Query 010796
Match_columns 501
No_of_seqs 387 out of 1645
Neff 5.9
Searched_HMMs 46136
Date Fri Mar 29 04:39:49 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/010796.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/010796hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PRK10907 intramembrane serine 100.0 1.5E-46 3.2E-51 377.5 21.2 251 137-400 1-262 (276)
2 PF05512 AWPM-19: AWPM-19-like 100.0 6E-33 1.3E-37 248.5 9.4 97 401-498 45-141 (142)
3 PTZ00101 rhomboid-1 protease; 100.0 2.9E-27 6.3E-32 237.9 20.7 184 214-400 43-232 (278)
4 COG0705 Membrane associated se 99.9 1.7E-23 3.7E-28 204.4 13.2 176 223-399 16-202 (228)
5 KOG2289 Rhomboid family protei 99.9 4.2E-23 9.1E-28 209.9 7.1 142 256-399 103-245 (316)
6 PF01694 Rhomboid: Rhomboid fa 99.8 3.2E-20 7E-25 167.6 4.0 131 268-400 2-134 (145)
7 PF12122 DUF3582: Protein of u 99.6 2.7E-16 5.9E-21 136.2 5.0 86 137-226 1-99 (101)
8 KOG2632 Rhomboid family protei 99.6 4.2E-15 9.1E-20 146.7 10.1 163 222-399 13-189 (258)
9 KOG2290 Rhomboid family protei 99.6 1.3E-15 2.9E-20 158.3 6.0 130 269-401 448-578 (652)
10 KOG2980 Integral membrane prot 98.2 7E-07 1.5E-11 90.4 3.0 166 225-399 117-292 (310)
11 PF04511 DER1: Der1-like famil 98.1 2.7E-05 5.8E-10 75.3 12.3 160 224-399 2-173 (197)
12 PF08551 DUF1751: Eukaryotic i 97.9 1.1E-05 2.3E-10 70.0 4.1 58 271-328 7-64 (99)
13 KOG0858 Predicted membrane pro 97.4 0.00089 1.9E-08 66.3 9.3 98 221-327 10-112 (239)
14 KOG4463 Uncharacterized conser 94.4 0.044 9.5E-07 55.1 4.2 60 268-328 47-106 (323)
15 KOG2890 Predicted membrane pro 94.0 0.053 1.2E-06 55.6 4.0 84 270-353 65-161 (326)
16 COG5291 Predicted membrane pro 93.1 0.15 3.3E-06 51.0 5.2 51 267-317 55-109 (313)
17 KOG3817 Uncharacterized conser 78.8 10 0.00023 40.2 8.7 43 444-498 252-294 (452)
18 PRK09765 PTS system 2-O-a-mann 56.3 3.4E+02 0.0075 31.1 15.7 23 148-170 182-204 (631)
19 COG0705 Membrane associated se 55.3 7.7 0.00017 37.8 2.1 75 267-354 135-209 (228)
20 PF09527 ATPase_gene1: Putativ 43.5 1E+02 0.0022 23.4 6.3 42 286-327 8-50 (55)
21 PF09413 DUF2007: Domain of un 33.9 50 0.0011 25.8 3.3 30 139-168 2-31 (67)
22 PF11823 DUF3343: Protein of u 31.8 80 0.0017 25.4 4.2 45 140-184 5-60 (73)
23 TIGR02854 spore_II_GA sigma-E 27.8 6.8E+02 0.015 25.7 12.1 30 285-314 10-39 (288)
24 PF03419 Peptidase_U4: Sporula 25.5 7.3E+02 0.016 25.3 11.6 29 285-313 10-38 (293)
25 PF07226 DUF1422: Protein of u 24.6 2.4E+02 0.0052 25.5 6.1 20 308-327 8-27 (117)
26 TIGR01299 synapt_SV2 synaptic 24.3 1E+03 0.023 27.8 13.1 30 296-325 612-641 (742)
27 PRK11056 hypothetical protein; 23.2 2.8E+02 0.006 25.2 6.3 20 308-327 8-27 (120)
28 PRK10263 DNA translocase FtsK; 23.1 2E+02 0.0042 36.0 7.0 15 228-242 27-41 (1355)
29 TIGR02230 ATPase_gene1 F0F1-AT 23.0 2.7E+02 0.0058 24.4 6.1 41 287-327 51-92 (100)
30 PF12156 ATPase-cat_bd: Putati 21.2 83 0.0018 26.6 2.5 42 110-155 43-84 (88)
31 COG1030 NfeD Membrane-bound se 21.1 1.1E+03 0.025 25.9 12.4 27 328-354 299-326 (436)
32 TIGR00834 ae anion exchange pr 20.8 5.7E+02 0.012 30.8 10.0 62 285-346 376-439 (900)
33 PF10066 DUF2304: Uncharacteri 20.2 3.8E+02 0.0083 23.5 6.7 18 382-399 47-65 (115)
34 TIGR02916 PEP_his_kin putative 20.0 1E+03 0.022 27.0 11.9 41 334-374 193-235 (679)
No 1
>PRK10907 intramembrane serine protease GlpG; Provisional
Probab=100.00 E-value=1.5e-46 Score=377.50 Aligned_cols=251 Identities=14% Similarity=0.096 Sum_probs=211.7
Q ss_pred hhhhccCCChhHHHHHHHHHhhcCCceeEecCccc-----hhhhHHHHHhhhh--hccCCCCCcchhhhhhccccCCc--
Q 010796 137 HSRSGEINAKTELDSLDAYLGKLNTDAKFSTDQTT-----ERNLVAAQLSISK--SSKRGYMGKLKGYRELRNKDGVR-- 207 (501)
Q Consensus 137 m~~~~~~~~~~~aqaf~dYl~~~~i~~~v~~~~~~-----de~~~~~~~~e~~--~~~p~~~~~~~rY~~asw~~g~~-- 207 (501)
|+++.+++|||+||+|+|||+++||+++++++++. ||+|.+++|+|++ ++||+|+ ||++++|+++++
T Consensus 1 M~~~~~~~~~~~a~~f~dyl~~~~i~~~~~~~~~~~lwl~d~~~~~~~~~~~~~f~~~p~~~----~y~~asw~~g~~~~ 76 (276)
T PRK10907 1 MLMITSFSNPRLAQAFVDYMATQGVILTIQQHNQSDIWLADESQAERVRAELARFLENPADP----RYLAASWQSGHTNS 76 (276)
T ss_pred CcchhcCCCHHHHHHHHHHHHHCCCcEEEecCCceEEEecCHHHHHHHHHHHHHHHhCCCch----hHHhcccccCCCCC
Confidence 78899999999999999999999999999854443 8899999999999 9999999 999999998864
Q ss_pred --cchhhHHHhhcccccchHHHHHHHHHHHHHHHHHhcCCCCcccccchhhhhhhcchhhhhhcCcceeeeecccccCCH
Q 010796 208 --SLERDLALQRTEETSNLYLIILVSIDVAVFLFEIASPIRNSEFGFFSLPLLYGAKINELILVGEWWRLVTPMFLHSGL 285 (501)
Q Consensus 208 --~~~~~~~~~~~~~~~~P~vT~LIai~v~VFll~~~~~~~~~~~~~l~~p~~~ga~~~~~i~~gq~WRl~Ts~FlH~s~ 285 (501)
.++++...++.+.+..|.+++++++|++||+++.+.+.. ..+.++.+| ......+||||++|++|+|+|+
T Consensus 77 ~~~~~~~~~~~~~~~~~~p~T~~li~i~i~vf~l~~~~~~~-~~~~~l~~~-------~~~~~~~q~WRl~T~~flH~~~ 148 (276)
T PRK10907 77 GLRYRRFPFLATLRERAGPLTLGVMIACVVVFILMQILGDQ-TVMLWLAWP-------FDPSLKFELWRYFTHALLHFSL 148 (276)
T ss_pred CcccccchHHHhhccCCCCHHHHHHHHHHHHHHHHHHhccH-HHHHHHhcc-------ccccccCCcHHHHhHHHHhCCH
Confidence 356677777777666654449999999999998775432 112221111 1123579999999999999999
Q ss_pred HHHHHHHHHHHHHHHHHHHhhchhHHHHHHHHHHHHHHHHhHhhCCCccccchHHHHHHHHHHHHHHhcccchhhhhhhH
Q 010796 286 FHVALSCWALLTFGPQVCKSYGPFTFFLIYTLGGISGNLTSFLHTPEPTVGGTGPVFAIIGAWLIYQFQNKDLIAKDVSE 365 (501)
Q Consensus 286 ~HLlfNml~L~~fG~~lE~~lGs~r~l~lyllsgl~g~l~~~l~~~~~~vGaSGaVfGLlGa~~v~~~~~~~~~~~~~~~ 365 (501)
+||+|||+++|++|+.+|+.+|+++++.+|++++++||++++++.+...+|+||+|||++|+.++...+.+.. ...+|.
T Consensus 149 ~Hl~fNml~l~~lG~~iE~~~G~~~~l~l~l~s~i~~~~~~~~~~~~~~gGaSGvVygL~g~~~~~~~~~p~~-~~~lp~ 227 (276)
T PRK10907 149 LHILFNLLWWWYLGGAVEKRLGSGKLIVITLISALLSGWVQSKFSGPWFGGLSGVVYALMGYVWLRGERDPQS-GIYLPR 227 (276)
T ss_pred HHHHHHHHHHHHHHHHHHHHHChHHHHHHHHHHHHHHHHHHHHHccchhhHHHHHHHHHHHHHHHHhcccccc-chhhhH
Confidence 9999999999999999999999999999999999999999999988778899999999999998887666554 345577
Q ss_pred HHHHHHHHHHHHHHHhhcCCCchhhhhHhhhhhhc
Q 010796 366 RMFQKAILSTALSFIISNFGPVDTWAHLGAAFTDL 400 (501)
Q Consensus 366 ~l~~~~li~l~l~~i~~~~~~Is~~AHLgGll~GL 400 (501)
.++.++++++++++.....++|+|.||++|+++|+
T Consensus 228 ~~~~f~llwl~~g~~~~~g~~Ian~AHlgGli~Gl 262 (276)
T PRK10907 228 GLIAFALLWLVAGYFDLFGMSIANAAHVAGLAVGL 262 (276)
T ss_pred HHHHHHHHHHHHHHHHccCcccHHHHHHHHHHHHH
Confidence 78888888888888765567899999999999994
No 2
>PF05512 AWPM-19: AWPM-19-like family; InterPro: IPR008390 Members of this family are 19 kDa membrane proteins. The levels of the plant protein AWPM-19 increase dramatically when there is an increase level of abscisic acid. The increase presence of this protein leads to greater tolerance of freezing [].
Probab=99.98 E-value=6e-33 Score=248.54 Aligned_cols=97 Identities=55% Similarity=0.870 Sum_probs=96.0
Q ss_pred cccchhHHHHHHHHhhhhhhhhhhhhhceeecccccchHHHHHHHHHHHHHHHHHHhhchheeEEeCcccCccchhHHHH
Q 010796 401 GGNTSTWFLLTFALTTGAIGVCSVTAGLMHLRAWRSESLAAASSLAILSWSVTAIAVGFVCKEIILGGHRGKRLQTLEAF 480 (501)
Q Consensus 401 ~G~~~t~f~i~f~Llagvvg~~~~~~g~~~~~~w~~~~~~aa~a~~~iaw~lt~lA~G~a~k~i~~~~~~~~~~~~le~~ 480 (501)
+||.+|+||++|+|+|||||+++.+.|+.|.|.|+.+++++|+++++++|++|+||||+|||||++|+ ||+||||||||
T Consensus 45 ~GN~AT~ffv~faLlAgVVG~aS~l~G~~h~r~W~~~sLaaAaa~a~iAW~lTlLAmGlACKeI~~g~-r~~rLrtlEaf 123 (142)
T PF05512_consen 45 MGNAATGFFVIFALLAGVVGAASVLAGLHHVRSWRSESLAAAAASALIAWALTLLAMGLACKEIHLGG-RNWRLRTLEAF 123 (142)
T ss_pred ccchhHHHHHHHHHHHHHHHHHHHHhhHHHHhhcCccchHHHHHHHHHHHHHHHHHHHHhHheeeecC-ccchhhHHHHH
Confidence 79999999999999999999999999999999999999999999999999999999999999999998 99999999999
Q ss_pred HHHHHHHHHHHHHHHhhh
Q 010796 481 AVISLLSQLLYLGLVHAW 498 (501)
Q Consensus 481 ~~i~~~~ql~~~~~~~~~ 498 (501)
+||+++|||+|++++|+|
T Consensus 124 ~IIl~~tQLly~l~lH~g 141 (142)
T PF05512_consen 124 TIILSATQLLYLLALHAG 141 (142)
T ss_pred HHHHHHHHHHHHHHHhcc
Confidence 999999999999999997
No 3
>PTZ00101 rhomboid-1 protease; Provisional
Probab=99.95 E-value=2.9e-27 Score=237.88 Aligned_cols=184 Identities=24% Similarity=0.330 Sum_probs=135.5
Q ss_pred HHhhcccccchHHH-HHHHHHHHHHHHHHhcCCCCcccccc-hhhhhhhcchhhhhhcCcceeeeecccccCCHHHHHHH
Q 010796 214 ALQRTEETSNLYLI-ILVSIDVAVFLFEIASPIRNSEFGFF-SLPLLYGAKINELILVGEWWRLVTPMFLHSGLFHVALS 291 (501)
Q Consensus 214 ~~~~~~~~~~P~vT-~LIai~v~VFll~~~~~~~~~~~~~l-~~p~~~ga~~~~~i~~gq~WRl~Ts~FlH~s~~HLlfN 291 (501)
...++++-+.+.+| .++++++++|++........ .+... .....+|+..++.+.++||||++|++|+|.|++|+++|
T Consensus 43 ler~Fp~f~i~~l~~~Iiii~iivfil~l~~~~~~-~l~p~~~~L~~~Ga~~~~~i~~gq~WRLiT~~FlH~~~~HLl~N 121 (278)
T PTZ00101 43 LNLIFPHFTWKSFIMAISIIQIIVFIISVSIKPAD-FLTPSDSLLVTLGANVASRIKQGEIHRLILPIFLHANIFHTFFN 121 (278)
T ss_pred HHHHcCCccHHHHHHHHHHHHHHHHHHHHHhcccc-cCCCCHHHHHHHhCcchhhhhcCCCHHHHHHHHHccCHHHHHHH
Confidence 44567777888888 99999999999876643211 11111 13456788777888899999999999999999999999
Q ss_pred HHHHHHHHHHHHHhhchhHHHHHHHHHHHHHHHHhHhhCCC-ccccchHHHHHHHHHHHHHHhcccchhhhhhhHHHHHH
Q 010796 292 CWALLTFGPQVCKSYGPFTFFLIYTLGGISGNLTSFLHTPE-PTVGGTGPVFAIIGAWLIYQFQNKDLIAKDVSERMFQK 370 (501)
Q Consensus 292 ml~L~~fG~~lE~~lGs~r~l~lyllsgl~g~l~~~l~~~~-~~vGaSGaVfGLlGa~~v~~~~~~~~~~~~~~~~l~~~ 370 (501)
|++++.+|..+|+.+|++|++.+|+++|++|++++.++.+. ..+||||++||++|++.......+..... +......
T Consensus 122 m~~l~~~G~~lE~~~G~~r~~ilYl~sGi~G~l~s~~~~~~~~svGASgAifGLiGa~~~~lil~w~~~~~--~~~~~~~ 199 (278)
T PTZ00101 122 VFFQLRMGFTLEKNYGIVKIIILYFLTGIYGNILSSSVTYCPIKVGASTSGMGLLGIVTSELILLWHVIRH--RERVVFN 199 (278)
T ss_pred HHHHHHHHHHHHHHHChHHHHHHHHHHHHHHHHHHHHHccCCcEEehhHHHHHHHHHHHHHHHHHHHhhcc--HHHHHHH
Confidence 99999999999999999999999999999999999887663 58999999999999987644333222111 1111111
Q ss_pred HHHHHHHH---HHhhcCCCchhhhhHhhhhhhc
Q 010796 371 AILSTALS---FIISNFGPVDTWAHLGAAFTDL 400 (501)
Q Consensus 371 ~li~l~l~---~i~~~~~~Is~~AHLgGll~GL 400 (501)
.++..++. ......+++|++||+||+++|+
T Consensus 200 ~i~~~li~~~l~~~~~g~~Id~~aHlGG~i~G~ 232 (278)
T PTZ00101 200 IIFFSLISFFYYFTFNGSNIDHVGHLGGLLSGI 232 (278)
T ss_pred HHHHHHHHHHHHHhcCCCCccHHHHHHHHHHHH
Confidence 11111111 1112246799999999999993
No 4
>COG0705 Membrane associated serine protease [Amino acid transport and metabolism]
Probab=99.90 E-value=1.7e-23 Score=204.42 Aligned_cols=176 Identities=26% Similarity=0.466 Sum_probs=138.6
Q ss_pred chHHH-HHHHHHHHHHHHHHhcCCCCcccccchhhhhhhcchhhhh-hcC--cceeeeecccccCCHHHHHHHHHHHHHH
Q 010796 223 NLYLI-ILVSIDVAVFLFEIASPIRNSEFGFFSLPLLYGAKINELI-LVG--EWWRLVTPMFLHSGLFHVALSCWALLTF 298 (501)
Q Consensus 223 ~P~vT-~LIai~v~VFll~~~~~~~~~~~~~l~~p~~~ga~~~~~i-~~g--q~WRl~Ts~FlH~s~~HLlfNml~L~~f 298 (501)
.++.+ .++.+|+++|+++...+.... .........++....... ... |+||++|++|+|.|+.|+++||+++|.+
T Consensus 16 ~~~~~~~~~~~~~~v~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~w~lit~~FlH~~~~Hll~N~~~l~~f 94 (228)
T COG0705 16 APPVTLFLILLNILVFLLELVLGWSAI-FLLTFLFRLFGLYPLNLLGALARDQLWRLITAIFLHAGFLHLLFNMLALWVF 94 (228)
T ss_pred cchHHHHHHHHHHHHHHHHHHccchHH-HHHHHhhhHHhhcchhhhccccccchHHHHHHHHHHhhHHHHHHHHHHHHHh
Confidence 46777 999999999999877654321 111000000111111111 111 8999999999999999999999999999
Q ss_pred HHHHHHhhchhHHHHHHHHHHHHHHHHhHhhCCC---ccccchHHHHHHHHHHHHHHhcccchhhhh-hhHHHHHHHHHH
Q 010796 299 GPQVCKSYGPFTFFLIYTLGGISGNLTSFLHTPE---PTVGGTGPVFAIIGAWLIYQFQNKDLIAKD-VSERMFQKAILS 374 (501)
Q Consensus 299 G~~lE~~lGs~r~l~lyllsgl~g~l~~~l~~~~---~~vGaSGaVfGLlGa~~v~~~~~~~~~~~~-~~~~l~~~~li~ 374 (501)
|..+|+.+|+.+++.+|+++|+++++++.++.+. +.+|+||++||++|++++..+..+...... .+..+..++.++
T Consensus 95 g~~le~~~G~~~f~~~yl~~gl~~~~~~~~~~~~~~~~~~GASG~i~gllga~~~~~~~~~~~~~~~~~~~~~~~~i~~~ 174 (228)
T COG0705 95 GSNLERRLGTLRFLLFYLLSGLLAGLAQVLFGPKGGAPSLGASGAIFGLLGAYFLLFPFARILLLFLSLPRPALILILIW 174 (228)
T ss_pred hHHHHHHhchhHHHHHHHHHHHHHHHHHHHHcccccCcccchhHHHHHHHHHHHHHccccchhhhhccCchhHHHHHHHH
Confidence 9999999999999999999999999999988873 689999999999999999999887765444 677777777888
Q ss_pred HHHHHHhhcCC---CchhhhhHhhhhhh
Q 010796 375 TALSFIISNFG---PVDTWAHLGAAFTD 399 (501)
Q Consensus 375 l~l~~i~~~~~---~Is~~AHLgGll~G 399 (501)
.+.+++..... ++++.||++|+++|
T Consensus 175 ~~~~~~~~~~~~~~~va~~aHl~G~i~G 202 (228)
T COG0705 175 LLYSLFSGAGSFGPSVAWSAHLGGLIGG 202 (228)
T ss_pred HHHHHHHHhcCCchHHHHHHHHHHHHHH
Confidence 88777765543 69999999999999
No 5
>KOG2289 consensus Rhomboid family proteins [Signal transduction mechanisms]
Probab=99.88 E-value=4.2e-23 Score=209.92 Aligned_cols=142 Identities=30% Similarity=0.505 Sum_probs=120.8
Q ss_pred hhhhhcchhhhhhcCcceeeeecccccCCHHHHHHHHHHHHHHHHHHHHhhchhHHHHHHHHHHHHHHHHhHhhCCC-cc
Q 010796 256 PLLYGAKINELILVGEWWRLVTPMFLHSGLFHVALSCWALLTFGPQVCKSYGPFTFFLIYTLGGISGNLTSFLHTPE-PT 334 (501)
Q Consensus 256 p~~~ga~~~~~i~~gq~WRl~Ts~FlH~s~~HLlfNml~L~~fG~~lE~~lGs~r~l~lyllsgl~g~l~~~l~~~~-~~ 334 (501)
+...+......+..+|+||++|++|+|+|+.||.+||+.+.++|..+|..+|.+|+.++|++||+.|++++.++.+. ..
T Consensus 103 ~~~~~~~i~~~~~r~E~WRllTym~LHaGi~HL~~N~~~ql~iGi~LE~~~G~~RiglIYl~gg~aGSlls~l~d~~~~s 182 (316)
T KOG2289|consen 103 EKMGGLLIYKPVHRGELWRLLTYMWLHAGIFHLLLNMLSQLFIGIPLEQVHGFLRIGLIYLAGGVAGSLLSSLFDPNSIS 182 (316)
T ss_pred cccCCceecChhhhchhHHHHHHHHHhcCHHHHHHHHHHHHhccccHHhhcCceEEeeehhhhhhhhHHHHHHhccCCce
Confidence 34455556566789999999999999999999999999999999999999999999999999999999999999986 59
Q ss_pred ccchHHHHHHHHHHHHHHhcccchhhhhhhHHHHHHHHHHHHHHHHhhcCCCchhhhhHhhhhhh
Q 010796 335 VGGTGPVFAIIGAWLIYQFQNKDLIAKDVSERMFQKAILSTALSFIISNFGPVDTWAHLGAAFTD 399 (501)
Q Consensus 335 vGaSGaVfGLlGa~~v~~~~~~~~~~~~~~~~l~~~~li~l~l~~i~~~~~~Is~~AHLgGll~G 399 (501)
|||||++|||+|+.+.....|+..+.... ..+..+++.+.+...++..+.+++++|+||+++|
T Consensus 183 VGASggvfaLlgA~Ls~l~~Nw~~m~~~~--~~l~~ll~Ii~i~l~~G~~~~~~~~~h~gg~~~G 245 (316)
T KOG2289|consen 183 VGASGGVFALLGAHLSNLLTNWTIMKNKF--AALRTLLIIIFINLDLGFAPYVDNFAHIGGLLAG 245 (316)
T ss_pred ecccHHHHHHHHHHHHHHHhhHHHhcchH--HHHHHHHHHHHHHHhhccccceeccccccccCCC
Confidence 99999999999999999999988753222 2233444444555555677889999999999999
No 6
>PF01694 Rhomboid: Rhomboid family; InterPro: IPR022764 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. Proteolytic enzymes that exploit serine in their catalytic activity are ubiquitous, being found in viruses, bacteria and eukaryotes []. They include a wide range of peptidase activity, including exopeptidase, endopeptidase, oligopeptidase and omega-peptidase activity. Over 20 families (denoted S1 - S66) of serine protease have been identified, these being grouped into clans on the basis of structural similarity and other functional evidence []. Structures are known for members of the clans and the structures indicate that some appear to be totally unrelated, suggesting different evolutionary origins for the serine peptidases []. Not withstanding their different evolutionary origins, there are similarities in the reaction mechanisms of several peptidases. Chymotrypsin, subtilisin and carboxypeptidase C have a catalytic triad of serine, aspartate and histidine in common: serine acts as a nucleophile, aspartate as an electrophile, and histidine as a base []. The geometric orientations of the catalytic residues are similar between families, despite different protein folds []. The linear arrangements of the catalytic residues commonly reflect clan relationships. For example the catalytic triad in the chymotrypsin clan (PA) is ordered HDS, but is ordered DHS in the subtilisin clan (SB) and SDH in the carboxypeptidase clan (SC) [, ]. This group of proteins contain serine peptidases belonging to the MEROPS peptidase family S54 (Rhomboid, clan ST). They are integral membrane proteins related to the Drosophila melanogaster (Fruit fly) rhomboid protein P20350 from SWISSPROT. Members of this family are found in archaea, bacteria and eukaryotes. The D. melanogaster rhomboid protease cleaves type-1 transmembrane domains using a catalytic triad composed of serine, histidine and asparagine contributed by different transmembrane domains. It cleaves the transmembrane proteins Spitz, Gurken and Keren within their transmembrane domains to release a soluble TGFalpha-like growth factor. Cleavage occurs in the Golgi, following translocation of the substrates from the endoplasmic reticulum membrane by Star, another transmembrane protein. The growth factors are then able to activate the epidermal growth factor receptor [, ]. Few substrates of mammalian rhomboid homologues have been determined, but rhomboid-like protein 2 (MEROPS S54.002) has been shown to cleave ephrin B3 []. Parasite-encoded rhomboid enzymes are also important for invasion of host cells by Toxoplasma and the malaria parasite. In Saccharomyces cerevisiae (Baker's yeast) the Pcp1 (MDM37) protein (MEROPS S54.007) is a mitochondrial endopeptidase required for the activation of cytochrome c peroxidase and for the processing of the mitochondrial dynamin-like protein Mgm1 [, ]. Mutations in Pcp1 result in cells have fragmented mitochondria, which have very few short tubulues []. This entry represents the 6 transmembrane helix rhomboid domain.; GO: 0004252 serine-type endopeptidase activity, 0016021 integral to membrane; PDB: 3UBB_A 3B45_A 3B44_A 2NRF_A 3TXT_A 2O7L_A 2XTU_A 2IRV_A 2XOW_A 2XTV_A ....
Probab=99.79 E-value=3.2e-20 Score=167.56 Aligned_cols=131 Identities=31% Similarity=0.584 Sum_probs=98.3
Q ss_pred hcCcceeeeecccccCCHHHHHHHHHHHHHHHHHHHHhhchhHHHHHHHHHHHHHHHHhHhhCCC--ccccchHHHHHHH
Q 010796 268 LVGEWWRLVTPMFLHSGLFHVALSCWALLTFGPQVCKSYGPFTFFLIYTLGGISGNLTSFLHTPE--PTVGGTGPVFAII 345 (501)
Q Consensus 268 ~~gq~WRl~Ts~FlH~s~~HLlfNml~L~~fG~~lE~~lGs~r~l~lyllsgl~g~l~~~l~~~~--~~vGaSGaVfGLl 345 (501)
.++||||++|++|+|.|+.|+++|++.++.+|..+|+.+|+++++.+|+++++.+++...++.+. +.+|+||+++|++
T Consensus 2 ~~~~~wrl~T~~f~h~~~~hl~~n~~~l~~~g~~lE~~~G~~~~~~~~l~~~~~~~l~~~~~~~~~~~~~G~Sg~~~~l~ 81 (145)
T PF01694_consen 2 QNGQWWRLFTSPFVHANFLHLLFNLLALWFFGSLLERRLGSRRFLALYLLSGLLGSLLSLLFSPPNQPYVGASGAVFGLL 81 (145)
T ss_dssp GCC-TTHHHHGGG--SSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-S-----SSHHHHHHHH
T ss_pred CCCcchhhhHHHHHccCHHHHHHHHHHHHHhhhhHhhhccchHHHHHHHHHHHhhhhccccccccccccCCCcccchHHH
Confidence 57999999999999999999999999999999999999999999999999999999999887764 5899999999999
Q ss_pred HHHHHHHhcccchhhhhhhHHHHHHHHHHHHHHHHhhcCCCchhhhhHhhhhhhc
Q 010796 346 GAWLIYQFQNKDLIAKDVSERMFQKAILSTALSFIISNFGPVDTWAHLGAAFTDL 400 (501)
Q Consensus 346 Ga~~v~~~~~~~~~~~~~~~~l~~~~li~l~l~~i~~~~~~Is~~AHLgGll~GL 400 (501)
++.....+..+........ ........+.+.+.....+++++.+|++|+++|+
T Consensus 82 ~~~~~~~~~~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~hl~G~~~G~ 134 (145)
T PF01694_consen 82 GAFLFLYPQNKKRLRFIYL--ALVVPIIVLVIILLLGFIPNISFLGHLGGFLAGL 134 (145)
T ss_dssp HHHHHHHHCCCCCS---HC--CCCCCCCCCCHHHCTSSSSTTTHHHHHHHHHHHH
T ss_pred HHHHHHHhhccchhhcchH--HHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHH
Confidence 9999988887554321100 0000011111222323367899999999999993
No 7
>PF12122 DUF3582: Protein of unknown function (DUF3582); InterPro: IPR022732 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. Proteolytic enzymes that exploit serine in their catalytic activity are ubiquitous, being found in viruses, bacteria and eukaryotes []. They include a wide range of peptidase activity, including exopeptidase, endopeptidase, oligopeptidase and omega-peptidase activity. Over 20 families (denoted S1 - S66) of serine protease have been identified, these being grouped into clans on the basis of structural similarity and other functional evidence []. Structures are known for members of the clans and the structures indicate that some appear to be totally unrelated, suggesting different evolutionary origins for the serine peptidases []. Not withstanding their different evolutionary origins, there are similarities in the reaction mechanisms of several peptidases. Chymotrypsin, subtilisin and carboxypeptidase C have a catalytic triad of serine, aspartate and histidine in common: serine acts as a nucleophile, aspartate as an electrophile, and histidine as a base []. The geometric orientations of the catalytic residues are similar between families, despite different protein folds []. The linear arrangements of the catalytic residues commonly reflect clan relationships. For example the catalytic triad in the chymotrypsin clan (PA) is ordered HDS, but is ordered DHS in the subtilisin clan (SB) and SDH in the carboxypeptidase clan (SC) [, ]. This entry represents the N-terminal domain of membrane-bound serine endopeptidases belonging to MEROPS peptidase family S54 (rhomboid-1, clan ST). This domain contains a conserved ASW sequence motif and a single completely conserved residue F that may be functionally important. The tertiary structure of the GlpG protein from Escherichia coli has been determined []. The GlpG protein has six transmembrane domains (other members of the family are predicted to have seven), with the N- and C-terminal ends anchored in the cytoplasm. One transmembrane domain is shorter than the rest, creating an internal, aqueous cavity just below the membrane surface and it is here were proteolysis occurs. There is also a membrane-embedded loop between the first and second transmembrane domains which is postulated to act as a gate controlling substrate access to the active site. No other family of serine peptidases is known to have active site residues within transmembrane domains (although transmembrane active sites are known for aspartic peptidase and metallopeptidases), and the GlpG protein has the type structure for clan ST.; GO: 0004252 serine-type endopeptidase activity, 0016021 integral to membrane; PDB: 3UBB_A 3B45_A 3B44_A 2NRF_A 3TXT_A 2O7L_A 2XTU_A 2IRV_A 2XOW_A 2XTV_A ....
Probab=99.62 E-value=2.7e-16 Score=136.22 Aligned_cols=86 Identities=10% Similarity=0.115 Sum_probs=48.1
Q ss_pred hhhhccCCChhHHHHHHHHHhhcCCceeEecCccc-------hhhhHHHHHhhhh--hccCCCCCcchhhhhhccccCCc
Q 010796 137 HSRSGEINAKTELDSLDAYLGKLNTDAKFSTDQTT-------ERNLVAAQLSISK--SSKRGYMGKLKGYRELRNKDGVR 207 (501)
Q Consensus 137 m~~~~~~~~~~~aqaf~dYl~~~~i~~~v~~~~~~-------de~~~~~~~~e~~--~~~p~~~~~~~rY~~asw~~g~~ 207 (501)
|+++++++|||+||+|+|||+++||++++++++++ ||++++++++|++ ++||+|+ ||++++|+.|++
T Consensus 1 M~~l~~~~n~r~AqaF~DYl~sqgI~~~i~~~~~~~~~lwl~de~~~~~a~~el~~Fl~nP~~~----rYqaASWq~g~~ 76 (101)
T PF12122_consen 1 MIRLGSLNNPRAAQAFIDYLASQGIELQIEPEGQGQFALWLHDEEHLEQAEQELEEFLQNPNDP----RYQAASWQTGST 76 (101)
T ss_dssp -EEEEEESSHHHHHHHHHHHHHTT--EEEE-SSSE--EEEES-GGGHHHHHHHHHHHHHS-SS-----------------
T ss_pred CeEEEecCCHHHHHHHHHHHHHCCCeEEEEECCCCceEEEEeCHHHHHHHHHHHHHHHHCCCCH----HHHHHHHhcCCc
Confidence 89999999999999999999999999999987665 8999999999999 9999999 999999999986
Q ss_pred c----chhhHHHhhcccccchHH
Q 010796 208 S----LERDLALQRTEETSNLYL 226 (501)
Q Consensus 208 ~----~~~~~~~~~~~~~~~P~v 226 (501)
. |+.+.++++++...+|.+
T Consensus 77 ~~~~~y~~~s~~~~l~~~aGplT 99 (101)
T PF12122_consen 77 RTQFSYQSPSLLQQLRAQAGPLT 99 (101)
T ss_dssp ------------------S-HHH
T ss_pred cCccCcCCchHHHHHHHcCCCee
Confidence 4 455667777766667543
No 8
>KOG2632 consensus Rhomboid family proteins [Function unknown]
Probab=99.59 E-value=4.2e-15 Score=146.67 Aligned_cols=163 Identities=18% Similarity=0.224 Sum_probs=124.7
Q ss_pred cchHHH-HHHHHHHHHHHHHHhcCCCCcccccchhhhhhhcchhhhhhcCcceeeeecccccCCHHHHHHHHHHHHHHHH
Q 010796 222 SNLYLI-ILVSIDVAVFLFEIASPIRNSEFGFFSLPLLYGAKINELILVGEWWRLVTPMFLHSGLFHVALSCWALLTFGP 300 (501)
Q Consensus 222 ~~P~vT-~LIai~v~VFll~~~~~~~~~~~~~l~~p~~~ga~~~~~i~~gq~WRl~Ts~FlH~s~~HLlfNml~L~~fG~ 300 (501)
..|..| .++.+|.++|++....+... + + ........+.|+||++|++++|.+..|+++||+.+|.+|.
T Consensus 13 ~~p~~ts~~~~~~~~i~lv~~~~~i~~-~---~-------~l~~~~l~~~ql~RL~Ty~l~H~s~~hllfnmlaL~~~g~ 81 (258)
T KOG2632|consen 13 KIPLLTSIVVVLAILIYLVSFFPGIVE-V---L-------GLPSELLINWQLYRLITYALVHLSLPHLLFNMLALWPLGS 81 (258)
T ss_pred cchHHHHHHHHHHHHHHHHhccchhhh-H---h-------cCCHHHhhhHHHHHHHHHHHHhccHHHHHHHHHHHHhchh
Confidence 456677 89999999998876544321 1 1 1122345789999999999999999999999999999999
Q ss_pred HHHHhhc-hhHHHHHHHHHHHHHHHHhHhhCC----------CccccchHHHHHHHHHHHHHHhcccchhh--hhhhHHH
Q 010796 301 QVCKSYG-PFTFFLIYTLGGISGNLTSFLHTP----------EPTVGGTGPVFAIIGAWLIYQFQNKDLIA--KDVSERM 367 (501)
Q Consensus 301 ~lE~~lG-s~r~l~lyllsgl~g~l~~~l~~~----------~~~vGaSGaVfGLlGa~~v~~~~~~~~~~--~~~~~~l 367 (501)
..|+.+| +.+++..+.+.+++++++..+... ...+|.||+.||+++......+.++.... ..+|..+
T Consensus 82 ~fE~~~G~t~~~l~~~~llalf~gIl~ll~~~~~~~~d~~~~~~a~G~s~v~Fam~~~~~~~sp~r~~~~fg~~siP~~l 161 (258)
T KOG2632|consen 82 QFERTHGTTVRILMFTVLLALFSGILYLLAYHVFLLSDLVYVEGAIGFSGVLFAMMAVLEVQSPVRSRSVFGLFSIPIVL 161 (258)
T ss_pred HHHhhccceehHHHHHHHHHHHHHHHHHHHHHHHhhcchhhhcccccccHHHHHHHHHHhhcCcccchhhcccccccHHH
Confidence 9999999 899999999999999998766531 23689999999999998887777664332 2245544
Q ss_pred HHHHHHHHHHHHHhhcCCCchhhhhHhhhhhh
Q 010796 368 FQKAILSTALSFIISNFGPVDTWAHLGAAFTD 399 (501)
Q Consensus 368 ~~~~li~l~l~~i~~~~~~Is~~AHLgGll~G 399 (501)
.+++. +..+....++.+..+|++|+++|
T Consensus 162 ~Pw~l----Li~~~~lvp~aSFlghl~GllvG 189 (258)
T KOG2632|consen 162 APWAL----LIATQILVPQASFLGHLCGLLVG 189 (258)
T ss_pred HHHHH----HHHHHHHccCchHHHHHHHHHHH
Confidence 44333 23333455889999999999999
No 9
>KOG2290 consensus Rhomboid family proteins [Signal transduction mechanisms]
Probab=99.58 E-value=1.3e-15 Score=158.27 Aligned_cols=130 Identities=29% Similarity=0.456 Sum_probs=111.3
Q ss_pred cCcceeeeecccccCCHHHHHHHHHHHHHHHHHHHHhhchhHHHHHHHHHHHHHHHHhHhhCC-CccccchHHHHHHHHH
Q 010796 269 VGEWWRLVTPMFLHSGLFHVALSCWALLTFGPQVCKSYGPFTFFLIYTLGGISGNLTSFLHTP-EPTVGGTGPVFAIIGA 347 (501)
Q Consensus 269 ~gq~WRl~Ts~FlH~s~~HLlfNml~L~~fG~~lE~~lGs~r~l~lyllsgl~g~l~~~l~~~-~~~vGaSGaVfGLlGa 347 (501)
..|+||++|+.|+|+++.|++..+....++-..+|+..|+.|..++|++||+.||+++..|.| .+.||-||+-||+++.
T Consensus 448 PdQfYRL~~SLFlHagviH~~vSi~FQm~vmrdlEkL~g~~riAIiy~~SGitGNLASAIFlpY~~eVgPa~sQ~Gila~ 527 (652)
T KOG2290|consen 448 PDQFYRLWLSLFLHAGVIHLLVSICFQMTVMRDLEKLAGWHRIAIIYFLSGITGNLASAIFLPYRAEVGPAGSQFGILAC 527 (652)
T ss_pred hhHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHhhcchhhheeeecccccccchheeeeccccccCCcccccchHHH
Confidence 468999999999999999999999999999999999999999999999999999999999988 4899999999999999
Q ss_pred HHHHHhcccchhhhhhhHHHHHHHHHHHHHHHHhhcCCCchhhhhHhhhhhhcc
Q 010796 348 WLIYQFQNKDLIAKDVSERMFQKAILSTALSFIISNFGPVDTWAHLGAAFTDLG 401 (501)
Q Consensus 348 ~~v~~~~~~~~~~~~~~~~l~~~~li~l~l~~i~~~~~~Is~~AHLgGll~GL~ 401 (501)
+++-...++..+..++ ..+.-++..+++.++ ++.|.|||+||+.|++.||.
T Consensus 528 l~vEl~qs~~il~~~w--~a~~~Lia~~L~L~i-GliPWiDN~aHlfG~i~GLl 578 (652)
T KOG2290|consen 528 LFVELFQSWQILERPW--RAFFHLIATLLVLCI-GLIPWIDNWAHLFGTIFGLL 578 (652)
T ss_pred HHHHHHhhhHhhhhHH--HHHHHHHHHHHHHHh-ccccchhhHHHHHHHHHHHH
Confidence 9998888888765432 333333333333333 67789999999999999974
No 10
>KOG2980 consensus Integral membrane protease of the rhomboid family involved in different forms of regulated intramembrane proteolysis [Signal transduction mechanisms]
Probab=98.21 E-value=7e-07 Score=90.41 Aligned_cols=166 Identities=17% Similarity=0.253 Sum_probs=110.7
Q ss_pred HHHHHHHHHHHHHHHHHhcCCCCcccccchhhhhhhcchhhhhhcCcceeeeecccccCCHHHHHHHHHHHHHHHH-HHH
Q 010796 225 YLIILVSIDVAVFLFEIASPIRNSEFGFFSLPLLYGAKINELILVGEWWRLVTPMFLHSGLFHVALSCWALLTFGP-QVC 303 (501)
Q Consensus 225 ~vT~LIai~v~VFll~~~~~~~~~~~~~l~~p~~~ga~~~~~i~~gq~WRl~Ts~FlH~s~~HLlfNml~L~~fG~-~lE 303 (501)
.+..++++|+++|.++.+....... .+.. ..++ +...--|.++++.|.|.+.+|+..||+.++.+.. .+-
T Consensus 117 ~v~~ll~~n~~vf~lWrv~~~~~~~-----~~~m---ls~~-~~~t~~w~i~~s~Fsh~~a~h~g~~~~~~~~y~~~a~~ 187 (310)
T KOG2980|consen 117 VVFGLLIANAFVFTLWRVPQKQFTM-----IPWM---LSRN-AYKTGCWKIILSTFSHYSALHLGPNMLVLKSYLAGALK 187 (310)
T ss_pred chhHHHHHHHHHHHHHHhcchhhhh-----hhHH---hhcc-cccccceeEEeehhcchhHhhhcHHHHHHHHHhccccc
Confidence 3338999999999998775432111 0100 1111 2233457799999999999999999998887777 788
Q ss_pred HhhchhHHHHHHHHHHHHHHHHhHhh-CC----CccccchHHHHHHHHHHHHHHhcccchhhhhhhHHHHHHHHHHHHHH
Q 010796 304 KSYGPFTFFLIYTLGGISGNLTSFLH-TP----EPTVGGTGPVFAIIGAWLIYQFQNKDLIAKDVSERMFQKAILSTALS 378 (501)
Q Consensus 304 ~~lGs~r~l~lyllsgl~g~l~~~l~-~~----~~~vGaSGaVfGLlGa~~v~~~~~~~~~~~~~~~~l~~~~li~l~l~ 378 (501)
-.+|...+..+|+.++..|......- .+ .+.+|+||++|++++......+.....+.+.++.+....+.+-.+..
T Consensus 188 ~~~~~~~~~AlylSa~~~~~~i~~~~~v~~~~~gp~LGAsGav~ai~a~~~~lfP~~~~~i~f~~~v~~ga~~~~~~i~~ 267 (310)
T KOG2980|consen 188 GSLGFSSFFALYLSAGVKGLFISVKDKVPTSWAGPSLGASGAVYAILALDCTLFPKTTLYILFVFPVPAGAGLAFKAIAA 267 (310)
T ss_pred CCcchhhcccceeccccccceeEeeccccccccccccccchHHHHHHHHHhhcCcCcceeEEEeecccccchhHHHHHHH
Confidence 88999999999996666665544322 11 36899999999999999999887766654444433322222222221
Q ss_pred HHh----hcCCCchhhhhHhhhhhh
Q 010796 379 FII----SNFGPVDTWAHLGAAFTD 399 (501)
Q Consensus 379 ~i~----~~~~~Is~~AHLgGll~G 399 (501)
+.+ ..+..-++.||++|-+.|
T Consensus 268 ~~~a~~~l~~~~~n~~Ah~~gsl~G 292 (310)
T KOG2980|consen 268 YDFAGLILGWGFFNHAAHLSGSLFG 292 (310)
T ss_pred hhhcceeeccccchhHhhhcchHHH
Confidence 111 122456777999999999
No 11
>PF04511 DER1: Der1-like family; InterPro: IPR007599 The endoplasmic reticulum (ER) of the yeast Saccharomyces cerevisiae (Baker's yeast) contains a proteolytic system able to selectively degrade misfolded lumenal secretory proteins. For examination of the components involved in this degradation process, mutants were isolated. They could be divided into four complementation groups. The mutations led to stabilisation of two different substrates for this process, and the classes were called der for degradation in the ER. DER1 was cloned by complementation of the der1-2 mutation. The DER1 gene codes for a novel, hydrophobic protein that is localized to the ER. Deletion of DER1 abolished degradation of the substrate proteins, suggesting that the function of the Der1 protein may be specifically required for the degradation process associated with the ER []. Interestingly this family seems distantly related to the Rhomboid family of membrane peptidases. This family may also mediate degradation of misfolded proteins.
Probab=98.14 E-value=2.7e-05 Score=75.26 Aligned_cols=160 Identities=12% Similarity=0.115 Sum_probs=92.4
Q ss_pred hHHH-HHHHHHHHHHHHHHhcCCCCcccccchhhhhhhcchhhhhhcCcceeeeecccccCCH-HHHHHHHHHHHHHHHH
Q 010796 224 LYLI-ILVSIDVAVFLFEIASPIRNSEFGFFSLPLLYGAKINELILVGEWWRLVTPMFLHSGL-FHVALSCWALLTFGPQ 301 (501)
Q Consensus 224 P~vT-~LIai~v~VFll~~~~~~~~~~~~~l~~p~~~ga~~~~~i~~gq~WRl~Ts~FlH~s~-~HLlfNml~L~~fG~~ 301 (501)
||+| ..++.++++.++....-... ...--.++....++|+||++|+.|.-.+. ++.++|+..++..+..
T Consensus 2 PpVTR~~~~~~~~~s~l~~~~~~~~---------~~l~~~~~~v~~~~q~WRl~Tsff~~g~~~~~~l~~~~~l~~~s~~ 72 (197)
T PF04511_consen 2 PPVTRYWLISTVALSLLVSFGIISP---------YYLYFDWELVFKKFQIWRLFTSFFYFGPFSLNFLFNLYFLYQYSSS 72 (197)
T ss_pred ChhHHHHHHHHHHHHHHHHCCCCCH---------HHeeECcHHHhhhcCceeeEEEEEEEcCCCHHHHHHHHHHHHHhhH
Confidence 7888 77777777777654422111 11111222234579999999999986554 7999999999999999
Q ss_pred HHHh-hch--hHHHHHHHHHHHHHHHHhHhhCCC----ccccchHHHHHHHHHHHH-HHhcccchhh--hhhhHHHHHHH
Q 010796 302 VCKS-YGP--FTFFLIYTLGGISGNLTSFLHTPE----PTVGGTGPVFAIIGAWLI-YQFQNKDLIA--KDVSERMFQKA 371 (501)
Q Consensus 302 lE~~-lGs--~r~l~lyllsgl~g~l~~~l~~~~----~~vGaSGaVfGLlGa~~v-~~~~~~~~~~--~~~~~~l~~~~ 371 (501)
+|+. +.. ..++...+++++.-.++..+.... +..| +. ....+.+.|. ..+....... ..++...++.+
T Consensus 73 LE~~~f~~~~ady~~~ll~~~~~i~~~~~~~~~~~~~~~~l~-~~-l~~~l~Y~wsr~np~~~v~~~g~~~i~a~ylP~~ 150 (197)
T PF04511_consen 73 LEEGHFQGRSADYLWFLLFGASLILILSLLIGPYFFNIPFLG-SS-LSFALTYIWSRKNPNAQVSFFGLFTIKAKYLPWV 150 (197)
T ss_pred hccCCCCCCHHHHHHHHHHHHHHHHHHHHhhccchhHHHHHH-HH-HHHHHHHHHHHhCcccceeeEEEEEEChhhHHHH
Confidence 9998 332 467766666666666666554321 1222 22 3333333333 3333333322 23444444433
Q ss_pred HHHHHHHHHhhcCCCchhhhhHhhhhhh
Q 010796 372 ILSTALSFIISNFGPVDTWAHLGAAFTD 399 (501)
Q Consensus 372 li~l~l~~i~~~~~~Is~~AHLgGll~G 399 (501)
.+++.++.. +-+...++-|+++|
T Consensus 151 --~~~~~~l~~---~~~~~~~l~Gi~~G 173 (197)
T PF04511_consen 151 --LLAFSLLFG---GSSPIPDLLGILVG 173 (197)
T ss_pred --HHHHHHHhC---CCcHHHHHHHHHHH
Confidence 333333332 22455788898888
No 12
>PF08551 DUF1751: Eukaryotic integral membrane protein (DUF1751); InterPro: IPR013861 This entry is found in eukaryotic integral membrane proteins. Q12239 from SWISSPROT, a Saccharomyces cerevisiae (Baker's yeast) protein, has been shown to localise COP II vesicles [].
Probab=97.91 E-value=1.1e-05 Score=70.05 Aligned_cols=58 Identities=22% Similarity=0.332 Sum_probs=54.7
Q ss_pred cceeeeecccccCCHHHHHHHHHHHHHHHHHHHHhhchhHHHHHHHHHHHHHHHHhHh
Q 010796 271 EWWRLVTPMFLHSGLFHVALSCWALLTFGPQVCKSYGPFTFFLIYTLGGISGNLTSFL 328 (501)
Q Consensus 271 q~WRl~Ts~FlH~s~~HLlfNml~L~~fG~~lE~~lGs~r~l~lyllsgl~g~l~~~l 328 (501)
.+|+++|+.|++.++..+++|.+.+++.|+.+|+.||++.++-.+++.++.+|+...+
T Consensus 7 ~pWtl~T~~fve~~i~~~l~~~~~l~~~g~~lE~~WGs~E~lkFi~vv~~~tnl~~~~ 64 (99)
T PF08551_consen 7 YPWTLFTAGFVETNIIGLLFSLLTLFYGGRYLEPIWGSREFLKFILVVNVITNLLTFL 64 (99)
T ss_pred ehHHHHHHHHHHhHHHHHHHHHHHHHHhhHHHHHhcChHHHHHHHHHHHHHhHHHHHH
Confidence 6899999999999999999999999999999999999999999999999999887654
No 13
>KOG0858 consensus Predicted membrane protein [Function unknown]
Probab=97.38 E-value=0.00089 Score=66.25 Aligned_cols=98 Identities=14% Similarity=0.178 Sum_probs=70.3
Q ss_pred ccchHHH-HHHHHHHHHHHHHHhcCCCCcccccchhhhhhhcchhhhhhcCcceeeeecccccCC-HHHHHHHHHHHHHH
Q 010796 221 TSNLYLI-ILVSIDVAVFLFEIASPIRNSEFGFFSLPLLYGAKINELILVGEWWRLVTPMFLHSG-LFHVALSCWALLTF 298 (501)
Q Consensus 221 ~~~P~vT-~LIai~v~VFll~~~~~~~~~~~~~l~~p~~~ga~~~~~i~~gq~WRl~Ts~FlH~s-~~HLlfNml~L~~f 298 (501)
...|++| .....|++.=++....-.. |...--.++-.+.+.|+||++|+.+.-.. -+|.++||+.++-.
T Consensus 10 ~~iPpVTR~~~~~~v~tt~~~~l~lIs---------P~~l~~~p~Lv~kk~QiWRliTs~lyfg~~gf~fl~n~~FlyrY 80 (239)
T KOG0858|consen 10 LQIPPVTRYYTTACVVTTLLVRLDLIS---------PFQLYLNPELVFKKFQIWRLITSFLYFGPFGFDFLMNLYFLYRY 80 (239)
T ss_pred hcCChHHHHHHHHHHHHHHHHhhcccC---------chheEecHHHHHhHhHHHHhhhhhheeccccHHHHHHHHHHHHH
Confidence 4678999 8888888887766543221 11100112223468999999999998866 69999999999999
Q ss_pred HHHHHHhh-c--hhHHHHHHHHHHHHHHHHhH
Q 010796 299 GPQVCKSY-G--PFTFFLIYTLGGISGNLTSF 327 (501)
Q Consensus 299 G~~lE~~l-G--s~r~l~lyllsgl~g~l~~~ 327 (501)
...+|+-. . +..|+..+++++++-.+...
T Consensus 81 ~~~LE~g~f~~rtadf~~mllf~~~l~~~~~~ 112 (239)
T KOG0858|consen 81 SSMLEEGSFRGRTADFLYMLLFGAVLLTLTGL 112 (239)
T ss_pred HHHHhcCCCCCchhHHHHHHHHHHHHHHHHHH
Confidence 99999863 2 36788888888777765555
No 14
>KOG4463 consensus Uncharacterized conserved protein [Function unknown]
Probab=94.43 E-value=0.044 Score=55.14 Aligned_cols=60 Identities=17% Similarity=0.314 Sum_probs=52.5
Q ss_pred hcCcceeeeecccccCCHHHHHHHHHHHHHHHHHHHHhhchhHHHHHHHHHHHHHHHHhHh
Q 010796 268 LVGEWWRLVTPMFLHSGLFHVALSCWALLTFGPQVCKSYGPFTFFLIYTLGGISGNLTSFL 328 (501)
Q Consensus 268 ~~gq~WRl~Ts~FlH~s~~HLlfNml~L~~fG~~lE~~lGs~r~l~lyllsgl~g~l~~~l 328 (501)
...|+||++..-|.-.+-..+.+-++.||++ +.+||.+|+-||..+.+.+++.+-++...
T Consensus 47 ~y~qywrlL~~qF~~~n~~e~~~~l~I~Y~f-R~~ERlLGShky~~fiv~s~~~~~l~~~i 106 (323)
T KOG4463|consen 47 KYFQYWRLLMSQFAFSNTPELMFGLYILYYF-RVFERLLGSHKYSVFIVFSGTVSLLLEVI 106 (323)
T ss_pred HHHHHHHHHHHHHHhcCChHHHHHHHHHHHH-HHHHHHhccccceeehhHHHHHHHHHHHH
Confidence 3589999999999999999999988888776 88999999999999999898888776543
No 15
>KOG2890 consensus Predicted membrane protein [Function unknown]
Probab=94.05 E-value=0.053 Score=55.59 Aligned_cols=84 Identities=21% Similarity=0.304 Sum_probs=65.4
Q ss_pred CcceeeeecccccCCHHHHHHHHHHHHHHHHHHHHhhchhHHHHHHHHHHHHHHHHhH--------hhCC-----Ccccc
Q 010796 270 GEWWRLVTPMFLHSGLFHVALSCWALLTFGPQVCKSYGPFTFFLIYTLGGISGNLTSF--------LHTP-----EPTVG 336 (501)
Q Consensus 270 gq~WRl~Ts~FlH~s~~HLlfNml~L~~fG~~lE~~lGs~r~l~lyllsgl~g~l~~~--------l~~~-----~~~vG 336 (501)
..+|+++|+.|+-.+++-.+.|++.+.+-|..+|+.||+..++..|.+.-...+++.. ++.. .+..|
T Consensus 65 ~~~WtliTs~fie~~vw~V~~sv~~L~v~G~~lEp~Wg~~e~lkff~ivn~~~~l~v~v~~~l~Y~it~n~v~L~~~i~G 144 (326)
T KOG2890|consen 65 FFPWTLITSGFIELNVWDVLVSVLTLSVGGKFLEPNWGSLELLKFFAIVNGSTTLVVLVPALLLYMITDNHVYLYIPIHG 144 (326)
T ss_pred hhhHHHHhcchhhhhHHHHHHHHHheeecceeeccCCCCHHHHHHHHHhhchhHHHHHHHHHHHHHHhcCceEEEEEecc
Confidence 4789999999999999999999999999999999999999998888766544444322 2222 24678
Q ss_pred chHHHHHHHHHHHHHHh
Q 010796 337 GTGPVFAIIGAWLIYQF 353 (501)
Q Consensus 337 aSGaVfGLlGa~~v~~~ 353 (501)
..|..-|++.++=-..+
T Consensus 145 ~~gilaGilVa~kQllp 161 (326)
T KOG2890|consen 145 TTGILAGILVAWKQLLP 161 (326)
T ss_pred chHHHHHHHHHHHHHcC
Confidence 88988888776654443
No 16
>COG5291 Predicted membrane protein [Function unknown]
Probab=93.09 E-value=0.15 Score=50.96 Aligned_cols=51 Identities=12% Similarity=0.324 Sum_probs=39.1
Q ss_pred hhcCcceeeeecccccCC-HHHHHHHHHHHHHHHHHHHHh-hchh--HHHHHHHH
Q 010796 267 ILVGEWWRLVTPMFLHSG-LFHVALSCWALLTFGPQVCKS-YGPF--TFFLIYTL 317 (501)
Q Consensus 267 i~~gq~WRl~Ts~FlH~s-~~HLlfNml~L~~fG~~lE~~-lGs~--r~l~lyll 317 (501)
+.+-||||+||+..+-++ -+..++|+..+|--...+|+- +|+. .++...++
T Consensus 55 ~k~~qiwRlfTs~~~~~~~~~d~~M~vyf~Y~yS~~LE~g~f~~~lv~Y~~yl~~ 109 (313)
T COG5291 55 LKRLQIWRLFTSFLYFGKPTLDMFMHVYFLYRYSRMLEEGCFNTSLVEYFWYLLV 109 (313)
T ss_pred HHHHHHHHHHHHHHhhcCcchhHHHHHHHHHHHHHHHhccccCccHHHHHHHHHH
Confidence 467899999998777765 588999999999999999985 4554 55433333
No 17
>KOG3817 consensus Uncharacterized conserved protein [Function unknown]
Probab=78.78 E-value=10 Score=40.15 Aligned_cols=43 Identities=16% Similarity=0.159 Sum_probs=26.1
Q ss_pred HHHHHHHHHHHHHhhchheeEEeCcccCccchhHHHHHHHHHHHHHHHHHHHhhh
Q 010796 444 SLAILSWSVTAIAVGFVCKEIILGGHRGKRLQTLEAFAVISLLSQLLYLGLVHAW 498 (501)
Q Consensus 444 a~~~iaw~lt~lA~G~a~k~i~~~~~~~~~~~~le~~~~i~~~~ql~~~~~~~~~ 498 (501)
+-.++.|.+-+++.=+++-.+..- + + .|..+.+++|.+.+|..
T Consensus 252 S~~ilmWtLqli~lvl~Yfsvq~p----------~-~-a~A~iI~~lc~~~l~~p 294 (452)
T KOG3817|consen 252 SQTILMWTLQLIGLVLAYFSVQHP----------S-A-AIAAIIMVLCFVALYFP 294 (452)
T ss_pred hhhHHHHHHHHHHHHHHHHhcccH----------H-H-HHHHHHHHHHHHHHhcc
Confidence 446788988887777766444432 1 1 12344567777777754
No 18
>PRK09765 PTS system 2-O-a-mannosyl-D-glycerate specific transporter subunit IIABC; Provisional
Probab=56.33 E-value=3.4e+02 Score=31.11 Aligned_cols=23 Identities=13% Similarity=0.104 Sum_probs=18.8
Q ss_pred HHHHHHHHHhhcCCceeEecCcc
Q 010796 148 ELDSLDAYLGKLNTDAKFSTDQT 170 (501)
Q Consensus 148 ~aqaf~dYl~~~~i~~~v~~~~~ 170 (501)
+|+++.+--+++|.+.++|.++.
T Consensus 182 Aae~L~~aA~~~g~~i~vE~~g~ 204 (631)
T PRK09765 182 AAEYLEKAGRKLGVNVYVEKQGA 204 (631)
T ss_pred HHHHHHHHHHHCCCeEEEEecCC
Confidence 57889999999999999886544
No 19
>COG0705 Membrane associated serine protease [Amino acid transport and metabolism]
Probab=55.30 E-value=7.7 Score=37.82 Aligned_cols=75 Identities=20% Similarity=0.091 Sum_probs=57.6
Q ss_pred hhcCcceeeeecccccCCHHHHHHHHHHHHHHHHHHHHhhchhHHHHHHHHHHHHHHHHhHhhCCCccccchHHHHHHHH
Q 010796 267 ILVGEWWRLVTPMFLHSGLFHVALSCWALLTFGPQVCKSYGPFTFFLIYTLGGISGNLTSFLHTPEPTVGGTGPVFAIIG 346 (501)
Q Consensus 267 i~~gq~WRl~Ts~FlH~s~~HLlfNml~L~~fG~~lE~~lGs~r~l~lyllsgl~g~l~~~l~~~~~~vGaSGaVfGLlG 346 (501)
...|++|+++++.++|....|...+... ..+...+++...++.+++.......+.++.++-+.|+++
T Consensus 135 GASG~i~gllga~~~~~~~~~~~~~~~~-------------~~~~~~~~i~~~~~~~~~~~~~~~~~~va~~aHl~G~i~ 201 (228)
T COG0705 135 GASGAIFGLLGAYFLLFPFARILLLFLS-------------LPRPALILILIWLLYSLFSGAGSFGPSVAWSAHLGGLIG 201 (228)
T ss_pred chhHHHHHHHHHHHHHccccchhhhhcc-------------CchhHHHHHHHHHHHHHHHHhcCCchHHHHHHHHHHHHH
Confidence 4678899999999999998888887765 445566777777888888777766567888899999987
Q ss_pred HHHHHHhc
Q 010796 347 AWLIYQFQ 354 (501)
Q Consensus 347 a~~v~~~~ 354 (501)
..+.....
T Consensus 202 G~l~~~~~ 209 (228)
T COG0705 202 GLLLAALL 209 (228)
T ss_pred HHHHHHHH
Confidence 66655433
No 20
>PF09527 ATPase_gene1: Putative F0F1-ATPase subunit (ATPase_gene1)
Probab=43.50 E-value=1e+02 Score=23.36 Aligned_cols=42 Identities=26% Similarity=0.241 Sum_probs=31.8
Q ss_pred HHHHHHHHHHHHHHHHHHHhhch-hHHHHHHHHHHHHHHHHhH
Q 010796 286 FHVALSCWALLTFGPQVCKSYGP-FTFFLIYTLGGISGNLTSF 327 (501)
Q Consensus 286 ~HLlfNml~L~~fG~~lE~~lGs-~r~l~lyllsgl~g~l~~~ 327 (501)
..++.++....++|..+++.+|+ ..+..+.++-|+.+++.+.
T Consensus 8 ~~~~~~i~~g~~~G~~lD~~~~t~p~~~~~g~llG~~~g~~~~ 50 (55)
T PF09527_consen 8 FTMAAPILVGFFLGYWLDKWFGTSPWFTLIGLLLGIAAGFYNV 50 (55)
T ss_pred HHHHHHHHHHHHHHHHHHHHcCCChHHHHHHHHHHHHHHHHHH
Confidence 35677888889999999999998 5556666666777766554
No 21
>PF09413 DUF2007: Domain of unknown function (DUF2007); InterPro: IPR018551 This is a family of proteins with unknown function. ; PDB: 2HFV_A.
Probab=33.93 E-value=50 Score=25.79 Aligned_cols=30 Identities=10% Similarity=0.051 Sum_probs=20.2
Q ss_pred hhccCCChhHHHHHHHHHhhcCCceeEecC
Q 010796 139 RSGEINAKTELDSLDAYLGKLNTDAKFSTD 168 (501)
Q Consensus 139 ~~~~~~~~~~aqaf~dYl~~~~i~~~v~~~ 168 (501)
++...+|+-.|+...+.|+..||++.++.+
T Consensus 2 ~l~~~~~~~ea~~i~~~L~~~gI~~~v~~~ 31 (67)
T PF09413_consen 2 KLYTAGDPIEAELIKGLLEENGIPAFVKNE 31 (67)
T ss_dssp EEEEE--HHHHHHHHHHHHHTT--EE--S-
T ss_pred EEEEcCCHHHHHHHHHHHHhCCCcEEEECC
Confidence 356778999999999999999999999853
No 22
>PF11823 DUF3343: Protein of unknown function (DUF3343); InterPro: IPR021778 This family of proteins are functionally uncharacterised. This protein is found in bacteria and archaea. Proteins in this family are typically between 78 to 102 amino acids in length.
Probab=31.83 E-value=80 Score=25.39 Aligned_cols=45 Identities=9% Similarity=-0.004 Sum_probs=35.0
Q ss_pred hccCCChhHHHHHHHHHhhcCCceeEecCccc-----------hhhhHHHHHhhhh
Q 010796 140 SGEINAKTELDSLDAYLGKLNTDAKFSTDQTT-----------ERNLVAAQLSISK 184 (501)
Q Consensus 140 ~~~~~~~~~aqaf~dYl~~~~i~~~v~~~~~~-----------de~~~~~~~~e~~ 184 (501)
+..|++...|-++.++|++.|++.++.|-..+ ++++.+.+++.++
T Consensus 5 ~i~F~st~~a~~~ek~lk~~gi~~~liP~P~~i~~~CG~al~~~~~d~~~i~~~l~ 60 (73)
T PF11823_consen 5 LITFPSTHDAMKAEKLLKKNGIPVRLIPTPREISAGCGLALRFEPEDLEKIKEILE 60 (73)
T ss_pred EEEECCHHHHHHHHHHHHHCCCcEEEeCCChhccCCCCEEEEEChhhHHHHHHHHH
Confidence 67789999999999999999999999875543 4444555555554
No 23
>TIGR02854 spore_II_GA sigma-E processing peptidase SpoIIGA. Members of this protein family are the stage II sporulation protein SpoIIGA. This protein acts as an activating protease for Sigma-E, one of several specialized sigma factors of the sporulation process in Bacillus subtilis and related endospore-forming bacteria.
Probab=27.84 E-value=6.8e+02 Score=25.69 Aligned_cols=30 Identities=10% Similarity=0.171 Sum_probs=24.9
Q ss_pred HHHHHHHHHHHHHHHHHHHHhhchhHHHHH
Q 010796 285 LFHVALSCWALLTFGPQVCKSYGPFTFFLI 314 (501)
Q Consensus 285 ~~HLlfNml~L~~fG~~lE~~lGs~r~l~l 314 (501)
+..+++|.+.|+..+..+-+....+|.++-
T Consensus 10 l~Nf~~d~~LL~~t~~~lk~~~~~~Rll~g 39 (288)
T TIGR02854 10 LENFIIDYFLLYLTARTLKDKVSQWRLLLA 39 (288)
T ss_pred HHHHHHHHHHHHHHHHHhhccchHHHHHHH
Confidence 356789999999999999998888887543
No 24
>PF03419 Peptidase_U4: Sporulation factor SpoIIGA This family belongs to family U4 of the peptidase classification.; InterPro: IPR005081 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. The peptidases families associated with clan U- have an unknown catalytic mechanism as the protein fold of the active site domain and the active site residues have not been reported. This group of peptidases belong to the MEROPS peptidase family U4 (SpoIIGA peptidase family, clan U-). Sporulation in bacteria such as Bacillus subtilis involves the formation of a polar septum, which divides the sporangium into a mother cell and a forespore. The sigma E factor, which is encoded within the spoIIG operon, is a cell-specific regulatory protein that directs gene transcription in the mother cell. Sigma E is synthesised as an inactive proprotein pro-sigma E, which is converted to the mature factor by the putative processing enzyme SpoIIGA []. ; GO: 0004190 aspartic-type endopeptidase activity, 0006508 proteolysis, 0030436 asexual sporulation
Probab=25.45 E-value=7.3e+02 Score=25.26 Aligned_cols=29 Identities=10% Similarity=0.202 Sum_probs=24.3
Q ss_pred HHHHHHHHHHHHHHHHHHHHhhchhHHHH
Q 010796 285 LFHVALSCWALLTFGPQVCKSYGPFTFFL 313 (501)
Q Consensus 285 ~~HLlfNml~L~~fG~~lE~~lGs~r~l~ 313 (501)
+..++.|.+.||..+..+-+....+|+++
T Consensus 10 l~N~~md~~lL~~t~~~~~~~~~~~Rll~ 38 (293)
T PF03419_consen 10 LVNFLMDYFLLWLTARLLKRRASRWRLLL 38 (293)
T ss_pred HHHHHHHHHHHHHHHHHhcCCCcHHHHHH
Confidence 35678999999999999999999898753
No 25
>PF07226 DUF1422: Protein of unknown function (DUF1422); InterPro: IPR009867 This family consists of several hypothetical bacterial proteins of around 120 residues in length. The function of this family is unknown.
Probab=24.64 E-value=2.4e+02 Score=25.49 Aligned_cols=20 Identities=25% Similarity=0.306 Sum_probs=12.4
Q ss_pred hhHHHHHHHHHHHHHHHHhH
Q 010796 308 PFTFFLIYTLGGISGNLTSF 327 (501)
Q Consensus 308 s~r~l~lyllsgl~g~l~~~ 327 (501)
.++.+++-++.|+.+|....
T Consensus 8 ek~tLlLaliaGl~~n~~~s 27 (117)
T PF07226_consen 8 EKKTLLLALIAGLCGNATFS 27 (117)
T ss_pred chhhHHHHHHHHHhccchhH
Confidence 35566677777777765443
No 26
>TIGR01299 synapt_SV2 synaptic vesicle protein SV2. This model describes a tightly conserved subfamily of the larger family of sugar (and other) transporters described by pfam model pfam00083. Members of this subfamily include closely related forms SV2A and SV2B of synaptic vesicle protein from vertebrates and a more distantly related homolog (below trusted cutoff) from Drosophila melanogaster. Members are predicted to have two sets of six transmembrane helices.
Probab=24.27 E-value=1e+03 Score=27.84 Aligned_cols=30 Identities=3% Similarity=-0.079 Sum_probs=19.1
Q ss_pred HHHHHHHHHhhchhHHHHHHHHHHHHHHHH
Q 010796 296 LTFGPQVCKSYGPFTFFLIYTLGGISGNLT 325 (501)
Q Consensus 296 ~~fG~~lE~~lGs~r~l~lyllsgl~g~l~ 325 (501)
.+++..+-+++|+++.+.+.++...++.++
T Consensus 612 ~il~g~L~Dr~GRr~~l~~~~~lsai~~ll 641 (742)
T TIGR01299 612 NIVSALLMDKIGRLRMLAGSMVLSCISCFF 641 (742)
T ss_pred HHHHHHHHHHhCCHHHHHHHHHHHHHHHHH
Confidence 345556667899998876666555544444
No 27
>PRK11056 hypothetical protein; Provisional
Probab=23.22 E-value=2.8e+02 Score=25.17 Aligned_cols=20 Identities=25% Similarity=0.092 Sum_probs=13.5
Q ss_pred hhHHHHHHHHHHHHHHHHhH
Q 010796 308 PFTFFLIYTLGGISGNLTSF 327 (501)
Q Consensus 308 s~r~l~lyllsgl~g~l~~~ 327 (501)
.++.+++-++.|+.++....
T Consensus 8 ek~tLlLaliaGl~~ng~fs 27 (120)
T PRK11056 8 EKGTLLLALIAGLSINGTFA 27 (120)
T ss_pred chhhHHHHHHHHHhhchhhH
Confidence 45667777777777766543
No 28
>PRK10263 DNA translocase FtsK; Provisional
Probab=23.12 E-value=2e+02 Score=35.98 Aligned_cols=15 Identities=20% Similarity=0.397 Sum_probs=8.1
Q ss_pred HHHHHHHHHHHHHHh
Q 010796 228 ILVSIDVAVFLFEIA 242 (501)
Q Consensus 228 ~LIai~v~VFll~~~ 242 (501)
.++++.+.+|++..+
T Consensus 27 gIlLlllAlfL~lAL 41 (1355)
T PRK10263 27 LILIVLFAVWLMAAL 41 (1355)
T ss_pred HHHHHHHHHHHHHHH
Confidence 455555566655433
No 29
>TIGR02230 ATPase_gene1 F0F1-ATPase subunit, putative. This model represents a protein found encoded in F1F0-ATPase operons in several genomes, including Methanosarcina barkeri (archaeal) and Chlorobium tepidum (bacterial). It is a small protein (about 100 amino acids) with long hydrophic stretches and is presumed to be a subunit of the enzyme.
Probab=22.96 E-value=2.7e+02 Score=24.45 Aligned_cols=41 Identities=17% Similarity=0.207 Sum_probs=29.3
Q ss_pred HHHHHHHHHHHHHHHHHHhhch-hHHHHHHHHHHHHHHHHhH
Q 010796 287 HVALSCWALLTFGPQVCKSYGP-FTFFLIYTLGGISGNLTSF 327 (501)
Q Consensus 287 HLlfNml~L~~fG~~lE~~lGs-~r~l~lyllsgl~g~l~~~ 327 (501)
+++.-.+.-.++|..+.+.+|+ ..+.+++++.|++.++...
T Consensus 51 ~~v~pil~G~~lG~WLD~~~~t~~~~tl~~lllGv~~G~~n~ 92 (100)
T TIGR02230 51 SVAIPTLLGVAVGIWLDRHYPSPFSWTLTMLIVGVVIGCLNA 92 (100)
T ss_pred HHHHHHHHHHHHHHHHHhhcCCCcHHHHHHHHHHHHHHHHHH
Confidence 5566667778899999999986 3455666677777766554
No 30
>PF12156 ATPase-cat_bd: Putative metal-binding domain of cation transport ATPase; InterPro: IPR021993 This domain is found in bacteria, and is approximately 90 amino acids in length. It is found associated with PF00403 from PFAM, PF00122 from PFAM, PF00702 from PFAM. The cysteine-rich nature and composition suggest this might be a cation-binding domain; most members are annotated as being cation transport ATPases.
Probab=21.23 E-value=83 Score=26.62 Aligned_cols=42 Identities=14% Similarity=0.122 Sum_probs=31.5
Q ss_pred HHHHHHhhhcccccCCCCCCchhhhhhhhhhccCCChhHHHHHHHH
Q 010796 110 ILESYLAKLKDDSIQNSSESSGEIEELHSRSGEINAKTELDSLDAY 155 (501)
Q Consensus 110 ~l~~y~~kl~~~~~~~s~~~~~~~~~~m~~~~~~~~~~~aqaf~dY 155 (501)
-||+|+++..+....|...-.++ ...+..+++|...+.|++.
T Consensus 43 gL~~yY~~r~~~~~~p~~~~~~~----~~~~~~~D~~~v~~~fv~~ 84 (88)
T PF12156_consen 43 GLESYYQKRTDPGLSPDPLVPDQ----LEDLAYYDDPEVQQKFVRF 84 (88)
T ss_pred chHHHHhccCccCCCCccccccc----HHHHHHcCCHHHHHHHhcc
Confidence 48999999988887776622222 3468889999999999864
No 31
>COG1030 NfeD Membrane-bound serine protease (ClpP class) [Posttranslational modification, protein turnover, chaperones]
Probab=21.13 E-value=1.1e+03 Score=25.93 Aligned_cols=27 Identities=26% Similarity=0.437 Sum_probs=17.6
Q ss_pred hhCCC-ccccchHHHHHHHHHHHHHHhc
Q 010796 328 LHTPE-PTVGGTGPVFAIIGAWLIYQFQ 354 (501)
Q Consensus 328 l~~~~-~~vGaSGaVfGLlGa~~v~~~~ 354 (501)
++.|. ..+|.+|++.-++|........
T Consensus 299 ~~~p~fGvigl~Gii~~iiG~~~L~~~~ 326 (436)
T COG1030 299 AFVPGFGVIGLLGIILFIIGLLLLFPSG 326 (436)
T ss_pred HhcccchHHHHHHHHHHHHhhhhccCCC
Confidence 34443 4677788888888877765543
No 32
>TIGR00834 ae anion exchange protein. They preferentially catalyze anion exchange (antiport) reactions, typically acting as HCO3-:Cl- antiporters, but also transporting a range of other inorganic and organic anions. Additionally, renal Na+:HCO3- cotransporters have been found to be members of the AE family. They catalyze the reabsorption of HCO3- in the renal proximal tubule.
Probab=20.84 E-value=5.7e+02 Score=30.83 Aligned_cols=62 Identities=16% Similarity=0.166 Sum_probs=44.9
Q ss_pred HHHHHHHHHHHHHHHHHHHHhhchhHHHHHHHHHHHHHHHHhHhhCCCc--cccchHHHHHHHH
Q 010796 285 LFHVALSCWALLTFGPQVCKSYGPFTFFLIYTLGGISGNLTSFLHTPEP--TVGGTGPVFAIIG 346 (501)
Q Consensus 285 ~~HLlfNml~L~~fG~~lE~~lGs~r~l~lyllsgl~g~l~~~l~~~~~--~vGaSGaVfGLlG 346 (501)
+.=.+.|+.--..||..+++.-+..-=..=.++|..++++.+.++.+.| .+|.+|-+.-+..
T Consensus 376 ifiyFA~L~PaIaFG~ll~~~T~g~~gv~E~Llstai~Giifslf~GQPL~IlG~TGPilvF~~ 439 (900)
T TIGR00834 376 IFIYFAALSPAITFGGLLGEKTRNMMGVSELLISTAVQGVLFALLAAQPLLVVGFSGPLLVFEE 439 (900)
T ss_pred HHHHHHHhhHHhhHHHHHHHhhCCcchHHHHHHHHHHHHHHHhhhcCCceEEecCcccHHHHHH
Confidence 4556778888899999999886665445556677777778888887764 6798996654444
No 33
>PF10066 DUF2304: Uncharacterized conserved protein (DUF2304); InterPro: IPR019277 This entry represents hypothetical archaeal and bacterial proteins that have no known function.
Probab=20.21 E-value=3.8e+02 Score=23.52 Aligned_cols=18 Identities=28% Similarity=0.012 Sum_probs=13.0
Q ss_pred hcCCC-chhhhhHhhhhhh
Q 010796 382 SNFGP-VDTWAHLGAAFTD 399 (501)
Q Consensus 382 ~~~~~-Is~~AHLgGll~G 399 (501)
..+|+ .++.||+-|+-.|
T Consensus 47 ~ifP~~~~~vA~~lGi~~~ 65 (115)
T PF10066_consen 47 SIFPNILDWVAKLLGIGRP 65 (115)
T ss_pred HhhhhHHHHHHHHHCCCch
Confidence 44555 6777999888777
No 34
>TIGR02916 PEP_his_kin putative PEP-CTERM system histidine kinase. Members of this protein family have a novel N-terminal domain, a single predicted membrane-spanning helix, and a predicted cystosolic histidine kinase domain. We designate this protein PrsK, and its companion DNA-binding response regulator protein (TIGR02915) PrsR. These predicted signal-transducing proteins appear to enable enhancer-dependent transcriptional activation. The prsK gene is often associated with exopolysaccharide biosynthesis genes.
Probab=20.02 E-value=1e+03 Score=27.02 Aligned_cols=41 Identities=15% Similarity=0.039 Sum_probs=22.4
Q ss_pred cccchHHHHHHHHHHHHHHhcccch--hhhhhhHHHHHHHHHH
Q 010796 334 TVGGTGPVFAIIGAWLIYQFQNKDL--IAKDVSERMFQKAILS 374 (501)
Q Consensus 334 ~vGaSGaVfGLlGa~~v~~~~~~~~--~~~~~~~~l~~~~li~ 374 (501)
..++-|++.+++-.+......+.+. ....+++.+....+..
T Consensus 193 ~~~~rg~~~~~~~~~~~~~~~r~~~~~~~~~~sr~~~~~~~~~ 235 (679)
T TIGR02916 193 VWPARGLVAALVVPLIAVSAARNPDWSVRIAVSREMAFHSATL 235 (679)
T ss_pred HHHHHHHHHHHHHHHHHHHHhcccCCCcceeechHHHHHHHHH
Confidence 4455788888887776665553222 2344455544443333
Done!