Query gi|254780944|ref|YP_003065357.1| hypothetical protein CLIBASIA_04215 [Candidatus Liberibacter asiaticus str. psy62]
Match_columns 228
No_of_seqs 121 out of 807
Neff 6.4
Searched_HMMs 39220
Date Mon May 30 03:22:07 2011
Command /home/congqian_1/programs/hhpred/hhsearch -i 254780944.hhm -d /home/congqian_1/database/cdd/Cdd.hhm
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 COG2928 Uncharacterized conser 100.0 0 0 427.2 22.7 206 9-218 1-206 (222)
2 pfam04367 DUF502 Protein of un 100.0 4.9E-34 1.2E-38 228.9 11.9 107 70-180 2-108 (108)
3 PRK10573 type IV pilin biogene 91.7 1.1 2.7E-05 24.2 10.7 29 91-119 240-270 (397)
4 COG1459 PulF Type II secretory 82.7 3.8 9.6E-05 20.8 8.8 23 89-111 238-260 (397)
5 PRK09824 beta-glucoside-specif 82.1 4 0.0001 20.7 10.2 19 26-44 218-236 (625)
6 PRK09796 cellobiose/arbutin/sa 79.5 4.9 0.00012 20.1 10.2 81 24-117 220-305 (472)
7 pfam01230 HIT HIT domain. 78.2 4.1 0.0001 20.6 4.3 42 162-204 10-52 (98)
8 PRK09586 murP N-acetylmuramic 67.7 9.5 0.00024 18.3 9.5 83 24-117 228-311 (474)
9 PRK11007 trehalose(maltose)-sp 67.6 9.6 0.00024 18.3 8.7 27 24-50 231-257 (473)
10 cd01277 HINT_subgroup HINT (hi 60.9 13 0.00033 17.5 4.0 42 162-204 18-60 (103)
11 PRK05700 fliQ flagellar biosyn 58.6 14 0.00036 17.3 11.0 82 10-105 6-87 (89)
12 pfam06160 EzrA Septation ring 52.2 18 0.00046 16.6 3.3 59 67-128 3-63 (559)
13 TIGR02120 GspF general secreti 50.5 19 0.00048 16.5 6.6 93 9-112 172-279 (414)
14 TIGR02518 EutH_ACDH acetaldehy 49.0 9.5 0.00024 18.3 1.5 93 81-181 18-121 (528)
15 PRK04778 septation ring format 48.4 20 0.00052 16.3 4.8 61 65-128 5-67 (569)
16 PRK12781 fliQ flagellar biosyn 47.7 21 0.00054 16.2 11.2 81 10-104 6-86 (88)
17 cd00468 HIT_like HIT family: H 47.4 21 0.00054 16.2 4.1 44 163-207 3-47 (86)
18 pfam02674 Colicin_V Colicin V 47.3 21 0.00054 16.2 12.5 96 10-115 13-108 (145)
19 COG0537 Hit Diadenosine tetrap 45.2 23 0.00059 16.0 4.0 43 163-206 20-63 (138)
20 PRK12772 bifunctional flagella 43.6 24 0.00062 15.8 10.4 40 7-46 165-204 (609)
21 PRK04949 putative sulfate tran 42.5 25 0.00064 15.7 9.1 28 23-50 29-60 (251)
22 KOG0125 consensus 40.6 26 0.00066 15.7 2.7 48 127-174 120-173 (376)
23 cd01276 PKCI_related Protein K 40.4 27 0.0007 15.5 3.4 38 162-200 18-56 (104)
24 COG4956 Integral membrane prot 38.9 29 0.00073 15.4 9.4 30 91-120 65-94 (356)
25 COG4794 EscS Type III secretor 38.5 29 0.00075 15.3 9.5 77 16-106 12-88 (89)
26 COG1684 FliR Flagellar biosynt 36.0 32 0.00082 15.1 11.9 44 3-46 164-207 (258)
27 pfam10173 DUF2343 Uncharacteri 35.7 32 0.00083 15.0 4.5 54 84-137 8-61 (106)
28 cd01275 FHIT FHIT (fragile his 35.3 33 0.00084 15.0 4.1 41 163-204 19-60 (126)
29 TIGR01995 PTS-II-ABC-beta PTS 35.1 33 0.00084 15.0 4.9 86 24-119 236-323 (660)
30 COG1987 FliQ Flagellar biosynt 34.1 34 0.00088 14.9 11.3 82 10-105 6-87 (89)
31 PRK11513 cytochrome b561; Prov 33.8 35 0.00089 14.9 6.5 15 67-81 48-62 (176)
32 PRK11365 ssuC alkanesulfonate 33.2 36 0.00091 14.8 6.5 40 66-105 70-110 (263)
33 pfam05552 TM_helix Conserved T 32.9 36 0.00092 14.8 4.3 28 70-97 18-45 (53)
34 pfam11969 DcpS_C Scavenger mRN 32.7 36 0.00092 14.8 3.3 37 163-200 19-56 (113)
35 TIGR01078 arcA arginine deimin 32.3 37 0.00094 14.7 2.9 33 109-141 244-276 (421)
36 pfam03596 Cad Cadmium resistan 32.0 37 0.00095 14.7 6.8 85 67-173 34-120 (192)
37 COG4756 Predicted cation trans 30.6 28 0.00071 15.5 1.5 18 200-217 306-323 (367)
38 PRK06010 fliQ flagellar biosyn 29.8 40 0.001 14.5 11.1 81 10-104 6-86 (88)
39 KOG2927 consensus 29.6 41 0.001 14.4 5.2 26 48-75 208-234 (372)
40 TIGR02119 panF sodium/pantothe 29.1 42 0.0011 14.4 6.2 27 65-91 73-99 (474)
41 COG3180 AbrB Putative ammonia 28.8 40 0.001 14.5 2.1 59 69-137 94-152 (352)
42 pfam07854 DUF1646 Protein of u 28.3 32 0.00081 15.1 1.5 25 194-218 284-312 (347)
43 PRK09765 2-O-a-mannosyl-D-glyc 27.9 44 0.0011 14.2 6.8 106 4-110 276-425 (638)
44 pfam06711 DUF1198 Protein of u 27.8 39 0.001 14.5 1.9 36 69-104 5-40 (148)
45 pfam02762 Cbl_N3 CBL proto-onc 27.3 38 0.00096 14.6 1.7 39 109-150 11-49 (86)
46 PRK03776 phosphoglycerol trans 27.2 45 0.0012 14.2 6.9 66 17-83 26-98 (762)
47 PRK11901 hypothetical protein; 27.1 45 0.0012 14.2 2.3 21 64-84 39-59 (329)
48 TIGR02823 oxido_YhdH putative 26.6 40 0.001 14.5 1.7 62 133-203 56-125 (330)
49 TIGR00630 uvra excinuclease AB 26.4 34 0.00087 14.9 1.3 16 188-203 814-830 (956)
50 pfam06695 Sm_multidrug_ex Puta 24.1 51 0.0013 13.8 2.9 53 89-142 35-92 (121)
51 TIGR00757 RNaseEG ribonuclease 24.0 52 0.0013 13.8 2.2 11 165-175 153-163 (464)
52 PRK10892 D-arabinose 5-phospha 23.9 52 0.0013 13.8 5.1 101 86-209 195-300 (326)
53 TIGR01937 nqrB NADH:ubiquinone 22.6 55 0.0014 13.6 5.6 32 14-45 115-146 (508)
54 TIGR02188 Ac_CoA_lig_AcsA acet 21.6 51 0.0013 13.9 1.5 60 67-134 131-211 (643)
55 PRK00042 tpiA triosephosphate 20.8 53 0.0013 13.7 1.4 37 111-152 143-179 (251)
56 cd02435 CCC1 CCC1. CCC1: This 20.2 62 0.0016 13.3 5.8 41 47-90 170-210 (241)
57 PRK11026 ftsX cell division pr 20.1 62 0.0016 13.3 9.8 11 140-150 94-104 (309)
58 COG0841 AcrB Cation/multidrug 20.0 62 0.0016 13.3 5.2 35 164-199 589-625 (1009)
No 1
>COG2928 Uncharacterized conserved protein [Function unknown]
Probab=100.00 E-value=0 Score=427.24 Aligned_cols=206 Identities=39% Similarity=0.806 Sum_probs=197.5
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf 69999999999999999999999999999999998764210512115011011023589999999999998777433788
Q gi|254780944|r 9 SISAKVRNNFFAGFIICAPIAITIWLSLSLIHWFDGFIVPYIPMQYNPEYYCDFSIPGFGLLVVIVGINIVGFFGRNLLG 88 (228)
Q Consensus 9 ~l~~~l~~~Fl~GLlvllPi~iTi~i~~~l~~~~~~~~~p~i~~~~~~~~~~~~~i~glg~~~~i~~i~liG~l~~~~~g 88 (228)
+.++|+||||+|||++++|+++|+|+++|+++|+|++++|.++..+.+..+.+..++|+|+++.+++++++|++++|.+|
T Consensus 1 k~~~~lk~~fltGLlvllPlaiT~~vv~~i~~~l~~~~~~~lp~~~~~~~~~~~~i~~lg~il~iili~l~G~l~~~~ig 80 (222)
T COG2928 1 KGAKRLKKYFLTGLLVLLPLAITLWVVSWIFGLLDQFVGPLLPDRLRPAVYFPFNIPGLGVILAIILIFLLGFLARNMIG 80 (222)
T ss_pred CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHCHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf 91788999999889999999999999999999998764430421212221476034788999999999999999998755
Q ss_pred HHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHCCCCCCCCEEEEEECCCCCEEEEEEEECCCHHHHHHHHCCCCCCCEEE
Q ss_conf 99999999999533238899999999999973177553310399984887579999970687156555302467773899
Q gi|254780944|r 89 RFVFFLSESILNNTPIVRHLYKSTKQIIRTLLKEDSTSFKNACLVEYPSAGFWSLCFLTTEVKGEIKEKFSNIGCEDMVT 168 (228)
Q Consensus 89 ~~~~~~~e~~l~rIP~v~~IY~sikqi~~~~~~~~~~~f~~vVlVe~P~~g~~~iGFvT~~~~~~~~~~~~~~~~~~~v~ 168 (228)
|++++++|++|.|||++|+||+++||+++++.++++++||+||+|||||+|+|++||+|++..+++++ ..+++|++
T Consensus 81 ~~l~~~~d~~L~RiPlv~~IY~s~kqi~etll~~~~~sfk~vvlVefP~~G~~~i~fvtg~~~~e~~~----~~~~~~v~ 156 (222)
T COG2928 81 RSLLSLGDSLLRRIPLVKSIYKSAKQVVETLLSDQSGSFKQVVLVEFPRRGIWAIAFVTGEKAGELKE----KEGRPMVA 156 (222)
T ss_pred HHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHCCCCCCEEEEEEECCCCCCEEEEEECCCCCCCHHC----CCCCCEEE
T ss_conf 48999999997007528889999999999997268845000489877999817999851677750001----35885079
Q ss_pred EEEECCCCCCCCEEEEEEHHHEEECCCCHHHHHHHHHHCCCCCCCCCCCC
Q ss_conf 99707985326889998777624779999999999870143378878876
Q gi|254780944|r 169 VFIPPTPLPTAGMLVFVPRNKVIMLKMSAEDSAKMLISGGLLIPDNISYD 218 (228)
Q Consensus 169 VfiPtsPnPtsG~~~~vp~~~v~~~dmsveeA~k~iiS~Gv~~P~~~~~~ 218 (228)
||+||||||||||+.+||+||++++||++|||+|+++|||+++|+.....
T Consensus 157 VfvPTTPNPTsGfl~~Vpkedi~~ldmtvEda~k~iIS~G~v~p~~~~~~ 206 (222)
T COG2928 157 VFVPTTPNPTSGFLLLVPKEDIVPLDMTVEDALKYIISGGVVAPDSLPAK 206 (222)
T ss_pred EECCCCCCCCCCEEEEEEHHHCEECCCCHHHHHHEEEECCCCCCCCCCCC
T ss_conf 98379998876459998889822353649877451666664489852311
No 2
>pfam04367 DUF502 Protein of unknown function (DUF502). Predicted to be an integral membrane protein.
Probab=100.00 E-value=4.9e-34 Score=228.88 Aligned_cols=107 Identities=46% Similarity=0.861 Sum_probs=99.1
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHCCCCCCCCEEEEEECCCCCEEEEEEEECC
Q ss_conf 99999999987774337889999999999953323889999999999997317755331039998488757999997068
Q gi|254780944|r 70 LVVIVGINIVGFFGRNLLGRFVFFLSESILNNTPIVRHLYKSTKQIIRTLLKEDSTSFKNACLVEYPSAGFWSLCFLTTE 149 (228)
Q Consensus 70 ~~~i~~i~liG~l~~~~~g~~~~~~~e~~l~rIP~v~~IY~sikqi~~~~~~~~~~~f~~vVlVe~P~~g~~~iGFvT~~ 149 (228)
++++++|+++|+++++++||++++++|+++.|||++|+||+++||++++++++++++|++||+||||++|+|++||+|+|
T Consensus 2 ~~~l~~i~~vG~l~~~~~g~~l~~~~e~~l~riP~v~~IY~~ikq~~~~~~~~~~~~f~~vVlV~~p~~g~~~iGFvT~~ 81 (108)
T pfam04367 2 ILTLLLIFLVGLLARNFIGRWLLSLGERLLNRIPLVRSIYSSVKQIVETLLGDKKKSFRKVVLVEYPRPGLWAIGFVTGE 81 (108)
T ss_pred EEEHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHCCCCCCCCEEEEEEECCCCCEEEEEEECC
T ss_conf 52089999999999959899999999999997861989999999999998458875632589999459992899999257
Q ss_pred CHHHHHHHHCCCCCCCEEEEEEECCCCCCCC
Q ss_conf 7156555302467773899997079853268
Q gi|254780944|r 150 VKGEIKEKFSNIGCEDMVTVFIPPTPLPTAG 180 (228)
Q Consensus 150 ~~~~~~~~~~~~~~~~~v~VfiPtsPnPtsG 180 (228)
..+++.+ ..++|+++||+|||||||||
T Consensus 82 ~~~~~~~----~~~~~~v~VfvPtspnPtsG 108 (108)
T pfam04367 82 VGGELAE----RLGEDLVAVFVPTTPNPTSG 108 (108)
T ss_pred CCCHHHC----CCCCCEEEEEECCCCCCCCC
T ss_conf 7304431----47996599992899999998
No 3
>PRK10573 type IV pilin biogenesis protein; Provisional
Probab=91.68 E-value=1.1 Score=24.18 Aligned_cols=29 Identities=21% Similarity=0.312 Sum_probs=19.8
Q ss_pred HHHHHHHHHHHCCHHHHHHHHH--HHHHHHH
Q ss_conf 9999999995332388999999--9999997
Q gi|254780944|r 91 VFFLSESILNNTPIVRHLYKST--KQIIRTL 119 (228)
Q Consensus 91 ~~~~~e~~l~rIP~v~~IY~si--kqi~~~~ 119 (228)
...+.|+++.|+|+++.+|... -++..++
T Consensus 240 ~~~~~~~~llkiP~~g~l~~~~~~~rf~~~L 270 (397)
T PRK10573 240 WQIREQRLLLRIPLMGSLIRGQKLSQIFTIL 270 (397)
T ss_pred HHHHHHHHHHCCHHHHHHHHHHHHHHHHHHH
T ss_conf 7699999972124465999999999999999
No 4
>COG1459 PulF Type II secretory pathway, component PulF [Cell motility and secretion / Intracellular trafficking and secretion]
Probab=82.72 E-value=3.8 Score=20.79 Aligned_cols=23 Identities=13% Similarity=0.059 Sum_probs=18.8
Q ss_pred HHHHHHHHHHHHHCCHHHHHHHH
Q ss_conf 99999999999533238899999
Q gi|254780944|r 89 RFVFFLSESILNNTPIVRHLYKS 111 (228)
Q Consensus 89 ~~~~~~~e~~l~rIP~v~~IY~s 111 (228)
.+.-.+.|+++.|+|+++.+...
T Consensus 238 ~~~r~~~~~~llrlP~~g~l~~~ 260 (397)
T COG1459 238 PAGRRRLDRLLLRLPLFGKLVRK 260 (397)
T ss_pred HHHHHHHHHHHHCCCCHHHHHHH
T ss_conf 47788888697607757799999
No 5
>PRK09824 beta-glucoside-specific PTS system components IIABC; Provisional
Probab=82.15 E-value=4 Score=20.66 Aligned_cols=19 Identities=26% Similarity=0.546 Sum_probs=6.7
Q ss_pred HHHHHHHHHHHHHHHHHHH
Q ss_conf 9999999999999999987
Q gi|254780944|r 26 APIAITIWLSLSLIHWFDG 44 (228)
Q Consensus 26 lPi~iTi~i~~~l~~~~~~ 44 (228)
+|+.++.|+..++-+|++.
T Consensus 218 iPiIl~v~~~s~vEk~l~K 236 (625)
T PRK09824 218 IPIIFSAWLCSILERRLNA 236 (625)
T ss_pred HHHHHHHHHHHHHHHHHHH
T ss_conf 9999999999999999987
No 6
>PRK09796 cellobiose/arbutin/salicin-specific PTS system components IIBC; Provisional
Probab=79.54 E-value=4.9 Score=20.11 Aligned_cols=81 Identities=14% Similarity=0.178 Sum_probs=41.1
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHCCCHHHHHHHHHH----HHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf 9999999999999999999876421051211501101102358999999----999999877743378899999999999
Q gi|254780944|r 24 ICAPIAITIWLSLSLIHWFDGFIVPYIPMQYNPEYYCDFSIPGFGLLVV----IVGINIVGFFGRNLLGRFVFFLSESIL 99 (228)
Q Consensus 24 vllPi~iTi~i~~~l~~~~~~~~~p~i~~~~~~~~~~~~~i~glg~~~~----i~~i~liG~l~~~~~g~~~~~~~e~~l 99 (228)
-++|+.++.|+..|+-+|++.++-..+...+ .|.+.++++ ++++=-+|....+.++ .....+.
T Consensus 220 sViPiil~v~~~s~ier~l~K~iP~~l~~i~---------~P~ltlli~~~l~l~viGPig~~i~~~i~----~~v~~l~ 286 (472)
T PRK09796 220 TVIPALVMTWCLSYIERWVDRITPAVTKNFL---------KPMLIVLIAAPLAILLIGPIGIWIGSAIS----ALVYTIH 286 (472)
T ss_pred CHHHHHHHHHHHHHHHHHHHHHCCHHHHHHH---------HHHHHHHHHHHHHHHHHHHHHHHHHHHHH----HHHHHHH
T ss_conf 0699999999999999999974819989989---------98999999999999999889999999999----9999998
Q ss_pred HHCCHH-HHHHHHHHHHHH
Q ss_conf 533238-899999999999
Q gi|254780944|r 100 NNTPIV-RHLYKSTKQIIR 117 (228)
Q Consensus 100 ~rIP~v-~~IY~sikqi~~ 117 (228)
.+.|.+ ..|++..-|.+=
T Consensus 287 ~~~~~i~g~i~g~~~~~lV 305 (472)
T PRK09796 287 GYLGWLSVAIMGALWPLLV 305 (472)
T ss_pred HCCHHHHHHHHHHHHHHHH
T ss_conf 6053999999999999999
No 7
>pfam01230 HIT HIT domain.
Probab=78.18 E-value=4.1 Score=20.57 Aligned_cols=42 Identities=19% Similarity=0.487 Sum_probs=34.2
Q ss_pred CCCCEEEEEEECCCCCCCCEEEEEEHHHEEEC-CCCHHHHHHHH
Q ss_conf 77738999970798532688999877762477-99999999998
Q gi|254780944|r 162 GCEDMVTVFIPPTPLPTAGMLVFVPRNKVIML-KMSAEDSAKML 204 (228)
Q Consensus 162 ~~~~~v~VfiPtsPnPtsG~~~~vp~~~v~~~-dmsveeA~k~i 204 (228)
-+++.+.+|+...|. +-|.++.+|+..+..+ |++.|+..++.
T Consensus 10 yed~~~~aflD~~P~-~~gH~LViPk~H~~~l~dl~~~~~~~l~ 52 (98)
T pfam01230 10 YEDDLVLAFLDIDPQ-APGHVLVIPKKHIRELHDLTPEELGDLM 52 (98)
T ss_pred EECCCEEEEECCCCC-CCCEEEEEEECCCCCCCCCCHHHHHHHH
T ss_conf 978979999878889-9971999961052851429999999999
No 8
>PRK09586 murP N-acetylmuramic acid phosphotransfer permease; Reviewed
Probab=67.73 E-value=9.5 Score=18.31 Aligned_cols=83 Identities=16% Similarity=0.109 Sum_probs=40.3
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHCCCHHHHHHHHHHHHH-HHHHHHHHHHHHHHHHHHHHHHHHHHC
Q ss_conf 9999999999999999999876421051211501101102358999999999-999877743378899999999999533
Q gi|254780944|r 24 ICAPIAITIWLSLSLIHWFDGFIVPYIPMQYNPEYYCDFSIPGFGLLVVIVG-INIVGFFGRNLLGRFVFFLSESILNNT 102 (228)
Q Consensus 24 vllPi~iTi~i~~~l~~~~~~~~~p~i~~~~~~~~~~~~~i~glg~~~~i~~-i~liG~l~~~~~g~~~~~~~e~~l~rI 102 (228)
.++|+.++.|+..++-+|++.++-..+... ..|.+.+++++.+ ++++|=+. ++++.-+-..+..+ .--
T Consensus 228 sViPiIl~v~~~s~iek~l~K~iP~~l~~i---------~~P~ltllI~~pl~l~viGPig-~~l~~gi~~~~~~~-~~~ 296 (474)
T PRK09586 228 NIIGVLIAAWAGARIERMVRRFMPDDLDML---------LTSLITLLITATLAYLIIMPLG-GWLFEGMSWLFMHL-NSN 296 (474)
T ss_pred CHHHHHHHHHHHHHHHHHHHHHCHHHHHHH---------HHHHHHHHHHHHHHHHHHHHHH-HHHHHHHHHHHHHH-CCC
T ss_conf 409999999999999999997472999998---------9989999999999999999899-99999999999980-211
Q ss_pred CHHHHHHHHHHHHHH
Q ss_conf 238899999999999
Q gi|254780944|r 103 PIVRHLYKSTKQIIR 117 (228)
Q Consensus 103 P~v~~IY~sikqi~~ 117 (228)
|+...++...-|++=
T Consensus 297 ~~~~~ii~g~~~~lV 311 (474)
T PRK09586 297 PLGCAVLAGLFLIAV 311 (474)
T ss_pred HHHHHHHHHHHHHHH
T ss_conf 899999999999996
No 9
>PRK11007 trehalose(maltose)-specific PTS system components IIBC; Provisional
Probab=67.58 E-value=9.6 Score=18.30 Aligned_cols=27 Identities=7% Similarity=0.033 Sum_probs=18.7
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHC
Q ss_conf 999999999999999999987642105
Q gi|254780944|r 24 ICAPIAITIWLSLSLIHWFDGFIVPYI 50 (228)
Q Consensus 24 vllPi~iTi~i~~~l~~~~~~~~~p~i 50 (228)
.++|+.++.|+..++-+|++.++-..+
T Consensus 231 sViPiIl~v~~~s~iEk~~~K~iP~~l 257 (473)
T PRK11007 231 QVIPALLAGLALGFIETRLKRIVPDYL 257 (473)
T ss_pred CHHHHHHHHHHHHHHHHHHHHHCHHHH
T ss_conf 089999999999999999986470998
No 10
>cd01277 HINT_subgroup HINT (histidine triad nucleotide-binding protein) subgroup: Members of this CD belong to the superfamily of histidine triad hydrolases that act on alpha-phosphate of ribonucleotides. This subgroup includes members from all three forms of cellular life. Although the biochemical function has not been characterised for many of the members of this subgroup, the proteins from Yeast have been shown to be involved in secretion, peroxisome formation and gene expression.
Probab=60.86 E-value=13 Score=17.52 Aligned_cols=42 Identities=21% Similarity=0.414 Sum_probs=33.9
Q ss_pred CCCCEEEEEEECCCCCCCCEEEEEEHHHEEEC-CCCHHHHHHHH
Q ss_conf 77738999970798532688999877762477-99999999998
Q gi|254780944|r 162 GCEDMVTVFIPPTPLPTAGMLVFVPRNKVIML-KMSAEDSAKML 204 (228)
Q Consensus 162 ~~~~~v~VfiPtsPnPtsG~~~~vp~~~v~~~-dmsveeA~k~i 204 (228)
-++|.+.+|.+..|. .-|-++.+||..+..+ |++-|+.-.+.
T Consensus 18 ~E~e~~~af~d~~P~-~pgH~LViPK~H~~~l~dl~~~~~~~l~ 60 (103)
T cd01277 18 YEDDHVLAFLDINPA-SKGHTLVIPKKHYENLLDLDPEELAELI 60 (103)
T ss_pred EECCCEEEEECCCCC-CCCEEEEEECCCCCCHHHCCHHHHHHHH
T ss_conf 979979999778889-9942999962577981139999999999
No 11
>PRK05700 fliQ flagellar biosynthesis protein FliQ; Validated
Probab=58.56 E-value=14 Score=17.28 Aligned_cols=82 Identities=9% Similarity=0.212 Sum_probs=54.6
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf 99999999999999999999999999999999987642105121150110110235899999999999987774337889
Q gi|254780944|r 10 ISAKVRNNFFAGFIICAPIAITIWLSLSLIHWFDGFIVPYIPMQYNPEYYCDFSIPGFGLLVVIVGINIVGFFGRNLLGR 89 (228)
Q Consensus 10 l~~~l~~~Fl~GLlvllPi~iTi~i~~~l~~~~~~~~~p~i~~~~~~~~~~~~~i~glg~~~~i~~i~liG~l~~~~~g~ 89 (228)
...-.|+.+...+.+..|+.+.-.++-.++..+. .....+. .-+.|+-=++.+++.=++.-.+.++
T Consensus 6 ~i~l~~~al~~~l~ls~P~L~~alvVGl~Isi~Q----A~TqIqE----------qTLsFvPKliav~~~l~~~g~Wm~~ 71 (89)
T PRK05700 6 VMDLFREAMKVALMLAAPLLLVALIVGLVVSIFQ----AATQINE----------QTLSFIPKILAVLLTLIIAGPWMLN 71 (89)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH----HHHHHHH----------HHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf 9999999999999998889999999999999999----9999999----------8998799999999999998789999
Q ss_pred HHHHHHHHHHHHCCHH
Q ss_conf 9999999999533238
Q gi|254780944|r 90 FVFFLSESILNNTPIV 105 (228)
Q Consensus 90 ~~~~~~e~~l~rIP~v 105 (228)
.+.++..+++++||-+
T Consensus 72 ~l~~f~~~if~~ip~l 87 (89)
T PRK05700 72 TLLDYTRTLFTNIPTL 87 (89)
T ss_pred HHHHHHHHHHHHHHHH
T ss_conf 9999999999987766
No 12
>pfam06160 EzrA Septation ring formation regulator, EzrA. During the bacterial cell cycle, the tubulin-like cell-division protein FtsZ polymerizes into a ring structure that establishes the location of the nascent division site. EzrA modulates the frequency and position of FtsZ ring formation.
Probab=52.22 E-value=18 Score=16.64 Aligned_cols=59 Identities=27% Similarity=0.464 Sum_probs=36.6
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH--HHHHCCHHHHHHHHHHHHHHHHHCCCCCCCC
Q ss_conf 9999999999998777433788999999999--9953323889999999999997317755331
Q gi|254780944|r 67 FGLLVVIVGINIVGFFGRNLLGRFVFFLSES--ILNNTPIVRHLYKSTKQIIRTLLKEDSTSFK 128 (228)
Q Consensus 67 lg~~~~i~~i~liG~l~~~~~g~~~~~~~e~--~l~rIP~v~~IY~sikqi~~~~~~~~~~~f~ 128 (228)
+|+++++++++++|++.++..-+.+-.+-++ -+...|+.--+-. +|++ .+.|+....|.
T Consensus 3 i~iivivii~~~~~~~~rk~~~k~I~~Le~rk~~l~~~pv~~el~k-vk~L--~l~Ges~~~f~ 63 (559)
T pfam06160 3 IGIIVIVIVAYLAGYFLRKKIYKQIDELEERKEELMNLPVNEELSK-VKKL--NLTGESEETFE 63 (559)
T ss_pred EEHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHH-HHCC--CCCHHHHHHHH
T ss_conf 4089999999999999988899999999999999874988999999-8829--89705699999
No 13
>TIGR02120 GspF general secretion pathway protein F; InterPro: IPR011850 This membrane protein is a component of the terminal branch complex of the general secretion pathway (GSP), also known as the "Type II" secretion pathway. The GSP transports proteins (generally virulence-associated cell wall hydrolases) across the outer membrase of the bacterial cell. Transport across the inner membrane is often, but not exclusively handled by the Sec system. GspF nearly always clusters with other GSP subunits. However, some genes from Xylella and Xanthomonas strains are excluded from this entry due to excessive divergence.; GO: 0008565 protein transporter activity, 0015628 protein secretion by the type II secretion system, 0015627 type II protein secretion system complex.
Probab=50.55 E-value=19 Score=16.48 Aligned_cols=93 Identities=16% Similarity=0.296 Sum_probs=46.0
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHCCCHHH--------------HHHHHHHHH
Q ss_conf 699999999999999999999999999999999987642105121150110110235--------------899999999
Q gi|254780944|r 9 SISAKVRNNFFAGFIICAPIAITIWLSLSLIHWFDGFIVPYIPMQYNPEYYCDFSIP--------------GFGLLVVIV 74 (228)
Q Consensus 9 ~l~~~l~~~Fl~GLlvllPi~iTi~i~~~l~~~~~~~~~p~i~~~~~~~~~~~~~i~--------------glg~~~~i~ 74 (228)
.+.+++.+. .+=|+.+|+--+.-+...+ +++-|=+-.+|. ...-.+| -.|+++.+
T Consensus 172 ~lr~Ki~~A------liYPa~l~vVa~~vv~~Ll-~~VVPkvV~~F~---~~~q~LPl~Tr~li~lSdFl~~~G~~~~~- 240 (414)
T TIGR02120 172 ALRSKITTA------LIYPAVLTVVAIGVVIFLL-AYVVPKVVEQFA---HMKQTLPLLTRALIALSDFLRSWGWALLA- 240 (414)
T ss_pred HHHHHHHHH------HHHHHHHHHHHHHHHHHHH-HHHCCCEECHHH---CCCCCCCHHHHHHHHHCHHHHHHHHHHHH-
T ss_conf 999999998------7658999999999999999-420444031023---19978748999999845168889999999-
Q ss_pred HHHHHHHHHHHHHHHH-HHHHHHHHHHHCCHHHHHHHHH
Q ss_conf 9999877743378899-9999999995332388999999
Q gi|254780944|r 75 GINIVGFFGRNLLGRF-VFFLSESILNNTPIVRHLYKST 112 (228)
Q Consensus 75 ~i~liG~l~~~~~g~~-~~~~~e~~l~rIP~v~~IY~si 112 (228)
.+..++++....+.+. .-..+|+++-|+|++|.+-..+
T Consensus 241 ~~~~~~~l~~~~Lr~p~~r~~~dr~LLr~PviG~L~r~l 279 (414)
T TIGR02120 241 ALAALVVLFRRLLRDPAFRLRFDRRLLRLPVIGRLVRGL 279 (414)
T ss_pred HHHHHHHHHHHHHCCCCCCHHHHHHHHCCHHHHHHHHHH
T ss_conf 999999999998438987504548783202456899999
No 14
>TIGR02518 EutH_ACDH acetaldehyde dehydrogenase (acetylating); InterPro: IPR013357 Aldehyde dehydrogenases (1.2.1.3 from EC and 1.2.1.5 from EC) are enzymes which oxidize a wide variety of aliphatic and aromatic aldehydes using NAD(P) as a cofactor. In eukaryotes, at least twenty distinct aldehyde dehydrogenase families have been classified . Many aldehyde dehydrogenases have also been found in prokaryotic species. A glutamic acid and a cysteine residue have been implicated in the catalytic activity of mammalian aldehyde dehydrogenase, though these residues are not necessarily conserved in all the enzymes of this family. The acetaldehyde dehydrogenase family (1.2.1.10 from EC) of bacterial enzymes catalyse the formation of acetyl-CoA from acetaldehyde in the degradation of phenols, cresols and catechol . Proteins in this entry occur in bacterial species and are annotated as probable acetaldehyde dehydrogenases, though this function has not been experimentally verified..
Probab=49.01 E-value=9.5 Score=18.33 Aligned_cols=93 Identities=16% Similarity=0.175 Sum_probs=53.1
Q ss_pred HHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHCCCCCCCCEE-----------EEEECCCCCEEEEEEEECC
Q ss_conf 77433788999999999995332388999999999999731775533103-----------9998488757999997068
Q gi|254780944|r 81 FFGRNLLGRFVFFLSESILNNTPIVRHLYKSTKQIIRTLLKEDSTSFKNA-----------CLVEYPSAGFWSLCFLTTE 149 (228)
Q Consensus 81 ~l~~~~~g~~~~~~~e~~l~rIP~v~~IY~sikqi~~~~~~~~~~~f~~v-----------VlVe~P~~g~~~iGFvT~~ 149 (228)
=-+++-+.+.-.+.+|+++..| +..-|...-++..+- ..+++|.++ -.|---=+++.++|.+.-+
T Consensus 18 k~Aq~~~a~~~q~qID~iv~ai--~~~~~~~~~~LAkmA--~EETGFGk~eDKv~KN~fA~~~vY~~IKDmKTvG~~~E~ 93 (528)
T TIGR02518 18 KVAQKKLANMTQEQIDKIVKAI--VDAAYENAVKLAKMA--NEETGFGKWEDKVIKNVFAAKIVYDSIKDMKTVGILEED 93 (528)
T ss_pred HHHHHHHHHHCHHHHHHHHHHH--HHHHHHHHHHHHHHC--CCCCCCCCEECHHHHHHHHHHHHHHHCCCCCEEEEEEEC
T ss_conf 9999998740577787999999--998752278888741--542577411020244678777765410554135556415
Q ss_pred CHHHHHHHHCCCCCCCEEEEEEECCCCCCCCE
Q ss_conf 71565553024677738999970798532688
Q gi|254780944|r 150 VKGEIKEKFSNIGCEDMVTVFIPPTPLPTAGM 181 (228)
Q Consensus 150 ~~~~~~~~~~~~~~~~~v~VfiPtsPnPtsG~ 181 (228)
....+-+. .-+-+.|+=.+|.| ||||-.
T Consensus 94 ~~~~~~ev---~vP~G~vagl~PST-NPTSTa 121 (528)
T TIGR02518 94 KEKKVIEV---AVPVGVVAGLIPST-NPTSTA 121 (528)
T ss_pred CCCCEEEE---ECCCEEEEECCCCC-CCHHHH
T ss_conf 54505885---05502344435878-854799
No 15
>PRK04778 septation ring formation regulator EzrA; Provisional
Probab=48.45 E-value=20 Score=16.27 Aligned_cols=61 Identities=25% Similarity=0.321 Sum_probs=38.2
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH--HHHHCCHHHHHHHHHHHHHHHHHCCCCCCCC
Q ss_conf 589999999999998777433788999999999--9953323889999999999997317755331
Q gi|254780944|r 65 PGFGLLVVIVGINIVGFFGRNLLGRFVFFLSES--ILNNTPIVRHLYKSTKQIIRTLLKEDSTSFK 128 (228)
Q Consensus 65 ~glg~~~~i~~i~liG~l~~~~~g~~~~~~~e~--~l~rIP~v~~IY~sikqi~~~~~~~~~~~f~ 128 (228)
..+++++++++++++|++.++..-+.+-++-++ -+..+|+.-.+-. +|++ .+.|+....|.
T Consensus 5 iii~iivlvii~~~~~~~~rr~~~k~I~~Le~rK~~l~~~pv~~el~k-vk~L--~l~Get~~~fe 67 (569)
T PRK04778 5 LIIAIVVIIIIAYLVGYILRKRNYKRIDELEERKQELEDLPVNEELEK-VKKL--NLTGQSETKFE 67 (569)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHH-HHCC--CCCCHHHHHHH
T ss_conf 789999999999999999999999899999999999876987999998-8808--67706599999
No 16
>PRK12781 fliQ flagellar biosynthesis protein FliQ; Reviewed
Probab=47.73 E-value=21 Score=16.21 Aligned_cols=81 Identities=16% Similarity=0.155 Sum_probs=55.7
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf 99999999999999999999999999999999987642105121150110110235899999999999987774337889
Q gi|254780944|r 10 ISAKVRNNFFAGFIICAPIAITIWLSLSLIHWFDGFIVPYIPMQYNPEYYCDFSIPGFGLLVVIVGINIVGFFGRNLLGR 89 (228)
Q Consensus 10 l~~~l~~~Fl~GLlvllPi~iTi~i~~~l~~~~~~~~~p~i~~~~~~~~~~~~~i~glg~~~~i~~i~liG~l~~~~~g~ 89 (228)
...-.|.-+..-+++-.|+.+.-.++-.++ ++++-....+. .-+.|+-=++.+++.-++...+.++
T Consensus 6 vi~l~r~al~~~l~~s~PiL~~aL~VGl~I----sifQA~TQIQE----------~TLsFVPKi~av~~~l~l~g~wm~~ 71 (88)
T PRK12781 6 ALELVRAAIWTIIVASGPAVGAAMLVGIAI----ALLQALTQIQE----------VTLTFVPKIVVILIVMAVTGSFVGA 71 (88)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH----HHHHHHHHHHH----------HHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf 999999999999999774999999999999----99999999999----------9998599899999999998779999
Q ss_pred HHHHHHHHHHHHCCH
Q ss_conf 999999999953323
Q gi|254780944|r 90 FVFFLSESILNNTPI 104 (228)
Q Consensus 90 ~~~~~~e~~l~rIP~ 104 (228)
.+.++.+++++|||-
T Consensus 72 ~l~~ft~~lf~~I~~ 86 (88)
T PRK12781 72 QIYAFTEMVYGRIES 86 (88)
T ss_pred HHHHHHHHHHHHHCC
T ss_conf 999999999986122
No 17
>cd00468 HIT_like HIT family: HIT (Histidine triad) proteins, named for a motif related to the sequence HxHxH/Qxx (x, a hydrophobic amino acid), are a superfamily of nucleotide hydrolases and transferases, which act on the alpha-phosphate of ribonucleotides. On the basis of sequence, substrate specificity, structure, evolution and mechanism, HIT proteins are classified in the literacture into three major branches: the Hint branch, which consists of adenosine 5' -monophosphoramide hydrolases, the Fhit branch, that consists of diadenosine polyphosphate hydrolases, and the GalT branch consisting of specific nucloside monophosphate transferases. Further sequence analysis reveals several new closely related, yet uncharacterized subgroups.
Probab=47.39 E-value=21 Score=16.17 Aligned_cols=44 Identities=18% Similarity=0.362 Sum_probs=34.8
Q ss_pred CCCEEEEEEECCCCCCCCEEEEEEHHHEEEC-CCCHHHHHHHHHHC
Q ss_conf 7738999970798532688999877762477-99999999998701
Q gi|254780944|r 163 CEDMVTVFIPPTPLPTAGMLVFVPRNKVIML-KMSAEDSAKMLISG 207 (228)
Q Consensus 163 ~~~~v~VfiPtsPnPtsG~~~~vp~~~v~~~-dmsveeA~k~iiS~ 207 (228)
++|.+-+|+-..|. +-|=++.+||+.+..+ |++.|+.-++...+
T Consensus 3 Ede~~~af~Di~P~-~~gH~LViPk~h~~~l~dl~~~~~~~l~~~~ 47 (86)
T cd00468 3 DDEHSFAFVNLKPA-APGHVLVCPKRHVETLPDLDEALLADLVITA 47 (86)
T ss_pred CCCCEEEEECCCCC-CCCCEEEECCHHHCCHHHCCHHHHHHHHHHH
T ss_conf 27858999779889-9972999702241993469999999999999
No 18
>pfam02674 Colicin_V Colicin V production protein. Colicin V production protein is required in E. Coli for colicin V production from plasmid pColV-K30. This protein is coded for in the purF operon.
Probab=47.28 E-value=21 Score=16.16 Aligned_cols=96 Identities=9% Similarity=0.146 Sum_probs=53.7
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf 99999999999999999999999999999999987642105121150110110235899999999999987774337889
Q gi|254780944|r 10 ISAKVRNNFFAGFIICAPIAITIWLSLSLIHWFDGFIVPYIPMQYNPEYYCDFSIPGFGLLVVIVGINIVGFFGRNLLGR 89 (228)
Q Consensus 10 l~~~l~~~Fl~GLlvllPi~iTi~i~~~l~~~~~~~~~p~i~~~~~~~~~~~~~i~glg~~~~i~~i~liG~l~~~~~g~ 89 (228)
...-.+|=|+..++.++=..+.+++..+....+.+++.+.+.. + .....+++++..+.+++++.+..+.+.+
T Consensus 13 ~~~G~~rG~i~e~~~l~~~i~~~~~a~~~~~~~~~~~~~~~~~----~----~~~~~~a~~iifi~~~~i~~~i~~~l~~ 84 (145)
T pfam02674 13 ALLGFRRGFVREVLSLLGWVVAFFVASLFYPPLAPLLAEYVLS----P----ALAAIIAFLLIFLLVLLIGSLLGVLLRK 84 (145)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCC----H----HHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf 9999999999999999999999999999999999998843797----8----9999999999999999999999999999
Q ss_pred HHHHHHHHHHHHCCHHHHHHHHHHHH
Q ss_conf 99999999995332388999999999
Q gi|254780944|r 90 FVFFLSESILNNTPIVRHLYKSTKQI 115 (228)
Q Consensus 90 ~~~~~~e~~l~rIP~v~~IY~sikqi 115 (228)
.+....-+.++| +.+.+.+.+|-.
T Consensus 85 ~~~~~~l~~~dr--~lG~~~G~~k~~ 108 (145)
T pfam02674 85 LVKLSGLGGLDR--LLGAVFGLLRGL 108 (145)
T ss_pred HHHHHCCCHHHH--HHHHHHHHHHHH
T ss_conf 998805343899--999999999999
No 19
>COG0537 Hit Diadenosine tetraphosphate (Ap4A) hydrolase and other HIT family hydrolases [Nucleotide transport and metabolism / Carbohydrate transport and metabolism / General function prediction only]
Probab=45.16 E-value=23 Score=15.96 Aligned_cols=43 Identities=21% Similarity=0.430 Sum_probs=33.4
Q ss_pred CCCEEEEEEECCCCCCCCEEEEEEHHHEEEC-CCCHHHHHHHHHH
Q ss_conf 7738999970798532688999877762477-9999999999870
Q gi|254780944|r 163 CEDMVTVFIPPTPLPTAGMLVFVPRNKVIML-KMSAEDSAKMLIS 206 (228)
Q Consensus 163 ~~~~v~VfiPtsPnPtsG~~~~vp~~~v~~~-dmsveeA~k~iiS 206 (228)
.++++.+|+=-.|. +-|.++.+|+..+..+ |++.++.-.+.-.
T Consensus 20 e~~~~~afld~~P~-~~gH~LviPk~h~~~l~~l~~~~~~~l~~~ 63 (138)
T COG0537 20 EDEHVLAFLDIYPA-APGHTLVIPKRHVSDLEDLDPEELAELFLL 63 (138)
T ss_pred ECCCEEEEECCCCC-CCCEEEEEECHHHHHHHHCCHHHHHHHHHH
T ss_conf 77988999777889-998699995554556760999999999999
No 20
>PRK12772 bifunctional flagellar biosynthesis protein FliR/FlhB; Provisional
Probab=43.55 E-value=24 Score=15.81 Aligned_cols=40 Identities=15% Similarity=0.210 Sum_probs=29.3
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf 2169999999999999999999999999999999998764
Q gi|254780944|r 7 HTSISAKVRNNFFAGFIICAPIAITIWLSLSLIHWFDGFI 46 (228)
Q Consensus 7 ~~~l~~~l~~~Fl~GLlvllPi~iTi~i~~~l~~~~~~~~ 46 (228)
...+.+...+.|..|+-+-+|+.+++.+....++.+....
T Consensus 165 ~~~~~~~~~~~F~~a~~iA~Pii~~lll~dv~lGilaR~~ 204 (609)
T PRK12772 165 IMHVINVFIQYFVIGIKIAIPIVLIILITDLTLGLISRTV 204 (609)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf 9999999999999999999999999999999999999813
No 21
>PRK04949 putative sulfate transport protein CysZ; Validated
Probab=42.54 E-value=25 Score=15.71 Aligned_cols=28 Identities=21% Similarity=0.317 Sum_probs=16.5
Q ss_pred HHHHHHHHHHHHH----HHHHHHHHHHHHHHC
Q ss_conf 9999999999999----999999987642105
Q gi|254780944|r 23 IICAPIAITIWLS----LSLIHWFDGFIVPYI 50 (228)
Q Consensus 23 lvllPi~iTi~i~----~~l~~~~~~~~~p~i 50 (228)
.+++|+.+++.++ +++++.+++++....
T Consensus 29 fv~iPlliNi~Lf~~~~~~l~~~~~~~~~~~~ 60 (251)
T PRK04949 29 FVILPLLVNILLFGGAFWWLFTQLDAWIDWLM 60 (251)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf 99989999999999999999999999999998
No 22
>KOG0125 consensus
Probab=40.64 E-value=26 Score=15.66 Aligned_cols=48 Identities=17% Similarity=0.151 Sum_probs=30.5
Q ss_pred CCEEEEEE--CCCCCEEEEEEEECCCHHHHHHHHC----CCCCCCEEEEEEECC
Q ss_conf 31039998--4887579999970687156555302----467773899997079
Q gi|254780944|r 127 FKNACLVE--YPSAGFWSLCFLTTEVKGEIKEKFS----NIGCEDMVTVFIPPT 174 (228)
Q Consensus 127 f~~vVlVe--~P~~g~~~iGFvT~~~~~~~~~~~~----~~~~~~~v~VfiPts 174 (228)
|.+|+=|| |-..|..-.||||=|++.+...... ..-+++.+-|=.-|+
T Consensus 120 fG~VldVEIIfNERGSKGFGFVTmen~~dadRARa~LHgt~VEGRkIEVn~ATa 173 (376)
T KOG0125 120 FGKVLDVEIIFNERGSKGFGFVTMENPADADRARAELHGTVVEGRKIEVNNATA 173 (376)
T ss_pred HCCEEEEEEEECCCCCCCCCEEEECCHHHHHHHHHHHHCCEEECEEEEEECCCH
T ss_conf 175046899863677775234872282468999998504643012788741431
No 23
>cd01276 PKCI_related Protein Kinase C Interacting protein related (PKCI): PKCI and related proteins belong to the ubiquitous HIT family of hydrolases that act on alpha-phosphates of ribonucleotides. The members of this subgroup have a conserved HxHxHxx motif (x is a hydrophobic residue) that is a signature for this family. No enzymatic activity has been reported however, for PKCI and its related members.
Probab=40.41 E-value=27 Score=15.51 Aligned_cols=38 Identities=21% Similarity=0.344 Sum_probs=31.1
Q ss_pred CCCCEEEEEEECCCCCCCCEEEEEEHHHEEEC-CCCHHHH
Q ss_conf 77738999970798532688999877762477-9999999
Q gi|254780944|r 162 GCEDMVTVFIPPTPLPTAGMLVFVPRNKVIML-KMSAEDS 200 (228)
Q Consensus 162 ~~~~~v~VfiPtsPnPtsG~~~~vp~~~v~~~-dmsveeA 200 (228)
-++|.+.+|+...|. +-|-++.+||..+..+ |++-|++
T Consensus 18 yede~~~aflD~~P~-~~GH~LViPK~H~~~l~~l~~~~~ 56 (104)
T cd01276 18 YEDDEVLAFHDINPQ-APVHILVIPKKHIASLSDATEEDE 56 (104)
T ss_pred EECCCEEEEECCCCC-CCCEEEEEEEEEECCHHHCCHHHH
T ss_conf 979979999888999-983299985422298588998589
No 24
>COG4956 Integral membrane protein (PIN domain superfamily) [General function prediction only]
Probab=38.95 E-value=29 Score=15.37 Aligned_cols=30 Identities=20% Similarity=0.261 Sum_probs=20.4
Q ss_pred HHHHHHHHHHHCCHHHHHHHHHHHHHHHHH
Q ss_conf 999999999533238899999999999973
Q gi|254780944|r 91 VFFLSESILNNTPIVRHLYKSTKQIIRTLL 120 (228)
Q Consensus 91 ~~~~~e~~l~rIP~v~~IY~sikqi~~~~~ 120 (228)
..+++|+.+.|+|...-+|.++-=++..+.
T Consensus 65 ~~~~le~~i~k~~~~~ilf~tiGLiiGLli 94 (356)
T COG4956 65 WLKRLEEQIRKLPVTTILFGTIGLIIGLLI 94 (356)
T ss_pred HHHHHHHHHHHCCHHHHHHHHHHHHHHHHH
T ss_conf 999999999836899999987889999999
No 25
>COG4794 EscS Type III secretory pathway, component EscS [Intracellular trafficking and secretion]
Probab=38.45 E-value=29 Score=15.32 Aligned_cols=77 Identities=17% Similarity=0.304 Sum_probs=46.9
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf 99999999999999999999999999987642105121150110110235899999999999987774337889999999
Q gi|254780944|r 16 NNFFAGFIICAPIAITIWLSLSLIHWFDGFIVPYIPMQYNPEYYCDFSIPGFGLLVVIVGINIVGFFGRNLLGRFVFFLS 95 (228)
Q Consensus 16 ~~Fl~GLlvllPi~iTi~i~~~l~~~~~~~~~p~i~~~~~~~~~~~~~i~glg~~~~i~~i~liG~l~~~~~g~~~~~~~ 95 (228)
+.+.-=|+.-+|-++ +..+++.+-++++.....+ |. -++|.+-++.++..=++...+.|..++++.
T Consensus 12 qaL~liLilSlPpvi----vAsvvGllVslvQA~TQiQ---dQ-------Tl~f~iKLl~V~~tl~lt~~Wlg~~ll~fa 77 (89)
T COG4794 12 QALWLILILSLPPVI----VASVVGLLVSLVQALTQIQ---DQ-------TLPFGIKLLAVSATLFLTAGWLGATLLNFA 77 (89)
T ss_pred HHHHHHHHHHCCHHH----HHHHHHHHHHHHHHHHHHH---HH-------HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf 999999999611999----9999999999999999999---86-------788999999999999997077588999999
Q ss_pred HHHHHHCCHHH
Q ss_conf 99995332388
Q gi|254780944|r 96 ESILNNTPIVR 106 (228)
Q Consensus 96 e~~l~rIP~v~ 106 (228)
|..+.++|..|
T Consensus 78 ~~i~~~~~~~~ 88 (89)
T COG4794 78 EQIFLNIPKAR 88 (89)
T ss_pred HHHHHHHHHCC
T ss_conf 99999866405
No 26
>COG1684 FliR Flagellar biosynthesis pathway, component FliR [Cell motility and secretion / Intracellular trafficking and secretion]
Probab=35.95 E-value=32 Score=15.08 Aligned_cols=44 Identities=11% Similarity=0.207 Sum_probs=35.6
Q ss_pred CCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf 76102169999999999999999999999999999999998764
Q gi|254780944|r 3 KKSFHTSISAKVRNNFFAGFIICAPIAITIWLSLSLIHWFDGFI 46 (228)
Q Consensus 3 ~~~~~~~l~~~l~~~Fl~GLlvllPi~iTi~i~~~l~~~~~~~~ 46 (228)
++.....+.+.+...|..|+..-+|+.....++...++.++...
T Consensus 164 ~~~~~~~l~~~l~~~F~~~l~iAlPii~~lLlvnlalGlv~R~~ 207 (258)
T COG1684 164 NDNAFLLLAKALSAIFLIGLRLALPIIALLLLVNLALGLLNRLA 207 (258)
T ss_pred CCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCC
T ss_conf 74099999999999999999999899999999999999998425
No 27
>pfam10173 DUF2343 Uncharacterized conserved protein (DUF2343). This entry is of a family of proteins conserved from plants to humans. The function is not known.
Probab=35.65 E-value=32 Score=15.05 Aligned_cols=54 Identities=19% Similarity=0.193 Sum_probs=28.4
Q ss_pred HHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHCCCCCCCCEEEEEECCC
Q ss_conf 337889999999999953323889999999999997317755331039998488
Q gi|254780944|r 84 RNLLGRFVFFLSESILNNTPIVRHLYKSTKQIIRTLLKEDSTSFKNACLVEYPS 137 (228)
Q Consensus 84 ~~~~g~~~~~~~e~~l~rIP~v~~IY~sikqi~~~~~~~~~~~f~~vVlVe~P~ 137 (228)
....-++++++++++++|||-=----.|+--.....-.++...-++.+-+-||.
T Consensus 8 ~~gwk~kiv~~g~~ll~rIpyeE~~LKSiP~~~~~~~~~~~~~~~~~i~v~yP~ 61 (106)
T pfam10173 8 EKGWKKKIVSLGNKLLDRIPYEEWGLKSIPSLSAILRRKELEGAKIPIEVYYPG 61 (106)
T ss_pred HHHHHHHHHHHHHHHHHHCCHHHHHHHHCCCCHHHHHHHHHCCCCCEEEEECCC
T ss_conf 088999999999999976784888886158602888874310457615687797
No 28
>cd01275 FHIT FHIT (fragile histidine family): FHIT proteins, related to the HIT family carry a motif HxHxH/Qxx (x, is a hydrophobic amino acid), On the basis of sequence, substrate specificity, structure, evolution and mechanism, HIT proteins are classified into three branches: the Hint branch, which consists of adenosine 5' -monophosphoramide hydrolases, the Fhit branch, that consists of diadenosine polyphosphate hydrolases, and the GalT branch consisting of specific nucloside monophosphate transferases. Fhit plays a very important role in the development of tumours. Infact, Fhit deletions are among the earliest and most frequent genetic alterations in the development of tumours.
Probab=35.30 E-value=33 Score=15.01 Aligned_cols=41 Identities=20% Similarity=0.325 Sum_probs=32.9
Q ss_pred CCCEEEEEEECCCCCCCCEEEEEEHHHEEEC-CCCHHHHHHHH
Q ss_conf 7738999970798532688999877762477-99999999998
Q gi|254780944|r 163 CEDMVTVFIPPTPLPTAGMLVFVPRNKVIML-KMSAEDSAKML 204 (228)
Q Consensus 163 ~~~~v~VfiPtsPnPtsG~~~~vp~~~v~~~-dmsveeA~k~i 204 (228)
+++++.+|+...|. +-|-++.+||..+..+ |++.|+...+.
T Consensus 19 ede~~~aflD~~P~-~~GH~LViPK~H~~~l~dl~~~e~~~l~ 60 (126)
T cd01275 19 RTKHSFAVVNLYPY-NPGHVLVVPYRHVPRLEDLTPEEIADLF 60 (126)
T ss_pred ECCCEEEEECCCCC-CCCEEEEECCHHCCHHHCCCHHHHHHHH
T ss_conf 79969999768889-9960999755330515309999999999
No 29
>TIGR01995 PTS-II-ABC-beta PTS system, beta-glucoside-specific IIABC component; InterPro: IPR011297 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 , , , . This entry represents a family of PTS enzyme II proteins in which all three domains are found in the same polypeptide chain and which appear to have a broad specificity for beta-glucosides including salicin (beta-D-glucose-1-salicylate) and arbutin (hydroquinone-O-beta-D-glucopyranoside) . These are distinct from the closely related sucrose-specific and trehalose-specific PTS transporters.; GO: 0008982 protein-N(PI)-phosphohistidine-sugar phosphotransferase activity, 0009401 phosphoenolpyruvate-dependent sugar phosphotransferase system.
Probab=35.08 E-value=33 Score=14.99 Aligned_cols=86 Identities=16% Similarity=0.236 Sum_probs=45.4
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHCCCHHHHHHHHHHHHHH-HHHHHHHHHHHHHHHHHHHHHHHHHC
Q ss_conf 99999999999999999998764210512115011011023589999999999-99877743378899999999999533
Q gi|254780944|r 24 ICAPIAITIWLSLSLIHWFDGFIVPYIPMQYNPEYYCDFSIPGFGLLVVIVGI-NIVGFFGRNLLGRFVFFLSESILNNT 102 (228)
Q Consensus 24 vllPi~iTi~i~~~l~~~~~~~~~p~i~~~~~~~~~~~~~i~glg~~~~i~~i-~liG~l~~~~~g~~~~~~~e~~l~rI 102 (228)
.++|+.+.+|+..++=+|+ ..++|..+.- +..|.+-+++++=+. +++|=+ .+++|.-+.+....+++..
T Consensus 236 sVIP~il~v~lm~y~eK~~----~K~~P~~~~~-----F~~Pll~~LI~~PltL~i~GP~-g~~~g~gi~~~~~~Ly~~~ 305 (660)
T TIGR01995 236 SVIPVILAVWLMSYVEKFL----KKVIPKALKN-----FLTPLLVMLITVPLTLLILGPV-GVYLGEGIASGILFLYEVS 305 (660)
T ss_pred HHHHHHHHHHHHHHHHEEE----ECCCCHHHHH-----HHHHHHHHHHHHHHHHHHHHHH-HHHHHHHHHHHHHHHHHHH
T ss_conf 3689999999985340122----3036467898-----6414999999888888654358-9999999999999887430
Q ss_pred CHH-HHHHHHHHHHHHHH
Q ss_conf 238-89999999999997
Q gi|254780944|r 103 PIV-RHLYKSTKQIIRTL 119 (228)
Q Consensus 103 P~v-~~IY~sikqi~~~~ 119 (228)
|.+ ..+|+++-|++=+|
T Consensus 306 p~~A~~llaa~~p~~V~~ 323 (660)
T TIGR01995 306 PWLAGALLAAVWPVLVMF 323 (660)
T ss_pred HHHHHHHHHHHHHHHHHH
T ss_conf 389999999888999997
No 30
>COG1987 FliQ Flagellar biosynthesis pathway, component FliQ [Cell motility and secretion / Intracellular trafficking and secretion]
Probab=34.12 E-value=34 Score=14.89 Aligned_cols=82 Identities=12% Similarity=0.202 Sum_probs=53.9
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf 99999999999999999999999999999999987642105121150110110235899999999999987774337889
Q gi|254780944|r 10 ISAKVRNNFFAGFIICAPIAITIWLSLSLIHWFDGFIVPYIPMQYNPEYYCDFSIPGFGLLVVIVGINIVGFFGRNLLGR 89 (228)
Q Consensus 10 l~~~l~~~Fl~GLlvllPi~iTi~i~~~l~~~~~~~~~p~i~~~~~~~~~~~~~i~glg~~~~i~~i~liG~l~~~~~g~ 89 (228)
...=.+.-+-.+|....|+.+.-.++.-++..+.+ ...... --+.|+=-++.++++-.+..-+.++
T Consensus 6 ~l~i~~~ai~~~L~l~~P~ll~alvvGLvIsifQA----~TQIqE----------qTLsFiPKIiai~~~l~~~gpWm~~ 71 (89)
T COG1987 6 VLDIGQEAIWLVLMLSAPVLLVALVVGLVISIFQA----ATQIQE----------QTLSFIPKIIAVFLVLILLGPWMLN 71 (89)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH----HHHHHH----------HHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf 99999999999999999899999999999999999----999999----------9998599899999999997589999
Q ss_pred HHHHHHHHHHHHCCHH
Q ss_conf 9999999999533238
Q gi|254780944|r 90 FVFFLSESILNNTPIV 105 (228)
Q Consensus 90 ~~~~~~e~~l~rIP~v 105 (228)
.+.++...+++|||..
T Consensus 72 ~l~dft~~if~~i~~~ 87 (89)
T COG1987 72 QLLDFTVTIFSNIPQI 87 (89)
T ss_pred HHHHHHHHHHHHHHHH
T ss_conf 9999999999988766
No 31
>PRK11513 cytochrome b561; Provisional
Probab=33.81 E-value=35 Score=14.86 Aligned_cols=15 Identities=7% Similarity=0.217 Sum_probs=6.4
Q ss_pred HHHHHHHHHHHHHHH
Q ss_conf 999999999999877
Q gi|254780944|r 67 FGLLVVIVGINIVGF 81 (228)
Q Consensus 67 lg~~~~i~~i~liG~ 81 (228)
+|+.+.++.+.-+.+
T Consensus 48 ~Gi~il~L~~~Rl~w 62 (176)
T PRK11513 48 CGISILVLMVVRLLI 62 (176)
T ss_pred HHHHHHHHHHHHHHH
T ss_conf 999999999999999
No 32
>PRK11365 ssuC alkanesulfonate transporter permease subunit; Provisional
Probab=33.18 E-value=36 Score=14.80 Aligned_cols=40 Identities=20% Similarity=0.139 Sum_probs=17.3
Q ss_pred HHHHHHHHHHHHHHHHHH-HHHHHHHHHHHHHHHHHHCCHH
Q ss_conf 899999999999987774-3378899999999999533238
Q gi|254780944|r 66 GFGLLVVIVGINIVGFFG-RNLLGRFVFFLSESILNNTPIV 105 (228)
Q Consensus 66 glg~~~~i~~i~liG~l~-~~~~g~~~~~~~e~~l~rIP~v 105 (228)
.+|+++..++=..+|.+. .+...+++++-.=..+.-+|.+
T Consensus 70 ~~Gf~l~~~~Gi~lGil~g~~~~~~~~~~P~~~~l~~iP~i 110 (263)
T PRK11365 70 LIGFSIGGSLGLILGLISGLSRWGERLLDTSIQMLRNVPHL 110 (263)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHCHHHHHHHHCCHH
T ss_conf 99999999999999999998699998758599999765799
No 33
>pfam05552 TM_helix Conserved TM helix. This alignment represents a conserved transmembrane helix as well as some flanking sequence. It is often found in association with pfam00924.
Probab=32.93 E-value=36 Score=14.77 Aligned_cols=28 Identities=29% Similarity=0.406 Sum_probs=19.6
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf 9999999998777433788999999999
Q gi|254780944|r 70 LVVIVGINIVGFFGRNLLGRFVFFLSES 97 (228)
Q Consensus 70 ~~~i~~i~liG~l~~~~~g~~~~~~~e~ 97 (228)
++..++++++|++..+.+++.+-+.+++
T Consensus 18 ii~AivIL~vG~~va~~v~~~v~k~L~~ 45 (53)
T pfam05552 18 LIAAILILLVGWLIAKIVRRLVTKLLEK 45 (53)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf 9999999999999999999999999998
No 34
>pfam11969 DcpS_C Scavenger mRNA decapping enzyme C-term binding. This family consists of several scavenger mRNA decapping enzymes (DcpS) and is the C-terminal region. DcpS is a scavenger pyrophosphatase that hydrolyses the residual cap structure following 3' to 5' decay of an mRNA. The association of DcpS with 3' to 5' exonuclease exosome components suggests that these two activities are linked and there is a coupled exonucleolytic decay-dependent decapping pathway. The C-terminal domain contains a histidine triad (HIT) sequence with three histidines separated by hydrophobic residues. The central histidine within the DcpS HIT motif is critical for decapping activity and defines the HIT motif as a new mRNA decapping domain, making DcpS the first member of the HIT family of proteins with a defined biological function.
Probab=32.72 E-value=36 Score=14.75 Aligned_cols=37 Identities=19% Similarity=0.309 Sum_probs=30.0
Q ss_pred CCCEEEEEEECCCCCCCCEEEEEEHHHEEEC-CCCHHHH
Q ss_conf 7738999970798532688999877762477-9999999
Q gi|254780944|r 163 CEDMVTVFIPPTPLPTAGMLVFVPRNKVIML-KMSAEDS 200 (228)
Q Consensus 163 ~~~~v~VfiPtsPnPtsG~~~~vp~~~v~~~-dmsveeA 200 (228)
++|.+.+|....|. ..|-++.+|++.+..+ |++.|+.
T Consensus 19 edd~~vaf~D~~P~-~~gH~LVIPk~h~~~~~dl~~~~~ 56 (113)
T pfam11969 19 EDDGFVAFKDIKPK-APLHLLVIPKKHIKSLRDLTKEHL 56 (113)
T ss_pred ECCCEEEEECCCCC-CCCEEEEEEEECCCCCCCCCHHHH
T ss_conf 79999998689989-997599999974044354898799
No 35
>TIGR01078 arcA arginine deiminase; InterPro: IPR003876 This is a family of arginine deiminases, 3.5.3.6 from EC. The aligned region corresponds to the C-terminal of the protein. These enzymes catalyse the conversion of arginine + H2O to citrulline + NH3. Also found in this family is the Streptococcus anti tumor glycoprotein .; GO: 0016990 arginine deiminase activity, 0006527 arginine catabolic process.
Probab=32.26 E-value=37 Score=14.71 Aligned_cols=33 Identities=15% Similarity=0.328 Sum_probs=27.3
Q ss_pred HHHHHHHHHHHHCCCCCCCCEEEEEECCCCCEE
Q ss_conf 999999999973177553310399984887579
Q gi|254780944|r 109 YKSTKQIIRTLLKEDSTSFKNACLVEYPSAGFW 141 (228)
Q Consensus 109 Y~sikqi~~~~~~~~~~~f~~vVlVe~P~~g~~ 141 (228)
-.|+-++..+++.+++..|++|+.++.|+.-.+
T Consensus 244 ~q~ve~LA~~LF~~k~~~f~~vlA~~~Pk~ra~ 276 (421)
T TIGR01078 244 AQSVEKLAKSLFANKEGGFKKVLAIKIPKNRAL 276 (421)
T ss_pred HHHHHHHHHHHHHCCCCCCCEEEEECCCCCCCC
T ss_conf 889999999998403376555899717555678
No 36
>pfam03596 Cad Cadmium resistance transporter.
Probab=31.99 E-value=37 Score=14.68 Aligned_cols=85 Identities=16% Similarity=0.217 Sum_probs=44.5
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHCCCCCC--CCEEEEEECCCCCEEEEE
Q ss_conf 999999999999877743378899999999999533238899999999999973177553--310399984887579999
Q gi|254780944|r 67 FGLLVVIVGINIVGFFGRNLLGRFVFFLSESILNNTPIVRHLYKSTKQIIRTLLKEDSTS--FKNACLVEYPSAGFWSLC 144 (228)
Q Consensus 67 lg~~~~i~~i~liG~l~~~~~g~~~~~~~e~~l~rIP~v~~IY~sikqi~~~~~~~~~~~--f~~vVlVe~P~~g~~~iG 144 (228)
+|+...++.=++.++......- +|+-.++.-+|+ |-.+|...+ +++++. -++..--.-.++..|+++
T Consensus 34 lGf~~Lv~~Sl~~a~g~~~ip~----~wilGlLGliPi----~lGi~~~~~---~~~~~~~~~~~~~~~~~~~~~~~~Va 102 (192)
T pfam03596 34 LGSVALVLVSLLFAFVLNLVPE----KWILGLLGLIPI----YLGIKVLIK---GDDDDEEEILELLNSGKNNSLFGTVA 102 (192)
T ss_pred HHHHHHHHHHHHHHHHHHHCCH----HHHHHHHHHHHH----HHHHHHHHH---CCCCCCHHHHHHHCCCCCCCCEEEEE
T ss_conf 7799999999999999874799----999998758999----999999972---76655134444420256677059999
Q ss_pred EEECCCHHHHHHHHCCCCCCCEEEEEEEC
Q ss_conf 97068715655530246777389999707
Q gi|254780944|r 145 FLTTEVKGEIKEKFSNIGCEDMVTVFIPP 173 (228)
Q Consensus 145 FvT~~~~~~~~~~~~~~~~~~~v~VfiPt 173 (228)
.+|=-+ .+.|-..||+|-
T Consensus 103 ~vTiAn-----------cGgDNIgiYvPl 120 (192)
T pfam03596 103 IITFAS-----------CGADNIGIFVPY 120 (192)
T ss_pred EEEEEC-----------CCCCEEEEEEEE
T ss_conf 999951-----------578516897521
No 37
>COG4756 Predicted cation transporter [General function prediction only]
Probab=30.61 E-value=28 Score=15.46 Aligned_cols=18 Identities=50% Similarity=0.863 Sum_probs=13.1
Q ss_pred HHHHHHHCCCCCCCCCCC
Q ss_conf 999987014337887887
Q gi|254780944|r 200 SAKMLISGGLLIPDNISY 217 (228)
Q Consensus 200 A~k~iiS~Gv~~P~~~~~ 217 (228)
-|.+++|||+..|.+++.
T Consensus 306 lmsLvIsGGmlIPGNiPN 323 (367)
T COG4756 306 LMSLVISGGMLIPGNIPN 323 (367)
T ss_pred HHHHHHCCCEECCCCCCC
T ss_conf 999977287335788862
No 38
>PRK06010 fliQ flagellar biosynthesis protein FliQ; Reviewed
Probab=29.84 E-value=40 Score=14.46 Aligned_cols=81 Identities=14% Similarity=0.143 Sum_probs=53.7
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf 99999999999999999999999999999999987642105121150110110235899999999999987774337889
Q gi|254780944|r 10 ISAKVRNNFFAGFIICAPIAITIWLSLSLIHWFDGFIVPYIPMQYNPEYYCDFSIPGFGLLVVIVGINIVGFFGRNLLGR 89 (228)
Q Consensus 10 l~~~l~~~Fl~GLlvllPi~iTi~i~~~l~~~~~~~~~p~i~~~~~~~~~~~~~i~glg~~~~i~~i~liG~l~~~~~g~ 89 (228)
...-.|+-+..-+.+-.|+.++-.++-.++. +++.....+. .-+.|+-=++.+++.-.+...+.++
T Consensus 6 vi~l~~~al~~~l~ls~P~L~valvVGl~Is----lfQA~TQIqE----------qTLsFvPKliav~~~l~~~~pwm~~ 71 (88)
T PRK06010 6 ALDVVRDAIWTVLIASGPAVLAAMVVGVAIA----LFQALTQIQE----------MTLTFVPKIVAIFVTLLLTLPFMGA 71 (88)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH----HHHHHHHHHH----------HHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf 9999999999999998769999999999999----9999999999----------8998799999999999998889999
Q ss_pred HHHHHHHHHHHHCCH
Q ss_conf 999999999953323
Q gi|254780944|r 90 FVFFLSESILNNTPI 104 (228)
Q Consensus 90 ~~~~~~e~~l~rIP~ 104 (228)
.+.++.++++.+||.
T Consensus 72 ~l~~ft~~if~~I~g 86 (88)
T PRK06010 72 QISAFTLRIYSRIAG 86 (88)
T ss_pred HHHHHHHHHHHHHCC
T ss_conf 999999999987134
No 39
>KOG2927 consensus
Probab=29.57 E-value=41 Score=14.43 Aligned_cols=26 Identities=31% Similarity=0.498 Sum_probs=10.2
Q ss_pred HHCCCCCCH-HHHCCCHHHHHHHHHHHHH
Q ss_conf 105121150-1101102358999999999
Q gi|254780944|r 48 PYIPMQYNP-EYYCDFSIPGFGLLVVIVG 75 (228)
Q Consensus 48 p~i~~~~~~-~~~~~~~i~glg~~~~i~~ 75 (228)
|+.|..... .+|+. +++.||+..++.
T Consensus 208 PLWP~~mR~gvyY~s--ig~~gfl~~Ilv 234 (372)
T KOG2927 208 PLWPRRMRQGVYYLS--IGAGGFLAFILV 234 (372)
T ss_pred CCCCHHHHCCEEEEE--CCHHHHHHHHHH
T ss_conf 358388742211344--031599999999
No 40
>TIGR02119 panF sodium/pantothenate symporter; InterPro: IPR011849 Pantothenate (vitamin B5) is a precursor of coenzyme A and is made from aspartate and 2-oxoisovalerate in most bacteria with completed genome sequences. However, some pathogens must import pantothenate. This entry describes PanF, a sodium/pantothenate symporter. Several species that have this transporter appear to lack all enzymes of pantothenate biosynthesis, namely Haemophilus influenzae, Pasteurella multocida, Fusobacterium nucleatum, and Borrelia burgdorferi (Lyme disease spirochete) .; GO: 0015081 sodium ion transmembrane transporter activity, 0015233 pantothenate transporter activity, 0031402 sodium ion binding, 0006814 sodium ion transport, 0015887 pantothenate transport, 0009276 1-2nm peptidoglycan-based cell wall, 0016021 integral to membrane.
Probab=29.05 E-value=42 Score=14.37 Aligned_cols=27 Identities=15% Similarity=0.212 Sum_probs=20.9
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf 589999999999998777433788999
Q gi|254780944|r 65 PGFGLLVVIVGINIVGFFGRNLLGRFV 91 (228)
Q Consensus 65 ~glg~~~~i~~i~liG~l~~~~~g~~~ 91 (228)
.|+|+++.-..=...||++=..+||++
T Consensus 73 ~GLGWVLLa~iQvpt~~~~LgVLGKKf 99 (474)
T TIGR02119 73 YGLGWVLLAMIQVPTVYLVLGVLGKKF 99 (474)
T ss_pred CCHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf 152699999999999999997899999
No 41
>COG3180 AbrB Putative ammonia monooxygenase [General function prediction only]
Probab=28.82 E-value=40 Score=14.49 Aligned_cols=59 Identities=12% Similarity=0.345 Sum_probs=32.6
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHCCCCCCCCEEEEEECCC
Q ss_conf 999999999987774337889999999999953323889999999999997317755331039998488
Q gi|254780944|r 69 LLVVIVGINIVGFFGRNLLGRFVFFLSESILNNTPIVRHLYKSTKQIIRTLLKEDSTSFKNACLVEYPS 137 (228)
Q Consensus 69 ~~~~i~~i~liG~l~~~~~g~~~~~~~e~~l~rIP~v~~IY~sikqi~~~~~~~~~~~f~~vVlVe~P~ 137 (228)
.+.+++.-.+.||+.+++- ..+..+.++.-.|+ ...++.. +..|.+...+.|.+++|=|
T Consensus 94 ~~~tl~~s~l~g~ll~r~~---~~~~~Ta~~gs~PG------gas~m~~-iA~d~gAd~~~VAl~Q~lR 152 (352)
T COG3180 94 LLLTLLSSILLGWLLKRFS---ILPGNTAFLGSSPG------GASAMVS-IAQDYGADLRLVALMQYLR 152 (352)
T ss_pred HHHHHHHHHHHHHHHHHHC---CCCCCHHHHHCCCC------HHHHHHH-HHHHHCCCHHHHHHHHHHH
T ss_conf 9999999999999999954---89962135752874------6899999-9998489735789999999
No 42
>pfam07854 DUF1646 Protein of unknown function (DUF1646). Some of the members of this family are hypothetical bacterial and archaeal proteins, but others are annotated as being cation transporters expressed by the archaebacterium Methanosarcina mazei.
Probab=28.29 E-value=32 Score=15.09 Aligned_cols=25 Identities=48% Similarity=0.737 Sum_probs=19.3
Q ss_pred CCCHHH----HHHHHHHCCCCCCCCCCCC
Q ss_conf 999999----9999870143378878876
Q gi|254780944|r 194 KMSAED----SAKMLISGGLLIPDNISYD 218 (228)
Q Consensus 194 dmsvee----A~k~iiS~Gv~~P~~~~~~ 218 (228)
.|+.|+ -|.+++|||+..|.+++.-
T Consensus 284 ~M~~~qI~aiLmgLliSGGMLIPGNIPNI 312 (347)
T pfam07854 284 EMTEEQIRSILMGLLISGGMLIPGNIPNI 312 (347)
T ss_pred CCCHHHHHHHHHHHHHCCCEECCCCCCHH
T ss_conf 24899999999999992871047886402
No 43
>PRK09765 2-O-a-mannosyl-D-glycerate specific PTS transporten components IIABC; Provisional
Probab=27.85 E-value=44 Score=14.24 Aligned_cols=106 Identities=16% Similarity=0.182 Sum_probs=54.9
Q ss_pred CCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH----------------------------HHCCCCCC
Q ss_conf 61021699999999999999999999999999999999987642----------------------------10512115
Q gi|254780944|r 4 KSFHTSISAKVRNNFFAGFIICAPIAITIWLSLSLIHWFDGFIV----------------------------PYIPMQYN 55 (228)
Q Consensus 4 ~~~~~~l~~~l~~~Fl~GLlvllPi~iTi~i~~~l~~~~~~~~~----------------------------p~i~~~~~ 55 (228)
...+++..+++++.+++|.=..+|+++.=-++.-+-..+++..+ |++.....
T Consensus 276 ~~~~~~~~~~iyk~lmtGVS~MlPfVVaGGiliAi~~l~~~~~g~~~~~~~~~~~~~~~~~igg~~~~~lmvPvla~yIA 355 (638)
T PRK09765 276 TQPVKSVKTELKQALLSGISFAVPLIVAGGTVLAVAVLLSQIFGLQDLFNEENSWLWMYRKLGGGLLGILMVPVLAAYTA 355 (638)
T ss_pred CCCCCCHHHHHHHHHHHCHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf 44433056899999983521546299985899999998602457653345666499999998789999999999999999
Q ss_pred HH-HHCCCHHH-----------HHHHHHHHHHHHHHHHHHHHHHHH--HHHHHHHHHHH--HCCHHHHHHH
Q ss_conf 01-10110235-----------899999999999987774337889--99999999995--3323889999
Q gi|254780944|r 56 PE-YYCDFSIP-----------GFGLLVVIVGINIVGFFGRNLLGR--FVFFLSESILN--NTPIVRHLYK 110 (228)
Q Consensus 56 ~~-~~~~~~i~-----------glg~~~~i~~i~liG~l~~~~~g~--~~~~~~e~~l~--rIP~v~~IY~ 110 (228)
.. ..-+-..| +.||+-.++.=|+.||++... .+ ++-++++.+.. -+|++.++-.
T Consensus 356 ySIadrpglapGfi~G~~A~~~~aGFlGaii~GflaGy~v~~l-kk~iklp~~l~gl~piliiPl~~~li~ 425 (638)
T PRK09765 356 YSLADKPALAPGFAAGLAANMIGSGFLGAVVGGLIAGYLMRWV-KNHLRLSSKFNGFLTFYLYPVLGTLGA 425 (638)
T ss_pred HHHCCCCCCHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHH-HHHCCCCHHHHCCCCEEEHHHHHHHHH
T ss_conf 9862874107899999997325640789999999999999999-985778776754477886168999999
No 44
>pfam06711 DUF1198 Protein of unknown function (DUF1198). This family consists of several bacterial proteins of around 150 residues in length which are specific to Escherichia coli, Salmonella species and Yersinia pestis. The function of this family is unknown.
Probab=27.78 E-value=39 Score=14.53 Aligned_cols=36 Identities=22% Similarity=0.184 Sum_probs=26.9
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCH
Q ss_conf 999999999987774337889999999999953323
Q gi|254780944|r 69 LLVVIVGINIVGFFGRNLLGRFVFFLSESILNNTPI 104 (228)
Q Consensus 69 ~~~~i~~i~liG~l~~~~~g~~~~~~~e~~l~rIP~ 104 (228)
++.+++.+|++|+=+-+.=.|+..+.+-..++--|+
T Consensus 5 ilAtLvVVFivGfRvLTSdtRrAi~rLs~rL~I~pv 40 (148)
T pfam06711 5 ILATLIVVFIVGFRVLTSDTRRAIDRLSERLKIKPV 40 (148)
T ss_pred HHHHHHHHHHEEEEEECCCHHHHHHHHHHHHCCCCE
T ss_conf 886889974202344346528999999987299835
No 45
>pfam02762 Cbl_N3 CBL proto-oncogene N-terminus, SH2-like domain. Cbl is an adaptor protein that binds EGF receptors (or other tyrosine kinases) and SH3 domains, functioning as a negative regulator of many signaling pathways. The N-terminal domain is evolutionarily conserved, and is known to bind to phosphorylated tyrosine residues. The so called N-terminal domain is actually 3 structural domains, of which this is the C-terminal SH2 domain.
Probab=27.34 E-value=38 Score=14.65 Aligned_cols=39 Identities=15% Similarity=0.445 Sum_probs=23.4
Q ss_pred HHHHHHHHHHHHCCCCCCCCEEEEEECCCCCEEEEEEEECCC
Q ss_conf 999999999973177553310399984887579999970687
Q gi|254780944|r 109 YKSTKQIIRTLLKEDSTSFKNACLVEYPSAGFWSLCFLTTEV 150 (228)
Q Consensus 109 Y~sikqi~~~~~~~~~~~f~~vVlVe~P~~g~~~iGFvT~~~ 150 (228)
|.-+|.-.+.+.. +-.++ +--..--|-|-|+||+||.|.
T Consensus 11 YDevk~rL~~~~~-kpGSY--iFRlSCTrlGQWAIgyVt~dg 49 (86)
T pfam02762 11 YDEVKARLQKFIH-KPGSY--IFRLSCTRLGQWAIGYVTADG 49 (86)
T ss_pred HHHHHHHHHHHHC-CCCCE--EEEEECCCCCCEEEEEECCCC
T ss_conf 9999999999745-99736--997523633525789985788
No 46
>PRK03776 phosphoglycerol transferase I; Provisional
Probab=27.16 E-value=45 Score=14.17 Aligned_cols=66 Identities=14% Similarity=0.339 Sum_probs=32.0
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHH--H----HHHHCCCCCCHHHHCCCHHHHHHHHHHHHHHHH-HHHHH
Q ss_conf 9999999999999999999999999987--6----421051211501101102358999999999999-87774
Q gi|254780944|r 17 NFFAGFIICAPIAITIWLSLSLIHWFDG--F----IVPYIPMQYNPEYYCDFSIPGFGLLVVIVGINI-VGFFG 83 (228)
Q Consensus 17 ~Fl~GLlvllPi~iTi~i~~~l~~~~~~--~----~~p~i~~~~~~~~~~~~~i~glg~~~~i~~i~l-iG~l~ 83 (228)
+.+.-++++|-+.+-+.+++++-+.+.| + +-.+. ..+.-..+..+.+|++++++.+.++|. ..+..
T Consensus 26 ~w~~~~l~~lg~~iiln~~l~asnYfTGdGINDAVifhLt-~~l~Gagv~~YIlP~I~~i~~l~lvF~~l~~~L 98 (762)
T PRK03776 26 WWFAATLTVLGLFVVLNITLFASDYFTGDGINDAVLYTLT-NSLTGAGVSKYILPGIGIVLALTAVFGALGWIL 98 (762)
T ss_pred CHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCEEEEEEE-CCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHE
T ss_conf 1699999999999999999999751267887712899996-267654501101688999999999999988740
No 47
>PRK11901 hypothetical protein; Reviewed
Probab=27.07 E-value=45 Score=14.16 Aligned_cols=21 Identities=29% Similarity=0.471 Sum_probs=15.0
Q ss_pred HHHHHHHHHHHHHHHHHHHHH
Q ss_conf 358999999999999877743
Q gi|254780944|r 64 IPGFGLLVVIVGINIVGFFGR 84 (228)
Q Consensus 64 i~glg~~~~i~~i~liG~l~~ 84 (228)
+-|+|+++++++|..||-..+
T Consensus 39 MiGiGILVLLLLIIgIgSALK 59 (329)
T PRK11901 39 MIGIGILVLLLLIIAIGSALK 59 (329)
T ss_pred HHHHHHHHHHHHHHHHHHHHC
T ss_conf 999999999999998656432
No 48
>TIGR02823 oxido_YhdH putative quinone oxidoreductase, YhdH/YhfP family; InterPro: IPR014188 This entry represents a subfamily of the alcohol dehydrogenase, a superfamily in which some members are zinc-binding medium-chain alcohol dehydrogenases while others are quinone oxidoreductases with no bound zinc. This entry includes YhdH from Escherichia coli and YhfP from Bacillus subtilis both of which bind NADPH or NAD, but not zinc. Both proteins have been studied crystallographically for insight into function. .
Probab=26.55 E-value=40 Score=14.50 Aligned_cols=62 Identities=18% Similarity=0.191 Sum_probs=39.0
Q ss_pred EECCC-CCEEEEEEEECCCHHHHHHHHCCCCCCCEEEEE---EECCCCCCCCE--EEEEEHHHEEEC--CCCHHHHHHH
Q ss_conf 98488-757999997068715655530246777389999---70798532688--999877762477--9999999999
Q gi|254780944|r 133 VEYPS-AGFWSLCFLTTEVKGEIKEKFSNIGCEDMVTVF---IPPTPLPTAGM--LVFVPRNKVIML--KMSAEDSAKM 203 (228)
Q Consensus 133 Ve~P~-~g~~~iGFvT~~~~~~~~~~~~~~~~~~~v~Vf---iPtsPnPtsG~--~~~vp~~~v~~~--dmsveeA~k~ 203 (228)
=+||. +|+=.-|-|-....+ .+..+|.|-|. +=. +-++|| ..-||-|++.++ +||..|||-+
T Consensus 56 R~yP~~PGID~aG~Vv~S~dp-------~F~~GD~VivTGyglG~--~H~GGysqyaRVp~dWlVpLP~glsl~eAM~~ 125 (330)
T TIGR02823 56 RSYPMIPGIDLAGTVVSSEDP-------RFRPGDEVIVTGYGLGV--SHDGGYSQYARVPADWLVPLPEGLSLREAMAL 125 (330)
T ss_pred EECCCCCCCCCEEEEEECCCC-------CCCCCCEEEEEEECCCC--CCCCCCEEEEEECHHHEECCCCCCCHHHHHHH
T ss_conf 877876881754689844887-------75788718997402456--51576223567332310158898898899986
No 49
>TIGR00630 uvra excinuclease ABC, A subunit; InterPro: IPR004602 ABC transporters belong to the ATP-Binding Cassette (ABC) superfamily, which uses the hydrolysis of ATP to energize diverse biological systems. ABC transporters are minimally constituted of two conserved regions: a highly conserved ATP binding cassette (ABC) and a less conserved transmembrane domain (TMD). These regions can be found on the same protein or on two different ones. Most ABC transporters function as a dimer and therefore are constituted of four domains, two ABC modules and two TMDs. ABC transporters are involved in the export or import of a wide variety of substrates ranging from small ions to macromolecules. The major function of ABC import systems is to provide essential nutrients to bacteria. They are found only in prokaryotes and their four constitutive domains are usually encoded by independent polypeptides (two ABC proteins and two TMD proteins). Prokaryotic importers require additional extracytoplasmic binding proteins (one or more per systems) for function. In contrast, export systems are involved in the extrusion of noxious substances, the export of extracellular toxins and the targeting of membrane components. They are found in all living organisms and in general the TMD is fused to the ABC module in a variety of combinations. Some eukaryotic exporters encode the four domains on the same polypeptide chain . The ABC module (approximately two hundred amino acid residues) is known to bind and hydrolyze ATP, thereby coupling transport to ATP hydrolysis in a large number of biological processes. The cassette is duplicated in several subfamilies. Its primary sequence is highly conserved, displaying a typical phosphate-binding loop: Walker A, and a magnesium binding site: Walker B. Besides these two regions, three other conserved motifs are present in the ABC cassette: the switch region which contains a histidine loop, postulated to polarize the attaching water molecule for hydrolysis, the signature conserved motif (LSGGQ) specific to the ABC transporter, and the Q-motif (between Walker A and the signature), which interacts with the gamma phosphate through a water bond. The Walker A, Walker B, Q-loop and switch region form the nucleotide binding site , , . The 3D structure of a monomeric ABC module adopts a stubby L-shape with two distinct arms. ArmI (mainly beta-strand) contains Walker A and Walker B. The important residues for ATP hydrolysis and/or binding are located in the P-loop. The ATP-binding pocket is located at the extremity of armI. The perpendicular armII contains mostly the alpha helical subdomain with the signature motif. It only seems to be required for structural integrity of the ABC module. ArmII is in direct contact with the TMD. The hinge between armI and armII contains both the histidine loop and the Q-loop, making contact with the gamma phosphate of the ATP molecule. ATP hydrolysis leads to a conformational change that could facilitate ADP release. In the dimer the two ABC cassettes contact each other through hydrophobic interactions at the antiparallel beta-sheet of armI by a two-fold axis , , , , , . Proteins known to belong to this family are classified in several functional subfamilies depending on the substrate used (for further information see http://www.tcdb.org/tcdb/index.php?tc=3.A.1). During the process of Escherichia coli nucleotide excision repair, DNA damage recognition and processing are achieved by the action of the uvrA, uvrB, and uvrC gene products . The UvrC protein contain 4 conserved regions: a central region which interact with UvrB (Uvr domain), a Helix hairpin Helix (HhH) domain important for 5 prime incision of damage DNA and the homology regions 1 and 2 of unknown function. UvrC homology region 2 is specific for UvrC proteins, whereas UvrC homology region 1 is also shared by few other nucleases.; GO: 0009381 excinuclease ABC activity, 0006289 nucleotide-excision repair, 0009380 excinuclease repair complex.
Probab=26.37 E-value=34 Score=14.92 Aligned_cols=16 Identities=19% Similarity=0.437 Sum_probs=8.0
Q ss_pred HHEEE-CCCCHHHHHHH
Q ss_conf 76247-79999999999
Q gi|254780944|r 188 NKVIM-LKMSAEDSAKM 203 (228)
Q Consensus 188 ~~v~~-~dmsveeA~k~ 203 (228)
..|.+ ||||||||-.|
T Consensus 814 K~IadVLdMtveEA~eF 830 (956)
T TIGR00630 814 KNIADVLDMTVEEAREF 830 (956)
T ss_pred CEEHHHHCCCHHHHHHH
T ss_conf 71123315866899887
No 50
>pfam06695 Sm_multidrug_ex Putative small multi-drug export protein. This family contains a small number of putative small multi-drug export proteins.
Probab=24.07 E-value=51 Score=13.81 Aligned_cols=53 Identities=13% Similarity=0.236 Sum_probs=27.8
Q ss_pred HHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHCCCCCCCCE-----EEEEECCCCCEEE
Q ss_conf 99999999999533238899999999999973177553310-----3999848875799
Q gi|254780944|r 89 RFVFFLSESILNNTPIVRHLYKSTKQIIRTLLKEDSTSFKN-----ACLVEYPSAGFWS 142 (228)
Q Consensus 89 ~~~~~~~e~~l~rIP~v~~IY~sikqi~~~~~~~~~~~f~~-----vVlVe~P~~g~~~ 142 (228)
-.++++..+++.|.|..+.+|.-..+=.+.- +++=+++.- -|.+..|..|.|+
T Consensus 35 l~~~~~i~~~~~~~~~~~k~~~~~~~k~~k~-~~~iekyg~~gL~lFVaIPLPgTGawT 92 (121)
T pfam06695 35 LLFLRKVFKWLKRTKLFKKIYDWLEERARKG-SGKVEKYGFLGLILFVAIPLPGTGAWT 92 (121)
T ss_pred HHHHHHHHHHHHHCHHHHHHHHHHHHHHHHH-HHHHHHHHHHHHHHHHHCCCCCCCHHH
T ss_conf 9999999999985715899999999999854-078999999999999957888750899
No 51
>TIGR00757 RNaseEG ribonuclease, Rne/Rng family; InterPro: IPR004659 The eubacterial degradosome is a large, multiprotein, multienzyme complex involved in RNA processing and degradation in Escherichia coli and other proteobacteria . The components of the RNA degradosome in E. coli (EBI-1169250 from INTACT) are: Ribonuclease E (Rne), P21513 from SWISSPROT, IPR004659 from INTERPRO ATP-dependent RNA helicase (RhlB), P0A8J8 from SWISSPROT, IPR000629 from INTERPRO Polynucleotide phosphorylase (Pnp), , IPR012162 from INTERPRO Enolase (Eno), P0A6P9 from SWISSPROT, IPR000941 from INTERPRO Associated components: The chaperone protein DnaK (,IPR012725 from INTERPRO) associates to abnormal complexes in which the canonical components RhlB and PNPase are not present or present in limiting amount and could be involved in repairing such incorrectly assembled degradosomes. Polyphosphate kinase (Ppk), P0A7B1 from SWISSPROT, IPR003414 from INTERPRO appears to maintain an appropriate microenvironment, removing inhibitory polyphosphate and NDPs and regenerating ATP. Subunit composition of the E. coli degradosome(see: http://biocyc.org/ECOLI/NEW-IMAGE?type=POLYPEPTIDE&object=CPLX0-2381): [(Ppk)4][(Rne)4][(RhlB)2][(Pnp)3][(Eno)2] In vitro a "minimal" degradosome composed of only RNase E, PNPase and RhlB degrades malEF REP RNA in an ATP-dependent manner in vitro, with activity equivalent to purified whole degradosomes. RNase E enzymatic function is dispensible, whereas PNPase must be catalytically active and incorporated into the degradosome for degradation to occur . RNase E provides the organizational structure for the degradosome . It is tethered to the cytoplasmic membrane via its amino-terminus and its carboxy-terminal half, which is largly unstructured and poorly conserved, cooridnates the binding of PNPase, RhlB and enolase. The loss of this portion of the protein prevents degradation of a number of degradosome substrates, including the ptsG and mukB mRNAs and RNA I , , . Ribonuclease E 3.1.4 from EC is responsible for maturing 5S rRNA from its precursors from all the rRNA genes. It also cleaves RNA I, a molecule that controls the replication of ColE1 plasmid DNA. It is the major endoribonuclease participating in mRNA turnover in Escherichia coli, and initiates decay of RNAs by cutting them internally near their 5'-end. It is able to remove poly A tails by an endonucleolytic process. Ribonuclease G is smaller than RNase E lacking the C-terminal region. It is involved in processing of the 5' end of 16S rRNA, and may be involved in chromosome segregation and cell division too. RNase E is a major subunit the eubacterial degradosome. It is a large, multiprotein, multienzyme complex involved in RNA processing and degradation in Escherichia coli and other proteobacteria . It consists of the RNA degradation enzymes RNase E (Rne) and PNPase (Pnp), as well as the ATP-dependent RNA helicase (RhlB) and the metabolic enzyme enolase (Eno) , , .; GO: 0004540 ribonuclease activity, 0006396 RNA processing, 0005737 cytoplasm.
Probab=24.00 E-value=52 Score=13.81 Aligned_cols=11 Identities=27% Similarity=0.410 Sum_probs=5.3
Q ss_pred CEEEEEEECCC
Q ss_conf 38999970798
Q gi|254780944|r 165 DMVTVFIPPTP 175 (228)
Q Consensus 165 ~~v~VfiPtsP 175 (228)
+.|.||+|.+|
T Consensus 153 GrYlVlmP~~~ 163 (464)
T TIGR00757 153 GRYLVLMPNTS 163 (464)
T ss_pred CCEEEECCCCC
T ss_conf 21078557889
No 52
>PRK10892 D-arabinose 5-phosphate isomerase; Provisional
Probab=23.86 E-value=52 Score=13.79 Aligned_cols=101 Identities=16% Similarity=0.236 Sum_probs=59.2
Q ss_pred HHHHHHHHHHHHHHH---HCCHHHHHHHHHHHHHHHHHCCCCCCCCEEEEEECCCCCEEEEEEEECCCHHHHHHHHCCCC
Q ss_conf 788999999999995---33238899999999999973177553310399984887579999970687156555302467
Q gi|254780944|r 86 LLGRFVFFLSESILN---NTPIVRHLYKSTKQIIRTLLKEDSTSFKNACLVEYPSAGFWSLCFLTTEVKGEIKEKFSNIG 162 (228)
Q Consensus 86 ~~g~~~~~~~e~~l~---rIP~v~~IY~sikqi~~~~~~~~~~~f~~vVlVe~P~~g~~~iGFvT~~~~~~~~~~~~~~~ 162 (228)
.+||+++-..++++. ++|+++. ..+++|.+..++. +.+.-++.++ +.-...|.+|. +++...+..
T Consensus 195 ~LGk~Ll~~V~dlM~~~~~lP~v~~-~~~l~dai~~mt~---k~lG~v~Vvd---~~gkL~GIiTD---GDLRR~l~~-- 262 (326)
T PRK10892 195 ALGRKLLLRVSDIMHTGDEIPHVKK-TASLRDALLEITR---KNLGMTVICD---DNMMIEGIFTD---GDLRRVFDM-- 262 (326)
T ss_pred HHHHHHHHHHHHHHHCCCCCCCCCC-CCHHHHHHHHHCC---CCCEEEEEEC---CCCCEEEEEEC---HHHHHHHHH--
T ss_conf 7778888789998513765885377-6029999998745---8934999985---89968999862---689999870--
Q ss_pred CCCEEEEE--EECCCCCCCCEEEEEEHHHEEECCCCHHHHHHHHHHCCC
Q ss_conf 77389999--707985326889998777624779999999999870143
Q gi|254780944|r 163 CEDMVTVF--IPPTPLPTAGMLVFVPRNKVIMLKMSAEDSAKMLISGGL 209 (228)
Q Consensus 163 ~~~~v~Vf--iPtsPnPtsG~~~~vp~~~v~~~dmsveeA~k~iiS~Gv 209 (228)
+.+....- ==+++||.+ ..-|+.+.||+++.=.--+
T Consensus 263 ~~~i~~~~~~diMT~nP~t-----------I~~d~la~eAL~iMe~~kI 300 (326)
T PRK10892 263 GVDLRQLSIADVMTPGGIR-----------VRPGILAVDALNLMQSRHI 300 (326)
T ss_pred CCCCCCCCHHHHHCCCCCE-----------ECCCCCHHHHHHHHHHCCC
T ss_conf 6883128799971899967-----------8998869999999986398
No 53
>TIGR01937 nqrB NADH:ubiquinone oxidoreductase, Na(+)-translocating, B subunit; InterPro: IPR010966 This entry represents the NqrB subunit of the six-protein (NqrA to NqrF), membrane-associated Na(+)-pumping NADH-quinone reductase of a number of marine and pathogenic Gram-negative bacteria . The Nqr complex catalyses the reduction of ubiquinone-1 to ubiquinol by two successive reactions, coupled with the transport of sodium ions from the cytoplasm to the periplasm. NqrA to NqrE are probably involved in the second step, the conversion of ubisemiquinone to ubiquinol. Both the NqrB and NqrC subunits contain a FMN cofactor that is covalently attached by a phosphate group to a threonine residue .; GO: 0010181 FMN binding, 0016655 oxidoreductase activity acting on NADH or NADPH quinone or similar compound as acceptor, 0006118 electron transport, 0009276 1-2nm peptidoglycan-based cell wall, 0016021 integral to membrane.
Probab=22.61 E-value=55 Score=13.64 Aligned_cols=32 Identities=9% Similarity=0.124 Sum_probs=25.4
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf 99999999999999999999999999999876
Q gi|254780944|r 14 VRNNFFAGFIICAPIAITIWLSLSLIHWFDGF 45 (228)
Q Consensus 14 l~~~Fl~GLlvllPi~iTi~i~~~l~~~~~~~ 45 (228)
+...++.|+...||+.++.|++--..+.+-..
T Consensus 115 ~~~~l~~G~~~fLP~l~~~y~VG~~~Evlfa~ 146 (508)
T TIGR01937 115 IGSKLLLGAKIFLPLLLVSYAVGGTWEVLFAV 146 (508)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf 35689964899868999999898789888876
No 54
>TIGR02188 Ac_CoA_lig_AcsA acetate--CoA ligase; InterPro: IPR011904 Acetyl-CoA synthetase (also known as acetate-CoA ligase and acetyl-activating enzyme) is a ubiquitous enzyme, found in both prokaryotes and eukaryotes, which catalyses the formation of acetyl-CoA from acetate, coenzyme A (CoA) and ATP as shown below : ATP + acetate + CoA = AMP + diphosphate + acetyl-CoA The activity of this enzyme is crucial for maintaining the required levels of acetyl-CoA, a key intermediate in many important biosynthetic and catabolic processes. It is especially important in eukayotic species as it is the only route for the activation of acetate to acetyl-CoA in these organisms (some prokaryotic species can also activate acetate by either acetate kinase/phosphotransacetylase or by ADP-forming acetyl-CoA synthase). Eukaryotes typically have two isoforms of acetyl-CoA synthase, a cytosolic form involved in biosynthetic processes and a mitochondrial form primarily involved in energy generation. The crystal structures of a eukaryotic (Q01574 from SWISSPROT, from yeast) and bacterial (Q8ZKF6 from SWISSPROT, from Salmonella) form of this enzyme have been determined , . The yeast enzyme is trimeric, while the bacterial enzyme is monomeric. The trimeric state of the yeast protein may be unique to this organism however, as the residues involved in the trimer interface are poorly conserved in other sequences. Despite differences in the oligomeric state of the two enzyme, the structures of the monomers are almost identical. A large N-terminal domain (~500 residues) containing two parallel beta sheets is followed by a small (~110 residues) C-terminal domain containing a three-stranded beta sheet with helices. The active site occurs at the domain interface, with its contents determining the orientation of the C-terminal domain.; GO: 0003987 acetate-CoA ligase activity, 0016208 AMP binding.
Probab=21.58 E-value=51 Score=13.87 Aligned_cols=60 Identities=18% Similarity=0.288 Sum_probs=32.9
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHH-HHHHHHHH-----------------HCCHHHHHHHHHHHHHHHHHCCCCC---
Q ss_conf 99999999999987774337889999-99999995-----------------3323889999999999997317755---
Q gi|254780944|r 67 FGLLVVIVGINIVGFFGRNLLGRFVF-FLSESILN-----------------NTPIVRHLYKSTKQIIRTLLKEDST--- 125 (228)
Q Consensus 67 lg~~~~i~~i~liG~l~~~~~g~~~~-~~~e~~l~-----------------rIP~v~~IY~sikqi~~~~~~~~~~--- 125 (228)
-..++++++|.-+|.+-+-+||-.-= .+-||+.. .||| |+.+|--.....+
T Consensus 131 PEa~~AMLACaRIGA~HSVVFgGFSa~aL~~Ri~Da~ak~VITAD~g~RgGK~~~L--------K~~VD~AL~~~~~~~~ 202 (643)
T TIGR02188 131 PEAAIAMLACARIGAIHSVVFGGFSAEALADRINDAGAKLVITADEGLRGGKVIPL--------KAIVDEALEKCPDTCP 202 (643)
T ss_pred HHHHHHHHHHHHCCCEEEEECCCCCHHHHHHHHHCCCCCEEEECCCCCCCCCCCCH--------HHHHHHHHHHCCCCCC
T ss_conf 89999998864368526787257747899887532777589943774058864303--------6899999960786745
Q ss_pred CCCEEEEEE
Q ss_conf 331039998
Q gi|254780944|r 126 SFKNACLVE 134 (228)
Q Consensus 126 ~f~~vVlVe 134 (228)
+-++|-.++
T Consensus 203 ~V~~VlV~~ 211 (643)
T TIGR02188 203 SVEKVLVVR 211 (643)
T ss_pred CCCEEEEEE
T ss_conf 300678998
No 55
>PRK00042 tpiA triosephosphate isomerase; Provisional
Probab=20.83 E-value=53 Score=13.74 Aligned_cols=37 Identities=19% Similarity=0.372 Sum_probs=24.2
Q ss_pred HHHHHHHHHHCCCCCCCCEEEEEECCCCCEEEEEEEECCCHH
Q ss_conf 999999997317755331039998488757999997068715
Q gi|254780944|r 111 STKQIIRTLLKEDSTSFKNACLVEYPSAGFWSLCFLTTEVKG 152 (228)
Q Consensus 111 sikqi~~~~~~~~~~~f~~vVlVe~P~~g~~~iGFvT~~~~~ 152 (228)
-.+|+-+.+.+-++..++++++ -| +-+|+|| |+..+.
T Consensus 143 l~~Ql~~~l~~~~~~~~~~iiI-AY--EPvWAIG--TG~~as 179 (251)
T PRK00042 143 VARQLEAALAGLGAEDFANLVI-AY--EPVWAIG--TGKTAT 179 (251)
T ss_pred HHHHHHHHHHCCCHHHCCCEEE-EE--CCHHHCC--CCCCCC
T ss_conf 9999999996689877053599-96--7577507--999999
No 56
>cd02435 CCC1 CCC1. CCC1: This domain is present in the CCC1, an iron and manganese transporter of Saccharomyces cerevisiae. CCC1 is a transmembrane protein that is located in the vacuole and transfers the iron and manganese ions from the cytosol to the vacuole. This domain may be unique to certain fungi and plants.
Probab=20.19 E-value=62 Score=13.33 Aligned_cols=41 Identities=15% Similarity=0.374 Sum_probs=22.9
Q ss_pred HHHCCCCCCHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf 21051211501101102358999999999999877743378899
Q gi|254780944|r 47 VPYIPMQYNPEYYCDFSIPGFGLLVVIVGINIVGFFGRNLLGRF 90 (228)
Q Consensus 47 ~p~i~~~~~~~~~~~~~i~glg~~~~i~~i~liG~l~~~~~g~~ 90 (228)
-|++|..+.+... ......++++.+.++++|++...+.|++
T Consensus 170 iPLlpy~~~~~~~---~al~~S~~~t~~aL~~~G~~k~~~tg~~ 210 (241)
T cd02435 170 IPLLPYFFVSTVG---EALLLSVIVTLVALFVFGYVKTWFTGGW 210 (241)
T ss_pred HHHHHHHHCCCCH---HHHHHHHHHHHHHHHHHHHHHHHHCCCC
T ss_conf 8878999705503---8999999999999999999987201678
No 57
>PRK11026 ftsX cell division protein FtsX; Provisional
Probab=20.06 E-value=62 Score=13.31 Aligned_cols=11 Identities=18% Similarity=0.244 Sum_probs=4.4
Q ss_pred EEEEEEEECCC
Q ss_conf 79999970687
Q gi|254780944|r 140 FWSLCFLTTEV 150 (228)
Q Consensus 140 ~~~iGFvT~~~ 150 (228)
+..+-|+++|.
T Consensus 94 V~~v~~vskee 104 (309)
T PRK11026 94 VEKVNYLSREE 104 (309)
T ss_pred CCEEEEECHHH
T ss_conf 43798867999
No 58
>COG0841 AcrB Cation/multidrug efflux pump [Defense mechanisms]
Probab=20.00 E-value=62 Score=13.31 Aligned_cols=35 Identities=14% Similarity=-0.060 Sum_probs=13.2
Q ss_pred CCEEEEEEEC--CCCCCCCEEEEEEHHHEEECCCCHHH
Q ss_conf 7389999707--98532688999877762477999999
Q gi|254780944|r 164 EDMVTVFIPP--TPLPTAGMLVFVPRNKVIMLKMSAED 199 (228)
Q Consensus 164 ~~~v~VfiPt--sPnPtsG~~~~vp~~~v~~~dmsvee 199 (228)
-+.+.-++-. ++| .+|..+..-+++-.+.+-+.++
T Consensus 589 v~~v~~~~G~g~~~~-~~~~~~~~Lk~~~er~~~~~~~ 625 (1009)
T COG0841 589 VESVFTVVGFGSGQN-NAGRAFVSLKPWSERKENSAQA 625 (1009)
T ss_pred EEEEEEEECCCCCCC-CCCEEEEECCCHHHCCCCCHHH
T ss_conf 169999845677777-7615999448735355655789
Done!