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Conserved domains on  [gi|653594746|ref|WP_027607638|]
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MULTISPECIES: PAS domain-containing protein [Pseudomonas]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
PRK13558 super family cl36264
bacterio-opsin activator; Provisional
 17-129 1.03e-32

bacterio-opsin activator; Provisional


The actual alignment was detected with superfamily member PRK13558:

Pssm-ID: 237426 [Multi-domain]  Cd Length: 665  Bit Score: 121.48  E-value: 1.03e-32
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 653594746  17 GIVVAEREGKDKPLIYVNPAFERLTGYTLDEILYQDCRFLQSGDRDQPALMAIREALENGGACRETLRNYRKDGSHFWNE 96
Cdd:PRK13558 160 GITIADATLPDEPLIYINDAFERITGYSPDEVLGRNCRFLQGEDTNEERVAELREAIDEERPTSVELRNYRKDGSTFWNQ 239

                         90       100       110
                 ....*....|....*....|....*....|...
gi 653594746  97 LSLSTVYNAADKQTYFVGVQKDVTLQVKAQQRV 129
Cdd:PRK13558 240 VDIAPIRDEDGTVTHYVGFQTDVTERKEAELAL 272
 
Name Accession Description Interval E-value
PRK13558 PRK13558
bacterio-opsin activator; Provisional
 17-129 1.03e-32

bacterio-opsin activator; Provisional


Pssm-ID: 237426 [Multi-domain]  Cd Length: 665  Bit Score: 121.48  E-value: 1.03e-32
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 653594746  17 GIVVAEREGKDKPLIYVNPAFERLTGYTLDEILYQDCRFLQSGDRDQPALMAIREALENGGACRETLRNYRKDGSHFWNE 96
Cdd:PRK13558 160 GITIADATLPDEPLIYINDAFERITGYSPDEVLGRNCRFLQGEDTNEERVAELREAIDEERPTSVELRNYRKDGSTFWNQ 239

                         90       100       110
                 ....*....|....*....|....*....|...
gi 653594746  97 LSLSTVYNAADKQTYFVGVQKDVTLQVKAQQRV 129
Cdd:PRK13558 240 VDIAPIRDEDGTVTHYVGFQTDVTERKEAELAL 272
PAS COG2202
PAS domain [Signal transduction mechanisms];
6-139 1.18e-30

PAS domain [Signal transduction mechanisms];


Pssm-ID: 441804 [Multi-domain]  Cd Length: 258  Bit Score: 110.88  E-value: 1.18e-30
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 653594746   6 LMQMVINASNDGIVVAEREGKdkpLIYVNPAFERLTGYTLDEILYQDCRFLQSGDRDQPALMAIREALENGGACRETLRN 85
Cdd:COG2202   12 RLRALVESSPDAIIITDLDGR---ILYVNPAFERLTGYSAEELLGKTLRDLLPPEDDDEFLELLRAALAGGGVWRGELRN 88

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....
gi 653594746  86 YRKDGSHFWNELSLSTVYNAADKQTYFVGVQKDVTLQVKAQQRVAQLESELAEV 139
Cdd:COG2202   89 RRKDGSLFWVELSISPVRDEDGEITGFVGIARDITERKRAEEALRESEERLRLL 142
PAS_9 pfam13426
PAS domain; This domain is found in many signalling proteins in which it functions as a sensor ...
 27-120 5.34e-19

PAS domain; This domain is found in many signalling proteins in which it functions as a sensor domain. It recognizes FMN, Zn(II), FAD and riboflavin (MAtilla et. al., FEMS Microbiology Reviews, fuab043, 45, 2021, 1. https://doi.org/10.1093/femsre/fuab043).


Pssm-ID: 463873 [Multi-domain]  Cd Length: 93  Bit Score: 76.35  E-value: 5.34e-19
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 653594746   27 DKPLIYVNPAFERLTGYTLDEILYQDCRFLQSGDRDQpalMAIREALENGGACRE-TLRNYRKDGSHFWNELSLSTVYNA 105
Cdd:pfam13426   1 DGRIIYVNDAALRLLGYTREELLGKSITDLFAEPEDS---ERLREALREGKAVREfEVVLYRKDGEPFPVLVSLAPIRDD 77

                          90
                  ....*....|....*
gi 653594746  106 ADKQTYFVGVQKDVT 120
Cdd:pfam13426  78 GGELVGIIAILRDIT 92
sensory_box TIGR00229
PAS domain S-box; The PAS domain was previously described. This sensory box, or S-box domain ...
 14-128 1.51e-17

PAS domain S-box; The PAS domain was previously described. This sensory box, or S-box domain occupies the central portion of the PAS domain but is more widely distributed. It is often tandemly repeated. Known prosthetic groups bound in the S-box domain include heme in the oxygen sensor FixL, FAD in the redox potential sensor NifL, and a 4-hydroxycinnamyl chromophore in photoactive yellow protein. Proteins containing the domain often contain other regulatory domains such as response regulator or sensor histidine kinase domains. Other S-box proteins include phytochromes and the aryl hydrocarbon receptor nuclear translocator. [Regulatory functions, Small molecule interactions]


Pssm-ID: 272971 [Multi-domain]  Cd Length: 124  Bit Score: 73.48  E-value: 1.51e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 653594746   14 SNDGIVVAEREGKdkpLIYVNPAFERLTGYTLDEILYQDCRFL-QSGDRDQPALMAIREALENGGACRETLRNYRKDGSH 92
Cdd:TIGR00229  12 SPDAIIVIDLEGN---ILYVNPAFEEIFGYSAEELIGRNVLELiPEEDREEVRERIERRLEGEPEPVSEERRVRRKDGSE 88

                          90       100       110
                  ....*....|....*....|....*....|....*.
gi 653594746   93 FWNELSLSTVYnAADKQTYFVGVQKDVTLQVKAQQR 128
Cdd:TIGR00229  89 IWVEVSVSPIR-TNGGELGVVGIVRDITERKEAEEA 123
PAS cd00130
PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising ...
 14-119 3.65e-11

PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in signal transduction.


Pssm-ID: 238075 [Multi-domain]  Cd Length: 103  Bit Score: 56.49  E-value: 3.65e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 653594746  14 SNDGIVVAEREGKdkpLIYVNPAFERLTGYTLDEILYQDCRFLQSGDRDQPALMAIREALENGGACRETLRNYRKDGSHF 93
Cdd:cd00130    1 LPDGVIVLDLDGR---ILYANPAAEQLLGYSPEELIGKSLLDLIHPEDREELRERLENLLSGGEPVTLEVRLRRKDGSVI 77

                         90       100
                 ....*....|....*....|....*.
gi 653594746  94 WNELSLSTVYNAADKQTYFVGVQKDV 119
Cdd:cd00130   78 WVLVSLTPIRDEGGEVIGLLGVVRDI 103
PAC smart00086
Motif C-terminal to PAS motifs (likely to contribute to PAS structural domain); PAC motif ...
 83-120 4.82e-08

Motif C-terminal to PAS motifs (likely to contribute to PAS structural domain); PAC motif occurs C-terminal to a subset of all known PAS motifs. It is proposed to contribute to the PAS domain fold.


Pssm-ID: 197509  Cd Length: 43  Bit Score: 46.79  E-value: 4.82e-08
                           10        20        30
                   ....*....|....*....|....*....|....*...
gi 653594746    83 LRNYRKDGSHFWNELSLSTVYNAADKQTYFVGVQKDVT 120
Cdd:smart00086   4 YRLRRKDGSYIWVLVSASPIRDEDGEVEGILGVVRDIT 41
 
Name Accession Description Interval E-value
PRK13558 PRK13558
bacterio-opsin activator; Provisional
 17-129 1.03e-32

bacterio-opsin activator; Provisional


Pssm-ID: 237426 [Multi-domain]  Cd Length: 665  Bit Score: 121.48  E-value: 1.03e-32
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 653594746  17 GIVVAEREGKDKPLIYVNPAFERLTGYTLDEILYQDCRFLQSGDRDQPALMAIREALENGGACRETLRNYRKDGSHFWNE 96
Cdd:PRK13558 160 GITIADATLPDEPLIYINDAFERITGYSPDEVLGRNCRFLQGEDTNEERVAELREAIDEERPTSVELRNYRKDGSTFWNQ 239

                         90       100       110
                 ....*....|....*....|....*....|...
gi 653594746  97 LSLSTVYNAADKQTYFVGVQKDVTLQVKAQQRV 129
Cdd:PRK13558 240 VDIAPIRDEDGTVTHYVGFQTDVTERKEAELAL 272
PAS COG2202
PAS domain [Signal transduction mechanisms];
6-139 1.18e-30

PAS domain [Signal transduction mechanisms];


Pssm-ID: 441804 [Multi-domain]  Cd Length: 258  Bit Score: 110.88  E-value: 1.18e-30
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 653594746   6 LMQMVINASNDGIVVAEREGKdkpLIYVNPAFERLTGYTLDEILYQDCRFLQSGDRDQPALMAIREALENGGACRETLRN 85
Cdd:COG2202   12 RLRALVESSPDAIIITDLDGR---ILYVNPAFERLTGYSAEELLGKTLRDLLPPEDDDEFLELLRAALAGGGVWRGELRN 88

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....
gi 653594746  86 YRKDGSHFWNELSLSTVYNAADKQTYFVGVQKDVTLQVKAQQRVAQLESELAEV 139
Cdd:COG2202   89 RRKDGSLFWVELSISPVRDEDGEITGFVGIARDITERKRAEEALRESEERLRLL 142
PRK13559 PRK13559
hypothetical protein; Provisional
 18-136 9.34e-30

hypothetical protein; Provisional


Pssm-ID: 237427 [Multi-domain]  Cd Length: 361  Bit Score: 110.68  E-value: 9.34e-30
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 653594746  18 IVVAEREGKDKPLIYVNPAFERLTGYTLDEILYQDCRFLQSGDRDQPALMAIREALENGGACRETLRNYRKDGSHFWNEL 97
Cdd:PRK13559  56 MCITDPHQPDLPIVLANQAFLDLTGYAAEEVVGRNCRFLQGAATDPIAVAKIRAAIAAEREIVVELLNYRKDGEPFWNAL 135

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|..
gi 653594746  98 SLSTVYNAADKQTYFVGVQKDVT--LQVKAQQRVA-QLESEL 136
Cdd:PRK13559 136 HLGPVYGEDGRLLYFFGSQWDVTdiRAVRALEAHErRLAREV 177
PRK13557 PRK13557
histidine kinase; Provisional
 27-131 7.74e-28

histidine kinase; Provisional


Pssm-ID: 237425 [Multi-domain]  Cd Length: 540  Bit Score: 107.45  E-value: 7.74e-28
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 653594746  27 DKPLIYVNPAFERLTGYTLDEILYQDCRFLQSGDRDQPALMAIREALENGGACRETLRNYRKDGSHFWNELSLSTVYNAA 106
Cdd:PRK13557  52 DNPIVFANRAFLEMTGYAAEEIIGNNCRFLQGPETDRATVAEVRDAIAERREIATEILNYRKDGSSFWNALFVSPVYNDA 131

                         90       100
                 ....*....|....*....|....*
gi 653594746 107 DKQTYFVGVQKDVTLQVKAQQRVAQ 131
Cdd:PRK13557 132 GDLVYFFGSQLDVSRRRDAEDALRQ 156
PAS_9 pfam13426
PAS domain; This domain is found in many signalling proteins in which it functions as a sensor ...
 27-120 5.34e-19

PAS domain; This domain is found in many signalling proteins in which it functions as a sensor domain. It recognizes FMN, Zn(II), FAD and riboflavin (MAtilla et. al., FEMS Microbiology Reviews, fuab043, 45, 2021, 1. https://doi.org/10.1093/femsre/fuab043).


Pssm-ID: 463873 [Multi-domain]  Cd Length: 93  Bit Score: 76.35  E-value: 5.34e-19
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 653594746   27 DKPLIYVNPAFERLTGYTLDEILYQDCRFLQSGDRDQpalMAIREALENGGACRE-TLRNYRKDGSHFWNELSLSTVYNA 105
Cdd:pfam13426   1 DGRIIYVNDAALRLLGYTREELLGKSITDLFAEPEDS---ERLREALREGKAVREfEVVLYRKDGEPFPVLVSLAPIRDD 77

                          90
                  ....*....|....*
gi 653594746  106 ADKQTYFVGVQKDVT 120
Cdd:pfam13426  78 GGELVGIIAILRDIT 92
sensory_box TIGR00229
PAS domain S-box; The PAS domain was previously described. This sensory box, or S-box domain ...
 14-128 1.51e-17

PAS domain S-box; The PAS domain was previously described. This sensory box, or S-box domain occupies the central portion of the PAS domain but is more widely distributed. It is often tandemly repeated. Known prosthetic groups bound in the S-box domain include heme in the oxygen sensor FixL, FAD in the redox potential sensor NifL, and a 4-hydroxycinnamyl chromophore in photoactive yellow protein. Proteins containing the domain often contain other regulatory domains such as response regulator or sensor histidine kinase domains. Other S-box proteins include phytochromes and the aryl hydrocarbon receptor nuclear translocator. [Regulatory functions, Small molecule interactions]


Pssm-ID: 272971 [Multi-domain]  Cd Length: 124  Bit Score: 73.48  E-value: 1.51e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 653594746   14 SNDGIVVAEREGKdkpLIYVNPAFERLTGYTLDEILYQDCRFL-QSGDRDQPALMAIREALENGGACRETLRNYRKDGSH 92
Cdd:TIGR00229  12 SPDAIIVIDLEGN---ILYVNPAFEEIFGYSAEELIGRNVLELiPEEDREEVRERIERRLEGEPEPVSEERRVRRKDGSE 88

                          90       100       110
                  ....*....|....*....|....*....|....*.
gi 653594746   93 FWNELSLSTVYnAADKQTYFVGVQKDVTLQVKAQQR 128
Cdd:TIGR00229  89 IWVEVSVSPIR-TNGGELGVVGIVRDITERKEAEEA 123
NtrB COG3852
Signal transduction histidine kinase NtrB, nitrogen specific [Signal transduction mechanisms];
5-133 3.18e-17

Signal transduction histidine kinase NtrB, nitrogen specific [Signal transduction mechanisms];


Pssm-ID: 443061 [Multi-domain]  Cd Length: 361  Bit Score: 76.81  E-value: 3.18e-17
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 653594746   5 KLMQMVINASNDGIVVAEREGKdkpLIYVNPAFERLTGYTLDEILYQDCRFLQSGDRdqPALMAIREALENGGACRET-L 83
Cdd:COG3852    7 ELLRAILDSLPDAVIVLDADGR---ITYVNPAAERLLGLSAEELLGRPLAELFPEDS--PLRELLERALAEGQPVTEReV 81

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|
gi 653594746  84 RNYRKDGSHFWNELSLSTVYNaADKQTYFVGVQKDVTLQVKAQQRVAQLE 133
Cdd:COG3852   82 TLRRKDGEERPVDVSVSPLRD-AEGEGGVLLVLRDITERKRLERELRRAE 130
PAS COG2202
PAS domain [Signal transduction mechanisms];
5-128 1.62e-12

PAS domain [Signal transduction mechanisms];


Pssm-ID: 441804 [Multi-domain]  Cd Length: 258  Bit Score: 63.12  E-value: 1.62e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 653594746   5 KLMQMVINASNDGIVVAEREGKdkpLIYVNPAFERLTGYTLDEILYQDCRFLQSGDRDQPALMAIREALENGGACRET-L 83
Cdd:COG2202  137 ERLRLLVENAPDGIFVLDLDGR---ILYVNPAAEELLGYSPEELLGKSLLDLLHPEDRERLLELLRRLLEGGRESYELeL 213

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*
gi 653594746  84 RNYRKDGSHFWNELSLSTVYNaADKQTYFVGVQKDVTLQVKAQQR 128
Cdd:COG2202  214 RLKDGDGRWVWVEASAVPLRD-GGEVIGVLGIVRDITERKRAEEA 257
PAS_3 pfam08447
PAS fold; The PAS fold corresponds to the structural domain that has previously been defined ...
 31-115 5.68e-12

PAS fold; The PAS fold corresponds to the structural domain that has previously been defined as PAS and PAC motifs. The PAS fold appears in archaea, eubacteria and eukarya.


Pssm-ID: 430001 [Multi-domain]  Cd Length: 89  Bit Score: 58.12  E-value: 5.68e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 653594746   31 IYVNPAFERLTGYTLDEILYQDCRFLQS---GDRDQpALMAIREALENGGACRETLRNYRKDGSHFWNELSLSTVYNAAD 107
Cdd:pfam08447   2 IYWSPRFEEILGYTPEELLGKGESWLDLvhpDDRER-VREALWEALKGGEPYSGEYRIRRKDGEYRWVEARARPIRDENG 80


                  ....*...
gi 653594746  108 KQTYFVGV 115
Cdd:pfam08447  81 KPVRVIGV 88
KinE COG5809
Sporulation sensor histidine kinase E [Cell cycle control, cell division, chromosome ...
 10-145 1.85e-11

Sporulation sensor histidine kinase E [Cell cycle control, cell division, chromosome partitioning, Signal transduction mechanisms];


Pssm-ID: 444511 [Multi-domain]  Cd Length: 489  Bit Score: 60.76  E-value: 1.85e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 653594746  10 VINASNDGIVVAEREGKdkpLIYVNPAFERLTGYTLDEILYQDC-RFLQSGDRDQpALMAIREALENGGACRETLRNYRK 88
Cdd:COG5809  146 IFNHSPDGIIVTDLDGR---IIYANPAACKLLGISIEELIGKSIlELIHSDDQEN-VAAFISQLLKDGGIAQGEVRFWTK 221

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 653594746  89 DGSHFWNELSLSTVyNAADKQTYFVGVQKDVTLQVKAQQRVAQLESeLAeVKAELAA 145
Cdd:COG5809  222 DGRWRLLEASGAPI-KKNGEVDGIVIIFRDITERKKLEELLRKSEK-LS-VVGELAA 275
PAS pfam00989
PAS fold; The PAS fold corresponds to the structural domain that has previously been defined ...
 5-119 2.14e-11

PAS fold; The PAS fold corresponds to the structural domain that has previously been defined as PAS and PAC motifs. The PAS fold appears in archaea, eubacteria and eukarya. This domain can bind gases (O2, CO and NO), FAD, 4-hydroxycinnamic acid and NAD+ (Matilla et.al., FEMS Microbiology Reviews, fuab043, 45, 2021, 1. https://doi.org/10.1093/femsre/fuab043).


Pssm-ID: 395786 [Multi-domain]  Cd Length: 113  Bit Score: 57.43  E-value: 2.14e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 653594746    5 KLMQMVINASNDGIVVAEREGKdkpLIYVNPAFERLTGYTLDEILYQDCRFLQSGDRDQPALMAIREALENGGACRETLR 84
Cdd:pfam00989   1 EDLRAILESLPDGIFVVDEDGR---ILYVNAAAEELLGLSREEVIGKSLLDLIPEEDDAEVAELLRQALLQGEESRGFEV 77

                          90       100       110
                  ....*....|....*....|....*....|....*.
gi 653594746   85 NYR-KDGSHFWNELSLSTVYNAADKQTYFVGVQKDV 119
Cdd:pfam00989  78 SFRvPDGRPRHVEVRASPVRDAGGEILGFLGVLRDI 113
PAS cd00130
PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising ...
 14-119 3.65e-11

PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in signal transduction.


Pssm-ID: 238075 [Multi-domain]  Cd Length: 103  Bit Score: 56.49  E-value: 3.65e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 653594746  14 SNDGIVVAEREGKdkpLIYVNPAFERLTGYTLDEILYQDCRFLQSGDRDQPALMAIREALENGGACRETLRNYRKDGSHF 93
Cdd:cd00130    1 LPDGVIVLDLDGR---ILYANPAAEQLLGYSPEELIGKSLLDLIHPEDREELRERLENLLSGGEPVTLEVRLRRKDGSVI 77

                         90       100
                 ....*....|....*....|....*.
gi 653594746  94 WNELSLSTVYNAADKQTYFVGVQKDV 119
Cdd:cd00130   78 WVLVSLTPIRDEGGEVIGLLGVVRDI 103
KinE COG5809
Sporulation sensor histidine kinase E [Cell cycle control, cell division, chromosome ...
 10-136 3.40e-10

Sporulation sensor histidine kinase E [Cell cycle control, cell division, chromosome partitioning, Signal transduction mechanisms];


Pssm-ID: 444511 [Multi-domain]  Cd Length: 489  Bit Score: 56.91  E-value: 3.40e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 653594746  10 VINASNDGIVVAEREGKdkpLIYVNPAFERLTGYTLDEILYQdcRFLQ-SGDRDQPALMAIREALENGGACRETLRNYR- 87
Cdd:COG5809   20 LFENAPDAILILDLEGK---ILKVNPAAERIFGYTEDELLGT--NILDfLHPDDEKELREILKLLKEGESRDELEFELRh 94

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*....
gi 653594746  88 KDGSHFWNELSLSTVYNAADKQTYFVGVQKDVTLQVKAQQRVAQLESEL 136
Cdd:COG5809   95 KNGKRLEFSSKLSPIFDQNGDIEGMLAISRDITERKRMEEALRESEEKF 143
RocR COG3829
RocR-type transcriptional regulator, contains PAS, AAA-type ATPase, and DNA-binding Fis ...
 5-135 4.07e-09

RocR-type transcriptional regulator, contains PAS, AAA-type ATPase, and DNA-binding Fis domains [Transcription, Signal transduction mechanisms];


Pssm-ID: 443041 [Multi-domain]  Cd Length: 448  Bit Score: 54.01  E-value: 4.07e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 653594746   5 KLMQMVINASNDGIVVAEREGKdkpLIYVNPAFERLTGYTLDEILYQDCRFLQSGDRdqpalmaIREALENGGACRETLR 84
Cdd:COG3829   11 EELEAILDSLDDGIIVVDADGR---ITYVNRAAERILGLPREEVIGKNVTELIPNSP-------LLEVLKTGKPVTGVIQ 80

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|.
gi 653594746  85 NYRKDGSHFwneLSLSTVYNAADKQTYFVGVQKDVTLQVKAQQRVAQLESE 135
Cdd:COG3829   81 KTGGKGKTV---IVTAIPIFEDGEVIGAVETFRDITELKRLERKLREEELE 128
PRK11359 PRK11359
cyclic-di-GMP phosphodiesterase; Provisional
 30-132 4.27e-09

cyclic-di-GMP phosphodiesterase; Provisional


Pssm-ID: 183097 [Multi-domain]  Cd Length: 799  Bit Score: 54.01  E-value: 4.27e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 653594746  30 LIYVNPAFERLTGYTLDEILYQDCRFLQSGDRDQPALMAIREALENG-----GACRETLRNyRKDGSHFWNELSLSTVyn 104
Cdd:PRK11359  34 VLFFNPAAEKLWGYKREEVIGNNIDMLIPRDLRPAHPEYIRHNREGGkarveGMSRELQLE-KKDGSKIWTRFALSKV-- 110

                         90       100
                 ....*....|....*....|....*...
gi 653594746 105 AADKQTYFVGVQKDVTLQVKAQQRVAQL 132
Cdd:PRK11359 111 SAEGKVYYLALVRDASVEMAQKEQTRQL 138
PRK11360 PRK11360
two-component system sensor histidine kinase AtoS;
1-145 2.38e-08

two-component system sensor histidine kinase AtoS;


Pssm-ID: 236901 [Multi-domain]  Cd Length: 607  Bit Score: 51.89  E-value: 2.38e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 653594746   1 MINAKLMQMVINAS-NDGIVVAEREGKdkpLIYVNPAFERLTGYTLDEILYQDCRFLQSGdrDQPALMAIREALENGGAC 79
Cdd:PRK11360 257 LRETRSLNELILESiADGVIAIDRQGK---ITTMNPAAEVITGLQRHELVGKPYSELFPP--NTPFASPLLDTLEHGTEH 331

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 653594746  80 REtlRNYRKDGSHFWNELSLST--VYNAADKQTYFVGVQKDVTLQVKAQQRVAQLEsELAEVkAELAA 145
Cdd:PRK11360 332 VD--LEISFPGRDRTIELSVSTslLHNTHGEMIGALVIFSDLTERKRLQRRVARQE-RLAAL-GELVA 395
PAC smart00086
Motif C-terminal to PAS motifs (likely to contribute to PAS structural domain); PAC motif ...
 83-120 4.82e-08

Motif C-terminal to PAS motifs (likely to contribute to PAS structural domain); PAC motif occurs C-terminal to a subset of all known PAS motifs. It is proposed to contribute to the PAS domain fold.


Pssm-ID: 197509  Cd Length: 43  Bit Score: 46.79  E-value: 4.82e-08
                           10        20        30
                   ....*....|....*....|....*....|....*...
gi 653594746    83 LRNYRKDGSHFWNELSLSTVYNAADKQTYFVGVQKDVT 120
Cdd:smart00086   4 YRLRRKDGSYIWVLVSASPIRDEDGEVEGILGVVRDIT 41
KinA COG5805
Sporulation sensor histidine kinase A (Stage II sporulation protein SpoIIF/SpoIIJ) [Cell cycle ...
 2-113 3.84e-06

Sporulation sensor histidine kinase A (Stage II sporulation protein SpoIIF/SpoIIJ) [Cell cycle control, cell division, chromosome partitioning, Signal transduction mechanisms];


Pssm-ID: 444507 [Multi-domain]  Cd Length: 496  Bit Score: 45.49  E-value: 3.84e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 653594746   2 INAKLMQMVINASNDGIVVAEREGKdkpLIYVNPAFERLTGYTLDEILYQD-CRFLQSGDRDQpaLMAIREALENGGACR 80
Cdd:COG5805   31 EITEELETILENLPDAIIAVNREGK---VIYINPAMEKLLGYTSEEIIGKTiFDFLEKEYHYR--VKTRIERLQKGYDVV 105

                         90       100       110
                 ....*....|....*....|....*....|...
gi 653594746  81 ETLRNYRKDGSHFWNELSLSTVYNAADKQTYFV 113
Cdd:COG5805  106 MIEQIYCKDGELIYVEVKLFPIYNQNGQAAILA 138
PAS smart00091
PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising ...
 6-49 5.18e-06

PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels.


Pssm-ID: 214512  Cd Length: 67  Bit Score: 42.00  E-value: 5.18e-06
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....
gi 653594746     6 LMQMVINASNDGIVVAEREGKdkpLIYVNPAFERLTGYTLDEIL 49
Cdd:smart00091   2 RLRAILESLPDGIFVLDLDGR---ILYANPAAEELLGYSPEELI 42
PAS_8 pfam13188
PAS domain; PAS domains are involved in many signalling proteins where they are used as a ...
 8-63 4.78e-05

PAS domain; PAS domains are involved in many signalling proteins where they are used as a signal sensor domain. PAS domains appear in archaea, bacteria and eukaryotes. Several PAS-domain proteins are known to detect their signal by way of an associated cofactor. Heme, flavin, and a 4-hydroxycinnamyl chromophore are used in different proteins. This domain recognizes oxygen and CO (Matilla et al., FEMS Microbiology Reviews, fuab043, 45, 2021, 1. https://doi.org/10.1093/femsre/fuab043).


Pssm-ID: 463802 [Multi-domain]  Cd Length: 65  Bit Score: 39.45  E-value: 4.78e-05
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 653594746    8 QMVINASNDGIVVAEREGKdkpLIYVNPAFERLTGYT-LDEILYQDCRFLQSGDRDQ 63
Cdd:pfam13188   4 RALFESSPDGILVLDEGGR---IIYVNPAALELLGYElLGELLGELLDLLDPLLEDA 57
PAS_4 pfam08448
PAS fold; The PAS fold corresponds to the structural domain that has previously been defined ...
 12-120 7.71e-05

PAS fold; The PAS fold corresponds to the structural domain that has previously been defined as PAS and PAC motifs. The PAS fold appears in archaea, eubacteria and eukarya. This domain is associated to signalling systems and works as a signal sensor domain. It recognizes differently substituted aromatic hydrocarbons, oxygen, different dodecanoic acids, autoinducers, 3,5-dimethyl-pyrazin-2-ol and N-alanyl-aminoacetone (Matilla et. al., FEMS Microbiology Reviews, fuab043, 45, 2021, 1. https://doi.org/10.1093/femsre/fuab043).


Pssm-ID: 312075 [Multi-domain]  Cd Length: 110  Bit Score: 39.70  E-value: 7.71e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 653594746   12 NASNDGIVVAEREGKdkpLIYVNPAFERLTGYTLDEILyqDCRFLQS-GDRDQPALM-AIREALEnGGACRETLRNYRKD 89
Cdd:pfam08448   2 DSLPDALAVLDPDGR---VRYANAAAAELFGLPPEELL--GKTLAELlPPEDAARLErALRRALE-GEEPIDFLEELLLN 75

                          90       100       110
                  ....*....|....*....|....*....|.
gi 653594746   90 GSHFWNELSLSTVYNAADKQTYFVGVQKDVT 120
Cdd:pfam08448  76 GEERHYELRLTPLRDPDGEVIGVLVISRDIT 106
PRK11359 PRK11359
cyclic-di-GMP phosphodiesterase; Provisional
 5-146 8.40e-04

cyclic-di-GMP phosphodiesterase; Provisional


Pssm-ID: 183097 [Multi-domain]  Cd Length: 799  Bit Score: 38.60  E-value: 8.40e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 653594746   5 KLMQMVINASNDGIVVAEREGKdkpLIYVNPAFERLTGYTLDEILYQDC-RFLQSGDRDQPALMAIREALENGGACRETL 83
Cdd:PRK11359 136 RQLIIAVDHLDRPVIVLDPERR---IVQCNRAFTEMFGYCISEASGMQPdTLLNIPEFPADNRIRLQQLLWKTARDQDEF 212

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 653594746  84 RNYRKDGSHFWNELSLSTVYNAADKQTYFVGVQKDVTlqvkAQQRVAQLESELaevkaeLAAL 146
Cdd:PRK11359 213 LLLTRTGEKIWIKASISPVYDVLAHLQNLVMTFSDIT----EERQIRQLEGNI------LAAM 265
NtrY COG5000
Signal transduction histidine kinase NtrY involved in nitrogen fixation and metabolism ...
 6-130 7.02e-03

Signal transduction histidine kinase NtrY involved in nitrogen fixation and metabolism regulation [Signal transduction mechanisms];


Pssm-ID: 444024 [Multi-domain]  Cd Length: 422  Bit Score: 35.71  E-value: 7.02e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 653594746   6 LMQMVINASNDGIVVAEREGKdkpLIYVNPAFERLTGYTLDEILYQDcrfLQSGDRDQPALMAIREALENGGACRETLRN 85
Cdd:COG5000   91 YLETILENLPAGVIVLDADGR---ITLANPAAERLLGIPLEELIGKP---LEELLPELDLAELLREALERGWQEEIELTR 164

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*
gi 653594746  86 yrkDGSHFWNelslstVYNAADKQTYFVGVQKDVTLQVKAQQRVA 130
Cdd:COG5000  165 ---DGRRTLL------VRASPLRDDGYVIVFDDITELLRAERLAA 200
 
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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