Query psy17845
Match_columns 81
No_of_seqs 115 out of 486
Neff 6.0
Searched_HMMs 46136
Date Sat Aug 17 00:29:26 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy17845.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/17845hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG3646|consensus 99.1 5.7E-11 1.2E-15 92.6 3.8 50 2-53 436-485 (486)
2 PF02932 Neur_chan_memb: Neuro 99.0 1.8E-10 4E-15 74.8 1.7 45 2-46 193-237 (237)
3 TIGR00860 LIC Cation transport 98.9 3.3E-10 7.1E-15 87.5 1.7 45 2-47 413-457 (459)
4 KOG3645|consensus 97.8 3.8E-06 8.3E-11 65.0 -0.9 34 2-35 415-448 (449)
5 PF13721 SecD-TM1: SecD export 70.3 3.1 6.7E-05 26.4 1.6 35 28-62 3-37 (101)
6 PF06796 NapE: Periplasmic nit 35.7 91 0.002 18.0 3.8 36 8-45 7-42 (56)
7 PRK13743 conjugal transfer pro 33.6 54 0.0012 22.3 2.8 35 10-45 21-55 (141)
8 PRK12933 secD preprotein trans 27.7 53 0.0011 27.2 2.4 38 25-62 9-46 (604)
9 KOG4647|consensus 27.3 98 0.0021 23.0 3.5 27 20-46 97-123 (263)
10 PRK10629 EnvZ/OmpR regulon mod 25.3 70 0.0015 21.0 2.3 35 26-62 7-41 (127)
11 PF09879 DUF2106: Predicted me 25.2 1.8E+02 0.0038 20.1 4.2 19 16-34 4-24 (153)
12 PF05484 LRV_FeS: LRV protein 20.7 74 0.0016 18.5 1.5 10 23-32 40-49 (57)
13 cd00928 Cyt_c_Oxidase_VIIa Cyt 20.6 1.5E+02 0.0033 17.0 2.8 24 24-47 25-48 (55)
No 1
>KOG3646|consensus
Probab=99.11 E-value=5.7e-11 Score=92.62 Aligned_cols=50 Identities=30% Similarity=0.561 Sum_probs=45.1
Q ss_pred cchhcccCccchhhhhchhhhHhhHHHHHHHHHHHHHHhhhhHhhhcCCccc
Q psy17845 2 NGRQVVTHPDTNHIVEDWKYVSMVLDRFFLCVFTAACVLGTCGIIFQAPSLY 53 (81)
Q Consensus 2 i~eh~k~~d~~~~~~~eWk~vA~ViDRlfl~if~~~~~~~t~~i~~~~p~~~ 53 (81)
+.+++++++++++.++||||+|||+||+||++|.++++++ +++.++|++.
T Consensus 436 ~~~r~~~~~~~~~~~~dWkFAAmvVDRlCL~~Fs~fiii~--~i~~~~p~l~ 485 (486)
T KOG3646|consen 436 ILDRMEEDDKEEALQSDWKFAAMVVDRLCLLAFSVFIVMC--GILLSAPHLV 485 (486)
T ss_pred HHHHhhhhhHHHHHHhhhhHHHHHHHHHHHHHHHHHHHHH--HHhhcCCccC
Confidence 4578889999999999999999999999999999999888 8888888874
No 2
>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=98.98 E-value=1.8e-10 Score=74.77 Aligned_cols=45 Identities=29% Similarity=0.518 Sum_probs=41.0
Q ss_pred cchhcccCccchhhhhchhhhHhhHHHHHHHHHHHHHHhhhhHhh
Q psy17845 2 NGRQVVTHPDTNHIVEDWKYVSMVLDRFFLCVFTAACVLGTCGII 46 (81)
Q Consensus 2 i~eh~k~~d~~~~~~~eWk~vA~ViDRlfl~if~~~~~~~t~~i~ 46 (81)
+++|++++++.++.++||+++|+|+||+|+|+|.+++++.++++.
T Consensus 193 i~~~~~~~~~~~~~~~ew~~~A~viDR~~~~~F~i~f~~~~i~yw 237 (237)
T PF02932_consen 193 IAEHLREQDEEEEIKEEWKFVAMVIDRLFRILFPIAFILFNIVYW 237 (237)
T ss_dssp HHHHHHHHHHHHHHHHHHHSTSHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred eecccccccccccccccccccHHHHHHHHHHHHHHHHHHHHhhhC
Confidence 567889999999999999999999999999999999999988763
No 3
>TIGR00860 LIC Cation transporter family protein. selective while glycine receptors are anion selective).
Probab=98.93 E-value=3.3e-10 Score=87.51 Aligned_cols=45 Identities=22% Similarity=0.447 Sum_probs=42.5
Q ss_pred cchhcccCccchhhhhchhhhHhhHHHHHHHHHHHHHHhhhhHhhh
Q psy17845 2 NGRQVVTHPDTNHIVEDWKYVSMVLDRFFLCVFTAACVLGTCGIIF 47 (81)
Q Consensus 2 i~eh~k~~d~~~~~~~eWk~vA~ViDRlfl~if~~~~~~~t~~i~~ 47 (81)
| +|++++++.++.++|||++|+|+||+|+|+|.++++++|++++.
T Consensus 413 i-~~~~~~~~~~~~~~~W~~~a~viDr~~~~~f~~~~~~~~~~~~~ 457 (459)
T TIGR00860 413 A-HRFRKRDESEEVVRDWKFRAKVIDKLSRMAFPLAFLLFNIGYWM 457 (459)
T ss_pred H-HHHHhhhhhhcccchhhhccchhhHHHHHHHHHHHHHhhhhheE
Confidence 5 88999999999999999999999999999999999999998875
No 4
>KOG3645|consensus
Probab=97.76 E-value=3.8e-06 Score=64.96 Aligned_cols=34 Identities=41% Similarity=0.770 Sum_probs=31.7
Q ss_pred cchhcccCccchhhhhchhhhHhhHHHHHHHHHH
Q psy17845 2 NGRQVVTHPDTNHIVEDWKYVSMVLDRFFLCVFT 35 (81)
Q Consensus 2 i~eh~k~~d~~~~~~~eWk~vA~ViDRlfl~if~ 35 (81)
|++|+++++..++..+||+++|+|+||+|+|+|+
T Consensus 415 i~~~~~~~~~~~~~~~~w~~va~v~dr~~l~~f~ 448 (449)
T KOG3645|consen 415 IAEHLKSEDNFQEIREDWKYVAMVLDRLLLWIFL 448 (449)
T ss_pred HHHHHHhHHHHhhhhHHHHHHHHHHHHHhhheEe
Confidence 6889999999999999999999999999999875
No 5
>PF13721 SecD-TM1: SecD export protein N-terminal TM region
Probab=70.31 E-value=3.1 Score=26.36 Aligned_cols=35 Identities=23% Similarity=0.458 Sum_probs=25.4
Q ss_pred HHHHHHHHHHHHhhhhHhhhcCCccccCCCccchh
Q psy17845 28 RFFLCVFTAACVLGTCGIIFQAPSLYDNTAPIDIQ 62 (81)
Q Consensus 28 Rlfl~if~~~~~~~t~~i~~~~p~~~~~~~~~~~~ 62 (81)
|.-.|.|.++.++-.++++...|++|...+.+++.
T Consensus 3 ~yp~WKyllil~vl~~~~lyALPnlyge~pAvqIs 37 (101)
T PF13721_consen 3 RYPLWKYLLILVVLLLGALYALPNLYGEDPAVQIS 37 (101)
T ss_pred CcchHHHHHHHHHHHHHHHHHhhhccCCCCcEEEe
Confidence 45567777777777777788889998776666554
No 6
>PF06796 NapE: Periplasmic nitrate reductase protein NapE; InterPro: IPR010649 This family consists of several bacterial periplasmic nitrate reductase NapE proteins. Seven genes, napKEFDABC, encoding the periplasmic nitrate reductase system were cloned from the denitrifying phototrophic bacterium Rhodobacter sphaeroides. NapE is thought to be a transmembrane protein [].
Probab=35.65 E-value=91 Score=18.01 Aligned_cols=36 Identities=17% Similarity=0.246 Sum_probs=18.3
Q ss_pred cCccchhhhhchhhhHhhHHHHHHHHHHHHHHhhhhHh
Q psy17845 8 THPDTNHIVEDWKYVSMVLDRFFLCVFTAACVLGTCGI 45 (81)
Q Consensus 8 ~~d~~~~~~~eWk~vA~ViDRlfl~if~~~~~~~t~~i 45 (81)
.++..++.+.||+- ...=-+++|-.+.+.+++.-++
T Consensus 7 ~~~~~~~k~~E~~~--flfl~~~l~PiL~v~~Vg~YGF 42 (56)
T PF06796_consen 7 SESDKSTKRSELKA--FLFLAVVLFPILAVAFVGGYGF 42 (56)
T ss_pred CccccchhHHHHHH--HHHHHHHHHHHHHHHHHHHHHH
Confidence 33446777889983 2222233444444455555443
No 7
>PRK13743 conjugal transfer protein TrbF; Provisional
Probab=33.59 E-value=54 Score=22.30 Aligned_cols=35 Identities=20% Similarity=0.250 Sum_probs=26.1
Q ss_pred ccchhhhhchhhhHhhHHHHHHHHHHHHHHhhhhHh
Q psy17845 10 PDTNHIVEDWKYVSMVLDRFFLCVFTAACVLGTCGI 45 (81)
Q Consensus 10 d~~~~~~~eWk~vA~ViDRlfl~if~~~~~~~t~~i 45 (81)
.+.++.+.|-++...+.||-+ ++|+++...|.++.
T Consensus 21 ~KIrq~~rd~~y~~R~~~~Y~-~LfiVFl~AG~vLw 55 (141)
T PRK13743 21 LKIRQTKRDYDYERRVSDIYF-DLFIVFLTAGIVLW 55 (141)
T ss_pred HHHHhhhhhHHHHHHHHHHHH-HHHHHHHHhhHHHH
Confidence 455677889999999999865 67777766666554
No 8
>PRK12933 secD preprotein translocase subunit SecD; Reviewed
Probab=27.71 E-value=53 Score=27.24 Aligned_cols=38 Identities=13% Similarity=0.268 Sum_probs=31.5
Q ss_pred hHHHHHHHHHHHHHHhhhhHhhhcCCccccCCCccchh
Q psy17845 25 VLDRFFLCVFTAACVLGTCGIIFQAPSLYDNTAPIDIQ 62 (81)
Q Consensus 25 ViDRlfl~if~~~~~~~t~~i~~~~p~~~~~~~~~~~~ 62 (81)
.+.|.-+|.|+++.++-.++.+...|++|...+.+++.
T Consensus 9 m~n~yp~wky~~i~~~l~~~~lyalPn~y~~~pavqis 46 (604)
T PRK12933 9 LLNHYSAWKYVVLIVTIIILLLSAIPTWYGEDAAVQVS 46 (604)
T ss_pred hhccChhHHHHHHHHHHHHHHHHhChhccCCCCeEEEe
Confidence 47778889999999888899999999999777766654
No 9
>KOG4647|consensus
Probab=27.28 E-value=98 Score=23.03 Aligned_cols=27 Identities=30% Similarity=0.491 Sum_probs=20.7
Q ss_pred hhhHhhHHHHHHHHHHHHHHhhhhHhh
Q psy17845 20 KYVSMVLDRFFLCVFTAACVLGTCGII 46 (81)
Q Consensus 20 k~vA~ViDRlfl~if~~~~~~~t~~i~ 46 (81)
+++|..+|-++++.|-++++.|++-++
T Consensus 97 R~~AE~IDffilf~~K~~Iv~g~~~l~ 123 (263)
T KOG4647|consen 97 RLLAELIDFFILFSFKLAIVGGTLSLL 123 (263)
T ss_pred HHHHHHHHHHHHHHHHHHHHHhHHHhh
Confidence 458889999988888887777776543
No 10
>PRK10629 EnvZ/OmpR regulon moderator; Provisional
Probab=25.33 E-value=70 Score=21.05 Aligned_cols=35 Identities=11% Similarity=0.150 Sum_probs=21.1
Q ss_pred HHHHHHHHHHHHHHhhhhHhhhcCCccccCCCccchh
Q psy17845 26 LDRFFLCVFTAACVLGTCGIIFQAPSLYDNTAPIDIQ 62 (81)
Q Consensus 26 iDRlfl~if~~~~~~~t~~i~~~~p~~~~~~~~~~~~ 62 (81)
+-|.-+|.|.++.++-. ++...|++|...+.+++.
T Consensus 7 ~nryp~WKylli~~vl~--~lyAlPnlygedpavQIs 41 (127)
T PRK10629 7 SLRQLAWLGAVLLLLAA--LLLAWSALRQQESTLAIR 41 (127)
T ss_pred ccccHHHHHHHHHHHHH--HHHHChhccCCCceEEEe
Confidence 45556677755544333 566679988766555543
No 11
>PF09879 DUF2106: Predicted membrane protein (DUF2106); InterPro: IPR011313 [NiFe] hydrogenases function in H2 metabolism in a variety of microorganisms, enabling them to use H2 as a source of reducing equivalent under aerobic and anaerobic conditions [NiFe] hydrogenases consist of two subunits, hydrogenase large and hydrogenase small. The large subunit contains the binuclear [NiFe] active site, while the small subunit binds at least one [4Fe-4S] cluster []. Energy-converting [NiFe] hydrogenases (or [NiFe]-hydrogenase-3-type) form a distinct group within the [NiFe] hydrogenase family [, ]. Members of this subgroup include: Hydrogenase 3 and 4 (Hyc and Hyf) from Escherichia coli CO-induced hydrogenase (Coo) from Rhodospirillum rubrum Mbh hydrogenase from Pyrococcus furiosus Eha and Ehb hydrogenases from Methanothermobacter species Ech hydrogenase from Methanosarcina barkeri Energy-converting [NiFe] hydrogenases are membrane-bound enzymes with a six-subunit core: the large and small hydrogenase subunits, plus two hydrophilic proteins and two integral membrane proteins. Their large and small subunits show little sequence similarity to other [NiFe] hydrogenases, except for key conserved residues coordinating the active site and [FeS] cluster. However, they show considerable sequence similarity to the six-subunit, energy-conserving NADH:quinone oxidoreductases (complex I), which are present in cytoplasmic membranes of many bacteria and in inner mitochondrial membranes. However, the reactions they catalyse differ significantly from complex I. Energy-converting [NiFe] hydrogenases function as ion pumps. Eha and Ehb hydrogenases contain extra subunits in addition to those shared by other energy-converting [NiFe] hydrogenases (or [NiFe]-hydrogenase-3-type). Eha contains a 6[4Fe-4S] polyferredoxin, a 10[4F-4S] polyferredoxin, ten other predicted integral membrane proteins (EhaA IPR011306 from INTERPRO, EhaB IPR011314 from INTERPRO, EhaC IPR011316 from INTERPRO, EhaD IPR011308 from INTERPRO, EhaE IPR011317 from INTERPRO, EhaF IPR011313 from INTERPRO, EhaG IPR011311 from INTERPRO, EhaI IPR011318 from INTERPRO, EhaK IPR011319 from INTERPRO, EhaL IPR011305 from INTERPRO) and four hydrophobic subunits (EhaM, EhaR IPR014502 from INTERPRO, EhS, EhT) []. The ten predicted integral membrane proteins are absent from Ech, Coo, Hyc and Hyf complexes, which may have simpler membrane components than Eha. Eha and Ehb catalyse the reduction of low-potential redox carriers (e.g. ferredoxins or polyferredoxins), which then might function as electron donors to oxidoreductases. Based on sequence similarity and genome context analysis, other organisms such as Methanopyrus kandleri, Methanocaldococcus jannaschii, and Methanothermobacter marburgensis also encode Eha-like [NiFe]-hydrogenase-3-type complexes and have very similar eha operon structure. This entry represents small membrane proteins that are predicted to be the EhaF transmembrane subunits of multi-subunit membrane-bound [NiFe]-hydrogenase Eha complexes.
Probab=25.16 E-value=1.8e+02 Score=20.10 Aligned_cols=19 Identities=26% Similarity=0.553 Sum_probs=11.5
Q ss_pred hhchhhhHh--hHHHHHHHHH
Q psy17845 16 VEDWKYVSM--VLDRFFLCVF 34 (81)
Q Consensus 16 ~~eWk~vA~--ViDRlfl~if 34 (81)
..-|..++. .+-|+|-.+-
T Consensus 4 ~~i~n~ls~p~~v~rlfa~~l 24 (153)
T PF09879_consen 4 GKIWNYLSKPENVPRLFALFL 24 (153)
T ss_pred HHHHHHhcCchhHHHHHHHHH
Confidence 345777665 6777775433
No 12
>PF05484 LRV_FeS: LRV protein FeS4 cluster; InterPro: IPR008665 This iron sulphur cluster is found at the N terminus of some proteins containing leucine-repeat variant (LRV) repeats (IPR004830 from INTERPRO). These proteins have a two-domain structure, composed of a small N-terminal domain containing a cluster of four Cys residues that houses the 4Fe:4S cluster, and a larger C-terminal domain containing the LRV repeats []. Biochemical studies revealed that the 4Fe:4S cluster is sensitive to oxygen, but does not appear to have reversible redox activity.; PDB: 1LRV_A.
Probab=20.70 E-value=74 Score=18.47 Aligned_cols=10 Identities=40% Similarity=0.680 Sum_probs=8.2
Q ss_pred HhhHHHHHHH
Q psy17845 23 SMVLDRFFLC 32 (81)
Q Consensus 23 A~ViDRlfl~ 32 (81)
|.-|||||-|
T Consensus 40 aRrIdRFF~~ 49 (57)
T PF05484_consen 40 ARRIDRFFRW 49 (57)
T ss_dssp HHHHHHHHHH
T ss_pred HHHHHHHHHh
Confidence 7789999865
No 13
>cd00928 Cyt_c_Oxidase_VIIa Cytochrome c oxidase subunit VIIa. 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 VIIa has two tissue-specific isoforms that are expressed in a developmental manner. VIIa-H is expressed in heart and skeletal muscle but not smooth muscle. VIIa-L is expressed in liver and non-muscle tissues.
Probab=20.58 E-value=1.5e+02 Score=16.97 Aligned_cols=24 Identities=29% Similarity=0.362 Sum_probs=18.8
Q ss_pred hhHHHHHHHHHHHHHHhhhhHhhh
Q psy17845 24 MVLDRFFLCVFTAACVLGTCGIIF 47 (81)
Q Consensus 24 ~ViDRlfl~if~~~~~~~t~~i~~ 47 (81)
=+.|+++...-+..+++++...+.
T Consensus 25 G~~D~~LYr~Tm~L~~vG~~~~~~ 48 (55)
T cd00928 25 GVVDRILYRLTMALTVVGTGYSLY 48 (55)
T ss_pred CchhHHHHHHHHHHHHHhHHHHHH
Confidence 378999988888888888866543
Done!