Query 034120
Match_columns 103
No_of_seqs 101 out of 143
Neff 4.0
Searched_HMMs 46136
Date Fri Mar 29 09:59:37 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/034120.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/034120hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG3468 NADH:ubiquinone oxidor 100.0 2.8E-43 6E-48 253.8 5.4 97 5-103 32-128 (128)
2 PF05676 NDUF_B7: NADH-ubiquin 100.0 3.7E-40 8.1E-45 216.3 3.1 66 9-74 1-66 (66)
3 PF08583 Cmc1: Cytochrome c ox 89.1 0.13 2.8E-06 32.1 0.2 56 27-82 10-67 (69)
4 PF06747 CHCH: CHCH domain; I 74.3 0.48 1E-05 26.2 -1.3 33 30-62 1-33 (35)
5 PF10200 Ndufs5: NADH:ubiquino 66.0 13 0.00028 26.1 4.1 72 17-93 20-94 (96)
6 PLN00190 60S ribosomal protein 45.7 33 0.00071 26.2 3.7 27 52-81 94-120 (158)
7 KOG3039 Uncharacterized conser 41.6 28 0.00061 29.0 2.9 52 26-80 42-95 (303)
8 PF12597 DUF3767: Protein of u 32.4 42 0.00092 23.9 2.3 22 56-81 82-103 (118)
9 PF11414 Suppressor_APC: Adeno 23.1 73 0.0016 21.7 2.1 14 65-78 4-17 (84)
10 PTZ00189 60S ribosomal protein 21.7 1.3E+02 0.0029 22.9 3.5 27 52-81 94-120 (160)
11 KOG2880 SMAD6 interacting prot 20.3 85 0.0019 27.4 2.4 22 59-80 108-137 (424)
12 PF15279 SOBP: Sine oculis-bin 20.1 27 0.00059 28.9 -0.6 15 49-67 4-18 (306)
No 1
>KOG3468 consensus NADH:ubiquinone oxidoreductase, NDUFB7/B18 subunit [Energy production and conversion]
Probab=100.00 E-value=2.8e-43 Score=253.84 Aligned_cols=97 Identities=57% Similarity=0.945 Sum_probs=90.7
Q ss_pred CCCCCccCCHHHHHhCCCCCCCCcchhhhccChhhhhhhccCCCcCCCccccccccchHHHHHHHHHHHHHHHHHHHHHh
Q 034120 5 GSSKKMIATQEEMVEARVPIPYRDQCAHLLIPLNKCRQAEFYLPWKCENERHSYEKCEYELVMERMLQMQKIREEEAKLK 84 (103)
Q Consensus 5 ~~~r~m~aTqeEM~~ArlPl~~RDyCAh~LI~l~kCr~~~~~~~~~C~hErH~YekCqy~D~~~Rmke~er~r~~~~~~~ 84 (103)
+++|+|+||||||++|+|+|+.||||||+||+|++|++++||++|+|.+|||+|++|+|+||+.|||||||+|++-+|.+
T Consensus 32 Rk~r~MiATqeEM~~akl~l~~RDyCAH~lI~l~kCr~~~fp~~~kC~~erh~~dkCEyed~vmRmkefeRErrlLqrq~ 111 (128)
T KOG3468|consen 32 RKEREMIATQEEMEAAKLALGSRDYCAHLLIPLNKCRQDEFPFPWKCEDERHVYDKCEYEDYVMRMKEFERERRLLQRQK 111 (128)
T ss_pred hhHHHHHhhHHHHHhhhcCcchHHHHHHHHHHHHHhhcccCCcchhccccccchhhhhHHHHHHHHHHHHHHHHHHHHHH
Confidence 37889999999999999999999999999999999999999999999999999999999999999999999999888764
Q ss_pred hhhhcCCCCcccccCCcCC
Q 034120 85 QSQTQKGAPIPLIPKTANA 103 (103)
Q Consensus 85 ~~~~~~~~~~~~~~~~~~~ 103 (103)
.. .|...+||||+|||+
T Consensus 112 r~--e~~Aa~~~~~~~~~~ 128 (128)
T KOG3468|consen 112 RL--EKNAAVPLIPKTANA 128 (128)
T ss_pred HH--hhcccccccCCCCCC
Confidence 44 446899999999996
No 2
>PF05676 NDUF_B7: NADH-ubiquinone oxidoreductase B18 subunit (NDUFB7); InterPro: IPR008698 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 NADH-ubiquinone oxidoreductase B18 subunit proteins from different eukaryotic organisms. Oxidative phosphorylation is the well-characterised process in which ATP, the principal carrier of chemical energy of individual cells, is produced due to a mitochondrial proton gradient formed by the transfer of electrons from NADH and FADH2 to molecular oxygen. The oxidative phosphorylation (OXPHOS) system is located in the mitochondrial inner membrane and consists of five multi-subunit enzyme complexes and two small electron carriers: coenzyme Q10 and cytochrome C. At least 70 structural proteins involved in the formation of the whole OXPHOS system are encoded by nuclear genes, whereas 13 structural proteins are encoded by the mitochondrial genome. Deficiency of NADH ubiquinone oxidoreductase, the first enzyme complex of the mitochondrial respiratory chain, is one of the most frequent causes of Homo sapiens mitochondrial encephalomyopathies [].; GO: 0003954 NADH dehydrogenase activity, 0008137 NADH dehydrogenase (ubiquinone) activity, 0005739 mitochondrion
Probab=100.00 E-value=3.7e-40 Score=216.32 Aligned_cols=66 Identities=62% Similarity=1.187 Sum_probs=64.9
Q ss_pred CccCCHHHHHhCCCCCCCCcchhhhccChhhhhhhccCCCcCCCccccccccchHHHHHHHHHHHH
Q 034120 9 KMIATQEEMVEARVPIPYRDQCAHLLIPLNKCRQAEFYLPWKCENERHSYEKCEYELVMERMLQMQ 74 (103)
Q Consensus 9 ~m~aTqeEM~~ArlPl~~RDyCAh~LI~l~kCr~~~~~~~~~C~hErH~YekCqy~D~~~Rmke~e 74 (103)
+|+||||||++|+||+++||||||+||+|++|++++||++|+|+||||+|++|||+||++||||||
T Consensus 1 ~m~aTqeEM~~a~lPl~~RDyCAh~Li~l~kCrr~~~p~~~~C~~erH~y~~C~y~dy~~Rmke~E 66 (66)
T PF05676_consen 1 EMIATQEEMEDAKLPLQYRDYCAHLLIPLNKCRRDNFPFPWKCEHERHEYEKCQYDDYVMRMKEYE 66 (66)
T ss_pred CCCcCHHHHHHcCCChhhhhhHHHHHHHHHHHHHhCCCCcccCCcchhhHHHccHHHHHHHHHhcC
Confidence 599999999999999999999999999999999999999999999999999999999999999986
No 3
>PF08583 Cmc1: Cytochrome c oxidase biogenesis protein Cmc1 like; InterPro: IPR013892 Cmc1 is a metallo-chaperone like protein which is known to localise to the inner mitochondrial membrane in Saccharomyces cerevisiae. It is essential for full expression of cytochrome c oxidase and respiration []. Cmc1 contains two Cx9C motifs and is able to bind copper(I). Cmc1 is thought to play a role in mitochondrial copper trafficking and transfer to cytochrome c oxidase.
Probab=89.14 E-value=0.13 Score=32.05 Aligned_cols=56 Identities=16% Similarity=0.343 Sum_probs=43.6
Q ss_pred CcchhhhccChhhhhhhcc-CCCcCCCccccccccchHHHHHHHHH-HHHHHHHHHHH
Q 034120 27 RDQCAHLLIPLNKCRQAEF-YLPWKCENERHSYEKCEYELVMERML-QMQKIREEEAK 82 (103)
Q Consensus 27 RDyCAh~LI~l~kCr~~~~-~~~~~C~hErH~YekCqy~D~~~Rmk-e~er~r~~~~~ 82 (103)
+..|+...-.|..|-.+.+ .+.|.|..++.+-..|-...+..+-. +.++.+..++|
T Consensus 10 ~~~C~~~i~~~~~C~~~~~~~~~~~C~~~~~~m~~Cl~~~~~~~~~~~~~~~~~~~~r 67 (69)
T PF08583_consen 10 HKKCADEIEAFAECHKDRTFKFVGKCREEKKAMNECLKEERNDERFRNREKAEYLKER 67 (69)
T ss_pred HHHhHHHHHHHHHHHhcchHHHHHhhhHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHh
Confidence 4789999999999999854 47799999999999999988877655 44444444443
No 4
>PF06747 CHCH: CHCH domain; InterPro: IPR010625 A conserved motif was identified in the LOC118487 protein was called the CHCH motif. Alignment of this protein with related members showed the presence of three subgroups of proteins, which are called the S (Small), N (N-terminal extended) and C (C-terminal extended) subgroups. All three sub-groups of proteins have in common that they contain a predicted conserved [coiled coil 1]-[helix 1]-[coiled coil 2]-[helix 2] domain (CHCH domain). Within each helix of the CHCH domain, there are two cysteines present in a C-X9-C motif. The N-group contains an additional double helix domain, and each helix contains the C-X9-C motif. This family contains a number of characterised proteins: Cox19 protein - a nuclear gene of Saccharomyces cerevisiae, codes for an 11 kDa protein (Cox19p) required for expression of cytochrome oxidase. Because cox19 mutants are able to synthesise the mitochondrial and nuclear gene products of cytochrome oxidase, Cox19p probably functions post-translationally during assembly of the enzyme. Cox19p is present in the cytoplasm and mitochondria, where it exists as a soluble intermembrane protein. This dual location is similar to what was previously reported for Cox17p, a low molecular weight copper protein thought to be required for maturation of the CuA centre of subunit 2 of cytochrome oxidase. Cox19p have four conserved potential metal ligands, these are three cysteines and one histidine. Mrp10 - belongs to the class of yeast mitochondrial ribosomal proteins that are essential for translation []. Eukaryotic NADH-ubiquinone oxidoreductase 19 kDa (NDUFA8) subunit []. The CHCH domain was previously called DUF657 []. ; PDB: 2ZXT_A 3A3C_A 2L0Y_A 2K3J_A.
Probab=74.27 E-value=0.48 Score=26.19 Aligned_cols=33 Identities=24% Similarity=0.512 Sum_probs=27.3
Q ss_pred hhhhccChhhhhhhccCCCcCCCccccccccch
Q 034120 30 CAHLLIPLNKCRQAEFYLPWKCENERHSYEKCE 62 (103)
Q Consensus 30 CAh~LI~l~kCr~~~~~~~~~C~hErH~YekCq 62 (103)
|++..-.+..|..++.+...+|..+--+|..|.
T Consensus 1 C~~e~~~~~~Cl~~n~~~~~~C~~~~~~~~~C~ 33 (35)
T PF06747_consen 1 CAEEMKAYLACLKENNFDWSKCRKEFKAYKECR 33 (35)
T ss_dssp THHHHHHHHHHHHCH-SSTCCCHHHHHHHHHHH
T ss_pred CHHHHHHHHHHHHHCCCcHHhhHHHHHHHHHHh
Confidence 667777899999999888889999988888874
No 5
>PF10200 Ndufs5: NADH:ubiquinone oxidoreductase, NDUFS5-15kDa; InterPro: IPR019342 Proteins in this entry form part of the NADH:ubiquinone oxidoreductase complex I. Complex I is the first multisubunit inner membrane protein complex of the mitochondrial electron transport chain and it transfers two electrons from NADH to ubiquinone. The mammalian complex I is composed of 45 different subunits. The proteins in this entry represent a component of the iron-sulphur (IP) fragment of the enzyme, that is not involved in catalysis. These proteins carry four highly conserved cysteine residues, but these do not appear to be in a configuration which would favour metal binding, so the exact function of the protein is uncertain [].
Probab=66.00 E-value=13 Score=26.14 Aligned_cols=72 Identities=21% Similarity=0.275 Sum_probs=49.1
Q ss_pred HHhCCCCCCCCcchhhhccChhhhhhhcc--CCCcCCCccccccccchHHHHHHHHHHHHHHHHH-HHHHhhhhhcCCCC
Q 034120 17 MVEARVPIPYRDQCAHLLIPLNKCRQAEF--YLPWKCENERHSYEKCEYELVMERMLQMQKIREE-EAKLKQSQTQKGAP 93 (103)
Q Consensus 17 M~~ArlPl~~RDyCAh~LI~l~kCr~~~~--~~~~~C~hErH~YekCqy~D~~~Rmke~er~r~~-~~~~~~~~~~~~~~ 93 (103)
+.++--|...-..|..+=..+..|-.... -+.=.|..+..+|..|.+ +-|++.|..+- +++-++.+.||-.|
T Consensus 20 ~~s~~q~~~~~~RC~~FE~e~i~C~~~~G~~r~kKeC~~e~EDy~EClh-----~~Ke~~R~~aI~kqR~K~~keGk~tp 94 (96)
T PF10200_consen 20 IQSAEQPYKQPSRCHPFEKEWIECAEAYGQTRGKKECKLELEDYYECLH-----HTKEMKRMRAIRKQRDKQIKEGKYTP 94 (96)
T ss_pred HhcccCCCCCCCchHHHHHHHHHHHHHHcccchhhhchhHHhHHHHHHh-----hHHHHHHHHHHHHHHHHHHHccCCCC
Confidence 34556688899999999889999975442 345689999999998866 44555554432 24445566666554
No 6
>PLN00190 60S ribosomal protein L21; Provisional
Probab=45.67 E-value=33 Score=26.15 Aligned_cols=27 Identities=22% Similarity=0.340 Sum_probs=17.8
Q ss_pred CccccccccchHHHHHHHHHHHHHHHHHHH
Q 034120 52 ENERHSYEKCEYELVMERMLQMQKIREEEA 81 (103)
Q Consensus 52 ~hErH~YekCqy~D~~~Rmke~er~r~~~~ 81 (103)
+|-+|. +|. +||+.|+|+-++.+.+..
T Consensus 94 EHlk~s--k~r-~~Fl~Rvk~n~~~~~eak 120 (158)
T PLN00190 94 EHVQPS--RCR-EEFLLRKKSNDEAKAEAK 120 (158)
T ss_pred HHccCc--cCH-HHHHHHHHHhHHHHHHHH
Confidence 444453 444 699999999876654443
No 7
>KOG3039 consensus Uncharacterized conserved protein [Function unknown]
Probab=41.58 E-value=28 Score=28.96 Aligned_cols=52 Identities=19% Similarity=0.156 Sum_probs=31.9
Q ss_pred CCcchhhhccChhhhhhhcc--CCCcCCCccccccccchHHHHHHHHHHHHHHHHHH
Q 034120 26 YRDQCAHLLIPLNKCRQAEF--YLPWKCENERHSYEKCEYELVMERMLQMQKIREEE 80 (103)
Q Consensus 26 ~RDyCAh~LI~l~kCr~~~~--~~~~~C~hErH~YekCqy~D~~~Rmke~er~r~~~ 80 (103)
.-|-|.=.|- -|++--. -+.++|..---+|--=|-.||-+|||+||++|++.
T Consensus 42 ~FdcCsLtLq---Pc~dPvit~~GylfdrEaILe~ilaqKke~arrlkayekqrr~e 95 (303)
T KOG3039|consen 42 PFDCCSLTLQ---PCRDPVITPDGYLFDREAILEYILAQKKEIARRLKAYEKQRRAE 95 (303)
T ss_pred Ccceeeeecc---cccCCccCCCCeeeeHHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Confidence 3455554433 3544332 13345555555566667889999999999988444
No 8
>PF12597 DUF3767: Protein of unknown function (DUF3767); InterPro: IPR022533 This group of proteins includes mitochodrial cytochrome c oxidase proteins [], and some transmembrane domain-containing proteins of unknown function known as FAM36A. Proteins in this family are typically between 112 and 199 amino acids in length.
Probab=32.39 E-value=42 Score=23.93 Aligned_cols=22 Identities=27% Similarity=0.543 Sum_probs=13.5
Q ss_pred cccccchHHHHHHHHHHHHHHHHHHH
Q 034120 56 HSYEKCEYELVMERMLQMQKIREEEA 81 (103)
Q Consensus 56 H~YekCqy~D~~~Rmke~er~r~~~~ 81 (103)
-.|+.|+|. |-++.++.+++.+
T Consensus 82 ~~we~Cr~~----r~~~~~~~~~~~e 103 (118)
T PF12597_consen 82 GSWEYCRYN----RRKERQQMKRAVE 103 (118)
T ss_pred HHHHHHHHH----HHHHHHHHHHHHH
Confidence 469999996 4445444444443
No 9
>PF11414 Suppressor_APC: Adenomatous polyposis coli tumour suppressor protein; PDB: 1M5I_A.
Probab=23.07 E-value=73 Score=21.65 Aligned_cols=14 Identities=14% Similarity=0.475 Sum_probs=9.8
Q ss_pred HHHHHHHHHHHHHH
Q 034120 65 LVMERMLQMQKIRE 78 (103)
Q Consensus 65 D~~~Rmke~er~r~ 78 (103)
..++|||++|++|.
T Consensus 4 ~~lk~mkeLEqEkd 17 (84)
T PF11414_consen 4 NMLKRMKELEQEKD 17 (84)
T ss_dssp ---HHHHHHHHHHH
T ss_pred hHHHHHHHHHHHHH
Confidence 45789999999984
No 10
>PTZ00189 60S ribosomal protein L21; Provisional
Probab=21.74 E-value=1.3e+02 Score=22.93 Aligned_cols=27 Identities=30% Similarity=0.490 Sum_probs=18.6
Q ss_pred CccccccccchHHHHHHHHHHHHHHHHHHH
Q 034120 52 ENERHSYEKCEYELVMERMLQMQKIREEEA 81 (103)
Q Consensus 52 ~hErH~YekCqy~D~~~Rmke~er~r~~~~ 81 (103)
+|-+|. +| -+||+.|+|+-++.+.+..
T Consensus 94 EHlk~s--k~-r~~fl~Rvk~n~~~~~~ak 120 (160)
T PTZ00189 94 EHVRKS--RC-REDFLKRVAANDAIKAEAK 120 (160)
T ss_pred hHcCCc--CC-HHHHHHHHHHhHHHHHHHH
Confidence 344443 45 6899999999887665443
No 11
>KOG2880 consensus SMAD6 interacting protein AMSH, contains JAB/MPN/Mov34 domain [Signal transduction mechanisms]
Probab=20.30 E-value=85 Score=27.36 Aligned_cols=22 Identities=36% Similarity=0.444 Sum_probs=13.3
Q ss_pred ccchHHHHH--------HHHHHHHHHHHHH
Q 034120 59 EKCEYELVM--------ERMLQMQKIREEE 80 (103)
Q Consensus 59 ekCqy~D~~--------~Rmke~er~r~~~ 80 (103)
+.|||.+|. .|.++||.++..+
T Consensus 108 Y~~eyn~y~~~K~k~~~E~~k~le~~~~~E 137 (424)
T KOG2880|consen 108 YNVEYNEYDHSKKKNLAERFKKLEVQREEE 137 (424)
T ss_pred HhhHHHHHHHHHhhhHHHHHHHhhcchhhH
Confidence 456777765 4677777644333
No 12
>PF15279 SOBP: Sine oculis-binding protein
Probab=20.09 E-value=27 Score=28.90 Aligned_cols=15 Identities=33% Similarity=0.833 Sum_probs=11.3
Q ss_pred cCCCccccccccchHHHHH
Q 034120 49 WKCENERHSYEKCEYELVM 67 (103)
Q Consensus 49 ~~C~hErH~YekCqy~D~~ 67 (103)
| |+|-||.- +|.||-
T Consensus 4 w-ckh~rh~~---~y~d~~ 18 (306)
T PF15279_consen 4 W-CKHVRHTK---SYVDFQ 18 (306)
T ss_pred c-hhcccchh---heeccc
Confidence 5 99999987 556654
Done!