Query psy7749
Match_columns 319
No_of_seqs 245 out of 471
Neff 3.3
Searched_HMMs 46136
Date Fri Aug 16 17:48:43 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy7749.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/7749hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PTZ00072 40S ribosomal protein 100.0 7E-78 1.5E-82 519.7 14.3 148 172-319 1-148 (148)
2 PRK08561 rps15p 30S ribosomal 100.0 1.5E-74 3.2E-79 501.2 15.2 151 169-319 1-151 (151)
3 KOG0400|consensus 100.0 3.2E-74 6.9E-79 493.1 10.0 151 169-319 1-151 (151)
4 PTZ00072 40S ribosomal protein 100.0 9.9E-58 2.2E-62 394.5 9.9 125 12-136 16-148 (148)
5 KOG0400|consensus 100.0 2.6E-53 5.6E-58 364.3 6.1 125 12-136 19-151 (151)
6 PRK08561 rps15p 30S ribosomal 100.0 6.9E-52 1.5E-56 359.7 10.7 125 12-136 19-151 (151)
7 PF08069 Ribosomal_S13_N: Ribo 100.0 7.9E-34 1.7E-38 214.8 3.0 60 169-228 1-60 (60)
8 COG0184 RpsO Ribosomal protein 99.9 5.5E-25 1.2E-29 177.5 5.0 88 212-315 1-88 (89)
9 COG0184 RpsO Ribosomal protein 99.9 7E-23 1.5E-27 165.4 4.5 83 33-131 5-87 (89)
10 cd00353 Ribosomal_S15p_S13e Ri 99.5 9.3E-14 2E-18 109.2 5.5 73 239-311 2-78 (80)
11 PF00312 Ribosomal_S15: Riboso 99.4 4.5E-14 9.9E-19 111.5 3.4 81 234-318 2-82 (83)
12 PF00312 Ribosomal_S15: Riboso 99.4 7.1E-14 1.5E-18 110.4 3.8 80 51-134 2-81 (83)
13 cd00353 Ribosomal_S15p_S13e Ri 99.4 1.7E-13 3.6E-18 107.8 5.5 73 56-128 2-78 (80)
14 cd00677 S15_NS1_EPRS_RNA-bind 98.8 5.3E-09 1.2E-13 74.2 5.1 46 253-298 1-46 (46)
15 cd00677 S15_NS1_EPRS_RNA-bind 98.8 7.2E-09 1.6E-13 73.5 5.1 46 70-115 1-46 (46)
16 PF08069 Ribosomal_S13_N: Ribo 98.6 6.3E-09 1.4E-13 79.5 0.4 34 12-45 19-60 (60)
17 TIGR00952 S15_bact ribosomal p 96.6 0.004 8.8E-08 50.6 5.2 46 256-301 26-71 (86)
18 TIGR00952 S15_bact ribosomal p 96.6 0.0045 9.7E-08 50.3 5.4 46 73-118 26-71 (86)
19 CHL00027 rps15 ribosomal prote 96.4 0.0057 1.2E-07 50.3 4.8 46 256-301 26-71 (90)
20 PRK05626 rpsO 30S ribosomal pr 96.3 0.0062 1.3E-07 49.8 4.6 45 257-301 30-74 (89)
21 CHL00027 rps15 ribosomal prote 96.3 0.0086 1.9E-07 49.3 5.5 47 72-118 25-71 (90)
22 PRK05626 rpsO 30S ribosomal pr 96.3 0.0071 1.5E-07 49.4 4.8 46 73-118 29-74 (89)
23 PTZ00119 40S ribosomal protein 95.5 0.019 4.1E-07 55.9 4.8 44 258-301 133-176 (302)
24 PTZ00119 40S ribosomal protein 95.4 0.023 5.1E-07 55.2 4.9 98 54-156 108-211 (302)
25 COG2257 Uncharacterized homolo 93.5 0.31 6.8E-06 40.6 6.8 70 188-274 20-89 (92)
26 COG2257 Uncharacterized homolo 85.2 2.2 4.8E-05 35.7 5.4 59 26-91 31-89 (92)
27 PF13565 HTH_32: Homeodomain-l 80.9 2.2 4.7E-05 31.8 3.5 44 198-243 32-77 (77)
28 TIGR00789 flhB_rel flhB C-term 80.7 3 6.5E-05 33.6 4.4 60 15-81 15-74 (82)
29 TIGR00789 flhB_rel flhB C-term 76.5 6.6 0.00014 31.6 5.2 60 189-265 16-75 (82)
30 PF13276 HTH_21: HTH-like doma 74.5 5.5 0.00012 29.0 3.9 51 199-253 4-57 (60)
31 COG3328 Transposase and inacti 68.5 4 8.8E-05 41.0 2.7 48 177-228 69-116 (379)
32 PF00292 PAX: 'Paired box' dom 66.0 3.2 6.9E-05 36.1 1.3 31 197-227 18-48 (125)
33 PRK01322 6-carboxyhexanoate--C 64.8 6.1 0.00013 37.9 3.0 77 171-266 6-111 (242)
34 PF07750 GcrA: GcrA cell cycle 64.4 4.9 0.00011 35.8 2.2 25 199-223 5-29 (162)
35 PHA02591 hypothetical protein; 61.0 6.1 0.00013 32.6 1.9 28 195-222 42-69 (83)
36 PF11740 KfrA_N: Plasmid repli 57.7 16 0.00036 29.5 4.0 58 196-260 1-67 (120)
37 PF00356 LacI: Bacterial regul 56.6 5.2 0.00011 28.9 0.8 37 211-250 9-45 (46)
38 PF13361 UvrD_C: UvrD-like hel 53.0 8.6 0.00019 34.3 1.8 43 199-249 61-103 (351)
39 COG1202 Superfamily II helicas 52.8 7.8 0.00017 42.2 1.7 46 200-266 754-799 (830)
40 TIGR00328 flhB flagellar biosy 52.7 37 0.0008 33.8 6.2 62 189-267 278-340 (347)
41 KOG1802|consensus 52.2 7.5 0.00016 42.8 1.5 50 198-260 709-760 (935)
42 PRK06298 type III secretion sy 51.9 37 0.00079 34.0 6.1 73 15-94 278-352 (356)
43 PRK15364 pathogenicity island 51.2 39 0.00084 31.8 5.7 81 197-285 77-162 (196)
44 PF13276 HTH_21: HTH-like doma 48.5 15 0.00032 26.6 2.1 33 34-70 25-57 (60)
45 PHA02517 putative transposase 48.1 21 0.00046 32.6 3.5 48 198-250 28-78 (277)
46 PRK13902 alaS alanyl-tRNA synt 47.6 31 0.00068 38.4 5.3 55 204-264 419-474 (900)
47 COG1964 Predicted Fe-S oxidore 46.4 49 0.0011 34.8 6.2 83 170-277 64-149 (475)
48 PRK05702 flhB flagellar biosyn 45.8 59 0.0013 32.5 6.5 67 189-272 285-352 (359)
49 PF15652 Tox-SHH: HNH/Endo VII 44.3 15 0.00033 31.2 1.9 34 193-226 63-96 (100)
50 PF00872 Transposase_mut: Tran 43.7 15 0.00033 36.1 2.0 38 191-229 94-132 (381)
51 PF02899 Phage_int_SAM_1: Phag 43.5 21 0.00046 26.2 2.3 32 190-221 38-69 (84)
52 PRK06298 type III secretion sy 43.4 71 0.0015 32.0 6.6 71 189-276 279-351 (356)
53 smart00354 HTH_LACI helix_turn 43.1 18 0.00039 27.2 1.9 39 211-252 10-48 (70)
54 PF13551 HTH_29: Winged helix- 43.0 63 0.0014 24.9 5.0 51 191-247 54-112 (112)
55 PF13936 HTH_38: Helix-turn-he 42.5 13 0.00027 26.1 0.9 26 196-222 5-30 (44)
56 TIGR00328 flhB flagellar biosy 42.4 60 0.0013 32.3 5.9 63 15-84 277-340 (347)
57 PF06983 3-dmu-9_3-mt: 3-demet 42.4 14 0.0003 30.6 1.3 32 197-229 81-112 (116)
58 PRK05702 flhB flagellar biosyn 42.0 57 0.0012 32.6 5.7 67 16-89 285-352 (359)
59 cd01106 HTH_TipAL-Mta Helix-Tu 39.6 30 0.00065 27.7 2.8 38 187-224 30-69 (103)
60 TIGR01204 bioW 6-carboxyhexano 39.3 21 0.00046 34.1 2.2 62 197-267 15-104 (232)
61 PF10593 Z1: Z1 domain; Inter 39.3 8.4 0.00018 36.0 -0.5 58 169-226 172-233 (239)
62 PF02885 Glycos_trans_3N: Glyc 39.0 26 0.00055 26.3 2.2 28 195-222 14-41 (66)
63 TIGR02884 spore_pdaA delta-lac 38.5 42 0.0009 30.5 3.9 153 39-218 58-220 (224)
64 KOG3862|consensus 37.1 49 0.0011 33.0 4.3 51 197-253 26-76 (327)
65 smart00845 GatB_Yqey GatB doma 36.5 1.1E+02 0.0023 26.3 5.9 64 195-265 38-102 (147)
66 KOG3517|consensus 36.2 24 0.00051 34.9 2.0 31 198-228 22-52 (334)
67 PF11338 DUF3140: Protein of u 35.9 68 0.0015 26.9 4.4 38 50-89 37-75 (92)
68 PF02637 GatB_Yqey: GatB domai 35.3 69 0.0015 27.2 4.5 64 195-265 39-103 (148)
69 TIGR03859 PQQ_PqqD coenzyme PQ 32.8 30 0.00064 27.2 1.7 52 197-248 28-79 (81)
70 COG3415 Transposase and inacti 32.3 97 0.0021 27.4 5.0 70 177-253 48-117 (138)
71 PF13592 HTH_33: Winged helix- 31.8 29 0.00063 25.6 1.5 37 214-254 6-42 (60)
72 PRK05537 bifunctional sulfate 31.5 38 0.00083 35.5 2.8 55 96-157 347-401 (568)
73 cd08045 TAF4 TATA Binding Prot 31.3 62 0.0013 29.5 3.8 34 233-267 48-81 (212)
74 COG3028 Uncharacterized protei 30.3 62 0.0013 30.3 3.6 65 212-290 26-90 (187)
75 PF12990 DUF3874: Domain of un 30.2 32 0.00068 27.4 1.5 35 213-248 26-60 (73)
76 cd04766 HTH_HspR Helix-Turn-He 30.2 1.7E+02 0.0036 23.0 5.6 35 189-223 32-69 (91)
77 PF06676 DUF1178: Protein of u 30.0 1.6E+02 0.0035 26.4 6.0 116 12-141 11-137 (148)
78 PRK09108 type III secretion sy 29.6 1.2E+02 0.0026 30.3 5.7 67 15-88 279-345 (353)
79 COG2445 Uncharacterized conser 29.5 81 0.0018 27.7 4.1 60 217-281 50-109 (138)
80 PF00196 GerE: Bacterial regul 29.5 45 0.00098 23.9 2.1 25 196-222 4-28 (58)
81 PF06056 Terminase_5: Putative 29.4 36 0.00079 25.6 1.6 26 200-229 1-26 (58)
82 PF07508 Recombinase: Recombin 29.4 74 0.0016 24.5 3.4 48 198-246 3-52 (102)
83 TIGR01404 FlhB_rel_III type II 29.4 96 0.0021 30.8 5.0 60 15-81 276-336 (342)
84 cd03750 proteasome_alpha_type_ 29.1 37 0.00079 30.8 1.9 127 69-221 74-206 (227)
85 COG3028 Uncharacterized protei 28.8 68 0.0015 30.0 3.6 51 51-108 41-91 (187)
86 PF09860 DUF2087: Uncharacteri 28.7 34 0.00074 26.9 1.4 21 130-150 49-69 (71)
87 cd01104 HTH_MlrA-CarA Helix-Tu 28.3 92 0.002 22.4 3.6 31 192-222 35-67 (68)
88 smart00422 HTH_MERR helix_turn 28.3 1E+02 0.0022 22.1 3.8 33 191-223 34-68 (70)
89 cd05116 PTKc_Syk Catalytic dom 28.3 86 0.0019 27.1 4.0 77 26-114 175-256 (257)
90 cd01392 HTH_LacI Helix-turn-he 28.0 33 0.00072 23.5 1.2 39 211-252 7-45 (52)
91 cd08045 TAF4 TATA Binding Prot 27.9 77 0.0017 28.9 3.8 33 50-83 48-80 (212)
92 PF02796 HTH_7: Helix-turn-hel 27.6 34 0.00074 23.9 1.2 26 196-222 6-31 (45)
93 PRK13413 mpi multiple promoter 27.5 52 0.0011 29.0 2.6 61 175-249 139-199 (200)
94 PF11338 DUF3140: Protein of u 27.3 1.3E+02 0.0028 25.3 4.6 38 233-272 37-75 (92)
95 smart00733 Mterf Mitochondrial 27.3 73 0.0016 18.7 2.5 27 188-214 5-31 (31)
96 PRK03996 proteasome subunit al 26.8 54 0.0012 29.9 2.6 151 69-245 83-238 (241)
97 TIGR03683 A-tRNA_syn_arch alan 26.7 99 0.0021 34.6 5.0 55 204-264 423-478 (902)
98 COG2445 Uncharacterized conser 26.7 98 0.0021 27.2 4.0 58 35-97 51-108 (138)
99 PF04947 Pox_VLTF3: Poxvirus L 26.6 1.7E+02 0.0037 26.5 5.7 36 196-247 31-66 (171)
100 cd00592 HTH_MerR-like Helix-Tu 26.3 1E+02 0.0022 24.1 3.8 38 187-224 29-68 (100)
101 smart00550 Zalpha Z-DNA-bindin 26.3 80 0.0017 23.9 3.0 49 196-251 2-54 (68)
102 PRK12721 secretion system appa 25.8 1.6E+02 0.0034 29.5 5.8 62 15-83 277-339 (349)
103 PRK05290 hybrid cluster protei 25.7 1.1E+02 0.0024 32.7 4.9 169 70-263 77-255 (546)
104 PF01522 Polysacc_deac_1: Poly 25.0 14 0.0003 28.9 -1.4 93 37-141 24-122 (123)
105 TIGR02764 spore_ybaN_pdaB poly 24.9 78 0.0017 27.4 3.1 22 120-141 102-123 (191)
106 PRK13902 alaS alanyl-tRNA synt 24.6 73 0.0016 35.6 3.5 41 34-80 433-473 (900)
107 COG2771 CsgD DNA-binding HTH d 24.5 75 0.0016 22.1 2.5 29 195-225 4-32 (65)
108 PF04947 Pox_VLTF3: Poxvirus L 24.1 36 0.00077 30.8 0.9 57 7-65 8-67 (171)
109 PF11181 YflT: Heat induced st 23.7 53 0.0011 26.6 1.7 35 197-231 8-42 (103)
110 PF13411 MerR_1: MerR HTH fami 23.5 61 0.0013 23.4 1.9 36 189-224 31-68 (69)
111 COG2046 MET3 ATP sulfurylase ( 23.4 71 0.0015 33.0 2.9 87 126-222 294-391 (397)
112 PF11829 DUF3349: Protein of u 23.2 2.4E+02 0.0051 23.8 5.5 21 196-216 36-56 (96)
113 COG5352 Uncharacterized protei 23.1 57 0.0012 29.8 2.0 24 199-222 5-28 (169)
114 PRK12772 bifunctional flagella 22.7 1.4E+02 0.003 31.9 5.0 61 15-82 540-601 (609)
115 PRK12773 flhB flagellar biosyn 22.6 1.8E+02 0.0039 31.9 5.8 61 15-82 576-637 (646)
116 PLN02389 biotin synthase 22.1 1.1E+02 0.0023 30.8 3.8 38 190-227 110-147 (379)
117 PRK14810 formamidopyrimidine-D 21.9 2.2E+02 0.0048 27.1 5.8 71 186-268 131-210 (272)
118 KOG4279|consensus 21.7 78 0.0017 35.9 3.0 44 40-83 1002-1048(1226)
119 TIGR01293 Kv_beta voltage-depe 21.6 1.3E+02 0.0029 28.3 4.2 60 202-263 251-316 (317)
120 cd04398 RhoGAP_fRGD1 RhoGAP_fR 21.6 2.4E+02 0.0052 24.7 5.6 95 53-166 2-101 (192)
121 PF14057 GGGtGRT: GGGtGRT prot 21.5 43 0.00094 33.2 1.0 21 165-185 278-298 (328)
122 PRK12721 secretion system appa 21.4 2E+02 0.0042 28.8 5.5 62 188-266 277-339 (349)
123 cd03753 proteasome_alpha_type_ 20.9 74 0.0016 28.4 2.3 119 69-207 74-193 (213)
124 TIGR00180 parB_part ParB-like 20.8 2.8E+02 0.006 24.5 5.8 62 197-272 104-168 (187)
125 PF00690 Cation_ATPase_N: Cati 20.7 49 0.0011 24.5 0.9 53 193-246 1-53 (69)
126 PRK09108 type III secretion sy 20.5 2.6E+02 0.0056 28.1 6.1 66 189-271 280-345 (353)
127 PF10752 DUF2533: Protein of u 20.5 79 0.0017 26.3 2.1 20 198-217 50-69 (84)
128 cd04786 HTH_MerR-like_sg7 Heli 20.4 5.3E+02 0.012 22.0 7.3 40 185-224 28-69 (131)
129 PF13495 Phage_int_SAM_4: Phag 20.2 84 0.0018 23.3 2.1 30 194-223 39-69 (85)
130 KOG4279|consensus 20.2 86 0.0019 35.6 2.9 51 216-266 987-1048(1226)
131 cd03527 RuBisCO_small Ribulose 20.1 84 0.0018 26.4 2.3 21 196-216 12-32 (99)
No 1
>PTZ00072 40S ribosomal protein S13; Provisional
Probab=100.00 E-value=7e-78 Score=519.68 Aligned_cols=148 Identities=76% Similarity=1.159 Sum_probs=147.2
Q ss_pred cCCCCCCCCCcCCCCCCCCCCCccCChhHHHHHHHHHhhCCCCccchhhhhhcccCCCceeeeccchHHHHHHHcCCCCC
Q psy7749 172 MHTPGKGISKSALPYRRSVPNWLKLTSEDVKDHIFKLSKKGLTPSQIGVILRDSHGVAQVRFVSGNKILRIMKAMGLAPN 251 (319)
Q Consensus 172 Mhs~~kG~S~S~~Py~~~~P~Wl~~s~eEVe~~IvkLaKkG~tpSqIG~iLRD~~GIP~VK~vtGkkI~~ILk~nGlape 251 (319)
||++|||+|+|++||++++|+|+++++||||++||+|||+|+||||||++|||||||||||.|||+||++||++||+||+
T Consensus 1 Mhs~gkG~S~S~~P~~r~~P~w~~~~~eeVe~~I~klaKkG~~pSqIG~iLRD~~gi~~vk~vtG~kI~rILk~~Glap~ 80 (148)
T PTZ00072 1 MYGKGKGISSSALPYRRKPPSWLKLSSSEVEDQICKLAKKGLTPSQIGVILRDSMGIPQVKNVTGSKILRILKKNGLAPE 80 (148)
T ss_pred CCCCCCCCCCCCCCCCCCCCchhcCCHHHHHHHHHHHHHCCCCHhHhhhhhhhccCccceeeccchHHHHHHHhcCCCCC
Confidence 89999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred ChhhHHHHHHHHHHHHHHHhhhcCcccchhhHHHHHHhhhhhHHHHHhcCcCCCCCccchhhhhhhhC
Q psy7749 252 LPEDLYCLIKKAVAIRKHLERSRKDKDSKFRLILVESRIHRLARYYKTKAVLPPNWKYESATASALVA 319 (319)
Q Consensus 252 IPEDL~~LIkKAv~iRKHLe~n~KD~~sKr~L~LiESkI~RL~rYYK~~~~LP~~WkY~~~tA~~lv~ 319 (319)
||||||+||||||+||||||+|+||+||||+|||||||||||+||||++++||+||+|+|+||++||+
T Consensus 81 iPeDly~LikKAv~iRkHLe~n~kD~~sK~~LiLiESkI~RL~rYYk~~~~lP~~WkY~~~tA~~Lv~ 148 (148)
T PTZ00072 81 IPEDLYFLIKKAVSIRKHLEKNRKDKDSKFRLILVESRIHRLARYYKRTKQLPPNWKYESSTASALVA 148 (148)
T ss_pred CchHHHHHHHHHHHHHHHHHHcccchhhhHHHHHHHHHHHHHHHHHhhccCCCCCCcCCHHHHHHHhC
Confidence 99999999999999999999999999999999999999999999999999999999999999999985
No 2
>PRK08561 rps15p 30S ribosomal protein S15P; Reviewed
Probab=100.00 E-value=1.5e-74 Score=501.19 Aligned_cols=151 Identities=47% Similarity=0.836 Sum_probs=150.2
Q ss_pred hhccCCCCCCCCCcCCCCCCCCCCCccCChhHHHHHHHHHhhCCCCccchhhhhhcccCCCceeeeccchHHHHHHHcCC
Q psy7749 169 MGRMHTPGKGISKSALPYRRSVPNWLKLTSEDVKDHIFKLSKKGLTPSQIGVILRDSHGVAQVRFVSGNKILRIMKAMGL 248 (319)
Q Consensus 169 MaRMhs~~kG~S~S~~Py~~~~P~Wl~~s~eEVe~~IvkLaKkG~tpSqIG~iLRD~~GIP~VK~vtGkkI~~ILk~nGl 248 (319)
|||||++|||+|+|++||++++|+|+++++||||++||+|||+|+||||||++||||||||+||.|||+||++||++||+
T Consensus 1 M~rmh~~~kG~S~S~~P~~~~~P~W~~~~~eeve~~I~~lakkG~~pSqIG~~LRD~~gip~Vk~vtG~ki~~iLk~~gl 80 (151)
T PRK08561 1 MARMHTRRRGKSGSTRPARTEPPEWVDYSPEEIEELVVELAKQGYSPSMIGIILRDQYGIPDVKLITGKKITEILEENGL 80 (151)
T ss_pred CCCcCCCCCCCCCCCCCCCCCCCccccCCHHHHHHHHHHHHHCCCCHHHhhhhHhhccCCCceeeeccchHHHHHHHcCC
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CCCChhhHHHHHHHHHHHHHHHhhhcCcccchhhHHHHHHhhhhhHHHHHhcCcCCCCCccchhhhhhhhC
Q psy7749 249 APNLPEDLYCLIKKAVAIRKHLERSRKDKDSKFRLILVESRIHRLARYYKTKAVLPPNWKYESATASALVA 319 (319)
Q Consensus 249 apeIPEDL~~LIkKAv~iRKHLe~n~KD~~sKr~L~LiESkI~RL~rYYK~~~~LP~~WkY~~~tA~~lv~ 319 (319)
+|+|||||||||+||++|++||+.|+||+||||+|+++|||+|||++||+++++||+||+|+|+||++||+
T Consensus 81 ~p~iPEDL~~L~~ri~~L~~HL~~nkKD~~skRgL~~~~skrrRLl~Yyk~~~~LP~~WkY~~~~A~~lv~ 151 (151)
T PRK08561 81 APEIPEDLRNLIKKAVNLRKHLEENPKDLHNKRGLQLIESKIRRLVKYYKRTGVLPADWRYSPETAELLVS 151 (151)
T ss_pred CCCCcHHHHHHHHHHHHHHHHHHhCCCcchhHHHHHHHHHHHHHHHHHHHhcCCCCCCCcCCHHHHHHHhC
Confidence 99999999999999999999999999999999999999999999999999999999999999999999985
No 3
>KOG0400|consensus
Probab=100.00 E-value=3.2e-74 Score=493.11 Aligned_cols=151 Identities=86% Similarity=1.329 Sum_probs=150.2
Q ss_pred hhccCCCCCCCCCcCCCCCCCCCCCccCChhHHHHHHHHHhhCCCCccchhhhhhcccCCCceeeeccchHHHHHHHcCC
Q psy7749 169 MGRMHTPGKGISKSALPYRRSVPNWLKLTSEDVKDHIFKLSKKGLTPSQIGVILRDSHGVAQVRFVSGNKILRIMKAMGL 248 (319)
Q Consensus 169 MaRMhs~~kG~S~S~~Py~~~~P~Wl~~s~eEVe~~IvkLaKkG~tpSqIG~iLRD~~GIP~VK~vtGkkI~~ILk~nGl 248 (319)
|||||++|||+|+|++||++++|+|+++++|||.|+|++|||||+||||||++|||+||||+|+.|||+||+|||+.||+
T Consensus 1 MgrMHs~GKGis~SAlPY~r~~PtWlK~~~ddvkeqI~K~akKGltpsqIGviLRDshGi~q~r~v~G~kI~Rilk~~Gl 80 (151)
T KOG0400|consen 1 MGRMHSPGKGISGSALPYRRSVPTWLKLTADDVKEQIYKLAKKGLTPSQIGVILRDSHGIGQVRFVTGNKILRILKSNGL 80 (151)
T ss_pred CCcccCCCcccccCccccccCCcHHHhcCHHHHHHHHHHHHHcCCChhHceeeeecccCcchhheechhHHHHHHHHcCC
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CCCChhhHHHHHHHHHHHHHHHhhhcCcccchhhHHHHHHhhhhhHHHHHhcCcCCCCCccchhhhhhhhC
Q psy7749 249 APNLPEDLYCLIKKAVAIRKHLERSRKDKDSKFRLILVESRIHRLARYYKTKAVLPPNWKYESATASALVA 319 (319)
Q Consensus 249 apeIPEDL~~LIkKAv~iRKHLe~n~KD~~sKr~L~LiESkI~RL~rYYK~~~~LP~~WkY~~~tA~~lv~ 319 (319)
+||||||||+||+|||++|||||+|+||+|+|||||||||||||||||||++++||+||||++.||+.||+
T Consensus 81 ~PeiPeDLy~likkAv~iRkHLer~RKD~d~K~RLILveSRihRlARYYk~~~~lPp~WKyes~tas~lv~ 151 (151)
T KOG0400|consen 81 APEIPEDLYHLIKKAVAIRKHLERNRKDKDAKFRLILVESRIHRLARYYKTKMVLPPNWKYESATASALVA 151 (151)
T ss_pred CCCCcHHHHHHHHHHHHHHHHHHHhccccccceEEEeehHHHHHHHHHHHhcccCCCCCCcchhhHhhhhC
Confidence 99999999999999999999999999999999999999999999999999999999999999999999986
No 4
>PTZ00072 40S ribosomal protein S13; Provisional
Probab=100.00 E-value=9.9e-58 Score=394.50 Aligned_cols=125 Identities=65% Similarity=1.002 Sum_probs=120.8
Q ss_pred CCCCCCceeecc-----cccccccchh---hhhhhhccccCCCceeeeccchHHHHHHHcCCCCCChhhHHHHHHHHHHH
Q psy7749 12 TTLGPNWFIKSG-----FYCNLKTDIV---LFCVILRDSHGVAQVRFVSGNKILRIMKAMGLAPNLPEDLYCLIKKAVAI 83 (319)
Q Consensus 12 ~~~~p~w~~~s~-----~~~~~~~~~~---~IG~iLRD~~GIp~VK~vtGkkI~~ILk~nGlapeIPEDL~~LikKAv~l 83 (319)
.+.+|+|++.|+ .+|++++++. |||++|||||||||||.|||+||++||++||+||+||||||+||||||+|
T Consensus 16 ~r~~P~w~~~~~eeVe~~I~klaKkG~~pSqIG~iLRD~~gi~~vk~vtG~kI~rILk~~Glap~iPeDly~LikKAv~i 95 (148)
T PTZ00072 16 RRKPPSWLKLSSSEVEDQICKLAKKGLTPSQIGVILRDSMGIPQVKNVTGSKILRILKKNGLAPEIPEDLYFLIKKAVSI 95 (148)
T ss_pred CCCCCchhcCCHHHHHHHHHHHHHCCCCHhHhhhhhhhccCccceeeccchHHHHHHHhcCCCCCCchHHHHHHHHHHHH
Confidence 467999999988 7888888885 99999999999999999999999999999999999999999999999999
Q ss_pred HHHHhhccCcccchhhHhHHHHhhhhhHHHHHhcCcCCCCCccchHHHHHHHh
Q psy7749 84 RKHLERSRKDKDSKFRLILVESRIHRLARYYKTKAVLPPNWKYESATASAFIL 136 (319)
Q Consensus 84 RkHLe~n~kDk~~Kr~L~LiESkI~RL~rYYk~~~~LP~~WkY~~~tA~~lv~ 136 (319)
|||||+|+||+||||+|||||||||||+||||++++||+||+|+|+||++||+
T Consensus 96 RkHLe~n~kD~~sK~~LiLiESkI~RL~rYYk~~~~lP~~WkY~~~tA~~Lv~ 148 (148)
T PTZ00072 96 RKHLEKNRKDKDSKFRLILVESRIHRLARYYKRTKQLPPNWKYESSTASALVA 148 (148)
T ss_pred HHHHHHcccchhhhHHHHHHHHHHHHHHHHHhhccCCCCCCcCCHHHHHHHhC
Confidence 99999999999999999999999999999999999999999999999999985
No 5
>KOG0400|consensus
Probab=100.00 E-value=2.6e-53 Score=364.30 Aligned_cols=125 Identities=70% Similarity=1.055 Sum_probs=118.1
Q ss_pred CCCCCCceeecc-----cccccccch---hhhhhhhccccCCCceeeeccchHHHHHHHcCCCCCChhhHHHHHHHHHHH
Q psy7749 12 TTLGPNWFIKSG-----FYCNLKTDI---VLFCVILRDSHGVAQVRFVSGNKILRIMKAMGLAPNLPEDLYCLIKKAVAI 83 (319)
Q Consensus 12 ~~~~p~w~~~s~-----~~~~~~~~~---~~IG~iLRD~~GIp~VK~vtGkkI~~ILk~nGlapeIPEDL~~LikKAv~l 83 (319)
.+.+|+||+.++ .++++++++ +|||++|||+||||+|++|||+||+|||+.||++|+||||||+||+|||++
T Consensus 19 ~r~~PtWlK~~~ddvkeqI~K~akKGltpsqIGviLRDshGi~q~r~v~G~kI~Rilk~~Gl~PeiPeDLy~likkAv~i 98 (151)
T KOG0400|consen 19 RRSVPTWLKLTADDVKEQIYKLAKKGLTPSQIGVILRDSHGIGQVRFVTGNKILRILKSNGLAPEIPEDLYHLIKKAVAI 98 (151)
T ss_pred ccCCcHHHhcCHHHHHHHHHHHHHcCCChhHceeeeecccCcchhheechhHHHHHHHHcCCCCCCcHHHHHHHHHHHHH
Confidence 478999999988 455555555 489999999999999999999999999999999999999999999999999
Q ss_pred HHHHhhccCcccchhhHhHHHHhhhhhHHHHHhcCcCCCCCccchHHHHHHHh
Q psy7749 84 RKHLERSRKDKDSKFRLILVESRIHRLARYYKTKAVLPPNWKYESATASAFIL 136 (319)
Q Consensus 84 RkHLe~n~kDk~~Kr~L~LiESkI~RL~rYYk~~~~LP~~WkY~~~tA~~lv~ 136 (319)
|||||+|+||+|+||||||||||||||+||||++.+||+||||++.||++||+
T Consensus 99 RkHLer~RKD~d~K~RLILveSRihRlARYYk~~~~lPp~WKyes~tas~lv~ 151 (151)
T KOG0400|consen 99 RKHLERNRKDKDAKFRLILVESRIHRLARYYKTKMVLPPNWKYESATASALVA 151 (151)
T ss_pred HHHHHHhccccccceEEEeehHHHHHHHHHHHhcccCCCCCCcchhhHhhhhC
Confidence 99999999999999999999999999999999999999999999999999985
No 6
>PRK08561 rps15p 30S ribosomal protein S15P; Reviewed
Probab=100.00 E-value=6.9e-52 Score=359.74 Aligned_cols=125 Identities=43% Similarity=0.730 Sum_probs=120.5
Q ss_pred CCCCCCceeecc-----cccccccch---hhhhhhhccccCCCceeeeccchHHHHHHHcCCCCCChhhHHHHHHHHHHH
Q psy7749 12 TTLGPNWFIKSG-----FYCNLKTDI---VLFCVILRDSHGVAQVRFVSGNKILRIMKAMGLAPNLPEDLYCLIKKAVAI 83 (319)
Q Consensus 12 ~~~~p~w~~~s~-----~~~~~~~~~---~~IG~iLRD~~GIp~VK~vtGkkI~~ILk~nGlapeIPEDL~~LikKAv~l 83 (319)
.+.+|+|++.|+ .+|++++++ +|||++||||||||+||.|||+||++||++||++|+|||||||||+||++|
T Consensus 19 ~~~~P~W~~~~~eeve~~I~~lakkG~~pSqIG~~LRD~~gip~Vk~vtG~ki~~iLk~~gl~p~iPEDL~~L~~ri~~L 98 (151)
T PRK08561 19 RTEPPEWVDYSPEEIEELVVELAKQGYSPSMIGIILRDQYGIPDVKLITGKKITEILEENGLAPEIPEDLRNLIKKAVNL 98 (151)
T ss_pred CCCCCccccCCHHHHHHHHHHHHHCCCCHHHhhhhHhhccCCCceeeeccchHHHHHHHcCCCCCCcHHHHHHHHHHHHH
Confidence 568999999988 678888888 499999999999999999999999999999999999999999999999999
Q ss_pred HHHHhhccCcccchhhHhHHHHhhhhhHHHHHhcCcCCCCCccchHHHHHHHh
Q psy7749 84 RKHLERSRKDKDSKFRLILVESRIHRLARYYKTKAVLPPNWKYESATASAFIL 136 (319)
Q Consensus 84 RkHLe~n~kDk~~Kr~L~LiESkI~RL~rYYk~~~~LP~~WkY~~~tA~~lv~ 136 (319)
++||+.|+||+||||+|+++|||+|||++||+++++||+||+|+|++|++||+
T Consensus 99 ~~HL~~nkKD~~skRgL~~~~skrrRLl~Yyk~~~~LP~~WkY~~~~A~~lv~ 151 (151)
T PRK08561 99 RKHLEENPKDLHNKRGLQLIESKIRRLVKYYKRTGVLPADWRYSPETAELLVS 151 (151)
T ss_pred HHHHHhCCCcchhHHHHHHHHHHHHHHHHHHHhcCCCCCCCcCCHHHHHHHhC
Confidence 99999999999999999999999999999999999999999999999999985
No 7
>PF08069 Ribosomal_S13_N: Ribosomal S13/S15 N-terminal domain; InterPro: IPR012606 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. This domain is found at the N terminus of ribosomal S13 and S15 proteins. This domain is also identified as NUC021 [].; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005840 ribosome; PDB: 3U5C_N 3O30_G 3IZB_O 3O2Z_G 3U5G_N 2XZN_O 2XZM_O 3IZ6_O.
Probab=99.98 E-value=7.9e-34 Score=214.76 Aligned_cols=60 Identities=68% Similarity=1.114 Sum_probs=41.8
Q ss_pred hhccCCCCCCCCCcCCCCCCCCCCCccCChhHHHHHHHHHhhCCCCccchhhhhhcccCC
Q psy7749 169 MGRMHTPGKGISKSALPYRRSVPNWLKLTSEDVKDHIFKLSKKGLTPSQIGVILRDSHGV 228 (319)
Q Consensus 169 MaRMhs~~kG~S~S~~Py~~~~P~Wl~~s~eEVe~~IvkLaKkG~tpSqIG~iLRD~~GI 228 (319)
|||||++|||+|+|++||++++|+|+++++||||++||+|||+|+||||||++|||||||
T Consensus 1 M~RMh~~~kG~S~S~~P~~~~~P~W~~~~~~eVe~~I~klakkG~tpSqIG~iLRD~~GI 60 (60)
T PF08069_consen 1 MGRMHSRGKGISGSTRPYRRSPPSWLKYSPEEVEELIVKLAKKGLTPSQIGVILRDQYGI 60 (60)
T ss_dssp ---TTSSS---------S-SS--TT--S-HHHHHHHHHHHCCTTHCHHHHHHHHHHSCTC
T ss_pred CCCccCCCCCccCCCCCCCCCCCCCcCCCHHHHHHHHHHHHHcCCCHHHhhhhhhhccCC
Confidence 999999999999999999999999999999999999999999999999999999999998
No 8
>COG0184 RpsO Ribosomal protein S15P/S13E [Translation, ribosomal structure and biogenesis]
Probab=99.91 E-value=5.5e-25 Score=177.53 Aligned_cols=88 Identities=31% Similarity=0.403 Sum_probs=84.9
Q ss_pred CCCccchhhhhhcccCCCceeeeccchHHHHHHHcCCCCCChhhHHHHHHHHHHHHHHHhhhcCcccchhhHHHHHHhhh
Q psy7749 212 GLTPSQIGVILRDSHGVAQVRFVSGNKILRIMKAMGLAPNLPEDLYCLIKKAVAIRKHLERSRKDKDSKFRLILVESRIH 291 (319)
Q Consensus 212 G~tpSqIG~iLRD~~GIP~VK~vtGkkI~~ILk~nGlapeIPEDL~~LIkKAv~iRKHLe~n~KD~~sKr~L~LiESkI~ 291 (319)
|..|||||..|||+||+|.++..+| |||+.+|+++|++|++|++.|+||.||||+|++++||++
T Consensus 1 m~~~~~~k~~l~~eyg~~~~dtgs~----------------evq~a~Lt~ri~~L~~Hlk~hkKD~~srRGL~~~vskrr 64 (89)
T COG0184 1 MSLTSEIKQELRDEYGIPEVDTGSG----------------EVQLALLTERINNLTEHLKEHKKDHHSRRGLLLLVSKRR 64 (89)
T ss_pred CCchHHHHHHHHHHhCCCCCCCCCc----------------HHHHHHHHHHHHHHHHHHHHCCcchhHHHHHHHHHHHHH
Confidence 6789999999999999999999888 999999999999999999999999999999999999999
Q ss_pred hhHHHHHhcCcCCCCCccchhhhh
Q psy7749 292 RLARYYKTKAVLPPNWKYESATAS 315 (319)
Q Consensus 292 RL~rYYK~~~~LP~~WkY~~~tA~ 315 (319)
||++|||+++++|.+|.|++..++
T Consensus 65 rLl~Ylk~~~~~~y~~li~~l~lr 88 (89)
T COG0184 65 RLLKYLKRKDVLRYRWLIKKLGLR 88 (89)
T ss_pred HHHHHHHhcCcchHHHHHHHhhcc
Confidence 999999999999999999987653
No 9
>COG0184 RpsO Ribosomal protein S15P/S13E [Translation, ribosomal structure and biogenesis]
Probab=99.87 E-value=7e-23 Score=165.36 Aligned_cols=83 Identities=30% Similarity=0.405 Sum_probs=80.4
Q ss_pred hhhhhhhccccCCCceeeeccchHHHHHHHcCCCCCChhhHHHHHHHHHHHHHHHhhccCcccchhhHhHHHHhhhhhHH
Q psy7749 33 VLFCVILRDSHGVAQVRFVSGNKILRIMKAMGLAPNLPEDLYCLIKKAVAIRKHLERSRKDKDSKFRLILVESRIHRLAR 112 (319)
Q Consensus 33 ~~IG~iLRD~~GIp~VK~vtGkkI~~ILk~nGlapeIPEDL~~LikKAv~lRkHLe~n~kDk~~Kr~L~LiESkI~RL~r 112 (319)
++||..|||+||+|.++..+| |||+.+|+++|++|++|++.|+||.||||+|++++||++||++
T Consensus 5 ~~~k~~l~~eyg~~~~dtgs~----------------evq~a~Lt~ri~~L~~Hlk~hkKD~~srRGL~~~vskrrrLl~ 68 (89)
T COG0184 5 SEIKQELRDEYGIPEVDTGSG----------------EVQLALLTERINNLTEHLKEHKKDHHSRRGLLLLVSKRRRLLK 68 (89)
T ss_pred HHHHHHHHHHhCCCCCCCCCc----------------HHHHHHHHHHHHHHHHHHHHCCcchhHHHHHHHHHHHHHHHHH
Confidence 689999999999999999888 9999999999999999999999999999999999999999999
Q ss_pred HHHhcCcCCCCCccchHHH
Q psy7749 113 YYKTKAVLPPNWKYESATA 131 (319)
Q Consensus 113 YYk~~~~LP~~WkY~~~tA 131 (319)
|||+++++|.+|.|++..+
T Consensus 69 Ylk~~~~~~y~~li~~l~l 87 (89)
T COG0184 69 YLKRKDVLRYRWLIKKLGL 87 (89)
T ss_pred HHHhcCcchHHHHHHHhhc
Confidence 9999999999999998765
No 10
>cd00353 Ribosomal_S15p_S13e Ribosomal protein S15 (prokaryotic)_S13 (eukaryotic) binds the central domain of 16S rRNA and is required for assembly of the small ribosomal subunit and for intersubunit association, thus representing a key element in the assembly of the whole ribosome. S15 also plays an important autoregulatory role by binding and preventing its own mRNA from being translated. S15 has a predominantly alpha-helical fold that is highly structured except for the N-terminal alpha helix.
Probab=99.45 E-value=9.3e-14 Score=109.24 Aligned_cols=73 Identities=37% Similarity=0.525 Sum_probs=69.6
Q ss_pred HHHHHHHcCCC----CCChhhHHHHHHHHHHHHHHHhhhcCcccchhhHHHHHHhhhhhHHHHHhcCcCCCCCccch
Q psy7749 239 ILRIMKAMGLA----PNLPEDLYCLIKKAVAIRKHLERSRKDKDSKFRLILVESRIHRLARYYKTKAVLPPNWKYES 311 (319)
Q Consensus 239 I~~ILk~nGla----peIPEDL~~LIkKAv~iRKHLe~n~KD~~sKr~L~LiESkI~RL~rYYK~~~~LP~~WkY~~ 311 (319)
+.+|+++.|.. +.+|+++..|..|+.+|++||+.|+||++|+++|+.++||.+||.+||++++..|-+|.|+.
T Consensus 2 ~~~i~~~~~~~~~DtGs~evQia~LT~rI~~L~~Hl~~~~KD~~~krgL~~lv~kRrrLL~YLk~~~~~~y~~~i~~ 78 (80)
T cd00353 2 KQEILKEFGLAEGDTGSPEVQLALLTERIVNLTEHLEKNKKDKHSKRGLLLLVSKRRRLLKYLKRKDRLRYEWLIEK 78 (80)
T ss_pred HHHHHHHhCCCCCCCCChHHHHHHHHHHHHHHHHHHHHccccchHHHhHHHHHHHHHHHHHHHHHcCchhHHHHHHh
Confidence 57899999988 89999999999999999999999999999999999999999999999999999999998764
No 11
>PF00312 Ribosomal_S15: Ribosomal protein S15; InterPro: IPR000589 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. Ribosomal protein S15 is one of the proteins from the small ribosomal subunit. In Escherichia coli, this protein binds to 16S ribosomal RNA and functions at early steps in ribosome assembly. It belongs to a family of ribosomal proteins which, on the basis of sequence similarities [, ,], groups bacterial and plant chloroplast S15; archaeal Haloarcula marismortui HmaS15 (HS11); yeast mitochondrial S28; and mammalian, yeast, Brugia pahangi and Wuchereria bancrofti S13. S15 is a protein of 80 to 250 amino-acid residues.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 1YSH_E 3U5C_N 3O30_G 3IZB_O 3O2Z_G 3U5G_N 1S1H_O 3MR8_O 3D5C_O 3MS0_O ....
Probab=99.45 E-value=4.5e-14 Score=111.52 Aligned_cols=81 Identities=21% Similarity=0.262 Sum_probs=76.3
Q ss_pred eccchHHHHHHHcCCCCCChhhHHHHHHHHHHHHHHHhhhcCcccchhhHHHHHHhhhhhHHHHHhcCcCCCCCccchhh
Q psy7749 234 VSGNKILRIMKAMGLAPNLPEDLYCLIKKAVAIRKHLERSRKDKDSKFRLILVESRIHRLARYYKTKAVLPPNWKYESAT 313 (319)
Q Consensus 234 vtGkkI~~ILk~nGlapeIPEDL~~LIkKAv~iRKHLe~n~KD~~sKr~L~LiESkI~RL~rYYK~~~~LP~~WkY~~~t 313 (319)
++++.|.++++.+|-.+.+|+++..|..|+.+|++|++.|+||++|+++|..++||.+||.+||+++. .|.|....
T Consensus 2 ~k~~~i~~~~~~~~dtgs~evqia~LT~rI~~L~~Hl~~~kkD~~skr~L~~lv~kRrrlL~YLrr~~----~~~Y~~~~ 77 (83)
T PF00312_consen 2 RKQKSIKKFQRHPNDTGSPEVQIAILTERIRNLQEHLKKNKKDKHSKRGLLKLVSKRRRLLKYLRRKD----FERYEWVL 77 (83)
T ss_dssp HHHHHHHHHSSSTTSSSSHHHHHHHHHHHHHHHHHHHHHTTTSHHHHHHHHHHHHHHHHHHHHHHHHT----HHHHHHHH
T ss_pred hHHHHHHHHHhcCCCCCCCHHHHHHHHHHHHHHHHHHHHhccccccceehhHHHHHHHHHHHHHHhCC----HHHHHHHH
Confidence 46788999999999999999999999999999999999999999999999999999999999999988 78999888
Q ss_pred hhhhh
Q psy7749 314 ASALV 318 (319)
Q Consensus 314 A~~lv 318 (319)
+++-+
T Consensus 78 ~~Lgl 82 (83)
T PF00312_consen 78 KKLGL 82 (83)
T ss_dssp HHHTT
T ss_pred HHhCc
Confidence 87644
No 12
>PF00312 Ribosomal_S15: Ribosomal protein S15; InterPro: IPR000589 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. Ribosomal protein S15 is one of the proteins from the small ribosomal subunit. In Escherichia coli, this protein binds to 16S ribosomal RNA and functions at early steps in ribosome assembly. It belongs to a family of ribosomal proteins which, on the basis of sequence similarities [, ,], groups bacterial and plant chloroplast S15; archaeal Haloarcula marismortui HmaS15 (HS11); yeast mitochondrial S28; and mammalian, yeast, Brugia pahangi and Wuchereria bancrofti S13. S15 is a protein of 80 to 250 amino-acid residues.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 1YSH_E 3U5C_N 3O30_G 3IZB_O 3O2Z_G 3U5G_N 1S1H_O 3MR8_O 3D5C_O 3MS0_O ....
Probab=99.43 E-value=7.1e-14 Score=110.42 Aligned_cols=80 Identities=21% Similarity=0.254 Sum_probs=75.5
Q ss_pred eccchHHHHHHHcCCCCCChhhHHHHHHHHHHHHHHHhhccCcccchhhHhHHHHhhhhhHHHHHhcCcCCCCCccchHH
Q psy7749 51 VSGNKILRIMKAMGLAPNLPEDLYCLIKKAVAIRKHLERSRKDKDSKFRLILVESRIHRLARYYKTKAVLPPNWKYESAT 130 (319)
Q Consensus 51 vtGkkI~~ILk~nGlapeIPEDL~~LikKAv~lRkHLe~n~kDk~~Kr~L~LiESkI~RL~rYYk~~~~LP~~WkY~~~t 130 (319)
++++.|.++++++|-.+.+|+++..|..|+.+|++|++.|+||++|+++|..++||.+||.+||+++. .|.|....
T Consensus 2 ~k~~~i~~~~~~~~dtgs~evqia~LT~rI~~L~~Hl~~~kkD~~skr~L~~lv~kRrrlL~YLrr~~----~~~Y~~~~ 77 (83)
T PF00312_consen 2 RKQKSIKKFQRHPNDTGSPEVQIAILTERIRNLQEHLKKNKKDKHSKRGLLKLVSKRRRLLKYLRRKD----FERYEWVL 77 (83)
T ss_dssp HHHHHHHHHSSSTTSSSSHHHHHHHHHHHHHHHHHHHHHTTTSHHHHHHHHHHHHHHHHHHHHHHHHT----HHHHHHHH
T ss_pred hHHHHHHHHHhcCCCCCCCHHHHHHHHHHHHHHHHHHHHhccccccceehhHHHHHHHHHHHHHHhCC----HHHHHHHH
Confidence 46889999999999999999999999999999999999999999999999999999999999999988 78898887
Q ss_pred HHHH
Q psy7749 131 ASAF 134 (319)
Q Consensus 131 A~~l 134 (319)
+++-
T Consensus 78 ~~Lg 81 (83)
T PF00312_consen 78 KKLG 81 (83)
T ss_dssp HHHT
T ss_pred HHhC
Confidence 7753
No 13
>cd00353 Ribosomal_S15p_S13e Ribosomal protein S15 (prokaryotic)_S13 (eukaryotic) binds the central domain of 16S rRNA and is required for assembly of the small ribosomal subunit and for intersubunit association, thus representing a key element in the assembly of the whole ribosome. S15 also plays an important autoregulatory role by binding and preventing its own mRNA from being translated. S15 has a predominantly alpha-helical fold that is highly structured except for the N-terminal alpha helix.
Probab=99.43 E-value=1.7e-13 Score=107.82 Aligned_cols=73 Identities=37% Similarity=0.525 Sum_probs=69.2
Q ss_pred HHHHHHHcCCC----CCChhhHHHHHHHHHHHHHHHhhccCcccchhhHhHHHHhhhhhHHHHHhcCcCCCCCccch
Q psy7749 56 ILRIMKAMGLA----PNLPEDLYCLIKKAVAIRKHLERSRKDKDSKFRLILVESRIHRLARYYKTKAVLPPNWKYES 128 (319)
Q Consensus 56 I~~ILk~nGla----peIPEDL~~LikKAv~lRkHLe~n~kDk~~Kr~L~LiESkI~RL~rYYk~~~~LP~~WkY~~ 128 (319)
+.+|+++.|.. +.+|+++..|..|+.+|++||+.|+||++|+++|..++||.+||.+||++++..|-+|.|+.
T Consensus 2 ~~~i~~~~~~~~~DtGs~evQia~LT~rI~~L~~Hl~~~~KD~~~krgL~~lv~kRrrLL~YLk~~~~~~y~~~i~~ 78 (80)
T cd00353 2 KQEILKEFGLAEGDTGSPEVQLALLTERIVNLTEHLEKNKKDKHSKRGLLLLVSKRRRLLKYLKRKDRLRYEWLIEK 78 (80)
T ss_pred HHHHHHHhCCCCCCCCChHHHHHHHHHHHHHHHHHHHHccccchHHHhHHHHHHHHHHHHHHHHHcCchhHHHHHHh
Confidence 57889999988 89999999999999999999999999999999999999999999999999999999888764
No 14
>cd00677 S15_NS1_EPRS_RNA-bind S15/NS1/EPRS_RNA-binding domain. This short domain consists of a helix-turn-helix structure, which can bind to several types of RNA. It is found in the ribosomal protein S15, the influenza A viral nonstructural protein (NSA) and in several eukaryotic aminoacyl tRNA synthetases (aaRSs), where it occurs as a single or a repeated unit. It is involved in both protein-RNA interactions by binding tRNA and protein-protein interactions in the formation of tRNA-synthetases into multienzyme complexes. While this domain lacks significant sequence similarity between the subgroups in which it is found, they share similar electrostatic surface potentials and thus are likely to bind to RNA via the same mechanism.
Probab=98.84 E-value=5.3e-09 Score=74.15 Aligned_cols=46 Identities=33% Similarity=0.460 Sum_probs=44.5
Q ss_pred hhhHHHHHHHHHHHHHHHhhhcCcccchhhHHHHHHhhhhhHHHHH
Q psy7749 253 PEDLYCLIKKAVAIRKHLERSRKDKDSKFRLILVESRIHRLARYYK 298 (319)
Q Consensus 253 PEDL~~LIkKAv~iRKHLe~n~KD~~sKr~L~LiESkI~RL~rYYK 298 (319)
|+++..|..++.++..|++.|+||+++|++|..++++++||.+||+
T Consensus 1 ~vqia~lt~~i~~L~~hl~~~~kD~~~kr~L~~~v~kr~rLl~ylk 46 (46)
T cd00677 1 EVQIALLTERIRNLKEHLAKNKKDKHSKRGLDLLVSKRLRLLKYLK 46 (46)
T ss_pred CHHHHHHHHHHHHHHHHHHHCCCCcchHHHHHHHHHHHHHHHHHhC
Confidence 6789999999999999999999999999999999999999999996
No 15
>cd00677 S15_NS1_EPRS_RNA-bind S15/NS1/EPRS_RNA-binding domain. This short domain consists of a helix-turn-helix structure, which can bind to several types of RNA. It is found in the ribosomal protein S15, the influenza A viral nonstructural protein (NSA) and in several eukaryotic aminoacyl tRNA synthetases (aaRSs), where it occurs as a single or a repeated unit. It is involved in both protein-RNA interactions by binding tRNA and protein-protein interactions in the formation of tRNA-synthetases into multienzyme complexes. While this domain lacks significant sequence similarity between the subgroups in which it is found, they share similar electrostatic surface potentials and thus are likely to bind to RNA via the same mechanism.
Probab=98.81 E-value=7.2e-09 Score=73.50 Aligned_cols=46 Identities=33% Similarity=0.460 Sum_probs=44.4
Q ss_pred hhhHHHHHHHHHHHHHHHhhccCcccchhhHhHHHHhhhhhHHHHH
Q psy7749 70 PEDLYCLIKKAVAIRKHLERSRKDKDSKFRLILVESRIHRLARYYK 115 (319)
Q Consensus 70 PEDL~~LikKAv~lRkHLe~n~kDk~~Kr~L~LiESkI~RL~rYYk 115 (319)
|+++..|..++.++..|++.|+||++++++|..++++++||.+||+
T Consensus 1 ~vqia~lt~~i~~L~~hl~~~~kD~~~kr~L~~~v~kr~rLl~ylk 46 (46)
T cd00677 1 EVQIALLTERIRNLKEHLAKNKKDKHSKRGLDLLVSKRLRLLKYLK 46 (46)
T ss_pred CHHHHHHHHHHHHHHHHHHHCCCCcchHHHHHHHHHHHHHHHHHhC
Confidence 5789999999999999999999999999999999999999999996
No 16
>PF08069 Ribosomal_S13_N: Ribosomal S13/S15 N-terminal domain; InterPro: IPR012606 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. This domain is found at the N terminus of ribosomal S13 and S15 proteins. This domain is also identified as NUC021 [].; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005840 ribosome; PDB: 3U5C_N 3O30_G 3IZB_O 3O2Z_G 3U5G_N 2XZN_O 2XZM_O 3IZ6_O.
Probab=98.64 E-value=6.3e-09 Score=79.46 Aligned_cols=34 Identities=29% Similarity=0.429 Sum_probs=25.0
Q ss_pred CCCCCCceeecc-----cccccccch---hhhhhhhccccCC
Q psy7749 12 TTLGPNWFIKSG-----FYCNLKTDI---VLFCVILRDSHGV 45 (319)
Q Consensus 12 ~~~~p~w~~~s~-----~~~~~~~~~---~~IG~iLRD~~GI 45 (319)
.+.+|+|++.|+ .+|++++++ +|||++|||||||
T Consensus 19 ~~~~P~W~~~~~~eVe~~I~klakkG~tpSqIG~iLRD~~GI 60 (60)
T PF08069_consen 19 RRSPPSWLKYSPEEVEELIVKLAKKGLTPSQIGVILRDQYGI 60 (60)
T ss_dssp -SS--TT--S-HHHHHHHHHHHCCTTHCHHHHHHHHHHSCTC
T ss_pred CCCCCCCcCCCHHHHHHHHHHHHHcCCCHHHhhhhhhhccCC
Confidence 567899999987 788888888 5999999999998
No 17
>TIGR00952 S15_bact ribosomal protein S15, bacterial/organelle. This model is built to recognize specifically bacterial, chloroplast, and mitochondrial ribosomal protein S15. The homologous proteins of Archaea and Eukarya are designated S13.
Probab=96.62 E-value=0.004 Score=50.56 Aligned_cols=46 Identities=26% Similarity=0.432 Sum_probs=41.4
Q ss_pred HHHHHHHHHHHHHHHhhhcCcccchhhHHHHHHhhhhhHHHHHhcC
Q psy7749 256 LYCLIKKAVAIRKHLERSRKDKDSKFRLILVESRIHRLARYYKTKA 301 (319)
Q Consensus 256 L~~LIkKAv~iRKHLe~n~KD~~sKr~L~LiESkI~RL~rYYK~~~ 301 (319)
...|=.+-.+|..|++.|+||++|+++|.-.-+|=+||.+|-+++.
T Consensus 26 iA~LT~rI~~L~~Hl~~h~KD~~srrgL~~lv~kRkrlL~YL~~~d 71 (86)
T TIGR00952 26 IALLTERINQLTEHLKANKKDHHSRRGLLKLVGRRRRLLKYLKRTD 71 (86)
T ss_pred HHHHHHHHHHHHHHHHHCCCchHHHHHHHHHHHHHHHHHHHHHhCC
Confidence 3456678889999999999999999999999999999999998864
No 18
>TIGR00952 S15_bact ribosomal protein S15, bacterial/organelle. This model is built to recognize specifically bacterial, chloroplast, and mitochondrial ribosomal protein S15. The homologous proteins of Archaea and Eukarya are designated S13.
Probab=96.61 E-value=0.0045 Score=50.31 Aligned_cols=46 Identities=26% Similarity=0.432 Sum_probs=41.7
Q ss_pred HHHHHHHHHHHHHHHhhccCcccchhhHhHHHHhhhhhHHHHHhcC
Q psy7749 73 LYCLIKKAVAIRKHLERSRKDKDSKFRLILVESRIHRLARYYKTKA 118 (319)
Q Consensus 73 L~~LikKAv~lRkHLe~n~kDk~~Kr~L~LiESkI~RL~rYYk~~~ 118 (319)
...|=.+-.+|..|++.|+||++|+++|...-+|=+||.+|-+++.
T Consensus 26 iA~LT~rI~~L~~Hl~~h~KD~~srrgL~~lv~kRkrlL~YL~~~d 71 (86)
T TIGR00952 26 IALLTERINQLTEHLKANKKDHHSRRGLLKLVGRRRRLLKYLKRTD 71 (86)
T ss_pred HHHHHHHHHHHHHHHHHCCCchHHHHHHHHHHHHHHHHHHHHHhCC
Confidence 4566678889999999999999999999999999999999999854
No 19
>CHL00027 rps15 ribosomal protein S15
Probab=96.40 E-value=0.0057 Score=50.34 Aligned_cols=46 Identities=26% Similarity=0.370 Sum_probs=41.4
Q ss_pred HHHHHHHHHHHHHHHhhhcCcccchhhHHHHHHhhhhhHHHHHhcC
Q psy7749 256 LYCLIKKAVAIRKHLERSRKDKDSKFRLILVESRIHRLARYYKTKA 301 (319)
Q Consensus 256 L~~LIkKAv~iRKHLe~n~KD~~sKr~L~LiESkI~RL~rYYK~~~ 301 (319)
..-|=.+-..+..||+.|+||.+++++|.-.-++=+||.+|.+++.
T Consensus 26 iA~LT~rI~~Lt~Hlk~hkKD~~s~RgL~~lv~kRkrLL~YL~r~d 71 (90)
T CHL00027 26 VFSFTNKIRRLTSHLELHKKDYSSQRGLRKILGKRQRLLAYLSKKN 71 (90)
T ss_pred HHHHHHHHHHHHHHHHHCCCcchhHHHHHHHHHHHHHHHHHHHhCC
Confidence 4556678889999999999999999999999999999999999864
No 20
>PRK05626 rpsO 30S ribosomal protein S15; Reviewed
Probab=96.32 E-value=0.0062 Score=49.79 Aligned_cols=45 Identities=24% Similarity=0.379 Sum_probs=40.4
Q ss_pred HHHHHHHHHHHHHHhhhcCcccchhhHHHHHHhhhhhHHHHHhcC
Q psy7749 257 YCLIKKAVAIRKHLERSRKDKDSKFRLILVESRIHRLARYYKTKA 301 (319)
Q Consensus 257 ~~LIkKAv~iRKHLe~n~KD~~sKr~L~LiESkI~RL~rYYK~~~ 301 (319)
.-|=.|-.+|..|++.|+||++|+++|...=++=+||-+|-+++.
T Consensus 30 A~LT~rI~~L~~Hlk~~~KD~~srrgL~~lv~kRkrlL~YL~~~d 74 (89)
T PRK05626 30 ALLTERINHLTEHLKEHKKDHHSRRGLLKMVGQRRKLLDYLKKKD 74 (89)
T ss_pred HHHHHHHHHHHHHHHHcccchhhHHHHHHHHHhHHHHHHHHHhcC
Confidence 445568889999999999999999999999999999999998864
No 21
>CHL00027 rps15 ribosomal protein S15
Probab=96.32 E-value=0.0086 Score=49.28 Aligned_cols=47 Identities=26% Similarity=0.369 Sum_probs=41.9
Q ss_pred hHHHHHHHHHHHHHHHhhccCcccchhhHhHHHHhhhhhHHHHHhcC
Q psy7749 72 DLYCLIKKAVAIRKHLERSRKDKDSKFRLILVESRIHRLARYYKTKA 118 (319)
Q Consensus 72 DL~~LikKAv~lRkHLe~n~kDk~~Kr~L~LiESkI~RL~rYYk~~~ 118 (319)
-..-|=.+...+..||+.|+||.+++++|.-.-++=+||.+|.+++.
T Consensus 25 QiA~LT~rI~~Lt~Hlk~hkKD~~s~RgL~~lv~kRkrLL~YL~r~d 71 (90)
T CHL00027 25 QVFSFTNKIRRLTSHLELHKKDYSSQRGLRKILGKRQRLLAYLSKKN 71 (90)
T ss_pred HHHHHHHHHHHHHHHHHHCCCcchhHHHHHHHHHHHHHHHHHHHhCC
Confidence 34556678889999999999999999999999999999999999864
No 22
>PRK05626 rpsO 30S ribosomal protein S15; Reviewed
Probab=96.28 E-value=0.0071 Score=49.44 Aligned_cols=46 Identities=24% Similarity=0.384 Sum_probs=41.4
Q ss_pred HHHHHHHHHHHHHHHhhccCcccchhhHhHHHHhhhhhHHHHHhcC
Q psy7749 73 LYCLIKKAVAIRKHLERSRKDKDSKFRLILVESRIHRLARYYKTKA 118 (319)
Q Consensus 73 L~~LikKAv~lRkHLe~n~kDk~~Kr~L~LiESkI~RL~rYYk~~~ 118 (319)
..-|=.+-.+|..|++.|+||++|+++|...=++=+||.+|-+++.
T Consensus 29 iA~LT~rI~~L~~Hlk~~~KD~~srrgL~~lv~kRkrlL~YL~~~d 74 (89)
T PRK05626 29 VALLTERINHLTEHLKEHKKDHHSRRGLLKMVGQRRKLLDYLKKKD 74 (89)
T ss_pred HHHHHHHHHHHHHHHHHcccchhhHHHHHHHHHhHHHHHHHHHhcC
Confidence 4556678889999999999999999999999999999999999854
No 23
>PTZ00119 40S ribosomal protein S15; Provisional
Probab=95.49 E-value=0.019 Score=55.85 Aligned_cols=44 Identities=27% Similarity=0.449 Sum_probs=40.1
Q ss_pred HHHHHHHHHHHHHhhhcCcccchhhHHHHHHhhhhhHHHHHhcC
Q psy7749 258 CLIKKAVAIRKHLERSRKDKDSKFRLILVESRIHRLARYYKTKA 301 (319)
Q Consensus 258 ~LIkKAv~iRKHLe~n~KD~~sKr~L~LiESkI~RL~rYYK~~~ 301 (319)
-|=.|-.+|..||+.|+||.+|+++|...-+|=+||.+|.+++.
T Consensus 133 iLTeRI~~LTeHLk~hkKD~~SrRGLlkLV~KRRKLLkYLKrkD 176 (302)
T PTZ00119 133 CLTEKILNLRAHLILRCKDHPKKRTMSILLARRQKLMKYLYKTD 176 (302)
T ss_pred HHHHHHHHHHHHHHhCCCccHhHHHHHHHHHHHHHHHHHHHhcC
Confidence 45567889999999999999999999999999999999999864
No 24
>PTZ00119 40S ribosomal protein S15; Provisional
Probab=95.37 E-value=0.023 Score=55.24 Aligned_cols=98 Identities=21% Similarity=0.308 Sum_probs=66.7
Q ss_pred chHHHHHHHcCCCC----CChhhHHHHHHHHHHHHHHHhhccCcccchhhHhHHHHhhhhhHHHHHhcCcCCCCCccchH
Q psy7749 54 NKILRIMKAMGLAP----NLPEDLYCLIKKAVAIRKHLERSRKDKDSKFRLILVESRIHRLARYYKTKAVLPPNWKYESA 129 (319)
Q Consensus 54 kkI~~ILk~nGlap----eIPEDL~~LikKAv~lRkHLe~n~kDk~~Kr~L~LiESkI~RL~rYYk~~~~LP~~WkY~~~ 129 (319)
.+..+|.++-+..+ ...--..-|=.|-.+|..||+.|+||++|+++|...-+|=+||.+|.+++. +. .|..
T Consensus 108 ~rK~eIIkkfqr~~~DTGS~EVQIAiLTeRI~~LTeHLk~hkKD~~SrRGLlkLV~KRRKLLkYLKrkD--~e--rY~~- 182 (302)
T PTZ00119 108 YKKLCIRRCLQRRPFDTGSAPVQIGCLTEKILNLRAHLILRCKDHPKKRTMSILLARRQKLMKYLYKTD--FE--LYKH- 182 (302)
T ss_pred HHHHHHHHHhcCCCCCCCCHHHHHHHHHHHHHHHHHHHHhCCCccHhHHHHHHHHHHHHHHHHHHHhcC--HH--HHHH-
Confidence 44456666666543 233345667789999999999999999999999999999999999999964 11 2333
Q ss_pred HHHHHHhcCccccccCC--cceeeccccc
Q psy7749 130 TASAFILEGFRFRTRRG--FRYKIDLVGL 156 (319)
Q Consensus 130 tA~~lv~~~~~~~~~~~--~~~~~~~~~~ 156 (319)
+-+.|-....+|-++.- -.=.+.++|+
T Consensus 183 lIkkLGLRkv~f~~~~~~~~~k~i~~~~v 211 (302)
T PTZ00119 183 TCNLLKIKCILFAIPDSRDRSKAINAAAV 211 (302)
T ss_pred HHHHhCCceEEeecccccChhhccchhee
Confidence 33335555666655532 1123556653
No 25
>COG2257 Uncharacterized homolog of the cytoplasmic domain of flagellar protein FhlB [Function unknown]
Probab=93.52 E-value=0.31 Score=40.62 Aligned_cols=70 Identities=17% Similarity=0.361 Sum_probs=60.6
Q ss_pred CCCCCCccCChhHHHHHHHHHhhCCCCccchhhhhhcccCCCceeeeccchHHHHHHHcCCCCCChhhHHHHHHHHHHHH
Q psy7749 188 RSVPNWLKLTSEDVKDHIFKLSKKGLTPSQIGVILRDSHGVAQVRFVSGNKILRIMKAMGLAPNLPEDLYCLIKKAVAIR 267 (319)
Q Consensus 188 ~~~P~Wl~~s~eEVe~~IvkLaKkG~tpSqIG~iLRD~~GIP~VK~vtGkkI~~ILk~nGlapeIPEDL~~LIkKAv~iR 267 (319)
..+|.=+-.-.-+|-+.|++.||+ ||||.+.. .-+.+.|-.-.+..+|||.||.-|-.-...-
T Consensus 20 ~~AP~vvA~G~G~iAe~II~~Ake--------------~~Vpi~ed---p~Lv~~L~~lelg~~IPeelY~vVAEifafi 82 (92)
T COG2257 20 DKAPKVVASGKGEIAEKIIEKAKE--------------HGVPIQED---PLLVELLLKLELGDEIPEELYEVVAEIFAFI 82 (92)
T ss_pred CCCCEEEeecchHHHHHHHHHHHH--------------cCCCcccC---HHHHHHHHhccccccCCHHHHHHHHHHHHHH
Confidence 457887877888999999999985 89998775 5599999999999999999999999888888
Q ss_pred HHHhhhc
Q psy7749 268 KHLERSR 274 (319)
Q Consensus 268 KHLe~n~ 274 (319)
.|++.|-
T Consensus 83 ~~~~~~~ 89 (92)
T COG2257 83 YEVDNNV 89 (92)
T ss_pred HHHHccC
Confidence 8887763
No 26
>COG2257 Uncharacterized homolog of the cytoplasmic domain of flagellar protein FhlB [Function unknown]
Probab=85.20 E-value=2.2 Score=35.66 Aligned_cols=59 Identities=17% Similarity=0.329 Sum_probs=48.5
Q ss_pred cccccchhhhhhhhccccCCCceeeeccchHHHHHHHcCCCCCChhhHHHHHHHHHHHHHHHhhcc
Q psy7749 26 CNLKTDIVLFCVILRDSHGVAQVRFVSGNKILRIMKAMGLAPNLPEDLYCLIKKAVAIRKHLERSR 91 (319)
Q Consensus 26 ~~~~~~~~~IG~iLRD~~GIp~VK~vtGkkI~~ILk~nGlapeIPEDL~~LikKAv~lRkHLe~n~ 91 (319)
-+++++|..+. ..||||-+.. .-+.+.|-...+..+|||.||.-|-.-...-.|++.|-
T Consensus 31 G~iAe~II~~A----ke~~Vpi~ed---p~Lv~~L~~lelg~~IPeelY~vVAEifafi~~~~~~~ 89 (92)
T COG2257 31 GEIAEKIIEKA----KEHGVPIQED---PLLVELLLKLELGDEIPEELYEVVAEIFAFIYEVDNNV 89 (92)
T ss_pred hHHHHHHHHHH----HHcCCCcccC---HHHHHHHHhccccccCCHHHHHHHHHHHHHHHHHHccC
Confidence 56777766544 4699999875 56999999999999999999999988888888887663
No 27
>PF13565 HTH_32: Homeodomain-like domain
Probab=80.94 E-value=2.2 Score=31.77 Aligned_cols=44 Identities=25% Similarity=0.465 Sum_probs=33.9
Q ss_pred hhHHHHHHHHHhhCC--CCccchhhhhhcccCCCceeeeccchHHHHH
Q psy7749 198 SEDVKDHIFKLSKKG--LTPSQIGVILRDSHGVAQVRFVSGNKILRIM 243 (319)
Q Consensus 198 ~eEVe~~IvkLaKkG--~tpSqIG~iLRD~~GIP~VK~vtGkkI~~IL 243 (319)
++|+++.|+++.... .|+.+|...|.++|||.. .+.-..|.++|
T Consensus 32 ~~e~~~~i~~~~~~~p~wt~~~i~~~L~~~~g~~~--~~S~~tv~R~L 77 (77)
T PF13565_consen 32 DPEQRERIIALIEEHPRWTPREIAEYLEEEFGISV--RVSRSTVYRIL 77 (77)
T ss_pred cHHHHHHHHHHHHhCCCCCHHHHHHHHHHHhCCCC--CccHhHHHHhC
Confidence 677778888887765 899999999999999865 44444555554
No 28
>TIGR00789 flhB_rel flhB C-terminus-related protein. This model describes a short protein (80-93 residues) homologous to the C-terminus of the flagellar biosynthetic protein FlhB. It is found so far only in species that also have FlhB. In a phylogenetic tree based on alignment of both this family and the homologous region of FlhB and its homologs, the members of this family form a monophyletic set.
Probab=80.70 E-value=3 Score=33.59 Aligned_cols=60 Identities=15% Similarity=0.289 Sum_probs=45.2
Q ss_pred CCCceeecccccccccchhhhhhhhccccCCCceeeeccchHHHHHHHcCCCCCChhhHHHHHHHHH
Q psy7749 15 GPNWFIKSGFYCNLKTDIVLFCVILRDSHGVAQVRFVSGNKILRIMKAMGLAPNLPEDLYCLIKKAV 81 (319)
Q Consensus 15 ~p~w~~~s~~~~~~~~~~~~IG~iLRD~~GIp~VK~vtGkkI~~ILk~nGlapeIPEDL~~LikKAv 81 (319)
.|.+.+..+...+++..|..++ .+||||.+.. ..+.+.|-.-++..+|||+||.-+-...
T Consensus 15 ~~aP~VvAKG~g~~A~~I~~~A----~e~~VPi~~~---~~LAr~L~~~~ig~~IP~~ly~aVAeil 74 (82)
T TIGR00789 15 DKAPKVVASGVGEVAERIIEIA----KKHGIPIVED---PDLVDVLLKLDLDDEIPEELYEVVAEIF 74 (82)
T ss_pred CCCCEEEEEeCCHHHHHHHHHH----HHcCCCEEeC---HHHHHHHHhCCCCCccCHHHHHHHHHHH
Confidence 3455555454577777777665 4799999887 5688888888999999999997765544
No 29
>TIGR00789 flhB_rel flhB C-terminus-related protein. This model describes a short protein (80-93 residues) homologous to the C-terminus of the flagellar biosynthetic protein FlhB. It is found so far only in species that also have FlhB. In a phylogenetic tree based on alignment of both this family and the homologous region of FlhB and its homologs, the members of this family form a monophyletic set.
Probab=76.51 E-value=6.6 Score=31.64 Aligned_cols=60 Identities=23% Similarity=0.491 Sum_probs=47.2
Q ss_pred CCCCCccCChhHHHHHHHHHhhCCCCccchhhhhhcccCCCceeeeccchHHHHHHHcCCCCCChhhHHHHHHHHHH
Q psy7749 189 SVPNWLKLTSEDVKDHIFKLSKKGLTPSQIGVILRDSHGVAQVRFVSGNKILRIMKAMGLAPNLPEDLYCLIKKAVA 265 (319)
Q Consensus 189 ~~P~Wl~~s~eEVe~~IvkLaKkG~tpSqIG~iLRD~~GIP~VK~vtGkkI~~ILk~nGlapeIPEDL~~LIkKAv~ 265 (319)
.+|-=+-.-.+++-+.|.++|++ +|||.+.. ..+.+.|-.-++..+||||||.-+-....
T Consensus 16 ~aP~VvAKG~g~~A~~I~~~A~e--------------~~VPi~~~---~~LAr~L~~~~ig~~IP~~ly~aVAeil~ 75 (82)
T TIGR00789 16 KAPKVVASGVGEVAERIIEIAKK--------------HGIPIVED---PDLVDVLLKLDLDDEIPEELYEVVAEIFA 75 (82)
T ss_pred CCCEEEEEeCCHHHHHHHHHHHH--------------cCCCEEeC---HHHHHHHHhCCCCCccCHHHHHHHHHHHH
Confidence 45655556678888899998874 79999887 45888888889999999999977655543
No 30
>PF13276 HTH_21: HTH-like domain
Probab=74.54 E-value=5.5 Score=28.95 Aligned_cols=51 Identities=27% Similarity=0.380 Sum_probs=39.0
Q ss_pred hHHHHHHHHHhhC---CCCccchhhhhhcccCCCceeeeccchHHHHHHHcCCCCCCh
Q psy7749 199 EDVKDHIFKLSKK---GLTPSQIGVILRDSHGVAQVRFVSGNKILRIMKAMGLAPNLP 253 (319)
Q Consensus 199 eEVe~~IvkLaKk---G~tpSqIG~iLRD~~GIP~VK~vtGkkI~~ILk~nGlapeIP 253 (319)
+++.+.|.++... -+-.-.|-..|++++|+ .|.-++|.++++++||...++
T Consensus 4 ~~l~~~I~~i~~~~~~~yG~rri~~~L~~~~~~----~v~~krV~RlM~~~gL~~~~r 57 (60)
T PF13276_consen 4 EALRELIKEIFKESKPTYGYRRIWAELRREGGI----RVSRKRVRRLMREMGLRSKRR 57 (60)
T ss_pred HHHHHHHHHHHHHcCCCeehhHHHHHHhccCcc----cccHHHHHHHHHHcCCcccCC
Confidence 4566666666653 34556888999999987 477888999999999987654
No 31
>COG3328 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=68.49 E-value=4 Score=41.01 Aligned_cols=48 Identities=17% Similarity=0.239 Sum_probs=42.9
Q ss_pred CCCCCcCCCCCCCCCCCccCChhHHHHHHHHHhhCCCCccchhhhhhcccCC
Q psy7749 177 KGISKSALPYRRSVPNWLKLTSEDVKDHIFKLSKKGLTPSQIGVILRDSHGV 228 (319)
Q Consensus 177 kG~S~S~~Py~~~~P~Wl~~s~eEVe~~IvkLaKkG~tpSqIG~iLRD~~GI 228 (319)
|+..||-.| .++|.+.....+++.|..|-++|+|+.+|...++..|+.
T Consensus 69 r~r~g~f~p----l~~~~~r~~~~~~~~v~~~y~~gv~Tr~i~~~~~~~~~~ 116 (379)
T COG3328 69 RDRKGSFEP----LIERYQRRERALDLPVLSMYAKGVTTREIEALLEELYGH 116 (379)
T ss_pred cccccCccc----cchhhHhhhhhHHHHHHHHHHcCCcHHHHHHHHHHhhCc
Confidence 455667666 689999999999999999999999999999999999988
No 32
>PF00292 PAX: 'Paired box' domain; InterPro: IPR001523 The paired box is a conserved 124 amino acid N-terminal domain of unknown function that usually, but not always, precedes a homeobox domain (see IPR001356 from INTERPRO) [, ]. Paired box genes are expressed in alternate segments of the developing fruit fly, the observed grouping of segments into pairs depending on the position of the segment in the segmental array, and not on the identity of the segment as in the case of homeotic genes. This implies that the genes affect different processes from those altered by homeotic genes.; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 6PAX_A 1K78_E 1MDM_A 2K27_A 1PDN_C.
Probab=66.00 E-value=3.2 Score=36.13 Aligned_cols=31 Identities=35% Similarity=0.661 Sum_probs=24.1
Q ss_pred ChhHHHHHHHHHhhCCCCccchhhhhhcccC
Q psy7749 197 TSEDVKDHIFKLSKKGLTPSQIGVILRDSHG 227 (319)
Q Consensus 197 s~eEVe~~IvkLaKkG~tpSqIG~iLRD~~G 227 (319)
=++|+-+.|++||+.|+.|.+|--.|+=+||
T Consensus 18 Lp~~~R~rIvela~~G~rp~~Isr~l~Vs~g 48 (125)
T PF00292_consen 18 LPNELRQRIVELAKEGVRPCDISRQLRVSHG 48 (125)
T ss_dssp S-HHHHHHHHHHHHTT--HHHHHHHHT--HH
T ss_pred CcHHHHHHHHHHhhhcCCHHHHHHHHccchh
Confidence 3688999999999999999999999998886
No 33
>PRK01322 6-carboxyhexanoate--CoA ligase; Provisional
Probab=64.77 E-value=6.1 Score=37.89 Aligned_cols=77 Identities=22% Similarity=0.322 Sum_probs=55.2
Q ss_pred ccCCC--CCCCCCcCCCCCCCCCCCccCChhHHHHHHHHHhhCCCCccchhhhhhcccCCCceeeeccchH---------
Q psy7749 171 RMHTP--GKGISKSALPYRRSVPNWLKLTSEDVKDHIFKLSKKGLTPSQIGVILRDSHGVAQVRFVSGNKI--------- 239 (319)
Q Consensus 171 RMhs~--~kG~S~S~~Py~~~~P~Wl~~s~eEVe~~IvkLaKkG~tpSqIG~iLRD~~GIP~VK~vtGkkI--------- 239 (319)
||.+. |+=+||--+=. +.++|++.+.+|.+++++- +.|.|+--+++=.+|
T Consensus 6 kMRAs~~g~HISGAErIv----------~~~~i~~~~~~L~~Ral~H---------~~G~pDfinIkve~i~~~I~~i~~ 66 (242)
T PRK01322 6 KMRASKNGKHISGAERIV----------EFEKIEETVSELLKRALFH---------ENGKPDFINIKIEKIEEPIQYIKA 66 (242)
T ss_pred EeEccCCCCccccccccC----------CHHHHHHHHHHHHHhhhhc---------cCCCCCeeEEEEEEccCcceeccC
Confidence 45443 46677765443 6899999999999998765 567766544333332
Q ss_pred ------------------HHHHHHcCCCCCChhhHHHHHHHHHHH
Q psy7749 240 ------------------LRIMKAMGLAPNLPEDLYCLIKKAVAI 266 (319)
Q Consensus 240 ------------------~~ILk~nGlapeIPEDL~~LIkKAv~i 266 (319)
..+|++.|+.++.+|..+.+|.+--+|
T Consensus 67 LpV~t~~~~~~eea~~~a~~lL~~~gv~~~~~~~~~~~l~~~~~M 111 (242)
T PRK01322 67 LPIKTIDVKSVEEARALARELLQEEGVSEEAIEKAFELIKEGTNM 111 (242)
T ss_pred cceeEEecCCHHHHHHHHHHHHHhcCCCHHHHHHHHHHHhcCCCC
Confidence 455999999999999999998885333
No 34
>PF07750 GcrA: GcrA cell cycle regulator; InterPro: IPR011681 GcrA, together with CtrA (see IPR001789 from INTERPRO and IPR001867 from INTERPRO), form a master cell cycle regulator. These bacterial regulators are involved in controlling the progression and asymmetric polar morphogenesis []. During this process, there are temporal and spatial variations in the concentrations of GcrA and CtrA. The variation in concentration produces time and space dependent transcriptional regulation of modular functions that implement cell-cycle processes []. More specifically, GcrA acts as an activator of components of the replisome and the segregation machinery [].
Probab=64.39 E-value=4.9 Score=35.81 Aligned_cols=25 Identities=32% Similarity=0.404 Sum_probs=21.2
Q ss_pred hHHHHHHHHHhhCCCCccchhhhhh
Q psy7749 199 EDVKDHIFKLSKKGLTPSQIGVILR 223 (319)
Q Consensus 199 eEVe~~IvkLaKkG~tpSqIG~iLR 223 (319)
||-.+.+.+|.++|+|-|||+..|=
T Consensus 5 de~~~~L~~lw~~G~SasqIA~~lg 29 (162)
T PF07750_consen 5 DERVERLRKLWAEGLSASQIARQLG 29 (162)
T ss_pred HHHHHHHHHHHHcCCCHHHHHHHhC
Confidence 4455689999999999999998874
No 35
>PHA02591 hypothetical protein; Provisional
Probab=60.96 E-value=6.1 Score=32.58 Aligned_cols=28 Identities=25% Similarity=0.425 Sum_probs=25.2
Q ss_pred cCChhHHHHHHHHHhhCCCCccchhhhh
Q psy7749 195 KLTSEDVKDHIFKLSKKGLTPSQIGVIL 222 (319)
Q Consensus 195 ~~s~eEVe~~IvkLaKkG~tpSqIG~iL 222 (319)
--+.||+....-+|++.|+|.+||+..|
T Consensus 42 i~~~dd~~~vA~eL~eqGlSqeqIA~~L 69 (83)
T PHA02591 42 VESEDDLISVTHELARKGFTVEKIASLL 69 (83)
T ss_pred EeccchHHHHHHHHHHcCCCHHHHHHHh
Confidence 3478899999999999999999999877
No 36
>PF11740 KfrA_N: Plasmid replication region DNA-binding N-term; InterPro: IPR021104 The KfrA family of protiens are encoded on plasmids, generally in or near gene clusters invloved in stable inheritance functions. These proteins are thought to form an all-helical structure, consisting of an N-terminal helix-turn-helix DNA binding domain and an extended coiled-coil tail. The best-characterised KfrA protein, encoded on the broad host-range Plasmid RK2, is a site-specific DNA-binding protein whose operator overlaps its own promoter. The DNA-binding domain is essential for function, while the coiled-coil domain is probably responsible for formation of multimers, and may provide an example of a bridge to host structures required for plasmid partitioning []. This entry represents the N-terminal DNA-binding domain.
Probab=57.68 E-value=16 Score=29.45 Aligned_cols=58 Identities=29% Similarity=0.394 Sum_probs=37.8
Q ss_pred CChhHHHHHHHHHhhCCCCccchhhhhhcccCCCceeeeccchHHHHHHH------cC---CCCCChhhHHHHH
Q psy7749 196 LTSEDVKDHIFKLSKKGLTPSQIGVILRDSHGVAQVRFVSGNKILRIMKA------MG---LAPNLPEDLYCLI 260 (319)
Q Consensus 196 ~s~eEVe~~IvkLaKkG~tpSqIG~iLRD~~GIP~VK~vtGkkI~~ILk~------nG---lapeIPEDL~~LI 260 (319)
+|.++|.+....|...|-.||- ..+|..-|-++- ..|.+.|++ .. ..|++|++|-..+
T Consensus 1 IT~e~V~~Aa~~L~~~G~~pT~--~~Vr~~lG~GS~-----~ti~~~l~~w~~~~~~~~~~~~~~lP~~l~~~~ 67 (120)
T PF11740_consen 1 ITYEDVIEAADELLAAGKKPTV--RAVRERLGGGSM-----STISKHLKEWREEREAQVSEAAPDLPEALQDAL 67 (120)
T ss_pred CcHHHHHHHHHHHHHcCCCCCH--HHHHHHHCCCCH-----HHHHHHHHHHHHhhhccccccccCCChhHHHHH
Confidence 4789999999999999999974 334555552211 235555553 12 3678888884433
No 37
>PF00356 LacI: Bacterial regulatory proteins, lacI family; InterPro: IPR000843 Numerous bacterial transcription regulatory proteins bind DNA via a helix-turn-helix (HTH) motif. These proteins are very diverse, but for convenience may be grouped into subfamilies on the basis of sequence similarity. One such family groups together a range of proteins, including ascG, ccpA, cytR, ebgR, fruR, galR, galS, lacI, malI, opnR, purF, rafR, rbtR and scrR [, ]. Within this family, the HTH motif is situated towards the N terminus.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 3KJX_C 1ZAY_A 1VPW_A 2PUA_A 1QQA_A 1PNR_A 1JFT_A 1QP4_A 2PUD_A 1JH9_A ....
Probab=56.60 E-value=5.2 Score=28.90 Aligned_cols=37 Identities=22% Similarity=0.436 Sum_probs=32.6
Q ss_pred CCCCccchhhhhhcccCCCceeeeccchHHHHHHHcCCCC
Q psy7749 211 KGLTPSQIGVILRDSHGVAQVRFVSGNKILRIMKAMGLAP 250 (319)
Q Consensus 211 kG~tpSqIG~iLRD~~GIP~VK~vtGkkI~~ILk~nGlap 250 (319)
-|+|+|-+-.+|.+. |.|..-|-.+|.++.++.|-.|
T Consensus 9 agvS~~TVSr~ln~~---~~vs~~tr~rI~~~a~~lgY~p 45 (46)
T PF00356_consen 9 AGVSKSTVSRVLNGP---PRVSEETRERILEAAEELGYRP 45 (46)
T ss_dssp HTSSHHHHHHHHTTC---SSSTHHHHHHHHHHHHHHTB-S
T ss_pred HCcCHHHHHHHHhCC---CCCCHHHHHHHHHHHHHHCCCC
Confidence 599999999999998 7788899999999999998766
No 38
>PF13361 UvrD_C: UvrD-like helicase C-terminal domain; PDB: 1UAA_B 3U4Q_A 3U44_A 1W36_B 3K70_B 2IS6_B 3LFU_A 2IS2_B 2IS1_B 2IS4_A ....
Probab=53.02 E-value=8.6 Score=34.34 Aligned_cols=43 Identities=30% Similarity=0.525 Sum_probs=29.9
Q ss_pred hHHHHHHHHHhhCCCCccchhhhhhcccCCCceeeeccchHHHHHHHcCCC
Q psy7749 199 EDVKDHIFKLSKKGLTPSQIGVILRDSHGVAQVRFVSGNKILRIMKAMGLA 249 (319)
Q Consensus 199 eEVe~~IvkLaKkG~tpSqIG~iLRD~~GIP~VK~vtGkkI~~ILk~nGla 249 (319)
+.|.+.|.++...|.+|+.|++..|+.. + +..|.+.|+++|+.
T Consensus 61 ~~i~~~I~~l~~~~~~~~diAVL~R~~~---~-----~~~i~~~L~~~gIp 103 (351)
T PF13361_consen 61 EYIAEEIKELIRNGIPPSDIAVLVRTNS---Q-----IKEIEDALKEAGIP 103 (351)
T ss_dssp HHHHHHHHHHHHTTS-GGGEEEEESSGG---H-----HHHHHHHHHHTTS-
T ss_pred HHHHHHHHHHhhcCCCcccEEEEEECch---h-----HHHHHHHHhhhcce
Confidence 4477888888888999999999999942 2 22355566666654
No 39
>COG1202 Superfamily II helicase, archaea-specific [General function prediction only]
Probab=52.76 E-value=7.8 Score=42.17 Aligned_cols=46 Identities=28% Similarity=0.545 Sum_probs=38.2
Q ss_pred HHHHHHHHHhhCCCCccchhhhhhcccCCCceeeeccchHHHHHHHcCCCCCChhhHHHHHHHHHHH
Q psy7749 200 DVKDHIFKLSKKGLTPSQIGVILRDSHGVAQVRFVSGNKILRIMKAMGLAPNLPEDLYCLIKKAVAI 266 (319)
Q Consensus 200 EVe~~IvkLaKkG~tpSqIG~iLRD~~GIP~VK~vtGkkI~~ILk~nGlapeIPEDL~~LIkKAv~i 266 (319)
-.-++|++|.-.|.+|+||-.+|++.|||- ..|-|.++-...+|++
T Consensus 754 ~lse~ii~lR~~gk~p~~Isr~l~~~Ygi~---------------------aYpgDif~wLd~~vr~ 799 (830)
T COG1202 754 RLSEKIIELRIEGKDPSQISRILEKRYGIQ---------------------AYPGDIFTWLDTLVRL 799 (830)
T ss_pred HHHHHHHHHHhcCCCHHHHHHHHHHhhCee---------------------ecChhHHHHHHHHHHH
Confidence 344889999999999999999999999983 3677888777777665
No 40
>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=52.69 E-value=37 Score=33.76 Aligned_cols=62 Identities=15% Similarity=0.312 Sum_probs=50.5
Q ss_pred CCCCCccCChhHHHHHHHHHhhCCCCccchhhhhhcccCCCceeeeccchHHHHH-HHcCCCCCChhhHHHHHHHHHHHH
Q psy7749 189 SVPNWLKLTSEDVKDHIFKLSKKGLTPSQIGVILRDSHGVAQVRFVSGNKILRIM-KAMGLAPNLPEDLYCLIKKAVAIR 267 (319)
Q Consensus 189 ~~P~Wl~~s~eEVe~~IvkLaKkG~tpSqIG~iLRD~~GIP~VK~vtGkkI~~IL-k~nGlapeIPEDL~~LIkKAv~iR 267 (319)
.+|-=+-.-.+++-..|.++|++ ||||-|.. ..+.|-| +.-.+..+|||+||.-+-.....-
T Consensus 278 ~aP~vvakG~~~~A~~I~~~A~~--------------~~vPi~~~---~~LAr~Ly~~~~~g~~IP~~ly~aVA~il~~v 340 (347)
T TIGR00328 278 PAPVVVAKGVDELALKIKEIARE--------------NNVPIVEN---PPLARALYRQVEIGQEIPPELYKAVAEVLAYV 340 (347)
T ss_pred CCCEEEEeeCcHHHHHHHHHHHH--------------cCCCEEeC---HHHHHHHHHcCCCCCcCCHHHHHHHHHHHHHH
Confidence 45777777889999999999986 89999887 4588888 677889999999998877665543
No 41
>KOG1802|consensus
Probab=52.18 E-value=7.5 Score=42.79 Aligned_cols=50 Identities=40% Similarity=0.577 Sum_probs=38.3
Q ss_pred hhHHHHHHHHHhhCCCCccchhhhhhcccCCCceeeeccc--hHHHHHHHcCCCCCChhhHHHHH
Q psy7749 198 SEDVKDHIFKLSKKGLTPSQIGVILRDSHGVAQVRFVSGN--KILRIMKAMGLAPNLPEDLYCLI 260 (319)
Q Consensus 198 ~eEVe~~IvkLaKkG~tpSqIG~iLRD~~GIP~VK~vtGk--kI~~ILk~nGlapeIPEDL~~LI 260 (319)
+-++|.+|-+|-+.|+.|||||+|- +.-|. .|..+|..+| .++-|||.-|
T Consensus 709 a~~~ekii~~l~~~gv~~~qIGVIT----------pYegQr~~i~~ym~~~g---sl~~~ly~~v 760 (935)
T KOG1802|consen 709 AANCEKIITKLLKSGVKPSQIGVIT----------PYEGQRSYIVNYMQTNG---SLHKDLYKEV 760 (935)
T ss_pred HHHHHHHHHHHHHcCCCHHHeeeec----------ccchhHHHHHHHHHhcC---ccccchhhee
Confidence 5578999999999999999999863 33343 3788886666 5677888655
No 42
>PRK06298 type III secretion system protein; Validated
Probab=51.89 E-value=37 Score=33.96 Aligned_cols=73 Identities=15% Similarity=0.062 Sum_probs=49.8
Q ss_pred CCCceeecccccccccchhhhhhhhccccCCCceeeeccchHHHHH-HHcCCCCCChhhHHHHHHHHHHHHHHHh-hccC
Q psy7749 15 GPNWFIKSGFYCNLKTDIVLFCVILRDSHGVAQVRFVSGNKILRIM-KAMGLAPNLPEDLYCLIKKAVAIRKHLE-RSRK 92 (319)
Q Consensus 15 ~p~w~~~s~~~~~~~~~~~~IG~iLRD~~GIp~VK~vtGkkI~~IL-k~nGlapeIPEDL~~LikKAv~lRkHLe-~n~k 92 (319)
.|.+.+..+..++++..|..|. .+||||-|.. ..+-|-| +.-.+..+|||+||.-+-...+---.++ +||.
T Consensus 278 ~~AP~VvAKG~d~~A~~Ir~iA----~e~~VPiven---~pLARaLy~~~evg~~IP~ely~AVA~IL~~v~~l~~~~~~ 350 (356)
T PRK06298 278 YKAPWIIAMGINLRAKRIIAEA----EKYGVPIMRN---VPLAHQLLDEGKELKFIPESTYEAIGEILLYITSLNAQNPN 350 (356)
T ss_pred CCCCEEEEeeCcHHHHHHHHHH----HHcCCCEEeC---HHHHHHHHHcCCCCCcCCHHHHHHHHHHHHHHHHHhCcCcC
Confidence 3555555555567777666555 3699999886 5688888 4667888999999977766665544444 4444
Q ss_pred cc
Q psy7749 93 DK 94 (319)
Q Consensus 93 Dk 94 (319)
++
T Consensus 351 ~~ 352 (356)
T PRK06298 351 NK 352 (356)
T ss_pred CC
Confidence 43
No 43
>PRK15364 pathogenicity island 2 effector protein SseB; Provisional
Probab=51.15 E-value=39 Score=31.77 Aligned_cols=81 Identities=22% Similarity=0.255 Sum_probs=58.4
Q ss_pred ChhHHHHHHHHHhhCCC-----CccchhhhhhcccCCCceeeeccchHHHHHHHcCCCCCChhhHHHHHHHHHHHHHHHh
Q psy7749 197 TSEDVKDHIFKLSKKGL-----TPSQIGVILRDSHGVAQVRFVSGNKILRIMKAMGLAPNLPEDLYCLIKKAVAIRKHLE 271 (319)
Q Consensus 197 s~eEVe~~IvkLaKkG~-----tpSqIG~iLRD~~GIP~VK~vtGkkI~~ILk~nGlapeIPEDL~~LIkKAv~iRKHLe 271 (319)
.+.+|.+.|.+++|.|= -|-.+=..+|| +||- |.|++|-..|+++|..+++-.-=...||-|+.--.
T Consensus 77 mAN~VDevIA~v~k~ddK~k~~LPddVI~Ymrd-NgI~----VdG~sid~Yl~k~~~~~~LdkG~LqAVKAALd~~s--- 148 (196)
T PRK15364 77 KSNEMDEVIAKAAKGDAKTKEEVPEDVIKYMRD-NGIL----IDGMTIDDYMAKYGDHGKLDKGGLQAIKAALDNDA--- 148 (196)
T ss_pred HHHHHHHHHHHHhcCCCcccccCCHHHHHHHHH-cCce----ecccchHHHHhccCCccCCChhhHHHHHHHHHhhc---
Confidence 46789999999977442 25555678899 8984 79999999999999999998877777887754321
Q ss_pred hhcCcccchhhHHH
Q psy7749 272 RSRKDKDSKFRLIL 285 (319)
Q Consensus 272 ~n~KD~~sKr~L~L 285 (319)
-+--|.-+.-+|++
T Consensus 149 nr~TD~vsQsQLqi 162 (196)
T PRK15364 149 NRNTDLMSQGQITI 162 (196)
T ss_pred cccchhhhHHHHHH
Confidence 22345555555543
No 44
>PF13276 HTH_21: HTH-like domain
Probab=48.52 E-value=15 Score=26.64 Aligned_cols=33 Identities=30% Similarity=0.453 Sum_probs=28.0
Q ss_pred hhhhhhccccCCCceeeeccchHHHHHHHcCCCCCCh
Q psy7749 34 LFCVILRDSHGVAQVRFVSGNKILRIMKAMGLAPNLP 70 (319)
Q Consensus 34 ~IG~iLRD~~GIp~VK~vtGkkI~~ILk~nGlapeIP 70 (319)
.|-..|++++|+ .|.-++|.++++++||...++
T Consensus 25 ri~~~L~~~~~~----~v~~krV~RlM~~~gL~~~~r 57 (60)
T PF13276_consen 25 RIWAELRREGGI----RVSRKRVRRLMREMGLRSKRR 57 (60)
T ss_pred HHHHHHhccCcc----cccHHHHHHHHHHcCCcccCC
Confidence 588899999887 477889999999999987654
No 45
>PHA02517 putative transposase OrfB; Reviewed
Probab=48.12 E-value=21 Score=32.58 Aligned_cols=48 Identities=23% Similarity=0.313 Sum_probs=39.4
Q ss_pred hhHHHHHHHHHhhC---CCCccchhhhhhcccCCCceeeeccchHHHHHHHcCCCC
Q psy7749 198 SEDVKDHIFKLSKK---GLTPSQIGVILRDSHGVAQVRFVSGNKILRIMKAMGLAP 250 (319)
Q Consensus 198 ~eEVe~~IvkLaKk---G~tpSqIG~iLRD~~GIP~VK~vtGkkI~~ILk~nGlap 250 (319)
.+++.+.|.++..+ .+...+|-..|+++ |+ .+.-+.|.++|+++|+..
T Consensus 28 ~~~l~~~I~~i~~~~~~~~G~r~I~~~L~~~-g~----~vs~~tV~Rim~~~gl~~ 78 (277)
T PHA02517 28 DDWLKSEILRVYDENHQVYGVRKVWRQLNRE-GI----RVARCTVGRLMKELGLAG 78 (277)
T ss_pred hHHHHHHHHHHHHHhCCCCCHHHHHHHHHhc-Cc----ccCHHHHHHHHHHcCCce
Confidence 56889999999633 46889999999987 76 367788999999999965
No 46
>PRK13902 alaS alanyl-tRNA synthetase; Provisional
Probab=47.60 E-value=31 Score=38.41 Aligned_cols=55 Identities=27% Similarity=0.423 Sum_probs=41.9
Q ss_pred HHHHHhhC-CCCccchhhhhhcccCCCceeeeccchHHHHHHHcCCCCCChhhHHHHHHHHH
Q psy7749 204 HIFKLSKK-GLTPSQIGVILRDSHGVAQVRFVSGNKILRIMKAMGLAPNLPEDLYCLIKKAV 264 (319)
Q Consensus 204 ~IvkLaKk-G~tpSqIG~iLRD~~GIP~VK~vtGkkI~~ILk~nGlapeIPEDL~~LIkKAv 264 (319)
++-+++++ +.=|-+.-..|-|+||+|.= =+.+|.+++|+.-++|++.+.+|.+.-
T Consensus 419 ~~~~~~~~~~~l~g~~~f~LYDt~G~P~d------l~~eia~e~g~~vd~p~~F~~~~~~~~ 474 (900)
T PRK13902 419 IVERLAKKKEEIPLDDLIELYDSHGIPPE------IVKEIAKKKGVEVEVPDNFYSLVAERH 474 (900)
T ss_pred HHHHHHHhcCCCCHHHHhhhhhcCCCCHH------HHHHHHHHcCCccCchhhHHHHHHHHH
Confidence 33445544 55577888999999999952 145789999999999999999886643
No 47
>COG1964 Predicted Fe-S oxidoreductases [General function prediction only]
Probab=46.44 E-value=49 Score=34.76 Aligned_cols=83 Identities=23% Similarity=0.300 Sum_probs=61.6
Q ss_pred hccCCCC-CCCCCcCCCCCCCCCCCccCChhHHHHHHHHHhhCCCCccchhhhhhccc-CCCceeeeccchHHHHHHHcC
Q psy7749 170 GRMHTPG-KGISKSALPYRRSVPNWLKLTSEDVKDHIFKLSKKGLTPSQIGVILRDSH-GVAQVRFVSGNKILRIMKAMG 247 (319)
Q Consensus 170 aRMhs~~-kG~S~S~~Py~~~~P~Wl~~s~eEVe~~IvkLaKkG~tpSqIG~iLRD~~-GIP~VK~vtGkkI~~ILk~nG 247 (319)
++-.-.| .|.+..+-+|...++-=..-|-|+|++++-.|.++ + +.|.+-++||
T Consensus 64 ~~~~~~g~~g~~~~CFa~A~~ag~vYEpt~eqi~~Ml~~lk~e--------------~p~~~~aIq~tG----------- 118 (475)
T COG1964 64 ARWEFEGKFGVNNECFAYAEEAGYIYEPTLEQIREMLRNLKKE--------------HPVGANAVQFTG----------- 118 (475)
T ss_pred HhhcccCCcCCCCcCcCchhhcCcccCCCHHHHHHHHHHHHhc--------------CCCCCceeEecC-----------
Confidence 3445566 88888899999998888899999999999887654 3 3345556665
Q ss_pred CCCCChhhHHHHHHHHHHH-HHHHhhhcCcc
Q psy7749 248 LAPNLPEDLYCLIKKAVAI-RKHLERSRKDK 277 (319)
Q Consensus 248 lapeIPEDL~~LIkKAv~i-RKHLe~n~KD~ 277 (319)
=.|.|++||+.||+-|-.. =+|.+.|..-.
T Consensus 119 GEPTvr~DL~eiv~~a~e~g~~hVqinTnGi 149 (475)
T COG1964 119 GEPTLRDDLIEIIKIAREEGYDHVQLNTNGI 149 (475)
T ss_pred CCccchhhHHHHHHHHhhcCccEEEEccCce
Confidence 4699999999999988655 23555554433
No 48
>PRK05702 flhB flagellar biosynthesis protein FlhB; Reviewed
Probab=45.81 E-value=59 Score=32.52 Aligned_cols=67 Identities=21% Similarity=0.365 Sum_probs=52.8
Q ss_pred CCCCCccCChhHHHHHHHHHhhCCCCccchhhhhhcccCCCceeeeccchHHHHHH-HcCCCCCChhhHHHHHHHHHHHH
Q psy7749 189 SVPNWLKLTSEDVKDHIFKLSKKGLTPSQIGVILRDSHGVAQVRFVSGNKILRIMK-AMGLAPNLPEDLYCLIKKAVAIR 267 (319)
Q Consensus 189 ~~P~Wl~~s~eEVe~~IvkLaKkG~tpSqIG~iLRD~~GIP~VK~vtGkkI~~ILk-~nGlapeIPEDL~~LIkKAv~iR 267 (319)
.+|-=+-.-.+++-..|.++|+ +||||-+.. ..+.|-|= .-.+..+|||+||.-+-.....-
T Consensus 285 ~aP~vvakg~~~~A~~i~~~A~--------------~~~vpi~~~---~~LAr~Ly~~~~~g~~Ip~~~~~aVA~il~~v 347 (359)
T PRK05702 285 AAPVVVAKGVDEVALKIREIAR--------------EHNVPIVEN---PPLARALYATVEIGQEIPEELYKAVAEVLAYV 347 (359)
T ss_pred CCCEEEEeeCcHHHHHHHHHHH--------------HcCCCEEeC---HHHHHHHHHcCCCCCccCHHHHHHHHHHHHHH
Confidence 4576677778899999999997 689999887 45888885 66788999999998888776665
Q ss_pred HHHhh
Q psy7749 268 KHLER 272 (319)
Q Consensus 268 KHLe~ 272 (319)
..++.
T Consensus 348 ~~~~~ 352 (359)
T PRK05702 348 YQLKR 352 (359)
T ss_pred HHHHh
Confidence 55544
No 49
>PF15652 Tox-SHH: HNH/Endo VII superfamily toxin with a SHH signature
Probab=44.32 E-value=15 Score=31.18 Aligned_cols=34 Identities=12% Similarity=0.217 Sum_probs=32.9
Q ss_pred CccCChhHHHHHHHHHhhCCCCccchhhhhhccc
Q psy7749 193 WLKLTSEDVKDHIFKLSKKGLTPSQIGVILRDSH 226 (319)
Q Consensus 193 Wl~~s~eEVe~~IvkLaKkG~tpSqIG~iLRD~~ 226 (319)
|-....+|+....-+|-+.|++++++=..|+|+|
T Consensus 63 w~t~~~~Ef~~~~~eM~dAGV~~~~~~~~l~~~Y 96 (100)
T PF15652_consen 63 WSTTLQEEFNNSYREMFDAGVSKECRKKALKAQY 96 (100)
T ss_pred ccchHHHHHHHHHHHHHHcCCCHHHHHHHHHHHH
Confidence 9999999999999999999999999999999987
No 50
>PF00872 Transposase_mut: Transposase, Mutator family; InterPro: IPR001207 Autonomous mobile genetic elements such as transposon or insertion sequences (IS) encode an enzyme, transposase, that is required for excising and inserting the mobile element. Transposases have been grouped into various families [, , ]. The mutator family of transposases consists of a number of elements that include, mutator from maize, IsT2 from Thiobacillus ferrooxidans, Is256 from Staphylococcus aureus, Is1201 from Lactobacillus helveticus, Is1081 from Mycobacterium bovis, IsRm3 from Rhizobium meliloti and others. More information about these proteins can be found at Protein of the Month: Transposase [].; GO: 0003677 DNA binding, 0004803 transposase activity, 0006313 transposition, DNA-mediated
Probab=43.65 E-value=15 Score=36.15 Aligned_cols=38 Identities=26% Similarity=0.486 Sum_probs=33.2
Q ss_pred CCCccCChhHHHHHHHHHhhCCCCccchhhhhhcccC-CC
Q psy7749 191 PNWLKLTSEDVKDHIFKLSKKGLTPSQIGVILRDSHG-VA 229 (319)
Q Consensus 191 P~Wl~~s~eEVe~~IvkLaKkG~tpSqIG~iLRD~~G-IP 229 (319)
|.|-. ..+++++.|..|.-+|+|..+|+.+|.+-|| .+
T Consensus 94 ~~y~r-~~~~l~~~i~~ly~~G~Str~i~~~l~~l~g~~~ 132 (381)
T PF00872_consen 94 PKYQR-REDSLEELIISLYLKGVSTRDIEEALEELYGEVA 132 (381)
T ss_pred chhhh-hhhhhhhhhhhhhccccccccccchhhhhhcccc
Confidence 44443 4679999999999999999999999999999 87
No 51
>PF02899 Phage_int_SAM_1: Phage integrase, N-terminal SAM-like domain; InterPro: IPR004107 Proteins containing this domain cleave DNA substrates by a series of staggered cuts, during which the protein becomes covalently linked to the DNA through a catalytic tyrosine residue at the carboxy end of the alignment [, ]. The phage integrase N-terminal SAM-like domain is almost always found with the signature that defines the phage integrase family (see IPR002104 from INTERPRO).; GO: 0003677 DNA binding, 0015074 DNA integration; PDB: 1Z1G_B 1Z19_A 1Z1B_A 2OXO_A 1P7D_B 3NRW_A 1A0P_A.
Probab=43.48 E-value=21 Score=26.17 Aligned_cols=32 Identities=41% Similarity=0.701 Sum_probs=23.8
Q ss_pred CCCCccCChhHHHHHHHHHhhCCCCccchhhh
Q psy7749 190 VPNWLKLTSEDVKDHIFKLSKKGLTPSQIGVI 221 (319)
Q Consensus 190 ~P~Wl~~s~eEVe~~IvkLaKkG~tpSqIG~i 221 (319)
...|.+++.++|++-+..+.++|++|+-|-..
T Consensus 38 ~~~~~~i~~~~v~~f~~~~~~~~~s~~T~~~~ 69 (84)
T PF02899_consen 38 IIDWEDITEEDVRDFLEYLAKEGLSPSTINRR 69 (84)
T ss_dssp S-CGGG--HHHHHHHHHHHHCTT--HHHHHHH
T ss_pred hhhhhhhhhHHHHHHHHHHHccCCCHHHHHHH
Confidence 47899999999999999999999999877644
No 52
>PRK06298 type III secretion system protein; Validated
Probab=43.35 E-value=71 Score=31.98 Aligned_cols=71 Identities=15% Similarity=0.154 Sum_probs=53.4
Q ss_pred CCCCCccCChhHHHHHHHHHhhCCCCccchhhhhhcccCCCceeeeccchHHHHH-HHcCCCCCChhhHHHHHHHHHHHH
Q psy7749 189 SVPNWLKLTSEDVKDHIFKLSKKGLTPSQIGVILRDSHGVAQVRFVSGNKILRIM-KAMGLAPNLPEDLYCLIKKAVAIR 267 (319)
Q Consensus 189 ~~P~Wl~~s~eEVe~~IvkLaKkG~tpSqIG~iLRD~~GIP~VK~vtGkkI~~IL-k~nGlapeIPEDL~~LIkKAv~iR 267 (319)
.+|-=+-.-.+++-..|.++|++ ||||-|.. ..+.|-| +.-.+..+|||+||.-+-....-=
T Consensus 279 ~AP~VvAKG~d~~A~~Ir~iA~e--------------~~VPiven---~pLARaLy~~~evg~~IP~ely~AVA~IL~~v 341 (356)
T PRK06298 279 KAPWIIAMGINLRAKRIIAEAEK--------------YGVPIMRN---VPLAHQLLDEGKELKFIPESTYEAIGEILLYI 341 (356)
T ss_pred CCCEEEEeeCcHHHHHHHHHHHH--------------cCCCEEeC---HHHHHHHHHcCCCCCcCCHHHHHHHHHHHHHH
Confidence 45777777789999999999874 89999886 4588888 456688999999997777666554
Q ss_pred HHHh-hhcCc
Q psy7749 268 KHLE-RSRKD 276 (319)
Q Consensus 268 KHLe-~n~KD 276 (319)
-.++ +||.+
T Consensus 342 ~~l~~~~~~~ 351 (356)
T PRK06298 342 TSLNAQNPNN 351 (356)
T ss_pred HHHhCcCcCC
Confidence 4444 44443
No 53
>smart00354 HTH_LACI helix_turn _helix lactose operon repressor.
Probab=43.07 E-value=18 Score=27.22 Aligned_cols=39 Identities=23% Similarity=0.416 Sum_probs=33.2
Q ss_pred CCCCccchhhhhhcccCCCceeeeccchHHHHHHHcCCCCCC
Q psy7749 211 KGLTPSQIGVILRDSHGVAQVRFVSGNKILRIMKAMGLAPNL 252 (319)
Q Consensus 211 kG~tpSqIG~iLRD~~GIP~VK~vtGkkI~~ILk~nGlapeI 252 (319)
-|+|.+.|..+|++.-+| ..-|-.+|.+++++.|..|..
T Consensus 10 ~gvS~~TVSr~ln~~~~v---~~~t~~~i~~~~~~~gy~~~~ 48 (70)
T smart00354 10 AGVSKATVSRVLNGNGRV---SEETREKVLAAMEELGYIPNR 48 (70)
T ss_pred HCCCHHHHHHHHCCCCCC---CHHHHHHHHHHHHHhCCCCCH
Confidence 499999999999887554 678888999999999997764
No 54
>PF13551 HTH_29: Winged helix-turn helix
Probab=43.00 E-value=63 Score=24.88 Aligned_cols=51 Identities=29% Similarity=0.509 Sum_probs=33.8
Q ss_pred CCCccCChhHHHHHHHHHhhC----C---CCccchhhhh-hcccCCCceeeeccchHHHHHHHcC
Q psy7749 191 PNWLKLTSEDVKDHIFKLSKK----G---LTPSQIGVIL-RDSHGVAQVRFVSGNKILRIMKAMG 247 (319)
Q Consensus 191 P~Wl~~s~eEVe~~IvkLaKk----G---~tpSqIG~iL-RD~~GIP~VK~vtGkkI~~ILk~nG 247 (319)
|.+. +++++ ++.|+++..+ | .|+.+|-..| ..++|+. +.-..|.++|+++|
T Consensus 54 ~~~~-l~~~~-~~~l~~~~~~~p~~g~~~~t~~~l~~~l~~~~~~~~----~s~~ti~r~L~~~G 112 (112)
T PF13551_consen 54 PRKR-LSEEQ-RAQLIELLRENPPEGRSRWTLEELAEWLIEEEFGID----VSPSTIRRILKRAG 112 (112)
T ss_pred CCCC-CCHHH-HHHHHHHHHHCCCCCCCcccHHHHHHHHHHhccCcc----CCHHHHHHHHHHCc
Confidence 4443 45444 4466666654 3 5677887765 7888886 45567999999887
No 55
>PF13936 HTH_38: Helix-turn-helix domain; PDB: 2W48_A.
Probab=42.54 E-value=13 Score=26.13 Aligned_cols=26 Identities=31% Similarity=0.404 Sum_probs=13.6
Q ss_pred CChhHHHHHHHHHhhCCCCccchhhhh
Q psy7749 196 LTSEDVKDHIFKLSKKGLTPSQIGVIL 222 (319)
Q Consensus 196 ~s~eEVe~~IvkLaKkG~tpSqIG~iL 222 (319)
+|.+|... |..|.++|+|.++|+..|
T Consensus 5 Lt~~eR~~-I~~l~~~G~s~~~IA~~l 30 (44)
T PF13936_consen 5 LTPEERNQ-IEALLEQGMSIREIAKRL 30 (44)
T ss_dssp -------H-HHHHHCS---HHHHHHHT
T ss_pred hhhhHHHH-HHHHHHcCCCHHHHHHHH
Confidence 45666544 778999999999999876
No 56
>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=42.41 E-value=60 Score=32.34 Aligned_cols=63 Identities=16% Similarity=0.202 Sum_probs=45.5
Q ss_pred CCCceeecccccccccchhhhhhhhccccCCCceeeeccchHHHHH-HHcCCCCCChhhHHHHHHHHHHHH
Q psy7749 15 GPNWFIKSGFYCNLKTDIVLFCVILRDSHGVAQVRFVSGNKILRIM-KAMGLAPNLPEDLYCLIKKAVAIR 84 (319)
Q Consensus 15 ~p~w~~~s~~~~~~~~~~~~IG~iLRD~~GIp~VK~vtGkkI~~IL-k~nGlapeIPEDL~~LikKAv~lR 84 (319)
.|.+.+..+..++++..|..|+. +||||-|.. ..+.|-| +.-.+..+||++||.-+-.....-
T Consensus 277 ~~aP~vvakG~~~~A~~I~~~A~----~~~vPi~~~---~~LAr~Ly~~~~~g~~IP~~ly~aVA~il~~v 340 (347)
T TIGR00328 277 MPAPVVVAKGVDELALKIKEIAR----ENNVPIVEN---PPLARALYRQVEIGQEIPPELYKAVAEVLAYV 340 (347)
T ss_pred CCCCEEEEeeCcHHHHHHHHHHH----HcCCCEEeC---HHHHHHHHHcCCCCCcCCHHHHHHHHHHHHHH
Confidence 34555554445677777766664 599999887 5688888 677888999999998877665543
No 57
>PF06983 3-dmu-9_3-mt: 3-demethylubiquinone-9 3-methyltransferase; PDB: 1U7I_A 1TSJ_A 1U69_D 3L20_B 3OMS_A.
Probab=42.36 E-value=14 Score=30.64 Aligned_cols=32 Identities=31% Similarity=0.382 Sum_probs=26.2
Q ss_pred ChhHHHHHHHHHhhCCCCccchhhhhhcccCCC
Q psy7749 197 TSEDVKDHIFKLSKKGLTPSQIGVILRDSHGVA 229 (319)
Q Consensus 197 s~eEVe~~IvkLaKkG~tpSqIG~iLRD~~GIP 229 (319)
+.||++..=-+|+..|-.-|.-| .|.|+|||.
T Consensus 81 ~~ee~~~~f~~Ls~gG~~~~~~G-~v~DkFGv~ 112 (116)
T PF06983_consen 81 DEEEIDRIFDKLSEGGQWFSRYG-WVTDKFGVS 112 (116)
T ss_dssp SHHHHHHHHHHHHTTTETCCEEE-EEE-TTS-E
T ss_pred CHHHHHHHHHHHHcCCCccceeE-EEEeCCCCE
Confidence 78999999999999998556777 799999985
No 58
>PRK05702 flhB flagellar biosynthesis protein FlhB; Reviewed
Probab=41.96 E-value=57 Score=32.60 Aligned_cols=67 Identities=18% Similarity=0.228 Sum_probs=47.8
Q ss_pred CCceeecccccccccchhhhhhhhccccCCCceeeeccchHHHHHH-HcCCCCCChhhHHHHHHHHHHHHHHHhh
Q psy7749 16 PNWFIKSGFYCNLKTDIVLFCVILRDSHGVAQVRFVSGNKILRIMK-AMGLAPNLPEDLYCLIKKAVAIRKHLER 89 (319)
Q Consensus 16 p~w~~~s~~~~~~~~~~~~IG~iLRD~~GIp~VK~vtGkkI~~ILk-~nGlapeIPEDL~~LikKAv~lRkHLe~ 89 (319)
|.+.+..+..++++..|..|+. +||||-+.. ..+.|-|= .-.+..+|||+||.-+-.....-..++.
T Consensus 285 ~aP~vvakg~~~~A~~i~~~A~----~~~vpi~~~---~~LAr~Ly~~~~~g~~Ip~~~~~aVA~il~~v~~~~~ 352 (359)
T PRK05702 285 AAPVVVAKGVDEVALKIREIAR----EHNVPIVEN---PPLARALYATVEIGQEIPEELYKAVAEVLAYVYQLKR 352 (359)
T ss_pred CCCEEEEeeCcHHHHHHHHHHH----HcCCCEEeC---HHHHHHHHHcCCCCCccCHHHHHHHHHHHHHHHHHHh
Confidence 4445544445677777766664 899999887 46888885 6678899999999888776665544443
No 59
>cd01106 HTH_TipAL-Mta Helix-Turn-Helix DNA binding domain of the transcription regulators TipAL, Mta, and SkgA. Helix-turn-helix (HTH) TipAL, Mta, and SkgA transcription regulators, and related proteins, N-terminal domain. TipAL regulates resistance to and activation by numerous cyclic thiopeptide antibiotics, such as thiostrepton. Mta is a global transcriptional regulator; the N-terminal DNA-binding domain of Mta interacts directly with the promoters of mta, bmr, blt, and ydfK, and induces transcription of these multidrug-efflux transport genes. SkgA has been shown to control stationary-phase expression of catalase-peroxidase in Caulobacter crescentus. These proteins are comprised of distinct domains that harbor an N-terminal active (DNA-binding) site and a regulatory (effector-binding) site. The conserved N-terminal domain of these transcription regulators contains winged HTH motifs that mediate DNA binding. These proteins share the N-terminal DNA binding domain with other transcrip
Probab=39.61 E-value=30 Score=27.71 Aligned_cols=38 Identities=29% Similarity=0.447 Sum_probs=30.1
Q ss_pred CCCCCCCccCChhHHHHH--HHHHhhCCCCccchhhhhhc
Q psy7749 187 RRSVPNWLKLTSEDVKDH--IFKLSKKGLTPSQIGVILRD 224 (319)
Q Consensus 187 ~~~~P~Wl~~s~eEVe~~--IvkLaKkG~tpSqIG~iLRD 224 (319)
++..--|-.++.+||..+ |+.|..-|+|.++|..++..
T Consensus 30 ~~~~~g~R~y~~~di~~l~~i~~lr~~g~~l~~i~~~~~~ 69 (103)
T cd01106 30 RRTENGYRLYTEEDLERLQQILFLKELGFSLKEIKELLKD 69 (103)
T ss_pred ccCCCCceeeCHHHHHHHHHHHHHHHcCCCHHHHHHHHHc
Confidence 344445666899999865 88899999999999999854
No 60
>TIGR01204 bioW 6-carboxyhexanoate--CoA ligase. Alternate name: pimeloyl-CoA synthase.
Probab=39.33 E-value=21 Score=34.13 Aligned_cols=62 Identities=15% Similarity=0.224 Sum_probs=45.2
Q ss_pred ChhHHHHHHHHHhhCCCCccchhhhhhcccCCCceeeeccch----------------------------HHHHHHHcCC
Q psy7749 197 TSEDVKDHIFKLSKKGLTPSQIGVILRDSHGVAQVRFVSGNK----------------------------ILRIMKAMGL 248 (319)
Q Consensus 197 s~eEVe~~IvkLaKkG~tpSqIG~iLRD~~GIP~VK~vtGkk----------------------------I~~ILk~nGl 248 (319)
+.++|++.+.+|.+++++. +.|.|+--+++=.+ +..+|++.|+
T Consensus 15 ~~~~ie~~~~~L~~Ral~H---------~~G~pDfinIkve~v~~~~i~~i~~LpV~t~~~~~~ee~~~~a~~lL~~~gv 85 (232)
T TIGR01204 15 KKEELETAVKELLNKPKSH---------SRGEFDFMQIKVEKVKDFEIVKFNPLKISTYSFSSPEEARKFARKKLTQEGV 85 (232)
T ss_pred CHHHHHHHHHHHHHhhhhc---------cCCCCCeeEEEEEEccCccceeecccceEEEecCCHHHHHHHHHHHHHhCCC
Confidence 6899999999999999876 34555443322222 3455999999
Q ss_pred CCCChhhHHHHHHHHHHHH
Q psy7749 249 APNLPEDLYCLIKKAVAIR 267 (319)
Q Consensus 249 apeIPEDL~~LIkKAv~iR 267 (319)
.++++|..+.+|.+--+||
T Consensus 86 ~~~~~~~~~~~l~~~~~MR 104 (232)
T TIGR01204 86 SEEVAKKAVEILSKGANMR 104 (232)
T ss_pred CHHHHHHHHHHHhcCCCCc
Confidence 9999999999988844444
No 61
>PF10593 Z1: Z1 domain; InterPro: IPR018310 This entry represents the Z1 domain of unknown function that is found in a group of putative endonucleases. This domain is found associated with a helicase domain of superfamily type II [].
Probab=39.29 E-value=8.4 Score=35.99 Aligned_cols=58 Identities=24% Similarity=0.511 Sum_probs=44.5
Q ss_pred hhccCCCCCCCCCcCCCCCC-CCCCCccC---ChhHHHHHHHHHhhCCCCccchhhhhhccc
Q psy7749 169 MGRMHTPGKGISKSALPYRR-SVPNWLKL---TSEDVKDHIFKLSKKGLTPSQIGVILRDSH 226 (319)
Q Consensus 169 MaRMhs~~kG~S~S~~Py~~-~~P~Wl~~---s~eEVe~~IvkLaKkG~tpSqIG~iLRD~~ 226 (319)
||||.+=++|=-.-+|=|.+ ..=+|+.- ..||+.+.|.+++..|+||.++|..+|..-
T Consensus 172 mgRwFGYR~gY~dl~Ri~~~~~l~~~f~~i~~~~e~lr~~i~~~~~~~~tp~~~~~~vr~~~ 233 (239)
T PF10593_consen 172 MGRWFGYRPGYEDLCRIYMPEELYDWFRHIAEAEEELREEIKEMANNGLTPKDFGLRVRSHP 233 (239)
T ss_pred HhhcccCCcccccceEEecCHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCHHHhcccccCCC
Confidence 99999999996666666532 22234332 567888999999999999999999998764
No 62
>PF02885 Glycos_trans_3N: Glycosyl transferase family, helical bundle domain Prosite entry for Thymidine and pyrimidine-nucleoside phosphorylases; InterPro: IPR017459 The biosynthesis of disaccharides, oligosaccharides and polysaccharides involves the action of hundreds of different glycosyltransferases. These enzymes catalyse the transfer of sugar moieties from activated donor molecules to specific acceptor molecules, forming glycosidic bonds. A classification of glycosyltransferases using nucleotide diphospho-sugar, nucleotide monophospho-sugar and sugar phosphates (2.4.1.- from EC) and related proteins into distinct sequence based families has been described []. This classification is available on the CAZy (CArbohydrate-Active EnZymes) web site. The same three-dimensional fold is expected to occur within each of the families. Because 3-D structures are better conserved than sequences, several of the families defined on the basis of sequence similarities may have similar 3-D structures and therefore form 'clans'. The glycosyl transferase family includes anthranilate phosphoribosyltransferase (TrpD, 2.4.2.18 from EC) and thymidine phosphorylase (2.4.2.2 from EC). All these proteins can transfer a phosphorylated ribose substrate. Thymidine phosphorylase (2.4.2.2 from EC) catalyses the reversible phosphorolysis of thymidine, deoxyuridine and their analogues to their respective bases and 2-deoxyribose 1-phosphate. This enzyme regulates the availability of thymidine and is therefore essential to nucleic acid metabolism. This N-terminal domain is found in various family 3 glycosyl transferases, including anthranilate phosphoribosyltransferase (TrpD, 2.4.2.18 from EC) and thymidine phosphorylase (2.4.2.2 from EC). All these proteins can transfer a phosphorylated ribose substrate. Thymidine phosphorylase catalyses the reversible phosphorolysis of thymidine, deoxyuridine and their analogues to their respective bases and 2-deoxyribose 1-phosphate. This enzyme regulates the availability of thymidine and is therefore essential to nucleic acid metabolism.; PDB: 2DSJ_B 2ELC_B 2BPQ_A 1ZVW_B 3QR9_B 1V8G_B 2WK5_C 2J0F_C 2WK6_B 1UOU_A ....
Probab=38.99 E-value=26 Score=26.31 Aligned_cols=28 Identities=21% Similarity=0.307 Sum_probs=22.3
Q ss_pred cCChhHHHHHHHHHhhCCCCccchhhhh
Q psy7749 195 KLTSEDVKDHIFKLSKKGLTPSQIGVIL 222 (319)
Q Consensus 195 ~~s~eEVe~~IvkLaKkG~tpSqIG~iL 222 (319)
.+|.+|+.+.+-.+...-++|.|||-.|
T Consensus 14 ~Ls~~e~~~~~~~i~~g~~s~~qiaAfL 41 (66)
T PF02885_consen 14 DLSREEAKAAFDAILDGEVSDAQIAAFL 41 (66)
T ss_dssp ---HHHHHHHHHHHHTTSS-HHHHHHHH
T ss_pred CCCHHHHHHHHHHHHcCCCCHHHHHHHH
Confidence 4689999999999999999999999866
No 63
>TIGR02884 spore_pdaA delta-lactam-biosynthetic de-N-acetylase. Muramic delta-lactam is an unusual constituent of peptidoglycan, found only in bacterial spores in the peptidoglycan wall, or spore cortex. The proteins in this family are PdaA (yfjS), a member of a larger family of polysaccharide deacetylases, and are specificially involved in delta-lactam biosynthesis. PdaA acts immediately after CwlD, an N-acetylmuramoyl-L-alanine amidase and performs a de-N-acetylation. PdaA may also perform the following transpeptidation for lactam ring formation, as heterologous expression in E. coli of CwlD and PdaA together is sufficient for delta-lactam production.
Probab=38.50 E-value=42 Score=30.48 Aligned_cols=153 Identities=14% Similarity=0.161 Sum_probs=71.4
Q ss_pred hccccCCCceeeeccchHHHHHHHcCCCCCChhhHHHHHHHHHHHHHHHhhccCcccchhhHhHHHHhhhhhHHHHHh-c
Q psy7749 39 LRDSHGVAQVRFVSGNKILRIMKAMGLAPNLPEDLYCLIKKAVAIRKHLERSRKDKDSKFRLILVESRIHRLARYYKT-K 117 (319)
Q Consensus 39 LRD~~GIp~VK~vtGkkI~~ILk~nGlapeIPEDL~~LikKAv~lRkHLe~n~kDk~~Kr~L~LiESkI~RL~rYYk~-~ 117 (319)
+-++||||-.=+++|..+.+ -|+.+..+.+.=-.|--|--.|+ +.. ...-.-++.-|.+..+.... +
T Consensus 58 ~L~~~~vkATFFv~G~~~~~----------~p~~ir~i~~~GheIgnHt~~H~-~~~-~ls~~~~~~ei~~~~~~i~~~~ 125 (224)
T TIGR02884 58 VLKEKKVPAAFFVTGHYIKT----------QPDLIKRMVDEGHIVGNHSVHHP-SLT-AVNDEKFKEELTGVEEEFKKVT 125 (224)
T ss_pred HHHHcCCCeEEEeechhhHH----------CHHHHHHHHHcCCEeeecCccCc-Ccc-cCCHHHHHHHHHHHHHHHHHHh
Confidence 44668888888888876532 25444333332222333333222 111 11112223333333322221 2
Q ss_pred CcC------CCCCccchHHHHHHHhcCccccccCCcceeecccccc-c--cchhhhcchhhhccCCCCCCCCCcCCCCCC
Q psy7749 118 AVL------PPNWKYESATASAFILEGFRFRTRRGFRYKIDLVGLL-D--DNFYNKKSLKMGRMHTPGKGISKSALPYRR 188 (319)
Q Consensus 118 ~~L------P~~WkY~~~tA~~lv~~~~~~~~~~~~~~~~~~~~~~-~--~~~~~~~~~~MaRMhs~~kG~S~S~~Py~~ 188 (319)
|.- ||.+.|++.+.+++...||++=. +.+|...-. + .+--......|.+.+ .||+.-...
T Consensus 126 G~~~~~~fR~P~G~~~~~~~~~l~~~Gy~~v~-----w~v~~~Dw~~~~~~~~~~~~~~v~~~~~------~g~IiLlHd 194 (224)
T TIGR02884 126 GQKEMKYFRPPRGVFSERTLAYTKELGYYTVF-----WSLAFKDWKVDEQPGWQYAYKQIMKKIH------PGAILLLHA 194 (224)
T ss_pred CCCCCCEEeCCCCCcCHHHHHHHHHcCCcEEe-----ccccCcccCCCCCCCHHHHHHHHHhcCC------CCcEEEEEC
Confidence 222 56678899999999999987521 111111000 0 000001122333322 234444433
Q ss_pred CCCCCccCChhHHHHHHHHHhhCCCCccch
Q psy7749 189 SVPNWLKLTSEDVKDHIFKLSKKGLTPSQI 218 (319)
Q Consensus 189 ~~P~Wl~~s~eEVe~~IvkLaKkG~tpSqI 218 (319)
..+ .+.+-+.++|..|..+|++..-+
T Consensus 195 ~~~----~t~~aL~~ii~~lk~~Gy~fvtl 220 (224)
T TIGR02884 195 VSK----DNAEALDKIIKDLKEQGYTFKSL 220 (224)
T ss_pred CCC----CHHHHHHHHHHHHHHCCCEEEEh
Confidence 222 36777888888888888875544
No 64
>KOG3862|consensus
Probab=37.06 E-value=49 Score=33.01 Aligned_cols=51 Identities=25% Similarity=0.435 Sum_probs=41.2
Q ss_pred ChhHHHHHHHHHhhCCCCccchhhhhhcccCCCceeeeccchHHHHHHHcCCCCCCh
Q psy7749 197 TSEDVKDHIFKLSKKGLTPSQIGVILRDSHGVAQVRFVSGNKILRIMKAMGLAPNLP 253 (319)
Q Consensus 197 s~eEVe~~IvkLaKkG~tpSqIG~iLRD~~GIP~VK~vtGkkI~~ILk~nGlapeIP 253 (319)
-++-|-..|++||..|.-|+-|..-||-+||-|. +.+++.++.--.+|-.|
T Consensus 26 lpd~Vr~rIv~La~~gvrpcdisrQl~vShGcvS------kil~r~yEtgS~~pg~i 76 (327)
T KOG3862|consen 26 LPDVVRQRIVELAQNGVRPCDISRQLRVSHGCVS------KILGRYYETGSIRPGVI 76 (327)
T ss_pred CchHHHHHHHHHHHcCCcchhHHHHHhhccCCch------hHHHHHHHhcCcccCCC
Confidence 3577889999999999999999999999999875 44677777665555443
No 65
>smart00845 GatB_Yqey GatB domain. This domain is found in GatB and proteins related to bacterial Yqey. It is about 140 amino acid residues long. This domain is found at the C terminus of GatB which transamidates Glu-tRNA to Gln-tRNA. The function of this domain is uncertain. It does however suggest that Yqey and its relatives have a role in tRNA metabolism.
Probab=36.47 E-value=1.1e+02 Score=26.25 Aligned_cols=64 Identities=17% Similarity=0.248 Sum_probs=49.3
Q ss_pred cCChhHHHHHHHHHhhCCCCccchhhhhhcccCCCceeeeccchHHHHHHHcCCCCCChh-hHHHHHHHHHH
Q psy7749 195 KLTSEDVKDHIFKLSKKGLTPSQIGVILRDSHGVAQVRFVSGNKILRIMKAMGLAPNLPE-DLYCLIKKAVA 265 (319)
Q Consensus 195 ~~s~eEVe~~IvkLaKkG~tpSqIG~iLRD~~GIP~VK~vtGkkI~~ILk~nGlapeIPE-DL~~LIkKAv~ 265 (319)
.++++.+.++|.-++..-+|.+++=.+|+.-. -.|..+.+|++++|+.+--.| +|..+|+++++
T Consensus 38 ~i~~~~l~~li~lv~~g~It~~~ak~vl~~~~-------~~~~~~~~ii~~~~l~~isd~~el~~~v~~vi~ 102 (147)
T smart00845 38 PITPEHLAELLKLIEDGTISGKIAKEVLEELL-------ESGKSPEEIVEEKGLKQISDEGELEAIVDEVIA 102 (147)
T ss_pred CCCHHHHHHHHHHHHcCCCcHHHHHHHHHHHH-------HcCCCHHHHHHHcCCccCCCHHHHHHHHHHHHH
Confidence 46799999998888888888888777776321 126679999999999875444 69999999864
No 66
>KOG3517|consensus
Probab=36.21 E-value=24 Score=34.92 Aligned_cols=31 Identities=32% Similarity=0.574 Sum_probs=28.7
Q ss_pred hhHHHHHHHHHhhCCCCccchhhhhhcccCC
Q psy7749 198 SEDVKDHIFKLSKKGLTPSQIGVILRDSHGV 228 (319)
Q Consensus 198 ~eEVe~~IvkLaKkG~tpSqIG~iLRD~~GI 228 (319)
+.++.-.||+||+.|.-|..|...||-+||.
T Consensus 22 Pna~RlrIVELarlGiRPCDISRQLrvSHGC 52 (334)
T KOG3517|consen 22 PNAIRLRIVELARLGIRPCDISRQLRVSHGC 52 (334)
T ss_pred cchhhhhHHHHHHcCCCccchhhhhhhccch
Confidence 4678889999999999999999999999986
No 67
>PF11338 DUF3140: Protein of unknown function (DUF3140); InterPro: IPR021487 Some members in this family of proteins are annotated as DNA binding proteins. No function is currently known.
Probab=35.93 E-value=68 Score=26.91 Aligned_cols=38 Identities=29% Similarity=0.598 Sum_probs=32.0
Q ss_pred eeccchHHHHHHHcCCCCCChhhHHHHHHHHHH-HHHHHhh
Q psy7749 50 FVSGNKILRIMKAMGLAPNLPEDLYCLIKKAVA-IRKHLER 89 (319)
Q Consensus 50 ~vtGkkI~~ILk~nGlapeIPEDL~~LikKAv~-lRkHLe~ 89 (319)
.-+|.+|++||..+ ..++-+|=+.-|+|.|. ++.|+..
T Consensus 37 h~sGRrIv~IL~K~--k~dltddD~~hMrkVV~yv~rhlaq 75 (92)
T PF11338_consen 37 HESGRRIVEILRKR--KTDLTDDDYEHMRKVVGYVKRHLAQ 75 (92)
T ss_pred cchhhHHHHHHhcC--cccCCHHHHHHHHHHHHHHHHHHhc
Confidence 56899999999966 46677888899999985 7999988
No 68
>PF02637 GatB_Yqey: GatB domain; InterPro: IPR018027 The GatB domain, the function of which is uncertain, is associated with aspartyl/glutamyl amidotransferase subunit B and glutamyl amidotransferase subunit E. These are involved in the formation of correctly charged Asn-tRNA(Asn) or Gln-tRNA(Gln) through the transamidation of misacylated Asp-tRNA(Asn) or Glu-tRNA(Gln) in organisms which lack either or both of asparaginyl-tRNA or glutaminyl-tRNA synthetases. The reaction takes place in the presence of glutamine and ATP through an activated phospho-Asp-tRNA(Asn) or phospho-Glu-tRNA(Gln). ; GO: 0016884 carbon-nitrogen ligase activity, with glutamine as amido-N-donor; PDB: 2D6F_D 3H0M_H 3H0R_K 3H0L_K 3KFU_F 3AL0_B 3IP4_B 2DF4_B 2G5I_B 2F2A_B ....
Probab=35.30 E-value=69 Score=27.22 Aligned_cols=64 Identities=20% Similarity=0.281 Sum_probs=48.8
Q ss_pred cCChhHHHHHHHHHhhCCCCccchhhhhhcccCCCceeeeccchHHHHHHHcCCCCCC-hhhHHHHHHHHHH
Q psy7749 195 KLTSEDVKDHIFKLSKKGLTPSQIGVILRDSHGVAQVRFVSGNKILRIMKAMGLAPNL-PEDLYCLIKKAVA 265 (319)
Q Consensus 195 ~~s~eEVe~~IvkLaKkG~tpSqIG~iLRD~~GIP~VK~vtGkkI~~ILk~nGlapeI-PEDL~~LIkKAv~ 265 (319)
.++++++.++|.-+...-+|.++.-.+|+.-. -+|..+.++.+++|+..-- ++.|..++..+++
T Consensus 39 ~i~~~~l~~li~l~~~~~Is~~~ak~ll~~~~-------~~~~~~~~ii~~~~l~~i~d~~el~~~v~~vi~ 103 (148)
T PF02637_consen 39 PISPEHLAELINLLEDGKISKKSAKELLRELL-------ENGKSPEEIIEENGLWQISDEEELEALVEEVIA 103 (148)
T ss_dssp SSTHHHHHHHHHHHHTTSSGHHHHHHHHHHHH-------HHTS-HHHHHHHTT---B--CCHHHHHHHHHHH
T ss_pred CCCHHHHHHHHHHHHcCCCCHHHHHHHHHHHH-------HcCCCHHHHHHHcCCCcCCCHHHHHHHHHHHHH
Confidence 56999999999888888888888877776544 2388899999999997654 5789999999854
No 69
>TIGR03859 PQQ_PqqD coenzyme PQQ biosynthesis protein PqqD. This model identifies PqqD, a protein involved in the final steps of the biosynthesis of pyrroloquinoline quinone, coenzyme PQQ.
Probab=32.81 E-value=30 Score=27.16 Aligned_cols=52 Identities=15% Similarity=0.036 Sum_probs=36.0
Q ss_pred ChhHHHHHHHHHhhCCCCccchhhhhhcccCCCceeeeccchHHHHHHHcCC
Q psy7749 197 TSEDVKDHIFKLSKKGLTPSQIGVILRDSHGVAQVRFVSGNKILRIMKAMGL 248 (319)
Q Consensus 197 s~eEVe~~IvkLaKkG~tpSqIG~iLRD~~GIP~VK~vtGkkI~~ILk~nGl 248 (319)
.-+++-..|.+|-...-|.++|...|-++|+++..-.--=...+..|.++|+
T Consensus 28 ~Ln~~g~~Iw~lldg~~tv~eI~~~L~~~Y~~~e~~~~dV~~fL~~L~~~gl 79 (81)
T TIGR03859 28 KLNDSAGEILELCDGKRSLAEIIQELAQRFPAAEEIEDDVIAFLAVARAKHW 79 (81)
T ss_pred eeChHHHHHHHHccCCCcHHHHHHHHHHHcCChhhHHHHHHHHHHHHHHCcC
Confidence 5667888999999989999999999999998843211111223444446654
No 70
>COG3415 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=32.31 E-value=97 Score=27.35 Aligned_cols=70 Identities=21% Similarity=0.256 Sum_probs=54.5
Q ss_pred CCCCCcCCCCCCCCCCCccCChhHHHHHHHHHhhCCCCccchhhhhhcccCCCceeeeccchHHHHHHHcCCCCCCh
Q psy7749 177 KGISKSALPYRRSVPNWLKLTSEDVKDHIFKLSKKGLTPSQIGVILRDSHGVAQVRFVSGNKILRIMKAMGLAPNLP 253 (319)
Q Consensus 177 kG~S~S~~Py~~~~P~Wl~~s~eEVe~~IvkLaKkG~tpSqIG~iLRD~~GIP~VK~vtGkkI~~ILk~nGlapeIP 253 (319)
.|.- ....++...|+++ +.++++.+...+..+-.|...+=.+|--.+||..... .+.++|++-|+...=|
T Consensus 48 ~G~~-l~~~~~~GrP~kl--~~~q~~~l~e~~~~k~wTl~~~~~~l~~e~gv~y~~~----~v~~~l~~~GlsykK~ 117 (138)
T COG3415 48 TGLD-LPPKPRKGRPRKL--SEEQLEILLERLREKDWTLKELVEELGLEFGVWYHAS----AVRRLLHELGLSYKKP 117 (138)
T ss_pred cccc-ccCccCCCCCccc--CHHHHHHHHHHHhcccchHHHHHHHHhhhcCeEEeHH----HHHHHHHHcCCCcCCC
Confidence 3433 3444677889888 7777778888888888999999888888999976553 6999999999987654
No 71
>PF13592 HTH_33: Winged helix-turn helix
Probab=31.78 E-value=29 Score=25.59 Aligned_cols=37 Identities=24% Similarity=0.477 Sum_probs=29.7
Q ss_pred CccchhhhhhcccCCCceeeeccchHHHHHHHcCCCCCChh
Q psy7749 214 TPSQIGVILRDSHGVAQVRFVSGNKILRIMKAMGLAPNLPE 254 (319)
Q Consensus 214 tpSqIG~iLRD~~GIP~VK~vtGkkI~~ILk~nGlapeIPE 254 (319)
|..+|...+..+|||- ++-..|.++|+..|+...-|-
T Consensus 6 t~~~i~~~I~~~fgv~----ys~~~v~~lL~r~G~s~~kp~ 42 (60)
T PF13592_consen 6 TLKEIAAYIEEEFGVK----YSPSGVYRLLKRLGFSYQKPR 42 (60)
T ss_pred cHHHHHHHHHHHHCCE----EcHHHHHHHHHHcCCccccCC
Confidence 5567888888889885 467789999999999887763
No 72
>PRK05537 bifunctional sulfate adenylyltransferase subunit 1/adenylylsulfate kinase protein; Validated
Probab=31.50 E-value=38 Score=35.54 Aligned_cols=55 Identities=18% Similarity=0.318 Sum_probs=45.1
Q ss_pred chhhHhHHHHhhhhhHHHHHhcCcCCCCCccchHHHHHHHhcCccccccCCcceeecccccc
Q psy7749 96 SKFRLILVESRIHRLARYYKTKAVLPPNWKYESATASAFILEGFRFRTRRGFRYKIDLVGLL 157 (319)
Q Consensus 96 ~Kr~L~LiESkI~RL~rYYk~~~~LP~~WkY~~~tA~~lv~~~~~~~~~~~~~~~~~~~~~~ 157 (319)
...++.+-.++|+++.+ .|..||.|--.|+.|+ .+++.|+-|+.+|+- +=++|+-
T Consensus 347 ~~~~~~~sgt~ir~~l~----~G~~pP~~f~rpeV~~-iL~~~~~~r~~~g~~--Ivl~Gl~ 401 (568)
T PRK05537 347 GATVLTISGTELRRRLR----EGLEIPEWFSFPEVVA-ELRRTYPPRHKQGFT--VFFTGLS 401 (568)
T ss_pred CcceeccCHHHHHHHHH----CCCCCChhhcHHHHHH-HHHHHhccccCCCeE--EEEECCC
Confidence 33478888899999886 7999999999999999 667889999999984 4456654
No 73
>cd08045 TAF4 TATA Binding Protein (TBP) Associated Factor 4 (TAF4) is one of several TAFs that bind TBP and is involved in forming Transcription Factor IID (TFIID) complex. The TATA Binding Protein (TBP) Associated Factor 4 (TAF4) is one of several TAFs that bind TBP and are involved in forming the Transcription Factor IID (TFIID) complex. TFIID is one of seven General Transcription Factors (GTF) (TFIIA, TFIIB, TFIID, TFIIE, TFIIF, and TFIID) that are involved in accurate initiation of transcription by RNA polymerase II in eukaryote. TFIID plays an important role in the recognition of promoter DNA and assembly of the pre-initiation complex. TFIID complex is composed of the TBP and at least 13 TAFs. TAFs from various species were originally named by their predicted molecular weight or their electrophoretic mobility in polyacrylamide gels. A new, unified nomenclature for the pol II TAFs has been suggested to show the relationship between TAF orthologs and paralogs. Several hypotheses are
Probab=31.28 E-value=62 Score=29.50 Aligned_cols=34 Identities=35% Similarity=0.378 Sum_probs=28.2
Q ss_pred eeccchHHHHHHHcCCCCCChhhHHHHHHHHHHHH
Q psy7749 233 FVSGNKILRIMKAMGLAPNLPEDLYCLIKKAVAIR 267 (319)
Q Consensus 233 ~vtGkkI~~ILk~nGlapeIPEDL~~LIkKAv~iR 267 (319)
....++|.+|++++|+. ++.+|+.+||--|+..|
T Consensus 48 ~~l~~~~~~i~~~~g~~-~~~~d~~~lis~a~e~r 81 (212)
T cd08045 48 SPLAKKIRKIAKKHGLK-EVDEDVLDLISLALEER 81 (212)
T ss_pred HHHHHHHHHHHHHcCCC-CCCHHHHHHHHHHHHHH
Confidence 35567899999999999 99999999888876543
No 74
>COG3028 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=30.31 E-value=62 Score=30.27 Aligned_cols=65 Identities=26% Similarity=0.299 Sum_probs=44.1
Q ss_pred CCCccchhhhhhcccCCCceeeeccchHHHHHHHcCCCCCChhhHHHHHHHHHHHHHHHhhhcCcccchhhHHHHHHhh
Q psy7749 212 GLTPSQIGVILRDSHGVAQVRFVSGNKILRIMKAMGLAPNLPEDLYCLIKKAVAIRKHLERSRKDKDSKFRLILVESRI 290 (319)
Q Consensus 212 G~tpSqIG~iLRD~~GIP~VK~vtGkkI~~ILk~nGlapeIPEDL~~LIkKAv~iRKHLe~n~KD~~sKr~L~LiESkI 290 (319)
+.|-|||- ||-+++ ...|.+|+..=+..=-.-.+||||+.-|.-|-++.+|..+ ||+||.|---+
T Consensus 26 wvSKSqiK---Rd~~aL----q~LGe~L~~L~~~~L~KiPL~E~L~~Ai~~aqri~~~~ar-------rRQlQyIGKlm 90 (187)
T COG3028 26 WVSKSQIK---RDAEAL----QDLGEELVDLTKAALAKIPLDEDLLEAIELAQRIKSEIAR-------RRQLQYIGKLM 90 (187)
T ss_pred cccHHHHH---HHHHHH----HHHHHHHHhcCHHHHhhCCCChHHHHHHHHHHHHHHHHHH-------HHHHHHHHHHH
Confidence 56666663 343332 2456666655455545678999999999999999999766 56777764333
No 75
>PF12990 DUF3874: Domain of unknonw function from B. Theta Gene description (DUF3874); InterPro: IPR024450 This domain of unknown function if found in uncharacterised proteins from Bacteroides thetaiotaomicron and other Bacteroidetes.
Probab=30.24 E-value=32 Score=27.43 Aligned_cols=35 Identities=26% Similarity=0.338 Sum_probs=16.6
Q ss_pred CCccchhhhhhcccCCCceeeeccchHHHHHHHcCC
Q psy7749 213 LTPSQIGVILRDSHGVAQVRFVSGNKILRIMKAMGL 248 (319)
Q Consensus 213 ~tpSqIG~iLRD~~GIP~VK~vtGkkI~~ILk~nGl 248 (319)
+|+++|=..|.-+++++ .+..+=....|||+.+|+
T Consensus 26 lsa~~If~~L~k~~~~~-l~~~~~~~FGriL~~~gi 60 (73)
T PF12990_consen 26 LSAAEIFERLQKKSPAA-LRGSNPNHFGRILQKLGI 60 (73)
T ss_pred ecHHHHHHHHHHhCccc-cccCCHHHHHHHHHHcCC
Confidence 34444444555555443 333444444555555554
No 76
>cd04766 HTH_HspR Helix-Turn-Helix DNA binding domain of the HspR transcription regulator. Helix-turn-helix (HTH) transcription regulator HspR, N-terminal domain. Heat shock protein regulators (HspR) have been shown to regulate expression of specific regulons in response to high temperature or high osmolarity in Streptomyces and Helicobacter, respectively. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules.
Probab=30.17 E-value=1.7e+02 Score=22.97 Aligned_cols=35 Identities=17% Similarity=0.286 Sum_probs=27.3
Q ss_pred CCCCCccCChhHHHH--HHHHHhh-CCCCccchhhhhh
Q psy7749 189 SVPNWLKLTSEDVKD--HIFKLSK-KGLTPSQIGVILR 223 (319)
Q Consensus 189 ~~P~Wl~~s~eEVe~--~IvkLaK-kG~tpSqIG~iLR 223 (319)
+.+..-.+++++|.. .|+.|.. .|++.+.|-.+|.
T Consensus 32 ~~~g~R~y~~~dv~~l~~i~~L~~d~g~~l~~i~~~l~ 69 (91)
T cd04766 32 TDGGTRRYSERDIERLRRIQRLTQELGVNLAGVKRILE 69 (91)
T ss_pred CCCCCeeECHHHHHHHHHHHHHHHHcCCCHHHHHHHHH
Confidence 334555578888874 6888888 9999999988886
No 77
>PF06676 DUF1178: Protein of unknown function (DUF1178); InterPro: IPR009562 This family consists of several hypothetical bacterial proteins of around 150 residues in length. The function of this family is unknown.
Probab=29.96 E-value=1.6e+02 Score=26.45 Aligned_cols=116 Identities=18% Similarity=0.188 Sum_probs=68.0
Q ss_pred CCCCCCceeecccccccccchhh----hh-hhhccccCCCceeeeccchHHHHHHHcCCCCC---ChhhHHHHHHHHHHH
Q psy7749 12 TTLGPNWFIKSGFYCNLKTDIVL----FC-VILRDSHGVAQVRFVSGNKILRIMKAMGLAPN---LPEDLYCLIKKAVAI 83 (319)
Q Consensus 12 ~~~~p~w~~~s~~~~~~~~~~~~----IG-~iLRD~~GIp~VK~vtGkkI~~ILk~nGlape---IPEDL~~LikKAv~l 83 (319)
.-.|-.||-.|..++..+..+.. -| ..+.-.---|.|..-.+..-. ...-+++ -++....+.+....+
T Consensus 11 gH~FEgWF~ss~~fd~Q~~~glv~CP~Cgs~~V~K~lmAP~v~~~~~~~~~----~~~~~~~~~~~~~~~~~~~~~l~~~ 86 (148)
T PF06676_consen 11 GHEFEGWFRSSAAFDRQQARGLVSCPVCGSTEVSKALMAPAVATSRSKEAA----AAAPAPAAPSAAEPPAELEAALRKL 86 (148)
T ss_pred CCccceecCCHHHHHHHHHcCCccCCCCCCCeEeeecCCCeecCCCCCccc----ccCCccccccccccHHHHHHHHHHH
Confidence 45677899999888777777631 11 111112223333321111100 0001111 123446777788889
Q ss_pred HHHHhhccCcccchhhHhHHHHhhhhhHHHHHhcCcCCCCC---ccchHHHHHHHhcCccc
Q psy7749 84 RKHLERSRKDKDSKFRLILVESRIHRLARYYKTKAVLPPNW---KYESATASAFILEGFRF 141 (319)
Q Consensus 84 RkHLe~n~kDk~~Kr~L~LiESkI~RL~rYYk~~~~LP~~W---kY~~~tA~~lv~~~~~~ 141 (319)
|+|+++|-.|.-..|.=.-- ||| | |.-|.-= .=+++.|+.|+.||..+
T Consensus 87 ~~~v~~n~e~VG~~FAeEAR--~iH-----y---Gea~~R~I~G~at~eE~~~L~eEGI~v 137 (148)
T PF06676_consen 87 RRHVEKNSEDVGDRFAEEAR--KIH-----Y---GEAEERGIYGEATPEEAKELIEEGIEV 137 (148)
T ss_pred HHHHHHhCcchhHHHHHHHH--HHH-----c---CCCccccCcCcCCHHHHHHHHHcCCeE
Confidence 99999999999999975543 566 4 3333332 45788999999999764
No 78
>PRK09108 type III secretion system protein HrcU; Validated
Probab=29.56 E-value=1.2e+02 Score=30.32 Aligned_cols=67 Identities=13% Similarity=0.091 Sum_probs=47.4
Q ss_pred CCCceeecccccccccchhhhhhhhccccCCCceeeeccchHHHHHHHcCCCCCChhhHHHHHHHHHHHHHHHh
Q psy7749 15 GPNWFIKSGFYCNLKTDIVLFCVILRDSHGVAQVRFVSGNKILRIMKAMGLAPNLPEDLYCLIKKAVAIRKHLE 88 (319)
Q Consensus 15 ~p~w~~~s~~~~~~~~~~~~IG~iLRD~~GIp~VK~vtGkkI~~ILk~nGlapeIPEDL~~LikKAv~lRkHLe 88 (319)
.|.+.+..+..+.++..|..|+. +||||-|.. ..+-|-|=.-.+..+|||+||.-+-..++---.++
T Consensus 279 ~~AP~VvAKG~d~~A~~Ir~~A~----e~~VPvven---~pLARaLy~~~vg~~IP~ely~aVA~iL~~v~~l~ 345 (353)
T PRK09108 279 HPLPRVIAKGVDDGALALRRHAH----ALGIPIVGN---PPVARALYRVELDEPIPEELFETVAAILRWVDELG 345 (353)
T ss_pred CCCCEEEEEeCcHHHHHHHHHHH----HcCCCEEeC---HHHHHHHhcCCCCCcCCHHHHHHHHHHHHHHHHHh
Confidence 45555555545777777766664 699999886 46788887567889999999987776665544443
No 79
>COG2445 Uncharacterized conserved protein [Function unknown]
Probab=29.55 E-value=81 Score=27.70 Aligned_cols=60 Identities=23% Similarity=0.276 Sum_probs=43.9
Q ss_pred chhhhhhcccCCCceeeeccchHHHHHHHcCCCCCChhhHHHHHHHHHHHHHHHhhhcCcccchh
Q psy7749 217 QIGVILRDSHGVAQVRFVSGNKILRIMKAMGLAPNLPEDLYCLIKKAVAIRKHLERSRKDKDSKF 281 (319)
Q Consensus 217 qIG~iLRD~~GIP~VK~vtGkkI~~ILk~nGlapeIPEDL~~LIkKAv~iRKHLe~n~KD~~sKr 281 (319)
-||..+-+..|.-. +-|...+.++|.++|+ |||+....+++++++|+=|=.-=-+.|...
T Consensus 50 Di~~~li~~~~~~~--p~~y~d~~~~L~~~gv---i~~e~~e~L~~~~gfRN~lVH~Y~~vD~~~ 109 (138)
T COG2445 50 DIGNMLISKFGLRD--PGTYDDCIDILVEEGV---IPEEEAEELKKMVGFRNILVHRYWAVDPEK 109 (138)
T ss_pred HHHHHHHHHhCCCC--CCCHHHHHHHHHHcCC---CCHHHHHHHHHHHHHHHHHHHHHhcCCHHH
Confidence 46666666666422 2467789999999998 789999999999999997765444444443
No 80
>PF00196 GerE: Bacterial regulatory proteins, luxR family; InterPro: IPR000792 This domain is a DNA-binding, helix-turn-helix (HTH) domain of about 65 amino acids, present in transcription regulators of the LuxR/FixJ family of response regulators. The domain is named after Vibrio fischeri luxR, a transcriptional activator for quorum-sensing control of luminescence. LuxR-type HTH domain proteins occur in a variety of organisms. The DNA-binding HTH domain is usually located in the C-terminal region; the N-terminal region often containing an autoinducer-binding domain or a response regulatory domain. Most luxR-type regulators act as transcription activators, but some can be repressors or have a dual role for different sites. LuxR-type HTH regulators control a wide variety of activities in various biological processes. The luxR-type, DNA-binding HTH domain forms a four-helical bundle structure. The HTH motif comprises the second and third helices, known as the scaffold and recognition helix, respectively. The HTH binds DNA in the major groove, where the N-terminal part of the recognition helix makes most of the DNA contacts. The fourth helix is involved in dimerisation of gerE and traR. Signalling events by one of the four activation mechanisms described below lead to multimerisation of the regulator. The regulators bind DNA as multimers [, , ]. LuxR-type HTH proteins can be activated by one of four different mechanisms: 1) Regulators which belong to a two-component sensory transduction system where the protein is activated by its phosphorylation, generally on an aspartate residue, by a transmembrane kinase [, ]. Some proteins that belong to this category are: Rhizobiaceae fixJ (global regulator inducing expression of nitrogen-fixation genes in microaerobiosis) Escherichia coli and Salmonella typhimurium uhpA (activates hexose phosphate transport gene uhpT) E. coli narL and narP (activate nitrate reductase operon) Enterobacteria rcsB (regulation of exopolysaccharide biosynthesis in enteric and plant pathogenesis) Bordetella pertussis bvgA (virulence factor) Bacillus subtilis coma (involved in expression of late-expressing competence genes) 2) Regulators which are activated, or in very rare cases repressed, when bound to N-acyl homoserine lactones, which are used as quorum sensing molecules in a variety of Gram-negative bacteria []: V. fischeri luxR (activates bioluminescence operon) Agrobacterium tumefaciens traR (regulation of Ti plasmid transfer) Erwinia carotovora carR (control of carbapenem antibiotics biosynthesis) E. carotovora expR (virulence factor for soft rot disease; activates plant tissue macerating enzyme genes) Pseudomonas aeruginosa lasR (activates elastase gene lasB) Erwinia chrysanthemi echR and Erwinia stewartii esaR Pseudomonas chlororaphis phzR (positive regulator of phenazine antibiotic production) Pseudomonas aeruginosa rhlR (activates rhlAB operon and lasB gene) 3) Autonomous effector domain regulators, without a regulatory domain, represented by gerE []. B. subtilis gerE (transcription activator and repressor for the regulation of spore formation) 4) Multiple ligand-binding regulators, exemplified by malT []. E. coli malT (activates maltose operon; MalT binds ATP and maltotriose); GO: 0003700 sequence-specific DNA binding transcription factor activity, 0043565 sequence-specific DNA binding, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 3SZT_A 3CLO_A 1H0M_A 1L3L_A 3C57_B 1ZLK_B 1ZLJ_H 3C3W_B 1RNL_A 1ZG1_A ....
Probab=29.52 E-value=45 Score=23.89 Aligned_cols=25 Identities=24% Similarity=0.437 Sum_probs=19.1
Q ss_pred CChhHHHHHHHHHhhCCCCccchhhhh
Q psy7749 196 LTSEDVKDHIFKLSKKGLTPSQIGVIL 222 (319)
Q Consensus 196 ~s~eEVe~~IvkLaKkG~tpSqIG~iL 222 (319)
+|+.| -.|+.+.-.|+++.+|+..|
T Consensus 4 LT~~E--~~vl~~l~~G~~~~eIA~~l 28 (58)
T PF00196_consen 4 LTERE--LEVLRLLAQGMSNKEIAEEL 28 (58)
T ss_dssp S-HHH--HHHHHHHHTTS-HHHHHHHH
T ss_pred cCHHH--HHHHHHHHhcCCcchhHHhc
Confidence 35555 55999999999999999887
No 81
>PF06056 Terminase_5: Putative ATPase subunit of terminase (gpP-like); InterPro: IPR010332 This family of proteins are annotated as ATPase subunits of phage terminase after []. Terminases are viral proteins that are involved in packaging viral DNA into the capsid.; GO: 0005524 ATP binding, 0019069 viral capsid assembly
Probab=29.45 E-value=36 Score=25.62 Aligned_cols=26 Identities=31% Similarity=0.406 Sum_probs=22.1
Q ss_pred HHHHHHHHHhhCCCCccchhhhhhcccCCC
Q psy7749 200 DVKDHIFKLSKKGLTPSQIGVILRDSHGVA 229 (319)
Q Consensus 200 EVe~~IvkLaKkG~tpSqIG~iLRD~~GIP 229 (319)
||.+....|.-+|+++++|...| |||
T Consensus 1 e~k~~A~~LY~~G~~~~eIA~~L----g~~ 26 (58)
T PF06056_consen 1 EVKEQARSLYLQGWSIKEIAEEL----GVP 26 (58)
T ss_pred CHHHHHHHHHHcCCCHHHHHHHH----CCC
Confidence 57888899999999999998765 666
No 82
>PF07508 Recombinase: Recombinase; InterPro: IPR011109 This domain is usually found associated with IPR006119 from INTERPRO in putative integrases/recombinases of mobile genetic elements of diverse bacteria and phages.
Probab=29.38 E-value=74 Score=24.46 Aligned_cols=48 Identities=25% Similarity=0.368 Sum_probs=37.1
Q ss_pred hhHHHHHHHHHhhCCCCccchhhhhhcccCC--CceeeeccchHHHHHHHc
Q psy7749 198 SEDVKDHIFKLSKKGLTPSQIGVILRDSHGV--AQVRFVSGNKILRIMKAM 246 (319)
Q Consensus 198 ~eEVe~~IvkLaKkG~tpSqIG~iLRD~~GI--P~VK~vtGkkI~~ILk~n 246 (319)
..+|...|.++.-.|++..+|...|-+. || |.-+..+...|.+||+.-
T Consensus 3 ea~vVr~if~~~~~g~s~~~I~~~ln~~-gi~~~~~~~W~~~~v~~iL~np 52 (102)
T PF07508_consen 3 EAEVVREIFELYLEGYSLRQIARELNEK-GIPTPRGKKWSKSTVRRILRNP 52 (102)
T ss_pred HHHHHHHHHHHHHcCCCHHHHHHHHHhc-CCccccCCcccHHHHHHHHhhh
Confidence 3567778888877999999999999655 54 445567788899999853
No 83
>TIGR01404 FlhB_rel_III type III secretion protein, YscU/HrpY 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 FlhB (TIGRFAMs model TIGR00328). This model may not identify all type III secretion system FlhB homologs.
Probab=29.37 E-value=96 Score=30.78 Aligned_cols=60 Identities=15% Similarity=0.167 Sum_probs=43.0
Q ss_pred CCCceeecccccccccchhhhhhhhccccCCCceeeeccchHHHHHH-HcCCCCCChhhHHHHHHHHH
Q psy7749 15 GPNWFIKSGFYCNLKTDIVLFCVILRDSHGVAQVRFVSGNKILRIMK-AMGLAPNLPEDLYCLIKKAV 81 (319)
Q Consensus 15 ~p~w~~~s~~~~~~~~~~~~IG~iLRD~~GIp~VK~vtGkkI~~ILk-~nGlapeIPEDL~~LikKAv 81 (319)
.|.+.+..+..++++..|..|+. +||||-|.. ..+-|-|= .-.+..+|||+||.-+-...
T Consensus 276 ~~AP~VvAKG~d~~A~~Ir~iA~----e~~VPiven---~pLAR~Ly~~~evg~~IP~ely~aVA~IL 336 (342)
T TIGR01404 276 TPLPLIICKGTDAQALAVRAYAE----EAGIPVVRD---IPLARQLYRTARVGQYIPEELFEAVAELL 336 (342)
T ss_pred CCCCEEEEeeCcHHHHHHHHHHH----HcCCCEeeC---HHHHHHHHHcCCCCCcCCHHHHHHHHHHH
Confidence 45556665556777777776663 799999886 45777665 56788999999997665443
No 84
>cd03750 proteasome_alpha_type_2 proteasome_alpha_type_2. The 20S proteasome, multisubunit proteolytic complex, is the central enzyme of nonlysosomal protein degradation in both the cytosol and nucleus. It is composed of 28 subunits arranged as four homoheptameric rings that stack on top of one another forming an elongated alpha-beta-beta-alpha cylinder with a central cavity. The proteasome alpha and beta subunits are members of the N-terminal nucleophile (Ntn)-hydrolase superfamily. Their N-terminal threonine residues are exposed as a nucleophile in peptide bond hydrolysis. Mammals have 7 alpha and 7 beta proteasome subunits while archaea have one of each.
Probab=29.07 E-value=37 Score=30.76 Aligned_cols=127 Identities=18% Similarity=0.134 Sum_probs=64.0
Q ss_pred ChhhHHHHHHHHHHH-HHHHhhccCcccchhhHhHHHHhhhhhHHHHHhcCcCCCCCccchHHHHHHHhcCccccccCCc
Q psy7749 69 LPEDLYCLIKKAVAI-RKHLERSRKDKDSKFRLILVESRIHRLARYYKTKAVLPPNWKYESATASAFILEGFRFRTRRGF 147 (319)
Q Consensus 69 IPEDL~~LikKAv~l-RkHLe~n~kDk~~Kr~L~LiESkI~RL~rYYk~~~~LP~~WkY~~~tA~~lv~~~~~~~~~~~~ 147 (319)
+.-|-..|++.+... ..|-..+..+. -+++=.+.|++.+.. .-..|.+.|-.+++|++ ||.- ..++
T Consensus 74 ~~~D~~~l~~~~r~~~~~~~~~~~~~~-------~v~~la~~l~~~~~~---~t~~~~~rP~~v~~li~-G~D~--~g~~ 140 (227)
T cd03750 74 MGPDFRVLVKKARKIAQQYYLVYGEPI-------PVSQLVREIASVMQE---YTQSGGVRPFGVSLLIA-GWDE--GGPY 140 (227)
T ss_pred cHHhHHHHHHHHHHHHHHHHHHHCCCC-------CHHHHHHHHHHHHHH---hcCCCCCCChheEEEEE-EEeC--CCCE
Confidence 445777777766332 12222222222 233334445443321 11124456666776665 8873 2468
Q ss_pred ceeeccccccccchhhhcchhhhccCCCCCCCCCcCCCCCC-CCCCCccCChhHHHHHHHH----HhhCCCCccchhhh
Q psy7749 148 RYKIDLVGLLDDNFYNKKSLKMGRMHTPGKGISKSALPYRR-SVPNWLKLTSEDVKDHIFK----LSKKGLTPSQIGVI 221 (319)
Q Consensus 148 ~~~~~~~~~~~~~~~~~~~~~MaRMhs~~kG~S~S~~Py~~-~~P~Wl~~s~eEVe~~Ivk----LaKkG~tpSqIG~i 221 (319)
=|++|+.|......+..+ |.|.. -+.|+=. ...+ ++|.||..+++.+ ..+..+++..|-+.
T Consensus 141 Ly~~d~~G~~~~~~~~a~----------G~g~~-~~~~~Le~~~~~--~ms~eeai~l~~~~l~~~~~~~l~~~~iev~ 206 (227)
T cd03750 141 LYQVDPSGSYFTWKATAI----------GKNYS-NAKTFLEKRYNE--DLELEDAIHTAILTLKEGFEGQMTEKNIEIG 206 (227)
T ss_pred EEEECCCCCEEeeeEEEE----------CCCCH-HHHHHHHhhccC--CCCHHHHHHHHHHHHHHHhcccCCCCcEEEE
Confidence 899999998766554432 22211 1223211 1111 5799998888776 22334555554433
No 85
>COG3028 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=28.76 E-value=68 Score=30.00 Aligned_cols=51 Identities=24% Similarity=0.273 Sum_probs=37.0
Q ss_pred eccchHHHHHHHcCCCCCChhhHHHHHHHHHHHHHHHhhccCcccchhhHhHHHHhhh
Q psy7749 51 VSGNKILRIMKAMGLAPNLPEDLYCLIKKAVAIRKHLERSRKDKDSKFRLILVESRIH 108 (319)
Q Consensus 51 vtGkkI~~ILk~nGlapeIPEDL~~LikKAv~lRkHLe~n~kDk~~Kr~L~LiESkI~ 108 (319)
..|.+|+..=+..=..-.+||||+.-|.-|-++.+|..+ ||+||.|---++
T Consensus 41 ~LGe~L~~L~~~~L~KiPL~E~L~~Ai~~aqri~~~~ar-------rRQlQyIGKlmR 91 (187)
T COG3028 41 DLGEELVDLTKAALAKIPLDEDLLEAIELAQRIKSEIAR-------RRQLQYIGKLMR 91 (187)
T ss_pred HHHHHHHhcCHHHHhhCCCChHHHHHHHHHHHHHHHHHH-------HHHHHHHHHHHH
Confidence 345555555444445678999999999999999999766 678888744333
No 86
>PF09860 DUF2087: Uncharacterized protein conserved in bacteria (DUF2087); InterPro: IPR018656 This domain, found in various hypothetical prokaryotic proteins and transcriptional activators, has no known function.
Probab=28.72 E-value=34 Score=26.89 Aligned_cols=21 Identities=33% Similarity=0.335 Sum_probs=18.4
Q ss_pred HHHHHHhcCccccccCCccee
Q psy7749 130 TASAFILEGFRFRTRRGFRYK 150 (319)
Q Consensus 130 tA~~lv~~~~~~~~~~~~~~~ 150 (319)
.-..||..||=-||+.|+.|-
T Consensus 49 LRR~LVd~g~L~R~~dg~~Yw 69 (71)
T PF09860_consen 49 LRRYLVDYGLLERTRDGSRYW 69 (71)
T ss_pred HHHHHHHcCCeeecCCCCeee
Confidence 446799999999999999995
No 87
>cd01104 HTH_MlrA-CarA Helix-Turn-Helix DNA binding domain of the transcription regulators MlrA and CarA. Helix-turn-helix (HTH) transcription regulator MlrA (merR-like regulator A), N-terminal domain. The MlrA protein, also known as YehV, has been shown to control cell-cell aggregation by co-regulating the expression of curli and extracellular matrix production in Escherichia coli and Salmonella typhimurium. Its close homolog, CarA from Myxococcus xanthus, is involved in activation of the carotenoid biosynthesis genes by light. These proteins belong to the MerR superfamily of transcription regulators that promote expression of several stress regulon genes by reconfiguring the spacer between the -35 and -10 promoter elements. Their conserved N-terminal domains contain predicted HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules. Many MlrA- and CarA-like proteins in this group appear to lack the long dimerization helix seen i
Probab=28.28 E-value=92 Score=22.43 Aligned_cols=31 Identities=23% Similarity=0.267 Sum_probs=23.9
Q ss_pred CCccCChhHHHH--HHHHHhhCCCCccchhhhh
Q psy7749 192 NWLKLTSEDVKD--HIFKLSKKGLTPSQIGVIL 222 (319)
Q Consensus 192 ~Wl~~s~eEVe~--~IvkLaKkG~tpSqIG~iL 222 (319)
..-.++.+||.. .|..|.+.|+|..+|...|
T Consensus 35 ~~r~yt~~~v~~l~~i~~l~~~g~~l~~i~~~~ 67 (68)
T cd01104 35 GHRLYSEADVARLRLIRRLTSEGVRISQAAALA 67 (68)
T ss_pred CCeecCHHHHHHHHHHHHHHHCCCCHHHHHHHh
Confidence 444568888765 4788889999999997665
No 88
>smart00422 HTH_MERR helix_turn_helix, mercury resistance.
Probab=28.26 E-value=1e+02 Score=22.15 Aligned_cols=33 Identities=21% Similarity=0.365 Sum_probs=25.6
Q ss_pred CCCccCChhHHHH--HHHHHhhCCCCccchhhhhh
Q psy7749 191 PNWLKLTSEDVKD--HIFKLSKKGLTPSQIGVILR 223 (319)
Q Consensus 191 P~Wl~~s~eEVe~--~IvkLaKkG~tpSqIG~iLR 223 (319)
..--.++.+||.. .|..|...|+++++|..+|.
T Consensus 34 ~g~r~y~~~dl~~l~~i~~lr~~g~~~~~i~~~l~ 68 (70)
T smart00422 34 GGYRLYSDEDLERLRFIKRLKELGFSLEEIKELLE 68 (70)
T ss_pred CCCEecCHHHHHHHHHHHHHHHcCCCHHHHHHHHh
Confidence 3444578888764 58999999999999988763
No 89
>cd05116 PTKc_Syk Catalytic domain of the Protein Tyrosine Kinase, Spleen tyrosine kinase. Protein Tyrosine Kinase (PTK) family; Spleen tyrosine kinase (Syk); catalytic (c) domain. The PTKc family is part of a larger superfamily that includes the catalytic domains of other kinases such as protein serine/threonine kinases, RIO kinases, and phosphoinositide 3-kinase (PI3K). PTKs catalyze the transfer of the gamma-phosphoryl group from ATP to tyrosine (tyr) residues in protein substrates. Syk, together with Zap-70, form the Syk subfamily of kinases which are cytoplasmic (or nonreceptor) tyr kinases containing two Src homology 2 (SH2) domains N-terminal to the catalytic tyr kinase domain. Syk was first cloned from the spleen, and its function in hematopoietic cells is well-established. Syk is involved in the signaling downstream of activated receptors (including B-cell and Fc receptors) that contain ITAMs (immunoreceptor tyr activation motifs), leading to processes such as cell proliferatio
Probab=28.26 E-value=86 Score=27.11 Aligned_cols=77 Identities=22% Similarity=0.374 Sum_probs=47.3
Q ss_pred cccccchhhhhhhhccc--cCCCceeeeccchHHHHHHHcC---CCCCChhhHHHHHHHHHHHHHHHhhccCcccchhhH
Q psy7749 26 CNLKTDIVLFCVILRDS--HGVAQVRFVSGNKILRIMKAMG---LAPNLPEDLYCLIKKAVAIRKHLERSRKDKDSKFRL 100 (319)
Q Consensus 26 ~~~~~~~~~IG~iLRD~--~GIp~VK~vtGkkI~~ILk~nG---lapeIPEDL~~LikKAv~lRkHLe~n~kDk~~Kr~L 100 (319)
...+.|+--.|++|-.- +|-+--....+..+.+.+++.. ..+.+|+++.+||.+..+ .++ +.+-..
T Consensus 175 ~~~~~Di~slG~~l~el~t~g~~p~~~~~~~~~~~~i~~~~~~~~~~~~~~~l~~li~~~~~------~~p---~~Rp~~ 245 (257)
T cd05116 175 FSSKSDVWSFGVLMWEAFSYGQKPYKGMKGNEVTQMIESGERMECPQRCPPEMYDLMKLCWT------YGV---DERPGF 245 (257)
T ss_pred cCchhHHHHHHHHHHHHHhCCCCCCCCCCHHHHHHHHHCCCCCCCCCCCCHHHHHHHHHHhc------cCc---hhCcCH
Confidence 33467777788887765 4665555566777777776533 223467889999888743 333 333333
Q ss_pred hHHHHhhhhhHHHH
Q psy7749 101 ILVESRIHRLARYY 114 (319)
Q Consensus 101 ~LiESkI~RL~rYY 114 (319)
..| +.+|..||
T Consensus 246 ~~i---~~~l~~~~ 256 (257)
T cd05116 246 AVV---ELRLRNYY 256 (257)
T ss_pred HHH---HHHHhccc
Confidence 333 56677776
No 90
>cd01392 HTH_LacI Helix-turn-helix (HTH) DNA binding domain of the LacI family of transcriptional regulators. HTH-DNA binding domain of the LacI (lactose operon repressor) family of bacterial transcriptional regulators and their putative homologs found in plants. The LacI family has more than 500 members distributed among almost all bacterial species. The monomeric proteins of the LacI family contain common structural features that include a small DNA-binding domain with a helix-turn-helix motif in the N-terminus, a regulatory ligand-binding domain which exhibits the type I periplasmic binding protein fold in the C-terminus for oligomerization and for effector binding, and an approximately 18-amino acid linker connecting these two functional domains. In LacI-like transcriptional regulators, the ligands are monosaccharides including lactose, ribose, fructose, xylose, arabinose, galactose/glucose, and other sugars, with a few exceptions. When the C-terminal domain of the LacI family repre
Probab=28.05 E-value=33 Score=23.52 Aligned_cols=39 Identities=18% Similarity=0.386 Sum_probs=32.2
Q ss_pred CCCCccchhhhhhcccCCCceeeeccchHHHHHHHcCCCCCC
Q psy7749 211 KGLTPSQIGVILRDSHGVAQVRFVSGNKILRIMKAMGLAPNL 252 (319)
Q Consensus 211 kG~tpSqIG~iLRD~~GIP~VK~vtGkkI~~ILk~nGlapeI 252 (319)
-|++++.|-.+|++.. .|..-|-.+|.+++++-|..|+-
T Consensus 7 ~gvs~~tvs~~l~g~~---~vs~~~~~~i~~~~~~l~~~~~~ 45 (52)
T cd01392 7 AGVSVATVSRVLNGKP---RVSEETRERVLAAAEELGYRPNA 45 (52)
T ss_pred HCcCHHHHHHHHcCCC---CCCHHHHHHHHHHHHHhCCCCCH
Confidence 4999999999998765 56777888999999999986653
No 91
>cd08045 TAF4 TATA Binding Protein (TBP) Associated Factor 4 (TAF4) is one of several TAFs that bind TBP and is involved in forming Transcription Factor IID (TFIID) complex. The TATA Binding Protein (TBP) Associated Factor 4 (TAF4) is one of several TAFs that bind TBP and are involved in forming the Transcription Factor IID (TFIID) complex. TFIID is one of seven General Transcription Factors (GTF) (TFIIA, TFIIB, TFIID, TFIIE, TFIIF, and TFIID) that are involved in accurate initiation of transcription by RNA polymerase II in eukaryote. TFIID plays an important role in the recognition of promoter DNA and assembly of the pre-initiation complex. TFIID complex is composed of the TBP and at least 13 TAFs. TAFs from various species were originally named by their predicted molecular weight or their electrophoretic mobility in polyacrylamide gels. A new, unified nomenclature for the pol II TAFs has been suggested to show the relationship between TAF orthologs and paralogs. Several hypotheses are
Probab=27.85 E-value=77 Score=28.91 Aligned_cols=33 Identities=33% Similarity=0.342 Sum_probs=27.7
Q ss_pred eeccchHHHHHHHcCCCCCChhhHHHHHHHHHHH
Q psy7749 50 FVSGNKILRIMKAMGLAPNLPEDLYCLIKKAVAI 83 (319)
Q Consensus 50 ~vtGkkI~~ILk~nGlapeIPEDL~~LikKAv~l 83 (319)
....++|.+|++++|+. ++.+|+.+||--|+..
T Consensus 48 ~~l~~~~~~i~~~~g~~-~~~~d~~~lis~a~e~ 80 (212)
T cd08045 48 SPLAKKIRKIAKKHGLK-EVDEDVLDLISLALEE 80 (212)
T ss_pred HHHHHHHHHHHHHcCCC-CCCHHHHHHHHHHHHH
Confidence 45678899999999999 9999999888777543
No 92
>PF02796 HTH_7: Helix-turn-helix domain of resolvase; InterPro: IPR006120 Site-specific recombination plays an important role in DNA rearrangement in prokaryotic organisms. Two types of site-specific recombination are known to occur: Recombination between inverted repeats resulting in the reversal of a DNA segment. Recombination between repeat sequences on two DNA molecules resulting in their cointegration, or between repeats on one DNA molecule resulting in the excision of a DNA fragment. Site-specific recombination is characterised by a strand exchange mechanism that requires no DNA synthesis or high energy cofactor; the phosphodiester bond energy is conserved in a phospho-protein linkage during strand cleavage and re-ligation. Two unrelated families of recombinases are currently known []. The first, called the 'phage integrase' family, groups a number of bacterial phage and yeast plasmid enzymes. The second [], called the 'resolvase' family, groups enzymes which share the following structural characteristics: an N-terminal catalytic and dimerization domain that contains a conserved serine residue involved in the transient covalent attachment to DNA IPR006119 from INTERPRO, and a C-terminal helix-turn-helix DNA-binding domain. ; GO: 0000150 recombinase activity, 0003677 DNA binding, 0006310 DNA recombination; PDB: 1ZR2_A 2GM4_B 1RES_A 1ZR4_A 1RET_A 1GDT_B 2R0Q_C 1JKP_C 1IJW_C 1JJ6_C ....
Probab=27.60 E-value=34 Score=23.87 Aligned_cols=26 Identities=23% Similarity=0.385 Sum_probs=17.6
Q ss_pred CChhHHHHHHHHHhhCCCCccchhhhh
Q psy7749 196 LTSEDVKDHIFKLSKKGLTPSQIGVIL 222 (319)
Q Consensus 196 ~s~eEVe~~IvkLaKkG~tpSqIG~iL 222 (319)
+++++ .+.|++|.+.|+|.++|-..+
T Consensus 6 ~~~~~-~~~i~~l~~~G~si~~IA~~~ 31 (45)
T PF02796_consen 6 LSKEQ-IEEIKELYAEGMSIAEIAKQF 31 (45)
T ss_dssp SSHCC-HHHHHHHHHTT--HHHHHHHT
T ss_pred CCHHH-HHHHHHHHHCCCCHHHHHHHH
Confidence 34443 567888999999999997653
No 93
>PRK13413 mpi multiple promoter invertase; Provisional
Probab=27.48 E-value=52 Score=29.04 Aligned_cols=61 Identities=36% Similarity=0.496 Sum_probs=40.3
Q ss_pred CCCCCCCcCCCCCCCCCCCccCChhHHHHHHHHHhhCCCCccchhhhhhcccCCCceeeeccchHHHHHHHcCCC
Q psy7749 175 PGKGISKSALPYRRSVPNWLKLTSEDVKDHIFKLSKKGLTPSQIGVILRDSHGVAQVRFVSGNKILRIMKAMGLA 249 (319)
Q Consensus 175 ~~kG~S~S~~Py~~~~P~Wl~~s~eEVe~~IvkLaKkG~tpSqIG~iLRD~~GIP~VK~vtGkkI~~ILk~nGla 249 (319)
+.+|.... +|+ ...|.+.... +.++.|.++..+|+|.++|...| || .-..+-+++++.||.
T Consensus 139 ~~~G~~~G-rp~-g~~~~~~~~~--~~~~~i~~~~~~g~s~~~iak~l----gi------s~~Tv~r~~k~~~~~ 199 (200)
T PRK13413 139 KAEGVTLG-RPK-GSTPKKYKLT--GKEEKIKKLLDKGTSKSEIARKL----GV------SRTTLARFLKTRGLR 199 (200)
T ss_pred HHcCCccC-CCC-CCcchhhhcc--hhHHHHHHHHHCCCCHHHHHHHH----CC------CHHHHHHHHHhcccC
Confidence 34444432 365 3455554443 23467889999999999999888 44 344578888887763
No 94
>PF11338 DUF3140: Protein of unknown function (DUF3140); InterPro: IPR021487 Some members in this family of proteins are annotated as DNA binding proteins. No function is currently known.
Probab=27.33 E-value=1.3e+02 Score=25.31 Aligned_cols=38 Identities=29% Similarity=0.598 Sum_probs=32.4
Q ss_pred eeccchHHHHHHHcCCCCCChhhHHHHHHHHHH-HHHHHhh
Q psy7749 233 FVSGNKILRIMKAMGLAPNLPEDLYCLIKKAVA-IRKHLER 272 (319)
Q Consensus 233 ~vtGkkI~~ILk~nGlapeIPEDL~~LIkKAv~-iRKHLe~ 272 (319)
.-+|.+|++||.++ ..++-+|=+.-|+|.|. ++.|+..
T Consensus 37 h~sGRrIv~IL~K~--k~dltddD~~hMrkVV~yv~rhlaq 75 (92)
T PF11338_consen 37 HESGRRIVEILRKR--KTDLTDDDYEHMRKVVGYVKRHLAQ 75 (92)
T ss_pred cchhhHHHHHHhcC--cccCCHHHHHHHHHHHHHHHHHHhc
Confidence 57899999999966 46778888999999995 7999988
No 95
>smart00733 Mterf Mitochondrial termination factor repeats. Human mitochondrial termination factor is a DNA-binding protein that acts as a transcription termination factor. Six repeats occur in human mTERF, that also are present in numerous plant proteins.
Probab=27.28 E-value=73 Score=18.68 Aligned_cols=27 Identities=19% Similarity=0.369 Sum_probs=21.7
Q ss_pred CCCCCCccCChhHHHHHHHHHhhCCCC
Q psy7749 188 RSVPNWLKLTSEDVKDHIFKLSKKGLT 214 (319)
Q Consensus 188 ~~~P~Wl~~s~eEVe~~IvkLaKkG~t 214 (319)
...|.++..+.+.++..+--|...|++
T Consensus 5 ~~~P~il~~~~~~l~~~~~~l~~~g~~ 31 (31)
T smart00733 5 KKFPQILGYSEKKLKPKVEFLKELGFS 31 (31)
T ss_pred hhCcCcccccHHHhhHHHHHHHHcCCC
Confidence 356999999988888888887777754
No 96
>PRK03996 proteasome subunit alpha; Provisional
Probab=26.85 E-value=54 Score=29.90 Aligned_cols=151 Identities=16% Similarity=0.187 Sum_probs=73.0
Q ss_pred ChhhHHHHHHHHHHHHHHHhhccCcccchhhHhHHHHhhhhhHHHHHhcCcCCCCCccchHHHHHHHhcCccccccCCcc
Q psy7749 69 LPEDLYCLIKKAVAIRKHLERSRKDKDSKFRLILVESRIHRLARYYKTKAVLPPNWKYESATASAFILEGFRFRTRRGFR 148 (319)
Q Consensus 69 IPEDL~~LikKAv~lRkHLe~n~kDk~~Kr~L~LiESkI~RL~rYYk~~~~LP~~WkY~~~tA~~lv~~~~~~~~~~~~~ 148 (319)
+.-|.++|++.+... ...++...+..-...-+=+.+.++...|-+ .|.+.|--+++++ -||. ...+.=
T Consensus 83 ~~~D~~~l~~~~~~~---~~~~~~~~~~~i~~~~la~~ls~~~~~~~~------~~~~rP~~~~~il-aG~d--~~gp~L 150 (241)
T PRK03996 83 LVADARVLIDRARVE---AQINRLTYGEPIGVETLTKKICDHKQQYTQ------HGGVRPFGVALLI-AGVD--DGGPRL 150 (241)
T ss_pred cHHHHHHHHHHHHHH---HHHHHHHhCCCCCHHHHHHHHHHHHHHhcC------CCCccchheEEEE-EEEe--CCcCEE
Confidence 457888888876432 222221111122222222333343333322 2555666666444 4665 223688
Q ss_pred eeeccccccccchhhhcchhhhccCCCCCCCCCcCCCCCCCCCCC-ccCChhHHHHHHHHH----hhCCCCccchhhhhh
Q psy7749 149 YKIDLVGLLDDNFYNKKSLKMGRMHTPGKGISKSALPYRRSVPNW-LKLTSEDVKDHIFKL----SKKGLTPSQIGVILR 223 (319)
Q Consensus 149 ~~~~~~~~~~~~~~~~~~~~MaRMhs~~kG~S~S~~Py~~~~P~W-l~~s~eEVe~~IvkL----aKkG~tpSqIG~iLR 223 (319)
|++|+.|-.....+ .+-|.|.. .+.|+=.. .| -+++.||..+++.+- .+...+...|=+..-
T Consensus 151 y~id~~G~~~~~~~----------~a~G~g~~-~~~~~Le~--~~~~~~s~eeai~l~~~al~~~~~~~~~~~~i~i~ii 217 (241)
T PRK03996 151 FETDPSGAYLEYKA----------TAIGAGRD-TVMEFLEK--NYKEDLSLEEAIELALKALAKANEGKLDPENVEIAYI 217 (241)
T ss_pred EEECCCCCeecceE----------EEECCCcH-HHHHHHHH--hcccCCCHHHHHHHHHHHHHHHhccCCCCCcEEEEEE
Confidence 99999997655433 12333322 23333111 12 147888888887662 222333322222222
Q ss_pred cccCCCceeeeccchHHHHHHH
Q psy7749 224 DSHGVAQVRFVSGNKILRIMKA 245 (319)
Q Consensus 224 D~~GIP~VK~vtGkkI~~ILk~ 245 (319)
+..|. -.+.++...|.+.++.
T Consensus 218 ~~~~~-~~~~~~~~ei~~~~~~ 238 (241)
T PRK03996 218 DVETK-KFRKLSVEEIEKYLEK 238 (241)
T ss_pred ECCCC-cEEECCHHHHHHHHHH
Confidence 33343 3566666666666543
No 97
>TIGR03683 A-tRNA_syn_arch alanyl-tRNA synthetase. This family of alanyl-tRNA synthetases is limited to the archaea, and is a subset of those sequences identified by the model pfam07973 covering the second additional domain (SAD) of alanyl and threonyl tRNA synthetases.
Probab=26.69 E-value=99 Score=34.65 Aligned_cols=55 Identities=22% Similarity=0.370 Sum_probs=41.0
Q ss_pred HHHHHhhC-CCCccchhhhhhcccCCCceeeeccchHHHHHHHcCCCCCChhhHHHHHHHHH
Q psy7749 204 HIFKLSKK-GLTPSQIGVILRDSHGVAQVRFVSGNKILRIMKAMGLAPNLPEDLYCLIKKAV 264 (319)
Q Consensus 204 ~IvkLaKk-G~tpSqIG~iLRD~~GIP~VK~vtGkkI~~ILk~nGlapeIPEDL~~LIkKAv 264 (319)
++-+++++ +.=|-+.-..|-|.||+|.= =+..|.+++|+.-++|++.+.+|.+.-
T Consensus 423 ~~~~~~~~~~~i~g~~~f~LyDTyGfP~d------l~~eia~e~g~~vd~~~~F~~~~~~~~ 478 (902)
T TIGR03683 423 IVERLLKTKKEIPLDDLIELYDSHGIPPE------IVKEIAAELGAEVEIPDNFYSIVAERH 478 (902)
T ss_pred HHHHHHhcCCcCCHHHHHHHHHccCCCHH------HHHHHHHHcCCcccCCccHHHHHHHHH
Confidence 34445543 23366778899999999952 145789999999999999999887653
No 98
>COG2445 Uncharacterized conserved protein [Function unknown]
Probab=26.66 E-value=98 Score=27.20 Aligned_cols=58 Identities=21% Similarity=0.244 Sum_probs=44.1
Q ss_pred hhhhhccccCCCceeeeccchHHHHHHHcCCCCCChhhHHHHHHHHHHHHHHHhhccCcccch
Q psy7749 35 FCVILRDSHGVAQVRFVSGNKILRIMKAMGLAPNLPEDLYCLIKKAVAIRKHLERSRKDKDSK 97 (319)
Q Consensus 35 IG~iLRD~~GIp~VK~vtGkkI~~ILk~nGlapeIPEDL~~LikKAv~lRkHLe~n~kDk~~K 97 (319)
||..+-+..|.-.+ -|...+.++|.++|+ |||+....+++++++|+=|=..=-+.|..
T Consensus 51 i~~~li~~~~~~~p--~~y~d~~~~L~~~gv---i~~e~~e~L~~~~gfRN~lVH~Y~~vD~~ 108 (138)
T COG2445 51 IGNMLISKFGLRDP--GTYDDCIDILVEEGV---IPEEEAEELKKMVGFRNILVHRYWAVDPE 108 (138)
T ss_pred HHHHHHHHhCCCCC--CCHHHHHHHHHHcCC---CCHHHHHHHHHHHHHHHHHHHHHhcCCHH
Confidence 77777777774222 468889999999997 78999999999999998776544444433
No 99
>PF04947 Pox_VLTF3: Poxvirus Late Transcription Factor VLTF3 like ; InterPro: IPR007031 Members of this family are approximately 26 kDa, and are involved in trans-activation of late transcription [].; GO: 0046782 regulation of viral transcription
Probab=26.58 E-value=1.7e+02 Score=26.48 Aligned_cols=36 Identities=17% Similarity=0.302 Sum_probs=27.7
Q ss_pred CChhHHHHHHHHHhhCCCCccchhhhhhcccCCCceeeeccchHHHHHHHcC
Q psy7749 196 LTSEDVKDHIFKLSKKGLTPSQIGVILRDSHGVAQVRFVSGNKILRIMKAMG 247 (319)
Q Consensus 196 ~s~eEVe~~IvkLaKkG~tpSqIG~iLRD~~GIP~VK~vtGkkI~~ILk~nG 247 (319)
.+.+=++++..+|++.+++ ...||-..|..+||++|
T Consensus 31 i~~~V~~~l~~~l~k~~i~----------------~~~it~~~V~~~LK~l~ 66 (171)
T PF04947_consen 31 IPDEVYEELRKELKKYNID----------------ISDITKNHVREFLKKLG 66 (171)
T ss_pred CCHHHHHHHHHHHHHcCCC----------------HHHcCHHHHHHHHHHcC
Confidence 3455567777788889988 44578888999999988
No 100
>cd00592 HTH_MerR-like Helix-Turn-Helix DNA binding domain of MerR-like transcription regulators. Helix-turn-helix (HTH) MerR-like transcription regulator, N-terminal domain. The MerR family transcription regulators have been shown to mediate responses to stress including exposure to heavy metals, drugs, or oxygen radicals in eubacterial and some archaeal species. They regulate transcription of multidrug/metal ion transporter genes and oxidative stress regulons by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.
Probab=26.30 E-value=1e+02 Score=24.12 Aligned_cols=38 Identities=26% Similarity=0.359 Sum_probs=30.2
Q ss_pred CCCCCCCccCChhHHH--HHHHHHhhCCCCccchhhhhhc
Q psy7749 187 RRSVPNWLKLTSEDVK--DHIFKLSKKGLTPSQIGVILRD 224 (319)
Q Consensus 187 ~~~~P~Wl~~s~eEVe--~~IvkLaKkG~tpSqIG~iLRD 224 (319)
.+..+.+-.++.+||. ..|..|.+.|++.++|..++..
T Consensus 29 ~~~~~g~r~y~~~dv~~l~~i~~l~~~g~~~~~i~~~l~~ 68 (100)
T cd00592 29 ERSENGYRLYSEEDLERLRLIRRLRELGLSLKEIRELLDA 68 (100)
T ss_pred CcCCCCCcccCHHHHHHHHHHHHHHHcCCCHHHHHHHHhc
Confidence 3555577788999987 4578888899999999988854
No 101
>smart00550 Zalpha Z-DNA-binding domain in adenosine deaminases. Helix-turn-helix-containing domain. Also known as Zab.
Probab=26.29 E-value=80 Score=23.90 Aligned_cols=49 Identities=18% Similarity=0.297 Sum_probs=35.8
Q ss_pred CChhHHHHHHHHHhhC--C--CCccchhhhhhcccCCCceeeeccchHHHHHHHcCCCCC
Q psy7749 196 LTSEDVKDHIFKLSKK--G--LTPSQIGVILRDSHGVAQVRFVSGNKILRIMKAMGLAPN 251 (319)
Q Consensus 196 ~s~eEVe~~IvkLaKk--G--~tpSqIG~iLRD~~GIP~VK~vtGkkI~~ILk~nGlape 251 (319)
.++++.++.|+++-+. | ++.++|... -||+.. +..+++.-|++.|+.-.
T Consensus 2 ~~~~~~~~~IL~~L~~~g~~~~ta~eLa~~----lgl~~~---~v~r~L~~L~~~G~V~~ 54 (68)
T smart00550 2 LTQDSLEEKILEFLENSGDETSTALQLAKN----LGLPKK---EVNRVLYSLEKKGKVCK 54 (68)
T ss_pred CCchHHHHHHHHHHHHCCCCCcCHHHHHHH----HCCCHH---HHHHHHHHHHHCCCEEe
Confidence 3678888888887764 3 777777654 477653 67788888889887543
No 102
>PRK12721 secretion system apparatus protein SsaU; Reviewed
Probab=25.81 E-value=1.6e+02 Score=29.45 Aligned_cols=62 Identities=16% Similarity=0.168 Sum_probs=43.3
Q ss_pred CCCceeecccccccccchhhhhhhhccccCCCceeeeccchHHHHH-HHcCCCCCChhhHHHHHHHHHHH
Q psy7749 15 GPNWFIKSGFYCNLKTDIVLFCVILRDSHGVAQVRFVSGNKILRIM-KAMGLAPNLPEDLYCLIKKAVAI 83 (319)
Q Consensus 15 ~p~w~~~s~~~~~~~~~~~~IG~iLRD~~GIp~VK~vtGkkI~~IL-k~nGlapeIPEDL~~LikKAv~l 83 (319)
.|.+.+..+..++++..|-.|+ .+||||-|.. ..+-|-| +.-.+..+||+|||.-+-...+-
T Consensus 277 ~~aP~VvAKG~d~~A~~Ir~iA----~e~~VPiven---~pLARaLY~~~~vg~~IP~ely~aVA~ILa~ 339 (349)
T PRK12721 277 TPLPRVLEKGKDAQALHIVKLA----ERNGIPVVEN---IPLARALFKEVECGDYIPETLFEPVAALLRM 339 (349)
T ss_pred CCCCEEEEEeCcHHHHHHHHHH----HHcCCCEEeC---HHHHHHHHHhCCCCCcCCHHHHHHHHHHHHH
Confidence 3455555444567777666665 3689999886 4577766 56778899999999777655544
No 103
>PRK05290 hybrid cluster protein; Provisional
Probab=25.74 E-value=1.1e+02 Score=32.67 Aligned_cols=169 Identities=15% Similarity=0.130 Sum_probs=94.2
Q ss_pred hhhHHHHHHHHHHHHHHHhhc-------cCcccchhhHhHHHHhhhhhHHHHHhcCcCCCCCccchHHHHHHHhcCcccc
Q psy7749 70 PEDLYCLIKKAVAIRKHLERS-------RKDKDSKFRLILVESRIHRLARYYKTKAVLPPNWKYESATASAFILEGFRFR 142 (319)
Q Consensus 70 PEDL~~LikKAv~lRkHLe~n-------~kDk~~Kr~L~LiESkI~RL~rYYk~~~~LP~~WkY~~~tA~~lv~~~~~~~ 142 (319)
++++..++.++..+|..|..- +.+...--....-++. .-+..-=+..+.+.. |..++++|++--.-=|.++
T Consensus 77 ~~~l~~li~e~g~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~-~~K~~DvasLqDLLiYgLK 154 (546)
T PRK05290 77 DERIVGYIKEAIALREALKAKLAADGNAPEDLPDAALWLPADDL-EELLAQAAEVGVLAD-ATENEDIRSLRELLLYGLK 154 (546)
T ss_pred HHHHHHHHHHHHHHHHHHHhhhhcccccccCCcchhhccCCCCH-HHHHHHhhhcccccc-ccCChHHHHHHHHHHHHHH
Confidence 578999999999999999753 1111111111110110 000110112222222 4456666654333222222
Q ss_pred ccCCcceeeccccccccchhhhcchhhhccCCCCCCCCCcCCCCCCCCCCCccCChhHHHHHHHHHhhCCCCccchhhhh
Q psy7749 143 TRRGFRYKIDLVGLLDDNFYNKKSLKMGRMHTPGKGISKSALPYRRSVPNWLKLTSEDVKDHIFKLSKKGLTPSQIGVIL 222 (319)
Q Consensus 143 ~~~~~~~~~~~~~~~~~~~~~~~~~~MaRMhs~~kG~S~S~~Py~~~~P~Wl~~s~eEVe~~IvkLaKkG~tpSqIG~iL 222 (319)
--.-.-+.---.|..|.+-+.-+...|...++ . +.|++++.+++.+..+-+++-+++...+
T Consensus 155 GlAaYa~hAr~LGi~D~eVd~FI~eALfaTiT------------------N-nfD~e~Ll~lvLe~G~~n~~~m~ll~~~ 215 (546)
T PRK05290 155 GMAAYAEHARVLGQTDEEIYAFYHKALAALGD------------------D-PLDVDELLALVLECGKMNVKVMALLDKA 215 (546)
T ss_pred HHHHHHHHHHHcCCCchHHHHHHHHHHHHHcc------------------C-CCCHHHHHHHHHHHHHHHhHHHHHHHHH
Confidence 22222222334566777777777777764332 1 4699999999999999999999999999
Q ss_pred hcc-cCCCceeeeccchHHHHHHHcC--CCCCChhhHHHHHHHH
Q psy7749 223 RDS-HGVAQVRFVSGNKILRIMKAMG--LAPNLPEDLYCLIKKA 263 (319)
Q Consensus 223 RD~-~GIP~VK~vtGkkI~~ILk~nG--lapeIPEDL~~LIkKA 263 (319)
.|. ||.|..-.|.=. +++..+ +..-=|-||..|++.+
T Consensus 216 ~~~~fG~P~pt~v~~g----~~~~~~IlVsGHd~~~le~ll~qt 255 (546)
T PRK05290 216 NTETYGHPEPTKVNIG----VRKGPGILVSGHDLKDLEELLEQT 255 (546)
T ss_pred HhccCCCCceeeeccc----cCCCCeEEEECCChHHHHHHHHHh
Confidence 987 599987443311 222222 2233467777777765
No 104
>PF01522 Polysacc_deac_1: Polysaccharide deacetylase; InterPro: IPR002509 This domain is found in polysaccharide deacetylase. This family of polysaccharide deacetylases includes NodB (nodulation protein B from Rhizobium) which is a chitooligosaccharide deacetylase []. It also includes chitin deacetylase from yeast [], and endoxylanases which hydrolyses glucosidic bonds in xylan [].; GO: 0016810 hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, 0005975 carbohydrate metabolic process; PDB: 2IW0_A 2CC0_B 2VYO_A 2J13_A 2C71_A 2C79_A 1W1A_1 1W1B_1 1W17_A 1NY1_B ....
Probab=24.99 E-value=14 Score=28.92 Aligned_cols=93 Identities=20% Similarity=0.230 Sum_probs=52.5
Q ss_pred hhhccccCCCceeeeccchHHHHHHHcCCCCCChhhHHHHHHHHHHHHHHHhhccCcccchhhHhHHHHhhhhhHHHHHh
Q psy7749 37 VILRDSHGVAQVRFVSGNKILRIMKAMGLAPNLPEDLYCLIKKAVAIRKHLERSRKDKDSKFRLILVESRIHRLARYYKT 116 (319)
Q Consensus 37 ~iLRD~~GIp~VK~vtGkkI~~ILk~nGlapeIPEDL~~LikKAv~lRkHLe~n~kDk~~Kr~L~LiESkI~RL~rYYk~ 116 (319)
.-+-++||||-+=+++|.-+.+- |+.|..|.+.=..|--|=-.|+. .......-++..|.+-.++++.
T Consensus 24 ~~~l~~~~i~at~fv~~~~~~~~----------~~~l~~l~~~G~ei~~H~~~H~~--~~~~~~~~~~~ei~~~~~~l~~ 91 (123)
T PF01522_consen 24 LPLLKKYGIPATFFVIGSWVERY----------PDQLRELAAAGHEIGNHGWSHPN--LSTLSPEELRREIERSREILEE 91 (123)
T ss_dssp HHHHHHTT--EEEEE-HHHHHHH----------HHHHHHHHHTT-EEEEE-SSSSC--GGGS-HHHHHHHHHHHHHHHHH
T ss_pred HHHHHhcccceeeeecccccccc----------cccchhHHHHHHHHHhcCCcccc--cccCCHHHHHHHHHHHHHHHHH
Confidence 34557799999999999864443 56665555443333334333332 1333444555666666666554
Q ss_pred -c-----CcCCCCCccchHHHHHHHhcCccc
Q psy7749 117 -K-----AVLPPNWKYESATASAFILEGFRF 141 (319)
Q Consensus 117 -~-----~~LP~~WkY~~~tA~~lv~~~~~~ 141 (319)
. ...||-+.|+..+-++|.+.||+.
T Consensus 92 ~~g~~~~~f~~P~g~~~~~~~~~l~~~G~~y 122 (123)
T PF01522_consen 92 ITGRPPKGFRYPFGSYDDNTLQALREAGYKY 122 (123)
T ss_dssp HHSSEESEEE-GGGEECHHHHHHHHHTT-EE
T ss_pred HhCCCCcEEECCCCCCCHHHHHHHHHcCCCc
Confidence 2 344667788999999999999863
No 105
>TIGR02764 spore_ybaN_pdaB polysaccharide deacetylase family sporulation protein PdaB. This model describes the YbaN protein family, also called PdaB and SpoVIE, of Gram-positive bacteria. Although ybaN null mutants have only a mild sporulation defect, ybaN/ytrI double mutants show drastically reducted sporulation efficiencies. This synthetic defect suggests the role of this sigmaE-controlled gene in sporulation had been masked by functional redundancy. Members of this family are homologous to a characterized polysaccharide deacetylase; the exact function this protein family is unknown.
Probab=24.90 E-value=78 Score=27.39 Aligned_cols=22 Identities=23% Similarity=0.320 Sum_probs=16.1
Q ss_pred CCCCCccchHHHHHHHhcCccc
Q psy7749 120 LPPNWKYESATASAFILEGFRF 141 (319)
Q Consensus 120 LP~~WkY~~~tA~~lv~~~~~~ 141 (319)
-||.+.|++.+.+++...||+.
T Consensus 102 r~P~G~~~~~~~~~l~~~G~~~ 123 (191)
T TIGR02764 102 RPPSGAFNKAVLKAAESLGYTV 123 (191)
T ss_pred ECCCcCCCHHHHHHHHHcCCeE
Confidence 4666678888888888777763
No 106
>PRK13902 alaS alanyl-tRNA synthetase; Provisional
Probab=24.56 E-value=73 Score=35.62 Aligned_cols=41 Identities=27% Similarity=0.502 Sum_probs=33.4
Q ss_pred hhhhhhccccCCCceeeeccchHHHHHHHcCCCCCChhhHHHHHHHH
Q psy7749 34 LFCVILRDSHGVAQVRFVSGNKILRIMKAMGLAPNLPEDLYCLIKKA 80 (319)
Q Consensus 34 ~IG~iLRD~~GIp~VK~vtGkkI~~ILk~nGlapeIPEDL~~LikKA 80 (319)
..-..|-|+||+|-= + +.+|.+++|+.-++|++.+.+|.+.
T Consensus 433 ~~~f~LYDt~G~P~d--l----~~eia~e~g~~vd~p~~F~~~~~~~ 473 (900)
T PRK13902 433 DDLIELYDSHGIPPE--I----VKEIAKKKGVEVEVPDNFYSLVAER 473 (900)
T ss_pred HHHhhhhhcCCCCHH--H----HHHHHHHcCCccCchhhHHHHHHHH
Confidence 355679999999952 1 4578999999999999999998654
No 107
>COG2771 CsgD DNA-binding HTH domain-containing proteins [Transcription]
Probab=24.51 E-value=75 Score=22.13 Aligned_cols=29 Identities=31% Similarity=0.440 Sum_probs=22.1
Q ss_pred cCChhHHHHHHHHHhhCCCCccchhhhhhcc
Q psy7749 195 KLTSEDVKDHIFKLSKKGLTPSQIGVILRDS 225 (319)
Q Consensus 195 ~~s~eEVe~~IvkLaKkG~tpSqIG~iLRD~ 225 (319)
.+|+-| ..|..+...|.++.+|+..|--+
T Consensus 4 ~Lt~rE--~~v~~l~~~G~s~~eia~~l~is 32 (65)
T COG2771 4 DLTPRE--REILRLVAQGKSNKEIARILGIS 32 (65)
T ss_pred cCCHHH--HHHHHHHHCCCCHHHHHHHHCCC
Confidence 445555 56788888999999999988543
No 108
>PF04947 Pox_VLTF3: Poxvirus Late Transcription Factor VLTF3 like ; InterPro: IPR007031 Members of this family are approximately 26 kDa, and are involved in trans-activation of late transcription [].; GO: 0046782 regulation of viral transcription
Probab=24.10 E-value=36 Score=30.80 Aligned_cols=57 Identities=11% Similarity=0.169 Sum_probs=36.5
Q ss_pred cccccCCCCCCceee-cc-cccccccchh-hhhhhhccccCCCceeeeccchHHHHHHHcCC
Q psy7749 7 PQFNETTLGPNWFIK-SG-FYCNLKTDIV-LFCVILRDSHGVAQVRFVSGNKILRIMKAMGL 65 (319)
Q Consensus 7 ~~~~~~~~~p~w~~~-s~-~~~~~~~~~~-~IG~iLRD~~GIp~VK~vtGkkI~~ILk~nGl 65 (319)
+.+|-..|+-+||.. .+ .-+.|-+++. +|=..| ..++|. ...||-..|..+||++|+
T Consensus 8 ~~y~r~~Hf~e~L~~~q~k~~~~i~~~V~~~l~~~l-~k~~i~-~~~it~~~V~~~LK~l~~ 67 (171)
T PF04947_consen 8 YSYNRLNHFREVLRQFQGKQNTTIPDEVYEELRKEL-KKYNID-ISDITKNHVREFLKKLGY 67 (171)
T ss_pred ccccchHHHHHHHHHHhcCCCCCCCHHHHHHHHHHH-HHcCCC-HHHcCHHHHHHHHHHcCC
Confidence 456777788888877 22 1122444442 222222 335665 778999999999999994
No 109
>PF11181 YflT: Heat induced stress protein YflT
Probab=23.69 E-value=53 Score=26.57 Aligned_cols=35 Identities=20% Similarity=0.341 Sum_probs=29.7
Q ss_pred ChhHHHHHHHHHhhCCCCccchhhhhhcccCCCce
Q psy7749 197 TSEDVKDHIFKLSKKGLTPSQIGVILRDSHGVAQV 231 (319)
Q Consensus 197 s~eEVe~~IvkLaKkG~tpSqIG~iLRD~~GIP~V 231 (319)
+.+|+.+.|-+|..+|+....|-++-.|..-+-.+
T Consensus 8 ~~~E~~~~I~~L~~~Gy~~ddI~Vva~d~~~~~~l 42 (103)
T PF11181_consen 8 NEEEALSAIEELKAQGYSEDDIYVVAKDKDRTERL 42 (103)
T ss_pred CHHHHHHHHHHHHHcCCCcccEEEEEcCchHHHHH
Confidence 78999999999999999999999988777544333
No 110
>PF13411 MerR_1: MerR HTH family regulatory protein; PDB: 2JML_A 3GP4_A 3GPV_B.
Probab=23.50 E-value=61 Score=23.45 Aligned_cols=36 Identities=25% Similarity=0.419 Sum_probs=27.1
Q ss_pred CCCCCccCChhHHHH--HHHHHhhCCCCccchhhhhhc
Q psy7749 189 SVPNWLKLTSEDVKD--HIFKLSKKGLTPSQIGVILRD 224 (319)
Q Consensus 189 ~~P~Wl~~s~eEVe~--~IvkLaKkG~tpSqIG~iLRD 224 (319)
..-.+-.++.++|+. .|..|.+.|+|.++|-..|..
T Consensus 31 ~~~g~r~y~~~dv~~l~~i~~l~~~G~sl~~I~~~l~~ 68 (69)
T PF13411_consen 31 DENGYRYYSEEDVERLREIKELRKQGMSLEEIKKLLKQ 68 (69)
T ss_dssp STTSSEEE-HHHHHHHHHHHHHHHTTTHHHHHHHHH--
T ss_pred ccCceeeccHHHHHHHHHHHHHHHCcCCHHHHHHHHcc
Confidence 445567788888875 688999999999999888764
No 111
>COG2046 MET3 ATP sulfurylase (sulfate adenylyltransferase) [Inorganic ion transport and metabolism]
Probab=23.38 E-value=71 Score=32.96 Aligned_cols=87 Identities=25% Similarity=0.198 Sum_probs=59.4
Q ss_pred cchHHHHHHHhcCccccccCCcceeeccccccccchhhhcchhhhccCCCCCC------CCCcCCC----CCCCCCCCcc
Q psy7749 126 YESATASAFILEGFRFRTRRGFRYKIDLVGLLDDNFYNKKSLKMGRMHTPGKG------ISKSALP----YRRSVPNWLK 195 (319)
Q Consensus 126 Y~~~tA~~lv~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~MaRMhs~~kG------~S~S~~P----y~~~~P~Wl~ 195 (319)
|.+-.|+.|..++-. -+.|.++ .+.+.||-.+|+.|+---+-.+| +|||..= --..+|+|+
T Consensus 294 Yg~Y~aq~if~~f~~-------eLgI~p~-~f~e~~YC~~c~~~~~~~~cph~~~~~~~~SGt~lR~~Lr~G~~PP~~f- 364 (397)
T COG2046 294 YGPYDAQEIFDEFSP-------ELGITPV-FFEEFFYCPKCGQMVSTKTCPHGDEHHLHISGTKLREMLRAGVKPPEEF- 364 (397)
T ss_pred CCcccHHHHHHhccc-------ccCcEEE-eccceeecccccCCcccccCCCCCcceEEEccHHHHHHHHcCCCCCccc-
Confidence 778888888877654 5667776 47899999999999977766666 3444221 223688998
Q ss_pred CChhHHHHHHHHHhh-CCCCccchhhhh
Q psy7749 196 LTSEDVKDHIFKLSK-KGLTPSQIGVIL 222 (319)
Q Consensus 196 ~s~eEVe~~IvkLaK-kG~tpSqIG~iL 222 (319)
+--||-+.|++-.. +++.|.-+..-|
T Consensus 365 -~RPEV~~vl~k~~~~~~~~~~v~~~~l 391 (397)
T COG2046 365 -SRPEVADVLRKSLFPYRLKPQVIYNYL 391 (397)
T ss_pred -ccHHHHHHHHHhcccccccceeeechh
Confidence 66788887777544 444455555554
No 112
>PF11829 DUF3349: Protein of unknown function (DUF3349); InterPro: IPR021784 This family of proteins are functionally uncharacterised. This protein is found in bacteria. Proteins in this family are typically between 99 to 124 amino acids in length. ; PDB: 2KVC_A 3OL3_B 3OL4_A 2LKY_A.
Probab=23.19 E-value=2.4e+02 Score=23.78 Aligned_cols=21 Identities=29% Similarity=0.491 Sum_probs=16.8
Q ss_pred CChhHHHHHHHHHhhCCCCcc
Q psy7749 196 LTSEDVKDHIFKLSKKGLTPS 216 (319)
Q Consensus 196 ~s~eEVe~~IvkLaKkG~tpS 216 (319)
+|.|||.+.+.+|++.|..|.
T Consensus 36 Ltd~ev~~Va~~L~~~~~~~~ 56 (96)
T PF11829_consen 36 LTDDEVAEVAAELAARGDPPV 56 (96)
T ss_dssp S-HHHHHHHHHHHHHHTSS-B
T ss_pred CCHHHHHHHHHHHHhcCCCCC
Confidence 689999999999999987543
No 113
>COG5352 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=23.12 E-value=57 Score=29.80 Aligned_cols=24 Identities=33% Similarity=0.457 Sum_probs=20.6
Q ss_pred hHHHHHHHHHhhCCCCccchhhhh
Q psy7749 199 EDVKDHIFKLSKKGLTPSQIGVIL 222 (319)
Q Consensus 199 eEVe~~IvkLaKkG~tpSqIG~iL 222 (319)
||=.+..-||.-.|+|.|||...|
T Consensus 5 dERve~LkKLWseGLSASQIAaQL 28 (169)
T COG5352 5 DERVETLKKLWSEGLSASQIAAQL 28 (169)
T ss_pred HHHHHHHHHHHHcccCHHHHHHHh
Confidence 566678899999999999998766
No 114
>PRK12772 bifunctional flagellar biosynthesis protein FliR/FlhB; Provisional
Probab=22.66 E-value=1.4e+02 Score=31.93 Aligned_cols=61 Identities=13% Similarity=0.198 Sum_probs=43.3
Q ss_pred CCCceeecccccccccchhhhhhhhccccCCCceeeeccchHHHHH-HHcCCCCCChhhHHHHHHHHHH
Q psy7749 15 GPNWFIKSGFYCNLKTDIVLFCVILRDSHGVAQVRFVSGNKILRIM-KAMGLAPNLPEDLYCLIKKAVA 82 (319)
Q Consensus 15 ~p~w~~~s~~~~~~~~~~~~IG~iLRD~~GIp~VK~vtGkkI~~IL-k~nGlapeIPEDL~~LikKAv~ 82 (319)
.|.+.+..+..++++..|..|+ .+||||-|.. ..+-|-| +.-.+..+|||+||.-+-...+
T Consensus 540 ~~aP~VvAKG~d~~A~~Ir~~A----~e~~VPive~---~~LAR~Ly~~~evg~~IP~ely~aVA~iL~ 601 (609)
T PRK12772 540 DEAPKVVAKGADYVALKIKEIA----KENDVPIIEN---KPLARLIYKKVEIDQEIPQDMYQAVAEILA 601 (609)
T ss_pred CCCCEEEEeeCcHHHHHHHHHH----HHCCCcEEeC---HHHHHHHHHcCCCCCCCCHHHHHHHHHHHH
Confidence 3455555444577777776665 4799999887 4678877 4667889999999976655443
No 115
>PRK12773 flhB flagellar biosynthesis protein FlhB; Reviewed
Probab=22.58 E-value=1.8e+02 Score=31.90 Aligned_cols=61 Identities=15% Similarity=0.170 Sum_probs=43.8
Q ss_pred CCCceeecccccccccchhhhhhhhccccCCCceeeeccchHHHHH-HHcCCCCCChhhHHHHHHHHHH
Q psy7749 15 GPNWFIKSGFYCNLKTDIVLFCVILRDSHGVAQVRFVSGNKILRIM-KAMGLAPNLPEDLYCLIKKAVA 82 (319)
Q Consensus 15 ~p~w~~~s~~~~~~~~~~~~IG~iLRD~~GIp~VK~vtGkkI~~IL-k~nGlapeIPEDL~~LikKAv~ 82 (319)
.|++.+..+..+++|..|..|+ .+||||.|.. ..+-|-| +.-.+..+||++||.-+-..++
T Consensus 576 ~~APiVVAKG~D~lAlrIReiA----eE~gVPIVEN---pPLARALY~~veVGq~IP~eLYeAVAeILa 637 (646)
T PRK12773 576 HKAPIVIAKGVDDFALLIIRIA----RENGVPTVED---RLQARGLYEEVELGAEVPQQFYRAIATILS 637 (646)
T ss_pred CCCCEEEEEeCcHHHHHHHHHH----HHcCCcEEEC---HHHHHHHHHcCCCCCcCCHHHHHHHHHHHH
Confidence 4555655555577777776665 4799999886 4577766 5777889999999976655443
No 116
>PLN02389 biotin synthase
Probab=22.07 E-value=1.1e+02 Score=30.76 Aligned_cols=38 Identities=24% Similarity=0.291 Sum_probs=26.8
Q ss_pred CCCCccCChhHHHHHHHHHhhCCCCccchhhhhhcccC
Q psy7749 190 VPNWLKLTSEDVKDHIFKLSKKGLTPSQIGVILRDSHG 227 (319)
Q Consensus 190 ~P~Wl~~s~eEVe~~IvkLaKkG~tpSqIG~iLRD~~G 227 (319)
.|.|-.+++|||.+.+.++.+.|.+---||.-.|+.+|
T Consensus 110 ~~~~~~Ls~EeIl~~a~~~~~~G~~~~~ivts~rg~~~ 147 (379)
T PLN02389 110 VKAQKLMSKDDVLEAAKRAKEAGSTRFCMGAAWRDTVG 147 (379)
T ss_pred CcccccCCHHHHHHHHHHHHHcCCCEEEEEecccCCCC
Confidence 35577789999999999999888875444433444444
No 117
>PRK14810 formamidopyrimidine-DNA glycosylase; Provisional
Probab=21.94 E-value=2.2e+02 Score=27.06 Aligned_cols=71 Identities=20% Similarity=0.233 Sum_probs=51.1
Q ss_pred CCCCCCCCccCChhHHHHHHHHHhhCCCCccchhhhhhcc---cCCCceeeeccchHHHHHHHcCCCCCCh------hhH
Q psy7749 186 YRRSVPNWLKLTSEDVKDHIFKLSKKGLTPSQIGVILRDS---HGVAQVRFVSGNKILRIMKAMGLAPNLP------EDL 256 (319)
Q Consensus 186 y~~~~P~Wl~~s~eEVe~~IvkLaKkG~tpSqIG~iLRD~---~GIP~VK~vtGkkI~~ILk~nGlapeIP------EDL 256 (319)
+..--|+=+..+.+++.+.+. + +-..|+..|-|| -||+++= -.+||=..|+.|.-| +|+
T Consensus 131 ~~~LGpdpl~~~~~~~~~~~~---~---~~~~ik~~Lldq~viaGiGNiy------a~EiLf~a~i~P~~~~~~l~~~~~ 198 (272)
T PRK14810 131 FARPGPEPLEISFEDFAALFR---G---RKTRIKSALLNQTLLRGVGNIY------ADEALFRAGIRPQRLASSLSRERL 198 (272)
T ss_pred hhhCCCCCCCCCHHHHHHHHh---c---CCccHHHHhhcCceeccccHhH------HHHHHHHcCCCCCCCcccCCHHHH
Confidence 345556667778887766653 2 235699999999 8888764 478999999999887 788
Q ss_pred HHHHHHHHHHHH
Q psy7749 257 YCLIKKAVAIRK 268 (319)
Q Consensus 257 ~~LIkKAv~iRK 268 (319)
..|...+..+-.
T Consensus 199 ~~l~~a~~~vl~ 210 (272)
T PRK14810 199 RKLHDAIGEVLR 210 (272)
T ss_pred HHHHHHHHHHHH
Confidence 777665555533
No 118
>KOG4279|consensus
Probab=21.69 E-value=78 Score=35.87 Aligned_cols=44 Identities=23% Similarity=0.370 Sum_probs=38.5
Q ss_pred ccccCCCceee---eccchHHHHHHHcCCCCCChhhHHHHHHHHHHH
Q psy7749 40 RDSHGVAQVRF---VSGNKILRIMKAMGLAPNLPEDLYCLIKKAVAI 83 (319)
Q Consensus 40 RD~~GIp~VK~---vtGkkI~~ILk~nGlapeIPEDL~~LikKAv~l 83 (319)
-|++||.+++. -.--.+..+|+.+.+.|.-=--|-|||++||.-
T Consensus 1002 ~d~~~ia~~~~~lf~f~DaV~~VLR~~~IkPHWMFaLdnli~rAVqa 1048 (1226)
T KOG4279|consen 1002 ADTAGIAQINLALFHFSDAVQPVLRRHDIKPHWMFALDNLITRAVQA 1048 (1226)
T ss_pred ccccchhhhhhhhccchHHHHHHHHhcCCChhHHHHHHHHHHHHHHH
Confidence 37899999996 456789999999999999999999999999864
No 119
>TIGR01293 Kv_beta voltage-dependent potassium channel beta subunit, animal. Plant beta subunits and their closely related bacterial homologs (in Deinococcus radiudurans, Xylella fastidiosa, etc.) appear more closely related to each other than to animal forms. However, the bacterial species lack convincing counterparts the Kv alpha subunit and the Kv beta homolog may serve as an enzyme. Cutoffs are set for this model such that yeast and plant forms and bacterial close homologs score between trusted and noise cutoffs.
Probab=21.59 E-value=1.3e+02 Score=28.34 Aligned_cols=60 Identities=15% Similarity=0.271 Sum_probs=34.0
Q ss_pred HHHHHHHhh-CCCCccchhhhhhccc-CCCceeeeccch----HHHHHHHcCCCCCChhhHHHHHHHH
Q psy7749 202 KDHIFKLSK-KGLTPSQIGVILRDSH-GVAQVRFVSGNK----ILRIMKAMGLAPNLPEDLYCLIKKA 263 (319)
Q Consensus 202 e~~IvkLaK-kG~tpSqIG~iLRD~~-GIP~VK~vtGkk----I~~ILk~nGlapeIPEDL~~LIkKA 263 (319)
.+.+.++|+ .|.||+||-+.=-=++ || +-.+.|.+ +.+.++.-.+..+++++-+.-|.++
T Consensus 251 ~~~l~~ia~~~g~s~aqlal~w~l~~~~v--~~~i~G~~~~~ql~en~~a~~~~~~Ls~e~~~~l~~~ 316 (317)
T TIGR01293 251 LKDLQAIAERLGCTLPQLAIAWCLRNEGV--SSVLLGASSAEQLMENLGSLQVLPKLSSSIIHEIDSI 316 (317)
T ss_pred HHHHHHHHHHHCcCHHHHHHHHHhcCCCC--eEEEeCCCCHHHHHHHHHHhhccCCCCHHHHHHHHhh
Confidence 345666665 6999999877322233 33 13344444 3333433343347888888777653
No 120
>cd04398 RhoGAP_fRGD1 RhoGAP_fRGD1: RhoGAP (GTPase-activator protein [GAP] for Rho-like small GTPases) domain of fungal RGD1-like proteins. Yeast Rgd1 is a GAP protein for Rho3 and Rho4 and plays a role in low-pH response. Small GTPases cluster into distinct families, and all act as molecular switches, active in their GTP-bound form but inactive when GDP-bound. The Rho family of GTPases activates effectors involved in a wide variety of developmental processes, including regulation of cytoskeleton formation, cell proliferation and the JNK signaling pathway. GTPases generally have a low intrinsic GTPase hydrolytic activity but there are family-specific groups of GAPs that enhance the rate of GTP hydrolysis by several orders of magnitude.
Probab=21.59 E-value=2.4e+02 Score=24.72 Aligned_cols=95 Identities=18% Similarity=0.285 Sum_probs=64.9
Q ss_pred cchHHHHHHHcCCCCCChhhHHHHHHHHHHHHHHHhhccCcccchhhHhHHHHhhhhhHHHHHhcC----cC-CCCCccc
Q psy7749 53 GNKILRIMKAMGLAPNLPEDLYCLIKKAVAIRKHLERSRKDKDSKFRLILVESRIHRLARYYKTKA----VL-PPNWKYE 127 (319)
Q Consensus 53 GkkI~~ILk~nGlapeIPEDL~~LikKAv~lRkHLe~n~kDk~~Kr~L~LiESkI~RL~rYYk~~~----~L-P~~WkY~ 127 (319)
|..|..+++..| ..||-=+..+| .|++.+.-+...-||.-=-.++|.+|...+.+.. .+ |..|.++
T Consensus 2 G~~L~~~~~~~~--~~iP~~v~~~i-------~~l~~~gl~~eGiFR~~g~~~~i~~l~~~~d~~~~~~~~~~~~~~~~d 72 (192)
T cd04398 2 GVPLEDLILREG--DNVPNIVYQCI-------QAIENFGLNLEGIYRLSGNVSRVNKLKELFDKDPLNVLLISPEDYESD 72 (192)
T ss_pred CCChHHHHHHcC--CCCCHHHHHHH-------HHHHHhCCCCCCeeecCCcHHHHHHHHHHHccCCcccccccccccccc
Confidence 677888888887 56776554443 3577777778888998888889999988876533 23 4556778
Q ss_pred hHHHHHHHhcCccccccCCcceeeccccccccchhhhcc
Q psy7749 128 SATASAFILEGFRFRTRRGFRYKIDLVGLLDDNFYNKKS 166 (319)
Q Consensus 128 ~~tA~~lv~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 166 (319)
+-++..++..-||-- |.+|++.++|...-
T Consensus 73 ~~~va~~LK~fLreL----------p~pLi~~~~~~~~~ 101 (192)
T cd04398 73 IHSVASLLKLFFREL----------PEPLLTKALSREFI 101 (192)
T ss_pred HHHHHHHHHHHHHhC----------CCccCCHHHHHHHH
Confidence 876666666654421 23468888887443
No 121
>PF14057 GGGtGRT: GGGtGRT protein
Probab=21.54 E-value=43 Score=33.16 Aligned_cols=21 Identities=33% Similarity=0.510 Sum_probs=13.3
Q ss_pred cchhhhccCCCCCCCCCcCCC
Q psy7749 165 KSLKMGRMHTPGKGISKSALP 185 (319)
Q Consensus 165 ~~~~MaRMhs~~kG~S~S~~P 185 (319)
.+|.|||||+.-.=--+|..|
T Consensus 278 mTDtMGRMh~DAQFAGSSSVP 298 (328)
T PF14057_consen 278 MTDTMGRMHSDAQFAGSSSVP 298 (328)
T ss_pred ccchhhhccccccccCCCccc
Confidence 467899999876533333333
No 122
>PRK12721 secretion system apparatus protein SsaU; Reviewed
Probab=21.44 E-value=2e+02 Score=28.82 Aligned_cols=62 Identities=21% Similarity=0.362 Sum_probs=48.2
Q ss_pred CCCCCCccCChhHHHHHHHHHhhCCCCccchhhhhhcccCCCceeeeccchHHHHH-HHcCCCCCChhhHHHHHHHHHHH
Q psy7749 188 RSVPNWLKLTSEDVKDHIFKLSKKGLTPSQIGVILRDSHGVAQVRFVSGNKILRIM-KAMGLAPNLPEDLYCLIKKAVAI 266 (319)
Q Consensus 188 ~~~P~Wl~~s~eEVe~~IvkLaKkG~tpSqIG~iLRD~~GIP~VK~vtGkkI~~IL-k~nGlapeIPEDL~~LIkKAv~i 266 (319)
..+|-=+---.+++-..|.++|++ ||||-|.+ ..+.|-| +.-.+..+||||||.-+-...+-
T Consensus 277 ~~aP~VvAKG~d~~A~~Ir~iA~e--------------~~VPiven---~pLARaLY~~~~vg~~IP~ely~aVA~ILa~ 339 (349)
T PRK12721 277 TPLPRVLEKGKDAQALHIVKLAER--------------NGIPVVEN---IPLARALFKEVECGDYIPETLFEPVAALLRM 339 (349)
T ss_pred CCCCEEEEEeCcHHHHHHHHHHHH--------------cCCCEEeC---HHHHHHHHHhCCCCCcCCHHHHHHHHHHHHH
Confidence 345777777889999999998874 79999886 4577766 56778899999999777665544
No 123
>cd03753 proteasome_alpha_type_5 proteasome_alpha_type_5. The 20S proteasome, multisubunit proteolytic complex, is the central enzyme of nonlysosomal protein degradation in both the cytosol and nucleus. It is composed of 28 subunits arranged as four homoheptameric rings that stack on top of one another forming an elongated alpha-beta-beta-alpha cylinder with a central cavity. The proteasome alpha and beta subunits are members of the N-terminal nucleophile (Ntn)-hydrolase superfamily. Their N-terminal threonine residues are exposed as a nucleophile in peptide bond hydrolysis. Mammals have 7 alpha and 7 beta proteasome subunits while archaea have one of each.
Probab=20.95 E-value=74 Score=28.39 Aligned_cols=119 Identities=16% Similarity=0.116 Sum_probs=61.0
Q ss_pred ChhhHHHHHHHHHHHHHHHhhccCcccchhhHhHHHHhhhhhHHHHHhcCcCCCCCccchHHHHHHHhcCccccccCCcc
Q psy7749 69 LPEDLYCLIKKAVAIRKHLERSRKDKDSKFRLILVESRIHRLARYYKTKAVLPPNWKYESATASAFILEGFRFRTRRGFR 148 (319)
Q Consensus 69 IPEDL~~LikKAv~lRkHLe~n~kDk~~Kr~L~LiESkI~RL~rYYk~~~~LP~~WkY~~~tA~~lv~~~~~~~~~~~~~ 148 (319)
+.-|-+.|++.+ |.+.+..+.....+-...-+-+.+.++..-|.+...- ..|.+.|--++++++ ||.- ...+=
T Consensus 74 ~~~D~~~l~~~~---r~~~~~~~~~~~~~i~~~~~~~~ls~~~~~~~~~~~~-~~~~~rP~~v~~ii~-G~D~--~gp~L 146 (213)
T cd03753 74 LIADARTLIDHA---RVEAQNHRFTYNEPMTVESVTQAVSDLALQFGEGDDG-KKAMSRPFGVALLIA-GVDE--NGPQL 146 (213)
T ss_pred CHHHHHHHHHHH---HHHHHHHHHHhCCCCCHHHHHHHHHHHHHHHhCcccc-cccccccceEEEEEE-EEcC--CCCEE
Confidence 457888888765 3333332222222222222223344444333332211 345566666776665 8862 23477
Q ss_pred eeeccccccccchhhhcchhhhccCCCCCCCCCcCCCCCCCCCCCc-cCChhHHHHHHHH
Q psy7749 149 YKIDLVGLLDDNFYNKKSLKMGRMHTPGKGISKSALPYRRSVPNWL-KLTSEDVKDHIFK 207 (319)
Q Consensus 149 ~~~~~~~~~~~~~~~~~~~~MaRMhs~~kG~S~S~~Py~~~~P~Wl-~~s~eEVe~~Ivk 207 (319)
|.+|+.|-.....|.. -|.|. ..+.|+=.. .|- ++|.||..+++++
T Consensus 147 y~vd~~G~~~~~~~~a----------~G~~~-~~~~~~L~~--~~~~~ls~eeai~l~~~ 193 (213)
T cd03753 147 FHTDPSGTFTRCDAKA----------IGSGS-EGAQSSLQE--KYHKDMTLEEAEKLALS 193 (213)
T ss_pred EEECCCCCeecccEEE----------ECCCc-HHHHHHHHh--hccCCCCHHHHHHHHHH
Confidence 9999999776644432 12221 123333111 122 5799999888877
No 124
>TIGR00180 parB_part ParB-like partition proteins. This model represents the most well-conserved core of a set of chromosomal and plasmid partition proteins related to ParB, including Spo0J, RepB, and SopB. Spo0J has been shown to bind a specific DNA sequence that, when introduced into a plasmid, can serve as partition site. Study of RepB, which has nicking-closing activity, suggests that it forms a transient protein-DNA covalent intermediate during the strand transfer reaction.
Probab=20.78 E-value=2.8e+02 Score=24.55 Aligned_cols=62 Identities=15% Similarity=0.256 Sum_probs=35.3
Q ss_pred ChhHHHHHHHHHhh-CCCCccchhhhhhcccCCCceeeeccchHHHHHHHcCCCCCChhhHHHHHHH--HHHHHHHHhh
Q psy7749 197 TSEDVKDHIFKLSK-KGLTPSQIGVILRDSHGVAQVRFVSGNKILRIMKAMGLAPNLPEDLYCLIKK--AVAIRKHLER 272 (319)
Q Consensus 197 s~eEVe~~IvkLaK-kG~tpSqIG~iLRD~~GIP~VK~vtGkkI~~ILk~nGlapeIPEDL~~LIkK--Av~iRKHLe~ 272 (319)
++-|.-..+.+|.. .|.|+.+|+..| | ++-..|.+.|.-. ++|+++..++.. ...-..|.+.
T Consensus 104 t~~e~a~~~~~l~~~~g~s~~~iA~~l----g------~s~~~V~r~l~l~----~lp~~v~~~~~~~~~~~~~~~~~~ 168 (187)
T TIGR00180 104 SPIEEAQAYKRLLEKFSMTQEDLAKKI----G------KSRAHITNLLRLL----KLPSEIQSAIPEASGLLSSGHARL 168 (187)
T ss_pred CHHHHHHHHHHHHHHhCCCHHHHHHHH----C------cCHHHHHHHHHHH----cCCHHHHHHHHhccCCCcHHHHHH
Confidence 44444445555443 466666666544 2 2334566666653 489999999987 3333444443
No 125
>PF00690 Cation_ATPase_N: Cation transporter/ATPase, N-terminus; InterPro: IPR004014 ATPases (or ATP synthases) are membrane-bound enzyme complexes/ion transporters that combine ATP synthesis and/or hydrolysis with the transport of protons across a membrane. ATPases can harness the energy from a proton gradient, using the flux of ions across the membrane via the ATPase proton channel to drive the synthesis of ATP. Some ATPases work in reverse, using the energy from the hydrolysis of ATP to create a proton gradient. There are different types of ATPases, which can differ in function (ATP synthesis and/or hydrolysis), structure (e.g., F-, V- and A-ATPases, which contain rotary motors) and in the type of ions they transport [, ]. The different types include: F-ATPases (F1F0-ATPases), which are found in mitochondria, chloroplasts and bacterial plasma membranes where they are the prime producers of ATP, using the proton gradient generated by oxidative phosphorylation (mitochondria) or photosynthesis (chloroplasts). V-ATPases (V1V0-ATPases), which are primarily found in eukaryotic vacuoles and catalyse ATP hydrolysis to transport solutes and lower pH in organelles. A-ATPases (A1A0-ATPases), which are found in Archaea and function like F-ATPases (though with respect to their structure and some inhibitor responses, A-ATPases are more closely related to the V-ATPases). P-ATPases (E1E2-ATPases), which are found in bacteria and in eukaryotic plasma membranes and organelles, and function to transport a variety of different ions across membranes. E-ATPases, which are cell-surface enzymes that hydrolyse a range of NTPs, including extracellular ATP. P-ATPases (sometime known as E1-E2 ATPases) (3.6.3.- from EC) are found in bacteria and in a number of eukaryotic plasma membranes and organelles []. P-ATPases function to transport a variety of different compounds, including ions and phospholipids, across a membrane using ATP hydrolysis for energy. There are many different classes of P-ATPases, each of which transports a specific type of ion: H+, Na+, K+, Mg2+, Ca2+, Ag+ and Ag2+, Zn2+, Co2+, Pb2+, Ni2+, Cd2+, Cu+ and Cu2+. P-ATPases can be composed of one or two polypeptides, and can usually assume two main conformations called E1 and E2. This entry represents the conserved N-terminal region found in several classes of cation-transporting P-type ATPases, including those that transport H+ (3.6.3.6 from EC), Na+ (3.6.3.7 from EC), Ca2+ (3.6.3.8 from EC), Na+/K+ (3.6.3.9 from EC), and H+/K+ (3.6.3.10 from EC). In the H+/K+- and Na+/K+-exchange P-ATPases, this domain is found in the catalytic alpha chain. In gastric H+/K+-ATPases, this domain undergoes reversible sequential phosphorylation inducing conformational changes that may be important for regulating the function of these ATPases [, ]. More information about this protein can be found at Protein of the Month: ATP Synthases [].; PDB: 3KDP_C 3N2F_A 3B8E_A 3N23_A 2XZB_A 1MHS_B 3A3Y_A 2ZXE_A 3B8C_A 3B9B_A ....
Probab=20.75 E-value=49 Score=24.52 Aligned_cols=53 Identities=21% Similarity=0.342 Sum_probs=38.3
Q ss_pred CccCChhHHHHHHHHHhhCCCCccchhhhhhcccCCCceeeeccchHHHHHHHc
Q psy7749 193 WLKLTSEDVKDHIFKLSKKGLTPSQIGVILRDSHGVAQVRFVSGNKILRIMKAM 246 (319)
Q Consensus 193 Wl~~s~eEVe~~IvkLaKkG~tpSqIG~iLRD~~GIP~VK~vtGkkI~~ILk~n 246 (319)
|-..+.|||.+..--=...|++..|+-.. |.+||--.+......++.+++-+.
T Consensus 1 w~~~~~~~v~~~l~t~~~~GLs~~ev~~r-~~~~G~N~l~~~~~~s~~~~~~~~ 53 (69)
T PF00690_consen 1 WHQLSVEEVLKRLNTSSSQGLSSEEVEER-RKKYGPNELPEPKKKSLWRIFLKQ 53 (69)
T ss_dssp -TTSSHHHHHHHHTTBTSSBBTHHHHHHH-HHHHSSSSTTTTTSSSHHHHHHHH
T ss_pred CCCCCHHHHHHHHCcCCCCCCCHHHHHHH-HHhcccccccccccCcHHHHHHHH
Confidence 77788888887775445899999887654 578887777777777777766543
No 126
>PRK09108 type III secretion system protein HrcU; Validated
Probab=20.54 E-value=2.6e+02 Score=28.05 Aligned_cols=66 Identities=15% Similarity=0.223 Sum_probs=51.3
Q ss_pred CCCCCccCChhHHHHHHHHHhhCCCCccchhhhhhcccCCCceeeeccchHHHHHHHcCCCCCChhhHHHHHHHHHHHHH
Q psy7749 189 SVPNWLKLTSEDVKDHIFKLSKKGLTPSQIGVILRDSHGVAQVRFVSGNKILRIMKAMGLAPNLPEDLYCLIKKAVAIRK 268 (319)
Q Consensus 189 ~~P~Wl~~s~eEVe~~IvkLaKkG~tpSqIG~iLRD~~GIP~VK~vtGkkI~~ILk~nGlapeIPEDL~~LIkKAv~iRK 268 (319)
.+|-=+---.+++-..|.+.|++ ||||-|.+ ..+.|-|=.-.+..+|||+||.-+-..++---
T Consensus 280 ~AP~VvAKG~d~~A~~Ir~~A~e--------------~~VPvven---~pLARaLy~~~vg~~IP~ely~aVA~iL~~v~ 342 (353)
T PRK09108 280 PLPRVIAKGVDDGALALRRHAHA--------------LGIPIVGN---PPVARALYRVELDEPIPEELFETVAAILRWVD 342 (353)
T ss_pred CCCEEEEEeCcHHHHHHHHHHHH--------------cCCCEEeC---HHHHHHHhcCCCCCcCCHHHHHHHHHHHHHHH
Confidence 45777777889999999999874 89999886 45788887567889999999987777665544
Q ss_pred HHh
Q psy7749 269 HLE 271 (319)
Q Consensus 269 HLe 271 (319)
.++
T Consensus 343 ~l~ 345 (353)
T PRK09108 343 ELG 345 (353)
T ss_pred HHh
Confidence 443
No 127
>PF10752 DUF2533: Protein of unknown function (DUF2533) ; InterPro: IPR019688 This entry represents proteins with unknown function, and appear to be restricted to Bacillus spp.
Probab=20.51 E-value=79 Score=26.29 Aligned_cols=20 Identities=25% Similarity=0.611 Sum_probs=16.6
Q ss_pred hhHHHHHHHHHhhCCCCccc
Q psy7749 198 SEDVKDHIFKLSKKGLTPSQ 217 (319)
Q Consensus 198 ~eEVe~~IvkLaKkG~tpSq 217 (319)
-.||.+.|-+|||+|+.|..
T Consensus 50 IN~vT~~mN~LAk~givP~R 69 (84)
T PF10752_consen 50 INEVTKEMNELAKQGIVPTR 69 (84)
T ss_pred HHHHHHHHHHHHHcCCCCcc
Confidence 45788899999999988763
No 128
>cd04786 HTH_MerR-like_sg7 Helix-Turn-Helix DNA binding domain of putative transcription regulators from the MerR superfamily. Putative helix-turn-helix (HTH) MerR-like transcription regulators (subgroup 7) with a conserved cysteine present in the C-terminal portion of the protein. Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic su
Probab=20.42 E-value=5.3e+02 Score=21.97 Aligned_cols=40 Identities=20% Similarity=0.265 Sum_probs=30.9
Q ss_pred CCCCCCCCCccCChhHHH--HHHHHHhhCCCCccchhhhhhc
Q psy7749 185 PYRRSVPNWLKLTSEDVK--DHIFKLSKKGLTPSQIGVILRD 224 (319)
Q Consensus 185 Py~~~~P~Wl~~s~eEVe--~~IvkLaKkG~tpSqIG~iLRD 224 (319)
|.+++...+=.|+.++|+ ..|..|.+-|+|-++|..+|-.
T Consensus 28 p~~r~~~gyR~Y~~~~v~~l~~I~~lr~~GfsL~eI~~ll~~ 69 (131)
T cd04786 28 SVERSANGYRDYPPETVWVLEIISSAQQAGFSLDEIRQLLPA 69 (131)
T ss_pred CCCcCCCCCeecCHHHHHHHHHHHHHHHcCCCHHHHHHHHhc
Confidence 334555566677888886 5788899999999999999854
No 129
>PF13495 Phage_int_SAM_4: Phage integrase, N-terminal SAM-like domain; PDB: 2A3V_A.
Probab=20.23 E-value=84 Score=23.27 Aligned_cols=30 Identities=33% Similarity=0.532 Sum_probs=20.9
Q ss_pred ccCChhHHHHHHHHHh-hCCCCccchhhhhh
Q psy7749 194 LKLTSEDVKDHIFKLS-KKGLTPSQIGVILR 223 (319)
Q Consensus 194 l~~s~eEVe~~IvkLa-KkG~tpSqIG~iLR 223 (319)
-.+++++|++-+..|. .+|++||-|-..++
T Consensus 39 ~~it~~~i~~y~~~l~~~~~~s~~T~~~~~~ 69 (85)
T PF13495_consen 39 DEITPEDIEQYLNYLQNERGLSPSTINQYLS 69 (85)
T ss_dssp GG--HHHHHHHHHHHHTTT---HHHHHHHHH
T ss_pred chhHHHHHHHHHHHHHHhcCCCHHHHHHHHH
Confidence 4569999999999999 89999998866553
No 130
>KOG4279|consensus
Probab=20.22 E-value=86 Score=35.57 Aligned_cols=51 Identities=24% Similarity=0.402 Sum_probs=42.3
Q ss_pred cchhhhhh--------cccCCCceee---eccchHHHHHHHcCCCCCChhhHHHHHHHHHHH
Q psy7749 216 SQIGVILR--------DSHGVAQVRF---VSGNKILRIMKAMGLAPNLPEDLYCLIKKAVAI 266 (319)
Q Consensus 216 SqIG~iLR--------D~~GIP~VK~---vtGkkI~~ILk~nGlapeIPEDL~~LIkKAv~i 266 (319)
++|..+|+ |++||.+++. -.--.+..||+.+.+.|--=--|-|||++||.-
T Consensus 987 ~kia~~l~~lkg~ld~d~~~ia~~~~~lf~f~DaV~~VLR~~~IkPHWMFaLdnli~rAVqa 1048 (1226)
T KOG4279|consen 987 TKIAKMLDDLKGLLDADTAGIAQINLALFHFSDAVQPVLRRHDIKPHWMFALDNLITRAVQA 1048 (1226)
T ss_pred HHHHHHHHHHhhhccccccchhhhhhhhccchHHHHHHHHhcCCChhHHHHHHHHHHHHHHH
Confidence 55666553 6799999986 455679999999999999999999999999963
No 131
>cd03527 RuBisCO_small Ribulose bisphosphate carboxylase/oxygenase (Rubisco), small subunit. Rubisco is a bifunctional enzyme catalyzes the initial steps of two opposing metabolic pathways: photosynthetic carbon fixation and the competing process of photorespiration. Rubisco Form I, present in plants and green algae, is composed of eight large and eight small subunits. The nearly identical small subunits are encoded by a family of nuclear genes. After translation, the small subunits are translocated across the chloroplast membrane, where an N-terminal signal peptide is cleaved off. While the large subunits contain the catalytic activities, it has been shown that the small subunits are important for catalysis by enhancing the catalytic rate through inducing conformational changes in the large subunits.
Probab=20.06 E-value=84 Score=26.43 Aligned_cols=21 Identities=29% Similarity=0.468 Sum_probs=19.2
Q ss_pred CChhHHHHHHHHHhhCCCCcc
Q psy7749 196 LTSEDVKDHIFKLSKKGLTPS 216 (319)
Q Consensus 196 ~s~eEVe~~IvkLaKkG~tpS 216 (319)
+|.+||.++|.-+..+|..|+
T Consensus 12 lt~~~i~~QI~yll~qG~~~~ 32 (99)
T cd03527 12 LTDEQIAKQIDYIISNGWAPC 32 (99)
T ss_pred CCHHHHHHHHHHHHhCCCEEE
Confidence 589999999999999999775
Done!