Query 045959
Match_columns 303
No_of_seqs 310 out of 1882
Neff 6.9
Searched_HMMs 46136
Date Fri Mar 29 07:19:48 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/045959.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/045959hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG2289 Rhomboid family protei 100.0 5.6E-37 1.2E-41 285.9 6.8 261 29-295 30-316 (316)
2 PTZ00101 rhomboid-1 protease; 100.0 5.8E-30 1.3E-34 236.7 20.4 168 32-227 46-240 (278)
3 KOG2290 Rhomboid family protei 100.0 1.3E-28 2.9E-33 234.3 7.9 199 87-302 421-643 (652)
4 PRK10907 intramembrane serine 99.9 2.6E-24 5.7E-29 199.3 15.5 154 38-227 93-270 (276)
5 COG0705 Membrane associated se 99.9 1.6E-21 3.5E-26 175.8 13.4 167 38-230 16-214 (228)
6 PF01694 Rhomboid: Rhomboid fa 99.8 2.5E-19 5.3E-24 149.6 6.4 118 112-229 2-144 (145)
7 KOG2632 Rhomboid family protei 99.4 9.1E-12 2E-16 113.0 12.5 117 108-224 45-195 (258)
8 PF08551 DUF1751: Eukaryotic i 98.1 4.7E-06 1E-10 66.1 5.3 54 115-168 7-60 (99)
9 PF04511 DER1: Der1-like famil 97.8 0.00038 8.3E-09 61.7 12.2 63 106-168 32-98 (197)
10 KOG2980 Integral membrane prot 97.6 3E-05 6.6E-10 72.2 2.0 54 115-168 154-208 (310)
11 KOG0858 Predicted membrane pro 97.0 0.0028 6.1E-08 57.4 7.6 96 36-168 10-109 (239)
12 KOG2890 Predicted membrane pro 93.4 0.099 2.2E-06 49.1 4.3 54 115-168 66-119 (326)
13 KOG4463 Uncharacterized conser 93.4 0.048 1E-06 50.2 2.1 57 111-168 46-102 (323)
14 KOG2290 Rhomboid family protei 90.0 0.37 7.9E-06 47.8 4.1 84 37-121 198-286 (652)
15 COG5291 Predicted membrane pro 89.6 1.1 2.4E-05 41.2 6.5 42 107-148 51-93 (313)
16 TIGR00341 conserved hypothetic 56.9 99 0.0021 29.7 9.7 81 154-235 210-296 (325)
17 PF09527 ATPase_gene1: Putativ 42.6 1.1E+02 0.0024 20.9 6.4 39 130-168 8-47 (55)
18 COG2056 Predicted permease [Ge 34.6 76 0.0017 31.2 5.1 25 212-236 198-222 (444)
19 PF12669 P12: Virus attachment 32.9 86 0.0019 22.2 4.0 18 284-302 29-47 (58)
20 TIGR02854 spore_II_GA sigma-E 30.3 3.1E+02 0.0068 25.6 8.5 35 130-168 11-45 (288)
21 PF07895 DUF1673: Protein of u 25.4 2.9E+02 0.0063 24.5 7.0 12 213-224 83-94 (205)
22 PF01944 DUF95: Integral membr 25.1 4E+02 0.0086 22.1 8.7 22 207-228 111-132 (173)
23 TIGR02230 ATPase_gene1 F0F1-AT 24.1 3.4E+02 0.0073 21.5 6.3 39 130-168 50-89 (100)
24 PF12732 YtxH: YtxH-like prote 23.8 88 0.0019 22.9 2.9 22 210-231 4-25 (74)
25 PF03419 Peptidase_U4: Sporula 23.1 4.6E+02 0.0099 24.3 8.2 35 130-168 11-45 (293)
26 PF01034 Syndecan: Syndecan do 22.9 26 0.00057 25.5 -0.1 20 209-228 12-31 (64)
27 PF05546 She9_MDM33: She9 / Md 22.3 73 0.0016 28.6 2.5 22 38-59 151-172 (207)
28 TIGR02302 aProt_lowcomp conser 20.3 3.9E+02 0.0085 29.2 7.9 20 252-271 137-156 (851)
No 1
>KOG2289 consensus Rhomboid family proteins [Signal transduction mechanisms]
Probab=100.00 E-value=5.6e-37 Score=285.95 Aligned_cols=261 Identities=52% Similarity=0.885 Sum_probs=223.7
Q ss_pred CCCCCCCcccccHHHHHHHHHHHHHHHHHHHhcCCCCCCC-CCCchhhh-hhcccccccCCCCCCCCCChhHHHhhcccc
Q 045959 29 VEPGSDQQWTSWLIPMFVVANVAVFIVAMYINNCPKNNWE-GGRGCVAR-FLGRLSFEPLKENPLFGPSSSTLQKLGALE 106 (303)
Q Consensus 29 ~~~~~~~~~~p~vt~~li~inv~VFl~~~~~~~~~~~~~~-~~~~~~~~-~l~~~~~~P~~~n~l~gp~~~~L~~~Ga~~ 106 (303)
+++..++.++++....+...|+..|+..++.++|+...++ .-..|... ++.+|.|++.++|+..+|+..++..+|+..
T Consensus 30 ~~~~~~~~~~~~~i~~~~~~~~~~~~~~~~~~d~~~~~~~~~f~~~~~~~~l~~f~~~~~~~n~~~~~s~~~~~~~~~~~ 109 (316)
T KOG2289|consen 30 RDKLLPRSWTKWLIPRFAVANVPEFIVVMYVNDCPKCCPPPIFMLCLAIVFLGRFSFQGLRENPLLGPSSLTLEKMGGLL 109 (316)
T ss_pred ccccccchhhHHHHhHHHhhccchhheeeeeecccccCCCchhhhhhhhhhhheeeeeeeccCCccCcCCCCccccCCce
Confidence 4444557788899999999999999888999998764433 12236666 899999999999999999999999999999
Q ss_pred hhhhhccCceeeeehhhhccccHHHHHHHHHHHHHHHHHHHHHhchHHHHHHHHHHHHHHHH-HHHHhcCCcee------
Q 045959 107 WDRVVHEHQGWRLITCIWLHAGVIHLLANMLSLVFIGIRLEQQFGFVRVGFVYLLSGFGGAY-YLLFLFNAVSL------ 179 (303)
Q Consensus 107 ~~~i~~~~q~wRl~T~~FlH~~~~HLl~Nm~~l~~~G~~lE~~~G~~r~~~lyl~sgi~g~l-~~~~~~~~~~v------ 179 (303)
....+.++|+||++|++|+|+|+.||++||+.|.++|..+|+.+|.+|+.++|+++|++|++ ++++.+.+.+|
T Consensus 110 i~~~~~r~E~WRllTym~LHaGi~HL~~N~~~ql~iGi~LE~~~G~~RiglIYl~gg~aGSlls~l~d~~~~sVGASggv 189 (316)
T KOG2289|consen 110 IYKPVHRGELWRLLTYMWLHAGIFHLLLNMLSQLFIGIPLEQVHGFLRIGLIYLAGGVAGSLLSSLFDPNSISVGASGGV 189 (316)
T ss_pred ecChhhhchhHHHHHHHHHhcCHHHHHHHHHHHHhccccHHhhcCceEEeeehhhhhhhhHHHHHHhccCCceecccHHH
Confidence 99999999999999999999999999999999999999999999999999999999999999 99998876544
Q ss_pred eehhHHHH-----------------HHHHHHHHHHHHHhcCchHhHHHHHHHHHHHHHHHHHHhhccccchhhhccCchh
Q 045959 180 LVLLAAAL-----------------LTLVVIIAINLAVGILPHVDNFAHIGGFMAGFLLGFVLLLRPQFGWAERHQLPAQ 242 (303)
Q Consensus 180 ~Gll~~~l-----------------~~l~~~~~~~l~~g~~p~v~~~aHlgG~l~G~l~g~~l~~~~~~~~~~~~~~p~~ 242 (303)
||++++.+ ..+++++.+++.+|+.|++|+++|+||+++|..+++++.++.++++......+
T Consensus 190 faLlgA~Ls~l~~Nw~~m~~~~~~l~~ll~Ii~i~l~~G~~~~~~~~~h~gg~~~G~~~~fil~~~g~~~~~~~~~~~-- 267 (316)
T KOG2289|consen 190 FALLGAHLSNLLTNWTIMKNKFAALRTLLIIIFINLDLGFAPYVDNFAHIGGLLAGFLLGFVLHIGGQLGGITIGLIV-- 267 (316)
T ss_pred HHHHHHHHHHHHhhHHHhcchHHHHHHHHHHHHHHHhhccccceeccccccccCCCcchhHHhhhccceeEEecccee--
Confidence 88886544 35566778889999999999999999999999999999999999987765444
Q ss_pred hhhcccCchhHHHHHHHHHHHHHHHHHHHHHHHHccCCCCCCCCccceeeeee
Q 045959 243 ARVKSRHNPYQYVLCIVALVLLIVGFTVGLVMLFRGENGNDHCSWCHYLSCVP 295 (303)
Q Consensus 243 ~~~~~~~~~~~~~~~~~~~~ll~~~~~~~~~~~~~~~~~~~~C~~c~y~~C~p 295 (303)
.+.+.|++.+|.+.|++..+.++.++.++++.++++ +.|.||+++.|+|
T Consensus 268 ~~~~~~~~~~q~~~w~~~~~~~v~~~~~~~~~if~~----~~~~~~~~~~~~~ 316 (316)
T KOG2289|consen 268 LRVFSKRLPYQLLLWIVLLVYLVAGLFASLFNIFDG----KYCLWCHPLSCVP 316 (316)
T ss_pred eeccccccccchHHHHHHHHHHHHHHHHHHHHhhcC----CccccccccCCCC
Confidence 224455667777888888888888888888887765 7999999999986
No 2
>PTZ00101 rhomboid-1 protease; Provisional
Probab=99.97 E-value=5.8e-30 Score=236.73 Aligned_cols=168 Identities=24% Similarity=0.388 Sum_probs=131.8
Q ss_pred CCCCcccccHHHHHHHHHHHHHHHHHHHhcCCCCCCCCCCchhhhhhcccccccCCCCCCCCCChhHHHhhcccchhhhh
Q 045959 32 GSDQQWTSWLIPMFVVANVAVFIVAMYINNCPKNNWEGGRGCVARFLGRLSFEPLKENPLFGPSSSTLQKLGALEWDRVV 111 (303)
Q Consensus 32 ~~~~~~~p~vt~~li~inv~VFl~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~P~~~n~l~gp~~~~L~~~Ga~~~~~i~ 111 (303)
+-++...+.+|..++++|+++|++..... .+..++|+.+.+.++|+++++.+
T Consensus 46 ~Fp~f~i~~l~~~Iiii~iivfil~l~~~---------------------------~~~~l~p~~~~L~~~Ga~~~~~i- 97 (278)
T PTZ00101 46 IFPHFTWKSFIMAISIIQIIVFIISVSIK---------------------------PADFLTPSDSLLVTLGANVASRI- 97 (278)
T ss_pred HcCCccHHHHHHHHHHHHHHHHHHHHHhc---------------------------ccccCCCCHHHHHHHhCcchhhh-
Confidence 33445578899999999999999876321 11235788889999999987665
Q ss_pred ccCceeeeehhhhccccHHHHHHHHHHHHHHHHHHHHHhchHHHHHHHHHHHHHHHH-HHHHhcC------CceeeehhH
Q 045959 112 HEHQGWRLITCIWLHAGVIHLLANMLSLVFIGIRLEQQFGFVRVGFVYLLSGFGGAY-YLLFLFN------AVSLLVLLA 184 (303)
Q Consensus 112 ~~~q~wRl~T~~FlH~~~~HLl~Nm~~l~~~G~~lE~~~G~~r~~~lyl~sgi~g~l-~~~~~~~------~~~v~Gll~ 184 (303)
.++||||++|++|+|.|+.|+++||+.++.+|..+|+.+|++|+..+|++||++|++ ++.+.+. |+++||+++
T Consensus 98 ~~gq~WRLiT~~FlH~~~~HLl~Nm~~l~~~G~~lE~~~G~~r~~ilYl~sGi~G~l~s~~~~~~~~svGASgAifGLiG 177 (278)
T PTZ00101 98 KQGEIHRLILPIFLHANIFHTFFNVFFQLRMGFTLEKNYGIVKIIILYFLTGIYGNILSSSVTYCPIKVGASTSGMGLLG 177 (278)
T ss_pred hcCCCHHHHHHHHHccCHHHHHHHHHHHHHHHHHHHHHHChHHHHHHHHHHHHHHHHHHHHHccCCcEEehhHHHHHHHH
Confidence 579999999999999999999999999999999999999999999999999999999 7766543 345588887
Q ss_pred HHHHH-----------------HHHHHHHHHH--Hhc-CchHhHHHHHHHHHHHHHHHHHHhh
Q 045959 185 AALLT-----------------LVVIIAINLA--VGI-LPHVDNFAHIGGFMAGFLLGFVLLL 227 (303)
Q Consensus 185 ~~l~~-----------------l~~~~~~~l~--~g~-~p~v~~~aHlgG~l~G~l~g~~l~~ 227 (303)
+.+.. ++.+.++.+. .+. .|++|+.||+||+++|+++|.++.+
T Consensus 178 a~~~~lil~w~~~~~~~~~~~~~i~~~li~~~l~~~~~g~~Id~~aHlGG~i~G~llg~~~~~ 240 (278)
T PTZ00101 178 IVTSELILLWHVIRHRERVVFNIIFFSLISFFYYFTFNGSNIDHVGHLGGLLSGISMGILYNS 240 (278)
T ss_pred HHHHHHHHHHHhhccHHHHHHHHHHHHHHHHHHHHhcCCCCccHHHHHHHHHHHHHHHHHHHh
Confidence 65321 1111222221 222 4789999999999999999988653
No 3
>KOG2290 consensus Rhomboid family proteins [Signal transduction mechanisms]
Probab=99.95 E-value=1.3e-28 Score=234.26 Aligned_cols=199 Identities=25% Similarity=0.463 Sum_probs=148.9
Q ss_pred CCCCCCCCChhHHHh-hcccchhhhhccCceeeeehhhhccccHHHHHHHHHHHHHHHHHHHHHhchHHHHHHHHHHHHH
Q 045959 87 KENPLFGPSSSTLQK-LGALEWDRVVHEHQGWRLITCIWLHAGVIHLLANMLSLVFIGIRLEQQFGFVRVGFVYLLSGFG 165 (303)
Q Consensus 87 ~~n~l~gp~~~~L~~-~Ga~~~~~i~~~~q~wRl~T~~FlH~~~~HLl~Nm~~l~~~G~~lE~~~G~~r~~~lyl~sgi~ 165 (303)
++|..+......+.. .|.+..-.-..+.|+|||+|+.|+|+|++|++..|.+++.+-+.+|+..|+.|+.++|++||+.
T Consensus 421 HEeAtLCSQVhC~d~VCGllPFln~e~PdQfYRL~~SLFlHagviH~~vSi~FQm~vmrdlEkL~g~~riAIiy~~SGit 500 (652)
T KOG2290|consen 421 HEEATLCSQVHCFDGVCGLLPFLNPEVPDQFYRLWLSLFLHAGVIHLLVSICFQMTVMRDLEKLAGWHRIAIIYFLSGIT 500 (652)
T ss_pred hhhhhhhhhhhhhhcccccccccCCCChhHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHhhcchhhheeeeccccc
Confidence 445444444444444 3444333344578999999999999999999999999999999999999999999999999999
Q ss_pred HHH-HHHHhcCCcee------eehhHHHHHH----------------HHHHHHHHHHHhcCchHhHHHHHHHHHHHHHHH
Q 045959 166 GAY-YLLFLFNAVSL------LVLLAAALLT----------------LVVIIAINLAVGILPHVDNFAHIGGFMAGFLLG 222 (303)
Q Consensus 166 g~l-~~~~~~~~~~v------~Gll~~~l~~----------------l~~~~~~~l~~g~~p~v~~~aHlgG~l~G~l~g 222 (303)
||+ +++|.|+...| +|++.+..+- =++.+.+.+.+|+.|.|||+||+.|+++|++.+
T Consensus 501 GNLASAIFlpY~~eVgPa~sQ~Gila~l~vEl~qs~~il~~~w~a~~~Lia~~L~L~iGliPWiDN~aHlfG~i~GLl~s 580 (652)
T KOG2290|consen 501 GNLASAIFLPYRAEVGPAGSQFGILACLFVELFQSWQILERPWRAFFHLIATLLVLCIGLIPWIDNWAHLFGTIFGLLTS 580 (652)
T ss_pred ccchheeeeccccccCCcccccchHHHHHHHHHhhhHhhhhHHHHHHHHHHHHHHHHhccccchhhHHHHHHHHHHHHHH
Confidence 999 99998876555 9999665431 122333445569999999999999999999999
Q ss_pred HHHhhccccchhhhccCchhhhhcccCchhHHHHHHHHHHHHHHHHHHHHHHHHccCCCCCCCCccceeeeeeCCCCCCC
Q 045959 223 FVLLLRPQFGWAERHQLPAQARVKSRHNPYQYVLCIVALVLLIVGFTVGLVMLFRGENGNDHCSWCHYLSCVPTSKWKCG 302 (303)
Q Consensus 223 ~~l~~~~~~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~ll~~~~~~~~~~~~~~~~~~~~C~~c~y~~C~p~~~~~c~ 302 (303)
++++++-.++..+. + +|+.+.+++.+++...+...+|+||. -.-.||||.|+||+|+++-+|+
T Consensus 581 ~~~~PYi~Fg~~d~------------y--rKr~~ilIs~ivf~~Lla~Lvv~fy~---~~i~cpWce~ltClP~~~~~~e 643 (652)
T KOG2290|consen 581 IIFLPYIDFGDFDL------------Y--RKRFYILISQIVFSGLLAILVVVFYN---YPIDCPWCEHLTCLPFTDCFCE 643 (652)
T ss_pred HHhhccccccchhh------------h--hhHHHHHHHHHHHHHHHHHHHHheee---cccCCchhhhccccchhhhhhh
Confidence 99998877764322 1 12233344444444444444455553 3468999999999999999997
No 4
>PRK10907 intramembrane serine protease GlpG; Provisional
Probab=99.92 E-value=2.6e-24 Score=199.28 Aligned_cols=154 Identities=22% Similarity=0.254 Sum_probs=112.6
Q ss_pred cccHHHHHHHHHHHHHHHHHHHhcCCCCCCCCCCchhhhhhcccccccCCCCCCCCCChhHHHhhcccchhhhhccCcee
Q 045959 38 TSWLIPMFVVANVAVFIVAMYINNCPKNNWEGGRGCVARFLGRLSFEPLKENPLFGPSSSTLQKLGALEWDRVVHEHQGW 117 (303)
Q Consensus 38 ~p~vt~~li~inv~VFl~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~P~~~n~l~gp~~~~L~~~Ga~~~~~i~~~~q~w 117 (303)
..++|..++++|++||++.....+ +.. .. +.. .+......+|||
T Consensus 93 ~~p~T~~li~i~i~vf~l~~~~~~----------~~~---~~----------------------~l~-~~~~~~~~~q~W 136 (276)
T PRK10907 93 AGPLTLGVMIACVVVFILMQILGD----------QTV---ML----------------------WLA-WPFDPSLKFELW 136 (276)
T ss_pred CCCHHHHHHHHHHHHHHHHHHhcc----------HHH---HH----------------------HHh-ccccccccCCcH
Confidence 346899999999999998764321 000 00 111 011223478999
Q ss_pred eeehhhhccccHHHHHHHHHHHHHHHHHHHHHhchHHHHHHHHHHHHHHHH-HHHHhc-----CCceeeehhHHHHH---
Q 045959 118 RLITCIWLHAGVIHLLANMLSLVFIGIRLEQQFGFVRVGFVYLLSGFGGAY-YLLFLF-----NAVSLLVLLAAALL--- 188 (303)
Q Consensus 118 Rl~T~~FlH~~~~HLl~Nm~~l~~~G~~lE~~~G~~r~~~lyl~sgi~g~l-~~~~~~-----~~~~v~Gll~~~l~--- 188 (303)
|++|++|+|.|+.|+++||++++.+|..+|+.+|++|++.+|++++++|++ ..++.+ .|+.|||+++....
T Consensus 137 Rl~T~~flH~~~~Hl~fNml~l~~lG~~iE~~~G~~~~l~l~l~s~i~~~~~~~~~~~~~~gGaSGvVygL~g~~~~~~~ 216 (276)
T PRK10907 137 RYFTHALLHFSLLHILFNLLWWWYLGGAVEKRLGSGKLIVITLISALLSGWVQSKFSGPWFGGLSGVVYALMGYVWLRGE 216 (276)
T ss_pred HHHhHHHHhCCHHHHHHHHHHHHHHHHHHHHHHChHHHHHHHHHHHHHHHHHHHHHccchhhHHHHHHHHHHHHHHHHhc
Confidence 999999999999999999999999999999999999999999999999999 665543 23445777743221
Q ss_pred -----------HHHHHHHHHHHHhc----CchHhHHHHHHHHHHHHHHHHHHhh
Q 045959 189 -----------TLVVIIAINLAVGI----LPHVDNFAHIGGFMAGFLLGFVLLL 227 (303)
Q Consensus 189 -----------~l~~~~~~~l~~g~----~p~v~~~aHlgG~l~G~l~g~~l~~ 227 (303)
.++.+.++.++.|+ .++|+|.||+||+++|+++|+...+
T Consensus 217 ~~p~~~~~lp~~~~~f~llwl~~g~~~~~g~~Ian~AHlgGli~Gll~g~~~~~ 270 (276)
T PRK10907 217 RDPQSGIYLPRGLIAFALLWLVAGYFDLFGMSIANAAHVAGLAVGLAMAFWDTR 270 (276)
T ss_pred cccccchhhhHHHHHHHHHHHHHHHHHccCcccHHHHHHHHHHHHHHHHHHhhh
Confidence 22333344443333 3689999999999999999987653
No 5
>COG0705 Membrane associated serine protease [Amino acid transport and metabolism]
Probab=99.87 E-value=1.6e-21 Score=175.77 Aligned_cols=167 Identities=30% Similarity=0.473 Sum_probs=116.7
Q ss_pred cccHHHHHHHHHHHHHHHHHHHhcCCCCCCCCCCchhhhhhcccccccCCCCCCCCCChhHHHhhcccchhhhhccCcee
Q 045959 38 TSWLIPMFVVANVAVFIVAMYINNCPKNNWEGGRGCVARFLGRLSFEPLKENPLFGPSSSTLQKLGALEWDRVVHEHQGW 117 (303)
Q Consensus 38 ~p~vt~~li~inv~VFl~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~P~~~n~l~gp~~~~L~~~Ga~~~~~i~~~~q~w 117 (303)
.+.+|..++++|+++|+.+.+..... ..........+...|.... ......|+|
T Consensus 16 ~~~~~~~~~~~~~~v~~~~~~~~~~~-------~~~~~~~~~~~~~~~~~~~-------------------~~~~~~~~w 69 (228)
T COG0705 16 APPVTLFLILLNILVFLLELVLGWSA-------IFLLTFLFRLFGLYPLNLL-------------------GALARDQLW 69 (228)
T ss_pred cchHHHHHHHHHHHHHHHHHHccchH-------HHHHHHhhhHHhhcchhhh-------------------ccccccchH
Confidence 37899999999999999887543210 0000000111222222110 000111999
Q ss_pred eeehhhhccccHHHHHHHHHHHHHHHHHHHHHhchHHHHHHHHHHHHHHHH-HHHHhcCC--------ceeeehhHHHH-
Q 045959 118 RLITCIWLHAGVIHLLANMLSLVFIGIRLEQQFGFVRVGFVYLLSGFGGAY-YLLFLFNA--------VSLLVLLAAAL- 187 (303)
Q Consensus 118 Rl~T~~FlH~~~~HLl~Nm~~l~~~G~~lE~~~G~~r~~~lyl~sgi~g~l-~~~~~~~~--------~~v~Gll~~~l- 187 (303)
|++|++|+|+|+.|+++||+.++.+|..+|+.+|+.||+.+|+++|+++++ ...+.+.. +++||++++..
T Consensus 70 ~lit~~FlH~~~~Hll~N~~~l~~fg~~le~~~G~~~f~~~yl~~gl~~~~~~~~~~~~~~~~~~GASG~i~gllga~~~ 149 (228)
T COG0705 70 RLITAIFLHAGFLHLLFNMLALWVFGSNLERRLGTLRFLLFYLLSGLLAGLAQVLFGPKGGAPSLGASGAIFGLLGAYFL 149 (228)
T ss_pred HHHHHHHHHhhHHHHHHHHHHHHHhhHHHHHHhchhHHHHHHHHHHHHHHHHHHHHcccccCcccchhHHHHHHHHHHHH
Confidence 999999999999999999999999999999999999999999999999999 77776443 34477775432
Q ss_pred -------------------HHHHHHHHHHHHHhcC---chHhHHHHHHHHHHHHHHHHHHhhccc
Q 045959 188 -------------------LTLVVIIAINLAVGIL---PHVDNFAHIGGFMAGFLLGFVLLLRPQ 230 (303)
Q Consensus 188 -------------------~~l~~~~~~~l~~g~~---p~v~~~aHlgG~l~G~l~g~~l~~~~~ 230 (303)
..+.+++..+++.+.. ++|+++||++|+++|++++..+.++.+
T Consensus 150 ~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~~~~~va~~aHl~G~i~G~l~~~~~~~~~~ 214 (228)
T COG0705 150 LFPFARILLLFLSLPRPALILILIWLLYSLFSGAGSFGPSVAWSAHLGGLIGGLLLAALLSRKLR 214 (228)
T ss_pred HccccchhhhhccCchhHHHHHHHHHHHHHHHHhcCCchHHHHHHHHHHHHHHHHHHHHHhhhhh
Confidence 1222333444444443 379999999999999999988875443
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=99.78 E-value=2.5e-19 Score=149.55 Aligned_cols=118 Identities=41% Similarity=0.730 Sum_probs=88.9
Q ss_pred ccCceeeeehhhhccccHHHHHHHHHHHHHHHHHHHHHhchHHHHHHHHHHHHHHHH-HHHHhcCC-c------eeeehh
Q 045959 112 HEHQGWRLITCIWLHAGVIHLLANMLSLVFIGIRLEQQFGFVRVGFVYLLSGFGGAY-YLLFLFNA-V------SLLVLL 183 (303)
Q Consensus 112 ~~~q~wRl~T~~FlH~~~~HLl~Nm~~l~~~G~~lE~~~G~~r~~~lyl~sgi~g~l-~~~~~~~~-~------~v~Gll 183 (303)
+++|+||++|++|+|.|+.|+++|++.++.+|..+|+.+|++|+..+|+.+++++++ ..++.+.. . .++|++
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 578999999999999999999999999999999999999999999999999999999 66665544 2 235555
Q ss_pred HHHHHHH-----------------HHHHHHHHHHhcCchHhHHHHHHHHHHHHHHHHHHhhcc
Q 045959 184 AAALLTL-----------------VVIIAINLAVGILPHVDNFAHIGGFMAGFLLGFVLLLRP 229 (303)
Q Consensus 184 ~~~l~~l-----------------~~~~~~~l~~g~~p~v~~~aHlgG~l~G~l~g~~l~~~~ 229 (303)
+...... ...+.+.+..+..|++++.+|++|+++|++++..+.+|+
T Consensus 82 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~hl~G~~~G~~~~~~~~~~~ 144 (145)
T PF01694_consen 82 GAFLFLYPQNKKRLRFIYLALVVPIIVLVIILLLGFIPNISFLGHLGGFLAGLLYGFLILRRP 144 (145)
T ss_dssp HHHHHHHHCCCCCS---HCCCCCCCCCCCHHHCTSSSSTTTHHHHHHHHHHHHHHHHHHCH--
T ss_pred HHHHHHHhhccchhhcchHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHcc
Confidence 4432211 011223344455789999999999999999999988654
No 7
>KOG2632 consensus Rhomboid family proteins [Function unknown]
Probab=99.35 E-value=9.1e-12 Score=113.05 Aligned_cols=117 Identities=26% Similarity=0.408 Sum_probs=83.3
Q ss_pred hhhhccCceeeeehhhhccccHHHHHHHHHHHHHHHHHHHHHhc-hHHHHHHHHHHHHHHHH-HHHHhc-----CCc---
Q 045959 108 DRVVHEHQGWRLITCIWLHAGVIHLLANMLSLVFIGIRLEQQFG-FVRVGFVYLLSGFGGAY-YLLFLF-----NAV--- 177 (303)
Q Consensus 108 ~~i~~~~q~wRl~T~~FlH~~~~HLl~Nm~~l~~~G~~lE~~~G-~~r~~~lyl~sgi~g~l-~~~~~~-----~~~--- 177 (303)
.....+.|.||++|++++|.+..|+++||+.++.+|...|+.+| +.+++....+.++..++ ..+... +..
T Consensus 45 ~~~l~~~ql~RL~Ty~l~H~s~~hllfnmlaL~~~g~~fE~~~G~t~~~l~~~~llalf~gIl~ll~~~~~~~~d~~~~~ 124 (258)
T KOG2632|consen 45 SELLINWQLYRLITYALVHLSLPHLLFNMLALWPLGSQFERTHGTTVRILMFTVLLALFSGILYLLAYHVFLLSDLVYVE 124 (258)
T ss_pred HHHhhhHHHHHHHHHHHHhccHHHHHHHHHHHHhchhHHHhhccceehHHHHHHHHHHHHHHHHHHHHHHHhhcchhhhc
Confidence 34456889999999999999999999999999999999999999 88888888888888777 332221 111
Q ss_pred -ee--eehhHHHH---------------------HHHHHHHHHHHHHhcCchHhHHHHHHHHHHHHHHHHH
Q 045959 178 -SL--LVLLAAAL---------------------LTLVVIIAINLAVGILPHVDNFAHIGGFMAGFLLGFV 224 (303)
Q Consensus 178 -~v--~Gll~~~l---------------------~~l~~~~~~~l~~g~~p~v~~~aHlgG~l~G~l~g~~ 224 (303)
++ .|+..+.+ ..+..++.+-...=+.|+.|..+|++|+++|+.+++.
T Consensus 125 ~a~G~s~v~Fam~~~~~~~sp~r~~~~fg~~siP~~l~Pw~lLi~~~~lvp~aSFlghl~GllvG~ay~~~ 195 (258)
T KOG2632|consen 125 GAIGFSGVLFAMMAVLEVQSPVRSRSVFGLFSIPIVLAPWALLIATQILVPQASFLGHLCGLLVGYAYAFS 195 (258)
T ss_pred ccccccHHHHHHHHHHhhcCcccchhhcccccccHHHHHHHHHHHHHHHccCchHHHHHHHHHHHHHHHHH
Confidence 11 22221111 1122222222222246999999999999999999884
No 8
>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=98.11 E-value=4.7e-06 Score=66.07 Aligned_cols=54 Identities=24% Similarity=0.317 Sum_probs=51.9
Q ss_pred ceeeeehhhhccccHHHHHHHHHHHHHHHHHHHHHhchHHHHHHHHHHHHHHHH
Q 045959 115 QGWRLITCIWLHAGVIHLLANMLSLVFIGIRLEQQFGFVRVGFVYLLSGFGGAY 168 (303)
Q Consensus 115 q~wRl~T~~FlH~~~~HLl~Nm~~l~~~G~~lE~~~G~~r~~~lyl~sgi~g~l 168 (303)
..|+++|+.|++.++..+++|.+.++..|+.+|+.+|+++++-...+.+..+|+
T Consensus 7 ~pWtl~T~~fve~~i~~~l~~~~~l~~~g~~lE~~WGs~E~lkFi~vv~~~tnl 60 (99)
T PF08551_consen 7 YPWTLFTAGFVETNIIGLLFSLLTLFYGGRYLEPIWGSREFLKFILVVNVITNL 60 (99)
T ss_pred ehHHHHHHHHHHhHHHHHHHHHHHHHHhhHHHHHhcChHHHHHHHHHHHHHhHH
Confidence 679999999999999999999999999999999999999999999999988887
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=97.79 E-value=0.00038 Score=61.69 Aligned_cols=63 Identities=22% Similarity=0.333 Sum_probs=47.0
Q ss_pred chhhhhccCceeeeehhhhccccH-HHHHHHHHHHHHHHHHHHHH-hc-h-HHHHHHHHHHHHHHHH
Q 045959 106 EWDRVVHEHQGWRLITCIWLHAGV-IHLLANMLSLVFIGIRLEQQ-FG-F-VRVGFVYLLSGFGGAY 168 (303)
Q Consensus 106 ~~~~i~~~~q~wRl~T~~FlH~~~-~HLl~Nm~~l~~~G~~lE~~-~G-~-~r~~~lyl~sgi~g~l 168 (303)
+++.+.++.|+||++|+.|.-++. .+.++|++.++..+..+|+. +. + ..++...+.+++.-.+
T Consensus 32 ~~~~v~~~~q~WRl~Tsff~~g~~~~~~l~~~~~l~~~s~~LE~~~f~~~~ady~~~ll~~~~~i~~ 98 (197)
T PF04511_consen 32 DWELVFKKFQIWRLFTSFFYFGPFSLNFLFNLYFLYQYSSSLEEGHFQGRSADYLWFLLFGASLILI 98 (197)
T ss_pred CcHHHhhhcCceeeEEEEEEEcCCCHHHHHHHHHHHHHhhHhccCCCCCCHHHHHHHHHHHHHHHHH
Confidence 345566789999999999987655 69999999999999999997 22 2 4566555555444333
No 10
>KOG2980 consensus Integral membrane protease of the rhomboid family involved in different forms of regulated intramembrane proteolysis [Signal transduction mechanisms]
Probab=97.58 E-value=3e-05 Score=72.16 Aligned_cols=54 Identities=30% Similarity=0.480 Sum_probs=45.5
Q ss_pred ceeeeehhhhccccHHHHHHHHHHHHHHHH-HHHHHhchHHHHHHHHHHHHHHHH
Q 045959 115 QGWRLITCIWLHAGVIHLLANMLSLVFIGI-RLEQQFGFVRVGFVYLLSGFGGAY 168 (303)
Q Consensus 115 q~wRl~T~~FlH~~~~HLl~Nm~~l~~~G~-~lE~~~G~~r~~~lyl~sgi~g~l 168 (303)
--|.++++.|.|.+..|+..||+.+..+.. .+....|...+..+|+.++..|..
T Consensus 154 ~~w~i~~s~Fsh~~a~h~g~~~~~~~~y~~~a~~~~~~~~~~~AlylSa~~~~~~ 208 (310)
T KOG2980|consen 154 GCWKIILSTFSHYSALHLGPNMLVLKSYLAGALKGSLGFSSFFALYLSAGVKGLF 208 (310)
T ss_pred cceeEEeehhcchhHhhhcHHHHHHHHHhcccccCCcchhhcccceeccccccce
Confidence 347799999999999999999999888877 777788899999999966666554
No 11
>KOG0858 consensus Predicted membrane protein [Function unknown]
Probab=96.98 E-value=0.0028 Score=57.44 Aligned_cols=96 Identities=18% Similarity=0.141 Sum_probs=69.2
Q ss_pred cccccHHHHHHHHHHHHHHHHHHHhcCCCCCCCCCCchhhhhhcccccccCCCCCCCCCChhHHHhhcccchhhhhccCc
Q 045959 36 QWTSWLIPMFVVANVAVFIVAMYINNCPKNNWEGGRGCVARFLGRLSFEPLKENPLFGPSSSTLQKLGALEWDRVVHEHQ 115 (303)
Q Consensus 36 ~~~p~vt~~li~inv~VFl~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~P~~~n~l~gp~~~~L~~~Ga~~~~~i~~~~q 115 (303)
..+|.+|.....+++++=++....- + .|.. =-.+++.+.++.|
T Consensus 10 ~~iPpVTR~~~~~~v~tt~~~~l~l-----------------I-----sP~~---------------l~~~p~Lv~kk~Q 52 (239)
T KOG0858|consen 10 LQIPPVTRYYTTACVVTTLLVRLDL-----------------I-----SPFQ---------------LYLNPELVFKKFQ 52 (239)
T ss_pred hcCChHHHHHHHHHHHHHHHHhhcc-----------------c-----Cchh---------------eEecHHHHHhHhH
Confidence 3468899999999988777654210 0 1111 0124567888999
Q ss_pred eeeeehhhhcccc-HHHHHHHHHHHHHHHHHHHHHh-c--hHHHHHHHHHHHHHHHH
Q 045959 116 GWRLITCIWLHAG-VIHLLANMLSLVFIGIRLEQQF-G--FVRVGFVYLLSGFGGAY 168 (303)
Q Consensus 116 ~wRl~T~~FlH~~-~~HLl~Nm~~l~~~G~~lE~~~-G--~~r~~~lyl~sgi~g~l 168 (303)
+||++|+.+.-+. -+|.++||+.++--.+.+|+-. . +..|+...+.+++.-.+
T Consensus 53 iWRliTs~lyfg~~gf~fl~n~~FlyrY~~~LE~g~f~~rtadf~~mllf~~~l~~~ 109 (239)
T KOG0858|consen 53 IWRLITSFLYFGPFGFDFLMNLYFLYRYSSMLEEGSFRGRTADFLYMLLFGAVLLTL 109 (239)
T ss_pred HHHhhhhhheeccccHHHHHHHHHHHHHHHHHhcCCCCCchhHHHHHHHHHHHHHHH
Confidence 9999999999876 6899999999999999999732 2 36677776666655444
No 12
>KOG2890 consensus Predicted membrane protein [Function unknown]
Probab=93.44 E-value=0.099 Score=49.10 Aligned_cols=54 Identities=22% Similarity=0.313 Sum_probs=48.2
Q ss_pred ceeeeehhhhccccHHHHHHHHHHHHHHHHHHHHHhchHHHHHHHHHHHHHHHH
Q 045959 115 QGWRLITCIWLHAGVIHLLANMLSLVFIGIRLEQQFGFVRVGFVYLLSGFGGAY 168 (303)
Q Consensus 115 q~wRl~T~~FlH~~~~HLl~Nm~~l~~~G~~lE~~~G~~r~~~lyl~sgi~g~l 168 (303)
..|+++|+.|+-.+++-.+.|.+.+.+-|..+|+.+|+..++.+|.+.-..-++
T Consensus 66 ~~WtliTs~fie~~vw~V~~sv~~L~v~G~~lEp~Wg~~e~lkff~ivn~~~~l 119 (326)
T KOG2890|consen 66 FPWTLITSGFIELNVWDVLVSVLTLSVGGKFLEPNWGSLELLKFFAIVNGSTTL 119 (326)
T ss_pred hhHHHHhcchhhhhHHHHHHHHHheeecceeeccCCCCHHHHHHHHHhhchhHH
Confidence 679999999999999999999999999999999999999999888776544443
No 13
>KOG4463 consensus Uncharacterized conserved protein [Function unknown]
Probab=93.37 E-value=0.048 Score=50.24 Aligned_cols=57 Identities=18% Similarity=0.277 Sum_probs=48.8
Q ss_pred hccCceeeeehhhhccccHHHHHHHHHHHHHHHHHHHHHhchHHHHHHHHHHHHHHHH
Q 045959 111 VHEHQGWRLITCIWLHAGVIHLLANMLSLVFIGIRLEQQFGFVRVGFVYLLSGFGGAY 168 (303)
Q Consensus 111 ~~~~q~wRl~T~~FlH~~~~HLl~Nm~~l~~~G~~lE~~~G~~r~~~lyl~sgi~g~l 168 (303)
....|+||++...|.-.+-..+.+-++.++.+ +.+||.+|+.||..+.+.+++.+-+
T Consensus 46 ~~y~qywrlL~~qF~~~n~~e~~~~l~I~Y~f-R~~ERlLGShky~~fiv~s~~~~~l 102 (323)
T KOG4463|consen 46 EKYFQYWRLLMSQFAFSNTPELMFGLYILYYF-RVFERLLGSHKYSVFIVFSGTVSLL 102 (323)
T ss_pred HHHHHHHHHHHHHHHhcCChHHHHHHHHHHHH-HHHHHHhccccceeehhHHHHHHHH
Confidence 34689999999999999988888877666655 6999999999999998888888877
No 14
>KOG2290 consensus Rhomboid family proteins [Signal transduction mechanisms]
Probab=89.95 E-value=0.37 Score=47.79 Aligned_cols=84 Identities=25% Similarity=0.340 Sum_probs=54.7
Q ss_pred ccccHHHHHHHHHHHHHHHHHHHhcCCCCCCCCCCchhhhhhc-ccccc----cCCCCCCCCCChhHHHhhcccchhhhh
Q 045959 37 WTSWLIPMFVVANVAVFIVAMYINNCPKNNWEGGRGCVARFLG-RLSFE----PLKENPLFGPSSSTLQKLGALEWDRVV 111 (303)
Q Consensus 37 ~~p~vt~~li~inv~VFl~~~~~~~~~~~~~~~~~~~~~~~l~-~~~~~----P~~~n~l~gp~~~~L~~~Ga~~~~~i~ 111 (303)
.+||+|+.+..+++.|=++.....+..-.+- +-.+..+..++ .+.++ -.++|+.+||+.+.|+.+||++.+-+.
T Consensus 198 ~RP~FTyWlt~Vh~~V~iLsl~~YG~aP~gf-~~~et~~~Vl~n~~v~e~VkYlqQeN~WiGP~~~dLI~LGA~fSPCmr 276 (652)
T KOG2290|consen 198 HRPWFTYWLTFVHSFVTILSLCIYGIAPVGF-SQHETVGDVLDNTLVYERVKYLQQENFWIGPSSADLIHLGAKFSPCMR 276 (652)
T ss_pred CCchhHHHHHHHHHHHHHHHHHHhcCCcccc-hhhHhHHHHHhhhhhhhhhHHHHhcCCccCccHHHHHHhccccChhhh
Confidence 3589999999999888877665443210000 00111122221 11111 135799999999999999999999999
Q ss_pred ccCceeeeeh
Q 045959 112 HEHQGWRLIT 121 (303)
Q Consensus 112 ~~~q~wRl~T 121 (303)
+..|.|.++-
T Consensus 277 rd~q~~~~I~ 286 (652)
T KOG2290|consen 277 RDPQVWSAIE 286 (652)
T ss_pred cChHHHHHHH
Confidence 9999887653
No 15
>COG5291 Predicted membrane protein [Function unknown]
Probab=89.59 E-value=1.1 Score=41.17 Aligned_cols=42 Identities=19% Similarity=0.248 Sum_probs=35.2
Q ss_pred hhhhhccCceeeeehhhhcccc-HHHHHHHHHHHHHHHHHHHH
Q 045959 107 WDRVVHEHQGWRLITCIWLHAG-VIHLLANMLSLVFIGIRLEQ 148 (303)
Q Consensus 107 ~~~i~~~~q~wRl~T~~FlH~~-~~HLl~Nm~~l~~~G~~lE~ 148 (303)
.+...++-||||++|+..+-++ -+..++|++.++--.+++|+
T Consensus 51 ~pL~~k~~qiwRlfTs~~~~~~~~~d~~M~vyf~Y~yS~~LE~ 93 (313)
T COG5291 51 SPLFLKRLQIWRLFTSFLYFGKPTLDMFMHVYFLYRYSRMLEE 93 (313)
T ss_pred chhHHHHHHHHHHHHHHHhhcCcchhHHHHHHHHHHHHHHHhc
Confidence 4455678899999998777765 46889999999999999997
No 16
>TIGR00341 conserved hypothetical protein TIGR00341. This conserved hypothetical protein is found so far only in three archaeal genomes and in Streptomyces coelicolor. It shares a hydrophobic uncharacterized domain (see model TIGR00271) of about 180 residues with several eubacterial proteins, including the much longer protein sll1151 of Synechocystis PCC6803.
Probab=56.92 E-value=99 Score=29.75 Aligned_cols=81 Identities=22% Similarity=0.242 Sum_probs=39.9
Q ss_pred HHHHHHHHHHHHHHHHHHHhcCCceeeehhHH-HHHHHHHHHHHHHHHhcC-----chHhHHHHHHHHHHHHHHHHHHhh
Q 045959 154 RVGFVYLLSGFGGAYYLLFLFNAVSLLVLLAA-ALLTLVVIIAINLAVGIL-----PHVDNFAHIGGFMAGFLLGFVLLL 227 (303)
Q Consensus 154 r~~~lyl~sgi~g~l~~~~~~~~~~v~Gll~~-~l~~l~~~~~~~l~~g~~-----p~v~~~aHlgG~l~G~l~g~~l~~ 227 (303)
--+.+-+.+|+.|.++. ....+.++-|+..+ .++.=....++.+..|-. ...-...++.|+..+-...+.+.-
T Consensus 210 ~~l~vAl~aG~AGalsl-~~~~s~aLvGVaIAvaLvPPa~~~Gi~la~g~~~~a~ga~~L~~~Nl~~I~la~~~vf~~~g 288 (325)
T TIGR00341 210 VSEILAVLAGIAGILSL-SSGILESLAGVAISASLLPPAVATGILLVISPLPLAVKSLILTLINVAGLMAGSLAGVYVYG 288 (325)
T ss_pred HHHHHHHHHHHHHHHHH-hhccccchHHHHHHHHhhchHHHHHHHHHhccHHHHHHHHHHHHHHHHHHHHHHHHHHHHhC
Confidence 33566667777776642 23344444555422 222222222333333221 233456677787777776666655
Q ss_pred ccccchhh
Q 045959 228 RPQFGWAE 235 (303)
Q Consensus 228 ~~~~~~~~ 235 (303)
.+.++|.+
T Consensus 289 ~~p~~~~~ 296 (325)
T TIGR00341 289 IRAYRYYK 296 (325)
T ss_pred CCcchhhh
Confidence 44445443
No 17
>PF09527 ATPase_gene1: Putative F0F1-ATPase subunit (ATPase_gene1)
Probab=42.61 E-value=1.1e+02 Score=20.94 Aligned_cols=39 Identities=26% Similarity=0.452 Sum_probs=31.0
Q ss_pred HHHHHHHHHHHHHHHHHHHHhch-HHHHHHHHHHHHHHHH
Q 045959 130 IHLLANMLSLVFIGIRLEQQFGF-VRVGFVYLLSGFGGAY 168 (303)
Q Consensus 130 ~HLl~Nm~~l~~~G~~lE~~~G~-~r~~~lyl~sgi~g~l 168 (303)
..++.+++.-..+|..+++.+++ ..+.++.++-|+.+++
T Consensus 8 ~~~~~~i~~g~~~G~~lD~~~~t~p~~~~~g~llG~~~g~ 47 (55)
T PF09527_consen 8 FTMAAPILVGFFLGYWLDKWFGTSPWFTLIGLLLGIAAGF 47 (55)
T ss_pred HHHHHHHHHHHHHHHHHHHHcCCChHHHHHHHHHHHHHHH
Confidence 35677888889999999999999 6666677777777776
No 18
>COG2056 Predicted permease [General function prediction only]
Probab=34.62 E-value=76 Score=31.16 Aligned_cols=25 Identities=20% Similarity=0.319 Sum_probs=18.7
Q ss_pred HHHHHHHHHHHHHHhhccccchhhh
Q 045959 212 IGGFMAGFLLGFVLLLRPQFGWAER 236 (303)
Q Consensus 212 lgG~l~G~l~g~~l~~~~~~~~~~~ 236 (303)
--|++.|+++++++.+||+..+.++
T Consensus 198 ~lgMi~GLl~ai~~~YrKpReY~~~ 222 (444)
T COG2056 198 GLGMIVGLLLAIFVSYRKPREYQTN 222 (444)
T ss_pred HHHHHHHHHHHHHHhhcCCcccccc
Confidence 4589999999999866666666543
No 19
>PF12669 P12: Virus attachment protein p12 family
Probab=32.88 E-value=86 Score=22.20 Aligned_cols=18 Identities=33% Similarity=0.571 Sum_probs=8.8
Q ss_pred CCCccceee-eeeCCCCCCC
Q 045959 284 HCSWCHYLS-CVPTSKWKCG 302 (303)
Q Consensus 284 ~C~~c~y~~-C~p~~~~~c~ 302 (303)
-|..|.-=+ | +-+...|+
T Consensus 29 ~c~gCs~~sgC-~~~~~~C~ 47 (58)
T PF12669_consen 29 CCCGCSGCSGC-CGSSSSCH 47 (58)
T ss_pred CCCCCCCCCCc-CCCCCCCC
Confidence 455554433 5 45555554
No 20
>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=30.29 E-value=3.1e+02 Score=25.62 Aligned_cols=35 Identities=17% Similarity=0.295 Sum_probs=28.3
Q ss_pred HHHHHHHHHHHHHHHHHHHHhchHHHHHHHHHHHHHHHH
Q 045959 130 IHLLANMLSLVFIGIRLEQQFGFVRVGFVYLLSGFGGAY 168 (303)
Q Consensus 130 ~HLl~Nm~~l~~~G~~lE~~~G~~r~~~lyl~sgi~g~l 168 (303)
..+++|.+.|+..+..+.+....+|. +++++.|++
T Consensus 11 ~Nf~~d~~LL~~t~~~lk~~~~~~Rl----l~ga~iGa~ 45 (288)
T TIGR02854 11 ENFIIDYFLLYLTARTLKDKVSQWRL----LLAALIGSL 45 (288)
T ss_pred HHHHHHHHHHHHHHHHhhccchHHHH----HHHHHHHHH
Confidence 46889999999999999998888887 455566666
No 21
>PF07895 DUF1673: Protein of unknown function (DUF1673); InterPro: IPR012874 This family contains hypothetical proteins of unknown function found in Methanosarcina acetivorans and Methanosarcina mazei.
Probab=25.39 E-value=2.9e+02 Score=24.54 Aligned_cols=12 Identities=25% Similarity=0.398 Sum_probs=5.9
Q ss_pred HHHHHHHHHHHH
Q 045959 213 GGFMAGFLLGFV 224 (303)
Q Consensus 213 gG~l~G~l~g~~ 224 (303)
.+++.|+++++.
T Consensus 83 ~~ll~g~~~~L~ 94 (205)
T PF07895_consen 83 LFLLAGLILSLY 94 (205)
T ss_pred HHHHHHHHHHHH
Confidence 445555555433
No 22
>PF01944 DUF95: Integral membrane protein DUF95; InterPro: IPR002798 Many members of this family have no known function and are predicted to be integral membrane proteins. Q9V182 from SWISSPROT is annotated as "Stage II sporulation protein M related"; and weakly related to other proteins with similar annotation.
Probab=25.14 E-value=4e+02 Score=22.10 Aligned_cols=22 Identities=27% Similarity=0.273 Sum_probs=12.6
Q ss_pred hHHHHHHHHHHHHHHHHHHhhc
Q 045959 207 DNFAHIGGFMAGFLLGFVLLLR 228 (303)
Q Consensus 207 ~~~aHlgG~l~G~l~g~~l~~~ 228 (303)
-..|-+-....|+-++..+.++
T Consensus 111 Eipa~~ia~~~g~~~~~~li~~ 132 (173)
T PF01944_consen 111 EIPAIIIAAAAGLRLSYYLIKK 132 (173)
T ss_pred HHHHHHHHHHHHHHHHHHHHhc
Confidence 4455555566677766555543
No 23
>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=24.08 E-value=3.4e+02 Score=21.51 Aligned_cols=39 Identities=18% Similarity=0.171 Sum_probs=30.0
Q ss_pred HHHHHHHHHHHHHHHHHHHHhch-HHHHHHHHHHHHHHHH
Q 045959 130 IHLLANMLSLVFIGIRLEQQFGF-VRVGFVYLLSGFGGAY 168 (303)
Q Consensus 130 ~HLl~Nm~~l~~~G~~lE~~~G~-~r~~~lyl~sgi~g~l 168 (303)
++++.=.+.-.++|.-+.+.+|+ ..+.+++++.|++.++
T Consensus 50 ~~~v~pil~G~~lG~WLD~~~~t~~~~tl~~lllGv~~G~ 89 (100)
T TIGR02230 50 WSVAIPTLLGVAVGIWLDRHYPSPFSWTLTMLIVGVVIGC 89 (100)
T ss_pred HHHHHHHHHHHHHHHHHHhhcCCCcHHHHHHHHHHHHHHH
Confidence 46666677778899999999985 4566777778887777
No 24
>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=23.82 E-value=88 Score=22.87 Aligned_cols=22 Identities=18% Similarity=0.294 Sum_probs=15.8
Q ss_pred HHHHHHHHHHHHHHHHhhcccc
Q 045959 210 AHIGGFMAGFLLGFVLLLRPQF 231 (303)
Q Consensus 210 aHlgG~l~G~l~g~~l~~~~~~ 231 (303)
+-+.|.++|.+.|+++.|++-.
T Consensus 4 g~l~Ga~~Ga~~glL~aP~sG~ 25 (74)
T PF12732_consen 4 GFLAGAAAGAAAGLLFAPKSGK 25 (74)
T ss_pred HHHHHHHHHHHHHHHhCCCCcH
Confidence 4567888888888888765443
No 25
>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=23.08 E-value=4.6e+02 Score=24.35 Aligned_cols=35 Identities=23% Similarity=0.271 Sum_probs=27.8
Q ss_pred HHHHHHHHHHHHHHHHHHHHhchHHHHHHHHHHHHHHHH
Q 045959 130 IHLLANMLSLVFIGIRLEQQFGFVRVGFVYLLSGFGGAY 168 (303)
Q Consensus 130 ~HLl~Nm~~l~~~G~~lE~~~G~~r~~~lyl~sgi~g~l 168 (303)
..+++|.+.|+..+..+-+....+|. ++++..|++
T Consensus 11 ~N~~md~~lL~~t~~~~~~~~~~~Rl----l~~A~~Gal 45 (293)
T PF03419_consen 11 VNFLMDYFLLWLTARLLKRRASRWRL----LLGAAIGAL 45 (293)
T ss_pred HHHHHHHHHHHHHHHHhcCCCcHHHH----HHHHHHHHH
Confidence 46789999999999999988888888 445555555
No 26
>PF01034 Syndecan: Syndecan domain; InterPro: IPR001050 The syndecans are transmembrane proteoglycans which are involved in the organisation of cytoskeleton and/or actin microfilaments, and have important roles as cell surface receptors during cell-cell and/or cell-matrix interactions [, ]. Structurally, these proteins consist of four separate domains: A signal sequence; An extracellular domain (ectodomain) of variable length whose sequence is not evolutionary conserved in the various forms of syndecans. The ectodomain contains the sites of attachment of the heparan sulphate glycosaminoglycan side chains; A transmembrane region; A highly conserved cytoplasmic domain of about 30 to 35 residues, which could interact with cytoskeletal proteins. The proteins known to belong to this family are: Syndecan 1. Syndecan 2 or fibroglycan. Syndecan 3 or neuroglycan or N-syndecan. Syndecan 4 or amphiglycan or ryudocan. Drosophila syndecan. Caenorhabditis elegans probable syndecan (F57C7.3). Syndecan-4, a transmembrane heparan sulphate proteoglycan, is a coreceptor with integrins in cell adhesion. It has been suggested to form a ternary signalling complex with protein kinase Calpha and phosphatidylinositol 4,5-bisphosphate (PIP2). Structural studies have demonstrated that the cytoplasmic domain undergoes a conformational transition and forms a symmetric dimer in the presence of phospholipid activator PIP2, and whose overall structure in solution exhibits a twisted clamp shape having a cavity in the centre of dimeric interface. In addition, it has been observed that the syndecan-4 variable domain interacts, strongly, not only with fatty acyl groups but also the anionic head group of PIP2. These findings indicate that PIP2 promotes oligomerisation of the syndecan-4 cytoplasmic domain for transmembrane signalling and cell-matrix adhesion [, ].; GO: 0008092 cytoskeletal protein binding, 0016020 membrane; PDB: 1EJQ_B 1EJP_B 1YBO_C 1OBY_Q.
Probab=22.87 E-value=26 Score=25.51 Aligned_cols=20 Identities=35% Similarity=0.521 Sum_probs=0.0
Q ss_pred HHHHHHHHHHHHHHHHHhhc
Q 045959 209 FAHIGGFMAGFLLGFVLLLR 228 (303)
Q Consensus 209 ~aHlgG~l~G~l~g~~l~~~ 228 (303)
.|-++|.++|+++++++..-
T Consensus 12 aavIaG~Vvgll~ailLIlf 31 (64)
T PF01034_consen 12 AAVIAGGVVGLLFAILLILF 31 (64)
T ss_dssp --------------------
T ss_pred HHHHHHHHHHHHHHHHHHHH
Confidence 56778888888888766533
No 27
>PF05546 She9_MDM33: She9 / Mdm33 family; InterPro: IPR008839 Members of this family are mitochondrial inner membrane proteins with a role in inner mitochondrial membrane organisation and biogenesis []. The yeast Mdm33 protein assembles into an oligomeric complex in the inner membrane where it performs homotypic protein-protein interactions. It has been suggested that Mdm33 plays a distinct role, possibly involved in fission of the mitochondrial inner membrane [].
Probab=22.28 E-value=73 Score=28.63 Aligned_cols=22 Identities=27% Similarity=0.445 Sum_probs=18.7
Q ss_pred cccHHHHHHHHHHHHHHHHHHH
Q 045959 38 TSWLIPMFVVANVAVFIVAMYI 59 (303)
Q Consensus 38 ~p~vt~~li~inv~VFl~~~~~ 59 (303)
..|-|++++++|+++|++....
T Consensus 151 STwgT~~lmgvNvllFl~~~~~ 172 (207)
T PF05546_consen 151 STWGTWGLMGVNVLLFLVAQLL 172 (207)
T ss_pred HHHHHHHHHHHHHHHHHHHHHH
Confidence 4688999999999999987643
No 28
>TIGR02302 aProt_lowcomp conserved hypothetical protein TIGR02302. Members of this family are long (~850 residue) bacterial proteins from the alpha Proteobacteria. Each has 2-3 predicted transmembrane helices near the N-terminus and a long C-terminal region that includes stretches of Gln/Gly-rich low complexity sequence, predicted by TMHMM to be outside the membrane. In Bradyrhizobium japonicum, two tandem reading frames are together homologous the single members found in other species; the cutoffs scores are set low enough that the longer scores above the trusted cutoff and the shorter above the noise cutoff for this model.
Probab=20.34 E-value=3.9e+02 Score=29.23 Aligned_cols=20 Identities=20% Similarity=0.383 Sum_probs=14.0
Q ss_pred hHHHHHHHHHHHHHHHHHHH
Q 045959 252 YQYVLCIVALVLLIVGFTVG 271 (303)
Q Consensus 252 ~~~~~~~~~~~ll~~~~~~~ 271 (303)
-.+.++.+++++++++|+++
T Consensus 137 DP~aLR~~~~l~lv~a~~~a 156 (851)
T TIGR02302 137 DPWGLRALVVLLLVAAFAYS 156 (851)
T ss_pred CcHHHHHHHHHHHHHHHHHh
Confidence 34578888888777777654
Done!