Query 027362
Match_columns 224
No_of_seqs 169 out of 1306
Neff 5.5
Searched_HMMs 46136
Date Fri Mar 29 08:49:25 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/027362.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/027362hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PRK10907 intramembrane serine 99.9 4.1E-26 9E-31 204.7 8.6 146 73-223 35-187 (276)
2 PTZ00101 rhomboid-1 protease; 99.8 1.1E-18 2.5E-23 156.9 8.2 95 129-223 51-154 (278)
3 COG0705 Membrane associated se 99.6 3.8E-15 8.2E-20 128.4 6.8 94 130-223 16-120 (228)
4 PF01694 Rhomboid: Rhomboid fa 99.4 6.1E-13 1.3E-17 105.7 4.7 57 167-223 2-58 (145)
5 KOG2289 Rhomboid family protei 99.2 2.3E-12 5.1E-17 117.8 -1.2 65 159-223 107-171 (316)
6 KOG2632 Rhomboid family protei 99.0 7.7E-10 1.7E-14 98.6 6.0 92 129-222 13-105 (258)
7 PF08551 DUF1751: Eukaryotic i 98.3 5E-07 1.1E-11 69.9 2.7 54 170-223 7-60 (99)
8 PF04511 DER1: Der1-like famil 98.1 8.6E-06 1.9E-10 69.7 7.2 89 131-219 2-94 (197)
9 KOG2290 Rhomboid family protei 97.9 2.3E-06 5.1E-11 81.9 0.1 57 168-224 448-504 (652)
10 KOG2980 Integral membrane prot 97.8 2E-05 4.3E-10 72.0 4.0 87 133-221 117-206 (310)
11 KOG0858 Predicted membrane pro 97.8 4E-05 8.6E-10 67.9 5.7 90 131-220 13-106 (239)
12 PF12122 DUF3582: Protein of u 97.6 1.9E-05 4E-10 61.6 0.6 57 74-135 38-100 (101)
13 KOG4463 Uncharacterized conser 96.9 0.00053 1.1E-08 62.0 2.3 91 129-221 9-100 (323)
14 KOG2890 Predicted membrane pro 95.6 0.012 2.6E-07 54.2 3.7 52 169-220 65-116 (326)
15 COG5291 Predicted membrane pro 95.0 0.026 5.6E-07 50.9 3.8 43 166-208 55-99 (313)
16 PF09527 ATPase_gene1: Putativ 43.7 65 0.0014 21.6 4.7 38 185-222 8-46 (55)
17 TIGR00667 aat leucyl/phenylala 32.5 23 0.0005 30.6 1.2 61 14-78 22-82 (185)
18 COG3809 Uncharacterized protei 26.8 23 0.0005 26.8 0.2 35 64-98 19-53 (88)
19 PF05546 She9_MDM33: She9 / Md 26.6 65 0.0014 28.4 2.9 19 132-150 153-171 (207)
No 1
>PRK10907 intramembrane serine protease GlpG; Provisional
Probab=99.93 E-value=4.1e-26 Score=204.69 Aligned_cols=146 Identities=22% Similarity=0.205 Sum_probs=117.6
Q ss_pred Cccccccccccccc-----cccccCCcccceeceeecCCCc-cCCCCCCCCCCccccccccCCChhHHHHHHHHHHHHHH
Q 027362 73 KDQWCENAFRFNGV-----NFFRFTNDAFASSLSFFNGGGT-RKNSGHEGTSHLDTARTNLFIGRQWTNILLAVNVLVYI 146 (224)
Q Consensus 73 ~~~w~~~~~~~~~~-----~fl~~p~~~~~~~~s~~~g~~~-~~~y~~~g~~~~~~~~~~~~~~~pvT~~LI~inv~vFi 146 (224)
.+.|.....+.+.+ +|++||+|+||+++||++|++. +.+|... ...++.+.+..|+|..++++|+++|+
T Consensus 35 ~~lwl~d~~~~~~~~~~~~~f~~~p~~~~y~~asw~~g~~~~~~~~~~~-----~~~~~~~~~~~p~T~~li~i~i~vf~ 109 (276)
T PRK10907 35 SDIWLADESQAERVRAELARFLENPADPRYLAASWQSGHTNSGLRYRRF-----PFLATLRERAGPLTLGVMIACVVVFI 109 (276)
T ss_pred eEEEecCHHHHHHHHHHHHHHHhCCCchhHHhcccccCCCCCCcccccc-----hHHHhhccCCCCHHHHHHHHHHHHHH
Confidence 45888765555544 7999999999999999999875 6777652 33344444567899999999999999
Q ss_pred HHHhchH-HHHHhhhhhhhhhccCCcceeeecccccCcHHHHHHHHHHHHHHHHHHHhhhchHHHHHHHHHHHhhhcC
Q 027362 147 AQFATQD-KLLLWGAKINSLIDKGQFWRLATSAFLHANIAHLMVNCYSLNSIGPTMEKICGPRRYLGVYFSSAIASNN 223 (224)
Q Consensus 147 l~~~~~~-~l~~~g~~~~~ii~~gq~WRLiTs~FlH~~~lHLlfNml~L~~~G~~LE~~lGs~rfl~lYL~Sgl~gsl 223 (224)
++.+..+ ....+...+......+||||++|++|+|+|++||+|||++||++|+.+|+.+|+++|+.+|++++++|++
T Consensus 110 l~~~~~~~~~~~~l~~~~~~~~~~q~WRl~T~~flH~~~~Hl~fNml~l~~lG~~iE~~~G~~~~l~l~l~s~i~~~~ 187 (276)
T PRK10907 110 LMQILGDQTVMLWLAWPFDPSLKFELWRYFTHALLHFSLLHILFNLLWWWYLGGAVEKRLGSGKLIVITLISALLSGW 187 (276)
T ss_pred HHHHhccHHHHHHHhccccccccCCcHHHHhHHHHhCCHHHHHHHHHHHHHHHHHHHHHHChHHHHHHHHHHHHHHHH
Confidence 9766543 3333333232334679999999999999999999999999999999999999999999999999999875
No 2
>PTZ00101 rhomboid-1 protease; Provisional
Probab=99.76 E-value=1.1e-18 Score=156.85 Aligned_cols=95 Identities=28% Similarity=0.443 Sum_probs=83.5
Q ss_pred CChhHHHHHHHHHHHHHHHHHhch---------HHHHHhhhhhhhhhccCCcceeeecccccCcHHHHHHHHHHHHHHHH
Q 027362 129 IGRQWTNILLAVNVLVYIAQFATQ---------DKLLLWGAKINSLIDKGQFWRLATSAFLHANIAHLMVNCYSLNSIGP 199 (224)
Q Consensus 129 ~~~pvT~~LI~inv~vFil~~~~~---------~~l~~~g~~~~~ii~~gq~WRLiTs~FlH~~~lHLlfNml~L~~~G~ 199 (224)
.-..+|..|+++|+++|++....+ +.+..+|++.++.+.++||||++|++|+|.+++|+++||+++|.+|.
T Consensus 51 ~i~~l~~~Iiii~iivfil~l~~~~~~~l~p~~~~L~~~Ga~~~~~i~~gq~WRLiT~~FlH~~~~HLl~Nm~~l~~~G~ 130 (278)
T PTZ00101 51 TWKSFIMAISIIQIIVFIISVSIKPADFLTPSDSLLVTLGANVASRIKQGEIHRLILPIFLHANIFHTFFNVFFQLRMGF 130 (278)
T ss_pred cHHHHHHHHHHHHHHHHHHHHHhcccccCCCCHHHHHHHhCcchhhhhcCCCHHHHHHHHHccCHHHHHHHHHHHHHHHH
Confidence 445678899999999999875521 24567788777777889999999999999999999999999999999
Q ss_pred HHHhhhchHHHHHHHHHHHhhhcC
Q 027362 200 TMEKICGPRRYLGVYFSSAIASNN 223 (224)
Q Consensus 200 ~LE~~lGs~rfl~lYL~Sgl~gsl 223 (224)
.+|+.+|+.||+.+|++||++|++
T Consensus 131 ~lE~~~G~~r~~ilYl~sGi~G~l 154 (278)
T PTZ00101 131 TLEKNYGIVKIIILYFLTGIYGNI 154 (278)
T ss_pred HHHHHHChHHHHHHHHHHHHHHHH
Confidence 999999999999999999999875
No 3
>COG0705 Membrane associated serine protease [Amino acid transport and metabolism]
Probab=99.57 E-value=3.8e-15 Score=128.37 Aligned_cols=94 Identities=30% Similarity=0.493 Sum_probs=75.1
Q ss_pred ChhHHHHHHHHHHHHHHHHHhchHH-HHH-------hhhhhhhhhccC---CcceeeecccccCcHHHHHHHHHHHHHHH
Q 027362 130 GRQWTNILLAVNVLVYIAQFATQDK-LLL-------WGAKINSLIDKG---QFWRLATSAFLHANIAHLMVNCYSLNSIG 198 (224)
Q Consensus 130 ~~pvT~~LI~inv~vFil~~~~~~~-l~~-------~g~~~~~ii~~g---q~WRLiTs~FlH~~~lHLlfNml~L~~~G 198 (224)
..+.|..++++|+++|+........ ... +...+....... |+||++|++|+|.|++|+++||+++|.+|
T Consensus 16 ~~~~~~~~~~~~~~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~w~lit~~FlH~~~~Hll~N~~~l~~fg 95 (228)
T COG0705 16 APPVTLFLILLNILVFLLELVLGWSAIFLLTFLFRLFGLYPLNLLGALARDQLWRLITAIFLHAGFLHLLFNMLALWVFG 95 (228)
T ss_pred cchHHHHHHHHHHHHHHHHHHccchHHHHHHHhhhHHhhcchhhhccccccchHHHHHHHHHHhhHHHHHHHHHHHHHhh
Confidence 3678999999999999997654321 111 222222221111 89999999999999999999999999999
Q ss_pred HHHHhhhchHHHHHHHHHHHhhhcC
Q 027362 199 PTMEKICGPRRYLGVYFSSAIASNN 223 (224)
Q Consensus 199 ~~LE~~lGs~rfl~lYL~Sgl~gsl 223 (224)
..+|+.+|+.+|+.+|+++|+++++
T Consensus 96 ~~le~~~G~~~f~~~yl~~gl~~~~ 120 (228)
T COG0705 96 SNLERRLGTLRFLLFYLLSGLLAGL 120 (228)
T ss_pred HHHHHHhchhHHHHHHHHHHHHHHH
Confidence 9999999999999999999999875
No 4
>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=99.36 E-value=6.1e-13 Score=105.68 Aligned_cols=57 Identities=40% Similarity=0.730 Sum_probs=51.9
Q ss_pred ccCCcceeeecccccCcHHHHHHHHHHHHHHHHHHHhhhchHHHHHHHHHHHhhhcC
Q 027362 167 DKGQFWRLATSAFLHANIAHLMVNCYSLNSIGPTMEKICGPRRYLGVYFSSAIASNN 223 (224)
Q Consensus 167 ~~gq~WRLiTs~FlH~~~lHLlfNml~L~~~G~~LE~~lGs~rfl~lYL~Sgl~gsl 223 (224)
+++|+||++|+.|+|.|+.|+++|++.++.+|..+|+.+|+.+++.+|+++++++++
T Consensus 2 ~~~~~wrl~T~~f~h~~~~hl~~n~~~l~~~g~~lE~~~G~~~~~~~~l~~~~~~~l 58 (145)
T PF01694_consen 2 QNGQWWRLFTSPFVHANFLHLLFNLLALWFFGSLLERRLGSRRFLALYLLSGLLGSL 58 (145)
T ss_dssp GCC-TTHHHHGGG--SSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred CCCcchhhhHHHHHccCHHHHHHHHHHHHHhhhhHhhhccchHHHHHHHHHHHhhhh
Confidence 579999999999999999999999999999999999999999999999999998864
No 5
>KOG2289 consensus Rhomboid family proteins [Signal transduction mechanisms]
Probab=99.17 E-value=2.3e-12 Score=117.83 Aligned_cols=65 Identities=34% Similarity=0.537 Sum_probs=59.7
Q ss_pred hhhhhhhhccCCcceeeecccccCcHHHHHHHHHHHHHHHHHHHhhhchHHHHHHHHHHHhhhcC
Q 027362 159 GAKINSLIDKGQFWRLATSAFLHANIAHLMVNCYSLNSIGPTMEKICGPRRYLGVYFSSAIASNN 223 (224)
Q Consensus 159 g~~~~~ii~~gq~WRLiTs~FlH~~~lHLlfNml~L~~~G~~LE~~lGs~rfl~lYL~Sgl~gsl 223 (224)
+.+.....+.+|+||++|++|+|.|+.||++||+.+.++|..+|...|..|+..+|+++++.||+
T Consensus 107 ~~~i~~~~~r~E~WRllTym~LHaGi~HL~~N~~~ql~iGi~LE~~~G~~RiglIYl~gg~aGSl 171 (316)
T KOG2289|consen 107 GLLIYKPVHRGELWRLLTYMWLHAGIFHLLLNMLSQLFIGIPLEQVHGFLRIGLIYLAGGVAGSL 171 (316)
T ss_pred CceecChhhhchhHHHHHHHHHhcCHHHHHHHHHHHHhccccHHhhcCceEEeeehhhhhhhhHH
Confidence 33444556889999999999999999999999999999999999999999999999999999985
No 6
>KOG2632 consensus Rhomboid family proteins [Function unknown]
Probab=98.97 E-value=7.7e-10 Score=98.56 Aligned_cols=92 Identities=25% Similarity=0.305 Sum_probs=74.0
Q ss_pred CChhHHHHHHHHHHHHHHHHHhchHHHHHhhhhhhhhhccCCcceeeecccccCcHHHHHHHHHHHHHHHHHHHhhhc-h
Q 027362 129 IGRQWTNILLAVNVLVYIAQFATQDKLLLWGAKINSLIDKGQFWRLATSAFLHANIAHLMVNCYSLNSIGPTMEKICG-P 207 (224)
Q Consensus 129 ~~~pvT~~LI~inv~vFil~~~~~~~l~~~g~~~~~ii~~gq~WRLiTs~FlH~~~lHLlfNml~L~~~G~~LE~~lG-s 207 (224)
+...+|-.+..++.++|++.....-. .....+...+.+.|.||++|++++|.+..|++|||+.+|.+|...|+..| +
T Consensus 13 ~~p~~ts~~~~~~~~i~lv~~~~~i~--~~~~l~~~~l~~~ql~RL~Ty~l~H~s~~hllfnmlaL~~~g~~fE~~~G~t 90 (258)
T KOG2632|consen 13 KIPLLTSIVVVLAILIYLVSFFPGIV--EVLGLPSELLINWQLYRLITYALVHLSLPHLLFNMLALWPLGSQFERTHGTT 90 (258)
T ss_pred cchHHHHHHHHHHHHHHHHhccchhh--hHhcCCHHHhhhHHHHHHHHHHHHhccHHHHHHHHHHHHhchhHHHhhccce
Confidence 34567888999999999886544322 22233455567899999999999999999999999999999999999999 8
Q ss_pred HHHHHHHHHHHhhhc
Q 027362 208 RRYLGVYFSSAIASN 222 (224)
Q Consensus 208 ~rfl~lYL~Sgl~gs 222 (224)
.+++.+..+.+++++
T Consensus 91 ~~~l~~~~llalf~g 105 (258)
T KOG2632|consen 91 VRILMFTVLLALFSG 105 (258)
T ss_pred ehHHHHHHHHHHHHH
Confidence 888877777777655
No 7
>PF08551 DUF1751: Eukaryotic integral membrane protein (DUF1751); InterPro: IPR013861 This entry is found in eukaryotic integral membrane proteins. Q12239 from SWISSPROT, a Saccharomyces cerevisiae (Baker's yeast) protein, has been shown to localise COP II vesicles [].
Probab=98.27 E-value=5e-07 Score=69.91 Aligned_cols=54 Identities=28% Similarity=0.423 Sum_probs=51.7
Q ss_pred CcceeeecccccCcHHHHHHHHHHHHHHHHHHHhhhchHHHHHHHHHHHhhhcC
Q 027362 170 QFWRLATSAFLHANIAHLMVNCYSLNSIGPTMEKICGPRRYLGVYFSSAIASNN 223 (224)
Q Consensus 170 q~WRLiTs~FlH~~~lHLlfNml~L~~~G~~LE~~lGs~rfl~lYL~Sgl~gsl 223 (224)
.+|+++|+.|++.++..+++|.+.++..|+.+|+.+|++.++.++++.++++|+
T Consensus 7 ~pWtl~T~~fve~~i~~~l~~~~~l~~~g~~lE~~WGs~E~lkFi~vv~~~tnl 60 (99)
T PF08551_consen 7 YPWTLFTAGFVETNIIGLLFSLLTLFYGGRYLEPIWGSREFLKFILVVNVITNL 60 (99)
T ss_pred ehHHHHHHHHHHhHHHHHHHHHHHHHHhhHHHHHhcChHHHHHHHHHHHHHhHH
Confidence 789999999999999999999999999999999999999999999999888775
No 8
>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=98.11 E-value=8.6e-06 Score=69.65 Aligned_cols=89 Identities=21% Similarity=0.175 Sum_probs=63.8
Q ss_pred hhHHHHHHHHHHHHHHHHHhchHHHHHhhhhhhhhhccCCcceeeecccccCcH-HHHHHHHHHHHHHHHHHHhh-h-ch
Q 027362 131 RQWTNILLAVNVLVYIAQFATQDKLLLWGAKINSLIDKGQFWRLATSAFLHANI-AHLMVNCYSLNSIGPTMEKI-C-GP 207 (224)
Q Consensus 131 ~pvT~~LI~inv~vFil~~~~~~~l~~~g~~~~~ii~~gq~WRLiTs~FlH~~~-lHLlfNml~L~~~G~~LE~~-l-Gs 207 (224)
+|+|...++.++++.++..+.--........+..+..++|+||++|+.|.-++. +..++|++.++..++.+|+. + |+
T Consensus 2 PpVTR~~~~~~~~~s~l~~~~~~~~~~l~~~~~~v~~~~q~WRl~Tsff~~g~~~~~~l~~~~~l~~~s~~LE~~~f~~~ 81 (197)
T PF04511_consen 2 PPVTRYWLISTVALSLLVSFGIISPYYLYFDWELVFKKFQIWRLFTSFFYFGPFSLNFLFNLYFLYQYSSSLEEGHFQGR 81 (197)
T ss_pred ChhHHHHHHHHHHHHHHHHCCCCCHHHeeECcHHHhhhcCceeeEEEEEEEcCCCHHHHHHHHHHHHHhhHhccCCCCCC
Confidence 378988888888888876554222222223344455789999999999986554 79999999999999999998 2 33
Q ss_pred -HHHHHHHHHHHh
Q 027362 208 -RRYLGVYFSSAI 219 (224)
Q Consensus 208 -~rfl~lYL~Sgl 219 (224)
..|+...+.+++
T Consensus 82 ~ady~~~ll~~~~ 94 (197)
T PF04511_consen 82 SADYLWFLLFGAS 94 (197)
T ss_pred HHHHHHHHHHHHH
Confidence 467655555443
No 9
>KOG2290 consensus Rhomboid family proteins [Signal transduction mechanisms]
Probab=97.91 E-value=2.3e-06 Score=81.87 Aligned_cols=57 Identities=37% Similarity=0.516 Sum_probs=54.6
Q ss_pred cCCcceeeecccccCcHHHHHHHHHHHHHHHHHHHhhhchHHHHHHHHHHHhhhcCC
Q 027362 168 KGQFWRLATSAFLHANIAHLMVNCYSLNSIGPTMEKICGPRRYLGVYFSSAIASNNS 224 (224)
Q Consensus 168 ~gq~WRLiTs~FlH~~~lHLlfNml~L~~~G~~LE~~lGs~rfl~lYL~Sgl~gsls 224 (224)
..|++||+|+.|+|+++.|++..|...+.+-+.+|+..|..|+.++|++||+.||++
T Consensus 448 PdQfYRL~~SLFlHagviH~~vSi~FQm~vmrdlEkL~g~~riAIiy~~SGitGNLA 504 (652)
T KOG2290|consen 448 PDQFYRLWLSLFLHAGVIHLLVSICFQMTVMRDLEKLAGWHRIAIIYFLSGITGNLA 504 (652)
T ss_pred hhHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHhhcchhhheeeecccccccch
Confidence 358999999999999999999999999999999999999999999999999999985
No 10
>KOG2980 consensus Integral membrane protease of the rhomboid family involved in different forms of regulated intramembrane proteolysis [Signal transduction mechanisms]
Probab=97.80 E-value=2e-05 Score=72.00 Aligned_cols=87 Identities=23% Similarity=0.328 Sum_probs=70.5
Q ss_pred HHHHHHHHHHHHHHHHHhchHH--HHHhhhhhhhhhccCCcceeeecccccCcHHHHHHHHHHHHHHHH-HHHhhhchHH
Q 027362 133 WTNILLAVNVLVYIAQFATQDK--LLLWGAKINSLIDKGQFWRLATSAFLHANIAHLMVNCYSLNSIGP-TMEKICGPRR 209 (224)
Q Consensus 133 vT~~LI~inv~vFil~~~~~~~--l~~~g~~~~~ii~~gq~WRLiTs~FlH~~~lHLlfNml~L~~~G~-~LE~~lGs~r 209 (224)
+.+.|+++|+++|.+|.+.+.. ...|....+ +...-.|.++++.|.|.+.+|+..||+.++.+.. .+....|...
T Consensus 117 ~v~~ll~~n~~vf~lWrv~~~~~~~~~~mls~~--~~~t~~w~i~~s~Fsh~~a~h~g~~~~~~~~y~~~a~~~~~~~~~ 194 (310)
T KOG2980|consen 117 VVFGLLIANAFVFTLWRVPQKQFTMIPWMLSRN--AYKTGCWKIILSTFSHYSALHLGPNMLVLKSYLAGALKGSLGFSS 194 (310)
T ss_pred chhHHHHHHHHHHHHHHhcchhhhhhhHHhhcc--cccccceeEEeehhcchhHhhhcHHHHHHHHHhcccccCCcchhh
Confidence 6789999999999999887543 344443222 3445678899999999999999999999998888 8999999999
Q ss_pred HHHHHHHHHhhh
Q 027362 210 YLGVYFSSAIAS 221 (224)
Q Consensus 210 fl~lYL~Sgl~g 221 (224)
+.++|+.++..|
T Consensus 195 ~~AlylSa~~~~ 206 (310)
T KOG2980|consen 195 FFALYLSAGVKG 206 (310)
T ss_pred cccceecccccc
Confidence 999999655544
No 11
>KOG0858 consensus Predicted membrane protein [Function unknown]
Probab=97.79 E-value=4e-05 Score=67.93 Aligned_cols=90 Identities=17% Similarity=0.102 Sum_probs=66.7
Q ss_pred hhHHHHHHHHHHHHHHHHHhchHHHHHhhhhhhhhhccCCcceeeecccccCc-HHHHHHHHHHHHHHHHHHHhhhc---
Q 027362 131 RQWTNILLAVNVLVYIAQFATQDKLLLWGAKINSLIDKGQFWRLATSAFLHAN-IAHLMVNCYSLNSIGPTMEKICG--- 206 (224)
Q Consensus 131 ~pvT~~LI~inv~vFil~~~~~~~l~~~g~~~~~ii~~gq~WRLiTs~FlH~~-~lHLlfNml~L~~~G~~LE~~lG--- 206 (224)
.|+|.....+|++..++..+.--+....-.++.-++.+.|+||++|+.+.-+. -+|.++||+.++--.+.+|+-.=
T Consensus 13 PpVTR~~~~~~v~tt~~~~l~lIsP~~l~~~p~Lv~kk~QiWRliTs~lyfg~~gf~fl~n~~FlyrY~~~LE~g~f~~r 92 (239)
T KOG0858|consen 13 PPVTRYYTTACVVTTLLVRLDLISPFQLYLNPELVFKKFQIWRLITSFLYFGPFGFDFLMNLYFLYRYSSMLEEGSFRGR 92 (239)
T ss_pred ChHHHHHHHHHHHHHHHHhhcccCchheEecHHHHHhHhHHHHhhhhhheeccccHHHHHHHHHHHHHHHHHhcCCCCCc
Confidence 57899999999998888654321111122223334688999999999998866 68999999999999999999432
Q ss_pred hHHHHHHHHHHHhh
Q 027362 207 PRRYLGVYFSSAIA 220 (224)
Q Consensus 207 s~rfl~lYL~Sgl~ 220 (224)
+..|+..+++++++
T Consensus 93 tadf~~mllf~~~l 106 (239)
T KOG0858|consen 93 TADFLYMLLFGAVL 106 (239)
T ss_pred hhHHHHHHHHHHHH
Confidence 36788777777664
No 12
>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=97.59 E-value=1.9e-05 Score=61.62 Aligned_cols=57 Identities=12% Similarity=0.091 Sum_probs=18.0
Q ss_pred cccccccccccc-----ccccccCCcccceeceeecCCCc-cCCCCCCCCCCccccccccCCChhHHH
Q 027362 74 DQWCENAFRFNG-----VNFFRFTNDAFASSLSFFNGGGT-RKNSGHEGTSHLDTARTNLFIGRQWTN 135 (224)
Q Consensus 74 ~~w~~~~~~~~~-----~~fl~~p~~~~~~~~s~~~g~~~-~~~y~~~g~~~~~~~~~~~~~~~pvT~ 135 (224)
+.|.....++.. .+|++||+|+||+++||++|++. +..|+.. .+.++......|+|.
T Consensus 38 ~lwl~de~~~~~a~~el~~Fl~nP~~~rYqaASWq~g~~~~~~~y~~~-----s~~~~l~~~aGplTl 100 (101)
T PF12122_consen 38 ALWLHDEEHLEQAEQELEEFLQNPNDPRYQAASWQTGSTRTQFSYQSP-----SLLQQLRAQAGPLTL 100 (101)
T ss_dssp EEEES-GGGHHHHHHHHHHHHHS-SS------------------------------------S-HHHH
T ss_pred EEEEeCHHHHHHHHHHHHHHHHCCCCHHHHHHHHhcCCccCccCcCCc-----hHHHHHHHcCCCeec
Confidence 578776666544 47999999999999999999997 5777763 355555567778885
No 13
>KOG4463 consensus Uncharacterized conserved protein [Function unknown]
Probab=96.90 E-value=0.00053 Score=62.02 Aligned_cols=91 Identities=22% Similarity=0.310 Sum_probs=64.2
Q ss_pred CChhHHHHHHHHHHHHHHHHHhchHHHHHhhhhhhhhh-ccCCcceeeecccccCcHHHHHHHHHHHHHHHHHHHhhhch
Q 027362 129 IGRQWTNILLAVNVLVYIAQFATQDKLLLWGAKINSLI-DKGQFWRLATSAFLHANIAHLMVNCYSLNSIGPTMEKICGP 207 (224)
Q Consensus 129 ~~~pvT~~LI~inv~vFil~~~~~~~l~~~g~~~~~ii-~~gq~WRLiTs~FlH~~~lHLlfNml~L~~~G~~LE~~lGs 207 (224)
.+.|+|...++...++-++..+..-+ -.++..+.+.+ .+.|+||++-+.|.--+-..+++-++.+|.+ +.+||.+|+
T Consensus 9 ~nmpVTK~~~iT~~~~~vvagI~~~k-~~f~l~y~~~l~~y~qywrlL~~qF~~~n~~e~~~~l~I~Y~f-R~~ERlLGS 86 (323)
T KOG4463|consen 9 HNMPVTKAFVITSALFTVVAGIQGRK-SKFGLSYQDILEKYFQYWRLLMSQFAFSNTPELMFGLYILYYF-RVFERLLGS 86 (323)
T ss_pred cccchHHHHHHHHHHHHHHHHhhhcc-cccccchhHHHHHHHHHHHHHHHHHHhcCChHHHHHHHHHHHH-HHHHHHhcc
Confidence 45678866655544444443222110 11223333333 3479999999999999999999999988887 999999999
Q ss_pred HHHHHHHHHHHhhh
Q 027362 208 RRYLGVYFSSAIAS 221 (224)
Q Consensus 208 ~rfl~lYL~Sgl~g 221 (224)
-||..+.+.+++.+
T Consensus 87 hky~~fiv~s~~~~ 100 (323)
T KOG4463|consen 87 HKYSVFIVFSGTVS 100 (323)
T ss_pred ccceeehhHHHHHH
Confidence 99998888888765
No 14
>KOG2890 consensus Predicted membrane protein [Function unknown]
Probab=95.61 E-value=0.012 Score=54.22 Aligned_cols=52 Identities=23% Similarity=0.281 Sum_probs=47.7
Q ss_pred CCcceeeecccccCcHHHHHHHHHHHHHHHHHHHhhhchHHHHHHHHHHHhh
Q 027362 169 GQFWRLATSAFLHANIAHLMVNCYSLNSIGPTMEKICGPRRYLGVYFSSAIA 220 (224)
Q Consensus 169 gq~WRLiTs~FlH~~~lHLlfNml~L~~~G~~LE~~lGs~rfl~lYL~Sgl~ 220 (224)
...|+++|+.|+-.+++-.++|.+.+-+.|+.+|+.+|+..++.+|.+.-..
T Consensus 65 ~~~WtliTs~fie~~vw~V~~sv~~L~v~G~~lEp~Wg~~e~lkff~ivn~~ 116 (326)
T KOG2890|consen 65 FFPWTLITSGFIELNVWDVLVSVLTLSVGGKFLEPNWGSLELLKFFAIVNGS 116 (326)
T ss_pred hhhHHHHhcchhhhhHHHHHHHHHheeecceeeccCCCCHHHHHHHHHhhch
Confidence 4789999999999999999999999999999999999999999888776443
No 15
>COG5291 Predicted membrane protein [Function unknown]
Probab=95.00 E-value=0.026 Score=50.89 Aligned_cols=43 Identities=21% Similarity=0.380 Sum_probs=36.0
Q ss_pred hccCCcceeeecccccCc-HHHHHHHHHHHHHHHHHHHh-hhchH
Q 027362 166 IDKGQFWRLATSAFLHAN-IAHLMVNCYSLNSIGPTMEK-ICGPR 208 (224)
Q Consensus 166 i~~gq~WRLiTs~FlH~~-~lHLlfNml~L~~~G~~LE~-~lGs~ 208 (224)
+.+.|+||++|+..+-.+ -+..++|++.+|--.+.+|+ .+|+.
T Consensus 55 ~k~~qiwRlfTs~~~~~~~~~d~~M~vyf~Y~yS~~LE~g~f~~~ 99 (313)
T COG5291 55 LKRLQIWRLFTSFLYFGKPTLDMFMHVYFLYRYSRMLEEGCFNTS 99 (313)
T ss_pred HHHHHHHHHHHHHHhhcCcchhHHHHHHHHHHHHHHHhccccCcc
Confidence 467799999998887765 47899999999999999998 45554
No 16
>PF09527 ATPase_gene1: Putative F0F1-ATPase subunit (ATPase_gene1)
Probab=43.66 E-value=65 Score=21.62 Aligned_cols=38 Identities=13% Similarity=0.038 Sum_probs=29.8
Q ss_pred HHHHHHHHHHHHHHHHHHhhhch-HHHHHHHHHHHhhhc
Q 027362 185 AHLMVNCYSLNSIGPTMEKICGP-RRYLGVYFSSAIASN 222 (224)
Q Consensus 185 lHLlfNml~L~~~G~~LE~~lGs-~rfl~lYL~Sgl~gs 222 (224)
..+..+++.-..+|..+++.+|+ ..+..+.++-|++++
T Consensus 8 ~~~~~~i~~g~~~G~~lD~~~~t~p~~~~~g~llG~~~g 46 (55)
T PF09527_consen 8 FTMAAPILVGFFLGYWLDKWFGTSPWFTLIGLLLGIAAG 46 (55)
T ss_pred HHHHHHHHHHHHHHHHHHHHcCCChHHHHHHHHHHHHHH
Confidence 35677888889999999999999 666666666666654
No 17
>TIGR00667 aat leucyl/phenylalanyl-tRNA--protein transferase. The N-terminal residue controls the biological half-life of many proteins via the N-end rule pathway. This enzyme transfers a Leu or Phe to the amino end of certain proteins to enable degradation.
Probab=32.55 E-value=23 Score=30.61 Aligned_cols=61 Identities=16% Similarity=0.308 Sum_probs=44.9
Q ss_pred CCCccccCCCcchhhhhhhhcchhhhhhhhhcccCcchhhhhhhccccccccccCCCCCCccccc
Q 027362 14 REPFDWLTRPPLNLITTTAKHSLSVSLSRRLLHHHPLHARRLLHSSVKKLSRLCHIPRLKDQWCE 78 (224)
Q Consensus 14 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~w~~ 78 (224)
.+|+.|..|.|--++-. ..+|+++|++|.+.+-. +..-+-..|.+|-..|..||-.++|-.
T Consensus 22 ~~pi~WwsP~pR~vl~p-~~~hvsrsL~k~lr~~~---f~vtin~~F~~Vi~~Ca~~r~~gTWI~ 82 (185)
T TIGR00667 22 GDPILWWSPDPRAVLWP-ESLHIARSMKRFLKRSP---YRVSVNYAFGQVIEGCASDRPEGTWIS 82 (185)
T ss_pred CCCeeEEcCCCCeEecc-cccccCHHHHHHHcCCC---eEEEEcCcHHHHHHHHcCCCCCCCCCC
Confidence 36899998888877755 58999999998743211 123456788899999999886668973
No 18
>COG3809 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=26.78 E-value=23 Score=26.85 Aligned_cols=35 Identities=17% Similarity=0.156 Sum_probs=25.6
Q ss_pred ccccCCCCCCccccccccccccccccccCCcccce
Q 027362 64 SRLCHIPRLKDQWCENAFRFNGVNFFRFTNDAFAS 98 (224)
Q Consensus 64 ~~~~~~~~~~~~w~~~~~~~~~~~fl~~p~~~~~~ 98 (224)
-..|-||||..+|.++++--+.++--+-|+..-|+
T Consensus 19 vEiD~CPrCrGVWLDrGELdKli~r~r~pqpa~ys 53 (88)
T COG3809 19 VEIDYCPRCRGVWLDRGELDKLIERSRYPQPAEYS 53 (88)
T ss_pred ceeeeCCccccEeecchhHHHHHHHhcCCCCcccC
Confidence 35788999999999998877766555555544444
No 19
>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=26.61 E-value=65 Score=28.40 Aligned_cols=19 Identities=32% Similarity=0.272 Sum_probs=16.2
Q ss_pred hHHHHHHHHHHHHHHHHHh
Q 027362 132 QWTNILLAVNVLVYIAQFA 150 (224)
Q Consensus 132 pvT~~LI~inv~vFil~~~ 150 (224)
..|++++++|+++|++..+
T Consensus 153 wgT~~lmgvNvllFl~~~~ 171 (207)
T PF05546_consen 153 WGTWGLMGVNVLLFLVAQL 171 (207)
T ss_pred HHHHHHHHHHHHHHHHHHH
Confidence 5689999999999998644
Done!