Query psy12043
Match_columns 143
No_of_seqs 169 out of 1052
Neff 8.7
Searched_HMMs 46136
Date Fri Aug 16 17:09:41 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy12043.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/12043hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG3646|consensus 100.0 5E-40 1.1E-44 255.5 7.4 142 1-143 56-213 (486)
2 KOG3645|consensus 100.0 6.7E-36 1.4E-40 239.1 12.8 137 5-142 63-216 (449)
3 TIGR00860 LIC Cation transport 100.0 1.5E-35 3.2E-40 237.7 12.8 136 4-139 62-215 (459)
4 PF02931 Neur_chan_LBD: Neurot 100.0 7.1E-35 1.5E-39 212.9 14.2 137 5-141 37-192 (217)
5 KOG3643|consensus 100.0 3.9E-31 8.5E-36 205.2 7.6 122 4-130 69-196 (459)
6 KOG3644|consensus 99.9 4.6E-26 9.9E-31 181.5 13.1 119 7-125 79-201 (457)
7 KOG3642|consensus 99.9 6E-23 1.3E-27 160.5 9.0 117 8-128 82-202 (466)
8 PF15363 DUF4596: Domain of un 71.9 8.2 0.00018 21.0 3.2 34 101-138 11-44 (46)
9 PF06107 DUF951: Bacterial pro 51.6 10 0.00022 21.9 1.3 17 127-143 17-33 (57)
10 PRK14751 tetracycline resistan 50.0 13 0.00027 17.8 1.3 19 95-113 5-23 (28)
11 KOG1332|consensus 47.0 68 0.0015 24.5 5.3 62 70-136 223-296 (299)
12 PF08076 TetM_leader: Tetracyc 44.3 11 0.00023 18.2 0.5 20 95-114 5-24 (28)
13 PF11211 DUF2997: Protein of u 37.4 20 0.00044 19.8 1.1 23 73-95 2-24 (48)
14 PRK03174 sspH acid-soluble spo 34.8 35 0.00075 19.9 1.8 18 1-18 23-40 (59)
15 PRK01625 sspH acid-soluble spo 33.9 36 0.00077 19.8 1.7 18 1-18 23-40 (59)
16 TIGR02861 SASP_H small acid-so 33.1 42 0.00092 19.4 2.0 18 1-18 23-40 (58)
17 PF09732 CactinC_cactus: Cactu 30.2 1.1E+02 0.0024 20.6 3.9 30 104-134 69-98 (125)
18 PF08141 SspH: Small acid-solu 28.9 54 0.0012 18.9 2.0 17 2-18 24-40 (58)
19 PF15016 DUF4520: Domain of un 26.3 1.7E+02 0.0037 18.3 5.1 39 71-112 15-55 (85)
20 PF11455 DUF3018: Protein of 23.4 32 0.00069 20.4 0.3 10 47-56 19-28 (65)
21 COG2158 Uncharacterized protei 23.3 51 0.0011 21.5 1.3 17 100-116 25-43 (112)
22 COG3557 Uncharacterized domain 22.3 3E+02 0.0064 19.6 7.3 101 13-136 13-121 (177)
23 KOG1344|consensus 22.0 66 0.0014 24.4 1.8 33 50-83 246-278 (324)
24 PRK04257 hypothetical protein; 20.1 2.2E+02 0.0048 17.3 3.8 19 69-87 56-76 (78)
No 1
>KOG3646|consensus
Probab=100.00 E-value=5e-40 Score=255.51 Aligned_cols=142 Identities=34% Similarity=0.740 Sum_probs=129.9
Q ss_pred CceEEEEeec---eeEEEEEeeeeeeEEEcCCceeCCCCCCCeeEEEECCCCcccCCccccccCCCCCCCCCcceEEEEe
Q psy12043 1 MPCIIQSILN---SKLVSYLTADIGVKWYDPVLQWDPKKYGDIKQIYLAPQEVWQPDLSTFNSAGGNDVSPFGETYHIAS 77 (143)
Q Consensus 1 ~~v~i~~i~~---~~~~~~~~~~l~~~W~D~rL~w~p~~~~~i~~i~~~~~~iW~Pdi~~~n~~~~~~~~~~~~~~v~v~ 77 (143)
+++++|||++ +.+...+++|++++|+|.+|+|||++||||+.+++|.++||+||+.+||+++.+ ......+++.++
T Consensus 56 ~~~~lqQIidVDEKnQvl~~naWl~y~W~D~~LrW~pseygnI~dvR~p~~~iWkPDVLLYNSade~-FDsTy~tN~Vv~ 134 (486)
T KOG3646|consen 56 LGVFLQQIIDVDEKNQVLSVNAWLQYQWNDYKLRWDPSEYGNITDIRFPGGNIWKPDVLLYNSADEQ-FDSTYKTNYVVY 134 (486)
T ss_pred eeeeEeccCCCcccccchhhhhhhheeehhhhhccCHHHhCCceeeccCCccccCCceecccccccc-CCCcceeeEEEc
Confidence 4688999987 447788999999999999999999999999999999999999999999999842 334568999999
Q ss_pred eCCeEEEecCcEEEEEecccccccCCccceEEEEEeccccCCCeEEEE-------------eecCcEEEEeeeEeEEeC
Q psy12043 78 SDGLISWVPPCQFQVYCRLDLTYWPFDSQVCELILGSWVYDGNNIDFH-------------FEDGNWRMNGDASEFKIK 143 (143)
Q Consensus 78 ~~G~V~~~~~~~~~~~C~~~~~~fPfD~q~C~l~f~s~~y~~~~v~l~-------------~~n~EW~l~~~~~~~~~~ 143 (143)
++|.|.|.||.+++++|.+|.+.||||.|.|.++||||+|+|..++|+ .+||||+|++.++...+|
T Consensus 135 ~tG~v~~vPPGIfk~sCkiDItwFPFD~Q~C~mKFGSWTY~G~~lDL~~~~~~g~~Dls~yi~NGEW~Ll~~pakr~~~ 213 (486)
T KOG3646|consen 135 STGSVLWVPPGIFKSSCKIDITWFPFDDQVCYLKFGSWTYAGILLDLRIDDEDGGIDLSTYIPNGEWDLLGTPAKREEK 213 (486)
T ss_pred cCCeeeecCCceeeeeeEEEEEEecccccEEEEEeeeEEEcceeeeeeeccccCCcchhhcccCCceeeccccccceee
Confidence 999999999999999999999999999999999999999999988876 689999999999876654
No 2
>KOG3645|consensus
Probab=100.00 E-value=6.7e-36 Score=239.13 Aligned_cols=137 Identities=29% Similarity=0.699 Sum_probs=120.4
Q ss_pred EEEeec---eeEEEEEeeeeeeEEEcCCceeCCCCCCCeeEEEECCCCcccCCccccccCCCCCCCCCcceEEEEeeCCe
Q psy12043 5 IQSILN---SKLVSYLTADIGVKWYDPVLQWDPKKYGDIKQIYLAPQEVWQPDLSTFNSAGGNDVSPFGETYHIASSDGL 81 (143)
Q Consensus 5 i~~i~~---~~~~~~~~~~l~~~W~D~rL~w~p~~~~~i~~i~~~~~~iW~Pdi~~~n~~~~~~~~~~~~~~v~v~~~G~ 81 (143)
+.++++ ..+.+++++|+.++|+|+||+|||++|+||+.+++|.++||+||++++|+++++ .......++.++++|+
T Consensus 63 l~qii~VdE~~q~~t~~~wl~~~W~D~~L~Wnp~~~~~I~~i~vp~~~IW~Pdi~l~N~~~~~-~~~~~~~~v~v~~~G~ 141 (449)
T KOG3645|consen 63 LYQIIEVDEKNQIMTTNVWLKQSWTDERLSWDPSDYGGITKIRVPSSKIWLPDIVLYNNADGD-FEVEDLTNVLVTYTGE 141 (449)
T ss_pred EEEEEeeccccceEEEEEEeeeEEeccCcccChHHcCCceEEEecHHHcCcCcEEEEeccccc-ccccccceEEEEECCE
Confidence 445554 557788888999999999999999999999999999999999999999977642 3334556699999999
Q ss_pred EEEecCcEEEEEecccccccCCccceEEEEEeccccCCCeEE-EE-------------eecCcEEEEeeeEeEEe
Q psy12043 82 ISWVPPCQFQVYCRLDLTYWPFDSQVCELILGSWVYDGNNID-FH-------------FEDGNWRMNGDASEFKI 142 (143)
Q Consensus 82 V~~~~~~~~~~~C~~~~~~fPfD~q~C~l~f~s~~y~~~~v~-l~-------------~~n~EW~l~~~~~~~~~ 142 (143)
|.|.+++..+++|++|+++||||.|+|.++||||+|++.+++ +. .+|+||++++..+....
T Consensus 142 V~~~~p~i~~s~C~idv~~FPfD~Q~C~i~f~sw~~~~~~i~~~~~~~~~~~~~~~~~~~n~eW~l~~~~~~~~~ 216 (449)
T KOG3645|consen 142 VLWYPPAIYKSSCPIDVTYFPFDVQNCSIKFGSWTYDGSEVDGLDLNAQTIEVDLSDFIENSEWELLSVTVVREE 216 (449)
T ss_pred EEEEcceEEEeecccccccCCCcceeEeEEEeccccCccccceeeeccccccCCHHHcCCCCcEEEEeeeeEEee
Confidence 999999999999999999999999999999999999999776 32 68999999999886643
No 3
>TIGR00860 LIC Cation transporter family protein. selective while glycine receptors are anion selective).
Probab=100.00 E-value=1.5e-35 Score=237.73 Aligned_cols=136 Identities=22% Similarity=0.468 Sum_probs=116.0
Q ss_pred EEEEe---eceeEEEEEeeeeeeEEEcCCceeCCCCCCCeeEEEECCCCcccCCccccccCCCCCC-CCCcceEEEEeeC
Q psy12043 4 IIQSI---LNSKLVSYLTADIGVKWYDPVLQWDPKKYGDIKQIYLAPQEVWQPDLSTFNSAGGNDV-SPFGETYHIASSD 79 (143)
Q Consensus 4 ~i~~i---~~~~~~~~~~~~l~~~W~D~rL~w~p~~~~~i~~i~~~~~~iW~Pdi~~~n~~~~~~~-~~~~~~~v~v~~~ 79 (143)
.+.+| .+.++++++++|++++|+|+||+|||++|+|++.+.++.++||+||++++|+++.... ....+..+++++|
T Consensus 62 ~l~~i~~vde~~q~~t~~~wl~~~W~D~rL~Wnp~~y~~i~~i~~~~~~IW~PDi~l~N~~~~~~~~~~~~~~~v~~~~~ 141 (459)
T TIGR00860 62 FLRSIMDVDEKNMDYTTNIWLRQEWTDERLQWNPEEYPGVTLVRTPDDSIWVPDIFFYNEKDARFHGITMTNVLVRIHPN 141 (459)
T ss_pred EEEEecccccccceEEEeeeeeeEEeCCccCCCCccCCCceeccccccccccCcEEeecCccccccccccCceEEEEcCC
Confidence 44455 4466889999999999999999999999999999999999999999999999874311 1123445555669
Q ss_pred CeEEEecCcEEEEEecccccccCCccceEEEEEeccccCCCeEEEE--------------eecCcEEEEeeeEe
Q psy12043 80 GLISWVPPCQFQVYCRLDLTYWPFDSQVCELILGSWVYDGNNIDFH--------------FEDGNWRMNGDASE 139 (143)
Q Consensus 80 G~V~~~~~~~~~~~C~~~~~~fPfD~q~C~l~f~s~~y~~~~v~l~--------------~~n~EW~l~~~~~~ 139 (143)
|+|.|.++.++++.|++|+++||||+|+|+++|+||+|+++++++. .+++||++.+..+.
T Consensus 142 G~V~~~~~~~~~~~C~~d~~~FPfD~Q~C~l~fgSw~y~~~~i~l~~~~~~~v~~~~~~~~~~~eW~l~~~~~~ 215 (459)
T TIGR00860 142 GSVLYSPRITLTLACPMDLRNFPFDVQNCSLKFESWGYTTNDIKLEWKEQGAVQVDDSLFISLPEFELLGVYGT 215 (459)
T ss_pred CcEEEecCceEEecccceeccCCCCCccccEEEhhhccccceEEEEECCCCceEechhhccccCceEEEeeeee
Confidence 9999999999999999999999999999999999999999999885 26889999986543
No 4
>PF02931 Neur_chan_LBD: Neurotransmitter-gated ion-channel ligand binding domain ion channel family signature gamma-aminobutyric acid (GABA) receptor signature nicotinic acetylcholine receptor signature; InterPro: IPR006202 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 entry presents the extracellular ligand binding domain of these ion channels. This domain forms a pentameric arrangement in the known structure. ; GO: 0005230 extracellular ligand-gated ion channel activity, 0006810 transport, 0016020 membrane; PDB: 1LXH_B 1ABT_B 1TOS_A 1LXG_B 1IDG_B 1TOR_A 1IDH_B 3IGQ_B 3TLU_B 3UU5_A ....
Probab=100.00 E-value=7.1e-35 Score=212.90 Aligned_cols=137 Identities=28% Similarity=0.624 Sum_probs=115.0
Q ss_pred EEEeeceeEEEEEeeeeeeEEEcCCceeCCCCCCCeeEEEECCCCcccCCccccccCCCCCCCCCcceEEEEeeCCeEEE
Q psy12043 5 IQSILNSKLVSYLTADIGVKWYDPVLQWDPKKYGDIKQIYLAPQEVWQPDLSTFNSAGGNDVSPFGETYHIASSDGLISW 84 (143)
Q Consensus 5 i~~i~~~~~~~~~~~~l~~~W~D~rL~w~p~~~~~i~~i~~~~~~iW~Pdi~~~n~~~~~~~~~~~~~~v~v~~~G~V~~ 84 (143)
|.++.+..+++.+++++.+.|+|+||+|+|++|+|++.+.++.+.||+|++++.|+.+...........+.|+++|+|.+
T Consensus 37 i~~v~e~~~~~~~~~~~~~~W~D~rL~w~~~~~~~i~~~~v~~~~iW~P~l~~~n~~~~~~~~~~~~~~~~v~~~G~V~~ 116 (217)
T PF02931_consen 37 IVEVDESEQTFTVDGFIRLSWKDPRLKWNPSDYGGIESIRVPSSQIWTPDLYFYNSVSGSFEITEPNSNVRVYSDGTVRY 116 (217)
T ss_dssp EEEEETTTTEEEEEEEEEEEEEECCGE-STTTTTTESEEEEEGGGS----EEETTBSSSEEECS-SSEEEEEETTSEEEE
T ss_pred eeccccccchhhhhhhhceeccccccccChhhccCcccccccccceEecccccccccccceecccccccccccccchhee
Confidence 34455567889999999999999999999999999999999999999999999996553212223579999999999999
Q ss_pred ecCcEEEEEecccccccCCccceEEEEEeccccCCCeEEEE-------------------eecCcEEEEeeeEeEE
Q psy12043 85 VPPCQFQVYCRLDLTYWPFDSQVCELILGSWVYDGNNIDFH-------------------FEDGNWRMNGDASEFK 141 (143)
Q Consensus 85 ~~~~~~~~~C~~~~~~fPfD~q~C~l~f~s~~y~~~~v~l~-------------------~~n~EW~l~~~~~~~~ 141 (143)
..++.+++.|+|++.+||||+|+|.|+|+||.|+..+|.+. ..++||++.+.....+
T Consensus 117 ~~~~~~~~~C~~d~~~fPfD~q~C~i~~~s~~~~~~~v~l~~~~~~~~~~~~~~~~~~~~~~~~ew~~~~~~~~~~ 192 (217)
T PF02931_consen 117 SPRFTLTFSCPMDLRDFPFDSQNCSIKFGSWSYNSEEVQLKWENKNPPIDENDEVSLSDFVSNSEWKIVSVTSTRR 192 (217)
T ss_dssp EEEEEEEEEECETTTSSSSSEEEEEEEEEESSSSTTTEEEEESCSSS-TTSSTTTSCTTCETTSSEEEEEEEEEEE
T ss_pred eecccccccccccccccccccceeEEEEecccccccceeeeecccCceeeeeccccHHHccccceEEEEeeEEEEE
Confidence 99999999999999999999999999999999999999998 5579999999766543
No 5
>KOG3643|consensus
Probab=99.97 E-value=3.9e-31 Score=205.15 Aligned_cols=122 Identities=24% Similarity=0.435 Sum_probs=109.6
Q ss_pred EEEEeeceeEEEEEeeeeeeEEEcCCceeCCCCCCCeeEEEECC---CCcccCCccccccCCCCCCCC---CcceEEEEe
Q psy12043 4 IIQSILNSKLVSYLTADIGVKWYDPVLQWDPKKYGDIKQIYLAP---QEVWQPDLSTFNSAGGNDVSP---FGETYHIAS 77 (143)
Q Consensus 4 ~i~~i~~~~~~~~~~~~l~~~W~D~rL~w~p~~~~~i~~i~~~~---~~iW~Pdi~~~n~~~~~~~~~---~~~~~v~v~ 77 (143)
.|.+|+|.+|.++++++++|.|+||||+|+ .+++..+.+.. ++||.||.++-|+++. .++ ..+..+++.
T Consensus 69 SI~~vSEV~MDyTlt~y~rq~W~D~RLay~---~~~~~slTl~~~~~~~LWvPDTff~N~KkS--f~H~~T~~N~~lRl~ 143 (459)
T KOG3643|consen 69 SIDAVSEVNMDYTLTMYLRQTWRDPRLAYS---SKNIDSLTLDVRYVDKLWVPDTFFPNSKKS--FFHDVTTHNSLLRLH 143 (459)
T ss_pred eechhccccchhhhhhhhhhhhcCcccccC---CCCCceEEEchhhhhccccCceecccCccc--ccceeeecceEEEEc
Confidence 467788899999999999999999999998 46778999984 7999999999998763 333 468999999
Q ss_pred eCCeEEEecCcEEEEEecccccccCCccceEEEEEeccccCCCeEEEEeecCc
Q psy12043 78 SDGLISWVPPCQFQVYCRLDLTYWPFDSQVCELILGSWVYDGNNIDFHFEDGN 130 (143)
Q Consensus 78 ~~G~V~~~~~~~~~~~C~~~~~~fPfD~q~C~l~f~s~~y~~~~v~l~~~n~E 130 (143)
+||+|.+..|++.++.|+|||++||+|+|+|+|.++||+|+.++|.+.|..|.
T Consensus 144 ~dGtVlys~RlT~Ta~C~MDL~~fPmD~Q~C~LeiESYGYt~~DI~y~W~~g~ 196 (459)
T KOG3643|consen 144 PDGTVLYSIRLTVTAACPMDLKLFPMDSQNCKLEIESYGYTTDDIEYYWSKGD 196 (459)
T ss_pred CCCeEEEEEEEEEEEecccccccCCCcccceeEEEEecccccccEEEEEcCCC
Confidence 99999999999999999999999999999999999999999999999976543
No 6
>KOG3644|consensus
Probab=99.94 E-value=4.6e-26 Score=181.52 Aligned_cols=119 Identities=24% Similarity=0.397 Sum_probs=98.3
Q ss_pred EeeceeEEEEEeeeeeeEEEcCCceeC-CC-CCCCeeEEEEC-CCCcccCCccccccCCCC-CCCCCcceEEEEeeCCeE
Q psy12043 7 SILNSKLVSYLTADIGVKWYDPVLQWD-PK-KYGDIKQIYLA-PQEVWQPDLSTFNSAGGN-DVSPFGETYHIASSDGLI 82 (143)
Q Consensus 7 ~i~~~~~~~~~~~~l~~~W~D~rL~w~-p~-~~~~i~~i~~~-~~~iW~Pdi~~~n~~~~~-~~~~~~~~~v~v~~~G~V 82 (143)
+|.+..+.+.+++++++.|+||||+.+ .+ ++-+.-...+. .++||.||+++.|++... +.....+..+.|++||+|
T Consensus 79 ~ise~~mdf~~di~~~~~W~DpRL~~~~~~~~~~~~~~~~l~~~~~iW~Pd~~F~NsK~a~~H~~~~~N~ll~I~pnGtV 158 (457)
T KOG3644|consen 79 SISEITMDFEVDIYFRERWQDPRLAYNALKFDHILPCKLNLSLKQKIWTPDTFFANSKSAEFHKSTKPNVLLMIFPNGTV 158 (457)
T ss_pred ceecccceEEeeeeeeeeEeCccccccccCcccccccccccccCCceecCceeeecccceeeecCCCCceEEEEecCCeE
Confidence 344467889999999999999999998 34 32222222222 257999999999998753 222346899999999999
Q ss_pred EEecCcEEEEEecccccccCCccceEEEEEeccccCCCeEEEE
Q psy12043 83 SWVPPCQFQVYCRLDLTYWPFDSQVCELILGSWVYDGNNIDFH 125 (143)
Q Consensus 83 ~~~~~~~~~~~C~~~~~~fPfD~q~C~l~f~s~~y~~~~v~l~ 125 (143)
.+..|+.++.+|+|++.+||+|+|+|.+.|+||+|+.++|++.
T Consensus 159 ~~~~Ri~l~~~C~m~L~~fP~D~Q~C~l~~eSy~Yn~~~v~~~ 201 (457)
T KOG3644|consen 159 WYSYRISLTLPCNMDLSKFPMDSQECKLQLESYAYNTDDVRLE 201 (457)
T ss_pred EEEEEEEEeeceeeehhhCCCccceeeEEEEEeccccceEEEE
Confidence 9999999999999999999999999999999999999999998
No 7
>KOG3642|consensus
Probab=99.89 E-value=6e-23 Score=160.52 Aligned_cols=117 Identities=20% Similarity=0.399 Sum_probs=100.7
Q ss_pred eeceeEEEEEeeeeeeEEEcCCceeCCCCCCCeeEEEEC---CCCcccCCccccccCCCC-CCCCCcceEEEEeeCCeEE
Q psy12043 8 ILNSKLVSYLTADIGVKWYDPVLQWDPKKYGDIKQIYLA---PQEVWQPDLSTFNSAGGN-DVSPFGETYHIASSDGLIS 83 (143)
Q Consensus 8 i~~~~~~~~~~~~l~~~W~D~rL~w~p~~~~~i~~i~~~---~~~iW~Pdi~~~n~~~~~-~~~~~~~~~v~v~~~G~V~ 83 (143)
+++.+++..++++++|.|.|.||.++ +-.+.+.+. ..+||.||.++.|+++.. +.....+..++|..||+|.
T Consensus 82 VSd~~meytid~~FrQ~W~D~RL~f~----~~~~~L~Ln~~m~~kiW~PDTfF~NgkkS~~H~iT~pN~l~Ri~~dG~vl 157 (466)
T KOG3642|consen 82 VSDSDMEYTIDCFFRQTWVDDRLKFN----GPQEALPLNSLMLSKIWIPDTFFRNGKKSYAHNITTPNKLVRIYIDGTVL 157 (466)
T ss_pred ccccCceEEEEEEEEEeehhhhhccc----CcchhhccchhhhcCcccCCcccccCcccceeeccCCCceEEEeECCcce
Confidence 34578999999999999999999998 323344444 369999999999998753 3344679999999999999
Q ss_pred EecCcEEEEEecccccccCCccceEEEEEeccccCCCeEEEEeec
Q psy12043 84 WVPPCQFQVYCRLDLTYWPFDSQVCELILGSWVYDGNNIDFHFED 128 (143)
Q Consensus 84 ~~~~~~~~~~C~~~~~~fPfD~q~C~l~f~s~~y~~~~v~l~~~n 128 (143)
|..|++..+.|+|++.+||+|.|.|.++|||++|+++|+.+.+.+
T Consensus 158 yt~RlTi~A~C~m~l~~fPMD~haCpl~fgSy~Y~~~evvY~W~~ 202 (466)
T KOG3642|consen 158 YTMRLTIPAECPMHLARFPMDSHACPLKFGSYAYPGSEVVYKWKK 202 (466)
T ss_pred EEEEEeecccCcchhhcCCCCcccCcceecccCcCCCCEEEEEec
Confidence 999999999999999999999999999999999999999997443
No 8
>PF15363 DUF4596: Domain of unknown function (DUF4596)
Probab=71.92 E-value=8.2 Score=21.02 Aligned_cols=34 Identities=15% Similarity=0.337 Sum_probs=23.7
Q ss_pred cCCccceEEEEEeccccCCCeEEEEeecCcEEEEeeeE
Q psy12043 101 WPFDSQVCELILGSWVYDGNNIDFHFEDGNWRMNGDAS 138 (143)
Q Consensus 101 fPfD~q~C~l~f~s~~y~~~~v~l~~~n~EW~l~~~~~ 138 (143)
-|+|.-.-++...|++- ++ -.-+.|||.++....
T Consensus 11 sPld~s~asitvtsfSp--ed--~sSpqGeWTivElET 44 (46)
T PF15363_consen 11 SPLDDSSASITVTSFSP--ED--CSSPQGEWTIVELET 44 (46)
T ss_pred CCCCCCcceeEEeecCc--cc--cCCCCCceEEEEEee
Confidence 37787777777776554 22 225899999998754
No 9
>PF06107 DUF951: Bacterial protein of unknown function (DUF951); InterPro: IPR009296 This family consists of several short hypothetical bacterial proteins of unknown function.
Probab=51.59 E-value=10 Score=21.89 Aligned_cols=17 Identities=24% Similarity=0.515 Sum_probs=14.9
Q ss_pred ecCcEEEEeeeEeEEeC
Q psy12043 127 EDGNWRMNGDASEFKIK 143 (143)
Q Consensus 127 ~n~EW~l~~~~~~~~~~ 143 (143)
++.+|+++.+.++|++|
T Consensus 17 G~~~Wei~R~GaDikik 33 (57)
T PF06107_consen 17 GSNEWEIIRIGADIKIK 33 (57)
T ss_pred CCCEEEEEEccCcEEEE
Confidence 46799999999999876
No 10
>PRK14751 tetracycline resistance determinant leader peptide; Provisional
Probab=49.98 E-value=13 Score=17.79 Aligned_cols=19 Identities=11% Similarity=0.039 Sum_probs=15.3
Q ss_pred cccccccCCccceEEEEEe
Q psy12043 95 RLDLTYWPFDSQVCELILG 113 (143)
Q Consensus 95 ~~~~~~fPfD~q~C~l~f~ 113 (143)
+|-+..||-|..-|...|-
T Consensus 5 ~mi~h~~psdksi~hwdf~ 23 (28)
T PRK14751 5 PMVMHKNPSDKSIYHWDFY 23 (28)
T ss_pred eeeeecCCCcCceeeeeeh
Confidence 5777899999999887663
No 11
>KOG1332|consensus
Probab=46.97 E-value=68 Score=24.53 Aligned_cols=62 Identities=23% Similarity=0.358 Sum_probs=36.9
Q ss_pred cceEEEEeeCCeEEE-ecCcEEEEEecccccccCCccceEEEEEeccccCCCeEEEE-----------eecCcEEEEee
Q psy12043 70 GETYHIASSDGLISW-VPPCQFQVYCRLDLTYWPFDSQVCELILGSWVYDGNNIDFH-----------FEDGNWRMNGD 136 (143)
Q Consensus 70 ~~~~v~v~~~G~V~~-~~~~~~~~~C~~~~~~fPfD~q~C~l~f~s~~y~~~~v~l~-----------~~n~EW~l~~~ 136 (143)
....+....||+|.. ........-=.--+..|| |.+-=.||+.+++-+.+. ..+|+|+.++.
T Consensus 223 ~s~iAS~SqDg~viIwt~~~e~e~wk~tll~~f~-----~~~w~vSWS~sGn~LaVs~GdNkvtlwke~~~Gkw~~v~~ 296 (299)
T KOG1332|consen 223 KSTIASCSQDGTVIIWTKDEEYEPWKKTLLEEFP-----DVVWRVSWSLSGNILAVSGGDNKVTLWKENVDGKWEEVGE 296 (299)
T ss_pred ceeeEEecCCCcEEEEEecCccCcccccccccCC-----cceEEEEEeccccEEEEecCCcEEEEEEeCCCCcEEEccc
Confidence 356777888998654 333221111122234454 666667888888877665 34788988764
No 12
>PF08076 TetM_leader: Tetracycline resistance determinant leader peptide; InterPro: IPR012992 The antibiotic tetracycline has a broad spectrum of activity, acting to inhibit bacterial protein synthesis by binding to the 30S ribosomal subunit, which prevents the association of the aminoacyl-tRNA to the ribosomal acceptor A site. Tetracycline binding is reversible, therefore diluting out the antibiotic can reverse its effects. Tetracycline resistance genes are often located on mobile elements, such as plasmids, transposons and/or conjugative transposons, which can sometimes be transferred between bacterial species. In certain cases, tetracycline can enhance the transfer of these elements, thereby promoting resistance amongst a bacterial colony. There are three types of tetracycline resistance: tetracycline efflux, ribosomal protection, and tetracycline modification [, ]: Tetracycline efflux proteins belong to the major facilitator superfamily. Efflux proteins are membrane-associated proteins that recognise and export tetracycline from the cell. They are found in both Gram-positive and Gram-negative bacteria []. There are at least 22 different tetracycline efflux proteins, grouped according to sequence similarity: Group 1 are Tet(A), Tet(B), Tet(C), Tet(D), Tet(E), Tet(G), Tet(H), Tet(J), Tet(Z) and Tet(30); Group 2 are Tet(K) and Tet(L); Group 3 are Otr(B) and Tcr(3); Group 4 is TetA(P); Group 5 is Tet(V). In addition, there are the efflux proteins Tet(31), Tet(33), Tet(V), Tet(Y), Tet(34), and Tet(35). Ribosomal protection proteins are cytoplasmic proteins that display homology with the elongation factors EF-Tu and EF-G. Protection proteins bind the ribosome, causing an alteration in ribosomal conformation that prevents tetracycline from binding. There are at least ten ribosomal protection proteins: Tet(M), Tet(O), Tet(S), Tet(W), Tet(32), Tet(36), Tet(Q), Tet(T), Otr(A), and TetB(P). Both Tet(M) and Tet(O) have ribosome-dependent GTPase activity, the hydrolysis of GTP providing the energy for the ribosomal conformational changes. Tetracycline modification proteins include the enzymes Tet(37) and Tet(X), both of which inactivate tetracycline. In addition, there are the tetracycline resistance proteins Tet(U) and Otr(C). The expression of several of these tet genes is controlled by a family of tetracycline transcriptional regulators known as TetR. TetR family regulators are involved in the transcriptional control of multidrug efflux pumps, pathways for the biosynthesis of antibiotics, response to osmotic stress and toxic chemicals, control of catabolic pathways, differentiation processes, and pathogenicity []. The TetR proteins identified in over 115 genera of bacteria and archaea share a common helix-turn-helix (HTH) structure in their DNA-binding domain. However, TetR proteins can work in different ways: they can bind a target operator directly to exert their effect (e.g. TetR binds Tet(A) gene to repress it in the absence of tetracycline), or they can be involved in complex regulatory cascades in which the TetR protein can either be modulated by another regulator or TetR can trigger the cellular response. This entry represents the tetracycline resistance leader peptide, which can be found in Tet(M) ribosomal protection proteins. A short open reading frame corresponding to a 28 amino acid peptide, which contains a number of inverted repeat sequences was found immediately upstream of tet(M). Transcriptional analyses has found that expression of tet(M) resulted from an extension of a small transcript representing the upstream leader region into the resistance determinant. Therefore, this leader sequence is responsible for transcriptional attenuation and thus regulation of the transcription of tet(M) [].
Probab=44.28 E-value=11 Score=18.22 Aligned_cols=20 Identities=15% Similarity=0.198 Sum_probs=15.9
Q ss_pred cccccccCCccceEEEEEec
Q psy12043 95 RLDLTYWPFDSQVCELILGS 114 (143)
Q Consensus 95 ~~~~~~fPfD~q~C~l~f~s 114 (143)
|+-+..||-|...|...|-+
T Consensus 5 p~~m~~fP~D~S~y~WDF~~ 24 (28)
T PF08076_consen 5 PMFMHHFPSDKSIYHWDFCS 24 (28)
T ss_pred eeeeccCCCccceeehhhhh
Confidence 67788999999988876643
No 13
>PF11211 DUF2997: Protein of unknown function (DUF2997); InterPro: IPR021375 This family of proteins has no known function.
Probab=37.42 E-value=20 Score=19.83 Aligned_cols=23 Identities=13% Similarity=-0.059 Sum_probs=18.2
Q ss_pred EEEEeeCCeEEEecCcEEEEEec
Q psy12043 73 YHIASSDGLISWVPPCQFQVYCR 95 (143)
Q Consensus 73 ~v~v~~~G~V~~~~~~~~~~~C~ 95 (143)
.+.|++||+|.-......-.+|.
T Consensus 2 ~~~I~~dG~V~~~v~G~~G~~C~ 24 (48)
T PF11211_consen 2 EFTIYPDGRVEEEVEGFKGSSCL 24 (48)
T ss_pred EEEECCCcEEEEEEEeccChhHH
Confidence 47899999999887777767774
No 14
>PRK03174 sspH acid-soluble spore protein H; Provisional
Probab=34.75 E-value=35 Score=19.85 Aligned_cols=18 Identities=17% Similarity=0.229 Sum_probs=15.1
Q ss_pred CceEEEEeeceeEEEEEe
Q psy12043 1 MPCIIQSILNSKLVSYLT 18 (143)
Q Consensus 1 ~~v~i~~i~~~~~~~~~~ 18 (143)
.||+|+.+.++..+..+.
T Consensus 23 ~pV~Ie~vde~~~tA~I~ 40 (59)
T PRK03174 23 VPIYIQHVDEQNGTARIH 40 (59)
T ss_pred EEEEEEEEcCCCCeEEEE
Confidence 489999999988887774
No 15
>PRK01625 sspH acid-soluble spore protein H; Provisional
Probab=33.86 E-value=36 Score=19.80 Aligned_cols=18 Identities=22% Similarity=0.182 Sum_probs=14.9
Q ss_pred CceEEEEeeceeEEEEEe
Q psy12043 1 MPCIIQSILNSKLVSYLT 18 (143)
Q Consensus 1 ~~v~i~~i~~~~~~~~~~ 18 (143)
+||.|+.+.++..+..+.
T Consensus 23 ~pV~Iq~vde~~~tA~V~ 40 (59)
T PRK01625 23 VPVWIESCDEQSGVAQVY 40 (59)
T ss_pred EEEEEEEEcCCCCeEEEE
Confidence 489999999988887774
No 16
>TIGR02861 SASP_H small acid-soluble spore protein, H-type. This model is derived from pfam08141 but has been expanded to include in the seed corresponding proteins from three species of Clostridium. Members of this family should occur only in endospore-forming bacteria, typically with two members per genome, but may be absent from the genomes of some endospore-forming bacteria. SspH (previously designated YfjU) was shown to be expressed specifically in spores of Bacillus subtilis.
Probab=33.08 E-value=42 Score=19.39 Aligned_cols=18 Identities=11% Similarity=0.170 Sum_probs=15.0
Q ss_pred CceEEEEeeceeEEEEEe
Q psy12043 1 MPCIIQSILNSKLVSYLT 18 (143)
Q Consensus 1 ~~v~i~~i~~~~~~~~~~ 18 (143)
.||+|+++.++..+..++
T Consensus 23 ~pV~Ie~vde~~~tA~V~ 40 (58)
T TIGR02861 23 VPVYIEHVDEQSGTARVY 40 (58)
T ss_pred EEEEEEEEcCCCCeEEEE
Confidence 389999999988887774
No 17
>PF09732 CactinC_cactus: Cactus-binding C-terminus of cactin protein; InterPro: IPR019134 This entry represents the C-terminal 200 residues of the cactin protein which is necessary for the association of cactin with IkappaB-cactus, as one of the intracellular members of the Rel complex. The Rel (NF-kappaB) pathway is conserved in invertebrates and vertebrates. In mammals, it controls the activities of the immune and inflammatory response genes as well as viral genes, and is critical for cell growth and survival. In Drosophila, the Rel pathway functions in the innate cellular and humoral immune response, in muscle development and in the establishment of dorsal-ventral polarity in the early embryo []. Most members of the family also have the conserved mid region of cactin (IPR018816 from INTERPRO) further upstream.
Probab=30.21 E-value=1.1e+02 Score=20.57 Aligned_cols=30 Identities=17% Similarity=0.388 Sum_probs=22.7
Q ss_pred ccceEEEEEeccccCCCeEEEEeecCcEEEE
Q psy12043 104 DSQVCELILGSWVYDGNNIDFHFEDGNWRMN 134 (143)
Q Consensus 104 D~q~C~l~f~s~~y~~~~v~l~~~n~EW~l~ 134 (143)
+...|-|.|.+ +-+=++|.+.+.|-||+..
T Consensus 69 ~~~~~~L~F~A-gpPYeDIAFkIvnrEWd~s 98 (125)
T PF09732_consen 69 NPDFCILRFHA-GPPYEDIAFKIVNREWDYS 98 (125)
T ss_pred CCCEEEEEEeC-CCCCcCEEEEEecCeeecC
Confidence 56789999964 2344789999999999874
No 18
>PF08141 SspH: Small acid-soluble spore protein H family; InterPro: IPR012610 This family consists of the small acid-soluble spore proteins (SASP) of the H type (sspH). SspH are unique to spores of Bacillus subtilis and are expressed only in the forespore compartment during sporulation of this organism. The sspH genes are monocistronic and are recognised by the forespore-specific sigma factor for RNA polymerase - sigma-G. The specific role of this protein is unclear but is thought to play a role in sporulation under conditions different from that of the common laboratory tests of spore properties [].; GO: 0030436 asexual sporulation, 0042601 endospore-forming forespore
Probab=28.91 E-value=54 Score=18.93 Aligned_cols=17 Identities=12% Similarity=0.173 Sum_probs=14.5
Q ss_pred ceEEEEeeceeEEEEEe
Q psy12043 2 PCIIQSILNSKLVSYLT 18 (143)
Q Consensus 2 ~v~i~~i~~~~~~~~~~ 18 (143)
||+|+++.++..+..++
T Consensus 24 pV~Ie~vde~~~tA~V~ 40 (58)
T PF08141_consen 24 PVWIEHVDEENGTARVH 40 (58)
T ss_pred EEEEEEEcCCCCeEEEE
Confidence 89999999988888775
No 19
>PF15016 DUF4520: Domain of unknown function (DUF4520)
Probab=26.34 E-value=1.7e+02 Score=18.27 Aligned_cols=39 Identities=15% Similarity=0.128 Sum_probs=25.0
Q ss_pred ceEEEEeeCCeEEE--ecCcEEEEEecccccccCCccceEEEEE
Q psy12043 71 ETYHIASSDGLISW--VPPCQFQVYCRLDLTYWPFDSQVCELIL 112 (143)
Q Consensus 71 ~~~v~v~~~G~V~~--~~~~~~~~~C~~~~~~fPfD~q~C~l~f 112 (143)
.-....++||+|.. ..+.++...+.++-.. +...|++.|
T Consensus 15 ~GrF~AysDgrVr~~F~Drt~L~l~~~~~~~~---~~~~c~l~~ 55 (85)
T PF15016_consen 15 VGRFTAYSDGRVRVHFDDRTILTLIWNFSSRE---ELGWCKLTF 55 (85)
T ss_pred ceEEEEEcCCeEEEEEcCCCEEEEEeCCCCcc---cCCEEEEEc
Confidence 34677888887654 6777888777544433 455566554
No 20
>PF11455 DUF3018: Protein of unknown function (DUF3018); InterPro: IPR021558 This is a bacterial family of uncharacterised proteins.
Probab=23.36 E-value=32 Score=20.42 Aligned_cols=10 Identities=40% Similarity=1.145 Sum_probs=7.5
Q ss_pred CCCcccCCcc
Q psy12043 47 PQEVWQPDLS 56 (143)
Q Consensus 47 ~~~iW~Pdi~ 56 (143)
+=.||+||+.
T Consensus 19 PVqiWVPDtr 28 (65)
T PF11455_consen 19 PVQIWVPDTR 28 (65)
T ss_pred cceeeCCCCC
Confidence 3468999985
No 21
>COG2158 Uncharacterized protein containing a Zn-finger-like domain [General function prediction only]
Probab=23.30 E-value=51 Score=21.55 Aligned_cols=17 Identities=35% Similarity=0.835 Sum_probs=13.6
Q ss_pred ccC--CccceEEEEEeccc
Q psy12043 100 YWP--FDSQVCELILGSWV 116 (143)
Q Consensus 100 ~fP--fD~q~C~l~f~s~~ 116 (143)
.|| ||.|+|.+++-++-
T Consensus 25 YYPCHfdgQnC~fCyCPfY 43 (112)
T COG2158 25 YYPCHFDGQNCLFCYCPFY 43 (112)
T ss_pred EecceecCCceeEEecccc
Confidence 454 89999999998754
No 22
>COG3557 Uncharacterized domain/protein associated with RNAses G and E [Translation, ribosomal structure and biogenesis]
Probab=22.29 E-value=3e+02 Score=19.58 Aligned_cols=101 Identities=16% Similarity=0.355 Sum_probs=57.5
Q ss_pred EEEEEeeeeeeEEEcCCceeCCCCC---CCeeEEEEC-CCCccc---CCccccccCCCCCCCCCcceEEEEeeCCeEEEe
Q psy12043 13 LVSYLTADIGVKWYDPVLQWDPKKY---GDIKQIYLA-PQEVWQ---PDLSTFNSAGGNDVSPFGETYHIASSDGLISWV 85 (143)
Q Consensus 13 ~~~~~~~~l~~~W~D~rL~w~p~~~---~~i~~i~~~-~~~iW~---Pdi~~~n~~~~~~~~~~~~~~v~v~~~G~V~~~ 85 (143)
+..+.++++.-.|+++..--+.+.. +|-..+... .++-|. |.+..+.+.. =.+..+.+..+|.-
T Consensus 13 qsYKhnG~LhR~W~~t~Vlk~t~~~iIg~NdhtlV~esdgr~w~TrEpai~yF~k~~------wFNvi~mir~dGi~--- 83 (177)
T COG3557 13 QSYKHNGSLHRTWNETKVLKSTEQLIIGGNDHTLVTESDGRTWVTREPAIWYFHKNE------WFNVIAMIREDGIY--- 83 (177)
T ss_pred EEEecCCceeeeecCcEEEeecCcEEEeccCcEEEEecCCccceecCCEEEEEeccc------ceeeEEEEecCCeE---
Confidence 4566788899999999876654421 122222222 234452 4443332211 23667777888865
Q ss_pred cCcEEEEEecccccccCCccceEEEEEeccccCCCeEEEE-eecCcEEEEee
Q psy12043 86 PPCQFQVYCRLDLTYWPFDSQVCELILGSWVYDGNNIDFH-FEDGNWRMNGD 136 (143)
Q Consensus 86 ~~~~~~~~C~~~~~~fPfD~q~C~l~f~s~~y~~~~v~l~-~~n~EW~l~~~ 136 (143)
..|.+. +-|++|.|+.. |-.-++++. .+.|||.++.+
T Consensus 84 ------yY~Nl~-sPf~~deealK-------YiDyDLDiKV~~d~~~~llDv 121 (177)
T COG3557 84 ------YYCNLA-SPFIMDEEALK-------YIDYDLDIKVFPDGEKKLLDV 121 (177)
T ss_pred ------EEEEcC-CCceechhhhc-------eEeeeeeEEEccCCceEEccH
Confidence 345543 45788888643 222234444 78999999865
No 23
>KOG1344|consensus
Probab=22.01 E-value=66 Score=24.37 Aligned_cols=33 Identities=18% Similarity=0.278 Sum_probs=22.5
Q ss_pred cccCCccccccCCCCCCCCCcceEEEEeeCCeEE
Q psy12043 50 VWQPDLSTFNSAGGNDVSPFGETYHIASSDGLIS 83 (143)
Q Consensus 50 iW~Pdi~~~n~~~~~~~~~~~~~~v~v~~~G~V~ 83 (143)
=.+||+++||+..+ ......-..+.|+++|-+.
T Consensus 246 ef~Pd~VvYNAGTD-iLeGDpLG~L~ISp~Gi~~ 278 (324)
T KOG1344|consen 246 EFRPDMVVYNAGTD-ILEGDPLGNLAISPEGIIE 278 (324)
T ss_pred hhCCcEEEEeCCCc-cccCCCCCCeeecccccch
Confidence 37899999998653 2333445667788888654
No 24
>PRK04257 hypothetical protein; Provisional
Probab=20.13 E-value=2.2e+02 Score=17.32 Aligned_cols=19 Identities=11% Similarity=-0.137 Sum_probs=13.9
Q ss_pred CcceEEEEe--eCCeEEEecC
Q psy12043 69 FGETYHIAS--SDGLISWVPP 87 (143)
Q Consensus 69 ~~~~~v~v~--~~G~V~~~~~ 87 (143)
+...-+.|. .||.|.|..+
T Consensus 56 P~HRI~~I~~~~dG~vvw~r~ 76 (78)
T PRK04257 56 PYHRILEIVNKKTGEILYKKR 76 (78)
T ss_pred cceEEEEEEEcCCCeEEEEEe
Confidence 445666777 8999999753
Done!