254781079

254781079

diguanylate cyclase

GeneID in NCBI database:8210103Locus tag:CLIBASIA_04905
Protein GI in NCBI database:254781079Protein Accession:YP_003065492.1
Gene range:+(1080234, 1081034)Protein Length:266aa
Gene description:diguanylate cyclase
COG prediction:[T] FOG: GGDEF domain
KEGG prediction:diguanylate cyclase
SEED prediction:diguanylate cyclase (GGDEF domain)
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
TMHMM2 TM-Helix
TOPPREDnone TM-Helix
HMMTOP5 TM-Helix
MEMSAT2 TM-Helix
MEMSAT_SVM2 TM-Helix
PHOBIUS2 TM-Helix
SignalP_HMMno
SignalP_NNno
COILScoiled coil
70% MSAconservation map
90% MSAconservation map
  
--------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------
MTRSLKDFLSIWLCHEKNLESFSPHTFMIYFSIFFSIFIATVIFIANIFLFYIGLTPFYGLEYILVENLSLVIISITISLLLGYISGSILKELFISYNRISQLSRIDCLSGLLNHSAFISSLGSYNEKLSIVFFDIDYFKQINDNFGHPVGDKVIAFLSDQLVVVFGTPMFVGRLGGEEFAAAALGSSEQEAAILANDLRKIIENSQINISSGPSIHITISAGIAERCHKEPISTIIYRADQALYVAKKSGRNRVVCFSDIENNTC
ccHHHHHHHHHHHHHHHHHHHcccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHccccccccHHHHHHHHHHHHccccEEEEEEEcccHHHHHHHccHHHHHHHHHHHHHHHHHccccccEEEEEcccEEEEEEccccHHHHHHHHHHHHHHHHHcccccccccEEEEEEEEEEEcccccccHHHHHHHHHHHHHHHHHccccEEEEccHHHHHcc
ccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccccccccccEEEccEEEEEEccccEEEEEEEEEHHHHHHHHHHHHHHHHHHcccccccccHHHHHHHHHHccccEEEEEEEcHHcccccccccccHHHHHHHHHHHHHHHHHccccEEEEccccEEEEEEccccHHHHHHHHHHHHHHHccccEEEEcccEEEEEEEEEEEEccccccHHHHHHHHHHHHHHHHHcccccEEEEcHHHcccc
MTRSLKDFLSIWLCHeknlesfsphtfMIYFSIFFSIFIATVIFIANIFLFYIGLTPFYGLEYILVENLSLVIISITISLLLGYISGSILKELFISYNRISQLSRIDCLSGLLNHSAFISSlgsyneklsivffdidyfkqindnfghpvgDKVIAFLSDQLVVVfgtpmfvgrlggEEFAAAALGSSEQEAAILANDLRKIIEnsqinissgpsiHITISAGIaerchkepistiIYRADQALYVAkksgrnrvvcfsdienntc
MTRSLKDFLSIWLCHEKNLESFSPHTFMIYFSIFFSIFIATVIFIANIFLFYIGLTPFYGLEYILVENLSLVIISITISLLLGYISGSILKELFISYNRISQLSRIDCLSGLLNHSAFISSLGSYNEKLSIVFFDIDYFKQINDNFGHPVGDKVIAFLSDQLVVVFGTPMFVGRLGGEEFAAAALGSSEQEAAILANDLRKIIENsqinissgpsIHITISAGIAERCHKEPISTIIYRADQALYVAKksgrnrvvcfsdienntc
MTRSLKDFLSIWLCHEKNLESFSPHtfmiyfsiffsifiatvifiaNIFLFYIGLTPFYGLEYILVENlslviisitislllgyisgsilKELFISYNRISQLSRIDCLSGLLNHSAFISSLGSYNEKLSIVFFDIDYFKQINDNFGHPVGDKVIAFLSDQLVVVFGTPMFVgrlggeefaaaalgSSEQEAAILANDLRKIIENSQINISSGPSIHITISAGIAERCHKEPISTIIYRADQALYVAKKSGRNRVVCFSDIENNTC
*TRSLKDFLSIWLCHEKNLESFSPHTFMIYFSIFFSIFIATVIFIANIFLFYIGLTPFYGLEYILVENLSLVIISITISLLLGYISGSILKELFISYNRISQLSRIDCLSGLLNHSAFISSLGSYNEKLSIVFFDIDYFKQINDNFGHPVGDKVIAFLSDQLVVVFGTPMFVGRLGGEEFAAAALGSSEQEAAILANDLRKIIENSQINISSGPSIHITISAGIAERCHKEPISTIIYRADQALYVAKKSGRNRVVCFSD*E****
MTRSLKDFLSIWLCHEKNLESFSPHTFMIYFSIFFSIFIATVIFIANIFLFYIGLTPFYGLEYILVENLSLVIISITISLLLGYISGSILKELFISYNRISQLSRIDCLSGLLNHSAFISSLGSYNEKLSIVFFDIDYFKQINDNFGHPVGDKVIAFLSDQLVVVFGTPMFVGRLGGEEFAAAALGSSEQEAAILANDLRKIIENSQINISSGPSIHITISAGIAERCHKEPISTIIYRADQALYVAKKSGRNRVVCFSDIENNTC
**RSLKDFLSIWLCHEKNLESFSPHTFMIYFSIFFSIFIATVIFIANIFLFYIGLTPFYGLEYILVENLSLVIISITISLLLGYISGSILKELFISYNRISQLSRIDCLSGLLNHSAFISSLGSYNEKLSIVFFDIDYFKQINDNFGHPVGDKVIAFLSDQLVVVFGTPMFVGRLGGEEFAAAALGSSEQEAAILANDLRKIIENSQINISSGPSIHITISAGIAERCHKEPISTIIYRADQALYVAKKSGRNRVVCFSDI****C
ooooooooooooooooooooooooooooooooHHHHHHHHHHHHHHHHHHHHHHHiiiiiiiiiiiiHHHHHHHHHHHHHHHHHHHHHHHoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
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iiiiiiiiiiiiiiiiiiiiiiiiiiHHHHHHHHHHHHHHHHHHHHHHHHHooooooooooooooooooooHHHHHHHHHHHHHHHHHHiiiiiiiiiiiiiiiiHHHHHHHHHHHHHHHHHHooooooooooooooooooooooooooooooHHHHHHHHHHHHHHHHHHiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiHHHHHHHHHHHHHHHHHHooooooooooooooooooooooooooooooooooooooooo
iiiiiiiiiiiiiiiiiiiiiiiiiiiiHHHHHHHHHHHHHHHHHHHHHHooooooooooooooooHHHHHHHHHHHHHHHHHHHHHHHHiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSiiHHHHHHHHHHHHHHHHHoooooooooHHHHHHHHHHHHHHHHHHHHiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
iiiiiiiiiiiiiiiiiiiiiiiiiiHHHHHHHHHHHHHHHHHHHHHHHHHHHoooooooooooHHHHHHHHHHHHHHHHHHHHHiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
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MTRSLKDFLSIWLCHEKNLESFSPHTFMIYFSIFFSIFIATVIFIANIFLFYIGLTPFYGLEYILVENLSLVIISITISLLLGYISGSILKELFISYNRISQLSRIDCLSGLLNHSAFISSLGSYNEKLSIVFFDIDYFKQINDNFGHPVGDKVIAFLSDQLVVVFGTPMFVGRLGGEEFAAAALGSSEQEAAILANDLRKIIENSQINISSGPSIHITISAGIAERCHKEPISTIIYRADQALYVAKKSGRNRVVCFSDIENNTC
MTRSLKDFLSIWLCHEKNLESFSPHTFMIYFSIFFSIFIATVIFIANIFLFYIGLTPFYGLEYILVENLSLVIISITISLLLGYISGSILKELFISYNRISQLSRIDCLSGLLNHSAFISSLGSYNEKLSIVFFDIDYFKQINDNFGHPVGDKVIAFLSDQLVVVFGTPMFVGRLGGEEFAAAALGSSEQEAAILANDLRKIIENSQINISSGPSIHITISAGIAERCHKEPISTIIYRADQALYVAKKSGRNRVVCFSDIENNTC
MTRSLKDFLSIWLCHEKNLESFSPHTFMIYFSIFFSIFIATVIFIANIFLFYIGLTPFYGLEYILVENLSLVIISITISLLLGYISGSILKELFISYNRISQLSRIDCLSGLLNHSAFISSLGSYNEKLSIVFFDIDYFKQINDNFGHPVGDKVIAFLSDQLVVVFGTPMFVGRLGGEEFAAAALGSSEQEAAILANDLRKIIENSQINISSGPSIHITISAGIAERCHKEPISTIIYRADQALYVAKKSGRNRVVCFSDIENNTC

Close Homologs Detected by BLAST or PSI-BLAST

Homolog within the Genome Detected by BLAST

IdentityAlignment graphLength Definition E-value
Target266 diguanylate cyclase [Candidatus Liberibacter asiaticus
254780468 963 sensory box/GGDEF family protein [Candidatus Liber 3e-09
>gi|254780468|ref|YP_003064881.1| sensory box/GGDEF family protein [Candidatus Liberibacter asiaticus str. psy62] Length = 963 Back     alignment
 Score = 53.9 bits (128), Expect = 3e-09,   Method: Compositional matrix adjust.
 Identities = 47/162 (29%), Positives = 76/162 (46%), Gaps = 12/162 (7%)

Query: 107 DCLSGLLNHSAFISSLGSY--------NEKLSIVFFDIDYFKQINDNFGHPVGDKVIAFL 158
           D L+G+ N  +F+  L +         N + +++  DID +K+IND  G  VGD V+  L
Sbjct: 536 DNLTGIPNRQSFLDRLTTILDLSATDDNLRPTVMVIDIDKYKKINDVLGIAVGDDVLVSL 595

Query: 159 SDQLVVVFGTPMFVGRLGGEEFAAAALGSSEQ-EAAILANDLRKIIENSQINISSGPSIH 217
           + ++  +   P  + RL G  F    +  +   + A  A  +RK I    IN+     I 
Sbjct: 596 TRRIGELLKFPDILARLSGNRFGIILISENNSLKIADFAIAMRKSIA-MPINLLER-EIT 653

Query: 218 ITISAGIAERCHKEPIST-IIYRADQALYVAKKSGRNRVVCF 258
           +T S G A     +  S+ ++  A+ A+Y AK  G N V  F
Sbjct: 654 VTASIGFASWTSSKITSSEMLKNAELAMYHAKHRGGNHVESF 695

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

IdentityAlignment graphLength Definition Round E-value
Target266 diguanylate cyclase [Candidatus Liberibacter asiaticus
315122462259 diguanylate cyclase [Candidatus Liberibacter solanacear 1 3e-99
163760787261 probable urease-associated protein [Hoeflea phototrophi 1 3e-27
19070379287 urease-associated hypothetical protein [Rhizobium legum 1 5e-26
218680699287 urease-associated protein [Rhizobium etli CIAT 894] Len 1 8e-26
88798529476 GGDEF domain protein [Reinekea sp. MED297] Length = 476 1 8e-26
190893128282 urease-associated protein [Rhizobium etli CIAT 652] Len 1 1e-25
241205995286 diguanylate cyclase [Rhizobium leguminosarum bv. trifol 1 2e-25
218673892283 probable urease-associated protein [Rhizobium etli GR56 1 2e-25
91774395521 diguanylate cyclase [Methylobacillus flagellatus KT] Le 1 2e-25
222086805285 urease-associated protein [Agrobacterium radiobacter K8 1 3e-25
>gi|315122462|ref|YP_004062951.1| diguanylate cyclase [Candidatus Liberibacter solanacearum CLso-ZC1] Length = 259 Back     alignment and organism information
 Score =  365 bits (938), Expect = 3e-99,   Method: Compositional matrix adjust.
 Identities = 206/259 (79%), Positives = 234/259 (90%)

Query: 1   MTRSLKDFLSIWLCHEKNLESFSPHTFMIYFSIFFSIFIATVIFIANIFLFYIGLTPFYG 60
           MT+ LKD L IWL +EKNLESFSP+ FM YFSIFF+IFI ++IFI N+ LFYIGL PFYG
Sbjct: 1   MTKYLKDLLRIWLLYEKNLESFSPNAFMTYFSIFFTIFITSIIFITNVVLFYIGLIPFYG 60

Query: 61  LEYILVENLSLVIISITISLLLGYISGSILKELFISYNRISQLSRIDCLSGLLNHSAFIS 120
           +EYIL+EN+SLVIISI ISL+LGYISGSILKELF++YN++S+LSRIDCLSGLLNHSAFIS
Sbjct: 61  VEYILLENISLVIISIVISLILGYISGSILKELFVAYNKMSRLSRIDCLSGLLNHSAFIS 120

Query: 121 SLGSYNEKLSIVFFDIDYFKQINDNFGHPVGDKVIAFLSDQLVVVFGTPMFVGRLGGEEF 180
           +LGS +EKLSIVFFDID FK IND+FGHPVGDKVIAFLS++LV VF +PMFVGRLGGEEF
Sbjct: 121 NLGSCSEKLSIVFFDIDNFKFINDSFGHPVGDKVIAFLSEKLVYVFQSPMFVGRLGGEEF 180

Query: 181 AAAALGSSEQEAAILANDLRKIIENSQINISSGPSIHITISAGIAERCHKEPISTIIYRA 240
           AAAALG SE+EAAILANDLRKIIENS I ISS   + ITISAGI+ERC+KEPISTI+Y+A
Sbjct: 181 AAAALGLSEKEAAILANDLRKIIENSFIKISSSQFVQITISAGISERCNKEPISTIVYQA 240

Query: 241 DQALYVAKKSGRNRVVCFS 259
           DQALYVAKK GRNRVVCF 
Sbjct: 241 DQALYVAKKLGRNRVVCFK 259


Species: Candidatus Liberibacter solanacearum
Genus: Candidatus Liberibacter
Family: Rhizobiaceae
Order: Rhizobiales
Class: Alphaproteobacteria
Phylum: Proteobacteria
Superkingdom: Bacteria
>gi|163760787|ref|ZP_02167867.1| probable urease-associated protein [Hoeflea phototrophica DFL-43] Length = 261 Back     alignment and organism information
>gi|19070379|gb|AAL83832.1|AF347070_9 urease-associated hypothetical protein [Rhizobium leguminosarum bv. viciae] Length = 287 Back     alignment and organism information
>gi|218680699|ref|ZP_03528596.1| urease-associated protein [Rhizobium etli CIAT 894] Length = 287 Back     alignment and organism information
>gi|88798529|ref|ZP_01114113.1| GGDEF domain protein [Reinekea sp. MED297] Length = 476 Back     alignment and organism information
>gi|190893128|ref|YP_001979670.1| urease-associated protein [Rhizobium etli CIAT 652] Length = 282 Back     alignment and organism information
>gi|241205995|ref|YP_002977091.1| diguanylate cyclase [Rhizobium leguminosarum bv. trifolii WSM1325] Length = 286 Back     alignment and organism information
>gi|218673892|ref|ZP_03523561.1| probable urease-associated protein [Rhizobium etli GR56] Length = 283 Back     alignment and organism information
>gi|91774395|ref|YP_544151.1| diguanylate cyclase [Methylobacillus flagellatus KT] Length = 521 Back     alignment and organism information
>gi|222086805|ref|YP_002545339.1| urease-associated protein [Agrobacterium radiobacter K84] Length = 285 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
Target266 diguanylate cyclase [Candidatus Liberibacter asiaticus
COG2199181 COG2199, COG2199, FOG: GGDEF domain [Signal transductio 2e-33
smart00267163 smart00267, GGDEF, diguanylate cyclase 1e-29
pfam00990159 pfam00990, GGDEF, GGDEF domain 2e-29
COG3706435 COG3706, PleD, Response regulator containing a CheY-lik 3e-29
TIGR00254165 TIGR00254, GGDEF, diguanylate cyclase (GGDEF) domain 9e-29
PRK09581457 PRK09581, pleD, response regulator PleD; Reviewed 2e-27
PRK09894296 PRK09894, PRK09894, diguanylate cyclase; Provisional 4e-25
PRK15426570 PRK15426, PRK15426, putative diguanylate cyclase YedQ; 1e-24
PRK10245366 PRK10245, adrA, diguanylate cyclase AdrA; Provisional 5e-19
COG5001 663 COG5001, COG5001, Predicted signal transduction protein 5e-17
PRK10060 663 PRK10060, PRK10060, RNase II stability modulator; Provi 8e-16
PRK09776 1092 PRK09776, PRK09776, putative diguanylate cyclase; Provi 6e-12
PRK11359 799 PRK11359, PRK11359, cyclic-di-GMP phosphodiesterase; Pr 7e-12
PRK09966407 PRK09966, PRK09966, putative inner membrane diguanylate 3e-11
cd01949158 cd01949, GGDEF, Diguanylate-cyclase (DGC) or GGDEF doma 3e-38
cd07556133 cd07556, Nucleotidyl_cyc_III, Class III nucleotidyl cyc 5e-07
>gnl|CDD|32381 COG2199, COG2199, FOG: GGDEF domain [Signal transduction mechanisms] Back     alignment and domain information
>gnl|CDD|128563 smart00267, GGDEF, diguanylate cyclase Back     alignment and domain information
>gnl|CDD|144545 pfam00990, GGDEF, GGDEF domain Back     alignment and domain information
>gnl|CDD|33501 COG3706, PleD, Response regulator containing a CheY-like receiver domain and a GGDEF domain [Signal transduction mechanisms] Back     alignment and domain information
>gnl|CDD|161790 TIGR00254, GGDEF, diguanylate cyclase (GGDEF) domain Back     alignment and domain information
>gnl|CDD|181966 PRK09581, pleD, response regulator PleD; Reviewed Back     alignment and domain information
>gnl|CDD|182133 PRK09894, PRK09894, diguanylate cyclase; Provisional Back     alignment and domain information
>gnl|CDD|185324 PRK15426, PRK15426, putative diguanylate cyclase YedQ; Provisional Back     alignment and domain information
>gnl|CDD|182329 PRK10245, adrA, diguanylate cyclase AdrA; Provisional Back     alignment and domain information
>gnl|CDD|34606 COG5001, COG5001, Predicted signal transduction protein containing a membrane domain, an EAL and a GGDEF domain [Signal transduction mechanisms] Back     alignment and domain information
>gnl|CDD|182215 PRK10060, PRK10060, RNase II stability modulator; Provisional Back     alignment and domain information
>gnl|CDD|182070 PRK09776, PRK09776, putative diguanylate cyclase; Provisional Back     alignment and domain information
>gnl|CDD|183097 PRK11359, PRK11359, cyclic-di-GMP phosphodiesterase; Provisional Back     alignment and domain information
>gnl|CDD|182171 PRK09966, PRK09966, putative inner membrane diguanylate cyclase; Provisional Back     alignment and domain information
>gnl|CDD|143635 cd01949, GGDEF, Diguanylate-cyclase (DGC) or GGDEF domain Back     alignment and domain information
>gnl|CDD|143637 cd07556, Nucleotidyl_cyc_III, Class III nucleotidyl cyclases Back     alignment and domain information

Conserved Domains in CDD Database Detected by HHsearch

IdentityAlignment graphLength Definition Probability
Target 266 diguanylate cyclase [Candidatus Liberibacter asiaticus
PRK10245371 adrA diguanylate cyclase AdrA; Provisional 100.0
PRK09581457 pleD response regulator PleD; Reviewed 100.0
PRK09894293 hypothetical protein; Provisional 100.0
PRK09966407 hypothetical protein; Provisional 100.0
PRK13561 651 putative phosphodiesterase; Provisional 100.0
PRK10060 663 RNase II stability modulator; Provisional 100.0
PRK11359 799 cAMP phosphodiesterase; Provisional 100.0
PRK09776 1116 putative sensor protein; Provisional 100.0
COG3706435 PleD Response regulator containing a CheY-like receiver 100.0
PRK11059 642 regulatory protein CsrD; Provisional 100.0
smart00267163 GGDEF diguanylate cyclase. Diguanylate cyclase, present 99.97
COG2199181 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) 99.97
PRK11829 728 biofilm formation regulator HmsP; Provisional 99.96
COG5001 663 Predicted signal transduction protein containing a memb 99.95
TIGR00254171 GGDEF diguanylate cyclase (GGDEF) domain; InterPro: IPR 99.89
pfam00990159 GGDEF GGDEF domain. This domain is found linked to a wi 99.96
cd01949158 GGDEF Diguanylate-cyclase (DGC) or GGDEF domain. Diguan 99.95
COG3887 655 Predicted signaling protein consisting of a modified GG 98.33
PRK02240254 GTP cyclohydrolase III; Provisional 96.05
pfam05165246 GGDN GGDN family. I have named this protein family of u 95.5
TIGR02578 802 cas_TM1811_Csm1 CRISPR-associated protein, Csm1 family; 95.44
TIGR02578802 cas_TM1811_Csm1 CRISPR-associated protein, Csm1 family; 93.45
cd07302177 CHD cyclase homology domain. Catalytic domains of the m 92.54
PRK11477385 carbohydrate diacid transcriptional activator CdaR; Pro 90.06
cd07556133 Nucleotidyl_cyc_III Class III nucleotidyl cyclases. Cla 97.17
pfam00211186 Guanylate_cyc Adenylate and Guanylate cyclase catalytic 92.26
COG1353 799 Predicted CRISPR-associated polymerase [Defense mechani 96.55
TIGR02577665 cas_TM1794_Crm2 CRISPR-associated protein, Crm2 family; 94.44
COG2429250 Archaeal GTP cyclohydrolase III [Nucleotide transport a 92.19
PRK02240 254 GTP cyclohydrolase III; Provisional 91.21
>PRK10245 adrA diguanylate cyclase AdrA; Provisional Back     alignment and domain information
>PRK09581 pleD response regulator PleD; Reviewed Back     alignment and domain information
>PRK09894 hypothetical protein; Provisional Back     alignment and domain information
>PRK09966 hypothetical protein; Provisional Back     alignment and domain information
>PRK13561 putative phosphodiesterase; Provisional Back     alignment and domain information
>PRK10060 RNase II stability modulator; Provisional Back     alignment and domain information
>PRK11359 cAMP phosphodiesterase; Provisional Back     alignment and domain information
>PRK09776 putative sensor protein; Provisional Back     alignment and domain information
>COG3706 PleD Response regulator containing a CheY-like receiver domain and a GGDEF domain [Signal transduction mechanisms] Back     alignment and domain information
>PRK11059 regulatory protein CsrD; Provisional Back     alignment and domain information
>smart00267 GGDEF diguanylate cyclase Back     alignment and domain information
>COG2199 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms] Back     alignment and domain information
>PRK11829 biofilm formation regulator HmsP; Provisional Back     alignment and domain information
>COG5001 Predicted signal transduction protein containing a membrane domain, an EAL and a GGDEF domain [Signal transduction mechanisms] Back     alignment and domain information
>TIGR00254 GGDEF diguanylate cyclase (GGDEF) domain; InterPro: IPR000160 This domain appears to be ubiquitous in bacteria and is often linked to a regulatory domain, such as a phosphorylation receiver or oxygen sensing domain Back     alignment and domain information
>pfam00990 GGDEF GGDEF domain Back     alignment and domain information
>cd01949 GGDEF Diguanylate-cyclase (DGC) or GGDEF domain Back     alignment and domain information
>COG3887 Predicted signaling protein consisting of a modified GGDEF domain and a DHH domain [Signal transduction mechanisms] Back     alignment and domain information
>PRK02240 GTP cyclohydrolase III; Provisional Back     alignment and domain information
>pfam05165 GGDN GGDN family Back     alignment and domain information
>TIGR02578 cas_TM1811_Csm1 CRISPR-associated protein, Csm1 family; InterPro: IPR013408 CRISPR are Clustered Regularly Interspaced Short Palindromic Repeats Back     alignment and domain information
>TIGR02578 cas_TM1811_Csm1 CRISPR-associated protein, Csm1 family; InterPro: IPR013408 CRISPR are Clustered Regularly Interspaced Short Palindromic Repeats Back     alignment and domain information
>cd07302 CHD cyclase homology domain Back     alignment and domain information
>PRK11477 carbohydrate diacid transcriptional activator CdaR; Provisional Back     alignment and domain information
>cd07556 Nucleotidyl_cyc_III Class III nucleotidyl cyclases Back     alignment and domain information
>pfam00211 Guanylate_cyc Adenylate and Guanylate cyclase catalytic domain Back     alignment and domain information
>COG1353 Predicted CRISPR-associated polymerase [Defense mechanisms] Back     alignment and domain information
>TIGR02577 cas_TM1794_Crm2 CRISPR-associated protein, Crm2 family; InterPro: IPR013407 This entry is encoded within the CRISPR-associated RAMP module, a set of six genes found together in prokaryotic genomes Back     alignment and domain information
>COG2429 Archaeal GTP cyclohydrolase III [Nucleotide transport and metabolism] Back     alignment and domain information
>PRK02240 GTP cyclohydrolase III; Provisional 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
Target266 diguanylate cyclase [Candidatus Liberibacter asiaticus
1w25_A459 Response Regulator Pled In Complex With C-Digmp Len 1e-28
2wb4_A459 Activated Diguanylate Cyclase Pled In Complex With 3e-28
3i5c_A206 Crystal Structure Of A Fusion Protein Containing Th 5e-27
3ign_A177 Crystal Structure Of The Ggdef Domain From Marinoba 3e-25
3i5b_A179 Crystal Structure Of The Isolated Ggdef Domain Of W 6e-25
3bre_A358 Crystal Structure Of P.Aeruginosa Pa3702 Length = 3 3e-27
>gi|56966618|pdb|1W25|A Chain A, Response Regulator Pled In Complex With C-Digmp Length = 459 Back     alignment and structure
 Score =  130 bits (328), Expect = 1e-28,   Method: Composition-based stats.
 Identities = 52/164 (31%), Positives = 82/164 (50%), Gaps = 9/164 (5%)

Query: 102 QLSRIDCLSGLLNHSAFISSLGSY-------NEKLSIVFFDIDYFKQINDNFGHPVGDKV 154
           +L+  D L+GL N       L S         + +S +  DID+FK+IND FGH +GD+V
Sbjct: 286 ELAVTDQLTGLHNRRYMTGQLDSLVKRATLGGDPVSALLIDIDFFKKINDTFGHDIGDEV 345

Query: 155 IAFLSDQLVVVFGTPMFVGRLGGEEFAAAALGSSEQEAAILANDLRKIIENSQINISSGP 214
           +   + +L           R GGEEF      ++  +A  +A  +R  +  S   ++ G 
Sbjct: 346 LREFALRLASNVRAIDLPCRYGGEEFVVIMPDTALADALRIAERIRMHVSGSPFTVAHGR 405

Query: 215 S-IHITISAGI-AERCHKEPISTIIYRADQALYVAKKSGRNRVV 256
             +++TIS G+ A     +    ++ RAD+ +Y AK SGRN VV
Sbjct: 406 EMLNVTISIGVSATAGEGDTPEALLKRADEGVYQAKASGRNAVV 449


>gi|294979306|pdb|2WB4|A Chain A, Activated Diguanylate Cyclase Pled In Complex With C-Di-Gmp Length = 459 Back     alignment and structure
>gi|256032862|pdb|3I5C|A Chain A, Crystal Structure Of A Fusion Protein Containing The Leucine Zipper Of Gcn4 And The Ggdef Domain Of Wspr From Pseudomonas Aeruginosa Length = 206 Back     alignment and structure
>gi|255918034|pdb|3IGN|A Chain A, Crystal Structure Of The Ggdef Domain From Marinobacter Aquaeolei Diguanylate Cyclase Complexed With C-Di-Gmp - Northeast Structural Genomics Consortium Target Mqr89a Length = 177 Back     alignment and structure
>gi|256032860|pdb|3I5B|A Chain A, Crystal Structure Of The Isolated Ggdef Domain Of Wpsr From Pseudomonas Aeruginosa Length = 179 Back     alignment and structure
>gi|171849031|pdb|3BRE|A Chain A, Crystal Structure Of P.Aeruginosa Pa3702 Length = 358 Back     alignment and structure

Homologous Structures in PDB70 Database Detected by RPS-BLAST

IdentityAlignment graphLength Definition E-value
Target266 diguanylate cyclase [Candidatus Liberibacter asiaticus
1w25_A459 Stalked-cell differentiation controlling protein; two-c 3e-36
3ezu_A342 Ggdef domain protein; multidomain protein of unknown fu 2e-33
3bre_A358 Probable two-component response regulator; protein-nucl 3e-33
3ign_A177 Diguanylate cyclase; ggdef domain, A1U3W3_marav, NESG, 1e-28
3mtk_A178 Diguanylate cyclase/phosphodiesterase; structural genom 2e-28
3icl_A171 EAL/ggdef domain protein; structural genomics, PSI-2, p 1e-25
3hvw_A176 Diguanylate-cyclase (DGC); alpha-beta protein., structu 2e-24
3hvb_A 437 Protein FIMX; EAL phosphodiesterase, biofilm, C-DI-GMP, 3e-17
3i5c_A206 Fusion of general control protein GCN4 and WSPR respons 4e-15
3hva_A177 Protein FIMX; ggdef diguanylate cyclase, biofilm, C-DI- 6e-13
>1w25_A Stalked-cell differentiation controlling protein; two-component system, response regulator, diguanylate cyclase, ggdef domain; HET: C2E; 2.70A {Caulobacter vibrioides} SCOP: c.23.1.1 c.23.1.1 d.58.29.2 PDB: 2v0n_A* Length = 459 Back     alignment and structure
 Score =  147 bits (371), Expect = 3e-36
 Identities = 51/170 (30%), Positives = 84/170 (49%), Gaps = 9/170 (5%)

Query: 96  SYNRISQLSRIDCLSGLLNHSAFISSLGS-------YNEKLSIVFFDIDYFKQINDNFGH 148
           + +   +L+  D L+GL N       L S         + +S +  DID+FK+IND FGH
Sbjct: 280 NLDHSLELAVTDQLTGLHNRRYMTGQLDSLVKRATLGGDPVSALLIDIDFFKKINDTFGH 339

Query: 149 PVGDKVIAFLSDQLVVVFGTPMFVGRLGGEEFAAAALGSSEQEAAILANDLRKIIENSQI 208
            +GD+V+   + +L           R GGEEF      ++  +A  +A  +R  +  S  
Sbjct: 340 DIGDEVLREFALRLASNVRAIDLPCRYGGEEFVVIMPDTALADALRIAERIRMHVSGSPF 399

Query: 209 NISSG-PSIHITISAGIAE-RCHKEPISTIIYRADQALYVAKKSGRNRVV 256
            ++ G   +++TIS G++      +    ++ RAD+ +Y AK SGRN VV
Sbjct: 400 TVAHGREMLNVTISIGVSATAGEGDTPEALLKRADEGVYQAKASGRNAVV 449


>3ezu_A Ggdef domain protein; multidomain protein of unknown function with ggdef-domain, structural genomics; 1.95A {Geobacter sulfurreducens} Length = 342 Back     alignment and structure
>3bre_A Probable two-component response regulator; protein-nucleotide complex, signaling protein; HET: C2E; 2.40A {Pseudomonas aeruginosa PAO1} PDB: 3i5a_A* Length = 358 Back     alignment and structure
>3ign_A Diguanylate cyclase; ggdef domain, A1U3W3_marav, NESG, MQR89A, structural genomics, PSI-2, protein structure initiative; HET: C2E; 1.83A {Marinobacter aquaeolei VT8} Length = 177 Back     alignment and structure
>3mtk_A Diguanylate cyclase/phosphodiesterase; structural genomics, PSI-2, protein structure initiative; 2.24A {Caldicellulosiruptor saccharolyticus} Length = 178 Back     alignment and structure
>3icl_A EAL/ggdef domain protein; structural genomics, PSI-2, protein structure initiative, northeast structural genomics, consortium, NESG; HET: MSE; 2.00A {Methylococcus capsulatus} Length = 171 Back     alignment and structure
>3hvw_A Diguanylate-cyclase (DGC); alpha-beta protein., structural genomics, PSI-2, protein structure initiative; 1.70A {Pseudomonas aeruginosa} Length = 176 Back     alignment and structure
>3hvb_A Protein FIMX; EAL phosphodiesterase, biofilm, C-DI-GMP, hydrolase; 2.99A {Pseudomonas aeruginosa PAO1} Length = 437 Back     alignment and structure
>3i5c_A Fusion of general control protein GCN4 and WSPR response regulator protein; C-DI-GMP, ggdef, leucine zipper, signaling protein; HET: C2E; 1.94A {Pseudomonas aeruginosa PAO1} PDB: 3i5b_A* Length = 206 Back     alignment and structure
>3hva_A Protein FIMX; ggdef diguanylate cyclase, biofilm, C-DI-GMP, transferase; 2.04A {Pseudomonas aeruginosa PAO1} Length = 177 Back     alignment and structure

Homologous Structures in PDB70 Database Detected by HHsearch

IdentityAlignment graphLength Definition Probability
Target266 diguanylate cyclase [Candidatus Liberibacter asiaticus
1w25_A459 Stalked-cell differentiation controlling protein; two-c 100.0
3ezu_A342 Ggdef domain protein; multidomain protein of unknown fu 99.98
3bre_A358 Probable two-component response regulator; protein-nucl 99.98
3mtk_A178 Diguanylate cyclase/phosphodiesterase; structural genom 99.95
3i5c_A206 Fusion of general control protein GCN4 and WSPR R regul 99.95
3ign_A177 Diguanylate cyclase; ggdef domain, A1U3W3_marav, NESG, 99.95
3hva_A177 Protein FIMX; ggdef diguanylate cyclase, biofilm, C-DI- 99.95
3icl_A171 EAL/ggdef domain protein; structural genomics, PSI-2, p 99.92
3hvb_A 437 Protein FIMX; EAL phosphodiesterase, biofilm, C-DI-GMP, 99.88
3hvw_A176 Diguanylate-cyclase (DGC); alpha-beta protein., structu 99.82
2qv6_A268 MJ0145, GTP cyclohydrolase III, MJGC; enzyme, FAPY; HET 96.25
3et6_A190 Soluble guanylyl cyclase beta; guanylate cyclase, dimet 93.8
1y10_A407 Hypothetical protein RV1264/MT1302; adenylyl cyclase fo 93.53
1ybt_A184 Hydrolase, alpha/beta hydrolase fold family; cyclase ho 92.51
1azs_A220 VC1; complex (lyase/hydrolase), hydrolase, signal trans 91.58
3mr7_A189 Adenylate/guanylate cyclase/hydrolase, alpha/beta famil 91.15
1yk9_A204 Adenylate cyclase; beta-alpha-beta sandwich, structural 94.11
>1w25_A Stalked-cell differentiation controlling protein; two-component system, response regulator, diguanylate cyclase, ggdef domain; HET: C2E; 2.70A {Caulobacter vibrioides} SCOP: c.23.1.1 c.23.1.1 d.58.29.2 PDB: 2v0n_A* 2wb4_A* Back     alignment and structure
Probab=100.00  E-value=1.2e-39  Score=320.21  Aligned_cols=166  Identities=30%  Similarity=0.465  Sum_probs=149.6

Q ss_pred             HHHHHHHHHHHCCCHHCCCCHHHHHHHHHH-------CCCCEEEEEEECCCCCCCCCCCCCCCCCCCCCHHHCCCCCCCC
Q ss_conf             999999999610401050204899988877-------0897257554422100011468865444311000000011111
Q gi|254781079|r   95 ISYNRISQLSRIDCLSGLLNHSAFISSLGS-------YNEKLSIVFFDIDYFKQINDNFGHPVGDKVIAFLSDQLVVVFG  167 (266)
Q Consensus        95 ~~~~~l~~~a~~D~LTgL~NR~~f~~~l~~-------~~~~~~l~~idid~fk~iNd~~G~~~gD~~L~~va~~l~~~~~  167 (266)
                      +..+++.++|++|||||||||++|.+++++       .+.+++|+++|||+||.|||+|||.+||++|+++|++|+.++|
T Consensus       279 ~~~~~l~~la~~D~LTgL~NR~~~~~~l~~~i~~a~r~~~~~al~~lDlD~FK~iND~~GH~~GD~vL~~va~~L~~~~r  358 (459)
T 1w25_A          279 NNLDHSLELAVTDQLTGLHNRRYMTGQLDSLVKRATLGGDPVSALLIDIDFFKKINDTFGHDIGDEVLREFALRLASNVR  358 (459)
T ss_dssp             SSSSCCSTTCCBCTTTCCBCHHHHHHHHHHHHHHHHTSSCCCEEEEEEETTHHHHHHHSCHHHHHHHHHHHHHHHHHTSC
T ss_pred             HHHHHHHHHCCCCCCCCCHHHHHHHHHHHHHHHHHHHCCCEEEEEEECCCHHCCHHHCCCCHHHHHHHHHHHHHHHHHCC
T ss_conf             99987664127686568712999999889999998742987999996043014021134826789999999999997289


Q ss_pred             CCHHHCCCCCCEEEEECCCCCHHHHHHHHHHHHHHHHHCCCCCCC-CCEEEEEEEEEEEECC-CCCCHHHHHHHHHHHHH
Q ss_conf             000000133430365016861012344458999998631540679-9568999999998779-98998999999999999
Q gi|254781079|r  168 TPMFVGRLGGEEFAAAALGSSEQEAAILANDLRKIIENSQINISS-GPSIHITISAGIAERC-HKEPISTIIYRADQALY  245 (266)
Q Consensus       168 ~~~~~~R~~gdeF~ill~~~~~~~~~~~~~~l~~~l~~~~~~~~~-~~~~~~t~s~Gia~~~-~~~~~~~ll~~Ad~Al~  245 (266)
                      ++|+++|+|||||+|++|+++.+++..++++|+..+...++...+ +..+.+|+|+||+.++ +++++++|+++||.|||
T Consensus       359 ~~d~vaR~GGDEF~ill~~~~~~~a~~~a~ri~~~i~~~~f~~~~~~~~~~vt~SiGia~~~~~~~~~~~Ll~~AD~Amy  438 (459)
T 1w25_A          359 AIDLPCRYGGEEFVVIMPDTALADALRIAERIRMHVSGSPFTVAHGREMLNVTISIGVSATAGEGDTPEALLKRADEGVY  438 (459)
T ss_dssp             TTSEEEECSSSEEEEEETTCCHHHHHHHHHHHHHHHHTSCEECGGGSCEECCCEEEEEEECCSTTCCHHHHHHHHHHHHH
T ss_pred             CCCEEEEECCCEEEEEECCCCHHHHHHHHHHHHHHHHCCCCEECCCCEEEEEEEEEEEEEECCCCCCHHHHHHHHHHHHH
T ss_conf             88689998576799997899999999999999999966893665898899999999999717999989999999999999


Q ss_pred             HHHHCCCCEEEECCH
Q ss_conf             999709968999402
Q gi|254781079|r  246 VAKKSGRNRVVCFSD  260 (266)
Q Consensus       246 ~AK~~gkn~~~~~~~  260 (266)
                      +||++||||||..+-
T Consensus       439 ~AK~~Grnrvv~~~~  453 (459)
T 1w25_A          439 QAKASGRNAVVGKAA  453 (459)
T ss_dssp             HHHHTTSSCEEECCC
T ss_pred             HHHHHCCCEEEECCC
T ss_conf             999719995998000



>3ezu_A Ggdef domain protein; multidomain protein of unknown function with ggdef-domain, structural genomics; 1.95A {Geobacter sulfurreducens} Back     alignment and structure
>3bre_A Probable two-component response regulator; protein-nucleotide complex, signaling protein; HET: C2E; 2.40A {Pseudomonas aeruginosa PAO1} PDB: 3i5a_A* Back     alignment and structure
>3mtk_A Diguanylate cyclase/phosphodiesterase; structural genomics, PSI-2, protein structure initiative; 2.24A {Caldicellulosiruptor saccharolyticus} Back     alignment and structure
>3i5c_A Fusion of general control protein GCN4 and WSPR R regulator protein; C-DI-GMP, ggdef, leucine zipper, signaling protein; HET: C2E; 1.94A {Pseudomonas aeruginosa PAO1} PDB: 3i5b_A* Back     alignment and structure
>3ign_A Diguanylate cyclase; ggdef domain, A1U3W3_marav, NESG, MQR89A, structural genomics, PSI-2, protein structure initiative; HET: C2E; 1.83A {Marinobacter aquaeolei VT8} Back     alignment and structure
>3hva_A Protein FIMX; ggdef diguanylate cyclase, biofilm, C-DI-GMP, transferase; 2.04A {Pseudomonas aeruginosa PAO1} Back     alignment and structure
>3icl_A EAL/ggdef domain protein; structural genomics, PSI-2, protein structure initiative, northeast structural genomics, consortium, NESG; HET: MSE; 2.00A {Methylococcus capsulatus} Back     alignment and structure
>3hvb_A Protein FIMX; EAL phosphodiesterase, biofilm, C-DI-GMP, hydrolase; 2.99A {Pseudomonas aeruginosa PAO1} Back     alignment and structure
>3hvw_A Diguanylate-cyclase (DGC); alpha-beta protein., structural genomics, PSI-2, protein structure initiative; 1.70A {Pseudomonas aeruginosa} Back     alignment and structure
>2qv6_A MJ0145, GTP cyclohydrolase III, MJGC; enzyme, FAPY; HET: GTP; 2.00A {Methanocaldococcus jannaschii} Back     alignment and structure
>3et6_A Soluble guanylyl cyclase beta; guanylate cyclase, dimethylarsenic, lyase, membrane, transmembrane; 2.55A {Chlamydomonas reinhardtii} PDB: 3et6_B Back     alignment and structure
>1y10_A Hypothetical protein RV1264/MT1302; adenylyl cyclase fold, lyase; HET: 1PE; 2.30A {Mycobacterium tuberculosis} PDB: 1y11_A* Back     alignment and structure
>1ybt_A Hydrolase, alpha/beta hydrolase fold family; cyclase homology domain, CHD, RV1900C; 2.31A {Mycobacterium tuberculosis CDC1551} PDB: 1ybu_A* Back     alignment and structure
>1azs_A VC1; complex (lyase/hydrolase), hydrolase, signal transducing protein, cyclase, effector enzyme; HET: GSP FKP; 2.30A {Canis lupus familiaris} SCOP: d.58.29.1 PDB: 1cs4_A* 1u0h_A* 2gvd_A* 2gvz_A* 3c14_A* 3c15_A* 3c16_A* 3e8a_A* 3g82_A* 3maa_A* 1cul_A* 1cjk_A* 1cju_A* 1cjv_A* 1cjt_A* 1tl7_A* Back     alignment and structure
>3mr7_A Adenylate/guanylate cyclase/hydrolase, alpha/beta family; alpha-beta fold, structural genomics, PSI-2, protein structu initiative; 2.60A {Ruegeria pomeroyi} Back     alignment and structure
>1yk9_A Adenylate cyclase; beta-alpha-beta sandwich, structural genomics, PSI, protein structure initiative; 2.70A {Mycobacterium tuberculosis} Back     alignment and structure

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 266 diguanylate cyclase [Candidatus Liberibacter asiaticus
d1w25a3162 d.58.29.2 (A:294-455) Response regulator PleD, C-termin 7e-16
>d1w25a3 d.58.29.2 (A:294-455) Response regulator PleD, C-terminal domain {Caulobacter crescentus [TaxId: 155892]} Length = 162 Back     information, alignment and structure

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: Nucleotide cyclase
family: GGDEF domain
domain: Response regulator PleD, C-terminal domain
species: Caulobacter crescentus [TaxId: 155892]
 Score = 77.9 bits (190), Expect = 7e-16
 Identities = 48/160 (30%), Positives = 76/160 (47%), Gaps = 9/160 (5%)

Query: 109 LSGLLNHSAFISSLGS-------YNEKLSIVFFDIDYFKQINDNFGHPVGDKVIAFLSDQ 161
           L+GL N       L S         + +S +  DID+FK+IND FGH +GD+V+   + +
Sbjct: 1   LTGLHNRRYMTGQLDSLVKRATLGGDPVSALLIDIDFFKKINDTFGHDIGDEVLREFALR 60

Query: 162 LVVVFGTPMFVGRLGGEEFAAAALGSSEQEAAILANDLRKIIENSQ-INISSGPSIHITI 220
           L           R GGEEF      ++  +A  +A  +R  +  S          +++TI
Sbjct: 61  LASNVRAIDLPCRYGGEEFVVIMPDTALADALRIAERIRMHVSGSPFTVAHGREMLNVTI 120

Query: 221 SAGIAE-RCHKEPISTIIYRADQALYVAKKSGRNRVVCFS 259
           S G++      +    ++ RAD+ +Y AK SGRN VV  +
Sbjct: 121 SIGVSATAGEGDTPEALLKRADEGVYQAKASGRNAVVGKA 160


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

IdentityAlignment graphLength Definition Probability
Target266 diguanylate cyclase [Candidatus Liberibacter asiaticus
d1w25a3162 Response regulator PleD, C-terminal domain {Caulobacter 99.94
d1azsa_190 Adenylyl cyclase VC1, domain C1a {Dog (Canis familiaris 90.81
>d1w25a3 d.58.29.2 (A:294-455) Response regulator PleD, C-terminal domain {Caulobacter crescentus [TaxId: 155892]} Back     information, alignment and structure
class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: Nucleotide cyclase
family: GGDEF domain
domain: Response regulator PleD, C-terminal domain
species: Caulobacter crescentus [TaxId: 155892]
Probab=99.94  E-value=6.1e-27  Score=221.45  Aligned_cols=152  Identities=32%  Similarity=0.502  Sum_probs=136.9

Q ss_pred             HHCCCCHHHHHHHHHH-------CCCCEEEEEEECCCCCCCCCCCCCCCCCCCCCHHHCCCCCCCCCCHHHCCCCCCEEE
Q ss_conf             1050204899988877-------089725755442210001146886544431100000001111100000013343036
Q gi|254781079|r  109 LSGLLNHSAFISSLGS-------YNEKLSIVFFDIDYFKQINDNFGHPVGDKVIAFLSDQLVVVFGTPMFVGRLGGEEFA  181 (266)
Q Consensus       109 LTgL~NR~~f~~~l~~-------~~~~~~l~~idid~fk~iNd~~G~~~gD~~L~~va~~l~~~~~~~~~~~R~~gdeF~  181 (266)
                      |||||||++|.+++++       .+.++++++++||+|+.||+.||++.||++|++++++|+..++++++++|+++|+|+
T Consensus         1 LTGL~Nr~~f~~~l~~~l~~~~~~~~~~~l~~i~id~~~~in~~~G~~~~d~ll~~~a~~l~~~~~~~d~~~R~~~~~F~   80 (162)
T d1w25a3           1 LTGLHNRRYMTGQLDSLVKRATLGGDPVSALLIDIDFFKKINDTFGHDIGDEVLREFALRLASNVRAIDLPCRYGGEEFV   80 (162)
T ss_dssp             TTCCBCHHHHHHHHHHHHHHHHTSSCCCEEEEEEETTHHHHHHHSCHHHHHHHHHHHHHHHHHTSCTTSEEEECSSSEEE
T ss_pred             CCCCHHHHHHHHHHHHHHHHHHHCCCCEEEEEECCCCCHHCCCCCCCCCCCHHHHHHHHHHHHCCCCCCEEEECCCCEEE
T ss_conf             98816889999999999999986599789999526311110443321112101356666566304876644414897689


Q ss_pred             EECCCCCHHHHHHHHHHHHHHHHHCCCCCC-CCCEEEEEEEEEEEECC-CCCCHHHHHHHHHHHHHHHHHCCCCEEEECC
Q ss_conf             501686101234445899999863154067-99568999999998779-9899899999999999999970996899940
Q gi|254781079|r  182 AAALGSSEQEAAILANDLRKIIENSQINIS-SGPSIHITISAGIAERC-HKEPISTIIYRADQALYVAKKSGRNRVVCFS  259 (266)
Q Consensus       182 ill~~~~~~~~~~~~~~l~~~l~~~~~~~~-~~~~~~~t~s~Gia~~~-~~~~~~~ll~~Ad~Al~~AK~~gkn~~~~~~  259 (266)
                      +++|..+.+++...+.++...+.+.++... ....+.+++|+|++.++ ++.++++++.+|+.||++||++|||+||+++
T Consensus        81 il~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~siGia~~~~~~~~~~~ll~~A~~AL~~AK~~G~n~v~~~~  160 (162)
T d1w25a3          81 VIMPDTALADALRIAERIRMHVSGSPFTVAHGREMLNVTISIGVSATAGEGDTPEALLKRADEGVYQAKASGRNAVVGKA  160 (162)
T ss_dssp             EEETTCCHHHHHHHHHHHHHHHHTSCEECGGGSCEECCCEEEEEEECCSTTCCHHHHHHHHHHHHHHHHHTTSSCEEECC
T ss_pred             EEEECCCHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCEEECCCCCCCHHHHHHHHHHHHHHHHHHCCCEEEEEC
T ss_conf             87602320345667777788998640332232211023333765505899999999999999999999982999299826


Q ss_pred             H
Q ss_conf             2
Q gi|254781079|r  260 D  260 (266)
Q Consensus       260 ~  260 (266)
                      -
T Consensus       161 ~  161 (162)
T d1w25a3         161 A  161 (162)
T ss_dssp             C
T ss_pred             C
T ss_conf             8



>d1azsa_ d.58.29.1 (A:) Adenylyl cyclase VC1, domain C1a {Dog (Canis familiaris) [TaxId: 9615]} Back     information, alignment and structure

Homologous Domains in MMDB70 Database Detected by RPS-BLAST

IdentityAlignment graphLength Definition E-value
Target 266 diguanylate cyclase [Candidatus Liberibacter asiat
3ezu_A_187-342156 (A:187-342) Ggdef domain protein; multidomain prot 1e-29
3ign_A_177 (A:) Diguanylate cyclase; ggdef domain, A1U3W3_mar 7e-28
1w25_A_285-459175 (A:285-459) Stalked-cell differentiation controlli 4e-25
3icl_A_171 (A:) EAL/ggdef domain protein; structural genomics 5e-24
3i5c_A_31-206176 (A:31-206) Fusion of general control protein GCN4 5e-23
3hvw_A_176 (A:) Diguanylate-cyclase (DGC); alpha-beta protein 3e-22
3bre_A_176-358183 (A:176-358) Probable two-component response regula 2e-19
3hva_A_177 (A:) Protein FIMX; ggdef diguanylate cyclase, biof 3e-14
3hvb_A_ 437 (A:) Protein FIMX; EAL phosphodiesterase, biofilm, 1e-04
2r6o_A_ 294 (A:) Putative diguanylate cyclase/phosphodiesteras 3e-04
>3ezu_A (A:187-342) Ggdef domain protein; multidomain protein of unknown function with ggdef-domain, structural genomics; 1.95A {Geobacter sulfurreducens}Length = 156 Back     alignment and structure
 Score =  124 bits (312), Expect = 1e-29
 Identities = 41/156 (26%), Positives = 70/156 (44%), Gaps = 8/156 (5%)

Query: 109 LSGLLNHSAFISSLGS-------YNEKLSIVFFDIDYFKQINDNFGHPVGDKVIAFLSDQ 161
           L+G+   + F  ++GS           + I   D+DYFK + DN+GH  GD+++  +++ 
Sbjct: 1   LTGVXTRAGFFKTVGSLAYAAQRSGSNVGIXLIDLDYFKLVGDNYGHQTGDRILQLVAET 60

Query: 162 LVVVFGTPMFVGRLGGEEFAAAALGSSEQEAAILANDLRKIIENSQINISSGPSIHITIS 221
           +         VGR  G+EF              +A +LR+ IE          +  I ++
Sbjct: 61  ITSHLRRSDVVGRYDGDEFVVYLSPVEPASLRTVAENLRRSIEEESAR-XVPVTASIGVA 119

Query: 222 AGIAERCHKEPISTIIYRADQALYVAKKSGRNRVVC 257
            GI        I  ++  AD+ L  AK +G+N+VV 
Sbjct: 120 QGILGTDVDGGIEELVRLADECLXQAKYTGKNKVVV 155


>3ign_A (A:) Diguanylate cyclase; ggdef domain, A1U3W3_marav, NESG, MQR89A, structural genomics, PSI-2, protein structure initiative; HET: C2E; 1.83A {Marinobacter aquaeolei VT8}Length = 177 Back     alignment and structure
>1w25_A (A:285-459) Stalked-cell differentiation controlling protein; two-component system, response regulator, diguanylate cyclase, ggdef domain; HET: C2E; 2.70A {Caulobacter vibrioides}Length = 175 Back     alignment and structure
>3icl_A (A:) EAL/ggdef domain protein; structural genomics, PSI-2, protein structure initiative, northeast structural genomics, consortium, NESG; HET: MSE; 2.00A {Methylococcus capsulatus}Length = 171 Back     alignment and structure
>3i5c_A (A:31-206) Fusion of general control protein GCN4 and WSPR response regulator protein; C-DI-GMP, ggdef, leucine zipper, signaling protein; HET: C2E; 1.94A {Pseudomonas aeruginosa PAO1} PDB: 3i5b_A*Length = 176 Back     alignment and structure
>3hvw_A (A:) Diguanylate-cyclase (DGC); alpha-beta protein., structural genomics, PSI-2, protein structure initiative; 1.70A {Pseudomonas aeruginosa}Length = 176 Back     alignment and structure
>3bre_A (A:176-358) Probable two-component response regulator; protein-nucleotide complex, signaling protein; HET: C2E; 2.40A {Pseudomonas aeruginosa PAO1} PDB: 3i5a_A*Length = 183 Back     alignment and structure
>3hva_A (A:) Protein FIMX; ggdef diguanylate cyclase, biofilm, C-DI-GMP, transferase; 2.04A {Pseudomonas aeruginosa PAO1}Length = 177 Back     alignment and structure
>3hvb_A (A:) Protein FIMX; EAL phosphodiesterase, biofilm, C-DI-GMP, hydrolase; 2.99A {Pseudomonas aeruginosa PAO1}Length = 437 Back     alignment and structure
>2r6o_A (A:) Putative diguanylate cyclase/phosphodiesterase (ggdef & EAL domains); ggdef and EAL domains, structural genomics, PSI-2; 1.80A {Thiobacillus denitrificans atcc 25259} PDB: 3ii8_A*Length = 294 Back     alignment and structure

Homologous Domains in MMDB70 Database Detected by HHsearch

IdentityAlignment graphLength Definition Probability
Target266 diguanylate cyclase [Candidatus Liberibacter asiaticus
3ign_A_177 Diguanylate cyclase; ggdef domain, A1U3W3_marav, N 99.95
1w25_A_285-459175 Stalked-cell differentiation controlling protein; 99.94
3ezu_A_187-342156 Ggdef domain protein; multidomain protein of unkno 99.93
3icl_A_171 EAL/ggdef domain protein; structural genomics, PSI 99.92
3hva_A_177 Protein FIMX; ggdef diguanylate cyclase, biofilm, 99.92
3i5c_A_31-206176 Fusion of general control protein GCN4 and WSPR re 99.91
3bre_A_176-358183 Probable two-component response regulator; protein 99.89
3hvw_A_176 Diguanylate-cyclase (DGC); alpha-beta protein., st 99.85
3hvb_A_ 437 Protein FIMX; EAL phosphodiesterase, biofilm, C-DI 99.76
2qv6_A_128-268141 MJ0145, GTP cyclohydrolase III, MJGC; enzyme, FAPY 96.08
1yk9_A_204 Adenylate cyclase; beta-alpha-beta sandwich, struc 94.48
3gqc_A_1-96_213-314198 DNA repair protein REV1; protein-DNA complex, alte 93.68
2qv6_A_1-127127 MJ0145, GTP cyclohydrolase III, MJGC; enzyme, FAPY 93.47
3et6_A_190 Soluble guanylyl cyclase beta; guanylate cyclase, 93.1
1jx4_A_1-10_78-182115 DNA polymerase IV (family Y); protein-DNA complex, 92.29
1azs_A_220 VC1; complex (lyase/hydrolase), hydrolase, signal 90.13
3bq0_A_1-10_78-169_236-244111 POL IV, DBH, DNA polymerase IV; Y-family, lesion b 92.97
>3ign_A (A:) Diguanylate cyclase; ggdef domain, A1U3W3_marav, NESG, MQR89A, structural genomics, PSI-2, protein structure initiative; HET: C2E; 1.83A {Marinobacter aquaeolei VT8} Back     alignment and structure
Probab=99.95  E-value=1.6e-28  Score=236.41  Aligned_cols=167  Identities=35%  Similarity=0.544  Sum_probs=149.6

Q ss_pred             HHHHHHHHCCCHHCCCCHHHHHHHHHH-------CCCCEEEEEEECCCCCCCCCCCCCCCCCCCCCHHHCCCCCCCCCCH
Q ss_conf             999999610401050204899988877-------0897257554422100011468865444311000000011111000
Q gi|254781079|r   98 NRISQLSRIDCLSGLLNHSAFISSLGS-------YNEKLSIVFFDIDYFKQINDNFGHPVGDKVIAFLSDQLVVVFGTPM  170 (266)
Q Consensus        98 ~~l~~~a~~D~LTgL~NR~~f~~~l~~-------~~~~~~l~~idid~fk~iNd~~G~~~gD~~L~~va~~l~~~~~~~~  170 (266)
                      +++++++++|||||||||++|.+++++       .+.++++++||||+||.|||.|||..||++|+.+|++|+..+++.+
T Consensus         2 q~l~~la~~D~LTgL~NR~~f~~~l~~~l~~~~~~~~~~~l~~idid~fk~ind~~G~~~gD~~l~~~a~~l~~~~~~~~   81 (177)
T 3ign_A            2 EQLAKLSXTDRLTGLLNRGTWENLVDAEYERFRRYGQATSLVXFDIDHFKPVNDTYGHLAGDEVIRHTADVTRNNIRQSD   81 (177)
T ss_dssp             ---CTTSSBCTTTCSEEHHHHHHHHHHHHHHHHHHCCCEEEEEEEETTHHHHHHHHCHHHHHHHHHHHHHHHHTTSCTTS
T ss_pred             HHHHHHHCCCCCCCCCHHHHHHHHHHHHHHHHHHCCCCEEEEEEECCHHHCCCCCCCCHHHHHHHHHHHHHHHHCCCCCC
T ss_conf             78998749652548555899999999999998850996799998443320024667807898988887777653045666


Q ss_pred             HHCCCCCCEEEEECCCCCHHHHHHHHHHHHHHHHHCCCCCCCCCEEEEEEEEEEEECC-CCCCHHHHHHHHHHHHHHHHH
Q ss_conf             0001334303650168610123444589999986315406799568999999998779-989989999999999999997
Q gi|254781079|r  171 FVGRLGGEEFAAAALGSSEQEAAILANDLRKIIENSQINISSGPSIHITISAGIAERC-HKEPISTIIYRADQALYVAKK  249 (266)
Q Consensus       171 ~~~R~~gdeF~ill~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~~~t~s~Gia~~~-~~~~~~~ll~~Ad~Al~~AK~  249 (266)
                      .++|++||+|++++++..........+++........+ ..++....+++|+|++.++ ++.++++++.+||.|||+||+
T Consensus        82 ~~~r~~~~~f~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~s~g~~~~~~~~~~~~~ll~~A~~Al~~AK~  160 (177)
T 3ign_A           82 SAGRYGGEEFGIILPETDAESARVICERIREAIEKSTV-STSAGDIQYTVSXGIAQLTETPENYXQWXQKADEALYKAKE  160 (177)
T ss_dssp             EEEECSSSEEEEEEETCCHHHHHHHHHHHHHHHHTCCE-ECSSCEECCCEEEEEEECCSCCSSHHHHHHHHHHHHHHHHH
T ss_pred             CCEECCCCEEEEEECCCCHHHHHHHHHHHHHHHHHCCC-CCCCCCCEEEEEEEEEECCCCCCCHHHHHHHHHHHHHHHHH
T ss_conf             52022588799997898989999999999999982765-45788731678899996479988899999999999999998


Q ss_pred             CCCCEEEECCHHHCCC
Q ss_conf             0996899940210056
Q gi|254781079|r  250 SGRNRVVCFSDIENNT  265 (266)
Q Consensus       250 ~gkn~~~~~~~~~~~~  265 (266)
                      +|+|++++|++--+++
T Consensus       161 ~G~n~~~~y~~~~~~~  176 (177)
T 3ign_A          161 SGRNKVVVSLEHHHHH  176 (177)
T ss_dssp             TTSSSEEECC------
T ss_pred             HCCCEEEEEEECCCCC
T ss_conf             4999699988424447



>1w25_A (A:285-459) Stalked-cell differentiation controlling protein; two-component system, response regulator, diguanylate cyclase, ggdef domain; HET: C2E; 2.70A {Caulobacter vibrioides} Back     alignment and structure
>3ezu_A (A:187-342) Ggdef domain protein; multidomain protein of unknown function with ggdef-domain, structural genomics; 1.95A {Geobacter sulfurreducens} Back     alignment and structure
>3icl_A (A:) EAL/ggdef domain protein; structural genomics, PSI-2, protein structure initiative, northeast structural genomics, consortium, NESG; HET: MSE; 2.00A {Methylococcus capsulatus} Back     alignment and structure
>3hva_A (A:) Protein FIMX; ggdef diguanylate cyclase, biofilm, C-DI-GMP, transferase; 2.04A {Pseudomonas aeruginosa PAO1} Back     alignment and structure
>3i5c_A (A:31-206) Fusion of general control protein GCN4 and WSPR response regulator protein; C-DI-GMP, ggdef, leucine zipper, signaling protein; HET: C2E; 1.94A {Pseudomonas aeruginosa PAO1} PDB: 3i5b_A* Back     alignment and structure
>3bre_A (A:176-358) Probable two-component response regulator; protein-nucleotide complex, signaling protein; HET: C2E; 2.40A {Pseudomonas aeruginosa PAO1} PDB: 3i5a_A* Back     alignment and structure
>3hvw_A (A:) Diguanylate-cyclase (DGC); alpha-beta protein., structural genomics, PSI-2, protein structure initiative; 1.70A {Pseudomonas aeruginosa} Back     alignment and structure
>3hvb_A (A:) Protein FIMX; EAL phosphodiesterase, biofilm, C-DI-GMP, hydrolase; 2.99A {Pseudomonas aeruginosa PAO1} Back     alignment and structure
>2qv6_A (A:128-268) MJ0145, GTP cyclohydrolase III, MJGC; enzyme, FAPY; HET: GTP; 2.00A {Methanocaldococcus jannaschii} Back     alignment and structure
>1yk9_A (A:) Adenylate cyclase; beta-alpha-beta sandwich, structural genomics, PSI, protein structure initiative; 2.70A {Mycobacterium tuberculosis} Back     alignment and structure
>3gqc_A (A:1-96,A:213-314) DNA repair protein REV1; protein-DNA complex, alternative splicing, DNA damage, DNA repair, DNA synthesis; HET: DNA DOC DCP; 2.50A {Homo sapiens} Back     alignment and structure
>2qv6_A (A:1-127) MJ0145, GTP cyclohydrolase III, MJGC; enzyme, FAPY; HET: GTP; 2.00A {Methanocaldococcus jannaschii} Back     alignment and structure
>3et6_A (A:) Soluble guanylyl cyclase beta; guanylate cyclase, dimethylarsenic, lyase, membrane, transmembrane; 2.55A {Chlamydomonas reinhardtii} PDB: 3et6_B Back     alignment and structure
>1jx4_A (A:1-10,A:78-182) DNA polymerase IV (family Y); protein-DNA complex, Y-family, transferase/DNA complex; HET: DNA MSE ADI; 1.70A {Sulfolobus solfataricus} Back     alignment and structure
>1azs_A (A:) VC1; complex (lyase/hydrolase), hydrolase, signal transducing protein, cyclase, effector enzyme; HET: GSP FKP; 2.30A {Canis familiaris} Back     alignment and structure
>3bq0_A (A:1-10,A:78-169,A:236-244) POL IV, DBH, DNA polymerase IV; Y-family, lesion bypass; HET: DNA; 2.60A {Sulfolobus acidocaldarius} Back     alignment and structure