Query psy14129
Match_columns 160
No_of_seqs 158 out of 1069
Neff 8.3
Searched_HMMs 46136
Date Fri Aug 16 20:16:21 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy14129.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/14129hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG3646|consensus 100.0 4.7E-34 1E-38 231.8 8.8 145 7-152 37-202 (486)
2 PF02931 Neur_chan_LBD: Neurot 100.0 2.3E-32 5E-37 207.8 15.4 139 4-143 14-161 (217)
3 TIGR00860 LIC Cation transport 100.0 1.7E-32 3.6E-37 229.7 14.4 151 5-155 45-211 (459)
4 KOG3645|consensus 100.0 1.5E-32 3.2E-37 229.5 13.1 147 8-155 41-209 (449)
5 KOG3643|consensus 100.0 2.7E-32 5.9E-37 220.7 10.0 134 6-142 50-194 (459)
6 KOG3644|consensus 99.9 2.5E-26 5.5E-31 190.9 14.3 132 12-144 63-206 (457)
7 KOG3642|consensus 99.9 3.6E-25 7.7E-30 180.3 9.3 136 3-143 56-203 (466)
8 COG2158 Uncharacterized protei 60.7 6.7 0.00014 26.6 1.8 13 117-129 30-42 (112)
9 PF11455 DUF3018: Protein of 30.2 20 0.00044 22.1 0.3 10 61-70 19-28 (65)
10 PF11211 DUF2997: Protein of u 25.9 34 0.00073 19.7 0.7 23 87-109 2-24 (48)
11 PF00928 Adap_comp_sub: Adapto 24.9 1.6E+02 0.0034 22.6 4.6 43 82-129 19-61 (262)
12 PRK14751 tetracycline resistan 22.9 72 0.0016 15.9 1.5 19 109-127 5-23 (28)
No 1
>KOG3646|consensus
Probab=100.00 E-value=4.7e-34 Score=231.81 Aligned_cols=145 Identities=32% Similarity=0.615 Sum_probs=128.4
Q ss_pred CCCCCCCCeEEeeecEEEEEeeeeEEE--------------EEEeEEecCCcccCCCCCCCeeEEEeCCCCcccCCccce
Q psy14129 7 RTLSSLHPVHRCTQTSLHSIEKKVDQT--------------LNFKKWYDPVLQWDPKKYGDIKQIYLAPQEVWQPDLSTF 72 (160)
Q Consensus 7 r~~~~~rPv~~~~~~~~~~i~~~~~~~--------------~~~~~W~D~rL~wn~~~~~~i~~i~~~~~~iW~Pdi~~~ 72 (160)
-|+.-.|||.|...+..|++...+.|+ |+++.|+|-+|+|||++||||+.+++|.++||+||+.+|
T Consensus 37 nYn~leRPV~N~Sepl~V~~~~~lqQIidVDEKnQvl~~naWl~y~W~D~~LrW~pseygnI~dvR~p~~~iWkPDVLLY 116 (486)
T KOG3646|consen 37 NYNPLERPVANESEPLQVKLGVFLQQIIDVDEKNQVLSVNAWLQYQWNDYKLRWDPSEYGNITDIRFPGGNIWKPDVLLY 116 (486)
T ss_pred hcCccCCCccccCcCEEEEeeeeEeccCCCcccccchhhhhhhheeehhhhhccCHHHhCCceeeccCCccccCCceecc
Confidence 366777888877777777764433332 289999999999999999999999999999999999999
Q ss_pred ecCCCCCCCCCcceEEEEeecCeEEEecCcEEEEEEeecccCCCCccceEEEEEeccccccCcEEEEECC-------CCC
Q psy14129 73 NSAGGNDVSPFGETYHIASSDGLISWVPPCQFQVYCHLDLTYWPFDSQVCELILGSWVYDGNNIDFLACP-------SRS 145 (160)
Q Consensus 73 n~~~~~~~~~~~~~~v~v~~~G~V~~~~~~~~~~~C~~~l~~fPfD~q~C~l~~~s~~y~~~~l~l~~~~-------~~~ 145 (160)
|+++ +.+..+..+.+.++++|.|.|.++.+.+++|.+|.+.||||+|.|.++||||+|++..++|+... +..
T Consensus 117 NSad-e~FDsTy~tN~Vv~~tG~v~~vPPGIfk~sCkiDItwFPFD~Q~C~mKFGSWTY~G~~lDL~~~~~~g~~Dls~y 195 (486)
T KOG3646|consen 117 NSAD-EQFDSTYKTNYVVYSTGSVLWVPPGIFKSSCKIDITWFPFDDQVCYLKFGSWTYAGILLDLRIDDEDGGIDLSTY 195 (486)
T ss_pred cccc-ccCCCcceeeEEEccCCeeeecCCceeeeeeEEEEEEecccccEEEEEeeeEEEcceeeeeeeccccCCcchhhc
Confidence 9998 78889999999999999999999999999999999999999999999999999999999998553 456
Q ss_pred CCccccc
Q psy14129 146 MPLIRWA 152 (160)
Q Consensus 146 ~~~~ew~ 152 (160)
.+||||.
T Consensus 196 i~NGEW~ 202 (486)
T KOG3646|consen 196 IPNGEWD 202 (486)
T ss_pred ccCCcee
Confidence 7899993
No 2
>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=2.3e-32 Score=207.83 Aligned_cols=139 Identities=29% Similarity=0.573 Sum_probs=110.6
Q ss_pred CCCCCC-CCCCCeEEeeecEEEEEe--------eeeEEEEEEeEEecCCcccCCCCCCCeeEEEeCCCCcccCCccceec
Q psy14129 4 AHTRTL-SSLHPVHRCTQTSLHSIE--------KKVDQTLNFKKWYDPVLQWDPKKYGDIKQIYLAPQEVWQPDLSTFNS 74 (160)
Q Consensus 4 ~~~r~~-~~~rPv~~~~~~~~~~i~--------~~~~~~~~~~~W~D~rL~wn~~~~~~i~~i~~~~~~iW~Pdi~~~n~ 74 (160)
++.||. ....|+.|..++.+.+|. +++.. .+.+.|+|+||+|||++|+|++.+.++.++||+||+++.|.
T Consensus 14 ~~~rP~~~~~~~~~V~v~~~~~~i~~v~e~~~~~~~~~-~~~~~W~D~rL~w~~~~~~~i~~~~v~~~~iW~P~l~~~n~ 92 (217)
T PF02931_consen 14 KRVRPVKNEGDPTNVSVSIYLNSIVEVDESEQTFTVDG-FIRLSWKDPRLKWNPSDYGGIESIRVPSSQIWTPDLYFYNS 92 (217)
T ss_dssp STS-SSSSSSS-EEEEEEEEEEEEEEEETTTTEEEEEE-EEEEEEEECCGE-STTTTTTESEEEEEGGGS----EEETTB
T ss_pred CCCCCCCCCCCeEEEEEEEEHhheeccccccchhhhhh-hhceeccccccccChhhccCcccccccccceEecccccccc
Confidence 455665 455677888888776652 22222 28999999999999999999999999999999999999995
Q ss_pred CCCCCCCCCcceEEEEeecCeEEEecCcEEEEEEeecccCCCCccceEEEEEeccccccCcEEEEECCC
Q psy14129 75 AGGNDVSPFGETYHIASSDGLISWVPPCQFQVYCHLDLTYWPFDSQVCELILGSWVYDGNNIDFLACPS 143 (160)
Q Consensus 75 ~~~~~~~~~~~~~v~v~~~G~V~~~~~~~~~~~C~~~l~~fPfD~q~C~l~~~s~~y~~~~l~l~~~~~ 143 (160)
.............+.|+++|+|.+..++++++.|+|++.+||||+|.|.|.|+||.|+..++.+.+...
T Consensus 93 ~~~~~~~~~~~~~~~v~~~G~V~~~~~~~~~~~C~~d~~~fPfD~q~C~i~~~s~~~~~~~v~l~~~~~ 161 (217)
T PF02931_consen 93 VSGSFEITEPNSNVRVYSDGTVRYSPRFTLTFSCPMDLRDFPFDSQNCSIKFGSWSYNSEEVQLKWENK 161 (217)
T ss_dssp SSSEEECS-SSEEEEEETTSEEEEEEEEEEEEEECETTTSSSSSEEEEEEEEEESSSSTTTEEEEESCS
T ss_pred cccceecccccccccccccchheeeecccccccccccccccccccceeEEEEecccccccceeeeeccc
Confidence 542222344679999999999999999999999999999999999999999999999999999998873
No 3
>TIGR00860 LIC Cation transporter family protein. selective while glycine receptors are anion selective).
Probab=100.00 E-value=1.7e-32 Score=229.74 Aligned_cols=151 Identities=24% Similarity=0.447 Sum_probs=117.5
Q ss_pred CCCCCCCCCCeEEeeecEEEEE---eee-eE---EEEEEeEEecCCcccCCCCCCCeeEEEeCCCCcccCCccceecCCC
Q psy14129 5 HTRTLSSLHPVHRCTQTSLHSI---EKK-VD---QTLNFKKWYDPVLQWDPKKYGDIKQIYLAPQEVWQPDLSTFNSAGG 77 (160)
Q Consensus 5 ~~r~~~~~rPv~~~~~~~~~~i---~~~-~~---~~~~~~~W~D~rL~wn~~~~~~i~~i~~~~~~iW~Pdi~~~n~~~~ 77 (160)
..||.....||.|..++.+.+| +++ +. .++++|+|+|+||+|||++|+|++.+.++.++||+||++++|++++
T Consensus 45 ~~RPv~~~~~v~V~~~i~l~~i~~vde~~q~~t~~~wl~~~W~D~rL~Wnp~~y~~i~~i~~~~~~IW~PDi~l~N~~~~ 124 (459)
T TIGR00860 45 RVRPVFGGPPVTVSFNLFLRSIMDVDEKNMDYTTNIWLRQEWTDERLQWNPEEYPGVTLVRTPDDSIWVPDIFFYNEKDA 124 (459)
T ss_pred CcCCCCCCCCEEEEEEEEEEEecccccccceEEEeeeeeeEEeCCccCCCCccCCCceeccccccccccCcEEeecCccc
Confidence 3444444445566666666555 221 11 1248999999999999999999999999999999999999999873
Q ss_pred CCCC-CCcceEEEEeecCeEEEecCcEEEEEEeecccCCCCccceEEEEEeccccccCcEEEEECCC--------CCCCc
Q psy14129 78 NDVS-PFGETYHIASSDGLISWVPPCQFQVYCHLDLTYWPFDSQVCELILGSWVYDGNNIDFLACPS--------RSMPL 148 (160)
Q Consensus 78 ~~~~-~~~~~~v~v~~~G~V~~~~~~~~~~~C~~~l~~fPfD~q~C~l~~~s~~y~~~~l~l~~~~~--------~~~~~ 148 (160)
.... ...+..+++++||+|.|.++.+.++.|+||+++||||+|+|+++|+||+|+++++++.+.++ ....+
T Consensus 125 ~~~~~~~~~~~v~~~~~G~V~~~~~~~~~~~C~~d~~~FPfD~Q~C~l~fgSw~y~~~~i~l~~~~~~~v~~~~~~~~~~ 204 (459)
T TIGR00860 125 RFHGITMTNVLVRIHPNGSVLYSPRITLTLACPMDLRNFPFDVQNCSLKFESWGYTTNDIKLEWKEQGAVQVDDSLFISL 204 (459)
T ss_pred cccccccCceEEEEcCCCcEEEecCceEEecccceeccCCCCCccccEEEhhhccccceEEEEECCCCceEechhhcccc
Confidence 3221 23345556666999999999999999999999999999999999999999999999998643 12267
Q ss_pred ccccccc
Q psy14129 149 IRWARRD 155 (160)
Q Consensus 149 ~ew~~~~ 155 (160)
+||...+
T Consensus 205 ~eW~l~~ 211 (459)
T TIGR00860 205 PEFELLG 211 (459)
T ss_pred CceEEEe
Confidence 8996654
No 4
>KOG3645|consensus
Probab=100.00 E-value=1.5e-32 Score=229.45 Aligned_cols=147 Identities=29% Similarity=0.604 Sum_probs=122.7
Q ss_pred CCCCCCCeEEeeecEEEEEeeeeEEE--------------EEEeEEecCCcccCCCCCCCeeEEEeCCCCcccCCcccee
Q psy14129 8 TLSSLHPVHRCTQTSLHSIEKKVDQT--------------LNFKKWYDPVLQWDPKKYGDIKQIYLAPQEVWQPDLSTFN 73 (160)
Q Consensus 8 ~~~~~rPv~~~~~~~~~~i~~~~~~~--------------~~~~~W~D~rL~wn~~~~~~i~~i~~~~~~iW~Pdi~~~n 73 (160)
|.+..||+.+...+..|.++..+.++ ++.++|+|+||+|||++|+||+.+++|.++||+||++++|
T Consensus 41 Y~~~vrPv~~~~~~v~V~~~~~l~qii~VdE~~q~~t~~~wl~~~W~D~~L~Wnp~~~~~I~~i~vp~~~IW~Pdi~l~N 120 (449)
T KOG3645|consen 41 YNKLVRPVKNSSDPVTVNFGLVLYQIIEVDEKNQIMTTNVWLKQSWTDERLSWDPSDYGGITKIRVPSSKIWLPDIVLYN 120 (449)
T ss_pred ccccCCccCCCCCcEEEEEEEEEEEEEeeccccceEEEEEEeeeEEeccCcccChHHcCCceEEEecHHHcCcCcEEEEe
Confidence 78888888887776666653333222 2789999999999999999999999999999999999999
Q ss_pred cCCCCCCCCCcceEEEEeecCeEEEecCcEEEEEEeecccCCCCccceEEEEEeccccccCcEE-EEECC-------CCC
Q psy14129 74 SAGGNDVSPFGETYHIASSDGLISWVPPCQFQVYCHLDLTYWPFDSQVCELILGSWVYDGNNID-FLACP-------SRS 145 (160)
Q Consensus 74 ~~~~~~~~~~~~~~v~v~~~G~V~~~~~~~~~~~C~~~l~~fPfD~q~C~l~~~s~~y~~~~l~-l~~~~-------~~~ 145 (160)
+.. +.........+.++++|+|.|.+++..++.|++|+++||||.|+|.++||||+|++.++. +.... +..
T Consensus 121 ~~~-~~~~~~~~~~v~v~~~G~V~~~~p~i~~s~C~idv~~FPfD~Q~C~i~f~sw~~~~~~i~~~~~~~~~~~~~~~~~ 199 (449)
T KOG3645|consen 121 NAD-GDFEVEDLTNVLVTYTGEVLWYPPAIYKSSCPIDVTYFPFDVQNCSIKFGSWTYDGSEVDGLDLNAQTIEVDLSDF 199 (449)
T ss_pred ccc-ccccccccceEEEEECCEEEEEcceEEEeecccccccCCCcceeEeEEEeccccCccccceeeeccccccCCHHHc
Confidence 766 566666677799999999999999999999999999999999999999999999999776 44332 233
Q ss_pred CCcccccccc
Q psy14129 146 MPLIRWARRD 155 (160)
Q Consensus 146 ~~~~ew~~~~ 155 (160)
+++.||...+
T Consensus 200 ~~n~eW~l~~ 209 (449)
T KOG3645|consen 200 IENSEWELLS 209 (449)
T ss_pred CCCCcEEEEe
Confidence 7799996543
No 5
>KOG3643|consensus
Probab=99.97 E-value=2.7e-32 Score=220.67 Aligned_cols=134 Identities=25% Similarity=0.376 Sum_probs=121.3
Q ss_pred CCCCCCCCCeEEeeecEEEEE----eeeeEEEE---EEeEEecCCcccCCCCCCCeeEEEeCC---CCcccCCccceecC
Q psy14129 6 TRTLSSLHPVHRCTQTSLHSI----EKKVDQTL---NFKKWYDPVLQWDPKKYGDIKQIYLAP---QEVWQPDLSTFNSA 75 (160)
Q Consensus 6 ~r~~~~~rPv~~~~~~~~~~i----~~~~~~~~---~~~~W~D~rL~wn~~~~~~i~~i~~~~---~~iW~Pdi~~~n~~ 75 (160)
.||+.++.||.|...+.+.|| |.+||+++ ++|.|+||||+|+ .+++..+.+.. ++||+||.+|.|++
T Consensus 50 lRP~fGG~pv~Vgi~i~VaSI~~vSEV~MDyTlt~y~rq~W~D~RLay~---~~~~~slTl~~~~~~~LWvPDTff~N~K 126 (459)
T KOG3643|consen 50 LRPNFGGPPVDVGITIHVASIDAVSEVNMDYTLTMYLRQTWRDPRLAYS---SKNIDSLTLDVRYVDKLWVPDTFFPNSK 126 (459)
T ss_pred cCCCCCCCCeEEEEEEEEeeechhccccchhhhhhhhhhhhcCcccccC---CCCCceEEEchhhhhccccCceecccCc
Confidence 689999999999999999998 45666554 8999999999998 46778888886 59999999999988
Q ss_pred CCC-CCCCCcceEEEEeecCeEEEecCcEEEEEEeecccCCCCccceEEEEEeccccccCcEEEEECC
Q psy14129 76 GGN-DVSPFGETYHIASSDGLISWVPPCQFQVYCHLDLTYWPFDSQVCELILGSWVYDGNNIDFLACP 142 (160)
Q Consensus 76 ~~~-~~~~~~~~~v~v~~~G~V~~~~~~~~~~~C~~~l~~fPfD~q~C~l~~~s~~y~~~~l~l~~~~ 142 (160)
++- +..++.+..++|.+||+|.+..|++.++.|+|||++||+|+|+|+|.++||+|++++|.+.|+.
T Consensus 127 kSf~H~~T~~N~~lRl~~dGtVlys~RlT~Ta~C~MDL~~fPmD~Q~C~LeiESYGYt~~DI~y~W~~ 194 (459)
T KOG3643|consen 127 KSFFHDVTTHNSLLRLHPDGTVLYSIRLTVTAACPMDLKLFPMDSQNCKLEIESYGYTTDDIEYYWSK 194 (459)
T ss_pred ccccceeeecceEEEEcCCCeEEEEEEEEEEEecccccccCCCcccceeEEEEecccccccEEEEEcC
Confidence 743 4457899999999999999999999999999999999999999999999999999999999985
No 6
>KOG3644|consensus
Probab=99.94 E-value=2.5e-26 Score=190.92 Aligned_cols=132 Identities=24% Similarity=0.384 Sum_probs=107.2
Q ss_pred CCCeEEeeecEEEEE--------eeeeEEEEEEeEEecCCcccC-CC-CCCCeeEEEeC-CCCcccCCccceecCCCC-C
Q psy14129 12 LHPVHRCTQTSLHSI--------EKKVDQTLNFKKWYDPVLQWD-PK-KYGDIKQIYLA-PQEVWQPDLSTFNSAGGN-D 79 (160)
Q Consensus 12 ~rPv~~~~~~~~~~i--------~~~~~~~~~~~~W~D~rL~wn-~~-~~~~i~~i~~~-~~~iW~Pdi~~~n~~~~~-~ 79 (160)
+.||.|...+.+.+| ++.++. +++|+|+||||+.+ .+ ++.......+. ..+||.||++|.|++.+. +
T Consensus 63 ~~pv~V~v~i~vq~i~~ise~~mdf~~di-~~~~~W~DpRL~~~~~~~~~~~~~~~~l~~~~~iW~Pd~~F~NsK~a~~H 141 (457)
T KOG3644|consen 63 GGPVSVSVEITVQSISSISEITMDFEVDI-YFRERWQDPRLAYNALKFDHILPCKLNLSLKQKIWTPDTFFANSKSAEFH 141 (457)
T ss_pred CCceEEEEEEEEEeecceecccceEEeee-eeeeeEeCccccccccCcccccccccccccCCceecCceeeecccceeee
Confidence 456888888888887 233333 38999999999998 33 32222222221 257999999999998744 3
Q ss_pred CCCCcceEEEEeecCeEEEecCcEEEEEEeecccCCCCccceEEEEEeccccccCcEEEEECCCC
Q psy14129 80 VSPFGETYHIASSDGLISWVPPCQFQVYCHLDLTYWPFDSQVCELILGSWVYDGNNIDFLACPSR 144 (160)
Q Consensus 80 ~~~~~~~~v~v~~~G~V~~~~~~~~~~~C~~~l~~fPfD~q~C~l~~~s~~y~~~~l~l~~~~~~ 144 (160)
.....+..+.|++||+|.+..|+.++.+|.|+|.+||+|+|.|.+.|+||+|+.+++++.|.+..
T Consensus 142 ~~~~~N~ll~I~pnGtV~~~~Ri~l~~~C~m~L~~fP~D~Q~C~l~~eSy~Yn~~~v~~~W~~~~ 206 (457)
T KOG3644|consen 142 KSTKPNVLLMIFPNGTVWYSYRISLTLPCNMDLSKFPMDSQECKLQLESYAYNTDDVRLEWKEWN 206 (457)
T ss_pred cCCCCceEEEEecCCeEEEEEEEEEeeceeeehhhCCCccceeeEEEEEeccccceEEEEecCCC
Confidence 45788999999999999999999999999999999999999999999999999999999998754
No 7
>KOG3642|consensus
Probab=99.92 E-value=3.6e-25 Score=180.31 Aligned_cols=136 Identities=21% Similarity=0.330 Sum_probs=117.2
Q ss_pred CCCCCCCCCCCCeEEeeecEEEEE--------eeeeEEEEEEeEEecCCcccCCCCCCCeeEEEeC---CCCcccCCccc
Q psy14129 3 NAHTRTLSSLHPVHRCTQTSLHSI--------EKKVDQTLNFKKWYDPVLQWDPKKYGDIKQIYLA---PQEVWQPDLST 71 (160)
Q Consensus 3 ~~~~r~~~~~rPv~~~~~~~~~~i--------~~~~~~~~~~~~W~D~rL~wn~~~~~~i~~i~~~---~~~iW~Pdi~~ 71 (160)
..+.||+.+.+|..+.+.+++-++ +..+|.+ ++|.|.|.||++| +-.+.+.+. ..+||+||.+|
T Consensus 56 D~~lRP~~g~~pt~v~~di~V~S~GPVSd~~meytid~~-FrQ~W~D~RL~f~----~~~~~L~Ln~~m~~kiW~PDTfF 130 (466)
T KOG3642|consen 56 DNKLRPDIGSKPTEVETDIYVRSMGPVSDSDMEYTIDCF-FRQTWVDDRLKFN----GPQEALPLNSLMLSKIWIPDTFF 130 (466)
T ss_pred hcccCCCCCCCCcEEEEEEEEeecccccccCceEEEEEE-EEEeehhhhhccc----CcchhhccchhhhcCcccCCccc
Confidence 356799999999999999988776 4555555 9999999999998 223334333 36999999999
Q ss_pred eecCCCC-CCCCCcceEEEEeecCeEEEecCcEEEEEEeecccCCCCccceEEEEEeccccccCcEEEEECCC
Q psy14129 72 FNSAGGN-DVSPFGETYHIASSDGLISWVPPCQFQVYCHLDLTYWPFDSQVCELILGSWVYDGNNIDFLACPS 143 (160)
Q Consensus 72 ~n~~~~~-~~~~~~~~~v~v~~~G~V~~~~~~~~~~~C~~~l~~fPfD~q~C~l~~~s~~y~~~~l~l~~~~~ 143 (160)
.|++++. +..+..+..++|..||+|.|..++++.+.|+|++.+||||.|.|.+.|||++|..+|+.+.|...
T Consensus 131 ~NgkkS~~H~iT~pN~l~Ri~~dG~vlyt~RlTi~A~C~m~l~~fPMD~haCpl~fgSy~Y~~~evvY~W~~~ 203 (466)
T KOG3642|consen 131 RNGKKSYAHNITTPNKLVRIYIDGTVLYTMRLTIPAECPMHLARFPMDSHACPLKFGSYAYPGSEVVYKWKKR 203 (466)
T ss_pred ccCcccceeeccCCCceEEEeECCcceEEEEEeecccCcchhhcCCCCcccCcceecccCcCCCCEEEEEecc
Confidence 9998864 55689999999999999999999999999999999999999999999999999999999998753
No 8
>COG2158 Uncharacterized protein containing a Zn-finger-like domain [General function prediction only]
Probab=60.71 E-value=6.7 Score=26.63 Aligned_cols=13 Identities=31% Similarity=0.621 Sum_probs=11.4
Q ss_pred CccceEEEEEecc
Q psy14129 117 FDSQVCELILGSW 129 (160)
Q Consensus 117 fD~q~C~l~~~s~ 129 (160)
||.|+|.+.+-.+
T Consensus 30 fdgQnC~fCyCPf 42 (112)
T COG2158 30 FDGQNCLFCYCPF 42 (112)
T ss_pred ecCCceeEEeccc
Confidence 8999999999873
No 9
>PF11455 DUF3018: Protein of unknown function (DUF3018); InterPro: IPR021558 This is a bacterial family of uncharacterised proteins.
Probab=30.23 E-value=20 Score=22.14 Aligned_cols=10 Identities=40% Similarity=1.145 Sum_probs=7.6
Q ss_pred CCCcccCCcc
Q psy14129 61 PQEVWQPDLS 70 (160)
Q Consensus 61 ~~~iW~Pdi~ 70 (160)
+=+||+||+-
T Consensus 19 PVqiWVPDtr 28 (65)
T PF11455_consen 19 PVQIWVPDTR 28 (65)
T ss_pred cceeeCCCCC
Confidence 3478999974
No 10
>PF11211 DUF2997: Protein of unknown function (DUF2997); InterPro: IPR021375 This family of proteins has no known function.
Probab=25.92 E-value=34 Score=19.69 Aligned_cols=23 Identities=13% Similarity=-0.055 Sum_probs=17.7
Q ss_pred EEEEeecCeEEEecCcEEEEEEe
Q psy14129 87 YHIASSDGLISWVPPCQFQVYCH 109 (160)
Q Consensus 87 ~v~v~~~G~V~~~~~~~~~~~C~ 109 (160)
.++|++||+|.-...-..-..|.
T Consensus 2 ~~~I~~dG~V~~~v~G~~G~~C~ 24 (48)
T PF11211_consen 2 EFTIYPDGRVEEEVEGFKGSSCL 24 (48)
T ss_pred EEEECCCcEEEEEEEeccChhHH
Confidence 47899999998887766666663
No 11
>PF00928 Adap_comp_sub: Adaptor complexes medium subunit family; InterPro: IPR008968 Proteins synthesized on the ribosome and processed in the endoplasmic reticulum are transported from the Golgi apparatus to the trans-Golgi network (TGN), and from there via small carrier vesicles to their final destination compartment. These vesicles have specific coat proteins (such as clathrin or coatomer) that are important for cargo selection and direction of transport []. Clathrin coats contain both clathrin (acts as a scaffold) and adaptor complexes that link clathrin to receptors in coated vesicles. Clathrin-associated protein complexes are believed to interact with the cytoplasmic tails of membrane proteins, leading to their selection and concentration. The two major types of clathrin adaptor complexes are the heterotetrameric adaptor protein (AP) complexes, and the monomeric GGA (Golgi-localising, Gamma-adaptin ear domain homology, ARF-binding proteins) adaptors [, ]. AP (adaptor protein) complexes are found in coated vesicles and clathrin-coated pits. AP complexes connect cargo proteins and lipids to clathrin at vesicle budding sites, as well as binding accessory proteins that regulate coat assembly and disassembly (such as AP180, epsins and auxilin). There are different AP complexes in mammals. AP1 is responsible for the transport of lysosomal hydrolases between the TGN and endosomes []. AP2 associates with the plasma membrane and is responsible for endocytosis []. AP3 is responsible for protein trafficking to lysosomes and other related organelles []. AP4 is less well characterised. AP complexes are heterotetramers composed of two large subunits (adaptins), a medium subunit (mu) and a small subunit (sigma). For example, in AP1 these subunits are gamma-1-adaptin, beta-1-adaptin, mu-1 and sigma-1, while in AP2 they are alpha-adaptin, beta-2-adaptin, mu-2 and sigma-2. Each subunit has a specific function. Adaptins recognise and bind to clathrin through their hinge region (clathrin box), and recruit accessory proteins that modulate AP function through their C-terminal ear (appendage) domains. Mu recognises tyrosine-based sorting signals within the cytoplasmic domains of transmembrane cargo proteins []. One function of clathrin and AP2 complex-mediated endocytosis is to regulate the number of GABA(A) receptors available at the cell surface []. This entry represents the C-terminal domain of the mu subunit from various clathrin adaptors (AP1, AP2 and AP3) []. The C-teminal domain has an immunoglobulin-like beta-sandwich fold consisting of 9 strands in 2 sheets with a Greek key topology, similar to that found in cytochrome f and certain transcription factors []. The mu subunit regulates the coupling of clathrin lattices with particular membrane proteins by self-phosphorylation via a mechanism that is still unclear []. The mu subunit possesses a highly conserved N-terminal domain of around 230 amino acids, which may be the region of interaction with other AP proteins; a linker region of between 10 and 42 amino acids; and a less well-conserved C-terminal domain of around 190 amino acids, which may be the site of specific interaction with the protein being transported in the vesicle []. More information about these proteins can be found at Protein of the Month: Clathrin [].; GO: 0005515 protein binding, 0006886 intracellular protein transport, 0016192 vesicle-mediated transport, 0030131 clathrin adaptor complex; PDB: 1H6E_A 3L81_A 1W63_V 4EMZ_A 4EN2_A 2VGL_M 3ML6_F 2PR9_A 2JKT_M 1I31_A ....
Probab=24.92 E-value=1.6e+02 Score=22.55 Aligned_cols=43 Identities=21% Similarity=0.131 Sum_probs=29.4
Q ss_pred CCcceEEEEeecCeEEEecCcEEEEEEeecccCCCCccceEEEEEecc
Q psy14129 82 PFGETYHIASSDGLISWVPPCQFQVYCHLDLTYWPFDSQVCELILGSW 129 (160)
Q Consensus 82 ~~~~~~v~v~~~G~V~~~~~~~~~~~C~~~l~~fPfD~q~C~l~~~s~ 129 (160)
..+...+.+..+|.+.... +.....|.-.+.-.| .|.|.|..-
T Consensus 19 v~E~i~~~~~~~G~~~~~~-v~G~v~~~~~l~g~p----~i~l~l~~~ 61 (262)
T PF00928_consen 19 VVEKISAVLDRDGNILSSE-VKGSVQCKSFLSGMP----EIKLTLNNP 61 (262)
T ss_dssp EEEEEEEEEETTSEEEEEE-EEEEEEEEEE-SST-----EEEEEESSS
T ss_pred EEEEEEEEEccCCcEEEEE-EEEEEEEEEeCCCCC----eEEEEecCc
Confidence 4455677888899876655 777777777777766 577777654
No 12
>PRK14751 tetracycline resistance determinant leader peptide; Provisional
Probab=22.89 E-value=72 Score=15.86 Aligned_cols=19 Identities=11% Similarity=0.036 Sum_probs=15.2
Q ss_pred eecccCCCCccceEEEEEe
Q psy14129 109 HLDLTYWPFDSQVCELILG 127 (160)
Q Consensus 109 ~~~l~~fPfD~q~C~l~~~ 127 (160)
+|-+.+||-|...|.-.|-
T Consensus 5 ~mi~h~~psdksi~hwdf~ 23 (28)
T PRK14751 5 PMVMHKNPSDKSIYHWDFY 23 (28)
T ss_pred eeeeecCCCcCceeeeeeh
Confidence 6778899999988876653
Done!