254780304

254780304

DNA protecting protein DprA

GeneID in NCBI database:8209286Locus tag:CLIBASIA_00945
Protein GI in NCBI database:254780304Protein Accession:YP_003064717.1
Gene range:+(194079, 194183)Protein Length:34aa
Gene description:DNA protecting protein DprA
COG prediction:[L] [U] Predicted Rossmann fold nucleotide-binding protein involved in DNA uptake
KEGG prediction:DNA protecting protein DprA
SEED prediction:not defined as a protein in SEED
Pathway involved in KEGG:not defined
Subsystem involved in KEGG:not defined
sequencesequence profile

Prediction of Local Sequence Properties

SourceSummaryResult
scaler
NCBI Databasesequence
PSIPREDsecondary structure
SSPROsecondary structure
DISEMBLcoil and loop
DISEMBLflexible loop
SEGlow complexity
DISOPREDdisordered
DISEMBLmissing residues
DISPROdisordered
TMHMMnone TM-Helix
TOPPREDnone TM-Helix
HMMTOPnone TM-Helix
MEMSATnone TM-Helix
MEMSAT_SVMnone TM-Helix
PHOBIUSnone TM-Helix
SignalP_HMMno
SignalP_NNno
COILScoiled coil
70% MSAconservation map
90% MSAconservation map
  
--------10--------20--------30----
MAGGLDCLYPPENRNLLEEIWDNGGIAISEIPFG
cccccccccccHHHHHHHHHHHcccccHHccccc
cccccccccccHHccHHHHHHccccEEEEEcccc
maggldclyppenrNLLEEIWDnggiaiseipfg
maggldclYPPENRNLLEEIWDNGGIAISEIPFG
MAGGLDCLYPPENRNLLEEIWDNGGIAISEIPFG
**GGLDCLYPPENRNLLEEIWDNGGIAISEIPFG
MAGGLDCLYPPENRNLLEEIWDNGGIAISEIPFG
***GLDCLYPPENRNLLEEIWDNGGIAISEIPFG
oooooooooooooooooooooooooooooooooo
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
oooooooooooooooooooooooooooooooooo
iiiiiiiihhhhhhhhhhhhhhhhhhhooooooo
iiiiiiiiiiiiiihhhhhhhhhhhhhhhhoooo
oooooooooooooooooooooooooooooooooo
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
MAGGLDCLYPPENRNLLEEIWDNGGIAISEIPFG
MAGGLDCLYPPENRNLLEEIWDNGGIAISEIPFG
MAGGLDCLYPPENRNLLEEIWDNGGIAISEIPFG

Close Homologs Detected by BLAST or PSI-BLAST

Homolog within the Genome Detected by BLAST

No hits with e-value below 0.05

Close Homologs Detected BLAST or PSI-BLAST in the First 2 Iterations

IdentityAlignment graphLength Definition Round E-value
Target34 DNA protecting protein DprA [Candidatus Liberibacter as
315122272298 hypothetical protein CKC_02620 [Candidatus Liberibacter 1 6e-08
222085614 383 DNA protecting protein DprA [Agrobacterium radiobacter 1 4e-06
222148310 383 DNA protecting protein DprA [Agrobacterium vitis S4] Le 1 1e-05
150396156 383 DNA protecting protein DprA [Sinorhizobium medicae WSM4 1 1e-04
319405728 383 DNA processing chain A [Bartonella sp. AR 15-3] Length 1 2e-04
49475582 410 DNA processing chain A [Bartonella henselae str. Housto 1 2e-04
319898957 383 DNA processing chain A [Bartonella clarridgeiae 73] Len 1 3e-04
319408534 404 DNA processing chain A [Bartonella schoenbuchensis R1] 1 4e-04
319407290 383 DNA processing chain A [Bartonella sp. 1-1C] Length = 3 1 4e-04
319404285 383 DNA processing chain A [Bartonella rochalimae ATCC BAA- 1 5e-04
>gi|315122272|ref|YP_004062761.1| hypothetical protein CKC_02620 [Candidatus Liberibacter solanacearum CLso-ZC1] Length = 298 Back     alignment and organism information
 Score = 60.8 bits (146), Expect = 6e-08,   Method: Compositional matrix adjust.
 Identities = 29/34 (85%), Positives = 31/34 (91%), Gaps = 1/34 (2%)

Query: 1   MAGGLDCLYPPENRNLLEEIWDNGGIAISEIPFG 34
           MAGGLDCLYPPENR+LLEEIW   GIAISE+PFG
Sbjct: 179 MAGGLDCLYPPENRSLLEEIWHE-GIAISEMPFG 211


Species: Candidatus Liberibacter solanacearum
Genus: Candidatus Liberibacter
Family: Rhizobiaceae
Order: Rhizobiales
Class: Alphaproteobacteria
Phylum: Proteobacteria
Superkingdom: Bacteria
>gi|222085614|ref|YP_002544144.1| DNA protecting protein DprA [Agrobacterium radiobacter K84] Length = 383 Back     alignment and organism information
>gi|222148310|ref|YP_002549267.1| DNA protecting protein DprA [Agrobacterium vitis S4] Length = 383 Back     alignment and organism information
>gi|150396156|ref|YP_001326623.1| DNA protecting protein DprA [Sinorhizobium medicae WSM419] Length = 383 Back     alignment and organism information
>gi|319405728|emb|CBI79351.1| DNA processing chain A [Bartonella sp. AR 15-3] Length = 383 Back     alignment and organism information
>gi|49475582|ref|YP_033623.1| DNA processing chain A [Bartonella henselae str. Houston-1] Length = 410 Back     alignment and organism information
>gi|319898957|ref|YP_004159050.1| DNA processing chain A [Bartonella clarridgeiae 73] Length = 383 Back     alignment and organism information
>gi|319408534|emb|CBI82187.1| DNA processing chain A [Bartonella schoenbuchensis R1] Length = 404 Back     alignment and organism information
>gi|319407290|emb|CBI80931.1| DNA processing chain A [Bartonella sp. 1-1C] Length = 383 Back     alignment and organism information
>gi|319404285|emb|CBI77878.1| DNA processing chain A [Bartonella rochalimae ATCC BAA-1498] Length = 383 Back     alignment and organism information

Conserved Domains in CDD Database
Detected by RPS-BLAST and HHsearch

Conserved Domains in CDD Database Detected by RPS-BLAST

IdentityAlignment graphLength Definition E-value
Target34 DNA protecting protein DprA [Candidatus Liberibacter as
COG0758 350 COG0758, Smf, Predicted Rossmann fold nucleotide-bindin 5e-04
TIGR00732220 TIGR00732, dprA, DNA protecting protein DprA 0.001
pfam02481210 pfam02481, DNA_processg_A, DNA recombination-mediator p 2e-07
>gnl|CDD|31101 COG0758, Smf, Predicted Rossmann fold nucleotide-binding protein involved in DNA uptake [DNA replication, recombination, and repair / Intracellular trafficking and secretion] Back     alignment and domain information
>gnl|CDD|129815 TIGR00732, dprA, DNA protecting protein DprA Back     alignment and domain information
>gnl|CDD|145559 pfam02481, DNA_processg_A, DNA recombination-mediator protein A Back     alignment and domain information

Conserved Domains in CDD Database Detected by HHsearch

IdentityAlignment graphLength Definition Probability
Target 34 DNA protecting protein DprA [Candidatus Liberibacter as
PRK10736 364 hypothetical protein; Provisional 99.44
TIGR00732238 dprA DNA protecting protein DprA; InterPro: IPR003488 T 99.44
pfam02481210 DNA_processg_A DNA recombination-mediator protein A. Th 99.18
COG0758 350 Smf Predicted Rossmann fold nucleotide-binding protein 99.17
>PRK10736 hypothetical protein; Provisional Back     alignment and domain information
>TIGR00732 dprA DNA protecting protein DprA; InterPro: IPR003488 The SMF family (DNA processing chain A, dprA) are a group of bacterial proteins Back     alignment and domain information
>pfam02481 DNA_processg_A DNA recombination-mediator protein A Back     alignment and domain information
>COG0758 Smf Predicted Rossmann fold nucleotide-binding protein involved in DNA uptake [DNA replication, recombination, and repair / Intracellular trafficking and secretion] Back     alignment and domain information

Homologous Structures in PDB Database
Detected by PSI-BLAST, RPS-BLAST and HHsearch

Homologous Structures Detected by PSI-BLAST against Nonredundant Database

IdentityAlignment graphLength Definition E-value
Target34 DNA protecting protein DprA [Candidatus Liberibacter as
3maj_A 382 Crystal Structure Of Putative Dna Processing Protei 8e-06
>gi|295982522|pdb|3MAJ|A Chain A, Crystal Structure Of Putative Dna Processing Protein Dpra Fr Rhodopseudomonas Palustris Cga009 Length = 382 Back     alignment and structure
 Score = 53.8 bits (130), Expect = 8e-06,   Method: Composition-based stats.
 Identities = 17/34 (50%), Positives = 22/34 (64%)

Query: 1   MAGGLDCLYPPENRNLLEEIWDNGGIAISEIPFG 34
           +AGG D +YP E+ +LL +I    G AISE P G
Sbjct: 185 LAGGHDKIYPAEHEDLLLDIIQTRGAAISEXPLG 218


Homologous Structures in PDB70 Database Detected by RPS-BLAST

No hit with e-value below 0.005

Homologous Structures in PDB70 Database Detected by HHsearch

IdentityAlignment graphLength Definition Probability
Target34 DNA protecting protein DprA [Candidatus Liberibacter as
3maj_A 382 DNA processing chain A; MCSG, PSI-2, structural genomic 99.19
>3maj_A DNA processing chain A; MCSG, PSI-2, structural genomics, protein structure initiati midwest center for structural genomics; HET: DNA; 2.05A {Rhodopseudomonas palustris} Back     alignment and structure
Probab=99.19  E-value=8.4e-12  Score=77.65  Aligned_cols=34  Identities=50%  Similarity=0.897  Sum_probs=32.8

Q ss_pred             CCCCCCCCCCHHHHHHHHHHHHHCCEEEEECCCC
Q ss_conf             9873881089899999999998399599706998
Q gi|254780304|r    1 MAGGLDCLYPPENRNLLEEIWDNGGIAISEIPFG   34 (34)
Q Consensus         1 l~~GiD~iYP~~n~~L~~~I~~~gG~liSE~P~G   34 (34)
                      ||+|+|++||++|++|+++|++++|++|||||+|
T Consensus       185 l~~Gld~~yP~~n~~l~~~ii~~~GllISE~pp~  218 (382)
T 3maj_A          185 LAGGHDKIYPAEHEDLLLDIIQTRGAAISEMPLG  218 (382)
T ss_dssp             CSSCTTSCSSGGGHHHHHHHHHTTCEEEECSCTT
T ss_pred             ECCCCCCCCCCCCHHHHHHHHHCCCEEEEECCCC
T ss_conf             5036773157520899999997097798716988




Homologous Domains in SCOP and MMDB Database
Detected by RPS-BLAST and HHsearch

Homologous Domains in SCOP70 (Version1.75) Database Detected by RPS-BLAST

No hit with e-value below 0.005

Homologous Domains in SCOP70 (Version 1.75) Database Detected by HHsearch

No hit with probability above 90.00

Homologous Domains in MMDB70 Database Detected by RPS-BLAST

No hit with e-value below 0.005

Homologous Domains in MMDB70 Database Detected by HHsearch

IdentityAlignment graphLength Definition Probability
Target34 DNA protecting protein DprA [Candidatus Liberibacter as
2nx2_A_181 Hypothetical protein YPSA; structural genomics, un 96.62
>2nx2_A (A:) Hypothetical protein YPSA; structural genomics, unknown function, PSI, protein structure initiative; 2.00A {Bacillus subtilis} Back     alignment and structure
Probab=96.62  E-value=0.0025  Score=37.59  Aligned_cols=31  Identities=6%  Similarity=0.004  Sum_probs=28.2

Q ss_pred             CCCCCCCCHHHHHHHHHHHHHCCEEEEECCCC
Q ss_conf             73881089899999999998399599706998
Q gi|254780304|r    3 GGLDCLYPPENRNLLEEIWDNGGIAISEIPFG   34 (34)
Q Consensus         3 ~GiD~iYP~~n~~L~~~I~~~gG~liSE~P~G   34 (34)
                      .+++..||++|+.++++|+++ |.++||++++
T Consensus        82 ~~~~~~~~~~~r~~~~~i~~~-~~~vs~~~~~  112 (181)
T 2nx2_A           82 YEQEKNWKEPNKEQYEAVLAQ-ADYEASLTHR  112 (181)
T ss_dssp             BCTTTTSCHHHHHHHHHHHHH-CSEEEESSSS
T ss_pred             HHHHCCCCHHHHHHHHHHHHH-CCEEEEECCC
T ss_conf             313007998999999999973-8878971558