Query 034645
Match_columns 88
No_of_seqs 102 out of 125
Neff 4.9
Searched_HMMs 46136
Date Fri Mar 29 05:00:46 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/034645.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/034645hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG4695 Uncharacterized conser 99.0 3.2E-10 7E-15 78.2 4.9 46 19-64 37-82 (122)
2 PF06747 CHCH: CHCH domain; I 98.5 6.6E-08 1.4E-12 52.6 2.7 34 30-63 1-34 (35)
3 PF08991 DUF1903: Domain of un 97.0 0.00072 1.6E-08 42.6 3.1 38 28-65 2-39 (67)
4 KOG4618 Uncharacterized conser 93.4 0.26 5.6E-06 31.7 4.9 38 27-64 21-58 (74)
5 PF07802 GCK: GCK domain; Int 91.7 0.54 1.2E-05 30.3 4.7 40 27-66 11-55 (76)
6 PF08583 Cmc1: Cytochrome c ox 87.6 1.2 2.6E-05 26.6 3.8 39 28-66 11-50 (69)
7 KOG4090 Uncharacterized conser 87.6 1.3 2.8E-05 32.3 4.5 39 27-65 115-153 (157)
8 KOG4149 Uncharacterized conser 85.2 1.7 3.6E-05 30.8 4.0 40 26-65 66-107 (129)
9 KOG4138 Unchracterized conserv 81.4 2.7 5.8E-05 28.3 3.6 41 27-68 40-80 (96)
10 smart00511 ORANGE Orange domai 76.8 9.7 0.00021 21.2 4.6 36 28-65 8-43 (45)
11 KOG4083 Head-elevated expressi 75.1 4.2 9.1E-05 30.4 3.4 41 26-66 144-184 (192)
12 KOG3477 Putative cytochrome c 71.3 5.9 0.00013 26.6 3.1 36 27-62 27-62 (97)
13 PF07527 Hairy_orange: Hairy O 70.6 15 0.00033 20.4 4.4 34 29-64 9-42 (43)
14 PF05051 COX17: Cytochrome C o 70.3 5.3 0.00012 23.9 2.5 36 28-65 10-45 (49)
15 PF11326 DUF3128: Protein of u 59.3 14 0.00031 23.3 3.1 42 26-67 3-52 (84)
16 KOG4453 Predicted ER membrane 59.0 11 0.00023 29.5 2.9 44 2-45 168-211 (269)
17 KOG4624 Uncharacterized conser 56.9 20 0.00044 24.5 3.6 41 25-65 28-69 (104)
18 PHA02629 A-type inclusion body 44.0 15 0.00032 22.6 1.3 28 39-66 23-50 (61)
19 PF02297 COX6B: Cytochrome oxi 41.0 14 0.0003 23.0 0.9 39 26-64 8-56 (76)
20 cd00926 Cyt_c_Oxidase_VIb Cyto 39.7 80 0.0017 19.9 4.2 35 26-60 19-53 (75)
21 PF07956 DUF1690: Protein of U 37.8 43 0.00093 23.5 3.0 36 27-62 106-141 (142)
22 PF10200 Ndufs5: NADH:ubiquino 35.0 31 0.00066 23.1 1.8 59 26-86 29-89 (96)
23 PF10811 DUF2532: Protein of u 30.1 49 0.0011 23.8 2.3 25 57-82 104-128 (158)
24 PF08095 Toxin_25: Hefutoxin f 29.9 28 0.0006 17.5 0.7 15 38-53 6-20 (22)
25 PRK11477 carbohydrate diacid t 25.0 1.1E+02 0.0025 23.6 3.8 38 33-84 322-359 (385)
26 PF05924 SAMP: SAMP Motif; In 24.3 64 0.0014 15.9 1.5 16 55-70 3-18 (20)
27 PF05676 NDUF_B7: NADH-ubiquin 22.9 67 0.0015 20.0 1.7 35 28-62 20-54 (66)
28 PF00196 GerE: Bacterial regul 21.9 18 0.00039 20.7 -1.0 13 74-86 33-45 (58)
29 COG0640 ArsR Predicted transcr 21.8 42 0.0009 19.3 0.6 16 70-85 50-65 (110)
No 1
>KOG4695 consensus Uncharacterized conserved protein [Function unknown]
Probab=99.04 E-value=3.2e-10 Score=78.23 Aligned_cols=46 Identities=15% Similarity=0.481 Sum_probs=42.2
Q ss_pred CcCCCCCCCCChHHHHHHHHHHHhcCCCChHHHHHHHHHHHHHHHh
Q 034645 19 NPKKFGNIAKPCMKEMITFLNCMSLNQMNSEKCARQKELLSACMDA 64 (88)
Q Consensus 19 ~pKk~~~~~~pC~~eMs~lL~Cwasng~~~~~Ca~~~~~L~~Cm~~ 64 (88)
-.++.+.+++.|++||++|++||+.|.|++..|.++++.|.+|...
T Consensus 37 ~g~~~~gs~~tC~qEm~vlfaClK~nEF~d~~C~Kei~~f~dC~~~ 82 (122)
T KOG4695|consen 37 EGRREKGSEATCIQEMSVLFACLKQNEFRDDACRKEIQGFLDCAAR 82 (122)
T ss_pred cccCCcccchHHHHHHHHHHHHHHhccccchHHHHHHHHHHHHHHH
Confidence 3567777899999999999999999999999999999999999765
No 2
>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=98.54 E-value=6.6e-08 Score=52.58 Aligned_cols=34 Identities=26% Similarity=0.648 Sum_probs=31.8
Q ss_pred hHHHHHHHHHHHhcCCCChHHHHHHHHHHHHHHH
Q 034645 30 CMKEMITFLNCMSLNQMNSEKCARQKELLSACMD 63 (88)
Q Consensus 30 C~~eMs~lL~Cwasng~~~~~Ca~~~~~L~~Cm~ 63 (88)
|..||..+|.||.+|+++.+.|..+.++|++|+.
T Consensus 1 C~~e~~~~~~Cl~~n~~~~~~C~~~~~~~~~C~~ 34 (35)
T PF06747_consen 1 CAEEMKAYLACLKENNFDWSKCRKEFKAYKECRM 34 (35)
T ss_dssp THHHHHHHHHHHHCH-SSTCCCHHHHHHHHHHHC
T ss_pred CHHHHHHHHHHHHHCCCcHHhhHHHHHHHHHHhh
Confidence 8899999999999999999999999999999974
No 3
>PF08991 DUF1903: Domain of unknown function (DUF1903); InterPro: IPR009069 The mature-T-cell-proliferation (MTCP1) putative oncogene was identified for its involvement in t(X:14)(q28;q11)-associated T-cell leukaemia []. MTCP1 is alternatively spliced to produce two completely distinct proteins: the small mitochondrial protein, p8MTCP1, and the protein p13MTCP1, which shows strong homology to another oncogene product, p14TCL1. While p13MTCP1 expression appears to be restricted to mature T-cell proliferation with t(X,14) translocations, the mitochondrial p8MTCP1 is expressed at low levels in most human tissues, and is over-expressed in the proliferating T-cells. The biological function of p8MTCP1 is still unknown, but it appears to play a role in oncogenesis. The structure of p8MTCP1 reveals a disulphide-rich, irregular array of three helices [].; PDB: 2HP8_A 1EI0_A 1HP8_A.
Probab=97.02 E-value=0.00072 Score=42.56 Aligned_cols=38 Identities=26% Similarity=0.577 Sum_probs=34.7
Q ss_pred CChHHHHHHHHHHHhcCCCChHHHHHHHHHHHHHHHhh
Q 034645 28 KPCMKEMITFLNCMSLNQMNSEKCARQKELLSACMDAQ 65 (88)
Q Consensus 28 ~pC~~eMs~lL~Cwasng~~~~~Ca~~~~~L~~Cm~~~ 65 (88)
+||..+--.+..|+..|+|+.+.|...+++|+.|-...
T Consensus 2 ~PC~~~Ac~iq~CL~~N~Yd~~kC~~~i~~l~~Cck~~ 39 (67)
T PF08991_consen 2 DPCQKEACAIQKCLQRNNYDESKCQDYIDALYECCKKF 39 (67)
T ss_dssp -TTHHHHHHHHHHHHHTTT-CCCTHHHHHHHHHHHTTS
T ss_pred cchHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHHH
Confidence 69999999999999999999999999999999998777
No 4
>KOG4618 consensus Uncharacterized conserved protein [Function unknown]
Probab=93.38 E-value=0.26 Score=31.74 Aligned_cols=38 Identities=21% Similarity=0.524 Sum_probs=35.6
Q ss_pred CCChHHHHHHHHHHHhcCCCChHHHHHHHHHHHHHHHh
Q 034645 27 AKPCMKEMITFLNCMSLNQMNSEKCARQKELLSACMDA 64 (88)
Q Consensus 27 ~~pC~~eMs~lL~Cwasng~~~~~Ca~~~~~L~~Cm~~ 64 (88)
-+||+.|-++-+.|+-.|+|+-++|...-...++|-..
T Consensus 21 ~nPCl~es~aSfkCLeennyDRsKCq~yFd~YkeCKkf 58 (74)
T KOG4618|consen 21 YNPCLLESSASFKCLEENNYDRSKCQDYFDVYKECKKF 58 (74)
T ss_pred CChHHHHHHHHHHHHHhcCccHHHHHHHHHHHHHHHHH
Confidence 49999999999999999999999999999999999754
No 5
>PF07802 GCK: GCK domain; InterPro: IPR012891 This domain is found in proteins carrying other domains known to be involved in intracellular signalling pathways (such as IPR001806 from INTERPRO) indicating that it might also be involved in these pathways. It has 4 highly conserved cysteine residues, suggesting that it can bind zinc ions. Moreover, it is found repeated in some members of this family (such as Q9LMF3 from SWISSPROT); this may indicate that these domains are able to interact with one another, raising the possibility that this domain mediates heterodimerisation.
Probab=91.67 E-value=0.54 Score=30.28 Aligned_cols=40 Identities=23% Similarity=0.514 Sum_probs=33.5
Q ss_pred CCChHHHHHHHHHHH----hcCC-CChHHHHHHHHHHHHHHHhhc
Q 034645 27 AKPCMKEMITFLNCM----SLNQ-MNSEKCARQKELLSACMDAQT 66 (88)
Q Consensus 27 ~~pC~~eMs~lL~Cw----asng-~~~~~Ca~~~~~L~~Cm~~~~ 66 (88)
..+|-....+...|+ ++++ -....|...-..|+.||+..+
T Consensus 11 gG~Cke~F~awe~C~~ea~~~~~~d~v~kC~e~~~~L~kCM~ahs 55 (76)
T PF07802_consen 11 GGGCKESFTAWEDCVDEAEKNKEEDFVEKCFEATAALRKCMEAHS 55 (76)
T ss_pred CCChhHHHHHHHHHHHHHHhccCCchHHHHHHHHHHHHHHHHhch
Confidence 468999999999999 3333 566899999999999999764
No 6
>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=87.60 E-value=1.2 Score=26.61 Aligned_cols=39 Identities=23% Similarity=0.576 Sum_probs=34.9
Q ss_pred CChHHHHHHHHHHHhcCCC-ChHHHHHHHHHHHHHHHhhc
Q 034645 28 KPCMKEMITFLNCMSLNQM-NSEKCARQKELLSACMDAQT 66 (88)
Q Consensus 28 ~pC~~eMs~lL~Cwasng~-~~~~Ca~~~~~L~~Cm~~~~ 66 (88)
..|..++..|..|-+..++ ....|..+..+|+.|+....
T Consensus 11 ~~C~~~i~~~~~C~~~~~~~~~~~C~~~~~~m~~Cl~~~~ 50 (69)
T PF08583_consen 11 KKCADEIEAFAECHKDRTFKFVGKCREEKKAMNECLKEER 50 (69)
T ss_pred HHhHHHHHHHHHHHhcchHHHHHhhhHHHHHHHHHHHHHH
Confidence 6899999999999999664 66999999999999998775
No 7
>KOG4090 consensus Uncharacterized conserved protein [Function unknown]
Probab=87.59 E-value=1.3 Score=32.25 Aligned_cols=39 Identities=26% Similarity=0.618 Sum_probs=36.0
Q ss_pred CCChHHHHHHHHHHHhcCCCChHHHHHHHHHHHHHHHhh
Q 034645 27 AKPCMKEMITFLNCMSLNQMNSEKCARQKELLSACMDAQ 65 (88)
Q Consensus 27 ~~pC~~eMs~lL~Cwasng~~~~~Ca~~~~~L~~Cm~~~ 65 (88)
..+|.-|.-.||.|....|-|.+.|.-..+.|+.|-...
T Consensus 115 ~~~C~~e~kqF~dCa~~~~~d~slC~~f~e~Lk~Ck~~~ 153 (157)
T KOG4090|consen 115 QQPCFIEIKQFLDCAQNQGSDISLCEGYNEMLKQCKKNS 153 (157)
T ss_pred cCchHHHHHHHHHHHHhcCcchHHHHHHHHHHHHHHHHh
Confidence 567999999999999999999999999999999997654
No 8
>KOG4149 consensus Uncharacterized conserved protein [Function unknown]
Probab=85.17 E-value=1.7 Score=30.75 Aligned_cols=40 Identities=23% Similarity=0.552 Sum_probs=35.4
Q ss_pred CCCChHHHHHHHHHHHhcCC--CChHHHHHHHHHHHHHHHhh
Q 034645 26 IAKPCMKEMITFLNCMSLNQ--MNSEKCARQKELLSACMDAQ 65 (88)
Q Consensus 26 ~~~pC~~eMs~lL~Cwasng--~~~~~Ca~~~~~L~~Cm~~~ 65 (88)
...||..|+-..++|+..++ --...|.++-.++..||.+.
T Consensus 66 ~a~pCG~eFreA~sCf~~s~~e~kg~dC~~qf~a~~~C~qk~ 107 (129)
T KOG4149|consen 66 VAGPCGEEFREAFSCFKYSDTEPKGGDCVKQFVAMQECMQKY 107 (129)
T ss_pred ccCccHHHHHHHHhhccccCCCcCccchHHHHHHHHHHHHhC
Confidence 56799999999999999998 45678999999999999844
No 9
>KOG4138 consensus Unchracterized conserved protein (estrogen up-regulated protein E2IG2 in human) [General function prediction only]
Probab=81.43 E-value=2.7 Score=28.26 Aligned_cols=41 Identities=22% Similarity=0.545 Sum_probs=35.1
Q ss_pred CCChHHHHHHHHHHHhcCCCChHHHHHHHHHHHHHHHhhcCC
Q 034645 27 AKPCMKEMITFLNCMSLNQMNSEKCARQKELLSACMDAQTNK 68 (88)
Q Consensus 27 ~~pC~~eMs~lL~Cwasng~~~~~Ca~~~~~L~~Cm~~~~~~ 68 (88)
..-|..|=.+|=-|.|..+ +=-+|..+.++|+.|++++..+
T Consensus 40 k~GC~~ehlalq~C~a~t~-DWRqC~~qm~~FrkCwek~~g~ 80 (96)
T KOG4138|consen 40 KSGCAAEHLALQECMAQTQ-DWRQCQPQMQAFRKCWEKQQGR 80 (96)
T ss_pred ccchHHHHHHHHHHHHhhc-cHHHHHHHHHHHHHHHHHHcCC
Confidence 4579999999999999876 4579999999999999996543
No 10
>smart00511 ORANGE Orange domain. This domain confers specificity among members of the Hairy/E(SPL) family.
Probab=76.78 E-value=9.7 Score=21.25 Aligned_cols=36 Identities=22% Similarity=0.375 Sum_probs=29.7
Q ss_pred CChHHHHHHHHHHHhcCCCChHHHHHHHHHHHHHHHhh
Q 034645 28 KPCMKEMITFLNCMSLNQMNSEKCARQKELLSACMDAQ 65 (88)
Q Consensus 28 ~pC~~eMs~lL~Cwasng~~~~~Ca~~~~~L~~Cm~~~ 65 (88)
..|+.|.+.+|+ +..+.+.+.+..+..-|..|++..
T Consensus 8 ~~C~~Ev~~fLs--~~~~~~~~~~~~Ll~HL~~~~~~~ 43 (45)
T smart00511 8 RECANEVSRFLS--QLPGTDPDVRARLLSHLQTHLNQL 43 (45)
T ss_pred HHHHHHHHHHHh--cCCCCChHHHHHHHHHHHHHHHhh
Confidence 469999999998 344567889999999999998754
No 11
>KOG4083 consensus Head-elevated expression protein [Transcription]
Probab=75.06 E-value=4.2 Score=30.43 Aligned_cols=41 Identities=17% Similarity=0.286 Sum_probs=38.7
Q ss_pred CCCChHHHHHHHHHHHhcCCCChHHHHHHHHHHHHHHHhhc
Q 034645 26 IAKPCMKEMITFLNCMSLNQMNSEKCARQKELLSACMDAQT 66 (88)
Q Consensus 26 ~~~pC~~eMs~lL~Cwasng~~~~~Ca~~~~~L~~Cm~~~~ 66 (88)
..++|.+.=+-+|.|.-.|....-+|+.+..+|..|.+.+.
T Consensus 144 ~~pvCqdlq~qil~Cyr~~p~e~LkC~~lv~af~~Cv~~~r 184 (192)
T KOG4083|consen 144 REPVCQDLQAQILRCYRENPGEVLKCSPLVAAFMKCVSLAR 184 (192)
T ss_pred cCCcccccHHHHHHHHhcCCCccccccHHHHHHHHHHHHHH
Confidence 48899999999999999999999999999999999998775
No 12
>KOG3477 consensus Putative cytochrome c oxidase, subunit COX19 [Energy production and conversion]
Probab=71.32 E-value=5.9 Score=26.61 Aligned_cols=36 Identities=28% Similarity=0.537 Sum_probs=33.6
Q ss_pred CCChHHHHHHHHHHHhcCCCChHHHHHHHHHHHHHH
Q 034645 27 AKPCMKEMITFLNCMSLNQMNSEKCARQKELLSACM 62 (88)
Q Consensus 27 ~~pC~~eMs~lL~Cwasng~~~~~Ca~~~~~L~~Cm 62 (88)
...|-.||-..|.|+.+...+.+.|--+++..-.|-
T Consensus 27 ~geC~~em~eYl~Cl~~k~e~~~eCR~laK~YlqCR 62 (97)
T KOG3477|consen 27 LGECTAEMKEYLGCLKSKAENSEECRLLAKKYLQCR 62 (97)
T ss_pred ccccHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHh
Confidence 457999999999999999999999999999999994
No 13
>PF07527 Hairy_orange: Hairy Orange; InterPro: IPR003650 This domain confers specificity among members of the Hairy/E(SPL) family. HES-2 (hairy and enhancer of split 2) is a transcription factor, and the hairy protein is a pair-rule protein that regulates embryonic segmentation and adult bristle patterning. These proteins are transcriptional repressors of genes that require the BHLH protein for their transcription.; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 2DB7_A.
Probab=70.57 E-value=15 Score=20.36 Aligned_cols=34 Identities=26% Similarity=0.531 Sum_probs=27.2
Q ss_pred ChHHHHHHHHHHHhcCCCChHHHHHHHHHHHHHHHh
Q 034645 29 PCMKEMITFLNCMSLNQMNSEKCARQKELLSACMDA 64 (88)
Q Consensus 29 pC~~eMs~lL~Cwasng~~~~~Ca~~~~~L~~Cm~~ 64 (88)
.|+.|.+.+| -...+.+.+.++.+..-|..|+..
T Consensus 9 ~C~~Ev~~fL--~~~~~~~~~~~~rLl~HL~~~~~~ 42 (43)
T PF07527_consen 9 ECLNEVSRFL--SSVEGVDPGVRARLLSHLQSCLNQ 42 (43)
T ss_dssp HHHHHHHHHH--HHTS---THHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHH--hcCCCCChHHHHHHHHHHHHHhcC
Confidence 5999999999 566667889999999999999864
No 14
>PF05051 COX17: Cytochrome C oxidase copper chaperone (COX17); InterPro: IPR007745 Cox17p is essential for the assembly of functional cytochrome c oxidase (CCO) and for delivery of copper ions to the mitochondrion for insertion into the enzyme in Saccharomyces cerevisiae [].; GO: 0005507 copper ion binding, 0016531 copper chaperone activity, 0006825 copper ion transport, 0005758 mitochondrial intermembrane space; PDB: 1U97_A 1U96_A 1Z2G_A 2RNB_A 2RN9_A 2LGQ_A 2L0Y_B.
Probab=70.31 E-value=5.3 Score=23.87 Aligned_cols=36 Identities=22% Similarity=0.400 Sum_probs=28.4
Q ss_pred CChHHHHHHHHHHHhcCCCChHHHHHHHHHHHHHHHhh
Q 034645 28 KPCMKEMITFLNCMSLNQMNSEKCARQKELLSACMDAQ 65 (88)
Q Consensus 28 ~pC~~eMs~lL~Cwasng~~~~~Ca~~~~~L~~Cm~~~ 65 (88)
=.|-.+=.+==.|.-.||.++ |..++++.+.||...
T Consensus 10 CaCpetK~aRDeC~l~~g~e~--C~~~Ieahk~Cmr~~ 45 (49)
T PF05051_consen 10 CACPETKKARDECILFNGEED--CKELIEAHKACMRGE 45 (49)
T ss_dssp TTSHHHHHHHHHHHHHC-CCC--CHHHHHHHHHHHHHH
T ss_pred ccChhHHHHhHhhHHhcChHH--HHHHHHHHHHHHHHc
Confidence 346666667778899999876 999999999999865
No 15
>PF11326 DUF3128: Protein of unknown function (DUF3128); InterPro: IPR021475 This eukaryotic family of proteins has no known function.
Probab=59.34 E-value=14 Score=23.34 Aligned_cols=42 Identities=17% Similarity=0.354 Sum_probs=35.8
Q ss_pred CCCChHHHHHHHHHHHhcCC-------C-ChHHHHHHHHHHHHHHHhhcC
Q 034645 26 IAKPCMKEMITFLNCMSLNQ-------M-NSEKCARQKELLSACMDAQTN 67 (88)
Q Consensus 26 ~~~pC~~eMs~lL~Cwasng-------~-~~~~Ca~~~~~L~~Cm~~~~~ 67 (88)
....|...+-.++.|-+--| | ....|....+.|..||.....
T Consensus 3 ~~~sC~~~fd~~~~C~S~~~q~~~yYryG~~~~C~~~~~df~~C~~~k~~ 52 (84)
T PF11326_consen 3 TTMSCMDAFDELWFCYSPGGQFRNYYRYGEFDDCSQWWEDFKFCLRWKSK 52 (84)
T ss_pred CCccHHHHHHHHHHcCCchHhheeeeecCCCccHHHHHHHHHHHHHhccC
Confidence 36789999999999999887 2 347899999999999988764
No 16
>KOG4453 consensus Predicted ER membrane protein [Function unknown]
Probab=58.96 E-value=11 Score=29.47 Aligned_cols=44 Identities=18% Similarity=0.185 Sum_probs=30.4
Q ss_pred cchhhhhhhccCCcceeCcCCCCCCCCChHHHHHHHHHHHhcCC
Q 034645 2 CSLKHKIMGRKAGTLYINPKKFGNIAKPCMKEMITFLNCMSLNQ 45 (88)
Q Consensus 2 ~~~~~~~m~~k~~~Lkv~pKk~~~~~~pC~~eMs~lL~Cwasng 45 (88)
|.---.|||||.+.++..-.|.+.-+..=...-..++.||+--+
T Consensus 168 cDt~AdtvGRKfG~~tpk~aknKSlAGSIgaft~Gvf~c~vy~g 211 (269)
T KOG4453|consen 168 CDTIADTVGRKFGSTTPKYAKNKSLAGSIGAFTFGVFICIVYLG 211 (269)
T ss_pred hhhHHHHHhhhccccCCCcCCCccccchHHHHHHHHHHHHHHHH
Confidence 44456799999999886433333455666666778899998655
No 17
>KOG4624 consensus Uncharacterized conserved protein [Function unknown]
Probab=56.89 E-value=20 Score=24.49 Aligned_cols=41 Identities=17% Similarity=0.428 Sum_probs=35.4
Q ss_pred CCCCChHHHHHHHHHHHhcCCC-ChHHHHHHHHHHHHHHHhh
Q 034645 25 NIAKPCMKEMITFLNCMSLNQM-NSEKCARQKELLSACMDAQ 65 (88)
Q Consensus 25 ~~~~pC~~eMs~lL~Cwasng~-~~~~Ca~~~~~L~~Cm~~~ 65 (88)
.++.-|..+.+.|-.|...+|+ .-..|-++..+|+.|.-..
T Consensus 28 akt~~C~~~v~~~a~C~k~~~v~vv~TCrkq~~elk~Cl~~~ 69 (104)
T KOG4624|consen 28 AKTEKCSEFVQDFADCAKASGVSVVPTCRKQNSELKECLTQY 69 (104)
T ss_pred HHHHHHHHHHHHHHHHHhcCCeeeehhhHHHHHHHHHHHHHH
Confidence 3457899999999999999995 6789999999999997543
No 18
>PHA02629 A-type inclusion body protein; Provisional
Probab=43.97 E-value=15 Score=22.59 Aligned_cols=28 Identities=18% Similarity=0.217 Sum_probs=22.8
Q ss_pred HHHhcCCCChHHHHHHHHHHHHHHHhhc
Q 034645 39 NCMSLNQMNSEKCARQKELLSACMDAQT 66 (88)
Q Consensus 39 ~Cwasng~~~~~Ca~~~~~L~~Cm~~~~ 66 (88)
.|-++.+|....=+-++.+|+.||++-+
T Consensus 23 gc~s~c~ferk~iavleaelr~~metik 50 (61)
T PHA02629 23 GCTSSCEFERKIIAVLEAELRKSMETIK 50 (61)
T ss_pred CccchhHhhHHHHHHHHHHHHHHHHHHH
Confidence 3667777888888889999999998764
No 19
>PF02297 COX6B: Cytochrome oxidase c subunit VIb; InterPro: IPR003213 Cytochrome c oxidase (1.9.3.1 from EC) is an oligomeric enzymatic complex that is a component of the respiratory chain complex and is involved in the transfer of electrons from cytochrome c to oxygen []. In eukaryotes this enzyme complex is located in the mitochondrial inner membrane; in aerobic prokaryotes it is found in the plasma membrane. In eukaryotes, in addition to the three large subunits, I, II and III, that form the catalytic centre of the enzyme complex, there are a variable number of small polypeptide subunits. One of these subunits is the potentially haem-binding subunit, VIb, which is encoded in the nucleus []. ; GO: 0004129 cytochrome-c oxidase activity, 0005739 mitochondrion; PDB: 1OCC_U 1OCR_U 2DYS_H 3ASO_H 3AG3_U 2EIL_H 2EIJ_U 3AG2_U 3ABM_U 2EIN_U ....
Probab=40.95 E-value=14 Score=23.02 Aligned_cols=39 Identities=15% Similarity=0.427 Sum_probs=32.2
Q ss_pred CCCChHHHHHHHHHHHhcCCC---------ChHHHHHHHHHHHH-HHHh
Q 034645 26 IAKPCMKEMITFLNCMSLNQM---------NSEKCARQKELLSA-CMDA 64 (88)
Q Consensus 26 ~~~pC~~eMs~lL~Cwasng~---------~~~~Ca~~~~~L~~-Cm~~ 64 (88)
....|-+.=-.++.|...+|. +.+.|..+...+.. |...
T Consensus 8 ~r~~Cw~arD~y~~Cl~~~~~~~~~~~~~~~~~~C~~~~~~ye~~Cp~s 56 (76)
T PF02297_consen 8 QRKKCWQARDDYFKCLDKNGEPDSEKEKKKDESACKYFRKNYESNCPSS 56 (76)
T ss_dssp -HHHHHHHHHHHHHHHHHHHH------TTTTGGGGHHHHHHHHHHS-HH
T ss_pred HHHHHHHHHHHHHHHHHHcCccccccccccchhhhHHHHHHHHHhCcHH
Confidence 467888888999999999998 88999999999965 8754
No 20
>cd00926 Cyt_c_Oxidase_VIb Cytochrome c oxidase subunit VIb. Cytochrome c oxidase (CcO), the terminal oxidase in the respiratory chains of eukaryotes and most bacteria, is a multi-chain transmembrane protein located in the inner membrane of mitochondria and the cell membrane of prokaryotes. It catalyzes the reduction of O2 and simultaneously pumps protons across the membrane. The number of subunits varies from three to five in bacteria and up to 13 in mammalian mitochondria. Subunits I, II, and III of mammalian CcO are encoded within the mitochondrial genome and the remaining 10 subunits are encoded within the nuclear genome. Found only in eukaryotes, subunit VIb is one of three mammalian subunits that lacks a transmembrane region. It is located on the cytosolic side of the membrane and helps form the dimer interface with the corresponding subunit on the other monomer complex.
Probab=39.69 E-value=80 Score=19.87 Aligned_cols=35 Identities=11% Similarity=0.483 Sum_probs=31.5
Q ss_pred CCCChHHHHHHHHHHHhcCCCChHHHHHHHHHHHH
Q 034645 26 IAKPCMKEMITFLNCMSLNQMNSEKCARQKELLSA 60 (88)
Q Consensus 26 ~~~pC~~eMs~lL~Cwasng~~~~~Ca~~~~~L~~ 60 (88)
....|.+--..++.|...+|.+.+.|..+...++.
T Consensus 19 q~k~Cw~~y~~y~~Cl~~~ged~~~C~~~~~~~es 53 (75)
T cd00926 19 QTKHCWQRYVDYHRCIKAKGEDASPCKKFRRVYES 53 (75)
T ss_pred HHHHHHHHHHHHHHHHHHcCCchHHHHHHHHHHHH
Confidence 46789999999999999999999999999988764
No 21
>PF07956 DUF1690: Protein of Unknown function (DUF1690) ; InterPro: IPR012471 Family of uncharacterised fungal proteins.
Probab=37.78 E-value=43 Score=23.53 Aligned_cols=36 Identities=14% Similarity=0.229 Sum_probs=31.8
Q ss_pred CCChHHHHHHHHHHHhcCCCChHHHHHHHHHHHHHH
Q 034645 27 AKPCMKEMITFLNCMSLNQMNSEKCARQKELLSACM 62 (88)
Q Consensus 27 ~~pC~~eMs~lL~Cwasng~~~~~Ca~~~~~L~~Cm 62 (88)
...+-..=+.+..|+..|+--.=.|-.++++|+.|.
T Consensus 106 ~~~v~~aR~~vv~CL~~N~~rPLnCw~EVe~FKk~V 141 (142)
T PF07956_consen 106 SEEVEKARSAVVRCLRENDGRPLNCWEEVEAFKKEV 141 (142)
T ss_pred chhhHHHHHHHHHHHHHCCCCCCchHHHHHHHHHHh
Confidence 446777789999999999998899999999999885
No 22
>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=35.03 E-value=31 Score=23.11 Aligned_cols=59 Identities=10% Similarity=0.234 Sum_probs=45.8
Q ss_pred CCCChHHHHHHHHHHHhcCCC--ChHHHHHHHHHHHHHHHhhcCCCCCCCCChHHHHHhhcCC
Q 034645 26 IAKPCMKEMITFLNCMSLNQM--NSEKCARQKELLSACMDAQTNKKRKPWGSINYHLQRLNRG 86 (88)
Q Consensus 26 ~~~pC~~eMs~lL~Cwasng~--~~~~Ca~~~~~L~~Cm~~~~~~~k~~~stINYHL~Rl~~~ 86 (88)
-+..|..+=..++.|.-..|. ....|.-+..+|..|+-..+ ..++. .+|--...|+++.
T Consensus 29 ~~~RC~~FE~e~i~C~~~~G~~r~kKeC~~e~EDy~EClh~~K-e~~R~-~aI~kqR~K~~ke 89 (96)
T PF10200_consen 29 QPSRCHPFEKEWIECAEAYGQTRGKKECKLELEDYYECLHHTK-EMKRM-RAIRKQRDKQIKE 89 (96)
T ss_pred CCCchHHHHHHHHHHHHHHcccchhhhchhHHhHHHHHHhhHH-HHHHH-HHHHHHHHHHHHc
Confidence 478899998999999988774 57899999999999997665 33444 6777666666653
No 23
>PF10811 DUF2532: Protein of unknown function (DUF2532); InterPro: IPR024386 This bacterial family of proteins has no known function.
Probab=30.11 E-value=49 Score=23.79 Aligned_cols=25 Identities=32% Similarity=0.634 Sum_probs=19.9
Q ss_pred HHHHHHHhhcCCCCCCCCChHHHHHh
Q 034645 57 LLSACMDAQTNKKRKPWGSINYHLQR 82 (88)
Q Consensus 57 ~L~~Cm~~~~~~~k~~~stINYHL~R 82 (88)
-|+-|-|..+.-+-+. ++.|||++.
T Consensus 104 flkfcednfqts~sk~-nsln~~~kk 128 (158)
T PF10811_consen 104 FLKFCEDNFQTSKSKS-NSLNYQIKK 128 (158)
T ss_pred HHHHHHhhcccccCCC-cchhHHHHH
Confidence 3677988888776777 999999874
No 24
>PF08095 Toxin_25: Hefutoxin family; InterPro: IPR012630 This family consists of the hefutoxins that are found in the venom of the scorpion Heterometrus fulvipes (Indian black scorpion). These toxins, kappa-hefutoxin1 and kappa-hefutoxin2, exhibit no homology to any known toxins. The hefutoxins are potassium channel toxins [].; GO: 0009405 pathogenesis, 0005576 extracellular region; PDB: 1HP9_A.
Probab=29.91 E-value=28 Score=17.52 Aligned_cols=15 Identities=20% Similarity=0.521 Sum_probs=9.2
Q ss_pred HHHHhcCCCChHHHHH
Q 034645 38 LNCMSLNQMNSEKCAR 53 (88)
Q Consensus 38 L~Cwasng~~~~~Ca~ 53 (88)
-+||.. |+++..|.+
T Consensus 6 rscwk~-g~deetck~ 20 (22)
T PF08095_consen 6 RSCWKA-GHDEETCKE 20 (22)
T ss_dssp THHHHH-HS-TTHHHH
T ss_pred HHHHHc-cCcHHHHHh
Confidence 379975 556666754
No 25
>PRK11477 carbohydrate diacid transcriptional activator CdaR; Provisional
Probab=24.98 E-value=1.1e+02 Score=23.60 Aligned_cols=38 Identities=11% Similarity=0.133 Sum_probs=27.8
Q ss_pred HHHHHHHHHhcCCCChHHHHHHHHHHHHHHHhhcCCCCCCCCChHHHHHhhc
Q 034645 33 EMITFLNCMSLNQMNSEKCARQKELLSACMDAQTNKKRKPWGSINYHLQRLN 84 (88)
Q Consensus 33 eMs~lL~Cwasng~~~~~Ca~~~~~L~~Cm~~~~~~~k~~~stINYHL~Rl~ 84 (88)
++...|.+|-.++.+.+.+|+.. -=+.||++|.|.|+.
T Consensus 322 ~L~~TL~~y~~~~~ni~~tA~~L--------------~iHrNTL~YRL~kI~ 359 (385)
T PRK11477 322 LLRRTLAAWFRHNVQPLATSKAL--------------FIHRNTLEYRLNRIS 359 (385)
T ss_pred hHHHHHHHHHHcCCCHHHHHHHh--------------CCCHhhHHHHHHHHH
Confidence 56667778888888888777633 123499999999975
No 26
>PF05924 SAMP: SAMP Motif; InterPro: IPR009224 This short region is found repeated in the mid region of the adenomatous polyposis proteins (APCs). This motif binds axin [].; GO: 0008013 beta-catenin binding, 0016055 Wnt receptor signaling pathway; PDB: 1EMU_B 2RQU_B.
Probab=24.34 E-value=64 Score=15.93 Aligned_cols=16 Identities=31% Similarity=0.733 Sum_probs=9.9
Q ss_pred HHHHHHHHHhhcCCCC
Q 034645 55 KELLSACMDAQTNKKR 70 (88)
Q Consensus 55 ~~~L~~Cm~~~~~~~k 70 (88)
+..|+.|+..+-|+.+
T Consensus 3 deiL~~CI~sAmPk~~ 18 (20)
T PF05924_consen 3 DEILQECIGSAMPKRR 18 (20)
T ss_dssp HHHHHHHHHCTS----
T ss_pred HHHHHHHHHHhccccc
Confidence 4789999988775543
No 27
>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=22.87 E-value=67 Score=19.98 Aligned_cols=35 Identities=20% Similarity=0.360 Sum_probs=28.1
Q ss_pred CChHHHHHHHHHHHhcCCCChHHHHHHHHHHHHHH
Q 034645 28 KPCMKEMITFLNCMSLNQMNSEKCARQKELLSACM 62 (88)
Q Consensus 28 ~pC~~eMs~lL~Cwasng~~~~~Ca~~~~~L~~Cm 62 (88)
.-|+-.+..|..|-..+-+..-.|..+.-+...|.
T Consensus 20 DyCAh~Li~l~kCrr~~~p~~~~C~~erH~y~~C~ 54 (66)
T PF05676_consen 20 DYCAHLLIPLNKCRRDNFPFPWKCEHERHEYEKCQ 54 (66)
T ss_pred hhHHHHHHHHHHHHHhCCCCcccCCcchhhHHHcc
Confidence 45888888888888888777788888888888875
No 28
>PF00196 GerE: Bacterial regulatory proteins, luxR family; InterPro: IPR000792 This domain is a DNA-binding, helix-turn-helix (HTH) domain of about 65 amino acids, present in transcription regulators of the LuxR/FixJ family of response regulators. The domain is named after Vibrio fischeri luxR, a transcriptional activator for quorum-sensing control of luminescence. LuxR-type HTH domain proteins occur in a variety of organisms. The DNA-binding HTH domain is usually located in the C-terminal region; the N-terminal region often containing an autoinducer-binding domain or a response regulatory domain. Most luxR-type regulators act as transcription activators, but some can be repressors or have a dual role for different sites. LuxR-type HTH regulators control a wide variety of activities in various biological processes. The luxR-type, DNA-binding HTH domain forms a four-helical bundle structure. The HTH motif comprises the second and third helices, known as the scaffold and recognition helix, respectively. The HTH binds DNA in the major groove, where the N-terminal part of the recognition helix makes most of the DNA contacts. The fourth helix is involved in dimerisation of gerE and traR. Signalling events by one of the four activation mechanisms described below lead to multimerisation of the regulator. The regulators bind DNA as multimers [, , ]. LuxR-type HTH proteins can be activated by one of four different mechanisms: 1) Regulators which belong to a two-component sensory transduction system where the protein is activated by its phosphorylation, generally on an aspartate residue, by a transmembrane kinase [, ]. Some proteins that belong to this category are: Rhizobiaceae fixJ (global regulator inducing expression of nitrogen-fixation genes in microaerobiosis) Escherichia coli and Salmonella typhimurium uhpA (activates hexose phosphate transport gene uhpT) E. coli narL and narP (activate nitrate reductase operon) Enterobacteria rcsB (regulation of exopolysaccharide biosynthesis in enteric and plant pathogenesis) Bordetella pertussis bvgA (virulence factor) Bacillus subtilis coma (involved in expression of late-expressing competence genes) 2) Regulators which are activated, or in very rare cases repressed, when bound to N-acyl homoserine lactones, which are used as quorum sensing molecules in a variety of Gram-negative bacteria []: V. fischeri luxR (activates bioluminescence operon) Agrobacterium tumefaciens traR (regulation of Ti plasmid transfer) Erwinia carotovora carR (control of carbapenem antibiotics biosynthesis) E. carotovora expR (virulence factor for soft rot disease; activates plant tissue macerating enzyme genes) Pseudomonas aeruginosa lasR (activates elastase gene lasB) Erwinia chrysanthemi echR and Erwinia stewartii esaR Pseudomonas chlororaphis phzR (positive regulator of phenazine antibiotic production) Pseudomonas aeruginosa rhlR (activates rhlAB operon and lasB gene) 3) Autonomous effector domain regulators, without a regulatory domain, represented by gerE []. B. subtilis gerE (transcription activator and repressor for the regulation of spore formation) 4) Multiple ligand-binding regulators, exemplified by malT []. E. coli malT (activates maltose operon; MalT binds ATP and maltotriose); GO: 0003700 sequence-specific DNA binding transcription factor activity, 0043565 sequence-specific DNA binding, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 3SZT_A 3CLO_A 1H0M_A 1L3L_A 3C57_B 1ZLK_B 1ZLJ_H 3C3W_B 1RNL_A 1ZG1_A ....
Probab=21.88 E-value=18 Score=20.69 Aligned_cols=13 Identities=15% Similarity=0.376 Sum_probs=11.1
Q ss_pred CChHHHHHhhcCC
Q 034645 74 GSINYHLQRLNRG 86 (88)
Q Consensus 74 stINYHL~Rl~~~ 86 (88)
+||.+|+.+++++
T Consensus 33 ~tV~~~~~~i~~K 45 (58)
T PF00196_consen 33 KTVKSHRRRIMKK 45 (58)
T ss_dssp HHHHHHHHHHHHH
T ss_pred hhHHHHHHHHHHH
Confidence 7999999998764
No 29
>COG0640 ArsR Predicted transcriptional regulators [Transcription]
Probab=21.80 E-value=42 Score=19.33 Aligned_cols=16 Identities=19% Similarity=0.262 Sum_probs=12.0
Q ss_pred CCCCCChHHHHHhhcC
Q 034645 70 RKPWGSINYHLQRLNR 85 (88)
Q Consensus 70 k~~~stINYHL~Rl~~ 85 (88)
.-.++|+.|||..|..
T Consensus 50 ~~~~~~v~~hL~~L~~ 65 (110)
T COG0640 50 GLSQSTVSHHLKVLRE 65 (110)
T ss_pred CCChhHHHHHHHHHHH
Confidence 3344999999998754
Done!