Query 017952
Match_columns 363
No_of_seqs 16 out of 18
Neff 1.7
Searched_HMMs 46136
Date Fri Mar 29 04:52:15 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/017952.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/017952hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF02517 Abi: CAAX protease se 98.1 6.1E-06 1.3E-10 60.7 4.6 89 178-330 3-91 (91)
2 TIGR03008 pepcterm_CAAX CAAX p 95.6 0.014 3.1E-07 53.0 4.1 38 301-338 179-220 (222)
3 COG1266 Predicted metal-depend 95.2 0.043 9.4E-07 44.5 5.3 27 302-328 185-211 (226)
4 PF04604 L_biotic_typeA: Type- 65.5 3.6 7.8E-05 31.4 1.3 26 160-185 10-49 (51)
5 PF03116 NQR2_RnfD_RnfE: NQR2, 64.0 14 0.00031 35.2 5.3 84 152-247 2-104 (313)
6 PRK00816 rnfD electron transpo 50.0 29 0.00063 34.2 5.0 85 153-247 4-106 (350)
7 PF13556 HTH_30: PucR C-termin 46.7 16 0.00035 26.4 2.1 19 338-356 21-39 (59)
8 PF04995 CcmD: Heme exporter p 40.7 20 0.00043 25.5 1.7 29 329-357 15-43 (46)
9 PF07219 HemY_N: HemY protein 39.9 44 0.00095 26.7 3.8 30 279-308 44-73 (108)
10 PF08172 CASP_C: CASP C termin 36.9 32 0.0007 32.2 2.9 28 313-357 75-102 (248)
11 KOG0835 Cyclin L [General func 36.7 9.6 0.00021 38.4 -0.6 16 305-320 23-38 (367)
12 PF08285 DPM3: Dolichol-phosph 35.6 19 0.00041 29.4 1.1 35 322-356 46-83 (91)
13 smart00582 RPR domain present 32.7 35 0.00077 26.7 2.1 21 273-297 93-113 (121)
14 TIGR00035 asp_race aspartate r 32.5 1.1E+02 0.0024 26.9 5.4 52 300-356 135-186 (229)
15 PRK14713 multifunctional hydro 31.9 75 0.0016 31.7 4.7 42 109-150 30-72 (530)
16 PRK09804 putative cryptic C4-d 28.9 30 0.00066 35.4 1.5 74 160-250 293-370 (455)
17 PF12666 PrgI: PrgI family pro 28.1 26 0.00057 26.9 0.7 28 163-192 4-32 (93)
18 PF12725 DUF3810: Protein of u 27.8 1E+02 0.0022 29.5 4.7 77 220-350 12-88 (318)
19 PLN03160 uncharacterized prote 24.5 89 0.0019 28.3 3.5 28 245-272 51-78 (219)
20 cd08316 Death_FAS_TNFRSF6 Deat 24.4 98 0.0021 25.4 3.4 34 272-305 46-79 (97)
21 PRK12757 cell division protein 24.2 69 0.0015 30.8 2.8 29 238-270 3-31 (256)
22 PF11160 DUF2945: Protein of u 24.1 45 0.00098 25.8 1.3 15 252-266 30-44 (62)
23 PF00076 RRM_1: RNA recognitio 23.8 60 0.0013 21.6 1.8 19 163-181 8-26 (70)
24 cd07962 Anticodon_Ia_Val Antic 23.7 45 0.00098 26.5 1.3 27 276-302 52-78 (135)
25 PF09496 CENP-O: Cenp-O kineto 23.0 1.3E+02 0.0027 24.2 3.7 18 228-245 39-56 (90)
26 COG0798 ACR3 Arsenite efflux p 22.6 26 0.00056 35.0 -0.3 42 263-307 184-226 (342)
27 PF02525 Flavodoxin_2: Flavodo 22.0 1.3E+02 0.0028 25.3 3.8 47 288-352 149-197 (199)
28 PF03613 EIID-AGA: PTS system 21.8 1.2E+02 0.0027 28.6 4.0 48 274-323 4-72 (264)
29 PF00536 SAM_1: SAM domain (St 21.6 75 0.0016 22.3 2.0 14 341-354 51-64 (64)
30 PF01117 Aerolysin: Aerolysin 21.5 65 0.0014 32.1 2.2 22 293-316 16-37 (360)
31 KOG0193 Serine/threonine prote 21.1 1.6E+02 0.0035 32.1 5.0 67 237-306 577-654 (678)
32 PRK10927 essential cell divisi 20.9 1.3E+02 0.0028 30.1 4.0 31 230-260 30-60 (319)
33 PLN03155 cytochrome c oxidase 20.9 47 0.001 26.6 0.9 26 332-357 29-56 (63)
34 PF13994 PgaD: PgaD-like prote 20.7 77 0.0017 26.6 2.2 43 294-336 31-76 (138)
35 TIGR01946 rnfD electron transp 20.3 1.4E+02 0.0031 29.2 4.2 63 173-247 30-100 (327)
No 1
>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=98.06 E-value=6.1e-06 Score=60.69 Aligned_cols=89 Identities=22% Similarity=0.347 Sum_probs=65.7
Q ss_pred CchhhhHHhhhccchhHHHHHHHHhhhhHHHHhhCCCcccccccchhhcccCCCcchHHHHHHHHHHHHHhcceeeeecC
Q 017952 178 SPWQFVLIVAASSVGEELFYRAAVQGALADIFLRGTDFLTDAQGMASLTGVLPPFVPFAQAFAAVITAALTGSLYYVATS 257 (363)
Q Consensus 178 spwQFiliVaAssvgEElFyR~AvQGaladiflrgt~l~~d~~GmasLtgv~PpFvPFAq~fAavltaaLTGSlYyva~s 257 (363)
..+.++..+....+.||++||..+|..+.+. .+. ..|.++++.+=|.+.+..
T Consensus 3 ~~~~~~~~~~~~~~~EEl~fRg~l~~~l~~~--~~~------------------------~~a~~is~~~f~~~H~~~-- 54 (91)
T PF02517_consen 3 FLIFFLVMILIAPIAEELFFRGFLFNRLRRR--FNP------------------------WFAILISSLLFALWHLPN-- 54 (91)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh--cch------------------------HHHHHHHHHHHHHHHHhh--
Confidence 3466777888899999999999999877654 110 456666666666554432
Q ss_pred CCCCceEEeecccCccchHHHHHHHHHHHHHHhhhHhhhHHHHHHHHHHhcceeeeeCcchhhHHHhhhhhhh
Q 017952 258 PKDPTYVVAPVLRSRSGREDLKKLFAAWYERRQMKKIYSPLLEGLLALYLGFEWIQTNNILAPIITHGIYSAV 330 (363)
Q Consensus 258 pkDPtYvvaPv~~sr~~r~dlkklf~aWyErRqmkKIYSPLlEglLalYLGfEWiqT~NILAPiiTHgiYS~V 330 (363)
-.. -+.-.++|+.+|.-+..|+|+++|++.|+++..+
T Consensus 55 -----------------------------------~~~-~~~~~~~g~~~~~~~~~t~sl~~~i~~H~~~n~~ 91 (91)
T PF02517_consen 55 -----------------------------------GPQ-FIYAFLFGLLFGYLYLRTGSLWAAIIAHALWNLV 91 (91)
T ss_pred -----------------------------------hHH-HHHHHHHHHHHHHHHHHcCChHHHHHHHHHHHcC
Confidence 001 2666788999999999999999999999998653
No 2
>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=95.60 E-value=0.014 Score=53.04 Aligned_cols=38 Identities=24% Similarity=0.413 Sum_probs=30.5
Q ss_pred HHHHHHhcceeeeeCcchhhHHHhhhhh----hhhhccccch
Q 017952 301 GLLALYLGFEWIQTNNILAPIITHGIYS----AVILGHGLWK 338 (363)
Q Consensus 301 glLalYLGfEWiqT~NILAPiiTHgiYS----~VvlghGLwk 338 (363)
.+.|+.+|.-+..|+|+.+||+.|.+.. ..|+.-|=|.
T Consensus 179 ~l~Gli~~~l~~~tgsL~~~I~~H~~~N~ll~~~vl~~~~w~ 220 (222)
T TIGR03008 179 LIAGLAYNLLLLRTGSIMACILAHAVTNGLLGLWVLLTGAWS 220 (222)
T ss_pred HHHHHHHHHHHHHhCChHHHHHHHHHHHHHHHHHHHHcCCcC
Confidence 4558889999999999999999998754 4567777664
No 3
>COG1266 Predicted metal-dependent membrane protease [General function prediction only]
Probab=95.20 E-value=0.043 Score=44.51 Aligned_cols=27 Identities=26% Similarity=0.645 Sum_probs=21.4
Q ss_pred HHHHHhcceeeeeCcchhhHHHhhhhh
Q 017952 302 LLALYLGFEWIQTNNILAPIITHGIYS 328 (363)
Q Consensus 302 lLalYLGfEWiqT~NILAPiiTHgiYS 328 (363)
..++-+|+-+.-|+|+..||+.|..+.
T Consensus 185 ~~gli~~~~~~~t~~l~~~i~~H~~~N 211 (226)
T COG1266 185 IAGLILGLLYLRTGSLWVPILLHALIN 211 (226)
T ss_pred HHHHHHHHHHHHhCCcHHHHHHHHHHH
Confidence 344455555679999999999999998
No 4
>PF04604 L_biotic_typeA: Type-A lantibiotic; InterPro: IPR007682 Lantibiotics are antibiotic peptides distinguished by the presence of the rare thioether amino acids lanthionine and/or methyllanthionine. They are produced by Gram-positive bacteria as gene-encoded precursor peptides and undergo post-translational modification to generate the mature peptide. Based on their structural and functional features lantibiotics are currently divided into two major groups: the flexible amphiphilic type-A and the rather rigid and globular type-B. Type-A lantibiotics act primarily by pore formation in the bacterial membrane by a mechanism involving the interaction with specific docking molecules such as the membrane precursor lipid II [].; GO: 0019748 secondary metabolic process, 0005576 extracellular region
Probab=65.51 E-value=3.6 Score=31.41 Aligned_cols=26 Identities=38% Similarity=0.864 Sum_probs=21.9
Q ss_pred ccccccchHHHHHHhhc--------------CCchhhhHH
Q 017952 160 RAIRDVEDEELRSFFYG--------------MSPWQFVLI 185 (363)
Q Consensus 160 RAIRDVEDeEL~~fF~G--------------MspwQFili 185 (363)
-++..|+||||...--| |..|||++-
T Consensus 10 ~~lqevs~eELd~ilGg~g~Gv~~Tis~eC~~ns~q~~ft 49 (51)
T PF04604_consen 10 NSLQEVSDEELDQILGGAGNGVIKTISHECRMNSWQFIFT 49 (51)
T ss_pred HHHHhcCHHHHHHHhCCCCCCceeecccccccccHHHHhc
Confidence 46778999999999998 777999873
No 5
>PF03116 NQR2_RnfD_RnfE: NQR2, RnfD, RnfE family; InterPro: IPR004338 This family of proteins describes the Nqr2 (NqrB) subunit of the bacterial 6-subunit sodium-translocating NADH-ubiquinone oxidoreductase (i.e. a respiration linked sodium pump). In Vibrio cholerae, it negatively regulates the expression of virulence factors through inhibiting (by an unknown mechanism) the transcription of the transcriptional activator ToxT []. The family also includes RnfD, which is involved in nitrogen fixation. The similarity of RnfD to NADH-ubiquinone oxidoreductases was previously noted [].; GO: 0006810 transport, 0016020 membrane
Probab=63.96 E-value=14 Score=35.24 Aligned_cols=84 Identities=30% Similarity=0.455 Sum_probs=54.8
Q ss_pred hhccCcccccccccchHH------------HHHHhhcCCchhhhHHhhhccchhHHHHHHHHhhhhHHHHhhCCCc--cc
Q 017952 152 VVKLSPHARAIRDVEDEE------------LRSFFYGMSPWQFVLIVAASSVGEELFYRAAVQGALADIFLRGTDF--LT 217 (363)
Q Consensus 152 VVk~sp~ARAIRDVEDeE------------L~~fF~GMspwQFiliVaAssvgEElFyR~AvQGaladiflrgt~l--~~ 217 (363)
+++.+||.|.=+|+..-- .--|++|+.+.-.+++..++++.=|..+.. +++++. .+
T Consensus 2 ~~~~sPhi~~~~~~~~~M~~VilaLlP~~~~~~~~fG~~~l~~~~~av~~a~l~E~l~~~----------l~~~~~~~~~ 71 (313)
T PF03116_consen 2 VVSSSPHIRDGRSTQKIMWDVILALLPALLASIYFFGFRALLVILVAVLTAVLAEALFAK----------LRKRPIPTLK 71 (313)
T ss_pred ccCCCCccCCCCCHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHH----------HhcCCCCCCC
Confidence 688999999888776532 124788998877777766666666655542 344443 33
Q ss_pred ccccchhhcc-----cCCCcchHHHHHHHHHHHHH
Q 017952 218 DAQGMASLTG-----VLPPFVPFAQAFAAVITAAL 247 (363)
Q Consensus 218 d~~GmasLtg-----v~PpFvPFAq~fAavltaaL 247 (363)
|-. +-+|| .+||.+|+-+++.++.-|.+
T Consensus 72 d~s--a~vTglLlal~LP~~~P~w~v~ig~~~aI~ 104 (313)
T PF03116_consen 72 DLS--AVVTGLLLALLLPPSVPLWVVAIGSFFAIV 104 (313)
T ss_pred Ccc--HHHHHHHHHHhCCCCCcHHHHHHHHHHHHH
Confidence 333 33344 58999999887766665554
No 6
>PRK00816 rnfD electron transport complex protein RnfD; Reviewed
Probab=49.99 E-value=29 Score=34.22 Aligned_cols=85 Identities=21% Similarity=0.339 Sum_probs=50.6
Q ss_pred hccCcccccccccchHHH------------HHHhhcCCchhhhHHhhhccchhHHHHHHHHhhhhHHHHhhCCCccc-cc
Q 017952 153 VKLSPHARAIRDVEDEEL------------RSFFYGMSPWQFVLIVAASSVGEELFYRAAVQGALADIFLRGTDFLT-DA 219 (363)
Q Consensus 153 Vk~sp~ARAIRDVEDeEL------------~~fF~GMspwQFiliVaAssvgEElFyR~AvQGaladiflrgt~l~~-d~ 219 (363)
|..|||.|.=+++..-=+ --||+|+.+..-+++-.++++.-|..+.. +|++.... -.
T Consensus 4 v~~sPh~~~~~s~~~iM~~VllALlP~~~~~i~~fG~~al~~~~~~v~~av~~E~l~~k----------~~~k~~~~~l~ 73 (350)
T PRK00816 4 IASSPHTHNQRQTSRIMLWVILAALPGIAAQTYFFGWGTLIQILLAIVTALLAEAAVLK----------LRKRPVAATLK 73 (350)
T ss_pred CCCCCcccCCCcHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHH----------HhCCCCccccC
Confidence 578999986555543211 12899998877666666666666654442 24433221 12
Q ss_pred ccchhhcc-----cCCCcchHHHHHHHHHHHHH
Q 017952 220 QGMASLTG-----VLPPFVPFAQAFAAVITAAL 247 (363)
Q Consensus 220 ~GmasLtg-----v~PpFvPFAq~fAavltaaL 247 (363)
.|=+-+|| .+||.+|+-++..++.-|.+
T Consensus 74 D~Sa~vTglLlal~lPp~~P~W~~~iG~~fAI~ 106 (350)
T PRK00816 74 DNSALLTALLLAVSIPPLAPWWMIVIGTVFAII 106 (350)
T ss_pred cccHHHHHHHHHHhcCCCCcHHHHHHHHHHHHH
Confidence 24455565 47999998876655554443
No 7
>PF13556 HTH_30: PucR C-terminal helix-turn-helix domain; PDB: 3ONQ_B.
Probab=46.71 E-value=16 Score=26.40 Aligned_cols=19 Identities=32% Similarity=0.541 Sum_probs=15.8
Q ss_pred hhchhhHHHHHHHHHHhhc
Q 017952 338 KIHDHRRRLHQRIQRLELE 356 (363)
Q Consensus 338 kihdhr~rlRqRiq~i~~~ 356 (363)
++|=||.-++.|+++|+.-
T Consensus 21 ~L~iHrNTl~yRl~ki~~l 39 (59)
T PF13556_consen 21 ALHIHRNTLRYRLKKIEEL 39 (59)
T ss_dssp HHTS-HHHHHHHHHHHHHH
T ss_pred HHCCCHHHHHHHHHHHHHH
Confidence 5789999999999999864
No 8
>PF04995 CcmD: Heme exporter protein D (CcmD); InterPro: IPR007078 The CcmD protein is part of a C-type cytochrome biogenesis operon []. The exact function of this protein is uncertain. It has been proposed that CcmC, CcmD and CcmE interact directly with each other, establishing a cytoplasm to periplasm haem delivery pathway for cytochrome c maturation []. This protein is found fused to CcmE in P52224 from SWISSPROT. These proteins contain a predicted transmembrane helix.; GO: 0006810 transport, 0016021 integral to membrane
Probab=40.68 E-value=20 Score=25.53 Aligned_cols=29 Identities=31% Similarity=0.402 Sum_probs=17.8
Q ss_pred hhhhccccchhchhhHHHHHHHHHHhhcc
Q 017952 329 AVILGHGLWKIHDHRRRLHQRIQRLELEG 357 (363)
Q Consensus 329 ~VvlghGLwkihdhr~rlRqRiq~i~~~~ 357 (363)
+++++==++-..-.|+++++++++++..+
T Consensus 15 ~~~l~~l~~~~~~~~r~~~~~l~~~~~r~ 43 (46)
T PF04995_consen 15 ALVLAGLIVWSLRRRRRLRKELKRLEARE 43 (46)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHhH
Confidence 34444334445556777888888877654
No 9
>PF07219 HemY_N: HemY protein N-terminus; InterPro: IPR010817 This entry represents the N terminus (approximately 150 residues) of bacterial HemY porphyrin biosynthesis proteins. These are membrane protein involved in a late step of protoheme IX synthesis [].
Probab=39.93 E-value=44 Score=26.68 Aligned_cols=30 Identities=33% Similarity=0.505 Sum_probs=26.0
Q ss_pred HHHHHHHHHHHhhhHhhhHHHHHHHHHHhc
Q 017952 279 KKLFAAWYERRQMKKIYSPLLEGLLALYLG 308 (363)
Q Consensus 279 kklf~aWyErRqmkKIYSPLlEglLalYLG 308 (363)
-..+..|.++|..+|=+.-|.+||+++--|
T Consensus 44 p~~~~~~~~~rr~~ka~~al~~Gl~al~~G 73 (108)
T PF07219_consen 44 PSRVRRWRRRRRRRKAQRALSRGLIALAEG 73 (108)
T ss_pred hHHHHHHHHHHHHHHHHHHHHHHHHHHHCC
Confidence 356889999999999999999999997654
No 10
>PF08172 CASP_C: CASP C terminal; InterPro: IPR012955 This domain is the C-terminal region of the CASP family of proteins. These are Golgi membrane proteins which are thought to have a role in vesicle transport [].; GO: 0006891 intra-Golgi vesicle-mediated transport, 0030173 integral to Golgi membrane
Probab=36.90 E-value=32 Score=32.19 Aligned_cols=28 Identities=36% Similarity=0.479 Sum_probs=22.5
Q ss_pred eeCcchhhHHHhhhhhhhhhccccchhchhhHHHHHHHHHHhhcc
Q 017952 313 QTNNILAPIITHGIYSAVILGHGLWKIHDHRRRLHQRIQRLELEG 357 (363)
Q Consensus 313 qT~NILAPiiTHgiYS~VvlghGLwkihdhr~rlRqRiq~i~~~~ 357 (363)
..++=|-|||| .+|.|.|+|.++|+.|.
T Consensus 75 ~~~~siLpIVt-----------------sQRDRFR~Rn~ELE~el 102 (248)
T PF08172_consen 75 GGDSSILPIVT-----------------SQRDRFRQRNAELEEEL 102 (248)
T ss_pred CCcccHHHHHH-----------------HHHHHHHHHHHHHHHHH
Confidence 55666777777 49999999999998764
No 11
>KOG0835 consensus Cyclin L [General function prediction only]
Probab=36.68 E-value=9.6 Score=38.38 Aligned_cols=16 Identities=44% Similarity=0.468 Sum_probs=14.1
Q ss_pred HHhcceeeeeCcchhh
Q 017952 305 LYLGFEWIQTNNILAP 320 (363)
Q Consensus 305 lYLGfEWiqT~NILAP 320 (363)
.|||+||||+.-||--
T Consensus 23 ~~LG~e~Iqea~ILL~ 38 (367)
T KOG0835|consen 23 RILGCELIQEAGILLN 38 (367)
T ss_pred HHHhHHHHHhhhHhhc
Confidence 5999999999999853
No 12
>PF08285 DPM3: Dolichol-phosphate mannosyltransferase subunit 3 (DPM3); InterPro: IPR013174 This family corresponds to subunit 3 of dolichol-phosphate mannosyltransferase, an enzyme which generates mannosyl donors for glycosylphosphatidylinositols, N-glycan and protein O- and C-mannosylation. DPM3 is an integral membrane protein and plays a role in stabilising the dolichol-phosphate mannosyl transferase complex [].
Probab=35.57 E-value=19 Score=29.44 Aligned_cols=35 Identities=26% Similarity=0.492 Sum_probs=27.7
Q ss_pred HHhhhhhhhhhccccchhchhhH---HHHHHHHHHhhc
Q 017952 322 ITHGIYSAVILGHGLWKIHDHRR---RLHQRIQRLELE 356 (363)
Q Consensus 322 iTHgiYS~VvlghGLwkihdhr~---rlRqRiq~i~~~ 356 (363)
+.-|.||...+|-|++..||.-+ .|.+-|++-|.+
T Consensus 46 v~fG~Ysl~~lgy~v~tFnDcpeA~~eL~~eI~eAK~d 83 (91)
T PF08285_consen 46 VSFGCYSLFTLGYGVATFNDCPEAAKELQKEIKEAKAD 83 (91)
T ss_pred HHHHHHHHHHHHHhhhccCCCHHHHHHHHHHHHHHHHH
Confidence 67899999999999999998754 566666665544
No 13
>smart00582 RPR domain present in proteins, which are involved in regulation of nuclear pre-mRNA.
Probab=32.69 E-value=35 Score=26.70 Aligned_cols=21 Identities=29% Similarity=0.832 Sum_probs=17.7
Q ss_pred cchHHHHHHHHHHHHHHhhhHhhhH
Q 017952 273 SGREDLKKLFAAWYERRQMKKIYSP 297 (363)
Q Consensus 273 ~~r~dlkklf~aWyErRqmkKIYSP 297 (363)
..++.++|++..|.+| .||+|
T Consensus 93 ~~~~ki~kll~iW~~~----~iF~~ 113 (121)
T smart00582 93 ETKKKIRRLLNIWEER----GIFPP 113 (121)
T ss_pred HHHHHHHHHHHHHhcC----CCCCH
Confidence 5589999999999997 57776
No 14
>TIGR00035 asp_race aspartate racemase.
Probab=32.48 E-value=1.1e+02 Score=26.90 Aligned_cols=52 Identities=27% Similarity=0.293 Sum_probs=38.3
Q ss_pred HHHHHHHhcceeeeeCcchhhHHHhhhhhhhhhccccchhchhhHHHHHHHHHHhhc
Q 017952 300 EGLLALYLGFEWIQTNNILAPIITHGIYSAVILGHGLWKIHDHRRRLHQRIQRLELE 356 (363)
Q Consensus 300 EglLalYLGfEWiqT~NILAPiiTHgiYS~VvlghGLwkihdhr~rlRqRiq~i~~~ 356 (363)
+..|.-+ |++.++-..-+.+.|.++||..+--| +..+-++.+++-++++..+
T Consensus 135 ~~~l~~~-g~~v~~p~~~~~~~i~~~i~~~~~~g----~~~~~~~~l~~~~~~l~~~ 186 (229)
T TIGR00035 135 EREMKKH-GIEIVTPDKEEQEAIMSGIYDEVKAG----NIELGRELLLKIAKELEER 186 (229)
T ss_pred HHHHHHC-CCEEECCCHHHHHHHHHHHHHHHhcC----CcHHHHHHHHHHHHHHHhC
Confidence 3344444 78888877778999999999876666 3367788899988888643
No 15
>PRK14713 multifunctional hydroxymethylpyrimidine phosphokinase/4-amino-5-aminomethyl-2-methylpyrimidine hydrolase; Provisional
Probab=31.92 E-value=75 Score=31.75 Aligned_cols=42 Identities=21% Similarity=0.264 Sum_probs=29.5
Q ss_pred ceeeeeeecccCCCCCCCHH-HHHhccCCChhhHHHHHhhccc
Q 017952 109 RFICSITGVDSMGGFHPSLD-AIVEGLGYAAPPIMALLFILDD 150 (363)
Q Consensus 109 ~fIC~~tGiD~~GGF~~Sld-ai~~GlGYA~pPimaLLFIldD 150 (363)
..|+.|.|.|+.||--+.-| .+++.+|.-.-++.--+..++.
T Consensus 30 ~~vl~Iag~D~sGgaGi~aDl~t~~a~g~~~~~v~Talt~q~t 72 (530)
T PRK14713 30 PRVLSIAGTDPSGGAGIQADLKSIAAAGGYGMAVITALVAQNT 72 (530)
T ss_pred CeEEEEeCcCCCcHHHHHHHHHHHHHcCCeecchhheEeeecC
Confidence 35789999999999887776 3678888555455444445554
No 16
>PRK09804 putative cryptic C4-dicarboxylate transporter DcuD; Provisional
Probab=28.89 E-value=30 Score=35.43 Aligned_cols=74 Identities=31% Similarity=0.508 Sum_probs=39.5
Q ss_pred ccccccchHHHHHHhhcCCchhhh----HHhhhccchhHHHHHHHHhhhhHHHHhhCCCcccccccchhhcccCCCcchH
Q 017952 160 RAIRDVEDEELRSFFYGMSPWQFV----LIVAASSVGEELFYRAAVQGALADIFLRGTDFLTDAQGMASLTGVLPPFVPF 235 (363)
Q Consensus 160 RAIRDVEDeEL~~fF~GMspwQFi----liVaAssvgEElFyR~AvQGaladiflrgt~l~~d~~GmasLtgv~PpFvPF 235 (363)
|..+.+- |++..||.||+ -+|. |+|||+ .|=----.=++-|.++..- ++. | +.| .+.+.
T Consensus 293 r~~k~~~-~~~~~ff~GMG-~~f~~VV~LIVAA~-----vFa~GL~aiG~Id~Li~~~---~~~-g---~g~---~~~~l 355 (455)
T PRK09804 293 HNLRETM-DDVQAFFDGMG-TQFANVVTLVVAGE-----IFAKGLTTIGTVDAVIRGA---EHS-G---LGG---IGVMI 355 (455)
T ss_pred ccchhHH-HHHHHHHHHHH-HHHHHHHHHHHhHH-----HHHhHHHHhhHHHHHHHHH---HhC-C---Cch---HHHHH
Confidence 3444443 57999999999 7776 556654 3322222234556655331 111 1 111 23344
Q ss_pred HHHHHHHHHHHHhcc
Q 017952 236 AQAFAAVITAALTGS 250 (363)
Q Consensus 236 Aq~fAavltaaLTGS 250 (363)
.=.....+.+.+|||
T Consensus 356 v~~~i~~l~a~l~GS 370 (455)
T PRK09804 356 IMALVIAICAIVMGS 370 (455)
T ss_pred HHHHHHHHHHhhhcC
Confidence 445566677778877
No 17
>PF12666 PrgI: PrgI family protein; InterPro: IPR024414 This family of bacterial proteins is functionally uncharacterised. Proteins in this family are typically between 116 and 146 amino acids in length. PrgI is found encoded on plasmids of Enterococcus faecalis, its function is not known.
Probab=28.05 E-value=26 Score=26.91 Aligned_cols=28 Identities=29% Similarity=0.673 Sum_probs=21.4
Q ss_pred cccch-HHHHHHhhcCCchhhhHHhhhccch
Q 017952 163 RDVED-EELRSFFYGMSPWQFVLIVAASSVG 192 (363)
Q Consensus 163 RDVED-eEL~~fF~GMspwQFiliVaAssvg 192 (363)
+|+++ || ..+.|+|--|++.++++..++
T Consensus 4 kdi~~~e~--ki~~GlT~RQl~~l~~~~~~~ 32 (93)
T PF12666_consen 4 KDISKYEE--KIFFGLTLRQLICLAIGALVG 32 (93)
T ss_pred cchhhccc--hhccCCCHHHHHHHHHHHHHH
Confidence 35555 43 678899999999998887766
No 18
>PF12725 DUF3810: Protein of unknown function (DUF3810); InterPro: IPR024294 This family of bacterial proteins is functionally uncharacterised. Proteins in this family are typically between 333 and 377 amino acids in length and contain a conserved HEXXH sequence motif that is characteristic of metallopeptidases. This family may therefore belong to an as yet uncharacterised family of peptidase enzymes.
Probab=27.76 E-value=1e+02 Score=29.50 Aligned_cols=77 Identities=22% Similarity=0.265 Sum_probs=46.5
Q ss_pred ccchhhcccCCCcchHHHHHHHHHHHHHhcceeeeecCCCCCceEEeecccCccchHHHHHHHHHHHHHHhhhHhhhHHH
Q 017952 220 QGMASLTGVLPPFVPFAQAFAAVITAALTGSLYYVATSPKDPTYVVAPVLRSRSGREDLKKLFAAWYERRQMKKIYSPLL 299 (363)
Q Consensus 220 ~GmasLtgv~PpFvPFAq~fAavltaaLTGSlYyva~spkDPtYvvaPv~~sr~~r~dlkklf~aWyErRqmkKIYSPLl 299 (363)
+.+..++|.+| +++++++-+++...+-..++ .-+||++..|..++ ..=++
T Consensus 12 ~~l~~~~g~~P--FSvgdi~~~~~il~ll~~~~-----------------------~~~~~~~k~~~~~~-----l~~~~ 61 (318)
T PF12725_consen 12 KLLRRLFGWFP--FSVGDILYYLLILFLLYYLI-----------------------RLIRKIFKKKKRFK-----LLNIL 61 (318)
T ss_pred HHHHHhccCcC--hhHHHHHHHHHHHHHHHHHH-----------------------HHHHHHHhhhhHHH-----HHHHH
Confidence 45677889987 46778887776665544433 23455555554444 23334
Q ss_pred HHHHHHHhcceeeeeCcchhhHHHhhhhhhhhhccccchhchhhHHHHHHH
Q 017952 300 EGLLALYLGFEWIQTNNILAPIITHGIYSAVILGHGLWKIHDHRRRLHQRI 350 (363)
Q Consensus 300 EglLalYLGfEWiqT~NILAPiiTHgiYS~VvlghGLwkihdhr~rlRqRi 350 (363)
..++-+|+-| |.+|-+++||.-|-+|.
T Consensus 62 ~~~~~~y~~F------------------------~~~WGlNY~R~pl~~~l 88 (318)
T PF12725_consen 62 FFLSVLYFLF------------------------YLLWGLNYYRPPLSERL 88 (318)
T ss_pred HHHHHHHHHH------------------------HHHhhhhcCCcCHHHHc
Confidence 4455555544 55788888887666654
No 19
>PLN03160 uncharacterized protein; Provisional
Probab=24.55 E-value=89 Score=28.31 Aligned_cols=28 Identities=21% Similarity=0.201 Sum_probs=23.2
Q ss_pred HHHhcceeeeecCCCCCceEEeecccCc
Q 017952 245 AALTGSLYYVATSPKDPTYVVAPVLRSR 272 (363)
Q Consensus 245 aaLTGSlYyva~spkDPtYvvaPv~~sr 272 (363)
+++.+.++|..--||||+|-|..+-=++
T Consensus 51 ~~v~~~l~~~vfrPk~P~~~v~~v~l~~ 78 (219)
T PLN03160 51 ATTILVLVFTVFRVKDPVIKMNGVTVTK 78 (219)
T ss_pred HHHHHheeeEEEEccCCeEEEEEEEEee
Confidence 7777888899999999999998876443
No 20
>cd08316 Death_FAS_TNFRSF6 Death domain of FAS or TNF receptor superfamily member 6. Death Domain (DD) found in the FS7-associated cell surface antigen (FAS). FAS, also known as TNFRSF6 (TNF receptor superfamily member 6), APT1, CD95, FAS1, or APO-1, together with FADD (Fas-associating via Death Domain) and caspase 8, is an integral part of the death inducing signalling complex (DISC), which plays an important role in the induction of apoptosis and is activated by binding of the ligand FasL to FAS. FAS also plays a critical role in self-tolerance by eliminating cell types (autoreactive T and B cells) that contribute to autoimmunity. DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily including CARD (Caspase activation and recruitment domain), DED (Death Effector Domain), and PYRIN. They serve as adaptors in sign
Probab=24.43 E-value=98 Score=25.44 Aligned_cols=34 Identities=24% Similarity=0.442 Sum_probs=29.0
Q ss_pred ccchHHHHHHHHHHHHHHhhhHhhhHHHHHHHHH
Q 017952 272 RSGREDLKKLFAAWYERRQMKKIYSPLLEGLLAL 305 (363)
Q Consensus 272 r~~r~dlkklf~aWyErRqmkKIYSPLlEglLal 305 (363)
+..++.--+++.+||++--++--|.-|++.|-..
T Consensus 46 ~d~~Eq~~qmL~~W~~~~G~~a~~~~Li~aLr~~ 79 (97)
T cd08316 46 QDTAEQKVQLLRAWYQSHGKTGAYRTLIKTLRKA 79 (97)
T ss_pred CChHHHHHHHHHHHHHHhCCCchHHHHHHHHHHc
Confidence 4557888899999999999999999999888763
No 21
>PRK12757 cell division protein FtsN; Provisional
Probab=24.24 E-value=69 Score=30.75 Aligned_cols=29 Identities=31% Similarity=0.676 Sum_probs=23.4
Q ss_pred HHHHHHHHHHhcceeeeecCCCCCceEEeeccc
Q 017952 238 AFAAVITAALTGSLYYVATSPKDPTYVVAPVLR 270 (363)
Q Consensus 238 ~fAavltaaLTGSlYyva~spkDPtYvvaPv~~ 270 (363)
++|+++...+.|.|||++...||. +|++.
T Consensus 3 alava~lv~f~gGLyfi~h~k~~~----~~~~~ 31 (256)
T PRK12757 3 ALAVAVLVTFIGGLYFITHNKKEE----APLLP 31 (256)
T ss_pred HHHHHHHHHHhhheEEEecCCCCC----CCccc
Confidence 578889999999999999987764 55554
No 22
>PF11160 DUF2945: Protein of unknown function (DUF2945); InterPro: IPR021331 This family of proteins has no known function.
Probab=24.12 E-value=45 Score=25.79 Aligned_cols=15 Identities=33% Similarity=0.516 Sum_probs=12.5
Q ss_pred eeeecCCCCCceEEe
Q 017952 252 YYVATSPKDPTYVVA 266 (363)
Q Consensus 252 Yyva~spkDPtYvva 266 (363)
.=+.+||.||.|+|-
T Consensus 30 ~~v~AS~ddP~Y~I~ 44 (62)
T PF11160_consen 30 RTVNASKDDPRYEIE 44 (62)
T ss_pred EEecCCCCCCEEEEE
Confidence 347899999999984
No 23
>PF00076 RRM_1: RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain); InterPro: IPR000504 Many eukaryotic proteins containing one or more copies of a putative RNA-binding domain of about 90 amino acids are known to bind single-stranded RNAs [, , ]. The largest group of single strand RNA-binding proteins is the eukaryotic RNA recognition motif (RRM) family that contains an eight amino acid RNP-1 consensus sequence [, ]. RRM proteins have a variety of RNA binding preferences and functions, and include heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing (SR, U2AF, Sxl), protein components of small nuclear ribonucleoproteins (U1 and U2 snRNPs), and proteins that regulate RNA stability and translation (PABP, La, Hu) [, , ]. The RRM in heterodimeric splicing factor U2 snRNP auxiliary factor (U2AF) appears to have two RRM-like domains with specialised features for protein recognition []. The motif also appears in a few single stranded DNA binding proteins. The typical RRM consists of four anti-parallel beta-strands and two alpha-helices arranged in a beta-alpha-beta-beta-alpha-beta fold with side chains that stack with RNA bases. Specificity of RNA binding is determined by multiple contacts with surrounding amino acids. A third helix is present during RNA binding in some cases []. The RRM is reviewed in a number of publications [, , ].; GO: 0003676 nucleic acid binding; PDB: 2RNE_A 2DGO_A 2DO4_A 1YTY_B 2VOO_B 2VOP_A 2VON_B 1ZH5_B 2VOD_A 1S79_A ....
Probab=23.77 E-value=60 Score=21.64 Aligned_cols=19 Identities=42% Similarity=0.677 Sum_probs=15.4
Q ss_pred cccchHHHHHHhhcCCchh
Q 017952 163 RDVEDEELRSFFYGMSPWQ 181 (363)
Q Consensus 163 RDVEDeEL~~fF~GMspwQ 181 (363)
.|++++||+++|.-.++-.
T Consensus 8 ~~~t~~~l~~~f~~~g~i~ 26 (70)
T PF00076_consen 8 PDVTEEELRDFFSQFGKIE 26 (70)
T ss_dssp TTSSHHHHHHHHHTTSTEE
T ss_pred CcCCHHHHHHHHHHhhhcc
Confidence 3789999999998887653
No 24
>cd07962 Anticodon_Ia_Val Anticodon-binding domain of valyl tRNA synthetases. This domain is found in valyl tRNA synthetases (ValRS), which belong to the class Ia aminoacyl tRNA synthetases. It lies C-terminal to the catalytic core domain, and recognizes and specifically binds to the tRNA anticodon. ValRS catalyzes the transfer of valine to the 3'-end of its tRNA.
Probab=23.72 E-value=45 Score=26.50 Aligned_cols=27 Identities=11% Similarity=0.047 Sum_probs=18.0
Q ss_pred HHHHHHHHHHHHHHhhhHhhhHHHHHH
Q 017952 276 EDLKKLFAAWYERRQMKKIYSPLLEGL 302 (363)
Q Consensus 276 ~dlkklf~aWyErRqmkKIYSPLlEgl 302 (363)
.++.|-+...||+.+.+|...-+++-+
T Consensus 52 ~~~~~~~~~~~e~~~~~~al~~i~~~~ 78 (135)
T cd07962 52 NKTVEEVTEALENYRFSEAATALYEFF 78 (135)
T ss_pred HHHHHHHHHHHHhcCHHHHHHHHHHHH
Confidence 345666677777777777766666654
No 25
>PF09496 CENP-O: Cenp-O kinetochore centromere component; InterPro: IPR018464 Chromosome segregation in eukaryotes requires the kinetochore, a multi-protein structure that assembles on centromeric DNA, and which acts to link chromosomes to spindle microtubules. Kinetochore structure and composition is highly conserved among vertebrates. The inner kinetochore is essential for kinetochore assembly, and is involved in chromosome segregation via regulation of the spindle. Inner kinetochore components include the multi-subunit CENP-H/I complex, which may function, in part, in directing centromere protein A (CENP-A) deposition to centromeres, where CENP-A is a centromere-specific histone H3 variant required for the organisation of centromeric chromatin during interphase. The CENP-H/I complex contains three functional classes of proteins [, ]: CENP-H class (includes CENP-H, -I, -K, -L) CENP-M class (includes CENP-M) CENP-O class (includes CENP-O, -P, -Q, -R, -50) The CENP-O class proteins form a stable complex and are required for proper kinetochore function. They are involved in the prevention of premature sister chromatid separation during recovery from spindle damage []. CENP-O mediates the attachment of the centromere to the mitotic spindle by forming essential interactions between the microtubule-associated outer kinetochore proteins and the centromere-associated inner kinetochore proteins. It has been shown to be involved in chromosome segregation via regulation of the spindle in both yeast [] and human [].; GO: 0007059 chromosome segregation, 0051301 cell division, 0000775 chromosome, centromeric region, 0005634 nucleus; PDB: 3ZXU_C.
Probab=23.04 E-value=1.3e+02 Score=24.21 Aligned_cols=18 Identities=28% Similarity=0.744 Sum_probs=11.4
Q ss_pred cCCCcchHHHHHHHHHHH
Q 017952 228 VLPPFVPFAQAFAAVITA 245 (363)
Q Consensus 228 v~PpFvPFAq~fAavlta 245 (363)
-+|+|+|..+..+-.+.+
T Consensus 39 TIP~~IPl~~l~~~~l~~ 56 (90)
T PF09496_consen 39 TIPPFIPLEELAAKYLPG 56 (90)
T ss_dssp ---TTS-HHHHHHHHHTT
T ss_pred CCCCcCcHHHHHHHHccc
Confidence 389999999998877643
No 26
>COG0798 ACR3 Arsenite efflux pump ACR3 and related permeases [Inorganic ion transport and metabolism]
Probab=22.62 E-value=26 Score=34.99 Aligned_cols=42 Identities=38% Similarity=0.595 Sum_probs=31.1
Q ss_pred eEEeecccCccchHHHHHHH-HHHHHHHhhhHhhhHHHHHHHHHHh
Q 017952 263 YVVAPVLRSRSGREDLKKLF-AAWYERRQMKKIYSPLLEGLLALYL 307 (363)
Q Consensus 263 YvvaPv~~sr~~r~dlkklf-~aWyErRqmkKIYSPLlEglLalYL 307 (363)
|++.|..-+.--|.-+.|-. ..|||+|-+.|| ||+ .++|+|+
T Consensus 184 yl~iPli~G~lTR~i~~k~kg~~~~~~~f~p~i-spi--~ligLl~ 226 (342)
T COG0798 184 YLGIPLIAGVLTRYILIKKKGREWYESRFLPKI-SPI--ALIGLLL 226 (342)
T ss_pred HHHHHHHHHHHHHHHHHHhccchHHHHHHHhhc-ChH--HHHHHHH
Confidence 77889888877777665555 469999998886 665 3666665
No 27
>PF02525 Flavodoxin_2: Flavodoxin-like fold; InterPro: IPR003680 This family consists of a domain with a flavodoxin-like fold. The family includes bacterial and eukaryotic NAD(P)H dehydrogenase (quinone) 1.6.99.2 from EC. These enzymes catalyse the NAD(P)H-dependent two-electron reductions of quinones and protect cells against damage by free radicals and reactive oxygen species []. This enzyme uses a FAD cofactor. The equation for this reaction is NAD(P)H + acceptor = NAD(P)(+) + reduced acceptor. This enzyme is also involved in the bioactivation of prodrugs used in chemotherapy []. The family also includes acyl carrier protein phosphodiesterase 3.1.4.14 from EC. This enzyme converts holo-ACP to apo-ACP by hydrolytic cleavage of the phosphopantetheine residue from ACP []. This family is related to FMN_red IPR005025 from INTERPRO and Flavodoxin_1 IPR008254 from INTERPRO.; GO: 0009055 electron carrier activity, 0016491 oxidoreductase activity, 0050662 coenzyme binding; PDB: 1T5B_B 1DXQ_B 2B3D_A 2Z9D_B 2Z9C_A 2Z98_A 2D5I_A 2Z9B_A 1TIK_A 1V4B_A ....
Probab=22.03 E-value=1.3e+02 Score=25.27 Aligned_cols=47 Identities=17% Similarity=0.285 Sum_probs=31.3
Q ss_pred HHhhhHhhhHHHHHHHHHHhcceeeeeCcchhhHHHhhhhhhhhhccccchh--chhhHHHHHHHHH
Q 017952 288 RRQMKKIYSPLLEGLLALYLGFEWIQTNNILAPIITHGIYSAVILGHGLWKI--HDHRRRLHQRIQR 352 (363)
Q Consensus 288 rRqmkKIYSPLlEglLalYLGfEWiqT~NILAPiiTHgiYS~VvlghGLwki--hdhr~rlRqRiq~ 352 (363)
.+.|+.+..| +++++ -|+|++|+++ +.-+|+... .+.+++..+|+++
T Consensus 149 ~~~~~~~~~~-~~~~~-~~~G~~~~~~----------------~~~~~~~~~~~~~~~~~~~~~~~~ 197 (199)
T PF02525_consen 149 GRSMDHLLPY-LRGIL-KFCGIKDVES----------------FSFEGVDNPDREEALEKALERAAE 197 (199)
T ss_dssp TSHHHHHHHH-HHHHH-HHTTEEEEEE----------------EEEESTTTCCHHHHHHHHHHHHHH
T ss_pred CCChhhhHHH-HHHHH-HhCCCceeeE----------------EEEeCCCCCChHHHHHHHHHHHHh
Confidence 4577777777 67776 8999999975 234555521 4556666666654
No 28
>PF03613 EIID-AGA: PTS system mannose/fructose/sorbose family IID component; InterPro: IPR004704 The phosphoenolpyruvate-dependent sugar phosphotransferase system (PTS) [, ] is a major carbohydrate transport system in bacteria. The PTS catalyses the phosphorylation of incoming sugar substrates and coupled with translocation across the cell membrane, makes the PTS a link between the uptake and metabolism of sugars. The general mechanism of the PTS is the following: a phosphoryl group from phosphoenolpyruvate (PEP) is transferred via a signal transduction pathway, to enzyme I (EI) which in turn transfers it to a phosphoryl carrier, the histidine protein (HPr). Phospho-HPr then transfers the phosphoryl group to a sugar-specific permease, a membrane-bound complex known as enzyme 2 (EII), which transports the sugar to the cell. EII consists of at least three structurally distinct domains IIA, IIB and IIC []. These can either be fused together in a single polypeptide chain or exist as two or three interactive chains, formerly called enzymes II (EII) and III (EIII). The first domain (IIA or EIIA) carries the first permease-specific phosphorylation site, a histidine which is phosphorylated by phospho-HPr. The second domain (IIB or EIIB) is phosphorylated by phospho-IIA on a cysteinyl or histidyl residue, depending on the sugar transported. Finally, the phosphoryl group is transferred from the IIB domain to the sugar substrate concomitantly with the sugar uptake processed by the IIC domain. This third domain (IIC or EIIC) forms the translocation channel and the specific substrate-binding site. An additional transmembrane domain IID, homologous to IIC, can be found in some PTSs, e.g. for mannose [, , , ]. Bacterial PTS transporters transport and concomitantly phosphorylate their sugar substrates, and typically consist of multiple subunits or protein domains.The Man family is unique in several respects among PTS permease families. It is the only PTS family in which members possess a IID protein. It is the only PTS family in which the IIB constituent is phosphorylated on a histidyl rather than a cysteyl residue. Its permease members exhibit broad specificity for a range of sugars, rather than being specific for just one or a few sugars. The mannose permease of Escherichia coli, for example, can transport and phosphorylate glucose, mannose, fructose, glucosamine,N-acetylglucosamine, and other sugars. Other members of this can transport sorbose, fructose and N-acetylglucosamine. This family is specific for the IID subunits of this family of PTS transporters.; GO: 0009401 phosphoenolpyruvate-dependent sugar phosphotransferase system, 0016021 integral to membrane
Probab=21.81 E-value=1.2e+02 Score=28.63 Aligned_cols=48 Identities=38% Similarity=0.595 Sum_probs=34.0
Q ss_pred chHHHHHHHHHH--------HHHHh-----------hhHhhhH--HHHHHHHHHhcceeeeeCcchhhHHH
Q 017952 274 GREDLKKLFAAW--------YERRQ-----------MKKIYSP--LLEGLLALYLGFEWIQTNNILAPIIT 323 (363)
Q Consensus 274 ~r~dlkklf~aW--------yErRq-----------mkKIYSP--LlEglLalYLGfEWiqT~NILAPiiT 323 (363)
.++|++|.|-.| |||=| .||||.- -+...+--++ |+..|+..++|+|.
T Consensus 4 tkkdl~k~~~R~~~~q~~~nyErmq~~gf~~~m~P~lkklY~~~e~~~~al~rh~--~fFNT~p~~~~~I~ 72 (264)
T PF03613_consen 4 TKKDLRKVFWRSLFLQASWNYERMQGLGFAYSMLPALKKLYKDKEELKEALKRHM--EFFNTEPFLGPFIL 72 (264)
T ss_pred CHHHHHHHHHHHHHHhCCCCHHHHHhHhHHHHHHHHHHHHcCCHHHHHHHHHHHH--HHHCCCChhhhHHH
Confidence 478999999888 67765 5899965 2223344454 56888888888774
No 29
>PF00536 SAM_1: SAM domain (Sterile alpha motif); InterPro: IPR021129 The sterile alpha motif (SAM) domain is a putative protein interaction module present in a wide variety of proteins [] involved in many biological processes. The SAM domain that spreads over around 70 residues is found in diverse eukaryotic organisms []. SAM domains have been shown to homo- and hetero-oligomerise, forming multiple self-association architectures and also binding to various non-SAM domain-containing proteins [], nevertheless with a low affinity constant []. SAM domains also appear to possess the ability to bind RNA []. Smaug, a protein that helps to establish a morphogen gradient in Drosophila embryos by repressing the translation of nanos (nos) mRNA, binds to the 3' untranslated region (UTR) of nos mRNA via two similar hairpin structures. The 3D crystal structure of the Smaug RNA-binding region shows a cluster of positively charged residues on the Smaug-SAM domain, which could be the RNA-binding surface. This electropositive potential is unique among all previously determined SAM-domain structures and is conserved among Smaug-SAM homologs. These results suggest that the SAM domain might have a primary role in RNA binding. Structural analyses show that the SAM domain is arranged in a small five-helix bundle with two large interfaces []. In the case of the SAM domain of EphB2, each of these interfaces is able to form dimers. The presence of these two distinct intermonomers binding surface suggest that SAM could form extended polymeric structures []. This entry represents type 1 SAM domains. ; PDB: 2KIV_A 3HIL_B 3KKA_A 3K1R_B 3SEN_B 3SEI_B 1V85_A 2KE7_A 2EAM_A 1WWV_A ....
Probab=21.64 E-value=75 Score=22.32 Aligned_cols=14 Identities=36% Similarity=0.776 Sum_probs=11.8
Q ss_pred hhhHHHHHHHHHHh
Q 017952 341 DHRRRLHQRIQRLE 354 (363)
Q Consensus 341 dhr~rlRqRiq~i~ 354 (363)
.||+|+.+.|+++|
T Consensus 51 ghr~ki~~~i~~Lk 64 (64)
T PF00536_consen 51 GHRKKILRAIQKLK 64 (64)
T ss_dssp HHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHhC
Confidence 48999999998876
No 30
>PF01117 Aerolysin: Aerolysin toxin; InterPro: IPR005830 This family represents the pore forming lobe of aerolysin, and the related toxins haemolysin and the leukocidin S subunit. Aerolysin [] is a cytolytic toxin exported by Aeromonas hydrophila, a Gram-negative bacterium associated with diarrhoeal diseases and deep wound infections []. The mature toxin binds to eukaryotic cells and aggregates to form holes (approximately 3 nm in diameter) leading to the destruction of the membrane permeability barrier and osmotic lysis. The structure of proaerolysin has been determined to 2.8A resolution and shows the protoxin to adopt a novel fold []. Images of an aerolysin oligomer derived from electron microscopy have helped to construct a model of the protein and to outline a mechanism by which it might insert into lipid bilayers to form ion channels [].; GO: 0009405 pathogenesis, 0005576 extracellular region; PDB: 3G4N_B 3C0N_B 3C0O_B 1PRE_A 1Z52_B 3C0M_A 3G4O_A.
Probab=21.46 E-value=65 Score=32.08 Aligned_cols=22 Identities=41% Similarity=0.922 Sum_probs=15.6
Q ss_pred HhhhHHHHHHHHHHhcceeeeeCc
Q 017952 293 KIYSPLLEGLLALYLGFEWIQTNN 316 (363)
Q Consensus 293 KIYSPLlEglLalYLGfEWiqT~N 316 (363)
.++.|| ..||-||||.|+--+|
T Consensus 16 ~firp~--a~LAh~LGy~W~gg~~ 37 (360)
T PF01117_consen 16 DFIRPL--AYLAHYLGYAWVGGNH 37 (360)
T ss_dssp TTHHHH--HHHHHHTTBS--S-TT
T ss_pred hhhhhH--HHHHhhhCceEECCCC
Confidence 678898 5789999999986553
No 31
>KOG0193 consensus Serine/threonine protein kinase RAF [Signal transduction mechanisms]
Probab=21.06 E-value=1.6e+02 Score=32.10 Aligned_cols=67 Identities=27% Similarity=0.404 Sum_probs=50.5
Q ss_pred HHHHHHHHHHHhcceeeeecCCCCCceEEeecccC----------ccchHHHHHHHHH-HHHHHhhhHhhhHHHHHHHHH
Q 017952 237 QAFAAVITAALTGSLYYVATSPKDPTYVVAPVLRS----------RSGREDLKKLFAA-WYERRQMKKIYSPLLEGLLAL 305 (363)
Q Consensus 237 q~fAavltaaLTGSlYyva~spkDPtYvvaPv~~s----------r~~r~dlkklf~a-WyErRqmkKIYSPLlEglLal 305 (363)
-+|..|.==.|||.|-|-+ .++ .-|+-=|=|+ .+++++||+|.+. |.-.||=+-.|.+||+.|+.+
T Consensus 577 YaFGiV~YELltg~lPysi-~~~--dqIifmVGrG~l~pd~s~~~s~~pk~mk~Ll~~C~~~~~~eRP~F~~il~~l~~l 653 (678)
T KOG0193|consen 577 YAFGIVWYELLTGELPYSI-QNR--DQIIFMVGRGYLMPDLSKIRSNCPKAMKRLLSDCWKFDREERPLFPQLLSKLEEL 653 (678)
T ss_pred hhhhHHHHHHHhCcCCcCC-CCh--hheEEEecccccCccchhhhccCHHHHHHHHHHHHhcCcccCccHHHHHHHHHHh
Confidence 3688899999999999983 333 3344434343 3567799999865 998999999999999988876
Q ss_pred H
Q 017952 306 Y 306 (363)
Q Consensus 306 Y 306 (363)
-
T Consensus 654 ~ 654 (678)
T KOG0193|consen 654 L 654 (678)
T ss_pred h
Confidence 4
No 32
>PRK10927 essential cell division protein FtsN; Provisional
Probab=20.86 E-value=1.3e+02 Score=30.08 Aligned_cols=31 Identities=29% Similarity=0.589 Sum_probs=24.4
Q ss_pred CCcchHHHHHHHHHHHHHhcceeeeecCCCC
Q 017952 230 PPFVPFAQAFAAVITAALTGSLYYVATSPKD 260 (363)
Q Consensus 230 PpFvPFAq~fAavltaaLTGSlYyva~spkD 260 (363)
|-+-|-.=++|+++..++.|.|||+....|+
T Consensus 30 ~~~~~~m~alAvavlv~fiGGLyFith~k~~ 60 (319)
T PRK10927 30 PAVSPAMVAIAAAVLVTFIGGLYFITHHKKE 60 (319)
T ss_pred CCcchHHHHHHHHHHHHHhhheEEEecCCCC
Confidence 3344555688999999999999999987764
No 33
>PLN03155 cytochrome c oxidase subunit 5C; Provisional
Probab=20.86 E-value=47 Score=26.62 Aligned_cols=26 Identities=31% Similarity=0.543 Sum_probs=18.0
Q ss_pred hccccchhch--hhHHHHHHHHHHhhcc
Q 017952 332 LGHGLWKIHD--HRRRLHQRIQRLELEG 357 (363)
Q Consensus 332 lghGLwkihd--hr~rlRqRiq~i~~~~ 357 (363)
..-|+||+|+ ||||-|.=-+.|+..+
T Consensus 29 ~AG~~WKmhHWn~qrkt~~fY~~Lekge 56 (63)
T PLN03155 29 AAGGLWKMHHWNEQRKTRSFYDLLEKGE 56 (63)
T ss_pred hhhhHHHHhhhhhHHHHHHHHHHHhcCc
Confidence 3468999996 6666666667776544
No 34
>PF13994 PgaD: PgaD-like protein
Probab=20.68 E-value=77 Score=26.63 Aligned_cols=43 Identities=28% Similarity=0.409 Sum_probs=33.2
Q ss_pred hhhH---HHHHHHHHHhcceeeeeCcchhhHHHhhhhhhhhhcccc
Q 017952 294 IYSP---LLEGLLALYLGFEWIQTNNILAPIITHGIYSAVILGHGL 336 (363)
Q Consensus 294 IYSP---LlEglLalYLGfEWiqT~NILAPiiTHgiYS~VvlghGL 336 (363)
+..| ++-.+++.+++-+.+--..+.++.-|=.+|..++++++.
T Consensus 31 L~~pl~~ll~~ll~~~~~~~~~~~~~~~~~~~~l~~y~~i~~~~a~ 76 (138)
T PF13994_consen 31 LWRPLLTLLAWLLGLHLFYPQMSLGGFLSSLNTLQIYLLIALVNAV 76 (138)
T ss_pred HHHHHHHHHHHHHccccccchhhhcchhhHHHHHHHHHHHHHHHHH
Confidence 4578 566677777777766566677888888999999999984
No 35
>TIGR01946 rnfD electron transport complex, RnfABCDGE type, D subunit. The six subunit complex RnfABCDGE in Rhodobacter capsulatus encodes an apparent NADH oxidoreductase responsible for electron transport to nitrogenase, necessary for nitrogen fixation. A closely related complex in E. coli, RsxABCDGE (Reducer of SoxR), reduces the 2Fe-2S-containing superoxide sensor SoxR, active as a transcription factor when oxidized. This family of putative NADH oxidoreductase complexes exists in many of the same species as the related NQR, a Na(+)-translocating NADH-quinone reductase, but is distinct. This model describes the A subunit.
Probab=20.32 E-value=1.4e+02 Score=29.23 Aligned_cols=63 Identities=25% Similarity=0.405 Sum_probs=39.9
Q ss_pred HhhcCCchhhhHHhhhccchhHHHHHHHHhhhhHHHHhhCCCc---ccccccchhhcc-----cCCCcchHHHHHHHHHH
Q 017952 173 FFYGMSPWQFVLIVAASSVGEELFYRAAVQGALADIFLRGTDF---LTDAQGMASLTG-----VLPPFVPFAQAFAAVIT 244 (363)
Q Consensus 173 fF~GMspwQFiliVaAssvgEElFyR~AvQGaladiflrgt~l---~~d~~GmasLtg-----v~PpFvPFAq~fAavlt 244 (363)
||+|+.+..-+++..++++.=|..+.. +|++.. .+|- =+-+|| .+||.+|+-++..++.-
T Consensus 30 ~~fG~~al~~~~~~v~~av~~E~l~~~----------l~~k~~~~~~~D~--Sa~vTglLlal~lP~~~P~W~~~ig~~f 97 (327)
T TIGR01946 30 YFFGWGTLIQIALAILTALILEAAILK----------LRKRSIKAFLKDG--SAILTGLLLAVAIPPLAPWWMIVIGTIF 97 (327)
T ss_pred HHHhHHHHHHHHHHHHHHHHHHHHHHH----------HhCCCCccccCCc--cHHHHHHHHHHHcCCCCcHHHHHHHHHH
Confidence 889998877776666677766655443 244333 3343 344555 57999999887666655
Q ss_pred HHH
Q 017952 245 AAL 247 (363)
Q Consensus 245 aaL 247 (363)
|.+
T Consensus 98 aI~ 100 (327)
T TIGR01946 98 AIV 100 (327)
T ss_pred HHH
Confidence 544
Done!