Query psy11692
Match_columns 171
No_of_seqs 126 out of 1094
Neff 8.4
Searched_HMMs 46136
Date Fri Aug 16 16:26:39 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy11692.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/11692hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG3646|consensus 100.0 1.1E-41 2.4E-46 278.8 7.2 169 1-170 167-337 (486)
2 TIGR00860 LIC Cation transport 100.0 1.6E-34 3.4E-39 244.9 14.4 161 1-163 172-335 (459)
3 KOG3643|consensus 100.0 4.7E-34 1E-38 233.2 15.2 155 1-158 176-331 (459)
4 KOG3645|consensus 100.0 7.2E-34 1.6E-38 240.2 14.6 169 1-170 170-343 (449)
5 KOG3644|consensus 100.0 3.4E-32 7.4E-37 228.4 11.4 155 1-159 186-341 (457)
6 KOG3642|consensus 100.0 1.2E-31 2.6E-36 220.2 5.2 157 1-160 184-341 (466)
7 PF02932 Neur_chan_memb: Neuro 99.9 4.1E-24 9E-29 160.9 1.3 97 74-171 1-98 (237)
8 PF02931 Neur_chan_LBD: Neurot 98.7 8E-08 1.7E-12 73.7 8.4 67 1-67 142-217 (217)
9 PF10856 DUF2678: Protein of u 65.0 13 0.00028 25.9 3.8 13 132-144 62-74 (118)
10 PF14494 DUF4436: Domain of un 53.7 71 0.0015 25.4 6.8 70 55-125 152-225 (256)
11 COG3671 Predicted membrane pro 43.6 69 0.0015 22.5 4.6 15 156-170 110-125 (125)
12 PF15102 TMEM154: TMEM154 prot 33.6 40 0.00086 24.5 2.3 14 152-165 77-90 (146)
13 PF01350 Flavi_NS4A: Flaviviru 27.5 77 0.0017 23.0 3.0 37 80-116 56-94 (144)
14 PF13119 DUF3973: Domain of un 27.4 28 0.0006 19.4 0.5 16 88-103 24-39 (41)
15 TIGR03068 srtB_sig_NPQTN sorta 25.8 1.2E+02 0.0025 16.2 3.5 9 121-129 2-10 (33)
16 PHA03042 CD47-like protein; Pr 23.9 1.3E+02 0.0029 24.3 3.9 14 8-21 46-59 (286)
17 TIGR01432 QOXA cytochrome aa3 22.5 2.1E+02 0.0045 21.9 4.8 21 149-169 42-62 (217)
18 PF03350 UPF0114: Uncharacteri 22.3 46 0.00099 23.3 1.0 41 127-170 56-96 (124)
19 COG3374 Predicted membrane pro 21.5 2E+02 0.0043 22.0 4.2 44 101-145 48-91 (197)
20 TIGR03063 srtB_target sortase 21.4 1.4E+02 0.003 15.4 2.7 12 121-133 2-13 (29)
21 TIGR01294 P_lamban phospholamb 20.8 1.8E+02 0.004 16.7 3.3 21 129-149 28-48 (52)
22 PRK10525 cytochrome o ubiquino 20.3 98 0.0021 25.5 2.7 12 160-171 74-85 (315)
23 TIGR02896 spore_III_AF stage I 20.0 2.4E+02 0.0051 19.3 4.1 26 104-130 8-33 (106)
No 1
>KOG3646|consensus
Probab=100.00 E-value=1.1e-41 Score=278.82 Aligned_cols=169 Identities=38% Similarity=0.707 Sum_probs=158.5
Q ss_pred CeEecceecCCeEEEEEcCCCcccccccccccccEEEeEeeeEEEE--ecCCCCCeeEEEEEEEEEeecceeEEEEehhh
Q psy11692 1 MKFGSWTFNGDQVSLALYNDKNFVDLSDYWKSGTWDIIEVPAYLNV--YDEHQPTETDITFYIIIRRKTLFYTVNLILPT 78 (171)
Q Consensus 1 L~f~Sw~y~~~~v~l~~~~~~~~~~~~~~~~~~eW~l~~~~~~~~~--~~~~~~~y~~i~~~~~l~R~~~~y~~~~~iP~ 78 (171)
||||||+|++..++++.......+|++.|++||||++.+.+..+.. |+||+++|++++|++++|||..||.+|+++||
T Consensus 167 mKFGSWTY~G~~lDL~~~~~~g~~Dls~yi~NGEW~Ll~~pakr~~~~y~cC~epY~dv~F~l~irRRTLyYgfNlIiP~ 246 (486)
T KOG3646|consen 167 LKFGSWTYAGILLDLRIDDEDGGIDLSTYIPNGEWDLLGTPAKREEKTYDCCPEPYPDVTFYLHIRRRTLYYGFNLIIPS 246 (486)
T ss_pred EEeeeEEEcceeeeeeeccccCCcchhhcccCCceeeccccccceeeecccCCCCcceeEEEEEEEehhhHHHHHHHHHH
Confidence 6999999999999999866555678999999999999999987654 67999999999999999999999999999999
Q ss_pred HHHHHHHHHhhcccCCCCceEEehhHHHHHHHHHHHHhhhcCCCCccCcCchhhHHHHHHHHHHHHHHHHHHhhhhhhhc
Q psy11692 79 VLISFLCVLVFYLPAEAGEKVTLGISILLSLVVFLLLVSKILPPTSLVLPLIAKYLLFTFIMNTVKSACLHYFLLYELLA 158 (171)
Q Consensus 79 ~li~~l~~~~F~lp~~~~~r~~l~~t~lL~~~~~l~~v~~~lP~~s~~~p~i~~y~~~~~~~v~~s~~~~~~~~~~~~~~ 158 (171)
+++.++++.+|-+|+|+|||+++++|++|+..+|+..+++..|++|+++|++|.||.+||+++++|+ ..+++++|+|+|
T Consensus 247 lLIs~m~lLgFtlppD~gEKitL~iTilLsvc~FL~mvse~~PpTSeaVPllg~fFsc~m~iv~~Sv-vfTv~vLn~h~R 325 (486)
T KOG3646|consen 247 LLISLMSLLGFTLPPDAGEKITLQITILLSVCFFLTMVSEMTPPTSEAVPLLGAFFSCCMFIVAASV-VFTVIVLNLHHR 325 (486)
T ss_pred HHHHHHHHhccccCccccceeeeeeehHHHHHHHHHHHHhhcCCccccccHHHHHHHHHHHHHHhhh-eeEEEEEeeecc
Confidence 9999999999999999999999999999999999999999999999999999999999999999996 467889999999
Q ss_pred cCCCCCCCcccc
Q psy11692 159 TGNTFDMNTYQK 170 (171)
Q Consensus 159 ~~~~~~~p~w~~ 170 (171)
+..+.+|+.|.+
T Consensus 326 ~p~~h~m~p~~r 337 (486)
T KOG3646|consen 326 TPETHEMSPWTR 337 (486)
T ss_pred CccccccCHHHH
Confidence 999999888876
No 2
>TIGR00860 LIC Cation transporter family protein. selective while glycine receptors are anion selective).
Probab=100.00 E-value=1.6e-34 Score=244.90 Aligned_cols=161 Identities=25% Similarity=0.418 Sum_probs=138.9
Q ss_pred CeEecceecCCeEEEEEcCCC-cccccccccccccEEEeEeeeEEE-EecCCCCCeeEEEEEEEEEeecceeEEEEehhh
Q psy11692 1 MKFGSWTFNGDQVSLALYNDK-NFVDLSDYWKSGTWDIIEVPAYLN-VYDEHQPTETDITFYIIIRRKTLFYTVNLILPT 78 (171)
Q Consensus 1 L~f~Sw~y~~~~v~l~~~~~~-~~~~~~~~~~~~eW~l~~~~~~~~-~~~~~~~~y~~i~~~~~l~R~~~~y~~~~~iP~ 78 (171)
|+||||+|+++++++.|.+++ ..++.+.|..++||++.+....+. .+.+|+++|++++|++++||+++||++++++||
T Consensus 172 l~fgSw~y~~~~i~l~~~~~~~v~~~~~~~~~~~eW~l~~~~~~~~~~~~~~~~~y~~l~~~~~l~R~~~~y~~~l~iP~ 251 (459)
T TIGR00860 172 LKFESWGYTTNDIKLEWKEQGAVQVDDSLFISLPEFELLGVYGTRYCTSETNTGEYPCLTFSFVLRRRPLYYLLQLYIPS 251 (459)
T ss_pred EEEhhhccccceEEEEECCCCceEechhhccccCceEEEeeeeeeeEecccCCCCcCeEEEEEEEEEcccceeeeehHHH
Confidence 689999999999999986542 234566678999999999655443 356788999999999999999999999999999
Q ss_pred HHHHHHHHHhhcccCC-CCceEEehhHHHHHHHHHHHHhhhcCCCCccCcCchhhHHHHHHHHHHHHHHHHHHhhhhhhh
Q psy11692 79 VLISFLCVLVFYLPAE-AGEKVTLGISILLSLVVFLLLVSKILPPTSLVLPLIAKYLLFTFIMNTVKSACLHYFLLYELL 157 (171)
Q Consensus 79 ~li~~l~~~~F~lp~~-~~~r~~l~~t~lL~~~~~l~~v~~~lP~~s~~~p~i~~y~~~~~~~v~~s~~~~~~~~~~~~~ 157 (171)
+++++++|++||+|++ +|||+++|+|++|++++|+..+++.+|++|+ +|+||+|+.+||+++++|++. .+++.+.++
T Consensus 252 ~li~~ls~~sF~Lp~~a~~eRi~L~it~lLs~~vf~~~v~~~lP~~S~-vpli~~y~~~~~~~v~~sli~-tv~V~~~~~ 329 (459)
T TIGR00860 252 ILIVILSWVSFWLPADASGARVSLGITTLLTMTTFSSGVRESLPAVSY-VKAIDVYFAVCMAFVFLALLE-TAFVNYVHH 329 (459)
T ss_pred HHHHHHhheeEecCCCCCCCcEEEEEEHHHHHHHHHHHHHhhCCCcch-HHHHHHHHHHHHHHHHHHHHH-HHhheeEEc
Confidence 9999999999999999 6999999999999999999999999999995 999999999999999999653 344555566
Q ss_pred ccCCCC
Q psy11692 158 ATGNTF 163 (171)
Q Consensus 158 ~~~~~~ 163 (171)
|++...
T Consensus 330 ~~~~~~ 335 (459)
T TIGR00860 330 KDPAQG 335 (459)
T ss_pred cCCCCC
Confidence 654433
No 3
>KOG3643|consensus
Probab=100.00 E-value=4.7e-34 Score=233.15 Aligned_cols=155 Identities=19% Similarity=0.335 Sum_probs=143.5
Q ss_pred CeEecceecCCeEEEEEcCCCcccccccccccccEEEeEeeeEEEEecCCCCCeeEEEEEEEEEeecceeEEEEehhhHH
Q psy11692 1 MKFGSWTFNGDQVSLALYNDKNFVDLSDYWKSGTWDIIEVPAYLNVYDEHQPTETDITFYIIIRRKTLFYTVNLILPTVL 80 (171)
Q Consensus 1 L~f~Sw~y~~~~v~l~~~~~~~~~~~~~~~~~~eW~l~~~~~~~~~~~~~~~~y~~i~~~~~l~R~~~~y~~~~~iP~~l 80 (171)
|+++||+|+.+|+.+.|.++++++...+-.+.+++.+.+...........+|.|+.+...|.++|+.+||++++++|+.+
T Consensus 176 LeiESYGYt~~DI~y~W~~g~~av~~~e~i~LpqFti~~~~~~s~~~~~sTG~Y~RL~l~F~l~Rnigf~ilQ~y~PS~L 255 (459)
T KOG3643|consen 176 LEIESYGYTTDDIEYYWSKGDNAVKGDEKIELPQFTITEYHVTSRLVSFSTGNYSRLSLSFQLRRNIGFYILQTYIPSTL 255 (459)
T ss_pred EEEEecccccccEEEEEcCCCccccceeeeeccceEEEEEEEEEEEEEEccccceeEEEEEEEEeeccEEEEeeecchhh
Confidence 57999999999999999887777776666788999999998877766667999999999999999999999999999999
Q ss_pred HHHHHHHhhcccCCC-CceEEehhHHHHHHHHHHHHhhhcCCCCccCcCchhhHHHHHHHHHHHHHHHHHHhhhhhhhc
Q psy11692 81 ISFLCVLVFYLPAEA-GEKVTLGISILLSLVVFLLLVSKILPPTSLVLPLIAKYLLFTFIMNTVKSACLHYFLLYELLA 158 (171)
Q Consensus 81 i~~l~~~~F~lp~~~-~~r~~l~~t~lL~~~~~l~~v~~~lP~~s~~~p~i~~y~~~~~~~v~~s~~~~~~~~~~~~~~ 158 (171)
++++||+|||+..|+ ++|+.+|+|++|+++++....+++||++|+ ++.||+|+.+|+++|++| ++|++++|+...
T Consensus 256 iVilSWVSFWin~~a~pARv~lGITTVLTMTTl~t~~n~slPrvSY-VKAiDiYL~vCFvfVF~s--LLEYA~V~Y~~~ 331 (459)
T KOG3643|consen 256 IVILSWVSFWINRDASPARVALGITTVLTMTTLMTSTNESLPRVSY-VKAIDVYLGVCFVFVFLS--LLEYAAVNYMFK 331 (459)
T ss_pred hhHHhHhHhhhccccchhheeeceehHHhHHHHHhhhhccCCCccc-eeeehhhhhHHHHHHHHH--HHHHHHHHHHHH
Confidence 999999999999998 999999999999999999999999999998 999999999999999999 459999998443
No 4
>KOG3645|consensus
Probab=100.00 E-value=7.2e-34 Score=240.19 Aligned_cols=169 Identities=47% Similarity=0.814 Sum_probs=148.8
Q ss_pred CeEecceecCCeEE-EEEcCCCcccccccccccccEEEeEeeeEEEE--ecCCCCCeeEEEEEEEEEeecceeEEEEehh
Q psy11692 1 MKFGSWTFNGDQVS-LALYNDKNFVDLSDYWKSGTWDIIEVPAYLNV--YDEHQPTETDITFYIIIRRKTLFYTVNLILP 77 (171)
Q Consensus 1 L~f~Sw~y~~~~v~-l~~~~~~~~~~~~~~~~~~eW~l~~~~~~~~~--~~~~~~~y~~i~~~~~l~R~~~~y~~~~~iP 77 (171)
++||||+|++++++ +.........+.+++.+|+||++.+....+.. +.|+++.|++++|.+++||||.||++++++|
T Consensus 170 i~f~sw~~~~~~i~~~~~~~~~~~~~~~~~~~n~eW~l~~~~~~~~~~~~~~~~~~~~~i~f~l~irRkplyY~v~liiP 249 (449)
T KOG3645|consen 170 IKFGSWTYDGSEVDGLDLNAQTIEVDLSDFIENSEWELLSVTVVREEKKYDCCPGPYSDITFTITIRRKPLYYTVNLIIP 249 (449)
T ss_pred EEEeccccCccccceeeeccccccCCHHHcCCCCcEEEEeeeeEEeecccCCCCCceeEEEEEEEEEeccceEEEehhhh
Confidence 58999999999887 54332211167889999999999999987765 3467788999999999999999999999999
Q ss_pred hHHHHHHHHHhhcccCCCC-ceEEehhHHHHHHHHHHHHhhhcCCCCccCcCchhhHHHHHHHHHHHHHHHHHHhhhhhh
Q psy11692 78 TVLISFLCVLVFYLPAEAG-EKVTLGISILLSLVVFLLLVSKILPPTSLVLPLIAKYLLFTFIMNTVKSACLHYFLLYEL 156 (171)
Q Consensus 78 ~~li~~l~~~~F~lp~~~~-~r~~l~~t~lL~~~~~l~~v~~~lP~~s~~~p~i~~y~~~~~~~v~~s~~~~~~~~~~~~ 156 (171)
|+++++++.++||+|++.+ ||+++|++++|++++++..+++.+|++|..+|+||+|+.++|+++++|++ ..+++++.+
T Consensus 250 ~~lis~l~il~fflp~~~~~eki~L~it~Ll~~tv~ll~vs~~~P~ts~~iPLig~y~~~~m~~~~~sv~-~tv~i~~~~ 328 (449)
T KOG3645|consen 250 CFLISFLSILGFFLPSDSGTEKVTLGITVLLAMTVFLLLVSDKMPPTSSVIPLIGKYLLFTMVLVTISVV-VTVVILNLH 328 (449)
T ss_pred HHHHHHHHhheEEccCCCCCceEEEEHHHHHHHHHHHHHHHhhcCCccCcchHHHHHHHHHHHHHHHHHH-HheeEEeee
Confidence 9999999999999998875 99999999999999999999999999998899999999999999999965 566788888
Q ss_pred hccCCCC-CCCcccc
Q psy11692 157 LATGNTF-DMNTYQK 170 (171)
Q Consensus 157 ~~~~~~~-~~p~w~~ 170 (171)
+|+.... ++|+|++
T Consensus 329 ~~~~~~~~~~~~~~~ 343 (449)
T KOG3645|consen 329 HRSPTTHPPMPPWVR 343 (449)
T ss_pred cccCCCCCCCchHHH
Confidence 8886666 8999975
No 5
>KOG3644|consensus
Probab=99.98 E-value=3.4e-32 Score=228.45 Aligned_cols=155 Identities=18% Similarity=0.222 Sum_probs=139.5
Q ss_pred CeEecceecCCeEEEEEcCCCcccccccccccccEEEeEeeeEEEEecCCCCCeeEEEEEEEEEeecceeEEEEehhhHH
Q psy11692 1 MKFGSWTFNGDQVSLALYNDKNFVDLSDYWKSGTWDIIEVPAYLNVYDEHQPTETDITFYIIIRRKTLFYTVNLILPTVL 80 (171)
Q Consensus 1 L~f~Sw~y~~~~v~l~~~~~~~~~~~~~~~~~~eW~l~~~~~~~~~~~~~~~~y~~i~~~~~l~R~~~~y~~~~~iP~~l 80 (171)
|+++||+|+.+|++++|.+++ .+..+.-...++.++.+.+..........|.|++++++++++|+.+||+++.++|+.+
T Consensus 186 l~~eSy~Yn~~~v~~~W~~~~-pv~~~~~i~LPdf~l~~~~~~~~~~~y~~G~~scL~v~~~f~R~~g~yllQ~YiPT~l 264 (457)
T KOG3644|consen 186 LQLESYAYNTDDVRLEWKEWN-PVQVKKDIKLPDFSLPSFSTEKCTGSYTTGVYSCLRVTFTFKRRYGYYLLQTYIPTLL 264 (457)
T ss_pred EEEEEeccccceEEEEecCCC-CcccccCccCCceeccceeeccccccccCcceEEEEEEEEEEEeehhhhhHHHhhhHh
Confidence 579999999999999998765 4555556778999999887655443344899999999999999999999999999999
Q ss_pred HHHHHHHhhcccCCC-CceEEehhHHHHHHHHHHHHhhhcCCCCccCcCchhhHHHHHHHHHHHHHHHHHHhhhhhhhcc
Q psy11692 81 ISFLCVLVFYLPAEA-GEKVTLGISILLSLVVFLLLVSKILPPTSLVLPLIAKYLLFTFIMNTVKSACLHYFLLYELLAT 159 (171)
Q Consensus 81 i~~l~~~~F~lp~~~-~~r~~l~~t~lL~~~~~l~~v~~~lP~~s~~~p~i~~y~~~~~~~v~~s~~~~~~~~~~~~~~~ 159 (171)
++++||++||+++++ ++|+++|+|+||++++....+..+||++|| +++||+|+++|++++++|+ +|+++|++..|+
T Consensus 265 ~ViiSWvSFWLd~~A~PARv~LgvtsLLtLttq~~~i~~~LP~VSY-vKAIDVWm~~C~~FIF~sL--lE~A~V~~~~~~ 341 (457)
T KOG3644|consen 265 IVIISWVSFWLDPKAVPARVTLGVTSLLTLTTQSGGIRRNLPKVSY-VKAIDVWMGVCMTFIFGSL--LELAVVNYVGRR 341 (457)
T ss_pred hhhhhhhheecCCCcccceEEehHHHHHHHHHHhcchhhcCCchhh-HHHHHHHHHHHHHHHHHHH--HHHHHHHHhhhc
Confidence 999999999999998 999999999999999999999999999999 9999999999999999994 599999987664
No 6
>KOG3642|consensus
Probab=99.97 E-value=1.2e-31 Score=220.15 Aligned_cols=157 Identities=20% Similarity=0.383 Sum_probs=143.6
Q ss_pred CeEecceecCCeEEEEEcCCCcccccccccccccEEEeEeeeEEEEecCCCCCeeEEEEEEEEEeecceeEEEEehhhHH
Q psy11692 1 MKFGSWTFNGDQVSLALYNDKNFVDLSDYWKSGTWDIIEVPAYLNVYDEHQPTETDITFYIIIRRKTLFYTVNLILPTVL 80 (171)
Q Consensus 1 L~f~Sw~y~~~~v~l~~~~~~~~~~~~~~~~~~eW~l~~~~~~~~~~~~~~~~y~~i~~~~~l~R~~~~y~~~~~iP~~l 80 (171)
|+||||+|..+|+.+.|...+..++.++...+.|+++.+.++..+......|+|..++.+|+++||.|||++|.++||++
T Consensus 184 l~fgSy~Y~~~evvY~W~~~~VeV~~~~~~~L~Qf~l~g~~~~te~i~t~~gey~vmtv~F~L~R~~GYf~iQ~YlPC~l 263 (466)
T KOG3642|consen 184 LKFGSYAYPGSEVVYKWKKRSVEVNETDSWSLDQFDLLGVSVGTEDIKTSSGEYSVMTVYFHLSRRQGYFIIQIYLPCIL 263 (466)
T ss_pred ceecccCcCCCCEEEEEecccEEEcCCCCccccceeeecccccccceEecCCCEEEEEEEEeccceeeEEEEeeccceee
Confidence 68999999999999999876455666667788999999998877766677899999999999999999999999999999
Q ss_pred HHHHHHHhhcccCCC-CceEEehhHHHHHHHHHHHHhhhcCCCCccCcCchhhHHHHHHHHHHHHHHHHHHhhhhhhhcc
Q psy11692 81 ISFLCVLVFYLPAEA-GEKVTLGISILLSLVVFLLLVSKILPPTSLVLPLIAKYLLFTFIMNTVKSACLHYFLLYELLAT 159 (171)
Q Consensus 81 i~~l~~~~F~lp~~~-~~r~~l~~t~lL~~~~~l~~v~~~lP~~s~~~p~i~~y~~~~~~~v~~s~~~~~~~~~~~~~~~ 159 (171)
+++|+|++||+..|+ ++|.++|+|++|+|++.....++++||.|+ .+++|+|...|+++++.++ +|++++|++...
T Consensus 264 tViLSwVSFWinrEs~paRt~lGITtVLTMTtLs~~aR~slPKVsy-~TAmD~fIavCf~FvFsal--iEfa~vNYft~~ 340 (466)
T KOG3642|consen 264 TVVLSWVSFWINREATPARTSLGITTVLTMTTLSTSARKSLPKVSY-ATALDVFIAVCFIFVFAAL--VEFAVVNYFTLN 340 (466)
T ss_pred eeeeeeeehhccccccccceeeeeeeeeeeeeeeehhccCCCcccc-chhHHHHHHHHHHHHHHHH--HHHHheeeeeec
Confidence 999999999999998 999999999999999999999999999998 8999999999999998885 499999987644
Q ss_pred C
Q psy11692 160 G 160 (171)
Q Consensus 160 ~ 160 (171)
+
T Consensus 341 ~ 341 (466)
T KOG3642|consen 341 Q 341 (466)
T ss_pred c
Confidence 3
No 7
>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=99.88 E-value=4.1e-24 Score=160.95 Aligned_cols=97 Identities=37% Similarity=0.581 Sum_probs=76.7
Q ss_pred EehhhHHHHHHHHHhhcccCCCC-ceEEehhHHHHHHHHHHHHhhhcCCCCccCcCchhhHHHHHHHHHHHHHHHHHHhh
Q psy11692 74 LILPTVLISFLCVLVFYLPAEAG-EKVTLGISILLSLVVFLLLVSKILPPTSLVLPLIAKYLLFTFIMNTVKSACLHYFL 152 (171)
Q Consensus 74 ~~iP~~li~~l~~~~F~lp~~~~-~r~~l~~t~lL~~~~~l~~v~~~lP~~s~~~p~i~~y~~~~~~~v~~s~~~~~~~~ 152 (171)
+|+||+++++++|++||+|++++ ||+++|+|++|++++++..+++.+|++|+.+|+++.|+.+++++++++ ++..+++
T Consensus 1 l~~P~~li~~~s~~~f~~~~~~~~~rv~l~it~lL~~~~~~~~~~~~lP~~s~~~pl~~~~~~~~~~v~~~~-~~~avv~ 79 (237)
T PF02932_consen 1 LIIPCILIVVLSWLSFWLPPESGPERVTLGITTLLAMTVFLLMVAENLPPTSYAKPLDGWYFICTMFVFSAS-LEFAVVV 79 (237)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHSTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHSHHHHHHHHHHHHHHHHH-HHHHHHH
T ss_pred CeehHHHHHHHHHhheEeCccccccccccchhHHHHHHHHHhhhhhhhcccccccchhhhhccccchhhhHH-HHhhhhh
Confidence 37999999999999999999997 999999999999999999999999999998888877766655555554 4556667
Q ss_pred hhhhhccCCCCCCCccccC
Q psy11692 153 LYELLATGNTFDMNTYQKN 171 (171)
Q Consensus 153 ~~~~~~~~~~~~~p~w~~~ 171 (171)
++.|+|+++.+++|+|+|.
T Consensus 80 ~~~~~~~~~~~~~~~~~r~ 98 (237)
T PF02932_consen 80 YNIHHRGPRTRPMPPWVRR 98 (237)
T ss_dssp HHHHHHSTTT-S-------
T ss_pred hhhcccccccccccchhHH
Confidence 7778888889999999873
No 8
>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=98.71 E-value=8e-08 Score=73.70 Aligned_cols=67 Identities=28% Similarity=0.594 Sum_probs=55.1
Q ss_pred CeEecceecCCeEEEEEcCCC------cccccccccccccEEEeEeeeEEEE--ecCCCCC-eeEEEEEEEEEeec
Q psy11692 1 MKFGSWTFNGDQVSLALYNDK------NFVDLSDYWKSGTWDIIEVPAYLNV--YDEHQPT-ETDITFYIIIRRKT 67 (171)
Q Consensus 1 L~f~Sw~y~~~~v~l~~~~~~------~~~~~~~~~~~~eW~l~~~~~~~~~--~~~~~~~-y~~i~~~~~l~R~~ 67 (171)
|+|+||.|+.+++.+.+.... ...+.+.+..++||++.+....... +.++.+. |+.+.|.+++||||
T Consensus 142 i~~~s~~~~~~~v~l~~~~~~~~~~~~~~~~~~~~~~~~ew~~~~~~~~~~~~~~~~~~~~~ys~l~~~~~l~R~~ 217 (217)
T PF02931_consen 142 IKFGSWSYNSEEVQLKWENKNPPIDENDEVSLSDFVSNSEWKIVSVTSTRRETTYGCYNEPTYSMLSFTFTLKRRP 217 (217)
T ss_dssp EEEEESSSSTTTEEEEESCSSS-TTSSTTTSCTTCETTSSEEEEEEEEEEEEEEESTSSSCSEEEEEEEEEEEEST
T ss_pred EEEecccccccceeeeecccCceeeeeccccHHHccccceEEEEeeEEEEEEEccCCcCCCCEeeEEEEEEEEECc
Confidence 579999999999999997643 2456778899999999998766544 4556665 99999999999996
No 9
>PF10856 DUF2678: Protein of unknown function (DUF2678); InterPro: IPR022564 This family of proteins has no known function.
Probab=64.98 E-value=13 Score=25.94 Aligned_cols=13 Identities=0% Similarity=0.255 Sum_probs=5.8
Q ss_pred hHHHHHHHHHHHH
Q psy11692 132 KYLLFTFIMNTVK 144 (171)
Q Consensus 132 ~y~~~~~~~v~~s 144 (171)
.|+.+|+++++.+
T Consensus 62 iffavcI~l~~~s 74 (118)
T PF10856_consen 62 IFFAVCILLICIS 74 (118)
T ss_pred EehHHHHHHHHHH
Confidence 4444444444443
No 10
>PF14494 DUF4436: Domain of unknown function (DUF4436)
Probab=53.65 E-value=71 Score=25.45 Aligned_cols=70 Identities=16% Similarity=0.225 Sum_probs=42.0
Q ss_pred eEEEEEEEEEeecceeEEEEehhhHHHHHHHHHhhcccCCC---CceEEehhHHHHHHHHHHH-HhhhcCCCCcc
Q psy11692 55 TDITFYIIIRRKTLFYTVNLILPTVLISFLCVLVFYLPAEA---GEKVTLGISILLSLVVFLL-LVSKILPPTSL 125 (171)
Q Consensus 55 ~~i~~~~~l~R~~~~y~~~~~iP~~li~~l~~~~F~lp~~~---~~r~~l~~t~lL~~~~~l~-~v~~~lP~~s~ 125 (171)
....+.++++|..+--.+.+ +=++++..|+.++++.-... ..|+.......++-++|.. -+++.+|..+.
T Consensus 152 ~~~~~~i~l~Rs~~~~~F~~-~i~~vm~~L~~~al~~ai~~~~~rr~~~~~~l~w~aA~LFAlp~lRN~lPGaPP 225 (256)
T PF14494_consen 152 GGDGVDITLKRSRGVLFFAL-FICLVMWALATLALFVAIQVLRRRRKFEPPMLTWMAAMLFALPPLRNILPGAPP 225 (256)
T ss_pred CceeEEEEEEccCcceehHH-HHHHHHHHHHHHHHHHHHHHHhCccccccchHHHHHHHHHhhhhHhccCCCCCC
Confidence 56778889998877655433 33344455666666654432 3445555555555555544 47999998663
No 11
>COG3671 Predicted membrane protein [Function unknown]
Probab=43.60 E-value=69 Score=22.49 Aligned_cols=15 Identities=20% Similarity=0.410 Sum_probs=11.5
Q ss_pred hhccCCCCCCCc-ccc
Q psy11692 156 LLATGNTFDMNT-YQK 170 (171)
Q Consensus 156 ~~~~~~~~~~p~-w~~ 170 (171)
+..+++..|.|+ |++
T Consensus 110 yl~~g~ayp~p~~Wi~ 125 (125)
T COG3671 110 YLNEGKAYPNPKTWIK 125 (125)
T ss_pred HHhCCCcCCCcccccC
Confidence 455688899998 975
No 12
>PF15102 TMEM154: TMEM154 protein family
Probab=33.57 E-value=40 Score=24.53 Aligned_cols=14 Identities=14% Similarity=-0.107 Sum_probs=7.5
Q ss_pred hhhhhhccCCCCCC
Q psy11692 152 LLYELLATGNTFDM 165 (171)
Q Consensus 152 ~~~~~~~~~~~~~~ 165 (171)
++-.++|++|.|+-
T Consensus 77 ~lv~~~kRkr~K~~ 90 (146)
T PF15102_consen 77 CLVIYYKRKRTKQE 90 (146)
T ss_pred HheeEEeecccCCC
Confidence 33345566666663
No 13
>PF01350 Flavi_NS4A: Flavivirus non-structural protein NS4A; InterPro: IPR000404 Flaviviruses encode a single polyprotein. This is cleaved into three structural and seven non-structural proteins. The NS4A protein is small and poorly conserved among the Flaviviruses. NS4A contains multiple hydrophobic potential membrane spanning regions []. NS4A has only been found in cells infected by Kunjin virus [].; GO: 0016032 viral reproduction, 0016070 RNA metabolic process, 0044423 virion part
Probab=27.50 E-value=77 Score=22.99 Aligned_cols=37 Identities=16% Similarity=0.345 Sum_probs=25.2
Q ss_pred HHHHHHHHhhcc--cCCCCceEEehhHHHHHHHHHHHHh
Q psy11692 80 LISFLCVLVFYL--PAEAGEKVTLGISILLSLVVFLLLV 116 (171)
Q Consensus 80 li~~l~~~~F~l--p~~~~~r~~l~~t~lL~~~~~l~~v 116 (171)
++.+.+...||. .+....|+++|..++...+.++..-
T Consensus 56 ll~~~T~G~~~~lm~~kgi~rm~lG~~vm~~~~~llw~g 94 (144)
T PF01350_consen 56 LLGVMTLGVFWFLMRRKGIGRMSLGMLVMAVAGYLLWMG 94 (144)
T ss_pred HHHHHHHHHHHhhhcCCCcchhhHHHHHHHHHHHHHHhc
Confidence 344444444444 6666899999999988877776654
No 14
>PF13119 DUF3973: Domain of unknown function (DUF3973)
Probab=27.39 E-value=28 Score=19.39 Aligned_cols=16 Identities=44% Similarity=0.706 Sum_probs=12.7
Q ss_pred hhcccCCCCceEEehh
Q psy11692 88 VFYLPAEAGEKVTLGI 103 (171)
Q Consensus 88 ~F~lp~~~~~r~~l~~ 103 (171)
+|+++|--|||+-+|+
T Consensus 24 gfYIdPflgek~hLGM 39 (41)
T PF13119_consen 24 GFYIDPFLGEKYHLGM 39 (41)
T ss_pred ceeecccccceeeccc
Confidence 6788887788888875
No 15
>TIGR03068 srtB_sig_NPQTN sortase B signal domain, NPQTN class. This model represents one of the boutique (rare) sortase signals, recognized by sortase B (SrtB) rather than by the housekeeping-type SrtA class sortase. This sequence, beginning NPQTN, shows little similarity to several other SrtB substrates.
Probab=25.78 E-value=1.2e+02 Score=16.17 Aligned_cols=9 Identities=33% Similarity=0.423 Sum_probs=7.6
Q ss_pred CCCccCcCc
Q psy11692 121 PPTSLVLPL 129 (171)
Q Consensus 121 P~~s~~~p~ 129 (171)
|++|+.+|.
T Consensus 2 PQTs~gtp~ 10 (33)
T TIGR03068 2 PQTNAGTPA 10 (33)
T ss_pred CCCCCCCcc
Confidence 888888885
No 16
>PHA03042 CD47-like protein; Provisional
Probab=23.92 E-value=1.3e+02 Score=24.29 Aligned_cols=14 Identities=7% Similarity=0.195 Sum_probs=8.9
Q ss_pred ecCCeEEEEEcCCC
Q psy11692 8 FNGDQVSLALYNDK 21 (171)
Q Consensus 8 y~~~~v~l~~~~~~ 21 (171)
+|.+++..+|+-++
T Consensus 46 ~ni~~~~V~Wkf~~ 59 (286)
T PHA03042 46 YNISNIHINWKFNN 59 (286)
T ss_pred cCccceEEEEEeCC
Confidence 45567777776554
No 17
>TIGR01432 QOXA cytochrome aa3 quinol oxidase, subunit II. This enzyme catalyzes the oxidation of quinol with the concomitant reduction of molecular oxygen to water. This acts as the terminal electron acceptor in the respiratory chain. This subunit contains two transmembrane helices and a large external domain responsible for the binding and oxidation of quinol. QuoX is (presently) only found in gram positive bacteria of the Bacillus/Staphylococcus group. Like CyoA, the ubiquinol oxidase found in proteobacteria, the residues responsible for the ligation of Cu(a) and cytochrome c (found in the related cyt. c oxidases) are absent. Unlike CyoA, QoxA is in complex with a subunit I which contains cytochromes a similar to the cyt. c oxidases (as opposed to cytochromes b).
Probab=22.50 E-value=2.1e+02 Score=21.94 Aligned_cols=21 Identities=14% Similarity=0.015 Sum_probs=8.4
Q ss_pred HHhhhhhhhccCCCCCCCccc
Q psy11692 149 HYFLLYELLATGNTFDMNTYQ 169 (171)
Q Consensus 149 ~~~~~~~~~~~~~~~~~p~w~ 169 (171)
.+++.++..|+++....|++-
T Consensus 42 i~~~~kyr~r~~~~~~~~~~~ 62 (217)
T TIGR01432 42 TIFLVKYRYRKDNGAYSPKMH 62 (217)
T ss_pred HHHHHHHHhccccccCCcccc
Confidence 344444433333223345543
No 18
>PF03350 UPF0114: Uncharacterized protein family, UPF0114; InterPro: IPR005134 This conserved hypothetical protein family with four predicted transmembrane regions is found in Escherichia coli, Haemophilus influenzae, and Helicobacter pylori 26695, among completed genomes.
Probab=22.30 E-value=46 Score=23.29 Aligned_cols=41 Identities=15% Similarity=0.216 Sum_probs=21.3
Q ss_pred cCchhhHHHHHHHHHHHHHHHHHHhhhhhhhccCCCCCCCcccc
Q psy11692 127 LPLIAKYLLFTFIMNTVKSACLHYFLLYELLATGNTFDMNTYQK 170 (171)
Q Consensus 127 ~p~i~~y~~~~~~~v~~s~~~~~~~~~~~~~~~~~~~~~p~w~~ 170 (171)
+..+|.|+....+++ ++.-.-|.++-+ ...+++.+.|+|++
T Consensus 56 l~~vD~~Lia~vllI-~~~g~YelFIs~--~~~~~~~~~p~wL~ 96 (124)
T PF03350_consen 56 LELVDLFLIANVLLI-FAFGLYELFISK--LDIAEHDDRPKWLG 96 (124)
T ss_pred HHHHHHHHHHHHHHH-HHHcCeeeeEec--ccccccCcccCccc
Confidence 345777777665555 332233333322 11234458999986
No 19
>COG3374 Predicted membrane protein [Function unknown]
Probab=21.52 E-value=2e+02 Score=21.99 Aligned_cols=44 Identities=20% Similarity=0.294 Sum_probs=33.0
Q ss_pred ehhHHHHHHHHHHHHhhhcCCCCccCcCchhhHHHHHHHHHHHHH
Q psy11692 101 LGISILLSLVVFLLLVSKILPPTSLVLPLIAKYLLFTFIMNTVKS 145 (171)
Q Consensus 101 l~~t~lL~~~~~l~~v~~~lP~~s~~~p~i~~y~~~~~~~v~~s~ 145 (171)
+++-.+...+-+-....+-+|. |+++-+.|.|....++++..++
T Consensus 48 ~~lG~~~~itGl~g~~tWPLPg-SyNIlF~Dp~lllGi~ll~~ai 91 (197)
T COG3374 48 AGLGIFILITGLWGEFTWPLPG-SYNILFYDPYLLLGIVLLSVAI 91 (197)
T ss_pred HHHHHHHHHHHHHhheeecCCC-ccceeecChHHHHHHHHHHHHH
Confidence 3455555566666777889998 6889999999998888776663
No 20
>TIGR03063 srtB_target sortase B cell surface sorting signal. Two different classes of sorting signal, both analogous to the sortase A signal LPXTG, may be recognized by the sortase SrtB. These are given as NXZTN and NPKXZ. Proteins sorted by this class of sortase are less common than the sortase A and LPXTG system. This model describes a number of cell surface protein C-terminal regions from Gram-positive bacteria that appear to be sortase B (SrtB) sorting signals.
Probab=21.36 E-value=1.4e+02 Score=15.45 Aligned_cols=12 Identities=33% Similarity=0.382 Sum_probs=8.4
Q ss_pred CCCccCcCchhhH
Q psy11692 121 PPTSLVLPLIAKY 133 (171)
Q Consensus 121 P~~s~~~p~i~~y 133 (171)
|++|+..| |+.|
T Consensus 2 PkT~D~a~-i~ly 13 (29)
T TIGR03063 2 PKTGDSAQ-IGLY 13 (29)
T ss_pred CCCccchh-HHHH
Confidence 89998544 5666
No 21
>TIGR01294 P_lamban phospholamban. This model represents the short (52 residue) transmembrane phosphoprotein phospholamban. Phospholamban, in its unphosphorylated form, inhibits SERCA2, the cardiac sarcoplasmic reticulum Ca-ATPase.
Probab=20.84 E-value=1.8e+02 Score=16.66 Aligned_cols=21 Identities=19% Similarity=0.406 Sum_probs=15.0
Q ss_pred chhhHHHHHHHHHHHHHHHHH
Q psy11692 129 LIAKYLLFTFIMNTVKSACLH 149 (171)
Q Consensus 129 ~i~~y~~~~~~~v~~s~~~~~ 149 (171)
+-..|.-+|++++++-+++..
T Consensus 28 lq~lfvnf~lilicllli~ii 48 (52)
T TIGR01294 28 LQNLFINFCLILICLLLICII 48 (52)
T ss_pred HHHHHHHHHHHHHHHHHHHHH
Confidence 456788889988887765443
No 22
>PRK10525 cytochrome o ubiquinol oxidase subunit II; Provisional
Probab=20.35 E-value=98 Score=25.49 Aligned_cols=12 Identities=0% Similarity=-0.009 Sum_probs=6.7
Q ss_pred CCCCCCCccccC
Q psy11692 160 GNTFDMNTYQKN 171 (171)
Q Consensus 160 ~~~~~~p~w~~~ 171 (171)
++....|.|.++
T Consensus 74 ~~a~y~p~~~~s 85 (315)
T PRK10525 74 KDAKYSPNWSHS 85 (315)
T ss_pred CcCCCCCcccCC
Confidence 334456777654
No 23
>TIGR02896 spore_III_AF stage III sporulation protein AF. This family represents the stage III sporulation protein AF of the bacterial endospore formation program, which exists in some but not all members of the Firmicutes (formerly called low-GC Gram-positives). The C-terminal region of this protein is poorly conserved, so only the N-terminal region, which includes two predicted transmembrane domains, is included in the seed alignment.
Probab=20.02 E-value=2.4e+02 Score=19.25 Aligned_cols=26 Identities=19% Similarity=0.471 Sum_probs=17.2
Q ss_pred HHHHHHHHHHHHhhhcCCCCccCcCch
Q psy11692 104 SILLSLVVFLLLVSKILPPTSLVLPLI 130 (171)
Q Consensus 104 t~lL~~~~~l~~v~~~lP~~s~~~p~i 130 (171)
.++....++...+-..+|..++ -+.+
T Consensus 8 ~~i~~~~il~t~~~~llP~~~~-kkYv 33 (106)
T TIGR02896 8 TNIIVLILLATILEMLLPNSSL-KKYV 33 (106)
T ss_pred HHHHHHHHHHHHHHHHCCCccH-HHHH
Confidence 4556666777777778898765 3443
Done!