Query psy4842
Match_columns 95
No_of_seqs 157 out of 1047
Neff 9.5
Searched_HMMs 46136
Date Fri Aug 16 19:08:09 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy4842.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/4842hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 TIGR00860 LIC Cation transport 100.0 2.8E-31 6.1E-36 183.6 7.7 94 1-95 82-178 (459)
2 KOG3643|consensus 100.0 9.7E-31 2.1E-35 176.2 6.1 95 1-95 86-182 (459)
3 PF02931 Neur_chan_LBD: Neurot 100.0 3.1E-29 6.6E-34 158.7 8.1 93 1-95 53-148 (217)
4 KOG3645|consensus 100.0 1.5E-29 3.3E-34 174.6 6.7 92 1-95 82-176 (449)
5 KOG3646|consensus 100.0 2.7E-29 5.8E-34 170.0 4.3 92 1-95 79-173 (486)
6 KOG3644|consensus 99.9 4.4E-26 9.5E-31 157.0 8.6 95 1-95 93-192 (457)
7 KOG3642|consensus 99.9 1.1E-24 2.3E-29 147.8 3.9 95 1-95 95-190 (466)
8 PF11211 DUF2997: Protein of u 70.7 3.8 8.3E-05 20.0 1.6 22 53-74 3-24 (48)
9 KOG1344|consensus 58.0 11 0.00023 25.1 2.3 34 27-62 245-278 (324)
10 PRK14751 tetracycline resistan 54.8 9.3 0.0002 16.1 1.1 18 74-91 5-22 (28)
11 PF11455 DUF3018: Protein of 47.9 7 0.00015 20.4 0.2 9 26-34 20-28 (65)
12 PF14494 DUF4436: Domain of un 45.6 18 0.00038 24.1 1.9 21 73-93 95-116 (256)
13 PF00928 Adap_comp_sub: Adapto 43.7 65 0.0014 20.9 4.3 34 53-91 25-58 (262)
14 PF14208 DUF4320: Domain of un 38.4 29 0.00064 20.2 1.9 35 57-91 70-105 (116)
15 PF08076 TetM_leader: Tetracyc 37.0 18 0.00039 15.4 0.6 19 74-92 5-23 (28)
16 PF08910 Aida_N: Aida N-termin 31.6 18 0.0004 20.8 0.3 8 78-85 99-106 (106)
17 PF13356 DUF4102: Domain of un 31.4 91 0.002 16.7 3.3 18 50-67 24-41 (89)
18 PRK04257 hypothetical protein; 28.2 1.1E+02 0.0023 16.5 3.6 15 52-66 60-76 (78)
19 PF06200 tify: tify domain; I 26.7 77 0.0017 14.4 2.0 15 51-65 6-20 (36)
20 KOG1379|consensus 26.3 1.1E+02 0.0024 21.3 3.3 30 53-82 193-223 (330)
21 PF13186 SPASM: Iron-sulfur cl 25.6 62 0.0014 15.6 1.7 12 53-64 8-19 (64)
22 PF13103 TonB_2: TonB C termin 25.0 1.2E+02 0.0025 15.8 2.8 14 49-62 28-41 (85)
23 PF06554 Olfactory_mark: Olfac 21.3 17 0.00037 21.8 -1.1 10 25-34 72-81 (151)
24 KOG2139|consensus 21.2 3.2E+02 0.007 19.7 4.7 18 52-69 243-260 (445)
25 PF08758 Cadherin_pro: Cadheri 20.5 1.2E+02 0.0025 16.8 2.2 19 51-69 46-64 (90)
26 PF15016 DUF4520: Domain of un 20.3 1.7E+02 0.0037 16.1 4.7 20 54-73 19-40 (85)
27 PF15008 DUF4518: Domain of un 20.3 1.3E+02 0.0027 20.3 2.6 42 51-92 213-254 (262)
No 1
>TIGR00860 LIC Cation transporter family protein. selective while glycine receptors are anion selective).
Probab=99.97 E-value=2.8e-31 Score=183.62 Aligned_cols=94 Identities=40% Similarity=0.847 Sum_probs=84.7
Q ss_pred CceEEeCCCcccCCCCccccccc---ccCceeecceEEeecccceeeccCcceeEEEEcCCCeEEEeecceEEEEecccC
Q psy4842 1 MRYRWVDPRLAHNAKENYLGEIN---LRDRVWTPHLYLVNEHDSRIMGSGRQDILISVQPDGTVLYSTRLKVTLLCLMNL 77 (95)
Q Consensus 1 l~~~W~D~rL~w~~~~~~~~~~~---~~~~iW~P~i~~~n~~~~~~~~~~~~~~~~~i~~~G~v~~~~~~~~~~~C~~d~ 77 (95)
++|+|+|+||+|||+ +++++.. +.++||+||++++|++++..+.....+..+++++||+|.|.++++.++.|+||+
T Consensus 82 l~~~W~D~rL~Wnp~-~y~~i~~i~~~~~~IW~PDi~l~N~~~~~~~~~~~~~~~v~~~~~G~V~~~~~~~~~~~C~~d~ 160 (459)
T TIGR00860 82 LRQEWTDERLQWNPE-EYPGVTLVRTPDDSIWVPDIFFYNEKDARFHGITMTNVLVRIHPNGSVLYSPRITLTLACPMDL 160 (459)
T ss_pred eeeEEeCCccCCCCc-cCCCceeccccccccccCcEEeecCccccccccccCceEEEEcCCCcEEEecCceEEeccccee
Confidence 478999999999997 7777654 478999999999999998777666667778888899999999999999999999
Q ss_pred cccCCCCceeeeEEeecC
Q psy4842 78 KKFPFDEQECPLVLESCK 95 (95)
Q Consensus 78 ~~fPfD~q~C~l~~~S~~ 95 (95)
++||||+|+|+|+||||+
T Consensus 161 ~~FPfD~Q~C~l~fgSw~ 178 (459)
T TIGR00860 161 RNFPFDVQNCSLKFESWG 178 (459)
T ss_pred ccCCCCCccccEEEhhhc
Confidence 999999999999999995
No 2
>KOG3643|consensus
Probab=99.97 E-value=9.7e-31 Score=176.21 Aligned_cols=95 Identities=40% Similarity=0.738 Sum_probs=86.8
Q ss_pred CceEEeCCCcccCCC--CcccccccccCceeecceEEeecccceeeccCcceeEEEEcCCCeEEEeecceEEEEecccCc
Q psy4842 1 MRYRWVDPRLAHNAK--ENYLGEINLRDRVWTPHLYLVNEHDSRIMGSGRQDILISVQPDGTVLYSTRLKVTLLCLMNLK 78 (95)
Q Consensus 1 l~~~W~D~rL~w~~~--~~~~~~~~~~~~iW~P~i~~~n~~~~~~~~~~~~~~~~~i~~~G~v~~~~~~~~~~~C~~d~~ 78 (95)
++|.|+||||+|+.. .+........++||+||.++.|++++.+|..+..|.++++++||+|.+..|++.++.|+|||+
T Consensus 86 ~rq~W~D~RLay~~~~~~slTl~~~~~~~LWvPDTff~N~KkSf~H~~T~~N~~lRl~~dGtVlys~RlT~Ta~C~MDL~ 165 (459)
T KOG3643|consen 86 LRQTWRDPRLAYSSKNIDSLTLDVRYVDKLWVPDTFFPNSKKSFFHDVTTHNSLLRLHPDGTVLYSIRLTVTAACPMDLK 165 (459)
T ss_pred hhhhhcCcccccCCCCCceEEEchhhhhccccCceecccCcccccceeeecceEEEEcCCCeEEEEEEEEEEEecccccc
Confidence 578999999999932 344555566899999999999999999999999999999999999999999999999999999
Q ss_pred ccCCCCceeeeEEeecC
Q psy4842 79 KFPFDEQECPLVLESCK 95 (95)
Q Consensus 79 ~fPfD~q~C~l~~~S~~ 95 (95)
+||+|+|+|++.++||.
T Consensus 166 ~fPmD~Q~C~LeiESYG 182 (459)
T KOG3643|consen 166 LFPMDSQNCKLEIESYG 182 (459)
T ss_pred cCCCcccceeEEEEecc
Confidence 99999999999999983
No 3
>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=99.96 E-value=3.1e-29 Score=158.69 Aligned_cols=93 Identities=37% Similarity=0.711 Sum_probs=73.3
Q ss_pred CceEEeCCCcccCCCCccccccc---ccCceeecceEEeecccceeeccCcceeEEEEcCCCeEEEeecceEEEEecccC
Q psy4842 1 MRYRWVDPRLAHNAKENYLGEIN---LRDRVWTPHLYLVNEHDSRIMGSGRQDILISVQPDGTVLYSTRLKVTLLCLMNL 77 (95)
Q Consensus 1 l~~~W~D~rL~w~~~~~~~~~~~---~~~~iW~P~i~~~n~~~~~~~~~~~~~~~~~i~~~G~v~~~~~~~~~~~C~~d~ 77 (95)
+.+.|.|+||+|+++ +++++.. ..+.||+|++++.|...... ........+.|+++|+|.+..++.+++.|+|++
T Consensus 53 ~~~~W~D~rL~w~~~-~~~~i~~~~v~~~~iW~P~l~~~n~~~~~~-~~~~~~~~~~v~~~G~V~~~~~~~~~~~C~~d~ 130 (217)
T PF02931_consen 53 IRLSWKDPRLKWNPS-DYGGIESIRVPSSQIWTPDLYFYNSVSGSF-EITEPNSNVRVYSDGTVRYSPRFTLTFSCPMDL 130 (217)
T ss_dssp EEEEEEECCGE-STT-TTTTESEEEEEGGGS----EEETTBSSSEE-ECS-SSEEEEEETTSEEEEEEEEEEEEEECETT
T ss_pred hceeccccccccChh-hccCcccccccccceEecccccccccccce-ecccccccccccccchheeeecccccccccccc
Confidence 368999999999997 6766654 46899999999999554433 233345668899999999999999999999999
Q ss_pred cccCCCCceeeeEEeecC
Q psy4842 78 KKFPFDEQECPLVLESCK 95 (95)
Q Consensus 78 ~~fPfD~q~C~l~~~S~~ 95 (95)
.+||||+|.|.|.|+||.
T Consensus 131 ~~fPfD~q~C~i~~~s~~ 148 (217)
T PF02931_consen 131 RDFPFDSQNCSIKFGSWS 148 (217)
T ss_dssp TSSSSSEEEEEEEEEESS
T ss_pred cccccccceeEEEEeccc
Confidence 999999999999999984
No 4
>KOG3645|consensus
Probab=99.96 E-value=1.5e-29 Score=174.61 Aligned_cols=92 Identities=25% Similarity=0.536 Sum_probs=81.1
Q ss_pred CceEEeCCCcccCCCCcccccccc---cCceeecceEEeecccceeeccCcceeEEEEcCCCeEEEeecceEEEEecccC
Q psy4842 1 MRYRWVDPRLAHNAKENYLGEINL---RDRVWTPHLYLVNEHDSRIMGSGRQDILISVQPDGTVLYSTRLKVTLLCLMNL 77 (95)
Q Consensus 1 l~~~W~D~rL~w~~~~~~~~~~~~---~~~iW~P~i~~~n~~~~~~~~~~~~~~~~~i~~~G~v~~~~~~~~~~~C~~d~ 77 (95)
+.++|+|+||+|||+ ++++++.. .++||+||++++|++.+........+ +.+.++|+|.+.+++..++.|++|+
T Consensus 82 l~~~W~D~~L~Wnp~-~~~~I~~i~vp~~~IW~Pdi~l~N~~~~~~~~~~~~~--v~v~~~G~V~~~~p~i~~s~C~idv 158 (449)
T KOG3645|consen 82 LKQSWTDERLSWDPS-DYGGITKIRVPSSKIWLPDIVLYNNADGDFEVEDLTN--VLVTYTGEVLWYPPAIYKSSCPIDV 158 (449)
T ss_pred eeeEEeccCcccChH-HcCCceEEEecHHHcCcCcEEEEecccccccccccce--EEEEECCEEEEEcceEEEeeccccc
Confidence 357899999999997 78877664 79999999999998777665555544 7789999999999999999999999
Q ss_pred cccCCCCceeeeEEeecC
Q psy4842 78 KKFPFDEQECPLVLESCK 95 (95)
Q Consensus 78 ~~fPfD~q~C~l~~~S~~ 95 (95)
++||||.|+|.++||||+
T Consensus 159 ~~FPfD~Q~C~i~f~sw~ 176 (449)
T KOG3645|consen 159 TYFPFDVQNCSIKFGSWT 176 (449)
T ss_pred ccCCCcceeEeEEEeccc
Confidence 999999999999999996
No 5
>KOG3646|consensus
Probab=99.95 E-value=2.7e-29 Score=169.98 Aligned_cols=92 Identities=25% Similarity=0.528 Sum_probs=83.8
Q ss_pred CceEEeCCCcccCCCCcccccccc---cCceeecceEEeecccceeeccCcceeEEEEcCCCeEEEeecceEEEEecccC
Q psy4842 1 MRYRWVDPRLAHNAKENYLGEINL---RDRVWTPHLYLVNEHDSRIMGSGRQDILISVQPDGTVLYSTRLKVTLLCLMNL 77 (95)
Q Consensus 1 l~~~W~D~rL~w~~~~~~~~~~~~---~~~iW~P~i~~~n~~~~~~~~~~~~~~~~~i~~~G~v~~~~~~~~~~~C~~d~ 77 (95)
++++|+|-+|+|||+ +|+|+... .++||+||+.+||+++..+.....++ +.++++|.|.|.++-+.+++|.+|.
T Consensus 79 l~y~W~D~~LrW~ps-eygnI~dvR~p~~~iWkPDVLLYNSade~FDsTy~tN--~Vv~~tG~v~~vPPGIfk~sCkiDI 155 (486)
T KOG3646|consen 79 LQYQWNDYKLRWDPS-EYGNITDIRFPGGNIWKPDVLLYNSADEQFDSTYKTN--YVVYSTGSVLWVPPGIFKSSCKIDI 155 (486)
T ss_pred hheeehhhhhccCHH-HhCCceeeccCCccccCCceeccccccccCCCcceee--EEEccCCeeeecCCceeeeeeEEEE
Confidence 467999999999997 88887765 58999999999999999887766666 5589999999999999999999999
Q ss_pred cccCCCCceeeeEEeecC
Q psy4842 78 KKFPFDEQECPLVLESCK 95 (95)
Q Consensus 78 ~~fPfD~q~C~l~~~S~~ 95 (95)
+.||||+|.|.++|||||
T Consensus 156 twFPFD~Q~C~mKFGSWT 173 (486)
T KOG3646|consen 156 TWFPFDDQVCYLKFGSWT 173 (486)
T ss_pred EEecccccEEEEEeeeEE
Confidence 999999999999999997
No 6
>KOG3644|consensus
Probab=99.93 E-value=4.4e-26 Score=156.96 Aligned_cols=95 Identities=44% Similarity=0.802 Sum_probs=82.8
Q ss_pred CceEEeCCCcccC-CC-Ccccccc-ccc--CceeecceEEeecccceeeccCcceeEEEEcCCCeEEEeecceEEEEecc
Q psy4842 1 MRYRWVDPRLAHN-AK-ENYLGEI-NLR--DRVWTPHLYLVNEHDSRIMGSGRQDILISVQPDGTVLYSTRLKVTLLCLM 75 (95)
Q Consensus 1 l~~~W~D~rL~w~-~~-~~~~~~~-~~~--~~iW~P~i~~~n~~~~~~~~~~~~~~~~~i~~~G~v~~~~~~~~~~~C~~ 75 (95)
++++|.||||+++ .+ +...... ... .+||.||++|.|++.+.+|.....|..++|++||+|.+..|+.++.+|+|
T Consensus 93 ~~~~W~DpRL~~~~~~~~~~~~~~~~l~~~~~iW~Pd~~F~NsK~a~~H~~~~~N~ll~I~pnGtV~~~~Ri~l~~~C~m 172 (457)
T KOG3644|consen 93 FRERWQDPRLAYNALKFDHILPCKLNLSLKQKIWTPDTFFANSKSAEFHKSTKPNVLLMIFPNGTVWYSYRISLTLPCNM 172 (457)
T ss_pred eeeeEeCccccccccCcccccccccccccCCceecCceeeecccceeeecCCCCceEEEEecCCeEEEEEEEEEeeceee
Confidence 5789999999988 44 2221111 123 56999999999999999999999999999999999999999999999999
Q ss_pred cCcccCCCCceeeeEEeecC
Q psy4842 76 NLKKFPFDEQECPLVLESCK 95 (95)
Q Consensus 76 d~~~fPfD~q~C~l~~~S~~ 95 (95)
|+.+||+|+|+|.+.++||.
T Consensus 173 ~L~~fP~D~Q~C~l~~eSy~ 192 (457)
T KOG3644|consen 173 DLSKFPMDSQECKLQLESYA 192 (457)
T ss_pred ehhhCCCccceeeEEEEEec
Confidence 99999999999999999984
No 7
>KOG3642|consensus
Probab=99.90 E-value=1.1e-24 Score=147.75 Aligned_cols=95 Identities=33% Similarity=0.608 Sum_probs=84.9
Q ss_pred CceEEeCCCcccCCC-CcccccccccCceeecceEEeecccceeeccCcceeEEEEcCCCeEEEeecceEEEEecccCcc
Q psy4842 1 MRYRWVDPRLAHNAK-ENYLGEINLRDRVWTPHLYLVNEHDSRIMGSGRQDILISVQPDGTVLYSTRLKVTLLCLMNLKK 79 (95)
Q Consensus 1 l~~~W~D~rL~w~~~-~~~~~~~~~~~~iW~P~i~~~n~~~~~~~~~~~~~~~~~i~~~G~v~~~~~~~~~~~C~~d~~~ 79 (95)
++|.|.|+||+++.. +..........+||+||.++.|++++..|.....+.+++|..||+|.|..++++.+.|+|++.+
T Consensus 95 FrQ~W~D~RL~f~~~~~~L~Ln~~m~~kiW~PDTfF~NgkkS~~H~iT~pN~l~Ri~~dG~vlyt~RlTi~A~C~m~l~~ 174 (466)
T KOG3642|consen 95 FRQTWVDDRLKFNGPQEALPLNSLMLSKIWIPDTFFRNGKKSYAHNITTPNKLVRIYIDGTVLYTMRLTIPAECPMHLAR 174 (466)
T ss_pred EEEeehhhhhcccCcchhhccchhhhcCcccCCcccccCcccceeeccCCCceEEEeECCcceEEEEEeecccCcchhhc
Confidence 479999999999965 2222223347999999999999999999999999999999999999999999999999999999
Q ss_pred cCCCCceeeeEEeecC
Q psy4842 80 FPFDEQECPLVLESCK 95 (95)
Q Consensus 80 fPfD~q~C~l~~~S~~ 95 (95)
||+|.|+|.++||||.
T Consensus 175 fPMD~haCpl~fgSy~ 190 (466)
T KOG3642|consen 175 FPMDSHACPLKFGSYA 190 (466)
T ss_pred CCCCcccCcceecccC
Confidence 9999999999999984
No 8
>PF11211 DUF2997: Protein of unknown function (DUF2997); InterPro: IPR021375 This family of proteins has no known function.
Probab=70.70 E-value=3.8 Score=20.01 Aligned_cols=22 Identities=27% Similarity=0.333 Sum_probs=17.3
Q ss_pred EEEcCCCeEEEeecceEEEEec
Q psy4842 53 ISVQPDGTVLYSTRLKVTLLCL 74 (95)
Q Consensus 53 ~~i~~~G~v~~~~~~~~~~~C~ 74 (95)
++|++||.|.-...-..-.+|.
T Consensus 3 ~~I~~dG~V~~~v~G~~G~~C~ 24 (48)
T PF11211_consen 3 FTIYPDGRVEEEVEGFKGSSCL 24 (48)
T ss_pred EEECCCcEEEEEEEeccChhHH
Confidence 5789999999887766666663
No 9
>KOG1344|consensus
Probab=57.97 E-value=11 Score=25.14 Aligned_cols=34 Identities=15% Similarity=0.402 Sum_probs=22.0
Q ss_pred ceeecceEEeecccceeeccCcceeEEEEcCCCeEE
Q psy4842 27 RVWTPHLYLVNEHDSRIMGSGRQDILISVQPDGTVL 62 (95)
Q Consensus 27 ~iW~P~i~~~n~~~~~~~~~~~~~~~~~i~~~G~v~ 62 (95)
.=..||+++||+...-..+..-.+ +.|+++|-+.
T Consensus 245 ~ef~Pd~VvYNAGTDiLeGDpLG~--L~ISp~Gi~~ 278 (324)
T KOG1344|consen 245 AEFRPDMVVYNAGTDILEGDPLGN--LAISPEGIIE 278 (324)
T ss_pred HhhCCcEEEEeCCCccccCCCCCC--eeecccccch
Confidence 446799999998665433333322 5678888654
No 10
>PRK14751 tetracycline resistance determinant leader peptide; Provisional
Probab=54.85 E-value=9.3 Score=16.12 Aligned_cols=18 Identities=22% Similarity=0.156 Sum_probs=14.0
Q ss_pred cccCcccCCCCceeeeEE
Q psy4842 74 LMNLKKFPFDEQECPLVL 91 (95)
Q Consensus 74 ~~d~~~fPfD~q~C~l~~ 91 (95)
+|-...||-|..-|.-.|
T Consensus 5 ~mi~h~~psdksi~hwdf 22 (28)
T PRK14751 5 PMVMHKNPSDKSIYHWDF 22 (28)
T ss_pred eeeeecCCCcCceeeeee
Confidence 466778999988887665
No 11
>PF11455 DUF3018: Protein of unknown function (DUF3018); InterPro: IPR021558 This is a bacterial family of uncharacterised proteins.
Probab=47.91 E-value=7 Score=20.45 Aligned_cols=9 Identities=22% Similarity=0.770 Sum_probs=7.1
Q ss_pred CceeecceE
Q psy4842 26 DRVWTPHLY 34 (95)
Q Consensus 26 ~~iW~P~i~ 34 (95)
-.||+||+-
T Consensus 20 VqiWVPDtr 28 (65)
T PF11455_consen 20 VQIWVPDTR 28 (65)
T ss_pred ceeeCCCCC
Confidence 479999983
No 12
>PF14494 DUF4436: Domain of unknown function (DUF4436)
Probab=45.63 E-value=18 Score=24.11 Aligned_cols=21 Identities=14% Similarity=0.411 Sum_probs=15.8
Q ss_pred ecccCcccCCCCceee-eEEee
Q psy4842 73 CLMNLKKFPFDEQECP-LVLES 93 (95)
Q Consensus 73 C~~d~~~fPfD~q~C~-l~~~S 93 (95)
-.-+..+||||+..=. +.+..
T Consensus 95 ~~G~~~~yPFD~Y~~~~i~v~~ 116 (256)
T PF14494_consen 95 ADGDINNYPFDRYRTDPIRVSA 116 (256)
T ss_pred ecCCccCCCCcccccceEEEEE
Confidence 3467889999998877 56544
No 13
>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=43.66 E-value=65 Score=20.87 Aligned_cols=34 Identities=32% Similarity=0.486 Sum_probs=19.5
Q ss_pred EEEcCCCeEEEeecceEEEEecccCcccCCCCceeeeEE
Q psy4842 53 ISVQPDGTVLYSTRLKVTLLCLMNLKKFPFDEQECPLVL 91 (95)
Q Consensus 53 ~~i~~~G~v~~~~~~~~~~~C~~d~~~fPfD~q~C~l~~ 91 (95)
+.+..+|.+.... ......|...+.-.| .|.|.|
T Consensus 25 ~~~~~~G~~~~~~-v~G~v~~~~~l~g~p----~i~l~l 58 (262)
T PF00928_consen 25 AVLDRDGNILSSE-VKGSVQCKSFLSGMP----EIKLTL 58 (262)
T ss_dssp EEEETTSEEEEEE-EEEEEEEEEE-SST-----EEEEEE
T ss_pred EEEccCCcEEEEE-EEEEEEEEEeCCCCC----eEEEEe
Confidence 5567777766654 566666665555555 355554
No 14
>PF14208 DUF4320: Domain of unknown function (DUF4320)
Probab=38.37 E-value=29 Score=20.18 Aligned_cols=35 Identities=17% Similarity=0.209 Sum_probs=28.0
Q ss_pred CCCeEEEeecceEEEEecccCccc-CCCCceeeeEE
Q psy4842 57 PDGTVLYSTRLKVTLLCLMNLKKF-PFDEQECPLVL 91 (95)
Q Consensus 57 ~~G~v~~~~~~~~~~~C~~d~~~f-PfD~q~C~l~~ 91 (95)
.+|.|-+...+.++.....++..| ||+...-+|+.
T Consensus 70 ~~~kVq~n~~v~vtvt~~~~~~~F~~~~~~~i~i~a 105 (116)
T PF14208_consen 70 TTGKVQLNEEVTVTVTGEYKIGIFKGFGSFPITIRA 105 (116)
T ss_pred cCCcccCCCEEEEEEEEEEEEEEECCCCCccEEEEE
Confidence 688888888888888888888777 88877766665
No 15
>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=37.04 E-value=18 Score=15.40 Aligned_cols=19 Identities=21% Similarity=0.211 Sum_probs=14.7
Q ss_pred cccCcccCCCCceeeeEEe
Q psy4842 74 LMNLKKFPFDEQECPLVLE 92 (95)
Q Consensus 74 ~~d~~~fPfD~q~C~l~~~ 92 (95)
|+-+..||-|...|+-.|-
T Consensus 5 p~~m~~fP~D~S~y~WDF~ 23 (28)
T PF08076_consen 5 PMFMHHFPSDKSIYHWDFC 23 (28)
T ss_pred eeeeccCCCccceeehhhh
Confidence 5777889999888876553
No 16
>PF08910 Aida_N: Aida N-terminus; InterPro: IPR015006 This entry represents the axin interactor, dorsalization-associated protein family AIDA [].; PDB: 1UG7_A.
Probab=31.57 E-value=18 Score=20.78 Aligned_cols=8 Identities=75% Similarity=1.310 Sum_probs=2.0
Q ss_pred cccCCCCc
Q psy4842 78 KKFPFDEQ 85 (95)
Q Consensus 78 ~~fPfD~q 85 (95)
.-||||.|
T Consensus 99 ~~FP~dv~ 106 (106)
T PF08910_consen 99 KEFPFDVQ 106 (106)
T ss_dssp S--SS---
T ss_pred CCCCCCCC
Confidence 35777765
No 17
>PF13356 DUF4102: Domain of unknown function (DUF4102); PDB: 3JU0_A 3RMP_A 3JTZ_A 2KJ8_A.
Probab=31.40 E-value=91 Score=16.72 Aligned_cols=18 Identities=22% Similarity=0.515 Sum_probs=11.6
Q ss_pred eeEEEEcCCCeEEEeecc
Q psy4842 50 DILISVQPDGTVLYSTRL 67 (95)
Q Consensus 50 ~~~~~i~~~G~v~~~~~~ 67 (95)
.-.++|.++|...|..+.
T Consensus 24 GL~l~v~~~G~kt~~~r~ 41 (89)
T PF13356_consen 24 GLYLRVTPSGSKTFYFRY 41 (89)
T ss_dssp TEEEEE-TTS-EEEEEEE
T ss_pred CcEEEEEeCCCeEEEEEE
Confidence 345788999988887655
No 18
>PRK04257 hypothetical protein; Provisional
Probab=28.19 E-value=1.1e+02 Score=16.49 Aligned_cols=15 Identities=27% Similarity=0.736 Sum_probs=11.0
Q ss_pred EEEEc--CCCeEEEeec
Q psy4842 52 LISVQ--PDGTVLYSTR 66 (95)
Q Consensus 52 ~~~i~--~~G~v~~~~~ 66 (95)
.+.|. .+|.|.|.-+
T Consensus 60 I~~I~~~~dG~vvw~r~ 76 (78)
T PRK04257 60 ILEIVNKKTGEILYKKR 76 (78)
T ss_pred EEEEEEcCCCeEEEEEe
Confidence 35677 8999998643
No 19
>PF06200 tify: tify domain; InterPro: IPR010399 The tify domain is a 36-amino acid domain only found among Embryophyta (land plants). It has been named after the most conserved amino acid pattern (TIF[F/Y]XG) it contains, but was previously known as the Zim domain. As the use of uppercase characters (TIFY) might imply that the domain is fully conserved across proteins, a lowercase lettering has been chosen in an attempt to highlight the reality of its natural variability. Based on the domain architecture, tify domain containing proteins can be classified into two groups. Group I is formed by proteins possessing a CCT (CONSTANS, CO-like, and TOC1) domain and a GATA-type zinc finger in addition to the tify domain. Group II contains proteins characterised by the tify domain but lacking a GATA-type zinc finger. Tify domain containing proteins might be involved in developmental processes and some of them have features that are characteristic for transcription factors: a nuclear localisation and the presence of a putative DNA-binding domain []. Some proteins known to contain a tify domain include: Arabidopsis thaliana Zinc-finger protein expressed in Inflorescence Meristem (ZIM), a putative transcription factor involved in inflorescence and flower development [, ]. A. thaliana ZIM-like proteins (ZML) []. A. thaliana PEAPOD1 and PEAPOD2 (PPD1 and PPD2) [].
Probab=26.72 E-value=77 Score=14.43 Aligned_cols=15 Identities=13% Similarity=0.091 Sum_probs=11.2
Q ss_pred eEEEEcCCCeEEEee
Q psy4842 51 ILISVQPDGTVLYST 65 (95)
Q Consensus 51 ~~~~i~~~G~v~~~~ 65 (95)
..++|.++|.|....
T Consensus 6 ~qLTIfY~G~V~Vfd 20 (36)
T PF06200_consen 6 AQLTIFYGGQVCVFD 20 (36)
T ss_pred CcEEEEECCEEEEeC
Confidence 347899999987654
No 20
>KOG1379|consensus
Probab=26.34 E-value=1.1e+02 Score=21.26 Aligned_cols=30 Identities=17% Similarity=0.187 Sum_probs=21.3
Q ss_pred EEEcCCCeEEEe-ecceEEEEecccCcccCC
Q psy4842 53 ISVQPDGTVLYS-TRLKVTLLCLMNLKKFPF 82 (95)
Q Consensus 53 ~~i~~~G~v~~~-~~~~~~~~C~~d~~~fPf 82 (95)
..|-.+|+|.+. +.....+.||..|...|-
T Consensus 193 F~VvR~G~vv~~S~~Q~H~FN~PyQLs~~p~ 223 (330)
T KOG1379|consen 193 FLVVREGKVVFRSPEQQHYFNTPYQLSSPPE 223 (330)
T ss_pred eEEEECCEEEEcCchheeccCCceeeccCCc
Confidence 446789998884 445555677888888773
No 21
>PF13186 SPASM: Iron-sulfur cluster-binding domain
Probab=25.58 E-value=62 Score=15.58 Aligned_cols=12 Identities=33% Similarity=0.672 Sum_probs=9.4
Q ss_pred EEEcCCCeEEEe
Q psy4842 53 ISVQPDGTVLYS 64 (95)
Q Consensus 53 ~~i~~~G~v~~~ 64 (95)
+.|.+||.|.--
T Consensus 8 ~~I~~dG~v~pC 19 (64)
T PF13186_consen 8 LYIDPDGDVYPC 19 (64)
T ss_pred EEEeeCccEEeC
Confidence 668899998753
No 22
>PF13103 TonB_2: TonB C terminal; PDB: 1LR0_A.
Probab=24.97 E-value=1.2e+02 Score=15.84 Aligned_cols=14 Identities=36% Similarity=0.805 Sum_probs=10.2
Q ss_pred ceeEEEEcCCCeEE
Q psy4842 49 QDILISVQPDGTVL 62 (95)
Q Consensus 49 ~~~~~~i~~~G~v~ 62 (95)
....++|.++|+|.
T Consensus 28 ~~V~i~i~~dG~v~ 41 (85)
T PF13103_consen 28 VTVRITIDPDGRVI 41 (85)
T ss_dssp EEEEEEE-TTSBEE
T ss_pred EEEEEEECCCCCEE
Confidence 34568899999996
No 23
>PF06554 Olfactory_mark: Olfactory marker protein; InterPro: IPR009103 Olfactory marker protein (OMP) is a highly expressed, cytoplasmic protein found in mature olfactory sensory receptor neurons of all vertebrates. OMP is a modulator of the olfactory signal transduction cascade. The crystal structure of OMP reveals a beta sandwich consisting of eight strands in two sheets with a jelly-roll topology []. Three highly conserved regions have been identified as possible protein-protein interaction sites in OMP, indicating a possible role for OMP in modulating such interactions, thereby acting as a molecular switch [].; GO: 0004871 signal transducer activity, 0007165 signal transduction, 0007608 sensory perception of smell; PDB: 1ZRI_A 1JYT_A 1JOD_B 1F35_A 1JOB_A.
Probab=21.26 E-value=17 Score=21.81 Aligned_cols=10 Identities=40% Similarity=1.012 Sum_probs=6.7
Q ss_pred cCceeecceE
Q psy4842 25 RDRVWTPHLY 34 (95)
Q Consensus 25 ~~~iW~P~i~ 34 (95)
.+.+|+||+.
T Consensus 72 tsQ~WTPDLT 81 (151)
T PF06554_consen 72 TSQLWTPDLT 81 (151)
T ss_dssp B-TTS-TTTS
T ss_pred eccccCcchh
Confidence 5899999985
No 24
>KOG2139|consensus
Probab=21.20 E-value=3.2e+02 Score=19.70 Aligned_cols=18 Identities=33% Similarity=0.676 Sum_probs=12.4
Q ss_pred EEEEcCCCeEEEeecceE
Q psy4842 52 LISVQPDGTVLYSTRLKV 69 (95)
Q Consensus 52 ~~~i~~~G~v~~~~~~~~ 69 (95)
+++-++||.+.+-.....
T Consensus 243 lLkwSPdgd~lfaAt~da 260 (445)
T KOG2139|consen 243 LLKWSPDGDVLFAATCDA 260 (445)
T ss_pred eEEEcCCCCEEEEecccc
Confidence 567788998887654443
No 25
>PF08758 Cadherin_pro: Cadherin prodomain like; InterPro: IPR014868 Cadherins are a group of proteins that mediate calcium dependent cell-cell adhesion. They are activated through cleavage of a prosequence in the late Golgi. This protein corresponds to the folded region of the prosequence, and is termed the prodomain. The prodomain shows structural resemblance to the cadherin domain, but lacks all the features known to be important for cadherin-cadherin interactions []. ; GO: 0007155 cell adhesion, 0016021 integral to membrane; PDB: 1OP4_A.
Probab=20.51 E-value=1.2e+02 Score=16.77 Aligned_cols=19 Identities=21% Similarity=0.240 Sum_probs=13.0
Q ss_pred eEEEEcCCCeEEEeecceE
Q psy4842 51 ILISVQPDGTVLYSTRLKV 69 (95)
Q Consensus 51 ~~~~i~~~G~v~~~~~~~~ 69 (95)
...+|..||.|.....+.+
T Consensus 46 pdF~V~~DGsVy~~r~v~l 64 (90)
T PF08758_consen 46 PDFRVLEDGSVYAKRPVQL 64 (90)
T ss_dssp SEEEEETTTEEEEES--S-
T ss_pred CCEEEcCCCeEEEeeeEec
Confidence 3478999999998776665
No 26
>PF15016 DUF4520: Domain of unknown function (DUF4520)
Probab=20.31 E-value=1.7e+02 Score=16.09 Aligned_cols=20 Identities=30% Similarity=0.494 Sum_probs=10.8
Q ss_pred EEcCCCeEE--EeecceEEEEe
Q psy4842 54 SVQPDGTVL--YSTRLKVTLLC 73 (95)
Q Consensus 54 ~i~~~G~v~--~~~~~~~~~~C 73 (95)
.-++||+|. +.-+.+++..+
T Consensus 19 ~AysDgrVr~~F~Drt~L~l~~ 40 (85)
T PF15016_consen 19 TAYSDGRVRVHFDDRTILTLIW 40 (85)
T ss_pred EEEcCCeEEEEEcCCCEEEEEe
Confidence 356677643 35555555555
No 27
>PF15008 DUF4518: Domain of unknown function (DUF4518)
Probab=20.29 E-value=1.3e+02 Score=20.31 Aligned_cols=42 Identities=21% Similarity=0.173 Sum_probs=33.6
Q ss_pred eEEEEcCCCeEEEeecceEEEEecccCcccCCCCceeeeEEe
Q psy4842 51 ILISVQPDGTVLYSTRLKVTLLCLMNLKKFPFDEQECPLVLE 92 (95)
Q Consensus 51 ~~~~i~~~G~v~~~~~~~~~~~C~~d~~~fPfD~q~C~l~~~ 92 (95)
-+|.|..=|+|--.......+.|-+-+.+=||+..+=+++|.
T Consensus 213 GlV~V~v~GTvH~~~~ClGiFEq~FGLiRdP~~~N~WKiK~~ 254 (262)
T PF15008_consen 213 GLVLVAVCGTVHRDNTCLGIFEQIFGLIRDPFAENNWKIKFV 254 (262)
T ss_pred CcEEEEEeeeEecCCceEeehhhhhhcccCccccCceeEEEE
Confidence 345566667777777788889999999999999998888864
Done!