Query 045334
Match_columns 80
No_of_seqs 102 out of 180
Neff 3.3
Searched_HMMs 46136
Date Fri Mar 29 12:12:26 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/045334.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/045334hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG3496 Cytochrome c oxidase a 100.0 1E-33 2.3E-38 183.4 6.2 72 1-80 1-72 (72)
2 PF05051 COX17: Cytochrome C o 100.0 2.8E-32 6E-37 166.0 1.2 48 33-80 2-49 (49)
3 PF06747 CHCH: CHCH domain; I 90.2 0.076 1.7E-06 28.4 -0.2 30 45-74 3-34 (35)
4 PLN03079 Uncharacterized prote 89.9 0.24 5.2E-06 33.6 1.9 33 43-75 18-60 (91)
5 PF08583 Cmc1: Cytochrome c ox 88.0 0.37 8E-06 28.7 1.7 20 60-79 11-30 (69)
6 PF08991 DUF1903: Domain of un 84.1 0.52 1.1E-05 29.9 1.0 26 51-76 12-39 (67)
7 PF05254 UPF0203: Uncharacteri 83.6 0.68 1.5E-05 29.4 1.4 34 42-75 8-51 (68)
8 PF06747 CHCH: CHCH domain; I 83.1 1.1 2.3E-05 23.8 1.9 18 62-79 1-18 (35)
9 KOG4114 Cytochrome c oxidase a 52.7 16 0.00035 24.1 2.5 29 48-76 27-59 (73)
10 KOG3481 Uncharacterized conser 51.5 13 0.00029 25.2 2.0 34 42-75 12-55 (87)
11 KOG4138 Unchracterized conserv 47.0 21 0.00045 24.6 2.5 33 43-75 43-76 (96)
12 PF07956 DUF1690: Protein of U 44.1 13 0.00029 26.2 1.3 24 51-74 117-142 (142)
13 KOG3284 Vacuolar sorting prote 43.8 24 0.00052 27.3 2.6 17 60-76 56-72 (213)
14 KOG0957 PHD finger protein [Ge 40.6 16 0.00035 32.2 1.4 20 30-49 111-131 (707)
15 PF10249 NDUFB10: NADH-ubiquin 39.5 23 0.0005 25.1 1.9 27 49-75 69-98 (128)
16 KOG4624 Uncharacterized conser 37.1 34 0.00073 23.9 2.4 21 60-80 31-51 (104)
17 KOG4618 Uncharacterized conser 34.8 41 0.00088 22.2 2.3 32 43-74 24-57 (74)
18 PF00998 RdRP_3: Viral RNA dep 33.5 25 0.00054 29.5 1.5 29 51-79 304-332 (486)
19 KOG4009 NADH-ubiquinone oxidor 31.6 46 0.00099 24.7 2.4 26 51-76 87-115 (156)
20 PF08036 Antimicrobial_6: Diap 31.5 29 0.00063 20.5 1.1 17 42-58 9-25 (39)
21 PF03997 VPS28: VPS28 protein; 30.8 48 0.001 24.6 2.4 18 59-76 29-46 (188)
22 PF03489 SapB_2: Saposin-like 29.8 51 0.0011 17.2 1.8 11 60-70 2-12 (35)
23 PF01841 Transglut_core: Trans 29.2 27 0.00059 21.2 0.8 25 55-79 47-71 (113)
24 smart00460 TGc Transglutaminas 29.0 44 0.00096 18.7 1.6 25 55-79 2-26 (68)
25 cd03715 RT_ZFREV_like RT_ZFREV 24.6 80 0.0017 22.1 2.6 30 51-80 161-191 (210)
26 PF08676 MutL_C: MutL C termin 24.5 56 0.0012 21.4 1.7 18 63-80 65-82 (144)
27 PF09034 TRADD_N: TRADD, N-ter 24.1 64 0.0014 22.7 2.0 17 56-72 27-43 (111)
28 PF10203 Pet191_N: Cytochrome 23.5 79 0.0017 19.8 2.2 25 52-76 31-58 (68)
29 PF11326 DUF3128: Protein of u 22.3 60 0.0013 20.5 1.5 22 57-78 30-52 (84)
30 PF03790 KNOX1: KNOX1 domain ; 21.5 77 0.0017 18.9 1.7 13 62-74 13-25 (45)
31 KOG4148 Uncharacterized conser 20.3 80 0.0017 22.1 1.8 18 59-76 10-27 (106)
No 1
>KOG3496 consensus Cytochrome c oxidase assembly protein/Cu2+ chaperone COX17 [Posttranslational modification, protein turnover, chaperones]
Probab=100.00 E-value=1e-33 Score=183.39 Aligned_cols=72 Identities=54% Similarity=0.989 Sum_probs=59.2
Q ss_pred CCCCCCCCCccccCCCCCCCCCCCccccCCCCCCCCCCccccCccchhhhhhhhhhccHHHHHHHHHHHHHHHHhcCCCC
Q 045334 1 MGGLPLQDASSTLALPGSQPNQGLEVTKSGTESKPKKKICCACPETKKLRDECIVEHGEEACAKWIEAHRKCLRAEGFNV 80 (80)
Q Consensus 1 Mg~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~k~KpCCaCpetK~~RDeCil~~ge~~C~~~Ieahk~Cmr~~GF~v 80 (80)
|.|++.+++.+..+-++ ..+..++.++|+|||||||+||++||.|||+||+++|.+|||+||.|||+|||+|
T Consensus 1 m~~l~~~s~at~~~~~~--------~~~~a~eek~K~KpCCaCpetK~~RDaCIle~gee~C~~lIEahk~CMr~~GF~v 72 (72)
T KOG3496|consen 1 MSGLTAQSSATESDKPA--------PQANAAEEKPKPKPCCACPETKKARDACILENGEEKCGKLIEAHKECMRAYGFEV 72 (72)
T ss_pred CCcccccchhhccCCCc--------cccccccccCCCCccccCCchhhhhhhHhhhcCHHHHHHHHHHHHHHHHHcCCCC
Confidence 66766666555544441 2223456788999999999999999999999999999999999999999999997
No 2
>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=99.97 E-value=2.8e-32 Score=166.03 Aligned_cols=48 Identities=69% Similarity=1.288 Sum_probs=41.6
Q ss_pred CCCCCCccccCccchhhhhhhhhhccHHHHHHHHHHHHHHHHhcCCCC
Q 045334 33 SKPKKKICCACPETKKLRDECIVEHGEEACAKWIEAHRKCLRAEGFNV 80 (80)
Q Consensus 33 ~~~k~KpCCaCpetK~~RDeCil~~ge~~C~~~Ieahk~Cmr~~GF~v 80 (80)
++|++||||||||||++||+|||+||+++|++|||+||+|||+|||+|
T Consensus 2 ~kP~~KpCCaCpetK~aRDeC~l~~g~e~C~~~Ieahk~Cmr~~GF~v 49 (49)
T PF05051_consen 2 EKPKKKPCCACPETKKARDECILFNGEEDCKELIEAHKACMRGEGFKV 49 (49)
T ss_dssp SS----TTTTSHHHHHHHHHHHHHC-CCCCHHHHHHHHHHHHHHTCCS
T ss_pred CCCCCCcCccChhHHHHhHhhHHhcChHHHHHHHHHHHHHHHHcCCCC
Confidence 456689999999999999999999999999999999999999999997
No 3
>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=90.16 E-value=0.076 Score=28.36 Aligned_cols=30 Identities=27% Similarity=0.398 Sum_probs=20.7
Q ss_pred cchhhhhhhhhhccH--HHHHHHHHHHHHHHH
Q 045334 45 ETKKLRDECIVEHGE--EACAKWIEAHRKCLR 74 (80)
Q Consensus 45 etK~~RDeCil~~ge--~~C~~~Ieahk~Cmr 74 (80)
++.++==+|+-.|+. ..|.+++++|++|+.
T Consensus 3 ~e~~~~~~Cl~~n~~~~~~C~~~~~~~~~C~~ 34 (35)
T PF06747_consen 3 EEMKAYLACLKENNFDWSKCRKEFKAYKECRM 34 (35)
T ss_dssp HHHHHHHHHHHCH-SSTCCCHHHHHHHHHHHC
T ss_pred HHHHHHHHHHHHCCCcHHhhHHHHHHHHHHhh
Confidence 333344467777654 489999999999975
No 4
>PLN03079 Uncharacterized protein At4g33100; Provisional
Probab=89.86 E-value=0.24 Score=33.65 Aligned_cols=33 Identities=27% Similarity=0.608 Sum_probs=28.2
Q ss_pred Cccchhhhhhhhhh-------cc---HHHHHHHHHHHHHHHHh
Q 045334 43 CPETKKLRDECIVE-------HG---EEACAKWIEAHRKCLRA 75 (80)
Q Consensus 43 CpetK~~RDeCil~-------~g---e~~C~~~Ieahk~Cmr~ 75 (80)
|.+.|..=|.|+.. .| ++.|.++.+.|++|+..
T Consensus 18 CtelK~~YD~CFN~WYsEkFLKG~~~~~eC~~~w~~Yq~Cv~~ 60 (91)
T PLN03079 18 CAELRTAYHNCFNRWYSEKFVKGQWDKEDCVAEWHKYRACLSE 60 (91)
T ss_pred cHHHHHHHHHHHHHHHHHhhhcCCcccchHHHHHHHHHHHHHH
Confidence 99999999999982 23 46899999999999864
No 5
>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=87.99 E-value=0.37 Score=28.65 Aligned_cols=20 Identities=35% Similarity=0.675 Sum_probs=17.4
Q ss_pred HHHHHHHHHHHHHHHhcCCC
Q 045334 60 EACAKWIEAHRKCLRAEGFN 79 (80)
Q Consensus 60 ~~C~~~Ieahk~Cmr~~GF~ 79 (80)
..|.++|++|..|.++.+|.
T Consensus 11 ~~C~~~i~~~~~C~~~~~~~ 30 (69)
T PF08583_consen 11 KKCADEIEAFAECHKDRTFK 30 (69)
T ss_pred HHhHHHHHHHHHHHhcchHH
Confidence 68999999999999987664
No 6
>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=84.06 E-value=0.52 Score=29.88 Aligned_cols=26 Identities=23% Similarity=0.657 Sum_probs=21.1
Q ss_pred hhhhhhcc--HHHHHHHHHHHHHHHHhc
Q 045334 51 DECIVEHG--EEACAKWIEAHRKCLRAE 76 (80)
Q Consensus 51 DeCil~~g--e~~C~~~Ieahk~Cmr~~ 76 (80)
-.|+-.|+ ++.|.++|++|+.|-+.+
T Consensus 12 q~CL~~N~Yd~~kC~~~i~~l~~Cck~~ 39 (67)
T PF08991_consen 12 QKCLQRNNYDESKCQDYIDALYECCKKF 39 (67)
T ss_dssp HHHHHHTTT-CCCTHHHHHHHHHHHTTS
T ss_pred HHHHHHcCCCHHHHHHHHHHHHHHHHHH
Confidence 46777775 679999999999997765
No 7
>PF05254 UPF0203: Uncharacterised protein family (UPF0203); InterPro: IPR007918 This is a family of small highly conserved proteins. In Saccharomyces cerevisiae (Baker's yeast) the gene YKL053C-A (MDM35) O60200 from SWISSPROT is one of the genes essential for maintenance of normal mitochondrial distribution and morphology (MDM) []; wherease in Homo sapiens (Human), p53CSV, O43715 from SWISSPROT is a direct transcriptional target for p53 and appears to be a cell-survival mediator in response to genotoxic stress including low-levels of DNA damage. It is suggested that p53CSV modulates the apoptotic pathway through interaction with HSP70 and Apaf-1 thereby inhibiting activation of procaspase-3 and procaspase-9 [].
Probab=83.63 E-value=0.68 Score=29.36 Aligned_cols=34 Identities=24% Similarity=0.716 Sum_probs=28.1
Q ss_pred cCccchhhhhhhhhh-------cc---HHHHHHHHHHHHHHHHh
Q 045334 42 ACPETKKLRDECIVE-------HG---EEACAKWIEAHRKCLRA 75 (80)
Q Consensus 42 aCpetK~~RDeCil~-------~g---e~~C~~~Ieahk~Cmr~ 75 (80)
.|.+-|..=|.|+.. .| ...|.++-+.|++|+..
T Consensus 8 eC~~lK~~YD~CFn~WfsekfLkG~~~~~~C~~~~~~Y~~Cv~~ 51 (68)
T PF05254_consen 8 ECTELKEKYDQCFNKWFSEKFLKGDSSDNECGELFKEYQQCVQK 51 (68)
T ss_pred HHHHHHHHHHHHHHHHHHHhhhcCCCCCCcHHHHHHHHHHHHHH
Confidence 488999999999982 24 35899999999999864
No 8
>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=83.12 E-value=1.1 Score=23.77 Aligned_cols=18 Identities=33% Similarity=0.756 Sum_probs=15.5
Q ss_pred HHHHHHHHHHHHHhcCCC
Q 045334 62 CAKWIEAHRKCLRAEGFN 79 (80)
Q Consensus 62 C~~~Ieahk~Cmr~~GF~ 79 (80)
|...+.+|-.||+..+|+
T Consensus 1 C~~e~~~~~~Cl~~n~~~ 18 (35)
T PF06747_consen 1 CAEEMKAYLACLKENNFD 18 (35)
T ss_dssp THHHHHHHHHHHHCH-SS
T ss_pred CHHHHHHHHHHHHHCCCc
Confidence 788999999999999985
No 9
>KOG4114 consensus Cytochrome c oxidase assembly protein PET191 [Posttranslational modification, protein turnover, chaperones]
Probab=52.75 E-value=16 Score=24.09 Aligned_cols=29 Identities=28% Similarity=0.499 Sum_probs=22.1
Q ss_pred hhhhhhhhhcc----HHHHHHHHHHHHHHHHhc
Q 045334 48 KLRDECIVEHG----EEACAKWIEAHRKCLRAE 76 (80)
Q Consensus 48 ~~RDeCil~~g----e~~C~~~Ieahk~Cmr~~ 76 (80)
+.=.||+-.++ .++|..+|++|..|=|+.
T Consensus 27 ks~reCldn~~~~~vPeeC~al~~af~dCKRsl 59 (73)
T KOG4114|consen 27 KSPRECLDNPELKDVPEECIALMKAFLDCKRSL 59 (73)
T ss_pred CCHHHHhcCCccccCcHHHHHHHHHHHHHHHHH
Confidence 33347777666 479999999999998863
No 10
>KOG3481 consensus Uncharacterized conserved protein [Function unknown]
Probab=51.47 E-value=13 Score=25.18 Aligned_cols=34 Identities=26% Similarity=0.762 Sum_probs=27.7
Q ss_pred cCccchhhhhhhhhh-------cc---HHHHHHHHHHHHHHHHh
Q 045334 42 ACPETKKLRDECIVE-------HG---EEACAKWIEAHRKCLRA 75 (80)
Q Consensus 42 aCpetK~~RDeCil~-------~g---e~~C~~~Ieahk~Cmr~ 75 (80)
.|-+-|..=|.|+-. .| .+.|..|-..|++|+..
T Consensus 12 eCt~lk~~YD~CFn~Wf~eKflKG~~~~~pC~~l~k~Y~~Cv~k 55 (87)
T KOG3481|consen 12 ECTDLKQKYDQCFNEWFSEKFLKGDSSGEPCSRLFKVYKQCVQK 55 (87)
T ss_pred cchHHHHHHHHHHHHHHHHHhcCCccccCcHHHHHHHHHHHHHH
Confidence 378899999999863 23 46899999999999853
No 11
>KOG4138 consensus Unchracterized conserved protein (estrogen up-regulated protein E2IG2 in human) [General function prediction only]
Probab=47.04 E-value=21 Score=24.59 Aligned_cols=33 Identities=24% Similarity=0.626 Sum_probs=24.6
Q ss_pred CccchhhhhhhhhhccH-HHHHHHHHHHHHHHHh
Q 045334 43 CPETKKLRDECIVEHGE-EACAKWIEAHRKCLRA 75 (80)
Q Consensus 43 CpetK~~RDeCil~~ge-~~C~~~Ieahk~Cmr~ 75 (80)
|-++--+=.+|+..++. -.|...+++||.||..
T Consensus 43 C~~ehlalq~C~a~t~DWRqC~~qm~~FrkCwek 76 (96)
T KOG4138|consen 43 CAAEHLALQECMAQTQDWRQCQPQMQAFRKCWEK 76 (96)
T ss_pred hHHHHHHHHHHHHhhccHHHHHHHHHHHHHHHHH
Confidence 44455555667666654 5899999999999976
No 12
>PF07956 DUF1690: Protein of Unknown function (DUF1690) ; InterPro: IPR012471 Family of uncharacterised fungal proteins.
Probab=44.05 E-value=13 Score=26.18 Aligned_cols=24 Identities=25% Similarity=0.446 Sum_probs=19.7
Q ss_pred hhhhhhccH--HHHHHHHHHHHHHHH
Q 045334 51 DECIVEHGE--EACAKWIEAHRKCLR 74 (80)
Q Consensus 51 DeCil~~ge--~~C~~~Ieahk~Cmr 74 (80)
=.|+..|.- =+|-+.||+||.|.+
T Consensus 117 v~CL~~N~~rPLnCw~EVe~FKk~V~ 142 (142)
T PF07956_consen 117 VRCLRENDGRPLNCWEEVEAFKKEVK 142 (142)
T ss_pred HHHHHHCCCCCCchHHHHHHHHHHhC
Confidence 369998853 499999999999864
No 13
>KOG3284 consensus Vacuolar sorting protein VPS28 [Intracellular trafficking, secretion, and vesicular transport]
Probab=43.75 E-value=24 Score=27.28 Aligned_cols=17 Identities=24% Similarity=0.440 Sum_probs=15.3
Q ss_pred HHHHHHHHHHHHHHHhc
Q 045334 60 EACAKWIEAHRKCLRAE 76 (80)
Q Consensus 60 ~~C~~~Ieahk~Cmr~~ 76 (80)
..|..||.+||.||++.
T Consensus 56 s~c~kLi~Q~k~~~~~~ 72 (213)
T KOG3284|consen 56 SECSKLIVQYKVAFRSV 72 (213)
T ss_pred HHHHHHHHHHHHHHHHh
Confidence 47999999999999974
No 14
>KOG0957 consensus PHD finger protein [General function prediction only]
Probab=40.61 E-value=16 Score=32.16 Aligned_cols=20 Identities=45% Similarity=0.941 Sum_probs=13.8
Q ss_pred CCCCCCCCC-ccccCccchhh
Q 045334 30 GTESKPKKK-ICCACPETKKL 49 (80)
Q Consensus 30 ~~~~~~k~K-pCCaCpetK~~ 49 (80)
...+.|++. +||||.-.+..
T Consensus 111 ~~~Sapkk~~iCcVClg~rs~ 131 (707)
T KOG0957|consen 111 RTPSAPKKAVICCVCLGQRSV 131 (707)
T ss_pred cccCccccceEEEEeecCccc
Confidence 334556655 99999988743
No 15
>PF10249 NDUFB10: NADH-ubiquinone oxidoreductase subunit 10; InterPro: IPR019377 NADH-ubiquinone oxidoreductase subunit 10 of (NDUFB10) is a member of a family of conserved proteins of up to 180 residues. It is one of the 41 protein subunits within the hydrophobic fraction of the NADH:ubiquinone oxidoreductase (complex I), a multiprotein complex located in the inner mitochondrial membrane whose 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. NDUFB10 is encoded in the nucleus.
Probab=39.48 E-value=23 Score=25.13 Aligned_cols=27 Identities=19% Similarity=0.433 Sum_probs=20.8
Q ss_pred hhhhhhhhccH---HHHHHHHHHHHHHHHh
Q 045334 49 LRDECIVEHGE---EACAKWIEAHRKCLRA 75 (80)
Q Consensus 49 ~RDeCil~~ge---~~C~~~Ieahk~Cmr~ 75 (80)
..++|...+|. .+|+++|++|..=.+.
T Consensus 69 Rl~~C~~~EG~nh~qnC~~l~~qy~ea~~~ 98 (128)
T PF10249_consen 69 RLEACYRREGVNHYQNCRKLVEQYEEAAKN 98 (128)
T ss_pred HHHHHHHHHCcCHhhhhHHHHHHHHHHHHH
Confidence 34689998886 5799999999865443
No 16
>KOG4624 consensus Uncharacterized conserved protein [Function unknown]
Probab=37.13 E-value=34 Score=23.86 Aligned_cols=21 Identities=29% Similarity=0.817 Sum_probs=18.8
Q ss_pred HHHHHHHHHHHHHHHhcCCCC
Q 045334 60 EACAKWIEAHRKCLRAEGFNV 80 (80)
Q Consensus 60 ~~C~~~Ieahk~Cmr~~GF~v 80 (80)
++|.+++.+|-.|-++-||.|
T Consensus 31 ~~C~~~v~~~a~C~k~~~v~v 51 (104)
T KOG4624|consen 31 EKCSEFVQDFADCAKASGVSV 51 (104)
T ss_pred HHHHHHHHHHHHHHhcCCeee
Confidence 689999999999999999864
No 17
>KOG4618 consensus Uncharacterized conserved protein [Function unknown]
Probab=34.84 E-value=41 Score=22.23 Aligned_cols=32 Identities=16% Similarity=0.554 Sum_probs=25.2
Q ss_pred Cccchhhhhhhhhhcc--HHHHHHHHHHHHHHHH
Q 045334 43 CPETKKLRDECIVEHG--EEACAKWIEAHRKCLR 74 (80)
Q Consensus 43 CpetK~~RDeCil~~g--e~~C~~~Ieahk~Cmr 74 (80)
|..+-.+-=.|+=+|+ -++|.+..+.||.|=+
T Consensus 24 Cl~es~aSfkCLeennyDRsKCq~yFd~YkeCKk 57 (74)
T KOG4618|consen 24 CLLESSASFKCLEENNYDRSKCQDYFDVYKECKK 57 (74)
T ss_pred HHHHHHHHHHHHHhcCccHHHHHHHHHHHHHHHH
Confidence 4566666667887776 4699999999999965
No 18
>PF00998 RdRP_3: Viral RNA dependent RNA polymerase; InterPro: IPR002166 The RNA dependent RNA polymerase is also known as non-structural protein NS5B. NS5B is a 65 kDa protein that resembles other viral RNA polymerases. Hepatitis C virus (HCV) replication is thought to occur in membrane bound replication complexes. These complexes transcribe the positive strand and the resulting minus strand is used as a template for the synthesis of genomic RNA. There are two viral proteins involved in the reaction, NS3 and NS5B [, , ].; GO: 0003723 RNA binding, 0003968 RNA-directed RNA polymerase activity, 0005524 ATP binding, 0006351 transcription, DNA-dependent, 0019079 viral genome replication; PDB: 2XYM_A 3I5K_D 4AEX_A 4E7A_A 2XXD_A 4E78_A 4AEP_A 4E76_A 1S4F_D 1S48_A ....
Probab=33.55 E-value=25 Score=29.45 Aligned_cols=29 Identities=21% Similarity=0.318 Sum_probs=22.6
Q ss_pred hhhhhhccHHHHHHHHHHHHHHHHhcCCC
Q 045334 51 DECIVEHGEEACAKWIEAHRKCLRAEGFN 79 (80)
Q Consensus 51 DeCil~~ge~~C~~~Ieahk~Cmr~~GF~ 79 (80)
|+|+|.--...+.++.++...-|..|||.
T Consensus 304 DD~vvi~E~~~~~~~~~~l~~~~~~~Gf~ 332 (486)
T PF00998_consen 304 DDCVVICESAGVDEDEAALTEAFTRYGFP 332 (486)
T ss_dssp TEEEEEEEHCHHHHHHHHHHHHHHHTT-B
T ss_pred CceEEEecccchHHHHHHHHHHHHhcCCC
Confidence 67777665667777778999999999996
No 19
>KOG4009 consensus NADH-ubiquinone oxidoreductase, subunit NDUFB10/PDSW [Energy production and conversion]
Probab=31.58 E-value=46 Score=24.65 Aligned_cols=26 Identities=23% Similarity=0.419 Sum_probs=20.7
Q ss_pred hhhhhhccHH---HHHHHHHHHHHHHHhc
Q 045334 51 DECIVEHGEE---ACAKWIEAHRKCLRAE 76 (80)
Q Consensus 51 DeCil~~ge~---~C~~~Ieahk~Cmr~~ 76 (80)
+.|++.+|.. +|.++||+|.+=-+.|
T Consensus 87 k~C~lye~pnh~q~C~k~veq~e~~~~n~ 115 (156)
T KOG4009|consen 87 KWCYLYEGPNHYQKCRKLVEQYEDATRNY 115 (156)
T ss_pred HHHHHHhCcchHhHHHHHHHHHHHHHHHH
Confidence 5799988864 7999999998765543
No 20
>PF08036 Antimicrobial_6: Diapausin family of antimicrobial peptide; InterPro: IPR012525 This family consists of diapausin-related antimicrobial peptides. Diapause during periods of environmental adversity is an essential part of the life cycle of many organisms with the molecular basis being different among animals. Diapause-specific peptides provide anti-fungal activity and act as N-type voltage-gated calcium channel blocker [].; GO: 0050832 defense response to fungus, 0005576 extracellular region; PDB: 2E2F_A.
Probab=31.46 E-value=29 Score=20.46 Aligned_cols=17 Identities=41% Similarity=0.798 Sum_probs=14.0
Q ss_pred cCccchhhhhhhhhhcc
Q 045334 42 ACPETKKLRDECIVEHG 58 (80)
Q Consensus 42 aCpetK~~RDeCil~~g 58 (80)
||+-+-..||||---||
T Consensus 9 vC~R~~~Er~eCCrAhG 25 (39)
T PF08036_consen 9 VCSRIVPERDECCRAHG 25 (39)
T ss_dssp STTS-STTTHHHHHHTT
T ss_pred cccCcchhHHHHHHHcC
Confidence 79999999999987776
No 21
>PF03997 VPS28: VPS28 protein; InterPro: IPR007143 The Endosomal Sorting Complex Required for Transport (ESCRT) complexes form the machinery driving protein sorting from endosomes to lysosomes. ESCRT complexes are central to receptor down-regulation, lysosome biogenesis, and budding of HIV. Yeast ESCRT-I consists of three protein subunits, VPS23, VPS28, and VPS37. In humans, ESCRT-I comprises TSG101, VPS28, and one of four potential human VPS37 homologues. The main role of ESCRT-I is to recognise ubiquitinated cargo via the UEV domain of the VPS23/TSG101 subunit. The assembly of the ESCRT-I complex is directed by the C-terminal steadiness box (SB) of VPS23, the N-terminal half of VPS28, and the C-terminal half of VPS37. The structure is primarily composed of three long, parallel helical hairpins, each corresponding to a different subunit. The additional domains and motifs extending beyond the core serve as gripping tools for ESCRT-I critical functions [, ].; PDB: 2J9W_B 2J9U_C 2G3K_A 2F66_E 2F6M_D 2J9V_A 2CAZ_E 2P22_B.
Probab=30.83 E-value=48 Score=24.60 Aligned_cols=18 Identities=22% Similarity=0.420 Sum_probs=15.5
Q ss_pred HHHHHHHHHHHHHHHHhc
Q 045334 59 EEACAKWIEAHRKCLRAE 76 (80)
Q Consensus 59 e~~C~~~Ieahk~Cmr~~ 76 (80)
...|..||.+||..++..
T Consensus 29 t~~c~kLl~Qyk~~~~~~ 46 (188)
T PF03997_consen 29 TTACNKLLNQYKTILKQL 46 (188)
T ss_dssp HHHHHHHHHHHHHHHTST
T ss_pred HHHHHHHHHHHHHHHHHc
Confidence 458999999999999865
No 22
>PF03489 SapB_2: Saposin-like type B, region 2; InterPro: IPR008138 Saposins are small lysosomal proteins that serve as activators of various lysosomal lipid-degrading enzymes []. They probably act by isolating the lipid substrate from the membrane surroundings, thus making it more accessible to the soluble degradative enzymes. All mammalian saposins are synthesized as a single precursor molecule (prosaposin) which contains four Saposin-B domains, yielding the active saposins after proteolytic cleavage, and two Saposin-A domains that are removed in the activation reaction. The Saposin-B domains also occur in other proteins, many of them active in the lysis of membranes [, ].; PDB: 3BQQ_A 2RB3_B 2R0R_A 3BQP_A 2R1Q_A 1NKL_A 1L9L_A 1QDM_C 3RFI_A 4DDJ_A ....
Probab=29.77 E-value=51 Score=17.17 Aligned_cols=11 Identities=9% Similarity=0.625 Sum_probs=9.1
Q ss_pred HHHHHHHHHHH
Q 045334 60 EACAKWIEAHR 70 (80)
Q Consensus 60 ~~C~~~Ieahk 70 (80)
+.|+.+|+.|-
T Consensus 2 ~~C~~~V~~y~ 12 (35)
T PF03489_consen 2 DECKNFVDQYG 12 (35)
T ss_dssp HHHHHHHHHHH
T ss_pred cHHHHHHHHHH
Confidence 57999999984
No 23
>PF01841 Transglut_core: Transglutaminase-like superfamily; InterPro: IPR002931 This domain is found in many proteins known to have transglutaminase activity, i.e. which cross-link proteins through an acyl-transfer reaction between the gamma-carboxamide group of peptide-bound glutamine and the epsilon-amino group of peptide-bound lysine, resulting in a epsilon-(gamma-glutamyl)lysine isopeptide bond. Tranglutaminases have been found in a diverse range of species, from bacteria through to mammals. The enzymes require calcium binding and their activity leads to post-translational modification of proteins through acyl-transfer reactions, involving peptidyl glutamine residues as acyl donors and a variety of primary amines as acyl acceptors, with the generation of proteinase resistant isopeptide bonds []. Sequence conservation in this superfamily primarily involves three motifs that centre around conserved cysteine, histidine, and aspartate residues that form the catalytic triad in the structurally characterised transglutaminase, the human blood clotting factor XIIIa' []. On the basis of the experimentally demonstrated activity of the Methanobacterium phage psiM2 pseudomurein endoisopeptidase [], it is proposed that many, if not all, microbial homologs of the transglutaminases are proteases and that the eukaryotic transglutaminases have evolved from an ancestral protease []. A subunit of plasma Factor XIII revealed that each Factor XIIIA subunit is composed of four domains (termed N-terminal beta-sandwich, core domain (containing the catalytic and the regulatory sites), and C-terminal beta-barrels 1 and 2) and that two monomers assemble into the native dimer through the surfaces in domains 1 and 2, in opposite orientation. This organisation in four domains is highly conserved during evolution among transglutaminase isoforms [].; PDB: 2F4M_A 2F4O_A 1GGY_B 1FIE_B 1GGU_B 1GGT_B 1F13_A 1QRK_B 1EVU_A 1EX0_B ....
Probab=29.24 E-value=27 Score=21.24 Aligned_cols=25 Identities=24% Similarity=0.444 Sum_probs=19.7
Q ss_pred hhccHHHHHHHHHHHHHHHHhcCCC
Q 045334 55 VEHGEEACAKWIEAHRKCLRAEGFN 79 (80)
Q Consensus 55 l~~ge~~C~~~Ieahk~Cmr~~GF~ 79 (80)
|+.+...|.++=..+...||..|+.
T Consensus 47 l~~~~G~C~~~a~l~~allr~~Gip 71 (113)
T PF01841_consen 47 LRSGRGDCEDYASLFVALLRALGIP 71 (113)
T ss_dssp HHCEEESHHHHHHHHHHHHHHHT--
T ss_pred HHcCCCccHHHHHHHHHHHhhCCCc
Confidence 3455568999999999999999985
No 24
>smart00460 TGc Transglutaminase/protease-like homologues. Transglutaminases are enzymes that establish covalent links between proteins. A subset of transglutaminase homologues appear to catalyse the reverse reaction, the hydrolysis of peptide bonds. Proteins with this domain are both extracellular and intracellular, and it is likely that the eukaryotic intracellular proteins are involved in signalling events.
Probab=29.05 E-value=44 Score=18.71 Aligned_cols=25 Identities=16% Similarity=0.311 Sum_probs=21.3
Q ss_pred hhccHHHHHHHHHHHHHHHHhcCCC
Q 045334 55 VEHGEEACAKWIEAHRKCLRAEGFN 79 (80)
Q Consensus 55 l~~ge~~C~~~Ieahk~Cmr~~GF~ 79 (80)
|.++...|.++...+..=||..|+.
T Consensus 2 ~~~~~G~C~~~a~l~~~llr~~GIp 26 (68)
T smart00460 2 LKTKYGTCGEFAALFVALLRSLGIP 26 (68)
T ss_pred CcccceeeHHHHHHHHHHHHHCCCC
Confidence 4566778999999999999999975
No 25
>cd03715 RT_ZFREV_like RT_ZFREV_like: A subfamily of reverse transcriptases (RTs) found in sequences similar to the intact endogenous retrovirus ZFERV from zebrafish and to Moloney murine leukemia virus RT. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs. Phylogenetic analysis suggests that ZFERV belongs to a distinct group of retroviruses.
Probab=24.59 E-value=80 Score=22.07 Aligned_cols=30 Identities=30% Similarity=0.465 Sum_probs=23.2
Q ss_pred hhhhhhc-cHHHHHHHHHHHHHHHHhcCCCC
Q 045334 51 DECIVEH-GEEACAKWIEAHRKCLRAEGFNV 80 (80)
Q Consensus 51 DeCil~~-ge~~C~~~Ieahk~Cmr~~GF~v 80 (80)
|+.++.. ..++|.+.++.-...|+.+||.+
T Consensus 161 DDili~s~~~~e~~~~l~~v~~~l~~~gl~l 191 (210)
T cd03715 161 DDLLLAADSEEDCLKGTDALLTHLGELGYKV 191 (210)
T ss_pred CcEEEecCCHHHHHHHHHHHHHHHHHCCCCc
Confidence 4444433 46789999999999999999975
No 26
>PF08676 MutL_C: MutL C terminal dimerisation domain; InterPro: IPR014790 MutL and MutS are key components of the DNA repair machinery that corrects replication errors []. MutS recognises mispaired or unpaired bases in a DNA duplex and in the presence of ATP, recruits MutL to form a DNA signalling complex for repair. The N-terminal region of MutL contains the ATPase domain and the C-terminal is involved in dimerisation []. ; GO: 0005524 ATP binding, 0006298 mismatch repair; PDB: 3NCV_B 1X9Z_B 3GAB_C 3KDK_A 3KDG_A.
Probab=24.50 E-value=56 Score=21.40 Aligned_cols=18 Identities=28% Similarity=0.560 Sum_probs=14.8
Q ss_pred HHHHHHHHHHHHhcCCCC
Q 045334 63 AKWIEAHRKCLRAEGFNV 80 (80)
Q Consensus 63 ~~~Ieahk~Cmr~~GF~v 80 (80)
.++++.|+.=|+..||++
T Consensus 65 ~~~l~~~~~~L~~~Gf~~ 82 (144)
T PF08676_consen 65 AELLEENKEELEKLGFEI 82 (144)
T ss_dssp HHHHHHHHHHHHHTT-EE
T ss_pred HHHHHHHHHHHHhCCeEE
Confidence 478999999999999974
No 27
>PF09034 TRADD_N: TRADD, N-terminal domain; InterPro: IPR009095 TRADD is a signalling adaptor protein involved in tumour necrosis factor-receptor I (TNFR1)-associated apoptosis and cell survival. The decision between apoptosis and cell survival involves the interplay between two sequential signalling complexes. The plasma membrane-bound complex I is comprised of TNFR1, TRADD, the kinase RIP1, and TRAF2, which together mediate the activation of NF-kappaB. Subsequently, complex II is formed in the cytoplasm, where TRADD and RIP1 associate with FADD and caspase-8. If NF-kappaB is activated by complex I, then complex II will associate with the caspase-8 inhibitor FLIP(L) and the cell survives, while the failure to activate NF-kappaB leads to apoptosis []. The TRADD C-terminal death domain is responsible for its association with TNFR1, and with the death-domain proteins FADD and RIP1, which promote apoptosis. The TRADD N-terminal domain binds TRAF2 and promotes TRAF2 recruitment to TNFR1, thereby mediating the activation of NK-kappaB and JNK/AP1, which promote cell survival []. The N-terminal TRADD domain is composed of an alpha-beta sandwich, where the beta strands form an antiparallel beta-sheet.; GO: 0004871 signal transducer activity, 0006917 induction of apoptosis, 0043123 positive regulation of I-kappaB kinase/NF-kappaB cascade, 0005737 cytoplasm; PDB: 1F3V_A 1F2H_A.
Probab=24.13 E-value=64 Score=22.74 Aligned_cols=17 Identities=24% Similarity=0.567 Sum_probs=15.2
Q ss_pred hccHHHHHHHHHHHHHH
Q 045334 56 EHGEEACAKWIEAHRKC 72 (80)
Q Consensus 56 ~~ge~~C~~~Ieahk~C 72 (80)
|.|.+.|..|+++|+.+
T Consensus 27 F~~~~~C~rFL~sYreG 43 (111)
T PF09034_consen 27 FCGREPCRRFLRSYREG 43 (111)
T ss_dssp EESHHHHHHHHHHHHCC
T ss_pred EcCchhHHHHHHHHhcc
Confidence 77999999999999864
No 28
>PF10203 Pet191_N: Cytochrome c oxidase assembly protein PET191; InterPro: IPR018793 This entry represents a family of conserved proteins found from nematodes to humans. Cytochrome c oxidase assembly protein Pet191 carries six highly conserved cysteine residues. Pet191 is required for the assembly of active cytochrome c oxidase but does not form part of the final assembled complex [].
Probab=23.51 E-value=79 Score=19.85 Aligned_cols=25 Identities=24% Similarity=0.590 Sum_probs=18.7
Q ss_pred hhhhhcc---HHHHHHHHHHHHHHHHhc
Q 045334 52 ECIVEHG---EEACAKWIEAHRKCLRAE 76 (80)
Q Consensus 52 eCil~~g---e~~C~~~Ieahk~Cmr~~ 76 (80)
+|+-.+. .++|..|..+|-+|=|+.
T Consensus 31 ~Cl~~~~~~~p~eC~~lr~~f~eCKrg~ 58 (68)
T PF10203_consen 31 DCLKDPSDELPEECQQLRKAFFECKRGM 58 (68)
T ss_pred HHHcCCCCcCCHHHHHHHHHHHHHhccc
Confidence 4555442 468999999999998763
No 29
>PF11326 DUF3128: Protein of unknown function (DUF3128); InterPro: IPR021475 This eukaryotic family of proteins has no known function.
Probab=22.33 E-value=60 Score=20.50 Aligned_cols=22 Identities=36% Similarity=0.824 Sum_probs=18.2
Q ss_pred ccH-HHHHHHHHHHHHHHHhcCC
Q 045334 57 HGE-EACAKWIEAHRKCLRAEGF 78 (80)
Q Consensus 57 ~ge-~~C~~~Ieahk~Cmr~~GF 78 (80)
+|+ ..|....+.|+.||+-..+
T Consensus 30 yG~~~~C~~~~~df~~C~~~k~~ 52 (84)
T PF11326_consen 30 YGEFDDCSQWWEDFKFCLRWKSK 52 (84)
T ss_pred cCCCccHHHHHHHHHHHHHhccC
Confidence 466 5899999999999986654
No 30
>PF03790 KNOX1: KNOX1 domain ; InterPro: IPR005540 The MEINOX region is comprised of two domains, KNOX1 and KNOX2. KNOX1 plays a role in suppressing target gene expression. KNOX2, essential for function, is thought to be necessary for homo-dimerization [].; GO: 0003677 DNA binding, 0005634 nucleus
Probab=21.48 E-value=77 Score=18.93 Aligned_cols=13 Identities=15% Similarity=0.399 Sum_probs=11.0
Q ss_pred HHHHHHHHHHHHH
Q 045334 62 CAKWIEAHRKCLR 74 (80)
Q Consensus 62 C~~~Ieahk~Cmr 74 (80)
.-.|++||-.|+|
T Consensus 13 Y~~Ll~Ayi~C~K 25 (45)
T PF03790_consen 13 YPRLLAAYIDCQK 25 (45)
T ss_pred cHHHHHHHHHHHh
Confidence 4579999999987
No 31
>KOG4148 consensus Uncharacterized conserved protein [Function unknown]
Probab=20.32 E-value=80 Score=22.07 Aligned_cols=18 Identities=28% Similarity=0.680 Sum_probs=14.7
Q ss_pred HHHHHHHHHHHHHHHHhc
Q 045334 59 EEACAKWIEAHRKCLRAE 76 (80)
Q Consensus 59 e~~C~~~Ieahk~Cmr~~ 76 (80)
.+.|.+||.|-+.|-+..
T Consensus 10 ~~~C~dlInaL~eCH~~~ 27 (106)
T KOG4148|consen 10 HEECNDLINALKECHKNH 27 (106)
T ss_pred HHHHHHHHHHHHHHHhhh
Confidence 468999999999997544
Done!