Query 033425
Match_columns 119
No_of_seqs 104 out of 178
Neff 4.1
Searched_HMMs 46136
Date Fri Mar 29 13:44:39 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/033425.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/033425hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF02297 COX6B: Cytochrome oxi 99.9 1.7E-25 3.6E-30 151.3 4.2 75 17-94 2-76 (76)
2 cd00926 Cyt_c_Oxidase_VIb Cyto 99.8 1.3E-18 2.9E-23 118.6 5.9 54 19-84 15-68 (75)
3 KOG3057 Cytochrome c oxidase, 99.1 2E-10 4.4E-15 84.2 5.8 50 19-80 50-99 (112)
4 KOG4618 Uncharacterized conser 85.8 1.6 3.4E-05 30.3 4.0 41 26-79 23-63 (74)
5 PF06747 CHCH: CHCH domain; I 83.2 1 2.2E-05 25.5 1.9 28 32-72 6-33 (35)
6 PLN03079 Uncharacterized prote 82.5 2.4 5.2E-05 30.4 4.0 17 82-98 60-76 (91)
7 KOG4695 Uncharacterized conser 65.2 16 0.00035 27.4 4.7 46 25-86 46-91 (122)
8 PF10762 DUF2583: Protein of u 58.2 3.5 7.5E-05 29.5 0.1 13 74-86 74-86 (89)
9 PF08583 Cmc1: Cytochrome c ox 46.6 72 0.0016 20.0 5.5 43 21-75 7-49 (69)
10 PF10200 Ndufs5: NADH:ubiquino 45.7 98 0.0021 22.2 5.9 60 26-98 32-92 (96)
11 PRK10692 hypothetical protein; 41.6 9.8 0.00021 27.4 0.3 12 74-85 74-85 (92)
12 KOG3466 NADH:ubiquinone oxidor 40.9 17 0.00037 28.3 1.5 34 85-119 55-88 (157)
13 KOG3458 NADH:ubiquinone oxidor 33.5 37 0.0008 26.8 2.3 52 20-82 71-128 (170)
14 KOG4114 Cytochrome c oxidase a 32.6 68 0.0015 22.2 3.3 24 56-80 41-64 (73)
15 KOG4624 Uncharacterized conser 28.8 2.1E+02 0.0046 21.0 5.5 62 19-95 25-86 (104)
16 PRK12271 rps10p 30S ribosomal 27.3 42 0.00091 24.0 1.6 18 90-108 25-42 (102)
17 PF03221 HTH_Tnp_Tc5: Tc5 tran 26.8 36 0.00078 20.7 1.0 17 71-87 48-64 (66)
18 PF08991 DUF1903: Domain of un 26.7 43 0.00093 22.4 1.5 37 27-76 4-40 (67)
19 TIGR01046 S10_Arc_S20_Euk ribo 24.5 51 0.0011 23.4 1.6 16 92-108 26-41 (99)
20 COG0051 RpsJ Ribosomal protein 23.7 57 0.0012 23.8 1.7 18 90-108 27-44 (104)
21 PTZ00039 40S ribosomal protein 23.7 52 0.0011 24.1 1.6 18 90-108 40-57 (115)
22 PF05254 UPF0203: Uncharacteri 22.4 1E+02 0.0023 20.5 2.7 23 58-81 7-30 (68)
No 1
>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=1.7e-25 Score=151.35 Aligned_cols=75 Identities=25% Similarity=0.531 Sum_probs=52.7
Q ss_pred chhchHHHHHHHHcchhhHhhhhhcCCCCcchhhhcCCCchhhhHHHHHHHHHhcHHHHHHHHHHHHHHHHHHHHHHh
Q 033425 17 TDVLLKARQACYKSRDAFYDCLEKESNKKPTEIASVGLLYPAECKALRAQFVNHCRASWVKHFDRLYCKNKRVTRLLD 94 (119)
Q Consensus 17 ~~~~r~~Rk~CW~aRD~YF~CLDk~~i~~p~e~~~v~~~~~~~C~~er~~FE~~C~~SWVkyF~rr~~~~kr~~kll~ 94 (119)
..|++++|++||++||.||.|||.+++.++. +.+..+.+.|+.+++.||++||.|||+||++++..++|.++++.
T Consensus 2 rfP~~~~r~~Cw~arD~y~~Cl~~~~~~~~~---~~~~~~~~~C~~~~~~ye~~Cp~sWv~~f~~~R~~~~~k~~~~~ 76 (76)
T PF02297_consen 2 RFPNRNQRKKCWQARDDYFKCLDKNGEPDSE---KEKKKDESACKYFRKNYESNCPSSWVKYFDEKRVYDQRKEGTLK 76 (76)
T ss_dssp TS-SSB-HHHHHHHHHHHHHHHHHHHH---------TTTTGGGGHHHHHHHHHHS-HHHHHHHHHH-----HHHT---
T ss_pred CCCChHHHHHHHHHHHHHHHHHHHcCccccc---cccccchhhhHHHHHHHHHhCcHHHHHHHHHHhhHHHHHhhccC
Confidence 3478999999999999999999999985543 22334568899999999999999999999999999999888763
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=99.76 E-value=1.3e-18 Score=118.59 Aligned_cols=54 Identities=15% Similarity=0.490 Sum_probs=48.1
Q ss_pred hchHHHHHHHHcchhhHhhhhhcCCCCcchhhhcCCCchhhhHHHHHHHHHhcHHHHHHHHHHHHH
Q 033425 19 VLLKARQACYKSRDAFYDCLEKESNKKPTEIASVGLLYPAECKALRAQFVNHCRASWVKHFDRLYC 84 (119)
Q Consensus 19 ~~r~~Rk~CW~aRD~YF~CLDk~~i~~p~e~~~v~~~~~~~C~~er~~FE~~C~~SWVkyF~rr~~ 84 (119)
|++++|+.||.+||.||.||+++++.. +.|+.+++.|+.+||.|||+||++++.
T Consensus 15 P~~nq~k~Cw~~y~~y~~Cl~~~ged~------------~~C~~~~~~~es~Cp~~Wve~w~ekR~ 68 (75)
T cd00926 15 PNQNQTKHCWQRYVDYHRCIKAKGEDA------------SPCKKFRRVYESLCPQEWLEKWDEQRE 68 (75)
T ss_pred CChHHHHHHHHHHHHHHHHHHHcCCch------------HHHHHHHHHHHHhCcHHHHHHHHHHHH
Confidence 679999999999999999999987432 679999999999999999999995543
No 3
>KOG3057 consensus Cytochrome c oxidase, subunit VIb/COX12 [Energy production and conversion]
Probab=99.09 E-value=2e-10 Score=84.23 Aligned_cols=50 Identities=16% Similarity=0.568 Sum_probs=45.2
Q ss_pred hchHHHHHHHHcchhhHhhhhhcCCCCcchhhhcCCCchhhhHHHHHHHHHhcHHHHHHHHH
Q 033425 19 VLLKARQACYKSRDAFYDCLEKESNKKPTEIASVGLLYPAECKALRAQFVNHCRASWVKHFD 80 (119)
Q Consensus 19 ~~r~~Rk~CW~aRD~YF~CLDk~~i~~p~e~~~v~~~~~~~C~~er~~FE~~C~~SWVkyF~ 80 (119)
|+-.+++.||.+++.|+.|++.++.+ ...|+.+++.|+..||.+||++|+
T Consensus 50 P~~nqtrhCf~~y~dyhrC~~~~geD------------~~~Ck~f~~~y~SlCP~~WV~kWd 99 (112)
T KOG3057|consen 50 PNTNQTRHCFQRYVDYHRCIKAKGED------------ANPCKKFQKVYRSLCPGEWVEKWD 99 (112)
T ss_pred CCcchhHHHHHHHHHHHHHHHHhccc------------chhHHHHHHHHHHhCcHHHHHHHH
Confidence 56689999999999999999998732 377999999999999999999998
No 4
>KOG4618 consensus Uncharacterized conserved protein [Function unknown]
Probab=85.77 E-value=1.6 Score=30.28 Aligned_cols=41 Identities=20% Similarity=0.567 Sum_probs=34.1
Q ss_pred HHHHcchhhHhhhhhcCCCCcchhhhcCCCchhhhHHHHHHHHHhcHHHHHHHH
Q 033425 26 ACYKSRDAFYDCLEKESNKKPTEIASVGLLYPAECKALRAQFVNHCRASWVKHF 79 (119)
Q Consensus 26 ~CW~aRD~YF~CLDk~~i~~p~e~~~v~~~~~~~C~~er~~FE~~C~~SWVkyF 79 (119)
-|...-++=|.||++|+-. +++|..--..|. +|-.-|-+-=
T Consensus 23 PCl~es~aSfkCLeennyD------------RsKCq~yFd~Yk-eCKkfwn~ar 63 (74)
T KOG4618|consen 23 PCLLESSASFKCLEENNYD------------RSKCQDYFDVYK-ECKKFWNEAR 63 (74)
T ss_pred hHHHHHHHHHHHHHhcCcc------------HHHHHHHHHHHH-HHHHHHHHHH
Confidence 5999999999999998843 488999988886 8998887543
No 5
>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=83.24 E-value=1 Score=25.46 Aligned_cols=28 Identities=21% Similarity=0.611 Sum_probs=21.2
Q ss_pred hhhHhhhhhcCCCCcchhhhcCCCchhhhHHHHHHHHHhcH
Q 033425 32 DAFYDCLEKESNKKPTEIASVGLLYPAECKALRAQFVNHCR 72 (119)
Q Consensus 32 D~YF~CLDk~~i~~p~e~~~v~~~~~~~C~~er~~FE~~C~ 72 (119)
.+|+.||+.|+... ..|..+.+.|.+ |.
T Consensus 6 ~~~~~Cl~~n~~~~------------~~C~~~~~~~~~-C~ 33 (35)
T PF06747_consen 6 KAYLACLKENNFDW------------SKCRKEFKAYKE-CR 33 (35)
T ss_dssp HHHHHHHHCH-SST------------CCCHHHHHHHHH-HH
T ss_pred HHHHHHHHHCCCcH------------HhhHHHHHHHHH-Hh
Confidence 47999999987532 679999999974 54
No 6
>PLN03079 Uncharacterized protein At4g33100; Provisional
Probab=82.54 E-value=2.4 Score=30.41 Aligned_cols=17 Identities=18% Similarity=0.368 Sum_probs=12.2
Q ss_pred HHHHHHHHHHHHhcCCC
Q 033425 82 LYCKNKRVTRLLDDGGE 98 (119)
Q Consensus 82 r~~~~kr~~kll~ega~ 98 (119)
+...++-+.+||++...
T Consensus 60 ~aL~ek~I~~lLe~ar~ 76 (91)
T PLN03079 60 EHLEDKHLSQILEVDGT 76 (91)
T ss_pred HHHHHcChHHHHHHHhh
Confidence 44457778888888665
No 7
>KOG4695 consensus Uncharacterized conserved protein [Function unknown]
Probab=65.16 E-value=16 Score=27.42 Aligned_cols=46 Identities=15% Similarity=0.437 Sum_probs=33.6
Q ss_pred HHHHHcchhhHhhhhhcCCCCcchhhhcCCCchhhhHHHHHHHHHhcHHHHHHHHHHHHHHH
Q 033425 25 QACYKSRDAFYDCLEKESNKKPTEIASVGLLYPAECKALRAQFVNHCRASWVKHFDRLYCKN 86 (119)
Q Consensus 25 k~CW~aRD~YF~CLDk~~i~~p~e~~~v~~~~~~~C~~er~~FE~~C~~SWVkyF~rr~~~~ 86 (119)
..|-.-=-..|+||-+|.-.+ ..|.++...|- +|.+ +|-++.+...
T Consensus 46 ~tC~qEm~vlfaClK~nEF~d------------~~C~Kei~~f~-dC~~---~ya~ea~~~r 91 (122)
T KOG4695|consen 46 ATCIQEMSVLFACLKQNEFRD------------DACRKEIQGFL-DCAA---RYAQEARKMR 91 (122)
T ss_pred hHHHHHHHHHHHHHHhccccc------------hHHHHHHHHHH-HHHH---HHHHHHHHHH
Confidence 468887888999999975432 67999999997 8876 4555444333
No 8
>PF10762 DUF2583: Protein of unknown function (DUF2583) ; InterPro: IPR019698 Some members in this entry are annotated as YchH however currently no function is known.
Probab=58.23 E-value=3.5 Score=29.51 Aligned_cols=13 Identities=54% Similarity=1.012 Sum_probs=9.5
Q ss_pred HHHHHHHHHHHHH
Q 033425 74 SWVKHFDRLYCKN 86 (119)
Q Consensus 74 SWVkyF~rr~~~~ 86 (119)
=||+|||+|..++
T Consensus 74 wWvkh~DkRcrr~ 86 (89)
T PF10762_consen 74 WWVKHFDKRCRRN 86 (89)
T ss_pred HHHHhhhHhhccc
Confidence 4999999765443
No 9
>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=46.58 E-value=72 Score=19.97 Aligned_cols=43 Identities=19% Similarity=0.445 Sum_probs=33.7
Q ss_pred hHHHHHHHHcchhhHhhhhhcCCCCcchhhhcCCCchhhhHHHHHHHHHhcHHHH
Q 033425 21 LKARQACYKSRDAFYDCLEKESNKKPTEIASVGLLYPAECKALRAQFVNHCRASW 75 (119)
Q Consensus 21 r~~Rk~CW~aRD~YF~CLDk~~i~~p~e~~~v~~~~~~~C~~er~~FE~~C~~SW 75 (119)
...+..|.+.=++|-.|... .... +-..|.+++..+. .|...+
T Consensus 7 ~~~~~~C~~~i~~~~~C~~~-~~~~----------~~~~C~~~~~~m~-~Cl~~~ 49 (69)
T PF08583_consen 7 EEAHKKCADEIEAFAECHKD-RTFK----------FVGKCREEKKAMN-ECLKEE 49 (69)
T ss_pred HHHHHHhHHHHHHHHHHHhc-chHH----------HHHhhhHHHHHHH-HHHHHH
Confidence 34679999999999999988 3221 1256999999997 899876
No 10
>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=45.68 E-value=98 Score=22.22 Aligned_cols=60 Identities=18% Similarity=0.400 Sum_probs=38.2
Q ss_pred HHHHcchhhHhhhhhcCCCCcchhhhcCCCchhhhHHHHHHHHHhcHHHHHHHHHH-HHHHHHHHHHHHhcCCC
Q 033425 26 ACYKSRDAFYDCLEKESNKKPTEIASVGLLYPAECKALRAQFVNHCRASWVKHFDR-LYCKNKRVTRLLDDGGE 98 (119)
Q Consensus 26 ~CW~aRD~YF~CLDk~~i~~p~e~~~v~~~~~~~C~~er~~FE~~C~~SWVkyF~r-r~~~~kr~~kll~ega~ 98 (119)
.|..==-+|..|+...+... .++.|..+...|. -|..- .|=+.| +-...+| ++++.+|--
T Consensus 32 RC~~FE~e~i~C~~~~G~~r----------~kKeC~~e~EDy~-EClh~-~Ke~~R~~aI~kqR-~K~~keGk~ 92 (96)
T PF10200_consen 32 RCHPFEKEWIECAEAYGQTR----------GKKECKLELEDYY-ECLHH-TKEMKRMRAIRKQR-DKQIKEGKY 92 (96)
T ss_pred chHHHHHHHHHHHHHHcccc----------hhhhchhHHhHHH-HHHhh-HHHHHHHHHHHHHH-HHHHHccCC
Confidence 46655567889998766432 2478999999998 57642 222223 2334444 788888766
No 11
>PRK10692 hypothetical protein; Provisional
Probab=41.64 E-value=9.8 Score=27.38 Aligned_cols=12 Identities=33% Similarity=0.924 Sum_probs=9.1
Q ss_pred HHHHHHHHHHHH
Q 033425 74 SWVKHFDRLYCK 85 (119)
Q Consensus 74 SWVkyF~rr~~~ 85 (119)
=||||||+++.+
T Consensus 74 wwvkh~d~rcrr 85 (92)
T PRK10692 74 WWVRHYDKRCRR 85 (92)
T ss_pred HHHhhccHhhcc
Confidence 499999976543
No 12
>KOG3466 consensus NADH:ubiquinone oxidoreductase, NDUFB9/B22 subunit [Energy production and conversion]
Probab=40.87 E-value=17 Score=28.32 Aligned_cols=34 Identities=35% Similarity=0.548 Sum_probs=26.4
Q ss_pred HHHHHHHHHhcCCCcccCCCCCCCcccccCCCCCC
Q 033425 85 KNKRVTRLLDDGGETRRGPLTLPQPYTFKPSSGSS 119 (119)
Q Consensus 85 ~~kr~~kll~ega~~~~g~~~~p~~~~~~~~~~~~ 119 (119)
+-.+..+||++|.. .==.---|+||.|-=+||.|
T Consensus 55 D~~k~~~LLa~ge~-E~w~~rHpqP~ifp~spGGs 88 (157)
T KOG3466|consen 55 DVDKAIRLLAEGER-ELWEWRHPQPYIFPDSPGGS 88 (157)
T ss_pred hHHHHHHHHHHHHH-HHHhhcCCCccccCCCCCCC
Confidence 45667899999887 44555679999999888865
No 13
>KOG3458 consensus NADH:ubiquinone oxidoreductase, NDUFA8/PGIV/19 kDa subunit [Energy production and conversion]
Probab=33.50 E-value=37 Score=26.77 Aligned_cols=52 Identities=19% Similarity=0.501 Sum_probs=40.5
Q ss_pred chHHHHHHHHcchhhHhhhhhcCCCCcchhhhcCCCchhhhHHHHHHHHHhcHHH--HH----HHHHHH
Q 033425 20 LLKARQACYKSRDAFYDCLEKESNKKPTEIASVGLLYPAECKALRAQFVNHCRAS--WV----KHFDRL 82 (119)
Q Consensus 20 ~r~~Rk~CW~aRD~YF~CLDk~~i~~p~e~~~v~~~~~~~C~~er~~FE~~C~~S--WV----kyF~rr 82 (119)
++.=-+.|-+-=|.|+.|+|..+ .+ + =+.|.++...|++-|+.- |+ -||.+-
T Consensus 71 lr~lkr~C~~e~~~y~~C~dyss-t~--~--------f~~Crk~Q~~fdkcv~~kl~w~RP~lGyfSk~ 128 (170)
T KOG3458|consen 71 LRDLKRSCLEEFTKYATCMDYSS-TN--E--------FSHCRKEQEAFDKCVPDKLNWTRPKLGYFSKL 128 (170)
T ss_pred HHHHHHHhhHHHHHHHHHHHHHh-hH--H--------HHHHHHHHHHHHHHhHhhcCCCCcccccccee
Confidence 45667889999999999999965 21 1 278999999999999874 65 378763
No 14
>KOG4114 consensus Cytochrome c oxidase assembly protein PET191 [Posttranslational modification, protein turnover, chaperones]
Probab=32.64 E-value=68 Score=22.20 Aligned_cols=24 Identities=38% Similarity=0.664 Sum_probs=19.3
Q ss_pred chhhhHHHHHHHHHhcHHHHHHHHH
Q 033425 56 YPAECKALRAQFVNHCRASWVKHFD 80 (119)
Q Consensus 56 ~~~~C~~er~~FE~~C~~SWVkyF~ 80 (119)
.|..|..+.+.|- .|-.|-|.-=+
T Consensus 41 vPeeC~al~~af~-dCKRslvDmrk 64 (73)
T KOG4114|consen 41 VPEECIALMKAFL-DCKRSLVDMRK 64 (73)
T ss_pred CcHHHHHHHHHHH-HHHHHHHHHHH
Confidence 3588999999997 89888886543
No 15
>KOG4624 consensus Uncharacterized conserved protein [Function unknown]
Probab=28.82 E-value=2.1e+02 Score=21.03 Aligned_cols=62 Identities=15% Similarity=0.375 Sum_probs=44.1
Q ss_pred hchHHHHHHHHcchhhHhhhhhcCCCCcchhhhcCCCchhhhHHHHHHHHHhcHHHHHHHHHHHHHHHHHHHHHHhc
Q 033425 19 VLLKARQACYKSRDAFYDCLEKESNKKPTEIASVGLLYPAECKALRAQFVNHCRASWVKHFDRLYCKNKRVTRLLDD 95 (119)
Q Consensus 19 ~~r~~Rk~CW~aRD~YF~CLDk~~i~~p~e~~~v~~~~~~~C~~er~~FE~~C~~SWVkyF~rr~~~~kr~~kll~e 95 (119)
.+++++..|=+.=-.|=.|...+++.. --.|.+++..|. .|...|.. |..|..+.| ..|+.|
T Consensus 25 n~kakt~~C~~~v~~~a~C~k~~~v~v-----------v~TCrkq~~elk-~Cl~~~~~--D~af~e~~r-d~yv~E 86 (104)
T KOG4624|consen 25 NLKAKTEKCSEFVQDFADCAKASGVSV-----------VPTCRKQNSELK-ECLTQYYN--DEAFLEECR-DEYVQE 86 (104)
T ss_pred HHHHHHHHHHHHHHHHHHHHhcCCeee-----------ehhhHHHHHHHH-HHHHHHhc--CHHHHHHHH-HHHHHH
Confidence 467888999999999999988876532 145999999997 89988732 334555555 444443
No 16
>PRK12271 rps10p 30S ribosomal protein S10P; Reviewed
Probab=27.35 E-value=42 Score=23.98 Aligned_cols=18 Identities=28% Similarity=0.497 Sum_probs=13.5
Q ss_pred HHHHhcCCCcccCCCCCCC
Q 033425 90 TRLLDDGGETRRGPLTLPQ 108 (119)
Q Consensus 90 ~kll~ega~~~~g~~~~p~ 108 (119)
......|+. .+||+.||-
T Consensus 25 ~~~k~~g~~-~~GPipLPt 42 (102)
T PRK12271 25 EIAEKTGVD-MSGPIPLPT 42 (102)
T ss_pred HHHHHcCCe-EECCCcCCc
Confidence 334456777 999999995
No 17
>PF03221 HTH_Tnp_Tc5: Tc5 transposase DNA-binding domain; InterPro: IPR006600 This entry represents a DNA-binding helix-turn-helix domain found in the pogo family of transposable elements, the centromere protein Cenp-B, and yeast PCD2. There is extensive sequence similarity between Cenp-B and transposase proteins encoded by the pogo superfamily of transposable elements, which includes the human Tigger and Jerky elements []. The HTH domain is composed of three alpha-helices, with the second and third helices connected via a turn comprise the helix-turn-helix motif. Helix 3 is termed the recognition helix as it binds the DNA major groove, as in other HTHs []. This conserved DNA-binding domain is found in the following proteins: Cenp-B (major centromere autoantigen B or centromere protein B), which appears to organise arrays of centromere satellite DNA into a higher order structure that then direct centromere formation and kinetochore assembly in mammalian chromosomes. The N terminus of Cenp-B contains two DNA-binding HTH domains, which bind to adjacent major grooves of DNA: a psq-type HTH domain followed by a CenpB-type HTH domain, which together bind specifically to the Cenp-B box, which occurs in alpha-satellite DNA in human centromeres []. Pogo family transposable elements includes both Tigger and Jerky elements []. Pogo contains two open reading frames flanked by inverted repeats. The N-terminal region of pogo transposase contains a Cenp-B-type HTH DNA-binding domain []. Mammalian jerky protein, involved in epileptic seizures in mice []. PDC2 (Pyruvate DeCarboxylase 2), which is a transcription factor required for the synthesis of the glycolytic enzyme pyruvate decarboxylase, required for high level expression of both the THI and the PDC genes. PDC2 may be important for a high basal level of PDC gene expression or play a positive role in the autoregulation control of PDC1 and PDC5 [, ]. ; PDB: 1HLV_A 1IUF_A.
Probab=26.76 E-value=36 Score=20.66 Aligned_cols=17 Identities=12% Similarity=0.350 Sum_probs=10.4
Q ss_pred cHHHHHHHHHHHHHHHH
Q 033425 71 CRASWVKHFDRLYCKNK 87 (119)
Q Consensus 71 C~~SWVkyF~rr~~~~k 87 (119)
-..+|+..|.+||....
T Consensus 48 ~s~~W~~~F~~Rh~i~~ 64 (66)
T PF03221_consen 48 ASKGWLDRFKKRHGIKL 64 (66)
T ss_dssp --CHHHHHHHHHTS---
T ss_pred cccHHHHHHHHHcCCCC
Confidence 34679999999885443
No 18
>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=26.70 E-value=43 Score=22.38 Aligned_cols=37 Identities=19% Similarity=0.512 Sum_probs=25.6
Q ss_pred HHHcchhhHhhhhhcCCCCcchhhhcCCCchhhhHHHHHHHHHhcHHHHH
Q 033425 27 CYKSRDAFYDCLEKESNKKPTEIASVGLLYPAECKALRAQFVNHCRASWV 76 (119)
Q Consensus 27 CW~aRD~YF~CLDk~~i~~p~e~~~v~~~~~~~C~~er~~FE~~C~~SWV 76 (119)
|=..-.+-..||++|+-. ++.|...-..|- .|-.+|.
T Consensus 4 C~~~Ac~iq~CL~~N~Yd------------~~kC~~~i~~l~-~Cck~~y 40 (67)
T PF08991_consen 4 CQKEACAIQKCLQRNNYD------------ESKCQDYIDALY-ECCKKFY 40 (67)
T ss_dssp THHHHHHHHHHHHHTTT-------------CCCTHHHHHHHH-HHHTTS-
T ss_pred hHHHHHHHHHHHHHcCCC------------HHHHHHHHHHHH-HHHHHHH
Confidence 344445778999998843 266999988887 5666663
No 19
>TIGR01046 S10_Arc_S20_Euk ribosomal protein S10(archaeal)/S20(eukaryotic). its equivalents in eukaryotes.
Probab=24.47 E-value=51 Score=23.36 Aligned_cols=16 Identities=31% Similarity=0.542 Sum_probs=12.4
Q ss_pred HHhcCCCcccCCCCCCC
Q 033425 92 LLDDGGETRRGPLTLPQ 108 (119)
Q Consensus 92 ll~ega~~~~g~~~~p~ 108 (119)
....|+. ..||+.||-
T Consensus 26 ak~~g~~-~~GPipLPt 41 (99)
T TIGR01046 26 AEKTGVR-MSGPVPLPT 41 (99)
T ss_pred HHHcCCE-EECCccCCc
Confidence 3446777 999999995
No 20
>COG0051 RpsJ Ribosomal protein S10 [Translation, ribosomal structure and biogenesis]
Probab=23.74 E-value=57 Score=23.79 Aligned_cols=18 Identities=28% Similarity=0.654 Sum_probs=13.9
Q ss_pred HHHHhcCCCcccCCCCCCC
Q 033425 90 TRLLDDGGETRRGPLTLPQ 108 (119)
Q Consensus 90 ~kll~ega~~~~g~~~~p~ 108 (119)
+.-...|+. .+||+.||-
T Consensus 27 e~akrtg~~-v~GPiPLPT 44 (104)
T COG0051 27 ETAKRTGAD-VKGPIPLPT 44 (104)
T ss_pred HHHHHhCCe-eeCCccCCC
Confidence 344457888 999999996
No 21
>PTZ00039 40S ribosomal protein S20; Provisional
Probab=23.72 E-value=52 Score=24.13 Aligned_cols=18 Identities=22% Similarity=0.392 Sum_probs=13.8
Q ss_pred HHHHhcCCCcccCCCCCCC
Q 033425 90 TRLLDDGGETRRGPLTLPQ 108 (119)
Q Consensus 90 ~kll~ega~~~~g~~~~p~ 108 (119)
......|+. .+||+.||-
T Consensus 40 ~~ak~~g~~-v~GPipLPt 57 (115)
T PTZ00039 40 TGAKEKNLK-VTGPVRMPV 57 (115)
T ss_pred HHHHHcCCE-eECCccCCc
Confidence 344457777 999999995
No 22
>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=22.37 E-value=1e+02 Score=20.52 Aligned_cols=23 Identities=26% Similarity=0.826 Sum_probs=19.0
Q ss_pred hhhHHHHHHHHHhcHHHHH-HHHHH
Q 033425 58 AECKALRAQFVNHCRASWV-KHFDR 81 (119)
Q Consensus 58 ~~C~~er~~FE~~C~~SWV-kyF~r 81 (119)
..|.+++..|. +|=..|. ..|-+
T Consensus 7 ~eC~~lK~~YD-~CFn~WfsekfLk 30 (68)
T PF05254_consen 7 PECTELKEKYD-QCFNKWFSEKFLK 30 (68)
T ss_pred hHHHHHHHHHH-HHHHHHHHHhhhc
Confidence 66999999998 8999998 66654
Done!