Query 033442
Match_columns 119
No_of_seqs 134 out of 214
Neff 3.7
Searched_HMMs 46136
Date Fri Mar 29 13:55:54 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/033442.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/033442hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PLN02294 cytochrome c oxidase 100.0 3.9E-43 8.4E-48 272.4 9.6 116 1-116 1-123 (174)
2 cd00924 Cyt_c_Oxidase_Vb Cytoc 100.0 8.7E-32 1.9E-36 192.0 5.8 65 55-119 2-66 (97)
3 PF01215 COX5B: Cytochrome c o 100.0 3.7E-32 8E-37 204.0 3.3 67 53-119 32-98 (136)
4 KOG3352 Cytochrome c oxidase, 100.0 9.6E-31 2.1E-35 199.9 5.9 67 53-119 54-120 (153)
5 PTZ00043 cytochrome c oxidase 99.6 1.1E-15 2.5E-20 124.7 4.4 63 57-119 103-166 (268)
6 PLN00128 Succinate dehydrogena 78.6 1.6 3.5E-05 39.4 2.5 18 1-18 1-18 (635)
7 COG3542 Uncharacterized conser 22.1 49 0.0011 26.2 1.2 26 92-118 106-131 (162)
8 PF07710 P53_tetramer: P53 tet 19.9 78 0.0017 19.8 1.6 15 65-79 14-28 (42)
9 PF00278 Orn_DAP_Arg_deC: Pyri 15.0 1.1E+02 0.0023 20.6 1.5 14 106-119 58-71 (116)
10 PF09680 Tiny_TM_bacill: Prote 14.4 41 0.00089 19.0 -0.6 6 110-115 18-23 (24)
No 1
>PLN02294 cytochrome c oxidase subunit Vb
Probab=100.00 E-value=3.9e-43 Score=272.38 Aligned_cols=116 Identities=64% Similarity=0.988 Sum_probs=97.8
Q ss_pred ChhhHhhhhhHHHHHHhhhccCCCCCC-CCc----ccc-cccccccccccccccCCCC-CCccccCCCCCccccchhHHH
Q 033442 1 MWRRICSSQLKAQALALAQYSCRSAPV-NPS----IAS-RSLISRPLFASRHFSADSG-TSVKKRVEDVNPVATGHEREE 73 (119)
Q Consensus 1 mwrr~~~~~l~~~~~~~~~~~~~~~~~-~~~----~~~-~~~~~~~~~~s~~~~~~~~-~~~~g~vpdd~EqATGlER~E 73 (119)
||||++++|||+|+++.++.++++.++ ++. +++ +++.++.++|+|+|++.++ +.++++|+|++||||||||+|
T Consensus 1 MwRr~~ss~L~~la~~~~~~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~s~~~~~~~~~~d~~~~ATGLER~E 80 (174)
T PLN02294 1 MWRRIVSSHLKTLAASVVAASPRRTVVATTRPLYLSRSRSSISASSSVFSRYFSSESADTAVKKRVEDVMPIATGHEREE 80 (174)
T ss_pred ChhhHHHHHHHHHHHhhcccCcccccccccccccccccccccCchhhhhhhccccccccccccccCCCchhhccchHHHH
Confidence 999999999999998866554454442 221 112 3333444899999998877 678999999999999999999
Q ss_pred HHHHHhCCCCCCCCCCCCCCCCCCCCeeeeccCCceeEeeCCC
Q 033442 74 LEAELEGKNILEIDYPTGPFGTKDAPAVVKSYYDKRIVGCPGG 116 (119)
Q Consensus 74 Lla~~~G~DpFdm~~~~~~~GTke~P~lVpS~~~~RIVGC~g~ 116 (119)
|+++++|+|||||+++++++||||||+||||++|+|||||+|+
T Consensus 81 Lla~leG~D~Fd~~~~~gp~GTke~P~lVpS~~d~RiVGCtg~ 123 (174)
T PLN02294 81 LEAELEGRKLLDIDFPEGPFGTKEAPAVVKSYYDKRIVGCPGG 123 (174)
T ss_pred HHHHHcCCCccccccccCCCCCccCCcEeccCCCceEEeeCCC
Confidence 9999999999999999999999999999999999999999993
No 2
>cd00924 Cyt_c_Oxidase_Vb Cytochrome c oxidase subunit Vb. 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 Vb is one of three mammalian subunits that lacks a transmembrane region. Subunit Vb is located on the matrix side of the membrane and binds the regulatory subunit of protein kinase A. The abnormally extended conformation is stable only in the CcO assembly.
Probab=99.97 E-value=8.7e-32 Score=191.98 Aligned_cols=65 Identities=43% Similarity=0.624 Sum_probs=62.9
Q ss_pred ccccCCCCCccccchhHHHHHHHHhCCCCCCCCCCCCCCCCCCCCeeeeccCCceeEeeCCCCCC
Q 033442 55 VKKRVEDVNPVATGHEREELEAELEGKNILEIDYPTGPFGTKDAPAVVKSYYDKRIVGCPGGEGG 119 (119)
Q Consensus 55 ~~g~vpdd~EqATGlER~ELla~~~G~DpFdm~~~~~~~GTke~P~lVpS~~~~RIVGC~g~p~e 119 (119)
++|+||||+||||||||+||+++++|+|+|+|+++++++||++||+||||++++|||||+|+|++
T Consensus 2 ~~g~vp~d~e~aTGlEr~ELl~~~~G~d~f~~~~~~~~~GT~e~P~lVpS~~~~RiVGC~g~~~~ 66 (97)
T cd00924 2 AEGEVPTDLEQATGLERKELLAKLEGIDDFDMKPLKGPFGTKEDPNLVPSAFDKRIVGCICEPDS 66 (97)
T ss_pred CCcccCCchHhhhccHHHHHHHHHcCCccccccccccCCCCccCCeEecCCCCCeEEeeeCCCCC
Confidence 67899999999999999999999999999999999999999999999999999999999999873
No 3
>PF01215 COX5B: Cytochrome c oxidase subunit Vb This family consists of chains F and S ; InterPro: IPR002124 Cytochrome c oxidase (1.9.3.1 from EC) is an oligomeric enzymatic complex which 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 polypeptidic subunits. One of these subunits, which is known as Vb in mammals, V in Dictyostelium discoideum (Slime mold) and IV in yeast, binds a zinc atom. The sequence of subunit Vb is well conserved and includes three conserved cysteines that coordinate the zinc ion [, ]. Two of these cysteines are clustered in the C-terminal section of the subunit.; GO: 0004129 cytochrome-c oxidase activity, 0005740 mitochondrial envelope; PDB: 2EIL_S 2ZXW_S 3ASN_S 1OCO_S 3AG4_S 3ABK_S 1OCZ_S 1OCC_F 3ASO_S 3ABL_S ....
Probab=99.97 E-value=3.7e-32 Score=204.02 Aligned_cols=67 Identities=43% Similarity=0.664 Sum_probs=45.6
Q ss_pred CCccccCCCCCccccchhHHHHHHHHhCCCCCCCCCCCCCCCCCCCCeeeeccCCceeEeeCCCCCC
Q 033442 53 TSVKKRVEDVNPVATGHEREELEAELEGKNILEIDYPTGPFGTKDAPAVVKSYYDKRIVGCPGGEGG 119 (119)
Q Consensus 53 ~~~~g~vpdd~EqATGlER~ELla~~~G~DpFdm~~~~~~~GTke~P~lVpS~~~~RIVGC~g~p~e 119 (119)
++++|+||||+||||||||+||+++++|+|||||+++++++||+||||||||++++|||||+|+|++
T Consensus 32 ~a~~G~vptd~eqATGlER~Ella~~~G~D~Fd~~~~~~~~GT~e~P~lVpS~~~~RiVGC~g~~~~ 98 (136)
T PF01215_consen 32 GAKPGTVPTDLEQATGLEREELLAKLEGIDPFDMKPLKAPFGTKEDPILVPSYFDERIVGCTGEPDD 98 (136)
T ss_dssp -----BS--HHHH--HHHHHHHHHHHTT--TT--S--B----SSSS-CEEEESSSCEEEEESSSTT-
T ss_pred cccCCCCCChhHhhhHHHHHHHHHHhcCcCcccccCccCCCCCccCCeEccCCCCceEEeeccCCCC
Confidence 6789999999999999999999999999999999999999999999999999999999999999975
No 4
>KOG3352 consensus Cytochrome c oxidase, subunit Vb/COX4 [Energy production and conversion]
Probab=99.96 E-value=9.6e-31 Score=199.92 Aligned_cols=67 Identities=49% Similarity=0.745 Sum_probs=64.6
Q ss_pred CCccccCCCCCccccchhHHHHHHHHhCCCCCCCCCCCCCCCCCCCCeeeeccCCceeEeeCCCCCC
Q 033442 53 TSVKKRVEDVNPVATGHEREELEAELEGKNILEIDYPTGPFGTKDAPAVVKSYYDKRIVGCPGGEGG 119 (119)
Q Consensus 53 ~~~~g~vpdd~EqATGlER~ELla~~~G~DpFdm~~~~~~~GTke~P~lVpS~~~~RIVGC~g~p~e 119 (119)
+++.|+||||+||||||||+|||++++|.|||||+.+++++||||||||||||||+|||||.|++|+
T Consensus 54 ~~~~g~vpddle~aTGlEk~eLla~l~G~d~~d~k~~~~~~GTkedP~lV~S~~d~RiVGC~c~eD~ 120 (153)
T KOG3352|consen 54 MAKGGGVPDDLEQATGLEKEELLAELEGRDPFDMKVPRGPSGTKEDPNLVPSYYDKRIVGCGCEEDS 120 (153)
T ss_pred cccCCCCCCchhhhhhHHHHHHHHHhhCCCccccccccCCCCcccCCccccccCCceEEeecccCCC
Confidence 7789999999999999999999999999999999988999999999999999999999999999874
No 5
>PTZ00043 cytochrome c oxidase subunit; Provisional
Probab=99.58 E-value=1.1e-15 Score=124.70 Aligned_cols=63 Identities=32% Similarity=0.467 Sum_probs=55.3
Q ss_pred ccCCCCCc-cccchhHHHHHHHHhCCCCCCCCCCCCCCCCCCCCeeeeccCCceeEeeCCCCCC
Q 033442 57 KRVEDVNP-VATGHEREELEAELEGKNILEIDYPTGPFGTKDAPAVVKSYYDKRIVGCPGGEGG 119 (119)
Q Consensus 57 g~vpdd~E-qATGlER~ELla~~~G~DpFdm~~~~~~~GTke~P~lVpS~~~~RIVGC~g~p~e 119 (119)
+.+.-||. |...-+.++|+|.++|.+.+.++++.+|+||+|+|+||||++++|||||+|+++|
T Consensus 103 kqla~d~gmqi~~~~~~hm~~~le~y~~Lk~~~~~GPfGTkEdPiLVpSy~deRyVGCTGg~~E 166 (268)
T PTZ00043 103 KQLARDMGMQIVNEPSEHMLGLLELYEYLKSSSFVGPFGTIENPVLVPSVGTERVVGCTGGTGE 166 (268)
T ss_pred HHHHHHhCceecCCchHHHHHHHHHHHhcCcCCCCCCCCCccCCeEeccCCCceEEeccCCCcc
Confidence 33444555 6777889999999999999999999999999999999999999999999996554
No 6
>PLN00128 Succinate dehydrogenase [ubiquinone] flavoprotein subunit
Probab=78.64 E-value=1.6 Score=39.35 Aligned_cols=18 Identities=39% Similarity=0.599 Sum_probs=15.3
Q ss_pred ChhhHhhhhhHHHHHHhh
Q 033442 1 MWRRICSSQLKAQALALA 18 (119)
Q Consensus 1 mwrr~~~~~l~~~~~~~~ 18 (119)
||||-+..-|+-|+++..
T Consensus 1 ~~~~~~~~~~~~~~~~~~ 18 (635)
T PLN00128 1 MWRRCVARGLRLLASSSA 18 (635)
T ss_pred CcccchhhHHHHHhhhhc
Confidence 999999999999986554
No 7
>COG3542 Uncharacterized conserved protein [Function unknown]
Probab=22.06 E-value=49 Score=26.21 Aligned_cols=26 Identities=42% Similarity=0.501 Sum_probs=21.1
Q ss_pred CCCCCCCCeeeeccCCceeEeeCCCCC
Q 033442 92 PFGTKDAPAVVKSYYDKRIVGCPGGEG 118 (119)
Q Consensus 92 ~~GTke~P~lVpS~~~~RIVGC~g~p~ 118 (119)
|.||.-.-.+.++- |+-+|||+.-||
T Consensus 106 P~g~w~aS~~~~g~-~~tLVgCtVaPG 131 (162)
T COG3542 106 PAGTWWASAVSLGE-DYTLVGCTVAPG 131 (162)
T ss_pred eCCcEEEEEEecCC-CceEEEEEecCC
Confidence 67777777777766 999999999886
No 8
>PF07710 P53_tetramer: P53 tetramerisation motif; InterPro: IPR010991 The p53 protein is a tetrameric transcription factor that plays a central role in the prevention of neoplastic transformation []. Oligomerization appears to be essential for the tumour suppressing activity of p53. p53 can be divided into different functional domains: an N-terminal transactivation domain, a proline-rich domain, a DNA-binding domain (IPR008967 from INTERPRO), a tetramerisation domain and a C-terminal regulatory region. The tetramerisation domain of human p53 extends from residues 325 to 356, and has a 4-helical bundle fold. The tetramerisation domain is essential for DNA binding, protein-protein interactions, post-translational modifications, and p53 degradation [].; GO: 0051262 protein tetramerization; PDB: 3Q06_B 1SAL_B 1OLH_B 1AIE_A 1PES_D 1SAK_D 1SAE_B 2J11_D 1PET_A 1OLG_A ....
Probab=19.94 E-value=78 Score=19.79 Aligned_cols=15 Identities=27% Similarity=0.430 Sum_probs=12.9
Q ss_pred cccchhHHHHHHHHh
Q 033442 65 VATGHEREELEAELE 79 (119)
Q Consensus 65 qATGlER~ELla~~~ 79 (119)
|.-|.||+||+-++.
T Consensus 14 ~VrGRe~yE~l~kin 28 (42)
T PF07710_consen 14 QVRGRERYEMLKKIN 28 (42)
T ss_dssp EEESHHHHHHHHHHH
T ss_pred EEecHHHHHHHHHHH
Confidence 678999999998874
No 9
>PF00278 Orn_DAP_Arg_deC: Pyridoxal-dependent decarboxylase, C-terminal sheet domain; InterPro: IPR022643 These enzymes are collectively known as group IV decarboxylases []. Pyridoxal-dependent decarboxylases acting on ornithine, lysine, arginine and related substrates can be classified into two different families on the basis of sequence similarities [, ]. Members of this family while most probably evolutionary related, do not share extensive regions of sequence similarities. The proteins contain a conserved lysine residue which is known, in mouse ODC [], to be the site of attachment of the pyridoxal-phosphate group. The proteins also contain a stretch of three consecutive glycine residues and has been proposed to be part of a substrate- binding region []. This entry represents the C-terminal region of the Orn/DAP/Arg decarboxylases.; GO: 0003824 catalytic activity; PDB: 1TWI_B 1TUF_A 3MT1_A 3N2B_C 2O0T_A 1HKW_A 1HKV_A 3VAB_A 3N2O_A 7ODC_A ....
Probab=15.01 E-value=1.1e+02 Score=20.60 Aligned_cols=14 Identities=29% Similarity=0.406 Sum_probs=11.1
Q ss_pred CCceeEeeCCCCCC
Q 033442 106 YDKRIVGCPGGEGG 119 (119)
Q Consensus 106 ~~~RIVGC~g~p~e 119 (119)
....|.|++|.+.|
T Consensus 58 ~~~~i~GptC~~~D 71 (116)
T PF00278_consen 58 YPSTIWGPTCDSGD 71 (116)
T ss_dssp EEEEEEESSSSTTS
T ss_pred EEEEEEECCcCCCc
Confidence 35678999999875
No 10
>PF09680 Tiny_TM_bacill: Protein of unknown function (Tiny_TM_bacill); InterPro: IPR010070 This entry represents a family of hypothetical proteins, half of which are 40 residues or less in length. Members are found only in spore-forming species. A Gly-rich variable region is followed by a strongly conserved, highly hydrophobic region, predicted to form a transmembrane helix, ending with an invariant Gly. The consensus for this stretch is FALLVVFILLIIV.
Probab=14.41 E-value=41 Score=18.98 Aligned_cols=6 Identities=50% Similarity=0.717 Sum_probs=3.7
Q ss_pred eEeeCC
Q 033442 110 IVGCPG 115 (119)
Q Consensus 110 IVGC~g 115 (119)
||||.|
T Consensus 18 IvG~s~ 23 (24)
T PF09680_consen 18 IVGASC 23 (24)
T ss_pred Hhccee
Confidence 566665
Done!