Query 029541
Match_columns 192
No_of_seqs 115 out of 295
Neff 3.3
Searched_HMMs 46136
Date Fri Mar 29 14:34:16 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/029541.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/029541hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG3057 Cytochrome c oxidase, 100.0 5.8E-37 1.3E-41 240.3 7.8 80 113-192 32-111 (112)
2 cd00926 Cyt_c_Oxidase_VIb Cyto 100.0 3.6E-36 7.8E-41 220.0 8.5 73 119-191 3-75 (75)
3 PF02297 COX6B: Cytochrome oxi 99.9 3.5E-25 7.5E-30 160.5 4.7 60 128-187 1-69 (76)
4 PF06747 CHCH: CHCH domain; I 92.4 0.098 2.1E-06 32.2 1.9 31 139-169 1-31 (35)
5 KOG4618 Uncharacterized conser 92.1 0.26 5.6E-06 37.1 4.1 47 137-184 22-68 (74)
6 CHL00088 apcB allophycocyanin 71.6 7.9 0.00017 32.2 4.6 61 123-184 66-135 (161)
7 KOG4090 Uncharacterized conser 62.3 7.9 0.00017 32.8 2.9 40 135-175 114-153 (157)
8 TIGR01337 apcB allophycocyanin 59.4 23 0.00051 29.6 5.2 54 123-177 66-127 (167)
9 PF08991 DUF1903: Domain of un 55.6 8.4 0.00018 28.1 1.8 33 139-171 4-36 (67)
10 KOG3458 NADH:ubiquinone oxidor 41.8 21 0.00046 30.6 2.3 40 135-174 74-114 (170)
11 KOG4763 Ubiquinol-cytochrome c 39.2 18 0.00039 27.5 1.3 20 133-152 47-66 (77)
12 PF11326 DUF3128: Protein of u 37.4 15 0.00034 26.9 0.8 18 136-153 4-21 (84)
13 CHL00090 apcD allophycocyanin 36.6 83 0.0018 26.2 5.0 54 123-177 66-127 (161)
14 PF11357 Spy1: Cell cycle regu 35.9 31 0.00066 28.4 2.3 45 133-183 86-131 (131)
15 CHL00089 apcF allophycocyanin 35.2 86 0.0019 26.5 4.9 55 122-177 66-128 (169)
16 PF05676 NDUF_B7: NADH-ubiquin 32.4 73 0.0016 23.2 3.6 44 134-177 17-60 (66)
17 PF14345 GDYXXLXY: GDYXXLXY pr 31.5 19 0.00041 28.4 0.5 18 115-132 19-36 (144)
18 TIGR01339 phycocy_beta phycocy 26.6 73 0.0016 27.0 3.1 55 121-176 63-125 (170)
19 KOG4624 Uncharacterized conser 25.1 1E+02 0.0023 24.7 3.6 54 133-186 27-94 (104)
20 PF05240 APOBEC_C: APOBEC-like 23.7 46 0.00099 23.6 1.2 18 131-148 21-38 (55)
21 PF10203 Pet191_N: Cytochrome 23.5 70 0.0015 23.3 2.2 40 137-177 19-60 (68)
22 PF13982 YbfN: YbfN-like lipop 22.9 76 0.0017 24.8 2.4 24 142-165 55-83 (89)
23 CHL00171 cpcB phycocyanin beta 21.5 1.8E+02 0.004 24.5 4.6 53 123-176 67-127 (172)
No 1
>KOG3057 consensus Cytochrome c oxidase, subunit VIb/COX12 [Energy production and conversion]
Probab=100.00 E-value=5.8e-37 Score=240.26 Aligned_cols=80 Identities=65% Similarity=1.292 Sum_probs=76.4
Q ss_pred cccCCCcccccCCCCCCCCChHHHHHHHHhhhhhhhhhhhcCCChhhHHHHHHHHHhhChHHHHHHHHHhhhcCCCCCCC
Q 029541 113 SEETPDIKLETAPADFRFPTTNQTRHCFTRYIEYHRCVAAKGEGAPECDKFAKYYRALCPSDWIEKWNEQRENGTFPGPL 192 (192)
Q Consensus 113 ~~~~~~~~l~TaP~DpRFPn~NQrK~CW~~YddY~rCl~~kGED~s~Ckkfrk~YeSlCP~sWVE~WDEqRe~GtFpgki 192 (192)
......+.|.|+|+|+||||+|||||||++|+|||||++++|+|+..|++|+++|+|+||.+||++||+||++|+|||+|
T Consensus 32 ~~~~~~~~l~tap~d~RFP~~nqtrhCf~~y~dyhrC~~~~geD~~~Ck~f~~~y~SlCP~~WV~kWdeqre~G~Fpg~~ 111 (112)
T KOG3057|consen 32 PETPKSKLLTTAPVDARFPNTNQTRHCFQRYVDYHRCIKAKGEDANPCKKFQKVYRSLCPGEWVEKWDEQRENGTFPGPI 111 (112)
T ss_pred cccccccccccccccccCCCcchhHHHHHHHHHHHHHHHHhcccchhHHHHHHHHHHhCcHHHHHHHHHhhhcCCCCCCC
Confidence 35566778999999999999999999999999999999999999999999999999999999999999999999999986
No 2
>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=100.00 E-value=3.6e-36 Score=220.02 Aligned_cols=73 Identities=60% Similarity=1.257 Sum_probs=71.4
Q ss_pred cccccCCCCCCCCChHHHHHHHHhhhhhhhhhhhcCCChhhHHHHHHHHHhhChHHHHHHHHHhhhcCCCCCC
Q 029541 119 IKLETAPADFRFPTTNQTRHCFTRYIEYHRCVAAKGEGAPECDKFAKYYRALCPSDWIEKWNEQRENGTFPGP 191 (192)
Q Consensus 119 ~~l~TaP~DpRFPn~NQrK~CW~~YddY~rCl~~kGED~s~Ckkfrk~YeSlCP~sWVE~WDEqRe~GtFpgk 191 (192)
+.|+|+|+||||||+|||+|||++||+||+||+++|+|+++|++|++.|+++||.+||++|++||++|+||++
T Consensus 3 ~~~~t~~~D~RfP~~nq~k~Cw~~y~~y~~Cl~~~ged~~~C~~~~~~~es~Cp~~Wve~w~ekR~~g~f~~~ 75 (75)
T cd00926 3 GPLTTAPFDPRFPNQNQTKHCWQRYVDYHRCIKAKGEDASPCKKFRRVYESLCPQEWLEKWDEQREEGTFPGK 75 (75)
T ss_pred ccccCCCCCCCCCChHHHHHHHHHHHHHHHHHHHcCCchHHHHHHHHHHHHhCcHHHHHHHHHHHHhCCCCCC
Confidence 5699999999999999999999999999999999999999999999999999999999999999999999986
No 3
>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=99.91 E-value=3.5e-25 Score=160.53 Aligned_cols=60 Identities=33% Similarity=0.814 Sum_probs=50.4
Q ss_pred CCCCChHHHHHHHHhhhhhhhhhhhcCC---------ChhhHHHHHHHHHhhChHHHHHHHHHhhhcCC
Q 029541 128 FRFPTTNQTRHCFTRYIEYHRCVAAKGE---------GAPECDKFAKYYRALCPSDWIEKWNEQRENGT 187 (192)
Q Consensus 128 pRFPn~NQrK~CW~~YddY~rCl~~kGE---------D~s~Ckkfrk~YeSlCP~sWVE~WDEqRe~Gt 187 (192)
||||++|||++||++||+||+||+.+|+ +.+.|+.|++.|+++||.+||+||+++|.+.+
T Consensus 1 ~rfP~~~~r~~Cw~arD~y~~Cl~~~~~~~~~~~~~~~~~~C~~~~~~ye~~Cp~sWv~~f~~~R~~~~ 69 (76)
T PF02297_consen 1 PRFPNRNQRKKCWQARDDYFKCLDKNGEPDSEKEKKKDESACKYFRKNYESNCPSSWVKYFDEKRVYDQ 69 (76)
T ss_dssp -TS-SSB-HHHHHHHHHHHHHHHHHHHH------TTTTGGGGHHHHHHHHHHS-HHHHHHHHHH-----
T ss_pred CCCCChHHHHHHHHHHHHHHHHHHHcCccccccccccchhhhHHHHHHHHHhCcHHHHHHHHHHhhHHH
Confidence 7999999999999999999999999999 89999999999999999999999999955443
No 4
>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=92.43 E-value=0.098 Score=32.17 Aligned_cols=31 Identities=23% Similarity=0.436 Sum_probs=26.4
Q ss_pred HHHhhhhhhhhhhhcCCChhhHHHHHHHHHh
Q 029541 139 CFTRYIEYHRCVAAKGEGAPECDKFAKYYRA 169 (192)
Q Consensus 139 CW~~YddY~rCl~~kGED~s~Ckkfrk~YeS 169 (192)
|-.-...|+.|++.++.+...|.++.+.|+.
T Consensus 1 C~~e~~~~~~Cl~~n~~~~~~C~~~~~~~~~ 31 (35)
T PF06747_consen 1 CAEEMKAYLACLKENNFDWSKCRKEFKAYKE 31 (35)
T ss_dssp THHHHHHHHHHHHCH-SSTCCCHHHHHHHHH
T ss_pred CHHHHHHHHHHHHHCCCcHHhhHHHHHHHHH
Confidence 4556788999999999999999999999986
No 5
>KOG4618 consensus Uncharacterized conserved protein [Function unknown]
Probab=92.06 E-value=0.26 Score=37.05 Aligned_cols=47 Identities=19% Similarity=0.511 Sum_probs=41.4
Q ss_pred HHHHHhhhhhhhhhhhcCCChhhHHHHHHHHHhhChHHHHHHHHHhhh
Q 029541 137 RHCFTRYIEYHRCVAAKGEGAPECDKFAKYYRALCPSDWIEKWNEQRE 184 (192)
Q Consensus 137 K~CW~~YddY~rCl~~kGED~s~Ckkfrk~YeSlCP~sWVE~WDEqRe 184 (192)
.-|...+..=++||..+|-|-+.|..++..|+ .|-..|.+-=-++|.
T Consensus 22 nPCl~es~aSfkCLeennyDRsKCq~yFd~Yk-eCKkfwn~ar~errk 68 (74)
T KOG4618|consen 22 NPCLLESSASFKCLEENNYDRSKCQDYFDVYK-ECKKFWNEARLERRK 68 (74)
T ss_pred ChHHHHHHHHHHHHHhcCccHHHHHHHHHHHH-HHHHHHHHHHHHHhh
Confidence 56999999999999999999999999999997 599999887666654
No 6
>CHL00088 apcB allophycocyanin beta subunit
Probab=71.56 E-value=7.9 Score=32.17 Aligned_cols=61 Identities=16% Similarity=0.240 Sum_probs=42.6
Q ss_pred cCCCCCCCCChHHHHHHHHhhhhhhhhhhh--cCCC----hhhH-HHHHHHHHhh-ChHHHH-HHHHHhhh
Q 029541 123 TAPADFRFPTTNQTRHCFTRYIEYHRCVAA--KGEG----APEC-DKFAKYYRAL-CPSDWI-EKWNEQRE 184 (192)
Q Consensus 123 TaP~DpRFPn~NQrK~CW~~YddY~rCl~~--kGED----~s~C-kkfrk~YeSl-CP~sWV-E~WDEqRe 184 (192)
+.|....+++.+ ...||.=+.-|.||+.- ..+| ...| .-+|..|+++ ||..|+ .-+...|.
T Consensus 66 ~~~Gg~~y~~~r-~~~C~RD~~~~LR~itYaivaGd~~~L~e~~L~GlrE~y~~Lgvp~~~~i~al~~mk~ 135 (161)
T CHL00088 66 TRPGGNMYTTRR-YAACIRDLDYYLRYATYGMLAGDPSILDERVLNGLKETYNSLGVPIGATIQAIQAMKE 135 (161)
T ss_pred cCCCCCccChHH-HHHHHHHHhhhccceeeeeecCCchHHHHHHHHHHHHHHHHhCCCHHHHHHHHHHHHH
Confidence 455555665544 77899999999999862 2222 4557 7799999995 999997 44444443
No 7
>KOG4090 consensus Uncharacterized conserved protein [Function unknown]
Probab=62.33 E-value=7.9 Score=32.85 Aligned_cols=40 Identities=18% Similarity=0.535 Sum_probs=31.6
Q ss_pred HHHHHHHhhhhhhhhhhhcCCChhhHHHHHHHHHhhChHHH
Q 029541 135 QTRHCFTRYIEYHRCVAAKGEGAPECDKFAKYYRALCPSDW 175 (192)
Q Consensus 135 QrK~CW~~YddY~rCl~~kGED~s~Ckkfrk~YeSlCP~sW 175 (192)
|..-|.----.|..|+..+|.|.+.|..|.. .-+-|-..|
T Consensus 114 ~~~~C~~e~kqF~dCa~~~~~d~slC~~f~e-~Lk~Ck~~~ 153 (157)
T KOG4090|consen 114 QQQPCFIEIKQFLDCAQNQGSDISLCEGYNE-MLKQCKKNS 153 (157)
T ss_pred hcCchHHHHHHHHHHHHhcCcchHHHHHHHH-HHHHHHHHh
Confidence 4567999999999999999999999987744 445565544
No 8
>TIGR01337 apcB allophycocyanin, beta subunit. The alpha and beta subunits of allophycocyanin form heterodimers, six of which associate into larger aggregates as part of the phycobilisome, a light-harvesting complex of phycobiliproteins and linker proteins. This model describes allophycocyanin beta subunit. Other, homologous phyobiliproteins include allophycocyanin alpha chain and the phycocyanin and phycoerythrin alpha and beta chains.
Probab=59.37 E-value=23 Score=29.56 Aligned_cols=54 Identities=15% Similarity=0.228 Sum_probs=40.7
Q ss_pred cCCCCCCCCChHHHHHHHHhhhhhhhhhhh---cCCC---hhhH-HHHHHHHHh-hChHHHHH
Q 029541 123 TAPADFRFPTTNQTRHCFTRYIEYHRCVAA---KGEG---APEC-DKFAKYYRA-LCPSDWIE 177 (192)
Q Consensus 123 TaP~DpRFPn~NQrK~CW~~YddY~rCl~~---kGED---~s~C-kkfrk~YeS-lCP~sWVE 177 (192)
+.|....||+.+ ...||.=+.-|.||+.- -|+. ...| .-+|..|++ .||..|+-
T Consensus 66 ~~~GG~~y~~~r-~~aC~RD~~~~LR~itYailaGd~~~L~~~~L~GlrE~y~~LgvP~~~~v 127 (167)
T TIGR01337 66 IRPGGNAYTTRR-YAACLRDIDYYLRYATYAIIAGDNSILEERVLNGLKETYNSLGVPIGPTV 127 (167)
T ss_pred CCCCCCCCCHHH-HHHHHHHHHHHhhhhheeeecCCchHHHHHHHHHHHHHHHHcCCCHHHHH
Confidence 456667777655 78899999999999862 2322 4556 678999999 69999973
No 9
>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=55.62 E-value=8.4 Score=28.07 Aligned_cols=33 Identities=12% Similarity=0.463 Sum_probs=24.5
Q ss_pred HHHhhhhhhhhhhhcCCChhhHHHHHHHHHhhC
Q 029541 139 CFTRYIEYHRCVAAKGEGAPECDKFAKYYRALC 171 (192)
Q Consensus 139 CW~~YddY~rCl~~kGED~s~Ckkfrk~YeSlC 171 (192)
|-..-..-++||..+|-+.+.|..+...|+.-|
T Consensus 4 C~~~Ac~iq~CL~~N~Yd~~kC~~~i~~l~~Cc 36 (67)
T PF08991_consen 4 CQKEACAIQKCLQRNNYDESKCQDYIDALYECC 36 (67)
T ss_dssp THHHHHHHHHHHHHTTT-CCCTHHHHHHHHHHH
T ss_pred hHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHH
Confidence 334445678899999999999999888887644
No 10
>KOG3458 consensus NADH:ubiquinone oxidoreductase, NDUFA8/PGIV/19 kDa subunit [Energy production and conversion]
Probab=41.84 E-value=21 Score=30.56 Aligned_cols=40 Identities=18% Similarity=0.499 Sum_probs=34.7
Q ss_pred HHHHHHHhhhhhhhhhhhcC-CChhhHHHHHHHHHhhChHH
Q 029541 135 QTRHCFTRYIEYHRCVAAKG-EGAPECDKFAKYYRALCPSD 174 (192)
Q Consensus 135 QrK~CW~~YddY~rCl~~kG-ED~s~Ckkfrk~YeSlCP~s 174 (192)
--++|-.-+++|+-|++..| -..+.|.+-+..|..-||.-
T Consensus 74 lkr~C~~e~~~y~~C~dysst~~f~~Crk~Q~~fdkcv~~k 114 (170)
T KOG3458|consen 74 LKRSCLEEFTKYATCMDYSSTNEFSHCRKEQEAFDKCVPDK 114 (170)
T ss_pred HHHHhhHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHhHhh
Confidence 34889999999999999886 44889999999999999874
No 11
>KOG4763 consensus Ubiquinol-cytochrome c reductase hinge protein [Energy production and conversion]
Probab=39.18 E-value=18 Score=27.51 Aligned_cols=20 Identities=25% Similarity=0.810 Sum_probs=16.5
Q ss_pred hHHHHHHHHhhhhhhhhhhh
Q 029541 133 TNQTRHCFTRYIEYHRCVAA 152 (192)
Q Consensus 133 ~NQrK~CW~~YddY~rCl~~ 152 (192)
.+--++|-+-|-|||+|++.
T Consensus 47 s~tee~Ct~e~fDy~h~~Dh 66 (77)
T KOG4763|consen 47 SSTEEHCTGEYFDYWHCLDH 66 (77)
T ss_pred cccchhhHHHHHHHHHHHHH
Confidence 34458999999999999863
No 12
>PF11326 DUF3128: Protein of unknown function (DUF3128); InterPro: IPR021475 This eukaryotic family of proteins has no known function.
Probab=37.45 E-value=15 Score=26.93 Aligned_cols=18 Identities=22% Similarity=0.458 Sum_probs=14.0
Q ss_pred HHHHHHhhhhhhhhhhhc
Q 029541 136 TRHCFTRYIEYHRCVAAK 153 (192)
Q Consensus 136 rK~CW~~YddY~rCl~~k 153 (192)
+--|...+|.|+.|....
T Consensus 4 ~~sC~~~fd~~~~C~S~~ 21 (84)
T PF11326_consen 4 TMSCMDAFDELWFCYSPG 21 (84)
T ss_pred CccHHHHHHHHHHcCCch
Confidence 446899999999997644
No 13
>CHL00090 apcD allophycocyanin gamma subunit
Probab=36.57 E-value=83 Score=26.17 Aligned_cols=54 Identities=20% Similarity=0.225 Sum_probs=38.5
Q ss_pred cCCCCCCCCChHHHHHHHHhhhhhhhhhhh---cCCC---hhhH-HHHHHHHHhh-ChHHHHH
Q 029541 123 TAPADFRFPTTNQTRHCFTRYIEYHRCVAA---KGEG---APEC-DKFAKYYRAL-CPSDWIE 177 (192)
Q Consensus 123 TaP~DpRFPn~NQrK~CW~~YddY~rCl~~---kGED---~s~C-kkfrk~YeSl-CP~sWVE 177 (192)
+.|...-||+. ....||.=+.-|.||+.- -|+. ...| .-+|..|+++ ||..|+-
T Consensus 66 ~~~Gg~~y~~~-r~~aC~RD~~~~LR~itYa~lagd~~~L~~~~l~GlrE~Y~~LgvP~~~~v 127 (161)
T CHL00090 66 IAPGGNASGSR-QRSLCLRDYGWYLRLITYGVLAGDKNSIEKIGIIGVREMYNSLGVPIIGMV 127 (161)
T ss_pred cCCCCCCcchH-HHHHHHHhHHHhhhhheeeeecCChHHHHHHHHHHHHHHHHHhCCChHHHH
Confidence 34555566664 488999999999999862 2322 2334 4588999998 9999964
No 14
>PF11357 Spy1: Cell cycle regulatory protein; InterPro: IPR020984 Speedy (Spy1) is a cell cycle regulatory protein which activates CDK2, the major kinase that allows progression through G1/S phase and further replication events. Spy1 expression overcomes a p27-induced cell cycle arrest to allow for DNA synthesis, so cell cycle progression occurs due to an interaction between Spy1 and p27 []. Spy1 is also known as Ringo protein A.
Probab=35.94 E-value=31 Score=28.43 Aligned_cols=45 Identities=20% Similarity=0.508 Sum_probs=35.5
Q ss_pred hHHHHHHHHhhhhhhhhhhhcC-CChhhHHHHHHHHHhhChHHHHHHHHHhh
Q 029541 133 TNQTRHCFTRYIEYHRCVAAKG-EGAPECDKFAKYYRALCPSDWIEKWNEQR 183 (192)
Q Consensus 133 ~NQrK~CW~~YddY~rCl~~kG-ED~s~Ckkfrk~YeSlCP~sWVE~WDEqR 183 (192)
.+|...=...|+.|++|++=+. .....|... ++.+|.-|| |.+.|
T Consensus 86 ~~~~~~F~klr~~~~~~m~~Ra~Vsre~cEEi----~a~~P~hwv--W~R~R 131 (131)
T PF11357_consen 86 RSQIPQFHKLRDQFWRRMDWRAWVSREECEEI----QAYDPEHWV--WKRDR 131 (131)
T ss_pred HHHhHHHHHHHHHHHHHcCCceeeCHHHHHHH----HHhCCcchh--hccCC
Confidence 6777888889999999998664 667778665 556799999 87765
No 15
>CHL00089 apcF allophycocyanin beta 18 subunit
Probab=35.23 E-value=86 Score=26.46 Aligned_cols=55 Identities=16% Similarity=0.210 Sum_probs=40.4
Q ss_pred ccCCCCCCCCChHHHHHHHHhhhhhhhhhhh---cCCC---hhhH-HHHHHHHHh-hChHHHHH
Q 029541 122 ETAPADFRFPTTNQTRHCFTRYIEYHRCVAA---KGEG---APEC-DKFAKYYRA-LCPSDWIE 177 (192)
Q Consensus 122 ~TaP~DpRFPn~NQrK~CW~~YddY~rCl~~---kGED---~s~C-kkfrk~YeS-lCP~sWVE 177 (192)
-+.|....||+.+ ...||.=+.-|.||+.- -|+. ...| .-+|..|++ .||..|+-
T Consensus 66 l~~~GG~~y~~~r-~~aC~RD~~~~LR~itYalvaGd~~~L~e~~L~GlrE~Y~~LgvP~~~~i 128 (169)
T CHL00089 66 LLRPGGNAYTTRR-YAACLRDIEYYLRYASYAIVAGDTNILDERVLDGLKDTYNSLGVPIAPTV 128 (169)
T ss_pred ccCCCCCCcchHH-HHHHHHHHHhhhhheeeeeecCCchHHhHHHHHHHHHHHHHhCCCHHHHH
Confidence 4557777887755 88999999999999862 2322 3333 458899999 89999964
No 16
>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=32.35 E-value=73 Score=23.25 Aligned_cols=44 Identities=14% Similarity=0.190 Sum_probs=34.5
Q ss_pred HHHHHHHHhhhhhhhhhhhcCCChhhHHHHHHHHHhhChHHHHH
Q 029541 134 NQTRHCFTRYIEYHRCVAAKGEGAPECDKFAKYYRALCPSDWIE 177 (192)
Q Consensus 134 NQrK~CW~~YddY~rCl~~kGED~s~Ckkfrk~YeSlCP~sWVE 177 (192)
.+|-.|--.++.|.+|.+.+---.-.|...|..|..-=-..+|.
T Consensus 17 ~~RDyCAh~Li~l~kCrr~~~p~~~~C~~erH~y~~C~y~dy~~ 60 (66)
T PF05676_consen 17 QYRDYCAHLLIPLNKCRRDNFPFPWKCEHERHEYEKCQYDDYVM 60 (66)
T ss_pred hhhhhHHHHHHHHHHHHHhCCCCcccCCcchhhHHHccHHHHHH
Confidence 57899999999999999988766678999988887643344443
No 17
>PF14345 GDYXXLXY: GDYXXLXY protein
Probab=31.51 E-value=19 Score=28.41 Aligned_cols=18 Identities=33% Similarity=0.394 Sum_probs=14.4
Q ss_pred cCCCcccccCCCCCCCCC
Q 029541 115 ETPDIKLETAPADFRFPT 132 (192)
Q Consensus 115 ~~~~~~l~TaP~DpRFPn 132 (192)
....+.|+|+|.|||=+-
T Consensus 19 ~G~~v~L~~~PvDPRdll 36 (144)
T PF14345_consen 19 QGKEVTLKTAPVDPRDLL 36 (144)
T ss_pred CCCEEEEEecccCccccc
Confidence 356788999999999653
No 18
>TIGR01339 phycocy_beta phycocyanin, beta subunit. This model excludes the closely related phycoerythrocyanin beta subunit.
Probab=26.60 E-value=73 Score=27.02 Aligned_cols=55 Identities=18% Similarity=0.248 Sum_probs=42.0
Q ss_pred cccCCCCCCCCChHHHHHHHHhhhhhhhhhh---hcCC---ChhhHH-HHHHHHHh-hChHHHH
Q 029541 121 LETAPADFRFPTTNQTRHCFTRYIEYHRCVA---AKGE---GAPECD-KFAKYYRA-LCPSDWI 176 (192)
Q Consensus 121 l~TaP~DpRFPn~NQrK~CW~~YddY~rCl~---~kGE---D~s~Ck-kfrk~YeS-lCP~sWV 176 (192)
--|.|....||+.+ ...||.=..-|.||+. .-|+ -...|. -+|..|++ ..|..|+
T Consensus 63 ~l~~pGG~~y~~~r-~~aClRD~~~yLR~itYalvaGd~~~ld~~gl~GLrE~Y~aLgVP~~~~ 125 (170)
T TIGR01339 63 QLIAPGGNAYTSRR-MAACLRDMEIILRYVTYAIFTGDASVLEDRCLNGLRETYLALGTPGSSV 125 (170)
T ss_pred CCCCCCCCCCcHHH-HHHHHhhccceeceeeEEeecCCCchhhHHHHHHHHHHHHHhCCCchHH
Confidence 34678888998766 8999999999999986 2222 255565 68999999 5999887
No 19
>KOG4624 consensus Uncharacterized conserved protein [Function unknown]
Probab=25.14 E-value=1e+02 Score=24.67 Aligned_cols=54 Identities=20% Similarity=0.513 Sum_probs=35.9
Q ss_pred hHHHHHHHHhhhhhhhhhhhcCCC-hhhHHHHHHH-------------HHhhChHHHHHHHHHhhhcC
Q 029541 133 TNQTRHCFTRYIEYHRCVAAKGEG-APECDKFAKY-------------YRALCPSDWIEKWNEQRENG 186 (192)
Q Consensus 133 ~NQrK~CW~~YddY~rCl~~kGED-~s~Ckkfrk~-------------YeSlCP~sWVE~WDEqRe~G 186 (192)
+..|..|-+.+.+|-.|.+..|.. ...|++.+.. |+..|-...|.-=-..|..|
T Consensus 27 kakt~~C~~~v~~~a~C~k~~~v~vv~TCrkq~~elk~Cl~~~~~D~af~e~~rd~yv~Er~~~ratg 94 (104)
T KOG4624|consen 27 KAKTEKCSEFVQDFADCAKASGVSVVPTCRKQNSELKECLTQYYNDEAFLEECRDEYVQERINKRATG 94 (104)
T ss_pred HHHHHHHHHHHHHHHHHHhcCCeeeehhhHHHHHHHHHHHHHHhcCHHHHHHHHHHHHHHHHHHHhcc
Confidence 566789999999999999999854 5556655443 44455555555444444444
No 20
>PF05240 APOBEC_C: APOBEC-like C-terminal domain; InterPro: IPR007904 This domain is found at the C terminus of the Apolipoprotein B mRNA editing enzyme. Apobec-1 catalyzes C to U editing of apolipoprotein B (apoB) mRNA in the mammalian intestine. C to U RNA editing of mammalian apolipoprotein B (apoB) RNA is a site-specific posttranscriptional modification in which a single cytidine is enzymatically deaminated to uridine, thereby generating a UAA stop codon in the edited mRNA. The function of this domain is currently unknown.; GO: 0008270 zinc ion binding, 0016814 hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in cyclic amidines; PDB: 2NYT_D.
Probab=23.72 E-value=46 Score=23.62 Aligned_cols=18 Identities=11% Similarity=0.425 Sum_probs=11.4
Q ss_pred CChHHHHHHHHhhhhhhh
Q 029541 131 PTTNQTRHCFTRYIEYHR 148 (192)
Q Consensus 131 Pn~NQrK~CW~~YddY~r 148 (192)
.+-..-.+||++++++-.
T Consensus 21 M~~~eF~~CW~nFV~~~~ 38 (55)
T PF05240_consen 21 MTYSEFQYCWENFVDNQG 38 (55)
T ss_dssp --HHHHHHHHHHCB--TT
T ss_pred cCcHHHHHHHHHHhcCCC
Confidence 455678899999998763
No 21
>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=23.48 E-value=70 Score=23.28 Aligned_cols=40 Identities=18% Similarity=0.420 Sum_probs=24.9
Q ss_pred HHHHH-hhhhhhhhhhhc-CCChhhHHHHHHHHHhhChHHHHH
Q 029541 137 RHCFT-RYIEYHRCVAAK-GEGAPECDKFAKYYRALCPSDWIE 177 (192)
Q Consensus 137 K~CW~-~YddY~rCl~~k-GED~s~Ckkfrk~YeSlCP~sWVE 177 (192)
..|+. ..-.|..||+.. .+-...|..+++.|- .|--++|+
T Consensus 19 SdCv~~~~~t~~~Cl~~~~~~~p~eC~~lr~~f~-eCKrg~lD 60 (68)
T PF10203_consen 19 SDCVKKEKRTPKDCLKDPSDELPEECQQLRKAFF-ECKRGMLD 60 (68)
T ss_pred ChhhccCCCCHHHHHcCCCCcCCHHHHHHHHHHH-HHhccccc
Confidence 34554 445666676666 344678988888874 46666654
No 22
>PF13982 YbfN: YbfN-like lipoprotein
Probab=22.85 E-value=76 Score=24.76 Aligned_cols=24 Identities=38% Similarity=0.967 Sum_probs=15.7
Q ss_pred hhhhhhhhhhhc--CCC---hhhHHHHHH
Q 029541 142 RYIEYHRCVAAK--GEG---APECDKFAK 165 (192)
Q Consensus 142 ~YddY~rCl~~k--GED---~s~Ckkfrk 165 (192)
+-.||.+|+.+. |.+ ...|.++++
T Consensus 55 rvlDYQ~CIqAa~tGngqa~~a~C~kiwq 83 (89)
T PF13982_consen 55 RVLDYQQCIQAAMTGNGQAYTARCDKIWQ 83 (89)
T ss_pred hhccHHHHHHHHHcCCchHHHHHHHHHHH
Confidence 567999999754 544 455666633
No 23
>CHL00171 cpcB phycocyanin beta subunit; Reviewed
Probab=21.50 E-value=1.8e+02 Score=24.53 Aligned_cols=53 Identities=19% Similarity=0.367 Sum_probs=39.0
Q ss_pred cCCCCCCCCChHHHHHHHHhhhhhhhhhhh---cCCC---hhhHH-HHHHHHHhh-ChHHHH
Q 029541 123 TAPADFRFPTTNQTRHCFTRYIEYHRCVAA---KGEG---APECD-KFAKYYRAL-CPSDWI 176 (192)
Q Consensus 123 TaP~DpRFPn~NQrK~CW~~YddY~rCl~~---kGED---~s~Ck-kfrk~YeSl-CP~sWV 176 (192)
+.|....||+.. ...||.=+.-|.||+.- -|+. ...|. -+|..|+++ .|..|+
T Consensus 67 ~~~GG~~y~~~r-~~aC~RD~~~~LR~itYailaGd~~~L~e~~L~GlrE~Y~~lgvP~~~~ 127 (172)
T CHL00171 67 IQPGGNAYTNRR-MAACLRDMEIVLRYVSYAMIAGDSSVLDDRCLNGLRETYQALGVPGSSV 127 (172)
T ss_pred cCCCCCCCCHHH-HHHHHHhHHhhhhhheeeeecCCchHHhHHHHHHHHHHHHHhCCCchHH
Confidence 567778887655 88999999999999862 2322 34454 688999996 888765
Done!