Query 024772
Match_columns 262
No_of_seqs 135 out of 225
Neff 5.7
Searched_HMMs 46136
Date Fri Mar 29 07:18:24 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/024772.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/024772hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG2890 Predicted membrane pro 100.0 2.8E-62 6.1E-67 445.8 14.8 245 12-256 22-321 (326)
2 PF08551 DUF1751: Eukaryotic i 99.5 2.4E-15 5.2E-20 118.8 -1.1 54 46-99 1-99 (99)
3 KOG2632 Rhomboid family protei 96.6 0.0031 6.8E-08 57.8 5.4 128 20-153 20-194 (258)
4 COG0705 Membrane associated se 96.1 0.022 4.7E-07 50.3 7.5 115 42-158 52-212 (228)
5 PRK10907 intramembrane serine 95.6 0.032 6.9E-07 51.8 6.5 59 14-73 96-155 (276)
6 PF01694 Rhomboid: Rhomboid fa 95.2 0.0016 3.5E-08 52.7 -3.0 69 52-120 5-108 (145)
7 PF04511 DER1: Der1-like famil 94.7 0.03 6.5E-07 49.0 3.4 133 14-156 4-180 (197)
8 KOG0858 Predicted membrane pro 93.6 0.069 1.5E-06 48.6 3.4 132 13-154 14-184 (239)
9 PTZ00101 rhomboid-1 protease; 92.8 0.26 5.6E-06 45.9 6.0 59 15-73 53-122 (278)
10 PF06946 Phage_holin_5: Phage 74.0 8.2 0.00018 30.4 5.0 47 111-157 31-84 (93)
11 PRK10862 SoxR reducing system 70.3 9.4 0.0002 32.4 5.0 44 115-158 83-127 (154)
12 KOG3142 Prenylated rab accepto 67.6 11 0.00023 33.4 4.9 26 134-159 87-112 (187)
13 COG5291 Predicted membrane pro 62.8 6.8 0.00015 36.3 2.9 112 12-126 20-171 (313)
14 PF04246 RseC_MucC: Positive r 62.8 19 0.00042 29.3 5.3 44 115-158 76-120 (135)
15 KOG3249 Uncharacterized conser 38.9 70 0.0015 27.9 5.1 27 137-168 125-151 (181)
16 PF03082 MAGSP: Male accessory 36.4 29 0.00062 31.6 2.4 29 218-246 107-139 (264)
17 PF04528 Adeno_E4_34: Adenovir 34.0 26 0.00056 29.8 1.7 17 222-238 125-141 (148)
18 TIGR03766 conserved hypothetic 33.1 1.9E+02 0.0042 28.7 8.0 21 222-243 330-350 (483)
19 TIGR03759 conj_TIGR03759 integ 32.6 35 0.00076 30.5 2.3 23 221-243 47-71 (200)
20 PF02654 CobS: Cobalamin-5-pho 29.4 1.1E+02 0.0024 27.4 5.1 27 140-167 193-219 (235)
21 KOG2289 Rhomboid family protei 27.7 29 0.00062 33.1 1.0 22 52-73 118-139 (316)
22 COG3086 RseC Positive regulato 26.1 1.6E+02 0.0035 25.2 5.1 44 115-158 83-127 (150)
23 TIGR00908 2A0305 ethanolamine 24.3 3.7E+02 0.008 25.7 8.0 53 115-169 388-441 (442)
24 PRK15065 PTS system mannose-sp 23.6 2.3E+02 0.005 26.3 6.1 39 111-153 202-240 (262)
25 PF04217 DUF412: Protein of un 22.3 64 0.0014 27.4 2.0 33 98-131 23-56 (143)
26 PRK08965 putative monovalent c 22.2 1.7E+02 0.0036 24.8 4.6 17 141-157 31-47 (162)
27 COG1377 FlhB Flagellar biosynt 21.2 87 0.0019 30.5 3.0 23 221-243 237-259 (363)
28 PF12023 DUF3511: Domain of un 20.9 68 0.0015 22.2 1.6 13 221-233 4-16 (47)
29 cd03211 GST_C_Metaxin2 GST_C f 20.3 98 0.0021 24.8 2.7 24 221-244 54-77 (126)
30 KOG4453 Predicted ER membrane 20.1 86 0.0019 28.9 2.5 22 137-158 195-216 (269)
No 1
>KOG2890 consensus Predicted membrane protein [Function unknown]
Probab=100.00 E-value=2.8e-62 Score=445.83 Aligned_cols=245 Identities=36% Similarity=0.577 Sum_probs=217.9
Q ss_pred cchhHHHHHHHHHHHHHHHHHHhh----hhhcceeEeecCccccchhHHHHHHhhccccceEEeec--------------
Q 024772 12 TGFTKLCKGLAVVLVGGHILVQLL----PASVSVLALIPARTIPFAWNLLTAGYIEQTVHGVRPSF-------------- 73 (262)
Q Consensus 12 ~~~tr~~k~i~~vl~~~~~Ls~~~----~~~~~~L~liP~~~~~~pWtl~T~~fvE~~i~~~i~s~-------------- 73 (262)
.......+.||++..++|.+|+.- ..+.|+++++|+++++||||++|++|+|.|+|++++|+
T Consensus 22 ~n~~vvvs~ic~~tlf~yi~sf~~~t~~l~~~p~y~lvp~~~~~~~WtliTs~fie~~vw~V~~sv~~L~v~G~~lEp~W 101 (326)
T KOG2890|consen 22 LNLEVVVSAICVLTLFGYILSFGNFTILLATLPGYQLVPNALFFFPWTLITSGFIELNVWDVLVSVLTLSVGGKFLEPNW 101 (326)
T ss_pred hhchhHHHHHHHHHHHHHHHHHHHhHHHHHhccccccCCcchhhhhHHHHhcchhhhhHHHHHHHHHheeecceeeccCC
Confidence 445567888998999999999762 34689999999999999999999999999999999888
Q ss_pred -------------------------------ccceeeeeeccchHHHHHHHHHHhhhhcCCceeEE---eccccchhHHH
Q 024772 74 -------------------------------DVKKFTYMPLSGFQGVLAGFLVGIKQIVPDQELYL---LKIKAKWLPSL 119 (262)
Q Consensus 74 -------------------------------g~~~~l~~~i~G~~~~~~g~lVA~kQl~Pd~~v~~---~~ir~K~lP~i 119 (262)
.|..|||.+++|+.|+++|++||+||++||+.|.. .++.+||+|++
T Consensus 102 g~~e~lkff~ivn~~~~l~v~v~~~l~Y~it~n~v~L~~~i~G~~gilaGilVa~kQllpd~~il~~~~~r~~~~~lP~~ 181 (326)
T KOG2890|consen 102 GSLELLKFFAIVNGSTTLVVLVPALLLYMITDNHVYLYIPIHGTTGILAGILVAWKQLLPDTIILELKSGRFLYAHLPLL 181 (326)
T ss_pred CCHHHHHHHHHhhchhHHHHHHHHHHHHHHhcCceEEEEEeccchHHHHHHHHHHHHHcCceeEEeccchhhhhhhCCHH
Confidence 38889999999999999999999999999999886 68888999999
Q ss_pred HHHHHHHHHHHhhhhhhhHHHHHHHHHHHHHHHhhhccCCCCcccCCCCCCccccccCCcccccccchhhhhhhhheecc
Q 024772 120 MLLLSIAISFFTAESAAYLPTLIFGTYMGWIYLRYLQKKPETKLSGDPSDDFAFSSFFPEFIRPVIDPIASIFHRMLCGR 199 (262)
Q Consensus 120 ~l~~~~~~~~~~~~~~~~~~~~~~G~~~sW~YLRF~Q~~p~~~~rGD~Sd~Fafa~FFP~~l~p~i~~is~~~~~l~c~~ 199 (262)
.+.++++++++.+....+++++++|+++||+||||||+||++..|||+||+|+|++|||+.+||++++++|.+|+++|++
T Consensus 182 ~l~~~~il~i~~f~~f~~l~s~~~g~~~sWtYLRfyq~h~~~~~rGD~Sd~F~fvsFFP~v~qp~~~li~n~~~~~l~~~ 261 (326)
T KOG2890|consen 182 VLFLSLILSIITFLVFASLPSITFGVLVSWTYLRFYQRHPTDELRGDCSDSFTFVSFFPEVLQPFFHLIANTIYRILVRM 261 (326)
T ss_pred HHHHHHHHHHHHHHHhhhhHHHHHhhhhhhhhheecccCCcccccCCchhceehhhhchhhhhHHHHHHHHHHHHHHHHh
Confidence 99999999999999999999999999999999999999988889999999999999999999999999999999999665
Q ss_pred cccc--cCC-CCCCcccCCCCCCCCchhhhHHHHHHHHHHHHHHhccccccccccccccc
Q 024772 200 RTET--SGD-DHGYTLGGASLPGSDPIEASRRRERGARALEERLATEKLAAAQSVEESKK 256 (262)
Q Consensus 200 ~~~~--~~~-~~~~~~~~~~lpg~~~~eAERRR~~ALkaL~eRL~~~~~~~~~~~~~~~~ 256 (262)
.+.+ ..| ..+.+..++++||.|++|||||||+|||||||||++...+++++.+|.++
T Consensus 262 ~~~~~~~~d~~~~~~s~~~~lpg~d~~d~eRRRQ~alkaL~eRl~~~~~~p~~~~~~~~~ 321 (326)
T KOG2890|consen 262 GVVKKPHVDIDLDSGSVGANLPGLDPKDAERRRQLALKALEERLKKTRTAPVASYDEWDD 321 (326)
T ss_pred ccccccceecccCcccccccCCCCChhHHHHHHHHHHHHHHHHhcCcccCccccccchhh
Confidence 5321 112 14455666899999999999999999999999999999887776666553
No 2
>PF08551 DUF1751: Eukaryotic integral membrane protein (DUF1751); InterPro: IPR013861 This entry is found in eukaryotic integral membrane proteins. Q12239 from SWISSPROT, a Saccharomyces cerevisiae (Baker's yeast) protein, has been shown to localise COP II vesicles [].
Probab=99.49 E-value=2.4e-15 Score=118.84 Aligned_cols=54 Identities=46% Similarity=0.987 Sum_probs=51.7
Q ss_pred cCccccchhHHHHHHhhccccceEEeec---------------------------------------------ccceeee
Q 024772 46 PARTIPFAWNLLTAGYIEQTVHGVRPSF---------------------------------------------DVKKFTY 80 (262)
Q Consensus 46 P~~~~~~pWtl~T~~fvE~~i~~~i~s~---------------------------------------------g~~~~l~ 80 (262)
||++++||||++|++|+|+|++++++++ +|+.+++
T Consensus 1 P~~~~~~pWtl~T~~fve~~i~~~l~~~~~l~~~g~~lE~~WGs~E~lkFi~vv~~~tnl~~~~~~~~~y~i~~~~~~l~ 80 (99)
T PF08551_consen 1 PGRSFPYPWTLFTAGFVETNIIGLLFSLLTLFYGGRYLEPIWGSREFLKFILVVNVITNLLTFLLYLLLYAITGNESYLF 80 (99)
T ss_pred CCceeeehHHHHHHHHHHhHHHHHHHHHHHHHHhhHHHHHhcChHHHHHHHHHHHHHhHHHHHHHHHHHHHHhCCCceeE
Confidence 8999999999999999999999999888 5888899
Q ss_pred eeccchHHHHHHHHHHhhh
Q 024772 81 MPLSGFQGVLAGFLVGIKQ 99 (262)
Q Consensus 81 ~~i~G~~~~~~g~lVA~kQ 99 (262)
.++||++|+++|++||+||
T Consensus 81 ~~i~G~~~~~~g~lVa~kQ 99 (99)
T PF08551_consen 81 VPISGFMGVLAGFLVAFKQ 99 (99)
T ss_pred EEecCcHHhHhheEEEEeC
Confidence 9999999999999999999
No 3
>KOG2632 consensus Rhomboid family proteins [Function unknown]
Probab=96.65 E-value=0.0031 Score=57.83 Aligned_cols=128 Identities=18% Similarity=0.234 Sum_probs=88.1
Q ss_pred HHHHHHHHHHHHHHhhhhhcceeEeecCcccc-chhHHHHHHhhccccceEEeec--------------c----------
Q 024772 20 GLAVVLVGGHILVQLLPASVSVLALIPARTIP-FAWNLLTAGYIEQTVHGVRPSF--------------D---------- 74 (262)
Q Consensus 20 ~i~~vl~~~~~Ls~~~~~~~~~L~liP~~~~~-~pWtl~T~~fvE~~i~~~i~s~--------------g---------- 74 (262)
.+.+...+.|+++. .+.....+.+-+...+. ..|+++|+.++|.|..++++|+ |
T Consensus 20 ~~~~~~~~i~lv~~-~~~i~~~~~l~~~~l~~~ql~RL~Ty~l~H~s~~hllfnmlaL~~~g~~fE~~~G~t~~~l~~~~ 98 (258)
T KOG2632|consen 20 IVVVLAILIYLVSF-FPGIVEVLGLPSELLINWQLYRLITYALVHLSLPHLLFNMLALWPLGSQFERTHGTTVRILMFTV 98 (258)
T ss_pred HHHHHHHHHHHHhc-cchhhhHhcCCHHHhhhHHHHHHHHHHHHhccHHHHHHHHHHHHhchhHHHhhccceehHHHHHH
Confidence 33444566677774 45555566666666666 6999999999999999999988 1
Q ss_pred -------------------cceeeeeeccchHHHHHHHHHHhhhhcCCceeEE---eccccchhHHHHHHHHHHHHHHhh
Q 024772 75 -------------------VKKFTYMPLSGFQGVLAGFLVGIKQIVPDQELYL---LKIKAKWLPSLMLLLSIAISFFTA 132 (262)
Q Consensus 75 -------------------~~~~l~~~i~G~~~~~~g~lVA~kQl~Pd~~v~~---~~ir~K~lP~i~l~~~~~~~~~~~ 132 (262)
++.+.-...+|+.+++.+++++..-..|+....+ .++..|+.|.+++....+ +..
T Consensus 99 llalf~gIl~ll~~~~~~~~d~~~~~~a~G~s~v~Fam~~~~~~~sp~r~~~~fg~~siP~~l~Pw~lLi~~~~---lvp 175 (258)
T KOG2632|consen 99 LLALFSGILYLLAYHVFLLSDLVYVEGAIGFSGVLFAMMAVLEVQSPVRSRSVFGLFSIPIVLAPWALLIATQI---LVP 175 (258)
T ss_pred HHHHHHHHHHHHHHHHHhhcchhhhcccccccHHHHHHHHHHhhcCcccchhhcccccccHHHHHHHHHHHHHH---Hcc
Confidence 1112223578999999999999888888888443 788999999998744322 111
Q ss_pred hhhhhHHHHHHHHHHHHHHHh
Q 024772 133 ESAAYLPTLIFGTYMGWIYLR 153 (262)
Q Consensus 133 ~~~~~~~~~~~G~~~sW~YLR 153 (262)
..+++ --..|++++..|.-
T Consensus 176 -~aSFl-ghl~GllvG~ay~~ 194 (258)
T KOG2632|consen 176 -QASFL-GHLCGLLVGYAYAF 194 (258)
T ss_pred -CchHH-HHHHHHHHHHHHHH
Confidence 22222 34567777777765
No 4
>COG0705 Membrane associated serine protease [Amino acid transport and metabolism]
Probab=96.11 E-value=0.022 Score=50.34 Aligned_cols=115 Identities=19% Similarity=0.321 Sum_probs=74.0
Q ss_pred eEeecCcccc-----chhHHHHHHhhccccceEEeec--------------ccce----------------eee-----e
Q 024772 42 LALIPARTIP-----FAWNLLTAGYIEQTVHGVRPSF--------------DVKK----------------FTY-----M 81 (262)
Q Consensus 42 L~liP~~~~~-----~pWtl~T~~fvE~~i~~~i~s~--------------g~~~----------------~l~-----~ 81 (262)
..+.|..... .+|+++|+.|+|.++++.+.|. |... +++ .
T Consensus 52 ~~~~~~~~~~~~~~~~~w~lit~~FlH~~~~Hll~N~~~l~~fg~~le~~~G~~~f~~~yl~~gl~~~~~~~~~~~~~~~ 131 (228)
T COG0705 52 FGLYPLNLLGALARDQLWRLITAIFLHAGFLHLLFNMLALWVFGSNLERRLGTLRFLLFYLLSGLLAGLAQVLFGPKGGA 131 (228)
T ss_pred HhhcchhhhccccccchHHHHHHHHHHhhHHHHHHHHHHHHHhhHHHHHHhchhHHHHHHHHHHHHHHHHHHHHcccccC
Confidence 5666655533 5899999999999999999888 2111 111 2
Q ss_pred eccchHHHHHHHHHHhhhhcCCceeEEec--cccchhHHHHHHHHHHHHHHhhhh----hhhHHHHHHHHHHHHHHHhhh
Q 024772 82 PLSGFQGVLAGFLVGIKQIVPDQELYLLK--IKAKWLPSLMLLLSIAISFFTAES----AAYLPTLIFGTYMGWIYLRYL 155 (262)
Q Consensus 82 ~i~G~~~~~~g~lVA~kQl~Pd~~v~~~~--ir~K~lP~i~l~~~~~~~~~~~~~----~~~~~~~~~G~~~sW~YLRF~ 155 (262)
+..|.+|.+.|++-|+-++.|...+.... +....+ +++.+..+.+++.... .....--+.|++.++.|..++
T Consensus 132 ~~~GASG~i~gllga~~~~~~~~~~~~~~~~~~~~~~--~~i~~~~~~~~~~~~~~~~~~va~~aHl~G~i~G~l~~~~~ 209 (228)
T COG0705 132 PSLGASGAIFGLLGAYFLLFPFARILLLFLSLPRPAL--ILILIWLLYSLFSGAGSFGPSVAWSAHLGGLIGGLLLAALL 209 (228)
T ss_pred cccchhHHHHHHHHHHHHHccccchhhhhccCchhHH--HHHHHHHHHHHHHHhcCCchHHHHHHHHHHHHHHHHHHHHH
Confidence 56699999999999999999997776522 222111 1222233333332221 122233668888888888777
Q ss_pred ccC
Q 024772 156 QKK 158 (262)
Q Consensus 156 Q~~ 158 (262)
.+.
T Consensus 210 ~~~ 212 (228)
T COG0705 210 SRK 212 (228)
T ss_pred hhh
Confidence 764
No 5
>PRK10907 intramembrane serine protease GlpG; Provisional
Probab=95.59 E-value=0.032 Score=51.81 Aligned_cols=59 Identities=12% Similarity=0.002 Sum_probs=35.5
Q ss_pred hhHHHHHHHHHHHHHHHHHHhhhhhcceeEeecCcccc-chhHHHHHHhhccccceEEeec
Q 024772 14 FTKLCKGLAVVLVGGHILVQLLPASVSVLALIPARTIP-FAWNLLTAGYIEQTVHGVRPSF 73 (262)
Q Consensus 14 ~tr~~k~i~~vl~~~~~Ls~~~~~~~~~L~liP~~~~~-~pWtl~T~~fvE~~i~~~i~s~ 73 (262)
+|-.+..+|++++++..+.. ......++......... .+|+++|+.|+|.++.++++|+
T Consensus 96 ~T~~li~i~i~vf~l~~~~~-~~~~~~~l~~~~~~~~~~q~WRl~T~~flH~~~~Hl~fNm 155 (276)
T PRK10907 96 LTLGVMIACVVVFILMQILG-DQTVMLWLAWPFDPSLKFELWRYFTHALLHFSLLHILFNL 155 (276)
T ss_pred HHHHHHHHHHHHHHHHHHhc-cHHHHHHHhccccccccCCcHHHHhHHHHhCCHHHHHHHH
Confidence 55556666666544433321 12233333321111112 6899999999999999999998
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=95.22 E-value=0.0016 Score=52.75 Aligned_cols=69 Identities=17% Similarity=0.236 Sum_probs=44.0
Q ss_pred chhHHHHHHhhccccceEEeec--------------c---------------ccee-e---ee-eccchHHHHHHHHHHh
Q 024772 52 FAWNLLTAGYIEQTVHGVRPSF--------------D---------------VKKF-T---YM-PLSGFQGVLAGFLVGI 97 (262)
Q Consensus 52 ~pWtl~T~~fvE~~i~~~i~s~--------------g---------------~~~~-l---~~-~i~G~~~~~~g~lVA~ 97 (262)
..|+++|+.|++.|+++++.|+ | +-.+ + .. +..|.+|.+.|++.+.
T Consensus 5 ~~wrl~T~~f~h~~~~hl~~n~~~l~~~g~~lE~~~G~~~~~~~~l~~~~~~~l~~~~~~~~~~~~~G~Sg~~~~l~~~~ 84 (145)
T PF01694_consen 5 QWWRLFTSPFVHANFLHLLFNLLALWFFGSLLERRLGSRRFLALYLLSGLLGSLLSLLFSPPNQPYVGASGAVFGLLGAF 84 (145)
T ss_dssp -TTHHHHGGG--SSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-S-----SSHHHHHHHHHHH
T ss_pred cchhhhHHHHHccCHHHHHHHHHHHHHhhhhHhhhccchHHHHHHHHHHHhhhhccccccccccccCCCcccchHHHHHH
Confidence 5899999999999999999988 1 1000 0 01 6789999999999999
Q ss_pred hhhcCCceeEE-eccccchhHHHH
Q 024772 98 KQIVPDQELYL-LKIKAKWLPSLM 120 (262)
Q Consensus 98 kQl~Pd~~v~~-~~ir~K~lP~i~ 120 (262)
-...|+..... .+.+...++.++
T Consensus 85 ~~~~~~~~~~~~~~~~~~~~~~~~ 108 (145)
T PF01694_consen 85 LFLYPQNKKRLRFIYLALVVPIIV 108 (145)
T ss_dssp HHHHHCCCCCS---HCCCCCCCCC
T ss_pred HHHHhhccchhhcchHHHHHHHHH
Confidence 99988886544 233344444433
No 7
>PF04511 DER1: Der1-like family; InterPro: IPR007599 The endoplasmic reticulum (ER) of the yeast Saccharomyces cerevisiae (Baker's yeast) contains a proteolytic system able to selectively degrade misfolded lumenal secretory proteins. For examination of the components involved in this degradation process, mutants were isolated. They could be divided into four complementation groups. The mutations led to stabilisation of two different substrates for this process, and the classes were called der for degradation in the ER. DER1 was cloned by complementation of the der1-2 mutation. The DER1 gene codes for a novel, hydrophobic protein that is localized to the ER. Deletion of DER1 abolished degradation of the substrate proteins, suggesting that the function of the Der1 protein may be specifically required for the degradation process associated with the ER []. Interestingly this family seems distantly related to the Rhomboid family of membrane peptidases. This family may also mediate degradation of misfolded proteins.
Probab=94.70 E-value=0.03 Score=49.03 Aligned_cols=133 Identities=17% Similarity=0.181 Sum_probs=81.3
Q ss_pred hhHHHHHHHHHHHHHHHHHHhhhhhcceeEeecCcccc--chhHHHHHHhh-ccccceEEeec----------------c
Q 024772 14 FTKLCKGLAVVLVGGHILVQLLPASVSVLALIPARTIP--FAWNLLTAGYI-EQTVHGVRPSF----------------D 74 (262)
Q Consensus 14 ~tr~~k~i~~vl~~~~~Ls~~~~~~~~~L~liP~~~~~--~pWtl~T~~fv-E~~i~~~i~s~----------------g 74 (262)
+||...+.++++.++..+... -...+.+.|...+. -+|.++|+.|+ ...-++.++++ +
T Consensus 4 VTR~~~~~~~~~s~l~~~~~~---~~~~l~~~~~~v~~~~q~WRl~Tsff~~g~~~~~~l~~~~~l~~~s~~LE~~~f~~ 80 (197)
T PF04511_consen 4 VTRYWLISTVALSLLVSFGII---SPYYLYFDWELVFKKFQIWRLFTSFFYFGPFSLNFLFNLYFLYQYSSSLEEGHFQG 80 (197)
T ss_pred hHHHHHHHHHHHHHHHHCCCC---CHHHeeECcHHHhhhcCceeeEEEEEEEcCCCHHHHHHHHHHHHHhhHhccCCCCC
Confidence 455555544444444333221 12245678877664 79999999887 33334445444 1
Q ss_pred c-ceeeee------------ecc---------chHHHHHHHHHHhhhhcCCceeEE---eccccchhHHHHHHHHHHHHH
Q 024772 75 V-KKFTYM------------PLS---------GFQGVLAGFLVGIKQIVPDQELYL---LKIKAKWLPSLMLLLSIAISF 129 (262)
Q Consensus 75 ~-~~~l~~------------~i~---------G~~~~~~g~lVA~kQl~Pd~~v~~---~~ir~K~lP~i~l~~~~~~~~ 129 (262)
+ .+|++. .+. -..++...++=.+.|..|+.++.+ .++|.||+|.+.++++.++.
T Consensus 81 ~~ady~~~ll~~~~~i~~~~~~~~~~~~~~~~l~~~l~~~l~Y~wsr~np~~~v~~~g~~~i~a~ylP~~~~~~~~l~~- 159 (197)
T PF04511_consen 81 RSADYLWFLLFGASLILILSLLIGPYFFNIPFLGSSLSFALTYIWSRKNPNAQVSFFGLFTIKAKYLPWVLLAFSLLFG- 159 (197)
T ss_pred CHHHHHHHHHHHHHHHHHHHHhhccchhHHHHHHHHHHHHHHHHHHHhCcccceeeEEEEEEChhhHHHHHHHHHHHhC-
Confidence 1 234431 111 123455566667889999999986 69999999998876665533
Q ss_pred HhhhhhhhHHHHHHHHHHHHHHHhhhc
Q 024772 130 FTAESAAYLPTLIFGTYMGWIYLRYLQ 156 (262)
Q Consensus 130 ~~~~~~~~~~~~~~G~~~sW~YLRF~Q 156 (262)
+. +.. ..+.|++++-+|. |++
T Consensus 160 ---~~-~~~-~~l~Gi~~Ghly~-fl~ 180 (197)
T PF04511_consen 160 ---GS-SPI-PDLLGILVGHLYY-FLK 180 (197)
T ss_pred ---CC-cHH-HHHHHHHHHHHHH-HHH
Confidence 21 222 4678999999988 554
No 8
>KOG0858 consensus Predicted membrane protein [Function unknown]
Probab=93.58 E-value=0.069 Score=48.61 Aligned_cols=132 Identities=22% Similarity=0.243 Sum_probs=85.2
Q ss_pred chhHHHHHHHHHHHHHHHHHHhhhhhcceeEeecCcccc--chhHHHHHHhhccc-cceEEeec----------------
Q 024772 13 GFTKLCKGLAVVLVGGHILVQLLPASVSVLALIPARTIP--FAWNLLTAGYIEQT-VHGVRPSF---------------- 73 (262)
Q Consensus 13 ~~tr~~k~i~~vl~~~~~Ls~~~~~~~~~L~liP~~~~~--~pWtl~T~~fvE~~-i~~~i~s~---------------- 73 (262)
.+||.-...|+++.+..-|....| -+|-+.|...+. -.|.++|+.++=.. -+..++++
T Consensus 14 pVTR~~~~~~v~tt~~~~l~lIsP---~~l~~~p~Lv~kk~QiWRliTs~lyfg~~gf~fl~n~~FlyrY~~~LE~g~f~ 90 (239)
T KOG0858|consen 14 PVTRYYTTACVVTTLLVRLDLISP---FQLYLNPELVFKKFQIWRLITSFLYFGPFGFDFLMNLYFLYRYSSMLEEGSFR 90 (239)
T ss_pred hHHHHHHHHHHHHHHHHhhcccCc---hheEecHHHHHhHhHHHHhhhhhheeccccHHHHHHHHHHHHHHHHHhcCCCC
Confidence 467777777777666555543322 356677776666 58999999988744 34445555
Q ss_pred c-cceeeee-ecc-------ch--------HHHHHHHHHHhhhhcCCceeEE---eccccchhHHHHHHHHHHHHHHhhh
Q 024772 74 D-VKKFTYM-PLS-------GF--------QGVLAGFLVGIKQIVPDQELYL---LKIKAKWLPSLMLLLSIAISFFTAE 133 (262)
Q Consensus 74 g-~~~~l~~-~i~-------G~--------~~~~~g~lVA~kQl~Pd~~v~~---~~ir~K~lP~i~l~~~~~~~~~~~~ 133 (262)
| ..+|++. -++ |. .+..+.++=.+.|.-|+..+.+ .+++.+|+|-+.+.++.+.. .
T Consensus 91 ~rtadf~~mllf~~~l~~~~~~~~~~~fLg~~l~~~l~YvWs~~Np~~~v~F~g~~~f~a~YlPwvll~fs~l~g----~ 166 (239)
T KOG0858|consen 91 GRTADFLYMLLFGAVLLTLTGLFVYIVFLGQSLVFMLVYVWSKRNPDVIVSFFGLITFKAPYLPWVLLGFSFLFG----G 166 (239)
T ss_pred CchhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhCCCceEEEEEEecCccccchHHHHHHHHHhC----C
Confidence 1 3445542 111 21 2333444555678889999987 79999999999988777643 2
Q ss_pred hhhhHHHHHHHHHHHHHHHhh
Q 024772 134 SAAYLPTLIFGTYMGWIYLRY 154 (262)
Q Consensus 134 ~~~~~~~~~~G~~~sW~YLRF 154 (262)
+. ....+|+.++-+|-=+
T Consensus 167 ~~---~~dllGi~~GHiy~fl 184 (239)
T KOG0858|consen 167 SI---LVDLLGIIVGHIYYFL 184 (239)
T ss_pred ch---HHHHHhhhhheeEEEE
Confidence 22 2367899999887543
No 9
>PTZ00101 rhomboid-1 protease; Provisional
Probab=92.78 E-value=0.26 Score=45.92 Aligned_cols=59 Identities=10% Similarity=0.151 Sum_probs=37.4
Q ss_pred hHHHHHHHHHHHHHHHHHHhh-------hh--hccee-EeecCcccc-chhHHHHHHhhccccceEEeec
Q 024772 15 TKLCKGLAVVLVGGHILVQLL-------PA--SVSVL-ALIPARTIP-FAWNLLTAGYIEQTVHGVRPSF 73 (262)
Q Consensus 15 tr~~k~i~~vl~~~~~Ls~~~-------~~--~~~~L-~liP~~~~~-~pWtl~T~~fvE~~i~~~i~s~ 73 (262)
...++.+.++.++.|+++... |+ ....+ ++.|..... .+|.++|+.|++.+++++++|+
T Consensus 53 ~~l~~~Iiii~iivfil~l~~~~~~~l~p~~~~L~~~Ga~~~~~i~~gq~WRLiT~~FlH~~~~HLl~Nm 122 (278)
T PTZ00101 53 KSFIMAISIIQIIVFIISVSIKPADFLTPSDSLLVTLGANVASRIKQGEIHRLILPIFLHANIFHTFFNV 122 (278)
T ss_pred HHHHHHHHHHHHHHHHHHHHhcccccCCCCHHHHHHHhCcchhhhhcCCCHHHHHHHHHccCHHHHHHHH
Confidence 344555555666666665442 11 22222 334443333 6999999999999999999888
No 10
>PF06946 Phage_holin_5: Phage holin; InterPro: IPR009708 This entry represents the Bacteriophage A118, holin protein. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This protein family represent one of a large number of mutually dissimilar families of phage holins. It is thought that the temporal precision of holin-mediated lysis may occur through the build-up of a holin oligomer which causes the lysis [].
Probab=73.98 E-value=8.2 Score=30.43 Aligned_cols=47 Identities=11% Similarity=0.268 Sum_probs=30.5
Q ss_pred cccchhHHHHHHHHHHHHHHhh---hhhhhHHHHHHH----HHHHHHHHhhhcc
Q 024772 111 IKAKWLPSLMLLLSIAISFFTA---ESAAYLPTLIFG----TYMGWIYLRYLQK 157 (262)
Q Consensus 111 ir~K~lP~i~l~~~~~~~~~~~---~~~~~~~~~~~G----~~~sW~YLRF~Q~ 157 (262)
++.||+|.+.+++..++.++.. .......++|.| +-.+|.+--|=+|
T Consensus 31 v~~K~iPlIs~viGilLG~~~~~~~~~~~l~~~~~aG~laGlAaTGL~e~~t~r 84 (93)
T PF06946_consen 31 VPNKWIPLISVVIGILLGAAAYPLTGDGNLALMAWAGGLAGLAATGLFEQFTNR 84 (93)
T ss_pred CCcchhhHHHHHHHHHHHHHhhhcCCCccHHHHHHHHHHhhhhhhhHHHHHHhh
Confidence 7899999999988888776632 222333344544 4456777666654
No 11
>PRK10862 SoxR reducing system protein RseC; Provisional
Probab=70.30 E-value=9.4 Score=32.39 Aligned_cols=44 Identities=25% Similarity=0.288 Sum_probs=29.2
Q ss_pred hhHHHHHHHHHHHHH-HhhhhhhhHHHHHHHHHHHHHHHhhhccC
Q 024772 115 WLPSLMLLLSIAISF-FTAESAAYLPTLIFGTYMGWIYLRYLQKK 158 (262)
Q Consensus 115 ~lP~i~l~~~~~~~~-~~~~~~~~~~~~~~G~~~sW~YLRF~Q~~ 158 (262)
-+|++.+++..++.- ++..........+.|+.++|.+.|++.++
T Consensus 83 llPLl~li~ga~l~~~~~~~e~~~~~~~~~g~~~g~~~~r~~~~~ 127 (154)
T PRK10862 83 MTPLVGLFLGAALFQLLFGSDLAALCGALLGGVGGFLLARGLSRK 127 (154)
T ss_pred HHHHHHHHHHHHHHHHHhcchHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 488888776544432 22222223334678999999999999976
No 12
>KOG3142 consensus Prenylated rab acceptor 1 [Intracellular trafficking, secretion, and vesicular transport]
Probab=67.61 E-value=11 Score=33.40 Aligned_cols=26 Identities=15% Similarity=0.574 Sum_probs=19.5
Q ss_pred hhhhHHHHHHHHHHHHHHHhhhccCC
Q 024772 134 SAAYLPTLIFGTYMGWIYLRYLQKKP 159 (262)
Q Consensus 134 ~~~~~~~~~~G~~~sW~YLRF~Q~~p 159 (262)
.......++.++..+|+||+|++-+|
T Consensus 87 ~~P~~Livl~~lv~~w~~LY~~rd~p 112 (187)
T KOG3142|consen 87 THPLSLIVLLALVAAWLFLYFLRDEP 112 (187)
T ss_pred HhHHHHHHHHHHHHHHHheeeecCCC
Confidence 33333457889999999999999554
No 13
>COG5291 Predicted membrane protein [Function unknown]
Probab=62.84 E-value=6.8 Score=36.33 Aligned_cols=112 Identities=13% Similarity=0.117 Sum_probs=59.5
Q ss_pred cchhHHHHHHHHHHHHHHHHHHhhhhhcceeEeecCcccc--chhHHHHHHhhccc-cceEEeec---------------
Q 024772 12 TGFTKLCKGLAVVLVGGHILVQLLPASVSVLALIPARTIP--FAWNLLTAGYIEQT-VHGVRPSF--------------- 73 (262)
Q Consensus 12 ~~~tr~~k~i~~vl~~~~~Ls~~~~~~~~~L~liP~~~~~--~pWtl~T~~fvE~~-i~~~i~s~--------------- 73 (262)
-..||-...++.+..++-.+....|+ |+-..-..++. -.|.++|+.++=.. -+..+..+
T Consensus 20 PPITRy~~ll~~a~til~~~~lvsPw---y~ly~~pL~~k~~qiwRlfTs~~~~~~~~~d~~M~vyf~Y~yS~~LE~g~f 96 (313)
T COG5291 20 PPITRYMTLLISAVTILVYVDLVSPW---YSLYYSPLFLKRLQIWRLFTSFLYFGKPTLDMFMHVYFLYRYSRMLEEGCF 96 (313)
T ss_pred CcHHHHHHHHHHHHHHHHHHhhcCcc---ceeeechhHHHHHHHHHHHHHHHhhcCcchhHHHHHHHHHHHHHHHhcccc
Confidence 35788777766665555555444443 22222223333 59999997765432 22233233
Q ss_pred cc--ceeee------------eeccc-hHHHHHHH----HHHhhhhcCCceeEE---eccccchhHHHHHHHHHH
Q 024772 74 DV--KKFTY------------MPLSG-FQGVLAGF----LVGIKQIVPDQELYL---LKIKAKWLPSLMLLLSIA 126 (262)
Q Consensus 74 g~--~~~l~------------~~i~G-~~~~~~g~----lVA~kQl~Pd~~v~~---~~ir~K~lP~i~l~~~~~ 126 (262)
+. ..|.+ ..|.| ..++-.|| .--|.-.-|...|.+ ..+.-||+|+|.+.++.+
T Consensus 97 ~~~lv~Y~~yl~~~~l~i~a~s~I~gg~saL~tsf~a~ItY~WS~~N~~~~Iqf~g~i~v~gkYlP~Illgfsfl 171 (313)
T COG5291 97 NTSLVEYFWYLLVISLVIFAISNIYGGISALGTSFSATITYIWSKRNPRAIIQFFGFISVPGKYLPFILLGFSFL 171 (313)
T ss_pred CccHHHHHHHHHHHHHHHHHHHHHhcchhhhcchhhhheeeeeeecCCceEEEEEEeeecchhhhhHHHHHHHHH
Confidence 11 12322 12333 22222222 223344556666765 688899999999887776
No 14
>PF04246 RseC_MucC: Positive regulator of sigma(E), RseC/MucC; InterPro: IPR007359 This bacterial family of integral membrane proteins represents a positive regulator of the sigma(E) transcription factor, namely RseC/MucC. The sigma(E) transcription factor is up-regulated by cell envelope protein misfolding, and regulates the expression of genes that are collectively termed ECF (devoted to Extra-Cellular Functions) []. In Pseudomonas aeruginosa, derepression of sigma(E) is associated with the alginate-overproducing phenotype characteristic of chronic respiratory tract colonization in cystic fibrosis patients. The mechanism by which RseC/MucC positively regulates the sigma(E) transcription factor is unknown. RseC is also thought to have a role in thiamine biosynthesis in Salmonella typhimurium []. In addition, this family also includes an N-terminal part of RnfF, a Rhodobacter capsulatus protein, of unknown function, that is essential for nitrogen fixation. This protein also contains a domain found in ApbE protein IPR003374 from INTERPRO, which is itself involved in thiamine biosynthesis.
Probab=62.76 E-value=19 Score=29.29 Aligned_cols=44 Identities=18% Similarity=0.376 Sum_probs=30.6
Q ss_pred hhHHHHHHHHHHHHHHhhh-hhhhHHHHHHHHHHHHHHHhhhccC
Q 024772 115 WLPSLMLLLSIAISFFTAE-SAAYLPTLIFGTYMGWIYLRYLQKK 158 (262)
Q Consensus 115 ~lP~i~l~~~~~~~~~~~~-~~~~~~~~~~G~~~sW~YLRF~Q~~ 158 (262)
-+|++.+++..++.-.... ........+.|+..+|.++|+|.++
T Consensus 76 ~lPll~li~g~~l~~~~~~~e~~~~l~~l~~l~~~~~~~~~~~~~ 120 (135)
T PF04246_consen 76 LLPLLALIAGAVLGSYLGGSELWAILGGLLGLALGFLILRLFDRR 120 (135)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Confidence 3788887776665544332 2233345788999999999999986
No 15
>KOG3249 consensus Uncharacterized conserved protein [Function unknown]
Probab=38.94 E-value=70 Score=27.93 Aligned_cols=27 Identities=19% Similarity=0.319 Sum_probs=19.4
Q ss_pred hHHHHHHHHHHHHHHHhhhccCCCCcccCCCC
Q 024772 137 YLPTLIFGTYMGWIYLRYLQKKPETKLSGDPS 168 (262)
Q Consensus 137 ~~~~~~~G~~~sW~YLRF~Q~~p~~~~rGD~S 168 (262)
+-+..+.+-+++|+|+- ++...+||+|
T Consensus 125 fGlvff~lSlf~~iy~n-----~~~rk~gEmS 151 (181)
T KOG3249|consen 125 FGLVFFLLSLFSIIYLN-----TGKRKRGEMS 151 (181)
T ss_pred hhHHHHHHHHHHHheec-----CCCCCCCccc
Confidence 33345567778999987 3456899998
No 16
>PF03082 MAGSP: Male accessory gland secretory protein; InterPro: IPR004315 The accessory gland of male insects is a genital tissue that secretes many components of the ejaculatory fluid, some of which affect the female's receptivity to courtship and her rate of oviposition. The protein is expressed exclusively in the male accessory glands of adult Drosophila melanogaster. During copulation it is transferred to the female genital tract where it is rapidly altered [].; GO: 0007618 mating, 0005576 extracellular region
Probab=36.43 E-value=29 Score=31.57 Aligned_cols=29 Identities=31% Similarity=0.426 Sum_probs=21.2
Q ss_pred CCCCchhhhHHH----HHHHHHHHHHHhccccc
Q 024772 218 PGSDPIEASRRR----ERGARALEERLATEKLA 246 (262)
Q Consensus 218 pg~~~~eAERRR----~~ALkaL~eRL~~~~~~ 246 (262)
+|.++-+||.|| |.|+|||.+||.-++..
T Consensus 107 kg~~~~p~~~~~~~~~q~alraLqqrL~~E~n~ 139 (264)
T PF03082_consen 107 KGLPDFPAKKRNNGSNQNALRALQQRLLLEQNN 139 (264)
T ss_pred cCCCCcchhhhccchHHHHHHHHHHHHHHhhcc
Confidence 466666665555 79999999999765543
No 17
>PF04528 Adeno_E4_34: Adenovirus early E4 34 kDa protein conserved region; InterPro: IPR007615 Adenoviruses E4 is essential for DNA replication and late protein synthesis []. The adenovirus, early region 4 open reading frame 3 (E4 ORF3) protein is required for viral DNA replication during the interferon (IFN)-induced antiviral state []. The E4 ORF3 protein reorganises the promyelocytic leukemia (PML) protein nuclear bodies. These normally punctate structures are reorganised by E4 ORF3 into tracks that eventually surround viral replication centres. PML rearrangement is an evolutionarily conserved function of E4 ORF3 []. The product of adenovirus early region 4 (E4), open reading frame 6, is E4 34k. It modulates viral late gene expression, DNA replication, apoptosis, double strand break repair, and transformation through multiple interactions with components in infected and transformed cells [, ]. Conservation of several cysteine and histidine residues among E4 34k sequences suggests the presence of a zinc binding domain, which is important for its function []. This entry is a conserved region found in the Adenovirus E4 34 kDa protein.
Probab=33.98 E-value=26 Score=29.85 Aligned_cols=17 Identities=35% Similarity=0.392 Sum_probs=13.5
Q ss_pred chhhhHHHHHHHHHHHH
Q 024772 222 PIEASRRRERGARALEE 238 (262)
Q Consensus 222 ~~eAERRR~~ALkaL~e 238 (262)
+..+|||||++|+.|=+
T Consensus 125 ~s~~E~~RQr~Lr~~m~ 141 (148)
T PF04528_consen 125 RSRTERRRQRLLRRLMR 141 (148)
T ss_pred ccchHHHHHHHHHHHHH
Confidence 56679999999997643
No 18
>TIGR03766 conserved hypothetical integral membrane protein. Models TIGR03110, TIGR03111, and TIGR03112 describe a three-gene system found in several Gram-positive bacteria, where TIGR03110 is distantly related to a putative transpeptidase, exosortase (TIGR02602). This model describes a small clade that correlates by both gene clustering and phyletic pattern, although imperfectly, to the three gene system. Both this narrow clade, and the larger set of full-length homologous integral membrane proteins, have an especially well-conserved region near the C-terminus with an invariant tyrosine. The function is unknown.
Probab=33.07 E-value=1.9e+02 Score=28.67 Aligned_cols=21 Identities=19% Similarity=0.466 Sum_probs=16.1
Q ss_pred chhhhHHHHHHHHHHHHHHhcc
Q 024772 222 PIEASRRRERGARALEERLATE 243 (262)
Q Consensus 222 ~~eAERRR~~ALkaL~eRL~~~ 243 (262)
+..+| |++.+.|.+-||+++.
T Consensus 330 ~~~~~-k~~~~~k~I~~Rl~~~ 350 (483)
T TIGR03766 330 PTKAE-KNKYSIKEIKRRLKEK 350 (483)
T ss_pred CCHHH-HHHhhHHHHHHHHHHc
Confidence 44456 6778999999999973
No 19
>TIGR03759 conj_TIGR03759 integrating conjugative element protein, PFL_4693 family. Members of this protein family, such as model protein PFL_4693 from Pseudomonas fluorescens Pf-5, belong to extended genomic regions that appear to be spread by conjugative transfer. Most members have a predicted N-terminal signal sequence. The function is unknown.
Probab=32.62 E-value=35 Score=30.51 Aligned_cols=23 Identities=26% Similarity=0.336 Sum_probs=17.0
Q ss_pred CchhhhHHH--HHHHHHHHHHHhcc
Q 024772 221 DPIEASRRR--ERGARALEERLATE 243 (262)
Q Consensus 221 ~~~eAERRR--~~ALkaL~eRL~~~ 243 (262)
.+.|+|||| +++.|.=-+|..++
T Consensus 47 Arsd~ERrryAEl~vk~E~~rveke 71 (200)
T TIGR03759 47 ARSDEERRRYAELWVKQEAQRVEKE 71 (200)
T ss_pred cCCHHHHHHHHHHHHHHHHHHHHHH
Confidence 577889999 77777777776543
No 20
>PF02654 CobS: Cobalamin-5-phosphate synthase; InterPro: IPR003805 Cobalamin (vitamin B12) is a structurally complex cofactor, consisting of a modified tetrapyrrole with a centrally chelated cobalt. Cobalamin is usually found in one of two biologically active forms: methylcobalamin and adocobalamin. Most prokaryotes, as well as animals, have cobalamin-dependent enzymes, whereas plants and fungi do not appear to use it. In bacteria and archaea, these include methionine synthase, ribonucleotide reductase, glutamate and methylmalonyl-CoA mutases, ethanolamine ammonia lyase, and diol dehydratase []. In mammals, cobalamin is obtained through the diet, and is required for methionine synthase and methylmalonyl-CoA mutase []. There are at least two distinct cobalamin biosynthetic pathways in bacteria []: Aerobic pathway that requires oxygen and in which cobalt is inserted late in the pathway []; found in Pseudomonas denitrificans and Rhodobacter capsulatus. Anaerobic pathway in which cobalt insertion is the first committed step towards cobalamin synthesis []; found in Salmonella typhimurium, Bacillus megaterium, and Propionibacterium freudenreichii subsp. shermanii. Either pathway can be divided into two parts: (1) corrin ring synthesis (differs in aerobic and anaerobic pathways) and (2) adenosylation of corrin ring, attachment of aminopropanol arm, and assembly of the nucleotide loop (common to both pathways) []. There are about 30 enzymes involved in either pathway, where those involved in the aerobic pathway are prefixed Cob and those of the anaerobic pathway Cbi. Several of these enzymes are pathway-specific: CbiD, CbiG, and CbiK are specific to the anaerobic route of S. typhimurium, whereas CobE, CobF, CobG, CobN, CobS, CobT, and CobW are unique to the aerobic pathway of P. denitrificans. This entry represents the CobS protein, a cobalamin-5-phosphate synthase that catyalzes the reactions: Adenosylcobinamide-GDP + alpha-ribazole-5'-P = adenosylcobalamin-5'-phosphate + GMP Adenosylcobinamide-GDP + alpha-ribazole = adenosylcobalamin + GMP The protein product from these catalyses is associated with a large complex of proteins and is induced by cobinamide. CobS is involved in part III of cobalamin biosynthesis, one of the late steps in adenosylcobalamin synthesis that, together with CobU, CobT, and CobC proteins, defines the nucleotide loop assembly pathway [, ].; GO: 0008818 cobalamin 5'-phosphate synthase activity, 0009236 cobalamin biosynthetic process
Probab=29.43 E-value=1.1e+02 Score=27.36 Aligned_cols=27 Identities=19% Similarity=0.469 Sum_probs=22.4
Q ss_pred HHHHHHHHHHHHHhhhccCCCCcccCCC
Q 024772 140 TLIFGTYMGWIYLRYLQKKPETKLSGDP 167 (262)
Q Consensus 140 ~~~~G~~~sW~YLRF~Q~~p~~~~rGD~ 167 (262)
....++..+|.+-|+.+++ -.|..||.
T Consensus 193 ~~~~~~~~~~~~~~~~~r~-lGG~tGD~ 219 (235)
T PF02654_consen 193 ALLVALLLALLLARYARRR-LGGITGDV 219 (235)
T ss_pred HHHHHHHHHHHHHHHHHHH-cCCcChHH
Confidence 3667889999999999988 47888984
No 21
>KOG2289 consensus Rhomboid family proteins [Signal transduction mechanisms]
Probab=27.75 E-value=29 Score=33.12 Aligned_cols=22 Identities=18% Similarity=0.329 Sum_probs=20.9
Q ss_pred chhHHHHHHhhccccceEEeec
Q 024772 52 FAWNLLTAGYIEQTVHGVRPSF 73 (262)
Q Consensus 52 ~pWtl~T~~fvE~~i~~~i~s~ 73 (262)
-.|.++|+.|+|.+++++.+|+
T Consensus 118 E~WRllTym~LHaGi~HL~~N~ 139 (316)
T KOG2289|consen 118 ELWRLLTYMWLHAGIFHLLLNM 139 (316)
T ss_pred hhHHHHHHHHHhcCHHHHHHHH
Confidence 5899999999999999999888
No 22
>COG3086 RseC Positive regulator of sigma E activity [Signal transduction mechanisms]
Probab=26.08 E-value=1.6e+02 Score=25.17 Aligned_cols=44 Identities=16% Similarity=0.320 Sum_probs=27.9
Q ss_pred hhHHHHHHHHHHH-HHHhhhhhhhHHHHHHHHHHHHHHHhhhccC
Q 024772 115 WLPSLMLLLSIAI-SFFTAESAAYLPTLIFGTYMGWIYLRYLQKK 158 (262)
Q Consensus 115 ~lP~i~l~~~~~~-~~~~~~~~~~~~~~~~G~~~sW~YLRF~Q~~ 158 (262)
-+|.+.+++..++ ..++.........+..|...+|.-+|=|.|+
T Consensus 83 i~PL~~l~v~~~La~~L~~~e~~~~~~~~lg~~l~fl~~r~ysRk 127 (150)
T COG3086 83 IFPLVGLFLGAILAQYLFFSELIVIFGAFLGLALGFLLARRYSRK 127 (150)
T ss_pred HHHHHHHHHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 4677777666655 3333333333334677888888888888765
No 23
>TIGR00908 2A0305 ethanolamine permease. The three genes used as the seed for this model (from Burkholderia pseudomallei, Pseudomonas aeruginosa and Clostridium acetobutylicum are all adjacent to genes for the catabolism of ethanolamine. Most if not all of the hits to this model have a similar arrangement of genes. This group is a member of the Amino Acid-Polyamine-Organocation (APC) Superfamily.
Probab=24.29 E-value=3.7e+02 Score=25.71 Aligned_cols=53 Identities=13% Similarity=0.086 Sum_probs=25.2
Q ss_pred hhHHHHHHHHHHHHHHhhh-hhhhHHHHHHHHHHHHHHHhhhccCCCCcccCCCCC
Q 024772 115 WLPSLMLLLSIAISFFTAE-SAAYLPTLIFGTYMGWIYLRYLQKKPETKLSGDPSD 169 (262)
Q Consensus 115 ~lP~i~l~~~~~~~~~~~~-~~~~~~~~~~G~~~sW~YLRF~Q~~p~~~~rGD~Sd 169 (262)
..|.+.++++.++.+.... ..........-+...++|..++.+| ...|||+.|
T Consensus 388 ~~~~l~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~--~~~~~~~~~ 441 (442)
T TIGR00908 388 LTPGVALVLACVALVTGFYVDPRVVVGAVAIFVVLIGYYFLYSRH--HLVSGTPEE 441 (442)
T ss_pred hHHHHHHHHHHHHHHHHHHcChHHHHHHHHHHHHHHHHHHhhhhc--hhhccCccc
Confidence 4566655554443322211 1112211344566667777667665 345666433
No 24
>PRK15065 PTS system mannose-specific transporter subunit IIC; Provisional
Probab=23.56 E-value=2.3e+02 Score=26.25 Aligned_cols=39 Identities=18% Similarity=0.296 Sum_probs=25.7
Q ss_pred cccchhHHHHHHHHHHHHHHhhhhhhhHHHHHHHHHHHHHHHh
Q 024772 111 IKAKWLPSLMLLLSIAISFFTAESAAYLPTLIFGTYMGWIYLR 153 (262)
Q Consensus 111 ir~K~lP~i~l~~~~~~~~~~~~~~~~~~~~~~G~~~sW~YLR 153 (262)
.+-|++|++++.+.++.. .. .+.+...++|..++++|..
T Consensus 202 ~~k~~~~ff~lGFvl~ay-l~---l~~l~iAiig~~iA~i~~~ 240 (262)
T PRK15065 202 ATRELMPFFYLGFVLAAF-TN---LNLIALGVIGVVLALIYLQ 240 (262)
T ss_pred hccchHHHHHHHHHHHHH-hC---CcHHHHHHHHHHHHHHHHH
Confidence 456789999886655433 21 2233457899999999843
No 25
>PF04217 DUF412: Protein of unknown function, DUF412; InterPro: IPR007334 This family consists of bacterial uncharacterised proteins.
Probab=22.32 E-value=64 Score=27.41 Aligned_cols=33 Identities=18% Similarity=0.397 Sum_probs=24.1
Q ss_pred hhhcCCceeEE-eccccchhHHHHHHHHHHHHHHh
Q 024772 98 KQIVPDQELYL-LKIKAKWLPSLMLLLSIAISFFT 131 (262)
Q Consensus 98 kQl~Pd~~v~~-~~ir~K~lP~i~l~~~~~~~~~~ 131 (262)
..++||+.|+- -++=.|.+|.+.+ +++++.+..
T Consensus 23 ~~~FPE~RvIkaTrfa~k~MP~lAv-~s~~~Q~~~ 56 (143)
T PF04217_consen 23 APIFPENRVIKATRFAIKFMPALAV-FSLLWQIAF 56 (143)
T ss_pred HccCcHHHHHHHHHHHHHHhhHHHH-HHHHHHHHH
Confidence 35688888876 6777788999986 566666554
No 26
>PRK08965 putative monovalent cation/H+ antiporter subunit E; Reviewed
Probab=22.19 E-value=1.7e+02 Score=24.82 Aligned_cols=17 Identities=24% Similarity=0.434 Sum_probs=11.3
Q ss_pred HHHHHHHHHHHHhhhcc
Q 024772 141 LIFGTYMGWIYLRYLQK 157 (262)
Q Consensus 141 ~~~G~~~sW~YLRF~Q~ 157 (262)
...|+.+|..=..++.+
T Consensus 31 l~~G~~~~~~v~~~~~~ 47 (162)
T PRK08965 31 LLLGLLLGLLIPLLLAL 47 (162)
T ss_pred HHHHHHHHHHHHHHhcc
Confidence 55677777766666665
No 27
>COG1377 FlhB Flagellar biosynthesis pathway, component FlhB [Cell motility and secretion / Intracellular trafficking and secretion]
Probab=21.24 E-value=87 Score=30.48 Aligned_cols=23 Identities=26% Similarity=0.365 Sum_probs=20.8
Q ss_pred CchhhhHHHHHHHHHHHHHHhcc
Q 024772 221 DPIEASRRRERGARALEERLATE 243 (262)
Q Consensus 221 ~~~eAERRR~~ALkaL~eRL~~~ 243 (262)
||+.-.||||++.+.+.+||.++
T Consensus 237 dPeVKsr~Rq~~re~a~~rm~~~ 259 (363)
T COG1377 237 DPEVKSRIRQMQREIARRRMMSD 259 (363)
T ss_pred ChhhhHHHHHHHHHHHHHHHHhh
Confidence 88899999999999999999644
No 28
>PF12023 DUF3511: Domain of unknown function (DUF3511); InterPro: IPR021899 This presumed domain is functionally uncharacterised. This domain is found in eukaryotes. This domain is about 50 amino acids in length. This domain has two completely conserved residues (Y and K) that may be functionally important.
Probab=20.92 E-value=68 Score=22.22 Aligned_cols=13 Identities=15% Similarity=0.309 Sum_probs=10.2
Q ss_pred CchhhhHHHHHHH
Q 024772 221 DPIEASRRRERGA 233 (262)
Q Consensus 221 ~~~eAERRR~~AL 233 (262)
+..|..|||.+|.
T Consensus 4 ~dpE~kRkkRVA~ 16 (47)
T PF12023_consen 4 NDPEMKRKKRVAS 16 (47)
T ss_pred CCHHHHHHHHHHh
Confidence 4558899998886
No 29
>cd03211 GST_C_Metaxin2 GST_C family, Metaxin subfamily, Metaxin 2; a metaxin 1 binding protein identified through a yeast two-hybrid system using metaxin 1 as the bait. Metaxin 2 shares sequence similarity with metaxin 1 but does not contain a C-terminal mitochondrial outer membrane signal-anchor domain. It associates with mitochondrial membranes through its interaction with metaxin 1, which is a component of the mitochondrial preprotein import complex of the outer membrane. The biological function of metaxin 2 is unknown. It is likely that it also plays a role in protein translocation into the mitochondria. However, this has not been experimentally validated. In a recent proteomics study, it has been shown that metaxin 2 is overexpressed in response to lipopolysaccharide-induced liver injury.
Probab=20.29 E-value=98 Score=24.76 Aligned_cols=24 Identities=21% Similarity=0.252 Sum_probs=18.4
Q ss_pred CchhhhHHHHHHHHHHHHHHhccc
Q 024772 221 DPIEASRRRERGARALEERLATEK 244 (262)
Q Consensus 221 ~~~eAERRR~~ALkaL~eRL~~~~ 244 (262)
+.+|..++-+..|+||+++|.+++
T Consensus 54 ~~ee~~~~~~~~l~aLs~~Lg~~~ 77 (126)
T cd03211 54 TLDQVIEEVDQCCQALSQRLGTQP 77 (126)
T ss_pred CHHHHHHHHHHHHHHHHHHHCCCC
Confidence 345556667889999999998754
No 30
>KOG4453 consensus Predicted ER membrane protein [Function unknown]
Probab=20.05 E-value=86 Score=28.89 Aligned_cols=22 Identities=23% Similarity=0.615 Sum_probs=18.6
Q ss_pred hHHHHHHHHHHHHHHHhhhccC
Q 024772 137 YLPTLIFGTYMGWIYLRYLQKK 158 (262)
Q Consensus 137 ~~~~~~~G~~~sW~YLRF~Q~~ 158 (262)
.+.+..+|+++||+|+-||...
T Consensus 195 SIgaft~Gvf~c~vy~gyf~s~ 216 (269)
T KOG4453|consen 195 SIGAFTFGVFICIVYLGYFSSL 216 (269)
T ss_pred hHHHHHHHHHHHHHHHHHHhcc
Confidence 4556789999999999999953
Done!