Query 022623
Match_columns 294
No_of_seqs 209 out of 1132
Neff 4.9
Searched_HMMs 46136
Date Fri Mar 29 04:56:57 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/022623.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/022623hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 TIGR03008 pepcterm_CAAX CAAX p 99.6 4.8E-15 1E-19 135.5 12.9 74 206-286 120-204 (222)
2 COG1266 Predicted metal-depend 99.6 5.3E-14 1.2E-18 122.3 14.0 85 203-287 123-210 (226)
3 PF02517 Abi: CAAX protease se 99.6 2.4E-14 5.3E-19 110.6 9.6 80 204-286 5-87 (91)
4 KOG4130 Prenyl protein proteas 98.1 8.6E-05 1.9E-09 69.5 13.6 77 210-286 135-231 (291)
5 COG4449 Predicted protease of 97.3 0.00016 3.6E-09 73.3 3.5 89 206-294 712-817 (827)
6 PRK11901 hypothetical protein; 57.4 22 0.00047 35.0 5.4 52 80-131 3-55 (327)
7 PF10086 DUF2324: Putative mem 47.5 1.8E+02 0.0039 26.8 9.6 45 202-250 60-107 (223)
8 KOG4753 Predicted membrane pro 44.3 72 0.0016 27.3 5.9 61 71-131 3-70 (124)
9 PF05437 AzlD: Branched-chain 43.6 62 0.0013 25.4 5.2 55 233-292 44-98 (99)
10 PF03189 Otopetrin: Otopetrin; 43.5 3E+02 0.0066 27.9 11.3 16 125-140 188-203 (441)
11 PF10329 DUF2417: Region of un 42.0 3E+02 0.0065 25.9 11.6 38 191-228 101-138 (232)
12 TIGR02185 Trep_Strep conserved 38.2 2.9E+02 0.0063 24.6 9.3 43 233-279 40-82 (189)
13 PF10766 DUF2592: Protein of u 37.2 40 0.00087 23.5 2.7 26 238-270 2-27 (41)
14 PHA03242 envelope glycoprotein 36.9 32 0.00069 35.1 3.1 27 55-81 366-392 (428)
15 PF11712 Vma12: Endoplasmic re 31.3 2.8E+02 0.006 23.5 7.6 13 58-70 27-39 (142)
16 PF09605 Trep_Strep: Hypotheti 30.9 3.8E+02 0.0083 23.8 9.5 41 233-277 38-78 (186)
17 PF06679 DUF1180: Protein of u 29.2 17 0.00038 32.3 -0.1 23 46-68 110-132 (163)
18 COG4317 Uncharacterized protei 25.9 1.3E+02 0.0028 24.4 4.2 34 235-269 10-43 (93)
19 PRK10862 SoxR reducing system 25.2 1.6E+02 0.0034 25.6 5.1 56 213-273 67-122 (154)
20 PHA03237 envelope glycoprotein 24.3 68 0.0015 32.7 3.0 16 56-71 370-385 (424)
21 COG3105 Uncharacterized protei 22.8 97 0.0021 27.0 3.2 22 253-274 7-28 (138)
22 PF11947 DUF3464: Protein of u 22.6 4.1E+02 0.0088 23.5 7.2 31 107-137 54-84 (153)
23 PF04142 Nuc_sug_transp: Nucle 21.5 6.5E+02 0.014 23.2 10.6 72 210-281 126-212 (244)
24 KOG4544 Uncharacterized conser 21.5 92 0.002 27.3 2.9 49 242-290 43-92 (144)
No 1
>TIGR03008 pepcterm_CAAX CAAX prenyl protease-related protein. The CAAX prenyl protease, in eukaryotes, catalyzes three covalent modifications, including cleavage and acylation, at the C-terminus of certain proteins in a process connected to protein sorting. This family describes a bacterial protein family homologous to one domain of the CAAX-processing enzyme. Members of this protein family are found in genomes that carry a predicted protein sorting system, PEP-CTERM/exosortase, usually in the vicinity of the EpsH homolog that is the hallmark of the system. The function of this protein is unknown, but it may relate to protein motification.
Probab=99.62 E-value=4.8e-15 Score=135.50 Aligned_cols=74 Identities=24% Similarity=0.261 Sum_probs=65.0
Q ss_pred HHHHHHhhHHHHHHHHHHHhHhhhcc-----------hhHHHHHHHHHHHHhhcCCCchhHHHHHHHHHHHHHHHHHHHh
Q 022623 206 YLVVAFLPGISEELLFRGALLPLFGM-----------DWRSVLAVATVFGALHLGSGRKYSFAVCHDLRLPLSGQRLLAS 274 (294)
Q Consensus 206 il~v~iLapI~EELLFRGiLl~~fg~-----------~w~aIviSSllFGllH~~~~~~~~~~i~a~llGliLG~vYl~T 274 (294)
++..++++|++||++|||++++.+.+ .|.++++||++||+.|.. .+.+++.|+++|++|.+|
T Consensus 120 l~~~~l~vpi~EElfFRG~l~~~l~~~~f~~~~~~~~~~~a~lisSllFal~H~~-------~~~~~l~Gli~~~l~~~t 192 (222)
T TIGR03008 120 LAGATLVVPVMEELFWRSFLLRYLQQSDFESVPGGRFHWPSFLAVTLLFGLEHHL-------IVAGLIAGLAYNLLLLRT 192 (222)
T ss_pred HHHHHhhHHHHHHHHHHHHHHHHHHHhcccccccccccHHHHHHHHHHHHHHHHH-------HHHHHHHHHHHHHHHHHh
Confidence 35568899999999999999998832 388999999999999983 445678899999999999
Q ss_pred CCchhhHHHHHH
Q 022623 275 HMATRQLYPRAL 286 (294)
Q Consensus 275 GSL~~~I~~~a~ 286 (294)
|||+.+|..|++
T Consensus 193 gsL~~~I~~H~~ 204 (222)
T TIGR03008 193 GSIMACILAHAV 204 (222)
T ss_pred CChHHHHHHHHH
Confidence 999999999987
No 2
>COG1266 Predicted metal-dependent membrane protease [General function prediction only]
Probab=99.57 E-value=5.3e-14 Score=122.33 Aligned_cols=85 Identities=26% Similarity=0.294 Sum_probs=74.6
Q ss_pred chhHHHHHHhhHHHHHHHHHHHhHhhhcc---hhHHHHHHHHHHHHhhcCCCchhHHHHHHHHHHHHHHHHHHHhCCchh
Q 022623 203 PLDYLVVAFLPGISEELLFRGALLPLFGM---DWRSVLAVATVFGALHLGSGRKYSFAVCHDLRLPLSGQRLLASHMATR 279 (294)
Q Consensus 203 ~~~il~v~iLapI~EELLFRGiLl~~fg~---~w~aIviSSllFGllH~~~~~~~~~~i~a~llGliLG~vYl~TGSL~~ 279 (294)
...++...+.+|++||++|||++++.+.+ .+.++++||++||+.|..+...+.++++.+.+|++++++|.+|||+++
T Consensus 123 ~~~~~~~~i~~~l~EEl~fRg~l~~~l~~~~~~~~a~iissllFal~H~~~~~~~~~~~~~~~~gli~~~~~~~t~~l~~ 202 (226)
T COG1266 123 LLFFLVLLILAPLAEELLFRGYLLGALARRFGPLLAIIISSLLFALLHLPNGLLLLYFLLYFIAGLILGLLYLRTGSLWV 202 (226)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHhHHHHHHhcCcHHHHHHHHHHHHHHHhcccchHHHHHHHHHHHHHHHHHHHHhCCcHH
Confidence 34567778999999999999999999865 388999999999999998764467788889999999999999999999
Q ss_pred hHHHHHHH
Q 022623 280 QLYPRALS 287 (294)
Q Consensus 280 ~I~~~a~~ 287 (294)
|+..|++.
T Consensus 203 ~i~~H~~~ 210 (226)
T COG1266 203 PILLHALI 210 (226)
T ss_pred HHHHHHHH
Confidence 99988873
No 3
>PF02517 Abi: CAAX protease self-immunity; InterPro: IPR003675 Members of this family are probably proteases (after a isoprenyl group is attached to the Cys residue in the C-terminal CAAX motif of a protein to attach it to the membrane, the AAX tripeptide is removed by one of the CAAX prenyl proteases). The family contains the Q03530 from SWISSPROT CAAX prenyl protease []. The proteins contain a highly conserved Glu-Glu motif at the amino end of the alignment. The alignment also contains two histidine residues that may be involved in zinc binding []. While these proteins are involved in membrane anchoring of proteins in eukaryotes, little is known about their function in prokaryotes. In some known bacteriocin loci, Abi genes have been found downstream of bacteriocin structural genes where they are probably involved in self-immunity. Investigation of the bacteriocin-like loci in the Gram positive bacteria locus from Lactobacillus sakei 23K confirmed that the bacteriocin-like genes (sak23Kalphabeta) exhibited antimicrobial activity when expressed in a heterologous host and that the associated Abi gene (sak23Ki) conferred immunity against the cognate bacteriocin. Interestingly, the immunity genes from three similar systems conferred a high degree of cross-immunity against each other's bacteriocins, suggesting the recognition of a common receptor. Site-directed mutagenesis demonstrated that the conserved motifs constituting the putative proteolytic active site of the Abi proteins are essential for the immunity function of Sak23Ki - thus a new concept in self-immunity []. This family also includes lysostaphin resistance protein A [].; GO: 0016020 membrane
Probab=99.55 E-value=2.4e-14 Score=110.63 Aligned_cols=80 Identities=26% Similarity=0.334 Sum_probs=70.0
Q ss_pred hhHHHHHHhhHHHHHHHHHHHhHhhhcc---hhHHHHHHHHHHHHhhcCCCchhHHHHHHHHHHHHHHHHHHHhCCchhh
Q 022623 204 LDYLVVAFLPGISEELLFRGALLPLFGM---DWRSVLAVATVFGALHLGSGRKYSFAVCHDLRLPLSGQRLLASHMATRQ 280 (294)
Q Consensus 204 ~~il~v~iLapI~EELLFRGiLl~~fg~---~w~aIviSSllFGllH~~~~~~~~~~i~a~llGliLG~vYl~TGSL~~~ 280 (294)
+..+...++.|+.||++|||++++.+.+ ++.++++|+++||+.|... .+. ++..++.|++++++|.+|||++++
T Consensus 5 ~~~~~~~~~~~~~EEl~fRg~l~~~l~~~~~~~~a~~is~~~f~~~H~~~--~~~-~~~~~~~g~~~~~~~~~t~sl~~~ 81 (91)
T PF02517_consen 5 IFFLVMILIAPIAEELFFRGFLFNRLRRRFNPWFAILISSLLFALWHLPN--GPQ-FIYAFLFGLLFGYLYLRTGSLWAA 81 (91)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHhcchHHHHHHHHHHHHHHHHhh--hHH-HHHHHHHHHHHHHHHHHcCChHHH
Confidence 4567788999999999999999998854 3899999999999999986 233 677889999999999999999999
Q ss_pred HHHHHH
Q 022623 281 LYPRAL 286 (294)
Q Consensus 281 I~~~a~ 286 (294)
+..|++
T Consensus 82 i~~H~~ 87 (91)
T PF02517_consen 82 IIAHAL 87 (91)
T ss_pred HHHHHH
Confidence 998775
No 4
>KOG4130 consensus Prenyl protein protease [Posttranslational modification, protein turnover, chaperones]
Probab=98.08 E-value=8.6e-05 Score=69.49 Aligned_cols=77 Identities=18% Similarity=0.205 Sum_probs=62.7
Q ss_pred HHhhHHHHHHHHHHHhHhhhcc----hhHHHHHHHHHHHHhhcCC-------Cch----h-----HHHHHHHHHHHHHHH
Q 022623 210 AFLPGISEELLFRGALLPLFGM----DWRSVLAVATVFGALHLGS-------GRK----Y-----SFAVCHDLRLPLSGQ 269 (294)
Q Consensus 210 ~iLapI~EELLFRGiLl~~fg~----~w~aIviSSllFGllH~~~-------~~~----~-----~~~i~a~llGliLG~ 269 (294)
-+++|++||++||..+++.+.. ...++.+..+.||+.|.-. .+. . ..+.++++.|..-+.
T Consensus 135 ~iiaPLtEElvfracmlp~~l~~~~s~l~avF~~PLfFGvAH~HHiyEqL~~g~~~~~~ilL~t~fQfsYTtlFG~yTaf 214 (291)
T KOG4130|consen 135 FIIAPLTEELVFRACMLPTYLNLIQSSLQAVFWQPLFFGVAHAHHIYEQLQEGSMTTVSILLTTCFQFSYTTLFGGYTAF 214 (291)
T ss_pred hhhccchHHHHHHHHHHHHHHHhhhcchhhHHHhhHHHhHHHHHHHHHHHHhcchHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3799999999999999987643 4678888889999999632 100 0 126778899999999
Q ss_pred HHHHhCCchhhHHHHHH
Q 022623 270 RLLASHMATRQLYPRAL 286 (294)
Q Consensus 270 vYl~TGSL~~~I~~~a~ 286 (294)
++++||++|.||+.||.
T Consensus 215 lF~rTghl~~~iLvHAf 231 (291)
T KOG4130|consen 215 LFVRTGHLWCPILVHAF 231 (291)
T ss_pred HhhhcCCchHHHHHHHH
Confidence 99999999999999986
No 5
>COG4449 Predicted protease of the Abi (CAAX) family [General function prediction only]
Probab=97.31 E-value=0.00016 Score=73.30 Aligned_cols=89 Identities=25% Similarity=0.277 Sum_probs=67.9
Q ss_pred HHHHHHhhHHHHHHHHHHHhHhhhc---chhHHHHHHHH--HHHHhhcCCCc-----------hhHHHHHHHHHHHHHHH
Q 022623 206 YLVVAFLPGISEELLFRGALLPLFG---MDWRSVLAVAT--VFGALHLGSGR-----------KYSFAVCHDLRLPLSGQ 269 (294)
Q Consensus 206 il~v~iLapI~EELLFRGiLl~~fg---~~w~aIviSSl--lFGllH~~~~~-----------~~~~~i~a~llGliLG~ 269 (294)
++.+.+.|++.||+.||-++.+.=+ ++|.-+..... +|-+.|.-+.. .+.|.....++|+-...
T Consensus 712 iL~vIl~PAl~EElvFRvvLlP~P~E~r~~W~tl~a~~~l~LfvLyHplnA~T~y~rg~PvFf~PiFL~ltglLGL~Ctv 791 (827)
T COG4449 712 ILTVILIPALGEELVFRVVLLPGPGEGRRPWVTLGAATGLVLFVLYHPLNALTFYPRGAPVFFRPIFLLLTGLLGLGCTV 791 (827)
T ss_pred hhhheehhhccccceeEEEecCCCCccccchHhHHHHHHHHHHHHhhhhhhhhccccCCcceeccHHHHHHHHHhhhhhh
Confidence 4556678999999999999998753 36876666555 89999965421 23456666789999999
Q ss_pred HHHHhCCchhhHHHH-HHHhHHhhcC
Q 022623 270 RLLASHMATRQLYPR-ALSCQWLLML 294 (294)
Q Consensus 270 vYl~TGSL~~~I~~~-a~~~~~~~~~ 294 (294)
.|..|||+|+-++-+ |+..+|++.|
T Consensus 792 ty~vT~SlW~iV~lHW~vVvVWl~~L 817 (827)
T COG4449 792 TYRVTGSLWPIVLLHWAVVVVWLTWL 817 (827)
T ss_pred hHHhccchHHHHHHHHHHHHHHHHHh
Confidence 999999999988755 5678888643
No 6
>PRK11901 hypothetical protein; Reviewed
Probab=57.45 E-value=22 Score=35.05 Aligned_cols=52 Identities=15% Similarity=0.118 Sum_probs=33.4
Q ss_pred CCCCCcccccccCCCCccc-ccccCCccCchhHHHHHHHHHHHHHHHHHHHHH
Q 022623 80 RSGTEDDYVKDESKESTDD-NFTSQTLVTIPSRSNVLQACTVTCGLITALGVI 131 (294)
Q Consensus 80 ~~~~~~~~~~~~~~~~~~~-~~~~~~l~~~~~R~~lL~~~~lT~illLiial~ 131 (294)
++-.||++.+|.++--+.- .-..+.......|+.++..+|+-.+|||+||+.
T Consensus 3 Efkpe~elkPDtSDRrp~Rsr~~~~~pk~~vSRQh~MiGiGilVLlLLIi~Ig 55 (327)
T PRK11901 3 EFKPEDELKPDTSDRRPTRSRKSSNGPKLAVSRQHMMIGIGILVLLLLIIAIG 55 (327)
T ss_pred cCCcccccCCCcccCCCcccccCCCCCCchHHHHHHHHHHHHHHHHHHHHHHh
Confidence 3444555666644432221 112223457789999999999999999999964
No 7
>PF10086 DUF2324: Putative membrane peptidase family (DUF2324); InterPro: IPR011397 There are currently no experimental data for members of this group or their homologues, nor do they exhibit features indicative of any function. However, they are predicted to be integral membrane proteins (with several transmembrane segments).
Probab=47.52 E-value=1.8e+02 Score=26.80 Aligned_cols=45 Identities=29% Similarity=0.244 Sum_probs=27.8
Q ss_pred cchhHHHHHHhhHHHHHHHHHHHhHhhhcc---hhHHHHHHHHHHHHhhcCC
Q 022623 202 EPLDYLVVAFLPGISEELLFRGALLPLFGM---DWRSVLAVATVFGALHLGS 250 (294)
Q Consensus 202 ~~~~il~v~iLapI~EELLFRGiLl~~fg~---~w~aIviSSllFGllH~~~ 250 (294)
++...++.++.+++.||. .|=+-.+.+.+ .+.. .++.||+-|...
T Consensus 60 ~~l~~ly~~l~AGiFEE~-gR~i~~k~l~kk~~~~~~---~al~~GlGhGg~ 107 (223)
T PF10086_consen 60 PILYALYGGLMAGIFEET-GRYIGFKYLLKKRRDWSD---DALAYGLGHGGI 107 (223)
T ss_pred HHHHHHHHHHHHHHHHHH-HHHHHHHHHHHcccchhh---HHHHHHcchHHH
Confidence 445568889999999993 23333333321 1111 358999999853
No 8
>KOG4753 consensus Predicted membrane protein [Function unknown]
Probab=44.35 E-value=72 Score=27.30 Aligned_cols=61 Identities=16% Similarity=0.177 Sum_probs=28.5
Q ss_pred hhcCCCccCCCCCCcccccccCCCCccc-------ccccCCccCchhHHHHHHHHHHHHHHHHHHHHH
Q 022623 71 AEKGNGVADRSGTEDDYVKDESKESTDD-------NFTSQTLVTIPSRSNVLQACTVTCGLITALGVI 131 (294)
Q Consensus 71 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~-------~~~~~~l~~~~~R~~lL~~~~lT~illLiial~ 131 (294)
++++++++-+++++++---.+--.|..| |.-..++..+-.+.++-..+.....+++.++++
T Consensus 3 p~rdv~~~~~dss~~~~~y~~~~~s~~Dsd~~~~~~~~~s~tr~P~k~i~lavvL~~fg~Lli~lg~f 70 (124)
T KOG4753|consen 3 PERDVGVGTRDSSRTSMAYSDHAFSISDSDIQIDYSYKVSNTRHPVKEIALAVVLLVFGLLLIGLGFF 70 (124)
T ss_pred CcCcCceeccCCCccchhhcccccccccccceeecccccCCCCCchHHHHHHHHHHHHHHHHHHHHHH
Confidence 4567777777775432111111111222 223333445555555555555555555555544
No 9
>PF05437 AzlD: Branched-chain amino acid transport protein (AzlD); InterPro: IPR008407 This family consists of a number of bacterial and archaeal branched-chain amino acid transport proteins. AzlD, a member of this group, has been shown by mutational analysis to be involved in branched-chain amino acid transport, and to be involved in conferring resistance to 4-azaleucine []. However, its exact role in these processes is not yet clear []. Based on its hydropathy profile, it has been suggested to be a membrane protein [].
Probab=43.64 E-value=62 Score=25.43 Aligned_cols=55 Identities=9% Similarity=0.050 Sum_probs=31.4
Q ss_pred hHHHHHHHHHHHHhhcCCCchhHHHHHHHHHHHHHHHHHHHhCCchhhHHHHHHHhHHhh
Q 022623 233 WRSVLAVATVFGALHLGSGRKYSFAVCHDLRLPLSGQRLLASHMATRQLYPRALSCQWLL 292 (294)
Q Consensus 233 w~aIviSSllFGllH~~~~~~~~~~i~a~llGliLG~vYl~TGSL~~~I~~~a~~~~~~~ 292 (294)
..++++.++++.--|......++.. +..++-..++++|+|+..++. -++.+.|++
T Consensus 44 l~aLv~~~i~~~~~~~~~~~~~~~l----~a~~~~~~~~~~~~~~~~~v~-~G~~~~~ll 98 (99)
T PF05437_consen 44 LAALVVPSIFFPTGSLELSLGNPYL----IAALVAALVALRTRNLLLSVL-AGVAAFALL 98 (99)
T ss_pred HHHHHHHHHccCccccccccchHHH----HHHHHHHHHHHHHcchHHHHH-HHHHHHHHh
Confidence 3445555555554444332222332 234455567788899988887 666666654
No 10
>PF03189 Otopetrin: Otopetrin; InterPro: IPR004878 The otopetrins are a group of proteins that are restricted to the metazoa. The structure of otopetrin-1 (Q80VM9 from SWISSPROT) shows it to have 12 transmembrane domains, with three conserved sub-domains (OD-1 to OD-III) []. Otopetrins modulate calcium homeostasis and influx of calcium in response to extracellular ATP. The otopetrins are required for normal formation of otoconia/otoliths in the inner ear. Otoconia are minute biomineral particles embedded in a gelatinous membrane that overlies the sensory epithelium in the inner ear. Gravity and acceleration cause the octoconia to deflect the stereocilia of sensory hair cells. Otoconia are required for normal processing of information regarding spatial orientation and acceleration.
Probab=43.47 E-value=3e+02 Score=27.92 Aligned_cols=16 Identities=13% Similarity=0.150 Sum_probs=11.5
Q ss_pred HHHHHHHHHHhhhhcc
Q 022623 125 ITALGVIIRQGSHVAS 140 (294)
Q Consensus 125 lLiial~i~lw~~~~~ 140 (294)
++..|...-.|...+.
T Consensus 188 LIaAavlyvmWknigr 203 (441)
T PF03189_consen 188 LIAAAVLYVMWKNIGR 203 (441)
T ss_pred HHHHHHHHHHHHHhcc
Confidence 6666666677988766
No 11
>PF10329 DUF2417: Region of unknown function (DUF2417); InterPro: IPR019431 This entry represents a family of fungal proteins with no known function. In some cases these proteins also contain an alpha/beta hydrolase fold (IPR000073 from INTERPRO).
Probab=41.99 E-value=3e+02 Score=25.87 Aligned_cols=38 Identities=21% Similarity=0.199 Sum_probs=30.2
Q ss_pred HHHHHHHHhcccchhHHHHHHhhHHHHHHHHHHHhHhh
Q 022623 191 EAANQQVLTSLEPLDYLVVAFLPGISEELLFRGALLPL 228 (294)
Q Consensus 191 ~~~ne~vl~~l~~~~il~v~iLapI~EELLFRGiLl~~ 228 (294)
+.....+...+...+++.+..++.+=+|.=|.|+..-.
T Consensus 101 ~r~l~~vl~~Lllvdlilil~V~~~R~~eG~vGi~s~i 138 (232)
T PF10329_consen 101 ERILNIVLAGLLLVDLILILAVPYTRHEEGWVGIASVI 138 (232)
T ss_pred HHHHHHHHHHHHHHHHHHHHhhHhHHhHhhHhhHHHHH
Confidence 44555666666788899999999999999999988754
No 12
>TIGR02185 Trep_Strep conserved hypothetical integral membrane protein TIGR02185. This family consists of strongly hydrophobic proteins about 190 amino acids in length with a strongly basic motif near the C-terminus. If is found in rather few species, but in paralogous families of 12 members in the oral pathogenic spirochaete Treponema denticola and 2 in Streptococcus pneumoniae R6.
Probab=38.22 E-value=2.9e+02 Score=24.63 Aligned_cols=43 Identities=12% Similarity=-0.106 Sum_probs=21.1
Q ss_pred hHHHHHHHHHHHHhhcCCCchhHHHHHHHHHHHHHHHHHHHhCCchh
Q 022623 233 WRSVLAVATVFGALHLGSGRKYSFAVCHDLRLPLSGQRLLASHMATR 279 (294)
Q Consensus 233 w~aIviSSllFGllH~~~~~~~~~~i~a~llGliLG~vYl~TGSL~~ 279 (294)
..+.++++.+|=++-..-.+ .-..+++|++.|..+..+|+.|+
T Consensus 40 ~i~al~~g~vyml~~~KV~K----~G~~~i~~~i~gl~~~~~G~~~~ 82 (189)
T TIGR02185 40 GITAFLVGIIFFLMVAKVPK----RGVIFIFGILLGLLFFLMGMYWP 82 (189)
T ss_pred HHHHHHHhHHHhhhhhhcCC----ccHHHHHHHHHHHHHHHHcccHH
Confidence 34444555555554444333 22223456666666666666443
No 13
>PF10766 DUF2592: Protein of unknown function (DUF2592); InterPro: IPR019702 This entry represents proteins with unknown function, and appear to be restricted to Enterobacteriaceae. Some members are annotated as ybhY.
Probab=37.20 E-value=40 Score=23.52 Aligned_cols=26 Identities=12% Similarity=0.039 Sum_probs=18.3
Q ss_pred HHHHHHHHhhcCCCchhHHHHHHHHHHHHHHHH
Q 022623 238 AVATVFGALHLGSGRKYSFAVCHDLRLPLSGQR 270 (294)
Q Consensus 238 iSSllFGllH~~~~~~~~~~i~a~llGliLG~v 270 (294)
+-|+.|+++..+ .+.+.++|+++|.-
T Consensus 2 lkSl~fa~iMVP-------Vvma~ilglIyGlG 27 (41)
T PF10766_consen 2 LKSLAFAVIMVP-------VVMALILGLIYGLG 27 (41)
T ss_pred hHHHHHHHHHHH-------HHHHHHHHHHHHHH
Confidence 347888888775 45566778887764
No 14
>PHA03242 envelope glycoprotein M; Provisional
Probab=36.86 E-value=32 Score=35.09 Aligned_cols=27 Identities=15% Similarity=0.129 Sum_probs=13.8
Q ss_pred chhhHHHHHHHHhhhhhhcCCCccCCC
Q 022623 55 SKKSVKKLKRDRQLRLAEKGNGVADRS 81 (294)
Q Consensus 55 ~~~~~~~~~~~~~~~~~~~~~~~~~~~ 81 (294)
+++-++++||.+..|+.++++-.+++.
T Consensus 366 ~~~~~~~~~r~r~~~~~~~~~~~~~~~ 392 (428)
T PHA03242 366 RHRARSYIRRVRSSMRNSREAPYAGES 392 (428)
T ss_pred HHHHHHHHHHhhCcCCCCccccccccc
Confidence 444555666666655545443333333
No 15
>PF11712 Vma12: Endoplasmic reticulum-based factor for assembly of V-ATPase; InterPro: IPR021013 ATPases (or ATP synthases) are membrane-bound enzyme complexes/ion transporters that combine ATP synthesis and/or hydrolysis with the transport of protons across a membrane. ATPases can harness the energy from a proton gradient, using the flux of ions across the membrane via the ATPase proton channel to drive the synthesis of ATP. Some ATPases work in reverse, using the energy from the hydrolysis of ATP to create a proton gradient. There are different types of ATPases, which can differ in function (ATP synthesis and/or hydrolysis), structure (e.g., F-, V- and A-ATPases, which contain rotary motors) and in the type of ions they transport [, ]. The different types include: F-ATPases (F1F0-ATPases), which are found in mitochondria, chloroplasts and bacterial plasma membranes where they are the prime producers of ATP, using the proton gradient generated by oxidative phosphorylation (mitochondria) or photosynthesis (chloroplasts). V-ATPases (V1V0-ATPases), which are primarily found in eukaryotic vacuoles and catalyse ATP hydrolysis to transport solutes and lower pH in organelles. A-ATPases (A1A0-ATPases), which are found in Archaea and function like F-ATPases (though with respect to their structure and some inhibitor responses, A-ATPases are more closely related to the V-ATPases). P-ATPases (E1E2-ATPases), which are found in bacteria and in eukaryotic plasma membranes and organelles, and function to transport a variety of different ions across membranes. E-ATPases, which are cell-surface enzymes that hydrolyse a range of NTPs, including extracellular ATP. V-ATPases (also known as V1V0-ATPase or vacuolar ATPase) (3.6.3.14 from EC) are found in the eukaryotic endomembrane system, and in the plasma membrane of prokaryotes and certain specialised eukaryotic cells. V-ATPases hydrolyse ATP to drive a proton pump, and are involved in a variety of vital intra- and inter-cellular processes such as receptor mediated endocytosis, protein trafficking, active transport of metabolites, homeostasis and neurotransmitter release []. V-ATPases are composed of two linked complexes: the V1 complex (subunits A-H) contains the catalytic core that hydrolyses ATP, while the V0 complex (subunits a, c, c', c'', d) forms the membrane-spanning pore. V-ATPases may have an additional role in membrane fusion through binding to t-SNARE proteins []. The yeast vacuolar proton-translocating ATPase (V-ATPase) is the best characterised member of the V-ATPase family. A total of thirteen genes are required for encoding the subunits of the enzyme complex itself and an additional three for providing factors necessary for the assembly of the whole. Vma12 is one of these latter, all three of which are localised to the endoplasmic reticulum [].
Probab=31.29 E-value=2.8e+02 Score=23.50 Aligned_cols=13 Identities=15% Similarity=0.427 Sum_probs=7.6
Q ss_pred hHHHHHHHHhhhh
Q 022623 58 SVKKLKRDRQLRL 70 (294)
Q Consensus 58 ~~~~~~~~~~~~~ 70 (294)
...|||++.+.++
T Consensus 27 ~le~Lr~~~ee~e 39 (142)
T PF11712_consen 27 RLERLRAEQEERE 39 (142)
T ss_pred HHHHHHHHHHHHH
Confidence 4566666665544
No 16
>PF09605 Trep_Strep: Hypothetical bacterial integral membrane protein (Trep_Strep); InterPro: IPR011733 This family consists of strongly hydrophobic proteins about 190 amino acids in length with a strongly basic motif near the C terminus. If is found in rather few species, but in paralogous families of 12 members in the oral pathogenic spirochaete Treponema denticola and 2 in Streptococcus pneumoniae (strain ATCC BAA-255 / R6).
Probab=30.85 E-value=3.8e+02 Score=23.77 Aligned_cols=41 Identities=7% Similarity=-0.049 Sum_probs=20.8
Q ss_pred hHHHHHHHHHHHHhhcCCCchhHHHHHHHHHHHHHHHHHHHhCCc
Q 022623 233 WRSVLAVATVFGALHLGSGRKYSFAVCHDLRLPLSGQRLLASHMA 277 (294)
Q Consensus 233 w~aIviSSllFGllH~~~~~~~~~~i~a~llGliLG~vYl~TGSL 277 (294)
..+.++++.+|-++-..-++... .++.|++.|.++..+|.-
T Consensus 38 ~i~ali~g~vyml~~~KV~K~G~----~~i~~~i~gl~~~~~G~~ 78 (186)
T PF09605_consen 38 AIAALICGIVYMLMVAKVPKRGA----FLIMGIIMGLIFFLMGHG 78 (186)
T ss_pred HHHHHHHHHHHHHHHHHcCchHH----HHHHHHHHHHHHHHHhhh
Confidence 44445555555555554444222 234555555556666654
No 17
>PF06679 DUF1180: Protein of unknown function (DUF1180); InterPro: IPR009565 This entry consists of several hypothetical eukaryotic proteins thought to be membrane proteins. Their function is unknown.
Probab=29.24 E-value=17 Score=32.31 Aligned_cols=23 Identities=30% Similarity=0.473 Sum_probs=16.6
Q ss_pred cchhhhhhhchhhHHHHHHHHhh
Q 022623 46 LKFRMRTFASKKSVKKLKRDRQL 68 (294)
Q Consensus 46 ~~~~~~~~~~~~~~~~~~~~~~~ 68 (294)
+-|.+|+|-.||..||.||-.=+
T Consensus 110 ~yfvir~~R~r~~~rktRkYgvl 132 (163)
T PF06679_consen 110 LYFVIRTFRLRRRNRKTRKYGVL 132 (163)
T ss_pred HHHHHHHHhhccccccceeeccc
Confidence 45888999877777777765555
No 18
>COG4317 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=25.94 E-value=1.3e+02 Score=24.38 Aligned_cols=34 Identities=21% Similarity=0.162 Sum_probs=24.0
Q ss_pred HHHHHHHHHHHhhcCCCchhHHHHHHHHHHHHHHH
Q 022623 235 SVLAVATVFGALHLGSGRKYSFAVCHDLRLPLSGQ 269 (294)
Q Consensus 235 aIviSSllFGllH~~~~~~~~~~i~a~llGliLG~ 269 (294)
+=+..+++|+++|.+.+.- +-.....++|++.|+
T Consensus 10 AGllVGiiyaLl~vrsPAP-P~iAlvGllGilvGe 43 (93)
T COG4317 10 AGLLVGIIYALLKVRSPAP-PAIALVGLLGILVGE 43 (93)
T ss_pred hhHHHHHHHHHHhCCCCCC-cHHHHHHHHHHHHHH
Confidence 3455679999999987653 333345678888887
No 19
>PRK10862 SoxR reducing system protein RseC; Provisional
Probab=25.22 E-value=1.6e+02 Score=25.64 Aligned_cols=56 Identities=29% Similarity=0.274 Sum_probs=32.0
Q ss_pred hHHHHHHHHHHHhHhhhcchhHHHHHHHHHHHHhhcCCCchhHHHHHHHHHHHHHHHHHHH
Q 022623 213 PGISEELLFRGALLPLFGMDWRSVLAVATVFGALHLGSGRKYSFAVCHDLRLPLSGQRLLA 273 (294)
Q Consensus 213 apI~EELLFRGiLl~~fg~~w~aIviSSllFGllH~~~~~~~~~~i~a~llGliLG~vYl~ 273 (294)
..+-|--+.|+.++-++-+ ..++++.+++...++.+ . .+.+.+.+.|+++||.+.+
T Consensus 67 v~i~e~~llkaa~lvYllP-Ll~li~ga~l~~~~~~~--e--~~~~~~~~~g~~~g~~~~r 122 (154)
T PRK10862 67 LGIAEGSLLRSALLVYMTP-LVGLFLGAALFQLLFGS--D--LAALCGALLGGVGGFLLAR 122 (154)
T ss_pred EecchhhHHHHHHHHHHHH-HHHHHHHHHHHHHHhcc--h--HHHHHHHHHHHHHHHHHHH
Confidence 4566777777777655443 34444444444444332 2 2244556778888887776
No 20
>PHA03237 envelope glycoprotein M; Provisional
Probab=24.26 E-value=68 Score=32.73 Aligned_cols=16 Identities=31% Similarity=0.218 Sum_probs=7.8
Q ss_pred hhhHHHHHHHHhhhhh
Q 022623 56 KKSVKKLKRDRQLRLA 71 (294)
Q Consensus 56 ~~~~~~~~~~~~~~~~ 71 (294)
+|-++.+||.|..|+.
T Consensus 370 ~~~~~~~~r~r~~~~~ 385 (424)
T PHA03237 370 QKVKRYLNRVRGGRRR 385 (424)
T ss_pred HHHHHHHHHhhcCCCC
Confidence 3444455555554443
No 21
>COG3105 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=22.76 E-value=97 Score=26.96 Aligned_cols=22 Identities=9% Similarity=0.064 Sum_probs=18.4
Q ss_pred hhHHHHHHHHHHHHHHHHHHHh
Q 022623 253 KYSFAVCHDLRLPLSGQRLLAS 274 (294)
Q Consensus 253 ~~~~~i~a~llGliLG~vYl~T 274 (294)
.|.|.+.+.++|+++|++..+-
T Consensus 7 ~W~~a~igLvvGi~IG~li~Rl 28 (138)
T COG3105 7 TWEYALIGLVVGIIIGALIARL 28 (138)
T ss_pred HHHHHHHHHHHHHHHHHHHHHH
Confidence 4788888899999999987664
No 22
>PF11947 DUF3464: Protein of unknown function (DUF3464); InterPro: IPR021855 This family of proteins are functionally uncharacterised. This protein is found in bacteria and eukaryotes. Proteins in this family are typically between 137 to 196 amino acids in length.
Probab=22.62 E-value=4.1e+02 Score=23.51 Aligned_cols=31 Identities=26% Similarity=0.195 Sum_probs=17.1
Q ss_pred CchhHHHHHHHHHHHHHHHHHHHHHHHHhhh
Q 022623 107 TIPSRSNVLQACTVTCGLITALGVIIRQGSH 137 (294)
Q Consensus 107 ~~~~R~~lL~~~~lT~illLiial~i~lw~~ 137 (294)
+...=+.++.=|.++.++=.++|+......+
T Consensus 54 P~~Vs~RM~rRm~~~~GiP~~lG~~~f~~~y 84 (153)
T PF11947_consen 54 PEVVSNRMLRRMAVFVGIPTALGVAVFVVFY 84 (153)
T ss_pred CHHHHHHHHHHHHHHhchHHHHHHHHHHHHH
Confidence 3333344666677777776666654444443
No 23
>PF04142 Nuc_sug_transp: Nucleotide-sugar transporter; InterPro: IPR007271 This family of membrane proteins transport nucleotide sugars from the cytoplasm into golgi vesicles. P78382 from SWISSPROT transports CMP-sialic acid, P78381 from SWISSPROT transports UDP-galactose and Q9Y2D2 from SWISSPROT transports UDP-GlcNAc. This family has some but not complete overlap with the UDP-galactose transporter family IPR004689 from INTERPRO.; GO: 0005351 sugar:hydrogen symporter activity, 0008643 carbohydrate transport, 0000139 Golgi membrane, 0016021 integral to membrane
Probab=21.55 E-value=6.5e+02 Score=23.24 Aligned_cols=72 Identities=13% Similarity=-0.018 Sum_probs=41.1
Q ss_pred HHhhHHHHHHHHHHHhHhhhcc----hhHHHHHHHHHHHH-----------hhcCCCchhHHHHHHHHHHHHHHHHHHHh
Q 022623 210 AFLPGISEELLFRGALLPLFGM----DWRSVLAVATVFGA-----------LHLGSGRKYSFAVCHDLRLPLSGQRLLAS 274 (294)
Q Consensus 210 ~iLapI~EELLFRGiLl~~fg~----~w~aIviSSllFGl-----------lH~~~~~~~~~~i~a~llGliLG~vYl~T 274 (294)
.-++++.||-+..+-=.+...+ ...+++.+.+..-+ .|..+...|.....-.+.|++.++++.+.
T Consensus 126 S~~agVy~E~~lK~~~~s~~~~N~qL~~~gi~~~~~~~~~~~~~~~~~~g~f~G~~~~~~~~i~~~a~gGllva~v~Kya 205 (244)
T PF04142_consen 126 SGFAGVYFEKLLKRSNVSLWIQNMQLYLFGILFNLLALLLSDGSAISESGFFHGYSWWVWIVIFLQAIGGLLVAFVLKYA 205 (244)
T ss_pred HHHHHHHHHHHhcccchhHHHHHHHHHHHHHHHHHHHHhcccccccccCCchhhcchHHHHHHHHHHHhhHHHHHHHHHH
Confidence 3477788999887754333333 24455555444322 22222212222222345799999999999
Q ss_pred CCchhhH
Q 022623 275 HMATRQL 281 (294)
Q Consensus 275 GSL~~~I 281 (294)
+|+.-..
T Consensus 206 dnI~K~f 212 (244)
T PF04142_consen 206 DNIVKGF 212 (244)
T ss_pred hHHHHHH
Confidence 9997643
No 24
>KOG4544 consensus Uncharacterized conserved protein [Function unknown]
Probab=21.49 E-value=92 Score=27.27 Aligned_cols=49 Identities=8% Similarity=-0.059 Sum_probs=30.8
Q ss_pred HHHHhhcCCCchhHH-HHHHHHHHHHHHHHHHHhCCchhhHHHHHHHhHH
Q 022623 242 VFGALHLGSGRKYSF-AVCHDLRLPLSGQRLLASHMATRQLYPRALSCQW 290 (294)
Q Consensus 242 lFGllH~~~~~~~~~-~i~a~llGliLG~vYl~TGSL~~~I~~~a~~~~~ 290 (294)
.|.++|....-+|.- +....++++..++.-++--+-++||+|.++.|+.
T Consensus 43 A~~Ia~~RE~f~w~~~f~~~avv~laa~~~~~Kr~~~liPIvPL~f~~gY 92 (144)
T KOG4544|consen 43 AFKIAEEREKFNWIACFGSLAVVLLAASSFHHKRLLHLIPIVPLAFFIGY 92 (144)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhccchheechhhHhhhhh
Confidence 356666654333321 2222356777777777777888889998887763
Done!