YRC Public Data Repository - Protein Structure Prediction

Protein:	gi\|29139464, gi\|...
Organism:	Salmonella enterica subsp. enterica serovar Typhi str. Ty2
Length:	732 amino acids
Reference:	Drew K, et al. (2011) The proteome folding project: Proteome-scale prediction of structure and function. Genome Res. 2011 Sep 16

[What does the above image mean?]

[Show Ginzu Version Information]

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|29139464, gi|....

Description	E-value	Query Range	Subject Range
gi\|205329942, gi... - gi\|205329942\|gb\|EDZ16706.1\| primosomal protein N' [Salmonella enterica subsp. enterica serovar 4,[5]... lcl\|NC_016856.1_... - [gene=priA] [protein=primosome assembly protein PriA] [protein_id=YP_005240376.1] [location=compleme... gi\|16767361, gi\|... - gi\|16767361\|ref\|NP_462976.1\| primosome assembly protein PriA [Salmonella typhimurium LT2], gi\|164226...	0.0	[1..732]	[1..732]
gi\|197364866, gi... - gi\|197364866\|ref\|YP_002144503.1\| primosome assembly protein PriA [Salmonella enterica subsp. enteric... gi\|56130196, gi\|... - gi\|56415939\|ref\|YP_153014.1\| primosome assembly protein PriA [Salmonella enterica subsp. enterica se...	0.0	[1..732]	[1..732]
gi\|62182554, gi\|... - gi\|62182554\|ref\|YP_218971.1\| primosome assembly protein PriA [Salmonella enterica subsp. enterica se...	0.0	[1..732]	[1..732]
gi\|81243037, gi\|... - gi\|82778889\|ref\|YP_405238.1\| primosome assembly protein PriA [Shigella dysenteriae Sd197], gi\|812430...	0.0	[1..732]	[1..732]
gi\|30064772, gi\|... - gi\|30064772\|ref\|NP_838943.1\| primosome assembly protein PriA [Shigella flexneri 2a str. 2457T], gi\|3... gi\|110617344, gi... - gi\|110807796\|ref\|YP_691316.1\| primosome assembly protein PriA [Shigella flexneri 5 str. 8401], gi\|11... gi\|56384037, gi\|... - gi\|56480486\|ref\|NP_709739.2\| primosome assembly protein PriA [Shigella flexneri 2a str. 301], gi\|563...	0.0	[1..732]	[1..732]
gi\|238903001, gi... - gi\|238903001\|ref\|YP_002928797.1\| Primosome factor n' (replication factor Y) [Escherichia coli BW2952... gi\|242379471, gi... - gi\|251787198\|ref\|YP_003001502.1\| hypothetical protein B21_03769 [Escherichia coli BL21], gi\|24237947... gi\|83586221, gi\|... - gi\|83586221\|ref\|ZP_00924857.1\| COG1198: Primosomal protein N' (replication factor Y) - superfamily I... gi\|254290636, gi... - gi\|254290636\|ref\|YP_003056384.1\| primosome assembly protein PriA [Escherichia coli BL21(DE3)], gi\|25... gi\|253975786, gi... - gi\|254163885\|ref\|YP_003046993.1\| primosome assembly protein PriA [Escherichia coli B str. REL606], g... PRIA_ECOLI - Primosomal protein N' (EC 3.6.1.-) (ATP-dependent helicase priA) (Replication factor Y) - Escherichi... gi\|89110094, gi\|... - gi\|89110094\|ref\|AP_003874.1\| primosome factor n' [Escherichia coli str. K-12 substr. W3110], gi\|8567... gi\|169891240, gi... - gi\|170083405\|ref\|YP_001732725.1\| primosome factor n' (replication factor Y) [Escherichia coli str. K... EG10763 - Primosome factor n' (replication factor Y) / Primosome factor Y, also called protein n'; ATP-depende... EG10763 - Primosome factor n' (replication factor Y) / Primosome factor Y, also called protein n'; ATP-depende...	0.0	[1..732]	[1..732]
gi\|194418498, gi... - gi\|83569799\|ref\|ZP_00921248.1\| COG1198: Primosomal protein N' (replication factor Y) - superfamily I...	0.0	[1..732]	[1..732]
gi\|216620 - gi\|216620\|dbj\|BAA00491.1\| PriA [Escherichia coli]	0.0	[1..732]	[1..732]
gi\|187429604, gi... - gi\|75176678\|ref\|ZP_00696806.1\| COG1198: Primosomal protein N' (replication factor Y) - superfamily I...	0.0	[1..732]	[1..732]

Back

Predicted Domain #1

Region A:
Residues: [1-134]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 MSVAHVALPV PLPRTFDYLL PEGGVAKAGC RVRVPFGKQQ ERVGIVVSVS DHSELPLDEL  60
   61 KSVIEILDNE PIFSPSIWRL LLWAADYYHH PLGDVLFHAL PVLLRQGKPA SNAPLWYWFA 120
  121 TEEGQAVDIN SLKR

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	22.30103
Match:	2d7eA
Description:	No description for 2d7eA was found.

Predicted Domain #2

Region A:
Residues: [135-670]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 SAKQQQALAA LRQGKIWRYQ VAELDFTDAT LQTLRRKGLC ELASETPAFT DWREHYAVAG  60
   61 ERLRLNTEQA TAVGAIHSAS DGFSAWLLAG VTGSGKTEVY LSVLENVLAQ GKQALVMVPE 120
  121 IGLTPQTIAR FRERFNTPVE VLHSGLNDSE RLSAWLKAKN GEAAIVIGTR SSLFTPFKNL 180
  181 GVIVIDEEHD SSYKQQEGWR YHARDLAVYR AHSEQIPIIL GSATPALETL CNVRQKKYRM 240
  241 LRLTRRAGNA RPALQHVLDL KGQRLQAGLA PALIARMRQH LQADNQVILF LNRRGFAPAL 300
  301 LCHDCGWIAE CPRCDHYYTL HQAQHHLRCH HCDSQRPVPR QCPSCGSTHM LPVGLGTEQL 360
  361 EQVLAPFFPG VPISRIDRDT TSRKGALEQH LAEVHRGGAR ILIGTQMLAK GHHFPDVTLV 420
  421 ALLDVDGALF SADFRSAERF AQLYTQVSGR AGRAGKQGEV VLQTHHPEHP LLQTLLYKGY 480
  481 DAFAEQALAE RQTLQLPPWT SHVIIRAEDH NNQQAPVFLQ QLRNVIQASP LSDDKL

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	10.30103
Match:	1gl9B
Description:	Helicase-like "domain" of reverse gyrase; Topoisomerase "domain" of reverse gyrase
Matching Structure (courtesy of the PDB):

Predicted functions:

Term	Confidence	Notes
DNA clamp loader activity	4.91429252297969	bayes_pls_golite062009
protein-DNA loading ATPase activity	4.80695929076807	bayes_pls_golite062009
binding	3.20817609308002	bayes_pls_golite062009
DNA-dependent ATPase activity	2.72462789867829	bayes_pls_golite062009
DNA helicase activity	2.2817164193758	bayes_pls_golite062009
nucleic acid binding	2.2502397577006	bayes_pls_golite062009
transcription regulator activity	2.19474222771129	bayes_pls_golite062009
pyrophosphatase activity	2.13284212711072	bayes_pls_golite062009
DNA binding	2.03222535159295	bayes_pls_golite062009
ATP-dependent DNA helicase activity	1.88455339138556	bayes_pls_golite062009
helicase activity	1.70242731830224	bayes_pls_golite062009
purine NTP-dependent helicase activity	1.19311444180077	bayes_pls_golite062009
ATP-dependent helicase activity	1.19311444180077	bayes_pls_golite062009
catalytic activity	1.00104173493322	bayes_pls_golite062009
DNA-directed DNA polymerase activity	0.971476020912368	bayes_pls_golite062009
DNA polymerase activity	0.928091843881235	bayes_pls_golite062009
transcription factor activity	0.802855430913287	bayes_pls_golite062009
structure-specific DNA binding	0.782430219754236	bayes_pls_golite062009
double-stranded DNA binding	0.6071273686445	bayes_pls_golite062009
RNA helicase activity	0.18426050934025	bayes_pls_golite062009
nucleoside-triphosphatase activity	0.147579541298736	bayes_pls_golite062009
RNA-dependent ATPase activity	0.14606996093053	bayes_pls_golite062009
ATP-dependent RNA helicase activity	0.13050483816765	bayes_pls_golite062009
nucleotide binding	0.114848452385726	bayes_pls_golite062009
hydrolase activity, acting on acid anhydrides	0.113504049290503	bayes_pls_golite062009
hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides	0.111293884322157	bayes_pls_golite062009
purine nucleotide binding	0.10713474095071	bayes_pls_golite062009
purine ribonucleotide binding	0.0916519414118148	bayes_pls_golite062009
ribonucleotide binding	0.0915913646217636	bayes_pls_golite062009
structural constituent of ribosome	0.089234257580272	bayes_pls_golite062009
3'-5' DNA helicase activity	0.0769112340058804	bayes_pls_golite062009

Predicted Domain #3

Region A:
Residues: [671-732]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 WILGPVPALA PKRGGRYRWQ ILLQHPSRIL LQHIISGTLA LINTLPEARK VKWVLDVDPI  60
   61 EG

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	4.0
Match:	2qsrA
Description:	No description for 2qsrA was found.

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: