Query 027966
Match_columns 216
No_of_seqs 112 out of 428
Neff 6.3
Searched_HMMs 46136
Date Fri Mar 29 04:13:28 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/027966.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/027966hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG0858 Predicted membrane pro 100.0 4.1E-54 8.9E-59 367.2 14.7 179 2-192 22-210 (239)
2 PF04511 DER1: Der1-like famil 100.0 4.8E-49 1E-53 331.7 14.8 176 2-184 11-197 (197)
3 COG5291 Predicted membrane pro 100.0 8.3E-38 1.8E-42 267.6 5.6 177 4-192 31-217 (313)
4 KOG2632 Rhomboid family protei 98.7 1.2E-07 2.7E-12 82.8 9.5 147 17-167 46-195 (258)
5 PF01694 Rhomboid: Rhomboid fa 97.5 0.00039 8.5E-09 54.4 7.0 140 20-170 2-142 (145)
6 PTZ00101 rhomboid-1 protease; 96.9 0.0041 8.9E-08 55.5 8.2 55 16-75 94-149 (278)
7 COG0705 Membrane associated se 96.4 0.019 4.1E-07 48.8 8.4 133 23-167 67-208 (228)
8 PRK10907 intramembrane serine 96.2 0.045 9.7E-07 48.8 10.1 132 20-170 131-270 (276)
9 KOG2890 Predicted membrane pro 90.3 0.56 1.2E-05 42.5 5.2 145 22-173 65-222 (326)
10 PF08551 DUF1751: Eukaryotic i 84.3 2.9 6.2E-05 31.5 5.3 51 23-78 7-57 (99)
11 PF12841 YvrJ: YvrJ protein fa 56.2 13 0.00028 23.4 2.5 25 35-59 3-27 (38)
12 KOG2289 Rhomboid family protei 52.7 22 0.00049 32.4 4.4 141 20-175 115-259 (316)
13 KOG4463 Uncharacterized conser 49.0 26 0.00057 31.4 4.1 51 21-77 48-98 (323)
14 PF11169 DUF2956: Protein of u 38.3 23 0.00049 27.2 1.8 18 129-146 78-95 (103)
15 PHA02132 hypothetical protein 27.6 14 0.0003 26.6 -0.8 29 113-143 33-69 (86)
No 1
>KOG0858 consensus Predicted membrane protein [Function unknown]
Probab=100.00 E-value=4.1e-54 Score=367.22 Aligned_cols=179 Identities=55% Similarity=0.947 Sum_probs=169.1
Q ss_pred cceeehhhhhhcccccee---------ecccccchhhccceecCCCCHHHHHHHHHHHHHhhhhhhcCCCCCchhHHHHH
Q 027966 2 HCVLLNMLQATHMFDCFY---------IDGATNTVTINMAIFFVMTDLDFLFHMFFLARYCKLLEENSFRGRTADFLYML 72 (216)
Q Consensus 2 ~~~~~t~~~~~~~~~~~~---------~~~q~wR~liTsf~f~G~~sl~~l~~l~fl~~yss~LE~~~f~~~~aDyl~~L 72 (216)
.|+++|++.++.+++|.. +|+|+|| ++|+++|+|+++++++|+++|+||||++||+++|++|++||+||+
T Consensus 22 ~~v~tt~~~~l~lIsP~~l~~~p~Lv~kk~QiWR-liTs~lyfg~~gf~fl~n~~FlyrY~~~LE~g~f~~rtadf~~ml 100 (239)
T KOG0858|consen 22 ACVVTTLLVRLDLISPFQLYLNPELVFKKFQIWR-LITSFLYFGPFGFDFLMNLYFLYRYSSMLEEGSFRGRTADFLYML 100 (239)
T ss_pred HHHHHHHHHhhcccCchheEecHHHHHhHhHHHH-hhhhhheeccccHHHHHHHHHHHHHHHHHhcCCCCCchhHHHHHH
Confidence 589999999999998876 5899999 999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHHHhhcccccccchhHHHhHHHHHHHHHHHHHhhhcCCCceeEEEEeecccccchHHHHHHHHHHhcchhH
Q 027966 73 LFGATFLTGTVLIGGMIPYLSESFAKIIFLSNSLTLMMVYVWSKQNPFIHMSFLGLFTFTAAYLPWVLLGFSVFVGASAW 152 (216)
Q Consensus 73 l~~~~~i~~~s~~~~~~~y~~~~~~~~~fL~~~L~~~liYiWsr~np~~~V~~~G~~~i~a~ylP~~~l~~~~l~~~s~~ 152 (216)
+++++++.+.+ .+.+.++|+++|+.+++|+|||+||+.+||++|++++||+|+||++++++++.+++.+
T Consensus 101 lf~~~l~~~~~-----------~~~~~~fLg~~l~~~l~YvWs~~Np~~~v~F~g~~~f~a~YlPwvll~fs~l~g~~~~ 169 (239)
T KOG0858|consen 101 LFGAVLLTLTG-----------LFVYIVFLGQSLVFMLVYVWSKRNPDVIVSFFGLITFKAPYLPWVLLGFSFLFGGSIL 169 (239)
T ss_pred HHHHHHHHHHH-----------HHHHHHHHHHHHHHHHHHHHHhhCCCceEEEEEEecCccccchHHHHHHHHHhCCchH
Confidence 99999888663 2457889999999999999999999999999999999999999999999999998779
Q ss_pred HHHHHhhHHHHHHHhhhhccCCC-CCCCcCChHHHHHhhcc
Q 027966 153 VDLLGMIAGHAYYFLEDVYPRMT-GRRPLKTPSFIKALFAD 192 (216)
Q Consensus 153 ~~liGi~~GHly~fL~~i~P~~~-g~~~l~TP~fl~~l~~~ 192 (216)
.|++||++||+|+|++|++|+.. |+|++|||+|++|++++
T Consensus 170 ~dllGi~~GHiy~fl~~~~p~~~gg~~~l~TP~~l~rl~~~ 210 (239)
T KOG0858|consen 170 VDLLGIIVGHIYYFLDDVYPRDYGGRDLLKTPQFLKRLFAD 210 (239)
T ss_pred HHHHhhhhheeEEEEeeeccCCcCCcCcccCHHHHHHhcCC
Confidence 99999999999999999999954 69999999999999998
No 2
>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=100.00 E-value=4.8e-49 Score=331.69 Aligned_cols=176 Identities=43% Similarity=0.828 Sum_probs=160.7
Q ss_pred cceeehhhhhhcccccee---------ecccccchhhccceecCCCCHHHHHHHHHHHHHhhhhhhcCCCCCchhHHHHH
Q 027966 2 HCVLLNMLQATHMFDCFY---------IDGATNTVTINMAIFFVMTDLDFLFHMFFLARYCKLLEENSFRGRTADFLYML 72 (216)
Q Consensus 2 ~~~~~t~~~~~~~~~~~~---------~~~q~wR~liTsf~f~G~~sl~~l~~l~fl~~yss~LE~~~f~~~~aDyl~~L 72 (216)
.++++|++++++.+||.. ++.|+|| ++|+++++|+.|+++++++|++++||++||+++|++|++||+|++
T Consensus 11 ~~~~~s~l~~~~~~~~~~l~~~~~~v~~~~q~WR-l~Tsff~~g~~~~~~l~~~~~l~~~s~~LE~~~f~~~~ady~~~l 89 (197)
T PF04511_consen 11 STVALSLLVSFGIISPYYLYFDWELVFKKFQIWR-LFTSFFYFGPFSLNFLFNLYFLYQYSSSLEEGHFQGRSADYLWFL 89 (197)
T ss_pred HHHHHHHHHHCCCCCHHHeeECcHHHhhhcCcee-eEEEEEEEcCCCHHHHHHHHHHHHHhhHhccCCCCCCHHHHHHHH
Confidence 367788899999887663 5799999 999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHHHhhcccccccchhHHHhHHHHHHHHHHHHHhhhcCCCceeEEEEeecccccchHHHHHHHHHHhcc-hh
Q 027966 73 LFGATFLTGTVLIGGMIPYLSESFAKIIFLSNSLTLMMVYVWSKQNPFIHMSFLGLFTFTAAYLPWVLLGFSVFVGA-SA 151 (216)
Q Consensus 73 l~~~~~i~~~s~~~~~~~y~~~~~~~~~fL~~~L~~~liYiWsr~np~~~V~~~G~~~i~a~ylP~~~l~~~~l~~~-s~ 151 (216)
+++++++.+++.+.+ ....+.++++++++.+++|+|||+||+++||++|++++||+|+||+++++++++++ +.
T Consensus 90 l~~~~~i~~~~~~~~------~~~~~~~~l~~~l~~~l~Y~wsr~np~~~v~~~g~~~i~a~ylP~~~~~~~~l~~~~~~ 163 (197)
T PF04511_consen 90 LFGASLILILSLLIG------PYFFNIPFLGSSLSFALTYIWSRKNPNAQVSFFGLFTIKAKYLPWVLLAFSLLFGGSSP 163 (197)
T ss_pred HHHHHHHHHHHHhhc------cchhHHHHHHHHHHHHHHHHHHHhCcccceeeEEEEEEChhhHHHHHHHHHHHhCCCcH
Confidence 999999988865431 11246689999999999999999999999999999999999999999999999987 89
Q ss_pred HHHHHHhhHHHHHHHhhhhccCCC-CCCCcCChH
Q 027966 152 WVDLLGMIAGHAYYFLEDVYPRMT-GRRPLKTPS 184 (216)
Q Consensus 152 ~~~liGi~~GHly~fL~~i~P~~~-g~~~l~TP~ 184 (216)
..|++||++||+|||++|++|+.+ |+|+||||+
T Consensus 164 ~~~l~Gi~~Ghly~fl~~~~p~~~~G~~~l~tP~ 197 (197)
T PF04511_consen 164 IPDLLGILVGHLYYFLKDIYPRLPGGKDLLKTPQ 197 (197)
T ss_pred HHHHHHHHHHHHHHHHHHhcccccCCCccCCCcC
Confidence 999999999999999999999975 899999995
No 3
>COG5291 Predicted membrane protein [Function unknown]
Probab=100.00 E-value=8.3e-38 Score=267.63 Aligned_cols=177 Identities=30% Similarity=0.619 Sum_probs=159.3
Q ss_pred eeehhhhhhcccccee---------ecccccchhhccceecCCCCHHHHHHHHHHHHHhhhhhhcCCCCCchhHHHHHHH
Q 027966 4 VLLNMLQATHMFDCFY---------IDGATNTVTINMAIFFVMTDLDFLFHMFFLARYCKLLEENSFRGRTADFLYMLLF 74 (216)
Q Consensus 4 ~~~t~~~~~~~~~~~~---------~~~q~wR~liTsf~f~G~~sl~~l~~l~fl~~yss~LE~~~f~~~~aDyl~~Ll~ 74 (216)
.++|++....+++|++ ++.|+|| ++||+.++|+..++.+|++|++|+||+.||+++|...-.||+|||++
T Consensus 31 ~a~til~~~~lvsPwy~ly~~pL~~k~~qiwR-lfTs~~~~~~~~~d~~M~vyf~Y~yS~~LE~g~f~~~lv~Y~~yl~~ 109 (313)
T COG5291 31 SAVTILVYVDLVSPWYSLYYSPLFLKRLQIWR-LFTSFLYFGKPTLDMFMHVYFLYRYSRMLEEGCFNTSLVEYFWYLLV 109 (313)
T ss_pred HHHHHHHHHhhcCccceeeechhHHHHHHHHH-HHHHHHhhcCcchhHHHHHHHHHHHHHHHhccccCccHHHHHHHHHH
Confidence 4678888888888855 5799999 99999999999999999999999999999999998666799999999
Q ss_pred HHHHHHHHHHhhcccccccchhHHHhHHHHHHHHHHHHHhhhcCCCceeEEEEeecccccchHHHHHHHHHHhc-chhHH
Q 027966 75 GATFLTGTVLIGGMIPYLSESFAKIIFLSNSLTLMMVYVWSKQNPFIHMSFLGLFTFTAAYLPWVLLGFSVFVG-ASAWV 153 (216)
Q Consensus 75 ~~~~i~~~s~~~~~~~y~~~~~~~~~fL~~~L~~~liYiWsr~np~~~V~~~G~~~i~a~ylP~~~l~~~~l~~-~s~~~ 153 (216)
+..+|..++.+.+ +..-|+++++.+++|+||++||+.+++|+|+|+++++|+|+++++++++.+ +....
T Consensus 110 ~~l~i~a~s~I~g----------g~saL~tsf~a~ItY~WS~~N~~~~Iqf~g~i~v~gkYlP~Illgfsfl~~~g~~i~ 179 (313)
T COG5291 110 ISLVIFAISNIYG----------GISALGTSFSATITYIWSKRNPRAIIQFFGFISVPGKYLPFILLGFSFLSRRGISID 179 (313)
T ss_pred HHHHHHHHHHHhc----------chhhhcchhhhheeeeeeecCCceEEEEEEeeecchhhhhHHHHHHHHHhcCCccce
Confidence 9999988876632 234589999999999999999999999999999999999999999999998 78899
Q ss_pred HHHHhhHHHHHHHhhhhccCCCCCCCcCChHHHHHhhcc
Q 027966 154 DLLGMIAGHAYYFLEDVYPRMTGRRPLKTPSFIKALFAD 192 (216)
Q Consensus 154 ~liGi~~GHly~fL~~i~P~~~g~~~l~TP~fl~~l~~~ 192 (216)
|++|+.+||..+++.++||+. |++.+.||.|.++++.+
T Consensus 180 ~vlGf~~g~~~h~~g~I~~mi-~r~~~~t~~~~~~~~~~ 217 (313)
T COG5291 180 DVLGFVVGHLFHYFGDIYPMI-GRDILSTPCWVKKLFNE 217 (313)
T ss_pred eeeeeeeccccccccchhhhh-hcccCCCcccccccccC
Confidence 999999999999999999987 67788888888777644
No 4
>KOG2632 consensus Rhomboid family proteins [Function unknown]
Probab=98.67 E-value=1.2e-07 Score=82.84 Aligned_cols=147 Identities=25% Similarity=0.303 Sum_probs=102.5
Q ss_pred ceeecccccchhhccceecCCCCHHHHHHHHHHHHHhhhhhhcCCCCCchhHHHHHHHHHHHHHHHHHhhcccccccchh
Q 027966 17 CFYIDGATNTVTINMAIFFVMTDLDFLFHMFFLARYCKLLEENSFRGRTADFLYMLLFGATFLTGTVLIGGMIPYLSESF 96 (216)
Q Consensus 17 ~~~~~~q~wR~liTsf~f~G~~sl~~l~~l~fl~~yss~LE~~~f~~~~aDyl~~Ll~~~~~i~~~s~~~~~~~y~~~~~ 96 (216)
....+.|.|| ++|..++.... +++++++.-+..-++..|+.+ |.++-++.+..+.+..=-++.++..-..+.....
T Consensus 46 ~~l~~~ql~R-L~Ty~l~H~s~-~hllfnmlaL~~~g~~fE~~~--G~t~~~l~~~~llalf~gIl~ll~~~~~~~~d~~ 121 (258)
T KOG2632|consen 46 ELLINWQLYR-LITYALVHLSL-PHLLFNMLALWPLGSQFERTH--GTTVRILMFTVLLALFSGILYLLAYHVFLLSDLV 121 (258)
T ss_pred HHhhhHHHHH-HHHHHHHhccH-HHHHHHHHHHHhchhHHHhhc--cceehHHHHHHHHHHHHHHHHHHHHHHHhhcchh
Confidence 3346799999 99999987755 899999999999999999987 6688888777555432111111111000000000
Q ss_pred HHHhHHH-HHHHHHHHHHhhhcCCCceeEEEEeecccccchHHHHHHHH-HHhc-chhHHHHHHhhHHHHHHHh
Q 027966 97 AKIIFLS-NSLTLMMVYVWSKQNPFIHMSFLGLFTFTAAYLPWVLLGFS-VFVG-ASAWVDLLGMIAGHAYYFL 167 (216)
Q Consensus 97 ~~~~fL~-~~L~~~liYiWsr~np~~~V~~~G~~~i~a~ylP~~~l~~~-~l~~-~s~~~~liGi~~GHly~fL 167 (216)
....--| +.-.++++=+-+-+.|..+.+++|.+++|++|-||+++++. ++.. .|++..+.|+++|..|-+.
T Consensus 122 ~~~~a~G~s~v~Fam~~~~~~~sp~r~~~~fg~~siP~~l~Pw~lLi~~~~lvp~aSFlghl~GllvG~ay~~~ 195 (258)
T KOG2632|consen 122 YVEGAIGFSGVLFAMMAVLEVQSPVRSRSVFGLFSIPIVLAPWALLIATQILVPQASFLGHLCGLLVGYAYAFS 195 (258)
T ss_pred hhcccccccHHHHHHHHHHhhcCcccchhhcccccccHHHHHHHHHHHHHHHccCchHHHHHHHHHHHHHHHHH
Confidence 0000001 22334555555778899999999999999999999999888 5565 4999999999999999994
No 5
>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=97.49 E-value=0.00039 Score=54.37 Aligned_cols=140 Identities=17% Similarity=0.102 Sum_probs=73.3
Q ss_pred ecccccchhhccceecCCCCHHHHHHHHHHHHHhhhhhhcCCCCCchhHHHHHHHHHHHHHHHHHhhcccccccchhHH-
Q 027966 20 IDGATNTVTINMAIFFVMTDLDFLFHMFFLARYCKLLEENSFRGRTADFLYMLLFGATFLTGTVLIGGMIPYLSESFAK- 98 (216)
Q Consensus 20 ~~~q~wR~liTsf~f~G~~sl~~l~~l~fl~~yss~LE~~~f~~~~aDyl~~Ll~~~~~i~~~s~~~~~~~y~~~~~~~- 98 (216)
.+.|+|| ++|+.+..++. .+++++++.++..+..+|+.. .+.++.-..+..+..-.+......-... +..+
T Consensus 2 ~~~~~wr-l~T~~f~h~~~-~hl~~n~~~l~~~g~~lE~~~---G~~~~~~~~l~~~~~~~l~~~~~~~~~~---~~~G~ 73 (145)
T PF01694_consen 2 QNGQWWR-LFTSPFVHANF-LHLLFNLLALWFFGSLLERRL---GSRRFLALYLLSGLLGSLLSLLFSPPNQ---PYVGA 73 (145)
T ss_dssp GCC-TTH-HHHGGG--SSH-HHHHHHHHHHHHHHHHHHHHH---HHHHHHHHHHHHHHHHHHHHHHHH-S--------SS
T ss_pred CCCcchh-hhHHHHHccCH-HHHHHHHHHHHHhhhhHhhhc---cchHHHHHHHHHHHhhhhcccccccccc---ccCCC
Confidence 3689999 99999887655 999999999999999999886 3445544443333322222211110000 0000
Q ss_pred HhHHHHHHHHHHHHHhhhcCCCceeEEEEeecccccchHHHHHHHHHHhcchhHHHHHHhhHHHHHHHhhhh
Q 027966 99 IIFLSNSLTLMMVYVWSKQNPFIHMSFLGLFTFTAAYLPWVLLGFSVFVGASAWVDLLGMIAGHAYYFLEDV 170 (216)
Q Consensus 99 ~~fL~~~L~~~liYiWsr~np~~~V~~~G~~~i~a~ylP~~~l~~~~l~~~s~~~~liGi~~GHly~fL~~i 170 (216)
..-....+.......+.++... +. ....+.+...+++..+.... ..+.+...++.|+++|-++-+.-..
T Consensus 74 Sg~~~~l~~~~~~~~~~~~~~~-~~-~~~~~~~~~~~~~~~~~~~~-~~~~~~~~hl~G~~~G~~~~~~~~~ 142 (145)
T PF01694_consen 74 SGAVFGLLGAFLFLYPQNKKRL-RF-IYLALVVPIIVLVIILLLGF-IPNISFLGHLGGFLAGLLYGFLILR 142 (145)
T ss_dssp HHHHHHHHHHHHHHHHCCCCCS-----HCCCCCCCCCCCHHHCTSS-SSTTTHHHHHHHHHHHHHHHHHHCH
T ss_pred cccchHHHHHHHHHHhhccchh-hc-chHHHHHHHHHHHHHHHHHH-HHhHHHHHHHHHHHHHHHHHHHHHH
Confidence 0111112222222222222222 11 22234555556665555443 2234778899999999998876443
No 6
>PTZ00101 rhomboid-1 protease; Provisional
Probab=96.93 E-value=0.0041 Score=55.47 Aligned_cols=55 Identities=20% Similarity=0.244 Sum_probs=42.4
Q ss_pred cceeecccccchhhccceecCCCCHHHHHHHHHHHHHhhhhhhcCCCCCchhHH-HHHHHH
Q 027966 16 DCFYIDGATNTVTINMAIFFVMTDLDFLFHMFFLARYCKLLEENSFRGRTADFL-YMLLFG 75 (216)
Q Consensus 16 ~~~~~~~q~wR~liTsf~f~G~~sl~~l~~l~fl~~yss~LE~~~f~~~~aDyl-~~Ll~~ 75 (216)
++....+|+|| ++|+.|..++ -++.++++++++..++.+|+.. .+..|. -|++-+
T Consensus 94 ~~~i~~gq~WR-LiT~~FlH~~-~~HLl~Nm~~l~~~G~~lE~~~---G~~r~~ilYl~sG 149 (278)
T PTZ00101 94 ASRIKQGEIHR-LILPIFLHAN-IFHTFFNVFFQLRMGFTLEKNY---GIVKIIILYFLTG 149 (278)
T ss_pred hhhhhcCCCHH-HHHHHHHccC-HHHHHHHHHHHHHHHHHHHHHH---ChHHHHHHHHHHH
Confidence 34445799999 9999888765 4899999999999999999986 455665 444333
No 7
>COG0705 Membrane associated serine protease [Amino acid transport and metabolism]
Probab=96.39 E-value=0.019 Score=48.81 Aligned_cols=133 Identities=23% Similarity=0.200 Sum_probs=88.7
Q ss_pred cccchhhccceecCCCCHHHHHHHHHHHHHhhhhhhcCCCCCchhHHHHHHHHHHHHHHHHHhhcccccccchhHHHhHH
Q 027966 23 ATNTVTINMAIFFVMTDLDFLFHMFFLARYCKLLEENSFRGRTADFLYMLLFGATFLTGTVLIGGMIPYLSESFAKIIFL 102 (216)
Q Consensus 23 q~wR~liTsf~f~G~~sl~~l~~l~fl~~yss~LE~~~f~~~~aDyl~~Ll~~~~~i~~~s~~~~~~~y~~~~~~~~~fL 102 (216)
|+|| ++|+-|..++. .+.++|+..++.+.+.+|+.. .+..|+.+.+.++..-.+.....+...+ .+.+
T Consensus 67 ~~w~-lit~~FlH~~~-~Hll~N~~~l~~fg~~le~~~---G~~~f~~~yl~~gl~~~~~~~~~~~~~~-------~~~~ 134 (228)
T COG0705 67 QLWR-LITAIFLHAGF-LHLLFNMLALWVFGSNLERRL---GTLRFLLFYLLSGLLAGLAQVLFGPKGG-------APSL 134 (228)
T ss_pred chHH-HHHHHHHHhhH-HHHHHHHHHHHHhhHHHHHHh---chhHHHHHHHHHHHHHHHHHHHHccccc-------Cccc
Confidence 8999 89998887766 889999999999999999976 3444666666655543333322211110 1111
Q ss_pred H-HHHHHHHHHHhhhcCCCceeEEEEe-ecccccchHHHHHHHHHHhcc-h------hHHHHHHhhHHHHHHHh
Q 027966 103 S-NSLTLMMVYVWSKQNPFIHMSFLGL-FTFTAAYLPWVLLGFSVFVGA-S------AWVDLLGMIAGHAYYFL 167 (216)
Q Consensus 103 ~-~~L~~~liYiWsr~np~~~V~~~G~-~~i~a~ylP~~~l~~~~l~~~-s------~~~~liGi~~GHly~fL 167 (216)
| +.-...++=.++...|..++..... ++.++..+=.+.++.+++.+. + ...++-|.+.|=++-.+
T Consensus 135 GASG~i~gllga~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~~~~~va~~aHl~G~i~G~l~~~~ 208 (228)
T COG0705 135 GASGAIFGLLGAYFLLFPFARILLLFLSLPRPALILILIWLLYSLFSGAGSFGPSVAWSAHLGGLIGGLLLAAL 208 (228)
T ss_pred chhHHHHHHHHHHHHHccccchhhhhccCchhHHHHHHHHHHHHHHHHhcCCchHHHHHHHHHHHHHHHHHHHH
Confidence 1 3334445555566777777776644 666667777777778887652 2 56788999999888765
No 8
>PRK10907 intramembrane serine protease GlpG; Provisional
Probab=96.24 E-value=0.045 Score=48.79 Aligned_cols=132 Identities=16% Similarity=0.205 Sum_probs=76.4
Q ss_pred ecccccchhhccceecCCCCHHHHHHHHHHHHHhhhhhhcCCCCCchhHHHHHHHHHHHHHHHHHhhcccccccchhHHH
Q 027966 20 IDGATNTVTINMAIFFVMTDLDFLFHMFFLARYCKLLEENSFRGRTADFLYMLLFGATFLTGTVLIGGMIPYLSESFAKI 99 (216)
Q Consensus 20 ~~~q~wR~liTsf~f~G~~sl~~l~~l~fl~~yss~LE~~~f~~~~aDyl~~Ll~~~~~i~~~s~~~~~~~y~~~~~~~~ 99 (216)
...|+|| ++|+-|..++. ++.+||++.++..++.+|+.. .+..++...+..++.=-+...... .+ ..
T Consensus 131 ~~~q~WR-l~T~~flH~~~-~Hl~fNml~l~~lG~~iE~~~---G~~~~l~l~l~s~i~~~~~~~~~~------~~--~~ 197 (276)
T PRK10907 131 LKFELWR-YFTHALLHFSL-LHILFNLLWWWYLGGAVEKRL---GSGKLIVITLISALLSGWVQSKFS------GP--WF 197 (276)
T ss_pred ccCCcHH-HHhHHHHhCCH-HHHHHHHHHHHHHHHHHHHHH---ChHHHHHHHHHHHHHHHHHHHHHc------cc--hh
Confidence 3689999 99999887765 899999999999999999875 456666555544432111111110 10 00
Q ss_pred hHHHHHHHHHHHHHhhh--cCCCceeEEEEeecccccchHHHHHHHH--H--Hhcc--hhHHHHHHhhHHHHHHHhhhh
Q 027966 100 IFLSNSLTLMMVYVWSK--QNPFIHMSFLGLFTFTAAYLPWVLLGFS--V--FVGA--SAWVDLLGMIAGHAYYFLEDV 170 (216)
Q Consensus 100 ~fL~~~L~~~liYiWsr--~np~~~V~~~G~~~i~a~ylP~~~l~~~--~--l~~~--s~~~~liGi~~GHly~fL~~i 170 (216)
.=++-++...+.|+|-+ ++|+..+ .+|..++-++.+-+- + +.+. +-..++.|.++|-+.-+++..
T Consensus 198 gGaSGvVygL~g~~~~~~~~~p~~~~------~lp~~~~~f~llwl~~g~~~~~g~~Ian~AHlgGli~Gll~g~~~~~ 270 (276)
T PRK10907 198 GGLSGVVYALMGYVWLRGERDPQSGI------YLPRGLIAFALLWLVAGYFDLFGMSIANAAHVAGLAVGLAMAFWDTR 270 (276)
T ss_pred hHHHHHHHHHHHHHHHHhccccccch------hhhHHHHHHHHHHHHHHHHHccCcccHHHHHHHHHHHHHHHHHHhhh
Confidence 01445555666677754 4554322 334444443333111 1 1121 336678888888877666433
No 9
>KOG2890 consensus Predicted membrane protein [Function unknown]
Probab=90.29 E-value=0.56 Score=42.46 Aligned_cols=145 Identities=21% Similarity=0.184 Sum_probs=95.1
Q ss_pred ccccchhhccceecCCCCHHHHHHHHHHHHHhhhhhhcCCCCCchhHHHHHHHHHHHHHHHHHhhcccccccchhHH---
Q 027966 22 GATNTVTINMAIFFVMTDLDFLFHMFFLARYCKLLEENSFRGRTADFLYMLLFGATFLTGTVLIGGMIPYLSESFAK--- 98 (216)
Q Consensus 22 ~q~wR~liTsf~f~G~~sl~~l~~l~fl~~yss~LE~~~f~~~~aDyl~~Ll~~~~~i~~~s~~~~~~~y~~~~~~~--- 98 (216)
...|+ ++|+. |++.--++.+.++.-+.-+++.+|.+- .+.+++.+..+...+..+...+..+..| ....+
T Consensus 65 ~~~Wt-liTs~-fie~~vw~V~~sv~~L~v~G~~lEp~W---g~~e~lkff~ivn~~~~l~v~v~~~l~Y--~it~n~v~ 137 (326)
T KOG2890|consen 65 FFPWT-LITSG-FIELNVWDVLVSVLTLSVGGKFLEPNW---GSLELLKFFAIVNGSTTLVVLVPALLLY--MITDNHVY 137 (326)
T ss_pred hhhHH-HHhcc-hhhhhHHHHHHHHHheeecceeeccCC---CCHHHHHHHHHhhchhHHHHHHHHHHHH--HHhcCceE
Confidence 57899 89995 668888999999999999999999875 4555555544332221111111111111 00000
Q ss_pred --HhHH-HHHHHHHHHHHhhhcCCCceeEEEEeecccccchHHHHHHHHHHhc-------chhHHHHHHhhHHHHHHHhh
Q 027966 99 --IIFL-SNSLTLMMVYVWSKQNPFIHMSFLGLFTFTAAYLPWVLLGFSVFVG-------ASAWVDLLGMIAGHAYYFLE 168 (216)
Q Consensus 99 --~~fL-~~~L~~~liYiWsr~np~~~V~~~G~~~i~a~ylP~~~l~~~~l~~-------~s~~~~liGi~~GHly~fL~ 168 (216)
+++- .......+.-.|-|.-|+..|--.=.-.++++-+|...+.++++.. .++..-..|..++-.|..+-
T Consensus 138 L~~~i~G~~gilaGilVa~kQllpd~~il~~~~~r~~~~~lP~~~l~~~~il~i~~f~~f~~l~s~~~g~~~sWtYLRfy 217 (326)
T KOG2890|consen 138 LYIPIHGTTGILAGILVAWKQLLPDTIILELKSGRFLYAHLPLLVLFLSLILSIITFLVFASLPSITFGVLVSWTYLRFY 217 (326)
T ss_pred EEEEeccchHHHHHHHHHHHHHcCceeEEeccchhhhhhhCCHHHHHHHHHHHHHHHHHhhhhHHHHHhhhhhhhhheec
Confidence 1110 1345556777899999998776554456666679999888887754 24566778999999999888
Q ss_pred hhccC
Q 027966 169 DVYPR 173 (216)
Q Consensus 169 ~i~P~ 173 (216)
.-.|.
T Consensus 218 q~h~~ 222 (326)
T KOG2890|consen 218 QRHPT 222 (326)
T ss_pred ccCCc
Confidence 88883
No 10
>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=84.26 E-value=2.9 Score=31.50 Aligned_cols=51 Identities=18% Similarity=0.168 Sum_probs=42.9
Q ss_pred cccchhhccceecCCCCHHHHHHHHHHHHHhhhhhhcCCCCCchhHHHHHHHHHHH
Q 027966 23 ATNTVTINMAIFFVMTDLDFLFHMFFLARYCKLLEENSFRGRTADFLYMLLFGATF 78 (216)
Q Consensus 23 q~wR~liTsf~f~G~~sl~~l~~l~fl~~yss~LE~~~f~~~~aDyl~~Ll~~~~~ 78 (216)
.+|+ ++|+.++ ...-+..+++...+.-.++.+|+.- .+.+++.+++++.+.
T Consensus 7 ~pWt-l~T~~fv-e~~i~~~l~~~~~l~~~g~~lE~~W---Gs~E~lkFi~vv~~~ 57 (99)
T PF08551_consen 7 YPWT-LFTAGFV-ETNIIGLLFSLLTLFYGGRYLEPIW---GSREFLKFILVVNVI 57 (99)
T ss_pred ehHH-HHHHHHH-HhHHHHHHHHHHHHHHhhHHHHHhc---ChHHHHHHHHHHHHH
Confidence 7899 9999766 5556889999999999999999875 588999998877654
No 11
>PF12841 YvrJ: YvrJ protein family; InterPro: IPR024419 This entry is represents a family of uncharacterised protein. The function of the Bacillus subtilis YvrJ protein is not known, but its expression is regulated by the cell envelope stress-inducible sigma factor YvrI [].
Probab=56.17 E-value=13 Score=23.39 Aligned_cols=25 Identities=20% Similarity=0.287 Sum_probs=22.5
Q ss_pred cCCCCHHHHHHHHHHHHHhhhhhhc
Q 027966 35 FVMTDLDFLFHMFFLARYCKLLEEN 59 (216)
Q Consensus 35 ~G~~sl~~l~~l~fl~~yss~LE~~ 59 (216)
.|+.|++....+|++.|..+.||+-
T Consensus 3 I~n~GFPi~va~yLL~R~E~kld~L 27 (38)
T PF12841_consen 3 ISNVGFPIAVAIYLLVRIEKKLDEL 27 (38)
T ss_pred hhhcCcHHHHHHHHHHHHHHHHHHH
Confidence 5788999999999999999999964
No 12
>KOG2289 consensus Rhomboid family proteins [Signal transduction mechanisms]
Probab=52.68 E-value=22 Score=32.41 Aligned_cols=141 Identities=11% Similarity=0.059 Sum_probs=80.6
Q ss_pred ecccccchhhccceecCCCCHHHHHHHHHHHHHhhhhhhcCCCCCchhHHHHHHHHHHHHHHHHHhhcccccccchhHHH
Q 027966 20 IDGATNTVTINMAIFFVMTDLDFLFHMFFLARYCKLLEENSFRGRTADFLYMLLFGATFLTGTVLIGGMIPYLSESFAKI 99 (216)
Q Consensus 20 ~~~q~wR~liTsf~f~G~~sl~~l~~l~fl~~yss~LE~~~f~~~~aDyl~~Ll~~~~~i~~~s~~~~~~~y~~~~~~~~ 99 (216)
.+.|.|| ++|+-+-..+. +++.+++...--..-.||..+ ..-..--+|++-..+.+++.. ++..-.++.+.-...
T Consensus 115 ~r~E~WR-llTym~LHaGi-~HL~~N~~~ql~iGi~LE~~~-G~~RiglIYl~gg~aGSlls~--l~d~~~~sVGASggv 189 (316)
T KOG2289|consen 115 HRGELWR-LLTYMWLHAGI-FHLLLNMLSQLFIGIPLEQVH-GFLRIGLIYLAGGVAGSLLSS--LFDPNSISVGASGGV 189 (316)
T ss_pred hhchhHH-HHHHHHHhcCH-HHHHHHHHHHHhccccHHhhc-CceEEeeehhhhhhhhHHHHH--HhccCCceecccHHH
Confidence 4699999 89987665544 899999999999999999886 213344556664444444321 111111110111122
Q ss_pred hHHHHHHHHHHHHHhhhcCCCceeEEEEeecccccchHHHHHHHHHHhcch----hHHHHHHhhHHHHHHHhhhhccCCC
Q 027966 100 IFLSNSLTLMMVYVWSKQNPFIHMSFLGLFTFTAAYLPWVLLGFSVFVGAS----AWVDLLGMIAGHAYYFLEDVYPRMT 175 (216)
Q Consensus 100 ~fL~~~L~~~liYiWsr~np~~~V~~~G~~~i~a~ylP~~~l~~~~l~~~s----~~~~liGi~~GHly~fL~~i~P~~~ 175 (216)
.=|-.+....++--|...+.... +.-.=.+++++++-+|.. -+.++=|...|=.+-|+..+-|.++
T Consensus 190 faLlgA~Ls~l~~Nw~~m~~~~~----------~l~~ll~Ii~i~l~~G~~~~~~~~~h~gg~~~G~~~~fil~~~g~~~ 259 (316)
T KOG2289|consen 190 FALLGAHLSNLLTNWTIMKNKFA----------ALRTLLIIIFINLDLGFAPYVDNFAHIGGLLAGFLLGFVLHIGGQLG 259 (316)
T ss_pred HHHHHHHHHHHHhhHHHhcchHH----------HHHHHHHHHHHHHhhccccceeccccccccCCCcchhHHhhhcccee
Confidence 22444666677777876654422 111222333555556642 2344556777777777777777754
No 13
>KOG4463 consensus Uncharacterized conserved protein [Function unknown]
Probab=48.95 E-value=26 Score=31.44 Aligned_cols=51 Identities=14% Similarity=0.262 Sum_probs=33.7
Q ss_pred cccccchhhccceecCCCCHHHHHHHHHHHHHhhhhhhcCCCCCchhHHHHHHHHHH
Q 027966 21 DGATNTVTINMAIFFVMTDLDFLFHMFFLARYCKLLEENSFRGRTADFLYMLLFGAT 77 (216)
Q Consensus 21 ~~q~wR~liTsf~f~G~~sl~~l~~l~fl~~yss~LE~~~f~~~~aDyl~~Ll~~~~ 77 (216)
..|+||+++.-|+|..+ -+.++-+|.+| |-+.+|+.- .+-.|+-++++.++
T Consensus 48 y~qywrlL~~qF~~~n~--~e~~~~l~I~Y-~fR~~ERlL---GShky~~fiv~s~~ 98 (323)
T KOG4463|consen 48 YFQYWRLLMSQFAFSNT--PELMFGLYILY-YFRVFERLL---GSHKYSVFIVFSGT 98 (323)
T ss_pred HHHHHHHHHHHHHhcCC--hHHHHHHHHHH-HHHHHHHHh---ccccceeehhHHHH
Confidence 48999977777888653 45566666665 458899865 44556656555544
No 14
>PF11169 DUF2956: Protein of unknown function (DUF2956); InterPro: IPR021339 This family of proteins with unknown function appears to be restricted to Gammaproteobacteria.
Probab=38.30 E-value=23 Score=27.18 Aligned_cols=18 Identities=33% Similarity=0.562 Sum_probs=15.0
Q ss_pred ecccccchHHHHHHHHHH
Q 027966 129 FTFTAAYLPWVLLGFSVF 146 (216)
Q Consensus 129 ~~i~a~ylP~~~l~~~~l 146 (216)
..-...+|||+++++||+
T Consensus 78 ~~~~~~~LPW~LL~lSW~ 95 (103)
T PF11169_consen 78 SQSRSSWLPWGLLVLSWI 95 (103)
T ss_pred ccccccchhHHHHHHHHH
Confidence 455677999999999994
No 15
>PHA02132 hypothetical protein
Probab=27.64 E-value=14 Score=26.59 Aligned_cols=29 Identities=21% Similarity=0.498 Sum_probs=21.5
Q ss_pred HhhhcCCCce--------eEEEEeecccccchHHHHHHH
Q 027966 113 VWSKQNPFIH--------MSFLGLFTFTAAYLPWVLLGF 143 (216)
Q Consensus 113 iWsr~np~~~--------V~~~G~~~i~a~ylP~~~l~~ 143 (216)
-|.|+.|+.+ |+.+| +|.+.+||.++.+.
T Consensus 33 ewr~~~pdsk~pa~sl~~vqiyg--~ia~awlp~~~~l~ 69 (86)
T PHA02132 33 EWRQKRPDSKMPARSLCAVQVYG--MIAGAWLPLAIYLV 69 (86)
T ss_pred HHHcCCCCccCchhhhhhhHHHH--HHHHHHHHHHHHHH
Confidence 5999999975 46676 67778888876544
Done!