Query 026159
Match_columns 242
No_of_seqs 95 out of 112
Neff 4.8
Searched_HMMs 46136
Date Fri Mar 29 04:27:10 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/026159.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/026159hhsearch_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 6.4E-85 1.4E-89 581.9 21.1 227 2-236 1-229 (238)
2 KOG3972 Predicted membrane pro 100.0 5.9E-78 1.3E-82 525.4 13.8 226 1-236 1-227 (252)
3 PF10086 DUF2324: Putative mem 98.2 1.8E-05 3.9E-10 70.6 10.5 171 15-203 5-204 (223)
4 PF13367 PrsW-protease: Protea 92.3 6.2 0.00013 33.5 13.5 95 67-182 43-139 (191)
5 COG4377 Predicted membrane pro 86.0 8.8 0.00019 34.9 9.9 123 61-203 74-220 (258)
6 COG2443 Sss1 Preprotein transl 46.0 42 0.00092 25.0 4.2 47 77-137 11-57 (65)
7 PF04387 PTPLA: Protein tyrosi 45.8 15 0.00032 31.4 2.1 39 51-89 33-71 (164)
8 PLN02838 3-hydroxyacyl-CoA deh 43.5 31 0.00067 31.2 3.8 38 51-88 87-124 (221)
9 COG2339 prsW Membrane proteina 33.7 4E+02 0.0088 24.9 16.7 149 7-182 41-197 (274)
10 PRK10497 peripheral inner memb 31.7 50 0.0011 25.2 2.7 28 10-37 26-55 (73)
11 COG5198 Ptpl Protein tyrosine 28.3 3.8E+02 0.0082 24.0 7.9 59 33-106 12-70 (209)
12 TIGR00327 secE_euk_arch protei 27.9 84 0.0018 23.0 3.3 26 111-136 26-51 (61)
13 TIGR02979 phageshock_pspD phag 27.8 62 0.0014 23.7 2.5 27 11-37 15-43 (59)
14 PRK09400 secE preprotein trans 27.5 85 0.0018 22.9 3.2 26 111-136 30-55 (61)
15 PRK14818 NADH dehydrogenase su 26.5 57 0.0012 28.6 2.6 24 143-166 129-152 (173)
16 COG4657 RnfA Predicted NADH:ub 23.9 5.2E+02 0.011 23.0 8.3 105 54-167 62-184 (193)
17 PF09584 Phageshock_PspD: Phag 23.1 1E+02 0.0022 23.2 2.9 28 10-37 19-48 (66)
18 PF01058 Oxidored_q6: NADH ubi 22.4 63 0.0014 26.2 2.0 21 145-165 111-131 (131)
19 PTZ00478 Sec superfamily; Prov 20.5 1.2E+02 0.0026 23.6 3.0 25 112-136 44-68 (81)
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=6.4e-85 Score=581.91 Aligned_cols=227 Identities=39% Similarity=0.693 Sum_probs=220.9
Q ss_pred cchhhHHHHHHHHhhHHHHhHHhhcCCchhHHHHHHHHHHHHHHHHHHHhHHhhcccCCCCCchhhHHHHHHHHHHHHHH
Q 026159 2 TVAAGIGYALIALGPSLSLFVAVISKKPFLILTVLSSTLLWLISLIVLSGIWRAFLPLKSTTWWPFALLIISSVGFQEGL 81 (242)
Q Consensus 2 t~~~~fGc~~iafGP~lalF~~tIa~~P~lIIili~gaFfWLvSLLlsS~iW~~~~pl~~~~~~~l~~~v~~sV~~QE~f 81 (242)
|+++++||+||||||++++|.+||||||+|||++++||||||+|+|+||++|++++|++|+ +++++++||++||.+
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 7899999999999999999999999999999999999999999999999999999999997 668999999999999
Q ss_pred HHHHHHHHHHHHHHHHHhhcccCCCccccchhhHHHHHhccchhhHHHHHHHhhcccccccCcccccCCCCCchHHHHHH
Q 026159 82 RVLFWKVYKRLEDTLDAFADRVGKPRLFLTDKMQIALAGGLGHGVAHAVFFCLSLLTPAFGPATFYVDRCPQMPFFLISA 161 (242)
Q Consensus 82 R~~~y~ll~kae~gL~~i~~~~~~~~~~~~~~~~la~v~GlGfG~ms~~f~~~n~Lads~GpGt~~~~~c~~~~~fl~SA 161 (242)
|++|||++||||||||+++||+++| +|||++|||+|+|||+|||+|+++|+|+|++||||+|+|+||++|||++||
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 9999999999999999999987655 678999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHHHHHHHhhcccccCceeeEEehhhhHHHHHHHhhhc--cCCCCceehHHHHHHHHHHHHHHhhhhhe
Q 026159 162 IIALAFVTIHTFSMVIAFNGYAEGNTTDQYFVPVVHLVAGMVTLVN--FASGGCVVGIPLLYILASLILLHCGKMVW 236 (242)
Q Consensus 162 ~~tl~~~llH~fW~Vi~F~g~~~~~~~~~~~V~~~Hl~vs~lTllN--~~~~gc~~s~~~~~~~~~~~~~~~~~~~w 236 (242)
++|+++++||+|||||+|||||||||+++++|+++|+++|++|++| .++++|+.+.|+++++++++..+|++.+|
T Consensus 153 ~~tl~~~lLH~fW~VI~F~g~~~~~~~~i~~V~~~Hl~vs~lTllN~~~~~~~~v~~~~il~~~~~~a~~~~gg~~~ 229 (238)
T PF06105_consen 153 FMTLAFILLHTFWMVIFFDGCEKKNWWLIAFVVISHLLVSCLTLLNSPLYSGGCVPSYPILVLTGAWAFFVAGGSVR 229 (238)
T ss_pred HHHHHHHHHHHHHHHhhhhhhccCCceEEEehHHHHHHHHHHHHcCccccccchHHHHHHHHHHHHHHHHHhCccHH
Confidence 9999999999999999999999999999999999999999999999 67789999999999999999999999998
No 2
>KOG3972 consensus Predicted membrane protein [Function unknown]
Probab=100.00 E-value=5.9e-78 Score=525.39 Aligned_cols=226 Identities=26% Similarity=0.421 Sum_probs=215.6
Q ss_pred CcchhhHHHHHHHHhhHHHHhHHhhcCCchhHHHHHHHHHHHHHHHHHHHhHHhhc-ccCCCCCchhhHHHHHHHHHHHH
Q 026159 1 MTVAAGIGYALIALGPSLSLFVAVISKKPFLILTVLSSTLLWLISLIVLSGIWRAF-LPLKSTTWWPFALLIISSVGFQE 79 (242)
Q Consensus 1 Mt~~~~fGc~~iafGP~lalF~~tIa~~P~lIIili~gaFfWLvSLLlsS~iW~~~-~pl~~~~~~~l~~~v~~sV~~QE 79 (242)
||.+++|||+++||||++|+|.+|||+||.|||++++||||||||||+||++|++. .|++|+ ++|++.+||++||
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 566664 7899999999999
Q ss_pred HHHHHHHHHHHHHHHHHHHhhcccCCCccccchhhHHHHHhccchhhHHHHHHHhhcccccccCcccccCCCCCchHHHH
Q 026159 80 GLRVLFWKVYKRLEDTLDAFADRVGKPRLFLTDKMQIALAGGLGHGVAHAVFFCLSLLTPAFGPATFYVDRCPQMPFFLI 159 (242)
Q Consensus 80 ~fR~~~y~ll~kae~gL~~i~~~~~~~~~~~~~~~~la~v~GlGfG~ms~~f~~~n~Lads~GpGt~~~~~c~~~~~fl~ 159 (242)
.||++|||++|||||||++++||+ |. +++||++|||+|+|||+|||+|+.+|.|+|+.||||+|+||++++ ||+.
T Consensus 77 ~fR~ayyklLkka~~GL~si~~d~---~~-~~s~h~lAyVsGLgfGIiSgvFs~vN~lad~sGPGtvGl~g~s~~-~fl~ 151 (252)
T KOG3972|consen 77 LFRFAYYKLLKKAQEGLNSITEDG---RL-HNSRHMLAYVSGLGFGIISGVFSTVNALADFSGPGTVGLHGDSPY-FFLT 151 (252)
T ss_pred HHHHHHHHHHHHHHHHHHhcCccC---CC-chhHHHHHHHhccchhHHHHHHHHHHHHHhccCCCeeccCCCcch-hhHH
Confidence 999999999999999999999974 33 588999999999999999999999999999999999999999995 9999
Q ss_pred HHHHHHHHHHHHHHHHHHhhcccccCceeeEEehhhhHHHHHHHhhhccCCCCceehHHHHHHHHHHHHHHhhhhhe
Q 026159 160 SAIIALAFVTIHTFSMVIAFNGYAEGNTTDQYFVPVVHLVAGMVTLVNFASGGCVVGIPLLYILASLILLHCGKMVW 236 (242)
Q Consensus 160 SA~~tl~~~llH~fW~Vi~F~g~~~~~~~~~~~V~~~Hl~vs~lTllN~~~~gc~~s~~~~~~~~~~~~~~~~~~~w 236 (242)
||++++.++|+|+||+|++||+|||+||+....|+.+|+++|.+|++|+++. +..+..++|++.+++.++|.++.-
T Consensus 152 sa~~al~iiLlHvfW~ivffdac~k~~~~~l~~vv~SHLlvs~lt~lns~~~-y~~~la~~flilvl~g~~af~~aG 227 (252)
T KOG3972|consen 152 SAFSALLIILLHVFWGIVFFDACEKIAYVPLGAVVVSHLLVSFLTFLNSRGF-YVLVLAVQFLILVLMGAWAFVIAG 227 (252)
T ss_pred HHHHHHHHHHHHHHHHheeehhhhhhchhhhHHHHHHHHHHHHHHHhCccch-hHHHHHHHHHHHHHHHHHHHHHhC
Confidence 9999999999999999999999999999999999999999999999999877 888888999999999999988753
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=98.15 E-value=1.8e-05 Score=70.60 Aligned_cols=171 Identities=18% Similarity=0.121 Sum_probs=115.7
Q ss_pred hhHHHHhHHhhcCCchhHHHHHHHHHHHHHHHHHHHhHH--hhcccCCC------CCchhhHHHHHHHHHHHHHHHHHHH
Q 026159 15 GPSLSLFVAVISKKPFLILTVLSSTLLWLISLIVLSGIW--RAFLPLKS------TTWWPFALLIISSVGFQEGLRVLFW 86 (242)
Q Consensus 15 GP~lalF~~tIa~~P~lIIili~gaFfWLvSLLlsS~iW--~~~~pl~~------~~~~~l~~~v~~sV~~QE~fR~~~y 86 (242)
-|.. ++...=.|+.......+.|+..|.++..+.-... ....+.++ +++.....+-+.+=.+||..||.-+
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 5566667888889999999999988777665433 22233322 2222234467788899999999999
Q ss_pred HHHHHHHHHHHHhhcccCCCccccchhhHHHHHhccchhhHHHHHHH----hhccccc--ccCcccccC-----------
Q 026159 87 KVYKRLEDTLDAFADRVGKPRLFLTDKMQIALAGGLGHGVAHAVFFC----LSLLTPA--FGPATFYVD----------- 149 (242)
Q Consensus 87 ~ll~kae~gL~~i~~~~~~~~~~~~~~~~la~v~GlGfG~ms~~f~~----~n~Lads--~GpGt~~~~----------- 149 (242)
|.++|-++..+ .-+..-|+|||.+=+++-. +|.+.-+ .-.|+....
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 99886431111 1377899999988655443 3543222 222332110
Q ss_pred ----CCCCchHHHHHHHHHHHHHHHHHHHHHHhhcccccCceeeEEehhhhHHHHHHH
Q 026159 150 ----RCPQMPFFLISAIIALAFVTIHTFSMVIAFNGYAEGNTTDQYFVPVVHLVAGMV 203 (242)
Q Consensus 150 ----~c~~~~~fl~SA~~tl~~~llH~fW~Vi~F~g~~~~~~~~~~~V~~~Hl~vs~l 203 (242)
.+.+-..++.+.+.-.+=+++|+..+++.+.|.++||++.....+..|.++=..
T Consensus 147 ~~~l~~~~~~~~~l~~~ERi~Al~~hi~lSvlV~~av~~~k~~~l~~AIllHaliD~~ 204 (223)
T PF10086_consen 147 QSALASLPPWSFLLGGVERIFALLFHIGLSVLVWYAVRQRKKWYLVLAILLHALIDFP 204 (223)
T ss_pred HHHHHcCcHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCchHHHHHHHHHHHHHHH
Confidence 022224788999999999999999999999999999888888888999887663
No 4
>PF13367 PrsW-protease: Protease prsW family
Probab=92.26 E-value=6.2 Score=33.51 Aligned_cols=95 Identities=18% Similarity=0.079 Sum_probs=60.5
Q ss_pred hHHHHHHHHHHHHHHHHHHHHHHHH-HHHHHHHhhcccCCCccccchhhHHHHHhccchhhHHHHHHHhhcccccccCcc
Q 026159 67 FALLIISSVGFQEGLRVLFWKVYKR-LEDTLDAFADRVGKPRLFLTDKMQIALAGGLGHGVAHAVFFCLSLLTPAFGPAT 145 (242)
Q Consensus 67 l~~~v~~sV~~QE~fR~~~y~ll~k-ae~gL~~i~~~~~~~~~~~~~~~~la~v~GlGfG~ms~~f~~~n~Lads~GpGt 145 (242)
.....+.+=...|..++.-..++.. .++..++. .|-...+.++|+||+.+=-+....|-..|..+.
T Consensus 43 ~~~~~~~a~~~EE~~K~l~v~~~~~~~~~~~~~~-----------~d~~~~g~a~GlGFa~~En~~Y~~~~~~~~~~~-- 109 (191)
T PF13367_consen 43 LWGAFLIAPLVEEFAKLLPVLLLLLLRRRRFDEP-----------MDGLVYGAAVGLGFAIMENILYILNAAEDNGGS-- 109 (191)
T ss_pred HHHHHHHhHHHHHHHHHHHHHHHHHHhhHhhcCc-----------chhhhhhhHHHHHHHHHHHHHHHHHhhhcccch--
Confidence 4456778888999999887666652 33322111 244688999999999999999998866444332
Q ss_pred cccCCCCCchHHHHHHHHHHHH-HHHHHHHHHHhhccc
Q 026159 146 FYVDRCPQMPFFLISAIIALAF-VTIHTFSMVIAFNGY 182 (242)
Q Consensus 146 ~~~~~c~~~~~fl~SA~~tl~~-~llH~fW~Vi~F~g~ 182 (242)
.+ .-+.+ ++.-... ...|..|+.++.-|.
T Consensus 110 ------~~-~~~~~-~~~R~~~~~~~H~~~t~i~g~~l 139 (191)
T PF13367_consen 110 ------VQ-GGLST-AILRGITSVPGHALFTAIFGYGL 139 (191)
T ss_pred ------hh-hHHHH-HHHHHHHHHhHHHHHHHHHHHHH
Confidence 11 11111 2222222 579999999975444
No 5
>COG4377 Predicted membrane protein [Function unknown]
Probab=85.99 E-value=8.8 Score=34.93 Aligned_cols=123 Identities=17% Similarity=0.206 Sum_probs=71.6
Q ss_pred CCCchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhcccCCCccccchhhHHHHHhccchhhHHHHHHHhhccccc
Q 026159 61 STTWWPFALLIISSVGFQEGLRVLFWKVYKRLEDTLDAFADRVGKPRLFLTDKMQIALAGGLGHGVAHAVFFCLSLLTPA 140 (242)
Q Consensus 61 ~~~~~~l~~~v~~sV~~QE~fR~~~y~ll~kae~gL~~i~~~~~~~~~~~~~~~~la~v~GlGfG~ms~~f~~~n~Lads 140 (242)
++|.+--+.|.+..=++.|.-|+.++|.+.| + -++ .--+.+-|+|||..-+.+-.+.-+.+-
T Consensus 74 ~hPl~y~IYG~lMAg~FEE~gR~l~~rfl~k-R-~~~----------------~Ad~lAyglGHgGlEail~g~~S~~~l 135 (258)
T COG4377 74 DHPLIYIIYGLLMAGFFEETGRLLFFRFLEK-R-SLE----------------KADALAYGLGHGGLEAILLGLTSLLNL 135 (258)
T ss_pred hCCcHHHHHHHHHHHHHHHHhHHHHHHHHHh-C-ccc----------------chhHHHHhcccccHHHHHHHHHhHhhH
Confidence 3444445568899999999999999999875 1 111 122456789998876655433322111
Q ss_pred ccCcccccCCCCCchHHHHHH------------------------HHHHHHHHHHHHHHHHhhcccccCceeeEEehhhh
Q 026159 141 FGPATFYVDRCPQMPFFLISA------------------------IIALAFVTIHTFSMVIAFNGYAEGNTTDQYFVPVV 196 (242)
Q Consensus 141 ~GpGt~~~~~c~~~~~fl~SA------------------------~~tl~~~llH~fW~Vi~F~g~~~~~~~~~~~V~~~ 196 (242)
.==+.--..|+||. .+.|. +.-..=+..+..-++..+++.++||+.........
T Consensus 136 ~i~~~Avn~g~~~~--L~~sGaeal~~~~~~ll~~lS~W~~~g~~~ERI~A~~vQ~~Ltl~V~~AVrqrrpi~Ll~ai~L 213 (258)
T COG4377 136 YIVLSAVNTGNPQV--LMQSGAEALSENMLKLLQSLSVWQIYGLGFERILALGVQLLLTLWVYQAVRQRRPIYLLAAIGL 213 (258)
T ss_pred HHhhhhhccCCHHH--HHHhhHHHhhHHHHHHHhCCcHHHHhhHHHHHHHHHHHHHHHHHHHHHHHHccccHHHHHHHHH
Confidence 11111112233332 12211 11112233445556778999999999999888889
Q ss_pred HHHHHHH
Q 026159 197 HLVAGMV 203 (242)
Q Consensus 197 Hl~vs~l 203 (242)
|-+.-.=
T Consensus 214 HAlfdlp 220 (258)
T COG4377 214 HALFDLP 220 (258)
T ss_pred HHHhcCC
Confidence 9765443
No 6
>COG2443 Sss1 Preprotein translocase subunit Sss1 [Intracellular trafficking and secretion]
Probab=45.97 E-value=42 Score=25.00 Aligned_cols=47 Identities=28% Similarity=0.352 Sum_probs=32.9
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHhhcccCCCccccchhhHHHHHhccchhhHHHHHHHhhcc
Q 026159 77 FQEGLRVLFWKVYKRLEDTLDAFADRVGKPRLFLTDKMQIALAGGLGHGVAHAVFFCLSLL 137 (242)
Q Consensus 77 ~QE~fR~~~y~ll~kae~gL~~i~~~~~~~~~~~~~~~~la~v~GlGfG~ms~~f~~~n~L 137 (242)
+||.+| .|.|++|+|. +|+- ++--+.|-+.|+|+.++-++=+.+-++
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 6777887776 3432 344677888999999998887777655
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=45.77 E-value=15 Score=31.41 Aligned_cols=39 Identities=15% Similarity=0.355 Sum_probs=28.2
Q ss_pred hHHhhcccCCCCCchhhHHHHHHHHHHHHHHHHHHHHHH
Q 026159 51 GIWRAFLPLKSTTWWPFALLIISSVGFQEGLRVLFWKVY 89 (242)
Q Consensus 51 ~iW~~~~pl~~~~~~~l~~~v~~sV~~QE~fR~~~y~ll 89 (242)
++|-++.+.++....+....++++-.+.|..||.||-+-
T Consensus 33 vv~~v~~~~p~~~~~~~~~~l~~aWsl~EviRY~yY~~~ 71 (164)
T PF04387_consen 33 VVWGVIYPFPEVQSSPAVPLLLIAWSLTEVIRYPYYALK 71 (164)
T ss_pred eehhhhccccccccccchhhHHHHHHhhhcchhHHHHHH
Confidence 567766665543223455688999999999999998653
No 8
>PLN02838 3-hydroxyacyl-CoA dehydratase subunit of elongase
Probab=43.50 E-value=31 Score=31.15 Aligned_cols=38 Identities=13% Similarity=0.196 Sum_probs=27.4
Q ss_pred hHHhhcccCCCCCchhhHHHHHHHHHHHHHHHHHHHHH
Q 026159 51 GIWRAFLPLKSTTWWPFALLIISSVGFQEGLRVLFWKV 88 (242)
Q Consensus 51 ~iW~~~~pl~~~~~~~l~~~v~~sV~~QE~fR~~~y~l 88 (242)
++|-++.+.++....+....++++-.+.|..||.||-+
T Consensus 87 iv~~v~~~~p~~~~~~~~~~l~~aWs~tEvIRY~yY~~ 124 (221)
T PLN02838 87 LTWGILWSFPEVRSHILVTSLVISWSITEIIRYSFFGM 124 (221)
T ss_pred HHHHHhhcCcchhcccHHHHHHHHHHHHHHHHHHHHHH
Confidence 66777666654332334456899999999999999954
No 9
>COG2339 prsW Membrane proteinase, regulator of anti-sigma factor [Posttranslational modification, protein turnover, chaperones]
Probab=33.75 E-value=4e+02 Score=24.93 Aligned_cols=149 Identities=17% Similarity=0.178 Sum_probs=73.7
Q ss_pred HHHHHHHHhhHHHHhHHhhcCCch-------hHHHHHHHHHHHHHHHHHH-HhHHhhcccCCCCCchhhHHHHHHHHHHH
Q 026159 7 IGYALIALGPSLSLFVAVISKKPF-------LILTVLSSTLLWLISLIVL-SGIWRAFLPLKSTTWWPFALLIISSVGFQ 78 (242)
Q Consensus 7 fGc~~iafGP~lalF~~tIa~~P~-------lIIili~gaFfWLvSLLls-S~iW~~~~pl~~~~~~~l~~~v~~sV~~Q 78 (242)
+-..++++-|++++-....-+|+. .+...+.|+++++.+..+- ..+=....|-+. -+.+....+..=.+.
T Consensus 41 ~~lv~~~~~~~~~~L~yFy~~~~~~~~pl~vvv~tfl~G~~l~~~~~~~~~~~v~~~~~~~~l--~~~~l~~al~~G~vE 118 (274)
T COG2339 41 FALVLIAIAPALALLWYFYLRDAHKPEPLWVVVRTFLLGAFLSLFAVMLIYHFVLVLLWPSSL--ALLFLGSALLAGLVE 118 (274)
T ss_pred HHHHHHHHHHHHHHHHHHhcccCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhccccc--HHHHHHHHHhhhhhH
Confidence 334567777777766665555544 5566677777664332221 111111112111 112222233333455
Q ss_pred HHHHHHHHHHHHHHHHHHHHhhcccCCCccccchhhHHHHHhccchhhHHHHHHHhhcccccccCcccccCCCCCchHHH
Q 026159 79 EGLRVLFWKVYKRLEDTLDAFADRVGKPRLFLTDKMQIALAGGLGHGVAHAVFFCLSLLTPAFGPATFYVDRCPQMPFFL 158 (242)
Q Consensus 79 E~fR~~~y~ll~kae~gL~~i~~~~~~~~~~~~~~~~la~v~GlGfG~ms~~f~~~n~Lads~GpGt~~~~~c~~~~~fl 158 (242)
|.....=-++.- +... +.-++.|......++|+||-++=.+-...|- + +. ++..+ -+
T Consensus 119 E~~KaL~v~~~~--------~~~~---~~~~~~~g~l~Gaa~gLGFa~~Enl~Y~l~~-~-~~---------~~gv~-v~ 175 (274)
T COG2339 119 EPLKALAVVLFV--------LRSL---PLDELLDGLLYGAAAGLGFAATENLLYLLTG-A-SI---------GFGVE-VA 175 (274)
T ss_pred HHHHHHHHHHHH--------Hccc---cccchHHHHHHHHHHhccHHHHhhhHHHhcc-c-cc---------cchHH-HH
Confidence 554433222110 1111 1112346688999999999999888888774 1 22 22221 11
Q ss_pred HHHHHHHHHHHHHHHHHHHhhccc
Q 026159 159 ISAIIALAFVTIHTFSMVIAFNGY 182 (242)
Q Consensus 159 ~SA~~tl~~~llH~fW~Vi~F~g~ 182 (242)
.+.... -++-|+.|..+..-+.
T Consensus 176 ~~r~~~--~~~gHa~~s~i~Gy~L 197 (274)
T COG2339 176 FERALL--AILGHALLSAIVGYYL 197 (274)
T ss_pred HHHHHH--hhhhHHHHHHHHHHHH
Confidence 222211 2223999999987666
No 10
>PRK10497 peripheral inner membrane phage-shock protein; Provisional
Probab=31.70 E-value=50 Score=25.18 Aligned_cols=28 Identities=18% Similarity=0.322 Sum_probs=21.0
Q ss_pred HHHHHhhHHHHhH--HhhcCCchhHHHHHH
Q 026159 10 ALIALGPSLSLFV--AVISKKPFLILTVLS 37 (242)
Q Consensus 10 ~~iafGP~lalF~--~tIa~~P~lIIili~ 37 (242)
..+-|||+=+-=. -+|+++|+|.+++++
T Consensus 26 ~al~YgPAG~aG~~vKsVarkPLR~lL~~~ 55 (73)
T PRK10497 26 TALRYGPAGVAGWAVKSVARKPLKMLLAVA 55 (73)
T ss_pred HHHHhCchHHHHHHHHHHhhccHHHHHHHH
Confidence 4567999865443 489999999988754
No 11
>COG5198 Ptpl Protein tyrosine phosphatase-like protein (contains Pro instead of catalytic Arg) [General function prediction only]
Probab=28.27 E-value=3.8e+02 Score=23.97 Aligned_cols=59 Identities=22% Similarity=0.275 Sum_probs=36.6
Q ss_pred HHHHHHHHHHHHHHHHHHhHHhhcccCCCCCchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhcccCCC
Q 026159 33 LTVLSSTLLWLISLIVLSGIWRAFLPLKSTTWWPFALLIISSVGFQEGLRVLFWKVYKRLEDTLDAFADRVGKP 106 (242)
Q Consensus 33 Iili~gaFfWLvSLLlsS~iW~~~~pl~~~~~~~l~~~v~~sV~~QE~fR~~~y~ll~kae~gL~~i~~~~~~~ 106 (242)
+-=++|+|.|-.-+++++++|...- ++ . .+.|..|++=+-=--..-|..+......+++
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 3446899999999999999997532 11 1 5778887765433333334445555443333
No 12
>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=27.89 E-value=84 Score=23.00 Aligned_cols=26 Identities=12% Similarity=0.323 Sum_probs=20.7
Q ss_pred chhhHHHHHhccchhhHHHHHHHhhc
Q 026159 111 TDKMQIALAGGLGHGVAHAVFFCLSL 136 (242)
Q Consensus 111 ~~~~~la~v~GlGfG~ms~~f~~~n~ 136 (242)
++..++|.++|+|+.+|-.+=+.+-+
T Consensus 26 ~Ef~~iak~t~iG~~i~G~IGf~Ikl 51 (61)
T TIGR00327 26 EEYLKVAKVTGIGIIIVGIIGYIIKI 51 (61)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 45589999999999999887666543
No 13
>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=27.82 E-value=62 Score=23.70 Aligned_cols=27 Identities=15% Similarity=0.332 Sum_probs=20.2
Q ss_pred HHHHhhHHHHhH--HhhcCCchhHHHHHH
Q 026159 11 LIALGPSLSLFV--AVISKKPFLILTVLS 37 (242)
Q Consensus 11 ~iafGP~lalF~--~tIa~~P~lIIili~ 37 (242)
-+-|||+=+-=+ -+|+++|+|.+++++
T Consensus 15 Al~YGPAG~aGw~vKsVsrkPLr~lLa~a 43 (59)
T TIGR02979 15 ALRYGPAGVAGWAMKSVARRPLKMLLAIA 43 (59)
T ss_pred HHHhCchhHHHHHHHHHhhccHHHHHHHH
Confidence 466899765544 489999999888754
No 14
>PRK09400 secE preprotein translocase subunit SecE; Reviewed
Probab=27.53 E-value=85 Score=22.87 Aligned_cols=26 Identities=23% Similarity=0.266 Sum_probs=20.6
Q ss_pred chhhHHHHHhccchhhHHHHHHHhhc
Q 026159 111 TDKMQIALAGGLGHGVAHAVFFCLSL 136 (242)
Q Consensus 111 ~~~~~la~v~GlGfG~ms~~f~~~n~ 136 (242)
++..++|.++|+|+.+|-.+=+.+-+
T Consensus 30 ~Ef~~ia~~~~iG~~i~G~iGf~Ikl 55 (61)
T PRK09400 30 EEFLLVAKVTGLGILLIGLIGFIIYL 55 (61)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 35588999999999999887666543
No 15
>PRK14818 NADH dehydrogenase subunit B; Provisional
Probab=26.47 E-value=57 Score=28.62 Aligned_cols=24 Identities=33% Similarity=0.678 Sum_probs=20.7
Q ss_pred CcccccCCCCCchHHHHHHHHHHH
Q 026159 143 PATFYVDRCPQMPFFLISAIIALA 166 (242)
Q Consensus 143 pGt~~~~~c~~~~~fl~SA~~tl~ 166 (242)
|=.++++|||+.|--+..+++.+.
T Consensus 129 pVDvyIPGCPP~PeaIl~gil~L~ 152 (173)
T PRK14818 129 PVDVYVPGCPPRPEALTEGLLRLQ 152 (173)
T ss_pred CCcEEccCCCCCHHHHHHHHHHHH
Confidence 677899999999999999987763
No 16
>COG4657 RnfA Predicted NADH:ubiquinone oxidoreductase, subunit RnfA [Energy production and conversion]
Probab=23.89 E-value=5.2e+02 Score=22.97 Aligned_cols=105 Identities=15% Similarity=0.226 Sum_probs=57.0
Q ss_pred hhcccCCCCCchhhHHHHHHHHHHHHHH---H---HHHHHHHHH---------HHHHHHHhhcccCCCccccchhhHHHH
Q 026159 54 RAFLPLKSTTWWPFALLIISSVGFQEGL---R---VLFWKVYKR---------LEDTLDAFADRVGKPRLFLTDKMQIAL 118 (242)
Q Consensus 54 ~~~~pl~~~~~~~l~~~v~~sV~~QE~f---R---~~~y~ll~k---------ae~gL~~i~~~~~~~~~~~~~~~~la~ 118 (242)
++..|++-+.-...+|.++++|..|-.= | -..||++-- |.-|...++..+ ++.+ .+-.....
T Consensus 62 ~iL~pl~l~yLRtiafIlVIAv~VQf~Em~v~KtsP~LYr~LGIfLPLITTNCaVLgvaLln~~~-~~~f--~qsv~~gf 138 (193)
T COG4657 62 FILIPLGLEYLRTIAFILVIAVVVQFTEMVVRKTSPTLYRLLGIFLPLITTNCAVLGVALLNINE-GHNF--LQSVVYGF 138 (193)
T ss_pred HhhhccChHHHHHHHHHHHHHHHHHHHHHHHHccCHHHHHHHHHhhhhHhhchHHHHHHHHHhhh-hhhH--HHHHHHHh
Confidence 6778998776666888999999988321 1 122333321 111111122111 1212 11234456
Q ss_pred HhccchhhHHHHHHHhhc---ccccccCcccccCCCCCchHHHHHHHHHHHH
Q 026159 119 AGGLGHGVAHAVFFCLSL---LTPAFGPATFYVDRCPQMPFFLISAIIALAF 167 (242)
Q Consensus 119 v~GlGfG~ms~~f~~~n~---Lads~GpGt~~~~~c~~~~~fl~SA~~tl~~ 167 (242)
.+|+||.+.--+|..+.= ++| =|..+ +|-|- -+++..+++++|
T Consensus 139 ~a~lGfslvmvlfA~iRER~~~ad--vP~~f--rG~~i--alitagLmSlaF 184 (193)
T COG4657 139 GAALGFSLVMVLFAAIRERLALAD--VPAPF--RGAAI--ALITAGLMSLAF 184 (193)
T ss_pred hhHhhHHHHHHHHHHHHHHHHHhc--CCCCC--CCcch--HHHHHHHHHHHH
Confidence 788899888777777653 222 24333 33333 377777777766
No 17
>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=23.12 E-value=1e+02 Score=23.15 Aligned_cols=28 Identities=25% Similarity=0.350 Sum_probs=20.4
Q ss_pred HHHHHhhHHHHh--HHhhcCCchhHHHHHH
Q 026159 10 ALIALGPSLSLF--VAVISKKPFLILTVLS 37 (242)
Q Consensus 10 ~~iafGP~lalF--~~tIa~~P~lIIili~ 37 (242)
..+-|||+=+-= +-+|+++|.|.+++++
T Consensus 19 ~aL~ygPAGiAg~~vk~VarkPLR~lLa~~ 48 (66)
T PF09584_consen 19 LALTYGPAGIAGWAVKSVARKPLRWLLALA 48 (66)
T ss_pred HHHHhCcHHHHHHHHHHHhhccHHHHHHHH
Confidence 456789975443 3489999999988753
No 18
>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=22.36 E-value=63 Score=26.17 Aligned_cols=21 Identities=24% Similarity=0.694 Sum_probs=14.2
Q ss_pred ccccCCCCCchHHHHHHHHHH
Q 026159 145 TFYVDRCPQMPFFLISAIIAL 165 (242)
Q Consensus 145 t~~~~~c~~~~~fl~SA~~tl 165 (242)
.+.++|||+.|=-+..++..|
T Consensus 111 Di~IpGCPp~pd~i~~~l~~L 131 (131)
T PF01058_consen 111 DINIPGCPPHPDWILETLLAL 131 (131)
T ss_dssp CEEE-SSS--HHHHHHHHHHH
T ss_pred EEEeeCCCCCHHHHHHHHhhC
Confidence 379999999998888877654
No 19
>PTZ00478 Sec superfamily; Provisional
Probab=20.48 E-value=1.2e+02 Score=23.59 Aligned_cols=25 Identities=20% Similarity=0.264 Sum_probs=20.3
Q ss_pred hhhHHHHHhccchhhHHHHHHHhhc
Q 026159 112 DKMQIALAGGLGHGVAHAVFFCLSL 136 (242)
Q Consensus 112 ~~~~la~v~GlGfG~ms~~f~~~n~ 136 (242)
+-.++|.+.|+||.+|..+=+++-+
T Consensus 44 Ef~kiakat~iGf~imG~IGy~IKL 68 (81)
T PTZ00478 44 EYTNIAYACSVGFFIMGFIGYSIKL 68 (81)
T ss_pred HHHHHHHHHHHHHHHHHHHHHhhhe
Confidence 4578999999999999877666543
Done!