Query 029538
Match_columns 192
No_of_seqs 119 out of 258
Neff 3.1
Searched_HMMs 46136
Date Fri Mar 29 14:31:21 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/029538.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/029538hhsearch_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 8.1E-35 1.8E-39 228.2 6.9 76 112-187 31-106 (112)
2 cd00926 Cyt_c_Oxidase_VIb Cyto 100.0 1.6E-34 3.5E-39 211.1 7.7 72 119-190 3-74 (75)
3 PF02297 COX6B: Cytochrome oxi 99.9 1.1E-24 2.3E-29 157.7 4.5 59 128-186 1-68 (76)
4 PF06747 CHCH: CHCH domain; I 90.5 0.22 4.8E-06 30.5 2.0 31 139-169 1-31 (35)
5 KOG4618 Uncharacterized conser 89.8 0.54 1.2E-05 35.4 4.0 47 137-184 22-68 (74)
6 KOG4090 Uncharacterized conser 63.1 8.1 0.00018 32.8 3.1 38 135-173 114-151 (157)
7 CHL00088 apcB allophycocyanin 61.1 16 0.00034 30.4 4.4 54 123-177 66-127 (161)
8 TIGR01337 apcB allophycocyanin 58.7 26 0.00056 29.3 5.4 55 122-177 65-127 (167)
9 PF05676 NDUF_B7: NADH-ubiquin 45.8 17 0.00038 26.5 2.1 35 134-168 17-51 (66)
10 PF08991 DUF1903: Domain of un 41.2 15 0.00032 26.8 1.2 36 141-177 6-41 (67)
11 KOG3458 NADH:ubiquinone oxidor 38.6 26 0.00057 30.0 2.4 40 135-174 74-114 (170)
12 PF14345 GDYXXLXY: GDYXXLXY pr 38.2 12 0.00027 29.4 0.4 18 115-132 19-36 (144)
13 KOG4624 Uncharacterized conser 37.8 49 0.0011 26.5 3.6 43 133-176 27-70 (104)
14 KOG4763 Ubiquinol-cytochrome c 37.6 22 0.00048 27.1 1.6 19 133-151 47-65 (77)
15 PF05240 APOBEC_C: APOBEC-like 33.1 22 0.00048 25.2 1.0 18 131-148 21-38 (55)
16 PF09717 CPW_WPC: Plasmodium f 32.4 6.8 0.00015 27.0 -1.7 20 165-189 3-22 (60)
17 CHL00090 apcD allophycocyanin 30.6 1.3E+02 0.0027 25.1 5.1 55 123-178 66-128 (161)
18 PF15199 DAOA: D-amino acid ox 24.8 42 0.00091 25.5 1.2 14 163-178 3-16 (82)
19 CHL00089 apcF allophycocyanin 23.0 1.9E+02 0.004 24.4 4.9 55 122-177 66-128 (169)
20 PF08057 Ery_res_leader2: Eryt 21.4 30 0.00066 18.7 -0.1 10 126-135 5-14 (14)
21 PF00502 Phycobilisome: Phycob 21.3 2.6E+02 0.0057 22.6 5.3 58 122-180 61-127 (157)
No 1
>KOG3057 consensus Cytochrome c oxidase, subunit VIb/COX12 [Energy production and conversion]
Probab=100.00 E-value=8.1e-35 Score=228.21 Aligned_cols=76 Identities=53% Similarity=0.932 Sum_probs=71.9
Q ss_pred ccccCCCcccccCCCCCCCCChhHHhHHHHhhhhHHHhHhhcCCChhhHHHHHHHHHhcChHHHHHHHHhhhccch
Q 029538 112 ASEETPDIKLETAPADFRFPTTNQTRHCFTRYIEYHRCVAAKGEGAPECDKFAKYYRALCPSDWVCFTKASCALIT 187 (192)
Q Consensus 112 ~~~~~~~~~l~TaP~DpRFPnqNQTrhCwq~Y~DYhRClkekGED~~~Ck~frk~Y~SLCP~~WVekWDEqR~y~t 187 (192)
.......+.|.|+|+|+||||+|||||||++|+|||||++++|+|+.+|++|+++|+||||.+||++||+||.-||
T Consensus 31 ~~~~~~~~~l~tap~d~RFP~~nqtrhCf~~y~dyhrC~~~~geD~~~Ck~f~~~y~SlCP~~WV~kWdeqre~G~ 106 (112)
T KOG3057|consen 31 GPETPKSKLLTTAPVDARFPNTNQTRHCFQRYVDYHRCIKAKGEDANPCKKFQKVYRSLCPGEWVEKWDEQRENGT 106 (112)
T ss_pred ccccccccccccccccccCCCcchhHHHHHHHHHHHHHHHHhcccchhHHHHHHHHHHhCcHHHHHHHHHhhhcCC
Confidence 3355667789999999999999999999999999999999999999999999999999999999999999999887
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=1.6e-34 Score=211.09 Aligned_cols=72 Identities=46% Similarity=0.844 Sum_probs=69.8
Q ss_pred cccccCCCCCCCCChhHHhHHHHhhhhHHHhHhhcCCChhhHHHHHHHHHhcChHHHHHHHHhhhccchhcc
Q 029538 119 IKLETAPADFRFPTTNQTRHCFTRYIEYHRCVAAKGEGAPECDKFAKYYRALCPSDWVCFTKASCALITCML 190 (192)
Q Consensus 119 ~~l~TaP~DpRFPnqNQTrhCwq~Y~DYhRClkekGED~~~Ck~frk~Y~SLCP~~WVekWDEqR~y~tc~~ 190 (192)
+.++|+|+||||||+|||+|||++|++||||++++|+|.++|++|++.|+++||.+||++||+||..||+-+
T Consensus 3 ~~~~t~~~D~RfP~~nq~k~Cw~~y~~y~~Cl~~~ged~~~C~~~~~~~es~Cp~~Wve~w~ekR~~g~f~~ 74 (75)
T cd00926 3 GPLTTAPFDPRFPNQNQTKHCWQRYVDYHRCIKAKGEDASPCKKFRRVYESLCPQEWLEKWDEQREEGTFPG 74 (75)
T ss_pred ccccCCCCCCCCCChHHHHHHHHHHHHHHHHHHHcCCchHHHHHHHHHHHHhCcHHHHHHHHHHHHhCCCCC
Confidence 569999999999999999999999999999999999999999999999999999999999999999999865
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=99.90 E-value=1.1e-24 Score=157.74 Aligned_cols=59 Identities=32% Similarity=0.735 Sum_probs=50.3
Q ss_pred CCCCChhHHhHHHHhhhhHHHhHhhcCC---------ChhhHHHHHHHHHhcChHHHHHHHHhhhccc
Q 029538 128 FRFPTTNQTRHCFTRYIEYHRCVAAKGE---------GAPECDKFAKYYRALCPSDWVCFTKASCALI 186 (192)
Q Consensus 128 pRFPnqNQTrhCwq~Y~DYhRClkekGE---------D~~~Ck~frk~Y~SLCP~~WVekWDEqR~y~ 186 (192)
||||++|||++||++||+||+|++.+|. +...|.+|++.|+++||.+||+|||++|.+.
T Consensus 1 ~rfP~~~~r~~Cw~arD~y~~Cl~~~~~~~~~~~~~~~~~~C~~~~~~ye~~Cp~sWv~~f~~~R~~~ 68 (76)
T PF02297_consen 1 PRFPNRNQRKKCWQARDDYFKCLDKNGEPDSEKEKKKDESACKYFRKNYESNCPSSWVKYFDEKRVYD 68 (76)
T ss_dssp -TS-SSB-HHHHHHHHHHHHHHHHHHHH------TTTTGGGGHHHHHHHHHHS-HHHHHHHHHH----
T ss_pred CCCCChHHHHHHHHHHHHHHHHHHHcCccccccccccchhhhHHHHHHHHHhCcHHHHHHHHHHhhHH
Confidence 7999999999999999999999999998 8999999999999999999999999998764
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=90.45 E-value=0.22 Score=30.54 Aligned_cols=31 Identities=23% Similarity=0.436 Sum_probs=26.4
Q ss_pred HHHhhhhHHHhHhhcCCChhhHHHHHHHHHh
Q 029538 139 CFTRYIEYHRCVAAKGEGAPECDKFAKYYRA 169 (192)
Q Consensus 139 Cwq~Y~DYhRClkekGED~~~Ck~frk~Y~S 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 4556788999999999999999999999984
No 5
>KOG4618 consensus Uncharacterized conserved protein [Function unknown]
Probab=89.83 E-value=0.54 Score=35.43 Aligned_cols=47 Identities=13% Similarity=0.374 Sum_probs=42.1
Q ss_pred hHHHHhhhhHHHhHhhcCCChhhHHHHHHHHHhcChHHHHHHHHhhhc
Q 029538 137 RHCFTRYIEYHRCVAAKGEGAPECDKFAKYYRALCPSDWVCFTKASCA 184 (192)
Q Consensus 137 rhCwq~Y~DYhRClkekGED~~~Ck~frk~Y~SLCP~~WVekWDEqR~ 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 45999999999999999999999999999999 899999887777654
No 6
>KOG4090 consensus Uncharacterized conserved protein [Function unknown]
Probab=63.06 E-value=8.1 Score=32.78 Aligned_cols=38 Identities=18% Similarity=0.619 Sum_probs=32.3
Q ss_pred HHhHHHHhhhhHHHhHhhcCCChhhHHHHHHHHHhcChH
Q 029538 135 QTRHCFTRYIEYHRCVAAKGEGAPECDKFAKYYRALCPS 173 (192)
Q Consensus 135 QTrhCwq~Y~DYhRClkekGED~~~Ck~frk~Y~SLCP~ 173 (192)
|.+-|+----.|..|+...|.|.+.|.+|....+ -|=.
T Consensus 114 ~~~~C~~e~kqF~dCa~~~~~d~slC~~f~e~Lk-~Ck~ 151 (157)
T KOG4090|consen 114 QQQPCFIEIKQFLDCAQNQGSDISLCEGYNEMLK-QCKK 151 (157)
T ss_pred hcCchHHHHHHHHHHHHhcCcchHHHHHHHHHHH-HHHH
Confidence 4567999999999999999999999999988765 4543
No 7
>CHL00088 apcB allophycocyanin beta subunit
Probab=61.12 E-value=16 Score=30.41 Aligned_cols=54 Identities=17% Similarity=0.243 Sum_probs=39.6
Q ss_pred cCCCCCCCCChhHHhHHHHhhhhHHHhHh--hcCCC----hhhH-HHHHHHHHhc-ChHHHHH
Q 029538 123 TAPADFRFPTTNQTRHCFTRYIEYHRCVA--AKGEG----APEC-DKFAKYYRAL-CPSDWVC 177 (192)
Q Consensus 123 TaP~DpRFPnqNQTrhCwq~Y~DYhRClk--ekGED----~~~C-k~frk~Y~SL-CP~~WVe 177 (192)
+.|....+++.+ ...||.-+.-|-||+. ...+| ...| .-+|-.|++| ||..|+-
T Consensus 66 ~~~Gg~~y~~~r-~~~C~RD~~~~LR~itYaivaGd~~~L~e~~L~GlrE~y~~Lgvp~~~~i 127 (161)
T CHL00088 66 TRPGGNMYTTRR-YAACIRDLDYYLRYATYGMLAGDPSILDERVLNGLKETYNSLGVPIGATI 127 (161)
T ss_pred cCCCCCccChHH-HHHHHHHHhhhccceeeeeecCCchHHHHHHHHHHHHHHHHhCCCHHHHH
Confidence 456666665433 7789999999999986 22333 3446 7899999996 9999973
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=58.73 E-value=26 Score=29.29 Aligned_cols=55 Identities=15% Similarity=0.211 Sum_probs=41.3
Q ss_pred ccCCCCCCCCChhHHhHHHHhhhhHHHhHh--hcCCC----hhhH-HHHHHHHHhc-ChHHHHH
Q 029538 122 ETAPADFRFPTTNQTRHCFTRYIEYHRCVA--AKGEG----APEC-DKFAKYYRAL-CPSDWVC 177 (192)
Q Consensus 122 ~TaP~DpRFPnqNQTrhCwq~Y~DYhRClk--ekGED----~~~C-k~frk~Y~SL-CP~~WVe 177 (192)
-+.|....||+.+ ...||.-+..|-||+. ...+| ...| .-+|-.|++| ||..|+-
T Consensus 65 l~~~GG~~y~~~r-~~aC~RD~~~~LR~itYailaGd~~~L~~~~L~GlrE~y~~LgvP~~~~v 127 (167)
T TIGR01337 65 LIRPGGNAYTTRR-YAACLRDIDYYLRYATYAIIAGDNSILEERVLNGLKETYNSLGVPIGPTV 127 (167)
T ss_pred cCCCCCCCCCHHH-HHHHHHHHHHHhhhhheeeecCCchHHHHHHHHHHHHHHHHcCCCHHHHH
Confidence 3457777887655 8889999999999986 22333 3445 7789999995 9999974
No 9
>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=45.78 E-value=17 Score=26.49 Aligned_cols=35 Identities=14% Similarity=0.209 Sum_probs=30.3
Q ss_pred hHHhHHHHhhhhHHHhHhhcCCChhhHHHHHHHHH
Q 029538 134 NQTRHCFTRYIEYHRCVAAKGEGAPECDKFAKYYR 168 (192)
Q Consensus 134 NQTrhCwq~Y~DYhRClkekGED~~~Ck~frk~Y~ 168 (192)
.+|-.|--.++.|++|.+.+-.-.-.|...++.|.
T Consensus 17 ~~RDyCAh~Li~l~kCrr~~~p~~~~C~~erH~y~ 51 (66)
T PF05676_consen 17 QYRDYCAHLLIPLNKCRRDNFPFPWKCEHERHEYE 51 (66)
T ss_pred hhhhhHHHHHHHHHHHHHhCCCCcccCCcchhhHH
Confidence 46789999999999999887766678999998887
No 10
>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=41.24 E-value=15 Score=26.80 Aligned_cols=36 Identities=8% Similarity=0.328 Sum_probs=25.0
Q ss_pred HhhhhHHHhHhhcCCChhhHHHHHHHHHhcChHHHHH
Q 029538 141 TRYIEYHRCVAAKGEGAPECDKFAKYYRALCPSDWVC 177 (192)
Q Consensus 141 q~Y~DYhRClkekGED~~~Ck~frk~Y~SLCP~~WVe 177 (192)
..-..-++|+..+|-|...|..+...|+. |=..|.+
T Consensus 6 ~~Ac~iq~CL~~N~Yd~~kC~~~i~~l~~-Cck~~y~ 41 (67)
T PF08991_consen 6 KEACAIQKCLQRNNYDESKCQDYIDALYE-CCKKFYE 41 (67)
T ss_dssp HHHHHHHHHHHHTTT-CCCTHHHHHHHHH-HHTTS--
T ss_pred HHHHHHHHHHHHcCCCHHHHHHHHHHHHH-HHHHHHH
Confidence 33346678999999999999999998884 4455543
No 11
>KOG3458 consensus NADH:ubiquinone oxidoreductase, NDUFA8/PGIV/19 kDa subunit [Energy production and conversion]
Probab=38.56 E-value=26 Score=30.02 Aligned_cols=40 Identities=18% Similarity=0.499 Sum_probs=33.2
Q ss_pred HHhHHHHhhhhHHHhHhhcC-CChhhHHHHHHHHHhcChHH
Q 029538 135 QTRHCFTRYIEYHRCVAAKG-EGAPECDKFAKYYRALCPSD 174 (192)
Q Consensus 135 QTrhCwq~Y~DYhRClkekG-ED~~~Ck~frk~Y~SLCP~~ 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 34789999999999998775 45788999999999988874
No 12
>PF14345 GDYXXLXY: GDYXXLXY protein
Probab=38.24 E-value=12 Score=29.42 Aligned_cols=18 Identities=33% Similarity=0.394 Sum_probs=14.2
Q ss_pred cCCCcccccCCCCCCCCC
Q 029538 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 346678999999999553
No 13
>KOG4624 consensus Uncharacterized conserved protein [Function unknown]
Probab=37.77 E-value=49 Score=26.53 Aligned_cols=43 Identities=21% Similarity=0.482 Sum_probs=32.1
Q ss_pred hhHHhHHHHhhhhHHHhHhhcC-CChhhHHHHHHHHHhcChHHHH
Q 029538 133 TNQTRHCFTRYIEYHRCVAAKG-EGAPECDKFAKYYRALCPSDWV 176 (192)
Q Consensus 133 qNQTrhCwq~Y~DYhRClkekG-ED~~~Ck~frk~Y~SLCP~~WV 176 (192)
+..|..|-+.+.+|-.|.+..| .....|+.....+. -|-.+|.
T Consensus 27 kakt~~C~~~v~~~a~C~k~~~v~vv~TCrkq~~elk-~Cl~~~~ 70 (104)
T KOG4624|consen 27 KAKTEKCSEFVQDFADCAKASGVSVVPTCRKQNSELK-ECLTQYY 70 (104)
T ss_pred HHHHHHHHHHHHHHHHHHhcCCeeeehhhHHHHHHHH-HHHHHHh
Confidence 4556899999999999999887 34566777777666 4655553
No 14
>KOG4763 consensus Ubiquinol-cytochrome c reductase hinge protein [Energy production and conversion]
Probab=37.59 E-value=22 Score=27.09 Aligned_cols=19 Identities=26% Similarity=0.866 Sum_probs=16.1
Q ss_pred hhHHhHHHHhhhhHHHhHh
Q 029538 133 TNQTRHCFTRYIEYHRCVA 151 (192)
Q Consensus 133 qNQTrhCwq~Y~DYhRClk 151 (192)
.+--.||-+-|-|||.|++
T Consensus 47 s~tee~Ct~e~fDy~h~~D 65 (77)
T KOG4763|consen 47 SSTEEHCTGEYFDYWHCLD 65 (77)
T ss_pred cccchhhHHHHHHHHHHHH
Confidence 4456899999999999986
No 15
>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=33.07 E-value=22 Score=25.21 Aligned_cols=18 Identities=11% Similarity=0.425 Sum_probs=11.6
Q ss_pred CChhHHhHHHHhhhhHHH
Q 029538 131 PTTNQTRHCFTRYIEYHR 148 (192)
Q Consensus 131 PnqNQTrhCwq~Y~DYhR 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 445678999999999864
No 16
>PF09717 CPW_WPC: Plasmodium falciparum domain of unknown function (CPW_WPC); InterPro: IPR006387 This entry represents a domain of about 61 residues in length with six well-conserved cysteine residues and six well-conserved aromatic sites. The domain can be found in tandem repeats. It is named for motifs of CPxxW and (less well conserved) WPC. Its function is unknown.
Probab=32.37 E-value=6.8 Score=27.03 Aligned_cols=20 Identities=25% Similarity=0.773 Sum_probs=14.0
Q ss_pred HHHHhcChHHHHHHHHhhhccchhc
Q 029538 165 KYYRALCPSDWVCFTKASCALITCM 189 (192)
Q Consensus 165 k~Y~SLCP~~WVekWDEqR~y~tc~ 189 (192)
+.|...||..|+ +.+-+.|.
T Consensus 3 rdys~~CP~~W~-----~~~~~~C~ 22 (60)
T PF09717_consen 3 RDYSQPCPEGWI-----LSDDGSCI 22 (60)
T ss_pred Cccccccccccc-----cCCCCeEc
Confidence 458889999999 44444453
No 17
>CHL00090 apcD allophycocyanin gamma subunit
Probab=30.56 E-value=1.3e+02 Score=25.10 Aligned_cols=55 Identities=18% Similarity=0.153 Sum_probs=39.7
Q ss_pred cCCCCCCCCChhHHhHHHHhhhhHHHhHh--hcCCCh----hhH-HHHHHHHHhc-ChHHHHHH
Q 029538 123 TAPADFRFPTTNQTRHCFTRYIEYHRCVA--AKGEGA----PEC-DKFAKYYRAL-CPSDWVCF 178 (192)
Q Consensus 123 TaP~DpRFPnqNQTrhCwq~Y~DYhRClk--ekGED~----~~C-k~frk~Y~SL-CP~~WVek 178 (192)
+.|...-||+ .+...||.-+..|-||+. ...+|. +.| .-+|-.|++| ||..|+-.
T Consensus 66 ~~~Gg~~y~~-~r~~aC~RD~~~~LR~itYa~lagd~~~L~~~~l~GlrE~Y~~LgvP~~~~v~ 128 (161)
T CHL00090 66 IAPGGNASGS-RQRSLCLRDYGWYLRLITYGVLAGDKNSIEKIGIIGVREMYNSLGVPIIGMVD 128 (161)
T ss_pred cCCCCCCcch-HHHHHHHHhHHHhhhhheeeeecCChHHHHHHHHHHHHHHHHHhCCChHHHHH
Confidence 3566666766 448999999999999986 223332 233 5689999999 99999743
No 18
>PF15199 DAOA: D-amino acid oxidase activator
Probab=24.79 E-value=42 Score=25.49 Aligned_cols=14 Identities=43% Similarity=1.127 Sum_probs=11.1
Q ss_pred HHHHHHhcChHHHHHH
Q 029538 163 FAKYYRALCPSDWVCF 178 (192)
Q Consensus 163 frk~Y~SLCP~~WVek 178 (192)
+|+.-+|||| ||.+
T Consensus 3 qrhlqrslcp--wvsy 16 (82)
T PF15199_consen 3 QRHLQRSLCP--WVSY 16 (82)
T ss_pred HHHHHHhhcc--hhhh
Confidence 5778899999 7765
No 19
>CHL00089 apcF allophycocyanin beta 18 subunit
Probab=23.00 E-value=1.9e+02 Score=24.44 Aligned_cols=55 Identities=15% Similarity=0.166 Sum_probs=40.5
Q ss_pred ccCCCCCCCCChhHHhHHHHhhhhHHHhHh--hcCCC----hhh-HHHHHHHHHh-cChHHHHH
Q 029538 122 ETAPADFRFPTTNQTRHCFTRYIEYHRCVA--AKGEG----APE-CDKFAKYYRA-LCPSDWVC 177 (192)
Q Consensus 122 ~TaP~DpRFPnqNQTrhCwq~Y~DYhRClk--ekGED----~~~-Ck~frk~Y~S-LCP~~WVe 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 4567778887655 8899999999999986 22222 222 3568889999 89999974
No 20
>PF08057 Ery_res_leader2: Erythromycin resistance leader peptide; InterPro: IPR012559 This family consists of erythromycin resistance gene leader peptides. These leader peptides are involved in the transcriptional attenuation control of the synthesis of the macrolide-lincosamide -streptogramin B resistance protein. It acts as a transcriptional attenuator, in contrast to other inducible erm genes. The mRNA leader sequence can fold in either of two mutually exclusive conformations, one of which is postulated to form in the absence of induction, and to contain two rho factor-independent terminators [].; GO: 0046677 response to antibiotic
Probab=21.35 E-value=30 Score=18.74 Aligned_cols=10 Identities=60% Similarity=0.933 Sum_probs=7.2
Q ss_pred CCCCCCChhH
Q 029538 126 ADFRFPTTNQ 135 (192)
Q Consensus 126 ~DpRFPnqNQ 135 (192)
.--|||.-||
T Consensus 5 mrlrfptlnq 14 (14)
T PF08057_consen 5 MRLRFPTLNQ 14 (14)
T ss_pred eeeeccccCC
Confidence 3458998886
No 21
>PF00502 Phycobilisome: Phycobilisome protein; InterPro: IPR012128 Cyanobacteria and red algae harvest light through water-soluble complexes, called phycobilisomes, which are attached to the outer face of the thylakoid membrane []. These complexes are capable of transferring the absorbed energy to the photosynthetic reaction centre with greater than 95% efficiency. Phycobilisomes contain various photosynthetic light harvesting proteins known as biliproteins, and linker proteins which help assemble the structure. The two main structural elements of the complex are a core located near the photosynthetic reaction centre, and rods attached to this core. Allophycocyanin is the major component of the core, while the rods contain phycocyanins, phycoerythrins and linker proteins. The rod biliproteins harvest photons, with the excitation energy being passed through the rods into the allophycocyanin in the core. Other core biliproteins subsequently pass this energy to chlorophyll within the thylakoid membrane. This entry represents the alpha and beta subunits found in biliproteins from cyanobacteria and red algae. Structural studies indicate that the basic structural unit of most biliproteins is a heterodimer composed of these alpha and beta subunits [, , , ]. The full protein is a ring-like trimer assembly of these heterodimers. Each subunit of the heterodimer has eight helices and binds chromophores through thioester bonds formed at particular cysteine residues. These chromophores, also known as bilins, are open-chain tetrapyrroles whose number and type vary with the particular biliprotein eg R-phyocerythrin binds five phycoerythrobilins per heterodimer, while allophycocyanin binds two phycocyanobilins per heterodimer.; GO: 0015979 photosynthesis, 0030089 phycobilisome; PDB: 2VML_I 2VJR_A 1KTP_B 3L0F_B 1JBO_B 3KVS_B 1PHN_B 3BRP_B 2C7K_B 2C7L_B ....
Probab=21.25 E-value=2.6e+02 Score=22.57 Aligned_cols=58 Identities=24% Similarity=0.425 Sum_probs=36.4
Q ss_pred ccCCCCCCCCChhHHhHHHHhhhhHHHhHh---hcCCCh---hhH-HHHHHHHHhc-ChHHH-HHHHH
Q 029538 122 ETAPADFRFPTTNQTRHCFTRYIEYHRCVA---AKGEGA---PEC-DKFAKYYRAL-CPSDW-VCFTK 180 (192)
Q Consensus 122 ~TaP~DpRFPnqNQTrhCwq~Y~DYhRClk---ekGED~---~~C-k~frk~Y~SL-CP~~W-VekWD 180 (192)
-+.|....|+... +..||.-...|.||+. .-|+.. ..+ .+++..|+++ +|..| |.-..
T Consensus 61 l~~~gg~~y~~~~-~~~C~RD~~~~LR~i~ya~l~gd~~~l~~~~l~~l~ei~~al~vp~~~~v~al~ 127 (157)
T PF00502_consen 61 LTQPGGNLYPSRR-REACWRDIWHYLRYITYAMLAGDTDPLDERGLNGLREIYRALGVPIDAYVEALQ 127 (157)
T ss_dssp GGSTTSTTSSHHH-HHHHHHHHHHHHHHHHHHHHHTSSHHHHHHTTTTHHHHHHHHT--HHHHHHHHH
T ss_pred cccccccccchHH-HHHHHHHHHHHHHHHHHHHHhcchhHHHHHHHHHHHHHHHHHcCCchHHHHHHH
Confidence 4556666666544 4899999999999876 223321 112 3599999995 99877 44344
Done!