254780853

254780853

NADH dehydrogenase subunit B

GeneID in NCBI database:8209868Locus tag:CLIBASIA_03740
Protein GI in NCBI database:254780853Protein Accession:YP_003065266.1
Gene range:+(822929, 823486)Protein Length:185aa
Gene description:NADH dehydrogenase subunit B
COG prediction:[C] NADH:ubiquinone oxidoreductase 20 kD subunit and related Fe-S oxidoreductases
KEGG prediction:nuoB; NADH dehydrogenase subunit B (EC:1.6.99.5); K00331 NADH dehydrogenase I subunit B [EC:1.6.5.3]
SEED prediction:NADH-ubiquinone oxidoreductase chain B (EC 1.6.5.3)
Pathway involved in KEGG:Oxidative phosphorylation [PATH:las00190]
Subsystem involved in SEED:Respiratory Complex I
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
TOPPRED2 TM-Helix
HMMTOP1 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--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170-------180-----
MGLTTVNQKIISGQSSCSLEKVDADFSRISSEITHKGFLVTSVDQLVTWARTGSLMWMTFGLACCAVEMMQASMPRYDLERFGFAPRASPRQSDVMIVAGTLTNKMASALRRVYDQMPEPRYVISMGSCANGGGYYHYSYSVVRGCDRIVPVDIYVPGCPPTAEALIYGILLLQKKIRRVGNVKC
ccHHHHHHHHHccccccccccccHHHHHHHHHcccccEEEEEHHHHHHHHHHcccEEEEccccHHHHHHHHHccccccHHHcccEEccccccccEEEEEccccHHHHHHHHHHHHHcccccEEEEEccccccccccccccHHHcccHHEEEEEEEcccccccHHHHHHHHHHHHHHHHHHccccc
ccccccccccccccccccccccccccccccHHHHccccEEEcHHHHHHHHHccccccccccHHHHHHHHHccccccccHHcccccccccccccHHHHHHcHHHHHHHHHHHHHHHHcccccEEEEccccccccccEEEEEEEEccccccEcEcEEccccccHHHHHHHHHHHHHHHHHHcccccc
MGLTTVNQKIisgqsscslekvdaDFSRisseithkgfLVTSVDQLVTWARTGSLMWMTFGLACCAVEMmqasmprydlerfgfaprasprqsdvMIVAGTLTNKMASALRRvydqmpepryvismgscangggyyhysysvvrgcdrivpvdiyvpgcpptAEALIYGILLLQKKIRRVGNVKC
mglttvnqkiisgqsscsleKVDADFSRISseithkgflvtsVDQLVTWARTGSLMWMTFGLACCAVEMMQASMPRYDLERFgfaprasprqsDVMIVAGTLTNKMASALRRVYDQMPEPRYVISMGSCANGGGYYHYSYSVVRGCDRIVPVDIYVPGCPPTAEALIYGILLLQKKIrrvgnvkc
MGLTTVNQKIISGQSSCSLEKVDADFSRISSEITHKGFLVTSVDQLVTWARTGSLMWMTFGLACCAVEMMQASMPRYDLERFGFAPRASPRQSDVMIVAGTLTNKMASALRRVYDQMPEPRYVISMGSCANgggyyhysysvvrgCDRIVPVDIYVPGCPPTAEALIYGILLLQKKIRRVGNVKC
*************************************FLVTSVDQLVTWARTGSLMWMTFGLACCAVEMMQASMPRYDLERFGFAPRASPRQSDVMIVAGTLTNKMASALRRVYDQMPEPRYVISMGSCANGGGYYHYSYSVVRGCDRIVPVDIYVPGCPPTAEALIYGILLLQKKIR*******
MGLTTVNQKIISGQSSCSLEKVDADFSRISSEITHKGFLVTSVDQLVTWARTGSLMWMTFGLACCAVEMMQASMPRYDLERFGFAPRASPRQSDVMIVAGTLTNKMASALRRVYDQMPEPRYVISMGSCANGGGYYHYSYSVVRGCDRIVPVDIYVPGCPPTAEALIYGILLLQKKIRRVGNVKC
****************CSLEKVDADFSRISSEITHKGFLVTSVDQLVTWARTGSLMWMTFGLACCAVEMMQASMPRYDLERFGFAPRASPRQSDVMIVAGTLTNKMASALRRVYDQMPEPRYVISMGSCANGGGYYHYSYSVVRGCDRIVPVDIYVPGCPPTAEALIYGILLLQKKIRRV*****
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxHHHHHHHHHHHHHHHHHHHHxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxhhhhhhhhhhhhhhhhhhhhxxxxxxxxxxxx
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooHHHHHHHHHHHHHHHHHHHHHHHHHiiiiiiiiiiii
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oooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
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MGLTTVNQKIISGQSSCSLEKVDADFSRISSEITHKGFLVTSVDQLVTWARTGSLMWMTFGLACCAVEMMQASMPRYDLERFGFAPRASPRQSDVMIVAGTLTNKMASALRRVYDQMPEPRYVISMGSCANGGGYYHYSYSVVRGCDRIVPVDIYVPGCPPTAEALIYGILLLQKKIRRVGNVKC
MGLTTVNQKIISGQSSCSLEKVDADFSRISSEITHKGFLVTSVDQLVTWARTGSLMWMTFGLACCAVEMMQASMPRYDLERFGFAPRASPRQSDVMIVAGTLTNKMASALRRVYDQMPEPRYVISMGSCANGGGYYHYSYSVVRGCDRIVPVDIYVPGCPPTAEALIYGILLLQKKIRRVGNVKC
MGLTTVNQKIISGQSSCSLEKVDADFSRISSEITHKGFLVTSVDQLVTWARTGSLMWMTFGLACCAVEMMQASMPRYDLERFGFAPRASPRQSDVMIVAGTLTNKMASALRRVYDQMPEPRYVISMGSCANGGGYYHYSYSVVRGCDRIVPVDIYVPGCPPTAEALIYGILLLQKKIRRVGNVKC

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
Target185 NADH dehydrogenase subunit B [Candidatus Liberibacter a
315122725185 NADH dehydrogenase subunit B [Candidatus Liberibacter s 1 8e-91
300023456198 NADH-quinone oxidoreductase subunit beta [Hyphomicrobiu 1 3e-82
327188488201 NADH dehydrogenase subunit B [Rhizobium etli CNPAF512] 1 9e-82
86357237194 NADH dehydrogenase subunit B [Rhizobium etli CFN 42] Le 1 1e-81
153009751193 NADH dehydrogenase subunit B [Ochrobactrum anthropi ATC 1 1e-81
150396112192 NADH dehydrogenase subunit B [Sinorhizobium medicae WSM 1 1e-81
190891286194 NADH-ubiquinone oxidoreductase, chain B [Rhizobium etli 1 2e-81
209548863194 NADH dehydrogenase subunit B [Rhizobium leguminosarum b 1 2e-81
118590038192 NADH dehydrogenase subunit B [Stappia aggregata IAM 126 1 2e-81
239831687193 NADH-quinone oxidoreductase, B subunit [Ochrobactrum in 1 3e-81
>gi|315122725|ref|YP_004063214.1| NADH dehydrogenase subunit B [Candidatus Liberibacter solanacearum CLso-ZC1] Length = 185 Back     alignment and organism information
 Score =  336 bits (862), Expect = 8e-91,   Method: Compositional matrix adjust.
 Identities = 158/184 (85%), Positives = 168/184 (91%)

Query: 1   MGLTTVNQKIISGQSSCSLEKVDADFSRISSEITHKGFLVTSVDQLVTWARTGSLMWMTF 60
           MGLT  ++KI+   SS SLEK   DF    +E+ +KGFLV  +DQLVTWARTGSLMWMTF
Sbjct: 1   MGLTKFDRKIVVDHSSFSLEKAGMDFPSTDTELMNKGFLVAPIDQLVTWARTGSLMWMTF 60

Query: 61  GLACCAVEMMQASMPRYDLERFGFAPRASPRQSDVMIVAGTLTNKMASALRRVYDQMPEP 120
           GLACCAVEMMQASMPRYDLERFGFAPRASPRQSDVMIVAGTLTNKMASALRRVYDQMPEP
Sbjct: 61  GLACCAVEMMQASMPRYDLERFGFAPRASPRQSDVMIVAGTLTNKMASALRRVYDQMPEP 120

Query: 121 RYVISMGSCANGGGYYHYSYSVVRGCDRIVPVDIYVPGCPPTAEALIYGILLLQKKIRRV 180
           RYVISMGSCANGGGYYHYSYSVVRGCDRIVPVD+YVPGCPPTAEALIYGILLLQKKIRR+
Sbjct: 121 RYVISMGSCANGGGYYHYSYSVVRGCDRIVPVDVYVPGCPPTAEALIYGILLLQKKIRRI 180

Query: 181 GNVK 184
           GN+K
Sbjct: 181 GNIK 184


Species: Candidatus Liberibacter solanacearum
Genus: Candidatus Liberibacter
Family: Rhizobiaceae
Order: Rhizobiales
Class: Alphaproteobacteria
Phylum: Proteobacteria
Superkingdom: Bacteria
>gi|300023456|ref|YP_003756067.1| NADH-quinone oxidoreductase subunit beta [Hyphomicrobium denitrificans ATCC 51888] Length = 198 Back     alignment and organism information
>gi|327188488|gb|EGE55702.1| NADH dehydrogenase subunit B [Rhizobium etli CNPAF512] Length = 201 Back     alignment and organism information
>gi|86357237|ref|YP_469129.1| NADH dehydrogenase subunit B [Rhizobium etli CFN 42] Length = 194 Back     alignment and organism information
>gi|153009751|ref|YP_001370966.1| NADH dehydrogenase subunit B [Ochrobactrum anthropi ATCC 49188] Length = 193 Back     alignment and organism information
>gi|150396112|ref|YP_001326579.1| NADH dehydrogenase subunit B [Sinorhizobium medicae WSM419] Length = 192 Back     alignment and organism information
>gi|190891286|ref|YP_001977828.1| NADH-ubiquinone oxidoreductase, chain B [Rhizobium etli CIAT 652] Length = 194 Back     alignment and organism information
>gi|209548863|ref|YP_002280780.1| NADH dehydrogenase subunit B [Rhizobium leguminosarum bv. trifolii WSM2304] Length = 194 Back     alignment and organism information
>gi|118590038|ref|ZP_01547442.1| NADH dehydrogenase subunit B [Stappia aggregata IAM 12614] Length = 192 Back     alignment and organism information
>gi|239831687|ref|ZP_04680016.1| NADH-quinone oxidoreductase, B subunit [Ochrobactrum intermedium LMG 3301] Length = 193 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
Target185 NADH dehydrogenase subunit B [Candidatus Liberibacter a
PRK06411183 PRK06411, PRK06411, NADH dehydrogenase subunit B; Valid 6e-85
TIGR01957145 TIGR01957, nuoB_fam, NADH-quinone oxidoreductase, B sub 9e-72
KOG1687168 KOG1687, KOG1687, KOG1687, NADH-ubiquinone oxidoreducta 1e-68
PRK14813189 PRK14813, PRK14813, NADH dehydrogenase subunit B; Provi 7e-56
PRK14818173 PRK14818, PRK14818, NADH dehydrogenase subunit B; Provi 4e-55
PRK14819264 PRK14819, PRK14819, NADH dehydrogenase subunit B; Provi 3e-52
PRK13292 788 PRK13292, PRK13292, trifunctional NADH dehydrogenase I 2e-51
PRK14815183 PRK14815, PRK14815, NADH dehydrogenase subunit B; Provi 2e-47
PRK14816182 PRK14816, PRK14816, NADH dehydrogenase subunit B; Provi 1e-46
CHL00023225 CHL00023, ndhK, NADH dehydrogenase subunit K 4e-42
PRK14817181 PRK14817, PRK14817, NADH dehydrogenase subunit B; Provi 2e-40
PRK14814186 PRK14814, PRK14814, NADH dehydrogenase subunit B; Provi 4e-39
PRK14820180 PRK14820, PRK14820, NADH dehydrogenase subunit B; Provi 2e-38
COG0377194 COG0377, NuoB, NADH:ubiquinone oxidoreductase 20 kD sub 7e-75
COG3260148 COG3260, COG3260, Ni,Fe-hydrogenase III small subunit [ 5e-34
pfam01058124 pfam01058, Oxidored_q6, NADH ubiquinone oxidoreductase, 1e-28
COG1941247 COG1941, FrhG, Coenzyme F420-reducing hydrogenase, gamm 2e-04
TIGR03294228 TIGR03294, FrhG, coenzyme F420 hydrogenase, subunit gam 0.001
>gnl|CDD|180557 PRK06411, PRK06411, NADH dehydrogenase subunit B; Validated Back     alignment and domain information
>gnl|CDD|162625 TIGR01957, nuoB_fam, NADH-quinone oxidoreductase, B subunit Back     alignment and domain information
>gnl|CDD|36900 KOG1687, KOG1687, KOG1687, NADH-ubiquinone oxidoreductase, NUFS7/PSST/20 kDa subunit [Energy production and conversion] Back     alignment and domain information
>gnl|CDD|173274 PRK14813, PRK14813, NADH dehydrogenase subunit B; Provisional Back     alignment and domain information
>gnl|CDD|173279 PRK14818, PRK14818, NADH dehydrogenase subunit B; Provisional Back     alignment and domain information
>gnl|CDD|173280 PRK14819, PRK14819, NADH dehydrogenase subunit B; Provisional Back     alignment and domain information
>gnl|CDD|183955 PRK13292, PRK13292, trifunctional NADH dehydrogenase I subunit B/C/D; Provisional Back     alignment and domain information
>gnl|CDD|184832 PRK14815, PRK14815, NADH dehydrogenase subunit B; Provisional Back     alignment and domain information
>gnl|CDD|173277 PRK14816, PRK14816, NADH dehydrogenase subunit B; Provisional Back     alignment and domain information
>gnl|CDD|176965 CHL00023, ndhK, NADH dehydrogenase subunit K Back     alignment and domain information
>gnl|CDD|173278 PRK14817, PRK14817, NADH dehydrogenase subunit B; Provisional Back     alignment and domain information
>gnl|CDD|173275 PRK14814, PRK14814, NADH dehydrogenase subunit B; Provisional Back     alignment and domain information
>gnl|CDD|184833 PRK14820, PRK14820, NADH dehydrogenase subunit B; Provisional Back     alignment and domain information
>gnl|CDD|30726 COG0377, NuoB, NADH:ubiquinone oxidoreductase 20 kD subunit and related Fe-S oxidoreductases [Energy production and conversion] Back     alignment and domain information
>gnl|CDD|33071 COG3260, COG3260, Ni,Fe-hydrogenase III small subunit [Energy production and conversion] Back     alignment and domain information
>gnl|CDD|144593 pfam01058, Oxidored_q6, NADH ubiquinone oxidoreductase, 20 Kd subunit Back     alignment and domain information
>gnl|CDD|32124 COG1941, FrhG, Coenzyme F420-reducing hydrogenase, gamma subunit [Energy production and conversion] Back     alignment and domain information
>gnl|CDD|132337 TIGR03294, FrhG, coenzyme F420 hydrogenase, subunit gamma Back     alignment and domain information

Conserved Domains in CDD Database Detected by HHsearch

IdentityAlignment graphLength Definition Probability
Target 185 NADH dehydrogenase subunit B [Candidatus Liberibacter a
TIGR01957146 nuoB_fam NADH-quinone oxidoreductase, B subunit; InterP 100.0
COG0377194 NuoB NADH:ubiquinone oxidoreductase 20 kD subunit and r 100.0
CHL00023225 ndhK NADH dehydrogenase subunit K 100.0
PRK06411195 NADH dehydrogenase subunit B; Validated 100.0
PRK13292 784 trifunctional NADH dehydrogenase I subunit B/C/D; Provi 100.0
KOG1687168 consensus 100.0
COG3260148 Ni,Fe-hydrogenase III small subunit [Energy production 100.0
COG1740 355 HyaA Ni,Fe-hydrogenase I small subunit [Energy producti 98.99
PRK10468 371 hydrogenase 2 small subunit; Provisional 98.84
TIGR00391 370 hydA hydrogenase (NiFe) small subunit (hydA); InterPro: 95.94
pfam01058124 Oxidored_q6 NADH ubiquinone oxidoreductase, 20 Kd subun 99.97
TIGR03294228 FrhG coenzyme F420 hydrogenase, subunit gamma. This mod 99.7
COG1941247 FrhG Coenzyme F420-reducing hydrogenase, gamma subunit 99.61
>TIGR01957 nuoB_fam NADH-quinone oxidoreductase, B subunit; InterPro: IPR006138 Respiratory-chain NADH dehydrogenase (1 Back     alignment and domain information
>COG0377 NuoB NADH:ubiquinone oxidoreductase 20 kD subunit and related Fe-S oxidoreductases [Energy production and conversion] Back     alignment and domain information
>CHL00023 ndhK NADH dehydrogenase subunit K Back     alignment and domain information
>PRK06411 NADH dehydrogenase subunit B; Validated Back     alignment and domain information
>PRK13292 trifunctional NADH dehydrogenase I subunit B/C/D; Provisional Back     alignment and domain information
>KOG1687 consensus Back     alignment and domain information
>COG3260 Ni,Fe-hydrogenase III small subunit [Energy production and conversion] Back     alignment and domain information
>COG1740 HyaA Ni,Fe-hydrogenase I small subunit [Energy production and conversion] Back     alignment and domain information
>PRK10468 hydrogenase 2 small subunit; Provisional Back     alignment and domain information
>TIGR00391 hydA hydrogenase (NiFe) small subunit (hydA); InterPro: IPR001821 Hydrogenases catalyse the reversible oxidation of molecular hydrogen and play a vital role in anaerobic metabolism Back     alignment and domain information
>pfam01058 Oxidored_q6 NADH ubiquinone oxidoreductase, 20 Kd subunit Back     alignment and domain information
>TIGR03294 FrhG coenzyme F420 hydrogenase, subunit gamma Back     alignment and domain information
>COG1941 FrhG Coenzyme F420-reducing hydrogenase, gamma subunit [Energy production and conversion] 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
Target185 NADH dehydrogenase subunit B [Candidatus Liberibacter a
2fug_6181 Crystal Structure Of The Hydrophilic Domain Of Resp 1e-53
2wpn_A317 Structure Of The Oxidised, As-Isolated Nifese Hydro 2e-04
gi|90109659|pdb|2FUG|6 Chain 6, Crystal Structure Of The Hydrophilic Domain Of Respiratory Complex I From Thermus Thermophilus Length = 181 Back     alignment and structure
 Score =  213 bits (542), Expect = 1e-53,   Method: Composition-based stats.
 Identities = 86/160 (53%), Positives = 118/160 (73%), Gaps = 2/160 (1%)

Query: 20  EKVDADFSRISSEITHKGFLVTSVDQLVTWARTGSLMWMTFGLACCAVEMMQASMPRYDL 79
             +   F R   E+  +G L T++++LV W R+ SL   TFGLACCA+EMM ++  R DL
Sbjct: 1   MALKDLFERDVQELEREGILFTTLEKLVAWGRSNSLWPATFGLACCAIEMMASTDARNDL 60

Query: 80  ERFGFA-PRASPRQSDVMIVAGTLTNKMASALRRVYDQMPEPRYVISMGSCANGGGYYHY 138
            RFG    RASPRQ+DVMIVAG L+ KMA  +RRV++QMP+P++VISMG+CA+ GG ++ 
Sbjct: 61  ARFGSEVFRASPRQADVMIVAGRLSKKMAPVMRRVWEQMPDPKWVISMGACASSGGMFN- 119

Query: 139 SYSVVRGCDRIVPVDIYVPGCPPTAEALIYGILLLQKKIR 178
           +Y++V+  D +VPVD+YVPGCPP  EALIY ++ LQKK+R
Sbjct: 120 NYAIVQNVDSVVPVDVYVPGCPPRPEALIYAVMQLQKKVR 159


gi|284449405|pdb|2WPN|A Chain A, Structure Of The Oxidised, As-Isolated Nifese Hydrogenase From D. Vulgaris Hildenborough Length = 317 Back     alignment and structure

Homologous Structures in PDB70 Database Detected by RPS-BLAST

IdentityAlignment graphLength Definition E-value
Target185 NADH dehydrogenase subunit B [Candidatus Liberibacter a
3i9v_6181 NADH-quinone oxidoreductase subunit 6; electron transpo 2e-55
1h2a_S317 Hydrogenase; SO ligand, hydrogen metabolism, Mg center, 1e-16
1wui_S267 Periplasmic [NIFE] hydrogenase small subunit; high reso 3e-16
1yq9_A264 Periplasmic [NIFE] hydrogenase small subunit; oxidoredu 1e-15
1yqw_A264 Periplasmic [NIFE] hydrogenase small subunit; NI-Fe hyd 3e-13
1cc1_S283 Hydrogenase (small subunit); NI-Fe-Se hydrogenase, oxid 2e-13
3myr_A269 Hydrogenase (NIFE) small subunit HYDA; [NIFE] hydrogena 5e-13
2wpn_A317 Periplasmic [nifese] hydrogenase, small subunit; metal- 3e-06
3nb0_A725 Glycogen [starch] synthase isoform 2; glycogen synthase 3e-05
>3i9v_6 NADH-quinone oxidoreductase subunit 6; electron transport, respiratory chain, 4Fe- 4S, cell membrane, flavoprotein, FMN, iron; HET: FMN; 3.10A {Thermus thermophilus HB8} PDB: 2fug_6* 3iam_6* 3ias_6* Length = 181 Back     alignment and structure
 Score =  210 bits (535), Expect = 2e-55
 Identities = 86/155 (55%), Positives = 117/155 (75%), Gaps = 2/155 (1%)

Query: 26  FSRISSEITHKGFLVTSVDQLVTWARTGSLMWMTFGLACCAVEMMQASMPRYDLERFGFA 85
           F R   E+  +G L T++++LV W R+ SL   TFGLACCA+EMM ++  R DL RFG  
Sbjct: 7   FERDVQELEREGILFTTLEKLVAWGRSNSLWPATFGLACCAIEMMASTDARNDLARFGSE 66

Query: 86  -PRASPRQSDVMIVAGTLTNKMASALRRVYDQMPEPRYVISMGSCANGGGYYHYSYSVVR 144
             RASPRQ+DVMIVAG L+ KMA  +RRV++QMP+P++VISMG+CA+ GG ++ +Y++V+
Sbjct: 67  VFRASPRQADVMIVAGRLSKKMAPVMRRVWEQMPDPKWVISMGACASSGGMFN-NYAIVQ 125

Query: 145 GCDRIVPVDIYVPGCPPTAEALIYGILLLQKKIRR 179
             D +VPVD+YVPGCPP  EALIY ++ LQKK+R 
Sbjct: 126 NVDSVVPVDVYVPGCPPRPEALIYAVMQLQKKVRG 160


>1h2a_S Hydrogenase; SO ligand, hydrogen metabolism, Mg center, MIR, MAD, oxidoreductase; 1.80A {Desulfovibrio vulgaris str} SCOP: e.19.1.1 Length = 317 Back     alignment and structure
>1wui_S Periplasmic [NIFE] hydrogenase small subunit; high resolution [NIFE]hydrogenase, oxidoreductase, NI-A state, unready state; HET: NFC; 1.04A {Desulfovibrio vulgaris str} SCOP: e.19.1.1 PDB: 1h2r_S 1ubj_S 1ubh_S 1ubl_S 1ubm_S 1ubo_S 1ubr_S 1ubt_S 1ubu_S 1wuh_S* 1ubk_S* 1wuj_S 1wuk_S 1wul_S 1e3d_A* Length = 267 Back     alignment and structure
>1yq9_A Periplasmic [NIFE] hydrogenase small subunit; oxidoreductase; 2.35A {Desulfovibrio gigas} SCOP: e.19.1.1 PDB: 2frv_S 1frv_A Length = 264 Back     alignment and structure
>1yqw_A Periplasmic [NIFE] hydrogenase small subunit; NI-Fe hydrogenase unready state, oxidoreductase; 1.83A {Desulfovibrio fructosovorans} PDB: 3cur_A 3cus_A 3h3x_A 1yrq_A 1frf_S Length = 264 Back     alignment and structure
>1cc1_S Hydrogenase (small subunit); NI-Fe-Se hydrogenase, oxidoreductase; 2.15A {Desulfovibrio baculatus} SCOP: e.19.1.1 Length = 283 Back     alignment and structure
>3myr_A Hydrogenase (NIFE) small subunit HYDA; [NIFE] hydrogenase, photosynthetic P sulfur bacterium, iron-sulfur cluster, NI-A state; HET: SF4; 2.10A {Allochromatium vinosum} Length = 269 Back     alignment and structure
>2wpn_A Periplasmic [nifese] hydrogenase, small subunit; metal-binding, oxidoreductase, oxygen tolerance; HET: FSX SBY PSW; 2.04A {Desulfovibrio vulgaris} Length = 317 Back     alignment and structure
>3nb0_A Glycogen [starch] synthase isoform 2; glycogen synthase, glucose-6-phosphate, yeast, allosteric AC transferase; HET: G6P; 2.41A {Saccharomyces cerevisiae} PDB: 3nch_A 3naz_A 3o3c_A* Length = 725 Back     alignment and structure

Homologous Structures in PDB70 Database Detected by HHsearch

IdentityAlignment graphLength Definition Probability
Target185 NADH dehydrogenase subunit B [Candidatus Liberibacter a
3i9v_6181 NADH-quinone oxidoreductase subunit 6; electron transpo 100.0
1h2a_S317 Hydrogenase; SO ligand, hydrogen metabolism, Mg center, 99.68
1yq9_A264 Periplasmic [NIFE] hydrogenase small subunit; oxidoredu 99.81
3myr_A269 Hydrogenase (NIFE) small subunit HYDA; [NIFE] hydrogena 99.81
1yqw_A264 Periplasmic [NIFE] hydrogenase small subunit; NI-Fe hyd 99.81
1wui_S267 Periplasmic [NIFE] hydrogenase small subunit; high reso 99.8
1cc1_S283 Hydrogenase (small subunit); NI-Fe-Se hydrogenase, oxid 99.73
2wpn_A317 Periplasmic [nifese] hydrogenase, small subunit; metal- 99.51
>3i9v_6 NADH-quinone oxidoreductase subunit 6; electron transport, respiratory chain, 4Fe- 4S, cell membrane, flavoprotein, FMN, iron; HET: FMN; 3.10A {Thermus thermophilus HB8} PDB: 2fug_6* 3iam_6* 3ias_6* 3m9s_6* Back     alignment and structure
Probab=100.00  E-value=0  Score=460.20  Aligned_cols=160  Identities=54%  Similarity=0.985  Sum_probs=153.9

Q ss_pred             CCHHHHHHHHHHHHCCEEEEEHHHHHHHHHCCCCEEEEECCCCCCHHHHHHCCCCCCHHHCCEE-ECCCCCCCCEEEEEC
Q ss_conf             6425777667541087688559999845612883477523546521356633666786764848-706822060799714
Q gi|254780853|r   22 VDADFSRISSEITHKGFLVTSVDQLVTWARTGSLMWMTFGLACCAVEMMQASMPRYDLERFGFA-PRASPRQSDVMIVAG  100 (185)
Q Consensus        22 i~~~~~~~~~~~~~~~~i~t~~d~l~nW~R~~Slwp~~fg~aCC~iE~~a~~~p~yD~eRfG~~-~~~sPRqADvliVtG  100 (185)
                      +.+.|++...++..+|++.|++|+++||+|++|+||+|||++||+|||+++.+|+||++|||++ |++||||||+|||+|
T Consensus         3 ~~~~~~~~~~~~~~~~~i~t~~~~~~nw~R~~Slw~~~~g~~cC~iE~~a~~~p~yD~eRfG~~~~~aSPR~ADvllVtG   82 (181)
T 3i9v_6            3 LKDLFERDVQELEREGILFTTLEKLVAWGRSNSLWPATFGLACCAIEMMASTDARNDLARFGSEVFRASPRQADVMIVAG   82 (181)
T ss_dssp             ------------CTTSHHHHHHHHHHHHHHTTSCCCEEEECSTHHHHHTTTTTTC----------------CCCCEEEES
T ss_pred             CHHHHHHHHHHHHHCCEEEEEHHHHHHHHHCCCCCCCCCCCCCHHHHHHHCCCCCCCHHHHCCCCCCCCCCCCCEEEECC
T ss_conf             20577889998753786875799998798718975010557763989976149877777732424468998677889717


Q ss_pred             CCCHHHHHHHHHHHHHCCCCCEEEEECCCCCCCCCCCCCCCEECCCCCCCCCEEECCCCCCCHHHHHHHHHHHHHHHHHH
Q ss_conf             13455699999999846866619985355668863478872207722232230674887689899999999999999641
Q gi|254780853|r  101 TLTNKMASALRRVYDQMPEPRYVISMGSCANGGGYYHYSYSVVRGCDRIVPVDIYVPGCPPTAEALIYGILLLQKKIRRV  180 (185)
Q Consensus       101 ~vT~km~~~l~~~yeqmpePK~ViA~G~Ca~sGG~f~~sY~v~~g~d~~iPVDvyVPGCPPrPeail~gl~~L~~ki~~~  180 (185)
                      +||+||+++|+++|||||+||||||+|+||++||+| +||++++|+|++||||+||||||||||+||+||++||+||+++
T Consensus        83 ~vT~km~~~l~~~yeqmp~PK~VIA~GaCa~sGG~f-~sy~vv~gvd~~iPVDv~IPGCPPrPeail~gl~~L~~ki~~~  161 (181)
T 3i9v_6           83 RLSKKMAPVMRRVWEQMPDPKWVISMGACASSGGMF-NNYAIVQNVDSVVPVDVYVPGCPPRPEALIYAVMQLQKKVRGQ  161 (181)
T ss_dssp             CCBTTTHHHHHHHHHSSCSSCCEEEEHHHHHSCTTC-CSTTBCSCGGGTSCCSEEECCSSCCHHHHHHHHHHHHHHHTTC
T ss_pred             CCHHHHHHHHHHHHHHCCCCCEEEEECCCCCCCCCC-CCCCCCCCCCCCCCCCEECCCCCCCHHHHHHHHHHHHHHHHHH
T ss_conf             115878999999998488985389855236788635-6775557866647578777898859999999999999998621


Q ss_pred             CC
Q ss_conf             26
Q gi|254780853|r  181 GN  182 (185)
Q Consensus       181 ~~  182 (185)
                      ..
T Consensus       162 ~~  163 (181)
T 3i9v_6          162 AY  163 (181)
T ss_dssp             CB
T ss_pred             HH
T ss_conf             10



>1h2a_S Hydrogenase; SO ligand, hydrogen metabolism, Mg center, MIR, MAD, oxidoreductase; 1.80A {Desulfovibrio vulgaris str} SCOP: e.19.1.1 Back     alignment and structure
>1yq9_A Periplasmic [NIFE] hydrogenase small subunit; oxidoreductase; 2.35A {Desulfovibrio gigas} SCOP: e.19.1.1 PDB: 2frv_S 1frv_A Back     alignment and structure
>3myr_A Hydrogenase (NIFE) small subunit HYDA; [NIFE] hydrogenase, photosynthetic P sulfur bacterium, iron-sulfur cluster, NI-A state; HET: SF4; 2.10A {Allochromatium vinosum} Back     alignment and structure
>1yqw_A Periplasmic [NIFE] hydrogenase small subunit; NI-Fe hydrogenase unready state, oxidoreductase; 1.83A {Desulfovibrio fructosovorans} PDB: 3cur_A 3cus_A 3h3x_A 1yrq_A 1frf_S Back     alignment and structure
>1wui_S Periplasmic [NIFE] hydrogenase small subunit; high resolution [NIFE]hydrogenase, oxidoreductase, NI-A state, unready state; HET: NFC; 1.04A {Desulfovibrio vulgaris str} SCOP: e.19.1.1 PDB: 1h2r_S 1ubj_S 1ubh_S 1ubl_S 1ubm_S 1ubo_S 1ubr_S 1ubt_S 1ubu_S 1wuh_S* 1ubk_S* 1wuj_S 1wuk_S 1wul_S 1e3d_A* Back     alignment and structure
>1cc1_S Hydrogenase (small subunit); NI-Fe-Se hydrogenase, oxidoreductase; 2.15A {Desulfomicrobium baculatum} SCOP: e.19.1.1 Back     alignment and structure
>2wpn_A Periplasmic [nifese] hydrogenase, small subunit; metal-binding, oxidoreductase, oxygen tolerance; HET: FSX SBY PSW; 2.04A {Desulfovibrio vulgaris} 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 185 NADH dehydrogenase subunit B [Candidatus Liberibacter a
d2fug61161 e.19.1.2 (6:15-175) NAD-quinone oxidoreductase chain 6, 9e-56
d1wuis1267 e.19.1.1 (S:1-267) Nickel-iron hydrogenase, small subun 9e-16
d1yq9a1261 e.19.1.1 (A:4-264) Nickel-iron hydrogenase, small subun 1e-14
d1frfs_261 e.19.1.1 (S:) Nickel-iron hydrogenase, small subunit {D 2e-12
d1cc1s_278 e.19.1.1 (S:) Nickel-iron hydrogenase, small subunit {D 1e-12
>d2fug61 e.19.1.2 (6:15-175) NAD-quinone oxidoreductase chain 6, Nqo6 {Thermus thermophilus [TaxId: 274]} Length = 161 Back     information, alignment and structure

class: Multi-domain proteins (alpha and beta)
fold: HydA/Nqo6-like
superfamily: HydA/Nqo6-like
family: Nq06-like
domain: NAD-quinone oxidoreductase chain 6, Nqo6
species: Thermus thermophilus [TaxId: 274]
 Score =  209 bits (534), Expect = 9e-56
 Identities = 83/145 (57%), Positives = 113/145 (77%), Gaps = 2/145 (1%)

Query: 36  KGFLVTSVDQLVTWARTGSLMWMTFGLACCAVEMMQASMPRYDLERFGF-APRASPRQSD 94
           +G L T++++LV W R+ SL   TFGLACCA+EMM ++  R DL RFG    RASPRQ+D
Sbjct: 3   EGILFTTLEKLVAWGRSNSLWPATFGLACCAIEMMASTDARNDLARFGSEVFRASPRQAD 62

Query: 95  VMIVAGTLTNKMASALRRVYDQMPEPRYVISMGSCANGGGYYHYSYSVVRGCDRIVPVDI 154
           VMIVAG L+ KMA  +RRV++QMP+P++VISMG+CA+ GG ++ +Y++V+  D +VPVD+
Sbjct: 63  VMIVAGRLSKKMAPVMRRVWEQMPDPKWVISMGACASSGGMFN-NYAIVQNVDSVVPVDV 121

Query: 155 YVPGCPPTAEALIYGILLLQKKIRR 179
           YVPGCPP  EALIY ++ LQKK+R 
Sbjct: 122 YVPGCPPRPEALIYAVMQLQKKVRG 146


>d1wuis1 e.19.1.1 (S:1-267) Nickel-iron hydrogenase, small subunit {Desulfovibrio vulgaris [TaxId: 881]} Length = 267 Back     information, alignment and structure
>d1yq9a1 e.19.1.1 (A:4-264) Nickel-iron hydrogenase, small subunit {Desulfovibrio gigas [TaxId: 879]} Length = 261 Back     information, alignment and structure
>d1frfs_ e.19.1.1 (S:) Nickel-iron hydrogenase, small subunit {Desulfovibrio fructosovorans [TaxId: 878]} Length = 261 Back     information, alignment and structure
>d1cc1s_ e.19.1.1 (S:) Nickel-iron hydrogenase, small subunit {Desulfomicrobium baculatum [TaxId: 899]} Length = 278 Back     information, alignment and structure

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

IdentityAlignment graphLength Definition Probability
Target185 NADH dehydrogenase subunit B [Candidatus Liberibacter a
d2fug61161 NAD-quinone oxidoreductase chain 6, Nqo6 {Thermus therm 100.0
d1wuis1267 Nickel-iron hydrogenase, small subunit {Desulfovibrio v 99.88
d1frfs_261 Nickel-iron hydrogenase, small subunit {Desulfovibrio f 99.84
d1cc1s_278 Nickel-iron hydrogenase, small subunit {Desulfomicrobiu 99.82
d1yq9a1261 Nickel-iron hydrogenase, small subunit {Desulfovibrio g 99.8
>d2fug61 e.19.1.2 (6:15-175) NAD-quinone oxidoreductase chain 6, Nqo6 {Thermus thermophilus [TaxId: 274]} Back     information, alignment and structure
class: Multi-domain proteins (alpha and beta)
fold: HydA/Nqo6-like
superfamily: HydA/Nqo6-like
family: Nq06-like
domain: NAD-quinone oxidoreductase chain 6, Nqo6
species: Thermus thermophilus [TaxId: 274]
Probab=100.00  E-value=0  Score=456.96  Aligned_cols=147  Identities=56%  Similarity=1.045  Sum_probs=142.5

Q ss_pred             HCCEEEEEHHHHHHHHHCCCCEEEEECCCCCCHHHHHHCCCCCCHHHCCEE-ECCCCCCCCEEEEECCCCHHHHHHHHHH
Q ss_conf             087688559999845612883477523546521356633666786764848-7068220607997141345569999999
Q gi|254780853|r   35 HKGFLVTSVDQLVTWARTGSLMWMTFGLACCAVEMMQASMPRYDLERFGFA-PRASPRQSDVMIVAGTLTNKMASALRRV  113 (185)
Q Consensus        35 ~~~~i~t~~d~l~nW~R~~Slwp~~fg~aCC~iE~~a~~~p~yD~eRfG~~-~~~sPRqADvliVtG~vT~km~~~l~~~  113 (185)
                      ++|+++|++|+++||+|++|+||+|||++||+|||+++.+|+||+||||+. |++||||||+|||+|+||+||+++|+++
T Consensus         2 ~~~~i~t~~~~~~nw~r~~Slw~~~~g~~cC~iE~~a~~~p~yD~eRfG~~~~~~sPR~ADvllVtG~vT~km~~~l~~~   81 (161)
T d2fug61           2 REGILFTTLEKLVAWGRSNSLWPATFGLACCAIEMMASTDARNDLARFGSEVFRASPRQADVMIVAGRLSKKMAPVMRRV   81 (161)
T ss_dssp             TTSHHHHHHHHHHHHHHHHCCCCCCEECSHHHHHTGGGCCC-----------------CCCCEEEESCCBTTTHHHHHHH
T ss_pred             CCCEEEEEHHHHHHHHHHCCCCEEECCCCCCHHHHHHCCCCCCCHHHHCCCCCCCCCCCCCEEEEECCCHHHHHHHHHHH
T ss_conf             88568756999988998088730020556308777531387665666234235788654767897063308889999999


Q ss_pred             HHHCCCCCEEEEECCCCCCCCCCCCCCCEECCCCCCCCCEEECCCCCCCHHHHHHHHHHHHHHHHHHCC
Q ss_conf             984686661998535566886347887220772223223067488768989999999999999964126
Q gi|254780853|r  114 YDQMPEPRYVISMGSCANGGGYYHYSYSVVRGCDRIVPVDIYVPGCPPTAEALIYGILLLQKKIRRVGN  182 (185)
Q Consensus       114 yeqmpePK~ViA~G~Ca~sGG~f~~sY~v~~g~d~~iPVDvyVPGCPPrPeail~gl~~L~~ki~~~~~  182 (185)
                      ||||||||||||+|+||++||+| +||++++|+|++||||+||||||||||+||+||++||+||+++..
T Consensus        82 y~qmPePK~VIA~GaCa~sGG~f-~~y~v~~gvd~~iPVDvyIPGCPPrPeail~gl~~l~~ki~~~~~  149 (161)
T d2fug61          82 WEQMPDPKWVISMGACASSGGMF-NNYAIVQNVDSVVPVDVYVPGCPPRPEALIYAVMQLQKKVRGQAY  149 (161)
T ss_dssp             HHTSCSSCCEEEEHHHHHSCTTC-CSTTBCSCGGGTSCCSEEECCSSCCHHHHHHHHHHHHHHHHSSCC
T ss_pred             HHHCCCCCEEEEECCCCCCCCCC-CCCCCCCCCCCCCCCCEECCCCCCCHHHHHHHHHHHHHHHHHHCC
T ss_conf             99678976699855445678766-876445785755767516899874989999999999999863000



>d1wuis1 e.19.1.1 (S:1-267) Nickel-iron hydrogenase, small subunit {Desulfovibrio vulgaris [TaxId: 881]} Back     information, alignment and structure
>d1frfs_ e.19.1.1 (S:) Nickel-iron hydrogenase, small subunit {Desulfovibrio fructosovorans [TaxId: 878]} Back     information, alignment and structure
>d1cc1s_ e.19.1.1 (S:) Nickel-iron hydrogenase, small subunit {Desulfomicrobium baculatum [TaxId: 899]} Back     information, alignment and structure
>d1yq9a1 e.19.1.1 (A:4-264) Nickel-iron hydrogenase, small subunit {Desulfovibrio gigas [TaxId: 879]} Back     information, alignment and structure

Homologous Domains in MMDB70 Database Detected by RPS-BLAST

IdentityAlignment graphLength Definition E-value
Target 185 NADH dehydrogenase subunit B [Candidatus Liberibac
3i9v_6_181 (6:) NADH-quinone oxidoreductase subunit 6; electr 7e-43
1cc1_S_1-198198 (S:1-198) Hydrogenase (small subunit); NI-Fe-Se hy 2e-40
2wpn_A_1-240240 (A:1-240) Periplasmic [nifese] hydrogenase, small 2e-39
1yq9_A_1-177177 (A:1-177) Periplasmic [NIFE] hydrogenase small sub 4e-36
1yqw_A_1-182182 (A:1-182) Periplasmic [NIFE] hydrogenase small sub 5e-36
1wui_S_1-180180 (S:1-180) Periplasmic [NIFE] hydrogenase small sub 4e-35
1h2a_S_1-236236 (S:1-236) Hydrogenase; SO ligand, hydrogen metabol 7e-35
>3i9v_6 (6:) NADH-quinone oxidoreductase subunit 6; electron transport, respiratory chain, 4Fe- 4S, cell membrane, flavoprotein, FMN, iron; HET: FMN; 3.10A {Thermus thermophilus HB8} PDB: 2fug_6* 3iam_6* 3ias_6*Length = 181 Back     alignment and structure
 Score =  167 bits (425), Expect = 7e-43
 Identities = 86/160 (53%), Positives = 118/160 (73%), Gaps = 2/160 (1%)

Query: 21  KVDADFSRISSEITHKGFLVTSVDQLVTWARTGSLMWMTFGLACCAVEMMQASMPRYDLE 80
            +   F R   E+  +G L T++++LV W R+ SL   TFGLACCA+EMM ++  R DL 
Sbjct: 2   ALKDLFERDVQELEREGILFTTLEKLVAWGRSNSLWPATFGLACCAIEMMASTDARNDLA 61

Query: 81  RFGFAP-RASPRQSDVMIVAGTLTNKMASALRRVYDQMPEPRYVISMGSCANGGGYYHYS 139
           RFG    RASPRQ+DVMIVAG L+ KMA  +RRV++QMP+P++VISMG+CA+ GG ++ +
Sbjct: 62  RFGSEVFRASPRQADVMIVAGRLSKKMAPVMRRVWEQMPDPKWVISMGACASSGGMFN-N 120

Query: 140 YSVVRGCDRIVPVDIYVPGCPPTAEALIYGILLLQKKIRR 179
           Y++V+  D +VPVD+YVPGCPP  EALIY ++ LQKK+R 
Sbjct: 121 YAIVQNVDSVVPVDVYVPGCPPRPEALIYAVMQLQKKVRG 160


>1cc1_S (S:1-198) Hydrogenase (small subunit); NI-Fe-Se hydrogenase, oxidoreductase; 2.15A {Desulfovibrio baculatus}Length = 198 Back     alignment and structure
>2wpn_A (A:1-240) Periplasmic [nifese] hydrogenase, small subunit; metal-binding, oxidoreductase, oxygen tolerance; HET: FSX SBY PSW; 2.04A {Desulfovibrio vulgaris}Length = 240 Back     alignment and structure
>1yq9_A (A:1-177) Periplasmic [NIFE] hydrogenase small subunit; oxidoreductase; 2.35A {Desulfovibrio gigas}Length = 177 Back     alignment and structure
>1yqw_A (A:1-182) Periplasmic [NIFE] hydrogenase small subunit; NI-Fe hydrogenase unready state, oxidoreductase; 1.83A {Desulfovibrio fructosovorans} PDB: 3cur_A 3cus_A 3h3x_A 1yrq_A 1frf_SLength = 182 Back     alignment and structure
>1wui_S (S:1-180) Periplasmic [NIFE] hydrogenase small subunit; high resolution [NIFE]hydrogenase, oxidoreductase, NI-A state, unready state; HET: NFC; 1.04A {Desulfovibrio vulgaris str}Length = 180 Back     alignment and structure
>1h2a_S (S:1-236) Hydrogenase; SO ligand, hydrogen metabolism, Mg center, MIR, MAD, oxidoreductase; 1.80A {Desulfovibrio vulgaris str}Length = 236 Back     alignment and structure

Homologous Domains in MMDB70 Database Detected by HHsearch

IdentityAlignment graphLength Definition Probability
Target185 NADH dehydrogenase subunit B [Candidatus Liberibacter a
3i9v_6_181 NADH-quinone oxidoreductase subunit 6; electron tr 100.0
1h2a_S_1-236236 Hydrogenase; SO ligand, hydrogen metabolism, Mg ce 100.0
2wpn_A_1-240240 Periplasmic [nifese] hydrogenase, small subunit; m 99.98
1wui_S_1-180180 Periplasmic [NIFE] hydrogenase small subunit; high 99.97
1yqw_A_1-182182 Periplasmic [NIFE] hydrogenase small subunit; NI-F 99.97
1cc1_S_1-198198 Hydrogenase (small subunit); NI-Fe-Se hydrogenase, 99.97
1yq9_A_1-177177 Periplasmic [NIFE] hydrogenase small subunit; oxid 99.97
2wpn_A_1-240240 Periplasmic [nifese] hydrogenase, small subunit; m 91.08
>3i9v_6 (6:) NADH-quinone oxidoreductase subunit 6; electron transport, respiratory chain, 4Fe- 4S, cell membrane, flavoprotein, FMN, iron; HET: FMN; 3.10A {Thermus thermophilus HB8} PDB: 2fug_6* 3iam_6* 3ias_6* Back     alignment and structure
Probab=100.00  E-value=7e-45  Score=282.47  Aligned_cols=157  Identities=55%  Similarity=1.007  Sum_probs=145.2

Q ss_pred             HHHHHHHHHHHHCCEEEEEHHHHHHHHHCCCCEEEEECCCCCCHHHHHHCCCCCCHHHCCE-EECCCCCCCCEEEEECCC
Q ss_conf             2577766754108768855999984561288347752354652135663366678676484-870682206079971413
Q gi|254780853|r   24 ADFSRISSEITHKGFLVTSVDQLVTWARTGSLMWMTFGLACCAVEMMQASMPRYDLERFGF-APRASPRQSDVMIVAGTL  102 (185)
Q Consensus        24 ~~~~~~~~~~~~~~~i~t~~d~l~nW~R~~Slwp~~fg~aCC~iE~~a~~~p~yD~eRfG~-~~~~sPRqADvliVtG~v  102 (185)
                      +.+.....+.+..+++.++.+++.||+|.+++|+.++|++||.+|++++..+.+|++|||. .++++|||||+++|+|+|
T Consensus         5 ~~~~~~~~~~~~~~~~~~~~~~~~~~~r~~~iw~~~~~C~GC~~s~l~~~~~~~~~~~~~~~~~~~~~~~aDiliveG~v   84 (181)
T 3i9v_6            5 DLFERDVQELEREGILFTTLEKLVAWGRSNSLWPATFGLACCAIEMMASTDARNDLARFGSEVFRASPRQADVMIVAGRL   84 (181)
T ss_dssp             ----------CTTSHHHHHHHHHHHHHHTTSCCCEEEECSTHHHHHTTTTTTC----------------CCCCEEEESCC
T ss_pred             HHHHHHHHHHHHCCEEEEEHHHHHHHHHHCCCCCCCCCCCCCHHHHHHCCCCCCCHHCCCCCCCCCCCCCCCEEEEECCC
T ss_conf             56788899876478388579999889982787502135764332343313888634205451147898768789970633


Q ss_pred             CHHHHHHHHHHHHHCCCCCEEEEECCCCCCCCCCCCCCCEECCCCCCCCCEEECCCCCCCHHHHHHHHHHHHHHHHHHC
Q ss_conf             4556999999998468666199853556688634788722077222322306748876898999999999999996412
Q gi|254780853|r  103 TNKMASALRRVYDQMPEPRYVISMGSCANGGGYYHYSYSVVRGCDRIVPVDIYVPGCPPTAEALIYGILLLQKKIRRVG  181 (185)
Q Consensus       103 T~km~~~l~~~yeqmpePK~ViA~G~Ca~sGG~f~~sY~v~~g~d~~iPVDvyVPGCPPrPeail~gl~~L~~ki~~~~  181 (185)
                      |.+|.+.++++||++|+||+|||+|+||++||+|. +|+..+|++++++||+|||||||+||+|+++|..|++++..+-
T Consensus        85 ~~~~~~~~~~~~e~~~~ak~vVA~G~CA~~GGi~~-~~~~~~gv~~~i~vd~~IpGCPp~Pe~i~~~l~~l~~~~~~~~  162 (181)
T 3i9v_6           85 SKKMAPVMRRVWEQMPDPKWVISMGACASSGGMFN-NYAIVQNVDSVVPVDVYVPGCPPRPEALIYAVMQLQKKVRGQA  162 (181)
T ss_dssp             BTTTHHHHHHHHHSSCSSCCEEEEHHHHHSCTTCC-STTBCSCGGGTSCCSEEECCSSCCHHHHHHHHHHHHHHHTTCC
T ss_pred             HHHHHHHHHHHHHHCCCCCEEEEECCCCCCCCCCC-CCCCCCCCCCCCCCCEECCCCCCCHHHHHHHHHHHHHHHHHHH
T ss_conf             07779999999984899856997454466797057-7644478454675775778988599999999999999986323



>1h2a_S (S:1-236) Hydrogenase; SO ligand, hydrogen metabolism, Mg center, MIR, MAD, oxidoreductase; 1.80A {Desulfovibrio vulgaris str} Back     alignment and structure
>2wpn_A (A:1-240) Periplasmic [nifese] hydrogenase, small subunit; metal-binding, oxidoreductase, oxygen tolerance; HET: FSX SBY PSW; 2.04A {Desulfovibrio vulgaris} Back     alignment and structure
>1wui_S (S:1-180) Periplasmic [NIFE] hydrogenase small subunit; high resolution [NIFE]hydrogenase, oxidoreductase, NI-A state, unready state; HET: NFC; 1.04A {Desulfovibrio vulgaris str} Back     alignment and structure
>1yqw_A (A:1-182) Periplasmic [NIFE] hydrogenase small subunit; NI-Fe hydrogenase unready state, oxidoreductase; 1.83A {Desulfovibrio fructosovorans} PDB: 3cur_A 3cus_A 3h3x_A 1yrq_A 1frf_S Back     alignment and structure
>1cc1_S (S:1-198) Hydrogenase (small subunit); NI-Fe-Se hydrogenase, oxidoreductase; 2.15A {Desulfovibrio baculatus} Back     alignment and structure
>1yq9_A (A:1-177) Periplasmic [NIFE] hydrogenase small subunit; oxidoreductase; 2.35A {Desulfovibrio gigas} Back     alignment and structure
>2wpn_A (A:1-240) Periplasmic [nifese] hydrogenase, small subunit; metal-binding, oxidoreductase, oxygen tolerance; HET: FSX SBY PSW; 2.04A {Desulfovibrio vulgaris} Back     alignment and structure