254780469

254780469

zinc-binding protein

GeneID in NCBI database:8209458Locus tag:CLIBASIA_01770
Protein GI in NCBI database:254780469Protein Accession:YP_003064882.1
Gene range:-(392578, 392769)Protein Length:63aa
Gene description:zinc-binding protein
COG prediction:[S] Uncharacterized protein conserved in bacteria
KEGG prediction:zinc-binding protein; K09862 hypothetical protein
SEED prediction:hypothetical protein
Pathway involved in KEGG:not defined
Subsystem involved in SEED:- none -
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--------40--------50--------60---
MQTSDFRSLKSICPECRKGSMVEFYPFCSTQCRSIDLSRWLHGEYVIAAVEDEKSEEEVKDIL
cccccccccccccccccccccccccccHHHHHHHHHHHHHHcccEEEccccccccHHHHHHHc
ccccccccccccccccccccccccccccccccccccHHHHHcccEEEccccccccHHHHHHHc
mqtsdfrslksicpecrkgsmvefypfcstqcrsidlsrwLHGEYVIAAVEDEKSEEEVKDIL
mqtsdfrslksicpecrkgsmVEFYPFCSTQCRSIDLSRWLHGEYVIaavedekseeevkdil
MQTSDFRSLKSICPECRKGSMVEFYPFCSTQCRSIDLSRWLHGEYViaavedekseeevkdiL
***************CRKGSMVEFYPFCSTQCRSIDLSRWLHGEYV*****************
MQTSDFRSLKSICPECRKGSMVEFYPFCSTQCRSIDLSRWLHGEYVIAAVE************
*********KSICPECRKGSMVEFYPFCSTQCRSIDLSRWLHGEYVIAAV****S*EE***IL
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iiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhoooooooooooooooooooooo
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MQTSDFRSLKSICPECRKGSMVEFYPFCSTQCRSIDLSRWLHGEYVIAAVEDEKSEEEVKDIL
MQTSDFRSLKSICPECRKGSMVEFYPFCSTQCRSIDLSRWLHGEYVIAAVEDEKSEEEVKDIL
MQTSDFRSLKSICPECRKGSMVEFYPFCSTQCRSIDLSRWLHGEYVIAAVEDEKSEEEVKDIL

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
Target63 zinc-binding protein [Candidatus Liberibacter asiaticus
31512207562 zinc-binding protein [Candidatus Liberibacter solanacea 1 1e-11
32529192275 hypothetical protein AGROH133_03916 [Agrobacterium sp. 1 1e-08
11063254770 zinc-binding protein [Mesorhizobium sp. BNC1] Length = 1 2e-08
19089028770 hypothetical protein RHECIAT_CH0000661 [Rhizobium etli 1 3e-08
31989932974 hypothetical protein BARCL_1184 [Bartonella clarridgeia 1 4e-08
31978208465 hypothetical protein Mesci_2363 [Mesorhizobium ciceri b 1 4e-08
20954785370 zinc-binding protein [Rhizobium leguminosarum bv. trifo 1 5e-08
12160168560 hypothetical protein BARBAKC583_0213 [Bartonella bacill 1 5e-08
21851474284 zinc-binding protein [Rhizobium etli 8C-3] Length = 84 1 5e-08
8635623870 zinc-binding protein [Rhizobium etli CFN 42] Length = 7 1 7e-08
>gi|315122075|ref|YP_004062564.1| zinc-binding protein [Candidatus Liberibacter solanacearum CLso-ZC1] Length = 62 Back     alignment and organism information
 Score = 73.2 bits (178), Expect = 1e-11,   Method: Compositional matrix adjust.
 Identities = 34/58 (58%), Positives = 41/58 (70%)

Query: 1  MQTSDFRSLKSICPECRKGSMVEFYPFCSTQCRSIDLSRWLHGEYVIAAVEDEKSEEE 58
          MQ SD   ++ +CPECRK S+  FYPFCST+CRSIDLSRWL   YVI   E+E   +E
Sbjct: 1  MQKSDCELVRCLCPECRKDSVSAFYPFCSTRCRSIDLSRWLSDGYVIVRTENEAFNKE 58


Species: Candidatus Liberibacter solanacearum
Genus: Candidatus Liberibacter
Family: Rhizobiaceae
Order: Rhizobiales
Class: Alphaproteobacteria
Phylum: Proteobacteria
Superkingdom: Bacteria
>gi|325291922|ref|YP_004277786.1| hypothetical protein AGROH133_03916 [Agrobacterium sp. H13-3] Length = 75 Back     alignment and organism information
>gi|110632547|ref|YP_672755.1| zinc-binding protein [Mesorhizobium sp. BNC1] Length = 70 Back     alignment and organism information
>gi|190890287|ref|YP_001976829.1| hypothetical protein RHECIAT_CH0000661 [Rhizobium etli CIAT 652] Length = 70 Back     alignment and organism information
>gi|319899329|ref|YP_004159426.1| hypothetical protein BARCL_1184 [Bartonella clarridgeiae 73] Length = 74 Back     alignment and organism information
>gi|319782084|ref|YP_004141560.1| hypothetical protein Mesci_2363 [Mesorhizobium ciceri biovar biserrulae WSM1271] Length = 65 Back     alignment and organism information
>gi|209547853|ref|YP_002279770.1| zinc-binding protein [Rhizobium leguminosarum bv. trifolii WSM2304] Length = 70 Back     alignment and organism information
>gi|121601685|ref|YP_988549.1| hypothetical protein BARBAKC583_0213 [Bartonella bacilliformis KC583] Length = 60 Back     alignment and organism information
>gi|218514742|ref|ZP_03511582.1| zinc-binding protein [Rhizobium etli 8C-3] Length = 84 Back     alignment and organism information
>gi|86356238|ref|YP_468130.1| zinc-binding protein [Rhizobium etli CFN 42] Length = 70 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
Target63 zinc-binding protein [Candidatus Liberibacter asiaticus
PRK0134357 PRK01343, PRK01343, zinc-binding protein; Provisional 4e-13
COG302465 COG3024, COG3024, Uncharacterized protein conserved in 2e-07
pfam0388457 pfam03884, DUF329, Domain of unknown function (DUF329) 7e-08
>gnl|CDD|167213 PRK01343, PRK01343, zinc-binding protein; Provisional Back     alignment and domain information
>gnl|CDD|32840 COG3024, COG3024, Uncharacterized protein conserved in bacteria [Function unknown] Back     alignment and domain information
>gnl|CDD|146490 pfam03884, DUF329, Domain of unknown function (DUF329) Back     alignment and domain information

Conserved Domains in CDD Database Detected by HHsearch

IdentityAlignment graphLength Definition Probability
Target 63 zinc-binding protein [Candidatus Liberibacter asiaticus
PRK0041862 zinc-binding protein; Reviewed 99.87
pfam0388457 DUF329 Domain of unknown function (DUF329). The functio 99.85
PRK0134356 zinc-binding protein; Provisional 99.84
COG302465 Uncharacterized protein conserved in bacteria [Function 99.83
pfam0988959 DUF2116 Uncharacterized protein containing a Zn-ribbon 91.09
COG406864 Uncharacterized protein containing a Zn-ribbon [Functio 90.72
>PRK00418 zinc-binding protein; Reviewed Back     alignment and domain information
>pfam03884 DUF329 Domain of unknown function (DUF329) Back     alignment and domain information
>PRK01343 zinc-binding protein; Provisional Back     alignment and domain information
>COG3024 Uncharacterized protein conserved in bacteria [Function unknown] Back     alignment and domain information
>pfam09889 DUF2116 Uncharacterized protein containing a Zn-ribbon (DUF2116) Back     alignment and domain information
>COG4068 Uncharacterized protein containing a Zn-ribbon [Function unknown] 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
Target63 zinc-binding protein [Candidatus Liberibacter asiaticus
1lv3_A68 Solution Nmr Structure Of Zinc Finger Protein Yacg 9e-12
>gi|24158901|pdb|1LV3|A Chain A, Solution Nmr Structure Of Zinc Finger Protein Yacg From Escherichia Coli. Northeast Structural Genomics Consortium Target Et92 Length = 68 Back     alignment and structure
 Score = 73.3 bits (179), Expect = 9e-12,   Method: Composition-based stats.
 Identities = 17/58 (29%), Positives = 26/58 (44%), Gaps = 4/58 (6%)

Query: 8  SLKSICPECRKGSM----VEFYPFCSTQCRSIDLSRWLHGEYVIAAVEDEKSEEEVKD 61
          ++   CP C K  +      F PFCS +C+ IDL  W   E  I +  D    ++  +
Sbjct: 7  TITVNCPTCGKTVVWGEISPFRPFCSKRCQLIDLGEWAAEEKRIPSSGDLSESDDWSE 64


Homologous Structures in PDB70 Database Detected by RPS-BLAST

IdentityAlignment graphLength Definition E-value
Target63 zinc-binding protein [Candidatus Liberibacter asiaticus
1lv3_A68 Hypothetical protein YACG; zinc finger, rubredoxin knuc 1e-08
>1lv3_A Hypothetical protein YACG; zinc finger, rubredoxin knuckle, C4 tetrahedral Zn+2, antiparallel beta strand and alpha helix, NESG project; NMR {Escherichia coli} SCOP: g.39.1.9 Length = 68 Back     alignment and structure
 Score = 53.4 bits (128), Expect = 1e-08
 Identities = 18/50 (36%), Positives = 24/50 (48%), Gaps = 4/50 (8%)

Query: 13 CPECRK----GSMVEFYPFCSTQCRSIDLSRWLHGEYVIAAVEDEKSEEE 58
          CP C K    G +  F PFCS +C+ IDL  W   E  I +  D    ++
Sbjct: 12 CPTCGKTVVWGEISPFRPFCSKRCQLIDLGEWAAEEKRIPSSGDLSESDD 61


Homologous Structures in PDB70 Database Detected by HHsearch

IdentityAlignment graphLength Definition Probability
Target63 zinc-binding protein [Candidatus Liberibacter asiaticus
1lv3_A68 Hypothetical protein YACG; zinc finger, rubredoxin knuc 99.87
>1lv3_A Hypothetical protein YACG; zinc finger, rubredoxin knuckle, C4 tetrahedral Zn+2, antiparallel beta strand and alpha helix, NESG project; NMR {Escherichia coli} SCOP: g.39.1.9 Back     alignment and structure
Probab=99.87  E-value=1.5e-23  Score=154.17  Aligned_cols=54  Identities=31%  Similarity=0.673  Sum_probs=46.5

Q ss_pred             CCCEECCCCCCCCCC----CCCCCCCHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCHH
Q ss_conf             663044568887877----788687610777443356530898303578888668714
Q gi|254780469|r    6 FRSLKSICPECRKGS----MVEFYPFCSTQCRSIDLSRWLHGEYVIAAVEDEKSEEEV   59 (63)
Q Consensus         6 ~k~~k~~CP~C~k~~----~~~~rPFCS~RC~~iDLg~W~~e~Y~Ip~~~~~~~~~e~   59 (63)
                      -+.++++||+|+|++    +++||||||+||++||||+||+|+|+||+.+.++.+++.
T Consensus         5 ~~~~~v~CP~C~k~v~w~~~~~~rPFCS~RCk~IDLg~W~~e~y~Ip~~~~~~~~~~~   62 (68)
T 1lv3_A            5 SETITVNCPTCGKTVVWGEISPFRPFCSKRCQLIDLGEWAAEEKRIPSSGDLSESDDW   62 (68)
T ss_dssp             CCCCEEECTTTCCEEECSSSSSCCSSSSHHHHHHHHSCSSSSSCCCCSSSCCSSSCSC
T ss_pred             CCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHCCCCHHHHHCCCCCCCCCCCCCCCCCC
T ss_conf             8885214889998444577787687254766105087886678015798878766575




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

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

IdentityAlignment graphLength Definition E-value
Target 63 zinc-binding protein [Candidatus Liberibacter asiaticus
d1lv3a_65 g.39.1.9 (A:) Hypothetical zinc finger protein YacG {Es 6e-09
>d1lv3a_ g.39.1.9 (A:) Hypothetical zinc finger protein YacG {Escherichia coli [TaxId: 562]} Length = 65 Back     information, alignment and structure

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: Hypothetical zinc finger protein YacG
domain: Hypothetical zinc finger protein YacG
species: Escherichia coli [TaxId: 562]
 Score = 53.4 bits (128), Expect = 6e-09
 Identities = 18/50 (36%), Positives = 24/50 (48%), Gaps = 4/50 (8%)

Query: 13 CPECRK----GSMVEFYPFCSTQCRSIDLSRWLHGEYVIAAVEDEKSEEE 58
          CP C K    G +  F PFCS +C+ IDL  W   E  I +  D    ++
Sbjct: 9  CPTCGKTVVWGEISPFRPFCSKRCQLIDLGEWAAEEKRIPSSGDLSESDD 58


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

IdentityAlignment graphLength Definition Probability
Target63 zinc-binding protein [Candidatus Liberibacter asiaticus
d1lv3a_65 Hypothetical zinc finger protein YacG {Escherichia coli 99.87
>d1lv3a_ g.39.1.9 (A:) Hypothetical zinc finger protein YacG {Escherichia coli [TaxId: 562]} Back     information, alignment and structure
class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: Hypothetical zinc finger protein YacG
domain: Hypothetical zinc finger protein YacG
species: Escherichia coli [TaxId: 562]
Probab=99.87  E-value=9.6e-24  Score=153.88  Aligned_cols=52  Identities=33%  Similarity=0.733  Sum_probs=45.4

Q ss_pred             CCEECCCCCCCCCC----CCCCCCCHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCH
Q ss_conf             63044568887877----78868761077744335653089830357888866871
Q gi|254780469|r    7 RSLKSICPECRKGS----MVEFYPFCSTQCRSIDLSRWLHGEYVIAAVEDEKSEEE   58 (63)
Q Consensus         7 k~~k~~CP~C~k~~----~~~~rPFCS~RC~~iDLg~W~~e~Y~Ip~~~~~~~~~e   58 (63)
                      +.++++||+|+|++    +++||||||+||++||||+||+|+|+||+.+.++.+++
T Consensus         3 ~~~~v~CP~C~k~~~w~~~~~~rPFCS~RCk~IDLg~W~~e~y~Ip~~~~~~~~~~   58 (65)
T d1lv3a_           3 ETITVNCPTCGKTVVWGEISPFRPFCSKRCQLIDLGEWAAEEKRIPSSGDLSESDD   58 (65)
T ss_dssp             CCCEEECTTTCCEEECSSSSSCCSSSSHHHHHHHHSCSSSSSCCCCSSSCCSSSCS
T ss_pred             CCCEEECCCCCCCCCCCCCCCCCCCHHHHHHHCCHHHHHCCCCCCCCCCCCCCCCC
T ss_conf             87350488999834457778858725476600508788667812578887776667



Homologous Domains in MMDB70 Database Detected by RPS-BLAST

IdentityAlignment graphLength Definition E-value
Target 63 zinc-binding protein [Candidatus Liberibacter asia
1lv3_A_68 (A:) Hypothetical protein YACG; zinc finger, rubre 4e-09
>1lv3_A (A:) Hypothetical protein YACG; zinc finger, rubredoxin knuckle, C4 tetrahedral Zn+2, antiparallel beta strand and alpha helix, NESG project; NMR {Escherichia coli}Length = 68 Back     alignment and structure
 Score = 54.9 bits (132), Expect = 4e-09
 Identities = 18/50 (36%), Positives = 24/50 (48%), Gaps = 4/50 (8%)

Query: 13 CPECRK----GSMVEFYPFCSTQCRSIDLSRWLHGEYVIAAVEDEKSEEE 58
          CP C K    G +  F PFCS +C+ IDL  W   E  I +  D    ++
Sbjct: 12 CPTCGKTVVWGEISPFRPFCSKRCQLIDLGEWAAEEKRIPSSGDLSESDD 61


Homologous Domains in MMDB70 Database Detected by HHsearch

IdentityAlignment graphLength Definition Probability
Target63 zinc-binding protein [Candidatus Liberibacter asiaticus
1lv3_A_68 Hypothetical protein YACG; zinc finger, rubredoxin 99.87
>1lv3_A (A:) Hypothetical protein YACG; zinc finger, rubredoxin knuckle, C4 tetrahedral Zn+2, antiparallel beta strand and alpha helix, NESG project; NMR {Escherichia coli} Back     alignment and structure
Probab=99.87  E-value=2.2e-23  Score=154.03  Aligned_cols=57  Identities=30%  Similarity=0.628  Sum_probs=48.2

Q ss_pred             CCCCCCEECCCCCCCCCC----CCCCCCCHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCHH
Q ss_conf             777663044568887877----788687610777443356530898303578888668714
Q gi|254780469|r    3 TSDFRSLKSICPECRKGS----MVEFYPFCSTQCRSIDLSRWLHGEYVIAAVEDEKSEEEV   59 (63)
Q Consensus         3 ~~~~k~~k~~CP~C~k~~----~~~~rPFCS~RC~~iDLg~W~~e~Y~Ip~~~~~~~~~e~   59 (63)
                      ++--+.++++||+|||++    +++||||||+|||+||||+||+|+|+||+.+.++.+++.
T Consensus         2 ~~m~~~~~v~CP~C~k~~~w~~~~~~rPFCS~RCk~IDLg~W~~e~y~Ip~~~~~~~~~~~   62 (68)
T 1lv3_A            2 SHMSETITVNCPTCGKTVVWGEISPFRPFCSKRCQLIDLGEWAAEEKRIPSSGDLSESDDW   62 (68)
T ss_dssp             --CCCCCEEECTTTCCEEECSSSSSCCSSSSHHHHHHHHSCSSSSSCCCCSSSCCSSSCSC
T ss_pred             CCCCCCCEEECCCCCCCCCCCCCCCCCCCHHHHHHHCCHHHHHCCCCCCCCCCCCCCCCCC
T ss_conf             8678885205889998444576687587253766105087886678015798888765565