Query 012374
Match_columns 465
No_of_seqs 287 out of 1704
Neff 6.1
Searched_HMMs 46136
Date Fri Mar 29 01:58:26 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/012374.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/012374hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PTZ00101 rhomboid-1 protease; 100.0 6.3E-32 1.4E-36 268.5 20.7 193 215-409 44-241 (278)
2 KOG2289 Rhomboid family protei 100.0 1.1E-29 2.3E-34 254.9 5.4 235 218-455 64-300 (316)
3 PRK10907 intramembrane serine 100.0 1.1E-27 2.5E-32 238.3 16.9 174 226-408 96-270 (276)
4 COG0705 Membrane associated se 99.9 1.7E-24 3.7E-29 209.4 14.0 188 223-412 16-215 (228)
5 KOG2290 Rhomboid family protei 99.9 1.7E-23 3.7E-28 213.9 9.4 173 269-457 448-623 (652)
6 PF01694 Rhomboid: Rhomboid fa 99.9 1.6E-22 3.4E-27 181.0 3.6 140 268-409 2-143 (145)
7 KOG2632 Rhomboid family protei 99.6 1E-15 2.2E-20 149.2 10.8 172 221-405 12-195 (258)
8 KOG2980 Integral membrane prot 98.9 2E-09 4.3E-14 107.2 5.7 180 225-413 117-306 (310)
9 PF04511 DER1: Der1-like famil 98.4 4E-06 8.7E-11 80.1 12.0 170 223-406 1-180 (197)
10 PF08551 DUF1751: Eukaryotic i 98.2 2.7E-07 5.9E-12 78.9 0.3 58 271-328 7-64 (99)
11 KOG0858 Predicted membrane pro 97.7 8.1E-05 1.8E-09 72.5 6.4 168 222-405 11-184 (239)
12 KOG2890 Predicted membrane pro 97.4 0.00017 3.6E-09 72.4 5.3 142 270-414 65-221 (326)
13 KOG4463 Uncharacterized conser 93.6 0.055 1.2E-06 53.7 3.0 60 268-328 47-106 (323)
14 COG5291 Predicted membrane pro 91.9 0.15 3.3E-06 50.2 3.5 43 267-309 55-99 (313)
15 COG0705 Membrane associated se 70.6 7.7 0.00017 37.4 5.2 74 268-354 136-209 (228)
16 PF11992 DUF3488: Domain of un 70.6 72 0.0016 32.8 12.6 60 385-459 121-180 (325)
17 PF03419 Peptidase_U4: Sporula 65.6 45 0.00097 33.7 9.7 70 286-359 11-84 (293)
18 TIGR01299 synapt_SV2 synaptic 64.6 2.7E+02 0.0059 32.2 19.0 38 288-326 212-249 (742)
19 TIGR00834 ae anion exchange pr 48.9 1.5E+02 0.0033 35.0 11.4 65 284-349 375-442 (900)
20 PF11833 DUF3353: Protein of u 48.1 2E+02 0.0044 27.6 10.4 21 391-411 145-165 (194)
21 TIGR01299 synapt_SV2 synaptic 46.5 3.8E+02 0.0083 31.0 14.1 28 297-324 613-640 (742)
22 TIGR02854 spore_II_GA sigma-E 45.2 2E+02 0.0044 29.1 10.5 71 285-359 10-84 (288)
23 PF10011 DUF2254: Predicted me 43.5 4.1E+02 0.0089 27.9 14.1 27 388-414 93-119 (371)
24 PRK10255 PTS system N-acetyl g 42.7 47 0.001 37.7 5.9 63 389-461 95-157 (648)
25 PF06609 TRI12: Fungal trichot 39.4 6.1E+02 0.013 28.7 14.8 43 287-330 87-129 (599)
26 KOG1172 Na+-independent Cl/HCO 39.3 3.3E+02 0.0071 32.1 11.8 118 284-407 366-490 (876)
27 PF09527 ATPase_gene1: Putativ 38.3 95 0.0021 23.2 5.3 42 286-327 8-50 (55)
28 KOG0255 Synaptic vesicle trans 37.3 1.7E+02 0.0037 31.3 9.1 45 285-330 125-169 (521)
29 COG4769 Predicted membrane pro 35.6 2.3E+02 0.0051 26.8 8.3 50 305-354 51-101 (181)
30 COG1575 MenA 1,4-dihydroxy-2-n 35.0 5.3E+02 0.011 26.7 12.1 20 337-356 153-172 (303)
31 TIGR02185 Trep_Strep conserved 30.9 4.7E+02 0.01 24.8 10.2 17 337-353 37-53 (189)
32 PF07301 DUF1453: Protein of u 30.6 3.3E+02 0.0071 25.2 8.4 29 386-414 54-82 (148)
33 PF01032 FecCD: FecCD transpor 29.2 2.5E+02 0.0054 28.8 8.3 31 434-464 174-204 (311)
34 PRK10263 DNA translocase FtsK; 28.7 1.2E+02 0.0027 37.1 6.6 13 228-240 27-39 (1355)
35 TIGR02005 PTS-IIBC-alpha PTS s 25.8 82 0.0018 34.9 4.3 63 389-461 136-198 (524)
36 PF10066 DUF2304: Uncharacteri 25.7 2E+02 0.0043 25.0 5.9 20 381-400 46-66 (115)
37 PF15183 MRAP: Melanocortin-2 25.2 56 0.0012 27.4 2.1 24 432-455 33-56 (90)
38 COG4393 Predicted membrane pro 25.1 8.3E+02 0.018 25.8 11.9 97 306-408 29-138 (405)
39 PF04632 FUSC: Fusaric acid re 25.0 3.8E+02 0.0083 29.7 9.5 15 392-406 471-485 (650)
40 COG3263 NhaP-type Na+/H+ and K 24.2 7E+02 0.015 27.5 10.6 56 283-341 182-246 (574)
41 TIGR03869 F420-0_ABCperm propo 23.7 8E+02 0.017 25.4 10.9 28 437-464 186-213 (325)
42 TIGR00806 rfc RFC reduced fola 23.6 1E+03 0.023 26.4 12.6 32 292-324 76-107 (511)
43 KOG2533 Permease of the major 22.7 3.5E+02 0.0077 29.7 8.4 16 391-406 179-194 (495)
44 PTZ00207 hypothetical protein; 22.6 1.1E+03 0.025 26.4 15.4 31 297-328 80-110 (591)
45 PRK10263 DNA translocase FtsK; 22.2 1.6E+03 0.035 28.1 15.0 14 337-350 141-154 (1355)
46 PF12732 YtxH: YtxH-like prote 22.1 95 0.0021 24.7 3.0 20 390-409 3-22 (74)
47 PF03814 KdpA: Potassium-trans 22.1 4.1E+02 0.009 29.7 8.6 142 299-464 46-196 (552)
48 cd03381 PAP2_glucose_6_phospha 21.8 7.1E+02 0.015 24.6 9.6 17 392-408 136-152 (235)
49 COG3105 Uncharacterized protei 21.5 92 0.002 28.2 2.9 22 388-409 7-28 (138)
50 TIGR00680 kdpA K+-transporting 21.2 7.1E+02 0.015 27.9 10.1 144 298-464 53-204 (563)
51 PRK10712 PTS system fructose-s 20.9 1.6E+02 0.0035 32.9 5.4 19 389-407 313-331 (563)
52 COG4395 Uncharacterized protei 20.9 2E+02 0.0042 29.4 5.5 27 437-463 58-84 (281)
53 COG1296 AzlC Predicted branche 20.6 6E+02 0.013 25.2 8.8 21 388-408 210-230 (238)
54 PF12122 DUF3582: Protein of u 20.4 74 0.0016 27.4 2.1 25 104-128 43-67 (101)
No 1
>PTZ00101 rhomboid-1 protease; Provisional
Probab=100.00 E-value=6.3e-32 Score=268.54 Aligned_cols=193 Identities=26% Similarity=0.333 Sum_probs=148.5
Q ss_pred hhhcccCcchHHH-HHHHHHHHHHHHHHhcCCCCccccchhhhhhhhchhhhhhhcCceeeeeecccccCCHHHHHHHHH
Q 012374 215 LQRTEETSNLYLI-ILVSIDVAVFLFEIASPIRNSEFGFFSLPLLYGAKINELILVGEWWRLVTPMFLHSGLFHVALSCW 293 (465)
Q Consensus 215 ~~~~~~~~~p~vt-~Li~inv~VFil~~~~~~~~~~~~l~~~~l~~ga~~~~~i~~gq~WRL~Ts~FlH~gl~HLl~Nml 293 (465)
++++++.+.+.+| .++++|+++|++............-.+....+|++.++.+.++||||++|++|+|.|+.|+++||+
T Consensus 44 er~Fp~f~i~~l~~~Iiii~iivfil~l~~~~~~~l~p~~~~L~~~Ga~~~~~i~~gq~WRLiT~~FlH~~~~HLl~Nm~ 123 (278)
T PTZ00101 44 NLIFPHFTWKSFIMAISIIQIIVFIISVSIKPADFLTPSDSLLVTLGANVASRIKQGEIHRLILPIFLHANIFHTFFNVF 123 (278)
T ss_pred HHHcCCccHHHHHHHHHHHHHHHHHHHHHhcccccCCCCHHHHHHHhCcchhhhhcCCCHHHHHHHHHccCHHHHHHHHH
Confidence 3478999999999 999999999998766322111001112345678888888899999999999999999999999999
Q ss_pred HHHHHHHHHHHhhchhHHHHHHHHHhhhhhhhhcccCC-CCccCchHHHHHHHHHHHHHHhcchhhhhhhhHHHHHHHHH
Q 012374 294 ALLTFGPQVCKSYGPFTFFLIYTLGGISGNLTSFLHTP-EPTVGGTGPVFAIIGAWLIYQFQNKDLIAKDVSERMFQKAI 372 (465)
Q Consensus 294 ~L~~fG~~LE~~~Gs~rfl~lYllsGi~G~l~s~l~~p-~~~VGaSGaVfGLlga~~~~~~~~~~~l~~~~~~~l~~~~i 372 (465)
+++.+|..+|+.+|++|++++|+++|++|++++.++.+ ..++||||++||++|++++.....|.....+ .+.....+
T Consensus 124 ~l~~~G~~lE~~~G~~r~~ilYl~sGi~G~l~s~~~~~~~~svGASgAifGLiGa~~~~lil~w~~~~~~--~~~~~~~i 201 (278)
T PTZ00101 124 FQLRMGFTLEKNYGIVKIIILYFLTGIYGNILSSSVTYCPIKVGASTSGMGLLGIVTSELILLWHVIRHR--ERVVFNII 201 (278)
T ss_pred HHHHHHHHHHHHHChHHHHHHHHHHHHHHHHHHHHHccCCcEEehhHHHHHHHHHHHHHHHHHHHhhccH--HHHHHHHH
Confidence 99999999999999999999999999999999988765 4689999999999999987766555543221 11111111
Q ss_pred HHHHHHH--HH-hcCCchhHHHHHHHHHHHHHHHHHhhcc
Q 012374 373 LSTALSF--II-SNFGPVDTWAHLGAAFTGIIYGFLTCPL 409 (465)
Q Consensus 373 i~~~l~~--ll-~~~~~is~~aHLgG~L~G~llg~l~~~~ 409 (465)
++.++.+ .. ...+++|++||+||+++|+++|+++.++
T Consensus 202 ~~~li~~~l~~~~~g~~Id~~aHlGG~i~G~llg~~~~~~ 241 (278)
T PTZ00101 202 FFSLISFFYYFTFNGSNIDHVGHLGGLLSGISMGILYNSQ 241 (278)
T ss_pred HHHHHHHHHHHhcCCCCccHHHHHHHHHHHHHHHHHHHhh
Confidence 1111111 11 2246799999999999999999998654
No 2
>KOG2289 consensus Rhomboid family proteins [Signal transduction mechanisms]
Probab=99.96 E-value=1.1e-29 Score=254.91 Aligned_cols=235 Identities=24% Similarity=0.326 Sum_probs=167.6
Q ss_pred cccCcchHHH-HHHHHHHHHHHHHHhcCCCCccccchhhhhhhhchhhhhhhcCceeeeeecccccCCHHHHHHHHHHHH
Q 012374 218 TEETSNLYLI-ILVSIDVAVFLFEIASPIRNSEFGFFSLPLLYGAKINELILVGEWWRLVTPMFLHSGLFHVALSCWALL 296 (465)
Q Consensus 218 ~~~~~~p~vt-~Li~inv~VFil~~~~~~~~~~~~l~~~~l~~ga~~~~~i~~gq~WRL~Ts~FlH~gl~HLl~Nml~L~ 296 (465)
.+..+.|.+. .+..+.+..|.++..................++.+....+.++|+||++||||+|+|+.||++||+.++
T Consensus 64 ~~~~~~~~f~~~~~~~~l~~f~~~~~~~n~~~~~s~~~~~~~~~~~i~~~~~r~E~WRllTym~LHaGi~HL~~N~~~ql 143 (316)
T KOG2289|consen 64 PKCCPPPIFMLCLAIVFLGRFSFQGLRENPLLGPSSLTLEKMGGLLIYKPVHRGELWRLLTYMWLHAGIFHLLLNMLSQL 143 (316)
T ss_pred cccCCCchhhhhhhhhhhheeeeeeeccCCccCcCCCCccccCCceecChhhhchhHHHHHHHHHhcCHHHHHHHHHHHH
Confidence 3444555454 444446666665533111110000001223455556666789999999999999999999999999999
Q ss_pred HHHHHHHHhhchhHHHHHHHHHhhhhhhhhcccCCC-CccCchHHHHHHHHHHHHHHhcchhhhhhhhHHHHHHHHHHHH
Q 012374 297 TFGPQVCKSYGPFTFFLIYTLGGISGNLTSFLHTPE-PTVGGTGPVFAIIGAWLIYQFQNKDLIAKDVSERMFQKAILST 375 (465)
Q Consensus 297 ~fG~~LE~~~Gs~rfl~lYllsGi~G~l~s~l~~p~-~~VGaSGaVfGLlga~~~~~~~~~~~l~~~~~~~l~~~~ii~~ 375 (465)
++|..+|..+|.+|+.++|++||++|++++.++.+. ++|||||++|||+||++.....||..+.... .++..+++++
T Consensus 144 ~iGi~LE~~~G~~RiglIYl~gg~aGSlls~l~d~~~~sVGASggvfaLlgA~Ls~l~~Nw~~m~~~~--~~l~~ll~Ii 221 (316)
T KOG2289|consen 144 FIGIPLEQVHGFLRIGLIYLAGGVAGSLLSSLFDPNSISVGASGGVFALLGAHLSNLLTNWTIMKNKF--AALRTLLIII 221 (316)
T ss_pred hccccHHhhcCceEEeeehhhhhhhhHHHHHHhccCCceecccHHHHHHHHHHHHHHHhhHHHhcchH--HHHHHHHHHH
Confidence 999999999999999999999999999999999986 5999999999999999999999999875332 2344455666
Q ss_pred HHHHHHhcCCchhHHHHHHHHHHHHHHHHHhhcccccCCcCcCCccchhhHHhhhccccchhHHHHHHHHHHHHHHHHhh
Q 012374 376 ALSFIISNFGPVDTWAHLGAAFTGIIYGFLTCPLVQLGDASSRNSQEEGITLIRQYANPCKSLIVFTIFVIILGSFIFVF 455 (465)
Q Consensus 376 ~l~~ll~~~~~is~~aHLgG~L~G~llg~l~~~~~~~~~~~~~~~~~~~~~~~r~~~~~~~~ll~f~i~vivl~~~lf~i 455 (465)
+++..++..+++++++|+||+++|..+|++..+..++.....+..... ....++..+.++.+..++.+++.+.+.+|.+
T Consensus 222 ~i~l~~G~~~~~~~~~h~gg~~~G~~~~fil~~~g~~~~~~~~~~~~~-~~~~~~~~q~~~w~~~~~~~v~~~~~~~~~i 300 (316)
T KOG2289|consen 222 FINLDLGFAPYVDNFAHIGGLLAGFLLGFVLHIGGQLGGITIGLIVLR-VFSKRLPYQLLLWIVLLVYLVAGLFASLFNI 300 (316)
T ss_pred HHHHhhccccceeccccccccCCCcchhHHhhhccceeEEeccceeee-ccccccccchHHHHHHHHHHHHHHHHHHHHh
Confidence 677778888999999999999999999999999888776554332100 0111222223445555555555554433333
No 3
>PRK10907 intramembrane serine protease GlpG; Provisional
Probab=99.95 E-value=1.1e-27 Score=238.29 Aligned_cols=174 Identities=18% Similarity=0.155 Sum_probs=129.0
Q ss_pred HH-HHHHHHHHHHHHHHhcCCCCccccchhhhhhhhchhhhhhhcCceeeeeecccccCCHHHHHHHHHHHHHHHHHHHH
Q 012374 226 LI-ILVSIDVAVFLFEIASPIRNSEFGFFSLPLLYGAKINELILVGEWWRLVTPMFLHSGLFHVALSCWALLTFGPQVCK 304 (465)
Q Consensus 226 vt-~Li~inv~VFil~~~~~~~~~~~~l~~~~l~~ga~~~~~i~~gq~WRL~Ts~FlH~gl~HLl~Nml~L~~fG~~LE~ 304 (465)
+| +++++|++||++........ ...+..........+||||++|++|+|.|+.||++||+++|.+|..+|+
T Consensus 96 ~T~~li~i~i~vf~l~~~~~~~~--------~~~~l~~~~~~~~~~q~WRl~T~~flH~~~~Hl~fNml~l~~lG~~iE~ 167 (276)
T PRK10907 96 LTLGVMIACVVVFILMQILGDQT--------VMLWLAWPFDPSLKFELWRYFTHALLHFSLLHILFNLLWWWYLGGAVEK 167 (276)
T ss_pred HHHHHHHHHHHHHHHHHHhccHH--------HHHHHhccccccccCCcHHHHhHHHHhCCHHHHHHHHHHHHHHHHHHHH
Confidence 66 99999999999876643211 0111111112235789999999999999999999999999999999999
Q ss_pred hhchhHHHHHHHHHhhhhhhhhcccCCCCccCchHHHHHHHHHHHHHHhcchhhhhhhhHHHHHHHHHHHHHHHHHHhcC
Q 012374 305 SYGPFTFFLIYTLGGISGNLTSFLHTPEPTVGGTGPVFAIIGAWLIYQFQNKDLIAKDVSERMFQKAILSTALSFIISNF 384 (465)
Q Consensus 305 ~~Gs~rfl~lYllsGi~G~l~s~l~~p~~~VGaSGaVfGLlga~~~~~~~~~~~l~~~~~~~l~~~~ii~~~l~~ll~~~ 384 (465)
.+|+++++.+|+++|++|+++++++.+...+|+||+|||++|+........+.. ...++..+...+++.+++.+.-...
T Consensus 168 ~~G~~~~l~l~l~s~i~~~~~~~~~~~~~~gGaSGvVygL~g~~~~~~~~~p~~-~~~lp~~~~~f~llwl~~g~~~~~g 246 (276)
T PRK10907 168 RLGSGKLIVITLISALLSGWVQSKFSGPWFGGLSGVVYALMGYVWLRGERDPQS-GIYLPRGLIAFALLWLVAGYFDLFG 246 (276)
T ss_pred HHChHHHHHHHHHHHHHHHHHHHHHccchhhHHHHHHHHHHHHHHHHhcccccc-chhhhHHHHHHHHHHHHHHHHHccC
Confidence 999999999999999999999988877788999999999999866554322221 1112222222233333333332334
Q ss_pred CchhHHHHHHHHHHHHHHHHHhhc
Q 012374 385 GPVDTWAHLGAAFTGIIYGFLTCP 408 (465)
Q Consensus 385 ~~is~~aHLgG~L~G~llg~l~~~ 408 (465)
++|+++||++|+++|+++|++..+
T Consensus 247 ~~Ian~AHlgGli~Gll~g~~~~~ 270 (276)
T PRK10907 247 MSIANAAHVAGLAVGLAMAFWDTR 270 (276)
T ss_pred cccHHHHHHHHHHHHHHHHHHhhh
Confidence 679999999999999999998754
No 4
>COG0705 Membrane associated serine protease [Amino acid transport and metabolism]
Probab=99.92 E-value=1.7e-24 Score=209.44 Aligned_cols=188 Identities=23% Similarity=0.390 Sum_probs=139.9
Q ss_pred chHHH-HHHHHHHHHHHHHHhcCCCCccccchhhhhhhhchhhhhh--hc--CceeeeeecccccCCHHHHHHHHHHHHH
Q 012374 223 NLYLI-ILVSIDVAVFLFEIASPIRNSEFGFFSLPLLYGAKINELI--LV--GEWWRLVTPMFLHSGLFHVALSCWALLT 297 (465)
Q Consensus 223 ~p~vt-~Li~inv~VFil~~~~~~~~~~~~l~~~~l~~ga~~~~~i--~~--gq~WRL~Ts~FlH~gl~HLl~Nml~L~~ 297 (465)
.+.++ .++++|+++|++....+....... .... ......+..+ .. .||||++|++|+|.|+.|+++||+.+|.
T Consensus 16 ~~~~~~~~~~~~~~v~~~~~~~~~~~~~~~-~~~~-~~~~~~~~~~~~~~~~~~~w~lit~~FlH~~~~Hll~N~~~l~~ 93 (228)
T COG0705 16 APPVTLFLILLNILVFLLELVLGWSAIFLL-TFLF-RLFGLYPLNLLGALARDQLWRLITAIFLHAGFLHLLFNMLALWV 93 (228)
T ss_pred cchHHHHHHHHHHHHHHHHHHccchHHHHH-HHhh-hHHhhcchhhhccccccchHHHHHHHHHHhhHHHHHHHHHHHHH
Confidence 45677 999999999999876553221110 0000 0011111111 11 1999999999999999999999999999
Q ss_pred HHHHHHHhhchhHHHHHHHHHhhhhhhhhcccCCC---CccCchHHHHHHHHHHHHHHhcchhhhhhh-hHHHHHHHHHH
Q 012374 298 FGPQVCKSYGPFTFFLIYTLGGISGNLTSFLHTPE---PTVGGTGPVFAIIGAWLIYQFQNKDLIAKD-VSERMFQKAIL 373 (465)
Q Consensus 298 fG~~LE~~~Gs~rfl~lYllsGi~G~l~s~l~~p~---~~VGaSGaVfGLlga~~~~~~~~~~~l~~~-~~~~l~~~~ii 373 (465)
+|..+|+.+|+.+|+.+|+++|+++++++..+.+. +.+||||++||+++++....+..+...... .+..+...+.+
T Consensus 94 fg~~le~~~G~~~f~~~yl~~gl~~~~~~~~~~~~~~~~~~GASG~i~gllga~~~~~~~~~~~~~~~~~~~~~~~~i~~ 173 (228)
T COG0705 94 FGSNLERRLGTLRFLLFYLLSGLLAGLAQVLFGPKGGAPSLGASGAIFGLLGAYFLLFPFARILLLFLSLPRPALILILI 173 (228)
T ss_pred hhHHHHHHhchhHHHHHHHHHHHHHHHHHHHHcccccCcccchhHHHHHHHHHHHHHccccchhhhhccCchhHHHHHHH
Confidence 99999999999999999999999999998888763 699999999999999999988766655433 44444434444
Q ss_pred HHHHHHHHhcCC---chhHHHHHHHHHHHHHHHHHhhccccc
Q 012374 374 STALSFIISNFG---PVDTWAHLGAAFTGIIYGFLTCPLVQL 412 (465)
Q Consensus 374 ~~~l~~ll~~~~---~is~~aHLgG~L~G~llg~l~~~~~~~ 412 (465)
.....++..... ++++.||++|+++|++++..+.++.+.
T Consensus 174 ~~~~~~~~~~~~~~~~va~~aHl~G~i~G~l~~~~~~~~~~~ 215 (228)
T COG0705 174 WLLYSLFSGAGSFGPSVAWSAHLGGLIGGLLLAALLSRKLRK 215 (228)
T ss_pred HHHHHHHHHhcCCchHHHHHHHHHHHHHHHHHHHHHhhhhhh
Confidence 444444444333 699999999999999999998776443
No 5
>KOG2290 consensus Rhomboid family proteins [Signal transduction mechanisms]
Probab=99.89 E-value=1.7e-23 Score=213.89 Aligned_cols=173 Identities=28% Similarity=0.447 Sum_probs=142.7
Q ss_pred cCceeeeeecccccCCHHHHHHHHHHHHHHHHHHHHhhchhHHHHHHHHHhhhhhhhhcccCCC-CccCchHHHHHHHHH
Q 012374 269 VGEWWRLVTPMFLHSGLFHVALSCWALLTFGPQVCKSYGPFTFFLIYTLGGISGNLTSFLHTPE-PTVGGTGPVFAIIGA 347 (465)
Q Consensus 269 ~gq~WRL~Ts~FlH~gl~HLl~Nml~L~~fG~~LE~~~Gs~rfl~lYllsGi~G~l~s~l~~p~-~~VGaSGaVfGLlga 347 (465)
.+|+|||+||+|+|+|+.|++..|.+++.+-+.+|+..|+.|+.++|++||+.||+++.++.|. +.||+||+-||++++
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 4699999999999999999999999999999999999999999999999999999999999985 899999999999999
Q ss_pred HHHHHhcchhhhhhhhHHHHHHHHHHHHHHHHHHhcCCchhHHHHHHHHHHHHHHHHHhhcccccCCcCcCCccchhhHH
Q 012374 348 WLIYQFQNKDLIAKDVSERMFQKAILSTALSFIISNFGPVDTWAHLGAAFTGIIYGFLTCPLVQLGDASSRNSQEEGITL 427 (465)
Q Consensus 348 ~~~~~~~~~~~l~~~~~~~l~~~~ii~~~l~~ll~~~~~is~~aHLgG~L~G~llg~l~~~~~~~~~~~~~~~~~~~~~~ 427 (465)
.++...++|..+..+ ++.+.-+++.+.+. .++..|+||||||+.|++.|++.+++++|++.+++...
T Consensus 528 l~vEl~qs~~il~~~--w~a~~~Lia~~L~L-~iGliPWiDN~aHlfG~i~GLl~s~~~~PYi~Fg~~d~---------- 594 (652)
T KOG2290|consen 528 LFVELFQSWQILERP--WRAFFHLIATLLVL-CIGLIPWIDNWAHLFGTIFGLLTSIIFLPYIDFGDFDL---------- 594 (652)
T ss_pred HHHHHHhhhHhhhhH--HHHHHHHHHHHHHH-HhccccchhhHHHHHHHHHHHHHHHHhhccccccchhh----------
Confidence 999999999988763 33443333333333 33777999999999999999999999999998877432
Q ss_pred hhhccccchhHHHHHHHHHHHHH--HHHhhcC
Q 012374 428 IRQYANPCKSLIVFTIFVIILGS--FIFVFEP 457 (465)
Q Consensus 428 ~r~~~~~~~~ll~f~i~vivl~~--~lf~i~p 457 (465)
|..++..++..++|.+++.. ++|+..|
T Consensus 595 ---yrKr~~ilIs~ivf~~Lla~Lvv~fy~~~ 623 (652)
T KOG2290|consen 595 ---YRKRFYILISQIVFSGLLAILVVVFYNYP 623 (652)
T ss_pred ---hhhHHHHHHHHHHHHHHHHHHHHheeecc
Confidence 23335566666666666644 4455444
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=99.86 E-value=1.6e-22 Score=180.98 Aligned_cols=140 Identities=31% Similarity=0.614 Sum_probs=106.7
Q ss_pred hcCceeeeeecccccCCHHHHHHHHHHHHHHHHHHHHhhchhHHHHHHHHHhhhhhhhhcccCCC--CccCchHHHHHHH
Q 012374 268 LVGEWWRLVTPMFLHSGLFHVALSCWALLTFGPQVCKSYGPFTFFLIYTLGGISGNLTSFLHTPE--PTVGGTGPVFAII 345 (465)
Q Consensus 268 ~~gq~WRL~Ts~FlH~gl~HLl~Nml~L~~fG~~LE~~~Gs~rfl~lYllsGi~G~l~s~l~~p~--~~VGaSGaVfGLl 345 (465)
.++||||++|+.|+|.|+.|+++|++.++.+|..+|+.+|+.++..+|++++++++++..++.+. +.+|+||+++|++
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 57899999999999999999999999999999999999999999999999999999999877654 5999999999999
Q ss_pred HHHHHHHhcchhhhhhhhHHHHHHHHHHHHHHHHHHhcCCchhHHHHHHHHHHHHHHHHHhhcc
Q 012374 346 GAWLIYQFQNKDLIAKDVSERMFQKAILSTALSFIISNFGPVDTWAHLGAAFTGIIYGFLTCPL 409 (465)
Q Consensus 346 ga~~~~~~~~~~~l~~~~~~~l~~~~ii~~~l~~ll~~~~~is~~aHLgG~L~G~llg~l~~~~ 409 (465)
++.+...+..+........ ........+.+.+.....+++++.+|++|+++|+++++.+.++
T Consensus 82 ~~~~~~~~~~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~hl~G~~~G~~~~~~~~~~ 143 (145)
T PF01694_consen 82 GAFLFLYPQNKKRLRFIYL--ALVVPIIVLVIILLLGFIPNISFLGHLGGFLAGLLYGFLILRR 143 (145)
T ss_dssp HHHHHHHHCCCCCS---HC--CCCCCCCCCCHHHCTSSSSTTTHHHHHHHHHHHHHHHHHHCH-
T ss_pred HHHHHHHhhccchhhcchH--HHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHc
Confidence 9999998877554331000 0000111122333333468899999999999999999998765
No 7
>KOG2632 consensus Rhomboid family proteins [Function unknown]
Probab=99.63 E-value=1e-15 Score=149.15 Aligned_cols=172 Identities=18% Similarity=0.230 Sum_probs=127.0
Q ss_pred CcchHHH-HHHHHHHHHHHHHHhcCCCCccccchhhhhhhhchhhhhhhcCceeeeeecccccCCHHHHHHHHHHHHHHH
Q 012374 221 TSNLYLI-ILVSIDVAVFLFEIASPIRNSEFGFFSLPLLYGAKINELILVGEWWRLVTPMFLHSGLFHVALSCWALLTFG 299 (465)
Q Consensus 221 ~~~p~vt-~Li~inv~VFil~~~~~~~~~~~~l~~~~l~~ga~~~~~i~~gq~WRL~Ts~FlH~gl~HLl~Nml~L~~fG 299 (465)
.+.|.+| +++.++.++|++....+.. . .+ .+....+.+.|.||++||.++|.+..|+++||+.+|.+|
T Consensus 12 ~~~p~~ts~~~~~~~~i~lv~~~~~i~-~---------~~-~l~~~~l~~~ql~RL~Ty~l~H~s~~hllfnmlaL~~~g 80 (258)
T KOG2632|consen 12 MKIPLLTSIVVVLAILIYLVSFFPGIV-E---------VL-GLPSELLINWQLYRLITYALVHLSLPHLLFNMLALWPLG 80 (258)
T ss_pred ccchHHHHHHHHHHHHHHHHhccchhh-h---------Hh-cCCHHHhhhHHHHHHHHHHHHhccHHHHHHHHHHHHhch
Confidence 3457777 8888889999886554332 1 11 123344578899999999999999999999999999999
Q ss_pred HHHHHhhc-hhHHHHHHHHHhhhhhhhhcccC------C----CCccCchHHHHHHHHHHHHHHhcchhhhhhhhHHHHH
Q 012374 300 PQVCKSYG-PFTFFLIYTLGGISGNLTSFLHT------P----EPTVGGTGPVFAIIGAWLIYQFQNKDLIAKDVSERMF 368 (465)
Q Consensus 300 ~~LE~~~G-s~rfl~lYllsGi~G~l~s~l~~------p----~~~VGaSGaVfGLlga~~~~~~~~~~~l~~~~~~~l~ 368 (465)
...|+.+| +.+++.+..+.++..+++..+.. + ...+|.||..||+++......+...............
T Consensus 81 ~~fE~~~G~t~~~l~~~~llalf~gIl~ll~~~~~~~~d~~~~~~a~G~s~v~Fam~~~~~~~sp~r~~~~fg~~siP~~ 160 (258)
T KOG2632|consen 81 SQFERTHGTTVRILMFTVLLALFSGILYLLAYHVFLLSDLVYVEGAIGFSGVLFAMMAVLEVQSPVRSRSVFGLFSIPIV 160 (258)
T ss_pred hHHHhhccceehHHHHHHHHHHHHHHHHHHHHHHHhhcchhhhcccccccHHHHHHHHHHhhcCcccchhhcccccccHH
Confidence 99999999 88888888888888888765543 2 3579999999999999888877766443332322222
Q ss_pred HHHHHHHHHHHHHhcCCchhHHHHHHHHHHHHHHHHH
Q 012374 369 QKAILSTALSFIISNFGPVDTWAHLGAAFTGIIYGFL 405 (465)
Q Consensus 369 ~~~ii~~~l~~ll~~~~~is~~aHLgG~L~G~llg~l 405 (465)
...++.++.. ....++.|+++|++|+++|+.+++-
T Consensus 161 l~Pw~lLi~~--~~lvp~aSFlghl~GllvG~ay~~~ 195 (258)
T KOG2632|consen 161 LAPWALLIAT--QILVPQASFLGHLCGLLVGYAYAFS 195 (258)
T ss_pred HHHHHHHHHH--HHHccCchHHHHHHHHHHHHHHHHH
Confidence 2222222222 1234889999999999999999994
No 8
>KOG2980 consensus Integral membrane protease of the rhomboid family involved in different forms of regulated intramembrane proteolysis [Signal transduction mechanisms]
Probab=98.88 E-value=2e-09 Score=107.19 Aligned_cols=180 Identities=18% Similarity=0.249 Sum_probs=122.9
Q ss_pred HHHHHHHHHHHHHHHHHhcCCCCccccchhhhhhhhchhhhhhhcCceeeeeecccccCCHHHHHHHHHHHHHHHH-HHH
Q 012374 225 YLIILVSIDVAVFLFEIASPIRNSEFGFFSLPLLYGAKINELILVGEWWRLVTPMFLHSGLFHVALSCWALLTFGP-QVC 303 (465)
Q Consensus 225 ~vt~Li~inv~VFil~~~~~~~~~~~~l~~~~l~~ga~~~~~i~~gq~WRL~Ts~FlH~gl~HLl~Nml~L~~fG~-~LE 303 (465)
.+..++++|+++|.++.+...+..+. .|- ..+. +..---|-+++|.|.|.+..|+..||+.++.++. .+-
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 VVFGLLIANAFVFTLWRVPQKQFTMI-------PWM-LSRN-AYKTGCWKIILSTFSHYSALHLGPNMLVLKSYLAGALK 187 (310)
T ss_pred chhHHHHHHHHHHHHHHhcchhhhhh-------hHH-hhcc-cccccceeEEeehhcchhHhhhcHHHHHHHHHhccccc
Confidence 34499999999999886643221111 111 1111 1223446699999999999999999999998887 788
Q ss_pred HhhchhHHHHHHHHHhhhhhhhhccc-CC----CCccCchHHHHHHHHHHHHHHhcchhhhhhhhHHHHHHH----HHHH
Q 012374 304 KSYGPFTFFLIYTLGGISGNLTSFLH-TP----EPTVGGTGPVFAIIGAWLIYQFQNKDLIAKDVSERMFQK----AILS 374 (465)
Q Consensus 304 ~~~Gs~rfl~lYllsGi~G~l~s~l~-~p----~~~VGaSGaVfGLlga~~~~~~~~~~~l~~~~~~~l~~~----~ii~ 374 (465)
...|...+..+|+.++..|......- .+ .+.+||||+++++++.....+|.....+.+..+...... +++.
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 88999999999997777777665543 12 478999999999999999998876655543333222111 1111
Q ss_pred HHHHHHHhcCCchhHHHHHHHHHHHHHHHHHhhcccccC
Q 012374 375 TALSFIISNFGPVDTWAHLGAAFTGIIYGFLTCPLVQLG 413 (465)
Q Consensus 375 ~~l~~ll~~~~~is~~aHLgG~L~G~llg~l~~~~~~~~ 413 (465)
..+..+......-++.||++|.+.|+.++.+..+++..+
T Consensus 268 ~~~a~~~l~~~~~n~~Ah~~gsl~Gv~va~~~~~ri~kg 306 (310)
T KOG2980|consen 268 YDFAGLILGWGFFNHAAHLSGSLFGVVVATYLWARIRKG 306 (310)
T ss_pred hhhcceeeccccchhHhhhcchHHHHHHHHHHHHHHHcC
Confidence 111111122345677899999999999999987766544
No 9
>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=98.37 E-value=4e-06 Score=80.07 Aligned_cols=170 Identities=17% Similarity=0.191 Sum_probs=99.7
Q ss_pred chHHH-HHHHHHHHHHHHHHhcCCCCccccchhhhhhhhchhhhh-hhcCceeeeeecccccCCH-HHHHHHHHHHHHHH
Q 012374 223 NLYLI-ILVSIDVAVFLFEIASPIRNSEFGFFSLPLLYGAKINEL-ILVGEWWRLVTPMFLHSGL-FHVALSCWALLTFG 299 (465)
Q Consensus 223 ~p~vt-~Li~inv~VFil~~~~~~~~~~~~l~~~~l~~ga~~~~~-i~~gq~WRL~Ts~FlH~gl-~HLl~Nml~L~~fG 299 (465)
.|++| ..++..+++.++....-.. +... ...++. +.+.|+||++|+.|.-++. .+.++|++.++..+
T Consensus 1 iPpVTR~~~~~~~~~s~l~~~~~~~---------~~~l-~~~~~~v~~~~q~WRl~Tsff~~g~~~~~~l~~~~~l~~~s 70 (197)
T PF04511_consen 1 IPPVTRYWLISTVALSLLVSFGIIS---------PYYL-YFDWELVFKKFQIWRLFTSFFYFGPFSLNFLFNLYFLYQYS 70 (197)
T ss_pred CChhHHHHHHHHHHHHHHHHCCCCC---------HHHe-eECcHHHhhhcCceeeEEEEEEEcCCCHHHHHHHHHHHHHh
Confidence 37788 7777776666665432111 1111 122333 3579999999999987655 79999999999999
Q ss_pred HHHHHh-hch--hHHHHHHHHHhhhhhhhhcccCCC----CccCchHHHHHHHHHHHHHHhcchhhhhhhhHHHHHHHHH
Q 012374 300 PQVCKS-YGP--FTFFLIYTLGGISGNLTSFLHTPE----PTVGGTGPVFAIIGAWLIYQFQNKDLIAKDVSERMFQKAI 372 (465)
Q Consensus 300 ~~LE~~-~Gs--~rfl~lYllsGi~G~l~s~l~~p~----~~VGaSGaVfGLlga~~~~~~~~~~~l~~~~~~~l~~~~i 372 (465)
..+|+. ++. ..++...+.+++.-.+++.+.... +..| .+-.+.++=.+.-..+.....+.+.++.+....-+
T Consensus 71 ~~LE~~~f~~~~ady~~~ll~~~~~i~~~~~~~~~~~~~~~~l~-~~l~~~l~Y~wsr~np~~~v~~~g~~~i~a~ylP~ 149 (197)
T PF04511_consen 71 SSLEEGHFQGRSADYLWFLLFGASLILILSLLIGPYFFNIPFLG-SSLSFALTYIWSRKNPNAQVSFFGLFTIKAKYLPW 149 (197)
T ss_pred hHhccCCCCCCHHHHHHHHHHHHHHHHHHHHhhccchhHHHHHH-HHHHHHHHHHHHHhCcccceeeEEEEEEChhhHHH
Confidence 999998 332 457666666666655555543321 1111 22222333233333333333222223334444455
Q ss_pred HHHHHHHHHhcCCchhHHHHHHHHHHHHHHHHHh
Q 012374 373 LSTALSFIISNFGPVDTWAHLGAAFTGIIYGFLT 406 (465)
Q Consensus 373 i~~~l~~ll~~~~~is~~aHLgG~L~G~llg~l~ 406 (465)
+.+++.++... -+...++.|+++|-++-++-
T Consensus 150 ~~~~~~~l~~~---~~~~~~l~Gi~~Ghly~fl~ 180 (197)
T PF04511_consen 150 VLLAFSLLFGG---SSPIPDLLGILVGHLYYFLK 180 (197)
T ss_pred HHHHHHHHhCC---CcHHHHHHHHHHHHHHHHHH
Confidence 55555655532 24568999999999988763
No 10
>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=98.22 E-value=2.7e-07 Score=78.92 Aligned_cols=58 Identities=22% Similarity=0.332 Sum_probs=54.6
Q ss_pred ceeeeeecccccCCHHHHHHHHHHHHHHHHHHHHhhchhHHHHHHHHHhhhhhhhhcc
Q 012374 271 EWWRLVTPMFLHSGLFHVALSCWALLTFGPQVCKSYGPFTFFLIYTLGGISGNLTSFL 328 (465)
Q Consensus 271 q~WRL~Ts~FlH~gl~HLl~Nml~L~~fG~~LE~~~Gs~rfl~lYllsGi~G~l~s~l 328 (465)
.+|+++|+.|++.++..+++|.+.++..|+.+|+.||++.++..+++.+++.|++..+
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 7899999999999999999999999999999999999999999999999988887654
No 11
>KOG0858 consensus Predicted membrane protein [Function unknown]
Probab=97.67 E-value=8.1e-05 Score=72.52 Aligned_cols=168 Identities=17% Similarity=0.165 Sum_probs=95.5
Q ss_pred cchHHH-HHHHHHHHHHHHHHhcCCCCccccchhhhhhhhchhhhh-hhcCceeeeeecccccCC-HHHHHHHHHHHHHH
Q 012374 222 SNLYLI-ILVSIDVAVFLFEIASPIRNSEFGFFSLPLLYGAKINEL-ILVGEWWRLVTPMFLHSG-LFHVALSCWALLTF 298 (465)
Q Consensus 222 ~~p~vt-~Li~inv~VFil~~~~~~~~~~~~l~~~~l~~ga~~~~~-i~~gq~WRL~Ts~FlH~g-l~HLl~Nml~L~~f 298 (465)
.+|.+| ....+|++.-++....-.. | .+-...+++ +.+.|+||++|+.+.-+. -+|.++||++++-.
T Consensus 11 ~iPpVTR~~~~~~v~tt~~~~l~lIs---------P-~~l~~~p~Lv~kk~QiWRliTs~lyfg~~gf~fl~n~~FlyrY 80 (239)
T KOG0858|consen 11 QIPPVTRYYTTACVVTTLLVRLDLIS---------P-FQLYLNPELVFKKFQIWRLITSFLYFGPFGFDFLMNLYFLYRY 80 (239)
T ss_pred cCChHHHHHHHHHHHHHHHHhhcccC---------c-hheEecHHHHHhHhHHHHhhhhhheeccccHHHHHHHHHHHHH
Confidence 467888 7777777777665332111 1 111223333 478899999999999866 69999999999999
Q ss_pred HHHHHHhh-c--hhHHHHHHHHHhhhhhhhhcccCCCCccCchHHHHHHHHHHHHHHhcchhhhhhhhHHHHHHHHHHHH
Q 012374 299 GPQVCKSY-G--PFTFFLIYTLGGISGNLTSFLHTPEPTVGGTGPVFAIIGAWLIYQFQNKDLIAKDVSERMFQKAILST 375 (465)
Q Consensus 299 G~~LE~~~-G--s~rfl~lYllsGi~G~l~s~l~~p~~~VGaSGaVfGLlga~~~~~~~~~~~l~~~~~~~l~~~~ii~~ 375 (465)
.+.||+-. . +..|+.+.+.++++-.+.+.... ...+|-+ -++.+.=.+.-..+.....+.+.+..+....-+++.
T Consensus 81 ~~~LE~g~f~~rtadf~~mllf~~~l~~~~~~~~~-~~fLg~~-l~~~l~YvWs~~Np~~~v~F~g~~~f~a~YlPwvll 158 (239)
T KOG0858|consen 81 SSMLEEGSFRGRTADFLYMLLFGAVLLTLTGLFVY-IVFLGQS-LVFMLVYVWSKRNPDVIVSFFGLITFKAPYLPWVLL 158 (239)
T ss_pred HHHHhcCCCCCchhHHHHHHHHHHHHHHHHHHHHH-HHHHHHH-HHHHHHHHHHhhCCCceEEEEEEecCccccchHHHH
Confidence 99999864 2 36777777787777775554211 1111111 111111111111111111111222333344445556
Q ss_pred HHHHHHhcCCchhHHHHHHHHHHHHHHHHH
Q 012374 376 ALSFIISNFGPVDTWAHLGAAFTGIIYGFL 405 (465)
Q Consensus 376 ~l~~ll~~~~~is~~aHLgG~L~G~llg~l 405 (465)
++.++... .+ ..-+-|+++|-++-++
T Consensus 159 ~fs~l~g~---~~-~~dllGi~~GHiy~fl 184 (239)
T KOG0858|consen 159 GFSFLFGG---SI-LVDLLGIIVGHIYYFL 184 (239)
T ss_pred HHHHHhCC---ch-HHHHHhhhhheeEEEE
Confidence 66666532 23 6778888888766543
No 12
>KOG2890 consensus Predicted membrane protein [Function unknown]
Probab=97.44 E-value=0.00017 Score=72.40 Aligned_cols=142 Identities=21% Similarity=0.238 Sum_probs=95.0
Q ss_pred CceeeeeecccccCCHHHHHHHHHHHHHHHHHHHHhhchhHHHHHHHHHhhhhhhhhc--------ccCC-----CCccC
Q 012374 270 GEWWRLVTPMFLHSGLFHVALSCWALLTFGPQVCKSYGPFTFFLIYTLGGISGNLTSF--------LHTP-----EPTVG 336 (465)
Q Consensus 270 gq~WRL~Ts~FlH~gl~HLl~Nml~L~~fG~~LE~~~Gs~rfl~lYllsGi~G~l~s~--------l~~p-----~~~VG 336 (465)
-.+|+++|+.|+-.+++-.++|.+.+.+-|..+|+.||+..++.+|.+.-..-+++.. +... .+..|
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 3689999999999999999999999999999999999999999888765444444321 1111 25889
Q ss_pred chHHHHHHHHHHHHHHhcchhhhhhhhHHHHHH--HHHHHHHHHHHHhcCCchhHHHHHHHHHHHHHHHHHhhcccccCC
Q 012374 337 GTGPVFAIIGAWLIYQFQNKDLIAKDVSERMFQ--KAILSTALSFIISNFGPVDTWAHLGAAFTGIIYGFLTCPLVQLGD 414 (465)
Q Consensus 337 aSGaVfGLlga~~~~~~~~~~~l~~~~~~~l~~--~~ii~~~l~~ll~~~~~is~~aHLgG~L~G~llg~l~~~~~~~~~ 414 (465)
..|.+.|++.++=-..|..-..... .. ++.. .-++.+.+.+++.. -.....+.+.-+..|...+|.+++.-+.+.
T Consensus 145 ~~gilaGilVa~kQllpd~~il~~~-~~-r~~~~~lP~~~l~~~~il~i-~~f~~f~~l~s~~~g~~~sWtYLRfyq~h~ 221 (326)
T KOG2890|consen 145 TTGILAGILVAWKQLLPDTIILELK-SG-RFLYAHLPLLVLFLSLILSI-ITFLVFASLPSITFGVLVSWTYLRFYQRHP 221 (326)
T ss_pred chHHHHHHHHHHHHHcCceeEEecc-ch-hhhhhhCCHHHHHHHHHHHH-HHHHHhhhhHHHHHhhhhhhhhheecccCC
Confidence 9999999998887666543111100 00 1110 00111111111111 123456777888899999999998877665
No 13
>KOG4463 consensus Uncharacterized conserved protein [Function unknown]
Probab=93.57 E-value=0.055 Score=53.73 Aligned_cols=60 Identities=15% Similarity=0.246 Sum_probs=50.8
Q ss_pred hcCceeeeeecccccCCHHHHHHHHHHHHHHHHHHHHhhchhHHHHHHHHHhhhhhhhhcc
Q 012374 268 LVGEWWRLVTPMFLHSGLFHVALSCWALLTFGPQVCKSYGPFTFFLIYTLGGISGNLTSFL 328 (465)
Q Consensus 268 ~~gq~WRL~Ts~FlH~gl~HLl~Nml~L~~fG~~LE~~~Gs~rfl~lYllsGi~G~l~s~l 328 (465)
...|+||++.+.|.-.+-..+.+-++.++. .+.+||.+|+.||..+.+.+++.+.++...
T Consensus 47 ~y~qywrlL~~qF~~~n~~e~~~~l~I~Y~-fR~~ERlLGShky~~fiv~s~~~~~l~~~i 106 (323)
T KOG4463|consen 47 KYFQYWRLLMSQFAFSNTPELMFGLYILYY-FRVFERLLGSHKYSVFIVFSGTVSLLLEVI 106 (323)
T ss_pred HHHHHHHHHHHHHHhcCChHHHHHHHHHHH-HHHHHHHhccccceeehhHHHHHHHHHHHH
Confidence 457999999999999998888887766655 568999999999999999999988886543
No 14
>COG5291 Predicted membrane protein [Function unknown]
Probab=91.93 E-value=0.15 Score=50.23 Aligned_cols=43 Identities=12% Similarity=0.298 Sum_probs=35.2
Q ss_pred hhcCceeeeeecccccCC-HHHHHHHHHHHHHHHHHHHHh-hchh
Q 012374 267 ILVGEWWRLVTPMFLHSG-LFHVALSCWALLTFGPQVCKS-YGPF 309 (465)
Q Consensus 267 i~~gq~WRL~Ts~FlH~g-l~HLl~Nml~L~~fG~~LE~~-~Gs~ 309 (465)
+.+-||||++|+..+-++ -+..++|+++++--.+.||+- +|+.
T Consensus 55 ~k~~qiwRlfTs~~~~~~~~~d~~M~vyf~Y~yS~~LE~g~f~~~ 99 (313)
T COG5291 55 LKRLQIWRLFTSFLYFGKPTLDMFMHVYFLYRYSRMLEEGCFNTS 99 (313)
T ss_pred HHHHHHHHHHHHHHhhcCcchhHHHHHHHHHHHHHHHhccccCcc
Confidence 366799999997766654 578999999999999999985 5655
No 15
>COG0705 Membrane associated serine protease [Amino acid transport and metabolism]
Probab=70.63 E-value=7.7 Score=37.39 Aligned_cols=74 Identities=20% Similarity=0.113 Sum_probs=58.8
Q ss_pred hcCceeeeeecccccCCHHHHHHHHHHHHHHHHHHHHhhchhHHHHHHHHHhhhhhhhhcccCCCCccCchHHHHHHHHH
Q 012374 268 LVGEWWRLVTPMFLHSGLFHVALSCWALLTFGPQVCKSYGPFTFFLIYTLGGISGNLTSFLHTPEPTVGGTGPVFAIIGA 347 (465)
Q Consensus 268 ~~gq~WRL~Ts~FlH~gl~HLl~Nml~L~~fG~~LE~~~Gs~rfl~lYllsGi~G~l~s~l~~p~~~VGaSGaVfGLlga 347 (465)
..|.+|+++++.++|....|...+... ..+...+++..++..+++.....+.+.|+.++-+.|+++.
T Consensus 136 ASG~i~gllga~~~~~~~~~~~~~~~~-------------~~~~~~~~i~~~~~~~~~~~~~~~~~~va~~aHl~G~i~G 202 (228)
T COG0705 136 ASGAIFGLLGAYFLLFPFARILLLFLS-------------LPRPALILILIWLLYSLFSGAGSFGPSVAWSAHLGGLIGG 202 (228)
T ss_pred hhHHHHHHHHHHHHHccccchhhhhcc-------------CchhHHHHHHHHHHHHHHHHhcCCchHHHHHHHHHHHHHH
Confidence 567888999999999988888877665 5566678888888888888877766788999999999987
Q ss_pred HHHHHhc
Q 012374 348 WLIYQFQ 354 (465)
Q Consensus 348 ~~~~~~~ 354 (465)
.+.....
T Consensus 203 ~l~~~~~ 209 (228)
T COG0705 203 LLLAALL 209 (228)
T ss_pred HHHHHHH
Confidence 7665443
No 16
>PF11992 DUF3488: Domain of unknown function (DUF3488); InterPro: IPR021878 This presumed domain is functionally uncharacterised. This domain is found in bacteria. This domain is typically between 323 to 339 amino acids in length. This domain is found associated with PF01841 from PFAM. This domain has a conserved PLW sequence motif. This domain contains 6 transmembrane helices.
Probab=70.57 E-value=72 Score=32.78 Aligned_cols=60 Identities=10% Similarity=0.049 Sum_probs=31.6
Q ss_pred CchhHHHHHHHHHHHHHHHHHhhcccccCCcCcCCccchhhHHhhhccccchhHHHHHHHHHHHHHHHHhhcCCc
Q 012374 385 GPVDTWAHLGAAFTGIIYGFLTCPLVQLGDASSRNSQEEGITLIRQYANPCKSLIVFTIFVIILGSFIFVFEPPL 459 (465)
Q Consensus 385 ~~is~~aHLgG~L~G~llg~l~~~~~~~~~~~~~~~~~~~~~~~r~~~~~~~~ll~f~i~vivl~~~lf~i~pp~ 459 (465)
..+-....+...+...+.+++....... . +......+....+++..+.++.++|++-|=.
T Consensus 121 qs~~~~l~~ll~~~~~~~~L~~l~~~~~---~------------~~~~~~~~~~~~l~l~alpl~~vlFl~fPR~ 180 (325)
T PF11992_consen 121 QSLLFALYLLLFLVLLLAALVLLHQPDS---R------------RSLRQLLRRALKLLLQALPLALVLFLLFPRL 180 (325)
T ss_pred ccHHHHHHHHHHHHHHHHHHHHHhCccc---c------------chHHHHHHHHHHHHHHHHHHHHHHHHHhhcc
Confidence 4455666777777777776665422100 0 1112233444555555556666777776633
No 17
>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=65.57 E-value=45 Score=33.73 Aligned_cols=70 Identities=9% Similarity=0.092 Sum_probs=41.6
Q ss_pred HHHHHHHHHHHHHHHHHHHhhchhHHHHHHHHHhhhhhhhhc-ccCCCCc-c--CchHHHHHHHHHHHHHHhcchhhh
Q 012374 286 FHVALSCWALLTFGPQVCKSYGPFTFFLIYTLGGISGNLTSF-LHTPEPT-V--GGTGPVFAIIGAWLIYQFQNKDLI 359 (465)
Q Consensus 286 ~HLl~Nml~L~~fG~~LE~~~Gs~rfl~lYllsGi~G~l~s~-l~~p~~~-V--GaSGaVfGLlga~~~~~~~~~~~l 359 (465)
..+++|.+.|+..+..+-+....+|.++- +++|++.++ ++.|... + -..-.+.+++..++++.+..+..+
T Consensus 11 ~N~~md~~lL~~t~~~~~~~~~~~Rll~~----A~~Gal~~~~~~~p~~~~~~~~~~k~l~s~lmv~iaf~~~~~~~~ 84 (293)
T PF03419_consen 11 VNFLMDYFLLWLTARLLKRRASRWRLLLG----AAIGALYSLLIFFPPLSFLYSILFKLLISVLMVLIAFGPKRWRQF 84 (293)
T ss_pred HHHHHHHHHHHHHHHHhcCCCcHHHHHHH----HHHHHHHHHHHhhcCHHHHHHHHHHHHHHHHHHHHHhCCCcHHHH
Confidence 46789999999999999888888888543 333333332 2223211 1 122245555566666666655544
No 18
>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=64.62 E-value=2.7e+02 Score=32.19 Aligned_cols=38 Identities=13% Similarity=-0.059 Sum_probs=23.1
Q ss_pred HHHHHHHHHHHHHHHHHhhchhHHHHHHHHHhhhhhhhh
Q 012374 288 VALSCWALLTFGPQVCKSYGPFTFFLIYTLGGISGNLTS 326 (465)
Q Consensus 288 Ll~Nml~L~~fG~~LE~~~Gs~rfl~lYllsGi~G~l~s 326 (465)
.+..++..++.|. +-..+|+++.+++.++...++.++.
T Consensus 212 ~lG~iiG~li~G~-LsDR~GRR~~lii~lil~~i~~ll~ 249 (742)
T TIGR01299 212 YLGMMVGAFFWGG-LADKLGRKQCLLICLSVNGFFAFFS 249 (742)
T ss_pred HHHHHHHHHHHHH-HHHHhCcHHHHHHHHHHHHHHHHHH
Confidence 4555566666665 4456898888766655444444443
No 19
>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=48.94 E-value=1.5e+02 Score=34.97 Aligned_cols=65 Identities=18% Similarity=0.192 Sum_probs=40.5
Q ss_pred CHHHHHHHHHHHHHHHHHHHHhhch-hHHHHHHHHHhhhhhhhhcccCC--CCccCchHHHHHHHHHHH
Q 012374 284 GLFHVALSCWALLTFGPQVCKSYGP-FTFFLIYTLGGISGNLTSFLHTP--EPTVGGTGPVFAIIGAWL 349 (465)
Q Consensus 284 gl~HLl~Nml~L~~fG~~LE~~~Gs-~rfl~lYllsGi~G~l~s~l~~p--~~~VGaSGaVfGLlga~~ 349 (465)
-++=.+.|+..-..||..+++.-+. .-..-..+.++++|-+ ..++.+ -..+|.+|.+.-...+..
T Consensus 375 ~ifiyFA~L~PaIaFG~ll~~~T~g~~gv~E~Llstai~Gii-fslf~GQPL~IlG~TGPilvF~~~ly 442 (900)
T TIGR00834 375 VIFIYFAALSPAITFGGLLGEKTRNMMGVSELLISTAVQGVL-FALLAAQPLLVVGFSGPLLVFEEAFF 442 (900)
T ss_pred HHHHHHHHhhHHhhHHHHHHHhhCCcchHHHHHHHHHHHHHH-HhhhcCCceEEecCcccHHHHHHHHH
Confidence 3555677888888999888876544 3444444444555444 444544 358899998765554433
No 20
>PF11833 DUF3353: Protein of unknown function (DUF3353); InterPro: IPR021788 This family of proteins are functionally uncharacterised. This protein is found in bacteria and eukaryotes. Proteins in this family are typically between 205 to 258 amino acids in length.
Probab=48.10 E-value=2e+02 Score=27.61 Aligned_cols=21 Identities=29% Similarity=0.442 Sum_probs=12.6
Q ss_pred HHHHHHHHHHHHHHHhhcccc
Q 012374 391 AHLGAAFTGIIYGFLTCPLVQ 411 (465)
Q Consensus 391 aHLgG~L~G~llg~l~~~~~~ 411 (465)
--++|+++|.++|-++...++
T Consensus 145 ~~~~~L~~G~~lGs~l~~~l~ 165 (194)
T PF11833_consen 145 WTLGGLVVGLILGSLLASWLP 165 (194)
T ss_pred HHHHHHHHHHHHHHHHHhhcc
Confidence 345666677777766654433
No 21
>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=46.53 E-value=3.8e+02 Score=31.02 Aligned_cols=28 Identities=4% Similarity=-0.024 Sum_probs=16.9
Q ss_pred HHHHHHHHhhchhHHHHHHHHHhhhhhh
Q 012374 297 TFGPQVCKSYGPFTFFLIYTLGGISGNL 324 (465)
Q Consensus 297 ~fG~~LE~~~Gs~rfl~lYllsGi~G~l 324 (465)
+++..+-..+|+++.+++.++.+.++.+
T Consensus 613 il~g~L~Dr~GRr~~l~~~~~lsai~~l 640 (742)
T TIGR01299 613 IVSALLMDKIGRLRMLAGSMVLSCISCF 640 (742)
T ss_pred HHHHHHHHHhCCHHHHHHHHHHHHHHHH
Confidence 3344455678998887666555444443
No 22
>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=45.19 E-value=2e+02 Score=29.13 Aligned_cols=71 Identities=10% Similarity=0.203 Sum_probs=41.5
Q ss_pred HHHHHHHHHHHHHHHHHHHHhhchhHHHHHHHHHhhhhhhhhcc-cCCCCccCch---HHHHHHHHHHHHHHhcchhhh
Q 012374 285 LFHVALSCWALLTFGPQVCKSYGPFTFFLIYTLGGISGNLTSFL-HTPEPTVGGT---GPVFAIIGAWLIYQFQNKDLI 359 (465)
Q Consensus 285 l~HLl~Nml~L~~fG~~LE~~~Gs~rfl~lYllsGi~G~l~s~l-~~p~~~VGaS---GaVfGLlga~~~~~~~~~~~l 359 (465)
+..+++|.+.|+..+..+-+....+|.++--+ +|++.+++ +.|....=.+ =.+++++..++++.+..++.+
T Consensus 10 l~Nf~~d~~LL~~t~~~lk~~~~~~Rll~ga~----iGa~~~~~~~~p~~~~~~~~~~k~~~s~lmv~iafg~~~~~~f 84 (288)
T TIGR02854 10 LENFIIDYFLLYLTARTLKDKVSQWRLLLAAL----IGSLYVLFMFTPKASFFTSPIAKLLYSFLIIFIAFGPKSLRFF 84 (288)
T ss_pred HHHHHHHHHHHHHHHHHhhccchHHHHHHHHH----HHHHHHHHHHhccHHHHHHHHHHHHHHHHHHHHHhcCCCHHHH
Confidence 35678999999999999999888888854433 34433322 3342211111 123455555566655555443
No 23
>PF10011 DUF2254: Predicted membrane protein (DUF2254); InterPro: IPR018723 Members of this family of proteins comprises various hypothetical and putative membrane proteins. Their exact function, has not, as yet, been defined.
Probab=43.48 E-value=4.1e+02 Score=27.86 Aligned_cols=27 Identities=26% Similarity=0.365 Sum_probs=20.0
Q ss_pred hHHHHHHHHHHHHHHHHHhhcccccCC
Q 012374 388 DTWAHLGAAFTGIIYGFLTCPLVQLGD 414 (465)
Q Consensus 388 s~~aHLgG~L~G~llg~l~~~~~~~~~ 414 (465)
.+..-+|-|+++++|+++.+..++...
T Consensus 93 ~~q~vLg~Figtfvy~l~~l~~i~~~~ 119 (371)
T PF10011_consen 93 VTQVVLGTFIGTFVYSLLVLIAIRSGD 119 (371)
T ss_pred hHHHHHHHHHHHHHHHHHHHHHccccc
Confidence 455668889999999998877655433
No 24
>PRK10255 PTS system N-acetyl glucosamine specific transporter subunits IIABC; Provisional
Probab=42.66 E-value=47 Score=37.71 Aligned_cols=63 Identities=14% Similarity=0.174 Sum_probs=37.3
Q ss_pred HHHHHHHHHHHHHHHHHhhcccccCCcCcCCccchhhHHhhhccccchhHHHHHHHHHHHHHHHHhhcCCccc
Q 012374 389 TWAHLGAAFTGIIYGFLTCPLVQLGDASSRNSQEEGITLIRQYANPCKSLIVFTIFVIILGSFIFVFEPPLDT 461 (465)
Q Consensus 389 ~~aHLgG~L~G~llg~l~~~~~~~~~~~~~~~~~~~~~~~r~~~~~~~~ll~f~i~vivl~~~lf~i~pp~~~ 461 (465)
+.+-+||+++|++.++++-+.-..+- ++- +.-|....-..++-.+..++++..+.+++||.+.
T Consensus 95 ~~gvfgGIi~G~i~a~l~nkf~~~kl-------P~~---l~fF~G~rfVpii~~~~~~~~g~i~~~iWP~v~~ 157 (648)
T PRK10255 95 NMGVLAGIITGLVGGAAYNRWSDIKL-------PDF---LSFFGGKRFVPIATGFFCLVLAAIFGYVWPPVQH 157 (648)
T ss_pred chhhhhhhHHHHHHHHHHHHhccccC-------Cce---eeecCCcchhHhHHHHHHHHHHHHHHHhHHHHHH
Confidence 45669999999999998865422211 111 1122322223333344456777788999998763
No 25
>PF06609 TRI12: Fungal trichothecene efflux pump (TRI12); InterPro: IPR010573 This family consists of several fungal specific trichothecene efflux pump proteins. Many of the genes involved in trichothecene toxin biosynthesis in Fusarium sporotrichioides are present within a gene cluster. It has been suggested that TRI12 may play a role in F. sporotrichioides self-protection against trichothecenes [].
Probab=39.37 E-value=6.1e+02 Score=28.67 Aligned_cols=43 Identities=21% Similarity=0.329 Sum_probs=31.8
Q ss_pred HHHHHHHHHHHHHHHHHHhhchhHHHHHHHHHhhhhhhhhcccC
Q 012374 287 HVALSCWALLTFGPQVCKSYGPFTFFLIYTLGGISGNLTSFLHT 330 (465)
Q Consensus 287 HLl~Nml~L~~fG~~LE~~~Gs~rfl~lYllsGi~G~l~s~l~~ 330 (465)
..+.+.....++| .+-..+|++.+++.=.+.+++|.+...--.
T Consensus 87 ~~l~~av~~~~~G-~LSDlfGRr~~~i~g~~l~vvG~Iv~atA~ 129 (599)
T PF06609_consen 87 WTLASAVSFPFVG-RLSDLFGRRYFFIIGSLLGVVGSIVCATAQ 129 (599)
T ss_pred HHHHHHHHHHhhH-HHHHHhcchHHHHHHHHHHHhHHHHhhcCC
Confidence 5556666666666 577999999998888888888888765443
No 26
>KOG1172 consensus Na+-independent Cl/HCO3 exchanger AE1 and related transporters (SLC4 family) [Inorganic ion transport and metabolism]
Probab=39.27 E-value=3.3e+02 Score=32.07 Aligned_cols=118 Identities=15% Similarity=0.169 Sum_probs=60.6
Q ss_pred CHHHHHHHHHHHHHHHHHHHHhh-chhHHHHHHHHHhhhhhhhhcccCCC--CccCchHHHHHHHHHHHHHHhc-chhhh
Q 012374 284 GLFHVALSCWALLTFGPQVCKSY-GPFTFFLIYTLGGISGNLTSFLHTPE--PTVGGTGPVFAIIGAWLIYQFQ-NKDLI 359 (465)
Q Consensus 284 gl~HLl~Nml~L~~fG~~LE~~~-Gs~rfl~lYllsGi~G~l~s~l~~p~--~~VGaSGaVfGLlga~~~~~~~-~~~~l 359 (465)
-+.=.+.++.....||..+++.- |.....-..+.+++ ++++..++... ..+|.+|.+.=..-+..-+.-. .+.++
T Consensus 366 ~lfiYfa~l~P~ItFG~ll~~~Tdg~~~v~E~L~stal-~GiifslfggQPLlIlg~TgP~lVfe~~lf~f~~~~~~dyl 444 (876)
T KOG1172|consen 366 TLFIYFACLLPAITFGGLLGEATDGLIGVVETLLSTAL-CGIIFSLFGGQPLLILGVTGPLLVFEKALFKFCKDNGLDYL 444 (876)
T ss_pred HHHHHHHhhhhHhhHHHHhhhhccchHHHHHHHHHHHH-HHHHHHHhcCCceEEEecCccHHHHHHHHHHHHhhCCCchh
Confidence 34456667777889998887765 33344444444444 44444445443 5889999865444333322211 12222
Q ss_pred hhhhHHHHHHHHHHHHHHHHHHhcC---CchhHHHHHHHHHHHHHHHHHhh
Q 012374 360 AKDVSERMFQKAILSTALSFIISNF---GPVDTWAHLGAAFTGIIYGFLTC 407 (465)
Q Consensus 360 ~~~~~~~l~~~~ii~~~l~~ll~~~---~~is~~aHLgG~L~G~llg~l~~ 407 (465)
.. +++..++. .++.+++... .-+.....+.+=+.|++++++|.
T Consensus 445 ~~----r~wVglW~-~~l~illaa~~as~lv~~~TRfteEiF~~LIs~iFi 490 (876)
T KOG1172|consen 445 AF----RAWVGLWT-AFLLILLAATNASSLVKYITRFTEEIFGLLISLIFI 490 (876)
T ss_pred hH----HHHHHHHH-HHHHHHHHHhhhhHHHHHHHHhHHHHHHHHHHHHHH
Confidence 21 22111111 1111111111 22566677778888888887775
No 27
>PF09527 ATPase_gene1: Putative F0F1-ATPase subunit (ATPase_gene1)
Probab=38.33 E-value=95 Score=23.18 Aligned_cols=42 Identities=26% Similarity=0.241 Sum_probs=31.4
Q ss_pred HHHHHHHHHHHHHHHHHHHhhch-hHHHHHHHHHhhhhhhhhc
Q 012374 286 FHVALSCWALLTFGPQVCKSYGP-FTFFLIYTLGGISGNLTSF 327 (465)
Q Consensus 286 ~HLl~Nml~L~~fG~~LE~~~Gs-~rfl~lYllsGi~G~l~s~ 327 (465)
..++.+++.-..+|..+++.+|+ ..+.++.++-|+++++.+.
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 34667777788999999999999 5666666777777766543
No 28
>KOG0255 consensus Synaptic vesicle transporter SVOP and related transporters (major facilitator superfamily) [General function prediction only]
Probab=37.35 E-value=1.7e+02 Score=31.30 Aligned_cols=45 Identities=18% Similarity=0.124 Sum_probs=32.6
Q ss_pred HHHHHHHHHHHHHHHHHHHHhhchhHHHHHHHHHhhhhhhhhcccC
Q 012374 285 LFHVALSCWALLTFGPQVCKSYGPFTFFLIYTLGGISGNLTSFLHT 330 (465)
Q Consensus 285 l~HLl~Nml~L~~fG~~LE~~~Gs~rfl~lYllsGi~G~l~s~l~~ 330 (465)
-.+++.-++.=+++|..-++ +|++..+.+-++..+++++.+.+..
T Consensus 125 s~~~~G~~vG~~i~g~lsD~-~GRk~~~~~~~~~~~i~~~~~a~a~ 169 (521)
T KOG0255|consen 125 SLFFLGVLVGSLIFGPLSDR-FGRKPVLLVSLLLFIIFGILTAFAP 169 (521)
T ss_pred HHHHHHHHHHHhhheehHhh-cccHHHHHHHHHHHHHHHHHHHHhC
Confidence 45566666666778887777 9999988887777777776655443
No 29
>COG4769 Predicted membrane protein [Function unknown]
Probab=35.64 E-value=2.3e+02 Score=26.82 Aligned_cols=50 Identities=20% Similarity=0.168 Sum_probs=27.7
Q ss_pred hhchhHHHHHHHHHhhhhhhhhc-ccCCCCccCchHHHHHHHHHHHHHHhc
Q 012374 305 SYGPFTFFLIYTLGGISGNLTSF-LHTPEPTVGGTGPVFAIIGAWLIYQFQ 354 (465)
Q Consensus 305 ~~Gs~rfl~lYllsGi~G~l~s~-l~~p~~~VGaSGaVfGLlga~~~~~~~ 354 (465)
.++.+..+.+-++=.+++++++- ++.|.-..+++|++.+.++.++.....
T Consensus 51 ~l~~~~~~~~i~lr~il~AL~sGtlfs~~Fl~sfaG~i~S~L~m~~l~~f~ 101 (181)
T COG4769 51 TLNFKDALQTILLRVILQALFSGTLFSPVFLYSFAGAILSTLFMYFLYQFG 101 (181)
T ss_pred hccHHHHHHHHHHHHHHHHHHcCccchHHHHHHHHHHHHHHHHHHHHHHcC
Confidence 34555555555555555555443 344445666777777777666665543
No 30
>COG1575 MenA 1,4-dihydroxy-2-naphthoate octaprenyltransferase [Coenzyme metabolism]
Probab=35.00 E-value=5.3e+02 Score=26.66 Aligned_cols=20 Identities=20% Similarity=0.107 Sum_probs=14.6
Q ss_pred chHHHHHHHHHHHHHHhcch
Q 012374 337 GTGPVFAIIGAWLIYQFQNK 356 (465)
Q Consensus 337 aSGaVfGLlga~~~~~~~~~ 356 (465)
.+|..||.++....++.+..
T Consensus 153 ~~~vffG~l~v~g~~yiqt~ 172 (303)
T COG1575 153 FVGVFFGPLIVLGAYYIQTG 172 (303)
T ss_pred HHHHHHHHHHHHHHHHHhcc
Confidence 57888888887777776543
No 31
>TIGR02185 Trep_Strep conserved hypothetical integral membrane protein TIGR02185. This family consists of strongly hydrophobic proteins about 190 amino acids in length with a strongly basic motif near the C-terminus. If is found in rather few species, but in paralogous families of 12 members in the oral pathogenic spirochaete Treponema denticola and 2 in Streptococcus pneumoniae R6.
Probab=30.89 E-value=4.7e+02 Score=24.78 Aligned_cols=17 Identities=6% Similarity=0.090 Sum_probs=10.1
Q ss_pred chHHHHHHHHHHHHHHh
Q 012374 337 GTGPVFAIIGAWLIYQF 353 (465)
Q Consensus 337 aSGaVfGLlga~~~~~~ 353 (465)
.+.++.+++++-.....
T Consensus 37 ~~p~i~al~~g~vyml~ 53 (189)
T TIGR02185 37 FSPGITAFLVGIIFFLM 53 (189)
T ss_pred HHHHHHHHHHhHHHhhh
Confidence 45667777766554443
No 32
>PF07301 DUF1453: Protein of unknown function (DUF1453); InterPro: IPR009916 This family consists of several hypothetical bacterial proteins of around 150 residues in length. The function of this family is unknown. Members of this family seem to be found exclusively in the Order Bacillales.
Probab=30.65 E-value=3.3e+02 Score=25.23 Aligned_cols=29 Identities=10% Similarity=0.084 Sum_probs=21.8
Q ss_pred chhHHHHHHHHHHHHHHHHHhhcccccCC
Q 012374 386 PVDTWAHLGAAFTGIIYGFLTCPLVQLGD 414 (465)
Q Consensus 386 ~is~~aHLgG~L~G~llg~l~~~~~~~~~ 414 (465)
.+.++--+.+++.|.++++.+....+++.
T Consensus 54 ~~~~~~~l~A~~~G~lFs~~Li~ts~fEv 82 (148)
T PF07301_consen 54 RPPWLEVLEAFLVGALFSYPLIKTSKFEV 82 (148)
T ss_pred cchHHHHHHHHHHHHHHHHHHHHhceEEE
Confidence 45667778899999999998876655443
No 33
>PF01032 FecCD: FecCD transport family; InterPro: IPR000522 This is a subfamily of bacterial binding-protein-dependent transport systems family, and includes transport system permease proteins involved in the transport across the membrane of several compounds. This entry contains the inner components of this multicomponent transport system.; GO: 0005215 transporter activity, 0016020 membrane; PDB: 4DBL_A 1L7V_B 2QI9_B 2NQ2_A.
Probab=29.18 E-value=2.5e+02 Score=28.75 Aligned_cols=31 Identities=19% Similarity=0.343 Sum_probs=21.3
Q ss_pred cchhHHHHHHHHHHHHHHHHhhcCCccccCC
Q 012374 434 PCKSLIVFTIFVIILGSFIFVFEPPLDTLAL 464 (465)
Q Consensus 434 ~~~~ll~f~i~vivl~~~lf~i~pp~~~~~~ 464 (465)
.+..+......+++....+++.++++|.+.+
T Consensus 174 ~~~~~~~~~~~~~i~~~~~~~~~~~L~~l~l 204 (311)
T PF01032_consen 174 SWEQLYILLPLLLIGLILLLLLSRKLDILSL 204 (311)
T ss_dssp SHHHHHHHHHHHHHHHHHHCCTCCHHHHHCT
T ss_pred cchhHHHHHHHHHHHHHHHHHHHhHHHHHhc
Confidence 3445555555666666688889999887764
No 34
>PRK10263 DNA translocase FtsK; Provisional
Probab=28.74 E-value=1.2e+02 Score=37.14 Aligned_cols=13 Identities=23% Similarity=0.508 Sum_probs=6.5
Q ss_pred HHHHHHHHHHHHH
Q 012374 228 ILVSIDVAVFLFE 240 (465)
Q Consensus 228 ~Li~inv~VFil~ 240 (465)
.++++.+++|++.
T Consensus 27 gIlLlllAlfL~l 39 (1355)
T PRK10263 27 LILIVLFAVWLMA 39 (1355)
T ss_pred HHHHHHHHHHHHH
Confidence 4444555555543
No 35
>TIGR02005 PTS-IIBC-alpha PTS system, alpha-glucoside-specific IIBC component. This model represents a family of fused PTS enzyme II B and C domains. A gene from Clostridium has been partially characterized as a maltose transporter, while genes from Fusobacterium and Klebsiella have been proposed to transport the five non-standard isomers of sucrose.
Probab=25.84 E-value=82 Score=34.92 Aligned_cols=63 Identities=6% Similarity=0.055 Sum_probs=36.9
Q ss_pred HHHHHHHHHHHHHHHHHhhcccccCCcCcCCccchhhHHhhhccccchhHHHHHHHHHHHHHHHHhhcCCccc
Q 012374 389 TWAHLGAAFTGIIYGFLTCPLVQLGDASSRNSQEEGITLIRQYANPCKSLIVFTIFVIILGSFIFVFEPPLDT 461 (465)
Q Consensus 389 ~~aHLgG~L~G~llg~l~~~~~~~~~~~~~~~~~~~~~~~r~~~~~~~~ll~f~i~vivl~~~lf~i~pp~~~ 461 (465)
+.+-+||+++|++.++++-+.-+.+ .++-.. -|..+.-.-++-.+..++++.++.+++||.+.
T Consensus 136 ~~gVfgGIi~G~i~a~l~Nkf~~ik-------LP~~L~---FF~G~RfVpIi~~~~~~~l~~~~~~iWP~i~~ 198 (524)
T TIGR02005 136 DTSIIGAIIISGIITYIHNRFFDKR-------LPVFLG---IFQGTTFVVTIAFFVMLPCAAITCLVWPKVQM 198 (524)
T ss_pred cchhHHHHHHHHHHHHHHHHHhccc-------cchhhh---hcCCCcchHhHHHHHHHHHHHHHHHHHHHHHH
Confidence 5667999999999999986542211 111122 22222222333333346667788899998763
No 36
>PF10066 DUF2304: Uncharacterized conserved protein (DUF2304); InterPro: IPR019277 This entry represents hypothetical archaeal and bacterial proteins that have no known function.
Probab=25.69 E-value=2e+02 Score=24.99 Aligned_cols=20 Identities=25% Similarity=-0.001 Sum_probs=12.6
Q ss_pred HhcCCc-hhHHHHHHHHHHHH
Q 012374 381 ISNFGP-VDTWAHLGAAFTGI 400 (465)
Q Consensus 381 l~~~~~-is~~aHLgG~L~G~ 400 (465)
++.+|+ .++.||+-|+-.|.
T Consensus 46 ~~ifP~~~~~vA~~lGi~~~~ 66 (115)
T PF10066_consen 46 LSIFPNILDWVAKLLGIGRPP 66 (115)
T ss_pred HHhhhhHHHHHHHHHCCCchh
Confidence 344555 56668888866553
No 37
>PF15183 MRAP: Melanocortin-2 receptor accessory protein family
Probab=25.16 E-value=56 Score=27.36 Aligned_cols=24 Identities=25% Similarity=0.426 Sum_probs=19.9
Q ss_pred cccchhHHHHHHHHHHHHHHHHhh
Q 012374 432 ANPCKSLIVFTIFVIILGSFIFVF 455 (465)
Q Consensus 432 ~~~~~~ll~f~i~vivl~~~lf~i 455 (465)
.+++.++++|++.++++++++|++
T Consensus 33 a~kysIVI~FWv~LA~FV~~lF~i 56 (90)
T PF15183_consen 33 ANKYSIVIAFWVSLAAFVVFLFLI 56 (90)
T ss_pred ccceeeehhHHHHHHHHHHHHHHH
Confidence 456779999999999999977765
No 38
>COG4393 Predicted membrane protein [Function unknown]
Probab=25.13 E-value=8.3e+02 Score=25.79 Aligned_cols=97 Identities=16% Similarity=0.096 Sum_probs=54.3
Q ss_pred hchhHHHHHHHHHhhhhhhhhcccCC--CCccCchHHHHHHHHHHHHHHhcchhhhhhhhHHHHHHHHHHHHHHHHHHhc
Q 012374 306 YGPFTFFLIYTLGGISGNLTSFLHTP--EPTVGGTGPVFAIIGAWLIYQFQNKDLIAKDVSERMFQKAILSTALSFIISN 383 (465)
Q Consensus 306 ~Gs~rfl~lYllsGi~G~l~s~l~~p--~~~VGaSGaVfGLlga~~~~~~~~~~~l~~~~~~~l~~~~ii~~~l~~ll~~ 383 (465)
+-..+...+-++.|+.|...+..+.. ....-.++...|.+-.++..+...+..+. -++.+++..+..+..+.
T Consensus 29 ~~~~~vvwl~~L~~~~g~~~~~y~pKsq~~~l~l~~v~i~sLLlf~~sqfw~~i~l~------~Fw~~lLsF~aaL~wg~ 102 (405)
T COG4393 29 FKSFFVVWLGFLFGYFGFFIAAYFPKSQNLILNLDFVFIGSLLLFFISQFWKKIELL------NFWLLLLSFCAALHWGF 102 (405)
T ss_pred hhHHHHHHHHHHHHHHHHHHHHhcccccceeehhHHHHHHHHHHHHHHHHHHHHHHH------HHHHHHHHHHHHHhhcc
Confidence 34455566667778888777665532 34566788887777666665443222211 12222222222221121
Q ss_pred C-----------CchhHHHHHHHHHHHHHHHHHhhc
Q 012374 384 F-----------GPVDTWAHLGAAFTGIIYGFLTCP 408 (465)
Q Consensus 384 ~-----------~~is~~aHLgG~L~G~llg~l~~~ 408 (465)
. -+.+...|+||++.|++..++..-
T Consensus 103 ~~n~f~if~tdvinTd~ll~lg~i~lall~~ilia~ 138 (405)
T COG4393 103 MPNLFAIFGTDVINTDSLLRLGAILLALLTIILIAL 138 (405)
T ss_pred CccccccccccccccHHHHHhHHHHHHHHHHHHHHH
Confidence 1 135777899999999987776643
No 39
>PF04632 FUSC: Fusaric acid resistance protein family; InterPro: IPR006726 This entry represents the p-hydroxybenzoic acid efflux pump subunit AaeB (pHBA efflux pump protein B) whose substrates are p-hydroxybenzoic acid (pHBA), 6-hydroxy-2-naphthoic and 2-hydroxycinnamate. It could function as a metabolic relief valve, allowing to eliminate certain compounds when they accumulate to high levels in the cell []. This family also includes fusaric acid resistance proteins [], which are likely to be membrane transporter proteins, and uncharacterised transporter YdhK.; GO: 0006810 transport, 0005886 plasma membrane
Probab=25.02 E-value=3.8e+02 Score=29.72 Aligned_cols=15 Identities=27% Similarity=0.279 Sum_probs=7.0
Q ss_pred HHHHHHHHHHHHHHh
Q 012374 392 HLGAAFTGIIYGFLT 406 (465)
Q Consensus 392 HLgG~L~G~llg~l~ 406 (465)
...|.+.|++++++.
T Consensus 471 ~~la~l~G~~~a~l~ 485 (650)
T PF04632_consen 471 RALAILLGIVIAALV 485 (650)
T ss_pred HHHHHHHHHHHHHHH
Confidence 344455555544443
No 40
>COG3263 NhaP-type Na+/H+ and K+/H+ antiporters with a unique C-terminal domain [Inorganic ion transport and metabolism]
Probab=24.22 E-value=7e+02 Score=27.50 Aligned_cols=56 Identities=18% Similarity=0.215 Sum_probs=29.8
Q ss_pred CCHHHHHHHHHHHHHHHHHHHHhhchhHH---------HHHHHHHhhhhhhhhcccCCCCccCchHHH
Q 012374 283 SGLFHVALSCWALLTFGPQVCKSYGPFTF---------FLIYTLGGISGNLTSFLHTPEPTVGGTGPV 341 (465)
Q Consensus 283 ~gl~HLl~Nml~L~~fG~~LE~~~Gs~rf---------l~lYllsGi~G~l~s~l~~p~~~VGaSGaV 341 (465)
-++.|++. .+.++-+|..+--..|..-. -.+|-+-.+.++++.+.+. ..+|+||-+
T Consensus 182 l~~~~ll~-f~~q~glG~l~G~~gg~l~~~~Inr~nLd~GL~pil~la~~Ll~fs~t--~aiGGsG~L 246 (574)
T COG3263 182 LSWGFLLG-FLQQFGLGLLLGLGGGKLLLQLINRINLDSGLYPILALAGGLLIFSLT--GAIGGSGIL 246 (574)
T ss_pred cCHHHHHH-HHHHhhHHHHHHHHHHHHHHHHHHhhccccchhHHHHHHHHHHHHHHH--HHhcCcccH
Confidence 45666666 44444444444333333211 1345556666666666554 578999854
No 41
>TIGR03869 F420-0_ABCperm proposed F420-0 ABC transporter, permease protein. his small clade of ABC-type transporter permease protein components is found as a three gene cassette along with a periplasmic substrate-binding protein (TIGR03868) and an ATPase (TIGR03873). The organisms containing this cassette are all Actinobacteria and all contain numerous genes requiring the coenzyme F420. This model was defined based on five such organisms, four of which are lacking all F420 biosynthetic capability save the final side-chain polyglutamate attachment step (via the gene cofE: TIGR01916). In Jonesia denitrificans DSM 20603 and marine actinobacterium PHSC20C1 this cassette is in an apparent operon with the cofE gene and, in PHSC20C1, also with an F420-dependent glucose-6-phosphate dehydrogenase (TIGR03554). Based on these observations we propose that this permease protein is a component of a F420-0 (that is, F420 lacking only the polyglutamate tail) transporter.
Probab=23.74 E-value=8e+02 Score=25.43 Aligned_cols=28 Identities=18% Similarity=0.293 Sum_probs=17.8
Q ss_pred hHHHHHHHHHHHHHHHHhhcCCccccCC
Q 012374 437 SLIVFTIFVIILGSFIFVFEPPLDTLAL 464 (465)
Q Consensus 437 ~ll~f~i~vivl~~~lf~i~pp~~~~~~ 464 (465)
.+......+++...+++...+++|.+++
T Consensus 186 ~~~~~~~~~~~~~~~~~~~~~~L~~L~L 213 (325)
T TIGR03869 186 SVAIAGGALLVVGLVLLASGRVLDAFAF 213 (325)
T ss_pred HHHHHHHHHHHHHHHHHHHHHhCccccc
Confidence 4444444444455567778999998875
No 42
>TIGR00806 rfc RFC reduced folate carrier. Proteins of the RFC family are so-far restricted to animals. RFC proteins possess 12 putative transmembrane a-helical spanners (TMSs) and evidence for a 12 TMS topology has been published for the human RFC. The RFC transporters appear to transport reduced folate by an energy-dependent, pH-dependent, Na+-independent mechanism. Folate:H+ symport, folate:OH- antiport and folate:anion antiport mechanisms have been proposed, but the energetic mechanism is not well defined.
Probab=23.56 E-value=1e+03 Score=26.39 Aligned_cols=32 Identities=9% Similarity=-0.082 Sum_probs=18.0
Q ss_pred HHHHHHHHHHHHHhhchhHHHHHHHHHhhhhhh
Q 012374 292 CWALLTFGPQVCKSYGPFTFFLIYTLGGISGNL 324 (465)
Q Consensus 292 ml~L~~fG~~LE~~~Gs~rfl~lYllsGi~G~l 324 (465)
++.+...| .+-..+|.++++.+-+++..+..+
T Consensus 76 al~qIp~G-lLaDrlG~K~vL~l~~l~Wsl~t~ 107 (511)
T TIGR00806 76 LAVLVPVF-LLTDYLRYKPVLVLQALSFVCVWL 107 (511)
T ss_pred HHHHHHHH-HHHHHhCchHHHHHHHHHHHHHHH
Confidence 34444444 566778888876655544444433
No 43
>KOG2533 consensus Permease of the major facilitator superfamily [Carbohydrate transport and metabolism]
Probab=22.70 E-value=3.5e+02 Score=29.67 Aligned_cols=16 Identities=38% Similarity=0.401 Sum_probs=11.3
Q ss_pred HHHHHHHHHHHHHHHh
Q 012374 391 AHLGAAFTGIIYGFLT 406 (465)
Q Consensus 391 aHLgG~L~G~llg~l~ 406 (465)
+-+|++++|++.+.++
T Consensus 179 ~~~g~i~ggliA~g~~ 194 (495)
T KOG2533|consen 179 ASLGNIFGGLIAYGVF 194 (495)
T ss_pred cchhhHHHHHHHHHhh
Confidence 4578888888766654
No 44
>PTZ00207 hypothetical protein; Provisional
Probab=22.57 E-value=1.1e+03 Score=26.45 Aligned_cols=31 Identities=19% Similarity=0.229 Sum_probs=21.2
Q ss_pred HHHHHHHHhhchhHHHHHHHHHhhhhhhhhcc
Q 012374 297 TFGPQVCKSYGPFTFFLIYTLGGISGNLTSFL 328 (465)
Q Consensus 297 ~fG~~LE~~~Gs~rfl~lYllsGi~G~l~s~l 328 (465)
..| .+-..+|+++.+.+-.+...+|.+...+
T Consensus 80 p~G-~L~Dr~G~R~vllig~ll~~iG~ll~al 110 (591)
T PTZ00207 80 PYS-FIYDYLGPRPIFVLSMTVFCLGTLLFAL 110 (591)
T ss_pred HHH-HHHHHhCcHHHHHHHHHHHHHHHHHHHH
Confidence 345 4556789999887777766666665544
No 45
>PRK10263 DNA translocase FtsK; Provisional
Probab=22.18 E-value=1.6e+03 Score=28.09 Aligned_cols=14 Identities=14% Similarity=0.183 Sum_probs=7.8
Q ss_pred chHHHHHHHHHHHH
Q 012374 337 GTGPVFAIIGAWLI 350 (465)
Q Consensus 337 aSGaVfGLlga~~~ 350 (465)
.+|++.|.+.+.+.
T Consensus 141 ~gGGIIG~lLs~lL 154 (1355)
T PRK10263 141 ASGGVIGSLLSTTL 154 (1355)
T ss_pred cccchHHHHHHHHH
Confidence 45666666554443
No 46
>PF12732 YtxH: YtxH-like protein; InterPro: IPR024623 This family of uncharacterised proteins is found in bacteria. Proteins in this family are typically between 100 and 143 amino acids in length. The N-terminal region is the most conserved.
Probab=22.14 E-value=95 Score=24.70 Aligned_cols=20 Identities=30% Similarity=0.411 Sum_probs=16.6
Q ss_pred HHHHHHHHHHHHHHHHhhcc
Q 012374 390 WAHLGAAFTGIIYGFLTCPL 409 (465)
Q Consensus 390 ~aHLgG~L~G~llg~l~~~~ 409 (465)
.+-+.|+++|.+.|+++.|.
T Consensus 3 ~g~l~Ga~~Ga~~glL~aP~ 22 (74)
T PF12732_consen 3 LGFLAGAAAGAAAGLLFAPK 22 (74)
T ss_pred HHHHHHHHHHHHHHHHhCCC
Confidence 45678999999999999875
No 47
>PF03814 KdpA: Potassium-transporting ATPase A subunit; InterPro: IPR004623 Kdp is a high affinity ATP-driven K+ transport system in Escherichia coli. It is composed of three membrane-bound subunits, KdpA, KdpB and KdpC and one small peptide, KdpF. KdpA is the K+-transporting subunit of this complex. During assembly of the complex, KdpA and KdpC bind to each other. This interaction is thought to stabilise the complex. Data indicates that KdpC might connect the KdpA, the K+-transporting subunit, to KdpB, the ATP-hydrolysing (energy providing) subunit [].; GO: 0008556 potassium-transporting ATPase activity, 0006813 potassium ion transport, 0005886 plasma membrane
Probab=22.12 E-value=4.1e+02 Score=29.67 Aligned_cols=142 Identities=14% Similarity=0.060 Sum_probs=67.4
Q ss_pred HHHHHHhhchhHHHHHHHHHhhhhhhhhccc---------CCCCccCchHHHHHHHHHHHHHHhcchhhhhhhhHHHHHH
Q 012374 299 GPQVCKSYGPFTFFLIYTLGGISGNLTSFLH---------TPEPTVGGTGPVFAIIGAWLIYQFQNKDLIAKDVSERMFQ 369 (465)
Q Consensus 299 G~~LE~~~Gs~rfl~lYllsGi~G~l~s~l~---------~p~~~VGaSGaVfGLlga~~~~~~~~~~~l~~~~~~~l~~ 369 (465)
|..=++..++++|..-.++.-+++.++.++. .|...-|.| .-.++=.|....--.||+.+........+.
T Consensus 46 Gvd~~~em~Wk~Ya~alL~fN~~~~l~~~~ll~~Q~~LPlNP~~~~~~s-~dlAfNTAiSFvTNTNwQ~YsGEstlSyls 124 (552)
T PF03814_consen 46 GVDPEEEMSWKQYALALLAFNLIGFLLLYLLLRLQGWLPLNPQGFPGMS-PDLAFNTAISFVTNTNWQHYSGESTLSYLS 124 (552)
T ss_pred CCCCcCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHhccCccCCCCCC-cchhhhhhhhhhccCcccccCCcchHHHHH
Confidence 3333455666666655555554444443322 122222222 233444444444456777665543333333
Q ss_pred HHHHHHHHHHHHhcCCchhHHHHHHHHHHHHHHHHHhhcccccCCcCcCCccchhhHHhhhccccchhHHHHHHHHHHHH
Q 012374 370 KAILSTALSFIISNFGPVDTWAHLGAAFTGIIYGFLTCPLVQLGDASSRNSQEEGITLIRQYANPCKSLIVFTIFVIILG 449 (465)
Q Consensus 370 ~~ii~~~l~~ll~~~~~is~~aHLgG~L~G~llg~l~~~~~~~~~~~~~~~~~~~~~~~r~~~~~~~~ll~f~i~vivl~ 449 (465)
....+...+ +..+.+|++.++.+.|.+..++... .-.-|.+..|.++..++=+.++.
T Consensus 125 Qm~gLtvqn--------------FvSAAtGiAv~~AliRg~~~~~~~~---------iGNFwvDl~R~~l~vLLPlS~v~ 181 (552)
T PF03814_consen 125 QMAGLTVQN--------------FVSAATGIAVAIALIRGFARKETKT---------IGNFWVDLVRSTLRVLLPLSFVF 181 (552)
T ss_pred HHHHHHHHH--------------HHhHHHHHHHHHHHHHHHHhccCCC---------CCchHHHHHHHHHHHHHHHHHHH
Confidence 333333223 2345567777777776654332111 11123333444444444344445
Q ss_pred HHHHhhcCCccccCC
Q 012374 450 SFIFVFEPPLDTLAL 464 (465)
Q Consensus 450 ~~lf~i~pp~~~~~~ 464 (465)
.++++.-.+.||+++
T Consensus 182 AliLv~qGVpQtf~~ 196 (552)
T PF03814_consen 182 ALILVSQGVPQTFSG 196 (552)
T ss_pred HHHHHhcCccccccC
Confidence 577777778887754
No 48
>cd03381 PAP2_glucose_6_phosphatase PAP2_like proteins, glucose-6-phosphatase subfamily. Glucose-6-phosphatase converts glucose-6-phosphate into free glucose and is active in the lumen of the endoplasmic reticulum, where it is bound to the membrane. The generation of free glucose is an important control point in metabolism, and stands at the end of gluconeogenesis and the release of glucose from glycogen. Deficiency of glucose-6-phosphatase leads to von Gierke's disease.
Probab=21.79 E-value=7.1e+02 Score=24.60 Aligned_cols=17 Identities=12% Similarity=0.104 Sum_probs=13.6
Q ss_pred HHHHHHHHHHHHHHhhc
Q 012374 392 HLGAAFTGIIYGFLTCP 408 (465)
Q Consensus 392 HLgG~L~G~llg~l~~~ 408 (465)
.++|.+.|++.+..+..
T Consensus 136 VlaG~~lGi~~~~~~~~ 152 (235)
T cd03381 136 VIAGVISGIAVAETFSH 152 (235)
T ss_pred HHHHHHHHHHHHHHHHH
Confidence 48899999988887754
No 49
>COG3105 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=21.53 E-value=92 Score=28.20 Aligned_cols=22 Identities=32% Similarity=0.204 Sum_probs=17.0
Q ss_pred hHHHHHHHHHHHHHHHHHhhcc
Q 012374 388 DTWAHLGAAFTGIIYGFLTCPL 409 (465)
Q Consensus 388 s~~aHLgG~L~G~llg~l~~~~ 409 (465)
.|.+-+.|+++|+++|+++.+-
T Consensus 7 ~W~~a~igLvvGi~IG~li~Rl 28 (138)
T COG3105 7 TWEYALIGLVVGIIIGALIARL 28 (138)
T ss_pred HHHHHHHHHHHHHHHHHHHHHH
Confidence 3556777899999999988754
No 50
>TIGR00680 kdpA K+-transporting ATPase, KdpA. Kdp is a high affinity ATP-driven K+ transport system in Escherichia coli. It is composed of three membrane-bound subunits, KdpA, KdpB and KdpC and one small peptide, KdpF. KdpA is the K+-transporting subunit of this complex. During assembly of the complex, KdpA and KdpC bind to each other. This interaction is thought to stabilize the complex [PubMed:9858692]. Data indicates that KdpC might connect the KdpA, the K+-transporting subunit, to KdpB, the ATP-hydrolyzing (energy providing) subunit PubMed:9858692].
Probab=21.15 E-value=7.1e+02 Score=27.91 Aligned_cols=144 Identities=13% Similarity=0.082 Sum_probs=73.5
Q ss_pred HHHHHHHhhchhHHHHHHHHHhhhhhhhhcccC------C-C-CccCchHHHHHHHHHHHHHHhcchhhhhhhhHHHHHH
Q 012374 298 FGPQVCKSYGPFTFFLIYTLGGISGNLTSFLHT------P-E-PTVGGTGPVFAIIGAWLIYQFQNKDLIAKDVSERMFQ 369 (465)
Q Consensus 298 fG~~LE~~~Gs~rfl~lYllsGi~G~l~s~l~~------p-~-~~VGaSGaVfGLlga~~~~~~~~~~~l~~~~~~~l~~ 369 (465)
.|..-++..++++|..-.+..-+++.++.++.. | . ...++-..-.++=.+....--.||+.+........+.
T Consensus 53 ~Gvd~~~em~Wk~Ya~alL~fn~~~~~~~~~il~~Q~~LPlNP~~~~~~s~~lAfNTavSFvTNTNwQ~YsGE~tlSy~s 132 (563)
T TIGR00680 53 SGVTKHPEMGWTQYVSAALISNLVMGVFLFLILMFQGSLPLNPTGLPAPSWDLALNTAVSFVTNTNWQSYSGETTYSYFS 132 (563)
T ss_pred HCCCCcccCCHHHHHHHHHHHHHHHHHHHHHHHHHHhhCCCCcccCCCCChhHHHHhHhhhhccCccccccCcchHHHHH
Confidence 354445667788887777666666665554321 2 1 1233323334444455554556777766544333333
Q ss_pred HHHHHHHHHHHHhcCCchhHHHHHHHHHHHHHHHHHhhcccccCCcCcCCccchhhHHhhhccccchhHHHHHHHHHHHH
Q 012374 370 KAILSTALSFIISNFGPVDTWAHLGAAFTGIIYGFLTCPLVQLGDASSRNSQEEGITLIRQYANPCKSLIVFTIFVIILG 449 (465)
Q Consensus 370 ~~ii~~~l~~ll~~~~~is~~aHLgG~L~G~llg~l~~~~~~~~~~~~~~~~~~~~~~~r~~~~~~~~ll~f~i~vivl~ 449 (465)
..+.+...+ +..+.+|+..+..+.|.+..++... .-.-|.+..|.++..++=+.++.
T Consensus 133 Qm~gl~~~n--------------F~SAAtGiava~AliRgl~~~~~~~---------lGNFwvDl~R~~l~vLLPlS~i~ 189 (563)
T TIGR00680 133 QMGGLGVQN--------------FTSAATGIAVAIALIRGLTRQSMST---------LGNFWVDLVRSILRILLPISLVG 189 (563)
T ss_pred HHHHHHHHH--------------HHhHHHHHHHHHHHHHHHhccCCCC---------CCchhHHHHHHHHHHHHHHHHHH
Confidence 333333233 2345567777777766554332100 11223334444444444445555
Q ss_pred HHHHhhcCCccccCC
Q 012374 450 SFIFVFEPPLDTLAL 464 (465)
Q Consensus 450 ~~lf~i~pp~~~~~~ 464 (465)
.++++.-...||++.
T Consensus 190 Al~lv~qGvpQt~~~ 204 (563)
T TIGR00680 190 AILLLVQGVPQNLAG 204 (563)
T ss_pred HHHHHhCCCCcccCC
Confidence 577777778777653
No 51
>PRK10712 PTS system fructose-specific transporter subunits IIBC; Provisional
Probab=20.91 E-value=1.6e+02 Score=32.93 Aligned_cols=19 Identities=16% Similarity=0.461 Sum_probs=15.1
Q ss_pred HHHHHHHHHHHHHHHHHhh
Q 012374 389 TWAHLGAAFTGIIYGFLTC 407 (465)
Q Consensus 389 ~~aHLgG~L~G~llg~l~~ 407 (465)
..+-+||+++|++.|++..
T Consensus 313 ~~GFlG~Ilag~lagyv~~ 331 (563)
T PRK10712 313 GSGFIGGIIAGFLAGYVAK 331 (563)
T ss_pred CchHHHHHHHHHHHHHHHH
Confidence 3678888999999888763
No 52
>COG4395 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=20.89 E-value=2e+02 Score=29.43 Aligned_cols=27 Identities=15% Similarity=0.427 Sum_probs=20.2
Q ss_pred hHHHHHHHHHHHHHHHHhhcCCccccC
Q 012374 437 SLIVFTIFVIILGSFIFVFEPPLDTLA 463 (465)
Q Consensus 437 ~ll~f~i~vivl~~~lf~i~pp~~~~~ 463 (465)
.++.++.++.+++..++...|+.++-.
T Consensus 58 ~~~~~l~l~~lig~~~~~~~r~f~~~r 84 (281)
T COG4395 58 AFLIFLLLITLIGFVIMLEMRFFDPYR 84 (281)
T ss_pred HHHHHHHHHHHHHHHHHHhcccccccc
Confidence 556667777778888888888888643
No 53
>COG1296 AzlC Predicted branched-chain amino acid permease (azaleucine resistance) [Amino acid transport and metabolism]
Probab=20.56 E-value=6e+02 Score=25.25 Aligned_cols=21 Identities=24% Similarity=0.597 Sum_probs=15.6
Q ss_pred hHHHHHHHHHHHHHHHHHhhc
Q 012374 388 DTWAHLGAAFTGIIYGFLTCP 408 (465)
Q Consensus 388 s~~aHLgG~L~G~llg~l~~~ 408 (465)
..+.-+.|.++|++...+..+
T Consensus 210 ~~~~v~~~~la~l~~~~l~~~ 230 (238)
T COG1296 210 GPWAVLAGILAGLLAALLLAA 230 (238)
T ss_pred HHHHHHHHHHHHHHHHHHhcc
Confidence 456778888888888777654
No 54
>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=20.40 E-value=74 Score=27.37 Aligned_cols=25 Identities=12% Similarity=0.121 Sum_probs=18.5
Q ss_pred cHHHHHHHHHHHHHhhcCcCCCCCc
Q 012374 104 SECQIRILESYLAKLKDDSIQNSSE 128 (465)
Q Consensus 104 ~~~~~~~~~~~~~~~~~~~~~~s~~ 128 (465)
||+++++++..++.|..||.++...
T Consensus 43 de~~~~~a~~el~~Fl~nP~~~rYq 67 (101)
T PF12122_consen 43 DEEHLEQAEQELEEFLQNPNDPRYQ 67 (101)
T ss_dssp -GGGHHHHHHHHHHHHHS-SS----
T ss_pred CHHHHHHHHHHHHHHHHCCCCHHHH
Confidence 8999999999999999999988654
Done!