Query 034876
Match_columns 80
No_of_seqs 110 out of 132
Neff 4.1
Searched_HMMs 46136
Date Fri Mar 29 07:17:06 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/034876.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/034876hhsearch_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 2E-36 4.4E-41 190.6 5.7 65 1-65 1-65 (68)
2 KOG4114 Cytochrome c oxidase a 100.0 8.9E-32 1.9E-36 172.2 3.9 66 1-66 1-67 (73)
3 PF06747 CHCH: CHCH domain; I 82.3 0.55 1.2E-05 24.8 0.5 27 29-56 8-34 (35)
4 KOG3477 Putative cytochrome c 57.1 3.8 8.2E-05 27.8 0.1 27 29-56 37-63 (97)
5 PF08991 DUF1903: Domain of un 39.1 44 0.00095 20.8 2.9 42 3-62 2-43 (67)
6 PF08583 Cmc1: Cytochrome c ox 29.5 34 0.00074 19.9 1.2 14 4-17 12-25 (69)
7 cd08817 CARD_RIG-I_2 Caspase a 29.4 35 0.00075 22.8 1.4 12 9-20 53-64 (88)
8 PF11857 DUF3377: Domain of un 23.0 28 0.00061 22.5 0.0 11 51-61 63-73 (74)
9 PF10200 Ndufs5: NADH:ubiquino 21.8 46 0.001 22.3 0.9 18 40-57 52-69 (96)
10 COG2938 Uncharacterized conser 18.6 44 0.00096 22.3 0.3 17 46-62 14-30 (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=2e-36 Score=190.57 Aligned_cols=65 Identities=48% Similarity=0.836 Sum_probs=64.4
Q ss_pred CcchHHHHHHHHHHHHhcCccccccCCChhHHhCCCCCCCchhhHHHHhHHHhcccCcccCcchH
Q 034876 1 MSKSCKGLAMELVKCLSESDCVKVEKRSFRECAGEKSPCIPSECVGLRETYFNCKRGQACSLFSS 65 (80)
Q Consensus 1 M~~SCk~lr~~L~~CL~~SdCv~~~~~tpkeCL~~~~~~lP~eC~~Lr~affeCKRgmlDmr~rf 65 (80)
|++||+++++||++||++||||+++++||+|||+++++++|+||++|+++||||||||||||+||
T Consensus 1 m~~sC~~~~~~L~~Cl~~SdCv~~~~~t~~~Cl~~~~~~~p~eC~~lr~~f~eCKrg~lDmr~Rf 65 (68)
T PF10203_consen 1 MSKSCKGIREALAECLQESDCVKKEKRTPKDCLKDPSDELPEECQQLRKAFFECKRGMLDMRKRF 65 (68)
T ss_pred CCchHHHHHHHHHHHHhhChhhccCCCCHHHHHcCCCCcCCHHHHHHHHHHHHHhcccccccccc
Confidence 99999999999999999999999999999999999999999999999999999999999999998
No 2
>KOG4114 consensus Cytochrome c oxidase assembly protein PET191 [Posttranslational modification, protein turnover, chaperones]
Probab=99.97 E-value=8.9e-32 Score=172.21 Aligned_cols=66 Identities=36% Similarity=0.611 Sum_probs=63.4
Q ss_pred CcchHHHHHHHHHHHHhcCccccccCCChhHHhCCC-CCCCchhhHHHHhHHHhcccCcccCcchHH
Q 034876 1 MSKSCKGLAMELVKCLSESDCVKVEKRSFRECAGEK-SPCIPSECVGLRETYFNCKRGQACSLFSSF 66 (80)
Q Consensus 1 M~~SCk~lr~~L~~CL~~SdCv~~~~~tpkeCL~~~-~~~lP~eC~~Lr~affeCKRgmlDmr~rf~ 66 (80)
|+.||+++|+||+.||++||||+++++||+|||.++ ..+||+||++++++|.+|||||||||+||-
T Consensus 1 ~g~sC~~~r~alk~Cl~~S~Cv~v~~ks~reCldn~~~~~vPeeC~al~~af~dCKRslvDmrkRfr 67 (73)
T KOG4114|consen 1 MGASCKDQRKALKICLLRSDCVMVERKSPRECLDNPELKDVPEECIALMKAFLDCKRSLVDMRKRFR 67 (73)
T ss_pred CcccHHHHHHHHHHHHhcCcceeeecCCHHHHhcCCccccCcHHHHHHHHHHHHHHHHHHHHHHHHc
Confidence 789999999999999999999999999999999997 567999999999999999999999999993
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=82.34 E-value=0.55 Score=24.79 Aligned_cols=27 Identities=22% Similarity=0.383 Sum_probs=20.3
Q ss_pred hhHHhCCCCCCCchhhHHHHhHHHhccc
Q 034876 29 FRECAGEKSPCIPSECVGLRETYFNCKR 56 (80)
Q Consensus 29 pkeCL~~~~~~lP~eC~~Lr~affeCKR 56 (80)
+-+|++++..+ .+.|+.+.++|.+|+.
T Consensus 8 ~~~Cl~~n~~~-~~~C~~~~~~~~~C~~ 34 (35)
T PF06747_consen 8 YLACLKENNFD-WSKCRKEFKAYKECRM 34 (35)
T ss_dssp HHHHHHCH-SS-TCCCHHHHHHHHHHHC
T ss_pred HHHHHHHCCCc-HHhhHHHHHHHHHHhh
Confidence 45677765433 7799999999999975
No 4
>KOG3477 consensus Putative cytochrome c oxidase, subunit COX19 [Energy production and conversion]
Probab=57.06 E-value=3.8 Score=27.75 Aligned_cols=27 Identities=26% Similarity=0.571 Sum_probs=19.5
Q ss_pred hhHHhCCCCCCCchhhHHHHhHHHhccc
Q 034876 29 FRECAGEKSPCIPSECVGLRETYFNCKR 56 (80)
Q Consensus 29 pkeCL~~~~~~lP~eC~~Lr~affeCKR 56 (80)
+-.|++.. .+-.+||..|-+.|++||-
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 33455543 2446799999999999984
No 5
>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=39.13 E-value=44 Score=20.83 Aligned_cols=42 Identities=19% Similarity=0.384 Sum_probs=27.9
Q ss_pred chHHHHHHHHHHHHhcCccccccCCChhHHhCCCCCCCchhhHHHHhHHHhcccCcccCc
Q 034876 3 KSCKGLAMELVKCLSESDCVKVEKRSFRECAGEKSPCIPSECVGLRETYFNCKRGQACSL 62 (80)
Q Consensus 3 ~SCk~lr~~L~~CL~~SdCv~~~~~tpkeCL~~~~~~lP~eC~~Lr~affeCKRgmlDmr 62 (80)
.+|+....++-.||.+. .--++.|+....+|.+|+....+-+
T Consensus 2 ~PC~~~Ac~iq~CL~~N------------------~Yd~~kC~~~i~~l~~Cck~~y~~~ 43 (67)
T PF08991_consen 2 DPCQKEACAIQKCLQRN------------------NYDESKCQDYIDALYECCKKFYEQR 43 (67)
T ss_dssp -TTHHHHHHHHHHHHHT------------------TT-CCCTHHHHHHHHHHHTTS----
T ss_pred cchHHHHHHHHHHHHHc------------------CCCHHHHHHHHHHHHHHHHHHHHcc
Confidence 46777777777777631 1346689999999999998886654
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=29.52 E-value=34 Score=19.94 Aligned_cols=14 Identities=14% Similarity=0.446 Sum_probs=7.8
Q ss_pred hHHHHHHHHHHHHh
Q 034876 4 SCKGLAMELVKCLS 17 (80)
Q Consensus 4 SCk~lr~~L~~CL~ 17 (80)
.|.++-++|++|..
T Consensus 12 ~C~~~i~~~~~C~~ 25 (69)
T PF08583_consen 12 KCADEIEAFAECHK 25 (69)
T ss_pred HhHHHHHHHHHHHh
Confidence 45555555555554
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=29.42 E-value=35 Score=22.82 Aligned_cols=12 Identities=58% Similarity=0.858 Sum_probs=10.4
Q ss_pred HHHHHHHHhcCc
Q 034876 9 AMELVKCLSESD 20 (80)
Q Consensus 9 r~~L~~CL~~Sd 20 (80)
.+.|++||++||
T Consensus 53 aeKl~ecLlRSD 64 (88)
T cd08817 53 AEKLVECLLRSD 64 (88)
T ss_pred HHHHHHHHHHhc
Confidence 367999999998
No 8
>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=22.98 E-value=28 Score=22.52 Aligned_cols=11 Identities=27% Similarity=0.374 Sum_probs=8.6
Q ss_pred HHhcccCcccC
Q 034876 51 YFNCKRGQACS 61 (80)
Q Consensus 51 ffeCKRgmlDm 61 (80)
..-||||+.|+
T Consensus 63 llYckRSlqew 73 (74)
T PF11857_consen 63 LLYCKRSLQEW 73 (74)
T ss_pred EEEEecchhhc
Confidence 34699999886
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=21.82 E-value=46 Score=22.27 Aligned_cols=18 Identities=28% Similarity=0.464 Sum_probs=14.4
Q ss_pred CchhhHHHHhHHHhcccC
Q 034876 40 IPSECVGLRETYFNCKRG 57 (80)
Q Consensus 40 lP~eC~~Lr~affeCKRg 57 (80)
-+.+|......|.||-.+
T Consensus 52 ~kKeC~~e~EDy~EClh~ 69 (96)
T PF10200_consen 52 GKKECKLELEDYYECLHH 69 (96)
T ss_pred hhhhchhHHhHHHHHHhh
Confidence 356899999999999654
No 10
>COG2938 Uncharacterized conserved protein [Function unknown]
Probab=18.61 E-value=44 Score=22.26 Aligned_cols=17 Identities=12% Similarity=0.020 Sum_probs=14.0
Q ss_pred HHHhHHHhcccCcccCc
Q 034876 46 GLRETYFNCKRGQACSL 62 (80)
Q Consensus 46 ~Lr~affeCKRgmlDmr 62 (80)
.+++-++.|+|||+-|=
T Consensus 14 ~~~RL~~rsrRGmrElD 30 (94)
T COG2938 14 RKARLRWRSRRGMRELD 30 (94)
T ss_pred HHHHHHHHHHhccHHHH
Confidence 56788999999998763
Done!