Query 025213
Match_columns 256
No_of_seqs 94 out of 112
Neff 4.4
Searched_HMMs 46136
Date Fri Mar 29 03:41:04 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/025213.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/025213hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF06105 Aph-1: Aph-1 protein; 100.0 2.7E-82 5.7E-87 569.9 20.0 218 2-227 1-220 (238)
2 KOG3972 Predicted membrane pro 100.0 2.7E-75 6E-80 514.7 12.4 206 1-217 1-207 (252)
3 PF10086 DUF2324: Putative mem 98.1 1.9E-05 4E-10 71.1 10.0 169 15-202 5-203 (223)
4 PF13367 PrsW-protease: Protea 90.7 7.6 0.00017 33.2 12.5 93 67-180 43-137 (191)
5 COG4377 Predicted membrane pro 83.9 18 0.00039 33.5 11.0 153 63-238 76-252 (258)
6 COG2339 prsW Membrane proteina 62.8 1.4E+02 0.0031 28.3 11.9 150 7-184 41-199 (274)
7 PF04387 PTPLA: Protein tyrosi 50.4 12 0.00025 32.5 2.1 39 51-89 33-71 (164)
8 PLN02838 3-hydroxyacyl-CoA deh 46.9 24 0.00053 32.2 3.7 38 51-88 87-124 (221)
9 COG2443 Sss1 Preprotein transl 37.0 59 0.0013 24.6 3.8 47 77-137 11-57 (65)
10 COG5198 Ptpl Protein tyrosine 35.7 2.2E+02 0.0048 25.8 7.8 59 33-106 12-70 (209)
11 PRK10497 peripheral inner memb 34.6 41 0.00088 26.1 2.7 28 10-37 26-55 (73)
12 TIGR02979 phageshock_pspD phag 31.0 49 0.0011 24.7 2.5 27 11-37 15-43 (59)
13 PF09584 Phageshock_PspD: Phag 24.8 85 0.0019 23.9 2.9 28 10-37 19-48 (66)
14 PRK14818 NADH dehydrogenase su 20.9 88 0.0019 27.9 2.7 24 143-166 129-152 (173)
15 PF01058 Oxidored_q6: NADH ubi 20.0 79 0.0017 25.9 2.1 23 143-165 109-131 (131)
No 1
>PF06105 Aph-1: Aph-1 protein; InterPro: IPR009294 This family consists of several eukaryotic Aph-1 proteins. Gamma-secretase catalyses the intramembrane proteolysis of Notch, beta-amyloid precursor protein, and other substrates as part of a new signalling paradigm and as a key step in the pathogenesis of Alzheimer's disease. It is thought that the presenilin heterodimer comprises the catalytic site and that a highly glycosylated form of nicastrin associates with it. Aph-1 and Pen-2, two membrane proteins genetically linked to gamma-secretase, associate directly with presenilin and nicastrin in the active protease complex. Co-expression of all four proteins leads to marked increases in presenilin heterodimers, full glycosylation of nicastrin, and enhanced gamma-secretase activity [].; GO: 0016485 protein processing, 0043085 positive regulation of catalytic activity, 0016021 integral to membrane
Probab=100.00 E-value=2.7e-82 Score=569.90 Aligned_cols=218 Identities=36% Similarity=0.625 Sum_probs=209.8
Q ss_pred cchhhHhHHHHHHhhHHHHhhHhhcCCchhHHHHHHHHHHHHHHHHHHHhHHhhcccCCCCCcchhHHHHHHHHHHHHHH
Q 025213 2 TVAAGIGYALIALGPSLSLFVAVISKKPFLILTVLSSTLLWLISLIVLSGIWRAFLPLKSTTWWPFALLIISSVGFQEGL 81 (256)
Q Consensus 2 t~~~~fGc~fIAfGP~laLF~~tIa~~P~lIIiliagAFfWLvSLLlsSliW~i~~pl~~~~~~~l~f~v~~SV~iQE~f 81 (256)
|+++++||+||||||++++|++||||||+|||++++||||||+|+|++|++|++++|++|+ +++++++||++||.+
T Consensus 1 T~~~f~Gc~liafgP~lalf~~tIa~~p~liIi~i~~aFfWLvSLLlss~iW~i~~pl~~~----l~f~v~~sV~~QE~f 76 (238)
T PF06105_consen 1 TLAVFFGCALIAFGPALALFVFTIARDPQLIIILIAGAFFWLVSLLLSSLIWFIVVPLRDN----LAFGVLFSVLIQEAF 76 (238)
T ss_pred ChHHHHHHHHHHHCHHHHhhheeeeCCCchhHHHHHHHHHHHHHHHHHHHHHHhhhccccc----hhHHHHHHHHHHHHH
Confidence 7889999999999999999999999999999999999999999999999999999999988 568999999999999
Q ss_pred HHHHHHHHHHHHHHHHhhhcccCCCccccchhhHHHHhhccchhhHHHHHHHhhcccccccCceeccCCCCCchHHHHHH
Q 025213 82 RVLFWKVYKRLEDTLDAFADRVGKPRLFLTDKMQIALAGGLGHGVAHAVFFCLSLLTPAFGPATFYVDRCPQMPFFLISA 161 (256)
Q Consensus 82 R~~~y~llkkae~gL~~i~~~~~~~~~~~~~~~~lA~v~GlGfGimsg~f~~in~Lads~GPGt~g~~~c~~~~ffl~SA 161 (256)
|++|||++||||||||+++||+++| +|||++|||+|+|||+|||+|+++|+|+|++||||+|+|+||++|||++||
T Consensus 77 R~~~~~ll~kae~gL~~i~~~~~~~----~~~~~lA~v~GlGfGimsg~f~~~n~Lads~GPGt~g~~~c~~~~ffl~SA 152 (238)
T PF06105_consen 77 RYLYYKLLKKAEEGLQSIAEDGTSP----ISRHQLAYVSGLGFGIMSGVFSFVNILADSLGPGTVGIHGCPSMPFFLTSA 152 (238)
T ss_pred HHHHHHHHHHHHHHHHHhccccCCC----CccceeeehhccchHHHHHHHHHHhhhhhccCCceeccCCCCCccchHHHH
Confidence 9999999999999999999998776 789999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHHHHHHHhhcccccCceeeEEehhhHHHHHHHHhhhc--CCCCceeEehHHHHHHHHHH
Q 025213 162 IIALAFVTIHTFSMVIAFNGYAEGNTTDQYFVPVVHLVAGMVVKSA--FARCFCLLSQKFSLLRILFL 227 (256)
Q Consensus 162 ~~tl~~iLLH~fW~VI~F~g~~~k~~~~~~~V~~~Hl~vS~lTllN--~~~~gC~vsi~i~l~~i~~~ 227 (256)
++|+++++||+|||||+|||||||||+++++|+++|+++|++|++| .+.+||+.+.|+-.++....
T Consensus 153 ~~tl~~~lLH~fW~VI~F~g~~~~~~~~i~~V~~~Hl~vs~lTllN~~~~~~~~v~~~~il~~~~~~a 220 (238)
T PF06105_consen 153 FMTLAFILLHTFWMVIFFDGCEKKNWWLIAFVVISHLLVSCLTLLNSPLYSGGCVPSYPILVLTGAWA 220 (238)
T ss_pred HHHHHHHHHHHHHHHhhhhhhccCCceEEEehHHHHHHHHHHHHcCccccccchHHHHHHHHHHHHHH
Confidence 9999999999999999999999999999999999999999999999 56789999999877776655
No 2
>KOG3972 consensus Predicted membrane protein [Function unknown]
Probab=100.00 E-value=2.7e-75 Score=514.73 Aligned_cols=206 Identities=26% Similarity=0.403 Sum_probs=195.3
Q ss_pred CcchhhHhHHHHHHhhHHHHhhHhhcCCchhHHHHHHHHHHHHHHHHHHHhHHhhc-ccCCCCCcchhHHHHHHHHHHHH
Q 025213 1 MTVAAGIGYALIALGPSLSLFVAVISKKPFLILTVLSSTLLWLISLIVLSGIWRAF-LPLKSTTWWPFALLIISSVGFQE 79 (256)
Q Consensus 1 Mt~~~~fGc~fIAfGP~laLF~~tIa~~P~lIIiliagAFfWLvSLLlsSliW~i~-~pl~~~~~~~l~f~v~~SV~iQE 79 (256)
||++++|||+|+||||++|+|++|||+||.|||++++||||||+|||+||++|++. .|++|+ ++|+..+||.+||
T Consensus 1 M~~~~ffgC~fiaFgPa~ALf~~tIA~dPvRIIiliagaFFWLvSLLisSl~W~~l~i~l~~~----lifg~~vsV~~qE 76 (252)
T KOG3972|consen 1 MGAAVFFGCTFIAFGPAFALFVFTIAHDPVRIIILIAGAFFWLVSLLISSLVWFGLSIVLPDD----LIFGATVSVIAQE 76 (252)
T ss_pred CCcceeeeeEEeeeCcchhhheeeecCCCeeehhhHHHHHHHHHHHHHHHHHHHheEccchhh----hhhHHHHHHHHHH
Confidence 99999999999999999999999999999999999999999999999999999998 566554 7899999999999
Q ss_pred HHHHHHHHHHHHHHHHHHhhhcccCCCccccchhhHHHHhhccchhhHHHHHHHhhcccccccCceeccCCCCCchHHHH
Q 025213 80 GLRVLFWKVYKRLEDTLDAFADRVGKPRLFLTDKMQIALAGGLGHGVAHAVFFCLSLLTPAFGPATFYVDRCPQMPFFLI 159 (256)
Q Consensus 80 ~fR~~~y~llkkae~gL~~i~~~~~~~~~~~~~~~~lA~v~GlGfGimsg~f~~in~Lads~GPGt~g~~~c~~~~ffl~ 159 (256)
.||++|||++|||||||++++||++. +++||++|||+|+|||+|||+|+.+|.|+|+.||||+|+||++++ ||+.
T Consensus 77 ~fR~ayyklLkka~~GL~si~~d~~~----~~s~h~lAyVsGLgfGIiSgvFs~vN~lad~sGPGtvGl~g~s~~-~fl~ 151 (252)
T KOG3972|consen 77 LFRFAYYKLLKKAQEGLNSITEDGRL----HNSRHMLAYVSGLGFGIISGVFSTVNALADFSGPGTVGLHGDSPY-FFLT 151 (252)
T ss_pred HHHHHHHHHHHHHHHHHHhcCccCCC----chhHHHHHHHhccchhHHHHHHHHHHHHHhccCCCeeccCCCcch-hhHH
Confidence 99999999999999999999998554 489999999999999999999999999999999999999999996 9999
Q ss_pred HHHHHHHHHHHHHHHHHHhhcccccCceeeEEehhhHHHHHHHHhhhcCCCCceeEeh
Q 025213 160 SAIIALAFVTIHTFSMVIAFNGYAEGNTTDQYFVPVVHLVAGMVVKSAFARCFCLLSQ 217 (256)
Q Consensus 160 SA~~tl~~iLLH~fW~VI~F~g~~~k~~~~~~~V~~~Hl~vS~lTllN~~~~gC~vsi 217 (256)
||++|+.++|+|+||+|++||+|||+||+....|+.+|+++|.+|++|++ |-.+..
T Consensus 152 sa~~al~iiLlHvfW~ivffdac~k~~~~~l~~vv~SHLlvs~lt~lns~--~~y~~~ 207 (252)
T KOG3972|consen 152 SAFSALLIILLHVFWGIVFFDACEKIAYVPLGAVVVSHLLVSFLTFLNSR--GFYVLV 207 (252)
T ss_pred HHHHHHHHHHHHHHHHheeehhhhhhchhhhHHHHHHHHHHHHHHHhCcc--chhHHH
Confidence 99999999999999999999999999999999999999999999999995 444444
No 3
>PF10086 DUF2324: Putative membrane peptidase family (DUF2324); InterPro: IPR011397 There are currently no experimental data for members of this group or their homologues, nor do they exhibit features indicative of any function. However, they are predicted to be integral membrane proteins (with several transmembrane segments).
Probab=98.12 E-value=1.9e-05 Score=71.11 Aligned_cols=169 Identities=18% Similarity=0.153 Sum_probs=115.3
Q ss_pred hhHHHHhhHhhcCCchhHHHHHHHHHHHHHHHHHHHhHH--hhcccCCCC------CcchhHHHHHHHHHHHHHHHHHHH
Q 025213 15 GPSLSLFVAVISKKPFLILTVLSSTLLWLISLIVLSGIW--RAFLPLKST------TWWPFALLIISSVGFQEGLRVLFW 86 (256)
Q Consensus 15 GP~laLF~~tIa~~P~lIIiliagAFfWLvSLLlsSliW--~i~~pl~~~------~~~~l~f~v~~SV~iQE~fR~~~y 86 (256)
-|.. ++...=.|+.......+.|+..|.++..+.-... ....+.++. ++.-...+-+.+=.+||..||.-+
T Consensus 5 ~pi~-l~~~~rk~~~~~~~~f~~Ga~~F~v~~~vle~~l~~~~~~~~~~~~~~~~~~~l~~ly~~l~AGiFEE~gR~i~~ 83 (223)
T PF10086_consen 5 LPIL-LFIYFRKRKKISWKPFILGALVFFVFAQVLELPLHQIVLSPNADGLIWTSNPILYALYGGLMAGIFEETGRYIGF 83 (223)
T ss_pred HHHH-HHHHHHHhccchHHHHHHHHHHHHHHHHHHHHHHHHHHHhcchhhHHHHhhHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3555 5666667888889999999999988777665433 222333222 211234456778889999999999
Q ss_pred HHHHHHHHHHHhhhcccCCCccccchhhHHHHhhccchhhHHHHHH----Hhhccccc--ccCceecc------------
Q 025213 87 KVYKRLEDTLDAFADRVGKPRLFLTDKMQIALAGGLGHGVAHAVFF----CLSLLTPA--FGPATFYV------------ 148 (256)
Q Consensus 87 ~llkkae~gL~~i~~~~~~~~~~~~~~~~lA~v~GlGfGimsg~f~----~in~Lads--~GPGt~g~------------ 148 (256)
|.++|-++..+ .-+..-|+|||.+=+++- .+|.+.-+ .-.|+...
T Consensus 84 k~l~kk~~~~~-----------------~~al~~GlGhGg~Eailvg~~~~l~~~v~~~~in~g~~~~~~~~~~~~~~~~ 146 (223)
T PF10086_consen 84 KYLLKKRRDWS-----------------DDALAYGLGHGGIEAILVGGLSLLNNLVLAMMINSGSLDQLLEQPAELLEQI 146 (223)
T ss_pred HHHHHcccchh-----------------hHHHHHHcchHHHHHHHHHHHHHHHHHHHHHHHhcCChhhhhhhhhhHHHHH
Confidence 99886432111 137788999998755443 44544222 11222211
Q ss_pred ----CCCCCchHHHHHHHHHHHHHHHHHHHHHHhhcccccCceeeEEehhhHHHHHHH
Q 025213 149 ----DRCPQMPFFLISAIIALAFVTIHTFSMVIAFNGYAEGNTTDQYFVPVVHLVAGM 202 (256)
Q Consensus 149 ----~~c~~~~ffl~SA~~tl~~iLLH~fW~VI~F~g~~~k~~~~~~~V~~~Hl~vS~ 202 (256)
..-|. ..++.+.+....=+.+|+..+++.+.|.++||++.....+..|.++=.
T Consensus 147 ~~~l~~~~~-~~~~l~~~ERi~Al~~hi~lSvlV~~av~~~k~~~l~~AIllHaliD~ 203 (223)
T PF10086_consen 147 QSALASLPP-WSFLLGGVERIFALLFHIGLSVLVWYAVRQRKKWYLVLAILLHALIDF 203 (223)
T ss_pred HHHHHcCcH-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCchHHHHHHHHHHHHHH
Confidence 11233 378899999999999999999999999999999888888899988766
No 4
>PF13367 PrsW-protease: Protease prsW family
Probab=90.69 E-value=7.6 Score=33.24 Aligned_cols=93 Identities=17% Similarity=0.070 Sum_probs=59.5
Q ss_pred hHHHHHHHHHHHHHHHHHHHHHHHH-HHHHHHhhhcccCCCccccchhhHHHHhhccchhhHHHHHHHhhcccccccCce
Q 025213 67 FALLIISSVGFQEGLRVLFWKVYKR-LEDTLDAFADRVGKPRLFLTDKMQIALAGGLGHGVAHAVFFCLSLLTPAFGPAT 145 (256)
Q Consensus 67 l~f~v~~SV~iQE~fR~~~y~llkk-ae~gL~~i~~~~~~~~~~~~~~~~lA~v~GlGfGimsg~f~~in~Lads~GPGt 145 (256)
.....+.+=...|..++.-..++.. .++..++ +.|....+.++|+||+.+=-+....|-..|.-+.
T Consensus 43 ~~~~~~~a~~~EE~~K~l~v~~~~~~~~~~~~~-----------~~d~~~~g~a~GlGFa~~En~~Y~~~~~~~~~~~-- 109 (191)
T PF13367_consen 43 LWGAFLIAPLVEEFAKLLPVLLLLLLRRRRFDE-----------PMDGLVYGAAVGLGFAIMENILYILNAAEDNGGS-- 109 (191)
T ss_pred HHHHHHHhHHHHHHHHHHHHHHHHHHhhHhhcC-----------cchhhhhhhHHHHHHHHHHHHHHHHHhhhcccch--
Confidence 4456777888999999877666552 3332211 1345788999999999999999988876444332
Q ss_pred eccCCCCCchHHHHHHHHHHHH-HHHHHHHHHHhhc
Q 025213 146 FYVDRCPQMPFFLISAIIALAF-VTIHTFSMVIAFN 180 (256)
Q Consensus 146 ~g~~~c~~~~ffl~SA~~tl~~-iLLH~fW~VI~F~ 180 (256)
.+ .-+. .++.-... ...|..|+.++.-
T Consensus 110 ------~~-~~~~-~~~~R~~~~~~~H~~~t~i~g~ 137 (191)
T PF13367_consen 110 ------VQ-GGLS-TAILRGITSVPGHALFTAIFGY 137 (191)
T ss_pred ------hh-hHHH-HHHHHHHHHHhHHHHHHHHHHH
Confidence 11 1111 12332222 5799999999743
No 5
>COG4377 Predicted membrane protein [Function unknown]
Probab=83.87 E-value=18 Score=33.50 Aligned_cols=153 Identities=17% Similarity=0.152 Sum_probs=87.7
Q ss_pred CcchhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhcccCCCccccchhhHHHHhhccchhhHHHHHHHhhccccccc
Q 025213 63 TWWPFALLIISSVGFQEGLRVLFWKVYKRLEDTLDAFADRVGKPRLFLTDKMQIALAGGLGHGVAHAVFFCLSLLTPAFG 142 (256)
Q Consensus 63 ~~~~l~f~v~~SV~iQE~fR~~~y~llkkae~gL~~i~~~~~~~~~~~~~~~~lA~v~GlGfGimsg~f~~in~Lads~G 142 (256)
|.+--+.|.+..=++.|.-|+.++|.+.| + -++ .--+.+-|+|||..-+.+-.+.-+..-.=
T Consensus 76 Pl~y~IYG~lMAg~FEE~gR~l~~rfl~k-R-~~~----------------~Ad~lAyglGHgGlEail~g~~S~~~l~i 137 (258)
T COG4377 76 PLIYIIYGLLMAGFFEETGRLLFFRFLEK-R-SLE----------------KADALAYGLGHGGLEAILLGLTSLLNLYI 137 (258)
T ss_pred CcHHHHHHHHHHHHHHHHhHHHHHHHHHh-C-ccc----------------chhHHHHhcccccHHHHHHHHHhHhhHHH
Confidence 33334567899999999999999999876 1 111 11245668999877665543322211111
Q ss_pred CceeccCCCCCchHHHHHH------------------------HHHHHHHHHHHHHHHHhhcccccCceeeEEehhhHHH
Q 025213 143 PATFYVDRCPQMPFFLISA------------------------IIALAFVTIHTFSMVIAFNGYAEGNTTDQYFVPVVHL 198 (256)
Q Consensus 143 PGt~g~~~c~~~~ffl~SA------------------------~~tl~~iLLH~fW~VI~F~g~~~k~~~~~~~V~~~Hl 198 (256)
=+.---.|+||. .+.|. +--..=+..+..-++..+++.++||+.........|-
T Consensus 138 ~~~Avn~g~~~~--L~~sGaeal~~~~~~ll~~lS~W~~~g~~~ERI~A~~vQ~~Ltl~V~~AVrqrrpi~Ll~ai~LHA 215 (258)
T COG4377 138 VLSAVNTGNPQV--LMQSGAEALSENMLKLLQSLSVWQIYGLGFERILALGVQLLLTLWVYQAVRQRRPIYLLAAIGLHA 215 (258)
T ss_pred hhhhhccCCHHH--HHHhhHHHhhHHHHHHHhCCcHHHHhhHHHHHHHHHHHHHHHHHHHHHHHHccccHHHHHHHHHHH
Confidence 111112233332 11211 1111223344555677899999999999999899997
Q ss_pred HHHHHhhhcCCCCceeEehHHHHHHHHHHHHHhccccCcc
Q 025213 199 VAGMVVKSAFARCFCLLSQKFSLLRILFLIVLKNCQLSPE 238 (256)
Q Consensus 199 ~vS~lTllN~~~~gC~vsi~i~l~~i~~~~~~~~~~~~~~ 238 (256)
+.-.=.-+-+ -| .++-|+..=+|+-++.+-.|--.||
T Consensus 216 lfdlpa~LyQ--vg-~~~~~v~vevi~AL~lal~~yw~~~ 252 (258)
T COG4377 216 LFDLPASLYQ--VG-WLTNPVLVEVILALELALVAYWTKE 252 (258)
T ss_pred HhcCCHHHHH--cc-cccchHHHHHHHHHHHHHHhcCcHh
Confidence 6433222222 23 3344667777777777777766665
No 6
>COG2339 prsW Membrane proteinase, regulator of anti-sigma factor [Posttranslational modification, protein turnover, chaperones]
Probab=62.80 E-value=1.4e+02 Score=28.27 Aligned_cols=150 Identities=18% Similarity=0.204 Sum_probs=75.2
Q ss_pred HhHHHHHHhhHHHHhhHhhcCCch-------hHHHHHHHHHHHHHHHHHHHhHHhhc-ccC-CCCCcchhHHHHHHHHHH
Q 025213 7 IGYALIALGPSLSLFVAVISKKPF-------LILTVLSSTLLWLISLIVLSGIWRAF-LPL-KSTTWWPFALLIISSVGF 77 (256)
Q Consensus 7 fGc~fIAfGP~laLF~~tIa~~P~-------lIIiliagAFfWLvSLLlsSliW~i~-~pl-~~~~~~~l~f~v~~SV~i 77 (256)
+-..++++-|++++-....-+|+. .+...+.|+++++.+..+ ....+ .+. .+..-+.+....+..=.+
T Consensus 41 ~~lv~~~~~~~~~~L~yFy~~~~~~~~pl~vvv~tfl~G~~l~~~~~~~---~~~~v~~~~~~~~l~~~~l~~al~~G~v 117 (274)
T COG2339 41 FALVLIAIAPALALLWYFYLRDAHKPEPLWVVVRTFLLGAFLSLFAVML---IYHFVLVLLWPSSLALLFLGSALLAGLV 117 (274)
T ss_pred HHHHHHHHHHHHHHHHHHhcccCCCCCCHHHHHHHHHHHHHHHHHHHHH---HHHHHHHhhcccccHHHHHHHHHhhhhh
Confidence 344567777777776666665554 555667777766433222 22111 111 111112222223333345
Q ss_pred HHHHHHHHHHHHHHHHHHHHhhhcccCCCccccchhhHHHHhhccchhhHHHHHHHhhcccccccCceeccCCCCCchHH
Q 025213 78 QEGLRVLFWKVYKRLEDTLDAFADRVGKPRLFLTDKMQIALAGGLGHGVAHAVFFCLSLLTPAFGPATFYVDRCPQMPFF 157 (256)
Q Consensus 78 QE~fR~~~y~llkkae~gL~~i~~~~~~~~~~~~~~~~lA~v~GlGfGimsg~f~~in~Lads~GPGt~g~~~c~~~~ff 157 (256)
.|.....=-++.- +..++.+ .+.|......++|+||-++=..-...|- + +.|+| .+ -
T Consensus 118 EE~~KaL~v~~~~--------~~~~~~~---~~~~g~l~Gaa~gLGFa~~Enl~Y~l~~-~-~~~~g---------v~-v 174 (274)
T COG2339 118 EEPLKALAVVLFV--------LRSLPLD---ELLDGLLYGAAAGLGFAATENLLYLLTG-A-SIGFG---------VE-V 174 (274)
T ss_pred HHHHHHHHHHHHH--------Hcccccc---chHHHHHHHHHHhccHHHHhhhHHHhcc-c-cccch---------HH-H
Confidence 5555443222210 1111111 2356688999999999999887777765 2 22222 21 1
Q ss_pred HHHHHHHHHHHHHHHHHHHHhhccccc
Q 025213 158 LISAIIALAFVTIHTFSMVIAFNGYAE 184 (256)
Q Consensus 158 l~SA~~tl~~iLLH~fW~VI~F~g~~~ 184 (256)
+.+..... ++-|+.|+.+..-+.-+
T Consensus 175 ~~~r~~~~--~~gHa~~s~i~Gy~Lgl 199 (274)
T COG2339 175 AFERALLA--ILGHALLSAIVGYYLGL 199 (274)
T ss_pred HHHHHHHh--hhhHHHHHHHHHHHHHH
Confidence 22222222 22399999998765543
No 7
>PF04387 PTPLA: Protein tyrosine phosphatase-like protein, PTPLA; InterPro: IPR007482 Protein tyrosine (pTyr) phosphorylation is a common post-translational modification which can create novel recognition motifs for protein interactions and cellular localisation, affect protein stability, and regulate enzyme activity. Consequently, maintaining an appropriate level of protein tyrosine phosphorylation is essential for many cellular functions. Tyrosine-specific protein phosphatases (PTPase; 3.1.3.48 from EC) catalyse the removal of a phosphate group attached to a tyrosine residue, using a cysteinyl-phosphate enzyme intermediate. These enzymes are key regulatory components in signal transduction pathways (such as the MAP kinase pathway) and cell cycle control, and are important in the control of cell growth, proliferation, differentiation and transformation [, ]. The PTP superfamily can be divided into four subfamilies []: (1) pTyr-specific phosphatases (2) dual specificity phosphatases (dTyr and dSer/dThr) (3) Cdc25 phosphatases (dTyr and/or dThr) (4) LMW (low molecular weight) phosphatases Based on their cellular localisation, PTPases are also classified as: Receptor-like, which are transmembrane receptors that contain PTPase domains [] Non-receptor (intracellular) PTPases [] All PTPases carry the highly conserved active site motif C(X)5R (PTP signature motif), employ a common catalytic mechanism, and share a similar core structure made of a central parallel beta-sheet with flanking alpha-helices containing a beta-loop-alpha-loop that encompasses the PTP signature motif []. Functional diversity between PTPases is endowed by regulatory domains and subunits. This family includes the mammalian protein tyrosine phosphatase-like protein, PTPLA. A significant variation of PTPLA from other protein tyrosine phosphatases is the presence of proline instead of catalytic arginine at the active site. It is thought that PTPLA proteins have a role in the development, differentiation, and maintenance of a number of tissue types [].
Probab=50.45 E-value=12 Score=32.47 Aligned_cols=39 Identities=15% Similarity=0.355 Sum_probs=29.3
Q ss_pred hHHhhcccCCCCCcchhHHHHHHHHHHHHHHHHHHHHHH
Q 025213 51 GIWRAFLPLKSTTWWPFALLIISSVGFQEGLRVLFWKVY 89 (256)
Q Consensus 51 liW~i~~pl~~~~~~~l~f~v~~SV~iQE~fR~~~y~ll 89 (256)
++|-++.+.++.+..+....++++-.+.|..||.||-+-
T Consensus 33 vv~~v~~~~p~~~~~~~~~~l~~aWsl~EviRY~yY~~~ 71 (164)
T PF04387_consen 33 VVWGVIYPFPEVQSSPAVPLLLIAWSLTEVIRYPYYALK 71 (164)
T ss_pred eehhhhccccccccccchhhHHHHHHhhhcchhHHHHHH
Confidence 567777666654334456789999999999999998653
No 8
>PLN02838 3-hydroxyacyl-CoA dehydratase subunit of elongase
Probab=46.94 E-value=24 Score=32.18 Aligned_cols=38 Identities=13% Similarity=0.196 Sum_probs=28.6
Q ss_pred hHHhhcccCCCCCcchhHHHHHHHHHHHHHHHHHHHHH
Q 025213 51 GIWRAFLPLKSTTWWPFALLIISSVGFQEGLRVLFWKV 88 (256)
Q Consensus 51 liW~i~~pl~~~~~~~l~f~v~~SV~iQE~fR~~~y~l 88 (256)
++|-++.+.++.+..+....++++-.+.|..||.||-+
T Consensus 87 iv~~v~~~~p~~~~~~~~~~l~~aWs~tEvIRY~yY~~ 124 (221)
T PLN02838 87 LTWGILWSFPEVRSHILVTSLVISWSITEIIRYSFFGM 124 (221)
T ss_pred HHHHHhhcCcchhcccHHHHHHHHHHHHHHHHHHHHHH
Confidence 67777766665444444556899999999999999954
No 9
>COG2443 Sss1 Preprotein translocase subunit Sss1 [Intracellular trafficking and secretion]
Probab=36.96 E-value=59 Score=24.63 Aligned_cols=47 Identities=28% Similarity=0.352 Sum_probs=32.3
Q ss_pred HHHHHHHHHHHHHHHHHHHHHhhhcccCCCccccchhhHHHHhhccchhhHHHHHHHhhcc
Q 025213 77 FQEGLRVLFWKVYKRLEDTLDAFADRVGKPRLFLTDKMQIALAGGLGHGVAHAVFFCLSLL 137 (256)
Q Consensus 77 iQE~fR~~~y~llkkae~gL~~i~~~~~~~~~~~~~~~~lA~v~GlGfGimsg~f~~in~L 137 (256)
+||-+| .|.|++|+|. +|+- ++=.+.|-+.|+|+.++.++=+.+-++
T Consensus 11 ~~~~lk-e~~rvl~~ar-----------KP~~--eEy~~~aKi~~~Gi~liG~IGfiI~li 57 (65)
T COG2443 11 LREFLK-EYRRVLKVAR-----------KPDW--EEYSKIAKITGLGILLIGIIGFIIYLI 57 (65)
T ss_pred HHHHHH-HHHHHHHHHh-----------CCCH--HHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 455555 6788888776 3422 233667778999999998887776665
No 10
>COG5198 Ptpl Protein tyrosine phosphatase-like protein (contains Pro instead of catalytic Arg) [General function prediction only]
Probab=35.73 E-value=2.2e+02 Score=25.83 Aligned_cols=59 Identities=22% Similarity=0.275 Sum_probs=37.8
Q ss_pred HHHHHHHHHHHHHHHHHHhHHhhcccCCCCCcchhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhcccCCC
Q 025213 33 LTVLSSTLLWLISLIVLSGIWRAFLPLKSTTWWPFALLIISSVGFQEGLRVLFWKVYKRLEDTLDAFADRVGKP 106 (256)
Q Consensus 33 IiliagAFfWLvSLLlsSliW~i~~pl~~~~~~~l~f~v~~SV~iQE~fR~~~y~llkkae~gL~~i~~~~~~~ 106 (256)
+-=.+|+|.|-.-+++++++|...- ++ . .+.|..|.+-+-=--..-|..++.....+++
T Consensus 12 lYN~~s~f~w~~vlll~~lv~~kt~----dp----------a-~f~et~~va~lvQt~ai~E~~ns~~g~v~S~ 70 (209)
T COG5198 12 LYNTASCFIWCIVLLLASLVFYKTM----DP----------A-VFHETLRVAGLVQTFAIMEAANSSAGKVNSR 70 (209)
T ss_pred HHHHHHHHHHHHHHHHHHHHhhhcc----Ch----------H-HHHHHHHHHHHHHHHHHHHHHHHHhhhccCc
Confidence 3446899999999999999997631 11 1 4688888765433333334455555544444
No 11
>PRK10497 peripheral inner membrane phage-shock protein; Provisional
Probab=34.57 E-value=41 Score=26.09 Aligned_cols=28 Identities=18% Similarity=0.322 Sum_probs=20.9
Q ss_pred HHHHHhhHHHHhh--HhhcCCchhHHHHHH
Q 025213 10 ALIALGPSLSLFV--AVISKKPFLILTVLS 37 (256)
Q Consensus 10 ~fIAfGP~laLF~--~tIa~~P~lIIilia 37 (256)
..+-|||+=+-=+ -+|+++|+|.+++++
T Consensus 26 ~al~YgPAG~aG~~vKsVarkPLR~lL~~~ 55 (73)
T PRK10497 26 TALRYGPAGVAGWAVKSVARKPLKMLLAVA 55 (73)
T ss_pred HHHHhCchHHHHHHHHHHhhccHHHHHHHH
Confidence 4577999865443 489999999988664
No 12
>TIGR02979 phageshock_pspD phage shock protein PspD. Members of this family are phage shock protein PspD, found in a minority of bacteria that carry the defining genes of the phage shock regulon (pspA, pspB, pspC, and pspF). It is found in Escherichia coli, Yersinia pestis, and closely related species, where it is part of the phage shock operon. It is known to be expressed but its function is unknown.
Probab=31.03 E-value=49 Score=24.66 Aligned_cols=27 Identities=15% Similarity=0.332 Sum_probs=20.2
Q ss_pred HHHHhhHHHHhh--HhhcCCchhHHHHHH
Q 025213 11 LIALGPSLSLFV--AVISKKPFLILTVLS 37 (256)
Q Consensus 11 fIAfGP~laLF~--~tIa~~P~lIIilia 37 (256)
-+-|||+=+-=+ -+|+++|+|.+++++
T Consensus 15 Al~YGPAG~aGw~vKsVsrkPLr~lLa~a 43 (59)
T TIGR02979 15 ALRYGPAGVAGWAMKSVARRPLKMLLAIA 43 (59)
T ss_pred HHHhCchhHHHHHHHHHhhccHHHHHHHH
Confidence 466899866544 489999999888664
No 13
>PF09584 Phageshock_PspD: Phage shock protein PspD (Phageshock_PspD); InterPro: IPR014321 Members of this entry are phage shock protein PspD, they are found in a minority of bacteria that carry the defining genes of the phage shock regulon (pspA, pspB, pspC, and pspF). It is found in Escherichia coli, Yersinia pestis, and closely related species, where it is part of the phage shock operon. It is known to be expressed but its function is unknown.
Probab=24.84 E-value=85 Score=23.92 Aligned_cols=28 Identities=25% Similarity=0.350 Sum_probs=20.3
Q ss_pred HHHHHhhHHHHh--hHhhcCCchhHHHHHH
Q 025213 10 ALIALGPSLSLF--VAVISKKPFLILTVLS 37 (256)
Q Consensus 10 ~fIAfGP~laLF--~~tIa~~P~lIIilia 37 (256)
..+-|||+=+-= +-+|+++|+|.+++++
T Consensus 19 ~aL~ygPAGiAg~~vk~VarkPLR~lLa~~ 48 (66)
T PF09584_consen 19 LALTYGPAGIAGWAVKSVARKPLRWLLALA 48 (66)
T ss_pred HHHHhCcHHHHHHHHHHHhhccHHHHHHHH
Confidence 456789975443 3489999999988653
No 14
>PRK14818 NADH dehydrogenase subunit B; Provisional
Probab=20.89 E-value=88 Score=27.87 Aligned_cols=24 Identities=33% Similarity=0.678 Sum_probs=21.1
Q ss_pred CceeccCCCCCchHHHHHHHHHHH
Q 025213 143 PATFYVDRCPQMPFFLISAIIALA 166 (256)
Q Consensus 143 PGt~g~~~c~~~~ffl~SA~~tl~ 166 (256)
|=.++++|||+.|--+..+++.+.
T Consensus 129 pVDvyIPGCPP~PeaIl~gil~L~ 152 (173)
T PRK14818 129 PVDVYVPGCPPRPEALTEGLLRLQ 152 (173)
T ss_pred CCcEEccCCCCCHHHHHHHHHHHH
Confidence 778999999999999999988764
No 15
>PF01058 Oxidored_q6: NADH ubiquinone oxidoreductase, 20 Kd subunit; InterPro: IPR006137 NADH:ubiquinone oxidoreductase (complex I) (1.6.5.3 from EC) is a respiratory-chain enzyme that catalyses the transfer of two electrons from NADH to ubiquinone in a reaction that is associated with proton translocation across the membrane (NADH + ubiquinone = NAD+ + ubiquinol) []. Complex I is a major source of reactive oxygen species (ROS) that are predominantly formed by electron transfer from FMNH(2). Complex I is found in bacteria, cyanobacteria (as a NADH-plastoquinone oxidoreductase), archaea [], mitochondira, and in the hydrogenosome, a mitochondria-derived organelle. In general, the bacterial complex consists of 14 different subunits, while the mitochondrial complex contains homologues to these subunits in addition to approximately 31 additional proteins []. Mitochondrial complex I, which is located in the inner mitochondrial membrane, is the largest multimeric respiratory enzyme in the mitochondria, consisting of more than 40 subunits, one FMN co-factor and eight FeS clusters []. The assembly of mitochondrial complex I is an intricate process that requires the cooperation of the nuclear and mitochondrial genomes [, ]. Mitochondrial complex I can cycle between active and deactive forms that can be distinguished by the reactivity towards divalent cations and thiol-reactive agents. All redox prosthetic groups reside in the peripheral arm of the L-shaped structure. The NADH oxidation domain harbouring the FMN cofactor is connected via a chain of iron-sulphur clusters to the ubiquinone reduction site that is located in a large pocket formed by the PSST and 49kDa subunits of complex I []. Among the many polypeptide subunits that make up complex I, there is one with a molecular weight of 20 kDa (in mammals) [], which is a component of the iron-sulphur (IP) fragment of the enzyme. It seems to bind a 4Fe-4S iron-sulphur cluster. The 20 kDa subunit has been found to be nuclear encoded, as a precursor form with a transit peptide in mammals, and in Neurospora crassa. It is and chloroplast encoded in various higher plants (gene ndhK or psbG).; GO: 0008137 NADH dehydrogenase (ubiquinone) activity, 0048038 quinone binding, 0051539 4 iron, 4 sulfur cluster binding, 0055114 oxidation-reduction process; PDB: 3MYR_E 3RGW_S 2FUG_F 3IAS_6 3I9V_F 3IAM_F 2YBB_6 3M9S_F 2FRV_G 1YQ9_B ....
Probab=20.02 E-value=79 Score=25.91 Aligned_cols=23 Identities=26% Similarity=0.745 Sum_probs=14.9
Q ss_pred CceeccCCCCCchHHHHHHHHHH
Q 025213 143 PATFYVDRCPQMPFFLISAIIAL 165 (256)
Q Consensus 143 PGt~g~~~c~~~~ffl~SA~~tl 165 (256)
|=.+.++|||+.|--+..++..|
T Consensus 109 ~VDi~IpGCPp~pd~i~~~l~~L 131 (131)
T PF01058_consen 109 PVDINIPGCPPHPDWILETLLAL 131 (131)
T ss_dssp -ECEEE-SSS--HHHHHHHHHHH
T ss_pred cEEEEeeCCCCCHHHHHHHHhhC
Confidence 44489999999998888877654
Done!