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Conserved domains on  [gi|1088166532|gb|OHA27103|]
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MAG: hypothetical protein A3D52_02220 [Candidatus Taylorbacteria bacterium RIFCSPHIGHO2_02_FULL_44_36]

Protein Classification

CCA tRNA nucleotidyltransferase( domain architecture ID 11427658)

[cytidine(C)-cytidine(C)-adenosine (A)] tRNA nucleotidyltransferase adds the CCA sequence one nucleotide at a time onto the 3' end of tRNA

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
PcnB COG0617
tRNA nucleotidyltransferase/poly(A) polymerase [Translation, ribosomal structure and ...
 11-456 9.03e-123

tRNA nucleotidyltransferase/poly(A) polymerase [Translation, ribosomal structure and biogenesis]; tRNA nucleotidyltransferase/poly(A) polymerase is part of the Pathway/BioSystem: tRNA modification


:

Pssm-ID: 440382 [Multi-domain]  Cd Length: 391  Bit Score: 364.52  E-value: 9.03e-123
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1088166532  11 AIPKEITEVAKTLEKADFEAYLIGGCVRDLLLDKKPKDWDFTTNATPEEIMKIFSNTFyeN------EYGTVGVINENVs 84
Cdd:COG0617     1 RLSPNALKVLEALEEAGFEAYLVGGAVRDLLLGRPPKDIDIVTVATPEEVAALFRKAL--RtvpvgrDFGTVTVVFGGE- 77

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1088166532  85 detlrVVEVTPYRLEAKYSNKRHPDaVTFGKKLDDDLKRRDFTMNAIALKIEKENdagcevsVIDLFGGQEDLKTGIIRA 164
Cdd:COG0617    78 -----KIEVATARTERYYGDGRRPF-VEFGDTLEEDLARRDFTINALAYDLNDGE-------LIDPFGGLADLEARVIRT 144

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1088166532 165 VGEPAARFAEDALRILRAIRLSAELDFTIEEKTAEAIKANARHLENISAERIRDEFSSILLSDNPQKALILshnlcilpf 244
Cdd:COG0617   145 VGDPEERFREDPLRILRAVRFAARLGFTIEPETLAAIREMAGLLDRLSAERVWDELLKLLLSPHPSRGLEL--------- 215

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1088166532 245 vlpelekgisvkqnsAHAYDVWEHslrtlqhaakrnfvFEVRLAALLHDLGKiparRWSEEKKDWTFYGHDVVGAKIAAK 324
Cdd:COG0617   216 ---------------LRETGLLEV--------------LALRLAALLHDLGK----PATREDGLPTFHGHEEAGAELAEA 262

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1088166532 325 ILSRLKFPKKTIDDVVKLVRWHMFFSDTEVITLSSVRRMIRNvGQENIWKLMDVRAAdrigtgrpkesPYRLRKYQAMVE 404
Cdd:COG0617   263 LLKRLRLPNRERKLVRELVELHLRFHGLGELRDSAVRRLLER-GPEALEDLLLLREN-----------GLEYPELQERLA 330

                         410       420       430       440       450
                  ....*....|....*....|....*....|....*....|....*....|..
gi 1088166532 405 EASRDPISVSMLKIAGGKIMEItNLKPGPKIGFILHALLEEVLEDPKLNTAE 456
Cdd:COG0617   331 ELLEAAWRRFQPPVDGEDLMAL-GLKPGPEIGEILRALREAVLDGGIPNRRE 381
 
Name Accession Description Interval E-value
PcnB COG0617
tRNA nucleotidyltransferase/poly(A) polymerase [Translation, ribosomal structure and ...
 11-456 9.03e-123

tRNA nucleotidyltransferase/poly(A) polymerase [Translation, ribosomal structure and biogenesis]; tRNA nucleotidyltransferase/poly(A) polymerase is part of the Pathway/BioSystem: tRNA modification


Pssm-ID: 440382 [Multi-domain]  Cd Length: 391  Bit Score: 364.52  E-value: 9.03e-123
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1088166532  11 AIPKEITEVAKTLEKADFEAYLIGGCVRDLLLDKKPKDWDFTTNATPEEIMKIFSNTFyeN------EYGTVGVINENVs 84
Cdd:COG0617     1 RLSPNALKVLEALEEAGFEAYLVGGAVRDLLLGRPPKDIDIVTVATPEEVAALFRKAL--RtvpvgrDFGTVTVVFGGE- 77

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1088166532  85 detlrVVEVTPYRLEAKYSNKRHPDaVTFGKKLDDDLKRRDFTMNAIALKIEKENdagcevsVIDLFGGQEDLKTGIIRA 164
Cdd:COG0617    78 -----KIEVATARTERYYGDGRRPF-VEFGDTLEEDLARRDFTINALAYDLNDGE-------LIDPFGGLADLEARVIRT 144

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1088166532 165 VGEPAARFAEDALRILRAIRLSAELDFTIEEKTAEAIKANARHLENISAERIRDEFSSILLSDNPQKALILshnlcilpf 244
Cdd:COG0617   145 VGDPEERFREDPLRILRAVRFAARLGFTIEPETLAAIREMAGLLDRLSAERVWDELLKLLLSPHPSRGLEL--------- 215

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1088166532 245 vlpelekgisvkqnsAHAYDVWEHslrtlqhaakrnfvFEVRLAALLHDLGKiparRWSEEKKDWTFYGHDVVGAKIAAK 324
Cdd:COG0617   216 ---------------LRETGLLEV--------------LALRLAALLHDLGK----PATREDGLPTFHGHEEAGAELAEA 262

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1088166532 325 ILSRLKFPKKTIDDVVKLVRWHMFFSDTEVITLSSVRRMIRNvGQENIWKLMDVRAAdrigtgrpkesPYRLRKYQAMVE 404
Cdd:COG0617   263 LLKRLRLPNRERKLVRELVELHLRFHGLGELRDSAVRRLLER-GPEALEDLLLLREN-----------GLEYPELQERLA 330

                         410       420       430       440       450
                  ....*....|....*....|....*....|....*....|....*....|..
gi 1088166532 405 EASRDPISVSMLKIAGGKIMEItNLKPGPKIGFILHALLEEVLEDPKLNTAE 456
Cdd:COG0617   331 ELLEAAWRRFQPPVDGEDLMAL-GLKPGPEIGEILRALREAVLDGGIPNRRE 381
PRK13299 PRK13299
tRNA CCA-pyrophosphorylase; Provisional
 12-448 6.96e-84

tRNA CCA-pyrophosphorylase; Provisional


Pssm-ID: 237339 [Multi-domain]  Cd Length: 394  Bit Score: 264.78  E-value: 6.96e-84
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1088166532  12 IPKEITE---VAKTLEKADFEAYLIGGCVRDLLLDKKPKDWDFTTNATPEEIMKIFSNTFYEN-EYGTVGVINENVSdet 87
Cdd:PRK13299    2 MPSEFQKalpILEKIKEAGFEAYFVGGSVRDYLLGRPIHDVDIATSAYPEEVKAIFPRTVDVGiEHGTVLVLENGEE--- 78

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1088166532  88 lrvVEVTPYRLEAKYSNKRHPDAVTFGKKLDDDLKRRDFTMNAIALKIEKEndagcevsVIDLFGGQEDLKTGIIRAVGE 167
Cdd:PRK13299   79 ---YEVTTFRTESEYVDYRRPSEVTFVRSLEEDLKRRDFTINAIAMDENGE--------IIDLFDGLEDLKNRLIRAVGN 147

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1088166532 168 PAARFAEDALRILRAIRLSAELDFTIEEKTAEAIKANARHLENISAERIRDEFSSILLSDNPQKALILSHNLCILPFvLP 247
Cdd:PRK13299  148 AEERFQEDALRMMRAVRFASQLGFDLETETFEAMKTQAPLLEKISVERIFVEFEKLLLGPFWRKGLKLLIETGLYNY-LP 226

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1088166532 248 ELE-KGISVKQNSAHAYDVWEHSlrtlqhaakrnfvfEVRLAALLHDLGKIPARRWseekkdwtfyghdvvgakiaakiL 326
Cdd:PRK13299  227 GLKgKEENLLKLTQLLWFSFETS--------------EQAWAALLISLKIENIKSF-----------------------L 269

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1088166532 327 SRLKFPKKTIDDVVKLVrwhMFFSDTEVITLSSVrrMIRNVGQENIWKLMDVRAAdrigTGRPKESPYRLRKYQAMveea 406
Cdd:PRK13299  270 KAWKLSNKFIKDVVKLL---ALYALRSERSWEKL--DLYQYGKEIALLAEDLRQA----QGLSVDEEAIQELYQAL---- 336

                         410       420       430       440
                  ....*....|....*....|....*....|....*....|...
gi 1088166532 407 srdPI-SVSMLKIAGGKIMEITNLKPGPKIGFILHALLEEVLE 448
Cdd:PRK13299  337 ---PIhDKKELAVNGGDLLKHFGKKPGPWLGETLRKIEEAIVT 376
pcnB TIGR01942
poly(A) polymerase; This model describes the pcnB family of poly(A) polymerases (also known as ...
 19-291 1.27e-45

poly(A) polymerase; This model describes the pcnB family of poly(A) polymerases (also known as plasmid copy number protein). These enzymes sequentially add adenosine nucleotides to the 3' end of RNAs, targeting them for degradation by the cell. This was originally described for anti-sense RNAs, but was later demonstrated for mRNAs as well. Members of this family are as yet limited to the gamma- and beta-proteobacteria, with putative members in the Chlamydiacae and spirochetes. This family has homology to tRNA nucleotidyltransferase (cca).


Pssm-ID: 130997 [Multi-domain]  Cd Length: 410  Bit Score: 164.59  E-value: 1.27e-45
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1088166532  19 VAKTLEKADFEAYLIGGCVRDLLLDKKPKDWDFTTNATPEEIMKIFSNT-FYENEYGTVGVINENvsdetlRVVEVTPYR 97
Cdd:TIGR01942  21 VVERLKGAGYQAYIVGGAVRDLLLGIEPKDFDVVTSATPEEVRKLFRNSrIVGRRFRLVHVSFGR------QIIEVATFR 94

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1088166532  98 LEAKYSNKRHPDAV---TFGkKLDDDLKRRDFTMNAIALKIEKEndagcevSVIDLFGGQEDLKTGIIRAVGEPAARFAE 174
Cdd:TIGR01942  95 SGHKSSVNAEGRILkdnVYG-TLEEDAWRRDFTVNALYYDPSRE-------VIIDYVGGMEDLKNRRLRLIGDPRSRYQE 166

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1088166532 175 DALRILRAIRLSAELDFTIEEKTAEAIKANARHLENISAERIRDEFSSILLSDNPQKALILSHNLCILPFVLPELEKGIS 254
Cdd:TIGR01942 167 DPVRMLRALRFSVKLEFTIDESTARPIRESAPLLKGIPPARLFEEILKLLFSGRSAALFRMLCGYQLLEPLFPSVAYALR 246

                         250       260       270       280
                  ....*....|....*....|....*....|....*....|.
gi 1088166532 255 VKQNSAHAYDVwehSLRTLQHAAKRNFVFEVR----LAALL 291
Cdd:TIGR01942 247 ESPKFESAFTV---QALVNDTDFRVKRDKPVTpaflYAALL 284
PolyA_pol pfam01743
Poly A polymerase head domain; This family includes nucleic acid independent RNA polymerases, ...
 30-163 3.86e-38

Poly A polymerase head domain; This family includes nucleic acid independent RNA polymerases, such as Poly(A) polymerase, which adds the poly (A) tail to mRNA EC:2.7.7.19. This family also includes the tRNA nucleotidyltransferase that adds the CCA to the 3' of the tRNA EC:2.7.7.25. This family is part of the nucleotidyltransferase superfamily.


Pssm-ID: 396348 [Multi-domain]  Cd Length: 126  Bit Score: 135.49  E-value: 3.86e-38
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1088166532  30 AYLIGGCVRDLLLDKKPKDWDFTTNATPEEIMKIFSNTFYEN-----EYGTVGVINENvsdetlRVVEVTPYRLEAKYSN 104
Cdd:pfam01743   1 LYIVGGAVRDLLLGKTPKDVDIATDATPEQVATLFRRRRIVHllsgiEFGTIHVIFGN------QILEVATFRIEFDESD 74

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 1088166532 105 KRHPDAVTFGKKLDDDLKRRDFTMNAIALKIEKENdagcevsVIDLFGGQEDLKTGIIR 163
Cdd:pfam01743  75 FRNPRSEEYTGTLEEDAKRRDFTINALAYNPNSGE-------VIDYFGGIKDLKSGVIR 126
NT_ClassII-CCAase cd05398
Nucleotidyltransferase (NT) domain of ClassII CCA-adding enzymes; CCA-adding enzymes add the ...
 13-158 2.02e-36

Nucleotidyltransferase (NT) domain of ClassII CCA-adding enzymes; CCA-adding enzymes add the sequence [cytidine(C)-cytidine-adenosine (A)], one nucleotide at a time, onto the 3' end of tRNA, in a template-independent reaction. This Class II group is comprised mainly of eubacterial and eukaryotic enzymes and includes Bacillus stearothermophilus CCAase, Escherichia coli poly(A) polymerase I, human mitochondrial CCAase, and Saccharomyces cerevisiae CCAase (CCA1). CCA-adding enzymes have a single catalytic pocket, which recognizes both ATP and CTP substrates. Included in this subgroup are CC- and A-adding enzymes from various ancient species of bacteria such as Aquifex aeolicus; these enzymes collaborate to add CCA to tRNAs. This family belongs to the Pol beta-like NT superfamily. In the majority of enzymes in this superfamily, two carboxylates, Dx[D/E], together with a third more distal carboxylate, coordinate two divalent metal cations involved in a two-metal ion mechanism of nucleotide addition. These carboxylate residues are fairly well conserved in this family. Escherichia coli CCAase is related to this group but has not been included in this alignment as this enzyme lacks the N-terminal helix conserved in the remainder of the NT superfamily.


Pssm-ID: 143388 [Multi-domain]  Cd Length: 139  Bit Score: 131.56  E-value: 2.02e-36
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1088166532  13 PKEITEVAKTLEKA-DFEAYLIGGCVRDLLLDKKPKDWDFTTNA-TPEEIMKIFsntfyenEYGTVGVINENVSDETLRV 90
Cdd:cd05398     1 TPELLKLLRELKKAlGYEAYLVGGAVRDLLLGRPPKDIDIATDAdGPEFAEALF-------KKIGGRVVGLGEEFGTATV 73

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1088166532  91 ------VEVTPYRLEAKYSNKRHPDAVTFGkkLDDDLKRRDFTMNAIALKIEKENdagcevsVIDLFGGQEDLK 158
Cdd:cd05398    74 vingltIDVATLRTETYTDPGRRPPVVGFT--IEEDLLRRDFTINAMAYDLDDGE-------LIDPFGGLKDLE 138
HDc smart00471
Metal dependent phosphohydrolases with conserved 'HD' motif; Includes eukaryotic cyclic ...
 261-389 1.01e-11

Metal dependent phosphohydrolases with conserved 'HD' motif; Includes eukaryotic cyclic nucleotide phosphodiesterases (PDEc). This profile/HMM does not detect HD homologues in bacterial glycine aminoacyl-tRNA synthetases (beta subunit).


Pssm-ID: 214679 [Multi-domain]  Cd Length: 124  Bit Score: 61.93  E-value: 1.01e-11
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1088166532  261 HAYDVWEHSLRTLQHAAK------RNFVFEVRLAALLHDLGKIPARRWSEEKKDWTFyGHDVVGakiaAKILSRLKFPKK 334
Cdd:smart00471   1 SDYHVFEHSLRVAQLAAAlaeelgLLDIELLLLAALLHDIGKPGTPDSFLVKTSVLE-DHHFIG----AEILLEEEEPRI 75

                           90       100       110       120       130
                   ....*....|....*....|....*....|....*....|....*....|....*
gi 1088166532  335 TIDDVVKLVRWHMFFSDTEVITLSSVRRMIrnvgqeniwklmdVRAADRIGTGRP 389
Cdd:smart00471  76 LEEILRTAILSHHERPDGLRGEPITLEARI-------------VKVADRLDALRA 117
 
Name Accession Description Interval E-value
PcnB COG0617
tRNA nucleotidyltransferase/poly(A) polymerase [Translation, ribosomal structure and ...
 11-456 9.03e-123

tRNA nucleotidyltransferase/poly(A) polymerase [Translation, ribosomal structure and biogenesis]; tRNA nucleotidyltransferase/poly(A) polymerase is part of the Pathway/BioSystem: tRNA modification


Pssm-ID: 440382 [Multi-domain]  Cd Length: 391  Bit Score: 364.52  E-value: 9.03e-123
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1088166532  11 AIPKEITEVAKTLEKADFEAYLIGGCVRDLLLDKKPKDWDFTTNATPEEIMKIFSNTFyeN------EYGTVGVINENVs 84
Cdd:COG0617     1 RLSPNALKVLEALEEAGFEAYLVGGAVRDLLLGRPPKDIDIVTVATPEEVAALFRKAL--RtvpvgrDFGTVTVVFGGE- 77

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1088166532  85 detlrVVEVTPYRLEAKYSNKRHPDaVTFGKKLDDDLKRRDFTMNAIALKIEKENdagcevsVIDLFGGQEDLKTGIIRA 164
Cdd:COG0617    78 -----KIEVATARTERYYGDGRRPF-VEFGDTLEEDLARRDFTINALAYDLNDGE-------LIDPFGGLADLEARVIRT 144

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1088166532 165 VGEPAARFAEDALRILRAIRLSAELDFTIEEKTAEAIKANARHLENISAERIRDEFSSILLSDNPQKALILshnlcilpf 244
Cdd:COG0617   145 VGDPEERFREDPLRILRAVRFAARLGFTIEPETLAAIREMAGLLDRLSAERVWDELLKLLLSPHPSRGLEL--------- 215

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1088166532 245 vlpelekgisvkqnsAHAYDVWEHslrtlqhaakrnfvFEVRLAALLHDLGKiparRWSEEKKDWTFYGHDVVGAKIAAK 324
Cdd:COG0617   216 ---------------LRETGLLEV--------------LALRLAALLHDLGK----PATREDGLPTFHGHEEAGAELAEA 262

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1088166532 325 ILSRLKFPKKTIDDVVKLVRWHMFFSDTEVITLSSVRRMIRNvGQENIWKLMDVRAAdrigtgrpkesPYRLRKYQAMVE 404
Cdd:COG0617   263 LLKRLRLPNRERKLVRELVELHLRFHGLGELRDSAVRRLLER-GPEALEDLLLLREN-----------GLEYPELQERLA 330

                         410       420       430       440       450
                  ....*....|....*....|....*....|....*....|....*....|..
gi 1088166532 405 EASRDPISVSMLKIAGGKIMEItNLKPGPKIGFILHALLEEVLEDPKLNTAE 456
Cdd:COG0617   331 ELLEAAWRRFQPPVDGEDLMAL-GLKPGPEIGEILRALREAVLDGGIPNRRE 381
PRK13299 PRK13299
tRNA CCA-pyrophosphorylase; Provisional
 12-448 6.96e-84

tRNA CCA-pyrophosphorylase; Provisional


Pssm-ID: 237339 [Multi-domain]  Cd Length: 394  Bit Score: 264.78  E-value: 6.96e-84
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1088166532  12 IPKEITE---VAKTLEKADFEAYLIGGCVRDLLLDKKPKDWDFTTNATPEEIMKIFSNTFYEN-EYGTVGVINENVSdet 87
Cdd:PRK13299    2 MPSEFQKalpILEKIKEAGFEAYFVGGSVRDYLLGRPIHDVDIATSAYPEEVKAIFPRTVDVGiEHGTVLVLENGEE--- 78

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1088166532  88 lrvVEVTPYRLEAKYSNKRHPDAVTFGKKLDDDLKRRDFTMNAIALKIEKEndagcevsVIDLFGGQEDLKTGIIRAVGE 167
Cdd:PRK13299   79 ---YEVTTFRTESEYVDYRRPSEVTFVRSLEEDLKRRDFTINAIAMDENGE--------IIDLFDGLEDLKNRLIRAVGN 147

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1088166532 168 PAARFAEDALRILRAIRLSAELDFTIEEKTAEAIKANARHLENISAERIRDEFSSILLSDNPQKALILSHNLCILPFvLP 247
Cdd:PRK13299  148 AEERFQEDALRMMRAVRFASQLGFDLETETFEAMKTQAPLLEKISVERIFVEFEKLLLGPFWRKGLKLLIETGLYNY-LP 226

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1088166532 248 ELE-KGISVKQNSAHAYDVWEHSlrtlqhaakrnfvfEVRLAALLHDLGKIPARRWseekkdwtfyghdvvgakiaakiL 326
Cdd:PRK13299  227 GLKgKEENLLKLTQLLWFSFETS--------------EQAWAALLISLKIENIKSF-----------------------L 269

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1088166532 327 SRLKFPKKTIDDVVKLVrwhMFFSDTEVITLSSVrrMIRNVGQENIWKLMDVRAAdrigTGRPKESPYRLRKYQAMveea 406
Cdd:PRK13299  270 KAWKLSNKFIKDVVKLL---ALYALRSERSWEKL--DLYQYGKEIALLAEDLRQA----QGLSVDEEAIQELYQAL---- 336

                         410       420       430       440
                  ....*....|....*....|....*....|....*....|...
gi 1088166532 407 srdPI-SVSMLKIAGGKIMEITNLKPGPKIGFILHALLEEVLE 448
Cdd:PRK13299  337 ---PIhDKKELAVNGGDLLKHFGKKPGPWLGETLRKIEEAIVT 376
pcnB TIGR01942
poly(A) polymerase; This model describes the pcnB family of poly(A) polymerases (also known as ...
 19-291 1.27e-45

poly(A) polymerase; This model describes the pcnB family of poly(A) polymerases (also known as plasmid copy number protein). These enzymes sequentially add adenosine nucleotides to the 3' end of RNAs, targeting them for degradation by the cell. This was originally described for anti-sense RNAs, but was later demonstrated for mRNAs as well. Members of this family are as yet limited to the gamma- and beta-proteobacteria, with putative members in the Chlamydiacae and spirochetes. This family has homology to tRNA nucleotidyltransferase (cca).


Pssm-ID: 130997 [Multi-domain]  Cd Length: 410  Bit Score: 164.59  E-value: 1.27e-45
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1088166532  19 VAKTLEKADFEAYLIGGCVRDLLLDKKPKDWDFTTNATPEEIMKIFSNT-FYENEYGTVGVINENvsdetlRVVEVTPYR 97
Cdd:TIGR01942  21 VVERLKGAGYQAYIVGGAVRDLLLGIEPKDFDVVTSATPEEVRKLFRNSrIVGRRFRLVHVSFGR------QIIEVATFR 94

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1088166532  98 LEAKYSNKRHPDAV---TFGkKLDDDLKRRDFTMNAIALKIEKEndagcevSVIDLFGGQEDLKTGIIRAVGEPAARFAE 174
Cdd:TIGR01942  95 SGHKSSVNAEGRILkdnVYG-TLEEDAWRRDFTVNALYYDPSRE-------VIIDYVGGMEDLKNRRLRLIGDPRSRYQE 166

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1088166532 175 DALRILRAIRLSAELDFTIEEKTAEAIKANARHLENISAERIRDEFSSILLSDNPQKALILSHNLCILPFVLPELEKGIS 254
Cdd:TIGR01942 167 DPVRMLRALRFSVKLEFTIDESTARPIRESAPLLKGIPPARLFEEILKLLFSGRSAALFRMLCGYQLLEPLFPSVAYALR 246

                         250       260       270       280
                  ....*....|....*....|....*....|....*....|.
gi 1088166532 255 VKQNSAHAYDVwehSLRTLQHAAKRNFVFEVR----LAALL 291
Cdd:TIGR01942 247 ESPKFESAFTV---QALVNDTDFRVKRDKPVTpaflYAALL 284
PolyA_pol pfam01743
Poly A polymerase head domain; This family includes nucleic acid independent RNA polymerases, ...
 30-163 3.86e-38

Poly A polymerase head domain; This family includes nucleic acid independent RNA polymerases, such as Poly(A) polymerase, which adds the poly (A) tail to mRNA EC:2.7.7.19. This family also includes the tRNA nucleotidyltransferase that adds the CCA to the 3' of the tRNA EC:2.7.7.25. This family is part of the nucleotidyltransferase superfamily.


Pssm-ID: 396348 [Multi-domain]  Cd Length: 126  Bit Score: 135.49  E-value: 3.86e-38
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1088166532  30 AYLIGGCVRDLLLDKKPKDWDFTTNATPEEIMKIFSNTFYEN-----EYGTVGVINENvsdetlRVVEVTPYRLEAKYSN 104
Cdd:pfam01743   1 LYIVGGAVRDLLLGKTPKDVDIATDATPEQVATLFRRRRIVHllsgiEFGTIHVIFGN------QILEVATFRIEFDESD 74

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 1088166532 105 KRHPDAVTFGKKLDDDLKRRDFTMNAIALKIEKENdagcevsVIDLFGGQEDLKTGIIR 163
Cdd:pfam01743  75 FRNPRSEEYTGTLEEDAKRRDFTINALAYNPNSGE-------VIDYFGGIKDLKSGVIR 126
cca PRK10885
multifunctional CCA addition/repair protein;
31-346 7.74e-38

multifunctional CCA addition/repair protein;


Pssm-ID: 182810 [Multi-domain]  Cd Length: 409  Bit Score: 143.07  E-value: 7.74e-38
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1088166532  31 YLIGGCVRDLLLDKKPKDWDF-TTNATPEEIMKifsntfyeNEYGTVG----VINENVSDEtlrvvEVTPYRLEAKYSNK 105
Cdd:PRK10885    4 YLVGGAVRDALLGLPVKDRDWvVVGATPEEMLA--------QGYQQVGkdfpVFLHPKTHE-----EYALARTERKSGRG 70

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1088166532 106 RH-------PDaVTfgkkLDDDLKRRDFTMNAIAlkiekENDAGcevSVIDLFGGQEDLKTGIIRAVGePAarFAEDALR 178
Cdd:PRK10885   71 YTgftcyaaPD-VT----LEEDLIRRDLTINAMA-----QDDDG---ELIDPYGGQRDLEARLLRHVS-PA--FAEDPLR 134

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1088166532 179 ILRAIRLSA---ELDFTIEEKTAEAIK--ANARHLENISAERIRDEFSSILLSDNPQKALILSHNLCILPFVLPELEKGI 253
Cdd:PRK10885  135 VLRVARFAArfaHLGFRIAPETLALMRemVASGELDALTPERVWKETERALMERNPQVFFQVLRDCGALAVLLPEIDALF 214

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1088166532 254 SVKQNSAH--AYDVWEHSLRTLQHAAKRNFVFEVRLAALLHDLGK--IPARRWSEEkkdwtfYGHDVVGAKIAAKILSRL 329
Cdd:PRK10885  215 GVPQPAKWhpEIDTGIHTLMVLDQAAKLSPSLDVRFAALCHDLGKglTPPEEWPRH------HGHEPRGVKLVEQLCQRL 288

                         330
                  ....*....|....*...
gi 1088166532 330 KFPKKtIDDVVKLV-RWH 346
Cdd:PRK10885  289 RVPNE-CRDLALLVaEEH 305
NT_ClassII-CCAase cd05398
Nucleotidyltransferase (NT) domain of ClassII CCA-adding enzymes; CCA-adding enzymes add the ...
 13-158 2.02e-36

Nucleotidyltransferase (NT) domain of ClassII CCA-adding enzymes; CCA-adding enzymes add the sequence [cytidine(C)-cytidine-adenosine (A)], one nucleotide at a time, onto the 3' end of tRNA, in a template-independent reaction. This Class II group is comprised mainly of eubacterial and eukaryotic enzymes and includes Bacillus stearothermophilus CCAase, Escherichia coli poly(A) polymerase I, human mitochondrial CCAase, and Saccharomyces cerevisiae CCAase (CCA1). CCA-adding enzymes have a single catalytic pocket, which recognizes both ATP and CTP substrates. Included in this subgroup are CC- and A-adding enzymes from various ancient species of bacteria such as Aquifex aeolicus; these enzymes collaborate to add CCA to tRNAs. This family belongs to the Pol beta-like NT superfamily. In the majority of enzymes in this superfamily, two carboxylates, Dx[D/E], together with a third more distal carboxylate, coordinate two divalent metal cations involved in a two-metal ion mechanism of nucleotide addition. These carboxylate residues are fairly well conserved in this family. Escherichia coli CCAase is related to this group but has not been included in this alignment as this enzyme lacks the N-terminal helix conserved in the remainder of the NT superfamily.


Pssm-ID: 143388 [Multi-domain]  Cd Length: 139  Bit Score: 131.56  E-value: 2.02e-36
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1088166532  13 PKEITEVAKTLEKA-DFEAYLIGGCVRDLLLDKKPKDWDFTTNA-TPEEIMKIFsntfyenEYGTVGVINENVSDETLRV 90
Cdd:cd05398     1 TPELLKLLRELKKAlGYEAYLVGGAVRDLLLGRPPKDIDIATDAdGPEFAEALF-------KKIGGRVVGLGEEFGTATV 73

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1088166532  91 ------VEVTPYRLEAKYSNKRHPDAVTFGkkLDDDLKRRDFTMNAIALKIEKENdagcevsVIDLFGGQEDLK 158
Cdd:cd05398    74 vingltIDVATLRTETYTDPGRRPPVVGFT--IEEDLLRRDFTINAMAYDLDDGE-------LIDPFGGLKDLE 138
pcnB PRK11623
poly(A) polymerase I; Provisional
 14-219 5.08e-36

poly(A) polymerase I; Provisional


Pssm-ID: 236939 [Multi-domain]  Cd Length: 472  Bit Score: 139.50  E-value: 5.08e-36
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1088166532  14 KEITE----VAKTLEKADFEAYLIGGCVRDLLLDKKPKDWDFTTNATPEEIMKIFSNTfyeneyGTVGvinenvsdETLR 89
Cdd:PRK11623   49 KDISEnalkVLYRLNKAGYEAYLVGGGVRDLLLGKKPKDFDVTTNATPEQVRKLFRNC------RLVG--------RRFR 114

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1088166532  90 ---------VVEVTPYR------LEAKYSNKRHPDAV-----TFGKkLDDDLKRRDFTMNAIALKIEkendagcEVSVID 149
Cdd:PRK11623  115 lahvmfgpeIIEVATFRghhegnESDRNTSQRGQNGMllrdnIFGS-IEEDAQRRDFTINSLYYSVA-------DFTVRD 186

                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1088166532 150 LFGGQEDLKTGIIRAVGEPAARFAEDALRILRAIRLSAELDFTIEEKTAEAIKANARHLENISAERIRDE 219
Cdd:PRK11623  187 YVGGMKDLKEGVIRLIGNPETRYREDPVRMLRAVRFAAKLDMRISPETAEPIPRLATLLNDIPPARLFEE 256
PRK13298 PRK13298
tRNA CCA-pyrophosphorylase; Provisional
 29-351 6.09e-24

tRNA CCA-pyrophosphorylase; Provisional


Pssm-ID: 237338 [Multi-domain]  Cd Length: 417  Bit Score: 104.04  E-value: 6.09e-24
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1088166532  29 EAYLIGGCVRDLLLD--KKPKDWdFTTNATPEEIMKIfsntfyenEYGTVG----VINENVSDEtlrvvEVTPYRLEAK- 101
Cdd:PRK13298    2 KIYLVGGAVRDSLLNlpVKDKDW-VVVGGTPKILLSI--------NFQQVGkdfpVFLHPETHE-----EYALARTERKs 67

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1088166532 102 ----------YSNKrhpdaVTfgkkLDDDLKRRDFTMNAIAlkiEKENDagcevSVIDLFGGQEDLKTGIIRAVGEPaar 171
Cdd:PRK13298   68 gvgytgfitdTSSD-----VT----LEEDLIRRDLTINAIA---QDENG-----NYIDPFQGKKDIQLRLLRHVSES--- 127

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1088166532 172 FAEDALRILRAIRLSA---ELDFTIEEKTAEAIK--ANARHLENISAERIRDEFSSILLSDNPQKALILSHNLCILPFVL 246
Cdd:PRK13298  128 FIEDPLRVLRVARFAAllvHLGFKIAKETMILMCimVKKHELLYLTPERIWNETEKALKTDNPHVYFQVLYECNALKFLF 207

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1088166532 247 PEL----EKGISVKQNSAHAYDVwEHSLRTLQHAAKRNFVFEVRLAALLHDLGKIPArrWSEEKKDWTFYGHDVVGAKIA 322
Cdd:PRK13298  208 PEIdflyEKPYFLNSFFKKFNLG-NYILMGLSKISKLTKDIDIRFSYLCQFLGSMIP--INQIKRNYKKIFFDKYAASLI 284

                         330       340
                  ....*....|....*....|....*....
gi 1088166532 323 AKILSRLKFPKKTIDDVVKLVRWHMFFSD 351
Cdd:PRK13298  285 KNLCKRFKIPSYIRNIAVLNTGFYFFLYN 313
PRK13296 PRK13296
CCA tRNA nucleotidyltransferase;
29-258 5.83e-20

CCA tRNA nucleotidyltransferase;


Pssm-ID: 106256 [Multi-domain]  Cd Length: 360  Bit Score: 91.20  E-value: 5.83e-20
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1088166532  29 EAYLIGGCVRDLLLDKKPKDWDFTT-NATPEEIMKifsNTFYENEYGTVGVINENVSDETLRVvevtpyRLEAKYSNKRH 107
Cdd:PRK13296    2 KFYLVGGAVRDMLLGITPKDKDWVVvGATEDEMLA---NGFIKIAANFPVFIHPQTKQEYALA------RSEKKTASGYH 72

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1088166532 108 PDAVTFGK--KLDDDLKRRDFTMNAIAlkIEKENDagcevsVIDLFGGQEDLKTGIIRAVGEPaarFAEDALRILRAIRL 185
Cdd:PRK13296   73 GFEVNFSKyiTLEDDLKRRDLTINSIA--IDQNNK------VIDPFNGQADLQNRILRHTSIA---FIEDPLRVVRLARF 141

                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1088166532 186 SAEL---DFTIEEKTAEAIKA--NARHLENISAERIRDEFSSILlsDNPQKALILSHNLCILPFVLPELEKGISVKQN 258
Cdd:PRK13296  142 KAQLsnfNFSIAQEMLALIKElvKTGELNHLTRERLHIEFVKAL--NNPKIFFTTLKELEALKIIFPNISCILPLIPN 217
PRK13297 PRK13297
tRNA CCA-pyrophosphorylase; Provisional
 26-250 3.72e-17

tRNA CCA-pyrophosphorylase; Provisional


Pssm-ID: 139469 [Multi-domain]  Cd Length: 364  Bit Score: 83.12  E-value: 3.72e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1088166532  26 ADFEAYLIGGCVRDLLLDKKPKDWDFTT-NATPEEIMK-----------IFSNTFYENEYGTVgvinenvsdetlrvvev 93
Cdd:PRK13297   10 AGLQVYIVGGAVRDALLGLPAGDRDWVVvGATPEDMARrgfipvggdfpVFLHPRTKEEYALA----------------- 72

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1088166532  94 tpyRLEAKysNKRHPDAVTF----GKKLDDDLKRRDFTMNAIALKIEKEndagcevsVIDLFGGQEDLKTGIIRAVGEPa 169
Cdd:PRK13297   73 ---RTERK--SGRGYKGFTFytgaDVTLEQDLQRRDLTVNAIARTPQGE--------LVDPLDGVADVRARVLRHVGEA- 138

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1088166532 170 arFAEDALRILRAIRLSAEL-DFTIEEKTAEAIK--ANARHLENISAERIRDEFSSILLSDNPQKALILSHNLCILPFVL 246
Cdd:PRK13297  139 --FAEDPVRILRLGRFAARFgDFSIAPETMQLCRrmVEAGEADALVPERVWKEVSRGLMAQAPSRMLDVLARAGALARVM 216


                  ....
gi 1088166532 247 PELE 250
Cdd:PRK13297  217 PELH 220
PolyA_pol_RNAbd pfam12627
Probable RNA and SrmB- binding site of polymerase A; This region encompasses much of the RNA ...
 190-250 6.67e-16

Probable RNA and SrmB- binding site of polymerase A; This region encompasses much of the RNA and SrmB binding motifs on polymerase A.


Pssm-ID: 463648 [Multi-domain]  Cd Length: 64  Bit Score: 72.13  E-value: 6.67e-16
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1088166532 190 DFTIEEKTAEAIKANARHLENISAERIRDEFSSILLSDNPQKALILSHNLCILPFVLPELE 250
Cdd:pfam12627   1 GFTIEPETREAIRKLAPLLKKISPERIFEELLKLLLSGHPERGLELLRETGLLEYLFPELA 61
HDc smart00471
Metal dependent phosphohydrolases with conserved 'HD' motif; Includes eukaryotic cyclic ...
 261-389 1.01e-11

Metal dependent phosphohydrolases with conserved 'HD' motif; Includes eukaryotic cyclic nucleotide phosphodiesterases (PDEc). This profile/HMM does not detect HD homologues in bacterial glycine aminoacyl-tRNA synthetases (beta subunit).


Pssm-ID: 214679 [Multi-domain]  Cd Length: 124  Bit Score: 61.93  E-value: 1.01e-11
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1088166532  261 HAYDVWEHSLRTLQHAAK------RNFVFEVRLAALLHDLGKIPARRWSEEKKDWTFyGHDVVGakiaAKILSRLKFPKK 334
Cdd:smart00471   1 SDYHVFEHSLRVAQLAAAlaeelgLLDIELLLLAALLHDIGKPGTPDSFLVKTSVLE-DHHFIG----AEILLEEEEPRI 75

                           90       100       110       120       130
                   ....*....|....*....|....*....|....*....|....*....|....*
gi 1088166532  335 TIDDVVKLVRWHMFFSDTEVITLSSVRRMIrnvgqeniwklmdVRAADRIGTGRP 389
Cdd:smart00471  76 LEEILRTAILSHHERPDGLRGEPITLEARI-------------VKVADRLDALRA 117
HD pfam01966
HD domain; HD domains are metal dependent phosphohydrolases.
 265-353 1.39e-11

HD domain; HD domains are metal dependent phosphohydrolases.


Pssm-ID: 460398 [Multi-domain]  Cd Length: 110  Bit Score: 61.10  E-value: 1.39e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1088166532 265 VWEHSLRTLQHAAK------RNFVFEVRLAALLHDLGKIPARRwsEEKKDWTFYGHDVVGAKIAAKILSRLKFpkktiDD 338
Cdd:pfam01966   1 RLEHSLRVALLARElaeelgELDRELLLLAALLHDIGKGPFGD--EKPEFEIFLGHAVVGAEILRELEKRLGL-----ED 73

                          90
                  ....*....|....*
gi 1088166532 339 VVKLVRWHMFFSDTE 353
Cdd:pfam01966  74 VLKLILEHHESWEGA 88
GlnD COG2844
UTP:GlnB (protein PII) uridylyltransferase [Posttranslational modification, protein turnover, ...
 172-352 1.60e-10

UTP:GlnB (protein PII) uridylyltransferase [Posttranslational modification, protein turnover, chaperones, Signal transduction mechanisms];


Pssm-ID: 442092 [Multi-domain]  Cd Length: 864  Bit Score: 63.62  E-value: 1.60e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1088166532 172 FAEDALRILRAIRLSAELDfTIEEKTAEAIKANARHLENISAERIRDE-----FSSILLS-DNPQKALILSHNLCILPFV 245
Cdd:COG2844   341 FERDPVALLRLFLLAAQHP-EGLGIHPDTLRLLRRALRLIDDAFRRDPearrlFLEILRQpRGITRALRRMNEYGVLGRY 419

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1088166532 246 LPELEKGISVKQNSA-HAYDVWEHSLRTL---------QHAAKRNFVFEV----------RLAALLHDLGKipARrwsee 305
Cdd:COG2844   420 IPEFGRIVGQMQFDLfHVYTVDEHTLRVVrnlrrfergELAEEFPLASELiaelpkpellYLAALFHDIAK--GR----- 492

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....*..
gi 1088166532 306 KKDwtfygHDVVGAKIAAKILSRLKFPKKTIDDVVKLVRWHMFFSDT 352
Cdd:COG2844   493 GGD-----HSELGAEDARRFCPRHGLSPEDTELVAWLVRHHLLMSHT 534
HDc cd00077
Metal dependent phosphohydrolases with conserved 'HD' motif
 263-406 2.79e-10

Metal dependent phosphohydrolases with conserved 'HD' motif


Pssm-ID: 238032 [Multi-domain]  Cd Length: 145  Bit Score: 58.50  E-value: 2.79e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1088166532 263 YDVWEHSLRTLQHAAK--------RNFVFEVRLAALLHDLGKIPARRWSEEKKDWTFYGHDVVGAKIAAKILSRLKFpkK 334
Cdd:cd00077     1 EHRFEHSLRVAQLARRlaeelglsEEDIELLRLAALLHDIGKPGTPDAITEEESELEKDHAIVGAEILRELLLEEVI--K 78

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1088166532 335 TIDDVVKLVRWHmffsDTEVITLSSVRRMIRNVGQENIWKLmdVRAADRIGTGRPKESPYRLRKYQAMVEEA 406
Cdd:cd00077    79 LIDELILAVDAS----HHERLDGLGYPDGLKGEEITLEARI--VKLADRLDALRRDSREKRRRIAEEDLEEL 144
RnaY COG1418
HD superfamily phosphodieaserase, includes HD domain of RNase Y [Translation, ribosomal ...
 246-384 9.44e-10

HD superfamily phosphodieaserase, includes HD domain of RNase Y [Translation, ribosomal structure and biogenesis, General function prediction only];


Pssm-ID: 441028 [Multi-domain]  Cd Length: 191  Bit Score: 57.99  E-value: 9.44e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1088166532 246 LPELEKGISVKQNSAHAYDvWEHSLR----TLQHAAKRNF-VFEVRLAALLHDLGKIPArrWSEEKkdwtfyGHDVVGAK 320
Cdd:COG1418     1 LPELIKLVKYLRTSYGQHD-LQHSLRvaklAGLIAAEEGAdVEVAKRAALLHDIGKAKD--HEVEG------SHAEIGAE 71

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1088166532 321 IAAKILSRLKFPKKTIDDVVKLVRWHMFFSDTEVITLSSVrrmIrnvgqeniwklmdVRAADRI 384
Cdd:COG1418    72 LARKYLESLGFPEEEIEAVVHAIEAHSFSGGIEPESLEAK---I-------------VQDADRL 119
tRNA_NucTran2_2 pfam13735
tRNA nucleotidyltransferase domain 2 putative;
322-460 9.64e-09

tRNA nucleotidyltransferase domain 2 putative;


Pssm-ID: 433443 [Multi-domain]  Cd Length: 149  Bit Score: 54.20  E-value: 9.64e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1088166532 322 AAKILSRLKFPKKTIDDVVKLVRWHMFFSDTEVitlssVRRMIRNVGQENIWKLMDVRAADRIGTgrpkespyrlrKYQA 401
Cdd:pfam13735  24 ARSFLKSWKTSNKLIKAVVALLEALEKRQNGEW-----TRLLLYQAGLEALLLAEELAQALGQSI-----------DLEA 87

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 1088166532 402 MVEEASRDPI-SVSMLKIAGGKIMEITNLKPGPKIGFILHALLEEVLEDPKLNTAEYLEN 460
Cdd:pfam13735  88 LLERYQALPIkSKKELAITGGDLLKALGLKPGPWLGEILAALEQAVVEGELPNEKEALLE 147
PRK03381 PRK03381
PII uridylyl-transferase; Provisional
 169-352 3.33e-08

PII uridylyl-transferase; Provisional


Pssm-ID: 235123 [Multi-domain]  Cd Length: 774  Bit Score: 56.15  E-value: 3.33e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1088166532 169 AARFAEDALRILRAIRLSAELDFTIEEKTAEAIKANARHLENISAERIRDEFSSILLSDNPQKALILSHNLC-ILPFVLP 247
Cdd:PRK03381  323 DARPARDPGLVLRVAAAAATTGLPIAAATLSRLAASAPPLPTPWPAEARDDLLVLLGAGPAAVAVIEALDRTgLWGRLLP 402

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1088166532 248 ELEKGISVKQ-NSAHAYDVWEHSLRTLQHAAKrnFVFEVR------LAALLHDLGKiparRWSEEkkdwtfygHDVVGAK 320
Cdd:PRK03381  403 EWEAVRDLPPrDPVHRWTVDRHLVETAVRAAA--LTRRVArpdlllLGALLHDIGK----GRGGD--------HSVVGAE 468

                         170       180       190
                  ....*....|....*....|....*....|..
gi 1088166532 321 IAAKILSRLKFPKKTIDDVVKLVRWHMFFSDT 352
Cdd:PRK03381  469 LARQIGARLGLSPADVALLSALVRHHLLLPET 500
PRK05092 PRK05092
PII uridylyl-transferase; Provisional
 172-352 2.34e-07

PII uridylyl-transferase; Provisional


Pssm-ID: 235342 [Multi-domain]  Cd Length: 931  Bit Score: 53.72  E-value: 2.34e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1088166532 172 FAEDALRILRAIRLSAELDFTIEEKTAEAIKANARHL-----ENISAERIrdeFSSILLSD-NPQKALILSHNLCILPFV 245
Cdd:PRK05092  397 FERDPVNLIRLFHLADRHGLDIHPDAMRLVTRSLRLIdaalrEDPEANRL---FLDILTSRrNPERVLRRMNEAGVLGRF 473

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1088166532 246 LPELEKGISVKQ-NSAHAYDVWEHSLRTL-------QHAAKRNFVFEVRL------------AALLHDLGKipARrwsEE 305
Cdd:PRK05092  474 IPDFGRIVAMMQfNMYHHYTVDEHTIRAIgvlaeieRGELADEHPLASELmpkiesrralyvAVLLHDIAK--GR---PE 548

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....*..
gi 1088166532 306 kkdwtfyGHDVVGAKIAAKILSRLKFPKKTIDDVVKLVRWHMFFSDT 352
Cdd:PRK05092  549 -------DHSIAGARIARRLCPRLGLSPAETETVAWLVEHHLLMSDT 588
COG4339 COG4339
Predicted metal-dependent phosphohydrolase, HD superfamily [General function prediction only];
258-344 1.16e-04

Predicted metal-dependent phosphohydrolase, HD superfamily [General function prediction only];


Pssm-ID: 443480  Cd Length: 202  Bit Score: 43.34  E-value: 1.16e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1088166532 258 NSAHAYDVWEHsLRTLQHAAKRNFvfEVRLAALLHDLGKIPARRWSEEKkdwtfyghdvvGAKIAAKILSRLKFPKKTID 337
Cdd:COG4339    34 NLRHLQAVLAA-LDELAELAEDPD--AVRLAAWFHDAVYDTGAGDNEER-----------SAELAREFLTSLGVPEEVIE 99


                  ....*..
gi 1088166532 338 DVVKLVR 344
Cdd:COG4339   100 RVARLIL 106
HDIG TIGR00277
HDIG domain; This domain is found in a few known nucleotidyltransferes and in a large number ...
 285-333 1.42e-04

HDIG domain; This domain is found in a few known nucleotidyltransferes and in a large number of uncharacterized proteins. It contains four widely separated His residues, the second of which is part of an invariant dipeptide His-Asp in a region matched approximately by the motif HDIG. This model may annotate homologous domains in which one or more of the His residues is conserved but misaligned, and some probable false-positive hits.


Pssm-ID: 272994 [Multi-domain]  Cd Length: 80  Bit Score: 40.40  E-value: 1.42e-04
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*....
gi 1088166532 285 VRLAALLHDLGKiparrwSEEKKDWTFYGHDVVGAKIAAKILSRLKFPK 333
Cdd:TIGR00277  30 ARRGALLHDIGK------PITREGVIFESHVVVGAEIARKYGEPLEVID 72
Cas3''_I cd09641
CRISPR/Cas system-associated protein Cas3''; CRISPR (Clustered Regularly Interspaced Short ...
 260-346 6.10e-04

CRISPR/Cas system-associated protein Cas3''; CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) and associated Cas proteins comprise a system for heritable host defense by prokaryotic cells against phage and other foreign DNA; HD-like nuclease, specifically digesting double-stranded oligonucleotides and preferably cleaving at G:C pairs; signature gene for Type I


Pssm-ID: 193608 [Multi-domain]  Cd Length: 200  Bit Score: 41.11  E-value: 6.10e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1088166532 260 AHAYDVWEHSLRTLQHAAKR------NFVFEVRLAALLHDLGKI-PA--RRWSEEKKDWTFYG-----HDVVGAKIAAKI 325
Cdd:cd09641    11 EHLLDVAAWDAELAEEFARKlglelgLSRELLALAGLLHDLGKAtPAfqKYLRGGKEALREGKrkevrHSLLGALLLYEL 90

                          90       100
                  ....*....|....*....|.
gi 1088166532 326 LSRLKFPKKTIDDVVKLVRWH 346
Cdd:cd09641    91 LKELGLDEELALLLAYAIAGH 111
cas3_HD TIGR01596
CRISPR-associated endonuclease Cas3-HD; CRISPR/Cas systems are widespread, mobile systems for ...
 261-346 9.96e-04

CRISPR-associated endonuclease Cas3-HD; CRISPR/Cas systems are widespread, mobile systems for host defense against invasive elements such as phage. In these systems, Cas3 designates one of the core proteins shared widely by multiple types of CRISPR/Cas system. This model represents an HD-like endonuclease that occurs either separately or as the N-terminal region of Cas3, the helicase-containing CRISPR-associated protein.


Pssm-ID: 273711 [Multi-domain]  Cd Length: 176  Bit Score: 40.26  E-value: 9.96e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1088166532 261 HAYDVWE--HSLRTLQHAAKRNFVFEVR----LAALLHDLGKI-PA-----RRWSEEKKDWTFYgHDVVGAKIAAKILSR 328
Cdd:TIGR01596   4 HLLDVAAvaEALPALRPRLAEKLGLELRellkLAGLLHDLGKAsPAfqkklRKAEERGDRGEVR-HSTLSAALLYDLLEE 82

                          90
                  ....*....|....*...
gi 1088166532 329 LKFPKKTIDDVVKLVRWH 346
Cdd:TIGR01596  83 LGLEEELALLLALAIAGH 100
HDOD COG1639
HD-like signal output (HDOD) domain, no enzymatic activity [Signal transduction mechanisms];
264-346 4.52e-03

HD-like signal output (HDOD) domain, no enzymatic activity [Signal transduction mechanisms];


Pssm-ID: 441246 [Multi-domain]  Cd Length: 244  Bit Score: 38.79  E-value: 4.52e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1088166532 264 DVWEHSLRT------LQHAAKRNFVFEVRLAALLHDLGKIP------------ARRWSEEKKDWTFYGHDVVG---AKIA 322
Cdd:COG1639   104 RFWRHSLAVaaaaraLARRLGLLDPEEAFLAGLLHDIGKLVllslfpeeyaelLALAEADGLSLAEAEREVLGtdhAELG 183

                          90       100
                  ....*....|....*....|....
gi 1088166532 323 AKILSRLKFPkktiDDVVKLVRWH 346
Cdd:COG1639   184 AALARKWGLP----EELVEAIRYH 203
 
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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