Query 024694
Match_columns 264
No_of_seqs 139 out of 625
Neff 5.4
Searched_HMMs 46136
Date Fri Mar 29 06:39:03 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/024694.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/024694hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 COG2928 Uncharacterized conser 100.0 1.6E-54 3.4E-59 383.1 20.0 195 55-250 3-206 (222)
2 PF04367 DUF502: Protein of un 100.0 3.2E-30 6.8E-35 207.1 12.3 106 106-212 1-108 (108)
3 TIGR02120 GspF general secreti 87.5 7 0.00015 37.5 11.1 22 128-149 243-264 (399)
4 cd01277 HINT_subgroup HINT (hi 87.2 1.2 2.6E-05 34.0 4.7 42 196-237 19-61 (103)
5 PRK15350 type III secretion sy 87.0 13 0.00028 29.2 10.5 79 56-141 8-86 (88)
6 PRK05700 fliQ flagellar biosyn 85.7 16 0.00034 28.8 10.4 80 55-141 7-86 (89)
7 TIGR01402 fliQ flagellar biosy 84.9 17 0.00037 28.5 10.2 79 56-141 8-86 (88)
8 PRK06010 fliQ flagellar biosyn 84.1 19 0.0004 28.3 10.6 80 55-141 7-86 (88)
9 cd01275 FHIT FHIT (fragile his 82.8 2.4 5.1E-05 34.1 4.7 44 196-239 19-63 (126)
10 PRK12781 fliQ flagellar biosyn 81.8 23 0.0005 27.8 10.6 80 55-141 7-86 (88)
11 cd00468 HIT_like HIT family: H 81.8 2.4 5.1E-05 31.1 4.0 42 196-237 3-45 (86)
12 COG1459 PulF Type II secretory 81.5 8.3 0.00018 37.8 8.7 23 127-149 239-261 (397)
13 COG1684 FliR Flagellar biosynt 80.6 22 0.00047 33.1 10.7 45 46-90 163-207 (258)
14 TIGR01403 fliQ_rel_III type II 80.5 24 0.00053 27.2 10.0 77 57-140 5-81 (81)
15 PRK10573 type IV pilin biogene 78.3 22 0.00048 34.1 10.4 18 130-147 244-261 (399)
16 PF01230 HIT: HIT domain; Int 76.8 2.8 6E-05 32.1 3.1 41 196-236 11-52 (98)
17 PRK09824 PTS system beta-gluco 73.8 27 0.00058 36.4 10.2 69 69-140 219-288 (627)
18 cd01276 PKCI_related Protein K 73.7 4 8.7E-05 31.4 3.3 34 196-229 19-53 (104)
19 PRK12772 bifunctional flagella 73.1 36 0.00078 35.3 10.9 40 51-90 165-204 (609)
20 PRK11007 PTS system trehalose( 72.0 27 0.00059 35.1 9.5 86 68-156 231-319 (473)
21 PF01311 Bac_export_1: Bacteri 71.0 59 0.0013 29.6 10.8 43 48-90 163-205 (249)
22 PRK09796 PTS system cellobiose 70.5 34 0.00075 34.4 9.8 85 68-155 220-306 (472)
23 PRK15333 type III secretion sy 70.4 50 0.0011 25.8 9.7 79 56-141 6-84 (86)
24 COG1987 FliQ Flagellar biosynt 69.0 55 0.0012 25.8 10.4 76 59-141 11-86 (89)
25 PRK09765 PTS system 2-O-a-mann 68.5 22 0.00047 37.0 8.1 70 69-140 381-456 (631)
26 cd01278 aprataxin_related apra 68.3 9.8 0.00021 29.3 4.4 36 196-231 21-57 (104)
27 COG4794 EscS Type III secretor 67.9 59 0.0013 25.7 9.5 80 57-143 9-88 (89)
28 PRK09586 murP PTS system N-ace 66.8 44 0.00095 33.7 9.7 82 68-153 230-312 (476)
29 TIGR01992 PTS-IIBC-Tre PTS sys 66.5 44 0.00094 33.4 9.6 85 69-156 233-319 (462)
30 TIGR01996 PTS-II-BC-sucr PTS s 65.5 56 0.0012 32.6 10.1 85 69-156 230-316 (461)
31 TIGR02002 PTS-II-BC-glcB PTS s 64.8 37 0.00081 34.3 8.8 87 69-156 135-225 (502)
32 PF08566 Pam17: Mitochondrial 63.0 76 0.0016 28.0 9.2 67 66-134 42-108 (173)
33 PRK15083 PTS system mannitol-s 62.7 33 0.00072 35.6 8.2 83 68-153 101-190 (639)
34 PRK15071 lipopolysaccharide AB 59.1 43 0.00092 31.5 7.7 39 51-89 2-40 (356)
35 PRK15349 type III secretion sy 58.7 1.4E+02 0.003 27.4 10.8 41 50-90 169-209 (259)
36 COG3768 Predicted membrane pro 58.4 1E+02 0.0022 29.9 9.9 34 53-86 58-91 (350)
37 PRK10687 purine nucleoside pho 57.9 14 0.0003 30.0 3.6 36 196-231 22-58 (119)
38 TIGR00851 mtlA PTS system, man 57.1 92 0.002 29.9 9.6 83 68-153 93-182 (338)
39 PRK11404 putative PTS system 53.4 49 0.0011 33.4 7.3 67 68-137 228-300 (482)
40 COG3366 Uncharacterized protei 53.1 1.5E+02 0.0034 28.4 10.2 79 37-118 156-236 (311)
41 TIGR02004 PTS-IIBC-malX PTS sy 52.3 92 0.002 31.7 9.2 89 69-159 139-231 (517)
42 PF02674 Colicin_V: Colicin V 51.2 1.3E+02 0.0028 24.2 8.5 81 59-139 18-103 (146)
43 PF05552 TM_helix: Conserved T 51.2 41 0.00088 23.3 4.7 25 109-133 20-44 (53)
44 TIGR01400 fliR flagellar biosy 50.4 2E+02 0.0043 26.2 10.6 41 50-90 158-198 (245)
45 PF06596 PsbX: Photosystem II 50.0 38 0.00083 22.8 4.1 26 54-79 5-30 (39)
46 TIGR01427 PTS_IIC_fructo PTS s 49.8 81 0.0018 30.4 8.0 72 68-140 112-185 (346)
47 PF02355 SecD_SecF: Protein ex 49.6 1.5E+02 0.0033 25.9 9.1 70 44-133 118-187 (189)
48 PRK05701 fliR flagellar biosyn 48.2 2.1E+02 0.0046 25.9 10.8 40 51-90 161-200 (242)
49 PF01313 Bac_export_3: Bacteri 47.8 1.2E+02 0.0027 23.0 9.4 71 56-133 5-75 (76)
50 TIGR01401 fliR_like_III type I 47.8 2.2E+02 0.0049 26.0 10.6 42 49-90 164-205 (253)
51 COG2177 FtsX Cell division pro 47.4 2.3E+02 0.005 26.8 10.5 59 66-124 227-286 (297)
52 COG0537 Hit Diadenosine tetrap 46.9 35 0.00076 28.3 4.4 43 196-238 20-63 (138)
53 PRK10478 putative PTS system f 45.5 1.1E+02 0.0023 30.0 8.0 94 50-145 4-144 (359)
54 TIGR01995 PTS-II-ABC-beta PTS 45.4 1.6E+02 0.0035 30.5 9.9 80 69-151 211-292 (610)
55 PRK10110 bifunctional PTS syst 43.0 1.6E+02 0.0035 30.1 9.2 88 69-158 148-239 (530)
56 TIGR00852 pts-Glc PTS system, 40.7 1.9E+02 0.0041 26.7 8.8 87 68-156 66-154 (289)
57 PF03596 Cad: Cadmium resistan 38.8 59 0.0013 28.9 4.8 82 104-205 34-118 (191)
58 PRK12780 fliR flagellar biosyn 38.4 3.1E+02 0.0068 25.0 11.1 40 51-90 169-208 (251)
59 smart00743 Agenet Tudor-like d 38.1 1.3E+02 0.0029 20.7 6.2 50 167-225 7-56 (61)
60 PRK05415 hypothetical protein; 37.7 2.6E+02 0.0056 27.2 9.3 27 59-86 67-93 (341)
61 COG3763 Uncharacterized protei 35.0 93 0.002 23.6 4.6 35 104-142 5-39 (71)
62 PF07670 Gate: Nucleoside reco 34.5 1.2E+02 0.0027 23.1 5.6 33 67-99 2-40 (109)
63 PRK14762 membrane protein; Pro 34.3 70 0.0015 19.6 3.1 16 109-124 7-22 (27)
64 PRK10845 colicin V production 34.2 2.8E+02 0.0061 23.5 8.2 24 114-137 78-101 (162)
65 TIGR01427 PTS_IIC_fructo PTS s 34.2 3.6E+02 0.0077 26.0 9.7 21 56-76 13-33 (346)
66 PF09527 ATPase_gene1: Putativ 33.7 79 0.0017 21.8 3.9 12 65-76 7-18 (55)
67 PRK00665 petG cytochrome b6-f 33.1 64 0.0014 21.4 3.0 21 104-124 7-27 (37)
68 TIGR01620 hyp_HI0043 conserved 33.1 3.1E+02 0.0068 26.0 8.9 29 57-85 12-40 (289)
69 PF01594 UPF0118: Domain of un 33.0 3.8E+02 0.0082 24.4 10.2 31 122-155 69-99 (327)
70 PRK02870 heat shock protein Ht 32.7 4.6E+02 0.0099 25.2 11.5 36 144-183 116-151 (336)
71 PF14584 DUF4446: Protein of u 32.1 3.2E+02 0.007 23.3 8.8 27 162-188 77-109 (151)
72 COG4597 BatB ABC-type amino ac 32.0 2E+02 0.0044 27.9 7.4 47 110-156 110-156 (397)
73 TIGR02003 PTS-II-BC-unk1 PTS s 31.6 3.2E+02 0.007 28.1 9.4 89 69-158 142-238 (548)
74 PRK01844 hypothetical protein; 31.3 1E+02 0.0023 23.4 4.4 30 111-143 11-40 (72)
75 TIGR02872 spore_ytvI sporulati 31.3 4.1E+02 0.0088 24.2 11.3 19 123-141 72-90 (341)
76 CHL00008 petG cytochrome b6/f 31.2 71 0.0015 21.2 3.0 21 104-124 7-27 (37)
77 PF11241 DUF3043: Protein of u 31.0 1.5E+02 0.0032 26.0 6.0 15 68-82 80-94 (170)
78 PRK10494 hypothetical protein; 30.8 3.9E+02 0.0085 24.5 9.0 64 59-134 5-68 (259)
79 TIGR01183 ntrB nitrate ABC tra 29.6 3.8E+02 0.0083 23.4 9.7 67 49-117 14-80 (202)
80 PF14257 DUF4349: Domain of un 29.5 92 0.002 28.2 4.7 9 68-76 242-250 (262)
81 PRK11365 ssuC alkanesulfonate 29.5 3E+02 0.0065 24.8 8.0 67 48-116 56-122 (263)
82 PF02762 Cbl_N3: CBL proto-onc 28.8 81 0.0018 24.5 3.4 37 146-188 11-49 (86)
83 COG3125 CyoD Heme/copper-type 28.7 3.3E+02 0.0072 22.3 8.6 22 54-75 17-38 (111)
84 PF03739 YjgP_YjgQ: Predicted 28.4 2.9E+02 0.0063 25.4 7.9 30 60-89 5-34 (354)
85 PF02529 PetG: Cytochrome B6-F 27.3 1.1E+02 0.0024 20.4 3.4 21 104-124 7-27 (37)
86 PF02419 PsbL: PsbL protein; 27.0 1.1E+02 0.0024 20.3 3.4 20 105-124 16-35 (37)
87 PF11947 DUF3464: Protein of u 26.9 4.1E+02 0.0089 22.9 9.2 61 49-123 56-116 (153)
88 PF04459 DUF512: Protein of un 26.8 1.2E+02 0.0026 27.1 4.8 83 144-235 107-191 (204)
89 PF06305 DUF1049: Protein of u 26.6 1.3E+02 0.0028 21.2 4.2 21 104-124 18-38 (68)
90 PF03672 UPF0154: Uncharacteri 25.9 98 0.0021 23.0 3.3 29 110-141 3-31 (64)
91 PF07290 DUF1449: Protein of u 25.4 3.5E+02 0.0076 24.2 7.5 20 110-129 101-120 (202)
92 PF03547 Mem_trans: Membrane t 25.4 5.6E+02 0.012 23.9 9.7 36 49-84 229-264 (385)
93 PF14018 DUF4234: Domain of un 25.2 2.7E+02 0.0059 20.2 9.0 62 69-131 9-71 (75)
94 COG1286 CvpA Uncharacterized m 25.1 4.6E+02 0.01 22.8 9.7 25 60-84 22-46 (182)
95 COG2981 CysZ Uncharacterized p 24.9 5.7E+02 0.012 23.8 9.5 25 68-92 28-56 (250)
96 PF05283 MGC-24: Multi-glycosy 24.9 61 0.0013 28.8 2.5 26 59-84 160-185 (186)
97 PRK11720 galactose-1-phosphate 24.0 1.1E+02 0.0025 29.4 4.4 65 171-235 162-255 (346)
98 PRK00523 hypothetical protein; 23.7 1.9E+02 0.0041 22.0 4.6 27 112-141 13-39 (72)
99 TIGR03279 cyano_FeS_chp putati 23.3 2.1E+02 0.0046 28.7 6.2 82 144-234 329-412 (433)
100 KOG2927 Membrane component of 23.1 1.4E+02 0.0031 29.2 4.8 20 61-80 191-210 (372)
101 TIGR00834 ae anion exchange pr 22.9 2.6E+02 0.0055 30.7 7.1 46 113-158 467-512 (900)
102 TIGR00779 cad cadmium resistan 22.8 5.1E+02 0.011 23.1 7.9 57 134-206 59-119 (193)
103 PF00873 ACR_tran: AcrB/AcrD/A 22.7 2E+02 0.0044 31.2 6.5 82 65-151 865-961 (1021)
104 PF01594 UPF0118: Domain of un 22.4 5.9E+02 0.013 23.1 10.0 42 44-85 177-218 (327)
105 PRK04949 putative sulfate tran 21.9 6.2E+02 0.013 23.2 9.7 23 67-89 29-55 (251)
106 TIGR00209 galT_1 galactose-1-p 21.8 1.4E+02 0.0031 28.7 4.6 65 171-235 162-255 (347)
107 COG2928 Uncharacterized conser 21.7 6.3E+02 0.014 23.2 9.8 39 50-88 2-40 (222)
108 PRK15120 lipopolysaccharide AB 21.7 6.8E+02 0.015 23.6 9.2 37 54-90 3-39 (366)
109 PRK05886 yajC preprotein trans 21.4 92 0.002 25.3 2.7 8 150-157 33-40 (109)
110 PRK00753 psbL photosystem II r 21.3 1.3E+02 0.0028 20.2 2.9 20 105-124 18-37 (39)
111 TIGR00439 ftsX putative protei 21.2 6.9E+02 0.015 23.4 10.7 27 107-133 281-307 (309)
112 PRK10712 PTS system fructose-s 21.1 4.4E+02 0.0096 27.2 8.2 123 3-140 176-340 (563)
113 PF04854 DUF624: Protein of un 20.9 2.8E+02 0.006 20.1 5.1 31 50-80 44-74 (77)
114 PF07613 DUF1576: Protein of u 20.9 5.3E+02 0.012 22.9 7.6 62 58-119 103-180 (183)
115 cd00608 GalT Galactose-1-phosp 20.7 1.4E+02 0.003 28.2 4.2 37 197-233 206-243 (329)
116 TIGR00822 EII-Sor PTS system, 20.6 7E+02 0.015 23.3 9.4 29 101-129 188-224 (265)
117 CHL00114 psbX photosystem II p 20.5 1.1E+02 0.0023 20.7 2.4 24 54-77 5-28 (39)
118 PRK01821 hypothetical protein; 20.4 2E+02 0.0042 24.2 4.6 12 98-109 33-46 (133)
119 COG4956 Integral membrane prot 20.2 5E+02 0.011 25.3 7.7 29 128-156 65-93 (356)
120 COG3224 Uncharacterized protei 20.0 4.1E+02 0.0089 23.8 6.6 42 88-131 139-180 (195)
No 1
>COG2928 Uncharacterized conserved protein [Function unknown]
Probab=100.00 E-value=1.6e-54 Score=383.13 Aligned_cols=195 Identities=30% Similarity=0.640 Sum_probs=175.9
Q ss_pred HHHHHHHhhhhHHHHHHHHHHHHHHHHHHHHHHHHhHhhhh-------hhcccchhhHHHHHHHHHHHHHHHHHHHHHHH
Q 024694 55 RSWASKKFMTGCVILFPIAVTFYITWWFIHFVDGFFSPIYA-------QLGIDIFGLGFITSVTFIFLIGVFMSSWLGAS 127 (264)
Q Consensus 55 r~~l~~~FltGLlvLLPi~iTi~Il~w~~~~vd~~~~pi~~-------~lg~~ipGlgll~~llliflvG~l~~~~lg~~ 127 (264)
.+.+||+|+|||++++|+++|+|+++|+++++|+++.|.+. +++.+++|+|+++.+++++++|+++++.+||+
T Consensus 3 ~~~lk~~fltGLlvllPlaiT~~vv~~i~~~l~~~~~~~lp~~~~~~~~~~~~i~~lg~il~iili~l~G~l~~~~ig~~ 82 (222)
T COG2928 3 AKRLKKYFLTGLLVLLPLAITLWVVSWIFGLLDQFVGPLLPDRLRPAVYFPFNIPGLGVILAIILIFLLGFLARNMIGRS 82 (222)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhhccchhchhhcCchhhHHHHHHHHHHHHHHHHHHHHHHhhhH
Confidence 34567889999999999999999999999999999998552 34667899999999999999999999999999
Q ss_pred HHHHHHHhhchhceehhHHHHHHHHHHHhCCCcCcCCcccEEEEEeCCCCeeEEEEEccccccc-ccCCCCceEEEEecC
Q 024694 128 VLSLGEWFIKRMPFVRHIYNASKQISAAISPDQNTQAFKEVAIIRHPRIGEYAFGFITSSVVLQ-NYSGEEELCCVYVPT 206 (264)
Q Consensus 128 l~~~~E~~l~rIPlVk~IY~~iKqv~~~~~~~~~~~~Fk~VVlV~~P~~g~~~iGFvT~~~~~~-~~~~~e~~v~VfvPt 206 (264)
+++++|++++|||++|+||+++||+++++.+++ ..+||+||+||||++|+|++||+|++...+ +...++++++||+||
T Consensus 83 l~~~~d~~L~RiPlv~~IY~s~kqi~etll~~~-~~sfk~vvlVefP~~G~~~i~fvtg~~~~e~~~~~~~~~v~VfvPT 161 (222)
T COG2928 83 LLSLGDSLLRRIPLVKSIYKSAKQVVETLLSDQ-SGSFKQVVLVEFPRRGIWAIAFVTGEKAGELKEKEGRPMVAVFVPT 161 (222)
T ss_pred HHHHHHHHHccCccHHHHHHHHHHHHHHHHhcC-CccceeeEEEECCCCCcEEEEEeccCCCcchhcccCCceEEEEcCC
Confidence 999999999999999999999999999998765 458999999999999999999999996421 224467999999999
Q ss_pred CC-CCCeeEEEEeCCCeecCCCCHHHHHHHHhhccccCCCCcccc
Q 024694 207 NH-LYIGDIFLINTKDVIRPNLSVREGIEIVVSGGMSMPQILSTL 250 (264)
Q Consensus 207 sp-~tsG~l~lV~~~~V~~lDmsveeAmk~iiS~Gv~~p~~~~~~ 250 (264)
+| ||+||+++||+||++++|||+|||+|+++|||++.|+.....
T Consensus 162 TPNPTsGfl~~Vpkedi~~ldmtvEda~k~iIS~G~v~p~~~~~~ 206 (222)
T COG2928 162 TPNPTSGFLLLVPKEDIVPLDMTVEDALKYIISGGVVAPDSLPAK 206 (222)
T ss_pred CCCCCcceEEEEEHHHceeccccHHHHhheeeeccccCCCccccc
Confidence 99 789999999999999999999999999999999999855443
No 2
>PF04367 DUF502: Protein of unknown function (DUF502); InterPro: IPR007462 This entry contains proteins that are predicted to be integral membrane proteins.
Probab=99.97 E-value=3.2e-30 Score=207.05 Aligned_cols=106 Identities=33% Similarity=0.613 Sum_probs=93.4
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhchhceehhHHHHHHHHHHHhCCCcCcCCcccEEEEEeCCCCeeEEEEEc
Q 024694 106 FITSVTFIFLIGVFMSSWLGASVLSLGEWFIKRMPFVRHIYNASKQISAAISPDQNTQAFKEVAIIRHPRIGEYAFGFIT 185 (264)
Q Consensus 106 ll~~llliflvG~l~~~~lg~~l~~~~E~~l~rIPlVk~IY~~iKqv~~~~~~~~~~~~Fk~VVlV~~P~~g~~~iGFvT 185 (264)
+++++++||++|+++++++|+++++++|+++.|||+||+||+++||++++|+++++ +.|++||+||||++|.|++||+|
T Consensus 1 ~l~~l~~i~~iG~l~~~~~g~~l~~~~e~ll~riP~v~~iY~~~k~~~~~~~~~~~-~~f~~vVlV~~p~~g~~~igFvT 79 (108)
T PF04367_consen 1 FLILLLLIFLIGLLARNYFGKWLLNWLERLLQRIPLVKSIYSSIKQLVESFSGDKK-KSFKKVVLVEFPRPGMYVIGFVT 79 (108)
T ss_pred ChHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCchHHHHHHHHHHHHHHhhccc-ccCCeEEEEEecCCCcEEEEEEe
Confidence 35678899999999999999999999999999999999999999999999998754 44999999999999999999999
Q ss_pred cccccc-ccCCCCceEEEEecCCCC-CCe
Q 024694 186 SSVVLQ-NYSGEEELCCVYVPTNHL-YIG 212 (264)
Q Consensus 186 ~~~~~~-~~~~~e~~v~VfvPtsp~-tsG 212 (264)
++...+ ....++++++||+||||+ ++|
T Consensus 80 ~~~~~~~~~~~~~~~v~VfvPtsPnPtsG 108 (108)
T PF04367_consen 80 GEDPGELPGKTGEEMVAVFVPTSPNPTSG 108 (108)
T ss_pred ccCcchhhccCCCCEEEEEeCCCCCCCCC
Confidence 997532 222245999999999995 676
No 3
>TIGR02120 GspF general secretion pathway protein F. 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. This model was constructed from the broader subfamily model, pfam00482 which includes components of pilin complexes (PilC) as well as other related genes. GspF is nearly always gene clustered with other GSP subunits. Some genes from Xylella and Xanthomonas strains score below the trusted cutoff due to excessive divergence from the family such that a sequence from Deinococcus which does not appear to be GspF scores higher.
Probab=87.48 E-value=7 Score=37.45 Aligned_cols=22 Identities=9% Similarity=0.083 Sum_probs=18.0
Q ss_pred HHHHHHHhhchhceehhHHHHH
Q 024694 128 VLSLGEWFIKRMPFVRHIYNAS 149 (264)
Q Consensus 128 l~~~~E~~l~rIPlVk~IY~~i 149 (264)
.-.+.|+++.|+|+++.+|...
T Consensus 243 ~r~~~~~~l~kiP~~g~~~~~~ 264 (399)
T TIGR02120 243 FRLRFDRRLLRLPVIGRLVRGL 264 (399)
T ss_pred HHHHHHHHHhcccchHHHHHHH
Confidence 4457789999999999988754
No 4
>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=87.17 E-value=1.2 Score=34.02 Aligned_cols=42 Identities=19% Similarity=0.279 Sum_probs=35.6
Q ss_pred CCceEEEEecCCCCCCeeEEEEeCCCeecC-CCCHHHHHHHHh
Q 024694 196 EEELCCVYVPTNHLYIGDIFLINTKDVIRP-NLSVREGIEIVV 237 (264)
Q Consensus 196 ~e~~v~VfvPtsp~tsG~l~lV~~~~V~~l-DmsveeAmk~ii 237 (264)
+.+.+.+|+|-.|..-|.++++|++-+..+ |++.||...+..
T Consensus 19 e~~~~~a~~~~~~~~pg~~lI~Pk~H~~~~~~l~~~e~~~l~~ 61 (103)
T cd01277 19 EDDHVLAFLDINPASKGHTLVIPKKHYENLLDLDPEELAELIL 61 (103)
T ss_pred eCCCEEEEECCCCCCCeeEEEEeccccCChhhCCHHHHHHHHH
Confidence 467889999999999999999999999765 999988765543
No 5
>PRK15350 type III secretion system protein SsaS; Provisional
Probab=86.98 E-value=13 Score=29.16 Aligned_cols=79 Identities=11% Similarity=0.183 Sum_probs=51.9
Q ss_pred HHHHHHhhhhHHHHHHHHHHHHHHHHHHHHHHHHhHhhhhhhcccchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 024694 56 SWASKKFMTGCVILFPIAVTFYITWWFIHFVDGFFSPIYAQLGIDIFGLGFITSVTFIFLIGVFMSSWLGASVLSLGEWF 135 (264)
Q Consensus 56 ~~l~~~FltGLlvLLPi~iTi~Il~w~~~~vd~~~~pi~~~lg~~ipGlgll~~llliflvG~l~~~~lg~~l~~~~E~~ 135 (264)
...++.+...+.+.+|+.+.-.++.-+++++.... . + +-.-+.|+-=++.++++=++...|.++.+.++.+++
T Consensus 8 ~l~~~al~~~l~ls~P~L~~alvVGlvIsi~QA~T----Q-I--QEqTLsFvPKliav~~~l~~~gpWm~~~l~~ft~~i 80 (88)
T PRK15350 8 QFVTQLLWIVLFTSMPVVLVASVVGVIVSLVQALT----Q-I--QDQTLQFMIKLLAIAITLMVSYPWLSGILLNYTRQI 80 (88)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH----H-H--HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 44566688899999999888877776666543321 1 1 111234443344445555566678889999999999
Q ss_pred hchhce
Q 024694 136 IKRMPF 141 (264)
Q Consensus 136 l~rIPl 141 (264)
+.+||-
T Consensus 81 f~~i~~ 86 (88)
T PRK15350 81 MLRIGE 86 (88)
T ss_pred HHhhhh
Confidence 999983
No 6
>PRK05700 fliQ flagellar biosynthesis protein FliQ; Validated
Probab=85.68 E-value=16 Score=28.76 Aligned_cols=80 Identities=10% Similarity=0.225 Sum_probs=52.9
Q ss_pred HHHHHHHhhhhHHHHHHHHHHHHHHHHHHHHHHHHhHhhhhhhcccchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 024694 55 RSWASKKFMTGCVILFPIAVTFYITWWFIHFVDGFFSPIYAQLGIDIFGLGFITSVTFIFLIGVFMSSWLGASVLSLGEW 134 (264)
Q Consensus 55 r~~l~~~FltGLlvLLPi~iTi~Il~w~~~~vd~~~~pi~~~lg~~ipGlgll~~llliflvG~l~~~~lg~~l~~~~E~ 134 (264)
-...++.+...+.+-.|+.+.-.++.-+++++.... . + +-.-+.|+-=++.++++=++...|.++.+.++.++
T Consensus 7 ~~l~~~al~~~l~ls~P~l~~alvVGlvIsi~QA~T----Q-I--qEqTLsFvPKliav~~~l~~~g~Wm~~~l~~f~~~ 79 (89)
T PRK05700 7 MDLFREAMKVALMLAAPLLLVALVVGLVVSIFQAAT----Q-I--NEQTLSFIPKILAVLLTLIIAGPWMLNTLLDYTRT 79 (89)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH----H-H--HHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 345566688899999999888877776665543321 1 1 11123444334444455556668899999999999
Q ss_pred hhchhce
Q 024694 135 FIKRMPF 141 (264)
Q Consensus 135 ~l~rIPl 141 (264)
++.++|-
T Consensus 80 if~~i~~ 86 (89)
T PRK05700 80 LFSNIPT 86 (89)
T ss_pred HHHHHHh
Confidence 9999985
No 7
>TIGR01402 fliQ flagellar biosynthetic protein FliQ. This model describes FliQ, a protein involved in biosynthesis of bacterial flagella. A related family of proteins, excluded from this model, participates in bacterial type III protein secretion systems.
Probab=84.92 E-value=17 Score=28.52 Aligned_cols=79 Identities=14% Similarity=0.264 Sum_probs=52.6
Q ss_pred HHHHHHhhhhHHHHHHHHHHHHHHHHHHHHHHHHhHhhhhhhcccchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 024694 56 SWASKKFMTGCVILFPIAVTFYITWWFIHFVDGFFSPIYAQLGIDIFGLGFITSVTFIFLIGVFMSSWLGASVLSLGEWF 135 (264)
Q Consensus 56 ~~l~~~FltGLlvLLPi~iTi~Il~w~~~~vd~~~~pi~~~lg~~ipGlgll~~llliflvG~l~~~~lg~~l~~~~E~~ 135 (264)
...++.+...+.+..|+.+.-.++.-+++.+.... . + +-.-+.|+-=++.++++-++...|.++.+.++.+++
T Consensus 8 ~l~~~al~~~l~~s~P~l~~alvVGlvIsi~QA~T----Q-I--qEqTLsFvPKliav~~~l~~~gpWm~~~l~~f~~~~ 80 (88)
T TIGR01402 8 DLGREAIWLTLLLSAPVLLVALVVGLVISIFQAAT----Q-I--QEQTLSFIPKIIAILLALALLGPWMLTKLLDFTREI 80 (88)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH----H-H--HHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 44566688899999999888777776655543321 1 1 111234444444455555566688899999999999
Q ss_pred hchhce
Q 024694 136 IKRMPF 141 (264)
Q Consensus 136 l~rIPl 141 (264)
+.++|-
T Consensus 81 f~~i~~ 86 (88)
T TIGR01402 81 FQRIPQ 86 (88)
T ss_pred HHHhhh
Confidence 999985
No 8
>PRK06010 fliQ flagellar biosynthesis protein FliQ; Reviewed
Probab=84.05 E-value=19 Score=28.30 Aligned_cols=80 Identities=14% Similarity=0.166 Sum_probs=51.3
Q ss_pred HHHHHHHhhhhHHHHHHHHHHHHHHHHHHHHHHHHhHhhhhhhcccchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 024694 55 RSWASKKFMTGCVILFPIAVTFYITWWFIHFVDGFFSPIYAQLGIDIFGLGFITSVTFIFLIGVFMSSWLGASVLSLGEW 134 (264)
Q Consensus 55 r~~l~~~FltGLlvLLPi~iTi~Il~w~~~~vd~~~~pi~~~lg~~ipGlgll~~llliflvG~l~~~~lg~~l~~~~E~ 134 (264)
-...++.+...+.+.+|+.+.-.++.-+++.+.... . + +-.-+.++-=++.++++=++...|..+.+.++.++
T Consensus 7 ~~l~~~al~~~l~~s~P~L~~alvVGliIsi~QA~T----Q-I--qEqTLsFvPKliav~~~l~~~g~Wm~~~l~~f~~~ 79 (88)
T PRK06010 7 LDIVRDAIWTVLVASGPAVLAAMVVGVAIALFQALT----Q-I--QEMTLTFVPKIVAIFVTLLLTLPFMGAQISAFTLL 79 (88)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH----H-H--HHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 345566688899999999888877776665543321 1 1 11113333333344444455567888889999999
Q ss_pred hhchhce
Q 024694 135 FIKRMPF 141 (264)
Q Consensus 135 ~l~rIPl 141 (264)
++.+||-
T Consensus 80 if~~i~~ 86 (88)
T PRK06010 80 IYSRIAG 86 (88)
T ss_pred HHHhhcc
Confidence 9999983
No 9
>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=82.84 E-value=2.4 Score=34.14 Aligned_cols=44 Identities=14% Similarity=0.125 Sum_probs=36.1
Q ss_pred CCceEEEEecCCCCCCeeEEEEeCCCeecC-CCCHHHHHHHHhhc
Q 024694 196 EEELCCVYVPTNHLYIGDIFLINTKDVIRP-NLSVREGIEIVVSG 239 (264)
Q Consensus 196 ~e~~v~VfvPtsp~tsG~l~lV~~~~V~~l-DmsveeAmk~iiS~ 239 (264)
+++.+.+|+|-.|.+.|.++++|++.+..+ |++-||...+.-..
T Consensus 19 e~~~~~~~~~~~p~~~gh~lIiPk~H~~~~~~L~~~e~~~l~~~~ 63 (126)
T cd01275 19 RTKHSFAVVNLYPYNPGHVLVVPYRHVPRLEDLTPEEIADLFKLV 63 (126)
T ss_pred eCCCEEEEEcCCCCCCCcEEEEeccccCChhhCCHHHHHHHHHHH
Confidence 467889999999988999999999999765 89988877654443
No 10
>PRK12781 fliQ flagellar biosynthesis protein FliQ; Reviewed
Probab=81.84 E-value=23 Score=27.78 Aligned_cols=80 Identities=15% Similarity=0.187 Sum_probs=52.3
Q ss_pred HHHHHHHhhhhHHHHHHHHHHHHHHHHHHHHHHHHhHhhhhhhcccchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 024694 55 RSWASKKFMTGCVILFPIAVTFYITWWFIHFVDGFFSPIYAQLGIDIFGLGFITSVTFIFLIGVFMSSWLGASVLSLGEW 134 (264)
Q Consensus 55 r~~l~~~FltGLlvLLPi~iTi~Il~w~~~~vd~~~~pi~~~lg~~ipGlgll~~llliflvG~l~~~~lg~~l~~~~E~ 134 (264)
-...++.+...+.+-+|+.+.-.++.-+++.+.... . + +-.-+.++-=++.++++=++...|.++.+.++.++
T Consensus 7 i~~~~~al~~~l~ls~P~L~~alvVGlvIsi~QA~T----Q-I--QEqTLsFvPKliav~~~l~~~~~wm~~~l~~ft~~ 79 (88)
T PRK12781 7 LELVRAAIWTIIVASGPAVGAAMLVGIAIALLQALT----Q-I--QEVTLTFVPKIVVILIVMAVTGSFVGAQIYAFTEM 79 (88)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH----H-H--HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 445666788889999999888777776655543321 1 1 11123443334444555556668888999999999
Q ss_pred hhchhce
Q 024694 135 FIKRMPF 141 (264)
Q Consensus 135 ~l~rIPl 141 (264)
++.+||-
T Consensus 80 if~~i~~ 86 (88)
T PRK12781 80 VYGRIES 86 (88)
T ss_pred HHHhhcc
Confidence 9999983
No 11
>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=81.81 E-value=2.4 Score=31.14 Aligned_cols=42 Identities=14% Similarity=0.224 Sum_probs=33.8
Q ss_pred CCceEEEEecCCCCCCeeEEEEeCCCeecC-CCCHHHHHHHHh
Q 024694 196 EEELCCVYVPTNHLYIGDIFLINTKDVIRP-NLSVREGIEIVV 237 (264)
Q Consensus 196 ~e~~v~VfvPtsp~tsG~l~lV~~~~V~~l-DmsveeAmk~ii 237 (264)
+++.+.+|+|-.|...|-++++|++-+..+ |++.|+..++..
T Consensus 3 e~~~~~a~~~~~p~~~gh~lIipk~H~~~~~~l~~~~~~~l~~ 45 (86)
T cd00468 3 DDEHSFAFVNLKPAAPGHVLVCPKRHVETLPDLDEALLADLVI 45 (86)
T ss_pred ecCcEEEEECCCCCCCCcEEEeCchhhCChhHCCHHHHHHHHH
Confidence 457789999999988999999999988664 898876655443
No 12
>COG1459 PulF Type II secretory pathway, component PulF [Cell motility and secretion / Intracellular trafficking and secretion]
Probab=81.47 E-value=8.3 Score=37.83 Aligned_cols=23 Identities=9% Similarity=0.134 Sum_probs=18.4
Q ss_pred HHHHHHHHhhchhceehhHHHHH
Q 024694 127 SVLSLGEWFIKRMPFVRHIYNAS 149 (264)
Q Consensus 127 ~l~~~~E~~l~rIPlVk~IY~~i 149 (264)
+.-.+.|+++-|+|+++.+....
T Consensus 239 ~~r~~~~~~llrlP~~g~l~~~~ 261 (397)
T COG1459 239 AGRRRLDRLLLRLPLFGKLVRKY 261 (397)
T ss_pred HHHHHHHhHHhcCCcHHHHHHHH
Confidence 44567899999999999987643
No 13
>COG1684 FliR Flagellar biosynthesis pathway, component FliR [Cell motility and secretion / Intracellular trafficking and secretion]
Probab=80.64 E-value=22 Score=33.09 Aligned_cols=45 Identities=11% Similarity=0.148 Sum_probs=38.7
Q ss_pred ChhHHHHHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHHHHHHHHh
Q 024694 46 GRETFSKVVRSWASKKFMTGCVILFPIAVTFYITWWFIHFVDGFF 90 (264)
Q Consensus 46 ~~~~~~~~lr~~l~~~FltGLlvLLPi~iTi~Il~w~~~~vd~~~ 90 (264)
..+++..-+-+++...|..|+..-+|++....+++-.+..+++..
T Consensus 163 ~~~~~~~~l~~~l~~~F~~~l~iAlPii~~lLlvnlalGlv~R~~ 207 (258)
T COG1684 163 LNDNAFLLLAKALSAIFLIGLRLALPIIALLLLVNLALGLLNRLA 207 (258)
T ss_pred CCccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcc
Confidence 345778888889999999999999999999999998888887763
No 14
>TIGR01403 fliQ_rel_III type III secretion protein, HrpO family. This model represents one of several families of proteins related to bacterial flagellar biosynthesis proteins and involved in bacterial type III protein secretion systems. This family is homologous to, but distinguished from, flagellar biosynthetic protein FliQ. This model may not identify all type III secretion system FliQ homologs.
Probab=80.51 E-value=24 Score=27.21 Aligned_cols=77 Identities=16% Similarity=0.353 Sum_probs=48.8
Q ss_pred HHHHHhhhhHHHHHHHHHHHHHHHHHHHHHHHHhHhhhhhhcccchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Q 024694 57 WASKKFMTGCVILFPIAVTFYITWWFIHFVDGFFSPIYAQLGIDIFGLGFITSVTFIFLIGVFMSSWLGASVLSLGEWFI 136 (264)
Q Consensus 57 ~l~~~FltGLlvLLPi~iTi~Il~w~~~~vd~~~~pi~~~lg~~ipGlgll~~llliflvG~l~~~~lg~~l~~~~E~~l 136 (264)
..++.+...+.+-+|+.+.-.++.-+++++.... . + +-.-+.|+-=++.++++=++...|..+.+.++.++++
T Consensus 5 ~~~~al~~~l~~s~P~L~~alvVGLvIsi~QA~T----Q-I--qEqTLsFvPKliav~~~l~~~~pwm~~~l~~f~~~if 77 (81)
T TIGR01403 5 LTNQALLLVLILSLPPVLVAAIVGLLVSLLQALT----Q-L--QDQTLPFAIKLIAVFITLMLTAGWLGAEILNFANQIF 77 (81)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH----H-H--HHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 4566688899999999888887776665543321 1 1 1111333333333344444555788888899999999
Q ss_pred chhc
Q 024694 137 KRMP 140 (264)
Q Consensus 137 ~rIP 140 (264)
.+||
T Consensus 78 ~~i~ 81 (81)
T TIGR01403 78 TMIP 81 (81)
T ss_pred hhCC
Confidence 9887
No 15
>PRK10573 type IV pilin biogenesis protein; Provisional
Probab=78.30 E-value=22 Score=34.06 Aligned_cols=18 Identities=17% Similarity=0.366 Sum_probs=15.1
Q ss_pred HHHHHhhchhceehhHHH
Q 024694 130 SLGEWFIKRMPFVRHIYN 147 (264)
Q Consensus 130 ~~~E~~l~rIPlVk~IY~ 147 (264)
.+.++++.|+|+++.+|.
T Consensus 244 ~~~~~~l~~iP~~g~~~~ 261 (399)
T PRK10573 244 IREQRLLLRLPLVGSLIR 261 (399)
T ss_pred HHHHHHHhcCCeeccccc
Confidence 456899999999998776
No 16
>PF01230 HIT: HIT domain; InterPro: IPR001310 The Histidine Triad (HIT) motif, His-x-His-x-His-x-x (x, a hydrophobic amino acid) was identified as being highly conserved in a variety of organisms []. Crystal structure of rabbit Hint, purified as an adenosine and AMP-binding protein, showed that proteins in the HIT superfamily are conserved as nucleotide-binding proteins and that Hint homologues, which are found in all forms of life, are structurally related to Fhit homologues and GalT-related enzymes, which have more restricted phylogenetic profiles []. Hint homologues including rabbit Hint and yeast Hnt1 hydrolyse adenosine 5' monophosphoramide substrates such as AMP-NH2 and AMP-lysine to AMP plus the amine product and function as positive regulators of Cdk7/Kin28 in vivo []. Fhit homologues are diadenosine polyphosphate hydrolases [] and function as tumour suppressors in human and mouse [] though the tumour suppressing function of Fhit does not depend on ApppA hydrolysis []. The third branch of the HIT superfamily, which includes GalT homologues, contains a related His-X-His-X-Gln motif and transfers nucleoside monophosphate moieties to phosphorylated second substrates rather than hydrolysing them [].; PDB: 3LB5_B 1EMS_A 1Y23_A 3ANO_B 1KPE_B 1KPC_A 4EQE_B 1KPA_A 1KPB_B 4EQG_B ....
Probab=76.85 E-value=2.8 Score=32.11 Aligned_cols=41 Identities=17% Similarity=0.320 Sum_probs=33.7
Q ss_pred CCceEEEEecCCCCCCeeEEEEeCCCeecC-CCCHHHHHHHH
Q 024694 196 EEELCCVYVPTNHLYIGDIFLINTKDVIRP-NLSVREGIEIV 236 (264)
Q Consensus 196 ~e~~v~VfvPtsp~tsG~l~lV~~~~V~~l-DmsveeAmk~i 236 (264)
+.+.+.+|++..|..-|.++++|++.+..+ |++-++..++.
T Consensus 11 e~~~~~~~~~~~p~~~gh~LVipk~H~~~l~dl~~~~~~~l~ 52 (98)
T PF01230_consen 11 EDDHFVAFLDIFPISPGHLLVIPKRHVESLSDLPPEERAELM 52 (98)
T ss_dssp E-SSEEEEEESSTSSTTEEEEEESSTGSSGGGSHHHHHHHHH
T ss_pred ECCCEEEEEcCCCCCCeEEEEEecccccchhcCCHHHHHHHH
Confidence 356788899998988899999999999886 89977776654
No 17
>PRK09824 PTS system beta-glucoside-specific transporter subunits IIABC; Provisional
Probab=73.83 E-value=27 Score=36.40 Aligned_cols=69 Identities=16% Similarity=0.337 Sum_probs=39.8
Q ss_pred HHHHHHHHHHHHHHHHHHHHHhHhhhhhhcccchhhHHHHHH-HHHHHHHHHHHHHHHHHHHHHHHHhhchhc
Q 024694 69 LFPIAVTFYITWWFIHFVDGFFSPIYAQLGIDIFGLGFITSV-TFIFLIGVFMSSWLGASVLSLGEWFIKRMP 140 (264)
Q Consensus 69 LLPi~iTi~Il~w~~~~vd~~~~pi~~~lg~~ipGlgll~~l-lliflvG~l~~~~lg~~l~~~~E~~l~rIP 140 (264)
++|+.++.|+..|+-+++++.+...++.+ -.|-+.+++++ +.++++|=+. +++|..+-..+.|+...-|
T Consensus 219 ViPiil~v~~~s~iEk~l~K~iP~~l~~i--~~P~ltlli~~pl~l~viGPig-~~i~~~l~~~i~~l~~~~~ 288 (627)
T PRK09824 219 VIPIIFSAWLCSILERRLNAWLPSAIKNF--FTPLLCLMVIVPLTFLLIGPLA-TWLSELLAAGYQWLYQAVP 288 (627)
T ss_pred hHHHHHHHHHHHHHHHHHHHHHHHHHHHH--HHHHHHHHHHHHHHHHhHHHHH-HHHHHHHHHHHHHHHhhch
Confidence 79999999999999999988765544432 12434443332 3344444332 2444444444445544443
No 18
>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=73.69 E-value=4 Score=31.36 Aligned_cols=34 Identities=15% Similarity=0.149 Sum_probs=28.4
Q ss_pred CCceEEEEecCCCCCCeeEEEEeCCCeecC-CCCH
Q 024694 196 EEELCCVYVPTNHLYIGDIFLINTKDVIRP-NLSV 229 (264)
Q Consensus 196 ~e~~v~VfvPtsp~tsG~l~lV~~~~V~~l-Dmsv 229 (264)
+++.+.+|+|..|...|-++++|++.+..+ |++.
T Consensus 19 e~~~~~a~~~~~p~~~gh~lIiPk~H~~~~~dl~~ 53 (104)
T cd01276 19 EDDEVLAFHDINPQAPVHILVIPKKHIASLSDATE 53 (104)
T ss_pred ECCCEEEEECCCCCCCCEEEEEecceeCChHHccc
Confidence 467888999999988999999999998664 6654
No 19
>PRK12772 bifunctional flagellar biosynthesis protein FliR/FlhB; Provisional
Probab=73.13 E-value=36 Score=35.29 Aligned_cols=40 Identities=20% Similarity=0.164 Sum_probs=34.0
Q ss_pred HHHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHHHHHHHHh
Q 024694 51 SKVVRSWASKKFMTGCVILFPIAVTFYITWWFIHFVDGFF 90 (264)
Q Consensus 51 ~~~lr~~l~~~FltGLlvLLPi~iTi~Il~w~~~~vd~~~ 90 (264)
...+-+++...|..|+.+-+|++++..++.-.+.++....
T Consensus 165 ~~~~~~~~~~~F~~al~lAaP~i~~lll~~~~lGllsR~a 204 (609)
T PRK12772 165 IMHVINVFIQYFYIGIKIAIPIVLIILITDLTLGLISRTV 204 (609)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhC
Confidence 4556677888999999999999999999998888887764
No 20
>PRK11007 PTS system trehalose(maltose)-specific transporter subunits IIBC; Provisional
Probab=71.98 E-value=27 Score=35.08 Aligned_cols=86 Identities=12% Similarity=0.058 Sum_probs=54.8
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHhHhhhhhhcccchhhHHHHHHHH-HHHHHHHHHHHHHHHHHHHHHHhhc-hh-ceehh
Q 024694 68 ILFPIAVTFYITWWFIHFVDGFFSPIYAQLGIDIFGLGFITSVTF-IFLIGVFMSSWLGASVLSLGEWFIK-RM-PFVRH 144 (264)
Q Consensus 68 vLLPi~iTi~Il~w~~~~vd~~~~pi~~~lg~~ipGlgll~~lll-iflvG~l~~~~lg~~l~~~~E~~l~-rI-PlVk~ 144 (264)
-++|+.++.|+..|+-+++++.....++.+ -.|-+.++++..+ ++++|=+. ++++..+-+.++++.. .. ++-.-
T Consensus 231 sViP~Il~v~~~s~iek~l~K~~P~~l~~i--~~Plltlli~~~l~l~viGPig-~~i~~~i~~~i~~L~~~~~~~ig~~ 307 (473)
T PRK11007 231 QVIPALLAGLALGFIETRLKRIVPDYLYLV--VVPVCSLILAVFLAHALIGPFG-RMIGDGVAFAVKALMTGSFAPIGAA 307 (473)
T ss_pred CcHHHHHHHHHHHHHHHHHHHhCcHHHHHH--HHHHHHHHHHHHHHHHHHHHHH-HHHHHHHHHHHHHHHhcchHHHHHH
Confidence 578999999999999999988864444422 1355555544433 44666443 4667766677777762 33 45566
Q ss_pred HHHHHHHHHHHh
Q 024694 145 IYNASKQISAAI 156 (264)
Q Consensus 145 IY~~iKqv~~~~ 156 (264)
++.++-|..=.+
T Consensus 308 i~g~~~~~lV~~ 319 (473)
T PRK11007 308 LFGFLYAPLVIT 319 (473)
T ss_pred HHHHHHHHHHHh
Confidence 777777755443
No 21
>PF01311 Bac_export_1: Bacterial export proteins, family 1; InterPro: IPR002010 Secretion of virulence factors in Gram-negative bacteria involves transportation of the protein across two membranes to reach the cell exterior []. There have been four secretion systems described in animal enteropathogens such as Salmonella and Yersinia, with further sequence similarities in plant pathogens like Ralstonia and Erwinia []. The type III secretion system is of great interest, as it is used to transport virulence factors from the pathogen directly into the host cell [] and is only triggered when the bacterium comes into close contact with the host. The protein subunits of the system are very similar to those of bacterial flagellar biosynthesis []. However, while the latter forms a ring structure to allow secretion of flagellin and is an integral part of the flagellum itself [], type III subunits in the outer membrane translocate secreted proteins through a channel-like structure. It is believed that the family of type III inner membrane proteins are used as structural moieties in a complex with several other subunits []. One such set of inner membrane proteins, labeled "R" here for nomenclature purposes, includes the Salmonella and Shigella SpaR, the Yersinia YscT, Rhizobium Y4YN, and the Erwinia HrcT genes []. The flagellar protein FliR also shares similarity, probably due to evolution of the type III secretion system from the flagellar biosynthetic pathway. ; GO: 0006605 protein targeting, 0016020 membrane
Probab=71.00 E-value=59 Score=29.55 Aligned_cols=43 Identities=7% Similarity=0.060 Sum_probs=37.1
Q ss_pred hHHHHHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHHHHHHHHh
Q 024694 48 ETFSKVVRSWASKKFMTGCVILFPIAVTFYITWWFIHFVDGFF 90 (264)
Q Consensus 48 ~~~~~~lr~~l~~~FltGLlvLLPi~iTi~Il~w~~~~vd~~~ 90 (264)
+.+...+-++..+.|..|+.+-+|+++...++.-.+.++.+..
T Consensus 163 ~~~~~~~~~~~~~~f~~al~lAaP~i~~lll~~l~lG~l~R~~ 205 (249)
T PF01311_consen 163 EEALQFIIKLFGQMFSLALQLAAPVIAALLLVDLALGLLSRAA 205 (249)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhC
Confidence 5677788888899999999999999999999998888776664
No 22
>PRK09796 PTS system cellobiose/arbutin/salicin-specific transporter subunits IIBC; Provisional
Probab=70.54 E-value=34 Score=34.39 Aligned_cols=85 Identities=16% Similarity=0.177 Sum_probs=47.2
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHhHhhhhhhcccchhhHHHHH-HHHHHHHHHHHHHHHHHHHHHHHHHhhchhc-eehhH
Q 024694 68 ILFPIAVTFYITWWFIHFVDGFFSPIYAQLGIDIFGLGFITS-VTFIFLIGVFMSSWLGASVLSLGEWFIKRMP-FVRHI 145 (264)
Q Consensus 68 vLLPi~iTi~Il~w~~~~vd~~~~pi~~~lg~~ipGlgll~~-llliflvG~l~~~~lg~~l~~~~E~~l~rIP-lVk~I 145 (264)
-++|+.++.|+..++-+++++.....++.+ -.|-+.++++ .+.++++|=+ -+++|..+-..+.++....| +...|
T Consensus 220 sViPiil~v~~~s~vek~~~K~~P~~l~~i--~~P~ltlli~~pl~l~viGPi-g~~i~~~i~~~i~~l~~~~~~i~g~i 296 (472)
T PRK09796 220 TVIPALVMTWCLSYIERWVDRITPAVTKNF--LKPMLIVLIAAPLAILLIGPI-GIWIGSAISALVYTIHGYLGWLSVAI 296 (472)
T ss_pred chHHHHHHHHHHHHHHHHHHHhCHHHHHHH--HHHHHHHHHHHHHHHHhHHHH-HHHHHHHHHHHHHHHHhcchHHHHHH
Confidence 368999999999999999888764443321 1233333332 2234444433 23455555455555554443 44556
Q ss_pred HHHHHHHHHH
Q 024694 146 YNASKQISAA 155 (264)
Q Consensus 146 Y~~iKqv~~~ 155 (264)
+.++-+..=.
T Consensus 297 ~g~~~~~lV~ 306 (472)
T PRK09796 297 MGALWPLLVM 306 (472)
T ss_pred HHHHHHHHHH
Confidence 6666665433
No 23
>PRK15333 type III secretion system protein SpaQ; Provisional
Probab=70.44 E-value=50 Score=25.84 Aligned_cols=79 Identities=16% Similarity=0.078 Sum_probs=50.8
Q ss_pred HHHHHHhhhhHHHHHHHHHHHHHHHHHHHHHHHHhHhhhhhhcccchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 024694 56 SWASKKFMTGCVILFPIAVTFYITWWFIHFVDGFFSPIYAQLGIDIFGLGFITSVTFIFLIGVFMSSWLGASVLSLGEWF 135 (264)
Q Consensus 56 ~~l~~~FltGLlvLLPi~iTi~Il~w~~~~vd~~~~pi~~~lg~~ipGlgll~~llliflvG~l~~~~lg~~l~~~~E~~ 135 (264)
...++.+...+.+-.|+.+.-.++.-+++++.... . + +-.-+.|+-=++.++++=++...|.++.+.++.+++
T Consensus 6 ~~~~~al~~~l~ls~P~L~valvVGlvIsi~QA~T----Q-I--QEqTLsFvPKliav~~~l~~~~pwm~~~l~~f~~~i 78 (86)
T PRK15333 6 FAGNKALYLVLILSGWPTIVATIIGLLVGLFQTVT----Q-L--QEQTLPFGIKLLGVCLCLFLLSGWYGEVLLSYGRQV 78 (86)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH----H-H--HHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 34566788889999999888777776655543321 1 1 111233333334444444556688889999999999
Q ss_pred hchhce
Q 024694 136 IKRMPF 141 (264)
Q Consensus 136 l~rIPl 141 (264)
+..+|-
T Consensus 79 f~~~~~ 84 (86)
T PRK15333 79 IFLALA 84 (86)
T ss_pred HHhhhc
Confidence 988884
No 24
>COG1987 FliQ Flagellar biosynthesis pathway, component FliQ [Cell motility and secretion / Intracellular trafficking and secretion]
Probab=69.02 E-value=55 Score=25.83 Aligned_cols=76 Identities=14% Similarity=0.290 Sum_probs=49.1
Q ss_pred HHHhhhhHHHHHHHHHHHHHHHHHHHHHHHHhHhhhhhhcccchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhch
Q 024694 59 SKKFMTGCVILFPIAVTFYITWWFIHFVDGFFSPIYAQLGIDIFGLGFITSVTFIFLIGVFMSSWLGASVLSLGEWFIKR 138 (264)
Q Consensus 59 ~~~FltGLlvLLPi~iTi~Il~w~~~~vd~~~~pi~~~lg~~ipGlgll~~llliflvG~l~~~~lg~~l~~~~E~~l~r 138 (264)
++.+-.+|....|+.+.-.++.-++.++.... .+ +---+.|+==++.++++-.++.-|.++.+.++...+++|
T Consensus 11 ~~ai~~~L~l~~P~ll~alvvGLvIsifQA~T-----QI--qEqTLsFiPKIiai~~~l~~~gpWm~~~l~dft~~if~~ 83 (89)
T COG1987 11 QEAIWLVLMLSAPVLLVALVVGLVISIFQAAT-----QI--QEQTLSFIPKIIAVFLVLILLGPWMLNQLLDFTVTIFSN 83 (89)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-----HH--HHHHHHhHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHH
Confidence 34466788888998877766665554432221 11 101133333445566666677789999999999999999
Q ss_pred hce
Q 024694 139 MPF 141 (264)
Q Consensus 139 IPl 141 (264)
||.
T Consensus 84 i~~ 86 (89)
T COG1987 84 IPQ 86 (89)
T ss_pred HHh
Confidence 995
No 25
>PRK09765 PTS system 2-O-a-mannosyl-D-glycerate specific transporter subunit IIABC; Provisional
Probab=68.54 E-value=22 Score=36.95 Aligned_cols=70 Identities=13% Similarity=0.219 Sum_probs=46.8
Q ss_pred HHHHHHHHHHHHHHHHHHHHHhHhhhhhh----c-ccchhhHHHHHH-HHHHHHHHHHHHHHHHHHHHHHHHhhchhc
Q 024694 69 LFPIAVTFYITWWFIHFVDGFFSPIYAQL----G-IDIFGLGFITSV-TFIFLIGVFMSSWLGASVLSLGEWFIKRMP 140 (264)
Q Consensus 69 LLPi~iTi~Il~w~~~~vd~~~~pi~~~l----g-~~ipGlgll~~l-lliflvG~l~~~~lg~~l~~~~E~~l~rIP 140 (264)
++|.++..|+..|+.+++++.+ |.-+.+ . .-+|-++++++. +.++++|-.. ++++..+-+++.++...-|
T Consensus 381 flg~Ii~~~l~gyv~~~l~k~i-p~~~~~~~~~~~~~~Pllt~li~~~l~~~viGp~~-~~i~~~l~~~l~~l~~~~~ 456 (631)
T PRK09765 381 FLGAVVGGLIAGYLMRWVKNHL-RLSSKFNGFLTFYLYPVLGTLGAGSLMLFVVGEPV-AWINNSLTAWLNGLSGSNA 456 (631)
T ss_pred cHHHHHHHHHHHHHHHHHHHHC-CCchhhhhhcCEEeehHHHHHHHHHHHHHHHHHHH-HHHHHHHHHHHHHHHhhhH
Confidence 5888888888888888888876 432111 1 124666665544 4566888776 6788888888877765443
No 26
>cd01278 aprataxin_related aprataxin related: Aprataxin, a HINT family hydrolase is mutated in ataxia oculomotor apraxia syndrome. All the members of this subgroup have the conserved HxHxHxx (where x is a hydrophobic residue) signature motif. Members of this subgroup are predominantly eukaryotic in origin.
Probab=68.31 E-value=9.8 Score=29.27 Aligned_cols=36 Identities=11% Similarity=0.154 Sum_probs=30.2
Q ss_pred CCceEEEEecCCCCCCeeEEEEeCCCeecC-CCCHHH
Q 024694 196 EEELCCVYVPTNHLYIGDIFLINTKDVIRP-NLSVRE 231 (264)
Q Consensus 196 ~e~~v~VfvPtsp~tsG~l~lV~~~~V~~l-Dmsvee 231 (264)
.++.+.+|.|..|..-|-+.++|++.+..+ |++.||
T Consensus 21 ~~~~~~a~~~~~p~~~~h~lIiPk~h~~~~~~l~~~~ 57 (104)
T cd01278 21 EDDRVVVFKDIYPKARHHYLVIPKEHIASLKALTKED 57 (104)
T ss_pred eCCCEEEEECCCCCCCceEEEEecCCCCChHHCCHhH
Confidence 467889999999988899999999998665 787664
No 27
>COG4794 EscS Type III secretory pathway, component EscS [Intracellular trafficking and secretion]
Probab=67.86 E-value=59 Score=25.68 Aligned_cols=80 Identities=16% Similarity=0.257 Sum_probs=46.3
Q ss_pred HHHHHhhhhHHHHHHHHHHHHHHHHHHHHHHHHhHhhhhhhcccchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Q 024694 57 WASKKFMTGCVILFPIAVTFYITWWFIHFVDGFFSPIYAQLGIDIFGLGFITSVTFIFLIGVFMSSWLGASVLSLGEWFI 136 (264)
Q Consensus 57 ~l~~~FltGLlvLLPi~iTi~Il~w~~~~vd~~~~pi~~~lg~~ipGlgll~~llliflvG~l~~~~lg~~l~~~~E~~l 136 (264)
+-.+.+.-=|+.-+|-++.--++.-++.++ .-+.. +-. .-+++.+=++.++..=++...|.|..++++.|.++
T Consensus 9 ~~~qaL~liLilSlPpvivAsvvGllVslv----QA~TQ-iQd--QTl~f~iKLl~V~~tl~lt~~Wlg~~ll~fa~~i~ 81 (89)
T COG4794 9 LTSQALWLILILSLPPVIVASVVGLLVSLV----QALTQ-IQD--QTLPFGIKLLAVSATLFLTAGWLGATLLNFAEQIF 81 (89)
T ss_pred HHHHHHHHHHHHhccHHHHHHHHHHHHHHH----HHHHH-HHH--hHHHHHHHHHHHHHHHHHHhHHhHHHHHHHHHHHH
Confidence 333444444566667766555555444443 22221 111 11344443444444445677899999999999999
Q ss_pred chhceeh
Q 024694 137 KRMPFVR 143 (264)
Q Consensus 137 ~rIPlVk 143 (264)
.++|..|
T Consensus 82 ~~~~~~~ 88 (89)
T COG4794 82 LNIPKAR 88 (89)
T ss_pred HHhhhcc
Confidence 9999754
No 28
>PRK09586 murP PTS system N-acetylmuramic acid transporter subunits EIIBC; Reviewed
Probab=66.83 E-value=44 Score=33.67 Aligned_cols=82 Identities=11% Similarity=0.053 Sum_probs=44.5
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHhHhhhhhhcccchhhHHHH-HHHHHHHHHHHHHHHHHHHHHHHHHHhhchhceehhHH
Q 024694 68 ILFPIAVTFYITWWFIHFVDGFFSPIYAQLGIDIFGLGFIT-SVTFIFLIGVFMSSWLGASVLSLGEWFIKRMPFVRHIY 146 (264)
Q Consensus 68 vLLPi~iTi~Il~w~~~~vd~~~~pi~~~lg~~ipGlgll~-~llliflvG~l~~~~lg~~l~~~~E~~l~rIPlVk~IY 146 (264)
-++|+.++.|+..++-++++++....++.+- .|-+.+++ ..+.++++|=+. +|+|..+-..+.++... ++..-|+
T Consensus 230 sViPiil~v~~~s~iek~~~K~iP~~l~~i~--~P~ltlli~~p~~l~viGP~g-~~i~~~i~~~~~~l~~~-~~~~~i~ 305 (476)
T PRK09586 230 NIIGVLIAAIAGARIERMVRRFMPDDLDMIL--TSLITLLITGALAFLIIMPLG-GWLFEGMSWLFMHLNSN-PFGCAVL 305 (476)
T ss_pred chHHHHHHHHHHHHHHHHHHhhCHHHHHHHH--HHHHHHHHHHHHHHHhHHhHH-HHHHHHHHHHHHHHHhh-HHHHHHH
Confidence 4679999999999998888887644443321 23333332 222344444332 34454444444444432 4555566
Q ss_pred HHHHHHH
Q 024694 147 NASKQIS 153 (264)
Q Consensus 147 ~~iKqv~ 153 (264)
.++-|..
T Consensus 306 g~~~~~l 312 (476)
T PRK09586 306 AGLFLIA 312 (476)
T ss_pred HHHHHHH
Confidence 6666644
No 29
>TIGR01992 PTS-IIBC-Tre PTS system, trehalose-specific IIBC component. Trehalose may also be transported (in Salmonella) via the mannose PTS or galactose permease systems, or (in Sinorhizobium, Thermococcus and Sulfolobus, for instance) by ABC transporters.
Probab=66.51 E-value=44 Score=33.38 Aligned_cols=85 Identities=9% Similarity=0.081 Sum_probs=51.3
Q ss_pred HHHHHHHHHHHHHHHHHHHHHhHhhhhhhcccchhhHHHHHHHHH-HHHHHHHHHHHHHHHHHHHHHhhchhce-ehhHH
Q 024694 69 LFPIAVTFYITWWFIHFVDGFFSPIYAQLGIDIFGLGFITSVTFI-FLIGVFMSSWLGASVLSLGEWFIKRMPF-VRHIY 146 (264)
Q Consensus 69 LLPi~iTi~Il~w~~~~vd~~~~pi~~~lg~~ipGlgll~~llli-flvG~l~~~~lg~~l~~~~E~~l~rIPl-Vk~IY 146 (264)
++|..++.|+..++-+++++.+...++.+ -.|-+.+++++.+. +++|-+ -.+++..+...+.++....|. ..-+|
T Consensus 233 Vip~Il~g~i~~yiek~~~k~lP~~l~~~--~vP~lt~lv~~~l~~~vigPi-~~~i~~~i~~~~~~l~~~~~~i~g~i~ 309 (462)
T TIGR01992 233 VLPALLAGYVLAVIEKWLRKRVPDAIQLL--VVPPVSLLVTGFLAHAIIGPI-GRLIGNGITSGVTALFTSAAWLGGAIF 309 (462)
T ss_pred HHHHHHHHHHHHHHHHHHHcCChHHHHHH--HHHHHHHHHHHHHHHHHHHHH-HHHHHHHHHHHHHHHHHhCcHHHHHHH
Confidence 48899999999988888887654444432 13444444433333 344533 235566565555666666664 34588
Q ss_pred HHHHHHHHHh
Q 024694 147 NASKQISAAI 156 (264)
Q Consensus 147 ~~iKqv~~~~ 156 (264)
..+-+..=.+
T Consensus 310 G~l~~~lV~~ 319 (462)
T TIGR01992 310 GLLYAPLVIT 319 (462)
T ss_pred HHHHHHHHHh
Confidence 8888866544
No 30
>TIGR01996 PTS-II-BC-sucr PTS system, sucrose-specific IIBC component. This family is closely related to the trehalose transporting PTS IIBC enzymes and the B and C domains of each are described by subfamily-domain level TIGRFAMs models (TIGR00826 and TIGR00852, respectively).
Probab=65.45 E-value=56 Score=32.56 Aligned_cols=85 Identities=13% Similarity=0.214 Sum_probs=56.7
Q ss_pred HHHHHHHHHHHHHHHHHHHHHhHhhhhhhcccchhhHHHHH-HHHHHHHHHHHHHHHHHHHHHHHHHhhchhc-eehhHH
Q 024694 69 LFPIAVTFYITWWFIHFVDGFFSPIYAQLGIDIFGLGFITS-VTFIFLIGVFMSSWLGASVLSLGEWFIKRMP-FVRHIY 146 (264)
Q Consensus 69 LLPi~iTi~Il~w~~~~vd~~~~pi~~~lg~~ipGlgll~~-llliflvG~l~~~~lg~~l~~~~E~~l~rIP-lVk~IY 146 (264)
++|..++.|+..|+=++++..+...++.+ -.|-+.++++ ++..+++|.+. .+++..+.++++++...-+ +..-+|
T Consensus 230 Vip~Il~g~i~~~iek~~~k~~P~~l~~~--~vP~l~~lv~~~l~~~vigp~~-~~i~~~i~~~~~~l~~~~~~i~~~i~ 306 (461)
T TIGR01996 230 VLPVLVAVWILAKIEKFLRKVVPNALDLL--LTPFLTLLITGFLTLLVIGPIG-RWVGDVLTDGLQWLYDLPGGLGGLLF 306 (461)
T ss_pred HHHHHHHHHHHHHHHHHHHHhchhhhhhh--hHHHHHHHHHHHHHHHHHHHHH-HHHHHHHHHHHHHHHhccHHHHHHHH
Confidence 78999999999999888887765555533 1344554444 33444577554 4677777777777776433 456688
Q ss_pred HHHHHHHHHh
Q 024694 147 NASKQISAAI 156 (264)
Q Consensus 147 ~~iKqv~~~~ 156 (264)
....++.-.+
T Consensus 307 G~l~~~Lv~~ 316 (461)
T TIGR01996 307 GGLYSLIVIT 316 (461)
T ss_pred HHHHHHHHHh
Confidence 8888875544
No 31
>TIGR02002 PTS-II-BC-glcB PTS system, glucose-specific IIBC component. This model represents the combined B and C domains of the PTS transport system enzyme II specific for glucose transport. Many of the genes in this family also include an A domain as part of the same polypeptide and thus should be given the name "PTS system, glucose-specific IIABC component" while the B. subtilus enzyme also contains an enzyme III domain which appears to act independently of the enzyme II domains. This family is most closely related to the N-acetylglucosamine-specific PTS enzymes (TIGR01998).
Probab=64.77 E-value=37 Score=34.30 Aligned_cols=87 Identities=7% Similarity=0.060 Sum_probs=58.6
Q ss_pred HHHHHHHHHHHHHHH-HHHHHHhHhhhhhhccc--chhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhchhc-eehh
Q 024694 69 LFPIAVTFYITWWFI-HFVDGFFSPIYAQLGID--IFGLGFITSVTFIFLIGVFMSSWLGASVLSLGEWFIKRMP-FVRH 144 (264)
Q Consensus 69 LLPi~iTi~Il~w~~-~~vd~~~~pi~~~lg~~--ipGlgll~~llliflvG~l~~~~lg~~l~~~~E~~l~rIP-lVk~ 144 (264)
++|.++..++..|+. ++.+..+...+..++-. .|-+.+++.+.+.+++|.+- .+++..+-+..+++.+.-| +-.-
T Consensus 135 V~~~Il~g~i~a~l~nk~~~k~lP~~l~~f~G~rfvPiit~lv~~~l~~i~~~iw-p~i~~~i~~~~~~l~~~~~~~g~~ 213 (502)
T TIGR02002 135 VFGGIIIGAIAAYCYNRFYNIKLPEYLGFFAGKRFVPIITGLAAIVTGIVLSFIW-PPVQDALNTFSHWAAYQNPVVAFF 213 (502)
T ss_pred cHHHHHHHHHHHHHHHHHhcccCcHHHHhcCCCchHHHHHHHHHHHHHHHHHHHH-HHHHHHHHHHHHHHHHcCcHHHHH
Confidence 589999999999999 77777765555554221 45566665555555555443 3667777767777666554 6667
Q ss_pred HHHHHHHHHHHh
Q 024694 145 IYNASKQISAAI 156 (264)
Q Consensus 145 IY~~iKqv~~~~ 156 (264)
+|..+.++.=.+
T Consensus 214 i~G~l~r~Lv~~ 225 (502)
T TIGR02002 214 IFGFIERSLIPF 225 (502)
T ss_pred HHHHHHHHHHHh
Confidence 899998876544
No 32
>PF08566 Pam17: Mitochondrial import protein Pam17; InterPro: IPR013875 The presequence translocase-associated motor (PAM) drives the completion of preprotein translocation into the mitochondrial matrix. The Pam17 subunit is required for formation of a stable complex between cochaperones Pam16 and Pam18 and promotes the association of Pam16-Pam18 with the presequence translocase []. Mitochondria lacking Pam17 are selectively impaired in the import of matrix proteins [].
Probab=62.97 E-value=76 Score=27.97 Aligned_cols=67 Identities=16% Similarity=0.113 Sum_probs=38.0
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHhHhhhhhhcccchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 024694 66 CVILFPIAVTFYITWWFIHFVDGFFSPIYAQLGIDIFGLGFITSVTFIFLIGVFMSSWLGASVLSLGEW 134 (264)
Q Consensus 66 LlvLLPi~iTi~Il~w~~~~vd~~~~pi~~~lg~~ipGlgll~~llliflvG~l~~~~lg~~l~~~~E~ 134 (264)
++.-+|-+++-..+.|.+ +...-+.|.-..+|++ |-+.+.+..+.|-.+|+|+--.+|..++....+
T Consensus 42 ~~~si~t~~~g~~~g~~y-l~~~~~D~~~~I~GlD-P~~~~g~~t~a~g~lG~L~GP~~G~~vf~l~~r 108 (173)
T PF08566_consen 42 LVSSIPTGLLGSSAGWAY-LSTIEIDPTQQIMGLD-PFMVYGLATLACGALGWLVGPSLGNQVFRLLNR 108 (173)
T ss_pred HHhHHHHHHHHHHHHHHH-HhhccccccccccCcC-HHHHHHHHHHHHHHHHHHhcchHHHHHHHHHhH
Confidence 344444444444444333 1222223433334655 334455555678899999999999988877653
No 33
>PRK15083 PTS system mannitol-specific transporter subunit IICBA; Provisional
Probab=62.72 E-value=33 Score=35.55 Aligned_cols=83 Identities=13% Similarity=0.090 Sum_probs=52.3
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHhHhhhhhhcccchhhH----HHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhch--hce
Q 024694 68 ILFPIAVTFYITWWFIHFVDGFFSPIYAQLGIDIFGLG----FITSVTFIFLIGVFMSSWLGASVLSLGEWFIKR--MPF 141 (264)
Q Consensus 68 vLLPi~iTi~Il~w~~~~vd~~~~pi~~~lg~~ipGlg----ll~~llliflvG~l~~~~lg~~l~~~~E~~l~r--IPl 141 (264)
.++|..++.|+..|+-+++++.+...++.+- .|-+. +++..+.++++|-+. +|+|..+-+++.++... .|+
T Consensus 101 svip~il~~~~~~~vek~l~k~ip~~l~~~~--~P~~tlli~~i~~~l~~~viGP~g-~~i~~~l~~~i~~l~~~~~~~~ 177 (639)
T PRK15083 101 AMIAGPLGGWAIKHFDRWVDGKIKSGFEMLV--NNFSAGIIGMILAILAFLGIGPAV-EVLSKMLAAGVNFMVVHDLLPL 177 (639)
T ss_pred chHHHHHHHHHHHHHHHHHHhhccchhhHhh--hhHHHHHHHHHHHHHHheeeHHHH-HHHHHHHHHHHHHHHhCcchhH
Confidence 6899999999999999998887655544321 12222 223345567777654 36777777777777665 444
Q ss_pred e-hhHHHHHHHHH
Q 024694 142 V-RHIYNASKQIS 153 (264)
Q Consensus 142 V-k~IY~~iKqv~ 153 (264)
+ .-++++.-++.
T Consensus 178 ~a~~i~~~~~~~l 190 (639)
T PRK15083 178 TSIFVEPAKILFL 190 (639)
T ss_pred HHHHHHHHHHHHH
Confidence 3 33445555543
No 34
>PRK15071 lipopolysaccharide ABC transporter permease; Provisional
Probab=59.06 E-value=43 Score=31.46 Aligned_cols=39 Identities=5% Similarity=0.114 Sum_probs=31.7
Q ss_pred HHHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHHHHHHHH
Q 024694 51 SKVVRSWASKKFMTGCVILFPIAVTFYITWWFIHFVDGF 89 (264)
Q Consensus 51 ~~~lr~~l~~~FltGLlvLLPi~iTi~Il~w~~~~vd~~ 89 (264)
|+.+..++-|.++..+++.+-+.+.++++.++++.++.+
T Consensus 2 M~il~rYi~r~~l~~~~~~l~~l~~l~~~~~~~~~l~~~ 40 (356)
T PRK15071 2 FGILDRYIGRTILSTIMLTLFMLVGLSGIIKFVDQLRKV 40 (356)
T ss_pred chHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhc
Confidence 577888888889998888888888888888888766554
No 35
>PRK15349 type III secretion system protein SsaT; Provisional
Probab=58.67 E-value=1.4e+02 Score=27.43 Aligned_cols=41 Identities=7% Similarity=0.066 Sum_probs=33.6
Q ss_pred HHHHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHHHHHHHHh
Q 024694 50 FSKVVRSWASKKFMTGCVILFPIAVTFYITWWFIHFVDGFF 90 (264)
Q Consensus 50 ~~~~lr~~l~~~FltGLlvLLPi~iTi~Il~w~~~~vd~~~ 90 (264)
....+-++..+.|..|+..-+|++++..++.-.+..+.+..
T Consensus 169 ~~~~~~~~~~~~f~~al~lAaP~i~~lll~~~~lGll~R~~ 209 (259)
T PRK15349 169 FLKYIQAEWRTLYQLCISFSLPAIICMVLADLALGLLNRSA 209 (259)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhC
Confidence 34555567788899999999999999999998888777664
No 36
>COG3768 Predicted membrane protein [Function unknown]
Probab=58.38 E-value=1e+02 Score=29.86 Aligned_cols=34 Identities=24% Similarity=0.265 Sum_probs=27.9
Q ss_pred HHHHHHHHHhhhhHHHHHHHHHHHHHHHHHHHHH
Q 024694 53 VVRSWASKKFMTGCVILFPIAVTFYITWWFIHFV 86 (264)
Q Consensus 53 ~lr~~l~~~FltGLlvLLPi~iTi~Il~w~~~~v 86 (264)
|=|+++.|+++++..+|+-+++-.|...|+-+..
T Consensus 58 rpr~s~~k~~~~a~~vLf~~Av~~q~~qwi~d~~ 91 (350)
T COG3768 58 RPRSSFWKIMLGAGGVLFSLAVGLQSVQWIRDLF 91 (350)
T ss_pred cccchHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 4456678999999999999999888888877654
No 37
>PRK10687 purine nucleoside phosphoramidase; Provisional
Probab=57.94 E-value=14 Score=30.02 Aligned_cols=36 Identities=14% Similarity=0.169 Sum_probs=31.0
Q ss_pred CCceEEEEecCCCCCCeeEEEEeCCCeecC-CCCHHH
Q 024694 196 EEELCCVYVPTNHLYIGDIFLINTKDVIRP-NLSVRE 231 (264)
Q Consensus 196 ~e~~v~VfvPtsp~tsG~l~lV~~~~V~~l-Dmsvee 231 (264)
+++.+.+|....|..-|-++++|++-+..+ |++.|+
T Consensus 22 edd~~~aflD~~P~~~GH~LViPK~H~~~l~dl~~~~ 58 (119)
T PRK10687 22 QDELVTAFRDISPQAPTHILIIPNILIPTVNDVSAEH 58 (119)
T ss_pred ECCCEEEEEcCCCCCCccEEEEehhHhCChhHCChHH
Confidence 467888999888988999999999998776 898886
No 38
>TIGR00851 mtlA PTS system, mannitol-specific IIC component. Bacterial PTS transporters transport and concomitantly phosphorylate their sugar substrates, and typically consist of multiple subunits or protein domains. The Fru family is a large and complex family which includes several sequenced fructose and mannitol-specific permeases as well as several putative PTS permeases of unknown specificities.The Fru family PTS systems typically have 3 domains, IIA, IIB and IIC, which may be found as 1 or more proteins. The fructose and mannitol transporters form separate phylogenetic clusters in this family. This family is specific for the IIC domain of the mannitol PTS transporters.
Probab=57.10 E-value=92 Score=29.86 Aligned_cols=83 Identities=12% Similarity=-0.029 Sum_probs=49.9
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHhHhhhhhhcccchhhHH----HHHHHHHHHHHHHHHHHHHHHHHHHHHHhhch--hce
Q 024694 68 ILFPIAVTFYITWWFIHFVDGFFSPIYAQLGIDIFGLGF----ITSVTFIFLIGVFMSSWLGASVLSLGEWFIKR--MPF 141 (264)
Q Consensus 68 vLLPi~iTi~Il~w~~~~vd~~~~pi~~~lg~~ipGlgl----l~~llliflvG~l~~~~lg~~l~~~~E~~l~r--IPl 141 (264)
-++|+.++.|+..|+-+++++.+...++.+- .|-+.+ ++..+.++++|=+. +++|..+-...+++.+. -|.
T Consensus 93 sViP~il~v~~~s~iEk~l~K~iP~~l~~i~--~P~ltlli~li~~pl~l~viGPig-~~ig~~i~~~i~~l~~~~~~~~ 169 (338)
T TIGR00851 93 AMIMGPLGGWLIKKTDEFVQGKVKQGFEMLV--NNFSAGIIGFILTILAFEGIGPIV-KAISKILAAGVEAIVHAHLLPL 169 (338)
T ss_pred hHHHHHHHHHHHHHHHHHHHhhCcHHHHHhH--hhHHHHHHHHHHHHHHHHHHHHHH-HHHHHHHHHHHHHHHhCcchhH
Confidence 7899999999999999999887644444321 233332 22344456666543 46666666666676652 333
Q ss_pred -ehhHHHHHHHHH
Q 024694 142 -VRHIYNASKQIS 153 (264)
Q Consensus 142 -Vk~IY~~iKqv~ 153 (264)
-.-+....-++.
T Consensus 170 ~~g~i~g~~~~~l 182 (338)
T TIGR00851 170 ASIFVEPAKILFL 182 (338)
T ss_pred HHHHHHHHHHHHH
Confidence 334455555543
No 39
>PRK11404 putative PTS system transporter subunits IIBC; Provisional
Probab=53.38 E-value=49 Score=33.37 Aligned_cols=67 Identities=16% Similarity=0.129 Sum_probs=43.0
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHh-----HhhhhhhcccchhhHHHHH-HHHHHHHHHHHHHHHHHHHHHHHHHhhc
Q 024694 68 ILFPIAVTFYITWWFIHFVDGFF-----SPIYAQLGIDIFGLGFITS-VTFIFLIGVFMSSWLGASVLSLGEWFIK 137 (264)
Q Consensus 68 vLLPi~iTi~Il~w~~~~vd~~~-----~pi~~~lg~~ipGlgll~~-llliflvG~l~~~~lg~~l~~~~E~~l~ 137 (264)
-++|..++.|+..|+.++++++. ..+.+. .-.|-++++++ .+.++++|=... |++..+.+++.++..
T Consensus 228 gflg~Il~g~~~gyv~k~lkki~~p~~~p~~~~~--~~~Pllt~li~~~l~~~viGP~~~-~i~~~l~~~l~~l~~ 300 (482)
T PRK11404 228 GFLGAVVLGLAIGYFVFWFRKVRLGKALQPLLGS--MLIPFVTLLVFGVLTYYVIGPVMS-DLMGGLLHFLNTIPP 300 (482)
T ss_pred cHHHHHHHHHHHHHHHHHHHhCCCCcchhhhcce--eeHHHHHHHHHHHHHHHHHHHHHH-HHHHHHHHHHHHHHc
Confidence 46899999999999999888865 222222 11455665544 344557776654 666666666666544
No 40
>COG3366 Uncharacterized protein conserved in archaea [Function unknown]
Probab=53.06 E-value=1.5e+02 Score=28.38 Aligned_cols=79 Identities=18% Similarity=0.311 Sum_probs=44.9
Q ss_pred CCCCCCCCCChhHHHHHHHHHHHHHhhhhHHHHHHHHHHHHHH--HHHHHHHHHHhHhhhhhhcccchhhHHHHHHHHHH
Q 024694 37 SSSSSSHHAGRETFSKVVRSWASKKFMTGCVILFPIAVTFYIT--WWFIHFVDGFFSPIYAQLGIDIFGLGFITSVTFIF 114 (264)
Q Consensus 37 ~~~~~~~~~~~~~~~~~lr~~l~~~FltGLlvLLPi~iTi~Il--~w~~~~vd~~~~pi~~~lg~~ipGlgll~~lllif 114 (264)
+.+.....+++|+..+- +++ |+|.+=.-.+.|..+.+..+ .-+++.+..+++|+.+.++..-..+-.+++-+.=+
T Consensus 156 ~~~~~~~~~~k~a~~~~-kt~--k~~~rv~~~~~~~~~li~~L~~~G~~d~~~~~~~pl~~~L~lp~eav~v~~~~~~~~ 232 (311)
T COG3366 156 SNSELSIPANKEAVKEA-KTF--KVFKRVIPVVVPATVLIFFLIELGLFDYVEEFLHPLTNYLPLPPEAVTVVLTNLANI 232 (311)
T ss_pred ccCCCCcchHHHHHhhh-hhH--HHHHHHHHHHHHHHHHHHHHHHhhHHHHHHHHhhhHhhhcCCCcchHHHHHHHHHHH
Confidence 34444556777777765 222 34444445555555544433 45678889999999888765544444444433344
Q ss_pred HHHH
Q 024694 115 LIGV 118 (264)
Q Consensus 115 lvG~ 118 (264)
..|+
T Consensus 233 ~~g~ 236 (311)
T COG3366 233 IAGI 236 (311)
T ss_pred HHHH
Confidence 4444
No 41
>TIGR02004 PTS-IIBC-malX PTS system, maltose and glucose-specific IIBC component. This model represents a family of PTS enzyme II fused B and C components including and most closely related to the MalX maltose and glucose-specific transporter of E. coli. A pair of paralogous genes from E. coli strain CFT073 score between trusted and noise and may have diverged sufficiently to have an altered substrate specificity.
Probab=52.26 E-value=92 Score=31.69 Aligned_cols=89 Identities=10% Similarity=0.024 Sum_probs=55.1
Q ss_pred HHHHHHHHHHHHHHHHHHHHH-hHhhhhhhcc--cchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhchhceeh-h
Q 024694 69 LFPIAVTFYITWWFIHFVDGF-FSPIYAQLGI--DIFGLGFITSVTFIFLIGVFMSSWLGASVLSLGEWFIKRMPFVR-H 144 (264)
Q Consensus 69 LLPi~iTi~Il~w~~~~vd~~-~~pi~~~lg~--~ipGlgll~~llliflvG~l~~~~lg~~l~~~~E~~l~rIPlVk-~ 144 (264)
++|.+++.++..|+.+...+. +...+..++- -+|-+.+++.+.+-+++.+ -+.++...++.+.+++...+.+. -
T Consensus 139 V~ggIi~g~i~a~i~n~~~k~~lP~~L~ff~G~rfVPiit~li~~~l~~~~p~--~wp~~~~~i~~~~~~i~~~g~~g~f 216 (517)
T TIGR02004 139 VLGAVIVGLIVYKLHNRFYTVQMPDALAFFGGARFVPIISALVLAVVGLVIPL--VWPLFALMIMAIGQLIQRSGIFGPF 216 (517)
T ss_pred hHHHHHHHHHHHHHHHHHccccCchHHHHccCCcchHHHHHHHHHHHHHHHHH--HHHHHHHHHHHHHHHHHhcChHHHH
Confidence 689999999999999998875 3333343321 1444444444333333322 24555666666667776655444 4
Q ss_pred HHHHHHHHHHHhCCC
Q 024694 145 IYNASKQISAAISPD 159 (264)
Q Consensus 145 IY~~iKqv~~~~~~~ 159 (264)
+|..+.+..-.+.-+
T Consensus 217 iyG~l~rlLIp~GLH 231 (517)
T TIGR02004 217 LFGSGERLLLPIGLH 231 (517)
T ss_pred HHHHHHHHHHHhccc
Confidence 999999987776543
No 42
>PF02674 Colicin_V: Colicin V production protein; InterPro: IPR003825 Colicin V is a small extracellular protein toxin which kills sensitive cells by disrupting their membrane potential []. Colicin V is produced from large low-copy plasmids and requires four plasmid genes for synthesis export and immunity [ 3034857). The cvaC gene is the structural gene for colicin V and cvaA and cvaB are required for processing and export of the toxin through the inner and outer membranes cvi confers immunity to the host cell. There are several stages at which host factors could play a role in colicin V production and mutations that alter any of these functions should result in lowered levels of extracellular colicin V ]. Colicin V production protein is required in Escherichia coli for colicin V production from plasmid pColV-K30 []. This entry represent the CvpA protein, which is involved in colicin V production. It is coded for by the cvpA gene, which is found upstream of the purF gene in the purF operon []. ; GO: 0009403 toxin biosynthetic process, 0016020 membrane
Probab=51.18 E-value=1.3e+02 Score=24.22 Aligned_cols=81 Identities=14% Similarity=0.257 Sum_probs=37.6
Q ss_pred HHHhhhhHHHHHHHHHHHHHHHHHHHHHHHHhHhhh-hhhcccchhhHHHHHHHHHHHHHHHHHHHHHH----HHHHHHH
Q 024694 59 SKKFMTGCVILFPIAVTFYITWWFIHFVDGFFSPIY-AQLGIDIFGLGFITSVTFIFLIGVFMSSWLGA----SVLSLGE 133 (264)
Q Consensus 59 ~~~FltGLlvLLPi~iTi~Il~w~~~~vd~~~~pi~-~~lg~~ipGlgll~~llliflvG~l~~~~lg~----~l~~~~E 133 (264)
+|=|+.-++-++=+++.+++-.+....+...+.... ..-..-...++++++.+++++++....+.+.+ ...++.|
T Consensus 18 ~rG~~~~~~~l~~~i~a~~~a~~~~~~~~~~l~~~~~~~~~~~~~~iaf~~~f~~~~~i~~~i~~~l~~~~~~~~~~~~d 97 (146)
T PF02674_consen 18 RRGFIRELFSLIGLIVALFVAFLFYPPLAPFLSNYFSSLSPPFANIIAFIILFVLVYIIVRIIGKLLRRIVKKPFLGWLD 97 (146)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhcccccHHH
Confidence 344555556666666666666666665555443322 00000112344444444444444444443333 3445555
Q ss_pred Hhhchh
Q 024694 134 WFIKRM 139 (264)
Q Consensus 134 ~~l~rI 139 (264)
+++.-+
T Consensus 98 r~lG~~ 103 (146)
T PF02674_consen 98 RLLGAL 103 (146)
T ss_pred HHHHHH
Confidence 554443
No 43
>PF05552 TM_helix: Conserved TM helix; InterPro: IPR008910 This alignment represents a conserved transmembrane helix as well as some flanking sequence. It is often found in association with a Mechanosensitive (MS) channel IPR006685 from INTERPRO.; PDB: 2VV5_F 2OAU_E.
Probab=51.17 E-value=41 Score=23.25 Aligned_cols=25 Identities=20% Similarity=0.405 Sum_probs=17.0
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHH
Q 024694 109 SVTFIFLIGVFMSSWLGASVLSLGE 133 (264)
Q Consensus 109 ~llliflvG~l~~~~lg~~l~~~~E 133 (264)
..++++++|+++.+++.+.+-+.++
T Consensus 20 ~AilIl~vG~~va~~v~~~~~~~l~ 44 (53)
T PF05552_consen 20 GAILILIVGWWVAKFVRKLVRRLLE 44 (53)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 4456788999888877765544444
No 44
>TIGR01400 fliR flagellar biosynthetic protein FliR. This model recognizes the FliR protein of bacterial flagellar biosynthesis. It distinguishes FliR from the homologous proteins bacterial type III protein secretion systems, known by names such as YopT, EscT, and HrcT.
Probab=50.37 E-value=2e+02 Score=26.17 Aligned_cols=41 Identities=17% Similarity=0.320 Sum_probs=34.2
Q ss_pred HHHHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHHHHHHHHh
Q 024694 50 FSKVVRSWASKKFMTGCVILFPIAVTFYITWWFIHFVDGFF 90 (264)
Q Consensus 50 ~~~~lr~~l~~~FltGLlvLLPi~iTi~Il~w~~~~vd~~~ 90 (264)
..+.+-+.....|..|+.+-+|+++...++.-.+.++.+..
T Consensus 158 ~~~~~~~~~~~~f~~a~~lAaPvi~~~ll~~~~lGll~R~~ 198 (245)
T TIGR01400 158 FFELILKALSDMFLLGLLLALPIIAALLLVNLVLGLVNRAA 198 (245)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcc
Confidence 34566677788899999999999999999998888877764
No 45
>PF06596 PsbX: Photosystem II reaction centre X protein (PsbX); InterPro: IPR009518 Oxygenic photosynthesis uses two multi-subunit photosystems (I and II) located in the cell membranes of cyanobacteria and in the thylakoid membranes of chloroplasts in plants and algae. Photosystem II (PSII) has a P680 reaction centre containing chlorophyll 'a' that uses light energy to carry out the oxidation (splitting) of water molecules, and to produce ATP via a proton pump. Photosystem I (PSI) has a P700 reaction centre containing chlorophyll that takes the electron and associated hydrogen donated from PSII to reduce NADP+ to NADPH. Both ATP and NADPH are subsequently used in the light-independent reactions to convert carbon dioxide to glucose using the hydrogen atom extracted from water by PSII, releasing oxygen as a by-product. PSII is a multisubunit protein-pigment complex containing polypeptides both intrinsic and extrinsic to the photosynthetic membrane [, ]. Within the core of the complex, the chlorophyll and beta-carotene pigments are mainly bound to the antenna proteins CP43 (PsbC) and CP47 (PsbB), which pass the excitation energy on to the reaction centre proteins D1 (Qb, PsbA) and D2 (Qa, PsbD) that bind all the redox-active cofactors involved in the energy conversion process. The PSII oxygen-evolving complex (OEC) oxidises water to provide protons for use by PSI, and consists of OEE1 (PsbO), OEE2 (PsbP) and OEE3 (PsbQ). The remaining subunits in PSII are of low molecular weight (less than 10 kDa), and are involved in PSII assembly, stabilisation, dimerisation, and photo-protection []. The low molecular weight transmembrane protein PsbX found in PSII is associated with the oxygen-evolving complex. Its expression is light-regulated. PsbX appears to be involved in the regulation of the amount of PSII [], and may be involved in the binding or turnover of quinone molecules at the Qb (PsbA) site [].; GO: 0015979 photosynthesis, 0009523 photosystem II, 0016020 membrane; PDB: 3ARC_x 3A0H_X 3A0B_X 3PRR_X 1S5L_x 4FBY_j 3PRQ_X 3KZI_X 3BZ2_X 3BZ1_X.
Probab=50.04 E-value=38 Score=22.79 Aligned_cols=26 Identities=12% Similarity=0.286 Sum_probs=18.5
Q ss_pred HHHHHHHHhhhhHHHHHHHHHHHHHH
Q 024694 54 VRSWASKKFMTGCVILFPIAVTFYIT 79 (264)
Q Consensus 54 lr~~l~~~FltGLlvLLPi~iTi~Il 79 (264)
|.+++..-+.+|+++++|+++.+..+
T Consensus 5 L~nfl~Sl~aG~~iVv~~i~~ali~V 30 (39)
T PF06596_consen 5 LSNFLLSLVAGAVIVVIPIAGALIFV 30 (39)
T ss_dssp HHHHHHHHHHHH-HHHHHHHHHHHHH
T ss_pred HHHHHHHHHhhhhhhhhhhhhheEEE
Confidence 56677666777779999998776544
No 46
>TIGR01427 PTS_IIC_fructo PTS system, fructose subfamily, IIC component. This model represents the IIC component, or IIC region of a IIABC or IIBC polypeptide of a phosphotransferase system for carbohydrate transport. Members of this family belong to the fructose-specific subfamily of the broader family (pfam02378) of PTS IIC proteins. Members should be found as part of the same chain or in the same operon as fructose family IIA (TIGR00848) and IIB (TIGR00829) protein regions. A number of bacterial species have members in two different branches of this subfamily, suggesting some diversity in substrate specificity of its members.
Probab=49.82 E-value=81 Score=30.40 Aligned_cols=72 Identities=11% Similarity=0.036 Sum_probs=42.5
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHhHhhhhhh--cccchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhchhc
Q 024694 68 ILFPIAVTFYITWWFIHFVDGFFSPIYAQL--GIDIFGLGFITSVTFIFLIGVFMSSWLGASVLSLGEWFIKRMP 140 (264)
Q Consensus 68 vLLPi~iTi~Il~w~~~~vd~~~~pi~~~l--g~~ipGlgll~~llliflvG~l~~~~lg~~l~~~~E~~l~rIP 140 (264)
-++|..++.|+..|+-+++++.+...++.+ -.-+|-+.++++.+..+++|=.. ++++..+-+++.++.+.-|
T Consensus 112 gII~gilag~~~~~lek~ikK~lP~~l~g~~~i~iiP~lt~li~~~~~~vigppi-~~i~~~l~~~l~~l~~~~~ 185 (346)
T TIGR01427 112 GIIAGFLAGYVVKGLQKYIKKKLPQSLRGLKPILIIPLLGTLIVGALIYGINIPV-AYLNYGLSNWLNIMGSPNA 185 (346)
T ss_pred HHHHHHHHHHHHHHHHHHHHhhCcHHHHhCCceeehhHHHHHHHHHHHHHHHHHH-HHHHHHHHHHHHHHHhhhH
Confidence 356666677776666666655443322210 01245566665556666777666 6788888877777665444
No 47
>PF02355 SecD_SecF: Protein export membrane protein; InterPro: IPR022813 Secretion across the inner membrane in some Gram-negative bacteria occurs via the preprotein translocase pathway. Proteins are produced in the cytoplasm as precursors, and require a chaperone subunit to direct them to the translocase component []. From there, the mature proteins are either targeted to the outer membrane, or remain as periplasmic proteins. The translocase protein subunits are encoded on the bacterial chromosome. The translocase itself comprises 7 proteins, including a chaperone protein (SecB), an ATPase (SecA), an integral membrane complex (SecCY, SecE and SecG), and two additional membrane proteins that promote the release of the mature peptide into the periplasm (SecD and SecF) []. The chaperone protein SecB [] is a highly acidic homotetrameric protein that exists as a "dimer of dimers" in the bacterial cytoplasm. SecB maintains preproteins in an unfolded state after translation, and targets these to the peripheral membrane protein ATPase SecA for secretion []. Together with SecY and SecG, SecE forms a multimeric channel through which preproteins are translocated, using both proton motive forces and ATP-driven secretion. The latter is mediated by SecA. The structure of the Escherichia coli SecYEG assembly revealed a sandwich of two membranes interacting through the extensive cytoplasmic domains []. Each membrane is composed of dimers of SecYEG. The monomeric complex contains 15 transmembrane helices. The SecD and SecF equivalents of the Gram-positive bacterium Bacillus subtilis are jointly present in one polypeptide, denoted SecDF, that is required to maintain a high capacity for protein secretion. Unlike the SecD subunit of the pre-protein translocase of E. coli, SecDF of B. subtilis was not required for the release of a mature secretory protein from the membrane, indicating that SecDF is involved in earlier translocation steps []. Comparison with SecD and SecF proteins from other organisms revealed the presence of 10 conserved regions in SecDF, some of which appear to be important for SecDF function. Interestingly, the SecDF protein of B. subtilis has 12 putative transmembrane domains. Thus, SecDF does not only show sequence similarity but also structural similarity to secondary solute transporters []. This entry represents bacterial SecD and SecF protein export membrane proteins and their archaeal homologues []. It is found in association with PF07549 from PFAM SecD and SecF proteins are part of the multimeric protein export complex comprising SecA, D, E, F, G, Y, and YajC []. SecD and SecF are required to maintain a proton motive force []. ; PDB: 3AQP_A 2RRN_A 3AQO_B.
Probab=49.56 E-value=1.5e+02 Score=25.93 Aligned_cols=70 Identities=19% Similarity=0.236 Sum_probs=46.7
Q ss_pred CCChhHHHHHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHHHHHHHHhHhhhhhhcccchhhHHHHHHHHHHHHHHHHHHH
Q 024694 44 HAGRETFSKVVRSWASKKFMTGCVILFPIAVTFYITWWFIHFVDGFFSPIYAQLGIDIFGLGFITSVTFIFLIGVFMSSW 123 (264)
Q Consensus 44 ~~~~~~~~~~lr~~l~~~FltGLlvLLPi~iTi~Il~w~~~~vd~~~~pi~~~lg~~ipGlgll~~llliflvG~l~~~~ 123 (264)
.+-++++..-+++.+++.+.+.+.++++.+..++. |- -+--+|.+.+++-.++|.+.+.+
T Consensus 118 ~~~~~~~~~s~~~tl~r~i~t~~ttll~~~~L~~~-------------------g~-~~l~~Fa~~l~iGvi~~~~ss~~ 177 (189)
T PF02355_consen 118 KSLREAINISIKQTLSRTIDTSLTTLLAALILFFF-------------------GG-GSLKGFALTLIIGVIIGTYSSLF 177 (189)
T ss_dssp S-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHC----------------------CHHHHHHHHHHHHHHHHHHHHHH
T ss_pred CCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh-------------------cc-chHHHHHHHHHHHHHHHHHHHHH
Confidence 34467888888888888888887777666443211 10 01135556666667888888888
Q ss_pred HHHHHHHHHH
Q 024694 124 LGASVLSLGE 133 (264)
Q Consensus 124 lg~~l~~~~E 133 (264)
+.+.++.+++
T Consensus 178 ia~~l~~~l~ 187 (189)
T PF02355_consen 178 IARPLLYWLV 187 (189)
T ss_dssp HHHHHHHHHH
T ss_pred HHHHHHHHHh
Confidence 8888877664
No 48
>PRK05701 fliR flagellar biosynthesis protein FliR; Reviewed
Probab=48.17 E-value=2.1e+02 Score=25.91 Aligned_cols=40 Identities=15% Similarity=0.206 Sum_probs=33.6
Q ss_pred HHHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHHHHHHHHh
Q 024694 51 SKVVRSWASKKFMTGCVILFPIAVTFYITWWFIHFVDGFF 90 (264)
Q Consensus 51 ~~~lr~~l~~~FltGLlvLLPi~iTi~Il~w~~~~vd~~~ 90 (264)
.+.+-++....|..|+.+-+|+++...++.-.+.++.+..
T Consensus 161 ~~~~~~~~~~~f~~a~~lAaP~i~~~ll~~~~lGll~R~~ 200 (242)
T PRK05701 161 FLLLAKALSAMFLIGLQLALPIIVLLLLVNLALGLINRTA 200 (242)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcc
Confidence 4556677788899999999999999999998888777664
No 49
>PF01313 Bac_export_3: Bacterial export proteins, family 3; InterPro: IPR002191 The fliL operon of Escherichia coli contains seven genes (including fliO, fliP, fliQ and fliR) involved in the biosynthesis and functioning of the flagellar organelle []. The fliO, fliP, fliQ and fliR genes encode highly hydrophobic polypeptides. The fliQ gene product, a small integral membrane protein that contains two putative transmembrane (TM) regions, is required for the assembly of the rivet at the earliest stage of flagellar biosynthesis. Proteins sharing an evolutionary relationship with FliQ have been found in a range of bacteria: these include Yop translocation protein S from Yersinia pestis []; surface antigen-presentation protein SpaQ from Salmonella typhimurium and Shigella flexneri []; and probable translocation protein Y4YM from Rhizobium sp. (strain NGR234) []. All of these members export proteins, that do not possess signal peptides, through the membrane. Although the proteins that these exporters move may be different, the exporters are thought to function in similar ways [].; GO: 0009306 protein secretion, 0016020 membrane
Probab=47.77 E-value=1.2e+02 Score=23.02 Aligned_cols=71 Identities=11% Similarity=0.242 Sum_probs=42.9
Q ss_pred HHHHHHhhhhHHHHHHHHHHHHHHHHHHHHHHHHhHhhhhhhcccchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 024694 56 SWASKKFMTGCVILFPIAVTFYITWWFIHFVDGFFSPIYAQLGIDIFGLGFITSVTFIFLIGVFMSSWLGASVLSLGE 133 (264)
Q Consensus 56 ~~l~~~FltGLlvLLPi~iTi~Il~w~~~~vd~~~~pi~~~lg~~ipGlgll~~llliflvG~l~~~~lg~~l~~~~E 133 (264)
.+.++.+...+...+|+.+.-.++.-+++.+.... ..+-.-+.++-=++.++++-++...|.++.+.++.+
T Consensus 5 ~l~r~al~~~l~~~~P~L~~alvvGlvIsi~QA~T-------qIqEqTL~fvpKl~av~~~l~~~g~wm~~~l~~ft~ 75 (76)
T PF01313_consen 5 DLLRQALWLVLMLSAPVLLVALVVGLVISIFQAAT-------QIQEQTLSFVPKLLAVFLVLLLFGPWMLQQLVDFTR 75 (76)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-------HHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Confidence 45666788899999999888877776665543321 111123444444444455555555677777766654
No 50
>TIGR01401 fliR_like_III type III secretion protein SpaR/YscT/HrcT. This model represents members of bacterial type III secretion systems homologous to the flagellar biosynthetic protein FliR (TIGRFAMs:TIGR01400).
Probab=47.75 E-value=2.2e+02 Score=26.02 Aligned_cols=42 Identities=10% Similarity=0.138 Sum_probs=34.4
Q ss_pred HHHHHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHHHHHHHHh
Q 024694 49 TFSKVVRSWASKKFMTGCVILFPIAVTFYITWWFIHFVDGFF 90 (264)
Q Consensus 49 ~~~~~lr~~l~~~FltGLlvLLPi~iTi~Il~w~~~~vd~~~ 90 (264)
...+.+-+.+.+.|..|+-+-+|+++...++.-.+.++.+..
T Consensus 164 ~~~~~~~~~~~~~f~~al~lAaPvi~~~ll~~l~lGllsR~~ 205 (253)
T TIGR01401 164 QGLSFVLSQLDQMMALALLLAAPVIIVLFLIELALGLLSRFA 205 (253)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhc
Confidence 345666677788999999999999999999988887776654
No 51
>COG2177 FtsX Cell division protein [Cell division and chromosome partitioning]
Probab=47.41 E-value=2.3e+02 Score=26.81 Aligned_cols=59 Identities=17% Similarity=0.218 Sum_probs=30.8
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHhHhhhhhhcccchhh-HHHHHHHHHHHHHHHHHHHH
Q 024694 66 CVILFPIAVTFYITWWFIHFVDGFFSPIYAQLGIDIFGL-GFITSVTFIFLIGVFMSSWL 124 (264)
Q Consensus 66 LlvLLPi~iTi~Il~w~~~~vd~~~~pi~~~lg~~ipGl-gll~~llliflvG~l~~~~l 124 (264)
+-.++|.++.-+++++.-..++.+...+...++...++. ..+.+..+|.++|++...+-
T Consensus 227 ~Ga~~~~~l~~~l~~~~~~~~~~~~~~~~~~f~~~~~~~~~~l~l~~~~~~iG~~~~~l~ 286 (297)
T COG2177 227 LGALIALALAALLLAGYRSSVNNVAPQFGQAFGLLGLGLDEVLLLLGILLLIGVLIAWLA 286 (297)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhhcCCchHHHHHHHHHHHHHHHHHHHH
Confidence 345777777655444444444444333333344333333 33445556788887766543
No 52
>COG0537 Hit Diadenosine tetraphosphate (Ap4A) hydrolase and other HIT family hydrolases [Nucleotide transport and metabolism / Carbohydrate transport and metabolism / General function prediction only]
Probab=46.88 E-value=35 Score=28.31 Aligned_cols=43 Identities=19% Similarity=0.227 Sum_probs=35.2
Q ss_pred CCceEEEEecCCCCCCeeEEEEeCCCeecC-CCCHHHHHHHHhh
Q 024694 196 EEELCCVYVPTNHLYIGDIFLINTKDVIRP-NLSVREGIEIVVS 238 (264)
Q Consensus 196 ~e~~v~VfvPtsp~tsG~l~lV~~~~V~~l-DmsveeAmk~iiS 238 (264)
+++++.+|+=-.|..-|.++++|++.+..+ |++.++..++...
T Consensus 20 e~~~~~afld~~P~~~gH~LviPk~h~~~l~~l~~~~~~~l~~~ 63 (138)
T COG0537 20 EDEHVLAFLDIYPAAPGHTLVIPKRHVSDLEDLDPEELAELFLL 63 (138)
T ss_pred eCCCEEEEecCCCCCCCeEEEEeccchhhhhhCCHHHHHHHHHH
Confidence 466788999888888999999999988886 9999876655443
No 53
>PRK10478 putative PTS system fructose-like transporter subunit EIIC; Provisional
Probab=45.46 E-value=1.1e+02 Score=29.95 Aligned_cols=94 Identities=19% Similarity=0.322 Sum_probs=53.1
Q ss_pred HHHHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHHHHH------------------HH-------HhHhhhh-hhccc---
Q 024694 50 FSKVVRSWASKKFMTGCVILFPIAVTFYITWWFIHFV------------------DG-------FFSPIYA-QLGID--- 100 (264)
Q Consensus 50 ~~~~lr~~l~~~FltGLlvLLPi~iTi~Il~w~~~~v------------------d~-------~~~pi~~-~lg~~--- 100 (264)
.+|.+ +-+++++++|+--.+|+++.-=++.-+-..+ +. +.-|++. ++.+.
T Consensus 4 ~~~~~-~~~~~hlmtGvS~MlP~VvagGil~ai~~~~~g~~~~~~~~~~~~~~~l~~iG~~~f~lmvpvlaayIa~SIa~ 82 (359)
T PRK10478 4 LVQIL-KNTRQHLMTGVSHMIPFVVAGGILLAVSVMLYGKGAVPDAVADPNLKKLFDIGVAGLTLMVPFLAAYIGYSIAD 82 (359)
T ss_pred HHHHH-HHHHHHHHhChhHhHhHHHHHHHHHHHHHHHccccccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcC
Confidence 44544 4468999999999999988654443332211 11 1123321 11110
Q ss_pred ----c-----------hhhHHHHHHHHHHHHHHHHHHHHHH-HHHHHHHHhhc--hhceehhH
Q 024694 101 ----I-----------FGLGFITSVTFIFLIGVFMSSWLGA-SVLSLGEWFIK--RMPFVRHI 145 (264)
Q Consensus 101 ----i-----------pGlgll~~llliflvG~l~~~~lg~-~l~~~~E~~l~--rIPlVk~I 145 (264)
. .|.||+-.++.-|++||+++ ++.+ ++-++.+.+.. =+|++.++
T Consensus 83 kpglapg~i~G~~a~~~~~GFlGaii~G~laGy~v~-~lkki~lpk~l~~~~piliiP~l~~l 144 (359)
T PRK10478 83 RSALAPCAIGAWVGNSFGAGFFGALIAGIIGGIVVH-YLKKIPVHKVLRSVMPIFIIPIVGTL 144 (359)
T ss_pred CccccHHHHHHHHHhcCCcchHHHHHHHHHHHHHHH-HHHhcCCchhhHhhcceeeeHHHHHH
Confidence 1 23578888888999999988 6655 34444444322 25555443
No 54
>TIGR01995 PTS-II-ABC-beta PTS system, beta-glucoside-specific IIABC component. This model 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.
Probab=45.41 E-value=1.6e+02 Score=30.51 Aligned_cols=80 Identities=13% Similarity=0.215 Sum_probs=39.6
Q ss_pred HHHHHHHHHHHHHHHHHHHHHhHhhhhhhcccchhhHHHHHHH-HHHHHHHHHHHHHHHHHHHHHHHhhchhc-eehhHH
Q 024694 69 LFPIAVTFYITWWFIHFVDGFFSPIYAQLGIDIFGLGFITSVT-FIFLIGVFMSSWLGASVLSLGEWFIKRMP-FVRHIY 146 (264)
Q Consensus 69 LLPi~iTi~Il~w~~~~vd~~~~pi~~~lg~~ipGlgll~~ll-liflvG~l~~~~lg~~l~~~~E~~l~rIP-lVk~IY 146 (264)
++|..+..|+..++.+++++.+.+.+..+ -.|.+.++++.. .++++|-+. .+++..+-.++.++...-| +...+|
T Consensus 211 vip~Il~~~l~~~iek~~~k~vP~~l~~~--f~Pli~~li~~~l~l~vigPig-~~i~~~i~~~l~~l~~~~~~i~~~ii 287 (610)
T TIGR01995 211 VIPVILAVWLMSYVEKFLKKVIPGALKNF--LTPLLVMLITVPLTLLIIGPLG-NYAGEGISSGILFLYEVSPWLAGALL 287 (610)
T ss_pred HHHHHHHHHHHHHHHHHHHhhChHHHHHH--HHHHHHHHHHHHHHHHHHHHHH-HHHHHHHHHHHHHHHhcchHHHHHHH
Confidence 36777777777777777777654443321 123333333222 223345332 3445555555555544433 233455
Q ss_pred HHHHH
Q 024694 147 NASKQ 151 (264)
Q Consensus 147 ~~iKq 151 (264)
..+-+
T Consensus 288 g~l~~ 292 (610)
T TIGR01995 288 AALWP 292 (610)
T ss_pred HHHHH
Confidence 55544
No 55
>PRK10110 bifunctional PTS system maltose and glucose-specific transporter subunits IICB; Provisional
Probab=42.96 E-value=1.6e+02 Score=30.09 Aligned_cols=88 Identities=9% Similarity=0.021 Sum_probs=49.9
Q ss_pred HHHHHHHHHHHHHHHHHHHHH-hHhhhhhhc-c-cchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhchhceeh-h
Q 024694 69 LFPIAVTFYITWWFIHFVDGF-FSPIYAQLG-I-DIFGLGFITSVTFIFLIGVFMSSWLGASVLSLGEWFIKRMPFVR-H 144 (264)
Q Consensus 69 LLPi~iTi~Il~w~~~~vd~~-~~pi~~~lg-~-~ipGlgll~~llliflvG~l~~~~lg~~l~~~~E~~l~rIPlVk-~ 144 (264)
++|.+++.++..|+.+...+. +...+..++ . -.|-+.+++.+.+.+++.+ -.=++..+.+.+.+++...+.+. -
T Consensus 148 V~ggIi~g~i~a~l~~k~~k~~lP~~l~~f~G~rfvPiit~lv~~~l~~i~~~--iwP~~~~~~~~~~~~~~~~g~ig~~ 225 (530)
T PRK10110 148 ILGAVIAGIIVWMLHERFHNIRLPDALAFFGGTRFVPIISSLVMGLVGLVIPL--VWPIFAMGISGLGHMINSAGDFGPM 225 (530)
T ss_pred hHHHHHHHHHHHHHHHHHhcccCcHHHHhcCCCccHHHHHHHHHHHHHHHHHH--HHHHHHHHHHHHHHHHHhccHHHHH
Confidence 588889999999999987774 333334331 1 1344444433333222211 12234444455556666655444 4
Q ss_pred HHHHHHHHHHHhCC
Q 024694 145 IYNASKQISAAISP 158 (264)
Q Consensus 145 IY~~iKqv~~~~~~ 158 (264)
+|..+.++.=.+.-
T Consensus 226 i~G~l~r~LVp~GL 239 (530)
T PRK10110 226 LFGTGERLLLPFGL 239 (530)
T ss_pred HHHHHHHHHHHhcc
Confidence 89999998766543
No 56
>TIGR00852 pts-Glc PTS system, maltose and glucose-specific subfamily, IIC component. permeases are in this class, as the cellobiose (Cel) b-glucoside PTS permease is in the Lac family (TC #4.A.3). These permeases show limited sequence similarity with members of the Fru family (TC #4.A.2). Several of the E. coli PTS permeases in the Glc family lack their own IIA domains and instead use the glucose IIA protein (IIAglc or Crr). Most of these permeases have the B and C domains linked together in a single polypeptide chain, and a cysteyl residue in the IIB domain is phosphorylated by direct phosphoryl transfer from IIAglc(his~P). Those permeases which lack a IIA domain include the maltose (Mal), arbutin-salicin-cellobiose (ASC), trehalose (Tre), putative glucoside (Glv) and sucrose (Scr) permeases of E. coli. Most, but not all Scr permeases of other bacteria also lack a IIA domain. This model is specific for the IIC domain of the Glc family PTS transporters.
Probab=40.72 E-value=1.9e+02 Score=26.73 Aligned_cols=87 Identities=11% Similarity=0.036 Sum_probs=47.1
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHhHhhhhhhcccchhhHHHHHHHHHHHHHHHHHHHHHH-HHHHHHHHhhchh-ceehhH
Q 024694 68 ILFPIAVTFYITWWFIHFVDGFFSPIYAQLGIDIFGLGFITSVTFIFLIGVFMSSWLGA-SVLSLGEWFIKRM-PFVRHI 145 (264)
Q Consensus 68 vLLPi~iTi~Il~w~~~~vd~~~~pi~~~lg~~ipGlgll~~llliflvG~l~~~~lg~-~l~~~~E~~l~rI-PlVk~I 145 (264)
.++|+.+.+++.+++=++++..+-..++.+. .|-+.+++...++++++..+..+++. .+-+..+++.+.- +.-.-+
T Consensus 66 ~~~~ii~~~~~~~~~~k~~~~~lP~~l~~~~--~p~~~~li~~~~~~~v~~p~~~~~~~~~i~~~~~~i~~~~~~~g~~i 143 (289)
T TIGR00852 66 VVGPILVGAIALALHERFLDKKLPDVLGFFL--GPRFVVIIAGFVAILLIGPLGRVWPPVGISALLHWLYSAGGALGGAI 143 (289)
T ss_pred eeHHHHHHHHHHHHHHHHhhhhCchhhhhcc--cchHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHcchHHHHHH
Confidence 4789999998888877777665533333221 13344444444444444444444444 3334445544433 333457
Q ss_pred HHHHHHHHHHh
Q 024694 146 YNASKQISAAI 156 (264)
Q Consensus 146 Y~~iKqv~~~~ 156 (264)
|..+-|+.=.+
T Consensus 144 ~g~l~~lLv~~ 154 (289)
T TIGR00852 144 FGFLYRLLVPT 154 (289)
T ss_pred HHHHHHHHHHH
Confidence 88887765444
No 57
>PF03596 Cad: Cadmium resistance transporter; InterPro: IPR004676 These proteins are members of the Cadmium Resistance (CadD) Family. To date, this family of proteins has only been found in Gram-positive bacteria. The CadD family includes two close orthologues in two Staphylococcus species that have been reported to function in cadmium resistance, and another staphylococcal protein that has been reported to possibly function in quaternary ammonium ion export.
Probab=38.75 E-value=59 Score=28.86 Aligned_cols=82 Identities=18% Similarity=0.186 Sum_probs=41.6
Q ss_pred hHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhchhceehhHHHHHHHHHHHhCCCcCcC-CcccEEEEEe--CCCCeeE
Q 024694 104 LGFITSVTFIFLIGVFMSSWLGASVLSLGEWFIKRMPFVRHIYNASKQISAAISPDQNTQ-AFKEVAIIRH--PRIGEYA 180 (264)
Q Consensus 104 lgll~~llliflvG~l~~~~lg~~l~~~~E~~l~rIPlVk~IY~~iKqv~~~~~~~~~~~-~Fk~VVlV~~--P~~g~~~ 180 (264)
+|+.+++..-++.++.....--.|++ .++.=+|+ |=.+|... .++++++ .-++ -.+- .+...+.
T Consensus 34 lG~~~Lv~~Sl~~~~~l~~ip~~wiL----GlLGliPI----~lGi~~l~---~~~~~~e~~~~~--~~~~~~~~~~i~~ 100 (191)
T PF03596_consen 34 LGFTILVLASLLGAFGLLFIPPEWIL----GLLGLIPI----YLGIKALF---SGEDDDEEEAEE--KLNSPKSNSLILT 100 (191)
T ss_pred HHHHHHHHHHHHHHHHHHhCCHHHHH----HHHHHHHH----HHHHHHHH---cCCCcccccccc--ccccccccchhHH
Confidence 56655554444444444332233332 34778896 88888764 3322211 1000 0111 1223566
Q ss_pred EEEEcccccccccCCCCceEEEEec
Q 024694 181 FGFITSSVVLQNYSGEEELCCVYVP 205 (264)
Q Consensus 181 iGFvT~~~~~~~~~~~e~~v~VfvP 205 (264)
++++|=- ++.|-..||+|
T Consensus 101 Va~iTiA-------nGgDNigIYiP 118 (191)
T PF03596_consen 101 VAAITIA-------NGGDNIGIYIP 118 (191)
T ss_pred hhhhhhh-------cCCCeEEEeeh
Confidence 6666633 26788999999
No 58
>PRK12780 fliR flagellar biosynthesis protein FliR; Reviewed
Probab=38.41 E-value=3.1e+02 Score=25.03 Aligned_cols=40 Identities=15% Similarity=0.058 Sum_probs=34.1
Q ss_pred HHHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHHHHHHHHh
Q 024694 51 SKVVRSWASKKFMTGCVILFPIAVTFYITWWFIHFVDGFF 90 (264)
Q Consensus 51 ~~~lr~~l~~~FltGLlvLLPi~iTi~Il~w~~~~vd~~~ 90 (264)
.+.+-++....|..|+..-+|++++..+..-.+..+.+..
T Consensus 169 ~~~~~~~~~~~f~~al~lAaP~i~~lll~~l~lGll~R~~ 208 (251)
T PRK12780 169 LVQLVDQLSEAFTLALRIASPFIIYSVIVNLAVGLVNKLT 208 (251)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Confidence 4566777888999999999999999999998888777764
No 59
>smart00743 Agenet Tudor-like domain present in plant sequences. Domain in plant sequences with possible chromatin-associated functions.
Probab=38.12 E-value=1.3e+02 Score=20.71 Aligned_cols=50 Identities=8% Similarity=-0.128 Sum_probs=37.6
Q ss_pred cEEEEEeCCCCeeEEEEEcccccccccCCCCceEEEEecCCCCCCeeEEEEeCCCeecC
Q 024694 167 EVAIIRHPRIGEYAFGFITSSVVLQNYSGEEELCCVYVPTNHLYIGDIFLINTKDVIRP 225 (264)
Q Consensus 167 ~VVlV~~P~~g~~~iGFvT~~~~~~~~~~~e~~v~VfvPtsp~tsG~l~lV~~~~V~~l 225 (264)
..|-+.++.+|.|--|.|++.. +++.+.|+.++ ...|....++.+++.+.
T Consensus 7 ~~Ve~~~~~~~~W~~a~V~~~~-------~~~~~~V~~~~--~~~~~~e~v~~~~LRp~ 56 (61)
T smart00743 7 DRVEVFSKEEDSWWEAVVTKVL-------GDGKYLVRYLT--ESEPLKETVDWSDLRPH 56 (61)
T ss_pred CEEEEEECCCCEEEEEEEEEEC-------CCCEEEEEECC--CCcccEEEEeHHHcccC
Confidence 4677888778999999999774 35678999987 33456677777777654
No 60
>PRK05415 hypothetical protein; Provisional
Probab=37.69 E-value=2.6e+02 Score=27.17 Aligned_cols=27 Identities=19% Similarity=0.178 Sum_probs=18.3
Q ss_pred HHHhhhhHHHHHHHHHHHHHHHHHHHHH
Q 024694 59 SKKFMTGCVILFPIAVTFYITWWFIHFV 86 (264)
Q Consensus 59 ~~~FltGLlvLLPi~iTi~Il~w~~~~v 86 (264)
++.|.+++..++=+++..+ ..|+.+.+
T Consensus 67 ~~~~~~~l~~l~~~~~~~~-~~~i~~~~ 93 (341)
T PRK05415 67 RKLLWGGLGLLGSLVVGQA-VQWLRDAF 93 (341)
T ss_pred HHHHHHHHHHHHHHHHHHH-HHHHHHHH
Confidence 6778888888877777766 55554433
No 61
>COG3763 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=34.98 E-value=93 Score=23.58 Aligned_cols=35 Identities=14% Similarity=0.211 Sum_probs=22.8
Q ss_pred hHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhchhcee
Q 024694 104 LGFITSVTFIFLIGVFMSSWLGASVLSLGEWFIKRMPFV 142 (264)
Q Consensus 104 lgll~~llliflvG~l~~~~lg~~l~~~~E~~l~rIPlV 142 (264)
+++ +.+++++++|++.-.|+.++. .++.+++=|=+
T Consensus 5 lai-l~ivl~ll~G~~~G~fiark~---~~k~lk~NPpi 39 (71)
T COG3763 5 LAI-LLIVLALLAGLIGGFFIARKQ---MKKQLKDNPPI 39 (71)
T ss_pred HHH-HHHHHHHHHHHHHHHHHHHHH---HHHHHhhCCCC
Confidence 444 566678888888777777754 45666665543
No 62
>PF07670 Gate: Nucleoside recognition; InterPro: IPR011642 This region in the nucleoside transporter proteins are responsible for determining nucleoside specificity in the human CNT1 and CNT2 proteins (e.g. O00337 from SWISSPROT) []. In the FeoB proteins (e.g. O25396 from SWISSPROT), which are believed to be Fe2+ transporters, it includes the membrane pore region, so the function of this region is likely to be more general than just nucleoside specificity []. This family may represent the pore and gate, with a wide potential range of specificity. Hence its name - Gate.; GO: 0001882 nucleoside binding; PDB: 3TIJ_A.
Probab=34.51 E-value=1.2e+02 Score=23.09 Aligned_cols=33 Identities=24% Similarity=0.710 Sum_probs=21.8
Q ss_pred HHHHHHHHHHHHHHHHHH------HHHHHhHhhhhhhcc
Q 024694 67 VILFPIAVTFYITWWFIH------FVDGFFSPIYAQLGI 99 (264)
Q Consensus 67 lvLLPi~iTi~Il~w~~~------~vd~~~~pi~~~lg~ 99 (264)
.-++|+++.+.++.|+.. .+..++.|+.+.+|.
T Consensus 2 ~~~~p~i~~~~~l~~iL~~~g~l~~i~~~l~P~~~~lgL 40 (109)
T PF07670_consen 2 LRALPIIIPFSILIWILEESGLLERISRLLEPLFRPLGL 40 (109)
T ss_dssp HHTHHHHHHHHHHHHHHHHTTHHHHHHHHHHHHHHHH--
T ss_pred eeeHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHhhcCC
Confidence 346777777777777665 455677888887764
No 63
>PRK14762 membrane protein; Provisional
Probab=34.34 E-value=70 Score=19.64 Aligned_cols=16 Identities=38% Similarity=0.698 Sum_probs=10.5
Q ss_pred HHHHHHHHHHHHHHHH
Q 024694 109 SVTFIFLIGVFMSSWL 124 (264)
Q Consensus 109 ~llliflvG~l~~~~l 124 (264)
.+..+|++|+++-+-+
T Consensus 7 ~i~iifligllvvtgv 22 (27)
T PRK14762 7 AVLIIFLIGLLVVTGV 22 (27)
T ss_pred HHHHHHHHHHHHHHHH
Confidence 3456788888865543
No 64
>PRK10845 colicin V production protein; Provisional
Probab=34.19 E-value=2.8e+02 Score=23.54 Aligned_cols=24 Identities=8% Similarity=0.111 Sum_probs=10.7
Q ss_pred HHHHHHHHHHHHHHHHHHHHHhhc
Q 024694 114 FLIGVFMSSWLGASVLSLGEWFIK 137 (264)
Q Consensus 114 flvG~l~~~~lg~~l~~~~E~~l~ 137 (264)
-+++.+.+..+....+++.|+++.
T Consensus 78 ~i~~~~l~~l~~~~~Lg~~dr~lG 101 (162)
T PRK10845 78 AIVNYVIGQLVEKTGLSGTDRVLG 101 (162)
T ss_pred HHHHHHHHHHHHHcCCchHHHHHH
Confidence 333334443333344455565544
No 65
>TIGR01427 PTS_IIC_fructo PTS system, fructose subfamily, IIC component. This model represents the IIC component, or IIC region of a IIABC or IIBC polypeptide of a phosphotransferase system for carbohydrate transport. Members of this family belong to the fructose-specific subfamily of the broader family (pfam02378) of PTS IIC proteins. Members should be found as part of the same chain or in the same operon as fructose family IIA (TIGR00848) and IIB (TIGR00829) protein regions. A number of bacterial species have members in two different branches of this subfamily, suggesting some diversity in substrate specificity of its members.
Probab=34.17 E-value=3.6e+02 Score=26.01 Aligned_cols=21 Identities=24% Similarity=0.346 Sum_probs=17.7
Q ss_pred HHHHHHhhhhHHHHHHHHHHH
Q 024694 56 SWASKKFMTGCVILFPIAVTF 76 (264)
Q Consensus 56 ~~l~~~FltGLlvLLPi~iTi 76 (264)
+-++|++++|.--++|+++.-
T Consensus 13 ~~~~~~lm~gis~miP~ivag 33 (346)
T TIGR01427 13 KGIYKHLLTGVSYMLPFVVAG 33 (346)
T ss_pred HHHHHHHHhchHHHHHHHHHH
Confidence 446788999999999998865
No 66
>PF09527 ATPase_gene1: Putative F0F1-ATPase subunit (ATPase_gene1)
Probab=33.68 E-value=79 Score=21.83 Aligned_cols=12 Identities=42% Similarity=0.681 Sum_probs=5.2
Q ss_pred hHHHHHHHHHHH
Q 024694 65 GCVILFPIAVTF 76 (264)
Q Consensus 65 GLlvLLPi~iTi 76 (264)
|+-++.|+++-.
T Consensus 7 g~~~~~~i~~g~ 18 (55)
T PF09527_consen 7 GFTMAAPILVGF 18 (55)
T ss_pred HHHHHHHHHHHH
Confidence 444444444333
No 67
>PRK00665 petG cytochrome b6-f complex subunit PetG; Reviewed
Probab=33.13 E-value=64 Score=21.41 Aligned_cols=21 Identities=24% Similarity=0.638 Sum_probs=17.4
Q ss_pred hHHHHHHHHHHHHHHHHHHHH
Q 024694 104 LGFITSVTFIFLIGVFMSSWL 124 (264)
Q Consensus 104 lgll~~llliflvG~l~~~~l 124 (264)
.|+++.++-+.++|+++..|+
T Consensus 7 ~GiVLGlipiTl~GlfvaAyl 27 (37)
T PRK00665 7 CGIVLGLIPVTLAGLFVAAWN 27 (37)
T ss_pred hhHHHHhHHHHHHHHHHHHHH
Confidence 477888888999999988775
No 68
>TIGR01620 hyp_HI0043 conserved hypothetical protein, TIGR01620. This model includes putative membrane proteins from alpha and gamma proteobacteria, each making up their own clade. The two clades have less than 25% identity between them. We could not find support for the assignment to the sequence from Brucella of being a GTP-binding protein.
Probab=33.09 E-value=3.1e+02 Score=26.02 Aligned_cols=29 Identities=17% Similarity=0.217 Sum_probs=18.8
Q ss_pred HHHHHhhhhHHHHHHHHHHHHHHHHHHHH
Q 024694 57 WASKKFMTGCVILFPIAVTFYITWWFIHF 85 (264)
Q Consensus 57 ~l~~~FltGLlvLLPi~iTi~Il~w~~~~ 85 (264)
++.+.|..+++.++=+++.++...|+.+.
T Consensus 12 ~~~~~~~~~~~~l~~~~~~~~~~~~i~~~ 40 (289)
T TIGR01620 12 SFGKLGLGALGVLFGLAFVLQAVQWIRNL 40 (289)
T ss_pred chHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 34566888888877776665555555443
No 69
>PF01594 UPF0118: Domain of unknown function DUF20; InterPro: IPR002549 This is a family of hypothetical proteins. A number of the sequence records state they are transmembrane proteins or putative permeases. It is not clear what source suggested that these proteins might be permeases and this information should be treated with caution.
Probab=32.98 E-value=3.8e+02 Score=24.36 Aligned_cols=31 Identities=10% Similarity=0.130 Sum_probs=18.7
Q ss_pred HHHHHHHHHHHHHhhchhceehhHHHHHHHHHHH
Q 024694 122 SWLGASVLSLGEWFIKRMPFVRHIYNASKQISAA 155 (264)
Q Consensus 122 ~~lg~~l~~~~E~~l~rIPlVk~IY~~iKqv~~~ 155 (264)
..+...+.+....+.+.+| ...+.+++..+.
T Consensus 69 ~~~~~~i~~~~~~l~~~l~---~~~~~i~~~~~~ 99 (327)
T PF01594_consen 69 YLIIPQIIQQIQSLIENLP---QYLDKIKSWLND 99 (327)
T ss_pred HHHHHHHHHHHHHHHHhhh---HHHHHhhhhhhc
Confidence 4566667777777888888 334444444333
No 70
>PRK02870 heat shock protein HtpX; Provisional
Probab=32.75 E-value=4.6e+02 Score=25.23 Aligned_cols=36 Identities=25% Similarity=0.498 Sum_probs=19.7
Q ss_pred hHHHHHHHHHHHhCCCcCcCCcccEEEEEeCCCCeeEEEE
Q 024694 144 HIYNASKQISAAISPDQNTQAFKEVAIIRHPRIGEYAFGF 183 (264)
Q Consensus 144 ~IY~~iKqv~~~~~~~~~~~~Fk~VVlV~~P~~g~~~iGF 183 (264)
.+|+.++++..... -....+|.+++-+..+.++.|+
T Consensus 116 ~L~~~ve~La~~ag----~p~~p~V~vi~~~~~NAFA~G~ 151 (336)
T PRK02870 116 QLYNVVEELLVAAG----LRFMPKVYIIDAPYMNAFASGY 151 (336)
T ss_pred HHHHHHHHHHHHcC----CCCCCeEEEEcCCCCceEEecC
Confidence 56777776655431 1112367777665555666553
No 71
>PF14584 DUF4446: Protein of unknown function (DUF4446)
Probab=32.06 E-value=3.2e+02 Score=23.28 Aligned_cols=27 Identities=7% Similarity=0.247 Sum_probs=20.3
Q ss_pred cCCcccEEEEEeC---C---CCeeEEEEEcccc
Q 024694 162 TQAFKEVAIIRHP---R---IGEYAFGFITSSV 188 (264)
Q Consensus 162 ~~~Fk~VVlV~~P---~---~g~~~iGFvT~~~ 188 (264)
...+++|.+|+|. . +=+++++++-++.
T Consensus 77 ~~~~~kvgvvRYnAF~dmGg~LSFslAlLD~~~ 109 (151)
T PF14584_consen 77 RNCVQKVGVVRYNAFEDMGGDLSFSLALLDDNN 109 (151)
T ss_pred HhccceEEEEEccCcccccccceeeeEEEeCCC
Confidence 4578999999974 2 3378888888774
No 72
>COG4597 BatB ABC-type amino acid transport system, permease component [Amino acid transport and metabolism]
Probab=32.02 E-value=2e+02 Score=27.92 Aligned_cols=47 Identities=13% Similarity=0.230 Sum_probs=32.4
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHhhchhceehhHHHHHHHHHHHh
Q 024694 110 VTFIFLIGVFMSSWLGASVLSLGEWFIKRMPFVRHIYNASKQISAAI 156 (264)
Q Consensus 110 llliflvG~l~~~~lg~~l~~~~E~~l~rIPlVk~IY~~iKqv~~~~ 156 (264)
+.++.-+|-+..||+-+++-...=.++.+||..-.|+==-.-+...+
T Consensus 110 iGfliGIaRLS~NWLi~kl~~vYvEiFRNiPpLL~IfFWYf~Vl~~L 156 (397)
T COG4597 110 IGFLIGIARLSDNWLIRKLSTVYVEIFRNIPPLLQIFFWYFGVLSVL 156 (397)
T ss_pred HHHHHHHHHhchhHHHHHHHHHHHHHHhcCcHHHHHHHHHHHHHhhC
Confidence 33444445578888888887777788999998877765555555544
No 73
>TIGR02003 PTS-II-BC-unk1 PTS system, IIBC component. This model represents a family of fused B and C components of PTS enzyme II. This clade is a member of a larger family which contains enzyme II's specific for a variety of sugars including glucose (TIGR02002) and N-acetylglucosamine (TIGR01998). None of the members of this clade have been experimentally characterized. This clade includes sequences from Streptococcus and Enterococcus which also include a C-terminal A domain as well as Bacillus and Clostridium which do not. In nearly all cases, these species also contain an authentic glucose-specific PTS transporter.
Probab=31.61 E-value=3.2e+02 Score=28.15 Aligned_cols=89 Identities=8% Similarity=0.147 Sum_probs=54.6
Q ss_pred HHHHHHHHHHHHHHHHHHHH--HhHhhhhhhc-c-cchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhh---chhc-
Q 024694 69 LFPIAVTFYITWWFIHFVDG--FFSPIYAQLG-I-DIFGLGFITSVTFIFLIGVFMSSWLGASVLSLGEWFI---KRMP- 140 (264)
Q Consensus 69 LLPi~iTi~Il~w~~~~vd~--~~~pi~~~lg-~-~ipGlgll~~llliflvG~l~~~~lg~~l~~~~E~~l---~rIP- 140 (264)
++|.+++.++..|+.+..-+ .+...+..++ . -+|-+.+++.+.+-++.+++-= +++..+-+..+++. ..-|
T Consensus 142 VfggIi~g~i~a~l~n~~~~~k~lP~~L~ff~G~RfVPilt~lv~i~l~~i~~~iwP-~i~~gI~~~~~~i~~~g~~~~~ 220 (548)
T TIGR02003 142 VFVGIIAGFLGATAYNKYYNYDKLPEALAFFNGKRFVPFVVILRSIFTAIILSLLWP-FIQSGINEFGMWIAASKDSAPI 220 (548)
T ss_pred hHHHHHHHHHHHHHHHHHhccccCcHHHHHccCCcchHhHHHHHHHHHHHHHHHHhH-HHHHHHHHHHHHHHhcCCccch
Confidence 58999999999999998833 3433334332 1 1455555444444333333322 66666667777776 3334
Q ss_pred eehhHHHHHHHHHHHhCC
Q 024694 141 FVRHIYNASKQISAAISP 158 (264)
Q Consensus 141 lVk~IY~~iKqv~~~~~~ 158 (264)
+-.-+|..+.++.=.+.-
T Consensus 221 ~g~fiyG~l~rlLIp~GL 238 (548)
T TIGR02003 221 LAPFLYGTLERLLLPFGL 238 (548)
T ss_pred HHHHHHHHHHHHHHHhcc
Confidence 556799999998766543
No 74
>PRK01844 hypothetical protein; Provisional
Probab=31.34 E-value=1e+02 Score=23.39 Aligned_cols=30 Identities=10% Similarity=0.277 Sum_probs=19.8
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHhhchhceeh
Q 024694 111 TFIFLIGVFMSSWLGASVLSLGEWFIKRMPFVR 143 (264)
Q Consensus 111 lliflvG~l~~~~lg~~l~~~~E~~l~rIPlVk 143 (264)
++++++|++.--++.+ .++|+-+++=|=+.
T Consensus 11 I~~li~G~~~Gff~ar---k~~~k~lk~NPpin 40 (72)
T PRK01844 11 VVALVAGVALGFFIAR---KYMMNYLQKNPPIN 40 (72)
T ss_pred HHHHHHHHHHHHHHHH---HHHHHHHHHCCCCC
Confidence 3567777776666666 45677788776543
No 75
>TIGR02872 spore_ytvI sporulation integral membrane protein YtvI. Three lines of evidence show this protein to be involved in sporulation. First, it is under control of a sporulation-specific sigma factor, sigma-E. Second, mutation leads to a sporulation defect. Third, it if found in exactly those genomes whose bacteria are capable of sporulation, except for being absent in Clostridium acetobutylicum ATCC824. This protein has extensive hydrophobic regions and is likely an integral membrane protein.
Probab=31.28 E-value=4.1e+02 Score=24.21 Aligned_cols=19 Identities=16% Similarity=0.127 Sum_probs=12.2
Q ss_pred HHHHHHHHHHHHhhchhce
Q 024694 123 WLGASVLSLGEWFIKRMPF 141 (264)
Q Consensus 123 ~lg~~l~~~~E~~l~rIPl 141 (264)
+++..+.+..+++.+++|-
T Consensus 72 ~l~~~l~~q~~~l~~~lp~ 90 (341)
T TIGR02872 72 ILVTELVTETIALAKNLPQ 90 (341)
T ss_pred HHHHHHHHHHHHHHHHhhH
Confidence 4555566666677777774
No 76
>CHL00008 petG cytochrome b6/f complex subunit V
Probab=31.15 E-value=71 Score=21.20 Aligned_cols=21 Identities=29% Similarity=0.665 Sum_probs=17.3
Q ss_pred hHHHHHHHHHHHHHHHHHHHH
Q 024694 104 LGFITSVTFIFLIGVFMSSWL 124 (264)
Q Consensus 104 lgll~~llliflvG~l~~~~l 124 (264)
.|+++.++-+.++|+++..|+
T Consensus 7 ~GiVLGlipvTl~GlfvaAyl 27 (37)
T CHL00008 7 FGIVLGLIPITLAGLFVTAYL 27 (37)
T ss_pred hhHHHHhHHHHHHHHHHHHHH
Confidence 477788888999999988775
No 77
>PF11241 DUF3043: Protein of unknown function (DUF3043); InterPro: IPR021403 Some members in this family of proteins with unknown function are annotated as membrane proteins. This cannot be confirmed.
Probab=30.96 E-value=1.5e+02 Score=26.02 Aligned_cols=15 Identities=13% Similarity=0.527 Sum_probs=11.4
Q ss_pred HHHHHHHHHHHHHHH
Q 024694 68 ILFPIAVTFYITWWF 82 (264)
Q Consensus 68 vLLPi~iTi~Il~w~ 82 (264)
+++|+++.+.++.++
T Consensus 80 ~fmP~alv~lv~~~v 94 (170)
T PF11241_consen 80 FFMPVALVLLVLSFV 94 (170)
T ss_pred HHHHHHHHHHHHHHH
Confidence 357898888887765
No 78
>PRK10494 hypothetical protein; Provisional
Probab=30.76 E-value=3.9e+02 Score=24.47 Aligned_cols=64 Identities=13% Similarity=0.008 Sum_probs=30.9
Q ss_pred HHHhhhhHHHHHHHHHHHHHHHHHHHHHHHHhHhhhhhhcccchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 024694 59 SKKFMTGCVILFPIAVTFYITWWFIHFVDGFFSPIYAQLGIDIFGLGFITSVTFIFLIGVFMSSWLGASVLSLGEW 134 (264)
Q Consensus 59 ~~~FltGLlvLLPi~iTi~Il~w~~~~vd~~~~pi~~~lg~~ipGlgll~~llliflvG~l~~~~lg~~l~~~~E~ 134 (264)
-+++++.++.=+|+.+.+.++.|++-+... . ...+..++++.+.++-++...+++..++..+|.
T Consensus 5 l~K~i~~ll~P~~~~llll~l~~ll~~~~r-------~-----~r~~~~l~~~~~~~l~l~s~~~~~~~Ll~~LE~ 68 (259)
T PRK10494 5 LKKVIGGLLLPLPLLLLIIGAGLALLWFSR-------F-----QKTGKIFISIGWLALLLLSLQPVADRLLRPIES 68 (259)
T ss_pred HHHHHHHHHhhHHHHHHHHHHHHHHHHHHh-------H-----HHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHhc
Confidence 355666666666666665555543222100 0 011211222222333344556777778877775
No 79
>TIGR01183 ntrB nitrate ABC transporter, permease protein. This model describes the nitrate transport permease in bacteria. This is gene product of ntrB. The nitrate transport permease is the integral membrane component of the nitrate transport system and belongs to the ATP-binding cassette (ABC) superfamily. At least in photosynthetic bacteria nitrate assimilation is aided by other proteins derived from the operon which among others include products of ntrA, ntrB, ntrC, ntrD, narB. Functionally ntrC and ntrD resemble the ATP binding components of the binding protein-dependent transport systems. Mutational studies have shown that ntrB and ntrC are mandatory for nitrate accumulation. Nitrate reductase is encoded by narB.
Probab=29.63 E-value=3.8e+02 Score=23.40 Aligned_cols=67 Identities=16% Similarity=0.155 Sum_probs=41.2
Q ss_pred HHHHHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHHHHHHHHhHhhhhhhcccchhhHHHHHHHHHHHHH
Q 024694 49 TFSKVVRSWASKKFMTGCVILFPIAVTFYITWWFIHFVDGFFSPIYAQLGIDIFGLGFITSVTFIFLIG 117 (264)
Q Consensus 49 ~~~~~lr~~l~~~FltGLlvLLPi~iTi~Il~w~~~~vd~~~~pi~~~lg~~ipGlgll~~llliflvG 117 (264)
.++..+...+.+. +.|+.+-+-+.+.+-++-....+++..+.|++..+ ..+|-++++-.+++.|-.|
T Consensus 14 ~~~~~~~~Tl~r~-~~g~~ia~~ig~~lG~~~~~~~~~~~~~~p~~~~l-~~iP~~~~~pl~~~~fG~g 80 (202)
T TIGR01183 14 GLFWQIIASLTRV-AVGFSIAAIIGIAVGILIGLSKFLNAALDPIFQVL-RTIPPLAWLPIALAAFQDA 80 (202)
T ss_pred HHHHHHHHHHHHH-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-hhCCHHHHHHHHHHHHhcC
Confidence 4666666666654 44555555555555566666788999999987653 3456566655544444433
No 80
>PF14257 DUF4349: Domain of unknown function (DUF4349)
Probab=29.52 E-value=92 Score=28.19 Aligned_cols=9 Identities=22% Similarity=0.150 Sum_probs=3.3
Q ss_pred HHHHHHHHH
Q 024694 68 ILFPIAVTF 76 (264)
Q Consensus 68 vLLPi~iTi 76 (264)
.++|+++.+
T Consensus 242 ~l~p~~~~~ 250 (262)
T PF14257_consen 242 GLLPWLPLI 250 (262)
T ss_pred HHHHHHHHH
Confidence 333333333
No 81
>PRK11365 ssuC alkanesulfonate transporter permease subunit; Provisional
Probab=29.45 E-value=3e+02 Score=24.82 Aligned_cols=67 Identities=10% Similarity=0.041 Sum_probs=41.7
Q ss_pred hHHHHHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHHHHHHHHhHhhhhhhcccchhhHHHHHHHHHHHH
Q 024694 48 ETFSKVVRSWASKKFMTGCVILFPIAVTFYITWWFIHFVDGFFSPIYAQLGIDIFGLGFITSVTFIFLI 116 (264)
Q Consensus 48 ~~~~~~lr~~l~~~FltGLlvLLPi~iTi~Il~w~~~~vd~~~~pi~~~lg~~ipGlgll~~llliflv 116 (264)
+.+++.+-..+.+. +.|+++-+.+++.+-++....+++|.++.|+... ...+|-+.++..++..|-.
T Consensus 56 ~~l~~~l~~Tl~~~-~~g~~la~~igi~lGi~~~~~~~~~~~~~~~~~~-~~siP~~~~~~lli~~fg~ 122 (263)
T PRK11365 56 GELWQHLAISSWRA-LIGFSIGGSLGLILGLISGLSRWGERLLDTSIQM-LRNVPHLALIPLVILWFGI 122 (263)
T ss_pred CcHHHHHHHHHHHH-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-HhhCCHHHHHHHHHHHHcC
Confidence 35677777776553 4466666777777777666677888888887654 3345655555444444433
No 82
>PF02762 Cbl_N3: CBL proto-oncogene N-terminus, SH2-like domain; InterPro: IPR014742 Cbl (Casitas B-lineage lymphoma) is an adaptor protein that functions as a negative regulator of many signalling pathways that start from receptors at the cell surface. The N-terminal region of Cbl contains a Cbl-type phosphotyrosine-binding (Cbl-PTB) domain, which is composed of three evolutionarily conserved domains: an N-terminal four-helix bundle (4H) domain, an EF hand-like calcium-binding domain, and a divergent SH2-like domain. The calcium-bound EF-hand wedges between the 4H and SH2 domains, and roughly determines their relative orientation. The Cbl-PTB domain has also been named Cbl N-terminal (Cbl-N) or tyrosine kinase binding (TKB) domain [, ]. The N-terminal 4H domain contains four long alpha-helices. The C and D helices in this domain pack against the adjacent EF-hand-like domain, and a highly conserved loop connecting the A and B helices contacts the SH2-like domain. The EF-hand motif is similar to classical EF-hand proteins. The SH2-like domain retains the general helix-sheet-helix architecture of the SH2 fold, but lacks the secondary beta-sheet, comprising beta-strands D', E and F, and also a prominent BG loop []. This entry represents the SH2-like domain.; PDB: 3PFV_A 3VGO_A 3PLF_B 2Y1M_A 2CBL_A 3BUX_B 3BUN_B 3BUM_B 3OB1_B 3BUW_B ....
Probab=28.77 E-value=81 Score=24.54 Aligned_cols=37 Identities=24% Similarity=0.445 Sum_probs=24.7
Q ss_pred HHHHHHHHHHhCCCcCcCCcccEEEEEe--CCCCeeEEEEEcccc
Q 024694 146 YNASKQISAAISPDQNTQAFKEVAIIRH--PRIGEYAFGFITSSV 188 (264)
Q Consensus 146 Y~~iKqv~~~~~~~~~~~~Fk~VVlV~~--P~~g~~~iGFvT~~~ 188 (264)
|.-+|...+.+..+ ..+ -+.+. -+-|-|+||+||.+.
T Consensus 11 Ydevk~~L~~~~~k--pGs----YiFRlSCTrLGQWAIGyV~~dg 49 (86)
T PF02762_consen 11 YDEVKARLQHYRDK--PGS----YIFRLSCTRLGQWAIGYVTQDG 49 (86)
T ss_dssp HHHHHHHHGGGTTS--TTE----EEEEEESSSTTSEEEEEEETTS
T ss_pred HHHHHHHHHHHhCC--ccc----EEEeeccccccceeEEEEcCCC
Confidence 77888888877632 222 12232 366999999999873
No 83
>COG3125 CyoD Heme/copper-type cytochrome/quinol oxidase, subunit 4 [Energy production and conversion]
Probab=28.66 E-value=3.3e+02 Score=22.34 Aligned_cols=22 Identities=18% Similarity=0.256 Sum_probs=11.7
Q ss_pred HHHHHHHHhhhhHHHHHHHHHH
Q 024694 54 VRSWASKKFMTGCVILFPIAVT 75 (264)
Q Consensus 54 lr~~l~~~FltGLlvLLPi~iT 75 (264)
+++.+---.+.=++.++|..+.
T Consensus 17 ~k~y~iGFvLsIiLT~ipF~~v 38 (111)
T COG3125 17 LKSYLIGFVLSIILTLIPFWVV 38 (111)
T ss_pred HHHHHHHHHHHHHHHHHHHHHH
Confidence 5555444455555666666544
No 84
>PF03739 YjgP_YjgQ: Predicted permease YjgP/YjgQ family; InterPro: IPR005495 Members of this family are predicted integral membrane proteins of unknown function. They are about 350 amino acids long, contain about 6 transmembrane regions and may be permeases, although there is no verification of this.; GO: 0016021 integral to membrane
Probab=28.40 E-value=2.9e+02 Score=25.44 Aligned_cols=30 Identities=13% Similarity=0.375 Sum_probs=17.3
Q ss_pred HHhhhhHHHHHHHHHHHHHHHHHHHHHHHH
Q 024694 60 KKFMTGCVILFPIAVTFYITWWFIHFVDGF 89 (264)
Q Consensus 60 ~~FltGLlvLLPi~iTi~Il~w~~~~vd~~ 89 (264)
+.|+.=.++.+-....++++..+++.++.+
T Consensus 5 ~~~l~~f~~~l~~~~~i~~~~~l~~~l~~~ 34 (354)
T PF03739_consen 5 KEFLKTFLLVLLSFTGIFLIIDLFELLDDF 34 (354)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 344444555555556666666666666555
No 85
>PF02529 PetG: Cytochrome B6-F complex subunit 5; InterPro: IPR003683 This family consists of cytochrome b6/f complex subunit 5 (PetG). The cytochrome bf complex, found in green plants, eukaryotic algae and cyanobacteria, connects photosystem I to photosystem II in the electron transport chain, functioning as a plastoquinol:plastocyanin/cytochrome c6 oxidoreductase []. The purified complex from the unicellular alga Chlamydomonas reinhardtii contains seven subunits; namely four high molecular weight subunits (cytochrome f, Rieske iron-sulphur protein, cytochrome b6, and subunit IV) and three approximately miniproteins (PetG, PetL, and PetX) []. Stoichiometry measurements are consistent with every subunit being present as two copies per b6/f dimer. The absence of PetG affects either the assembly or stability of the cytochrome bf complex in C. reinhardtii [].; GO: 0009512 cytochrome b6f complex; PDB: 1Q90_G 2ZT9_G 1VF5_G 2D2C_G 2E74_G 2E75_G 2E76_G.
Probab=27.33 E-value=1.1e+02 Score=20.39 Aligned_cols=21 Identities=24% Similarity=0.580 Sum_probs=17.1
Q ss_pred hHHHHHHHHHHHHHHHHHHHH
Q 024694 104 LGFITSVTFIFLIGVFMSSWL 124 (264)
Q Consensus 104 lgll~~llliflvG~l~~~~l 124 (264)
.|+++.++-+.++|+++..|.
T Consensus 7 ~GiVlGli~vtl~Glfv~Ay~ 27 (37)
T PF02529_consen 7 SGIVLGLIPVTLAGLFVAAYL 27 (37)
T ss_dssp HHHHHHHHHHHHHHHHHHHHH
T ss_pred hhHHHHhHHHHHHHHHHHHHH
Confidence 477888888999999988764
No 86
>PF02419 PsbL: PsbL protein; InterPro: IPR003372 Oxygenic photosynthesis uses two multi-subunit photosystems (I and II) located in the cell membranes of cyanobacteria and in the thylakoid membranes of chloroplasts in plants and algae. Photosystem II (PSII) has a P680 reaction centre containing chlorophyll 'a' that uses light energy to carry out the oxidation (splitting) of water molecules, and to produce ATP via a proton pump. Photosystem I (PSI) has a P700 reaction centre containing chlorophyll that takes the electron and associated hydrogen donated from PSII to reduce NADP+ to NADPH. Both ATP and NADPH are subsequently used in the light-independent reactions to convert carbon dioxide to glucose using the hydrogen atom extracted from water by PSII, releasing oxygen as a by-product. PSII is a multisubunit protein-pigment complex containing polypeptides both intrinsic and extrinsic to the photosynthetic membrane [, ]. Within the core of the complex, the chlorophyll and beta-carotene pigments are mainly bound to the antenna proteins CP43 (PsbC) and CP47 (PsbB), which pass the excitation energy on to the reaction centre proteins D1 (Qb, PsbA) and D2 (Qa, PsbD) that bind all the redox-active cofactors involved in the energy conversion process. The PSII oxygen-evolving complex (OEC) oxidises water to provide protons for use by PSI, and consists of OEE1 (PsbO), OEE2 (PsbP) and OEE3 (PsbQ). The remaining subunits in PSII are of low molecular weight (less than 10 kDa), and are involved in PSII assembly, stabilisation, dimerisation, and photo-protection []. This family represents the low molecular weight transmembrane protein PsbL found in PSII. PsbL is located in a gene cluster with PsbE, PsbF and PsbJ (PsbEFJL). Both PsbL and PsbJ (IPR002682 from INTERPRO) are essential for proper assembly of the OEC. Mutations in PsbL prevent the formation of both PSII core dimers and PSII-light harvesting complex []. In addition, both PsbL and PsbJ are involved in the unidirectional flow of electrons, where PsbJ regulates the forward electron flow from D2 (Qa) to the plastoquinone pool, and PsbL prevents the reduction of PSII by back electron flow from plastoquinol protecting PSII from photo-inactivation [].; GO: 0015979 photosynthesis, 0009523 photosystem II, 0009539 photosystem II reaction center, 0016020 membrane; PDB: 3A0H_L 3A0B_l 3ARC_l 1S5L_l 2AXT_l 3BZ2_L 4FBY_L 3PRQ_L 3PRR_L 3KZI_L ....
Probab=27.04 E-value=1.1e+02 Score=20.31 Aligned_cols=20 Identities=25% Similarity=0.579 Sum_probs=15.2
Q ss_pred HHHHHHHHHHHHHHHHHHHH
Q 024694 105 GFITSVTFIFLIGVFMSSWL 124 (264)
Q Consensus 105 gll~~llliflvG~l~~~~l 124 (264)
.+-..++++|++|++.++++
T Consensus 16 SLY~GLllifvl~vLFssyf 35 (37)
T PF02419_consen 16 SLYWGLLLIFVLAVLFSSYF 35 (37)
T ss_dssp HHHHHHHHHHHHHHHHHHHH
T ss_pred hHHHHHHHHHHHHHHhhhhh
Confidence 45556778899999988875
No 87
>PF11947 DUF3464: Protein of unknown function (DUF3464); InterPro: IPR021855 This family of proteins are functionally uncharacterised. This protein is found in bacteria and eukaryotes. Proteins in this family are typically between 137 to 196 amino acids in length.
Probab=26.94 E-value=4.1e+02 Score=22.88 Aligned_cols=61 Identities=13% Similarity=0.113 Sum_probs=33.8
Q ss_pred HHHHHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHHHHHHHHhHhhhhhhcccchhhHHHHHHHHHHHHHHHHHHH
Q 024694 49 TFSKVVRSWASKKFMTGCVILFPIAVTFYITWWFIHFVDGFFSPIYAQLGIDIFGLGFITSVTFIFLIGVFMSSW 123 (264)
Q Consensus 49 ~~~~~lr~~l~~~FltGLlvLLPi~iTi~Il~w~~~~vd~~~~pi~~~lg~~ipGlgll~~llliflvG~l~~~~ 123 (264)
...+||..-+ ++.+-+|.++-+.++..++-.++.- .+++|-...+++-++||.+|++--+|
T Consensus 56 ~Vs~RM~rRm------~~~~GiP~~lG~~~f~~~y~l~~~~--------~~dvP~~~~~~~S~~~Fg~gllGisY 116 (153)
T PF11947_consen 56 VVSNRMLRRM------AVFVGIPTALGVAVFVVFYYLKSRQ--------IVDVPPWAVLLVSLVFFGLGLLGISY 116 (153)
T ss_pred HHHHHHHHHH------HHHhchHHHHHHHHHHHHHHHHhcc--------ccccCchHHHHHHHHHHHHHHHhhhh
Confidence 4455554443 5566778887776666555444321 23444444444445677777765543
No 88
>PF04459 DUF512: Protein of unknown function (DUF512); InterPro: IPR007549 This is a domain of uncharacterised prokaryotic proteins. It is often found C-terminal to the radical SAM domain (IPR007197 from INTERPRO).
Probab=26.84 E-value=1.2e+02 Score=27.14 Aligned_cols=83 Identities=16% Similarity=0.126 Sum_probs=51.9
Q ss_pred hHHHHHHHHHHHhCCCcCcCCcccEEEEE--eCCCCeeEEEEEcccccccccCCCCceEEEEecCCCCCCeeEEEEeCCC
Q 024694 144 HIYNASKQISAAISPDQNTQAFKEVAIIR--HPRIGEYAFGFITSSVVLQNYSGEEELCCVYVPTNHLYIGDIFLINTKD 221 (264)
Q Consensus 144 ~IY~~iKqv~~~~~~~~~~~~Fk~VVlV~--~P~~g~~~iGFvT~~~~~~~~~~~e~~v~VfvPtsp~tsG~l~lV~~~~ 221 (264)
.-|..++++++.+... ..-.. +|+.|+ |-+...-+-|++|+++..++..+.+.--.+++|..-- -..++
T Consensus 107 la~~~l~~~~~~l~~~-~~~~v-~V~~V~N~fFG~~ItVaGLLTg~Dii~~L~~~~~~d~lllP~~ml-------~~~~~ 177 (204)
T PF04459_consen 107 LAYPFLKPLVEKLNRI-PGLEV-EVVPVKNRFFGGTITVAGLLTGQDIIEQLKGKELGDLLLLPDVML-------RHGEG 177 (204)
T ss_pred HHHHHHHHHHHHHhcc-CCCeE-EEEEeecCCCCCCeEEeeCccHHHHHHHhCcCCCCCEEEECHHHh-------cCCCC
Confidence 4588999999998322 22233 466665 5567899999999998643222111113688887641 11244
Q ss_pred eecCCCCHHHHHHH
Q 024694 222 VIRPNLSVREGIEI 235 (264)
Q Consensus 222 V~~lDmsveeAmk~ 235 (264)
+.-=|||++|..+-
T Consensus 178 ~fLDD~t~~el~~~ 191 (204)
T PF04459_consen 178 VFLDDMTLEELEER 191 (204)
T ss_pred ccCCCCcHHHHHHH
Confidence 44458999987664
No 89
>PF06305 DUF1049: Protein of unknown function (DUF1049); InterPro: IPR010445 This entry consists of several hypothetical bacterial proteins of unknown function.
Probab=26.62 E-value=1.3e+02 Score=21.22 Aligned_cols=21 Identities=24% Similarity=0.385 Sum_probs=14.5
Q ss_pred hHHHHHHHHHHHHHHHHHHHH
Q 024694 104 LGFITSVTFIFLIGVFMSSWL 124 (264)
Q Consensus 104 lgll~~llliflvG~l~~~~l 124 (264)
+.+.+.++++|++|.++...+
T Consensus 18 ~pl~l~il~~f~~G~llg~l~ 38 (68)
T PF06305_consen 18 LPLGLLILIAFLLGALLGWLL 38 (68)
T ss_pred chHHHHHHHHHHHHHHHHHHH
Confidence 566667777788887766543
No 90
>PF03672 UPF0154: Uncharacterised protein family (UPF0154); InterPro: IPR005359 The proteins in this entry are functionally uncharacterised.
Probab=25.86 E-value=98 Score=22.98 Aligned_cols=29 Identities=14% Similarity=0.311 Sum_probs=16.5
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHhhchhce
Q 024694 110 VTFIFLIGVFMSSWLGASVLSLGEWFIKRMPF 141 (264)
Q Consensus 110 llliflvG~l~~~~lg~~l~~~~E~~l~rIPl 141 (264)
+++++++|+++-.++++ .++++-+++=|=
T Consensus 3 iilali~G~~~Gff~ar---~~~~k~l~~NPp 31 (64)
T PF03672_consen 3 IILALIVGAVIGFFIAR---KYMEKQLKENPP 31 (64)
T ss_pred HHHHHHHHHHHHHHHHH---HHHHHHHHHCCC
Confidence 34455666665555555 345666666554
No 91
>PF07290 DUF1449: Protein of unknown function (DUF1449); InterPro: IPR010840 This family consists of several bacterial proteins of around 210 residues in length. The function of this family is unknown.
Probab=25.37 E-value=3.5e+02 Score=24.21 Aligned_cols=20 Identities=15% Similarity=0.559 Sum_probs=12.6
Q ss_pred HHHHHHHHHHHHHHHHHHHH
Q 024694 110 VTFIFLIGVFMSSWLGASVL 129 (264)
Q Consensus 110 llliflvG~l~~~~lg~~l~ 129 (264)
+...+++++++.++.|+.+-
T Consensus 101 ~~~al~~sl~~~~~~~~~la 120 (202)
T PF07290_consen 101 APVALFLSLFFTRYLGRPLA 120 (202)
T ss_pred HHHHHHHHHHHHHHHhHHHH
Confidence 34466677777777665443
No 92
>PF03547 Mem_trans: Membrane transport protein; InterPro: IPR004776 This entry represents a mostly uncharacterised family of membrane transport proteins found in eukaryotes, bacteria and archaea. Most characterised members of this family are the PIN components of auxin efflux systems from plants. These carriers are saturable, auxin-specific, and localized to the basal ends of auxin transport-competent cells [, ]. Plants typically posses several of these proteins, each displaying a unique tissue-specific expression pattern. They are expressed in almost all plant tissues including vascular tissues and roots, and influence many processes including the establishment of embryonic polarity, plant growth, apical hook formation in seedlings and the photo- and gravitrophic responses. These plant proteins are typically 600-700 amino acyl residues long and exhibit 8-12 transmembrane segments.; GO: 0055085 transmembrane transport, 0016021 integral to membrane
Probab=25.37 E-value=5.6e+02 Score=23.89 Aligned_cols=36 Identities=11% Similarity=-0.028 Sum_probs=22.5
Q ss_pred HHHHHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHHH
Q 024694 49 TFSKVVRSWASKKFMTGCVILFPIAVTFYITWWFIH 84 (264)
Q Consensus 49 ~~~~~lr~~l~~~FltGLlvLLPi~iTi~Il~w~~~ 84 (264)
..++.+.+.+++.|.+=.++-.-+++++.++.|...
T Consensus 229 ~~~~~~~~~~~~~~~nP~~~a~~lgli~~~~~~~~~ 264 (385)
T PF03547_consen 229 STRKKLKKSILKLFKNPPLIAIILGLIIGLIPPLRP 264 (385)
T ss_pred hHHHHHHHHHHHHHhCcHHHHHHHHHHHHHHHHhcc
Confidence 344555556667777776666666666666655543
No 93
>PF14018 DUF4234: Domain of unknown function (DUF4234)
Probab=25.22 E-value=2.7e+02 Score=20.19 Aligned_cols=62 Identities=13% Similarity=0.217 Sum_probs=31.8
Q ss_pred HHHHHHHHHHHHHHHHHHHHHhHhhhhh-hcccchhhHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 024694 69 LFPIAVTFYITWWFIHFVDGFFSPIYAQ-LGIDIFGLGFITSVTFIFLIGVFMSSWLGASVLSL 131 (264)
Q Consensus 69 LLPi~iTi~Il~w~~~~vd~~~~pi~~~-lg~~ipGlgll~~llliflvG~l~~~~lg~~l~~~ 131 (264)
|--+..-+|-++|+++.-+.+ ...... .+..-..+.+++.++.|-+.++....-.++++-+.
T Consensus 9 LsiiT~GIY~l~W~y~~~~~~-~~~~~~~~~~~~~~~~lll~ilt~gi~~i~w~~k~~~~i~~~ 71 (75)
T PF14018_consen 9 LSIITCGIYGLYWLYKIWKEL-NQLTGRIISPRSMTLWLLLSILTCGIYSIYWAYKLGNRINEE 71 (75)
T ss_pred HHHHHHHHHHHHHHHHHHHHH-HHHhcCCCCCCcHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 334456689999999877664 221111 01112234444444455555555555555555443
No 94
>COG1286 CvpA Uncharacterized membrane protein, required for colicin V production [General function prediction only]
Probab=25.06 E-value=4.6e+02 Score=22.81 Aligned_cols=25 Identities=12% Similarity=0.344 Sum_probs=12.3
Q ss_pred HHhhhhHHHHHHHHHHHHHHHHHHH
Q 024694 60 KKFMTGCVILFPIAVTFYITWWFIH 84 (264)
Q Consensus 60 ~~FltGLlvLLPi~iTi~Il~w~~~ 84 (264)
|=|+..++-++=.++.+|+-+..+.
T Consensus 22 RGfi~e~~sl~s~i~a~~vA~~fy~ 46 (182)
T COG1286 22 RGFIREVLSLLSWILAAFVASLFYK 46 (182)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHhH
Confidence 4444445555555555555554444
No 95
>COG2981 CysZ Uncharacterized protein involved in cysteine biosynthesis [Amino acid transport and metabolism]
Probab=24.89 E-value=5.7e+02 Score=23.84 Aligned_cols=25 Identities=8% Similarity=0.324 Sum_probs=13.2
Q ss_pred HHHHHHHH----HHHHHHHHHHHHHHhHh
Q 024694 68 ILFPIAVT----FYITWWFIHFVDGFFSP 92 (264)
Q Consensus 68 vLLPi~iT----i~Il~w~~~~vd~~~~p 92 (264)
+++|+.+- +-+.||+++..+..+.-
T Consensus 28 vilpLl~ni~L~~gl~~~~~~~~~~wid~ 56 (250)
T COG2981 28 VILPLLLNILLWGGLFWLLFSQALPWIDT 56 (250)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 45555444 44456666665555433
No 96
>PF05283 MGC-24: Multi-glycosylated core protein 24 (MGC-24); InterPro: IPR007947 CD164 is a mucin-like receptor, or sialomucin, with specificity in receptor/ ligand interactions that depends on the structural characteristics of the mucin-like receptor. Its functions include mediating, or regulating, haematopoietic progenitor cell adhesion and the negative regulation of their growth and/or-differentiation. It exists in the native state as a disulphide- linked homodimer of two 80-85kDa subunits. It is usually expressed by CD34+ and CD341o/- haematopoietic stem cells and associated microenvironmental cells. It contains, in its extracellular region, two mucin domains (I and II) linked by a non-mucin domain, which has been predicted to contain intra- disulphide bridges. This receptor may play a key role in haematopoiesis by facilitating the adhesion of human CD34+ cells to bone marrow stroma and by negatively regulating CD34+ CD341o/- haematopoietic progenitor cell proliferation. These effects involve the CD164 class I and/or II epitopes recognised by the monoclonal antibodies (mAbs) 105A5 and 103B2/9E10. These epitopes are carbohydrate-dependent and are located on the N-terminal mucin domain I [, ]. It has been found that murine MGC-24v and rat endolyn share significant sequence similarities with human CD164. However, CD164 lacks the consensus glycosaminoglycan (GAG)-attachment site found in MGC-24; it is possible that GAG-association is responsible for the high molecular weight of the epithelial-derived MGC-24 glycoprotein []. Genomic structure studies have placed CD164 within the mucin-subgroup that comprises multiple exons, and demonstrate the diverse chromosomal distribution of this family of molecules. Molecules with such multiple exons may have sophisticated regulatory mechanisms that involve not only post-translational modifications of the oligosaccharide side chains, but also differential exon usage. Although differences in the intron and exon sizes are seen between the mouse and human genes, the predicted proteins are similar in size and structure, maintaining functionally important motifs that regulate cell proliferation or subcellular distribution []. CD164 is a gene whose expression depends on differential usage of poly- adenylation sites within the 3'-UTR. The conserved distribution of the 3.2- and 1.2-kb CD164 transcripts between mouse and human suggests that (i) a mechanism may exist to regulate tissue-specific polyadenylation, and (ii) differences in polyadenylation are important for the expression and function of CD164 in different tissues. Two other aspects of the structure of CD164 are of particular interest. First, it shares one of several conserved features of a cytokine-binding pocket - in this respect, it is notable that evidence exists for a class of cell-surface sialomucin modulators that directly interact with growth factor receptors to regulate their response to physiological ligands. Second, its cytoplasmic tail contains a C-terminal YHTL motif found in many endocytic membrane proteins or receptors. These Tyr-based motifs bind to adaptor proteins, which mediate the sorting of membrane proteins into transport vesicles from the plasma membrane to the endosomes, and between intracellular compartments.
Probab=24.89 E-value=61 Score=28.81 Aligned_cols=26 Identities=15% Similarity=0.441 Sum_probs=21.5
Q ss_pred HHHhhhhHHHHHHHHHHHHHHHHHHH
Q 024694 59 SKKFMTGCVILFPIAVTFYITWWFIH 84 (264)
Q Consensus 59 ~~~FltGLlvLLPi~iTi~Il~w~~~ 84 (264)
--.|+.|++..|=+...+|++|++++
T Consensus 160 ~~SFiGGIVL~LGv~aI~ff~~KF~k 185 (186)
T PF05283_consen 160 AASFIGGIVLTLGVLAIIFFLYKFCK 185 (186)
T ss_pred hhhhhhHHHHHHHHHHHHHHHhhhcc
Confidence 34699999999999888888887764
No 97
>PRK11720 galactose-1-phosphate uridylyltransferase; Provisional
Probab=24.03 E-value=1.1e+02 Score=29.36 Aligned_cols=65 Identities=20% Similarity=0.217 Sum_probs=48.8
Q ss_pred EEeCCCCeeEEEEEccccc---------------------ccc-------cCCCCceEEEEecCCCCCCeeEEEEeCCCe
Q 024694 171 IRHPRIGEYAFGFITSSVV---------------------LQN-------YSGEEELCCVYVPTNHLYIGDIFLINTKDV 222 (264)
Q Consensus 171 V~~P~~g~~~iGFvT~~~~---------------------~~~-------~~~~e~~v~VfvPtsp~tsG~l~lV~~~~V 222 (264)
..+||...|+..|++.+.. .+. ...+++...+|+|-+|-+-|-+.++|++.+
T Consensus 162 l~HPH~Qi~a~p~vP~~~~~e~~~~~~y~~~~g~Clfcdii~~E~~~~~RiV~End~fvAf~p~~p~~P~h~lIiPKrH~ 241 (346)
T PRK11720 162 NPHPHGQIWANSFLPNEAEREDRLQRAYFAEHGSPLLVDYVQRELADGERIVVETEHWLAVVPYWAAWPFETLLLPKAHV 241 (346)
T ss_pred CCCCceeeeeCCCCChHHHHHHHHHHHHHHHcCCeEHHHHHHhhhhcCCeEEEECCCEEEEeccccCCCCeEEEecccCC
Confidence 4678888999999987641 001 122367889999999988899999999999
Q ss_pred ecC-CCCHHHHHHH
Q 024694 223 IRP-NLSVREGIEI 235 (264)
Q Consensus 223 ~~l-DmsveeAmk~ 235 (264)
..+ |++-+|...+
T Consensus 242 ~~~~dl~dee~~~L 255 (346)
T PRK11720 242 LRLTDLTDAQRDDL 255 (346)
T ss_pred CChhhCCHHHHHHH
Confidence 765 8988866543
No 98
>PRK00523 hypothetical protein; Provisional
Probab=23.66 E-value=1.9e+02 Score=22.02 Aligned_cols=27 Identities=11% Similarity=0.238 Sum_probs=16.6
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHhhchhce
Q 024694 112 FIFLIGVFMSSWLGASVLSLGEWFIKRMPF 141 (264)
Q Consensus 112 liflvG~l~~~~lg~~l~~~~E~~l~rIPl 141 (264)
+++++|++.--++.+ .++|+-+++=|=
T Consensus 13 ~~li~G~~~Gffiar---k~~~k~l~~NPp 39 (72)
T PRK00523 13 PLLIVGGIIGYFVSK---KMFKKQIRENPP 39 (72)
T ss_pred HHHHHHHHHHHHHHH---HHHHHHHHHCcC
Confidence 357777776666666 355666664443
No 99
>TIGR03279 cyano_FeS_chp putative FeS-containing Cyanobacterial-specific oxidoreductase. Members of this protein family are predicted FeS-containing oxidoreductases of unknown function, apparently restricted to and universal across the Cyanobacteria. The high trusted cutoff score for this model, 700 bits, excludes homologs from other lineages. This exclusion seems justified because a significant number of sequence positions are simultaneously unique to and invariant across the Cyanobacteria, suggesting a specialized, conserved function, perhaps related to photosynthesis. A distantly related protein family, TIGR03278, in universal in and restricted to archaeal methanogens, and may be linked to methanogenesis.
Probab=23.30 E-value=2.1e+02 Score=28.69 Aligned_cols=82 Identities=15% Similarity=0.137 Sum_probs=50.8
Q ss_pred hHHHHHHHHHHHhCCCcCcCCcccEEEEE--eCCCCeeEEEEEcccccccccCCCCceEEEEecCCCCCCeeEEEEeCCC
Q 024694 144 HIYNASKQISAAISPDQNTQAFKEVAIIR--HPRIGEYAFGFITSSVVLQNYSGEEELCCVYVPTNHLYIGDIFLINTKD 221 (264)
Q Consensus 144 ~IY~~iKqv~~~~~~~~~~~~Fk~VVlV~--~P~~g~~~iGFvT~~~~~~~~~~~e~~v~VfvPtsp~tsG~l~lV~~~~ 221 (264)
..|..++++++.+....+. .. +|+-|+ |-++..-+-|++|+++...+..+.+---.+.+|..---.| ++
T Consensus 329 ~~~~~~~~~~~~l~~~~~~-~v-~v~~i~N~ffG~~vtV~GLltg~Dii~~l~~~~~gd~lliP~~ml~~~-------~~ 399 (433)
T TIGR03279 329 AVEQAFEPLVERLNAVEGL-EL-DLHGLASDYWGQEITVTGLLTGQDLIAGLKGKDLGDGLLLPSVMLKHG-------EL 399 (433)
T ss_pred cHHHHHHHHHHHHhcCCCc-EE-EEEEeccCCCCCCeeEeecccHHHHHHHhCCCCCCCeEEecHHHhcCC-------CC
Confidence 5799999999998754222 22 344454 5578899999999998643222111112577887653233 33
Q ss_pred eecCCCCHHHHHH
Q 024694 222 VIRPNLSVREGIE 234 (264)
Q Consensus 222 V~~lDmsveeAmk 234 (264)
+.-=|||++|.-+
T Consensus 400 ~fLDd~t~~~l~~ 412 (433)
T TIGR03279 400 VFLDDLTVEEVAE 412 (433)
T ss_pred eECCCCcHHHHHH
Confidence 4444899888654
No 100
>KOG2927 consensus Membrane component of ER protein translocation complex [Intracellular trafficking, secretion, and vesicular transport]
Probab=23.07 E-value=1.4e+02 Score=29.22 Aligned_cols=20 Identities=15% Similarity=0.527 Sum_probs=11.4
Q ss_pred HhhhhHHHHHHHHHHHHHHH
Q 024694 61 KFMTGCVILFPIAVTFYITW 80 (264)
Q Consensus 61 ~FltGLlvLLPi~iTi~Il~ 80 (264)
+.+.++++++=+++++|=+|
T Consensus 191 ~vl~~~fvl~tlaivLFPLW 210 (372)
T KOG2927|consen 191 QVLGVLFVLVTLAIVLFPLW 210 (372)
T ss_pred HHHHHHHHHHHHHHHhcccC
Confidence 35566666665665555544
No 101
>TIGR00834 ae anion exchange protein. They preferentially catalyze anion exchange (antiport) reactions, typically acting as HCO3-:Cl- antiporters, but also transporting a range of other inorganic and organic anions. Additionally, renal Na+:HCO3- cotransporters have been found to be members of the AE family. They catalyze the reabsorption of HCO3- in the renal proximal tubule.
Probab=22.92 E-value=2.6e+02 Score=30.74 Aligned_cols=46 Identities=11% Similarity=0.119 Sum_probs=34.0
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHhhchhceehhHHHHHHHHHHHhCC
Q 024694 113 IFLIGVFMSSWLGASVLSLGEWFIKRMPFVRHIYNASKQISAAISP 158 (264)
Q Consensus 113 iflvG~l~~~~lg~~l~~~~E~~l~rIPlVk~IY~~iKqv~~~~~~ 158 (264)
++++..+=...+-+.+-++.|.++.-.=-+-.||+++|.++..|..
T Consensus 467 ~~lla~~~~s~lvryiTRFTeEiFa~lIs~IFI~eai~~L~~~f~~ 512 (900)
T TIGR00834 467 VLLLVATEGSFLVRYISRFTQEIFSFLISLIFIYETFSKLIKIFQE 512 (900)
T ss_pred HHHHHHHhHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHHHhc
Confidence 4444444444566777778888888777788899999999998753
No 102
>TIGR00779 cad cadmium resistance transporter (or sequestration) family protein. These proteins are members of the Cadmium Resistance (CadD) Family (TC 2.A.77). To date, this family of proteins has only been found in Gram-positive bacteria. The CadD family includes several closely related Staphylococcal proteins reported to function in cadmium resistance. Members are predicted to span the membrane five times; the mechanism of resistance is believed to be export but has also been suggested to be binding and sequestration in the membrane. Closely related but outside the scope of this model is another staphylococcal protein that has been reported to possibly function in quaternary ammonium ion export. Still more distant are other members of the broader LysE family (see Vrljic. et al, PubMed:10943564).
Probab=22.79 E-value=5.1e+02 Score=23.14 Aligned_cols=57 Identities=16% Similarity=0.187 Sum_probs=31.3
Q ss_pred HhhchhceehhHHHHHHHHHHHhCCCcCcCCcccEEEE--EeC--CCCeeEEEEEcccccccccCCCCceEEEEecC
Q 024694 134 WFIKRMPFVRHIYNASKQISAAISPDQNTQAFKEVAII--RHP--RIGEYAFGFITSSVVLQNYSGEEELCCVYVPT 206 (264)
Q Consensus 134 ~~l~rIPlVk~IY~~iKqv~~~~~~~~~~~~Fk~VVlV--~~P--~~g~~~iGFvT~~~~~~~~~~~e~~v~VfvPt 206 (264)
.++.=+|+ |=.+|...+ ++++.+ ++.+.- +.+ +.-.+.++.+|=-+ +.|-..||+|-
T Consensus 59 GlLGliPI----~lGi~~l~~---~~~~~~--~~~~~~~~~~~~~~~~~~~Va~iTiAn-------GgDNIgIYvPl 119 (193)
T TIGR00779 59 GLLGLIPI----YLGIKVAIK---GECDED--ERAILSLNESGKLNKLFLTVAFITIAS-------GADNIGIYVPY 119 (193)
T ss_pred hHHhHHHH----HHHHHHHhc---cccccc--ccccccccccccCCCceEEEEEEEEec-------cCceeEEEeee
Confidence 45778886 888887655 222211 111100 011 12246777776432 67789999993
No 103
>PF00873 ACR_tran: AcrB/AcrD/AcrF family; InterPro: IPR001036 The Escherichia coli acrA and acrB genes encode a multi-drug efflux system that is believed to protect the bacterium against hydrophobic inhibitors []. The E. coli AcrB protein is a transporter that is energized by proton-motive force and that shows the widest substrate specificity among all known multidrug pumps, ranging from most of the currently used antibiotics, disinfectants, dyes, and detergents to simple solvents. The structure of ligand-free AcrB shows that it is a homotrimer of 110kDa per subunit. Each subunit contains 12 transmembrane helices and two large periplasmic domains (each exceeding 300 residues) between helices 1 and 2, and helices 7 and 8. X-ray analysis of the overexpressed AcrB protein demonstrated that the three periplasmic domains form, in the centre, a funnel-like structure and a connected narrow (or closed) pore. The pore is opened to the periplasm through three vestibules located at subunit interfaces. These vestibules were proposed to allow direct access of drugs from the periplasm as well as the outer leaflet of the cytoplasmic membrane. The three transmembrane domains of AcrB protomers form a large, 30A-wide central cavity that spans the cytoplasmic membrane and extends to the cytoplasm X-ray crystallographic structures of the trimeric AcrB pump from E. coli with four structurally diverse ligands demonstrated that three molecules of ligand bind simultaneously to the extremely large central cavity of 5000 cubic angstroms, primarily by hydrophobic, aromatic stacking and van der Waals interactions. Each ligand uses a slightly different subset of AcrB residues for binding. The bound ligand molecules often interact with each other, stabilising the binding. ; GO: 0005215 transporter activity, 0006810 transport, 0016020 membrane; PDB: 2V50_B 1T9U_A 2HRT_B 3NOC_A 3NOG_A 4DX7_A 1OYD_A 3AOB_A 1T9V_A 4DX6_B ....
Probab=22.71 E-value=2e+02 Score=31.24 Aligned_cols=82 Identities=23% Similarity=0.416 Sum_probs=0.0
Q ss_pred hHHHHHHHHHHHHHHHHHHHHHHHHhHhhh-----------hhhcccchh--hHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 024694 65 GCVILFPIAVTFYITWWFIHFVDGFFSPIY-----------AQLGIDIFG--LGFITSVTFIFLIGVFMSSWLGASVLSL 131 (264)
Q Consensus 65 GLlvLLPi~iTi~Il~w~~~~vd~~~~pi~-----------~~lg~~ipG--lgll~~llliflvG~l~~~~lg~~l~~~ 131 (264)
+..+++=+++.+.++.+.|+ ++..|++ ..+++.+.| +++..++.++.++|+.++|-+- ++++
T Consensus 865 ~~~~~~al~liyliL~~~F~---S~~~PliIm~~IPla~~G~~~~l~i~g~~l~~~s~iG~i~L~GIvVnNaIl--lvd~ 939 (1021)
T PF00873_consen 865 GFALILALLLIYLILAAQFE---SFRQPLIIMLTIPLALIGVLLGLFITGQPLSFMSLIGIIALIGIVVNNAIL--LVDF 939 (1021)
T ss_dssp HHHHHHHHHHHHHHHHHHTT---SSSTHHHHHTTHHHHHHHHHHHHHHTTBEBSHHHHHHHHHHHHHHHHHHHH--HHHH
T ss_pred hhhHHHHHHHHHHHHHHHhc---ceeeeEEEEeccchhhHHHHHHHhhccccccccceehHHHHHHHHHhhhHH--HHHH
Q ss_pred HHHhhc--hhceehhHHHHHHH
Q 024694 132 GEWFIK--RMPFVRHIYNASKQ 151 (264)
Q Consensus 132 ~E~~l~--rIPlVk~IY~~iKq 151 (264)
.++..+ .+|....|..+.++
T Consensus 940 ~~~~~~~~g~~~~eAi~~a~~~ 961 (1021)
T PF00873_consen 940 INELRKREGMPLEEAIIEAARS 961 (1021)
T ss_dssp HHHHHHTTCCHHHHHHHHHHHH
T ss_pred HHHHhhhccccHHHHHHHHHHH
No 104
>PF01594 UPF0118: Domain of unknown function DUF20; InterPro: IPR002549 This is a family of hypothetical proteins. A number of the sequence records state they are transmembrane proteins or putative permeases. It is not clear what source suggested that these proteins might be permeases and this information should be treated with caution.
Probab=22.39 E-value=5.9e+02 Score=23.08 Aligned_cols=42 Identities=10% Similarity=0.062 Sum_probs=30.5
Q ss_pred CCChhHHHHHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHHHH
Q 024694 44 HAGRETFSKVVRSWASKKFMTGCVILFPIAVTFYITWWFIHF 85 (264)
Q Consensus 44 ~~~~~~~~~~lr~~l~~~FltGLlvLLPi~iTi~Il~w~~~~ 85 (264)
++..+.+.+++.+.+++|+..=++..+=.++..++..|+++.
T Consensus 177 ~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~i~~~~~gi 218 (327)
T PF01594_consen 177 RERFEEILRKIDQSLSAYLKGQLILALIQGVLTFIGFSIFGI 218 (327)
T ss_pred hHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 455567888888888887777777766677777777777764
No 105
>PRK04949 putative sulfate transport protein CysZ; Validated
Probab=21.90 E-value=6.2e+02 Score=23.18 Aligned_cols=23 Identities=22% Similarity=0.895 Sum_probs=13.2
Q ss_pred HHHHHHHHHHHHH----HHHHHHHHHH
Q 024694 67 VILFPIAVTFYIT----WWFIHFVDGF 89 (264)
Q Consensus 67 lvLLPi~iTi~Il----~w~~~~vd~~ 89 (264)
++++|+++++.++ +|.++.++..
T Consensus 29 ~~liPl~inllLf~~~l~~~~~~~~~~ 55 (251)
T PRK04949 29 FVILPLLVNILLFGGAFWWLFTQLDAW 55 (251)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 4667777776655 4444444433
No 106
>TIGR00209 galT_1 galactose-1-phosphate uridylyltransferase, family 1. This enzyme is involved in glucose and galactose interconversion. This model describes one of two extremely distantly related branches of the model pfam01087 from PFAM.
Probab=21.79 E-value=1.4e+02 Score=28.70 Aligned_cols=65 Identities=20% Similarity=0.252 Sum_probs=48.6
Q ss_pred EEeCCCCeeEEEEEccccc---------------------ccc-------cCCCCceEEEEecCCCCCCeeEEEEeCCCe
Q 024694 171 IRHPRIGEYAFGFITSSVV---------------------LQN-------YSGEEELCCVYVPTNHLYIGDIFLINTKDV 222 (264)
Q Consensus 171 V~~P~~g~~~iGFvT~~~~---------------------~~~-------~~~~e~~v~VfvPtsp~tsG~l~lV~~~~V 222 (264)
..+||...|++.|+..+.. .+. ...+++.+.+|+|-+|-+-|-++++|++-+
T Consensus 162 l~HPH~Qi~a~p~vP~~~~~e~~~~~~y~~~~g~clfcdIi~~E~~~~~riV~End~fvAf~p~~p~~Pgh~lIiPKrH~ 241 (347)
T TIGR00209 162 NPHPHGQIWANSFLPNEVEREDRLQKEYFAEHKSPMLVDYVKRELADKSRTVVETEHWIAVVPYWAIWPFETLLLPKAHV 241 (347)
T ss_pred CCCCceeeeeCCCCChHHHHHHHHHHHHHHHcCCccHHHHHHhHhhcCCeEEEECCCEEEEeccCCCCCCeEEEeeccCC
Confidence 3688888999999987641 001 122367899999999988999999999999
Q ss_pred ecC-CCCHHHHHHH
Q 024694 223 IRP-NLSVREGIEI 235 (264)
Q Consensus 223 ~~l-DmsveeAmk~ 235 (264)
..+ |++-+|...+
T Consensus 242 ~~~~dl~d~e~~~L 255 (347)
T TIGR00209 242 LRITDLTDAQRSDL 255 (347)
T ss_pred CChhhCCHHHHHHH
Confidence 765 8887765443
No 107
>COG2928 Uncharacterized conserved protein [Function unknown]
Probab=21.66 E-value=6.3e+02 Score=23.16 Aligned_cols=39 Identities=13% Similarity=0.083 Sum_probs=35.1
Q ss_pred HHHHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHHHHHHH
Q 024694 50 FSKVVRSWASKKFMTGCVILFPIAVTFYITWWFIHFVDG 88 (264)
Q Consensus 50 ~~~~lr~~l~~~FltGLlvLLPi~iTi~Il~w~~~~vd~ 88 (264)
.+++|++++-.=++-=+=+.+=+++..|++.|+-+++..
T Consensus 2 ~~~~lk~~fltGLlvllPlaiT~~vv~~i~~~l~~~~~~ 40 (222)
T COG2928 2 GAKRLKKYFLTGLLVLLPLAITLWVVSWIFGLLDQFVGP 40 (222)
T ss_pred hHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhh
Confidence 468899998899999999999999999999999999874
No 108
>PRK15120 lipopolysaccharide ABC transporter permease LptF; Provisional
Probab=21.66 E-value=6.8e+02 Score=23.55 Aligned_cols=37 Identities=3% Similarity=0.161 Sum_probs=24.3
Q ss_pred HHHHHHHHhhhhHHHHHHHHHHHHHHHHHHHHHHHHh
Q 024694 54 VRSWASKKFMTGCVILFPIAVTFYITWWFIHFVDGFF 90 (264)
Q Consensus 54 lr~~l~~~FltGLlvLLPi~iTi~Il~w~~~~vd~~~ 90 (264)
+..++-|.++..+++.+=+.+.++++.-+++.+|.+.
T Consensus 3 l~RYi~re~l~~~~~~l~~l~~i~~~~~l~~~l~~~~ 39 (366)
T PRK15120 3 IIRYLVRETLKSQLAILFILLLIFFCQKLVRILGAAV 39 (366)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3456666666666666666677777777777666654
No 109
>PRK05886 yajC preprotein translocase subunit YajC; Validated
Probab=21.44 E-value=92 Score=25.34 Aligned_cols=8 Identities=0% Similarity=0.231 Sum_probs=4.0
Q ss_pred HHHHHHhC
Q 024694 150 KQISAAIS 157 (264)
Q Consensus 150 Kqv~~~~~ 157 (264)
+++.+++.
T Consensus 33 ~~m~~~Lk 40 (109)
T PRK05886 33 IDLHESLQ 40 (109)
T ss_pred HHHHHhcC
Confidence 34555554
No 110
>PRK00753 psbL photosystem II reaction center L; Provisional
Probab=21.29 E-value=1.3e+02 Score=20.17 Aligned_cols=20 Identities=20% Similarity=0.697 Sum_probs=15.1
Q ss_pred HHHHHHHHHHHHHHHHHHHH
Q 024694 105 GFITSVTFIFLIGVFMSSWL 124 (264)
Q Consensus 105 gll~~llliflvG~l~~~~l 124 (264)
++-..++++|++|++.++++
T Consensus 18 SLy~GlLlifvl~vLFssYf 37 (39)
T PRK00753 18 SLYLGLLLVFVLGILFSSYF 37 (39)
T ss_pred hHHHHHHHHHHHHHHHHhhc
Confidence 45556778899999988875
No 111
>TIGR00439 ftsX putative protein insertion permease FtsX. FtsX is an integral membrane protein encoded in the same operon as signal recognition particle docking protein FtsY and FtsE. It belongs to a family of predicted permeases and may play a role in the insertion of proteins required for potassium transport, cell division, and other activities. FtsE is a hydrophilic nucleotide-binding protein that associates with the inner membrane by means of association with FtsX.
Probab=21.22 E-value=6.9e+02 Score=23.44 Aligned_cols=27 Identities=15% Similarity=-0.023 Sum_probs=18.3
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 024694 107 ITSVTFIFLIGVFMSSWLGASVLSLGE 133 (264)
Q Consensus 107 l~~llliflvG~l~~~~lg~~l~~~~E 133 (264)
++++++..++|++.+.+.-++.++.+|
T Consensus 281 ~~l~~~g~~lg~lgs~~s~~r~Lr~~~ 307 (309)
T TIGR00439 281 GLLLGFCIALGVVGAWLATTQHLLCFK 307 (309)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHhC
Confidence 344555678888888877777666553
No 112
>PRK10712 PTS system fructose-specific transporter subunits IIBC; Provisional
Probab=21.07 E-value=4.4e+02 Score=27.23 Aligned_cols=123 Identities=18% Similarity=0.226 Sum_probs=0.0
Q ss_pred CcccccccccccccccccccccccCCCCCCCCCCCCCCCCCCCChhHHHHHHHHHHHHHhhhhHHHHHHHHHHHHHHHHH
Q 024694 3 DDKSTIVMASRERDRDRELLIPVADSGDESSKPSSSSSSSHHAGRETFSKVVRSWASKKFMTGCVILFPIAVTFYITWWF 82 (264)
Q Consensus 3 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lr~~l~~~FltGLlvLLPi~iTi~Il~w~ 82 (264)
+.|......-+|--+|-+.++--+-..+..-.++++..+......+ .++-+++.+++|+=..||+++.-=++.-+
T Consensus 176 ~gk~v~~~s~~~ai~~~~~~l~~a~~~a~~~~~~~~~~~~~~~~~~-----~~~~~~~hlmtGvS~mlP~vv~gGil~ai 250 (563)
T PRK10712 176 AGKPMYRTSTGLALKKTAQELDKAVAEATPYQPAGKAQTATTEGKK-----ESAGAYRHLLTGVSYMLPMVVAGGLCIAL 250 (563)
T ss_pred CCCceEEeCHHHHhhCHHHHHHHHHhhcccccccccccccccccch-----hhhHHHHHHHhhhhHHHHHHHHhHHHHHH
Q ss_pred HHHHH-------HHhHhhhhhhccc------------------------chhh-----------HHHHHHHHHHHHHHHH
Q 024694 83 IHFVD-------GFFSPIYAQLGID------------------------IFGL-----------GFITSVTFIFLIGVFM 120 (264)
Q Consensus 83 ~~~vd-------~~~~pi~~~lg~~------------------------ipGl-----------gll~~llliflvG~l~ 120 (264)
-..+. +-+.-.+..+|.. .||+ ||+-.++..|++||+.
T Consensus 251 ~~~~g~~~~~~~~~~~~~~~~~gg~~~~~lmvpvla~yia~sia~rpglapg~i~g~~a~~~~~GFlG~Ilag~lagyv~ 330 (563)
T PRK10712 251 SFAFGIEAFKEPGTLAAALMQIGGGSAFALMVPVLAGYIAFSIADRPGLTPGLIGGMLAVSTGSGFIGGIIAGFLAGYVA 330 (563)
T ss_pred HHHhCccccCCccHHHHHHHHhhhHHHHHHHHHHHHHHHHHHhcCCccchHHHHHHHHHhcCCchHHHHHHHHHHHHHHH
Q ss_pred HHHHHHHHHHHHHHhhchhc
Q 024694 121 SSWLGASVLSLGEWFIKRMP 140 (264)
Q Consensus 121 ~~~lg~~l~~~~E~~l~rIP 140 (264)
+ |+++. .|+|
T Consensus 331 ~---------~l~K~-~~lP 340 (563)
T PRK10712 331 K---------LISTK-LKLP 340 (563)
T ss_pred H---------HHHHh-ccCc
No 113
>PF04854 DUF624: Protein of unknown function, DUF624; InterPro: IPR006938 This family consists of uncharacterised or hypothetical bacterial proteins.
Probab=20.88 E-value=2.8e+02 Score=20.06 Aligned_cols=31 Identities=6% Similarity=0.073 Sum_probs=19.1
Q ss_pred HHHHHHHHHHHHhhhhHHHHHHHHHHHHHHH
Q 024694 50 FSKVVRSWASKKFMTGCVILFPIAVTFYITW 80 (264)
Q Consensus 50 ~~~~lr~~l~~~FltGLlvLLPi~iTi~Il~ 80 (264)
.++...+..|++|.++...-++..+.+.++.
T Consensus 44 ~~~~f~~~fk~nf~~~~~~~~~~~~~~~il~ 74 (77)
T PF04854_consen 44 LFRDFWRAFKQNFKQSLLLGLILLLLLAILY 74 (77)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3444444446667777777777766666554
No 114
>PF07613 DUF1576: Protein of unknown function (DUF1576); InterPro: IPR011470 This small family is found in several undescribed proteins. The alignment is distinguished by the frequent occurrence of conserved glycine and aromatic residues.
Probab=20.88 E-value=5.3e+02 Score=22.86 Aligned_cols=62 Identities=23% Similarity=0.413 Sum_probs=37.2
Q ss_pred HHHHhhhhHH--HHHHHHHHH--------HHHHHHHHHHHHHhHhh-hhh-----hcccchhhHHHHHHHHHHHHHHH
Q 024694 58 ASKKFMTGCV--ILFPIAVTF--------YITWWFIHFVDGFFSPI-YAQ-----LGIDIFGLGFITSVTFIFLIGVF 119 (264)
Q Consensus 58 l~~~FltGLl--vLLPi~iTi--------~Il~w~~~~vd~~~~pi-~~~-----lg~~ipGlgll~~llliflvG~l 119 (264)
++++.+..|+ .|.|++=-+ +++.|+...+-+++.|- ..+ -|.+..-.||...++..+++.++
T Consensus 103 ~~~~il~aLFgT~LAPi~s~~~f~~~~~~~~lG~~~Gi~~Gfi~~~la~~~~~~H~G~NLYN~GFa~Giva~~lv~il 180 (183)
T PF07613_consen 103 FSSYILIALFGTALAPIVSEFAFGLGLPLPILGILIGIIAGFIHPPLASNFGKLHGGYNLYNNGFAAGIVAMVLVPIL 180 (183)
T ss_pred hHHHHHHHHHHhhHHHHHHHHHHhcCCchHHHHHHHHHHHHHHHHHHHHHHHHHcCCchhhhchhHHHHHHHHHHHHH
Confidence 5556666664 456766544 46677777777766443 222 25555566777777766666654
No 115
>cd00608 GalT Galactose-1-phosphate uridyl transferase (GalT): This enzyme plays a key role in galactose metabolism by catalysing the transfer of a uridine 5'-phosphoryl group from UDP-galactose 1-phosphate. The structure of E.coli GalT reveals that the enzyme contains two identical subunits. It also demonstrates that the active site is formed by amino acid residues from both subunits of the dimer.
Probab=20.67 E-value=1.4e+02 Score=28.20 Aligned_cols=37 Identities=19% Similarity=0.187 Sum_probs=30.4
Q ss_pred CceEEEEecCCCCCCeeEEEEeCCCeecC-CCCHHHHH
Q 024694 197 EELCCVYVPTNHLYIGDIFLINTKDVIRP-NLSVREGI 233 (264)
Q Consensus 197 e~~v~VfvPtsp~tsG~l~lV~~~~V~~l-DmsveeAm 233 (264)
++.+.+|+|-++.+-|-+.++|++-+..+ |++-+|..
T Consensus 206 nd~~va~~p~~~~~P~e~lIiPKrH~~~~~dl~~~e~~ 243 (329)
T cd00608 206 NEHFVAVVPFWARWPFEVHILPKRHVSRFTDLTDEERE 243 (329)
T ss_pred CCCEEEEEecCCCCCcEEEEecCCCcCChhHCCHHHHH
Confidence 57889999999977789999999988664 88877654
No 116
>TIGR00822 EII-Sor PTS system, mannose/fructose/sorbose family, IIC component. Bacterial PTS transporters transport and concomitantly phosphorylate their sugar substrates, and typically consist of multiple subunits or protein domains. The Man (PTS splinter group) 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 E. coli, for example, can transport and phosphorylate glucose, mannose, fructose, glucosamine,N-acetylglucosamine, and other sugars. Other members of this family can transport sorbose, fructose and N-acetylglucosamine. This family is specific for the sorbose-specific IIC subunits of this family of PTS transporters.
Probab=20.58 E-value=7e+02 Score=23.27 Aligned_cols=29 Identities=21% Similarity=0.474 Sum_probs=19.2
Q ss_pred chhhHHHHHH--------HHHHHHHHHHHHHHHHHHH
Q 024694 101 IFGLGFITSV--------TFIFLIGVFMSSWLGASVL 129 (264)
Q Consensus 101 ipGlgll~~l--------lliflvG~l~~~~lg~~l~ 129 (264)
+|.+|+.+++ ..-|++|++...+++-.++
T Consensus 188 LPAvGfAmLl~~m~~k~~~~ff~lGF~laayl~l~~l 224 (265)
T TIGR00822 188 IVVVGYAMVLRMMFKAYLMPFFYLGFLFAAYTDFSLL 224 (265)
T ss_pred HHHHHHHHHHHHHhhcchHHHHHHHHHHHHHhCCcHH
Confidence 5667776643 3467889988888754433
No 117
>CHL00114 psbX photosystem II protein X; Reviewed
Probab=20.48 E-value=1.1e+02 Score=20.69 Aligned_cols=24 Identities=8% Similarity=0.461 Sum_probs=16.5
Q ss_pred HHHHHHHHhhhhHHHHHHHHHHHH
Q 024694 54 VRSWASKKFMTGCVILFPIAVTFY 77 (264)
Q Consensus 54 lr~~l~~~FltGLlvLLPi~iTi~ 77 (264)
|.+|+..-+.+++++++|+.+.+.
T Consensus 5 LsnF~~SL~~Ga~ivvipi~~aLi 28 (39)
T CHL00114 5 LSAFINSLLLGAIIVVIPITLALL 28 (39)
T ss_pred HHHHHHHHHHHHHHhHHHhhhheE
Confidence 456666667777777889876543
No 118
>PRK01821 hypothetical protein; Provisional
Probab=20.40 E-value=2e+02 Score=24.15 Aligned_cols=12 Identities=33% Similarity=0.564 Sum_probs=6.0
Q ss_pred cccchh--hHHHHH
Q 024694 98 GIDIFG--LGFITS 109 (264)
Q Consensus 98 g~~ipG--lgll~~ 109 (264)
+..+|| +|++++
T Consensus 33 ~lpiPGsViGmlLL 46 (133)
T PRK01821 33 PITIPGSIIGMLIL 46 (133)
T ss_pred CCCCcHHHHHHHHH
Confidence 445565 455443
No 119
>COG4956 Integral membrane protein (PIN domain superfamily) [General function prediction only]
Probab=20.21 E-value=5e+02 Score=25.33 Aligned_cols=29 Identities=17% Similarity=0.207 Sum_probs=23.1
Q ss_pred HHHHHHHhhchhceehhHHHHHHHHHHHh
Q 024694 128 VLSLGEWFIKRMPFVRHIYNASKQISAAI 156 (264)
Q Consensus 128 l~~~~E~~l~rIPlVk~IY~~iKqv~~~~ 156 (264)
..+++|..+.|+|...-+|.++-=+++.+
T Consensus 65 ~~~~le~~i~k~~~~~ilf~tiGLiiGLl 93 (356)
T COG4956 65 WLKRLEEQIRKLPVTTILFGTIGLIIGLL 93 (356)
T ss_pred HHHHHHHHHHhcCHHHHHHHHHHHHHHHH
Confidence 34677888999999999999888777654
No 120
>COG3224 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=20.03 E-value=4.1e+02 Score=23.84 Aligned_cols=42 Identities=12% Similarity=0.074 Sum_probs=24.8
Q ss_pred HHhHhhhhhhcccchhhHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 024694 88 GFFSPIYAQLGIDIFGLGFITSVTFIFLIGVFMSSWLGASVLSL 131 (264)
Q Consensus 88 ~~~~pi~~~lg~~ipGlgll~~llliflvG~l~~~~lg~~l~~~ 131 (264)
.+++|.+..+ ..|-.-++.+++.|.+.++++--++-+..-.|
T Consensus 139 ~~~gp~l~~~--~l~~~~Li~t~~~v~LltYf~iP~vs~l~~~W 180 (195)
T COG3224 139 LLLGPKLGFL--PLPTRVLIGTLCSVSLLTYFVIPLVSRLYAFW 180 (195)
T ss_pred HhhccccCCC--CccHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3445544432 34445667778888888888766555444333
Done!