254780854

254780854

NADH dehydrogenase subunit C

GeneID in NCBI database:8209869Locus tag:CLIBASIA_03745
Protein GI in NCBI database:254780854Protein Accession:YP_003065267.1
Gene range:+(823499, 824107)Protein Length:202aa
Gene description:NADH dehydrogenase subunit C
COG prediction:[C] NADH:ubiquinone oxidoreductase 27 kD subunit
KEGG prediction:nuoC; NADH dehydrogenase subunit C (EC:1.6.99.5); K00332 NADH dehydrogenase I subunit C [EC:1.6.5.3]
SEED prediction:NADH-ubiquinone oxidoreductase chain C (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
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--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170-------180-------190-------200--
MVRKIEDLGDYIVNSFSGSVRFAVNSVGELSLDVDCGDLVSLCSFLRDDPHCCFVNIIDLCGVDFLSRSNRFDVVYHFLSPKYNRRLRVKIAVAEGKSVPSIVGIYPGADWFEREVWDMYGIFFEGHPDLRRILTDYGFEGHPLRKDFPVTGFVELHYDDKVKKVVYRPVELMQEHRDYDFLSPWEGVNSLFAKEDSKDDMS
ccHHHHHHHHHHHHHHHHHHHHHHHHcccEEEEEcHHHHHHHHHHHHHcccccccEEEEEEEEEcccccccEEEEEEEEEcccccEEEEEEEccccccccccccccccccHHHHHHHHHHccEEcccccccccccccccccccEEccccccccEEEEEcccccEEEEccccccccHHcccccccccccccccccccccHHcc
ccHHHHHHHHHHHHHHHHHHEEEEEccccEEEEEcccccEcEHHHcccccccEEEEEEEcccccccccccccHEEEEHccccccccEEEEEEccccccccccccccccccHHHHHHHHHHcHcccccccHHHHHHccccccccccccccccEEEEEEEccccEEEEEccEEHHHHHHccccccccccccccccccccccccc
MVRKIEDLGDYIVNSFSGSVRFAVNSvgelsldvdcgdLVSLCsflrddphccfVNIIDlcgvdflsrsnrfdvvyhflspkynrRLRVKIAVAegksvpsivgiypgadwfeREVWDMYGIFFEGHPDLRRILTdygfeghplrkdfpvtgfvelhyddkvkkvvyrpvelmqehrdydflspwegvnslfakedskddms
MVRKIEDLGDYIVNSFSGSVRFAVNSVGELSLDVDCGDLVSLCSFLRDDPHCCFVNIIDLCGVDFLSRSNRFDVVYhflspkynrrLRVKIAvaegksvpsivgiypgADWFEREVWDMYGIFFEGHPDLRRILTDYGFEGHPLRKDFPVTGFVELHYDDKVKKVVYRPVELMqehrdydflspweGVNSlfakedskddms
MVRKIEDLGDYIVNSFSGSVRFAVNSVGELSLDVDCGDLVSLCSFLRDDPHCCFVNIIDLCGVDFLSRSNRFDVVYHFLSPKYNRRLRVKIAVAEGKSVPSIVGIYPGADWFEREVWDMYGIFFEGHPDLRRILTDYGFEGHPLRKDFPVTGFVELHYDDKVKKVVYRPVELMQEHRDYDFLSPWEGVNSLFAKEDSKDDMS
***KIEDLGDYIVNSFSGSVRFAVNSVGELSLDVDCGDLVSLCSFLRDDPHCCFVNIIDLCGVDFLSRSNRFDVVYHFLSPKYNRRLRVKIAVAEGKSVPSIVGIYPGADWFEREVWDMYGIFFEGHPDLRRILTDYGFEGHPLRKDFPVTGFVELHYDDKVKKVVYRPVELMQEHRDYDFLSPWEG***************
MVRKIEDLGDYIVNSFSGSVRFAVNSVGELSLDVDCGDLVSLCSFLRDDPHCCFVNIIDLCGVDFLSRSNRFDVVYHFLSPKYNRRLRVKIAVAEGKSVPSIVGIYPGADWFEREVWDMYGIFFEGHPDLRRILTDYGFEGHPLRKDFPVTGFVELHYDDKVKKVVYRPVELMQEHRDYDFLSPWEGVNSLFAK********
*VRKIEDLGDYIVNSFSGSVRFAVNSVGELSLDVDCGDLVSLCSFLRDDPHCCFVNIIDLCGVDFLSRSNRFDVVYHFLSPKYNRRLRVKIAVAEGKSVPSIVGIYPGADWFEREVWDMYGIFFEGHPDLRRILTDYGFEGHPLRKDFPVTGFVELHYDDKVKKVVYRPVELMQEHRDYDFLSPWEGVNSLFAK********
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MVRKIEDLGDYIVNSFSGSVRFAVNSVGELSLDVDCGDLVSLCSFLRDDPHCCFVNIIDLCGVDFLSRSNRFDVVYHFLSPKYNRRLRVKIAVAEGKSVPSIVGIYPGADWFEREVWDMYGIFFEGHPDLRRILTDYGFEGHPLRKDFPVTGFVELHYDDKVKKVVYRPVELMQEHRDYDFLSPWEGVNSLFAKEDSKDDMS
MVRKIEDLGDYIVNSFSGSVRFAVNSVGELSLDVDCGDLVSLCSFLRDDPHCCFVNIIDLCGVDFLSRSNRFDVVYHFLSPKYNRRLRVKIAVAEGKSVPSIVGIYPGADWFEREVWDMYGIFFEGHPDLRRILTDYGFEGHPLRKDFPVTGFVELHYDDKVKKVVYRPVELMQEHRDYDFLSPWEGVNSLFAKEDSKDDMS
MVRKIEDLGDYIVNSFSGSVRFAVNSVGELSLDVDCGDLVSLCSFLRDDPHCCFVNIIDLCGVDFLSRSNRFDVVYHFLSPKYNRRLRVKIAVAEGKSVPSIVGIYPGADWFEREVWDMYGIFFEGHPDLRRILTDYGFEGHPLRKDFPVTGFVELHYDDKVKKVVYRPVELMQEHRDYDFLSPWEGVNSLFAKEDSKDDMS

Close Homologs Detected by BLAST or PSI-BLAST

Homolog within the Genome Detected by BLAST

IdentityAlignment graphLength Definition E-value
Target202 NADH dehydrogenase subunit C [Candidatus Liberibacter a
254781103 598 penicillin-binding transmembrane protein [Candidat 0.029
>gi|254781103|ref|YP_003065516.1| penicillin-binding transmembrane protein [Candidatus Liberibacter asiaticus str. psy62] Length = 598 Back     alignment
 Score = 30.0 bits (66), Expect = 0.029,   Method: Compositional matrix adjust.
 Identities = 12/34 (35%), Positives = 20/34 (58%)

Query: 21  RFAVNSVGELSLDVDCGDLVSLCSFLRDDPHCCF 54
           ++   SVG + L+V  G+++S+ S    DPH  F
Sbjct: 278 KYNAESVGTVILNVSTGEVISMVSIPDYDPHEAF 311

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

IdentityAlignment graphLength Definition Round E-value
Target202 NADH dehydrogenase subunit C [Candidatus Liberibacter a
315122724198 NADH dehydrogenase subunit C [Candidatus Liberibacter s 1 2e-86
319782983200 NADH (or F420H2) dehydrogenase subunit C [Mesorhizobium 1 2e-64
222085577200 NADH-ubiquinone oxidoreductase chain C protein [Agrobac 1 3e-64
163759541200 NADH-ubiquinone oxidoreductase chain C protein [Hoeflea 1 5e-64
222148276200 NADH dehydrogenase subunit C [Agrobacterium vitis S4] L 1 8e-64
260462232200 NADH (or F420H2) dehydrogenase, subunit C [Mesorhizobiu 1 1e-63
190891287200 NADH-ubiquinone oxidoreductase, chain C [Rhizobium etli 1 2e-63
150396113201 NADH dehydrogenase subunit C [Sinorhizobium medicae WSM 1 2e-63
116251468200 NADH dehydrogenase subunit C [Rhizobium leguminosarum b 1 2e-63
86357238200 NADH dehydrogenase subunit C [Rhizobium etli CFN 42] Le 1 2e-63
>gi|315122724|ref|YP_004063213.1| NADH dehydrogenase subunit C [Candidatus Liberibacter solanacearum CLso-ZC1] Length = 198 Back     alignment and organism information
 Score =  322 bits (824), Expect = 2e-86,   Method: Compositional matrix adjust.
 Identities = 157/195 (80%), Positives = 176/195 (90%), Gaps = 1/195 (0%)

Query: 5   IEDLGDYIVNSFSGSVRFAVNSVGELSLDVDCGDLVSLCSFLRDDPHCCFVNIIDLCGVD 64
           +ED+GDYIVNSF  SVR  +NSVGELSLDVDCGDL+SLC FLRDD +C FVNI+DLCGVD
Sbjct: 1   MEDIGDYIVNSFGRSVRSTINSVGELSLDVDCGDLLSLCYFLRDDSNCRFVNIVDLCGVD 60

Query: 65  FLSRSNRFDVVYHFLSPKYNRRLRVKIAVAEGKSVPSIVGIYPGADWFEREVWDMYGIFF 124
           FLSRS+RFDVVYHFLSPKYN R+RVK+AV+EG S+PS+V +YP A+WFEREV DMYGI F
Sbjct: 61  FLSRSSRFDVVYHFLSPKYNCRVRVKVAVSEGDSIPSMVEVYPAANWFEREVLDMYGIKF 120

Query: 125 EGHPDLRRILTDYGFEGHPLRKDFPVTGFVELHYDDKVKKVVYRPVELMQEHRDYDFLSP 184
           EGHPDLRRILTDYGFEGHPLRKDFPVTGFVEL YDDK KKVVY PVELMQE+RDYDFLSP
Sbjct: 121 EGHPDLRRILTDYGFEGHPLRKDFPVTGFVELRYDDKAKKVVYSPVELMQEYRDYDFLSP 180

Query: 185 WEGVNSLFAKEDSKD 199
           WEG + LFA +DS++
Sbjct: 181 WEG-SPLFADKDSEN 194


Species: Candidatus Liberibacter solanacearum
Genus: Candidatus Liberibacter
Family: Rhizobiaceae
Order: Rhizobiales
Class: Alphaproteobacteria
Phylum: Proteobacteria
Superkingdom: Bacteria
>gi|319782983|ref|YP_004142459.1| NADH (or F420H2) dehydrogenase subunit C [Mesorhizobium ciceri biovar biserrulae WSM1271] Length = 200 Back     alignment and organism information
>gi|222085577|ref|YP_002544107.1| NADH-ubiquinone oxidoreductase chain C protein [Agrobacterium radiobacter K84] Length = 200 Back     alignment and organism information
>gi|163759541|ref|ZP_02166626.1| NADH-ubiquinone oxidoreductase chain C protein [Hoeflea phototrophica DFL-43] Length = 200 Back     alignment and organism information
>gi|222148276|ref|YP_002549233.1| NADH dehydrogenase subunit C [Agrobacterium vitis S4] Length = 200 Back     alignment and organism information
>gi|260462232|ref|ZP_05810476.1| NADH (or F420H2) dehydrogenase, subunit C [Mesorhizobium opportunistum WSM2075] Length = 200 Back     alignment and organism information
>gi|190891287|ref|YP_001977829.1| NADH-ubiquinone oxidoreductase, chain C [Rhizobium etli CIAT 652] Length = 200 Back     alignment and organism information
>gi|150396113|ref|YP_001326580.1| NADH dehydrogenase subunit C [Sinorhizobium medicae WSM419] Length = 201 Back     alignment and organism information
>gi|116251468|ref|YP_767306.1| NADH dehydrogenase subunit C [Rhizobium leguminosarum bv. viciae 3841] Length = 200 Back     alignment and organism information
>gi|86357238|ref|YP_469130.1| NADH dehydrogenase subunit C [Rhizobium etli CFN 42] Length = 200 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
Target202 NADH dehydrogenase subunit C [Candidatus Liberibacter a
PRK06074189 PRK06074, PRK06074, NADH dehydrogenase subunit C; Provi 6e-69
COG0852176 COG0852, NuoC, NADH:ubiquinone oxidoreductase 27 kD sub 4e-46
PRK08491263 PRK08491, PRK08491, NADH dehydrogenase subunit C; Provi 6e-24
KOG1713191 KOG1713, KOG1713, KOG1713, NADH-ubiquinone oxidoreducta 2e-50
TIGR01961121 TIGR01961, NuoC_fam, NADH (or F420H2) dehydrogenase, su 8e-44
pfam00329103 pfam00329, Complex1_30kDa, Respiratory-chain NADH dehyd 1e-33
PRK11742 575 PRK11742, PRK11742, bifunctional NADH:ubiquinone oxidor 2e-33
PRK07785235 PRK07785, PRK07785, NADH dehydrogenase subunit C; Provi 2e-30
PRK13292 788 PRK13292, PRK13292, trifunctional NADH dehydrogenase I 7e-25
PRK07735430 PRK07735, PRK07735, NADH dehydrogenase subunit C; Valid 3e-21
PRK12494172 PRK12494, PRK12494, NADH dehydrogenase subunit J; Provi 5e-17
COG3262165 COG3262, HycE, Ni,Fe-hydrogenase III component G [Energ 4e-13
CHL00012158 CHL00012, ndhJ, NADH dehydrogenase subunit J 1e-12
>gnl|CDD|180384 PRK06074, PRK06074, NADH dehydrogenase subunit C; Provisional Back     alignment and domain information
>gnl|CDD|31193 COG0852, NuoC, NADH:ubiquinone oxidoreductase 27 kD subunit [Energy production and conversion] Back     alignment and domain information
>gnl|CDD|181449 PRK08491, PRK08491, NADH dehydrogenase subunit C; Provisional Back     alignment and domain information
>gnl|CDD|36925 KOG1713, KOG1713, KOG1713, NADH-ubiquinone oxidoreductase, NDUFS3/30 kDa subunit [Energy production and conversion] Back     alignment and domain information
>gnl|CDD|162626 TIGR01961, NuoC_fam, NADH (or F420H2) dehydrogenase, subunit C Back     alignment and domain information
>gnl|CDD|144062 pfam00329, Complex1_30kDa, Respiratory-chain NADH dehydrogenase, 30 Kd subunit Back     alignment and domain information
>gnl|CDD|183294 PRK11742, PRK11742, bifunctional NADH:ubiquinone oxidoreductase subunit C/D; Provisional Back     alignment and domain information
>gnl|CDD|181115 PRK07785, PRK07785, NADH dehydrogenase subunit C; 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|181096 PRK07735, PRK07735, NADH dehydrogenase subunit C; Validated Back     alignment and domain information
>gnl|CDD|183557 PRK12494, PRK12494, NADH dehydrogenase subunit J; Provisional Back     alignment and domain information
>gnl|CDD|33073 COG3262, HycE, Ni,Fe-hydrogenase III component G [Energy production and conversion] Back     alignment and domain information
>gnl|CDD|176955 CHL00012, ndhJ, NADH dehydrogenase subunit J Back     alignment and domain information

Conserved Domains in CDD Database Detected by HHsearch

IdentityAlignment graphLength Definition Probability
Target 202 NADH dehydrogenase subunit C [Candidatus Liberibacter a
PRK06074190 NADH dehydrogenase subunit C; Provisional 100.0
KOG1713191 consensus 100.0
COG0852176 NuoC NADH:ubiquinone oxidoreductase 27 kD subunit [Ener 100.0
PRK07785238 NADH dehydrogenase subunit C; Provisional 100.0
TIGR01961136 NuoC_fam NADH (or F420H2) dehydrogenase, subunit C; Int 100.0
PRK08491263 NADH dehydrogenase subunit C; Provisional 100.0
PRK11742 575 bifunctional NADH:ubiquinone oxidoreductase subunit C/D 100.0
PRK13292 784 trifunctional NADH dehydrogenase I subunit B/C/D; Provi 100.0
CHL00012158 ndhJ NADH dehydrogenase subunit J 100.0
PRK12494172 NADH dehydrogenase subunit J; Provisional 100.0
PRK07735420 NADH dehydrogenase subunit C; Validated 100.0
COG3262165 HycE Ni,Fe-hydrogenase III component G [Energy producti 99.95
pfam00329103 Complex1_30kDa Respiratory-chain NADH dehydrogenase, 30 100.0
>PRK06074 NADH dehydrogenase subunit C; Provisional Back     alignment and domain information
>KOG1713 consensus Back     alignment and domain information
>COG0852 NuoC NADH:ubiquinone oxidoreductase 27 kD subunit [Energy production and conversion] Back     alignment and domain information
>PRK07785 NADH dehydrogenase subunit C; Provisional Back     alignment and domain information
>TIGR01961 NuoC_fam NADH (or F420H2) dehydrogenase, subunit C; InterPro: IPR010218 This entry describes the C subunit of the NADH dehydrogenase complex I in bacteria, as well as many instances of the corresponding mitochondrial subunit (NADH dehydrogenase subunit 9) and of the F420H2 dehydrogenase in Methanosarcina Back     alignment and domain information
>PRK08491 NADH dehydrogenase subunit C; Provisional Back     alignment and domain information
>PRK11742 bifunctional NADH:ubiquinone oxidoreductase subunit C/D; Provisional Back     alignment and domain information
>PRK13292 trifunctional NADH dehydrogenase I subunit B/C/D; Provisional Back     alignment and domain information
>CHL00012 ndhJ NADH dehydrogenase subunit J Back     alignment and domain information
>PRK12494 NADH dehydrogenase subunit J; Provisional Back     alignment and domain information
>PRK07735 NADH dehydrogenase subunit C; Validated Back     alignment and domain information
>COG3262 HycE Ni,Fe-hydrogenase III component G [Energy production and conversion] Back     alignment and domain information
>pfam00329 Complex1_30kDa Respiratory-chain NADH dehydrogenase, 30 Kd subunit 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
Target202 NADH dehydrogenase subunit C [Candidatus Liberibacter a
3mcr_A213 Crystal Structure Of Nadh Dehydrogenase Subunit C ( 2e-20
2fug_5207 Crystal Structure Of The Hydrophilic Domain Of Resp 2e-18
>gi|295982538|pdb|3MCR|A Chain A, Crystal Structure Of Nadh Dehydrogenase Subunit C (Tfu_2693) Thermobifida Fusca Yx-Er1 At 2.65 A Resolution Length = 213 Back     alignment and structure
 Score =  103 bits (256), Expect = 2e-20,   Method: Composition-based stats.
 Identities = 41/132 (31%), Positives = 65/132 (49%), Gaps = 5/132 (3%)

Query: 6   EDLGDYIVNS---FSGSVRFAVNSVGELSLDVDCGDLVSLCSFLRDDPHCCFVNIIDLCG 62
           + L   +      +  ++   V   GE++  V    L+ + + LRDDP   F   + + G
Sbjct: 82  DALERSLKEIGTPYDTAISRVVVDRGEITFHVQREHLLDVATRLRDDPALRFELCLGVTG 141

Query: 63  VDFLSRS-NRFDVVYHFLSPKYNRRLRVKIAVAE-GKSVPSIVGIYPGADWFEREVWDMY 120
           V +     N    VY   S  +N  +R++++  +    +PSIV +YP  DW ERE WD +
Sbjct: 142 VHYPEDEGNELHAVYALRSITHNYEIRLEVSCPDSDPHIPSIVSVYPTNDWHEREAWDFF 201

Query: 121 GIFFEGHPDLRR 132
           GI F+GHP L R
Sbjct: 202 GIIFDGHPALTR 213


gi|90109658|pdb|2FUG|5 Chain 5, Crystal Structure Of The Hydrophilic Domain Of Respiratory Complex I From Thermus Thermophilus Length = 207 Back     alignment and structure

Homologous Structures in PDB70 Database Detected by RPS-BLAST

IdentityAlignment graphLength Definition E-value
Target202 NADH dehydrogenase subunit C [Candidatus Liberibacter a
3mcr_A213 NADH dehydrogenase, subunit C; structural genomics, joi 6e-36
3i9v_5207 NADH-quinone oxidoreductase subunit 5; electron transpo 2e-32
>3mcr_A NADH dehydrogenase, subunit C; structural genomics, joint center for structural genomics, J protein structure initiative, PSI-2; 2.65A {Thermobifida fusca} Length = 213 Back     alignment and structure
 Score =  145 bits (367), Expect = 6e-36
 Identities = 42/130 (32%), Positives = 65/130 (50%), Gaps = 2/130 (1%)

Query: 5   IEDLGDYIVNSFSGSVRFAVNSVGELSLDVDCGDLVSLCSFLRDDPHCCFVNIIDLCGVD 64
           +E     I   +  ++   V   GE++  V    L+ + + LRDDP   F   + + GV 
Sbjct: 84  LERSLKEIGTPYDTAISRVVVDRGEITFHVQREHLLDVATRLRDDPALRFELCLGVTGVH 143

Query: 65  FLSR-SNRFDVVYHFLSPKYNRRLRVKIAVAEGK-SVPSIVGIYPGADWFEREVWDMYGI 122
           +     N    VY   S  +N  +R++++  +    +PSIV +YP  DW ERE WD +GI
Sbjct: 144 YPEDEGNELHAVYALRSITHNYEIRLEVSCPDSDPHIPSIVSVYPTNDWHEREAWDFFGI 203

Query: 123 FFEGHPDLRR 132
            F+GHP L R
Sbjct: 204 IFDGHPALTR 213


>3i9v_5 NADH-quinone oxidoreductase subunit 5; electron transport, respiratory chain, 4Fe- 4S, cell membrane, flavoprotein, FMN, iron; HET: FMN; 3.10A {Thermus thermophilus HB8} PDB: 2fug_5* 3iam_5* 3ias_5* Length = 207 Back     alignment and structure

Homologous Structures in PDB70 Database Detected by HHsearch

IdentityAlignment graphLength Definition Probability
Target202 NADH dehydrogenase subunit C [Candidatus Liberibacter a
3i9v_5207 NADH-quinone oxidoreductase subunit 5; electron transpo 100.0
3mcr_A213 NADH dehydrogenase, subunit C; structural genomics, joi 100.0
>3i9v_5 NADH-quinone oxidoreductase subunit 5; electron transport, respiratory chain, 4Fe- 4S, cell membrane, flavoprotein, FMN, iron; HET: FMN; 3.10A {Thermus thermophilus HB8} PDB: 2fug_5* 3iam_5* 3ias_5* 3m9s_5* Back     alignment and structure
Probab=100.00  E-value=0  Score=406.29  Aligned_cols=177  Identities=32%  Similarity=0.554  Sum_probs=157.4

Q ss_pred             HHHHHHHHCCCCEEEEEEECCCEEEEECHHHHHHHHHHHHHCCCCCCCEEEECCCCCCCC----CCCCEEEEEEEEECC-
Q ss_conf             999999861531145798479599998689899999998718789801475132568877----778579999966157-
Q gi|254780854|r    8 LGDYIVNSFSGSVRFAVNSVGELSLDVDCGDLVSLCSFLRDDPHCCFVNIIDLCGVDFLS----RSNRFDVVYHFLSPK-   82 (202)
Q Consensus         8 L~~~L~~~l~~~I~~~~~~~~el~i~V~~~~l~~vl~~LKdd~~~~F~~LiDItaVDyp~----~~~RFeVvY~LlS~~-   82 (202)
                      |.+.|++.+...+.......|+++|.|+++++.+++++||+   ++|++|+|||||||++    +++||+|||||+|++ 
T Consensus         3 le~~l~e~~~~~~~~e~~~~g~l~i~V~~e~l~~v~~~Lk~---~gf~~L~dit~vD~~~~~~~~~~rf~vvY~l~S~~~   79 (207)
T 3i9v_5            3 LERVLEEARAKGYPIEDNGLGNLWVVLPRERFKEEMAHYKA---MGFNFLADIVGLDYLTYPDPRPERFAVVYELVSLPG   79 (207)
T ss_dssp             THHHHHHHHHTTCCCCBCTTSCBEEECCHHHHHHHHHHHHH---TTCCCEEEEEEEECTTCSSCCSSSEEEEEEECCCTT
T ss_pred             HHHHHHHHHHCCCCEEECCCCCEEEEECHHHHHHHHHHHHH---CCCCCEEEEEEEECCCCCCCCCCEEEEEEEEECCCC
T ss_conf             89999986643672002458838999839999999999986---899928788848278776787875899999744655


Q ss_pred             ----CCCEEEEEEEECCC-CEEECCCCCEECCCCEECCCHHHCCCEECCCCCCCCCCCCCCCCCCCCCCCCCC----CCC
Q ss_conf             ----52059982120578-501012233025531011210113827356798767788998987871133778----984
Q gi|254780854|r   83 ----YNRRLRVKIAVAEG-KSVPSIVGIYPGADWFEREVWDMYGIFFEGHPDLRRILTDYGFEGHPLRKDFPV----TGF  153 (202)
Q Consensus        83 ----~n~ri~Vk~~v~e~-~~vpSi~~i~p~A~W~ERE~~DmfGI~F~gHPdlRRiL~d~~feGhPLRKDFPl----tG~  153 (202)
                          .|.||+||+.++++ +.||||++|||||||+|||+||||||.|+|||||||||+|++|+||||||||||    |||
T Consensus        80 ~~~~~~~rv~vk~~v~~~~p~ipSi~~i~p~A~w~ERE~~DmfGi~f~ghpdlrril~~~~~~g~PLRKDfpl~~~~~~~  159 (207)
T 3i9v_5           80 WKDGDGSRFFVRVYVPEEDPRLPTVTDLWGSANFLEREVYDLFGIVFEGHPDLRKILTPEDLEGHPLRKDYPLGETPTLF  159 (207)
T ss_dssp             SSSCCCCCEEEEEEECSSCCBCCCCTTTCSTHHHHHHHHHHTSCCBCTTCSCCCCCSSCTTCCSCTTSTTSCCCCCCEEC
T ss_pred             CCCCCCEEEEEEEECCCCCCCCCCEECCCCCCCCCCEEEEEECCEEECCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
T ss_conf             66677608999984676567667710305799812322026127676799998454588899989877674688866652


Q ss_pred             EEEEE----------CHHHCEEECCCCEEEEHHHCCCCCCCCCCCCCCC
Q ss_conf             47887----------6211513126642202221276656323453345
Q gi|254780854|r  154 VELHY----------DDKVKKVVYRPVELMQEHRDYDFLSPWEGVNSLF  192 (202)
Q Consensus       154 ~evry----------d~~~k~v~~epv~l~q~~r~f~~~spwe~~~~~~  192 (202)
                      +|+||          +..+++|+|+|+.+.|+||+     +|+|++++.
T Consensus       160 ~e~~~~~p~~~r~~~~~~~~~~~~~~~~~~~~~r~-----~~~~~~~~~  203 (207)
T 3i9v_5          160 REGRYIIPAEFRAALTGKDPGLTFYKGGSRKGYRS-----LWADLKKAR  203 (207)
T ss_dssp             TTSCEECGGGTCCSCCSSCCCSSSCCCGGGSCCCC-----CC-------
T ss_pred             EEEEECCCCCCCCCCCCCCCCCEEECCCCCCCCCC-----HHCCCHHHH
T ss_conf             46675586424444456565411301553635304-----111601320



>3mcr_A NADH dehydrogenase, subunit C; structural genomics, joint center for structural genomics, J protein structure initiative, PSI-2; 2.65A {Thermobifida fusca} 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 202 NADH dehydrogenase subunit C [Candidatus Liberibacter a
d2fug51196 d.307.1.1 (5:1-196) NADH-quinone oxidoreductase chain 5 1e-28
>d2fug51 d.307.1.1 (5:1-196) NADH-quinone oxidoreductase chain 5, Nqo5 {Thermus thermophilus [TaxId: 274]} Length = 196 Back     information, alignment and structure

class: Alpha and beta proteins (a+b)
fold: Nqo5-like
superfamily: Nqo5-like
family: Nqo5-like
domain: NADH-quinone oxidoreductase chain 5, Nqo5
species: Thermus thermophilus [TaxId: 274]
 Score =  119 bits (300), Expect = 1e-28
 Identities = 51/173 (29%), Positives = 82/173 (47%), Gaps = 15/173 (8%)

Query: 25  NSVGELSLDVDCGDLVSLCSFLRDDPHCCFVNIIDLCGVDFLS----RSNRFDVVYHFLS 80
           N +G L + +         +  +      F  + D+ G+D+L+    R  RF VVY  +S
Sbjct: 20  NGLGNLWVVLPRERFKEEMAHYKA---MGFNFLADIVGLDYLTYPDPRPERFAVVYELVS 76

Query: 81  PKY-----NRRLRVKIAV-AEGKSVPSIVGIYPGADWFEREVWDMYGIFFEGHPDLRRIL 134
                     R  V++ V  E   +P++  ++  A++ EREV+D++GI FEGHPDLR+IL
Sbjct: 77  LPGWKDGDGSRFFVRVYVPEEDPRLPTVTDLWGSANFLEREVYDLFGIVFEGHPDLRKIL 136

Query: 135 TDYGFEGHPLRKDFPVTGFVELHYDDKVKKVVYRPVELMQEHRDYDFLSPWEG 187
           T    EGHPLRKD+P+     L  +   + ++          +D        G
Sbjct: 137 TPEDLEGHPLRKDYPLGETPTLFRE--GRYIIPAEFRAALTGKDPGLTFYKGG 187


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

IdentityAlignment graphLength Definition Probability
Target202 NADH dehydrogenase subunit C [Candidatus Liberibacter a
d2fug51196 NADH-quinone oxidoreductase chain 5, Nqo5 {Thermus ther 100.0
>d2fug51 d.307.1.1 (5:1-196) NADH-quinone oxidoreductase chain 5, Nqo5 {Thermus thermophilus [TaxId: 274]} Back     information, alignment and structure
class: Alpha and beta proteins (a+b)
fold: Nqo5-like
superfamily: Nqo5-like
family: Nqo5-like
domain: NADH-quinone oxidoreductase chain 5, Nqo5
species: Thermus thermophilus [TaxId: 274]
Probab=100.00  E-value=0  Score=330.13  Aligned_cols=149  Identities=35%  Similarity=0.631  Sum_probs=127.5

Q ss_pred             HHHHHHHHCCCCEEEEEEECCCEEEEECHHHHHHHHHHHHHCCCCCCCEEEECCCCCCCC----CCCCEEEEEEEEECC-
Q ss_conf             999999861531145798479599998689899999998718789801475132568877----778579999966157-
Q gi|254780854|r    8 LGDYIVNSFSGSVRFAVNSVGELSLDVDCGDLVSLCSFLRDDPHCCFVNIIDLCGVDFLS----RSNRFDVVYHFLSPK-   82 (202)
Q Consensus         8 L~~~L~~~l~~~I~~~~~~~~el~i~V~~~~l~~vl~~LKdd~~~~F~~LiDItaVDyp~----~~~RFeVvY~LlS~~-   82 (202)
                      |.+.|++.....+.......|+++|.|+++++.+++++||+   ++|++|+|||||||+.    .++||+|||||+|+. 
T Consensus         3 le~~Le~a~~~g~~ve~~~~g~l~I~V~~e~l~evl~~LKe---~gF~~L~dITaVD~~~~~e~~~~rfevvYhL~S~~~   79 (196)
T d2fug51           3 LERVLEEARAKGYPIEDNGLGNLWVVLPRERFKEEMAHYKA---MGFNFLADIVGLDYLTYPDPRPERFAVVYELVSLPG   79 (196)
T ss_dssp             HHHHHHHHHTTTCCEEECSSSCEEEECCSTTHHHHHHHTTT---TTCCCCCCEEEEECTTCSSCCSSSEEEEEEEECCTT
T ss_pred             HHHHHHHHHHCCCEEEECCCCCEEEEECHHHHHHHHHHHHH---CCCCCEEEEEEECCCCCCCCCCCEEEEEEEEEEEEE
T ss_conf             89999986733770101348838999859999999999986---799816578848688767676640699987888864


Q ss_pred             ----CCCEEEEEEEECC-CCEEECCCCCEECCCCEECCCHHHCCCEECCCCCCCCCCCCCCCCCCCCCCCCCCCC----C
Q ss_conf             ----5205998212057-850101223302553101121011382735679876778899898787113377898----4
Q gi|254780854|r   83 ----YNRRLRVKIAVAE-GKSVPSIVGIYPGADWFEREVWDMYGIFFEGHPDLRRILTDYGFEGHPLRKDFPVTG----F  153 (202)
Q Consensus        83 ----~n~ri~Vk~~v~e-~~~vpSi~~i~p~A~W~ERE~~DmfGI~F~gHPdlRRiL~d~~feGhPLRKDFPltG----~  153 (202)
                          .+.+|+|||.+++ ++.||||++|||+|||+|||+||||||.|+|||||||||++++|+||||||||||.|    |
T Consensus        80 ~~~~~~~~v~vkv~vp~~~p~ipSi~~i~p~A~w~ERE~~dmfGi~f~ghpd~rr~llpd~~~g~PlRKdfpl~~~~~~~  159 (196)
T d2fug51          80 WKDGDGSRFFVRVYVPEEDPRLPTVTDLWGSANFLEREVYDLFGIVFEGHPDLRKILTPEDLEGHPLRKDYPLGETPTLF  159 (196)
T ss_dssp             SSSCCCCEEEEEEEECSSCCCCCCCCC-----CCCHHHHHHHHHHSSCCCSSCSCCCCSSCSSSCSSSTTSCCCCCCEEC
T ss_pred             CCCCCCCEEEEEEEECCCCCEEEEEECCEECCEEEECCCCEEECEEECCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
T ss_conf             04788638999997235663122342318065101303526608697898888565579999989877676688865555


Q ss_pred             EEEEEC
Q ss_conf             478876
Q gi|254780854|r  154 VELHYD  159 (202)
Q Consensus       154 ~evryd  159 (202)
                      .|+||+
T Consensus       160 ~~~~~~  165 (196)
T d2fug51         160 REGRYI  165 (196)
T ss_dssp             TTSCEE
T ss_pred             CCCCCC
T ss_conf             255307



Homologous Domains in MMDB70 Database Detected by RPS-BLAST

IdentityAlignment graphLength Definition E-value
Target 202 NADH dehydrogenase subunit C [Candidatus Liberibac
3i9v_5_1-141141 (5:1-141) NADH-quinone oxidoreductase subunit 5; e 1e-30
>3i9v_5 (5:1-141) NADH-quinone oxidoreductase subunit 5; electron transport, respiratory chain, 4Fe- 4S, cell membrane, flavoprotein, FMN, iron; HET: FMN; 3.10A {Thermus thermophilus HB8} PDB: 2fug_5* 3iam_5* 3ias_5*Length = 141 Back     alignment and structure
 Score =  126 bits (319), Expect = 1e-30
 Identities = 39/143 (27%), Positives = 67/143 (46%), Gaps = 13/143 (9%)

Query: 7   DLGDYIVNSFSGSVRFAVNSVGELSLDVDCGDLVSLCSFLRDDPHCCFVNIIDLCGVDFL 66
            L   +  + +       N +G L + +         +  +      F  + D+ G+D+L
Sbjct: 2   RLERVLEEARAKGYPIEDNGLGNLWVVLPRERFKEEMAHYKAMG---FNFLADIVGLDYL 58

Query: 67  SRSN----RFDVVYHFLSPKY-----NRRLRVKIAVAEGK-SVPSIVGIYPGADWFEREV 116
           +  +    RF VVY  +S          R  V++ V E    +P++  ++  A++ EREV
Sbjct: 59  TYPDPRPERFAVVYELVSLPGWKDGDGSRFFVRVYVPEEDPRLPTVTDLWGSANFLEREV 118

Query: 117 WDMYGIFFEGHPDLRRILTDYGF 139
           +D++GI FEGHPDLR+ILT    
Sbjct: 119 YDLFGIVFEGHPDLRKILTPEDL 141


Homologous Domains in MMDB70 Database Detected by HHsearch

IdentityAlignment graphLength Definition Probability
Target202 NADH dehydrogenase subunit C [Candidatus Liberibacter a
3i9v_5_1-141141 NADH-quinone oxidoreductase subunit 5; electron tr 100.0
>3i9v_5 (5:1-141) NADH-quinone oxidoreductase subunit 5; electron transport, respiratory chain, 4Fe- 4S, cell membrane, flavoprotein, FMN, iron; HET: FMN; 3.10A {Thermus thermophilus HB8} PDB: 2fug_5* 3iam_5* 3ias_5* Back     alignment and structure
Probab=100.00  E-value=6.8e-40  Score=263.59  Aligned_cols=130  Identities=30%  Similarity=0.542  Sum_probs=120.0

Q ss_pred             HHHHHHHHHCCCCEEEEEEECCCEEEEECHHHHHHHHHHHHHCCCCCCCEEEECCCCCCCCCC----CCEEEEEEEEECC
Q ss_conf             999999986153114579847959999868989999999871878980147513256887777----8579999966157
Q gi|254780854|r    7 DLGDYIVNSFSGSVRFAVNSVGELSLDVDCGDLVSLCSFLRDDPHCCFVNIIDLCGVDFLSRS----NRFDVVYHFLSPK   82 (202)
Q Consensus         7 ~L~~~L~~~l~~~I~~~~~~~~el~i~V~~~~l~~vl~~LKdd~~~~F~~LiDItaVDyp~~~----~RFeVvY~LlS~~   82 (202)
                      ++.+.|++.+++.+.......+++++.|+++.+.+++.+||+.   +|.+|++|||+||+++.    .+|+++|||.|++
T Consensus         2 ~l~~~l~~~~~~~~~~~~~~~~~~~v~i~~~~l~~v~~~Lk~~---~~~~l~~i~~~D~~~~~~~~~~~f~vvY~l~s~~   78 (141)
T 3i9v_5            2 RLERVLEEARAKGYPIEDNGLGNLWVVLPRERFKEEMAHYKAM---GFNFLADIVGLDYLTYPDPRPERFAVVYELVSLP   78 (141)
T ss_dssp             TTHHHHHHHHHTTCCCCBCTTSCBEEECCHHHHHHHHHHHHHT---TCCCEEEEEEEECTTCSSCCSSSEEEEEEECCCT
T ss_pred             CHHHHHHHHHHCCCCCCCCCCCCEEEEECHHHHHHHHHHHHHC---CCCCEEEEEEECCCCCCCCCCCEEEEEEEEEEEE
T ss_conf             5899999877426721103588289998699999999999867---9982646887767876777764179999998654


Q ss_pred             -----CCCEEEEEEEECC-CCEEECCCCCEECCCCEECCCHHHCCCEECCCCCCCCCCCCCCC
Q ss_conf             -----5205998212057-85010122330255310112101138273567987677889989
Q gi|254780854|r   83 -----YNRRLRVKIAVAE-GKSVPSIVGIYPGADWFEREVWDMYGIFFEGHPDLRRILTDYGF  139 (202)
Q Consensus        83 -----~n~ri~Vk~~v~e-~~~vpSi~~i~p~A~W~ERE~~DmfGI~F~gHPdlRRiL~d~~f  139 (202)
                           .|.+|+||+.+++ ++.+|||++|||+|+|+|||+||||||.|+|||||||||+|+||
T Consensus        79 ~~~~~~~~~v~v~~~v~~~~p~ipSi~~i~~~A~w~ERE~~DmfGI~f~ghPdlrrlll~ddf  141 (141)
T 3i9v_5           79 GWKDGDGSRFFVRVYVPEEDPRLPTVTDLWGSANFLEREVYDLFGIVFEGHPDLRKILTPEDL  141 (141)
T ss_dssp             TSSSCCCCCEEEEEEECSSCCBCCCCTTTCSTHHHHHHHHHHTSCCBCTTCSCCCCCSSCTTC
T ss_pred             CCCCCCCEEEEEEEECCCCCCEEEEEECCCCCCCCCEECCCEECCEEECCCCCCCCCCCCCCC
T ss_conf             256777508999861365553010001308275113301537438797898888463579899