Query psy1287
Match_columns 292
No_of_seqs 95 out of 106
Neff 3.0
Searched_HMMs 46136
Date Fri Aug 16 21:51:13 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy1287.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/1287hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF13903 Claudin_2: PMP-22/EMP 99.3 6.8E-12 1.5E-16 101.2 7.0 100 86-214 2-113 (172)
2 PF00822 PMP22_Claudin: PMP-22 98.4 4.2E-07 9E-12 74.3 4.9 109 80-214 7-116 (166)
3 PF07062 Clc-like: Clc-like; 97.9 0.0001 2.2E-09 67.1 10.9 113 79-195 6-135 (211)
4 PF10242 L_HGMIC_fpl: Lipoma H 97.8 0.00014 3E-09 63.5 8.9 115 81-214 6-124 (181)
5 KOG4026|consensus 96.8 0.0077 1.7E-07 55.4 9.3 100 76-194 9-108 (207)
6 KOG4671|consensus 95.6 0.031 6.7E-07 51.2 6.4 53 79-143 20-74 (201)
7 PF06653 Claudin_3: Tight junc 94.1 0.47 1E-05 40.9 9.2 65 83-185 11-75 (163)
8 PF13903 Claudin_2: PMP-22/EMP 89.5 0.29 6.3E-06 39.6 2.6 46 214-282 38-83 (172)
9 PF06687 SUR7: SUR7/PalI famil 82.2 11 0.00023 32.4 8.5 99 79-186 4-137 (212)
10 PF00822 PMP22_Claudin: PMP-22 73.2 6.9 0.00015 32.0 4.7 50 215-282 36-85 (166)
11 PF07062 Clc-like: Clc-like; 72.5 11 0.00023 34.9 6.1 99 170-282 4-119 (211)
12 PF03332 PMM: Eukaryotic phosp 69.0 2.3 5E-05 39.6 1.1 41 13-61 62-106 (220)
13 PF15108 TMEM37: Voltage-depen 64.0 51 0.0011 30.3 8.5 106 80-212 24-129 (184)
14 PF07344 Amastin: Amastin surf 59.3 45 0.00097 28.6 7.1 91 86-197 2-95 (155)
15 PF06966 DUF1295: Protein of u 58.9 12 0.00027 33.9 3.8 47 79-130 123-169 (235)
16 PF06687 SUR7: SUR7/PalI famil 56.6 2.7 5.9E-05 36.0 -0.8 57 170-227 2-63 (212)
17 PF07803 GSG-1: GSG1-like prot 53.4 11 0.00024 32.5 2.4 46 77-123 8-53 (118)
18 PF13127 DUF3955: Protein of u 36.3 37 0.00081 25.8 2.7 33 79-112 6-38 (63)
19 PRK09400 secE preprotein trans 32.5 35 0.00075 26.0 2.0 25 189-213 23-47 (61)
20 PF11309 DUF3112: Protein of u 32.1 2.2E+02 0.0047 25.2 7.2 79 166-249 51-139 (160)
21 PF06966 DUF1295: Protein of u 22.6 1.9E+02 0.004 26.4 5.2 76 151-234 71-169 (235)
22 PF08600 Rsm1: Rsm1-like; Int 21.4 46 0.001 26.5 1.0 61 209-273 19-90 (91)
23 PF11292 DUF3093: Protein of u 21.0 42 0.00092 29.5 0.7 8 97-104 125-132 (143)
24 TIGR00327 secE_euk_arch protei 20.7 87 0.0019 24.0 2.3 25 189-213 19-43 (61)
No 1
>PF13903 Claudin_2: PMP-22/EMP/MP20/Claudin tight junction
Probab=99.29 E-value=6.8e-12 Score=101.22 Aligned_cols=100 Identities=30% Similarity=0.509 Sum_probs=82.2
Q ss_pred HHHHHHHHHhcCcceeeecccccC------------CccceechhHHhhccCCCCCchhhhccccceeeeecCCccchhh
Q psy1287 86 IAFFCVVFAFFSASWLVSDSRITG------------AKFDRLGLWTHCFRSLPDPNDEYIRRFFVGCRWIFDPFTKGYDQ 153 (292)
Q Consensus 86 iAf~~v~IAF~SPyWLvSd~rl~~------------~kF~rlGLWe~CF~~F~dP~~~~~d~~F~GC~WIy~PFt~eYy~ 153 (292)
+|++++++|++||+|++++++.++ .++.+.|||+.|...-+++++..
T Consensus 2 la~~L~~ia~~T~~W~~~~~~~~~~~~~~~~~~~~~~~~~~~Glw~~c~~~~~~~~~~~--------------------- 60 (172)
T PF13903_consen 2 LALILLIIAFGTPYWVVSDPRRTGFNCTESNNSVNFGLFSHSGLWRICFQREYDSSNRN--------------------- 60 (172)
T ss_pred hHHHHHHHHHcCchHhEEeeeccCccccccccccccccccccCcceEeecCCcCcccch---------------------
Confidence 688999999999999999999775 38889999999999998888611
Q ss_pred hhcccchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCcchhHHHHHHHHHhHHhhhcCC
Q psy1287 154 IRGYLVPGFLVFTEFFYTLTFLATIFCAMLVLLFFLCFTPDHKRFVQLTLVIGSTLTCAGA 214 (292)
Q Consensus 154 Ird~LlPgffiAtQ~FfTl~~ll~l~s~~l~~l~~Lc~~~d~~ryv~ll~~~g~~l~~AgA 214 (292)
+...|.|..++|.|..+++++.+++.+..++- .|+.|. ...+..|.+.++||.
T Consensus 61 --~~~~~~~~~~~~~~~~l~~~~~~~a~~~~~~~-~~~~~~-----~~~~~~~~~~~~ag~ 113 (172)
T PF13903_consen 61 --ETTNPHWMRATIAFLILGLLLLLFAFVFALIG-FCKRSY-----TLYLFAGILFILAGL 113 (172)
T ss_pred --hhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHH-hhcccc-----chhHHHHHHHHHHHH
Confidence 67889999999999999999999999999877 555332 444446666666666
No 2
>PF00822 PMP22_Claudin: PMP-22/EMP/MP20/Claudin family; InterPro: IPR004031 Several vertebrate small integral membrane glycoproteins are evolutionary related [, , ], including eye lens specific membrane protein 20 (MP20 or MP19); epithelial membrane protein-1 (EMP-1), which is also known as tumor-associated membrane protein (TMP) or as squamous cell-specific protein Cl-20; epithelial membrane protein-2 (EMP-2), which is also known as XMP; epithelial membrane protein-3 (EMP-3), also known as YMP; and peripheral myelin protein 22 (PMP-22), which is expressed in many tissues but mainly by Schwann cells as a component of myelin of the peripheral nervous system (PNS). PMP-22 probably plays a role both in myelinization and in cell proliferation. Mutations affecting PMP-22 are associated with hereditary motor and sensory neuropathies such as Charcot-Marie-Tooth disease type 1A (CMT-1A) in human or the trembler phenotype in mice. The proteins of this family are about 160 to 173 amino acid residues in size, and contain four transmembrane segments. PMP-22, EMP-1, -2 and -3 are highly similar, while MP20 is more distantly related. This family also includes the claudins, which are components of tight junctions.; GO: 0016020 membrane
Probab=98.39 E-value=4.2e-07 Score=74.31 Aligned_cols=109 Identities=24% Similarity=0.374 Sum_probs=74.3
Q ss_pred hhhHHHHH-HHHHHHHhcCcceeeecccccCCccceechhHHhhccCCCCCchhhhccccceeeeecCCccchhhhhccc
Q psy1287 80 GIAVFVIA-FFCVVFAFFSASWLVSDSRITGAKFDRLGLWTHCFRSLPDPNDEYIRRFFVGCRWIFDPFTKGYDQIRGYL 158 (292)
Q Consensus 80 a~~~t~iA-f~~v~IAF~SPyWLvSd~rl~~~kF~rlGLWe~CF~~F~dP~~~~~d~~F~GC~WIy~PFt~eYy~Ird~L 158 (292)
|..++.++ ..++++|-.+|+|.+++..- +..+-|||+.|..+=..- -..|.-. |.+. -
T Consensus 7 ~~~~~~~~~~~~liva~~~~~W~~~~~~~---~~~~~GLW~~C~~~~~~~--------~~~c~~~-~~~~---------~ 65 (166)
T PF00822_consen 7 GFIVSSLGWLALLIVATATPYWRVSNVSG---QSRWSGLWRECIQQSCTG--------STQCDSY-DSFL---------S 65 (166)
T ss_pred HHHHHHHHHHHHHHHHcCchHheEecCcC---ccceeCCccccCCcCcCc--------eeccccc-Cccc---------c
Confidence 34445444 44788999999999999883 889999999999854111 1134321 2111 2
Q ss_pred chhhHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCcchhHHHHHHHHHhHHhhhcCC
Q psy1287 159 VPGFLVFTEFFYTLTFLATIFCAMLVLLFFLCFTPDHKRFVQLTLVIGSTLTCAGA 214 (292)
Q Consensus 159 lPgffiAtQ~FfTl~~ll~l~s~~l~~l~~Lc~~~d~~ryv~ll~~~g~~l~~AgA 214 (292)
.|+++.|+|.++.++.++.++++++..+- ++|.+..++... .|.+.++||.
T Consensus 66 ~~~~~~a~r~l~i~s~il~~l~~~l~~~g-~~~~~~~~~~~~----ag~l~~~agl 116 (166)
T PF00822_consen 66 LPGYLQAARALMILSIILGFLGLILALFG-LCCTKRGPRPKV----AGILFILAGL 116 (166)
T ss_pred hhHHHHHHHHHhHHHHHHHHHHHHHHHhc-ccccccCCCCCc----ceeeeHHHhh
Confidence 58999999999999999999999998887 555544433222 4445555554
No 3
>PF07062 Clc-like: Clc-like; InterPro: IPR010761 Clc proteins are a nine-member gene family of chloride channels that have diverse roles in the plasma membrane and in intracellular organelles, especially membrane excitability and the maintenance of osmotic balance [, ]. This family contains a number of Clc-like proteins that are approximately 250 residues long and their homologues. ; GO: 0016021 integral to membrane
Probab=97.93 E-value=0.0001 Score=67.06 Aligned_cols=113 Identities=19% Similarity=0.308 Sum_probs=80.2
Q ss_pred chhhHHHHHHHHHHHHhcCcce-eeecccccCCccceechhHHhhccCCCCCchh-hhccccceeeeecCCcc--chh--
Q psy1287 79 VGIAVFVIAFFCVVFAFFSASW-LVSDSRITGAKFDRLGLWTHCFRSLPDPNDEY-IRRFFVGCRWIFDPFTK--GYD-- 152 (292)
Q Consensus 79 ~a~~~t~iAf~~v~IAF~SPyW-LvSd~rl~~~kF~rlGLWe~CF~~F~dP~~~~-~d~~F~GC~WIy~PFt~--eYy-- 152 (292)
.+.+++.+|+++..+|-.||+| .+..+| .+.. .+=|||..|-+....+.... +|.-=.-|++.+|- +. .|+
T Consensus 6 ~s~vl~lig~~L~~~al~SPsWQvv~~~e-~~~~-h~hGLW~dC~~~~~~~~~~~~~~~~~~~C~ykFd~-~~~~~y~~~ 82 (211)
T PF07062_consen 6 FSFVLILIGLILTFIALFSPSWQVVNIRE-FRAY-HQHGLWLDCQRPESHLLARDDDDEGPLHCTYKFDY-DDEQNYDEK 82 (211)
T ss_pred HHHHHHHHHHHHHHHHHcCCceEEEEecc-cCcE-EecceeeecCCccccccchhcccCCCceEEEEcCc-cHHHHHHHH
Confidence 5788999999999999999999 556666 4555 88899999999888554311 11102459999762 22 344
Q ss_pred -----------hhhcccchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCcch
Q psy1287 153 -----------QIRGYLVPGFLVFTEFFYTLTFLATIFCAMLVLLFFLCFTPDH 195 (292)
Q Consensus 153 -----------~Ird~LlPgffiAtQ~FfTl~~ll~l~s~~l~~l~~Lc~~~d~ 195 (292)
+++.-..=||=.||=+++..++++.++|+....+- .|.++.-
T Consensus 83 ~~~~~~~~~~~~~~~h~F~gWh~AvLil~~~s~lf~~lsi~~~iCa-~c~~~~a 135 (211)
T PF07062_consen 83 VDNCDGNSNVGESETHCFFGWHKAVLILISFSMLFALLSICFGICA-PCHPSFA 135 (211)
T ss_pred HhhcccCCcccccccceehhHHHHHHHHHHHHHHHHHHHHHHHHhh-hcCCcHH
Confidence 23333445888999999999999999998776655 4554443
No 4
>PF10242 L_HGMIC_fpl: Lipoma HMGIC fusion partner-like protein; InterPro: IPR019372 This is a group of proteins expressed from a series of genes referred to as Lipoma HGMIC fusion partner-like. The proteins carry four highly conserved transmembrane domains. In certain instances, as in LHFPL5, mutations cause deafness in humans [] or hypospadias []. LHFPL1 is transcribed in six liver tumour cell lines [].
Probab=97.78 E-value=0.00014 Score=63.53 Aligned_cols=115 Identities=17% Similarity=0.276 Sum_probs=67.4
Q ss_pred hhHHHHHHHHHHHHhcCcceeeecccccCCccceechhHHhhccCCCCCchhhhccccceeeeecCCccchhhhhcccch
Q psy1287 81 IAVFVIAFFCVVFAFFSASWLVSDSRITGAKFDRLGLWTHCFRSLPDPNDEYIRRFFVGCRWIFDPFTKGYDQIRGYLVP 160 (292)
Q Consensus 81 ~~~t~iAf~~v~IAF~SPyWLvSd~rl~~~kF~rlGLWe~CF~~F~dP~~~~~d~~F~GC~WIy~PFt~eYy~Ird~LlP 160 (292)
++++.++.++.++||.+|+||+...+ ++.=-++|||.+|-++-.++ -.-|.--.+.| .|.--.
T Consensus 6 ~llsl~~ail~~vsfi~P~Wl~~~~~--~~~~~sfGlf~rC~~~~~~~--------~~~C~~~~~~f-------~~iPs~ 68 (181)
T PF10242_consen 6 ALLSLCAAILCVVSFISPYWLGGSES--TPYSGSFGLFRRCSGQMDEW--------EQECGGYAESF-------GDIPSS 68 (181)
T ss_pred HHHHHHHHHHHHHHHcCchhccCCcC--CCCCceEEeehhhCcCCCCC--------CCccCCcCCCc-------cccCcH
Confidence 56899999999999999999998654 56778999999999211111 23454321112 221122
Q ss_pred hhHHHHHHHHHHHHHHHHHHHHHHHHHHHhc----CcchhHHHHHHHHHhHHhhhcCC
Q psy1287 161 GFLVFTEFFYTLTFLATIFCAMLVLLFFLCF----TPDHKRFVQLTLVIGSTLTCAGA 214 (292)
Q Consensus 161 gffiAtQ~FfTl~~ll~l~s~~l~~l~~Lc~----~~d~~ryv~ll~~~g~~l~~AgA 214 (292)
.| -+.=+|+.++.++..+.. ++++..+|. ++.--+....+..++.++++.|.
T Consensus 69 ~W-kaa~~~~~~g~~Ll~~~~-~~~L~~~c~~~~~~~sv~~i~g~~Q~~A~l~~~~g~ 124 (181)
T PF10242_consen 69 AW-KAAAFFVGIGCVLLLLIA-LLSLFSCCFRSICSRSVFKICGWLQFVAGLCLLLGC 124 (181)
T ss_pred HH-HHHHHHHHHHHHHHHHHH-HHHHHHHHHhccCCceEeeechHHHHHHHHHHHHhh
Confidence 36 555677777777744444 444443665 23333334444444444444443
No 5
>KOG4026|consensus
Probab=96.85 E-value=0.0077 Score=55.39 Aligned_cols=100 Identities=19% Similarity=0.303 Sum_probs=69.8
Q ss_pred cccchhhHHHHHHHHHHHHhcCcceeeecccccCCccceechhHHhhccCCCCCchhhhccccceeeeecCCccchhhhh
Q psy1287 76 AGNVGIAVFVIAFFCVVFAFFSASWLVSDSRITGAKFDRLGLWTHCFRSLPDPNDEYIRRFFVGCRWIFDPFTKGYDQIR 155 (292)
Q Consensus 76 ~g~~a~~~t~iAf~~v~IAF~SPyWLvSd~rl~~~kF~rlGLWe~CF~~F~dP~~~~~d~~F~GC~WIy~PFt~eYy~Ir 155 (292)
+|.+=++++....++.++||.+|||+.++.- + |=-+.|||.+|-.+=.+++- .++ | +|- =+
T Consensus 9 ~gviW~l~t~c~a~l~~v~fi~P~Wig~~~~--~-~~g~fGl~~~C~~~~~~~~~--~~~---~-~~~----------~~ 69 (207)
T KOG4026|consen 9 VGVIWALCTICFAVLFMVAFIQPYWIGDSVN--G-KPGSFGLFTYCVGPVLPGSL--ECR---G-RLA----------SF 69 (207)
T ss_pred HHHHHHHHHHHHHHHHHHHhccceeccCCcC--C-CCccccceeeccCCCCCCcc--ccc---C-Ccc----------cc
Confidence 3445567899999999999999999997744 2 66789999999765444441 011 0 111 12
Q ss_pred cccchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCcc
Q psy1287 156 GYLVPGFLVFTEFFYTLTFLATIFCAMLVLLFFLCFTPD 194 (292)
Q Consensus 156 d~LlPgffiAtQ~FfTl~~ll~l~s~~l~~l~~Lc~~~d 194 (292)
--..|-++.+-=+|+-+++.+.+...+.+.+..+|++++
T Consensus 70 ~~ips~~~~~a~f~vlla~~Lill~i~~~~l~~~c~~~s 108 (207)
T KOG4026|consen 70 SSIPSNEFKLAAFFVLLAFVLILLLIVFLALLGCCRSKS 108 (207)
T ss_pred ccCCcHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhchhh
Confidence 224567888888999999999997777777774666533
No 6
>KOG4671|consensus
Probab=95.64 E-value=0.031 Score=51.21 Aligned_cols=53 Identities=25% Similarity=0.478 Sum_probs=41.0
Q ss_pred chhhHHHHHHHHHHHHhcCcceeeecccccCCccceechhHHhhccCCCCCchhhhcccc--ceeee
Q psy1287 79 VGIAVFVIAFFCVVFAFFSASWLVSDSRITGAKFDRLGLWTHCFRSLPDPNDEYIRRFFV--GCRWI 143 (292)
Q Consensus 79 ~a~~~t~iAf~~v~IAF~SPyWLvSd~rl~~~kF~rlGLWe~CF~~F~dP~~~~~d~~F~--GC~WI 143 (292)
.+.++-++|..+.++|-+||.||++++. |=|||+.|.+.=..|. ..|+ ||+|-
T Consensus 20 i~licl~~aial~IvAl~s~~Wl~as~~-------~q~Lw~~C~~~~~~~~-----~pfd~~~C~s~ 74 (201)
T KOG4671|consen 20 ILLICLLSAIALDIVALASRGWLQASDQ-------RQGLWWSCRKPASTHA-----APFDPGGCQST 74 (201)
T ss_pred HHHHHHHHHHHHHHHHhccchhhhcCCC-------CcceeeeecCcCCcCC-----CCcCCccCcCh
Confidence 3567778888889999999999999877 3469999998665222 2244 99998
No 7
>PF06653 Claudin_3: Tight junction protein, Claudin-like; InterPro: IPR009545 This family consists of several Caenorhabditis elegans specific proteins of unknown function.
Probab=94.06 E-value=0.47 Score=40.88 Aligned_cols=65 Identities=15% Similarity=0.417 Sum_probs=50.8
Q ss_pred HHHHHHHHHHHHhcCcceeeecccccCCccceechhHHhhccCCCCCchhhhccccceeeeecCCccchhhhhcccchhh
Q psy1287 83 VFVIAFFCVVFAFFSASWLVSDSRITGAKFDRLGLWTHCFRSLPDPNDEYIRRFFVGCRWIFDPFTKGYDQIRGYLVPGF 162 (292)
Q Consensus 83 ~t~iAf~~v~IAF~SPyWLvSd~rl~~~kF~rlGLWe~CF~~F~dP~~~~~d~~F~GC~WIy~PFt~eYy~Ird~LlPgf 162 (292)
+-.+++++..+|-.||.|.+.... + ...|..| -||.. -.|+|
T Consensus 11 ~i~i~~iL~~vgvFTp~W~~~~~~-----------------------~------~~~~~GI-vP~~~--------~~~~W 52 (163)
T PF06653_consen 11 LILIGFILNAVGVFTPCWITDSNY-----------------------K------ISISIGI-VPYSS--------SEPGW 52 (163)
T ss_pred HHHHHHHHHHHheECCceEEEeCC-----------------------c------ccceeeE-EeCCC--------CCccH
Confidence 378899999999999999998866 1 3468888 57663 56889
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHH
Q psy1287 163 LVFTEFFYTLTFLATIFCAMLVL 185 (292)
Q Consensus 163 fiAtQ~FfTl~~ll~l~s~~l~~ 185 (292)
+-|.=.++.+++.+.++..+...
T Consensus 53 ~~~as~lm~is~~~~~i~i~~~~ 75 (163)
T PF06653_consen 53 FAAASWLMYISFACFIIMIIFYI 75 (163)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHH
Confidence 99999999998887776664333
No 8
>PF13903 Claudin_2: PMP-22/EMP/MP20/Claudin tight junction
Probab=89.53 E-value=0.29 Score=39.60 Aligned_cols=46 Identities=26% Similarity=0.434 Sum_probs=37.1
Q ss_pred CCccEEeeehcccCCCCCCCCcccccCccceEeeecCCccchhhhhccccchhhHHHHHHHHHHHhhhc
Q psy1287 214 AKFDRLGLWTHCFRSLPDPNDEYIRRFFVGCRWIFDPFTKGYDQIRGYLVPGFLVFTEFFYTLTFLVHN 282 (292)
Q Consensus 214 AKF~rLGLWe~CF~~F~~P~~~y~~~~F~GC~wIf~p~s~EY~~Ird~LlPgwfiavQ~F~Tl~lll~~ 282 (292)
.++.+.|||+.|...-++++... +...|.|..++|++..+++++.+
T Consensus 38 ~~~~~~Glw~~c~~~~~~~~~~~-----------------------~~~~~~~~~~~~~~~~l~~~~~~ 83 (172)
T PF13903_consen 38 GLFSHSGLWRICFQREYDSSNRN-----------------------ETTNPHWMRATIAFLILGLLLLL 83 (172)
T ss_pred ccccccCcceEeecCCcCcccch-----------------------hhhhHHHHHHHHHHHHHHHHHHH
Confidence 46788899999998887776622 56789999999999999877654
No 9
>PF06687 SUR7: SUR7/PalI family; InterPro: IPR009571 This family consists of several fungal-specific SUR7 proteins. Its activity regulates expression of RVS161, a homologue of human endophilin, suggesting a function for both in endocytosis [, ]. The protein carries four transmembrane domains and is thus likely to act as an anchoring protein for the eisosome to the plasma membrane. Eisosomes are the immobile protein complexes, that include the proteins Pil1 and Lsp1, which co-localise with sites of protein and lipid endocytosis at the plasma membrane. SUR7 protein may play a role in sporulation []. Two-component signal transduction systems enable bacteria to sense, respond, and adapt to a wide range of environments, stressors, and growth conditions []. Some bacteria can contain up to as many as 200 two-component systems that need tight regulation to prevent unwanted cross-talk []. These pathways have been adapted to response to a wide variety of stimuli, including nutrients, cellular redox state, changes in osmolarity, quorum signals, antibiotics, and more []. Two-component systems are comprised of a sensor histidine kinase (HK) and its cognate response regulator (RR) []. The HK catalyses its own auto-phosphorylation followed by the transfer of the phosphoryl group to the receiver domain on RR; phosphorylation of the RR usually activates an attached output domain, which can then effect changes in cellular physiology, often by regulating gene expression. Some HK are bifunctional, catalysing both the phosphorylation and dephosphorylation of their cognate RR. The input stimuli can regulate either the kinase or phosphatase activity of the bifunctional HK. A variant of the two-component system is the phospho-relay system. Here a hybrid HK auto-phosphorylates and then transfers the phosphoryl group to an internal receiver domain, rather than to a separate RR protein. The phosphoryl group is then shuttled to histidine phosphotransferase (HPT) and subsequently to a terminal RR, which can evoke the desired response [, ]. This family also includes PalI which is part of a pH signal transduction cascade. Based on the similarity of PalI to the yeast Rim9 meiotic signal transduction component it has been suggested that PalI might be a membrane sensor for ambient pH [].
Probab=82.15 E-value=11 Score=32.43 Aligned_cols=99 Identities=23% Similarity=0.429 Sum_probs=57.5
Q ss_pred chhhHHHHHHHHHHHHhcCcc----e------eeecc-cc----cCCccceechhHHhhccCCCCCchhhhcccccee--
Q psy1287 79 VGIAVFVIAFFCVVFAFFSAS----W------LVSDS-RI----TGAKFDRLGLWTHCFRSLPDPNDEYIRRFFVGCR-- 141 (292)
Q Consensus 79 ~a~~~t~iAf~~v~IAF~SPy----W------LvSd~-rl----~~~kF~rlGLWe~CF~~F~dP~~~~~d~~F~GC~-- 141 (292)
++..++.+|+++++++..++. . ++-|- ++ .-+++-+.|+|.+|-. .+..+ -..|.
T Consensus 4 ~~~~~~~~a~il~il~~i~~~~~~~~~~~l~~~~~~~s~~~~~~g~~~~y~~gl~g~C~~--~~~~~------~~~Cs~~ 75 (212)
T PF06687_consen 4 IPLLLSLAAFILLILALISGPSNSSVLKSLYFLKLDTSGLGISLGLPDFYRFGLWGYCEG--NNGTN------ITSCSSP 75 (212)
T ss_pred HHHHHHHHHHHHHHHHHhcCCCCCCcccceEEEEEECCCCCccCCCCCeEEEEEEEEeee--CCCCC------CCccCCC
Confidence 467788888888877766554 4 44443 11 2357899999999998 11111 23454
Q ss_pred ---eeecCCccchh----hhhcccchhh-----------HHHHHHHHHHHHHHHHHHHHHHHH
Q psy1287 142 ---WIFDPFTKGYD----QIRGYLVPGF-----------LVFTEFFYTLTFLATIFCAMLVLL 186 (292)
Q Consensus 142 ---WIy~PFt~eYy----~Ird~LlPgf-----------fiAtQ~FfTl~~ll~l~s~~l~~l 186 (292)
+-+||- +..+ ...+.-+|+- .-++..+.-++..++++++++..+
T Consensus 76 ~~~y~f~~~-~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~l~~ia~~~t~l~~~~~~~ 137 (212)
T PF06687_consen 76 SPGYPFDPR-EILDSELNSLSDLGLPSSLRSALDYYNNLLKAMFILYPIAIVFTFLALILSGL 137 (212)
T ss_pred CCCCCCCHH-HHhcccchhhhhccCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 333332 1000 1234456664 444777777777777777777444
No 10
>PF00822 PMP22_Claudin: PMP-22/EMP/MP20/Claudin family; InterPro: IPR004031 Several vertebrate small integral membrane glycoproteins are evolutionary related [, , ], including eye lens specific membrane protein 20 (MP20 or MP19); epithelial membrane protein-1 (EMP-1), which is also known as tumor-associated membrane protein (TMP) or as squamous cell-specific protein Cl-20; epithelial membrane protein-2 (EMP-2), which is also known as XMP; epithelial membrane protein-3 (EMP-3), also known as YMP; and peripheral myelin protein 22 (PMP-22), which is expressed in many tissues but mainly by Schwann cells as a component of myelin of the peripheral nervous system (PNS). PMP-22 probably plays a role both in myelinization and in cell proliferation. Mutations affecting PMP-22 are associated with hereditary motor and sensory neuropathies such as Charcot-Marie-Tooth disease type 1A (CMT-1A) in human or the trembler phenotype in mice. The proteins of this family are about 160 to 173 amino acid residues in size, and contain four transmembrane segments. PMP-22, EMP-1, -2 and -3 are highly similar, while MP20 is more distantly related. This family also includes the claudins, which are components of tight junctions.; GO: 0016020 membrane
Probab=73.16 E-value=6.9 Score=32.00 Aligned_cols=50 Identities=20% Similarity=0.475 Sum_probs=32.8
Q ss_pred CccEEeeehcccCCCCCCCCcccccCccceEeeecCCccchhhhhccccchhhHHHHHHHHHHHhhhc
Q psy1287 215 KFDRLGLWTHCFRSLPDPNDEYIRRFFVGCRWIFDPFTKGYDQIRGYLVPGFLVFTEFFYTLTFLVHN 282 (292)
Q Consensus 215 KF~rLGLWe~CF~~F~~P~~~y~~~~F~GC~wIf~p~s~EY~~Ird~LlPgwfiavQ~F~Tl~lll~~ 282 (292)
...+-|||+.|...-.. .. ..|.- +| .+ .-.|+++-++|.++.+++++.+
T Consensus 36 ~~~~~GLW~~C~~~~~~------~~--~~c~~-~~-------~~--~~~~~~~~a~r~l~i~s~il~~ 85 (166)
T PF00822_consen 36 QSRWSGLWRECIQQSCT------GS--TQCDS-YD-------SF--LSLPGYLQAARALMILSIILGF 85 (166)
T ss_pred ccceeCCccccCCcCcC------ce--ecccc-cC-------cc--cchhHHHHHHHHHhHHHHHHHH
Confidence 67899999999985410 11 23322 22 11 1258899999999999977654
No 11
>PF07062 Clc-like: Clc-like; InterPro: IPR010761 Clc proteins are a nine-member gene family of chloride channels that have diverse roles in the plasma membrane and in intracellular organelles, especially membrane excitability and the maintenance of osmotic balance [, ]. This family contains a number of Clc-like proteins that are approximately 250 residues long and their homologues. ; GO: 0016021 integral to membrane
Probab=72.46 E-value=11 Score=34.87 Aligned_cols=99 Identities=18% Similarity=0.325 Sum_probs=58.4
Q ss_pred HHHHHHHHHHHHHHHHHHHHhcCcchhHHHHHHHHHhHHhhhcCCCccEEeeehcccCCCCCCCCccc--ccCccceEee
Q psy1287 170 YTLTFLATIFCAMLVLLFFLCFTPDHKRFVQLTLVIGSTLTCAGAKFDRLGLWTHCFRSLPDPNDEYI--RRFFVGCRWI 247 (292)
Q Consensus 170 fTl~~ll~l~s~~l~~l~~Lc~~~d~~ryv~ll~~~g~~l~~AgAKF~rLGLWe~CF~~F~~P~~~y~--~~~F~GC~wI 247 (292)
-..++++.++|.++++.= |.. |.=+ ++ ...=.++. .+=|||..|-+....+..+.+ .. =.-|++.
T Consensus 4 ~~~s~vl~lig~~L~~~a-l~S-PsWQ-vv--------~~~e~~~~-h~hGLW~dC~~~~~~~~~~~~~~~~-~~~C~yk 70 (211)
T PF07062_consen 4 LVFSFVLILIGLILTFIA-LFS-PSWQ-VV--------NIREFRAY-HQHGLWLDCQRPESHLLARDDDDEG-PLHCTYK 70 (211)
T ss_pred HHHHHHHHHHHHHHHHHH-HcC-CceE-EE--------EecccCcE-EecceeeecCCccccccchhcccCC-CceEEEE
Confidence 356778888888887766 433 5433 11 11113333 777999999998885533332 21 2469999
Q ss_pred ecCCcc--chh-------------hhhccccchhhHHHHHHHHHHHhhhc
Q psy1287 248 FDPFTK--GYD-------------QIRGYLVPGFLVFTEFFYTLTFLVHN 282 (292)
Q Consensus 248 f~p~s~--EY~-------------~Ird~LlPgwfiavQ~F~Tl~lll~~ 282 (292)
|| ++. .|+ .++.-..=||=.||=+++..++++.+
T Consensus 71 Fd-~~~~~~y~~~~~~~~~~~~~~~~~~h~F~gWh~AvLil~~~s~lf~~ 119 (211)
T PF07062_consen 71 FD-YDDEQNYDEKVDNCDGNSNVGESETHCFFGWHKAVLILISFSMLFAL 119 (211)
T ss_pred cC-ccHHHHHHHHHhhcccCCcccccccceehhHHHHHHHHHHHHHHHHH
Confidence 98 222 344 12333444777777777666665543
No 12
>PF03332 PMM: Eukaryotic phosphomannomutase; InterPro: IPR005002 This enzyme (5.4.2.8 from EC) is involved in the synthesis of the GDP-mannose and dolichol-phosphate-mannose required for a number of critical mannosyl transfer reactions.; GO: 0004615 phosphomannomutase activity, 0019307 mannose biosynthetic process, 0005737 cytoplasm; PDB: 2I55_B 2I54_C 3F9R_A 2FUE_A 2FUC_A 2AMY_A 2Q4R_A.
Probab=69.04 E-value=2.3 Score=39.62 Aligned_cols=41 Identities=39% Similarity=0.518 Sum_probs=27.7
Q ss_pred cccccHHHHHHhhccceeeeehhhhhHhhhcCCcE----Eeeecccccccccc
Q psy1287 13 VEQFSQEELSALINSAAIIYIKQYQDFISKLGAPV----VIEHLNSMIKDFTI 61 (292)
Q Consensus 13 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~----~~~~~~~~~~~~~~ 61 (292)
.+.+++|++.++||.+ . ..+|+++.|+ .||+|||||.=||+
T Consensus 62 ~~~lgee~~~~~in~~-l-------~~~~~l~lp~krGtfIE~R~gmIn~Spi 106 (220)
T PF03332_consen 62 AEFLGEEKLQKLINFC-L-------RYISDLDLPVKRGTFIEFRGGMINFSPI 106 (220)
T ss_dssp HHHHHHHHHHHHHHHH-H-------HHHHT---S---S-SEEEESSEEEE-SS
T ss_pred HHHcCHHHHHHHHHHH-H-------HHHHhCCCCccCCCceeecCCcEEECcc
Confidence 3567788899999843 2 3357788887 59999999999987
No 13
>PF15108 TMEM37: Voltage-dependent calcium channel gamma-like subunit protein family
Probab=64.04 E-value=51 Score=30.27 Aligned_cols=106 Identities=20% Similarity=0.343 Sum_probs=70.0
Q ss_pred hhhHHHHHHHHHHHHhcCcceeeecccccCCccceechhHHhhccCCCCCchhhhccccceeeeecCCccchhhhhcccc
Q psy1287 80 GIAVFVIAFFCVVFAFFSASWLVSDSRITGAKFDRLGLWTHCFRSLPDPNDEYIRRFFVGCRWIFDPFTKGYDQIRGYLV 159 (292)
Q Consensus 80 a~~~t~iAf~~v~IAF~SPyWLvSd~rl~~~kF~rlGLWe~CF~~F~dP~~~~~d~~F~GC~WIy~PFt~eYy~Ird~Ll 159 (292)
-+.++++|.++--||-|--+||-..+++ .|||.+|--+=+.+-+ |- +.-..-+---|
T Consensus 24 IilC~alavVLSSisiCDG~WLla~~~l-------FGLWhFCt~~n~s~~~---------C~-------rdL~~a~v~gL 80 (184)
T PF15108_consen 24 IILCTALAVVLSSISICDGHWLLAEDRL-------FGLWHFCTVSNQSSPH---------CL-------RDLSQAHVPGL 80 (184)
T ss_pred HHHHHHHHHHHhhheeecceEEEecCee-------eeeeeeeecCCCCcch---------hh-------HHHHHhcCchH
Confidence 5667889999999999999999998774 6999999654332222 10 00111122223
Q ss_pred hhhHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCcchhHHHHHHHHHhHHhhhc
Q psy1287 160 PGFLVFTEFFYTLTFLATIFCAMLVLLFFLCFTPDHKRFVQLTLVIGSTLTCA 212 (292)
Q Consensus 160 PgffiAtQ~FfTl~~ll~l~s~~l~~l~~Lc~~~d~~ryv~ll~~~g~~l~~A 212 (292)
--.+...-...|+++...+.++=++.+--.|.+.+-.| =+++|..|+..
T Consensus 81 ~~gm~l~Rs~~slAVV~AIFGLElLmvSQvcEd~~Srr----KWamGs~LlLv 129 (184)
T PF15108_consen 81 AVGMGLARSVGSLAVVVAIFGLELLMVSQVCEDAHSRR----KWAMGSVLLLV 129 (184)
T ss_pred HHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHhcchhhh----hhhhhhHHHHH
Confidence 44677788888899888888887777665888655443 24555555543
No 14
>PF07344 Amastin: Amastin surface glycoprotein; InterPro: IPR009944 This family contains the eukaryotic surface glycoprotein amastin (approximately 180 residues long).In Trypanosoma cruzi, amastin is particularly abundant during the amastigote stage.
Probab=59.34 E-value=45 Score=28.58 Aligned_cols=91 Identities=16% Similarity=0.202 Sum_probs=58.1
Q ss_pred HHHHHHHHHhcCcceeeecccccCCccceechhH---HhhccCCCCCchhhhccccceeeeecCCccchhhhhcccchhh
Q psy1287 86 IAFFCVVFAFFSASWLVSDSRITGAKFDRLGLWT---HCFRSLPDPNDEYIRRFFVGCRWIFDPFTKGYDQIRGYLVPGF 162 (292)
Q Consensus 86 iAf~~v~IAF~SPyWLvSd~rl~~~kF~rlGLWe---~CF~~F~dP~~~~~d~~F~GC~WIy~PFt~eYy~Ird~LlPgf 162 (292)
+|++++++|=.+|=+-...++ ..++=...-||- .|-+.=. +...+..+.+|.-. | .-
T Consensus 2 iaflfvlv~tp~~~fr~~~~~-~~~~~~c~TlWg~k~~c~~~~y---~~~~~~~~~~C~~~-----------~-----~~ 61 (155)
T PF07344_consen 2 IAFLFVLVGTPLDMFRVKGGD-AFGNKGCYTLWGYKNDCGSVSY---SLRVDDLWFNCPQR-----------R-----SR 61 (155)
T ss_pred hhHHHHHHhCCHHHHccCCCC-CCCCceEEEEeeeeccCCCCcc---ccchhhhhcCCcHH-----------H-----HH
Confidence 688888888766654443332 344556777886 4543322 22224445678433 2 24
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHhcCcchhH
Q psy1287 163 LVFTEFFYTLTFLATIFCAMLVLLFFLCFTPDHKR 197 (292)
Q Consensus 163 fiAtQ~FfTl~~ll~l~s~~l~~l~~Lc~~~d~~r 197 (292)
|-|.|.|.-++..+.+++.++..+. +|+-+..+-
T Consensus 62 f~aa~afaIisi~~~~~a~v~g~~~-l~~~~~~r~ 95 (155)
T PF07344_consen 62 FRAAQAFAIISIFVYGAAFVLGVLL-LCCCSCLRW 95 (155)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHH-HHHhhhHHH
Confidence 6789999999999999999999988 555344443
No 15
>PF06966 DUF1295: Protein of unknown function (DUF1295); InterPro: IPR010721 This family contains a number of bacterial and eukaryotic proteins of unknown function that are approximately 300 residues long.
Probab=58.86 E-value=12 Score=33.92 Aligned_cols=47 Identities=32% Similarity=0.484 Sum_probs=30.5
Q ss_pred chhhHHHHHHHHHHHHhcCcceeeecccccCCccceechhHHhhccCCCCCc
Q psy1287 79 VGIAVFVIAFFCVVFAFFSASWLVSDSRITGAKFDRLGLWTHCFRSLPDPND 130 (292)
Q Consensus 79 ~a~~~t~iAf~~v~IAF~SPyWLvSd~rl~~~kF~rlGLWe~CF~~F~dP~~ 130 (292)
+|+++.++|+++=.+|=.-.+=...+|+ ...||-+-|||.+| |+|||
T Consensus 123 ~g~~l~~~g~~~E~~AD~Q~~~fk~~~~-n~g~~~~~GLw~~s----RHPNY 169 (235)
T PF06966_consen 123 LGIALFLIGFLLETVADQQKYRFKKDPA-NKGKFCTTGLWRYS----RHPNY 169 (235)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHhhCcc-cCCccccCCeeeee----eCchH
Confidence 4555555666555555333332245666 45689999999986 88998
No 16
>PF06687 SUR7: SUR7/PalI family; InterPro: IPR009571 This family consists of several fungal-specific SUR7 proteins. Its activity regulates expression of RVS161, a homologue of human endophilin, suggesting a function for both in endocytosis [, ]. The protein carries four transmembrane domains and is thus likely to act as an anchoring protein for the eisosome to the plasma membrane. Eisosomes are the immobile protein complexes, that include the proteins Pil1 and Lsp1, which co-localise with sites of protein and lipid endocytosis at the plasma membrane. SUR7 protein may play a role in sporulation []. Two-component signal transduction systems enable bacteria to sense, respond, and adapt to a wide range of environments, stressors, and growth conditions []. Some bacteria can contain up to as many as 200 two-component systems that need tight regulation to prevent unwanted cross-talk []. These pathways have been adapted to response to a wide variety of stimuli, including nutrients, cellular redox state, changes in osmolarity, quorum signals, antibiotics, and more []. Two-component systems are comprised of a sensor histidine kinase (HK) and its cognate response regulator (RR) []. The HK catalyses its own auto-phosphorylation followed by the transfer of the phosphoryl group to the receiver domain on RR; phosphorylation of the RR usually activates an attached output domain, which can then effect changes in cellular physiology, often by regulating gene expression. Some HK are bifunctional, catalysing both the phosphorylation and dephosphorylation of their cognate RR. The input stimuli can regulate either the kinase or phosphatase activity of the bifunctional HK. A variant of the two-component system is the phospho-relay system. Here a hybrid HK auto-phosphorylates and then transfers the phosphoryl group to an internal receiver domain, rather than to a separate RR protein. The phosphoryl group is then shuttled to histidine phosphotransferase (HPT) and subsequently to a terminal RR, which can evoke the desired response [, ]. This family also includes PalI which is part of a pH signal transduction cascade. Based on the similarity of PalI to the yeast Rim9 meiotic signal transduction component it has been suggested that PalI might be a membrane sensor for ambient pH [].
Probab=56.56 E-value=2.7 Score=36.05 Aligned_cols=57 Identities=21% Similarity=0.367 Sum_probs=32.9
Q ss_pred HHHHHHHHHHHHHHHHHHHHhcCcchhH-----HHHHHHHHhHHhhhcCCCccEEeeehcccC
Q psy1287 170 YTLTFLATIFCAMLVLLFFLCFTPDHKR-----FVQLTLVIGSTLTCAGAKFDRLGLWTHCFR 227 (292)
Q Consensus 170 fTl~~ll~l~s~~l~~l~~Lc~~~d~~r-----yv~ll~~~g~~l~~AgAKF~rLGLWe~CF~ 227 (292)
..+.+++++++.++.++- +.-+|.++. |..-+-+-+.....+-+++-+.|+|.+|-.
T Consensus 2 ~~~~~~~~~~a~il~il~-~i~~~~~~~~~~~l~~~~~~~s~~~~~~g~~~~y~~gl~g~C~~ 63 (212)
T PF06687_consen 2 AIIPLLLSLAAFILLILA-LISGPSNSSVLKSLYFLKLDTSGLGISLGLPDFYRFGLWGYCEG 63 (212)
T ss_pred chHHHHHHHHHHHHHHHH-HhcCCCCCCcccceEEEEEECCCCCccCCCCCeEEEEEEEEeee
Confidence 356778888888888887 333342211 111111100111134567899999999998
No 17
>PF07803 GSG-1: GSG1-like protein; InterPro: IPR012478 This family contains sequences bearing similarity to a region of GSG1 (Q9Z1H7 from SWISSPROT), a protein specifically expressed in testicular germ cells []. It is possible that over expression of the human homologue may be involved in tumourigenesis of human testicular germ cell tumours []. The region in question has four highly conserved cysteine residues.
Probab=53.38 E-value=11 Score=32.51 Aligned_cols=46 Identities=15% Similarity=0.282 Sum_probs=35.4
Q ss_pred ccchhhHHHHHHHHHHHHhcCcceeeecccccCCccceechhHHhhc
Q psy1287 77 GNVGIAVFVIAFFCVVFAFFSASWLVSDSRITGAKFDRLGLWTHCFR 123 (292)
Q Consensus 77 g~~a~~~t~iAf~~v~IAF~SPyWLvSd~rl~~~kF~rlGLWe~CF~ 123 (292)
...+++++.+|+.+-+.||.|-||-|--.|...|-= .-|.=..|++
T Consensus 8 a~Ls~~ln~LAL~~S~tA~~sSyWC~GTqKVpKPlC-~~~~~~~Ci~ 53 (118)
T PF07803_consen 8 ALLSLILNLLALAFSTTALLSSYWCEGTQKVPKPLC-GKGKGTNCIH 53 (118)
T ss_pred HHHHHHHHHHHHHHHHHHHhcccccccceecCCCCC-CccccCcCcC
Confidence 347889999999999999999999998877655433 3355566664
No 18
>PF13127 DUF3955: Protein of unknown function (DUF3955)
Probab=36.32 E-value=37 Score=25.85 Aligned_cols=33 Identities=12% Similarity=0.400 Sum_probs=28.9
Q ss_pred chhhHHHHHHHHHHHHhcCcceeeecccccCCcc
Q psy1287 79 VGIAVFVIAFFCVVFAFFSASWLVSDSRITGAKF 112 (292)
Q Consensus 79 ~a~~~t~iAf~~v~IAF~SPyWLvSd~rl~~~kF 112 (292)
.|..+..+|.+++++.=.++++..+||-+..| |
T Consensus 6 l~~~~~llg~~~l~i~~~~~syVd~~G~L~Ep-F 38 (63)
T PF13127_consen 6 LSLILLLLGVVCLFIFNIIGSYVDEDGVLHEP-F 38 (63)
T ss_pred HHHHHHHHHHHHHHHHhcccceECCCCeEecc-c
Confidence 67888889999999999999999999998665 5
No 19
>PRK09400 secE preprotein translocase subunit SecE; Reviewed
Probab=32.48 E-value=35 Score=26.02 Aligned_cols=25 Identities=20% Similarity=0.381 Sum_probs=21.3
Q ss_pred HhcCcchhHHHHHHHHHhHHhhhcC
Q psy1287 189 LCFTPDHKRFVQLTLVIGSTLTCAG 213 (292)
Q Consensus 189 Lc~~~d~~ryv~ll~~~g~~l~~Ag 213 (292)
+|+.||.|.|.++.++.|.-.++-|
T Consensus 23 ~~~KPd~~Ef~~ia~~~~iG~~i~G 47 (61)
T PRK09400 23 VARKPTREEFLLVAKVTGLGILLIG 47 (61)
T ss_pred HhcCCCHHHHHHHHHHHHHHHHHHH
Confidence 7888999999999999887766655
No 20
>PF11309 DUF3112: Protein of unknown function (DUF3112); InterPro: IPR021460 This eukaryotic family of proteins has no known function.
Probab=32.12 E-value=2.2e+02 Score=25.20 Aligned_cols=79 Identities=24% Similarity=0.240 Sum_probs=52.2
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHhcCc---c-------hhHHHHHHHHHhHHhhhcCCCccEEeeehcccCCCCCCCCc
Q psy1287 166 TEFFYTLTFLATIFCAMLVLLFFLCFTP---D-------HKRFVQLTLVIGSTLTCAGAKFDRLGLWTHCFRSLPDPNDE 235 (292)
Q Consensus 166 tQ~FfTl~~ll~l~s~~l~~l~~Lc~~~---d-------~~ryv~ll~~~g~~l~~AgAKF~rLGLWe~CF~~F~~P~~~ 235 (292)
.|+-.|+-.++++..+.++++-.+.-++ . +-|.-.++..++++|+.-|+-|.-...|.. +.-.+|.-+
T Consensus 51 ~~~~~~~~~v~a~~pi~lv~la~~~P~~~p~~iE~Fg~g~~~~k~~il~~ts~lL~~ga~~R~~~~f~~--~~~~~~~~w 128 (160)
T PF11309_consen 51 QLFASTYLAVYAFLPIPLVALAFFLPRRKPWWIESFGPGSHRTKIIILIITSLLLTLGAIFRAGVAFQP--RPVNNPSAW 128 (160)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCCcccCCccchhHHHHHHHHHHHHHHHHHHHHheeEecc--cCCCCCCcc
Confidence 4566666667777777777765333323 1 223566777888888888999988888887 666666444
Q ss_pred ccccCccceEeeec
Q psy1287 236 YIRRFFVGCRWIFD 249 (292)
Q Consensus 236 y~~~~F~GC~wIf~ 249 (292)
|.+| .|-|++.
T Consensus 129 ~~sk---a~fYi~~ 139 (160)
T PF11309_consen 129 YHSK---AAFYIFN 139 (160)
T ss_pred cccc---eeeeeec
Confidence 5444 5888863
No 21
>PF06966 DUF1295: Protein of unknown function (DUF1295); InterPro: IPR010721 This family contains a number of bacterial and eukaryotic proteins of unknown function that are approximately 300 residues long.
Probab=22.60 E-value=1.9e+02 Score=26.37 Aligned_cols=76 Identities=24% Similarity=0.311 Sum_probs=39.9
Q ss_pred hhhhhcccchh-h-HHHHHHHHHHHHHHHHHHHHHHHHHHHhcCcchhHHHHHHHHHhHHhhhcCC--------------
Q psy1287 151 YDQIRGYLVPG-F-LVFTEFFYTLTFLATIFCAMLVLLFFLCFTPDHKRFVQLTLVIGSTLTCAGA-------------- 214 (292)
Q Consensus 151 Yy~Ird~LlPg-f-fiAtQ~FfTl~~ll~l~s~~l~~l~~Lc~~~d~~ryv~ll~~~g~~l~~AgA-------------- 214 (292)
|..+|+-.-+. | .-..-+++.-+++..++++...++. . .+++. -....-.+|..+.+.|.
T Consensus 71 ~~~~r~~~~~~~~~~~~~~~~~~q~~~~~~~~lP~~~~~-~-~~~~~--~~~~~~~~g~~l~~~g~~~E~~AD~Q~~~fk 146 (235)
T PF06966_consen 71 YDDLRKKWGEWFWPFSFFFIFLFQALLVWLISLPVYLAN-S-SPPNP--PLNWLDILGIALFLIGFLLETVADQQKYRFK 146 (235)
T ss_pred HHHHHHhcCcchhHHHHHHHHHHHHHHHHHHHHHHHHHH-H-hcccC--cchHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 45566654333 2 2222244444555556666555544 1 11211 13444455555555333
Q ss_pred -------CccEEeeehcccCCCCCCCC
Q psy1287 215 -------KFDRLGLWTHCFRSLPDPND 234 (292)
Q Consensus 215 -------KF~rLGLWe~CF~~F~~P~~ 234 (292)
+|.+-|||.+| ++|||
T Consensus 147 ~~~~n~g~~~~~GLw~~s----RHPNY 169 (235)
T PF06966_consen 147 KDPANKGKFCTTGLWRYS----RHPNY 169 (235)
T ss_pred hCcccCCccccCCeeeee----eCchH
Confidence 58999999987 57877
No 22
>PF08600 Rsm1: Rsm1-like; InterPro: IPR013909 This entry contains Nuclear-interacting partner of ALK (NIPA) and NIPA like proteins, as well as mRNA export factor Rsm1, all of which contain a C3HC-type zinc finger. The domain represented in this entry is found C-terminal to the zinc-finger like domain IPR012935 from INTERPRO. Rsm1 is involved in mRNA export from the nucleus []. NIPA is an essential component of an SCF-type E3 ligase complex, SCF(NIPA), a complex that controls mitotic entry by mediating ubiquitination and subsequent degradation of cyclin B1 (CCNB1). Its cell-cycle-dependent phosphorylation regulates the assembly of the SCF(NIPA) complex, restricting CCNB1 ubiquitination activity to interphase. Its inactivation results in nuclear accumulation of CCNB1 in interphase and premature mitotic entry [].
Probab=21.40 E-value=46 Score=26.52 Aligned_cols=61 Identities=30% Similarity=0.484 Sum_probs=35.8
Q ss_pred hhhcCCCccEEeeehcccC--------CCCCCCCcccccCccceEeeec-C--CccchhhhhccccchhhHHHHHH
Q psy1287 209 LTCAGAKFDRLGLWTHCFR--------SLPDPNDEYIRRFFVGCRWIFD-P--FTKGYDQIRGYLVPGFLVFTEFF 273 (292)
Q Consensus 209 l~~AgAKF~rLGLWe~CF~--------~F~~P~~~y~~~~F~GC~wIf~-p--~s~EY~~Ird~LlPgwfiavQ~F 273 (292)
++--+.|+.|+|||-+=-+ +.-||.++.. .+ |-||=. + -+.+...-.+-..|||=+..|+.
T Consensus 19 ~~~C~~C~Rr~GLW~f~~~~ss~~~~~~~~d~~~eHr-~~---CPwv~~~~q~~~~~~~~~~~~~~~GW~~l~~~l 90 (91)
T PF08600_consen 19 LLSCSYCFRRLGLWMFKSKESSDSDPMSPFDPLEEHR-EY---CPWVNPSTQSGTGRSSEAEQSLSPGWKVLLQAL 90 (91)
T ss_pred eEEccccCcEeeeeecccCccCCCCcCCCCCCccccc-cc---CCccCCcccccccccCCCCCCcCcHHHHHHHHh
Confidence 3445789999999998543 3455555442 22 777732 0 01123333344459999888863
No 23
>PF11292 DUF3093: Protein of unknown function (DUF3093); InterPro: IPR021443 This family of proteins with unknown function appears to be restricted to Actinobacteria. Some members are annotated as alanine rich membrane proteins however this cannot be confirmed.
Probab=21.00 E-value=42 Score=29.48 Aligned_cols=8 Identities=50% Similarity=0.987 Sum_probs=6.7
Q ss_pred Ccceeeec
Q psy1287 97 SASWLVSD 104 (292)
Q Consensus 97 SPyWLvSd 104 (292)
|||||+|-
T Consensus 125 TPYWlvST 132 (143)
T PF11292_consen 125 TPYWLVST 132 (143)
T ss_pred CceEEEee
Confidence 78888885
No 24
>TIGR00327 secE_euk_arch protein translocase SEC61 complex gamma subunit, archaeal and eukaryotic. This model describes archaeal SEC61-like and eukaryotic SEC61 but not bacterial secE proteins, for which a Pfam pfam00584 (SecE) has been created.
Probab=20.73 E-value=87 Score=24.02 Aligned_cols=25 Identities=24% Similarity=0.602 Sum_probs=20.4
Q ss_pred HhcCcchhHHHHHHHHHhHHhhhcC
Q psy1287 189 LCFTPDHKRFVQLTLVIGSTLTCAG 213 (292)
Q Consensus 189 Lc~~~d~~ryv~ll~~~g~~l~~Ag 213 (292)
.|+-||.|.|.+..++.|.-.++-|
T Consensus 19 ~~~KPd~~Ef~~iak~t~iG~~i~G 43 (61)
T TIGR00327 19 VCKKPDLEEYLKVAKVTGIGIIIVG 43 (61)
T ss_pred HhcCCCHHHHHHHHHHHHHHHHHHH
Confidence 6888999999999998877665533
Done!