YRC Public Data Repository - Protein Structure Prediction

Protein:	gi\|24346978, gi\|...
Organism:	Shewanella oneidensis MR-1
Length:	574 amino acids
Reference:	Drew K, et al. (2011) The proteome folding project: Proteome-scale prediction of structure and function. Genome Res. 2011 Sep 16

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Top Sequence Alignment Hits

Listed below are up to the top 10 sequence alignment matches, by species, for the PSI-BLAST search against the protein sequence for gi|24346978, gi|....

Description	E-value	Query Range	Subject Range
gi\|75176041, gi\|... - gi\|75176041\|ref\|ZP_00696209.1\| COG0358: DNA primase (bacterial type) [Shigella boydii BS512], gi\|187...	591.0	[0..2]	[573..4]
gi\|91212495, gi\|... - gi\|91212495\|ref\|YP_542481.1\| DNA primase [Escherichia coli UTI89], gi\|91074069\|gb\|ABE08950.1\| DNA pr... gi\|115514502, gi... - gi\|117625378\|ref\|YP_855495.1\| DNA primase [Escherichia coli APEC O1], gi\|115514502\|gb\|ABJ02577.1\| DN... gi\|218560153, gi... - gi\|218560153\|ref\|YP_002393066.1\| DNA primase [Escherichia coli S88], gi\|218366922\|emb\|CAR04693.1\| DN... DNAG_ECOL6 - DNA primase OS=Escherichia coli O6:H1 (strain CFT073 / ATCC 700928 / UPEC) GN=dnaG PE=3 SV=1 gi\|237706171, gi... - gi\|237706171\|ref\|ZP_04536652.1\| DNA primase [Escherichia sp. 3_2_53FAA], gi\|226899211\|gb\|EEH85470.1\|... gi\|227887790, gi... - gi\|227887790\|ref\|ZP_04005595.1\| DNA primase [Escherichia coli 83972], gi\|227835186\|gb\|EEJ45652.1\| DN... PRIM_ECOL6 - DNA primase OS=Escherichia coli O6 GN=dnaG PE=3 SV=1	590.0	[0..2]	[573..4]
gi\|75230016 - gi\|75230016\|ref\|ZP_00716529.1\| COG0358: DNA primase (bacterial type) [Escherichia coli B7A]	590.0	[0..2]	[573..5]
gi\|24053530, gi\|... - gi\|24114366\|ref\|NP_708876.1\| DNA primase [Shigella flexneri 2a str. 301], gi\|24053530\|gb\|AAN44583.1\|... gi\|30042671, gi\|... - gi\|30064414\|ref\|NP_838585.1\| DNA primase [Shigella flexneri 2a str. 2457T], gi\|30042671\|gb\|AAP18395.... DNAG_SHIFL - DNA primase OS=Shigella flexneri GN=dnaG PE=3 SV=1 DNAG_ECO57 - DNA primase OS=Escherichia coli O157:H7 GN=dnaG PE=3 SV=1 EG10239 - DNA primase / Primase for DNA replication; primer synthesis for leading- and lagging-strand synthesi... EG10239 - DNA primase / Primase for DNA replication; primer synthesis for leading- and lagging-strand synthesi... gi\|189001079, gi... - gi\|189001079\|gb\|EDU70065.1\| DNA primase [Escherichia coli O157:H7 str. EC4076], gi\|168781201\|ref\|ZP_... gi\|168773277, gi... - gi\|187770989\|gb\|EDU34833.1\| DNA primase [Escherichia coli O157:H7 str. EC4196], gi\|168773277\|ref\|ZP_... gi\|168797658, gi... - gi\|189379826\|gb\|EDU98242.1\| DNA primase [Escherichia coli O157:H7 str. EC508], gi\|168797658\|ref\|ZP_0... gi\|189374115, gi... - gi\|189374115\|gb\|EDU92531.1\| DNA primase [Escherichia coli O157:H7 str. EC869], gi\|168785941\|ref\|ZP_0... gi\|170518602, gi... - gi\|170680884\|ref\|YP_001745338.1\| DNA primase [Escherichia coli SMS-3-5], gi\|170518602\|gb\|ACB16780.1\|... gi\|169890444, gi... - gi\|170082609\|ref\|YP_001731929.1\| DNA primase [Escherichia coli str. K-12 substr. DH10B], gi\|16989044... gi\|208811926, gi... - gi\|208811926\|ref\|ZP_03253255.1\| DNA primase [Escherichia coli O157:H7 str. EC4045], gi\|208733203\|gb\|... gi\|195937212 - gi\|195937212\|ref\|ZP_03082594.1\| DNA primase [Escherichia coli O157:H7 str. EC4024] gi\|238902177, gi... - gi\|238902177\|ref\|YP_002927973.1\| DNA primase [Escherichia coli BW2952], gi\|238860841\|gb\|ACR62839.1\| ... gi\|242378616, gi... - gi\|251786343\|ref\|YP_003000647.1\| hypothetical protein B21_02886 [Escherichia coli BL21], gi\|24237861... gi\|253323142, gi... - gi\|254289763\|ref\|YP_003055511.1\| DNA primase [Escherichia coli BL21(DE3)], gi\|253979070\|gb\|ACT44740.... gi\|226839859, gi... - gi\|254038235\|ref\|ZP_04872293.1\| DNA primase [Escherichia sp. 1_1_43], gi\|226839859\|gb\|EEH71880.1\| DN... gi\|253974914, gi... - gi\|254163013\|ref\|YP_003046121.1\| DNA primase [Escherichia coli B str. REL606], gi\|253974914\|gb\|ACT40... gi\|189361484, gi... - gi\|189361484\|gb\|EDU79903.1\| DNA primase [Escherichia coli O157:H7 str. EC4486], gi\|168769475\|ref\|ZP_... gi\|254594417, gi... - gi\|254795017\|ref\|YP_003079854.1\| DNA primase [Escherichia coli O157:H7 str. TW14359], gi\|254594417\|g... gi\|189358475, gi... - gi\|189358475\|gb\|EDU76894.1\| DNA primase [Escherichia coli O157:H7 str. EC4401], gi\|168754038\|ref\|ZP_... gi\|13363422, gi\|... - gi\|15833203\|ref\|NP_311976.1\| DNA primase [Escherichia coli O157:H7 str. Sakai], gi\|13363422\|dbj\|BAB3... gi\|209157960, gi... - gi\|209396560\|ref\|YP_002272539.1\| DNA primase [Escherichia coli O157:H7 str. EC4115], gi\|209157960\|gb... PRIM_ECOLI - DNA primase (EC 2.7.7.-) - Escherichia coli gi\|110643310, gi... - gi\|110643310\|ref\|YP_671040.1\| DNA primase [Escherichia coli 536], gi\|110344902\|gb\|ABG71139.1\| DNA pr... gi\|208820632, gi... - gi\|208820632\|ref\|ZP_03260952.1\| DNA primase [Escherichia coli O157:H7 str. EC4042], gi\|208740755\|gb\|... gi\|89109836, gi\|... - gi\|89109836\|ref\|AP_003616.1\| DNA primase [Escherichia coli str. K-12 substr. W3110], gi\|85675867\|dbj... gi\|217327354, gi... - gi\|217327354\|ref\|ZP_03443437.1\| DNA primase [Escherichia coli O157:H7 str. TW14588], gi\|217319721\|gb... gi\|209920538, gi... - gi\|209920538\|ref\|YP_002294622.1\| DNA primase [Escherichia coli SE11], gi\|209913797\|dbj\|BAG78871.1\| D... gi\|218691371, gi... - gi\|218691371\|ref\|YP_002399583.1\| DNA primase [Escherichia coli ED1a], gi\|218428935\|emb\|CAR09738.1\| D... gi\|218555636, gi... - gi\|218555636\|ref\|YP_002388549.1\| DNA primase [Escherichia coli IAI1], gi\|218362404\|emb\|CAR00028.1\| D... gi\|218433788, gi... - gi\|218706691\|ref\|YP_002414210.1\| DNA primase [Escherichia coli UMN026], gi\|218433788\|emb\|CAR14705.1\|... gi\|218353503, gi... - gi\|218696771\|ref\|YP_002404438.1\| DNA primase [Escherichia coli 55989], gi\|218353503\|emb\|CAU99621.1\| ... gi\|83584790, gi\|... - gi\|83584790\|ref\|ZP_00923451.1\| COG0358: DNA primase (bacterial type) [Escherichia coli 101-1], gi\|19... gi\|193067246, gi... - gi\|75239363\|ref\|ZP_00723334.1\| COG0358: DNA primase (bacterial type) [Escherichia coli E110019], gi\|... gi\|74313601, gi\|... - gi\|74313601\|ref\|YP_312020.1\| DNA primase [Shigella sonnei Ss046], gi\|73857078\|gb\|AAZ89785.1\| DNA pri... gi\|157156565, gi... - gi\|75187876\|ref\|ZP_00701143.1\| COG0358: DNA primase (bacterial type) [Escherichia coli E24377A], gi\|... gi\|194414185, gi... - gi\|75210999\|ref\|ZP_00711112.1\| COG0358: DNA primase (bacterial type) [Escherichia coli B171], gi\|194...	589.0	[0..2]	[573..4]
gi\|75259999, gi\|... - gi\|75259999\|ref\|ZP_00731277.1\| COG0358: DNA primase (bacterial type) [Escherichia coli E22], gi\|1930...	589.0	[0..2]	[573..4]
gi\|110616501, gi... - gi\|110806953\|ref\|YP_690473.1\| DNA primase [Shigella flexneri 5 str. 8401], gi\|110616501\|gb\|ABF05168....	588.0	[0..2]	[573..4]
gi\|82778396, gi\|... - gi\|82778396\|ref\|YP_404745.1\| DNA primase [Shigella dysenteriae Sd197], gi\|81242544\|gb\|ABB63254.1\| DN...	588.0	[0..2]	[573..4]
gi\|75240902 - gi\|75240902\|ref\|ZP_00724800.1\| COG0358: DNA primase (bacterial type) [Escherichia coli F11]	588.0	[0..2]	[573..4]
gi\|81246732, gi\|... - gi\|82545321\|ref\|YP_409268.1\| DNA primase [Shigella boydii Sb227], gi\|81246732\|gb\|ABB67440.1\| DNA pri...	588.0	[0..2]	[573..4]
gi\|15803608, gi\|... - gi\|15803608\|ref\|NP_289641.1\| DNA primase [Escherichia coli O157:H7 EDL933], gi\|12517648\|gb\|AAG58200.... gi\|25298043 - gi\|25298043\|pir\|\|D85967 DNA biosynthesis, DNA primase [imported] - Escherichia coli (strain O157:H7...	586.0	[0..2]	[573..4]

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Predicted Domain #1

Region A:
Residues: [1-97]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 MAIPRDFINE LIARTDIVEL IDRKVPLKKA GKNYSACCPF HSEKSPSFTV SRDKQFYHCF  60
   61 GCGAHGNAID FVMEYDRLDF VDAIEDLAGQ LGLEVPR

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	36.39794
Match:	1d0qA
Description:	Zinc-binding domain of DNA primase
Matching Structure (courtesy of the PDB):

Predicted functions:

Term	Confidence	Notes
DNA primase activity	9.73419395042405	bayes_pls_golite062009
transcription regulator activity	3.46382129825313	bayes_pls_golite062009
DNA-directed RNA polymerase activity	3.39768224850127	bayes_pls_golite062009
RNA polymerase activity	3.39768224850127	bayes_pls_golite062009
nucleotidyltransferase activity	3.28799371541043	bayes_pls_golite062009
binding	2.62275087285714	bayes_pls_golite062009
nucleic acid binding	1.95935440221316	bayes_pls_golite062009
DNA binding	1.92092218509957	bayes_pls_golite062009
transcription elongation regulator activity	1.49626290953998	bayes_pls_golite062009
general RNA polymerase II transcription factor activity	1.23314259311645	bayes_pls_golite062009
RNA polymerase II transcription factor activity	0.730134088263314	bayes_pls_golite062009
catalytic activity	0.434839928397784	bayes_pls_golite062009
protein binding	0.265222284938592	bayes_pls_golite062009
transferase activity, transferring phosphorus-containing groups	0.240481799431949	bayes_pls_golite062009

Predicted Domain #2

Region A:
Residues: [98-158]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 EQGTGKRQDD GLSRDLYQLM EEASRFFQTQ LRQHQDKQKV IDYLAYRGLS DDIVEHFGIG  60
   61 F

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	93.522879
Match:	1dd9A
Description:	DNA primase DnaG catalytic core
Matching Structure (courtesy of the PDB):

Predicted Domain #3

Region A:
Residues: [159-574]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 APDGWDGLLS RYRQNQDAQD KLLTAGMLIS NDSGKRYDRF RDRLMFPIRD RRGRVIGFGG  60
   61 RVLGDGTPKY LNSPETPIFH KGNELYGLYE LKQRHRDPDK VLIVEGYMDV VALAQYGVDY 120
  121 AVASLGTSTT AEQFQLLLRS AKEVICCYDG DRAGNEAAWR ALETALPLLK PGDKVRFMFL 180
  181 PQSEDPDSMV RKIGKDPFEQ LMESAITLPE FLFDTLATKF GTDKGNLAKQ AFGLIEKIQD 240
  241 TVLQNLLLEN LAHKLGMNSS DDMKKKLGFT VKQPKPTAST GLKGRGTPLR LAIALLVQHP 300
  301 ELGVGLSPQP ALNHLQMPGI DLLPLLLALT REHRLNSAQL LEQFRDSPHS GTLHKLAQWD 360
  361 HQVAEENQLE KFKQTLVWLN NQYIEQRYQE LSLKQTHTKE EKIQLQKLIS VMKGLN

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	31.30103
Match:	1q57A
Description:	The Crystal Structure of the Bifunctional Primase-Helicase of Bacteriophage T7
Matching Structure (courtesy of the PDB):

Predicted functions:

Term	Confidence	Notes
DNA primase activity	11.9648478190162	bayes_pls_golite062009
DNA-directed RNA polymerase activity	4.35308216592295	bayes_pls_golite062009
RNA polymerase activity	4.35308216592295	bayes_pls_golite062009
nucleotidyltransferase activity	4.2392655850006	bayes_pls_golite062009
binding	2.46518385502315	bayes_pls_golite062009
catalytic activity	1.39967796334655	bayes_pls_golite062009
transferase activity, transferring phosphorus-containing groups	1.17252562283519	bayes_pls_golite062009
transferase activity	0.605239890876961	bayes_pls_golite062009
protein binding	0.11913220264667	bayes_pls_golite062009

TMHMM	2.0c	PSIPRED	v2.61
SignalP	3.0	COILS	1999
DISOPRED	v0.1	NCBI nr	06/2007
PSI-BLAST	2.2.18	FFAS	ffas03
PDB	06/2007	Pfam	22
HMMER	2.3.2

View Structure Prediction Details

Top Sequence Alignment Hits

Predicted functions:

Predicted functions: