Query 033216
Match_columns 125
No_of_seqs 39 out of 41
Neff 3.6
Searched_HMMs 46136
Date Fri Mar 29 11:13:24 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/033216.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/033216hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF05821 NDUF_B8: NADH-ubiquin 99.1 1.6E-10 3.4E-15 90.9 6.5 74 43-125 96-169 (179)
2 KOG4040 NADH:ubiquinone oxidor 96.7 0.0037 8E-08 50.1 5.2 53 71-125 123-176 (186)
3 PLN02720 complex II 29.1 40 0.00086 26.4 1.8 56 41-106 31-91 (140)
4 COG3477 Predicted periplasmic/ 26.8 56 0.0012 26.4 2.3 37 85-122 12-57 (176)
5 KOG1397 Ca2+/H+ antiporter VCX 26.2 1.2E+02 0.0026 27.7 4.6 33 67-99 280-314 (441)
6 PF12351 Fig1: Ca2+ regulator 24.8 95 0.002 24.2 3.3 28 71-98 152-180 (182)
7 PF06181 DUF989: Protein of un 24.2 2.1E+02 0.0045 25.0 5.5 42 54-95 57-103 (300)
8 PRK15126 thiamin pyrimidine py 22.9 60 0.0013 25.3 1.8 24 64-87 178-201 (272)
9 PF08802 CytB6-F_Fe-S: Cytochr 22.7 1.2E+02 0.0027 18.8 2.9 26 71-96 4-29 (39)
10 KOG0815 60S acidic ribosomal p 20.8 1.5E+02 0.0033 25.1 3.9 40 54-98 192-231 (245)
11 COG3748 Predicted membrane pro 20.2 1.4E+02 0.0031 26.8 3.8 42 54-95 54-100 (407)
12 PTZ00174 phosphomannomutase; P 20.1 71 0.0015 25.0 1.7 22 64-85 178-199 (247)
No 1
>PF05821 NDUF_B8: NADH-ubiquinone oxidoreductase ASHI subunit (CI-ASHI or NDUFB8); InterPro: IPR008699 NADH:ubiquinone oxidoreductase (complex I) (1.6.5.3 from EC) is a respiratory-chain enzyme that catalyses the transfer of two electrons from NADH to ubiquinone in a reaction that is associated with proton translocation across the membrane (NADH + ubiquinone = NAD+ + ubiquinol) []. Complex I is a major source of reactive oxygen species (ROS) that are predominantly formed by electron transfer from FMNH(2). Complex I is found in bacteria, cyanobacteria (as a NADH-plastoquinone oxidoreductase), archaea [], mitochondira, and in the hydrogenosome, a mitochondria-derived organelle. In general, the bacterial complex consists of 14 different subunits, while the mitochondrial complex contains homologues to these subunits in addition to approximately 31 additional proteins []. Mitochondrial complex I, which is located in the inner mitochondrial membrane, is the largest multimeric respiratory enzyme in the mitochondria, consisting of more than 40 subunits, one FMN co-factor and eight FeS clusters []. The assembly of mitochondrial complex I is an intricate process that requires the cooperation of the nuclear and mitochondrial genomes [, ]. Mitochondrial complex I can cycle between active and deactive forms that can be distinguished by the reactivity towards divalent cations and thiol-reactive agents. All redox prosthetic groups reside in the peripheral arm of the L-shaped structure. The NADH oxidation domain harbouring the FMN cofactor is connected via a chain of iron-sulphur clusters to the ubiquinone reduction site that is located in a large pocket formed by the PSST and 49kDa subunits of complex I []. This family consists of several eukaryotic NADH-ubiquinone oxidoreductase ASHI subunit (CI-ASHI) proteins. NADH:ubiquinone oxidoreductase (complex I) is an extremely complicated multiprotein complex located in the inner mitochondrial membrane. Its main function is the transport of electrons from NADH to ubiquinone, which is accompanied by translocation of protons from the mitochondrial matrix to the intermembrane space. Human complex I appears to consist of 41 subunits [].; GO: 0003954 NADH dehydrogenase activity, 0008137 NADH dehydrogenase (ubiquinone) activity, 0005739 mitochondrion
Probab=99.11 E-value=1.6e-10 Score=90.94 Aligned_cols=74 Identities=31% Similarity=0.512 Sum_probs=51.5
Q ss_pred CCCCCCCCccccccCCCCCCCccccccCCCcCHHHHHHHHHHHHHHHHHHhhhhhhccCCCCCCCCCCCCCCcchhHhhC
Q 033216 43 PNKPLSVNDELVWDNGTPFPEPCIDRIADTVGKYEALGWLLGGLGFFASLGALAVWNDKASKIPFTPKVYPYDNLRVELG 122 (125)
Q Consensus 43 p~kpLpe~~EL~Wd~G~a~PEp~iD~~~~~Isk~eAl~~l~~gl~fFa~lg~va~~~Dk~sk~P~~pR~yPyd~L~~ElG 122 (125)
-++|||++.|+ |. ++ ..|.....++-...+.+|++.++|+.++.++.... .+.+|++||+||||||+.|+|
T Consensus 96 fgEPvH~d~Dm-~s-----~d-r~d~~~~~~~w~~~~~~l~~flg~~~~~~~~~~~~--~~~~P~~pKqYP~~gL~~e~g 166 (179)
T PF05821_consen 96 FGEPVHEDFDM-YS-----PD-RYDTSPTPVSWQSMLKQLFGFLGFMLFMFYLGEMY--PPYRPVMPKQYPYNGLYLELG 166 (179)
T ss_pred CCCCCcccccc-ee-----ec-ccccCCCcccHHHHHHHHHHHHHHHHHHHHHhhhc--cCCCCCCcccCCCCCeecccC
Confidence 34678877775 33 21 12222223344567788888888887776665542 678999999999999999999
Q ss_pred CCC
Q 033216 123 GEP 125 (125)
Q Consensus 123 g~~ 125 (125)
|+|
T Consensus 167 gdp 169 (179)
T PF05821_consen 167 GDP 169 (179)
T ss_pred CCC
Confidence 975
No 2
>KOG4040 consensus NADH:ubiquinone oxidoreductase, NDUFB8/ASHI subunit [Energy production and conversion]
Probab=96.68 E-value=0.0037 Score=50.07 Aligned_cols=53 Identities=26% Similarity=0.332 Sum_probs=38.8
Q ss_pred CCcCHHHHHHHHHHHHHHHHHH-hhhhhhccCCCCCCCCCCCCCCcchhHhhCCCC
Q 033216 71 DTVGKYEALGWLLGGLGFFASL-GALAVWNDKASKIPFTPKVYPYDNLRVELGGEP 125 (125)
Q Consensus 71 ~~Isk~eAl~~l~~gl~fFa~l-g~va~~~Dk~sk~P~~pR~yPyd~L~~ElGg~~ 125 (125)
+..+.+.....++.||.-|+.| .++ .+++.--+|..||+||||++|.+-+++|
T Consensus 123 p~y~~w~~~~mcl~g~~~~~l~~~y~--~d~~p~ykPv~pKQYpy~~~~~y~f~dp 176 (186)
T KOG4040|consen 123 PDYTTWNSIVMCLRGLVPMALLAWYF--TDEHPRYKPVMPKQYPYDFYRAYPFDDP 176 (186)
T ss_pred CCcccHHHHHHHHHHHHHHHHHHHHH--cccccccccCCcccCCCCCeeeccCCCC
Confidence 4456666677777777666666 222 2456677899999999999999988865
No 3
>PLN02720 complex II
Probab=29.10 E-value=40 Score=26.38 Aligned_cols=56 Identities=23% Similarity=0.172 Sum_probs=30.7
Q ss_pred CCCCCCCCCCccccccCCCCCCCccccccC---CCc-CHHHHHHHHHHHHHH-HHHHhhhhhhccCCCCCC
Q 033216 41 IVPNKPLSVNDELVWDNGTPFPEPCIDRIA---DTV-GKYEALGWLLGGLGF-FASLGALAVWNDKASKIP 106 (125)
Q Consensus 41 ~~p~kpLpe~~EL~Wd~G~a~PEp~iD~~~---~~I-sk~eAl~~l~~gl~f-Fa~lg~va~~~Dk~sk~P 106 (125)
.-+|||||.+.+-- =|..|+-|+ |+. +..||....+.|... -+..+.++. |+||.|
T Consensus 31 ~~rdkPLP~Ws~sD-------VeeFIaSDPVyGPqLk~~rea~~fa~~Ga~vGa~~tag~a~---kysk~p 91 (140)
T PLN02720 31 SKRDKPLPPWSDSD-------VDEFIASDPVYGPQLKTMREAATFAVTGAAVGAVSTAGVAW---KYSKSP 91 (140)
T ss_pred hcCCCCCCCCchhh-------HHHHHhcCCCcchHHHHHHHHHHHHhhhhhhhhhhhhHHHH---HhhcCC
Confidence 35799999866542 255666665 334 346666555444322 222244444 466665
No 4
>COG3477 Predicted periplasmic/secreted protein [Function unknown]
Probab=26.78 E-value=56 Score=26.43 Aligned_cols=37 Identities=27% Similarity=0.481 Sum_probs=18.9
Q ss_pred HHHHHHHH--hhhhhhccCCCCCCCCCCC------C-CCcchhHhhC
Q 033216 85 GLGFFASL--GALAVWNDKASKIPFTPKV------Y-PYDNLRVELG 122 (125)
Q Consensus 85 gl~fFa~l--g~va~~~Dk~sk~P~~pR~------y-Pyd~L~~ElG 122 (125)
|+.+|+++ |+++..+.--=+.|+.||+ . |+-+|.+ ||
T Consensus 12 gl~~~igIi~G~vS~~VK~GwEv~~PPR~per~~~nPP~~~l~q-LG 57 (176)
T COG3477 12 GLAAFIGIIAGLVSAIVKWGWEVPLPPRTPERNETNPPQIFLQQ-LG 57 (176)
T ss_pred HHHHHHHHHHHHHHHHHHhcccccCCCCCcccccCCChHHHHHH-cC
Confidence 33334444 4444444223456666666 2 5556655 66
No 5
>KOG1397 consensus Ca2+/H+ antiporter VCX1 and related proteins [Inorganic ion transport and metabolism]
Probab=26.21 E-value=1.2e+02 Score=27.65 Aligned_cols=33 Identities=15% Similarity=0.225 Sum_probs=25.6
Q ss_pred cccCCCcCHHHHHHHHHHHHHHHHHH--hhhhhhc
Q 033216 67 DRIADTVGKYEALGWLLGGLGFFASL--GALAVWN 99 (125)
Q Consensus 67 D~~~~~Isk~eAl~~l~~gl~fFa~l--g~va~~~ 99 (125)
+.+.|++|++++..||++.-.+.+.+ |+|....
T Consensus 280 ~~e~p~is~~ss~~~L~~~T~~vsllaeyLV~~Id 314 (441)
T KOG1397|consen 280 EDEAPNISRWSSIIWLLIMTLLVSLLAEYLVDTID 314 (441)
T ss_pred cCCCCcchHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 45778899999999999887777777 5555543
No 6
>PF12351 Fig1: Ca2+ regulator and membrane fusion protein Fig1
Probab=24.81 E-value=95 Score=24.21 Aligned_cols=28 Identities=25% Similarity=0.476 Sum_probs=22.8
Q ss_pred CCcC-HHHHHHHHHHHHHHHHHHhhhhhh
Q 033216 71 DTVG-KYEALGWLLGGLGFFASLGALAVW 98 (125)
Q Consensus 71 ~~Is-k~eAl~~l~~gl~fFa~lg~va~~ 98 (125)
-+++ +.+++.|..++|.+..++|....|
T Consensus 152 ~~~G~~a~~l~W~aF~f~~l~~lgl~~~~ 180 (182)
T PF12351_consen 152 VKVGKAAMVLGWFAFAFLLLVCLGLWVMY 180 (182)
T ss_pred eccchhHHhHHHHHHHHHHHHHHHHHHee
Confidence 4455 699999999999988888887764
No 7
>PF06181 DUF989: Protein of unknown function (DUF989); InterPro: IPR010389 This entry consists of several hypothetical bacterial proteins of unknown function.
Probab=24.18 E-value=2.1e+02 Score=24.95 Aligned_cols=42 Identities=14% Similarity=0.220 Sum_probs=30.8
Q ss_pred cccCCCCCCC---ccccccCCCc--CHHHHHHHHHHHHHHHHHHhhh
Q 033216 54 VWDNGTPFPE---PCIDRIADTV--GKYEALGWLLGGLGFFASLGAL 95 (125)
Q Consensus 54 ~Wd~G~a~PE---p~iD~~~~~I--sk~eAl~~l~~gl~fFa~lg~v 95 (125)
+.+-|.+++| .+=+.+++|. .|.||-..|+.||+++..+|++
T Consensus 57 VHGGGFYh~~KY~vaP~~mP~~LhWfkWesY~TWlSGfaLl~~~Yy~ 103 (300)
T PF06181_consen 57 VHGGGFYHVQKYLVAPEKMPEHLHWFKWESYTTWLSGFALLIVVYYF 103 (300)
T ss_pred eecccccchhhhccCcccCCccceeehhHhHHHHHHHHHHHHHHHHh
Confidence 5787875443 1123466665 5999999999999999999774
No 8
>PRK15126 thiamin pyrimidine pyrophosphate hydrolase; Provisional
Probab=22.87 E-value=60 Score=25.30 Aligned_cols=24 Identities=29% Similarity=0.382 Sum_probs=21.1
Q ss_pred ccccccCCCcCHHHHHHHHHHHHH
Q 033216 64 PCIDRIADTVGKYEALGWLLGGLG 87 (125)
Q Consensus 64 p~iD~~~~~Isk~eAl~~l~~gl~ 87 (125)
-++|..+..++|..|+.+|+--++
T Consensus 178 ~~~eI~~~g~sKg~al~~l~~~~g 201 (272)
T PRK15126 178 DCLEVLPVGCNKGAALAVLSQHLG 201 (272)
T ss_pred cEEEeecCCCChHHHHHHHHHHhC
Confidence 489999999999999999986655
No 9
>PF08802 CytB6-F_Fe-S: Cytochrome B6-F complex Fe-S subunit ; InterPro: IPR014909 The cytochrome b6-f complex mediates electron transfer between photosystem II (PSII) and photosystem I (PSI), cyclic electron flow around PSI, and state transitions. The cytochrome b6-f complex has 4 large subunits, these are: cytochrome b6, subunit IV (17 kDa polypeptide, PetD), cytochrome f and the Rieske protein, while the 4 small subunits are: PetG, PetL, PetM and PetN. The complex functions as a dimer. This protein corresponds to the alpha helical transmembrane domain of the cytochrome b6-f complex Rieske iron-sulphur subunit. ; GO: 0009496 plastoquinol-plastocyanin reductase activity, 0051537 2 iron, 2 sulfur cluster binding, 0055114 oxidation-reduction process, 0042651 thylakoid membrane; PDB: 1Q90_R 1VF5_D 2E75_D 2E74_D 2E76_D 2D2C_Q 2ZT9_D.
Probab=22.68 E-value=1.2e+02 Score=18.82 Aligned_cols=26 Identities=23% Similarity=0.314 Sum_probs=18.5
Q ss_pred CCcCHHHHHHHHHHHHHHHHHHhhhh
Q 033216 71 DTVGKYEALGWLLGGLGFFASLGALA 96 (125)
Q Consensus 71 ~~Isk~eAl~~l~~gl~fFa~lg~va 96 (125)
+.+++++-+-+|++|.....+.+.+.
T Consensus 4 Pdm~RR~lmN~ll~Gava~~a~~~ly 29 (39)
T PF08802_consen 4 PDMSRRQLMNLLLGGAVAVPAGGMLY 29 (39)
T ss_dssp --HHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred CChhHHHHHHHHHHhhHHHHHHHHhh
Confidence 56789999999998887766655443
No 10
>KOG0815 consensus 60S acidic ribosomal protein P0 [Translation, ribosomal structure and biogenesis]
Probab=20.76 E-value=1.5e+02 Score=25.12 Aligned_cols=40 Identities=23% Similarity=0.347 Sum_probs=32.2
Q ss_pred cccCCCCCCCccccccCCCcCHHHHHHHHHHHHHHHHHHhhhhhh
Q 033216 54 VWDNGTPFPEPCIDRIADTVGKYEALGWLLGGLGFFASLGALAVW 98 (125)
Q Consensus 54 ~Wd~G~a~PEp~iD~~~~~Isk~eAl~~l~~gl~fFa~lg~va~~ 98 (125)
+.|||.-+.-- .=.|+..++...+..+++.++++++.+.|
T Consensus 192 VyDnGsiy~pe-----vLDiteE~l~~~f~~~vs~va~~sL~~~y 231 (245)
T KOG0815|consen 192 VYDNGSIYNPE-----VLDITEEDLFSKFLSGVSNVASVSLAAGY 231 (245)
T ss_pred EecCCcccChh-----hcCCcHHHHHHHHHHHHHHHHHHHHhcCC
Confidence 58999865432 23478899999999999999999888876
No 11
>COG3748 Predicted membrane protein [Function unknown]
Probab=20.19 E-value=1.4e+02 Score=26.83 Aligned_cols=42 Identities=17% Similarity=0.230 Sum_probs=28.8
Q ss_pred cccCCCCCCCccc---cccCCCcC--HHHHHHHHHHHHHHHHHHhhh
Q 033216 54 VWDNGTPFPEPCI---DRIADTVG--KYEALGWLLGGLGFFASLGAL 95 (125)
Q Consensus 54 ~Wd~G~a~PEp~i---D~~~~~Is--k~eAl~~l~~gl~fFa~lg~v 95 (125)
+..-|.++.|-.+ -.+++|.. |+|+-..|+.||..++.+|+.
T Consensus 54 vHGGGFYh~qKYlvAP~~mPEhL~WFkWEsY~TWlSGfalL~ivYY~ 100 (407)
T COG3748 54 VHGGGFYHIQKYLVAPAHMPEHLHWFKWEAYFTWLSGFALLCIVYYF 100 (407)
T ss_pred eeecceEEEEEeeecCccCCccccchhHHHHHHHHHHHHHHHHHHHc
Confidence 4566655443211 12556665 999999999999999988654
No 12
>PTZ00174 phosphomannomutase; Provisional
Probab=20.05 E-value=71 Score=24.99 Aligned_cols=22 Identities=18% Similarity=0.039 Sum_probs=20.0
Q ss_pred ccccccCCCcCHHHHHHHHHHH
Q 033216 64 PCIDRIADTVGKYEALGWLLGG 85 (125)
Q Consensus 64 p~iD~~~~~Isk~eAl~~l~~g 85 (125)
.++|..+..++|..|+.+|+-=
T Consensus 178 ~~leI~~~gvsKg~al~~L~~~ 199 (247)
T PTZ00174 178 ISFDVFPKGWDKTYCLRHLEND 199 (247)
T ss_pred eEEEeeeCCCcHHHHHHHHHhh
Confidence 4899999999999999999866
Done!