Query 035162
Match_columns 71
No_of_seqs 106 out of 137
Neff 4.6
Searched_HMMs 46136
Date Fri Mar 29 09:43:06 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/035162.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/035162hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF10203 Pet191_N: Cytochrome 100.0 6.7E-41 1.4E-45 204.8 6.4 68 1-68 1-68 (68)
2 KOG4114 Cytochrome c oxidase a 100.0 1.9E-37 4.2E-42 191.8 3.5 71 1-71 1-72 (73)
3 PF06747 CHCH: CHCH domain; I 85.7 0.46 9.9E-06 24.3 1.1 28 28-56 7-34 (35)
4 KOG3477 Putative cytochrome c 66.7 2.4 5.3E-05 27.6 0.6 27 29-56 37-63 (97)
5 KOG4618 Uncharacterized conser 52.9 6.4 0.00014 24.7 0.7 37 19-57 22-58 (74)
6 PF08991 DUF1903: Domain of un 37.2 24 0.00052 21.3 1.4 42 3-62 2-43 (67)
7 cd08817 CARD_RIG-I_2 Caspase a 36.8 21 0.00046 23.0 1.2 12 9-20 53-64 (88)
8 PF08583 Cmc1: Cytochrome c ox 32.1 31 0.00068 19.5 1.4 31 4-35 12-48 (69)
9 PF10200 Ndufs5: NADH:ubiquino 31.8 28 0.0006 22.6 1.2 19 39-57 51-69 (96)
10 PF11857 DUF3377: Domain of un 27.1 21 0.00046 22.3 0.0 10 52-61 64-73 (74)
11 PF13656 RNA_pol_L_2: RNA poly 23.8 15 0.00032 22.3 -1.1 24 28-51 54-77 (77)
12 PLN03079 Uncharacterized prote 23.4 56 0.0012 21.1 1.5 19 37-55 11-29 (91)
13 KOG4090 Uncharacterized conser 23.1 35 0.00076 24.1 0.5 37 18-56 115-151 (157)
14 PF05254 UPF0203: Uncharacteri 20.5 70 0.0015 19.2 1.4 16 39-54 4-19 (68)
15 COG2938 Uncharacterized conser 20.1 41 0.00089 21.7 0.3 16 46-61 14-29 (94)
No 1
>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=100.00 E-value=6.7e-41 Score=204.77 Aligned_cols=68 Identities=56% Similarity=1.045 Sum_probs=67.3
Q ss_pred CchhHHHHHHHHHHHHhcCccccccCCChhHHhcCCCCCChhhHHHHHHHHHhcccCCCCCCccccCC
Q 035162 1 MSKSCKGLAMELVKCLSESDCVKVEKRSFRECAGEKSPCIPSECVGLRETYFNCKRGQVDMRARIRGN 68 (71)
Q Consensus 1 M~~sC~~~r~~L~~Cl~~SdCv~~~~~t~~eCL~~~~~~lp~eC~~lr~~f~eCKR~~lD~r~RfRGn 68 (71)
|++||+++++||++||++||||+++++||+|||++++++||+||++|+++||||||||||||+|||||
T Consensus 1 m~~sC~~~~~~L~~Cl~~SdCv~~~~~t~~~Cl~~~~~~~p~eC~~lr~~f~eCKrg~lDmr~RfRGn 68 (68)
T PF10203_consen 1 MSKSCKGIREALAECLQESDCVKKEKRTPKDCLKDPSDELPEECQQLRKAFFECKRGMLDMRKRFRGN 68 (68)
T ss_pred CCchHHHHHHHHHHHHhhChhhccCCCCHHHHHcCCCCcCCHHHHHHHHHHHHHhcccccccccccCc
Confidence 99999999999999999999999999999999999999999999999999999999999999999998
No 2
>KOG4114 consensus Cytochrome c oxidase assembly protein PET191 [Posttranslational modification, protein turnover, chaperones]
Probab=100.00 E-value=1.9e-37 Score=191.76 Aligned_cols=71 Identities=46% Similarity=0.840 Sum_probs=68.3
Q ss_pred CchhHHHHHHHHHHHHhcCccccccCCChhHHhcCC-CCCChhhHHHHHHHHHhcccCCCCCCccccCCCCC
Q 035162 1 MSKSCKGLAMELVKCLSESDCVKVEKRSFRECAGEK-SPCIPSECVGLRETYFNCKRGQVDMRARIRGNKGY 71 (71)
Q Consensus 1 M~~sC~~~r~~L~~Cl~~SdCv~~~~~t~~eCL~~~-~~~lp~eC~~lr~~f~eCKR~~lD~r~RfRGnkgy 71 (71)
|+.||+++|+||+.||++||||+++++||+|||.+. ..+||+||++++++|.+|||||||||+||||++||
T Consensus 1 ~g~sC~~~r~alk~Cl~~S~Cv~v~~ks~reCldn~~~~~vPeeC~al~~af~dCKRslvDmrkRfrgrkg~ 72 (73)
T KOG4114|consen 1 MGASCKDQRKALKICLLRSDCVMVERKSPRECLDNPELKDVPEECIALMKAFLDCKRSLVDMRKRFRGRKGT 72 (73)
T ss_pred CcccHHHHHHHHHHHHhcCcceeeecCCHHHHhcCCccccCcHHHHHHHHHHHHHHHHHHHHHHHHccccCC
Confidence 789999999999999999999999999999999875 56799999999999999999999999999999997
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=85.65 E-value=0.46 Score=24.33 Aligned_cols=28 Identities=21% Similarity=0.382 Sum_probs=21.2
Q ss_pred ChhHHhcCCCCCChhhHHHHHHHHHhccc
Q 035162 28 SFRECAGEKSPCIPSECVGLRETYFNCKR 56 (71)
Q Consensus 28 t~~eCL~~~~~~lp~eC~~lr~~f~eCKR 56 (71)
.+-+||+++..+ .+.|..+..+|.+|+.
T Consensus 7 ~~~~Cl~~n~~~-~~~C~~~~~~~~~C~~ 34 (35)
T PF06747_consen 7 AYLACLKENNFD-WSKCRKEFKAYKECRM 34 (35)
T ss_dssp HHHHHHHCH-SS-TCCCHHHHHHHHHHHC
T ss_pred HHHHHHHHCCCc-HHhhHHHHHHHHHHhh
Confidence 356788765433 7799999999999975
No 4
>KOG3477 consensus Putative cytochrome c oxidase, subunit COX19 [Energy production and conversion]
Probab=66.71 E-value=2.4 Score=27.65 Aligned_cols=27 Identities=26% Similarity=0.571 Sum_probs=20.7
Q ss_pred hhHHhcCCCCCChhhHHHHHHHHHhccc
Q 035162 29 FRECAGEKSPCIPSECVGLRETYFNCKR 56 (71)
Q Consensus 29 ~~eCL~~~~~~lp~eC~~lr~~f~eCKR 56 (71)
+-.||+.. .+-.+||..|-+.|++|+-
T Consensus 37 Yl~Cl~~k-~e~~~eCR~laK~YlqCRM 63 (97)
T KOG3477|consen 37 YLGCLKSK-AENSEECRLLAKKYLQCRM 63 (97)
T ss_pred HHHHHHHH-HHhHHHHHHHHHHHHHHhh
Confidence 45666643 2557899999999999985
No 5
>KOG4618 consensus Uncharacterized conserved protein [Function unknown]
Probab=52.88 E-value=6.4 Score=24.65 Aligned_cols=37 Identities=27% Similarity=0.523 Sum_probs=26.8
Q ss_pred CccccccCCChhHHhcCCCCCChhhHHHHHHHHHhcccC
Q 035162 19 SDCVKVEKRSFRECAGEKSPCIPSECVGLRETYFNCKRG 57 (71)
Q Consensus 19 SdCv~~~~~t~~eCL~~~~~~lp~eC~~lr~~f~eCKR~ 57 (71)
++|.....-|+ .||.+. +.--+.|+.....|=+||+.
T Consensus 22 nPCl~es~aSf-kCLeen-nyDRsKCq~yFd~YkeCKkf 58 (74)
T KOG4618|consen 22 NPCLLESSASF-KCLEEN-NYDRSKCQDYFDVYKECKKF 58 (74)
T ss_pred ChHHHHHHHHH-HHHHhc-CccHHHHHHHHHHHHHHHHH
Confidence 45555554554 599764 35568999999999999974
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=37.17 E-value=24 Score=21.29 Aligned_cols=42 Identities=21% Similarity=0.482 Sum_probs=26.2
Q ss_pred hhHHHHHHHHHHHHhcCccccccCCChhHHhcCCCCCChhhHHHHHHHHHhcccCCCCCC
Q 035162 3 KSCKGLAMELVKCLSESDCVKVEKRSFRECAGEKSPCIPSECVGLRETYFNCKRGQVDMR 62 (71)
Q Consensus 3 ~sC~~~r~~L~~Cl~~SdCv~~~~~t~~eCL~~~~~~lp~eC~~lr~~f~eCKR~~lD~r 62 (71)
.+|+....++-.||.+ + .--++-|.....+|.+|.....+-+
T Consensus 2 ~PC~~~Ac~iq~CL~~-----------------N-~Yd~~kC~~~i~~l~~Cck~~y~~~ 43 (67)
T PF08991_consen 2 DPCQKEACAIQKCLQR-----------------N-NYDESKCQDYIDALYECCKKFYEQR 43 (67)
T ss_dssp -TTHHHHHHHHHHHHH-----------------T-TT-CCCTHHHHHHHHHHHTTS----
T ss_pred cchHHHHHHHHHHHHH-----------------c-CCCHHHHHHHHHHHHHHHHHHHHcc
Confidence 3566666666666552 1 2456789999999999998776554
No 7
>cd08817 CARD_RIG-I_2 Caspase activation and recruitment domain found in RIG-I, second repeat. Caspase activation and recruitment domain (CARD) found in RIG-I (Retinoic acid Inducible Gene I, also known as Ddx58), second repeat. RIG-I is a cytoplasmic RNA helicase that plays an important role in host antiviral response by sensing incoming viral RNA. RIG-I contains two N-terminal CARD domains and a C-terminal RNA helicase. Upon activation, the signal is transferred to downstream pathways via the adaptor molecule IPS-1 (MAVS, VISA, CARDIF), leading to the induction of type I interferons. Although very similar in sequence, RIG-I recognizes different sets of viruses compared to MDA5, a related RNA helicase. RIG-I associates with IPS-1 through a CARD-CARD interaction. In general, CARDs are death domains (DDs) found associated with caspases. They are known to be important in the signaling pathways for apoptosis, inflammation, and host-defense mechanisms. DDs are protein-protein interaction do
Probab=36.81 E-value=21 Score=23.02 Aligned_cols=12 Identities=58% Similarity=0.858 Sum_probs=10.4
Q ss_pred HHHHHHHHhcCc
Q 035162 9 AMELVKCLSESD 20 (71)
Q Consensus 9 r~~L~~Cl~~Sd 20 (71)
.+.|++||++||
T Consensus 53 aeKl~ecLlRSD 64 (88)
T cd08817 53 AEKLVECLLRSD 64 (88)
T ss_pred HHHHHHHHHHhc
Confidence 467999999998
No 8
>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=32.13 E-value=31 Score=19.49 Aligned_cols=31 Identities=23% Similarity=0.607 Sum_probs=18.4
Q ss_pred hHHHHHHHHHHHHhc------CccccccCCChhHHhcC
Q 035162 4 SCKGLAMELVKCLSE------SDCVKVEKRSFRECAGE 35 (71)
Q Consensus 4 sC~~~r~~L~~Cl~~------SdCv~~~~~t~~eCL~~ 35 (71)
.|..+-++|++|... ..|-.. ..-..+||+.
T Consensus 12 ~C~~~i~~~~~C~~~~~~~~~~~C~~~-~~~m~~Cl~~ 48 (69)
T PF08583_consen 12 KCADEIEAFAECHKDRTFKFVGKCREE-KKAMNECLKE 48 (69)
T ss_pred HhHHHHHHHHHHHhcchHHHHHhhhHH-HHHHHHHHHH
Confidence 566777777777654 555433 3446666654
No 9
>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=31.79 E-value=28 Score=22.55 Aligned_cols=19 Identities=26% Similarity=0.401 Sum_probs=14.6
Q ss_pred CChhhHHHHHHHHHhcccC
Q 035162 39 CIPSECVGLRETYFNCKRG 57 (71)
Q Consensus 39 ~lp~eC~~lr~~f~eCKR~ 57 (71)
.-+.+|......|+||-.+
T Consensus 51 r~kKeC~~e~EDy~EClh~ 69 (96)
T PF10200_consen 51 RGKKECKLELEDYYECLHH 69 (96)
T ss_pred chhhhchhHHhHHHHHHhh
Confidence 3467899999999999553
No 10
>PF11857 DUF3377: Domain of unknown function (DUF3377); InterPro: IPR021805 This domain is functionally uncharacterised and found at the C terminus of peptidases belonging to MEROPS peptidase family M10A, membrane-type matrix metallopeptidases (clan MA). ; GO: 0004222 metalloendopeptidase activity
Probab=27.11 E-value=21 Score=22.28 Aligned_cols=10 Identities=30% Similarity=0.634 Sum_probs=8.0
Q ss_pred HhcccCCCCC
Q 035162 52 FNCKRGQVDM 61 (71)
Q Consensus 52 ~eCKR~~lD~ 61 (71)
.-||||+.||
T Consensus 64 lYckRSlqew 73 (74)
T PF11857_consen 64 LYCKRSLQEW 73 (74)
T ss_pred EEEecchhhc
Confidence 4689999886
No 11
>PF13656 RNA_pol_L_2: RNA polymerase Rpb3/Rpb11 dimerisation domain; PDB: 2Y0S_L 1I3Q_K 4A3D_K 2JA8_K 3GTP_K 1R9T_K 3PO2_K 4A3J_K 3HOX_K 2JA7_K ....
Probab=23.82 E-value=15 Score=22.31 Aligned_cols=24 Identities=13% Similarity=0.160 Sum_probs=19.0
Q ss_pred ChhHHhcCCCCCChhhHHHHHHHH
Q 035162 28 SFRECAGEKSPCIPSECVGLRETY 51 (71)
Q Consensus 28 t~~eCL~~~~~~lp~eC~~lr~~f 51 (71)
+|.+.|++...++-..|..++..|
T Consensus 54 ~p~~~l~~a~~~l~~~~~~l~~~F 77 (77)
T PF13656_consen 54 TPIEALKKALEDLIKICEELKKEF 77 (77)
T ss_dssp -HHHHHHHHHHHHHHHHHHHHHHH
T ss_pred CHHHHHHHHHHHHHHHHHHHHhhC
Confidence 899999876667888888888776
No 12
>PLN03079 Uncharacterized protein At4g33100; Provisional
Probab=23.36 E-value=56 Score=21.14 Aligned_cols=19 Identities=42% Similarity=0.721 Sum_probs=15.7
Q ss_pred CCCChhhHHHHHHHHHhcc
Q 035162 37 SPCIPSECVGLRETYFNCK 55 (71)
Q Consensus 37 ~~~lp~eC~~lr~~f~eCK 55 (71)
..++.++|..|+..|-.|=
T Consensus 11 ~~~~g~eCtelK~~YD~CF 29 (91)
T PLN03079 11 SRSSTSPCAELRTAYHNCF 29 (91)
T ss_pred cCCCCcccHHHHHHHHHHH
Confidence 4578889999999998883
No 13
>KOG4090 consensus Uncharacterized conserved protein [Function unknown]
Probab=23.10 E-value=35 Score=24.10 Aligned_cols=37 Identities=32% Similarity=0.660 Sum_probs=26.2
Q ss_pred cCccccccCCChhHHhcCCCCCChhhHHHHHHHHHhccc
Q 035162 18 ESDCVKVEKRSFRECAGEKSPCIPSECVGLRETYFNCKR 56 (71)
Q Consensus 18 ~SdCv~~~~~t~~eCL~~~~~~lp~eC~~lr~~f~eCKR 56 (71)
...|.- |-+-|.||+.+...++ +.|..+...+-+||.
T Consensus 115 ~~~C~~-e~kqF~dCa~~~~~d~-slC~~f~e~Lk~Ck~ 151 (157)
T KOG4090|consen 115 QQPCFI-EIKQFLDCAQNQGSDI-SLCEGYNEMLKQCKK 151 (157)
T ss_pred cCchHH-HHHHHHHHHHhcCcch-HHHHHHHHHHHHHHH
Confidence 445643 3466899998764444 579999999999975
No 14
>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=20.52 E-value=70 Score=19.23 Aligned_cols=16 Identities=38% Similarity=0.912 Sum_probs=12.3
Q ss_pred CChhhHHHHHHHHHhc
Q 035162 39 CIPSECVGLRETYFNC 54 (71)
Q Consensus 39 ~lp~eC~~lr~~f~eC 54 (71)
++.++|..|+..|=.|
T Consensus 4 S~~~eC~~lK~~YD~C 19 (68)
T PF05254_consen 4 SLAPECTELKEKYDQC 19 (68)
T ss_pred chhhHHHHHHHHHHHH
Confidence 5677888888888777
No 15
>COG2938 Uncharacterized conserved protein [Function unknown]
Probab=20.06 E-value=41 Score=21.67 Aligned_cols=16 Identities=13% Similarity=0.295 Sum_probs=12.9
Q ss_pred HHHHHHHhcccCCCCC
Q 035162 46 GLRETYFNCKRGQVDM 61 (71)
Q Consensus 46 ~lr~~f~eCKR~~lD~ 61 (71)
.+++-++.|+|||+.|
T Consensus 14 ~~~RL~~rsrRGmrEl 29 (94)
T COG2938 14 RKARLRWRSRRGMREL 29 (94)
T ss_pred HHHHHHHHHHhccHHH
Confidence 4678899999999753
Done!