Citrus Sinensis ID: 042101

Local Sequence Feature Prediction

Prediction and (Method)Result
Residue Number Marker
Protein Sequence ?
Secondary Structure (PSIPRED) ?
Secondary Structure Prediction (SSPRO) ?
Coil and Loop (DISEMBL) ?
Flexible Loop (DISEMBL) ?
Low Complexity Region (SEG) ?
Disordered region (IsUnstruct) ?
Disordered Region (DISOPRED) ?
Disordered Region (DISEMBL) ?
Disordered Region (DISPRO) ?
Transmembrane Helix (TMHMM) ?
Transmembrane Helix (HMMTOP) ?
Transmembrane Helix (MEMSAT) ?
TM Helix, Signal Peptide (MEMSAT_SVM) ?
TM Helix, Signal Peptide (Phobius) ?
Signal Peptide (SignalP HMM Mode) ?
Signal Peptide (SignalP NN Mode) ?
Coiled Coils (COILS) ?
Positional Conservation ?
 
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170-------180-------190-------200-------210-------220-------230-------240-------250-------260-------270-------280-------290-------300-------310-------320-------330-------340-------350-------360-------370-------380
MPVRIMQPGHLSLTNGLATTSSVTVPRRLGRVWSRLLSYPTHVTGNPSLQCNSDAESFGEHKDDTIDISKLTEVKQKLKLVGINCDDSCIPGRYAHLLCPKCKGGGRSLERSLSVHIIQDGDFAMWRCFRVDCGWAGRAFAGSNKIRKVMSSRQVAEKSLGLEPLGEKLIAYLGERMISEGTLQRNSVMQRLHDQAIAFPYWHNGVLVGCKYRSMERKFRQEKGTEKWLYGLDDINETAEVIIVEGEIDKLSVEEAGFQNCVSVPSGAPPKVSNRELPPREKDTGYQYLWNCKEHLDKVSRIILGTDADTPGHALAEELARRLGKDRCWRVRWPKKDEFSYFKDANEVLKCLGPGALREVIENAELYQLHVSEEALQCTK
cccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccHHHHHHHHHHHHHHccccccccccccccccccccccccccccccccEEEEEEcccccEEEEEccccccccccccccHHHHHHHccHHHHHHccccccccHHHHHHHHHccccHHHHHHcccEEEcccEEEEEEEEEccEEEEEEEcccccccccccccccccccccccccccEEEEEEcHHHHHHHHHHccccccccccccccccccccccccccccccHHHHHHHHHcccccEEEEEEcccHHHHHHHHHHHHHHccccEEEEEccccccccccccHHHHHHHccHHHHHHHHHHccccccccHHHHHHccc
ccEEEEcccccccccccccccccccccccccEEEEEEccccccccccccccccccccccccccccccHHHHHHHHHHHHHccccHHHHccccccccEEcccccccccccccEEEEEEEcccccEEEEEEEcccccccccccccccccccccHccccHccccccccHHHHHHHHHHccccHHHHHHcccHccccccEEEEEEccccEEEEEEEccccccEEEccccccEEEcccHcccccEEEEEccHHHHHHHHHcccccEEEcccccccccccccccccccccHHHHHHHHHHHHHcccEEEEEEccccHHHHHHHHHHHHHccccEEEEEccccccccccccHHHHHHHccHHHHHHHHHHccccccEEEHHHHHccc
mpvrimqpghlsltnglattssvtvprrLGRVWSRLLsypthvtgnpslqcnsdaesfgehkddtidiSKLTEVKQKLKLVGincddscipgryahllcpkckgggrslerSLSVHIIQDGDFAMWRCFRVdcgwagrafagsnKIRKVMSSRQVAEKSLGLEPLGEKLIAYLGERMISEGTLQRNSVMQRLHDqaiafpywhngvlvgckyrsMERKFRQEKGTEKWLYGLDDINETAEVIIVEGeidklsveeagfqncvsvpsgappkvsnrelpprekdtgyQYLWNCKEHLDKVSRIilgtdadtpgHALAEELARRLgkdrcwrvrwpkkdefsyfkDANEVLKCLGPGALREVIENAELYQLHVSEEALQCTK
mpvrimqpghlsltnglattssvtvprRLGRVWSRLLSYpthvtgnpslQCNSDAESFGEHKDDTIDISKLTEVKQKLKLVGINCDDSCIPGRYAHLLCPKCKGGGRSLERSLSVHIIQDGDFAMWRCFRVDCGWAGRAFAGSNKIRKVMSSRQVaekslgleplGEKLIAYLGERMISEGTLQRNSVMQRLHDQAIAFPYWHNGVLVGCKYRSMERKFRQEKGTEKWLYGLDDINETAEVIIVEGEIDKLSVEEAGFQNcvsvpsgappkvsnrelppreKDTGYQYLWNCKEHLDKVSRIILGTDADTPGHALAEELArrlgkdrcwrvrwpkkdefsyfkdaNEVLKCLGPGALREVIENAELYQLhvseealqctk
MPVRIMQPGHLSLTNGLATTSSVTVPRRLGRVWSRLLSYPTHVTGNPSLQCNSDAESFGEHKDDTIDISKLTEVKQKLKLVGINCDDSCIPGRYAHLLCPKCKGGGRSLERSLSVHIIQDGDFAMWRCFRVDCGWAGRAFAGSNKIRKVMSSRQVAEKSLGLEPLGEKLIAYLGERMISEGTLQRNSVMQRLHDQAIAFPYWHNGVLVGCKYRSMERKFRQEKGTEKWLYGLDDINETAEVIIVEGEIDKLSVEEAGFQNCVSVPSGAPPKVSNRELPPREKDTGYQYLWNCKEHLDKVSRIILGTDADTPGHALAEELARRLGKDRCWRVRWPKKDEFSYFKDANEVLKCLGPGALREVIENAELYQLHVSEEALQCTK
***************GLATTSSVTVPRRLGRVWSRLLSYPTHVTG*******************TIDISKLTEVKQKLKLVGINCDDSCIPGRYAHLLCPKCKGGGRSLERSLSVHIIQDGDFAMWRCFRVDCGWAGRAFAGSNKIRKVM********SLGLEPLGEKLIAYLGERMISEGTLQRNSVMQRLHDQAIAFPYWHNGVLVGCKYRSMERKFRQEKGTEKWLYGLDDINETAEVIIVEGEIDKLSVEEAGFQNCV*********************TGYQYLWNCKEHLDKVSRIILGTDADTPGHALAEELARRLGKDRCWRVRWPKKDEFSYFKDANEVLKCLGPGALREVIENAELYQLHV*********
********GHL*************V*RRLGRV**************************************LTEVKQKLKLVGINCDDSCIPGRYAHLLCPKCK********S**VHIIQDGDFAMWRCFRVDCGWAGRAFAGS************AEKSLGLEPLGEKLIAYLGERMISEGTLQRNSVMQRLHDQAIAFPYWHNGVLVGCKYRSMERKFRQEKGTEKWLYGLDDINETAEVIIVEGEIDKLSVEEAGFQNCVSVPSGAPPKVSNRELPPREKDTGYQYLWNCKEHLDKVSRIILGTDADTPGHALAEELARRLGKDRCWRVRWPKKDEFSYFKDANEVLKCLGPGALREVIENAELYQLHVSEEALQ***
MPVRIMQPGHLSLTNGLATTSSVTVPRRLGRVWSRLLSYPTHVTGNPSLQCNSDAESFGEHKDDTIDISKLTEVKQKLKLVGINCDDSCIPGRYAHLLCPKCKGGGRSLERSLSVHIIQDGDFAMWRCFRVDCGWAGRAFAGSNKIRKVMSSRQVAEKSLGLEPLGEKLIAYLGERMISEGTLQRNSVMQRLHDQAIAFPYWHNGVLVGCKYRSMERKFRQEKGTEKWLYGLDDINETAEVIIVEGEIDKLSVEEAGFQNCVSVPSGAPPKVSNRELPPREKDTGYQYLWNCKEHLDKVSRIILGTDADTPGHALAEELARRLGKDRCWRVRWPKKDEFSYFKDANEVLKCLGPGALREVIENAELYQLHVSEEALQCTK
*PVRIMQPGHLSLTNGLATTSSVTVPRRLGRVWSRLLSYPTHVTGNPSLQCNSDAESF*EHKDDTIDISKLTEVKQKLKLVGINCDDSCIPGRYAHLLCPKCKGGGRSLERSLSVHIIQDGDFAMWRCFRVDCGWAGRAFAGSNKIRKVMSSRQVAEKSLGLEPLGEKLIAYLGERMISEGTLQRNSVMQRLHDQAIAFPYWHNGVLVGCKYRSMERKFRQEKGTEKWLYGLDDINETAEVIIVEGEIDKLSVEEAGFQNCVSVPSGAPPKVSNRELPPREKDTGYQYLWNCKEHLDKVSRIILGTDADTPGHALAEELARRLGKDRCWRVRWPKKDEFSYFKDANEVLKCLGPGALREVIENAELYQLHVSEEALQCT*
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
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SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
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MPVRIMQPGHLSLTNGLATTSSVTVPRRLGRVWSRLLSYPTHVTGNPSLQCNSDAESFGEHKDDTIDISKLTEVKQKLKLVGINCDDSCIPGRYAHLLCPKCKGGGRSLERSLSVHIIQDGDFAMWRCFRVDCGWAGRAFAGSNKIRKVMSSRQVAEKSLGLEPLGEKLIAYLGERMISEGTLQRNSVMQRLHDQAIAFPYWHNGVLVGCKYRSMERKFRQEKGTEKWLYGLDDINETAEVIIVEGEIDKLSVEEAGFQNCVSVPSGAPPKVSNRELPPREKDTGYQYLWNCKEHLDKVSRIILGTDADTPGHALAEELARRLGKDRCWRVRWPKKDEFSYFKDANEVLKCLGPGALREVIENAELYQLHVSEEALQCTK
no confident homologs detected

Close Homologs for Annotation Transfer

Close Homologs in SWISS-PROT Database Detected by BLAST ?

Original result of BLAST against SWISS-PROT Database

No hits with e-value below 0.001 by BLAST

Close Homologs in the Non-Redundant Database Detected by BLAST ?

Original result of BLAST against Nonredundant Database

GI ?Alignment Graph ?Length ? Definition ? Q cover ? H cover ? Identity ? E-value ?
Query380
255564297306 nucleic acid binding protein, putative [ 0.784 0.973 0.680 1e-117
359483975380 PREDICTED: uncharacterized protein LOC10 0.815 0.815 0.669 1e-116
388507530384 unknown [Lotus japonicus] 0.921 0.911 0.583 1e-113
356533161375 PREDICTED: uncharacterized protein LOC10 0.889 0.901 0.575 1e-110
449435924329 PREDICTED: uncharacterized protein LOC10 0.778 0.899 0.605 1e-103
357495669331 hypothetical protein MTR_5g099220 [Medic 0.768 0.882 0.624 1e-102
359483742 519 PREDICTED: uncharacterized protein LOC10 0.818 0.599 0.578 1e-100
296089225276 unnamed protein product [Vitis vinifera] 0.694 0.956 0.680 1e-100
297740895460 unnamed protein product [Vitis vinifera] 0.818 0.676 0.578 3e-99
302141745 696 unnamed protein product [Vitis vinifera] 0.960 0.524 0.521 2e-98
>gi|255564297|ref|XP_002523145.1| nucleic acid binding protein, putative [Ricinus communis] gi|223537552|gb|EEF39176.1| nucleic acid binding protein, putative [Ricinus communis] Back     alignment and taxonomy information
 Score =  426 bits (1096), Expect = e-117,   Method: Compositional matrix adjust.
 Identities = 209/307 (68%), Positives = 242/307 (78%), Gaps = 9/307 (2%)

Query: 78  LKLVGINCDDSCIPGRYAHLLCPKCKGGGRSLERSLSVHIIQDGDFAMWRCFRVDCGWAG 137
           ++ +GINCD S IPG+++HLLCPKCKGG +S+ERSLS+HIIQD DFAMWRC+R  CGWAG
Sbjct: 1   MEFLGINCDRSSIPGKFSHLLCPKCKGG-KSVERSLSLHIIQDADFAMWRCYRTCCGWAG 59

Query: 138 RAFA-------GSNKIRKVMSSRQVAEKSLGLEPLGEKLIAYLGERMISEGTLQRNSVMQ 190
           +AFA       G N + KV +SRQ   + + LEPLGEKLIAY  +R IS+ TL+RNSVMQ
Sbjct: 60  QAFADDRATNEGMNIMLKVNTSRQTTSEGIALEPLGEKLIAYFSDRGISKETLRRNSVMQ 119

Query: 191 RLHDQ-AIAFPYWHNGVLVGCKYRSMERKFRQEKGTEKWLYGLDDINETAEVIIVEGEID 249
              DQ  IAF Y  N VLVGCKYR+ E+KF Q+KGTEKWLYGLDDINET E+IIVEGEID
Sbjct: 120 MAADQDVIAFTYRQNRVLVGCKYRTTEKKFWQDKGTEKWLYGLDDINETTEIIIVEGEID 179

Query: 250 KLSVEEAGFQNCVSVPSGAPPKVSNRELPPREKDTGYQYLWNCKEHLDKVSRIILGTDAD 309
           KLSVEEAGF+NCVSVP GAP  VS +++PP E D  YQYLWNC+++LDKVSRIIL TD D
Sbjct: 180 KLSVEEAGFRNCVSVPGGAPQVVSTKDVPPLENDKAYQYLWNCRDYLDKVSRIILATDGD 239

Query: 310 TPGHALAEELARRLGKDRCWRVRWPKKDEFSYFKDANEVLKCLGPGALREVIENAELYQL 369
             G ALAEELARRLGK+RC  VRWPKKD    FKDANEVLKCLGP AL+EVIE AELY  
Sbjct: 240 VAGQALAEELARRLGKERCCIVRWPKKDHSRCFKDANEVLKCLGPIALKEVIETAELYHS 299

Query: 370 HVSEEAL 376
           H   +A+
Sbjct: 300 HAISQAI 306

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Class:

Phylum: Streptophyta

Superkingdom: Eukaryota
>gi|359483975|ref|XP_002270298.2| PREDICTED: uncharacterized protein LOC100263216 [Vitis vinifera] Back     alignment and taxonomy information
>gi|388507530|gb|AFK41831.1| unknown [Lotus japonicus] Back     alignment and taxonomy information
>gi|356533161|ref|XP_003535136.1| PREDICTED: uncharacterized protein LOC100814805 [Glycine max] Back     alignment and taxonomy information
>gi|449435924|ref|XP_004135744.1| PREDICTED: uncharacterized protein LOC101219541 [Cucumis sativus] Back     alignment and taxonomy information
>gi|357495669|ref|XP_003618123.1| hypothetical protein MTR_5g099220 [Medicago truncatula] gi|355519458|gb|AET01082.1| hypothetical protein MTR_5g099220 [Medicago truncatula] Back     alignment and taxonomy information
>gi|359483742|ref|XP_002268125.2| PREDICTED: uncharacterized protein LOC100247384 [Vitis vinifera] Back     alignment and taxonomy information
>gi|296089225|emb|CBI38997.3| unnamed protein product [Vitis vinifera] Back     alignment and taxonomy information
>gi|297740895|emb|CBI31077.3| unnamed protein product [Vitis vinifera] Back     alignment and taxonomy information
>gi|302141745|emb|CBI18948.3| unnamed protein product [Vitis vinifera] Back     alignment and taxonomy information

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST ?

Original result of BLAST against Gene Ontology (AMIGO)

ID ? Alignment graph ? Length ? Definition ? Q cover ? H cover ? Identity ? E-value ?
Query380
TAIR|locus:2204584 709 AT1G30680 [Arabidopsis thalian 0.797 0.427 0.525 1e-82
TAIR|locus:2204559337 AT1G30660 "AT1G30660" [Arabido 0.802 0.905 0.517 3.8e-78
UNIPROTKB|Q1L7I7 765 Q1L7I7 "Mitochondrial helicase 0.247 0.122 0.299 0.00099
TAIR|locus:2204584 AT1G30680 [Arabidopsis thaliana (taxid:3702)] Back     alignment and assigned GO terms
 Score = 829 (296.9 bits), Expect = 1.0e-82, P = 1.0e-82
 Identities = 165/314 (52%), Positives = 220/314 (70%)

Query:    63 DDTIDISKLTEVKQKLKLVGINCDDSCIPGRYAHLLCPKCKGGGRSLERSLSVHIIQDGD 122
             D  + +S+L  +++KL   G++ ++ C PG+++ L+CP C+GG  S E+SLS+ I  DG 
Sbjct:   101 DKRVVLSRLVTLRRKLAEQGVDAEN-CPPGQHSGLICPTCEGGN-SGEKSLSLFIAPDGS 158

Query:   123 FAMWRCFRVDCGWAG--RA---FAGSNKIRKVMSSRQVAEKSLGLEPLGEKLIAYLGERM 177
              A W CFR  CG  G  RA    A ++ I KV   R++  + + LEPL +++  Y   R 
Sbjct:   159 SATWNCFRGKCGLKGGVRADGGLASADPIEKV--ERKITVEGIELEPLCDEIQDYFAARA 216

Query:   178 ISEGTLQRNSVMQ-RLHDQ-AIAFPYWHNGVLVGCKYRSMERKFRQEKGTEKWLYGLDDI 235
             IS  TL+RN VMQ R+ D+  IAF YW  G LV CKYRS+ + F QE+ T + LYGLDDI
Sbjct:   217 ISRKTLERNRVMQKRIGDEIVIAFTYWQRGELVSCKYRSLTKMFFQERKTRRILYGLDDI 276

Query:   236 NETAEVIIVEGEIDKLSVEEAGFQNCVSVPSGAPPKVSNRELPPREKDTGYQYLWNCKEH 295
              +T+EVIIVEGEIDKL++EEAGF NCVSVP GAP KVS++E+P  +KDT Y++LWNC ++
Sbjct:   277 EKTSEVIIVEGEIDKLAMEEAGFLNCVSVPDGAPAKVSSKEIPSEDKDTKYKFLWNCNDY 336

Query:   296 LDKVSRIILGTDADTPGHALAEELARRLGKDRCWRVRWPKKDEFSYFKDANEVLKCLGPG 355
             L K SRI++ TD D PG A+AEE+ARRLGK+RCWRV+WPKK E  +FKDANEVL   GP 
Sbjct:   337 LKKASRIVIATDGDGPGQAMAEEIARRLGKERCWRVKWPKKSEDEHFKDANEVLMSKGPH 396

Query:   356 ALREVIENAELYQL 369
              L+E I +AE Y +
Sbjct:   397 LLKEAILDAEPYPI 410
GO:0003678 "DNA helicase activity" evidence=IEA
GO:0005524 "ATP binding" evidence=IEA
GO:0005739 "mitochondrion" evidence=ISM
GO:0006260 "DNA replication" evidence=IEA
TAIR|locus:2204559 AT1G30660 "AT1G30660" [Arabidopsis thaliana (taxid:3702)] Back     alignment and assigned GO terms
UNIPROTKB|Q1L7I7 Q1L7I7 "Mitochondrial helicase twinkle" [Acanthamoeba castellanii (taxid:5755)] Back     alignment and assigned GO terms

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries ?

Original result of BLAST against SWISS-PROT

No confident hit for EC number transfering in SWISSPROT detected by BLAST

EC Number Prediction by Ezypred Server ?

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software ?

No EC number assignment, probably not an enzyme!

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING ?

Original result from the STRING server

Your Input:
GSVIVG00035172001
SubName- Full=Chromosome chr10 scaffold_76, whole genome shotgun sequence; (334 aa)
(Vitis vinifera)
Predicted Functional Partners:
 
Sorry, there are no predicted associations at the current settings.
 

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST ?

Original result of RPS-BLAST against CDD database part I

ID ?Alignment Graph ?Length ? Definition ? E-value ?
Query380
pfam1366281 pfam13662, Toprim_4, Toprim domain 3e-10
pfam1315590 pfam13155, Toprim_2, Toprim-like 2e-08
cd0102979 cd01029, TOPRIM_primases, TOPRIM_primases: The top 9e-08
cd0018883 cd00188, TOPRIM, Topoisomerase-primase domain 2e-07
pfam0175186 pfam01751, Toprim, Toprim domain 3e-06
COG0358 568 COG0358, DnaG, DNA primase (bacterial type) [DNA r 5e-06
smart0049375 smart00493, TOPRIM, topoisomerases, DnaG-type prim 6e-06
cd0336479 cd03364, TOPRIM_DnaG_primases, TOPRIM_DnaG_primase 2e-04
TIGR01391415 TIGR01391, dnaG, DNA primase, catalytic core 0.004
>gnl|CDD|222298 pfam13662, Toprim_4, Toprim domain Back     alignment and domain information 
 Score = 55.7 bits (135), Expect = 3e-10
 Identities = 26/86 (30%), Positives = 36/86 (41%), Gaps = 15/86 (17%)

Query: 240 EVIIVEGEIDKLSVEEAGFQNCVSVPSGAPPKVSNRELPPREKDTGYQYLWNCKEHLDKV 299
            + IVEG  D L++E+AG++  V+V  GA        L P +         + KE     
Sbjct: 2   TICIVEGYADVLALEQAGYKGVVAVLGGA--------LSPLDGIGPEDLNIDVKE----- 48

Query: 300 SRIILGTDADTPGHALAEELARRLGK 325
             +IL  D D  G   A  LA  L  
Sbjct: 49  --VILAFDGDVAGEKAALRLAELLLA 72

The toprim domain is found in a wide variety of enzymes involved in nucleic acid manipulation. Length = 81
>gnl|CDD|221942 pfam13155, Toprim_2, Toprim-like Back     alignment and domain information
>gnl|CDD|173779 cd01029, TOPRIM_primases, TOPRIM_primases: The topoisomerase-primase (TORPIM) nucleotidyl transferase/hydrolase domain found in the active site regions of bacterial DnaG-type primases and their homologs Back     alignment and domain information
>gnl|CDD|173773 cd00188, TOPRIM, Topoisomerase-primase domain Back     alignment and domain information
>gnl|CDD|216679 pfam01751, Toprim, Toprim domain Back     alignment and domain information
>gnl|CDD|223435 COG0358, DnaG, DNA primase (bacterial type) [DNA replication, recombination, and repair] Back     alignment and domain information
>gnl|CDD|214695 smart00493, TOPRIM, topoisomerases, DnaG-type primases, OLD family nucleases and RecR proteins Back     alignment and domain information
>gnl|CDD|173784 cd03364, TOPRIM_DnaG_primases, TOPRIM_DnaG_primases: The topoisomerase-primase (TORPIM) nucleotidyl transferase/hydrolase domain found in the active site regions of proteins similar to Escherichia coli DnaG Back     alignment and domain information
>gnl|CDD|233392 TIGR01391, dnaG, DNA primase, catalytic core Back     alignment and domain information

Conserved Domains Detected by HHsearch ?

Original result of HHsearch against CDD database

ID ?Alignment Graph ?Length ? Definition ? Probability ?
Query 380
PRK05667 580 dnaG DNA primase; Validated 100.0
TIGR01391415 dnaG DNA primase, catalytic core. This protein con 100.0
PHA02540337 61 DNA primase; Provisional 100.0
COG0358 568 DnaG DNA primase (bacterial type) [DNA replication 100.0
PHA02415 930 DNA primase domain-containing protein 99.97
PRK08624373 hypothetical protein; Provisional 99.97
TIGR00646218 MG010 DNA primase-related protein. The DNA primase 99.97
PHA02031266 putative DnaG-like primase 99.94
TIGR027601960 TraI_TIGR conjugative transfer relaxase protein Tr 99.56
PF1315596 Toprim_2: Toprim-like 99.54
PRK07078 759 hypothetical protein; Validated 99.5
cd0336479 TOPRIM_DnaG_primases TOPRIM_DnaG_primases: The top 99.44
PF1366281 Toprim_4: Toprim domain; PDB: 1EQN_E 1DD9_A 3B39_B 99.33
PF1336296 Toprim_3: Toprim domain 99.27
cd0102979 TOPRIM_primases TOPRIM_primases: The topoisomerase 99.22
COG4643366 Uncharacterized protein conserved in bacteria [Fun 99.15
PRK04031 408 DNA primase; Provisional 99.15
PF0180797 zf-CHC2: CHC2 zinc finger; InterPro: IPR002694 Zin 99.13
PF08275128 Toprim_N: DNA primase catalytic core, N-terminal d 98.99
smart0049376 TOPRIM topoisomerases, DnaG-type primases, OLD fam 98.87
cd0102781 TOPRIM_RNase_M5_like TOPRIM_ RNase M5_like: The to 98.87
smart0040055 ZnF_CHCC zinc finger. 98.84
PF12965130 DUF3854: Domain of unknown function (DUF3854); Int 98.66
KOG2373 514 consensus Predicted mitochondrial DNA helicase twi 98.42
cd0018883 TOPRIM Topoisomerase-primase domain. This is a nuc 98.16
PF0827340 Prim_Zn_Ribbon: Zinc-binding domain of primase-hel 97.75
PF01751100 Toprim: Toprim domain; InterPro: IPR006171 This is 97.34
smart0077837 Prim_Zn_Ribbon Zinc-binding domain of primase-heli 97.29
COG1658127 Small primase-like proteins (Toprim domain) [DNA r 97.15
PRK04017132 hypothetical protein; Provisional 97.11
PF1315477 DUF3991: Protein of unknown function (DUF3991) 96.86
TIGR00334174 5S_RNA_mat_M5 ribonuclease M5. This family of orth 96.65
PRK14719 360 bifunctional RNAse/5-amino-6-(5-phosphoribosylamin 95.75
COG4026 290 Uncharacterized protein containing TOPRIM domain, 95.34
TIGR0365553 anti_R_Lar restriction alleviation protein, Lar fa 94.1
cd01025112 TOPRIM_recR TOPRIM_recR: topoisomerase-primase (TO 93.69
PRK0971064 lar restriction alleviation and modification prote 91.75
TIGR00615195 recR recombination protein RecR. This family is ba 91.47
PRK00076196 recR recombination protein RecR; Reviewed 90.93
PRK13844200 recombination protein RecR; Provisional 90.56
COG0353198 RecR Recombinational DNA repair protein (RecF path 90.03
PF1435461 Lar_restr_allev: Restriction alleviation protein L 87.43
PTZ0025590 60S ribosomal protein L37a; Provisional 86.29
PF0178090 Ribosomal_L37ae: Ribosomal L37ae protein family; I 85.74
TIGR0028091 L37a ribosomal protein L37a. This model finds euka 85.53
COG199789 RPL43A Ribosomal protein L37AE/L43A [Translation, 84.26
PRK0397690 rpl37ae 50S ribosomal protein L37Ae; Reviewed 84.2
PF1178136 RRN7: RNA polymerase I-specific transcription init 81.31
PF0512981 Elf1: Transcription elongation factor Elf1 like; I 80.48
>PRK05667 dnaG DNA primase; Validated Back     alignment and domain information 
Probab=100.00  E-value=1.6e-42  Score=362.41  Aligned_cols=273  Identities=24%  Similarity=0.366  Sum_probs=206.5

Q ss_pred             ccchhhHHHHH------HHHHHhCCccccCCCCCceeeecCCCCCCCCCCCCccceEEEEEcCCccEEEeCCccCCCCcc
Q 042101           65 TIDISKLTEVK------QKLKLVGINCDDSCIPGRYAHLLCPKCKGGGRSLERSLSVHIIQDGDFAMWRCFRVDCGWAGR  138 (380)
Q Consensus        65 ~~~~~~~~~~~------~~l~~~gi~~~~~~~~G~~~~~~CPfc~~~~~~~eks~s~~v~~d~~~g~~~Cf~~~CG~~G~  138 (380)
                      +++.+.+++|+      +++..+ +++++   +|++|.++||||++      ++|||+|++++  +.||||+  ||.+||
T Consensus         3 ~i~~~~i~~i~~~~dI~~vi~~~-v~Lkk---~G~~~~~~CPfH~e------ktpSf~V~~~k--~~~~CF~--Cg~~Gd   68 (580)
T PRK05667          3 RIPPEFIEELRARVDIVDVIGEY-VKLKK---AGRNYKGLCPFHDE------KTPSFTVSPDK--QFYHCFG--CGAGGD   68 (580)
T ss_pred             CCCHHHHHHHHhcCCHHHHHHHh-cceee---cCCceeecCCCCCC------CCCceEEECCC--CeEEECC--CCCCCC
Confidence            34555555544      455554 88877   89999999999985      78999999864  9999999  999999


Q ss_pred             cccC-----Cc---c------------chhc--cch--h-hhh---hh--cc---CC-CcccHHHHHHHHhCCCCHHHHh
Q 042101          139 AFAG-----SN---K------------IRKV--MSS--R-QVA---EK--SL---GL-EPLGEKLIAYLGERMISEGTLQ  184 (380)
Q Consensus       139 v~~~-----~~---e------------~~~~--~~~--~-~~~---~~--~~---~~-~pl~~~~~~YL~~RGIs~eti~  184 (380)
                      ++..     ..   +            ....  .+.  + +..   +.  .+   .+ .+.++.+++||.+|||++++++
T Consensus        69 ~i~fv~~~~~~sf~eAv~~La~~~gi~~~~~~~~~~~~~~~l~~~~~~a~~~y~~~L~~~~~~~a~~YL~~RGls~~~i~  148 (580)
T PRK05667         69 VIKFLMEYEGLSFVEAVEELADRAGIELPYEDQQERSRRQRLYEIMELAAKFYQQQLRTPEGAEARQYLYKRGLSEETIE  148 (580)
T ss_pred             HHHHHHHHhCCCHHHHHHHHHHHhCCCCCchhhhhhhhHHHHHHHHHHHHHHHHHHHcCccchHHHHHHHHcCCCHHHHH
Confidence            9852     10   1            0000  000  0 000   00  00   12 4667789999999999999999


Q ss_pred             hcceEEecC-------------------------------C-------cEEEEE-ecCCCEEEEEeeecCC---Cccccc
Q 042101          185 RNSVMQRLH-------------------------------D-------QAIAFP-YWHNGVLVGCKYRSME---RKFRQE  222 (380)
Q Consensus       185 ~f~~g~~~~-------------------------------g-------~~I~fP-~~~~G~vv~~~~R~~~---Kkf~~~  222 (380)
                      +|++||+++                               |       +||+|| +|.+|++|+|++|.++   .||.+.
T Consensus       149 ~f~lGyap~~~~~L~~~l~~~~~~~~~l~~~GL~~~~~~~~~~yd~Fr~RimfPI~d~~G~vigF~GR~l~~~~pKYlNS  228 (580)
T PRK05667        149 RFGIGYAPDGWDALLKHLGGKGFSEKELEEAGLLIKNEDGGGPYDRFRNRIMFPIRDLRGRVIGFGGRVLGDDKPKYLNS  228 (580)
T ss_pred             HhCCccCCChHHHHHHHHHhcCCCHHHHHHCCceEecCCCCCcchhcCCeEEEEEECCCCcEEEEEeeecCCCCCeeeCC
Confidence            999998641                               2       289999 5789999999999985   578775


Q ss_pred             c-----CCCCccccccccC----CCCEEEEEechhHHHHHHHhCCCcEEEcCCCCCCCccCCCCCCCcccchhhhhHHHH
Q 042101          223 K-----GTEKWLYGLDDIN----ETAEVIIVEGEIDKLSVEEAGFQNCVSVPSGAPPKVSNRELPPREKDTGYQYLWNCK  293 (380)
Q Consensus       223 ~-----~~~~~Lfgl~~i~----~~~~iiIvEG~~DaLSl~q~G~~~~Vs~~~Ga~~~~~~~~Lp~~~~~~~~~~l~~~~  293 (380)
                      +     .++..|||++.++    +.+.||||||++||||++|+|+.|||++ .|+..+  .                +|+
T Consensus       229 pet~iF~K~~~LYgl~~a~~~i~~~~~viivEG~~Dvisl~q~Gi~naVA~-lGtalt--~----------------~~~  289 (580)
T PRK05667        229 PETPLFHKGRVLYGLDEARKAIAKKKQVIVVEGYMDVIALHQAGITNAVAS-LGTALT--E----------------EHL  289 (580)
T ss_pred             CCCCCccCCccccCccHHHHhcccCCeEEEEeeHHHHHHHHHcCCCcEEEe-CCCCCC--H----------------HHH
Confidence            5     3678999998754    5789999999999999999999999976 465321  1                244


Q ss_pred             hhcCCC-CeEEEEeCCChhhHHHHHHHHHH---hC--CCceEEEEcCCCCCCCCCCCHHHHHHhcChHHHHHHHHhccCC
Q 042101          294 EHLDKV-SRIILGTDADTPGHALAEELARR---LG--KDRCWRVRWPKKDEFSYFKDANEVLKCLGPGALREVIENAELY  367 (380)
Q Consensus       294 ~~L~~~-~~Ivl~~DnD~AG~~aa~~la~~---L~--~~~v~iv~lP~~~~~~~~KD~ND~L~~~g~~~l~~~i~~A~~~  367 (380)
                      .+|.+. .+||+|||+|.||++||.++++.   +.  ...++++.+|+      +|||||+++++|.++|+++|++|.++
T Consensus       290 ~~L~r~~~~vil~~D~D~AG~~aa~r~~~~~~~l~~~g~~v~vv~lp~------gkDpdd~l~~~G~~~~~~~i~~a~~~  363 (580)
T PRK05667        290 KLLRRLTDEVILCFDGDKAGRKAALRALELALPLLKDGRQVRVAFLPD------GKDPDDLVRKEGPEAFRALLEQAIPL  363 (580)
T ss_pred             HHHHhcCCeEEEEeCCCHHHHHHHHHHHHHHHHHHhCCceEEEEECCC------CCChHHHHHHhCHHHHHHHHHcCCCH
Confidence            555443 58999999999999999998877   42  23688999997      49999999999999999999999998


Q ss_pred             Cccchhhhh
Q 042101          368 QLHVSEEAL  376 (380)
Q Consensus       368 ~~~~~~~~~  376 (380)
                      ....+...+
T Consensus       364 ~~f~~~~~~  372 (580)
T PRK05667        364 SEFLIRRLI  372 (580)
T ss_pred             HHHHHHHHH
Confidence            766555443

>TIGR01391 dnaG DNA primase, catalytic core Back     alignment and domain information
>PHA02540 61 DNA primase; Provisional Back     alignment and domain information
>COG0358 DnaG DNA primase (bacterial type) [DNA replication, recombination, and repair] Back     alignment and domain information
>PHA02415 DNA primase domain-containing protein Back     alignment and domain information
>PRK08624 hypothetical protein; Provisional Back     alignment and domain information
>TIGR00646 MG010 DNA primase-related protein Back     alignment and domain information
>PHA02031 putative DnaG-like primase Back     alignment and domain information
>TIGR02760 TraI_TIGR conjugative transfer relaxase protein TraI Back     alignment and domain information
>PF13155 Toprim_2: Toprim-like Back     alignment and domain information
>PRK07078 hypothetical protein; Validated Back     alignment and domain information
>cd03364 TOPRIM_DnaG_primases TOPRIM_DnaG_primases: The topoisomerase-primase (TORPIM) nucleotidyl transferase/hydrolase domain found in the active site regions of proteins similar to Escherichia coli DnaG Back     alignment and domain information
>PF13662 Toprim_4: Toprim domain; PDB: 1EQN_E 1DD9_A 3B39_B 1DDE_A Back     alignment and domain information
>PF13362 Toprim_3: Toprim domain Back     alignment and domain information
>cd01029 TOPRIM_primases TOPRIM_primases: The topoisomerase-primase (TORPIM) nucleotidyl transferase/hydrolase domain found in the active site regions of bacterial DnaG-type primases and their homologs Back     alignment and domain information
>COG4643 Uncharacterized protein conserved in bacteria [Function unknown] Back     alignment and domain information
>PRK04031 DNA primase; Provisional Back     alignment and domain information
>PF01807 zf-CHC2: CHC2 zinc finger; InterPro: IPR002694 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule Back     alignment and domain information
>PF08275 Toprim_N: DNA primase catalytic core, N-terminal domain; InterPro: IPR013264 This is the N-terminal, catalytic core domain of DNA primases Back     alignment and domain information
>smart00493 TOPRIM topoisomerases, DnaG-type primases, OLD family nucleases and RecR proteins Back     alignment and domain information
>cd01027 TOPRIM_RNase_M5_like TOPRIM_ RNase M5_like: The topoisomerase-primase (TOPRIM) nucleotidyl transferase/hydrolase domain found in Ribonuclease M5: (RNase M5) and other small primase-like proteins from bacteria and archaea Back     alignment and domain information
>smart00400 ZnF_CHCC zinc finger Back     alignment and domain information
>PF12965 DUF3854: Domain of unknown function (DUF3854); InterPro: IPR024385 This is a family of uncharacterised proteins, found by clustering human gut metagenomic sequences [] Back     alignment and domain information
>KOG2373 consensus Predicted mitochondrial DNA helicase twinkle [Replication, recombination and repair] Back     alignment and domain information
>cd00188 TOPRIM Topoisomerase-primase domain Back     alignment and domain information
>PF08273 Prim_Zn_Ribbon: Zinc-binding domain of primase-helicase; InterPro: IPR013237 This entry is represented by bacteriophage T7 Gp4 Back     alignment and domain information
>PF01751 Toprim: Toprim domain; InterPro: IPR006171 This is a conserved region from DNA primase Back     alignment and domain information
>smart00778 Prim_Zn_Ribbon Zinc-binding domain of primase-helicase Back     alignment and domain information
>COG1658 Small primase-like proteins (Toprim domain) [DNA replication, recombination, and repair] Back     alignment and domain information
>PRK04017 hypothetical protein; Provisional Back     alignment and domain information
>PF13154 DUF3991: Protein of unknown function (DUF3991) Back     alignment and domain information
>TIGR00334 5S_RNA_mat_M5 ribonuclease M5 Back     alignment and domain information
>PRK14719 bifunctional RNAse/5-amino-6-(5-phosphoribosylamino)uracil reductase; Provisional Back     alignment and domain information
>COG4026 Uncharacterized protein containing TOPRIM domain, potential nuclease [General function prediction only] Back     alignment and domain information
>TIGR03655 anti_R_Lar restriction alleviation protein, Lar family Back     alignment and domain information
>cd01025 TOPRIM_recR TOPRIM_recR: topoisomerase-primase (TOPRIM) nucleotidyl transferase/hydrolase domain of the type found in Escherichia coli RecR Back     alignment and domain information
>PRK09710 lar restriction alleviation and modification protein; Reviewed Back     alignment and domain information
>TIGR00615 recR recombination protein RecR Back     alignment and domain information
>PRK00076 recR recombination protein RecR; Reviewed Back     alignment and domain information
>PRK13844 recombination protein RecR; Provisional Back     alignment and domain information
>COG0353 RecR Recombinational DNA repair protein (RecF pathway) [DNA replication, recombination, and repair] Back     alignment and domain information
>PF14354 Lar_restr_allev: Restriction alleviation protein Lar Back     alignment and domain information
>PTZ00255 60S ribosomal protein L37a; Provisional Back     alignment and domain information
>PF01780 Ribosomal_L37ae: Ribosomal L37ae protein family; InterPro: IPR002674 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms Back     alignment and domain information
>TIGR00280 L37a ribosomal protein L37a Back     alignment and domain information
>COG1997 RPL43A Ribosomal protein L37AE/L43A [Translation, ribosomal structure and biogenesis] Back     alignment and domain information
>PRK03976 rpl37ae 50S ribosomal protein L37Ae; Reviewed Back     alignment and domain information
>PF11781 RRN7: RNA polymerase I-specific transcription initiation factor Rrn7; InterPro: IPR021752 Rrn7 is a transcription binding factor that associates strongly with both Rrn6 and Rrn11 to form a complex which itself binds the TATA-binding protein and is required for transcription by the core domain of the RNA PolI promoter [],[] Back     alignment and domain information
>PF05129 Elf1: Transcription elongation factor Elf1 like; InterPro: IPR007808 This family of uncharacterised, mostly short, proteins contain a putative zinc binding domain with four conserved cysteines Back     alignment and domain information

Homologous Structure Templates

Structure Templates Detected by BLAST ?

Original result of BLAST against Protein Data Bank

ID ?Alignment Graph ?Length ? Definition ? E-value ?
Query380
1q57_A 503 The Crystal Structure Of The Bifunctional Primase-h 2e-04
1nui_A255 Crystal Structure Of The Primase Fragment Of Bacter 3e-04
>pdb|1Q57|A Chain A, The Crystal Structure Of The Bifunctional Primase-helicase Of Bacteriophage T7 Length = 503 Back     alignment and structure 
Iteration: 1

 Score = 43.1 bits (100), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 50/166 (30%), Positives = 71/166 (42%), Gaps = 33/166 (19%)
Query: 203 HNGVLVGCKYRSMERKFRQEKGTEK--WLYGLDDINETAEVIIVEGEIDKLSVEEAGFQN 260
            NG +V  K R  ++ F+   G+ K   L+G    N   ++++ EGEID L+V E   Q+
Sbjct: 51  QNGNIVSQKVRDKDKNFKT-TGSHKSDALFGKHLWNGGKKIVVTEGEIDMLTVME--LQD 107
Query: 261 C----VSVPSGAPPKVSNRELPPREKDTGYQYLWNCKEHLDKVSRIILGTDADTPGHALA 316
           C    VS+  GA            +K     Y     E+ D+  +IIL  D D  G    
Sbjct: 108 CKYPVVSLGHGASAA---------KKTCAANY-----EYFDQFEQIILMFDMDEAGRKAV 153
Query: 317 EELARRLGKDRCWRVRWPKKDEFSYFKDANEVLKCLGPGALREVIE 362
           EE A+ L   +      P        KDANE   C   G  RE++E
Sbjct: 154 EEAAQVLPAGKVRVAVLP-------CKDANE---CHLNGHDREIME 189
>pdb|1NUI|A Chain A, Crystal Structure Of The Primase Fragment Of Bacteriophage T7 Primase- Helicase Protein Length = 255 Back     alignment and structure

Structure Templates Detected by RPS-BLAST ?

Original result of RPS-BLAST against PDB70 database

ID ?Alignment Graph ?Length ? Definition ? E-value ?
Query380
1q57_A 503 DNA primase/helicase; dntpase, DNA replication, tr 7e-36
1nui_A255 DNA primase/helicase; zinc-biding domain, toprim f 2e-27
1vt4_I 1221 APAF-1 related killer DARK; drosophila apoptosome, 5e-05
>1q57_A DNA primase/helicase; dntpase, DNA replication, transferase; HET: DNA; 3.45A {Enterobacteria phage T7} SCOP: c.37.1.11 e.13.1.2 Length = 503 Back     alignment and structure
 Score =  136 bits (342), Expect = 7e-36
 Identities = 52/214 (24%), Positives = 77/214 (35%), Gaps = 27/214 (12%)

Query: 170 IAYLGERMISEGTLQRNSVMQRLHDQ---AIAFPYWHNGVLVGCKYRSMERKFRQEKGTE 226
            + L  R IS+ T Q+        D     +A     NG +V  K R  ++ F+     +
Sbjct: 15  YSALTARGISKETCQKAGYWIAKVDGVMYQVADYRDQNGNIVSQKVRDKDKNFKTTGSHK 74

Query: 227 KW-LYGLDDINETAEVIIVEGEIDKLSVEEAGFQN--CVSVPSGAPPKVSNRELPPREKD 283
              L+G    N   ++++ EGEID L+V E        VS+  GA               
Sbjct: 75  SDALFGKHLWNGGKKIVVTEGEIDMLTVMELQDCKYPVVSLGHGASAAK----------- 123

Query: 284 TGYQYLWNCKEHLDKVSRIILGTDADTPGHALAEELARRLGKDRCWRVRWPKKDEFSYFK 343
              +      E+ D+  +IIL  D D  G    EE A+ L   +      P        K
Sbjct: 124 ---KTCAANYEYFDQFEQIILMFDMDEAGRKAVEEAAQVLPAGKVRVAVLP-------CK 173

Query: 344 DANEVLKCLGPGALREVIENAELYQLHVSEEALQ 377
           DANE         + E + NA  +       AL 
Sbjct: 174 DANECHLNGHDREIMEQVWNAGPWIPDGVVSALS 207
>1nui_A DNA primase/helicase; zinc-biding domain, toprim fold, DNA replication, DNA-direct polymerase, primosome, late protein, ATP-binding; HET: DNA; 2.90A {Enterobacteria phage T7} SCOP: e.13.1.2 g.41.3.2 Length = 255 Back     alignment and structure
>1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis, programmed cell death; HET: DTP; 6.90A {Drosophila melanogaster} PDB: 3iz8_A* Length = 1221 Back     alignment and structure

Structure Templates Detected by HHsearch ?

Original result of HHsearch against PDB70 database

ID ?Alignment Graph ?Length ? Definition ? Probability ?
Query380
2au3_A407 DNA primase; zinc ribbon, toprim, RNA polymerase, 100.0
1nui_A255 DNA primase/helicase; zinc-biding domain, toprim f 100.0
4edg_A329 DNA primase; catalytic domain, nucleoside triphosp 99.97
1dd9_A338 DNA primase, DNAG; toprim, 3-helix bundle, DNA-bin 99.97
1q57_A 503 DNA primase/helicase; dntpase, DNA replication, tr 99.95
1d0q_A103 DNA primase; zinc-binding motif, protein, transfer 99.27
1t6t_1118 Putative protein; structural genomics, PSI, protei 98.84
2fcj_A119 Small toprim domain protein; structural genomics, 98.23
1vdd_A228 Recombination protein RECR; helix-hairpin-helix, z 93.24
3j21_i83 50S ribosomal protein L37AE; archaea, archaeal, KI 91.53
4a17_Y103 RPL37A, 60S ribosomal protein L32; eukaryotic ribo 90.97
3iz5_m92 60S ribosomal protein L43 (L37AE); eukaryotic ribo 90.67
3izc_m92 60S ribosomal protein RPL43 (L37AE); eukaryotic ri 89.95
3vdp_A212 Recombination protein RECR; zinc finger, DNA repai 89.93
3cc2_Z116 50S ribosomal protein L37AE, 50S ribosomal protein 88.67
1ffk_W73 Ribosomal protein L37AE; ribosome assembly, RNA-RN 87.73
1vq8_Z83 50S ribosomal protein L37AE; ribosome 50S, protein 87.25
3jyw_972 60S ribosomal protein L43; eukaryotic ribosome, RA 86.15
1wii_A85 Hypothetical UPF0222 protein MGC4549; domain of un 83.1
>2au3_A DNA primase; zinc ribbon, toprim, RNA polymerase, DNA replication, transf; HET: DNA; 2.00A {Aquifex aeolicus} Back     alignment and structure
Probab=100.00  E-value=7.3e-43  Score=351.69  Aligned_cols=262  Identities=20%  Similarity=0.262  Sum_probs=198.8

Q ss_pred             HHHHHHHhCCccccCCCCCceeeecCCCCCCCCCCCCccceEEEEEcCCccEEEeCCccCCCCcccccCCc--------c
Q 042101           74 VKQKLKLVGINCDDSCIPGRYAHLLCPKCKGGGRSLERSLSVHIIQDGDFAMWRCFRVDCGWAGRAFAGSN--------K  145 (380)
Q Consensus        74 ~~~~l~~~gi~~~~~~~~G~~~~~~CPfc~~~~~~~eks~s~~v~~d~~~g~~~Cf~~~CG~~G~v~~~~~--------e  145 (380)
                      |.+++.++ +++++   .|++|+++||||++      |+|||+|++++  |.||||+  ||.+||+++.-.        |
T Consensus        16 I~dvi~~~-v~lkk---~G~~~~~~CPfh~e------ktpSf~V~~~k--~~~~CFg--Cg~gGd~i~fv~~~~~~sf~e   81 (407)
T 2au3_A           16 IVDVISEY-LNLEK---VGSNYRTNCPFHPD------DTPSFYVSPSK--QIFKCFG--CGVGGDAIKFVSLYEDISYFE   81 (407)
T ss_dssp             HHHHHHHH-SCCEE---ETTEEEECCSSSCC------SSCCEEEETTT--TEEEETT--TCCEECHHHHHHHHHTCCHHH
T ss_pred             HHHHHHHh-ccccc---CCCeEEeeCcCCCC------CCCeEEEECCC--CEEEECC--CCCCCCHHHHHHHHhCCCHHH
Confidence            45667666 88887   89999999999985      78999998764  8999999  999999985211        1


Q ss_pred             c------------hhcc-chh-hh---hhh--c-c-CCCcccHHHHHHHHhCCCCHHHHhhcceEEecC-----------
Q 042101          146 I------------RKVM-SSR-QV---AEK--S-L-GLEPLGEKLIAYLGERMISEGTLQRNSVMQRLH-----------  193 (380)
Q Consensus       146 ~------------~~~~-~~~-~~---~~~--~-~-~~~pl~~~~~~YL~~RGIs~eti~~f~~g~~~~-----------  193 (380)
                      +            .... ..+ +.   .+.  . + .....+..+.+||.+|||+.+++++|++||.++           
T Consensus        82 Av~~La~~~gi~~~~~~~~~~~~l~~~~~~a~~~~~~~L~~~~~a~~YL~~RGi~~~~i~~f~lGyap~~~~l~~~l~~~  161 (407)
T 2au3_A           82 AALELAKRYGKKLDLEKISKDEKVYVALDRVCDFYRESLLKNREASEYVKSRGIDPKVARKFDLGYAPSSEALVKVLKEN  161 (407)
T ss_dssp             HHHHHHHHHTCCCCTTSCCHHHHHHHHHHHHHHHHHHHHHHCHHHHHHHHHTTCCHHHHHHTTCEECCCHHHHHHHHHHH
T ss_pred             HHHHHHHHhCCCCCccchhHHHHHHHHHHHHHHHHHHHHhcChHHHHHHHHcCCCHHHHHHhCCCCCCchHHHHHHHHhc
Confidence            0            0000 000 00   000  0 0 001135678999999999999999999998653           


Q ss_pred             -----------------C-------cEEEEE-ecCCCEEEEEeee-cCC---Ccccccc-----CCCCccccccccC---
Q 042101          194 -----------------D-------QAIAFP-YWHNGVLVGCKYR-SME---RKFRQEK-----GTEKWLYGLDDIN---  236 (380)
Q Consensus       194 -----------------g-------~~I~fP-~~~~G~vv~~~~R-~~~---Kkf~~~~-----~~~~~Lfgl~~i~---  236 (380)
                                       |       ++|+|| +|.+|++++|++| .++   .||.+.+     .++..|||++.+.   
T Consensus       162 ~~~~~~l~~~Gl~~~~~g~~~d~f~~ri~fPi~d~~G~vigf~gRr~l~~~~pKylnspet~~f~k~~~lygl~~a~~~i  241 (407)
T 2au3_A          162 DLLEAYLETKNLLSPTKGVYRDLFLRRVVIPIKDPRGRVIGFGGRRIVEDKSPKYINSPDSRVFKKGENLFGLYEAKEYI  241 (407)
T ss_dssp             TCHHHHHTTTCEECSSTTCCEETTTTEEEEEEECTTSCEEEEEEEECSCCSSCSEEECCCCSSCCGGGCEETHHHHHHHH
T ss_pred             CCCHHHHHHCCceEecCCCcccccCCeEEEEEECCCCCEEEEEEEEecCCCCCeeecCCCCCCCCCCccccChHHHHHHh
Confidence                             1       389999 5799999999999 774   4677643     3567899998653   


Q ss_pred             -CCCEEEEEechhHHHHHHHhCCCcEEEcCCCCCCCccCCCCCCCcccchhhhhHHHHhhcCCC-CeEEEEeCCChhhHH
Q 042101          237 -ETAEVIIVEGEIDKLSVEEAGFQNCVSVPSGAPPKVSNRELPPREKDTGYQYLWNCKEHLDKV-SRIILGTDADTPGHA  314 (380)
Q Consensus       237 -~~~~iiIvEG~~DaLSl~q~G~~~~Vs~~~Ga~~~~~~~~Lp~~~~~~~~~~l~~~~~~L~~~-~~Ivl~~DnD~AG~~  314 (380)
                       +.+.|+||||++||||++|+|+.++|+.. |+..  +                .+++.+|.+. ++|+||+|||.||++
T Consensus       242 ~~~~~viivEG~~Dvlsl~q~G~~n~VA~l-Gtal--t----------------~~~~~~L~r~~~~vil~~D~D~AG~~  302 (407)
T 2au3_A          242 KEEGFAILVEGYFDLLRLFSEGIRNVVAPL-GTAL--T----------------QNQANLLSKFTKKVYILYDGDDAGRK  302 (407)
T ss_dssp             HHHTCEEECSSHHHHHHHHHTTCCSEEEES-SSSC--C----------------HHHHHHHHTTCSEEEEECCSSHHHHH
T ss_pred             ccCCeEEEEechHhHHHHHHCCCCcEEEcC-cccC--C----------------HHHHHHHHhcCCeEEEEEcCCHHHHH
Confidence             46789999999999999999999988764 5531  1                0245566555 799999999999999


Q ss_pred             HHHHHHHHhC--CCceEEEEcCCCCCCCCCCCHHHHHHhcChHHHHHHHHhccCCCccchhh
Q 042101          315 LAEELARRLG--KDRCWRVRWPKKDEFSYFKDANEVLKCLGPGALREVIENAELYQLHVSEE  374 (380)
Q Consensus       315 aa~~la~~L~--~~~v~iv~lP~~~~~~~~KD~ND~L~~~g~~~l~~~i~~A~~~~~~~~~~  374 (380)
                      ||.++++.|.  ..+++++.+|+      +|||||+|+++|.++|+++|++|.|+..-.+..
T Consensus       303 Aa~r~~~~l~~~g~~~~v~~lP~------gkDpdd~l~~~g~~~~~~~l~~a~~~~~~~~~~  358 (407)
T 2au3_A          303 AMKSAIPLLLSAGVEVYPVYLPE------GYDPDEFIKEFGKEELRRLINSSGELFETLIKT  358 (407)
T ss_dssp             HHHHHHHHHHHTTCEEEEECCCT------TCCHHHHHHHHCHHHHHHHHHHCCCHHHHHHHH
T ss_pred             HHHHHHHHHHhCCCeEEEEECCC------CCChHHHHHhcCHHHHHHHHHcCCCHHHHHHHH
Confidence            9999988874  23678888986      499999999999999999999999876544443
>1nui_A DNA primase/helicase; zinc-biding domain, toprim fold, DNA replication, DNA-direct polymerase, primosome, late protein, ATP-binding; HET: DNA; 2.90A {Enterobacteria phage T7} SCOP: e.13.1.2 g.41.3.2 Back     alignment and structure
>4edg_A DNA primase; catalytic domain, nucleoside triphosphate, nucleoside polyph protein-ligand complex, transferase; HET: DNA ATP; 2.00A {Staphylococcus aureus} PDB: 4e2k_A* 4edk_A* 4edr_A* 4edt_A* 4edv_A* 4ee1_A* Back     alignment and structure
>1dd9_A DNA primase, DNAG; toprim, 3-helix bundle, DNA-binding protein, RNA polymerase, replication protein, transferase; HET: DNA; 1.60A {Escherichia coli} SCOP: e.13.1.1 PDB: 1dde_A* 1eqn_A* 3b39_A* Back     alignment and structure
>1q57_A DNA primase/helicase; dntpase, DNA replication, transferase; HET: DNA; 3.45A {Enterobacteria phage T7} SCOP: c.37.1.11 e.13.1.2 Back     alignment and structure
>1d0q_A DNA primase; zinc-binding motif, protein, transferase; HET: DNA; 1.71A {Geobacillus stearothermophilus} SCOP: g.41.3.2 Back     alignment and structure
>1t6t_1 Putative protein; structural genomics, PSI, protein structur initiative, midwest center for structural genomics, MCSG, U function; 1.80A {Aquifex aeolicus} SCOP: c.136.1.1 Back     alignment and structure
>2fcj_A Small toprim domain protein; structural genomics, PSI, protein structure initiative, midwest center for structural genomics, MCSG; HET: MES; 1.30A {Geobacillus stearothermophilus} SCOP: c.136.1.1 PDB: 2i5r_A* Back     alignment and structure
>1vdd_A Recombination protein RECR; helix-hairpin-helix, zinc finger, toprim, walker B ATP binding motif; 2.50A {Deinococcus radiodurans} SCOP: e.49.1.1 PDB: 2v1c_A Back     alignment and structure
>3j21_i 50S ribosomal protein L37AE; archaea, archaeal, KINK-turn, protein synthe ribosome; 6.60A {Pyrococcus furiosus} Back     alignment and structure
>4a17_Y RPL37A, 60S ribosomal protein L32; eukaryotic ribosome, ribosome, eukaryotic initiation factor 60S, translation, large ribosomal subunit; 3.52A {Tetrahymena thermophila} PDB: 4a1a_Y 4a1c_Y 4a1e_Y Back     alignment and structure
>3vdp_A Recombination protein RECR; zinc finger, DNA repair, DNA binding; 2.45A {Thermoanaerobacter tengcongensis} PDB: 3vdu_A 3ve5_D Back     alignment and structure
>3cc2_Z 50S ribosomal protein L37AE, 50S ribosomal protein L32E; genomic sequnece for R-proteins, ribonucleoprotein, ribosoma protein, RNA-binding; HET: 1MA OMU OMG UR3 PSU; 2.40A {Haloarcula marismortui} SCOP: g.41.8.1 PDB: 3cc4_Z* 3cc7_Z* 3cce_Z* 3ccj_Z* 3ccl_Z* 3ccm_Z* 3ccq_Z* 3ccr_Z* 3ccs_Z* 3ccu_Z* 3ccv_Z* 3cd6_Z* 3cma_Z* 3cme_Z* 3i55_Z* 3i56_Z* 3cpw_Y* 4adx_Z Back     alignment and structure
>1ffk_W Ribosomal protein L37AE; ribosome assembly, RNA-RNA, protein-RNA, protein-protein; 2.40A {Haloarcula marismortui} SCOP: g.41.8.1 PDB: 1jj2_Y 1k73_1* 1k8a_1* 1k9m_1* 1kc8_1* 1kd1_1* 1kqs_Y* 1m1k_1* 1m90_1* 1n8r_1* 1nji_1* 1q7y_1* 1q81_1* 1q82_1* 1q86_1* 1qvf_Y 1qvg_Y 1w2b_Y 3cxc_Y* Back     alignment and structure
>1vq8_Z 50S ribosomal protein L37AE; ribosome 50S, protein-protein complex, RNA-RNA complex, PROT complex, peptidyl transferase reaction; HET: 1MA OMU OMG UR3 PSU SPS; 2.20A {Haloarcula marismortui} SCOP: g.41.8.1 PDB: 1vq4_Z* 1vq6_Z* 1vq5_Z* 1vq7_Z* 1vq9_Z* 1vqk_Z* 1vql_Z* 1vqm_Z* 1vqn_Z* 1vqo_Z* 1vqp_Z* 1yhq_Z* 1yi2_Z* 1yij_Z* 1yit_Z* 1yj9_Z* 1yjn_Z* 1yjw_Z* 2qa4_Z* 1s72_Z* ... Back     alignment and structure
>3jyw_9 60S ribosomal protein L43; eukaryotic ribosome, RACK1 protein, flexible fitting; 8.90A {Thermomyces lanuginosus} Back     alignment and structure
>1wii_A Hypothetical UPF0222 protein MGC4549; domain of unknown function, zinc finger, metal-binding protein, structural genomics; NMR {Mus musculus} SCOP: g.41.3.4 Back     alignment and structure

Homologous Structure Domains

Structure Domains Detected by RPS-BLAST ?

Original result of RPS-BLAST against SCOP70(version1.75) database

ID ?Alignment Graph ?Length ? Definition ? E-value ?
Query 380
d1nuia1192 e.13.1.2 (A:64-255) Primase fragment of primase-he 7e-20
d2fcja1114 c.136.1.1 (A:1-114) Hypothetical protein RBSTP2199 3e-15
d1t6t1_108 c.136.1.1 (1:) Hypothetical protein aq_2086 {Aquif 1e-05
>d1nuia1 e.13.1.2 (A:64-255) Primase fragment of primase-helicase protein {Bacteriophage T7 [TaxId: 10760]} Length = 192 Back     information, alignment and structure

class: Multi-domain proteins (alpha and beta)
fold: DNA primase core
superfamily: DNA primase core
family: Primase fragment of primase-helicase protein
domain: Primase fragment of primase-helicase protein
species: Bacteriophage T7 [TaxId: 10760]

 Score = 84.2 bits (207), Expect = 7e-20
 Identities = 45/197 (22%), Positives = 67/197 (34%), Gaps = 23/197 (11%)

Query: 169 LIAYLGERMISEGTLQRNSVMQRLHDQ---AIAFPYWHNGVLVGCKYRSMERK-FRQEKG 224
             + L  R IS+ T Q+        D     +A     NG +V  K R  ++        
Sbjct: 14  RYSALTARGISKETCQKAGYWIAKVDGVMYQVADYRDQNGNIVSQKVRDKDKNFKTTGSH 73

Query: 225 TEKWLYGLDDINETAEVIIVEGEIDKLSVEEAGFQNCVSVPSGAPPKVSNRELPPREKDT 284
               L+G    N   ++++ EGEID L+V E        V  G     +           
Sbjct: 74  KSDALFGKHLWNGGKKIVVTEGEIDMLTVMELQDCKYPVVSLGHGASAA----------- 122

Query: 285 GYQYLWNCKEHLDKVSRIILGTDADTPGHALAEELARRLGKDRCWRVRWPKKDEFSYFKD 344
             +      E+ D+  +IIL  D D  G    EE A+ L   +      P        KD
Sbjct: 123 -KKTCAANYEYFDQFEQIILMFDMDEAGRKAVEEAAQVLPAGKVRVAVLP-------CKD 174

Query: 345 ANEVLKCLGPGALREVI 361
           ANE         + E +
Sbjct: 175 ANECHLNGHDREIMEQV 191
>d2fcja1 c.136.1.1 (A:1-114) Hypothetical protein RBSTP2199 {Bacillus stearothermophilus [TaxId: 1422]} Length = 114 Back     information, alignment and structure
>d1t6t1_ c.136.1.1 (1:) Hypothetical protein aq_2086 {Aquifex aeolicus [TaxId: 63363]} Length = 108 Back     information, alignment and structure

Homologous Domains Detected by HHsearch ?

Original result of HHsearch against SCOP70(version1.75) database

ID ?Alignment Graph ?Length ? Definition ? Probability ?
Query380
d1dd9a_314 DNA primase DnaG catalytic core {Escherichia coli 99.97
d1nuia1192 Primase fragment of primase-helicase protein {Bact 99.97
d2fcja1114 Hypothetical protein RBSTP2199 {Bacillus stearothe 99.57
d1t6t1_108 Hypothetical protein aq_2086 {Aquifex aeolicus [Ta 99.54
d1d0qa_102 Zinc-binding domain of DNA primase {Bacillus stear 99.19
d1nuia254 Zinc-binding domain of primase-helicase {Bacteriop 96.42
d1vdda_199 Recombination protein RecR {Deinococcus radioduran 93.49
d1vqoz173 Ribosomal protein L37ae {Archaeon Haloarcula maris 88.16
d1jj2y_73 Ribosomal protein L37ae {Archaeon Haloarcula maris 87.56
d1wiia_85 Hypothetical UPF0222 protein MGC4549 {Mouse (Mus m 81.63
>d1dd9a_ e.13.1.1 (A:) DNA primase DnaG catalytic core {Escherichia coli [TaxId: 562]} Back     information, alignment and structure
class: Multi-domain proteins (alpha and beta)
fold: DNA primase core
superfamily: DNA primase core
family: DNA primase DnaG catalytic core
domain: DNA primase DnaG catalytic core
species: Escherichia coli [TaxId: 562]

Probab=99.97  E-value=5.7e-31  Score=253.99  Aligned_cols=188  Identities=19%  Similarity=0.274  Sum_probs=151.8

Q ss_pred             CcccHHHHHHHHhCCCCHHHHhhcceEEecC------------------------------C-------cEEEEE-ecCC
Q 042101          163 EPLGEKLIAYLGERMISEGTLQRNSVMQRLH------------------------------D-------QAIAFP-YWHN  204 (380)
Q Consensus       163 ~pl~~~~~~YL~~RGIs~eti~~f~~g~~~~------------------------------g-------~~I~fP-~~~~  204 (380)
                      ++.++.+++||++|||++++|++|++||++.                              |       +||+|| ++..
T Consensus        19 ~~~~~~a~~YL~~Rgl~~~~i~~f~lGyap~~~~~l~~~l~~~~~~~~~l~~~gl~~~~~~g~~~d~F~~ri~fPI~d~~   98 (314)
T d1dd9a_          19 QPVATSARQYLEKRGLSHEVIARFAIGFAPPGWDNVLKRFGGNPENRQSLIDAGMLVTNDQGRSYDRFRERVMFPIRDKR   98 (314)
T ss_dssp             SGGGHHHHHHHHHTTCCHHHHHHHTCEEECSSSCHHHHHHCSSHHHHHHHHHTTSEEEC---CEEESCCSEEEEEEECTT
T ss_pred             CCchHHHHHHHHHCCCCHHHHHHcccccCcccHHHHHHHHhhCCCchhhhhhhhheeeccccccchhccceeEEEEeccc
Confidence            4567789999999999999999999999741                              1       299999 5899


Q ss_pred             CEEEEEeeecCC---Ccccccc-----CCCCcccccccc----CCCCEEEEEechhHHHHHHHhCCCcEEEcCCCCCCCc
Q 042101          205 GVLVGCKYRSME---RKFRQEK-----GTEKWLYGLDDI----NETAEVIIVEGEIDKLSVEEAGFQNCVSVPSGAPPKV  272 (380)
Q Consensus       205 G~vv~~~~R~~~---Kkf~~~~-----~~~~~Lfgl~~i----~~~~~iiIvEG~~DaLSl~q~G~~~~Vs~~~Ga~~~~  272 (380)
                      |++|+|.+|.+.   +||.+.+     .++..|||++.+    .+.+++|||||++|||+++|+|+.|||+. .|++.+.
T Consensus        99 g~~i~f~gR~~~~~~~KY~ns~et~~f~k~~~ly~~~~a~~~~~~~~~~iivEG~~Dvi~l~q~Gi~n~Va~-~Gta~t~  177 (314)
T d1dd9a_          99 GRVIGFGGRVLGNDTPKYLNSPETDIFHKGRQLYGLYEAQQDNAEPNRLLVVEGYMDVVALAQYGINYAVAS-LGTSTTA  177 (314)
T ss_dssp             SCEEEEEEEESSSCSCSEEECCCCSSCCTTTCCBTHHHHHHTCSSCSCEEEESSHHHHHHHHHTTCCCEEEC-CC-CCCH
T ss_pred             ceEEEEeeeecccccccccCCCccccccchhhcccHHHHHhhhccccceEEEechHHHHHHHHcccccchhH-Hhhhhhh
Confidence            999999999984   4676654     478899999854    45788999999999999999999999985 5664321


Q ss_pred             cCCCCCCCcccchhhhhHHHHhhcCC-CCeEEEEeCCChhhHHHHHHHHHHhC-----CCceEEEEcCCCCCCCCCCCHH
Q 042101          273 SNRELPPREKDTGYQYLWNCKEHLDK-VSRIILGTDADTPGHALAEELARRLG-----KDRCWRVRWPKKDEFSYFKDAN  346 (380)
Q Consensus       273 ~~~~Lp~~~~~~~~~~l~~~~~~L~~-~~~Ivl~~DnD~AG~~aa~~la~~L~-----~~~v~iv~lP~~~~~~~~KD~N  346 (380)
                                        .|+..|.+ .++|++|||+|.||++|+.++.+.+-     ...++++.+|++      +||+
T Consensus       178 ------------------~~~~~l~~~~~~i~l~~D~D~AG~~A~~r~~~~~~~~~~~g~~v~v~~lp~g------~DPD  233 (314)
T d1dd9a_         178 ------------------DHIQLLFRATNNVICCYDGDRAGRDAAWRALETALPYMTDGRQLRFMFLPDG------EDPD  233 (314)
T ss_dssp             ------------------HHHHHHHHHCSEEEEEEESSHHHHHHHHHHHHHHGGGCCTTCEEEEEEECTT------CCHH
T ss_pred             ------------------HHHHHHHhcCCceEEEeecCcchhhHHHhHHHHhhHHhcCCCeEEEEeccCc------CCHH
Confidence                              23444433 47999999999999999998776641     236889999974      9999


Q ss_pred             HHHHhcChHHHHHHHHhccCCCccchhhh
Q 042101          347 EVLKCLGPGALREVIENAELYQLHVSEEA  375 (380)
Q Consensus       347 D~L~~~g~~~l~~~i~~A~~~~~~~~~~~  375 (380)
                      |+++++|.++|+++|++|.++.--.++..
T Consensus       234 e~l~k~G~e~~~~ll~~a~~~~eFli~~~  262 (314)
T d1dd9a_         234 TLVRKEGKEAFEARMEQAMPLSAFLFNSL  262 (314)
T ss_dssp             HHHHHHHHHHHHHHHTTCEEHHHHHHHHH
T ss_pred             HHHHhcCHHHHHHHHhcCCCHHHHHHHHH
Confidence            99999999999999999988765544443
>d1nuia1 e.13.1.2 (A:64-255) Primase fragment of primase-helicase protein {Bacteriophage T7 [TaxId: 10760]} Back     information, alignment and structure
>d2fcja1 c.136.1.1 (A:1-114) Hypothetical protein RBSTP2199 {Bacillus stearothermophilus [TaxId: 1422]} Back     information, alignment and structure
>d1t6t1_ c.136.1.1 (1:) Hypothetical protein aq_2086 {Aquifex aeolicus [TaxId: 63363]} Back     information, alignment and structure
>d1d0qa_ g.41.3.2 (A:) Zinc-binding domain of DNA primase {Bacillus stearothermophilus [TaxId: 1422]} Back     information, alignment and structure
>d1nuia2 g.41.3.2 (A:10-63) Zinc-binding domain of primase-helicase {Bacteriophage T7 [TaxId: 10760]} Back     information, alignment and structure
>d1vdda_ e.49.1.1 (A:) Recombination protein RecR {Deinococcus radiodurans [TaxId: 1299]} Back     information, alignment and structure
>d1vqoz1 g.41.8.1 (Z:10-82) Ribosomal protein L37ae {Archaeon Haloarcula marismortui [TaxId: 2238]} Back     information, alignment and structure
>d1jj2y_ g.41.8.1 (Y:) Ribosomal protein L37ae {Archaeon Haloarcula marismortui [TaxId: 2238]} Back     information, alignment and structure
>d1wiia_ g.41.3.4 (A:) Hypothetical UPF0222 protein MGC4549 {Mouse (Mus musculus) [TaxId: 10090]} Back     information, alignment and structure