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Conserved domains on  [gi|2024405217|ref|XP_040555673|]
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protein RUFY3 isoform X10 [Gallus gallus]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
RUN_RUFY3 cd17696
RUN domain found in RUN and FYVE domain-containing protein 3 (RUFY3) and similar proteins; ...
 108-263 3.73e-102

RUN domain found in RUN and FYVE domain-containing protein 3 (RUFY3) and similar proteins; RUFY3, also called Rap2-interacting protein x (RIPx or RPIPx), or single axon-regulated protein (singar), is an N-terminal RUN domain and a C-terminal FYVE domain containing protein predominantly expressed in the brain. It suppresses formation of surplus axons for neuronal polarity. Unlike other RUFY proteins, RUFY3 can associate with the GTP-bound active form of Rab5. This model represents the RUN domain of RUFY3.


:

Pssm-ID: 439058  Cd Length: 156  Bit Score: 303.84  E-value: 3.73e-102
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2024405217 108 ERMNLMNMAKLSIKGLIESALNLGRTLDSDYAPLQQFFVVMEHCLKHGLKAKKTFLGQNKSFWGPLELVEKLVPEAAEIT 187
Cdd:cd17696     1 ERMNLMNMAKLSIKGLIESALNLGRTLDSDYAPLQQFFVVMEHCLKHGLKAKKTFLGQNKSFWGPLELVEKLVPEAAEIT 80

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 2024405217 188 ASVKDLPGLKTPVGRGRAWLRLALMQKKLSEYMKALINRKDLLSEFYEPNALMMEEEGAIIAGLLVGLNVIDANFC 263
Cdd:cd17696    81 ASVKDLPGLKTPVGRGRAWLRLALMQKKLSEYMKALINRKDLLSEFYEPNALMMEEEGAIIAGLLVGLNVIDANFC 156
SMC_prok_B super family cl37069
chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of ...
 283-485 9.19e-10

chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]


The actual alignment was detected with superfamily member TIGR02168:

Pssm-ID: 274008 [Multi-domain]  Cd Length: 1179  Bit Score: 61.61  E-value: 9.19e-10
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2024405217  283 KDGNSTKGSegDGQITAILDQKNYVEELNRH---LSATVNNLQAKVDALEKSNTKLTEELAVANNRIITLQEEMERVKEE 359
Cdd:TIGR02168  657 PGGVITGGS--AKTNSSILERRREIEELEEKieeLEEKIAELEKALAELRKELEELEEELEQLRKELEELSRQISALRKD 734

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2024405217  360 SSYILESNRKVTKDRTADGQALTEARKQLKEETQLRLDVEKELEAQIGMRQEMELAMKMLEKDVCEKQDALVALRQQLDD 439
Cdd:TIGR02168  735 LARLEAEVEQLEERIAQLSKELTELEAEIEELEERLEEAEEELAEAEAEIEELEAQIEQLKEELKALREALDELRAELTL 814

                          170       180       190       200
                   ....*....|....*....|....*....|....*....|....*.
gi 2024405217  440 LRALKHELSFKLQSSDMGVKQKSELNSRLEEKTNQMAATIKQLEQS 485
Cdd:TIGR02168  815 LNEEAANLRERLESLERRIAATERRLEDLEEQIEELSEDIESLAAE 860
flhF super family cl35529
flagellar biosynthesis protein FlhF;
4-128 1.12e-04

flagellar biosynthesis protein FlhF;


The actual alignment was detected with superfamily member PRK06995:

Pssm-ID: 235904 [Multi-domain]  Cd Length: 484  Bit Score: 44.57  E-value: 1.12e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2024405217   4 AERAPLLPPPAESSRDGM-AAETPPGMERRAEPGPEEAAVTEEEDEARPASPPFFLLYPGHGGAAAPHGAWRPPAPRGGA 82
Cdd:PRK06995   61 AAQPPPAAAPAAVSRPAApAAEPAPWLVEHAKRLTAQREQLVARAAAPAAPEAQAPAAPAERAAAENAARRLARAAAAAP 140

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*..
gi 2024405217  83 ALPVLLLSYPGPDGASAHPNYLMANERMnlmnMAKL-SIKGLIESAL 128
Cdd:PRK06995  141 RPRVPADAAAAVADAVKARIERIVNDTV----MQELrSLRGMLEEQL 183
 
Name Accession Description Interval E-value
RUN_RUFY3 cd17696
RUN domain found in RUN and FYVE domain-containing protein 3 (RUFY3) and similar proteins; ...
 108-263 3.73e-102

RUN domain found in RUN and FYVE domain-containing protein 3 (RUFY3) and similar proteins; RUFY3, also called Rap2-interacting protein x (RIPx or RPIPx), or single axon-regulated protein (singar), is an N-terminal RUN domain and a C-terminal FYVE domain containing protein predominantly expressed in the brain. It suppresses formation of surplus axons for neuronal polarity. Unlike other RUFY proteins, RUFY3 can associate with the GTP-bound active form of Rab5. This model represents the RUN domain of RUFY3.


Pssm-ID: 439058  Cd Length: 156  Bit Score: 303.84  E-value: 3.73e-102
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2024405217 108 ERMNLMNMAKLSIKGLIESALNLGRTLDSDYAPLQQFFVVMEHCLKHGLKAKKTFLGQNKSFWGPLELVEKLVPEAAEIT 187
Cdd:cd17696     1 ERMNLMNMAKLSIKGLIESALNLGRTLDSDYAPLQQFFVVMEHCLKHGLKAKKTFLGQNKSFWGPLELVEKLVPEAAEIT 80

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 2024405217 188 ASVKDLPGLKTPVGRGRAWLRLALMQKKLSEYMKALINRKDLLSEFYEPNALMMEEEGAIIAGLLVGLNVIDANFC 263
Cdd:cd17696    81 ASVKDLPGLKTPVGRGRAWLRLALMQKKLSEYMKALINRKDLLSEFYEPNALMMEEEGAIIAGLLVGLNVIDANFC 156
RUN pfam02759
RUN domain; This domain is present in several proteins that are linked to the functions of ...
 143-266 6.34e-46

RUN domain; This domain is present in several proteins that are linked to the functions of GTPases in the Rap and Rab families. They could hence play important roles in multiple Ras-like GTPase signalling pathways. The domain is comprises six conserved regions, which in some proteins have considerable insertions between them. The domain core is thought to take up a predominantly alpha fold, with basic amino acids in regions A and D possibly playing a functional role in interactions with Ras GTPases.


Pssm-ID: 460679  Cd Length: 134  Bit Score: 157.05  E-value: 6.34e-46
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2024405217 143 QFFVVMEHCLKHGLKA------KKTFLGQNKSFWGPLELVEKLVPEAAEITASVKDLPGLKT---PVGRGRAWLRLALMQ 213
Cdd:pfam02759   1 QLCAALEALLSHGLKRssllilRAAGLLPERSFWALLERVGKLVPPAEELLSSVQELEQIHTpysPDGRGRAWIRLALNE 80

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....
gi 2024405217 214 KKLSEYMKALINRKDLLSEFYEPNALMMEEEGA-IIAGLLVGLNVIDANFCMKG 266
Cdd:pfam02759  81 KLLDQWLKLLLSNKELLSEYYEPWALLADPEFGeILLGLLVGLSALDFNLCLKL 134
RUN smart00593
domain involved in Ras-like GTPase signaling;
203-265 1.95e-18

domain involved in Ras-like GTPase signaling;


Pssm-ID: 214736 [Multi-domain]  Cd Length: 64  Bit Score: 79.19  E-value: 1.95e-18
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 2024405217  203 GRAWLRLALMQKKLSEYMKALINRKDLLSEFYEPNALMM-EEEGAIIAGLLVGLNVIDANFCMK 265
Cdd:smart00593   1 FRAWIRLALNEKLLSSWLNLLLSDEELLSKYYEPWAFLRdPEEGEQLLGLLVGLSALDFNLPVD 64
SMC_prok_B TIGR02168
chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of ...
 283-485 9.19e-10

chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]


Pssm-ID: 274008 [Multi-domain]  Cd Length: 1179  Bit Score: 61.61  E-value: 9.19e-10
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2024405217  283 KDGNSTKGSegDGQITAILDQKNYVEELNRH---LSATVNNLQAKVDALEKSNTKLTEELAVANNRIITLQEEMERVKEE 359
Cdd:TIGR02168  657 PGGVITGGS--AKTNSSILERRREIEELEEKieeLEEKIAELEKALAELRKELEELEEELEQLRKELEELSRQISALRKD 734

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2024405217  360 SSYILESNRKVTKDRTADGQALTEARKQLKEETQLRLDVEKELEAQIGMRQEMELAMKMLEKDVCEKQDALVALRQQLDD 439
Cdd:TIGR02168  735 LARLEAEVEQLEERIAQLSKELTELEAEIEELEERLEEAEEELAEAEAEIEELEAQIEQLKEELKALREALDELRAELTL 814

                          170       180       190       200
                   ....*....|....*....|....*....|....*....|....*.
gi 2024405217  440 LRALKHELSFKLQSSDMGVKQKSELNSRLEEKTNQMAATIKQLEQS 485
Cdd:TIGR02168  815 LNEEAANLRERLESLERRIAATERRLEDLEEQIEELSEDIESLAAE 860
CwlO1 COG3883
Uncharacterized N-terminal coiled-coil domain of peptidoglycan hydrolase CwlO [Function ...
 288-494 3.89e-07

Uncharacterized N-terminal coiled-coil domain of peptidoglycan hydrolase CwlO [Function unknown];


Pssm-ID: 443091 [Multi-domain]  Cd Length: 379  Bit Score: 52.14  E-value: 3.89e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2024405217 288 TKGSEGDGQITAILDQKNYVE-ELNRhLSATVNNLQAKVDALEKSNTKLTEELAVANNRIITLQEEMERVKEE------S 360
Cdd:COG3883    16 PQIQAKQKELSELQAELEAAQaELDA-LQAELEELNEEYNELQAELEALQAEIDKLQAEIAEAEAEIEERREElgerarA 94

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2024405217 361 SY-----------ILESN---------RKVTKDRTADGQALTEARKQLKEETQLRLDVEKELEAQIGMRQEMELAMKMLE 420
Cdd:COG3883    95 LYrsggsvsyldvLLGSEsfsdfldrlSALSKIADADADLLEELKADKAELEAKKAELEAKLAELEALKAELEAAKAELE 174

                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 2024405217 421 KDVCEKQDALVALRQQLDDLRALKHELSFKLQSSDMGVKQKSELNSRLEEKTNQMAATIKQLEQSSCGSNPDCG 494
Cdd:COG3883   175 AQQAEQEALLAQLSAEEAAAEAQLAELEAELAAAEAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAASAAG 248
Golgin_A5 pfam09787
Golgin subfamily A member 5; Members of this family of proteins are involved in maintaining ...
 317-483 2.52e-05

Golgin subfamily A member 5; Members of this family of proteins are involved in maintaining Golgi structure. They stimulate the formation of Golgi stacks and ribbons, and are involved in intra-Golgi retrograde transport. Two main interactions have been characterized: one with RAB1A that has been activated by GTP-binding and another with isoform CASP of CUTL1.


Pssm-ID: 462900 [Multi-domain]  Cd Length: 305  Bit Score: 46.29  E-value: 2.52e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2024405217 317 TVNNLQAKVDALEKSNTKLTEELAVANNRIITLQEEMERVKEESSYILESNRkvtkdrtadgQALTEARKQLKEETQLRL 396
Cdd:pfam09787  41 SSTALTLELEELRQERDLLREEIQKLRGQIQQLRTELQELEAQQQEEAESSR----------EQLQELEEQLATERSARR 110

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2024405217 397 DVEKELEAQigmRQEMElamKMLEKDVCEKQDALVALRQQLDDLRALKHELSFKLQSSdmgvKQKSELNSRLEEKTNQMA 476
Cdd:pfam09787 111 EAEAELERL---QEELR---YLEEELRRSKATLQSRIKDREAEIEKLRNQLTSKSQSS----SSQSELENRLHQLTETLI 180


                  ....*..
gi 2024405217 477 ATIKQLE 483
Cdd:pfam09787 181 QKQTMLE 187
flhF PRK06995
flagellar biosynthesis protein FlhF;
4-128 1.12e-04

flagellar biosynthesis protein FlhF;


Pssm-ID: 235904 [Multi-domain]  Cd Length: 484  Bit Score: 44.57  E-value: 1.12e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2024405217   4 AERAPLLPPPAESSRDGM-AAETPPGMERRAEPGPEEAAVTEEEDEARPASPPFFLLYPGHGGAAAPHGAWRPPAPRGGA 82
Cdd:PRK06995   61 AAQPPPAAAPAAVSRPAApAAEPAPWLVEHAKRLTAQREQLVARAAAPAAPEAQAPAAPAERAAAENAARRLARAAAAAP 140

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*..
gi 2024405217  83 ALPVLLLSYPGPDGASAHPNYLMANERMnlmnMAKL-SIKGLIESAL 128
Cdd:PRK06995  141 RPRVPADAAAAVADAVKARIERIVNDTV----MQELrSLRGMLEEQL 183
PRK11281 PRK11281
mechanosensitive channel MscK;
312-491 1.40e-04

mechanosensitive channel MscK;


Pssm-ID: 236892 [Multi-domain]  Cd Length: 1113  Bit Score: 44.90  E-value: 1.40e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2024405217  312 RHLSATVNNLQAKVDALEKSNTKLTEELAVANNRIITLQEEMERVKEE----SSYILESNRKVTKDRTADGQALTEARKQ 387
Cdd:PRK11281   117 TLSTLSLRQLESRLAQTLDQLQNAQNDLAEYNSQLVSLQTQPERAQAAlyanSQRLQQIRNLLKGGKVGGKALRPSQRVL 196

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2024405217  388 LKEETQLrldvekeLEAQIGMRQEmELAMKMLEKDVCEKQDALVALRQQLddlraLKHELSFkLQSSdmgVKQKselnsR 467
Cdd:PRK11281   197 LQAEQAL-------LNAQNDLQRK-SLEGNTQLQDLLQKQRDYLTARIQR-----LEHQLQL-LQEA---INSK-----R 254

                          170       180
                   ....*....|....*....|....
gi 2024405217  468 LEEKTNQMAATIKQLEQSSCGSNP 491
Cdd:PRK11281   255 LTLSEKTVQEAQSQDEAARIQANP 278
 
Name Accession Description Interval E-value
RUN_RUFY3 cd17696
RUN domain found in RUN and FYVE domain-containing protein 3 (RUFY3) and similar proteins; ...
 108-263 3.73e-102

RUN domain found in RUN and FYVE domain-containing protein 3 (RUFY3) and similar proteins; RUFY3, also called Rap2-interacting protein x (RIPx or RPIPx), or single axon-regulated protein (singar), is an N-terminal RUN domain and a C-terminal FYVE domain containing protein predominantly expressed in the brain. It suppresses formation of surplus axons for neuronal polarity. Unlike other RUFY proteins, RUFY3 can associate with the GTP-bound active form of Rab5. This model represents the RUN domain of RUFY3.


Pssm-ID: 439058  Cd Length: 156  Bit Score: 303.84  E-value: 3.73e-102
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2024405217 108 ERMNLMNMAKLSIKGLIESALNLGRTLDSDYAPLQQFFVVMEHCLKHGLKAKKTFLGQNKSFWGPLELVEKLVPEAAEIT 187
Cdd:cd17696     1 ERMNLMNMAKLSIKGLIESALNLGRTLDSDYAPLQQFFVVMEHCLKHGLKAKKTFLGQNKSFWGPLELVEKLVPEAAEIT 80

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 2024405217 188 ASVKDLPGLKTPVGRGRAWLRLALMQKKLSEYMKALINRKDLLSEFYEPNALMMEEEGAIIAGLLVGLNVIDANFC 263
Cdd:cd17696    81 ASVKDLPGLKTPVGRGRAWLRLALMQKKLSEYMKALINRKDLLSEFYEPNALMMEEEGAIIAGLLVGLNVIDANFC 156
RUN_RUFY2 cd17695
RUN domain found in RUN and FYVE domain-containing protein 2 (RUFY2) and similar proteins; ...
 108-263 2.23e-99

RUN domain found in RUN and FYVE domain-containing protein 2 (RUFY2) and similar proteins; RUFY2, also called Rab4-interacting protein related, is a novel embryonic factor that contains an N-terminal RUN domain and a C-terminal FYVE domain with two coiled-coil domains in-between. It is present in the nucleus at early stages of embryonic development. It may have both endosomal functions in the cytoplasm and nuclear functions. This model represents the RUN domain of RUFY2.


Pssm-ID: 439057  Cd Length: 156  Bit Score: 296.50  E-value: 2.23e-99
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2024405217 108 ERMNLMNMAKLSIKGLIESALNLGRTLDSDYAPLQQFFVVMEHCLKHGLKAKKTFLGQNKSFWGPLELVEKLVPEAAEIT 187
Cdd:cd17695     1 ERANLLNMAKLSIKGLIESALSFGRTLDSDYPPLQQFFVVMEHCLKHGLKVRKSFLSYNKTIWGPLELVEKLCPEAEEIA 80

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 2024405217 188 ASVKDLPGLKTPVGRGRAWLRLALMQKKLSEYMKALINRKDLLSEFYEPNALMMEEEGAIIAGLLVGLNVIDANFC 263
Cdd:cd17695    81 ASVRDLPGLKTPLGRARAWLRLALMQKKLADYLRCLIIRRDLLSEFYEYHALMMEEEGAVIVGLLVGLNVIDANLC 156
RUN_RUFY1_like cd17681
RUN domain found in RUN and FYVE domain-containing proteins, RUFY1, RUFY2, RUFY3 and similar ...
 108-262 3.93e-98

RUN domain found in RUN and FYVE domain-containing proteins, RUFY1, RUFY2, RUFY3 and similar proteins; This family includes RUN and FYVE domain-containing protein RUFY1, RUFY2, and RUFY3. RUFY1, also called FYVE-finger protein EIP1, or La-binding protein 1, or Rab4-interacting protein (Rabip4), or Zinc finger FYVE domain-containing protein 12 (ZFY12), a human homolog of mouse Rabip4, an effector of Rab4 GTPase that regulates recycling of endocytosed cargo. RUFY1 is an endosomal protein that functions as a dual effector of Rab4 and Rab14 and is involved in efficient recycling of transferrin (Tfn). It is a downstream effector of Etk, a downstream tyrosine kinase of PI3-kinase that is involved in regulation of vesicle trafficking. RUFY2, also called Rab4-interacting protein related, is a novel embryonic factor that is present in the nucleus at early stages of embryonic development. It may have both endosomal functions in the cytoplasm and nuclear functions. RUFY3, also called Rap2-interacting protein x (RIPx or RPIPx), or single axon-regulated protein (singar), is an N-terminal RUN domain and a C-terminal FYVE domain containing protein predominantly expressed in the brain. It suppresses formation of surplus axons for neuronal polarity. Unlike other RUFY proteins, RUFY3 can associate with the GTP-bound active form of Rab5. RUFY1, RUFY2, and RUFY3 contain an N-terminal RUN domain and a C-terminal FYVE domain with two coiled-coil domains in-between; this model represents the RUN domain.


Pssm-ID: 439043  Cd Length: 155  Bit Score: 293.32  E-value: 3.93e-98
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2024405217 108 ERMNLMNMAKLSIKGLIESALNLGRTLDSDYAPLQQFFVVMEHCLKHGLKAKKTFLGQNKSFWGPLELVEKLVPEAAEIT 187
Cdd:cd17681     1 ERRNLLNLAKLSIKELIESALSFGRTLDSDHVPLQQFFVILEHVLRHGLKVKKSFLGPNKSFWPVLEHVEKLVPEANEIT 80

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 2024405217 188 ASVKDLPGLKTPVGRGRAWLRLALMQKKLSEYMKALINRKDLLSEFYEPNALMMEEEGAIIAGLLVGLNVIDANF 262
Cdd:cd17681    81 ASVRDLPGIKTPLGRARAWLRLALMQKKLADYFRALIENKDLLSEFYEPGALMMSEEAVVIAGLLVGLNVIDCNL 155
RUN_RUFY1 cd17694
RUN domain found in RUN and FYVE domain-containing protein 1 (RUFY1) and similar proteins; ...
 108-263 1.08e-94

RUN domain found in RUN and FYVE domain-containing protein 1 (RUFY1) and similar proteins; RUFY1, also called FYVE-finger protein EIP1, or La-binding protein 1, or Rab4-interacting protein (Rabip4), or Zinc finger FYVE domain-containing protein 12 (ZFY12), a human homolog of mouse Rabip4, an effector of Rab4 GTPase that regulates recycling of endocytosed cargo. RUFY1 is an endosomal protein that functions as a dual effector of Rab4 and Rab14 and is involved in efficient recycling of transferrin (Tfn). It is a downstream effector of Etk, a downstream tyrosine kinase of PI3-kinase that is involved in regulation of vesicle trafficking. RUFY1 contains an N-terminal RUN domain and a C-terminal FYVE domain with two coiled-coil domains in-between; this model represents the RUN domain.


Pssm-ID: 439056  Cd Length: 156  Bit Score: 284.49  E-value: 1.08e-94
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2024405217 108 ERMNLMNMAKLSIKGLIESALNLGRTLDSDYAPLQQFFVVMEHCLKHGLKAKKTFLGQNKSFWGPLELVEKLVPEAAEIT 187
Cdd:cd17694     1 ERANLMNMMKLSIKVLIQSALSLGRTLDSDYPPLQQFFVVLEHCLKHGLKVKKSFIGQNKSFFGPLELVEKLCPEASDIA 80

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 2024405217 188 ASVKDLPGLKTPVGRGRAWLRLALMQKKLSEYMKALINRKDLLSEFYEPNALMMEEEGAIIAGLLVGLNVIDANFC 263
Cdd:cd17694    81 TSARNLPELKTAVGRGRAWLHLALMQKKLADYLKVLIDRKDLLSEFYEPGALMMEEEGAVIVGLLVGLNVIDANLC 156
RUN pfam02759
RUN domain; This domain is present in several proteins that are linked to the functions of ...
 143-266 6.34e-46

RUN domain; This domain is present in several proteins that are linked to the functions of GTPases in the Rap and Rab families. They could hence play important roles in multiple Ras-like GTPase signalling pathways. The domain is comprises six conserved regions, which in some proteins have considerable insertions between them. The domain core is thought to take up a predominantly alpha fold, with basic amino acids in regions A and D possibly playing a functional role in interactions with Ras GTPases.


Pssm-ID: 460679  Cd Length: 134  Bit Score: 157.05  E-value: 6.34e-46
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2024405217 143 QFFVVMEHCLKHGLKA------KKTFLGQNKSFWGPLELVEKLVPEAAEITASVKDLPGLKT---PVGRGRAWLRLALMQ 213
Cdd:pfam02759   1 QLCAALEALLSHGLKRssllilRAAGLLPERSFWALLERVGKLVPPAEELLSSVQELEQIHTpysPDGRGRAWIRLALNE 80

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....
gi 2024405217 214 KKLSEYMKALINRKDLLSEFYEPNALMMEEEGA-IIAGLLVGLNVIDANFCMKG 266
Cdd:pfam02759  81 KLLDQWLKLLLSNKELLSEYYEPWALLADPEFGeILLGLLVGLSALDFNLCLKL 134
RUN_RUNDC3 cd17684
RUN domain found in RUN domain-containing protein 3 (RUNDC3) and similar proteins; RUNDC3 ...
 111-262 8.74e-37

RUN domain found in RUN domain-containing protein 3 (RUNDC3) and similar proteins; RUNDC3 contains two isoforms, RUNDC3A and RUNDC3B. RUNDC3A, also called Rap2-interacting protein 8 (RPIP8), may act as an effector of Rap2A GTPase in neuronal cells. RUNDC3B, also called Rap2-binding protein 9, or Rap2-interacting protein 9 (RPIP-9), contains a RUN domain in its N-terminal region that mediates interaction with Rap2, an important component of the Mitogen-Activated Protein Kinase (MAPK) cascade, which regulates cellular proliferation and differentiation. It also contains characteristic binding sites for MAPK intermediates. Both RUNDC3A and RUNDC3B contain a RUN domain.


Pssm-ID: 439046  Cd Length: 150  Bit Score: 133.29  E-value: 8.74e-37
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2024405217 111 NLMNMAKLSIKGLIESALNlgRTLDSDYAPLQQFFVVMEHCLKHGLKAKKTFLG--QNKSFWGPLELVEKLVPEAAeiTA 188
Cdd:cd17684     1 NLVTVCRLSVKSLIDKACL--ETIDDSSEELINFAAILEQILSHRLKPVKPWYGseEPRTFWDYIRVACKKVPQNC--IA 76

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 2024405217 189 SVKDLPGLKTPVGRGRAWLRLALMQKKLSEYMKALINRKDLLSEFYEPNALMMEEEGAIIAGLLVGLNVIDANF 262
Cdd:cd17684    77 SIEQMENIKSPKAKGRAWIRVALMEKRLSEYLSTALKQTRLTRNFYQDGAIMLSEDATVLCGMLIGLNAIDFSF 150
RUN cd17671
RUN domain; RUN domain, named after RPIP8 (Rap2 interacting protein 8), UNC-14 and NESCA (new ...
 119-262 6.02e-34

RUN domain; RUN domain, named after RPIP8 (Rap2 interacting protein 8), UNC-14 and NESCA (new molecule containing SH3 at the carboxyl-terminus), is a less conserved protein motif that comprises six conserved regions, which in some proteins have considerable insertions between them. The domain core is thought to take up a predominantly alpha fold, with basic amino acids in regions A and D possibly playing a functional role in interactions with Ras GTPases. RUN domains are often found in proteins linked particularly to the functions of GTPases in the Rap and Rab families, suggesting the RUN domain may be involved in Rab-mediated membrane trafficking, possibly as a Rab-binding site. RUN domain-containing proteins could hence play important roles in multiple Ras-like GTPase signalling pathways.


Pssm-ID: 439038  Cd Length: 154  Bit Score: 125.62  E-value: 6.02e-34
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2024405217 119 SIKGLIESALNLGR-------TLDSDYAPLQQFFVVMEHCLKHGLKAKKtFLGQNKSFWGPLELVEKLVPEAAEITA--S 189
Cdd:cd17671     2 AVKELLESFADNGEaddsaalTLTDDDPVVGRLCAALEAILSHGLKPKR-FGGGKVSFWDFLEALEKLLPAPSLKQAirD 80

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 2024405217 190 VKDLPGLKTPVGRGRAWLRLALMQKKLSEYMKALINRKDLLSEFYEPNALMM-EEEGAIIAGLLVGLNVIDANF 262
Cdd:cd17671    81 INSLSNVKTDDGRGRAWIRLALNEKSLESYLAALLSDQSLLRKYYEPWALLRdPEEAELFLSLLVGLSSLDFNL 154
RUN_RUNDC3B cd17700
RUN domain found in RUN domain-containing protein 3B (RUNDC3B) and similar proteins; RUN ...
 111-263 2.72e-26

RUN domain found in RUN domain-containing protein 3B (RUNDC3B) and similar proteins; RUN domain-containing protein 3B (RUNDC3B), also called Rap2-binding protein 9, or Rap2-interacting protein 9 (RPIP-9), contains a RUN domain in its N-terminal region that mediates interaction with Rap2, an important component of the Mitogen-Activated Protein Kinase (MAPK) cascade, which regulates cellular proliferation and differentiation. It also contains characteristic binding sites for MAPK intermediates. RUNDC3B contains a RUN domain.


Pssm-ID: 439062  Cd Length: 151  Bit Score: 104.28  E-value: 2.72e-26
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2024405217 111 NLMNMAKLSIKGLIESALNlgRTLDSDYAPLQQFFVVMEHCLKHGLKAKKTFLGQN--KSFWGPLELVEKLVPEAAeiTA 188
Cdd:cd17700     1 NLITVCRFSVKTLIDRSCF--ETIDDSSPEFVNFAAILEQILSHRLKGQVTWFGYEspRSFWDYIRVACSKVPHNC--IC 76

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 2024405217 189 SVKDLPGLKTPVGRGRAWLRLALMQKKLSEYMKALINRKDLLSEFYEPNALMMEEEGAIIAGLLVGLNVIDANFC 263
Cdd:cd17700    77 SIENMENVSSSRAKGRAWIRVALMEKRLSEYISTALRDFKTTRRFYEDGAIVLGEEANMLAGMLLGLNAIDFSFC 151
RUN_RUNDC3A cd17699
RUN domain found in RUN domain-containing protein 3A (RUNDC3A) and similar proteins; RUN ...
 111-263 1.20e-23

RUN domain found in RUN domain-containing protein 3A (RUNDC3A) and similar proteins; RUN domain-containing protein 3A (RUNDC3A), also called Rap2-interacting protein 8 (RPIP8), may act as an effector of Rap2A GTPase in neuronal cells. It contains a RUN domain.


Pssm-ID: 439061  Cd Length: 151  Bit Score: 97.02  E-value: 1.20e-23
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2024405217 111 NLMNMAKLSIKGLIESALnlGRTLDSDYAPLQQFFVVMEHCLKHGLKAKKTFL---GQnKSFWGPLELVEKLVPEaaEIT 187
Cdd:cd17699     1 NLITVCRFSVKTLLEKYT--AEPIDDSSEEFVNFAAILEQILSHRFKGPVSWFssdGQ-RGFWDYIRLACSKVPN--NCI 75

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 2024405217 188 ASVKDLPGLKTPVGRGRAWLRLALMQKKLSEYMKALINRKDLLSEFYEPNALMMEEEGAIIAGLLVGLNVIDANFC 263
Cdd:cd17699    76 SSIENMENISTSRAKGRAWIRVALMEKRLSEYIATALRDTRTTRRFYDDGAIMLREESTVLTGMLIGLSAIDFSFC 151
RUN smart00593
domain involved in Ras-like GTPase signaling;
203-265 1.95e-18

domain involved in Ras-like GTPase signaling;


Pssm-ID: 214736 [Multi-domain]  Cd Length: 64  Bit Score: 79.19  E-value: 1.95e-18
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 2024405217  203 GRAWLRLALMQKKLSEYMKALINRKDLLSEFYEPNALMM-EEEGAIIAGLLVGLNVIDANFCMK 265
Cdd:smart00593   1 FRAWIRLALNEKLLSSWLNLLLSDEELLSKYYEPWAFLRdPEEGEQLLGLLVGLSALDFNLPVD 64
RUN_RUFY4_like cd17682
RUN domain found in RUN and FYVE domain-containing protein 4 (RUFY4), FYVE and coiled-coil ...
 120-259 3.99e-18

RUN domain found in RUN and FYVE domain-containing protein 4 (RUFY4), FYVE and coiled-coil domain-containing protein 1 (FYCO1), and similar proteins; The family includes RUFY4 and FYCO1. RUFY4 acts as a positive regulator that enhances autophagy and lysosome tethering in response to Interleukin-4. It is expressed in a cell-specific manner or under specific immunological conditions associated with IL4 expression such as allergic asthma. FYCO1, also called zinc finger FYVE domain-containing protein 7 (ZFYVE7), is a multidomain autophagy adaptor protein that interacts with kinesin motor proteins and with the autophagosomal membrane components microtubule-associated protein 1 light chain 3 (LC3), Rab7, and phosphatidylinositol 3-phosphate (PI3P), to mediate microtubule plus-end-directed autophagosome transport. Both RUFY4 and FYCO1 contain an N-terminal RUN domain and a C-terminal FYVE domain with two coiled-coil domains in-between; this model represents the RUN domain.


Pssm-ID: 439044  Cd Length: 150  Bit Score: 81.12  E-value: 3.99e-18
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2024405217 120 IKGLIESALNLGRTLDSDYAP-LQQFFVVMEHCLKHGLKAKKTFLGQNKSFWGPLE-LVEKLVPEA---AEITASVKDLP 194
Cdd:cd17682     2 LKGCVLDLKSEFGEITDPDNPyLRPFCETLEKILRKGLKEKVSLGGRRKDYWDWLEeLLKKLNKIPkslSDAVKFVKSCK 81

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 2024405217 195 GLKTPVGRGRAWLRLALMQKKLSEYMKALINRKDLLSEFYEPNALMMEEE-GAIIAGLLVGLNVID 259
Cdd:cd17682    82 KVKTNQGRGRLFIRYALNKKCLHDPVQQLVKNPKLLSDYYSPDSILGNEIlSEILLSLLYQLNEIN 147
RUN_PLEKHM1 cd17679
RUN domain found in pleckstrin homology domain-containing family M member 1 (PLEKHM1) and ...
 109-255 4.31e-14

RUN domain found in pleckstrin homology domain-containing family M member 1 (PLEKHM1) and similar proteins; PLEKHM1, also called PH domain-containing family M member 1, or 162 kDa adapter protein (AP162), may act as a multivalent adapter protein that regulates Rab7-dependent and HOPS complex-dependent fusion events in the endolysosomal system and couples autophagic and the endocytic trafficking pathways. This model represents the RUN domain of PLEKHM1.


Pssm-ID: 439041 [Multi-domain]  Cd Length: 171  Bit Score: 70.31  E-value: 4.31e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2024405217 109 RMNLMNMAKLSIKGLIESALNLGRTLDSDYAPLQQFFVVMEHCLKHGLKAK-----KTFLGQN------KSFWGPLELV- 176
Cdd:cd17679     1 KKSLTKELSSSVKELQLEYVSSDEVVTSSDDGANTLCCVLEAIFLHGLKDKfiskvSSVFSGDvdklpePNFWPLLLKFs 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2024405217 177 EKlvpeaaEITASVKDLPGLKTPVGRGRAWLRLALMQKKLSEYMKALINRKDLLSEFYEPNALMM-EEEGAIIAGLLVGL 255
Cdd:cd17679    81 HR------DVIDQIEHLSQITTDVGRCRAWIRLALNDGLLESYLEAILKDKSALKSYYNPSAFLRdPEQLDILKSLLQGL 154
RUN_SNX29 cd17689
RUN domain found in sorting nexin-29 (SNX29) and similar proteins; SNX29, also called RUN ...
 193-258 1.10e-12

RUN domain found in sorting nexin-29 (SNX29) and similar proteins; SNX29, also called RUN domain-containing protein 2A (RUNDC2A), belongs to the sorting nexin family. Sorting nexins are a large group of proteins that are localized in the cytoplasm and have the potential for membrane association either through their lipid-binding PX domain, a phospholipid-binding motif, or through protein-protein interactions with membrane-associated protein complexes. Some sorting nexin family members have been shown to facilitate protein sorting. This model contains the RUN domain of SNX29.


Pssm-ID: 439051  Cd Length: 166  Bit Score: 66.10  E-value: 1.10e-12
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 2024405217 193 LPGLKTPVGRGRAWLRLALMQKKLSEYMKALINRKDLLSEFYEPNALMM-EEEGAIIAGLLVGLNVI 258
Cdd:cd17689    93 LKNIWTDIGRGRAWLRSALNEHSLERYLHILLSNENLLRQYYEDWAFLRdEERSSMLPNMAAGLGSI 159
RUN_RUFY4 cd17697
RUN domain found in RUN and FYVE domain-containing protein 4 (RUFY4) and similar proteins; ...
 148-258 1.05e-11

RUN domain found in RUN and FYVE domain-containing protein 4 (RUFY4) and similar proteins; RUFY4 acts as a positive regulator that enhances autophagy and lysosome tethering in response to Interleukin-4. It is expressed in a cell-specific manner or under specific immunological conditions associated with IL4 expression such as allergic asthma. RUFY4 belongs to the FUFY protein family which is characterized by the presence of an N-terminal RUN domain and a C-terminal FYVE domain; this model represents the RUN domain of RUFY4.


Pssm-ID: 439059  Cd Length: 150  Bit Score: 62.89  E-value: 1.05e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2024405217 148 MEHCLKHGLKAKKTFLGQNKSFWGPLELVEKLVPEAAEITASVKDLPGLKTPVGRGRAWLRLALMQKKLSEYMKALINRK 227
Cdd:cd17697    35 LEYLLQFDQKEKKSFFGSRKDYWDFLCLCLNRHRGGTEGIHFVNSTDKLKTPLGKGRAFIRYCLVQQQLAESLQLCLLNP 114

                          90       100       110
                  ....*....|....*....|....*....|..
gi 2024405217 228 DLLSEFYEPNA-LMMEEEGAIIAGLLVGLNVI 258
Cdd:cd17697   115 ELTGEWYYARSpFLSPELRSDILDSLYELNGV 146
RUN_SGSM1_like cd17687
RUN domain found in small G protein signaling modulators, SGSM1, SGSM2, and similar proteins; ...
 149-259 2.24e-11

RUN domain found in small G protein signaling modulators, SGSM1, SGSM2, and similar proteins; SGSM1, also called RUN and TBC1 domain-containing protein 2 (RUTBC2), interacts with numerous Rab family members, functioning as Rab effector for some, and as GTPase activator for others. It is a Rab9A effector and GTPase-activating protein for Rab36, and links Rab9A function to Rab36 function in the endosomal system. SGSM2, also called RUN and TBC1 domain-containing protein 1 (RUTBC1), is a GTPase-activating protein for Rab32/38, and regulates melanogenic enzyme trafficking in melanocytes. It also acts as a Rab9A effector that activates GTP hydrolysis by Rab32 and Rab33B proteins. This model contains the RUN domain of SGSM1 and SGSM2.


Pssm-ID: 439049  Cd Length: 161  Bit Score: 62.30  E-value: 2.24e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2024405217 149 EHCLKHGLKAKK-TFLGQNKSFwGPLELVEKLVPEAAEITASVKDL------PGLKTPVGRGRA-------------WLR 208
Cdd:cd17687    31 DACLLHGLRKRAlGLFRSSSTF-SLLQKVAKSCPPAADILRKVQEIenlsenKRSSSSSGSNSSnshgnsssnrkilWIR 109

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|..
gi 2024405217 209 LALMQKKLSEYMKALINRKdllSEFYEPNALMME-EEGAIIAGLLVGLNVID 259
Cdd:cd17687   110 IALFEKVLDKIVDYLVENA---SKYYEKEALMADpVDGPLLASLLVGPCALD 158
RUN_PLEKHM2 cd17680
RUN domain found in pleckstrin homology domain-containing family M member 2 (PLEKHM2) and ...
 119-240 4.19e-11

RUN domain found in pleckstrin homology domain-containing family M member 2 (PLEKHM2) and similar proteins; PLEKHM2, also called PH domain-containing family M member 2, or Salmonella-induced filaments A (SifA) and Kinesin-Interacting Protein (SKIP), is the lysosome, melanosome and lytic granule cargo adaptor that controls lysosome positioning using a composite kinesin-1 heavy and light chain-binding domain. In addition to kinesin-1, it also interacts with several Rabs to affect endosomal trafficking. This model represents the RUN domain of PLEKHM2.


Pssm-ID: 439042  Cd Length: 145  Bit Score: 61.10  E-value: 4.19e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2024405217 119 SIKGLIESALNLGRTLDSDYAPLQQFFVVMEHCLKHGLKAKktflgqNKSFWGpleLVEKLVPEAAEItaSVKDLPGLKT 198
Cdd:cd17680    12 SLQSYSSSQEEEDVLITNENRELQRLCEALDHALLHGLRRG------NRGYWP---FVKEFTHKETIK--QIENLPNVTT 80

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|..
gi 2024405217 199 PVGRGRAWLRLALMQKKLSEYMKALINRKDLLSEFYEPNALM 240
Cdd:cd17680    81 DLGRGRAWLYLALNEGSLESYLRSFLENRKLVKKFYHKHALL 122
RUN1_DENND5 cd17677
RUN1 domain found in DENN domain-containing protein 5 (DENND5) and similar proteins; DENND5 ...
 154-263 2.63e-10

RUN1 domain found in DENN domain-containing protein 5 (DENND5) and similar proteins; DENND5 has been characterized as Rab6-interacting protein which is composed of an N-terminal DENN (Differentially Expressed in Normal and Neoplastic cells) domain followed by two RUN (RPIP8 [RaP2-interacting protein 8], UNC-14, and NESCA [new molecule containing SH3 at the carboxyl terminus]) domains flanking a PLAT (Polycystin-1, Lipoxygenase, Alpha-Toxin) domain. It functions in membrane trafficking at a crossroads between the Golgi and the endosomal system. DENND5 has two isoforms, DENND5A and DENND5B. This model represents the first RUN domain of DENND5.


Pssm-ID: 439039  Cd Length: 183  Bit Score: 59.72  E-value: 2.63e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2024405217 154 HGLKAKktflgQNKS-FWGPL----ELVEKLVPEAAEITA---SVKDLPGLKTPVGRGRAWLRLALMQKKLSEYMKALIN 225
Cdd:cd17677    65 HGLQTK-----QGKSaLWSHLlayqENEERLKPLPESLLFdmkNVQNMKEIKTDVGYARAWIRLALEKKLLSKHLKTLLS 139

                          90       100       110
                  ....*....|....*....|....*....|....*....
gi 2024405217 226 RKDLLSEFYEPNA-LMMEEEGAIIAGLLVGLNVIDAnFC 263
Cdd:cd17677   140 NQDLLRSLYKRYAfLRCEDEREQFLYHLLSLNAVDY-FC 177
RUN_FYCO1 cd17698
RUN domain found in FYVE and coiled-coil domain-containing protein 1 (FYCO1) and similar ...
 114-262 3.49e-10

RUN domain found in FYVE and coiled-coil domain-containing protein 1 (FYCO1) and similar proteins; FYCO1, also called zinc finger FYVE domain-containing protein 7 (ZFYVE7), is a multidomain autophagy adaptor protein that interacts with kinesin motor proteins and with the autophagosomal membrane components microtubule-associated protein 1 light chain 3 (LC3), Rab7, and Phosphatidylinositol 3-phosphate (PI3P), to mediate microtubule plus-end-directed autophagosome transport. This model represents the RUN domain of FYCO1.


Pssm-ID: 439060  Cd Length: 158  Bit Score: 58.55  E-value: 3.49e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2024405217 114 NMAKLSIKGLIESALNLGRTLDSDYAP-------LQQFFVVMEHCLKHGLKAKKTFLGQNKSFWGPL-ELVEKlVPEAAE 185
Cdd:cd17698     2 SQLQKIIRDLQDCVTELKKEFEETGEPitddsttLHKFCAKLEYLLQFDQKEKTTLLGGRKDYWDYFcECLAK-VKGLND 80

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 2024405217 186 ITASVKDLPGLKTPVGRGRAWLRLALMQKKLSEYMKALINRKDLLSEFYEP-NALMMEEEGAIIAGLLVGLNviDANF 262
Cdd:cd17698    81 GIRFVKSLKEVRTSLGKGRAFIRYSLVHQRLADTLQQCVMNGKVTSDWYYPrSVFLNHKYSSDIINSLYDLN--EVQF 156
SMC_prok_B TIGR02168
chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of ...
 283-485 9.19e-10

chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]


Pssm-ID: 274008 [Multi-domain]  Cd Length: 1179  Bit Score: 61.61  E-value: 9.19e-10
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2024405217  283 KDGNSTKGSegDGQITAILDQKNYVEELNRH---LSATVNNLQAKVDALEKSNTKLTEELAVANNRIITLQEEMERVKEE 359
Cdd:TIGR02168  657 PGGVITGGS--AKTNSSILERRREIEELEEKieeLEEKIAELEKALAELRKELEELEEELEQLRKELEELSRQISALRKD 734

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2024405217  360 SSYILESNRKVTKDRTADGQALTEARKQLKEETQLRLDVEKELEAQIGMRQEMELAMKMLEKDVCEKQDALVALRQQLDD 439
Cdd:TIGR02168  735 LARLEAEVEQLEERIAQLSKELTELEAEIEELEERLEEAEEELAEAEAEIEELEAQIEQLKEELKALREALDELRAELTL 814

                          170       180       190       200
                   ....*....|....*....|....*....|....*....|....*.
gi 2024405217  440 LRALKHELSFKLQSSDMGVKQKSELNSRLEEKTNQMAATIKQLEQS 485
Cdd:TIGR02168  815 LNEEAANLRERLESLERRIAATERRLEDLEEQIEELSEDIESLAAE 860
RUN_RUBCN cd17686
RUN domain found in Run domain Beclin-1-interacting and cysteine-rich domain-containing ...
 128-261 1.43e-09

RUN domain found in Run domain Beclin-1-interacting and cysteine-rich domain-containing protein (RUBCN) and similar proteins; RUBCN, also called rubicon, or beclin-1 associated RUN domain containing protein (Baron), is part of a Beclin-1-Vps34-containing autophagy complex. It negatively regulates endosome maturation and degradative endocytic trafficking and impairs autophagosome maturation process. It is also an important negative regulator of the innate immune response, enhances viral replication and may play a role in viral immune evasion. This model contains the RUN domain of RUBCN.


Pssm-ID: 439048  Cd Length: 151  Bit Score: 56.51  E-value: 1.43e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2024405217 128 LNLGRTLD--SDYAPLQQFFVVMEHCLKHGLKAKKTFLGQNkSFWGPLELVEKLVPEAAEITASVKDLPGLKTPVG-RGR 204
Cdd:cd17686     6 LLLSRSSNvwSTYGGLQRLCRAVENILQHGLKEFQGLNKEI-DDWEFVQGLRWLQPTLAPSIEQQSRSSPSESEVSdKGR 84

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 2024405217 205 AWLRLALMQKKLSEYMKALINRKDLLSEFYEPNALMMEEEGAiiAGLLVGLNVIDAN 261
Cdd:cd17686    85 LWLRQSLQQHCLSSQLQWLVSDKELLRKYYEDEAFLRQEGYA--TALLICLTAVELN 139
RUN1_DENND5B cd17691
RUN1 domain found in DENN domain-containing protein 5B (DENND5B) and similar proteins; DENND5B, ...
 190-263 1.56e-08

RUN1 domain found in DENN domain-containing protein 5B (DENND5B) and similar proteins; DENND5B, also called Rab6-interacting protein 1 (Rab6IP1)-like protein, functions in membrane trafficking at a crossroads between the Golgi and the endosomal system. It is composed of an N-terminal DENN (Differentially Expressed in Normal and Neoplastic cells) domain followed by two RUN (RPIP8 [RaP2-interacting protein 8], UNC-14, and NESCA [new molecule containing SH3 at the carboxyl terminus]) domains flanking a PLAT (Polycystin-1, Lipoxygenase, Alpha-Toxin) domain. This model represents the first RUN domain of DENND5B.


Pssm-ID: 439053 [Multi-domain]  Cd Length: 206  Bit Score: 55.06  E-value: 1.56e-08
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 2024405217 190 VKDLPGLKTPVGRGRAWLRLALMQKKLSEYMKALINRKDLLSEFYEPNA-LMMEEEGAIIAGLLVGLNVIDAnFC 263
Cdd:cd17691   127 IQNMSEIKTDVGRARAWIRLSLEKKLLSQHLKQLLSNQALTKKLYKRYAfLRCEEEKEQFLYHLLSLNAVDY-FC 200
SMC_prok_B TIGR02168
chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of ...
 304-484 8.51e-08

chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]


Pssm-ID: 274008 [Multi-domain]  Cd Length: 1179  Bit Score: 55.06  E-value: 8.51e-08
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2024405217  304 KNYVEELNRHLSAtVNNLQAKVDALEKSNTKLTEELAVANNRIITLQEEMERVKEESSYILESNRKVTKDRTADGQALTE 383
Cdd:TIGR02168  263 QELEEKLEELRLE-VSELEEEIEELQKELYALANEISRLEQQKQILRERLANLERQLEELEAQLEELESKLDELAEELAE 341

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2024405217  384 ARKQLKEETQLRLDVEKELEAQIGMRQEMELAMKMLEKDVCEKQDALVALRQQLDDLRALKHELSFKLQSSDMGVKQKSE 463
Cdd:TIGR02168  342 LEEKLEELKEELESLEAELEELEAELEELESRLEELEEQLETLRSKVAQLELQIASLNNEIERLEARLERLEDRRERLQQ 421

                          170       180
                   ....*....|....*....|...
gi 2024405217  464 LNSRLEEK--TNQMAATIKQLEQ 484
Cdd:TIGR02168  422 EIEELLKKleEAELKELQAELEE 444
SMC_prok_B TIGR02168
chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of ...
 287-484 3.14e-07

chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]


Pssm-ID: 274008 [Multi-domain]  Cd Length: 1179  Bit Score: 53.52  E-value: 3.14e-07
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2024405217  287 STKGSEGDGQITAILDQKNYVEELNRHLSATVNNLQAKVDALEKSNTKLTEELAVANNRIITLQEEMERVKEE---SSYI 363
Cdd:TIGR02168  725 SRQISALRKDLARLEAEVEQLEERIAQLSKELTELEAEIEELEERLEEAEEELAEAEAEIEELEAQIEQLKEElkaLREA 804

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2024405217  364 LESNRKVTKDRTADGQALTEARKQLKEETQLRLDVEKELEAQIGMRQE----MELAMKMLEKDVCEKQDALVALRQQLDD 439
Cdd:TIGR02168  805 LDELRAELTLLNEEAANLRERLESLERRIAATERRLEDLEEQIEELSEdiesLAAEIEELEELIEELESELEALLNERAS 884

                          170       180       190       200
                   ....*....|....*....|....*....|....*....|....*....
gi 2024405217  440 LRALKHELSFKLQSSDMGV----KQKSELNSRLEEKTNQMAATIKQLEQ 484
Cdd:TIGR02168  885 LEEALALLRSELEELSEELreleSKRSELRRELEELREKLAQLELRLEG 933
CwlO1 COG3883
Uncharacterized N-terminal coiled-coil domain of peptidoglycan hydrolase CwlO [Function ...
 288-494 3.89e-07

Uncharacterized N-terminal coiled-coil domain of peptidoglycan hydrolase CwlO [Function unknown];


Pssm-ID: 443091 [Multi-domain]  Cd Length: 379  Bit Score: 52.14  E-value: 3.89e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2024405217 288 TKGSEGDGQITAILDQKNYVE-ELNRhLSATVNNLQAKVDALEKSNTKLTEELAVANNRIITLQEEMERVKEE------S 360
Cdd:COG3883    16 PQIQAKQKELSELQAELEAAQaELDA-LQAELEELNEEYNELQAELEALQAEIDKLQAEIAEAEAEIEERREElgerarA 94

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2024405217 361 SY-----------ILESN---------RKVTKDRTADGQALTEARKQLKEETQLRLDVEKELEAQIGMRQEMELAMKMLE 420
Cdd:COG3883    95 LYrsggsvsyldvLLGSEsfsdfldrlSALSKIADADADLLEELKADKAELEAKKAELEAKLAELEALKAELEAAKAELE 174

                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 2024405217 421 KDVCEKQDALVALRQQLDDLRALKHELSFKLQSSDMGVKQKSELNSRLEEKTNQMAATIKQLEQSSCGSNPDCG 494
Cdd:COG3883   175 AQQAEQEALLAQLSAEEAAAEAQLAELEAELAAAEAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAASAAG 248
RUN_SGSM1 cd17703
RUN domain found in small G protein signaling modulator 1 (SGSM1) and similar proteins; SGSM1, ...
 120-254 1.09e-06

RUN domain found in small G protein signaling modulator 1 (SGSM1) and similar proteins; SGSM1, also called RUN and TBC1 domain-containing protein 2 (RUTBC2), interacts with numerous Rab family members, functioning as Rab effector for some, and as GTPase activator for others. It is a Rab9A effector and GTPase-activating protein for Rab36, and links Rab9A function to Rab36 function in the endosomal system. This model contains the RUN domain of SGSM1.


Pssm-ID: 439065  Cd Length: 177  Bit Score: 48.85  E-value: 1.09e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2024405217 120 IKGLIESALNLgRTLDSDYAPLQQFFVVMEHCLKHGLKAKKT-FLGQNK----------SFWGPLELVEKL--------- 179
Cdd:cd17703     3 VKQIMEEAVTR-KFVHEDSSHIISFCAAVEACVLHGLKRRAAgFLRSNKiaalfmkvgkSFPPAEELCRKVqeleqllen 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2024405217 180 ----VPEAAEITASVKDLPGLkTPVGRGRAWLRLALMQKKLSEYMKALINRKdllSEFYEPNALMMEE-EGAIIAGLLVG 254
Cdd:cd17703    82 krnqMQGLQENVRKMPKLPNL-SPQAIKHLWIRTALFEKVLDKIVHYLVENS---SKYYEKEALLMDPvDGPILASLLVG 157
Smc COG1196
Chromosome segregation ATPase Smc [Cell cycle control, cell division, chromosome partitioning]; ...
 296-484 1.64e-06

Chromosome segregation ATPase Smc [Cell cycle control, cell division, chromosome partitioning];


Pssm-ID: 440809 [Multi-domain]  Cd Length: 983  Bit Score: 51.09  E-value: 1.64e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2024405217 296 QITAILDQKNYVEELNRHLSATVNNLQAKVDALEKSNTKLTEELAVANNRIITLQEEMERVKEESSYILESNRKVTKDRT 375
Cdd:COG1196   233 KLRELEAELEELEAELEELEAELEELEAELAELEAELEELRLELEELELELEEAQAEEYELLAELARLEQDIARLEERRR 312

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2024405217 376 ADGQALTEARKQLKEETQLRLDVEKELEAQIGMRQEMELAMKMLEKDVCEKQDALVALRQQLDDLRALKHELSFKLQSSD 455
Cdd:COG1196   313 ELEERLEELEEELAELEEELEELEEELEELEEELEEAEEELEEAEAELAEAEEALLEAEAELAEAEEELEELAEELLEAL 392

                         170       180
                  ....*....|....*....|....*....
gi 2024405217 456 mgvKQKSELNSRLEEKTNQMAATIKQLEQ 484
Cdd:COG1196   393 ---RAAAELAAQLEELEEAEEALLERLER 418
Smc COG1196
Chromosome segregation ATPase Smc [Cell cycle control, cell division, chromosome partitioning]; ...
 296-485 2.33e-06

Chromosome segregation ATPase Smc [Cell cycle control, cell division, chromosome partitioning];


Pssm-ID: 440809 [Multi-domain]  Cd Length: 983  Bit Score: 50.32  E-value: 2.33e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2024405217 296 QITAILDQKNYVEELNRHLSATVNNLQAKVDALEKSNTKLTEELAVANNRIITLQEEMERVKEESSYILESNRKVTKDRT 375
Cdd:COG1196   296 ELARLEQDIARLEERRRELEERLEELEEELAELEEELEELEEELEELEEELEEAEEELEEAEAELAEAEEALLEAEAELA 375

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2024405217 376 ADGQALTEARKQLKEETQLRLDVEKELEAQIGMRQEMELAMKMLEKDVCEKQDALVALRQQLDDLRALKHELSFKLQSSD 455
Cdd:COG1196   376 EAEEELEELAEELLEALRAAAELAAQLEELEEAEEALLERLERLEEELEELEEALAELEEEEEEEEEALEEAAEEEAELE 455

                         170       180       190
                  ....*....|....*....|....*....|
gi 2024405217 456 MGVKQKSELNSRLEEKTNQMAATIKQLEQS 485
Cdd:COG1196   456 EEEEALLELLAELLEEAALLEAALAELLEE 485
RUN1_DENND5A cd17690
RUN1 domain found in DENN domain-containing protein 5A (DENND5A) and similar proteins; DENND5A, ...
 190-263 1.97e-05

RUN1 domain found in DENN domain-containing protein 5A (DENND5A) and similar proteins; DENND5A, also called Rab6-interacting protein 1 (Rab6IP1), is present predominantly in developing neuronal tissue, and functions in membrane trafficking at a crossroads between the Golgi and the endosomal system. It is composed of an N-terminal DENN (Differentially Expressed in Normal and Neoplastic cells) domain followed by two RUN (RPIP8 [RaP2-interacting protein 8], UNC-14, and NESCA [new molecule containing SH3 at the carboxyl terminus]) domains flanking a PLAT (Polycystin-1, Lipoxygenase, Alpha-Toxin) domain. This model represents the first RUN domain of DENND5A.


Pssm-ID: 439052 [Multi-domain]  Cd Length: 209  Bit Score: 45.77  E-value: 1.97e-05
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 2024405217 190 VKDLPGLKTPVGRGRAWLRLALMQKKLSEYMKALINRKDLLSEFYEPNA-LMMEEEGAIIAGLLVGLNVIDAnFC 263
Cdd:cd17690   130 IQNIGEIKTDVGKARAWVRLSMEKKLLSRHLKQLLSDHELTKKLYKRYAfLRCDDEKEQFLYHLLSFNAVDY-FC 203
HEC1 COG5185
Chromosome segregation protein NDC80, interacts with SMC proteins [Cell cycle control, cell ...
 298-485 2.34e-05

Chromosome segregation protein NDC80, interacts with SMC proteins [Cell cycle control, cell division, chromosome partitioning];


Pssm-ID: 444066 [Multi-domain]  Cd Length: 594  Bit Score: 46.87  E-value: 2.34e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2024405217 298 TAILDQKNYVEELNRHLSAT--VNNLQAKVDALEKSNTKLTEELAVANNriiTLQEEMERVKEESSYILESNRKVTKDRT 375
Cdd:COG5185   302 TKSIDIKKATESLEEQLAAAeaEQELEESKRETETGIQNLTAEIEQGQE---SLTENLEAIKEEIENIVGEVELSKSSEE 378

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2024405217 376 AD--GQALTEARKQLKEETQLRLDVEKELEAQIgmrqemELAMKMLEKDVCEKQDALVALRQQLDD----LRALKHELSF 449
Cdd:COG5185   379 LDsfKDTIESTKESLDEIPQNQRGYAQEILATL------EDTLKAADRQIEELQRQIEQATSSNEEvsklLNELISELNK 452

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|.
gi 2024405217 450 KLQSSDMGVKQK-----SELNSRLEEKTNQMAATIKQLEQS 485
Cdd:COG5185   453 VMREADEESQSRleeayDEINRSVRSKKEDLNEELTQIESR 493
Golgin_A5 pfam09787
Golgin subfamily A member 5; Members of this family of proteins are involved in maintaining ...
 317-483 2.52e-05

Golgin subfamily A member 5; Members of this family of proteins are involved in maintaining Golgi structure. They stimulate the formation of Golgi stacks and ribbons, and are involved in intra-Golgi retrograde transport. Two main interactions have been characterized: one with RAB1A that has been activated by GTP-binding and another with isoform CASP of CUTL1.


Pssm-ID: 462900 [Multi-domain]  Cd Length: 305  Bit Score: 46.29  E-value: 2.52e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2024405217 317 TVNNLQAKVDALEKSNTKLTEELAVANNRIITLQEEMERVKEESSYILESNRkvtkdrtadgQALTEARKQLKEETQLRL 396
Cdd:pfam09787  41 SSTALTLELEELRQERDLLREEIQKLRGQIQQLRTELQELEAQQQEEAESSR----------EQLQELEEQLATERSARR 110

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2024405217 397 DVEKELEAQigmRQEMElamKMLEKDVCEKQDALVALRQQLDDLRALKHELSFKLQSSdmgvKQKSELNSRLEEKTNQMA 476
Cdd:pfam09787 111 EAEAELERL---QEELR---YLEEELRRSKATLQSRIKDREAEIEKLRNQLTSKSQSS----SSQSELENRLHQLTETLI 180


                  ....*..
gi 2024405217 477 ATIKQLE 483
Cdd:pfam09787 181 QKQTMLE 187
DUF5401 pfam17380
Family of unknown function (DUF5401); This is a family of unknown function found in ...
 352-485 2.68e-05

Family of unknown function (DUF5401); This is a family of unknown function found in Chromadorea.


Pssm-ID: 375164 [Multi-domain]  Cd Length: 722  Bit Score: 47.04  E-value: 2.68e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2024405217 352 EMERVKEES---SYILESNRKVTKDRTADGQAL-TEARKQLKEETQLRLDVEKELEAQIGMRQEMELAMKMLEKDVCEKQ 427
Cdd:pfam17380 447 EMERVRLEEqerQQQVERLRQQEEERKRKKLELeKEKRDRKRAEEQRRKILEKELEERKQAMIEEERKRKLLEKEMEERQ 526

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 2024405217 428 DALV--ALRQQLDDLRALKHELSFKLQSSDMgVKQKSELNSRLE--EKTNQMAATIKQLEQS 485
Cdd:pfam17380 527 KAIYeeERRREAEEERRKQQEMEERRRIQEQ-MRKATEERSRLEamEREREMMRQIVESEKA 587
EnvC COG4942
Septal ring factor EnvC, activator of murein hydrolases AmiA and AmiB [Cell cycle control, ...
 295-485 3.03e-05

Septal ring factor EnvC, activator of murein hydrolases AmiA and AmiB [Cell cycle control, cell division, chromosome partitioning];


Pssm-ID: 443969 [Multi-domain]  Cd Length: 377  Bit Score: 46.30  E-value: 3.03e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2024405217 295 GQITAILDQKNYVEELNRHLSAtvnnLQAKVDALEKSNTKLTEELAVANNRIITLQEEMERVKEESSYILESNRKVTKDR 374
Cdd:COG4942    17 AQADAAAEAEAELEQLQQEIAE----LEKELAALKKEEKALLKQLAALERRIAALARRIRALEQELAALEAELAELEKEI 92

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2024405217 375 TADGQALTEARKQLKEETQLRLDVEKELEAQIGMRQE----MELAMKMLEKDVCEKQDALVALRQQLDDLRALKHELSFK 450
Cdd:COG4942    93 AELRAELEAQKEELAELLRALYRLGRQPPLALLLSPEdfldAVRRLQYLKYLAPARREQAEELRADLAELAALRAELEAE 172

                         170       180       190
                  ....*....|....*....|....*....|....*
gi 2024405217 451 LQSSDMGVKQKSELNSRLEEKTNQMAATIKQLEQS 485
Cdd:COG4942   173 RAELEALLAELEEERAALEALKAERQKLLARLEKE 207
Smc COG1196
Chromosome segregation ATPase Smc [Cell cycle control, cell division, chromosome partitioning]; ...
 308-484 4.39e-05

Chromosome segregation ATPase Smc [Cell cycle control, cell division, chromosome partitioning];


Pssm-ID: 440809 [Multi-domain]  Cd Length: 983  Bit Score: 46.47  E-value: 4.39e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2024405217 308 EELNRhLSATVNNLQAKVDALEKSNTKLTEELAVANNRIITLQEEMERVKEESSYILESNRKVTKDRTADGQALTEARKQ 387
Cdd:COG1196   281 LELEE-AQAEEYELLAELARLEQDIARLEERRRELEERLEELEEELAELEEELEELEEELEELEEELEEAEEELEEAEAE 359

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2024405217 388 LKEETQLRLDVEKELEAQIGMRQEMELAMKMLEKDVCEKQDALVALRQQLDDLRALKHELSfklqssdmgvKQKSELNSR 467
Cdd:COG1196   360 LAEAEEALLEAEAELAEAEEELEELAEELLEALRAAAELAAQLEELEEAEEALLERLERLE----------EELEELEEA 429

                         170
                  ....*....|....*..
gi 2024405217 468 LEEKTNQMAATIKQLEQ 484
Cdd:COG1196   430 LAELEEEEEEEEEALEE 446
flhF PRK06995
flagellar biosynthesis protein FlhF;
4-128 1.12e-04

flagellar biosynthesis protein FlhF;


Pssm-ID: 235904 [Multi-domain]  Cd Length: 484  Bit Score: 44.57  E-value: 1.12e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2024405217   4 AERAPLLPPPAESSRDGM-AAETPPGMERRAEPGPEEAAVTEEEDEARPASPPFFLLYPGHGGAAAPHGAWRPPAPRGGA 82
Cdd:PRK06995   61 AAQPPPAAAPAAVSRPAApAAEPAPWLVEHAKRLTAQREQLVARAAAPAAPEAQAPAAPAERAAAENAARRLARAAAAAP 140

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*..
gi 2024405217  83 ALPVLLLSYPGPDGASAHPNYLMANERMnlmnMAKL-SIKGLIESAL 128
Cdd:PRK06995  141 RPRVPADAAAAVADAVKARIERIVNDTV----MQELrSLRGMLEEQL 183
COG4372 COG4372
Uncharacterized protein, contains DUF3084 domain [Function unknown];
314-485 1.32e-04

Uncharacterized protein, contains DUF3084 domain [Function unknown];


Pssm-ID: 443500 [Multi-domain]  Cd Length: 370  Bit Score: 44.12  E-value: 1.32e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2024405217 314 LSATVNNLQAKVDALEKSNTKLTEELAVANNRIITLQEEMERVKEEssyilesnrkvtkdrtadgqaLTEARKQLKeetQ 393
Cdd:COG4372    29 LSEQLRKALFELDKLQEELEQLREELEQAREELEQLEEELEQARSE---------------------LEQLEEELE---E 84

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2024405217 394 LRLDVEKELEAQIGMRQEMElamkMLEKDVCEKQDALVALRQQLDDLRALKHELSFKLQSSDMGVKQKSELNSRLEEKTN 473
Cdd:COG4372    85 LNEQLQAAQAELAQAQEELE----SLQEEAEELQEELEELQKERQDLEQQRKQLEAQIAELQSEIAEREEELKELEEQLE 160

                         170
                  ....*....|..
gi 2024405217 474 QMAATIKQLEQS 485
Cdd:COG4372   161 SLQEELAALEQE 172
PRK11281 PRK11281
mechanosensitive channel MscK;
312-491 1.40e-04

mechanosensitive channel MscK;


Pssm-ID: 236892 [Multi-domain]  Cd Length: 1113  Bit Score: 44.90  E-value: 1.40e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2024405217  312 RHLSATVNNLQAKVDALEKSNTKLTEELAVANNRIITLQEEMERVKEE----SSYILESNRKVTKDRTADGQALTEARKQ 387
Cdd:PRK11281   117 TLSTLSLRQLESRLAQTLDQLQNAQNDLAEYNSQLVSLQTQPERAQAAlyanSQRLQQIRNLLKGGKVGGKALRPSQRVL 196

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2024405217  388 LKEETQLrldvekeLEAQIGMRQEmELAMKMLEKDVCEKQDALVALRQQLddlraLKHELSFkLQSSdmgVKQKselnsR 467
Cdd:PRK11281   197 LQAEQAL-------LNAQNDLQRK-SLEGNTQLQDLLQKQRDYLTARIQR-----LEHQLQL-LQEA---INSK-----R 254

                          170       180
                   ....*....|....*....|....
gi 2024405217  468 LEEKTNQMAATIKQLEQSSCGSNP 491
Cdd:PRK11281   255 LTLSEKTVQEAQSQDEAARIQANP 278
PRK04778 PRK04778
septation ring formation regulator EzrA; Provisional
 307-484 1.48e-04

septation ring formation regulator EzrA; Provisional


Pssm-ID: 179877 [Multi-domain]  Cd Length: 569  Bit Score: 44.44  E-value: 1.48e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2024405217 307 VEELNRHLSATVNNL----QAKVDA---LEKSNTKLTEELAVANNRIITLQEEMERVKEesSYIL-----ESNRKVTKDR 374
Cdd:PRK04778  280 AEEKNEEIQERIDQLydilEREVKArkyVEKNSDTLPDFLEHAKEQNKELKEEIDRVKQ--SYTLneselESVRQLEKQL 357

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2024405217 375 TADGQALTEARKQLKEETQLRLDVEKELEaqigmrqEMELAMKMLEKDVCEKQDALVAL-------RQQLDDLRALKHEL 447
Cdd:PRK04778  358 ESLEKQYDEITERIAEQEIAYSELQEELE-------EILKQLEEIEKEQEKLSEMLQGLrkdeleaREKLERYRNKLHEI 430

                         170       180       190
                  ....*....|....*....|....*....|....*...
gi 2024405217 448 SFKLQSSDM-GVKQksELNSRLEEKTNQMAATIKQLEQ 484
Cdd:PRK04778  431 KRYLEKSNLpGLPE--DYLEMFFEVSDEIEALAEELEE 466
COG4913 COG4913
Uncharacterized conserved protein, contains a C-terminal ATPase domain [Function unknown];
296-484 1.78e-04

Uncharacterized conserved protein, contains a C-terminal ATPase domain [Function unknown];


Pssm-ID: 443941 [Multi-domain]  Cd Length: 1089  Bit Score: 44.52  E-value: 1.78e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2024405217  296 QITAILDQKNYVEELNRHLSATVNnlQAKVDALEKSNTKLTEELAVANNRIITLQEEMERVKEEssyILESNRKVtkdRT 375
Cdd:COG4913    263 RYAAARERLAELEYLRAALRLWFA--QRRLELLEAELEELRAELARLEAELERLEARLDALREE---LDELEAQI---RG 334

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2024405217  376 ADGQALTEARKQLKeetqlrlDVEKELEAQIGMRQEMELAMKMLEKDVCEKQDALVALRQQLDDLRALKHELSFKLQSS- 454
Cdd:COG4913    335 NGGDRLEQLEREIE-------RLERELEERERRRARLEALLAALGLPLPASAEEFAALRAEAAALLEALEEELEALEEAl 407

                          170       180       190
                   ....*....|....*....|....*....|
gi 2024405217  455 DMGVKQKSELNSRLEEKTNQmaatIKQLEQ 484
Cdd:COG4913    408 AEAEAALRDLRRELRELEAE----IASLER 433
SMC_prok_A TIGR02169
chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of ...
 300-484 3.13e-04

chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]


Pssm-ID: 274009 [Multi-domain]  Cd Length: 1164  Bit Score: 43.52  E-value: 3.13e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2024405217  300 ILDQK--NYVEELnRHLSATVNNLQAKVDALEKSNTKLTEELAvaNNRIITLQEEMERVKEESSyileSNRKVTKDRTAD 377
Cdd:TIGR02169  748 SLEQEieNVKSEL-KELEARIEELEEDLHKLEEALNDLEARLS--HSRIPEIQAELSKLEEEVS----RIEARLREIEQK 820

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2024405217  378 GQALTEARKQLKEETQLRLDVEKELEAQIGM-RQEMELAMKMLEK---DVCEKQDALVALRQQLDDLRALKHELSFKLQS 453
Cdd:TIGR02169  821 LNRLTLEKEYLEKEIQELQEQRIDLKEQIKSiEKEIENLNGKKEEleeELEELEAALRDLESRLGDLKKERDELEAQLRE 900

                          170       180       190
                   ....*....|....*....|....*....|.
gi 2024405217  454 SDMGVKQKSELNSRLEEKTNQMAATIKQLEQ 484
Cdd:TIGR02169  901 LERKIEELEAQIEKKRKRLSELKAKLEALEE 931
Myosin_tail_1 pfam01576
Myosin tail; The myosin molecule is a multi-subunit complex made up of two heavy chains and ...
 308-484 3.65e-04

Myosin tail; The myosin molecule is a multi-subunit complex made up of two heavy chains and four light chains it is a fundamental contractile protein found in all eukaryote cell types. This family consists of the coiled-coil myosin heavy chain tail region. The coiled-coil is composed of the tail from two molecules of myosin. These can then assemble into the macromolecular thick filament. The coiled-coil region provides the structural backbone the thick filament.


Pssm-ID: 460256 [Multi-domain]  Cd Length: 1081  Bit Score: 43.24  E-value: 3.65e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2024405217  308 EELNRHLSATVNNLQAKVDALEKsntKLTEELAvANNRI----ITLQEEMERVKEESSYILESNRKVTKDRTADGQALTE 383
Cdd:pfam01576   88 EERSQQLQNEKKKMQQHIQDLEE---QLDEEEA-ARQKLqlekVTTEAKIKKLEEDILLLEDQNSKLSKERKLLEERISE 163

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2024405217  384 ARKQLKEE-------TQLRL-------DVEKELEAQIGMRQEMELAMKMLEKDVCEKQDALVALRQQLDDLRAL----KH 445
Cdd:pfam01576  164 FTSNLAEEeekakslSKLKNkheamisDLEERLKKEEKGRQELEKAKRKLEGESTDLQEQIAELQAQIAELRAQlakkEE 243

                          170       180       190
                   ....*....|....*....|....*....|....*....
gi 2024405217  446 ELSFKLQSSDMGVKQKSELNSRLEEKTNQMAATIKQLEQ 484
Cdd:pfam01576  244 ELQAALARLEEETAQKNNALKKIRELEAQISELQEDLES 282
Mplasa_alph_rch TIGR04523
helix-rich Mycoplasma protein; Members of this family occur strictly within a subset of ...
 308-484 3.65e-04

helix-rich Mycoplasma protein; Members of this family occur strictly within a subset of Mycoplasma species. Members average 750 amino acids in length, including signal peptide. Sequences are predicted (Jpred 3) to be almost entirely alpha-helical. These sequences show strong periodicity (consistent with long alpha helical structures) and low complexity rich in D,E,N,Q, and K. Genes encoding these proteins are often found in tandem. The function is unknown.


Pssm-ID: 275316 [Multi-domain]  Cd Length: 745  Bit Score: 43.47  E-value: 3.65e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2024405217 308 EELNRHLSATVNNLQAKVDALEKSNTKLTEELAVANNRIITLQEEMERVKEESSYILESNRKVTKDRTADGQALTEARKQ 387
Cdd:TIGR04523 210 IQKNKSLESQISELKKQNNQLKDNIEKKQQEINEKTTEISNTQTQLNQLKDEQNKIKKQLSEKQKELEQNNKKIKELEKQ 289

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2024405217 388 LKE-ETQLrLDVEKELEAQIgmrqemelaMKMLEKDVCEKQDALVALRQQLDDLRALKHELSFKLQSSDmgvKQKSELNS 466
Cdd:TIGR04523 290 LNQlKSEI-SDLNNQKEQDW---------NKELKSELKNQEKKLEEIQNQISQNNKIISQLNEQISQLK---KELTNSES 356

                         170
                  ....*....|....*...
gi 2024405217 467 RLEEKTNQMAATIKQLEQ 484
Cdd:TIGR04523 357 ENSEKQRELEEKQNEIEK 374
EzrA pfam06160
Septation ring formation regulator, EzrA; During the bacterial cell cycle, the tubulin-like ...
 307-485 3.85e-04

Septation ring formation regulator, EzrA; During the bacterial cell cycle, the tubulin-like cell-division protein FtsZ polymerizes into a ring structure that establishes the location of the nascent division site. EzrA modulates the frequency and position of FtsZ ring formation. The structure contains 5 spectrin like alpha helical repeats.


Pssm-ID: 428797 [Multi-domain]  Cd Length: 542  Bit Score: 42.92  E-value: 3.85e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2024405217 307 VEELNRHLSATVNNL----QAKVDA---LEKSNTKLTEEL--AVANNRiiTLQEEMERVKEesSYIL-----ESNRKVTK 372
Cdd:pfam06160 261 AEEALEEIEERIDQLydllEKEVDAkkyVEKNLPEIEDYLehAEEQNK--ELKEELERVQQ--SYTLnenelERVRGLEK 336

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2024405217 373 DRTADGQALTEARKQLKEETQLRLDVEKELEaqigmrqEMELAMKMLEKDVCEKQDALVALR-------QQLDDLRALKH 445
Cdd:pfam06160 337 QLEELEKRYDEIVERLEEKEVAYSELQEELE-------EILEQLEEIEEEQEEFKESLQSLRkdelearEKLDEFKLELR 409

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|.
gi 2024405217 446 ELSFKLQSSDM-GVKQksELNSRLEEKTNQMAATIKQLEQS 485
Cdd:pfam06160 410 EIKRLVEKSNLpGLPE--SYLDYFFDVSDEIEDLADELNEV 448
PRK03918 PRK03918
DNA double-strand break repair ATPase Rad50;
317-485 4.31e-04

DNA double-strand break repair ATPase Rad50;


Pssm-ID: 235175 [Multi-domain]  Cd Length: 880  Bit Score: 43.13  E-value: 4.31e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2024405217 317 TVNNLQAKVDALEKSNTKLTEELAVANNRIITLQEEMERVKEEssyiLESNRKVTKDRTADGQALTEA-RKQLKEETQLR 395
Cdd:PRK03918  385 TPEKLEKELEELEKAKEEIEEEISKITARIGELKKEIKELKKA----IEELKKAKGKCPVCGRELTEEhRKELLEEYTAE 460

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2024405217 396 L-DVEKELEAQIGMRQEMELAMKMLEKdVCEKQDALVALRQQLDDLRALKHELS-FKLQSsdmgVKQKSELNSRLEEKTN 473
Cdd:PRK03918  461 LkRIEKELKEIEEKERKLRKELRELEK-VLKKESELIKLKELAEQLKELEEKLKkYNLEE----LEKKAEEYEKLKEKLI 535

                         170
                  ....*....|..
gi 2024405217 474 QMAATIKQLEQS 485
Cdd:PRK03918  536 KLKGEIKSLKKE 547
CagA_N pfam18971
CagA protein; The Helicobacter pylori type IV secretion effector CagA is a major bacterial ...
 319-500 4.58e-04

CagA protein; The Helicobacter pylori type IV secretion effector CagA is a major bacterial virulence determinant and critical for gastric carcinogenesis. X-ray crystallographic analysis of the N-terminal CagA fragment (residues 1-876) revealed that the region has a structure comprised of three discrete domains. Domain I constitutes a mobile CagA N terminus, while Domain II tethers CagA to the plasma membrane by interacting with membrane phosphatidylserine. Domain III interacts intramolecularly with the intrinsically disordered C-terminal region, and this interaction potentiates the pathogenic scaffold/hub function of CagA.


Pssm-ID: 408741 [Multi-domain]  Cd Length: 876  Bit Score: 43.22  E-value: 4.58e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2024405217 319 NNLQAKVDALEKSNtKLTEELAVANnriitlqeemervKEESSYILESNRKVTKDRTADG-----QALTEARKQLKEETQ 393
Cdd:pfam18971 563 NKLTAKGLSLQEAN-KLIKDFLSSN-------------KELAGKALNFNKAVAEAKSTGNydevkKAQKDLEKSLRKREH 628

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2024405217 394 LRLDVEKELEAQIGMRQEMElamkmLEKDVCEKQDALVAL--RQQLDDLRALKHELSFKlqssdmGVKQksELNSRLEEK 471
Cdd:pfam18971 629 LEKEVEKKLESKSGNKNKME-----AKAQANSQKDEIFALinKEANRDARAIAYTQNLK------GIKR--ELSDKLEKI 695

                         170       180
                  ....*....|....*....|....*....
gi 2024405217 472 TNQMAATIKQLEQSSCGSNPDCGRRRKTV 500
Cdd:pfam18971 696 SKDLKDFSKSFDEFKNGKNKDFSKAEETL 724
COG4372 COG4372
Uncharacterized protein, contains DUF3084 domain [Function unknown];
307-442 5.47e-04

Uncharacterized protein, contains DUF3084 domain [Function unknown];


Pssm-ID: 443500 [Multi-domain]  Cd Length: 370  Bit Score: 42.20  E-value: 5.47e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2024405217 307 VEELNRHLSATVNNLQAKVDALEKSNTKLTEELAVANNRIITLQEEMERVKEESSYILESNRKVTKDRTADGQALTEARK 386
Cdd:COG4372    29 LSEQLRKALFELDKLQEELEQLREELEQAREELEQLEEELEQARSELEQLEEELEELNEQLQAAQAELAQAQEELESLQE 108

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 2024405217 387 QLKEETQLRLDVEKELEAQIGMRQEMELAMKMLEKDVCEKQDALVALRQQLDDLRA 442
Cdd:COG4372   109 EAEELQEELEELQKERQDLEQQRKQLEAQIAELQSEIAEREEELKELEEQLESLQE 164
Mplasa_alph_rch TIGR04523
helix-rich Mycoplasma protein; Members of this family occur strictly within a subset of ...
 324-485 9.02e-04

helix-rich Mycoplasma protein; Members of this family occur strictly within a subset of Mycoplasma species. Members average 750 amino acids in length, including signal peptide. Sequences are predicted (Jpred 3) to be almost entirely alpha-helical. These sequences show strong periodicity (consistent with long alpha helical structures) and low complexity rich in D,E,N,Q, and K. Genes encoding these proteins are often found in tandem. The function is unknown.


Pssm-ID: 275316 [Multi-domain]  Cd Length: 745  Bit Score: 41.93  E-value: 9.02e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2024405217 324 KVDALEKSNTKLTEELAVANNRIITLQEEMERVKEEssyILESNRKVTKDrtadgqaLTEARKQLKEETQLRLDVeKELE 403
Cdd:TIGR04523  97 KINKLNSDLSKINSEIKNDKEQKNKLEVELNKLEKQ---KKENKKNIDKF-------LTEIKKKEKELEKLNNKY-NDLK 165

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2024405217 404 AQIgmrQEMELAMKMLEKDVCEKQDALVALRQQlddLRALKHELSfKLQSSDMGVKQ-KSELNsRLEEKTNQMAATIKQL 482
Cdd:TIGR04523 166 KQK---EELENELNLLEKEKLNIQKNIDKIKNK---LLKLELLLS-NLKKKIQKNKSlESQIS-ELKKQNNQLKDNIEKK 237


                  ...
gi 2024405217 483 EQS 485
Cdd:TIGR04523 238 QQE 240
GumC COG3206
Exopolysaccharide export protein/domain GumC/Wzc1 [Cell wall/membrane/envelope biogenesis];
319-484 1.46e-03

Exopolysaccharide export protein/domain GumC/Wzc1 [Cell wall/membrane/envelope biogenesis];


Pssm-ID: 442439 [Multi-domain]  Cd Length: 687  Bit Score: 41.16  E-value: 1.46e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2024405217 319 NNLQAKVDALEKSNTKLTEELAVANNRIITLQEEMERVKEESSYI-LESNRKVTKDRTAD-GQALTEARKQLKE------ 390
Cdd:COG3206   164 QNLELRREEARKALEFLEEQLPELRKELEEAEAALEEFRQKNGLVdLSEEAKLLLQQLSElESQLAEARAELAEaearla 243

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2024405217 391 --ETQLRLDVE-----------KELEAQIgmrQEMELAMKMLEKDVCEKQDALVALRQQLDDLRA-LKHELSFKLQSSDM 456
Cdd:COG3206   244 alRAQLGSGPDalpellqspviQQLRAQL---AELEAELAELSARYTPNHPDVIALRAQIAALRAqLQQEAQRILASLEA 320

                         170       180       190
                  ....*....|....*....|....*....|..
gi 2024405217 457 GVK----QKSELNSRLEEkTNQMAATIKQLEQ 484
Cdd:COG3206   321 ELEalqaREASLQAQLAQ-LEARLAELPELEA 351
YhaN COG4717
Uncharacterized conserved protein YhaN, contains AAA domain [Function unknown];
295-442 1.64e-03

Uncharacterized conserved protein YhaN, contains AAA domain [Function unknown];


Pssm-ID: 443752 [Multi-domain]  Cd Length: 641  Bit Score: 41.29  E-value: 1.64e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2024405217 295 GQITAILDQKNYVEELNRHLSATVNNLQAKVDALEK--SNTKLTEELAVANNRIITLQEEMERVKEEssyiLESNRKVTK 372
Cdd:COG4717    88 EEYAELQEELEELEEELEELEAELEELREELEKLEKllQLLPLYQELEALEAELAELPERLEELEER----LEELRELEE 163

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 2024405217 373 DRTADGQALTEARKQLKEE-TQLRLDVEKELEAQIGMRQEMELAMKMLEKDVCEKQDALVALRQQLDDLRA 442
Cdd:COG4717   164 ELEELEAELAELQEELEELlEQLSLATEEELQDLAEELEELQQRLAELEEELEEAQEELEELEEELEQLEN 234
PRK12323 PRK12323
DNA polymerase III subunit gamma/tau;
2-99 1.98e-03

DNA polymerase III subunit gamma/tau;


Pssm-ID: 237057 [Multi-domain]  Cd Length: 700  Bit Score: 41.01  E-value: 1.98e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2024405217   2 AEAERAPLLPPPAESSRDGMAAETPPGMERRAEPGPEEAAVTEEEDEARPASPPffllYPGHGGAAAPHGAWRPPA--PR 79
Cdd:PRK12323  395 AAPAPAAPPAAPAAAPAAAAAARAVAAAPARRSPAPEALAAARQASARGPGGAP----APAPAPAAAPAAAARPAAagPR 470

                          90       100
                  ....*....|....*....|
gi 2024405217  80 GGAALPVLLLSYPGPDGASA 99
Cdd:PRK12323  471 PVAAAAAAAPARAAPAAAPA 490
EnvC COG4942
Septal ring factor EnvC, activator of murein hydrolases AmiA and AmiB [Cell cycle control, ...
 299-443 2.16e-03

Septal ring factor EnvC, activator of murein hydrolases AmiA and AmiB [Cell cycle control, cell division, chromosome partitioning];


Pssm-ID: 443969 [Multi-domain]  Cd Length: 377  Bit Score: 40.52  E-value: 2.16e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2024405217 299 AILDQKNYVEELNRHLSAT---VNNLQAKVDALEKSNTKLTEELAvanNRIITLQ-----------------EEMERVKE 358
Cdd:COG4942    63 RIAALARRIRALEQELAALeaeLAELEKEIAELRAELEAQKEELA---ELLRALYrlgrqpplalllspedfLDAVRRLQ 139

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2024405217 359 ESSYILESNRKVTKDRTADGQALTEARKQLKEETQLRLDVEKELEAQIG----MRQEMELAMKMLEKDVCEKQDALVALR 434
Cdd:COG4942   140 YLKYLAPARREQAEELRADLAELAALRAELEAERAELEALLAELEEERAaleaLKAERQKLLARLEKELAELAAELAELQ 219


                  ....*....
gi 2024405217 435 QQLDDLRAL 443
Cdd:COG4942   220 QEAEELEAL 228
PRK07764 PRK07764
DNA polymerase III subunits gamma and tau; Validated
 1-99 3.34e-03

DNA polymerase III subunits gamma and tau; Validated


Pssm-ID: 236090 [Multi-domain]  Cd Length: 824  Bit Score: 40.35  E-value: 3.34e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2024405217   1 MAEAERAPLLPPPAESSRDGMAAETPPGMERRAEPGPEEAAVTEEEDEARPASPP----FFLLYPGHGGAAAPHGAWRPP 76
Cdd:PRK07764  387 VAGGAGAPAAAAPSAAAAAPAAAPAPAAAAPAAAAAPAPAAAPQPAPAPAPAPAPpspaGNAPAGGAPSPPPAAAPSAQP 466

                          90       100
                  ....*....|....*....|...
gi 2024405217  77 APRGGAALPVLLLSYPGPDGASA 99
Cdd:PRK07764  467 APAPAAAPEPTAAPAPAPPAAPA 489
46 PHA02562
endonuclease subunit; Provisional
 303-481 3.42e-03

endonuclease subunit; Provisional


Pssm-ID: 222878 [Multi-domain]  Cd Length: 562  Bit Score: 40.00  E-value: 3.42e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2024405217 303 QKNYVEELNRHLSATVNNLQAKVDALEKSNTKLTEELAVANNRIITLQEEMErvkeessyilesnrkvtkDRTADGQALT 382
Cdd:PHA02562  200 YNKNIEEQRKKNGENIARKQNKYDELVEEAKTIKAEIEELTDELLNLVMDIE------------------DPSAALNKLN 261

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2024405217 383 EARKQLKEETQLrldVEKEleaqigmrqemelaMKMLEK-DVC---------------EKQDALVALRQQLDDLRALKHE 446
Cdd:PHA02562  262 TAAAKIKSKIEQ---FQKV--------------IKMYEKgGVCptctqqisegpdritKIKDKLKELQHSLEKLDTAIDE 324

                         170       180       190
                  ....*....|....*....|....*....|....*
gi 2024405217 447 LSFKLQSSDMGVKQKSELNSRLEEKTNQMAATIKQ 481
Cdd:PHA02562  325 LEEIMDEFNEQSKKLLELKNKISTNKQSLITLVDK 359
SMC_prok_B TIGR02168
chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of ...
 301-485 3.51e-03

chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]


Pssm-ID: 274008 [Multi-domain]  Cd Length: 1179  Bit Score: 40.43  E-value: 3.51e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2024405217  301 LDQKNYVEELNRHLSAT-VNNLQAKVDALEKSNTKLTEELAVANNRIITLQEEMERVKeesSYILESNRKVTkDRTADGQ 379
Cdd:TIGR02168  216 KELKAELRELELALLVLrLEELREELEELQEELKEAEEELEELTAELQELEEKLEELR---LEVSELEEEIE-ELQKELY 291

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2024405217  380 ALTEARKQLKEETQLRLDVEKELEAQIgmrQEMELAMKMLEKDVCEKQDALVALRQQLDDLRALKHELSFKLQSSdmgVK 459
Cdd:TIGR02168  292 ALANEISRLEQQKQILRERLANLERQL---EELEAQLEELESKLDELAEELAELEEKLEELKEELESLEAELEEL---EA 365

                          170       180
                   ....*....|....*....|....*....
gi 2024405217  460 QKSELNSRLEEKTNQM---AATIKQLEQS 485
Cdd:TIGR02168  366 ELEELESRLEELEEQLetlRSKVAQLELQ 394
SMC_prok_A TIGR02169
chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of ...
 291-485 3.98e-03

chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]


Pssm-ID: 274009 [Multi-domain]  Cd Length: 1164  Bit Score: 40.05  E-value: 3.98e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2024405217  291 SEGDGQITAILDQKNYVEELNRHLSATVNNLQAKVDALEKSNTKLTEElavannRIITLQEEMERVKEESSYiLESNRKV 370
Cdd:TIGR02169  240 EAIERQLASLEEELEKLTEEISELEKRLEEIEQLLEELNKKIKDLGEE------EQLRVKEKIGELEAEIAS-LERSIAE 312

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2024405217  371 TKDRTADGQA-----LTEARKQLKEETQLRLDVE---KELEAQIGMRQEMELAMKMLEKDVCEKQDALVALRQQLDDLR- 441
Cdd:TIGR02169  313 KERELEDAEErlaklEAEIDKLLAEIEELEREIEeerKRRDKLTEEYAELKEELEDLRAELEEVDKEFAETRDELKDYRe 392

                          170       180       190       200
                   ....*....|....*....|....*....|....*....|....*..
gi 2024405217  442 ---ALKHELSFKLQSSDMGVKQKSELNSRLEEKTNQMAATIKQLEQS 485
Cdd:TIGR02169  393 kleKLKREINELKRELDRLQEELQRLSEELADLNAAIAGIEAKINEL 439
DR0291 COG1579
Predicted nucleic acid-binding protein DR0291, contains C4-type Zn-ribbon domain [General ...
 321-484 4.36e-03

Predicted nucleic acid-binding protein DR0291, contains C4-type Zn-ribbon domain [General function prediction only];


Pssm-ID: 441187 [Multi-domain]  Cd Length: 236  Bit Score: 38.75  E-value: 4.36e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2024405217 321 LQAKVDALEKSNTKLTEELAVANNRIITLQEEMERVKEESSYILESNRKVTKDRTADGQALTEARKQLKEETQLR--LDV 398
Cdd:COG1579    15 LDSELDRLEHRLKELPAELAELEDELAALEARLEAAKTELEDLEKEIKRLELEIEEVEARIKKYEEQLGNVRNNKeyEAL 94

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2024405217 399 EKELEAQIGMRQEMELAMKMLEKDVCEKQDALVALRQQLDDLRAlkhELSFKLQSSDmgvKQKSELNSRLEEKTNQMAAT 478
Cdd:COG1579    95 QKEIESLKRRISDLEDEILELMERIEELEEELAELEAELAELEA---ELEEKKAELD---EELAELEAELEELEAEREEL 168


                  ....*.
gi 2024405217 479 IKQLEQ 484
Cdd:COG1579   169 AAKIPP 174
Mplasa_alph_rch TIGR04523
helix-rich Mycoplasma protein; Members of this family occur strictly within a subset of ...
 294-483 5.12e-03

helix-rich Mycoplasma protein; Members of this family occur strictly within a subset of Mycoplasma species. Members average 750 amino acids in length, including signal peptide. Sequences are predicted (Jpred 3) to be almost entirely alpha-helical. These sequences show strong periodicity (consistent with long alpha helical structures) and low complexity rich in D,E,N,Q, and K. Genes encoding these proteins are often found in tandem. The function is unknown.


Pssm-ID: 275316 [Multi-domain]  Cd Length: 745  Bit Score: 39.62  E-value: 5.12e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2024405217 294 DGQITAILDQKNYVEELNRHLSATVNNLQAKVDALEKSNTKLTEELAVANNRIITLQEEMERVKEESSYI---LESNRKV 370
Cdd:TIGR04523 411 DEQIKKLQQEKELLEKEIERLKETIIKNNSEIKDLTNQDSVKELIIKNLDNTRESLETQLKVLSRSINKIkqnLEQKQKE 490

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2024405217 371 TKDRTADGQALTEARKQLKEETQ-------LRLDVEKELEAQIGMRQ-------------EMELAMKMLEKDVCEKQDAL 430
Cdd:TIGR04523 491 LKSKEKELKKLNEEKKELEEKVKdltkkisSLKEKIEKLESEKKEKEskisdledelnkdDFELKKENLEKEIDEKNKEI 570

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|...
gi 2024405217 431 VALRQQLDDLRALKHELSFKLQSSDmgvKQKSELNSRLEEKTNQMAATIKQLE 483
Cdd:TIGR04523 571 EELKQTQKSLKKKQEEKQELIDQKE---KEKKDLIKEIEEKEKKISSLEKELE 620
SCP-1 pfam05483
Synaptonemal complex protein 1 (SCP-1); Synaptonemal complex protein 1 (SCP-1) is the major ...
 309-484 5.36e-03

Synaptonemal complex protein 1 (SCP-1); Synaptonemal complex protein 1 (SCP-1) is the major component of the transverse filaments of the synaptonemal complex. Synaptonemal complexes are structures that are formed between homologous chromosomes during meiotic prophase.


Pssm-ID: 114219 [Multi-domain]  Cd Length: 787  Bit Score: 39.70  E-value: 5.36e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2024405217 309 ELNRHLSATVNNLQAKVDALEKSNTKLTEELAVANNRIITLQEEMERVKEESSYILESNRKVTKDRTA-----------D 377
Cdd:pfam05483 289 EKKDHLTKELEDIKMSLQRSMSTQKALEEDLQIATKTICQLTEEKEAQMEELNKAKAAHSFVVTEFEAttcsleellrtE 368

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2024405217 378 GQALTEARKQLKEETQLRLDVEKELEAQIGMRQEMELAMKMLEKDVCEKQDALVALRQ---QLDDLRALKHELSFKLQSS 454
Cdd:pfam05483 369 QQRLEKNEDQLKIITMELQKKSSELEEMTKFKNNKEVELEELKKILAEDEKLLDEKKQfekIAEELKGKEQELIFLLQAR 448

                         170       180       190
                  ....*....|....*....|....*....|
gi 2024405217 455 DmgvKQKSELNSRLEEKTNQMAATIKQLEQ 484
Cdd:pfam05483 449 E---KEIHDLEIQLTAIKTSEEHYLKEVED 475
COG4913 COG4913
Uncharacterized conserved protein, contains a C-terminal ATPase domain [Function unknown];
322-471 5.43e-03

Uncharacterized conserved protein, contains a C-terminal ATPase domain [Function unknown];


Pssm-ID: 443941 [Multi-domain]  Cd Length: 1089  Bit Score: 39.51  E-value: 5.43e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2024405217  322 QAKVDALEKSNTKLTEELAVANNRIITLQEEMERVKEessyILESNRKVTKDRTA--DGQALTEARKQLKEE-TQLRLDV 398
Cdd:COG4913    609 RAKLAALEAELAELEEELAEAEERLEALEAELDALQE----RREALQRLAEYSWDeiDVASAEREIAELEAElERLDASS 684

                           90       100       110       120       130       140       150
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 2024405217  399 E--KELEAQIgmrQEMELAMKMLEKDVCEKQDALVALRQQLDDLRALKHELSFKLQssDMGVKQKSELNSRLEEK 471
Cdd:COG4913    685 DdlAALEEQL---EELEAELEELEEELDELKGEIGRLEKELEQAEEELDELQDRLE--AAEDLARLELRALLEER 754
UPF0242 pfam06785
Uncharacterized protein family (UPF0242) N-terminus; This region includes an N-terminal ...
 351-484 5.71e-03

Uncharacterized protein family (UPF0242) N-terminus; This region includes an N-terminal transmembrane region and a C-terminal coiled-coil.


Pssm-ID: 429117 [Multi-domain]  Cd Length: 194  Bit Score: 38.26  E-value: 5.71e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2024405217 351 EEMERVKEESSYILESNRKVTKDRTADGQALTEARKQLKEETQ-LRLDVEKELEAQIGMRQEMELAMKMLEKDVCEKQDA 429
Cdd:pfam06785  58 EDALKEKFEKSFLEEKEAKLTELDAEGFKILEETLEELQSEEErLEEELSQKEEELRRLTEENQQLQIQLQQISQDFAEF 137

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 2024405217 430 LVALRQQLDDLRALKHELSFKLQSSDMGVKQKSELNSRLEEKTNQMAATIKQLEQ 484
Cdd:pfam06785 138 RLESEEQLAEKQLLINEYQQTIEEQRSVLEKRQDQIENLESKVRDLNYEIKTLLQ 192
DUF5401 pfam17380
Family of unknown function (DUF5401); This is a family of unknown function found in ...
 282-475 6.39e-03

Family of unknown function (DUF5401); This is a family of unknown function found in Chromadorea.


Pssm-ID: 375164 [Multi-domain]  Cd Length: 722  Bit Score: 39.34  E-value: 6.39e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2024405217 282 LKDGNSTKGSEGDGQITAILDQKNYVEELNRHLSATvnNLQAKVDALEKSNTkltEELAVANNRIITL-------QEEME 354
Cdd:pfam17380 318 LEEAEKARQAEMDRQAAIYAEQERMAMERERELERI--RQEERKRELERIRQ---EEIAMEISRMRELerlqmerQQKNE 392

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2024405217 355 RVKEEssyiLESNRKVtkdRTADGQALTEARKQLKEETQLRLDVEKELEAQIG-MRQEMELAMKMLEKDVCEKQDALVAL 433
Cdd:pfam17380 393 RVRQE----LEAARKV---KILEEERQRKIQQQKVEMEQIRAEQEEARQREVRrLEEERAREMERVRLEEQERQQQVERL 465

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|...
gi 2024405217 434 RQQLDDLRALKHELSFKLQSSDMGVKQKSE-LNSRLEEKTNQM 475
Cdd:pfam17380 466 RQQEEERKRKKLELEKEKRDRKRAEEQRRKiLEKELEERKQAM 508
 
Blast search parameters
Data Source: Precalculated data, version = cdd.v.3.21
Preset Options:Database: CDSEARCH/cdd   Low complexity filter: no  Composition Based Adjustment: yes   E-value threshold: 0.01

References:

  • Wang J et al. (2023), "The conserved domain database in 2023", Nucleic Acids Res.51(D)384-8.
  • Lu S et al. (2020), "The conserved domain database in 2020", Nucleic Acids Res.48(D)265-8.
  • Marchler-Bauer A et al. (2017), "CDD/SPARCLE: functional classification of proteins via subfamily domain architectures.", Nucleic Acids Res.45(D)200-3.
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