Query psy4504
Match_columns 219
No_of_seqs 174 out of 721
Neff 6.3
Searched_HMMs 46136
Date Fri Aug 16 18:52:36 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy4504.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/4504hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG2289|consensus 99.9 4.4E-27 9.6E-32 210.6 5.1 192 9-216 81-306 (316)
2 PTZ00101 rhomboid-1 protease; 99.9 2.3E-21 5.1E-26 171.7 15.3 172 22-207 80-266 (278)
3 PRK10907 intramembrane serine 99.6 5.1E-15 1.1E-19 131.3 9.7 131 34-179 133-270 (276)
4 COG0705 Membrane associated se 99.6 4.1E-15 9E-20 127.2 8.5 138 35-183 67-215 (228)
5 KOG2290|consensus 99.5 1.1E-13 2.3E-18 128.4 9.2 162 35-211 450-621 (652)
6 PF01694 Rhomboid: Rhomboid fa 99.3 2.4E-13 5.2E-18 107.4 -1.9 130 34-180 4-143 (145)
7 KOG2289|consensus 99.1 2.3E-11 4.9E-16 109.6 2.2 49 1-49 163-211 (316)
8 PTZ00101 rhomboid-1 protease; 97.4 0.00086 1.9E-08 59.9 8.3 46 3-48 148-193 (278)
9 KOG2632|consensus 96.6 0.014 3.1E-07 51.5 8.6 131 32-176 49-195 (258)
10 COG0705 Membrane associated se 95.1 0.034 7.4E-07 47.4 4.8 94 4-117 115-212 (228)
11 KOG2980|consensus 92.5 0.084 1.8E-06 47.7 2.4 81 90-182 219-304 (310)
12 KOG2290|consensus 89.9 1.3 2.9E-05 42.4 7.6 99 3-126 497-599 (652)
13 PF01694 Rhomboid: Rhomboid fa 80.4 0.58 1.3E-05 36.3 0.2 44 4-47 53-97 (145)
14 PF11286 DUF3087: Protein of u 71.1 26 0.00056 29.2 7.6 32 156-187 45-76 (165)
15 PRK10907 intramembrane serine 64.7 10 0.00022 33.9 4.3 29 5-34 183-211 (276)
16 PF06912 DUF1275: Protein of u 52.1 44 0.00095 27.8 5.9 52 162-213 54-105 (209)
17 PF12732 YtxH: YtxH-like prote 40.7 49 0.0011 23.2 3.8 29 162-190 4-32 (74)
18 PRK12505 putative monovalent c 38.1 2.3E+02 0.005 23.4 9.7 13 165-177 47-59 (159)
19 PRK12574 putative monovalent c 34.2 2.5E+02 0.0053 22.6 7.8 13 165-177 36-48 (141)
20 PRK12437 prolipoprotein diacyl 34.1 1.1E+02 0.0025 26.9 5.9 63 93-183 52-115 (269)
21 PF01773 Nucleos_tra2_N: Na+ d 32.9 1.7E+02 0.0036 20.9 5.6 25 156-180 18-42 (75)
22 PRK13108 prolipoprotein diacyl 31.6 1.7E+02 0.0037 28.2 7.0 28 92-119 55-82 (460)
23 COG0038 EriC Chloride channel 26.7 5.5E+02 0.012 24.3 9.5 28 92-119 161-188 (443)
24 PRK12573 putative monovalent c 25.8 3.5E+02 0.0076 21.7 8.3 13 165-177 36-48 (140)
25 PF11992 DUF3488: Domain of un 25.8 4.9E+02 0.011 23.4 10.6 26 155-180 120-145 (325)
26 COG1299 FruA Phosphotransferas 25.2 87 0.0019 29.1 3.6 20 158-177 92-111 (343)
27 PRK05529 cell division protein 25.0 63 0.0014 28.3 2.6 37 180-217 26-62 (255)
28 PRK12509 putative monovalent c 24.9 3.6E+02 0.0078 21.5 8.2 13 165-177 34-46 (137)
29 PF04892 VanZ: VanZ like famil 24.5 3.1E+02 0.0067 20.6 6.9 78 94-181 53-130 (133)
30 KOG2980|consensus 24.5 1.2E+02 0.0025 27.8 4.2 17 17-33 220-236 (310)
31 cd00400 Voltage_gated_ClC CLC 22.1 6E+02 0.013 23.1 11.5 28 92-119 133-160 (383)
32 PF06295 DUF1043: Protein of u 21.5 80 0.0017 24.8 2.4 15 165-179 4-18 (128)
33 COG4059 MtrE Tetrahydromethano 20.1 1E+02 0.0022 27.2 2.8 54 157-210 223-281 (304)
No 1
>KOG2289|consensus
Probab=99.93 E-value=4.4e-27 Score=210.55 Aligned_cols=192 Identities=35% Similarity=0.550 Sum_probs=153.1
Q ss_pred cccccccC--CccccccchH---------hhHHHHHHHHHHhhcccccccChhHHHH----HHHHhcccC--ccchhhhh
Q psy4504 9 LGTSVIDS--DVYLVGASGG---------VYALLAAHLANVLLNYNQMEFGIVRLLA----IFVVGKFNT--TSFVQVSL 71 (219)
Q Consensus 9 l~~~~~~~--~~~l~gasgg---------~y~~~~ah~~~~~~n~~~m~~G~~rll~----iyll~~~~e--g~~~r~~l 71 (219)
|+....|| ++|+.|+|+- +|++.=.||.||+++|-.+|.|..|+++ ...+|.++| ++++|+.+
T Consensus 81 l~~f~~~~~~~n~~~~~s~~~~~~~~~~~i~~~~~r~E~WRllTym~LHaGi~HL~~N~~~ql~iGi~LE~~~G~~Rigl 160 (316)
T KOG2289|consen 81 LGRFSFQGLRENPLLGPSSLTLEKMGGLLIYKPVHRGELWRLLTYMWLHAGIFHLLLNMLSQLFIGIPLEQVHGFLRIGL 160 (316)
T ss_pred hheeeeeeeccCCccCcCCCCccccCCceecChhhhchhHHHHHHHHHhcCHHHHHHHHHHHHhccccHHhhcCceEEee
Confidence 45556666 3888888883 3445556999999999999999999999 567899999 78899977
Q ss_pred HHHHHHHhhhhhhhhccCCccchhhhhhHHHHHHHHHHHHHHHhccchhhhH--HHHHHHHHHHHHHHHHHHHHHhhhhh
Q psy4504 72 ITFFKDFLRGSLGTSVIDSDVYLVGASGGVYALLAAHLANVLLNYNQMEFGI--VRLLAIFVVASADVGFAVYNRYAGEL 149 (219)
Q Consensus 72 i~~l~gvi~Gsl~~~~~~p~~~~vGASGaifGLlga~l~~~~~~~~~~~~~~--~r~~~l~~~~~~~~~~~i~~~~~~~~ 149 (219)
+| +.|+++||+++.++||+.++||||||+|||+||+++++++||++++.+. .+.+++++++.++++++
T Consensus 161 IY-l~gg~aGSlls~l~d~~~~sVGASggvfaLlgA~Ls~l~~Nw~~m~~~~~~l~~ll~Ii~i~l~~G~~--------- 230 (316)
T KOG2289|consen 161 IY-LAGGVAGSLLSSLFDPNSISVGASGGVFALLGAHLSNLLTNWTIMKNKFAALRTLLIIIFINLDLGFA--------- 230 (316)
T ss_pred eh-hhhhhhhHHHHHHhccCCceecccHHHHHHHHHHHHHHHhhHHHhcchHHHHHHHHHHHHHHHhhccc---------
Confidence 65 5566799999999999999999999999999999999999999997543 44445555556666655
Q ss_pred cCCCCCCCcchhhhhHHHHHHHHHHHHHh---------------cchhhHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCC
Q psy4504 150 AGAGSGYPVSYVAHLTGALAGLTIGLLVL---------------KNFEQKLREQLMWWIALGVYVACTIFAVIYNVTSPS 214 (219)
Q Consensus 150 ~~~~~~~~Vs~~AHlGG~i~G~llg~~~~---------------~~~~~~~~~~~~~~~a~~~~~~~~~~~i~~n~~~~~ 214 (219)
|.+++++|+||+++|+.++++.. +++.+++.+|.++|++..++.++.++++++|+|...
T Consensus 231 ------~~~~~~~h~gg~~~G~~~~fil~~~g~~~~~~~~~~~~~~~~~~~~~q~~~w~~~~~~~v~~~~~~~~~if~~~ 304 (316)
T KOG2289|consen 231 ------PYVDNFAHIGGLLAGFLLGFVLHIGGQLGGITIGLIVLRVFSKRLPYQLLLWIVLLVYLVAGLFASLFNIFDGK 304 (316)
T ss_pred ------cceeccccccccCCCcchhHHhhhccceeEEeccceeeeccccccccchHHHHHHHHHHHHHHHHHHHHhhcCC
Confidence 55666777777777777776653 345566778889999999999999999999999954
Q ss_pred CC
Q psy4504 215 YN 216 (219)
Q Consensus 215 ~~ 216 (219)
|+
T Consensus 305 ~~ 306 (316)
T KOG2289|consen 305 YC 306 (316)
T ss_pred cc
Confidence 43
No 2
>PTZ00101 rhomboid-1 protease; Provisional
Probab=99.87 E-value=2.3e-21 Score=171.72 Aligned_cols=172 Identities=18% Similarity=0.251 Sum_probs=119.1
Q ss_pred ccchHhhHHHHH--------HHHHHhhcccccccChhHHHH----HHHHhcccC---ccchhhhhHHHHHHHhhhhhhhh
Q psy4504 22 GASGGVYALLAA--------HLANVLLNYNQMEFGIVRLLA----IFVVGKFNT---TSFVQVSLITFFKDFLRGSLGTS 86 (219)
Q Consensus 22 gasgg~y~~~~a--------h~~~~~~n~~~m~~G~~rll~----iyll~~~~e---g~~~r~~li~~l~gvi~Gsl~~~ 86 (219)
+++..++..+|+ +|.||+.++.++|.|..|+++ +|.++..+| |+ +|+.++|+++|+ .||+.+.
T Consensus 80 ~p~~~~L~~~Ga~~~~~i~~gq~WRLiT~~FlH~~~~HLl~Nm~~l~~~G~~lE~~~G~-~r~~ilYl~sGi-~G~l~s~ 157 (278)
T PTZ00101 80 TPSDSLLVTLGANVASRIKQGEIHRLILPIFLHANIFHTFFNVFFQLRMGFTLEKNYGI-VKIIILYFLTGI-YGNILSS 157 (278)
T ss_pred CCCHHHHHHHhCcchhhhhcCCCHHHHHHHHHccCHHHHHHHHHHHHHHHHHHHHHHCh-HHHHHHHHHHHH-HHHHHHH
Confidence 455444444443 799999999999999999988 688899999 55 898778877776 5589888
Q ss_pred ccCCccchhhhhhHHHHHHHHHHHHHHHhccchhhhHHHHHHHHHHHHHHHHHHHHHHhhhhhcCCCCCCCcchhhhhHH
Q psy4504 87 VIDSDVYLVGASGGVYALLAAHLANVLLNYNQMEFGIVRLLAIFVVASADVGFAVYNRYAGELAGAGSGYPVSYVAHLTG 166 (219)
Q Consensus 87 ~~~p~~~~vGASGaifGLlga~l~~~~~~~~~~~~~~~r~~~l~~~~~~~~~~~i~~~~~~~~~~~~~~~~Vs~~AHlGG 166 (219)
...|...++|||||+||++|++++.++.+|++++.+.........+..+.+. ++ + .. .+|+||++||+||
T Consensus 158 ~~~~~~~svGASgAifGLiGa~~~~lil~w~~~~~~~~~~~~~i~~~li~~~--l~--~-~~-----~g~~Id~~aHlGG 227 (278)
T PTZ00101 158 SVTYCPIKVGASTSGMGLLGIVTSELILLWHVIRHRERVVFNIIFFSLISFF--YY--F-TF-----NGSNIDHVGHLGG 227 (278)
T ss_pred HHccCCcEEehhHHHHHHHHHHHHHHHHHHHhhccHHHHHHHHHHHHHHHHH--HH--H-hc-----CCCCccHHHHHHH
Confidence 8888888999999999999999988888888765443222211111111111 11 1 11 1489999999999
Q ss_pred HHHHHHHHHHHhcchhhHHHHHHHHHHHHHHHHHHHHHHHH
Q psy4504 167 ALAGLTIGLLVLKNFEQKLREQLMWWIALGVYVACTIFAVI 207 (219)
Q Consensus 167 ~i~G~llg~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~i~ 207 (219)
+++|++++..+.++.+. ..|..+|.....+.+++...+.
T Consensus 228 ~i~G~llg~~~~~~l~~--~~~~~~~~~~~~~~~~~~~~i~ 266 (278)
T PTZ00101 228 LLSGISMGILYNSQMEN--KPSWYDHMKMASYACLALLAIV 266 (278)
T ss_pred HHHHHHHHHHHHhhhhh--cccHHHHHHHHHHHHHHHHHHH
Confidence 99999999887554432 2333445544445554444443
No 3
>PRK10907 intramembrane serine protease GlpG; Provisional
Probab=99.59 E-value=5.1e-15 Score=131.32 Aligned_cols=131 Identities=19% Similarity=0.226 Sum_probs=88.0
Q ss_pred HHHHHhhcccccccChhHHHH----HHHHhcccC---ccchhhhhHHHHHHHhhhhhhhhccCCccchhhhhhHHHHHHH
Q psy4504 34 HLANVLLNYNQMEFGIVRLLA----IFVVGKFNT---TSFVQVSLITFFKDFLRGSLGTSVIDSDVYLVGASGGVYALLA 106 (219)
Q Consensus 34 h~~~~~~n~~~m~~G~~rll~----iyll~~~~e---g~~~r~~li~~l~gvi~Gsl~~~~~~p~~~~vGASGaifGLlg 106 (219)
++.||+++..++|+|..|+++ ++.+++..| |+ +|++.+|+++++++ |+.++.+.+ ...+|+||++||++|
T Consensus 133 ~q~WRl~T~~flH~~~~Hl~fNml~l~~lG~~iE~~~G~-~~~l~l~l~s~i~~-~~~~~~~~~-~~~gGaSGvVygL~g 209 (276)
T PRK10907 133 FELWRYFTHALLHFSLLHILFNLLWWWYLGGAVEKRLGS-GKLIVITLISALLS-GWVQSKFSG-PWFGGLSGVVYALMG 209 (276)
T ss_pred CCcHHHHhHHHHhCCHHHHHHHHHHHHHHHHHHHHHHCh-HHHHHHHHHHHHHH-HHHHHHHcc-chhhHHHHHHHHHHH
Confidence 578999999999999999999 788999999 66 78877777777654 677666644 357899999999999
Q ss_pred HHHHHHHHhccchhhhHHHHHHHHHHHHHHHHHHHHHHhhhhhcCCCCCCCcchhhhhHHHHHHHHHHHHHhc
Q psy4504 107 AHLANVLLNYNQMEFGIVRLLAIFVVASADVGFAVYNRYAGELAGAGSGYPVSYVAHLTGALAGLTIGLLVLK 179 (219)
Q Consensus 107 a~l~~~~~~~~~~~~~~~r~~~l~~~~~~~~~~~i~~~~~~~~~~~~~~~~Vs~~AHlGG~i~G~llg~~~~~ 179 (219)
... ..-.+.++......+....... +.+.....+.+ +++|+++||+||+++|+++++.-.+
T Consensus 210 ~~~-~~~~~~p~~~~~lp~~~~~f~l--lwl~~g~~~~~---------g~~Ian~AHlgGli~Gll~g~~~~~ 270 (276)
T PRK10907 210 YVW-LRGERDPQSGIYLPRGLIAFAL--LWLVAGYFDLF---------GMSIANAAHVAGLAVGLAMAFWDTR 270 (276)
T ss_pred HHH-HHhccccccchhhhHHHHHHHH--HHHHHHHHHcc---------CcccHHHHHHHHHHHHHHHHHHhhh
Confidence 753 1111111111112222222211 11222222211 4789999999999999999976543
No 4
>COG0705 Membrane associated serine protease [Amino acid transport and metabolism]
Probab=99.59 E-value=4.1e-15 Score=127.19 Aligned_cols=138 Identities=21% Similarity=0.333 Sum_probs=95.2
Q ss_pred HHHHhhcccccccChhHHHH----HHHHhcccC---ccchhhhhHHHHHHHhhhhhhhhccCCc--cchhhhhhHHHHHH
Q psy4504 35 LANVLLNYNQMEFGIVRLLA----IFVVGKFNT---TSFVQVSLITFFKDFLRGSLGTSVIDSD--VYLVGASGGVYALL 105 (219)
Q Consensus 35 ~~~~~~n~~~m~~G~~rll~----iyll~~~~e---g~~~r~~li~~l~gvi~Gsl~~~~~~p~--~~~vGASGaifGLl 105 (219)
+.|++.++.++|.|+.|++. ++.++...| |+ .|+...|+.+|+++ ++.+..+.|. ++++||||++||++
T Consensus 67 ~~w~lit~~FlH~~~~Hll~N~~~l~~fg~~le~~~G~-~~f~~~yl~~gl~~-~~~~~~~~~~~~~~~~GASG~i~gll 144 (228)
T COG0705 67 QLWRLITAIFLHAGFLHLLFNMLALWVFGSNLERRLGT-LRFLLFYLLSGLLA-GLAQVLFGPKGGAPSLGASGAIFGLL 144 (228)
T ss_pred chHHHHHHHHHHhhHHHHHHHHHHHHHhhHHHHHHhch-hHHHHHHHHHHHHH-HHHHHHHcccccCcccchhHHHHHHH
Confidence 89999999999999999987 788898999 66 78888888888766 5666766664 48999999999999
Q ss_pred HHHHHHHHHhccchhhh--HHHHHHHHHHHHHHHHHHHHHHhhhhhcCCCCCCCcchhhhhHHHHHHHHHHHHHhcchhh
Q psy4504 106 AAHLANVLLNYNQMEFG--IVRLLAIFVVASADVGFAVYNRYAGELAGAGSGYPVSYVAHLTGALAGLTIGLLVLKNFEQ 183 (219)
Q Consensus 106 ga~l~~~~~~~~~~~~~--~~r~~~l~~~~~~~~~~~i~~~~~~~~~~~~~~~~Vs~~AHlGG~i~G~llg~~~~~~~~~ 183 (219)
+++.. ...+.+..... ..+...+.+ ...+ +++.+.... +..++|+|+||++|+++|.+++..+.|+.++
T Consensus 145 ga~~~-~~~~~~~~~~~~~~~~~~~~~i--~~~~---~~~~~~~~~---~~~~~va~~aHl~G~i~G~l~~~~~~~~~~~ 215 (228)
T COG0705 145 GAYFL-LFPFARILLLFLSLPRPALILI--LIWL---LYSLFSGAG---SFGPSVAWSAHLGGLIGGLLLAALLSRKLRK 215 (228)
T ss_pred HHHHH-HccccchhhhhccCchhHHHHH--HHHH---HHHHHHHhc---CCchHHHHHHHHHHHHHHHHHHHHHhhhhhh
Confidence 99872 22222222111 222222222 1122 233333222 1124799999999999999999887665443
No 5
>KOG2290|consensus
Probab=99.48 E-value=1.1e-13 Score=128.42 Aligned_cols=162 Identities=17% Similarity=0.230 Sum_probs=111.7
Q ss_pred HHHHhhcccccccChhHHHHH----HHHhcccC--ccchhhhhHHHHHHHhhhhhhhhccCCccchhhhhhHHHHHHHHH
Q psy4504 35 LANVLLNYNQMEFGIVRLLAI----FVVGKFNT--TSFVQVSLITFFKDFLRGSLGTSVIDSDVYLVGASGGVYALLAAH 108 (219)
Q Consensus 35 ~~~~~~n~~~m~~G~~rll~i----yll~~~~e--g~~~r~~li~~l~gvi~Gsl~~~~~~p~~~~vGASGaifGLlga~ 108 (219)
+-+|+....++|.|..|++.= +-+...+| -.+.|++++|+++| +.||+++.++-|..+.||-||+.+|++++.
T Consensus 450 QfYRL~~SLFlHagviH~~vSi~FQm~vmrdlEkL~g~~riAIiy~~SG-itGNLASAIFlpY~~eVgPa~sQ~Gila~l 528 (652)
T KOG2290|consen 450 QFYRLWLSLFLHAGVIHLLVSICFQMTVMRDLEKLAGWHRIAIIYFLSG-ITGNLASAIFLPYRAEVGPAGSQFGILACL 528 (652)
T ss_pred HHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHhhcchhhheeeeccc-ccccchheeeeccccccCCcccccchHHHH
Confidence 455666677899999999981 22233456 33578888777777 588999999999999999999999999999
Q ss_pred HHHHHHhccchhhhHHHHHHHHHHHHHHHHHHHHHHhhhhhcCCCCCCCcchhhhhHHHHHHHHHHHHHhcchh--h--H
Q psy4504 109 LANVLLNYNQMEFGIVRLLAIFVVASADVGFAVYNRYAGELAGAGSGYPVSYVAHLTGALAGLTIGLLVLKNFE--Q--K 184 (219)
Q Consensus 109 l~~~~~~~~~~~~~~~r~~~l~~~~~~~~~~~i~~~~~~~~~~~~~~~~Vs~~AHlGG~i~G~llg~~~~~~~~--~--~ 184 (219)
+..+..+|+.+++++....=++. +.+-+ +.+. -|-||++||+.|++.|++.++++++... . .
T Consensus 529 ~vEl~qs~~il~~~w~a~~~Lia-~~L~L-------~iGl------iPWiDN~aHlfG~i~GLl~s~~~~PYi~Fg~~d~ 594 (652)
T KOG2290|consen 529 FVELFQSWQILERPWRAFFHLIA-TLLVL-------CIGL------IPWIDNWAHLFGTIFGLLTSIIFLPYIDFGDFDL 594 (652)
T ss_pred HHHHHhhhHhhhhHHHHHHHHHH-HHHHH-------Hhcc------ccchhhHHHHHHHHHHHHHHHHhhccccccchhh
Confidence 99999999877666533322211 11101 1111 3999999999999999999999987433 2 1
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHhc
Q psy4504 185 LREQLMWWIALGVYVACTIFAVIYNVT 211 (219)
Q Consensus 185 ~~~~~~~~~a~~~~~~~~~~~i~~n~~ 211 (219)
-++|..-.++.+++..++..++++.+.
T Consensus 595 yrKr~~ilIs~ivf~~Lla~Lvv~fy~ 621 (652)
T KOG2290|consen 595 YRKRFYILISQIVFSGLLAILVVVFYN 621 (652)
T ss_pred hhhHHHHHHHHHHHHHHHHHHHHheee
Confidence 223444344455555555555555543
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=99.28 E-value=2.4e-13 Score=107.40 Aligned_cols=130 Identities=26% Similarity=0.317 Sum_probs=84.4
Q ss_pred HHHHHhhcccccccChhHHHH----HHHHhcccC---ccchhhhhHHHHHHHhhhhhhhhccCCcc-chhhhhhHHHHHH
Q psy4504 34 HLANVLLNYNQMEFGIVRLLA----IFVVGKFNT---TSFVQVSLITFFKDFLRGSLGTSVIDSDV-YLVGASGGVYALL 105 (219)
Q Consensus 34 h~~~~~~n~~~m~~G~~rll~----iyll~~~~e---g~~~r~~li~~l~gvi~Gsl~~~~~~p~~-~~vGASGaifGLl 105 (219)
++.||+.++...|.+..|++. ++.++...| |+ +|+..+++..++ .+++......+.. +.+|+||+++|++
T Consensus 4 ~~~wrl~T~~f~h~~~~hl~~n~~~l~~~g~~lE~~~G~-~~~~~~~l~~~~-~~~l~~~~~~~~~~~~~G~Sg~~~~l~ 81 (145)
T PF01694_consen 4 GQWWRLFTSPFVHANFLHLLFNLLALWFFGSLLERRLGS-RRFLALYLLSGL-LGSLLSLLFSPPNQPYVGASGAVFGLL 81 (145)
T ss_dssp C-TTHHHHGGG--SSHHHHHHHHHHHHHHHHHHHHHHHH-HHHHHHHHHHHH-HHHHHHHHHH-S-----SSHHHHHHHH
T ss_pred CcchhhhHHHHHccCHHHHHHHHHHHHHhhhhHhhhccc-hHHHHHHHHHHH-hhhhccccccccccccCCCcccchHHH
Confidence 578999999999999999998 778888899 44 777666555554 5588887766655 8999999999999
Q ss_pred HHHHHHHHHhccchhhhH--HHHHHHHHHHHHHHHHHHHHHhhhhhcCCCCCCCcchhhhhHHHHHHHHHHHHHhcc
Q psy4504 106 AAHLANVLLNYNQMEFGI--VRLLAIFVVASADVGFAVYNRYAGELAGAGSGYPVSYVAHLTGALAGLTIGLLVLKN 180 (219)
Q Consensus 106 ga~l~~~~~~~~~~~~~~--~r~~~l~~~~~~~~~~~i~~~~~~~~~~~~~~~~Vs~~AHlGG~i~G~llg~~~~~~ 180 (219)
+++......++++...+. .+.....+......+ ..|++|+.+|++|+++|.+++..+.|+
T Consensus 82 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---------------~~~~~~~~~hl~G~~~G~~~~~~~~~~ 143 (145)
T PF01694_consen 82 GAFLFLYPQNKKRLRFIYLALVVPIIVLVIILLLG---------------FIPNISFLGHLGGFLAGLLYGFLILRR 143 (145)
T ss_dssp HHHHHHHHCCCCCS---HCCCCCCCCCCCHHHCTS---------------SSSTTTHHHHHHHHHHHHHHHHHHCH-
T ss_pred HHHHHHHhhccchhhcchHHHHHHHHHHHHHHHHH---------------HHHhHHHHHHHHHHHHHHHHHHHHHHc
Confidence 999865555544443211 001011010111000 138999999999999999999887654
No 7
>KOG2289|consensus
Probab=99.11 E-value=2.3e-11 Score=109.58 Aligned_cols=49 Identities=43% Similarity=0.588 Sum_probs=45.4
Q ss_pred CccceeeccccccccCCccccccchHhhHHHHHHHHHHhhcccccccCh
Q psy4504 1 MSVWLRRSLGTSVIDSDVYLVGASGGVYALLAAHLANVLLNYNQMEFGI 49 (219)
Q Consensus 1 ~~~~~~g~l~~~~~~~~~~l~gasgg~y~~~~ah~~~~~~n~~~m~~G~ 49 (219)
|.+++||||+++++||+.++||||||+|+++|||+++.++||++|.-..
T Consensus 163 l~gg~aGSlls~l~d~~~~sVGASggvfaLlgA~Ls~l~~Nw~~m~~~~ 211 (316)
T KOG2289|consen 163 LAGGVAGSLLSSLFDPNSISVGASGGVFALLGAHLSNLLTNWTIMKNKF 211 (316)
T ss_pred hhhhhhhHHHHHHhccCCceecccHHHHHHHHHHHHHHHhhHHHhcchH
Confidence 4578999999999999999999999999999999999999999998333
No 8
>PTZ00101 rhomboid-1 protease; Provisional
Probab=97.36 E-value=0.00086 Score=59.93 Aligned_cols=46 Identities=17% Similarity=0.146 Sum_probs=40.2
Q ss_pred cceeeccccccccCCccccccchHhhHHHHHHHHHHhhcccccccC
Q psy4504 3 VWLRRSLGTSVIDSDVYLVGASGGVYALLAAHLANVLLNYNQMEFG 48 (219)
Q Consensus 3 ~~~~g~l~~~~~~~~~~l~gasgg~y~~~~ah~~~~~~n~~~m~~G 48 (219)
.++.|++.++.++|....+||||++|.++|++.+..+++|..+...
T Consensus 148 sGi~G~l~s~~~~~~~~svGASgAifGLiGa~~~~lil~w~~~~~~ 193 (278)
T PTZ00101 148 TGIYGNILSSSVTYCPIKVGASTSGMGLLGIVTSELILLWHVIRHR 193 (278)
T ss_pred HHHHHHHHHHHHccCCcEEehhHHHHHHHHHHHHHHHHHHHhhccH
Confidence 3567889999999988899999999999999999999999887543
No 9
>KOG2632|consensus
Probab=96.55 E-value=0.014 Score=51.47 Aligned_cols=131 Identities=19% Similarity=0.287 Sum_probs=74.8
Q ss_pred HHHHHHHhhcccccccChhHHHH----HHHHhcccC---ccchhhhhHHHHHHHhhhhhhh---h-cc-CCccc---hhh
Q psy4504 32 AAHLANVLLNYNQMEFGIVRLLA----IFVVGKFNT---TSFVQVSLITFFKDFLRGSLGT---S-VI-DSDVY---LVG 96 (219)
Q Consensus 32 ~ah~~~~~~n~~~m~~G~~rll~----iyll~~~~e---g~~~r~~li~~l~gvi~Gsl~~---~-~~-~p~~~---~vG 96 (219)
---+.+|+.+|...|-+..|+++ +...+...| |.-+|+.....+.++..|=+.- + .. .+... .+|
T Consensus 49 ~~~ql~RL~Ty~l~H~s~~hllfnmlaL~~~g~~fE~~~G~t~~~l~~~~llalf~gIl~ll~~~~~~~~d~~~~~~a~G 128 (258)
T KOG2632|consen 49 INWQLYRLITYALVHLSLPHLLFNMLALWPLGSQFERTHGTTVRILMFTVLLALFSGILYLLAYHVFLLSDLVYVEGAIG 128 (258)
T ss_pred hhHHHHHHHHHHHHhccHHHHHHHHHHHHhchhHHHhhccceehHHHHHHHHHHHHHHHHHHHHHHHhhcchhhhccccc
Confidence 33578889999999999999998 677788888 5457877777777776662221 1 11 23333 355
Q ss_pred hhhHHHHHHHHHHHHHHHhccc-hhhhHHHHHHHHHHHHHHHHHHHHHHhhhhhcCCCCCCCcchhhhhHHHHHHHHHHH
Q psy4504 97 ASGGVYALLAAHLANVLLNYNQ-MEFGIVRLLAIFVVASADVGFAVYNRYAGELAGAGSGYPVSYVAHLTGALAGLTIGL 175 (219)
Q Consensus 97 ASGaifGLlga~l~~~~~~~~~-~~~~~~r~~~l~~~~~~~~~~~i~~~~~~~~~~~~~~~~Vs~~AHlGG~i~G~llg~ 175 (219)
=||-.|+.++..- .....+. ..+....+-+.......-+.. +.. .|+.|+.+|++|++.|...++
T Consensus 129 ~s~v~Fam~~~~~--~~sp~r~~~~fg~~siP~~l~Pw~lLi~~---~~l---------vp~aSFlghl~GllvG~ay~~ 194 (258)
T KOG2632|consen 129 FSGVLFAMMAVLE--VQSPVRSRSVFGLFSIPIVLAPWALLIAT---QIL---------VPQASFLGHLCGLLVGYAYAF 194 (258)
T ss_pred ccHHHHHHHHHHh--hcCcccchhhcccccccHHHHHHHHHHHH---HHH---------ccCchHHHHHHHHHHHHHHHH
Confidence 5666665555421 1111111 111111000111111111111 111 499999999999999999998
Q ss_pred H
Q psy4504 176 L 176 (219)
Q Consensus 176 ~ 176 (219)
-
T Consensus 195 ~ 195 (258)
T KOG2632|consen 195 S 195 (258)
T ss_pred H
Confidence 4
No 10
>COG0705 Membrane associated serine protease [Amino acid transport and metabolism]
Probab=95.12 E-value=0.034 Score=47.37 Aligned_cols=94 Identities=21% Similarity=0.122 Sum_probs=53.1
Q ss_pred ceeeccccccccCCc--cccccchHhhHHHHHHHHHHhhcccccccC--hhHHHHHHHHhcccCccchhhhhHHHHHHHh
Q psy4504 4 WLRRSLGTSVIDSDV--YLVGASGGVYALLAAHLANVLLNYNQMEFG--IVRLLAIFVVGKFNTTSFVQVSLITFFKDFL 79 (219)
Q Consensus 4 ~~~g~l~~~~~~~~~--~l~gasgg~y~~~~ah~~~~~~n~~~m~~G--~~rll~iyll~~~~eg~~~r~~li~~l~gvi 79 (219)
++.++++...+.|.. +.+||||..|.++|+-....-.. ++.-.. ..+...+++.. . +
T Consensus 115 gl~~~~~~~~~~~~~~~~~~GASG~i~gllga~~~~~~~~-~~~~~~~~~~~~~~~~i~~-----------------~-~ 175 (228)
T COG0705 115 GLLAGLAQVLFGPKGGAPSLGASGAIFGLLGAYFLLFPFA-RILLLFLSLPRPALILILI-----------------W-L 175 (228)
T ss_pred HHHHHHHHHHHcccccCcccchhHHHHHHHHHHHHHcccc-chhhhhccCchhHHHHHHH-----------------H-H
Confidence 344556666777775 89999999999999844322111 000000 12222222221 1 2
Q ss_pred hhhhhhhccCCccchhhhhhHHHHHHHHHHHHHHHhcc
Q psy4504 80 RGSLGTSVIDSDVYLVGASGGVYALLAAHLANVLLNYN 117 (219)
Q Consensus 80 ~Gsl~~~~~~p~~~~vGASGaifGLlga~l~~~~~~~~ 117 (219)
..++.....++. .+++.++.+.|+++..+......++
T Consensus 176 ~~~~~~~~~~~~-~~va~~aHl~G~i~G~l~~~~~~~~ 212 (228)
T COG0705 176 LYSLFSGAGSFG-PSVAWSAHLGGLIGGLLLAALLSRK 212 (228)
T ss_pred HHHHHHHhcCCc-hHHHHHHHHHHHHHHHHHHHHHhhh
Confidence 224444443333 6899999999999888755544443
No 11
>KOG2980|consensus
Probab=92.53 E-value=0.084 Score=47.67 Aligned_cols=81 Identities=25% Similarity=0.247 Sum_probs=45.3
Q ss_pred CccchhhhhhHHHHHHHHHHHHHHHhccch---hhhH--HHHHHHHHHHHHHHHHHHHHHhhhhhcCCCCCCCcchhhhh
Q psy4504 90 SDVYLVGASGGVYALLAAHLANVLLNYNQM---EFGI--VRLLAIFVVASADVGFAVYNRYAGELAGAGSGYPVSYVAHL 164 (219)
Q Consensus 90 p~~~~vGASGaifGLlga~l~~~~~~~~~~---~~~~--~r~~~l~~~~~~~~~~~i~~~~~~~~~~~~~~~~Vs~~AHl 164 (219)
+..++.||||++|++.+... .++.+.+.+ ..+. .....+-.++..++...+ . +.-.-|+.||+
T Consensus 219 ~~gp~LGAsGav~ai~a~~~-~lfP~~~~~i~f~~~v~~ga~~~~~~i~~~~~a~~~--------l---~~~~~n~~Ah~ 286 (310)
T KOG2980|consen 219 WAGPSLGASGAVYAILALDC-TLFPKTTLYILFVFPVPAGAGLAFKAIAAYDFAGLI--------L---GWGFFNHAAHL 286 (310)
T ss_pred ccccccccchHHHHHHHHHh-hcCcCcceeEEEeecccccchhHHHHHHHhhhccee--------e---ccccchhHhhh
Confidence 35678999999999998875 233322222 1111 111111111111111111 1 12456778999
Q ss_pred HHHHHHHHHHHHHhcchh
Q psy4504 165 TGALAGLTIGLLVLKNFE 182 (219)
Q Consensus 165 GG~i~G~llg~~~~~~~~ 182 (219)
+|-+.|...+....++.+
T Consensus 287 ~gsl~Gv~va~~~~~ri~ 304 (310)
T KOG2980|consen 287 SGSLFGVVVATYLWARIR 304 (310)
T ss_pred cchHHHHHHHHHHHHHHH
Confidence 999999999987755544
No 12
>KOG2290|consensus
Probab=89.87 E-value=1.3 Score=42.42 Aligned_cols=99 Identities=16% Similarity=0.312 Sum_probs=67.0
Q ss_pred cceeeccccccccCCccccccchHhhHHHHHHHHHHhhccccccc---ChhHHHH-HHHHhcccCccchhhhhHHHHHHH
Q psy4504 3 VWLRRSLGTSVIDSDVYLVGASGGVYALLAAHLANVLLNYNQMEF---GIVRLLA-IFVVGKFNTTSFVQVSLITFFKDF 78 (219)
Q Consensus 3 ~~~~g~l~~~~~~~~~~l~gasgg~y~~~~ah~~~~~~n~~~m~~---G~~rll~-iyll~~~~eg~~~r~~li~~l~gv 78 (219)
.++.|-|++.++=|-.+=|||||.-+-++++-......||+-++= .+.|+++ +++++
T Consensus 497 SGitGNLASAIFlpY~~eVgPa~sQ~Gila~l~vEl~qs~~il~~~w~a~~~Lia~~L~L~------------------- 557 (652)
T KOG2290|consen 497 SGITGNLASAIFLPYRAEVGPAGSQFGILACLFVELFQSWQILERPWRAFFHLIATLLVLC------------------- 557 (652)
T ss_pred ccccccchheeeeccccccCCcccccchHHHHHHHHHhhhHhhhhHHHHHHHHHHHHHHHH-------------------
Confidence 467899999999999999999999999999999999999987653 2333333 22232
Q ss_pred hhhhhhhhccCCccchhhhhhHHHHHHHHHHHHHHHhccchhhhHHHH
Q psy4504 79 LRGSLGTSVIDSDVYLVGASGGVYALLAAHLANVLLNYNQMEFGIVRL 126 (219)
Q Consensus 79 i~Gsl~~~~~~p~~~~vGASGaifGLlga~l~~~~~~~~~~~~~~~r~ 126 (219)
+ | +.-++.+ -+--+|-|+||+.+.+..=...+...+....|.
T Consensus 558 i-G-liPWiDN----~aHlfG~i~GLl~s~~~~PYi~Fg~~d~yrKr~ 599 (652)
T KOG2290|consen 558 I-G-LIPWIDN----WAHLFGTIFGLLTSIIFLPYIDFGDFDLYRKRF 599 (652)
T ss_pred h-c-cccchhh----HHHHHHHHHHHHHHHHhhccccccchhhhhhHH
Confidence 2 2 2222222 344578999999998644445555544333443
No 13
>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=80.41 E-value=0.58 Score=36.31 Aligned_cols=44 Identities=34% Similarity=0.343 Sum_probs=31.8
Q ss_pred ceeeccccccccCCc-cccccchHhhHHHHHHHHHHhhccccccc
Q psy4504 4 WLRRSLGTSVIDSDV-YLVGASGGVYALLAAHLANVLLNYNQMEF 47 (219)
Q Consensus 4 ~~~g~l~~~~~~~~~-~l~gasgg~y~~~~ah~~~~~~n~~~m~~ 47 (219)
.+.|++.....+|.. +.+|+||++|++++++......++.++..
T Consensus 53 ~~~~~l~~~~~~~~~~~~~G~Sg~~~~l~~~~~~~~~~~~~~~~~ 97 (145)
T PF01694_consen 53 GLLGSLLSLLFSPPNQPYVGASGAVFGLLGAFLFLYPQNKKRLRF 97 (145)
T ss_dssp HHHHHHHHHHHH-S-----SSHHHHHHHHHHHHHHHHCCCCCS--
T ss_pred HHhhhhccccccccccccCCCcccchHHHHHHHHHHhhccchhhc
Confidence 356677888888887 99999999999999999999988877654
No 14
>PF11286 DUF3087: Protein of unknown function (DUF3087); InterPro: IPR021438 This family of proteins with unknown function appears to be restricted to Gammaproteobacteria.
Probab=71.10 E-value=26 Score=29.16 Aligned_cols=32 Identities=16% Similarity=0.200 Sum_probs=24.0
Q ss_pred CCcchhhhhHHHHHHHHHHHHHhcchhhHHHH
Q psy4504 156 YPVSYVAHLTGALAGLTIGLLVLKNFEQKLRE 187 (219)
Q Consensus 156 ~~Vs~~AHlGG~i~G~llg~~~~~~~~~~~~~ 187 (219)
++=++.=.+.|.+.|.++...++++.+.+++-
T Consensus 45 ~~~nf~~NllGVil~~~~~~~~l~~~k~~p~m 76 (165)
T PF11286_consen 45 SGGNFHWNLLGVILGLLLTSALLRQLKTHPFM 76 (165)
T ss_pred CCCceeeeHHHHHHHHHHHHHHHHHHccChHH
Confidence 44566778999999999988887776655443
No 15
>PRK10907 intramembrane serine protease GlpG; Provisional
Probab=64.66 E-value=10 Score=33.92 Aligned_cols=29 Identities=31% Similarity=0.347 Sum_probs=21.5
Q ss_pred eeeccccccccCCccccccchHhhHHHHHH
Q psy4504 5 LRRSLGTSVIDSDVYLVGASGGVYALLAAH 34 (219)
Q Consensus 5 ~~g~l~~~~~~~~~~l~gasgg~y~~~~ah 34 (219)
+.|.++.+.+++. +..|+||.+|+++|..
T Consensus 183 i~~~~~~~~~~~~-~~gGaSGvVygL~g~~ 211 (276)
T PRK10907 183 LLSGWVQSKFSGP-WFGGLSGVVYALMGYV 211 (276)
T ss_pred HHHHHHHHHHccc-hhhHHHHHHHHHHHHH
Confidence 4455666666664 4789999999999963
No 16
>PF06912 DUF1275: Protein of unknown function (DUF1275); InterPro: IPR010699 This family consists of several hypothetical bacterial proteins of around 200 residues in length. The function of this family is unknown although a few members are thought to be membrane proteins.
Probab=52.15 E-value=44 Score=27.83 Aligned_cols=52 Identities=13% Similarity=0.142 Sum_probs=23.9
Q ss_pred hhhHHHHHHHHHHHHHhcchhhHHHHHHHHHHHHHHHHHHHHHHHHHHhcCC
Q psy4504 162 AHLTGALAGLTIGLLVLKNFEQKLREQLMWWIALGVYVACTIFAVIYNVTSP 213 (219)
Q Consensus 162 AHlGG~i~G~llg~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~i~~n~~~~ 213 (219)
.=+.+++.|..++-.+.++.++++.++...+.-+.-.+++++..+......+
T Consensus 54 ~~i~~F~~G~~~~~~i~~~~~~~~~~~~~~~~l~~~~~ll~~~~~~~~~~~~ 105 (209)
T PF06912_consen 54 LAILSFILGAFLAGLIVRRSRRRRRRRWYRILLLLEAILLLIAALLPPAFPP 105 (209)
T ss_pred HHHHHHHHHHHHHHHHHHhccccchhHHHHHHHHHHHHHHHHHHHHHHhccc
Confidence 3355666666666655233333333344434433334444444444444433
No 17
>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=40.66 E-value=49 Score=23.19 Aligned_cols=29 Identities=38% Similarity=0.510 Sum_probs=19.4
Q ss_pred hhhHHHHHHHHHHHHHhcchhhHHHHHHH
Q psy4504 162 AHLTGALAGLTIGLLVLKNFEQKLREQLM 190 (219)
Q Consensus 162 AHlGG~i~G~llg~~~~~~~~~~~~~~~~ 190 (219)
+=+.|.++|..+++++-|+..+..++++.
T Consensus 4 g~l~Ga~~Ga~~glL~aP~sG~e~R~~l~ 32 (74)
T PF12732_consen 4 GFLAGAAAGAAAGLLFAPKSGKETREKLK 32 (74)
T ss_pred HHHHHHHHHHHHHHHhCCCCcHHHHHHHH
Confidence 34568888888888877766555444443
No 18
>PRK12505 putative monovalent cation/H+ antiporter subunit B; Reviewed
Probab=38.14 E-value=2.3e+02 Score=23.37 Aligned_cols=13 Identities=23% Similarity=0.427 Sum_probs=9.7
Q ss_pred HHHHHHHHHHHHH
Q psy4504 165 TGALAGLTIGLLV 177 (219)
Q Consensus 165 GG~i~G~llg~~~ 177 (219)
|||.+|.+++..+
T Consensus 47 GGFqgGlI~Aaa~ 59 (159)
T PRK12505 47 GGFQGGVIVASVV 59 (159)
T ss_pred chHHHHHHHHHHH
Confidence 7888888877653
No 19
>PRK12574 putative monovalent cation/H+ antiporter subunit B; Reviewed
Probab=34.24 E-value=2.5e+02 Score=22.58 Aligned_cols=13 Identities=23% Similarity=0.378 Sum_probs=10.1
Q ss_pred HHHHHHHHHHHHH
Q psy4504 165 TGALAGLTIGLLV 177 (219)
Q Consensus 165 GG~i~G~llg~~~ 177 (219)
|||.+|.+.+..+
T Consensus 36 GGF~gGli~a~a~ 48 (141)
T PRK12574 36 GGFIGGLIFSSAF 48 (141)
T ss_pred ccHHHHHHHHHHH
Confidence 7888888877664
No 20
>PRK12437 prolipoprotein diacylglyceryl transferase; Reviewed
Probab=34.10 E-value=1.1e+02 Score=26.91 Aligned_cols=63 Identities=14% Similarity=0.189 Sum_probs=40.3
Q ss_pred chhhhhhHHHHHHHHHHHHHHHhccchh-hhHHHHHHHHHHHHHHHHHHHHHHhhhhhcCCCCCCCcchhhhhHHHHHHH
Q psy4504 93 YLVGASGGVYALLAAHLANVLLNYNQME-FGIVRLLAIFVVASADVGFAVYNRYAGELAGAGSGYPVSYVAHLTGALAGL 171 (219)
Q Consensus 93 ~~vGASGaifGLlga~l~~~~~~~~~~~-~~~~r~~~l~~~~~~~~~~~i~~~~~~~~~~~~~~~~Vs~~AHlGG~i~G~ 171 (219)
....-...+.|++||=+..++.|+++.. ++. +. +.+| +.+-++. ||+++|+
T Consensus 52 ~~l~~~~~l~gilGARl~~Vl~~~~~y~~~p~-~i------------~~i~------------~GGls~~---GGligg~ 103 (269)
T PRK12437 52 SDLVLIAVPIAILGARIYYVLFEWDYYAQNPS-QI------------FNIW------------QGGLAIH---GGLIGAV 103 (269)
T ss_pred HHHHHHHHHHHHHHHHHHHHHcCHHHHHhCHH-HH------------HHHh------------cCCchHH---HHHHHHH
Confidence 4667778888999999988888887652 221 10 1122 2344443 8888888
Q ss_pred HHHHHHhcchhh
Q psy4504 172 TIGLLVLKNFEQ 183 (219)
Q Consensus 172 llg~~~~~~~~~ 183 (219)
+.+....|+++.
T Consensus 104 l~~~~~~r~~~~ 115 (269)
T PRK12437 104 LTGIIFAKKKKI 115 (269)
T ss_pred HHHHHHHHHhCC
Confidence 887776655443
No 21
>PF01773 Nucleos_tra2_N: Na+ dependent nucleoside transporter N-terminus; InterPro: IPR002668 This entry contains nucleoside transport proteins. S282_RAT is a purine-specific Na+-nucleoside cotransporter localised to the bile canalicular membrane []. S281_RAT is a a Na+-dependent nucleoside transporter selective for pyrimidine nucleosides and adenosine it also transports the anti-viral nucleoside analogues AZT and ddC [].; GO: 0005415 nucleoside:sodium symporter activity, 0006810 transport, 0016020 membrane; PDB: 3TIJ_A.
Probab=32.94 E-value=1.7e+02 Score=20.90 Aligned_cols=25 Identities=20% Similarity=0.303 Sum_probs=17.6
Q ss_pred CCcchhhhhHHHHHHHHHHHHHhcc
Q psy4504 156 YPVSYVAHLTGALAGLTIGLLVLKN 180 (219)
Q Consensus 156 ~~Vs~~AHlGG~i~G~llg~~~~~~ 180 (219)
..|+|-.=+.|+.-=++++..++|.
T Consensus 18 k~I~wr~V~~gl~lQ~~la~~vl~~ 42 (75)
T PF01773_consen 18 KAIKWRTVIWGLGLQFVLALFVLKT 42 (75)
T ss_dssp GG--HHHHHHHHHHHHHHHHHHHTS
T ss_pred CcCChHHHHHHHHHHHHHHHHHHhh
Confidence 4688888888888888888777654
No 22
>PRK13108 prolipoprotein diacylglyceryl transferase; Reviewed
Probab=31.58 E-value=1.7e+02 Score=28.20 Aligned_cols=28 Identities=11% Similarity=0.252 Sum_probs=19.8
Q ss_pred cchhhhhhHHHHHHHHHHHHHHHhccch
Q psy4504 92 VYLVGASGGVYALLAAHLANVLLNYNQM 119 (219)
Q Consensus 92 ~~~vGASGaifGLlga~l~~~~~~~~~~ 119 (219)
.....--..+.|++||=+.+++.+|++.
T Consensus 55 i~dl~i~~vi~giIGARL~yVl~~~~~y 82 (460)
T PRK13108 55 TYDIALWAVPFGLIGGRLYHLATDWRTY 82 (460)
T ss_pred HHHHHHHHHHHHHHHHhHHHHhcCHHHH
Confidence 3445555677888888888888777655
No 23
>COG0038 EriC Chloride channel protein EriC [Inorganic ion transport and metabolism]
Probab=26.68 E-value=5.5e+02 Score=24.28 Aligned_cols=28 Identities=29% Similarity=0.427 Sum_probs=21.5
Q ss_pred cchhhhhhHHHHHHHHHHHHHHHhccch
Q psy4504 92 VYLVGASGGVYALLAAHLANVLLNYNQM 119 (219)
Q Consensus 92 ~~~vGASGaifGLlga~l~~~~~~~~~~ 119 (219)
....|+++++.+.+.+=++-++.--+++
T Consensus 161 Ll~~GaAaGlaaaF~aPlagvlF~~E~l 188 (443)
T COG0038 161 LLAAGAAAGLAAAFNAPLAGALFAIEVL 188 (443)
T ss_pred HHHHHHHHHHHHHhCCcHHHHHHHHHHH
Confidence 5688999999999988776666655555
No 24
>PRK12573 putative monovalent cation/H+ antiporter subunit B; Reviewed
Probab=25.85 E-value=3.5e+02 Score=21.67 Aligned_cols=13 Identities=23% Similarity=0.383 Sum_probs=10.2
Q ss_pred HHHHHHHHHHHHH
Q psy4504 165 TGALAGLTIGLLV 177 (219)
Q Consensus 165 GG~i~G~llg~~~ 177 (219)
|||.+|.+.+..+
T Consensus 36 GGF~gGli~a~a~ 48 (140)
T PRK12573 36 GGFIGGLITASAL 48 (140)
T ss_pred ccHHHHHHHHHHH
Confidence 7888888887664
No 25
>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=25.76 E-value=4.9e+02 Score=23.38 Aligned_cols=26 Identities=19% Similarity=0.151 Sum_probs=20.8
Q ss_pred CCCcchhhhhHHHHHHHHHHHHHhcc
Q psy4504 155 GYPVSYVAHLTGALAGLTIGLLVLKN 180 (219)
Q Consensus 155 ~~~Vs~~AHlGG~i~G~llg~~~~~~ 180 (219)
++++-+..++...+...+.+.+....
T Consensus 120 ~qs~~~~l~~ll~~~~~~~~L~~l~~ 145 (325)
T PF11992_consen 120 SQSLLFALYLLLFLVLLLAALVLLHQ 145 (325)
T ss_pred hccHHHHHHHHHHHHHHHHHHHHHhC
Confidence 37788889999998888888776644
No 26
>COG1299 FruA Phosphotransferase system, fructose-specific IIC component [Carbohydrate transport and metabolism]
Probab=25.17 E-value=87 Score=29.06 Aligned_cols=20 Identities=25% Similarity=0.436 Sum_probs=17.0
Q ss_pred cchhhhhHHHHHHHHHHHHH
Q psy4504 158 VSYVAHLTGALAGLTIGLLV 177 (219)
Q Consensus 158 Vs~~AHlGG~i~G~llg~~~ 177 (219)
+.-.+++||.++|++.|++.
T Consensus 92 ~g~aGFlG~ii~GflAGy~v 111 (343)
T COG1299 92 IGGAGFLGAIIAGFLAGYVV 111 (343)
T ss_pred cccchhhHHHHHHHHHHHHH
Confidence 33569999999999999986
No 27
>PRK05529 cell division protein FtsQ; Provisional
Probab=25.00 E-value=63 Score=28.30 Aligned_cols=37 Identities=8% Similarity=0.114 Sum_probs=18.2
Q ss_pred chhhHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCC
Q psy4504 180 NFEQKLREQLMWWIALGVYVACTIFAVIYNVTSPSYNY 217 (219)
Q Consensus 180 ~~~~~~~~~~~~~~a~~~~~~~~~~~i~~n~~~~~~~~ 217 (219)
++.+|..+|...|.+.+. +++++.++++.+|.+|.-.
T Consensus 26 ~~~~~~~~r~~~~~~~~~-~~~~l~~l~~~~~~Sp~~~ 62 (255)
T PRK05529 26 RFTTRIRRRFILLACAVG-AVLTLLLFVMLSAYSPLLA 62 (255)
T ss_pred chhhhccchhhhHHHHHH-HHHHHHHHHHHheeCCceE
Confidence 333333334333444433 4444455556777777543
No 28
>PRK12509 putative monovalent cation/H+ antiporter subunit B; Reviewed
Probab=24.93 E-value=3.6e+02 Score=21.53 Aligned_cols=13 Identities=23% Similarity=0.373 Sum_probs=9.9
Q ss_pred HHHHHHHHHHHHH
Q psy4504 165 TGALAGLTIGLLV 177 (219)
Q Consensus 165 GG~i~G~llg~~~ 177 (219)
|||.+|.+.+..+
T Consensus 34 GGF~gGli~a~a~ 46 (137)
T PRK12509 34 GGFIGGLVAAAAF 46 (137)
T ss_pred ccHHHHHHHHHHH
Confidence 7888888877664
No 29
>PF04892 VanZ: VanZ like family ; InterPro: IPR006976 This entry represents a conserved sequence region found in the VanZ protein and also several phosphotransbutyrylases. VanZ confers low-level resistance to the glycopeptide antibiotic teicoplanin (Te). Analysis of cytoplasmic peptidoglycan precursors, accumulated in the presence of ramoplanin, showed that VanZ-mediated Te resistance does not involve incorporation of a substituent of D-alanine into the peptidoglycan precursors [].
Probab=24.55 E-value=3.1e+02 Score=20.61 Aligned_cols=78 Identities=14% Similarity=-0.007 Sum_probs=41.0
Q ss_pred hhhhhhHHHHHHHHHHHHHHHhccchhhhHHHHHHHHHHHHHHHHHHHHHHhhhhhcCCCCCCCcchhhhhHHHHHHHHH
Q psy4504 94 LVGASGGVYALLAAHLANVLLNYNQMEFGIVRLLAIFVVASADVGFAVYNRYAGELAGAGSGYPVSYVAHLTGALAGLTI 173 (219)
Q Consensus 94 ~vGASGaifGLlga~l~~~~~~~~~~~~~~~r~~~l~~~~~~~~~~~i~~~~~~~~~~~~~~~~Vs~~AHlGG~i~G~ll 173 (219)
...+.-..|..+|..+.....+.+ +..+.+..... ..+..=+.|.+.+.. ..+--|..+..-|...|.++
T Consensus 53 ~~~~hi~~f~plG~l~~~~~~~~~----~~~~~~~~~~~--~sl~iE~~Q~~~~~r----~~d~~Dv~~n~~G~~lG~~l 122 (133)
T PF04892_consen 53 DKIGHILLFFPLGFLLPLLFRRLR----SWLLAILIGFL--FSLFIELIQLFLPGR----SFDIDDVLANTLGALLGYLL 122 (133)
T ss_pred HHHHHHHHHHHHHHHHHHHHHccc----hHHHHHHHHHH--HHHHHHHHhccCCCC----CCCHHHHHHHHHHHHHHHHH
Confidence 445555566667766644444322 12222222211 112222245554332 13557889999999999998
Q ss_pred HHHHhcch
Q psy4504 174 GLLVLKNF 181 (219)
Q Consensus 174 g~~~~~~~ 181 (219)
...+.|++
T Consensus 123 ~~~~~~~~ 130 (133)
T PF04892_consen 123 YRLIRKRW 130 (133)
T ss_pred HHHHHHHh
Confidence 77665443
No 30
>KOG2980|consensus
Probab=24.51 E-value=1.2e+02 Score=27.80 Aligned_cols=17 Identities=53% Similarity=0.645 Sum_probs=14.6
Q ss_pred CccccccchHhhHHHHH
Q psy4504 17 DVYLVGASGGVYALLAA 33 (219)
Q Consensus 17 ~~~l~gasgg~y~~~~a 33 (219)
..|++||||.+|++++.
T Consensus 220 ~gp~LGAsGav~ai~a~ 236 (310)
T KOG2980|consen 220 AGPSLGASGAVYAILAL 236 (310)
T ss_pred cccccccchHHHHHHHH
Confidence 37899999999998765
No 31
>cd00400 Voltage_gated_ClC CLC voltage-gated chloride channel. The ClC chloride channels catalyse the selective flow of Cl- ions across cell membranes, thereby regulating electrical excitation in skeletal muscle and the flow of salt and water across epithelial barriers. This domain is found in the halogen ions (Cl-, Br- and I-) transport proteins of the ClC family. The ClC channels are found in all three kingdoms of life and perform a variety of functions including cellular excitability regulation, cell volume regulation, membrane potential stabilization, acidification of intracellular organelles, signal transduction, transepithelial transport in animals, and the extreme acid resistance response in eubacteria. They lack any structural or sequence similarity to other known ion channels and exhibit unique properties of ion permeation and gating. Unlike cation-selective ion channels, which form oligomers containing a single pore along the axis of symmetry, the ClC channels form two-pore
Probab=22.08 E-value=6e+02 Score=23.08 Aligned_cols=28 Identities=29% Similarity=0.428 Sum_probs=21.9
Q ss_pred cchhhhhhHHHHHHHHHHHHHHHhccch
Q psy4504 92 VYLVGASGGVYALLAAHLANVLLNYNQM 119 (219)
Q Consensus 92 ~~~vGASGaifGLlga~l~~~~~~~~~~ 119 (219)
...+|+.+++-+.+.+=++-++.-.++.
T Consensus 133 l~~~G~aaglaa~f~aPl~g~lf~~E~~ 160 (383)
T cd00400 133 LVACGAAAGIAAAFNAPLAGALFAIEVL 160 (383)
T ss_pred HHHHHHHHHHHHhcCChhHHHHHHHHHH
Confidence 5789999999999988777666665554
No 32
>PF06295 DUF1043: Protein of unknown function (DUF1043); InterPro: IPR009386 This entry consists of several hypothetical bacterial proteins of unknown function.
Probab=21.54 E-value=80 Score=24.78 Aligned_cols=15 Identities=40% Similarity=0.771 Sum_probs=10.3
Q ss_pred HHHHHHHHHHHHHhc
Q psy4504 165 TGALAGLTIGLLVLK 179 (219)
Q Consensus 165 GG~i~G~llg~~~~~ 179 (219)
-|++.|+++|+++.|
T Consensus 4 i~lvvG~iiG~~~~r 18 (128)
T PF06295_consen 4 IGLVVGLIIGFLIGR 18 (128)
T ss_pred HHHHHHHHHHHHHHH
Confidence 467777777777644
No 33
>COG4059 MtrE Tetrahydromethanopterin S-methyltransferase, subunit E [Coenzyme metabolism]
Probab=20.14 E-value=1e+02 Score=27.24 Aligned_cols=54 Identities=22% Similarity=0.435 Sum_probs=32.6
Q ss_pred CcchhhhhHHHHHHHHHHHHHhcc-hhhHHHH----HHHHHHHHHHHHHHHHHHHHHHh
Q psy4504 157 PVSYVAHLTGALAGLTIGLLVLKN-FEQKLRE----QLMWWIALGVYVACTIFAVIYNV 210 (219)
Q Consensus 157 ~Vs~~AHlGG~i~G~llg~~~~~~-~~~~~~~----~~~~~~a~~~~~~~~~~~i~~n~ 210 (219)
++-+-|.+||-++|+..+.+.+-. ......+ -...|+.++.=++.+..++.||.
T Consensus 223 ~~~FCak~GgplTGl~FGliVFl~~W~~~~~d~~~~i~~G~isiv~Gliiv~iLii~N~ 281 (304)
T COG4059 223 SSYFCAKFGGPLTGLAFGLIVFLSSWVTTVFDPAVSIQGGWISIVAGLIIVLILIIWNR 281 (304)
T ss_pred hhhhHHHhCCcchhhhhhhhhhhhhhhhhhcCcccccccchhhhHHHHHHHHHHHHhcc
Confidence 444568899999999999886432 1111111 01125665555566667778886
Done!