Query psy15248
Match_columns 75
No_of_seqs 101 out of 250
Neff 4.0
Searched_HMMs 46136
Date Sat Aug 17 01:09:31 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy15248.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/15248hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG1479|consensus 99.5 1.7E-14 3.7E-19 113.6 4.1 64 1-64 2-82 (406)
2 TIGR00939 2a57 Equilibrative N 98.5 3.9E-08 8.6E-13 76.6 1.4 23 22-44 1-23 (437)
3 PF04195 Transposase_28: Putat 64.2 11 0.00024 27.2 3.6 51 5-57 45-103 (181)
4 PF13817 DDE_Tnp_IS66_C: IS66 50.5 5.2 0.00011 22.3 -0.0 8 27-34 32-39 (39)
5 PF02932 Neur_chan_memb: Neuro 41.5 40 0.00086 20.9 3.0 27 20-46 37-63 (237)
6 PF10597 U5_2-snRNA_bdg: U5-sn 40.6 43 0.00092 23.7 3.3 42 32-73 54-109 (135)
7 PHA01474 nonstructural protein 38.6 14 0.0003 22.0 0.5 19 20-38 17-35 (52)
8 cd00929 Cyt_c_Oxidase_VIIc Cyt 32.1 34 0.00073 19.8 1.5 25 10-34 14-38 (46)
9 PRK10591 hypothetical protein; 30.6 25 0.00054 23.4 0.8 17 16-32 42-58 (92)
10 PHA02706 hypothetical protein; 29.6 26 0.00057 21.3 0.8 16 16-31 8-23 (58)
11 PF05787 DUF839: Bacterial pro 28.7 16 0.00036 29.9 -0.3 19 27-45 167-185 (524)
12 PF14654 Epiglycanin_C: Mucin, 26.0 1.1E+02 0.0023 20.9 3.2 11 28-38 13-23 (106)
13 PRK12887 ubiA tocopherol phyty 24.8 1.3E+02 0.0027 22.8 3.8 45 17-66 237-281 (308)
14 TIGR03782 Bac_Flav_CT_J Bacter 24.5 45 0.00098 26.5 1.4 19 12-30 260-278 (322)
15 PF02935 COX7C: Cytochrome c o 23.6 34 0.00074 20.8 0.5 24 10-33 32-55 (65)
16 PF07214 DUF1418: Protein of u 22.2 39 0.00085 22.6 0.6 18 17-34 43-60 (96)
No 1
>KOG1479|consensus
Probab=99.49 E-value=1.7e-14 Score=113.59 Aligned_cols=64 Identities=39% Similarity=0.704 Sum_probs=52.8
Q ss_pred CCccCCCCCCCCcccchhhhHHHHHhhhcccchhhhhhhhhhh-----------------hhhHHHHHHHHHHHhhhccc
Q psy15248 1 MENADLETNPPRDRWKLVYLTLLLHGVGTLMPWNMFITAKAQR-----------------LSANIIIIIIVLIYTARLGL 63 (75)
Q Consensus 1 ~~~~~~~~~~P~Dr~~~vyiif~llGiG~LlPWN~FITA~dY~-----------------~~~~~~~i~i~~~~~~r~~l 63 (75)
+|+++.+..+|+|+++.+|++|+++|+|+|+|||+||||.||| +..+.+..+++...+++++.
T Consensus 2 ~~~~~~~~~~p~d~~~~v~~i~~llGiG~LlpWN~fiTa~~y~~~~~~~~~~~~~F~~~~~~~a~i~~ll~~~~n~~~~~ 81 (406)
T KOG1479|consen 2 QDEVELDSPEPEDGYNLVYLIFLLLGIGTLLPWNMFITASDYYYYRFPGYHNSKNFTSSYTLAAQIPLLLFNLLNAFLNT 81 (406)
T ss_pred CccccccCCCcccccccHHHHHHHHhcccccchHhhhccHHHHHhhcCCCchHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 4678899999999999999999999999999999999999973 44455555666677776655
Q ss_pred c
Q psy15248 64 K 64 (75)
Q Consensus 64 ~ 64 (75)
+
T Consensus 82 ~ 82 (406)
T KOG1479|consen 82 R 82 (406)
T ss_pred H
Confidence 4
No 2
>TIGR00939 2a57 Equilibrative Nucleoside Transporter (ENT).
Probab=98.50 E-value=3.9e-08 Score=76.65 Aligned_cols=23 Identities=48% Similarity=0.959 Sum_probs=21.0
Q ss_pred HHHHhhhcccchhhhhhhhhhhh
Q psy15248 22 LLLHGVGTLMPWNMFITAKAQRL 44 (75)
Q Consensus 22 f~llGiG~LlPWN~FITA~dY~~ 44 (75)
|+++|+|+|+|||+||||.|||+
T Consensus 1 f~llG~~~L~pWN~fitA~~Yf~ 23 (437)
T TIGR00939 1 FFMLGVGVLLPWNAFITAPQYFI 23 (437)
T ss_pred CEEEeeeccchhHHHhhHHHHHH
Confidence 67899999999999999999854
No 3
>PF04195 Transposase_28: Putative gypsy type transposon; InterPro: IPR007321 This domain is found in a family of plant gene products and is thought to be related to gypsy type transposons. There is a domain of unknown function, (IPR007228 from INTERPRO), at the C terminus of the proteins. More information about these proteins can be found at Protein of the Month: Transposase [].
Probab=64.19 E-value=11 Score=27.19 Aligned_cols=51 Identities=16% Similarity=0.207 Sum_probs=37.8
Q ss_pred CCCCCCCCcccchhhhHHHHHhhhcccchhhhhhh-hhhh-------hhhHHHHHHHHHHH
Q psy15248 5 DLETNPPRDRWKLVYLTLLLHGVGTLMPWNMFITA-KAQR-------LSANIIIIIIVLIY 57 (75)
Q Consensus 5 ~~~~~~P~Dr~~~vyiif~llGiG~LlPWN~FITA-~dY~-------~~~~~~~i~i~~~~ 57 (75)
|..+.|+.++.-.+|..|+..|++ +|-|-|+-. .++| .++++..|+|+.+-
T Consensus 45 e~~P~P~~~g~~vvf~~f~~~Gl~--~P~~~f~~~vL~~y~v~l~~L~Pnai~~laiF~~l 103 (181)
T PF04195_consen 45 EAVPSPPYPGRIVVFADFFEAGLR--PPCSPFLREVLRFYGVELPQLNPNAIARLAIFAWL 103 (181)
T ss_pred ccccCCCCCCcEEEEhHHhhcCcc--CCchHHHHHHHHHhCccccccChHHHHHHHHHHHH
Confidence 444445556789999999997766 899999984 4654 56788888888764
No 4
>PF13817 DDE_Tnp_IS66_C: IS66 C-terminal element
Probab=50.53 E-value=5.2 Score=22.28 Aligned_cols=8 Identities=50% Similarity=1.477 Sum_probs=6.4
Q ss_pred hhcccchh
Q psy15248 27 VGTLMPWN 34 (75)
Q Consensus 27 iG~LlPWN 34 (75)
+.-|||||
T Consensus 32 ~~~LLPwn 39 (39)
T PF13817_consen 32 IDELLPWN 39 (39)
T ss_pred HHHhCCCC
Confidence 56689998
No 5
>PF02932 Neur_chan_memb: Neurotransmitter-gated ion-channel transmembrane region ion channel family signature gamma-aminobutyric acid (GABA) receptor signature nicotinic acetylcholine receptor signature; InterPro: IPR006029 Neurotransmitter ligand-gated ion channels are transmembrane receptor-ion channel complexes that open transiently upon binding of specific ligands, allowing rapid transmission of signals at chemical synapses [, ]. Five of these ion channel receptor families have been shown to form a sequence-related superfamily: Nicotinic acetylcholine receptor (AchR), an excitatory cation channel in vertebrates and invertebrates; in vertebrate motor endplates it is composed of alpha, beta, gamma and delta/epsilon subunits; in neurons it is composed of alpha and non-alpha (or beta) subunits []. Glycine receptor, an inhibitory chloride ion channel composed of alpha and beta subunits []. Gamma-aminobutyric acid (GABA) receptor, an inhibitory chloride ion channel; at least four types of subunits (alpha, beta, gamma and delta) are known []. Serotonin 5HT3 receptor, of which there are seven major types (5HT3-5HT7) []. Glutamate receptor, an excitatory cation channel of which at least three types have been described (kainate, N-methyl-D-aspartate (NMDA) and quisqualate) []. These receptors possess a pentameric structure (made up of varying subunits), surrounding a central pore. All known sequences of subunits from neurotransmitter-gated ion-channels are structurally related. They are composed of a large extracellular glycosylated N-terminal ligand-binding domain, followed by three hydrophobic transmembrane regions which form the ionic channel, followed by an intracellular region of variable length. A fourth hydrophobic region is found at the C-terminal of the sequence [, ]. This domain represents four transmembrane helices of a variety of neurotransmitter-gated ion-channels.; GO: 0006811 ion transport, 0016020 membrane; PDB: 1DXZ_A 3MRA_A 1EQ8_C 1OED_C 2PR9_P 1A11_A 1CEK_A 2BG9_E 2KSR_A 2K59_B ....
Probab=41.52 E-value=40 Score=20.95 Aligned_cols=27 Identities=15% Similarity=0.114 Sum_probs=21.3
Q ss_pred hHHHHHhhhcccchhhhhhhhhhhhhh
Q psy15248 20 LTLLLHGVGTLMPWNMFITAKAQRLSA 46 (75)
Q Consensus 20 iif~llGiG~LlPWN~FITA~dY~~~~ 46 (75)
++.+++++...+|.-+..+|.|-|...
T Consensus 37 ~~~~~~~~~~~lP~~s~~~pl~~~~~~ 63 (237)
T PF02932_consen 37 MTVFLLMVAENLPPTSYAKPLDGWYFI 63 (237)
T ss_dssp HHHHHHHHHHHHHHHHHHSHHHHHHHH
T ss_pred HHHHHhhhhhhhcccccccchhhhhcc
Confidence 456777888899999999999955443
No 6
>PF10597 U5_2-snRNA_bdg: U5-snRNA binding site 2 of PrP8; InterPro: IPR019581 The essential spliceosomal protein Prp8 interacts with U5 and U6 snRNAs and with specific pre-mRNA sequences that participate in catalysis []. This close association with crucial RNA sequences, together with extensive genetic evidence, suggests that Prp8 could directly affect the function of the catalytic core, perhaps acting as a splicing cofactor [].
Probab=40.61 E-value=43 Score=23.69 Aligned_cols=42 Identities=24% Similarity=0.509 Sum_probs=26.3
Q ss_pred chhhhhhhhhhhhhhHHH----HHHHHHHHhhhc------c----ccccCcccccc
Q psy15248 32 PWNMFITAKAQRLSANII----IIIIVLIYTARL------G----LKSPFTPAVGY 73 (75)
Q Consensus 32 PWN~FITA~dY~~~~~~~----~i~i~~~~~~r~------~----l~~~f~~~~~~ 73 (75)
=||..+++.-=|.+.+++ .+-++..+|.|+ + ..+||-|+|=|
T Consensus 54 KWNt~li~l~~YfREA~~~T~~lldil~k~E~kIq~RIK~gLNSkmPsRFPpvvFY 109 (135)
T PF10597_consen 54 KWNTALIGLMTYFREAIVNTEELLDILVKCENKIQNRIKIGLNSKMPSRFPPVVFY 109 (135)
T ss_pred HHHHHHHHHHHHHHHHHhccHHHHHHHHHHHHHHHHHHHHHhcccCCCCCCCeeec
Confidence 499999975544555554 335566777654 2 34688887744
No 7
>PHA01474 nonstructural protein
Probab=38.60 E-value=14 Score=22.04 Aligned_cols=19 Identities=26% Similarity=0.415 Sum_probs=13.1
Q ss_pred hHHHHHhhhcccchhhhhh
Q psy15248 20 LTLLLHGVGTLMPWNMFIT 38 (75)
Q Consensus 20 iif~llGiG~LlPWN~FIT 38 (75)
-.||--.--.|-|||+|-.
T Consensus 17 ssfwscariilspwnsfrs 35 (52)
T PHA01474 17 SSFWSCARIILSPWNSFRS 35 (52)
T ss_pred hhhhhhhheeeCcccccee
Confidence 3455555667889999854
No 8
>cd00929 Cyt_c_Oxidase_VIIc Cytochrome c oxidase subunit VIIc. 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. The VIIc subunit is found only in eukaryotes and its specific function remains unclear. Peroxide inactivation of bovine CcO coincides with the direct oxidation of tryptophan (W19) within subunit VIIc, along with other structural changes in other subunits.
Probab=32.06 E-value=34 Score=19.81 Aligned_cols=25 Identities=28% Similarity=0.579 Sum_probs=17.2
Q ss_pred CCCcccchhhhHHHHHhhhcccchh
Q psy15248 10 PPRDRWKLVYLTLLLHGVGTLMPWN 34 (75)
Q Consensus 10 ~P~Dr~~~vyiif~llGiG~LlPWN 34 (75)
.++.|+.+.-...+..|.|..+||=
T Consensus 14 ~~~nk~~~~~~~~~ffg~GF~~PF~ 38 (46)
T cd00929 14 SVTNKWRLTALFHLFFGSGFSAPFI 38 (46)
T ss_pred ccCccchHHHHHHHHHHHHHhhhHH
Confidence 3556665655566688888888873
No 9
>PRK10591 hypothetical protein; Provisional
Probab=30.59 E-value=25 Score=23.36 Aligned_cols=17 Identities=18% Similarity=0.407 Sum_probs=14.5
Q ss_pred chhhhHHHHHhhhcccc
Q psy15248 16 KLVYLTLLLHGVGTLMP 32 (75)
Q Consensus 16 ~~vyiif~llGiG~LlP 32 (75)
.-+-++.+++|+|+++|
T Consensus 42 ~~aai~mif~Gi~lmiP 58 (92)
T PRK10591 42 PTAAILMIFLGVLLMLP 58 (92)
T ss_pred chHHHHHHHHHHHHhhH
Confidence 35668889999999999
No 10
>PHA02706 hypothetical protein; Provisional
Probab=29.58 E-value=26 Score=21.33 Aligned_cols=16 Identities=13% Similarity=0.573 Sum_probs=12.5
Q ss_pred chhhhHHHHHhhhccc
Q psy15248 16 KLVYLTLLLHGVGTLM 31 (75)
Q Consensus 16 ~~vyiif~llGiG~Ll 31 (75)
-.+-||++++|+|++.
T Consensus 8 lviaiimmllgi~sii 23 (58)
T PHA02706 8 LVIAIIMMLLGIASII 23 (58)
T ss_pred HHHHHHHHHHhhHHHh
Confidence 3456889999999864
No 11
>PF05787 DUF839: Bacterial protein of unknown function (DUF839); InterPro: IPR008557 This family consists of bacterial proteins of unknown function.
Probab=28.74 E-value=16 Score=29.85 Aligned_cols=19 Identities=21% Similarity=0.635 Sum_probs=16.1
Q ss_pred hhcccchhhhhhhhhhhhh
Q psy15248 27 VGTLMPWNMFITAKAQRLS 45 (75)
Q Consensus 27 iG~LlPWN~FITA~dY~~~ 45 (75)
.|..-|||.+||.++++..
T Consensus 167 aGg~TPWGT~Lt~EEn~~~ 185 (524)
T PF05787_consen 167 AGGVTPWGTYLTCEENFPD 185 (524)
T ss_pred CCCCCCCcceEecccccCC
Confidence 4678899999999998665
No 12
>PF14654 Epiglycanin_C: Mucin, catalytic, TM and cytoplasmic tail region
Probab=25.97 E-value=1.1e+02 Score=20.92 Aligned_cols=11 Identities=45% Similarity=1.364 Sum_probs=9.4
Q ss_pred hcccchhhhhh
Q psy15248 28 GTLMPWNMFIT 38 (75)
Q Consensus 28 G~LlPWN~FIT 38 (75)
|+|-||-.|+.
T Consensus 13 GsL~PWeIfLI 23 (106)
T PF14654_consen 13 GSLKPWEIFLI 23 (106)
T ss_pred CCccchHHHHH
Confidence 78999998865
No 13
>PRK12887 ubiA tocopherol phytyltransferase; Reviewed
Probab=24.79 E-value=1.3e+02 Score=22.85 Aligned_cols=45 Identities=18% Similarity=0.305 Sum_probs=28.5
Q ss_pred hhhhHHHHHhhhcccchhhhhhhhhhhhhhHHHHHHHHHHHhhhcccccc
Q psy15248 17 LVYLTLLLHGVGTLMPWNMFITAKAQRLSANIIIIIIVLIYTARLGLKSP 66 (75)
Q Consensus 17 ~vyiif~llGiG~LlPWN~FITA~dY~~~~~~~~i~i~~~~~~r~~l~~~ 66 (75)
..|+...+.|++.+.+||...+. -.-.+...++.+...++|++++
T Consensus 237 ~~y~~~i~~~~~~~~~~~~~~~~-----~~~~~~~~~~~~~~~~~~~~~~ 281 (308)
T PRK12887 237 ACYLGMIAVGLLSLPTVNPAFLI-----VSHLILLALLWWRSQRVDLQDK 281 (308)
T ss_pred HHHHHHHHHHHHHhhhHHHHHHH-----HHHHHHHHHHHHHHhhcCcccc
Confidence 34677777788888888876543 1122344555567778888753
No 14
>TIGR03782 Bac_Flav_CT_J Bacteroides conjugative transposon TraJ protein. Members of this protein family are designated TraM and are found in a proposed transfer region of a class of conjugative transposon found in the Bacteroides lineage. This family is related conjugation system proteins in the Proteobacteria, including TrbL of Agrobacterium Ti plasmids and VirB6.
Probab=24.54 E-value=45 Score=26.54 Aligned_cols=19 Identities=21% Similarity=0.385 Sum_probs=16.5
Q ss_pred CcccchhhhHHHHHhhhcc
Q psy15248 12 RDRWKLVYLTLLLHGVGTL 30 (75)
Q Consensus 12 ~Dr~~~vyiif~llGiG~L 30 (75)
.|..+.+|++|++.|+...
T Consensus 260 ~d~sn~~yiiFmlIGi~gy 278 (322)
T TIGR03782 260 PDSSNSVYIIFMIIGIIGY 278 (322)
T ss_pred CCCccHHHHHHHHHHHHHh
Confidence 5788999999999998654
No 15
>PF02935 COX7C: Cytochrome c oxidase subunit VIIc; InterPro: IPR004202 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. This entry represents cytochrome C subunit 7C. The yeast member of this family is called cytochrome C subunit 8P.; GO: 0004129 cytochrome-c oxidase activity; PDB: 3ABL_Y 3ABM_L 2EIM_L 3ASO_L 3AG3_Y 3AG1_Y 1OCC_Y 2DYS_Y 2OCC_L 1V54_L ....
Probab=23.63 E-value=34 Score=20.77 Aligned_cols=24 Identities=17% Similarity=0.436 Sum_probs=17.3
Q ss_pred CCCcccchhhhHHHHHhhhcccch
Q psy15248 10 PPRDRWKLVYLTLLLHGVGTLMPW 33 (75)
Q Consensus 10 ~P~Dr~~~vyiif~llGiG~LlPW 33 (75)
.++.|+.++...+..+|+|..+|+
T Consensus 32 ~~~nK~~~~~~~~~f~g~GF~~PF 55 (65)
T PF02935_consen 32 NVKNKWPFAVKFWGFFGSGFAAPF 55 (65)
T ss_dssp --SSHHHHHHHHHHHHHHHHHHHH
T ss_pred cCcchhHHHHHHHHHHHHHHHhHH
Confidence 356677777777778899988886
No 16
>PF07214 DUF1418: Protein of unknown function (DUF1418); InterPro: IPR010815 This family consists of several hypothetical Enterobacterial proteins of around 100 residues in length. Members of this family are often described as YbjC. In Escherichia coli the ybjC gene is located downstream of nfsA (which encodes the major oxygen-insensitive nitroreductase). It is thought that nfsA and ybjC form an operon an its promoter is a class I SoxS-dependent promoter []. The function of this family is unknown.
Probab=22.18 E-value=39 Score=22.55 Aligned_cols=18 Identities=17% Similarity=0.554 Sum_probs=14.6
Q ss_pred hhhhHHHHHhhhcccchh
Q psy15248 17 LVYLTLLLHGVGTLMPWN 34 (75)
Q Consensus 17 ~vyiif~llGiG~LlPWN 34 (75)
.+-++.+++|+|+++|==
T Consensus 43 ~aai~MIf~Gi~lMlPAa 60 (96)
T PF07214_consen 43 TAAIAMIFVGIGLMLPAA 60 (96)
T ss_pred hHHHHHHHHHHHHHHHHH
Confidence 456788899999999943
Done!