Query 029429
Match_columns 193
No_of_seqs 110 out of 594
Neff 5.5
Searched_HMMs 46136
Date Fri Mar 29 12:46:48 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/029429.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/029429hhsearch_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 1.1E-37 2.4E-42 263.4 17.2 147 44-191 2-157 (222)
2 PF04367 DUF502: Protein of un 99.9 2.5E-25 5.4E-30 170.1 11.0 92 97-189 2-95 (108)
3 PRK15350 type III secretion sy 93.2 2.7 5.9E-05 31.4 11.7 80 45-131 7-86 (88)
4 PRK05700 fliQ flagellar biosyn 92.7 3.2 7E-05 31.0 11.7 81 45-132 7-87 (89)
5 TIGR01402 fliQ flagellar biosy 92.3 3.6 7.8E-05 30.7 11.7 81 45-132 7-87 (88)
6 PRK06010 fliQ flagellar biosyn 91.7 4.4 9.4E-05 30.3 11.7 80 45-131 7-86 (88)
7 PRK12781 fliQ flagellar biosyn 90.4 6 0.00013 29.5 11.7 80 45-131 7-86 (88)
8 TIGR01403 fliQ_rel_III type II 89.4 6.8 0.00015 28.8 11.3 78 46-130 4-81 (81)
9 TIGR02120 GspF general secreti 87.9 12 0.00026 33.9 12.3 21 118-138 243-263 (399)
10 PRK09824 PTS system beta-gluco 87.8 6.7 0.00015 38.7 11.1 85 59-146 219-305 (627)
11 PRK12772 bifunctional flagella 87.3 12 0.00027 36.6 12.6 41 40-80 164-204 (609)
12 COG1987 FliQ Flagellar biosynt 87.3 11 0.00023 28.4 11.8 80 46-132 8-87 (89)
13 PF01311 Bac_export_1: Bacteri 86.7 20 0.00043 30.9 12.6 43 38-80 163-205 (249)
14 PRK15333 type III secretion sy 86.2 12 0.00026 27.9 11.0 79 46-131 6-84 (86)
15 PRK09796 PTS system cellobiose 84.0 14 0.00031 35.1 11.0 87 58-147 220-308 (472)
16 PRK11007 PTS system trehalose( 83.9 14 0.00029 35.3 10.8 86 58-146 231-319 (473)
17 PRK10573 type IV pilin biogene 83.6 14 0.00031 33.5 10.5 18 120-137 244-261 (399)
18 PRK09586 murP PTS system N-ace 82.8 17 0.00037 34.7 11.0 85 58-146 230-315 (476)
19 TIGR01992 PTS-IIBC-Tre PTS sys 81.6 19 0.00042 34.0 10.9 87 58-147 232-320 (462)
20 COG1684 FliR Flagellar biosynt 81.5 30 0.00066 30.5 11.4 43 38-80 165-207 (258)
21 TIGR01996 PTS-II-BC-sucr PTS s 81.2 23 0.00051 33.4 11.2 86 59-147 230-317 (461)
22 TIGR00851 mtlA PTS system, man 80.0 27 0.00059 31.7 10.9 83 58-143 93-182 (338)
23 PRK09765 PTS system 2-O-a-mann 79.6 12 0.00025 36.9 8.9 70 59-130 381-456 (631)
24 PRK15083 PTS system mannitol-s 79.3 16 0.00035 35.9 9.8 83 58-143 101-190 (639)
25 COG1459 PulF Type II secretory 76.9 20 0.00044 33.3 9.3 23 116-138 238-260 (397)
26 PF11872 DUF3392: Protein of u 74.9 24 0.00052 27.2 7.7 65 47-112 39-105 (106)
27 COG4794 EscS Type III secretor 74.2 35 0.00075 25.6 11.0 78 49-133 11-88 (89)
28 TIGR02002 PTS-II-BC-glcB PTS s 71.2 37 0.0008 32.5 9.7 87 59-146 135-225 (502)
29 TIGR01427 PTS_IIC_fructo PTS s 69.4 35 0.00076 31.2 8.8 72 58-130 112-185 (346)
30 PRK11404 putative PTS system 69.0 27 0.00059 33.3 8.3 68 58-128 228-301 (482)
31 PF05552 TM_helix: Conserved T 68.9 16 0.00034 24.1 4.9 23 98-120 19-41 (53)
32 PF14584 DUF4446: Protein of u 68.2 58 0.0012 26.4 9.0 51 137-188 63-122 (151)
33 PRK15349 type III secretion sy 66.2 90 0.0019 27.2 11.9 75 41-116 170-244 (259)
34 TIGR01995 PTS-II-ABC-beta PTS 63.8 1E+02 0.0022 30.4 11.2 85 59-146 211-297 (610)
35 TIGR02004 PTS-IIBC-malX PTS sy 63.5 68 0.0015 30.9 9.9 90 58-149 138-231 (517)
36 PF02674 Colicin_V: Colicin V 63.3 65 0.0014 24.6 11.4 84 48-131 17-105 (146)
37 PRK10617 cytochrome c-type pro 63.1 21 0.00045 30.3 5.7 20 32-51 2-21 (200)
38 TIGR01400 fliR flagellar biosy 62.7 1E+02 0.0022 26.6 12.8 41 40-80 158-198 (245)
39 PRK10110 bifunctional PTS syst 62.5 82 0.0018 30.5 10.2 89 59-149 148-240 (530)
40 COG3768 Predicted membrane pro 54.7 58 0.0013 30.0 7.3 33 45-77 60-92 (350)
41 PF06596 PsbX: Photosystem II 54.1 46 0.00099 21.3 4.7 27 43-69 4-30 (39)
42 TIGR00852 pts-Glc PTS system, 52.0 1.6E+02 0.0035 25.7 9.7 28 58-85 66-93 (289)
43 PF14257 DUF4349: Domain of un 50.1 42 0.00091 28.8 5.6 14 33-47 215-228 (262)
44 PRK15071 lipopolysaccharide AB 48.9 1E+02 0.0023 27.3 8.1 39 42-80 3-41 (356)
45 PF04109 APG9: Autophagy prote 48.7 61 0.0013 30.1 6.7 49 30-79 103-151 (370)
46 COG2981 CysZ Uncharacterized p 48.1 2E+02 0.0043 25.5 9.5 28 57-84 27-54 (250)
47 TIGR03745 conj_TIGR03745 integ 47.6 1.3E+02 0.0028 23.2 9.6 63 44-108 31-99 (104)
48 PF04854 DUF624: Protein of un 47.4 56 0.0012 22.6 5.0 35 37-71 41-75 (77)
49 PF01313 Bac_export_3: Bacteri 47.3 1.1E+02 0.0023 22.2 10.5 36 45-80 4-39 (76)
50 PF08566 Pam17: Mitochondrial 46.5 1.8E+02 0.0038 24.4 9.9 37 87-124 72-108 (173)
51 PF02355 SecD_SecF: Protein ex 46.3 1.7E+02 0.0037 24.2 9.8 71 33-123 117-187 (189)
52 TIGR01183 ntrB nitrate ABC tra 46.0 1.7E+02 0.0038 24.2 11.0 68 39-108 14-81 (202)
53 TIGR01401 fliR_like_III type I 45.6 2E+02 0.0044 24.9 11.5 41 40-80 165-205 (253)
54 cd02433 Nodulin-21_like_2 Nodu 45.2 1.8E+02 0.0038 25.1 8.6 60 32-116 147-206 (234)
55 PRK05701 fliR flagellar biosyn 45.1 2E+02 0.0043 24.7 12.0 40 41-80 161-200 (242)
56 PF09527 ATPase_gene1: Putativ 44.1 90 0.0019 20.4 6.2 11 103-113 17-27 (55)
57 TIGR00437 feoB ferrous iron tr 44.1 2E+02 0.0043 28.1 9.7 52 38-89 462-522 (591)
58 COG3366 Uncharacterized protei 43.6 2.6E+02 0.0056 25.5 10.2 59 50-108 176-236 (311)
59 TIGR02003 PTS-II-BC-unk1 PTS s 43.1 2.4E+02 0.0053 27.6 10.0 88 59-147 142-237 (548)
60 PF02762 Cbl_N3: CBL proto-onc 42.8 32 0.00069 25.5 3.1 45 136-184 11-56 (86)
61 PRK09554 feoB ferrous iron tra 42.5 1.4E+02 0.0031 30.2 8.7 55 36-90 496-564 (772)
62 KOG1341 Na+/K+ transporter [In 42.2 33 0.00071 34.5 4.0 35 13-47 689-725 (854)
63 PF03213 Pox_P35: Poxvirus P35 40.8 51 0.0011 30.2 4.7 66 35-124 252-318 (325)
64 PHA02688 ORF059 IMV protein VP 40.6 47 0.001 30.4 4.5 42 79-124 274-316 (323)
65 PRK15082 glutathione ABC trans 40.5 2.6E+02 0.0056 24.6 10.4 27 34-60 85-111 (301)
66 PRK10478 putative PTS system f 40.2 1.9E+02 0.004 26.8 8.4 29 44-72 7-35 (359)
67 COG2059 ChrA Chromate transpor 39.8 1.5E+02 0.0033 25.0 7.2 47 33-79 62-108 (195)
68 PF11241 DUF3043: Protein of u 39.4 1.3E+02 0.0028 25.0 6.6 15 58-72 80-94 (170)
69 PRK00523 hypothetical protein; 37.5 93 0.002 22.5 4.8 40 103-147 14-53 (72)
70 COG3763 Uncharacterized protei 37.0 99 0.0021 22.3 4.8 44 98-146 8-51 (71)
71 PF12841 YvrJ: YvrJ protein fa 36.4 66 0.0014 20.3 3.4 25 60-84 8-32 (38)
72 PF05328 CybS: CybS; InterPro 35.7 2.2E+02 0.0048 22.5 9.7 42 47-88 36-77 (132)
73 PF05283 MGC-24: Multi-glycosy 35.5 1E+02 0.0023 26.0 5.5 24 50-73 161-184 (186)
74 PRK01844 hypothetical protein; 35.4 95 0.0021 22.4 4.5 42 101-147 11-52 (72)
75 PRK12287 tqsA pheromone autoin 35.1 3E+02 0.0066 24.5 8.9 37 38-74 183-219 (344)
76 PF03672 UPF0154: Uncharacteri 34.5 67 0.0015 22.7 3.6 42 101-147 4-45 (64)
77 PRK05415 hypothetical protein; 34.2 3.8E+02 0.0082 24.7 9.8 30 47-77 65-94 (341)
78 PF03739 YjgP_YjgQ: Predicted 34.1 3.2E+02 0.0069 23.8 9.0 31 50-80 5-35 (354)
79 PRK06298 type III secretion sy 33.6 3.6E+02 0.0078 24.8 9.2 18 99-116 90-107 (356)
80 PHA03231 glycoprotein BALF4; P 33.3 1.7E+02 0.0038 30.1 7.6 69 37-114 657-727 (829)
81 PRK10845 colicin V production 31.9 2.7E+02 0.0059 22.4 9.3 80 49-130 21-104 (162)
82 PF07670 Gate: Nucleoside reco 31.6 1.4E+02 0.0031 21.5 5.3 32 58-89 3-40 (109)
83 COG1286 CvpA Uncharacterized m 31.5 3E+02 0.0065 22.7 10.6 30 49-78 21-50 (182)
84 cd02432 Nodulin-21_like_1 Nodu 31.4 3.3E+02 0.0071 23.2 8.9 59 33-117 134-192 (218)
85 PRK02463 OxaA-like protein pre 30.9 2E+02 0.0043 25.9 6.9 22 46-67 3-24 (307)
86 TIGR00328 flhB flagellar biosy 30.1 4.3E+02 0.0094 24.2 9.4 47 99-145 89-146 (347)
87 PRK11365 ssuC alkanesulfonate 30.0 2.8E+02 0.006 23.7 7.5 65 39-105 57-121 (263)
88 PRK04949 putative sulfate tran 29.9 3.7E+02 0.0081 23.3 10.6 24 57-80 29-56 (251)
89 TIGR01427 PTS_IIC_fructo PTS s 29.0 4.5E+02 0.0097 24.0 10.1 25 46-70 13-37 (346)
90 PRK04897 heat shock protein Ht 28.7 4.1E+02 0.0089 23.4 12.9 35 134-173 81-115 (298)
91 PRK10519 hypothetical protein; 28.5 3.2E+02 0.0069 22.1 8.5 50 40-89 7-62 (151)
92 PF01988 VIT1: VIT family; In 28.3 3.5E+02 0.0076 22.5 7.8 49 48-116 139-187 (213)
93 PRK10417 nikC nickel transport 28.2 3.9E+02 0.0085 23.0 9.6 19 40-58 58-76 (272)
94 PF10112 Halogen_Hydrol: 5-bro 28.2 3.3E+02 0.0072 22.3 7.4 15 134-148 105-119 (199)
95 PF04341 DUF485: Protein of un 28.1 2.4E+02 0.0052 20.5 8.2 26 59-84 18-43 (91)
96 TIGR02790 nickel_nikC nickel A 28.0 3.8E+02 0.0082 22.8 10.4 21 40-60 53-73 (258)
97 PF00873 ACR_tran: AcrB/AcrD/A 27.7 3E+02 0.0064 28.4 8.3 46 94-141 914-961 (1021)
98 PRK14762 membrane protein; Pro 27.6 1E+02 0.0023 18.0 3.0 14 99-112 7-20 (27)
99 COG4171 SapC ABC-type antimicr 27.1 4.6E+02 0.0099 23.4 9.5 23 122-144 163-186 (296)
100 PF12729 4HB_MCP_1: Four helix 27.1 2.6E+02 0.0057 20.7 7.6 40 94-134 10-50 (181)
101 PRK11026 ftsX cell division AB 26.8 4.6E+02 0.0099 23.3 9.7 25 98-122 282-306 (309)
102 PHA01399 membrane protein P6 26.7 4.2E+02 0.0091 22.9 14.3 13 94-106 58-70 (242)
103 PF01594 UPF0118: Domain of un 26.5 4.1E+02 0.009 22.8 10.4 94 56-153 1-107 (327)
104 COG1380 Putative effector of m 26.4 2.6E+02 0.0057 22.1 6.1 16 65-80 13-28 (128)
105 cd02435 CCC1 CCC1. CCC1: This 26.3 3.2E+02 0.007 23.6 7.2 48 49-116 162-209 (241)
106 PF04971 Lysis_S: Lysis protei 26.2 1.6E+02 0.0035 21.0 4.4 41 68-116 17-57 (68)
107 PRK10755 sensor protein BasS/P 26.2 4.2E+02 0.0092 22.8 11.6 16 131-146 115-130 (356)
108 KOG2675 Adenylate cyclase-asso 26.2 89 0.0019 30.0 3.9 12 33-44 260-271 (480)
109 PF00159 Hormone_3: Pancreatic 26.0 1.2E+02 0.0026 19.0 3.3 26 27-52 3-28 (36)
110 PRK12780 fliR flagellar biosyn 25.7 4.4E+02 0.0095 22.8 12.6 41 40-80 168-208 (251)
111 PRK04125 murein hydrolase regu 25.7 1.8E+02 0.004 23.4 5.2 14 67-80 17-30 (141)
112 cd02434 Nodulin-21_like_3 Nodu 25.7 4.2E+02 0.0091 22.5 8.1 66 33-117 132-198 (225)
113 KOG3733 Mucolipidin and relate 25.6 1.1E+02 0.0025 29.4 4.5 43 5-47 5-47 (566)
114 PRK10983 putative inner membra 25.1 5.3E+02 0.011 23.5 11.9 9 125-133 112-120 (368)
115 PF11947 DUF3464: Protein of u 24.3 4E+02 0.0086 21.8 7.4 24 55-78 66-89 (153)
116 TIGR00834 ae anion exchange pr 24.1 4.3E+02 0.0093 27.6 8.6 46 103-148 467-512 (900)
117 PRK09881 D-ala-D-ala transport 24.0 5E+02 0.011 22.8 9.4 34 39-72 84-117 (296)
118 cd00126 PAH Pancreatic Hormone 23.6 1.6E+02 0.0035 18.4 3.6 26 27-52 3-28 (36)
119 PF14965 BRI3BP: Negative regu 23.4 3.6E+02 0.0079 22.7 6.6 74 56-129 73-168 (177)
120 TIGR00267 conserved hypothetic 23.3 2.7E+02 0.0059 22.6 5.9 26 94-119 121-146 (169)
121 PRK09108 type III secretion sy 23.0 3.5E+02 0.0075 24.9 7.1 52 29-80 6-57 (353)
122 smart00309 PAH Pancreatic horm 22.3 1.8E+02 0.0039 18.3 3.6 26 27-52 3-28 (36)
123 PRK01821 hypothetical protein; 21.8 3.4E+02 0.0074 21.5 6.0 15 66-80 18-32 (133)
124 PF03547 Mem_trans: Membrane t 21.6 5.6E+02 0.012 22.5 9.7 30 44-73 234-263 (385)
125 PF15485 DUF4643: Domain of un 21.5 1.3E+02 0.0028 27.0 3.8 40 8-47 104-143 (284)
126 PF14257 DUF4349: Domain of un 21.1 2.8E+02 0.0061 23.7 5.9 9 39-47 213-221 (262)
127 PF00672 HAMP: HAMP domain; I 20.8 1.1E+02 0.0024 19.9 2.7 22 97-118 6-27 (70)
128 PF07662 Nucleos_tra2_C: Na+ d 20.4 5.5E+02 0.012 22.0 8.1 44 45-88 44-87 (210)
129 PF05767 Pox_A14: Poxvirus vir 20.2 3.6E+02 0.0079 20.4 5.4 18 99-116 53-70 (92)
130 COG0600 TauC ABC-type nitrate/ 20.1 5.9E+02 0.013 22.2 10.5 108 39-149 58-165 (258)
131 PRK10160 taurine transporter s 20.1 5.7E+02 0.012 22.0 10.9 64 39-104 75-138 (275)
132 PRK10263 DNA translocase FtsK; 20.0 1.2E+03 0.026 25.7 15.5 30 36-65 62-91 (1355)
133 PF08934 Rb_C: Rb C-terminal d 20.0 38 0.00083 27.7 0.3 26 16-41 6-35 (155)
No 1
>COG2928 Uncharacterized conserved protein [Function unknown]
Probab=100.00 E-value=1.1e-37 Score=263.43 Aligned_cols=147 Identities=31% Similarity=0.628 Sum_probs=132.2
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhhhhh-------hhhhhhhhHHHHHHHHHHHHHHHHHHhhhhh
Q 029429 44 LQSWVSKKFMTGCVVLFPVAVTFLVTWWFIEFVDSFFSPIYA-------RLGVEIFGLGFLTSILFIFFVGVFASSWLGA 116 (193)
Q Consensus 44 ~~~~i~~~fl~GLlvlLPi~iTi~Il~~l~~~v~~~~~pl~~-------~l~~~~pglgl~~~l~~i~~iG~la~~~ig~ 116 (193)
.++++|++|++||++++|+++|+|+++|+++++|+++.|.+. +++.+++++|+++.+++++++|+++++.+||
T Consensus 2 ~~~~lk~~fltGLlvllPlaiT~~vv~~i~~~l~~~~~~~lp~~~~~~~~~~~~i~~lg~il~iili~l~G~l~~~~ig~ 81 (222)
T COG2928 2 GAKRLKKYFLTGLLVLLPLAITLWVVSWIFGLLDQFVGPLLPDRLRPAVYFPFNIPGLGVILAIILIFLLGFLARNMIGR 81 (222)
T ss_pred hHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhhccchhchhhcCchhhHHHHHHHHHHHHHHHHHHHHHHhhh
Confidence 356789999999999999999999999999999999998553 2345688999999999999999999999999
Q ss_pred HHHHHHHHHhhhhhhhhHHHHHHHHHHHHhCCCCCCccccceEEEEcCCCCeeEEEEEeccc--cccCCCCceeeee
Q 029429 117 TVFWLGEWFIKRLPFMKHIYSASKQISAAISPDQNTSAFKEVAIIRHPRLGEYAFGFITSSV--VLQVDTLPVQVDF 191 (193)
Q Consensus 117 ~ll~~~e~ll~rIP~V~sIYssiKqi~~~f~g~~~~~~f~~VVLVe~P~~g~~~iGFvT~~~--~~~~~~g~~~~~~ 191 (193)
++++++|++++|||++|+||+++||+++++.++++ ++||+||+||||++|+|++||+|++. +.+...|++.+.+
T Consensus 82 ~l~~~~d~~L~RiPlv~~IY~s~kqi~etll~~~~-~sfk~vvlVefP~~G~~~i~fvtg~~~~e~~~~~~~~~v~V 157 (222)
T COG2928 82 SLLSLGDSLLRRIPLVKSIYKSAKQVVETLLSDQS-GSFKQVVLVEFPRRGIWAIAFVTGEKAGELKEKEGRPMVAV 157 (222)
T ss_pred HHHHHHHHHHccCccHHHHHHHHHHHHHHHHhcCC-ccceeeEEEECCCCCcEEEEEeccCCCcchhcccCCceEEE
Confidence 99999999999999999999999999999998864 58999999999999999999999996 5555666665543
No 2
>PF04367 DUF502: Protein of unknown function (DUF502); InterPro: IPR007462 This entry contains proteins that are predicted to be integral membrane proteins.
Probab=99.93 E-value=2.5e-25 Score=170.12 Aligned_cols=92 Identities=34% Similarity=0.595 Sum_probs=81.7
Q ss_pred HHHHHHHHHHHHHHHhhhhhHHHHHHHHHhhhhhhhhHHHHHHHHHHHHhCCCCCCccccceEEEEcCCCCeeEEEEEec
Q 029429 97 LTSILFIFFVGVFASSWLGATVFWLGEWFIKRLPFMKHIYSASKQISAAISPDQNTSAFKEVAIIRHPRLGEYAFGFITS 176 (193)
Q Consensus 97 ~~~l~~i~~iG~la~~~ig~~ll~~~e~ll~rIP~V~sIYssiKqi~~~f~g~~~~~~f~~VVLVe~P~~g~~~iGFvT~ 176 (193)
++++++|+++|+++++++|+++++++|+++.|||+||+||+++||++++|+++++ ++|++||+||||++|+|++||+|+
T Consensus 2 l~~l~~i~~iG~l~~~~~g~~l~~~~e~ll~riP~v~~iY~~~k~~~~~~~~~~~-~~f~~vVlV~~p~~g~~~igFvT~ 80 (108)
T PF04367_consen 2 LILLLLIFLIGLLARNYFGKWLLNWLERLLQRIPLVKSIYSSIKQLVESFSGDKK-KSFKKVVLVEFPRPGMYVIGFVTG 80 (108)
T ss_pred hHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCchHHHHHHHHHHHHHHhhccc-ccCCeEEEEEecCCCcEEEEEEec
Confidence 5678899999999999999999999999999999999999999999999998864 459999999999999999999999
Q ss_pred cc--cccCCCCceee
Q 029429 177 SV--VLQVDTLPVQV 189 (193)
Q Consensus 177 ~~--~~~~~~g~~~~ 189 (193)
+. ..+...+++.+
T Consensus 81 ~~~~~~~~~~~~~~v 95 (108)
T PF04367_consen 81 EDPGELPGKTGEEMV 95 (108)
T ss_pred cCcchhhccCCCCEE
Confidence 97 33444444443
No 3
>PRK15350 type III secretion system protein SsaS; Provisional
Probab=93.17 E-value=2.7 Score=31.36 Aligned_cols=80 Identities=15% Similarity=0.198 Sum_probs=53.6
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhhhhhhhhhhhhhHHHHHHHHHHHHHHHHHHhhhhhHHHHHHHH
Q 029429 45 QSWVSKKFMTGCVVLFPVAVTFLVTWWFIEFVDSFFSPIYARLGVEIFGLGFLTSILFIFFVGVFASSWLGATVFWLGEW 124 (193)
Q Consensus 45 ~~~i~~~fl~GLlvlLPi~iTi~Il~~l~~~v~~~~~pl~~~l~~~~pglgl~~~l~~i~~iG~la~~~ig~~ll~~~e~ 124 (193)
....++.+...+.+.+|+.+.-.++..+++.+....+- .-.-++++-=++.++++=++...|.++.+.++.++
T Consensus 7 ~~l~~~al~~~l~ls~P~L~~alvVGlvIsi~QA~TQI-------QEqTLsFvPKliav~~~l~~~gpWm~~~l~~ft~~ 79 (88)
T PRK15350 7 TQFVTQLLWIVLFTSMPVVLVASVVGVIVSLVQALTQI-------QDQTLQFMIKLLAIAITLMVSYPWLSGILLNYTRQ 79 (88)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-------HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 44567889999999999999998888888777665421 11123333333333333344455666778889999
Q ss_pred Hhhhhhh
Q 029429 125 FIKRLPF 131 (193)
Q Consensus 125 ll~rIP~ 131 (193)
++.+||-
T Consensus 80 if~~i~~ 86 (88)
T PRK15350 80 IMLRIGE 86 (88)
T ss_pred HHHhhhh
Confidence 9999884
No 4
>PRK05700 fliQ flagellar biosynthesis protein FliQ; Validated
Probab=92.69 E-value=3.2 Score=30.97 Aligned_cols=81 Identities=14% Similarity=0.235 Sum_probs=55.6
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhhhhhhhhhhhhhHHHHHHHHHHHHHHHHHHhhhhhHHHHHHHH
Q 029429 45 QSWVSKKFMTGCVVLFPVAVTFLVTWWFIEFVDSFFSPIYARLGVEIFGLGFLTSILFIFFVGVFASSWLGATVFWLGEW 124 (193)
Q Consensus 45 ~~~i~~~fl~GLlvlLPi~iTi~Il~~l~~~v~~~~~pl~~~l~~~~pglgl~~~l~~i~~iG~la~~~ig~~ll~~~e~ 124 (193)
....++.+...+.+.+|+.+.-.++..+++.+....+- .-.-++++-=++.++++=++...|.++.+.++.++
T Consensus 7 ~~l~~~al~~~l~ls~P~l~~alvVGlvIsi~QA~TQI-------qEqTLsFvPKliav~~~l~~~g~Wm~~~l~~f~~~ 79 (89)
T PRK05700 7 MDLFREAMKVALMLAAPLLLVALVVGLVVSIFQAATQI-------NEQTLSFIPKILAVLLTLIIAGPWMLNTLLDYTRT 79 (89)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-------HHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 34567888999999999999998888888777665421 11223333333334444445556777888899999
Q ss_pred Hhhhhhhh
Q 029429 125 FIKRLPFM 132 (193)
Q Consensus 125 ll~rIP~V 132 (193)
++++||-+
T Consensus 80 if~~i~~~ 87 (89)
T PRK05700 80 LFSNIPTL 87 (89)
T ss_pred HHHHHHhh
Confidence 99999963
No 5
>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=92.35 E-value=3.6 Score=30.69 Aligned_cols=81 Identities=15% Similarity=0.184 Sum_probs=55.3
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhhhhhhhhhhhhhHHHHHHHHHHHHHHHHHHhhhhhHHHHHHHH
Q 029429 45 QSWVSKKFMTGCVVLFPVAVTFLVTWWFIEFVDSFFSPIYARLGVEIFGLGFLTSILFIFFVGVFASSWLGATVFWLGEW 124 (193)
Q Consensus 45 ~~~i~~~fl~GLlvlLPi~iTi~Il~~l~~~v~~~~~pl~~~l~~~~pglgl~~~l~~i~~iG~la~~~ig~~ll~~~e~ 124 (193)
..-.++.+...+.+.+|+.+.-.++..+++.+....+- .-.-++++-=++.++++-++.-.|.++.+.++.++
T Consensus 7 ~~l~~~al~~~l~~s~P~l~~alvVGlvIsi~QA~TQI-------qEqTLsFvPKliav~~~l~~~gpWm~~~l~~f~~~ 79 (88)
T TIGR01402 7 LDLGREAIWLTLLLSAPVLLVALVVGLVISIFQAATQI-------QEQTLSFIPKIIAILLALALLGPWMLTKLLDFTRE 79 (88)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-------HHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 34567888999999999999988888888777665421 11223333333334444445556677788899999
Q ss_pred Hhhhhhhh
Q 029429 125 FIKRLPFM 132 (193)
Q Consensus 125 ll~rIP~V 132 (193)
++++||-+
T Consensus 80 ~f~~i~~~ 87 (88)
T TIGR01402 80 IFQRIPQG 87 (88)
T ss_pred HHHHhhhh
Confidence 99999863
No 6
>PRK06010 fliQ flagellar biosynthesis protein FliQ; Reviewed
Probab=91.71 E-value=4.4 Score=30.27 Aligned_cols=80 Identities=18% Similarity=0.176 Sum_probs=52.6
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhhhhhhhhhhhhhHHHHHHHHHHHHHHHHHHhhhhhHHHHHHHH
Q 029429 45 QSWVSKKFMTGCVVLFPVAVTFLVTWWFIEFVDSFFSPIYARLGVEIFGLGFLTSILFIFFVGVFASSWLGATVFWLGEW 124 (193)
Q Consensus 45 ~~~i~~~fl~GLlvlLPi~iTi~Il~~l~~~v~~~~~pl~~~l~~~~pglgl~~~l~~i~~iG~la~~~ig~~ll~~~e~ 124 (193)
....++.+...+.+.+|+.+.-.++..+++.+....+- .-.-+.++-=++.++++=++...|.++.+.++.++
T Consensus 7 ~~l~~~al~~~l~~s~P~L~~alvVGliIsi~QA~TQI-------qEqTLsFvPKliav~~~l~~~g~Wm~~~l~~f~~~ 79 (88)
T PRK06010 7 LDIVRDAIWTVLVASGPAVLAAMVVGVAIALFQALTQI-------QEMTLTFVPKIVAIFVTLLLTLPFMGAQISAFTLL 79 (88)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-------HHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 34567889999999999999998888888777665421 11123333323333333334445666778889999
Q ss_pred Hhhhhhh
Q 029429 125 FIKRLPF 131 (193)
Q Consensus 125 ll~rIP~ 131 (193)
++.+||-
T Consensus 80 if~~i~~ 86 (88)
T PRK06010 80 IYSRIAG 86 (88)
T ss_pred HHHhhcc
Confidence 9999884
No 7
>PRK12781 fliQ flagellar biosynthesis protein FliQ; Reviewed
Probab=90.38 E-value=6 Score=29.52 Aligned_cols=80 Identities=19% Similarity=0.214 Sum_probs=53.6
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhhhhhhhhhhhhhHHHHHHHHHHHHHHHHHHhhhhhHHHHHHHH
Q 029429 45 QSWVSKKFMTGCVVLFPVAVTFLVTWWFIEFVDSFFSPIYARLGVEIFGLGFLTSILFIFFVGVFASSWLGATVFWLGEW 124 (193)
Q Consensus 45 ~~~i~~~fl~GLlvlLPi~iTi~Il~~l~~~v~~~~~pl~~~l~~~~pglgl~~~l~~i~~iG~la~~~ig~~ll~~~e~ 124 (193)
....++.+...+.+-+|..+.-.++.-+++.+....+- .-.-++++-=++.++++=++...+.++.+.++.++
T Consensus 7 i~~~~~al~~~l~ls~P~L~~alvVGlvIsi~QA~TQI-------QEqTLsFvPKliav~~~l~~~~~wm~~~l~~ft~~ 79 (88)
T PRK12781 7 LELVRAAIWTIIVASGPAVGAAMLVGIAIALLQALTQI-------QEVTLTFVPKIVVILIVMAVTGSFVGAQIYAFTEM 79 (88)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-------HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 45567888999999999999988888877776655411 11123333333333344444555667778889999
Q ss_pred Hhhhhhh
Q 029429 125 FIKRLPF 131 (193)
Q Consensus 125 ll~rIP~ 131 (193)
++.+||-
T Consensus 80 if~~i~~ 86 (88)
T PRK12781 80 VYGRIES 86 (88)
T ss_pred HHHhhcc
Confidence 9999883
No 8
>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=89.43 E-value=6.8 Score=28.77 Aligned_cols=78 Identities=12% Similarity=0.318 Sum_probs=49.6
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhhhhhhhhhhhhhHHHHHHHHHHHHHHHHHHhhhhhHHHHHHHHH
Q 029429 46 SWVSKKFMTGCVVLFPVAVTFLVTWWFIEFVDSFFSPIYARLGVEIFGLGFLTSILFIFFVGVFASSWLGATVFWLGEWF 125 (193)
Q Consensus 46 ~~i~~~fl~GLlvlLPi~iTi~Il~~l~~~v~~~~~pl~~~l~~~~pglgl~~~l~~i~~iG~la~~~ig~~ll~~~e~l 125 (193)
...++.+...+.+.+|..+.-.++..+++.+....+- .-+-+.++-=++.++++=++...+..+.+.++.+++
T Consensus 4 ~~~~~al~~~l~~s~P~L~~alvVGLvIsi~QA~TQI-------qEqTLsFvPKliav~~~l~~~~pwm~~~l~~f~~~i 76 (81)
T TIGR01403 4 QLTNQALLLVLILSLPPVLVAAIVGLLVSLLQALTQL-------QDQTLPFAIKLIAVFITLMLTAGWLGAEILNFANQI 76 (81)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-------HHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3457888899999999999998888888777665421 111122222222222222333445566778899999
Q ss_pred hhhhh
Q 029429 126 IKRLP 130 (193)
Q Consensus 126 l~rIP 130 (193)
+++||
T Consensus 77 f~~i~ 81 (81)
T TIGR01403 77 FTMIP 81 (81)
T ss_pred HhhCC
Confidence 98887
No 9
>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=87.89 E-value=12 Score=33.91 Aligned_cols=21 Identities=14% Similarity=0.126 Sum_probs=17.7
Q ss_pred HHHHHHHHhhhhhhhhHHHHH
Q 029429 118 VFWLGEWFIKRLPFMKHIYSA 138 (193)
Q Consensus 118 ll~~~e~ll~rIP~V~sIYss 138 (193)
.-...|+++.|||+++++|..
T Consensus 243 ~r~~~~~~l~kiP~~g~~~~~ 263 (399)
T TIGR02120 243 FRLRFDRRLLRLPVIGRLVRG 263 (399)
T ss_pred HHHHHHHHHhcccchHHHHHH
Confidence 446789999999999999864
No 10
>PRK09824 PTS system beta-glucoside-specific transporter subunits IIABC; Provisional
Probab=87.82 E-value=6.7 Score=38.68 Aligned_cols=85 Identities=13% Similarity=0.254 Sum_probs=57.3
Q ss_pred HHHHHHHHHHHHHHHHHHHhhhhhhhhhhhhhhhhHHHHHHH-HHHHHHHHHHHhhhhhHHHHHHHHHhhhhhhh-hHHH
Q 029429 59 LFPVAVTFLVTWWFIEFVDSFFSPIYARLGVEIFGLGFLTSI-LFIFFVGVFASSWLGATVFWLGEWFIKRLPFM-KHIY 136 (193)
Q Consensus 59 lLPi~iTi~Il~~l~~~v~~~~~pl~~~l~~~~pglgl~~~l-~~i~~iG~la~~~ig~~ll~~~e~ll~rIP~V-~sIY 136 (193)
++|+.+++|+..|+-.|+++++...++.+ -.|.+.+++++ +.++++|=+.. ++|..+-..++++.+.-|.+ +-|+
T Consensus 219 ViPiil~v~~~s~iEk~l~K~iP~~l~~i--~~P~ltlli~~pl~l~viGPig~-~i~~~l~~~i~~l~~~~~~i~g~i~ 295 (627)
T PRK09824 219 VIPIIFSAWLCSILERRLNAWLPSAIKNF--FTPLLCLMVIVPLTFLLIGPLAT-WLSELLAAGYQWLYQAVPAFAGAVM 295 (627)
T ss_pred hHHHHHHHHHHHHHHHHHHHHHHHHHHHH--HHHHHHHHHHHHHHHHhHHHHHH-HHHHHHHHHHHHHHhhchHHHHHHH
Confidence 89999999999999999999986665442 24555555543 44555665553 46666666777777766644 3467
Q ss_pred HHHHHHHHHh
Q 029429 137 SASKQISAAI 146 (193)
Q Consensus 137 ssiKqi~~~f 146 (193)
..+-+++=.+
T Consensus 296 g~~~~~lV~~ 305 (627)
T PRK09824 296 GAFWQVFVIF 305 (627)
T ss_pred HHHHHHHHHh
Confidence 7776665544
No 11
>PRK12772 bifunctional flagellar biosynthesis protein FliR/FlhB; Provisional
Probab=87.28 E-value=12 Score=36.65 Aligned_cols=41 Identities=12% Similarity=0.207 Sum_probs=36.5
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhh
Q 029429 40 CYAVLQSWVSKKFMTGCVVLFPVAVTFLVTWWFIEFVDSFF 80 (193)
Q Consensus 40 ~~~~~~~~i~~~fl~GLlvlLPi~iTi~Il~~l~~~v~~~~ 80 (193)
......+.+.+.|..|+...+|+++..+++...+++++...
T Consensus 164 ~~~~~~~~~~~~F~~al~lAaP~i~~lll~~~~lGllsR~a 204 (609)
T PRK12772 164 SIMHVINVFIQYFYIGIKIAIPIVLIILITDLTLGLISRTV 204 (609)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhC
Confidence 34566778899999999999999999999999999998876
No 12
>COG1987 FliQ Flagellar biosynthesis pathway, component FliQ [Cell motility and secretion / Intracellular trafficking and secretion]
Probab=87.27 E-value=11 Score=28.39 Aligned_cols=80 Identities=15% Similarity=0.214 Sum_probs=54.4
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhhhhhhhhhhhhhHHHHHHHHHHHHHHHHHHhhhhhHHHHHHHHH
Q 029429 46 SWVSKKFMTGCVVLFPVAVTFLVTWWFIEFVDSFFSPIYARLGVEIFGLGFLTSILFIFFVGVFASSWLGATVFWLGEWF 125 (193)
Q Consensus 46 ~~i~~~fl~GLlvlLPi~iTi~Il~~l~~~v~~~~~pl~~~l~~~~pglgl~~~l~~i~~iG~la~~~ig~~ll~~~e~l 125 (193)
+-.++.+-.+|...+|..+.-.++.-++..+.....- .-.-+.++==++.++++-.++..|.++.+.++...+
T Consensus 8 ~i~~~ai~~~L~l~~P~ll~alvvGLvIsifQA~TQI-------qEqTLsFiPKIiai~~~l~~~gpWm~~~l~dft~~i 80 (89)
T COG1987 8 DIGQEAIWLVLMLSAPVLLVALVVGLVISIFQAATQI-------QEQTLSFIPKIIAVFLVLILLGPWMLNQLLDFTVTI 80 (89)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-------HHHHHHhHHHHHHHHHHHHHHhHHHHHHHHHHHHHH
Confidence 4456778889999999998888877777666554311 111233333344455555566667788899999999
Q ss_pred hhhhhhh
Q 029429 126 IKRLPFM 132 (193)
Q Consensus 126 l~rIP~V 132 (193)
++|||..
T Consensus 81 f~~i~~~ 87 (89)
T COG1987 81 FSNIPQI 87 (89)
T ss_pred HHHHHhh
Confidence 9999963
No 13
>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=86.65 E-value=20 Score=30.93 Aligned_cols=43 Identities=9% Similarity=0.115 Sum_probs=39.0
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhh
Q 029429 38 KACYAVLQSWVSKKFMTGCVVLFPVAVTFLVTWWFIEFVDSFF 80 (193)
Q Consensus 38 ~~~~~~~~~~i~~~fl~GLlvlLPi~iTi~Il~~l~~~v~~~~ 80 (193)
++......+.+.+.|..|+..-+|+.+..+++.-.++.+++..
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 5677778888899999999999999999999999999998876
No 14
>PRK15333 type III secretion system protein SpaQ; Provisional
Probab=86.20 E-value=12 Score=27.88 Aligned_cols=79 Identities=11% Similarity=0.028 Sum_probs=52.1
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhhhhhhhhhhhhhHHHHHHHHHHHHHHHHHHhhhhhHHHHHHHHH
Q 029429 46 SWVSKKFMTGCVVLFPVAVTFLVTWWFIEFVDSFFSPIYARLGVEIFGLGFLTSILFIFFVGVFASSWLGATVFWLGEWF 125 (193)
Q Consensus 46 ~~i~~~fl~GLlvlLPi~iTi~Il~~l~~~v~~~~~pl~~~l~~~~pglgl~~~l~~i~~iG~la~~~ig~~ll~~~e~l 125 (193)
...++.+...+.+.+|+.+.-.++.-+++.+....+- .-.-+.++-=++.+++.=++...+.++.+.++.+++
T Consensus 6 ~~~~~al~~~l~ls~P~L~valvVGlvIsi~QA~TQI-------QEqTLsFvPKliav~~~l~~~~pwm~~~l~~f~~~i 78 (86)
T PRK15333 6 FAGNKALYLVLILSGWPTIVATIIGLLVGLFQTVTQL-------QEQTLPFGIKLLGVCLCLFLLSGWYGEVLLSYGRQV 78 (86)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-------HHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3457888899999999999988888887776655421 111233333333333333445556777788899999
Q ss_pred hhhhhh
Q 029429 126 IKRLPF 131 (193)
Q Consensus 126 l~rIP~ 131 (193)
+..+|-
T Consensus 79 f~~~~~ 84 (86)
T PRK15333 79 IFLALA 84 (86)
T ss_pred HHhhhc
Confidence 988874
No 15
>PRK09796 PTS system cellobiose/arbutin/salicin-specific transporter subunits IIBC; Provisional
Probab=84.00 E-value=14 Score=35.13 Aligned_cols=87 Identities=17% Similarity=0.162 Sum_probs=54.7
Q ss_pred HHHHHHHHHHHHHHHHHHHHhhhhhhhhhhhhhhhhHHHHHH-HHHHHHHHHHHHhhhhhHHHHHHHHHhhhhh-hhhHH
Q 029429 58 VLFPVAVTFLVTWWFIEFVDSFFSPIYARLGVEIFGLGFLTS-ILFIFFVGVFASSWLGATVFWLGEWFIKRLP-FMKHI 135 (193)
Q Consensus 58 vlLPi~iTi~Il~~l~~~v~~~~~pl~~~l~~~~pglgl~~~-l~~i~~iG~la~~~ig~~ll~~~e~ll~rIP-~V~sI 135 (193)
.++|+.+++|+..++-.+++++....++.+ -.|.+.++++ .+.++++|=+.. ++|..+-..++++.+.-| +..-|
T Consensus 220 sViPiil~v~~~s~vek~~~K~~P~~l~~i--~~P~ltlli~~pl~l~viGPig~-~i~~~i~~~i~~l~~~~~~i~g~i 296 (472)
T PRK09796 220 TVIPALVMTWCLSYIERWVDRITPAVTKNF--LKPMLIVLIAAPLAILLIGPIGI-WIGSAISALVYTIHGYLGWLSVAI 296 (472)
T ss_pred chHHHHHHHHHHHHHHHHHHHhCHHHHHHH--HHHHHHHHHHHHHHHHhHHHHHH-HHHHHHHHHHHHHHhcchHHHHHH
Confidence 479999999999999999999886655432 1344444432 233444444432 455555556666665554 55677
Q ss_pred HHHHHHHHHHhC
Q 029429 136 YSASKQISAAIS 147 (193)
Q Consensus 136 YssiKqi~~~f~ 147 (193)
+..+-+.+=.+.
T Consensus 297 ~g~~~~~lV~~G 308 (472)
T PRK09796 297 MGALWPLLVMTG 308 (472)
T ss_pred HHHHHHHHHHhc
Confidence 777777665443
No 16
>PRK11007 PTS system trehalose(maltose)-specific transporter subunits IIBC; Provisional
Probab=83.86 E-value=14 Score=35.31 Aligned_cols=86 Identities=9% Similarity=0.125 Sum_probs=57.0
Q ss_pred HHHHHHHHHHHHHHHHHHHHhhhhhhhhhhhhhhhhHHHHHHHHH-HHHHHHHHHhhhhhHHHHHHHHHhh-hh-hhhhH
Q 029429 58 VLFPVAVTFLVTWWFIEFVDSFFSPIYARLGVEIFGLGFLTSILF-IFFVGVFASSWLGATVFWLGEWFIK-RL-PFMKH 134 (193)
Q Consensus 58 vlLPi~iTi~Il~~l~~~v~~~~~pl~~~l~~~~pglgl~~~l~~-i~~iG~la~~~ig~~ll~~~e~ll~-rI-P~V~s 134 (193)
.++|+.++.|+..|+-.|++++....++. .-.|.+.++++..+ ++++|=+.. +++..+-+.++++.. .. ++-.-
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 QVIPALLAGLALGFIETRLKRIVPDYLYL--VVVPVCSLILAVFLAHALIGPFGR-MIGDGVAFAVKALMTGSFAPIGAA 307 (473)
T ss_pred CcHHHHHHHHHHHHHHHHHHHhCcHHHHH--HHHHHHHHHHHHHHHHHHHHHHHH-HHHHHHHHHHHHHHhcchHHHHHH
Confidence 58999999999999999999997555542 22455666554443 346665543 466666667777762 33 45666
Q ss_pred HHHHHHHHHHHh
Q 029429 135 IYSASKQISAAI 146 (193)
Q Consensus 135 IYssiKqi~~~f 146 (193)
++..+-+.+=.+
T Consensus 308 i~g~~~~~lV~~ 319 (473)
T PRK11007 308 LFGFLYAPLVIT 319 (473)
T ss_pred HHHHHHHHHHHh
Confidence 777777765544
No 17
>PRK10573 type IV pilin biogenesis protein; Provisional
Probab=83.58 E-value=14 Score=33.47 Aligned_cols=18 Identities=17% Similarity=0.344 Sum_probs=15.3
Q ss_pred HHHHHHhhhhhhhhHHHH
Q 029429 120 WLGEWFIKRLPFMKHIYS 137 (193)
Q Consensus 120 ~~~e~ll~rIP~V~sIYs 137 (193)
.+.|+++.|+|+++.+|.
T Consensus 244 ~~~~~~l~~iP~~g~~~~ 261 (399)
T PRK10573 244 IREQRLLLRLPLVGSLIR 261 (399)
T ss_pred HHHHHHHhcCCeeccccc
Confidence 467999999999998775
No 18
>PRK09586 murP PTS system N-acetylmuramic acid transporter subunits EIIBC; Reviewed
Probab=82.78 E-value=17 Score=34.69 Aligned_cols=85 Identities=14% Similarity=0.176 Sum_probs=52.8
Q ss_pred HHHHHHHHHHHHHHHHHHHHhhhhhhhhhhhhhhhhHHHHHH-HHHHHHHHHHHHhhhhhHHHHHHHHHhhhhhhhhHHH
Q 029429 58 VLFPVAVTFLVTWWFIEFVDSFFSPIYARLGVEIFGLGFLTS-ILFIFFVGVFASSWLGATVFWLGEWFIKRLPFMKHIY 136 (193)
Q Consensus 58 vlLPi~iTi~Il~~l~~~v~~~~~pl~~~l~~~~pglgl~~~-l~~i~~iG~la~~~ig~~ll~~~e~ll~rIP~V~sIY 136 (193)
.++|+.++.|+..++-.+++++....++.+ -.|.+.++++ .+.++++|=+. +++|..+-+.+.++... ++..-++
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 NIIGVLIAAIAGARIERMVRRFMPDDLDMI--LTSLITLLITGALAFLIIMPLG-GWLFEGMSWLFMHLNSN-PFGCAVL 305 (476)
T ss_pred chHHHHHHHHHHHHHHHHHHhhCHHHHHHH--HHHHHHHHHHHHHHHHhHHhHH-HHHHHHHHHHHHHHHhh-HHHHHHH
Confidence 578999999999999999999886655432 1344444432 33344444443 24555544555555443 6667777
Q ss_pred HHHHHHHHHh
Q 029429 137 SASKQISAAI 146 (193)
Q Consensus 137 ssiKqi~~~f 146 (193)
..+.+.+=.+
T Consensus 306 g~~~~~lV~~ 315 (476)
T PRK09586 306 AGLFLIAVVF 315 (476)
T ss_pred HHHHHHHhHh
Confidence 7777765444
No 19
>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=81.60 E-value=19 Score=33.97 Aligned_cols=87 Identities=8% Similarity=0.063 Sum_probs=55.7
Q ss_pred HHHHHHHHHHHHHHHHHHHHhhhhhhhhhhhhhhhhHHHHHHHHHHH-HHHHHHHhhhhhHHHHHHHHHhhhhhhh-hHH
Q 029429 58 VLFPVAVTFLVTWWFIEFVDSFFSPIYARLGVEIFGLGFLTSILFIF-FVGVFASSWLGATVFWLGEWFIKRLPFM-KHI 135 (193)
Q Consensus 58 vlLPi~iTi~Il~~l~~~v~~~~~pl~~~l~~~~pglgl~~~l~~i~-~iG~la~~~ig~~ll~~~e~ll~rIP~V-~sI 135 (193)
-++|..+..|+..|+-.|++..+...++.+ -.|.+.+++.+.+.+ ++|-+.. +++..+...+.++....|.+ .-+
T Consensus 232 sVip~Il~g~i~~yiek~~~k~lP~~l~~~--~vP~lt~lv~~~l~~~vigPi~~-~i~~~i~~~~~~l~~~~~~i~g~i 308 (462)
T TIGR01992 232 QVLPALLAGYVLAVIEKWLRKRVPDAIQLL--VVPPVSLLVTGFLAHAIIGPIGR-LIGNGITSGVTALFTSAAWLGGAI 308 (462)
T ss_pred cHHHHHHHHHHHHHHHHHHHcCChHHHHHH--HHHHHHHHHHHHHHHHHHHHHHH-HHHHHHHHHHHHHHHhCcHHHHHH
Confidence 358999999999999989988765555432 245555555443333 4464432 45555656666666666654 448
Q ss_pred HHHHHHHHHHhC
Q 029429 136 YSASKQISAAIS 147 (193)
Q Consensus 136 YssiKqi~~~f~ 147 (193)
|..+.+.+=.+-
T Consensus 309 ~G~l~~~lV~~G 320 (462)
T TIGR01992 309 FGLLYAPLVITG 320 (462)
T ss_pred HHHHHHHHHHhc
Confidence 888888765543
No 20
>COG1684 FliR Flagellar biosynthesis pathway, component FliR [Cell motility and secretion / Intracellular trafficking and secretion]
Probab=81.52 E-value=30 Score=30.54 Aligned_cols=43 Identities=14% Similarity=0.315 Sum_probs=38.5
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhh
Q 029429 38 KACYAVLQSWVSKKFMTGCVVLFPVAVTFLVTWWFIEFVDSFF 80 (193)
Q Consensus 38 ~~~~~~~~~~i~~~fl~GLlvlLPi~iTi~Il~~l~~~v~~~~ 80 (193)
+..+..+-+++...|..|+..-+|++....+++..++.+++..
T Consensus 165 ~~~~~~l~~~l~~~F~~~l~iAlPii~~lLlvnlalGlv~R~~ 207 (258)
T COG1684 165 DNAFLLLAKALSAIFLIGLRLALPIIALLLLVNLALGLLNRLA 207 (258)
T ss_pred ccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcc
Confidence 4566778888999999999999999999999999999998876
No 21
>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=81.19 E-value=23 Score=33.36 Aligned_cols=86 Identities=14% Similarity=0.213 Sum_probs=58.3
Q ss_pred HHHHHHHHHHHHHHHHHHHhhhhhhhhhhhhhhhhHHHHHH-HHHHHHHHHHHHhhhhhHHHHHHHHHhhhhh-hhhHHH
Q 029429 59 LFPVAVTFLVTWWFIEFVDSFFSPIYARLGVEIFGLGFLTS-ILFIFFVGVFASSWLGATVFWLGEWFIKRLP-FMKHIY 136 (193)
Q Consensus 59 lLPi~iTi~Il~~l~~~v~~~~~pl~~~l~~~~pglgl~~~-l~~i~~iG~la~~~ig~~ll~~~e~ll~rIP-~V~sIY 136 (193)
++|..++.|+..|+-++++..+...++.+ -.|.+.+++. ++.++++|.+.. +++..+.+.++.+.+.-+ +..-+|
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--LTPFLTLLITGFLTLLVIGPIGR-WVGDVLTDGLQWLYDLPGGLGGLLF 306 (461)
T ss_pred HHHHHHHHHHHHHHHHHHHHhchhhhhhh--hHHHHHHHHHHHHHHHHHHHHHH-HHHHHHHHHHHHHHhccHHHHHHHH
Confidence 89999999999999889988876666543 2455555554 344445776654 466667777777766433 455678
Q ss_pred HHHHHHHHHhC
Q 029429 137 SASKQISAAIS 147 (193)
Q Consensus 137 ssiKqi~~~f~ 147 (193)
..+.++...+.
T Consensus 307 G~l~~~Lv~~G 317 (461)
T TIGR01996 307 GGLYSLIVITG 317 (461)
T ss_pred HHHHHHHHHhc
Confidence 88877765443
No 22
>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=80.00 E-value=27 Score=31.70 Aligned_cols=83 Identities=13% Similarity=-0.049 Sum_probs=53.9
Q ss_pred HHHHHHHHHHHHHHHHHHHHhhhhhhhhhhhhhhhhHHHHH----HHHHHHHHHHHHHhhhhhHHHHHHHHHhhh--hhh
Q 029429 58 VLFPVAVTFLVTWWFIEFVDSFFSPIYARLGVEIFGLGFLT----SILFIFFVGVFASSWLGATVFWLGEWFIKR--LPF 131 (193)
Q Consensus 58 vlLPi~iTi~Il~~l~~~v~~~~~pl~~~l~~~~pglgl~~----~l~~i~~iG~la~~~ig~~ll~~~e~ll~r--IP~ 131 (193)
.++|+.++.|+..|+-+++++.+...++.+ -.|.+.+++ ..+.++++|=+.+ ++|+.+-+.++++.+. -|.
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 AMIMGPLGGWLIKKTDEFVQGKVKQGFEML--VNNFSAGIIGFILTILAFEGIGPIVK-AISKILAAGVEAIVHAHLLPL 169 (338)
T ss_pred hHHHHHHHHHHHHHHHHHHHhhCcHHHHHh--HhhHHHHHHHHHHHHHHHHHHHHHHH-HHHHHHHHHHHHHHhCcchhH
Confidence 899999999999999999999886655432 134444322 3445566666654 5677777777777763 443
Q ss_pred h-hHHHHHHHHHH
Q 029429 132 M-KHIYSASKQIS 143 (193)
Q Consensus 132 V-~sIYssiKqi~ 143 (193)
+ .-+....-+++
T Consensus 170 ~~g~i~g~~~~~l 182 (338)
T TIGR00851 170 ASIFVEPAKILFL 182 (338)
T ss_pred HHHHHHHHHHHHH
Confidence 3 34445555544
No 23
>PRK09765 PTS system 2-O-a-mannosyl-D-glycerate specific transporter subunit IIABC; Provisional
Probab=79.61 E-value=12 Score=36.85 Aligned_cols=70 Identities=14% Similarity=0.197 Sum_probs=49.3
Q ss_pred HHHHHHHHHHHHHHHHHHHhhhhhhhhhh----h-hhhhhHHHHHHHH-HHHHHHHHHHhhhhhHHHHHHHHHhhhhh
Q 029429 59 LFPVAVTFLVTWWFIEFVDSFFSPIYARL----G-VEIFGLGFLTSIL-FIFFVGVFASSWLGATVFWLGEWFIKRLP 130 (193)
Q Consensus 59 lLPi~iTi~Il~~l~~~v~~~~~pl~~~l----~-~~~pglgl~~~l~-~i~~iG~la~~~ig~~ll~~~e~ll~rIP 130 (193)
++|.++..|+..|+..|+++.+ |.-+.+ + +-.|.++++++.. .++++|-.. ++++..+.++++.+.+.-+
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 6899999999999999999987 432221 1 1257777766544 456888777 5688888888887776544
No 24
>PRK15083 PTS system mannitol-specific transporter subunit IICBA; Provisional
Probab=79.32 E-value=16 Score=35.86 Aligned_cols=83 Identities=13% Similarity=0.056 Sum_probs=55.8
Q ss_pred HHHHHHHHHHHHHHHHHHHHhhhhhhhhhhhhhhhhHH----HHHHHHHHHHHHHHHHhhhhhHHHHHHHHHhhh--hhh
Q 029429 58 VLFPVAVTFLVTWWFIEFVDSFFSPIYARLGVEIFGLG----FLTSILFIFFVGVFASSWLGATVFWLGEWFIKR--LPF 131 (193)
Q Consensus 58 vlLPi~iTi~Il~~l~~~v~~~~~pl~~~l~~~~pglg----l~~~l~~i~~iG~la~~~ig~~ll~~~e~ll~r--IP~ 131 (193)
.++|..++.|+..|+-.++++.+...++.+ -.|.+. ++...+.++++|-+.. ++|.++-++++++.+. .|.
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 AMIAGPLGGWAIKHFDRWVDGKIKSGFEML--VNNFSAGIIGMILAILAFLGIGPAVE-VLSKMLAAGVNFMVVHDLLPL 177 (639)
T ss_pred chHHHHHHHHHHHHHHHHHHhhccchhhHh--hhhHHHHHHHHHHHHHHheeeHHHHH-HHHHHHHHHHHHHHhCcchhH
Confidence 789999999999999999999886666543 123332 2233456677777764 5777777788887765 554
Q ss_pred h-hHHHHHHHHHH
Q 029429 132 M-KHIYSASKQIS 143 (193)
Q Consensus 132 V-~sIYssiKqi~ 143 (193)
+ .-++.+.-++.
T Consensus 178 ~a~~i~~~~~~~l 190 (639)
T PRK15083 178 TSIFVEPAKILFL 190 (639)
T ss_pred HHHHHHHHHHHHH
Confidence 4 34455555554
No 25
>COG1459 PulF Type II secretory pathway, component PulF [Cell motility and secretion / Intracellular trafficking and secretion]
Probab=76.91 E-value=20 Score=33.35 Aligned_cols=23 Identities=13% Similarity=0.154 Sum_probs=18.8
Q ss_pred hHHHHHHHHHhhhhhhhhHHHHH
Q 029429 116 ATVFWLGEWFIKRLPFMKHIYSA 138 (193)
Q Consensus 116 ~~ll~~~e~ll~rIP~V~sIYss 138 (193)
.+.-...|+++-|+|+++.+...
T Consensus 238 ~~~r~~~~~~llrlP~~g~l~~~ 260 (397)
T COG1459 238 PAGRRRLDRLLLRLPLFGKLVRK 260 (397)
T ss_pred hHHHHHHHhHHhcCCcHHHHHHH
Confidence 34557899999999999998763
No 26
>PF11872 DUF3392: Protein of unknown function (DUF3392); InterPro: IPR021813 This family of proteins are functionally uncharacterised. This protein is found in bacteria. Proteins in this family are about 110 amino acids in length.
Probab=74.87 E-value=24 Score=27.24 Aligned_cols=65 Identities=15% Similarity=0.316 Sum_probs=44.1
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhhhhhhh--hhhhhhHHHHHHHHHHHHHHHHHHh
Q 029429 47 WVSKKFMTGCVVLFPVAVTFLVTWWFIEFVDSFFSPIYARL--GVEIFGLGFLTSILFIFFVGVFASS 112 (193)
Q Consensus 47 ~i~~~fl~GLlvlLPi~iTi~Il~~l~~~v~~~~~pl~~~l--~~~~pglgl~~~l~~i~~iG~la~~ 112 (193)
+.-|..+.|.=+++=..+.+.+--+-|+.+.-...|++... ..+...++.+ +++..+++|++|++
T Consensus 39 ~~lrr~l~~~~Fi~Rt~~FIlicAFGYGll~v~~tP~l~~~L~~~~~~~l~~~-vl~~F~~iG~lAqR 105 (106)
T PF11872_consen 39 RFLRRLLSGYHFILRTLAFILICAFGYGLLIVWLTPLLARQLAQLPNYWLAPV-VLLSFILIGVLAQR 105 (106)
T ss_pred HHHHHHhcCCccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCchHHHHH-HHHHHHHHHHHhcc
Confidence 33455667777778788888888899999999999988542 1222223333 34556679999875
No 27
>COG4794 EscS Type III secretory pathway, component EscS [Intracellular trafficking and secretion]
Probab=74.19 E-value=35 Score=25.65 Aligned_cols=78 Identities=18% Similarity=0.259 Sum_probs=46.3
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhhhhhhhhhhhhhHHHHHHHHHHHHHHHHHHhhhhhHHHHHHHHHhhh
Q 029429 49 SKKFMTGCVVLFPVAVTFLVTWWFIEFVDSFFSPIYARLGVEIFGLGFLTSILFIFFVGVFASSWLGATVFWLGEWFIKR 128 (193)
Q Consensus 49 ~~~fl~GLlvlLPi~iTi~Il~~l~~~v~~~~~pl~~~l~~~~pglgl~~~l~~i~~iG~la~~~ig~~ll~~~e~ll~r 128 (193)
.+.+.-=|+.-+|-++.--++.-+++++.... ..=+. -+++.+=++.++..=++...+.|..++++.|+.+.+
T Consensus 11 ~qaL~liLilSlPpvivAsvvGllVslvQA~T----QiQdQ---Tl~f~iKLl~V~~tl~lt~~Wlg~~ll~fa~~i~~~ 83 (89)
T COG4794 11 SQALWLILILSLPPVIVASVVGLLVSLVQALT----QIQDQ---TLPFGIKLLAVSATLFLTAGWLGATLLNFAEQIFLN 83 (89)
T ss_pred HHHHHHHHHHhccHHHHHHHHHHHHHHHHHHH----HHHHh---HHHHHHHHHHHHHHHHHHhHHhHHHHHHHHHHHHHH
Confidence 34455556666676665555555555444333 11011 234444334444444456678899999999999999
Q ss_pred hhhhh
Q 029429 129 LPFMK 133 (193)
Q Consensus 129 IP~V~ 133 (193)
+|..|
T Consensus 84 ~~~~~ 88 (89)
T COG4794 84 IPKAR 88 (89)
T ss_pred hhhcc
Confidence 99865
No 28
>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=71.16 E-value=37 Score=32.54 Aligned_cols=87 Identities=9% Similarity=0.056 Sum_probs=56.9
Q ss_pred HHHHHHHHHHHHHHH-HHHHhhhhhhhhhh-hh-hhhhHHHHHHHHHHHHHHHHHHhhhhhHHHHHHHHHhhhhh-hhhH
Q 029429 59 LFPVAVTFLVTWWFI-EFVDSFFSPIYARL-GV-EIFGLGFLTSILFIFFVGVFASSWLGATVFWLGEWFIKRLP-FMKH 134 (193)
Q Consensus 59 lLPi~iTi~Il~~l~-~~v~~~~~pl~~~l-~~-~~pglgl~~~l~~i~~iG~la~~~ig~~ll~~~e~ll~rIP-~V~s 134 (193)
++|.++..|+..|++ .+.+..+...+..+ |. -.|.+.+++.+.+-+++|.+-. +++..+-+..+.+.+.-| +-.-
T Consensus 135 V~~~Il~g~i~a~l~nk~~~k~lP~~l~~f~G~rfvPiit~lv~~~l~~i~~~iwp-~i~~~i~~~~~~l~~~~~~~g~~ 213 (502)
T TIGR02002 135 VFGGIIIGAIAAYCYNRFYNIKLPEYLGFFAGKRFVPIITGLAAIVTGIVLSFIWP-PVQDALNTFSHWAAYQNPVVAFF 213 (502)
T ss_pred cHHHHHHHHHHHHHHHHHhcccCcHHHHhcCCCchHHHHHHHHHHHHHHHHHHHHH-HHHHHHHHHHHHHHHcCcHHHHH
Confidence 689999999999999 67777776666655 22 2566666655555545555544 466666666666665554 5556
Q ss_pred HHHHHHHHHHHh
Q 029429 135 IYSASKQISAAI 146 (193)
Q Consensus 135 IYssiKqi~~~f 146 (193)
+|..+.++.-.+
T Consensus 214 i~G~l~r~Lv~~ 225 (502)
T TIGR02002 214 IFGFIERSLIPF 225 (502)
T ss_pred HHHHHHHHHHHh
Confidence 787777655433
No 29
>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=69.35 E-value=35 Score=31.17 Aligned_cols=72 Identities=11% Similarity=-0.023 Sum_probs=43.5
Q ss_pred HHHHHHHHHHHHHHHHHHHHhhhhhhhhhh-h-hhhhhHHHHHHHHHHHHHHHHHHhhhhhHHHHHHHHHhhhhh
Q 029429 58 VLFPVAVTFLVTWWFIEFVDSFFSPIYARL-G-VEIFGLGFLTSILFIFFVGVFASSWLGATVFWLGEWFIKRLP 130 (193)
Q Consensus 58 vlLPi~iTi~Il~~l~~~v~~~~~pl~~~l-~-~~~pglgl~~~l~~i~~iG~la~~~ig~~ll~~~e~ll~rIP 130 (193)
-++|..++.|+..|+-+++++.+.-.++.+ + .-.|.++++++.+..+++|-.. ++++..+-++++.+.+.-|
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 345666667777666666665543333210 0 1256677776666666777766 4677777777777665443
No 30
>PRK11404 putative PTS system transporter subunits IIBC; Provisional
Probab=69.02 E-value=27 Score=33.34 Aligned_cols=68 Identities=13% Similarity=0.027 Sum_probs=45.7
Q ss_pred HHHHHHHHHHHHHHHHHHHHhhhhh-----hhhhhhhhhhhHHHHHHH-HHHHHHHHHHHhhhhhHHHHHHHHHhhh
Q 029429 58 VLFPVAVTFLVTWWFIEFVDSFFSP-----IYARLGVEIFGLGFLTSI-LFIFFVGVFASSWLGATVFWLGEWFIKR 128 (193)
Q Consensus 58 vlLPi~iTi~Il~~l~~~v~~~~~p-----l~~~l~~~~pglgl~~~l-~~i~~iG~la~~~ig~~ll~~~e~ll~r 128 (193)
-++|..+..|+..|+..++.++.-| +.+. +-.|.++++++. +.++++|=... +++..+.+++..+...
T Consensus 228 gflg~Il~g~~~gyv~k~lkki~~p~~~p~~~~~--~~~Pllt~li~~~l~~~viGP~~~-~i~~~l~~~l~~l~~~ 301 (482)
T PRK11404 228 GFLGAVVLGLAIGYFVFWFRKVRLGKALQPLLGS--MLIPFVTLLVFGVLTYYVIGPVMS-DLMGGLLHFLNTIPPS 301 (482)
T ss_pred cHHHHHHHHHHHHHHHHHHHhCCCCcchhhhcce--eeHHHHHHHHHHHHHHHHHHHHHH-HHHHHHHHHHHHHHcc
Confidence 5789999999999999999987622 3321 125667766644 34456777665 5666666666666553
No 31
>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=68.88 E-value=16 Score=24.10 Aligned_cols=23 Identities=17% Similarity=0.364 Sum_probs=15.0
Q ss_pred HHHHHHHHHHHHHHhhhhhHHHH
Q 029429 98 TSILFIFFVGVFASSWLGATVFW 120 (193)
Q Consensus 98 ~~l~~i~~iG~la~~~ig~~ll~ 120 (193)
+..++++++|+++.+.+.+.+-+
T Consensus 19 v~AilIl~vG~~va~~v~~~~~~ 41 (53)
T PF05552_consen 19 VGAILILIVGWWVAKFVRKLVRR 41 (53)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHHHHH
Confidence 34456788898887766653333
No 32
>PF14584 DUF4446: Protein of unknown function (DUF4446)
Probab=68.24 E-value=58 Score=26.42 Aligned_cols=51 Identities=10% Similarity=0.229 Sum_probs=32.4
Q ss_pred HHHHHHHHHhCCCCCCccccceEEEEcC---CCC---eeEEEEEeccc---cccCCCCcee
Q 029429 137 SASKQISAAISPDQNTSAFKEVAIIRHP---RLG---EYAFGFITSSV---VLQVDTLPVQ 188 (193)
Q Consensus 137 ssiKqi~~~f~g~~~~~~f~~VVLVe~P---~~g---~~~iGFvT~~~---~~~~~~g~~~ 188 (193)
...++-++.+-... +.++++|.+|+|. .-| .++++++-++. .++.-.|||.
T Consensus 63 ~~~~~~~~~l~~~~-~~~~~kvgvvRYnAF~dmGg~LSFslAlLD~~~nGvVltsI~~Re~ 122 (151)
T PF14584_consen 63 EELEKRIEELEEKL-RNCVQKVGVVRYNAFEDMGGDLSFSLALLDDNNNGVVLTSIHSREE 122 (151)
T ss_pred HHHHHHHHHHHHHH-HhccceEEEEEccCcccccccceeeeEEEeCCCCEEEEEeeecCCC
Confidence 33334444444332 3579999999965 333 78898888775 5566677764
No 33
>PRK15349 type III secretion system protein SsaT; Provisional
Probab=66.23 E-value=90 Score=27.20 Aligned_cols=75 Identities=5% Similarity=0.004 Sum_probs=47.5
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhhhhhhhhhhhhhHHHHHHHHHHHHHHHHHHhhhhh
Q 029429 41 YAVLQSWVSKKFMTGCVVLFPVAVTFLVTWWFIEFVDSFFSPIYARLGVEIFGLGFLTSILFIFFVGVFASSWLGA 116 (193)
Q Consensus 41 ~~~~~~~i~~~fl~GLlvlLPi~iTi~Il~~l~~~v~~~~~pl~~~l~~~~pglgl~~~l~~i~~iG~la~~~ig~ 116 (193)
.....+.+.+.|..|+..-+|+++...++...++.++....=+ +-+-...|.-.++..+++.+.++.+...+...
T Consensus 170 ~~~~~~~~~~~f~~al~lAaP~i~~lll~~~~lGll~R~~PQl-nvf~l~~P~k~~~gl~~l~l~~~~~~~~~~~~ 244 (259)
T PRK15349 170 LKYIQAEWRTLYQLCISFSLPAIICMVLADLALGLLNRSAQQL-NVFFFSMPLKSILVLLTLLISFPYALHHYLVE 244 (259)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCccc-chHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3445566778899999999999999999999999998876222 11112223222233333445566666554443
No 34
>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=63.82 E-value=1e+02 Score=30.37 Aligned_cols=85 Identities=11% Similarity=0.165 Sum_probs=53.3
Q ss_pred HHHHHHHHHHHHHHHHHHHhhhhhhhhhhhhhhhhHHHHHHHH-HHHHHHHHHHhhhhhHHHHHHHHHhhhhh-hhhHHH
Q 029429 59 LFPVAVTFLVTWWFIEFVDSFFSPIYARLGVEIFGLGFLTSIL-FIFFVGVFASSWLGATVFWLGEWFIKRLP-FMKHIY 136 (193)
Q Consensus 59 lLPi~iTi~Il~~l~~~v~~~~~pl~~~l~~~~pglgl~~~l~-~i~~iG~la~~~ig~~ll~~~e~ll~rIP-~V~sIY 136 (193)
++|..+..|+..++..|+++.+.+.+..+ -.|.+.++++.. .++++|-+.. +++..+-..+..+...-| +...+|
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--LTPLLVMLITVPLTLLIIGPLGN-YAGEGISSGILFLYEVSPWLAGALL 287 (610)
T ss_pred HHHHHHHHHHHHHHHHHHHhhChHHHHHH--HHHHHHHHHHHHHHHHHHHHHHH-HHHHHHHHHHHHHHhcchHHHHHHH
Confidence 57889999999999999988776655432 245555444333 2334565543 456666666666666554 345678
Q ss_pred HHHHHHHHHh
Q 029429 137 SASKQISAAI 146 (193)
Q Consensus 137 ssiKqi~~~f 146 (193)
..+-++.=.|
T Consensus 288 g~l~~~Lv~f 297 (610)
T TIGR01995 288 AALWPVLVMF 297 (610)
T ss_pred HHHHHHHhhc
Confidence 8877765433
No 35
>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=63.51 E-value=68 Score=30.94 Aligned_cols=90 Identities=10% Similarity=0.027 Sum_probs=57.1
Q ss_pred HHHHHHHHHHHHHHHHHHHHhh-hhhhhhhh-hh-hhhhHHHHHHHHHHHHHHHHHHhhhhhHHHHHHHHHhhhhhhhhH
Q 029429 58 VLFPVAVTFLVTWWFIEFVDSF-FSPIYARL-GV-EIFGLGFLTSILFIFFVGVFASSWLGATVFWLGEWFIKRLPFMKH 134 (193)
Q Consensus 58 vlLPi~iTi~Il~~l~~~v~~~-~~pl~~~l-~~-~~pglgl~~~l~~i~~iG~la~~~ig~~ll~~~e~ll~rIP~V~s 134 (193)
-++|.++..++..|++++..+. +...+..+ |. -.|.+.+++.+.+-+++ -.-+..++..++.+.++++..+.++.
T Consensus 138 gV~ggIi~g~i~a~i~n~~~k~~lP~~L~ff~G~rfVPiit~li~~~l~~~~--p~~wp~~~~~i~~~~~~i~~~g~~g~ 215 (517)
T TIGR02004 138 GVLGAVIVGLIVYKLHNRFYTVQMPDALAFFGGARFVPIISALVLAVVGLVI--PLVWPLFALMIMAIGQLIQRSGIFGP 215 (517)
T ss_pred chHHHHHHHHHHHHHHHHHccccCchHHHHccCCcchHHHHHHHHHHHHHHH--HHHHHHHHHHHHHHHHHHHhcChHHH
Confidence 3689999999999999999996 44455444 21 24555544433332222 22234555666667777776655444
Q ss_pred -HHHHHHHHHHHhCCC
Q 029429 135 -IYSASKQISAAISPD 149 (193)
Q Consensus 135 -IYssiKqi~~~f~g~ 149 (193)
+|..+.++.-.+.=+
T Consensus 216 fiyG~l~rlLIp~GLH 231 (517)
T TIGR02004 216 FLFGSGERLLLPIGLH 231 (517)
T ss_pred HHHHHHHHHHHHhccc
Confidence 999999988777544
No 36
>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=63.25 E-value=65 Score=24.56 Aligned_cols=84 Identities=11% Similarity=0.158 Sum_probs=44.9
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhhhh-hhhhhhhhhHHHHHHHHHHHHHHHH----HHhhhhhHHHHHH
Q 029429 48 VSKKFMTGCVVLFPVAVTFLVTWWFIEFVDSFFSPIY-ARLGVEIFGLGFLTSILFIFFVGVF----ASSWLGATVFWLG 122 (193)
Q Consensus 48 i~~~fl~GLlvlLPi~iTi~Il~~l~~~v~~~~~pl~-~~l~~~~pglgl~~~l~~i~~iG~l----a~~~ig~~ll~~~ 122 (193)
.+|=|+.-++-++=+++.+++-.+....+...+.... ..-......++++++.+++++++.. .++...+...+..
T Consensus 17 ~~rG~~~~~~~l~~~i~a~~~a~~~~~~~~~~l~~~~~~~~~~~~~~iaf~~~f~~~~~i~~~i~~~l~~~~~~~~~~~~ 96 (146)
T PF02674_consen 17 YRRGFIRELFSLIGLIVALFVAFLFYPPLAPFLSNYFSSLSPPFANIIAFIILFVLVYIIVRIIGKLLRRIVKKPFLGWL 96 (146)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhcccccHH
Confidence 4555666777777777777777777777666665532 1101112334444444444444444 4443333455566
Q ss_pred HHHhhhhhh
Q 029429 123 EWFIKRLPF 131 (193)
Q Consensus 123 e~ll~rIP~ 131 (193)
|+++.-+..
T Consensus 97 dr~lG~~~G 105 (146)
T PF02674_consen 97 DRLLGALLG 105 (146)
T ss_pred HHHHHHHHH
Confidence 666655443
No 37
>PRK10617 cytochrome c-type protein NapC; Provisional
Probab=63.09 E-value=21 Score=30.34 Aligned_cols=20 Identities=20% Similarity=0.252 Sum_probs=15.2
Q ss_pred CCCccHHHHHHHHHHHHHHH
Q 029429 32 PNSSTRKACYAVLQSWVSKK 51 (193)
Q Consensus 32 ~~~~~~~~~~~~~~~~i~~~ 51 (193)
+||+.++++++++++++++.
T Consensus 2 ~~~~~~~~~~~~~~~~~~k~ 21 (200)
T PRK10617 2 GNSDRKPGLIKRLWKWWRTP 21 (200)
T ss_pred CCCcCChHHHHHHHHHHHhh
Confidence 57888888888888886443
No 38
>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=62.72 E-value=1e+02 Score=26.60 Aligned_cols=41 Identities=15% Similarity=0.358 Sum_probs=36.1
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhh
Q 029429 40 CYAVLQSWVSKKFMTGCVVLFPVAVTFLVTWWFIEFVDSFF 80 (193)
Q Consensus 40 ~~~~~~~~i~~~fl~GLlvlLPi~iTi~Il~~l~~~v~~~~ 80 (193)
......+.+.+.|..|+-.-+|+.+...++...++.+++..
T Consensus 158 ~~~~~~~~~~~~f~~a~~lAaPvi~~~ll~~~~lGll~R~~ 198 (245)
T TIGR01400 158 FFELILKALSDMFLLGLLLALPIIAALLLVNLVLGLVNRAA 198 (245)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcc
Confidence 34566677889999999999999999999999999998876
No 39
>PRK10110 bifunctional PTS system maltose and glucose-specific transporter subunits IICB; Provisional
Probab=62.48 E-value=82 Score=30.50 Aligned_cols=89 Identities=9% Similarity=0.045 Sum_probs=52.7
Q ss_pred HHHHHHHHHHHHHHHHHHHhh-hhhhhhhh-hh-hhhhHHHHHHHHHHHHHHHHHHhhhhhHHHHHHHHHhhhhhhhhH-
Q 029429 59 LFPVAVTFLVTWWFIEFVDSF-FSPIYARL-GV-EIFGLGFLTSILFIFFVGVFASSWLGATVFWLGEWFIKRLPFMKH- 134 (193)
Q Consensus 59 lLPi~iTi~Il~~l~~~v~~~-~~pl~~~l-~~-~~pglgl~~~l~~i~~iG~la~~~ig~~ll~~~e~ll~rIP~V~s- 134 (193)
++|.+++.|+..|+.++..+. +...+..+ |. -.|.+.+++.+.+-+++.++ .=.++.+.+.+..+++.-+.++.
T Consensus 148 V~ggIi~g~i~a~l~~k~~k~~lP~~l~~f~G~rfvPiit~lv~~~l~~i~~~i--wP~~~~~~~~~~~~~~~~g~ig~~ 225 (530)
T PRK10110 148 ILGAVIAGIIVWMLHERFHNIRLPDALAFFGGTRFVPIISSLVMGLVGLVIPLV--WPIFAMGISGLGHMINSAGDFGPM 225 (530)
T ss_pred hHHHHHHHHHHHHHHHHHhcccCcHHHHhcCCCccHHHHHHHHHHHHHHHHHHH--HHHHHHHHHHHHHHHHhccHHHHH
Confidence 688899999999999998885 44444443 21 24555544433333332111 12334444555566666555444
Q ss_pred HHHHHHHHHHHhCCC
Q 029429 135 IYSASKQISAAISPD 149 (193)
Q Consensus 135 IYssiKqi~~~f~g~ 149 (193)
+|..+.+++=.+.-+
T Consensus 226 i~G~l~r~LVp~GLH 240 (530)
T PRK10110 226 LFGTGERLLLPFGLH 240 (530)
T ss_pred HHHHHHHHHHHhccc
Confidence 899998877666433
No 40
>COG3768 Predicted membrane protein [Function unknown]
Probab=54.69 E-value=58 Score=29.97 Aligned_cols=33 Identities=24% Similarity=0.338 Sum_probs=26.2
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 029429 45 QSWVSKKFMTGCVVLFPVAVTFLVTWWFIEFVD 77 (193)
Q Consensus 45 ~~~i~~~fl~GLlvlLPi~iTi~Il~~l~~~v~ 77 (193)
+..+.+.++++..+++-+++..|-..|+.+...
T Consensus 60 r~s~~k~~~~a~~vLf~~Av~~q~~qwi~d~~q 92 (350)
T COG3768 60 RSSFWKIMLGAGGVLFSLAVGLQSVQWIRDLFQ 92 (350)
T ss_pred cchHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 344668899999999999998888888877543
No 41
>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=54.05 E-value=46 Score=21.33 Aligned_cols=27 Identities=15% Similarity=0.357 Sum_probs=17.0
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 029429 43 VLQSWVSKKFMTGCVVLFPVAVTFLVT 69 (193)
Q Consensus 43 ~~~~~i~~~fl~GLlvlLPi~iTi~Il 69 (193)
.+.+++..-+.+|+++++|+++-+..+
T Consensus 4 SL~nfl~Sl~aG~~iVv~~i~~ali~V 30 (39)
T PF06596_consen 4 SLSNFLLSLVAGAVIVVIPIAGALIFV 30 (39)
T ss_dssp HHHHHHHHHHHHH-HHHHHHHHHHHHH
T ss_pred hHHHHHHHHHhhhhhhhhhhhhheEEE
Confidence 344555555555569999998776544
No 42
>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=52.01 E-value=1.6e+02 Score=25.72 Aligned_cols=28 Identities=18% Similarity=0.240 Sum_probs=21.7
Q ss_pred HHHHHHHHHHHHHHHHHHHHhhhhhhhh
Q 029429 58 VLFPVAVTFLVTWWFIEFVDSFFSPIYA 85 (193)
Q Consensus 58 vlLPi~iTi~Il~~l~~~v~~~~~pl~~ 85 (193)
.++|+.+.+|+..++-++++..+...++
T Consensus 66 ~~~~ii~~~~~~~~~~k~~~~~lP~~l~ 93 (289)
T TIGR00852 66 VVGPILVGAIALALHERFLDKKLPDVLG 93 (289)
T ss_pred eeHHHHHHHHHHHHHHHHhhhhCchhhh
Confidence 4789999999999888888876644443
No 43
>PF14257 DUF4349: Domain of unknown function (DUF4349)
Probab=50.09 E-value=42 Score=28.78 Aligned_cols=14 Identities=21% Similarity=-0.183 Sum_probs=5.8
Q ss_pred CCccHHHHHHHHHHH
Q 029429 33 NSSTRKACYAVLQSW 47 (193)
Q Consensus 33 ~~~~~~~~~~~~~~~ 47 (193)
.++-++++. ..++.
T Consensus 215 ~~~~~~al~-~~~~~ 228 (262)
T PF14257_consen 215 GSRFRDALK-NGWNA 228 (262)
T ss_pred chHHHHHHH-HHHHH
Confidence 334454443 33433
No 44
>PRK15071 lipopolysaccharide ABC transporter permease; Provisional
Probab=48.88 E-value=1e+02 Score=27.25 Aligned_cols=39 Identities=8% Similarity=0.192 Sum_probs=26.4
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhh
Q 029429 42 AVLQSWVSKKFMTGCVVLFPVAVTFLVTWWFIEFVDSFF 80 (193)
Q Consensus 42 ~~~~~~i~~~fl~GLlvlLPi~iTi~Il~~l~~~v~~~~ 80 (193)
+.+-+-+.|.++..+++.+-..+.++++.++++-++.+.
T Consensus 3 ~il~rYi~r~~l~~~~~~l~~l~~l~~~~~~~~~l~~~~ 41 (356)
T PRK15071 3 GILDRYIGRTILSTIMLTLFMLVGLSGIIKFVDQLRKVG 41 (356)
T ss_pred hHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhcc
Confidence 344455667777777777777777777777777666643
No 45
>PF04109 APG9: Autophagy protein Apg9 ; InterPro: IPR007241 Macroautophagy is a bulk degradation process induced by starvation in eukaryotic cells. In yeast, 15 Apg proteins coordinate the formation of autophagosomes. No molecule involved in autophagy has yet been identified in higher eukaryotes []. The pre-autophagosomal structure contains at least five Apg proteins: Apg1p, Apg2p, Apg5p, Aut7p/Apg8p and Apg16p. It is found in the vacuole []. The C-terminal glycine of Apg12p is conjugated to a lysine residue of Apg5p via an isopeptide bond. During autophagy, cytoplasmic components are enclosed in autophagosomes and delivered to lysosomes/vacuoles. Auotphagy protein 16 (Apg16) has been shown to be bind to Apg5 and is required for the function of the Apg12p-Apg5p conjugate []. Autophagy protein 5 (Apg5) is directly required for the import of aminopeptidase I via the cytoplasm-to-vacuole targeting pathway []. Apg9 plays a direct role in the formation of the cytoplasm to vacuole targeting and autophagic vesicles, possibly serving as a marker for a specialised compartment essential for these vesicle-mediated alternative targeting pathways [].
Probab=48.74 E-value=61 Score=30.07 Aligned_cols=49 Identities=16% Similarity=0.314 Sum_probs=38.6
Q ss_pred CCCCCccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Q 029429 30 HSPNSSTRKACYAVLQSWVSKKFMTGCVVLFPVAVTFLVTWWFIEFVDSF 79 (193)
Q Consensus 30 ~~~~~~~~~~~~~~~~~~i~~~fl~GLlvlLPi~iTi~Il~~l~~~v~~~ 79 (193)
+=-++.+|..+..+++++++-.-+--++ +.|+++...++++++.-.+.+
T Consensus 103 ~f~~~~~r~~l~~~Lr~Rf~~~gi~nll-l~Pfi~i~~il~~ff~y~e~~ 151 (370)
T PF04109_consen 103 EFLKNSRRKELAEELRKRFRLAGILNLL-LSPFILIYQILYFFFKYAEEF 151 (370)
T ss_pred HHcChhhHHHHHHHHHHHHHHHHHHHHH-HhHHHHHHHHHHHHHHHHHHH
Confidence 3345677888888888887766555544 899999999999999988876
No 46
>COG2981 CysZ Uncharacterized protein involved in cysteine biosynthesis [Amino acid transport and metabolism]
Probab=48.06 E-value=2e+02 Score=25.49 Aligned_cols=28 Identities=18% Similarity=0.150 Sum_probs=14.7
Q ss_pred HHHHHHHHHHHHHHHHHHHHHhhhhhhh
Q 029429 57 VVLFPVAVTFLVTWWFIEFVDSFFSPIY 84 (193)
Q Consensus 57 lvlLPi~iTi~Il~~l~~~v~~~~~pl~ 84 (193)
.+++|+.+-+.+..-++.++-+...|.+
T Consensus 27 fvilpLl~ni~L~~gl~~~~~~~~~~wi 54 (250)
T COG2981 27 FVILPLLLNILLWGGLFWLLFSQALPWI 54 (250)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3566776666555544444444444433
No 47
>TIGR03745 conj_TIGR03745 integrating conjugative element membrane protein, PFL_4702 family. Members of this protein family are found occasionally on plasmids such as the Pseudomonas putida TOL plasmid pWWO_p085. Usually, however, they are found on the bacterial main chromosome in a region flanked by markers of conjugative transfer and/or transposition.
Probab=47.64 E-value=1.3e+02 Score=23.23 Aligned_cols=63 Identities=10% Similarity=0.132 Sum_probs=34.1
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhhhhh----h--hhhhhhhHHHHHHHHHHHHHHH
Q 029429 44 LQSWVSKKFMTGCVVLFPVAVTFLVTWWFIEFVDSFFSPIYA----R--LGVEIFGLGFLTSILFIFFVGV 108 (193)
Q Consensus 44 ~~~~i~~~fl~GLlvlLPi~iTi~Il~~l~~~v~~~~~pl~~----~--l~~~~pglgl~~~l~~i~~iG~ 108 (193)
+++.+|+|+-.|.+.+.=++...-++.-...-+..+- -+.+ + +|. .-.+|.+++++.+++++-
T Consensus 31 ~~~tik~Y~~dg~~llgL~i~a~aFi~Va~~a~~ty~-Ei~~Gk~~W~~fg~-~v~VGviLLv~vIwLltk 99 (104)
T TIGR03745 31 IMQTIKNYGYDGGILLGLLIAAIAFIGVAYHALGTYH-EIRTGKATWGDFGA-TVVVGAILLVVIIWLLTK 99 (104)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-HHHcchhhHHhCcc-hhhhHhHHHHHHHHHHHH
Confidence 5566788888888877666655555554444443321 1110 0 111 124666666666666543
No 48
>PF04854 DUF624: Protein of unknown function, DUF624; InterPro: IPR006938 This family consists of uncharacterised or hypothetical bacterial proteins.
Probab=47.42 E-value=56 Score=22.56 Aligned_cols=35 Identities=3% Similarity=0.040 Sum_probs=26.5
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 029429 37 RKACYAVLQSWVSKKFMTGCVVLFPVAVTFLVTWW 71 (193)
Q Consensus 37 ~~~~~~~~~~~i~~~fl~GLlvlLPi~iTi~Il~~ 71 (193)
+...+++.++.+|++|.++...-++..+.+.++++
T Consensus 41 ~~~~~~~f~~~fk~nf~~~~~~~~~~~~~~~il~~ 75 (77)
T PF04854_consen 41 DSYLFRDFWRAFKQNFKQSLLLGLILLLLLAILYV 75 (77)
T ss_pred cChHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 34567777888888888888888888777776653
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=47.27 E-value=1.1e+02 Score=22.17 Aligned_cols=36 Identities=14% Similarity=0.089 Sum_probs=29.2
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhh
Q 029429 45 QSWVSKKFMTGCVVLFPVAVTFLVTWWFIEFVDSFF 80 (193)
Q Consensus 45 ~~~i~~~fl~GLlvlLPi~iTi~Il~~l~~~v~~~~ 80 (193)
....++.+...+...+|+.+.-.++..+++.+....
T Consensus 4 i~l~r~al~~~l~~~~P~L~~alvvGlvIsi~QA~T 39 (76)
T PF01313_consen 4 IDLLRQALWLVLMLSAPVLLVALVVGLVISIFQAAT 39 (76)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 345678899999999999999988888887776654
No 50
>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=46.49 E-value=1.8e+02 Score=24.43 Aligned_cols=37 Identities=22% Similarity=0.189 Sum_probs=27.9
Q ss_pred hhhhhhhHHHHHHHHHHHHHHHHHHhhhhhHHHHHHHH
Q 029429 87 LGVEIFGLGFLTSILFIFFVGVFASSWLGATVFWLGEW 124 (193)
Q Consensus 87 l~~~~pglgl~~~l~~i~~iG~la~~~ig~~ll~~~e~ 124 (193)
+|++ |.+.+.+..+.|-.+|+|+--.+|..++++..+
T Consensus 72 ~GlD-P~~~~g~~t~a~g~lG~L~GP~~G~~vf~l~~r 108 (173)
T PF08566_consen 72 MGLD-PFMVYGLATLACGALGWLVGPSLGNQVFRLLNR 108 (173)
T ss_pred cCcC-HHHHHHHHHHHHHHHHHHhcchHHHHHHHHHhH
Confidence 3554 345555666778899999999999988887775
No 51
>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=46.32 E-value=1.7e+02 Score=24.24 Aligned_cols=71 Identities=15% Similarity=0.269 Sum_probs=44.4
Q ss_pred CCccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhhhhhhhhhhhhhHHHHHHHHHHHHHHHHHHh
Q 029429 33 NSSTRKACYAVLQSWVSKKFMTGCVVLFPVAVTFLVTWWFIEFVDSFFSPIYARLGVEIFGLGFLTSILFIFFVGVFASS 112 (193)
Q Consensus 33 ~~~~~~~~~~~~~~~i~~~fl~GLlvlLPi~iTi~Il~~l~~~v~~~~~pl~~~l~~~~pglgl~~~l~~i~~iG~la~~ 112 (193)
..+-|.++.....+.+.|.+.+.+.++++.+..++.-. ++ .-++...+++=.++|.....
T Consensus 117 ~~~~~~~~~~s~~~tl~r~i~t~~ttll~~~~L~~~g~----------~~----------l~~Fa~~l~iGvi~~~~ss~ 176 (189)
T PF02355_consen 117 GKSLREAINISIKQTLSRTIDTSLTTLLAALILFFFGG----------GS----------LKGFALTLIIGVIIGTYSSL 176 (189)
T ss_dssp TS-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHC------------CH----------HHHHHHHHHHHHHHHHHHHH
T ss_pred CCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcc----------ch----------HHHHHHHHHHHHHHHHHHHH
Confidence 34557788888888899999988887776655432211 11 12444455555567777777
Q ss_pred hhhhHHHHHHH
Q 029429 113 WLGATVFWLGE 123 (193)
Q Consensus 113 ~ig~~ll~~~e 123 (193)
++.+.++.+++
T Consensus 177 ~ia~~l~~~l~ 187 (189)
T PF02355_consen 177 FIARPLLYWLV 187 (189)
T ss_dssp HHHHHHHHHHH
T ss_pred HHHHHHHHHHh
Confidence 77777666654
No 52
>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=45.95 E-value=1.7e+02 Score=24.22 Aligned_cols=68 Identities=15% Similarity=0.207 Sum_probs=41.7
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhhhhhhhhhhhhhHHHHHHHHHHHHHHH
Q 029429 39 ACYAVLQSWVSKKFMTGCVVLFPVAVTFLVTWWFIEFVDSFFSPIYARLGVEIFGLGFLTSILFIFFVGV 108 (193)
Q Consensus 39 ~~~~~~~~~i~~~fl~GLlvlLPi~iTi~Il~~l~~~v~~~~~pl~~~l~~~~pglgl~~~l~~i~~iG~ 108 (193)
.++......+.|.++ |+.+-+-+.+.+-++-....++++.+.|+...+ ..+|.++++-++++.+-.|-
T Consensus 14 ~~~~~~~~Tl~r~~~-g~~ia~~ig~~lG~~~~~~~~~~~~~~p~~~~l-~~iP~~~~~pl~~~~fG~g~ 81 (202)
T TIGR01183 14 GLFWQIIASLTRVAV-GFSIAAIIGIAVGILIGLSKFLNAALDPIFQVL-RTIPPLAWLPIALAAFQDAQ 81 (202)
T ss_pred HHHHHHHHHHHHHHH-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-hhCCHHHHHHHHHHHHhcCc
Confidence 566677777776444 555444455555555556778899999988654 33566666655554544443
No 53
>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=45.62 E-value=2e+02 Score=24.92 Aligned_cols=41 Identities=10% Similarity=0.181 Sum_probs=36.1
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhh
Q 029429 40 CYAVLQSWVSKKFMTGCVVLFPVAVTFLVTWWFIEFVDSFF 80 (193)
Q Consensus 40 ~~~~~~~~i~~~fl~GLlvlLPi~iTi~Il~~l~~~v~~~~ 80 (193)
......+.+.+.|..|+-.-+|+.+...+....++.+++..
T Consensus 165 ~~~~~~~~~~~~f~~al~lAaPvi~~~ll~~l~lGllsR~~ 205 (253)
T TIGR01401 165 GLSFVLSQLDQMMALALLLAAPVIIVLFLIELALGLLSRFA 205 (253)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhc
Confidence 44566677889999999999999999999999999998876
No 54
>cd02433 Nodulin-21_like_2 Nodulin-21 and CCC1-related protein family. Nodulin-21_like_2: This is a family of proteins closely related to nodulin-21, a plant nodule-specific protein that may be involved in symbiotic nitrogen fixation. This family is also related to CCC1, a yeast vacuole transmembrane protein that functions as an iron and manganese transporter.
Probab=45.19 E-value=1.8e+02 Score=25.12 Aligned_cols=60 Identities=12% Similarity=0.061 Sum_probs=35.3
Q ss_pred CCCccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhhhhhhhhhhhhhHHHHHHHHHHHHHHHHHH
Q 029429 32 PNSSTRKACYAVLQSWVSKKFMTGCVVLFPVAVTFLVTWWFIEFVDSFFSPIYARLGVEIFGLGFLTSILFIFFVGVFAS 111 (193)
Q Consensus 32 ~~~~~~~~~~~~~~~~i~~~fl~GLlvlLPi~iTi~Il~~l~~~v~~~~~pl~~~l~~~~pglgl~~~l~~i~~iG~la~ 111 (193)
.+||-+.+++. +--+++.|++=++|..+.. +. .....+.+++.++.++++|++..
T Consensus 147 ~~~P~~aAl~s-----flsF~ig~liPLLPf~~~~---------------~~-----~~~~~~s~~~~~~~L~~lG~~~a 201 (234)
T cd02433 147 LGNPWSAAVSS-----FLLFALGALIPVLPFLFGM---------------SG-----LAALVLSVLLVGLALLATGAVTG 201 (234)
T ss_pred cCCHHHHHHHH-----HHHHHHHHHHHHHHHHHhc---------------ch-----hHHHHHHHHHHHHHHHHHHHHHH
Confidence 34566666552 4478999999999964210 00 00112455666677777888766
Q ss_pred hhhhh
Q 029429 112 SWLGA 116 (193)
Q Consensus 112 ~~ig~ 116 (193)
.+-++
T Consensus 202 ~~s~~ 206 (234)
T cd02433 202 LLSGR 206 (234)
T ss_pred hhCCC
Confidence 65555
No 55
>PRK05701 fliR flagellar biosynthesis protein FliR; Reviewed
Probab=45.14 E-value=2e+02 Score=24.71 Aligned_cols=40 Identities=18% Similarity=0.346 Sum_probs=35.8
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhh
Q 029429 41 YAVLQSWVSKKFMTGCVVLFPVAVTFLVTWWFIEFVDSFF 80 (193)
Q Consensus 41 ~~~~~~~i~~~fl~GLlvlLPi~iTi~Il~~l~~~v~~~~ 80 (193)
.....+.+.+.|..|+...+|+.+...+.....+.+++..
T Consensus 161 ~~~~~~~~~~~f~~a~~lAaP~i~~~ll~~~~lGll~R~~ 200 (242)
T PRK05701 161 FLLLAKALSAMFLIGLQLALPIIVLLLLVNLALGLINRTA 200 (242)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcc
Confidence 4556677889999999999999999999999999998876
No 56
>PF09527 ATPase_gene1: Putative F0F1-ATPase subunit (ATPase_gene1)
Probab=44.11 E-value=90 Score=20.40 Aligned_cols=11 Identities=36% Similarity=1.029 Sum_probs=4.1
Q ss_pred HHHHHHHHHhh
Q 029429 103 IFFVGVFASSW 113 (193)
Q Consensus 103 i~~iG~la~~~ 113 (193)
.+.+|+...+.
T Consensus 17 g~~~G~~lD~~ 27 (55)
T PF09527_consen 17 GFFLGYWLDKW 27 (55)
T ss_pred HHHHHHHHHHH
Confidence 33333333333
No 57
>TIGR00437 feoB ferrous iron transporter FeoB. FeoB (773 amino acids in E. coli), a cytoplasmic membrane protein required for iron(II) update, is encoded in an operon with FeoA (75 amino acids), which is also required, and is regulated by Fur. There appear to be two copies in Archaeoglobus fulgidus and Clostridium acetobutylicum.
Probab=44.08 E-value=2e+02 Score=28.07 Aligned_cols=52 Identities=10% Similarity=0.199 Sum_probs=40.7
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH---------HHHHHHhhhhhhhhhhhh
Q 029429 38 KACYAVLQSWVSKKFMTGCVVLFPVAVTFLVTWW---------FIEFVDSFFSPIYARLGV 89 (193)
Q Consensus 38 ~~~~~~~~~~i~~~fl~GLlvlLPi~iTi~Il~~---------l~~~v~~~~~pl~~~l~~ 89 (193)
+..+.+.+.+.+.++.+-.-+++...+.+|++.. +.+.+.+.+.|++..+|.
T Consensus 462 r~v~~~~w~r~~~fl~~A~~ii~~~siviw~l~~~~~~~~~~S~l~~~g~~~~P~~~p~g~ 522 (591)
T TIGR00437 462 RVVFIQTWTRLRSFIKKAGTIIVIGSVLIWFLSSFPGGKILESWLAAIGSIMAPLFVPLGK 522 (591)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCchhhhHHHHHHHHHHHHHHHhcC
Confidence 5566677777777777788888888888888876 467788888999887776
No 58
>COG3366 Uncharacterized protein conserved in archaea [Function unknown]
Probab=43.62 E-value=2.6e+02 Score=25.54 Aligned_cols=59 Identities=19% Similarity=0.308 Sum_probs=34.9
Q ss_pred HHHHHHHHHHHHHHHHHHHH--HHHHHHHHhhhhhhhhhhhhhhhhHHHHHHHHHHHHHHH
Q 029429 50 KKFMTGCVVLFPVAVTFLVT--WWFIEFVDSFFSPIYARLGVEIFGLGFLTSILFIFFVGV 108 (193)
Q Consensus 50 ~~fl~GLlvlLPi~iTi~Il--~~l~~~v~~~~~pl~~~l~~~~pglgl~~~l~~i~~iG~ 108 (193)
|.+.+=.-.++|..+.+.++ .-++++++.+++|+.+.++..-..+-+++.-+.=+..|+
T Consensus 176 k~~~rv~~~~~~~~~li~~L~~~G~~d~~~~~~~pl~~~L~lp~eav~v~~~~~~~~~~g~ 236 (311)
T COG3366 176 KVFKRVIPVVVPATVLIFFLIELGLFDYVEEFLHPLTNYLPLPPEAVTVVLTNLANIIAGI 236 (311)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHhhHHHHHHHHhhhHhhhcCCCcchHHHHHHHHHHHHHHH
Confidence 44545455666665555433 367899999999999887655433334433333333333
No 59
>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=43.07 E-value=2.4e+02 Score=27.55 Aligned_cols=88 Identities=11% Similarity=0.181 Sum_probs=53.3
Q ss_pred HHHHHHHHHHHHHHHHHHHhh--hhhhhhhh-hh-hhhhHHHHHHHHHHHHHHHHHHhhhhhHHHHHHHHHh---hhhh-
Q 029429 59 LFPVAVTFLVTWWFIEFVDSF--FSPIYARL-GV-EIFGLGFLTSILFIFFVGVFASSWLGATVFWLGEWFI---KRLP- 130 (193)
Q Consensus 59 lLPi~iTi~Il~~l~~~v~~~--~~pl~~~l-~~-~~pglgl~~~l~~i~~iG~la~~~ig~~ll~~~e~ll---~rIP- 130 (193)
++|.+++.++..|+.++.-+. +...+..+ |. -.|.+.+++.+.+-++.+++-- +++..+-+..+.+. ..-|
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 589999999999999999443 54455444 22 2555555544443333333322 55555556666665 3334
Q ss_pred hhhHHHHHHHHHHHHhC
Q 029429 131 FMKHIYSASKQISAAIS 147 (193)
Q Consensus 131 ~V~sIYssiKqi~~~f~ 147 (193)
+-.-+|..+.++.=.+.
T Consensus 221 ~g~fiyG~l~rlLIp~G 237 (548)
T TIGR02003 221 LAPFLYGTLERLLLPFG 237 (548)
T ss_pred HHHHHHHHHHHHHHHhc
Confidence 55568888888765553
No 60
>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=42.75 E-value=32 Score=25.47 Aligned_cols=45 Identities=22% Similarity=0.410 Sum_probs=30.0
Q ss_pred HHHHHHHHHHhCCCCCCccccceEEEEcCCCCeeEEEEEeccc-cccCCC
Q 029429 136 YSASKQISAAISPDQNTSAFKEVAIIRHPRLGEYAFGFITSSV-VLQVDT 184 (193)
Q Consensus 136 YssiKqi~~~f~g~~~~~~f~~VVLVe~P~~g~~~iGFvT~~~-~~~~~~ 184 (193)
|.-+|...+.+..+.. ++ +-....-+-|-|+||+||.+- ..|+..
T Consensus 11 Ydevk~~L~~~~~kpG--sY--iFRlSCTrLGQWAIGyV~~dg~I~QTIP 56 (86)
T PF02762_consen 11 YDEVKARLQHYRDKPG--SY--IFRLSCTRLGQWAIGYVTQDGKILQTIP 56 (86)
T ss_dssp HHHHHHHHGGGTTSTT--EE--EEEEESSSTTSEEEEEEETTSEEEEE--
T ss_pred HHHHHHHHHHHhCCcc--cE--EEeeccccccceeEEEEcCCCcEEEecC
Confidence 7888888888875542 22 233445578999999999985 334433
No 61
>PRK09554 feoB ferrous iron transport protein B; Reviewed
Probab=42.54 E-value=1.4e+02 Score=30.20 Aligned_cols=55 Identities=15% Similarity=0.147 Sum_probs=43.1
Q ss_pred cHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH--------------HHHHHhhhhhhhhhhhhh
Q 029429 36 TRKACYAVLQSWVSKKFMTGCVVLFPVAVTFLVTWWF--------------IEFVDSFFSPIYARLGVE 90 (193)
Q Consensus 36 ~~~~~~~~~~~~i~~~fl~GLlvlLPi~iTi~Il~~l--------------~~~v~~~~~pl~~~l~~~ 90 (193)
+=+..+.+.+.+.|..+.+---++++..+.+|++..+ .+.+.+.+.|++..+|++
T Consensus 496 ~~~~v~~~~w~r~~~Fl~~Ag~iI~~~~iviw~l~~~~~~g~~~~~~~~S~l~~ig~~i~Pi~~plG~~ 564 (772)
T PRK09554 496 HLKSLLIQTWQRLKGFVLRAGKVIIIVSIFIGALNSFSLSGKIVDNINDSALASVSRVITPVLKPIGVH 564 (772)
T ss_pred CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCccccccchhhhHHHHHHHHHHHHHhccCCC
Confidence 3356677888888888888888999999999998754 556677788988887764
No 62
>KOG1341 consensus Na+/K+ transporter [Inorganic ion transport and metabolism]
Probab=42.16 E-value=33 Score=34.49 Aligned_cols=35 Identities=31% Similarity=0.290 Sum_probs=27.1
Q ss_pred cCCCCCCC--CCCCCCCCCCCCCCccHHHHHHHHHHH
Q 029429 13 SQGLTPHD--PEDVPKSPPHSPNSSTRKACYAVLQSW 47 (193)
Q Consensus 13 ~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~ 47 (193)
|-|.|++| +||-.+.--|-+||+.|+.+.+...++
T Consensus 689 slg~y~e~t~tEdd~ne~dhdg~s~~rKsf~~~hl~~ 725 (854)
T KOG1341|consen 689 SLGLYAEDTETEDDNNENDHDGNSKKRKSFLGDHLRR 725 (854)
T ss_pred cCCccccccccccCcccccccccchhhhhHHHHHHHH
Confidence 56999888 777777777999999998777555443
No 63
>PF03213 Pox_P35: Poxvirus P35 protein; InterPro: IPR004900 The Poxvirus P35 protein is an immunodominant envelope protein. It binds to heparan sulphate on the cell surface to provide virion attachment to target cell [].; GO: 0019031 viral envelope
Probab=40.77 E-value=51 Score=30.17 Aligned_cols=66 Identities=18% Similarity=0.441 Sum_probs=35.6
Q ss_pred ccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhhhhhhhhh-hhhhHHHHHHHHHHHHHHHHHHhh
Q 029429 35 STRKACYAVLQSWVSKKFMTGCVVLFPVAVTFLVTWWFIEFVDSFFSPIYARLGV-EIFGLGFLTSILFIFFVGVFASSW 113 (193)
Q Consensus 35 ~~~~~~~~~~~~~i~~~fl~GLlvlLPi~iTi~Il~~l~~~v~~~~~pl~~~l~~-~~pglgl~~~l~~i~~iG~la~~~ 113 (193)
+.|+++++|+-+|+.+.|=.. .--+..|++.++|. ++..+|+++++.+++++=+-+++
T Consensus 252 ~~~~~~wsrl~~Wla~~~P~~--------------------~y~lttPLfSfFGlfDInv~g~~iil~ii~l~iF~vnS- 310 (325)
T PF03213_consen 252 EMKNSIWSRLGKWLAKRFPGA--------------------YYFLTTPLFSFFGLFDINVIGVIIILFIIILVIFDVNS- 310 (325)
T ss_pred hhhhhHHHHHHHHHHhhCCCc--------------------hhhhhchHHHHcccchhHHHHHHHHHHHHHHHHhcCCc-
Confidence 567777777766666654332 22234677777763 45556666554444444333333
Q ss_pred hhhHHHHHHHH
Q 029429 114 LGATVFWLGEW 124 (193)
Q Consensus 114 ig~~ll~~~e~ 124 (193)
+++|++-.
T Consensus 311 ---kllWFLaG 318 (325)
T PF03213_consen 311 ---KLLWFLAG 318 (325)
T ss_pred ---hHHHHHHH
Confidence 45555443
No 64
>PHA02688 ORF059 IMV protein VP55; Provisional
Probab=40.58 E-value=47 Score=30.41 Aligned_cols=42 Identities=17% Similarity=0.437 Sum_probs=21.8
Q ss_pred hhhhhhhhhhh-hhhhHHHHHHHHHHHHHHHHHHhhhhhHHHHHHHH
Q 029429 79 FFSPIYARLGV-EIFGLGFLTSILFIFFVGVFASSWLGATVFWLGEW 124 (193)
Q Consensus 79 ~~~pl~~~l~~-~~pglgl~~~l~~i~~iG~la~~~ig~~ll~~~e~ 124 (193)
+..|++.++|. ++..+|+++++.++.++=+-+++ +++|++-.
T Consensus 274 lttPLfSfFGlfDInv~gviiil~ii~l~IF~vnS----kLlWFLaG 316 (323)
T PHA02688 274 LTTPLFSFFGLFDINVIGVIIILFIIVLLIFDVNS----KLLWFLAG 316 (323)
T ss_pred ecchHHHhhccchhHHHHHHHHHHHHHHHHhcCCc----hHHHHHHH
Confidence 44788877773 45556655544443333333333 45555443
No 65
>PRK15082 glutathione ABC transporter permease GsiD; Provisional
Probab=40.51 E-value=2.6e+02 Score=24.64 Aligned_cols=27 Identities=7% Similarity=0.080 Sum_probs=16.7
Q ss_pred CccHHHHHHHHHHHHHHHHHHHHHHHH
Q 029429 34 SSTRKACYAVLQSWVSKKFMTGCVVLF 60 (193)
Q Consensus 34 ~~~~~~~~~~~~~~i~~~fl~GLlvlL 60 (193)
.+.-...++|+....+.++.-+++..+
T Consensus 85 D~~Grdv~srl~~g~~~TL~ial~a~~ 111 (301)
T PRK15082 85 DSLGRDIFSRILVGARISLAAGFFSVA 111 (301)
T ss_pred CCCCccHHHHHHHHHHHHHHHHHHHHH
Confidence 334445667777777777766655544
No 66
>PRK10478 putative PTS system fructose-like transporter subunit EIIC; Provisional
Probab=40.18 E-value=1.9e+02 Score=26.84 Aligned_cols=29 Identities=17% Similarity=0.181 Sum_probs=23.6
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 029429 44 LQSWVSKKFMTGCVVLFPVAVTFLVTWWF 72 (193)
Q Consensus 44 ~~~~i~~~fl~GLlvlLPi~iTi~Il~~l 72 (193)
..+++++++.+|+--.+|+++.-=++.-+
T Consensus 7 ~~~~~~~hlmtGvS~MlP~VvagGil~ai 35 (359)
T PRK10478 7 ILKNTRQHLMTGVSHMIPFVVAGGILLAV 35 (359)
T ss_pred HHHHHHHHHHhChhHhHhHHHHHHHHHHH
Confidence 66789999999999999999876555433
No 67
>COG2059 ChrA Chromate transport protein ChrA [Inorganic ion transport and metabolism]
Probab=39.80 E-value=1.5e+02 Score=25.00 Aligned_cols=47 Identities=6% Similarity=0.077 Sum_probs=37.5
Q ss_pred CCccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Q 029429 33 NSSTRKACYAVLQSWVSKKFMTGCVVLFPVAVTFLVTWWFIEFVDSF 79 (193)
Q Consensus 33 ~~~~~~~~~~~~~~~i~~~fl~GLlvlLPi~iTi~Il~~l~~~v~~~ 79 (193)
+|.+=..+......-+.--+++++.+++|=++.++.+.++++...+.
T Consensus 62 ~a~~la~~vGy~~~G~~Ga~ia~lafvLPs~i~~~~l~~~~~~~~~~ 108 (195)
T COG2059 62 IATQLAIYVGYKLAGILGALIAGLAFVLPSILIMLGLALLLKRFGDL 108 (195)
T ss_pred HHHHHHHHHHHHHhchhHHHHHHHHHHHHHHHHHHHHHHHHHHcCcc
Confidence 44444555566666688889999999999999999999999987765
No 68
>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=39.37 E-value=1.3e+02 Score=25.04 Aligned_cols=15 Identities=33% Similarity=0.609 Sum_probs=11.6
Q ss_pred HHHHHHHHHHHHHHH
Q 029429 58 VLFPVAVTFLVTWWF 72 (193)
Q Consensus 58 vlLPi~iTi~Il~~l 72 (193)
+++|+++.+.++.++
T Consensus 80 ~fmP~alv~lv~~~v 94 (170)
T PF11241_consen 80 FFMPVALVLLVLSFV 94 (170)
T ss_pred HHHHHHHHHHHHHHH
Confidence 467888888887777
No 69
>PRK00523 hypothetical protein; Provisional
Probab=37.54 E-value=93 Score=22.48 Aligned_cols=40 Identities=10% Similarity=0.170 Sum_probs=21.8
Q ss_pred HHHHHHHHHhhhhhHHHHHHHHHhhhhhhhhHHHHHHHHHHHHhC
Q 029429 103 IFFVGVFASSWLGATVFWLGEWFIKRLPFMKHIYSASKQISAAIS 147 (193)
Q Consensus 103 i~~iG~la~~~ig~~ll~~~e~ll~rIP~V~sIYssiKqi~~~f~ 147 (193)
.+++|.+.--++.| +.+++-+.+=|=+.. +.+|.+..+..
T Consensus 14 ~li~G~~~Gffiar---k~~~k~l~~NPpine--~mir~M~~QMG 53 (72)
T PRK00523 14 LLIVGGIIGYFVSK---KMFKKQIRENPPITE--NMIRAMYMQMG 53 (72)
T ss_pred HHHHHHHHHHHHHH---HHHHHHHHHCcCCCH--HHHHHHHHHhC
Confidence 46667766666666 566766664444331 34444444443
No 70
>COG3763 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=37.02 E-value=99 Score=22.31 Aligned_cols=44 Identities=11% Similarity=0.179 Sum_probs=24.0
Q ss_pred HHHHHHHHHHHHHHhhhhhHHHHHHHHHhhhhhhhhHHHHHHHHHHHHh
Q 029429 98 TSILFIFFVGVFASSWLGATVFWLGEWFIKRLPFMKHIYSASKQISAAI 146 (193)
Q Consensus 98 ~~l~~i~~iG~la~~~ig~~ll~~~e~ll~rIP~V~sIYssiKqi~~~f 146 (193)
+++++++++|++.-.++.| +..++.+.+=|=++. ..+|-+..+.
T Consensus 8 l~ivl~ll~G~~~G~fiar---k~~~k~lk~NPpine--~~iR~M~~qm 51 (71)
T COG3763 8 LLIVLALLAGLIGGFFIAR---KQMKKQLKDNPPINE--EMIRMMMAQM 51 (71)
T ss_pred HHHHHHHHHHHHHHHHHHH---HHHHHHHhhCCCCCH--HHHHHHHHHh
Confidence 4455566677766666666 455566665554432 3444444444
No 71
>PF12841 YvrJ: YvrJ protein family; InterPro: IPR024419 This entry is represents a family of uncharacterised protein. The function of the Bacillus subtilis YvrJ protein is not known, but its expression is regulated by the cell envelope stress-inducible sigma factor YvrI [].
Probab=36.39 E-value=66 Score=20.34 Aligned_cols=25 Identities=24% Similarity=0.365 Sum_probs=21.1
Q ss_pred HHHHHHHHHHHHHHHHHHhhhhhhh
Q 029429 60 FPVAVTFLVTWWFIEFVDSFFSPIY 84 (193)
Q Consensus 60 LPi~iTi~Il~~l~~~v~~~~~pl~ 84 (193)
.|+++++|++.-+=+.+|.+...+.
T Consensus 8 FPi~va~yLL~R~E~kld~L~~~i~ 32 (38)
T PF12841_consen 8 FPIAVAIYLLVRIEKKLDELTESIN 32 (38)
T ss_pred cHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 5999999999999999888876543
No 72
>PF05328 CybS: CybS; InterPro: IPR007992 This family consists of several eukaryotic succinate dehydrogenase [ubiquinone] cytochrome B small subunit, mitochondrial precursor (CybS) proteins. SDHD encodes the small subunit (cybS) of cytochrome b in succinate-ubiquinone oxidoreductase (mitochondrial complex II). Mitochondrial complex II is involved in the Krebs cycle and in the aerobic electron transport chain. It contains four proteins. The catalytic core consists of a flavoprotein and an iron-sulphur protein; these proteins are anchored to the mitochondrial inner membrane by the large subunit of cytochrome b (cybL) and cybS, which together comprise the haem-protein cytochrome b. Mutations in the SDHD gene can lead to hereditary paraganglioma, characterised by the development of benign, vascularised tumours in the head and neck [].; GO: 0005506 iron ion binding, 0020037 heme binding, 0006099 tricarboxylic acid cycle, 0005740 mitochondrial envelope, 0016021 integral to membrane; PDB: 3AE7_D 3AEB_D 3AEC_D 3AE6_D 3AE4_D 3AE3_D 3AEG_D 3SFD_D 3AE9_D 1ZOY_D ....
Probab=35.68 E-value=2.2e+02 Score=22.47 Aligned_cols=42 Identities=12% Similarity=0.159 Sum_probs=25.1
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhhhhhhhh
Q 029429 47 WVSKKFMTGCVVLFPVAVTFLVTWWFIEFVDSFFSPIYARLG 88 (193)
Q Consensus 47 ~i~~~fl~GLlvlLPi~iTi~Il~~l~~~v~~~~~pl~~~l~ 88 (193)
.+.|.+-.+|+-+.|+....--..-+++.+-...-++..++|
T Consensus 36 ~~ER~~a~~Llpl~~~~~~~gs~~~~~D~~La~~l~~H~h~G 77 (132)
T PF05328_consen 36 KFERIVAAALLPLIPAAFASGSPNPVMDYLLAVALPLHSHIG 77 (132)
T ss_dssp HHHHHHHHHHHHHHHHHHHS---SHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHhcCCcHHHHHHHHHHHHHHHHHh
Confidence 456778889988888887763334455555444455544444
No 73
>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=35.50 E-value=1e+02 Score=25.96 Aligned_cols=24 Identities=21% Similarity=0.389 Sum_probs=20.3
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHH
Q 029429 50 KKFMTGCVVLFPVAVTFLVTWWFI 73 (193)
Q Consensus 50 ~~fl~GLlvlLPi~iTi~Il~~l~ 73 (193)
-.|++|++..|=+...+|++|.++
T Consensus 161 ~SFiGGIVL~LGv~aI~ff~~KF~ 184 (186)
T PF05283_consen 161 ASFIGGIVLTLGVLAIIFFLYKFC 184 (186)
T ss_pred hhhhhHHHHHHHHHHHHHHHhhhc
Confidence 569999999999988888887765
No 74
>PRK01844 hypothetical protein; Provisional
Probab=35.37 E-value=95 Score=22.44 Aligned_cols=42 Identities=10% Similarity=0.164 Sum_probs=24.1
Q ss_pred HHHHHHHHHHHhhhhhHHHHHHHHHhhhhhhhhHHHHHHHHHHHHhC
Q 029429 101 LFIFFVGVFASSWLGATVFWLGEWFIKRLPFMKHIYSASKQISAAIS 147 (193)
Q Consensus 101 ~~i~~iG~la~~~ig~~ll~~~e~ll~rIP~V~sIYssiKqi~~~f~ 147 (193)
++.+++|.+.--++.| +.+++-+.+=|=+.. +.+|.+..+..
T Consensus 11 I~~li~G~~~Gff~ar---k~~~k~lk~NPpine--~mir~Mm~QMG 52 (72)
T PRK01844 11 VVALVAGVALGFFIAR---KYMMNYLQKNPPINE--QMLKMMMMQMG 52 (72)
T ss_pred HHHHHHHHHHHHHHHH---HHHHHHHHHCCCCCH--HHHHHHHHHhC
Confidence 3456666666666666 567777776655432 34444444443
No 75
>PRK12287 tqsA pheromone autoinducer 2 transporter; Reviewed
Probab=35.12 E-value=3e+02 Score=24.52 Aligned_cols=37 Identities=8% Similarity=-0.042 Sum_probs=25.9
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 029429 38 KACYAVLQSWVSKKFMTGCVVLFPVAVTFLVTWWFIE 74 (193)
Q Consensus 38 ~~~~~~~~~~i~~~fl~GLlvlLPi~iTi~Il~~l~~ 74 (193)
.....+..+.+++|+.+.++..+=..+..++..|+++
T Consensus 183 ~~~l~~~~~~~~~Y~~g~~i~~~i~gv~~~i~l~ilg 219 (344)
T PRK12287 183 MAAIQRALDSVSHYLVLKTAISIITGLVAWAMLAALD 219 (344)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhC
Confidence 3456666778888888887776666666666666655
No 76
>PF03672 UPF0154: Uncharacterised protein family (UPF0154); InterPro: IPR005359 The proteins in this entry are functionally uncharacterised.
Probab=34.49 E-value=67 Score=22.66 Aligned_cols=42 Identities=12% Similarity=0.175 Sum_probs=20.9
Q ss_pred HHHHHHHHHHHhhhhhHHHHHHHHHhhhhhhhhHHHHHHHHHHHHhC
Q 029429 101 LFIFFVGVFASSWLGATVFWLGEWFIKRLPFMKHIYSASKQISAAIS 147 (193)
Q Consensus 101 ~~i~~iG~la~~~ig~~ll~~~e~ll~rIP~V~sIYssiKqi~~~f~ 147 (193)
++++++|.++-.+++| +.+++-+.+=|=+. =+.+|.+..+..
T Consensus 4 ilali~G~~~Gff~ar---~~~~k~l~~NPpin--e~mir~M~~QMG 45 (64)
T PF03672_consen 4 ILALIVGAVIGFFIAR---KYMEKQLKENPPIN--EKMIRAMMMQMG 45 (64)
T ss_pred HHHHHHHHHHHHHHHH---HHHHHHHHHCCCCC--HHHHHHHHHHhC
Confidence 4445566655555555 45666665554322 133444444443
No 77
>PRK05415 hypothetical protein; Provisional
Probab=34.21 E-value=3.8e+02 Score=24.72 Aligned_cols=30 Identities=17% Similarity=0.149 Sum_probs=20.3
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 029429 47 WVSKKFMTGCVVLFPVAVTFLVTWWFIEFVD 77 (193)
Q Consensus 47 ~i~~~fl~GLlvlLPi~iTi~Il~~l~~~v~ 77 (193)
+.++.|.+++..++=+++..+ ..|+.+...
T Consensus 65 ~w~~~~~~~l~~l~~~~~~~~-~~~i~~~~~ 94 (341)
T PRK05415 65 LWRKLLWGGLGLLGSLVVGQA-VQWLRDAFQ 94 (341)
T ss_pred HHHHHHHHHHHHHHHHHHHHH-HHHHHHHHH
Confidence 346778888888877777777 556555443
No 78
>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=34.07 E-value=3.2e+02 Score=23.79 Aligned_cols=31 Identities=16% Similarity=0.376 Sum_probs=19.8
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHhhh
Q 029429 50 KKFMTGCVVLFPVAVTFLVTWWFIEFVDSFF 80 (193)
Q Consensus 50 ~~fl~GLlvlLPi~iTi~Il~~l~~~v~~~~ 80 (193)
+.++.=.++++-....++++..+++.++.+.
T Consensus 5 ~~~l~~f~~~l~~~~~i~~~~~l~~~l~~~~ 35 (354)
T PF03739_consen 5 KEFLKTFLLVLLSFTGIFLIIDLFELLDDFL 35 (354)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 4455555566666667777777777776663
No 79
>PRK06298 type III secretion system protein; Validated
Probab=33.62 E-value=3.6e+02 Score=24.79 Aligned_cols=18 Identities=22% Similarity=0.265 Sum_probs=9.8
Q ss_pred HHHHHHHHHHHHHhhhhh
Q 029429 99 SILFIFFVGVFASSWLGA 116 (193)
Q Consensus 99 ~l~~i~~iG~la~~~ig~ 116 (193)
++++++++|.++.-..++
T Consensus 90 ~~~~~~~~~i~~~~~q~G 107 (356)
T PRK06298 90 LLGAVAFVGVLVGFLIVG 107 (356)
T ss_pred HHHHHHHHHHHHHHHhhC
Confidence 344555666666554444
No 80
>PHA03231 glycoprotein BALF4; Provisional
Probab=33.30 E-value=1.7e+02 Score=30.13 Aligned_cols=69 Identities=17% Similarity=0.056 Sum_probs=34.2
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHH--HHHHHHHHHHHHhhhhhhhhhhhhhhhhHHHHHHHHHHHHHHHHHHhhh
Q 029429 37 RKACYAVLQSWVSKKFMTGCVVLFPVAVT--FLVTWWFIEFVDSFFSPIYARLGVEIFGLGFLTSILFIFFVGVFASSWL 114 (193)
Q Consensus 37 ~~~~~~~~~~~i~~~fl~GLlvlLPi~iT--i~Il~~l~~~v~~~~~pl~~~l~~~~pglgl~~~l~~i~~iG~la~~~i 114 (193)
|++++..+ ..|+.||=.+-=.+.. .-+...+.++++|+++-+-+. +-|+.++++++++.++.+++.++.
T Consensus 657 ~~~~~~gl-----~~~~~gLG~vGk~vg~vv~~v~ga~~SiVsG~~sFl~NP----FGg~~iillvia~vv~v~l~~rr~ 727 (829)
T PHA03231 657 RNAFVRGL-----AEFMQGLGAVGKAVGNVVSGVAGAVGSIVSGVISFLKNP----FGGLAIGLLVIAVLVAVFLAYRRV 727 (829)
T ss_pred chHHHHHH-----HHHHhhhhhhchhhhhhhhhHHHHHHHHHHHHHHHhcCc----hHHHHHHHHHHHHhhhhhHHHHHH
Confidence 66666554 4455666544322221 112233334444444333333 335666666666667777766543
No 81
>PRK10845 colicin V production protein; Provisional
Probab=31.89 E-value=2.7e+02 Score=22.39 Aligned_cols=80 Identities=10% Similarity=0.152 Sum_probs=36.3
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhhhhhhhhhhhhhHHHHH----HHHHHHHHHHHHHhhhhhHHHHHHHH
Q 029429 49 SKKFMTGCVVLFPVAVTFLVTWWFIEFVDSFFSPIYARLGVEIFGLGFLT----SILFIFFVGVFASSWLGATVFWLGEW 124 (193)
Q Consensus 49 ~~~fl~GLlvlLPi~iTi~Il~~l~~~v~~~~~pl~~~l~~~~pglgl~~----~l~~i~~iG~la~~~ig~~ll~~~e~ 124 (193)
+|=|+.=++-++=.++-+|+-.+.++.+...+..+... ....+.++++ +++++-+++.+.+..+....++..|+
T Consensus 21 ~RGfv~ev~sl~g~i~a~~~A~~~~~~la~~l~~~~~~--~~~~~~af~~iFi~v~~~~~i~~~~l~~l~~~~~Lg~~dr 98 (162)
T PRK10845 21 IRGFVREALSLVTWGCAFFVASHYYTYLSVWFTGFEDE--LVRNGIAIAVLFIATLIVGAIVNYVIGQLVEKTGLSGTDR 98 (162)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhccH--HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCchHHH
Confidence 34444445555555555555555555444433221110 1112333333 33334445555555554455566777
Q ss_pred Hhhhhh
Q 029429 125 FIKRLP 130 (193)
Q Consensus 125 ll~rIP 130 (193)
++.-+=
T Consensus 99 ~lG~if 104 (162)
T PRK10845 99 VLGVCF 104 (162)
T ss_pred HHHHHH
Confidence 665433
No 82
>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=31.65 E-value=1.4e+02 Score=21.48 Aligned_cols=32 Identities=22% Similarity=0.721 Sum_probs=18.9
Q ss_pred HHHHHHHHHHHHHHHH------HHHHhhhhhhhhhhhh
Q 029429 58 VLFPVAVTFLVTWWFI------EFVDSFFSPIYARLGV 89 (193)
Q Consensus 58 vlLPi~iTi~Il~~l~------~~v~~~~~pl~~~l~~ 89 (193)
-++|+++...++.|+. +.+..++.|+++.+|.
T Consensus 3 ~~~p~i~~~~~l~~iL~~~g~l~~i~~~l~P~~~~lgL 40 (109)
T PF07670_consen 3 RALPIIIPFSILIWILEESGLLERISRLLEPLFRPLGL 40 (109)
T ss_dssp HTHHHHHHHHHHHHHHHHTTHHHHHHHHHHHHHHHH--
T ss_pred eeHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHhhcCC
Confidence 3455555555555544 4666778888877665
No 83
>COG1286 CvpA Uncharacterized membrane protein, required for colicin V production [General function prediction only]
Probab=31.48 E-value=3e+02 Score=22.73 Aligned_cols=30 Identities=13% Similarity=0.239 Sum_probs=15.6
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 029429 49 SKKFMTGCVVLFPVAVTFLVTWWFIEFVDS 78 (193)
Q Consensus 49 ~~~fl~GLlvlLPi~iTi~Il~~l~~~v~~ 78 (193)
+|=|+..++-++=.+.-+|+-+..+.-+..
T Consensus 21 ~RGfi~e~~sl~s~i~a~~vA~~fy~~~~~ 50 (182)
T COG1286 21 RRGFIREVLSLLSWILAAFVASLFYKPLAP 50 (182)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHhHHHHH
Confidence 455555555555555555555555543333
No 84
>cd02432 Nodulin-21_like_1 Nodulin-21 and CCC1-related protein family. Nodulin-21_like_1: This is a family of proteins closely related to nodulin-21, a plant nodule-specific protein that may be involved in symbiotic nitrogen fixation. This family is also related to CCC1, a yeast vacuole transmembrane protein that functions as an iron and manganese transporter.
Probab=31.42 E-value=3.3e+02 Score=23.17 Aligned_cols=59 Identities=10% Similarity=0.088 Sum_probs=35.0
Q ss_pred CCccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhhhhhhhhhhhhhHHHHHHHHHHHHHHHHHHh
Q 029429 33 NSSTRKACYAVLQSWVSKKFMTGCVVLFPVAVTFLVTWWFIEFVDSFFSPIYARLGVEIFGLGFLTSILFIFFVGVFASS 112 (193)
Q Consensus 33 ~~~~~~~~~~~~~~~i~~~fl~GLlvlLPi~iTi~Il~~l~~~v~~~~~pl~~~l~~~~pglgl~~~l~~i~~iG~la~~ 112 (193)
.|+-+.+.. .+-.+++.|++=++|..+. . . . . .-...++++.+.++++|++...
T Consensus 134 ~~p~~aal~-----s~~sf~lg~liPllpy~~~--------~---~-----~----~-~~~~s~~~~~~aL~~~G~~~a~ 187 (218)
T cd02432 134 ANPWQAALA-----SAISFSVGALLPLLAILLA--------P---A-----A----W-KVPVTIIATLLALALTGYVSAR 187 (218)
T ss_pred CCHHHHHHH-----HHHHHHHHHHHHHHHHHHh--------c---c-----h----H-HHHHHHHHHHHHHHHHHHHHHH
Confidence 345444444 3457899999999995421 0 0 0 0 0123556677778888888776
Q ss_pred hhhhH
Q 029429 113 WLGAT 117 (193)
Q Consensus 113 ~ig~~ 117 (193)
.-++.
T Consensus 188 ~~~~~ 192 (218)
T cd02432 188 LGGAS 192 (218)
T ss_pred HCCCC
Confidence 66653
No 85
>PRK02463 OxaA-like protein precursor; Provisional
Probab=30.89 E-value=2e+02 Score=25.93 Aligned_cols=22 Identities=9% Similarity=0.129 Sum_probs=17.5
Q ss_pred HHHHHHHHHHHHHHHHHHHHHH
Q 029429 46 SWVSKKFMTGCVVLFPVAVTFL 67 (193)
Q Consensus 46 ~~i~~~fl~GLlvlLPi~iTi~ 67 (193)
+..||.++.|+++.+.+++|--
T Consensus 3 ~~~k~~~~~~~~~~~~~~lsgc 24 (307)
T PRK02463 3 KTLKRILFSGLALSMLLTLTGC 24 (307)
T ss_pred hHHHHHHHHHHHHHHHHHHhcc
Confidence 5567888889999998888874
No 86
>TIGR00328 flhB flagellar biosynthetic protein FlhB. FlhB and its functionally equivalent orthologs, from among a larger superfamily of proteins involved in type III protein export systems, are specifically involved in flagellar protein export. The seed members are restricted and the trusted cutoff is set high such that the proteins gathered by this model play roles specifically related to flagellar structures. Full-length homologs scoring below the trusted cutoff are involved in peptide export but not necessarily in the creation of flagella.
Probab=30.07 E-value=4.3e+02 Score=24.16 Aligned_cols=47 Identities=17% Similarity=0.118 Sum_probs=23.7
Q ss_pred HHHHHHHHHHHHHhhhhhHHHHH------HHH-----HhhhhhhhhHHHHHHHHHHHH
Q 029429 99 SILFIFFVGVFASSWLGATVFWL------GEW-----FIKRLPFMKHIYSASKQISAA 145 (193)
Q Consensus 99 ~l~~i~~iG~la~~~ig~~ll~~------~e~-----ll~rIP~V~sIYssiKqi~~~ 145 (193)
++++++++|+++.-..++.++.. +++ -+.|+=..+++....|.+++.
T Consensus 89 ~~~~~~~~~i~~~~~q~G~~fs~k~l~Pk~~rlNPi~G~KriFS~~~l~el~KsllK~ 146 (347)
T TIGR00328 89 IFVLLLVVGVLSNIAQFGFLFTTKPLKPKFSKINPIKGLKRLFSLQSLVELLKSLLKV 146 (347)
T ss_pred HHHHHHHHHHHHHHHhhCcccccccCCCChhhcCHHHHHHHhcCHHHHHHHHHHHHHH
Confidence 34445666777665555543321 222 244555555555555555543
No 87
>PRK11365 ssuC alkanesulfonate transporter permease subunit; Provisional
Probab=30.00 E-value=2.8e+02 Score=23.73 Aligned_cols=65 Identities=8% Similarity=0.067 Sum_probs=37.4
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhhhhhhhhhhhhhHHHHHHHHHHHH
Q 029429 39 ACYAVLQSWVSKKFMTGCVVLFPVAVTFLVTWWFIEFVDSFFSPIYARLGVEIFGLGFLTSILFIFF 105 (193)
Q Consensus 39 ~~~~~~~~~i~~~fl~GLlvlLPi~iTi~Il~~l~~~v~~~~~pl~~~l~~~~pglgl~~~l~~i~~ 105 (193)
.++.++...+.+. +.|++.-+.+++.+-++.-...+++.++.|+...+ ..+|.+.++.+++..|-
T Consensus 57 ~l~~~l~~Tl~~~-~~g~~la~~igi~lGi~~~~~~~~~~~~~~~~~~~-~siP~~~~~~lli~~fg 121 (263)
T PRK11365 57 ELWQHLAISSWRA-LIGFSIGGSLGLILGLISGLSRWGERLLDTSIQML-RNVPHLALIPLVILWFG 121 (263)
T ss_pred cHHHHHHHHHHHH-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-hhCCHHHHHHHHHHHHc
Confidence 4555666665553 34666666666666666666678888888876432 23444444444333333
No 88
>PRK04949 putative sulfate transport protein CysZ; Validated
Probab=29.90 E-value=3.7e+02 Score=23.34 Aligned_cols=24 Identities=25% Similarity=0.663 Sum_probs=12.8
Q ss_pred HHHHHHHHHHHHHH----HHHHHHHhhh
Q 029429 57 VVLFPVAVTFLVTW----WFIEFVDSFF 80 (193)
Q Consensus 57 lvlLPi~iTi~Il~----~l~~~v~~~~ 80 (193)
.+++|+++++.++. |.++.++..+
T Consensus 29 ~~liPl~inllLf~~~l~~~~~~~~~~l 56 (251)
T PRK04949 29 FVILPLLVNILLFGGAFWWLFTQLDAWI 56 (251)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 45567666665544 4444444433
No 89
>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=29.01 E-value=4.5e+02 Score=24.00 Aligned_cols=25 Identities=20% Similarity=0.276 Sum_probs=20.2
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHH
Q 029429 46 SWVSKKFMTGCVVLFPVAVTFLVTW 70 (193)
Q Consensus 46 ~~i~~~fl~GLlvlLPi~iTi~Il~ 70 (193)
+.++|++.+|.--++|+++.-=++.
T Consensus 13 ~~~~~~lm~gis~miP~ivagGll~ 37 (346)
T TIGR01427 13 KGIYKHLLTGVSYMLPFVVAGGIII 37 (346)
T ss_pred HHHHHHHHhchHHHHHHHHHHHHHH
Confidence 5678999999999999988764433
No 90
>PRK04897 heat shock protein HtpX; Provisional
Probab=28.72 E-value=4.1e+02 Score=23.43 Aligned_cols=35 Identities=17% Similarity=0.303 Sum_probs=22.3
Q ss_pred HHHHHHHHHHHHhCCCCCCccccceEEEEcCCCCeeEEEE
Q 029429 134 HIYSASKQISAAISPDQNTSAFKEVAIIRHPRLGEYAFGF 173 (193)
Q Consensus 134 sIYssiKqi~~~f~g~~~~~~f~~VVLVe~P~~g~~~iGF 173 (193)
.+|+.++++.+...-. -.+|-.++-+..+.++.|+
T Consensus 81 ~L~~~v~~la~~~gip-----~p~v~v~~~~~~NAfa~G~ 115 (298)
T PRK04897 81 ELWHIVEDMAMVAQIP-----MPRVFIIDDPSPNAFATGS 115 (298)
T ss_pred HHHHHHHHHHHHcCCC-----CCcEEEecCCCCceEEecc
Confidence 4777777777754321 2457777766667777775
No 91
>PRK10519 hypothetical protein; Provisional
Probab=28.49 E-value=3.2e+02 Score=22.11 Aligned_cols=50 Identities=20% Similarity=0.335 Sum_probs=31.5
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH------HHHhhhhhhhhhhhh
Q 029429 40 CYAVLQSWVSKKFMTGCVVLFPVAVTFLVTWWFIE------FVDSFFSPIYARLGV 89 (193)
Q Consensus 40 ~~~~~~~~i~~~fl~GLlvlLPi~iTi~Il~~l~~------~v~~~~~pl~~~l~~ 89 (193)
.+....+--|+-|-..+=-++|..+..+++.++++ ++.+++.|+...+|.
T Consensus 7 v~d~Fv~GakeG~~i~~~~iiP~li~~~v~I~iL~~sG~ld~l~~~l~Pvm~llGL 62 (151)
T PRK10519 7 VTDIFIDGARKGFTIATTNLLPNVLMAFVIIQALNITGLLDLVGHIFGPVMALFGL 62 (151)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCHHHHHHHHHHHHHHHhCC
Confidence 33333344444444444457888888888887765 566678888876654
No 92
>PF01988 VIT1: VIT family; InterPro: IPR008217 Proteins containing this entry have no known function and are predicted to be integral membrane proteins. They include the Ccc1 protein from Saccharomyces cerevisiae (Baker's yeast) (P47818 from SWISSPROT) that may have a role in regulating calcium levels [].
Probab=28.32 E-value=3.5e+02 Score=22.50 Aligned_cols=49 Identities=20% Similarity=0.261 Sum_probs=28.0
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhhhhhhhhhhhhhHHHHHHHHHHHHHHHHHHhhhhh
Q 029429 48 VSKKFMTGCVVLFPVAVTFLVTWWFIEFVDSFFSPIYARLGVEIFGLGFLTSILFIFFVGVFASSWLGA 116 (193)
Q Consensus 48 i~~~fl~GLlvlLPi~iTi~Il~~l~~~v~~~~~pl~~~l~~~~pglgl~~~l~~i~~iG~la~~~ig~ 116 (193)
.--+++.|++-++|..+.- -.. . ...+.+++.++.++++|++..+..++
T Consensus 139 ~~sf~lg~liPllp~~~~~-~~~--~-----------------a~~~s~~~~~~~L~~~G~~~a~~~~~ 187 (213)
T PF01988_consen 139 FLSFILGGLIPLLPYFFLP-SVS--E-----------------AFIASIAVTILALFILGYFKARISGQ 187 (213)
T ss_pred HHHHHHHHHHHHHHHHHhh-hHH--H-----------------HHHHHHHHHHHHHHHHHHHHHHHcCC
Confidence 4467888888888876653 000 0 01134455556666666666655555
No 93
>PRK10417 nikC nickel transporter permease NikC; Provisional
Probab=28.21 E-value=3.9e+02 Score=23.03 Aligned_cols=19 Identities=5% Similarity=-0.045 Sum_probs=10.5
Q ss_pred HHHHHHHHHHHHHHHHHHH
Q 029429 40 CYAVLQSWVSKKFMTGCVV 58 (193)
Q Consensus 40 ~~~~~~~~i~~~fl~GLlv 58 (193)
.++++....+.++.-+++.
T Consensus 58 v~s~l~~g~~~TL~~~~~a 76 (272)
T PRK10417 58 IFSRLMAGTRVSLGSVMAC 76 (272)
T ss_pred HHHHHHHHHHHHHHHHHHH
Confidence 4556666666665554443
No 94
>PF10112 Halogen_Hydrol: 5-bromo-4-chloroindolyl phosphate hydrolysis protein; InterPro: IPR018770 This entry consists of prokaryotic proteins that mediate the hydrolysis of 5-bromo-4-chloroindolyl phosphate bonds.
Probab=28.17 E-value=3.3e+02 Score=22.27 Aligned_cols=15 Identities=13% Similarity=0.175 Sum_probs=8.0
Q ss_pred HHHHHHHHHHHHhCC
Q 029429 134 HIYSASKQISAAISP 148 (193)
Q Consensus 134 sIYssiKqi~~~f~g 148 (193)
.+++..|++.+.+-.
T Consensus 105 ~~~~~~~~I~~~v~~ 119 (199)
T PF10112_consen 105 RIEKIARRIFKYVEK 119 (199)
T ss_pred HHHHHHHHHHHHHHH
Confidence 345555556555543
No 95
>PF04341 DUF485: Protein of unknown function, DUF485; InterPro: IPR007436 This family includes several putative integral membrane proteins.
Probab=28.10 E-value=2.4e+02 Score=20.53 Aligned_cols=26 Identities=19% Similarity=0.510 Sum_probs=14.8
Q ss_pred HHHHHHHHHHHHHHHHHHHhhhhhhh
Q 029429 59 LFPVAVTFLVTWWFIEFVDSFFSPIY 84 (193)
Q Consensus 59 lLPi~iTi~Il~~l~~~v~~~~~pl~ 84 (193)
..|+.+...+.++.+-.+.++-..+.
T Consensus 18 ~~~l~~i~l~~y~~~~ll~a~~p~~m 43 (91)
T PF04341_consen 18 AWPLSAIFLVLYFGFVLLSAFAPELM 43 (91)
T ss_pred HHHHHHHHHHHHHHHHHHHHHCHHHH
Confidence 34555666666666666655554433
No 96
>TIGR02790 nickel_nikC nickel ABC transporter, permease subunit NikC. This family consists of the NikC family of nickel ABC transporter permeases. Operons that contain this protein also contain a homologous permease subunit NikB. Nickel is used in cells as part of urease or certain hydrogenases or superoxide dismutases.
Probab=27.96 E-value=3.8e+02 Score=22.79 Aligned_cols=21 Identities=14% Similarity=-0.002 Sum_probs=13.2
Q ss_pred HHHHHHHHHHHHHHHHHHHHH
Q 029429 40 CYAVLQSWVSKKFMTGCVVLF 60 (193)
Q Consensus 40 ~~~~~~~~i~~~fl~GLlvlL 60 (193)
.++|+.+..+.++.-+++..+
T Consensus 53 v~~~l~~g~~~TL~ia~~~~~ 73 (258)
T TIGR02790 53 IFSRLIFGARVSLGSALLVLG 73 (258)
T ss_pred HHHHHHHHHHHHHHHHHHHHH
Confidence 456667677777766665543
No 97
>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=27.66 E-value=3e+02 Score=28.41 Aligned_cols=46 Identities=20% Similarity=0.320 Sum_probs=30.9
Q ss_pred HHHHHHHHHHHHHHHHHHhhhhhHHHHHHHHHhh--hhhhhhHHHHHHHH
Q 029429 94 LGFLTSILFIFFVGVFASSWLGATVFWLGEWFIK--RLPFMKHIYSASKQ 141 (193)
Q Consensus 94 lgl~~~l~~i~~iG~la~~~ig~~ll~~~e~ll~--rIP~V~sIYssiKq 141 (193)
+++..++.++.++|..++|-+ -++++.++..+ ..|....+..+.++
T Consensus 914 l~~~s~iG~i~L~GIvVnNaI--llvd~~~~~~~~~g~~~~eAi~~a~~~ 961 (1021)
T PF00873_consen 914 LSFMSLIGIIALIGIVVNNAI--LLVDFINELRKREGMPLEEAIIEAARS 961 (1021)
T ss_dssp BSHHHHHHHHHHHHHHHHHHH--HHHHHHHHHHHTTCCHHHHHHHHHHHH
T ss_pred ccccceehHHHHHHHHHhhhH--HHHHHHHHHhhhccccHHHHHHHHHHH
Confidence 556667888999999999854 35666666655 56665555555443
No 98
>PRK14762 membrane protein; Provisional
Probab=27.63 E-value=1e+02 Score=18.00 Aligned_cols=14 Identities=29% Similarity=0.864 Sum_probs=9.6
Q ss_pred HHHHHHHHHHHHHh
Q 029429 99 SILFIFFVGVFASS 112 (193)
Q Consensus 99 ~l~~i~~iG~la~~ 112 (193)
.++++|++|+++-+
T Consensus 7 ~i~iifligllvvt 20 (27)
T PRK14762 7 AVLIIFLIGLLVVT 20 (27)
T ss_pred HHHHHHHHHHHHHH
Confidence 45667888888744
No 99
>COG4171 SapC ABC-type antimicrobial peptide transport system, permease component [Defense mechanisms]
Probab=27.08 E-value=4.6e+02 Score=23.43 Aligned_cols=23 Identities=30% Similarity=0.460 Sum_probs=15.8
Q ss_pred HHHHhhhhh-hhhHHHHHHHHHHH
Q 029429 122 GEWFIKRLP-FMKHIYSASKQISA 144 (193)
Q Consensus 122 ~e~ll~rIP-~V~sIYssiKqi~~ 144 (193)
+--++.-+| .|++||+++++=.+
T Consensus 163 fA~~LAllPrfirsiY~avh~Ele 186 (296)
T COG4171 163 FAVWLALLPRFIRSIYSAVHDELE 186 (296)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHH
Confidence 445555566 57999999987443
No 100
>PF12729 4HB_MCP_1: Four helix bundle sensory module for signal transduction; InterPro: IPR024478 This entry represents a four-helix bundle that operates as a ubiquitous sensory module in prokaryotic signal-transduction, which is known as four-helix bundles methyl-accepting chemotaxis protein (4HB_MCP) domain. The 4HB_MCP is always found between two predicted transmembrane helices indicating that it detects only extracellular signals. In many cases the domain is associated with a cytoplasmic HAMP domain suggesting that most proteins carrying the bundle might share the mechanism of transmembrane signalling which is well-characterised in E coli chemoreceptors [].
Probab=27.08 E-value=2.6e+02 Score=20.70 Aligned_cols=40 Identities=28% Similarity=0.330 Sum_probs=17.4
Q ss_pred HHHHHHHHHHHHHHHHHHhhhhhHHHHHHHHHhh-hhhhhhH
Q 029429 94 LGFLTSILFIFFVGVFASSWLGATVFWLGEWFIK-RLPFMKH 134 (193)
Q Consensus 94 lgl~~~l~~i~~iG~la~~~ig~~ll~~~e~ll~-rIP~V~s 134 (193)
++++++++++.++|.++-..+. .+-+..+.+.+ ++|.+..
T Consensus 10 ~~f~~~~~l~~~~~~~~~~~l~-~~~~~~~~i~~~~~~~~~~ 50 (181)
T PF12729_consen 10 LGFGLIILLLLIVGIVGLYSLS-QINQNVEEIYENNLPSIEL 50 (181)
T ss_pred HHHHHHHHHHHHHHHHHHHHHH-HHHHHHHHHHHhhhHHHHH
Confidence 3444455555555555433222 23334444433 3554433
No 101
>PRK11026 ftsX cell division ABC transporter subunit FtsX; Provisional
Probab=26.80 E-value=4.6e+02 Score=23.34 Aligned_cols=25 Identities=12% Similarity=-0.041 Sum_probs=16.9
Q ss_pred HHHHHHHHHHHHHHhhhhhHHHHHH
Q 029429 98 TSILFIFFVGVFASSWLGATVFWLG 122 (193)
Q Consensus 98 ~~l~~i~~iG~la~~~ig~~ll~~~ 122 (193)
+++++-.++|+++..+--++.++..
T Consensus 282 ~l~~~~~~ig~l~s~~s~~r~L~~~ 306 (309)
T PRK11026 282 LLLLVCSMIGWVAAWLATVQHLRRF 306 (309)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 3455556788888877777666654
No 102
>PHA01399 membrane protein P6
Probab=26.71 E-value=4.2e+02 Score=22.90 Aligned_cols=13 Identities=23% Similarity=0.641 Sum_probs=5.4
Q ss_pred HHHHHHHHHHHHH
Q 029429 94 LGFLTSILFIFFV 106 (193)
Q Consensus 94 lgl~~~l~~i~~i 106 (193)
+|++++++++.+.
T Consensus 58 ig~il~~il~~~~ 70 (242)
T PHA01399 58 IGIILIIILIIIA 70 (242)
T ss_pred ccHHHHHHHHHHH
Confidence 3444444444333
No 103
>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=26.54 E-value=4.1e+02 Score=22.76 Aligned_cols=94 Identities=16% Similarity=0.259 Sum_probs=0.0
Q ss_pred HHHHHHHHHHHHHHHHHHH-HHHhhh---------hhhhhhhhhh---hhhHHHHHHHHHHHHHHHHHHhhhhhHHHHHH
Q 029429 56 CVVLFPVAVTFLVTWWFIE-FVDSFF---------SPIYARLGVE---IFGLGFLTSILFIFFVGVFASSWLGATVFWLG 122 (193)
Q Consensus 56 LlvlLPi~iTi~Il~~l~~-~v~~~~---------~pl~~~l~~~---~pglgl~~~l~~i~~iG~la~~~ig~~ll~~~ 122 (193)
++.++=+++.++.++|.+. ++.-++ .|+.+++ .. -..++..+++++++.+=.+.-...+..+.+-.
T Consensus 1 ~~~~~~~~l~~~~~~~~~~~~~~p~~~a~~la~~~~p~~~~l-~~~~~~r~la~~l~~~~~~~il~l~~~~~~~~i~~~~ 79 (327)
T PF01594_consen 1 ILIILILLLLLFLFLWFISPFLLPFVLALVLAYLLNPLVRFL-RRFGIPRSLAALLVLLLLLLILVLLFYLIIPQIIQQI 79 (327)
T ss_pred ChHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-HHcCCCcHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_pred HHHhhhhhhhhHHHHHHHHHHHHhCCCCCCc
Q 029429 123 EWFIKRLPFMKHIYSASKQISAAISPDQNTS 153 (193)
Q Consensus 123 e~ll~rIP~V~sIYssiKqi~~~f~g~~~~~ 153 (193)
+++.+.+| ...+.+++..+.+....+..
T Consensus 80 ~~l~~~l~---~~~~~i~~~~~~~~~~~~~~ 107 (327)
T PF01594_consen 80 QSLIENLP---QYLDKIKSWLNDLPSWLQEL 107 (327)
T ss_pred HHHHHhhh---HHHHHhhhhhhccchhhhhh
No 104
>COG1380 Putative effector of murein hydrolase LrgA [General function prediction only]
Probab=26.42 E-value=2.6e+02 Score=22.14 Aligned_cols=16 Identities=19% Similarity=0.324 Sum_probs=9.9
Q ss_pred HHHHHHHHHHHHHhhh
Q 029429 65 TFLVTWWFIEFVDSFF 80 (193)
Q Consensus 65 Ti~Il~~l~~~v~~~~ 80 (193)
.+|.++++-+++.+++
T Consensus 13 ii~~~~~~G~~i~~~l 28 (128)
T COG1380 13 IILGFLFLGEWIASLL 28 (128)
T ss_pred HHHHHHHHHHHHHHHh
Confidence 4556666666666655
No 105
>cd02435 CCC1 CCC1. CCC1: This domain is present in the CCC1, an iron and manganese transporter of Saccharomyces cerevisiae. CCC1 is a transmembrane protein that is located in the vacuole and transfers the iron and manganese ions from the cytosol to the vacuole. This domain may be unique to certain fungi and plants.
Probab=26.27 E-value=3.2e+02 Score=23.60 Aligned_cols=48 Identities=21% Similarity=0.400 Sum_probs=28.9
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhhhhhhhhhhhhhHHHHHHHHHHHHHHHHHHhhhhh
Q 029429 49 SKKFMTGCVVLFPVAVTFLVTWWFIEFVDSFFSPIYARLGVEIFGLGFLTSILFIFFVGVFASSWLGA 116 (193)
Q Consensus 49 ~~~fl~GLlvlLPi~iTi~Il~~l~~~v~~~~~pl~~~l~~~~pglgl~~~l~~i~~iG~la~~~ig~ 116 (193)
--+++.|++-++|..+. .+. .......+++.++.++++|++....-++
T Consensus 162 lsf~lG~liPLlPy~~~---------------~~~-----~~a~~~si~l~~~aL~ilG~~~s~~s~~ 209 (241)
T cd02435 162 LSYFIGGLIPLLPYFFV---------------STV-----GEALLLSVIVTLVALFVFGYVKTWFTGG 209 (241)
T ss_pred HHHHHHHHHHHHHHHHc---------------cch-----hHHHHHHHHHHHHHHHHHHHHHHhhcCC
Confidence 36788888888885311 000 0011245666777788888887765544
No 106
>PF04971 Lysis_S: Lysis protein S ; InterPro: IPR007054 The lysis S protein is a cytotoxic protein forming holes in membranes causing cell lysis. The action of Lysis S is independent of the proportion of acidic phospholipids in the membrane [].
Probab=26.18 E-value=1.6e+02 Score=21.04 Aligned_cols=41 Identities=12% Similarity=0.477 Sum_probs=21.7
Q ss_pred HHHHHHHHHHhhhhhhhhhhhhhhhhHHHHHHHHHHHHHHHHHHhhhhh
Q 029429 68 VTWWFIEFVDSFFSPIYARLGVEIFGLGFLTSILFIFFVGVFASSWLGA 116 (193)
Q Consensus 68 Il~~l~~~v~~~~~pl~~~l~~~~pglgl~~~l~~i~~iG~la~~~ig~ 116 (193)
+.+|+++++|.+-. ..+-.+|++.. +++-+++++.+.++-.
T Consensus 17 ~~~wl~~lld~~sp-------~qW~aIGvi~g-i~~~~lt~ltN~YFK~ 57 (68)
T PF04971_consen 17 AGYWLLQLLDQFSP-------SQWAAIGVIGG-IFFGLLTYLTNLYFKI 57 (68)
T ss_pred HHHHHHHHHhccCc-------ccchhHHHHHH-HHHHHHHHHhHhhhhh
Confidence 45677777766541 22333455543 2345667777665443
No 107
>PRK10755 sensor protein BasS/PmrB; Provisional
Probab=26.17 E-value=4.2e+02 Score=22.75 Aligned_cols=16 Identities=19% Similarity=0.237 Sum_probs=8.9
Q ss_pred hhhHHHHHHHHHHHHh
Q 029429 131 FMKHIYSASKQISAAI 146 (193)
Q Consensus 131 ~V~sIYssiKqi~~~f 146 (193)
-++.+..++.++.+.+
T Consensus 115 E~~~l~~~~n~~~~~l 130 (356)
T PRK10755 115 EIEAVTSALNQLVSRL 130 (356)
T ss_pred HHHHHHHHHHHHHHHH
Confidence 4556666665555544
No 108
>KOG2675 consensus Adenylate cyclase-associated protein (CAP/Srv2p) [Cytoskeleton; Signal transduction mechanisms]
Probab=26.16 E-value=89 Score=29.98 Aligned_cols=12 Identities=42% Similarity=0.493 Sum_probs=5.6
Q ss_pred CCccHHHHHHHH
Q 029429 33 NSSTRKACYAVL 44 (193)
Q Consensus 33 ~~~~~~~~~~~~ 44 (193)
|+.-|.|+++++
T Consensus 260 ~k~~~~AlFaql 271 (480)
T KOG2675|consen 260 NKGGRGALFAQL 271 (480)
T ss_pred ccccHHHHHHHH
Confidence 334455555443
No 109
>PF00159 Hormone_3: Pancreatic hormone peptide; InterPro: IPR001955 Pancreatic hormone (PP) [] is a peptide synthesized in pancreatic islets of Langherhans, which acts as a regulator of pancreatic and gastrointestinal functions. The hormone is produced as a larger propeptide, which is enzymatically cleaved to yield the mature active peptide: this is 36 amino acids in length [] and has an amidated C terminus []. The hormone has a globular structure, residues 2-8 forming a left-handed poly-proline-II-like helix, residues 9-13 a beta turn, and 14-32 an alpha-helix,held close to the first helix by hydrophobic interactions []. Unlike glucagon, another peptide hormone, the structure of pancreatic peptide is preserved in aqueous solution []. Both N and C termini are required for activity: receptor binding and activation functions may reside in the N and C termini respectively []. Pancreatic hormone is part of a wider family of active peptides that includes: Neuropeptide Y (NPY) [], one of the most abundant peptides in the mammalian nervous system. NPY is implicated in the control of feeding and the secretion of the gonadotrophin-releasing hormone. Peptide YY (PYY) []. PPY is a gut peptide that inhibits exocrine pancreatic secretion, has a vasoconstrictory action and inhibits jejunal and colonic mobility. Various NPY and PYY-like polypeptides from fish and amphibians [, ]. Neuropeptide F (NPF) from invertebrates such as worms and snail. Skin peptide Tyr-Tyr (SPYY) from the frog Phyllomedusa bicolor. SPYY shows a large spectra of antibacterial and antifungal activity. All these peptides are 36 to 39 amino acids long. Like most active peptides, their C-terminal is amidated and they are synthesized as larger protein precursors.; GO: 0005179 hormone activity, 0005576 extracellular region; PDB: 1LJV_A 1BBA_A 1V1D_A 1PPT_A 2H3T_A 2H4B_A 2BF9_A 2H3S_B 1K8V_A 2DF0_A ....
Probab=26.01 E-value=1.2e+02 Score=19.01 Aligned_cols=26 Identities=15% Similarity=0.126 Sum_probs=17.1
Q ss_pred CCCCCCCCccHHHHHHHHHHHHHHHH
Q 029429 27 SPPHSPNSSTRKACYAVLQSWVSKKF 52 (193)
Q Consensus 27 ~~~~~~~~~~~~~~~~~~~~~i~~~f 52 (193)
+.|+.|..-+-++-+++..+.+++|+
T Consensus 3 ~~P~~P~~~aspeel~~Y~~~L~~Y~ 28 (36)
T PF00159_consen 3 SKPERPGDFASPEELAQYYAALRHYI 28 (36)
T ss_dssp SSSSSSSTTSSHHHHHHHHHHHHHHH
T ss_pred CCCCCCCCCCCHHHHHHHHHHHHHHH
Confidence 44555555555666778888887776
No 110
>PRK12780 fliR flagellar biosynthesis protein FliR; Reviewed
Probab=25.71 E-value=4.4e+02 Score=22.79 Aligned_cols=41 Identities=12% Similarity=0.155 Sum_probs=36.3
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhh
Q 029429 40 CYAVLQSWVSKKFMTGCVVLFPVAVTFLVTWWFIEFVDSFF 80 (193)
Q Consensus 40 ~~~~~~~~i~~~fl~GLlvlLPi~iTi~Il~~l~~~v~~~~ 80 (193)
......+.+.+.|..|+-.-+|+++...+....++.+++..
T Consensus 168 ~~~~~~~~~~~~f~~al~lAaP~i~~lll~~l~lGll~R~~ 208 (251)
T PRK12780 168 ALVQLVDQLSEAFTLALRIASPFIIYSVIVNLAVGLVNKLT 208 (251)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Confidence 34566777889999999999999999999999999998876
No 111
>PRK04125 murein hydrolase regulator LrgA; Provisional
Probab=25.71 E-value=1.8e+02 Score=23.38 Aligned_cols=14 Identities=14% Similarity=0.280 Sum_probs=6.1
Q ss_pred HHHHHHHHHHHhhh
Q 029429 67 LVTWWFIEFVDSFF 80 (193)
Q Consensus 67 ~Il~~l~~~v~~~~ 80 (193)
+.++++-+++..++
T Consensus 17 l~~~~lGe~i~~ll 30 (141)
T PRK04125 17 AAIMLISNIIASFL 30 (141)
T ss_pred HHHHHHHHHHHHHc
Confidence 34444444444443
No 112
>cd02434 Nodulin-21_like_3 Nodulin-21 and CCC1-related protein family. Nodulin-21_like_3: This is a family of proteins closely related to nodulin-21, a plant nodule-specific protein that may be involved in symbiotic nitrogen fixation. This family is also related to CCC1, a yeast vacuole transmembrane protein that functions as an iron and manganese transporter.
Probab=25.68 E-value=4.2e+02 Score=22.53 Aligned_cols=66 Identities=18% Similarity=0.260 Sum_probs=34.8
Q ss_pred CCccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhhhhhhhhhhhhhHHHHH-HHHHHHHHHHHHH
Q 029429 33 NSSTRKACYAVLQSWVSKKFMTGCVVLFPVAVTFLVTWWFIEFVDSFFSPIYARLGVEIFGLGFLT-SILFIFFVGVFAS 111 (193)
Q Consensus 33 ~~~~~~~~~~~~~~~i~~~fl~GLlvlLPi~iTi~Il~~l~~~v~~~~~pl~~~l~~~~pglgl~~-~l~~i~~iG~la~ 111 (193)
.||-+.++. .+-.+++.|++=++|..+.... + ...........++++ +++.++++|++..
T Consensus 132 ~~P~~aAl~-----sflsf~~ggliPLlp~~~~~~~----~----------~~~~~~~~~~~s~~~~~~~~L~~~G~~~~ 192 (225)
T cd02434 132 PSPLKTALV-----TFLSFLVFGIIPLLPYLLGLYY----Y----------SQKEIDSVFALSILIFVAFTLFLLGSFKS 192 (225)
T ss_pred CCHHHHHHH-----HHHHHHHHHHHHHHHHHHcccc----c----------ccccchhHHHHHHHHHHHHHHHHHHHHHH
Confidence 445555555 2346788898888886421100 0 000001111234444 6777788888877
Q ss_pred hhhhhH
Q 029429 112 SWLGAT 117 (193)
Q Consensus 112 ~~ig~~ 117 (193)
...++.
T Consensus 193 ~~~~~~ 198 (225)
T cd02434 193 KLYNGK 198 (225)
T ss_pred HhcCCc
Confidence 666663
No 113
>KOG3733 consensus Mucolipidin and related proteins (TRML subfamily of transient receptor potential proteins) [Inorganic ion transport and metabolism]
Probab=25.58 E-value=1.1e+02 Score=29.42 Aligned_cols=43 Identities=14% Similarity=0.178 Sum_probs=29.5
Q ss_pred cccccccccCCCCCCCCCCCCCCCCCCCCCccHHHHHHHHHHH
Q 029429 5 KESTSSSLSQGLTPHDPEDVPKSPPHSPNSSTRKACYAVLQSW 47 (193)
Q Consensus 5 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 47 (193)
.--.-||-++|.+|.+-......|.++++|+...+-|+|..++
T Consensus 5 ~~p~~~~~~~~~~p~~~~g~q~~ps~~~~~~~~ee~mrrklkf 47 (566)
T KOG3733|consen 5 VVPMPSSAGSGTAPPSVDGRQEQPSFPGSSAAQEERMRRKLKF 47 (566)
T ss_pred ccCCccccccCcCCCCCCCccCCCCCCCCCcchHHHHHHhhhh
Confidence 3445678888998887766666666777776666666666553
No 114
>PRK10983 putative inner membrane protein; Provisional
Probab=25.06 E-value=5.3e+02 Score=23.50 Aligned_cols=9 Identities=11% Similarity=0.770 Sum_probs=6.0
Q ss_pred Hhhhhhhhh
Q 029429 125 FIKRLPFMK 133 (193)
Q Consensus 125 ll~rIP~V~ 133 (193)
+++++|.++
T Consensus 112 ~l~~lp~ig 120 (368)
T PRK10983 112 WLNSIPLIG 120 (368)
T ss_pred HHHhCCccc
Confidence 466778764
No 115
>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=24.27 E-value=4e+02 Score=21.79 Aligned_cols=24 Identities=21% Similarity=0.146 Sum_probs=13.0
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHh
Q 029429 55 GCVVLFPVAVTFLVTWWFIEFVDS 78 (193)
Q Consensus 55 GLlvlLPi~iTi~Il~~l~~~v~~ 78 (193)
++.+-+|.++-+-++...|-.++.
T Consensus 66 ~~~~GiP~~lG~~~f~~~y~l~~~ 89 (153)
T PF11947_consen 66 AVFVGIPTALGVAVFVVFYYLKSR 89 (153)
T ss_pred HHHhchHHHHHHHHHHHHHHHHhc
Confidence 344556776666555555444443
No 116
>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=24.14 E-value=4.3e+02 Score=27.63 Aligned_cols=46 Identities=11% Similarity=0.110 Sum_probs=34.1
Q ss_pred HHHHHHHHHhhhhhHHHHHHHHHhhhhhhhhHHHHHHHHHHHHhCC
Q 029429 103 IFFVGVFASSWLGATVFWLGEWFIKRLPFMKHIYSASKQISAAISP 148 (193)
Q Consensus 103 i~~iG~la~~~ig~~ll~~~e~ll~rIP~V~sIYssiKqi~~~f~g 148 (193)
++++...-...+-|.+-++.|.++.-.=-+--||+++|.+++.|..
T Consensus 467 ~~lla~~~~s~lvryiTRFTeEiFa~lIs~IFI~eai~~L~~~f~~ 512 (900)
T TIGR00834 467 VLLLVATEGSFLVRYISRFTQEIFSFLISLIFIYETFSKLIKIFQE 512 (900)
T ss_pred HHHHHHHhHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHHHhc
Confidence 3344444334566777788888888777788899999999998864
No 117
>PRK09881 D-ala-D-ala transporter subunit; Provisional
Probab=24.02 E-value=5e+02 Score=22.83 Aligned_cols=34 Identities=9% Similarity=0.036 Sum_probs=20.3
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 029429 39 ACYAVLQSWVSKKFMTGCVVLFPVAVTFLVTWWF 72 (193)
Q Consensus 39 ~~~~~~~~~i~~~fl~GLlvlLPi~iTi~Il~~l 72 (193)
..++|+....+.++.-++...+=-.+.-.++..+
T Consensus 84 Dv~~rl~~g~~~sl~ia~~~~~is~iiG~~lG~~ 117 (296)
T PRK09881 84 DLFSRVLVGSQQSILAGLVVVAIAGMIGSLLGCL 117 (296)
T ss_pred cHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 4567777777777777766655444444444333
No 118
>cd00126 PAH Pancreatic Hormone domain, a regulator of pancreatic and gastrointestinal functions; neuropeptide Y (NPY)b, peptide YY (PYY), and pancreatic polypetide (PP) are closely related; propeptide is enzymatically cleaved to yield the mature active peptide with amidated C-terminal ends; receptor binding and activation functions may reside in the N- and C-termini respectively; occurs in neurons, intestinal endocrine cells, and pancreas; exist as monomers and dimers
Probab=23.62 E-value=1.6e+02 Score=18.43 Aligned_cols=26 Identities=12% Similarity=0.153 Sum_probs=17.4
Q ss_pred CCCCCCCCccHHHHHHHHHHHHHHHH
Q 029429 27 SPPHSPNSSTRKACYAVLQSWVSKKF 52 (193)
Q Consensus 27 ~~~~~~~~~~~~~~~~~~~~~i~~~f 52 (193)
+.|+.|.+-+=++-+++..+.++.|+
T Consensus 3 ~~P~~Pg~~a~~eel~~Y~~~L~~Yi 28 (36)
T cd00126 3 SKPENPGDDASPEELRQYLAALREYI 28 (36)
T ss_pred CCCCCCCCCCCHHHHHHHHHHHHHHH
Confidence 44555555555777778888887775
No 119
>PF14965 BRI3BP: Negative regulator of p53/TP53
Probab=23.38 E-value=3.6e+02 Score=22.68 Aligned_cols=74 Identities=15% Similarity=0.319 Sum_probs=37.9
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHhhhhhhhhhh-----------hh-----h------hhhHHHHHHHHHHHHHHHHHHhh
Q 029429 56 CVVLFPVAVTFLVTWWFIEFVDSFFSPIYARL-----------GV-----E------IFGLGFLTSILFIFFVGVFASSW 113 (193)
Q Consensus 56 LlvlLPi~iTi~Il~~l~~~v~~~~~pl~~~l-----------~~-----~------~pglgl~~~l~~i~~iG~la~~~ 113 (193)
+..++..+....+-||+..++-+++-+++..+ ++ . ...+=+..+.+.+++.|......
T Consensus 73 V~~~llw~~~aL~~YW~LSllLgl~~~lLgR~fW~lkv~lfl~~f~~Il~~~~~~~e~a~l~L~~lv~~~~l~g~~gs~~ 152 (177)
T PF14965_consen 73 VQTVLLWGAVALLAYWFLSLLLGLLFALLGRVFWLLKVVLFLLSFVYILQKYEGPPERAALLLCLLVLVCFLTGLVGSYW 152 (177)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCchHHHHHHHHHHHHHHHHccccCCCC
Confidence 33355555555666666666666554443211 00 0 11233444555566677766555
Q ss_pred hhhHHHHHHHHHhhhh
Q 029429 114 LGATVFWLGEWFIKRL 129 (193)
Q Consensus 114 ig~~ll~~~e~ll~rI 129 (193)
-+.++.+.++.+-.+|
T Consensus 153 ~~~~LE~kv~~LE~qv 168 (177)
T PF14965_consen 153 RSASLEAKVRHLERQV 168 (177)
T ss_pred CcccHHHHHHHHHHHH
Confidence 5555666666555544
No 120
>TIGR00267 conserved hypothetical protein TIGR00267. This family is represented in three of the first four completed archaeal genomes, with two members in A. fulgidus.
Probab=23.28 E-value=2.7e+02 Score=22.58 Aligned_cols=26 Identities=12% Similarity=0.383 Sum_probs=19.1
Q ss_pred HHHHHHHHHHHHHHHHHHhhhhhHHH
Q 029429 94 LGFLTSILFIFFVGVFASSWLGATVF 119 (193)
Q Consensus 94 lgl~~~l~~i~~iG~la~~~ig~~ll 119 (193)
+.+++.++.++++|++..+.-+++.+
T Consensus 121 ~s~~~~~~~L~ilG~~~a~~s~~~~~ 146 (169)
T TIGR00267 121 VTVLLTLIALLVLGVYLGRISRENIL 146 (169)
T ss_pred HHHHHHHHHHHHHHHHHHHHcCCcHH
Confidence 56677788888899988776666443
No 121
>PRK09108 type III secretion system protein HrcU; Validated
Probab=23.00 E-value=3.5e+02 Score=24.85 Aligned_cols=52 Identities=12% Similarity=0.082 Sum_probs=22.9
Q ss_pred CCCCCCccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhh
Q 029429 29 PHSPNSSTRKACYAVLQSWVSKKFMTGCVVLFPVAVTFLVTWWFIEFVDSFF 80 (193)
Q Consensus 29 ~~~~~~~~~~~~~~~~~~~i~~~fl~GLlvlLPi~iTi~Il~~l~~~v~~~~ 80 (193)
.|.|+++++....++-.-.=.+.+-+.+..+.-+.+..+...++++.+.+++
T Consensus 6 TE~pT~KKL~dARekGqV~kS~el~~a~~ll~~~~~l~~~~~~~~~~l~~~~ 57 (353)
T PRK09108 6 TEEPTEKKLKDARKDGEVAKSPDLTAAAVLLAALLVLTAAGSYLGDHLRALV 57 (353)
T ss_pred CCCCChhHHHHHHhcCCCCchHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 4555555544443322222223444444444444444444445555555544
No 122
>smart00309 PAH Pancreatic hormones / neuropeptide F / peptide YY family. Pancreatic hormone is a regulator of pancreatic and gastrointestinal functions.
Probab=22.33 E-value=1.8e+02 Score=18.26 Aligned_cols=26 Identities=12% Similarity=0.137 Sum_probs=15.2
Q ss_pred CCCCCCCCccHHHHHHHHHHHHHHHH
Q 029429 27 SPPHSPNSSTRKACYAVLQSWVSKKF 52 (193)
Q Consensus 27 ~~~~~~~~~~~~~~~~~~~~~i~~~f 52 (193)
+.|+.|.+.+=++=+++..+.++.|+
T Consensus 3 ~~P~~Pg~~a~~e~l~~Y~~~L~~Yi 28 (36)
T smart00309 3 SKPERPGDDASPEDLRQYLAALREYI 28 (36)
T ss_pred CCCCCCCCCCCHHHHHHHHHHHHHHH
Confidence 34444444444445777777777765
No 123
>PRK01821 hypothetical protein; Provisional
Probab=21.82 E-value=3.4e+02 Score=21.52 Aligned_cols=15 Identities=13% Similarity=0.235 Sum_probs=7.4
Q ss_pred HHHHHHHHHHHHhhh
Q 029429 66 FLVTWWFIEFVDSFF 80 (193)
Q Consensus 66 i~Il~~l~~~v~~~~ 80 (193)
++.++++-+.+...+
T Consensus 18 ll~~~~~Ge~i~~~l 32 (133)
T PRK01821 18 IYACLYAGIFIASLL 32 (133)
T ss_pred HHHHHHHHHHHHHHc
Confidence 344555555555444
No 124
>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=21.57 E-value=5.6e+02 Score=22.55 Aligned_cols=30 Identities=10% Similarity=-0.011 Sum_probs=15.7
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 029429 44 LQSWVSKKFMTGCVVLFPVAVTFLVTWWFI 73 (193)
Q Consensus 44 ~~~~i~~~fl~GLlvlLPi~iTi~Il~~l~ 73 (193)
..+.+++.+..=.+.-.-+++++-++.+..
T Consensus 234 ~~~~~~~~~~nP~~~a~~lgli~~~~~~~~ 263 (385)
T PF03547_consen 234 LKKSILKLFKNPPLIAIILGLIIGLIPPLR 263 (385)
T ss_pred HHHHHHHHHhCcHHHHHHHHHHHHHHHHhc
Confidence 344455555555555555555555554443
No 125
>PF15485 DUF4643: Domain of unknown function (DUF4643)
Probab=21.50 E-value=1.3e+02 Score=27.05 Aligned_cols=40 Identities=18% Similarity=0.137 Sum_probs=30.5
Q ss_pred ccccccCCCCCCCCCCCCCCCCCCCCCccHHHHHHHHHHH
Q 029429 8 TSSSLSQGLTPHDPEDVPKSPPHSPNSSTRKACYAVLQSW 47 (193)
Q Consensus 8 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 47 (193)
-.||.+++-.++.+-.+++.++.--.++.|.+.|.|+++.
T Consensus 104 ~v~S~~~as~~a~~s~P~~~p~P~~apkPk~SGWtRLKKq 143 (284)
T PF15485_consen 104 RVSSPSWASSPALPSGPHPCPVPKVAPKPKLSGWTRLKKQ 143 (284)
T ss_pred hccCCCcccCCCCCCCCCCCCCCcCCCCcccchHHHHHHH
Confidence 3466777777777777777777777777799999888876
No 126
>PF14257 DUF4349: Domain of unknown function (DUF4349)
Probab=21.12 E-value=2.8e+02 Score=23.66 Aligned_cols=9 Identities=0% Similarity=-0.153 Sum_probs=4.0
Q ss_pred HHHHHHHHH
Q 029429 39 ACYAVLQSW 47 (193)
Q Consensus 39 ~~~~~~~~~ 47 (193)
.++.++...
T Consensus 213 ~~~~~~~~a 221 (262)
T PF14257_consen 213 SFGSRFRDA 221 (262)
T ss_pred CcchHHHHH
Confidence 444444433
No 127
>PF00672 HAMP: HAMP domain; InterPro: IPR003660 The HAMP linker domain (present in Histidine kinases, Adenyl cyclases, Methyl-accepting proteins and Phosphatases) is an approximately 50-amino acid alpha-helical region. It is found in bacterial sensor and chemotaxis proteins and in eukaryotic histidine kinases. The bacterial proteins are usually integral membrane proteins and part of a two-component signal transduction pathway. One or several copies of the HAMP domain can be found in association with other domains, such as the histidine kinase domain, the bacterial chemotaxis sensory transducer domain, the PAS repeat, the EAL domain, the GGDEF domain, the protein phosphatase 2C-like domain, the guanylate cyclase domain, or the response regulatory domain. It has been suggested that the HAMP domain possesses a role of regulating the phosphorylation or methylation of homodimeric receptors by transmitting the conformational changes in periplasmic ligand-binding domains to cytoplasmic signalling kinase and methyl-acceptor domains.; GO: 0004871 signal transducer activity, 0007165 signal transduction, 0016021 integral to membrane; PDB: 3PJX_A 3PJW_A 3ZX6_B 2Y20_B 2Y0Q_D 2Y21_H 3ZRW_C 2L7H_B 2LFS_B 2L7I_B ....
Probab=20.85 E-value=1.1e+02 Score=19.93 Aligned_cols=22 Identities=9% Similarity=0.235 Sum_probs=10.0
Q ss_pred HHHHHHHHHHHHHHHhhhhhHH
Q 029429 97 LTSILFIFFVGVFASSWLGATV 118 (193)
Q Consensus 97 ~~~l~~i~~iG~la~~~ig~~l 118 (193)
++++++..+++++..+.+.+.+
T Consensus 6 ~~~~~~~~~~~~~~~~~i~~pl 27 (70)
T PF00672_consen 6 LIILLLSLLLAWLLARRITRPL 27 (70)
T ss_dssp HHHHHHHHHHHHH--HTTCCCH
T ss_pred HHHHHHHHHHHHHHHHHHHHHH
Confidence 3444445555565555555433
No 128
>PF07662 Nucleos_tra2_C: Na+ dependent nucleoside transporter C-terminus; InterPro: IPR011657 This entry consists of nucleoside transport proteins. Q62773 from SWISSPROT is a purine-specific Na+-nucleoside cotransporter localised to the bile canalicular membrane []. Q62674 from SWISSPROT is a Na+-dependent nucleoside transporter selective for pyrimidine nucleosides and adenosine. It also transports the anti-viral nucleoside analogues AZT and ddC []. This entry covers the C terminus of this family of transporters.; PDB: 3TIJ_A.
Probab=20.44 E-value=5.5e+02 Score=21.99 Aligned_cols=44 Identities=11% Similarity=0.168 Sum_probs=34.5
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhhhhhhhh
Q 029429 45 QSWVSKKFMTGCVVLFPVAVTFLVTWWFIEFVDSFFSPIYARLG 88 (193)
Q Consensus 45 ~~~i~~~fl~GLlvlLPi~iTi~Il~~l~~~v~~~~~pl~~~l~ 88 (193)
.+.+.+.-..|+=+.+=++..+..+.-++.++|+++..+-.++|
T Consensus 44 ~~A~~~Ga~~g~~la~~I~a~LIafvalial~N~~l~~ig~~~g 87 (210)
T PF07662_consen 44 FDAISNGALDGLKLALNIGAMLIAFVALIALLNGVLGWIGSLFG 87 (210)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHGGGT
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhcC
Confidence 34566778888888888888888888888999998877755555
No 129
>PF05767 Pox_A14: Poxvirus virion envelope protein A14; InterPro: IPR008785 This family consists of several Poxvirus virion envelope protein A14-like sequences. A14 is a component of the virion membrane and has been found to be an H1 phosphatase substrate in vivo and in vitro. A14 is hyperphosphorylated on serine residues in the absence of H1 expression [].; GO: 0019031 viral envelope
Probab=20.17 E-value=3.6e+02 Score=20.35 Aligned_cols=18 Identities=22% Similarity=0.309 Sum_probs=9.5
Q ss_pred HHHHHHHHHHHHHhhhhh
Q 029429 99 SILFIFFVGVFASSWLGA 116 (193)
Q Consensus 99 ~l~~i~~iG~la~~~ig~ 116 (193)
++.++..+|++.-..-||
T Consensus 53 I~giil~lG~~i~s~ygr 70 (92)
T PF05767_consen 53 ILGIILTLGIVIFSMYGR 70 (92)
T ss_pred HHHHHHHHHHHHHHHHhh
Confidence 444455566665444444
No 130
>COG0600 TauC ABC-type nitrate/sulfonate/bicarbonate transport system, permease component [Inorganic ion transport and metabolism]
Probab=20.08 E-value=5.9e+02 Score=22.23 Aligned_cols=108 Identities=10% Similarity=0.127 Sum_probs=58.6
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhhhhhhhhhhhhhHHHHHHHHHHHHHHHHHHhhhhhHH
Q 029429 39 ACYAVLQSWVSKKFMTGCVVLFPVAVTFLVTWWFIEFVDSFFSPIYARLGVEIFGLGFLTSILFIFFVGVFASSWLGATV 118 (193)
Q Consensus 39 ~~~~~~~~~i~~~fl~GLlvlLPi~iTi~Il~~l~~~v~~~~~pl~~~l~~~~pglgl~~~l~~i~~iG~la~~~ig~~l 118 (193)
.++......+.| .+.|++.-.=+.+.+-++-....+++..+.|++..+ ..+|-++++=++++-|-+|-.. ...--.+
T Consensus 58 ~L~~~~~~Sl~r-v~~Gf~la~~~gi~lgil~g~~~~~~~~l~P~i~~l-~~iP~lA~~Pl~ilwfG~g~~s-~i~i~~~ 134 (258)
T COG0600 58 ELFQHLLASLLR-VLLGFALAAVLGIPLGILMGLSRLLERLLDPLVQVL-RPIPPLALAPLAILWFGIGETS-KIVIAVL 134 (258)
T ss_pred hHHHHHHHHHHH-HHHHHHHHHHHHHHHHHHHHhHHHHHHHHhHHHHHH-hcCCHHHHHHHHHHHHhCCcch-HHHHHHH
Confidence 555555555555 455666666666666666677778888888877543 3355555555555555555444 1111111
Q ss_pred HHHHHHHhhhhhhhhHHHHHHHHHHHHhCCC
Q 029429 119 FWLGEWFIKRLPFMKHIYSASKQISAAISPD 149 (193)
Q Consensus 119 l~~~e~ll~rIP~V~sIYssiKqi~~~f~g~ 149 (193)
..++--.++-.=++|++=....++.+++.-+
T Consensus 135 ~~ffpi~int~~Gvr~v~~~~~~~ar~lgas 165 (258)
T COG0600 135 GAFFPILINTLDGVRSVDPDLLELARTLGAS 165 (258)
T ss_pred HHHHHHHHHHHHHHHhCCHHHHHHHHHcCCC
Confidence 2233333343444555555555666666533
No 131
>PRK10160 taurine transporter subunit; Provisional
Probab=20.07 E-value=5.7e+02 Score=22.01 Aligned_cols=64 Identities=9% Similarity=0.199 Sum_probs=28.0
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhhhhhhhhhhhhhHHHHHHHHHHH
Q 029429 39 ACYAVLQSWVSKKFMTGCVVLFPVAVTFLVTWWFIEFVDSFFSPIYARLGVEIFGLGFLTSILFIF 104 (193)
Q Consensus 39 ~~~~~~~~~i~~~fl~GLlvlLPi~iTi~Il~~l~~~v~~~~~pl~~~l~~~~pglgl~~~l~~i~ 104 (193)
.++..+...+.+.++ |+++-+-+++.+-++-.....+++++.|++..+ ..+|.+.++.++++.+
T Consensus 75 ~l~~~l~~Tl~~~~~-g~~ia~~ig~~lg~~~~~~~~~~~~l~~~~~~l-~~iP~i~~~pl~~~~f 138 (275)
T PRK10160 75 TLWQHLAASLTRIVL-ALLAAVVIGIPVGIAMGLSPTVRGILDPLIELY-RPVPPLAYLPLMVIWF 138 (275)
T ss_pred hHHHHHHHHHHHHHH-HHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHH-hhCCHHHHHHHHHHHH
Confidence 345555555554433 222222222222222223446777777766432 3345555443333333
No 132
>PRK10263 DNA translocase FtsK; Provisional
Probab=20.05 E-value=1.2e+03 Score=25.74 Aligned_cols=30 Identities=7% Similarity=-0.125 Sum_probs=18.5
Q ss_pred cHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 029429 36 TRKACYAVLQSWVSKKFMTGCVVLFPVAVT 65 (193)
Q Consensus 36 ~~~~~~~~~~~~i~~~fl~GLlvlLPi~iT 65 (193)
|.-+......+.+...+++-...++|+++.
T Consensus 62 Nl~GiVGA~LAD~L~~LFGl~AYLLP~LL~ 91 (1355)
T PRK10263 62 NLGGMPGAWLADTLFFIFGVMAYTIPVIIV 91 (1355)
T ss_pred cccchHHHHHHHHHHHHHhHHHHHHHHHHH
Confidence 444555555555556677777778886443
No 133
>PF08934 Rb_C: Rb C-terminal domain; InterPro: IPR015030 The Rb C-terminal domain is required for high-affinity binding to E2F-DP complexes and for maximal repression of E2F-responsive promoters, thereby acting as a growth suppressor by blocking the G1-S transition of the cell cycle. This domain has a strand-loop-helix structure, which directly interacts with both E2F1 and DP1, followed by a tail segment that lacks regular secondary structure []. ; PDB: 1H25_E 1GUX_B 3POM_A 1GH6_B 2AZE_C 1N4M_A 1O9K_H 4ELL_B 2R7G_C 4ELJ_A ....
Probab=20.04 E-value=38 Score=27.65 Aligned_cols=26 Identities=27% Similarity=0.142 Sum_probs=3.3
Q ss_pred CCCCCCCCCCCCCCCCC----CCccHHHHH
Q 029429 16 LTPHDPEDVPKSPPHSP----NSSTRKACY 41 (193)
Q Consensus 16 ~~~~~~~~~~~~~~~~~----~~~~~~~~~ 41 (193)
-+-+||++|+|.-|-|+ ||+.|..--
T Consensus 6 s~~~p~LSPiP~iprSPy~~~~SP~RVp~s 35 (155)
T PF08934_consen 6 STRPPTLSPIPHIPRSPYKFPNSPRRVPQS 35 (155)
T ss_dssp SSS-TT------------------------
T ss_pred cCCCCCCCCCCCCCCCcccCCCCCccccCc
Confidence 35579999999888887 999997654
Done!