Query 011129
Match_columns 493
No_of_seqs 375 out of 1617
Neff 6.0
Searched_HMMs 46136
Date Fri Mar 29 08:26:37 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/011129.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/011129hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PRK10907 intramembrane serine 100.0 3.6E-46 7.9E-51 373.7 20.0 251 137-401 1-263 (276)
2 PTZ00101 rhomboid-1 protease; 100.0 6.8E-28 1.5E-32 241.8 20.3 185 214-400 43-232 (278)
3 PF05512 AWPM-19: AWPM-19-like 99.9 1.7E-27 3.7E-32 212.7 8.5 90 401-491 45-142 (142)
4 COG0705 Membrane associated se 99.9 1.7E-23 3.6E-28 204.2 13.2 178 223-401 16-204 (228)
5 KOG2289 Rhomboid family protei 99.9 1.5E-24 3.3E-29 219.7 4.8 142 257-400 104-246 (316)
6 PF01694 Rhomboid: Rhomboid fa 99.8 1.5E-20 3.3E-25 169.5 2.5 131 268-400 2-134 (145)
7 KOG2290 Rhomboid family protei 99.7 9.7E-19 2.1E-23 180.7 3.6 173 269-451 448-635 (652)
8 KOG2632 Rhomboid family protei 99.7 4.8E-17 1E-21 159.8 10.9 214 222-473 13-240 (258)
9 PF12122 DUF3582: Protein of u 99.6 5.4E-16 1.2E-20 133.8 4.8 86 137-227 1-99 (101)
10 KOG2980 Integral membrane prot 98.3 3.6E-07 7.8E-12 92.1 4.3 167 225-400 117-293 (310)
11 PF04511 DER1: Der1-like famil 98.2 1.2E-05 2.7E-10 77.4 11.3 161 224-400 2-174 (197)
12 PF08551 DUF1751: Eukaryotic i 97.9 1.2E-05 2.6E-10 69.4 3.5 58 271-328 7-64 (99)
13 KOG0858 Predicted membrane pro 97.4 0.00046 1E-08 67.9 8.1 97 222-327 11-112 (239)
14 KOG4463 Uncharacterized conser 95.2 0.02 4.4E-07 57.2 4.2 59 268-327 47-105 (323)
15 COG5291 Predicted membrane pro 93.6 0.1 2.2E-06 51.9 4.9 48 267-314 55-106 (313)
16 KOG2890 Predicted membrane pro 93.6 0.052 1.1E-06 55.5 2.9 85 270-354 65-162 (326)
17 COG0705 Membrane associated se 59.0 6 0.00013 38.5 2.0 74 268-354 136-209 (228)
18 PF09527 ATPase_gene1: Putativ 45.0 92 0.002 23.5 6.2 42 286-327 8-50 (55)
19 PRK09765 PTS system 2-O-a-mann 44.2 4.8E+02 0.01 29.9 14.4 23 148-170 182-204 (631)
20 PRK10263 DNA translocase FtsK; 42.3 57 0.0012 40.2 6.8 14 228-241 27-40 (1355)
21 PF09413 DUF2007: Domain of un 31.0 57 0.0012 25.3 3.2 30 139-168 2-31 (67)
22 PF11823 DUF3343: Protein of u 29.5 88 0.0019 25.0 4.1 45 140-184 5-60 (73)
23 PF10066 DUF2304: Uncharacteri 28.8 1.6E+02 0.0034 25.9 5.9 20 381-400 46-66 (115)
24 KOG3966 p53-mediated apoptosis 27.9 5.7E+02 0.012 26.5 10.2 51 297-347 136-196 (360)
25 COG1823 Predicted Na+/dicarbox 25.3 8.3E+02 0.018 26.6 11.2 47 285-331 3-54 (458)
26 COG1030 NfeD Membrane-bound se 24.1 8.6E+02 0.019 26.7 11.4 19 334-352 306-324 (436)
27 TIGR00834 ae anion exchange pr 22.1 6E+02 0.013 30.6 10.5 63 284-346 375-439 (900)
28 PF12761 End3: Actin cytoskele 21.2 1.8E+02 0.0039 28.4 5.1 44 106-159 103-147 (195)
29 PF05546 She9_MDM33: She9 / Md 20.6 49 0.0011 32.5 1.2 33 210-242 138-171 (207)
30 PF06123 CreD: Inner membrane 20.3 5.5E+02 0.012 28.1 9.1 23 336-358 357-379 (430)
31 TIGR02230 ATPase_gene1 F0F1-AT 20.2 3.2E+02 0.0068 23.9 5.9 41 287-327 51-92 (100)
No 1
>PRK10907 intramembrane serine protease GlpG; Provisional
Probab=100.00 E-value=3.6e-46 Score=373.68 Aligned_cols=251 Identities=14% Similarity=0.100 Sum_probs=210.9
Q ss_pred hhhhccCCChhHHHHHHHHHhhcCCcceeecCccc-----hhhhHHHHHhhhh--hccCCCCCcchhhHhhhcccCCcc-
Q 011129 137 HSRSGEINAKTELDSLDAYLGKLNTDAKFSTDQTT-----ERNLVAAQLSISK--SSKRGYMGKLKGYRELRNKDGVRS- 208 (493)
Q Consensus 137 m~~~~~~~~~~~aqaf~dYl~~~~i~~~v~~~~~~-----de~~~~~~~~e~~--~~~p~~~~~~~rY~~as~~~g~~~- 208 (493)
|+++.+++|||+||+|+|||++|||+++++++++. ||++.+++++|++ ++||.|+ ||++++|+.++++
T Consensus 1 M~~~~~~~~~~~a~~f~dyl~~~~i~~~~~~~~~~~lwl~d~~~~~~~~~~~~~f~~~p~~~----~y~~asw~~g~~~~ 76 (276)
T PRK10907 1 MLMITSFSNPRLAQAFVDYMATQGVILTIQQHNQSDIWLADESQAERVRAELARFLENPADP----RYLAASWQSGHTNS 76 (276)
T ss_pred CcchhcCCCHHHHHHHHHHHHHCCCcEEEecCCceEEEecCHHHHHHHHHHHHHHHhCCCch----hHHhcccccCCCCC
Confidence 78899999999999999999999999999854443 8899999999999 9999999 9999999988643
Q ss_pred ---ccchHHhhhcccccchHHH-HHHHHHHHHHHHHHhcCCCCccccchhhhhhhhcchhhhhhcCccceeeecccccCC
Q 011129 209 ---LERDLALQRTEETSNLYLI-ILVSIDVAVFLFEIASPIRNSEFGFFSLPLLYGAKINELILVGEWWRLVTPMFLHSG 284 (493)
Q Consensus 209 ---~~~~~~~~~~~~~~~ppvT-~Liai~v~VFll~~~~~~~~~~~~~~~~p~~~Ga~~~~~i~~gq~WRl~Ts~FlH~s 284 (493)
++++..+++.+.+.. |+| +++++|++||+++.+.+.. .....+.+| . .....+||||++|++|+|+|
T Consensus 77 ~~~~~~~~~~~~~~~~~~-p~T~~li~i~i~vf~l~~~~~~~-~~~~~l~~~----~---~~~~~~q~WRl~T~~flH~~ 147 (276)
T PRK10907 77 GLRYRRFPFLATLRERAG-PLTLGVMIACVVVFILMQILGDQ-TVMLWLAWP----F---DPSLKFELWRYFTHALLHFS 147 (276)
T ss_pred CcccccchHHHhhccCCC-CHHHHHHHHHHHHHHHHHHhccH-HHHHHHhcc----c---cccccCCcHHHHhHHHHhCC
Confidence 566777777765554 677 9999999999998765532 111121111 1 12357999999999999999
Q ss_pred HHHHHHHHHHHHHHHHHHHHhcCChhHHHHHHHHHHHHHHhhhhcCCCceeccchHHHHHHHHHHHHHhcccchhhhhhh
Q 011129 285 LFHVALSCWALLTFGPQVCKSYGPFTFFLIYTLGGISGNLTSFLHTPEPTVGGTGPVFAIIGAWLIYQFQNKDLIAKDVS 364 (493)
Q Consensus 285 ~~HLlfNml~L~~~G~~lE~~lGs~r~l~lyLlsgi~g~l~~~l~~~~~~vGaSGaVfgLlga~~~~~~~~~~~~~~~~~ 364 (493)
++||+|||+++|++|..+|+.+|+++++.+|++++++||++++++.+...+|+||+|||++|+.+....+.+.. ...+|
T Consensus 148 ~~Hl~fNml~l~~lG~~iE~~~G~~~~l~l~l~s~i~~~~~~~~~~~~~~gGaSGvVygL~g~~~~~~~~~p~~-~~~lp 226 (276)
T PRK10907 148 LLHILFNLLWWWYLGGAVEKRLGSGKLIVITLISALLSGWVQSKFSGPWFGGLSGVVYALMGYVWLRGERDPQS-GIYLP 226 (276)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHChHHHHHHHHHHHHHHHHHHHHHccchhhHHHHHHHHHHHHHHHHhcccccc-chhhh
Confidence 99999999999999999999999999999999999999999999887778899999999999988877666554 34567
Q ss_pred HHHHHHHHHHHHHHhhhhcCCChhhhhhHhhhhhccc
Q 011129 365 ERMFQKAILSTALSFIISNFGPVDTWAHLGAAFTDLG 401 (493)
Q Consensus 365 ~~l~~~~li~l~l~~i~~~~~~Is~~AHLgGll~GLl 401 (493)
..++.++++++++++.....++|+|.||++|+++|++
T Consensus 227 ~~~~~f~llwl~~g~~~~~g~~Ian~AHlgGli~Gll 263 (276)
T PRK10907 227 RGLIAFALLWLVAGYFDLFGMSIANAAHVAGLAVGLA 263 (276)
T ss_pred HHHHHHHHHHHHHHHHHccCcccHHHHHHHHHHHHHH
Confidence 7788888888888877555578999999999999963
No 2
>PTZ00101 rhomboid-1 protease; Provisional
Probab=99.96 E-value=6.8e-28 Score=241.75 Aligned_cols=185 Identities=25% Similarity=0.326 Sum_probs=136.2
Q ss_pred HhhhcccccchHHH-HHHHHHHHHHHHHHhcCCCCccccchhhhhhhhcchhhhhhcCccceeeecccccCCHHHHHHHH
Q 011129 214 ALQRTEETSNLYLI-ILVSIDVAVFLFEIASPIRNSEFGFFSLPLLYGAKINELILVGEWWRLVTPMFLHSGLFHVALSC 292 (493)
Q Consensus 214 ~~~~~~~~~~ppvT-~Liai~v~VFll~~~~~~~~~~~~~~~~p~~~Ga~~~~~i~~gq~WRl~Ts~FlH~s~~HLlfNm 292 (493)
....+++-+.+.+| .++++++++|++...................+|+..++.+.++||||++|++|+|.|++|+++||
T Consensus 43 ler~Fp~f~i~~l~~~Iiii~iivfil~l~~~~~~~l~p~~~~L~~~Ga~~~~~i~~gq~WRLiT~~FlH~~~~HLl~Nm 122 (278)
T PTZ00101 43 LNLIFPHFTWKSFIMAISIIQIIVFIISVSIKPADFLTPSDSLLVTLGANVASRIKQGEIHRLILPIFLHANIFHTFFNV 122 (278)
T ss_pred HHHHcCCccHHHHHHHHHHHHHHHHHHHHHhcccccCCCCHHHHHHHhCcchhhhhcCCCHHHHHHHHHccCHHHHHHHH
Confidence 34455666777888 99999999999876643221100001134567888878888999999999999999999999999
Q ss_pred HHHHHHHHHHHHhcCChhHHHHHHHHHHHHHHhhhhcCC-CceeccchHHHHHHHHHHHHHhcccchhhhhhhHHHHHHH
Q 011129 293 WALLTFGPQVCKSYGPFTFFLIYTLGGISGNLTSFLHTP-EPTVGGTGPVFAIIGAWLIYQFQNKDLIAKDVSERMFQKA 371 (493)
Q Consensus 293 l~L~~~G~~lE~~lGs~r~l~lyLlsgi~g~l~~~l~~~-~~~vGaSGaVfgLlga~~~~~~~~~~~~~~~~~~~l~~~~ 371 (493)
++++.+|..+|+.+|++|++.+|+++|++|++++.++.+ ...+||||++||++|++.......+..... +.+....+
T Consensus 123 ~~l~~~G~~lE~~~G~~r~~ilYl~sGi~G~l~s~~~~~~~~svGASgAifGLiGa~~~~lil~w~~~~~--~~~~~~~~ 200 (278)
T PTZ00101 123 FFQLRMGFTLEKNYGIVKIIILYFLTGIYGNILSSSVTYCPIKVGASTSGMGLLGIVTSELILLWHVIRH--RERVVFNI 200 (278)
T ss_pred HHHHHHHHHHHHHHChHHHHHHHHHHHHHHHHHHHHHccCCcEEehhHHHHHHHHHHHHHHHHHHHhhcc--HHHHHHHH
Confidence 999999999999999999999999999999999988765 368999999999999987654444332211 11111111
Q ss_pred HHHHHHHhh--h-hcCCChhhhhhHhhhhhcc
Q 011129 372 ILSTALSFI--I-SNFGPVDTWAHLGAAFTDL 400 (493)
Q Consensus 372 li~l~l~~i--~-~~~~~Is~~AHLgGll~GL 400 (493)
++.+++.++ . ...+++|++||+||+++|+
T Consensus 201 i~~~li~~~l~~~~~g~~Id~~aHlGG~i~G~ 232 (278)
T PTZ00101 201 IFFSLISFFYYFTFNGSNIDHVGHLGGLLSGI 232 (278)
T ss_pred HHHHHHHHHHHHhcCCCCccHHHHHHHHHHHH
Confidence 111111111 1 1237799999999999996
No 3
>PF05512 AWPM-19: AWPM-19-like family; InterPro: IPR008390 Members of this family are 19 kDa membrane proteins. The levels of the plant protein AWPM-19 increase dramatically when there is an increase level of abscisic acid. The increase presence of this protein leads to greater tolerance of freezing [].
Probab=99.94 E-value=1.7e-27 Score=212.65 Aligned_cols=90 Identities=54% Similarity=0.817 Sum_probs=87.8
Q ss_pred cCCchhhHHHHHHHhhhhhhHHHHHHhhhhhhccccchHHHHHHhhHhhh--------hcccceeeccccCCccchhhHH
Q 011129 401 GGNTSTWFLLTFALTTGAIGVCSVTAGLMHLRAWRSESLAAASSLAILSC--------FVCKEIILGGHRGKRLQTLEAF 472 (493)
Q Consensus 401 lg~~~~~~~i~f~l~aG~vg~~~~l~~~~~~~~w~~~~l~a~~~~~~ls~--------~ack~i~l~~~r~~~l~~~e~~ 472 (493)
+||.+|+|+++|+++|||||++++++|+.|++.|+.|+++||++.++++| +|||||++|+ ||+||||||+|
T Consensus 45 ~GN~AT~ffv~faLlAgVVG~aS~l~G~~h~r~W~~~sLaaAaa~a~iAW~lTlLAmGlACKeI~~g~-r~~rLrtlEaf 123 (142)
T PF05512_consen 45 MGNAATGFFVIFALLAGVVGAASVLAGLHHVRSWRSESLAAAAASALIAWALTLLAMGLACKEIHLGG-RNWRLRTLEAF 123 (142)
T ss_pred ccchhHHHHHHHHHHHHHHHHHHHHhhHHHHhhcCccchHHHHHHHHHHHHHHHHHHHHhHheeeecC-ccchhhHHHHH
Confidence 69999999999999999999999999999999999999999999999999 6999999998 99999999999
Q ss_pred HHHHHHHHHHHHHHhhhhh
Q 011129 473 AVISLLSQLLYLGLVHAWF 491 (493)
Q Consensus 473 ~ii~~~~ql~~~~~~~~~~ 491 (493)
+|||+.|||+|++++|+|.
T Consensus 124 ~IIl~~tQLly~l~lH~g~ 142 (142)
T PF05512_consen 124 TIILSATQLLYLLALHAGV 142 (142)
T ss_pred HHHHHHHHHHHHHHHhccC
Confidence 9999999999999999983
No 4
>COG0705 Membrane associated serine protease [Amino acid transport and metabolism]
Probab=99.90 E-value=1.7e-23 Score=204.17 Aligned_cols=178 Identities=26% Similarity=0.454 Sum_probs=139.5
Q ss_pred chHHH-HHHHHHHHHHHHHHhcCCCCccccchhhhhhhhcchhhhhh-cC--ccceeeecccccCCHHHHHHHHHHHHHH
Q 011129 223 NLYLI-ILVSIDVAVFLFEIASPIRNSEFGFFSLPLLYGAKINELIL-VG--EWWRLVTPMFLHSGLFHVALSCWALLTF 298 (493)
Q Consensus 223 ~ppvT-~Liai~v~VFll~~~~~~~~~~~~~~~~p~~~Ga~~~~~i~-~g--q~WRl~Ts~FlH~s~~HLlfNml~L~~~ 298 (493)
.++.| .++.+|+++|+++...+.... .........++........ .. |+||++|++|+|.|+.|+++||+++|.+
T Consensus 16 ~~~~~~~~~~~~~~v~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~w~lit~~FlH~~~~Hll~N~~~l~~f 94 (228)
T COG0705 16 APPVTLFLILLNILVFLLELVLGWSAI-FLLTFLFRLFGLYPLNLLGALARDQLWRLITAIFLHAGFLHLLFNMLALWVF 94 (228)
T ss_pred cchHHHHHHHHHHHHHHHHHHccchHH-HHHHHhhhHHhhcchhhhccccccchHHHHHHHHHHhhHHHHHHHHHHHHHh
Confidence 46778 999999999999877654321 1110000001111111111 11 8999999999999999999999999999
Q ss_pred HHHHHHhcCChhHHHHHHHHHHHHHHhhhhcCCC---ceeccchHHHHHHHHHHHHHhcccchhhhh-hhHHHHHHHHHH
Q 011129 299 GPQVCKSYGPFTFFLIYTLGGISGNLTSFLHTPE---PTVGGTGPVFAIIGAWLIYQFQNKDLIAKD-VSERMFQKAILS 374 (493)
Q Consensus 299 G~~lE~~lGs~r~l~lyLlsgi~g~l~~~l~~~~---~~vGaSGaVfgLlga~~~~~~~~~~~~~~~-~~~~l~~~~li~ 374 (493)
|..+|+.+|+.+|+.+|+++|+++++.+..+.+. +.+|+||++||++|+++...+..+...... .+..+..++.++
T Consensus 95 g~~le~~~G~~~f~~~yl~~gl~~~~~~~~~~~~~~~~~~GASG~i~gllga~~~~~~~~~~~~~~~~~~~~~~~~i~~~ 174 (228)
T COG0705 95 GSNLERRLGTLRFLLFYLLSGLLAGLAQVLFGPKGGAPSLGASGAIFGLLGAYFLLFPFARILLLFLSLPRPALILILIW 174 (228)
T ss_pred hHHHHHHhchhHHHHHHHHHHHHHHHHHHHHcccccCcccchhHHHHHHHHHHHHHccccchhhhhccCchhHHHHHHHH
Confidence 9999999999999999999999999999988763 589999999999999999999887765444 777777778888
Q ss_pred HHHHhhhhcCC---ChhhhhhHhhhhhccc
Q 011129 375 TALSFIISNFG---PVDTWAHLGAAFTDLG 401 (493)
Q Consensus 375 l~l~~i~~~~~---~Is~~AHLgGll~GLl 401 (493)
++..++..... ++++.||++|++.|++
T Consensus 175 ~~~~~~~~~~~~~~~va~~aHl~G~i~G~l 204 (228)
T COG0705 175 LLYSLFSGAGSFGPSVAWSAHLGGLIGGLL 204 (228)
T ss_pred HHHHHHHHhcCCchHHHHHHHHHHHHHHHH
Confidence 88777765543 6999999999999963
No 5
>KOG2289 consensus Rhomboid family proteins [Signal transduction mechanisms]
Probab=99.90 E-value=1.5e-24 Score=219.71 Aligned_cols=142 Identities=30% Similarity=0.511 Sum_probs=123.2
Q ss_pred hhhhcchhhhhhcCccceeeecccccCCHHHHHHHHHHHHHHHHHHHHhcCChhHHHHHHHHHHHHHHhhhhcCCC-cee
Q 011129 257 LLYGAKINELILVGEWWRLVTPMFLHSGLFHVALSCWALLTFGPQVCKSYGPFTFFLIYTLGGISGNLTSFLHTPE-PTV 335 (493)
Q Consensus 257 ~~~Ga~~~~~i~~gq~WRl~Ts~FlH~s~~HLlfNml~L~~~G~~lE~~lGs~r~l~lyLlsgi~g~l~~~l~~~~-~~v 335 (493)
...+......+..+|+||++|++|+|+|+.||++||+.+.++|..+|+.+|.+|+.++|++||+.|++++.++.++ ..|
T Consensus 104 ~~~~~~i~~~~~r~E~WRllTym~LHaGi~HL~~N~~~ql~iGi~LE~~~G~~RiglIYl~gg~aGSlls~l~d~~~~sV 183 (316)
T KOG2289|consen 104 KMGGLLIYKPVHRGELWRLLTYMWLHAGIFHLLLNMLSQLFIGIPLEQVHGFLRIGLIYLAGGVAGSLLSSLFDPNSISV 183 (316)
T ss_pred ccCCceecChhhhchhHHHHHHHHHhcCHHHHHHHHHHHHhccccHHhhcCceEEeeehhhhhhhhHHHHHHhccCCcee
Confidence 4455666666789999999999999999999999999999999999999999999999999999999999999986 599
Q ss_pred ccchHHHHHHHHHHHHHhcccchhhhhhhHHHHHHHHHHHHHHhhhhcCCChhhhhhHhhhhhcc
Q 011129 336 GGTGPVFAIIGAWLIYQFQNKDLIAKDVSERMFQKAILSTALSFIISNFGPVDTWAHLGAAFTDL 400 (493)
Q Consensus 336 GaSGaVfgLlga~~~~~~~~~~~~~~~~~~~l~~~~li~l~l~~i~~~~~~Is~~AHLgGll~GL 400 (493)
||||++|||+|+.+.....||..+.... .....+++++.+...++..+.+++++|+||+++|.
T Consensus 184 GASggvfaLlgA~Ls~l~~Nw~~m~~~~--~~l~~ll~Ii~i~l~~G~~~~~~~~~h~gg~~~G~ 246 (316)
T KOG2289|consen 184 GASGGVFALLGAHLSNLLTNWTIMKNKF--AALRTLLIIIFINLDLGFAPYVDNFAHIGGLLAGF 246 (316)
T ss_pred cccHHHHHHHHHHHHHHHhhHHHhcchH--HHHHHHHHHHHHHHhhccccceeccccccccCCCc
Confidence 9999999999999999999998764222 23444555555666667789999999999999994
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=99.80 E-value=1.5e-20 Score=169.45 Aligned_cols=131 Identities=31% Similarity=0.584 Sum_probs=98.7
Q ss_pred hcCccceeeecccccCCHHHHHHHHHHHHHHHHHHHHhcCChhHHHHHHHHHHHHHHhhhhcCCC--ceeccchHHHHHH
Q 011129 268 LVGEWWRLVTPMFLHSGLFHVALSCWALLTFGPQVCKSYGPFTFFLIYTLGGISGNLTSFLHTPE--PTVGGTGPVFAII 345 (493)
Q Consensus 268 ~~gq~WRl~Ts~FlH~s~~HLlfNml~L~~~G~~lE~~lGs~r~l~lyLlsgi~g~l~~~l~~~~--~~vGaSGaVfgLl 345 (493)
+++||||++|++|+|.|+.|+++|++.++.+|..+|+.+|+.++..+|+++++.+++...+..+. +.+|+||+++|++
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 57999999999999999999999999999999999999999999999999999999999887664 5899999999999
Q ss_pred HHHHHHHhcccchhhhhhhHHHHHHHHHHHHHHhhhhcCCChhhhhhHhhhhhcc
Q 011129 346 GAWLIYQFQNKDLIAKDVSERMFQKAILSTALSFIISNFGPVDTWAHLGAAFTDL 400 (493)
Q Consensus 346 ga~~~~~~~~~~~~~~~~~~~l~~~~li~l~l~~i~~~~~~Is~~AHLgGll~GL 400 (493)
++.....+.++........ ........+.+.+.....+++++.+|++|+++|+
T Consensus 82 ~~~~~~~~~~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~hl~G~~~G~ 134 (145)
T PF01694_consen 82 GAFLFLYPQNKKRLRFIYL--ALVVPIIVLVIILLLGFIPNISFLGHLGGFLAGL 134 (145)
T ss_dssp HHHHHHHHCCCCCS---HC--CCCCCCCCCCHHHCTSSSSTTTHHHHHHHHHHHH
T ss_pred HHHHHHHhhccchhhcchH--HHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHH
Confidence 9999988887654421100 0000111112222333368899999999999995
No 7
>KOG2290 consensus Rhomboid family proteins [Signal transduction mechanisms]
Probab=99.73 E-value=9.7e-19 Score=180.74 Aligned_cols=173 Identities=25% Similarity=0.344 Sum_probs=133.8
Q ss_pred cCccceeeecccccCCHHHHHHHHHHHHHHHHHHHHhcCChhHHHHHHHHHHHHHHhhhhcCCC-ceeccchHHHHHHHH
Q 011129 269 VGEWWRLVTPMFLHSGLFHVALSCWALLTFGPQVCKSYGPFTFFLIYTLGGISGNLTSFLHTPE-PTVGGTGPVFAIIGA 347 (493)
Q Consensus 269 ~gq~WRl~Ts~FlH~s~~HLlfNml~L~~~G~~lE~~lGs~r~l~lyLlsgi~g~l~~~l~~~~-~~vGaSGaVfgLlga 347 (493)
.+|+||++|+.|+|+|++|++..|..++++-..+|+..|+.|..++|++||+.||+++..+.|. +.||-||+-||+++.
T Consensus 448 PdQfYRL~~SLFlHagviH~~vSi~FQm~vmrdlEkL~g~~riAIiy~~SGitGNLASAIFlpY~~eVgPa~sQ~Gila~ 527 (652)
T KOG2290|consen 448 PDQFYRLWLSLFLHAGVIHLLVSICFQMTVMRDLEKLAGWHRIAIIYFLSGITGNLASAIFLPYRAEVGPAGSQFGILAC 527 (652)
T ss_pred hhHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHhhcchhhheeeecccccccchheeeeccccccCCcccccchHHH
Confidence 4699999999999999999999999999999999999999999999999999999999999985 799999999999999
Q ss_pred HHHHHhcccchhhhhhhHHHHHHHHHHHHHHhhhhcCCChhhhhhHhhhhhcccCCchh--------------hHHHHHH
Q 011129 348 WLIYQFQNKDLIAKDVSERMFQKAILSTALSFIISNFGPVDTWAHLGAAFTDLGGNTST--------------WFLLTFA 413 (493)
Q Consensus 348 ~~~~~~~~~~~~~~~~~~~l~~~~li~l~l~~i~~~~~~Is~~AHLgGll~GLlg~~~~--------------~~~i~f~ 413 (493)
+++....+|..+..+ ...+.-++..+.+.++ ++.|.|||+||+.|++.||+-.++. .+.++.+
T Consensus 528 l~vEl~qs~~il~~~--w~a~~~Lia~~L~L~i-GliPWiDN~aHlfG~i~GLl~s~~~~PYi~Fg~~d~yrKr~~ilIs 604 (652)
T KOG2290|consen 528 LFVELFQSWQILERP--WRAFFHLIATLLVLCI-GLIPWIDNWAHLFGTIFGLLTSIIFLPYIDFGDFDLYRKRFYILIS 604 (652)
T ss_pred HHHHHHhhhHhhhhH--HHHHHHHHHHHHHHHh-ccccchhhHHHHHHHHHHHHHHHHhhccccccchhhhhhHHHHHHH
Confidence 999999998877553 3344444444333344 7889999999999999999655432 2222222
Q ss_pred HhhhhhhHHHHHHhhhhhhccccchHHHHHHhhHhhhh
Q 011129 414 LTTGAIGVCSVTAGLMHLRAWRSESLAAASSLAILSCF 451 (493)
Q Consensus 414 l~aG~vg~~~~l~~~~~~~~w~~~~l~a~~~~~~ls~~ 451 (493)
.+ ....+++++..+.+ +. -.-|-||.+++|+
T Consensus 605 ~i----vf~~Lla~Lvv~fy-~~--~i~cpWce~ltCl 635 (652)
T KOG2290|consen 605 QI----VFSGLLAILVVVFY-NY--PIDCPWCEHLTCL 635 (652)
T ss_pred HH----HHHHHHHHHHHhee-ec--ccCCchhhhcccc
Confidence 22 11233344433322 21 1348999999995
No 8
>KOG2632 consensus Rhomboid family proteins [Function unknown]
Probab=99.70 E-value=4.8e-17 Score=159.76 Aligned_cols=214 Identities=18% Similarity=0.190 Sum_probs=148.6
Q ss_pred cchHHH-HHHHHHHHHHHHHHhcCCCCccccchhhhhhhhcchhhhhhcCccceeeecccccCCHHHHHHHHHHHHHHHH
Q 011129 222 SNLYLI-ILVSIDVAVFLFEIASPIRNSEFGFFSLPLLYGAKINELILVGEWWRLVTPMFLHSGLFHVALSCWALLTFGP 300 (493)
Q Consensus 222 ~~ppvT-~Liai~v~VFll~~~~~~~~~~~~~~~~p~~~Ga~~~~~i~~gq~WRl~Ts~FlH~s~~HLlfNml~L~~~G~ 300 (493)
..|.+| .++.+|+++|+.....+.. +. ++ .......+.|+||++|++++|.+..|+++||+++|.+|.
T Consensus 13 ~~p~~ts~~~~~~~~i~lv~~~~~i~----~~------~~-l~~~~l~~~ql~RL~Ty~l~H~s~~hllfnmlaL~~~g~ 81 (258)
T KOG2632|consen 13 KIPLLTSIVVVLAILIYLVSFFPGIV----EV------LG-LPSELLINWQLYRLITYALVHLSLPHLLFNMLALWPLGS 81 (258)
T ss_pred cchHHHHHHHHHHHHHHHHhccchhh----hH------hc-CCHHHhhhHHHHHHHHHHHHhccHHHHHHHHHHHHhchh
Confidence 456788 9999999999987654422 11 11 122345789999999999999999999999999999999
Q ss_pred HHHHhcC-ChhHHHHHHHHHHHHHHhhhhcC------C----CceeccchHHHHHHHHHHHHHhcccchh--hhhhhHHH
Q 011129 301 QVCKSYG-PFTFFLIYTLGGISGNLTSFLHT------P----EPTVGGTGPVFAIIGAWLIYQFQNKDLI--AKDVSERM 367 (493)
Q Consensus 301 ~lE~~lG-s~r~l~lyLlsgi~g~l~~~l~~------~----~~~vGaSGaVfgLlga~~~~~~~~~~~~--~~~~~~~l 367 (493)
+.|+.+| +.+++..+.+.+++++++..+.. + +..+|.||+.||+++......+.++... ...+|..+
T Consensus 82 ~fE~~~G~t~~~l~~~~llalf~gIl~ll~~~~~~~~d~~~~~~a~G~s~v~Fam~~~~~~~sp~r~~~~fg~~siP~~l 161 (258)
T KOG2632|consen 82 QFERTHGTTVRILMFTVLLALFSGILYLLAYHVFLLSDLVYVEGAIGFSGVLFAMMAVLEVQSPVRSRSVFGLFSIPIVL 161 (258)
T ss_pred HHHhhccceehHHHHHHHHHHHHHHHHHHHHHHHhhcchhhhcccccccHHHHHHHHHHhhcCcccchhhcccccccHHH
Confidence 9999999 89999999999999998876543 2 2469999999999999888777766332 23356665
Q ss_pred HHHHHHHHHHHhhhhcCCChhhhhhHhhhhhcccCCchhhHHHHHHHhhhhhhHHHHHHhhhhhhccccchHHHHHHhhH
Q 011129 368 FQKAILSTALSFIISNFGPVDTWAHLGAAFTDLGGNTSTWFLLTFALTTGAIGVCSVTAGLMHLRAWRSESLAAASSLAI 447 (493)
Q Consensus 368 ~~~~li~l~l~~i~~~~~~Is~~AHLgGll~GLlg~~~~~~~i~f~l~aG~vg~~~~l~~~~~~~~w~~~~l~a~~~~~~ 447 (493)
..+++++ .+....|+.++++|++|+++|+ -+.|+.+ |..+. .++-.....++++
T Consensus 162 ~Pw~lLi----~~~~lvp~aSFlghl~GllvG~--------ay~~~~f-~lip~-----------~~~~~~v~~~~~~-- 215 (258)
T KOG2632|consen 162 APWALLI----ATQILVPQASFLGHLCGLLVGY--------AYAFSSF-GLIPG-----------IRNYRAVTEAAWS-- 215 (258)
T ss_pred HHHHHHH----HHHHHccCchHHHHHHHHHHHH--------HHHHHhh-ccCCc-----------chhHHHhhhhhhh--
Confidence 5554443 3333468999999999999994 3444333 33321 1111222233332
Q ss_pred hhhhcccceeeccccCCccchhhHHH
Q 011129 448 LSCFVCKEIILGGHRGKRLQTLEAFA 473 (493)
Q Consensus 448 ls~~ack~i~l~~~r~~~l~~~e~~~ 473 (493)
..-++|-++.++. +..+.++.|+.+
T Consensus 216 ~~~~~~~~~~~~~-~~~~~~v~~~~~ 240 (258)
T KOG2632|consen 216 LLRLAPWIQDLGS-NSGRGIVFPGLT 240 (258)
T ss_pred hhhcCCcHHHhcc-ccCCceeccCcC
Confidence 1225777778764 224777777643
No 9
>PF12122 DUF3582: Protein of unknown function (DUF3582); InterPro: IPR022732 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. Proteolytic enzymes that exploit serine in their catalytic activity are ubiquitous, being found in viruses, bacteria and eukaryotes []. They include a wide range of peptidase activity, including exopeptidase, endopeptidase, oligopeptidase and omega-peptidase activity. Over 20 families (denoted S1 - S66) of serine protease have been identified, these being grouped into clans on the basis of structural similarity and other functional evidence []. Structures are known for members of the clans and the structures indicate that some appear to be totally unrelated, suggesting different evolutionary origins for the serine peptidases []. Not withstanding their different evolutionary origins, there are similarities in the reaction mechanisms of several peptidases. Chymotrypsin, subtilisin and carboxypeptidase C have a catalytic triad of serine, aspartate and histidine in common: serine acts as a nucleophile, aspartate as an electrophile, and histidine as a base []. The geometric orientations of the catalytic residues are similar between families, despite different protein folds []. The linear arrangements of the catalytic residues commonly reflect clan relationships. For example the catalytic triad in the chymotrypsin clan (PA) is ordered HDS, but is ordered DHS in the subtilisin clan (SB) and SDH in the carboxypeptidase clan (SC) [, ]. This entry represents the N-terminal domain of membrane-bound serine endopeptidases belonging to MEROPS peptidase family S54 (rhomboid-1, clan ST). This domain contains a conserved ASW sequence motif and a single completely conserved residue F that may be functionally important. The tertiary structure of the GlpG protein from Escherichia coli has been determined []. The GlpG protein has six transmembrane domains (other members of the family are predicted to have seven), with the N- and C-terminal ends anchored in the cytoplasm. One transmembrane domain is shorter than the rest, creating an internal, aqueous cavity just below the membrane surface and it is here were proteolysis occurs. There is also a membrane-embedded loop between the first and second transmembrane domains which is postulated to act as a gate controlling substrate access to the active site. No other family of serine peptidases is known to have active site residues within transmembrane domains (although transmembrane active sites are known for aspartic peptidase and metallopeptidases), and the GlpG protein has the type structure for clan ST.; GO: 0004252 serine-type endopeptidase activity, 0016021 integral to membrane; PDB: 3UBB_A 3B45_A 3B44_A 2NRF_A 3TXT_A 2O7L_A 2XTU_A 2IRV_A 2XOW_A 2XTV_A ....
Probab=99.60 E-value=5.4e-16 Score=133.83 Aligned_cols=86 Identities=12% Similarity=0.130 Sum_probs=48.4
Q ss_pred hhhhccCCChhHHHHHHHHHhhcCCcceeecCccc-------hhhhHHHHHhhhh--hccCCCCCcchhhHhhhcccCCc
Q 011129 137 HSRSGEINAKTELDSLDAYLGKLNTDAKFSTDQTT-------ERNLVAAQLSISK--SSKRGYMGKLKGYRELRNKDGVR 207 (493)
Q Consensus 137 m~~~~~~~~~~~aqaf~dYl~~~~i~~~v~~~~~~-------de~~~~~~~~e~~--~~~p~~~~~~~rY~~as~~~g~~ 207 (493)
|+++++++|||+||+|+|||+++||++++++++++ ||++++++++|++ ++||+|+ ||++++|+.|++
T Consensus 1 M~~l~~~~n~r~AqaF~DYl~sqgI~~~i~~~~~~~~~lwl~de~~~~~a~~el~~Fl~nP~~~----rYqaASWq~g~~ 76 (101)
T PF12122_consen 1 MIRLGSLNNPRAAQAFIDYLASQGIELQIEPEGQGQFALWLHDEEHLEQAEQELEEFLQNPNDP----RYQAASWQTGST 76 (101)
T ss_dssp -EEEEEESSHHHHHHHHHHHHHTT--EEEE-SSSE--EEEES-GGGHHHHHHHHHHHHHS-SS-----------------
T ss_pred CeEEEecCCHHHHHHHHHHHHHCCCeEEEEECCCCceEEEEeCHHHHHHHHHHHHHHHHCCCCH----HHHHHHHhcCCc
Confidence 89999999999999999999999999999987665 8999999999999 9999999 999999999986
Q ss_pred c----ccchHHhhhcccccchHHH
Q 011129 208 S----LERDLALQRTEETSNLYLI 227 (493)
Q Consensus 208 ~----~~~~~~~~~~~~~~~ppvT 227 (493)
+ ++.+.++.+++...+ |+|
T Consensus 77 ~~~~~y~~~s~~~~l~~~aG-plT 99 (101)
T PF12122_consen 77 RTQFSYQSPSLLQQLRAQAG-PLT 99 (101)
T ss_dssp ------------------S--HHH
T ss_pred cCccCcCCchHHHHHHHcCC-Cee
Confidence 5 455666777765554 666
No 10
>KOG2980 consensus Integral membrane protease of the rhomboid family involved in different forms of regulated intramembrane proteolysis [Signal transduction mechanisms]
Probab=98.34 E-value=3.6e-07 Score=92.09 Aligned_cols=167 Identities=18% Similarity=0.252 Sum_probs=109.7
Q ss_pred HHHHHHHHHHHHHHHHHhcCCCCccccchhhhhhhhcchhhhhhcCccceeeecccccCCHHHHHHHHHHHHHHHH-HHH
Q 011129 225 YLIILVSIDVAVFLFEIASPIRNSEFGFFSLPLLYGAKINELILVGEWWRLVTPMFLHSGLFHVALSCWALLTFGP-QVC 303 (493)
Q Consensus 225 pvT~Liai~v~VFll~~~~~~~~~~~~~~~~p~~~Ga~~~~~i~~gq~WRl~Ts~FlH~s~~HLlfNml~L~~~G~-~lE 303 (493)
.++.++++|+++|.++.+....... .+ |- ..+. +..---|-++++.|.|.+.+|+..||+.++.+.. .+-
T Consensus 117 ~v~~ll~~n~~vf~lWrv~~~~~~~-----~~--~m-ls~~-~~~t~~w~i~~s~Fsh~~a~h~g~~~~~~~~y~~~a~~ 187 (310)
T KOG2980|consen 117 VVFGLLIANAFVFTLWRVPQKQFTM-----IP--WM-LSRN-AYKTGCWKIILSTFSHYSALHLGPNMLVLKSYLAGALK 187 (310)
T ss_pred chhHHHHHHHHHHHHHHhcchhhhh-----hh--HH-hhcc-cccccceeEEeehhcchhHhhhcHHHHHHHHHhccccc
Confidence 3448999999999988765432111 11 10 0111 1223356699999999999999999998887776 888
Q ss_pred HhcCChhHHHHHHHHHHHHHHhhhhc-CC----CceeccchHHHHHHHHHHHHHhcccchhhhhhhHHHHHHHHHHHH--
Q 011129 304 KSYGPFTFFLIYTLGGISGNLTSFLH-TP----EPTVGGTGPVFAIIGAWLIYQFQNKDLIAKDVSERMFQKAILSTA-- 376 (493)
Q Consensus 304 ~~lGs~r~l~lyLlsgi~g~l~~~l~-~~----~~~vGaSGaVfgLlga~~~~~~~~~~~~~~~~~~~l~~~~li~l~-- 376 (493)
-.+|...+..+|+.++..|......- .+ .+.+|+||++|++.++.....++....+....+.+....+.+-.+
T Consensus 188 ~~~~~~~~~AlylSa~~~~~~i~~~~~v~~~~~gp~LGAsGav~ai~a~~~~lfP~~~~~i~f~~~v~~ga~~~~~~i~~ 267 (310)
T KOG2980|consen 188 GSLGFSSFFALYLSAGVKGLFISVKDKVPTSWAGPSLGASGAVYAILALDCTLFPKTTLYILFVFPVPAGAGLAFKAIAA 267 (310)
T ss_pred CCcchhhcccceeccccccceeEeeccccccccccccccchHHHHHHHHHhhcCcCcceeEEEeecccccchhHHHHHHH
Confidence 88999999999996666665554332 11 368999999999999999888876665544333333222222111
Q ss_pred HHhhhh--cCCChhhhhhHhhhhhcc
Q 011129 377 LSFIIS--NFGPVDTWAHLGAAFTDL 400 (493)
Q Consensus 377 l~~i~~--~~~~Is~~AHLgGll~GL 400 (493)
+++... ....-++.||++|-+.|.
T Consensus 268 ~~~a~~~l~~~~~n~~Ah~~gsl~Gv 293 (310)
T KOG2980|consen 268 YDFAGLILGWGFFNHAAHLSGSLFGV 293 (310)
T ss_pred hhhcceeeccccchhHhhhcchHHHH
Confidence 122111 123467779999999884
No 11
>PF04511 DER1: Der1-like family; InterPro: IPR007599 The endoplasmic reticulum (ER) of the yeast Saccharomyces cerevisiae (Baker's yeast) contains a proteolytic system able to selectively degrade misfolded lumenal secretory proteins. For examination of the components involved in this degradation process, mutants were isolated. They could be divided into four complementation groups. The mutations led to stabilisation of two different substrates for this process, and the classes were called der for degradation in the ER. DER1 was cloned by complementation of the der1-2 mutation. The DER1 gene codes for a novel, hydrophobic protein that is localized to the ER. Deletion of DER1 abolished degradation of the substrate proteins, suggesting that the function of the Der1 protein may be specifically required for the degradation process associated with the ER []. Interestingly this family seems distantly related to the Rhomboid family of membrane peptidases. This family may also mediate degradation of misfolded proteins.
Probab=98.20 E-value=1.2e-05 Score=77.41 Aligned_cols=161 Identities=12% Similarity=0.100 Sum_probs=93.0
Q ss_pred hHHH-HHHHHHHHHHHHHHhcCCCCccccchhhhhhhhcchhhhhhcCccceeeecccccCCH-HHHHHHHHHHHHHHHH
Q 011129 224 LYLI-ILVSIDVAVFLFEIASPIRNSEFGFFSLPLLYGAKINELILVGEWWRLVTPMFLHSGL-FHVALSCWALLTFGPQ 301 (493)
Q Consensus 224 ppvT-~Liai~v~VFll~~~~~~~~~~~~~~~~p~~~Ga~~~~~i~~gq~WRl~Ts~FlH~s~-~HLlfNml~L~~~G~~ 301 (493)
||+| ..++.++++.++....-.. |...--.++....++|+||++|+.|.-.+. ++.++|++.++..+..
T Consensus 2 PpVTR~~~~~~~~~s~l~~~~~~~---------~~~l~~~~~~v~~~~q~WRl~Tsff~~g~~~~~~l~~~~~l~~~s~~ 72 (197)
T PF04511_consen 2 PPVTRYWLISTVALSLLVSFGIIS---------PYYLYFDWELVFKKFQIWRLFTSFFYFGPFSLNFLFNLYFLYQYSSS 72 (197)
T ss_pred ChhHHHHHHHHHHHHHHHHCCCCC---------HHHeeECcHHHhhhcCceeeEEEEEEEcCCCHHHHHHHHHHHHHhhH
Confidence 7899 7777777776665432111 111111222334679999999999986544 7999999999999999
Q ss_pred HHHhc-C-C-hhHHHHHHHHHHHHHHhhhhcCCC----ceeccchHHHHHHHHHHH-HHhcccchhh--hhhhHHHHHHH
Q 011129 302 VCKSY-G-P-FTFFLIYTLGGISGNLTSFLHTPE----PTVGGTGPVFAIIGAWLI-YQFQNKDLIA--KDVSERMFQKA 371 (493)
Q Consensus 302 lE~~l-G-s-~r~l~lyLlsgi~g~l~~~l~~~~----~~vGaSGaVfgLlga~~~-~~~~~~~~~~--~~~~~~l~~~~ 371 (493)
+|+.. + + ..++...+.+++.-.+++.+..+. +.. +.++...+.+.+. ..+....... ..++.+.+.+
T Consensus 73 LE~~~f~~~~ady~~~ll~~~~~i~~~~~~~~~~~~~~~~l--~~~l~~~l~Y~wsr~np~~~v~~~g~~~i~a~ylP~- 149 (197)
T PF04511_consen 73 LEEGHFQGRSADYLWFLLFGASLILILSLLIGPYFFNIPFL--GSSLSFALTYIWSRKNPNAQVSFFGLFTIKAKYLPW- 149 (197)
T ss_pred hccCCCCCCHHHHHHHHHHHHHHHHHHHHhhccchhHHHHH--HHHHHHHHHHHHHHhCcccceeeEEEEEEChhhHHH-
Confidence 99983 2 2 467776666666666666554321 112 2333333344443 2233322221 2345454443
Q ss_pred HHHHHHHhhhhcCCChhhhhhHhhhhhcc
Q 011129 372 ILSTALSFIISNFGPVDTWAHLGAAFTDL 400 (493)
Q Consensus 372 li~l~l~~i~~~~~~Is~~AHLgGll~GL 400 (493)
+.+++.++.+ +-+...++-|+++|-
T Consensus 150 -~~~~~~~l~~---~~~~~~~l~Gi~~Gh 174 (197)
T PF04511_consen 150 -VLLAFSLLFG---GSSPIPDLLGILVGH 174 (197)
T ss_pred -HHHHHHHHhC---CCcHHHHHHHHHHHH
Confidence 3334444432 224557888888884
No 12
>PF08551 DUF1751: Eukaryotic integral membrane protein (DUF1751); InterPro: IPR013861 This entry is found in eukaryotic integral membrane proteins. Q12239 from SWISSPROT, a Saccharomyces cerevisiae (Baker's yeast) protein, has been shown to localise COP II vesicles [].
Probab=97.85 E-value=1.2e-05 Score=69.44 Aligned_cols=58 Identities=22% Similarity=0.332 Sum_probs=54.4
Q ss_pred ccceeeecccccCCHHHHHHHHHHHHHHHHHHHHhcCChhHHHHHHHHHHHHHHhhhh
Q 011129 271 EWWRLVTPMFLHSGLFHVALSCWALLTFGPQVCKSYGPFTFFLIYTLGGISGNLTSFL 328 (493)
Q Consensus 271 q~WRl~Ts~FlH~s~~HLlfNml~L~~~G~~lE~~lGs~r~l~lyLlsgi~g~l~~~l 328 (493)
.+|+++|+.|++.++..+++|.+.++..|+.+|+.+|+++++-..++.++.+|++..+
T Consensus 7 ~pWtl~T~~fve~~i~~~l~~~~~l~~~g~~lE~~WGs~E~lkFi~vv~~~tnl~~~~ 64 (99)
T PF08551_consen 7 YPWTLFTAGFVETNIIGLLFSLLTLFYGGRYLEPIWGSREFLKFILVVNVITNLLTFL 64 (99)
T ss_pred ehHHHHHHHHHHhHHHHHHHHHHHHHHhhHHHHHhcChHHHHHHHHHHHHHhHHHHHH
Confidence 6899999999999999999999999999999999999999999999999888887654
No 13
>KOG0858 consensus Predicted membrane protein [Function unknown]
Probab=97.43 E-value=0.00046 Score=67.94 Aligned_cols=97 Identities=14% Similarity=0.170 Sum_probs=68.8
Q ss_pred cchHHH-HHHHHHHHHHHHHHhcCCCCccccchhhhhhhhcchhhhhhcCccceeeecccccCC-HHHHHHHHHHHHHHH
Q 011129 222 SNLYLI-ILVSIDVAVFLFEIASPIRNSEFGFFSLPLLYGAKINELILVGEWWRLVTPMFLHSG-LFHVALSCWALLTFG 299 (493)
Q Consensus 222 ~~ppvT-~Liai~v~VFll~~~~~~~~~~~~~~~~p~~~Ga~~~~~i~~gq~WRl~Ts~FlH~s-~~HLlfNml~L~~~G 299 (493)
..||+| .....|++.=++....-.. |...--.++..+++.|+||++|+.+.-.. -+|.++||+.++-..
T Consensus 11 ~iPpVTR~~~~~~v~tt~~~~l~lIs---------P~~l~~~p~Lv~kk~QiWRliTs~lyfg~~gf~fl~n~~FlyrY~ 81 (239)
T KOG0858|consen 11 QIPPVTRYYTTACVVTTLLVRLDLIS---------PFQLYLNPELVFKKFQIWRLITSFLYFGPFGFDFLMNLYFLYRYS 81 (239)
T ss_pred cCChHHHHHHHHHHHHHHHHhhcccC---------chheEecHHHHHhHhHHHHhhhhhheeccccHHHHHHHHHHHHHH
Confidence 457999 7777787776654332211 11111122234579999999999998865 699999999999999
Q ss_pred HHHHHhcC---ChhHHHHHHHHHHHHHHhhh
Q 011129 300 PQVCKSYG---PFTFFLIYTLGGISGNLTSF 327 (493)
Q Consensus 300 ~~lE~~lG---s~r~l~lyLlsgi~g~l~~~ 327 (493)
..+|+-.= +..|+..++.++++-.+..+
T Consensus 82 ~~LE~g~f~~rtadf~~mllf~~~l~~~~~~ 112 (239)
T KOG0858|consen 82 SMLEEGSFRGRTADFLYMLLFGAVLLTLTGL 112 (239)
T ss_pred HHHhcCCCCCchhHHHHHHHHHHHHHHHHHH
Confidence 99998642 37788888888777765555
No 14
>KOG4463 consensus Uncharacterized conserved protein [Function unknown]
Probab=95.22 E-value=0.02 Score=57.22 Aligned_cols=59 Identities=17% Similarity=0.303 Sum_probs=50.8
Q ss_pred hcCccceeeecccccCCHHHHHHHHHHHHHHHHHHHHhcCChhHHHHHHHHHHHHHHhhh
Q 011129 268 LVGEWWRLVTPMFLHSGLFHVALSCWALLTFGPQVCKSYGPFTFFLIYTLGGISGNLTSF 327 (493)
Q Consensus 268 ~~gq~WRl~Ts~FlH~s~~HLlfNml~L~~~G~~lE~~lGs~r~l~lyLlsgi~g~l~~~ 327 (493)
...|+||++..-|.-.+-.-+++-++.|+++ +.+||.+|+.||..+-+.+++.+-++..
T Consensus 47 ~y~qywrlL~~qF~~~n~~e~~~~l~I~Y~f-R~~ERlLGShky~~fiv~s~~~~~l~~~ 105 (323)
T KOG4463|consen 47 KYFQYWRLLMSQFAFSNTPELMFGLYILYYF-RVFERLLGSHKYSVFIVFSGTVSLLLEV 105 (323)
T ss_pred HHHHHHHHHHHHHHhcCChHHHHHHHHHHHH-HHHHHHhccccceeehhHHHHHHHHHHH
Confidence 4589999999999999999999987777775 8899999999999888888888766643
No 15
>COG5291 Predicted membrane protein [Function unknown]
Probab=93.61 E-value=0.1 Score=51.93 Aligned_cols=48 Identities=13% Similarity=0.341 Sum_probs=38.1
Q ss_pred hhcCccceeeecccccCC-HHHHHHHHHHHHHHHHHHHHh-cCCh--hHHHH
Q 011129 267 ILVGEWWRLVTPMFLHSG-LFHVALSCWALLTFGPQVCKS-YGPF--TFFLI 314 (493)
Q Consensus 267 i~~gq~WRl~Ts~FlH~s-~~HLlfNml~L~~~G~~lE~~-lGs~--r~l~l 314 (493)
+++-||||+||+..+-.+ -+-.++|++.++--...+|+- +|+. .++..
T Consensus 55 ~k~~qiwRlfTs~~~~~~~~~d~~M~vyf~Y~yS~~LE~g~f~~~lv~Y~~y 106 (313)
T COG5291 55 LKRLQIWRLFTSFLYFGKPTLDMFMHVYFLYRYSRMLEEGCFNTSLVEYFWY 106 (313)
T ss_pred HHHHHHHHHHHHHHhhcCcchhHHHHHHHHHHHHHHHhccccCccHHHHHHH
Confidence 468899999998777765 578899999999999999985 4555 55433
No 16
>KOG2890 consensus Predicted membrane protein [Function unknown]
Probab=93.57 E-value=0.052 Score=55.46 Aligned_cols=85 Identities=21% Similarity=0.302 Sum_probs=66.0
Q ss_pred CccceeeecccccCCHHHHHHHHHHHHHHHHHHHHhcCChhHHHHHHHHHHHHHHhh--------hhcCC-----Cceec
Q 011129 270 GEWWRLVTPMFLHSGLFHVALSCWALLTFGPQVCKSYGPFTFFLIYTLGGISGNLTS--------FLHTP-----EPTVG 336 (493)
Q Consensus 270 gq~WRl~Ts~FlH~s~~HLlfNml~L~~~G~~lE~~lGs~r~l~lyLlsgi~g~l~~--------~l~~~-----~~~vG 336 (493)
...|+++|+.|+-.+++-.++|++.+.+-|..+|+.+|+..++..|.+.-..-+++. .++.. .+..|
T Consensus 65 ~~~WtliTs~fie~~vw~V~~sv~~L~v~G~~lEp~Wg~~e~lkff~ivn~~~~l~v~v~~~l~Y~it~n~v~L~~~i~G 144 (326)
T KOG2890|consen 65 FFPWTLITSGFIELNVWDVLVSVLTLSVGGKFLEPNWGSLELLKFFAIVNGSTTLVVLVPALLLYMITDNHVYLYIPIHG 144 (326)
T ss_pred hhhHHHHhcchhhhhHHHHHHHHHheeecceeeccCCCCHHHHHHHHHhhchhHHHHHHHHHHHHHHhcCceEEEEEecc
Confidence 478999999999999999999999999999999999999999987776544433332 11222 24679
Q ss_pred cchHHHHHHHHHHHHHhc
Q 011129 337 GTGPVFAIIGAWLIYQFQ 354 (493)
Q Consensus 337 aSGaVfgLlga~~~~~~~ 354 (493)
..|.+-|++.++=-..+.
T Consensus 145 ~~gilaGilVa~kQllpd 162 (326)
T KOG2890|consen 145 TTGILAGILVAWKQLLPD 162 (326)
T ss_pred chHHHHHHHHHHHHHcCc
Confidence 999999988776544443
No 17
>COG0705 Membrane associated serine protease [Amino acid transport and metabolism]
Probab=58.97 E-value=6 Score=38.48 Aligned_cols=74 Identities=20% Similarity=0.113 Sum_probs=57.1
Q ss_pred hcCccceeeecccccCCHHHHHHHHHHHHHHHHHHHHhcCChhHHHHHHHHHHHHHHhhhhcCCCceeccchHHHHHHHH
Q 011129 268 LVGEWWRLVTPMFLHSGLFHVALSCWALLTFGPQVCKSYGPFTFFLIYTLGGISGNLTSFLHTPEPTVGGTGPVFAIIGA 347 (493)
Q Consensus 268 ~~gq~WRl~Ts~FlH~s~~HLlfNml~L~~~G~~lE~~lGs~r~l~lyLlsgi~g~l~~~l~~~~~~vGaSGaVfgLlga 347 (493)
..|++|+++++.++|....|...+... ..+.+.+++...++.+++....++.+.++.++-+.|+++.
T Consensus 136 ASG~i~gllga~~~~~~~~~~~~~~~~-------------~~~~~~~~i~~~~~~~~~~~~~~~~~~va~~aHl~G~i~G 202 (228)
T COG0705 136 ASGAIFGLLGAYFLLFPFARILLLFLS-------------LPRPALILILIWLLYSLFSGAGSFGPSVAWSAHLGGLIGG 202 (228)
T ss_pred hhHHHHHHHHHHHHHccccchhhhhcc-------------CchhHHHHHHHHHHHHHHHHhcCCchHHHHHHHHHHHHHH
Confidence 567888999999999888888777665 5566677888888888888777765678889999999976
Q ss_pred HHHHHhc
Q 011129 348 WLIYQFQ 354 (493)
Q Consensus 348 ~~~~~~~ 354 (493)
.+.....
T Consensus 203 ~l~~~~~ 209 (228)
T COG0705 203 LLLAALL 209 (228)
T ss_pred HHHHHHH
Confidence 6654433
No 18
>PF09527 ATPase_gene1: Putative F0F1-ATPase subunit (ATPase_gene1)
Probab=44.99 E-value=92 Score=23.51 Aligned_cols=42 Identities=26% Similarity=0.241 Sum_probs=31.7
Q ss_pred HHHHHHHHHHHHHHHHHHHhcCC-hhHHHHHHHHHHHHHHhhh
Q 011129 286 FHVALSCWALLTFGPQVCKSYGP-FTFFLIYTLGGISGNLTSF 327 (493)
Q Consensus 286 ~HLlfNml~L~~~G~~lE~~lGs-~r~l~lyLlsgi~g~l~~~ 327 (493)
..++.+++.-.++|..+++.+|+ ..+.++.++-|+.+++.+.
T Consensus 8 ~~~~~~i~~g~~~G~~lD~~~~t~p~~~~~g~llG~~~g~~~~ 50 (55)
T PF09527_consen 8 FTMAAPILVGFFLGYWLDKWFGTSPWFTLIGLLLGIAAGFYNV 50 (55)
T ss_pred HHHHHHHHHHHHHHHHHHHHcCCChHHHHHHHHHHHHHHHHHH
Confidence 35677888889999999999999 5555666677777766543
No 19
>PRK09765 PTS system 2-O-a-mannosyl-D-glycerate specific transporter subunit IIABC; Provisional
Probab=44.16 E-value=4.8e+02 Score=29.85 Aligned_cols=23 Identities=13% Similarity=0.104 Sum_probs=18.8
Q ss_pred HHHHHHHHHhhcCCcceeecCcc
Q 011129 148 ELDSLDAYLGKLNTDAKFSTDQT 170 (493)
Q Consensus 148 ~aqaf~dYl~~~~i~~~v~~~~~ 170 (493)
+|+++.+-.+++|.+.++|.++.
T Consensus 182 Aae~L~~aA~~~g~~i~vE~~g~ 204 (631)
T PRK09765 182 AAEYLEKAGRKLGVNVYVEKQGA 204 (631)
T ss_pred HHHHHHHHHHHCCCeEEEEecCC
Confidence 57889999999999999886544
No 20
>PRK10263 DNA translocase FtsK; Provisional
Probab=42.26 E-value=57 Score=40.20 Aligned_cols=14 Identities=21% Similarity=0.453 Sum_probs=7.3
Q ss_pred HHHHHHHHHHHHHH
Q 011129 228 ILVSIDVAVFLFEI 241 (493)
Q Consensus 228 ~Liai~v~VFll~~ 241 (493)
.++++.+.+|++..
T Consensus 27 gIlLlllAlfL~lA 40 (1355)
T PRK10263 27 LILIVLFAVWLMAA 40 (1355)
T ss_pred HHHHHHHHHHHHHH
Confidence 45555555565543
No 21
>PF09413 DUF2007: Domain of unknown function (DUF2007); InterPro: IPR018551 This is a family of proteins with unknown function. ; PDB: 2HFV_A.
Probab=30.96 E-value=57 Score=25.34 Aligned_cols=30 Identities=10% Similarity=0.051 Sum_probs=20.1
Q ss_pred hhccCCChhHHHHHHHHHhhcCCcceeecC
Q 011129 139 RSGEINAKTELDSLDAYLGKLNTDAKFSTD 168 (493)
Q Consensus 139 ~~~~~~~~~~aqaf~dYl~~~~i~~~v~~~ 168 (493)
++...+|+-.|+...+.|+..||++.++.+
T Consensus 2 ~l~~~~~~~ea~~i~~~L~~~gI~~~v~~~ 31 (67)
T PF09413_consen 2 KLYTAGDPIEAELIKGLLEENGIPAFVKNE 31 (67)
T ss_dssp EEEEE--HHHHHHHHHHHHHTT--EE--S-
T ss_pred EEEEcCCHHHHHHHHHHHHhCCCcEEEECC
Confidence 356678999999999999999999999853
No 22
>PF11823 DUF3343: Protein of unknown function (DUF3343); InterPro: IPR021778 This family of proteins are functionally uncharacterised. This protein is found in bacteria and archaea. Proteins in this family are typically between 78 to 102 amino acids in length.
Probab=29.55 E-value=88 Score=25.03 Aligned_cols=45 Identities=9% Similarity=-0.004 Sum_probs=34.7
Q ss_pred hccCCChhHHHHHHHHHhhcCCcceeecCccc-----------hhhhHHHHHhhhh
Q 011129 140 SGEINAKTELDSLDAYLGKLNTDAKFSTDQTT-----------ERNLVAAQLSISK 184 (493)
Q Consensus 140 ~~~~~~~~~aqaf~dYl~~~~i~~~v~~~~~~-----------de~~~~~~~~e~~ 184 (493)
+..|++...|-++.+.|++.|++.++.|-..+ ++++.+.++..++
T Consensus 5 ~i~F~st~~a~~~ek~lk~~gi~~~liP~P~~i~~~CG~al~~~~~d~~~i~~~l~ 60 (73)
T PF11823_consen 5 LITFPSTHDAMKAEKLLKKNGIPVRLIPTPREISAGCGLALRFEPEDLEKIKEILE 60 (73)
T ss_pred EEEECCHHHHHHHHHHHHHCCCcEEEeCCChhccCCCCEEEEEChhhHHHHHHHHH
Confidence 56789999999999999999999999975544 4444555555554
No 23
>PF10066 DUF2304: Uncharacterized conserved protein (DUF2304); InterPro: IPR019277 This entry represents hypothetical archaeal and bacterial proteins that have no known function.
Probab=28.80 E-value=1.6e+02 Score=25.85 Aligned_cols=20 Identities=25% Similarity=0.019 Sum_probs=14.5
Q ss_pred hhcCCC-hhhhhhHhhhhhcc
Q 011129 381 ISNFGP-VDTWAHLGAAFTDL 400 (493)
Q Consensus 381 ~~~~~~-Is~~AHLgGll~GL 400 (493)
...+|+ .+..||+-|+-.|.
T Consensus 46 ~~ifP~~~~~vA~~lGi~~~~ 66 (115)
T PF10066_consen 46 LSIFPNILDWVAKLLGIGRPP 66 (115)
T ss_pred HHhhhhHHHHHHHHHCCCchh
Confidence 355677 56779999988773
No 24
>KOG3966 consensus p53-mediated apoptosis protein EI24/PIG8 [Signal transduction mechanisms; Defense mechanisms]
Probab=27.86 E-value=5.7e+02 Score=26.50 Aligned_cols=51 Identities=16% Similarity=0.106 Sum_probs=29.0
Q ss_pred HHHHHHHHhcCChhHHHHHHHHHHHHHHh-----hhhc-----CCCceeccchHHHHHHHH
Q 011129 297 TFGPQVCKSYGPFTFFLIYTLGGISGNLT-----SFLH-----TPEPTVGGTGPVFAIIGA 347 (493)
Q Consensus 297 ~~G~~lE~~lGs~r~l~lyLlsgi~g~l~-----~~l~-----~~~~~vGaSGaVfgLlga 347 (493)
++++.+...+|-...+-+|++|-+..++- ...+ .|.+..|.|-.+-+.+..
T Consensus 136 wl~~~ls~lfg~iwVlPiF~lSkiV~alWF~DIa~aa~rv~k~~P~p~p~~Sk~~Ad~Lfs 196 (360)
T KOG3966|consen 136 WLHPILSLLFGYIWVLPIFFLSKIVQALWFSDIAGAAMRVLKLPPPPVPPFSKMLADTLFS 196 (360)
T ss_pred hhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCCCHHHHHHHHHHH
Confidence 34555555566666666777766654432 1111 234678888777666553
No 25
>COG1823 Predicted Na+/dicarboxylate symporter [General function prediction only]
Probab=25.34 E-value=8.3e+02 Score=26.59 Aligned_cols=47 Identities=9% Similarity=0.066 Sum_probs=27.7
Q ss_pred HHHHHHHHHHHHHHHHHHHHhcC-----ChhHHHHHHHHHHHHHHhhhhcCC
Q 011129 285 LFHVALSCWALLTFGPQVCKSYG-----PFTFFLIYTLGGISGNLTSFLHTP 331 (493)
Q Consensus 285 ~~HLlfNml~L~~~G~~lE~~lG-----s~r~l~lyLlsgi~g~l~~~l~~~ 331 (493)
-.|.+.|+..+..+-..+-+..- +.|.+.-.+++.++|-.+|+.+.+
T Consensus 3 ~~~tl~ni~if~~l~~~l~~~~~k~~slskrV~~aL~lG~vfG~~Lq~~~g~ 54 (458)
T COG1823 3 NFPTLANIAIFVVLLLALAQMRRKQISLSKRVLIALVLGVVFGLALQYIYGT 54 (458)
T ss_pred cHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcC
Confidence 35666776665555443333211 344555566777788888888765
No 26
>COG1030 NfeD Membrane-bound serine protease (ClpP class) [Posttranslational modification, protein turnover, chaperones]
Probab=24.05 E-value=8.6e+02 Score=26.73 Aligned_cols=19 Identities=32% Similarity=0.618 Sum_probs=11.9
Q ss_pred eeccchHHHHHHHHHHHHH
Q 011129 334 TVGGTGPVFAIIGAWLIYQ 352 (493)
Q Consensus 334 ~vGaSGaVfgLlga~~~~~ 352 (493)
.+|.+|.+.-++|......
T Consensus 306 vigl~Gii~~iiG~~~L~~ 324 (436)
T COG1030 306 VIGLLGIILFIIGLLLLFP 324 (436)
T ss_pred HHHHHHHHHHHHhhhhccC
Confidence 5666777777766665443
No 27
>TIGR00834 ae anion exchange protein. They preferentially catalyze anion exchange (antiport) reactions, typically acting as HCO3-:Cl- antiporters, but also transporting a range of other inorganic and organic anions. Additionally, renal Na+:HCO3- cotransporters have been found to be members of the AE family. They catalyze the reabsorption of HCO3- in the renal proximal tubule.
Probab=22.05 E-value=6e+02 Score=30.55 Aligned_cols=63 Identities=16% Similarity=0.146 Sum_probs=44.3
Q ss_pred CHHHHHHHHHHHHHHHHHHHHhcCChhHHHHHHHHHHHHHHhhhhcCCCc--eeccchHHHHHHH
Q 011129 284 GLFHVALSCWALLTFGPQVCKSYGPFTFFLIYTLGGISGNLTSFLHTPEP--TVGGTGPVFAIIG 346 (493)
Q Consensus 284 s~~HLlfNml~L~~~G~~lE~~lGs~r~l~lyLlsgi~g~l~~~l~~~~~--~vGaSGaVfgLlg 346 (493)
-+.=.+.|+.--..||..+++.-+..-=..=.++|..+++++..++.++| -+|.+|.+.-...
T Consensus 375 ~ifiyFA~L~PaIaFG~ll~~~T~g~~gv~E~Llstai~Giifslf~GQPL~IlG~TGPilvF~~ 439 (900)
T TIGR00834 375 VIFIYFAALSPAITFGGLLGEKTRNMMGVSELLISTAVQGVLFALLAAQPLLVVGFSGPLLVFEE 439 (900)
T ss_pred HHHHHHHHhhHHhhHHHHHHHhhCCcchHHHHHHHHHHHHHHHhhhcCCceEEecCcccHHHHHH
Confidence 34556778888889999998886655444555666666777777777754 6799997665544
No 28
>PF12761 End3: Actin cytoskeleton-regulatory complex protein END3
Probab=21.17 E-value=1.8e+02 Score=28.41 Aligned_cols=44 Identities=23% Similarity=0.249 Sum_probs=29.4
Q ss_pred HHHHHHHHHHhhhccccCCC-CCCCchhhhhhhhhhccCCChhHHHHHHHHHhhc
Q 011129 106 CQIRILESYLAKLKDDSIQN-SSESSGEIEELHSRSGEINAKTELDSLDAYLGKL 159 (493)
Q Consensus 106 ~~~~~~d~~~~kl~~~~~~~-s~~~~~~~~~~m~~~~~~~~~~~aqaf~dYl~~~ 159 (493)
++|..||.-+.+.+...... +..+++.. |+ .+..+++-||-+.+
T Consensus 103 rELa~Le~~l~~~~~~~~~~~~~~~~~~~---lv-------k~e~EqLL~YK~~q 147 (195)
T PF12761_consen 103 RELAELEEKLSKVEQAAESRRSDTDSKPA---LV-------KREFEQLLDYKERQ 147 (195)
T ss_pred HHHHHHHHHHHHHHHHHHhcccCCcchHH---HH-------HHHHHHHHHHHHHH
Confidence 58899999999999887763 22222221 22 25778899996665
No 29
>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=20.58 E-value=49 Score=32.49 Aligned_cols=33 Identities=12% Similarity=0.169 Sum_probs=21.9
Q ss_pred cchHHhhhcccccchHHH-HHHHHHHHHHHHHHh
Q 011129 210 ERDLALQRTEETSNLYLI-ILVSIDVAVFLFEIA 242 (493)
Q Consensus 210 ~~~~~~~~~~~~~~ppvT-~Liai~v~VFll~~~ 242 (493)
...+.+....+....|.| +++++|+++|++..+
T Consensus 138 HEEQiWSDKIRr~STwgT~~lmgvNvllFl~~~~ 171 (207)
T PF05546_consen 138 HEEQIWSDKIRRASTWGTWGLMGVNVLLFLVAQL 171 (207)
T ss_pred HHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHH
Confidence 334444333334445889 999999999987644
No 30
>PF06123 CreD: Inner membrane protein CreD; InterPro: IPR010364 This family consists of several bacterial CreD or Cet inner membrane proteins. Dominant mutations of the cet gene of Escherichia coli result in tolerance to colicin E2 and increased amounts of an inner membrane protein with a Mr of 42,000. The cet gene is shown to be in the same operon as the phoM gene, which is required in a phoR background for expression of the structural gene for alkaline phosphatase, phoA. Although the Cet protein is not required for phoA expression, it has been suggested that the Cet protein has an enhancing effect on the transcription of phoA [].
Probab=20.27 E-value=5.5e+02 Score=28.09 Aligned_cols=23 Identities=9% Similarity=0.033 Sum_probs=15.4
Q ss_pred ccchHHHHHHHHHHHHHhcccch
Q 011129 336 GGTGPVFAIIGAWLIYQFQNKDL 358 (493)
Q Consensus 336 GaSGaVfgLlga~~~~~~~~~~~ 358 (493)
=+|.++-++++.+.....++++.
T Consensus 357 iAa~a~i~Li~~Y~~~vl~~~k~ 379 (430)
T PF06123_consen 357 IAALACIGLISLYLSSVLKSWKR 379 (430)
T ss_pred HHHHHHHHHHHHHHHHHHhcchH
Confidence 34677777777777766666554
No 31
>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=20.17 E-value=3.2e+02 Score=23.88 Aligned_cols=41 Identities=15% Similarity=0.119 Sum_probs=27.9
Q ss_pred HHHHHHHHHHHHHHHHHHhcCCh-hHHHHHHHHHHHHHHhhh
Q 011129 287 HVALSCWALLTFGPQVCKSYGPF-TFFLIYTLGGISGNLTSF 327 (493)
Q Consensus 287 HLlfNml~L~~~G~~lE~~lGs~-r~l~lyLlsgi~g~l~~~ 327 (493)
+++.-.+.-.++|..+.+.+|+. .+.+++++.|++.++...
T Consensus 51 ~~v~pil~G~~lG~WLD~~~~t~~~~tl~~lllGv~~G~~n~ 92 (100)
T TIGR02230 51 SVAIPTLLGVAVGIWLDRHYPSPFSWTLTMLIVGVVIGCLNA 92 (100)
T ss_pred HHHHHHHHHHHHHHHHHhhcCCCcHHHHHHHHHHHHHHHHHH
Confidence 44555666778899999999863 455566667777665543
Done!