Citrus Sinensis ID: 013616

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-------390-------400-------410-------420-------430-------44

MLIDGPKQGNVIPDGFNPNYLKVYYGRLFPHADIFKWMSYGNDGRHPACDKSYFGRREFSFTLDNDIYLRFQSFNSESELENSIKEKCPSKIDIGPVYSVDPAKRHAYAQGGDNVFAPVERELIFDIDITDYDDVRYCCSGADVCLECWPLMTVAIKVIDTALRDDFGFDHILWVYSGRRGVHCWVCDGKARRLTNEQRGAIADYFRVYKGNENSNKKVSFPGPLHPFLVRSYTEVLREFFEEKLLLSQNLFSTEERYEKILSMIPDESVTSELRGKWQENRRSSNSKEDINFFRWEQLKNTLQSGKQKVQGLRRCVEEIVFAFTYPRLDMEVSKHRNHLLKAPFCVHPKTGRVCIPIDPKDCEEFDPTTVPTLSELLRELNTGDSRMDVDNEWEKTSLGKSIRFFRSSFLQPLLKSCKEEMESGYKAKIQQTKNSLSW

cccccccccccccccccHHHHHHHHHHHccHHHHHHHHccccccccccccccccccccEEEEEcccEEEEEcccccHHHHHHHHHHHccccEEEccccccccHHHHHHcccccccccccccHHHHccccccccccccccccHHHHHHHHHHHHHHHHHHHHHHHccccccEEEEEEEccccEEEEEEcHHHccccHHHHHHHHHHHHcccccccccccccccccccccccHHHHHHHHHHHHHHHHHcccccccHHHHHHHHcccccHHHHHHHHHHHHHHccccccccHHHHHHHHHHHHHHHHcHHHHHHHHHHHHHHHHHHHcccccccccccccccccccccccccccEEEEEccccccccccccccccHHHHHHHHcccccccccccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccccccc

cccccccccccccccccHHHHHHHHHHHccHHHHHHHHccccccccccccccHcccEEEEEEEcccEEEEEcccccHHHHHHHHHHHcccEEEEEEEEcccHHHHHccccccccccccHEEEEEEEEcccccccHHHccccccHHHHHHHHHHHHHHHHHHHHHHHccccEEEEEEcccccEEEEEccHHHHcccHHHHHHHHHHHHHHcccccccEEEEccccccHHHHHHHHHHHHHHHHHHHHHHccccccHHHHHHHHHHcccHHHHHHHHHHHHHcccccccHHccHHHHHHHHHHHHccccHHHHHHHHHHHHHHHHHHcccccHHHcHccccccccccEEcccccEEEEEccHHHHHcccccccccHHHHHHHHHHccccccccccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccccccc

mlidgpkqgnvipdgfnpnylkvyygrlfphadifkwmsygndgrhpacdksyfgrrefsftldndIYLRFQSFNSESELENsikekcpskidigpvysvdpakrhayaqggdnvfapverelifdiditdyddvryccsgadvclecwPLMTVAIKVIDTAlrddfgfdhILWVysgrrgvhcwvcdgkarrltneqRGAIADYFRVYkgnensnkkvsfpgplhpflVRSYTEVLREFFEEKLLLSQNLFSTEERYEKILsmipdesvtsELRGKWqenrrssnskediNFFRWEQLKNTLQSGKQKVQGLRRCVEEIVFAftyprldmEVSKHRnhllkapfcvhpktgrvcipidpkdceefdpttvPTLSELLRELntgdsrmdvdnewektslgksiRFFRSSFLQPLLKSCKEEMESGYKAKIQQTKNSLSW

mlidgpkqgnvipdgfnpNYLKVYYGRLFPHADIFKWMSYGNDGRHPACDKSYFGRREFSFTLDNDIYLRFQSFNSESELENsikekcpskidIGPVYSVDPAKRHAYAQGGDNVFAPVERELIFDIDITDYDDVRYCCSGADVCLECWPLMTVAIKVIDTALRDDFGFDHILWVYSGRRGVHCWVCDGKarrltneqrgaIADYFRVYKGNensnkkvsfpgplhPFLVRSYTEVLREFFEEKLLLSQNLFSTEERYEKIlsmipdesvtselrgkwqenrrssnskedinFFRWEQLKNTLQSGKQKVQGLRRCVEEIVFAFTYPRLDMEVSKHRNHLLkapfcvhpktgrVCIPIDPKDCEEFDPTTVPTLSELLRelntgdsrmdvdnewektslgksirffRSSFLQPLLKSCKEEmesgykakiqqtknslsw

**********VIPDGFNPNYLKVYYGRLFPHADIFKWMSYGNDGRHPACDKSYFGRREFSFTLDNDIYLRFQSFN**************SKIDIGPVYSVDPAKRHAYAQGGDNVFAPVERELIFDIDITDYDDVRYCCSGADVCLECWPLMTVAIKVIDTALRDDFGFDHILWVYSGRRGVHCWVCDGKARRLTNEQRGAIADYFRVYKGNENSNKKVSFPGPLHPFLVRSYTEVLREFFEEKLLLSQNLFSTEERYEKILSM**************************INFFRWEQLKNTLQSGKQKVQGLRRCVEEIVFAFTYPRLDMEVSKHRNHLLKAPFCVHPKTGRVCIPIDPKDCEEFDPTTVPTLSELL***************W**TSLGKSIRFFRSSFLQPLL************************

*******************YLKVYYGRLFPHADIFKWMSYGNDGRHPACDKSYFGRREFSFTLDNDIYLRFQSFNSESELENSIKEKCPSKIDIGPVYSVDPAK**********VFAPVERELIFDIDITDYDDVRYCCSGADVCLECWPLMTVAIKVIDTALRDDFGFDHILWVYSGRRGVHCWVCDGKARRLTNEQRGAIADYFRVYK**************LHPFLVRSYTEVLREFFEEKLLLSQNLFSTEERYEKILSMIPDESVT**********************FRWEQLKNTLQSGKQKVQGLRRCVEEIVFAFTYPRLDMEVSKHRNHLLKAPFCVHPKTGRVCIPIDPKDCEEFDPTTVPTLSELLRELNT**********WEKTSLGKSIRFFRSSFLQPL*************************

MLIDGPKQGNVIPDGFNPNYLKVYYGRLFPHADIFKWMSYGNDGRHPACDKSYFGRREFSFTLDNDIYLRFQSFNS********KEKCPSKIDIGPVYSVDPAKRHAYAQGGDNVFAPVERELIFDIDITDYDDVRYCCSGADVCLECWPLMTVAIKVIDTALRDDFGFDHILWVYSGRRGVHCWVCDGKARRLTNEQRGAIADYFRVYKGNENSNKKVSFPGPLHPFLVRSYTEVLREFFEEKLLLSQNLFSTEERYEKILSMIPDESVT****************KEDINFFRWEQLKN**********GLRRCVEEIVFAFTYPRLDMEVSKHRNHLLKAPFCVHPKTGRVCIPIDPKDCEEFDPTTVPTLSELLRELNTGDSRMDVDNEWEKTSLGKSIRFFRSSFLQPLLKSCKE*******************

*************DGFNPNYLKVYYGRLFPHADIFKWMSYGNDGRHPACDKSYFGRREFSFTLDNDIYLRFQSFNSESELENSIKEKCPSKIDIGPVYSVDPAKRHAYAQGGDNVFAPVERELIFDIDITDYDDVRYCCSGADVCLECWPLMTVAIKVIDTALRDDFGFDHILWVYSGRRGVHCWVCDGKARRLTNEQRGAIADYFRVYKGNENSNKKVSFPGPLHPFLVRSYTEVLREFFEEKLLLSQNLFSTEERYEKILSMIPDESVTSELRGKWQENRRSSNSKEDINFFRWEQLKNTLQSGKQKVQGLRRCVEEIVFAFTYPRLDMEVSKHRNHLLKAPFCVHPKTGRVCIPIDPKDCEEFDPTTVPTLSELLRELNTGDSRMDVDNEWEKTSLGKSIRFFRSSFLQPLLKSCKEEMESGYK************

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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

ID	Alignment graph	Length	Definition	RBH(Q2H)	RBH(H2Q)	Q cover	H cover	Identity	E-value
Query		439	2.2.26 [Sep-21-2011]
P20664		417	DNA primase small subunit	yes	no	0.870	0.916	0.441	3e-96
P49642		420	DNA primase small subunit	yes	no	0.876	0.916	0.437	5e-96
Q24317		438	DNA primase small subunit	yes	no	0.911	0.913	0.405	1e-88
O14215		454	DNA primase small subunit	yes	no	0.810	0.784	0.417	5e-81
Q25998		452	DNA primase small subunit	N/A	no	0.913	0.887	0.400	1e-77
Q7KQM1		452	DNA primase small subunit	yes	no	0.913	0.887	0.400	1e-77
P10363		409	DNA primase small subunit	yes	no	0.888	0.953	0.372	7e-70
P34471		410	DNA primase small subunit	yes	no	0.760	0.814	0.364	3e-61
B9LPT9		387	Probable DNA primase smal	yes	no	0.560	0.635	0.251	4e-08
Q6L0W5		370	Probable DNA primase smal	yes	no	0.651	0.772	0.223	6e-08

>sp\|P20664\|PRI1_MOUSE DNA primase small subunit OS=Mus musculus GN=Prim1 PE=1 SV=1	Back alignment and function desciption

 Score =  352 bits (904), Expect = 3e-96,   Method: Compositional matrix adjust.
 Identities = 186/421 (44%), Positives = 263/421 (62%), Gaps = 39/421 (9%)

Query: 18  PNYLKVYYGRLFPHADIFKWMSYGNDGRHPACDKSYFGRREFSFTLDNDIYLRFQSFNSE 77
           P  LK+YY RLFP+A  ++W++YG         K+YF  REFSFTL +DIY+R+QSFN++
Sbjct: 10  PELLKLYYRRLFPYAQYYRWLNYG------GVTKNYFQHREFSFTLKDDIYIRYQSFNNQ 63

Query: 78  SELENSIKEKCPSKIDIGPVYSVDPAKRHAYAQGGDNVFAPVERELIFDIDITDYDDVRY 137
           SELE  +++  P KIDIG VYS  P + +    G    F   E+EL+FDID+TDYDDVR 
Sbjct: 64  SELEKEMQKMNPYKIDIGAVYSHRPNQHNTVKLGA---FQAQEKELVFDIDMTDYDDVRR 120

Query: 138 CCSGADVCLECWPLMTVAIKVIDTALRDDFGFDHILWVYSGRRGVHCWVCDGKARRLTNE 197
           CCS AD+C +CW LMT+A+++ID AL++DFGF H LWVYSGRRGVHCWVCD   R+L++ 
Sbjct: 121 CCSSADICSKCWTLMTMAMRIIDRALKEDFGFKHRLWVYSGRRGVHCWVCDESVRKLSSA 180

Query: 198 QRGAIADYFRVYKGNENSNKKVSFPGPLHPFLVRSYTEVLREFFEEKLLLSQNLFSTEER 257
            R  I +Y  + KG ++  KKV     +HPF VR    +++++FEE  L+ Q++   +E 
Sbjct: 181 VRSGIVEYLSLVKGGQDVKKKVHLNEKVHPF-VRKSINIIKKYFEEYALVGQDILENKEN 239

Query: 258 YEKILSMIPDESVTSELRGKWQENRRSSNSKEDINFFRWEQLKNTLQSGKQKVQGLRRCV 317
           ++KIL+++P E++  EL+  +Q+   S          RWE L+    S +       +C 
Sbjct: 240 WDKILALVP-ETIHDELQRGFQKFHSSPQ--------RWEHLRKVANSSQNMKND--KCG 288

Query: 318 E----EIVFAFTYPRLDMEVSKHRNHLLKAPFCVHPKTGRVCIPIDPKDCEEFDPTTVPT 373
                E++  + +PRLD+ VSK  NHLLK+PF VHPKTGR+ +PID    ++FDP TVPT
Sbjct: 289 PWLEWEVMLQYCFPRLDVNVSKGVNHLLKSPFSVHPKTGRISVPIDFHKVDQFDPFTVPT 348

Query: 374 LSELLREL------------NTGDSRMDVDNEWEKTSLGKSIRFFRSSFLQPLLKSCKEE 421
           +S + REL            N  DS+  V   ++KTSL   ++ F   FL+ L KS K E
Sbjct: 349 ISAICRELDMVSTHEKEKEENEADSKHRVRG-YKKTSLAPYVKVF-EQFLENLDKSRKGE 406

Query: 422 M 422
           +
Sbjct: 407 L 407

DNA primase is the polymerase that synthesizes small RNA primers for the Okazaki fragments made during discontinuous DNA replication.
Mus musculus (taxid: 10090)
EC: 2EC: .EC: 7EC: .EC: 7EC: .EC: -

>sp\|P49642\|PRI1_HUMAN DNA primase small subunit OS=Homo sapiens GN=PRIM1 PE=1 SV=1	Back alignment and function description

>sp\|Q24317\|PRI1_DROME DNA primase small subunit OS=Drosophila melanogaster GN=DNApol-alpha50 PE=2 SV=2	Back alignment and function description

>sp\|O14215\|PRI1_SCHPO DNA primase small subunit OS=Schizosaccharomyces pombe (strain 972 / ATCC 24843) GN=pri1 PE=1 SV=1	Back alignment and function description

>sp\|Q25998\|PRI1_PLAFK DNA primase small subunit OS=Plasmodium falciparum (isolate K1 / Thailand) PE=3 SV=1	Back alignment and function description

>sp\|Q7KQM1\|PRI1_PLAF7 DNA primase small subunit OS=Plasmodium falciparum (isolate 3D7) GN=PF14_0366 PE=3 SV=1	Back alignment and function description

>sp\|P10363\|PRI1_YEAST DNA primase small subunit OS=Saccharomyces cerevisiae (strain ATCC 204508 / S288c) GN=PRI1 PE=1 SV=2	Back alignment and function description

>sp\|P34471\|PRI1_CAEEL DNA primase small subunit OS=Caenorhabditis elegans GN=pri-1 PE=3 SV=1	Back alignment and function description

>sp\|B9LPT9\|PRIS_HALLT Probable DNA primase small subunit OS=Halorubrum lacusprofundi (strain ATCC 49239 / DSM 5036 / JCM 8891 / ACAM 34) GN=priA PE=3 SV=1	Back alignment and function description

>sp\|Q6L0W5\|PRIS_PICTO Probable DNA primase small subunit OS=Picrophilus torridus (strain ATCC 700027 / DSM 9790 / JCM 10055 / NBRC 100828) GN=priA PE=3 SV=1	Back alignment and function description

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
Query		439
297742324		447	unnamed protein product [Vitis vinifera]	0.979	0.961	0.844	0.0
359473913		457	PREDICTED: DNA primase small subunit-lik	0.979	0.940	0.844	0.0
449447727		450	PREDICTED: DNA primase small subunit-lik	0.990	0.966	0.769	0.0
255549615		515	DNA primase, putative [Ricinus communis]	0.947	0.807	0.8	0.0
356501475		434	PREDICTED: DNA primase small subunit-lik	0.970	0.981	0.785	0.0
357142240		450	PREDICTED: DNA primase small subunit-lik	1.0	0.975	0.731	0.0
356553659		435	PREDICTED: LOW QUALITY PROTEIN: DNA prim	0.970	0.979	0.781	0.0
226492225		453	uncharacterized protein LOC100276095 [Ze	0.993	0.962	0.740	0.0
357460529		433	DNA primase small subunit [Medicago trun	0.965	0.979	0.76	0.0
388517081		433	unknown [Medicago truncatula]	0.965	0.979	0.752	0.0

>gi\|297742324\|emb\|CBI34473.3\| unnamed protein product [Vitis vinifera]	Back alignment and taxonomy information

 Score =  778 bits (2008), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 364/431 (84%), Positives = 394/431 (91%), Gaps = 1/431 (0%)

Query: 10  NVIPDGFNPNYLKVYYGRLFPHADIFKWMSYGNDGRHPACDKSYFGRREFSFTLDNDIYL 69
           N +PDGFN NYLKVYYG+LFPH+D+FKWMSYGNDG+HPACD+SY GRREFSFTL +DIYL
Sbjct: 17  NAVPDGFNANYLKVYYGKLFPHSDLFKWMSYGNDGKHPACDQSYIGRREFSFTLADDIYL 76

Query: 70  RFQSFNSESELENSIKEKCPSKIDIGPVYSVDPAKRHAYAQGGDNVFAPVERELIFDIDI 129
           RFQSFNS  E+ENSIKEKCP KIDIGPVYSVDP KRHAYAQ GDNVF PVEREL+FDIDI
Sbjct: 77  RFQSFNSVHEMENSIKEKCPFKIDIGPVYSVDPTKRHAYAQSGDNVFTPVERELVFDIDI 136

Query: 130 TDYDDVRYCCSGADVCLECWPLMTVAIKVIDTALRDDFGFDHILWVYSGRRGVHCWVCDG 189
           TDYDDVRYCCSGADVCL+CWPLMTVAIKVIDTALRDDFGF+HILWVYSGRRGVHCWVCDG
Sbjct: 137 TDYDDVRYCCSGADVCLDCWPLMTVAIKVIDTALRDDFGFNHILWVYSGRRGVHCWVCDG 196

Query: 190 KARRLTNEQRGAIADYFRVYKGNENSNKKVSFPGP-LHPFLVRSYTEVLREFFEEKLLLS 248
           +ARRL+NEQR AIADYFRVYKGNENS KKVS  GP LHPFL RSYTEVL++FFEEKLL  
Sbjct: 197 RARRLSNEQRAAIADYFRVYKGNENSQKKVSLVGPALHPFLARSYTEVLKDFFEEKLLPG 256

Query: 249 QNLFSTEERYEKILSMIPDESVTSELRGKWQENRRSSNSKEDINFFRWEQLKNTLQSGKQ 308
           Q LFSTEERYEKIL +IPDES+TSELRGKWQENRRSS SKEDIN  RWEQLK+ LQSGKQ
Sbjct: 257 QKLFSTEERYEKILKIIPDESITSELRGKWQENRRSSISKEDINAIRWEQLKHMLQSGKQ 316

Query: 309 KVQGLRRCVEEIVFAFTYPRLDMEVSKHRNHLLKAPFCVHPKTGRVCIPIDPKDCEEFDP 368
           K QGLRRCVEEIVF++TYPRLDMEVSKH NHLLKAPFCVHPKTGRVC+PIDPK CEEFDP
Sbjct: 317 KAQGLRRCVEEIVFSYTYPRLDMEVSKHMNHLLKAPFCVHPKTGRVCVPIDPKSCEEFDP 376

Query: 369 TTVPTLSELLRELNTGDSRMDVDNEWEKTSLGKSIRFFRSSFLQPLLKSCKEEMESGYKA 428
           T+VPTLS+LL ELN G  R D D+EWE+TSLGKS++FFR SFLQPLLKSCKEE+ES Y A
Sbjct: 377 TSVPTLSKLLEELNMGGFRADADDEWERTSLGKSVKFFRLSFLQPLLKSCKEEIESAYNA 436

Query: 429 KIQQTKNSLSW 439
           K+Q +KNSLSW
Sbjct: 437 KLQLSKNSLSW 447

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Class:

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi\|359473913\|ref\|XP_002270595.2\| PREDICTED: DNA primase small subunit-like [Vitis vinifera]	Back alignment and taxonomy information

>gi\|449447727\|ref\|XP_004141619.1\| PREDICTED: DNA primase small subunit-like [Cucumis sativus] gi\|449517297\|ref\|XP_004165682.1\| PREDICTED: DNA primase small subunit-like [Cucumis sativus]	Back alignment and taxonomy information

>gi\|255549615\|ref\|XP_002515859.1\| DNA primase, putative [Ricinus communis] gi\|223545014\|gb\|EEF46528.1\| DNA primase, putative [Ricinus communis]	Back alignment and taxonomy information

>gi\|356501475\|ref\|XP_003519550.1\| PREDICTED: DNA primase small subunit-like [Glycine max]	Back alignment and taxonomy information

>gi\|357142240\|ref\|XP_003572504.1\| PREDICTED: DNA primase small subunit-like [Brachypodium distachyon]	Back alignment and taxonomy information

>gi\|356553659\|ref\|XP_003545171.1\| PREDICTED: LOW QUALITY PROTEIN: DNA primase small subunit-like [Glycine max]	Back alignment and taxonomy information

>gi\|226492225\|ref\|NP_001143441.1\| uncharacterized protein LOC100276095 [Zea mays] gi\|195620552\|gb\|ACG32106.1\| hypothetical protein [Zea mays]	Back alignment and taxonomy information

>gi\|357460529\|ref\|XP_003600546.1\| DNA primase small subunit [Medicago truncatula] gi\|355489594\|gb\|AES70797.1\| DNA primase small subunit [Medicago truncatula]	Back alignment and taxonomy information

>gi\|388517081\|gb\|AFK46602.1\| unknown [Medicago truncatula]	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
Query		439
UNIPROTKB\|G8JKZ3		418	PRIM1 "DNA primase" [Bos tauru	0.890	0.935	0.444	6.3e-92
UNIPROTKB\|P49642		420	PRIM1 "DNA primase small subun	0.876	0.916	0.439	1.9e-90
ASPGD\|ASPL0000041026		521	AN3033 [Emericella nidulans (t	0.792	0.667	0.460	2.1e-90
ZFIN\|ZDB-GENE-990603-6		425	prim1 "primase polypeptide 1"	0.876	0.905	0.441	4e-90
MGI\|MGI:97757		417	Prim1 "DNA primase, p49 subuni	0.874	0.920	0.446	5.1e-90
UNIPROTKB\|I3LGL1		385	LOC100622817 "DNA primase" [Su	0.785	0.896	0.476	1.2e-88
UNIPROTKB\|F1LQA1		417	Prim1 "DNA primase" [Rattus no	0.888	0.935	0.418	5.4e-86
FB\|FBgn0011762		438	DNApol-alpha50 "DNA polymerase	0.913	0.915	0.411	9.1e-84
POMBASE\|SPAC6B12.10c		454	spp1 "DNA primase catalytic su	0.810	0.784	0.417	1.8e-80
UNIPROTKB\|F8VNY2		328	PRIM1 "DNA primase" [Homo sapi	0.717	0.960	0.461	1.1e-78

UNIPROTKB\|G8JKZ3 PRIM1 "DNA primase" [Bos taurus (taxid:9913)]	Back alignment and assigned GO terms

 Score = 916 (327.5 bits), Expect = 6.3e-92, P = 6.3e-92
 Identities = 185/416 (44%), Positives = 272/416 (65%)

Query:    18 PNYLKVYYGRLFPHADIFKWMSYGNDGRHPACDKSYFGRREFSFTLDNDIYLRFQSFNSE 77
             P  LK+YY RLFP+   ++W++YG         K+YF  REFSFTL +DIY+R+QSFN++
Sbjct:    10 PELLKLYYRRLFPYGQYYRWLNYGG------VVKNYFQHREFSFTLKDDIYIRYQSFNNQ 63

Query:    78 SELENSIKEKCPSKIDIGPVYSVDPAKRHAYAQGGDNVFAPVERELIFDIDITDYDDVRY 137
             S+LE  +++  P KIDIG VYS  P + +    G    F   E+EL+FDID+TDYDDVR 
Sbjct:    64 SDLEKEMQKMNPYKIDIGAVYSHRPNQHNTVKLGA---FQAQEKELVFDIDMTDYDDVRR 120

Query:   138 CCSGADVCLECWPLMTVAIKVIDTALRDDFGFDHILWVYSGRRGVHCWVCDGKARRLTNE 197
             CCS AD+C +CW LMT+AI +ID AL++DFGF H LWVYSGRRGVHCWVCD   R+L++ 
Sbjct:   121 CCSSADICSKCWTLMTMAIHIIDRALKEDFGFKHRLWVYSGRRGVHCWVCDESVRKLSSA 180

Query:   198 QRGAIADYFRVYKGNENSNKKVSFPGPLHPFLVRSYTEVLREFFEEKLLLSQNLFSTEER 257
              R  I +Y  + KG ++  KKV     +HPF VR    +++++FE+  L+ Q++   ++ 
Sbjct:   181 VRSGIVEYLSLVKGGQDVKKKVHLSEKIHPF-VRKSINIIKKYFEQYALVDQDILENKQS 239

Query:   258 YEKILSMIPDESVTSELRGKWQENRRSSNSKEDINFFRWEQLKNTLQSGKQKVQGLRRC- 316
             ++KIL+++P E+V  EL+  +Q   R SNS +     RWE LKNT+    QK     +C 
Sbjct:   240 WDKILALVP-ETVRDELQQGFQ---RQSNSPQ-----RWETLKNTINK-YQKNNKNDKCG 289

Query:   317 --VE-EIVFAFTYPRLDMEVSKHRNHLLKAPFCVHPKTGRVCIPIDPKDCEEFDPTTVPT 373
               +E EI+  + +PRLD+ VSK  NHLLK+PF VHPKTGR+ +PID +  ++FDP TVPT
Sbjct:   290 LWLEWEIMLQYCFPRLDINVSKGINHLLKSPFSVHPKTGRISVPIDLQKVDQFDPFTVPT 349

Query:   374 LSELLRELNTGDSRMDVDNEWEKTSLGKSIRFFRSSFLQPLLKSCKEEMESGYKAK 429
             +S +  EL+   ++ + +N  E  +  ++  + R+S L P +K  ++ +E+  K++
Sbjct:   350 ISSICHELDVISTKEEKENGTESDTKHRTRDYKRTS-LAPFVKVFEQFLENLDKSR 404

GO:0030894 "replisome" evidence=IEA

GO:0003896 "DNA primase activity" evidence=IEA

UNIPROTKB\|P49642 PRIM1 "DNA primase small subunit" [Homo sapiens (taxid:9606)]	Back alignment and assigned GO terms

ASPGD\|ASPL0000041026 AN3033 [Emericella nidulans (taxid:162425)]	Back alignment and assigned GO terms

ZFIN\|ZDB-GENE-990603-6 prim1 "primase polypeptide 1" [Danio rerio (taxid:7955)]	Back alignment and assigned GO terms

MGI\|MGI:97757 Prim1 "DNA primase, p49 subunit" [Mus musculus (taxid:10090)]	Back alignment and assigned GO terms

UNIPROTKB\|I3LGL1 LOC100622817 "DNA primase" [Sus scrofa (taxid:9823)]	Back alignment and assigned GO terms

UNIPROTKB\|F1LQA1 Prim1 "DNA primase" [Rattus norvegicus (taxid:10116)]	Back alignment and assigned GO terms

FB\|FBgn0011762 DNApol-alpha50 "DNA polymerase alpha 50kD" [Drosophila melanogaster (taxid:7227)]	Back alignment and assigned GO terms

POMBASE\|SPAC6B12.10c spp1 "DNA primase catalytic subunit Spp1" [Schizosaccharomyces pombe (taxid:4896)]	Back alignment and assigned GO terms

UNIPROTKB\|F8VNY2 PRIM1 "DNA primase" [Homo sapiens (taxid:9606)]	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

ID	Name	Annotated EC number	Identity	Query coverage	Hit coverage	RBH(Q2H)	RBH(H2Q)
Q24317	PRI1_DROME	2, ., 7, ., 7, ., -	0.4059	0.9111	0.9132	yes	no
P10363	PRI1_YEAST	2, ., 7, ., 7, ., -	0.3720	0.8883	0.9535	yes	no
P49642	PRI1_HUMAN	2, ., 7, ., 7, ., -	0.4370	0.8769	0.9166	yes	no
P20664	PRI1_MOUSE	2, ., 7, ., 7, ., -	0.4418	0.8701	0.9160	yes	no
Q7KQM1	PRI1_PLAF7	2, ., 7, ., 7, ., -	0.4004	0.9134	0.8871	yes	no

EC Number Prediction by Ezypred Server

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software

Prediction Level	EC number	Confidence of Prediction
3rd Layer	2.7.7	LOW CONFIDENCE prediction!

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Fail to connect to STRING server

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
Query		439
cd04860		232	cd04860, AE_Prim_S, AE_Prim_S: primase domain simi	5e-79
COG1467		341	COG1467, PRI1, Eukaryotic-type DNA primase, cataly	3e-50
TIGR00335		297	TIGR00335, primase_sml, DNA primase, eukaryotic-ty	2e-34
pfam01896		133	pfam01896, DNA_primase_S, Eukaryotic and archaeal	2e-26
PRK00419		376	PRK00419, PRK00419, DNA primase small subunit; Rev	6e-18
cd04860		232	cd04860, AE_Prim_S, AE_Prim_S: primase domain simi	4e-16
cd00525		136	cd00525, AE_Prim_S_like, AE_Prim_S_like: primase d	2e-12
pfam01896		133	pfam01896, DNA_primase_S, Eukaryotic and archaeal	8e-09

>gnl\|CDD\|240130 cd04860, AE_Prim_S, AE_Prim_S: primase domain similar to that found in the small subunit of archaeal and eukaryotic (A/E) DNA primases	Back alignment and domain information

 Score =  244 bits (624), Expect = 5e-79
 Identities = 84/191 (43%), Positives = 107/191 (56%), Gaps = 10/191 (5%)

Query: 45  RHPACDKSYFGRREFSFTLDNDIYLRFQSFNSESELENSIKEKCPSKIDIGPVYSVDPAK 104
            +      Y   REF FTL + +Y+R  SF+S  EL   +    P       VYS     
Sbjct: 10  NYGLEIPDYLENREFGFTLFDGVYIRHLSFSSAEELRKYLLRNVPR-----AVYSSSAYY 64

Query: 105 RHAYAQGGDNVFAPVERELIFDIDITDYDDVRYCCSGADVCLECWPLMTVAIKVIDTALR 164
           R   A+G       + REL+FDID  DYDDVR CCSGA +C +CW     A+K++D  LR
Sbjct: 65  RKPSAKGE---KGWLGRELVFDIDADDYDDVRTCCSGATICEKCWKFAKEAVKILDDILR 121

Query: 165 DDFGFDHILWVYSGRRGVHCWVCDGKARRLTNEQRGAIADYFRVYKGNENSNKKVSFPG- 223
           +DFGF HILWV+SGRRG H WVCD KAR+L +++R  I DY      NE+  KKV     
Sbjct: 122 EDFGFKHILWVFSGRRGYHVWVCDEKARKLDSDERREIVDYLNGIGLNEDKIKKVKVNLG 181

Query: 224 -PLHPFLVRSY 233
            PLHP + R+ 
Sbjct: 182 RPLHPGIRRAL 192

Primases are DNA-dependent RNA polymerases which synthesis the short RNA primers required for DNA replication. In addition to its catalytic role in replication, DNA primase may play a role in coupling replication to DNA damage repair and in checkpoint control during S phase. In eukaryotes, this small catalytically active primase subunit (p50) and a larger primase subunit (p60), referred to jointly as the core primase, associate with the B subunit and the DNA polymerase alpha subunit in a complex, called Pol alpha-pri. The function of the larger primase subunit is unclear. Included in this group are Pfu41 and Pfu46, these two proteins comprise the primase complex of the archaea Pyrococcus furiosus; Pfu41 and Pfu46 have sequence identity to the eukaryotic p50 and p60 primase proteins respectively. Pfu41 preferentially uses dNTPs as substrate. Pfu46 regulates the primase activity of Pfu41. Length = 232

>gnl\|CDD\|224384 COG1467, PRI1, Eukaryotic-type DNA primase, catalytic (small) subunit [DNA replication, recombination, and repair]	Back alignment and domain information

>gnl\|CDD\|232925 TIGR00335, primase_sml, DNA primase, eukaryotic-type, small subunit, putative	Back alignment and domain information

>gnl\|CDD\|216771 pfam01896, DNA_primase_S, Eukaryotic and archaeal DNA primase small subunit	Back alignment and domain information

>gnl\|CDD\|234755 PRK00419, PRK00419, DNA primase small subunit; Reviewed	Back alignment and domain information

>gnl\|CDD\|240130 cd04860, AE_Prim_S, AE_Prim_S: primase domain similar to that found in the small subunit of archaeal and eukaryotic (A/E) DNA primases	Back alignment and domain information

>gnl\|CDD\|238291 cd00525, AE_Prim_S_like, AE_Prim_S_like: primase domain similar to that found in the small subunit of archaeal and eukaryotic (A/E) DNA primases	Back alignment and domain information

>gnl\|CDD\|216771 pfam01896, DNA_primase_S, Eukaryotic and archaeal DNA primase small subunit	Back alignment and domain information

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Alignment Graph	Length	Definition	Probability
Query		439
KOG2851		412	consensus Eukaryotic-type DNA primase, catalytic (	100.0
cd04860		232	AE_Prim_S AE_Prim_S: primase domain similar to tha	100.0
TIGR00335		297	primase_sml DNA primase, eukaryotic-type, small su	100.0
PRK00419		376	DNA primase small subunit; Reviewed	100.0
COG1467		341	PRI1 Eukaryotic-type DNA primase, catalytic (small	100.0
PF01896		145	DNA_primase_S: Eukaryotic and archaeal DNA primase	99.97
cd00525		136	AE_Prim_S_like AE_Prim_S_like: primase domain simi	99.34
TIGR00335		297	primase_sml DNA primase, eukaryotic-type, small su	98.27
cd04861		227	LigD_Pol_like LigD_Pol_like: Polymerase (Pol) doma	95.14
cd04865		228	LigD_Pol_like_2 LigD_Pol_like_2: Polymerase (Pol)	94.96
cd04863		231	MtLigD_Pol_like MtLigD_Pol_like: Polymerase (Pol)	94.68
cd04862		227	PaeLigD_Pol_like PaeLigD_Pol_like: Polymerase (Pol	94.54
TIGR02778		245	ligD_pol DNA polymerase LigD, polymerase domain. D	94.23
cd04866		223	LigD_Pol_like_3 LigD_Pol_like_3: Polymerase (Pol)	94.17
cd04864		228	LigD_Pol_like_1 LigD_Pol_like_1: Polymerase (Pol)	93.97
TIGR02776		552	NHEJ_ligase_prk DNA ligase D. Members of this prot	92.71
PRK09633		610	ligD ATP-dependent DNA ligase; Reviewed	92.12
COG3285		299	Predicted eukaryotic-type DNA primase [DNA replica	92.05
PRK05972		860	ligD ATP-dependent DNA ligase; Reviewed	89.26
COG1467		341	PRI1 Eukaryotic-type DNA primase, catalytic (small	89.0
PRK09632		764	ATP-dependent DNA ligase; Reviewed	88.79

>KOG2851 consensus Eukaryotic-type DNA primase, catalytic (small) subunit [Replication, recombination and repair]	Back alignment and domain information

Probab=100.00  E-value=2.7e-130  Score=971.62  Aligned_cols=391  Identities=49%  Similarity=0.939  Sum_probs=365.4

Q ss_pred             CCCChHHHHHHhhhcCChhhhhhhhccCCCCCCCCCCCCCCCCceeEEEeCCCeeecccccCCHHHHHHHHHHhCCCcee
Q 013616           14 DGFNPNYLKVYYGRLFPHADIFKWMSYGNDGRHPACDKSYFGRREFSFTLDNDIYLRFQSFNSESELENSIKEKCPSKID   93 (439)
Q Consensus        14 ~~~~~~~l~~YY~~lfP~~~~~~WL~y~~~~~~~~~~~~~~~~REfaf~~~~~~y~R~~sF~~~~el~~~l~~~~P~~i~   93 (439)
                      .++++++|+.||++|||++++++||+||+.+      ..||.+||||||+.+++|+||+||+|+++|++.|.+++|.+||
T Consensus        10 ~~~~~~~l~~YYr~lFP~~~~~~wL~yg~~~------~~~f~~REfsFtL~ddvYiRY~sFn~~~~~~k~i~s~nP~KiD   83 (412)
T KOG2851|consen   10 PGVDSQDLPIYYRNLFPVKPFFRWLNYGPVP------GDYFNRREFSFTLADDVYIRYLSFNNASEFEKEISSTNPDKID   83 (412)
T ss_pred             CCCChhHHHHHHHhhCChHHHHHHHhCCCCc------chhhhhceEEEEecCCcEEEEeccCCHHHHHHHHhhcCCccee
Confidence            4578899999999999999999999999755      7899999999999999999999999999999999999999999


Q ss_pred             eccccccCccchhhhccCCCCCcCcccceEEEeccCCCCCCcccccCCCccccccHHHHHHHHHHHHHHHhhhcCCceeE
Q 013616           94 IGPVYSVDPAKRHAYAQGGDNVFAPVERELIFDIDITDYDDVRYCCSGADVCLECWPLMTVAIKVIDTALRDDFGFDHIL  173 (439)
Q Consensus        94 igavY~~~P~~~~~~~~~~~~~f~p~~~ELVFDID~~dyd~ir~CC~~~~iC~kCw~~~~~a~klld~~L~~dFGf~~i~  173 (439)
                      |||||+++|.++++..+   ++|+|++|||||||||||||+||+||+||+||+|||+||++|++|||.+|+|||||||++
T Consensus        84 IGaVY~~~P~~~~t~~~---s~~~~vekELVFDIDmTDYD~VR~CCS~a~VC~KCW~fm~lAvkIld~aLrEdFGFKh~l  160 (412)
T KOG2851|consen   84 IGAVYSHRPRNHKTLRK---SDFQAVEKELVFDIDMTDYDDVRTCCSGADVCPKCWKFMTLAVKILDTALREDFGFKHIL  160 (412)
T ss_pred             ecccccCCccccccccc---cccceeeeeeEEecccccChHHhhhcccccchHHHHHHHHHHHHHHHHHHHHhcCCceEE
Confidence            99999999999999887   789999999999999999999999999999999999999999999999999999999999


Q ss_pred             EEEeCCCceEEEeechhhccCChHHHHHHHhHhhhccCCCcccceeeCCCCCCcchhhHHHHHHHHHHHHHHhhhcCCCC
Q 013616          174 WVYSGRRGVHCWVCDGKARRLTNEQRGAIADYFRVYKGNENSNKKVSFPGPLHPFLVRSYTEVLREFFEEKLLLSQNLFS  253 (439)
Q Consensus       174 ~VFSGrRG~H~wV~D~~ar~L~~e~R~aIvdYl~vv~G~~~~~k~v~l~~~~hP~i~r~~~~il~~~f~~~il~~q~~l~  253 (439)
                      ||||||||+||||||++||.|++.+|++||+||++++|+++..+++.+..+.||++.|++ .+|+++|++++|++|++|+
T Consensus       161 WVfSGRRGvHCWVcD~~Ar~L~~~qR~aIa~Ylnvvk~n~~~~~~~~lk~~~hP~l~Rs~-~~lK~~f~e~~l~~Q~~w~  239 (412)
T KOG2851|consen  161 WVFSGRRGVHCWVCDKKARMLSDRQRSAIAEYLNVVKGNGQCGKRLGLKRKKHPHLARSL-NILKPFFEEIMLEDQNPWE  239 (412)
T ss_pred             EEEecCCceeeeeccHHHhhccchHHHHHHHHHHHhhcCcccccccccCCCCCcHHHHHH-HHHHHHHHHHHhhhcCccc
Confidence            999999999999999999999999999999999999999999999888789999999999 8999999999999999999


Q ss_pred             CHHHHHHHHccCCChhHHHHHHhhhhhccCCCCCcccchHHhHHHHHHHHhccchhh-----hhHHHHHHHHHHHhhccc
Q 013616          254 TEERYEKILSMIPDESVTSELRGKWQENRRSSNSKEDINFFRWEQLKNTLQSGKQKV-----QGLRRCVEEIVFAFTYPR  328 (439)
Q Consensus       254 ~~~~~~~lL~~lpd~~~~~~l~~~~~~~~~~~~~~~~~s~~~W~~l~~~~~~~~~~~-----~~~~~~~~eivl~~~ypR  328 (439)
                      ++++++++|+++||+.+++.|++.|+.+|      .+++.++|++|++++.+...++     ..+.++.++|+|+++|||
T Consensus       240 ~ke~~~k~l~~l~d~~~~d~Lr~~w~~~~------~~s~~erW~~i~~~~~s~~~~~~s~~~~k~~~~~~eivl~~~YPR  313 (412)
T KOG2851|consen  240 DKEGFEKLLKLLPDKDLIDDLRKYWESNP------RRSSKERWEDIDKVADSDYRKTLSPSDIKLKNCKSEIVLQYLYPR  313 (412)
T ss_pred             ChHHHHHHHhhcchhhhHHHHHHhhhcCc------ccchHHHHHHHHHHHhhhccccCChhhhhHHhhHHHHHHHHhccc
Confidence            99999999999999999999999999888      4689999999999998743322     346679999999999999


Q ss_pred             cccccccccccccccCccccCCCccEEEEcCCCCCCCCCCCCCCcHHHHHHhhhcCCCCC---Ccccchh-ccchhHHHH
Q 013616          329 LDMEVSKHRNHLLKAPFCVHPKTGRVCIPIDPKDCEEFDPTTVPTLSELLRELNTGDSRM---DVDNEWE-KTSLGKSIR  404 (439)
Q Consensus       329 LD~~VTkd~nHLLKsPfcvHpkTG~vcVPid~~~l~~FDP~~VPtl~~l~~e~~~~~~~~---~~~~~~~-~tsL~~yv~  404 (439)
                      ||+|||+++|||||||||||||||+||||||++++++|||++||||++|++|+++..+..   +...++. +.+|.|||.
T Consensus       314 LDveVtk~~nHLLKsPFcVHP~Tg~VcVPidv~~~d~Fdp~~vPti~~l~eEl~~~nd~~~~~e~~~d~~~~~aL~pyv~  393 (412)
T KOG2851|consen  314 LDVEVTKGTNHLLKSPFCVHPKTGRVCVPIDVSKVDEFDPEKVPTISDLLEELESLNDEKEYTENRKDLARHGALSPYVE  393 (412)
T ss_pred             hhhhhhhcchhhhcCCccccCCCCceEeecchhhccccCcccCCcHHHHHHHHhhcccccccccchhhhhhccccchHHH
Confidence            999999999999999999999999999999999999999999999999999999874321   1122322 449999999


Q ss_pred             HHHHHhHHHHHHHhHHh
Q 013616          405 FFRSSFLQPLLKSCKEE  421 (439)
Q Consensus       405 ~F~~~f~~~l~~~~~~~  421 (439)
                      +| +.|+..|.++.++.
T Consensus       394 ~F-e~F~s~l~~~~~g~  409 (412)
T KOG2851|consen  394 VF-EAFVSALIKSEKGS  409 (412)
T ss_pred             HH-HHHHHHHHHhhhcc
Confidence            99 99999999998876

>cd04860 AE_Prim_S AE_Prim_S: primase domain similar to that found in the small subunit of archaeal and eukaryotic (A/E) DNA primases	Back alignment and domain information

>TIGR00335 primase_sml DNA primase, eukaryotic-type, small subunit, putative	Back alignment and domain information

>PRK00419 DNA primase small subunit; Reviewed	Back alignment and domain information

>COG1467 PRI1 Eukaryotic-type DNA primase, catalytic (small) subunit [DNA replication, recombination, and repair]	Back alignment and domain information

>PF01896 DNA_primase_S: Eukaryotic and archaeal DNA primase small subunit; InterPro: IPR002755 DNA primase [] synthesizes the RNA primers for the Okazaki fragments in lagging strand DNA synthesis	Back alignment and domain information

>cd00525 AE_Prim_S_like AE_Prim_S_like: primase domain similar to that found in the small subunit of archaeal and eukaryotic (A/E) DNA primases	Back alignment and domain information

>TIGR00335 primase_sml DNA primase, eukaryotic-type, small subunit, putative	Back alignment and domain information

>cd04861 LigD_Pol_like LigD_Pol_like: Polymerase (Pol) domain of bacterial LigD proteins similar to Pseudomonas aeruginosa (Pae) LigD	Back alignment and domain information

>cd04865 LigD_Pol_like_2 LigD_Pol_like_2: Polymerase (Pol) domain of bacterial LigD proteins similar to Pseudomonas aeruginosa (Pae) LigD, subgroup 2	Back alignment and domain information

>cd04863 MtLigD_Pol_like MtLigD_Pol_like: Polymerase (Pol) domain of bacterial LigD proteins similar to Mycobacterium tuberculosis (Mt)LigD	Back alignment and domain information

>cd04862 PaeLigD_Pol_like PaeLigD_Pol_like: Polymerase (Pol) domain of bacterial LigD proteins similar to Pseudomonas aeruginosa (Pae) LigD	Back alignment and domain information

>TIGR02778 ligD_pol DNA polymerase LigD, polymerase domain	Back alignment and domain information

>cd04866 LigD_Pol_like_3 LigD_Pol_like_3: Polymerase (Pol) domain of bacterial LigD proteins similar to Pseudomonas aeruginosa (Pae) LigD, subgroup 3	Back alignment and domain information

>cd04864 LigD_Pol_like_1 LigD_Pol_like_1: Polymerase (Pol) domain of mostly bacterial LigD proteins similar to Pseudomonas aeruginosa (Pae) LigD, subgroup 1	Back alignment and domain information

>TIGR02776 NHEJ_ligase_prk DNA ligase D	Back alignment and domain information

>PRK09633 ligD ATP-dependent DNA ligase; Reviewed	Back alignment and domain information

>COG3285 Predicted eukaryotic-type DNA primase [DNA replication, recombination, and repair]	Back alignment and domain information

>PRK05972 ligD ATP-dependent DNA ligase; Reviewed	Back alignment and domain information

>COG1467 PRI1 Eukaryotic-type DNA primase, catalytic (small) subunit [DNA replication, recombination, and repair]	Back alignment and domain information

>PRK09632 ATP-dependent DNA ligase; Reviewed	Back alignment and domain information

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

No homologous structure with e-value below 0.005

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Alignment Graph	Length	Definition	E-value
Query		439
1v33_A		366	DNA primase small subunit; nucleotidyl transferase	1e-85
1zt2_A		330	DNA primase small subunit; heterodimeric complex,	6e-41

>1v33_A DNA primase small subunit; nucleotidyl transferase, riken structural genomics/proteomics initiative, RSGI, structural genomics; HET: DNA; 1.80A {Pyrococcus horikoshii} SCOP: d.264.1.1 PDB: 1v34_A* 1g71_A* Length = 366	Back alignment and structure

 Score =  265 bits (678), Expect = 1e-85
 Identities = 62/395 (15%), Positives = 119/395 (30%), Gaps = 51/395 (12%)

Query: 6   PKQGNVIPDGFNPNYLKVYYGRLFPHADIFKWMSYGNDGRHPACDKSYFGRREFSFTLDN 65
           P+  +++         K +Y   +   DI  ++                  REF F    
Sbjct: 16  PRGSHMLLREVTREERKNFYTNEWKVKDIPDFIVK------------TLELREFGFDHSG 63

Query: 66  D-IYLRFQSFNSESELENSIKEKCPSKIDIGPVYSVDPAKRHAYAQGGDNVFAPVERELI 124
           +    R   +    +LE+ I+   P  +         P +              +  EL+
Sbjct: 64  EGPSDRKNQYTDIRDLEDYIRATAPYAVYSSVALYEKPQEMEG----------WLGTELV 113

Query: 125 FDIDITDYDDVRYCCSGADVCLECWPLMTVAIKVIDTALRDDFGFDHILWVYSGRRGVHC 184
           FDID  D    R       VC  C       ++     LR++ GF+ I  +YSG RG H 
Sbjct: 114 FDIDAKDLPLRRCEHEPGTVCPICLNDAKEIVRDTVIILREELGFNDIHIIYSG-RGYHI 172

Query: 185 WVCDGKARRLTNEQRGAIADYFRVYKGNENSNKKVSFPG-PLHPFLVRSYTEVLREFFEE 243
            V D  A +L ++ R  I  +    +  +    +           L   Y    R  F  
Sbjct: 173 RVLDEWALKLDSKSRERILSFVSASEIEDVEEFRKLLLNKRGWFVLNHGYPRAFRLRFGY 232

Query: 244 KLLLSQNLFSTEERYEKILSMIPDESVTSELRGKWQENRRSSNSKEDINFFRWEQLKNTL 303
            +L  +          K ++    +S         ++   ++  +        +      
Sbjct: 233 FILRIKLPHLINAGIRKSIAKSILKSKEEIYEEFVRKAILAAFPQGVGIESLAKLF---- 288

Query: 304 QSGKQKVQGLRRCVEEIVFAFTYPRLDMEVSKHRNHLLKAPFCVHPKTGRVCIPIDP--K 361
                           +   F+    D  V+     +L+ P  +H K G +   +    +
Sbjct: 289 ---------------ALSTRFSKSYFDGRVTVDLKRILRLPSTLHSKVGLIAKYVGTNER 333

Query: 362 DCEEFDPTTVPTLSELLRELNTGDSRMDVDNEWEK 396
           D   F+P         + +    + +++     E 
Sbjct: 334 DVMRFNP-----FKHAVPKFRKEEVKVEYKKFLES 363

PyMOL of 1v33

>1zt2_A DNA primase small subunit; heterodimeric complex, replication, transferase; HET: DNA; 3.33A {Sulfolobus solfataricus} SCOP: d.264.1.1 Length = 330	Back alignment and structure

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Alignment Graph	Length	Definition	Probability
Query		439
1v33_A		366	DNA primase small subunit; nucleotidyl transferase	100.0
1zt2_A		330	DNA primase small subunit; heterodimeric complex,	100.0
2fao_A		309	Probable ATP-dependent DNA ligase; polymerase, pri	95.33
2iru_A		303	Putative DNA ligase-like protein RV0938/MT0965; po	95.31

>1v33_A DNA primase small subunit; nucleotidyl transferase, riken structural genomics/proteomics initiative, RSGI, structural genomics; HET: DNA; 1.80A {Pyrococcus horikoshii} SCOP: d.264.1.1 PDB: 1v34_A* 1g71_A*	Back alignment and structure

Probab=100.00  E-value=6.4e-90  Score=699.87  Aligned_cols=316  Identities=21%  Similarity=0.322  Sum_probs=265.1

Q ss_pred             CCCCCCChHHHHHHhhhcCChhhhhhhhccCCCCCCCCCCCCCCCCceeEEEe-CCCeeecccccCCHHHHHHHHHHhCC
Q 013616           11 VIPDGFNPNYLKVYYGRLFPHADIFKWMSYGNDGRHPACDKSYFGRREFSFTL-DNDIYLRFQSFNSESELENSIKEKCP   89 (439)
Q Consensus        11 ~~~~~~~~~~l~~YY~~lfP~~~~~~WL~y~~~~~~~~~~~~~~~~REfaf~~-~~~~y~R~~sF~~~~el~~~l~~~~P   89 (439)
                      |.-...++++|+.||+++||++++++||++            ++++|||||++ .+++|+||+||+|.+||+++|++++|
T Consensus        21 ~~~~~~~~~~l~~YY~r~fp~~~~~~wl~~------------~~~~REfaf~~~~~~~~~R~~sF~~~~el~~~l~~~~P   88 (366)
T 1v33_A           21 MLLREVTREERKNFYTNEWKVKDIPDFIVK------------TLELREFGFDHSGEGPSDRKNQYTDIRDLEDYIRATAP   88 (366)
T ss_dssp             CCSCCCCHHHHHHHHHHTCCGGGSCHHHHT------------TGGGCCEEEESSSSCSCEEEECCSSHHHHHHHHHHHCC
T ss_pred             eeeccCCHHHHHHHHHhhCCcccccccccc------------cCcCeEEEEEECCCCccccccccCCHHHHHHHHHHhCC
Confidence            555678899999999999999999999975            38999999997 68899999999999999999999999


Q ss_pred             CceeeccccccCccchhhhccCCCCCcCcccceEEEeccCCCCCCcccc-cCCCccccccHHHHHHHHHHHHHHHhhhcC
Q 013616           90 SKIDIGPVYSVDPAKRHAYAQGGDNVFAPVERELIFDIDITDYDDVRYC-CSGADVCLECWPLMTVAIKVIDTALRDDFG  168 (439)
Q Consensus        90 ~~i~igavY~~~P~~~~~~~~~~~~~f~p~~~ELVFDID~~dyd~ir~C-C~~~~iC~kCw~~~~~a~klld~~L~~dFG  168 (439)
                      .|+|+|||||.+|.+++        +|  .++||||||||||| ++|+| |++++||.+||.+|++|+++|+++|++|||
T Consensus        89 ~~iy~saayy~~P~~~k--------~~--~~~ELVFDID~~d~-diRtC~C~~~~iC~kC~~~~~~a~~~l~~~L~~dFG  157 (366)
T 1v33_A           89 YAVYSSVALYEKPQEME--------GW--LGTELVFDIDAKDL-PLRRCEHEPGTVCPICLNDAKEIVRDTVIILREELG  157 (366)
T ss_dssp             SEEEEESEEEEETTTTE--------EE--EEECEEEEEEGGGC-SSCSSCSCTTCCCHHHHHHHHHHHHHHHHHHHHTTC
T ss_pred             CEEEEcceeecChhhcC--------Cc--cccceEEEecCCcC-CcCccCCCCcchHHHHHHHHHHHHHHHHHHHHHHcC
Confidence            99999999999999853        35  78999999999999 69999 999999999999999999999999999999


Q ss_pred             CceeEEEEeCCCceEEEeechhhccCChHHHHHHHhHhhhccCCC-cccceeeCCCCCCcchh----hHHHHHHHHHHHH
Q 013616          169 FDHILWVYSGRRGVHCWVCDGKARRLTNEQRGAIADYFRVYKGNE-NSNKKVSFPGPLHPFLV----RSYTEVLREFFEE  243 (439)
Q Consensus       169 f~~i~~VFSGrRG~H~wV~D~~ar~L~~e~R~aIvdYl~vv~G~~-~~~k~v~l~~~~hP~i~----r~~~~il~~~f~~  243 (439)
                      |++++||||| |||||||||++||.|++++|+|||+||+++...+ +..+++++..+.||++.    |++ .++.++|..
T Consensus       158 f~~i~~vfSG-RG~HvwV~D~~ar~l~~~~R~~IvdYl~~~~~~~~~~~~~v~~~~~~h~~~~~~~~r~~-~~~~~~f~~  235 (366)
T 1v33_A          158 FNDIHIIYSG-RGYHIRVLDEWALKLDSKSRERILSFVSASEIEDVEEFRKLLLNKRGWFVLNHGYPRAF-RLRFGYFIL  235 (366)
T ss_dssp             CCCEEEEECS-SEEEEEECCHHHHTCCHHHHHHHHHHHTTCSSCCHHHHHHHHHHCGGGGGCSSSHHHHH-HHHHHHHHT
T ss_pred             CceeEEEEeC-CeEEEEEecHHhhhcCHHHHHHHhhhEEeeccCCccccceeeccCCCCcccchhHHHHH-HHHHHHHHH
Confidence            9999999999 9999999999999999999999999999765322 23456776667888766    667 667778876


Q ss_pred             HHhhhcCCCC---CHHHHHHHHccCCChhHHHHHHhhhhhccCCCCCcccchHHhHHHHHHHHhccchhhhhHHHHHHHH
Q 013616          244 KLLLSQNLFS---TEERYEKILSMIPDESVTSELRGKWQENRRSSNSKEDINFFRWEQLKNTLQSGKQKVQGLRRCVEEI  320 (439)
Q Consensus       244 ~il~~q~~l~---~~~~~~~lL~~lpd~~~~~~l~~~~~~~~~~~~~~~~~s~~~W~~l~~~~~~~~~~~~~~~~~~~ei  320 (439)
                      .++ +|++|.   +++.++++|+..      .++.+            ..++.++|+++++..     ....+.. +.++
T Consensus       236 ~~~-~~~~l~~g~~~~~~~~~l~~~------~~~~~------------~~~s~~~w~~~~~~~-----~~~~~~~-l~~~  290 (366)
T 1v33_A          236 RIK-LPHLINAGIRKSIAKSILKSK------EEIYE------------EFVRKAILAAFPQGV-----GIESLAK-LFAL  290 (366)
T ss_dssp             TCC-HHHHHHTTCCHHHHHHHHHTH------HHHHH------------HTTTTCCGGGSCTTC-----HHHHHHH-HHHH
T ss_pred             Hhh-hhhhhhccCCHHHHHHHHHHH------HHhhh------------cccchhhHHHHhhhh-----hhhHHHH-HHHH
Confidence            554 344544   677788877631      11111            124677888765321     1122333 3478


Q ss_pred             HHHhhccccccccccccccccccCccccCCCccEEEEcCCCC--CCCCCCC--CCCcHHH
Q 013616          321 VFAFTYPRLDMEVSKHRNHLLKAPFCVHPKTGRVCIPIDPKD--CEEFDPT--TVPTLSE  376 (439)
Q Consensus       321 vl~~~ypRLD~~VTkd~nHLLKsPfcvHpkTG~vcVPid~~~--l~~FDP~--~VPtl~~  376 (439)
                      +++++|||||+|||+|+|||||+|||||||||+|||||++++  ++.|||+  +|||+.+
T Consensus       291 v~~~~~~~lD~~VT~d~nhLLK~PfslHpkTG~vcvPid~~~~~~~~FDPl~daVPtf~~  350 (366)
T 1v33_A          291 STRFSKSYFDGRVTVDLKRILRLPSTLHSKVGLIAKYVGTNERDVMRFNPFKHAVPKFRK  350 (366)
T ss_dssp             HHHHHHTSSCHHHHHCTTCEEECTTSEETTTTEECCEEESSHHHHHHCCHHHHSCCGGGH
T ss_pred             HHHhhhcccCcccccCcceeeecCccccCCCCcEEEEeccccccccccCCccccCCeecC
Confidence            899999999999999999999999999999999999999988  9999995  8999753

PyMOL of 1v33

>1zt2_A DNA primase small subunit; heterodimeric complex, replication, transferase; HET: DNA; 3.33A {Sulfolobus solfataricus} SCOP: d.264.1.1	Back alignment and structure

>2fao_A Probable ATP-dependent DNA ligase; polymerase, primase, NHEJ, hydrolase/transferase complex; 1.50A {Pseudomonas aeruginosa} PDB: 2faq_A* 2far_A*	Back alignment and structure

>2iru_A Putative DNA ligase-like protein RV0938/MT0965; polymerase, primase, NHEJ, transferase; 1.65A {Mycobacterium tuberculosis} PDB: 2irx_A* 2iry_A* 2r9l_A* 3pky_A*	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		439
d1v33a_		346	d.264.1.1 (A:) DNA primase {Archaeon Pyrococcus ho	2e-88
d1zt2a1		327	d.264.1.1 (A:3-329) DNA primase small subunit PriA	2e-39

>d1v33a_ d.264.1.1 (A:) DNA primase {Archaeon Pyrococcus horikoshii [TaxId: 53953]} Length = 346	Back information, alignment and structure


class: Alpha and beta proteins (a+b)
fold: Prim-pol domain
superfamily: Prim-pol domain
family: PriA-like
domain: DNA primase
species: Archaeon Pyrococcus horikoshii [TaxId: 53953]

 Score =  271 bits (693), Expect = 2e-88
 Identities = 66/367 (17%), Positives = 114/367 (31%), Gaps = 48/367 (13%)

Query: 16  FNPNYLKVYYGRLFPHADIFKWMSYGNDGRHPACDKSYFGRREFSFTLDND-IYLRFQSF 74
                 K +Y   +   DI  ++                  REF F    +    R   +
Sbjct: 6   VTREERKNFYTNEWKVKDIPDFIV------------KTLELREFGFDHSGEGPSDRKNQY 53

Query: 75  NSESELENSIKEKCPSKIDIGPVYSVDPAKRHAYAQGGDNVFAPVERELIFDIDITDYDD 134
               +LE+ I+   P  +         P +              +  EL+FDID  D   
Sbjct: 54  TDIRDLEDYIRATAPYAVYSSVALYEKPQEMEG----------WLGTELVFDIDAKDLPL 103

Query: 135 VRYCCSGADVCLECWPLMTVAIKVIDTALRDDFGFDHILWVYSGRRGVHCWVCDGKARRL 194
            R       VC  C       ++     LR++ GF+ I  +YSG RG H  V D  A +L
Sbjct: 104 RRCEHEPGTVCPICLNDAKEIVRDTVIILREELGFNDIHIIYSG-RGYHIRVLDEWALKL 162

Query: 195 TNEQRGAIADYFRVYKGNENSNKKVSFPGP-LHPFLVRSYTEVLREFFEEKLLLSQNLFS 253
            ++ R  I  +    +  +    +           L   Y    R  F   +L  +    
Sbjct: 163 DSKSRERILSFVSASEIEDVEEFRKLLLNKRGWFVLNHGYPRAFRLRFGYFILRIK---- 218

Query: 254 TEERYEKILSMIPDESVTSELRGKWQENRRSSNSKEDINFFRWEQLKNTLQSGKQKVQGL 313
                           + + +R    ++   S  +    F R   L    Q    +    
Sbjct: 219 ------------LPHLINAGIRKSIAKSILKSKEEIYEEFVRKAILAAFPQGVGIE---S 263

Query: 314 RRCVEEIVFAFTYPRLDMEVSKHRNHLLKAPFCVHPKTGRVCIPI--DPKDCEEFDPTT- 370
              +  +   F+    D  V+     +L+ P  +H K G +   +  + +D   F+P   
Sbjct: 264 LAKLFALSTRFSKSYFDGRVTVDLKRILRLPSTLHSKVGLIAKYVGTNERDVMRFNPFKH 323

Query: 371 -VPTLSE 376
            VP   +
Sbjct: 324 AVPKFRK 330

PyMOL of d1v33a_

>d1zt2a1 d.264.1.1 (A:3-329) DNA primase small subunit PriA {Sulfolobus solfataricus [TaxId: 2287]} Length = 327	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
Query		439
d1v33a_		346	DNA primase {Archaeon Pyrococcus horikoshii [TaxId	100.0
d1zt2a1		327	DNA primase small subunit PriA {Sulfolobus solfata	100.0

>d1v33a_ d.264.1.1 (A:) DNA primase {Archaeon Pyrococcus horikoshii [TaxId: 53953]}	Back information, alignment and structure

class: Alpha and beta proteins (a+b)
fold: Prim-pol domain
superfamily: Prim-pol domain
family: PriA-like
domain: DNA primase
species: Archaeon Pyrococcus horikoshii [TaxId: 53953]

Probab=100.00  E-value=5.5e-87  Score=672.78  Aligned_cols=317  Identities=19%  Similarity=0.261  Sum_probs=238.6

Q ss_pred             CCCCCCChHHHHHHhhhcCChhhhhhhhccCCCCCCCCCCCCCCCCceeEEEeC-CCeeecccccCCHHHHHHHHHHhCC
Q 013616           11 VIPDGFNPNYLKVYYGRLFPHADIFKWMSYGNDGRHPACDKSYFGRREFSFTLD-NDIYLRFQSFNSESELENSIKEKCP   89 (439)
Q Consensus        11 ~~~~~~~~~~l~~YY~~lfP~~~~~~WL~y~~~~~~~~~~~~~~~~REfaf~~~-~~~y~R~~sF~~~~el~~~l~~~~P   89 (439)
                      |....++++.++.||+++||++.+++||+            ..+++|||||++. +++|+|||||+|.+||+++|++++|
T Consensus         1 ~~~~~~~~~~~~~yY~~~fp~~~~~~~~~------------~~~~~REf~f~~~~~~~~~R~~sF~s~~eL~~~l~~~~P   68 (346)
T d1v33a_           1 MLLREVTREERKNFYTNEWKVKDIPDFIV------------KTLELREFGFDHSGEGPSDRKNQYTDIRDLEDYIRATAP   68 (346)
T ss_dssp             CCSCCCCHHHHHHHHHHTCCGGGSCHHHH------------TTGGGCCEEEESSSSCSCEEEECCSSHHHHHHHHHHHCC
T ss_pred             CcchhhCHHHHHHHHHhhCCchhhhhhhc------------ccccccceEEEecCCCccchhhccCCHHHHHHHHHhhCC
Confidence            44568899999999999999999999994            4599999999976 5689999999999999999999999


Q ss_pred             CceeeccccccCccchhhhccCCCCCcCcccceEEEeccCCCCCCcccccCCCccccccHHHHHHHHHHHHHHHhhhcCC
Q 013616           90 SKIDIGPVYSVDPAKRHAYAQGGDNVFAPVERELIFDIDITDYDDVRYCCSGADVCLECWPLMTVAIKVIDTALRDDFGF  169 (439)
Q Consensus        90 ~~i~igavY~~~P~~~~~~~~~~~~~f~p~~~ELVFDID~~dyd~ir~CC~~~~iC~kCw~~~~~a~klld~~L~~dFGf  169 (439)
                      .|+|||||||.+|.+++        +|  +|+||||||||||||++|+||+++.||.+||.+|+.|+++|+.+|++||||
T Consensus        69 ~~vy~saayy~~P~~~k--------~~--~~~ELVFDID~ddy~~~r~cc~~~~iC~kCw~~~~~av~~L~~~L~~DFGf  138 (346)
T d1v33a_          69 YAVYSSVALYEKPQEME--------GW--LGTELVFDIDAKDLPLRRCEHEPGTVCPICLNDAKEIVRDTVIILREELGF  138 (346)
T ss_dssp             SEEEEESEEEEETTTTE--------EE--EEECEEEEEEGGGCSSCSSCSCTTCCCHHHHHHHHHHHHHHHHHHHHTTCC
T ss_pred             CeEEEecccccChhHcC--------Cc--cccccccccccccCCCcccccCCcchHHHHHHHHHHHHHHHHHHHHhcCCc
Confidence            99999999999996542        34  999999999999999999999999999999999999999999999999999


Q ss_pred             ceeEEEEeCCCceEEEeechhhccCChHHHHHHHhHhhhccCCCcccce-eeCCC----CCCcchhhHHHHHHHHHHHHH
Q 013616          170 DHILWVYSGRRGVHCWVCDGKARRLTNEQRGAIADYFRVYKGNENSNKK-VSFPG----PLHPFLVRSYTEVLREFFEEK  244 (439)
Q Consensus       170 ~~i~~VFSGrRG~H~wV~D~~ar~L~~e~R~aIvdYl~vv~G~~~~~k~-v~l~~----~~hP~i~r~~~~il~~~f~~~  244 (439)
                      +|++||||| |||||||||++||+|++++|+|||+||++.+++.....+ ..+..    ...+++.+.+    ...+...
T Consensus       139 ~~i~~vFSG-RG~H~wV~D~~ar~L~s~~RreIv~Yl~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~----~~~~~~~  213 (346)
T d1v33a_         139 NDIHIIYSG-RGYHIRVLDEWALKLDSKSRERILSFVSASEIEDVEEFRKLLLNKRGWFVLNHGYPRAF----RLRFGYF  213 (346)
T ss_dssp             CCEEEEECS-SEEEEEECCHHHHTCCHHHHHHHHHHHTTCSSCCHHHHHHHHHHCGGGGGCSSSHHHHH----HHHHHHH
T ss_pred             hhheeeecC-CeEEEEecCHHHHhccHHHHHHHHHHHhhcccccccccccccccccccccccchhHHHH----HHHHHhh
Confidence            999999999 999999999999999999999999999976654322111 11111    2223333333    3333322


Q ss_pred             HhhhcCCCCCHHHHHHHHccCCChhHHHHHHhhhhhccCCCCCcccchHHhHHHHHHHH--hcc-chhhhhHHHHHHHHH
Q 013616          245 LLLSQNLFSTEERYEKILSMIPDESVTSELRGKWQENRRSSNSKEDINFFRWEQLKNTL--QSG-KQKVQGLRRCVEEIV  321 (439)
Q Consensus       245 il~~q~~l~~~~~~~~lL~~lpd~~~~~~l~~~~~~~~~~~~~~~~~s~~~W~~l~~~~--~~~-~~~~~~~~~~~~eiv  321 (439)
                      .+..+        ...++..--.+.+...+.+              ...+.|..+....  ... ..........+.+++
T Consensus       214 ~~~~~--------~~~~~~~~~~~~~~~~~~~--------------~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~  271 (346)
T d1v33a_         214 ILRIK--------LPHLINAGIRKSIAKSILK--------------SKEEIYEEFVRKAILAAFPQGVGIESLAKLFALS  271 (346)
T ss_dssp             HTTCC--------HHHHHHTTCCHHHHHHHHH--------------THHHHHHHTTTTCCGGGSCTTCHHHHHHHHHHHH
T ss_pred             hhHhh--------hhhhhhhhhhHHHHHHHhh--------------hhHHHHHHHHHHHHhhhcccchhHHHHHHHHHHH
Confidence            22211        1222211111111111100              1111121111000  000 001122334567899


Q ss_pred             HHhhccccccccccccccccccCccccCCCccEEEEcCCCC--CCCCCCC--CCCcHHH
Q 013616          322 FAFTYPRLDMEVSKHRNHLLKAPFCVHPKTGRVCIPIDPKD--CEEFDPT--TVPTLSE  376 (439)
Q Consensus       322 l~~~ypRLD~~VTkd~nHLLKsPfcvHpkTG~vcVPid~~~--l~~FDP~--~VPtl~~  376 (439)
                      ++++|||||+|||+|+|||||+|||||||||++||||+++.  ++.|||+  +||.+.+
T Consensus       272 ~~~~~prlD~~VT~d~~rLlR~PfSlH~KTGlv~vpi~~~~ld~~~FDPl~daVp~f~~  330 (346)
T d1v33a_         272 TRFSKSYFDGRVTVDLKRILRLPSTLHSKVGLIAKYVGTNERDVMRFNPFKHAVPKFRK  330 (346)
T ss_dssp             HHHHHTSSCHHHHHCTTCEEECTTSEETTTTEECCEEESSHHHHHHCCHHHHSCCGGGH
T ss_pred             HhhccCcCCCccCCCCCceeeCCCCccCCCCCeEEEccCCccccccCCchhhhccccCC
Confidence            99999999999999999999999999999999999998774  6789998  8998754

PyMOL of d1v33a_

>d1zt2a1 d.264.1.1 (A:3-329) DNA primase small subunit PriA {Sulfolobus solfataricus [TaxId: 2287]}	Back information, alignment and structure