Query psy6649
Match_columns 242
No_of_seqs 123 out of 1333
Neff 8.5
Searched_HMMs 46136
Date Fri Aug 16 23:34:47 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy6649.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/6649hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG2632|consensus 99.9 7.5E-25 1.6E-29 180.8 15.9 184 22-210 10-195 (258)
2 PRK10907 intramembrane serine 99.9 5E-25 1.1E-29 187.7 15.3 170 25-212 92-269 (276)
3 PTZ00101 rhomboid-1 protease; 99.9 1.1E-24 2.3E-29 185.3 13.5 179 21-216 47-243 (278)
4 COG0705 Membrane associated se 99.9 1.2E-22 2.7E-27 169.9 14.7 183 26-218 16-216 (228)
5 KOG0858|consensus 99.8 4.6E-20 9.9E-25 150.5 13.5 171 23-210 9-184 (239)
6 PF01694 Rhomboid: Rhomboid fa 99.8 2.8E-21 6E-26 150.3 5.9 138 63-214 2-143 (145)
7 PF04511 DER1: Der1-like famil 99.8 1.5E-18 3.3E-23 142.0 15.7 174 26-210 1-179 (197)
8 KOG2289|consensus 99.7 1.1E-18 2.3E-23 150.0 0.8 136 60-212 112-253 (316)
9 COG5291 Predicted membrane pro 99.4 3.8E-13 8.2E-18 109.9 6.3 169 23-206 16-189 (313)
10 KOG2290|consensus 99.3 3.9E-13 8.4E-18 118.4 0.5 140 64-217 448-589 (652)
11 PF08551 DUF1751: Eukaryotic i 99.3 2.6E-12 5.7E-17 93.4 4.3 91 66-156 7-97 (99)
12 KOG2890|consensus 99.2 3.4E-11 7.4E-16 101.5 7.7 153 11-165 9-165 (326)
13 KOG4463|consensus 98.8 5.1E-09 1.1E-13 86.7 3.2 181 22-210 7-201 (323)
14 KOG2980|consensus 98.6 3.8E-08 8.3E-13 83.5 4.7 177 27-213 115-301 (310)
15 COG3105 Uncharacterized protei 37.8 27 0.00058 26.4 2.1 18 193-210 7-24 (138)
16 PRK11677 hypothetical protein; 28.6 45 0.00097 25.5 2.0 12 199-210 12-23 (134)
17 KOG0489|consensus 23.3 25 0.00055 30.0 -0.2 17 1-17 184-200 (261)
18 PF10066 DUF2304: Uncharacteri 23.0 72 0.0016 23.4 2.2 15 191-205 52-66 (115)
19 PF09946 DUF2178: Predicted me 22.5 94 0.002 22.8 2.8 28 190-217 23-50 (111)
20 PF09527 ATPase_gene1: Putativ 22.1 2.1E+02 0.0045 17.7 6.1 39 81-119 8-47 (55)
21 PF06295 DUF1043: Protein of u 21.0 53 0.0011 24.7 1.2 19 196-214 5-23 (128)
No 1
>KOG2632|consensus
Probab=99.93 E-value=7.5e-25 Score=180.83 Aligned_cols=184 Identities=32% Similarity=0.462 Sum_probs=161.3
Q ss_pred CCCCCchHHHHHHHHHHHHHHhhhcccccccchhcchhhhhccCccceeehhhhccCChhHHHHHHHHHHHhHHHHHHhh
Q psy6649 22 GADTIPPATLGLVFLQSMVYLNIFRKPWSTLDVCISADAVIQQRDYKRLILSAFEHGDDMHLYYNMVSLILKGRQLEKIY 101 (242)
Q Consensus 22 ~~~~~p~vt~~li~~~v~v~~l~~~~~~~~~~~~~~~~~v~~~~q~wrllT~~f~H~~~~hll~N~~~l~~~g~~lE~~~ 101 (242)
.+...|.+|..++.++.++|+....... .+.+..|...+++.|.||++||+++|.|..|+++||+.++..|..+|+.+
T Consensus 10 ~~~~~p~~ts~~~~~~~~i~lv~~~~~i--~~~~~l~~~~l~~~ql~RL~Ty~l~H~s~~hllfnmlaL~~~g~~fE~~~ 87 (258)
T KOG2632|consen 10 FWMKIPLLTSIVVVLAILIYLVSFFPGI--VEVLGLPSELLINWQLYRLITYALVHLSLPHLLFNMLALWPLGSQFERTH 87 (258)
T ss_pred ccccchHHHHHHHHHHHHHHHHhccchh--hhHhcCCHHHhhhHHHHHHHHHHHHhccHHHHHHHHHHHHhchhHHHhhc
Confidence 3457899999999999999998877643 36677777788899999999999999999999999999999999999999
Q ss_pred C-hHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCCCCcccccHHHHHHHHHHHHHhcCCCcceeEEe-eeehhhHHHH
Q psy6649 102 G-WGKFLSLVIFLTVFTSLYYILLAYIVFYITNDTSELSHCAIGFSAVLFAMKTILTRLQPDAYQQILN-INVKAIYAPW 179 (242)
Q Consensus 102 G-~~~fl~~~l~~~~~~~l~~~l~~~~~~~~~~~p~~~~~~~~G~Sg~v~all~~~~~~~p~~~~~i~~-i~i~~~~~~~ 179 (242)
| +.+++.+....+++++++.++..... ..++.......+|.|+++||+++......|.....++| +.||.++.||
T Consensus 88 G~t~~~l~~~~llalf~gIl~ll~~~~~---~~~d~~~~~~a~G~s~v~Fam~~~~~~~sp~r~~~~fg~~siP~~l~Pw 164 (258)
T KOG2632|consen 88 GTTVRILMFTVLLALFSGILYLLAYHVF---LLSDLVYVEGAIGFSGVLFAMMAVLEVQSPVRSRSVFGLFSIPIVLAPW 164 (258)
T ss_pred cceehHHHHHHHHHHHHHHHHHHHHHHH---hhcchhhhcccccccHHHHHHHHHHhhcCcccchhhcccccccHHHHHH
Confidence 9 89999999999999999998776522 12222225568999999999999988889998888898 7899999999
Q ss_pred HHHHHHHhhCCChhHHHHHHHHHHhHHHhhc
Q psy6649 180 FELIIIYLLVPNASFKGHLSGILVGLTYTDT 210 (242)
Q Consensus 180 i~~~~~~~~~~~~s~~~hl~G~l~G~~~~~~ 210 (242)
+.+..+.+..|+.|..+|++|+++|+.|++.
T Consensus 165 ~lLi~~~~lvp~aSFlghl~GllvG~ay~~~ 195 (258)
T KOG2632|consen 165 ALLIATQILVPQASFLGHLCGLLVGYAYAFS 195 (258)
T ss_pred HHHHHHHHHccCchHHHHHHHHHHHHHHHHH
Confidence 9999999999999999999999999999994
No 2
>PRK10907 intramembrane serine protease GlpG; Provisional
Probab=99.93 E-value=5e-25 Score=187.70 Aligned_cols=170 Identities=17% Similarity=0.172 Sum_probs=125.0
Q ss_pred CCchHHHHHHHHHHHHHHhhhccccc-ccchhcchhhhhccCccceeehhhhccCChhHHHHHHHHHHHhHHHHHHhhCh
Q psy6649 25 TIPPATLGLVFLQSMVYLNIFRKPWS-TLDVCISADAVIQQRDYKRLILSAFEHGDDMHLYYNMVSLILKGRQLEKIYGW 103 (242)
Q Consensus 25 ~~p~vt~~li~~~v~v~~l~~~~~~~-~~~~~~~~~~v~~~~q~wrllT~~f~H~~~~hll~N~~~l~~~g~~lE~~~G~ 103 (242)
+..|+|..++++|+++|++....... ...+...|....+++|+||++|+.|+|.|+.|+++|+++++.+|+.+|+.+|+
T Consensus 92 ~~~p~T~~li~i~i~vf~l~~~~~~~~~~~~l~~~~~~~~~~q~WRl~T~~flH~~~~Hl~fNml~l~~lG~~iE~~~G~ 171 (276)
T PRK10907 92 RAGPLTLGVMIACVVVFILMQILGDQTVMLWLAWPFDPSLKFELWRYFTHALLHFSLLHILFNLLWWWYLGGAVEKRLGS 171 (276)
T ss_pred CCCCHHHHHHHHHHHHHHHHHHhccHHHHHHHhccccccccCCcHHHHhHHHHhCCHHHHHHHHHHHHHHHHHHHHHHCh
Confidence 45679999999999999887665431 22233334344457899999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCCCCcccccHHHHHHHHHHHHHhc---CCCcceeEEeeeehhhHHH--
Q psy6649 104 GKFLSLVIFLTVFTSLYYILLAYIVFYITNDTSELSHCAIGFSAVLFAMKTILTRL---QPDAYQQILNINVKAIYAP-- 178 (242)
Q Consensus 104 ~~fl~~~l~~~~~~~l~~~l~~~~~~~~~~~p~~~~~~~~G~Sg~v~all~~~~~~---~p~~~~~i~~i~i~~~~~~-- 178 (242)
+|++.+|+++++.+++.+.. +..+ ...|+||++||++++.... .|+.. ..+|.....
T Consensus 172 ~~~l~l~l~s~i~~~~~~~~--------~~~~-----~~gGaSGvVygL~g~~~~~~~~~p~~~-----~~lp~~~~~f~ 233 (276)
T PRK10907 172 GKLIVITLISALLSGWVQSK--------FSGP-----WFGGLSGVVYALMGYVWLRGERDPQSG-----IYLPRGLIAFA 233 (276)
T ss_pred HHHHHHHHHHHHHHHHHHHH--------Hccc-----hhhHHHHHHHHHHHHHHHHhccccccc-----hhhhHHHHHHH
Confidence 99999999999999987632 2222 2579999999999865332 23322 123322222
Q ss_pred --HHHHHHHHhhCCChhHHHHHHHHHHhHHHhhccc
Q psy6649 179 --WFELIIIYLLVPNASFKGHLSGILVGLTYTDTPI 212 (242)
Q Consensus 179 --~i~~~~~~~~~~~~s~~~hl~G~l~G~~~~~~~~ 212 (242)
++.........+++++.+|++|+++|.++++...
T Consensus 234 llwl~~g~~~~~g~~Ian~AHlgGli~Gll~g~~~~ 269 (276)
T PRK10907 234 LLWLVAGYFDLFGMSIANAAHVAGLAVGLAMAFWDT 269 (276)
T ss_pred HHHHHHHHHHccCcccHHHHHHHHHHHHHHHHHHhh
Confidence 2212223344678999999999999999887543
No 3
>PTZ00101 rhomboid-1 protease; Provisional
Probab=99.92 E-value=1.1e-24 Score=185.33 Aligned_cols=179 Identities=19% Similarity=0.196 Sum_probs=128.6
Q ss_pred cCCCCCchHHHHHHHHHHHHHHhhhccc-c--------cccch-hcchhhhhccCccceeehhhhccCChhHHHHHHHHH
Q psy6649 21 LGADTIPPATLGLVFLQSMVYLNIFRKP-W--------STLDV-CISADAVIQQRDYKRLILSAFEHGDDMHLYYNMVSL 90 (242)
Q Consensus 21 ~~~~~~p~vt~~li~~~v~v~~l~~~~~-~--------~~~~~-~~~~~~v~~~~q~wrllT~~f~H~~~~hll~N~~~l 90 (242)
+|--++|.++..++++++++|++..... . ...++ ...|+.+ +++||||++|+.|+|.++.|+++|++++
T Consensus 47 Fp~f~i~~l~~~Iiii~iivfil~l~~~~~~~l~p~~~~L~~~Ga~~~~~i-~~gq~WRLiT~~FlH~~~~HLl~Nm~~l 125 (278)
T PTZ00101 47 FPHFTWKSFIMAISIIQIIVFIISVSIKPADFLTPSDSLLVTLGANVASRI-KQGEIHRLILPIFLHANIFHTFFNVFFQ 125 (278)
T ss_pred cCCccHHHHHHHHHHHHHHHHHHHHHhcccccCCCCHHHHHHHhCcchhhh-hcCCCHHHHHHHHHccCHHHHHHHHHHH
Confidence 6777889999999999999988765421 1 11223 2355554 6799999999999999999999999999
Q ss_pred HHhHHHHHHhhChHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCCCCcccccHHHHHHHHHHHHHhcC------CCcc
Q psy6649 91 ILKGRQLEKIYGWGKFLSLVIFLTVFTSLYYILLAYIVFYITNDTSELSHCAIGFSAVLFAMKTILTRLQ------PDAY 164 (242)
Q Consensus 91 ~~~g~~lE~~~G~~~fl~~~l~~~~~~~l~~~l~~~~~~~~~~~p~~~~~~~~G~Sg~v~all~~~~~~~------p~~~ 164 (242)
+.+|..+|+.+|+.|+..+|+.+++.+++..... .+ ....+|+||++||++++..... ...+
T Consensus 126 ~~~G~~lE~~~G~~r~~ilYl~sGi~G~l~s~~~---------~~---~~~svGASgAifGLiGa~~~~lil~w~~~~~~ 193 (278)
T PTZ00101 126 LRMGFTLEKNYGIVKIIILYFLTGIYGNILSSSV---------TY---CPIKVGASTSGMGLLGIVTSELILLWHVIRHR 193 (278)
T ss_pred HHHHHHHHHHHChHHHHHHHHHHHHHHHHHHHHH---------cc---CCcEEehhHHHHHHHHHHHHHHHHHHHhhccH
Confidence 9999999999999999999999999999876422 12 2347999999999998764211 0111
Q ss_pred eeEEeeeehhhHHHHHHH--HHHHhhCCChhHHHHHHHHHHhHHHhhccccchh
Q psy6649 165 QQILNINVKAIYAPWFEL--IIIYLLVPNASFKGHLSGILVGLTYTDTPIGWGL 216 (242)
Q Consensus 165 ~~i~~i~i~~~~~~~i~~--~~~~~~~~~~s~~~hl~G~l~G~~~~~~~~~~~~ 216 (242)
... +.......+.. .......+++|+.+|++|+++|++++..+.++..
T Consensus 194 ~~~----~~~~i~~~li~~~l~~~~~g~~Id~~aHlGG~i~G~llg~~~~~~l~ 243 (278)
T PTZ00101 194 ERV----VFNIIFFSLISFFYYFTFNGSNIDHVGHLGGLLSGISMGILYNSQME 243 (278)
T ss_pred HHH----HHHHHHHHHHHHHHHHhcCCCCccHHHHHHHHHHHHHHHHHHHhhhh
Confidence 000 00001111111 1122235789999999999999999998766443
No 4
>COG0705 Membrane associated serine protease [Amino acid transport and metabolism]
Probab=99.89 E-value=1.2e-22 Score=169.89 Aligned_cols=183 Identities=23% Similarity=0.296 Sum_probs=137.4
Q ss_pred CchHHHHHHHHHHHHHHhhhcccccc-cc-------hhcchhhhhccC---ccceeehhhhccCChhHHHHHHHHHHHhH
Q psy6649 26 IPPATLGLVFLQSMVYLNIFRKPWST-LD-------VCISADAVIQQR---DYKRLILSAFEHGDDMHLYYNMVSLILKG 94 (242)
Q Consensus 26 ~p~vt~~li~~~v~v~~l~~~~~~~~-~~-------~~~~~~~v~~~~---q~wrllT~~f~H~~~~hll~N~~~l~~~g 94 (242)
.|+++..++.+|+.++.......+.. .. ....|....... |+||++|+.|+|.|+.|+++|++.++.+|
T Consensus 16 ~~~~~~~~~~~~~~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~w~lit~~FlH~~~~Hll~N~~~l~~fg 95 (228)
T COG0705 16 APPVTLFLILLNILVFLLELVLGWSAIFLLTFLFRLFGLYPLNLLGALARDQLWRLITAIFLHAGFLHLLFNMLALWVFG 95 (228)
T ss_pred cchHHHHHHHHHHHHHHHHHHccchHHHHHHHhhhHHhhcchhhhccccccchHHHHHHHHHHhhHHHHHHHHHHHHHhh
Confidence 58999999999999999887765421 11 334444433322 89999999999999999999999999999
Q ss_pred HHHHHhhChHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCCCCcccccHHHHHHHHHHHHHhcCCCcceeEEe--eee
Q psy6649 95 RQLEKIYGWGKFLSLVIFLTVFTSLYYILLAYIVFYITNDTSELSHCAIGFSAVLFAMKTILTRLQPDAYQQILN--INV 172 (242)
Q Consensus 95 ~~lE~~~G~~~fl~~~l~~~~~~~l~~~l~~~~~~~~~~~p~~~~~~~~G~Sg~v~all~~~~~~~p~~~~~i~~--i~i 172 (242)
..+|+..|+.||+.+|+.+++++++.+...+. .. ..+.+|+||+++|+++++..+.|..+..... ++.
T Consensus 96 ~~le~~~G~~~f~~~yl~~gl~~~~~~~~~~~--------~~--~~~~~GASG~i~gllga~~~~~~~~~~~~~~~~~~~ 165 (228)
T COG0705 96 SNLERRLGTLRFLLFYLLSGLLAGLAQVLFGP--------KG--GAPSLGASGAIFGLLGAYFLLFPFARILLLFLSLPR 165 (228)
T ss_pred HHHHHHhchhHHHHHHHHHHHHHHHHHHHHcc--------cc--cCcccchhHHHHHHHHHHHHHccccchhhhhccCch
Confidence 99999999999999999999999998643221 11 2468999999999999999999987766654 333
Q ss_pred hhhHHHHHH--HHHHH-hhC--CChhHHHHHHHHHHhHHHhhccccchhhH
Q psy6649 173 KAIYAPWFE--LIIIY-LLV--PNASFKGHLSGILVGLTYTDTPIGWGLDY 218 (242)
Q Consensus 173 ~~~~~~~i~--~~~~~-~~~--~~~s~~~hl~G~l~G~~~~~~~~~~~~~~ 218 (242)
+......+. ...+. ... +++++.+|++|++.|.+++....++...+
T Consensus 166 ~~~~~i~~~~~~~~~~~~~~~~~~va~~aHl~G~i~G~l~~~~~~~~~~~~ 216 (228)
T COG0705 166 PALILILIWLLYSLFSGAGSFGPSVAWSAHLGGLIGGLLLAALLSRKLRKR 216 (228)
T ss_pred hHHHHHHHHHHHHHHHHhcCCchHHHHHHHHHHHHHHHHHHHHHhhhhhhh
Confidence 333322221 11111 112 25889999999999999998877655433
No 5
>KOG0858|consensus
Probab=99.84 E-value=4.6e-20 Score=150.50 Aligned_cols=171 Identities=23% Similarity=0.261 Sum_probs=142.2
Q ss_pred CCCCchHHHHHHHHHHHHHHhhhcccccccchhcchhhhhccCccceeehhhhccCC-hhHHHHHHHHHHHhHHHHHHhh
Q psy6649 23 ADTIPPATLGLVFLQSMVYLNIFRKPWSTLDVCISADAVIQQRDYKRLILSAFEHGD-DMHLYYNMVSLILKGRQLEKIY 101 (242)
Q Consensus 23 ~~~~p~vt~~li~~~v~v~~l~~~~~~~~~~~~~~~~~v~~~~q~wrllT~~f~H~~-~~hll~N~~~l~~~g~~lE~~~ 101 (242)
+.++||+||...++|+++.+++...-.++.++.++|+.++++.|+||++|+.+..+. -+|.++|+++++..++.+|+-.
T Consensus 9 ~~~iPpVTR~~~~~~v~tt~~~~l~lIsP~~l~~~p~Lv~kk~QiWRliTs~lyfg~~gf~fl~n~~FlyrY~~~LE~g~ 88 (239)
T KOG0858|consen 9 YLQIPPVTRYYTTACVVTTLLVRLDLISPFQLYLNPELVFKKFQIWRLITSFLYFGPFGFDFLMNLYFLYRYSSMLEEGS 88 (239)
T ss_pred HhcCChHHHHHHHHHHHHHHHHhhcccCchheEecHHHHHhHhHHHHhhhhhheeccccHHHHHHHHHHHHHHHHHhcCC
Confidence 478999999999999999999998888889999999999999999999999999987 5899999999999999999844
Q ss_pred -C--hHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCCCCcccccHHHHHHHHHHHHHhcCCCcceeEEe-eeehhhHH
Q psy6649 102 -G--WGKFLSLVIFLTVFTSLYYILLAYIVFYITNDTSELSHCAIGFSAVLFAMKTILTRLQPDAYQQILN-INVKAIYA 177 (242)
Q Consensus 102 -G--~~~fl~~~l~~~~~~~l~~~l~~~~~~~~~~~p~~~~~~~~G~Sg~v~all~~~~~~~p~~~~~i~~-i~i~~~~~ 177 (242)
. +++|+..++.++++-.+... .. + ...=.++.++++.+.|++.+|+.+++++| ++++++++
T Consensus 89 f~~rtadf~~mllf~~~l~~~~~~----~~-----~------~~fLg~~l~~~l~YvWs~~Np~~~v~F~g~~~f~a~Yl 153 (239)
T KOG0858|consen 89 FRGRTADFLYMLLFGAVLLTLTGL----FV-----Y------IVFLGQSLVFMLVYVWSKRNPDVIVSFFGLITFKAPYL 153 (239)
T ss_pred CCCchhHHHHHHHHHHHHHHHHHH----HH-----H------HHHHHHHHHHHHHHHHHhhCCCceEEEEEEecCccccc
Confidence 2 36788887766665554332 11 1 12234566788889999999999999999 89999999
Q ss_pred HHHHHHHHHhhCCChhHHHHHHHHHHhHHHhhc
Q psy6649 178 PWFELIIIYLLVPNASFKGHLSGILVGLTYTDT 210 (242)
Q Consensus 178 ~~i~~~~~~~~~~~~s~~~hl~G~l~G~~~~~~ 210 (242)
||++..+..+...+ + ...+.|+++|++|.+.
T Consensus 154 Pwvll~fs~l~g~~-~-~~dllGi~~GHiy~fl 184 (239)
T KOG0858|consen 154 PWVLLGFSFLFGGS-I-LVDLLGIIVGHIYYFL 184 (239)
T ss_pred hHHHHHHHHHhCCc-h-HHHHHhhhhheeEEEE
Confidence 99988777665544 3 7899999999998775
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=99.84 E-value=2.8e-21 Score=150.27 Aligned_cols=138 Identities=28% Similarity=0.446 Sum_probs=100.4
Q ss_pred ccCccceeehhhhccCChhHHHHHHHHHHHhHHHHHHhhChHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCCCCccc
Q psy6649 63 QQRDYKRLILSAFEHGDDMHLYYNMVSLILKGRQLEKIYGWGKFLSLVIFLTVFTSLYYILLAYIVFYITNDTSELSHCA 142 (242)
Q Consensus 63 ~~~q~wrllT~~f~H~~~~hll~N~~~l~~~g~~lE~~~G~~~fl~~~l~~~~~~~l~~~l~~~~~~~~~~~p~~~~~~~ 142 (242)
+++|+||++|++|+|.|+.|+++|++.++.+|..+|+.+|+.++..+++.+++.+++..++... + ....
T Consensus 2 ~~~~~wrl~T~~f~h~~~~hl~~n~~~l~~~g~~lE~~~G~~~~~~~~l~~~~~~~l~~~~~~~--------~---~~~~ 70 (145)
T PF01694_consen 2 QNGQWWRLFTSPFVHANFLHLLFNLLALWFFGSLLERRLGSRRFLALYLLSGLLGSLLSLLFSP--------P---NQPY 70 (145)
T ss_dssp GCC-TTHHHHGGG--SSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH---------S-------
T ss_pred CCCcchhhhHHHHHccCHHHHHHHHHHHHHhhhhHhhhccchHHHHHHHHHHHhhhhccccccc--------c---cccc
Confidence 6789999999999999999999999999999999999999999999999999999888754322 1 1157
Q ss_pred ccHHHHHHHHHHHHHhcCCCcceeEEe----eeehhhHHHHHHHHHHHhhCCChhHHHHHHHHHHhHHHhhccccc
Q psy6649 143 IGFSAVLFAMKTILTRLQPDAYQQILN----INVKAIYAPWFELIIIYLLVPNASFKGHLSGILVGLTYTDTPIGW 214 (242)
Q Consensus 143 ~G~Sg~v~all~~~~~~~p~~~~~i~~----i~i~~~~~~~i~~~~~~~~~~~~s~~~hl~G~l~G~~~~~~~~~~ 214 (242)
.|+||+++|+++.+....|+.+..... ..+.....++. ......++.++.+|++|+++|.+++...+|+
T Consensus 71 ~G~Sg~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---~~~~~~~~~~~~~hl~G~~~G~~~~~~~~~~ 143 (145)
T PF01694_consen 71 VGASGAVFGLLGAFLFLYPQNKKRLRFIYLALVVPIIVLVII---LLLGFIPNISFLGHLGGFLAGLLYGFLILRR 143 (145)
T ss_dssp -SSHHHHHHHHHHHHHHHHCCCCCS---HCCCCCCCCCCCHH---HCTSSSSTTTHHHHHHHHHHHHHHHHHHCH-
T ss_pred CCCcccchHHHHHHHHHHhhccchhhcchHHHHHHHHHHHHH---HHHHHHHhHHHHHHHHHHHHHHHHHHHHHHc
Confidence 999999999999987776655333221 12221111111 1111268899999999999999999988764
No 7
>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=99.80 E-value=1.5e-18 Score=141.98 Aligned_cols=174 Identities=23% Similarity=0.265 Sum_probs=136.7
Q ss_pred CchHHHHHHHHHHHHHHhhhcccccccchhcchhhhhccCccceeehhhhccCCh-hHHHHHHHHHHHhHHHHHHh-hC-
Q psy6649 26 IPPATLGLVFLQSMVYLNIFRKPWSTLDVCISADAVIQQRDYKRLILSAFEHGDD-MHLYYNMVSLILKGRQLEKI-YG- 102 (242)
Q Consensus 26 ~p~vt~~li~~~v~v~~l~~~~~~~~~~~~~~~~~v~~~~q~wrllT~~f~H~~~-~hll~N~~~l~~~g~~lE~~-~G- 102 (242)
+||+||.+++.++++.++......++.++.++++.++++.|+||++|+.|..++. .++++|++.++..++.+|+. ++
T Consensus 1 iPpVTR~~~~~~~~~s~l~~~~~~~~~~l~~~~~~v~~~~q~WRl~Tsff~~g~~~~~~l~~~~~l~~~s~~LE~~~f~~ 80 (197)
T PF04511_consen 1 IPPVTRYWLISTVALSLLVSFGIISPYYLYFDWELVFKKFQIWRLFTSFFYFGPFSLNFLFNLYFLYQYSSSLEEGHFQG 80 (197)
T ss_pred CChhHHHHHHHHHHHHHHHHCCCCCHHHeeECcHHHhhhcCceeeEEEEEEEcCCCHHHHHHHHHHHHHhhHhccCCCCC
Confidence 5999999999999999988877667788889999999999999999999998766 79999999999999999997 33
Q ss_pred h-HHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCCCCcccccHHHHHHHHHHHHHhcCCCcceeEEe-eeehhhHHHHH
Q psy6649 103 W-GKFLSLVIFLTVFTSLYYILLAYIVFYITNDTSELSHCAIGFSAVLFAMKTILTRLQPDAYQQILN-INVKAIYAPWF 180 (242)
Q Consensus 103 ~-~~fl~~~l~~~~~~~l~~~l~~~~~~~~~~~p~~~~~~~~G~Sg~v~all~~~~~~~p~~~~~i~~-i~i~~~~~~~i 180 (242)
+ .+++...+.+++...+.. ... ..+ . .....-.++...++.+.+++.+|+.+++++| +++|+++.|++
T Consensus 81 ~~ady~~~ll~~~~~i~~~~----~~~----~~~-~-~~~~~l~~~l~~~l~Y~wsr~np~~~v~~~g~~~i~a~ylP~~ 150 (197)
T PF04511_consen 81 RSADYLWFLLFGASLILILS----LLI----GPY-F-FNIPFLGSSLSFALTYIWSRKNPNAQVSFFGLFTIKAKYLPWV 150 (197)
T ss_pred CHHHHHHHHHHHHHHHHHHH----Hhh----ccc-h-hHHHHHHHHHHHHHHHHHHHhCcccceeeEEEEEEChhhHHHH
Confidence 2 567777664443333322 211 000 0 0112334668889999999999999999998 79999999999
Q ss_pred HHHHHHhhCCChhHHHHHHHHHHhHHHhhc
Q psy6649 181 ELIIIYLLVPNASFKGHLSGILVGLTYTDT 210 (242)
Q Consensus 181 ~~~~~~~~~~~~s~~~hl~G~l~G~~~~~~ 210 (242)
+..+..+..++ +...++.|+++|++|.+.
T Consensus 151 ~~~~~~l~~~~-~~~~~l~Gi~~Ghly~fl 179 (197)
T PF04511_consen 151 LLAFSLLFGGS-SPIPDLLGILVGHLYYFL 179 (197)
T ss_pred HHHHHHHhCCC-cHHHHHHHHHHHHHHHHH
Confidence 87776665553 566899999999999864
No 8
>KOG2289|consensus
Probab=99.71 E-value=1.1e-18 Score=149.95 Aligned_cols=136 Identities=21% Similarity=0.244 Sum_probs=101.9
Q ss_pred hhhccCccceeehhhhccCChhHHHHHHHHHHHhHHHHHHhhChHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCCCC
Q psy6649 60 AVIQQRDYKRLILSAFEHGDDMHLYYNMVSLILKGRQLEKIYGWGKFLSLVIFLTVFTSLYYILLAYIVFYITNDTSELS 139 (242)
Q Consensus 60 ~v~~~~q~wrllT~~f~H~~~~hll~N~~~l~~~g~~lE~~~G~~~fl~~~l~~~~~~~l~~~l~~~~~~~~~~~p~~~~ 139 (242)
+..+++|+||++|++++|+++.|+.+|+..+..+|..+|..+|..|+..+|+++++.|+++..+. +| +
T Consensus 112 ~~~~r~E~WRllTym~LHaGi~HL~~N~~~ql~iGi~LE~~~G~~RiglIYl~gg~aGSlls~l~---------d~---~ 179 (316)
T KOG2289|consen 112 KPVHRGELWRLLTYMWLHAGIFHLLLNMLSQLFIGIPLEQVHGFLRIGLIYLAGGVAGSLLSSLF---------DP---N 179 (316)
T ss_pred ChhhhchhHHHHHHHHHhcCHHHHHHHHHHHHhccccHHhhcCceEEeeehhhhhhhhHHHHHHh---------cc---C
Confidence 44567899999999999999999999999999999999999999999999999999999987432 44 4
Q ss_pred cccccHHHHHHHHHHHHHhcCCCcceeEEeeeehhhHHHHHHH------HHHHhhCCChhHHHHHHHHHHhHHHhhccc
Q psy6649 140 HCAIGFSAVLFAMKTILTRLQPDAYQQILNINVKAIYAPWFEL------IIIYLLVPNASFKGHLSGILVGLTYTDTPI 212 (242)
Q Consensus 140 ~~~~G~Sg~v~all~~~~~~~p~~~~~i~~i~i~~~~~~~i~~------~~~~~~~~~~s~~~hl~G~l~G~~~~~~~~ 212 (242)
...+|+||++||++++.....-..+.. ++.+...+... ..-....+..+..+|++|+..|..+++...
T Consensus 180 ~~sVGASggvfaLlgA~Ls~l~~Nw~~-----m~~~~~~l~~ll~Ii~i~l~~G~~~~~~~~~h~gg~~~G~~~~fil~ 253 (316)
T KOG2289|consen 180 SISVGASGGVFALLGAHLSNLLTNWTI-----MKNKFAALRTLLIIIFINLDLGFAPYVDNFAHIGGLLAGFLLGFVLH 253 (316)
T ss_pred CceecccHHHHHHHHHHHHHHHhhHHH-----hcchHHHHHHHHHHHHHHHhhccccceeccccccccCCCcchhHHhh
Confidence 558999999999998875332221111 22222211111 111123467788899999999998888633
No 9
>COG5291 Predicted membrane protein [Function unknown]
Probab=99.41 E-value=3.8e-13 Score=109.88 Aligned_cols=169 Identities=19% Similarity=0.251 Sum_probs=113.1
Q ss_pred CCCCchHHHHHHHHHHHHHHhhhcccccccchhcchhhhhccCccceeehhhhccCCh-hHHHHHHHHHHHhHHHHHHh-
Q psy6649 23 ADTIPPATLGLVFLQSMVYLNIFRKPWSTLDVCISADAVIQQRDYKRLILSAFEHGDD-MHLYYNMVSLILKGRQLEKI- 100 (242)
Q Consensus 23 ~~~~p~vt~~li~~~v~v~~l~~~~~~~~~~~~~~~~~v~~~~q~wrllT~~f~H~~~-~hll~N~~~l~~~g~~lE~~- 100 (242)
..++||+|+.+.++..++.++....-.+++...+..+..+++.|+||++|+....++. ...++|.+++|...+.+|+-
T Consensus 16 ~~~IPPITRy~~ll~~a~til~~~~lvsPwy~ly~~pL~~k~~qiwRlfTs~~~~~~~~~d~~M~vyf~Y~yS~~LE~g~ 95 (313)
T COG5291 16 MLRIPPITRYMTLLISAVTILVYVDLVSPWYSLYYSPLFLKRLQIWRLFTSFLYFGKPTLDMFMHVYFLYRYSRMLEEGC 95 (313)
T ss_pred cccCCcHHHHHHHHHHHHHHHHHHhhcCccceeeechhHHHHHHHHHHHHHHHhhcCcchhHHHHHHHHHHHHHHHhccc
Confidence 4569999999999988888877666556667777777788889999999999988865 89999999999999999983
Q ss_pred hChH--HHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCCCCcccccHHHHHHHHHHHHHhcCCCcceeEEe-eeehhhHH
Q psy6649 101 YGWG--KFLSLVIFLTVFTSLYYILLAYIVFYITNDTSELSHCAIGFSAVLFAMKTILTRLQPDAYQQILN-INVKAIYA 177 (242)
Q Consensus 101 ~G~~--~fl~~~l~~~~~~~l~~~l~~~~~~~~~~~p~~~~~~~~G~Sg~v~all~~~~~~~p~~~~~i~~-i~i~~~~~ 177 (242)
+++. ++....+..+ .++. ..+. +.+.+. .+ -++...++-+.|...+|+.+++++| ++++.|++
T Consensus 96 f~~~lv~Y~~yl~~~~---l~i~-a~s~----I~gg~s-----aL-~tsf~a~ItY~WS~~N~~~~Iqf~g~i~v~gkYl 161 (313)
T COG5291 96 FNTSLVEYFWYLLVIS---LVIF-AISN----IYGGIS-----AL-GTSFSATITYIWSKRNPRAIIQFFGFISVPGKYL 161 (313)
T ss_pred cCccHHHHHHHHHHHH---HHHH-HHHH----Hhcchh-----hh-cchhhhheeeeeeecCCceEEEEEEeeecchhhh
Confidence 4443 4444333222 1111 1111 111110 11 1222233345567788999999999 89999999
Q ss_pred HHHHHHHHHhhCCChhHHHHHHHHHHhHH
Q psy6649 178 PWFELIIIYLLVPNASFKGHLSGILVGLT 206 (242)
Q Consensus 178 ~~i~~~~~~~~~~~~s~~~hl~G~l~G~~ 206 (242)
|++.+.+..+...+. ..-.+.|+.+|+.
T Consensus 162 P~Illgfsfl~~~g~-~i~~vlGf~~g~~ 189 (313)
T COG5291 162 PFILLGFSFLSRRGI-SIDDVLGFVVGHL 189 (313)
T ss_pred hHHHHHHHHHhcCCc-cceeeeeeeeccc
Confidence 999877666554332 2224445555443
No 10
>KOG2290|consensus
Probab=99.30 E-value=3.9e-13 Score=118.43 Aligned_cols=140 Identities=21% Similarity=0.240 Sum_probs=102.6
Q ss_pred cCccceeehhhhccCChhHHHHHHHHHHHhHHHHHHhhChHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCCCCcccc
Q psy6649 64 QRDYKRLILSAFEHGDDMHLYYNMVSLILKGRQLEKIYGWGKFLSLVIFLTVFTSLYYILLAYIVFYITNDTSELSHCAI 143 (242)
Q Consensus 64 ~~q~wrllT~~f~H~~~~hll~N~~~l~~~g~~lE~~~G~~~fl~~~l~~~~~~~l~~~l~~~~~~~~~~~p~~~~~~~~ 143 (242)
..|.+||+|+.|+|++..|++.++.+.+.+-+.+|+..|+.|...+|+++|+-||+..-+ + -| +.+.+
T Consensus 448 PdQfYRL~~SLFlHagviH~~vSi~FQm~vmrdlEkL~g~~riAIiy~~SGitGNLASAI----F-----lp---Y~~eV 515 (652)
T KOG2290|consen 448 PDQFYRLWLSLFLHAGVIHLLVSICFQMTVMRDLEKLAGWHRIAIIYFLSGITGNLASAI----F-----LP---YRAEV 515 (652)
T ss_pred hhHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHhhcchhhheeeecccccccchhee----e-----ec---ccccc
Confidence 468999999999999999999999999999999999999999999999999999997521 1 23 45678
Q ss_pred cHHHHHHHHHHHHHhcCCCcceeEEeeeehhh--HHHHHHHHHHHhhCCChhHHHHHHHHHHhHHHhhccccchhh
Q psy6649 144 GFSAVLFAMKTILTRLQPDAYQQILNINVKAI--YAPWFELIIIYLLVPNASFKGHLSGILVGLTYTDTPIGWGLD 217 (242)
Q Consensus 144 G~Sg~v~all~~~~~~~p~~~~~i~~i~i~~~--~~~~i~~~~~~~~~~~~s~~~hl~G~l~G~~~~~~~~~~~~~ 217 (242)
|.+|..+|++....+-.-+.+ +++-=+..+. ..+.++.+.+ .+.|.+|+++|+.|.+.|++.+..+++....
T Consensus 516 gPa~sQ~Gila~l~vEl~qs~-~il~~~w~a~~~Lia~~L~L~i-GliPWiDN~aHlfG~i~GLl~s~~~~PYi~F 589 (652)
T KOG2290|consen 516 GPAGSQFGILACLFVELFQSW-QILERPWRAFFHLIATLLVLCI-GLIPWIDNWAHLFGTIFGLLTSIIFLPYIDF 589 (652)
T ss_pred CCcccccchHHHHHHHHHhhh-HhhhhHHHHHHHHHHHHHHHHh-ccccchhhHHHHHHHHHHHHHHHHhhccccc
Confidence 999999999876543222211 1110001111 1122222222 5679999999999999999999987775443
No 11
>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=99.29 E-value=2.6e-12 Score=93.37 Aligned_cols=91 Identities=27% Similarity=0.420 Sum_probs=82.1
Q ss_pred ccceeehhhhccCChhHHHHHHHHHHHhHHHHHHhhChHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCCCCcccccH
Q psy6649 66 DYKRLILSAFEHGDDMHLYYNMVSLILKGRQLEKIYGWGKFLSLVIFLTVFTSLYYILLAYIVFYITNDTSELSHCAIGF 145 (242)
Q Consensus 66 q~wrllT~~f~H~~~~hll~N~~~l~~~g~~lE~~~G~~~fl~~~l~~~~~~~l~~~l~~~~~~~~~~~p~~~~~~~~G~ 145 (242)
..||++|+.|++.|+..+++|...++..|+.+|+.||+++++.++....+.+|+...+.....+...+++.+...+..|.
T Consensus 7 ~pWtl~T~~fve~~i~~~l~~~~~l~~~g~~lE~~WGs~E~lkFi~vv~~~tnl~~~~~~~~~y~i~~~~~~l~~~i~G~ 86 (99)
T PF08551_consen 7 YPWTLFTAGFVETNIIGLLFSLLTLFYGGRYLEPIWGSREFLKFILVVNVITNLLTFLLYLLLYAITGNESYLFVPISGF 86 (99)
T ss_pred ehHHHHHHHHHHhHHHHHHHHHHHHHHhhHHHHHhcChHHHHHHHHHHHHHhHHHHHHHHHHHHHHhCCCceeEEEecCc
Confidence 67999999999999999999999999999999999999999999999999999999888887777888887656677899
Q ss_pred HHHHHHHHHHH
Q psy6649 146 SAVLFAMKTIL 156 (242)
Q Consensus 146 Sg~v~all~~~ 156 (242)
.|++.|+++++
T Consensus 87 ~~~~~g~lVa~ 97 (99)
T PF08551_consen 87 MGVLAGFLVAF 97 (99)
T ss_pred HHhHhheEEEE
Confidence 99998887654
No 12
>KOG2890|consensus
Probab=99.21 E-value=3.4e-11 Score=101.51 Aligned_cols=153 Identities=17% Similarity=0.152 Sum_probs=115.3
Q ss_pred HHHHHHHHhhcCCCCCchHHHHHHHHHHHHHHhhhcccc----cccchhcchhhhhccCccceeehhhhccCChhHHHHH
Q psy6649 11 LILLLVHILHLGADTIPPATLGLVFLQSMVYLNIFRKPW----STLDVCISADAVIQQRDYKRLILSAFEHGDDMHLYYN 86 (242)
Q Consensus 11 ~~~~~~~~~~~~~~~~p~vt~~li~~~v~v~~l~~~~~~----~~~~~~~~~~~v~~~~q~wrllT~~f~H~~~~hll~N 86 (242)
..+-.||-......+.-++...+..+.+..|..+..... ....+.+.|.+.+ ...|+++|+.|+..+.+..+.|
T Consensus 9 ~lp~~~~~~~~~l~n~~vvvs~ic~~tlf~yi~sf~~~t~~l~~~p~y~lvp~~~~--~~~WtliTs~fie~~vw~V~~s 86 (326)
T KOG2890|consen 9 NLPFSWQHLNALLLNLEVVVSAICVLTLFGYILSFGNFTILLATLPGYQLVPNALF--FFPWTLITSGFIELNVWDVLVS 86 (326)
T ss_pred cchHHHHHhhhHhhhchhHHHHHHHHHHHHHHHHHHHhHHHHHhccccccCCcchh--hhhHHHHhcchhhhhHHHHHHH
Confidence 456666666655555555555555555566666544221 1112333444332 4789999999999999999999
Q ss_pred HHHHHHhHHHHHHhhChHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCCCCcccccHHHHHHHHHHHHHhcCCCcce
Q psy6649 87 MVSLILKGRQLEKIYGWGKFLSLVIFLTVFTSLYYILLAYIVFYITNDTSELSHCAIGFSAVLFAMKTILTRLQPDAYQ 165 (242)
Q Consensus 87 ~~~l~~~g~~lE~~~G~~~fl~~~l~~~~~~~l~~~l~~~~~~~~~~~p~~~~~~~~G~Sg~v~all~~~~~~~p~~~~ 165 (242)
...+...|+.+|+.||+.+++.+|...-...++...+.+.+.+..++++.+...+.-|..|++-|+++++.+..|+..+
T Consensus 87 v~~L~v~G~~lEp~Wg~~e~lkff~ivn~~~~l~v~v~~~l~Y~it~n~v~L~~~i~G~~gilaGilVa~kQllpd~~i 165 (326)
T KOG2890|consen 87 VLTLSVGGKFLEPNWGSLELLKFFAIVNGSTTLVVLVPALLLYMITDNHVYLYIPIHGTTGILAGILVAWKQLLPDTII 165 (326)
T ss_pred HHheeecceeeccCCCCHHHHHHHHHhhchhHHHHHHHHHHHHHHhcCceEEEEEeccchHHHHHHHHHHHHHcCceeE
Confidence 9999999999999999999999999888888887776666666678888777777889999999999999999999743
No 13
>KOG4463|consensus
Probab=98.75 E-value=5.1e-09 Score=86.70 Aligned_cols=181 Identities=16% Similarity=0.226 Sum_probs=116.7
Q ss_pred CCCCCchHHHHHHHHHHHHHHhhhcccccccchhcchhhhhc-cCccceeehhhhccCChhHHHHHHHHHHHhHHHHHHh
Q psy6649 22 GADTIPPATLGLVFLQSMVYLNIFRKPWSTLDVCISADAVIQ-QRDYKRLILSAFEHGDDMHLYYNMVSLILKGRQLEKI 100 (242)
Q Consensus 22 ~~~~~p~vt~~li~~~v~v~~l~~~~~~~~~~~~~~~~~v~~-~~q~wrllT~~f~H~~~~hll~N~~~l~~~g~~lE~~ 100 (242)
+..++| ||+.+++....+.+........ ..+.+++...++ ++||||++-+.|+..|-..+.+-++.+|.+ +.+||.
T Consensus 7 g~~nmp-VTK~~~iT~~~~~vvagI~~~k-~~f~l~y~~~l~~y~qywrlL~~qF~~~n~~e~~~~l~I~Y~f-R~~ERl 83 (323)
T KOG4463|consen 7 GFHNMP-VTKAFVITSALFTVVAGIQGRK-SKFGLSYQDILEKYFQYWRLLMSQFAFSNTPELMFGLYILYYF-RVFERL 83 (323)
T ss_pred cccccc-hHHHHHHHHHHHHHHHHhhhcc-cccccchhHHHHHHHHHHHHHHHHHHhcCChHHHHHHHHHHHH-HHHHHH
Confidence 445554 7777776665555444333221 233445554444 489999999999999999999999988887 999999
Q ss_pred hChHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCCCCcccccHHHHHHHHHHHHHhcCCC-cceeEEeeeehhhHHHH
Q psy6649 101 YGWGKFLSLVIFLTVFTSLYYILLAYIVFYITNDTSELSHCAIGFSAVLFAMKTILTRLQPD-AYQQILNINVKAIYAPW 179 (242)
Q Consensus 101 ~G~~~fl~~~l~~~~~~~l~~~l~~~~~~~~~~~p~~~~~~~~G~Sg~v~all~~~~~~~p~-~~~~i~~i~i~~~~~~~ 179 (242)
.|+.||..+++.++..+.+....+..+.-..+++ -..++..|.+|+.++-+....|. .....+++.+.-|...+
T Consensus 84 LGShky~~fiv~s~~~~~l~~~il~~l~~~~~~n-----l~~~qp~~liFa~~~~~y~~ip~~~f~r~f~~~f~dkni~~ 158 (323)
T KOG4463|consen 84 LGSHKYSVFIVFSGTVSLLLEVILLSLLKDTTAN-----LLTSQPYGLIFASFIPFYLDIPVSTFFRVFGVNFSDKNISF 158 (323)
T ss_pred hccccceeehhHHHHHHHHHHHHHHHHHHHHHhh-----hhhcCCCceeeeeccceEEEecceeEEEeecccccccceee
Confidence 9999999999999999999988776654333332 22355556778887655555554 34455555555554222
Q ss_pred HHH-HHHHhhCCC-------hhH----HHHHHHHHHhHHHhhc
Q psy6649 180 FEL-IIIYLLVPN-------ASF----KGHLSGILVGLTYTDT 210 (242)
Q Consensus 180 i~~-~~~~~~~~~-------~s~----~~hl~G~l~G~~~~~~ 210 (242)
+.. .......++ ++| .--++|++.|++|-..
T Consensus 159 i~~~G~a~sh~~NkredksaveWk~~i~f~~~gLi~~~~~~~~ 201 (323)
T KOG4463|consen 159 IYLAGVALSHSSNKREDKSAVEWKRSIFFGICGLIAGSLYRLN 201 (323)
T ss_pred ecccchhhhcCcccccccccceeecccccccchhhhhhHhhcc
Confidence 211 111112221 122 2256788888887654
No 14
>KOG2980|consensus
Probab=98.62 E-value=3.8e-08 Score=83.45 Aligned_cols=177 Identities=21% Similarity=0.184 Sum_probs=118.6
Q ss_pred chHHHHHHHHHHHHHHhhhcccc-c-ccchhcchhhhhccCccceeehhhhccCChhHHHHHHHHHHHhHH-HHHHhhCh
Q psy6649 27 PPATLGLVFLQSMVYLNIFRKPW-S-TLDVCISADAVIQQRDYKRLILSAFEHGDDMHLYYNMVSLILKGR-QLEKIYGW 103 (242)
Q Consensus 27 p~vt~~li~~~v~v~~l~~~~~~-~-~~~~~~~~~~v~~~~q~wrllT~~f~H~~~~hll~N~~~l~~~g~-~lE~~~G~ 103 (242)
|-+...++..+++++.++..... . ...+...-+. .....|.++++.|.|-+..|+-.|++.+..+.. .+-...|.
T Consensus 115 ~g~v~~ll~~n~~vf~lWrv~~~~~~~~~~mls~~~--~~t~~w~i~~s~Fsh~~a~h~g~~~~~~~~y~~~a~~~~~~~ 192 (310)
T KOG2980|consen 115 NGVVFGLLIANAFVFTLWRVPQKQFTMIPWMLSRNA--YKTGCWKIILSTFSHYSALHLGPNMLVLKSYLAGALKGSLGF 192 (310)
T ss_pred CcchhHHHHHHHHHHHHHHhcchhhhhhhHHhhccc--ccccceeEEeehhcchhHhhhcHHHHHHHHHhcccccCCcch
Confidence 33778899999999988876532 1 2233332221 234567899999999999999999998887766 66667777
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCCCCcccccHHHHHHHHHHHHHhcCCCcceeEEe-eeehhhHHHHHHH
Q psy6649 104 GKFLSLVIFLTVFTSLYYILLAYIVFYITNDTSELSHCAIGFSAVLFAMKTILTRLQPDAYQQILN-INVKAIYAPWFEL 182 (242)
Q Consensus 104 ~~fl~~~l~~~~~~~l~~~l~~~~~~~~~~~p~~~~~~~~G~Sg~v~all~~~~~~~p~~~~~i~~-i~i~~~~~~~i~~ 182 (242)
..+..+|+.++..+..... .. ..+..+..+.+|+||.++++.++.+.+.|+.+..+.+ ++++......+..
T Consensus 193 ~~~~AlylSa~~~~~~i~~------~~--~v~~~~~gp~LGAsGav~ai~a~~~~lfP~~~~~i~f~~~v~~ga~~~~~~ 264 (310)
T KOG2980|consen 193 SSFFALYLSAGVKGLFISV------KD--KVPTSWAGPSLGASGAVYAILALDCTLFPKTTLYILFVFPVPAGAGLAFKA 264 (310)
T ss_pred hhcccceeccccccceeEe------ec--cccccccccccccchHHHHHHHHHhhcCcCcceeEEEeecccccchhHHHH
Confidence 7788888633333333210 00 0122224557999999999999999999998888777 6777654322211
Q ss_pred HH-HH-----hhCCChhHHHHHHHHHHhHHHhhcccc
Q psy6649 183 II-IY-----LLVPNASFKGHLSGILVGLTYTDTPIG 213 (242)
Q Consensus 183 ~~-~~-----~~~~~~s~~~hl~G~l~G~~~~~~~~~ 213 (242)
.. .. +.....++.+|++|-+.|..++...-+
T Consensus 265 i~~~~~a~~~l~~~~~n~~Ah~~gsl~Gv~va~~~~~ 301 (310)
T KOG2980|consen 265 IAAYDFAGLILGWGFFNHAAHLSGSLFGVVVATYLWA 301 (310)
T ss_pred HHHhhhcceeeccccchhHhhhcchHHHHHHHHHHHH
Confidence 11 11 112345677999999999998876543
No 15
>COG3105 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=37.78 E-value=27 Score=26.45 Aligned_cols=18 Identities=22% Similarity=0.440 Sum_probs=10.4
Q ss_pred hHHHHHHHHHHhHHHhhc
Q psy6649 193 SFKGHLSGILVGLTYTDT 210 (242)
Q Consensus 193 s~~~hl~G~l~G~~~~~~ 210 (242)
.|..-+.|+++|+++++.
T Consensus 7 ~W~~a~igLvvGi~IG~l 24 (138)
T COG3105 7 TWEYALIGLVVGIIIGAL 24 (138)
T ss_pred HHHHHHHHHHHHHHHHHH
Confidence 355555666666666554
No 16
>PRK11677 hypothetical protein; Provisional
Probab=28.63 E-value=45 Score=25.49 Aligned_cols=12 Identities=25% Similarity=0.434 Sum_probs=5.8
Q ss_pred HHHHHhHHHhhc
Q psy6649 199 SGILVGLTYTDT 210 (242)
Q Consensus 199 ~G~l~G~~~~~~ 210 (242)
.|+++|++.++.
T Consensus 12 vG~iiG~~~~R~ 23 (134)
T PRK11677 12 VGIIIGAVAMRF 23 (134)
T ss_pred HHHHHHHHHHhh
Confidence 444555544444
No 17
>KOG0489|consensus
Probab=23.33 E-value=25 Score=29.96 Aligned_cols=17 Identities=41% Similarity=0.563 Sum_probs=12.5
Q ss_pred CCCcccchhHHHHHHHH
Q psy6649 1 MTRPRRYELGLILLLVH 17 (242)
Q Consensus 1 ~~~~~~~~~~~~~~~~~ 17 (242)
.||+||.|++..|.+-+
T Consensus 184 LtR~RRiEiA~~L~LtE 200 (261)
T KOG0489|consen 184 LTRSRRIEIAHALNLTE 200 (261)
T ss_pred cchHHHHHHHhhcchhH
Confidence 48999999886665544
No 18
>PF10066 DUF2304: Uncharacterized conserved protein (DUF2304); InterPro: IPR019277 This entry represents hypothetical archaeal and bacterial proteins that have no known function.
Probab=22.95 E-value=72 Score=23.41 Aligned_cols=15 Identities=20% Similarity=0.040 Sum_probs=9.8
Q ss_pred ChhHHHHHHHHHHhH
Q psy6649 191 NASFKGHLSGILVGL 205 (242)
Q Consensus 191 ~~s~~~hl~G~l~G~ 205 (242)
-.++.+|+.|+-.|.
T Consensus 52 ~~~~vA~~lGi~~~~ 66 (115)
T PF10066_consen 52 ILDWVAKLLGIGRPP 66 (115)
T ss_pred HHHHHHHHHCCCchh
Confidence 356777877766553
No 19
>PF09946 DUF2178: Predicted membrane protein (DUF2178); InterPro: IPR019235 This entry, found in various hypothetical bacterial and archaeal proteins, has no known function, but contains several predicted transmembrane helices.
Probab=22.54 E-value=94 Score=22.80 Aligned_cols=28 Identities=11% Similarity=-0.141 Sum_probs=17.4
Q ss_pred CChhHHHHHHHHHHhHHHhhccccchhh
Q psy6649 190 PNASFKGHLSGILVGLTYTDTPIGWGLD 217 (242)
Q Consensus 190 ~~~s~~~hl~G~l~G~~~~~~~~~~~~~ 217 (242)
.+.+...-.+.+++|....+..+++..+
T Consensus 23 ~~g~~~la~i~~~~g~~~~~~~~~~v~~ 50 (111)
T PF09946_consen 23 SSGNPLLAVIVFLAGILLVYLYRRRVED 50 (111)
T ss_pred hcCChHHHHHHHHHHHHHHHHHHHhcCc
Confidence 3333444577888888877776654444
No 20
>PF09527 ATPase_gene1: Putative F0F1-ATPase subunit (ATPase_gene1)
Probab=22.15 E-value=2.1e+02 Score=17.72 Aligned_cols=39 Identities=15% Similarity=0.245 Sum_probs=27.0
Q ss_pred hHHHHHHHHHHHhHHHHHHhhChH-HHHHHHHHHHHHHHH
Q psy6649 81 MHLYYNMVSLILKGRQLEKIYGWG-KFLSLVIFLTVFTSL 119 (242)
Q Consensus 81 ~hll~N~~~l~~~g~~lE~~~G~~-~fl~~~l~~~~~~~l 119 (242)
..+..++..-...|..+++.+++. -+....++.++.++.
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 456677777788899999999984 455555555555554
No 21
>PF06295 DUF1043: Protein of unknown function (DUF1043); InterPro: IPR009386 This entry consists of several hypothetical bacterial proteins of unknown function.
Probab=21.02 E-value=53 Score=24.75 Aligned_cols=19 Identities=16% Similarity=0.349 Sum_probs=10.7
Q ss_pred HHHHHHHHhHHHhhccccc
Q psy6649 196 GHLSGILVGLTYTDTPIGW 214 (242)
Q Consensus 196 ~hl~G~l~G~~~~~~~~~~ 214 (242)
+-+.|+++|++.++...+.
T Consensus 5 ~lvvG~iiG~~~~r~~~~~ 23 (128)
T PF06295_consen 5 GLVVGLIIGFLIGRLTSSN 23 (128)
T ss_pred HHHHHHHHHHHHHHHhccc
Confidence 3445666666666554443
Done!