Query 013559
Match_columns 441
No_of_seqs 174 out of 788
Neff 7.6
Searched_HMMs 46136
Date Fri Mar 29 05:04:47 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/013559.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/013559hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG0686 COP9 signalosome, subu 100.0 8.3E-86 1.8E-90 641.1 37.6 434 1-439 1-452 (466)
2 KOG0687 26S proteasome regulat 100.0 4.3E-75 9.4E-80 551.9 35.4 370 46-423 17-388 (393)
3 COG5187 RPN7 26S proteasome re 100.0 7.4E-59 1.6E-63 435.1 32.3 372 50-423 25-402 (412)
4 KOG2758 Translation initiation 100.0 3.8E-49 8.2E-54 373.8 28.0 363 33-425 2-420 (432)
5 PF10602 RPN7: 26S proteasome 100.0 1.8E-42 3.8E-47 316.3 19.5 175 104-278 1-177 (177)
6 KOG1463 26S proteasome regulat 100.0 4.4E-27 9.4E-32 225.6 28.8 266 143-415 132-408 (411)
7 COG5159 RPN6 26S proteasome re 99.9 9.5E-25 2.1E-29 205.5 26.1 279 143-428 129-419 (421)
8 KOG1464 COP9 signalosome, subu 99.9 7E-25 1.5E-29 205.5 19.2 266 141-415 147-428 (440)
9 KOG1498 26S proteasome regulat 99.8 2.5E-18 5.5E-23 168.4 21.9 268 120-400 110-401 (439)
10 PF01399 PCI: PCI domain; Int 99.7 1.8E-17 4E-22 137.7 12.4 105 293-397 1-105 (105)
11 COG5071 RPN5 26S proteasome re 99.7 5.1E-16 1.1E-20 147.6 19.4 272 121-400 111-401 (439)
12 KOG1497 COP9 signalosome, subu 99.7 1.4E-14 3E-19 138.8 24.5 264 140-413 104-377 (399)
13 smart00088 PINT motif in prote 99.5 1.3E-13 2.8E-18 111.5 8.9 74 329-402 1-74 (88)
14 smart00753 PAM PCI/PINT associ 99.5 1.3E-13 2.8E-18 111.5 8.9 74 329-402 1-74 (88)
15 KOG2908 26S proteasome regulat 99.3 1.7E-09 3.6E-14 105.2 26.1 262 147-419 83-361 (380)
16 KOG2581 26S proteasome regulat 99.2 1.3E-07 2.9E-12 94.0 30.6 232 181-420 214-452 (493)
17 PF09440 eIF3_N: eIF3 subunit 99.1 7.2E-10 1.6E-14 96.0 10.6 106 36-148 1-132 (133)
18 KOG2582 COP9 signalosome, subu 98.7 3.7E-06 8E-11 82.9 20.6 272 141-419 104-385 (422)
19 KOG1076 Translation initiation 98.4 0.00053 1.2E-08 72.8 29.7 203 212-417 527-782 (843)
20 KOG2753 Uncharacterized conser 98.3 7.8E-05 1.7E-09 72.8 19.1 217 175-401 123-343 (378)
21 PF14938 SNAP: Soluble NSF att 97.6 0.0039 8.4E-08 61.3 17.0 193 140-334 76-277 (282)
22 PF09976 TPR_21: Tetratricopep 97.4 0.0054 1.2E-07 53.9 14.0 99 137-241 46-144 (145)
23 COG5600 Transcription-associat 97.2 0.17 3.6E-06 50.9 23.2 234 152-400 143-406 (413)
24 PF10255 Paf67: RNA polymerase 97.1 0.016 3.5E-07 59.5 15.3 186 178-375 124-344 (404)
25 KOG2688 Transcription-associat 97.1 0.019 4.1E-07 58.3 15.5 268 102-400 93-387 (394)
26 KOG2072 Translation initiation 97.0 0.046 1E-06 59.5 17.7 85 313-397 408-493 (988)
27 PF14938 SNAP: Soluble NSF att 96.9 0.52 1.1E-05 46.2 23.6 128 119-247 94-231 (282)
28 PF10075 PCI_Csn8: COP9 signal 96.8 0.0076 1.6E-07 53.0 8.9 78 295-376 44-121 (143)
29 TIGR02795 tol_pal_ybgF tol-pal 96.5 0.029 6.4E-07 46.2 10.4 104 141-246 4-107 (119)
30 cd00189 TPR Tetratricopeptide 96.3 0.055 1.2E-06 40.9 10.1 95 141-243 2-96 (100)
31 PF13424 TPR_12: Tetratricopep 96.3 0.027 6E-07 43.5 8.2 69 137-205 3-75 (78)
32 KOG1840 Kinesin light chain [C 96.2 0.27 5.9E-06 52.2 17.5 125 119-243 261-395 (508)
33 PF09756 DDRGK: DDRGK domain; 95.9 0.014 3E-07 53.7 5.5 59 340-398 101-159 (188)
34 KOG1174 Anaphase-promoting com 95.7 0.69 1.5E-05 47.3 16.9 194 140-346 233-494 (564)
35 PRK11788 tetratricopeptide rep 95.7 1.3 2.7E-05 44.9 19.7 101 140-243 108-208 (389)
36 PF12688 TPR_5: Tetratrico pep 95.7 0.2 4.3E-06 42.9 11.2 101 141-243 3-103 (120)
37 PF09012 FeoC: FeoC like trans 95.2 0.027 5.9E-07 43.1 4.1 49 341-389 3-51 (69)
38 PF13414 TPR_11: TPR repeat; P 95.2 0.12 2.5E-06 38.7 7.5 61 141-204 5-66 (69)
39 TIGR02552 LcrH_SycD type III s 94.9 0.4 8.6E-06 40.7 11.1 96 140-243 18-113 (135)
40 PF03399 SAC3_GANP: SAC3/GANP/ 94.9 0.42 9E-06 44.2 11.9 64 296-364 139-204 (204)
41 KOG0548 Molecular co-chaperone 94.9 2.5 5.4E-05 44.6 18.2 142 143-300 362-506 (539)
42 PF12895 Apc3: Anaphase-promot 94.7 0.18 3.9E-06 39.6 7.7 81 152-239 2-82 (84)
43 PF13432 TPR_16: Tetratricopep 94.7 0.16 3.5E-06 37.6 6.9 59 143-204 1-59 (65)
44 PRK02603 photosystem I assembl 94.7 0.4 8.7E-06 43.1 10.8 67 139-205 35-101 (172)
45 CHL00033 ycf3 photosystem I as 94.5 0.57 1.2E-05 41.8 11.4 104 139-242 35-140 (168)
46 KOG3677 RNA polymerase I-assoc 94.4 0.61 1.3E-05 47.6 12.2 236 178-423 237-513 (525)
47 PF13176 TPR_7: Tetratricopept 94.4 0.066 1.4E-06 35.2 3.8 30 141-170 1-30 (36)
48 PF08220 HTH_DeoR: DeoR-like h 94.3 0.07 1.5E-06 39.2 4.0 44 339-382 1-44 (57)
49 PRK15363 pathogenicity island 94.2 0.75 1.6E-05 41.1 11.2 102 134-243 29-131 (157)
50 TIGR02521 type_IV_pilW type IV 94.0 1.2 2.6E-05 40.4 12.8 98 140-244 66-164 (234)
51 TIGR00990 3a0801s09 mitochondr 94.0 7.9 0.00017 42.2 21.1 62 140-204 366-427 (615)
52 PF12895 Apc3: Anaphase-promot 93.9 0.16 3.5E-06 39.9 5.9 58 141-202 27-84 (84)
53 TIGR03302 OM_YfiO outer membra 93.9 0.59 1.3E-05 43.9 10.9 109 138-246 69-197 (235)
54 PRK15331 chaperone protein Sic 93.9 0.96 2.1E-05 40.7 11.3 104 132-243 30-133 (165)
55 COG3063 PilF Tfp pilus assembl 93.9 3.8 8.3E-05 38.9 15.6 161 138-318 34-200 (250)
56 KOG2003 TPR repeat-containing 93.8 7.8 0.00017 40.3 18.7 117 122-246 506-623 (840)
57 KOG1861 Leucine permease trans 93.8 2.2 4.7E-05 44.3 14.8 67 295-368 426-494 (540)
58 PRK11788 tetratricopeptide rep 93.7 3.5 7.5E-05 41.6 16.7 96 141-244 216-311 (389)
59 PF13429 TPR_15: Tetratricopep 93.6 0.44 9.5E-06 46.3 9.4 99 140-246 147-245 (280)
60 PRK10803 tol-pal system protei 93.3 0.41 9E-06 46.6 8.6 62 141-202 182-243 (263)
61 PRK15359 type III secretion sy 93.3 1.6 3.6E-05 38.1 11.7 94 142-243 27-120 (144)
62 TIGR02521 type_IV_pilW type IV 92.8 7 0.00015 35.2 19.2 96 140-243 32-127 (234)
63 PF13429 TPR_15: Tetratricopep 92.8 1.1 2.3E-05 43.6 10.8 178 141-337 80-260 (280)
64 KOG3054 Uncharacterized conser 92.7 0.29 6.4E-06 46.1 6.3 58 341-398 203-260 (299)
65 TIGR00990 3a0801s09 mitochondr 92.6 18 0.00039 39.4 23.9 60 141-203 401-460 (615)
66 TIGR02795 tol_pal_ybgF tol-pal 92.6 0.6 1.3E-05 38.2 7.6 66 140-205 40-105 (119)
67 TIGR02917 PEP_TPR_lipo putativ 92.4 16 0.00034 40.5 20.9 62 140-204 602-663 (899)
68 KOG2796 Uncharacterized conser 92.3 10 0.00022 37.0 16.0 98 141-244 179-281 (366)
69 TIGR03302 OM_YfiO outer membra 92.2 1.5 3.2E-05 41.2 10.7 105 140-246 34-146 (235)
70 PF07719 TPR_2: Tetratricopept 92.2 0.35 7.5E-06 30.6 4.4 29 141-169 3-31 (34)
71 PF13174 TPR_6: Tetratricopept 92.2 0.25 5.5E-06 31.0 3.8 31 140-170 1-31 (33)
72 KOG3081 Vesicle coat complex C 92.0 9.9 0.00022 37.0 15.7 116 141-271 110-256 (299)
73 PF13525 YfiO: Outer membrane 91.9 1.6 3.4E-05 40.6 10.3 68 140-207 6-74 (203)
74 PLN03088 SGT1, suppressor of 91.6 1.6 3.6E-05 44.3 10.9 94 142-243 5-98 (356)
75 KOG1127 TPR repeat-containing 91.5 30 0.00065 39.6 23.4 100 135-244 488-591 (1238)
76 PF09976 TPR_21: Tetratricopep 91.4 4.3 9.4E-05 35.2 12.1 92 147-240 19-110 (145)
77 PRK15431 ferrous iron transpor 91.4 0.29 6.3E-06 38.3 3.9 42 343-384 7-48 (78)
78 smart00345 HTH_GNTR helix_turn 91.3 0.51 1.1E-05 34.0 5.1 49 335-383 2-51 (60)
79 cd05804 StaR_like StaR_like; a 91.2 2 4.4E-05 42.8 11.0 98 141-242 116-213 (355)
80 PF13525 YfiO: Outer membrane 91.2 5.8 0.00013 36.8 13.3 110 138-247 41-173 (203)
81 PRK10370 formate-dependent nit 91.2 3.3 7.2E-05 38.3 11.6 96 140-243 74-172 (198)
82 PRK11447 cellulose synthase su 91.1 33 0.00071 40.6 22.4 100 140-244 304-414 (1157)
83 KOG0547 Translocase of outer m 91.0 0.76 1.6E-05 47.9 7.6 62 141-205 117-178 (606)
84 PRK12370 invasion protein regu 90.8 19 0.00041 38.8 18.7 95 140-242 339-433 (553)
85 PF13181 TPR_8: Tetratricopept 90.5 0.61 1.3E-05 29.5 4.4 29 141-169 3-31 (34)
86 PRK10866 outer membrane biogen 90.5 9.8 0.00021 36.5 14.5 111 136-246 66-206 (243)
87 PF08279 HTH_11: HTH domain; 89.9 0.79 1.7E-05 32.9 5.0 48 339-389 1-49 (55)
88 PRK10866 outer membrane biogen 89.8 19 0.00041 34.5 15.8 60 143-202 179-238 (243)
89 cd00189 TPR Tetratricopeptide 89.5 1.8 4E-05 32.1 7.2 62 140-204 35-96 (100)
90 PF00515 TPR_1: Tetratricopept 89.4 0.86 1.9E-05 28.9 4.4 30 140-169 2-31 (34)
91 PF10300 DUF3808: Protein of u 89.4 9.3 0.0002 40.4 14.5 99 141-243 269-375 (468)
92 PF14559 TPR_19: Tetratricopep 89.0 0.85 1.8E-05 33.8 4.7 53 150-205 2-54 (68)
93 smart00420 HTH_DEOR helix_turn 88.6 0.87 1.9E-05 31.8 4.3 41 344-384 6-46 (53)
94 PRK11189 lipoprotein NlpI; Pro 88.5 5.2 0.00011 39.4 11.3 94 141-242 66-159 (296)
95 PRK10803 tol-pal system protei 88.4 5.4 0.00012 38.8 11.0 103 141-246 144-248 (263)
96 PF13428 TPR_14: Tetratricopep 88.3 1.6 3.4E-05 29.8 5.3 32 141-172 3-34 (44)
97 PRK14574 hmsH outer membrane p 88.2 24 0.00053 40.0 17.5 95 142-244 37-131 (822)
98 PRK10049 pgaA outer membrane p 88.2 34 0.00074 38.5 18.8 96 141-245 51-146 (765)
99 KOG1126 DNA-binding cell divis 87.8 19 0.0004 39.1 15.3 189 140-340 354-606 (638)
100 PF12569 NARP1: NMDA receptor- 87.5 45 0.00097 35.8 23.6 129 137-274 192-320 (517)
101 PRK12370 invasion protein regu 87.2 5.2 0.00011 43.1 11.2 98 140-244 373-470 (553)
102 KOG1155 Anaphase-promoting com 87.2 8.6 0.00019 40.2 11.8 103 102-205 429-536 (559)
103 KOG1125 TPR repeat-containing 87.1 2.8 6.2E-05 44.5 8.6 136 134-282 428-567 (579)
104 PF13371 TPR_9: Tetratricopept 86.9 2.6 5.6E-05 31.5 6.4 57 145-204 1-57 (73)
105 PRK10049 pgaA outer membrane p 86.8 41 0.00089 37.9 18.5 167 145-325 278-461 (765)
106 PF13374 TPR_10: Tetratricopep 86.6 1.5 3.3E-05 28.8 4.4 30 140-169 3-32 (42)
107 PF13512 TPR_18: Tetratricopep 86.6 7.2 0.00016 34.3 9.6 28 141-168 49-76 (142)
108 KOG1586 Protein required for f 86.4 32 0.00069 33.1 18.6 193 140-338 55-280 (288)
109 PF00392 GntR: Bacterial regul 86.3 2.9 6.2E-05 31.1 6.2 52 332-383 3-55 (64)
110 COG1849 Uncharacterized protei 86.2 7.7 0.00017 31.2 8.6 52 113-164 8-66 (90)
111 PF08784 RPA_C: Replication pr 85.8 0.89 1.9E-05 37.3 3.5 39 350-388 63-101 (102)
112 KOG3785 Uncharacterized conser 85.7 5.3 0.00011 40.3 9.2 71 132-205 50-120 (557)
113 KOG2376 Signal recognition par 85.6 55 0.0012 35.4 17.0 103 141-243 112-252 (652)
114 KOG1840 Kinesin light chain [C 85.4 55 0.0012 35.0 17.3 105 136-241 238-351 (508)
115 COG3063 PilF Tfp pilus assembl 85.4 35 0.00076 32.6 14.9 97 140-243 104-200 (250)
116 TIGR02917 PEP_TPR_lipo putativ 85.2 65 0.0014 35.5 27.0 100 136-243 122-221 (899)
117 PRK11189 lipoprotein NlpI; Pro 85.1 40 0.00087 33.1 17.1 100 140-243 133-264 (296)
118 PF04733 Coatomer_E: Coatomer 84.9 3.1 6.6E-05 41.1 7.4 114 142-270 105-249 (290)
119 PF13412 HTH_24: Winged helix- 84.5 2.4 5.2E-05 29.5 4.7 42 341-382 6-47 (48)
120 COG1729 Uncharacterized protei 84.3 5.3 0.00012 38.7 8.4 65 140-204 179-243 (262)
121 PRK10747 putative protoheme IX 83.8 54 0.0012 33.6 16.4 59 145-206 159-217 (398)
122 PF13424 TPR_12: Tetratricopep 83.6 4.2 9.1E-05 30.9 6.2 68 175-242 4-73 (78)
123 COG4105 ComL DNA uptake lipopr 83.5 31 0.00068 33.3 13.2 110 136-246 68-198 (254)
124 PRK09782 bacteriophage N4 rece 83.4 75 0.0016 37.0 18.6 95 140-246 45-139 (987)
125 KOG2002 TPR-containing nuclear 83.3 25 0.00055 39.9 14.0 102 140-247 271-374 (1018)
126 PF09743 DUF2042: Uncharacteri 83.3 8.2 0.00018 37.8 9.4 66 324-396 107-172 (272)
127 KOG0543 FKBP-type peptidyl-pro 83.1 6 0.00013 40.5 8.5 95 144-243 213-319 (397)
128 KOG1585 Protein required for f 83.0 47 0.001 32.2 16.7 190 120-314 52-250 (308)
129 PF03704 BTAD: Bacterial trans 82.1 13 0.00028 32.0 9.5 65 140-207 63-127 (146)
130 COG4700 Uncharacterized protei 82.0 44 0.00095 31.1 13.9 117 140-269 90-207 (251)
131 COG2956 Predicted N-acetylgluc 82.0 60 0.0013 32.7 16.3 98 135-237 65-163 (389)
132 PF12862 Apc5: Anaphase-promot 81.9 5 0.00011 32.4 6.3 58 149-206 8-71 (94)
133 KOG2076 RNA polymerase III tra 81.9 11 0.00024 42.2 10.5 103 130-240 405-508 (895)
134 PRK10411 DNA-binding transcrip 81.9 7.8 0.00017 37.1 8.6 46 338-383 4-49 (240)
135 PF11817 Foie-gras_1: Foie gra 81.8 23 0.0005 33.9 11.9 83 116-198 155-240 (247)
136 PRK15174 Vi polysaccharide exp 81.8 65 0.0014 35.6 17.0 236 141-389 286-555 (656)
137 PRK11447 cellulose synthase su 81.7 80 0.0017 37.4 18.6 99 141-244 30-141 (1157)
138 PLN03098 LPA1 LOW PSII ACCUMUL 81.7 7 0.00015 40.8 8.6 27 141-167 114-140 (453)
139 PRK10434 srlR DNA-bindng trans 81.5 2.1 4.6E-05 41.4 4.6 45 338-382 5-49 (256)
140 KOG1070 rRNA processing protei 81.5 49 0.0011 39.3 15.6 100 141-246 1460-1561(1710)
141 COG4235 Cytochrome c biogenesi 81.3 18 0.0004 35.5 10.9 95 140-242 157-254 (287)
142 PRK04424 fatty acid biosynthes 80.6 1.9 4E-05 39.7 3.7 44 339-382 8-51 (185)
143 PF09295 ChAPs: ChAPs (Chs5p-A 80.5 40 0.00087 34.9 13.7 123 65-200 167-292 (395)
144 PRK04841 transcriptional regul 80.5 31 0.00067 39.2 14.3 102 140-241 532-638 (903)
145 TIGR00540 hemY_coli hemY prote 80.2 15 0.00032 38.0 10.6 94 141-242 120-214 (409)
146 COG1349 GlpR Transcriptional r 79.7 2.5 5.5E-05 40.9 4.5 46 338-383 5-50 (253)
147 PF10668 Phage_terminase: Phag 79.7 2.8 6.2E-05 31.1 3.7 37 339-375 9-45 (60)
148 KOG2003 TPR repeat-containing 79.6 9 0.0002 39.8 8.4 96 141-246 594-691 (840)
149 PLN03218 maturation of RBCL 1; 79.2 1.4E+02 0.003 35.2 26.2 96 141-242 509-606 (1060)
150 PLN03088 SGT1, suppressor of 79.2 14 0.00031 37.4 10.0 80 140-223 37-116 (356)
151 smart00550 Zalpha Z-DNA-bindin 79.1 4.1 8.9E-05 30.9 4.6 44 341-384 9-54 (68)
152 PRK14574 hmsH outer membrane p 79.0 1.2E+02 0.0027 34.5 18.2 95 141-246 104-200 (822)
153 PF04703 FaeA: FaeA-like prote 78.8 3.3 7.1E-05 31.0 3.8 40 344-383 6-46 (62)
154 PF14853 Fis1_TPR_C: Fis1 C-te 78.3 7.5 0.00016 28.1 5.5 37 139-175 1-37 (53)
155 cd07377 WHTH_GntR Winged helix 78.2 7.2 0.00016 28.4 5.7 51 333-383 5-56 (66)
156 TIGR03504 FimV_Cterm FimV C-te 77.8 2.9 6.3E-05 29.0 3.1 26 142-167 2-27 (44)
157 CHL00033 ycf3 photosystem I as 77.8 10 0.00022 33.6 7.6 67 140-206 73-143 (168)
158 PRK15359 type III secretion sy 77.8 11 0.00023 32.9 7.5 64 139-205 58-121 (144)
159 PRK09802 DNA-binding transcrip 77.7 3.3 7.1E-05 40.4 4.6 47 337-383 16-62 (269)
160 PF01047 MarR: MarR family; I 77.6 5.1 0.00011 28.9 4.6 46 346-391 11-56 (59)
161 PRK10906 DNA-binding transcrip 77.4 3.4 7.5E-05 39.9 4.6 46 338-383 5-50 (252)
162 TIGR02552 LcrH_SycD type III s 77.0 11 0.00024 31.6 7.3 63 140-205 52-114 (135)
163 PRK15179 Vi polysaccharide bio 76.9 97 0.0021 34.6 16.2 159 45-207 47-219 (694)
164 PRK13509 transcriptional repre 76.9 3.7 8.1E-05 39.6 4.7 45 339-383 6-50 (251)
165 KOG0553 TPR repeat-containing 76.7 20 0.00043 35.4 9.5 92 144-243 86-177 (304)
166 PF10345 Cohesin_load: Cohesin 76.1 1.3E+02 0.0027 33.0 17.0 100 141-241 102-205 (608)
167 KOG2002 TPR-containing nuclear 76.0 64 0.0014 36.8 14.2 130 67-202 233-368 (1018)
168 KOG1129 TPR repeat-containing 76.0 45 0.00097 33.6 11.7 87 152-243 337-423 (478)
169 PRK09782 bacteriophage N4 rece 75.8 96 0.0021 36.1 16.3 93 142-243 545-637 (987)
170 KOG0624 dsRNA-activated protei 75.5 99 0.0021 31.5 17.6 201 119-364 19-220 (504)
171 KOG4414 COP9 signalosome, subu 75.4 5.9 0.00013 34.8 4.9 76 296-375 80-155 (197)
172 KOG4234 TPR repeat-containing 75.3 9.3 0.0002 35.8 6.5 61 145-205 101-163 (271)
173 cd05804 StaR_like StaR_like; a 75.1 90 0.0019 30.8 18.6 64 140-203 149-213 (355)
174 PRK10681 DNA-binding transcrip 75.0 3.7 8.1E-05 39.6 4.2 41 337-377 6-46 (252)
175 TIGR03826 YvyF flagellar opero 74.5 3.5 7.5E-05 36.0 3.4 43 343-389 35-79 (137)
176 smart00028 TPR Tetratricopepti 74.1 6 0.00013 22.9 3.6 27 141-167 3-29 (34)
177 PF07721 TPR_4: Tetratricopept 73.9 4.7 0.0001 24.2 3.0 23 141-163 3-25 (26)
178 KOG0548 Molecular co-chaperone 73.2 49 0.0011 35.2 11.8 92 144-243 7-98 (539)
179 KOG0551 Hsp90 co-chaperone CNS 73.2 25 0.00055 35.3 9.3 96 137-237 79-175 (390)
180 PRK11014 transcriptional repre 73.0 9 0.0002 33.4 5.8 62 337-398 10-71 (141)
181 cd00090 HTH_ARSR Arsenical Res 73.0 21 0.00046 26.1 7.3 44 353-396 21-64 (78)
182 PF02064 MAS20: MAS20 protein 73.0 8.2 0.00018 33.0 5.2 41 140-180 64-104 (121)
183 PF13518 HTH_28: Helix-turn-he 72.7 9.5 0.00021 26.6 4.8 45 339-387 2-46 (52)
184 COG2976 Uncharacterized protei 72.7 78 0.0017 29.5 11.8 103 136-244 86-188 (207)
185 PF13432 TPR_16: Tetratricopep 72.5 7.2 0.00016 28.4 4.4 32 138-169 30-61 (65)
186 TIGR02844 spore_III_D sporulat 72.2 5.2 0.00011 31.6 3.6 34 339-373 7-40 (80)
187 PF01022 HTH_5: Bacterial regu 72.1 13 0.00028 25.8 5.3 43 338-382 3-45 (47)
188 PF13431 TPR_17: Tetratricopep 72.1 3.1 6.7E-05 26.9 1.9 21 140-160 14-34 (34)
189 PLN03218 maturation of RBCL 1; 72.0 2.1E+02 0.0046 33.7 28.7 172 141-331 616-795 (1060)
190 TIGR02787 codY_Gpos GTP-sensin 71.8 17 0.00036 34.9 7.5 60 326-385 152-231 (251)
191 PF01984 dsDNA_bind: Double-st 71.7 1.4 3.1E-05 36.8 0.3 52 336-387 31-82 (107)
192 KOG0396 Uncharacterized conser 71.4 90 0.0019 31.8 12.7 125 115-243 91-219 (389)
193 COG4649 Uncharacterized protei 71.1 84 0.0018 28.9 11.4 100 140-245 95-197 (221)
194 KOG1586 Protein required for f 71.0 1E+02 0.0022 29.7 14.4 106 142-248 116-231 (288)
195 PF09986 DUF2225: Uncharacteri 70.8 18 0.00038 34.1 7.5 73 106-178 125-206 (214)
196 PF14559 TPR_19: Tetratricopep 70.4 8.7 0.00019 28.1 4.4 32 140-171 26-57 (68)
197 KOG3431 Apoptosis-related prot 70.2 4.1 9E-05 34.5 2.7 53 335-387 38-90 (129)
198 KOG4626 O-linked N-acetylgluco 69.8 1.5E+02 0.0032 32.7 14.5 94 140-242 321-415 (966)
199 smart00344 HTH_ASNC helix_turn 69.7 8.3 0.00018 31.6 4.6 48 341-388 6-56 (108)
200 PF08631 SPO22: Meiosis protei 69.7 81 0.0018 30.7 12.3 106 134-244 30-150 (278)
201 KOG1155 Anaphase-promoting com 69.7 42 0.00091 35.3 10.3 100 134-238 427-530 (559)
202 PF12802 MarR_2: MarR family; 69.6 14 0.00031 26.7 5.4 40 352-391 21-60 (62)
203 KOG0550 Molecular chaperone (D 69.6 72 0.0016 33.1 11.8 132 141-277 251-392 (486)
204 smart00346 HTH_ICLR helix_turn 69.6 43 0.00094 26.1 8.6 46 339-384 6-52 (91)
205 KOG3060 Uncharacterized conser 69.5 1.1E+02 0.0025 29.7 13.6 93 106-202 19-112 (289)
206 PF13371 TPR_9: Tetratricopept 69.1 11 0.00023 28.1 4.7 34 140-173 30-63 (73)
207 PRK10857 DNA-binding transcrip 68.6 17 0.00037 32.7 6.6 69 341-411 14-82 (164)
208 PF02082 Rrf2: Transcriptional 68.5 26 0.00057 27.3 7.0 46 352-398 25-70 (83)
209 PRK15363 pathogenicity island 68.1 47 0.001 29.7 9.2 70 134-206 64-133 (157)
210 smart00419 HTH_CRP helix_turn_ 67.6 8.7 0.00019 26.1 3.6 32 352-383 8-39 (48)
211 PRK15179 Vi polysaccharide bio 67.6 52 0.0011 36.7 11.4 103 136-246 117-219 (694)
212 KOG1173 Anaphase-promoting com 67.3 27 0.00059 37.4 8.5 95 140-245 313-410 (611)
213 PRK04841 transcriptional regul 66.4 45 0.00098 37.9 11.1 103 141-243 493-601 (903)
214 PF06163 DUF977: Bacterial pro 66.2 8.8 0.00019 32.9 3.9 39 344-382 18-56 (127)
215 PRK04239 hypothetical protein; 65.5 5.7 0.00012 33.3 2.6 54 334-387 34-87 (110)
216 PF10300 DUF3808: Protein of u 64.9 69 0.0015 33.9 11.4 87 152-243 246-333 (468)
217 COG1729 Uncharacterized protei 64.4 86 0.0019 30.5 10.8 102 142-247 144-247 (262)
218 PLN03081 pentatricopeptide (PP 64.3 1.9E+02 0.0042 31.9 15.3 92 141-242 362-453 (697)
219 PF08281 Sigma70_r4_2: Sigma-7 64.2 21 0.00045 25.2 5.2 46 329-377 6-51 (54)
220 COG4783 Putative Zn-dependent 64.0 97 0.0021 32.7 11.7 69 139-207 374-456 (484)
221 KOG3252 Uncharacterized conser 63.9 64 0.0014 29.7 9.1 88 295-396 101-189 (217)
222 KOG3617 WD40 and TPR repeat-co 63.8 62 0.0013 36.5 10.6 104 138-241 857-993 (1416)
223 KOG3060 Uncharacterized conser 63.8 57 0.0012 31.7 9.3 42 124-167 141-182 (289)
224 PRK10747 putative protoheme IX 63.8 1.8E+02 0.0039 29.8 16.9 93 141-244 265-357 (398)
225 COG5010 TadD Flp pilus assembl 63.6 76 0.0016 30.7 10.2 93 143-243 104-196 (257)
226 smart00418 HTH_ARSR helix_turn 62.4 24 0.00051 25.0 5.4 43 350-392 8-50 (66)
227 KOG4555 TPR repeat-containing 61.8 1.1E+02 0.0024 26.8 10.1 95 142-241 46-141 (175)
228 PRK11534 DNA-binding transcrip 61.6 21 0.00046 33.3 6.2 65 330-396 8-72 (224)
229 KOG0276 Vesicle coat complex C 61.4 1.5E+02 0.0033 32.3 12.7 157 142-343 617-777 (794)
230 KOG0553 TPR repeat-containing 61.3 86 0.0019 31.0 10.3 84 84-169 95-179 (304)
231 cd00092 HTH_CRP helix_turn_hel 61.2 12 0.00027 27.3 3.7 34 351-384 24-57 (67)
232 TIGR00985 3a0801s04tom mitocho 61.2 1.1E+02 0.0023 27.2 10.0 43 140-182 91-134 (148)
233 PF09339 HTH_IclR: IclR helix- 60.9 20 0.00044 25.3 4.5 41 342-382 7-48 (52)
234 PRK09954 putative kinase; Prov 60.5 24 0.00051 35.7 6.7 54 343-396 8-64 (362)
235 KOG1156 N-terminal acetyltrans 60.5 2.7E+02 0.0058 30.7 20.0 120 119-243 115-247 (700)
236 TIGR02010 IscR iron-sulfur clu 60.5 39 0.00084 29.1 7.2 59 351-411 24-82 (135)
237 COG1802 GntR Transcriptional r 60.3 20 0.00044 33.7 5.9 67 330-398 17-83 (230)
238 PF13463 HTH_27: Winged helix 60.3 36 0.00079 24.9 6.2 48 344-391 9-57 (68)
239 smart00351 PAX Paired Box doma 60.1 19 0.00041 30.8 5.0 45 337-384 21-65 (125)
240 PRK03837 transcriptional regul 60.0 24 0.00053 33.2 6.4 64 331-396 15-79 (241)
241 PRK02603 photosystem I assembl 60.0 91 0.002 27.6 9.8 54 140-196 73-126 (172)
242 PRK15174 Vi polysaccharide exp 59.9 2.8E+02 0.006 30.7 23.4 97 140-244 145-241 (656)
243 TIGR03338 phnR_burk phosphonat 59.6 24 0.00052 32.6 6.1 64 331-396 13-76 (212)
244 PF13384 HTH_23: Homeodomain-l 59.2 9.9 0.00021 26.4 2.7 40 338-380 6-45 (50)
245 PF01726 LexA_DNA_bind: LexA D 59.1 15 0.00033 27.7 3.8 32 352-383 25-57 (65)
246 COG3355 Predicted transcriptio 58.4 1.2E+02 0.0026 26.1 10.6 84 342-425 32-117 (126)
247 TIGR03879 near_KaiC_dom probab 58.1 9.9 0.00021 29.5 2.6 33 350-382 30-62 (73)
248 cd00131 PAX Paired Box domain 57.6 23 0.0005 30.4 5.2 45 337-384 21-65 (128)
249 COG2118 DNA-binding protein [G 57.6 11 0.00024 31.6 2.9 53 335-387 38-90 (116)
250 TIGR02812 fadR_gamma fatty aci 57.6 1.2E+02 0.0026 28.4 10.7 64 331-396 8-72 (235)
251 PF04053 Coatomer_WDAD: Coatom 57.2 77 0.0017 33.3 10.0 132 142-318 298-429 (443)
252 PF13404 HTH_AsnC-type: AsnC-t 57.1 20 0.00043 24.5 3.7 35 342-376 7-41 (42)
253 COG2956 Predicted N-acetylgluc 57.0 2.2E+02 0.0049 28.8 18.2 98 141-243 143-242 (389)
254 KOG2235 Uncharacterized conser 56.6 35 0.00076 36.9 7.1 62 328-396 114-175 (776)
255 KOG3250 COP9 signalosome, subu 56.3 61 0.0013 30.6 7.9 121 293-423 60-184 (258)
256 PRK10225 DNA-binding transcrip 56.0 44 0.00096 31.9 7.5 65 331-397 11-76 (257)
257 TIGR01764 excise DNA binding d 55.8 21 0.00045 24.1 3.8 31 353-387 2-32 (49)
258 PF12840 HTH_20: Helix-turn-he 55.8 35 0.00076 24.9 5.3 50 334-384 7-56 (61)
259 PF13414 TPR_11: TPR repeat; P 55.6 42 0.0009 24.5 5.8 61 177-242 4-65 (69)
260 PF12862 Apc5: Anaphase-promot 55.3 84 0.0018 25.1 7.9 46 137-182 39-86 (94)
261 PF09613 HrpB1_HrpK: Bacterial 55.3 47 0.001 29.9 6.8 68 171-243 5-72 (160)
262 PRK11920 rirA iron-responsive 55.2 49 0.0011 29.3 7.0 61 349-411 21-81 (153)
263 TIGR02944 suf_reg_Xantho FeS a 55.0 40 0.00087 28.6 6.3 61 351-413 24-84 (130)
264 PF00325 Crp: Bacterial regula 54.7 24 0.00051 22.8 3.5 30 353-382 3-32 (32)
265 KOG4340 Uncharacterized conser 54.7 2.4E+02 0.0051 28.3 13.2 136 33-172 276-447 (459)
266 PF04733 Coatomer_E: Coatomer 54.5 72 0.0016 31.4 8.8 95 141-243 167-263 (290)
267 KOG2300 Uncharacterized conser 54.3 1.7E+02 0.0037 31.1 11.5 120 141-269 369-495 (629)
268 PF13812 PPR_3: Pentatricopept 53.7 33 0.00071 21.0 4.2 28 142-169 4-31 (34)
269 PF01325 Fe_dep_repress: Iron 53.5 34 0.00075 25.2 4.8 35 349-383 19-53 (60)
270 PF04967 HTH_10: HTH DNA bindi 53.1 24 0.00051 25.6 3.7 32 346-377 17-48 (53)
271 PF12487 DUF3703: Protein of u 53.0 94 0.002 26.2 7.8 60 143-202 13-73 (112)
272 PF13730 HTH_36: Helix-turn-he 52.9 21 0.00046 25.3 3.6 29 354-382 27-55 (55)
273 KOG1173 Anaphase-promoting com 52.8 1.8E+02 0.0039 31.4 11.6 62 141-205 457-518 (611)
274 COG1747 Uncharacterized N-term 52.7 3.3E+02 0.0071 29.4 19.5 163 141-314 207-385 (711)
275 PRK11179 DNA-binding transcrip 52.6 26 0.00057 30.8 4.9 48 341-388 12-62 (153)
276 KOG0495 HAT repeat protein [RN 52.2 1.3E+02 0.0029 33.1 10.6 62 141-205 586-647 (913)
277 smart00347 HTH_MARR helix_turn 51.6 1.1E+02 0.0025 23.7 8.2 45 346-390 18-62 (101)
278 PRK15481 transcriptional regul 51.3 32 0.00068 35.6 6.0 55 331-385 7-62 (431)
279 KOG2114 Vacuolar assembly/sort 51.1 45 0.00098 37.4 7.1 36 131-166 360-395 (933)
280 KOG2047 mRNA splicing factor [ 51.0 48 0.001 36.2 7.1 70 138-207 386-456 (835)
281 KOG4340 Uncharacterized conser 50.8 40 0.00086 33.6 6.0 114 138-253 43-180 (459)
282 PRK11169 leucine-responsive tr 50.8 31 0.00066 30.9 5.1 50 340-389 16-68 (164)
283 TIGR02337 HpaR homoprotocatech 50.6 1.4E+02 0.0031 24.6 9.0 43 349-391 39-81 (118)
284 PF12854 PPR_1: PPR repeat 50.3 23 0.00049 22.7 3.0 25 141-165 9-33 (34)
285 KOG1126 DNA-binding cell divis 49.8 1.5E+02 0.0032 32.5 10.5 94 140-241 490-583 (638)
286 PRK10370 formate-dependent nit 49.6 49 0.0011 30.5 6.4 65 140-207 108-175 (198)
287 COG1959 Predicted transcriptio 49.3 61 0.0013 28.6 6.7 50 349-398 22-71 (150)
288 PRK09464 pdhR transcriptional 49.3 42 0.00092 31.9 6.1 64 331-396 12-76 (254)
289 COG2345 Predicted transcriptio 48.9 39 0.00085 31.9 5.5 45 341-385 14-58 (218)
290 TIGR02561 HrpB1_HrpK type III 48.8 64 0.0014 28.7 6.5 68 171-244 5-73 (153)
291 COG2378 Predicted transcriptio 48.5 30 0.00066 34.5 5.1 54 335-391 5-58 (311)
292 PF04545 Sigma70_r4: Sigma-70, 48.3 52 0.0011 22.8 4.9 28 350-377 18-45 (50)
293 PLN03077 Protein ECB2; Provisi 47.7 4E+02 0.0088 30.2 14.7 23 143-165 226-248 (857)
294 PRK14720 transcript cleavage f 47.3 2.4E+02 0.0053 32.5 12.4 54 261-314 345-403 (906)
295 TIGR00756 PPR pentatricopeptid 47.0 40 0.00087 20.4 3.9 27 143-169 4-30 (35)
296 COG4105 ComL DNA uptake lipopr 46.9 2.8E+02 0.0061 26.9 15.0 57 143-199 171-227 (254)
297 PF13545 HTH_Crp_2: Crp-like h 46.9 34 0.00074 25.8 4.2 43 351-397 27-69 (76)
298 KOG1130 Predicted G-alpha GTPa 46.8 80 0.0017 32.9 7.6 85 119-204 168-263 (639)
299 KOG1156 N-terminal acetyltrans 46.8 4.4E+02 0.0095 29.1 17.1 66 138-206 370-435 (700)
300 PRK14165 winged helix-turn-hel 46.7 2.2E+02 0.0047 26.9 10.2 52 346-397 15-66 (217)
301 KOG0545 Aryl-hydrocarbon recep 46.7 87 0.0019 30.4 7.4 97 141-242 180-291 (329)
302 PF01535 PPR: PPR repeat; Int 46.4 31 0.00066 20.6 3.1 26 143-168 4-29 (31)
303 PF13041 PPR_2: PPR repeat fam 46.1 64 0.0014 22.1 5.2 33 141-173 5-37 (50)
304 PLN03081 pentatricopeptide (PP 45.9 4.5E+02 0.0098 29.0 20.0 28 141-168 191-218 (697)
305 PF12569 NARP1: NMDA receptor- 45.9 1.3E+02 0.0028 32.3 9.7 108 136-246 225-336 (517)
306 PRK11414 colanic acid/biofilm 45.7 49 0.0011 30.8 5.9 62 331-394 13-74 (221)
307 COG5010 TadD Flp pilus assembl 45.6 2.9E+02 0.0064 26.8 13.1 105 129-245 60-164 (257)
308 KOG2300 Uncharacterized conser 44.9 1.5E+02 0.0032 31.6 9.3 70 136-207 4-78 (629)
309 PRK11753 DNA-binding transcrip 44.7 1.6E+02 0.0034 26.7 9.1 42 352-397 168-209 (211)
310 PF13011 LZ_Tnp_IS481: leucine 44.7 31 0.00067 27.6 3.6 38 351-389 24-61 (85)
311 KOG2076 RNA polymerase III tra 44.4 5.4E+02 0.012 29.5 18.8 95 141-243 175-269 (895)
312 PF05843 Suf: Suppressor of fo 44.4 62 0.0013 31.6 6.5 67 141-207 72-138 (280)
313 PHA02943 hypothetical protein; 44.1 1.6E+02 0.0034 26.4 8.0 58 341-400 14-71 (165)
314 PLN03077 Protein ECB2; Provisi 43.9 5.3E+02 0.012 29.3 16.3 53 144-203 529-581 (857)
315 PF09986 DUF2225: Uncharacteri 43.7 2.5E+02 0.0053 26.4 10.2 70 138-207 117-196 (214)
316 PRK06266 transcription initiat 43.7 2.6E+02 0.0055 25.5 10.5 63 323-386 6-70 (178)
317 PF01476 LysM: LysM domain; I 43.4 23 0.0005 23.7 2.4 19 354-372 8-26 (44)
318 KOG2066 Vacuolar assembly/sort 43.4 5.3E+02 0.012 29.1 13.9 51 298-351 511-562 (846)
319 PRK04984 fatty acid metabolism 42.7 64 0.0014 30.4 6.2 63 332-396 10-73 (239)
320 PF01865 PhoU_div: Protein of 42.7 72 0.0016 29.5 6.4 80 293-379 25-104 (214)
321 PRK09990 DNA-binding transcrip 42.5 64 0.0014 30.7 6.2 64 331-396 9-73 (251)
322 PF04010 DUF357: Protein of un 42.1 75 0.0016 24.7 5.3 28 137-164 33-60 (75)
323 KOG0547 Translocase of outer m 41.7 4.7E+02 0.01 28.0 15.6 94 141-242 464-564 (606)
324 TIGR01884 cas_HTH CRISPR locus 41.5 77 0.0017 29.3 6.4 43 344-386 149-191 (203)
325 TIGR02702 SufR_cyano iron-sulf 41.4 69 0.0015 29.6 6.0 44 342-385 5-48 (203)
326 TIGR00952 S15_bact ribosomal p 41.4 33 0.00072 27.5 3.3 55 37-94 29-83 (86)
327 PF13601 HTH_34: Winged helix 41.3 1.6E+02 0.0035 22.9 7.3 50 342-391 4-53 (80)
328 TIGR00738 rrf2_super rrf2 fami 41.2 82 0.0018 26.6 6.1 43 351-393 24-66 (132)
329 PRK10421 DNA-binding transcrip 40.9 71 0.0015 30.4 6.2 64 331-396 4-68 (253)
330 KOG1130 Predicted G-alpha GTPa 40.7 2.5E+02 0.0054 29.4 10.1 73 130-202 226-301 (639)
331 COG1522 Lrp Transcriptional re 40.5 56 0.0012 28.3 5.0 43 346-388 16-61 (154)
332 PF08280 HTH_Mga: M protein tr 40.3 62 0.0013 23.6 4.4 39 339-377 6-44 (59)
333 KOG2561 Adaptor protein NUB1, 40.2 1.4E+02 0.0031 31.2 8.3 102 140-241 164-293 (568)
334 PRK11523 DNA-binding transcrip 40.0 73 0.0016 30.4 6.2 64 331-396 10-74 (253)
335 PLN03083 E3 UFM1-protein ligas 39.6 1.6E+02 0.0035 33.3 9.3 61 328-396 115-175 (803)
336 PF09295 ChAPs: ChAPs (Chs5p-A 39.4 1.9E+02 0.004 30.0 9.3 92 141-243 202-295 (395)
337 PF13512 TPR_18: Tetratricopep 39.2 2.7E+02 0.0058 24.5 10.5 56 141-196 12-67 (142)
338 KOG3850 Predicted membrane pro 39.2 4.5E+02 0.0097 27.1 12.0 85 67-163 262-359 (455)
339 PRK06771 hypothetical protein; 38.7 24 0.00051 28.6 2.0 30 352-381 36-67 (93)
340 PF01978 TrmB: Sugar-specific 37.9 86 0.0019 23.2 5.1 44 341-385 12-55 (68)
341 COG2963 Transposase and inacti 37.7 78 0.0017 26.2 5.3 46 336-383 10-56 (116)
342 COG3071 HemY Uncharacterized e 37.5 4.8E+02 0.01 26.9 12.0 132 146-288 91-227 (400)
343 PF03374 ANT: Phage antirepres 37.3 54 0.0012 27.0 4.2 35 341-375 13-47 (111)
344 PF03297 Ribosomal_S25: S25 ri 37.2 1.6E+02 0.0034 24.6 6.8 49 348-396 55-103 (105)
345 PF09743 DUF2042: Uncharacteri 36.8 93 0.002 30.5 6.3 56 333-388 173-228 (272)
346 PRK09391 fixK transcriptional 36.8 1.5E+02 0.0032 27.7 7.7 41 352-396 179-220 (230)
347 TIGR01610 phage_O_Nterm phage 36.7 1.1E+02 0.0025 24.5 5.9 48 349-398 44-91 (95)
348 TIGR00540 hemY_coli hemY prote 36.6 4.8E+02 0.01 26.7 26.2 100 143-245 157-293 (409)
349 KOG0543 FKBP-type peptidyl-pro 36.6 3E+02 0.0065 28.4 10.0 82 134-220 251-334 (397)
350 TIGR00498 lexA SOS regulatory 36.4 46 0.00099 30.5 4.0 33 353-385 26-59 (199)
351 PF07079 DUF1347: Protein of u 36.4 2.5E+02 0.0054 29.7 9.4 92 145-241 12-105 (549)
352 COG4565 CitB Response regulato 36.4 2.9E+02 0.0063 26.2 9.1 39 349-387 170-208 (224)
353 TIGR02018 his_ut_repres histid 36.0 99 0.0022 28.9 6.3 63 332-396 4-67 (230)
354 PF07106 TBPIP: Tat binding pr 35.4 3.2E+02 0.007 24.3 9.3 48 348-396 15-62 (169)
355 COG2976 Uncharacterized protei 35.4 3.8E+02 0.0082 25.1 12.7 24 142-165 129-152 (207)
356 TIGR03697 NtcA_cyano global ni 34.8 1.6E+02 0.0035 26.1 7.4 41 352-396 143-183 (193)
357 PF01710 HTH_Tnp_IS630: Transp 34.8 51 0.0011 27.8 3.7 43 337-383 6-48 (119)
358 PF14493 HTH_40: Helix-turn-he 34.8 55 0.0012 26.1 3.7 33 351-383 12-45 (91)
359 cd06171 Sigma70_r4 Sigma70, re 34.4 99 0.0021 20.6 4.7 27 351-377 25-51 (55)
360 PRK14999 histidine utilization 34.4 99 0.0021 29.2 6.1 65 331-397 14-79 (241)
361 PF14561 TPR_20: Tetratricopep 34.4 1.8E+02 0.004 23.2 6.7 44 118-167 7-50 (90)
362 smart00421 HTH_LUXR helix_turn 34.3 90 0.002 21.3 4.5 29 350-378 16-44 (58)
363 PRK09764 DNA-binding transcrip 34.2 1E+02 0.0023 29.1 6.2 63 332-396 8-71 (240)
364 cd06170 LuxR_C_like C-terminal 34.0 93 0.002 21.4 4.5 29 350-378 13-41 (57)
365 PRK11161 fumarate/nitrate redu 33.9 1.3E+02 0.0027 28.1 6.6 41 352-396 184-224 (235)
366 cd04761 HTH_MerR-SF Helix-Turn 33.8 77 0.0017 21.4 3.9 28 354-385 2-29 (49)
367 PF12324 HTH_15: Helix-turn-he 33.5 73 0.0016 25.0 4.0 36 341-376 27-62 (77)
368 PF01710 HTH_Tnp_IS630: Transp 33.5 47 0.001 28.0 3.3 36 341-376 60-95 (119)
369 PF07720 TPR_3: Tetratricopept 33.4 75 0.0016 20.9 3.5 23 141-163 3-25 (36)
370 PF12728 HTH_17: Helix-turn-he 33.3 63 0.0014 22.4 3.4 38 353-396 2-39 (51)
371 TIGR02675 tape_meas_nterm tape 33.3 48 0.001 25.6 3.0 27 355-385 47-73 (75)
372 TIGR00373 conserved hypothetic 32.9 3.5E+02 0.0077 24.0 11.1 46 349-394 25-72 (158)
373 PRK05626 rpsO 30S ribosomal pr 32.8 64 0.0014 26.0 3.7 55 37-94 32-86 (89)
374 PF06056 Terminase_5: Putative 32.6 73 0.0016 23.4 3.7 35 338-375 2-36 (58)
375 PF10771 DUF2582: Protein of u 32.1 1E+02 0.0022 23.3 4.5 51 343-395 13-63 (65)
376 KOG0495 HAT repeat protein [RN 31.8 7.7E+02 0.017 27.6 17.0 68 176-243 753-845 (913)
377 PF14502 HTH_41: Helix-turn-he 31.5 75 0.0016 22.5 3.4 30 354-383 8-37 (48)
378 COG1497 Predicted transcriptio 31.4 86 0.0019 30.1 4.8 44 341-384 14-57 (260)
379 PF12739 TRAPPC-Trs85: ER-Golg 31.2 2.4E+02 0.0052 29.3 8.7 59 135-193 204-264 (414)
380 PF12688 TPR_5: Tetratrico pep 31.0 3.3E+02 0.0071 23.0 9.1 62 136-199 35-98 (120)
381 PRK00215 LexA repressor; Valid 30.8 67 0.0015 29.6 4.1 34 352-385 23-57 (205)
382 TIGR00635 ruvB Holliday juncti 30.8 3.6E+02 0.0078 26.1 9.6 32 352-383 255-287 (305)
383 CHL00027 rps15 ribosomal prote 30.6 54 0.0012 26.5 2.9 55 37-94 29-83 (90)
384 COG4783 Putative Zn-dependent 30.5 6.8E+02 0.015 26.6 19.6 170 140-342 307-476 (484)
385 cd02680 MIT_calpain7_2 MIT: do 30.1 42 0.00092 26.1 2.2 27 145-171 12-38 (75)
386 PF13551 HTH_29: Winged helix- 30.0 83 0.0018 25.4 4.2 36 351-387 10-46 (112)
387 PRK10219 DNA-binding transcrip 30.0 1.3E+02 0.0028 24.3 5.3 38 335-375 7-44 (107)
388 PF10516 SHNi-TPR: SHNi-TPR; 29.9 1.1E+02 0.0024 20.4 3.9 27 141-167 3-29 (38)
389 PF00376 MerR: MerR family reg 29.9 51 0.0011 21.9 2.3 20 354-373 1-20 (38)
390 COG3413 Predicted DNA binding 29.7 62 0.0013 30.2 3.7 39 338-376 163-202 (215)
391 PF01527 HTH_Tnp_1: Transposas 29.7 92 0.002 23.4 4.1 41 335-377 8-48 (76)
392 PF13936 HTH_38: Helix-turn-he 29.6 63 0.0014 22.0 2.8 25 351-375 19-43 (44)
393 TIGR02997 Sig70-cyanoRpoD RNA 29.6 5.5E+02 0.012 25.1 11.0 36 352-387 177-212 (298)
394 PF06971 Put_DNA-bind_N: Putat 29.5 69 0.0015 22.9 3.0 25 350-374 26-50 (50)
395 PF14549 P22_Cro: DNA-binding 29.4 73 0.0016 23.6 3.3 19 354-372 11-29 (60)
396 TIGR02404 trehalos_R_Bsub treh 29.4 1.5E+02 0.0032 27.8 6.3 62 333-396 4-66 (233)
397 PRK09334 30S ribosomal protein 29.4 1.4E+02 0.003 24.0 5.0 38 348-385 37-74 (86)
398 PF08672 APC2: Anaphase promot 29.3 60 0.0013 24.1 2.8 26 360-385 29-54 (60)
399 smart00342 HTH_ARAC helix_turn 29.1 1.8E+02 0.0039 21.4 5.7 40 335-375 34-74 (84)
400 smart00668 CTLH C-terminal to 29.0 1.1E+02 0.0023 21.5 4.1 28 180-207 5-32 (58)
401 COG1516 FliS Flagellin-specifi 28.7 1.4E+02 0.0031 25.9 5.3 52 156-207 4-62 (132)
402 PF09182 PuR_N: Bacterial puri 28.3 1.2E+02 0.0026 23.3 4.3 37 337-373 3-41 (70)
403 KOG1941 Acetylcholine receptor 28.2 3.8E+02 0.0082 27.7 8.9 100 141-240 248-359 (518)
404 COG3415 Transposase and inacti 28.2 1E+02 0.0022 27.0 4.5 45 336-382 7-51 (138)
405 PF13959 DUF4217: Domain of un 28.1 2.3E+02 0.0051 21.1 5.9 49 317-365 6-58 (65)
406 KOG4626 O-linked N-acetylgluco 28.0 8E+02 0.017 27.3 11.7 67 134-204 383-450 (966)
407 TIGR02859 spore_sigH RNA polym 28.0 1.3E+02 0.0028 27.0 5.5 45 329-376 145-189 (198)
408 KOG1585 Protein required for f 27.9 5.8E+02 0.013 24.9 19.8 28 215-242 190-217 (308)
409 PRK05472 redox-sensing transcr 27.6 1.4E+02 0.003 27.7 5.7 46 335-380 13-60 (213)
410 KOG1538 Uncharacterized conser 27.6 4.2E+02 0.0091 29.4 9.6 86 137-241 745-830 (1081)
411 PF02259 FAT: FAT domain; Int 27.3 5.6E+02 0.012 24.9 10.5 68 135-202 142-210 (352)
412 cd00086 homeodomain Homeodomai 27.2 1.2E+02 0.0027 21.2 4.2 28 348-375 22-50 (59)
413 TIGR02325 C_P_lyase_phnF phosp 26.9 1.7E+02 0.0036 27.4 6.2 64 331-396 10-74 (238)
414 cd04762 HTH_MerR-trunc Helix-T 26.6 68 0.0015 21.3 2.6 28 354-385 2-29 (49)
415 PRK03902 manganese transport t 26.4 4.1E+02 0.009 22.7 9.4 43 342-384 12-54 (142)
416 PRK03573 transcriptional regul 26.3 3.7E+02 0.0079 22.9 7.8 43 352-394 46-88 (144)
417 PF13542 HTH_Tnp_ISL3: Helix-t 26.3 1.7E+02 0.0038 20.1 4.8 25 352-376 27-51 (52)
418 PRK10153 DNA-binding transcrip 26.2 4.3E+02 0.0093 28.4 9.7 51 186-242 430-480 (517)
419 PF04184 ST7: ST7 protein; In 25.8 2.6E+02 0.0057 29.9 7.6 63 141-204 261-323 (539)
420 PRK11512 DNA-binding transcrip 25.7 1.4E+02 0.0031 25.7 5.1 46 350-395 52-97 (144)
421 TIGR00331 hrcA heat shock gene 25.6 1.3E+02 0.0028 30.4 5.4 44 340-383 9-54 (337)
422 TIGR03362 VI_chp_7 type VI sec 25.6 1.8E+02 0.004 28.8 6.3 64 144-207 218-281 (301)
423 PRK10870 transcriptional repre 25.2 3.7E+02 0.008 24.2 7.8 43 351-393 70-112 (176)
424 KOG4648 Uncharacterized conser 25.0 1.1E+02 0.0024 31.1 4.6 26 143-168 101-126 (536)
425 PRK06759 RNA polymerase factor 24.8 1.7E+02 0.0037 25.0 5.5 45 330-377 103-147 (154)
426 KOG3617 WD40 and TPR repeat-co 24.7 1.8E+02 0.0038 33.2 6.3 88 141-242 1082-1172(1416)
427 smart00745 MIT Microtubule Int 24.7 2.5E+02 0.0055 21.2 5.8 26 144-169 13-38 (77)
428 PF13613 HTH_Tnp_4: Helix-turn 24.7 1.1E+02 0.0025 21.6 3.5 27 351-377 18-44 (53)
429 PF10345 Cohesin_load: Cohesin 24.5 9.4E+02 0.02 26.2 19.3 100 141-243 61-167 (608)
430 TIGR01716 RGG_Cterm transcript 24.0 4.6E+02 0.01 23.9 8.6 60 173-232 125-185 (220)
431 KOG1258 mRNA processing protei 24.0 9.6E+02 0.021 26.1 11.6 101 142-246 369-472 (577)
432 TIGR00122 birA_repr_reg BirA b 23.9 1.9E+02 0.004 21.4 4.8 29 353-381 14-42 (69)
433 PF10078 DUF2316: Uncharacteri 23.7 79 0.0017 25.5 2.7 23 351-373 22-44 (89)
434 PF07304 SRA1: Steroid recepto 23.6 3.8E+02 0.0083 23.8 7.5 49 113-165 68-116 (157)
435 PF02796 HTH_7: Helix-turn-hel 23.5 85 0.0018 21.4 2.6 21 353-373 22-42 (45)
436 PF04760 IF2_N: Translation in 23.3 62 0.0014 23.0 1.9 22 352-373 3-24 (54)
437 PF04348 LppC: LppC putative l 23.3 27 0.00059 37.6 0.0 251 140-414 25-280 (536)
438 KOG1127 TPR repeat-containing 23.3 1E+03 0.022 28.0 11.8 108 119-243 994-1103(1238)
439 PF05402 PqqD: Coenzyme PQQ sy 23.3 1E+02 0.0022 22.7 3.2 24 355-378 36-59 (68)
440 cd00569 HTH_Hin_like Helix-tur 22.8 1.6E+02 0.0036 17.2 3.8 21 352-372 21-41 (42)
441 PF10007 DUF2250: Uncharacteri 22.3 1.3E+02 0.0029 24.3 3.8 77 341-417 10-90 (92)
442 PHA00738 putative HTH transcri 22.2 4.3E+02 0.0094 22.1 6.8 60 338-398 13-72 (108)
443 PF08221 HTH_9: RNA polymerase 22.1 1.8E+02 0.0039 21.5 4.2 39 345-383 20-58 (62)
444 PRK00080 ruvB Holliday junctio 22.1 4.1E+02 0.009 26.3 8.3 33 351-383 275-308 (328)
445 PRK12537 RNA polymerase sigma 22.1 1.8E+02 0.0039 26.0 5.2 45 330-377 130-174 (182)
446 TIGR01889 Staph_reg_Sar staphy 21.7 4.4E+02 0.0096 21.4 10.4 65 349-413 40-105 (109)
447 PRK12534 RNA polymerase sigma 21.6 1.6E+02 0.0035 26.3 4.8 43 331-376 135-177 (187)
448 PF03444 HrcA_DNA-bdg: Winged 21.4 2.8E+02 0.0062 21.8 5.3 49 336-384 7-55 (78)
449 KOG4162 Predicted calmodulin-b 21.2 5.1E+02 0.011 29.1 9.0 99 137-243 682-782 (799)
450 PRK10046 dpiA two-component re 21.0 1.9E+02 0.0041 26.7 5.3 41 348-388 173-213 (225)
451 KOG3877 NADH:ubiquinone oxidor 20.9 2.3E+02 0.0049 28.1 5.6 68 300-374 150-236 (393)
452 PF04492 Phage_rep_O: Bacterio 20.8 2.6E+02 0.0056 23.0 5.3 36 347-382 49-84 (100)
453 smart00342 HTH_ARAC helix_turn 20.8 1.2E+02 0.0026 22.4 3.3 24 353-376 2-25 (84)
454 PRK11511 DNA-binding transcrip 20.6 2.4E+02 0.0051 23.8 5.3 26 350-375 23-48 (127)
455 PRK09413 IS2 repressor TnpA; R 20.5 5.1E+02 0.011 21.6 9.1 41 338-380 17-57 (121)
456 PF00046 Homeobox: Homeobox do 20.5 1.1E+02 0.0023 21.6 2.8 25 351-375 26-50 (57)
457 PF10579 Rapsyn_N: Rapsyn N-te 20.3 4.4E+02 0.0095 20.8 8.0 53 146-198 13-65 (80)
458 PRK12547 RNA polymerase sigma 20.3 2.2E+02 0.0049 24.8 5.4 47 328-377 107-153 (164)
459 PRK09642 RNA polymerase sigma 20.2 1.9E+02 0.004 25.1 4.8 46 328-376 101-146 (160)
460 TIGR02899 spore_safA spore coa 20.2 98 0.0021 20.0 2.3 17 354-370 6-22 (44)
461 KOG1125 TPR repeat-containing 20.1 8.7E+02 0.019 26.4 10.2 51 216-274 431-481 (579)
462 KOG2908 26S proteasome regulat 20.0 8.8E+02 0.019 24.7 9.7 84 80-167 55-143 (380)
No 1
>KOG0686 consensus COP9 signalosome, subunit CSN1 [Posttranslational modification, protein turnover, chaperones; Signal transduction mechanisms]
Probab=100.00 E-value=8.3e-86 Score=641.09 Aligned_cols=434 Identities=49% Similarity=0.811 Sum_probs=403.0
Q ss_pred CCCCccccchhhhhhhhcCCCCCCCCCccccC-CcCCHHHHhhccCchhhHHHHHHHHhcCCCchhHHHHHHHHHHHHHh
Q 013559 1 MEPEDEQSNSMMEEICSNGGEESARTRPIISG-EQLDVEAYASLYQGRTKITRLMFIADHCDIASMQLEALRMAYDEIKK 79 (441)
Q Consensus 1 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~-~~~Dl~~y~~~y~g~~~i~rL~fi~~~~~~~~~~~~a~~~~~~~lk~ 79 (441)
|+...+-++||+.+........ .+.-.+.. -++|+|+|.++|.|+.+|-||.|||+|| |.++.+|+++|++++|+
T Consensus 1 mp~~~~a~~pm~~d~~~~~~~~--~N~ee~~~~leidie~yA~~Y~g~~~i~RllfIA~~c--p~Lr~~Al~~Ai~~vk~ 76 (466)
T KOG0686|consen 1 MPAAEQAVEPMQIDREPTPEDI--ENDEELQLVLEIDIEAYAASYEGRNRILRLLFIARHC--PDLRVEALRMAIDEVKE 76 (466)
T ss_pred CCchhhcCccccccccCCCccC--CChHHHHhcccchHHHHHHhcccHHHHHHHHHHHHhC--chHHHHHHHHHHHHHHh
Confidence 6667778888885333321111 11111111 2389999999999999999999999999 99999999999999999
Q ss_pred -cCChHHHHHHHH--HhhccCC-----------CCCcCCHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhHHHHHhHHhHH
Q 013559 80 -GENTQLFREVVK--KIDGRLG-----------PNYAMDEAWCDSVDRRAEQRKEKLENELNAYRTNLIKESIRMGYNDF 145 (441)
Q Consensus 80 -t~~~~~Y~~~~~--~l~~~~~-----------~~~~~D~~~~~~~~~~~~~~~~~Le~el~~~~~n~~~esir~~~~~l 145 (441)
|.+++.|.++++ ++.+.+| ...+.|.+|+++...+..+++++|+.||+.||+|+||||||+++.++
T Consensus 77 ~t~nv~ly~~l~~~~k~~~~L~~~~~~~~~~~~e~~~~D~~WvE~~~~~a~~~le~L~~eLk~yK~n~iKEsiRra~~Dl 156 (466)
T KOG0686|consen 77 DTYNVDLYQELFNASKIQGELGRAPFKNPQLGFEGYLLDEKWVETNNKKAVLKLEKLDNELKSYKDNLIKESIRRALEDL 156 (466)
T ss_pred cCcchhHHHHHHHHHHhcchhhcCCCCCccccccccccchHHHHHhhHHHHHHHHHHHHHHHHhhcchhhHHHHHHHHHH
Confidence 999999999999 7776654 25788999999999999999999999999999999999999999999
Q ss_pred HHHHHHcCCHHHHHHHHHHHHhhhcCchhHHHHHHHHHHHHHHhcCHHHHHhHHHHHhcccc---cCChhhhhhHHHHHH
Q 013559 146 GDFYYAHGALGDAFKSYVRTRDYCTTSKHIIHMCMSAILVSIEMGQFTHVTSYVSKAEQTPE---ALEPVTIAKLRCAAG 222 (441)
Q Consensus 146 a~~~~~~Gd~~~A~~~~~~~r~~~~~~~~~~~~~l~~i~~~i~~~~~~~~~~~~~ka~~~~~---~~d~~~~~~l~~~~g 222 (441)
|+||++||+++.|+++|.++|+|||+.+|.++||+++|+++|+.|||.||..+++||++.++ ........+++|+.|
T Consensus 157 ~dhy~~cG~l~~Alr~YsR~RdYCTs~khvInm~ln~i~VSI~~~nw~hv~sy~~~A~st~~~~~~~~q~v~~kl~C~ag 236 (466)
T KOG0686|consen 157 GDHYLDCGQLDNALRCYSRARDYCTSAKHVINMCLNLILVSIYMGNWGHVLSYISKAESTPDANENLAQEVPAKLKCAAG 236 (466)
T ss_pred HHHHHHhccHHHHHhhhhhhhhhhcchHHHHHHHHHHHHHHHhhcchhhhhhHHHHHHhCchhhhhHHHhcCcchHHHHH
Confidence 99999999999999999999999999999999999999999999999999999999999985 334567789999999
Q ss_pred HHhcccccHHHHHHHHHhcCcCCCCCchhhhcHHHHHHHHHHHHHhcCChHHHHHhcccCHhhHhhhccchHHHHHHHHH
Q 013559 223 LAHLEARKYKLAARKFLEVGPDLGNSYNEVIAAQDVATYGGLCALASFDRAELKSKVIDNVNFRNFLELVPEVRELINDF 302 (441)
Q Consensus 223 l~~l~~r~y~~Aa~~Fl~~~~t~~~~~~el~s~~d~~~Y~~l~al~s~~R~eLk~~vl~~~~~~~~le~~p~~~~ll~~f 302 (441)
++++..|+|+.|+.+|+.+..+..+ ++|++++.|+++|++||||+||+|.+|+..|++|.+|+.|++.+|.++++|.+|
T Consensus 237 La~L~lkkyk~aa~~fL~~~~~~~d-~~~ivtpsdv~iYggLcALAtfdr~~Lk~~vi~n~~Fk~flel~Pqlr~il~~f 315 (466)
T KOG0686|consen 237 LANLLLKKYKSAAKYFLLAEFDHCD-YPEIVTPSDVAIYGGLCALATFDRQDLKLNVIKNESFKLFLELEPQLREILFKF 315 (466)
T ss_pred HHHHHHHHHHHHHHHHHhCCCCccC-ccceecchhhHHHHhhHhhccCCHHHHHHHHHcchhhhhHHhcChHHHHHHHHH
Confidence 9999999999999999999988776 899999999999999999999999999999999999999999999999999999
Q ss_pred hcCCHHHHHHHHHHhHHhhhhchhHHHHHHHHHHHHHHHHHHHhccccccccHHhHHHHcCCChHHHHHHHHHHHHcCcc
Q 013559 303 YSSRYASCLDYLGNLKANLLLDIHLHDHVETLYDQIRNKALIQYTHPFVSVDLHMMANAFKTSVAGIEKELEALITDNQI 382 (441)
Q Consensus 303 ~~~~y~~~~~~L~~~~~~l~~D~~L~~h~~~l~~~iR~~~i~qy~~pYs~I~L~~mA~~fg~s~~~~E~~L~~LI~~g~L 382 (441)
|+++|..|++.|.++++.+++|+||++||+.|+..||.|++.||+.||++++++.||.+||+|+.++|++|.+||.+|+|
T Consensus 316 y~sky~~cl~~L~~~k~~llLD~yLaphVd~Ly~~IR~r~llqy~~py~s~~m~~mA~af~~sv~~le~~l~~LI~~~~i 395 (466)
T KOG0686|consen 316 YSSKYASCLELLREIKPRLLLDMYLAPHVDNLYSLIRNRALLQYLSPYSSADMSKMAEAFNTSVAILESELLELILEGKI 395 (466)
T ss_pred hhhhHHHHHHHHHHhccceeechhcchhHHHHHHHHHHhhHHHhcCccccchHHHHHHHhcccHHHHHHHHHHHHHccch
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred ceEecCCCCeEEEecCCchhHHHHHHHHHHhhHHHHHHHHHHHHHHHhccceeccCC
Q 013559 383 QARIDSHNKILYARHADQRNATFQRVLQTGSEFDQDVRAMLLRANLLKHEYNVRAAR 439 (441)
Q Consensus 383 ~akID~~~gvv~~~~~d~r~~~~~~~i~~~~~~~~~~~~l~lR~~~~~~~~~v~~~~ 439 (441)
+||||+++|+|++.+.++++++++++.-.|+.+.+.++++++|+.++.+.+.+++.+
T Consensus 396 ~~rIDs~~ki~~~~~~~~en~~fe~~~~~~~~~~~~~kal~lr~~~~~~~~ht~s~~ 452 (466)
T KOG0686|consen 396 SGRIDSHNKILYARDADSENATFERVLPMGKRSQLEAKALLLRAALLKNKIHTKSLP 452 (466)
T ss_pred heeeccccceeeecccccccchhhhcchhhHHHHHHHHHHHHHHHHHhccccCCCcc
Confidence 999999999999999999999999999999999999999999999999999998754
No 2
>KOG0687 consensus 26S proteasome regulatory complex, subunit RPN7/PSMD6 [Posttranslational modification, protein turnover, chaperones]
Probab=100.00 E-value=4.3e-75 Score=551.87 Aligned_cols=370 Identities=21% Similarity=0.336 Sum_probs=356.5
Q ss_pred chhhHHHHHHHHhcCCCchhHHHHHHHHHHHHHhcCChHHHHHHHHHhhccCCCCCcCCHHHHHHHHHHHHHHHHHHHHH
Q 013559 46 GRTKITRLMFIADHCDIASMQLEALRMAYDEIKKGENTQLFREVVKKIDGRLGPNYAMDEAWCDSVDRRAEQRKEKLENE 125 (441)
Q Consensus 46 g~~~i~rL~fi~~~~~~~~~~~~a~~~~~~~lk~t~~~~~Y~~~~~~l~~~~~~~~~~D~~~~~~~~~~~~~~~~~Le~e 125 (441)
++..+..+.|+..|+.-+....++.+.+++.|+..+|+|+|+.+|+... |.+|.+.+++|.+.|..++++|+.+
T Consensus 17 p~le~sq~~FlLt~p~~~~~~~~~~e~l~~~Ird~~Map~Ye~lce~~~------i~~D~~~l~~m~~~neeki~eld~~ 90 (393)
T KOG0687|consen 17 PDLELSQLRFLLTHPEVLGQKAAAREKLLAAIRDEDMAPLYEYLCESLV------IKLDQDLLNSMKKANEEKIKELDEK 90 (393)
T ss_pred cchhHHHHHHHHcCccccCcCHHHHHHHHHHHHhcccchHHHHHHhhcc------eeccHHHHHHHHHhhHHHHHHHHHH
Confidence 4577899999999984222367788889999999999999999999865 9999999999999999999999999
Q ss_pred HHHHHhhhhHHHHHhHHhHHHHHHHHcCCHHHHHHHHHHHHhhhcCchhHHHHHHHHHHHHHHhcCHHHHHhHHHHHhcc
Q 013559 126 LNAYRTNLIKESIRMGYNDFGDFYYAHGALGDAFKSYVRTRDYCTTSKHIIHMCMSAILVSIEMGQFTHVTSYVSKAEQT 205 (441)
Q Consensus 126 l~~~~~n~~~esir~~~~~la~~~~~~Gd~~~A~~~~~~~r~~~~~~~~~~~~~l~~i~~~i~~~~~~~~~~~~~ka~~~ 205 (441)
+.++++|+++.++|.++..+|+||+++||.++|.+++.++.++.++.++++|+.|.++|++++.+|.+.+...+.||+.+
T Consensus 91 iedaeenlGE~ev~ea~~~kaeYycqigDkena~~~~~~t~~ktvs~g~kiDVvf~~iRlglfy~D~~lV~~~iekak~l 170 (393)
T KOG0687|consen 91 IEDAEENLGESEVREAMLRKAEYYCQIGDKENALEALRKTYEKTVSLGHKIDVVFYKIRLGLFYLDHDLVTESIEKAKSL 170 (393)
T ss_pred HHHHHHhcchHHHHHHHHHHHHHHHHhccHHHHHHHHHHHHHHHhhcccchhhHHHHHHHHHhhccHHHHHHHHHHHHHH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred cc-cCChhhhhhHHHHHHHHhcccccHHHHHHHHHhcCcCCCCCchhhhcHHHHHHHHHHHHHhcCChHHHHHhcccCHh
Q 013559 206 PE-ALEPVTIAKLRCAAGLAHLEARKYKLAARKFLEVGPDLGNSYNEVIAAQDVATYGGLCALASFDRAELKSKVIDNVN 284 (441)
Q Consensus 206 ~~-~~d~~~~~~l~~~~gl~~l~~r~y~~Aa~~Fl~~~~t~~~~~~el~s~~d~~~Y~~l~al~s~~R~eLk~~vl~~~~ 284 (441)
++ ||||+++||+|+|+|+++|+.|||++||.+|+++.+||+ ..|+++|.++++|+++|++.+++|.+|++||+++|+
T Consensus 171 iE~GgDWeRrNRlKvY~Gly~msvR~Fk~Aa~Lfld~vsTFt--S~El~~Y~~~v~Ytv~~g~i~leR~dlktKVi~~~E 248 (393)
T KOG0687|consen 171 IEEGGDWERRNRLKVYQGLYCMSVRNFKEAADLFLDSVSTFT--SYELMSYETFVRYTVITGLIALERVDLKTKVIKCPE 248 (393)
T ss_pred HHhCCChhhhhhHHHHHHHHHHHHHhHHHHHHHHHHHccccc--ceecccHHHHHHHHHHHhhheeccchHHhhhcCcHH
Confidence 99 999999999999999999999999999999999999998 589999999999999999999999999999999999
Q ss_pred hHhhhccchHHHHHHHHHhcCCHHHHHHHHHHh-HHhhhhchhHHHHHHHHHHHHHHHHHHHhccccccccHHhHHHHcC
Q 013559 285 FRNFLELVPEVRELINDFYSSRYASCLDYLGNL-KANLLLDIHLHDHVETLYDQIRNKALIQYTHPFVSVDLHMMANAFK 363 (441)
Q Consensus 285 ~~~~le~~p~~~~ll~~f~~~~y~~~~~~L~~~-~~~l~~D~~L~~h~~~l~~~iR~~~i~qy~~pYs~I~L~~mA~~fg 363 (441)
+..+++..|.+++++.++|+|+|+.||..|... .+.++.|.||++|.++++++||.++|.|+++||++++|++||++||
T Consensus 249 vl~vl~~l~~~~q~l~SLY~C~Y~~Ff~~L~~~~~~~lk~D~~l~~h~~yyvREMR~rvY~QlLESYrsl~l~~MA~aFg 328 (393)
T KOG0687|consen 249 VLEVLHKLPSVSQLLNSLYECDYSDFFNDLAAVEAKQLKDDRYLGPHYRYYVREMRRRVYAQLLESYRSLTLESMAKAFG 328 (393)
T ss_pred HHHHhhcCchHHHHHHHHHhccHHHHHHHHHHHHHHhhccchhcchHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhC
Confidence 999999999999999999999999999999655 8899999999999999999999999999999999999999999999
Q ss_pred CChHHHHHHHHHHHHcCccceEecCCCCeEEEecCCchhHHHHHHHHHHhhHHHHHHHHH
Q 013559 364 TSVAGIEKELEALITDNQIQARIDSHNKILYARHADQRNATFQRVLQTGSEFDQDVRAML 423 (441)
Q Consensus 364 ~s~~~~E~~L~~LI~~g~L~akID~~~gvv~~~~~d~r~~~~~~~i~~~~~~~~~~~~l~ 423 (441)
||+++++++|.+||.+|+|+||||+++|+|++++||.+|.+|+.+|++||.+.++.|++.
T Consensus 329 VSVefiDreL~rFI~~grL~ckIDrVnGVVEtNrpD~KN~qyq~vikqGd~LLnriQK~~ 388 (393)
T KOG0687|consen 329 VSVEFIDRELGRFIAAGRLHCKIDRVNGVVETNRPDEKNAQYQAVIKQGDLLLNRIQKLS 388 (393)
T ss_pred chHHHHHhHHHHhhccCceeeeeecccceeecCCccccchHHHHHHhhhHHHHHHHHHHH
Confidence 999999999999999999999999999999999999999999999999999999999874
No 3
>COG5187 RPN7 26S proteasome regulatory complex component, contains PCI domain [Posttranslational modification, protein turnover, chaperones]
Probab=100.00 E-value=7.4e-59 Score=435.09 Aligned_cols=372 Identities=16% Similarity=0.278 Sum_probs=338.3
Q ss_pred HHHHHHHHhcCCCchhHHHHHHHHHHHHHhcCChHHHHHHHHHhhccCC-CCCcCCHHHHHHHHHHHHHHHHHHHHHHHH
Q 013559 50 ITRLMFIADHCDIASMQLEALRMAYDEIKKGENTQLFREVVKKIDGRLG-PNYAMDEAWCDSVDRRAEQRKEKLENELNA 128 (441)
Q Consensus 50 i~rL~fi~~~~~~~~~~~~a~~~~~~~lk~t~~~~~Y~~~~~~l~~~~~-~~~~~D~~~~~~~~~~~~~~~~~Le~el~~ 128 (441)
+..-.|+...+.-.-.+..|++.+..+|+...|+|+|+.++++.+.... ..+.+|.+.++++-++|.+++++|++.+++
T Consensus 25 vs~~~fll~~~kl~n~~~ka~e~l~~~i~d~~maplYkyL~E~~n~kt~a~~ikfD~~~~n~l~kkneeki~Elde~i~~ 104 (412)
T COG5187 25 VSDAIFLLHGTKLGNPESKALEHLERLIIDKCMAPLYKYLAEKGNPKTSASVIKFDRGRMNTLLKKNEEKIEELDERIRE 104 (412)
T ss_pred hhhHHHHhcccccCChhhHHHHHHHHHHHHhhhhHHHHHHHhccCCcccchheehhhHHHHHHHHhhHHHHHHHHHHHHH
Confidence 4444555554321122344889999999999999999999998763221 136789999999999999999999999999
Q ss_pred HHhhhhHHHHHhHHhHHHHHHHHcCCHHHHHHHHHHHHhhhcCchhHHHHHHHHHHHHHHhcCHHHHHhHHHHHhcccc-
Q 013559 129 YRTNLIKESIRMGYNDFGDFYYAHGALGDAFKSYVRTRDYCTTSKHIIHMCMSAILVSIEMGQFTHVTSYVSKAEQTPE- 207 (441)
Q Consensus 129 ~~~n~~~esir~~~~~la~~~~~~Gd~~~A~~~~~~~r~~~~~~~~~~~~~l~~i~~~i~~~~~~~~~~~~~ka~~~~~- 207 (441)
.++-.++.++-.+...+|+||+++||.+++.++..+....-++.+-++|+.+.++|+++..||-.-|...+.+++.+++
T Consensus 105 ~eedngE~e~~ea~~n~aeyY~qi~D~~ng~~~~~~~~~~a~stg~KiDv~l~kiRlg~~y~d~~vV~e~lE~~~~~iEk 184 (412)
T COG5187 105 KEEDNGETEGSEADRNIAEYYCQIMDIQNGFEWMRRLMRDAMSTGLKIDVFLCKIRLGLIYGDRKVVEESLEVADDIIEK 184 (412)
T ss_pred HhhcccchHHHHHHHHHHHHHHHHhhhhhHHHHHHHHHHHHHhcccchhhHHHHHHHHHhhccHHHHHHHHHHHHHHHHh
Confidence 8887788999999999999999999999999999999877788889999999999999999999999999999999999
Q ss_pred cCChhhhhhHHHHHHHHhcccccHHHHHHHHHhcCcCCCCCchhhhcHHHHHHHHHHHHHhcCChHHHHHhcccCHhhHh
Q 013559 208 ALEPVTIAKLRCAAGLAHLEARKYKLAARKFLEVGPDLGNSYNEVIAAQDVATYGGLCALASFDRAELKSKVIDNVNFRN 287 (441)
Q Consensus 208 ~~d~~~~~~l~~~~gl~~l~~r~y~~Aa~~Fl~~~~t~~~~~~el~s~~d~~~Y~~l~al~s~~R~eLk~~vl~~~~~~~ 287 (441)
||||+++|++++|.|++.|..|+|++|+.+|.++.+||+ ..|++|+.++++|+++|++.+++|.++|++|+++|++..
T Consensus 185 GgDWeRrNRyK~Y~Gi~~m~~RnFkeAa~Ll~d~l~tF~--S~El~sY~~~vrYa~~~Gl~~leR~diktki~dspevl~ 262 (412)
T COG5187 185 GGDWERRNRYKVYKGIFKMMRRNFKEAAILLSDILPTFE--SSELISYSRAVRYAIFCGLLRLERRDIKTKILDSPEVLD 262 (412)
T ss_pred CCCHHhhhhHHHHHHHHHHHHHhhHHHHHHHHHHhcccc--ccccccHHHHHHHHHHhhhheeehhhhhhhhcCCHHHHH
Confidence 899999999999999999999999999999999999998 689999999999999999999999999999999999999
Q ss_pred hhccch---HHHHHHHHHhcCCHHHHHHH-HHHhHHhhhhchhHHHHHHHHHHHHHHHHHHHhccccccccHHhHHHHcC
Q 013559 288 FLELVP---EVRELINDFYSSRYASCLDY-LGNLKANLLLDIHLHDHVETLYDQIRNKALIQYTHPFVSVDLHMMANAFK 363 (441)
Q Consensus 288 ~le~~p---~~~~ll~~f~~~~y~~~~~~-L~~~~~~l~~D~~L~~h~~~l~~~iR~~~i~qy~~pYs~I~L~~mA~~fg 363 (441)
++.+.. .+..++.++|.|+|.++|.. |..+.+.|..|.||..|++.|+++||.|+|.|.+++|+..+|++||+.||
T Consensus 263 vi~~~e~l~sl~~l~~SLy~cdY~~~F~~ll~~~~n~L~~d~fl~rh~d~fvREMRrrvYaQlLESYr~lsl~sMA~tFg 342 (412)
T COG5187 263 VIGSSEKLGSLVQLATSLYECDYGGDFMNLLYLFCNSLQDDVFLGRHVDLFVREMRRRVYAQLLESYRLLSLESMAQTFG 342 (412)
T ss_pred hccchhhhhhHHHHHHHHHHhccchhhHHHHHHHHhhccchHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhHHHHHHHhC
Confidence 986654 45789999999999976665 45678999999999999999999999999999999999999999999999
Q ss_pred CChHHHHHHHHHHHHcCccceEecCCCCeEEEecCCchhHHHHHHHHHHhhHHHHHHHHH
Q 013559 364 TSVAGIEKELEALITDNQIQARIDSHNKILYARHADQRNATFQRVLQTGSEFDQDVRAML 423 (441)
Q Consensus 364 ~s~~~~E~~L~~LI~~g~L~akID~~~gvv~~~~~d~r~~~~~~~i~~~~~~~~~~~~l~ 423 (441)
+|++.+++.|..||-+|+|+|+||++||+|++++||++|..|+.++++|+.+.++.|+-.
T Consensus 343 VSV~yvdrDLg~FIp~~~LncvIDRvnGvVetnrpdekn~qy~~vVkqGd~ll~klqKy~ 402 (412)
T COG5187 343 VSVEYVDRDLGEFIPEGRLNCVIDRVNGVVETNRPDEKNQQYSSVVKQGDDLLRKLQKYV 402 (412)
T ss_pred ccHHHHhhhHHhhCCCCceeeeeecccceEeccCcchhhhhHHHHHhcchHHHHHHHHHH
Confidence 999999999999999999999999999999999999999999999999999999988753
No 4
>KOG2758 consensus Translation initiation factor 3, subunit e (eIF-3e) [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=3.8e-49 Score=373.76 Aligned_cols=363 Identities=12% Similarity=0.158 Sum_probs=297.1
Q ss_pred CcCCHHHHhhccCchh-hHHHHHHHHhcCCCchhHHHHHHHHHHHHHhcCChHHHHHHHHHhhccCCCCCcCCHHHHHHH
Q 013559 33 EQLDVEAYASLYQGRT-KITRLMFIADHCDIASMQLEALRMAYDEIKKGENTQLFREVVKKIDGRLGPNYAMDEAWCDSV 111 (441)
Q Consensus 33 ~~~Dl~~y~~~y~g~~-~i~rL~fi~~~~~~~~~~~~a~~~~~~~lk~t~~~~~Y~~~~~~l~~~~~~~~~~D~~~~~~~ 111 (441)
+.|||++.|+++.+++ .||.|+|+..+. .+...+.+++.++++++|||++|..++++.++- . -++ +.-+.+.
T Consensus 2 ~~yDLT~~ia~fLDrHLifPLlEFl~~r~--iy~~keLle~k~~ll~~TNMiDy~md~~k~l~~--s--ed~-p~a~~ek 74 (432)
T KOG2758|consen 2 ANYDLTQRIAQFLDRHLIFPLLEFLSLRQ--IYDEKELLEAKLQLLNKTNMIDYVMDTYKNLHT--S--EDM-PNALVEK 74 (432)
T ss_pred CccchhHHHHHhHhhHHHHHHHHHhhhhc--cCCHHHHHHHHHHHHcccchHHHHHHHHhcccc--c--ccc-hHHHHHH
Confidence 4699999999977665 789999999999 999999999999999999999999999988751 1 111 2334456
Q ss_pred HHHHHHHHHHHHHHHHHH---------------------------HhhhhHHHHHhHHhHHHHHHHHcCCHHHHHHHHHH
Q 013559 112 DRRAEQRKEKLENELNAY---------------------------RTNLIKESIRMGYNDFGDFYYAHGALGDAFKSYVR 164 (441)
Q Consensus 112 ~~~~~~~~~~Le~el~~~---------------------------~~n~~~esir~~~~~la~~~~~~Gd~~~A~~~~~~ 164 (441)
++++-+++++|+++.... +...++++..++++++|+|.|+||+|+.|..+++.
T Consensus 75 r~~Vla~lkeLe~ev~piv~~le~Pd~~~~~~~~k~~~~~l~~L~e~ynf~~e~i~~lykyakfqyeCGNY~gAs~yLY~ 154 (432)
T KOG2758|consen 75 RTEVLAELKELEEEVAPIVKVLENPDLIAALRSDKDRVQNLQHLQEHYNFTPERIETLYKYAKFQYECGNYSGASDYLYF 154 (432)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHcCHHHHHHHHhhhhHHHHHHHHHHhcCCCHHHHHHHHHHHHHHHhccCcccHHHHHHH
Confidence 667777777777776422 34457788889999999999999999999999999
Q ss_pred HHhhhcCchh-HHHHHHHHHHHHHHhcCHHHHHhHHHHHhcccccCChhhhhhHHHHHHHHhcccccHHHHHHHHH----
Q 013559 165 TRDYCTTSKH-IIHMCMSAILVSIEMGQFTHVTSYVSKAEQTPEALEPVTIAKLRCAAGLAHLEARKYKLAARKFL---- 239 (441)
Q Consensus 165 ~r~~~~~~~~-~~~~~l~~i~~~i~~~~~~~~~~~~~ka~~~~~~~d~~~~~~l~~~~gl~~l~~r~y~~Aa~~Fl---- 239 (441)
+|..|..++. .++..||.++..|+..||+.|.+.+.|+++.+|+..- -.....+.+|.|.-.+++|.
T Consensus 155 ~r~l~~~~d~n~lsalwGKlASEIL~qnWd~A~edL~rLre~IDs~~f--------~~~~~~l~qRtWLiHWslfv~fnh 226 (432)
T KOG2758|consen 155 YRALVSDPDRNYLSALWGKLASEILTQNWDGALEDLTRLREYIDSKSF--------STSAQQLQQRTWLIHWSLFVFFNH 226 (432)
T ss_pred HHHhcCCcchhhHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHccccc--------ccHHHHHHHHHHHHHHHHHhhccC
Confidence 9999987766 8999999999999999999999999999999983210 01122344455544444443
Q ss_pred --------hcC-------cCCCCCchhhhcHHHHHHHHHHHHHhcCC--hHHHHHhcccCHhhHhhhccchH-HHHHHHH
Q 013559 240 --------EVG-------PDLGNSYNEVIAAQDVATYGGLCALASFD--RAELKSKVIDNVNFRNFLELVPE-VRELIND 301 (441)
Q Consensus 240 --------~~~-------~t~~~~~~el~s~~d~~~Y~~l~al~s~~--R~eLk~~vl~~~~~~~~le~~p~-~~~ll~~ 301 (441)
+.+ .++++.|||++ +|++.+.+.+.. |+.||+ +.++++++.+ ++++|+.
T Consensus 227 pkgrd~iid~fly~p~YLNaIQt~cPhll------RYLatAvvtnk~~rr~~lkd-------lvkVIqqE~ysYkDPite 293 (432)
T KOG2758|consen 227 PKGRDTIIDMFLYQPPYLNAIQTSCPHLL------RYLATAVVTNKRRRRNRLKD-------LVKVIQQESYSYKDPITE 293 (432)
T ss_pred CChhhHHHHHHccCHHHHHHHHhhCHHHH------HHHHHHhhcchHhhHHHHHH-------HHHHHHHhccccCCcHHH
Confidence 221 13356689988 998877777632 455655 5566666653 4555544
Q ss_pred Hh-----cCCHHHHHHHHHHhHHhhhhchhHHHHHHHHHHHHHHHHHHHhccccccccHHhHHHHcCCChHHHHHHHHHH
Q 013559 302 FY-----SSRYASCLDYLGNLKANLLLDIHLHDHVETLYDQIRNKALIQYTHPFVSVDLHMMANAFKTSVAGIEKELEAL 376 (441)
Q Consensus 302 f~-----~~~y~~~~~~L~~~~~~l~~D~~L~~h~~~l~~~iR~~~i~qy~~pYs~I~L~~mA~~fg~s~~~~E~~L~~L 376 (441)
|. +-||.+++..|.+|+.++.+||||.+..+.|.++.|..+++.||++|+||+++.+|.+++|+++++|+|++++
T Consensus 294 Fl~clyvn~DFdgAq~kl~eCeeVl~nDfFLva~l~~F~E~ARl~ifEtfCRIHqcIti~mLA~kLnm~~eeaErwivnl 373 (432)
T KOG2758|consen 294 FLECLYVNYDFDGAQKKLRECEEVLVNDFFLVALLDEFLENARLLIFETFCRIHQCITIDMLADKLNMDPEEAERWIVNL 373 (432)
T ss_pred HHHHHhhccchHHHHHHHHHHHHHHhcchhHHHHHHHHHHHHHHHHHHHHHHHHHheeHHHHHHHhcCCHHHHHHHHHHH
Confidence 44 4588999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHcCccceEecCCCCeEEEecCCchhHHHHHHHHHHhhHHHHHHHHHHH
Q 013559 377 ITDNQIQARIDSHNKILYARHADQRNATFQRVLQTGSEFDQDVRAMLLR 425 (441)
Q Consensus 377 I~~g~L~akID~~~gvv~~~~~d~r~~~~~~~i~~~~~~~~~~~~l~lR 425 (441)
|++.+|+||||+..|.|+|.++ ..+.|+++|++++.+..|++.+..-
T Consensus 374 Ir~~rl~AkidSklg~Vvmg~~--~~s~~qQ~ie~tksLS~rsq~la~~ 420 (432)
T KOG2758|consen 374 IRTARLDAKIDSKLGHVVMGHP--TVSPHQQLIEKTKSLSFRSQNLAQQ 420 (432)
T ss_pred HHHhhhhhhhccccCceeecCC--CCCHHHHHHHhccccchhHHHHHHH
Confidence 9999999999999999999977 5589999999999999999988654
No 5
>PF10602 RPN7: 26S proteasome subunit RPN7; InterPro: IPR019585 This entry represents the regulatory subunit RPN7 (known as the non-ATPase regulatory subunit 6 in higher eukaryotes) of the 26S proteasome. This entry also matches the evolutionarily related subunit 1 of the COP9 signalosome complex (CSN) from Arabidopsis []. The 26S proteasome plays a major role in ATP-dependent degradation of ubiquitinated proteins. Substrate specificity is conferred by the regulatory particle (RP), which can dissociate into stable lid and base subcomplexes. The regulatory subunit RPN7 is one of the lid subunits of the 26S proteasome and has been shown in Saccharomyces cerevisiae (Baker's yeast) to be required for structural integrity []. The COP9 signalosome is a conserved protein complex composed of eight subunits, where Individual subunits of the complex have been linked to various signal transduction pathways leading to gene expression and cell cycle control []. The overall organisation and the amino acid sequences of the COP9 signalosome subunits resemble the lid subcomplex of the 19 S regulatory particle for the 26 S proteasome []. COP9 subunit 1 (CSN1 or GPS1) of the COP9 complex is an essential subunit of the complex with regard to both structural integrity and functionality. The N-terminal region of subunit 1 (CSN1-N) can inhibit c-fos expression from either a transfected template or a chromosomal transgene (fos-lacZ), and may contain the activity domain that confers most of the repression functions of CSN1. The C-terminal region of subunit 1 (CSN1-C) allows integration of the protein into the COP9 signalosome.
Probab=100.00 E-value=1.8e-42 Score=316.32 Aligned_cols=175 Identities=43% Similarity=0.703 Sum_probs=171.0
Q ss_pred CHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhHHHHHhHHhHHHHHHHHcCCHHHHHHHHHHHHhhhcCchhHHHHHHHHH
Q 013559 104 DEAWCDSVDRRAEQRKEKLENELNAYRTNLIKESIRMGYNDFGDFYYAHGALGDAFKSYVRTRDYCTTSKHIIHMCMSAI 183 (441)
Q Consensus 104 D~~~~~~~~~~~~~~~~~Le~el~~~~~n~~~esir~~~~~la~~~~~~Gd~~~A~~~~~~~r~~~~~~~~~~~~~l~~i 183 (441)
|++|+++++++|++++++|+.+|++|++|++++|||+++.++|+||+++||+++|+++|.++|++|++++|+++|++.+|
T Consensus 1 D~~w~~~~~~~~~~~~~~Le~elk~~~~n~~kesir~~~~~l~~~~~~~Gd~~~A~k~y~~~~~~~~~~~~~id~~l~~i 80 (177)
T PF10602_consen 1 DEEWIEETKAKNAEELEKLEAELKDAKSNLGKESIRMALEDLADHYCKIGDLEEALKAYSRARDYCTSPGHKIDMCLNVI 80 (177)
T ss_pred CHHHHHHHHHHHHHHHHHHHHHHHHHHhccchHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHhhhcCCHHHHHHHHHHHH
Confidence 78999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHhcCHHHHHhHHHHHhcccc-cCChhhhhhHHHHHHHHhcccccHHHHHHHHHhcCcCCC-CCchhhhcHHHHHHH
Q 013559 184 LVSIEMGQFTHVTSYVSKAEQTPE-ALEPVTIAKLRCAAGLAHLEARKYKLAARKFLEVGPDLG-NSYNEVIAAQDVATY 261 (441)
Q Consensus 184 ~~~i~~~~~~~~~~~~~ka~~~~~-~~d~~~~~~l~~~~gl~~l~~r~y~~Aa~~Fl~~~~t~~-~~~~el~s~~d~~~Y 261 (441)
|++|+.+||.+|.++++|++.+++ ++||++++++++|.|+++|.+|+|+.|+++|+++.+||+ .++++++||+|+|+|
T Consensus 81 rv~i~~~d~~~v~~~i~ka~~~~~~~~d~~~~nrlk~~~gL~~l~~r~f~~AA~~fl~~~~t~~~~~~~el~s~~d~a~Y 160 (177)
T PF10602_consen 81 RVAIFFGDWSHVEKYIEKAESLIEKGGDWERRNRLKVYEGLANLAQRDFKEAAELFLDSLSTFTSLQYTELISYNDFAIY 160 (177)
T ss_pred HHHHHhCCHHHHHHHHHHHHHHHhccchHHHHHHHHHHHHHHHHHhchHHHHHHHHHccCcCCCCCchhhhcCHHHHHHH
Confidence 999999999999999999999999 789999999999999999999999999999999999997 368999999999999
Q ss_pred HHHHHHhcCChHHHHHh
Q 013559 262 GGLCALASFDRAELKSK 278 (441)
Q Consensus 262 ~~l~al~s~~R~eLk~~ 278 (441)
++||||+|++|++||+|
T Consensus 161 ~~l~aLat~~R~eLk~K 177 (177)
T PF10602_consen 161 GGLCALATLDRSELKKK 177 (177)
T ss_pred HHHHHHHhCCHHHHccC
Confidence 99999999999999864
No 6
>KOG1463 consensus 26S proteasome regulatory complex, subunit RPN6/PSMD11 [Posttranslational modification, protein turnover, chaperones]
Probab=99.96 E-value=4.4e-27 Score=225.64 Aligned_cols=266 Identities=17% Similarity=0.242 Sum_probs=226.8
Q ss_pred hHHHHHHHHcCCHHHHHHHHHHH-HhhhcCchhHHHHHHHHHHHHHHhcCHHHHHhHHHHHhcccc---------cCChh
Q 013559 143 NDFGDFYYAHGALGDAFKSYVRT-RDYCTTSKHIIHMCMSAILVSIEMGQFTHVTSYVSKAEQTPE---------ALEPV 212 (441)
Q Consensus 143 ~~la~~~~~~Gd~~~A~~~~~~~-r~~~~~~~~~~~~~l~~i~~~i~~~~~~~~~~~~~ka~~~~~---------~~d~~ 212 (441)
-+|...|++.++|.+|+.....+ |+. .++|--..++.+.++...--+...++.|+++.+. -++|.
T Consensus 132 arli~Ly~d~~~YteAlaL~~~L~rEl-----KKlDDK~lLvev~llESK~y~~l~Nl~KakasLTsART~AnaiYcpPq 206 (411)
T KOG1463|consen 132 ARLIRLYNDTKRYTEALALINDLLREL-----KKLDDKILLVEVHLLESKAYHALRNLPKAKASLTSARTTANAIYCPPQ 206 (411)
T ss_pred HHHHHHHHhhHHHHHHHHHHHHHHHHH-----HhcccccceeeehhhhhHHHHHHhcchhHHHHHHHHHHhhcccccCHH
Confidence 36788999999999999999886 665 3444444555666665555556666666655432 27899
Q ss_pred hhhhHHHHHHHHhcccccHHHHHHHHHhcCcCCCCCchhhhcHHHHHHHHHHHHHhcCChHHHHHhcccCHhhHhhhc-c
Q 013559 213 TIAKLRCAAGLAHLEARKYKLAARKFLEVGPDLGNSYNEVIAAQDVATYGGLCALASFDRAELKSKVIDNVNFRNFLE-L 291 (441)
Q Consensus 213 ~~~~l~~~~gl~~l~~r~y~~Aa~~Fl~~~~t~~~~~~el~s~~d~~~Y~~l~al~s~~R~eLk~~vl~~~~~~~~le-~ 291 (441)
+++.+...+|+++...++|++|.++|++++..|.+ ...-..+....+|+.||.++-..+.++.. ++.++...++-. .
T Consensus 207 lQa~lDLqSGIlha~ekDykTafSYFyEAfEgf~s-~~~~v~A~~sLKYMlLcKIMln~~ddv~~-lls~K~~l~y~g~~ 284 (411)
T KOG1463|consen 207 LQATLDLQSGILHAAEKDYKTAFSYFYEAFEGFDS-LDDDVKALTSLKYMLLCKIMLNLPDDVAA-LLSAKLALKYAGRD 284 (411)
T ss_pred HHHHHHHhccceeecccccchHHHHHHHHHccccc-cCCcHHHHHHHHHHHHHHHHhcCHHHHHH-HHhhHHHHhccCcc
Confidence 99999999999999999999999999999998853 23334556667999999999999999866 777777777532 2
Q ss_pred chHHHHHHHHHhcCCHHHHHHHHHHhHHhhhhchhHHHHHHHHHHHHHHHHHHHhccccccccHHhHHHHcCCChHHHHH
Q 013559 292 VPEVRELINDFYSSRYASCLDYLGNLKANLLLDIHLHDHVETLYDQIRNKALIQYTHPFVSVDLHMMANAFKTSVAGIEK 371 (441)
Q Consensus 292 ~p~~~~ll~~f~~~~y~~~~~~L~~~~~~l~~D~~L~~h~~~l~~~iR~~~i~qy~~pYs~I~L~~mA~~fg~s~~~~E~ 371 (441)
...++.+..+|-+++...|..+|..++..|..|++++.|...|++++-.+.+...++|||+|.|+.+|+.+|+++..+|+
T Consensus 285 i~AmkavAeA~~nRSLkdF~~AL~~yk~eL~~D~ivr~Hl~~Lyd~lLEknl~riIEPyS~Vei~hIA~~IGl~~~~VEk 364 (411)
T KOG1463|consen 285 IDAMKAVAEAFGNRSLKDFEKALADYKKELAEDPIVRSHLQSLYDNLLEKNLCRIIEPYSRVEISHIAEVIGLDVPQVEK 364 (411)
T ss_pred hHHHHHHHHHhcCCcHHHHHHHHHHhHHHHhcChHHHHHHHHHHHHHHHHhHHHHcCchhhhhHHHHHHHHCCCcHHHHH
Confidence 33578899999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHcCccceEecCCCCeEEEecCCchhHHHHHHHHHHhhH
Q 013559 372 ELEALITDNQIQARIDSHNKILYARHADQRNATFQRVLQTGSEF 415 (441)
Q Consensus 372 ~L~~LI~~g~L~akID~~~gvv~~~~~d~r~~~~~~~i~~~~~~ 415 (441)
.|++||.|+++.|.+|+.+|++......+.+++|+.++++...+
T Consensus 365 KLsqMILDKkf~G~LDQg~g~Liv~~e~~~d~~y~~aLetI~~m 408 (411)
T KOG1463|consen 365 KLSQMILDKKFYGTLDQGEGCLIVFEEPPADNTYDAALETIQNM 408 (411)
T ss_pred HHHHHHHHHHhhcccccCCCeEEEeCCCCcchHHHHHHHHHHhc
Confidence 99999999999999999999999998888999999999997654
No 7
>COG5159 RPN6 26S proteasome regulatory complex component [Posttranslational modification, protein turnover, chaperones]
Probab=99.94 E-value=9.5e-25 Score=205.55 Aligned_cols=279 Identities=20% Similarity=0.253 Sum_probs=234.0
Q ss_pred hHHHHHHHHcCCHHHHHHHHHHH-HhhhcCchhHHHHHHHHHHHHHHhcCHHHHHhHHHHHhc-------ccc--cCChh
Q 013559 143 NDFGDFYYAHGALGDAFKSYVRT-RDYCTTSKHIIHMCMSAILVSIEMGQFTHVTSYVSKAEQ-------TPE--ALEPV 212 (441)
Q Consensus 143 ~~la~~~~~~Gd~~~A~~~~~~~-r~~~~~~~~~~~~~l~~i~~~i~~~~~~~~~~~~~ka~~-------~~~--~~d~~ 212 (441)
-++...+|+.|.|.+|+.....+ ++. .++|--.+++.+.++....-|...++.|+++ .-. -|+|.
T Consensus 129 ~Kli~l~y~~~~YsdalalIn~ll~El-----Kk~DDK~~Li~vhllESKvyh~irnv~KskaSLTaArt~Ans~YCPpq 203 (421)
T COG5159 129 CKLIYLLYKTGKYSDALALINPLLHEL-----KKYDDKINLITVHLLESKVYHEIRNVSKSKASLTAARTLANSAYCPPQ 203 (421)
T ss_pred HHHHHHHHhcccHHHHHHHHHHHHHHH-----HhhcCccceeehhhhhHHHHHHHHhhhhhhhHHHHHHHHhhccCCCHH
Confidence 36778899999999999988776 454 2233333444444444444444444444444 333 38999
Q ss_pred hhhhHHHHHHHHhcccccHHHHHHHHHhcCcCCCCCchhhhcHHHHHHHHHHHHHhcCChHHHHHhcccCHhhHhhhcc-
Q 013559 213 TIAKLRCAAGLAHLEARKYKLAARKFLEVGPDLGNSYNEVIAAQDVATYGGLCALASFDRAELKSKVIDNVNFRNFLEL- 291 (441)
Q Consensus 213 ~~~~l~~~~gl~~l~~r~y~~Aa~~Fl~~~~t~~~~~~el~s~~d~~~Y~~l~al~s~~R~eLk~~vl~~~~~~~~le~- 291 (441)
+++.+...+|+++...++|+.|.++|++++..|+.. ..-.-+....+|+.|+.++-+.|.+++. |+.++...+....
T Consensus 204 lqa~lDL~sGIlhcdd~dyktA~SYF~Ea~Egft~l-~~d~kAc~sLkYmlLSkIMlN~~~evk~-vl~~K~t~~~y~~r 281 (421)
T COG5159 204 LQAQLDLLSGILHCDDRDYKTASSYFIEALEGFTLL-KMDVKACVSLKYMLLSKIMLNRREEVKA-VLRNKNTLKHYDDR 281 (421)
T ss_pred HHHHHHHhccceeeccccchhHHHHHHHHHhccccc-cchHHHHHHHHHHHHHHHHHhhHHHHHH-HHccchhHhhhhhh
Confidence 999999999999999999999999999999888632 2223455567999999999999999976 8888887775533
Q ss_pred -chHHHHHHHHHhcCCHHHHHHHHHHhHHhhhhchhHHHHHHHHHHHHHHHHHHHhccccccccHHhHHHHcCCChHHHH
Q 013559 292 -VPEVRELINDFYSSRYASCLDYLGNLKANLLLDIHLHDHVETLYDQIRNKALIQYTHPFVSVDLHMMANAFKTSVAGIE 370 (441)
Q Consensus 292 -~p~~~~ll~~f~~~~y~~~~~~L~~~~~~l~~D~~L~~h~~~l~~~iR~~~i~qy~~pYs~I~L~~mA~~fg~s~~~~E 370 (441)
...++...++|-|++...|-..|+.+.+.+..|+|+..|...+|..+-.+.+...++||++|.++.+|+.+|+++..+|
T Consensus 282 ~I~am~avaea~~NRsL~df~~aL~qY~~el~~D~~iRsHl~~LYD~LLe~Nl~kiiEPfs~VeishIa~viGldt~qvE 361 (421)
T COG5159 282 MIRAMLAVAEAFGNRSLKDFSDALAQYSDELHQDSFIRSHLQYLYDVLLEKNLVKIIEPFSVVEISHIADVIGLDTNQVE 361 (421)
T ss_pred hHHHHHHHHHHhCCCcHhhHHHHHHHhhHHhccCHHHHHHHHHHHHHHHHhhhhhhcCcceeeehhHHHHHhcccHHHHH
Confidence 2457888999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHcCccceEecCCCCeEEEecCCchhHHHHHHHHHHhhHHHHHHHHHHHHHH
Q 013559 371 KELEALITDNQIQARIDSHNKILYARHADQRNATFQRVLQTGSEFDQDVRAMLLRANL 428 (441)
Q Consensus 371 ~~L~~LI~~g~L~akID~~~gvv~~~~~d~r~~~~~~~i~~~~~~~~~~~~l~lR~~~ 428 (441)
..|.+||.++-..+..|+.+|.+........+++|..++++...+...+..++.+++.
T Consensus 362 gKLsqMILDKifyG~LDqg~gcLivy~ep~qd~tyd~ale~v~~l~~vVd~l~ekas~ 419 (421)
T COG5159 362 GKLSQMILDKIFYGTLDQGDGCLIVYGEPAQDNTYDEALEQVEALDCVVDSLYEKASA 419 (421)
T ss_pred HHHHHHHHHHHHHhhhccCCceEEEeCCccccchHHHHHHHHHHhhhHHHHHHHHHhh
Confidence 9999999999999999999999999998889999999999999999999988887664
No 8
>KOG1464 consensus COP9 signalosome, subunit CSN2 [Posttranslational modification, protein turnover, chaperones; Signal transduction mechanisms]
Probab=99.93 E-value=7e-25 Score=205.45 Aligned_cols=266 Identities=17% Similarity=0.327 Sum_probs=224.4
Q ss_pred HHhHHHHHHHHcCCHHHHHHHHHHHHhhhcCc---------hhHHHHHHHHHHHHHHhcCHHHHHhHHHHHhcccc-cCC
Q 013559 141 GYNDFGDFYYAHGALGDAFKSYVRTRDYCTTS---------KHIIHMCMSAILVSIEMGQFTHVTSYVSKAEQTPE-ALE 210 (441)
Q Consensus 141 ~~~~la~~~~~~Gd~~~A~~~~~~~r~~~~~~---------~~~~~~~l~~i~~~i~~~~~~~~~~~~~ka~~~~~-~~d 210 (441)
...+||++|++.|+|.+-.+.+.+++..|.+. .+.++++-.-|.+.....|....+....++-.+-. -.+
T Consensus 147 TNtKLgkl~fd~~e~~kl~KIlkqLh~SCq~edGedD~kKGtQLLEiYAlEIQmYT~qKnNKkLK~lYeqalhiKSAIPH 226 (440)
T KOG1464|consen 147 TNTKLGKLYFDRGEYTKLQKILKQLHQSCQTEDGEDDQKKGTQLLEIYALEIQMYTEQKNNKKLKALYEQALHIKSAIPH 226 (440)
T ss_pred ccchHhhhheeHHHHHHHHHHHHHHHHHhccccCchhhhccchhhhhHhhHhhhhhhhcccHHHHHHHHHHHHhhccCCc
Confidence 45689999999999999999999999999532 45677777777777788888888877777755544 368
Q ss_pred hhhhhhHHHHHHHHhcccccHHHHHHHHHhcCcCCCCCchhhhcHHH--HHHHHHHHHHhcCChHHHHHhcccCHhhHhh
Q 013559 211 PVTIAKLRCAAGLAHLEARKYKLAARKFLEVGPDLGNSYNEVIAAQD--VATYGGLCALASFDRAELKSKVIDNVNFRNF 288 (441)
Q Consensus 211 ~~~~~~l~~~~gl~~l~~r~y~~Aa~~Fl~~~~t~~~~~~el~s~~d--~~~Y~~l~al~s~~R~eLk~~vl~~~~~~~~ 288 (441)
|.+...++.|.|.++|..|.|.+|...|.+++.. |.+..+|.. ..+|+||+.++-.+ .+ .++++.+.+.+
T Consensus 227 PlImGvIRECGGKMHlreg~fe~AhTDFFEAFKN----YDEsGspRRttCLKYLVLANMLmkS--~i--NPFDsQEAKPy 298 (440)
T KOG1464|consen 227 PLIMGVIRECGGKMHLREGEFEKAHTDFFEAFKN----YDESGSPRRTTCLKYLVLANMLMKS--GI--NPFDSQEAKPY 298 (440)
T ss_pred hHHHhHHHHcCCccccccchHHHHHhHHHHHHhc----ccccCCcchhHHHHHHHHHHHHHHc--CC--CCCcccccCCC
Confidence 9999999999999999999999999999999875 455566665 47999999888532 22 57888888777
Q ss_pred hccchH---HHHHHHHHhcCCHHHHHHHHHHhHHhhhhchhHHHHHHHHHHHHHHHHHHHhccccccccHHhHHHHcCCC
Q 013559 289 LELVPE---VRELINDFYSSRYASCLDYLGNLKANLLLDIHLHDHVETLYDQIRNKALIQYTHPFVSVDLHMMANAFKTS 365 (441)
Q Consensus 289 le~~p~---~~~ll~~f~~~~y~~~~~~L~~~~~~l~~D~~L~~h~~~l~~~iR~~~i~qy~~pYs~I~L~~mA~~fg~s 365 (441)
..+|+ +..++.+|.+.+..+|..+|...+..+..|||+.+|...++++||..++...++||+.|.|..+++.++++
T Consensus 299 -KNdPEIlAMTnlv~aYQ~NdI~eFE~Il~~~~~~IM~DpFIReh~EdLl~niRTQVLlkLIkPYt~i~Ipfis~~Lnv~ 377 (440)
T KOG1464|consen 299 -KNDPEILAMTNLVAAYQNNDIIEFERILKSNRSNIMDDPFIREHIEDLLRNIRTQVLLKLIKPYTNIGIPFISKELNVP 377 (440)
T ss_pred -CCCHHHHHHHHHHHHHhcccHHHHHHHHHhhhccccccHHHHHHHHHHHHHHHHHHHHHHhccccccCchhhHhhcCCC
Confidence 46776 47899999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred hHHHHHHHHHHHHcCccceEecCCCCeEEEecCCchhHH-HHHHHHHHhhH
Q 013559 366 VAGIEKELEALITDNQIQARIDSHNKILYARHADQRNAT-FQRVLQTGSEF 415 (441)
Q Consensus 366 ~~~~E~~L~~LI~~g~L~akID~~~gvv~~~~~d~r~~~-~~~~i~~~~~~ 415 (441)
+.+++..|+.+|.+.+|+||||.+++.+...+.....+. |..+=+....+
T Consensus 378 ~~dV~~LLV~~ILD~~i~g~Ide~n~~l~~~~~~~s~~k~~~al~kW~~ql 428 (440)
T KOG1464|consen 378 EADVESLLVSCILDDTIDGRIDEVNQYLELDKSKNSGSKLYKALDKWNNQL 428 (440)
T ss_pred HHHHHHHHHHHHhccccccchHHhhhHhccCccCCcchHHHHHHHHHHHHH
Confidence 999999999999999999999999999999876553333 44443343333
No 9
>KOG1498 consensus 26S proteasome regulatory complex, subunit RPN5/PSMD12 [Posttranslational modification, protein turnover, chaperones]
Probab=99.81 E-value=2.5e-18 Score=168.42 Aligned_cols=268 Identities=15% Similarity=0.222 Sum_probs=205.3
Q ss_pred HHHHHHHHHHHhhhhHHHHHhH--HhHHHHHHHHcCCHHHHHHHHHHH-Hhhhc--CchhHHHHHHHHHHHHHHhcCHHH
Q 013559 120 EKLENELNAYRTNLIKESIRMG--YNDFGDFYYAHGALGDAFKSYVRT-RDYCT--TSKHIIHMCMSAILVSIEMGQFTH 194 (441)
Q Consensus 120 ~~Le~el~~~~~n~~~esir~~--~~~la~~~~~~Gd~~~A~~~~~~~-r~~~~--~~~~~~~~~l~~i~~~i~~~~~~~ 194 (441)
.+|...|+..+++.|..||.++ .-.|++.+..+||..+|+..+..+ .+..+ ..+.++.+.+.++|+++..+||..
T Consensus 110 ~~li~tLr~VtegkIyvEvERarlTk~L~~ike~~Gdi~~Aa~il~el~VETygsm~~~ekV~fiLEQmrKOG~~~D~vr 189 (439)
T KOG1498|consen 110 IKLIETLRTVTEGKIYVEVERARLTKMLAKIKEEQGDIAEAADILCELQVETYGSMEKSEKVAFILEQMRLCLLRLDYVR 189 (439)
T ss_pred HHHHHHHHHhhcCceEEeehHHHHHHHHHHHHHHcCCHHHHHHHHHhcchhhhhhhHHHHHHHHHHHHHHHHHHhhhHHH
Confidence 4577778888999998888875 567999999999999999999987 66654 457789999999999999999999
Q ss_pred HHhHHHHHhc-ccccCChhhhhhHHHHHH--HHhcccccHHHHHHHHHhcCcCCC---CCchhhhcHHHHHHHHHHHHHh
Q 013559 195 VTSYVSKAEQ-TPEALEPVTIAKLRCAAG--LAHLEARKYKLAARKFLEVGPDLG---NSYNEVIAAQDVATYGGLCALA 268 (441)
Q Consensus 195 ~~~~~~ka~~-~~~~~d~~~~~~l~~~~g--l~~l~~r~y~~Aa~~Fl~~~~t~~---~~~~el~s~~d~~~Y~~l~al~ 268 (441)
+.....|++. .++..+ ....+++.|.- -..++.|.|..+++++..+..+.. ++..|.--...++.| |.++
T Consensus 190 a~i~skKI~~K~F~~~~-~~~lKlkyY~lmI~l~lh~~~Yl~v~~~Yraiy~t~~vk~d~~kw~~vL~~iv~f---~~LA 265 (439)
T KOG1498|consen 190 AQIISKKINKKFFEKPD-VQELKLKYYELMIRLGLHDRAYLNVCRSYRAIYDTGNVKEDPEKWIEVLRSIVSF---CVLA 265 (439)
T ss_pred HHHHHHHhhHHhcCCcc-HHHHHHHHHHHHHHhcccccchhhHHHHHHHHhcccccccChhhhhhhhhhheeE---Eeec
Confidence 9999999876 444322 33344555554 456779999999999999876542 122232222223333 3344
Q ss_pred c--CChHHHHHhcccCHhhHhhhccchHHHHHHHHHhcCCHHHHHHHHHHhHHhhhhchhH-H-----HH-----HHHHH
Q 013559 269 S--FDRAELKSKVIDNVNFRNFLELVPEVRELINDFYSSRYASCLDYLGNLKANLLLDIHL-H-----DH-----VETLY 335 (441)
Q Consensus 269 s--~~R~eLk~~vl~~~~~~~~le~~p~~~~ll~~f~~~~y~~~~~~L~~~~~~l~~D~~L-~-----~h-----~~~l~ 335 (441)
. ..+++|-.++-.+.. ++..|...+++.+|.+.....+-..-+.+.+.+..+.|+ . .| .+.+-
T Consensus 266 p~dneQsdll~~is~dKk----L~e~p~~k~lLklfv~~EL~rw~s~~~~yg~~l~~~~~~~~~~~gek~~~dL~~RIiE 341 (439)
T KOG1498|consen 266 PHDNEQSDLLARISNDKK----LSELPDYKELLKLFVTMELIRWVSLVESYGDELRTNDFFDGGEEGEKRWSDLKLRIIE 341 (439)
T ss_pred CCCcHHHHHHHHHhcccc----cccCccHHHHHHHHHhcceeeehhHhhhhHHHHhhcccccccchhhhHHHHHHHHHHH
Confidence 4 447777777665544 678899999999999998877776666677776655322 1 12 34455
Q ss_pred HHHHHHHHHHhccccccccHHhHHHHcCCChHHHHHHHHHHHHcCccceEecCCCCeEEEecCCc
Q 013559 336 DQIRNKALIQYTHPFVSVDLHMMANAFKTSVAGIEKELEALITDNQIQARIDSHNKILYARHADQ 400 (441)
Q Consensus 336 ~~iR~~~i~qy~~pYs~I~L~~mA~~fg~s~~~~E~~L~~LI~~g~L~akID~~~gvv~~~~~d~ 400 (441)
+|| |++..| |++|++.+||..+|++++++|+.|+.||..|.+.||||+++|+|.+..+..
T Consensus 342 HNi--RiiA~y---YSrIt~~rl~eLLdl~~ee~E~~LS~lv~t~ti~aKidrpsgII~F~k~K~ 401 (439)
T KOG1498|consen 342 HNI--RIIAKY---YSRITLKRLAELLDLPVEEMEKFLSDLVVTGTIYAKIDRPSGIINFQKVKD 401 (439)
T ss_pred HHH--HHHHHH---HhhccHHHHHHHhCCCHHHHHHHHHHHHhccceEEEecCCCceEEEEeccc
Confidence 555 788899 999999999999999999999999999999999999999999999998853
No 10
>PF01399 PCI: PCI domain; InterPro: IPR000717 A homology domain of unclear function, occurs in the C-terminal region of several regulatory components of the 26S proteasome as well as in other proteins. This domain has also been called the PINT motif (Proteasome, Int-6, Nip-1 and TRIP-15) []. Apparently, all of the characterised proteins containing PCI domains are parts of larger multi-protein complexes. Proteins with PCI domains include budding yeast proteasome regulatory components Rpn3(Sun2), Rpn5, Rpn6, Rpn7and Rpn9 []; mammalian proteasome regulatory components p55, p58 and p44.5, and translation initiation factor 3 complex subunits p110 and INT6 [, ]; Arabidopsis COP9 and FUS6/COP11 []; mammalian G-protein pathway suppressor GPS1, and several uncharacterised ORFs from plant, nematodes and mammals. The complete homology domain comprises approx. 200 residues, the highest conservation is found in the C-terminal half. Several of the proteins mentioned above have no detectable homology to the N-terminal half of the domain.; GO: 0005515 protein binding; PDB: 3TXM_A 3TXN_A 1UFM_A 3CHM_A 3T5X_A 3T5V_B.
Probab=99.74 E-value=1.8e-17 Score=137.74 Aligned_cols=105 Identities=29% Similarity=0.436 Sum_probs=99.3
Q ss_pred hHHHHHHHHHhcCCHHHHHHHHHHhHHhhhhchhHHHHHHHHHHHHHHHHHHHhccccccccHHhHHHHcCCChHHHHHH
Q 013559 293 PEVRELINDFYSSRYASCLDYLGNLKANLLLDIHLHDHVETLYDQIRNKALIQYTHPFVSVDLHMMANAFKTSVAGIEKE 372 (441)
Q Consensus 293 p~~~~ll~~f~~~~y~~~~~~L~~~~~~l~~D~~L~~h~~~l~~~iR~~~i~qy~~pYs~I~L~~mA~~fg~s~~~~E~~ 372 (441)
|++.+++++|..++|..|.+.++.+...+..|+++..|++.+.+.+|.+++.+++.+|++|+++.||+.|+++.+++|.+
T Consensus 1 ~~~~~l~~~~~~~~~~~~~~~l~~~~~~~~~~~~l~~~~~~l~~~i~~~~l~~l~~~y~~i~~~~ia~~l~~~~~~vE~~ 80 (105)
T PF01399_consen 1 PPYSELLRAFRSGDLQEFEEFLEKHSESLFKDPFLAEYVEQLKEKIRRRNLRQLSKPYSSISISEIAKALQLSEEEVESI 80 (105)
T ss_dssp HHHHHHHHHHHCT-HHHHHHHHHHTCHHHHHCTTHHHHHHHHHHHHHHHHHHHHHHC-SEEEHHHHHHHHTCCHHHHHHH
T ss_pred CHHHHHHHHHHhCCHHHHHHHHHHHHHHHHcCccHHHHHHHHHHHHHHHHHHHHHHHhcccchHHHHHHhccchHHHHHH
Confidence 78999999999999999999999998888899999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHcCccceEecCCCCeEEEec
Q 013559 373 LEALITDNQIQARIDSHNKILYARH 397 (441)
Q Consensus 373 L~~LI~~g~L~akID~~~gvv~~~~ 397 (441)
|++||.+|.|+||||+++|+|++++
T Consensus 81 l~~~I~~~~i~~~ID~~~~~v~~~k 105 (105)
T PF01399_consen 81 LIDLISNGLIKAKIDQVNGVVVFSK 105 (105)
T ss_dssp HHHHHHTTSSEEEEETTTTEEEE-S
T ss_pred HHHHHHCCCEEEEEECCCCEEEecC
Confidence 9999999999999999999999863
No 11
>COG5071 RPN5 26S proteasome regulatory complex component [Posttranslational modification, protein turnover, chaperones]
Probab=99.72 E-value=5.1e-16 Score=147.57 Aligned_cols=272 Identities=11% Similarity=0.110 Sum_probs=204.6
Q ss_pred HHHHHHHHHHhhhhHHHHHh--HHhHHHHHHHHcCCHHHHHHHHHHH-Hhhhc--CchhHHHHHHHHHHHHHHhcCHHHH
Q 013559 121 KLENELNAYRTNLIKESIRM--GYNDFGDFYYAHGALGDAFKSYVRT-RDYCT--TSKHIIHMCMSAILVSIEMGQFTHV 195 (441)
Q Consensus 121 ~Le~el~~~~~n~~~esir~--~~~~la~~~~~~Gd~~~A~~~~~~~-r~~~~--~~~~~~~~~l~~i~~~i~~~~~~~~ 195 (441)
-+.+-|+..++|.|..++.+ ...+|.+.+..+||...|+..+... .+..+ ..+.++.+.+.++|+++..+||..|
T Consensus 111 ~~ietlr~VtEgkIFvEvERariT~~L~~ikee~Gdi~sA~Dilcn~pVETygs~~~Sekv~fiLEQ~rL~vl~~Dy~~A 190 (439)
T COG5071 111 NLIETLRTVTEGKIFVEVERARLTQLLSQIKEEQGDIKSAQDILCNEPVETYGSFDLSEKVAFILEQVRLFLLRSDYYMA 190 (439)
T ss_pred hHHHHHHHHhcCceEEehhHHHHHHHHHHHHHHhcchhHHHHHHhcCchhhccchhHHHHHHHHHHHHHHHHhccchHHH
Confidence 45666788889988877766 4678999999999999999999876 55544 4567899999999999999999999
Q ss_pred HhHHHHHhc-ccccCC-hhhhhhHHHHHHHHhcccccHHHHHHHHHhcCcCC---CCCchhhhcHHHHHHHHHHHHHhcC
Q 013559 196 TSYVSKAEQ-TPEALE-PVTIAKLRCAAGLAHLEARKYKLAARKFLEVGPDL---GNSYNEVIAAQDVATYGGLCALASF 270 (441)
Q Consensus 196 ~~~~~ka~~-~~~~~d-~~~~~~l~~~~gl~~l~~r~y~~Aa~~Fl~~~~t~---~~~~~el~s~~d~~~Y~~l~al~s~ 270 (441)
..+..|+.. .++..| .+++.++....-..++++|.|..+++++.++..|. ++++.|-.-...++.|++ ......
T Consensus 191 ~~~~kKI~KK~Fe~~d~~slKlkyYeL~V~i~Lh~R~Yl~v~~y~~~vY~t~~~~~d~Akwk~VLS~~v~F~i-Ltpy~n 269 (439)
T COG5071 191 STYTKKINKKFFEKEDVQSLKLKYYELKVRIGLHDRAYLDVCKYYRAVYDTAVVQEDPAKWKEVLSNVVCFAL-LTPYDN 269 (439)
T ss_pred HHHHHHHHHHHhccccHHHHHHHHHHHhheeecccHHHHHHHHHHHHHHHHHHhccCcccccchhhcceeeEE-eccccc
Confidence 999999865 555333 34444444444556788999999999998887643 344555444444444432 233334
Q ss_pred ChHHHHHhcccCHhhHhhhccchHHHHHHHHHhcCCHHHHHHHHHHhHHhhhhchh-HH-----HHHHHHHHH---HHHH
Q 013559 271 DRAELKSKVIDNVNFRNFLELVPEVRELINDFYSSRYASCLDYLGNLKANLLLDIH-LH-----DHVETLYDQ---IRNK 341 (441)
Q Consensus 271 ~R~eLk~~vl~~~~~~~~le~~p~~~~ll~~f~~~~y~~~~~~L~~~~~~l~~D~~-L~-----~h~~~l~~~---iR~~ 341 (441)
...+|..++-++-. +...|...+++.+|....+-..--.-..+.+.+..|.| +. .|.+.+... ...|
T Consensus 270 eq~dlvhKi~~d~k----l~sl~~~~~lVk~f~vNelmrwp~V~~~y~~~l~~~~faF~~e~~~~~w~DL~krviEHN~R 345 (439)
T COG5071 270 EQADLLHKINADHK----LNSLPLLQQLVKCFIVNELMRWPKVAEIYGSALRSNVFAFNDEKGEKRWSDLRKRVIEHNIR 345 (439)
T ss_pred HHHHHHHHhhhhhh----hccchhhhhHHHHHHHHHHHhhhHHHHHhHHHHHhhhhhhccchhhhhHHHHHHHHHHhhHh
Confidence 56677666544322 34678889999999988887776666667777777743 32 344444333 3358
Q ss_pred HHHHhccccccccHHhHHHHcCCChHHHHHHHHHHHHcCccceEecCCCCeEEEecCCc
Q 013559 342 ALIQYTHPFVSVDLHMMANAFKTSVAGIEKELEALITDNQIQARIDSHNKILYARHADQ 400 (441)
Q Consensus 342 ~i~qy~~pYs~I~L~~mA~~fg~s~~~~E~~L~~LI~~g~L~akID~~~gvv~~~~~d~ 400 (441)
+|..| ||+|++.++...+++|++++|+.|+.|+..|-+.|||++++|+|.+.++..
T Consensus 346 vI~~y---YSrI~~~rl~~lld~~~s~te~~ISdlVN~G~~yaKiNrpa~Ii~FEK~~n 401 (439)
T COG5071 346 VIANY---YSRIHCSRLGVLLDMSPSETEQFISDLVNKGHFYAKINRPAQIISFEKSQN 401 (439)
T ss_pred HHHHH---hhhhhHHHHHHHHcCCHHHHHHHHHHHHhcCcEEEEecCccceEEeecccc
Confidence 89999 999999999999999999999999999999999999999999999998844
No 12
>KOG1497 consensus COP9 signalosome, subunit CSN4 [Posttranslational modification, protein turnover, chaperones; Signal transduction mechanisms]
Probab=99.68 E-value=1.4e-14 Score=138.81 Aligned_cols=264 Identities=14% Similarity=0.143 Sum_probs=188.7
Q ss_pred hHHhHHHHHHHHcCCHHHHHHHHHHHHhh----hcCchhHHHHHHHHHHHHHHhcCHHHHHhHHHHHhcccc-cCChhhh
Q 013559 140 MGYNDFGDFYYAHGALGDAFKSYVRTRDY----CTTSKHIIHMCMSAILVSIEMGQFTHVTSYVSKAEQTPE-ALEPVTI 214 (441)
Q Consensus 140 ~~~~~la~~~~~~Gd~~~A~~~~~~~r~~----~~~~~~~~~~~l~~i~~~i~~~~~~~~~~~~~ka~~~~~-~~d~~~~ 214 (441)
-....||.+|.+.|++..|...+.-+--- -.+.+.++..|+.+.|+.+..+|...+..+++|+.-.+. ..++.++
T Consensus 104 ~irl~LAsiYE~Eq~~~~aaq~L~~I~~~tg~~~~d~~~kl~l~iriarlyLe~~d~veae~~inRaSil~a~~~Ne~Lq 183 (399)
T KOG1497|consen 104 SIRLHLASIYEKEQNWRDAAQVLVGIPLDTGQKAYDVEQKLLLCIRIARLYLEDDDKVEAEAYINRASILQAESSNEQLQ 183 (399)
T ss_pred HHHHHHHHHHHHhhhHHHHHHHHhccCcccchhhhhhHHHHHHHHHHHHHHHhcCcHHHHHHHHHHHHHhhhcccCHHHH
Confidence 34589999999999999999999876221 235678899999999999999999999999999988765 5678999
Q ss_pred hhHHHHHHHHhcccccHHHHHHHHHhcCcCCCCCchhhhcHHHHHHHHHHHHHhcCChHHHHHhcccCHhhHhhhccchH
Q 013559 215 AKLRCAAGLAHLEARKYKLAARKFLEVGPDLGNSYNEVIAAQDVATYGGLCALASFDRAELKSKVIDNVNFRNFLELVPE 294 (441)
Q Consensus 215 ~~l~~~~gl~~l~~r~y~~Aa~~Fl~~~~t~~~~~~el~s~~d~~~Y~~l~al~s~~R~eLk~~vl~~~~~~~~le~~p~ 294 (441)
..+++|.+...-..|+|.+||..|++....-..+-.+...+-.-|.-+++.|.++-.|+.+...++.++..++. |
T Consensus 184 ie~kvc~ARvlD~krkFlEAAqrYyels~~ki~~e~~~~~aL~~a~~CtlLA~~gpqrsr~Latlfkder~~~l----~- 258 (399)
T KOG1497|consen 184 IEYKVCYARVLDYKRKFLEAAQRYYELSQRKIVDESERLEALKKALQCTLLASAGPQRSRMLATLFKDERCQKL----P- 258 (399)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcchHHHHHHHHHhHhheeecCCChHHHHHHHHHhcCcccccc----c-
Confidence 99999999999999999999999998865322122344444444555666677777788887777766543321 1
Q ss_pred HHHHHHHHhcCCHHHHHHHHHHhHHhhhhchhHH-H----HHHHHHHHHHHHHHHHhccccccccHHhHHHHcCCChHHH
Q 013559 295 VRELINDFYSSRYASCLDYLGNLKANLLLDIHLH-D----HVETLYDQIRNKALIQYTHPFVSVDLHMMANAFKTSVAGI 369 (441)
Q Consensus 295 ~~~ll~~f~~~~y~~~~~~L~~~~~~l~~D~~L~-~----h~~~l~~~iR~~~i~qy~~pYs~I~L~~mA~~fg~s~~~~ 369 (441)
...++..+|-.++-.= +.++.+.+.|+...-.+ + -.+.-+-+......+++ |..|+.+.+++.|+++++.+
T Consensus 259 ~y~ileKmyl~riI~k-~el~ef~~~L~pHQka~~~dgssil~ra~~EhNlls~Skl---y~nisf~~Lg~ll~i~~eka 334 (399)
T KOG1497|consen 259 AYGILEKMYLERIIRK-EELQEFEAFLQPHQKAHTMDGSSILDRAVIEHNLLSASKL---YNNISFEELGALLKIDAEKA 334 (399)
T ss_pred chHHHHHHHHHHHhcc-hhHHHHHHHhcchhhhcccCcchhhhhHHHHHhHHHHHHH---HHhccHHHHHHHhCCCHHHH
Confidence 2345555554433111 12222332222221111 0 12222222334778888 99999999999999999999
Q ss_pred HHHHHHHHHcCccceEecCCCCeEEEecCCchhHHHHHHHHHHh
Q 013559 370 EKELEALITDNQIQARIDSHNKILYARHADQRNATFQRVLQTGS 413 (441)
Q Consensus 370 E~~L~~LI~~g~L~akID~~~gvv~~~~~d~r~~~~~~~i~~~~ 413 (441)
|+..++||..||++|-||+.+|+|++.+.. .-.+|.+.|....
T Consensus 335 ekiaa~MI~qeRmng~IDQ~egiihFe~~e-~l~~wdkqi~sl~ 377 (399)
T KOG1497|consen 335 EKIAAQMITQERMNGSIDQIEGIIHFEDRE-ELPQWDKQIQSLC 377 (399)
T ss_pred HHHHHHHHhHHHhccchHhhcceEeecchh-hhhhhhHHHHHHH
Confidence 999999999999999999999999999632 2344566665433
No 13
>smart00088 PINT motif in proteasome subunits, Int-6, Nip-1 and TRIP-15. Also called the PCI (Proteasome, COP9, Initiation factor 3) domain. Unknown function.
Probab=99.49 E-value=1.3e-13 Score=111.48 Aligned_cols=74 Identities=34% Similarity=0.461 Sum_probs=71.0
Q ss_pred HHHHHHHHHHHHHHHHHhccccccccHHhHHHHcCCChHHHHHHHHHHHHcCccceEecCCCCeEEEecCCchh
Q 013559 329 DHVETLYDQIRNKALIQYTHPFVSVDLHMMANAFKTSVAGIEKELEALITDNQIQARIDSHNKILYARHADQRN 402 (441)
Q Consensus 329 ~h~~~l~~~iR~~~i~qy~~pYs~I~L~~mA~~fg~s~~~~E~~L~~LI~~g~L~akID~~~gvv~~~~~d~r~ 402 (441)
+|++.+.+.+|.+++.||+++|++|+++.||+.|+++.+++|.+|+++|.+|.|+||||+.+|+|++.+.++|.
T Consensus 1 ~~~~~l~~~~~~~~l~~l~~~y~~i~~~~i~~~~~l~~~~vE~~i~~~i~~~~l~~~ID~~~~~v~~~~~~~r~ 74 (88)
T smart00088 1 QLVERLQRKIRLTNLLQLSEPYSSISLSDLAKLLGLSVPEVEKLVSKAIRDGEISAKIDQVNGIVEFEEVDPRR 74 (88)
T ss_pred ChHHHHHHHHHHHHHHHHhHHhceeeHHHHHHHhCcCHHHHHHHHHHHHHCCCeEEEEcCcCCEEEECCCchhh
Confidence 47889999999999999999999999999999999999999999999999999999999999999999887764
No 14
>smart00753 PAM PCI/PINT associated module.
Probab=99.49 E-value=1.3e-13 Score=111.48 Aligned_cols=74 Identities=34% Similarity=0.461 Sum_probs=71.0
Q ss_pred HHHHHHHHHHHHHHHHHhccccccccHHhHHHHcCCChHHHHHHHHHHHHcCccceEecCCCCeEEEecCCchh
Q 013559 329 DHVETLYDQIRNKALIQYTHPFVSVDLHMMANAFKTSVAGIEKELEALITDNQIQARIDSHNKILYARHADQRN 402 (441)
Q Consensus 329 ~h~~~l~~~iR~~~i~qy~~pYs~I~L~~mA~~fg~s~~~~E~~L~~LI~~g~L~akID~~~gvv~~~~~d~r~ 402 (441)
+|++.+.+.+|.+++.||+++|++|+++.||+.|+++.+++|.+|+++|.+|.|+||||+.+|+|++.+.++|.
T Consensus 1 ~~~~~l~~~~~~~~l~~l~~~y~~i~~~~i~~~~~l~~~~vE~~i~~~i~~~~l~~~ID~~~~~v~~~~~~~r~ 74 (88)
T smart00753 1 QLVERLQRKIRLTNLLQLSEPYSSISLSDLAKLLGLSVPEVEKLVSKAIRDGEISAKIDQVNGIVEFEEVDPRR 74 (88)
T ss_pred ChHHHHHHHHHHHHHHHHhHHhceeeHHHHHHHhCcCHHHHHHHHHHHHHCCCeEEEEcCcCCEEEECCCchhh
Confidence 47889999999999999999999999999999999999999999999999999999999999999999887764
No 15
>KOG2908 consensus 26S proteasome regulatory complex, subunit RPN9/PSMD13 [Posttranslational modification, protein turnover, chaperones]
Probab=99.31 E-value=1.7e-09 Score=105.18 Aligned_cols=262 Identities=14% Similarity=0.115 Sum_probs=202.0
Q ss_pred HHHHHcCCHHHHHHHHHHHHhhh---cCchhHHHHHHHHHHHHHHhcCHHHHHhHHHHHhcccc---cCChhhhhhHHHH
Q 013559 147 DFYYAHGALGDAFKSYVRTRDYC---TTSKHIIHMCMSAILVSIEMGQFTHVTSYVSKAEQTPE---ALEPVTIAKLRCA 220 (441)
Q Consensus 147 ~~~~~~Gd~~~A~~~~~~~r~~~---~~~~~~~~~~l~~i~~~i~~~~~~~~~~~~~ka~~~~~---~~d~~~~~~l~~~ 220 (441)
.+..+++|.++|++.+.++.+.. ..+..++-+...+.|+.+..||...+++-+...++.+| +-++...+.++..
T Consensus 83 ~~~~~~~D~~~al~~Le~i~~~~~~~~e~~av~~~~t~~~r~~L~i~DLk~~kk~ldd~~~~ld~~~~v~~~Vh~~fY~l 162 (380)
T KOG2908|consen 83 VVSEQISDKDEALEFLEKIIEKLKEYKEPDAVIYILTEIARLKLEINDLKEIKKLLDDLKSMLDSLDGVTSNVHSSFYSL 162 (380)
T ss_pred HHHHHhccHHHHHHHHHHHHHHHHhhccchhHHHHHHHHHHHHHhcccHHHHHHHHHHHHHHHhcccCCChhhhhhHHHH
Confidence 44567889999999999996654 35556777888899999999999999999999999877 3455688888888
Q ss_pred HHHHhcccccHHHHHH---HHHhcCcCCCCCchhhhcHHHHHHHHHHHHHhcCC---hHHHHHhcccCHhhHhhhc-cch
Q 013559 221 AGLAHLEARKYKLAAR---KFLEVGPDLGNSYNEVIAAQDVATYGGLCALASFD---RAELKSKVIDNVNFRNFLE-LVP 293 (441)
Q Consensus 221 ~gl~~l~~r~y~~Aa~---~Fl~~~~t~~~~~~el~s~~d~~~Y~~l~al~s~~---R~eLk~~vl~~~~~~~~le-~~p 293 (441)
+..|+=..|+|..+.. .|+.+... +++++ --..+.|.-++++||++-. =.+|.. -|-+..... ...
T Consensus 163 ssqYyk~~~d~a~yYr~~L~YL~~~d~--~~l~~-se~~~lA~~L~~aALLGe~iyNfGELL~----HPilesL~gT~~e 235 (380)
T KOG2908|consen 163 SSQYYKKIGDFASYYRHALLYLGCSDI--DDLSE-SEKQDLAFDLSLAALLGENIYNFGELLA----HPILESLKGTNRE 235 (380)
T ss_pred HHHHHHHHHhHHHHHHHHHHHhccccc--cccCH-HHHHHHHHHHHHHHHhccccccHHHHHh----hHHHHHhcCCcHH
Confidence 8888888888876644 34444321 11222 1123678889999998732 223322 233333332 345
Q ss_pred HHHHHHHHHhcCCHHHHHHHHHHhHHhhhhchhHHHHHHHHHHHHHHHHHHHhc--c--ccccccHHhHHHHcCCChHHH
Q 013559 294 EVRELINDFYSSRYASCLDYLGNLKANLLLDIHLHDHVETLYDQIRNKALIQYT--H--PFVSVDLHMMANAFKTSVAGI 369 (441)
Q Consensus 294 ~~~~ll~~f~~~~y~~~~~~L~~~~~~l~~D~~L~~h~~~l~~~iR~~~i~qy~--~--pYs~I~L~~mA~~fg~s~~~~ 369 (441)
++.+++.+|-.++...|++.-... ..=|-|..|.+.+.+.||..|+...+ + .-+.|+++.+|++..+|.+++
T Consensus 236 WL~dll~Afn~Gdl~~f~~l~~~~----~~~p~L~~~e~~L~qKI~LmaLiEi~F~rpa~~R~lsf~~Ia~~tkip~~eV 311 (380)
T KOG2908|consen 236 WLKDLLIAFNSGDLKRFESLKGVW----GKQPDLASNEDFLLQKIRLLALIEITFSRPANERTLSFKEIAEATKIPNKEV 311 (380)
T ss_pred HHHHHHHHhccCCHHHHHHHHHHh----ccCchHHHHHHHHHHHHHHHHHHHHHhcCcchhccccHHHHHHHhCCCHHHH
Confidence 799999999999999986654443 33567899999999999999998764 4 457899999999999999999
Q ss_pred HHHHHHHHHcCccceEecCCCCeEEEecCCchhHHHHHHHHHHhhHHHHH
Q 013559 370 EKELEALITDNQIQARIDSHNKILYARHADQRNATFQRVLQTGSEFDQDV 419 (441)
Q Consensus 370 E~~L~~LI~~g~L~akID~~~gvv~~~~~d~r~~~~~~~i~~~~~~~~~~ 419 (441)
|--+.+-++-|-|.+.||.++|+|++...-+|.-.-+++.+.++.+...-
T Consensus 312 E~LVMKAlslgLikG~Idqv~~~v~~swvqPRvl~~~qI~~Mk~rl~~W~ 361 (380)
T KOG2908|consen 312 ELLVMKALSLGLIKGSIDQVEGVVYMSWVQPRVLDRSQIVKMKDRLDEWN 361 (380)
T ss_pred HHHHHHHHhccceeeeecccccEEEEecccccccCHHHHHhHHHHHHHHH
Confidence 99999999999999999999999999988888888889988887775543
No 16
>KOG2581 consensus 26S proteasome regulatory complex, subunit RPN3/PSMD3 [Posttranslational modification, protein turnover, chaperones]
Probab=99.15 E-value=1.3e-07 Score=93.98 Aligned_cols=232 Identities=15% Similarity=0.118 Sum_probs=157.9
Q ss_pred HHHHHHHHhcCHHHHHhHHHHHhcccccCChhhhhhHHHHHHHHhcccccHHHHHHHHHhcCcCCCCCchhhhcHHHHHH
Q 013559 181 SAILVSIEMGQFTHVTSYVSKAEQTPEALEPVTIAKLRCAAGLAHLEARKYKLAARKFLEVGPDLGNSYNEVIAAQDVAT 260 (441)
Q Consensus 181 ~~i~~~i~~~~~~~~~~~~~ka~~~~~~~d~~~~~~l~~~~gl~~l~~r~y~~Aa~~Fl~~~~t~~~~~~el~s~~d~~~ 260 (441)
.++|..+..+-++.+.+.+.|+. .++.....-.+|+..|.|....-+.+|..|.++|+.+.---+. -.-+.--..+-+
T Consensus 214 ~LLr~yL~n~lydqa~~lvsK~~-~pe~~snne~ARY~yY~GrIkaiqldYssA~~~~~qa~rkapq-~~alGf~q~v~k 291 (493)
T KOG2581|consen 214 LLLRNYLHNKLYDQADKLVSKSV-YPEAASNNEWARYLYYLGRIKAIQLDYSSALEYFLQALRKAPQ-HAALGFRQQVNK 291 (493)
T ss_pred HHHHHHhhhHHHHHHHHHhhccc-CccccccHHHHHHHHHHhhHHHhhcchhHHHHHHHHHHHhCcc-hhhhhHHHHHHH
Confidence 35677788888888888877753 3442222356788899999999999999999999998632111 111222333446
Q ss_pred HHHHHHHhcCChHHHHHhcccCHhhHhhhccchHHHHHHHHHhcCCHHHHHHHHHHhHHhhhhchhHHHHHHHHHHHHHH
Q 013559 261 YGGLCALASFDRAELKSKVIDNVNFRNFLELVPEVRELINDFYSSRYASCLDYLGNLKANLLLDIHLHDHVETLYDQIRN 340 (441)
Q Consensus 261 Y~~l~al~s~~R~eLk~~vl~~~~~~~~le~~p~~~~ll~~f~~~~y~~~~~~L~~~~~~l~~D~~L~~h~~~l~~~iR~ 340 (441)
..++..+...+-.+. .++.-|..++-| -++.++-++--.++.+.|-+.|+++.+.+..|--..-. -.|-+|+-.
T Consensus 292 ~~ivv~ll~geiPer--s~F~Qp~~~ksL---~~Yf~Lt~AVr~gdlkkF~~~leq~k~~f~~D~ty~Li-vRLR~NVIk 365 (493)
T KOG2581|consen 292 LMIVVELLLGEIPER--SVFRQPGMRKSL---RPYFKLTQAVRLGDLKKFNETLEQFKDKFQADGTYTLI-VRLRHNVIK 365 (493)
T ss_pred HHHHHHHHcCCCcch--hhhcCccHHHHH---HHHHHHHHHHHHhhHHHHHHHHHHHHHHHhhCCcchHH-HHHHHHHHH
Confidence 666666666443222 244444443322 34566777777889999999999999888877643222 234444444
Q ss_pred HHHHHhccccccccHHhHHHHcCCC-hHHHHHHHHHHHHcCccceEecCCCCeEEEec------CCchhHHHHHHHHHHh
Q 013559 341 KALIQYTHPFVSVDLHMMANAFKTS-VAGIEKELEALITDNQIQARIDSHNKILYARH------ADQRNATFQRVLQTGS 413 (441)
Q Consensus 341 ~~i~qy~~pYs~I~L~~mA~~fg~s-~~~~E~~L~~LI~~g~L~akID~~~gvv~~~~------~d~r~~~~~~~i~~~~ 413 (441)
-.|.+.=-+||+|++..+|+.+|++ ++++|--+++-|++|-|+|+||..+|.+.... .+.....|..-|.-+-
T Consensus 366 TgIR~ISlsYSRISl~DIA~kL~l~Seed~EyiVakAIRDGvIea~Id~~~g~m~skE~~diy~t~epQ~~f~~rI~fCl 445 (493)
T KOG2581|consen 366 TGIRKISLSYSRISLQDIAKKLGLNSEEDAEYIVAKAIRDGVIEAKIDHEDGFMQSKETFDIYSTREPQTAFDERIRFCL 445 (493)
T ss_pred HhhhheeeeeeeccHHHHHHHhcCCCchhHHHHHHHHHHhccceeeeccccCceehhhhhhhhccCCchhhHhHHHHHHH
Confidence 5555555689999999999999995 55699999999999999999999999776543 3445555666666655
Q ss_pred hHHHHHH
Q 013559 414 EFDQDVR 420 (441)
Q Consensus 414 ~~~~~~~ 420 (441)
.+.+.+.
T Consensus 446 ~LhN~~v 452 (493)
T KOG2581|consen 446 QLHNEAV 452 (493)
T ss_pred HHHHHHH
Confidence 5555543
No 17
>PF09440 eIF3_N: eIF3 subunit 6 N terminal domain; InterPro: IPR019010 This entry represents the N-terminal domain of subunit 6 (or e) (eIF3e) of the translation initiation factor eIF3. EIF3 is required in protein synthesis in mammalian cells and, together with other initiation factors, stimulates binding of initiator methionyl-tRNAi and mRNA to the 40S ribosomal subunit to form the 48 S initiation complex []. The eIF3 complex also prevents premature association of the 40 and 60 S ribosomal subunits and interacts with other initiation factors involved in start codon selection. EIF3 has at least 13 protein components (eIF3a-m or 1-13), where subunits h, i, k, and m are likely to be on the periphery of the complex []. Subunit 6 is produced by the int6 gene, one of the frequent integration sites for mouse mammary tumor viruses [].
Probab=99.09 E-value=7.2e-10 Score=95.98 Aligned_cols=106 Identities=16% Similarity=0.151 Sum_probs=77.7
Q ss_pred CHHHHhhccCchh-hHHHHHHHHhcCCCchhHHHHHHHHHHHHHhcCChHHHHHHHHHhhccCCCCCcCCHHHHHHHHHH
Q 013559 36 DVEAYASLYQGRT-KITRLMFIADHCDIASMQLEALRMAYDEIKKGENTQLFREVVKKIDGRLGPNYAMDEAWCDSVDRR 114 (441)
Q Consensus 36 Dl~~y~~~y~g~~-~i~rL~fi~~~~~~~~~~~~a~~~~~~~lk~t~~~~~Y~~~~~~l~~~~~~~~~~D~~~~~~~~~~ 114 (441)
||++.|++|.+++ .||.|.|+..+. ++.+.+.+++.++++++|||++|..++++.+++.- . -++-+.+.+.+
T Consensus 1 DLT~ki~~~LDrHLvfPLLeFl~~~~--iy~~~dl~~akl~LL~~TnMvDy~~d~~~~l~~~~----e-~p~e~~~kr~~ 73 (133)
T PF09440_consen 1 DLTSKIAPYLDRHLVFPLLEFLSDKG--IYDEEDLLKAKLDLLKKTNMVDYAMDLYKELYPDD----E-VPAELAEKREE 73 (133)
T ss_pred ChHHHHHHHhhHHHHHHHHHHHhhcc--cccHHHHHHHHHHHHHhccchHHHHHHHHHhcCCC----C-CcHHHHHHHHH
Confidence 8999999988876 789999999999 99999999999999999999999999999986321 1 12222233344
Q ss_pred HHHHHHHHHHHHHHH-------------------------HhhhhHHHHHhHHhHHHHH
Q 013559 115 AEQRKEKLENELNAY-------------------------RTNLIKESIRMGYNDFGDF 148 (441)
Q Consensus 115 ~~~~~~~Le~el~~~-------------------------~~n~~~esir~~~~~la~~ 148 (441)
+-++++.|+++.... +++.++.++.+++|++|+|
T Consensus 74 Vl~~l~~l~~~~~~v~~~~~~~ev~~~l~~dk~~nl~~L~~~h~it~e~id~LY~~akf 132 (133)
T PF09440_consen 74 VLAELKELEEETEPVLELLEDPEVVKNLRSDKKQNLEYLEENHGITPEMIDALYKYAKF 132 (133)
T ss_pred HHHHHHHHHHHHHHHHHHHcCHHHHHHHHccHHHHHHHHHHhcCCCHHHHHHHHHHhCc
Confidence 444444444433211 3566777888888888776
No 18
>KOG2582 consensus COP9 signalosome, subunit CSN3 [Posttranslational modification, protein turnover, chaperones; Signal transduction mechanisms]
Probab=98.67 E-value=3.7e-06 Score=82.89 Aligned_cols=272 Identities=11% Similarity=0.137 Sum_probs=174.6
Q ss_pred HHhHHHHHHHHcCCHHHHHHHHHHHHhhhc-CchhHHHHHHHHHHHHHHhcCHHHHHhHHHHHhccc---c-cCChhhhh
Q 013559 141 GYNDFGDFYYAHGALGDAFKSYVRTRDYCT-TSKHIIHMCMSAILVSIEMGQFTHVTSYVSKAEQTP---E-ALEPVTIA 215 (441)
Q Consensus 141 ~~~~la~~~~~~Gd~~~A~~~~~~~r~~~~-~~~~~~~~~l~~i~~~i~~~~~~~~~~~~~ka~~~~---~-~~d~~~~~ 215 (441)
...+++++..+.++-.-..+...+..++.. .+++...+...++.+++..++|..+..+++---.-+ + ..++....
T Consensus 104 lc~~l~~~~~~~~~p~~gi~ii~~av~k~~~~~~qlT~~H~~l~~~~L~ak~y~~~~p~ld~divei~~~n~h~~~k~fL 183 (422)
T KOG2582|consen 104 LCHDLTEAVVKKNKPLRGIRIIMQAVDKMQPSNGQLTSIHADLLQLCLEAKDYASVLPYLDDDIVEICKANPHLDPKYFL 183 (422)
T ss_pred HHHHHHHHHHhcCCccccchHHHHHHHHhccCccchhhhHHHHHHHHHHhhcccccCCccchhHHHHhccCCCCCHHHHH
Confidence 456778888876666666666666666654 334556677788899999999988765433211111 1 13556666
Q ss_pred hHHHHHHHHhcccccHHHHHHHHHhcCcCCCCCchhhhcHHHHHHHHHHHHHhcCChHHHHHhcccCHhhHhhh-ccchH
Q 013559 216 KLRCAAGLAHLEARKYKLAARKFLEVGPDLGNSYNEVIAAQDVATYGGLCALASFDRAELKSKVIDNVNFRNFL-ELVPE 294 (441)
Q Consensus 216 ~l~~~~gl~~l~~r~y~~Aa~~Fl~~~~t~~~~~~el~s~~d~~~Y~~l~al~s~~R~eLk~~vl~~~~~~~~l-e~~p~ 294 (441)
.+..|.|..++..++|..|.-+|..+..+.....+++ -.+..=+|+.+.-|.+..-.+|-+ -.++.+.++. ...|+
T Consensus 184 ~Y~yYgg~iciglk~fe~Al~~~e~~v~~Pa~~vs~~-hlEaYkkylLvsLI~~GK~~ql~k--~ts~~~~r~~K~ms~p 260 (422)
T KOG2582|consen 184 LYLYYGGMICIGLKRFERALYLLEICVTTPAMAVSHI-HLEAYKKYLLVSLILTGKVFQLPK--NTSQNAGRFFKPMSNP 260 (422)
T ss_pred HHHHhcceeeeccccHHHHHHHHHHHHhcchhHHHHH-HHHHHHHHHHHHhhhcCceeeccc--cchhhhHHhcccCCch
Confidence 6777889999999999998877777765432212221 122223564444444322112211 1223333433 35678
Q ss_pred HHHHHHHHhcCCHHHHHHHHHHhHHhhhhchhHHHHHHHHHHHHHHHHHHHhccccccccHHhHHHHcCC-ChHHHHHHH
Q 013559 295 VRELINDFYSSRYASCLDYLGNLKANLLLDIHLHDHVETLYDQIRNKALIQYTHPFVSVDLHMMANAFKT-SVAGIEKEL 373 (441)
Q Consensus 295 ~~~ll~~f~~~~y~~~~~~L~~~~~~l~~D~~L~~h~~~l~~~iR~~~i~qy~~pYs~I~L~~mA~~fg~-s~~~~E~~L 373 (441)
+.+++++|.+..-.+......+....+..|--.. -+......+-.+-|..+-+-|.+++|+.||+.-.+ +..++|++|
T Consensus 261 Y~ef~~~Y~~~~~~eLr~lVk~~~~rF~kDnnt~-l~k~av~sl~k~nI~rltktF~sLsL~dIA~~vQLa~~qevek~I 339 (422)
T KOG2582|consen 261 YHEFLNVYLKDSSTELRTLVKKHSERFTKDNNTG-LAKQAVSSLYKKNIQRLTKTFLSLSLSDIASRVQLASAQEVEKYI 339 (422)
T ss_pred HHHHHHHHhcCCcHHHHHHHHHHHHHHhhcCcHH-HHHHHHHHHHHHHHHHHHHHHHHhhHHHHHHHHHhcchHHHHHHH
Confidence 9999999998887776555666666666665322 24445555556667777778999999999996666 678999999
Q ss_pred HHHHHcCccceEecCCCCeEEEecC---CchhHHHHHHHHHHhhHHHHH
Q 013559 374 EALITDNQIQARIDSHNKILYARHA---DQRNATFQRVLQTGSEFDQDV 419 (441)
Q Consensus 374 ~~LI~~g~L~akID~~~gvv~~~~~---d~r~~~~~~~i~~~~~~~~~~ 419 (441)
.+||.+|++.|+|| |.|.+... +...+.++.=|..+..+....
T Consensus 340 lqmie~~~i~a~iN---G~v~f~~n~e~~~SpeM~~nk~~~~~~L~e~l 385 (422)
T KOG2582|consen 340 LQMIEDGEIFASIN---GMVFFTDNPEKYNSPEMHENKIDLCIQLIEAL 385 (422)
T ss_pred HHHhccCceEEEec---ceEEEecCcccCCCHHHHhhHHHHHHHHHHHH
Confidence 99999999999999 88887643 334455655445544444433
No 19
>KOG1076 consensus Translation initiation factor 3, subunit c (eIF-3c) [Translation, ribosomal structure and biogenesis]
Probab=98.41 E-value=0.00053 Score=72.79 Aligned_cols=203 Identities=15% Similarity=0.260 Sum_probs=131.9
Q ss_pred hhhhhHHHHHHHHhcccccHHHHHHHHHhcCcCCC-----------------CCchhh------hcHH-----HH--HHH
Q 013559 212 VTIAKLRCAAGLAHLEARKYKLAARKFLEVGPDLG-----------------NSYNEV------IAAQ-----DV--ATY 261 (441)
Q Consensus 212 ~~~~~l~~~~gl~~l~~r~y~~Aa~~Fl~~~~t~~-----------------~~~~el------~s~~-----d~--~~Y 261 (441)
-+.||.=+.-||..+..|--.+|-..+.+...+-. +.-.+. +++. ++ ++|
T Consensus 527 IL~NRtmvQLGLCAFR~Gmi~EaH~~L~dl~st~r~kELLgQgv~~~~~he~t~eQe~~eR~rQlPyHmHINLELlEcVy 606 (843)
T KOG1076|consen 527 ILFNRTMVQLGLCAFRQGMIKEAHQCLSDLQSTGRVKELLGQGVLQRRQHEKTAEQEKIERRRQLPYHMHINLELLECVY 606 (843)
T ss_pred HHHHHHHHHHHHHHHHcccHHHHHHHHHHHHhcchHHHHHhhhhhhhhhhccChhhHHHHHhhcCchhhhccHHHHHHHH
Confidence 35688888899999999999999888887654310 000111 1111 11 568
Q ss_pred HHHHHHhc-CC-----hHHHHHhcccCHhhHhhhccc--------h-----HHHHHHHHHhcCCHHHHHHHHHHhHHhhh
Q 013559 262 GGLCALAS-FD-----RAELKSKVIDNVNFRNFLELV--------P-----EVRELINDFYSSRYASCLDYLGNLKANLL 322 (441)
Q Consensus 262 ~~l~al~s-~~-----R~eLk~~vl~~~~~~~~le~~--------p-----~~~~ll~~f~~~~y~~~~~~L~~~~~~l~ 322 (441)
+ +|||+- .+ -.+-+.+++ +..|+..|+.. | ++...-+++..++|..|++.+-....++.
T Consensus 607 L-tcaMLlEIP~MAA~~~d~Rrr~i-Sk~frr~Le~serqsf~gPPEn~RehVvaAsKAm~~Gnw~~c~~fi~nn~KvW~ 684 (843)
T KOG1076|consen 607 L-TCAMLLEIPYMAAHESDARRRMI-SKSFRRQLEHSERQSFTGPPENTREHVVAASKAMQKGNWQKCFEFIVNNIKVWD 684 (843)
T ss_pred H-HHHHHHhhhHHhhhhhhhhcccc-cHHHHHHHHHHhhccccCCchhHHHHHHHHHHHHhcCCHHHHHHHHHhhhhHHH
Confidence 5 476652 11 123333333 45677766442 2 34456678899999999995554323322
Q ss_pred hchhHHHHHHHHHHHHHHHHHHHhc----cccccccHHhHHHHcCCChHHHHHHHHHHHHcCccceEecCCCCeEEEecC
Q 013559 323 LDIHLHDHVETLYDQIRNKALIQYT----HPFVSVDLHMMANAFKTSVAGIEKELEALITDNQIQARIDSHNKILYARHA 398 (441)
Q Consensus 323 ~D~~L~~h~~~l~~~iR~~~i~qy~----~pYs~I~L~~mA~~fg~s~~~~E~~L~~LI~~g~L~akID~~~gvv~~~~~ 398 (441)
+=+---.-.+-+.+.|+.-.+..|| ..|.+|+|..||+.|.+|+..+-.-|.+||.+..|.|..|.+.++|+|.+.
T Consensus 685 Lfpn~d~V~~Ml~~rIqEEsLRTYLftYss~Y~SvSl~~LA~mFdLp~~~VhsIiSkmiineEl~AslDqpt~~iv~hrv 764 (843)
T KOG1076|consen 685 LFPNADTVLDMLTERIQEESLRTYLFTYSSVYDSVSLAKLADMFDLPEPKVHSIISKMIINEELHASLDQPTQCIVMHRV 764 (843)
T ss_pred hcccHHHHHHHHHHHHHHHHHHHHHHHhhhhhhhccHHHHHHHhCCCchhHHHHHHHHHHHHHhhhccCCCcceEEEeec
Confidence 2111112233445556656665555 457789999999999999999999999999999999999999999999984
Q ss_pred CchhHHHHHHHHHHhhHHH
Q 013559 399 DQRNATFQRVLQTGSEFDQ 417 (441)
Q Consensus 399 d~r~~~~~~~i~~~~~~~~ 417 (441)
+.+....-+++..+.+..
T Consensus 765 -E~srlq~La~qL~eKl~~ 782 (843)
T KOG1076|consen 765 -EPSRLQSLAVQLSEKLAI 782 (843)
T ss_pred -cchHHHHHHHHHHHHHHH
Confidence 444445555655555443
No 20
>KOG2753 consensus Uncharacterized conserved protein, contains PCI domain [General function prediction only]
Probab=98.30 E-value=7.8e-05 Score=72.78 Aligned_cols=217 Identities=11% Similarity=0.105 Sum_probs=136.8
Q ss_pred HHHHHHHHHHHHHHhcCHHHHHhHHHHHhcccccCChhh---hhh-HHHHHHHHhcccccHHHHHHHHHhcCcCCCCCch
Q 013559 175 IIHMCMSAILVSIEMGQFTHVTSYVSKAEQTPEALEPVT---IAK-LRCAAGLAHLEARKYKLAARKFLEVGPDLGNSYN 250 (441)
Q Consensus 175 ~~~~~l~~i~~~i~~~~~~~~~~~~~ka~~~~~~~d~~~---~~~-l~~~~gl~~l~~r~y~~Aa~~Fl~~~~t~~~~~~ 250 (441)
...++...+.++...+-...+-.++.+...-+...+.+. +.- ..++.++ .....-.++.+.|.+...|++. .
T Consensus 123 R~~Vy~~lv~la~~~~~~~~i~~~lk~~~~~lkew~~~vedqrel~r~v~~al--~~~k~~~~s~kvmt~lLgtyt~--d 198 (378)
T KOG2753|consen 123 RYQVYMSLVTLAASCKLIEYIVPNLKQLDDWLKEWNISVEDQRELLRAVHKAL--KDNKSVDESSKVMTELLGTYTE--D 198 (378)
T ss_pred HHHHHHHHHHHHhhcceeeeecccHHHHHHHHHhCCCCHHHHHHHHHHHHHHH--HhcchhhhHHHHHHHHHHHhcc--c
Confidence 345556666666665555555555555555443111111 111 1122222 2233356677777777666652 3
Q ss_pred hhhcHHHHHHHHHHHHHhcCChHHHHHhcccCHhhHhhhccchHHHHHHHHHhcCCHHHHHHHHHHhHHhhhhchhHHHH
Q 013559 251 EVIAAQDVATYGGLCALASFDRAELKSKVIDNVNFRNFLELVPEVRELINDFYSSRYASCLDYLGNLKANLLLDIHLHDH 330 (441)
Q Consensus 251 el~s~~d~~~Y~~l~al~s~~R~eLk~~vl~~~~~~~~le~~p~~~~ll~~f~~~~y~~~~~~L~~~~~~l~~D~~L~~h 330 (441)
....+.+=|+=++..++..-+- =+=+-+++=|.+ ++||.++ +.+++.-|.......+.+--+....-+..--+.+
T Consensus 199 nas~AredA~rcV~~av~dP~~-F~fD~Ll~L~pV-~qLE~d~-i~qLL~IF~s~~L~aYveF~~~N~~Fvqs~gl~~-- 273 (378)
T KOG2753|consen 199 NASEAREDAMRCVVEAVKDPKI-FLFDHLLTLPPV-KQLEGDL-IHQLLKIFVSGKLDAYVEFVAANSGFVQSQGLVH-- 273 (378)
T ss_pred chhHHHHHHHHHHHHHHcCCce-eccchhccCchH-HHhccch-HHHHHHHHHhcchHHHHHHHHhChHHHHHhcccH--
Confidence 3455666666677777765210 000112233333 4466666 8899999998765554444443322222211222
Q ss_pred HHHHHHHHHHHHHHHhccccccccHHhHHHHcCCChHHHHHHHHHHHHcCccceEecCCCCeEEEecCCch
Q 013559 331 VETLYDQIRNKALIQYTHPFVSVDLHMMANAFKTSVAGIEKELEALITDNQIQARIDSHNKILYARHADQR 401 (441)
Q Consensus 331 ~~~l~~~iR~~~i~qy~~pYs~I~L~~mA~~fg~s~~~~E~~L~~LI~~g~L~akID~~~gvv~~~~~d~r 401 (441)
+..+..||..-+.+...+-..|+.+.|++.+.+..+++|-|+.+-|+.|-+.||||+.+++|+..+.-.|
T Consensus 274 -E~~~~KMRLLTlm~LA~es~eisy~~l~k~LqI~edeVE~fVIdaI~aklV~~kidq~~~~viVs~~~hR 343 (378)
T KOG2753|consen 274 -EQNMAKMRLLTLMSLAEESNEISYDTLAKELQINEDEVELFVIDAIRAKLVEGKIDQMNRTVIVSSSTHR 343 (378)
T ss_pred -HHHHHHHHHHHHHHHhccCCCCCHHHHHHHhccCHHHHHHHHHHHHHHHHHHhhHHhhcceEEeehhhhh
Confidence 3788999999999999999999999999999999999999999999999999999999999998866443
No 21
>PF14938 SNAP: Soluble NSF attachment protein, SNAP; PDB: 1QQE_A 2IFU_A.
Probab=97.58 E-value=0.0039 Score=61.27 Aligned_cols=193 Identities=14% Similarity=0.120 Sum_probs=113.4
Q ss_pred hHHhHHHHHHHHcCCHHHHHHHHHHHHhhhc---CchhHHHHHHHHHHHHHHh-cCHHHHHhHHHHHhcccc-cCChhhh
Q 013559 140 MGYNDFGDFYYAHGALGDAFKSYVRTRDYCT---TSKHIIHMCMSAILVSIEM-GQFTHVTSYVSKAEQTPE-ALEPVTI 214 (441)
Q Consensus 140 ~~~~~la~~~~~~Gd~~~A~~~~~~~r~~~~---~~~~~~~~~l~~i~~~i~~-~~~~~~~~~~~ka~~~~~-~~d~~~~ 214 (441)
..+...|..|.+. ++++|.++|.+..+... .+......+-.+.++.-.. |+++.+..+..+|-...+ .+.+...
T Consensus 76 ~~~~~Aa~~~k~~-~~~~Ai~~~~~A~~~y~~~G~~~~aA~~~~~lA~~ye~~~~d~e~Ai~~Y~~A~~~y~~e~~~~~a 154 (282)
T PF14938_consen 76 KAYEEAANCYKKG-DPDEAIECYEKAIEIYREAGRFSQAAKCLKELAEIYEEQLGDYEKAIEYYQKAAELYEQEGSPHSA 154 (282)
T ss_dssp HHHHHHHHHHHHT-THHHHHHHHHHHHHHHHHCT-HHHHHHHHHHHHHHHCCTT--HHHHHHHHHHHHHHHHHTT-HHHH
T ss_pred HHHHHHHHHHHhh-CHHHHHHHHHHHHHHHHhcCcHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHCCChhhH
Confidence 3555555555444 78888888877755443 2222233333333343344 689999999999988876 3344444
Q ss_pred hhHHHHHHHHhcccccHHHHHHHHHhcCcCCCCCchhhhcHHHHHHHHHHHHHhcCChHHHHHh----cccCHhhHhhhc
Q 013559 215 AKLRCAAGLAHLEARKYKLAARKFLEVGPDLGNSYNEVIAAQDVATYGGLCALASFDRAELKSK----VIDNVNFRNFLE 290 (441)
Q Consensus 215 ~~l~~~~gl~~l~~r~y~~Aa~~Fl~~~~t~~~~~~el~s~~d~~~Y~~l~al~s~~R~eLk~~----vl~~~~~~~~le 290 (441)
+.+..--|-++...++|.+|.+.|-++.......--.-.+..+...-.+||-|+..|-...+.. .-.+|.|..- +
T Consensus 155 ~~~~~~~A~l~~~l~~y~~A~~~~e~~~~~~l~~~l~~~~~~~~~l~a~l~~L~~~D~v~A~~~~~~~~~~~~~F~~s-~ 233 (282)
T PF14938_consen 155 AECLLKAADLYARLGRYEEAIEIYEEVAKKCLENNLLKYSAKEYFLKAILCHLAMGDYVAARKALERYCSQDPSFASS-R 233 (282)
T ss_dssp HHHHHHHHHHHHHTT-HHHHHHHHHHHHHTCCCHCTTGHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHGTTSTTSTTS-H
T ss_pred HHHHHHHHHHHHHhCCHHHHHHHHHHHHHHhhcccccchhHHHHHHHHHHHHHHcCCHHHHHHHHHHHHhhCCCCCCc-H
Confidence 4555455667778899999999998876543211001124556666778999998774433321 1112332221 1
Q ss_pred cchHHHHHHHHHhcCCHHHHHHHHHHhHHhhhhchhHHHHHHHH
Q 013559 291 LVPEVRELINDFYSSRYASCLDYLGNLKANLLLDIHLHDHVETL 334 (441)
Q Consensus 291 ~~p~~~~ll~~f~~~~y~~~~~~L~~~~~~l~~D~~L~~h~~~l 334 (441)
...-+.++|.+|-+.|-..|-+.+.++...-.+|.+...-+..+
T Consensus 234 E~~~~~~l~~A~~~~D~e~f~~av~~~d~~~~ld~w~~~~l~~~ 277 (282)
T PF14938_consen 234 EYKFLEDLLEAYEEGDVEAFTEAVAEYDSISRLDNWKTKMLLKI 277 (282)
T ss_dssp HHHHHHHHHHHHHTT-CCCHHHHCHHHTTSS---HHHHHHHHHH
T ss_pred HHHHHHHHHHHHHhCCHHHHHHHHHHHcccCccHHHHHHHHHHH
Confidence 11236889999999999999999999999999998876544433
No 22
>PF09976 TPR_21: Tetratricopeptide repeat; InterPro: IPR018704 This domain, found in various hypothetical prokaryotic proteins, has no known function.
Probab=97.41 E-value=0.0054 Score=53.87 Aligned_cols=99 Identities=10% Similarity=0.081 Sum_probs=78.9
Q ss_pred HHHhHHhHHHHHHHHcCCHHHHHHHHHHHHhhhcCchhHHHHHHHHHHHHHHhcCHHHHHhHHHHHhcccccCChhhhhh
Q 013559 137 SIRMGYNDFGDFYYAHGALGDAFKSYVRTRDYCTTSKHIIHMCMSAILVSIEMGQFTHVTSYVSKAEQTPEALEPVTIAK 216 (441)
Q Consensus 137 sir~~~~~la~~~~~~Gd~~~A~~~~~~~r~~~~~~~~~~~~~l~~i~~~i~~~~~~~~~~~~~ka~~~~~~~d~~~~~~ 216 (441)
--..+.+.+|+.++..|++++|.+.|..+.+...++.-.--..+.+.++.+..|+++.+...+.++ . ++.....
T Consensus 46 ya~~A~l~lA~~~~~~g~~~~A~~~l~~~~~~~~d~~l~~~a~l~LA~~~~~~~~~d~Al~~L~~~----~--~~~~~~~ 119 (145)
T PF09976_consen 46 YAALAALQLAKAAYEQGDYDEAKAALEKALANAPDPELKPLARLRLARILLQQGQYDEALATLQQI----P--DEAFKAL 119 (145)
T ss_pred HHHHHHHHHHHHHHHCCCHHHHHHHHHHHHhhCCCHHHHHHHHHHHHHHHHHcCCHHHHHHHHHhc----c--CcchHHH
Confidence 345688999999999999999999999998876555444456678888999999999999988652 1 2223455
Q ss_pred HHHHHHHHhcccccHHHHHHHHHhc
Q 013559 217 LRCAAGLAHLEARKYKLAARKFLEV 241 (441)
Q Consensus 217 l~~~~gl~~l~~r~y~~Aa~~Fl~~ 241 (441)
.....|-+++..|++.+|...|-.+
T Consensus 120 ~~~~~Gdi~~~~g~~~~A~~~y~~A 144 (145)
T PF09976_consen 120 AAELLGDIYLAQGDYDEARAAYQKA 144 (145)
T ss_pred HHHHHHHHHHHCCCHHHHHHHHHHh
Confidence 6678999999999999999888654
No 23
>COG5600 Transcription-associated recombination protein [DNA replication, recombination, and repair]
Probab=97.23 E-value=0.17 Score=50.94 Aligned_cols=234 Identities=12% Similarity=0.083 Sum_probs=145.8
Q ss_pred cCCHHHHHHHHHHHHhhhcC-------chhHHH--HHHH-HHHHHHHhcCHHHHHhHHHHHhcccccCC-----hhhhhh
Q 013559 152 HGALGDAFKSYVRTRDYCTT-------SKHIIH--MCMS-AILVSIEMGQFTHVTSYVSKAEQTPEALE-----PVTIAK 216 (441)
Q Consensus 152 ~Gd~~~A~~~~~~~r~~~~~-------~~~~~~--~~l~-~i~~~i~~~~~~~~~~~~~ka~~~~~~~d-----~~~~~~ 216 (441)
.-.++++.+.+.++...|.. ++.+.- +..+ ...+.+..+.+....+. -||....+..| -+-...
T Consensus 143 ~d~l~~~sr~l~R~Fn~il~dR~p~ln~skk~g~y~iaNlL~~iY~Rl~~~~l~~n~-lka~~~vs~~Di~~~~~sq~v~ 221 (413)
T COG5600 143 QDNLSKISRLLTRMFNSILNDRSPALNPSKKVGLYYIANLLFQIYLRLGRFKLCENF-LKASKEVSMPDISEYQKSQVVV 221 (413)
T ss_pred HhhHHHHHHHHHHHHHHhcCCcCccCChhhHHHHHHHHHHHHHHHHHhccHHHHHHH-HHhcccccccccchhhhcceee
Confidence 34567788888888777742 222322 1122 33445666777766543 34433322111 122345
Q ss_pred HHHHHHHHhcccccHHHHHHHHHhcCcCCCCCchhhhcHHH--HHHHHHHHHHhcCChHHHHHhcccCHhhHhhhccch-
Q 013559 217 LRCAAGLAHLEARKYKLAARKFLEVGPDLGNSYNEVIAAQD--VATYGGLCALASFDRAELKSKVIDNVNFRNFLELVP- 293 (441)
Q Consensus 217 l~~~~gl~~l~~r~y~~Aa~~Fl~~~~t~~~~~~el~s~~d--~~~Y~~l~al~s~~R~eLk~~vl~~~~~~~~le~~p- 293 (441)
+..|-|++++.+++|.+|.-.|-+++.. |+++++.+. ++.|.+-++|....-. .++.+++..|
T Consensus 222 f~YYLG~~~l~~en~heA~~~L~~aFl~----c~~l~~~n~~rIl~~~ipt~Llv~~~~----------Ptk~~L~r~~~ 287 (413)
T COG5600 222 FHYYLGIYYLLNENFHEAFLHLNEAFLQ----CPWLITRNRKRILPYYIPTSLLVNKFP----------PTKDLLERFKR 287 (413)
T ss_pred hhhHHHHHHHHHHhHHHHHHHHHHHHHh----ChhhhhcchheehhHHhhHHHHhCCCC----------CchHHHHhccc
Confidence 7889999999999999999999988753 677655443 5677777777765322 2344555555
Q ss_pred --HHHHHHHHHhcCCHHHHHHHHHHhHHhh-hhchhH--HHHHH-HHHHHHHHHHHHHhccccc-cccHHhHHHHcCCC-
Q 013559 294 --EVRELINDFYSSRYASCLDYLGNLKANL-LLDIHL--HDHVE-TLYDQIRNKALIQYTHPFV-SVDLHMMANAFKTS- 365 (441)
Q Consensus 294 --~~~~ll~~f~~~~y~~~~~~L~~~~~~l-~~D~~L--~~h~~-~l~~~iR~~~i~qy~~pYs-~I~L~~mA~~fg~s- 365 (441)
.+.-++.+.-.++++.+-..|+..+.-+ ..-.|+ ..|.. .+++++-.+...--...=+ .+++-..+..+..+
T Consensus 288 ~s~~~~LvkavrsGni~~~~~~l~~ner~~~~~~l~ltl~~~~~~V~~RNL~rk~w~~~~~qsrlp~sil~~~~qls~~d 367 (413)
T COG5600 288 CSVYSPLVKAVRSGNIEDFDLALSRNERKFAKRGLYLTLLAHYPLVCFRNLFRKIWRLHGKQSRLPLSILLIVLQLSAID 367 (413)
T ss_pred cchhHHHHHHHHcCCHHHHHHHHHHhHHHHHHcchHHHHHhhccHHHHHHHHHHHHhhccccccCcHHHHHHHHHccCCC
Confidence 3566777788889988888887765322 222222 23333 3333332233322222211 35556666666543
Q ss_pred ----hHHHHHHHHHHHHcCccceEecCCCCeEEEecCCc
Q 013559 366 ----VAGIEKELEALITDNQIQARIDSHNKILYARHADQ 400 (441)
Q Consensus 366 ----~~~~E~~L~~LI~~g~L~akID~~~gvv~~~~~d~ 400 (441)
.+++|--|+.+|..|.|.|-|=.....|++.+.|+
T Consensus 368 n~~~~~~VEciL~tlI~~G~lrgYis~s~~~vV~sk~~p 406 (413)
T COG5600 368 NFHSFKEVECILVTLIGLGLLRGYISHSRRTVVFSKKDP 406 (413)
T ss_pred cccChHHHHHHHHHHHhhhhhhheecccceEEEEecCCC
Confidence 57999999999999999999999999999998765
No 24
>PF10255 Paf67: RNA polymerase I-associated factor PAF67; InterPro: IPR019382 RNA polymerase I is a multi-subunit enzyme and its transcription competence is dependent on the presence of PAF67 [].
Probab=97.09 E-value=0.016 Score=59.45 Aligned_cols=186 Identities=13% Similarity=0.226 Sum_probs=108.9
Q ss_pred HHHHHHHHHHHhcCHHHHHhHHHHHhcccc---cCChhhhhhHHHHHHHHhcccccHHHHHHHHHhcCcCCC--------
Q 013559 178 MCMSAILVSIEMGQFTHVTSYVSKAEQTPE---ALEPVTIAKLRCAAGLAHLEARKYKLAARKFLEVGPDLG-------- 246 (441)
Q Consensus 178 ~~l~~i~~~i~~~~~~~~~~~~~ka~~~~~---~~d~~~~~~l~~~~gl~~l~~r~y~~Aa~~Fl~~~~t~~-------- 246 (441)
.+.+++|+..+.||+..|.+.+.-+.-... ..-+.....+..+-|.++|..|+|.+|.+.|..+...+.
T Consensus 124 SligLlRvh~LLGDY~~Alk~l~~idl~~~~l~~~V~~~~is~~YyvGFaylMlrRY~DAir~f~~iL~yi~r~k~~~~~ 203 (404)
T PF10255_consen 124 SLIGLLRVHCLLGDYYQALKVLENIDLNKKGLYTKVPACHISTYYYVGFAYLMLRRYADAIRTFSQILLYIQRTKNQYHQ 203 (404)
T ss_pred HHHHHHHHHHhccCHHHHHHHhhccCcccchhhccCcchheehHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhhcc
Confidence 357899999999999999876654432111 123445566778899999999999999999998754210
Q ss_pred -C-CchhhhcHHHHHHHH--HHHHHhcCChHHHHHhcccCHhhHhhhccchHHHHHHHHHhcCCHHHHHHHHHHhHHhhh
Q 013559 247 -N-SYNEVIAAQDVATYG--GLCALASFDRAELKSKVIDNVNFRNFLELVPEVRELINDFYSSRYASCLDYLGNLKANLL 322 (441)
Q Consensus 247 -~-~~~el~s~~d~~~Y~--~l~al~s~~R~eLk~~vl~~~~~~~~le~~p~~~~ll~~f~~~~y~~~~~~L~~~~~~l~ 322 (441)
+ .+..+.-..|= .|. ++|-..+-.| + + ..+...+.+ .+.+=+.....++...|-+......|.+-
T Consensus 204 ~~~q~d~i~K~~eq-MyaLlAic~~l~p~~--l-----d-e~i~~~lke--ky~ek~~kmq~gd~~~f~elF~~acPKFI 272 (404)
T PF10255_consen 204 RSYQYDQINKKNEQ-MYALLAICLSLCPQR--L-----D-ESISSQLKE--KYGEKMEKMQRGDEEAFEELFSFACPKFI 272 (404)
T ss_pred ccchhhHHHhHHHH-HHHHHHHHHHhCCCC--C-----C-HHHHHHHHH--HHHHHHHHHHccCHHHHHHHHHhhCCCcc
Confidence 1 12233333332 232 2233323222 1 1 111111111 12233333444455555444444433211
Q ss_pred h----------------chhHHHHHHHHHHHHH----HHHHHHhccccccccHHhHHHHcCCChHHHHHHHHH
Q 013559 323 L----------------DIHLHDHVETLYDQIR----NKALIQYTHPFVSVDLHMMANAFKTSVAGIEKELEA 375 (441)
Q Consensus 323 ~----------------D~~L~~h~~~l~~~iR----~~~i~qy~~pYs~I~L~~mA~~fg~s~~~~E~~L~~ 375 (441)
. |++ ..|.+.|.++++ ...+..|++-|++|+++.+|..++++++++-.+|..
T Consensus 273 sp~~pp~~~~~~~~~~~e~~-~~Ql~~Fl~eV~~q~~l~~lRSyLKLYtti~l~KLA~fl~vd~~~lr~~Ll~ 344 (404)
T PF10255_consen 273 SPVSPPDYDGPSQNKNKEPY-RRQLKLFLDEVKQQQKLPTLRSYLKLYTTIPLEKLASFLDVDEEELRSQLLC 344 (404)
T ss_pred CCCCCCCcccccchhhhhHH-HHHHHHHHHHHHHhhhhhHHHHHHHhhcCCCHHHHHHHcCCCHHHHHHHHHH
Confidence 0 332 335666666655 456778999999999999999999999987776643
No 25
>KOG2688 consensus Transcription-associated recombination protein - Thp1p [Cell cycle control, cell division, chromosome partitioning]
Probab=97.09 E-value=0.019 Score=58.34 Aligned_cols=268 Identities=13% Similarity=0.082 Sum_probs=160.4
Q ss_pred cCCHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhHHHHHhHHhHHHHHHHHcCCHHHHHHHHHHHHhhhcCc-------hh
Q 013559 102 AMDEAWCDSVDRRAEQRKEKLENELNAYRTNLIKESIRMGYNDFGDFYYAHGALGDAFKSYVRTRDYCTTS-------KH 174 (441)
Q Consensus 102 ~~D~~~~~~~~~~~~~~~~~Le~el~~~~~n~~~esir~~~~~la~~~~~~Gd~~~A~~~~~~~r~~~~~~-------~~ 174 (441)
.-|..|.-..--....++..|.......-. .+ .....--+++|.+...+.+..|-+. +.
T Consensus 93 ~~~~~w~~~~l~rv~~~l~~la~~~~~~~~------------~~--~s~~~~~le~~s~~i~~~f~~cl~d~~~~~~~~k 158 (394)
T KOG2688|consen 93 GNDENWILPNLYRVCKDLRYLAINADCALL------------SF--SSLPNQLLEAASRTISRLFSSCLSDRRADLEESK 158 (394)
T ss_pred ccccchHHHHHHHHHHHHHHHhhhhHHhhc------------Cc--ccCchHHHHHHHHHHHHHHHHHhCccccccccch
Confidence 346778766666666665555433321111 10 0000112567777777777776433 22
Q ss_pred HHHHH---HHHHHHHHHhcCHHHHHhHHHHHhccc--ccCChh--hhhhHHHHHHHHhcccccHHHHHHHHHhcCcCCCC
Q 013559 175 IIHMC---MSAILVSIEMGQFTHVTSYVSKAEQTP--EALEPV--TIAKLRCAAGLAHLEARKYKLAARKFLEVGPDLGN 247 (441)
Q Consensus 175 ~~~~~---l~~i~~~i~~~~~~~~~~~~~ka~~~~--~~~d~~--~~~~l~~~~gl~~l~~r~y~~Aa~~Fl~~~~t~~~ 247 (441)
+.-+. -...+++...+..... +.+.|+-... +..++. -...++.|-|.+.|.+.+|..|...+.+++..
T Consensus 159 k~~~~~i~n~lf~Iyfri~~~~L~-k~l~ra~~~~~~~~~~~~l~~~v~y~YylGr~a~~~~d~~~A~~~L~~af~~--- 234 (394)
T KOG2688|consen 159 KVAMLYIVNQLFQIYFRIEKLLLC-KNLIRAFDQSGSDISDFPLAQLVVYHYYLGRYAMFESDFLNAFLQLNEAFRL--- 234 (394)
T ss_pred hhHHHHHHHHHHHHHHHHhhHHHh-HHHHHHhhccccchhhcccccceeeeeeeeeehhhhhhHHHHHHHHHHHHHh---
Confidence 23222 2233344444444433 3444443322 111221 23446677789999999999999999998764
Q ss_pred Cchhhh--cHHHHHHHHHHHHHhcCChHHHHHhcccCHhhHhhhccch--HHHHHHHHHhcCCHHHHHHHHHHhHHh-hh
Q 013559 248 SYNEVI--AAQDVATYGGLCALASFDRAELKSKVIDNVNFRNFLELVP--EVRELINDFYSSRYASCLDYLGNLKAN-LL 322 (441)
Q Consensus 248 ~~~el~--s~~d~~~Y~~l~al~s~~R~eLk~~vl~~~~~~~~le~~p--~~~~ll~~f~~~~y~~~~~~L~~~~~~-l~ 322 (441)
|++.. ...-+.+|++-+++.... + | ...+++..+ .+..++.+.-.+++..+-..|+..+.. ++
T Consensus 235 -cp~~~~~n~~~iliylip~~~llg~---~-------P-t~~lL~~~~~~~~~~lv~aVr~Gnl~~f~~al~~~E~~f~~ 302 (394)
T KOG2688|consen 235 -CPDLLLKNKRLILIYLIPTGLLLGR---I-------P-TKELLDFYTLDKYSPLVQAVRSGNLRLFDLALADNERFFIR 302 (394)
T ss_pred -CcHHHHhhhhhHHHHHhHHHHHhcc---C-------c-chhhHhHhhHHhHHHHHHHHHhccHHHHHHHHhhhHHHHHH
Confidence 33322 344577999888887642 1 1 223344444 577888888899999998888887632 22
Q ss_pred hchhHH--HHHHHHHHHHHHHHHHHhccccccccHHhHHHHcCC------ChHHHHHHHHHHHHcCccceEecCCCCeEE
Q 013559 323 LDIHLH--DHVETLYDQIRNKALIQYTHPFVSVDLHMMANAFKT------SVAGIEKELEALITDNQIQARIDSHNKILY 394 (441)
Q Consensus 323 ~D~~L~--~h~~~l~~~iR~~~i~qy~~pYs~I~L~~mA~~fg~------s~~~~E~~L~~LI~~g~L~akID~~~gvv~ 394 (441)
.-.|+- ..--..+++.-.+++.=... =+.++++.+-.++.. +.+++|--|+++|..|+|.|-|+.....++
T Consensus 303 ~gi~l~l~~l~lv~yrnL~kkv~~~~~~-~~~lpls~~~~al~~~~~~~~~~deveciLa~lI~~G~ikgYish~~~~~V 381 (394)
T KOG2688|consen 303 SGIYLTLEKLPLVVYRNLFKKVIQLWGK-TSQLPLSRFLTALQFSGVTDVDLDEVECILANLIDLGRIKGYISHQLQTLV 381 (394)
T ss_pred hccHHHhhhhhHHHHHHHHHHHHHHhCC-CCCCCHHHHHHHHhhcCCCCCchhhHHHHHHhhhhhccccchhchhhheEE
Confidence 333331 22224445544444432212 267888888777754 358999999999999999999999999999
Q ss_pred EecCCc
Q 013559 395 ARHADQ 400 (441)
Q Consensus 395 ~~~~d~ 400 (441)
+.+.++
T Consensus 382 ~sK~~p 387 (394)
T KOG2688|consen 382 FSKKDP 387 (394)
T ss_pred EecCCC
Confidence 987764
No 26
>KOG2072 consensus Translation initiation factor 3, subunit a (eIF-3a) [Translation, ribosomal structure and biogenesis]
Probab=96.97 E-value=0.046 Score=59.46 Aligned_cols=85 Identities=20% Similarity=0.152 Sum_probs=70.8
Q ss_pred HHHHhHHhhhhchhHHHHHHHHHHHHHHHHHHHhccccccccHHhHHHHcC-CChHHHHHHHHHHHHcCccceEecCCCC
Q 013559 313 YLGNLKANLLLDIHLHDHVETLYDQIRNKALIQYTHPFVSVDLHMMANAFK-TSVAGIEKELEALITDNQIQARIDSHNK 391 (441)
Q Consensus 313 ~L~~~~~~l~~D~~L~~h~~~l~~~iR~~~i~qy~~pYs~I~L~~mA~~fg-~s~~~~E~~L~~LI~~g~L~akID~~~g 391 (441)
.++.+-..+..-+..++.+..|-..+-.|++.|.=..|.+|+++++-+.-- ++.-++|+-|++-...+-+..+||...+
T Consensus 408 ~lq~ll~~ls~~~~~~QYI~sLq~v~~~RllqQvSqiY~sIs~~~l~~La~F~~~~~lEk~~v~a~k~~~v~iriDH~~~ 487 (988)
T KOG2072|consen 408 KLQPLLDKLSESPDKSQYIPSLQDVIILRLLQQVSQIYESISFERLYKLAPFFSAFELEKLLVEAAKHNDVSIRIDHESN 487 (988)
T ss_pred HHHHHHHHHHcCCCccccchhHHHHHHHHHHHHHHHHHHHHhHHHHHHHHhhcCHHHHHHHHHHHHhccceeEEeccccc
Confidence 333334445555555778888999999999999999999999999887654 5888999999999999999999999999
Q ss_pred eEEEec
Q 013559 392 ILYARH 397 (441)
Q Consensus 392 vv~~~~ 397 (441)
.|.+..
T Consensus 488 ~v~Fgs 493 (988)
T KOG2072|consen 488 SVSFGS 493 (988)
T ss_pred eeeecc
Confidence 999983
No 27
>PF14938 SNAP: Soluble NSF attachment protein, SNAP; PDB: 1QQE_A 2IFU_A.
Probab=96.87 E-value=0.52 Score=46.19 Aligned_cols=128 Identities=15% Similarity=0.215 Sum_probs=86.1
Q ss_pred HHHHHHHHHHHHhhhhHHHHHhHHhHHHHHHHHc-CCHHHHHHHHHHHHhhhc---CchhHHHHHHHHHHHHHHhcCHHH
Q 013559 119 KEKLENELNAYRTNLIKESIRMGYNDFGDFYYAH-GALGDAFKSYVRTRDYCT---TSKHIIHMCMSAILVSIEMGQFTH 194 (441)
Q Consensus 119 ~~~Le~el~~~~~n~~~esir~~~~~la~~~~~~-Gd~~~A~~~~~~~r~~~~---~~~~~~~~~l~~i~~~i~~~~~~~ 194 (441)
.+-++.-+.-|.+++-....-..+..+|++|.+. ||+++|.++|.+..++.. .+....++...+..+.+..|+|..
T Consensus 94 i~~~~~A~~~y~~~G~~~~aA~~~~~lA~~ye~~~~d~e~Ai~~Y~~A~~~y~~e~~~~~a~~~~~~~A~l~~~l~~y~~ 173 (282)
T PF14938_consen 94 IECYEKAIEIYREAGRFSQAAKCLKELAEIYEEQLGDYEKAIEYYQKAAELYEQEGSPHSAAECLLKAADLYARLGRYEE 173 (282)
T ss_dssp HHHHHHHHHHHHHCT-HHHHHHHHHHHHHHHCCTT--HHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHTT-HHH
T ss_pred HHHHHHHHHHHHhcCcHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHCCChhhHHHHHHHHHHHHHHhCCHHH
Confidence 3445555566666665566667899999999999 999999999999977664 233345566788889999999999
Q ss_pred HHhHHHHHhcc-cc-c-CChhhhhhHHHHHHHHhcccccHHHHHHHHH---hcCcCCCC
Q 013559 195 VTSYVSKAEQT-PE-A-LEPVTIAKLRCAAGLAHLEARKYKLAARKFL---EVGPDLGN 247 (441)
Q Consensus 195 ~~~~~~ka~~~-~~-~-~d~~~~~~l~~~~gl~~l~~r~y~~Aa~~Fl---~~~~t~~~ 247 (441)
+...+.++-.. ++ . ..+..+ .+....+|.+|..+++..|...|- +..++|.+
T Consensus 174 A~~~~e~~~~~~l~~~l~~~~~~-~~~l~a~l~~L~~~D~v~A~~~~~~~~~~~~~F~~ 231 (282)
T PF14938_consen 174 AIEIYEEVAKKCLENNLLKYSAK-EYFLKAILCHLAMGDYVAARKALERYCSQDPSFAS 231 (282)
T ss_dssp HHHHHHHHHHTCCCHCTTGHHHH-HHHHHHHHHHHHTT-HHHHHHHHHHHGTTSTTSTT
T ss_pred HHHHHHHHHHHhhcccccchhHH-HHHHHHHHHHHHcCCHHHHHHHHHHHHhhCCCCCC
Confidence 99998887553 33 1 233322 234456889999999877655544 44556643
No 28
>PF10075 PCI_Csn8: COP9 signalosome, subunit CSN8; InterPro: IPR019280 The photomorphogenic 9 (COP9) signalosome or CSN complex is composed of eight subunits: Cops1/GPS1, Cops2, Cops3, Cops4, Cops5, Cop6, Cops7 (Cops7A or Cops7B) and Cops8. In the complex, Cops8, which is the smallest subunit, probably interacts directly with Cops3, Cops4 and Cops7 (Cops7A or Cops7B). This signalosome is homologous to the lid subcomplex of the 26S proteasome and regulates the ubiquitin-proteasome pathway. It functions as a structural scaffold for subunit-subunit interactions within the complex and is a key regulator of photomorphogenic development [].; PDB: 1RZ4_A.
Probab=96.80 E-value=0.0076 Score=53.05 Aligned_cols=78 Identities=17% Similarity=0.214 Sum_probs=58.3
Q ss_pred HHHHHHHHhcCCHHHHHHHHHHhHHhhhhchhHHHHHHHHHHHHHHHHHHHhccccccccHHhHHHHcCCChHHHHHHHH
Q 013559 295 VRELINDFYSSRYASCLDYLGNLKANLLLDIHLHDHVETLYDQIRNKALIQYTHPFVSVDLHMMANAFKTSVAGIEKELE 374 (441)
Q Consensus 295 ~~~ll~~f~~~~y~~~~~~L~~~~~~l~~D~~L~~h~~~l~~~iR~~~i~qy~~pYs~I~L~~mA~~fg~s~~~~E~~L~ 374 (441)
+..+...+.+|+|..+...+.... -...+.+.+..|.+.+|.+++.-.=..|++|+++.+|+.+|++.+++++++.
T Consensus 44 i~~l~~~L~~~~~~~~~~~~~~~~----~~~~~~~~v~~~~~~iR~~i~~~i~~aY~sIs~~~la~~Lg~~~~el~~~~~ 119 (143)
T PF10075_consen 44 IWSLGQALWEGDYSKFWQALRSNP----WSPDYKPFVPGFEDTIRERIAHLISKAYSSISLSDLAEMLGLSEEELEKFIK 119 (143)
T ss_dssp HHHHHHHHHTT-HHHHHHHS-TT--------HHHHTSTTHHHHHHHHHHHHHHHH-SEE-HHHHHHHTTS-HHHHHHHHH
T ss_pred HHHHHHHHHCCCHHHHHHHHHhcc----chHHHHHHHHHHHHHHHHHHHHHHHHHHhHcCHHHHHHHhCCCHHHHHHHHH
Confidence 456777888999999987776541 2246778889999999999999999999999999999999999777666666
Q ss_pred HH
Q 013559 375 AL 376 (441)
Q Consensus 375 ~L 376 (441)
+.
T Consensus 120 ~~ 121 (143)
T PF10075_consen 120 SR 121 (143)
T ss_dssp HH
T ss_pred Hc
Confidence 53
No 29
>TIGR02795 tol_pal_ybgF tol-pal system protein YbgF. Members of this protein family are the product of one of seven genes regularly clustered in operons to encode the proteins of the tol-pal system, which is critical for maintaining the integrity of the bacterial outer membrane. The gene for this periplasmic protein has been designated orf2 and ybgF. All members of the seed alignment were from unique tol-pal gene regions from completed bacterial genomes. The architecture of this protein is a signal sequence, a low-complexity region usually rich in Asn and Gln, a well-conserved region with tandem repeats that resemble the tetratricopeptide (TPR) repeat, involved in protein-protein interaction.
Probab=96.55 E-value=0.029 Score=46.22 Aligned_cols=104 Identities=12% Similarity=0.046 Sum_probs=77.9
Q ss_pred HHhHHHHHHHHcCCHHHHHHHHHHHHhhhcCchhHHHHHHHHHHHHHHhcCHHHHHhHHHHHhcccccCChhhhhhHHHH
Q 013559 141 GYNDFGDFYYAHGALGDAFKSYVRTRDYCTTSKHIIHMCMSAILVSIEMGQFTHVTSYVSKAEQTPEALEPVTIAKLRCA 220 (441)
Q Consensus 141 ~~~~la~~~~~~Gd~~~A~~~~~~~r~~~~~~~~~~~~~l~~i~~~i~~~~~~~~~~~~~ka~~~~~~~d~~~~~~l~~~ 220 (441)
.++.+|..+.+.|++++|.+.|.++.....+.....+..+.+.++....|++..+...+.++...... ++ ........
T Consensus 4 ~~~~~~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~p~-~~-~~~~~~~~ 81 (119)
T TIGR02795 4 AYYDAALLVLKAGDYADAIQAFQAFLKKYPKSTYAPNAHYWLGEAYYAQGKYADAAKAFLAVVKKYPK-SP-KAPDALLK 81 (119)
T ss_pred HHHHHHHHHHHcCCHHHHHHHHHHHHHHCCCccccHHHHHHHHHHHHhhccHHHHHHHHHHHHHHCCC-CC-cccHHHHH
Confidence 56899999999999999999999997765544444567788888999999999999999988664221 11 11122344
Q ss_pred HHHHhcccccHHHHHHHHHhcCcCCC
Q 013559 221 AGLAHLEARKYKLAARKFLEVGPDLG 246 (441)
Q Consensus 221 ~gl~~l~~r~y~~Aa~~Fl~~~~t~~ 246 (441)
.|..+...+++..|...|-.+...++
T Consensus 82 ~~~~~~~~~~~~~A~~~~~~~~~~~p 107 (119)
T TIGR02795 82 LGMSLQELGDKEKAKATLQQVIKRYP 107 (119)
T ss_pred HHHHHHHhCChHHHHHHHHHHHHHCc
Confidence 56677889999999998887765443
No 30
>cd00189 TPR Tetratricopeptide repeat domain; typically contains 34 amino acids [WLF]-X(2)-[LIM]-[GAS]-X(2)-[YLF]-X(8)-[ASE]-X(3)-[FYL]-X(2)-[ASL]-X(4)-[PKE] is the consensus sequence; found in a variety of organisms including bacteria, cyanobacteria, yeast, fungi, plants, and humans in various subcellular locations; involved in a variety of functions including protein-protein interactions, but common features in the interaction partners have not been defined; involved in chaperone, cell-cycle, transciption, and protein transport complexes; the number of TPR motifs varies among proteins (1,3-11,13 15,16,19); 5-6 tandem repeats generate a right-handed helical structure with an amphipathic channel that is thought to accomodate an alpha-helix of a target protein; it has been proposed that TPR proteins preferably interact with WD-40 repeat proteins, but in many instances several TPR-proteins seem to aggregate to multi-protein complexes; examples of TPR-proteins include, Cdc16p, Cdc23p and C
Probab=96.32 E-value=0.055 Score=40.93 Aligned_cols=95 Identities=17% Similarity=0.257 Sum_probs=69.6
Q ss_pred HHhHHHHHHHHcCCHHHHHHHHHHHHhhhcCchhHHHHHHHHHHHHHHhcCHHHHHhHHHHHhcccccCChhhhhhHHHH
Q 013559 141 GYNDFGDFYYAHGALGDAFKSYVRTRDYCTTSKHIIHMCMSAILVSIEMGQFTHVTSYVSKAEQTPEALEPVTIAKLRCA 220 (441)
Q Consensus 141 ~~~~la~~~~~~Gd~~~A~~~~~~~r~~~~~~~~~~~~~l~~i~~~i~~~~~~~~~~~~~ka~~~~~~~d~~~~~~l~~~ 220 (441)
+++.+|..++..|++++|.+.+.+......... ........+....+++..+...+.++-..... ++ .....
T Consensus 2 ~~~~~a~~~~~~~~~~~A~~~~~~~~~~~~~~~---~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~-~~----~~~~~ 73 (100)
T cd00189 2 ALLNLGNLYYKLGDYDEALEYYEKALELDPDNA---DAYYNLAAAYYKLGKYEEALEDYEKALELDPD-NA----KAYYN 73 (100)
T ss_pred HHHHHHHHHHHHhcHHHHHHHHHHHHhcCCccH---HHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCc-ch----hHHHH
Confidence 467899999999999999999999876654332 45556666777789999999988887654321 22 23345
Q ss_pred HHHHhcccccHHHHHHHHHhcCc
Q 013559 221 AGLAHLEARKYKLAARKFLEVGP 243 (441)
Q Consensus 221 ~gl~~l~~r~y~~Aa~~Fl~~~~ 243 (441)
.|..+...|++..|...|..+..
T Consensus 74 ~~~~~~~~~~~~~a~~~~~~~~~ 96 (100)
T cd00189 74 LGLAYYKLGKYEEALEAYEKALE 96 (100)
T ss_pred HHHHHHHHHhHHHHHHHHHHHHc
Confidence 56677788999999888876643
No 31
>PF13424 TPR_12: Tetratricopeptide repeat; PDB: 3RO2_A 3Q15_A 3ASG_A 3ASD_A 3AS5_A 3AS4_A 3ASH_B 4A1S_B 3CEQ_B 3EDT_H ....
Probab=96.30 E-value=0.027 Score=43.45 Aligned_cols=69 Identities=16% Similarity=0.229 Sum_probs=54.8
Q ss_pred HHHhHHhHHHHHHHHcCCHHHHHHHHHHHHhhhc--Cc--hhHHHHHHHHHHHHHHhcCHHHHHhHHHHHhcc
Q 013559 137 SIRMGYNDFGDFYYAHGALGDAFKSYVRTRDYCT--TS--KHIIHMCMSAILVSIEMGQFTHVTSYVSKAEQT 205 (441)
Q Consensus 137 sir~~~~~la~~~~~~Gd~~~A~~~~~~~r~~~~--~~--~~~~~~~l~~i~~~i~~~~~~~~~~~~~ka~~~ 205 (441)
.+-.++..+|..|...|++++|.++|.+..+.+. ++ ...+....++..+....|+++.+..++.|+-++
T Consensus 3 ~~a~~~~~la~~~~~~~~~~~A~~~~~~al~~~~~~~~~~~~~a~~~~~lg~~~~~~g~~~~A~~~~~~al~i 75 (78)
T PF13424_consen 3 DTANAYNNLARVYRELGRYDEALDYYEKALDIEEQLGDDHPDTANTLNNLGECYYRLGDYEEALEYYQKALDI 75 (78)
T ss_dssp HHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHTTTHHHHHHHHHHHHHHHHHHTTHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHhh
Confidence 4557889999999999999999999999865542 22 235677778888889999999999999987653
No 32
>KOG1840 consensus Kinesin light chain [Cytoskeleton]
Probab=96.21 E-value=0.27 Score=52.21 Aligned_cols=125 Identities=15% Similarity=0.175 Sum_probs=96.1
Q ss_pred HHHHHHHHHHHHhhhhH--HHHHhHHhHHHHHHHHcCCHHHHHHHHHHHHh-----hhcCchhHHHHHHHHHHHHHHhcC
Q 013559 119 KEKLENELNAYRTNLIK--ESIRMGYNDFGDFYYAHGALGDAFKSYVRTRD-----YCTTSKHIIHMCMSAILVSIEMGQ 191 (441)
Q Consensus 119 ~~~Le~el~~~~~n~~~--esir~~~~~la~~~~~~Gd~~~A~~~~~~~r~-----~~~~~~~~~~~~l~~i~~~i~~~~ 191 (441)
..-++.-|...++..+. +.+-..+.+||..|++.|++.+|..++.+..+ +..+.+++...+.++..+.-..+.
T Consensus 261 v~ly~~AL~i~e~~~G~~h~~va~~l~nLa~ly~~~GKf~EA~~~~e~Al~I~~~~~~~~~~~v~~~l~~~~~~~~~~~~ 340 (508)
T KOG1840|consen 261 VNLYEEALTIREEVFGEDHPAVAATLNNLAVLYYKQGKFAEAEEYCERALEIYEKLLGASHPEVAAQLSELAAILQSMNE 340 (508)
T ss_pred HHHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHhccCChHHHHHHHHHHHHHHHHhhccChHHHHHHHHHHHHHHHHhcc
Confidence 33445555555555544 45556899999999999999999999998643 234556666677778888888999
Q ss_pred HHHHHhHHHHHhcccc---cCChhhhhhHHHHHHHHhcccccHHHHHHHHHhcCc
Q 013559 192 FTHVTSYVSKAEQTPE---ALEPVTIAKLRCAAGLAHLEARKYKLAARKFLEVGP 243 (441)
Q Consensus 192 ~~~~~~~~~ka~~~~~---~~d~~~~~~l~~~~gl~~l~~r~y~~Aa~~Fl~~~~ 243 (441)
++.+..++.++-.++. +.+....+++++--|-.+...|+|.+|.+.|-+++.
T Consensus 341 ~Eea~~l~q~al~i~~~~~g~~~~~~a~~~~nl~~l~~~~gk~~ea~~~~k~ai~ 395 (508)
T KOG1840|consen 341 YEEAKKLLQKALKIYLDAPGEDNVNLAKIYANLAELYLKMGKYKEAEELYKKAIQ 395 (508)
T ss_pred hhHHHHHHHHHHHHHHhhccccchHHHHHHHHHHHHHHHhcchhHHHHHHHHHHH
Confidence 9999999999977654 344446677888888899999999999999988865
No 33
>PF09756 DDRGK: DDRGK domain; InterPro: IPR019153 This is a family of proteins of approximately 300 residues. They contain a highly conserved DDRGK motif. The function is unknown. ; PDB: 1WI9_A.
Probab=95.93 E-value=0.014 Score=53.69 Aligned_cols=59 Identities=19% Similarity=0.364 Sum_probs=43.7
Q ss_pred HHHHHHhccccccccHHhHHHHcCCChHHHHHHHHHHHHcCccceEecCCCCeEEEecC
Q 013559 340 NKALIQYTHPFVSVDLHMMANAFKTSVAGIEKELEALITDNQIQARIDSHNKILYARHA 398 (441)
Q Consensus 340 ~~~i~qy~~pYs~I~L~~mA~~fg~s~~~~E~~L~~LI~~g~L~akID~~~gvv~~~~~ 398 (441)
...|++|+...+.|.|..||..||+++.++-+-|-.|..+|+|.|-||-..+.|+.++.
T Consensus 101 L~~Fi~yIK~~Kvv~ledla~~f~l~t~~~i~ri~~L~~~g~ltGv~DdrGkfIyIs~e 159 (188)
T PF09756_consen 101 LQEFINYIKEHKVVNLEDLAAEFGLRTQDVINRIQELEAEGRLTGVIDDRGKFIYISEE 159 (188)
T ss_dssp HHHHHHHHHH-SEE-HHHHHHHH-S-HHHHHHHHHHHHHHSSS-EEE-TT--EEE----
T ss_pred HHHHHHHHHHcceeeHHHHHHHcCCCHHHHHHHHHHHHHCCCceeeEcCCCCeEEecHH
Confidence 36677899999999999999999999999999999999999999999998888887744
No 34
>KOG1174 consensus Anaphase-promoting complex (APC), subunit 7 [Cell cycle control, cell division, chromosome partitioning; Posttranslational modification, protein turnover, chaperones]
Probab=95.75 E-value=0.69 Score=47.32 Aligned_cols=194 Identities=15% Similarity=0.138 Sum_probs=112.7
Q ss_pred hHHhHHHHHHHHcCCHHHHHHHHHHHHh---hh-----------------cCchhHHHHHHHHH-----------HHHHH
Q 013559 140 MGYNDFGDFYYAHGALGDAFKSYVRTRD---YC-----------------TTSKHIIHMCMSAI-----------LVSIE 188 (441)
Q Consensus 140 ~~~~~la~~~~~~Gd~~~A~~~~~~~r~---~~-----------------~~~~~~~~~~l~~i-----------~~~i~ 188 (441)
..+..+|+.++.+||+.+|.--|.+++- |. .......+.+|.+. .+...
T Consensus 233 hLl~~lak~~~~~Gdn~~a~~~Fe~~~~~dpy~i~~MD~Ya~LL~~eg~~e~~~~L~~~Lf~~~~~ta~~wfV~~~~l~~ 312 (564)
T KOG1174|consen 233 HLMMALGKCLYYNGDYFQAEDIFSSTLCANPDNVEAMDLYAVLLGQEGGCEQDSALMDYLFAKVKYTASHWFVHAQLLYD 312 (564)
T ss_pred HHHHHHhhhhhhhcCchHHHHHHHHHhhCChhhhhhHHHHHHHHHhccCHhhHHHHHHHHHhhhhcchhhhhhhhhhhhh
Confidence 4678999999999999999998887532 11 11122223333333 12344
Q ss_pred hcCHHHHHhHHHHHhcccccCC---------------h------------hhhhhHHHHHHHH--hcccccHHHHHHHHH
Q 013559 189 MGQFTHVTSYVSKAEQTPEALE---------------P------------VTIAKLRCAAGLA--HLEARKYKLAARKFL 239 (441)
Q Consensus 189 ~~~~~~~~~~~~ka~~~~~~~d---------------~------------~~~~~l~~~~gl~--~l~~r~y~~Aa~~Fl 239 (441)
..++..+..+..|+-..-+... + -..-+|.+|.|++ +++.+++++|--.=-
T Consensus 313 ~K~~~rAL~~~eK~I~~~~r~~~alilKG~lL~~~~R~~~A~IaFR~Aq~Lap~rL~~Y~GL~hsYLA~~~~kEA~~~An 392 (564)
T KOG1174|consen 313 EKKFERALNFVEKCIDSEPRNHEALILKGRLLIALERHTQAVIAFRTAQMLAPYRLEIYRGLFHSYLAQKRFKEANALAN 392 (564)
T ss_pred hhhHHHHHHHHHHHhccCcccchHHHhccHHHHhccchHHHHHHHHHHHhcchhhHHHHHHHHHHHHhhchHHHHHHHHH
Confidence 5678888888888754422110 0 0124688999985 477888888865555
Q ss_pred hcCcCCCCCchhhhcHHHHHHHH-HHHHHhcCChHHHHHhcccCHhhHhhhccchHHHHHHH-----HHhcCCHHHHHHH
Q 013559 240 EVGPDLGNSYNEVIAAQDVATYG-GLCALASFDRAELKSKVIDNVNFRNFLELVPEVRELIN-----DFYSSRYASCLDY 313 (441)
Q Consensus 240 ~~~~t~~~~~~el~s~~d~~~Y~-~l~al~s~~R~eLk~~vl~~~~~~~~le~~p~~~~ll~-----~f~~~~y~~~~~~ 313 (441)
++..+++.++..+- .++ .+|.--+..|..-|+ ..+. -|..+|.+...+. +..+..|+.....
T Consensus 393 ~~~~~~~~sA~~Lt------L~g~~V~~~dp~~rEKAKk-f~ek-----~L~~~P~Y~~AV~~~AEL~~~Eg~~~D~i~L 460 (564)
T KOG1174|consen 393 WTIRLFQNSARSLT------LFGTLVLFPDPRMREKAKK-FAEK-----SLKINPIYTPAVNLIAELCQVEGPTKDIIKL 460 (564)
T ss_pred HHHHHhhcchhhhh------hhcceeeccCchhHHHHHH-HHHh-----hhccCCccHHHHHHHHHHHHhhCccchHHHH
Confidence 55555554333322 332 222222222322222 2221 1445675543332 2346788888777
Q ss_pred HHHhHHhhhhchhHHHHHHHHHHH--HHHHHHHHh
Q 013559 314 LGNLKANLLLDIHLHDHVETLYDQ--IRNKALIQY 346 (441)
Q Consensus 314 L~~~~~~l~~D~~L~~h~~~l~~~--iR~~~i~qy 346 (441)
|+..-... .|.-||.|+..++.. .-+.+..+|
T Consensus 461 Le~~L~~~-~D~~LH~~Lgd~~~A~Ne~Q~am~~y 494 (564)
T KOG1174|consen 461 LEKHLIIF-PDVNLHNHLGDIMRAQNEPQKAMEYY 494 (564)
T ss_pred HHHHHhhc-cccHHHHHHHHHHHHhhhHHHHHHHH
Confidence 77765443 677899999888764 557888888
No 35
>PRK11788 tetratricopeptide repeat protein; Provisional
Probab=95.74 E-value=1.3 Score=44.86 Aligned_cols=101 Identities=13% Similarity=0.125 Sum_probs=73.5
Q ss_pred hHHhHHHHHHHHcCCHHHHHHHHHHHHhhhcCchhHHHHHHHHHHHHHHhcCHHHHHhHHHHHhcccccCChhhhhhHHH
Q 013559 140 MGYNDFGDFYYAHGALGDAFKSYVRTRDYCTTSKHIIHMCMSAILVSIEMGQFTHVTSYVSKAEQTPEALEPVTIAKLRC 219 (441)
Q Consensus 140 ~~~~~la~~~~~~Gd~~~A~~~~~~~r~~~~~~~~~~~~~l~~i~~~i~~~~~~~~~~~~~ka~~~~~~~d~~~~~~l~~ 219 (441)
..+..+|..|...|++++|.++|.++.+... ........++.+....|+|..+...+.++...-....+.....+..
T Consensus 108 ~~~~~La~~~~~~g~~~~A~~~~~~~l~~~~---~~~~~~~~la~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~~~~ 184 (389)
T PRK11788 108 LALQELGQDYLKAGLLDRAEELFLQLVDEGD---FAEGALQQLLEIYQQEKDWQKAIDVAERLEKLGGDSLRVEIAHFYC 184 (389)
T ss_pred HHHHHHHHHHHHCCCHHHHHHHHHHHHcCCc---chHHHHHHHHHHHHHhchHHHHHHHHHHHHHhcCCcchHHHHHHHH
Confidence 4678999999999999999999999876522 2345566777788889999999988887755322111112223334
Q ss_pred HHHHHhcccccHHHHHHHHHhcCc
Q 013559 220 AAGLAHLEARKYKLAARKFLEVGP 243 (441)
Q Consensus 220 ~~gl~~l~~r~y~~Aa~~Fl~~~~ 243 (441)
.-|..++..+++.+|...|-++..
T Consensus 185 ~la~~~~~~~~~~~A~~~~~~al~ 208 (389)
T PRK11788 185 ELAQQALARGDLDAARALLKKALA 208 (389)
T ss_pred HHHHHHHhCCCHHHHHHHHHHHHh
Confidence 456677889999999999988765
No 36
>PF12688 TPR_5: Tetratrico peptide repeat
Probab=95.67 E-value=0.2 Score=42.85 Aligned_cols=101 Identities=15% Similarity=0.054 Sum_probs=83.2
Q ss_pred HHhHHHHHHHHcCCHHHHHHHHHHHHhhhcCchhHHHHHHHHHHHHHHhcCHHHHHhHHHHHhcccccCChhhhhhHHHH
Q 013559 141 GYNDFGDFYYAHGALGDAFKSYVRTRDYCTTSKHIIHMCMSAILVSIEMGQFTHVTSYVSKAEQTPEALEPVTIAKLRCA 220 (441)
Q Consensus 141 ~~~~la~~~~~~Gd~~~A~~~~~~~r~~~~~~~~~~~~~l~~i~~~i~~~~~~~~~~~~~ka~~~~~~~d~~~~~~l~~~ 220 (441)
+++.+|..+-..|+.++|...|.+..+..-+..+.....++.-.+.-..|+.+.+...+.++.... .+......+++.
T Consensus 3 ~~~~~A~a~d~~G~~~~Ai~~Y~~Al~~gL~~~~~~~a~i~lastlr~LG~~deA~~~L~~~~~~~--p~~~~~~~l~~f 80 (120)
T PF12688_consen 3 ALYELAWAHDSLGREEEAIPLYRRALAAGLSGADRRRALIQLASTLRNLGRYDEALALLEEALEEF--PDDELNAALRVF 80 (120)
T ss_pred hHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCchHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHC--CCccccHHHHHH
Confidence 578999999999999999999999977654555667788888888889999999999998875532 233345677788
Q ss_pred HHHHhcccccHHHHHHHHHhcCc
Q 013559 221 AGLAHLEARKYKLAARKFLEVGP 243 (441)
Q Consensus 221 ~gl~~l~~r~y~~Aa~~Fl~~~~ 243 (441)
.++.....|++++|.+.|+.+..
T Consensus 81 ~Al~L~~~gr~~eAl~~~l~~la 103 (120)
T PF12688_consen 81 LALALYNLGRPKEALEWLLEALA 103 (120)
T ss_pred HHHHHHHCCCHHHHHHHHHHHHH
Confidence 89999999999999999998763
No 37
>PF09012 FeoC: FeoC like transcriptional regulator; InterPro: IPR015102 This entry contains several transcriptional regulators, including FeoC, which contain a HTH motif. FeoC acts as a [Fe-S] dependent transcriptional repressor []. ; PDB: 1XN7_A 2K02_A.
Probab=95.23 E-value=0.027 Score=43.06 Aligned_cols=49 Identities=27% Similarity=0.250 Sum_probs=38.8
Q ss_pred HHHHHhccccccccHHhHHHHcCCChHHHHHHHHHHHHcCccceEecCC
Q 013559 341 KALIQYTHPFVSVDLHMMANAFKTSVAGIEKELEALITDNQIQARIDSH 389 (441)
Q Consensus 341 ~~i~qy~~pYs~I~L~~mA~~fg~s~~~~E~~L~~LI~~g~L~akID~~ 389 (441)
..+.+|++-...+++..||..||+|++.+|..|..||.-|+|...-+..
T Consensus 3 ~~i~~~l~~~~~~S~~eLa~~~~~s~~~ve~mL~~l~~kG~I~~~~~~~ 51 (69)
T PF09012_consen 3 QEIRDYLRERGRVSLAELAREFGISPEAVEAMLEQLIRKGYIRKVDMSS 51 (69)
T ss_dssp HHHHHHHHHS-SEEHHHHHHHTT--HHHHHHHHHHHHCCTSCEEEEEE-
T ss_pred HHHHHHHHHcCCcCHHHHHHHHCcCHHHHHHHHHHHHHCCcEEEecCCC
Confidence 3466778889999999999999999999999999999999997544433
No 38
>PF13414 TPR_11: TPR repeat; PDB: 2HO1_B 2FI7_B 2DBA_A 3Q4A_B 2C2L_D 3Q47_B 3Q49_B 2PL2_B 3IEG_B 2FBN_A ....
Probab=95.16 E-value=0.12 Score=38.74 Aligned_cols=61 Identities=13% Similarity=0.322 Sum_probs=51.2
Q ss_pred HHhHHHHHHHHcCCHHHHHHHHHHHHhhhcCchhHHHHHHHHHHHHHHhc-CHHHHHhHHHHHhc
Q 013559 141 GYNDFGDFYYAHGALGDAFKSYVRTRDYCTTSKHIIHMCMSAILVSIEMG-QFTHVTSYVSKAEQ 204 (441)
Q Consensus 141 ~~~~la~~~~~~Gd~~~A~~~~~~~r~~~~~~~~~~~~~l~~i~~~i~~~-~~~~~~~~~~ka~~ 204 (441)
.+..+|..++..|++++|.++|.+..++..+ -..+..++..+....| +|..+..++.++-.
T Consensus 5 ~~~~~g~~~~~~~~~~~A~~~~~~ai~~~p~---~~~~~~~~g~~~~~~~~~~~~A~~~~~~al~ 66 (69)
T PF13414_consen 5 AWYNLGQIYFQQGDYEEAIEYFEKAIELDPN---NAEAYYNLGLAYMKLGKDYEEAIEDFEKALK 66 (69)
T ss_dssp HHHHHHHHHHHTTHHHHHHHHHHHHHHHSTT---HHHHHHHHHHHHHHTTTHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHcCCHHHHHHHHHHHHHcCCC---CHHHHHHHHHHHHHhCccHHHHHHHHHHHHH
Confidence 5788999999999999999999999888633 2557777788888888 79999999888754
No 39
>TIGR02552 LcrH_SycD type III secretion low calcium response chaperone LcrH/SycD. ScyD/LcrH contains three central tetratricopeptide-like repeats that are predicted to fold into an all-alpha-helical array.
Probab=94.92 E-value=0.4 Score=40.72 Aligned_cols=96 Identities=10% Similarity=0.024 Sum_probs=73.3
Q ss_pred hHHhHHHHHHHHcCCHHHHHHHHHHHHhhhcCchhHHHHHHHHHHHHHHhcCHHHHHhHHHHHhcccccCChhhhhhHHH
Q 013559 140 MGYNDFGDFYYAHGALGDAFKSYVRTRDYCTTSKHIIHMCMSAILVSIEMGQFTHVTSYVSKAEQTPEALEPVTIAKLRC 219 (441)
Q Consensus 140 ~~~~~la~~~~~~Gd~~~A~~~~~~~r~~~~~~~~~~~~~l~~i~~~i~~~~~~~~~~~~~ka~~~~~~~d~~~~~~l~~ 219 (441)
.+++.+|..++..|++.+|.+.+.++....+. -.++...+..+....|+++.+...+.++..... .++ ....
T Consensus 18 ~~~~~~a~~~~~~~~~~~A~~~~~~~~~~~p~---~~~~~~~la~~~~~~~~~~~A~~~~~~~~~~~p-~~~----~~~~ 89 (135)
T TIGR02552 18 EQIYALAYNLYQQGRYDEALKLFQLLAAYDPY---NSRYWLGLAACCQMLKEYEEAIDAYALAAALDP-DDP----RPYF 89 (135)
T ss_pred HHHHHHHHHHHHcccHHHHHHHHHHHHHhCCC---cHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCC-CCh----HHHH
Confidence 45789999999999999999999988766433 245556667777888999999998888755421 122 2335
Q ss_pred HHHHHhcccccHHHHHHHHHhcCc
Q 013559 220 AAGLAHLEARKYKLAARKFLEVGP 243 (441)
Q Consensus 220 ~~gl~~l~~r~y~~Aa~~Fl~~~~ 243 (441)
..|..+...|+|..|...|-.+..
T Consensus 90 ~la~~~~~~g~~~~A~~~~~~al~ 113 (135)
T TIGR02552 90 HAAECLLALGEPESALKALDLAIE 113 (135)
T ss_pred HHHHHHHHcCCHHHHHHHHHHHHH
Confidence 578888899999999999887764
No 40
>PF03399 SAC3_GANP: SAC3/GANP/Nin1/mts3/eIF-3 p25 family; InterPro: IPR005062 This large family includes diverse proteins involved in large complexes [, , ]. The alignment contains one highly conserved negatively charged residue and one highly conserved positively charged residue that are probably important for the function of these proteins. The family includes the yeast nuclear export factor Sac3 [], and mammalian GANP/MCM3-associated proteins, which facilitate the nuclear localisation of MCM3, a protein that associates with chromatin in the G1 phase of the cell-cycle. The 26S protease (or 26S proteasome) is responsible for degrading ubiquitin conjugates. It consists of 19S regulatory complexes associated with the ends of 20S proteasomes. The 19S regulatory complex is composed of about 20 different polypeptides and confers ATP-dependence and substrate specificity to the 26S enzyme. The conserved region occurs at the C-terminal of the Nin1-like regulatory subunit [, , ]. This family includes several eukaryotic translation initiation factor 3 subunit 11 (eIF-3 p25) proteins. Eukaryotic initiation factor 3 (eIF3) is a multisubunit complex that is required for binding of mRNA to 40 S ribosomal subunits, stabilisation of ternary complex binding to 40 S subunits, and dissociation of 40 and 60 S subunits [].; PDB: 3T5V_D.
Probab=94.90 E-value=0.42 Score=44.23 Aligned_cols=64 Identities=17% Similarity=0.264 Sum_probs=48.2
Q ss_pred HHHHHHHhcCCHHHHHHHHHHhHHhhhhchhHHHHHH-HHHHHHHHHHHHHhcccccc-ccHHhHHHHcCC
Q 013559 296 RELINDFYSSRYASCLDYLGNLKANLLLDIHLHDHVE-TLYDQIRNKALIQYTHPFVS-VDLHMMANAFKT 364 (441)
Q Consensus 296 ~~ll~~f~~~~y~~~~~~L~~~~~~l~~D~~L~~h~~-~l~~~iR~~~i~qy~~pYs~-I~L~~mA~~fg~ 364 (441)
.++..++.+++|..|++.+.. ...+++..++- .++..+|.+++.....+|.+ |+++.+++.||.
T Consensus 139 l~l~~a~~~gny~~ff~l~~~-----~~~~~l~~~l~~~~~~~iR~~al~~i~~ay~~~i~l~~l~~~L~F 204 (204)
T PF03399_consen 139 LELCRALMEGNYVRFFRLYRS-----KSAPYLFACLMERFFNRIRLRALQSISKAYRSSIPLSFLAELLGF 204 (204)
T ss_dssp HHHHHHH--TTHHHHHHHHT------TTS-HHHHHHHGGGHHHHHHHHHHHHHHHS-T-EEHHHHHHHTT-
T ss_pred HHHHHHHHcCCHHHHHHHHhc-----cCCChHHHHHHHHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHcCC
Confidence 466788999999999988822 24455555544 59999999999999999999 999999998873
No 41
>KOG0548 consensus Molecular co-chaperone STI1 [Posttranslational modification, protein turnover, chaperones]
Probab=94.87 E-value=2.5 Score=44.56 Aligned_cols=142 Identities=16% Similarity=0.215 Sum_probs=94.5
Q ss_pred hHHHHHHHHcCCHHHHHHHHHHHHhhhcCchhHHHHHHHHHHHHHHhcCHHHHHhHHHHHhcccccCChhhhhhHHHHHH
Q 013559 143 NDFGDFYYAHGALGDAFKSYVRTRDYCTTSKHIIHMCMSAILVSIEMGQFTHVTSYVSKAEQTPEALEPVTIAKLRCAAG 222 (441)
Q Consensus 143 ~~la~~~~~~Gd~~~A~~~~~~~r~~~~~~~~~~~~~l~~i~~~i~~~~~~~~~~~~~ka~~~~~~~d~~~~~~l~~~~g 222 (441)
...|.=+++.|||.+|.+.|.++...-.+. --.+-+-..|.+-+|++..+.....++..+-. +| . +-....|
T Consensus 362 r~kGne~Fk~gdy~~Av~~YteAIkr~P~D---a~lYsNRAac~~kL~~~~~aL~Da~~~ieL~p--~~-~--kgy~RKg 433 (539)
T KOG0548|consen 362 REKGNEAFKKGDYPEAVKHYTEAIKRDPED---ARLYSNRAACYLKLGEYPEALKDAKKCIELDP--NF-I--KAYLRKG 433 (539)
T ss_pred HHHHHHHHhccCHHHHHHHHHHHHhcCCch---hHHHHHHHHHHHHHhhHHHHHHHHHHHHhcCc--hH-H--HHHHHHH
Confidence 345899999999999999999975543221 12334566677888999999988777766521 22 2 3334468
Q ss_pred HHhcccccHHHHHHHHHhcCcCCCCCchhhhcHHHHHHHHHHHHHh---cCChHHHHHhcccCHhhHhhhccchHHHHHH
Q 013559 223 LAHLEARKYKLAARKFLEVGPDLGNSYNEVIAAQDVATYGGLCALA---SFDRAELKSKVIDNVNFRNFLELVPEVRELI 299 (441)
Q Consensus 223 l~~l~~r~y~~Aa~~Fl~~~~t~~~~~~el~s~~d~~~Y~~l~al~---s~~R~eLk~~vl~~~~~~~~le~~p~~~~ll 299 (441)
.++...++|..|.+.|.+...--.+ ..+++ ..| .=|.-+ ..+..+++.+...+|+++.++ +.|.++-++
T Consensus 434 ~al~~mk~ydkAleay~eale~dp~-~~e~~-----~~~-~rc~~a~~~~~~~ee~~~r~~~dpev~~il-~d~~m~~~l 505 (539)
T KOG0548|consen 434 AALRAMKEYDKALEAYQEALELDPS-NAEAI-----DGY-RRCVEAQRGDETPEETKRRAMADPEVQAIL-QDPAMRQIL 505 (539)
T ss_pred HHHHHHHHHHHHHHHHHHHHhcCch-hHHHH-----HHH-HHHHHHhhcCCCHHHHHHhhccCHHHHHHH-cCHHHHHHH
Confidence 8999999999999999988642111 22322 122 223343 345678888888888888876 556666433
Q ss_pred H
Q 013559 300 N 300 (441)
Q Consensus 300 ~ 300 (441)
.
T Consensus 506 ~ 506 (539)
T KOG0548|consen 506 E 506 (539)
T ss_pred H
Confidence 3
No 42
>PF12895 Apc3: Anaphase-promoting complex, cyclosome, subunit 3; PDB: 3KAE_D 3Q4A_B 2C2L_D 3Q47_B 3Q49_B 2XPI_A 3ULQ_A.
Probab=94.73 E-value=0.18 Score=39.58 Aligned_cols=81 Identities=14% Similarity=0.180 Sum_probs=42.9
Q ss_pred cCCHHHHHHHHHHHHhhhcCchhHHHHHHHHHHHHHHhcCHHHHHhHHHHHhcccccCChhhhhhHHHHHHHHhcccccH
Q 013559 152 HGALGDAFKSYVRTRDYCTTSKHIIHMCMSAILVSIEMGQFTHVTSYVSKAEQTPEALEPVTIAKLRCAAGLAHLEARKY 231 (441)
Q Consensus 152 ~Gd~~~A~~~~~~~r~~~~~~~~~~~~~l~~i~~~i~~~~~~~~~~~~~ka~~~~~~~d~~~~~~l~~~~gl~~l~~r~y 231 (441)
.|+|++|+..+.++.+...+.. .....+.+..+....|+|..+...+.+.+. +..+ .......|..++..|+|
T Consensus 2 ~~~y~~Ai~~~~k~~~~~~~~~-~~~~~~~la~~~~~~~~y~~A~~~~~~~~~--~~~~----~~~~~l~a~~~~~l~~y 74 (84)
T PF12895_consen 2 QGNYENAIKYYEKLLELDPTNP-NSAYLYNLAQCYFQQGKYEEAIELLQKLKL--DPSN----PDIHYLLARCLLKLGKY 74 (84)
T ss_dssp TT-HHHHHHHHHHHHHHHCGTH-HHHHHHHHHHHHHHTTHHHHHHHHHHCHTH--HHCH----HHHHHHHHHHHHHTT-H
T ss_pred CccHHHHHHHHHHHHHHCCCCh-hHHHHHHHHHHHHHCCCHHHHHHHHHHhCC--CCCC----HHHHHHHHHHHHHhCCH
Confidence 4667777777776655543221 334455566666667777777666655111 1101 12223346666677777
Q ss_pred HHHHHHHH
Q 013559 232 KLAARKFL 239 (441)
Q Consensus 232 ~~Aa~~Fl 239 (441)
.+|.+.|-
T Consensus 75 ~eAi~~l~ 82 (84)
T PF12895_consen 75 EEAIKALE 82 (84)
T ss_dssp HHHHHHHH
T ss_pred HHHHHHHh
Confidence 77766653
No 43
>PF13432 TPR_16: Tetratricopeptide repeat; PDB: 3CVP_A 3CVL_A 3CVQ_A 3CV0_A 2GW1_B 3CVN_A 3QKY_A 2PL2_B.
Probab=94.66 E-value=0.16 Score=37.59 Aligned_cols=59 Identities=10% Similarity=0.160 Sum_probs=48.6
Q ss_pred hHHHHHHHHcCCHHHHHHHHHHHHhhhcCchhHHHHHHHHHHHHHHhcCHHHHHhHHHHHhc
Q 013559 143 NDFGDFYYAHGALGDAFKSYVRTRDYCTTSKHIIHMCMSAILVSIEMGQFTHVTSYVSKAEQ 204 (441)
Q Consensus 143 ~~la~~~~~~Gd~~~A~~~~~~~r~~~~~~~~~~~~~l~~i~~~i~~~~~~~~~~~~~ka~~ 204 (441)
+.+|..+++.|++++|.++|.++..... .-.+..+....+....|+++.+...+.++-.
T Consensus 1 ~~~a~~~~~~g~~~~A~~~~~~~l~~~P---~~~~a~~~lg~~~~~~g~~~~A~~~~~~a~~ 59 (65)
T PF13432_consen 1 YALARALYQQGDYDEAIAAFEQALKQDP---DNPEAWYLLGRILYQQGRYDEALAYYERALE 59 (65)
T ss_dssp HHHHHHHHHCTHHHHHHHHHHHHHCCST---THHHHHHHHHHHHHHTT-HHHHHHHHHHHHH
T ss_pred ChHHHHHHHcCCHHHHHHHHHHHHHHCC---CCHHHHHHHHHHHHHcCCHHHHHHHHHHHHH
Confidence 4689999999999999999999876642 3577888888899999999999988888743
No 44
>PRK02603 photosystem I assembly protein Ycf3; Provisional
Probab=94.65 E-value=0.4 Score=43.14 Aligned_cols=67 Identities=13% Similarity=0.132 Sum_probs=54.4
Q ss_pred HhHHhHHHHHHHHcCCHHHHHHHHHHHHhhhcCchhHHHHHHHHHHHHHHhcCHHHHHhHHHHHhcc
Q 013559 139 RMGYNDFGDFYYAHGALGDAFKSYVRTRDYCTTSKHIIHMCMSAILVSIEMGQFTHVTSYVSKAEQT 205 (441)
Q Consensus 139 r~~~~~la~~~~~~Gd~~~A~~~~~~~r~~~~~~~~~~~~~l~~i~~~i~~~~~~~~~~~~~ka~~~ 205 (441)
...++.+|..+...|++++|..+|.+.......+......+..+..+....|+++.+...+.++-..
T Consensus 35 a~~~~~lg~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~ 101 (172)
T PRK02603 35 AFVYYRDGMSAQADGEYAEALENYEEALKLEEDPNDRSYILYNMGIIYASNGEHDKALEYYHQALEL 101 (172)
T ss_pred HHHHHHHHHHHHHcCCHHHHHHHHHHHHHHhhccchHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHh
Confidence 3478999999999999999999999986654433334566777778888899999999999888764
No 45
>CHL00033 ycf3 photosystem I assembly protein Ycf3
Probab=94.47 E-value=0.57 Score=41.84 Aligned_cols=104 Identities=14% Similarity=0.116 Sum_probs=73.0
Q ss_pred HhHHhHHHHHHHHcCCHHHHHHHHHHHHhhhcCchhHHHHHHHHHHHHHHhcCHHHHHhHHHHHhcccc--cCChhhhhh
Q 013559 139 RMGYNDFGDFYYAHGALGDAFKSYVRTRDYCTTSKHIIHMCMSAILVSIEMGQFTHVTSYVSKAEQTPE--ALEPVTIAK 216 (441)
Q Consensus 139 r~~~~~la~~~~~~Gd~~~A~~~~~~~r~~~~~~~~~~~~~l~~i~~~i~~~~~~~~~~~~~ka~~~~~--~~d~~~~~~ 216 (441)
...++.+|..+...|++++|...|.+.......+........++..+....|+++.+...+.++-.... ...+.....
T Consensus 35 a~~~~~~g~~~~~~g~~~~A~~~~~~al~l~~~~~~~~~~~~~lg~~~~~~g~~~eA~~~~~~Al~~~~~~~~~~~~la~ 114 (168)
T CHL00033 35 AFTYYRDGMSAQSEGEYAEALQNYYEAMRLEIDPYDRSYILYNIGLIHTSNGEHTKALEYYFQALERNPFLPQALNNMAV 114 (168)
T ss_pred HHHHHHHHHHHHHcCCHHHHHHHHHHHHhccccchhhHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCcCcHHHHHHHHH
Confidence 457789999999999999999999998766444333444666777778889999999999999876533 112223333
Q ss_pred HHHHHHHHhcccccHHHHHHHHHhcC
Q 013559 217 LRCAAGLAHLEARKYKLAARKFLEVG 242 (441)
Q Consensus 217 l~~~~gl~~l~~r~y~~Aa~~Fl~~~ 242 (441)
+....|......|+|..|...|-++.
T Consensus 115 i~~~~~~~~~~~g~~~~A~~~~~~a~ 140 (168)
T CHL00033 115 ICHYRGEQAIEQGDSEIAEAWFDQAA 140 (168)
T ss_pred HHHHhhHHHHHcccHHHHHHHHHHHH
Confidence 44444555567888877666665543
No 46
>KOG3677 consensus RNA polymerase I-associated factor - PAF67 [Translation, ribosomal structure and biogenesis; Transcription]
Probab=94.42 E-value=0.61 Score=47.60 Aligned_cols=236 Identities=13% Similarity=0.149 Sum_probs=125.5
Q ss_pred HHHHHHHHHHHhcCHHHHHhHHHHHhcccccCChhhhhhHHHHHHHHhcccccHHHHHHHHHhcCcCC---------CCC
Q 013559 178 MCMSAILVSIEMGQFTHVTSYVSKAEQTPEALEPVTIAKLRCAAGLAHLEARKYKLAARKFLEVGPDL---------GNS 248 (441)
Q Consensus 178 ~~l~~i~~~i~~~~~~~~~~~~~ka~~~~~~~d~~~~~~l~~~~gl~~l~~r~y~~Aa~~Fl~~~~t~---------~~~ 248 (441)
.++|++|+.++.||+-.+...+.--..-+-+..|..+.. .+-|.++|..|+|.+|.+.|+++.... .+.
T Consensus 237 sL~GLlR~H~lLgDhQat~q~idi~pk~iy~t~p~c~VT--Y~VGFayLmmrryadai~~F~niLlyIqrtks~~~~~~y 314 (525)
T KOG3677|consen 237 SLLGLLRMHILLGDHQATSQILDIMPKEIYGTEPMCRVT--YQVGFAYLMMRRYADAIRVFLNILLYIQRTKSMFSRTTY 314 (525)
T ss_pred HHHHHHHHHHHhhhhHhhhhhhhcCchhhcCcccceeEe--eehhHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhcchhh
Confidence 568999999999995554433332222222334444444 567999999999999999999876421 111
Q ss_pred chhhhcHHHHHHHHHHH-HHhcCChHHHHHhcccCHhhHhhhccc---hH-------HHHHHHHH-hcC-CH-HHHHHHH
Q 013559 249 YNEVIAAQDVATYGGLC-ALASFDRAELKSKVIDNVNFRNFLELV---PE-------VRELINDF-YSS-RY-ASCLDYL 314 (441)
Q Consensus 249 ~~el~s~~d~~~Y~~l~-al~s~~R~eLk~~vl~~~~~~~~le~~---p~-------~~~ll~~f-~~~-~y-~~~~~~L 314 (441)
+.+.++...=-.+-.++ +++.-+ ..++ ..+..++.+. |- ...+=+.| |.| .| ..+...+
T Consensus 315 ~~d~inKq~eqm~~llai~l~~yP--q~iD-----ESi~s~l~Ek~~d~ml~mqng~~q~~ks~f~y~cpkflsp~~~~~ 387 (525)
T KOG3677|consen 315 QYDMINKQNEQMHHLLAICLSMYP--QMID-----ESIHSQLAEKYGDKMLPMQNGDPQVFKSLFSYLCPKFLSPVVPNY 387 (525)
T ss_pred hHhhhhhhHHHHHHHHHHHHHhCc--hhhh-----HHHHHHHHHHhcchhhhhhcCChHHHHHHHHHcCccccCCCCccc
Confidence 22333222212232221 122222 1111 2222222110 00 01111111 122 11 2222333
Q ss_pred HHhHHhhhhchhHHHHHHHHHHHHH----HHHHHHhccccccccHHhHHHHcCCChHHHHHHHHHHHH-----------c
Q 013559 315 GNLKANLLLDIHLHDHVETLYDQIR----NKALIQYTHPFVSVDLHMMANAFKTSVAGIEKELEALIT-----------D 379 (441)
Q Consensus 315 ~~~~~~l~~D~~L~~h~~~l~~~iR----~~~i~qy~~pYs~I~L~~mA~~fg~s~~~~E~~L~~LI~-----------~ 379 (441)
+..-+.+..+|+++. ...|...++ .-.+.+|++-|+......+|.-++++.++=++-++.|+. +
T Consensus 388 dgv~~~y~kePl~~q-lq~fld~v~qq~dl~~~rsylklyTt~P~kkla~F~D~~d~~~dk~li~Ll~~khkm~nlv~~s 466 (525)
T KOG3677|consen 388 DGVLPNYHKEPLLQQ-LQVFLDEVSQQADLPTIRSYLKLYTTLPVKKLASFLDLTDQERDKFLIQLLVFKHKMKNLVWTS 466 (525)
T ss_pred ccccccccccHHHHH-HHHHhHHHhhhccchHHHHHHHHHHhccHHHhhhccCCchhhhhhhHHHHHHHHHHHHHHHHhc
Confidence 333444556776654 334444444 456788999999999999999999998887788888774 5
Q ss_pred CccceEecCCCC-eEEEecCCchhHH-HHH-HHHHHhhHHHHHHHHH
Q 013559 380 NQIQARIDSHNK-ILYARHADQRNAT-FQR-VLQTGSEFDQDVRAML 423 (441)
Q Consensus 380 g~L~akID~~~g-vv~~~~~d~r~~~-~~~-~i~~~~~~~~~~~~l~ 423 (441)
|..+.+++...+ .|-+.-.+..... -++ +=+.|+.+.+.+++..
T Consensus 467 g~s~~d~~f~~~s~idfyid~dmi~iaDtkv~r~~gd~fir~i~kf~ 513 (525)
T KOG3677|consen 467 GPSDLDDAFFSRSEIDFYIDKDMIHIADTKVARRYGDIFIRQIHKFE 513 (525)
T ss_pred CCccccccccCcceeeEEechhHHHHHhHHHHHHHHHHHHHHHHHHH
Confidence 666777774443 4444433222111 122 2345666666666554
No 47
>PF13176 TPR_7: Tetratricopeptide repeat; PDB: 3SF4_C 3RO3_A 3RO2_A.
Probab=94.41 E-value=0.066 Score=35.24 Aligned_cols=30 Identities=20% Similarity=0.416 Sum_probs=24.3
Q ss_pred HHhHHHHHHHHcCCHHHHHHHHHHHHhhhc
Q 013559 141 GYNDFGDFYYAHGALGDAFKSYVRTRDYCT 170 (441)
Q Consensus 141 ~~~~la~~~~~~Gd~~~A~~~~~~~r~~~~ 170 (441)
++..||++|.+.|++++|.++|.+......
T Consensus 1 al~~Lg~~~~~~g~~~~Ai~~y~~aL~l~~ 30 (36)
T PF13176_consen 1 ALNNLGRIYRQQGDYEKAIEYYEQALALAR 30 (36)
T ss_dssp HHHHHHHHHHHCT-HHHHHHHHHHHHHHHH
T ss_pred CHHHHHHHHHHcCCHHHHHHHHHHHHHhcc
Confidence 467899999999999999999999654443
No 48
>PF08220 HTH_DeoR: DeoR-like helix-turn-helix domain; InterPro: IPR001034 The deoR-type HTH domain is a DNA-binding, helix-turn-helix (HTH) domain of about 50-60 amino acids present in transcription regulators of the deoR family, involved in sugar catabolism. This family of prokaryotic regulators is named after the Escherichia coli protein DeoR, a repressor of the deo operon, which encodes nucleotide and deoxyribonucleotide catabolic enzymes. DeoR also negatively regulates the expression of nupG and tsx, a nucleoside-specific transport protein and a channel-forming protein, respectively. DeoR-like transcription repressors occur in diverse bacteria as regulators of sugar and nucleoside metabolic systems. The effector molecules for deoR-like regulators are generally phosphorylated intermediates of the relevant metabolic pathway. The DNA-binding deoR-type HTH domain occurs usually in the N-terminal part. The C-terminal part can contain an effector-binding domain and/or an oligomerisation domain. DeoR occurs as an octamer, whilst glpR and agaR are tetramers. Several operators may be bound simultaneously, which could facilitate DNA looping [, ].; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular
Probab=94.26 E-value=0.07 Score=39.23 Aligned_cols=44 Identities=20% Similarity=0.308 Sum_probs=40.2
Q ss_pred HHHHHHHhccccccccHHhHHHHcCCChHHHHHHHHHHHHcCcc
Q 013559 339 RNKALIQYTHPFVSVDLHMMANAFKTSVAGIEKELEALITDNQI 382 (441)
Q Consensus 339 R~~~i~qy~~pYs~I~L~~mA~~fg~s~~~~E~~L~~LI~~g~L 382 (441)
|...|.+|+.....++++.+|+.||+|...+-+.|..|-..|.+
T Consensus 1 R~~~Il~~l~~~~~~s~~ela~~~~VS~~TiRRDl~~L~~~g~i 44 (57)
T PF08220_consen 1 RQQQILELLKEKGKVSVKELAEEFGVSEMTIRRDLNKLEKQGLI 44 (57)
T ss_pred CHHHHHHHHHHcCCEEHHHHHHHHCcCHHHHHHHHHHHHHCCCE
Confidence 45677888899999999999999999999999999999999974
No 49
>PRK15363 pathogenicity island 2 chaperone protein SscA; Provisional
Probab=94.23 E-value=0.75 Score=41.11 Aligned_cols=102 Identities=10% Similarity=-0.051 Sum_probs=81.6
Q ss_pred hH-HHHHhHHhHHHHHHHHcCCHHHHHHHHHHHHhhhcCchhHHHHHHHHHHHHHHhcCHHHHHhHHHHHhcccccCChh
Q 013559 134 IK-ESIRMGYNDFGDFYYAHGALGDAFKSYVRTRDYCTTSKHIIHMCMSAILVSIEMGQFTHVTSYVSKAEQTPEALEPV 212 (441)
Q Consensus 134 ~~-esir~~~~~la~~~~~~Gd~~~A~~~~~~~r~~~~~~~~~~~~~l~~i~~~i~~~~~~~~~~~~~ka~~~~~~~d~~ 212 (441)
+. ++..+..|.+|-.+++.|++++|.+.|.-+-.+- -.-.+.++++-.+.=..|+|..+.....++-.+-- .||
T Consensus 29 ~~~~~~l~~lY~~A~~ly~~G~l~~A~~~f~~L~~~D---p~~~~y~~gLG~~~Q~~g~~~~AI~aY~~A~~L~~-ddp- 103 (157)
T PRK15363 29 DDVTQPLNTLYRYAMQLMEVKEFAGAARLFQLLTIYD---AWSFDYWFRLGECCQAQKHWGEAIYAYGRAAQIKI-DAP- 103 (157)
T ss_pred CChHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhC---cccHHHHHHHHHHHHHHhhHHHHHHHHHHHHhcCC-CCc-
Confidence 44 6677899999999999999999999998764442 23467788888888899999999999988876532 243
Q ss_pred hhhhHHHHHHHHhcccccHHHHHHHHHhcCc
Q 013559 213 TIAKLRCAAGLAHLEARKYKLAARKFLEVGP 243 (441)
Q Consensus 213 ~~~~l~~~~gl~~l~~r~y~~Aa~~Fl~~~~ 243 (441)
+...+.|..++.-|+-..|...|-.++.
T Consensus 104 ---~~~~~ag~c~L~lG~~~~A~~aF~~Ai~ 131 (157)
T PRK15363 104 ---QAPWAAAECYLACDNVCYAIKALKAVVR 131 (157)
T ss_pred ---hHHHHHHHHHHHcCCHHHHHHHHHHHHH
Confidence 2346789999999999999999988764
No 50
>TIGR02521 type_IV_pilW type IV pilus biogenesis/stability protein PilW. Members of this family are designated PilF in ref (PubMed:8973346) and PilW in ref (PubMed:15612916). This outer membrane protein is required both for pilus stability and for pilus function such as adherence to human cells. Members of this family contain copies of the TPR (tetratricopeptide repeat) domain.
Probab=94.05 E-value=1.2 Score=40.36 Aligned_cols=98 Identities=16% Similarity=0.172 Sum_probs=71.3
Q ss_pred hHHhHHHHHHHHcCCHHHHHHHHHHHHhhhcCchhHHHHHHHHHHHHHHhcCHHHHHhHHHHHhcccc-cCChhhhhhHH
Q 013559 140 MGYNDFGDFYYAHGALGDAFKSYVRTRDYCTTSKHIIHMCMSAILVSIEMGQFTHVTSYVSKAEQTPE-ALEPVTIAKLR 218 (441)
Q Consensus 140 ~~~~~la~~~~~~Gd~~~A~~~~~~~r~~~~~~~~~~~~~l~~i~~~i~~~~~~~~~~~~~ka~~~~~-~~d~~~~~~l~ 218 (441)
.++..+|..+...|++++|.+.|.+..+..... .........+....|+++.+...+.++..... ...+ ...
T Consensus 66 ~~~~~la~~~~~~~~~~~A~~~~~~al~~~~~~---~~~~~~~~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~----~~~ 138 (234)
T TIGR02521 66 LAYLALALYYQQLGELEKAEDSFRRALTLNPNN---GDVLNNYGTFLCQQGKYEQAMQQFEQAIEDPLYPQPA----RSL 138 (234)
T ss_pred HHHHHHHHHHHHcCCHHHHHHHHHHHHhhCCCC---HHHHHHHHHHHHHcccHHHHHHHHHHHHhccccccch----HHH
Confidence 477788999999999999999999887765432 23455566677888999999999888876433 1121 122
Q ss_pred HHHHHHhcccccHHHHHHHHHhcCcC
Q 013559 219 CAAGLAHLEARKYKLAARKFLEVGPD 244 (441)
Q Consensus 219 ~~~gl~~l~~r~y~~Aa~~Fl~~~~t 244 (441)
..-|..+...|++..|...|-.+...
T Consensus 139 ~~l~~~~~~~g~~~~A~~~~~~~~~~ 164 (234)
T TIGR02521 139 ENAGLCALKAGDFDKAEKYLTRALQI 164 (234)
T ss_pred HHHHHHHHHcCCHHHHHHHHHHHHHh
Confidence 33477788899999999988887653
No 51
>TIGR00990 3a0801s09 mitochondrial precursor proteins import receptor (72 kDa mitochondrial outermembrane protein) (mitochondrial import receptor for the ADP/ATP carrier) (translocase of outermembrane tom70).
Probab=93.98 E-value=7.9 Score=42.23 Aligned_cols=62 Identities=10% Similarity=0.114 Sum_probs=36.7
Q ss_pred hHHhHHHHHHHHcCCHHHHHHHHHHHHhhhcCchhHHHHHHHHHHHHHHhcCHHHHHhHHHHHhc
Q 013559 140 MGYNDFGDFYYAHGALGDAFKSYVRTRDYCTTSKHIIHMCMSAILVSIEMGQFTHVTSYVSKAEQ 204 (441)
Q Consensus 140 ~~~~~la~~~~~~Gd~~~A~~~~~~~r~~~~~~~~~~~~~l~~i~~~i~~~~~~~~~~~~~ka~~ 204 (441)
.++..+|..+...|++++|..+|.+..+... .+ .+.......+....|+|+.+...+.++-.
T Consensus 366 ~~~~~la~~~~~~g~~~eA~~~~~~al~~~p--~~-~~~~~~lg~~~~~~g~~~~A~~~~~kal~ 427 (615)
T TIGR00990 366 QSYIKRASMNLELGDPDKAEEDFDKALKLNS--ED-PDIYYHRAQLHFIKGEFAQAGKDYQKSID 427 (615)
T ss_pred HHHHHHHHHHHHCCCHHHHHHHHHHHHHhCC--CC-HHHHHHHHHHHHHcCCHHHHHHHHHHHHH
Confidence 4566667777777777777777666644422 11 34444555555666666666666666644
No 52
>PF12895 Apc3: Anaphase-promoting complex, cyclosome, subunit 3; PDB: 3KAE_D 3Q4A_B 2C2L_D 3Q47_B 3Q49_B 2XPI_A 3ULQ_A.
Probab=93.95 E-value=0.16 Score=39.87 Aligned_cols=58 Identities=10% Similarity=0.195 Sum_probs=45.3
Q ss_pred HHhHHHHHHHHcCCHHHHHHHHHHHHhhhcCchhHHHHHHHHHHHHHHhcCHHHHHhHHHHH
Q 013559 141 GYNDFGDFYYAHGALGDAFKSYVRTRDYCTTSKHIIHMCMSAILVSIEMGQFTHVTSYVSKA 202 (441)
Q Consensus 141 ~~~~la~~~~~~Gd~~~A~~~~~~~r~~~~~~~~~~~~~l~~i~~~i~~~~~~~~~~~~~ka 202 (441)
..+.+|..|++.|+|.+|.+.+.+ .... ++ ..+..+...++.+..|+|+.+.+.+.++
T Consensus 27 ~~~~la~~~~~~~~y~~A~~~~~~-~~~~--~~-~~~~~~l~a~~~~~l~~y~eAi~~l~~~ 84 (84)
T PF12895_consen 27 YLYNLAQCYFQQGKYEEAIELLQK-LKLD--PS-NPDIHYLLARCLLKLGKYEEAIKALEKA 84 (84)
T ss_dssp HHHHHHHHHHHTTHHHHHHHHHHC-HTHH--HC-HHHHHHHHHHHHHHTT-HHHHHHHHHHH
T ss_pred HHHHHHHHHHHCCCHHHHHHHHHH-hCCC--CC-CHHHHHHHHHHHHHhCCHHHHHHHHhcC
Confidence 456789999999999999999988 2222 12 2566666789999999999999988875
No 53
>TIGR03302 OM_YfiO outer membrane assembly lipoprotein YfiO. Members of this protein family include YfiO, a near-essential protein of the outer membrane, part of a complex involved in protein insertion into the bacterial outer membrane. Many proteins in this family are annotated as ComL, based on the involvement of this protein in natural transformation with exogenous DNA in Neisseria gonorrhoeae. This protein family shows sequence similarity to, but is distinct from, the tol-pal system protein YbgF (TIGR02795).
Probab=93.94 E-value=0.59 Score=43.89 Aligned_cols=109 Identities=13% Similarity=0.065 Sum_probs=70.9
Q ss_pred HHhHHhHHHHHHHHcCCHHHHHHHHHHHHhhhcCchhHHHHHHHHHHHHHHh--------cCHHHHHhHHHHHhcc-ccc
Q 013559 138 IRMGYNDFGDFYYAHGALGDAFKSYVRTRDYCTTSKHIIHMCMSAILVSIEM--------GQFTHVTSYVSKAEQT-PEA 208 (441)
Q Consensus 138 ir~~~~~la~~~~~~Gd~~~A~~~~~~~r~~~~~~~~~~~~~l~~i~~~i~~--------~~~~~~~~~~~ka~~~-~~~ 208 (441)
...+++.+|..|+..|++++|.+.|.++.....+........+....+.... |++..+...+.++-.. ++.
T Consensus 69 ~~~a~~~la~~~~~~~~~~~A~~~~~~~l~~~p~~~~~~~a~~~~g~~~~~~~~~~~~~~~~~~~A~~~~~~~~~~~p~~ 148 (235)
T TIGR03302 69 AEQAQLDLAYAYYKSGDYAEAIAAADRFIRLHPNHPDADYAYYLRGLSNYNQIDRVDRDQTAAREAFEAFQELIRRYPNS 148 (235)
T ss_pred HHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHCcCCCchHHHHHHHHHHHHHhcccccCCHHHHHHHHHHHHHHHHHCCCC
Confidence 4467899999999999999999999999777665454333333333333322 6777888877776442 331
Q ss_pred C-ChhhhhhH----------HHHHHHHhcccccHHHHHHHHHhcCcCCC
Q 013559 209 L-EPVTIAKL----------RCAAGLAHLEARKYKLAARKFLEVGPDLG 246 (441)
Q Consensus 209 ~-d~~~~~~l----------~~~~gl~~l~~r~y~~Aa~~Fl~~~~t~~ 246 (441)
. .+.....+ ....|.+++..|+|..|...|-.+...++
T Consensus 149 ~~~~~a~~~~~~~~~~~~~~~~~~a~~~~~~g~~~~A~~~~~~al~~~p 197 (235)
T TIGR03302 149 EYAPDAKKRMDYLRNRLAGKELYVARFYLKRGAYVAAINRFETVVENYP 197 (235)
T ss_pred hhHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCChHHHHHHHHHHHHHCC
Confidence 1 11111111 12356677889999999998888876554
No 54
>PRK15331 chaperone protein SicA; Provisional
Probab=93.92 E-value=0.96 Score=40.73 Aligned_cols=104 Identities=18% Similarity=0.056 Sum_probs=81.7
Q ss_pred hhhHHHHHhHHhHHHHHHHHcCCHHHHHHHHHHHHhhhcCchhHHHHHHHHHHHHHHhcCHHHHHhHHHHHhcccccCCh
Q 013559 132 NLIKESIRMGYNDFGDFYYAHGALGDAFKSYVRTRDYCTTSKHIIHMCMSAILVSIEMGQFTHVTSYVSKAEQTPEALEP 211 (441)
Q Consensus 132 n~~~esir~~~~~la~~~~~~Gd~~~A~~~~~~~r~~~~~~~~~~~~~l~~i~~~i~~~~~~~~~~~~~ka~~~~~~~d~ 211 (441)
..+.++...+.+..|--+|..|++.+|.+.|.-+.-+-... -+.++++..|.=..++|..|.....-+-.+- ..||
T Consensus 30 ~gis~~~le~iY~~Ay~~y~~Gk~~eA~~~F~~L~~~d~~n---~~Y~~GLaa~~Q~~k~y~~Ai~~Y~~A~~l~-~~dp 105 (165)
T PRK15331 30 HGIPQDMMDGLYAHAYEFYNQGRLDEAETFFRFLCIYDFYN---PDYTMGLAAVCQLKKQFQKACDLYAVAFTLL-KNDY 105 (165)
T ss_pred hCCCHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhCcCc---HHHHHHHHHHHHHHHHHHHHHHHHHHHHHcc-cCCC
Confidence 44677888899999999999999999999998764442222 4567899999999999999998777765542 2333
Q ss_pred hhhhhHHHHHHHHhcccccHHHHHHHHHhcCc
Q 013559 212 VTIAKLRCAAGLAHLEARKYKLAARKFLEVGP 243 (441)
Q Consensus 212 ~~~~~l~~~~gl~~l~~r~y~~Aa~~Fl~~~~ 243 (441)
. --.+.|..++..|+-..|...|-.+..
T Consensus 106 ~----p~f~agqC~l~l~~~~~A~~~f~~a~~ 133 (165)
T PRK15331 106 R----PVFFTGQCQLLMRKAAKARQCFELVNE 133 (165)
T ss_pred C----ccchHHHHHHHhCCHHHHHHHHHHHHh
Confidence 2 136789999999999999999988875
No 55
>COG3063 PilF Tfp pilus assembly protein PilF [Cell motility and secretion / Intracellular trafficking and secretion]
Probab=93.89 E-value=3.8 Score=38.93 Aligned_cols=161 Identities=17% Similarity=0.136 Sum_probs=98.4
Q ss_pred HHhHHhHHHHHHHHcCCHHHHHHHHHHHHhhhcCchhHHHHHHHHHHHHHHhcCHHHHHhHHHHHhccc-ccCChhhhhh
Q 013559 138 IRMGYNDFGDFYYAHGALGDAFKSYVRTRDYCTTSKHIIHMCMSAILVSIEMGQFTHVTSYVSKAEQTP-EALEPVTIAK 216 (441)
Q Consensus 138 ir~~~~~la~~~~~~Gd~~~A~~~~~~~r~~~~~~~~~~~~~l~~i~~~i~~~~~~~~~~~~~ka~~~~-~~~d~~~~~~ 216 (441)
...++..||-=|++.||+..|.+.+.+..+.-. + .....+...-+.--.|+.+++.....||-++- ..+| +.|
T Consensus 34 aa~arlqLal~YL~~gd~~~A~~nlekAL~~DP--s-~~~a~~~~A~~Yq~~Ge~~~A~e~YrkAlsl~p~~Gd--VLN- 107 (250)
T COG3063 34 AAKARLQLALGYLQQGDYAQAKKNLEKALEHDP--S-YYLAHLVRAHYYQKLGENDLADESYRKALSLAPNNGD--VLN- 107 (250)
T ss_pred HHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhCc--c-cHHHHHHHHHHHHHcCChhhHHHHHHHHHhcCCCccc--hhh-
Confidence 344677889999999999999999998855422 1 22233333333445689999999999887653 3222 222
Q ss_pred HHHHHHHHhcccccHHHHHHHHHhcCcCCCCCchhhhcHHHHHHHHHHHHHh----cCChHHHHHhcccCHhhHhhhccc
Q 013559 217 LRCAAGLAHLEARKYKLAARKFLEVGPDLGNSYNEVIAAQDVATYGGLCALA----SFDRAELKSKVIDNVNFRNFLELV 292 (441)
Q Consensus 217 l~~~~gl~~l~~r~y~~Aa~~Fl~~~~t~~~~~~el~s~~d~~~Y~~l~al~----s~~R~eLk~~vl~~~~~~~~le~~ 292 (441)
= .|-+++.+|.|.+|-..|..+..... |++.- +.--=.++|++= ...+..++..+--+|+ ..
T Consensus 108 --N-YG~FLC~qg~~~eA~q~F~~Al~~P~--Y~~~s---~t~eN~G~Cal~~gq~~~A~~~l~raL~~dp~------~~ 173 (250)
T COG3063 108 --N-YGAFLCAQGRPEEAMQQFERALADPA--YGEPS---DTLENLGLCALKAGQFDQAEEYLKRALELDPQ------FP 173 (250)
T ss_pred --h-hhHHHHhCCChHHHHHHHHHHHhCCC--CCCcc---hhhhhhHHHHhhcCCchhHHHHHHHHHHhCcC------CC
Confidence 1 46678899999999999999986543 34332 222345789983 3334444443322221 11
Q ss_pred hHHHHHHHH-HhcCCHHHHHHHHHHhH
Q 013559 293 PEVRELIND-FYSSRYASCLDYLGNLK 318 (441)
Q Consensus 293 p~~~~ll~~-f~~~~y~~~~~~L~~~~ 318 (441)
|...++... |-.++|......++.+.
T Consensus 174 ~~~l~~a~~~~~~~~y~~Ar~~~~~~~ 200 (250)
T COG3063 174 PALLELARLHYKAGDYAPARLYLERYQ 200 (250)
T ss_pred hHHHHHHHHHHhcccchHHHHHHHHHH
Confidence 234444444 44678877766666553
No 56
>KOG2003 consensus TPR repeat-containing protein [General function prediction only]
Probab=93.79 E-value=7.8 Score=40.27 Aligned_cols=117 Identities=12% Similarity=0.073 Sum_probs=86.7
Q ss_pred HHHHHHHHHhhh-hHHHHHhHHhHHHHHHHHcCCHHHHHHHHHHHHhhhcCchhHHHHHHHHHHHHHHhcCHHHHHhHHH
Q 013559 122 LENELNAYRTNL-IKESIRMGYNDFGDFYYAHGALGDAFKSYVRTRDYCTTSKHIIHMCMSAILVSIEMGQFTHVTSYVS 200 (441)
Q Consensus 122 Le~el~~~~~n~-~~esir~~~~~la~~~~~~Gd~~~A~~~~~~~r~~~~~~~~~~~~~l~~i~~~i~~~~~~~~~~~~~ 200 (441)
|+..++.|++-+ .+.|...+++..|--+...|++++|++||.+++.-.-. -.+++..+..+.=.+.|-..+.+.+.
T Consensus 506 ~dka~~~ykeal~ndasc~ealfniglt~e~~~~ldeald~f~klh~il~n---n~evl~qianiye~led~aqaie~~~ 582 (840)
T KOG2003|consen 506 LDKAAEFYKEALNNDASCTEALFNIGLTAEALGNLDEALDCFLKLHAILLN---NAEVLVQIANIYELLEDPAQAIELLM 582 (840)
T ss_pred HHHHHHHHHHHHcCchHHHHHHHHhcccHHHhcCHHHHHHHHHHHHHHHHh---hHHHHHHHHHHHHHhhCHHHHHHHHH
Confidence 556666666554 33566779999999999999999999999998665432 24455555556666678888888888
Q ss_pred HHhcccccCChhhhhhHHHHHHHHhcccccHHHHHHHHHhcCcCCC
Q 013559 201 KAEQTPEALEPVTIAKLRCAAGLAHLEARKYKLAARKFLEVGPDLG 246 (441)
Q Consensus 201 ka~~~~~~~d~~~~~~l~~~~gl~~l~~r~y~~Aa~~Fl~~~~t~~ 246 (441)
.+.+++- .||.+..+|.- .+-..|+-..|.++.++..--|+
T Consensus 583 q~~slip-~dp~ilskl~d----lydqegdksqafq~~ydsyryfp 623 (840)
T KOG2003|consen 583 QANSLIP-NDPAILSKLAD----LYDQEGDKSQAFQCHYDSYRYFP 623 (840)
T ss_pred HhcccCC-CCHHHHHHHHH----HhhcccchhhhhhhhhhcccccC
Confidence 8888664 47776655543 45678999999999999987775
No 57
>KOG1861 consensus Leucine permease transcriptional regulator [Transcription]
Probab=93.76 E-value=2.2 Score=44.31 Aligned_cols=67 Identities=10% Similarity=0.166 Sum_probs=51.8
Q ss_pred HHHHHHHHhcCCHHHHHHHHHHhHHhhhhchhHHHH-HHHHHHHHHHHHHHHhccccc-cccHHhHHHHcCCChHH
Q 013559 295 VRELINDFYSSRYASCLDYLGNLKANLLLDIHLHDH-VETLYDQIRNKALIQYTHPFV-SVDLHMMANAFKTSVAG 368 (441)
Q Consensus 295 ~~~ll~~f~~~~y~~~~~~L~~~~~~l~~D~~L~~h-~~~l~~~iR~~~i~qy~~pYs-~I~L~~mA~~fg~s~~~ 368 (441)
..++-.+...++|..||..-. .-+-+..| ++.|++..|.+++.-.|++|. +|+++.+++.|.+...+
T Consensus 426 AL~vR~A~~~GNY~kFFrLY~-------~AP~M~~yLmdlF~erER~~Al~ii~KsyrP~i~~~fi~~~laf~~~e 494 (540)
T KOG1861|consen 426 ALEVRSAVTLGNYHKFFRLYL-------TAPNMSGYLMDLFLERERKKALTIICKSYRPTITVDFIASELAFDSME 494 (540)
T ss_pred HHHHHHHHHhccHHHHHHHHh-------hcccchhHHHHHHHHHHHHHHHHHHHHHcCCCccHHHHhhhhhhchHH
Confidence 345666778899999986433 22333444 678889999999999999999 99999999999986543
No 58
>PRK11788 tetratricopeptide repeat protein; Provisional
Probab=93.71 E-value=3.5 Score=41.60 Aligned_cols=96 Identities=14% Similarity=0.042 Sum_probs=54.7
Q ss_pred HHhHHHHHHHHcCCHHHHHHHHHHHHhhhcCchhHHHHHHHHHHHHHHhcCHHHHHhHHHHHhcccccCChhhhhhHHHH
Q 013559 141 GYNDFGDFYYAHGALGDAFKSYVRTRDYCTTSKHIIHMCMSAILVSIEMGQFTHVTSYVSKAEQTPEALEPVTIAKLRCA 220 (441)
Q Consensus 141 ~~~~la~~~~~~Gd~~~A~~~~~~~r~~~~~~~~~~~~~l~~i~~~i~~~~~~~~~~~~~ka~~~~~~~d~~~~~~l~~~ 220 (441)
+++.+|..|.+.|++++|.+.+.++.+.. +....+....+..+....|+++.+...+.++...-. +.. ....
T Consensus 216 ~~~~la~~~~~~g~~~~A~~~~~~~~~~~--p~~~~~~~~~l~~~~~~~g~~~~A~~~l~~~~~~~p--~~~----~~~~ 287 (389)
T PRK11788 216 ASILLGDLALAQGDYAAAIEALERVEEQD--PEYLSEVLPKLMECYQALGDEAEGLEFLRRALEEYP--GAD----LLLA 287 (389)
T ss_pred HHHHHHHHHHHCCCHHHHHHHHHHHHHHC--hhhHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCC--Cch----HHHH
Confidence 55667777777777777777777665442 222233334445555666777777776666554311 111 1133
Q ss_pred HHHHhcccccHHHHHHHHHhcCcC
Q 013559 221 AGLAHLEARKYKLAARKFLEVGPD 244 (441)
Q Consensus 221 ~gl~~l~~r~y~~Aa~~Fl~~~~t 244 (441)
.|..+...|++.+|...|-++...
T Consensus 288 la~~~~~~g~~~~A~~~l~~~l~~ 311 (389)
T PRK11788 288 LAQLLEEQEGPEAAQALLREQLRR 311 (389)
T ss_pred HHHHHHHhCCHHHHHHHHHHHHHh
Confidence 455566677777777777666543
No 59
>PF13429 TPR_15: Tetratricopeptide repeat; PDB: 2VQ2_A 2PL2_B.
Probab=93.55 E-value=0.44 Score=46.30 Aligned_cols=99 Identities=13% Similarity=0.124 Sum_probs=71.0
Q ss_pred hHHhHHHHHHHHcCCHHHHHHHHHHHHhhhcCchhHHHHHHHHHHHHHHhcCHHHHHhHHHHHhcccccCChhhhhhHHH
Q 013559 140 MGYNDFGDFYYAHGALGDAFKSYVRTRDYCTTSKHIIHMCMSAILVSIEMGQFTHVTSYVSKAEQTPEALEPVTIAKLRC 219 (441)
Q Consensus 140 ~~~~~la~~~~~~Gd~~~A~~~~~~~r~~~~~~~~~~~~~l~~i~~~i~~~~~~~~~~~~~ka~~~~~~~d~~~~~~l~~ 219 (441)
..+..+|.++.+.|+..+|.++|.+..+....... +....+-+.|..|+...+...+.+...... .++.+ ..
T Consensus 147 ~~~~~~a~~~~~~G~~~~A~~~~~~al~~~P~~~~---~~~~l~~~li~~~~~~~~~~~l~~~~~~~~-~~~~~----~~ 218 (280)
T PF13429_consen 147 RFWLALAEIYEQLGDPDKALRDYRKALELDPDDPD---ARNALAWLLIDMGDYDEAREALKRLLKAAP-DDPDL----WD 218 (280)
T ss_dssp HHHHHHHHHHHHCCHHHHHHHHHHHHHHH-TT-HH---HHHHHHHHHCTTCHHHHHHHHHHHHHHH-H-TSCCH----CH
T ss_pred HHHHHHHHHHHHcCCHHHHHHHHHHHHHcCCCCHH---HHHHHHHHHHHCCChHHHHHHHHHHHHHCc-CHHHH----HH
Confidence 46789999999999999999999999877654333 233444556788999988888777766542 23332 23
Q ss_pred HHHHHhcccccHHHHHHHHHhcCcCCC
Q 013559 220 AAGLAHLEARKYKLAARKFLEVGPDLG 246 (441)
Q Consensus 220 ~~gl~~l~~r~y~~Aa~~Fl~~~~t~~ 246 (441)
.-|..++..|++.+|...|-.+....+
T Consensus 219 ~la~~~~~lg~~~~Al~~~~~~~~~~p 245 (280)
T PF13429_consen 219 ALAAAYLQLGRYEEALEYLEKALKLNP 245 (280)
T ss_dssp HHHHHHHHHT-HHHHHHHHHHHHHHST
T ss_pred HHHHHhccccccccccccccccccccc
Confidence 457788889999999999999875433
No 60
>PRK10803 tol-pal system protein YbgF; Provisional
Probab=93.26 E-value=0.41 Score=46.60 Aligned_cols=62 Identities=11% Similarity=0.134 Sum_probs=33.3
Q ss_pred HHhHHHHHHHHcCCHHHHHHHHHHHHhhhcCchhHHHHHHHHHHHHHHhcCHHHHHhHHHHH
Q 013559 141 GYNDFGDFYYAHGALGDAFKSYVRTRDYCTTSKHIIHMCMSAILVSIEMGQFTHVTSYVSKA 202 (441)
Q Consensus 141 ~~~~la~~~~~~Gd~~~A~~~~~~~r~~~~~~~~~~~~~l~~i~~~i~~~~~~~~~~~~~ka 202 (441)
+++.+|..|+..|++.+|...|.++..........-+..+.+..+....|+++.+...+.++
T Consensus 182 A~y~LG~~y~~~g~~~~A~~~f~~vv~~yP~s~~~~dAl~klg~~~~~~g~~~~A~~~~~~v 243 (263)
T PRK10803 182 ANYWLGQLNYNKGKKDDAAYYFASVVKNYPKSPKAADAMFKVGVIMQDKGDTAKAKAVYQQV 243 (263)
T ss_pred HHHHHHHHHHHcCCHHHHHHHHHHHHHHCCCCcchhHHHHHHHHHHHHcCCHHHHHHHHHHH
Confidence 45555555555555555555555554444444444555555555555555555555555544
No 61
>PRK15359 type III secretion system chaperone protein SscB; Provisional
Probab=93.26 E-value=1.6 Score=38.09 Aligned_cols=94 Identities=12% Similarity=0.010 Sum_probs=73.2
Q ss_pred HhHHHHHHHHcCCHHHHHHHHHHHHhhhcCchhHHHHHHHHHHHHHHhcCHHHHHhHHHHHhcccccCChhhhhhHHHHH
Q 013559 142 YNDFGDFYYAHGALGDAFKSYVRTRDYCTTSKHIIHMCMSAILVSIEMGQFTHVTSYVSKAEQTPEALEPVTIAKLRCAA 221 (441)
Q Consensus 142 ~~~la~~~~~~Gd~~~A~~~~~~~r~~~~~~~~~~~~~l~~i~~~i~~~~~~~~~~~~~ka~~~~~~~d~~~~~~l~~~~ 221 (441)
++.+|..+...|++++|.++|.+....... ..+.......+....|++..+...+.++-..- ..++. ....-
T Consensus 27 ~~~~g~~~~~~g~~~~A~~~~~~al~~~P~---~~~a~~~lg~~~~~~g~~~~A~~~y~~Al~l~-p~~~~----a~~~l 98 (144)
T PRK15359 27 VYASGYASWQEGDYSRAVIDFSWLVMAQPW---SWRAHIALAGTWMMLKEYTTAINFYGHALMLD-ASHPE----PVYQT 98 (144)
T ss_pred HHHHHHHHHHcCCHHHHHHHHHHHHHcCCC---cHHHHHHHHHHHHHHhhHHHHHHHHHHHHhcC-CCCcH----HHHHH
Confidence 456799999999999999999998655332 35666777788888999999999999987642 22322 23556
Q ss_pred HHHhcccccHHHHHHHHHhcCc
Q 013559 222 GLAHLEARKYKLAARKFLEVGP 243 (441)
Q Consensus 222 gl~~l~~r~y~~Aa~~Fl~~~~ 243 (441)
|..+...|++.+|...|-.+..
T Consensus 99 g~~l~~~g~~~eAi~~~~~Al~ 120 (144)
T PRK15359 99 GVCLKMMGEPGLAREAFQTAIK 120 (144)
T ss_pred HHHHHHcCCHHHHHHHHHHHHH
Confidence 8888899999999999988764
No 62
>TIGR02521 type_IV_pilW type IV pilus biogenesis/stability protein PilW. Members of this family are designated PilF in ref (PubMed:8973346) and PilW in ref (PubMed:15612916). This outer membrane protein is required both for pilus stability and for pilus function such as adherence to human cells. Members of this family contain copies of the TPR (tetratricopeptide repeat) domain.
Probab=92.83 E-value=7 Score=35.17 Aligned_cols=96 Identities=13% Similarity=0.053 Sum_probs=73.3
Q ss_pred hHHhHHHHHHHHcCCHHHHHHHHHHHHhhhcCchhHHHHHHHHHHHHHHhcCHHHHHhHHHHHhcccccCChhhhhhHHH
Q 013559 140 MGYNDFGDFYYAHGALGDAFKSYVRTRDYCTTSKHIIHMCMSAILVSIEMGQFTHVTSYVSKAEQTPEALEPVTIAKLRC 219 (441)
Q Consensus 140 ~~~~~la~~~~~~Gd~~~A~~~~~~~r~~~~~~~~~~~~~l~~i~~~i~~~~~~~~~~~~~ka~~~~~~~d~~~~~~l~~ 219 (441)
..++.+|..+...|++++|.+.+.+..+.... ..........+....|+++.+...+.++-..... ++ ....
T Consensus 32 ~~~~~la~~~~~~~~~~~A~~~~~~~l~~~p~---~~~~~~~la~~~~~~~~~~~A~~~~~~al~~~~~-~~----~~~~ 103 (234)
T TIGR02521 32 KIRVQLALGYLEQGDLEVAKENLDKALEHDPD---DYLAYLALALYYQQLGELEKAEDSFRRALTLNPN-NG----DVLN 103 (234)
T ss_pred HHHHHHHHHHHHCCCHHHHHHHHHHHHHhCcc---cHHHHHHHHHHHHHcCCHHHHHHHHHHHHhhCCC-CH----HHHH
Confidence 46678899999999999999999998655322 2355566777888899999999999988765321 22 2234
Q ss_pred HHHHHhcccccHHHHHHHHHhcCc
Q 013559 220 AAGLAHLEARKYKLAARKFLEVGP 243 (441)
Q Consensus 220 ~~gl~~l~~r~y~~Aa~~Fl~~~~ 243 (441)
..|..++..|+|.+|.+.|-.+..
T Consensus 104 ~~~~~~~~~g~~~~A~~~~~~~~~ 127 (234)
T TIGR02521 104 NYGTFLCQQGKYEQAMQQFEQAIE 127 (234)
T ss_pred HHHHHHHHcccHHHHHHHHHHHHh
Confidence 457778899999999999998875
No 63
>PF13429 TPR_15: Tetratricopeptide repeat; PDB: 2VQ2_A 2PL2_B.
Probab=92.80 E-value=1.1 Score=43.61 Aligned_cols=178 Identities=15% Similarity=0.116 Sum_probs=80.5
Q ss_pred HHhHHHHHHHHcCCHHHHHHHHHHHHhhhcCchhHHHHHHHHHHHHHHhcCHHHHHhHHHHHhcccccCChhhhhhHHHH
Q 013559 141 GYNDFGDFYYAHGALGDAFKSYVRTRDYCTTSKHIIHMCMSAILVSIEMGQFTHVTSYVSKAEQTPEALEPVTIAKLRCA 220 (441)
Q Consensus 141 ~~~~la~~~~~~Gd~~~A~~~~~~~r~~~~~~~~~~~~~l~~i~~~i~~~~~~~~~~~~~ka~~~~~~~d~~~~~~l~~~ 220 (441)
.+..++.+ +..|++.+|.+++.+..+...+ -......+.+....++|+.+...+.++....... ....+...
T Consensus 80 ~~~~l~~l-~~~~~~~~A~~~~~~~~~~~~~----~~~l~~~l~~~~~~~~~~~~~~~l~~~~~~~~~~---~~~~~~~~ 151 (280)
T PF13429_consen 80 DYERLIQL-LQDGDPEEALKLAEKAYERDGD----PRYLLSALQLYYRLGDYDEAEELLEKLEELPAAP---DSARFWLA 151 (280)
T ss_dssp -------------------------------------------H-HHHTT-HHHHHHHHHHHHH-T------T-HHHHHH
T ss_pred cccccccc-cccccccccccccccccccccc----cchhhHHHHHHHHHhHHHHHHHHHHHHHhccCCC---CCHHHHHH
Confidence 45677777 7999999999998876554432 2334456667888899999999999987644311 12345566
Q ss_pred HHHHhcccccHHHHHHHHHhcCcCCCCCchhhhcHHHHHHHHHHHHHhc-CChHHHHHhcccCHhhHhhhccchHHHH-H
Q 013559 221 AGLAHLEARKYKLAARKFLEVGPDLGNSYNEVIAAQDVATYGGLCALAS-FDRAELKSKVIDNVNFRNFLELVPEVRE-L 298 (441)
Q Consensus 221 ~gl~~l~~r~y~~Aa~~Fl~~~~t~~~~~~el~s~~d~~~Y~~l~al~s-~~R~eLk~~vl~~~~~~~~le~~p~~~~-l 298 (441)
.|.++...|++.+|...|-.+..-.+++ +++. .. .+..++. .+..+++. ++.. ........|.+.. +
T Consensus 152 ~a~~~~~~G~~~~A~~~~~~al~~~P~~-~~~~------~~-l~~~li~~~~~~~~~~-~l~~--~~~~~~~~~~~~~~l 220 (280)
T PF13429_consen 152 LAEIYEQLGDPDKALRDYRKALELDPDD-PDAR------NA-LAWLLIDMGDYDEARE-ALKR--LLKAAPDDPDLWDAL 220 (280)
T ss_dssp HHHHHHHCCHHHHHHHHHHHHHHH-TT--HHHH------HH-HHHHHCTTCHHHHHHH-HHHH--HHHH-HTSCCHCHHH
T ss_pred HHHHHHHcCCHHHHHHHHHHHHHcCCCC-HHHH------HH-HHHHHHHCCChHHHHH-HHHH--HHHHCcCHHHHHHHH
Confidence 7888889999999999988776533321 2222 22 2223343 33344333 2211 2222245566543 4
Q ss_pred HHHHh-cCCHHHHHHHHHHhHHhhhhchhHHHHHHHHHHH
Q 013559 299 INDFY-SSRYASCLDYLGNLKANLLLDIHLHDHVETLYDQ 337 (441)
Q Consensus 299 l~~f~-~~~y~~~~~~L~~~~~~l~~D~~L~~h~~~l~~~ 337 (441)
..++. -.++..++..+......-..|+-..-|.-.++..
T Consensus 221 a~~~~~lg~~~~Al~~~~~~~~~~p~d~~~~~~~a~~l~~ 260 (280)
T PF13429_consen 221 AAAYLQLGRYEEALEYLEKALKLNPDDPLWLLAYADALEQ 260 (280)
T ss_dssp HHHHHHHT-HHHHHHHHHHHHHHSTT-HHHHHHHHHHHT-
T ss_pred HHHhcccccccccccccccccccccccccccccccccccc
Confidence 44443 4789999998888877777888777665554443
No 64
>KOG3054 consensus Uncharacterized conserved protein [Function unknown]
Probab=92.74 E-value=0.29 Score=46.14 Aligned_cols=58 Identities=16% Similarity=0.320 Sum_probs=52.6
Q ss_pred HHHHHhccccccccHHhHHHHcCCChHHHHHHHHHHHHcCccceEecCCCCeEEEecC
Q 013559 341 KALIQYTHPFVSVDLHMMANAFKTSVAGIEKELEALITDNQIQARIDSHNKILYARHA 398 (441)
Q Consensus 341 ~~i~qy~~pYs~I~L~~mA~~fg~s~~~~E~~L~~LI~~g~L~akID~~~gvv~~~~~ 398 (441)
.-|++|++--++|-|..||..||+-....-.-|-.|+.+|.|.+-||--.+.|++...
T Consensus 203 ~eFv~YIk~nKvV~ledLas~f~Lrtqd~inriq~~l~eg~ltGVmDDRGKfIYIS~e 260 (299)
T KOG3054|consen 203 SEFVEYIKKNKVVPLEDLASEFGLRTQDSINRIQELLAEGLLTGVMDDRGKFIYISME 260 (299)
T ss_pred HHHHHHHHhcCeeeHHHHHHHhCccHHHHHHHHHHHHHhhhheeeecCCCceEEecHH
Confidence 3467888889999999999999998888888999999999999999999999999844
No 65
>TIGR00990 3a0801s09 mitochondrial precursor proteins import receptor (72 kDa mitochondrial outermembrane protein) (mitochondrial import receptor for the ADP/ATP carrier) (translocase of outermembrane tom70).
Probab=92.64 E-value=18 Score=39.42 Aligned_cols=60 Identities=13% Similarity=0.179 Sum_probs=25.8
Q ss_pred HHhHHHHHHHHcCCHHHHHHHHHHHHhhhcCchhHHHHHHHHHHHHHHhcCHHHHHhHHHHHh
Q 013559 141 GYNDFGDFYYAHGALGDAFKSYVRTRDYCTTSKHIIHMCMSAILVSIEMGQFTHVTSYVSKAE 203 (441)
Q Consensus 141 ~~~~la~~~~~~Gd~~~A~~~~~~~r~~~~~~~~~~~~~l~~i~~~i~~~~~~~~~~~~~ka~ 203 (441)
+++.+|..|+..|++++|.++|.+..+...+. ......+..+....|+++.+...+.++.
T Consensus 401 ~~~~lg~~~~~~g~~~~A~~~~~kal~l~P~~---~~~~~~la~~~~~~g~~~eA~~~~~~al 460 (615)
T TIGR00990 401 IYYHRAQLHFIKGEFAQAGKDYQKSIDLDPDF---IFSHIQLGVTQYKEGSIASSMATFRRCK 460 (615)
T ss_pred HHHHHHHHHHHcCCHHHHHHHHHHHHHcCccC---HHHHHHHHHHHHHCCCHHHHHHHHHHHH
Confidence 44445555555555555555554443332111 1222333333344445555554444443
No 66
>TIGR02795 tol_pal_ybgF tol-pal system protein YbgF. Members of this protein family are the product of one of seven genes regularly clustered in operons to encode the proteins of the tol-pal system, which is critical for maintaining the integrity of the bacterial outer membrane. The gene for this periplasmic protein has been designated orf2 and ybgF. All members of the seed alignment were from unique tol-pal gene regions from completed bacterial genomes. The architecture of this protein is a signal sequence, a low-complexity region usually rich in Asn and Gln, a well-conserved region with tandem repeats that resemble the tetratricopeptide (TPR) repeat, involved in protein-protein interaction.
Probab=92.57 E-value=0.6 Score=38.19 Aligned_cols=66 Identities=17% Similarity=0.207 Sum_probs=53.7
Q ss_pred hHHhHHHHHHHHcCCHHHHHHHHHHHHhhhcCchhHHHHHHHHHHHHHHhcCHHHHHhHHHHHhcc
Q 013559 140 MGYNDFGDFYYAHGALGDAFKSYVRTRDYCTTSKHIIHMCMSAILVSIEMGQFTHVTSYVSKAEQT 205 (441)
Q Consensus 140 ~~~~~la~~~~~~Gd~~~A~~~~~~~r~~~~~~~~~~~~~l~~i~~~i~~~~~~~~~~~~~ka~~~ 205 (441)
.+++.+|..+++.|+++.|.++|.++.....+......+.+....+....|++..+...+.++...
T Consensus 40 ~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~A~~~~~~~~~~ 105 (119)
T TIGR02795 40 NAHYWLGEAYYAQGKYADAAKAFLAVVKKYPKSPKAPDALLKLGMSLQELGDKEKAKATLQQVIKR 105 (119)
T ss_pred HHHHHHHHHHHhhccHHHHHHHHHHHHHHCCCCCcccHHHHHHHHHHHHhCChHHHHHHHHHHHHH
Confidence 467889999999999999999999987765544444566677777788899999999998887654
No 67
>TIGR02917 PEP_TPR_lipo putative PEP-CTERM system TPR-repeat lipoprotein. This protein family occurs in strictly within a subset of Gram-negative bacterial species with the proposed PEP-CTERM/exosortase system, analogous to the LPXTG/sortase system common in Gram-positive bacteria. This protein occurs in a species if and only if a transmembrane histidine kinase (TIGR02916) and a DNA-binding response regulator (TIGR02915) also occur. The present of tetratricopeptide repeats (TPR) suggests protein-protein interaction, possibly for the regulation of PEP-CTERM protein expression, since many PEP-CTERM proteins in these genomes are preceded by a proposed DNA binding site for the response regulator.
Probab=92.41 E-value=16 Score=40.46 Aligned_cols=62 Identities=15% Similarity=0.116 Sum_probs=38.6
Q ss_pred hHHhHHHHHHHHcCCHHHHHHHHHHHHhhhcCchhHHHHHHHHHHHHHHhcCHHHHHhHHHHHhc
Q 013559 140 MGYNDFGDFYYAHGALGDAFKSYVRTRDYCTTSKHIIHMCMSAILVSIEMGQFTHVTSYVSKAEQ 204 (441)
Q Consensus 140 ~~~~~la~~~~~~Gd~~~A~~~~~~~r~~~~~~~~~~~~~l~~i~~~i~~~~~~~~~~~~~ka~~ 204 (441)
..+..+|..+...|++++|.++|.++.+..... ......+..+....|+|..+...+.++-.
T Consensus 602 ~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~~~---~~~~~~l~~~~~~~~~~~~A~~~~~~~~~ 663 (899)
T TIGR02917 602 EAWLMLGRAQLAAGDLNKAVSSFKKLLALQPDS---ALALLLLADAYAVMKNYAKAITSLKRALE 663 (899)
T ss_pred HHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCC---hHHHHHHHHHHHHcCCHHHHHHHHHHHHh
Confidence 356777777777777777777777765543221 22334455555566777777776666644
No 68
>KOG2796 consensus Uncharacterized conserved protein [Function unknown]
Probab=92.28 E-value=10 Score=37.01 Aligned_cols=98 Identities=13% Similarity=0.180 Sum_probs=74.2
Q ss_pred HHhHHHHHHHHcCCHHHHHHHHHHHHhhhcCchhHHHHHHHHHHHHHHhcCHHHHHhHHHHHhc---ccccCChhhhhhH
Q 013559 141 GYNDFGDFYYAHGALGDAFKSYVRTRDYCTTSKHIIHMCMSAILVSIEMGQFTHVTSYVSKAEQ---TPEALEPVTIAKL 217 (441)
Q Consensus 141 ~~~~la~~~~~~Gd~~~A~~~~~~~r~~~~~~~~~~~~~l~~i~~~i~~~~~~~~~~~~~ka~~---~~~~~d~~~~~~l 217 (441)
.++-++.++.-.|+|+-....+.+++++.. .+.-..+-.+.|++...||...++.+..+.+. .+++ ++++.
T Consensus 179 Vmy~~~~~llG~kEy~iS~d~~~~vi~~~~--e~~p~L~s~Lgr~~MQ~GD~k~a~~yf~~vek~~~kL~~----~q~~~ 252 (366)
T KOG2796|consen 179 VMYSMANCLLGMKEYVLSVDAYHSVIKYYP--EQEPQLLSGLGRISMQIGDIKTAEKYFQDVEKVTQKLDG----LQGKI 252 (366)
T ss_pred HHHHHHHHHhcchhhhhhHHHHHHHHHhCC--cccHHHHHHHHHHHHhcccHHHHHHHHHHHHHHHhhhhc----cchhH
Confidence 678899999999999999999999998753 34455566788999999999999988776543 3332 22222
Q ss_pred HH--HHHHHhcccccHHHHHHHHHhcCcC
Q 013559 218 RC--AAGLAHLEARKYKLAARKFLEVGPD 244 (441)
Q Consensus 218 ~~--~~gl~~l~~r~y~~Aa~~Fl~~~~t 244 (441)
-+ ..+..++.+.||..|..-|-++..+
T Consensus 253 ~V~~n~a~i~lg~nn~a~a~r~~~~i~~~ 281 (366)
T KOG2796|consen 253 MVLMNSAFLHLGQNNFAEAHRFFTEILRM 281 (366)
T ss_pred HHHhhhhhheecccchHHHHHHHhhcccc
Confidence 22 3456778899999999999888754
No 69
>TIGR03302 OM_YfiO outer membrane assembly lipoprotein YfiO. Members of this protein family include YfiO, a near-essential protein of the outer membrane, part of a complex involved in protein insertion into the bacterial outer membrane. Many proteins in this family are annotated as ComL, based on the involvement of this protein in natural transformation with exogenous DNA in Neisseria gonorrhoeae. This protein family shows sequence similarity to, but is distinct from, the tol-pal system protein YbgF (TIGR02795).
Probab=92.20 E-value=1.5 Score=41.21 Aligned_cols=105 Identities=10% Similarity=0.032 Sum_probs=72.7
Q ss_pred hHHhHHHHHHHHcCCHHHHHHHHHHHHhhhcCchhHHHHHHHHHHHHHHhcCHHHHHhHHHHHhcccccCChhhhhhHHH
Q 013559 140 MGYNDFGDFYYAHGALGDAFKSYVRTRDYCTTSKHIIHMCMSAILVSIEMGQFTHVTSYVSKAEQTPEALEPVTIAKLRC 219 (441)
Q Consensus 140 ~~~~~la~~~~~~Gd~~~A~~~~~~~r~~~~~~~~~~~~~l~~i~~~i~~~~~~~~~~~~~ka~~~~~~~d~~~~~~l~~ 219 (441)
..++.+|..++..|++++|...|.++.....+.....+..+....+....|+|..+...+.++-..-.. ++... ....
T Consensus 34 ~~~~~~g~~~~~~~~~~~A~~~~~~~~~~~p~~~~~~~a~~~la~~~~~~~~~~~A~~~~~~~l~~~p~-~~~~~-~a~~ 111 (235)
T TIGR03302 34 EELYEEAKEALDSGDYTEAIKYFEALESRYPFSPYAEQAQLDLAYAYYKSGDYAEAIAAADRFIRLHPN-HPDAD-YAYY 111 (235)
T ss_pred HHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCchhHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHCcC-CCchH-HHHH
Confidence 367899999999999999999999987665544444556677778888899999999999988654221 22110 1112
Q ss_pred HHHHHhcc--------cccHHHHHHHHHhcCcCCC
Q 013559 220 AAGLAHLE--------ARKYKLAARKFLEVGPDLG 246 (441)
Q Consensus 220 ~~gl~~l~--------~r~y~~Aa~~Fl~~~~t~~ 246 (441)
..|..+.. .+++..|.+.|-.+...++
T Consensus 112 ~~g~~~~~~~~~~~~~~~~~~~A~~~~~~~~~~~p 146 (235)
T TIGR03302 112 LRGLSNYNQIDRVDRDQTAAREAFEAFQELIRRYP 146 (235)
T ss_pred HHHHHHHHhcccccCCHHHHHHHHHHHHHHHHHCC
Confidence 23443433 3788888888887765443
No 70
>PF07719 TPR_2: Tetratricopeptide repeat; InterPro: IPR013105 The tetratrico peptide repeat (TPR) is a structural motif present in a wide range of proteins [, , ]. It mediates protein-protein interactions and the assembly of multiprotein complexes []. The TPR motif consists of 3-16 tandem-repeats of 34 amino acids residues, although individual TPR motifs can be dispersed in the protein sequence. Sequence alignment of the TPR domains reveals a consensus sequence defined by a pattern of small and large amino acids. TPR motifs have been identified in various different organisms, ranging from bacteria to humans. Proteins containing TPRs are involved in a variety of biological processes, such as cell cycle regulation, transcriptional control, mitochondrial and peroxisomal protein transport, neurogenesis and protein folding. This repeat includes outlying Tetratricopeptide-like repeats (TPR) that are not matched by IPR001440 from INTERPRO.; PDB: 1XNF_B 3Q15_A 4ABN_A 1OUV_A 3U4T_A 3MA5_C 2KCV_A 2KCL_A 2XEV_A 3NF1_A ....
Probab=92.16 E-value=0.35 Score=30.60 Aligned_cols=29 Identities=17% Similarity=0.413 Sum_probs=25.0
Q ss_pred HHhHHHHHHHHcCCHHHHHHHHHHHHhhh
Q 013559 141 GYNDFGDFYYAHGALGDAFKSYVRTRDYC 169 (441)
Q Consensus 141 ~~~~la~~~~~~Gd~~~A~~~~~~~r~~~ 169 (441)
+++.+|..|+..|++++|.++|.+.....
T Consensus 3 ~~~~lg~~~~~~~~~~~A~~~~~~al~l~ 31 (34)
T PF07719_consen 3 AWYYLGQAYYQLGNYEEAIEYFEKALELD 31 (34)
T ss_dssp HHHHHHHHHHHTT-HHHHHHHHHHHHHHS
T ss_pred HHHHHHHHHHHhCCHHHHHHHHHHHHHHC
Confidence 57899999999999999999999986654
No 71
>PF13174 TPR_6: Tetratricopeptide repeat; PDB: 3QKY_A 2XEV_A 3URZ_B 2Q7F_A.
Probab=92.15 E-value=0.25 Score=30.95 Aligned_cols=31 Identities=16% Similarity=0.273 Sum_probs=27.0
Q ss_pred hHHhHHHHHHHHcCCHHHHHHHHHHHHhhhc
Q 013559 140 MGYNDFGDFYYAHGALGDAFKSYVRTRDYCT 170 (441)
Q Consensus 140 ~~~~~la~~~~~~Gd~~~A~~~~~~~r~~~~ 170 (441)
++++.+|..|++.|++++|.+.|.++.+...
T Consensus 1 ~a~~~~a~~~~~~g~~~~A~~~~~~~~~~~P 31 (33)
T PF13174_consen 1 DALYRLARCYYKLGDYDEAIEYFQRLIKRYP 31 (33)
T ss_dssp HHHHHHHHHHHHHCHHHHHHHHHHHHHHHST
T ss_pred CHHHHHHHHHHHccCHHHHHHHHHHHHHHCc
Confidence 3789999999999999999999999866543
No 72
>KOG3081 consensus Vesicle coat complex COPI, epsilon subunit [Intracellular trafficking, secretion, and vesicular transport]
Probab=92.05 E-value=9.9 Score=36.99 Aligned_cols=116 Identities=15% Similarity=0.082 Sum_probs=69.3
Q ss_pred HHhHHHHHHHHcCCHHHHHHHHHHHHhhhcCchhHHHHHHHHHHHHHHhcCHHHHHhHHHHHhcccc-------------
Q 013559 141 GYNDFGDFYYAHGALGDAFKSYVRTRDYCTTSKHIIHMCMSAILVSIEMGQFTHVTSYVSKAEQTPE------------- 207 (441)
Q Consensus 141 ~~~~la~~~~~~Gd~~~A~~~~~~~r~~~~~~~~~~~~~l~~i~~~i~~~~~~~~~~~~~ka~~~~~------------- 207 (441)
.+..-|.+|.+-|++++|.+..... .-++.....+.+.+-...++.+.+.+.+..+.-+
T Consensus 110 ~~l~aa~i~~~~~~~deAl~~~~~~--------~~lE~~Al~VqI~lk~~r~d~A~~~lk~mq~ided~tLtQLA~awv~ 181 (299)
T KOG3081|consen 110 DLLLAAIIYMHDGDFDEALKALHLG--------ENLEAAALNVQILLKMHRFDLAEKELKKMQQIDEDATLTQLAQAWVK 181 (299)
T ss_pred HHHHhhHHhhcCCChHHHHHHHhcc--------chHHHHHHHHHHHHHHHHHHHHHHHHHHHHccchHHHHHHHHHHHHH
Confidence 3455688999999999999988652 2344444455555555555555555555544322
Q ss_pred --cCChhhhhhHHHH----------------HHHHhcccccHHHHHHHHHhcCcCCCCCchhhhcHHHHHHHHHHHHHhc
Q 013559 208 --ALEPVTIAKLRCA----------------AGLAHLEARKYKLAARKFLEVGPDLGNSYNEVIAAQDVATYGGLCALAS 269 (441)
Q Consensus 208 --~~d~~~~~~l~~~----------------~gl~~l~~r~y~~Aa~~Fl~~~~t~~~~~~el~s~~d~~~Y~~l~al~s 269 (441)
.+....+-.+.+| .+..+|+.|+|.+|-..+.++...-.. +++.+ .-+++|++..
T Consensus 182 la~ggek~qdAfyifeE~s~k~~~T~~llnG~Av~~l~~~~~eeAe~lL~eaL~kd~~-dpetL------~Nliv~a~~~ 254 (299)
T KOG3081|consen 182 LATGGEKIQDAFYIFEELSEKTPPTPLLLNGQAVCHLQLGRYEEAESLLEEALDKDAK-DPETL------ANLIVLALHL 254 (299)
T ss_pred HhccchhhhhHHHHHHHHhcccCCChHHHccHHHHHHHhcCHHHHHHHHHHHHhccCC-CHHHH------HHHHHHHHHh
Confidence 0111112112222 234678899999999988888764332 45544 5666777765
Q ss_pred CC
Q 013559 270 FD 271 (441)
Q Consensus 270 ~~ 271 (441)
..
T Consensus 255 Gk 256 (299)
T KOG3081|consen 255 GK 256 (299)
T ss_pred CC
Confidence 43
No 73
>PF13525 YfiO: Outer membrane lipoprotein; PDB: 3TGO_A 3Q5M_A 2YHC_A.
Probab=91.89 E-value=1.6 Score=40.59 Aligned_cols=68 Identities=10% Similarity=0.058 Sum_probs=55.1
Q ss_pred hHHhHHHHHHHHcCCHHHHHHHHHHHHhhhcCchhHHHHHHHHHHHHHHhcCHHHHHhHHHHHhc-ccc
Q 013559 140 MGYNDFGDFYYAHGALGDAFKSYVRTRDYCTTSKHIIHMCMSAILVSIEMGQFTHVTSYVSKAEQ-TPE 207 (441)
Q Consensus 140 ~~~~~la~~~~~~Gd~~~A~~~~~~~r~~~~~~~~~~~~~l~~i~~~i~~~~~~~~~~~~~ka~~-~~~ 207 (441)
..++..|.-+++.|+|.+|.+.|.++.....++...-+..+.+..+....|+|..+...+.+.-. .+.
T Consensus 6 ~~lY~~a~~~~~~g~y~~Ai~~f~~l~~~~P~s~~a~~A~l~la~a~y~~~~y~~A~~~~~~fi~~yP~ 74 (203)
T PF13525_consen 6 EALYQKALEALQQGDYEEAIKLFEKLIDRYPNSPYAPQAQLMLAYAYYKQGDYEEAIAAYERFIKLYPN 74 (203)
T ss_dssp HHHHHHHHHHHHCT-HHHHHHHHHHHHHH-TTSTTHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHH-TT
T ss_pred HHHHHHHHHHHHCCCHHHHHHHHHHHHHHCCCChHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHCCC
Confidence 36789999999999999999999999888877778888889999999999999999988887543 444
No 74
>PLN03088 SGT1, suppressor of G2 allele of SKP1; Provisional
Probab=91.60 E-value=1.6 Score=44.31 Aligned_cols=94 Identities=16% Similarity=0.179 Sum_probs=70.0
Q ss_pred HhHHHHHHHHcCCHHHHHHHHHHHHhhhcCchhHHHHHHHHHHHHHHhcCHHHHHhHHHHHhcccccCChhhhhhHHHHH
Q 013559 142 YNDFGDFYYAHGALGDAFKSYVRTRDYCTTSKHIIHMCMSAILVSIEMGQFTHVTSYVSKAEQTPEALEPVTIAKLRCAA 221 (441)
Q Consensus 142 ~~~la~~~~~~Gd~~~A~~~~~~~r~~~~~~~~~~~~~l~~i~~~i~~~~~~~~~~~~~ka~~~~~~~d~~~~~~l~~~~ 221 (441)
+...|.-.+..|+|.+|+++|.+......+. ...+.....+.+..|++..+...+.++-.+-- .++ ......
T Consensus 5 l~~~a~~a~~~~~~~~Ai~~~~~Al~~~P~~---~~a~~~~a~~~~~~g~~~eAl~~~~~Al~l~P-~~~----~a~~~l 76 (356)
T PLN03088 5 LEDKAKEAFVDDDFALAVDLYTQAIDLDPNN---AELYADRAQANIKLGNFTEAVADANKAIELDP-SLA----KAYLRK 76 (356)
T ss_pred HHHHHHHHHHcCCHHHHHHHHHHHHHhCCCC---HHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCc-CCH----HHHHHH
Confidence 3456888899999999999999987664432 34566777788888999999999888866522 122 223445
Q ss_pred HHHhcccccHHHHHHHHHhcCc
Q 013559 222 GLAHLEARKYKLAARKFLEVGP 243 (441)
Q Consensus 222 gl~~l~~r~y~~Aa~~Fl~~~~ 243 (441)
|.+++..|+|.+|...|-.+..
T Consensus 77 g~~~~~lg~~~eA~~~~~~al~ 98 (356)
T PLN03088 77 GTACMKLEEYQTAKAALEKGAS 98 (356)
T ss_pred HHHHHHhCCHHHHHHHHHHHHH
Confidence 7888899999999999887764
No 75
>KOG1127 consensus TPR repeat-containing protein [RNA processing and modification]
Probab=91.53 E-value=30 Score=39.56 Aligned_cols=100 Identities=16% Similarity=0.132 Sum_probs=72.5
Q ss_pred HHHHHhHHhHHHHHHHHcCCHHHHHHHHHHHHhhhcCchhHHHHHHHHHHHHHHhcCHHHHHhHHH-HHhcccc---cCC
Q 013559 135 KESIRMGYNDFGDFYYAHGALGDAFKSYVRTRDYCTTSKHIIHMCMSAILVSIEMGQFTHVTSYVS-KAEQTPE---ALE 210 (441)
Q Consensus 135 ~esir~~~~~la~~~~~~Gd~~~A~~~~~~~r~~~~~~~~~~~~~l~~i~~~i~~~~~~~~~~~~~-ka~~~~~---~~d 210 (441)
.++.--++--||.+|.+.-|...|.+||.+.++.-.+ . .+..-....+.....+|+.|..-.- +++..+. ...
T Consensus 488 d~~~apaf~~LG~iYrd~~Dm~RA~kCf~KAFeLDat--d-aeaaaa~adtyae~~~we~a~~I~l~~~qka~a~~~k~n 564 (1238)
T KOG1127|consen 488 DVSLAPAFAFLGQIYRDSDDMKRAKKCFDKAFELDAT--D-AEAAAASADTYAEESTWEEAFEICLRAAQKAPAFACKEN 564 (1238)
T ss_pred ccchhHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCch--h-hhhHHHHHHHhhccccHHHHHHHHHHHhhhchHHHHHhh
Confidence 3444458889999999999999999999999887432 1 3334456677888899999987533 3333322 123
Q ss_pred hhhhhhHHHHHHHHhcccccHHHHHHHHHhcCcC
Q 013559 211 PVTIAKLRCAAGLAHLEARKYKLAARKFLEVGPD 244 (441)
Q Consensus 211 ~~~~~~l~~~~gl~~l~~r~y~~Aa~~Fl~~~~t 244 (441)
|- .-|++++..+++..|...|-.+.-+
T Consensus 565 W~-------~rG~yyLea~n~h~aV~~fQsALR~ 591 (1238)
T KOG1127|consen 565 WV-------QRGPYYLEAHNLHGAVCEFQSALRT 591 (1238)
T ss_pred hh-------hccccccCccchhhHHHHHHHHhcC
Confidence 42 2799999999999999999887643
No 76
>PF09976 TPR_21: Tetratricopeptide repeat; InterPro: IPR018704 This domain, found in various hypothetical prokaryotic proteins, has no known function.
Probab=91.44 E-value=4.3 Score=35.23 Aligned_cols=92 Identities=13% Similarity=0.056 Sum_probs=71.7
Q ss_pred HHHHHcCCHHHHHHHHHHHHhhhcCchhHHHHHHHHHHHHHHhcCHHHHHhHHHHHhcccccCChhhhhhHHHHHHHHhc
Q 013559 147 DFYYAHGALGDAFKSYVRTRDYCTTSKHIIHMCMSAILVSIEMGQFTHVTSYVSKAEQTPEALEPVTIAKLRCAAGLAHL 226 (441)
Q Consensus 147 ~~~~~~Gd~~~A~~~~~~~r~~~~~~~~~~~~~l~~i~~~i~~~~~~~~~~~~~ka~~~~~~~d~~~~~~l~~~~gl~~l 226 (441)
.-....|+...+.+.+..+.....++.......|.+..+.+..|+++.+...+.++-... .++.++...+..-+..++
T Consensus 19 ~~~~~~~~~~~~~~~~~~l~~~~~~s~ya~~A~l~lA~~~~~~g~~~~A~~~l~~~~~~~--~d~~l~~~a~l~LA~~~~ 96 (145)
T PF09976_consen 19 LQALQAGDPAKAEAAAEQLAKDYPSSPYAALAALQLAKAAYEQGDYDEAKAALEKALANA--PDPELKPLARLRLARILL 96 (145)
T ss_pred HHHHHCCCHHHHHHHHHHHHHHCCCChHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHhhC--CCHHHHHHHHHHHHHHHH
Confidence 334479999999998999877666555556667788888899999999999999876643 356666666666678889
Q ss_pred ccccHHHHHHHHHh
Q 013559 227 EARKYKLAARKFLE 240 (441)
Q Consensus 227 ~~r~y~~Aa~~Fl~ 240 (441)
..++|.+|...+-.
T Consensus 97 ~~~~~d~Al~~L~~ 110 (145)
T PF09976_consen 97 QQGQYDEALATLQQ 110 (145)
T ss_pred HcCCHHHHHHHHHh
Confidence 99999999888744
No 77
>PRK15431 ferrous iron transport protein FeoC; Provisional
Probab=91.40 E-value=0.29 Score=38.29 Aligned_cols=42 Identities=10% Similarity=0.028 Sum_probs=37.9
Q ss_pred HHHhccccccccHHhHHHHcCCChHHHHHHHHHHHHcCccce
Q 013559 343 LIQYTHPFVSVDLHMMANAFKTSVAGIEKELEALITDNQIQA 384 (441)
Q Consensus 343 i~qy~~pYs~I~L~~mA~~fg~s~~~~E~~L~~LI~~g~L~a 384 (441)
+.+|+.-+.++++..||..|++|++.+|..|..++.-|++.-
T Consensus 7 lRd~l~~~gr~s~~~Ls~~~~~p~~~VeaMLe~l~~kGkver 48 (78)
T PRK15431 7 VRDLLALRGRMEAAQISQTLNTPQPMINAMLQQLESMGKAVR 48 (78)
T ss_pred HHHHHHHcCcccHHHHHHHHCcCHHHHHHHHHHHHHCCCeEe
Confidence 445666699999999999999999999999999999999854
No 78
>smart00345 HTH_GNTR helix_turn_helix gluconate operon transcriptional repressor.
Probab=91.32 E-value=0.51 Score=34.04 Aligned_cols=49 Identities=14% Similarity=0.180 Sum_probs=41.8
Q ss_pred HHHHHHHHHHHhccccccc-cHHhHHHHcCCChHHHHHHHHHHHHcCccc
Q 013559 335 YDQIRNKALIQYTHPFVSV-DLHMMANAFKTSVAGIEKELEALITDNQIQ 383 (441)
Q Consensus 335 ~~~iR~~~i~qy~~pYs~I-~L~~mA~~fg~s~~~~E~~L~~LI~~g~L~ 383 (441)
++.++.......+.|-..+ +...||+.||+|...+.+.+..|...|-|.
T Consensus 2 ~~~l~~~i~~~~~~~~~~l~s~~~la~~~~vs~~tv~~~l~~L~~~g~i~ 51 (60)
T smart00345 2 AERLREDIVSGELRPGDKLPSERELAAQLGVSRTTVREALSRLEAEGLVQ 51 (60)
T ss_pred HHHHHHHHHcCCCCCCCcCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCEE
Confidence 4566667777767777888 899999999999999999999999998774
No 79
>cd05804 StaR_like StaR_like; a well-conserved protein found in bacteria, plants, and animals. A family member from Streptomyces toyocaensis, StaR is part of a gene cluster involved in the biosynthesis of glycopeptide antibiotics (GPAs), specifically A47934. It has been speculated that StaR could be a flavoprotein hydroxylating a tyrosine sidechain. Some family members have been annotated as proteins containing tetratricopeptide (TPR) repeats, which may at least indicate mostly alpha-helical secondary structure.
Probab=91.19 E-value=2 Score=42.79 Aligned_cols=98 Identities=12% Similarity=-0.005 Sum_probs=70.7
Q ss_pred HHhHHHHHHHHcCCHHHHHHHHHHHHhhhcCchhHHHHHHHHHHHHHHhcCHHHHHhHHHHHhcccccCChhhhhhHHHH
Q 013559 141 GYNDFGDFYYAHGALGDAFKSYVRTRDYCTTSKHIIHMCMSAILVSIEMGQFTHVTSYVSKAEQTPEALEPVTIAKLRCA 220 (441)
Q Consensus 141 ~~~~la~~~~~~Gd~~~A~~~~~~~r~~~~~~~~~~~~~l~~i~~~i~~~~~~~~~~~~~ka~~~~~~~d~~~~~~l~~~ 220 (441)
++..+|..+...|++++|.+.+.+..+..... ......+..+....|+|+.+...+.++-..... ++.........
T Consensus 116 ~~~~~a~~~~~~G~~~~A~~~~~~al~~~p~~---~~~~~~la~i~~~~g~~~eA~~~l~~~l~~~~~-~~~~~~~~~~~ 191 (355)
T cd05804 116 LLGMLAFGLEEAGQYDRAEEAARRALELNPDD---AWAVHAVAHVLEMQGRFKEGIAFMESWRDTWDC-SSMLRGHNWWH 191 (355)
T ss_pred HHHHHHHHHHHcCCHHHHHHHHHHHHhhCCCC---cHHHHHHHHHHHHcCCHHHHHHHHHhhhhccCC-CcchhHHHHHH
Confidence 55677889999999999999999887764332 334455566778889999999988887664321 23333334445
Q ss_pred HHHHhcccccHHHHHHHHHhcC
Q 013559 221 AGLAHLEARKYKLAARKFLEVG 242 (441)
Q Consensus 221 ~gl~~l~~r~y~~Aa~~Fl~~~ 242 (441)
.|.+++..|++.+|...|-...
T Consensus 192 la~~~~~~G~~~~A~~~~~~~~ 213 (355)
T cd05804 192 LALFYLERGDYEAALAIYDTHI 213 (355)
T ss_pred HHHHHHHCCCHHHHHHHHHHHh
Confidence 6788899999999988887753
No 80
>PF13525 YfiO: Outer membrane lipoprotein; PDB: 3TGO_A 3Q5M_A 2YHC_A.
Probab=91.17 E-value=5.8 Score=36.75 Aligned_cols=110 Identities=15% Similarity=0.042 Sum_probs=63.0
Q ss_pred HHhHHhHHHHHHHHcCCHHHHHHHHHHHHhhhcCchhHHHHHHHHHHHHHHh--------cCHHHHHhHHHHHhcccc--
Q 013559 138 IRMGYNDFGDFYYAHGALGDAFKSYVRTRDYCTTSKHIIHMCMSAILVSIEM--------GQFTHVTSYVSKAEQTPE-- 207 (441)
Q Consensus 138 ir~~~~~la~~~~~~Gd~~~A~~~~~~~r~~~~~~~~~~~~~l~~i~~~i~~--------~~~~~~~~~~~ka~~~~~-- 207 (441)
...+.+.+|.-++..|||.+|...+.++.....+..+.-++.+.+..+.... .|-..+..-+...+.++.
T Consensus 41 a~~A~l~la~a~y~~~~y~~A~~~~~~fi~~yP~~~~~~~A~Y~~g~~~~~~~~~~~~~~~D~~~~~~A~~~~~~li~~y 120 (203)
T PF13525_consen 41 APQAQLMLAYAYYKQGDYEEAIAAYERFIKLYPNSPKADYALYMLGLSYYKQIPGILRSDRDQTSTRKAIEEFEELIKRY 120 (203)
T ss_dssp HHHHHHHHHHHHHHTT-HHHHHHHHHHHHHH-TT-TTHHHHHHHHHHHHHHHHHHHH-TT---HHHHHHHHHHHHHHHH-
T ss_pred HHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHCCCCcchhhHHHHHHHHHHHhCccchhcccChHHHHHHHHHHHHHHHHC
Confidence 3457899999999999999999999998766655555444433333332221 222222333333333332
Q ss_pred c-CCh---------hhhhh---HHHHHHHHhcccccHHHHHHHHHhcCcCCCC
Q 013559 208 A-LEP---------VTIAK---LRCAAGLAHLEARKYKLAARKFLEVGPDLGN 247 (441)
Q Consensus 208 ~-~d~---------~~~~~---l~~~~gl~~l~~r~y~~Aa~~Fl~~~~t~~~ 247 (441)
. ... .++++ --..-|.+++..|+|..|...|-.++..+++
T Consensus 121 P~S~y~~~A~~~l~~l~~~la~~e~~ia~~Y~~~~~y~aA~~r~~~v~~~yp~ 173 (203)
T PF13525_consen 121 PNSEYAEEAKKRLAELRNRLAEHELYIARFYYKRGKYKAAIIRFQYVIENYPD 173 (203)
T ss_dssp TTSTTHHHHHHHHHHHHHHHHHHHHHHHHHHHCTT-HHHHHHHHHHHHHHSTT
T ss_pred cCchHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccHHHHHHHHHHHHHHCCC
Confidence 1 111 12222 2234577889999999999999999877543
No 81
>PRK10370 formate-dependent nitrite reductase complex subunit NrfG; Provisional
Probab=91.17 E-value=3.3 Score=38.34 Aligned_cols=96 Identities=14% Similarity=0.132 Sum_probs=68.7
Q ss_pred hHHhHHHHHHHHcCCHHHHHHHHHHHHhhhcCchhHHHHHHHHHHHH-HHhcC--HHHHHhHHHHHhcccccCChhhhhh
Q 013559 140 MGYNDFGDFYYAHGALGDAFKSYVRTRDYCTTSKHIIHMCMSAILVS-IEMGQ--FTHVTSYVSKAEQTPEALEPVTIAK 216 (441)
Q Consensus 140 ~~~~~la~~~~~~Gd~~~A~~~~~~~r~~~~~~~~~~~~~l~~i~~~-i~~~~--~~~~~~~~~ka~~~~~~~d~~~~~~ 216 (441)
.++..||..|...|++++|..+|.+....-... .++......+- ...|+ ...+...+.++-..-- .++ .
T Consensus 74 ~~w~~Lg~~~~~~g~~~~A~~a~~~Al~l~P~~---~~~~~~lA~aL~~~~g~~~~~~A~~~l~~al~~dP-~~~----~ 145 (198)
T PRK10370 74 EQWALLGEYYLWRNDYDNALLAYRQALQLRGEN---AELYAALATVLYYQAGQHMTPQTREMIDKALALDA-NEV----T 145 (198)
T ss_pred HHHHHHHHHHHHCCCHHHHHHHHHHHHHhCCCC---HHHHHHHHHHHHHhcCCCCcHHHHHHHHHHHHhCC-CCh----h
Confidence 488999999999999999999999987765432 33444444432 33455 4788888888766422 122 2
Q ss_pred HHHHHHHHhcccccHHHHHHHHHhcCc
Q 013559 217 LRCAAGLAHLEARKYKLAARKFLEVGP 243 (441)
Q Consensus 217 l~~~~gl~~l~~r~y~~Aa~~Fl~~~~ 243 (441)
.....|..++..|+|.+|...|-.+..
T Consensus 146 al~~LA~~~~~~g~~~~Ai~~~~~aL~ 172 (198)
T PRK10370 146 ALMLLASDAFMQADYAQAIELWQKVLD 172 (198)
T ss_pred HHHHHHHHHHHcCCHHHHHHHHHHHHh
Confidence 335568888999999999999888764
No 82
>PRK11447 cellulose synthase subunit BcsC; Provisional
Probab=91.15 E-value=33 Score=40.62 Aligned_cols=100 Identities=11% Similarity=0.136 Sum_probs=71.2
Q ss_pred hHHhHHHHHHHHcCCHHHHHHHHHHHHhhhcCchh--HH---------HHHHHHHHHHHHhcCHHHHHhHHHHHhccccc
Q 013559 140 MGYNDFGDFYYAHGALGDAFKSYVRTRDYCTTSKH--II---------HMCMSAILVSIEMGQFTHVTSYVSKAEQTPEA 208 (441)
Q Consensus 140 ~~~~~la~~~~~~Gd~~~A~~~~~~~r~~~~~~~~--~~---------~~~l~~i~~~i~~~~~~~~~~~~~ka~~~~~~ 208 (441)
.++..+|..|++.|++++|.++|.+..+....... +. ...+....+.+..|+++.+...+.++-...-
T Consensus 304 ~a~~~Lg~~~~~~g~~~eA~~~l~~Al~~~p~~~~~~~~~~ll~~~~~~~~~~~g~~~~~~g~~~eA~~~~~~Al~~~P- 382 (1157)
T PRK11447 304 EALGALGQAYSQQGDRARAVAQFEKALALDPHSSNRDKWESLLKVNRYWLLIQQGDAALKANNLAQAERLYQQARQVDN- 382 (1157)
T ss_pred HHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCccchhHHHHHHHhhhHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhCC-
Confidence 57899999999999999999999998765543221 11 1122334456778999999999988877532
Q ss_pred CChhhhhhHHHHHHHHhcccccHHHHHHHHHhcCcC
Q 013559 209 LEPVTIAKLRCAAGLAHLEARKYKLAARKFLEVGPD 244 (441)
Q Consensus 209 ~d~~~~~~l~~~~gl~~l~~r~y~~Aa~~Fl~~~~t 244 (441)
.++. ....-|..++..|+|.+|.+.|-.+...
T Consensus 383 ~~~~----a~~~Lg~~~~~~g~~~eA~~~y~~aL~~ 414 (1157)
T PRK11447 383 TDSY----AVLGLGDVAMARKDYAAAERYYQQALRM 414 (1157)
T ss_pred CCHH----HHHHHHHHHHHCCCHHHHHHHHHHHHHh
Confidence 1221 1233477788899999999999888753
No 83
>KOG0547 consensus Translocase of outer mitochondrial membrane complex, subunit TOM70/TOM72 [Intracellular trafficking, secretion, and vesicular transport]
Probab=91.02 E-value=0.76 Score=47.93 Aligned_cols=62 Identities=15% Similarity=0.273 Sum_probs=51.1
Q ss_pred HHhHHHHHHHHcCCHHHHHHHHHHHHhhhcCchhHHHHHHHHHHHHHHhcCHHHHHhHHHHHhcc
Q 013559 141 GYNDFGDFYYAHGALGDAFKSYVRTRDYCTTSKHIIHMCMSAILVSIEMGQFTHVTSYVSKAEQT 205 (441)
Q Consensus 141 ~~~~la~~~~~~Gd~~~A~~~~~~~r~~~~~~~~~~~~~l~~i~~~i~~~~~~~~~~~~~ka~~~ 205 (441)
++-.+|+.+|..|+|++|+++|....+.|.+. --++-+...|..-.|||+.|.+..+|+-++
T Consensus 117 ~lK~~GN~~f~~kkY~eAIkyY~~AI~l~p~e---piFYsNraAcY~~lgd~~~Vied~TkALEl 178 (606)
T KOG0547|consen 117 ALKTKGNKFFRNKKYDEAIKYYTQAIELCPDE---PIFYSNRAACYESLGDWEKVIEDCTKALEL 178 (606)
T ss_pred HHHhhhhhhhhcccHHHHHHHHHHHHhcCCCC---chhhhhHHHHHHHHhhHHHHHHHHHHHhhc
Confidence 34577999999999999999999999999763 113446677888999999999999988765
No 84
>PRK12370 invasion protein regulator; Provisional
Probab=90.76 E-value=19 Score=38.80 Aligned_cols=95 Identities=8% Similarity=-0.100 Sum_probs=63.5
Q ss_pred hHHhHHHHHHHHcCCHHHHHHHHHHHHhhhcCchhHHHHHHHHHHHHHHhcCHHHHHhHHHHHhcccccCChhhhhhHHH
Q 013559 140 MGYNDFGDFYYAHGALGDAFKSYVRTRDYCTTSKHIIHMCMSAILVSIEMGQFTHVTSYVSKAEQTPEALEPVTIAKLRC 219 (441)
Q Consensus 140 ~~~~~la~~~~~~Gd~~~A~~~~~~~r~~~~~~~~~~~~~l~~i~~~i~~~~~~~~~~~~~ka~~~~~~~d~~~~~~l~~ 219 (441)
.++..+|..+...|++++|.++|.+..+...+.. +.......+....|+++.+...+.++..+-- .++.. ..
T Consensus 339 ~a~~~lg~~~~~~g~~~~A~~~~~~Al~l~P~~~---~a~~~lg~~l~~~G~~~eAi~~~~~Al~l~P-~~~~~----~~ 410 (553)
T PRK12370 339 QALGLLGLINTIHSEYIVGSLLFKQANLLSPISA---DIKYYYGWNLFMAGQLEEALQTINECLKLDP-TRAAA----GI 410 (553)
T ss_pred HHHHHHHHHHHHccCHHHHHHHHHHHHHhCCCCH---HHHHHHHHHHHHCCCHHHHHHHHHHHHhcCC-CChhh----HH
Confidence 4677888888999999999999998877764332 3344555667778899999888888866521 12111 11
Q ss_pred HHHHHhcccccHHHHHHHHHhcC
Q 013559 220 AAGLAHLEARKYKLAARKFLEVG 242 (441)
Q Consensus 220 ~~gl~~l~~r~y~~Aa~~Fl~~~ 242 (441)
..+..++..|+|.+|...|..+.
T Consensus 411 ~~~~~~~~~g~~eeA~~~~~~~l 433 (553)
T PRK12370 411 TKLWITYYHTGIDDAIRLGDELR 433 (553)
T ss_pred HHHHHHHhccCHHHHHHHHHHHH
Confidence 12333455678888888777654
No 85
>PF13181 TPR_8: Tetratricopeptide repeat; PDB: 3GW4_B 3MA5_C 2KCV_A 2KCL_A 3FP3_A 3LCA_A 3FP4_A 3FP2_A 1W3B_B 1ELW_A ....
Probab=90.55 E-value=0.61 Score=29.55 Aligned_cols=29 Identities=17% Similarity=0.453 Sum_probs=26.1
Q ss_pred HHhHHHHHHHHcCCHHHHHHHHHHHHhhh
Q 013559 141 GYNDFGDFYYAHGALGDAFKSYVRTRDYC 169 (441)
Q Consensus 141 ~~~~la~~~~~~Gd~~~A~~~~~~~r~~~ 169 (441)
+++.+|..|.+.|++++|.++|.+..+..
T Consensus 3 ~~~~lg~~y~~~~~~~~A~~~~~~a~~~~ 31 (34)
T PF13181_consen 3 AYYNLGKIYEQLGDYEEALEYFEKALELN 31 (34)
T ss_dssp HHHHHHHHHHHTTSHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHcCCHHHHHHHHHHHHhhC
Confidence 67899999999999999999999987664
No 86
>PRK10866 outer membrane biogenesis protein BamD; Provisional
Probab=90.46 E-value=9.8 Score=36.47 Aligned_cols=111 Identities=12% Similarity=-0.027 Sum_probs=69.6
Q ss_pred HHHHhHHhHHHHHHHHcCCHHHHHHHHHHHHhhhcCchhHHHHHHHHHHHHHH---------------hcCHHHHHhHHH
Q 013559 136 ESIRMGYNDFGDFYYAHGALGDAFKSYVRTRDYCTTSKHIIHMCMSAILVSIE---------------MGQFTHVTSYVS 200 (441)
Q Consensus 136 esir~~~~~la~~~~~~Gd~~~A~~~~~~~r~~~~~~~~~~~~~l~~i~~~i~---------------~~~~~~~~~~~~ 200 (441)
+....+.+.+|..|++.|||++|...+.++....++....-.+...+..+... .+|...+...+.
T Consensus 66 ~~a~~a~l~la~ayy~~~~y~~A~~~~e~fi~~~P~~~~~~~a~Y~~g~~~~~~~~~~~~~~~~~~~~~rD~~~~~~A~~ 145 (243)
T PRK10866 66 PYSQQVQLDLIYAYYKNADLPLAQAAIDRFIRLNPTHPNIDYVLYMRGLTNMALDDSALQGFFGVDRSDRDPQHARAAFR 145 (243)
T ss_pred hHHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHhCcCCCchHHHHHHHHHhhhhcchhhhhhccCCCccccCHHHHHHHHH
Confidence 45556789999999999999999999999977665554433333333222211 124455555455
Q ss_pred HHhcccc----c-CChh-------hhhhHH---HHHHHHhcccccHHHHHHHHHhcCcCCC
Q 013559 201 KAEQTPE----A-LEPV-------TIAKLR---CAAGLAHLEARKYKLAARKFLEVGPDLG 246 (441)
Q Consensus 201 ka~~~~~----~-~d~~-------~~~~l~---~~~gl~~l~~r~y~~Aa~~Fl~~~~t~~ 246 (441)
..+.+++ + -.++ ++++|. ..-|.+++..|+|..|+..|-.+...++
T Consensus 146 ~~~~li~~yP~S~ya~~A~~rl~~l~~~la~~e~~ia~~Y~~~~~y~AA~~r~~~v~~~Yp 206 (243)
T PRK10866 146 DFSKLVRGYPNSQYTTDATKRLVFLKDRLAKYELSVAEYYTKRGAYVAVVNRVEQMLRDYP 206 (243)
T ss_pred HHHHHHHHCcCChhHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCchHHHHHHHHHHHHHCC
Confidence 5555443 1 1112 222222 2346678889999999999999887654
No 87
>PF08279 HTH_11: HTH domain; InterPro: IPR013196 Winged helix DNA-binding proteins share a related winged helix-turn-helix DNA-binding motif, where the "wings", or loops, are small beta-sheets. The winged helix motif consists of two wings (W1, W2), three alpha helices (H1, H2, H3) and three beta-sheets (S1, S2, S3) arranged in the order H1-S1-H2-H3-S2-W1-S3-W2 []. The DNA-recognition helix makes sequence-specific DNA contacts with the major groove of DNA, while the wings make different DNA contacts, often with the minor groove or the backbone of DNA. Several winged-helix proteins display an exposed patch of hydrophobic residues thought to mediate protein-protein interactions. This entry represents a subset of the winged helix domain superfamily which is predominantly found in bacterial proteins, though there are also some archaeal and eukaryotic examples. This domain is commonly found in the biotin (vitamin H) repressor protein BirA which regulates transcription of the biotin operon []. It is also found in other proteins including regulators of amino acid biosynthsis such as LysM [], and regulators of carbohydrate metabolisms such as LicR and FrvR [, ].; PDB: 1HXD_B 2EWN_B 1BIA_A 1BIB_A 1J5Y_A 3V7S_A 3V7C_A 3RKW_A 3RIR_A 3RKX_A ....
Probab=89.88 E-value=0.79 Score=32.92 Aligned_cols=48 Identities=17% Similarity=0.241 Sum_probs=34.9
Q ss_pred HHHHHHHhc-cccccccHHhHHHHcCCChHHHHHHHHHHHHcCccceEecCC
Q 013559 339 RNKALIQYT-HPFVSVDLHMMANAFKTSVAGIEKELEALITDNQIQARIDSH 389 (441)
Q Consensus 339 R~~~i~qy~-~pYs~I~L~~mA~~fg~s~~~~E~~L~~LI~~g~L~akID~~ 389 (441)
|.+-+.+++ ..-..|+.+.||+.||+|...+.+.|..|-..| ..|.+.
T Consensus 1 R~~~il~~L~~~~~~it~~eLa~~l~vS~rTi~~~i~~L~~~~---~~I~~~ 49 (55)
T PF08279_consen 1 RQKQILKLLLESKEPITAKELAEELGVSRRTIRRDIKELREWG---IPIESK 49 (55)
T ss_dssp HHHHHHHHHHHTTTSBEHHHHHHHCTS-HHHHHHHHHHHHHTT----EEEEE
T ss_pred CHHHHHHHHHHcCCCcCHHHHHHHhCCCHHHHHHHHHHHHHCC---CeEEee
Confidence 344455555 444459999999999999999999999998877 444443
No 88
>PRK10866 outer membrane biogenesis protein BamD; Provisional
Probab=89.77 E-value=19 Score=34.52 Aligned_cols=60 Identities=5% Similarity=-0.055 Sum_probs=52.0
Q ss_pred hHHHHHHHHcCCHHHHHHHHHHHHhhhcCchhHHHHHHHHHHHHHHhcCHHHHHhHHHHH
Q 013559 143 NDFGDFYYAHGALGDAFKSYVRTRDYCTTSKHIIHMCMSAILVSIEMGQFTHVTSYVSKA 202 (441)
Q Consensus 143 ~~la~~~~~~Gd~~~A~~~~~~~r~~~~~~~~~~~~~l~~i~~~i~~~~~~~~~~~~~ka 202 (441)
+..|+||++.|.|..|+.-+..+.+...++...-+.++.++......|.-+.+.+....+
T Consensus 179 ~~ia~~Y~~~~~y~AA~~r~~~v~~~Yp~t~~~~eal~~l~~ay~~lg~~~~a~~~~~~l 238 (243)
T PRK10866 179 LSVAEYYTKRGAYVAVVNRVEQMLRDYPDTQATRDALPLMENAYRQLQLNAQADKVAKII 238 (243)
T ss_pred HHHHHHHHHcCchHHHHHHHHHHHHHCCCCchHHHHHHHHHHHHHHcCChHHHHHHHHHH
Confidence 467999999999999999999998887777888899999999999999998888765544
No 89
>cd00189 TPR Tetratricopeptide repeat domain; typically contains 34 amino acids [WLF]-X(2)-[LIM]-[GAS]-X(2)-[YLF]-X(8)-[ASE]-X(3)-[FYL]-X(2)-[ASL]-X(4)-[PKE] is the consensus sequence; found in a variety of organisms including bacteria, cyanobacteria, yeast, fungi, plants, and humans in various subcellular locations; involved in a variety of functions including protein-protein interactions, but common features in the interaction partners have not been defined; involved in chaperone, cell-cycle, transciption, and protein transport complexes; the number of TPR motifs varies among proteins (1,3-11,13 15,16,19); 5-6 tandem repeats generate a right-handed helical structure with an amphipathic channel that is thought to accomodate an alpha-helix of a target protein; it has been proposed that TPR proteins preferably interact with WD-40 repeat proteins, but in many instances several TPR-proteins seem to aggregate to multi-protein complexes; examples of TPR-proteins include, Cdc16p, Cdc23p and C
Probab=89.52 E-value=1.8 Score=32.14 Aligned_cols=62 Identities=16% Similarity=0.294 Sum_probs=48.5
Q ss_pred hHHhHHHHHHHHcCCHHHHHHHHHHHHhhhcCchhHHHHHHHHHHHHHHhcCHHHHHhHHHHHhc
Q 013559 140 MGYNDFGDFYYAHGALGDAFKSYVRTRDYCTTSKHIIHMCMSAILVSIEMGQFTHVTSYVSKAEQ 204 (441)
Q Consensus 140 ~~~~~la~~~~~~Gd~~~A~~~~~~~r~~~~~~~~~~~~~l~~i~~~i~~~~~~~~~~~~~ka~~ 204 (441)
.++..+|..+...|++++|.+++.+......... ...+.+..+....|++..+...+.++..
T Consensus 35 ~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~---~~~~~~~~~~~~~~~~~~a~~~~~~~~~ 96 (100)
T cd00189 35 DAYYNLAAAYYKLGKYEEALEDYEKALELDPDNA---KAYYNLGLAYYKLGKYEEALEAYEKALE 96 (100)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCcch---hHHHHHHHHHHHHHhHHHHHHHHHHHHc
Confidence 4678899999999999999999998866543322 5566677777888999999888777643
No 90
>PF00515 TPR_1: Tetratricopeptide repeat; InterPro: IPR001440 The tetratrico peptide repeat (TPR) is a structural motif present in a wide range of proteins [, , ]. It mediates protein-protein interactions and the assembly of multiprotein complexes []. The TPR motif consists of 3-16 tandem-repeats of 34 amino acids residues, although individual TPR motifs can be dispersed in the protein sequence. Sequence alignment of the TPR domains reveals a consensus sequence defined by a pattern of small and large amino acids. TPR motifs have been identified in various different organisms, ranging from bacteria to humans. Proteins containing TPRs are involved in a variety of biological processes, such as cell cycle regulation, transcriptional control, mitochondrial and peroxisomal protein transport, neurogenesis and protein folding. The X-ray structure of a domain containing three TPRs from protein phosphatase 5 revealed that TPR adopts a helix-turn-helix arrangement, with adjacent TPR motifs packing in a parallel fashion, resulting in a spiral of repeating anti-parallel alpha-helices []. The two helices are denoted helix A and helix B. The packing angle between helix A and helix B is ~24 degrees; within a single TPR and generates a right-handed superhelical shape. Helix A interacts with helix B and with helix A' of the next TPR. Two protein surfaces are generated: the inner concave surface is contributed to mainly by residue on helices A, and the other surface presents residues from both helices A and B. ; GO: 0005515 protein binding; PDB: 3SF4_C 2LNI_A 1ELW_A 2C0M_A 1FCH_B 3R9A_B 2J9Q_A 2C0L_A 1KT1_A 3FWV_A ....
Probab=89.42 E-value=0.86 Score=28.94 Aligned_cols=30 Identities=23% Similarity=0.525 Sum_probs=25.3
Q ss_pred hHHhHHHHHHHHcCCHHHHHHHHHHHHhhh
Q 013559 140 MGYNDFGDFYYAHGALGDAFKSYVRTRDYC 169 (441)
Q Consensus 140 ~~~~~la~~~~~~Gd~~~A~~~~~~~r~~~ 169 (441)
.+++.+|..|...|++++|.++|.+..+..
T Consensus 2 ~~~~~~g~~~~~~~~~~~A~~~~~~al~~~ 31 (34)
T PF00515_consen 2 EAYYNLGNAYFQLGDYEEALEYYQRALELD 31 (34)
T ss_dssp HHHHHHHHHHHHTT-HHHHHHHHHHHHHHS
T ss_pred HHHHHHHHHHHHhCCchHHHHHHHHHHHHC
Confidence 368899999999999999999999986553
No 91
>PF10300 DUF3808: Protein of unknown function (DUF3808); InterPro: IPR019412 This entry represents a family of proteins conserved from fungi to humans. In humans this protein is expressed in primary breast carcinomas but not in normal breast tissue, and has a putative eukaryotic RNP-1 RNA binding region and a candidate anchoring transmembrane domain. The human protein is coordinately regulated with oestrogen receptor, but is not necessarily oestradiol-responsive []. Members of this family carry a tetratricopeptide repeat (IPR013105 from INTERPRO) at their C terminus.
Probab=89.40 E-value=9.3 Score=40.42 Aligned_cols=99 Identities=16% Similarity=0.072 Sum_probs=74.6
Q ss_pred HHhHHHHHHHHcCCHHHHHHHHHHHHhhhcCchhHHH-HHHHHHHHHHHhcCHHHHHhHHHHHhcccccCChhhhhhHHH
Q 013559 141 GYNDFGDFYYAHGALGDAFKSYVRTRDYCTTSKHIIH-MCMSAILVSIEMGQFTHVTSYVSKAEQTPEALEPVTIAKLRC 219 (441)
Q Consensus 141 ~~~~la~~~~~~Gd~~~A~~~~~~~r~~~~~~~~~~~-~~l~~i~~~i~~~~~~~~~~~~~ka~~~~~~~d~~~~~~l~~ 219 (441)
-++-.|+++...||.++|.++|.+..+.....++.-. +.|.+.=+.+..+||..+..+..++... ..|+ ++.+..
T Consensus 269 fl~~~gR~~~~~g~~~~Ai~~~~~a~~~q~~~~Ql~~l~~~El~w~~~~~~~w~~A~~~f~~L~~~---s~WS-ka~Y~Y 344 (468)
T PF10300_consen 269 FLFFEGRLERLKGNLEEAIESFERAIESQSEWKQLHHLCYFELAWCHMFQHDWEEAAEYFLRLLKE---SKWS-KAFYAY 344 (468)
T ss_pred HHHHHHHHHHHhcCHHHHHHHHHHhccchhhHHhHHHHHHHHHHHHHHHHchHHHHHHHHHHHHhc---cccH-HHHHHH
Confidence 3577799999999999999999986543333344333 3477777789999999999988887663 4675 666677
Q ss_pred HHHHHhcccccH-------HHHHHHHHhcCc
Q 013559 220 AAGLAHLEARKY-------KLAARKFLEVGP 243 (441)
Q Consensus 220 ~~gl~~l~~r~y-------~~Aa~~Fl~~~~ 243 (441)
..|..+...++. ++|..+|-++..
T Consensus 345 ~~a~c~~~l~~~~~~~~~~~~a~~l~~~vp~ 375 (468)
T PF10300_consen 345 LAAACLLMLGREEEAKEHKKEAEELFRKVPK 375 (468)
T ss_pred HHHHHHHhhccchhhhhhHHHHHHHHHHHHH
Confidence 778888887777 888888887754
No 92
>PF14559 TPR_19: Tetratricopeptide repeat; PDB: 2R5S_A 3QDN_B 3QOU_A 3ASG_A 3ASD_A 3AS5_A 3AS4_A 3ASH_B 3FP3_A 3LCA_A ....
Probab=88.96 E-value=0.85 Score=33.76 Aligned_cols=53 Identities=8% Similarity=0.106 Sum_probs=40.9
Q ss_pred HHcCCHHHHHHHHHHHHhhhcCchhHHHHHHHHHHHHHHhcCHHHHHhHHHHHhcc
Q 013559 150 YAHGALGDAFKSYVRTRDYCTTSKHIIHMCMSAILVSIEMGQFTHVTSYVSKAEQT 205 (441)
Q Consensus 150 ~~~Gd~~~A~~~~~~~r~~~~~~~~~~~~~l~~i~~~i~~~~~~~~~~~~~ka~~~ 205 (441)
.+.|++++|.+.|.++...... -.++.+.+..+.+..|+++.+...+.++...
T Consensus 2 l~~~~~~~A~~~~~~~l~~~p~---~~~~~~~la~~~~~~g~~~~A~~~l~~~~~~ 54 (68)
T PF14559_consen 2 LKQGDYDEAIELLEKALQRNPD---NPEARLLLAQCYLKQGQYDEAEELLERLLKQ 54 (68)
T ss_dssp HHTTHHHHHHHHHHHHHHHTTT---SHHHHHHHHHHHHHTT-HHHHHHHHHCCHGG
T ss_pred hhccCHHHHHHHHHHHHHHCCC---CHHHHHHHHHHHHHcCCHHHHHHHHHHHHHH
Confidence 5679999999999998776543 3567778888999999999998888776543
No 93
>smart00420 HTH_DEOR helix_turn_helix, Deoxyribose operon repressor.
Probab=88.58 E-value=0.87 Score=31.81 Aligned_cols=41 Identities=15% Similarity=0.182 Sum_probs=34.0
Q ss_pred HHhccccccccHHhHHHHcCCChHHHHHHHHHHHHcCccce
Q 013559 344 IQYTHPFVSVDLHMMANAFKTSVAGIEKELEALITDNQIQA 384 (441)
Q Consensus 344 ~qy~~pYs~I~L~~mA~~fg~s~~~~E~~L~~LI~~g~L~a 384 (441)
.+++.....++...||+.||++...+.+.|..|...|.|..
T Consensus 6 l~~l~~~~~~s~~~l~~~l~~s~~tv~~~l~~L~~~g~i~~ 46 (53)
T smart00420 6 LELLAQQGKVSVEELAELLGVSEMTIRRDLNKLEEQGLLTR 46 (53)
T ss_pred HHHHHHcCCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEE
Confidence 33434345699999999999999999999999999988754
No 94
>PRK11189 lipoprotein NlpI; Provisional
Probab=88.46 E-value=5.2 Score=39.39 Aligned_cols=94 Identities=13% Similarity=0.051 Sum_probs=50.4
Q ss_pred HHhHHHHHHHHcCCHHHHHHHHHHHHhhhcCchhHHHHHHHHHHHHHHhcCHHHHHhHHHHHhcccccCChhhhhhHHHH
Q 013559 141 GYNDFGDFYYAHGALGDAFKSYVRTRDYCTTSKHIIHMCMSAILVSIEMGQFTHVTSYVSKAEQTPEALEPVTIAKLRCA 220 (441)
Q Consensus 141 ~~~~la~~~~~~Gd~~~A~~~~~~~r~~~~~~~~~~~~~l~~i~~~i~~~~~~~~~~~~~ka~~~~~~~d~~~~~~l~~~ 220 (441)
.++.+|..|...|++.+|...|.+....-... .+....+..+....|+++.+...+.++-.+--. +. .....
T Consensus 66 ~~~~~g~~~~~~g~~~~A~~~~~~Al~l~P~~---~~a~~~lg~~~~~~g~~~~A~~~~~~Al~l~P~-~~----~a~~~ 137 (296)
T PRK11189 66 LHYERGVLYDSLGLRALARNDFSQALALRPDM---ADAYNYLGIYLTQAGNFDAAYEAFDSVLELDPT-YN----YAYLN 137 (296)
T ss_pred HHHHHHHHHHHCCCHHHHHHHHHHHHHcCCCC---HHHHHHHHHHHHHCCCHHHHHHHHHHHHHhCCC-CH----HHHHH
Confidence 46666666666666666666666654443221 234444445556666666666666665443110 11 11123
Q ss_pred HHHHhcccccHHHHHHHHHhcC
Q 013559 221 AGLAHLEARKYKLAARKFLEVG 242 (441)
Q Consensus 221 ~gl~~l~~r~y~~Aa~~Fl~~~ 242 (441)
.|..+...|+|.+|.+.|-.+.
T Consensus 138 lg~~l~~~g~~~eA~~~~~~al 159 (296)
T PRK11189 138 RGIALYYGGRYELAQDDLLAFY 159 (296)
T ss_pred HHHHHHHCCCHHHHHHHHHHHH
Confidence 4555556666666666665554
No 95
>PRK10803 tol-pal system protein YbgF; Provisional
Probab=88.39 E-value=5.4 Score=38.85 Aligned_cols=103 Identities=10% Similarity=-0.011 Sum_probs=73.3
Q ss_pred HHhHHHHH-HHHcCCHHHHHHHHHHHHhhhcCchhHHHHHHHHHHHHHHhcCHHHHHhHHHHHhc-ccccCChhhhhhHH
Q 013559 141 GYNDFGDF-YYAHGALGDAFKSYVRTRDYCTTSKHIIHMCMSAILVSIEMGQFTHVTSYVSKAEQ-TPEALEPVTIAKLR 218 (441)
Q Consensus 141 ~~~~la~~-~~~~Gd~~~A~~~~~~~r~~~~~~~~~~~~~l~~i~~~i~~~~~~~~~~~~~ka~~-~~~~~d~~~~~~l~ 218 (441)
..|+.|.- +.+.|+|.+|...|..+..........-+..+.+..+.+..|++..+.....++-. .++. .+.-...
T Consensus 144 ~~Y~~A~~l~~~~~~y~~Ai~af~~fl~~yP~s~~a~~A~y~LG~~y~~~g~~~~A~~~f~~vv~~yP~s-~~~~dAl-- 220 (263)
T PRK10803 144 TDYNAAIALVQDKSRQDDAIVAFQNFVKKYPDSTYQPNANYWLGQLNYNKGKKDDAAYYFASVVKNYPKS-PKAADAM-- 220 (263)
T ss_pred HHHHHHHHHHHhcCCHHHHHHHHHHHHHHCcCCcchHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHCCCC-cchhHHH--
Confidence 44555554 47789999999999999777666555556667777788889999999999888754 3431 2111111
Q ss_pred HHHHHHhcccccHHHHHHHHHhcCcCCC
Q 013559 219 CAAGLAHLEARKYKLAARKFLEVGPDLG 246 (441)
Q Consensus 219 ~~~gl~~l~~r~y~~Aa~~Fl~~~~t~~ 246 (441)
..-|..+...|++..|...|-.+...++
T Consensus 221 ~klg~~~~~~g~~~~A~~~~~~vi~~yP 248 (263)
T PRK10803 221 FKVGVIMQDKGDTAKAKAVYQQVIKKYP 248 (263)
T ss_pred HHHHHHHHHcCCHHHHHHHHHHHHHHCc
Confidence 2246667788999999999888776554
No 96
>PF13428 TPR_14: Tetratricopeptide repeat
Probab=88.35 E-value=1.6 Score=29.84 Aligned_cols=32 Identities=13% Similarity=0.095 Sum_probs=28.3
Q ss_pred HHhHHHHHHHHcCCHHHHHHHHHHHHhhhcCc
Q 013559 141 GYNDFGDFYYAHGALGDAFKSYVRTRDYCTTS 172 (441)
Q Consensus 141 ~~~~la~~~~~~Gd~~~A~~~~~~~r~~~~~~ 172 (441)
+++.+|..|.+.|++++|.++|.++.....+.
T Consensus 3 ~~~~la~~~~~~G~~~~A~~~~~~~l~~~P~~ 34 (44)
T PF13428_consen 3 AWLALARAYRRLGQPDEAERLLRRALALDPDD 34 (44)
T ss_pred HHHHHHHHHHHcCCHHHHHHHHHHHHHHCcCC
Confidence 57899999999999999999999998876543
No 97
>PRK14574 hmsH outer membrane protein; Provisional
Probab=88.17 E-value=24 Score=40.05 Aligned_cols=95 Identities=7% Similarity=-0.030 Sum_probs=44.5
Q ss_pred HhHHHHHHHHcCCHHHHHHHHHHHHhhhcCchhHHHHHHHHHHHHHHhcCHHHHHhHHHHHhcccccCChhhhhhHHHHH
Q 013559 142 YNDFGDFYYAHGALGDAFKSYVRTRDYCTTSKHIIHMCMSAILVSIEMGQFTHVTSYVSKAEQTPEALEPVTIAKLRCAA 221 (441)
Q Consensus 142 ~~~la~~~~~~Gd~~~A~~~~~~~r~~~~~~~~~~~~~l~~i~~~i~~~~~~~~~~~~~ka~~~~~~~d~~~~~~l~~~~ 221 (441)
.+.-|-+.++.||+..|+..|.++...-......+. .++.+....|+...|..+++|+- ..+... .......
T Consensus 37 ~y~~aii~~r~Gd~~~Al~~L~qaL~~~P~~~~av~---dll~l~~~~G~~~~A~~~~eka~-~p~n~~----~~~llal 108 (822)
T PRK14574 37 QYDSLIIRARAGDTAPVLDYLQEESKAGPLQSGQVD---DWLQIAGWAGRDQEVIDVYERYQ-SSMNIS----SRGLASA 108 (822)
T ss_pred HHHHHHHHHhCCCHHHHHHHHHHHHhhCccchhhHH---HHHHHHHHcCCcHHHHHHHHHhc-cCCCCC----HHHHHHH
Confidence 344555566666666666666655433222110111 44444444566666666666555 111101 0111222
Q ss_pred HHHhcccccHHHHHHHHHhcCcC
Q 013559 222 GLAHLEARKYKLAARKFLEVGPD 244 (441)
Q Consensus 222 gl~~l~~r~y~~Aa~~Fl~~~~t 244 (441)
|..+...|+|.+|.+.|-.+...
T Consensus 109 A~ly~~~gdyd~Aiely~kaL~~ 131 (822)
T PRK14574 109 ARAYRNEKRWDQALALWQSSLKK 131 (822)
T ss_pred HHHHHHcCCHHHHHHHHHHHHhh
Confidence 33555556666666666655543
No 98
>PRK10049 pgaA outer membrane protein PgaA; Provisional
Probab=88.17 E-value=34 Score=38.49 Aligned_cols=96 Identities=11% Similarity=0.047 Sum_probs=72.5
Q ss_pred HHhHHHHHHHHcCCHHHHHHHHHHHHhhhcCchhHHHHHHHHHHHHHHhcCHHHHHhHHHHHhcccccCChhhhhhHHHH
Q 013559 141 GYNDFGDFYYAHGALGDAFKSYVRTRDYCTTSKHIIHMCMSAILVSIEMGQFTHVTSYVSKAEQTPEALEPVTIAKLRCA 220 (441)
Q Consensus 141 ~~~~la~~~~~~Gd~~~A~~~~~~~r~~~~~~~~~~~~~l~~i~~~i~~~~~~~~~~~~~ka~~~~~~~d~~~~~~l~~~ 220 (441)
++..+|..+...|++++|.+.|.+....-... .+....+..+.+..|++..+...+.++-...- .+.. ...
T Consensus 51 ~~~~lA~~~~~~g~~~~A~~~~~~al~~~P~~---~~a~~~la~~l~~~g~~~eA~~~l~~~l~~~P-~~~~-----~~~ 121 (765)
T PRK10049 51 GYAAVAVAYRNLKQWQNSLTLWQKALSLEPQN---DDYQRGLILTLADAGQYDEALVKAKQLVSGAP-DKAN-----LLA 121 (765)
T ss_pred HHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCC---HHHHHHHHHHHHHCCCHHHHHHHHHHHHHhCC-CCHH-----HHH
Confidence 57899999999999999999999987664322 34456777778889999999999998865421 1222 233
Q ss_pred HHHHhcccccHHHHHHHHHhcCcCC
Q 013559 221 AGLAHLEARKYKLAARKFLEVGPDL 245 (441)
Q Consensus 221 ~gl~~l~~r~y~~Aa~~Fl~~~~t~ 245 (441)
-|.++...+++.+|...|-.+..-.
T Consensus 122 la~~l~~~g~~~~Al~~l~~al~~~ 146 (765)
T PRK10049 122 LAYVYKRAGRHWDELRAMTQALPRA 146 (765)
T ss_pred HHHHHHHCCCHHHHHHHHHHHHHhC
Confidence 4777888999999999988876543
No 99
>KOG1126 consensus DNA-binding cell division cycle control protein [Cell cycle control, cell division, chromosome partitioning]
Probab=87.84 E-value=19 Score=39.09 Aligned_cols=189 Identities=13% Similarity=0.071 Sum_probs=104.1
Q ss_pred hHHhHHHHHHHHcCCHHHHHHHHHHHHhhhc---CchhHHH-HHHH------------------------H---HHHHHH
Q 013559 140 MGYNDFGDFYYAHGALGDAFKSYVRTRDYCT---TSKHIIH-MCMS------------------------A---ILVSIE 188 (441)
Q Consensus 140 ~~~~~la~~~~~~Gd~~~A~~~~~~~r~~~~---~~~~~~~-~~l~------------------------~---i~~~i~ 188 (441)
..+..+|+-|++.++|.+|.++|..+|..-. ..-.... .+|+ | -.|.=+
T Consensus 354 wvl~q~GrayFEl~~Y~~a~~~F~~~r~~~p~rv~~meiyST~LWHLq~~v~Ls~Laq~Li~~~~~sPesWca~GNcfSL 433 (638)
T KOG1126|consen 354 WVLSQLGRAYFELIEYDQAERIFSLVRRIEPYRVKGMEIYSTTLWHLQDEVALSYLAQDLIDTDPNSPESWCALGNCFSL 433 (638)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHhhccccccchhHHHHHHHHHHhhHHHHHHHHHHHhhCCCCcHHHHHhcchhhh
Confidence 4778999999999999999999998866421 1111111 1121 1 112234
Q ss_pred hcCHHHHHhHHHHHhccccc--------CChh------------hh-------hhHHHHH--HHHhcccccHHHHHHHHH
Q 013559 189 MGQFTHVTSYVSKAEQTPEA--------LEPV------------TI-------AKLRCAA--GLAHLEARKYKLAARKFL 239 (441)
Q Consensus 189 ~~~~~~~~~~~~ka~~~~~~--------~d~~------------~~-------~~l~~~~--gl~~l~~r~y~~Aa~~Fl 239 (441)
.+|.+.|.+...||-.+-.. |+.- .+ --+++.. |+.++-+++|..|--.|-
T Consensus 434 Qkdh~~Aik~f~RAiQldp~faYayTLlGhE~~~~ee~d~a~~~fr~Al~~~~rhYnAwYGlG~vy~Kqek~e~Ae~~fq 513 (638)
T KOG1126|consen 434 QKDHDTAIKCFKRAIQLDPRFAYAYTLLGHESIATEEFDKAMKSFRKALGVDPRHYNAWYGLGTVYLKQEKLEFAEFHFQ 513 (638)
T ss_pred hhHHHHHHHHHHHhhccCCccchhhhhcCChhhhhHHHHhHHHHHHhhhcCCchhhHHHHhhhhheeccchhhHHHHHHH
Confidence 67888888888888665321 1110 00 0133333 457788888888888887
Q ss_pred hcCcCCCCCchhhhcHHHHHHHHHHHHHhc-CChHHHHHhcccCHhhHhhh-ccch--HHHHHHHHHhcCCHHHHHHHHH
Q 013559 240 EVGPDLGNSYNEVIAAQDVATYGGLCALAS-FDRAELKSKVIDNVNFRNFL-ELVP--EVRELINDFYSSRYASCLDYLG 315 (441)
Q Consensus 240 ~~~~t~~~~~~el~s~~d~~~Y~~l~al~s-~~R~eLk~~vl~~~~~~~~l-e~~p--~~~~ll~~f~~~~y~~~~~~L~ 315 (441)
.++..-+. ..++-+.+..+.. +.+.+---.+++- .-++ ...| .+....--|...+|.+++..|+
T Consensus 514 kA~~INP~---------nsvi~~~~g~~~~~~k~~d~AL~~~~~---A~~ld~kn~l~~~~~~~il~~~~~~~eal~~LE 581 (638)
T KOG1126|consen 514 KAVEINPS---------NSVILCHIGRIQHQLKRKDKALQLYEK---AIHLDPKNPLCKYHRASILFSLGRYVEALQELE 581 (638)
T ss_pred hhhcCCcc---------chhHHhhhhHHHHHhhhhhHHHHHHHH---HHhcCCCCchhHHHHHHHHHhhcchHHHHHHHH
Confidence 77654321 1111111111111 1111110001110 0001 1223 2445555667789999999999
Q ss_pred HhHHhhhhchhHHHHHHHHHHHHHH
Q 013559 316 NLKANLLLDIHLHDHVETLYDQIRN 340 (441)
Q Consensus 316 ~~~~~l~~D~~L~~h~~~l~~~iR~ 340 (441)
+++.....+-..+--...+++.++.
T Consensus 582 eLk~~vP~es~v~~llgki~k~~~~ 606 (638)
T KOG1126|consen 582 ELKELVPQESSVFALLGKIYKRLGN 606 (638)
T ss_pred HHHHhCcchHHHHHHHHHHHHHHcc
Confidence 9998887777666556666666553
No 100
>PF12569 NARP1: NMDA receptor-regulated protein 1 ; InterPro: IPR021183 This group represents N-terminal acetyltransferase A (NatA) auxiliary subunit and represents a non-catalytic component of the NatA N-terminal acetyltransferase, which catalyzes acetylation of proteins beginning with Met-Ser, Met-Gly and Met-Ala. N-terminal acetylation plays a role in normal eukaryotic translation and processing, protect against proteolytic degradation and protein turnover. NAT1 anchors ARD1 and NAT5 to the ribosome and may present the N- terminal of nascent polypeptides for acetylation [], [].
Probab=87.45 E-value=45 Score=35.81 Aligned_cols=129 Identities=10% Similarity=0.086 Sum_probs=90.5
Q ss_pred HHHhHHhHHHHHHHHcCCHHHHHHHHHHHHhhhcCchhHHHHHHHHHHHHHHhcCHHHHHhHHHHHhcccccCChhhhhh
Q 013559 137 SIRMGYNDFGDFYYAHGALGDAFKSYVRTRDYCTTSKHIIHMCMSAILVSIEMGQFTHVTSYVSKAEQTPEALEPVTIAK 216 (441)
Q Consensus 137 sir~~~~~la~~~~~~Gd~~~A~~~~~~~r~~~~~~~~~~~~~l~~i~~~i~~~~~~~~~~~~~ka~~~~~~~d~~~~~~ 216 (441)
....+++=+|.||...|++++|++++.+..+.+.+ .++.++...++.-..|++..|...+..|+.+-- .|. .
T Consensus 192 ~~lw~~~~lAqhyd~~g~~~~Al~~Id~aI~htPt---~~ely~~KarilKh~G~~~~Aa~~~~~Ar~LD~-~DR----y 263 (517)
T PF12569_consen 192 TLLWTLYFLAQHYDYLGDYEKALEYIDKAIEHTPT---LVELYMTKARILKHAGDLKEAAEAMDEARELDL-ADR----Y 263 (517)
T ss_pred HHHHHHHHHHHHHHHhCCHHHHHHHHHHHHhcCCC---cHHHHHHHHHHHHHCCCHHHHHHHHHHHHhCCh-hhH----H
Confidence 34568899999999999999999999998777543 478999999999999999999999999998742 121 2
Q ss_pred HHHHHHHHhcccccHHHHHHHHHhcCcCCCCCchhhhcHHHHHHHHHHHHHhcCChHH
Q 013559 217 LRCAAGLAHLEARKYKLAARKFLEVGPDLGNSYNEVIAAQDVATYGGLCALASFDRAE 274 (441)
Q Consensus 217 l~~~~gl~~l~~r~y~~Aa~~Fl~~~~t~~~~~~el~s~~d~~~Y~~l~al~s~~R~e 274 (441)
+..-.+.+.+..|+..+|...+- .|.....+...-+.--+.++|.+=||-+-..+.+
T Consensus 264 iNsK~aKy~LRa~~~e~A~~~~~-~Ftr~~~~~~~~L~~mQc~Wf~~e~a~a~~r~~~ 320 (517)
T PF12569_consen 264 INSKCAKYLLRAGRIEEAEKTAS-LFTREDVDPLSNLNDMQCMWFETECAEAYLRQGD 320 (517)
T ss_pred HHHHHHHHHHHCCCHHHHHHHHH-hhcCCCCCcccCHHHHHHHHHHHHHHHHHHHHhh
Confidence 44556678889999988754332 2211111111112222346888888888765443
No 101
>PRK12370 invasion protein regulator; Provisional
Probab=87.20 E-value=5.2 Score=43.13 Aligned_cols=98 Identities=11% Similarity=0.041 Sum_probs=70.0
Q ss_pred hHHhHHHHHHHHcCCHHHHHHHHHHHHhhhcCchhHHHHHHHHHHHHHHhcCHHHHHhHHHHHhcccccCChhhhhhHHH
Q 013559 140 MGYNDFGDFYYAHGALGDAFKSYVRTRDYCTTSKHIIHMCMSAILVSIEMGQFTHVTSYVSKAEQTPEALEPVTIAKLRC 219 (441)
Q Consensus 140 ~~~~~la~~~~~~Gd~~~A~~~~~~~r~~~~~~~~~~~~~l~~i~~~i~~~~~~~~~~~~~ka~~~~~~~d~~~~~~l~~ 219 (441)
.+++.+|..+...|++++|...+.+..+....... ..+....+....|+++.+...+.++.......++. ...
T Consensus 373 ~a~~~lg~~l~~~G~~~eAi~~~~~Al~l~P~~~~---~~~~~~~~~~~~g~~eeA~~~~~~~l~~~~p~~~~----~~~ 445 (553)
T PRK12370 373 DIKYYYGWNLFMAGQLEEALQTINECLKLDPTRAA---AGITKLWITYYHTGIDDAIRLGDELRSQHLQDNPI----LLS 445 (553)
T ss_pred HHHHHHHHHHHHCCCHHHHHHHHHHHHhcCCCChh---hHHHHHHHHHhccCHHHHHHHHHHHHHhccccCHH----HHH
Confidence 47899999999999999999999998777543221 11223334566789999988888775442222332 234
Q ss_pred HHHHHhcccccHHHHHHHHHhcCcC
Q 013559 220 AAGLAHLEARKYKLAARKFLEVGPD 244 (441)
Q Consensus 220 ~~gl~~l~~r~y~~Aa~~Fl~~~~t 244 (441)
..|.++...|++.+|...|......
T Consensus 446 ~la~~l~~~G~~~eA~~~~~~~~~~ 470 (553)
T PRK12370 446 MQVMFLSLKGKHELARKLTKEISTQ 470 (553)
T ss_pred HHHHHHHhCCCHHHHHHHHHHhhhc
Confidence 5677888899999999998776544
No 102
>KOG1155 consensus Anaphase-promoting complex (APC), Cdc23 subunit [Cell cycle control, cell division, chromosome partitioning; Posttranslational modification, protein turnover, chaperones]
Probab=87.19 E-value=8.6 Score=40.16 Aligned_cols=103 Identities=12% Similarity=0.154 Sum_probs=65.1
Q ss_pred cCCHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhHHHH-HhHHhHHHHHHHHcCCHHHHHHHHHHHHh---hhcCc-hhHH
Q 013559 102 AMDEAWCDSVDRRAEQRKEKLENELNAYRTNLIKESI-RMGYNDFGDFYYAHGALGDAFKSYVRTRD---YCTTS-KHII 176 (441)
Q Consensus 102 ~~D~~~~~~~~~~~~~~~~~Le~el~~~~~n~~~esi-r~~~~~la~~~~~~Gd~~~A~~~~~~~r~---~~~~~-~~~~ 176 (441)
|-|+-....+-.-. .++.+++.-++-|+.-..-..+ -+++..||+.|.+.+|+++|..+|.+..+ .++.. .+.+
T Consensus 429 PnDsRlw~aLG~CY-~kl~~~~eAiKCykrai~~~dte~~~l~~LakLye~l~d~~eAa~~yek~v~~~~~eg~~~~~t~ 507 (559)
T KOG1155|consen 429 PNDSRLWVALGECY-EKLNRLEEAIKCYKRAILLGDTEGSALVRLAKLYEELKDLNEAAQYYEKYVEVSELEGEIDDETI 507 (559)
T ss_pred CCchHHHHHHHHHH-HHhccHHHHHHHHHHHHhccccchHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHhhcccchHHH
Confidence 55666655665554 6677788888777542211111 14788888888888888888888888744 23322 3345
Q ss_pred HHHHHHHHHHHHhcCHHHHHhHHHHHhcc
Q 013559 177 HMCMSAILVSIEMGQFTHVTSYVSKAEQT 205 (441)
Q Consensus 177 ~~~l~~i~~~i~~~~~~~~~~~~~ka~~~ 205 (441)
..++-+.+-.+-.+||+.+..+.+++...
T Consensus 508 ka~~fLA~~f~k~~~~~~As~Ya~~~~~~ 536 (559)
T KOG1155|consen 508 KARLFLAEYFKKMKDFDEASYYATLVLKG 536 (559)
T ss_pred HHHHHHHHHHHhhcchHHHHHHHHHHhcC
Confidence 55544444455567888888777766544
No 103
>KOG1125 consensus TPR repeat-containing protein [General function prediction only]
Probab=87.15 E-value=2.8 Score=44.48 Aligned_cols=136 Identities=16% Similarity=0.226 Sum_probs=84.3
Q ss_pred hHHHHHhHHhHHHHHHHHcCCHHHHHHHHHHHHhhhcCchhHHHHHHHHHHHHHHhcC-HHHHHhHHHHHhcccccCChh
Q 013559 134 IKESIRMGYNDFGDFYYAHGALGDAFKSYVRTRDYCTTSKHIIHMCMSAILVSIEMGQ-FTHVTSYVSKAEQTPEALEPV 212 (441)
Q Consensus 134 ~~esir~~~~~la~~~~~~Gd~~~A~~~~~~~r~~~~~~~~~~~~~l~~i~~~i~~~~-~~~~~~~~~ka~~~~~~~d~~ 212 (441)
++.+| +.-||-+|+-.|+|+.|.+||......-.+. ..+|+.+=..+--|+ ...|....++|..+.=+
T Consensus 428 ~Dpdv---Q~~LGVLy~ls~efdraiDcf~~AL~v~Pnd----~~lWNRLGAtLAN~~~s~EAIsAY~rALqLqP~---- 496 (579)
T KOG1125|consen 428 IDPDV---QSGLGVLYNLSGEFDRAVDCFEAALQVKPND----YLLWNRLGATLANGNRSEEAISAYNRALQLQPG---- 496 (579)
T ss_pred CChhH---HhhhHHHHhcchHHHHHHHHHHHHHhcCCch----HHHHHHhhHHhcCCcccHHHHHHHHHHHhcCCC----
Confidence 55554 4578899999999999999999875443221 234555555555553 44566677777765321
Q ss_pred hhhhHHHHHHHHhcccccHHHHHHHHHhcCcCCCC--Cchhhh-cHHHHHHHHHHHHHhcCChHHHHHhcccC
Q 013559 213 TIAKLRCAAGLAHLEARKYKLAARKFLEVGPDLGN--SYNEVI-AAQDVATYGGLCALASFDRAELKSKVIDN 282 (441)
Q Consensus 213 ~~~~l~~~~gl~~l~~r~y~~Aa~~Fl~~~~t~~~--~~~el~-s~~d~~~Y~~l~al~s~~R~eLk~~vl~~ 282 (441)
..|.+.=-|+.+|..|.|++|+.+|+.++.-... ...+.. +.+.|--++= .+|..+.|.++...+..+
T Consensus 497 -yVR~RyNlgIS~mNlG~ykEA~~hlL~AL~mq~ks~~~~~~~~~se~iw~tLR-~als~~~~~D~l~~a~~~ 567 (579)
T KOG1125|consen 497 -YVRVRYNLGISCMNLGAYKEAVKHLLEALSMQRKSRNHNKAPMASENIWQTLR-LALSAMNRSDLLQEAAPS 567 (579)
T ss_pred -eeeeehhhhhhhhhhhhHHHHHHHHHHHHHhhhcccccccCCcchHHHHHHHH-HHHHHcCCchHHHHhccc
Confidence 1233445799999999999999999998752110 011111 1222323333 567778888865544443
No 104
>PF13371 TPR_9: Tetratricopeptide repeat
Probab=86.85 E-value=2.6 Score=31.55 Aligned_cols=57 Identities=9% Similarity=0.190 Sum_probs=39.7
Q ss_pred HHHHHHHcCCHHHHHHHHHHHHhhhcCchhHHHHHHHHHHHHHHhcCHHHHHhHHHHHhc
Q 013559 145 FGDFYYAHGALGDAFKSYVRTRDYCTTSKHIIHMCMSAILVSIEMGQFTHVTSYVSKAEQ 204 (441)
Q Consensus 145 la~~~~~~Gd~~~A~~~~~~~r~~~~~~~~~~~~~l~~i~~~i~~~~~~~~~~~~~ka~~ 204 (441)
|+..|.+.|++++|.+++.++....+. -....+....+....|+|..+...+.++-.
T Consensus 1 l~~~~~~~~~~~~A~~~~~~~l~~~p~---~~~~~~~~a~~~~~~g~~~~A~~~l~~~l~ 57 (73)
T PF13371_consen 1 LKQIYLQQEDYEEALEVLERALELDPD---DPELWLQRARCLFQLGRYEEALEDLERALE 57 (73)
T ss_pred CHHHHHhCCCHHHHHHHHHHHHHhCcc---cchhhHHHHHHHHHhccHHHHHHHHHHHHH
Confidence 356778888888888888887665322 344555666677777888888877777654
No 105
>PRK10049 pgaA outer membrane protein PgaA; Provisional
Probab=86.85 E-value=41 Score=37.85 Aligned_cols=167 Identities=8% Similarity=-0.041 Sum_probs=82.3
Q ss_pred HHHHHHHcCCHHHHHHHHHHHHhhhcCc-hhHHHHHHHHHHHHHHhcCHHHHHhHHHHHhcc-cc--------cCChh-h
Q 013559 145 FGDFYYAHGALGDAFKSYVRTRDYCTTS-KHIIHMCMSAILVSIEMGQFTHVTSYVSKAEQT-PE--------ALEPV-T 213 (441)
Q Consensus 145 la~~~~~~Gd~~~A~~~~~~~r~~~~~~-~~~~~~~l~~i~~~i~~~~~~~~~~~~~ka~~~-~~--------~~d~~-~ 213 (441)
+|..|+..|++++|.+.|.++...-... ....+....+..+.+..++++.+...+.++... +. ...|. .
T Consensus 278 la~~yl~~g~~e~A~~~l~~~l~~~p~~~~~~~~~~~~L~~a~~~~g~~~eA~~~l~~~~~~~P~~~~~~~~~~~~p~~~ 357 (765)
T PRK10049 278 VASAYLKLHQPEKAQSILTELFYHPETIADLSDEELADLFYSLLESENYPGALTVTAHTINNSPPFLRLYGSPTSIPNDD 357 (765)
T ss_pred HHHHHHhcCCcHHHHHHHHHHhhcCCCCCCCChHHHHHHHHHHHhcccHHHHHHHHHHHhhcCCceEeecCCCCCCCCch
Confidence 5777777777777777777764322111 111223333333446667777777777766543 11 00111 1
Q ss_pred hhhHHHHHHHHhcccccHHHHHHHHHhcCcCCCCCchhhhcHHHHHHHHHHHHHh-cCChHHHHHhcccCHhhHhhhccc
Q 013559 214 IAKLRCAAGLAHLEARKYKLAARKFLEVGPDLGNSYNEVIAAQDVATYGGLCALA-SFDRAELKSKVIDNVNFRNFLELV 292 (441)
Q Consensus 214 ~~~l~~~~gl~~l~~r~y~~Aa~~Fl~~~~t~~~~~~el~s~~d~~~Y~~l~al~-s~~R~eLk~~vl~~~~~~~~le~~ 292 (441)
........|.++...|++.+|...|-++....+++ .++. . .++.+. ...+.+--. ..+...++..
T Consensus 358 ~~~a~~~~a~~l~~~g~~~eA~~~l~~al~~~P~n-~~l~------~--~lA~l~~~~g~~~~A~-----~~l~~al~l~ 423 (765)
T PRK10049 358 WLQGQSLLSQVAKYSNDLPQAEMRARELAYNAPGN-QGLR------I--DYASVLQARGWPRAAE-----NELKKAEVLE 423 (765)
T ss_pred HHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCC-HHHH------H--HHHHHHHhcCCHHHHH-----HHHHHHHhhC
Confidence 11223345556667788888877777765443322 2221 1 122222 111111000 1122333344
Q ss_pred hH-----HHHHHHHHhcCCHHHHHHHHHHhHHhhhhch
Q 013559 293 PE-----VRELINDFYSSRYASCLDYLGNLKANLLLDI 325 (441)
Q Consensus 293 p~-----~~~ll~~f~~~~y~~~~~~L~~~~~~l~~D~ 325 (441)
|. +.......-..+|......+..+......|+
T Consensus 424 Pd~~~l~~~~a~~al~~~~~~~A~~~~~~ll~~~Pd~~ 461 (765)
T PRK10049 424 PRNINLEVEQAWTALDLQEWRQMDVLTDDVVAREPQDP 461 (765)
T ss_pred CCChHHHHHHHHHHHHhCCHHHHHHHHHHHHHhCCCCH
Confidence 43 1333344445677777777777766666665
No 106
>PF13374 TPR_10: Tetratricopeptide repeat; PDB: 3CEQ_B 3EDT_H 3NF1_A.
Probab=86.61 E-value=1.5 Score=28.79 Aligned_cols=30 Identities=17% Similarity=0.282 Sum_probs=25.2
Q ss_pred hHHhHHHHHHHHcCCHHHHHHHHHHHHhhh
Q 013559 140 MGYNDFGDFYYAHGALGDAFKSYVRTRDYC 169 (441)
Q Consensus 140 ~~~~~la~~~~~~Gd~~~A~~~~~~~r~~~ 169 (441)
.++..+|..|...|++++|.+++.+..+.+
T Consensus 3 ~~~~~la~~~~~~g~~~~A~~~~~~al~~~ 32 (42)
T PF13374_consen 3 SALNNLANAYRAQGRYEEALELLEEALEIR 32 (42)
T ss_dssp HHHHHHHHHHHHCT-HHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHhhhhcchhhHHHHHHHHHH
Confidence 467899999999999999999999986554
No 107
>PF13512 TPR_18: Tetratricopeptide repeat
Probab=86.57 E-value=7.2 Score=34.32 Aligned_cols=28 Identities=25% Similarity=0.374 Sum_probs=14.0
Q ss_pred HHhHHHHHHHHcCCHHHHHHHHHHHHhh
Q 013559 141 GYNDFGDFYYAHGALGDAFKSYVRTRDY 168 (441)
Q Consensus 141 ~~~~la~~~~~~Gd~~~A~~~~~~~r~~ 168 (441)
+.++||.-|++.|+|.+|...+.++...
T Consensus 49 AqL~l~yayy~~~~y~~A~a~~~rFirL 76 (142)
T PF13512_consen 49 AQLDLAYAYYKQGDYEEAIAAYDRFIRL 76 (142)
T ss_pred HHHHHHHHHHHccCHHHHHHHHHHHHHh
Confidence 4445555555555555555555554433
No 108
>KOG1586 consensus Protein required for fusion of vesicles in vesicular transport, alpha-SNAP [Intracellular trafficking, secretion, and vesicular transport]
Probab=86.43 E-value=32 Score=33.05 Aligned_cols=193 Identities=19% Similarity=0.221 Sum_probs=108.9
Q ss_pred hHHhHHHHHHHHcCCHHHHHHHHHHHHhh--hcCchhHHHHHHHHHHHHHHhcCHHHHHhHHHHHhcccc----------
Q 013559 140 MGYNDFGDFYYAHGALGDAFKSYVRTRDY--CTTSKHIIHMCMSAILVSIEMGQFTHVTSYVSKAEQTPE---------- 207 (441)
Q Consensus 140 ~~~~~la~~~~~~Gd~~~A~~~~~~~r~~--~~~~~~~~~~~l~~i~~~i~~~~~~~~~~~~~ka~~~~~---------- 207 (441)
.++.+.|++|.+.|+..+|..+|..+-.- -..|..-++.+-.-|.+...+|+|.++-++--.+-++.+
T Consensus 55 ~aflkaA~~h~k~~skhDaat~YveA~~cykk~~~~eAv~cL~~aieIyt~~Grf~~aAk~~~~iaEiyEsdl~d~ekaI 134 (288)
T KOG1586|consen 55 DAFLKAADLHLKAGSKHDAATTYVEAANCYKKVDPEEAVNCLEKAIEIYTDMGRFTMAAKHHIEIAEIYESDLQDFEKAI 134 (288)
T ss_pred HHHHHHHHHHHhcCCchhHHHHHHHHHHHhhccChHHHHHHHHHHHHHHHhhhHHHHHHhhhhhHHHHHhhhHHHHHHHH
Confidence 47788888888888877777777665221 135566666666677777777777765443222211111
Q ss_pred -----cCCh-------hhhhh--HHHHHHHHhcccccHHHHHHHHHhcCc-CCCCCchhhh--cHHHHHHHHHHHHHhcC
Q 013559 208 -----ALEP-------VTIAK--LRCAAGLAHLEARKYKLAARKFLEVGP-DLGNSYNEVI--AAQDVATYGGLCALASF 270 (441)
Q Consensus 208 -----~~d~-------~~~~~--l~~~~gl~~l~~r~y~~Aa~~Fl~~~~-t~~~~~~el~--s~~d~~~Y~~l~al~s~ 270 (441)
.++| ..-|+ |+|. -+.-..+.|..|...|-++.. +.+ +.++ +..|-..=.+||=+..-
T Consensus 135 ~~YE~Aae~yk~ees~ssANKC~lKvA--~yaa~leqY~~Ai~iyeqva~~s~~---n~LLKys~KdyflkAgLChl~~~ 209 (288)
T KOG1586|consen 135 AHYEQAAEYYKGEESVSSANKCLLKVA--QYAAQLEQYSKAIDIYEQVARSSLD---NNLLKYSAKDYFLKAGLCHLCKA 209 (288)
T ss_pred HHHHHHHHHHcchhhhhhHHHHHHHHH--HHHHHHHHHHHHHHHHHHHHHHhcc---chHHHhHHHHHHHHHHHHhHhcc
Confidence 1111 12233 3332 233345778888887776643 222 1233 34444445677877754
Q ss_pred Ch----HHHHHhcccCHhhHhhhccchHHHHHHHHHhcCCHHHHHHHHHHhHHhhhhchhHHHHHHHHHHHH
Q 013559 271 DR----AELKSKVIDNVNFRNFLELVPEVRELINDFYSSRYASCLDYLGNLKANLLLDIHLHDHVETLYDQI 338 (441)
Q Consensus 271 ~R----~eLk~~vl~~~~~~~~le~~p~~~~ll~~f~~~~y~~~~~~L~~~~~~l~~D~~L~~h~~~l~~~i 338 (441)
+- ..|.+----+|.|-.- ....-+++|+.+.-..+-..|-+...++.+.-++|.+...++-.+-+.|
T Consensus 210 D~v~a~~ALeky~~~dP~F~ds-REckflk~L~~aieE~d~e~fte~vkefDsisrLD~W~ttiLlkiK~si 280 (288)
T KOG1586|consen 210 DEVNAQRALEKYQELDPAFTDS-RECKFLKDLLDAIEEQDIEKFTEVVKEFDSISRLDQWKTTILLKIKKSI 280 (288)
T ss_pred cHHHHHHHHHHHHhcCCccccc-HHHHHHHHHHHHHhhhhHHHHHHHHHhhhccchHHHHHHHHHHHHHHHH
Confidence 42 2222211112222110 1112357788888888888888888888888889988877766554443
No 109
>PF00392 GntR: Bacterial regulatory proteins, gntR family; InterPro: IPR000524 Many bacterial transcription regulation proteins bind DNA through a helix-turn-helix (HTH) motif, which can be classified into subfamilies on the basis of sequence similarities. The HTH GntR family has many members distributed among diverse bacterial groups that regulate various biological processes. It was named GntR after the Bacillus subtilis repressor of the gluconate operon []. Family members include GntR, HutC, KorA, NtaR, FadR, ExuR, FarR, DgoR and PhnF. The crystal structure of the FadR protein has been determined []. In general, these proteins contain a DNA-binding HTH domain at the N terminus, and an effector-binding or oligomerisation domain at the C terminus (IPR011711 from INTERPRO). The DNA-binding domain is well conserved in structure for the whole of the GntR family, consisting of a 3-helical bundle core with a small beta-sheet (wing); the GntR winged helix structure is similar to that found in several other transcriptional regulator families. The regions outside the DNA-binding domain are more variable and are consequently used to define GntR subfamilies []. This entry represents the N-terminal DNA-binding domain of the GntR family.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 1HW1_B 1H9T_A 1HW2_A 1H9G_A 1E2X_A 3IHU_A 3C7J_A 2RA5_A 3BY6_C 3IC7_A ....
Probab=86.27 E-value=2.9 Score=31.11 Aligned_cols=52 Identities=23% Similarity=0.321 Sum_probs=44.2
Q ss_pred HHHHHHHHHHHHHHhccccccc-cHHhHHHHcCCChHHHHHHHHHHHHcCccc
Q 013559 332 ETLYDQIRNKALIQYTHPFVSV-DLHMMANAFKTSVAGIEKELEALITDNQIQ 383 (441)
Q Consensus 332 ~~l~~~iR~~~i~qy~~pYs~I-~L~~mA~~fg~s~~~~E~~L~~LI~~g~L~ 383 (441)
..+++.++..+...-+.|=+.+ +...||+.||+|...+-+-+..|..+|-+.
T Consensus 3 ~~i~~~l~~~I~~g~~~~g~~lps~~~la~~~~vsr~tvr~al~~L~~~g~i~ 55 (64)
T PF00392_consen 3 EQIYDQLRQAILSGRLPPGDRLPSERELAERYGVSRTTVREALRRLEAEGLIE 55 (64)
T ss_dssp HHHHHHHHHHHHTTSS-TTSBE--HHHHHHHHTS-HHHHHHHHHHHHHTTSEE
T ss_pred HHHHHHHHHHHHcCCCCCCCEeCCHHHHHHHhccCCcHHHHHHHHHHHCCcEE
Confidence 4677888888888888999999 999999999999999999999999999874
No 110
>COG1849 Uncharacterized protein conserved in archaea [Function unknown]
Probab=86.24 E-value=7.7 Score=31.17 Aligned_cols=52 Identities=17% Similarity=0.290 Sum_probs=34.4
Q ss_pred HHHHHHHHHHHHHHHHHHhhhh-----HH--HHHhHHhHHHHHHHHcCCHHHHHHHHHH
Q 013559 113 RRAEQRKEKLENELNAYRTNLI-----KE--SIRMGYNDFGDFYYAHGALGDAFKSYVR 164 (441)
Q Consensus 113 ~~~~~~~~~Le~el~~~~~n~~-----~e--sir~~~~~la~~~~~~Gd~~~A~~~~~~ 164 (441)
.+..+=++.++..|+..+.-.. +. ++...++.=|+||++.||+..|+.++.-
T Consensus 8 ekiekYi~~leeaL~~~k~~~~~~s~ae~~~~ma~~Y~~Dakyf~ekGD~vtAfa~~sY 66 (90)
T COG1849 8 EKIEKYIELLEEALKEIKSRPGDRSAAEDFVDMAESYFEDAKYFLEKGDYVTAFAALSY 66 (90)
T ss_pred HHHHHHHHHHHHHHHHhccCCCcchHHHHHHHHHHHHHHHHHHHHHcCcHHHHHHHHHH
Confidence 3444445556666665544333 22 2334788889999999999999998764
No 111
>PF08784 RPA_C: Replication protein A C terminal; InterPro: IPR014892 This protein corresponds to the C-terminal of the single stranded DNA binding protein RPA (replication protein A). RPA is involved in many DNA metabolic pathways including DNA replication, DNA repair, recombination, cell cycle and DNA damage checkpoints. ; PDB: 1QUQ_C 2PQA_C 3KDF_B 2Z6K_B 2PI2_B 1L1O_E 1DPU_A 1Z1D_A.
Probab=85.81 E-value=0.89 Score=37.35 Aligned_cols=39 Identities=23% Similarity=0.292 Sum_probs=35.1
Q ss_pred cccccHHhHHHHcCCChHHHHHHHHHHHHcCccceEecC
Q 013559 350 FVSVDLHMMANAFKTSVAGIEKELEALITDNQIQARIDS 388 (441)
Q Consensus 350 Ys~I~L~~mA~~fg~s~~~~E~~L~~LI~~g~L~akID~ 388 (441)
=.=|.++.+++.|+++.+++.+.|-.|+.+|.|...||-
T Consensus 63 ~~Gv~v~~I~~~l~~~~~~v~~al~~L~~eG~IYsTiDd 101 (102)
T PF08784_consen 63 EEGVHVDEIAQQLGMSENEVRKALDFLSNEGHIYSTIDD 101 (102)
T ss_dssp TTTEEHHHHHHHSTS-HHHHHHHHHHHHHTTSEEESSST
T ss_pred CCcccHHHHHHHhCcCHHHHHHHHHHHHhCCeEecccCC
Confidence 346999999999999999999999999999999999883
No 112
>KOG3785 consensus Uncharacterized conserved protein [Function unknown]
Probab=85.68 E-value=5.3 Score=40.35 Aligned_cols=71 Identities=18% Similarity=0.199 Sum_probs=48.7
Q ss_pred hhhHHHHHhHHhHHHHHHHHcCCHHHHHHHHHHHHhhhcCchhHHHHHHHHHHHHHHhcCHHHHHhHHHHHhcc
Q 013559 132 NLIKESIRMGYNDFGDFYYAHGALGDAFKSYVRTRDYCTTSKHIIHMCMSAILVSIEMGQFTHVTSYVSKAEQT 205 (441)
Q Consensus 132 n~~~esir~~~~~la~~~~~~Gd~~~A~~~~~~~r~~~~~~~~~~~~~l~~i~~~i~~~~~~~~~~~~~ka~~~ 205 (441)
|...||--....-+|.-++..|||++|+..|.-+.+..+.++. +.+ ++.=+..+.|.+..++....|+-..
T Consensus 50 ~~~~EEE~~~~lWia~C~fhLgdY~~Al~~Y~~~~~~~~~~~e-l~v--nLAcc~FyLg~Y~eA~~~~~ka~k~ 120 (557)
T KOG3785|consen 50 NLDREEEDSLQLWIAHCYFHLGDYEEALNVYTFLMNKDDAPAE-LGV--NLACCKFYLGQYIEAKSIAEKAPKT 120 (557)
T ss_pred ccchhhhHHHHHHHHHHHHhhccHHHHHHHHHHHhccCCCCcc-cch--hHHHHHHHHHHHHHHHHHHhhCCCC
Confidence 4443333345567789999999999999999988765444332 332 3333557788999998887777554
No 113
>KOG2376 consensus Signal recognition particle, subunit Srp72 [Intracellular trafficking, secretion, and vesicular transport]
Probab=85.57 E-value=55 Score=35.38 Aligned_cols=103 Identities=12% Similarity=0.114 Sum_probs=68.8
Q ss_pred HHhHHHHHHHHcCCHHHHHHHHHHHHhh------------hc----------------CchhHHHHHHHHHHHHHHhcCH
Q 013559 141 GYNDFGDFYYAHGALGDAFKSYVRTRDY------------CT----------------TSKHIIHMCMSAILVSIEMGQF 192 (441)
Q Consensus 141 ~~~~la~~~~~~Gd~~~A~~~~~~~r~~------------~~----------------~~~~~~~~~l~~i~~~i~~~~~ 192 (441)
...=.|.++|+.|+|++|++.|.++... |. .+....+.+++..=+.|..|+|
T Consensus 112 ll~L~AQvlYrl~~ydealdiY~~L~kn~~dd~d~~~r~nl~a~~a~l~~~~~q~v~~v~e~syel~yN~Ac~~i~~gky 191 (652)
T KOG2376|consen 112 LLELRAQVLYRLERYDEALDIYQHLAKNNSDDQDEERRANLLAVAAALQVQLLQSVPEVPEDSYELLYNTACILIENGKY 191 (652)
T ss_pred HHHHHHHHHHHHhhHHHHHHHHHHHHhcCCchHHHHHHHHHHHHHHhhhHHHHHhccCCCcchHHHHHHHHHHHHhcccH
Confidence 4455688999999999999999976211 10 1122345677777777889999
Q ss_pred HHHHhHHHHH-----hcccc--cCChhhhhhHH---HHHHHHhcccccHHHHHHHHHhcCc
Q 013559 193 THVTSYVSKA-----EQTPE--ALEPVTIAKLR---CAAGLAHLEARKYKLAARKFLEVGP 243 (441)
Q Consensus 193 ~~~~~~~~ka-----~~~~~--~~d~~~~~~l~---~~~gl~~l~~r~y~~Aa~~Fl~~~~ 243 (441)
..|...+.++ +.+-+ .++.+....+. +.-+..+...|+=.+|.+.+-+++.
T Consensus 192 ~qA~elL~kA~~~~~e~l~~~d~~eEeie~el~~IrvQlayVlQ~~Gqt~ea~~iy~~~i~ 252 (652)
T KOG2376|consen 192 NQAIELLEKALRICREKLEDEDTNEEEIEEELNPIRVQLAYVLQLQGQTAEASSIYVDIIK 252 (652)
T ss_pred HHHHHHHHHHHHHHHHhhcccccchhhHHHHHHHHHHHHHHHHHHhcchHHHHHHHHHHHH
Confidence 9999999999 33332 23345554444 4444556668888888887776653
No 114
>KOG1840 consensus Kinesin light chain [Cytoskeleton]
Probab=85.44 E-value=55 Score=35.05 Aligned_cols=105 Identities=16% Similarity=0.182 Sum_probs=73.1
Q ss_pred HHHHhHHhHHHHHHHHcCCHHHHHHHHHHH---Hhhhc--CchhHHHHHHHHHHHHHHhcCHHHHHhHHHHHhcccc---
Q 013559 136 ESIRMGYNDFGDFYYAHGALGDAFKSYVRT---RDYCT--TSKHIIHMCMSAILVSIEMGQFTHVTSYVSKAEQTPE--- 207 (441)
Q Consensus 136 esir~~~~~la~~~~~~Gd~~~A~~~~~~~---r~~~~--~~~~~~~~~l~~i~~~i~~~~~~~~~~~~~ka~~~~~--- 207 (441)
..++.....+|.+|...|++.+|...|.++ ++.+- +..++...+.++--+..-.|++..+..++.+|-.+..
T Consensus 238 l~va~~l~~~a~~y~~~~k~~eAv~ly~~AL~i~e~~~G~~h~~va~~l~nLa~ly~~~GKf~EA~~~~e~Al~I~~~~~ 317 (508)
T KOG1840|consen 238 LVVASMLNILALVYRSLGKYDEAVNLYEEALTIREEVFGEDHPAVAATLNNLAVLYYKQGKFAEAEEYCERALEIYEKLL 317 (508)
T ss_pred HHHHHHHHHHHHHHHHhccHHHHHHHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHhccCChHHHHHHHHHHHHHHHHhh
Confidence 445555667999999999999999999986 45442 4445555666666667778999999999999977654
Q ss_pred -cCChhhhhhHHHHHHHHhcccccHHHHHHHHHhc
Q 013559 208 -ALEPVTIAKLRCAAGLAHLEARKYKLAARKFLEV 241 (441)
Q Consensus 208 -~~d~~~~~~l~~~~gl~~l~~r~y~~Aa~~Fl~~ 241 (441)
..++++...+.- .|..+...+.|.+|..++-.+
T Consensus 318 ~~~~~~v~~~l~~-~~~~~~~~~~~Eea~~l~q~a 351 (508)
T KOG1840|consen 318 GASHPEVAAQLSE-LAAILQSMNEYEEAKKLLQKA 351 (508)
T ss_pred ccChHHHHHHHHH-HHHHHHHhcchhHHHHHHHHH
Confidence 234455444443 344556677777776665543
No 115
>COG3063 PilF Tfp pilus assembly protein PilF [Cell motility and secretion / Intracellular trafficking and secretion]
Probab=85.42 E-value=35 Score=32.61 Aligned_cols=97 Identities=22% Similarity=0.301 Sum_probs=69.4
Q ss_pred hHHhHHHHHHHHcCCHHHHHHHHHHHHhhhcCchhHHHHHHHHHHHHHHhcCHHHHHhHHHHHhcccccCChhhhhhHHH
Q 013559 140 MGYNDFGDFYYAHGALGDAFKSYVRTRDYCTTSKHIIHMCMSAILVSIEMGQFTHVTSYVSKAEQTPEALEPVTIAKLRC 219 (441)
Q Consensus 140 ~~~~~la~~~~~~Gd~~~A~~~~~~~r~~~~~~~~~~~~~l~~i~~~i~~~~~~~~~~~~~ka~~~~~~~d~~~~~~l~~ 219 (441)
+.+..+|.|+|..|.+++|...|.+...... =++.-+..-+..-|++-.|+++.+..++.++-...-..++.+.
T Consensus 104 dVLNNYG~FLC~qg~~~eA~q~F~~Al~~P~-Y~~~s~t~eN~G~Cal~~gq~~~A~~~l~raL~~dp~~~~~~l----- 177 (250)
T COG3063 104 DVLNNYGAFLCAQGRPEEAMQQFERALADPA-YGEPSDTLENLGLCALKAGQFDQAEEYLKRALELDPQFPPALL----- 177 (250)
T ss_pred chhhhhhHHHHhCCChHHHHHHHHHHHhCCC-CCCcchhhhhhHHHHhhcCCchhHHHHHHHHHHhCcCCChHHH-----
Confidence 4789999999999999999999999855321 1233455567777889999999999999998775432233222
Q ss_pred HHHHHhcccccHHHHHHHHHhcCc
Q 013559 220 AAGLAHLEARKYKLAARKFLEVGP 243 (441)
Q Consensus 220 ~~gl~~l~~r~y~~Aa~~Fl~~~~ 243 (441)
-..-.++..|+|-.| ..|++...
T Consensus 178 ~~a~~~~~~~~y~~A-r~~~~~~~ 200 (250)
T COG3063 178 ELARLHYKAGDYAPA-RLYLERYQ 200 (250)
T ss_pred HHHHHHHhcccchHH-HHHHHHHH
Confidence 123356778999886 56666543
No 116
>TIGR02917 PEP_TPR_lipo putative PEP-CTERM system TPR-repeat lipoprotein. This protein family occurs in strictly within a subset of Gram-negative bacterial species with the proposed PEP-CTERM/exosortase system, analogous to the LPXTG/sortase system common in Gram-positive bacteria. This protein occurs in a species if and only if a transmembrane histidine kinase (TIGR02916) and a DNA-binding response regulator (TIGR02915) also occur. The present of tetratricopeptide repeats (TPR) suggests protein-protein interaction, possibly for the regulation of PEP-CTERM protein expression, since many PEP-CTERM proteins in these genomes are preceded by a proposed DNA binding site for the response regulator.
Probab=85.22 E-value=65 Score=35.55 Aligned_cols=100 Identities=15% Similarity=0.068 Sum_probs=64.4
Q ss_pred HHHHhHHhHHHHHHHHcCCHHHHHHHHHHHHhhhcCchhHHHHHHHHHHHHHHhcCHHHHHhHHHHHhcccccCChhhhh
Q 013559 136 ESIRMGYNDFGDFYYAHGALGDAFKSYVRTRDYCTTSKHIIHMCMSAILVSIEMGQFTHVTSYVSKAEQTPEALEPVTIA 215 (441)
Q Consensus 136 esir~~~~~la~~~~~~Gd~~~A~~~~~~~r~~~~~~~~~~~~~l~~i~~~i~~~~~~~~~~~~~ka~~~~~~~d~~~~~ 215 (441)
+.....+..+|..++..|++++|.+.|.++.+..... .+..+....+....|+|..+...+.++....- .+ .
T Consensus 122 ~~~~~~~~~~~~~~~~~~~~~~A~~~~~~a~~~~~~~---~~~~~~la~~~~~~~~~~~A~~~~~~~~~~~~-~~----~ 193 (899)
T TIGR02917 122 EGAAELLALRGLAYLGLGQLELAQKSYEQALAIDPRS---LYAKLGLAQLALAENRFDEARALIDEVLTADP-GN----V 193 (899)
T ss_pred hhhHHHHHHHHHHHHHcCCHHHHHHHHHHHHhcCCCC---hhhHHHHHHHHHHCCCHHHHHHHHHHHHHhCC-CC----h
Confidence 3344567778888888888888888888776554322 34556667777778888888877777644311 11 1
Q ss_pred hHHHHHHHHhcccccHHHHHHHHHhcCc
Q 013559 216 KLRCAAGLAHLEARKYKLAARKFLEVGP 243 (441)
Q Consensus 216 ~l~~~~gl~~l~~r~y~~Aa~~Fl~~~~ 243 (441)
......|..+...|+|..|...|-.+..
T Consensus 194 ~~~~~~~~~~~~~g~~~~A~~~~~~a~~ 221 (899)
T TIGR02917 194 DALLLKGDLLLSLGNIELALAAYRKAIA 221 (899)
T ss_pred HHHHHHHHHHHhcCCHHHHHHHHHHHHh
Confidence 2234446666677777777777766643
No 117
>PRK11189 lipoprotein NlpI; Provisional
Probab=85.13 E-value=40 Score=33.06 Aligned_cols=100 Identities=9% Similarity=-0.080 Sum_probs=63.7
Q ss_pred hHHhHHHHHHHHcCCHHHHHHHHHHHHhhhcCchhHHHHHHHHHHHHHHhcCHHHHHhHHHHHhcccccCChh-------
Q 013559 140 MGYNDFGDFYYAHGALGDAFKSYVRTRDYCTTSKHIIHMCMSAILVSIEMGQFTHVTSYVSKAEQTPEALEPV------- 212 (441)
Q Consensus 140 ~~~~~la~~~~~~Gd~~~A~~~~~~~r~~~~~~~~~~~~~l~~i~~~i~~~~~~~~~~~~~ka~~~~~~~d~~------- 212 (441)
.++..+|..++..|++++|.+.+.+......+.. .... +..+....+++..+...+.++-...+...|.
T Consensus 133 ~a~~~lg~~l~~~g~~~eA~~~~~~al~~~P~~~--~~~~--~~~l~~~~~~~~~A~~~l~~~~~~~~~~~~~~~~~~~~ 208 (296)
T PRK11189 133 YAYLNRGIALYYGGRYELAQDDLLAFYQDDPNDP--YRAL--WLYLAESKLDPKQAKENLKQRYEKLDKEQWGWNIVEFY 208 (296)
T ss_pred HHHHHHHHHHHHCCCHHHHHHHHHHHHHhCCCCH--HHHH--HHHHHHccCCHHHHHHHHHHHHhhCCccccHHHHHHHH
Confidence 4788999999999999999999999876654332 1122 2233344567777777775543221111110
Q ss_pred ----------------------h---hhhHHHHHHHHhcccccHHHHHHHHHhcCc
Q 013559 213 ----------------------T---IAKLRCAAGLAHLEARKYKLAARKFLEVGP 243 (441)
Q Consensus 213 ----------------------~---~~~l~~~~gl~~l~~r~y~~Aa~~Fl~~~~ 243 (441)
+ ......+-|..+...|++.+|..+|-.+..
T Consensus 209 lg~~~~~~~~~~~~~~~~~~~~l~~~~~ea~~~Lg~~~~~~g~~~~A~~~~~~Al~ 264 (296)
T PRK11189 209 LGKISEETLMERLKAGATDNTELAERLCETYFYLAKYYLSLGDLDEAAALFKLALA 264 (296)
T ss_pred ccCCCHHHHHHHHHhcCCCcHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 0 001234557888888999999988887764
No 118
>PF04733 Coatomer_E: Coatomer epsilon subunit; InterPro: IPR006822 Proteins synthesised on the ribosome and processed in the endoplasmic reticulum are transported from the Golgi apparatus to the trans-Golgi network (TGN), and from there via small carrier vesicles to their final destination compartment. This traffic is bidirectional, to ensure that proteins required to form vesicles are recycled. Vesicles have specific coat proteins (such as clathrin or coatomer) that are important for cargo selection and direction of transfer []. While clathrin mediates endocytic protein transport, and transport from ER to Golgi, coatomers primarily mediate intra-Golgi transport, as well as the reverse Golgi to ER transport of dilysine-tagged proteins []. For example, the coatomer COP1 (coat protein complex 1) is responsible for reverse transport of recycled proteins from Golgi and pre-Golgi compartments back to the ER, while COPII buds vesicles from the ER to the Golgi []. Coatomers reversibly associate with Golgi (non-clathrin-coated) vesicles to mediate protein transport and for budding from Golgi membranes []. Activated small guanine triphosphatases (GTPases) attract coat proteins to specific membrane export sites, thereby linking coatomers to export cargos. As coat proteins polymerise, vesicles are formed and budded from membrane-bound organelles. Coatomer complexes also influence Golgi structural integrity, as well as the processing, activity, and endocytic recycling of LDL receptors. In mammals, coatomer complexes can only be recruited by membranes associated to ADP-ribosylation factors (ARFs), which are small GTP-binding proteins. Coatomer complexes are hetero-oligomers composed of at least an alpha, beta, beta', gamma, delta, epsilon and zeta subunits. This entry represents the epsilon subunit of the coatomer complex, which is involved in the regulation of intracellular protein trafficking between the endoplasmic reticulum and the Golgi complex []. More information about these proteins can be found at Protein of the Month: Clathrin [].; GO: 0005198 structural molecule activity, 0006890 retrograde vesicle-mediated transport, Golgi to ER, 0030126 COPI vesicle coat; PDB: 3MV2_B 3MV3_F 3MKR_A.
Probab=84.95 E-value=3.1 Score=41.13 Aligned_cols=114 Identities=16% Similarity=0.120 Sum_probs=73.4
Q ss_pred HhHHHHHHHHcCCHHHHHHHHHHHHhhhcCchhHHHHHHHHHHHHHHhcCHHHHHhHHHHHhccccc-------CChh--
Q 013559 142 YNDFGDFYYAHGALGDAFKSYVRTRDYCTTSKHIIHMCMSAILVSIEMGQFTHVTSYVSKAEQTPEA-------LEPV-- 212 (441)
Q Consensus 142 ~~~la~~~~~~Gd~~~A~~~~~~~r~~~~~~~~~~~~~l~~i~~~i~~~~~~~~~~~~~ka~~~~~~-------~d~~-- 212 (441)
..-.|.++...|++++|++.+.+. ..++...-.+.+.+..+..+.|.+.+.+.+..-+. ..|.
T Consensus 105 ~~~~A~i~~~~~~~~~AL~~l~~~--------~~lE~~al~Vqi~L~~~R~dlA~k~l~~~~~~~eD~~l~qLa~awv~l 176 (290)
T PF04733_consen 105 QLLAATILFHEGDYEEALKLLHKG--------GSLELLALAVQILLKMNRPDLAEKELKNMQQIDEDSILTQLAEAWVNL 176 (290)
T ss_dssp HHHHHHHHCCCCHHHHHHCCCTTT--------TCHHHHHHHHHHHHHTT-HHHHHHHHHHHHCCSCCHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHcCCHHHHHHHHHcc--------CcccHHHHHHHHHHHcCCHHHHHHHHHHHHhcCCcHHHHHHHHHHHHH
Confidence 355677888899999999887542 33677778888889999999999988888765321 0010
Q ss_pred ----------------------hhhhHHHHHHHHhcccccHHHHHHHHHhcCcCCCCCchhhhcHHHHHHHHHHHHHhcC
Q 013559 213 ----------------------TIAKLRCAAGLAHLEARKYKLAARKFLEVGPDLGNSYNEVIAAQDVATYGGLCALASF 270 (441)
Q Consensus 213 ----------------------~~~~l~~~~gl~~l~~r~y~~Aa~~Fl~~~~t~~~~~~el~s~~d~~~Y~~l~al~s~ 270 (441)
-...+....++.+|+.|+|.+|-+.+.++....+. .++.+ .-.++|+....
T Consensus 177 ~~g~e~~~~A~y~f~El~~~~~~t~~~lng~A~~~l~~~~~~eAe~~L~~al~~~~~-~~d~L------aNliv~~~~~g 249 (290)
T PF04733_consen 177 ATGGEKYQDAFYIFEELSDKFGSTPKLLNGLAVCHLQLGHYEEAEELLEEALEKDPN-DPDTL------ANLIVCSLHLG 249 (290)
T ss_dssp HHTTTCCCHHHHHHHHHHCCS--SHHHHHHHHHHHHHCT-HHHHHHHHHHHCCC-CC-HHHHH------HHHHHHHHHTT
T ss_pred HhCchhHHHHHHHHHHHHhccCCCHHHHHHHHHHHHHhCCHHHHHHHHHHHHHhccC-CHHHH------HHHHHHHHHhC
Confidence 01223334566888999999999998888653322 23333 45555555543
No 119
>PF13412 HTH_24: Winged helix-turn-helix DNA-binding; PDB: 1I1G_B 2IA0_B 3I4P_A 2GQQ_A 2L4A_A 2CFX_B 2DBB_B 2EFO_A 2EFQ_A 2PN6_A ....
Probab=84.46 E-value=2.4 Score=29.48 Aligned_cols=42 Identities=14% Similarity=0.237 Sum_probs=34.3
Q ss_pred HHHHHhccccccccHHhHHHHcCCChHHHHHHHHHHHHcCcc
Q 013559 341 KALIQYTHPFVSVDLHMMANAFKTSVAGIEKELEALITDNQI 382 (441)
Q Consensus 341 ~~i~qy~~pYs~I~L~~mA~~fg~s~~~~E~~L~~LI~~g~L 382 (441)
+.+..++.-...++...+|+.+|+|...+-+.|-+|+..|-|
T Consensus 6 ~~Il~~l~~~~~~t~~ela~~~~is~~tv~~~l~~L~~~g~I 47 (48)
T PF13412_consen 6 RKILNYLRENPRITQKELAEKLGISRSTVNRYLKKLEEKGLI 47 (48)
T ss_dssp HHHHHHHHHCTTS-HHHHHHHHTS-HHHHHHHHHHHHHTTSE
T ss_pred HHHHHHHHHcCCCCHHHHHHHhCCCHHHHHHHHHHHHHCcCc
Confidence 444566666788999999999999999999999999999865
No 120
>COG1729 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=84.30 E-value=5.3 Score=38.74 Aligned_cols=65 Identities=15% Similarity=0.153 Sum_probs=47.0
Q ss_pred hHHhHHHHHHHHcCCHHHHHHHHHHHHhhhcCchhHHHHHHHHHHHHHHhcCHHHHHhHHHHHhc
Q 013559 140 MGYNDFGDFYYAHGALGDAFKSYVRTRDYCTTSKHIIHMCMSAILVSIEMGQFTHVTSYVSKAEQ 204 (441)
Q Consensus 140 ~~~~~la~~~~~~Gd~~~A~~~~~~~r~~~~~~~~~~~~~l~~i~~~i~~~~~~~~~~~~~ka~~ 204 (441)
+++|=||+.+|..|||++|...|..+..-.......=|+.|-+..+....|+-+.+...+..+-.
T Consensus 179 nA~yWLGe~~y~qg~y~~Aa~~f~~~~k~~P~s~KApdallKlg~~~~~l~~~d~A~atl~qv~k 243 (262)
T COG1729 179 NAYYWLGESLYAQGDYEDAAYIFARVVKDYPKSPKAPDALLKLGVSLGRLGNTDEACATLQQVIK 243 (262)
T ss_pred hhHHHHHHHHHhcccchHHHHHHHHHHHhCCCCCCChHHHHHHHHHHHHhcCHHHHHHHHHHHHH
Confidence 47888888888888888888888887433333333347777777777788888888877776644
No 121
>PRK10747 putative protoheme IX biogenesis protein; Provisional
Probab=83.76 E-value=54 Score=33.65 Aligned_cols=59 Identities=8% Similarity=-0.004 Sum_probs=41.8
Q ss_pred HHHHHHHcCCHHHHHHHHHHHHhhhcCchhHHHHHHHHHHHHHHhcCHHHHHhHHHHHhccc
Q 013559 145 FGDFYYAHGALGDAFKSYVRTRDYCTTSKHIIHMCMSAILVSIEMGQFTHVTSYVSKAEQTP 206 (441)
Q Consensus 145 la~~~~~~Gd~~~A~~~~~~~r~~~~~~~~~~~~~l~~i~~~i~~~~~~~~~~~~~ka~~~~ 206 (441)
.++++...|+++.|.+.+.+..+..+... ........+.+..|+|+.+...+.+++...
T Consensus 159 ~a~l~l~~g~~~~Al~~l~~~~~~~P~~~---~al~ll~~~~~~~gdw~~a~~~l~~l~k~~ 217 (398)
T PRK10747 159 RVRIQLARNENHAARHGVDKLLEVAPRHP---EVLRLAEQAYIRTGAWSSLLDILPSMAKAH 217 (398)
T ss_pred HHHHHHHCCCHHHHHHHHHHHHhcCCCCH---HHHHHHHHHHHHHHhHHHHHHHHHHHHHcC
Confidence 37888888888888888888877654333 333444566677788888887777776643
No 122
>PF13424 TPR_12: Tetratricopeptide repeat; PDB: 3RO2_A 3Q15_A 3ASG_A 3ASD_A 3AS5_A 3AS4_A 3ASH_B 4A1S_B 3CEQ_B 3EDT_H ....
Probab=83.56 E-value=4.2 Score=30.92 Aligned_cols=68 Identities=16% Similarity=0.110 Sum_probs=49.7
Q ss_pred HHHHHHHHHHHHHHhcCHHHHHhHHHHHhcccc-cCCh-hhhhhHHHHHHHHhcccccHHHHHHHHHhcC
Q 013559 175 IIHMCMSAILVSIEMGQFTHVTSYVSKAEQTPE-ALEP-VTIAKLRCAAGLAHLEARKYKLAARKFLEVG 242 (441)
Q Consensus 175 ~~~~~l~~i~~~i~~~~~~~~~~~~~ka~~~~~-~~d~-~~~~~l~~~~gl~~l~~r~y~~Aa~~Fl~~~ 242 (441)
...++.++..+....|+|+.+..+..|+-.... .++. ........--|..+...|+|.+|.+.|-.+.
T Consensus 4 ~a~~~~~la~~~~~~~~~~~A~~~~~~al~~~~~~~~~~~~~a~~~~~lg~~~~~~g~~~~A~~~~~~al 73 (78)
T PF13424_consen 4 TANAYNNLARVYRELGRYDEALDYYEKALDIEEQLGDDHPDTANTLNNLGECYYRLGDYEEALEYYQKAL 73 (78)
T ss_dssp HHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHTTTHHHHHHHHHHHHHHHHHHTTHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHH
Confidence 345667777888899999999999999988744 2332 2234445556778888999999999987764
No 123
>COG4105 ComL DNA uptake lipoprotein [General function prediction only]
Probab=83.54 E-value=31 Score=33.31 Aligned_cols=110 Identities=15% Similarity=0.051 Sum_probs=73.9
Q ss_pred HHHHhHHhHHHHHHHHcCCHHHHHHHHHHHHhhhcCchhHHHHHHHHHHHH-HH-----hcCHHHHHhHHHHHhccccc-
Q 013559 136 ESIRMGYNDFGDFYYAHGALGDAFKSYVRTRDYCTTSKHIIHMCMSAILVS-IE-----MGQFTHVTSYVSKAEQTPEA- 208 (441)
Q Consensus 136 esir~~~~~la~~~~~~Gd~~~A~~~~~~~r~~~~~~~~~~~~~l~~i~~~-i~-----~~~~~~~~~~~~ka~~~~~~- 208 (441)
+-.+.++++++--+++.|+|..|..+..++....++... ++..+-+.-++ ++ .+|-..+...+...+..+..
T Consensus 68 ~~~~qa~l~l~yA~Yk~~~y~~A~~~~drFi~lyP~~~n-~dY~~YlkgLs~~~~i~~~~rDq~~~~~A~~~f~~~i~ry 146 (254)
T COG4105 68 PYSEQAQLDLAYAYYKNGEYDLALAYIDRFIRLYPTHPN-ADYAYYLKGLSYFFQIDDVTRDQSAARAAFAAFKELVQRY 146 (254)
T ss_pred cccHHHHHHHHHHHHhcccHHHHHHHHHHHHHhCCCCCC-hhHHHHHHHHHHhccCCccccCHHHHHHHHHHHHHHHHHC
Confidence 444778999999999999999999999998555443333 44333322222 22 35666777767666666541
Q ss_pred ------CChh--------hhhhHHHHHHHHhcccccHHHHHHHHHhcCcCCC
Q 013559 209 ------LEPV--------TIAKLRCAAGLAHLEARKYKLAARKFLEVGPDLG 246 (441)
Q Consensus 209 ------~d~~--------~~~~l~~~~gl~~l~~r~y~~Aa~~Fl~~~~t~~ 246 (441)
.|.. ..+.....=|.+++..|.|..|+..|-++..+++
T Consensus 147 PnS~Ya~dA~~~i~~~~d~LA~~Em~IaryY~kr~~~~AA~nR~~~v~e~y~ 198 (254)
T COG4105 147 PNSRYAPDAKARIVKLNDALAGHEMAIARYYLKRGAYVAAINRFEEVLENYP 198 (254)
T ss_pred CCCcchhhHHHHHHHHHHHHHHHHHHHHHHHHHhcChHHHHHHHHHHHhccc
Confidence 1111 1233344457789999999999999999988764
No 124
>PRK09782 bacteriophage N4 receptor, outer membrane subunit; Provisional
Probab=83.35 E-value=75 Score=37.02 Aligned_cols=95 Identities=6% Similarity=-0.076 Sum_probs=71.3
Q ss_pred hHHhHHHHHHHHcCCHHHHHHHHHHHHhhhcCchhHHHHHHHHHHHHHHhcCHHHHHhHHHHHhcccccCChhhhhhHHH
Q 013559 140 MGYNDFGDFYYAHGALGDAFKSYVRTRDYCTTSKHIIHMCMSAILVSIEMGQFTHVTSYVSKAEQTPEALEPVTIAKLRC 219 (441)
Q Consensus 140 ~~~~~la~~~~~~Gd~~~A~~~~~~~r~~~~~~~~~~~~~l~~i~~~i~~~~~~~~~~~~~ka~~~~~~~d~~~~~~l~~ 219 (441)
..++..|..+...||+.+|+..|.++.+.-.+. ..+.+.+.+..+..|+++.+..++.|+-..-. .+......+
T Consensus 45 ~~~f~~a~~~~~~Gd~~~A~~~l~~Al~~dP~n---~~~~~~LA~~yl~~g~~~~A~~~~~kAv~ldP-~n~~~~~~L-- 118 (987)
T PRK09782 45 YPRLDKALKAQKNNDEATAIREFEYIHQQVPDN---IPLTLYLAEAYRHFGHDDRARLLLEDQLKRHP-GDARLERSL-- 118 (987)
T ss_pred HHHHHHHHHHHhCCCHHHHHHHHHHHHHhCCCC---HHHHHHHHHHHHHCCCHHHHHHHHHHHHhcCc-ccHHHHHHH--
Confidence 467888999999999999999999987765433 66668999999999999999999998866532 232222222
Q ss_pred HHHHHhcccccHHHHHHHHHhcCcCCC
Q 013559 220 AAGLAHLEARKYKLAARKFLEVGPDLG 246 (441)
Q Consensus 220 ~~gl~~l~~r~y~~Aa~~Fl~~~~t~~ 246 (441)
|. + ++|.+|+..|-+......
T Consensus 119 --a~--i--~~~~kA~~~ye~l~~~~P 139 (987)
T PRK09782 119 --AA--I--PVEVKSVTTVEELLAQQK 139 (987)
T ss_pred --HH--h--ccChhHHHHHHHHHHhCC
Confidence 22 2 999999988888775443
No 125
>KOG2002 consensus TPR-containing nuclear phosphoprotein that regulates K(+) uptake [Inorganic ion transport and metabolism]
Probab=83.33 E-value=25 Score=39.87 Aligned_cols=102 Identities=11% Similarity=0.062 Sum_probs=78.0
Q ss_pred hHHhHHHHHHHHcCCHHHHHHHHHHHHhhhcCchhHHHHHHHHHHHHHHhcCHHHHHhHHHHHhcccccCChhhhhhHHH
Q 013559 140 MGYNDFGDFYYAHGALGDAFKSYVRTRDYCTTSKHIIHMCMSAILVSIEMGQFTHVTSYVSKAEQTPEALEPVTIAKLRC 219 (441)
Q Consensus 140 ~~~~~la~~~~~~Gd~~~A~~~~~~~r~~~~~~~~~~~~~l~~i~~~i~~~~~~~~~~~~~ka~~~~~~~d~~~~~~l~~ 219 (441)
+++..||.|||--|||+.+......+...+....-+.+.++.+.|+.=-.|||+.+..+.-.+...-... .+..
T Consensus 271 ~~l~~LAn~fyfK~dy~~v~~la~~ai~~t~~~~~~aes~Y~~gRs~Ha~Gd~ekA~~yY~~s~k~~~d~------~~l~ 344 (1018)
T KOG2002|consen 271 VALNHLANHFYFKKDYERVWHLAEHAIKNTENKSIKAESFYQLGRSYHAQGDFEKAFKYYMESLKADNDN------FVLP 344 (1018)
T ss_pred HHHHHHHHHHhhcccHHHHHHHHHHHHHhhhhhHHHHHHHHHHHHHHHhhccHHHHHHHHHHHHccCCCC------cccc
Confidence 3778999999999999999999998877765555566788999999999999999999888776643311 2223
Q ss_pred HHHH--HhcccccHHHHHHHHHhcCcCCCC
Q 013559 220 AAGL--AHLEARKYKLAARKFLEVGPDLGN 247 (441)
Q Consensus 220 ~~gl--~~l~~r~y~~Aa~~Fl~~~~t~~~ 247 (441)
..|| .++..+++..|...|=.+....++
T Consensus 345 ~~GlgQm~i~~~dle~s~~~fEkv~k~~p~ 374 (1018)
T KOG2002|consen 345 LVGLGQMYIKRGDLEESKFCFEKVLKQLPN 374 (1018)
T ss_pred ccchhHHHHHhchHHHHHHHHHHHHHhCcc
Confidence 3444 567789999998888777665544
No 126
>PF09743 DUF2042: Uncharacterized conserved protein (DUF2042); InterPro: IPR018611 The ubiquitin fold modifier 1 (Ufm1) is the most recently discovered ubiquitin-like modifier whose conjugation (ufmylation) system is conserved in multicellular organisms. Ufm1 is known to covalently attach with cellular protein(s) via a specific E1-activating enzyme (Uba5), an E2-conjugating enzyme (Ufc1), and a E3-ligating enzyme []. This entry represents E3 UFM1-protein ligase 1.
Probab=83.29 E-value=8.2 Score=37.80 Aligned_cols=66 Identities=18% Similarity=0.295 Sum_probs=53.5
Q ss_pred chhHHHHHHHHHHHHHHHHHHHhccccccccHHhHHHHcCCChHHHHHHHHHHHHcCccceEecCCCCeEEEe
Q 013559 324 DIHLHDHVETLYDQIRNKALIQYTHPFVSVDLHMMANAFKTSVAGIEKELEALITDNQIQARIDSHNKILYAR 396 (441)
Q Consensus 324 D~~L~~h~~~l~~~iR~~~i~qy~~pYs~I~L~~mA~~fg~s~~~~E~~L~~LI~~g~L~akID~~~gvv~~~ 396 (441)
+.+-..+++.+.++|+.+.=. -..|+++.+|+.|++|.+++-+.+..-...+.|+|++|.. ++++.
T Consensus 107 elit~~Yld~l~~Eine~Lqe-----~G~vsi~eLa~~~~Lp~efl~~~li~~~lg~~I~g~~d~~--~lyT~ 172 (272)
T PF09743_consen 107 ELITDSYLDSLAEEINEKLQE-----SGQVSISELAKQYDLPSEFLKEELISKRLGKIIKGRLDGD--VLYTE 172 (272)
T ss_pred EEccHHHHHHHHHHHHHHHHH-----cCeEeHHHHHHhcCCcHHHHHHHHhhhhcCcceeEEEeCC--EEecH
Confidence 334456778888888766543 5899999999999999999998888889999999999998 55543
No 127
>KOG0543 consensus FKBP-type peptidyl-prolyl cis-trans isomerase [Posttranslational modification, protein turnover, chaperones]
Probab=83.06 E-value=6 Score=40.47 Aligned_cols=95 Identities=17% Similarity=0.207 Sum_probs=70.2
Q ss_pred HHHHHHHHcCCHHHHHHHHHHHHh---hhc--Cc-------hhHHHHHHHHHHHHHHhcCHHHHHhHHHHHhcccccCCh
Q 013559 144 DFGDFYYAHGALGDAFKSYVRTRD---YCT--TS-------KHIIHMCMSAILVSIEMGQFTHVTSYVSKAEQTPEALEP 211 (441)
Q Consensus 144 ~la~~~~~~Gd~~~A~~~~~~~r~---~~~--~~-------~~~~~~~l~~i~~~i~~~~~~~~~~~~~ka~~~~~~~d~ 211 (441)
.-|+.|++.|+|..|...|.+... ++. +. .-++-+.+++..|.+-++.|..+....+++-.+-..
T Consensus 213 e~Gn~~fK~gk~~~A~~~Yerav~~l~~~~~~~~ee~~~~~~~k~~~~lNlA~c~lKl~~~~~Ai~~c~kvLe~~~~--- 289 (397)
T KOG0543|consen 213 ERGNVLFKEGKFKLAKKRYERAVSFLEYRRSFDEEEQKKAEALKLACHLNLAACYLKLKEYKEAIESCNKVLELDPN--- 289 (397)
T ss_pred HhhhHHHhhchHHHHHHHHHHHHHHhhccccCCHHHHHHHHHHHHHHhhHHHHHHHhhhhHHHHHHHHHHHHhcCCC---
Confidence 458899999999999999998633 332 11 123446688888889999999999888887665431
Q ss_pred hhhhhHHHHHHHHhcccccHHHHHHHHHhcCc
Q 013559 212 VTIAKLRCAAGLAHLEARKYKLAARKFLEVGP 243 (441)
Q Consensus 212 ~~~~~l~~~~gl~~l~~r~y~~Aa~~Fl~~~~ 243 (441)
-.++-+ -.|.+++..++|..|...|..+..
T Consensus 290 N~KALy--RrG~A~l~~~e~~~A~~df~ka~k 319 (397)
T KOG0543|consen 290 NVKALY--RRGQALLALGEYDLARDDFQKALK 319 (397)
T ss_pred chhHHH--HHHHHHHhhccHHHHHHHHHHHHH
Confidence 122222 268889999999999999998865
No 128
>KOG1585 consensus Protein required for fusion of vesicles in vesicular transport, gamma-SNAP [Intracellular trafficking, secretion, and vesicular transport]
Probab=83.00 E-value=47 Score=32.16 Aligned_cols=190 Identities=14% Similarity=0.119 Sum_probs=97.3
Q ss_pred HHHHHHHHHHHhhhhHHHHHhHHhHHHHHHHHcCCHHHHHHHHHHHHh---hhcCchhHHHHHHHHHHHHHHhcCHHHHH
Q 013559 120 EKLENELNAYRTNLIKESIRMGYNDFGDFYYAHGALGDAFKSYVRTRD---YCTTSKHIIHMCMSAILVSIEMGQFTHVT 196 (441)
Q Consensus 120 ~~Le~el~~~~~n~~~esir~~~~~la~~~~~~Gd~~~A~~~~~~~r~---~~~~~~~~~~~~l~~i~~~i~~~~~~~~~ 196 (441)
+-|..-.+.|++|.--=---.++..-|-+.-+...++++...|.+.-. -|+++. ...|.++...=.++.-+-+.+.
T Consensus 52 dcLlkA~~~yEnnrslfhAAKayEqaamLake~~klsEvvdl~eKAs~lY~E~Gspd-tAAmaleKAak~lenv~Pd~Al 130 (308)
T KOG1585|consen 52 DCLLKASKGYENNRSLFHAAKAYEQAAMLAKELSKLSEVVDLYEKASELYVECGSPD-TAAMALEKAAKALENVKPDDAL 130 (308)
T ss_pred HHHHHHHHHHHhcccHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHhCCcc-hHHHHHHHHHHHhhcCCHHHHH
Confidence 346656666665542111111233333333344455666666655422 233332 3555556655566666777777
Q ss_pred hHHHHHhcccccCChhhhhh-HHHHHHHHhcccccHHHHHHHHHhcCcCCCCCchhhhcHHHHHHHHHHHHHhcCChHHH
Q 013559 197 SYVSKAEQTPEALEPVTIAK-LRCAAGLAHLEARKYKLAARKFLEVGPDLGNSYNEVIAAQDVATYGGLCALASFDRAEL 275 (441)
Q Consensus 197 ~~~~ka~~~~~~~d~~~~~~-l~~~~gl~~l~~r~y~~Aa~~Fl~~~~t~~~~~~el~s~~d~~~Y~~l~al~s~~R~eL 275 (441)
....++-..++.++...+.. +.--.|..+.--+.|.+|+..|+.-.. .+....++++..+-.+-..|+-+.+++.
T Consensus 131 qlYqralavve~~dr~~ma~el~gk~sr~lVrl~kf~Eaa~a~lKe~~----~~~~~~~y~~~~k~~va~ilv~L~~~Dy 206 (308)
T KOG1585|consen 131 QLYQRALAVVEEDDRDQMAFELYGKCSRVLVRLEKFTEAATAFLKEGV----AADKCDAYNSQCKAYVAAILVYLYAHDY 206 (308)
T ss_pred HHHHHHHHHHhccchHHHHHHHHHHhhhHhhhhHHhhHHHHHHHHhhh----HHHHHhhcccHHHHHHHHHHHHhhHHHH
Confidence 77777666655434332221 222234556667788888888875432 1223334444433333344555666665
Q ss_pred HH--hcccC-HhhHhhh--ccchHHHHHHHHHhcCCHHHHHHHH
Q 013559 276 KS--KVIDN-VNFRNFL--ELVPEVRELINDFYSSRYASCLDYL 314 (441)
Q Consensus 276 k~--~vl~~-~~~~~~l--e~~p~~~~ll~~f~~~~y~~~~~~L 314 (441)
+. ++... ..+-.|. ++.-.+.+||..|-..|-..+...+
T Consensus 207 v~aekc~r~~~qip~f~~sed~r~lenLL~ayd~gD~E~~~kvl 250 (308)
T KOG1585|consen 207 VQAEKCYRDCSQIPAFLKSEDSRSLENLLTAYDEGDIEEIKKVL 250 (308)
T ss_pred HHHHHHhcchhcCccccChHHHHHHHHHHHHhccCCHHHHHHHH
Confidence 43 23221 1222232 2333478899999888877765544
No 129
>PF03704 BTAD: Bacterial transcriptional activator domain; InterPro: IPR005158 Found in the DNRI/REDD/AFSR family of regulators, this region of AFSR (P25941 from SWISSPROT) along with the C-terminal region is capable of independently directing actinorhodin production. It is important for the formation of secondary metabolites.; PDB: 2FF4_B 2FEZ_A.
Probab=82.07 E-value=13 Score=32.01 Aligned_cols=65 Identities=6% Similarity=0.008 Sum_probs=51.0
Q ss_pred hHHhHHHHHHHHcCCHHHHHHHHHHHHhhhcCchhHHHHHHHHHHHHHHhcCHHHHHhHHHHHhcccc
Q 013559 140 MGYNDFGDFYYAHGALGDAFKSYVRTRDYCTTSKHIIHMCMSAILVSIEMGQFTHVTSYVSKAEQTPE 207 (441)
Q Consensus 140 ~~~~~la~~~~~~Gd~~~A~~~~~~~r~~~~~~~~~~~~~l~~i~~~i~~~~~~~~~~~~~ka~~~~~ 207 (441)
.+...++.++...|++++|.+.+.+....-... =.++...|++....|+...+.....+.+..+.
T Consensus 63 ~~~~~l~~~~~~~~~~~~a~~~~~~~l~~dP~~---E~~~~~lm~~~~~~g~~~~A~~~Y~~~~~~l~ 127 (146)
T PF03704_consen 63 DALERLAEALLEAGDYEEALRLLQRALALDPYD---EEAYRLLMRALAAQGRRAEALRVYERYRRRLR 127 (146)
T ss_dssp HHHHHHHHHHHHTT-HHHHHHHHHHHHHHSTT----HHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHhccCHHHHHHHHHHHHhcCCCC---HHHHHHHHHHHHHCcCHHHHHHHHHHHHHHHH
Confidence 466789999999999999999999986654322 34667789999999999999999999877653
No 130
>COG4700 Uncharacterized protein conserved in bacteria containing a divergent form of TPR repeats [Function unknown]
Probab=82.00 E-value=44 Score=31.11 Aligned_cols=117 Identities=12% Similarity=0.031 Sum_probs=80.8
Q ss_pred hHHhHHHHHHHHcCCHHHHHHHHHHHHhhhcCchhHHHHHHHHHHHHHHhcCHHHHHhHHHHHhccc-ccCChhhhhhHH
Q 013559 140 MGYNDFGDFYYAHGALGDAFKSYVRTRDYCTTSKHIIHMCMSAILVSIEMGQFTHVTSYVSKAEQTP-EALEPVTIAKLR 218 (441)
Q Consensus 140 ~~~~~la~~~~~~Gd~~~A~~~~~~~r~~~~~~~~~~~~~l~~i~~~i~~~~~~~~~~~~~ka~~~~-~~~d~~~~~~l~ 218 (441)
.-.+.||.-..+.|++.+|...|.+..-=.- -+--.|.++..+.-+..+++..+...+.++-... .+..|+-.
T Consensus 90 qnr~rLa~al~elGr~~EA~~hy~qalsG~f--A~d~a~lLglA~Aqfa~~~~A~a~~tLe~l~e~~pa~r~pd~~---- 163 (251)
T COG4700 90 QNRYRLANALAELGRYHEAVPHYQQALSGIF--AHDAAMLLGLAQAQFAIQEFAAAQQTLEDLMEYNPAFRSPDGH---- 163 (251)
T ss_pred HHHHHHHHHHHHhhhhhhhHHHHHHHhcccc--CCCHHHHHHHHHHHHhhccHHHHHHHHHHHhhcCCccCCCCch----
Confidence 4568999999999999999999988632111 1234578899999999999999999888875543 22222211
Q ss_pred HHHHHHhcccccHHHHHHHHHhcCcCCCCCchhhhcHHHHHHHHHHHHHhc
Q 013559 219 CAAGLAHLEARKYKLAARKFLEVGPDLGNSYNEVIAAQDVATYGGLCALAS 269 (441)
Q Consensus 219 ~~~gl~~l~~r~y~~Aa~~Fl~~~~t~~~~~~el~s~~d~~~Y~~l~al~s 269 (441)
...|..+-..|+|..|-.-|-.+..-.+ .+...+.|+...+-.+
T Consensus 164 Ll~aR~laa~g~~a~Aesafe~a~~~yp-------g~~ar~~Y~e~La~qg 207 (251)
T COG4700 164 LLFARTLAAQGKYADAESAFEVAISYYP-------GPQARIYYAEMLAKQG 207 (251)
T ss_pred HHHHHHHHhcCCchhHHHHHHHHHHhCC-------CHHHHHHHHHHHHHhc
Confidence 3345666778999888887776654322 2344558988655544
No 131
>COG2956 Predicted N-acetylglucosaminyl transferase [Carbohydrate transport and metabolism]
Probab=82.00 E-value=60 Score=32.67 Aligned_cols=98 Identities=10% Similarity=0.027 Sum_probs=64.9
Q ss_pred HHHHHhHHhHHHHHHHHcCCHHHHHHHHHHHHhhh-cCchhHHHHHHHHHHHHHHhcCHHHHHhHHHHHhcccccCChhh
Q 013559 135 KESIRMGYNDFGDFYYAHGALGDAFKSYVRTRDYC-TTSKHIIHMCMSAILVSIEMGQFTHVTSYVSKAEQTPEALEPVT 213 (441)
Q Consensus 135 ~esir~~~~~la~~~~~~Gd~~~A~~~~~~~r~~~-~~~~~~~~~~l~~i~~~i~~~~~~~~~~~~~ka~~~~~~~d~~~ 213 (441)
..|.-++++.||++|.+.|..+.|++.-.-+.+.. .+-.+++-....+.+=..-.|=++.+......+-+..+...+.+
T Consensus 65 d~~t~e~~ltLGnLfRsRGEvDRAIRiHQ~L~~spdlT~~qr~lAl~qL~~Dym~aGl~DRAE~~f~~L~de~efa~~Al 144 (389)
T COG2956 65 DPETFEAHLTLGNLFRSRGEVDRAIRIHQTLLESPDLTFEQRLLALQQLGRDYMAAGLLDRAEDIFNQLVDEGEFAEGAL 144 (389)
T ss_pred CchhhHHHHHHHHHHHhcchHHHHHHHHHHHhcCCCCchHHHHHHHHHHHHHHHHhhhhhHHHHHHHHHhcchhhhHHHH
Confidence 34556789999999999999999999988775543 34466666666666666666666777666555444433223334
Q ss_pred hhhHHHHHHHHhcccccHHHHHHH
Q 013559 214 IAKLRCAAGLAHLEARKYKLAARK 237 (441)
Q Consensus 214 ~~~l~~~~gl~~l~~r~y~~Aa~~ 237 (441)
+.-+.+| =.+++|.+|.+.
T Consensus 145 qqLl~IY-----Q~treW~KAId~ 163 (389)
T COG2956 145 QQLLNIY-----QATREWEKAIDV 163 (389)
T ss_pred HHHHHHH-----HHhhHHHHHHHH
Confidence 4333333 357899888553
No 132
>PF12862 Apc5: Anaphase-promoting complex subunit 5
Probab=81.92 E-value=5 Score=32.35 Aligned_cols=58 Identities=14% Similarity=0.222 Sum_probs=44.2
Q ss_pred HHHcCCHHHHHHHHHHHHhhhcCchh------HHHHHHHHHHHHHHhcCHHHHHhHHHHHhccc
Q 013559 149 YYAHGALGDAFKSYVRTRDYCTTSKH------IIHMCMSAILVSIEMGQFTHVTSYVSKAEQTP 206 (441)
Q Consensus 149 ~~~~Gd~~~A~~~~~~~r~~~~~~~~------~~~~~l~~i~~~i~~~~~~~~~~~~~ka~~~~ 206 (441)
..+.|||.+|.+.+.+..|++..... .--..++...+....|+++.+...+..+-.+.
T Consensus 8 ~~~~~dy~~A~d~L~~~fD~~~~~~~~~~~~~~~~all~lA~~~~~~G~~~~A~~~l~eAi~~A 71 (94)
T PF12862_consen 8 ALRSGDYSEALDALHRYFDYAKQSNNSSSNSGLAYALLNLAELHRRFGHYEEALQALEEAIRLA 71 (94)
T ss_pred HHHcCCHHHHHHHHHHHHHHHhhcccchhhHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHH
Confidence 46789999999999999998853332 22345667777888999999988888776543
No 133
>KOG2076 consensus RNA polymerase III transcription factor TFIIIC [Transcription]
Probab=81.89 E-value=11 Score=42.22 Aligned_cols=103 Identities=14% Similarity=0.136 Sum_probs=74.1
Q ss_pred HhhhhHHHHHhHHhHHHHHHHHcCCHHHHHHHHHHHHhhhcCchhHHHHHHHHHHHHHHhcCHHHHHhHHHHHhcc-ccc
Q 013559 130 RTNLIKESIRMGYNDFGDFYYAHGALGDAFKSYVRTRDYCTTSKHIIHMCMSAILVSIEMGQFTHVTSYVSKAEQT-PEA 208 (441)
Q Consensus 130 ~~n~~~esir~~~~~la~~~~~~Gd~~~A~~~~~~~r~~~~~~~~~~~~~l~~i~~~i~~~~~~~~~~~~~ka~~~-~~~ 208 (441)
+.|...++..+.++++++.|.++|.|.+|++.|..+...-+. +...+++.+.+|....+.+++|.....|+-.+ ++.
T Consensus 405 ~~n~~~~d~~dL~~d~a~al~~~~~~~~Al~~l~~i~~~~~~--~~~~vw~~~a~c~~~l~e~e~A~e~y~kvl~~~p~~ 482 (895)
T KOG2076|consen 405 EDNVWVSDDVDLYLDLADALTNIGKYKEALRLLSPITNREGY--QNAFVWYKLARCYMELGEYEEAIEFYEKVLILAPDN 482 (895)
T ss_pred HhcCChhhhHHHHHHHHHHHHhcccHHHHHHHHHHHhcCccc--cchhhhHHHHHHHHHHhhHHHHHHHHHHHHhcCCCc
Confidence 344456677789999999999999999999999988544322 33778899999999999999999999998654 332
Q ss_pred CChhhhhhHHHHHHHHhcccccHHHHHHHHHh
Q 013559 209 LEPVTIAKLRCAAGLAHLEARKYKLAARKFLE 240 (441)
Q Consensus 209 ~d~~~~~~l~~~~gl~~l~~r~y~~Aa~~Fl~ 240 (441)
.| +++...+ .+...|+..+|.+.+-.
T Consensus 483 ~D----~Ri~Las--l~~~~g~~EkalEtL~~ 508 (895)
T KOG2076|consen 483 LD----ARITLAS--LYQQLGNHEKALETLEQ 508 (895)
T ss_pred hh----hhhhHHH--HHHhcCCHHHHHHHHhc
Confidence 22 2222221 34456666666666555
No 134
>PRK10411 DNA-binding transcriptional activator FucR; Provisional
Probab=81.87 E-value=7.8 Score=37.13 Aligned_cols=46 Identities=22% Similarity=0.335 Sum_probs=42.3
Q ss_pred HHHHHHHHhccccccccHHhHHHHcCCChHHHHHHHHHHHHcCccc
Q 013559 338 IRNKALIQYTHPFVSVDLHMMANAFKTSVAGIEKELEALITDNQIQ 383 (441)
Q Consensus 338 iR~~~i~qy~~pYs~I~L~~mA~~fg~s~~~~E~~L~~LI~~g~L~ 383 (441)
-|.+.+.+++..+..++.+.||+.||+|...+.+.|..|...|.|.
T Consensus 4 ~R~~~Il~~l~~~~~~~~~eLa~~l~VS~~TiRRdL~~L~~~~~l~ 49 (240)
T PRK10411 4 ARQQAIVDLLLNHTSLTTEALAEQLNVSKETIRRDLNELQTQGKIL 49 (240)
T ss_pred HHHHHHHHHHHHcCCCcHHHHHHHHCcCHHHHHHHHHHHHHCCCEE
Confidence 4778889999999999999999999999999999999999988775
No 135
>PF11817 Foie-gras_1: Foie gras liver health family 1; InterPro: IPR021773 Mutating the gene foie gras in zebrafish has been shown to affect development; the mutants develop large, lipid-filled hepatocytes in the liver, resembling those in individuals with fatty liver disease []. Foie-gras protein is long and has several well-defined domains though none of them has a known function. We have annotated this one as the first []. THe C terminus of this region contains TPR repeats.
Probab=81.82 E-value=23 Score=33.94 Aligned_cols=83 Identities=11% Similarity=0.107 Sum_probs=56.3
Q ss_pred HHHHHHHHHHHHHHHhhhhHHHHHhHHhHHHHHHHHcCCHHHHHHHHHHHH-hhhc-Cc-hhHHHHHHHHHHHHHHhcCH
Q 013559 116 EQRKEKLENELNAYRTNLIKESIRMGYNDFGDFYYAHGALGDAFKSYVRTR-DYCT-TS-KHIIHMCMSAILVSIEMGQF 192 (441)
Q Consensus 116 ~~~~~~Le~el~~~~~n~~~esir~~~~~la~~~~~~Gd~~~A~~~~~~~r-~~~~-~~-~~~~~~~l~~i~~~i~~~~~ 192 (441)
...++-|+.-...++.....--......++|+.|+..||+++|.+.|..+- .|-. .- .-.-++++.+.+|+...||.
T Consensus 155 ~~iI~lL~~A~~~f~~~~~~R~~~~l~~~~A~ey~~~g~~~~A~~~l~~~~~~yr~egW~~l~~~~l~~l~~Ca~~~~~~ 234 (247)
T PF11817_consen 155 KLIIELLEKAYEQFKKYGQNRMASYLSLEMAEEYFRLGDYDKALKLLEPAASSYRREGWWSLLTEVLWRLLECAKRLGDV 234 (247)
T ss_pred HHHHHHHHHHHHHHHHhccchHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHhCCcHHHHHHHHHHHHHHHHHhCCH
Confidence 344555666666665544433333467899999999999999999999982 2221 11 22345677888889999988
Q ss_pred HHHHhH
Q 013559 193 THVTSY 198 (441)
Q Consensus 193 ~~~~~~ 198 (441)
......
T Consensus 235 ~~~l~~ 240 (247)
T PF11817_consen 235 EDYLTT 240 (247)
T ss_pred HHHHHH
Confidence 877654
No 136
>PRK15174 Vi polysaccharide export protein VexE; Provisional
Probab=81.81 E-value=65 Score=35.58 Aligned_cols=236 Identities=13% Similarity=0.051 Sum_probs=107.1
Q ss_pred HHhHHHHHHHHcCCHHHHHHHHHHHHhhhcCchhHHHHHHHHHHHHHHhcCHHHHHhHHHHHhcccccCChhhhhhHHHH
Q 013559 141 GYNDFGDFYYAHGALGDAFKSYVRTRDYCTTSKHIIHMCMSAILVSIEMGQFTHVTSYVSKAEQTPEALEPVTIAKLRCA 220 (441)
Q Consensus 141 ~~~~la~~~~~~Gd~~~A~~~~~~~r~~~~~~~~~~~~~l~~i~~~i~~~~~~~~~~~~~ka~~~~~~~d~~~~~~l~~~ 220 (441)
++..+|..+.+.|++++|..++.+......... ........+....|+++.+...+.++-.. +|.. ......
T Consensus 286 a~~~lg~~l~~~g~~~eA~~~l~~al~l~P~~~---~a~~~La~~l~~~G~~~eA~~~l~~al~~----~P~~-~~~~~~ 357 (656)
T PRK15174 286 IVTLYADALIRTGQNEKAIPLLQQSLATHPDLP---YVRAMYARALRQVGQYTAASDEFVQLARE----KGVT-SKWNRY 357 (656)
T ss_pred HHHHHHHHHHHCCCHHHHHHHHHHHHHhCCCCH---HHHHHHHHHHHHCCCHHHHHHHHHHHHHh----Cccc-hHHHHH
Confidence 455566666666666666666665554432211 22233344445556666666655554332 1110 012233
Q ss_pred HHHHhcccccHHHHHHHHHhcCcCCCCCchhhhcHHHHHHHHHHHHHhcCC--h-HHHHHhcccCHhh-Hhhhccc---h
Q 013559 221 AGLAHLEARKYKLAARKFLEVGPDLGNSYNEVIAAQDVATYGGLCALASFD--R-AELKSKVIDNVNF-RNFLELV---P 293 (441)
Q Consensus 221 ~gl~~l~~r~y~~Aa~~Fl~~~~t~~~~~~el~s~~d~~~Y~~l~al~s~~--R-~eLk~~vl~~~~~-~~~le~~---p 293 (441)
.|..+...|++.+|...|-.+....+...+.-.. ..+..|.-....+... | .=.+...++++++ +...+.- -
T Consensus 358 ~a~al~~~G~~deA~~~l~~al~~~P~~~~~~~~-ea~~~~~~~~~~~~~~~~~~~W~~~~~~~~~~~~~~~~~~~~~~~ 436 (656)
T PRK15174 358 AAAALLQAGKTSEAESVFEHYIQARASHLPQSFE-EGLLALDGQISAVNLPPERLDWAWEVAGRQSGIERDEWERRAKWG 436 (656)
T ss_pred HHHHHHHCCCHHHHHHHHHHHHHhChhhchhhHH-HHHHHHHHHHHhcCCccchhhHHHHHhcccccCChHHHHHHHHhh
Confidence 4566677888888888887765432211111110 1223343333333221 1 1223323333221 0000000 1
Q ss_pred H-HHHHHHHHhcCCHHHHHHHHHHhH----------Hhhhh---chhHHHHHHHHHHHHHHHHHHHhc----cccccccH
Q 013559 294 E-VRELINDFYSSRYASCLDYLGNLK----------ANLLL---DIHLHDHVETLYDQIRNKALIQYT----HPFVSVDL 355 (441)
Q Consensus 294 ~-~~~ll~~f~~~~y~~~~~~L~~~~----------~~l~~---D~~L~~h~~~l~~~iR~~~i~qy~----~pYs~I~L 355 (441)
+ .-.++-.+..|+=...-+.|..+. ..+.. =+++..|...+ ++-..++..+. ..|+.+..
T Consensus 437 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~a~~~~kgvi~~t~H~gnw--E~~~~~~~~~~~~~~~i~r~~~~ 514 (656)
T PRK15174 437 YLADNFLLDWLECRGEQADEPMYRLADISHVEQFFQRLQLDQRGCIIVSAHLGAM--YAGPMILSLLEMNSKWVASTPGV 514 (656)
T ss_pred HHHHHHHHHHHHhcccchhhHHHHHhhhhhHHHHHHHHHhcCCCEEEEecCcchh--hHHHHHHHHcCCCceeeecchHH
Confidence 2 234666666775444433333221 11111 13566787766 22223344442 24555443
Q ss_pred HhHHHHcCCCh--------HHHHHHHHHHHHcCccce-EecCC
Q 013559 356 HMMANAFKTSV--------AGIEKELEALITDNQIQA-RIDSH 389 (441)
Q Consensus 356 ~~mA~~fg~s~--------~~~E~~L~~LI~~g~L~a-kID~~ 389 (441)
+=..+|... ...=+.|.+.+.+|.+=| =+|+.
T Consensus 515 --~R~~~g~~~i~~~~~~~~~~~r~i~~aLk~g~~v~il~Dq~ 555 (656)
T PRK15174 515 --LKGGYGERLISVSDKSEADVVRACMQTLHSGQSLVVAIDGA 555 (656)
T ss_pred --HHHhcCCceeccCCCCcchHHHHHHHHHHcCCeEEEEeCCC
Confidence 346666431 223457888888887655 34555
No 137
>PRK11447 cellulose synthase subunit BcsC; Provisional
Probab=81.67 E-value=80 Score=37.40 Aligned_cols=99 Identities=7% Similarity=-0.066 Sum_probs=67.8
Q ss_pred HHhHHHHHHHHcCCHHHHHHHHHHHHhhhcCchhHHHHHHHHHHHHHHhcCHHHHHhHHHHHhcc-cccCChhhh---hh
Q 013559 141 GYNDFGDFYYAHGALGDAFKSYVRTRDYCTTSKHIIHMCMSAILVSIEMGQFTHVTSYVSKAEQT-PEALEPVTI---AK 216 (441)
Q Consensus 141 ~~~~la~~~~~~Gd~~~A~~~~~~~r~~~~~~~~~~~~~l~~i~~~i~~~~~~~~~~~~~ka~~~-~~~~d~~~~---~~ 216 (441)
.+++-+++....|+.+.|.+.+.++...-+. . .+.....+++.+..|+.+.+...+.|+... ++ ++... ..
T Consensus 30 ~Ll~q~~~~~~~~~~d~a~~~l~kl~~~~p~--~-p~~~~~~~~~~l~~g~~~~A~~~l~~l~~~~P~--~~~~~~~~~~ 104 (1157)
T PRK11447 30 QLLEQVRLGEATHREDLVRQSLYRLELIDPN--N-PDVIAARFRLLLRQGDSDGAQKLLDRLSQLAPD--SNAYRSSRTT 104 (1157)
T ss_pred HHHHHHHHHHhhCChHHHHHHHHHHHccCCC--C-HHHHHHHHHHHHhCCCHHHHHHHHHHHHhhCCC--ChHHHHHHHH
Confidence 4667788888888888888888887655332 2 566677888888888888888888888664 32 21111 00
Q ss_pred ---------HHHHHHHHhcccccHHHHHHHHHhcCcC
Q 013559 217 ---------LRCAAGLAHLEARKYKLAARKFLEVGPD 244 (441)
Q Consensus 217 ---------l~~~~gl~~l~~r~y~~Aa~~Fl~~~~t 244 (441)
-....|..+...|+|.+|...|-..+..
T Consensus 105 ~~~~~~~~~~~l~~A~ll~~~g~~~eA~~~~~~~l~~ 141 (1157)
T PRK11447 105 MLLSTPEGRQALQQARLLATTGRTEEALASYDKLFNG 141 (1157)
T ss_pred HHhcCCchhhHHHHHHHHHhCCCHHHHHHHHHHHccC
Confidence 1133455667788888888888887754
No 138
>PLN03098 LPA1 LOW PSII ACCUMULATION1; Provisional
Probab=81.66 E-value=7 Score=40.79 Aligned_cols=27 Identities=7% Similarity=-0.156 Sum_probs=16.2
Q ss_pred HHhHHHHHHHHcCCHHHHHHHHHHHHh
Q 013559 141 GYNDFGDFYYAHGALGDAFKSYVRTRD 167 (441)
Q Consensus 141 ~~~~la~~~~~~Gd~~~A~~~~~~~r~ 167 (441)
+++.+|-.|...|++++|.++|.+..+
T Consensus 114 A~yNLAcaya~LGr~dEAla~LrrALe 140 (453)
T PLN03098 114 AYYNKACCHAYREEGKKAADCLRTALR 140 (453)
T ss_pred HHHHHHHHHHHcCCHHHHHHHHHHHHH
Confidence 456666666666666666666665544
No 139
>PRK10434 srlR DNA-bindng transcriptional repressor SrlR; Provisional
Probab=81.52 E-value=2.1 Score=41.43 Aligned_cols=45 Identities=22% Similarity=0.313 Sum_probs=42.5
Q ss_pred HHHHHHHHhccccccccHHhHHHHcCCChHHHHHHHHHHHHcCcc
Q 013559 338 IRNKALIQYTHPFVSVDLHMMANAFKTSVAGIEKELEALITDNQI 382 (441)
Q Consensus 338 iR~~~i~qy~~pYs~I~L~~mA~~fg~s~~~~E~~L~~LI~~g~L 382 (441)
=|...|.+++..+..|+++.+|+.||+|.+.+-+.|..|-..|.|
T Consensus 5 eR~~~Il~~L~~~~~v~v~eLa~~l~VS~~TIRRDL~~Le~~g~l 49 (256)
T PRK10434 5 QRQAAILEYLQKQGKTSVEELAQYFDTTGTTIRKDLVILEHAGTV 49 (256)
T ss_pred HHHHHHHHHHHHcCCEEHHHHHHHHCCCHHHHHHHHHHHHHCCCE
Confidence 388999999999999999999999999999999999999999976
No 140
>KOG1070 consensus rRNA processing protein Rrp5 [RNA processing and modification]
Probab=81.46 E-value=49 Score=39.28 Aligned_cols=100 Identities=12% Similarity=0.055 Sum_probs=77.6
Q ss_pred HHhHHHHHHHHcCCHHHHHHHHHHHHhh--hcCchhHHHHHHHHHHHHHHhcCHHHHHhHHHHHhcccccCChhhhhhHH
Q 013559 141 GYNDFGDFYYAHGALGDAFKSYVRTRDY--CTTSKHIIHMCMSAILVSIEMGQFTHVTSYVSKAEQTPEALEPVTIAKLR 218 (441)
Q Consensus 141 ~~~~la~~~~~~Gd~~~A~~~~~~~r~~--~~~~~~~~~~~l~~i~~~i~~~~~~~~~~~~~ka~~~~~~~d~~~~~~l~ 218 (441)
.+..+-.|+.+.++.++|.+...++... ......++++|...+.+..+.|.-+.+++...+|....++ ++. +.
T Consensus 1460 ~WI~YMaf~LelsEiekAR~iaerAL~tIN~REeeEKLNiWiA~lNlEn~yG~eesl~kVFeRAcqycd~----~~V-~~ 1534 (1710)
T KOG1070|consen 1460 LWIRYMAFHLELSEIEKARKIAERALKTINFREEEEKLNIWIAYLNLENAYGTEESLKKVFERACQYCDA----YTV-HL 1534 (1710)
T ss_pred HHHHHHHHHhhhhhhHHHHHHHHHHhhhCCcchhHHHHHHHHHHHhHHHhhCcHHHHHHHHHHHHHhcch----HHH-HH
Confidence 5788889999999999999999998443 3566789999999999999999999999999999888652 111 12
Q ss_pred HHHHHHhcccccHHHHHHHHHhcCcCCC
Q 013559 219 CAAGLAHLEARKYKLAARKFLEVGPDLG 246 (441)
Q Consensus 219 ~~~gl~~l~~r~y~~Aa~~Fl~~~~t~~ 246 (441)
...|+|. -..+|.+|.++|-..+.-|.
T Consensus 1535 ~L~~iy~-k~ek~~~A~ell~~m~KKF~ 1561 (1710)
T KOG1070|consen 1535 KLLGIYE-KSEKNDEADELLRLMLKKFG 1561 (1710)
T ss_pred HHHHHHH-HhhcchhHHHHHHHHHHHhc
Confidence 2234433 34567899999888887765
No 141
>COG4235 Cytochrome c biogenesis factor [Posttranslational modification, protein turnover, chaperones]
Probab=81.30 E-value=18 Score=35.54 Aligned_cols=95 Identities=15% Similarity=0.119 Sum_probs=61.9
Q ss_pred hHHhHHHHHHHHcCCHHHHHHHHHHHHhhhcCchhHHHHHHHHHHHHHHhc---CHHHHHhHHHHHhcccccCChhhhhh
Q 013559 140 MGYNDFGDFYYAHGALGDAFKSYVRTRDYCTTSKHIIHMCMSAILVSIEMG---QFTHVTSYVSKAEQTPEALEPVTIAK 216 (441)
Q Consensus 140 ~~~~~la~~~~~~Gd~~~A~~~~~~~r~~~~~~~~~~~~~l~~i~~~i~~~---~~~~~~~~~~ka~~~~~~~d~~~~~~ 216 (441)
.++.-||..|...|+++.|..+|.+.....+.+ .+..++..++-.+.. +-..+...++++-..- +.+.+
T Consensus 157 egW~~Lg~~ym~~~~~~~A~~AY~~A~rL~g~n---~~~~~g~aeaL~~~a~~~~ta~a~~ll~~al~~D---~~~ir-- 228 (287)
T COG4235 157 EGWDLLGRAYMALGRASDALLAYRNALRLAGDN---PEILLGLAEALYYQAGQQMTAKARALLRQALALD---PANIR-- 228 (287)
T ss_pred hhHHHHHHHHHHhcchhHHHHHHHHHHHhCCCC---HHHHHHHHHHHHHhcCCcccHHHHHHHHHHHhcC---CccHH--
Confidence 478899999999999999999999987775433 455556655554443 2223334444443321 11222
Q ss_pred HHHHHHHHhcccccHHHHHHHHHhcC
Q 013559 217 LRCAAGLAHLEARKYKLAARKFLEVG 242 (441)
Q Consensus 217 l~~~~gl~~l~~r~y~~Aa~~Fl~~~ 242 (441)
-..+-|...+.+|+|.+|+..+--..
T Consensus 229 al~lLA~~afe~g~~~~A~~~Wq~lL 254 (287)
T COG4235 229 ALSLLAFAAFEQGDYAEAAAAWQMLL 254 (287)
T ss_pred HHHHHHHHHHHcccHHHHHHHHHHHH
Confidence 33566778899999999976654443
No 142
>PRK04424 fatty acid biosynthesis transcriptional regulator; Provisional
Probab=80.63 E-value=1.9 Score=39.71 Aligned_cols=44 Identities=20% Similarity=0.119 Sum_probs=41.5
Q ss_pred HHHHHHHhccccccccHHhHHHHcCCChHHHHHHHHHHHHcCcc
Q 013559 339 RNKALIQYTHPFVSVDLHMMANAFKTSVAGIEKELEALITDNQI 382 (441)
Q Consensus 339 R~~~i~qy~~pYs~I~L~~mA~~fg~s~~~~E~~L~~LI~~g~L 382 (441)
|...|..++.-+..+++..||+.||+|.+.+-+.|..|-..|.+
T Consensus 8 R~~~Il~~l~~~~~~~~~~La~~~~vS~~TiRRDl~~L~~~g~~ 51 (185)
T PRK04424 8 RQKALQELIEENPFITDEELAEKFGVSIQTIRLDRMELGIPELR 51 (185)
T ss_pred HHHHHHHHHHHCCCEEHHHHHHHHCcCHHHHHHHHHHHhcchHH
Confidence 78889999999999999999999999999999999999999966
No 143
>PF09295 ChAPs: ChAPs (Chs5p-Arf1p-binding proteins); InterPro: IPR015374 ChAPs (Chs5p-Arf1p-binding proteins) are required for the export of specialised cargo from the Golgi. They physically interact with Chs3, Chs5 and the small GTPase Arf1, and they also form interactions with each other [].
Probab=80.54 E-value=40 Score=34.85 Aligned_cols=123 Identities=11% Similarity=0.039 Sum_probs=72.2
Q ss_pred hHHHHHHHHHHHHHhcCChHHHHHHHHHhhccCCCCCcCCHHHHHHHHHHHHHHHH---HHHHHHHHHHhhhhHHHHHhH
Q 013559 65 MQLEALRMAYDEIKKGENTQLFREVVKKIDGRLGPNYAMDEAWCDSVDRRAEQRKE---KLENELNAYRTNLIKESIRMG 141 (441)
Q Consensus 65 ~~~~a~~~~~~~lk~t~~~~~Y~~~~~~l~~~~~~~~~~D~~~~~~~~~~~~~~~~---~Le~el~~~~~n~~~esir~~ 141 (441)
...-....++..++.|...+...++++++...- |.-.-++...--...++.+ -+.+.|+..... -..
T Consensus 167 ~~NyLv~~Ll~~l~~t~~~~~ai~lle~L~~~~----pev~~~LA~v~l~~~~E~~AI~ll~~aL~~~p~d------~~L 236 (395)
T PF09295_consen 167 VNNYLVDTLLKYLSLTQRYDEAIELLEKLRERD----PEVAVLLARVYLLMNEEVEAIRLLNEALKENPQD------SEL 236 (395)
T ss_pred cchHHHHHHHHHHhhcccHHHHHHHHHHHHhcC----CcHHHHHHHHHHhcCcHHHHHHHHHHHHHhCCCC------HHH
Confidence 345566677888888888888888888776321 1001111111111111111 122222111111 234
Q ss_pred HhHHHHHHHHcCCHHHHHHHHHHHHhhhcCchhHHHHHHHHHHHHHHhcCHHHHHhHHH
Q 013559 142 YNDFGDFYYAHGALGDAFKSYVRTRDYCTTSKHIIHMCMSAILVSIEMGQFTHVTSYVS 200 (441)
Q Consensus 142 ~~~la~~~~~~Gd~~~A~~~~~~~r~~~~~~~~~~~~~l~~i~~~i~~~~~~~~~~~~~ 200 (441)
+.-.|+|+.+.|+++.|+++..+..+... ..++....+.++.+..|+|+.|.-.++
T Consensus 237 L~~Qa~fLl~k~~~~lAL~iAk~av~lsP---~~f~~W~~La~~Yi~~~d~e~ALlaLN 292 (395)
T PF09295_consen 237 LNLQAEFLLSKKKYELALEIAKKAVELSP---SEFETWYQLAECYIQLGDFENALLALN 292 (395)
T ss_pred HHHHHHHHHhcCCHHHHHHHHHHHHHhCc---hhHHHHHHHHHHHHhcCCHHHHHHHHh
Confidence 56678889999999999888888766543 236666778888888899988876655
No 144
>PRK04841 transcriptional regulator MalT; Provisional
Probab=80.52 E-value=31 Score=39.25 Aligned_cols=102 Identities=10% Similarity=0.062 Sum_probs=68.5
Q ss_pred hHHhHHHHHHHHcCCHHHHHHHHHHHHhhhcCch---hH--HHHHHHHHHHHHHhcCHHHHHhHHHHHhcccccCChhhh
Q 013559 140 MGYNDFGDFYYAHGALGDAFKSYVRTRDYCTTSK---HI--IHMCMSAILVSIEMGQFTHVTSYVSKAEQTPEALEPVTI 214 (441)
Q Consensus 140 ~~~~~la~~~~~~Gd~~~A~~~~~~~r~~~~~~~---~~--~~~~l~~i~~~i~~~~~~~~~~~~~ka~~~~~~~d~~~~ 214 (441)
.++..+|..++..|++..|...+.+..+.+...+ .. ..+......+....|+|+.+...+.++-.......+...
T Consensus 532 ~~~~~la~~~~~~G~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~~la~~~~~~G~~~~A~~~~~~al~~~~~~~~~~~ 611 (903)
T PRK04841 532 WSLLQQSEILFAQGFLQAAYETQEKAFQLIEEQHLEQLPMHEFLLRIRAQLLWEWARLDEAEQCARKGLEVLSNYQPQQQ 611 (903)
T ss_pred HHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHhccccccHHHHHHHHHHHHHHHhcCHHHHHHHHHHhHHhhhccCchHH
Confidence 4677889999999999999999998876653221 11 112233445667789999999888888665442112222
Q ss_pred hhHHHHHHHHhcccccHHHHHHHHHhc
Q 013559 215 AKLRCAAGLAHLEARKYKLAARKFLEV 241 (441)
Q Consensus 215 ~~l~~~~gl~~l~~r~y~~Aa~~Fl~~ 241 (441)
.......|..++..|++..|...+-.+
T Consensus 612 ~~~~~~la~~~~~~G~~~~A~~~l~~a 638 (903)
T PRK04841 612 LQCLAMLAKISLARGDLDNARRYLNRL 638 (903)
T ss_pred HHHHHHHHHHHHHcCCHHHHHHHHHHH
Confidence 233344566778899999988777665
No 145
>TIGR00540 hemY_coli hemY protein. This is an uncharacterized protein encoded next to a heme-biosynthetic enzyme in two gamma division proteobacteria (E. coli and H. influenzae). It is known in no other species. The gene symbol hemY is unfortunate in that an unrelated protein, protoporphyrinogen oxidase, is designated as HemG in E. coli but as HemY in Bacillus subtilis.
Probab=80.22 E-value=15 Score=37.97 Aligned_cols=94 Identities=9% Similarity=0.037 Sum_probs=60.7
Q ss_pred HHhHHHHHHHHcCCHHHHHHHHHHHHhhhcCchhHHHHHHHHHHHHHHhcCHHHHHhHHHHHhcc-cccCChhhhhhHHH
Q 013559 141 GYNDFGDFYYAHGALGDAFKSYVRTRDYCTTSKHIIHMCMSAILVSIEMGQFTHVTSYVSKAEQT-PEALEPVTIAKLRC 219 (441)
Q Consensus 141 ~~~~la~~~~~~Gd~~~A~~~~~~~r~~~~~~~~~~~~~l~~i~~~i~~~~~~~~~~~~~ka~~~-~~~~d~~~~~~l~~ 219 (441)
.+.-.|..+...|+++.|.++|.+..+.... ..+.+-+...++.+..|+++.+...+.++... ++ ++ ....
T Consensus 120 ~~llaA~aa~~~g~~~~A~~~l~~a~~~~p~--~~l~~~~~~a~l~l~~~~~~~Al~~l~~l~~~~P~--~~----~~l~ 191 (409)
T TIGR00540 120 NLIKAAEAAQQRGDEARANQHLEEAAELAGN--DNILVEIARTRILLAQNELHAARHGVDKLLEMAPR--HK----EVLK 191 (409)
T ss_pred HHHHHHHHHHHCCCHHHHHHHHHHHHHhCCc--CchHHHHHHHHHHHHCCCHHHHHHHHHHHHHhCCC--CH----HHHH
Confidence 3456678888888888888888887654433 22334444577777788888888777776554 22 22 2233
Q ss_pred HHHHHhcccccHHHHHHHHHhcC
Q 013559 220 AAGLAHLEARKYKLAARKFLEVG 242 (441)
Q Consensus 220 ~~gl~~l~~r~y~~Aa~~Fl~~~ 242 (441)
..|..++..|+|..|.+.|-...
T Consensus 192 ll~~~~~~~~d~~~a~~~l~~l~ 214 (409)
T TIGR00540 192 LAEEAYIRSGAWQALDDIIDNMA 214 (409)
T ss_pred HHHHHHHHHhhHHHHHHHHHHHH
Confidence 55667788888887766655443
No 146
>COG1349 GlpR Transcriptional regulators of sugar metabolism [Transcription / Carbohydrate transport and metabolism]
Probab=79.72 E-value=2.5 Score=40.85 Aligned_cols=46 Identities=17% Similarity=0.249 Sum_probs=43.4
Q ss_pred HHHHHHHHhccccccccHHhHHHHcCCChHHHHHHHHHHHHcCccc
Q 013559 338 IRNKALIQYTHPFVSVDLHMMANAFKTSVAGIEKELEALITDNQIQ 383 (441)
Q Consensus 338 iR~~~i~qy~~pYs~I~L~~mA~~fg~s~~~~E~~L~~LI~~g~L~ 383 (441)
-|.+.|.++++....|+++.||+.||+|.+.+-+.|..|=..|.|.
T Consensus 5 eR~~~Il~~l~~~g~v~v~eLa~~~~VS~~TIRRDL~~Le~~g~l~ 50 (253)
T COG1349 5 ERHQKILELLKEKGKVSVEELAELFGVSEMTIRRDLNELEEQGLLL 50 (253)
T ss_pred HHHHHHHHHHHHcCcEEHHHHHHHhCCCHHHHHHhHHHHHHCCcEE
Confidence 3889999999999999999999999999999999999999999884
No 147
>PF10668 Phage_terminase: Phage terminase small subunit; InterPro: IPR018925 This entry describes the terminase small subunit from Enterococcus phage phiFL1A, related proteins in other bacteriophage, and prophage regions of bacterial genomes. Packaging of double-stranded viral DNA concatemers requires interaction of the prohead with virus DNA. This process is mediated by a phage-encoded DNA recognition and terminase protein. The terminase enzymes described so far, which are hetero-oligomers composed of a small and a large subunit, do not have a significant level of sequence homology. The small terminase subunit is thought to form a nucleoprotein structure that helps to position the terminase large subunit at the packaging initiation site [].
Probab=79.71 E-value=2.8 Score=31.15 Aligned_cols=37 Identities=24% Similarity=0.226 Sum_probs=32.4
Q ss_pred HHHHHHHhccccccccHHhHHHHcCCChHHHHHHHHH
Q 013559 339 RNKALIQYTHPFVSVDLHMMANAFKTSVAGIEKELEA 375 (441)
Q Consensus 339 R~~~i~qy~~pYs~I~L~~mA~~fg~s~~~~E~~L~~ 375 (441)
|.+|+.-|.+.=-.|++..+|+.||+|...|-+|=.+
T Consensus 9 rdkA~e~y~~~~g~i~lkdIA~~Lgvs~~tIr~WK~~ 45 (60)
T PF10668_consen 9 RDKAFEIYKESNGKIKLKDIAEKLGVSESTIRKWKSR 45 (60)
T ss_pred HHHHHHHHHHhCCCccHHHHHHHHCCCHHHHHHHhhh
Confidence 6788898988878999999999999999998887554
No 148
>KOG2003 consensus TPR repeat-containing protein [General function prediction only]
Probab=79.60 E-value=9 Score=39.82 Aligned_cols=96 Identities=15% Similarity=0.164 Sum_probs=70.2
Q ss_pred HHhHHHHHHHHcCCHHHHHHHHHHHHhhhcCchhHHHHHHHHHHH-HHHhcCHHHHHhHHHHHhccc-ccCChhhhhhHH
Q 013559 141 GYNDFGDFYYAHGALGDAFKSYVRTRDYCTTSKHIIHMCMSAILV-SIEMGQFTHVTSYVSKAEQTP-EALEPVTIAKLR 218 (441)
Q Consensus 141 ~~~~la~~~~~~Gd~~~A~~~~~~~r~~~~~~~~~~~~~l~~i~~-~i~~~~~~~~~~~~~ka~~~~-~~~d~~~~~~l~ 218 (441)
.+-+||++|-+.||.+.|+.|++....|+..+-..+ .|+.. .|..+=|+.+..++.|+.-+. ....|.++
T Consensus 594 ilskl~dlydqegdksqafq~~ydsyryfp~nie~i----ewl~ayyidtqf~ekai~y~ekaaliqp~~~kwqlm---- 665 (840)
T KOG2003|consen 594 ILSKLADLYDQEGDKSQAFQCHYDSYRYFPCNIETI----EWLAAYYIDTQFSEKAINYFEKAALIQPNQSKWQLM---- 665 (840)
T ss_pred HHHHHHHHhhcccchhhhhhhhhhcccccCcchHHH----HHHHHHHHhhHHHHHHHHHHHHHHhcCccHHHHHHH----
Confidence 456899999999999999999998877876554433 44444 577788999999999986643 24466544
Q ss_pred HHHHHHhcccccHHHHHHHHHhcCcCCC
Q 013559 219 CAAGLAHLEARKYKLAARKFLEVGPDLG 246 (441)
Q Consensus 219 ~~~gl~~l~~r~y~~Aa~~Fl~~~~t~~ 246 (441)
+. -..-..|+|..|..++-++---|+
T Consensus 666 ia--sc~rrsgnyqka~d~yk~~hrkfp 691 (840)
T KOG2003|consen 666 IA--SCFRRSGNYQKAFDLYKDIHRKFP 691 (840)
T ss_pred HH--HHHHhcccHHHHHHHHHHHHHhCc
Confidence 21 123458999999999999876554
No 149
>PLN03218 maturation of RBCL 1; Provisional
Probab=79.22 E-value=1.4e+02 Score=35.16 Aligned_cols=96 Identities=15% Similarity=0.156 Sum_probs=60.0
Q ss_pred HHhHHHHHHHHcCCHHHHHHHHHHHHhhhcCchhHHHHHHHHHHHHHHhcCHHHHHhHHHHHhcccccCChhhhhhHHHH
Q 013559 141 GYNDFGDFYYAHGALGDAFKSYVRTRDYCTTSKHIIHMCMSAILVSIEMGQFTHVTSYVSKAEQTPEALEPVTIAKLRCA 220 (441)
Q Consensus 141 ~~~~la~~~~~~Gd~~~A~~~~~~~r~~~~~~~~~~~~~l~~i~~~i~~~~~~~~~~~~~ka~~~~~~~d~~~~~~l~~~ 220 (441)
.+..+...|.+.|++++|.+.|..++.....++ ...+-.++......|+++.+...+.+....-.+..|+.. .|
T Consensus 509 TynaLI~gy~k~G~~eeAl~lf~~M~~~Gv~PD--~vTYnsLI~a~~k~G~~deA~~lf~eM~~~~~gi~PD~v----Ty 582 (1060)
T PLN03218 509 TFGALIDGCARAGQVAKAFGAYGIMRSKNVKPD--RVVFNALISACGQSGAVDRAFDVLAEMKAETHPIDPDHI----TV 582 (1060)
T ss_pred HHHHHHHHHHHCcCHHHHHHHHHHHHHcCCCCC--HHHHHHHHHHHHHCCCHHHHHHHHHHHHHhcCCCCCcHH----HH
Confidence 566777888888999999988888877655444 234455666677778888888777776542111122211 12
Q ss_pred HHH--HhcccccHHHHHHHHHhcC
Q 013559 221 AGL--AHLEARKYKLAARKFLEVG 242 (441)
Q Consensus 221 ~gl--~~l~~r~y~~Aa~~Fl~~~ 242 (441)
..+ .+...|++.+|.+.|-+..
T Consensus 583 naLI~ay~k~G~ldeA~elf~~M~ 606 (1060)
T PLN03218 583 GALMKACANAGQVDRAKEVYQMIH 606 (1060)
T ss_pred HHHHHHHHHCCCHHHHHHHHHHHH
Confidence 222 2344677777777776654
No 150
>PLN03088 SGT1, suppressor of G2 allele of SKP1; Provisional
Probab=79.19 E-value=14 Score=37.41 Aligned_cols=80 Identities=6% Similarity=0.037 Sum_probs=57.6
Q ss_pred hHHhHHHHHHHHcCCHHHHHHHHHHHHhhhcCchhHHHHHHHHHHHHHHhcCHHHHHhHHHHHhcccccCChhhhhhHHH
Q 013559 140 MGYNDFGDFYYAHGALGDAFKSYVRTRDYCTTSKHIIHMCMSAILVSIEMGQFTHVTSYVSKAEQTPEALEPVTIAKLRC 219 (441)
Q Consensus 140 ~~~~~la~~~~~~Gd~~~A~~~~~~~r~~~~~~~~~~~~~l~~i~~~i~~~~~~~~~~~~~ka~~~~~~~d~~~~~~l~~ 219 (441)
.+++.+|..|...|++++|+..+.++.+..... ....+....+....|+|..+...+.++-.+- ..++.....+..
T Consensus 37 ~a~~~~a~~~~~~g~~~eAl~~~~~Al~l~P~~---~~a~~~lg~~~~~lg~~~eA~~~~~~al~l~-P~~~~~~~~l~~ 112 (356)
T PLN03088 37 ELYADRAQANIKLGNFTEAVADANKAIELDPSL---AKAYLRKGTACMKLEEYQTAKAALEKGASLA-PGDSRFTKLIKE 112 (356)
T ss_pred HHHHHHHHHHHHcCCHHHHHHHHHHHHHhCcCC---HHHHHHHHHHHHHhCCHHHHHHHHHHHHHhC-CCCHHHHHHHHH
Confidence 367889999999999999999999987765432 3445666677788899999999998887643 234555444444
Q ss_pred HHHH
Q 013559 220 AAGL 223 (441)
Q Consensus 220 ~~gl 223 (441)
+.+.
T Consensus 113 ~~~k 116 (356)
T PLN03088 113 CDEK 116 (356)
T ss_pred HHHH
Confidence 4433
No 151
>smart00550 Zalpha Z-DNA-binding domain in adenosine deaminases. Helix-turn-helix-containing domain. Also known as Zab.
Probab=79.09 E-value=4.1 Score=30.92 Aligned_cols=44 Identities=7% Similarity=0.114 Sum_probs=36.8
Q ss_pred HHHHHhcccccc--ccHHhHHHHcCCChHHHHHHHHHHHHcCccce
Q 013559 341 KALIQYTHPFVS--VDLHMMANAFKTSVAGIEKELEALITDNQIQA 384 (441)
Q Consensus 341 ~~i~qy~~pYs~--I~L~~mA~~fg~s~~~~E~~L~~LI~~g~L~a 384 (441)
..+.+++..... ++...||+.+|++...+.+.|..|...|.+..
T Consensus 9 ~~IL~~L~~~g~~~~ta~eLa~~lgl~~~~v~r~L~~L~~~G~V~~ 54 (68)
T smart00550 9 EKILEFLENSGDETSTALQLAKNLGLPKKEVNRVLYSLEKKGKVCK 54 (68)
T ss_pred HHHHHHHHHCCCCCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEe
Confidence 344555565555 99999999999999999999999999999854
No 152
>PRK14574 hmsH outer membrane protein; Provisional
Probab=78.95 E-value=1.2e+02 Score=34.47 Aligned_cols=95 Identities=13% Similarity=0.042 Sum_probs=64.5
Q ss_pred HHhHHHHHHHHcCCHHHHHHHHHHHHhhhcCchhHHHHHHHHHHHHHHhcCHHHHHhHHHHHhcccccCChhhhhhHHHH
Q 013559 141 GYNDFGDFYYAHGALGDAFKSYVRTRDYCTTSKHIIHMCMSAILVSIEMGQFTHVTSYVSKAEQTPEALEPVTIAKLRCA 220 (441)
Q Consensus 141 ~~~~la~~~~~~Gd~~~A~~~~~~~r~~~~~~~~~~~~~l~~i~~~i~~~~~~~~~~~~~ka~~~~~~~d~~~~~~l~~~ 220 (441)
++..+|..|...|++++|++.|.++.+.-.+. .++..+++.+....++...+...+.++.... |... .+
T Consensus 104 ~llalA~ly~~~gdyd~Aiely~kaL~~dP~n---~~~l~gLa~~y~~~~q~~eAl~~l~~l~~~d----p~~~----~~ 172 (822)
T PRK14574 104 GLASAARAYRNEKRWDQALALWQSSLKKDPTN---PDLISGMIMTQADAGRGGVVLKQATELAERD----PTVQ----NY 172 (822)
T ss_pred HHHHHHHHHHHcCCHHHHHHHHHHHHhhCCCC---HHHHHHHHHHHhhcCCHHHHHHHHHHhcccC----cchH----HH
Confidence 44556889999999999999999997776544 3444566777888899999988888876652 2211 12
Q ss_pred HHHHhcc--cccHHHHHHHHHhcCcCCC
Q 013559 221 AGLAHLE--ARKYKLAARKFLEVGPDLG 246 (441)
Q Consensus 221 ~gl~~l~--~r~y~~Aa~~Fl~~~~t~~ 246 (441)
.++.++. .+++.+|...|-.+....+
T Consensus 173 l~layL~~~~~~~~~AL~~~ekll~~~P 200 (822)
T PRK14574 173 MTLSYLNRATDRNYDALQASSEAVRLAP 200 (822)
T ss_pred HHHHHHHHhcchHHHHHHHHHHHHHhCC
Confidence 3333333 4555558777777765443
No 153
>PF04703 FaeA: FaeA-like protein; PDB: 2JT1_A 2HTJ_A.
Probab=78.76 E-value=3.3 Score=31.04 Aligned_cols=40 Identities=18% Similarity=0.247 Sum_probs=33.0
Q ss_pred HHhccc-cccccHHhHHHHcCCChHHHHHHHHHHHHcCccc
Q 013559 344 IQYTHP-FVSVDLHMMANAFKTSVAGIEKELEALITDNQIQ 383 (441)
Q Consensus 344 ~qy~~p-Ys~I~L~~mA~~fg~s~~~~E~~L~~LI~~g~L~ 383 (441)
..|+.. +..++=..+|+++|+|.-.+-.+|..|-.+|++.
T Consensus 6 l~~i~~~~~p~~T~eiA~~~gls~~~aR~yL~~Le~eG~V~ 46 (62)
T PF04703_consen 6 LEYIKEQNGPLKTREIADALGLSIYQARYYLEKLEKEGKVE 46 (62)
T ss_dssp HHHHHHHTS-EEHHHHHHHHTS-HHHHHHHHHHHHHCTSEE
T ss_pred HHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHHHHHCCCEE
Confidence 344444 7889999999999999999999999999999884
No 154
>PF14853 Fis1_TPR_C: Fis1 C-terminal tetratricopeptide repeat; PDB: 1IYG_A 1PC2_A 1NZN_A 3UUX_C 1Y8M_A 2PQR_A 2PQN_A 3O48_A.
Probab=78.33 E-value=7.5 Score=28.11 Aligned_cols=37 Identities=11% Similarity=-0.050 Sum_probs=28.8
Q ss_pred HhHHhHHHHHHHHcCCHHHHHHHHHHHHhhhcCchhH
Q 013559 139 RMGYNDFGDFYYAHGALGDAFKSYVRTRDYCTTSKHI 175 (441)
Q Consensus 139 r~~~~~la~~~~~~Gd~~~A~~~~~~~r~~~~~~~~~ 175 (441)
|+.++-+|-=+++.|+|.+|.++...+.+.-+...+.
T Consensus 1 Rd~lY~lAig~ykl~~Y~~A~~~~~~lL~~eP~N~Qa 37 (53)
T PF14853_consen 1 RDCLYYLAIGHYKLGEYEKARRYCDALLEIEPDNRQA 37 (53)
T ss_dssp HHHHHHHHHHHHHTT-HHHHHHHHHHHHHHTTS-HHH
T ss_pred ChhHHHHHHHHHHhhhHHHHHHHHHHHHhhCCCcHHH
Confidence 5678889999999999999999999887765555543
No 155
>cd07377 WHTH_GntR Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators. This CD represents the winged HTH DNA-binding domain of the GntR (named after the gluconate operon repressor in Bacillus subtilis) family of bacterial transcriptional regulators and their putative homologs found in eukaryota and archaea. The GntR family has over 6000 members distributed among almost all bacterial species, which is comprised of FadR, HutC, MocR, YtrA, AraR, PlmA, and other subfamilies for the regulation of the most varied biological process. The monomeric proteins of the GntR family are characterized by two function domains: a small highly conserved winged helix-turn-helix prokaryotic DNA binding domain in the N-terminus, and a very diverse regulatory ligand-binding domain in the C-terminus for effector-binding/oligomerization, which provides the basis for the subfamily classifications. Binding of the effector to GntR-like transcriptional regulators is
Probab=78.25 E-value=7.2 Score=28.38 Aligned_cols=51 Identities=18% Similarity=0.219 Sum_probs=38.0
Q ss_pred HHHHHHHHHHHHHhcccccccc-HHhHHHHcCCChHHHHHHHHHHHHcCccc
Q 013559 333 TLYDQIRNKALIQYTHPFVSVD-LHMMANAFKTSVAGIEKELEALITDNQIQ 383 (441)
Q Consensus 333 ~l~~~iR~~~i~qy~~pYs~I~-L~~mA~~fg~s~~~~E~~L~~LI~~g~L~ 383 (441)
.+.+.++...+..-+.+-..+. ...||+.||+|...+.+.|..|...|-|.
T Consensus 5 ~~~~~i~~~i~~~~~~~~~~~~~~~~la~~~~is~~~v~~~l~~L~~~G~i~ 56 (66)
T cd07377 5 QIADQLREAILSGELKPGDRLPSERELAEELGVSRTTVREALRELEAEGLVE 56 (66)
T ss_pred HHHHHHHHHHHcCCCCCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEE
Confidence 4455555444444344555555 99999999999999999999999999764
No 156
>TIGR03504 FimV_Cterm FimV C-terminal domain. This protein is found at the extreme C-terminus of FimV from Pseudomonas aeruginosa, and of TspA of Neisseria meningitidis. Disruption of the former blocks twitching motility from type IV pili; Semmler, et al. suggest a role in peptidoglycan layer remodelling required by type IV fimbrial systems.
Probab=77.84 E-value=2.9 Score=29.01 Aligned_cols=26 Identities=19% Similarity=0.156 Sum_probs=23.4
Q ss_pred HhHHHHHHHHcCCHHHHHHHHHHHHh
Q 013559 142 YNDFGDFYYAHGALGDAFKSYVRTRD 167 (441)
Q Consensus 142 ~~~la~~~~~~Gd~~~A~~~~~~~r~ 167 (441)
.++||+-|.+.||++.|.+.+..+..
T Consensus 2 kLdLA~ayie~Gd~e~Ar~lL~evl~ 27 (44)
T TIGR03504 2 KLDLARAYIEMGDLEGARELLEEVIE 27 (44)
T ss_pred chHHHHHHHHcCChHHHHHHHHHHHH
Confidence 47899999999999999999998764
No 157
>CHL00033 ycf3 photosystem I assembly protein Ycf3
Probab=77.81 E-value=10 Score=33.59 Aligned_cols=67 Identities=13% Similarity=0.137 Sum_probs=47.7
Q ss_pred hHHhHHHHHHHHcCCHHHHHHHHHHHHhhhcCc----hhHHHHHHHHHHHHHHhcCHHHHHhHHHHHhccc
Q 013559 140 MGYNDFGDFYYAHGALGDAFKSYVRTRDYCTTS----KHIIHMCMSAILVSIEMGQFTHVTSYVSKAEQTP 206 (441)
Q Consensus 140 ~~~~~la~~~~~~Gd~~~A~~~~~~~r~~~~~~----~~~~~~~l~~i~~~i~~~~~~~~~~~~~ka~~~~ 206 (441)
.++..+|..|...|++++|.++|.+....-... .....+....-++.+..|++..+.....++....
T Consensus 73 ~~~~~lg~~~~~~g~~~eA~~~~~~Al~~~~~~~~~~~~la~i~~~~~~~~~~~g~~~~A~~~~~~a~~~~ 143 (168)
T CHL00033 73 YILYNIGLIHTSNGEHTKALEYYFQALERNPFLPQALNNMAVICHYRGEQAIEQGDSEIAEAWFDQAAEYW 143 (168)
T ss_pred HHHHHHHHHHHHcCCHHHHHHHHHHHHHhCcCcHHHHHHHHHHHHHhhHHHHHcccHHHHHHHHHHHHHHH
Confidence 378899999999999999999999875543221 1122233444455568889998888888776653
No 158
>PRK15359 type III secretion system chaperone protein SscB; Provisional
Probab=77.79 E-value=11 Score=32.90 Aligned_cols=64 Identities=8% Similarity=-0.092 Sum_probs=52.9
Q ss_pred HhHHhHHHHHHHHcCCHHHHHHHHHHHHhhhcCchhHHHHHHHHHHHHHHhcCHHHHHhHHHHHhcc
Q 013559 139 RMGYNDFGDFYYAHGALGDAFKSYVRTRDYCTTSKHIIHMCMSAILVSIEMGQFTHVTSYVSKAEQT 205 (441)
Q Consensus 139 r~~~~~la~~~~~~Gd~~~A~~~~~~~r~~~~~~~~~~~~~l~~i~~~i~~~~~~~~~~~~~ka~~~ 205 (441)
..++..+|..+...|++++|..+|.+....... -.+..+++..+....|++..+...+.++-..
T Consensus 58 ~~a~~~lg~~~~~~g~~~~A~~~y~~Al~l~p~---~~~a~~~lg~~l~~~g~~~eAi~~~~~Al~~ 121 (144)
T PRK15359 58 WRAHIALAGTWMMLKEYTTAINFYGHALMLDAS---HPEPVYQTGVCLKMMGEPGLAREAFQTAIKM 121 (144)
T ss_pred HHHHHHHHHHHHHHhhHHHHHHHHHHHHhcCCC---CcHHHHHHHHHHHHcCCHHHHHHHHHHHHHh
Confidence 457899999999999999999999998776432 2556677777888899999999999988664
No 159
>PRK09802 DNA-binding transcriptional regulator AgaR; Provisional
Probab=77.67 E-value=3.3 Score=40.42 Aligned_cols=47 Identities=19% Similarity=0.191 Sum_probs=43.3
Q ss_pred HHHHHHHHHhccccccccHHhHHHHcCCChHHHHHHHHHHHHcCccc
Q 013559 337 QIRNKALIQYTHPFVSVDLHMMANAFKTSVAGIEKELEALITDNQIQ 383 (441)
Q Consensus 337 ~iR~~~i~qy~~pYs~I~L~~mA~~fg~s~~~~E~~L~~LI~~g~L~ 383 (441)
.-|...|.++++....|+...||+.||+|...+-+.|..|-..|.+.
T Consensus 16 ~eR~~~Il~~L~~~~~vtv~eLa~~l~VS~~TIRRDL~~Le~~G~l~ 62 (269)
T PRK09802 16 SERREQIIQRLRQQGSVQVNDLSALYGVSTVTIRNDLAFLEKQGIAV 62 (269)
T ss_pred HHHHHHHHHHHHHcCCEeHHHHHHHHCCCHHHHHHHHHHHHhCCCeE
Confidence 45888999999999999999999999999999999999998888875
No 160
>PF01047 MarR: MarR family; InterPro: IPR000835 The MarR-type HTH domain is a DNA-binding, winged helix-turn-helix (wHTH) domain of about 135 amino acids present in transcription regulators of the MarR/SlyA family, involved in the development of antibiotic resistance. This family of transcription regulators is named after Escherichia coli MarR, a repressor of genes which activate the multiple antibiotic resistance and oxidative stress regulons, and after slyA from Salmonella typhimurium and E. coli, a transcription regulator that is required for virulence and survival in the macrophage environment. Regulators with the MarR-type HTH domain are present in bacteria and archaea and control a variety of biological functions, including resistance to multiple antibiotics, household disinfectants, organic solvents, oxidative stress agents and regulation of the virulence factor synthesis in pathogens of humans and plants. Many of the MarR-like regulators respond to aromatic compounds [, , ]. The crystal structures of MarR, MexR and SlyA have been determined and show a winged HTH DNA-binding core flanked by helices involved in dimerisation. The DNA-binding domains are ascribed to the superfamily of winged helix proteins, containing a three (four)-helix (H) bundle and a three-stranded antiparallel beta-sheet (B) in the topology: H1-(H1')-H2-B1-H3-H4-B2-B3-H5-H6. Helices 3 and 4 comprise the helix-turn-helix motif and the beta-sheet is called the wing. Helix 4 is termed the recognition helix, like in other HTHs where it binds the DNA major groove. The helices 1, 5 and 6 are involved in dimerisation, as most MarR-like transcription regulators form dimers [, ]. ; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 1JGS_A 2NYX_D 2PEX_B 2PFB_A 3BPX_A 3BPV_A 2BV6_A 3BJA_A 3E6M_B 2ETH_A ....
Probab=77.63 E-value=5.1 Score=28.93 Aligned_cols=46 Identities=11% Similarity=0.114 Sum_probs=39.1
Q ss_pred hccccccccHHhHHHHcCCChHHHHHHHHHHHHcCccceEecCCCC
Q 013559 346 YTHPFVSVDLHMMANAFKTSVAGIEKELEALITDNQIQARIDSHNK 391 (441)
Q Consensus 346 y~~pYs~I~L~~mA~~fg~s~~~~E~~L~~LI~~g~L~akID~~~g 391 (441)
++..+..+++..||+.+|++...+-+.+.+|+..|-|.-..|..++
T Consensus 11 ~l~~~~~~~~~~la~~~~~~~~~~t~~i~~L~~~g~I~r~~~~~D~ 56 (59)
T PF01047_consen 11 ILYENGGITQSELAEKLGISRSTVTRIIKRLEKKGLIERERDPDDR 56 (59)
T ss_dssp HHHHHSSEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEEEETTET
T ss_pred HHHHcCCCCHHHHHHHHCCChhHHHHHHHHHHHCCCEEeccCCCCC
Confidence 3444677999999999999999999999999999999888777654
No 161
>PRK10906 DNA-binding transcriptional repressor GlpR; Provisional
Probab=77.41 E-value=3.4 Score=39.88 Aligned_cols=46 Identities=24% Similarity=0.323 Sum_probs=42.5
Q ss_pred HHHHHHHHhccccccccHHhHHHHcCCChHHHHHHHHHHHHcCccc
Q 013559 338 IRNKALIQYTHPFVSVDLHMMANAFKTSVAGIEKELEALITDNQIQ 383 (441)
Q Consensus 338 iR~~~i~qy~~pYs~I~L~~mA~~fg~s~~~~E~~L~~LI~~g~L~ 383 (441)
-|...|..+++-+..+++..+|+.||+|.+.+-+.|..|-..|.|.
T Consensus 5 ~R~~~Il~~l~~~~~~~~~ela~~l~vS~~TiRRdL~~Le~~g~l~ 50 (252)
T PRK10906 5 QRHDAIIELVKQQGYVSTEELVEHFSVSPQTIRRDLNDLAEQNKIL 50 (252)
T ss_pred HHHHHHHHHHHHcCCEeHHHHHHHhCCCHHHHHHHHHHHHHCCCEE
Confidence 4778888899999999999999999999999999999999999873
No 162
>TIGR02552 LcrH_SycD type III secretion low calcium response chaperone LcrH/SycD. ScyD/LcrH contains three central tetratricopeptide-like repeats that are predicted to fold into an all-alpha-helical array.
Probab=77.00 E-value=11 Score=31.59 Aligned_cols=63 Identities=8% Similarity=-0.013 Sum_probs=45.0
Q ss_pred hHHhHHHHHHHHcCCHHHHHHHHHHHHhhhcCchhHHHHHHHHHHHHHHhcCHHHHHhHHHHHhcc
Q 013559 140 MGYNDFGDFYYAHGALGDAFKSYVRTRDYCTTSKHIIHMCMSAILVSIEMGQFTHVTSYVSKAEQT 205 (441)
Q Consensus 140 ~~~~~la~~~~~~Gd~~~A~~~~~~~r~~~~~~~~~~~~~l~~i~~~i~~~~~~~~~~~~~ka~~~ 205 (441)
..+..+|..++..|++.+|.++|.+......+ ..+.......+....|++..+...+.++-..
T Consensus 52 ~~~~~la~~~~~~~~~~~A~~~~~~~~~~~p~---~~~~~~~la~~~~~~g~~~~A~~~~~~al~~ 114 (135)
T TIGR02552 52 RYWLGLAACCQMLKEYEEAIDAYALAAALDPD---DPRPYFHAAECLLALGEPESALKALDLAIEI 114 (135)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCC---ChHHHHHHHHHHHHcCCHHHHHHHHHHHHHh
Confidence 46678888888889999999888887555322 1334445555677788888888888777654
No 163
>PRK15179 Vi polysaccharide biosynthesis protein TviE; Provisional
Probab=76.94 E-value=97 Score=34.60 Aligned_cols=159 Identities=9% Similarity=-0.023 Sum_probs=93.4
Q ss_pred CchhhHHHHHHHHhcCCCchhHHHHHHHHHHHHHh-cCChHHHHHHHHHhhccCCC------------CCcCCHHHHHHH
Q 013559 45 QGRTKITRLMFIADHCDIASMQLEALRMAYDEIKK-GENTQLFREVVKKIDGRLGP------------NYAMDEAWCDSV 111 (441)
Q Consensus 45 ~g~~~i~rL~fi~~~~~~~~~~~~a~~~~~~~lk~-t~~~~~Y~~~~~~l~~~~~~------------~~~~D~~~~~~~ 111 (441)
-|+-..+.+.-+.+.+-......+++-.++++++. -.+++.|.-+..... ..|- ++..|-.-.-..
T Consensus 47 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~La~i~~-~~g~~~ea~~~l~~~~~~~Pd~~~a~~~ 125 (694)
T PRK15179 47 AGRELLQQARQVLERHAAVHKPAAALPELLDYVRRYPHTELFQVLVARALE-AAHRSDEGLAVWRGIHQRFPDSSEAFIL 125 (694)
T ss_pred HHHHHHHHHHHHHHHhhhhcchHhhHHHHHHHHHhccccHHHHHHHHHHHH-HcCCcHHHHHHHHHHHhhCCCcHHHHHH
Confidence 34566777777777653234456777778888877 355666655543322 1110 111121111112
Q ss_pred HHHHHHHHHHHHHHHHHHHhhh-hHHHHHhHHhHHHHHHHHcCCHHHHHHHHHHHHhhhcCchhHHHHHHHHHHHHHHhc
Q 013559 112 DRRAEQRKEKLENELNAYRTNL-IKESIRMGYNDFGDFYYAHGALGDAFKSYVRTRDYCTTSKHIIHMCMSAILVSIEMG 190 (441)
Q Consensus 112 ~~~~~~~~~~Le~el~~~~~n~-~~esir~~~~~la~~~~~~Gd~~~A~~~~~~~r~~~~~~~~~~~~~l~~i~~~i~~~ 190 (441)
....-.+.+++++-+..++.-+ ..++-..+++.+|..+-+.|+|++|..+|.++.. +.... -++.+++--+-...|
T Consensus 126 ~a~~L~~~~~~eeA~~~~~~~l~~~p~~~~~~~~~a~~l~~~g~~~~A~~~y~~~~~-~~p~~--~~~~~~~a~~l~~~G 202 (694)
T PRK15179 126 MLRGVKRQQGIEAGRAEIELYFSGGSSSAREILLEAKSWDEIGQSEQADACFERLSR-QHPEF--ENGYVGWAQSLTRRG 202 (694)
T ss_pred HHHHHHHhccHHHHHHHHHHHhhcCCCCHHHHHHHHHHHHHhcchHHHHHHHHHHHh-cCCCc--HHHHHHHHHHHHHcC
Confidence 2233344445555554443222 2233345889999999999999999999999876 32222 344455555566778
Q ss_pred CHHHHHhHHHHHhcccc
Q 013559 191 QFTHVTSYVSKAEQTPE 207 (441)
Q Consensus 191 ~~~~~~~~~~ka~~~~~ 207 (441)
+.+.+...+.++-+...
T Consensus 203 ~~~~A~~~~~~a~~~~~ 219 (694)
T PRK15179 203 ALWRARDVLQAGLDAIG 219 (694)
T ss_pred CHHHHHHHHHHHHHhhC
Confidence 88888888888766554
No 164
>PRK13509 transcriptional repressor UlaR; Provisional
Probab=76.94 E-value=3.7 Score=39.60 Aligned_cols=45 Identities=13% Similarity=0.232 Sum_probs=41.6
Q ss_pred HHHHHHHhccccccccHHhHHHHcCCChHHHHHHHHHHHHcCccc
Q 013559 339 RNKALIQYTHPFVSVDLHMMANAFKTSVAGIEKELEALITDNQIQ 383 (441)
Q Consensus 339 R~~~i~qy~~pYs~I~L~~mA~~fg~s~~~~E~~L~~LI~~g~L~ 383 (441)
|...+..++..+..++...+|+.||+|...+.+.|..|-..|.|.
T Consensus 6 R~~~Il~~l~~~~~~~~~ela~~l~vS~~TirRdL~~Le~~g~i~ 50 (251)
T PRK13509 6 RHQILLELLAQLGFVTVEKVIERLGISPATARRDINKLDESGKLK 50 (251)
T ss_pred HHHHHHHHHHHcCCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCEE
Confidence 677788899999999999999999999999999999998888874
No 165
>KOG0553 consensus TPR repeat-containing protein [General function prediction only]
Probab=76.68 E-value=20 Score=35.44 Aligned_cols=92 Identities=17% Similarity=0.248 Sum_probs=64.3
Q ss_pred HHHHHHHHcCCHHHHHHHHHHHHhhhcCchhHHHHHHHHHHHHHHhcCHHHHHhHHHHHhcccccCChhhhhhHHHHHHH
Q 013559 144 DFGDFYYAHGALGDAFKSYVRTRDYCTTSKHIIHMCMSAILVSIEMGQFTHVTSYVSKAEQTPEALEPVTIAKLRCAAGL 223 (441)
Q Consensus 144 ~la~~~~~~Gd~~~A~~~~~~~r~~~~~~~~~~~~~l~~i~~~i~~~~~~~~~~~~~ka~~~~~~~d~~~~~~l~~~~gl 223 (441)
.=|+=+.+.|+|++|+..|.+..++..+ .-+-+| +...+...+|.++.|.+...++-.+ || .-.|...--|+
T Consensus 86 ~eGN~~m~~~~Y~eAv~kY~~AI~l~P~--nAVyyc-NRAAAy~~Lg~~~~AVkDce~Al~i----Dp-~yskay~RLG~ 157 (304)
T KOG0553|consen 86 NEGNKLMKNKDYQEAVDKYTEAIELDPT--NAVYYC-NRAAAYSKLGEYEDAVKDCESALSI----DP-HYSKAYGRLGL 157 (304)
T ss_pred HHHHHHHHhhhHHHHHHHHHHHHhcCCC--cchHHH-HHHHHHHHhcchHHHHHHHHHHHhc----Ch-HHHHHHHHHHH
Confidence 3466688899999999999998887533 223233 4455667778888887776665554 22 12344455699
Q ss_pred HhcccccHHHHHHHHHhcCc
Q 013559 224 AHLEARKYKLAARKFLEVGP 243 (441)
Q Consensus 224 ~~l~~r~y~~Aa~~Fl~~~~ 243 (441)
+++..|+|.+|.+.|-.+..
T Consensus 158 A~~~~gk~~~A~~aykKaLe 177 (304)
T KOG0553|consen 158 AYLALGKYEEAIEAYKKALE 177 (304)
T ss_pred HHHccCcHHHHHHHHHhhhc
Confidence 99999999999998866553
No 166
>PF10345 Cohesin_load: Cohesin loading factor; InterPro: IPR019440 Cohesin loading factor is a conserved protein that has been characterised in fungi. It is associated with the cohesin complex and is required in G1 for cohesin binding to chromosomes, but is dispensable in G2 when cohesion has been established. It is often referred to as Ssl3 in Schizosaccharomyces pombe (Fission yeast), and Scc4 in Saccharomyces cerevisiae (Baker's yeast). It complexes with Mis4 [].
Probab=76.14 E-value=1.3e+02 Score=33.01 Aligned_cols=100 Identities=9% Similarity=0.085 Sum_probs=76.1
Q ss_pred HHhHHHHHHHHcCCHHHHHHHHHHHHhhhcCc-hhHHHHHHHHHHHHHH--hcCHHHHHhHHHHHhcccc-cCChhhhhh
Q 013559 141 GYNDFGDFYYAHGALGDAFKSYVRTRDYCTTS-KHIIHMCMSAILVSIE--MGQFTHVTSYVSKAEQTPE-ALEPVTIAK 216 (441)
Q Consensus 141 ~~~~la~~~~~~Gd~~~A~~~~~~~r~~~~~~-~~~~~~~l~~i~~~i~--~~~~~~~~~~~~ka~~~~~-~~d~~~~~~ 216 (441)
+..-+++++++.|-.. |.+.+.+..+++.+. ..-.-.++..+++.+. .+|+..|...+.++..... .+||.....
T Consensus 102 ~~~ll~~i~~~~~~~~-a~~~l~~~I~~~~~~~~~~w~~~frll~~~l~~~~~d~~~Al~~L~~~~~~a~~~~d~~~~v~ 180 (608)
T PF10345_consen 102 CQFLLARIYFKTNPKA-ALKNLDKAIEDSETYGHSAWYYAFRLLKIQLALQHKDYNAALENLQSIAQLANQRGDPAVFVL 180 (608)
T ss_pred HHHHHHHHHHhcCHHH-HHHHHHHHHHHHhccCchhHHHHHHHHHHHHHHhcccHHHHHHHHHHHHHHhhhcCCHHHHHH
Confidence 4456699999999999 999999987777553 3335566666666443 4699999999999888766 689999999
Q ss_pred HHHHHHHHhcccccHHHHHHHHHhc
Q 013559 217 LRCAAGLAHLEARKYKLAARKFLEV 241 (441)
Q Consensus 217 l~~~~gl~~l~~r~y~~Aa~~Fl~~ 241 (441)
+....|+.++..+...++.+..-.+
T Consensus 181 ~~l~~~~l~l~~~~~~d~~~~l~~~ 205 (608)
T PF10345_consen 181 ASLSEALLHLRRGSPDDVLELLQRA 205 (608)
T ss_pred HHHHHHHHHhcCCCchhHHHHHHHH
Confidence 9999999999988665555544433
No 167
>KOG2002 consensus TPR-containing nuclear phosphoprotein that regulates K(+) uptake [Inorganic ion transport and metabolism]
Probab=76.02 E-value=64 Score=36.82 Aligned_cols=130 Identities=13% Similarity=0.124 Sum_probs=70.6
Q ss_pred HHHHHHHHHHHHhcCChHHHHHHHHHhhccCCCCCcCCHHHHHHHHHHH------HHHHHHHHHHHHHHHhhhhHHHHHh
Q 013559 67 LEALRMAYDEIKKGENTQLFREVVKKIDGRLGPNYAMDEAWCDSVDRRA------EQRKEKLENELNAYRTNLIKESIRM 140 (441)
Q Consensus 67 ~~a~~~~~~~lk~t~~~~~Y~~~~~~l~~~~~~~~~~D~~~~~~~~~~~------~~~~~~Le~el~~~~~n~~~esir~ 140 (441)
..++-++-..-..+++.+-|......+.+... .-+-+|.....+.... ..-+.--+.-++ ++-.+.-+-.
T Consensus 233 v~alv~L~~~~l~~~d~~s~~~~~~ll~~ay~-~n~~nP~~l~~LAn~fyfK~dy~~v~~la~~ai~---~t~~~~~~ae 308 (1018)
T KOG2002|consen 233 VSALVALGEVDLNFNDSDSYKKGVQLLQRAYK-ENNENPVALNHLANHFYFKKDYERVWHLAEHAIK---NTENKSIKAE 308 (1018)
T ss_pred HHHHHHHHHHHHHccchHHHHHHHHHHHHHHh-hcCCCcHHHHHHHHHHhhcccHHHHHHHHHHHHH---hhhhhHHHHH
Confidence 44444444444568888888877766653211 1233344443333221 111111111111 2222222335
Q ss_pred HHhHHHHHHHHcCCHHHHHHHHHHHHhhhcCchhHHHHHHHHHHHHHHhcCHHHHHhHHHHH
Q 013559 141 GYNDFGDFYYAHGALGDAFKSYVRTRDYCTTSKHIIHMCMSAILVSIEMGQFTHVTSYVSKA 202 (441)
Q Consensus 141 ~~~~la~~~~~~Gd~~~A~~~~~~~r~~~~~~~~~~~~~l~~i~~~i~~~~~~~~~~~~~ka 202 (441)
++|.+|+-|...|||++|.++|........ ++-+--.+++..+.|..|+...+.....|+
T Consensus 309 s~Y~~gRs~Ha~Gd~ekA~~yY~~s~k~~~--d~~~l~~~GlgQm~i~~~dle~s~~~fEkv 368 (1018)
T KOG2002|consen 309 SFYQLGRSYHAQGDFEKAFKYYMESLKADN--DNFVLPLVGLGQMYIKRGDLEESKFCFEKV 368 (1018)
T ss_pred HHHHHHHHHHhhccHHHHHHHHHHHHccCC--CCccccccchhHHHHHhchHHHHHHHHHHH
Confidence 899999999999999999999998755432 222333445556666666666555444444
No 168
>KOG1129 consensus TPR repeat-containing protein [General function prediction only]
Probab=75.95 E-value=45 Score=33.63 Aligned_cols=87 Identities=18% Similarity=0.155 Sum_probs=54.2
Q ss_pred cCCHHHHHHHHHHHHhhhcCchhHHHHHHHHHHHHHHhcCHHHHHhHHHHHhcccccCChhhhhhHHHHHHHHhcccccH
Q 013559 152 HGALGDAFKSYVRTRDYCTTSKHIIHMCMSAILVSIEMGQFTHVTSYVSKAEQTPEALEPVTIAKLRCAAGLAHLEARKY 231 (441)
Q Consensus 152 ~Gd~~~A~~~~~~~r~~~~~~~~~~~~~l~~i~~~i~~~~~~~~~~~~~ka~~~~~~~d~~~~~~l~~~~gl~~l~~r~y 231 (441)
-|+-+-|+.+|.++......+. +...++--|++..+.++.+...+.+|.++... +...+-+..--|-.....|+|
T Consensus 337 ~~~PE~AlryYRRiLqmG~~sp---eLf~NigLCC~yaqQ~D~~L~sf~RAlstat~--~~~aaDvWYNlg~vaV~iGD~ 411 (478)
T KOG1129|consen 337 DNNPEMALRYYRRILQMGAQSP---ELFCNIGLCCLYAQQIDLVLPSFQRALSTATQ--PGQAADVWYNLGFVAVTIGDF 411 (478)
T ss_pred CCChHHHHHHHHHHHHhcCCCh---HHHhhHHHHHHhhcchhhhHHHHHHHHhhccC--cchhhhhhhccceeEEeccch
Confidence 3444444444444444332222 23456667888899999999999999887652 122222223335556678999
Q ss_pred HHHHHHHHhcCc
Q 013559 232 KLAARKFLEVGP 243 (441)
Q Consensus 232 ~~Aa~~Fl~~~~ 243 (441)
..|.++|.-+..
T Consensus 412 nlA~rcfrlaL~ 423 (478)
T KOG1129|consen 412 NLAKRCFRLALT 423 (478)
T ss_pred HHHHHHHHHHhc
Confidence 999999987764
No 169
>PRK09782 bacteriophage N4 receptor, outer membrane subunit; Provisional
Probab=75.78 E-value=96 Score=36.15 Aligned_cols=93 Identities=9% Similarity=-0.097 Sum_probs=47.0
Q ss_pred HhHHHHHHHHcCCHHHHHHHHHHHHhhhcCchhHHHHHHHHHHHHHHhcCHHHHHhHHHHHhcccccCChhhhhhHHHHH
Q 013559 142 YNDFGDFYYAHGALGDAFKSYVRTRDYCTTSKHIIHMCMSAILVSIEMGQFTHVTSYVSKAEQTPEALEPVTIAKLRCAA 221 (441)
Q Consensus 142 ~~~la~~~~~~Gd~~~A~~~~~~~r~~~~~~~~~~~~~l~~i~~~i~~~~~~~~~~~~~ka~~~~~~~d~~~~~~l~~~~ 221 (441)
++.+|..+.+.|++++|.++|.+....... . ......+.......|+++.+...+.++-.. +|. .....-.
T Consensus 545 ~~~la~all~~Gd~~eA~~~l~qAL~l~P~--~-~~l~~~La~~l~~~Gr~~eAl~~~~~AL~l----~P~--~~a~~~L 615 (987)
T PRK09782 545 LLAAANTAQAAGNGAARDRWLQQAEQRGLG--D-NALYWWLHAQRYIPGQPELALNDLTRSLNI----APS--ANAYVAR 615 (987)
T ss_pred HHHHHHHHHHCCCHHHHHHHHHHHHhcCCc--c-HHHHHHHHHHHHhCCCHHHHHHHHHHHHHh----CCC--HHHHHHH
Confidence 345566666666666666666665443221 1 111111111111236666666666665433 121 1223344
Q ss_pred HHHhcccccHHHHHHHHHhcCc
Q 013559 222 GLAHLEARKYKLAARKFLEVGP 243 (441)
Q Consensus 222 gl~~l~~r~y~~Aa~~Fl~~~~ 243 (441)
|.++...|++.+|...|-.+..
T Consensus 616 A~~l~~lG~~deA~~~l~~AL~ 637 (987)
T PRK09782 616 ATIYRQRHNVPAAVSDLRAALE 637 (987)
T ss_pred HHHHHHCCCHHHHHHHHHHHHH
Confidence 5566667777777777766654
No 170
>KOG0624 consensus dsRNA-activated protein kinase inhibitor P58, contains TPR and DnaJ domains [Defense mechanisms]
Probab=75.50 E-value=99 Score=31.49 Aligned_cols=201 Identities=16% Similarity=0.100 Sum_probs=120.1
Q ss_pred HHHHHHHHHHHHhhhhHHHHHhHHhHHHHHHHHcCCHHHHHHHHHHHHhhhcCchhHHHHHHHHHHHHHHhcCHHHHHhH
Q 013559 119 KEKLENELNAYRTNLIKESIRMGYNDFGDFYYAHGALGDAFKSYVRTRDYCTTSKHIIHMCMSAILVSIEMGQFTHVTSY 198 (441)
Q Consensus 119 ~~~Le~el~~~~~n~~~esir~~~~~la~~~~~~Gd~~~A~~~~~~~r~~~~~~~~~~~~~l~~i~~~i~~~~~~~~~~~ 198 (441)
+--|+.-+..++......++ .-++.+|+-++..|++..|+..|-...+.-. .. ...++.-..+.+.+|.-..+...
T Consensus 19 Lvll~~~~e~a~~~~~~adv-ekhlElGk~lla~~Q~sDALt~yHaAve~dp--~~-Y~aifrRaT~yLAmGksk~al~D 94 (504)
T KOG0624|consen 19 LVLLELFLEGAESTASPADV-EKHLELGKELLARGQLSDALTHYHAAVEGDP--NN-YQAIFRRATVYLAMGKSKAALQD 94 (504)
T ss_pred HHHHHHHHHHHHhcCCHHHH-HHHHHHHHHHHHhhhHHHHHHHHHHHHcCCc--hh-HHHHHHHHHHHhhhcCCccchhh
Confidence 33456666666665555555 4688999999999999999999887766532 22 33445566677778877777777
Q ss_pred HHHHhcc-cccCChhhhhhHHHHHHHHhcccccHHHHHHHHHhcCcCCCCCchhhhcHHHHHHHHHHHHHhcCChHHHHH
Q 013559 199 VSKAEQT-PEALEPVTIAKLRCAAGLAHLEARKYKLAARKFLEVGPDLGNSYNEVIAAQDVATYGGLCALASFDRAELKS 277 (441)
Q Consensus 199 ~~ka~~~-~~~~d~~~~~~l~~~~gl~~l~~r~y~~Aa~~Fl~~~~t~~~~~~el~s~~d~~~Y~~l~al~s~~R~eLk~ 277 (441)
+.++-++ +|. .--+...|..+|-+|.+..|...|-.+...-.++-...- .+ .
T Consensus 95 l~rVlelKpDF------~~ARiQRg~vllK~Gele~A~~DF~~vl~~~~s~~~~~e------aq---------------s 147 (504)
T KOG0624|consen 95 LSRVLELKPDF------MAARIQRGVVLLKQGELEQAEADFDQVLQHEPSNGLVLE------AQ---------------S 147 (504)
T ss_pred HHHHHhcCccH------HHHHHHhchhhhhcccHHHHHHHHHHHHhcCCCcchhHH------HH---------------H
Confidence 7776554 331 112456788999999999999999888754322111111 11 1
Q ss_pred hcccCHhhHhhhccchHHHHHHHHHhcCCHHHHHHHHHHhHHhhhhchhHHHHHHHHHHHHHHHHHHHhccccccccHHh
Q 013559 278 KVIDNVNFRNFLELVPEVRELINDFYSSRYASCLDYLGNLKANLLLDIHLHDHVETLYDQIRNKALIQYTHPFVSVDLHM 357 (441)
Q Consensus 278 ~vl~~~~~~~~le~~p~~~~ll~~f~~~~y~~~~~~L~~~~~~l~~D~~L~~h~~~l~~~iR~~~i~qy~~pYs~I~L~~ 357 (441)
++.-..+ .--....+++.|-++++....+.+..+-..-. .+.=++.+|.+|++.-=+|-+.|.==.
T Consensus 148 kl~~~~e------~~~l~~ql~s~~~~GD~~~ai~~i~~llEi~~--------Wda~l~~~Rakc~i~~~e~k~AI~Dlk 213 (504)
T KOG0624|consen 148 KLALIQE------HWVLVQQLKSASGSGDCQNAIEMITHLLEIQP--------WDASLRQARAKCYIAEGEPKKAIHDLK 213 (504)
T ss_pred HHHhHHH------HHHHHHHHHHHhcCCchhhHHHHHHHHHhcCc--------chhHHHHHHHHHHHhcCcHHHHHHHHH
Confidence 1100000 01113455666667787777666655432211 123345667777777666666654444
Q ss_pred HHHHcCC
Q 013559 358 MANAFKT 364 (441)
Q Consensus 358 mA~~fg~ 364 (441)
.|..+.-
T Consensus 214 ~askLs~ 220 (504)
T KOG0624|consen 214 QASKLSQ 220 (504)
T ss_pred HHHhccc
Confidence 4444443
No 171
>KOG4414 consensus COP9 signalosome, subunit CSN8 [Posttranslational modification, protein turnover, chaperones; Signal transduction mechanisms]
Probab=75.39 E-value=5.9 Score=34.80 Aligned_cols=76 Identities=11% Similarity=0.120 Sum_probs=57.2
Q ss_pred HHHHHHHhcCCHHHHHHHHHHhHHhhhhchhHHHHHHHHHHHHHHHHHHHhccccccccHHhHHHHcCCChHHHHHHHHH
Q 013559 296 RELINDFYSSRYASCLDYLGNLKANLLLDIHLHDHVETLYDQIRNKALIQYTHPFVSVDLHMMANAFKTSVAGIEKELEA 375 (441)
Q Consensus 296 ~~ll~~f~~~~y~~~~~~L~~~~~~l~~D~~L~~h~~~l~~~iR~~~i~qy~~pYs~I~L~~mA~~fg~s~~~~E~~L~~ 375 (441)
..+-+.....+|.+..+.+....-. .-..+-+..|-..-|.|++.-.+..|++|.+..+|..+|+++++.-+-+.+
T Consensus 80 WgiGQkiWq~Df~GiYeaI~~~dWS----eeak~imaAf~D~~~kR~FaLl~qAYssI~~~D~A~FlGl~~ddAtk~ilE 155 (197)
T KOG4414|consen 80 WGIGQKIWQHDFAGIYEAINAHDWS----EEAKDIMAAFRDATRKRAFALLLQAYSSIIADDFAAFLGLPEDDATKGILE 155 (197)
T ss_pred hhhhHHHHhcccchHHHHHhhhcch----HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCHHHHHHHHHH
Confidence 4466677788888888877764211 012334567777788899999999999999999999999999987666544
No 172
>KOG4234 consensus TPR repeat-containing protein [General function prediction only]
Probab=75.29 E-value=9.3 Score=35.77 Aligned_cols=61 Identities=15% Similarity=0.210 Sum_probs=44.9
Q ss_pred HHHHHHHcCCHHHHHHHHHHHHhhhcCchhHHHHHHH--HHHHHHHhcCHHHHHhHHHHHhcc
Q 013559 145 FGDFYYAHGALGDAFKSYVRTRDYCTTSKHIIHMCMS--AILVSIEMGQFTHVTSYVSKAEQT 205 (441)
Q Consensus 145 la~~~~~~Gd~~~A~~~~~~~r~~~~~~~~~~~~~l~--~i~~~i~~~~~~~~~~~~~ka~~~ 205 (441)
=|+-++.-|+|.+|..-|....+.|.+.......++- -..+-|-++.|..+.....|+-.+
T Consensus 101 EGN~~F~ngdyeeA~skY~~Ale~cp~~~~e~rsIly~Nraaa~iKl~k~e~aI~dcsKaiel 163 (271)
T KOG4234|consen 101 EGNELFKNGDYEEANSKYQEALESCPSTSTEERSILYSNRAAALIKLRKWESAIEDCSKAIEL 163 (271)
T ss_pred HHHHhhhcccHHHHHHHHHHHHHhCccccHHHHHHHHhhhHHHHHHhhhHHHHHHHHHhhHhc
Confidence 3677899999999999999999999866665554333 333446677888887777776554
No 173
>cd05804 StaR_like StaR_like; a well-conserved protein found in bacteria, plants, and animals. A family member from Streptomyces toyocaensis, StaR is part of a gene cluster involved in the biosynthesis of glycopeptide antibiotics (GPAs), specifically A47934. It has been speculated that StaR could be a flavoprotein hydroxylating a tyrosine sidechain. Some family members have been annotated as proteins containing tetratricopeptide (TPR) repeats, which may at least indicate mostly alpha-helical secondary structure.
Probab=75.10 E-value=90 Score=30.81 Aligned_cols=64 Identities=13% Similarity=0.074 Sum_probs=53.6
Q ss_pred hHHhHHHHHHHHcCCHHHHHHHHHHHHhhhc-CchhHHHHHHHHHHHHHHhcCHHHHHhHHHHHh
Q 013559 140 MGYNDFGDFYYAHGALGDAFKSYVRTRDYCT-TSKHIIHMCMSAILVSIEMGQFTHVTSYVSKAE 203 (441)
Q Consensus 140 ~~~~~la~~~~~~Gd~~~A~~~~~~~r~~~~-~~~~~~~~~l~~i~~~i~~~~~~~~~~~~~ka~ 203 (441)
.++..+|..+++.|++++|..++.+..+... .+...+...+...++.+..|+++.+...+.++.
T Consensus 149 ~~~~~la~i~~~~g~~~eA~~~l~~~l~~~~~~~~~~~~~~~~la~~~~~~G~~~~A~~~~~~~~ 213 (355)
T cd05804 149 WAVHAVAHVLEMQGRFKEGIAFMESWRDTWDCSSMLRGHNWWHLALFYLERGDYEAALAIYDTHI 213 (355)
T ss_pred HHHHHHHHHHHHcCCHHHHHHHHHhhhhccCCCcchhHHHHHHHHHHHHHCCCHHHHHHHHHHHh
Confidence 4778899999999999999999999866543 334445677888999999999999999999874
No 174
>PRK10681 DNA-binding transcriptional repressor DeoR; Provisional
Probab=75.05 E-value=3.7 Score=39.58 Aligned_cols=41 Identities=22% Similarity=0.130 Sum_probs=37.6
Q ss_pred HHHHHHHHHhccccccccHHhHHHHcCCChHHHHHHHHHHH
Q 013559 337 QIRNKALIQYTHPFVSVDLHMMANAFKTSVAGIEKELEALI 377 (441)
Q Consensus 337 ~iR~~~i~qy~~pYs~I~L~~mA~~fg~s~~~~E~~L~~LI 377 (441)
+=|...|.+++..+..|+...||+.||+|++.+-+.|..|=
T Consensus 6 ~eR~~~I~~~l~~~~~v~v~eLa~~~~VS~~TIRRDL~~Le 46 (252)
T PRK10681 6 DERIGQLLQALKRSDKLHLKDAAALLGVSEMTIRRDLNAHS 46 (252)
T ss_pred HHHHHHHHHHHHHcCCCcHHHHHHHhCCCHHHHHHHHHHhh
Confidence 34889999999999999999999999999999999999754
No 175
>TIGR03826 YvyF flagellar operon protein TIGR03826. This gene is found in flagellar operons of Bacillus-related organisms. Its function has not been determined and an official gene symbol has not been assigned, although the gene is designated yvyF in B. subtilus. A tentative assignment as a regulator is suggested in the NCBI record GI:16080597.
Probab=74.47 E-value=3.5 Score=36.05 Aligned_cols=43 Identities=7% Similarity=0.100 Sum_probs=33.2
Q ss_pred HHHhcccccc--ccHHhHHHHcCCChHHHHHHHHHHHHcCccceEecCC
Q 013559 343 LIQYTHPFVS--VDLHMMANAFKTSVAGIEKELEALITDNQIQARIDSH 389 (441)
Q Consensus 343 i~qy~~pYs~--I~L~~mA~~fg~s~~~~E~~L~~LI~~g~L~akID~~ 389 (441)
+.+|++-+.. .++..+|++.|||++. |.++|.+|||.-.-++.
T Consensus 35 V~~yLr~~p~~~ati~eV~e~tgVs~~~----I~~~IreGRL~~~~~~n 79 (137)
T TIGR03826 35 VYKFLRKHENRQATVSEIVEETGVSEKL----ILKFIREGRLQLKHFPN 79 (137)
T ss_pred HHHHHHHCCCCCCCHHHHHHHHCcCHHH----HHHHHHcCCeeccCCCC
Confidence 4457775666 9999999999999877 56778899997655443
No 176
>smart00028 TPR Tetratricopeptide repeats. Repeats present in 4 or more copies in proteins. Contain a minimum of 34 amino acids each and self-associate via a "knobs and holes" mechanism.
Probab=74.07 E-value=6 Score=22.87 Aligned_cols=27 Identities=19% Similarity=0.468 Sum_probs=23.4
Q ss_pred HHhHHHHHHHHcCCHHHHHHHHHHHHh
Q 013559 141 GYNDFGDFYYAHGALGDAFKSYVRTRD 167 (441)
Q Consensus 141 ~~~~la~~~~~~Gd~~~A~~~~~~~r~ 167 (441)
++..+|..+...|++++|..++.+...
T Consensus 3 ~~~~~a~~~~~~~~~~~a~~~~~~~~~ 29 (34)
T smart00028 3 ALYNLGNAYLKLGDYDEALEYYEKALE 29 (34)
T ss_pred HHHHHHHHHHHHhhHHHHHHHHHHHHc
Confidence 567899999999999999999987643
No 177
>PF07721 TPR_4: Tetratricopeptide repeat; InterPro: IPR011717 This entry includes tetratricopeptide-like repeats not detected by the IPR001440 from INTERPRO, IPR013105 from INTERPRO and IPR011716 from INTERPRO models. The tetratricopeptide repeat (TPR) motif is a protein-protein interaction module found in multiple copies in a number of functionally different proteins that facilitates specific interactions with a partner protein(s) [].; GO: 0042802 identical protein binding
Probab=73.91 E-value=4.7 Score=24.24 Aligned_cols=23 Identities=13% Similarity=0.043 Sum_probs=20.2
Q ss_pred HHhHHHHHHHHcCCHHHHHHHHH
Q 013559 141 GYNDFGDFYYAHGALGDAFKSYV 163 (441)
Q Consensus 141 ~~~~la~~~~~~Gd~~~A~~~~~ 163 (441)
+++.+|..+...||.++|...+.
T Consensus 3 a~~~la~~~~~~G~~~eA~~~l~ 25 (26)
T PF07721_consen 3 ARLALARALLAQGDPDEAERLLR 25 (26)
T ss_pred HHHHHHHHHHHcCCHHHHHHHHh
Confidence 56789999999999999998764
No 178
>KOG0548 consensus Molecular co-chaperone STI1 [Posttranslational modification, protein turnover, chaperones]
Probab=73.18 E-value=49 Score=35.22 Aligned_cols=92 Identities=14% Similarity=0.173 Sum_probs=68.6
Q ss_pred HHHHHHHHcCCHHHHHHHHHHHHhhhcCchhHHHHHHHHHHHHHHhcCHHHHHhHHHHHhcccccCChhhhhhHHHHHHH
Q 013559 144 DFGDFYYAHGALGDAFKSYVRTRDYCTTSKHIIHMCMSAILVSIEMGQFTHVTSYVSKAEQTPEALEPVTIAKLRCAAGL 223 (441)
Q Consensus 144 ~la~~~~~~Gd~~~A~~~~~~~r~~~~~~~~~~~~~l~~i~~~i~~~~~~~~~~~~~ka~~~~~~~d~~~~~~l~~~~gl 223 (441)
..|+.-++.||+..|..+|...-....+ .|++ +-+-..+....|+|..+.+.-.|...+- .+|. +=..-.|-
T Consensus 7 ~kgnaa~s~~d~~~ai~~~t~ai~l~p~-nhvl--ySnrsaa~a~~~~~~~al~da~k~~~l~--p~w~---kgy~r~Ga 78 (539)
T KOG0548|consen 7 EKGNAAFSSGDFETAIRLFTEAIMLSPT-NHVL--YSNRSAAYASLGSYEKALKDATKTRRLN--PDWA---KGYSRKGA 78 (539)
T ss_pred HHHHhhcccccHHHHHHHHHHHHccCCC-ccch--hcchHHHHHHHhhHHHHHHHHHHHHhcC--Cchh---hHHHHhHH
Confidence 4578889999999999999998776544 5543 3355667788899999988888776652 3553 21233578
Q ss_pred HhcccccHHHHHHHHHhcCc
Q 013559 224 AHLEARKYKLAARKFLEVGP 243 (441)
Q Consensus 224 ~~l~~r~y~~Aa~~Fl~~~~ 243 (441)
.++..|+|.+|...|-+-..
T Consensus 79 a~~~lg~~~eA~~ay~~GL~ 98 (539)
T KOG0548|consen 79 ALFGLGDYEEAILAYSEGLE 98 (539)
T ss_pred HHHhcccHHHHHHHHHHHhh
Confidence 88999999999999887664
No 179
>KOG0551 consensus Hsp90 co-chaperone CNS1 (contains TPR repeats) [Posttranslational modification, protein turnover, chaperones]
Probab=73.18 E-value=25 Score=35.30 Aligned_cols=96 Identities=17% Similarity=0.218 Sum_probs=69.9
Q ss_pred HHHhHHhHHHHHHHHcCCHHHHHHHHHHH-HhhhcCchhHHHHHHHHHHHHHHhcCHHHHHhHHHHHhcccccCChhhhh
Q 013559 137 SIRMGYNDFGDFYYAHGALGDAFKSYVRT-RDYCTTSKHIIHMCMSAILVSIEMGQFTHVTSYVSKAEQTPEALEPVTIA 215 (441)
Q Consensus 137 sir~~~~~la~~~~~~Gd~~~A~~~~~~~-r~~~~~~~~~~~~~l~~i~~~i~~~~~~~~~~~~~ka~~~~~~~d~~~~~ 215 (441)
++-.-+-+=|+.|++.-+|..|..+|++- ...|.+++--.-.+.+-.++.++.||+..+.+...++...-- . -+++
T Consensus 79 E~Aen~KeeGN~~fK~Kryk~A~~~Yt~Glk~kc~D~dlnavLY~NRAAa~~~l~NyRs~l~Dcs~al~~~P-~--h~Ka 155 (390)
T KOG0551|consen 79 EQAENYKEEGNEYFKEKRYKDAVESYTEGLKKKCADPDLNAVLYTNRAAAQLYLGNYRSALNDCSAALKLKP-T--HLKA 155 (390)
T ss_pred HHHHHHHHHhHHHHHhhhHHHHHHHHHHHHhhcCCCccHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHhcCc-c--hhhh
Confidence 35455666789999999999999999985 788988887677778888889999999999999998877521 1 1344
Q ss_pred hHHHHHHHHhcccccHHHHHHH
Q 013559 216 KLRCAAGLAHLEARKYKLAARK 237 (441)
Q Consensus 216 ~l~~~~gl~~l~~r~y~~Aa~~ 237 (441)
.++. +..++.-..|.+|.+.
T Consensus 156 ~~R~--Akc~~eLe~~~~a~nw 175 (390)
T KOG0551|consen 156 YIRG--AKCLLELERFAEAVNW 175 (390)
T ss_pred hhhh--hHHHHHHHHHHHHHHH
Confidence 4443 3344444555555443
No 180
>PRK11014 transcriptional repressor NsrR; Provisional
Probab=73.04 E-value=9 Score=33.35 Aligned_cols=62 Identities=11% Similarity=0.067 Sum_probs=49.5
Q ss_pred HHHHHHHHHhccccccccHHhHHHHcCCChHHHHHHHHHHHHcCccceEecCCCCeEEEecC
Q 013559 337 QIRNKALIQYTHPFVSVDLHMMANAFKTSVAGIEKELEALITDNQIQARIDSHNKILYARHA 398 (441)
Q Consensus 337 ~iR~~~i~qy~~pYs~I~L~~mA~~fg~s~~~~E~~L~~LI~~g~L~akID~~~gvv~~~~~ 398 (441)
-+|..++.....|=..++...||+.+|+|...+.+-+..|-..|-+..+==...|.....+|
T Consensus 10 Al~~~i~la~~~~g~~~s~~~ia~~~~is~~~vrk~l~~L~~~Glv~s~~G~~GG~~l~~~~ 71 (141)
T PRK11014 10 GLRALIYMASLPEGRMTSISEVTEVYGVSRNHMVKIINQLSRAGYVTAVRGKNGGIRLGKPA 71 (141)
T ss_pred HHHHHHHHhcCCCCCccCHHHHHHHHCcCHHHHHHHHHHHHhCCEEEEecCCCCCeeecCCH
Confidence 35556666666776789999999999999999999999999999987766555666665544
No 181
>cd00090 HTH_ARSR Arsenical Resistance Operon Repressor and similar prokaryotic, metal regulated homodimeric repressors. ARSR subfamily of helix-turn-helix bacterial transcription regulatory proteins (winged helix topology). Includes several proteins that appear to dissociate from DNA in the presence of metal ions.
Probab=73.00 E-value=21 Score=26.10 Aligned_cols=44 Identities=11% Similarity=0.188 Sum_probs=36.8
Q ss_pred ccHHhHHHHcCCChHHHHHHHHHHHHcCccceEecCCCCeEEEe
Q 013559 353 VDLHMMANAFKTSVAGIEKELEALITDNQIQARIDSHNKILYAR 396 (441)
Q Consensus 353 I~L~~mA~~fg~s~~~~E~~L~~LI~~g~L~akID~~~gvv~~~ 396 (441)
++.+.+|+.||++...+-+.|..|...|-|...-+...+....+
T Consensus 21 ~~~~ei~~~~~i~~~~i~~~l~~L~~~g~i~~~~~~~~~~~~~~ 64 (78)
T cd00090 21 LTVSELAERLGLSQSTVSRHLKKLEEAGLVESRREGRRVYYSLT 64 (78)
T ss_pred cCHHHHHHHHCcCHhHHHHHHHHHHHCCCeEEEEeccEEEEEeC
Confidence 99999999999999999999999999999988766644443333
No 182
>PF02064 MAS20: MAS20 protein import receptor; InterPro: IPR002056 Virtually all mitochondrial precursors are imported via the same mechanism []: precursors first bind to receptors on the mitochondrial surface, then insert into the translocation channel in the outer membrane. Many outer-membrane proteins participate in the early stages of import, four of which (MAS20, MAS22, MAS37 and MAS70) are components of the receptor. MAS20, which forms a subcomplex with MAS22, seems to interact with most or all mitochondrial precursors, suggesting that the protein binds directly to mitochondrial targeting sequences. The MAS37 and MAS70 components also form a subcomplex, the two subcomplexes possibly binding via their trans- membrane (TM) regions - the TM region of MAS70 promotes oligomerisation of attatched protein domains and shares sequence similarity with the TM region of MAS20 []. MAS20 is also known as TOM20.; GO: 0006605 protein targeting, 0006886 intracellular protein transport, 0005742 mitochondrial outer membrane translocase complex; PDB: 3AX3_A 3AWR_B 2V1S_A 3AX5_C 3AX2_C 1OM2_A 2V1T_B.
Probab=72.97 E-value=8.2 Score=33.01 Aligned_cols=41 Identities=12% Similarity=0.345 Sum_probs=34.3
Q ss_pred hHHhHHHHHHHHcCCHHHHHHHHHHHHhhhcCchhHHHHHH
Q 013559 140 MGYNDFGDFYYAHGALGDAFKSYVRTRDYCTTSKHIIHMCM 180 (441)
Q Consensus 140 ~~~~~la~~~~~~Gd~~~A~~~~~~~r~~~~~~~~~~~~~l 180 (441)
+-...+|+-+...|++.+|+.++++..--|+.|.+.+.++=
T Consensus 64 l~qV~lGE~L~~~G~~~~aa~hf~nAl~V~~qP~~LL~i~q 104 (121)
T PF02064_consen 64 LQQVQLGEQLLAQGDYEEAAEHFYNALKVCPQPAELLQIYQ 104 (121)
T ss_dssp HHHHHHHHHHHHTT-HHHHHHHHHHHHHTSSSHHHHHHHHH
T ss_pred HHHHHHHHHHHhCCCHHHHHHHHHHHHHhCCCHHHHHHHHH
Confidence 45568899999999999999999999999999988776653
No 183
>PF13518 HTH_28: Helix-turn-helix domain
Probab=72.66 E-value=9.5 Score=26.56 Aligned_cols=45 Identities=13% Similarity=0.138 Sum_probs=34.8
Q ss_pred HHHHHHHhccccccccHHhHHHHcCCChHHHHHHHHHHHHcCccceEec
Q 013559 339 RNKALIQYTHPFVSVDLHMMANAFKTSVAGIEKELEALITDNQIQARID 387 (441)
Q Consensus 339 R~~~i~qy~~pYs~I~L~~mA~~fg~s~~~~E~~L~~LI~~g~L~akID 387 (441)
|..++..|.+ ..++..+|..||+|...+..|+..+=..| +++-.+
T Consensus 2 r~~iv~~~~~---g~s~~~~a~~~gis~~tv~~w~~~y~~~G-~~~l~~ 46 (52)
T PF13518_consen 2 RLQIVELYLE---GESVREIAREFGISRSTVYRWIKRYREGG-IEGLKP 46 (52)
T ss_pred HHHHHHHHHc---CCCHHHHHHHHCCCHhHHHHHHHHHHhcC-HHHhcc
Confidence 4466777754 44999999999999999999999987776 444333
No 184
>COG2976 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=72.66 E-value=78 Score=29.51 Aligned_cols=103 Identities=7% Similarity=-0.085 Sum_probs=74.9
Q ss_pred HHHHhHHhHHHHHHHHcCCHHHHHHHHHHHHhhhcCchhHHHHHHHHHHHHHHhcCHHHHHhHHHHHhcccccCChhhhh
Q 013559 136 ESIRMGYNDFGDFYYAHGALGDAFKSYVRTRDYCTTSKHIIHMCMSAILVSIEMGQFTHVTSYVSKAEQTPEALEPVTIA 215 (441)
Q Consensus 136 esir~~~~~la~~~~~~Gd~~~A~~~~~~~r~~~~~~~~~~~~~l~~i~~~i~~~~~~~~~~~~~ka~~~~~~~d~~~~~ 215 (441)
..-..+.+.+|+-+.++|++++|...+......+.+..-+.=.-+.+.|+-+..|.++.+.+.+... .+.+| .+
T Consensus 86 ~Ya~laaL~lAk~~ve~~~~d~A~aqL~~~l~~t~De~lk~l~~lRLArvq~q~~k~D~AL~~L~t~----~~~~w--~~ 159 (207)
T COG2976 86 IYAVLAALELAKAEVEANNLDKAEAQLKQALAQTKDENLKALAALRLARVQLQQKKADAALKTLDTI----KEESW--AA 159 (207)
T ss_pred HHHHHHHHHHHHHHHhhccHHHHHHHHHHHHccchhHHHHHHHHHHHHHHHHHhhhHHHHHHHHhcc----ccccH--HH
Confidence 3445688999999999999999999999887776655555555677888889999999887655432 22233 34
Q ss_pred hHHHHHHHHhcccccHHHHHHHHHhcCcC
Q 013559 216 KLRCAAGLAHLEARKYKLAARKFLEVGPD 244 (441)
Q Consensus 216 ~l~~~~gl~~l~~r~y~~Aa~~Fl~~~~t 244 (441)
++....|=.++..|+=.+|...|-.+...
T Consensus 160 ~~~elrGDill~kg~k~~Ar~ay~kAl~~ 188 (207)
T COG2976 160 IVAELRGDILLAKGDKQEARAAYEKALES 188 (207)
T ss_pred HHHHHhhhHHHHcCchHHHHHHHHHHHHc
Confidence 55566777888888877777776666543
No 185
>PF13432 TPR_16: Tetratricopeptide repeat; PDB: 3CVP_A 3CVL_A 3CVQ_A 3CV0_A 2GW1_B 3CVN_A 3QKY_A 2PL2_B.
Probab=72.51 E-value=7.2 Score=28.42 Aligned_cols=32 Identities=19% Similarity=0.324 Sum_probs=26.8
Q ss_pred HHhHHhHHHHHHHHcCCHHHHHHHHHHHHhhh
Q 013559 138 IRMGYNDFGDFYYAHGALGDAFKSYVRTRDYC 169 (441)
Q Consensus 138 ir~~~~~la~~~~~~Gd~~~A~~~~~~~r~~~ 169 (441)
-..+++.+|..++..|++++|...|.++.+..
T Consensus 30 ~~~a~~~lg~~~~~~g~~~~A~~~~~~a~~~~ 61 (65)
T PF13432_consen 30 NPEAWYLLGRILYQQGRYDEALAYYERALELD 61 (65)
T ss_dssp HHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHS
T ss_pred CHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHC
Confidence 44688999999999999999999999886553
No 186
>TIGR02844 spore_III_D sporulation transcriptional regulator SpoIIID. Members of this protein are the transcriptional regulator SpoIIID, or stage III sporulation protein D. It is present in genomes if and only if the species is capable of endospore formation as occurs in the model species Bacillus subtilis. SpoIIID is a DNA binding protein that, in B. subtilis, downregulates many genes but also turns on ten genes.
Probab=72.18 E-value=5.2 Score=31.60 Aligned_cols=34 Identities=18% Similarity=0.255 Sum_probs=30.6
Q ss_pred HHHHHHHhccccccccHHhHHHHcCCChHHHHHHH
Q 013559 339 RNKALIQYTHPFVSVDLHMMANAFKTSVAGIEKEL 373 (441)
Q Consensus 339 R~~~i~qy~~pYs~I~L~~mA~~fg~s~~~~E~~L 373 (441)
|...|.+++.- ..+++..+|+.||+|...+-+.|
T Consensus 7 R~~~I~e~l~~-~~~ti~dvA~~~gvS~~TVsr~L 40 (80)
T TIGR02844 7 RVLEIGKYIVE-TKATVRETAKVFGVSKSTVHKDV 40 (80)
T ss_pred HHHHHHHHHHH-CCCCHHHHHHHhCCCHHHHHHHh
Confidence 77888999999 99999999999999999987744
No 187
>PF01022 HTH_5: Bacterial regulatory protein, arsR family; InterPro: IPR001845 Bacterial transcription regulatory proteins that bind DNA via a helix-turn-helix (HTH) motif can be grouped into families on the basis of sequence similarities. One such group, termed arsR, includes several proteins that appear to dissociate from DNA in the presence of metal ions: arsR, which functions as a transcriptional repressor of an arsenic resistance operon; smtB from Synechococcus sp. (strain PCC 7942), which acts as a transcriptional repressor of the smtA gene that codes for a metallothionein; cadC, a protein required for cadmium-resistance; and hypothetical protein yqcJ from Bacillus subtilis. The HTH motif is thought to be located in the central part of these proteins []. The motif is characterised by a number of well-conserved residues: at its N-terminal extremity is a cysteine residue; a second Cys is found in arsR and cadC, but not in smtA; and at the C terminus lie one or two histidines. These residues may be involved in metal-binding (Zn in smtB; metal-oxyanions such as arsenite, antimonite and arsenate for arsR; and cadmium for cadC) []. It is believed that binding of a metal ion could induce a conformational change that would prevent the protein from binding DNA []. The crystal structure of the cyanobacterial smtB shows a fold of five alpha-helices (H) and a pair of antiparallel beta-strands (B) in the topology H1-H2-H3-H4-B1-B2-H5. Helices 3 and 4 comprise the helix-turn-helix motif and the beta-sheet is called the wing as in other wHTH, such as the dtxR-type or the merR-type. Helix 4 is termed the recognition helix, like in other HTHs where it binds the DNA major groove. Most arsR/smtB-like metalloregulators form homodimers []. The dimer interface is formed by helix 5 and an N-terminal part []. Two distinct metal-binding sites have been identified. The first site comprises cysteine thiolates located in the HTH in helix 3 and for some cases in the N terminus, called the alpha3(N) site []. The second metal-binding site is located in helix 5 (and C terminus) and is called the alpha5(C) site. The alpha3N site binds large thiophilic, toxic metals including Cd, Pb, and Bi, as in S. aureus cadC. ArsR lacks the N-terminal arm and its alpha3 site coordinates smaller thiophilic ions like As and Sb. The alpha5 site contains carboxylate and imidazole ligands and interacts preferentially with biologically required metal ions including Zn, Co, and Ni. ArsR-type metalloregulators contain one of these sites, both, or other potential metal-binding sites [, ]. Binding of metal ions to these sites leads to allosteric changes that can derepress the operator/promotor DNA. The metal-inducible operons contain one or two imperfect 12-2-12 inverted repeats, which can be recognised by multimeric arsR-type metalloregulators. ; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 3CUO_A 1U2W_C 3F72_C 3F6V_A 3JTH_B 2P4W_B 1KU9_B 2LKP_B 1SMT_A 1R22_B ....
Probab=72.12 E-value=13 Score=25.76 Aligned_cols=43 Identities=14% Similarity=0.175 Sum_probs=35.0
Q ss_pred HHHHHHHHhccccccccHHhHHHHcCCChHHHHHHHHHHHHcCcc
Q 013559 338 IRNKALIQYTHPFVSVDLHMMANAFKTSVAGIEKELEALITDNQI 382 (441)
Q Consensus 338 iR~~~i~qy~~pYs~I~L~~mA~~fg~s~~~~E~~L~~LI~~g~L 382 (441)
.|.+++....+ ...+...+|+.||++...+-..|..|...|-+
T Consensus 3 ~R~~Il~~L~~--~~~~~~el~~~l~~s~~~vs~hL~~L~~~glV 45 (47)
T PF01022_consen 3 TRLRILKLLSE--GPLTVSELAEELGLSQSTVSHHLKKLREAGLV 45 (47)
T ss_dssp HHHHHHHHHTT--SSEEHHHHHHHHTS-HHHHHHHHHHHHHTTSE
T ss_pred HHHHHHHHHHh--CCCchhhHHHhccccchHHHHHHHHHHHCcCe
Confidence 45566665555 77899999999999999999999999998865
No 188
>PF13431 TPR_17: Tetratricopeptide repeat
Probab=72.09 E-value=3.1 Score=26.91 Aligned_cols=21 Identities=24% Similarity=0.618 Sum_probs=18.9
Q ss_pred hHHhHHHHHHHHcCCHHHHHH
Q 013559 140 MGYNDFGDFYYAHGALGDAFK 160 (441)
Q Consensus 140 ~~~~~la~~~~~~Gd~~~A~~ 160 (441)
.+++.||.+|...|++++|.+
T Consensus 14 ~a~~nla~~~~~~g~~~~A~~ 34 (34)
T PF13431_consen 14 EAYNNLANLYLNQGDYEEAIA 34 (34)
T ss_pred HHHHHHHHHHHHCcCHHhhcC
Confidence 589999999999999999863
No 189
>PLN03218 maturation of RBCL 1; Provisional
Probab=72.02 E-value=2.1e+02 Score=33.71 Aligned_cols=172 Identities=15% Similarity=0.121 Sum_probs=86.4
Q ss_pred HHhHHHHHHHHcCCHHHHHHHHHHHHhhhcCchhHHHHHHHHHHHHHHhcCHHHHHhHHHHHhcccccCChhhhhhHHHH
Q 013559 141 GYNDFGDFYYAHGALGDAFKSYVRTRDYCTTSKHIIHMCMSAILVSIEMGQFTHVTSYVSKAEQTPEALEPVTIAKLRCA 220 (441)
Q Consensus 141 ~~~~la~~~~~~Gd~~~A~~~~~~~r~~~~~~~~~~~~~l~~i~~~i~~~~~~~~~~~~~ka~~~~~~~d~~~~~~l~~~ 220 (441)
.+..+...|.+.|++++|.+.|.++......++ ...+-.++..+...|+++.+...+.+.... +..|... .|
T Consensus 616 tynsLI~ay~k~G~~deAl~lf~eM~~~Gv~PD--~~TynsLI~a~~k~G~~eeA~~l~~eM~k~--G~~pd~~----ty 687 (1060)
T PLN03218 616 VYTIAVNSCSQKGDWDFALSIYDDMKKKGVKPD--EVFFSALVDVAGHAGDLDKAFEILQDARKQ--GIKLGTV----SY 687 (1060)
T ss_pred HHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCC--HHHHHHHHHHHHhCCCHHHHHHHHHHHHHc--CCCCCHH----HH
Confidence 455666677777777777777777765544443 223334555566667777777766665432 1112111 22
Q ss_pred HHH--HhcccccHHHHHHHHHhcCcCCCCCchhhhcHHHHHHHHHHHHHh-cCChHHHHHhcccCHhhHhhhccch---H
Q 013559 221 AGL--AHLEARKYKLAARKFLEVGPDLGNSYNEVIAAQDVATYGGLCALA-SFDRAELKSKVIDNVNFRNFLELVP---E 294 (441)
Q Consensus 221 ~gl--~~l~~r~y~~Aa~~Fl~~~~t~~~~~~el~s~~d~~~Y~~l~al~-s~~R~eLk~~vl~~~~~~~~le~~p---~ 294 (441)
..+ .+...|++.+|.+.|-+.... + ..+.+. .|..+.... ...+-+--..+++. .+. ....| .
T Consensus 688 nsLI~ay~k~G~~eeA~~lf~eM~~~-g-~~Pdvv------tyN~LI~gy~k~G~~eeAlelf~e--M~~-~Gi~Pd~~T 756 (1060)
T PLN03218 688 SSLMGACSNAKNWKKALELYEDIKSI-K-LRPTVS------TMNALITALCEGNQLPKALEVLSE--MKR-LGLCPNTIT 756 (1060)
T ss_pred HHHHHHHHhCCCHHHHHHHHHHHHHc-C-CCCCHH------HHHHHHHHHHHCCCHHHHHHHHHH--HHH-cCCCCCHHH
Confidence 222 334578888888888766421 0 123333 232222222 22221100111110 000 01123 2
Q ss_pred HHHHHHHHh-cCCHHHHHHHHHHhHH-hhhhchhHHHHH
Q 013559 295 VRELINDFY-SSRYASCLDYLGNLKA-NLLLDIHLHDHV 331 (441)
Q Consensus 295 ~~~ll~~f~-~~~y~~~~~~L~~~~~-~l~~D~~L~~h~ 331 (441)
+.-++.++. ..++....+.+..+.. -+..|.+....+
T Consensus 757 y~sLL~a~~k~G~le~A~~l~~~M~k~Gi~pd~~tynsL 795 (1060)
T PLN03218 757 YSILLVASERKDDADVGLDLLSQAKEDGIKPNLVMCRCI 795 (1060)
T ss_pred HHHHHHHHHHCCCHHHHHHHHHHHHHcCCCCCHHHHHHH
Confidence 456677765 4678888887777643 456666554443
No 190
>TIGR02787 codY_Gpos GTP-sensing transcriptional pleiotropic repressor CodY. This model represents the full length of CodY, a pleiotropic repressor in Bacillus subtilis and other Firmicutes (low-GC Gram-positive bacteria) that responds to intracellular levels of GTP and branched chain amino acids. The C-terminal helix-turn-helix DNA-binding region is modeled by pfam08222 in Pfam.
Probab=71.75 E-value=17 Score=34.86 Aligned_cols=60 Identities=20% Similarity=0.253 Sum_probs=50.6
Q ss_pred hHHHHHHHHHHHHHHHHHHHhcc---ccc-----------------cccHHhHHHHcCCChHHHHHHHHHHHHcCccceE
Q 013559 326 HLHDHVETLYDQIRNKALIQYTH---PFV-----------------SVDLHMMANAFKTSVAGIEKELEALITDNQIQAR 385 (441)
Q Consensus 326 ~L~~h~~~l~~~iR~~~i~qy~~---pYs-----------------~I~L~~mA~~fg~s~~~~E~~L~~LI~~g~L~ak 385 (441)
.|+...+.+-++.|.++.+|..- +|| +++-..||+.+|+|...+-+-+.+|-..|-|..+
T Consensus 152 ilr~~~~~iEee~Rkka~Vq~Ai~tLSySEleAv~~IL~~L~~~egrlse~eLAerlGVSRs~ireAlrkLE~aGvIe~r 231 (251)
T TIGR02787 152 LLRAQAEEIEEEARKKAAVQMAINTLSYSELEAVEHIFEELDGNEGLLVASKIADRVGITRSVIVNALRKLESAGVIESR 231 (251)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHhccHhHHHHHHHHHHHhccccccccHHHHHHHHCCCHHHHHHHHHHHHHCCCEEec
Confidence 35566778888899999888732 666 8899999999999999999999999999988664
No 191
>PF01984 dsDNA_bind: Double-stranded DNA-binding domain; InterPro: IPR002836 This protein family is found in archaea and eukaryota. The human TFAR19 (TF-1 cell apoptosis-related protein 19) encodes a protein which shares significant homology to the corresponding proteins of species ranging from yeast to mice. TFAR19 exhibits a ubiquitous expression pattern and its expression is up-regulated in the tumour cells undergoing apoptosis. TFAR19 may play a general role in the apoptotic process []. Also included in this family is a DNA-binding protein from the archaea, Methanobacterium thermoautotrophicum.; GO: 0003677 DNA binding; PDB: 1EIJ_A 2K6B_A 2CRU_A 1YYB_A 2JXN_A 2FH0_A.
Probab=71.70 E-value=1.4 Score=36.76 Aligned_cols=52 Identities=21% Similarity=0.260 Sum_probs=39.5
Q ss_pred HHHHHHHHHHhccccccccHHhHHHHcCCChHHHHHHHHHHHHcCccceEec
Q 013559 336 DQIRNKALIQYTHPFVSVDLHMMANAFKTSVAGIEKELEALITDNQIQARID 387 (441)
Q Consensus 336 ~~iR~~~i~qy~~pYs~I~L~~mA~~fg~s~~~~E~~L~~LI~~g~L~akID 387 (441)
++.|..++.|++.|=..=.|++++-...=-...+|..|..|...|+|.++||
T Consensus 31 ee~~~~iL~qiLt~eAreRL~rI~lvkPe~A~~VE~~Liqlaq~G~l~~kI~ 82 (107)
T PF01984_consen 31 EEQRRAILRQILTPEARERLNRIKLVKPEKARQVENQLIQLAQSGQLRGKID 82 (107)
T ss_dssp HHCCHHHHHTCB-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCTSSSS-B-
T ss_pred HHHHHHHHHHHcCHHHHHHHHHHHhcCHHHHHHHHHHHHHHHHcCCCCCCcC
Confidence 3455677888888888878888776665456789999999999999999987
No 192
>KOG0396 consensus Uncharacterized conserved protein [Function unknown]
Probab=71.44 E-value=90 Score=31.76 Aligned_cols=125 Identities=14% Similarity=0.032 Sum_probs=76.2
Q ss_pred HHHHHHHHHHHHHHHH-hhhhHHHHHhHHhHHHHHHHHcCCHHHHHHHHHHH-HhhhcCchhHHHHH--HHHHHHHHHhc
Q 013559 115 AEQRKEKLENELNAYR-TNLIKESIRMGYNDFGDFYYAHGALGDAFKSYVRT-RDYCTTSKHIIHMC--MSAILVSIEMG 190 (441)
Q Consensus 115 ~~~~~~~Le~el~~~~-~n~~~esir~~~~~la~~~~~~Gd~~~A~~~~~~~-r~~~~~~~~~~~~~--l~~i~~~i~~~ 190 (441)
.+..++.+..++++-. .|..+=+.-..-.-.++|..++|-++.|.....++ .+..++ +|++ ...|+-+|..|
T Consensus 91 iksRid~m~e~~~~d~~~~~~~w~r~~l~r~vvdhmlr~gy~~~A~~L~K~s~ledlvD----~Dv~~~~~~I~~sll~~ 166 (389)
T KOG0396|consen 91 IKSRIDFMHEEISSDTPANSRKWPRNKLDRFVVDHMLRNGYFGAAVLLGKKSQLEDLVD----SDVYKRAYGIRDSLLAG 166 (389)
T ss_pred HHHHHHHHHHHhcccCchHHHHhHHHHHHHHHHHHHHHcCchhHHHHHHHhhhhhhhHh----HHHHHHHHHHHHHHHhc
Confidence 3444555555544433 34443333334556789999999888888777554 222222 2333 33566788888
Q ss_pred CHHHHHhHHHHHhcccccCChhhhhhHHHHHHHHhcccccHHHHHHHHHhcCc
Q 013559 191 QFTHVTSYVSKAEQTPEALEPVTIAKLRCAAGLAHLEARKYKLAARKFLEVGP 243 (441)
Q Consensus 191 ~~~~~~~~~~ka~~~~~~~d~~~~~~l~~~~gl~~l~~r~y~~Aa~~Fl~~~~ 243 (441)
++..+..-.+.-+..+....-.+-..++..+.+-.+..++|.+|...+-.-+.
T Consensus 167 ~l~~~Lswc~ehk~~LkK~~S~lEf~lRlQefIELi~~~~~~~Ai~~akk~f~ 219 (389)
T KOG0396|consen 167 ELEPALSWCKEHKVELKKEESSLEFQLRLQEFIELIKVDNYDKAIAFAKKHFA 219 (389)
T ss_pred chHHHHHHHHHHHHHHHhccchhhhHHHHHHHHHHHHhccHHHHHHHHHHHHh
Confidence 88888776665555443223344456667777888888899999776655443
No 193
>COG4649 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=71.14 E-value=84 Score=28.92 Aligned_cols=100 Identities=15% Similarity=0.156 Sum_probs=67.1
Q ss_pred hHHhHHHHHHHHcCCHHHHHHHHHHHHhhhcCchhHHHHHHHHHHHHHH---hcCHHHHHhHHHHHhcccccCChhhhhh
Q 013559 140 MGYNDFGDFYYAHGALGDAFKSYVRTRDYCTTSKHIIHMCMSAILVSIE---MGQFTHVTSYVSKAEQTPEALEPVTIAK 216 (441)
Q Consensus 140 ~~~~~la~~~~~~Gd~~~A~~~~~~~r~~~~~~~~~~~~~l~~i~~~i~---~~~~~~~~~~~~ka~~~~~~~d~~~~~~ 216 (441)
.+.++.|.+..+-||-..|..+|..+-.-...|.-.-| +.-+|.+.+ .|.|+.+.. +++.+-..++ ..+..
T Consensus 95 LA~mr~at~~a~kgdta~AV~aFdeia~dt~~P~~~rd--~ARlraa~lLvD~gsy~dV~s---rvepLa~d~n-~mR~s 168 (221)
T COG4649 95 LARMRAATLLAQKGDTAAAVAAFDEIAADTSIPQIGRD--LARLRAAYLLVDNGSYDDVSS---RVEPLAGDGN-PMRHS 168 (221)
T ss_pred HHHHHHHHHHhhcccHHHHHHHHHHHhccCCCcchhhH--HHHHHHHHHHhccccHHHHHH---HhhhccCCCC-hhHHH
Confidence 36788899999999999999999998544433332112 223444443 455555543 4444433223 34455
Q ss_pred HHHHHHHHhcccccHHHHHHHHHhcCcCC
Q 013559 217 LRCAAGLAHLEARKYKLAARKFLEVGPDL 245 (441)
Q Consensus 217 l~~~~gl~~l~~r~y~~Aa~~Fl~~~~t~ 245 (441)
-+..-|+.....|+|..|.++|..+..+-
T Consensus 169 ArEALglAa~kagd~a~A~~~F~qia~Da 197 (221)
T COG4649 169 AREALGLAAYKAGDFAKAKSWFVQIANDA 197 (221)
T ss_pred HHHHHhHHHHhccchHHHHHHHHHHHccc
Confidence 66788999999999999999999987643
No 194
>KOG1586 consensus Protein required for fusion of vesicles in vesicular transport, alpha-SNAP [Intracellular trafficking, secretion, and vesicular transport]
Probab=71.01 E-value=1e+02 Score=29.71 Aligned_cols=106 Identities=16% Similarity=0.310 Sum_probs=68.9
Q ss_pred HhHHHHHHHHc-CCHHHHHHHHHHHHhhhcCchhHHHH--H-HHHHHHHHHhcCHHHHHhHHHHH-hccccc--CChhhh
Q 013559 142 YNDFGDFYYAH-GALGDAFKSYVRTRDYCTTSKHIIHM--C-MSAILVSIEMGQFTHVTSYVSKA-EQTPEA--LEPVTI 214 (441)
Q Consensus 142 ~~~la~~~~~~-Gd~~~A~~~~~~~r~~~~~~~~~~~~--~-l~~i~~~i~~~~~~~~~~~~~ka-~~~~~~--~d~~~~ 214 (441)
+..+|++|..- -|+++|+.+|...-++..+....-.. | +.+...+-..+.+..+..-..++ +..++. ..|..+
T Consensus 116 ~~~iaEiyEsdl~d~ekaI~~YE~Aae~yk~ees~ssANKC~lKvA~yaa~leqY~~Ai~iyeqva~~s~~n~LLKys~K 195 (288)
T KOG1586|consen 116 HIEIAEIYESDLQDFEKAIAHYEQAAEYYKGEESVSSANKCLLKVAQYAAQLEQYSKAIDIYEQVARSSLDNNLLKYSAK 195 (288)
T ss_pred hhhHHHHHhhhHHHHHHHHHHHHHHHHHHcchhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhccchHHHhHHH
Confidence 45788888877 89999999999998887544333332 2 33333445566777776644433 334441 245554
Q ss_pred hhHHHHHHHHhcccccH---HHHHHHHHhcCcCCCCC
Q 013559 215 AKLRCAAGLAHLEARKY---KLAARKFLEVGPDLGNS 248 (441)
Q Consensus 215 ~~l~~~~gl~~l~~r~y---~~Aa~~Fl~~~~t~~~~ 248 (441)
..+ .-.|+.+|...+- ..|.+.|.+..|+|+++
T Consensus 196 dyf-lkAgLChl~~~D~v~a~~ALeky~~~dP~F~ds 231 (288)
T KOG1586|consen 196 DYF-LKAGLCHLCKADEVNAQRALEKYQELDPAFTDS 231 (288)
T ss_pred HHH-HHHHHHhHhcccHHHHHHHHHHHHhcCCccccc
Confidence 433 2368888886654 67788999999999753
No 195
>PF09986 DUF2225: Uncharacterized protein conserved in bacteria (DUF2225); InterPro: IPR018708 This conserved bacterial family has no known function.
Probab=70.82 E-value=18 Score=34.11 Aligned_cols=73 Identities=21% Similarity=0.190 Sum_probs=45.8
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHhhhhHH-------HHHhHHhHHHHHHHHcCCHHHHHHHHHHHHhhhcCch--hHH
Q 013559 106 AWCDSVDRRAEQRKEKLENELNAYRTNLIKE-------SIRMGYNDFGDFYYAHGALGDAFKSYVRTRDYCTTSK--HII 176 (441)
Q Consensus 106 ~~~~~~~~~~~~~~~~Le~el~~~~~n~~~e-------sir~~~~~la~~~~~~Gd~~~A~~~~~~~r~~~~~~~--~~~ 176 (441)
+|+=....+..++..-|..-++.+++....+ +--..++-+|+++++.|++++|.++|+++...-..+. ..+
T Consensus 125 AWlyR~~~~~~~E~~fl~~Al~~y~~a~~~e~~~~~~~~~~~l~YLigeL~rrlg~~~eA~~~fs~vi~~~~~s~~~~l~ 204 (214)
T PF09986_consen 125 AWLYRDLGDEENEKRFLRKALEFYEEAYENEDFPIEGMDEATLLYLIGELNRRLGNYDEAKRWFSRVIGSKKASKEPKLK 204 (214)
T ss_pred HHHhhccCCHHHHHHHHHHHHHHHHHHHHhCcCCCCCchHHHHHHHHHHHHHHhCCHHHHHHHHHHHHcCCCCCCcHHHH
Confidence 4554443444555555666666654433222 1124778899999999999999999999855433332 444
Q ss_pred HH
Q 013559 177 HM 178 (441)
Q Consensus 177 ~~ 178 (441)
++
T Consensus 205 ~~ 206 (214)
T PF09986_consen 205 DM 206 (214)
T ss_pred HH
Confidence 44
No 196
>PF14559 TPR_19: Tetratricopeptide repeat; PDB: 2R5S_A 3QDN_B 3QOU_A 3ASG_A 3ASD_A 3AS5_A 3AS4_A 3ASH_B 3FP3_A 3LCA_A ....
Probab=70.36 E-value=8.7 Score=28.13 Aligned_cols=32 Identities=13% Similarity=0.030 Sum_probs=26.5
Q ss_pred hHHhHHHHHHHHcCCHHHHHHHHHHHHhhhcC
Q 013559 140 MGYNDFGDFYYAHGALGDAFKSYVRTRDYCTT 171 (441)
Q Consensus 140 ~~~~~la~~~~~~Gd~~~A~~~~~~~r~~~~~ 171 (441)
.+++.+|..|.+.|++++|.+.+.++.....+
T Consensus 26 ~~~~~la~~~~~~g~~~~A~~~l~~~~~~~~~ 57 (68)
T PF14559_consen 26 EARLLLAQCYLKQGQYDEAEELLERLLKQDPD 57 (68)
T ss_dssp HHHHHHHHHHHHTT-HHHHHHHHHCCHGGGTT
T ss_pred HHHHHHHHHHHHcCCHHHHHHHHHHHHHHCcC
Confidence 36679999999999999999999988776554
No 197
>KOG3431 consensus Apoptosis-related protein/predicted DNA-binding protein [Cell cycle control, cell division, chromosome partitioning]
Probab=70.17 E-value=4.1 Score=34.45 Aligned_cols=53 Identities=17% Similarity=0.184 Sum_probs=44.5
Q ss_pred HHHHHHHHHHHhccccccccHHhHHHHcCCChHHHHHHHHHHHHcCccceEec
Q 013559 335 YDQIRNKALIQYTHPFVSVDLHMMANAFKTSVAGIEKELEALITDNQIQARID 387 (441)
Q Consensus 335 ~~~iR~~~i~qy~~pYs~I~L~~mA~~fg~s~~~~E~~L~~LI~~g~L~akID 387 (441)
-+++|.-++.|++.+-.+-.|+++|-.=-=-...+|..|.+|+.-|.|..||+
T Consensus 38 q~e~r~~~lsQvLdqqAr~RLsrlAlvkpekAq~VE~~lirma~~gQvs~Kis 90 (129)
T KOG3431|consen 38 QEEMRQSMLSQVLDQQARERLSRLALVKPEKAQAVENYLIRMAQTGQVSHKIS 90 (129)
T ss_pred HHHHHHhHHHHHhhHHHHHHHHhhhhcCHHHHHHHHHHHHHHHHhCCcccccc
Confidence 67899999999999988888888875433345679999999999999999886
No 198
>KOG4626 consensus O-linked N-acetylglucosamine transferase OGT [Carbohydrate transport and metabolism; Posttranslational modification, protein turnover, chaperones; Signal transduction mechanisms]
Probab=69.76 E-value=1.5e+02 Score=32.68 Aligned_cols=94 Identities=16% Similarity=0.147 Sum_probs=61.6
Q ss_pred hHHhHHHHHHHHcCCHHHHHHHHHHHHhhhcCchhHHHHHHHHHHHHHHhcCHHHHHhHHHHHhcc-cccCChhhhhhHH
Q 013559 140 MGYNDFGDFYYAHGALGDAFKSYVRTRDYCTTSKHIIHMCMSAILVSIEMGQFTHVTSYVSKAEQT-PEALEPVTIAKLR 218 (441)
Q Consensus 140 ~~~~~la~~~~~~Gd~~~A~~~~~~~r~~~~~~~~~~~~~l~~i~~~i~~~~~~~~~~~~~ka~~~-~~~~d~~~~~~l~ 218 (441)
+++..+|.-+-+.|+..+|..+|.+...+|.+ ..|..-++..+.-++|.++.+.....|+-+. ++... ..+-
T Consensus 321 ~Ay~NlanALkd~G~V~ea~~cYnkaL~l~p~---hadam~NLgni~~E~~~~e~A~~ly~~al~v~p~~aa--a~nN-- 393 (966)
T KOG4626|consen 321 DAYNNLANALKDKGSVTEAVDCYNKALRLCPN---HADAMNNLGNIYREQGKIEEATRLYLKALEVFPEFAA--AHNN-- 393 (966)
T ss_pred HHHhHHHHHHHhccchHHHHHHHHHHHHhCCc---cHHHHHHHHHHHHHhccchHHHHHHHHHHhhChhhhh--hhhh--
Confidence 46777777777788888888888887777753 2444455566667777788877777776553 22100 0111
Q ss_pred HHHHHHhcccccHHHHHHHHHhcC
Q 013559 219 CAAGLAHLEARKYKLAARKFLEVG 242 (441)
Q Consensus 219 ~~~gl~~l~~r~y~~Aa~~Fl~~~ 242 (441)
-|..+-++|++.+|..++-+++
T Consensus 394 --La~i~kqqgnl~~Ai~~Ykeal 415 (966)
T KOG4626|consen 394 --LASIYKQQGNLDDAIMCYKEAL 415 (966)
T ss_pred --HHHHHHhcccHHHHHHHHHHHH
Confidence 2345567889999988887765
No 199
>smart00344 HTH_ASNC helix_turn_helix ASNC type. AsnC: an autogenously regulated activator of asparagine synthetase A transcription in Escherichia coli
Probab=69.72 E-value=8.3 Score=31.60 Aligned_cols=48 Identities=15% Similarity=0.227 Sum_probs=39.1
Q ss_pred HHHHHhccccccccHHhHHHHcCCChHHHHHHHHHHHHcCccc---eEecC
Q 013559 341 KALIQYTHPFVSVDLHMMANAFKTSVAGIEKELEALITDNQIQ---ARIDS 388 (441)
Q Consensus 341 ~~i~qy~~pYs~I~L~~mA~~fg~s~~~~E~~L~~LI~~g~L~---akID~ 388 (441)
+.+..++....+++.+.||+.+|+|...+-+.+.+|..+|-|. +.+|.
T Consensus 6 ~~il~~L~~~~~~~~~~la~~l~~s~~tv~~~l~~L~~~g~i~~~~~~~~~ 56 (108)
T smart00344 6 RKILEELQKDARISLAELAKKVGLSPSTVHNRVKRLEEEGVIKGYTAVINP 56 (108)
T ss_pred HHHHHHHHHhCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCeeceEEEeCH
Confidence 3444555556789999999999999999999999999999775 45563
No 200
>PF08631 SPO22: Meiosis protein SPO22/ZIP4 like; InterPro: IPR013940 SPO22 is a meiosis-specific protein with similarity to phospholipase A2, involved in completion of nuclear divisions during meiosis; induced early in meiosis []. It is also involved in sporulation [].
Probab=69.72 E-value=81 Score=30.66 Aligned_cols=106 Identities=10% Similarity=0.056 Sum_probs=66.1
Q ss_pred hHHHHHhHHhHHHHHHHHcC-CHHHHHHHHHHHHhhhcCc-----------hhHHHHHHHHHHHHHHhcCHHHHHhHHHH
Q 013559 134 IKESIRMGYNDFGDFYYAHG-ALGDAFKSYVRTRDYCTTS-----------KHIIHMCMSAILVSIEMGQFTHVTSYVSK 201 (441)
Q Consensus 134 ~~esir~~~~~la~~~~~~G-d~~~A~~~~~~~r~~~~~~-----------~~~~~~~l~~i~~~i~~~~~~~~~~~~~k 201 (441)
..+++-+..|..|.-.++.+ ++++|.+++.+..++|..+ ..++.++-.++++.+..++.+.+.+..+-
T Consensus 30 ~~~~La~~~yn~G~~l~~~~~~~~~a~~wL~~a~~~l~~~~~~~~~~~~~~elr~~iL~~La~~~l~~~~~~~~~ka~~~ 109 (278)
T PF08631_consen 30 MAEELARVCYNIGKSLLSKKDKYEEAVKWLQRAYDILEKPGKMDKLSPDGSELRLSILRLLANAYLEWDTYESVEKALNA 109 (278)
T ss_pred HHHHHHHHHHHHHHHHHHcCCChHHHHHHHHHHHHHHHhhhhccccCCcHHHHHHHHHHHHHHHHHcCCChHHHHHHHHH
Confidence 34566778999999999999 9999999999998886321 22344555566667777766655443333
Q ss_pred Hhcccc--cCChhhh-hhHHHHHHHHhcccccHHHHHHHHHhcCcC
Q 013559 202 AEQTPE--ALEPVTI-AKLRCAAGLAHLEARKYKLAARKFLEVGPD 244 (441)
Q Consensus 202 a~~~~~--~~d~~~~-~~l~~~~gl~~l~~r~y~~Aa~~Fl~~~~t 244 (441)
++.+.. +.++... -++++..+ ..+...+.+.+...+.+
T Consensus 110 l~~l~~e~~~~~~~~~L~l~il~~-----~~~~~~~~~~L~~mi~~ 150 (278)
T PF08631_consen 110 LRLLESEYGNKPEVFLLKLEILLK-----SFDEEEYEEILMRMIRS 150 (278)
T ss_pred HHHHHHhCCCCcHHHHHHHHHHhc-----cCChhHHHHHHHHHHHh
Confidence 332222 2234433 56666555 55555555555555443
No 201
>KOG1155 consensus Anaphase-promoting complex (APC), Cdc23 subunit [Cell cycle control, cell division, chromosome partitioning; Posttranslational modification, protein turnover, chaperones]
Probab=69.71 E-value=42 Score=35.27 Aligned_cols=100 Identities=16% Similarity=0.138 Sum_probs=63.5
Q ss_pred hHHHHHhHHhHHHHHHHHcCCHHHHHHHHHHHHhhhcCchhHHHHHHHHHHHHHHhcCHHHHHhHHHHHhccc--cc--C
Q 013559 134 IKESIRMGYNDFGDFYYAHGALGDAFKSYVRTRDYCTTSKHIIHMCMSAILVSIEMGQFTHVTSYVSKAEQTP--EA--L 209 (441)
Q Consensus 134 ~~esir~~~~~la~~~~~~Gd~~~A~~~~~~~r~~~~~~~~~~~~~l~~i~~~i~~~~~~~~~~~~~ka~~~~--~~--~ 209 (441)
.++--.+.+..||+.|.+.+..++|.+||.+......+.+ +.++.+..+.=..++...+..+..|--... ++ .
T Consensus 427 ~kPnDsRlw~aLG~CY~kl~~~~eAiKCykrai~~~dte~---~~l~~LakLye~l~d~~eAa~~yek~v~~~~~eg~~~ 503 (559)
T KOG1155|consen 427 LKPNDSRLWVALGECYEKLNRLEEAIKCYKRAILLGDTEG---SALVRLAKLYEELKDLNEAAQYYEKYVEVSELEGEID 503 (559)
T ss_pred cCCCchHHHHHHHHHHHHhccHHHHHHHHHHHHhccccch---HHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHhhcccc
Confidence 3333445778999999999999999999999866653322 455666667777778888877766654422 22 2
Q ss_pred ChhhhhhHHHHHHHHhcccccHHHHHHHH
Q 013559 210 EPVTIAKLRCAAGLAHLEARKYKLAARKF 238 (441)
Q Consensus 210 d~~~~~~l~~~~gl~~l~~r~y~~Aa~~F 238 (441)
+..+++++ .-+.+....++|.+|..+-
T Consensus 504 ~~t~ka~~--fLA~~f~k~~~~~~As~Ya 530 (559)
T KOG1155|consen 504 DETIKARL--FLAEYFKKMKDFDEASYYA 530 (559)
T ss_pred hHHHHHHH--HHHHHHHhhcchHHHHHHH
Confidence 32344333 2344555566666654433
No 202
>PF12802 MarR_2: MarR family; PDB: 3ECO_B 2QWW_B 3KP6_B 3KP4_B 3KP2_A 3KP5_A 3KP3_B 3KP7_A 3NQO_B 3K0L_B ....
Probab=69.64 E-value=14 Score=26.65 Aligned_cols=40 Identities=10% Similarity=0.183 Sum_probs=33.7
Q ss_pred cccHHhHHHHcCCChHHHHHHHHHHHHcCccceEecCCCC
Q 013559 352 SVDLHMMANAFKTSVAGIEKELEALITDNQIQARIDSHNK 391 (441)
Q Consensus 352 ~I~L~~mA~~fg~s~~~~E~~L~~LI~~g~L~akID~~~g 391 (441)
.++...+|+.+|++...+-+.+.+|+..|-+.-.-|..++
T Consensus 21 ~~t~~~la~~l~~~~~~vs~~v~~L~~~Glv~r~~~~~D~ 60 (62)
T PF12802_consen 21 ELTQSELAERLGISKSTVSRIVKRLEKKGLVERERDPGDR 60 (62)
T ss_dssp GEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEEE-SSST
T ss_pred CcCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEeCCCCCC
Confidence 3999999999999999999999999999998776665543
No 203
>KOG0550 consensus Molecular chaperone (DnaJ superfamily) [Posttranslational modification, protein turnover, chaperones]
Probab=69.64 E-value=72 Score=33.14 Aligned_cols=132 Identities=16% Similarity=0.159 Sum_probs=82.9
Q ss_pred HHhHHHHHHHHcCCHHHHHHHHHHHHhhhcCc-hhHHHHHHHHHHHHHHhcCHHHHHhHHHHHhcccccCChhhhhhHHH
Q 013559 141 GYNDFGDFYYAHGALGDAFKSYVRTRDYCTTS-KHIIHMCMSAILVSIEMGQFTHVTSYVSKAEQTPEALEPVTIAKLRC 219 (441)
Q Consensus 141 ~~~~la~~~~~~Gd~~~A~~~~~~~r~~~~~~-~~~~~~~l~~i~~~i~~~~~~~~~~~~~ka~~~~~~~d~~~~~~l~~ 219 (441)
....-|+-.++.|+|..|.++|.+......+. +...-.+++...+.+-.|....+...-+.+-.+ |++.. +-..
T Consensus 251 ~~k~~gN~~fk~G~y~~A~E~Yteal~idP~n~~~naklY~nra~v~~rLgrl~eaisdc~~Al~i----D~syi-kall 325 (486)
T KOG0550|consen 251 VKKERGNDAFKNGNYRKAYECYTEALNIDPSNKKTNAKLYGNRALVNIRLGRLREAISDCNEALKI----DSSYI-KALL 325 (486)
T ss_pred HHHhhhhhHhhccchhHHHHHHHHhhcCCccccchhHHHHHHhHhhhcccCCchhhhhhhhhhhhc----CHHHH-HHHH
Confidence 44556788999999999999999986554322 233445677777777777777777666655544 22211 1112
Q ss_pred HHHHHhcccccHHHHHHHHHhcCcCCCCC--------c-hhhhcHHHHHHHHHHHHHhcCChHHHHH
Q 013559 220 AAGLAHLEARKYKLAARKFLEVGPDLGNS--------Y-NEVIAAQDVATYGGLCALASFDRAELKS 277 (441)
Q Consensus 220 ~~gl~~l~~r~y~~Aa~~Fl~~~~t~~~~--------~-~el~s~~d~~~Y~~l~al~s~~R~eLk~ 277 (441)
..|..++..++|..|.+.|-.+...-.+. + -.+--......|.+|...-.-++.++|+
T Consensus 326 ~ra~c~l~le~~e~AV~d~~~a~q~~~s~e~r~~l~~A~~aLkkSkRkd~ykilGi~~~as~~eikk 392 (486)
T KOG0550|consen 326 RRANCHLALEKWEEAVEDYEKAMQLEKDCEIRRTLREAQLALKKSKRKDWYKILGISRNASDDEIKK 392 (486)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHhhccccchHHHHHHHHHHHHHhhhhhHHHHhhhhhhcccchhhh
Confidence 25677888999999999998877543220 0 0111223456676555555566777765
No 204
>smart00346 HTH_ICLR helix_turn_helix isocitrate lyase regulation.
Probab=69.63 E-value=43 Score=26.13 Aligned_cols=46 Identities=15% Similarity=0.109 Sum_probs=38.1
Q ss_pred HHHHHHHhcccc-ccccHHhHHHHcCCChHHHHHHHHHHHHcCccce
Q 013559 339 RNKALIQYTHPF-VSVDLHMMANAFKTSVAGIEKELEALITDNQIQA 384 (441)
Q Consensus 339 R~~~i~qy~~pY-s~I~L~~mA~~fg~s~~~~E~~L~~LI~~g~L~a 384 (441)
|...+..++.-. ..+++..+|+.+|++...+-+.|..|...|-|.-
T Consensus 6 r~~~Il~~l~~~~~~~t~~~ia~~l~i~~~tv~r~l~~L~~~g~l~~ 52 (91)
T smart00346 6 RGLAVLRALAEEPGGLTLAELAERLGLSKSTAHRLLNTLQELGYVEQ 52 (91)
T ss_pred HHHHHHHHHHhCCCCcCHHHHHHHhCCCHHHHHHHHHHHHHCCCeee
Confidence 344455566555 5799999999999999999999999999998864
No 205
>KOG3060 consensus Uncharacterized conserved protein [Function unknown]
Probab=69.53 E-value=1.1e+02 Score=29.68 Aligned_cols=93 Identities=19% Similarity=0.229 Sum_probs=62.4
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHhhh-hHHHHHhHHhHHHHHHHHcCCHHHHHHHHHHHHhhhcCchhHHHHHHHHHH
Q 013559 106 AWCDSVDRRAEQRKEKLENELNAYRTNL-IKESIRMGYNDFGDFYYAHGALGDAFKSYVRTRDYCTTSKHIIHMCMSAIL 184 (441)
Q Consensus 106 ~~~~~~~~~~~~~~~~Le~el~~~~~n~-~~esir~~~~~la~~~~~~Gd~~~A~~~~~~~r~~~~~~~~~~~~~l~~i~ 184 (441)
.|-+ .+..+-+++-++..++..+.... ...++...+.+.+-...++|...-|.+|+..+++....+..+.- +.-++
T Consensus 19 ~wr~-~~~rnseevv~l~~~~~~~~k~~~~g~e~w~l~EqV~IAAld~~~~~lAq~C~~~L~~~fp~S~RV~~--lkam~ 95 (289)
T KOG3060|consen 19 KWRE-ETVRNSEEVVQLGSEVLNYSKSGALGDEIWTLYEQVFIAALDTGRDDLAQKCINQLRDRFPGSKRVGK--LKAML 95 (289)
T ss_pred HHHh-ccccCHHHHHHHHHHHHHHhhhcccCchHHHHHHHHHHHHHHhcchHHHHHHHHHHHHhCCCChhHHH--HHHHH
Confidence 5643 33445566666777766654444 77889999999999999999999999999999888744333221 22222
Q ss_pred HHHHhcCHHHHHhHHHHH
Q 013559 185 VSIEMGQFTHVTSYVSKA 202 (441)
Q Consensus 185 ~~i~~~~~~~~~~~~~ka 202 (441)
+.. .|+|..|.++++.+
T Consensus 96 lEa-~~~~~~A~e~y~~l 112 (289)
T KOG3060|consen 96 LEA-TGNYKEAIEYYESL 112 (289)
T ss_pred HHH-hhchhhHHHHHHHH
Confidence 222 36788887776654
No 206
>PF13371 TPR_9: Tetratricopeptide repeat
Probab=69.06 E-value=11 Score=28.06 Aligned_cols=34 Identities=9% Similarity=0.128 Sum_probs=29.9
Q ss_pred hHHhHHHHHHHHcCCHHHHHHHHHHHHhhhcCch
Q 013559 140 MGYNDFGDFYYAHGALGDAFKSYVRTRDYCTTSK 173 (441)
Q Consensus 140 ~~~~~la~~~~~~Gd~~~A~~~~~~~r~~~~~~~ 173 (441)
..++.+|..+++.|++++|.+.+.++.+.+.+..
T Consensus 30 ~~~~~~a~~~~~~g~~~~A~~~l~~~l~~~p~~~ 63 (73)
T PF13371_consen 30 ELWLQRARCLFQLGRYEEALEDLERALELSPDDP 63 (73)
T ss_pred hhhHHHHHHHHHhccHHHHHHHHHHHHHHCCCcH
Confidence 4788999999999999999999999988876443
No 207
>PRK10857 DNA-binding transcriptional regulator IscR; Provisional
Probab=68.64 E-value=17 Score=32.75 Aligned_cols=69 Identities=12% Similarity=0.092 Sum_probs=48.7
Q ss_pred HHHHHhccccccccHHhHHHHcCCChHHHHHHHHHHHHcCccceEecCCCCeEEEecCCchhHHHHHHHHH
Q 013559 341 KALIQYTHPFVSVDLHMMANAFKTSVAGIEKELEALITDNQIQARIDSHNKILYARHADQRNATFQRVLQT 411 (441)
Q Consensus 341 ~~i~qy~~pYs~I~L~~mA~~fg~s~~~~E~~L~~LI~~g~L~akID~~~gvv~~~~~d~r~~~~~~~i~~ 411 (441)
..+..+...-..++++.||+.+|+|..++++-|..|-..|-+...=....|..-..+| ..-...++++.
T Consensus 14 l~~lA~~~~~~~vs~~eIA~~~~ip~~~l~kIl~~L~~aGLv~s~rG~~GGy~Lar~p--~~Itl~dIl~a 82 (164)
T PRK10857 14 MLDVALNSEAGPVPLADISERQGISLSYLEQLFSRLRKNGLVSSVRGPGGGYLLGKDA--SSIAVGEVISA 82 (164)
T ss_pred HHHHHhCCCCCcCcHHHHHHHHCcCHHHHHHHHHHHHHCCCEEeCCCCCCCeeccCCH--HHCCHHHHHHH
Confidence 3333344444679999999999999999999999999999988755555565555544 33334444443
No 208
>PF02082 Rrf2: Transcriptional regulator; InterPro: IPR000944 The following uncharacterised bacterial proteins have been shown to be evolutionary related, Desulfovibrio vulgaris protein Rrf2; Escherichia coli hypothetical proteins yfhP and yjeB; Bacillus subtilis hypothetical proteins yhdE, yrzC and ywgB; Mycobacterium tuberculosis hypothetical protein Rv1287; and Synechocystis sp. (strain PCC 6803) hypothetical protein slr0846. These are small proteins of 12 to 18kDa which seem to contain a signal sequence, and may represent a family of probable transcriptional regulators.; PDB: 3T8T_A 3T8R_A 3K69_A 3LWF_C 1XD7_A 2Y75_E 1YLF_C.
Probab=68.48 E-value=26 Score=27.34 Aligned_cols=46 Identities=15% Similarity=0.079 Sum_probs=34.7
Q ss_pred cccHHhHHHHcCCChHHHHHHHHHHHHcCccceEecCCCCeEEEecC
Q 013559 352 SVDLHMMANAFKTSVAGIEKELEALITDNQIQARIDSHNKILYARHA 398 (441)
Q Consensus 352 ~I~L~~mA~~fg~s~~~~E~~L~~LI~~g~L~akID~~~gvv~~~~~ 398 (441)
.++...+|+.+|+|+..+++-+..|...|-|..+= ..+|-....++
T Consensus 25 ~~s~~eiA~~~~i~~~~l~kil~~L~~~Gli~s~~-G~~GGy~L~~~ 70 (83)
T PF02082_consen 25 PVSSKEIAERLGISPSYLRKILQKLKKAGLIESSR-GRGGGYRLARP 70 (83)
T ss_dssp -BEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEET-STTSEEEESS-
T ss_pred CCCHHHHHHHHCcCHHHHHHHHHHHhhCCeeEecC-CCCCceeecCC
Confidence 39999999999999999999999999999886543 33444444433
No 209
>PRK15363 pathogenicity island 2 chaperone protein SscA; Provisional
Probab=68.15 E-value=47 Score=29.71 Aligned_cols=70 Identities=10% Similarity=-0.006 Sum_probs=52.6
Q ss_pred hHHHHHhHHhHHHHHHHHcCCHHHHHHHHHHHHhhhcCchhHHHHHHHHHHHHHHhcCHHHHHhHHHHHhccc
Q 013559 134 IKESIRMGYNDFGDFYYAHGALGDAFKSYVRTRDYCTTSKHIIHMCMSAILVSIEMGQFTHVTSYVSKAEQTP 206 (441)
Q Consensus 134 ~~esir~~~~~la~~~~~~Gd~~~A~~~~~~~r~~~~~~~~~~~~~l~~i~~~i~~~~~~~~~~~~~ka~~~~ 206 (441)
+.....+.++-||-.+-..|+|++|+.+|.+.-..-.+ --...++.-.|.+..||...+.+....+-..-
T Consensus 64 ~Dp~~~~y~~gLG~~~Q~~g~~~~AI~aY~~A~~L~~d---dp~~~~~ag~c~L~lG~~~~A~~aF~~Ai~~~ 133 (157)
T PRK15363 64 YDAWSFDYWFRLGECCQAQKHWGEAIYAYGRAAQIKID---APQAPWAAAECYLACDNVCYAIKALKAVVRIC 133 (157)
T ss_pred hCcccHHHHHHHHHHHHHHhhHHHHHHHHHHHHhcCCC---CchHHHHHHHHHHHcCCHHHHHHHHHHHHHHh
Confidence 33455568899999999999999999999987554321 12344566677888999999998888776654
No 210
>smart00419 HTH_CRP helix_turn_helix, cAMP Regulatory protein.
Probab=67.60 E-value=8.7 Score=26.11 Aligned_cols=32 Identities=13% Similarity=0.204 Sum_probs=29.7
Q ss_pred cccHHhHHHHcCCChHHHHHHHHHHHHcCccc
Q 013559 352 SVDLHMMANAFKTSVAGIEKELEALITDNQIQ 383 (441)
Q Consensus 352 ~I~L~~mA~~fg~s~~~~E~~L~~LI~~g~L~ 383 (441)
.++...||+.+|++...+-+.|..|...|-+.
T Consensus 8 ~~s~~~la~~l~~s~~tv~~~l~~L~~~g~l~ 39 (48)
T smart00419 8 PLTRQEIAELLGLTRETVSRTLKRLEKEGLIS 39 (48)
T ss_pred ccCHHHHHHHHCCCHHHHHHHHHHHHHCCCEE
Confidence 47889999999999999999999999999885
No 211
>PRK15179 Vi polysaccharide biosynthesis protein TviE; Provisional
Probab=67.58 E-value=52 Score=36.69 Aligned_cols=103 Identities=6% Similarity=-0.154 Sum_probs=52.9
Q ss_pred HHHHhHHhHHHHHHHHcCCHHHHHHHHHHHHhhhcCchhHHHHHHHHHHHHHHhcCHHHHHhHHHHHhcccccCChhhhh
Q 013559 136 ESIRMGYNDFGDFYYAHGALGDAFKSYVRTRDYCTTSKHIIHMCMSAILVSIEMGQFTHVTSYVSKAEQTPEALEPVTIA 215 (441)
Q Consensus 136 esir~~~~~la~~~~~~Gd~~~A~~~~~~~r~~~~~~~~~~~~~l~~i~~~i~~~~~~~~~~~~~ka~~~~~~~d~~~~~ 215 (441)
+..-.++..+|....+.+.+++|...+.+..+....+ .+.....-.+-...|.++.+...+.|+-. ....++
T Consensus 117 Pd~~~a~~~~a~~L~~~~~~eeA~~~~~~~l~~~p~~---~~~~~~~a~~l~~~g~~~~A~~~y~~~~~-~~p~~~---- 188 (694)
T PRK15179 117 PDSSEAFILMLRGVKRQQGIEAGRAEIELYFSGGSSS---AREILLEAKSWDEIGQSEQADACFERLSR-QHPEFE---- 188 (694)
T ss_pred CCcHHHHHHHHHHHHHhccHHHHHHHHHHHhhcCCCC---HHHHHHHHHHHHHhcchHHHHHHHHHHHh-cCCCcH----
Confidence 3444455566666666666666666655554433211 22233333344455666666666666554 111111
Q ss_pred hHHHHHHHHhcccccHHHHHHHHHhcCcCCC
Q 013559 216 KLRCAAGLAHLEARKYKLAARKFLEVGPDLG 246 (441)
Q Consensus 216 ~l~~~~gl~~l~~r~y~~Aa~~Fl~~~~t~~ 246 (441)
...+-.|..++..|+..+|...|..++.-+.
T Consensus 189 ~~~~~~a~~l~~~G~~~~A~~~~~~a~~~~~ 219 (694)
T PRK15179 189 NGYVGWAQSLTRRGALWRARDVLQAGLDAIG 219 (694)
T ss_pred HHHHHHHHHHHHcCCHHHHHHHHHHHHHhhC
Confidence 1223445556666777777777776665443
No 212
>KOG1173 consensus Anaphase-promoting complex (APC), Cdc16 subunit [Cell cycle control, cell division, chromosome partitioning; Posttranslational modification, protein turnover, chaperones]
Probab=67.29 E-value=27 Score=37.38 Aligned_cols=95 Identities=13% Similarity=0.136 Sum_probs=69.3
Q ss_pred hHHhHHHHHHHHcCCHHHHHHHHHHHHh--hhcCchhHHHHHHHHHHHHHHhcCHHHHHhHHHHHhcccccCC-hhhhhh
Q 013559 140 MGYNDFGDFYYAHGALGDAFKSYVRTRD--YCTTSKHIIHMCMSAILVSIEMGQFTHVTSYVSKAEQTPEALE-PVTIAK 216 (441)
Q Consensus 140 ~~~~~la~~~~~~Gd~~~A~~~~~~~r~--~~~~~~~~~~~~l~~i~~~i~~~~~~~~~~~~~ka~~~~~~~d-~~~~~~ 216 (441)
-.++..|-||+-+|.+++|.++|++.-. ..-+++ .++..-..-..+.-+.+.....+|..++.|++ |
T Consensus 313 ~sW~aVg~YYl~i~k~seARry~SKat~lD~~fgpa-----Wl~fghsfa~e~EhdQAmaaY~tAarl~~G~hlP----- 382 (611)
T KOG1173|consen 313 LSWFAVGCYYLMIGKYSEARRYFSKATTLDPTFGPA-----WLAFGHSFAGEGEHDQAMAAYFTAARLMPGCHLP----- 382 (611)
T ss_pred cchhhHHHHHHHhcCcHHHHHHHHHHhhcCccccHH-----HHHHhHHhhhcchHHHHHHHHHHHHHhccCCcch-----
Confidence 3789999999999999999999998522 211111 11222222345678888889999999888655 3
Q ss_pred HHHHHHHHhcccccHHHHHHHHHhcCcCC
Q 013559 217 LRCAAGLAHLEARKYKLAARKFLEVGPDL 245 (441)
Q Consensus 217 l~~~~gl~~l~~r~y~~Aa~~Fl~~~~t~ 245 (441)
..|-|+-++..++++.|-+.|.++..-.
T Consensus 383 -~LYlgmey~~t~n~kLAe~Ff~~A~ai~ 410 (611)
T KOG1173|consen 383 -SLYLGMEYMRTNNLKLAEKFFKQALAIA 410 (611)
T ss_pred -HHHHHHHHHHhccHHHHHHHHHHHHhcC
Confidence 3678999999999999999999876543
No 213
>PRK04841 transcriptional regulator MalT; Provisional
Probab=66.39 E-value=45 Score=37.90 Aligned_cols=103 Identities=13% Similarity=-0.031 Sum_probs=70.8
Q ss_pred HHhHHHHHHHHcCCHHHHHHHHHHHHhhhc---CchhHHHHHHHHHHHHHHhcCHHHHHhHHHHHhcccc-cCCh--hhh
Q 013559 141 GYNDFGDFYYAHGALGDAFKSYVRTRDYCT---TSKHIIHMCMSAILVSIEMGQFTHVTSYVSKAEQTPE-ALEP--VTI 214 (441)
Q Consensus 141 ~~~~la~~~~~~Gd~~~A~~~~~~~r~~~~---~~~~~~~~~l~~i~~~i~~~~~~~~~~~~~ka~~~~~-~~d~--~~~ 214 (441)
+...+|..+...|++.+|...+.+...... ..............+.+..|++..+...+.++..... .+.+ ...
T Consensus 493 a~~~lg~~~~~~G~~~~A~~~~~~al~~~~~~g~~~~~~~~~~~la~~~~~~G~~~~A~~~~~~al~~~~~~~~~~~~~~ 572 (903)
T PRK04841 493 ATSVLGEVHHCKGELARALAMMQQTEQMARQHDVYHYALWSLLQQSEILFAQGFLQAAYETQEKAFQLIEEQHLEQLPMH 572 (903)
T ss_pred HHHHHHHHHHHcCCHHHHHHHHHHHHHHHhhhcchHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHhccccccHH
Confidence 556788888999999999999988765443 2222333445556677889999999999888877654 1111 112
Q ss_pred hhHHHHHHHHhcccccHHHHHHHHHhcCc
Q 013559 215 AKLRCAAGLAHLEARKYKLAARKFLEVGP 243 (441)
Q Consensus 215 ~~l~~~~gl~~l~~r~y~~Aa~~Fl~~~~ 243 (441)
..+....|..+...|++.+|...+-++..
T Consensus 573 ~~~~~~la~~~~~~G~~~~A~~~~~~al~ 601 (903)
T PRK04841 573 EFLLRIRAQLLWEWARLDEAEQCARKGLE 601 (903)
T ss_pred HHHHHHHHHHHHHhcCHHHHHHHHHHhHH
Confidence 23344567777888999999888777644
No 214
>PF06163 DUF977: Bacterial protein of unknown function (DUF977); InterPro: IPR010382 This entry consists of several hypothetical bacterial proteins of unknown function.
Probab=66.19 E-value=8.8 Score=32.88 Aligned_cols=39 Identities=8% Similarity=0.218 Sum_probs=36.2
Q ss_pred HHhccccccccHHhHHHHcCCChHHHHHHHHHHHHcCcc
Q 013559 344 IQYTHPFVSVDLHMMANAFKTSVAGIEKELEALITDNQI 382 (441)
Q Consensus 344 ~qy~~pYs~I~L~~mA~~fg~s~~~~E~~L~~LI~~g~L 382 (441)
+-+++-+-++|+..|+..+|++...+.+.+.+|+..|.|
T Consensus 18 vElVRe~GRiTi~ql~~~TGasR~Tvk~~lreLVa~G~l 56 (127)
T PF06163_consen 18 VELVREHGRITIKQLVAKTGASRNTVKRYLRELVARGDL 56 (127)
T ss_pred HHHHHHcCCccHHHHHHHHCCCHHHHHHHHHHHHHcCCe
Confidence 446677999999999999999999999999999999988
No 215
>PRK04239 hypothetical protein; Provisional
Probab=65.48 E-value=5.7 Score=33.29 Aligned_cols=54 Identities=20% Similarity=0.181 Sum_probs=40.7
Q ss_pred HHHHHHHHHHHHhccccccccHHhHHHHcCCChHHHHHHHHHHHHcCccceEec
Q 013559 334 LYDQIRNKALIQYTHPFVSVDLHMMANAFKTSVAGIEKELEALITDNQIQARID 387 (441)
Q Consensus 334 l~~~iR~~~i~qy~~pYs~I~L~~mA~~fg~s~~~~E~~L~~LI~~g~L~akID 387 (441)
-.+..+.-++.|++.|=.+=.|++++=.=-=-...+|..|..|...|+|.+|||
T Consensus 34 ~~e~qk~~iL~qiLt~eAreRL~rI~lvkPe~A~~VE~~liqlAq~G~i~~ki~ 87 (110)
T PRK04239 34 QAEAQKQAILRQILTPEARERLNRIKLVKPEFAEQVEQQLIQLAQSGRIQGPID 87 (110)
T ss_pred HHHHHHHHHHHHHCCHHHHHHHHhhhhcCHHHHHHHHHHHHHHHHcCCCCCCcC
Confidence 345677788999999877777766653221124579999999999999999986
No 216
>PF10300 DUF3808: Protein of unknown function (DUF3808); InterPro: IPR019412 This entry represents a family of proteins conserved from fungi to humans. In humans this protein is expressed in primary breast carcinomas but not in normal breast tissue, and has a putative eukaryotic RNP-1 RNA binding region and a candidate anchoring transmembrane domain. The human protein is coordinately regulated with oestrogen receptor, but is not necessarily oestradiol-responsive []. Members of this family carry a tetratricopeptide repeat (IPR013105 from INTERPRO) at their C terminus.
Probab=64.92 E-value=69 Score=33.86 Aligned_cols=87 Identities=14% Similarity=0.043 Sum_probs=62.0
Q ss_pred cCCHHHHHHHHHHHHhhhcCchhHHHHHHHHHHHHHHhcCHHHHHhHHHHHhcccccCChhhhhhHHHH-HHHHhccccc
Q 013559 152 HGALGDAFKSYVRTRDYCTTSKHIIHMCMSAILVSIEMGQFTHVTSYVSKAEQTPEALEPVTIAKLRCA-AGLAHLEARK 230 (441)
Q Consensus 152 ~Gd~~~A~~~~~~~r~~~~~~~~~~~~~l~~i~~~i~~~~~~~~~~~~~ka~~~~~~~d~~~~~~l~~~-~gl~~l~~r~ 230 (441)
-++...|.+.+...+...+.. .=..+..-|+....||.+.+...++++-... .+|.--..+-.+ -|..++..++
T Consensus 246 ~~~~~~a~~lL~~~~~~yP~s---~lfl~~~gR~~~~~g~~~~Ai~~~~~a~~~q--~~~~Ql~~l~~~El~w~~~~~~~ 320 (468)
T PF10300_consen 246 DVPLEEAEELLEEMLKRYPNS---ALFLFFEGRLERLKGNLEEAIESFERAIESQ--SEWKQLHHLCYFELAWCHMFQHD 320 (468)
T ss_pred CCCHHHHHHHHHHHHHhCCCc---HHHHHHHHHHHHHhcCHHHHHHHHHHhccch--hhHHhHHHHHHHHHHHHHHHHch
Confidence 357788889998887766432 3345667788899999999999888765322 233322223333 4778899999
Q ss_pred HHHHHHHHHhcCc
Q 013559 231 YKLAARKFLEVGP 243 (441)
Q Consensus 231 y~~Aa~~Fl~~~~ 243 (441)
|.+|+..|.....
T Consensus 321 w~~A~~~f~~L~~ 333 (468)
T PF10300_consen 321 WEEAAEYFLRLLK 333 (468)
T ss_pred HHHHHHHHHHHHh
Confidence 9999999999875
No 217
>COG1729 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=64.38 E-value=86 Score=30.53 Aligned_cols=102 Identities=12% Similarity=0.071 Sum_probs=75.2
Q ss_pred HhHHHHHHHHcCCHHHHHHHHHHHHhhhcCchhHHHHHHHHHHHHHHhcCHHHHHhHHHHH-hcccc-cCChhhhhhHHH
Q 013559 142 YNDFGDFYYAHGALGDAFKSYVRTRDYCTTSKHIIHMCMSAILVSIEMGQFTHVTSYVSKA-EQTPE-ALEPVTIAKLRC 219 (441)
Q Consensus 142 ~~~la~~~~~~Gd~~~A~~~~~~~r~~~~~~~~~~~~~l~~i~~~i~~~~~~~~~~~~~ka-~~~~~-~~d~~~~~~l~~ 219 (441)
.|+.|-=++..|||.+|...|.............-+..+-+..+..-.||+..+.....++ +..++ ...|+-..|+
T Consensus 144 ~Y~~A~~~~ksgdy~~A~~~F~~fi~~YP~s~~~~nA~yWLGe~~y~qg~y~~Aa~~f~~~~k~~P~s~KApdallKl-- 221 (262)
T COG1729 144 LYNAALDLYKSGDYAEAEQAFQAFIKKYPNSTYTPNAYYWLGESLYAQGDYEDAAYIFARVVKDYPKSPKAPDALLKL-- 221 (262)
T ss_pred HHHHHHHHHHcCCHHHHHHHHHHHHHcCCCCcccchhHHHHHHHHHhcccchHHHHHHHHHHHhCCCCCCChHHHHHH--
Confidence 5788888999999999999999987766554444555556667888899999988755554 56666 3344544443
Q ss_pred HHHHHhcccccHHHHHHHHHhcCcCCCC
Q 013559 220 AAGLAHLEARKYKLAARKFLEVGPDLGN 247 (441)
Q Consensus 220 ~~gl~~l~~r~y~~Aa~~Fl~~~~t~~~ 247 (441)
|+.....|+-.+|+..|-++...+++
T Consensus 222 --g~~~~~l~~~d~A~atl~qv~k~YP~ 247 (262)
T COG1729 222 --GVSLGRLGNTDEACATLQQVIKRYPG 247 (262)
T ss_pred --HHHHHHhcCHHHHHHHHHHHHHHCCC
Confidence 44556688889999999999887654
No 218
>PLN03081 pentatricopeptide (PPR) repeat-containing protein; Provisional
Probab=64.29 E-value=1.9e+02 Score=31.94 Aligned_cols=92 Identities=14% Similarity=0.082 Sum_probs=57.0
Q ss_pred HHhHHHHHHHHcCCHHHHHHHHHHHHhhhcCchhHHHHHHHHHHHHHHhcCHHHHHhHHHHHhcccccCChhhhhhHHHH
Q 013559 141 GYNDFGDFYYAHGALGDAFKSYVRTRDYCTTSKHIIHMCMSAILVSIEMGQFTHVTSYVSKAEQTPEALEPVTIAKLRCA 220 (441)
Q Consensus 141 ~~~~la~~~~~~Gd~~~A~~~~~~~r~~~~~~~~~~~~~l~~i~~~i~~~~~~~~~~~~~ka~~~~~~~d~~~~~~l~~~ 220 (441)
.+..|.+.|.++|++++|.+.|.++.+.. +..+-.+|......|+++.|...+.+.... +..|+......+.
T Consensus 362 ~~~~Li~~y~k~G~~~~A~~vf~~m~~~d------~~t~n~lI~~y~~~G~~~~A~~lf~~M~~~--g~~Pd~~T~~~ll 433 (697)
T PLN03081 362 ANTALVDLYSKWGRMEDARNVFDRMPRKN------LISWNALIAGYGNHGRGTKAVEMFERMIAE--GVAPNHVTFLAVL 433 (697)
T ss_pred ehHHHHHHHHHCCCHHHHHHHHHhCCCCC------eeeHHHHHHHHHHcCCHHHHHHHHHHHHHh--CCCCCHHHHHHHH
Confidence 57788999999999999999998875421 122334555566778888888888776542 2222222211111
Q ss_pred HHHHhcccccHHHHHHHHHhcC
Q 013559 221 AGLAHLEARKYKLAARKFLEVG 242 (441)
Q Consensus 221 ~gl~~l~~r~y~~Aa~~Fl~~~ 242 (441)
. .+...|.+.+|.+.|-...
T Consensus 434 ~--a~~~~g~~~~a~~~f~~m~ 453 (697)
T PLN03081 434 S--ACRYSGLSEQGWEIFQSMS 453 (697)
T ss_pred H--HHhcCCcHHHHHHHHHHHH
Confidence 1 2345666777666666554
No 219
>PF08281 Sigma70_r4_2: Sigma-70, region 4; InterPro: IPR013249 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognised by the major sigma factors [, ]. Region 4 of sigma-70 like sigma-factors are involved in binding to the -35 promoter element via a helix-turn-helix motif [].; GO: 0003677 DNA binding, 0003700 sequence-specific DNA binding transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, DNA-dependent, 0006355 regulation of transcription, DNA-dependent; PDB: 2LFW_A 1OR7_B 2H27_D 2O8X_B.
Probab=64.20 E-value=21 Score=25.19 Aligned_cols=46 Identities=17% Similarity=0.297 Sum_probs=30.2
Q ss_pred HHHHHHHHHHHHHHHHHhccccccccHHhHHHHcCCChHHHHHHHHHHH
Q 013559 329 DHVETLYDQIRNKALIQYTHPFVSVDLHMMANAFKTSVAGIEKELEALI 377 (441)
Q Consensus 329 ~h~~~l~~~iR~~~i~qy~~pYs~I~L~~mA~~fg~s~~~~E~~L~~LI 377 (441)
.++..+=..-|.-....| +.-.+...+|+.+|+|+..+..++.+-.
T Consensus 6 ~~l~~L~~~~r~i~~l~~---~~g~s~~eIa~~l~~s~~~v~~~l~ra~ 51 (54)
T PF08281_consen 6 QALAQLPERQREIFLLRY---FQGMSYAEIAEILGISESTVKRRLRRAR 51 (54)
T ss_dssp HHHHCS-HHHHHHHHHHH---TS---HHHHHHHCTS-HHHHHHHHHHHH
T ss_pred HHHHCCCHHHHHHHHHHH---HHCcCHHHHHHHHCcCHHHHHHHHHHHH
Confidence 344444445555555667 7888999999999999999999987643
No 220
>COG4783 Putative Zn-dependent protease, contains TPR repeats [General function prediction only]
Probab=63.99 E-value=97 Score=32.69 Aligned_cols=69 Identities=9% Similarity=0.031 Sum_probs=50.4
Q ss_pred HhHHhHHHHHHHHcCCHHHHHHHHHHH-Hhh-------------hcCchhHHHHHHHHHHHHHHhcCHHHHHhHHHHHhc
Q 013559 139 RMGYNDFGDFYYAHGALGDAFKSYVRT-RDY-------------CTTSKHIIHMCMSAILVSIEMGQFTHVTSYVSKAEQ 204 (441)
Q Consensus 139 r~~~~~la~~~~~~Gd~~~A~~~~~~~-r~~-------------~~~~~~~~~~~l~~i~~~i~~~~~~~~~~~~~ka~~ 204 (441)
+-..+.+|+.+.+.|++.+|.+.+.+. +.. |...+.........-....+.|+|..+...+.+++.
T Consensus 374 ~~l~~~~a~all~~g~~~eai~~L~~~~~~~p~dp~~w~~LAqay~~~g~~~~a~~A~AE~~~~~G~~~~A~~~l~~A~~ 453 (484)
T COG4783 374 PLLQLNLAQALLKGGKPQEAIRILNRYLFNDPEDPNGWDLLAQAYAELGNRAEALLARAEGYALAGRLEQAIIFLMRASQ 453 (484)
T ss_pred cHHHHHHHHHHHhcCChHHHHHHHHHHhhcCCCCchHHHHHHHHHHHhCchHHHHHHHHHHHHhCCCHHHHHHHHHHHHH
Confidence 446688899999999999999988865 222 122344455555566667788999999999999988
Q ss_pred ccc
Q 013559 205 TPE 207 (441)
Q Consensus 205 ~~~ 207 (441)
..+
T Consensus 454 ~~~ 456 (484)
T COG4783 454 QVK 456 (484)
T ss_pred hcc
Confidence 776
No 221
>KOG3252 consensus Uncharacterized conserved protein [Function unknown]
Probab=63.93 E-value=64 Score=29.66 Aligned_cols=88 Identities=11% Similarity=0.144 Sum_probs=62.2
Q ss_pred HHHHHHHHhcCCHHHHHHHHHHhHHhhhhchhHHHHHHHHHHHHHHHHHHHhccccccccHHhHHHHcCC-ChHHHHHHH
Q 013559 295 VRELINDFYSSRYASCLDYLGNLKANLLLDIHLHDHVETLYDQIRNKALIQYTHPFVSVDLHMMANAFKT-SVAGIEKEL 373 (441)
Q Consensus 295 ~~~ll~~f~~~~y~~~~~~L~~~~~~l~~D~~L~~h~~~l~~~iR~~~i~qy~~pYs~I~L~~mA~~fg~-s~~~~E~~L 373 (441)
+.++-.-+..|+|..|-..++.. +.+-+|+.-|-+.+|.-+---.=-.|+.|+=.-+|+++|- +-.++|.|+
T Consensus 101 ii~L~~~LEt~~Fq~FW~~~~~N-------~~mle~itGFedsvr~yachvv~iTyQkI~k~lLaellG~~sDs~le~~~ 173 (217)
T KOG3252|consen 101 IIDLGDYLETCRFQQFWQEADEN-------RDMLEGITGFEDSVRKYACHVVGITYQKIDKWLLAELLGGLSDSQLEVWM 173 (217)
T ss_pred HHhHHHHHhhchHHHHhhhhccc-------hHHhcCCCcHHHHHHHHHHHheechHhhchHHHHHHhhCcccHHHHHHHH
Confidence 44555556689999998666654 4555677777777764443333457999999999999985 677899999
Q ss_pred HHHHHcCccceEecCCCCeEEEe
Q 013559 374 EALITDNQIQARIDSHNKILYAR 396 (441)
Q Consensus 374 ~~LI~~g~L~akID~~~gvv~~~ 396 (441)
.+ .+-|-..+|.+..-
T Consensus 174 ~~-------~GW~a~e~G~ifv~ 189 (217)
T KOG3252|consen 174 TK-------YGWIADESGQIFVA 189 (217)
T ss_pred HH-------ccceecCCceEEEe
Confidence 88 66666777755443
No 222
>KOG3617 consensus WD40 and TPR repeat-containing protein [General function prediction only]
Probab=63.83 E-value=62 Score=36.52 Aligned_cols=104 Identities=15% Similarity=0.184 Sum_probs=61.9
Q ss_pred HHhHHhHHHHHHHHcCCHHHHHHHHHHH-----------HhhhcCchhHH-----HHHHHHHHHHHH-hcCHHHHHhHHH
Q 013559 138 IRMGYNDFGDFYYAHGALGDAFKSYVRT-----------RDYCTTSKHII-----HMCMSAILVSIE-MGQFTHVTSYVS 200 (441)
Q Consensus 138 ir~~~~~la~~~~~~Gd~~~A~~~~~~~-----------r~~~~~~~~~~-----~~~l~~i~~~i~-~~~~~~~~~~~~ 200 (441)
.|..|+.+|.++...||.+.|+++|.+. .++....++.+ ..+|.|---+|+ .|+.+.+..+..
T Consensus 857 Lr~Tyy~yA~~Lear~Di~~AleyyEK~~~hafev~rmL~e~p~~~e~Yv~~~~d~~L~~WWgqYlES~GemdaAl~~Y~ 936 (1416)
T KOG3617|consen 857 LRNTYYNYAKYLEARRDIEAALEYYEKAGVHAFEVFRMLKEYPKQIEQYVRRKRDESLYSWWGQYLESVGEMDAALSFYS 936 (1416)
T ss_pred hhhhHHHHHHHHHhhccHHHHHHHHHhcCChHHHHHHHHHhChHHHHHHHHhccchHHHHHHHHHHhcccchHHHHHHHH
Confidence 4668999999999999999999999863 11111111111 123555555565 378888888888
Q ss_pred HHhccccc-------CC--------hhhhhhHHHHH-HHHhcccccHHHHHHHHHhc
Q 013559 201 KAEQTPEA-------LE--------PVTIAKLRCAA-GLAHLEARKYKLAARKFLEV 241 (441)
Q Consensus 201 ka~~~~~~-------~d--------~~~~~~l~~~~-gl~~l~~r~y~~Aa~~Fl~~ 241 (441)
+|++...- |. .+-.++-.+|- |..+=.+|++-+|..-|..+
T Consensus 937 ~A~D~fs~VrI~C~qGk~~kAa~iA~esgd~AAcYhlaR~YEn~g~v~~Av~FfTrA 993 (1416)
T KOG3617|consen 937 SAKDYFSMVRIKCIQGKTDKAARIAEESGDKAACYHLARMYENDGDVVKAVKFFTRA 993 (1416)
T ss_pred HhhhhhhheeeEeeccCchHHHHHHHhcccHHHHHHHHHHhhhhHHHHHHHHHHHHH
Confidence 88875330 11 01112222221 34444567777776666654
No 223
>KOG3060 consensus Uncharacterized conserved protein [Function unknown]
Probab=63.80 E-value=57 Score=31.69 Aligned_cols=42 Identities=17% Similarity=0.280 Sum_probs=31.5
Q ss_pred HHHHHHHhhhhHHHHHhHHhHHHHHHHHcCCHHHHHHHHHHHHh
Q 013559 124 NELNAYRTNLIKESIRMGYNDFGDFYYAHGALGDAFKSYVRTRD 167 (441)
Q Consensus 124 ~el~~~~~n~~~esir~~~~~la~~~~~~Gd~~~A~~~~~~~r~ 167 (441)
.+|+.|.+.. ..--+++..|+++|...|+|.+|.-||.++.-
T Consensus 141 k~ln~YL~~F--~~D~EAW~eLaeiY~~~~~f~kA~fClEE~ll 182 (289)
T KOG3060|consen 141 KELNEYLDKF--MNDQEAWHELAEIYLSEGDFEKAAFCLEELLL 182 (289)
T ss_pred HHHHHHHHHh--cCcHHHHHHHHHHHHhHhHHHHHHHHHHHHHH
Confidence 4555554422 23335889999999999999999999998743
No 224
>PRK10747 putative protoheme IX biogenesis protein; Provisional
Probab=63.79 E-value=1.8e+02 Score=29.81 Aligned_cols=93 Identities=6% Similarity=0.018 Sum_probs=65.1
Q ss_pred HHhHHHHHHHHcCCHHHHHHHHHHHHhhhcCchhHHHHHHHHHHHHHHhcCHHHHHhHHHHHhcccccCChhhhhhHHHH
Q 013559 141 GYNDFGDFYYAHGALGDAFKSYVRTRDYCTTSKHIIHMCMSAILVSIEMGQFTHVTSYVSKAEQTPEALEPVTIAKLRCA 220 (441)
Q Consensus 141 ~~~~la~~~~~~Gd~~~A~~~~~~~r~~~~~~~~~~~~~l~~i~~~i~~~~~~~~~~~~~ka~~~~~~~d~~~~~~l~~~ 220 (441)
....+|..+...|+.++|.+.+.+.... .+...+- .+...+..++...+...+.+....- ..|+ .+..+
T Consensus 265 ~~~~~A~~l~~~g~~~~A~~~L~~~l~~--~~~~~l~----~l~~~l~~~~~~~al~~~e~~lk~~-P~~~----~l~l~ 333 (398)
T PRK10747 265 LQVAMAEHLIECDDHDTAQQIILDGLKR--QYDERLV----LLIPRLKTNNPEQLEKVLRQQIKQH-GDTP----LLWST 333 (398)
T ss_pred HHHHHHHHHHHCCCHHHHHHHHHHHHhc--CCCHHHH----HHHhhccCCChHHHHHHHHHHHhhC-CCCH----HHHHH
Confidence 6678999999999999999999887653 2222221 2223344578777776666554321 1243 35578
Q ss_pred HHHHhcccccHHHHHHHHHhcCcC
Q 013559 221 AGLAHLEARKYKLAARKFLEVGPD 244 (441)
Q Consensus 221 ~gl~~l~~r~y~~Aa~~Fl~~~~t 244 (441)
.|..++..++|.+|.+.|-.+...
T Consensus 334 lgrl~~~~~~~~~A~~~le~al~~ 357 (398)
T PRK10747 334 LGQLLMKHGEWQEASLAFRAALKQ 357 (398)
T ss_pred HHHHHHHCCCHHHHHHHHHHHHhc
Confidence 899999999999999999887653
No 225
>COG5010 TadD Flp pilus assembly protein TadD, contains TPR repeats [Intracellular trafficking and secretion]
Probab=63.61 E-value=76 Score=30.74 Aligned_cols=93 Identities=15% Similarity=0.104 Sum_probs=53.1
Q ss_pred hHHHHHHHHcCCHHHHHHHHHHHHhhhcCchhHHHHHHHHHHHHHHhcCHHHHHhHHHHHhcccccCChhhhhhHHHHHH
Q 013559 143 NDFGDFYYAHGALGDAFKSYVRTRDYCTTSKHIIHMCMSAILVSIEMGQFTHVTSYVSKAEQTPEALEPVTIAKLRCAAG 222 (441)
Q Consensus 143 ~~la~~~~~~Gd~~~A~~~~~~~r~~~~~~~~~~~~~l~~i~~~i~~~~~~~~~~~~~ka~~~~~~~d~~~~~~l~~~~g 222 (441)
..+|+-+...||+..|...+.+.-....+.. +.....--+.-..|+++.+...+.++-++.- .+|...+- -|
T Consensus 104 ~~~gk~~~~~g~~~~A~~~~rkA~~l~p~d~---~~~~~lgaaldq~Gr~~~Ar~ay~qAl~L~~-~~p~~~nN----lg 175 (257)
T COG5010 104 AAQGKNQIRNGNFGEAVSVLRKAARLAPTDW---EAWNLLGAALDQLGRFDEARRAYRQALELAP-NEPSIANN----LG 175 (257)
T ss_pred HHHHHHHHHhcchHHHHHHHHHHhccCCCCh---hhhhHHHHHHHHccChhHHHHHHHHHHHhcc-CCchhhhh----HH
Confidence 3367777777777777777776644432222 1222222334455677777777776666543 23333222 35
Q ss_pred HHhcccccHHHHHHHHHhcCc
Q 013559 223 LAHLEARKYKLAARKFLEVGP 243 (441)
Q Consensus 223 l~~l~~r~y~~Aa~~Fl~~~~ 243 (441)
+.++-+|++..|..+++....
T Consensus 176 ms~~L~gd~~~A~~lll~a~l 196 (257)
T COG5010 176 MSLLLRGDLEDAETLLLPAYL 196 (257)
T ss_pred HHHHHcCCHHHHHHHHHHHHh
Confidence 566677777777777777654
No 226
>smart00418 HTH_ARSR helix_turn_helix, Arsenical Resistance Operon Repressor.
Probab=62.38 E-value=24 Score=25.01 Aligned_cols=43 Identities=12% Similarity=0.115 Sum_probs=35.7
Q ss_pred cccccHHhHHHHcCCChHHHHHHHHHHHHcCccceEecCCCCe
Q 013559 350 FVSVDLHMMANAFKTSVAGIEKELEALITDNQIQARIDSHNKI 392 (441)
Q Consensus 350 Ys~I~L~~mA~~fg~s~~~~E~~L~~LI~~g~L~akID~~~gv 392 (441)
-..+++..+++.||++...+-+.|..|...|-+...-+...+.
T Consensus 8 ~~~~~~~~i~~~l~is~~~v~~~l~~L~~~g~i~~~~~~~~~~ 50 (66)
T smart00418 8 EGELCVCELAEILGLSQSTVSHHLKKLREAGLVESRREGKRVY 50 (66)
T ss_pred cCCccHHHHHHHHCCCHHHHHHHHHHHHHCCCeeeeecCCEEE
Confidence 4678999999999999999999999999999997554443333
No 227
>KOG4555 consensus TPR repeat-containing protein [Function unknown]
Probab=61.75 E-value=1.1e+02 Score=26.82 Aligned_cols=95 Identities=11% Similarity=-0.032 Sum_probs=65.0
Q ss_pred HhHHHHHHHHcCCHHHHHHHHHHHHhhhcCchhHHHHHHHHHHHHHHhcCHHHHHhHHHHHhcccccCChhhh-hhHHHH
Q 013559 142 YNDFGDFYYAHGALGDAFKSYVRTRDYCTTSKHIIHMCMSAILVSIEMGQFTHVTSYVSKAEQTPEALEPVTI-AKLRCA 220 (441)
Q Consensus 142 ~~~la~~~~~~Gd~~~A~~~~~~~r~~~~~~~~~~~~~l~~i~~~i~~~~~~~~~~~~~ka~~~~~~~d~~~~-~~l~~~ 220 (441)
+.-.|-...+.|+++.|++.|.+....|... .+.+-+-....-+.|+-+.+...++|+-++-. +..+. -.-.|.
T Consensus 46 LEl~~valaE~g~Ld~AlE~F~qal~l~P~r---aSayNNRAQa~RLq~~~e~ALdDLn~AleLag--~~trtacqa~vQ 120 (175)
T KOG4555|consen 46 LELKAIALAEAGDLDGALELFGQALCLAPER---ASAYNNRAQALRLQGDDEEALDDLNKALELAG--DQTRTACQAFVQ 120 (175)
T ss_pred HHHHHHHHHhccchHHHHHHHHHHHHhcccc---hHhhccHHHHHHHcCChHHHHHHHHHHHHhcC--ccchHHHHHHHH
Confidence 3445667889999999999999988887532 34444555556677999999999999887754 22211 123455
Q ss_pred HHHHhcccccHHHHHHHHHhc
Q 013559 221 AGLAHLEARKYKLAARKFLEV 241 (441)
Q Consensus 221 ~gl~~l~~r~y~~Aa~~Fl~~ 241 (441)
.|+.+--.|+-..|...|-.+
T Consensus 121 Rg~lyRl~g~dd~AR~DFe~A 141 (175)
T KOG4555|consen 121 RGLLYRLLGNDDAARADFEAA 141 (175)
T ss_pred HHHHHHHhCchHHHHHhHHHH
Confidence 677777777766666666544
No 228
>PRK11534 DNA-binding transcriptional regulator CsiR; Provisional
Probab=61.56 E-value=21 Score=33.33 Aligned_cols=65 Identities=11% Similarity=0.203 Sum_probs=56.1
Q ss_pred HHHHHHHHHHHHHHHHhccccccccHHhHHHHcCCChHHHHHHHHHHHHcCccceEecCCCCeEEEe
Q 013559 330 HVETLYDQIRNKALIQYTHPFVSVDLHMMANAFKTSVAGIEKELEALITDNQIQARIDSHNKILYAR 396 (441)
Q Consensus 330 h~~~l~~~iR~~~i~qy~~pYs~I~L~~mA~~fg~s~~~~E~~L~~LI~~g~L~akID~~~gvv~~~ 396 (441)
-.+.+++.||..++..-+.|=..++-..||+.||+|-.-+-.-|..|..+|-+.- -+..|+.+..
T Consensus 8 ~~~~vy~~i~~~I~~g~l~pG~~L~e~eLae~lgVSRtpVREAL~~L~~eGlv~~--~~~~G~~V~~ 72 (224)
T PRK11534 8 TALDGYRWLKNDIIRGNFQPDEKLRMSLLTSRYALGVGPLREALSQLVAERLVTV--VNQKGYRVAS 72 (224)
T ss_pred hhHHHHHHHHHHHHhCCCCCCCcCCHHHHHHHHCCChHHHHHHHHHHHHCCCEEE--eCCCceEeCC
Confidence 3567899999999999999999999999999999999999999999999998863 3555655543
No 229
>KOG0276 consensus Vesicle coat complex COPI, beta' subunit [Intracellular trafficking, secretion, and vesicular transport]
Probab=61.42 E-value=1.5e+02 Score=32.31 Aligned_cols=157 Identities=17% Similarity=0.222 Sum_probs=92.0
Q ss_pred HhHHHHHHHHcCCHHHHHHHHHHHHhhhcCchhHHHHHHHHHHHHHHhcCHHHHHhHHHHHhcccccCChhhhhhHHHHH
Q 013559 142 YNDFGDFYYAHGALGDAFKSYVRTRDYCTTSKHIIHMCMSAILVSIEMGQFTHVTSYVSKAEQTPEALEPVTIAKLRCAA 221 (441)
Q Consensus 142 ~~~la~~~~~~Gd~~~A~~~~~~~r~~~~~~~~~~~~~l~~i~~~i~~~~~~~~~~~~~ka~~~~~~~d~~~~~~l~~~~ 221 (441)
+-+.++|+.+.|=+++|++ .|+++.|++++.+. .|+.+.|.....++.+.. .|. .-
T Consensus 617 rt~va~Fle~~g~~e~AL~-------~s~D~d~rFelal~-------lgrl~iA~~la~e~~s~~---Kw~-------~L 672 (794)
T KOG0276|consen 617 RTKVAHFLESQGMKEQALE-------LSTDPDQRFELALK-------LGRLDIAFDLAVEANSEV---KWR-------QL 672 (794)
T ss_pred hhhHHhHhhhccchHhhhh-------cCCChhhhhhhhhh-------cCcHHHHHHHHHhhcchH---HHH-------HH
Confidence 3578999999998888765 67889988876654 455555554444443332 342 23
Q ss_pred HHHhcccccHHHHHHHHHhcCcCCCCCchhhhcHHHHHHHHHHHHHhcCChHHHHHhcccCHhhHhhhccchHHHHHHHH
Q 013559 222 GLAHLEARKYKLAARKFLEVGPDLGNSYNEVIAAQDVATYGGLCALASFDRAELKSKVIDNVNFRNFLELVPEVRELIND 301 (441)
Q Consensus 222 gl~~l~~r~y~~Aa~~Fl~~~~t~~~~~~el~s~~d~~~Y~~l~al~s~~R~eLk~~vl~~~~~~~~le~~p~~~~ll~~ 301 (441)
|-+.+..+++..|.++|..+-. +..++ |+.-++.+++-|.. +-. ..+ .+...=..++..
T Consensus 673 g~~al~~~~l~lA~EC~~~a~d-----~~~Ll----------Ll~t~~g~~~~l~~-la~--~~~---~~g~~N~AF~~~ 731 (794)
T KOG0276|consen 673 GDAALSAGELPLASECFLRARD-----LGSLL----------LLYTSSGNAEGLAV-LAS--LAK---KQGKNNLAFLAY 731 (794)
T ss_pred HHHHhhcccchhHHHHHHhhcc-----hhhhh----------hhhhhcCChhHHHH-HHH--HHH---hhcccchHHHHH
Confidence 5567888999999999988742 22222 22333444443322 100 000 011122446667
Q ss_pred HhcCCHHHHHHHHHHhH----HhhhhchhHHHHHHHHHHHHHHHHH
Q 013559 302 FYSSRYASCLDYLGNLK----ANLLLDIHLHDHVETLYDQIRNKAL 343 (441)
Q Consensus 302 f~~~~y~~~~~~L~~~~----~~l~~D~~L~~h~~~l~~~iR~~~i 343 (441)
|..++|.+|++.|.+-. ..+..--|+-..+..++..-|....
T Consensus 732 ~l~g~~~~C~~lLi~t~r~peAal~ArtYlps~vs~iv~~wk~~l~ 777 (794)
T KOG0276|consen 732 FLSGDYEECLELLISTQRLPEAALFARTYLPSQVSRIVELWKEDLS 777 (794)
T ss_pred HHcCCHHHHHHHHHhcCcCcHHHHHHhhhChHHHHHHHHHHHHHhh
Confidence 88999999999998752 2333333444556666666665544
No 230
>KOG0553 consensus TPR repeat-containing protein [General function prediction only]
Probab=61.29 E-value=86 Score=31.05 Aligned_cols=84 Identities=17% Similarity=0.264 Sum_probs=58.4
Q ss_pred HHHHHHHHHhhccCCCCCcCCHHHHHHHHHHHHHHHHHHHHHHHHHHhhh-hHHHHHhHHhHHHHHHHHcCCHHHHHHHH
Q 013559 84 QLFREVVKKIDGRLGPNYAMDEAWCDSVDRRAEQRKEKLENELNAYRTNL-IKESIRMGYNDFGDFYYAHGALGDAFKSY 162 (441)
Q Consensus 84 ~~Y~~~~~~l~~~~~~~~~~D~~~~~~~~~~~~~~~~~Le~el~~~~~n~-~~esir~~~~~la~~~~~~Gd~~~A~~~~ 162 (441)
..|++.+..+..... --|-|+-++ ..++.+--+|..-+.-+++.+.-+ +.+.--.+|-+||..|+..|++.+|.++|
T Consensus 95 ~~Y~eAv~kY~~AI~-l~P~nAVyy-cNRAAAy~~Lg~~~~AVkDce~Al~iDp~yskay~RLG~A~~~~gk~~~A~~ay 172 (304)
T KOG0553|consen 95 KDYQEAVDKYTEAIE-LDPTNAVYY-CNRAAAYSKLGEYEDAVKDCESALSIDPHYSKAYGRLGLAYLALGKYEEAIEAY 172 (304)
T ss_pred hhHHHHHHHHHHHHh-cCCCcchHH-HHHHHHHHHhcchHHHHHHHHHHHhcChHHHHHHHHHHHHHHccCcHHHHHHHH
Confidence 567777666552210 123455555 556666677777777777765543 55666679999999999999999999999
Q ss_pred HHHHhhh
Q 013559 163 VRTRDYC 169 (441)
Q Consensus 163 ~~~r~~~ 169 (441)
.+..+.-
T Consensus 173 kKaLeld 179 (304)
T KOG0553|consen 173 KKALELD 179 (304)
T ss_pred HhhhccC
Confidence 8876653
No 231
>cd00092 HTH_CRP helix_turn_helix, cAMP Regulatory protein C-terminus; DNA binding domain of prokaryotic regulatory proteins belonging to the catabolite activator protein family.
Probab=61.21 E-value=12 Score=27.35 Aligned_cols=34 Identities=12% Similarity=0.211 Sum_probs=31.1
Q ss_pred ccccHHhHHHHcCCChHHHHHHHHHHHHcCccce
Q 013559 351 VSVDLHMMANAFKTSVAGIEKELEALITDNQIQA 384 (441)
Q Consensus 351 s~I~L~~mA~~fg~s~~~~E~~L~~LI~~g~L~a 384 (441)
-.++...+|+.+|++...+.+.|..|...|-|..
T Consensus 24 ~~~s~~ela~~~g~s~~tv~r~l~~L~~~g~i~~ 57 (67)
T cd00092 24 LPLTRQEIADYLGLTRETVSRTLKELEEEGLISR 57 (67)
T ss_pred CCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEe
Confidence 4589999999999999999999999999998854
No 232
>TIGR00985 3a0801s04tom mitochondrial import receptor subunit translocase of outer membrane 20 kDa subunit.
Probab=61.17 E-value=1.1e+02 Score=27.21 Aligned_cols=43 Identities=7% Similarity=0.217 Sum_probs=36.2
Q ss_pred hHHhHHHHHHHHcC-CHHHHHHHHHHHHhhhcCchhHHHHHHHH
Q 013559 140 MGYNDFGDFYYAHG-ALGDAFKSYVRTRDYCTTSKHIIHMCMSA 182 (441)
Q Consensus 140 ~~~~~la~~~~~~G-d~~~A~~~~~~~r~~~~~~~~~~~~~l~~ 182 (441)
+....+|+-+...| +..+|+.+|++..--|..|...+.++=..
T Consensus 91 l~eV~~GE~L~~~g~~~~ega~hf~nAl~Vc~qP~~LL~iyq~t 134 (148)
T TIGR00985 91 LQEVQLGEELMAQGTNVDEGAVHFYNALKVYPQPQQLLSIYQQT 134 (148)
T ss_pred HHHHHHHHHHHhCCCchHHHHHHHHHHHHhCCCHHHHHHHHHhh
Confidence 34568899999999 99999999999999999998877665443
No 233
>PF09339 HTH_IclR: IclR helix-turn-helix domain; InterPro: IPR005471 The many bacterial transcription regulation proteins which bind DNA through a 'helix-turn-helix' motif can be classified into subfamilies on the basis of sequence similarities. One of these subfamilies, called 'iclR', groups several proteins including: gylR, a possible activator protein for the gylABX glycerol operon in Streptomyces. iclR, the repressor of the acetate operon (also known as glyoxylate bypass operon) in Escherichia coli and Salmonella typhimurium. These proteins have a Helix-Turn-Helix motif at the N terminus that is similar to that of other DNA-binding proteins [].; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 1MKM_A 3MQ0_A 3R4K_A 2G7U_C 2O0Y_C 2XRO_F 2XRN_B 2IA2_D.
Probab=60.87 E-value=20 Score=25.30 Aligned_cols=41 Identities=12% Similarity=0.221 Sum_probs=32.0
Q ss_pred HHHHhcccc-ccccHHhHHHHcCCChHHHHHHHHHHHHcCcc
Q 013559 342 ALIQYTHPF-VSVDLHMMANAFKTSVAGIEKELEALITDNQI 382 (441)
Q Consensus 342 ~i~qy~~pY-s~I~L~~mA~~fg~s~~~~E~~L~~LI~~g~L 382 (441)
.+..++... ..+++..+|+.+|++...+-+.|..|...|-+
T Consensus 7 ~iL~~l~~~~~~~t~~eia~~~gl~~stv~r~L~tL~~~g~v 48 (52)
T PF09339_consen 7 RILEALAESGGPLTLSEIARALGLPKSTVHRLLQTLVEEGYV 48 (52)
T ss_dssp HHHHCHHCTBSCEEHHHHHHHHTS-HHHHHHHHHHHHHTTSE
T ss_pred HHHHHHHcCCCCCCHHHHHHHHCcCHHHHHHHHHHHHHCcCe
Confidence 334444444 44899999999999999999999999998865
No 234
>PRK09954 putative kinase; Provisional
Probab=60.53 E-value=24 Score=35.69 Aligned_cols=54 Identities=7% Similarity=0.139 Sum_probs=45.1
Q ss_pred HHHhccccccccHHhHHHHcCCChHHHHHHHHHHHHcCccc---eEecCCCCeEEEe
Q 013559 343 LIQYTHPFVSVDLHMMANAFKTSVAGIEKELEALITDNQIQ---ARIDSHNKILYAR 396 (441)
Q Consensus 343 i~qy~~pYs~I~L~~mA~~fg~s~~~~E~~L~~LI~~g~L~---akID~~~gvv~~~ 396 (441)
+..+++-..+++...||+.||+|...+-+.|.+|..+|.|. ..+|...+++...
T Consensus 8 il~~l~~~~~~s~~~la~~l~~s~~~v~~~i~~L~~~g~i~~~~~~l~~~~~v~viG 64 (362)
T PRK09954 8 ILAILRRNPLIQQNEIADILQISRSRVAAHIMDLMRKGRIKGKGYILTEQEYCVVVG 64 (362)
T ss_pred HHHHHHHCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCcCCcEEEEcCCccEEEEE
Confidence 44555666799999999999999999999999999999885 4688888776543
No 235
>KOG1156 consensus N-terminal acetyltransferase [Chromatin structure and dynamics]
Probab=60.50 E-value=2.7e+02 Score=30.70 Aligned_cols=120 Identities=13% Similarity=0.090 Sum_probs=80.6
Q ss_pred HHHHHHHHHHHHh------hh--hHHHHHhHHhHHHHHHHHcCCHHHHHHHHHHHHhhhc--CchhH---HHHHHHHHHH
Q 013559 119 KEKLENELNAYRT------NL--IKESIRMGYNDFGDFYYAHGALGDAFKSYVRTRDYCT--TSKHI---IHMCMSAILV 185 (441)
Q Consensus 119 ~~~Le~el~~~~~------n~--~~esir~~~~~la~~~~~~Gd~~~A~~~~~~~r~~~~--~~~~~---~~~~l~~i~~ 185 (441)
+.-|+..+++++. .+ ...+.|.-+..+|--+.-.|+|..|.+.+..+...+. .+.+. .++.+-...+
T Consensus 115 lslLQ~QmRd~~~~~~tr~~LLql~~~~ra~w~~~Avs~~L~g~y~~A~~il~ef~~t~~~~~s~~~~e~se~~Ly~n~i 194 (700)
T KOG1156|consen 115 LSLLQIQMRDYEGYLETRNQLLQLRPSQRASWIGFAVAQHLLGEYKMALEILEEFEKTQNTSPSKEDYEHSELLLYQNQI 194 (700)
T ss_pred HHHHHHHHHhhhhHHHHHHHHHHhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhccCCCHHHHHHHHHHHHHHHH
Confidence 3456666666532 11 3457777888999999999999999999998877662 22222 4466777777
Q ss_pred HHHhcCHHHHHhHHHHHhcccccCChhhhhhHHHHHHHHhcccccHHHHHHHHHhcCc
Q 013559 186 SIEMGQFTHVTSYVSKAEQTPEALEPVTIAKLRCAAGLAHLEARKYKLAARKFLEVGP 243 (441)
Q Consensus 186 ~i~~~~~~~~~~~~~ka~~~~~~~d~~~~~~l~~~~gl~~l~~r~y~~Aa~~Fl~~~~ 243 (441)
-+..|....+.+.+.+-+.-+. | +..+....|-+.+..+++++|...+.-...
T Consensus 195 ~~E~g~~q~ale~L~~~e~~i~--D---kla~~e~ka~l~~kl~~lEeA~~~y~~Ll~ 247 (700)
T KOG1156|consen 195 LIEAGSLQKALEHLLDNEKQIV--D---KLAFEETKADLLMKLGQLEEAVKVYRRLLE 247 (700)
T ss_pred HHHcccHHHHHHHHHhhhhHHH--H---HHHHhhhHHHHHHHHhhHHhHHHHHHHHHh
Confidence 8888888888777766554332 1 122334456677788888888777665543
No 236
>TIGR02010 IscR iron-sulfur cluster assembly transcription factor IscR. This model describes IscR, an iron-sulfur binding transcription factor of the ISC iron-sulfur cluster assembly system.
Probab=60.47 E-value=39 Score=29.12 Aligned_cols=59 Identities=12% Similarity=0.129 Sum_probs=43.1
Q ss_pred ccccHHhHHHHcCCChHHHHHHHHHHHHcCccceEecCCCCeEEEecCCchhHHHHHHHHH
Q 013559 351 VSVDLHMMANAFKTSVAGIEKELEALITDNQIQARIDSHNKILYARHADQRNATFQRVLQT 411 (441)
Q Consensus 351 s~I~L~~mA~~fg~s~~~~E~~L~~LI~~g~L~akID~~~gvv~~~~~d~r~~~~~~~i~~ 411 (441)
..++.+.||+.+++|..++++-+..|...|=+..+=....|..-..+| ..-+..++++.
T Consensus 24 ~~~s~~~ia~~~~ip~~~l~kil~~L~~~glv~s~~G~~Ggy~l~~~~--~~Itl~dv~~a 82 (135)
T TIGR02010 24 GPVTLADISERQGISLSYLEQLFAKLRKAGLVKSVRGPGGGYQLGRPA--EDISVADIIDA 82 (135)
T ss_pred CcCcHHHHHHHHCcCHHHHHHHHHHHHHCCceEEEeCCCCCEeccCCH--HHCcHHHHHHH
Confidence 469999999999999999999999999999887654444554444433 22334444443
No 237
>COG1802 GntR Transcriptional regulators [Transcription]
Probab=60.32 E-value=20 Score=33.66 Aligned_cols=67 Identities=13% Similarity=0.205 Sum_probs=58.8
Q ss_pred HHHHHHHHHHHHHHHHhccccccccHHhHHHHcCCChHHHHHHHHHHHHcCccceEecCCCCeEEEecC
Q 013559 330 HVETLYDQIRNKALIQYTHPFVSVDLHMMANAFKTSVAGIEKELEALITDNQIQARIDSHNKILYARHA 398 (441)
Q Consensus 330 h~~~l~~~iR~~~i~qy~~pYs~I~L~~mA~~fg~s~~~~E~~L~~LI~~g~L~akID~~~gvv~~~~~ 398 (441)
-.+.+++.+|..++.-=+.|=+.++-..||+.||+|..-+-+-|.+|-.+|-|.-. ...|.++..-.
T Consensus 17 ~~~~vy~~Lr~~Il~g~l~pG~~l~e~~La~~~gvSrtPVReAL~rL~~eGlv~~~--p~rG~~V~~~~ 83 (230)
T COG1802 17 LADQVYEELREAILSGELAPGERLSEEELAEELGVSRTPVREALRRLEAEGLVEIE--PNRGAFVAPLS 83 (230)
T ss_pred HHHHHHHHHHHHHHhCCCCCCCCccHHHHHHHhCCCCccHHHHHHHHHHCCCeEec--CCCCCeeCCCC
Confidence 45678999999999999999999999999999999999999999999999998654 66677766543
No 238
>PF13463 HTH_27: Winged helix DNA-binding domain; PDB: 3GFL_A 2YR2_B 3GFM_A 3GFJ_A 3GF2_A 3GEZ_A 2GXG_A 3GFI_A 2EB7_A.
Probab=60.30 E-value=36 Score=24.94 Aligned_cols=48 Identities=13% Similarity=0.158 Sum_probs=35.4
Q ss_pred HHhcc-ccccccHHhHHHHcCCChHHHHHHHHHHHHcCccceEecCCCC
Q 013559 344 IQYTH-PFVSVDLHMMANAFKTSVAGIEKELEALITDNQIQARIDSHNK 391 (441)
Q Consensus 344 ~qy~~-pYs~I~L~~mA~~fg~s~~~~E~~L~~LI~~g~L~akID~~~g 391 (441)
..++. ....+++..+|+.+|++...+-+.|-+|+..|-|.=.=|..++
T Consensus 9 L~~l~~~~~~~t~~~l~~~~~~~~~~vs~~i~~L~~~glv~~~~~~~d~ 57 (68)
T PF13463_consen 9 LRALAHSDGPMTQSDLAERLGISKSTVSRIIKKLEEKGLVEKERDPHDK 57 (68)
T ss_dssp HHHHT--TS-BEHHHHHHHTT--HHHHHHHHHHHHHTTSEEEEEESSCT
T ss_pred HHHHHccCCCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEecCCCCcC
Confidence 33444 7899999999999999999999999999999999555444443
No 239
>smart00351 PAX Paired Box domain.
Probab=60.10 E-value=19 Score=30.78 Aligned_cols=45 Identities=13% Similarity=0.056 Sum_probs=37.5
Q ss_pred HHHHHHHHHhccccccccHHhHHHHcCCChHHHHHHHHHHHHcCccce
Q 013559 337 QIRNKALIQYTHPFVSVDLHMMANAFKTSVAGIEKELEALITDNQIQA 384 (441)
Q Consensus 337 ~iR~~~i~qy~~pYs~I~L~~mA~~fg~s~~~~E~~L~~LI~~g~L~a 384 (441)
..|.+++.-| -.-.+...+|+.||+|...+-+|+.++-..|.+..
T Consensus 21 ~~R~riv~~~---~~G~s~~~iA~~~gvs~~tV~kwi~r~~~~G~~~p 65 (125)
T smart00351 21 EERQRIVELA---QNGVRPCDISRQLCVSHGCVSKILGRYYETGSIRP 65 (125)
T ss_pred HHHHHHHHHH---HcCCCHHHHHHHHCcCHHHHHHHHHHHHHcCCcCC
Confidence 4677777666 25678899999999999999999999999997654
No 240
>PRK03837 transcriptional regulator NanR; Provisional
Probab=60.03 E-value=24 Score=33.23 Aligned_cols=64 Identities=13% Similarity=0.111 Sum_probs=56.4
Q ss_pred HHHHHHHHHHHHHHHhccccccc-cHHhHHHHcCCChHHHHHHHHHHHHcCccceEecCCCCeEEEe
Q 013559 331 VETLYDQIRNKALIQYTHPFVSV-DLHMMANAFKTSVAGIEKELEALITDNQIQARIDSHNKILYAR 396 (441)
Q Consensus 331 ~~~l~~~iR~~~i~qy~~pYs~I-~L~~mA~~fg~s~~~~E~~L~~LI~~g~L~akID~~~gvv~~~ 396 (441)
.+.+++.||.+++...+.|=..+ +...||+.||||...+-+-|..|-.+|-|.-+ ...|+.+..
T Consensus 15 ~~~v~~~l~~~I~~g~l~pG~~Lp~E~~Lae~~gVSRt~VREAL~~L~~eGlv~~~--~~~G~~V~~ 79 (241)
T PRK03837 15 SEEVEERLEQMIRSGEFGPGDQLPSERELMAFFGVGRPAVREALQALKRKGLVQIS--HGERARVSR 79 (241)
T ss_pred HHHHHHHHHHHHHhCCCCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHCCCEEEe--cCCceeEec
Confidence 46789999999999999999999 99999999999999999999999999988653 555766654
No 241
>PRK02603 photosystem I assembly protein Ycf3; Provisional
Probab=59.96 E-value=91 Score=27.61 Aligned_cols=54 Identities=11% Similarity=0.141 Sum_probs=36.3
Q ss_pred hHHhHHHHHHHHcCCHHHHHHHHHHHHhhhcCchhHHHHHHHHHHHHHHhcCHHHHH
Q 013559 140 MGYNDFGDFYYAHGALGDAFKSYVRTRDYCTTSKHIIHMCMSAILVSIEMGQFTHVT 196 (441)
Q Consensus 140 ~~~~~la~~~~~~Gd~~~A~~~~~~~r~~~~~~~~~~~~~l~~i~~~i~~~~~~~~~ 196 (441)
.++..+|..+...|++++|.++|.+........ ......+..+....|+...+.
T Consensus 73 ~~~~~la~~~~~~g~~~~A~~~~~~al~~~p~~---~~~~~~lg~~~~~~g~~~~a~ 126 (172)
T PRK02603 73 YILYNMGIIYASNGEHDKALEYYHQALELNPKQ---PSALNNIAVIYHKRGEKAEEA 126 (172)
T ss_pred HHHHHHHHHHHHcCCHHHHHHHHHHHHHhCccc---HHHHHHHHHHHHHcCChHhHh
Confidence 478899999999999999999999886654321 233334444444445544433
No 242
>PRK15174 Vi polysaccharide export protein VexE; Provisional
Probab=59.90 E-value=2.8e+02 Score=30.69 Aligned_cols=97 Identities=6% Similarity=-0.173 Sum_probs=59.8
Q ss_pred hHHhHHHHHHHHcCCHHHHHHHHHHHHhhhcCchhHHHHHHHHHHHHHHhcCHHHHHhHHHHHhcccccCChhhhhhHHH
Q 013559 140 MGYNDFGDFYYAHGALGDAFKSYVRTRDYCTTSKHIIHMCMSAILVSIEMGQFTHVTSYVSKAEQTPEALEPVTIAKLRC 219 (441)
Q Consensus 140 ~~~~~la~~~~~~Gd~~~A~~~~~~~r~~~~~~~~~~~~~l~~i~~~i~~~~~~~~~~~~~ka~~~~~~~d~~~~~~l~~ 219 (441)
.++..+|..+...|++++|...+.++......+... .... ...+..|++..+...+.++-......++. ...
T Consensus 145 ~a~~~la~~l~~~g~~~eA~~~~~~~~~~~P~~~~a---~~~~-~~l~~~g~~~eA~~~~~~~l~~~~~~~~~----~~~ 216 (656)
T PRK15174 145 QIFALHLRTLVLMDKELQAISLARTQAQEVPPRGDM---IATC-LSFLNKSRLPEDHDLARALLPFFALERQE----SAG 216 (656)
T ss_pred HHHHHHHHHHHHCCChHHHHHHHHHHHHhCCCCHHH---HHHH-HHHHHcCCHHHHHHHHHHHHhcCCCcchh----HHH
Confidence 467788888889999999988888765443332221 1122 23566788888887777654332111111 112
Q ss_pred HHHHHhcccccHHHHHHHHHhcCcC
Q 013559 220 AAGLAHLEARKYKLAARKFLEVGPD 244 (441)
Q Consensus 220 ~~gl~~l~~r~y~~Aa~~Fl~~~~t 244 (441)
..|..+...|+|.+|...|-.+...
T Consensus 217 ~l~~~l~~~g~~~eA~~~~~~al~~ 241 (656)
T PRK15174 217 LAVDTLCAVGKYQEAIQTGESALAR 241 (656)
T ss_pred HHHHHHHHCCCHHHHHHHHHHHHhc
Confidence 3355667788888888888777643
No 243
>TIGR03338 phnR_burk phosphonate utilization associated transcriptional regulator. This family of proteins are members of the GntR family (pfam00392) containing an N-terminal helix-turn-helix (HTH) motif. This clade is found adjacent to or inside of operons for the degradation of 2-aminoethylphosphonate (AEP) in Polaromonas, Burkholderia, Ralstonia and Verminephrobacter.
Probab=59.58 E-value=24 Score=32.57 Aligned_cols=64 Identities=13% Similarity=0.157 Sum_probs=56.2
Q ss_pred HHHHHHHHHHHHHHHhccccccccHHhHHHHcCCChHHHHHHHHHHHHcCccceEecCCCCeEEEe
Q 013559 331 VETLYDQIRNKALIQYTHPFVSVDLHMMANAFKTSVAGIEKELEALITDNQIQARIDSHNKILYAR 396 (441)
Q Consensus 331 ~~~l~~~iR~~~i~qy~~pYs~I~L~~mA~~fg~s~~~~E~~L~~LI~~g~L~akID~~~gvv~~~ 396 (441)
.+.+++.||.+++..-+.|=..++-..||+.||+|..-+-+-|..|-.+|-+.- -+..|+.+..
T Consensus 13 ~~~v~~~l~~~I~~g~l~pG~~L~e~~La~~lgVSRtpVReAL~~L~~eGlv~~--~~~~G~~V~~ 76 (212)
T TIGR03338 13 TTLVQDEIERAILSGELPPGAKLNESDIAARLGVSRGPVREAFRALEEAGLVRN--EKNRGVFVRE 76 (212)
T ss_pred HHHHHHHHHHHHHcCCCCCCCEecHHHHHHHhCCChHHHHHHHHHHHHCCCEEE--ecCCCeEEec
Confidence 457889999999999999999999999999999999999999999999999853 4556776665
No 244
>PF13384 HTH_23: Homeodomain-like domain; PDB: 2X48_C.
Probab=59.21 E-value=9.9 Score=26.44 Aligned_cols=40 Identities=8% Similarity=0.089 Sum_probs=23.1
Q ss_pred HHHHHHHHhccccccccHHhHHHHcCCChHHHHHHHHHHHHcC
Q 013559 338 IRNKALIQYTHPFVSVDLHMMANAFKTSVAGIEKELEALITDN 380 (441)
Q Consensus 338 iR~~~i~qy~~pYs~I~L~~mA~~fg~s~~~~E~~L~~LI~~g 380 (441)
.|..++..+.+ -.+...+|+.||+|...+-+|+.++-..|
T Consensus 6 ~R~~ii~l~~~---G~s~~~ia~~lgvs~~Tv~~w~kr~~~~G 45 (50)
T PF13384_consen 6 RRAQIIRLLRE---GWSIREIAKRLGVSRSTVYRWIKRYREEG 45 (50)
T ss_dssp ----HHHHHHH---T--HHHHHHHHTS-HHHHHHHHT------
T ss_pred HHHHHHHHHHC---CCCHHHHHHHHCcCHHHHHHHHHHccccc
Confidence 35556666633 78899999999999999999998876655
No 245
>PF01726 LexA_DNA_bind: LexA DNA binding domain; InterPro: IPR006199 This is the DNA binding domain of the LexA SOS regulon repressor which prevents expression of DNA repair proteins in bacteria. The aligned region contains a variant form of the helix-turn-helix DNA binding motif []. This domain usually at the N terminus is found associated with IPR006198 from INTERPRO the auto-proteolytic domain of LexA 3.4.21.88 from EC.; GO: 0004252 serine-type endopeptidase activity, 0006508 proteolysis; PDB: 1LEA_A 1JHH_A 3JSP_A 1JHF_A 3JSO_B 1LEB_A 3K2Z_A.
Probab=59.13 E-value=15 Score=27.67 Aligned_cols=32 Identities=19% Similarity=0.295 Sum_probs=26.9
Q ss_pred cccHHhHHHHcCCC-hHHHHHHHHHHHHcCccc
Q 013559 352 SVDLHMMANAFKTS-VAGIEKELEALITDNQIQ 383 (441)
Q Consensus 352 ~I~L~~mA~~fg~s-~~~~E~~L~~LI~~g~L~ 383 (441)
.-|+..||+.||++ +..+...|..|...|-|.
T Consensus 25 ~Pt~rEIa~~~g~~S~~tv~~~L~~Le~kG~I~ 57 (65)
T PF01726_consen 25 PPTVREIAEALGLKSTSTVQRHLKALERKGYIR 57 (65)
T ss_dssp ---HHHHHHHHTSSSHHHHHHHHHHHHHTTSEE
T ss_pred CCCHHHHHHHhCCCChHHHHHHHHHHHHCcCcc
Confidence 35999999999995 999999999999999874
No 246
>COG3355 Predicted transcriptional regulator [Transcription]
Probab=58.41 E-value=1.2e+02 Score=26.10 Aligned_cols=84 Identities=8% Similarity=0.180 Sum_probs=65.4
Q ss_pred HHHHhccccccccHHhHHHHcCCChHHHHHHHHHHHHcCccce-Eec-CCCCeEEEecCCchhHHHHHHHHHHhhHHHHH
Q 013559 342 ALIQYTHPFVSVDLHMMANAFKTSVAGIEKELEALITDNQIQA-RID-SHNKILYARHADQRNATFQRVLQTGSEFDQDV 419 (441)
Q Consensus 342 ~i~qy~~pYs~I~L~~mA~~fg~s~~~~E~~L~~LI~~g~L~a-kID-~~~gvv~~~~~d~r~~~~~~~i~~~~~~~~~~ 419 (441)
++..++++..-.|.+.+|+.+|.+-..+.+-|-+|+..|-+.= |+- ..-|-.+.+.|-+...+.+.+.+.-+......
T Consensus 32 v~~~LL~~~~~~tvdelae~lnr~rStv~rsl~~L~~~GlV~Rek~~~~~Ggy~yiY~~i~~ee~k~~i~~~l~~w~~~~ 111 (126)
T COG3355 32 VYKALLEENGPLTVDELAEILNRSRSTVYRSLQNLLEAGLVEREKVNLKGGGYYYLYKPIDPEEIKKKILKDLDEWYDKM 111 (126)
T ss_pred HHHHHHhhcCCcCHHHHHHHHCccHHHHHHHHHHHHHcCCeeeeeeccCCCceeEEEecCCHHHHHHHHHHHHHHHHHHH
Confidence 3444444578899999999999999999999999999998853 333 56678888888888888888888877776666
Q ss_pred HHHHHH
Q 013559 420 RAMLLR 425 (441)
Q Consensus 420 ~~l~lR 425 (441)
..++-.
T Consensus 112 ~~~i~~ 117 (126)
T COG3355 112 KQLIEE 117 (126)
T ss_pred HHHHHH
Confidence 665544
No 247
>TIGR03879 near_KaiC_dom probable regulatory domain. This model describes a common domain shared by two different families of proteins, each of which occurs regularly next to its corresponding partner family, a probable regulatory with homology to KaiC. By implication, this protein family likely is also involved in sensory transduction and/or regulation.
Probab=58.12 E-value=9.9 Score=29.47 Aligned_cols=33 Identities=6% Similarity=0.056 Sum_probs=30.3
Q ss_pred cccccHHhHHHHcCCChHHHHHHHHHHHHcCcc
Q 013559 350 FVSVDLHMMANAFKTSVAGIEKELEALITDNQI 382 (441)
Q Consensus 350 Ys~I~L~~mA~~fg~s~~~~E~~L~~LI~~g~L 382 (441)
+.-.+...+|+.+|+|+..+..++..+...|.+
T Consensus 30 ~eGlS~kEIAe~LGIS~~TVk~~l~~~~~~~~~ 62 (73)
T TIGR03879 30 EAGKTASEIAEELGRTEQTVRNHLKGETKAGGL 62 (73)
T ss_pred HcCCCHHHHHHHHCcCHHHHHHHHhcCcccchH
Confidence 588899999999999999999999998888876
No 248
>cd00131 PAX Paired Box domain
Probab=57.59 E-value=23 Score=30.44 Aligned_cols=45 Identities=13% Similarity=0.155 Sum_probs=39.0
Q ss_pred HHHHHHHHHhccccccccHHhHHHHcCCChHHHHHHHHHHHHcCccce
Q 013559 337 QIRNKALIQYTHPFVSVDLHMMANAFKTSVAGIEKELEALITDNQIQA 384 (441)
Q Consensus 337 ~iR~~~i~qy~~pYs~I~L~~mA~~fg~s~~~~E~~L~~LI~~g~L~a 384 (441)
..|.+++.-| ..-.+...+|+.||+|...+-+|+.++-..|.+..
T Consensus 21 d~R~rIv~~~---~~G~s~~~iA~~~~Vs~~tV~r~i~r~~e~G~v~p 65 (128)
T cd00131 21 SIRQRIVELA---QSGIRPCDISRQLRVSHGCVSKILNRYYETGSIRP 65 (128)
T ss_pred HHHHHHHHHH---HcCCCHHHHHHHHCcCHHHHHHHHHHHHHcCCcCC
Confidence 4677888766 46789999999999999999999999999998764
No 249
>COG2118 DNA-binding protein [General function prediction only]
Probab=57.58 E-value=11 Score=31.65 Aligned_cols=53 Identities=19% Similarity=0.176 Sum_probs=38.1
Q ss_pred HHHHHHHHHHHhccccccccHHhHHHHcCCChHHHHHHHHHHHHcCccceEec
Q 013559 335 YDQIRNKALIQYTHPFVSVDLHMMANAFKTSVAGIEKELEALITDNQIQARID 387 (441)
Q Consensus 335 ~~~iR~~~i~qy~~pYs~I~L~~mA~~fg~s~~~~E~~L~~LI~~g~L~akID 387 (441)
.+.-+.-++.|++.|=.+=.|..++=.=-==.+.+|..|..|+..|+|..+||
T Consensus 38 ~eaqkqaiLrqiLtpeAreRL~~irLvRPe~AeavE~qLi~LaqtGri~~~I~ 90 (116)
T COG2118 38 EEAQKQAILRQILTPEARERLARVRLVRPELAEAVENQLIQLAQTGRITHKID 90 (116)
T ss_pred HHHHHHHHHHHHCCHHHHHHHHHhhhcCHHHHHHHHHHHHHHHHcCCCCCCCC
Confidence 44566677888888877666655542111114578999999999999999997
No 250
>TIGR02812 fadR_gamma fatty acid metabolism transcriptional regulator FadR. Members of this family are FadR, a transcriptional regulator of fatty acid metabolism, including both biosynthesis and beta-oxidation. It is found exclusively in a subset of Gammaproteobacteria, with strictly one copy per genome. It has an N-terminal DNA-binding domain and a less well conserved C-terminal long chain acyl-CoA-binding domain. FadR from this family heterologously expressed in Escherichia coli show differences in regulatory response and fatty acid binding profiles. The family is nevertheless designated equivalog, as all member proteins have at least nominally the same function.
Probab=57.57 E-value=1.2e+02 Score=28.41 Aligned_cols=64 Identities=9% Similarity=0.020 Sum_probs=55.8
Q ss_pred HHHHHHHHHHHHHHHhccccccc-cHHhHHHHcCCChHHHHHHHHHHHHcCccceEecCCCCeEEEe
Q 013559 331 VETLYDQIRNKALIQYTHPFVSV-DLHMMANAFKTSVAGIEKELEALITDNQIQARIDSHNKILYAR 396 (441)
Q Consensus 331 ~~~l~~~iR~~~i~qy~~pYs~I-~L~~mA~~fg~s~~~~E~~L~~LI~~g~L~akID~~~gvv~~~ 396 (441)
.+..++.||..++..-+.|=..+ +-..||+.||||-.-+-.-|..|-.+|-|. +-+..|+.+..
T Consensus 8 ~~~v~~~l~~~I~~g~l~pG~~LpsE~~La~~lgVSRtpVREAL~~Le~eGlV~--~~~~~G~~V~~ 72 (235)
T TIGR02812 8 AGFAEEYIVESIWNNRFPPGSILPAERELSELIGVTRTTLREVLQRLARDGWLT--IQHGKPTKVNN 72 (235)
T ss_pred HHHHHHHHHHHHHcCCCCCCCcCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCEE--EeCCCccEecC
Confidence 45678899999999999999999 899999999999999999999999999986 44456776654
No 251
>PF04053 Coatomer_WDAD: Coatomer WD associated region ; InterPro: IPR006692 Proteins synthesised on the ribosome and processed in the endoplasmic reticulum are transported from the Golgi apparatus to the trans-Golgi network (TGN), and from there via small carrier vesicles to their final destination compartment. This traffic is bidirectional, to ensure that proteins required to form vesicles are recycled. Vesicles have specific coat proteins (such as clathrin or coatomer) that are important for cargo selection and direction of transfer []. While clathrin mediates endocytic protein transport, and transport from ER to Golgi, coatomers primarily mediate intra-Golgi transport, as well as the reverse Golgi to ER transport of dilysine-tagged proteins []. For example, the coatomer COP1 (coat protein complex 1) is responsible for reverse transport of recycled proteins from Golgi and pre-Golgi compartments back to the ER, while COPII buds vesicles from the ER to the Golgi []. Coatomers reversibly associate with Golgi (non-clathrin-coated) vesicles to mediate protein transport and for budding from Golgi membranes []. Activated small guanine triphosphatases (GTPases) attract coat proteins to specific membrane export sites, thereby linking coatomers to export cargos. As coat proteins polymerise, vesicles are formed and budded from membrane-bound organelles. Coatomer complexes also influence Golgi structural integrity, as well as the processing, activity, and endocytic recycling of LDL receptors. In mammals, coatomer complexes can only be recruited by membranes associated to ADP-ribosylation factors (ARFs), which are small GTP-binding proteins. Coatomer complexes are hetero-oligomers composed of at least an alpha, beta, beta', gamma, delta, epsilon and zeta subunits. This entry represents the WD-associated region found in coatomer subunits alpha, beta and beta' subunits. The alpha-subunit (RET1P) of the coatomer complex in Saccharomyces cerevisiae (Baker's yeast), participates in membrane transport between the endoplasmic reticulum and Golgi apparatus. The protein contains six WD-40 repeat motifs in its N-terminal region []. More information about these proteins can be found at Protein of the Month: Clathrin [].; GO: 0005198 structural molecule activity, 0006886 intracellular protein transport, 0016192 vesicle-mediated transport, 0030117 membrane coat; PDB: 3MKQ_B.
Probab=57.19 E-value=77 Score=33.32 Aligned_cols=132 Identities=14% Similarity=0.140 Sum_probs=81.0
Q ss_pred HhHHHHHHHHcCCHHHHHHHHHHHHhhhcCchhHHHHHHHHHHHHHHhcCHHHHHhHHHHHhcccccCChhhhhhHHHHH
Q 013559 142 YNDFGDFYYAHGALGDAFKSYVRTRDYCTTSKHIIHMCMSAILVSIEMGQFTHVTSYVSKAEQTPEALEPVTIAKLRCAA 221 (441)
Q Consensus 142 ~~~la~~~~~~Gd~~~A~~~~~~~r~~~~~~~~~~~~~l~~i~~~i~~~~~~~~~~~~~ka~~~~~~~d~~~~~~l~~~~ 221 (441)
....+.|+.+.|-.+.|+.. ++++.++++ +++..||.+.|.+... .+.+..-|. .-
T Consensus 298 ~~~i~~fL~~~G~~e~AL~~-------~~D~~~rFe-------LAl~lg~L~~A~~~a~---~~~~~~~W~-------~L 353 (443)
T PF04053_consen 298 GQSIARFLEKKGYPELALQF-------VTDPDHRFE-------LALQLGNLDIALEIAK---ELDDPEKWK-------QL 353 (443)
T ss_dssp HHHHHHHHHHTT-HHHHHHH-------SS-HHHHHH-------HHHHCT-HHHHHHHCC---CCSTHHHHH-------HH
T ss_pred HHHHHHHHHHCCCHHHHHhh-------cCChHHHhH-------HHHhcCCHHHHHHHHH---hcCcHHHHH-------HH
Confidence 45778999999999988864 456666554 5677888887765322 222222343 23
Q ss_pred HHHhcccccHHHHHHHHHhcCcCCCCCchhhhcHHHHHHHHHHHHHhcCChHHHHHhcccCHhhHhhhccchHHHHHHHH
Q 013559 222 GLAHLEARKYKLAARKFLEVGPDLGNSYNEVIAAQDVATYGGLCALASFDRAELKSKVIDNVNFRNFLELVPEVRELIND 301 (441)
Q Consensus 222 gl~~l~~r~y~~Aa~~Fl~~~~t~~~~~~el~s~~d~~~Y~~l~al~s~~R~eLk~~vl~~~~~~~~le~~p~~~~ll~~ 301 (441)
|-..|.+|++..|...|..+-. +..++ +...++.++..|++ +.+-. .+.......+..+
T Consensus 354 g~~AL~~g~~~lAe~c~~k~~d-----~~~L~----------lLy~~~g~~~~L~k-l~~~a-----~~~~~~n~af~~~ 412 (443)
T PF04053_consen 354 GDEALRQGNIELAEECYQKAKD-----FSGLL----------LLYSSTGDREKLSK-LAKIA-----EERGDINIAFQAA 412 (443)
T ss_dssp HHHHHHTTBHHHHHHHHHHCT------HHHHH----------HHHHHCT-HHHHHH-HHHHH-----HHTT-HHHHHHHH
T ss_pred HHHHHHcCCHHHHHHHHHhhcC-----ccccH----------HHHHHhCCHHHHHH-HHHHH-----HHccCHHHHHHHH
Confidence 5567889999999999988742 23222 33466777777765 22111 1122345677788
Q ss_pred HhcCCHHHHHHHHHHhH
Q 013559 302 FYSSRYASCLDYLGNLK 318 (441)
Q Consensus 302 f~~~~y~~~~~~L~~~~ 318 (441)
|+..++.+|.+.|.+..
T Consensus 413 ~~lgd~~~cv~lL~~~~ 429 (443)
T PF04053_consen 413 LLLGDVEECVDLLIETG 429 (443)
T ss_dssp HHHT-HHHHHHHHHHTT
T ss_pred HHcCCHHHHHHHHHHcC
Confidence 89999999999998753
No 252
>PF13404 HTH_AsnC-type: AsnC-type helix-turn-helix domain; PDB: 2ZNY_E 2ZNZ_G 1RI7_A 2CYY_A 2E1C_A 2VC1_B 2QZ8_A 2W29_C 2IVM_B 2VBX_B ....
Probab=57.06 E-value=20 Score=24.49 Aligned_cols=35 Identities=9% Similarity=0.126 Sum_probs=24.3
Q ss_pred HHHHhccccccccHHhHHHHcCCChHHHHHHHHHH
Q 013559 342 ALIQYTHPFVSVDLHMMANAFKTSVAGIEKELEAL 376 (441)
Q Consensus 342 ~i~qy~~pYs~I~L~~mA~~fg~s~~~~E~~L~~L 376 (441)
.|...+..-.+.+...+|+.+|+|...+-+-+.+|
T Consensus 7 ~Il~~Lq~d~r~s~~~la~~lglS~~~v~~Ri~rL 41 (42)
T PF13404_consen 7 KILRLLQEDGRRSYAELAEELGLSESTVRRRIRRL 41 (42)
T ss_dssp HHHHHHHH-TTS-HHHHHHHHTS-HHHHHHHHHHH
T ss_pred HHHHHHHHcCCccHHHHHHHHCcCHHHHHHHHHHh
Confidence 34444444589999999999999999987776654
No 253
>COG2956 Predicted N-acetylglucosaminyl transferase [Carbohydrate transport and metabolism]
Probab=57.01 E-value=2.2e+02 Score=28.76 Aligned_cols=98 Identities=13% Similarity=0.106 Sum_probs=69.0
Q ss_pred HHhHHHHHHHHcCCHHHHHHHHHHHHhhhcC--chhHHHHHHHHHHHHHHhcCHHHHHhHHHHHhcccccCChhhhhhHH
Q 013559 141 GYNDFGDFYYAHGALGDAFKSYVRTRDYCTT--SKHIIHMCMSAILVSIEMGQFTHVTSYVSKAEQTPEALEPVTIAKLR 218 (441)
Q Consensus 141 ~~~~la~~~~~~Gd~~~A~~~~~~~r~~~~~--~~~~~~~~l~~i~~~i~~~~~~~~~~~~~ka~~~~~~~d~~~~~~l~ 218 (441)
++..|..+|-...++.+|+++-.++...... .-++..++-.+...+....|.+.+...+.||-..--. -.+-.
T Consensus 143 AlqqLl~IYQ~treW~KAId~A~~L~k~~~q~~~~eIAqfyCELAq~~~~~~~~d~A~~~l~kAlqa~~~-----cvRAs 217 (389)
T COG2956 143 ALQQLLNIYQATREWEKAIDVAERLVKLGGQTYRVEIAQFYCELAQQALASSDVDRARELLKKALQADKK-----CVRAS 217 (389)
T ss_pred HHHHHHHHHHHhhHHHHHHHHHHHHHHcCCccchhHHHHHHHHHHHHHhhhhhHHHHHHHHHHHHhhCcc-----ceehh
Confidence 7888999999999999999988776444321 2233444555555667777888888888887554221 12344
Q ss_pred HHHHHHhcccccHHHHHHHHHhcCc
Q 013559 219 CAAGLAHLEARKYKLAARKFLEVGP 243 (441)
Q Consensus 219 ~~~gl~~l~~r~y~~Aa~~Fl~~~~ 243 (441)
+..|-..+..|+|..|.+.+-.+..
T Consensus 218 i~lG~v~~~~g~y~~AV~~~e~v~e 242 (389)
T COG2956 218 IILGRVELAKGDYQKAVEALERVLE 242 (389)
T ss_pred hhhhHHHHhccchHHHHHHHHHHHH
Confidence 6788899999999999888776654
No 254
>KOG2235 consensus Uncharacterized conserved protein [Function unknown]
Probab=56.56 E-value=35 Score=36.88 Aligned_cols=62 Identities=18% Similarity=0.296 Sum_probs=53.3
Q ss_pred HHHHHHHHHHHHHHHHHHhccccccccHHhHHHHcCCChHHHHHHHHHHHHcCccceEecCCCCeEEEe
Q 013559 328 HDHVETLYDQIRNKALIQYTHPFVSVDLHMMANAFKTSVAGIEKELEALITDNQIQARIDSHNKILYAR 396 (441)
Q Consensus 328 ~~h~~~l~~~iR~~~i~qy~~pYs~I~L~~mA~~fg~s~~~~E~~L~~LI~~g~L~akID~~~gvv~~~ 396 (441)
.+.++.+-++|+.+.-++ ..|++..+|+.|+++.+++...|..=....-+.|++|. |++++.
T Consensus 114 e~Y~d~iaeEinekLqE~-----gqvtiaeLakq~dl~sellqs~l~ek~lg~iikgr~dg--gviyT~ 175 (776)
T KOG2235|consen 114 EEYVDRIAEEINEKLQEQ-----GQVTIAELAKQWDLPSELLQSLLIEKLLGSIIKGRVDG--GVIYTS 175 (776)
T ss_pred HHHHHHHHHHHHHHHHHh-----cchHHHHHHHhcCCcHHHHHHHHHHHhhccceeeeecC--CEEeeH
Confidence 457888888888887764 78999999999999999999999888777778999998 888775
No 255
>KOG3250 consensus COP9 signalosome, subunit CSN7 [Posttranslational modification, protein turnover, chaperones; Signal transduction mechanisms]
Probab=56.33 E-value=61 Score=30.56 Aligned_cols=121 Identities=12% Similarity=0.143 Sum_probs=72.0
Q ss_pred hHHHHHHHHHhcCCHHHHHHHHHHhHHhhhhchhHHHHHHHHHHHHHHHHHHHhccccccccHHhHHHHcCC-ChHHHHH
Q 013559 293 PEVRELINDFYSSRYASCLDYLGNLKANLLLDIHLHDHVETLYDQIRNKALIQYTHPFVSVDLHMMANAFKT-SVAGIEK 371 (441)
Q Consensus 293 p~~~~ll~~f~~~~y~~~~~~L~~~~~~l~~D~~L~~h~~~l~~~iR~~~i~qy~~pYs~I~L~~mA~~fg~-s~~~~E~ 371 (441)
..+.++++-|..+.|..+...-.. -+.|..+..+. ++.+-+......-+++--..+=..+.+ ++-++|.
T Consensus 60 sa~lrlL~lFa~Gt~~Dy~aea~r-lp~Ls~~q~~k---------Lk~ltV~slas~~k~lpy~~Ll~~l~~~nvrelEd 129 (258)
T KOG3250|consen 60 SAYLRLLELFAYGTYRDYSAEALR-LPKLSLAQLNK---------LKHLTVVSLASFEKCLPYLVLLRLLPSRNVRELED 129 (258)
T ss_pred HHHHHHHHHHhcCchhhhhhhhhc-CCCCCHHHHHh---------hhcceehhhhhhchhhhHHHHHhhccCCchhHHHH
Confidence 357889999999888776433211 12233222211 111112222222344444555667777 5789999
Q ss_pred HHHHHHHcCccceEecCCCCeEEEec---CCchhHHHHHHHHHHhhHHHHHHHHH
Q 013559 372 ELEALITDNQIQARIDSHNKILYARH---ADQRNATFQRVLQTGSEFDQDVRAML 423 (441)
Q Consensus 372 ~L~~LI~~g~L~akID~~~gvv~~~~---~d~r~~~~~~~i~~~~~~~~~~~~l~ 423 (441)
.|.+.+-++-|.+|||+.+..++..= .|-+.........+-+.+..+...++
T Consensus 130 ~iieamya~IlrGkldqr~q~leV~faigRdlr~k~i~nm~~TL~~w~~~cenvL 184 (258)
T KOG3250|consen 130 LIIEAMYADILRGKLDQRNQTLEVDFAIGRDLRSKDIDNMKYTLDEWCEGCENVL 184 (258)
T ss_pred HHHHHHHHHHHHhhHHhhcceEeechhhcccccHhHHHHHHHHHHHHHHHHHHHH
Confidence 99999999999999999999998853 23344444444444455554444443
No 256
>PRK10225 DNA-binding transcriptional repressor UxuR; Provisional
Probab=55.96 E-value=44 Score=31.93 Aligned_cols=65 Identities=11% Similarity=0.077 Sum_probs=56.5
Q ss_pred HHHHHHHHHHHHHHHhccccccc-cHHhHHHHcCCChHHHHHHHHHHHHcCccceEecCCCCeEEEec
Q 013559 331 VETLYDQIRNKALIQYTHPFVSV-DLHMMANAFKTSVAGIEKELEALITDNQIQARIDSHNKILYARH 397 (441)
Q Consensus 331 ~~~l~~~iR~~~i~qy~~pYs~I-~L~~mA~~fg~s~~~~E~~L~~LI~~g~L~akID~~~gvv~~~~ 397 (441)
.+.+++.||..++..-+.|=..+ +-..||+.||||..-+-+-|..|-..|-|. +-+..|+.+...
T Consensus 11 ~~~v~~~l~~~I~~g~l~pG~~LpsE~eLa~~~gVSRtpVREAL~~L~~eGlV~--~~~~~G~~V~~~ 76 (257)
T PRK10225 11 YQEVGAMIRDLIIKTPYNPGERLPPEREIAEMLDVTRTVVREALIMLEIKGLVE--VRRGAGIYVLDS 76 (257)
T ss_pred HHHHHHHHHHHHHhCCCCCCCcCcCHHHHHHHhCCCHHHHHHHHHHHHHCCCEE--EecCCEEEEeCC
Confidence 56889999999999999999999 699999999999999999999999999986 334567766553
No 257
>TIGR01764 excise DNA binding domain, excisionase family. An excisionase, or Xis protein, is a small protein that binds and promotes excisive recombination; it is not enzymatically active. This model represents a number of putative excisionases and related proteins from temperate phage, plasmids, and transposons, as well as DNA binding domains of other proteins, such as a DNA modification methylase. This model identifies mostly small proteins and N-terminal regions of large proteins, but some proteins appear to have two copies. This domain appears similar, in both sequence and predicted secondary structure (PSIPRED) to the MerR family of transcriptional regulators (pfam00376).
Probab=55.82 E-value=21 Score=24.12 Aligned_cols=31 Identities=16% Similarity=0.138 Sum_probs=24.6
Q ss_pred ccHHhHHHHcCCChHHHHHHHHHHHHcCccceEec
Q 013559 353 VDLHMMANAFKTSVAGIEKELEALITDNQIQARID 387 (441)
Q Consensus 353 I~L~~mA~~fg~s~~~~E~~L~~LI~~g~L~akID 387 (441)
+++..+|+.||++...+. ++|.+|+|.+...
T Consensus 2 lt~~e~a~~lgis~~ti~----~~~~~g~i~~~~~ 32 (49)
T TIGR01764 2 LTVEEAAEYLGVSKDTVY----RLIHEGELPAYRV 32 (49)
T ss_pred CCHHHHHHHHCCCHHHHH----HHHHcCCCCeEEe
Confidence 478999999999988754 4568899987543
No 258
>PF12840 HTH_20: Helix-turn-helix domain; PDB: 1ULY_A 2CWE_A 1Y0U_B 2QUF_B 2QLZ_C 2OQG_B 2ZKZ_C 3PQK_A 3PQJ_D 3F6O_B ....
Probab=55.75 E-value=35 Score=24.88 Aligned_cols=50 Identities=18% Similarity=0.160 Sum_probs=38.1
Q ss_pred HHHHHHHHHHHHhccccccccHHhHHHHcCCChHHHHHHHHHHHHcCccce
Q 013559 334 LYDQIRNKALIQYTHPFVSVDLHMMANAFKTSVAGIEKELEALITDNQIQA 384 (441)
Q Consensus 334 l~~~iR~~~i~qy~~pYs~I~L~~mA~~fg~s~~~~E~~L~~LI~~g~L~a 384 (441)
|-+-.|.+++. ++......+...+|+.||++...+-..|..|...|-|..
T Consensus 7 L~~p~R~~Il~-~L~~~~~~t~~ela~~l~~~~~t~s~hL~~L~~aGli~~ 56 (61)
T PF12840_consen 7 LSDPTRLRILR-LLASNGPMTVSELAEELGISQSTVSYHLKKLEEAGLIEV 56 (61)
T ss_dssp HTSHHHHHHHH-HHHHCSTBEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEE
T ss_pred hCCHHHHHHHH-HHhcCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCeEE
Confidence 33444544444 446678999999999999999999999999999887754
No 259
>PF13414 TPR_11: TPR repeat; PDB: 2HO1_B 2FI7_B 2DBA_A 3Q4A_B 2C2L_D 3Q47_B 3Q49_B 2PL2_B 3IEG_B 2FBN_A ....
Probab=55.62 E-value=42 Score=24.46 Aligned_cols=61 Identities=16% Similarity=0.198 Sum_probs=44.8
Q ss_pred HHHHHHHHHHHHhcCHHHHHhHHHHHhcccccCChhhhhhHHHHHHHHhcccc-cHHHHHHHHHhcC
Q 013559 177 HMCMSAILVSIEMGQFTHVTSYVSKAEQTPEALEPVTIAKLRCAAGLAHLEAR-KYKLAARKFLEVG 242 (441)
Q Consensus 177 ~~~l~~i~~~i~~~~~~~~~~~~~ka~~~~~~~d~~~~~~l~~~~gl~~l~~r-~y~~Aa~~Fl~~~ 242 (441)
..+.....+.+..|+|+.+..+..++-..- ..++ .+...-|+.++..+ +|.+|...|-.+.
T Consensus 4 ~~~~~~g~~~~~~~~~~~A~~~~~~ai~~~-p~~~----~~~~~~g~~~~~~~~~~~~A~~~~~~al 65 (69)
T PF13414_consen 4 EAWYNLGQIYFQQGDYEEAIEYFEKAIELD-PNNA----EAYYNLGLAYMKLGKDYEEAIEDFEKAL 65 (69)
T ss_dssp HHHHHHHHHHHHTTHHHHHHHHHHHHHHHS-TTHH----HHHHHHHHHHHHTTTHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHcCCHHHHHHHHHHHHHcC-CCCH----HHHHHHHHHHHHhCccHHHHHHHHHHHH
Confidence 344556667788999999999999987752 1122 34466788888898 7999998887654
No 260
>PF12862 Apc5: Anaphase-promoting complex subunit 5
Probab=55.30 E-value=84 Score=25.07 Aligned_cols=46 Identities=7% Similarity=0.156 Sum_probs=33.1
Q ss_pred HHHhHHhHHHHHHHHcCCHHHHHHHHHHHHhhhc--CchhHHHHHHHH
Q 013559 137 SIRMGYNDFGDFYYAHGALGDAFKSYVRTRDYCT--TSKHIIHMCMSA 182 (441)
Q Consensus 137 sir~~~~~la~~~~~~Gd~~~A~~~~~~~r~~~~--~~~~~~~~~l~~ 182 (441)
....+...+|.++...|++++|.+.+.+...... .....+..++.|
T Consensus 39 ~~~~all~lA~~~~~~G~~~~A~~~l~eAi~~Are~~D~~~l~~al~~ 86 (94)
T PF12862_consen 39 GLAYALLNLAELHRRFGHYEEALQALEEAIRLARENGDRRCLAYALSW 86 (94)
T ss_pred HHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHCCHHHHHHHHHH
Confidence 4455788999999999999999999998766543 233334444443
No 261
>PF09613 HrpB1_HrpK: Bacterial type III secretion protein (HrpB1_HrpK); InterPro: IPR013394 This family of proteins is encoded by genes found within type III secretion operons in a limited range of species including Xanthomonas, Ralstonia and Burkholderia.
Probab=55.26 E-value=47 Score=29.86 Aligned_cols=68 Identities=16% Similarity=0.230 Sum_probs=49.2
Q ss_pred CchhHHHHHHHHHHHHHHhcCHHHHHhHHHHHhcccccCChhhhhhHHHHHHHHhcccccHHHHHHHHHhcCc
Q 013559 171 TSKHIIHMCMSAILVSIEMGQFTHVTSYVSKAEQTPEALEPVTIAKLRCAAGLAHLEARKYKLAARKFLEVGP 243 (441)
Q Consensus 171 ~~~~~~~~~l~~i~~~i~~~~~~~~~~~~~ka~~~~~~~d~~~~~~l~~~~gl~~l~~r~y~~Aa~~Fl~~~~ 243 (441)
.++..+.-++.++.+++..++.+.+...+.-++-+- |. ...+..+.|..++..|+|.+|...|-++..
T Consensus 5 C~~~iv~gLie~~~~al~~~~~~D~e~lL~ALrvLR----P~-~~e~~~~~~~l~i~r~~w~dA~rlLr~l~~ 72 (160)
T PF09613_consen 5 CSDEIVGGLIEVLSVALRLGDPDDAEALLDALRVLR----PE-FPELDLFDGWLHIVRGDWDDALRLLRELEE 72 (160)
T ss_pred CcHHHHHHHHHHHHHHHccCChHHHHHHHHHHHHhC----CC-chHHHHHHHHHHHHhCCHHHHHHHHHHHhc
Confidence 455677778888888888888887777666655541 11 124567888888999999999888888754
No 262
>PRK11920 rirA iron-responsive transcriptional regulator; Reviewed
Probab=55.20 E-value=49 Score=29.32 Aligned_cols=61 Identities=15% Similarity=0.122 Sum_probs=43.7
Q ss_pred ccccccHHhHHHHcCCChHHHHHHHHHHHHcCccceEecCCCCeEEEecCCchhHHHHHHHHH
Q 013559 349 PFVSVDLHMMANAFKTSVAGIEKELEALITDNQIQARIDSHNKILYARHADQRNATFQRVLQT 411 (441)
Q Consensus 349 pYs~I~L~~mA~~fg~s~~~~E~~L~~LI~~g~L~akID~~~gvv~~~~~d~r~~~~~~~i~~ 411 (441)
+-..++.+.||+..|+|..++++-+..|...|-|...==..-|..-..+| ..-+..++++.
T Consensus 21 ~~~~~s~~eIA~~~~is~~~L~kIl~~L~~aGlv~S~rG~~GGy~La~~p--~eItl~dIi~a 81 (153)
T PRK11920 21 DGKLSRIPEIARAYGVSELFLFKILQPLVEAGLVETVRGRNGGVRLGRPA--ADISLFDVVRV 81 (153)
T ss_pred CCCcCcHHHHHHHHCcCHHHHHHHHHHHHHCCCEEeecCCCCCeeecCCH--HHCcHHHHHHH
Confidence 33568999999999999999999999999999887655444454444444 22334444443
No 263
>TIGR02944 suf_reg_Xantho FeS assembly SUF system regulator, gammaproteobacterial. The SUF system is an oxygen-resistant iron-sulfur cluster assembly system found in both aerobes and facultative anaerobes. Its presence appears to be a marker of oxygen tolerance; strict anaerobes and microaerophiles tend to have different FeS cluster biosynthesis systems. Members of this protein family belong to the rrf2 family of transcriptional regulators and are found, typically, as the first gene of a SUF operon. It is found only in a subset of genomes that encode the SUF system, including the genus Xanthomonas. The conserved location suggests an autoregulatory role.
Probab=55.04 E-value=40 Score=28.64 Aligned_cols=61 Identities=13% Similarity=0.130 Sum_probs=43.6
Q ss_pred ccccHHhHHHHcCCChHHHHHHHHHHHHcCccceEecCCCCeEEEecCCchhHHHHHHHHHHh
Q 013559 351 VSVDLHMMANAFKTSVAGIEKELEALITDNQIQARIDSHNKILYARHADQRNATFQRVLQTGS 413 (441)
Q Consensus 351 s~I~L~~mA~~fg~s~~~~E~~L~~LI~~g~L~akID~~~gvv~~~~~d~r~~~~~~~i~~~~ 413 (441)
..++...||+.+|+|...+.+-|..|...|-|...-....|......+ ......++++..+
T Consensus 24 ~~~s~~eia~~l~is~~~v~~~l~~L~~~Gli~~~~g~~ggy~l~~~~--~~it~~~v~~~l~ 84 (130)
T TIGR02944 24 QPYSAAEIAEQTGLNAPTVSKILKQLSLAGIVTSKRGVEGGYTLARAP--RDITVADIVKAVE 84 (130)
T ss_pred CCccHHHHHHHHCcCHHHHHHHHHHHHHCCcEEecCCCCCChhhcCCc--cccCHHHHHHHHc
Confidence 579999999999999999999999999999997654333343333323 2333556655543
No 264
>PF00325 Crp: Bacterial regulatory proteins, crp family; InterPro: IPR001808 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. This family groups together a range of proteins, including anr, crp, clp, cysR, fixK, flp, fnr, fnrN, hlyX and ntcA [, ]. Within this family, the HTH motif is situated towards the C terminus.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 2OZ6_A 1CGP_B 2GZW_C 1O3T_B 3ROU_A 2CGP_A 3RDI_A 1I5Z_A 3IYD_H 3FWE_B ....
Probab=54.68 E-value=24 Score=22.77 Aligned_cols=30 Identities=13% Similarity=0.151 Sum_probs=24.1
Q ss_pred ccHHhHHHHcCCChHHHHHHHHHHHHcCcc
Q 013559 353 VDLHMMANAFKTSVAGIEKELEALITDNQI 382 (441)
Q Consensus 353 I~L~~mA~~fg~s~~~~E~~L~~LI~~g~L 382 (441)
++-..||..+|++.+.+-+.+.+|-.+|-|
T Consensus 3 mtr~diA~~lG~t~ETVSR~l~~l~~~glI 32 (32)
T PF00325_consen 3 MTRQDIADYLGLTRETVSRILKKLERQGLI 32 (32)
T ss_dssp --HHHHHHHHTS-HHHHHHHHHHHHHTTSE
T ss_pred cCHHHHHHHhCCcHHHHHHHHHHHHHcCCC
Confidence 566889999999999999999999888754
No 265
>KOG4340 consensus Uncharacterized conserved protein [Function unknown]
Probab=54.68 E-value=2.4e+02 Score=28.31 Aligned_cols=136 Identities=13% Similarity=0.164 Sum_probs=72.8
Q ss_pred CcCCHHHH-hhccCch--hhHHHHHHHHhcCCCchh------------HHHHHHHHHHHHHhcCChHHH---HHHHHHhh
Q 013559 33 EQLDVEAY-ASLYQGR--TKITRLMFIADHCDIASM------------QLEALRMAYDEIKKGENTQLF---REVVKKID 94 (441)
Q Consensus 33 ~~~Dl~~y-~~~y~g~--~~i~rL~fi~~~~~~~~~------------~~~a~~~~~~~lk~t~~~~~Y---~~~~~~l~ 94 (441)
++.-|.+- +++-.|+ .-+..|.|+.... |.. ..+-+..|.+.+-++....|| ..+++-+.
T Consensus 276 DPvTLHN~Al~n~~~~p~~g~~KLqFLL~~n--PfP~ETFANlLllyCKNeyf~lAADvLAEn~~lTyk~L~~Yly~LLd 353 (459)
T KOG4340|consen 276 DPVTLHNQALMNMDARPTEGFEKLQFLLQQN--PFPPETFANLLLLYCKNEYFDLAADVLAENAHLTYKFLTPYLYDLLD 353 (459)
T ss_pred CchhhhHHHHhcccCCccccHHHHHHHHhcC--CCChHHHHHHHHHHhhhHHHhHHHHHHhhCcchhHHHhhHHHHHHHH
Confidence 44455444 6666664 3577777877764 322 345666777888776555444 12222222
Q ss_pred ccCCCCCcCCHH----HHHHHHHHHHHHHHHHHHHHHHHHhhhhHHHHHh--------------HHhHHHHHHHHcCCHH
Q 013559 95 GRLGPNYAMDEA----WCDSVDRRAEQRKEKLENELNAYRTNLIKESIRM--------------GYNDFGDFYYAHGALG 156 (441)
Q Consensus 95 ~~~~~~~~~D~~----~~~~~~~~~~~~~~~Le~el~~~~~n~~~esir~--------------~~~~la~~~~~~Gd~~ 156 (441)
... ..+..++ -++.+...-..++.++-.++...+++.-++++|. ..+..|++|.+-.||.
T Consensus 354 aLI--t~qT~pEea~KKL~~La~~l~~kLRklAi~vQe~r~~~dd~a~R~ai~~Yd~~LE~YLPVlMa~AkiyW~~~Dy~ 431 (459)
T KOG4340|consen 354 ALI--TCQTAPEEAFKKLDGLAGMLTEKLRKLAIQVQEARHNRDDEAIRKAVNEYDETLEKYLPVLMAQAKIYWNLEDYP 431 (459)
T ss_pred HHH--hCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcccHHHHHHHHHHHHHHHHHHHHHHHHHHHhhccccccH
Confidence 110 0111111 1222223333334444444444444444444444 3456688888888888
Q ss_pred HHHHHHHHHHhhhcCc
Q 013559 157 DAFKSYVRTRDYCTTS 172 (441)
Q Consensus 157 ~A~~~~~~~r~~~~~~ 172 (441)
.+-+.|....++|...
T Consensus 432 ~vEk~Fr~SvefC~eh 447 (459)
T KOG4340|consen 432 MVEKIFRKSVEFCNDH 447 (459)
T ss_pred HHHHHHHHHHhhhccc
Confidence 8888888888888643
No 266
>PF04733 Coatomer_E: Coatomer epsilon subunit; InterPro: IPR006822 Proteins synthesised on the ribosome and processed in the endoplasmic reticulum are transported from the Golgi apparatus to the trans-Golgi network (TGN), and from there via small carrier vesicles to their final destination compartment. This traffic is bidirectional, to ensure that proteins required to form vesicles are recycled. Vesicles have specific coat proteins (such as clathrin or coatomer) that are important for cargo selection and direction of transfer []. While clathrin mediates endocytic protein transport, and transport from ER to Golgi, coatomers primarily mediate intra-Golgi transport, as well as the reverse Golgi to ER transport of dilysine-tagged proteins []. For example, the coatomer COP1 (coat protein complex 1) is responsible for reverse transport of recycled proteins from Golgi and pre-Golgi compartments back to the ER, while COPII buds vesicles from the ER to the Golgi []. Coatomers reversibly associate with Golgi (non-clathrin-coated) vesicles to mediate protein transport and for budding from Golgi membranes []. Activated small guanine triphosphatases (GTPases) attract coat proteins to specific membrane export sites, thereby linking coatomers to export cargos. As coat proteins polymerise, vesicles are formed and budded from membrane-bound organelles. Coatomer complexes also influence Golgi structural integrity, as well as the processing, activity, and endocytic recycling of LDL receptors. In mammals, coatomer complexes can only be recruited by membranes associated to ADP-ribosylation factors (ARFs), which are small GTP-binding proteins. Coatomer complexes are hetero-oligomers composed of at least an alpha, beta, beta', gamma, delta, epsilon and zeta subunits. This entry represents the epsilon subunit of the coatomer complex, which is involved in the regulation of intracellular protein trafficking between the endoplasmic reticulum and the Golgi complex []. More information about these proteins can be found at Protein of the Month: Clathrin [].; GO: 0005198 structural molecule activity, 0006890 retrograde vesicle-mediated transport, Golgi to ER, 0030126 COPI vesicle coat; PDB: 3MV2_B 3MV3_F 3MKR_A.
Probab=54.50 E-value=72 Score=31.44 Aligned_cols=95 Identities=16% Similarity=0.175 Sum_probs=59.5
Q ss_pred HHhHHHHHHHHcC--CHHHHHHHHHHHHhhhcCchhHHHHHHHHHHHHHHhcCHHHHHhHHHHHhcccccCChhhhhhHH
Q 013559 141 GYNDFGDFYYAHG--ALGDAFKSYVRTRDYCTTSKHIIHMCMSAILVSIEMGQFTHVTSYVSKAEQTPEALEPVTIAKLR 218 (441)
Q Consensus 141 ~~~~la~~~~~~G--d~~~A~~~~~~~r~~~~~~~~~~~~~l~~i~~~i~~~~~~~~~~~~~ka~~~~~~~d~~~~~~l~ 218 (441)
..+.-|.+.+..| .+++|.-.|.++-+.++.+ ..+..++..+.+..|+|+.|...+..+-.. +..+++..
T Consensus 167 ~qLa~awv~l~~g~e~~~~A~y~f~El~~~~~~t---~~~lng~A~~~l~~~~~~eAe~~L~~al~~-~~~~~d~L---- 238 (290)
T PF04733_consen 167 TQLAEAWVNLATGGEKYQDAFYIFEELSDKFGST---PKLLNGLAVCHLQLGHYEEAEELLEEALEK-DPNDPDTL---- 238 (290)
T ss_dssp HHHHHHHHHHHHTTTCCCHHHHHHHHHHCCS--S---HHHHHHHHHHHHHCT-HHHHHHHHHHHCCC--CCHHHHH----
T ss_pred HHHHHHHHHHHhCchhHHHHHHHHHHHHhccCCC---HHHHHHHHHHHHHhCCHHHHHHHHHHHHHh-ccCCHHHH----
Confidence 4455555666666 5999999999987776433 344567778889999999999998886432 23344422
Q ss_pred HHHHHHhcccccHHHHHHHHHhcCc
Q 013559 219 CAAGLAHLEARKYKLAARKFLEVGP 243 (441)
Q Consensus 219 ~~~gl~~l~~r~y~~Aa~~Fl~~~~ 243 (441)
+-.+.+..+.|+-..+.+.+++-..
T Consensus 239 aNliv~~~~~gk~~~~~~~~l~qL~ 263 (290)
T PF04733_consen 239 ANLIVCSLHLGKPTEAAERYLSQLK 263 (290)
T ss_dssp HHHHHHHHHTT-TCHHHHHHHHHCH
T ss_pred HHHHHHHHHhCCChhHHHHHHHHHH
Confidence 2234445667776555666665543
No 267
>KOG2300 consensus Uncharacterized conserved protein [Function unknown]
Probab=54.30 E-value=1.7e+02 Score=31.11 Aligned_cols=120 Identities=11% Similarity=-0.034 Sum_probs=62.6
Q ss_pred HHhHHHHHHHHcCCHHHHHHHHHHHHhhhcCchhHHHHHHHHHHHHHHhcCHHHHHhHHHHHhccccc------CChhhh
Q 013559 141 GYNDFGDFYYAHGALGDAFKSYVRTRDYCTTSKHIIHMCMSAILVSIEMGQFTHVTSYVSKAEQTPEA------LEPVTI 214 (441)
Q Consensus 141 ~~~~la~~~~~~Gd~~~A~~~~~~~r~~~~~~~~~~~~~l~~i~~~i~~~~~~~~~~~~~ka~~~~~~------~d~~~~ 214 (441)
.++-+|-+-...|-|++|...+......+...+-.....++..-+++-.++-+ .+.++-+.+.. +.-.++
T Consensus 369 ih~LlGlys~sv~~~enAe~hf~~a~k~t~~~dl~a~~nlnlAi~YL~~~~~e----d~y~~ld~i~p~nt~s~ssq~l~ 444 (629)
T KOG2300|consen 369 IHMLLGLYSHSVNCYENAEFHFIEATKLTESIDLQAFCNLNLAISYLRIGDAE----DLYKALDLIGPLNTNSLSSQRLE 444 (629)
T ss_pred HHHHHhhHhhhcchHHHHHHHHHHHHHhhhHHHHHHHHHHhHHHHHHHhccHH----HHHHHHHhcCCCCCCcchHHHHH
Confidence 34555666666666777766665544333221211111222222233333322 23333333321 223467
Q ss_pred hhHHHHHHHHhcccccHHHHHHHHHhcCcCCCCCchhhhcHHH-HHHHHHHHHHhc
Q 013559 215 AKLRCAAGLAHLEARKYKLAARKFLEVGPDLGNSYNEVIAAQD-VATYGGLCALAS 269 (441)
Q Consensus 215 ~~l~~~~gl~~l~~r~y~~Aa~~Fl~~~~t~~~~~~el~s~~d-~~~Y~~l~al~s 269 (441)
+-++...|+..+.+++|.+|-....++...-. ....+. .+-|++|.+.+.
T Consensus 445 a~~~~v~glfaf~qn~lnEaK~~l~e~Lkman-----aed~~rL~a~~LvLLs~v~ 495 (629)
T KOG2300|consen 445 ASILYVYGLFAFKQNDLNEAKRFLRETLKMAN-----AEDLNRLTACSLVLLSHVF 495 (629)
T ss_pred HHHHHHHHHHHHHhccHHHHHHHHHHHHhhcc-----hhhHHHHHHHHHHHHHHHH
Confidence 88888999999999999998777777754211 112222 245666666654
No 268
>PF13812 PPR_3: Pentatricopeptide repeat domain
Probab=53.67 E-value=33 Score=21.04 Aligned_cols=28 Identities=14% Similarity=0.165 Sum_probs=23.1
Q ss_pred HhHHHHHHHHcCCHHHHHHHHHHHHhhh
Q 013559 142 YNDFGDFYYAHGALGDAFKSYVRTRDYC 169 (441)
Q Consensus 142 ~~~la~~~~~~Gd~~~A~~~~~~~r~~~ 169 (441)
+..+-+.+.+.|+.+.|.+.+..+++..
T Consensus 4 y~~ll~a~~~~g~~~~a~~~~~~M~~~g 31 (34)
T PF13812_consen 4 YNALLRACAKAGDPDAALQLFDEMKEQG 31 (34)
T ss_pred HHHHHHHHHHCCCHHHHHHHHHHHHHhC
Confidence 4556678899999999999999987653
No 269
>PF01325 Fe_dep_repress: Iron dependent repressor, N-terminal DNA binding domain; InterPro: IPR022687 The DtxR-type HTH domain is a DNA-binding, winged helix-turn-helix (wHTH) domain of about 65 residues present in metalloregulators of the DtxR/MntR family. The family is named after Corynebacterium diphtheriae DtxR, an iron-specific diphtheria toxin repressor, and Bacillus subtilis MntR, a manganese transport regulator. Iron-responsive metalloregulators such as DtxR and IdeR occur in Gram-positive bacteria of the high GC branch, while manganese-responsive metalloregulators like MntR are described in diverse genera of Gram-positive and Gram-negative bacteria and also in Archaea [].The metalloregulators like DtxR/MntR contain the DNA-binding DtxR-type HTH domain usually in the N-terminal part. The C-terminal part contains a dimerisation domain with two metal-binding sites, although the primary metal-binding site is less conserved in the Mn(II)-regulators. Fe(II)-regulated proteins contain an SH3-like domain as a C-terminal extension, which is absent in Mn(II)-regulated MntR [, ]. Metal-ion dependent regulators orchestrate the virulence of several important human pathogens. The DtxR protein regulates the expression of diphtheria toxinin response to environmental iron concentrations. Furthermore, DtxR and IdeR control iron uptake []. Homeostasis of manganese, which is an essential nutrient, is regulated by MntR. A typical DtxR-type metalloregulator binds two divalent metal effectors per monomer, upon which allosteric changes occur that moderate binding to the cognate DNA operators. Iron-bound DtxR homodimers bind to an interrupted palindrome of 19 bp, protecting a sequence of ~30 bp. The crystal structures of iron-regulated and manganese-regulated repressors show that the DNA binding domain contains three alpha-helices and a pair of antiparallel beta-strands. Helices 2 and 3 comprise the helix-turn-helix motif and the beta-strands are called the wing []. This wHTH topology is similar to the lysR-type HTH (see PDOC00043 from PROSITEDOC). Most DtxR-type metalloregulators bind as dimers to the DNA major groove. Several proteins are known to contain a DtxR-type HTH domain. These include- Corynebacterium diphtheriae DtxR, a diphtheria toxin repressor [], which regulates the expression of the high-affinity iron uptake system, other iron-sensitive genes, and the bacteriophage tox gene. Metal-bound DtxR represses transcription by binding the tox operator; if iron is limiting, conformational changes of the wHTH disrupt DNA-binding and the diphtheria toxin is produced. Mycobacterium tuberculosis IdeR, an iron-dependent regulator that is essential for this pathogen. The regulator represses genes for iron acquisition and activates iron storage genes, and is a positive regulator of oxidative stress responses []. Bacillus subtilis MntR, a manganese transport regulator, binds Mn2+ as an effector and is a transcriptional repressor of transporters for the import of manganese. Treponema pallidum troR, a metal-dependent transcriptional repressor. Archaeoglobus fulgidus MDR1 (troR), a metal-dependent transcriptional repressor, which negatively regulates its own transcription. This entry covers the entire DtxR-type HTH domain.; GO: 0005506 iron ion binding; PDB: 3HRT_B 3HRS_A 3HRU_B 2X4H_D 1ON1_B 2HYF_C 2F5E_A 3R60_B 1ON2_B 2F5F_A ....
Probab=53.46 E-value=34 Score=25.20 Aligned_cols=35 Identities=14% Similarity=0.102 Sum_probs=30.8
Q ss_pred ccccccHHhHHHHcCCChHHHHHHHHHHHHcCccc
Q 013559 349 PFVSVDLHMMANAFKTSVAGIEKELEALITDNQIQ 383 (441)
Q Consensus 349 pYs~I~L~~mA~~fg~s~~~~E~~L~~LI~~g~L~ 383 (441)
.=..|+...+|+.||+++..+-+.+.+|-..|-+.
T Consensus 19 ~~~~v~~~~iA~~L~vs~~tvt~ml~~L~~~GlV~ 53 (60)
T PF01325_consen 19 EGGPVRTKDIAERLGVSPPTVTEMLKRLAEKGLVE 53 (60)
T ss_dssp CTSSBBHHHHHHHHTS-HHHHHHHHHHHHHTTSEE
T ss_pred CCCCccHHHHHHHHCCChHHHHHHHHHHHHCCCEE
Confidence 46889999999999999999999999999988764
No 270
>PF04967 HTH_10: HTH DNA binding domain; InterPro: IPR007050 Numerous bacterial transcription regulatory proteins bind DNA via a helix-turn-helix (HTH) motif. This entry represents the HTH DNA binding domain found in Halobacterium salinarium (Halobacterium halobium) and described as a putative bacterio-opsin activator.
Probab=53.09 E-value=24 Score=25.56 Aligned_cols=32 Identities=16% Similarity=0.162 Sum_probs=27.2
Q ss_pred hccccccccHHhHHHHcCCChHHHHHHHHHHH
Q 013559 346 YTHPFVSVDLHMMANAFKTSVAGIEKELEALI 377 (441)
Q Consensus 346 y~~pYs~I~L~~mA~~fg~s~~~~E~~L~~LI 377 (441)
|+..=..+++..+|+.||+|...+...|.+-+
T Consensus 17 Yfd~PR~~tl~elA~~lgis~st~~~~LRrae 48 (53)
T PF04967_consen 17 YFDVPRRITLEELAEELGISKSTVSEHLRRAE 48 (53)
T ss_pred CCCCCCcCCHHHHHHHhCCCHHHHHHHHHHHH
Confidence 77766899999999999999998887776643
No 271
>PF12487 DUF3703: Protein of unknown function (DUF3703) ; InterPro: IPR022172 This family of proteins is found in bacteria. Proteins in this family are typically between 113 and 135 amino acids in length.
Probab=53.04 E-value=94 Score=26.19 Aligned_cols=60 Identities=10% Similarity=0.022 Sum_probs=47.5
Q ss_pred hHHHHHHHHcCCHHHHHHHHHHHHhhhc-CchhHHHHHHHHHHHHHHhcCHHHHHhHHHHH
Q 013559 143 NDFGDFYYAHGALGDAFKSYVRTRDYCT-TSKHIIHMCMSAILVSIEMGQFTHVTSYVSKA 202 (441)
Q Consensus 143 ~~la~~~~~~Gd~~~A~~~~~~~r~~~~-~~~~~~~~~l~~i~~~i~~~~~~~~~~~~~ka 202 (441)
+..++..++.||+..|...+++.+.... .+....-..|..++.++..+|+.++.--+-++
T Consensus 13 l~~a~~a~~~~~~~~aw~hLErAHIlgQ~~~~~H~~~H~~ML~~a~r~rd~rEv~GQ~~Rl 73 (112)
T PF12487_consen 13 LEAAREALAAGDLQQAWRHLERAHILGQPYPWLHTRVHWAMLRFALRQRDRREVLGQLLRL 73 (112)
T ss_pred HHHHHHHHHcCCHHHHHHHHHhhHHhcCCchhHHHHHHHHHHHHHHHccCHHHHHHHHHHH
Confidence 3456677888999999999999877653 34445677899999999999999998665554
No 272
>PF13730 HTH_36: Helix-turn-helix domain
Probab=52.86 E-value=21 Score=25.28 Aligned_cols=29 Identities=14% Similarity=0.229 Sum_probs=26.6
Q ss_pred cHHhHHHHcCCChHHHHHHHHHHHHcCcc
Q 013559 354 DLHMMANAFKTSVAGIEKELEALITDNQI 382 (441)
Q Consensus 354 ~L~~mA~~fg~s~~~~E~~L~~LI~~g~L 382 (441)
+.+.||+.+|++...+.+.|..|+..|-|
T Consensus 27 S~~~la~~~g~s~~Tv~~~i~~L~~~G~I 55 (55)
T PF13730_consen 27 SQETLAKDLGVSRRTVQRAIKELEEKGLI 55 (55)
T ss_pred CHHHHHHHHCcCHHHHHHHHHHHHHCcCC
Confidence 79999999999999999999999988753
No 273
>KOG1173 consensus Anaphase-promoting complex (APC), Cdc16 subunit [Cell cycle control, cell division, chromosome partitioning; Posttranslational modification, protein turnover, chaperones]
Probab=52.80 E-value=1.8e+02 Score=31.42 Aligned_cols=62 Identities=15% Similarity=0.134 Sum_probs=50.1
Q ss_pred HHhHHHHHHHHcCCHHHHHHHHHHHHhhhcCchhHHHHHHHHHHHHHHhcCHHHHHhHHHHHhcc
Q 013559 141 GYNDFGDFYYAHGALGDAFKSYVRTRDYCTTSKHIIHMCMSAILVSIEMGQFTHVTSYVSKAEQT 205 (441)
Q Consensus 141 ~~~~la~~~~~~Gd~~~A~~~~~~~r~~~~~~~~~~~~~l~~i~~~i~~~~~~~~~~~~~ka~~~ 205 (441)
....||..+.++|.+.+|+.+|.+....|+.. .+..-.+.-+....||++.|.++..|+-.+
T Consensus 457 ~~~NLGH~~Rkl~~~~eAI~~~q~aL~l~~k~---~~~~asig~iy~llgnld~Aid~fhKaL~l 518 (611)
T KOG1173|consen 457 TLNNLGHAYRKLNKYEEAIDYYQKALLLSPKD---ASTHASIGYIYHLLGNLDKAIDHFHKALAL 518 (611)
T ss_pred HHHhHHHHHHHHhhHHHHHHHHHHHHHcCCCc---hhHHHHHHHHHHHhcChHHHHHHHHHHHhc
Confidence 46789999999999999999999987777522 344445556778899999999999998765
No 274
>COG1747 Uncharacterized N-terminal domain of the transcription elongation factor GreA [Function unknown]
Probab=52.73 E-value=3.3e+02 Score=29.37 Aligned_cols=163 Identities=12% Similarity=0.133 Sum_probs=88.6
Q ss_pred HHhHHHHHHHHcCCHHHHHHHHHHHHhhhcCchhHH-HHHHHHHHHHHHhcCHHHHHhHHHHHhcccccCChhhhhhHHH
Q 013559 141 GYNDFGDFYYAHGALGDAFKSYVRTRDYCTTSKHII-HMCMSAILVSIEMGQFTHVTSYVSKAEQTPEALEPVTIAKLRC 219 (441)
Q Consensus 141 ~~~~la~~~~~~Gd~~~A~~~~~~~r~~~~~~~~~~-~~~l~~i~~~i~~~~~~~~~~~~~ka~~~~~~~d~~~~~~l~~ 219 (441)
++.++-++|....|+.+|++.+.++.+.-.. .+.. .-+..-+|.- .++......|+.+..- +..+....--+.-
T Consensus 207 l~qdv~~~Ys~~eN~~eai~Ilk~il~~d~k-~~~ar~~~i~~lRd~--y~~~~~~e~yl~~s~i--~~~~rnf~~~l~d 281 (711)
T COG1747 207 LMQDVYKKYSENENWTEAIRILKHILEHDEK-DVWARKEIIENLRDK--YRGHSQLEEYLKISNI--SQSGRNFFEALND 281 (711)
T ss_pred HHHHHHHHhccccCHHHHHHHHHHHhhhcch-hhhHHHHHHHHHHHH--hccchhHHHHHHhcch--hhccccHHHHHHH
Confidence 6688889999999999999999977544211 1100 0111112221 1234444444443221 1111111112223
Q ss_pred HHHHHhcccccHHHHHHHHHhcCc-------CCCC----CchhhhcHHHHHHHHHHHHHhcCChHHH--HHhcccCHhhH
Q 013559 220 AAGLAHLEARKYKLAARKFLEVGP-------DLGN----SYNEVIAAQDVATYGGLCALASFDRAEL--KSKVIDNVNFR 286 (441)
Q Consensus 220 ~~gl~~l~~r~y~~Aa~~Fl~~~~-------t~~~----~~~el~s~~d~~~Y~~l~al~s~~R~eL--k~~vl~~~~~~ 286 (441)
+.-+++++.|+|- |.+.+. .|++ .+.... +.++.+=+++.+|..++|.++ .+++.+-.++-
T Consensus 282 Fek~m~f~eGnFV-----fHqtWgVG~i~~VsfqqkvlidF~~~r-ah~I~femA~saL~pLs~edi~vlk~v~~~d~la 355 (711)
T COG1747 282 FEKLMHFDEGNFV-----FHQTWGVGEIMGVSFQQKVLIDFEGRR-AHDISFEMAFSALQPLSKEDIFVLKRVGDPDDLA 355 (711)
T ss_pred HHHHheeccCceE-----Eecccccceeeecccccceeeeehhhh-hhhhhHHHHHHHhCcCCccceehhhhcCCHHHHH
Confidence 3445667777752 111110 0100 012222 667777788899999887653 34466666788
Q ss_pred hhhccchH--HHHHHHHHhcCCHHHHHHHH
Q 013559 287 NFLELVPE--VRELINDFYSSRYASCLDYL 314 (441)
Q Consensus 287 ~~le~~p~--~~~ll~~f~~~~y~~~~~~L 314 (441)
.+...+|. +.=+|++|-.++.++.-+.|
T Consensus 356 a~arkdpewAikviiks~~~~nlKeIK~EL 385 (711)
T COG1747 356 AFARKDPEWAIKVIIKSLGPKNLKEIKQEL 385 (711)
T ss_pred HHHhhChHHHHHHHHHhcCCccHHHHHHHH
Confidence 88888886 67788888888776654444
No 275
>PRK11179 DNA-binding transcriptional regulator AsnC; Provisional
Probab=52.56 E-value=26 Score=30.84 Aligned_cols=48 Identities=13% Similarity=0.186 Sum_probs=39.8
Q ss_pred HHHHHhccccccccHHhHHHHcCCChHHHHHHHHHHHHcCccc---eEecC
Q 013559 341 KALIQYTHPFVSVDLHMMANAFKTSVAGIEKELEALITDNQIQ---ARIDS 388 (441)
Q Consensus 341 ~~i~qy~~pYs~I~L~~mA~~fg~s~~~~E~~L~~LI~~g~L~---akID~ 388 (441)
+.|...+.-=.+++...+|+.+|+|+..+-+-+.+|..+|-|. |-+|.
T Consensus 12 ~~Il~~Lq~d~R~s~~eiA~~lglS~~tV~~Ri~rL~~~GvI~~~~~~v~~ 62 (153)
T PRK11179 12 RGILEALMENARTPYAELAKQFGVSPGTIHVRVEKMKQAGIITGTRVDVNP 62 (153)
T ss_pred HHHHHHHHHcCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCeeeEEEEECH
Confidence 3444444545899999999999999999999999999999885 56774
No 276
>KOG0495 consensus HAT repeat protein [RNA processing and modification]
Probab=52.19 E-value=1.3e+02 Score=33.12 Aligned_cols=62 Identities=10% Similarity=0.093 Sum_probs=53.5
Q ss_pred HHhHHHHHHHHcCCHHHHHHHHHHHHhhhcCchhHHHHHHHHHHHHHHhcCHHHHHhHHHHHhcc
Q 013559 141 GYNDFGDFYYAHGALGDAFKSYVRTRDYCTTSKHIIHMCMSAILVSIEMGQFTHVTSYVSKAEQT 205 (441)
Q Consensus 141 ~~~~la~~~~~~Gd~~~A~~~~~~~r~~~~~~~~~~~~~l~~i~~~i~~~~~~~~~~~~~ka~~~ 205 (441)
.++.+|+-+...||...|...+....++.. |..++.|..+++.+....++.+...+.|++..
T Consensus 586 lwlM~ake~w~agdv~~ar~il~~af~~~p---nseeiwlaavKle~en~e~eraR~llakar~~ 647 (913)
T KOG0495|consen 586 LWLMYAKEKWKAGDVPAARVILDQAFEANP---NSEEIWLAAVKLEFENDELERARDLLAKARSI 647 (913)
T ss_pred HHHHHHHHHHhcCCcHHHHHHHHHHHHhCC---CcHHHHHHHHHHhhccccHHHHHHHHHHHhcc
Confidence 455667788888999999999999998864 45788899999999999999999999999874
No 277
>smart00347 HTH_MARR helix_turn_helix multiple antibiotic resistance protein.
Probab=51.65 E-value=1.1e+02 Score=23.73 Aligned_cols=45 Identities=11% Similarity=0.086 Sum_probs=37.2
Q ss_pred hccccccccHHhHHHHcCCChHHHHHHHHHHHHcCccceEecCCC
Q 013559 346 YTHPFVSVDLHMMANAFKTSVAGIEKELEALITDNQIQARIDSHN 390 (441)
Q Consensus 346 y~~pYs~I~L~~mA~~fg~s~~~~E~~L~~LI~~g~L~akID~~~ 390 (441)
.+.....++...+|+.++++...+-+.|.+|...|-+...-|..+
T Consensus 18 ~l~~~~~~~~~~la~~~~~s~~~i~~~l~~L~~~g~v~~~~~~~~ 62 (101)
T smart00347 18 ILYEEGPLSVSELAKRLGVSPSTVTRVLDRLEKKGLIRRLPSPED 62 (101)
T ss_pred HHHHcCCcCHHHHHHHHCCCchhHHHHHHHHHHCCCeEecCCCCC
Confidence 333345699999999999999999999999999999987666443
No 278
>PRK15481 transcriptional regulatory protein PtsJ; Provisional
Probab=51.26 E-value=32 Score=35.64 Aligned_cols=55 Identities=16% Similarity=0.231 Sum_probs=49.2
Q ss_pred HHHHHHHHHHHHHHHhccccccc-cHHhHHHHcCCChHHHHHHHHHHHHcCccceE
Q 013559 331 VETLYDQIRNKALIQYTHPFVSV-DLHMMANAFKTSVAGIEKELEALITDNQIQAR 385 (441)
Q Consensus 331 ~~~l~~~iR~~~i~qy~~pYs~I-~L~~mA~~fg~s~~~~E~~L~~LI~~g~L~ak 385 (441)
...+++.|+..+....+.|=..+ +...||+.||+|...+.+-+..|..+|-|.++
T Consensus 7 ~~~~~~~i~~~i~~g~l~~g~~lps~r~la~~~~vsr~tv~~a~~~L~~~g~i~~~ 62 (431)
T PRK15481 7 ANEIFDSIRQLIQAGRLRPGDSLPPVRELASELGVNRNTVAAAYKRLVTAGLAQSQ 62 (431)
T ss_pred HHHHHHHHHHHHHcCCCCCCCcCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEe
Confidence 35678888889999999999999 89999999999999999999999999988653
No 279
>KOG2114 consensus Vacuolar assembly/sorting protein PEP5/VPS11 [Intracellular trafficking, secretion, and vesicular transport]
Probab=51.13 E-value=45 Score=37.40 Aligned_cols=36 Identities=22% Similarity=0.509 Sum_probs=29.4
Q ss_pred hhhhHHHHHhHHhHHHHHHHHcCCHHHHHHHHHHHH
Q 013559 131 TNLIKESIRMGYNDFGDFYYAHGALGDAFKSYVRTR 166 (441)
Q Consensus 131 ~n~~~esir~~~~~la~~~~~~Gd~~~A~~~~~~~r 166 (441)
.++..+-++..+.++|+|.|..||+++|...|-+.-
T Consensus 360 ~~~d~d~~~~i~~kYgd~Ly~Kgdf~~A~~qYI~tI 395 (933)
T KOG2114|consen 360 QHLDEDTLAEIHRKYGDYLYGKGDFDEATDQYIETI 395 (933)
T ss_pred cCCCHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHc
Confidence 344445666788999999999999999999998753
No 280
>KOG2047 consensus mRNA splicing factor [RNA processing and modification]
Probab=51.02 E-value=48 Score=36.24 Aligned_cols=70 Identities=14% Similarity=0.235 Sum_probs=58.7
Q ss_pred HHhHHhHHHHHHHHcCCHHHHHHHHHHHHh-hhcCchhHHHHHHHHHHHHHHhcCHHHHHhHHHHHhcccc
Q 013559 138 IRMGYNDFGDFYYAHGALGDAFKSYVRTRD-YCTTSKHIIHMCMSAILVSIEMGQFTHVTSYVSKAEQTPE 207 (441)
Q Consensus 138 ir~~~~~la~~~~~~Gd~~~A~~~~~~~r~-~~~~~~~~~~~~l~~i~~~i~~~~~~~~~~~~~ka~~~~~ 207 (441)
.....-.+|++|...|+++.|...+.+... -..+..+..++...|....+...+++.+.+.+.+|...+.
T Consensus 386 ~~~Lw~~faklYe~~~~l~~aRvifeka~~V~y~~v~dLa~vw~~waemElrh~~~~~Al~lm~~A~~vP~ 456 (835)
T KOG2047|consen 386 PGTLWVEFAKLYENNGDLDDARVIFEKATKVPYKTVEDLAEVWCAWAEMELRHENFEAALKLMRRATHVPT 456 (835)
T ss_pred hhhHHHHHHHHHHhcCcHHHHHHHHHHhhcCCccchHHHHHHHHHHHHHHHhhhhHHHHHHHHHhhhcCCC
Confidence 345678999999999999999999998732 3345667778888899999999999999999999987765
No 281
>KOG4340 consensus Uncharacterized conserved protein [Function unknown]
Probab=50.78 E-value=40 Score=33.56 Aligned_cols=114 Identities=16% Similarity=0.187 Sum_probs=71.0
Q ss_pred HHhHHhHHHHHHHHcCCHHHHHHHHHHHHhhhcCchh----------HHHHHHHHHHHHHHhcCHHHHHhHHHHHhcccc
Q 013559 138 IRMGYNDFGDFYYAHGALGDAFKSYVRTRDYCTTSKH----------IIHMCMSAILVSIEMGQFTHVTSYVSKAEQTPE 207 (441)
Q Consensus 138 ir~~~~~la~~~~~~Gd~~~A~~~~~~~r~~~~~~~~----------~~~~~l~~i~~~i~~~~~~~~~~~~~ka~~~~~ 207 (441)
-|.++--||.-||..-+|.+|.+||.++-.....-.+ ..-..-.-+|+....+|-+...+..-++++.+.
T Consensus 43 ~rAgLSlLgyCYY~~Q~f~~AA~CYeQL~ql~P~~~qYrlY~AQSLY~A~i~ADALrV~~~~~D~~~L~~~~lqLqaAIk 122 (459)
T KOG4340|consen 43 SRAGLSLLGYCYYRLQEFALAAECYEQLGQLHPELEQYRLYQAQSLYKACIYADALRVAFLLLDNPALHSRVLQLQAAIK 122 (459)
T ss_pred chHHHHHHHHHHHHHHHHHHHHHHHHHHHhhChHHHHHHHHHHHHHHHhcccHHHHHHHHHhcCCHHHHHHHHHHHHHHh
Confidence 4668889999999999999999999986443321111 111123456777777887777777667766543
Q ss_pred --cCC----hhhhhhH--------HHHHHHHhcccccHHHHHHHHHhcCcCCCCCchhhh
Q 013559 208 --ALE----PVTIAKL--------RCAAGLAHLEARKYKLAARKFLEVGPDLGNSYNEVI 253 (441)
Q Consensus 208 --~~d----~~~~~~l--------~~~~gl~~l~~r~y~~Aa~~Fl~~~~t~~~~~~el~ 253 (441)
.+| ..+-+++ -.-.|-.....|+|..|.+.|-++..- + .+..++
T Consensus 123 Yse~Dl~g~rsLveQlp~en~Ad~~in~gCllykegqyEaAvqkFqaAlqv-s-Gyqpll 180 (459)
T KOG4340|consen 123 YSEGDLPGSRSLVEQLPSENEADGQINLGCLLYKEGQYEAAVQKFQAALQV-S-GYQPLL 180 (459)
T ss_pred cccccCcchHHHHHhccCCCccchhccchheeeccccHHHHHHHHHHHHhh-c-CCCchh
Confidence 111 1111111 122344556799999999999988642 1 144455
No 282
>PRK11169 leucine-responsive transcriptional regulator; Provisional
Probab=50.77 E-value=31 Score=30.85 Aligned_cols=50 Identities=12% Similarity=0.100 Sum_probs=42.1
Q ss_pred HHHHHHhccccccccHHhHHHHcCCChHHHHHHHHHHHHcCccc---eEecCC
Q 013559 340 NKALIQYTHPFVSVDLHMMANAFKTSVAGIEKELEALITDNQIQ---ARIDSH 389 (441)
Q Consensus 340 ~~~i~qy~~pYs~I~L~~mA~~fg~s~~~~E~~L~~LI~~g~L~---akID~~ 389 (441)
.+.|...+.-=.+++...+|+.+|+|...+-+-+.+|..+|-|. |.||..
T Consensus 16 D~~IL~~Lq~d~R~s~~eiA~~lglS~~tv~~Ri~rL~~~GvI~~~~~~v~p~ 68 (164)
T PRK11169 16 DRNILNELQKDGRISNVELSKRVGLSPTPCLERVRRLERQGFIQGYTALLNPH 68 (164)
T ss_pred HHHHHHHhccCCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCeEEEEEEECHH
Confidence 34555567778999999999999999999999999999999884 567743
No 283
>TIGR02337 HpaR homoprotocatechuate degradation operon regulator, HpaR. This Helix-Turn-Helix transcriptional regulator is a member of the MarR family (pfam01047) and is found in association with operons for the degradation of 4-hydroxyphenylacetic acid via homoprotocatechuate.
Probab=50.59 E-value=1.4e+02 Score=24.61 Aligned_cols=43 Identities=16% Similarity=0.098 Sum_probs=38.4
Q ss_pred ccccccHHhHHHHcCCChHHHHHHHHHHHHcCccceEecCCCC
Q 013559 349 PFVSVDLHMMANAFKTSVAGIEKELEALITDNQIQARIDSHNK 391 (441)
Q Consensus 349 pYs~I~L~~mA~~fg~s~~~~E~~L~~LI~~g~L~akID~~~g 391 (441)
-...++.+.||+.+|++...+-+.|.+|...|-|...-|..++
T Consensus 39 ~~~~~t~~ela~~~~~~~~tvs~~l~~Le~~GlI~r~~~~~D~ 81 (118)
T TIGR02337 39 EQGSMEFTQLANQACILRPSLTGILARLERDGLVTRLKASNDQ 81 (118)
T ss_pred HcCCcCHHHHHHHhCCCchhHHHHHHHHHHCCCEEeccCCCCC
Confidence 3567999999999999999999999999999999888777665
No 284
>PF12854 PPR_1: PPR repeat
Probab=50.34 E-value=23 Score=22.73 Aligned_cols=25 Identities=28% Similarity=0.464 Sum_probs=21.3
Q ss_pred HHhHHHHHHHHcCCHHHHHHHHHHH
Q 013559 141 GYNDFGDFYYAHGALGDAFKSYVRT 165 (441)
Q Consensus 141 ~~~~la~~~~~~Gd~~~A~~~~~~~ 165 (441)
.+..+-+-|++.|++++|.+.+.++
T Consensus 9 ty~~lI~~~Ck~G~~~~A~~l~~~M 33 (34)
T PF12854_consen 9 TYNTLIDGYCKAGRVDEAFELFDEM 33 (34)
T ss_pred HHHHHHHHHHHCCCHHHHHHHHHhC
Confidence 4566778899999999999999875
No 285
>KOG1126 consensus DNA-binding cell division cycle control protein [Cell cycle control, cell division, chromosome partitioning]
Probab=49.82 E-value=1.5e+02 Score=32.52 Aligned_cols=94 Identities=12% Similarity=0.146 Sum_probs=63.9
Q ss_pred hHHhHHHHHHHHcCCHHHHHHHHHHHHhhhcCchhHHHHHHHHHHHHHHhcCHHHHHhHHHHHhcccccCChhhhhhHHH
Q 013559 140 MGYNDFGDFYYAHGALGDAFKSYVRTRDYCTTSKHIIHMCMSAILVSIEMGQFTHVTSYVSKAEQTPEALEPVTIAKLRC 219 (441)
Q Consensus 140 ~~~~~la~~~~~~Gd~~~A~~~~~~~r~~~~~~~~~~~~~l~~i~~~i~~~~~~~~~~~~~ka~~~~~~~d~~~~~~l~~ 219 (441)
+|+|-+|-.|.+.|.++.|.-.|.++++-...... +-.+.+. ..-..|..+.+...+++|-.+-- .++-. +.
T Consensus 490 nAwYGlG~vy~Kqek~e~Ae~~fqkA~~INP~nsv-i~~~~g~--~~~~~k~~d~AL~~~~~A~~ld~-kn~l~----~~ 561 (638)
T KOG1126|consen 490 NAWYGLGTVYLKQEKLEFAEFHFQKAVEINPSNSV-ILCHIGR--IQHQLKRKDKALQLYEKAIHLDP-KNPLC----KY 561 (638)
T ss_pred HHHHhhhhheeccchhhHHHHHHHhhhcCCccchh-HHhhhhH--HHHHhhhhhHHHHHHHHHHhcCC-CCchh----HH
Confidence 48999999999999999999999998887654442 3333333 34456777888888888765422 23221 23
Q ss_pred HHHHHhcccccHHHHHHHHHhc
Q 013559 220 AAGLAHLEARKYKLAARKFLEV 241 (441)
Q Consensus 220 ~~gl~~l~~r~y~~Aa~~Fl~~ 241 (441)
..|......++|.+|...|=+.
T Consensus 562 ~~~~il~~~~~~~eal~~LEeL 583 (638)
T KOG1126|consen 562 HRASILFSLGRYVEALQELEEL 583 (638)
T ss_pred HHHHHHHhhcchHHHHHHHHHH
Confidence 4566677788888887765544
No 286
>PRK10370 formate-dependent nitrite reductase complex subunit NrfG; Provisional
Probab=49.64 E-value=49 Score=30.47 Aligned_cols=65 Identities=9% Similarity=0.079 Sum_probs=44.4
Q ss_pred hHHhHHHHH-HHHcCC--HHHHHHHHHHHHhhhcCchhHHHHHHHHHHHHHHhcCHHHHHhHHHHHhcccc
Q 013559 140 MGYNDFGDF-YYAHGA--LGDAFKSYVRTRDYCTTSKHIIHMCMSAILVSIEMGQFTHVTSYVSKAEQTPE 207 (441)
Q Consensus 140 ~~~~~la~~-~~~~Gd--~~~A~~~~~~~r~~~~~~~~~~~~~l~~i~~~i~~~~~~~~~~~~~ka~~~~~ 207 (441)
..+..+|.. ++..|+ +.+|.+.+.+....-.+ + .+..+.+.......|+|+.+.....++-....
T Consensus 108 ~~~~~lA~aL~~~~g~~~~~~A~~~l~~al~~dP~--~-~~al~~LA~~~~~~g~~~~Ai~~~~~aL~l~~ 175 (198)
T PRK10370 108 ELYAALATVLYYQAGQHMTPQTREMIDKALALDAN--E-VTALMLLASDAFMQADYAQAIELWQKVLDLNS 175 (198)
T ss_pred HHHHHHHHHHHHhcCCCCcHHHHHHHHHHHHhCCC--C-hhHHHHHHHHHHHcCCHHHHHHHHHHHHhhCC
Confidence 456777874 567777 48888888887555322 1 34555556666778888888888888766554
No 287
>COG1959 Predicted transcriptional regulator [Transcription]
Probab=49.34 E-value=61 Score=28.62 Aligned_cols=50 Identities=18% Similarity=0.012 Sum_probs=40.7
Q ss_pred ccccccHHhHHHHcCCChHHHHHHHHHHHHcCccceEecCCCCeEEEecC
Q 013559 349 PFVSVDLHMMANAFKTSVAGIEKELEALITDNQIQARIDSHNKILYARHA 398 (441)
Q Consensus 349 pYs~I~L~~mA~~fg~s~~~~E~~L~~LI~~g~L~akID~~~gvv~~~~~ 398 (441)
....++++.+|+..|+|+.++++-+..|-..|-+..+==+.-|..-..+|
T Consensus 22 ~~~~~s~~~IA~~~~is~~~L~kil~~L~kaGlV~S~rG~~GGy~Lar~~ 71 (150)
T COG1959 22 GGGPVSSAEIAERQGISPSYLEKILSKLRKAGLVKSVRGKGGGYRLARPP 71 (150)
T ss_pred CCCcccHHHHHHHhCcCHHHHHHHHHHHHHcCCEEeecCCCCCccCCCCh
Confidence 34479999999999999999999999999999887766666665555543
No 288
>PRK09464 pdhR transcriptional regulator PdhR; Reviewed
Probab=49.29 E-value=42 Score=31.95 Aligned_cols=64 Identities=13% Similarity=0.131 Sum_probs=55.9
Q ss_pred HHHHHHHHHHHHHHHhccccccc-cHHhHHHHcCCChHHHHHHHHHHHHcCccceEecCCCCeEEEe
Q 013559 331 VETLYDQIRNKALIQYTHPFVSV-DLHMMANAFKTSVAGIEKELEALITDNQIQARIDSHNKILYAR 396 (441)
Q Consensus 331 ~~~l~~~iR~~~i~qy~~pYs~I-~L~~mA~~fg~s~~~~E~~L~~LI~~g~L~akID~~~gvv~~~ 396 (441)
.+.+++.||..++..-+.|=..+ +-..||+.||||..-+-.-|..|-..|-|.-+ +..|+.+..
T Consensus 12 ~~~v~~~l~~~I~~g~l~pG~~LpsE~eLa~~lgVSRtpVREAL~~L~~eGlv~~~--~~~G~~V~~ 76 (254)
T PRK09464 12 SDVIEQQLEFLILEGTLRPGEKLPPERELAKQFDVSRPSLREAIQRLEAKGLLLRR--QGGGTFVQS 76 (254)
T ss_pred HHHHHHHHHHHHHcCCCCCCCcCCCHHHHHHHhCCCHHHHHHHHHHHHHCCCEEEe--cCceeEEec
Confidence 35788999999999999999999 89999999999999999999999999999754 456766655
No 289
>COG2345 Predicted transcriptional regulator [Transcription]
Probab=48.90 E-value=39 Score=31.94 Aligned_cols=45 Identities=11% Similarity=0.226 Sum_probs=40.2
Q ss_pred HHHHHhccccccccHHhHHHHcCCChHHHHHHHHHHHHcCccceE
Q 013559 341 KALIQYTHPFVSVDLHMMANAFKTSVAGIEKELEALITDNQIQAR 385 (441)
Q Consensus 341 ~~i~qy~~pYs~I~L~~mA~~fg~s~~~~E~~L~~LI~~g~L~ak 385 (441)
..|.-+|.-...++...||+.+|+|...+-+.|-+|+.+|-+...
T Consensus 14 ~~il~lL~~~g~~sa~elA~~Lgis~~avR~HL~~Le~~Glv~~~ 58 (218)
T COG2345 14 ERILELLKKSGPVSADELAEELGISPMAVRRHLDDLEAEGLVEVE 58 (218)
T ss_pred HHHHHHHhccCCccHHHHHHHhCCCHHHHHHHHHHHHhCcceeee
Confidence 344556777899999999999999999999999999999999887
No 290
>TIGR02561 HrpB1_HrpK type III secretion protein HrpB1/HrpK. This gene is found within type III secretion operons in a limited range of species including Xanthomonas, Ralstonia and Burkholderia.
Probab=48.76 E-value=64 Score=28.69 Aligned_cols=68 Identities=13% Similarity=0.196 Sum_probs=50.9
Q ss_pred CchhHHHHHHHHHHHHHHhcCHHHHHhHHHHHhcc-cccCChhhhhhHHHHHHHHhcccccHHHHHHHHHhcCcC
Q 013559 171 TSKHIIHMCMSAILVSIEMGQFTHVTSYVSKAEQT-PEALEPVTIAKLRCAAGLAHLEARKYKLAARKFLEVGPD 244 (441)
Q Consensus 171 ~~~~~~~~~l~~i~~~i~~~~~~~~~~~~~ka~~~-~~~~d~~~~~~l~~~~gl~~l~~r~y~~Aa~~Fl~~~~t 244 (441)
-++..+.-++.++.+++...+.+.+...+.-++-+ ++ ..-+..+.|..++..|+|.+|.+.|-++...
T Consensus 5 Cs~~iv~gLi~~~~~aL~~~d~~D~e~lLdALrvLrP~------~~e~d~~dg~l~i~rg~w~eA~rvlr~l~~~ 73 (153)
T TIGR02561 5 CSNRLLGGLIEVLMYALRSADPYDAQAMLDALRVLRPN------LKELDMFDGWLLIARGNYDEAARILRELLSS 73 (153)
T ss_pred CcHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHhCCC------ccccchhHHHHHHHcCCHHHHHHHHHhhhcc
Confidence 34566777788888888888888887777766654 22 1234578899999999999999999988754
No 291
>COG2378 Predicted transcriptional regulator [Transcription]
Probab=48.53 E-value=30 Score=34.48 Aligned_cols=54 Identities=20% Similarity=0.210 Sum_probs=45.8
Q ss_pred HHHHHHHHHHHhccccccccHHhHHHHcCCChHHHHHHHHHHHHcCccceEecCCCC
Q 013559 335 YDQIRNKALIQYTHPFVSVDLHMMANAFKTSVAGIEKELEALITDNQIQARIDSHNK 391 (441)
Q Consensus 335 ~~~iR~~~i~qy~~pYs~I~L~~mA~~fg~s~~~~E~~L~~LI~~g~L~akID~~~g 391 (441)
....|...+.+|+..+.+++-..||+.||+|.-.+.+.|..|=..|-= |+...|
T Consensus 5 ~ka~RL~~ii~~L~~~~~vta~~lA~~~~VS~RTi~RDi~~L~~~gvP---I~~e~G 58 (311)
T COG2378 5 RKAERLLQIIQILRAKETVTAAELADEFEVSVRTIYRDIATLRAAGVP---IEGERG 58 (311)
T ss_pred hHHHHHHHHHHHHHhCccchHHHHHHhcCCCHHHHHHHHHHHHHCCCC---eEeecC
Confidence 345688899999999999999999999999999999999988766643 666666
No 292
>PF04545 Sigma70_r4: Sigma-70, region 4; InterPro: IPR007630 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognised by the major sigma factors [, ]. Region 4 of sigma-70 like sigma-factors is involved in binding to the -35 promoter element via a helix-turn-helix motif []. Due to the way Pfam works, the threshold has been set artificially high to prevent overlaps with other helix-turn-helix families. Therefore there are many false negatives.; GO: 0003677 DNA binding, 0003700 sequence-specific DNA binding transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, DNA-dependent, 0006355 regulation of transcription, DNA-dependent; PDB: 2P7V_B 3IYD_F 1TLH_B 1KU7_A 1RIO_H 3N97_A 1KU3_A 1RP3_C 1SC5_A 1NR3_A ....
Probab=48.27 E-value=52 Score=22.81 Aligned_cols=28 Identities=18% Similarity=0.300 Sum_probs=23.4
Q ss_pred cccccHHhHHHHcCCChHHHHHHHHHHH
Q 013559 350 FVSVDLHMMANAFKTSVAGIEKELEALI 377 (441)
Q Consensus 350 Ys~I~L~~mA~~fg~s~~~~E~~L~~LI 377 (441)
|...|+..+|+.+|+|...+-....+.+
T Consensus 18 ~~~~t~~eIa~~lg~s~~~V~~~~~~al 45 (50)
T PF04545_consen 18 FEGLTLEEIAERLGISRSTVRRILKRAL 45 (50)
T ss_dssp TST-SHHHHHHHHTSCHHHHHHHHHHHH
T ss_pred cCCCCHHHHHHHHCCcHHHHHHHHHHHH
Confidence 7889999999999999998887776655
No 293
>PLN03077 Protein ECB2; Provisional
Probab=47.74 E-value=4e+02 Score=30.23 Aligned_cols=23 Identities=22% Similarity=0.223 Sum_probs=11.9
Q ss_pred hHHHHHHHHcCCHHHHHHHHHHH
Q 013559 143 NDFGDFYYAHGALGDAFKSYVRT 165 (441)
Q Consensus 143 ~~la~~~~~~Gd~~~A~~~~~~~ 165 (441)
..|-..|.++|++++|.+.|.++
T Consensus 226 n~Li~~y~k~g~~~~A~~lf~~m 248 (857)
T PLN03077 226 NALITMYVKCGDVVSARLVFDRM 248 (857)
T ss_pred hHHHHHHhcCCCHHHHHHHHhcC
Confidence 34445555555555555555544
No 294
>PRK14720 transcript cleavage factor/unknown domain fusion protein; Provisional
Probab=47.33 E-value=2.4e+02 Score=32.48 Aligned_cols=54 Identities=11% Similarity=0.148 Sum_probs=33.4
Q ss_pred HHHHHHHhcCChHHHHH-hcccCH-hhHhhhccchH--HHHHHHHHhc-CCHHHHHHHH
Q 013559 261 YGGLCALASFDRAELKS-KVIDNV-NFRNFLELVPE--VRELINDFYS-SRYASCLDYL 314 (441)
Q Consensus 261 Y~~l~al~s~~R~eLk~-~vl~~~-~~~~~le~~p~--~~~ll~~f~~-~~y~~~~~~L 314 (441)
=+++.+|-.+++..+.- +.+.++ .+...+..+|. ++.+|++|-+ +.-....+.|
T Consensus 345 ~~A~~sL~pL~~dHi~v~k~~~~~~~l~~~~~~dp~~~ik~~lks~~~~~t~~~ik~eL 403 (906)
T PRK14720 345 QMAITALKPLKRDHIWVLKAVEPKEELVDKFKKDIPWALKTIIKSYDNRMDLKDIKSEL 403 (906)
T ss_pred HHHHHhcCcCChhheehhHhhCCHHHHHHHHHhCHHHHHHHHHHhcCCccCHHHHHHHH
Confidence 34567777788877766 555554 34445555554 6788888876 6555544433
No 295
>TIGR00756 PPR pentatricopeptide repeat domain (PPR motif). This family has a similar consensus to the TPR domain (tetratricopeptide), pfam pfam00515, a 33-residue repeat. It is predicted to form a pair of antiparallel helices similar to that of TPR.
Probab=46.96 E-value=40 Score=20.41 Aligned_cols=27 Identities=15% Similarity=0.153 Sum_probs=21.8
Q ss_pred hHHHHHHHHcCCHHHHHHHHHHHHhhh
Q 013559 143 NDFGDFYYAHGALGDAFKSYVRTRDYC 169 (441)
Q Consensus 143 ~~la~~~~~~Gd~~~A~~~~~~~r~~~ 169 (441)
..+-.-|.+.|++++|.+.|.+++...
T Consensus 4 n~li~~~~~~~~~~~a~~~~~~M~~~g 30 (35)
T TIGR00756 4 NTLIDGLCKAGRVEEALELFKEMLERG 30 (35)
T ss_pred HHHHHHHHHCCCHHHHHHHHHHHHHcC
Confidence 345567899999999999999987653
No 296
>COG4105 ComL DNA uptake lipoprotein [General function prediction only]
Probab=46.88 E-value=2.8e+02 Score=26.89 Aligned_cols=57 Identities=9% Similarity=0.105 Sum_probs=47.1
Q ss_pred hHHHHHHHHcCCHHHHHHHHHHHHhhhcCchhHHHHHHHHHHHHHHhcCHHHHHhHH
Q 013559 143 NDFGDFYYAHGALGDAFKSYVRTRDYCTTSKHIIHMCMSAILVSIEMGQFTHVTSYV 199 (441)
Q Consensus 143 ~~la~~~~~~Gd~~~A~~~~~~~r~~~~~~~~~~~~~l~~i~~~i~~~~~~~~~~~~ 199 (441)
+..|+||.+.|.+..|..-+..+.+...++.+.-+.+..+......+|-.+.+.+.-
T Consensus 171 m~IaryY~kr~~~~AA~nR~~~v~e~y~~t~~~~eaL~~l~eaY~~lgl~~~a~~~~ 227 (254)
T COG4105 171 MAIARYYLKRGAYVAAINRFEEVLENYPDTSAVREALARLEEAYYALGLTDEAKKTA 227 (254)
T ss_pred HHHHHHHHHhcChHHHHHHHHHHHhccccccchHHHHHHHHHHHHHhCChHHHHHHH
Confidence 466899999999999999999998777777787888888888888888777776543
No 297
>PF13545 HTH_Crp_2: Crp-like helix-turn-helix domain; PDB: 3LA2_A 3LA3_B 3LA7_A 3B02_A 3E97_A 2H6C_B 1OMI_A 2BGC_H 2BEO_A 2GAU_A ....
Probab=46.85 E-value=34 Score=25.77 Aligned_cols=43 Identities=12% Similarity=0.158 Sum_probs=35.5
Q ss_pred ccccHHhHHHHcCCChHHHHHHHHHHHHcCccceEecCCCCeEEEec
Q 013559 351 VSVDLHMMANAFKTSVAGIEKELEALITDNQIQARIDSHNKILYARH 397 (441)
Q Consensus 351 s~I~L~~mA~~fg~s~~~~E~~L~~LI~~g~L~akID~~~gvv~~~~ 397 (441)
-.++...||..+|+|.+.+-+.|..|..+|-|. ...|.+...+
T Consensus 27 ~~lt~~~iA~~~g~sr~tv~r~l~~l~~~g~I~----~~~~~i~I~d 69 (76)
T PF13545_consen 27 LPLTQEEIADMLGVSRETVSRILKRLKDEGIIE----VKRGKIIILD 69 (76)
T ss_dssp EESSHHHHHHHHTSCHHHHHHHHHHHHHTTSEE----EETTEEEESS
T ss_pred ecCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEE----EcCCEEEECC
Confidence 347899999999999999999999999999775 4555666553
No 298
>KOG1130 consensus Predicted G-alpha GTPase interaction protein, contains GoLoco domain [Signal transduction mechanisms]
Probab=46.83 E-value=80 Score=32.87 Aligned_cols=85 Identities=18% Similarity=0.208 Sum_probs=54.3
Q ss_pred HHHHHHHHHHHHhhhhHH-------HHHhHHhHHHHHHHHcCCHHHHHHHHHHH----HhhhcCchhHHHHHHHHHHHHH
Q 013559 119 KEKLENELNAYRTNLIKE-------SIRMGYNDFGDFYYAHGALGDAFKSYVRT----RDYCTTSKHIIHMCMSAILVSI 187 (441)
Q Consensus 119 ~~~Le~el~~~~~n~~~e-------sir~~~~~la~~~~~~Gd~~~A~~~~~~~----r~~~~~~~~~~~~~l~~i~~~i 187 (441)
.+.|+...+-|++|+--. ..-+++-.||+-||=.|||+.|+..-..- +++ ++..-.-...-++-.+.|
T Consensus 168 ~~al~~Av~fy~eNL~l~~~lgDr~aqGRa~GnLGNTyYlLGdf~~ai~~H~~RL~ia~ef-GDrAaeRRA~sNlgN~hi 246 (639)
T KOG1130|consen 168 TSALENAVKFYMENLELSEKLGDRLAQGRAYGNLGNTYYLLGDFDQAIHFHKLRLEIAQEF-GDRAAERRAHSNLGNCHI 246 (639)
T ss_pred HHHHHHHHHHHHHHHHHHHHhhhHHhhcchhcccCceeeeeccHHHHHHHHHHHHHHHHHh-hhHHHHHHhhcccchhhh
Confidence 344555556666655211 12246778889999999999999876542 222 222222224456777889
Q ss_pred HhcCHHHHHhHHHHHhc
Q 013559 188 EMGQFTHVTSYVSKAEQ 204 (441)
Q Consensus 188 ~~~~~~~~~~~~~ka~~ 204 (441)
+.|+|+.+..+..++-.
T Consensus 247 flg~fe~A~ehYK~tl~ 263 (639)
T KOG1130|consen 247 FLGNFELAIEHYKLTLN 263 (639)
T ss_pred hhcccHhHHHHHHHHHH
Confidence 99999999888887655
No 299
>KOG1156 consensus N-terminal acetyltransferase [Chromatin structure and dynamics]
Probab=46.82 E-value=4.4e+02 Score=29.11 Aligned_cols=66 Identities=12% Similarity=0.145 Sum_probs=58.5
Q ss_pred HHhHHhHHHHHHHHcCCHHHHHHHHHHHHhhhcCchhHHHHHHHHHHHHHHhcCHHHHHhHHHHHhccc
Q 013559 138 IRMGYNDFGDFYYAHGALGDAFKSYVRTRDYCTTSKHIIHMCMSAILVSIEMGQFTHVTSYVSKAEQTP 206 (441)
Q Consensus 138 ir~~~~~la~~~~~~Gd~~~A~~~~~~~r~~~~~~~~~~~~~l~~i~~~i~~~~~~~~~~~~~ka~~~~ 206 (441)
+...++-++.+|..+|+++.|.+++....+.|+| .++.++...|+.-..|+.+.+...+..++++-
T Consensus 370 llWt~y~laqh~D~~g~~~~A~~yId~AIdHTPT---liEly~~KaRI~kH~G~l~eAa~~l~ea~elD 435 (700)
T KOG1156|consen 370 LLWTLYFLAQHYDKLGDYEVALEYIDLAIDHTPT---LIELYLVKARIFKHAGLLDEAAAWLDEAQELD 435 (700)
T ss_pred HHHHHHHHHHHHHHcccHHHHHHHHHHHhccCch---HHHHHHHHHHHHHhcCChHHHHHHHHHHHhcc
Confidence 4457899999999999999999999998888753 58889999999999999999999999888763
No 300
>PRK14165 winged helix-turn-helix domain-containing protein/riboflavin kinase; Provisional
Probab=46.69 E-value=2.2e+02 Score=26.95 Aligned_cols=52 Identities=17% Similarity=0.142 Sum_probs=44.2
Q ss_pred hccccccccHHhHHHHcCCChHHHHHHHHHHHHcCccceEecCCCCeEEEec
Q 013559 346 YTHPFVSVDLHMMANAFKTSVAGIEKELEALITDNQIQARIDSHNKILYARH 397 (441)
Q Consensus 346 y~~pYs~I~L~~mA~~fg~s~~~~E~~L~~LI~~g~L~akID~~~gvv~~~~ 397 (441)
.+.-...|+.+.||+.+|+|...+-+.|.+|-..|-|.-++|.....|..+.
T Consensus 15 ~l~~~~~IS~~eLA~~L~iS~~Tvsr~Lk~LEe~GlI~R~~~~r~~~v~LTe 66 (217)
T PRK14165 15 AVNNTVKISSSEFANHTGTSSKTAARILKQLEDEGYITRTIVPRGQLITITE 66 (217)
T ss_pred ccCCCCCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEEEcCCceEEEECH
Confidence 4445567999999999999999999999999999999998887666666653
No 301
>KOG0545 consensus Aryl-hydrocarbon receptor-interacting protein [Posttranslational modification, protein turnover, chaperones]
Probab=46.69 E-value=87 Score=30.41 Aligned_cols=97 Identities=14% Similarity=0.105 Sum_probs=58.1
Q ss_pred HHhHHHHHHHHcCCHHHHHHHHHHH---------HhhhcCc------hhHHHHHHHHHHHHHHhcCHHHHHhHHHHHhcc
Q 013559 141 GYNDFGDFYYAHGALGDAFKSYVRT---------RDYCTTS------KHIIHMCMSAILVSIEMGQFTHVTSYVSKAEQT 205 (441)
Q Consensus 141 ~~~~la~~~~~~Gd~~~A~~~~~~~---------r~~~~~~------~~~~~~~l~~i~~~i~~~~~~~~~~~~~ka~~~ 205 (441)
++..-|+-+|+.|+|.+|..+|... +++-.++ +.+.-.+++...|.+-.+++-.|.++.+.+-..
T Consensus 180 ~l~q~GN~lfk~~~ykEA~~~YreAi~~l~~L~lkEkP~e~eW~eLdk~~tpLllNy~QC~L~~~e~yevleh~seiL~~ 259 (329)
T KOG0545|consen 180 VLHQEGNRLFKLGRYKEASSKYREAIICLRNLQLKEKPGEPEWLELDKMITPLLLNYCQCLLKKEEYYEVLEHCSEILRH 259 (329)
T ss_pred HHHHhhhhhhhhccHHHHHHHHHHHHHHHHHHHhccCCCChHHHHHHHhhhHHHHhHHHHHhhHHHHHHHHHHHHHHHhc
Confidence 4456788889999999999888864 2222222 234456788888888889999988876655333
Q ss_pred cccCChhhhhhHHHHHHHHhcccccHHHHHHHHHhcC
Q 013559 206 PEALEPVTIAKLRCAAGLAHLEARKYKLAARKFLEVG 242 (441)
Q Consensus 206 ~~~~d~~~~~~l~~~~gl~~l~~r~y~~Aa~~Fl~~~ 242 (441)
-++ -.++.++ .|.++..--|-.+|-..|..+.
T Consensus 260 ~~~---nvKA~fr--RakAhaa~Wn~~eA~~D~~~vL 291 (329)
T KOG0545|consen 260 HPG---NVKAYFR--RAKAHAAVWNEAEAKADLQKVL 291 (329)
T ss_pred CCc---hHHHHHH--HHHHHHhhcCHHHHHHHHHHHH
Confidence 221 1111111 2334444445556666666554
No 302
>PF01535 PPR: PPR repeat; InterPro: IPR002885 This entry represents the PPR repeat. Pentatricopeptide repeat (PPR) proteins are characterised by tandem repeats of a degenerate 35 amino acid motif []. Most of PPR proteins have roles in mitochondria or plastid []. PPR repeats were discovered while screening Arabidopsis proteins for those predicted to be targeted to mitochondria or chloroplast [, ]. Some of these proteins have been shown to play a role in post-transcriptional processes within organelles and they are thought to be sequence-specific RNA-binding proteins [, , ]. Plant genomes have between one hundred to five hundred PPR genes per genome whereas non-plant genomes encode two to six PPR proteins. Although no PPR structures are yet known, the motif is predicted to fold into a helix-turn-helix structure similar to those found in the tetratricopeptide repeat (TPR) family (see PDOC50005 from PROSITEDOC) []. The plant PPR protein family has been divided in two subfamilies on the basis of their motif content and organisation [, ]. Examples of PPR repeat-containing proteins include PET309 P32522 from SWISSPROT, which may be involved in RNA stabilisation [], and crp1, which is involved in RNA processing []. The repeat is associated with a predicted plant protein O49549 from SWISSPROT that has a domain organisation similar to the human BRCA1 protein.
Probab=46.40 E-value=31 Score=20.60 Aligned_cols=26 Identities=19% Similarity=0.324 Sum_probs=21.2
Q ss_pred hHHHHHHHHcCCHHHHHHHHHHHHhh
Q 013559 143 NDFGDFYYAHGALGDAFKSYVRTRDY 168 (441)
Q Consensus 143 ~~la~~~~~~Gd~~~A~~~~~~~r~~ 168 (441)
..+-+.|.+.|++++|.+.|.++++.
T Consensus 4 ~~li~~~~~~~~~~~a~~~~~~M~~~ 29 (31)
T PF01535_consen 4 NSLISGYCKMGQFEEALEVFDEMRER 29 (31)
T ss_pred HHHHHHHHccchHHHHHHHHHHHhHC
Confidence 44567899999999999999988653
No 303
>PF13041 PPR_2: PPR repeat family
Probab=46.11 E-value=64 Score=22.12 Aligned_cols=33 Identities=18% Similarity=0.284 Sum_probs=26.3
Q ss_pred HHhHHHHHHHHcCCHHHHHHHHHHHHhhhcCch
Q 013559 141 GYNDFGDFYYAHGALGDAFKSYVRTRDYCTTSK 173 (441)
Q Consensus 141 ~~~~la~~~~~~Gd~~~A~~~~~~~r~~~~~~~ 173 (441)
.+..+-+.|.+.|++++|.+.|.++.+....++
T Consensus 5 ~yn~li~~~~~~~~~~~a~~l~~~M~~~g~~P~ 37 (50)
T PF13041_consen 5 TYNTLISGYCKAGKFEEALKLFKEMKKRGIKPD 37 (50)
T ss_pred HHHHHHHHHHHCcCHHHHHHHHHHHHHcCCCCC
Confidence 345566889999999999999999977654443
No 304
>PLN03081 pentatricopeptide (PPR) repeat-containing protein; Provisional
Probab=45.93 E-value=4.5e+02 Score=29.02 Aligned_cols=28 Identities=11% Similarity=0.124 Sum_probs=18.2
Q ss_pred HHhHHHHHHHHcCCHHHHHHHHHHHHhh
Q 013559 141 GYNDFGDFYYAHGALGDAFKSYVRTRDY 168 (441)
Q Consensus 141 ~~~~la~~~~~~Gd~~~A~~~~~~~r~~ 168 (441)
.+..+..-|.+.|++++|.+.|.++.+.
T Consensus 191 t~n~li~~~~~~g~~~~A~~lf~~M~~~ 218 (697)
T PLN03081 191 SWGTIIGGLVDAGNYREAFALFREMWED 218 (697)
T ss_pred eHHHHHHHHHHCcCHHHHHHHHHHHHHh
Confidence 4555666666777777777777766544
No 305
>PF12569 NARP1: NMDA receptor-regulated protein 1 ; InterPro: IPR021183 This group represents N-terminal acetyltransferase A (NatA) auxiliary subunit and represents a non-catalytic component of the NatA N-terminal acetyltransferase, which catalyzes acetylation of proteins beginning with Met-Ser, Met-Gly and Met-Ala. N-terminal acetylation plays a role in normal eukaryotic translation and processing, protect against proteolytic degradation and protein turnover. NAT1 anchors ARD1 and NAT5 to the ribosome and may present the N- terminal of nascent polypeptides for acetylation [], [].
Probab=45.92 E-value=1.3e+02 Score=32.32 Aligned_cols=108 Identities=15% Similarity=0.136 Sum_probs=68.3
Q ss_pred HHHHhHHhHHHHHHHHcCCHHHHHHHHHHHHhhhcCchhHHHHHHHHHHHHHHhcCHHHHHhHHHHHhccc-ccC-C-hh
Q 013559 136 ESIRMGYNDFGDFYYAHGALGDAFKSYVRTRDYCTTSKHIIHMCMSAILVSIEMGQFTHVTSYVSKAEQTP-EAL-E-PV 212 (441)
Q Consensus 136 esir~~~~~la~~~~~~Gd~~~A~~~~~~~r~~~~~~~~~~~~~l~~i~~~i~~~~~~~~~~~~~ka~~~~-~~~-d-~~ 212 (441)
+...+.++-.|+++-..||+.+|++++...|..-+..+. ++. ..+.-.+..|+.+.+...+..-..-- ++. + .+
T Consensus 225 Pt~~ely~~KarilKh~G~~~~Aa~~~~~Ar~LD~~DRy-iNs--K~aKy~LRa~~~e~A~~~~~~Ftr~~~~~~~~L~~ 301 (517)
T PF12569_consen 225 PTLVELYMTKARILKHAGDLKEAAEAMDEARELDLADRY-INS--KCAKYLLRAGRIEEAEKTASLFTREDVDPLSNLND 301 (517)
T ss_pred CCcHHHHHHHHHHHHHCCCHHHHHHHHHHHHhCChhhHH-HHH--HHHHHHHHCCCHHHHHHHHHhhcCCCCCcccCHHH
Confidence 344568999999999999999999999999887544332 211 11223355566666665444331111 100 0 01
Q ss_pred hh-hhHHHHHHHHhcccccHHHHHHHHHhcCcCCC
Q 013559 213 TI-AKLRCAAGLAHLEARKYKLAARKFLEVGPDLG 246 (441)
Q Consensus 213 ~~-~~l~~~~gl~~l~~r~y~~Aa~~Fl~~~~t~~ 246 (441)
.+ .-+-.-.|.++...|+|..|...|..+...|.
T Consensus 302 mQc~Wf~~e~a~a~~r~~~~~~ALk~~~~v~k~f~ 336 (517)
T PF12569_consen 302 MQCMWFETECAEAYLRQGDYGLALKRFHAVLKHFD 336 (517)
T ss_pred HHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHH
Confidence 11 11335578888999999999999998876554
No 306
>PRK11414 colanic acid/biofilm transcriptional regulator; Provisional
Probab=45.73 E-value=49 Score=30.79 Aligned_cols=62 Identities=11% Similarity=0.152 Sum_probs=53.3
Q ss_pred HHHHHHHHHHHHHHHhccccccccHHhHHHHcCCChHHHHHHHHHHHHcCccceEecCCCCeEE
Q 013559 331 VETLYDQIRNKALIQYTHPFVSVDLHMMANAFKTSVAGIEKELEALITDNQIQARIDSHNKILY 394 (441)
Q Consensus 331 ~~~l~~~iR~~~i~qy~~pYs~I~L~~mA~~fg~s~~~~E~~L~~LI~~g~L~akID~~~gvv~ 394 (441)
.+.+++.||.+++..=+.|=..++-..||+.||||-.-+-+-|..|...|-+.-+ +..|+++
T Consensus 13 ~e~v~~~l~~~I~~g~l~pG~~L~e~~La~~lgVSRtpVREAL~~L~~eGLV~~~--~~~g~~v 74 (221)
T PRK11414 13 TLQVENDLKHQLSIGALKPGARLITKNLAEQLGMSITPVREALLRLVSVNALSVA--PAQAFTV 74 (221)
T ss_pred HHHHHHHHHHHHHhCCCCCCCccCHHHHHHHHCCCchhHHHHHHHHHHCCCEEec--CCCceee
Confidence 4678999999999999999999999999999999999999999999999988642 3345443
No 307
>COG5010 TadD Flp pilus assembly protein TadD, contains TPR repeats [Intracellular trafficking and secretion]
Probab=45.57 E-value=2.9e+02 Score=26.77 Aligned_cols=105 Identities=14% Similarity=0.091 Sum_probs=77.3
Q ss_pred HHhhhhHHHHHhHHhHHHHHHHHcCCHHHHHHHHHHHHhhhcCchhHHHHHHHHHHHHHHhcCHHHHHhHHHHHhccccc
Q 013559 129 YRTNLIKESIRMGYNDFGDFYYAHGALGDAFKSYVRTRDYCTTSKHIIHMCMSAILVSIEMGQFTHVTSYVSKAEQTPEA 208 (441)
Q Consensus 129 ~~~n~~~esir~~~~~la~~~~~~Gd~~~A~~~~~~~r~~~~~~~~~~~~~l~~i~~~i~~~~~~~~~~~~~ka~~~~~~ 208 (441)
+..|-...+| ..++.-++-.|+=..++.+......+.++... ......+..+-.||+..+...+.|+-.. ..
T Consensus 60 ~~~~p~d~~i----~~~a~a~~~~G~a~~~l~~~~~~~~~~~~d~~---ll~~~gk~~~~~g~~~~A~~~~rkA~~l-~p 131 (257)
T COG5010 60 VLRNPEDLSI----AKLATALYLRGDADSSLAVLQKSAIAYPKDRE---LLAAQGKNQIRNGNFGEAVSVLRKAARL-AP 131 (257)
T ss_pred HhcCcchHHH----HHHHHHHHhcccccchHHHHhhhhccCcccHH---HHHHHHHHHHHhcchHHHHHHHHHHhcc-CC
Confidence 3444455555 78889999999999999999987554433222 2223777889999999999999998664 23
Q ss_pred CChhhhhhHHHHHHHHhcccccHHHHHHHHHhcCcCC
Q 013559 209 LEPVTIAKLRCAAGLAHLEARKYKLAARKFLEVGPDL 245 (441)
Q Consensus 209 ~d~~~~~~l~~~~gl~~l~~r~y~~Aa~~Fl~~~~t~ 245 (441)
.||+.. -..|..+...|++..|...|.++..=+
T Consensus 132 ~d~~~~----~~lgaaldq~Gr~~~Ar~ay~qAl~L~ 164 (257)
T COG5010 132 TDWEAW----NLLGAALDQLGRFDEARRAYRQALELA 164 (257)
T ss_pred CChhhh----hHHHHHHHHccChhHHHHHHHHHHHhc
Confidence 477544 456888999999999999998876543
No 308
>KOG2300 consensus Uncharacterized conserved protein [Function unknown]
Probab=44.94 E-value=1.5e+02 Score=31.59 Aligned_cols=70 Identities=7% Similarity=0.085 Sum_probs=50.2
Q ss_pred HHHHhHHhHHHHHHHHcC--CHHHHHHHHHHHHhhhcCchhHHHH--HHHHHHHH-HHhcCHHHHHhHHHHHhcccc
Q 013559 136 ESIRMGYNDFGDFYYAHG--ALGDAFKSYVRTRDYCTTSKHIIHM--CMSAILVS-IEMGQFTHVTSYVSKAEQTPE 207 (441)
Q Consensus 136 esir~~~~~la~~~~~~G--d~~~A~~~~~~~r~~~~~~~~~~~~--~l~~i~~~-i~~~~~~~~~~~~~ka~~~~~ 207 (441)
..+-.++.-+|+++...| +...+.+|+..+...-.+ ..++. -+.+..+- -...|+++|+.++.||.....
T Consensus 4 dAva~aLlGlAe~~rt~~PPkIkk~IkClqA~~~~~is--~~veart~LqLg~lL~~yT~N~elAksHLekA~~i~~ 78 (629)
T KOG2300|consen 4 DAVAEALLGLAEHFRTSGPPKIKKCIKCLQAIFQFQIS--FLVEARTHLQLGALLLRYTKNVELAKSHLEKAWLISK 78 (629)
T ss_pred hHHHHHHHHHHHHHhhcCChhHHHHHHHHHHHhccCCh--HHHHHHHHHHHHHHHHHHhccHHHHHHHHHHHHHHHc
Confidence 345568899999999999 999999999887554322 33333 23333333 345799999999999977655
No 309
>PRK11753 DNA-binding transcriptional dual regulator Crp; Provisional
Probab=44.72 E-value=1.6e+02 Score=26.70 Aligned_cols=42 Identities=12% Similarity=0.097 Sum_probs=33.9
Q ss_pred cccHHhHHHHcCCChHHHHHHHHHHHHcCccceEecCCCCeEEEec
Q 013559 352 SVDLHMMANAFKTSVAGIEKELEALITDNQIQARIDSHNKILYARH 397 (441)
Q Consensus 352 ~I~L~~mA~~fg~s~~~~E~~L~~LI~~g~L~akID~~~gvv~~~~ 397 (441)
.++...||+.+|++.+.+-+.+.+|-.+|-|. ++ .+.|...+
T Consensus 168 ~~t~~~lA~~lG~tr~tvsR~l~~l~~~gii~--~~--~~~i~i~~ 209 (211)
T PRK11753 168 KITRQEIGRIVGCSREMVGRVLKMLEDQGLIS--AH--GKTIVVYG 209 (211)
T ss_pred CCCHHHHHHHhCCCHHHHHHHHHHHHHCCCEE--ec--CCEEEEec
Confidence 68889999999999999999999999999773 33 44455543
No 310
>PF13011 LZ_Tnp_IS481: leucine-zipper of insertion element IS481
Probab=44.70 E-value=31 Score=27.56 Aligned_cols=38 Identities=16% Similarity=0.032 Sum_probs=30.7
Q ss_pred ccccHHhHHHHcCCChHHHHHHHHHHHHcCccceEecCC
Q 013559 351 VSVDLHMMANAFKTSVAGIEKELEALITDNQIQARIDSH 389 (441)
Q Consensus 351 s~I~L~~mA~~fg~s~~~~E~~L~~LI~~g~L~akID~~ 389 (441)
...++...|+.||+|...+-+|+.++-.+|. .+-.|.-
T Consensus 24 ~g~~~a~aA~~~gVS~~Ta~kW~~Ryra~G~-~GL~DRS 61 (85)
T PF13011_consen 24 QGWPVAHAAAEFGVSRRTAYKWLARYRAEGE-AGLQDRS 61 (85)
T ss_pred cCCcHHHHHHHhCCCHHHHHHHHHHHHHcCc-ccccccC
Confidence 3467899999999999999999999998875 3344433
No 311
>KOG2076 consensus RNA polymerase III transcription factor TFIIIC [Transcription]
Probab=44.41 E-value=5.4e+02 Score=29.45 Aligned_cols=95 Identities=17% Similarity=0.201 Sum_probs=69.0
Q ss_pred HHhHHHHHHHHcCCHHHHHHHHHHHHhhhcCchhHHHHHHHHHHHHHHhcCHHHHHhHHHHHhcccccCChhhhhhHHHH
Q 013559 141 GYNDFGDFYYAHGALGDAFKSYVRTRDYCTTSKHIIHMCMSAILVSIEMGQFTHVTSYVSKAEQTPEALEPVTIAKLRCA 220 (441)
Q Consensus 141 ~~~~la~~~~~~Gd~~~A~~~~~~~r~~~~~~~~~~~~~l~~i~~~i~~~~~~~~~~~~~ka~~~~~~~d~~~~~~l~~~ 220 (441)
+++.||.+|.+.||.++|+.+.--+-..- ++.. +++..+...+..+|+|..+.-..+||-..- +.+|... .-
T Consensus 175 ay~tL~~IyEqrGd~eK~l~~~llAAHL~--p~d~-e~W~~ladls~~~~~i~qA~~cy~rAI~~~-p~n~~~~----~e 246 (895)
T KOG2076|consen 175 AYYTLGEIYEQRGDIEKALNFWLLAAHLN--PKDY-ELWKRLADLSEQLGNINQARYCYSRAIQAN-PSNWELI----YE 246 (895)
T ss_pred hHHHHHHHHHHcccHHHHHHHHHHHHhcC--CCCh-HHHHHHHHHHHhcccHHHHHHHHHHHHhcC-CcchHHH----HH
Confidence 89999999999999999998876653332 2233 777777788888999999999888886642 1245432 22
Q ss_pred HHHHhcccccHHHHHHHHHhcCc
Q 013559 221 AGLAHLEARKYKLAARKFLEVGP 243 (441)
Q Consensus 221 ~gl~~l~~r~y~~Aa~~Fl~~~~ 243 (441)
....+...|+...|+..|+..+.
T Consensus 247 rs~L~~~~G~~~~Am~~f~~l~~ 269 (895)
T KOG2076|consen 247 RSSLYQKTGDLKRAMETFLQLLQ 269 (895)
T ss_pred HHHHHHHhChHHHHHHHHHHHHh
Confidence 33344556999999999998875
No 312
>PF05843 Suf: Suppressor of forked protein (Suf); InterPro: IPR008847 This domain consists of several eukaryotic suppressor of forked (Suf) like proteins. The Drosophila melanogaster suppressor of forked [Su(f)] protein shares homology with the Saccharomyces cerevisiae RNA14 protein and the 77 kDa subunit of Homo sapiens cleavage stimulation factor, which are proteins involved in mRNA 3' end formation. This suggests a role for Su(f) in mRNA 3' end formation in Drosophila. The su(f) gene produces three transcripts; two of them are polyadenylated at the end of the transcription unit, and one is a truncated transcript, polyadenylated in intron 4. It is thought that su(f) plays a role in the regulation of poly(A) site utilisation and the GU-rich sequence is important for this regulation to occur [].; GO: 0006397 mRNA processing, 0005634 nucleus; PDB: 2L9B_B 2OND_B 2OOE_A 4E85_B 4EBA_C 4E6H_A 2UY1_B.
Probab=44.39 E-value=62 Score=31.58 Aligned_cols=67 Identities=15% Similarity=0.141 Sum_probs=52.4
Q ss_pred HHhHHHHHHHHcCCHHHHHHHHHHHHhhhcCchhHHHHHHHHHHHHHHhcCHHHHHhHHHHHhcccc
Q 013559 141 GYNDFGDFYYAHGALGDAFKSYVRTRDYCTTSKHIIHMCMSAILVSIEMGQFTHVTSYVSKAEQTPE 207 (441)
Q Consensus 141 ~~~~la~~~~~~Gd~~~A~~~~~~~r~~~~~~~~~~~~~l~~i~~~i~~~~~~~~~~~~~ka~~~~~ 207 (441)
-+..+.+|+.+.||.++|...|.+....+....+.-.++-.+++.+-..||++.+.+...|+.....
T Consensus 72 ~~~~Y~~~l~~~~d~~~aR~lfer~i~~l~~~~~~~~iw~~~i~fE~~~Gdl~~v~~v~~R~~~~~~ 138 (280)
T PF05843_consen 72 FWLEYLDFLIKLNDINNARALFERAISSLPKEKQSKKIWKKFIEFESKYGDLESVRKVEKRAEELFP 138 (280)
T ss_dssp HHHHHHHHHHHTT-HHHHHHHHHHHCCTSSCHHHCHHHHHHHHHHHHHHS-HHHHHHHHHHHHHHTT
T ss_pred HHHHHHHHHHHhCcHHHHHHHHHHHHHhcCchhHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHhh
Confidence 3567779999999999999999998776655444556777789999999999999988888877654
No 313
>PHA02943 hypothetical protein; Provisional
Probab=44.10 E-value=1.6e+02 Score=26.37 Aligned_cols=58 Identities=10% Similarity=0.081 Sum_probs=44.1
Q ss_pred HHHHHhccccccccHHhHHHHcCCChHHHHHHHHHHHHcCccceEecCCCCeEEEecCCc
Q 013559 341 KALIQYTHPFVSVDLHMMANAFKTSVAGIEKELEALITDNQIQARIDSHNKILYARHADQ 400 (441)
Q Consensus 341 ~~i~qy~~pYs~I~L~~mA~~fg~s~~~~E~~L~~LI~~g~L~akID~~~gvv~~~~~d~ 400 (441)
.-+..|+ -.-+.+.+.+|+++|+|..+++--|--|=.+|.+.- +-.-...+..-.+|.
T Consensus 14 ~eILE~L-k~G~~TtseIAkaLGlS~~qa~~~LyvLErEG~Vkr-V~~G~~tyw~l~~da 71 (165)
T PHA02943 14 IKTLRLL-ADGCKTTSRIANKLGVSHSMARNALYQLAKEGMVLK-VEIGRAAIWCLDEDA 71 (165)
T ss_pred HHHHHHH-hcCCccHHHHHHHHCCCHHHHHHHHHHHHHcCceEE-EeecceEEEEEChHH
Confidence 4555666 678899999999999999999999999999999854 333344555554543
No 314
>PLN03077 Protein ECB2; Provisional
Probab=43.93 E-value=5.3e+02 Score=29.27 Aligned_cols=53 Identities=9% Similarity=0.153 Sum_probs=26.4
Q ss_pred HHHHHHHHcCCHHHHHHHHHHHHhhhcCchhHHHHHHHHHHHHHHhcCHHHHHhHHHHHh
Q 013559 144 DFGDFYYAHGALGDAFKSYVRTRDYCTTSKHIIHMCMSAILVSIEMGQFTHVTSYVSKAE 203 (441)
Q Consensus 144 ~la~~~~~~Gd~~~A~~~~~~~r~~~~~~~~~~~~~l~~i~~~i~~~~~~~~~~~~~ka~ 203 (441)
.|-+.|.++|++++|.+.|..+ . ++ +..+-.+|......|+++.|...+.+..
T Consensus 529 aLi~~y~k~G~~~~A~~~f~~~-~----~d--~~s~n~lI~~~~~~G~~~~A~~lf~~M~ 581 (857)
T PLN03077 529 ALLDLYVRCGRMNYAWNQFNSH-E----KD--VVSWNILLTGYVAHGKGSMAVELFNRMV 581 (857)
T ss_pred HHHHHHHHcCCHHHHHHHHHhc-C----CC--hhhHHHHHHHHHHcCCHHHHHHHHHHHH
Confidence 4455666666666666665554 1 11 1122223444445566666665555543
No 315
>PF09986 DUF2225: Uncharacterized protein conserved in bacteria (DUF2225); InterPro: IPR018708 This conserved bacterial family has no known function.
Probab=43.71 E-value=2.5e+02 Score=26.37 Aligned_cols=70 Identities=9% Similarity=0.040 Sum_probs=49.0
Q ss_pred HHhHHhHHHHHHHHcCCHHH-------HHHHHHHHHhhhcC---chhHHHHHHHHHHHHHHhcCHHHHHhHHHHHhcccc
Q 013559 138 IRMGYNDFGDFYYAHGALGD-------AFKSYVRTRDYCTT---SKHIIHMCMSAILVSIEMGQFTHVTSYVSKAEQTPE 207 (441)
Q Consensus 138 ir~~~~~la~~~~~~Gd~~~-------A~~~~~~~r~~~~~---~~~~~~~~l~~i~~~i~~~~~~~~~~~~~ka~~~~~ 207 (441)
+-...+++|.+|...||.++ |++.|.+..+.-.. .-....+..-+..++-..|+++.|...+.++-....
T Consensus 117 ~A~l~LrlAWlyR~~~~~~~E~~fl~~Al~~y~~a~~~e~~~~~~~~~~~l~YLigeL~rrlg~~~eA~~~fs~vi~~~~ 196 (214)
T PF09986_consen 117 KAGLCLRLAWLYRDLGDEENEKRFLRKALEFYEEAYENEDFPIEGMDEATLLYLIGELNRRLGNYDEAKRWFSRVIGSKK 196 (214)
T ss_pred HHHHHHHHHHHhhccCCHHHHHHHHHHHHHHHHHHHHhCcCCCCCchHHHHHHHHHHHHHHhCCHHHHHHHHHHHHcCCC
Confidence 34578899999999999554 45555554333222 223345666677788899999999999999877665
No 316
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=43.69 E-value=2.6e+02 Score=25.51 Aligned_cols=63 Identities=11% Similarity=-0.042 Sum_probs=46.1
Q ss_pred hchhHHHHHHHHH--HHHHHHHHHHhccccccccHHhHHHHcCCChHHHHHHHHHHHHcCccceEe
Q 013559 323 LDIHLHDHVETLY--DQIRNKALIQYTHPFVSVDLHMMANAFKTSVAGIEKELEALITDNQIQARI 386 (441)
Q Consensus 323 ~D~~L~~h~~~l~--~~iR~~~i~qy~~pYs~I~L~~mA~~fg~s~~~~E~~L~~LI~~g~L~akI 386 (441)
.|+.+...+..++ ..-..+++. .+..+..+|-+.||+.+|++...+-+-|..|-.+|-+..+-
T Consensus 6 ~~~~v~~~l~~~~~~~~~~~~Vl~-~L~~~g~~tdeeLA~~Lgi~~~~VRk~L~~L~e~gLv~~~r 70 (178)
T PRK06266 6 NNPLVQKVLFEIMEGDEEGFEVLK-ALIKKGEVTDEEIAEQTGIKLNTVRKILYKLYDARLADYKR 70 (178)
T ss_pred cCHHHHHHHHHHhcCCccHhHHHH-HHHHcCCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCeEEee
Confidence 5555555555555 222333333 34567889999999999999999999999999999887544
No 317
>PF01476 LysM: LysM domain; InterPro: IPR018392 This domain is about 40 residues long and is found in a variety of enzymes involved in bacterial cell wall degradation []. This domain may have a general peptidoglycan binding function.; GO: 0016998 cell wall macromolecule catabolic process; PDB: 2DJP_A 3ZQD_A 1Y7M_B 4A52_A 2L9Y_A 1E0G_A.
Probab=43.44 E-value=23 Score=23.67 Aligned_cols=19 Identities=21% Similarity=0.247 Sum_probs=14.9
Q ss_pred cHHhHHHHcCCChHHHHHH
Q 013559 354 DLHMMANAFKTSVAGIEKE 372 (441)
Q Consensus 354 ~L~~mA~~fg~s~~~~E~~ 372 (441)
++..+|++||++.+++.++
T Consensus 8 tl~~IA~~~~~~~~~l~~~ 26 (44)
T PF01476_consen 8 TLWSIAKRYGISVDELMEL 26 (44)
T ss_dssp -HHHHHHHTTS-HHHHHHH
T ss_pred cHHHHHhhhhhhHhHHHHh
Confidence 6889999999999988764
No 318
>KOG2066 consensus Vacuolar assembly/sorting protein VPS41 [Intracellular trafficking, secretion, and vesicular transport]
Probab=43.40 E-value=5.3e+02 Score=29.12 Aligned_cols=51 Identities=20% Similarity=0.307 Sum_probs=35.5
Q ss_pred HHHH-HhcCCHHHHHHHHHHhHHhhhhchhHHHHHHHHHHHHHHHHHHHhccccc
Q 013559 298 LIND-FYSSRYASCLDYLGNLKANLLLDIHLHDHVETLYDQIRNKALIQYTHPFV 351 (441)
Q Consensus 298 ll~~-f~~~~y~~~~~~L~~~~~~l~~D~~L~~h~~~l~~~iR~~~i~qy~~pYs 351 (441)
|+.. +++++|..++..+...++.--.| .-+...|+..+|.++..+...++.
T Consensus 511 La~LYl~d~~Y~~Al~~ylklk~~~vf~---lI~k~nL~d~i~~~Iv~Lmll~sk 562 (846)
T KOG2066|consen 511 LAHLYLYDNKYEKALPIYLKLQDKDVFD---LIKKHNLFDQIKDQIVLLMLLDSK 562 (846)
T ss_pred HHHHHHHccChHHHHHHHHhccChHHHH---HHHHHhhHHHHHHHHHHHHccchh
Confidence 4443 47899999998887765433333 335568888888888888777766
No 319
>PRK04984 fatty acid metabolism regulator; Provisional
Probab=42.75 E-value=64 Score=30.37 Aligned_cols=63 Identities=8% Similarity=-0.007 Sum_probs=54.5
Q ss_pred HHHHHHHHHHHHHHhccccccc-cHHhHHHHcCCChHHHHHHHHHHHHcCccceEecCCCCeEEEe
Q 013559 332 ETLYDQIRNKALIQYTHPFVSV-DLHMMANAFKTSVAGIEKELEALITDNQIQARIDSHNKILYAR 396 (441)
Q Consensus 332 ~~l~~~iR~~~i~qy~~pYs~I-~L~~mA~~fg~s~~~~E~~L~~LI~~g~L~akID~~~gvv~~~ 396 (441)
+.+++.|+.++...-+.|=..+ +-..||+.||||-..+-+-|..|..+|-|.. -+..|+++..
T Consensus 10 ~~~~~~l~~~I~~g~l~pG~~LPsE~eLae~~gVSRt~VReAL~~L~~eGlv~~--~~g~G~~V~~ 73 (239)
T PRK04984 10 GFAEEYIIESIWNNRFPPGSILPAERELSELIGVTRTTLREVLQRLARDGWLTI--QHGKPTKVNN 73 (239)
T ss_pred HHHHHHHHHHHHcCCCCCCCcCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEE--eCCCeeEeCC
Confidence 4678889999999999999999 7999999999999999999999999999974 3455776654
No 320
>PF01865 PhoU_div: Protein of unknown function DUF47; InterPro: IPR018445 This family includes prokaryotic proteins of unknown function, as well as a protein annotated as the pit accessory protein from Rhizobium meliloti (Sinorhizobium meliloti) (O30498 from SWISSPROT). However, the function of this protein is also unknown (Pit stands for Phosphate transport) [].; PDB: 2OLT_C 2IIU_C 3L39_A.
Probab=42.73 E-value=72 Score=29.55 Aligned_cols=80 Identities=18% Similarity=0.305 Sum_probs=57.0
Q ss_pred hHHHHHHHHHhcCCHHHHHHHHHHhHHhhhhchhHHHHHHHHHHHHHHHHHHHhccccccccHHhHHHHcCCChHHHHHH
Q 013559 293 PEVRELINDFYSSRYASCLDYLGNLKANLLLDIHLHDHVETLYDQIRNKALIQYTHPFVSVDLHMMANAFKTSVAGIEKE 372 (441)
Q Consensus 293 p~~~~ll~~f~~~~y~~~~~~L~~~~~~l~~D~~L~~h~~~l~~~iR~~~i~qy~~pYs~I~L~~mA~~fg~s~~~~E~~ 372 (441)
-.+.+++.++.+++|..+-..+..+.. +-...+.+.++++......|+-|+.+-++-.++..++--.+.++.-
T Consensus 25 ~~~~e~l~~~~~~~~~~~~~~~~~i~~-------lE~~aD~i~~~i~~~L~~~fitP~dRedi~~L~~~lD~I~d~i~~~ 97 (214)
T PF01865_consen 25 VLLAELLEAYLEGDYEDVEELLEEIKE-------LEHEADEIKREIREELYKSFITPFDREDILRLISSLDDIADYIEDA 97 (214)
T ss_dssp HCHHHHHHHHCTT-CHHHHHHHHHHHH-------HHHHHHHHHHHHHHHHHH-SS-SS-HHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHhCCHHHHHHHHHHHHH-------HHHHHHHHHHHHHHHHHHhccCCCcHHHHHHHHHHHHHHHHHHHHH
Confidence 346788888888887666555555432 3356889999999999999999999999999999887666677666
Q ss_pred HHHHHHc
Q 013559 373 LEALITD 379 (441)
Q Consensus 373 L~~LI~~ 379 (441)
...|..-
T Consensus 98 a~~l~~~ 104 (214)
T PF01865_consen 98 AKRLSLY 104 (214)
T ss_dssp HHHHHHH
T ss_pred HHHHHHh
Confidence 6555443
No 321
>PRK09990 DNA-binding transcriptional regulator GlcC; Provisional
Probab=42.48 E-value=64 Score=30.66 Aligned_cols=64 Identities=11% Similarity=0.081 Sum_probs=54.8
Q ss_pred HHHHHHHHHHHHHHHhccccccc-cHHhHHHHcCCChHHHHHHHHHHHHcCccceEecCCCCeEEEe
Q 013559 331 VETLYDQIRNKALIQYTHPFVSV-DLHMMANAFKTSVAGIEKELEALITDNQIQARIDSHNKILYAR 396 (441)
Q Consensus 331 ~~~l~~~iR~~~i~qy~~pYs~I-~L~~mA~~fg~s~~~~E~~L~~LI~~g~L~akID~~~gvv~~~ 396 (441)
.+.+++.||..++..=+.|=..+ +-..||+.||||-.-+-.-|..|-..|-|..+ +..|+.+..
T Consensus 9 ~~~v~~~i~~~I~~g~l~pG~~LPsE~eLa~~~gVSRtpVREAL~~L~~eGlV~~~--~~~G~~V~~ 73 (251)
T PRK09990 9 ADVVAERIERLIVDGVLKVGQALPSERRLCEKLGFSRSALREGLTVLRGRGIIETA--QGRGSFVAR 73 (251)
T ss_pred HHHHHHHHHHHHHcCCCCCCCcCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEe--CCCeeEEec
Confidence 45788899999999999999999 89999999999999999999999999988643 345666554
No 322
>PF04010 DUF357: Protein of unknown function (DUF357); InterPro: IPR023140 This domain is found in a family of proteins, which have no known function.; PDB: 2OO2_A 2PMR_A.
Probab=42.15 E-value=75 Score=24.70 Aligned_cols=28 Identities=14% Similarity=0.394 Sum_probs=22.4
Q ss_pred HHHhHHhHHHHHHHHcCCHHHHHHHHHH
Q 013559 137 SIRMGYNDFGDFYYAHGALGDAFKSYVR 164 (441)
Q Consensus 137 sir~~~~~la~~~~~~Gd~~~A~~~~~~ 164 (441)
++-..++.=|++|++.||+..|+.++.-
T Consensus 33 ~mA~~Y~~D~~~fl~~gD~v~Ala~~sY 60 (75)
T PF04010_consen 33 EMAESYLEDGKYFLEKGDYVNALACFSY 60 (75)
T ss_dssp HHHHHHHHHHHHHHHTT-HHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHCCCHHHHHHHHHH
Confidence 3445788889999999999999998764
No 323
>KOG0547 consensus Translocase of outer mitochondrial membrane complex, subunit TOM70/TOM72 [Intracellular trafficking, secretion, and vesicular transport]
Probab=41.67 E-value=4.7e+02 Score=28.02 Aligned_cols=94 Identities=15% Similarity=0.161 Sum_probs=56.6
Q ss_pred HHhHHHHHHHHcCCHHHHHHHHHHHHhhhc-------CchhHHHHHHHHHHHHHHhcCHHHHHhHHHHHhcccccCChhh
Q 013559 141 GYNDFGDFYYAHGALGDAFKSYVRTRDYCT-------TSKHIIHMCMSAILVSIEMGQFTHVTSYVSKAEQTPEALEPVT 213 (441)
Q Consensus 141 ~~~~la~~~~~~Gd~~~A~~~~~~~r~~~~-------~~~~~~~~~l~~i~~~i~~~~~~~~~~~~~ka~~~~~~~d~~~ 213 (441)
++.-+|+++.+.++++.|.+.|.+..+.-. +....+.-.+.+++ ..+|+..+.+.++||-++--.|+
T Consensus 464 vy~~fAeiLtDqqqFd~A~k~YD~ai~LE~~~~~~~v~~~plV~Ka~l~~q---wk~d~~~a~~Ll~KA~e~Dpkce--- 537 (606)
T KOG0547|consen 464 VYNLFAEILTDQQQFDKAVKQYDKAIELEPREHLIIVNAAPLVHKALLVLQ---WKEDINQAENLLRKAIELDPKCE--- 537 (606)
T ss_pred HHHHHHHHHhhHHhHHHHHHHHHHHHhhccccccccccchhhhhhhHhhhc---hhhhHHHHHHHHHHHHccCchHH---
Confidence 666778888888888888888887654421 11111111111222 33677777777777766522222
Q ss_pred hhhHHHHHHHHhcccccHHHHHHHHHhcC
Q 013559 214 IAKLRCAAGLAHLEARKYKLAARKFLEVG 242 (441)
Q Consensus 214 ~~~l~~~~gl~~l~~r~y~~Aa~~Fl~~~ 242 (441)
.-+.--|-+.+++++-.+|.++|=++.
T Consensus 538 --~A~~tlaq~~lQ~~~i~eAielFEksa 564 (606)
T KOG0547|consen 538 --QAYETLAQFELQRGKIDEAIELFEKSA 564 (606)
T ss_pred --HHHHHHHHHHHHHhhHHHHHHHHHHHH
Confidence 112233446678999999999998765
No 324
>TIGR01884 cas_HTH CRISPR locus-related DNA-binding protein. Most but not all examples of this family are associated with CRISPR loci, a combination of DNA repeats and characteristic proteins encoded near the repeat cluster. The C-terminal region of this protein is homologous to DNA-binding helix-turn-helix domains with predicted transcriptional regulatory activity.
Probab=41.45 E-value=77 Score=29.27 Aligned_cols=43 Identities=12% Similarity=0.161 Sum_probs=35.8
Q ss_pred HHhccccccccHHhHHHHcCCChHHHHHHHHHHHHcCccceEe
Q 013559 344 IQYTHPFVSVDLHMMANAFKTSVAGIEKELEALITDNQIQARI 386 (441)
Q Consensus 344 ~qy~~pYs~I~L~~mA~~fg~s~~~~E~~L~~LI~~g~L~akI 386 (441)
..++..+..+++..+|+.+|+|...+-+.|..|...|-+.-.-
T Consensus 149 L~~l~~~g~~s~~eia~~l~is~stv~r~L~~Le~~GlI~r~~ 191 (203)
T TIGR01884 149 LEVLKAEGEKSVKNIAKKLGKSLSTISRHLRELEKKGLVEQKG 191 (203)
T ss_pred HHHHHHcCCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEEc
Confidence 3444445679999999999999999999999999999886543
No 325
>TIGR02702 SufR_cyano iron-sulfur cluster biosynthesis transcriptional regulator SufR. All members of this cyanobacterial protein family are the transcriptional regulator SufR and regulate the SUF system, which makes possible iron-sulfur cluster biosynthesis despite exposure to oxygen. In all cases, the sufR gene is encoded near SUF system genes but in the opposite direction. This DNA-binding protein belongs to the the DeoR family of helix-loop-helix proteins. All members also have a probable metal-binding motif C-X(12)-C-X(13)-C-X(14)-C near the C-terminus.
Probab=41.44 E-value=69 Score=29.60 Aligned_cols=44 Identities=18% Similarity=0.245 Sum_probs=37.6
Q ss_pred HHHHhccccccccHHhHHHHcCCChHHHHHHHHHHHHcCccceE
Q 013559 342 ALIQYTHPFVSVDLHMMANAFKTSVAGIEKELEALITDNQIQAR 385 (441)
Q Consensus 342 ~i~qy~~pYs~I~L~~mA~~fg~s~~~~E~~L~~LI~~g~L~ak 385 (441)
.+..++.....++...||+.+|++...+-+.|..|...|-|.-+
T Consensus 5 ~IL~~L~~~~~~t~~eLA~~lgis~~tV~~~L~~Le~~GlV~r~ 48 (203)
T TIGR02702 5 DILSYLLKQGQATAAALAEALAISPQAVRRHLKDLETEGLIEYE 48 (203)
T ss_pred HHHHHHHHcCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCeEEe
Confidence 34455555677999999999999999999999999999999755
No 326
>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=41.36 E-value=33 Score=27.46 Aligned_cols=55 Identities=9% Similarity=0.117 Sum_probs=35.5
Q ss_pred HHHHhhccCchhhHHHHHHHHhcCCCchhHHHHHHHHHHHHHhcCChHHHHHHHHHhh
Q 013559 37 VEAYASLYQGRTKITRLMFIADHCDIASMQLEALRMAYDEIKKGENTQLFREVVKKID 94 (441)
Q Consensus 37 l~~y~~~y~g~~~i~rL~fi~~~~~~~~~~~~a~~~~~~~lk~t~~~~~Y~~~~~~l~ 94 (441)
||..|.+++.|....+-.|-...+ -..-..--+.++.+++++ +.+.|..+++.|+
T Consensus 29 LT~rI~~L~~Hl~~h~KD~~srrg--L~~lv~kRkrlL~YL~~~-d~~~Y~~li~~Lg 83 (86)
T TIGR00952 29 LTERINQLTEHLKANKKDHHSRRG--LLKLVGRRRRLLKYLKRT-DVERYRSLIKRLG 83 (86)
T ss_pred HHHHHHHHHHHHHHCCCchHHHHH--HHHHHHHHHHHHHHHHhC-CHHHHHHHHHHhC
Confidence 466666666665555555555544 322333445678888877 6899999999875
No 327
>PF13601 HTH_34: Winged helix DNA-binding domain; PDB: 1UB9_A.
Probab=41.27 E-value=1.6e+02 Score=22.86 Aligned_cols=50 Identities=8% Similarity=0.133 Sum_probs=40.6
Q ss_pred HHHHhccccccccHHhHHHHcCCChHHHHHHHHHHHHcCccceEecCCCC
Q 013559 342 ALIQYTHPFVSVDLHMMANAFKTSVAGIEKELEALITDNQIQARIDSHNK 391 (441)
Q Consensus 342 ~i~qy~~pYs~I~L~~mA~~fg~s~~~~E~~L~~LI~~g~L~akID~~~g 391 (441)
.+..++..-..++++.+.+.+|++...+-+.|..|..+|-+..+-....+
T Consensus 4 ~Il~~L~~~~~~~f~~L~~~l~lt~g~Ls~hL~~Le~~GyV~~~k~~~~~ 53 (80)
T PF13601_consen 4 AILALLYANEEATFSELKEELGLTDGNLSKHLKKLEEAGYVEVEKEFEGR 53 (80)
T ss_dssp HHHHHHHHHSEEEHHHHHHHTT--HHHHHHHHHHHHHTTSEEEEEE-SSS
T ss_pred HHHHHHhhcCCCCHHHHHHHhCcCHHHHHHHHHHHHHCCCEEEEEeccCC
Confidence 44556666789999999999999999999999999999999887766655
No 328
>TIGR00738 rrf2_super rrf2 family protein (putative transcriptional regulator). This model represents a superfamily of probable transcriptional regulators. One member, RRF2 of Desulfovibrio vulgaris is an apparent regulatory protein experimentally (MEDLINE:97293189). The N-terminal region appears related to the DNA-binding biotin repressor region of the BirA bifunctional according to results after three rounds of PSI-BLAST with a fairly high stringency.
Probab=41.15 E-value=82 Score=26.57 Aligned_cols=43 Identities=16% Similarity=0.067 Sum_probs=35.1
Q ss_pred ccccHHhHHHHcCCChHHHHHHHHHHHHcCccceEecCCCCeE
Q 013559 351 VSVDLHMMANAFKTSVAGIEKELEALITDNQIQARIDSHNKIL 393 (441)
Q Consensus 351 s~I~L~~mA~~fg~s~~~~E~~L~~LI~~g~L~akID~~~gvv 393 (441)
..++.+.||+.+|+|...+.+-+..|...|-|...-....|..
T Consensus 24 ~~~s~~eia~~~~i~~~~v~~il~~L~~~gli~~~~g~~ggy~ 66 (132)
T TIGR00738 24 GPVSVKEIAERQGISRSYLEKILRTLRRAGLVESVRGPGGGYR 66 (132)
T ss_pred CcCcHHHHHHHHCcCHHHHHHHHHHHHHCCcEEeccCCCCCcc
Confidence 3799999999999999999999999999998866333333433
No 329
>PRK10421 DNA-binding transcriptional repressor LldR; Provisional
Probab=40.87 E-value=71 Score=30.43 Aligned_cols=64 Identities=11% Similarity=0.139 Sum_probs=55.6
Q ss_pred HHHHHHHHHHHHHHHhccccccc-cHHhHHHHcCCChHHHHHHHHHHHHcCccceEecCCCCeEEEe
Q 013559 331 VETLYDQIRNKALIQYTHPFVSV-DLHMMANAFKTSVAGIEKELEALITDNQIQARIDSHNKILYAR 396 (441)
Q Consensus 331 ~~~l~~~iR~~~i~qy~~pYs~I-~L~~mA~~fg~s~~~~E~~L~~LI~~g~L~akID~~~gvv~~~ 396 (441)
.+.+++.||..++..=+.|=..+ +-..||+.||||-.-+-.-|..|-..|-+..+ +..|+.+..
T Consensus 4 ~~~v~~~L~~~I~~g~l~pG~~LpsE~eLae~~gVSRtpVREAL~~Le~~GlV~~~--~~~G~~V~~ 68 (253)
T PRK10421 4 SDEVADRVRALIEEKNLEAGMKLPAERQLAMQLGVSRNSLREALAKLVSEGVLLSR--RGGGTFIRW 68 (253)
T ss_pred HHHHHHHHHHHHHcCCCCCCCcCCCHHHHHHHhCCCHHHHHHHHHHHHHCCCEEEe--CCCeEEEec
Confidence 45788899999999999999999 79999999999999999999999999999754 456776665
No 330
>KOG1130 consensus Predicted G-alpha GTPase interaction protein, contains GoLoco domain [Signal transduction mechanisms]
Probab=40.75 E-value=2.5e+02 Score=29.38 Aligned_cols=73 Identities=12% Similarity=0.093 Sum_probs=57.6
Q ss_pred HhhhhHHHHHhHHhHHHHHHHHcCCHHHHHHHHHHHHhhhc---CchhHHHHHHHHHHHHHHhcCHHHHHhHHHHH
Q 013559 130 RTNLIKESIRMGYNDFGDFYYAHGALGDAFKSYVRTRDYCT---TSKHIIHMCMSAILVSIEMGQFTHVTSYVSKA 202 (441)
Q Consensus 130 ~~n~~~esir~~~~~la~~~~~~Gd~~~A~~~~~~~r~~~~---~~~~~~~~~l~~i~~~i~~~~~~~~~~~~~ka 202 (441)
++-+-+-+.|+++-.+|+-|.=.|+++.|+++|........ .......+|..+-....+..++..+..|-.|-
T Consensus 226 ~efGDrAaeRRA~sNlgN~hiflg~fe~A~ehYK~tl~LAielg~r~vEAQscYSLgNtytll~e~~kAI~Yh~rH 301 (639)
T KOG1130|consen 226 QEFGDRAAERRAHSNLGNCHIFLGNFELAIEHYKLTLNLAIELGNRTVEAQSCYSLGNTYTLLKEVQKAITYHQRH 301 (639)
T ss_pred HHhhhHHHHHHhhcccchhhhhhcccHhHHHHHHHHHHHHHHhcchhHHHHHHHHhhhHHHHHHHHHHHHHHHHHH
Confidence 45555678899999999999999999999999998755432 33344668888888888888888888776654
No 331
>COG1522 Lrp Transcriptional regulators [Transcription]
Probab=40.52 E-value=56 Score=28.34 Aligned_cols=43 Identities=14% Similarity=0.142 Sum_probs=36.8
Q ss_pred hccccccccHHhHHHHcCCChHHHHHHHHHHHHcCcc---ceEecC
Q 013559 346 YTHPFVSVDLHMMANAFKTSVAGIEKELEALITDNQI---QARIDS 388 (441)
Q Consensus 346 y~~pYs~I~L~~mA~~fg~s~~~~E~~L~~LI~~g~L---~akID~ 388 (441)
.++--.++++..+|+.+|+|+..+-+-+-+|..+|-| .+.+|.
T Consensus 16 ~L~~d~r~~~~eia~~lglS~~~v~~Ri~~L~~~GiI~~~~~~v~~ 61 (154)
T COG1522 16 LLQEDARISNAELAERVGLSPSTVLRRIKRLEEEGVIKGYTAVLDP 61 (154)
T ss_pred HHHHhCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCceeeEEEEECH
Confidence 3333566999999999999999999999999999977 578885
No 332
>PF08280 HTH_Mga: M protein trans-acting positive regulator (MGA) HTH domain; InterPro: IPR013199 Mga is a DNA-binding protein that activates the expression of several important virulence genes in group A streptococcus in response to changing environmental conditions [].; PDB: 2WTE_A 3SQN_A.
Probab=40.34 E-value=62 Score=23.57 Aligned_cols=39 Identities=18% Similarity=0.217 Sum_probs=28.9
Q ss_pred HHHHHHHhccccccccHHhHHHHcCCChHHHHHHHHHHH
Q 013559 339 RNKALIQYTHPFVSVDLHMMANAFKTSVAGIEKELEALI 377 (441)
Q Consensus 339 R~~~i~qy~~pYs~I~L~~mA~~fg~s~~~~E~~L~~LI 377 (441)
|..-+..++---..+++..+|+.+|+|.-.+-..|..+=
T Consensus 6 rq~~Ll~~L~~~~~~~~~ela~~l~~S~rti~~~i~~L~ 44 (59)
T PF08280_consen 6 RQLKLLELLLKNKWITLKELAKKLNISERTIKNDINELN 44 (59)
T ss_dssp HHHHHHHHHHHHTSBBHHHHHHHCTS-HHHHHHHHHHHH
T ss_pred HHHHHHHHHHcCCCCcHHHHHHHHCCCHHHHHHHHHHHH
Confidence 334444444447899999999999999999988887753
No 333
>KOG2561 consensus Adaptor protein NUB1, contains UBA domain [Posttranslational modification, protein turnover, chaperones; Signal transduction mechanisms]
Probab=40.15 E-value=1.4e+02 Score=31.25 Aligned_cols=102 Identities=9% Similarity=0.162 Sum_probs=59.4
Q ss_pred hHHhHHHHHHHHcCCHHHHHHHHHHHHhhhc-CchhHHHH-------HHHHHHHHHHhcCHH---HHHhHHHHH------
Q 013559 140 MGYNDFGDFYYAHGALGDAFKSYVRTRDYCT-TSKHIIHM-------CMSAILVSIEMGQFT---HVTSYVSKA------ 202 (441)
Q Consensus 140 ~~~~~la~~~~~~Gd~~~A~~~~~~~r~~~~-~~~~~~~~-------~l~~i~~~i~~~~~~---~~~~~~~ka------ 202 (441)
+++...|+.+.+.-.|++|+.++-..-+++. -....++. -+.++=|++...|.. .|..-+.++
T Consensus 164 lg~hekaRa~m~re~y~eAl~~LleADe~F~~Cd~klLe~VDNyallnLDIVWCYfrLknitcL~DAe~RL~ra~kgf~~ 243 (568)
T KOG2561|consen 164 LGLHEKARAAMEREMYSEALLVLLEADESFSLCDSKLLELVDNYALLNLDIVWCYFRLKNITCLPDAEVRLVRARKGFER 243 (568)
T ss_pred HhHHHHHHHHHHHHHHHHHHHHHHHhhHHHHhhhHHHHHhhcchhhhhcchhheehhhcccccCChHHHHHHHHHHhhhh
Confidence 4788899999999999999999988755432 12222221 112222222222222 222223333
Q ss_pred ---------hcccccCCh--hhhhhHHHHHHHHhcccccHHHHHHHHHhc
Q 013559 203 ---------EQTPEALEP--VTIAKLRCAAGLAHLEARKYKLAARKFLEV 241 (441)
Q Consensus 203 ---------~~~~~~~d~--~~~~~l~~~~gl~~l~~r~y~~Aa~~Fl~~ 241 (441)
..+..++.| .+.-||...+|+...|+|+-.+|.+.|=.+
T Consensus 244 syGenl~Rl~~lKg~~spEraL~lRL~LLQGV~~yHqg~~deAye~le~a 293 (568)
T KOG2561|consen 244 SYGENLSRLRSLKGGQSPERALILRLELLQGVVAYHQGQRDEAYEALESA 293 (568)
T ss_pred hhhhhhHhhhhccCCCChhHHHHHHHHHHHHHHHHHcCCcHHHHHHHHHH
Confidence 332222334 466788999999999999876666655443
No 334
>PRK11523 DNA-binding transcriptional repressor ExuR; Provisional
Probab=40.00 E-value=73 Score=30.37 Aligned_cols=64 Identities=8% Similarity=0.031 Sum_probs=54.5
Q ss_pred HHHHHHHHHHHHHHHhccccccc-cHHhHHHHcCCChHHHHHHHHHHHHcCccceEecCCCCeEEEe
Q 013559 331 VETLYDQIRNKALIQYTHPFVSV-DLHMMANAFKTSVAGIEKELEALITDNQIQARIDSHNKILYAR 396 (441)
Q Consensus 331 ~~~l~~~iR~~~i~qy~~pYs~I-~L~~mA~~fg~s~~~~E~~L~~LI~~g~L~akID~~~gvv~~~ 396 (441)
.+.+++.||..++..-+.|=..+ +-..||+.||||..-+-+-|..|-..|-|.- -+..|+.+..
T Consensus 10 ~~~v~~~l~~~I~~g~l~pG~~LpsE~eLae~~gVSRtpVREAL~~L~~eGlV~~--~~~~G~~V~~ 74 (253)
T PRK11523 10 YQQLAAELKERIEQGVYLVGDKLPAERFIADEKNVSRTVVREAIIMLEVEGYVEV--RKGSGIHVVS 74 (253)
T ss_pred HHHHHHHHHHHHHcCCCCCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEE--ecCCeeEEec
Confidence 46788999999999999999999 5889999999999999999999999998863 3445666654
No 335
>PLN03083 E3 UFM1-protein ligase 1 homolog; Provisional
Probab=39.60 E-value=1.6e+02 Score=33.25 Aligned_cols=61 Identities=15% Similarity=0.248 Sum_probs=46.2
Q ss_pred HHHHHHHHHHHHHHHHHHhccccccccHHhHHHHcCCChHHHHHHHHHHHHcCccceEecCCCCeEEEe
Q 013559 328 HDHVETLYDQIRNKALIQYTHPFVSVDLHMMANAFKTSVAGIEKELEALITDNQIQARIDSHNKILYAR 396 (441)
Q Consensus 328 ~~h~~~l~~~iR~~~i~qy~~pYs~I~L~~mA~~fg~s~~~~E~~L~~LI~~g~L~akID~~~gvv~~~ 396 (441)
..+++.+.++|..+.=+ -..|++..+|+.|+++.+++-+.|..- ..+.|+|+++ .|+|++.
T Consensus 115 ~~Yld~iaeEIne~LqE-----~G~isI~eLa~~~~Lpsefl~~~l~~r-lG~iI~g~~~--g~~lyT~ 175 (803)
T PLN03083 115 QSYWDSIAEEINERLQE-----CSQIALAELARQLQVGSELVTSMLEPR-LGTIVKARLE--GGQLYTP 175 (803)
T ss_pred hHHHHHHHHHHHHHHHH-----cCcChHHHHHHhcCChHHHHHHHHHHH-hccceEEEec--CCEEecH
Confidence 34556666666444322 589999999999999999999999877 5578899993 5777653
No 336
>PF09295 ChAPs: ChAPs (Chs5p-Arf1p-binding proteins); InterPro: IPR015374 ChAPs (Chs5p-Arf1p-binding proteins) are required for the export of specialised cargo from the Golgi. They physically interact with Chs3, Chs5 and the small GTPase Arf1, and they also form interactions with each other [].
Probab=39.39 E-value=1.9e+02 Score=30.02 Aligned_cols=92 Identities=9% Similarity=-0.030 Sum_probs=66.1
Q ss_pred HHhHHHHHHHHcCCHHHHHHHHHHHHhhhcCchhHHHHHHHHHHHHHHhcCHHHHHhHHHHHhcc-cc-cCChhhhhhHH
Q 013559 141 GYNDFGDFYYAHGALGDAFKSYVRTRDYCTTSKHIIHMCMSAILVSIEMGQFTHVTSYVSKAEQT-PE-ALEPVTIAKLR 218 (441)
Q Consensus 141 ~~~~la~~~~~~Gd~~~A~~~~~~~r~~~~~~~~~~~~~l~~i~~~i~~~~~~~~~~~~~ka~~~-~~-~~d~~~~~~l~ 218 (441)
+..-+|+.+...++-.+|.+.+.+.....+.. .+++..+.+..+..++++.|.....++-.. ++ ...|.
T Consensus 202 v~~~LA~v~l~~~~E~~AI~ll~~aL~~~p~d---~~LL~~Qa~fLl~k~~~~lAL~iAk~av~lsP~~f~~W~------ 272 (395)
T PF09295_consen 202 VAVLLARVYLLMNEEVEAIRLLNEALKENPQD---SELLNLQAEFLLSKKKYELALEIAKKAVELSPSEFETWY------ 272 (395)
T ss_pred HHHHHHHHHHhcCcHHHHHHHHHHHHHhCCCC---HHHHHHHHHHHHhcCCHHHHHHHHHHHHHhCchhHHHHH------
Confidence 34568999999999999999988876544322 566667777788889999999888888663 44 33453
Q ss_pred HHHHHHhcccccHHHHHHHHHhcCc
Q 013559 219 CAAGLAHLEARKYKLAARKFLEVGP 243 (441)
Q Consensus 219 ~~~gl~~l~~r~y~~Aa~~Fl~~~~ 243 (441)
.-+.+++..|+|+.|. .-+++.+
T Consensus 273 -~La~~Yi~~~d~e~AL-laLNs~P 295 (395)
T PF09295_consen 273 -QLAECYIQLGDFENAL-LALNSCP 295 (395)
T ss_pred -HHHHHHHhcCCHHHHH-HHHhcCc
Confidence 3445677899999986 5555544
No 337
>PF13512 TPR_18: Tetratricopeptide repeat
Probab=39.24 E-value=2.7e+02 Score=24.50 Aligned_cols=56 Identities=7% Similarity=0.017 Sum_probs=26.8
Q ss_pred HHhHHHHHHHHcCCHHHHHHHHHHHHhhhcCchhHHHHHHHHHHHHHHhcCHHHHH
Q 013559 141 GYNDFGDFYYAHGALGDAFKSYVRTRDYCTTSKHIIHMCMSAILVSIEMGQFTHVT 196 (441)
Q Consensus 141 ~~~~la~~~~~~Gd~~~A~~~~~~~r~~~~~~~~~~~~~l~~i~~~i~~~~~~~~~ 196 (441)
.++.-|.-.++.|+|.+|.+.|..+......+...-..-|.++-+....++|+.+.
T Consensus 12 ~ly~~a~~~l~~~~Y~~A~~~le~L~~ryP~g~ya~qAqL~l~yayy~~~~y~~A~ 67 (142)
T PF13512_consen 12 ELYQEAQEALQKGNYEEAIKQLEALDTRYPFGEYAEQAQLDLAYAYYKQGDYEEAI 67 (142)
T ss_pred HHHHHHHHHHHhCCHHHHHHHHHHHHhcCCCCcccHHHHHHHHHHHHHccCHHHHH
Confidence 34455555555555555555555554444333333334444444444444444443
No 338
>KOG3850 consensus Predicted membrane protein [Function unknown]
Probab=39.23 E-value=4.5e+02 Score=27.06 Aligned_cols=85 Identities=22% Similarity=0.326 Sum_probs=45.8
Q ss_pred HHHHHHHHHHHHhcCC--hHHHHHHHHHhhccCCCCCcCCHHHHHHHHHHHHHHHHHHHHHHHHHHh-----------hh
Q 013559 67 LEALRMAYDEIKKGEN--TQLFREVVKKIDGRLGPNYAMDEAWCDSVDRRAEQRKEKLENELNAYRT-----------NL 133 (441)
Q Consensus 67 ~~a~~~~~~~lk~t~~--~~~Y~~~~~~l~~~~~~~~~~D~~~~~~~~~~~~~~~~~Le~el~~~~~-----------n~ 133 (441)
.+++..-+.+||+|.| -.-|..+-+.+. -|=.++.++-++-.-+.++||+.|++.++ ++
T Consensus 262 l~aileeL~eIk~~q~~Leesye~Lke~~k--------rdy~fi~etLQEERyR~erLEEqLNdlteLqQnEi~nLKqEl 333 (455)
T KOG3850|consen 262 LDAILEELREIKETQALLEESYERLKEQIK--------RDYKFIAETLQEERYRYERLEEQLNDLTELQQNEIANLKQEL 333 (455)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH--------HHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHH
Confidence 4555666666677654 345544444432 23345544444444555667777765532 22
Q ss_pred hHHHHHhHHhHHHHHHHHcCCHHHHHHHHH
Q 013559 134 IKESIRMGYNDFGDFYYAHGALGDAFKSYV 163 (441)
Q Consensus 134 ~~esir~~~~~la~~~~~~Gd~~~A~~~~~ 163 (441)
--.+-|.+| ..|.+..|.++|.+.+.
T Consensus 334 asmeervaY----QsyERaRdIqEalEscq 359 (455)
T KOG3850|consen 334 ASMEERVAY----QSYERARDIQEALESCQ 359 (455)
T ss_pred HHHHHHHHH----HHHHHHHHHHHHHHHHH
Confidence 222333333 34666778888888765
No 339
>PRK06771 hypothetical protein; Provisional
Probab=38.71 E-value=24 Score=28.65 Aligned_cols=30 Identities=20% Similarity=0.334 Sum_probs=26.0
Q ss_pred cccHHhHHHHcCCChH--HHHHHHHHHHHcCc
Q 013559 352 SVDLHMMANAFKTSVA--GIEKELEALITDNQ 381 (441)
Q Consensus 352 ~I~L~~mA~~fg~s~~--~~E~~L~~LI~~g~ 381 (441)
...|+.+++.+|++.. .+.+++.+||.+|+
T Consensus 36 e~~L~~I~~~~Gi~~~~~~~~~e~~~Li~~Gk 67 (93)
T PRK06771 36 EDRLQLITKEMGIVDREPPVNKELRQLMEEGQ 67 (93)
T ss_pred HHHHHHHHHHcCCCCCcccccHHHHHHHHcCC
Confidence 4578999999999866 68899999999996
No 340
>PF01978 TrmB: Sugar-specific transcriptional regulator TrmB; InterPro: IPR002831 TrmB, is a protein of 38,800 apparent molecular weight, that is involved in the maltose-specific regulation of the trehalose/maltose ABC transport operon in Thermococcus litoralis. TrmB has been shown to be a maltose-specific repressor, and this inhibition is counteracted by maltose and trehalose. TrmB binds maltose and trehalose half-maximally at 20 uM and 0.5 mM sugar concentration, respectively []. Other members of this family are annotated as either transcriptional regulators or hypothetical proteins. ; PDB: 2D1H_A 3QPH_A 1SFX_A.
Probab=37.88 E-value=86 Score=23.21 Aligned_cols=44 Identities=11% Similarity=0.124 Sum_probs=36.6
Q ss_pred HHHHHhccccccccHHhHHHHcCCChHHHHHHHHHHHHcCccceE
Q 013559 341 KALIQYTHPFVSVDLHMMANAFKTSVAGIEKELEALITDNQIQAR 385 (441)
Q Consensus 341 ~~i~qy~~pYs~I~L~~mA~~fg~s~~~~E~~L~~LI~~g~L~ak 385 (441)
++|...+ .....+...+|+.+|++...+-+.|.+|...|-+.-.
T Consensus 12 ~vy~~Ll-~~~~~t~~eIa~~l~i~~~~v~~~L~~L~~~GlV~~~ 55 (68)
T PF01978_consen 12 KVYLALL-KNGPATAEEIAEELGISRSTVYRALKSLEEKGLVERE 55 (68)
T ss_dssp HHHHHHH-HHCHEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEEE
T ss_pred HHHHHHH-HcCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEE
Confidence 3444333 5789999999999999999999999999999988543
No 341
>COG2963 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=37.67 E-value=78 Score=26.24 Aligned_cols=46 Identities=15% Similarity=0.085 Sum_probs=38.6
Q ss_pred HHHHHHHHHHhccccccccHHhHHHHcCC-ChHHHHHHHHHHHHcCccc
Q 013559 336 DQIRNKALIQYTHPFVSVDLHMMANAFKT-SVAGIEKELEALITDNQIQ 383 (441)
Q Consensus 336 ~~iR~~~i~qy~~pYs~I~L~~mA~~fg~-s~~~~E~~L~~LI~~g~L~ 383 (441)
.+-+..++.+|++|=. +++.+|..||+ +...+-+|+.++...+...
T Consensus 10 ~EfK~~iv~~~~~~g~--sv~~vAr~~gv~~~~~l~~W~~~~~~~~~~~ 56 (116)
T COG2963 10 PEFKLEAVALYLRGGD--TVSEVAREFGIVSATQLYKWRIQLQKGGGLA 56 (116)
T ss_pred HHHHHHHHHHHHhcCc--cHHHHHHHhCCCChHHHHHHHHHHHHccccc
Confidence 4556788889987644 89999999996 9999999999999987664
No 342
>COG3071 HemY Uncharacterized enzyme of heme biosynthesis [Coenzyme metabolism]
Probab=37.49 E-value=4.8e+02 Score=26.94 Aligned_cols=132 Identities=14% Similarity=0.126 Sum_probs=0.0
Q ss_pred HHHHHHcCCHHHHHHHHHHHHhhhcCchhHHHHHHHHHHHHHHhcCHHHHHhHHHHHhcccccCChhhhhhHHHHHHHHh
Q 013559 146 GDFYYAHGALGDAFKSYVRTRDYCTTSKHIIHMCMSAILVSIEMGQFTHVTSYVSKAEQTPEALEPVTIAKLRCAAGLAH 225 (441)
Q Consensus 146 a~~~~~~Gd~~~A~~~~~~~r~~~~~~~~~~~~~l~~i~~~i~~~~~~~~~~~~~ka~~~~~~~d~~~~~~l~~~~gl~~ 225 (441)
|-.-+..|||+.|-+...+--+.. .+-+-.++.-.+.+=..||.+.+..+++++.+..+ +-..-......-..
T Consensus 91 gl~~l~eG~~~qAEkl~~rnae~~---e~p~l~~l~aA~AA~qrgd~~~an~yL~eaae~~~----~~~l~v~ltrarll 163 (400)
T COG3071 91 GLLKLFEGDFQQAEKLLRRNAEHG---EQPVLAYLLAAEAAQQRGDEDRANRYLAEAAELAG----DDTLAVELTRARLL 163 (400)
T ss_pred HHHHHhcCcHHHHHHHHHHhhhcC---cchHHHHHHHHHHHHhcccHHHHHHHHHHHhccCC----CchHHHHHHHHHHH
Q ss_pred cccccHHHHHHHHHhcCcCCCCCchhhh-----cHHHHHHHHHHHHHhcCChHHHHHhcccCHhhHhh
Q 013559 226 LEARKYKLAARKFLEVGPDLGNSYNEVI-----AAQDVATYGGLCALASFDRAELKSKVIDNVNFRNF 288 (441)
Q Consensus 226 l~~r~y~~Aa~~Fl~~~~t~~~~~~el~-----s~~d~~~Y~~l~al~s~~R~eLk~~vl~~~~~~~~ 288 (441)
+.+|+|..|.+...+....-..+ ++++ .+.+..-|--+|++.- .--|.++++++++..+
T Consensus 164 l~~~d~~aA~~~v~~ll~~~pr~-~~vlrLa~r~y~~~g~~~~ll~~l~---~L~ka~~l~~~e~~~l 227 (400)
T COG3071 164 LNRRDYPAARENVDQLLEMTPRH-PEVLRLALRAYIRLGAWQALLAILP---KLRKAGLLSDEEAARL 227 (400)
T ss_pred HhCCCchhHHHHHHHHHHhCcCC-hHHHHHHHHHHHHhccHHHHHHHHH---HHHHccCCChHHHHHH
No 343
>PF03374 ANT: Phage antirepressor protein KilAC domain; InterPro: IPR005039 This entry is represented by Bacteriophage P1, Ant1 C-terminal domain, which represents the processed Ant2 chain. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. Prophages P1 and P7 exist as unit copy DNA plasmids in the bacterial cell. Maintenance of the prophage state requires the continuous expression of two repressors: (i) C1 is a protein which negatively regulates the expression of lytic genes including the C1 inactivator gene coi, and (ii) C4 is an antisense RNA which specifically inhibits the synthesis of an anti-repressor Ant.; GO: 0003677 DNA binding
Probab=37.33 E-value=54 Score=26.96 Aligned_cols=35 Identities=6% Similarity=-0.089 Sum_probs=29.4
Q ss_pred HHHHHhccccccccHHhHHHHcCCChHHHHHHHHH
Q 013559 341 KALIQYTHPFVSVDLHMMANAFKTSVAGIEKELEA 375 (441)
Q Consensus 341 ~~i~qy~~pYs~I~L~~mA~~fg~s~~~~E~~L~~ 375 (441)
..+.+|+.+=.++++...|+.||++...+=+||.+
T Consensus 13 ~~~d~~~~~~~~~ti~~~AK~L~i~~~~l~~~Lr~ 47 (111)
T PF03374_consen 13 EFYDAFVDSDGLYTIREAAKLLGIGRNKLFQWLRE 47 (111)
T ss_pred HHHHHHHcCCCCccHHHHHHHhCCCHHHHHHHHHh
Confidence 45666777778999999999999998888888765
No 344
>PF03297 Ribosomal_S25: S25 ribosomal protein; InterPro: IPR004977 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 [, ]. The S25 ribosomal protein is a component of the 40S ribosomal subunit.; PDB: 2XZM_8 2XZN_8 3O30_Q 3U5G_Z 3IZB_V 3U5C_Z 3O2Z_Q 3IZ6_V.
Probab=37.23 E-value=1.6e+02 Score=24.57 Aligned_cols=49 Identities=16% Similarity=0.235 Sum_probs=42.3
Q ss_pred cccccccHHhHHHHcCCChHHHHHHHHHHHHcCccceEecCCCCeEEEe
Q 013559 348 HPFVSVDLHMMANAFKTSVAGIEKELEALITDNQIQARIDSHNKILYAR 396 (441)
Q Consensus 348 ~pYs~I~L~~mA~~fg~s~~~~E~~L~~LI~~g~L~akID~~~gvv~~~ 396 (441)
..|+-||-..+|+.|+++..-+-+-|..|-..|.|..-.=.....|+++
T Consensus 55 ~~~K~ITp~~lserlkI~~SlAr~~Lr~L~~kG~Ik~V~k~~~~~IYtr 103 (105)
T PF03297_consen 55 PKMKLITPSVLSERLKINGSLARKALRELESKGLIKPVSKHHRQRIYTR 103 (105)
T ss_dssp TTSSCECHHHHHHHHCCSCHHHHHHHHHHHHCCSSEEEECCTTCEEEEE
T ss_pred ccCcEeeHHHHHHhHhhHHHHHHHHHHHHHHCCCEEEEeccCCeEEEec
Confidence 5589999999999999999999999999999999987765666666654
No 345
>PF09743 DUF2042: Uncharacterized conserved protein (DUF2042); InterPro: IPR018611 The ubiquitin fold modifier 1 (Ufm1) is the most recently discovered ubiquitin-like modifier whose conjugation (ufmylation) system is conserved in multicellular organisms. Ufm1 is known to covalently attach with cellular protein(s) via a specific E1-activating enzyme (Uba5), an E2-conjugating enzyme (Ufc1), and a E3-ligating enzyme []. This entry represents E3 UFM1-protein ligase 1.
Probab=36.83 E-value=93 Score=30.46 Aligned_cols=56 Identities=11% Similarity=0.074 Sum_probs=43.3
Q ss_pred HHHHHHHHHHHHHhccccccccHHhHHHHcCCChHHHHHHHHHHHHcCccceEecC
Q 013559 333 TLYDQIRNKALIQYTHPFVSVDLHMMANAFKTSVAGIEKELEALITDNQIQARIDS 388 (441)
Q Consensus 333 ~l~~~iR~~~i~qy~~pYs~I~L~~mA~~fg~s~~~~E~~L~~LI~~g~L~akID~ 388 (441)
.|+...+.++---+...=+-+.++.+.+.+|++...+-.-+.+||.+|+|.|+|-.
T Consensus 173 ayv~r~ka~iRG~l~a~T~Pt~l~~l~~~~~~~~~l~~~il~~Li~~~~l~G~i~G 228 (272)
T PF09743_consen 173 AYVARQKARIRGALSAITRPTPLSSLLKRYGFEEKLFQSILEELIKSGELPGSIVG 228 (272)
T ss_pred HHHHHHHHHHHHHHhcCccceEHHHHHHHhCCcHHHHHHHHHHHHhcCcceEEEEC
Confidence 33333333333334444567999999999999999999999999999999999877
No 346
>PRK09391 fixK transcriptional regulator FixK; Provisional
Probab=36.79 E-value=1.5e+02 Score=27.73 Aligned_cols=41 Identities=12% Similarity=0.181 Sum_probs=32.9
Q ss_pred cccHHhHHHHcCCChHHHHHHHHHHHHcCccceEecCCC-CeEEEe
Q 013559 352 SVDLHMMANAFKTSVAGIEKELEALITDNQIQARIDSHN-KILYAR 396 (441)
Q Consensus 352 ~I~L~~mA~~fg~s~~~~E~~L~~LI~~g~L~akID~~~-gvv~~~ 396 (441)
.++-..+|+.+|++.+.+-+.|.+|-.+|-|. ... |.|+..
T Consensus 179 ~lt~~~IA~~lGisretlsR~L~~L~~~GlI~----~~~~~~i~I~ 220 (230)
T PRK09391 179 PMSRRDIADYLGLTIETVSRALSQLQDRGLIG----LSGARQIELR 220 (230)
T ss_pred cCCHHHHHHHHCCCHHHHHHHHHHHHHCCcEE----ecCCceEEEc
Confidence 46789999999999999999999999988773 332 455555
No 347
>TIGR01610 phage_O_Nterm phage replication protein O, N-terminal domain. This model represents the N-terminal region of the phage lambda replication protein O and homologous regions of other phage proteins.
Probab=36.70 E-value=1.1e+02 Score=24.53 Aligned_cols=48 Identities=13% Similarity=0.034 Sum_probs=40.2
Q ss_pred ccccccHHhHHHHcCCChHHHHHHHHHHHHcCccceEecCCCCeEEEecC
Q 013559 349 PFVSVDLHMMANAFKTSVAGIEKELEALITDNQIQARIDSHNKILYARHA 398 (441)
Q Consensus 349 pYs~I~L~~mA~~fg~s~~~~E~~L~~LI~~g~L~akID~~~gvv~~~~~ 398 (441)
....++-..||+.+|++.+.+-+.|.+|...|-|. .+...|.+-++++
T Consensus 44 ~~~~is~~eLa~~~g~sr~tVsr~L~~Le~~GlI~--r~~~~~~~~~n~~ 91 (95)
T TIGR01610 44 KQDRVTATVIAELTGLSRTHVSDAIKSLARRRIIF--RQGMMGIVGVNTP 91 (95)
T ss_pred cCCccCHHHHHHHHCcCHHHHHHHHHHHHHCCCee--eecCCceeecCCC
Confidence 46788999999999999999999999999999995 3455677777643
No 348
>TIGR00540 hemY_coli hemY protein. This is an uncharacterized protein encoded next to a heme-biosynthetic enzyme in two gamma division proteobacteria (E. coli and H. influenzae). It is known in no other species. The gene symbol hemY is unfortunate in that an unrelated protein, protoporphyrinogen oxidase, is designated as HemG in E. coli but as HemY in Bacillus subtilis.
Probab=36.56 E-value=4.8e+02 Score=26.66 Aligned_cols=100 Identities=12% Similarity=0.062 Sum_probs=68.4
Q ss_pred hHHHHHHHHcCCHHHHHHHHHHHHhhhcCchhHHHHHHHHHHHHHHhcCHHHHHhHHHHHhcc--cccC-----------
Q 013559 143 NDFGDFYYAHGALGDAFKSYVRTRDYCTTSKHIIHMCMSAILVSIEMGQFTHVTSYVSKAEQT--PEAL----------- 209 (441)
Q Consensus 143 ~~la~~~~~~Gd~~~A~~~~~~~r~~~~~~~~~~~~~l~~i~~~i~~~~~~~~~~~~~ka~~~--~~~~----------- 209 (441)
..++.++.+.|+++.|.+.+.++.+..+... .+......+.+..|||+.+...+.++... .++.
T Consensus 157 ~~~a~l~l~~~~~~~Al~~l~~l~~~~P~~~---~~l~ll~~~~~~~~d~~~a~~~l~~l~k~~~~~~~~~~~l~~~a~~ 233 (409)
T TIGR00540 157 IARTRILLAQNELHAARHGVDKLLEMAPRHK---EVLKLAEEAYIRSGAWQALDDIIDNMAKAGLFDDEEFADLEQKAEI 233 (409)
T ss_pred HHHHHHHHHCCCHHHHHHHHHHHHHhCCCCH---HHHHHHHHHHHHHhhHHHHHHHHHHHHHcCCCCHHHHHHHHHHHHH
Confidence 3458999999999999999999877753332 45556677789999999888888777643 1100
Q ss_pred ---------------------Chh---hhhhHHHHHHHHhcccccHHHHHHHHHhcCcCC
Q 013559 210 ---------------------EPV---TIAKLRCAAGLAHLEARKYKLAARKFLEVGPDL 245 (441)
Q Consensus 210 ---------------------d~~---~~~~l~~~~gl~~l~~r~y~~Aa~~Fl~~~~t~ 245 (441)
.|. -...+..+.|..++..|++..|...+-+.....
T Consensus 234 ~~l~~~~~~~~~~~L~~~~~~~p~~~~~~~~l~~~~a~~l~~~g~~~~A~~~l~~~l~~~ 293 (409)
T TIGR00540 234 GLLDEAMADEGIDGLLNWWKNQPRHRRHNIALKIALAEHLIDCDDHDSAQEIIFDGLKKL 293 (409)
T ss_pred HHHHHHHHhcCHHHHHHHHHHCCHHHhCCHHHHHHHHHHHHHCCChHHHHHHHHHHHhhC
Confidence 010 023455666667777778888777777766543
No 349
>KOG0543 consensus FKBP-type peptidyl-prolyl cis-trans isomerase [Posttranslational modification, protein turnover, chaperones]
Probab=36.56 E-value=3e+02 Score=28.44 Aligned_cols=82 Identities=12% Similarity=0.152 Sum_probs=61.4
Q ss_pred hHHHHHh-HHhHHHHHHHHcCCHHHHHHHHHHHHhhhcCchhHHHHHHHHHHHHHHhcCHHHHHhHHHHHhcc-cccCCh
Q 013559 134 IKESIRM-GYNDFGDFYYAHGALGDAFKSYVRTRDYCTTSKHIIHMCMSAILVSIEMGQFTHVTSYVSKAEQT-PEALEP 211 (441)
Q Consensus 134 ~~esir~-~~~~la~~~~~~Gd~~~A~~~~~~~r~~~~~~~~~~~~~l~~i~~~i~~~~~~~~~~~~~ka~~~-~~~~d~ 211 (441)
.-.+++. +++.+|--|.+.++|.+|+++..++.+.-.. + .-.++..-++.+..++++.|...+.|+... ++ +.
T Consensus 251 ~~~~~k~~~~lNlA~c~lKl~~~~~Ai~~c~kvLe~~~~--N-~KALyRrG~A~l~~~e~~~A~~df~ka~k~~P~--Nk 325 (397)
T KOG0543|consen 251 KAEALKLACHLNLAACYLKLKEYKEAIESCNKVLELDPN--N-VKALYRRGQALLALGEYDLARDDFQKALKLEPS--NK 325 (397)
T ss_pred HHHHHHHHHhhHHHHHHHhhhhHHHHHHHHHHHHhcCCC--c-hhHHHHHHHHHHhhccHHHHHHHHHHHHHhCCC--cH
Confidence 3345554 7999999999999999999999988665322 2 445678888899999999999999999775 33 34
Q ss_pred hhhhhHHHH
Q 013559 212 VTIAKLRCA 220 (441)
Q Consensus 212 ~~~~~l~~~ 220 (441)
+.++.|..+
T Consensus 326 a~~~el~~l 334 (397)
T KOG0543|consen 326 AARAELIKL 334 (397)
T ss_pred HHHHHHHHH
Confidence 455554444
No 350
>TIGR00498 lexA SOS regulatory protein LexA. LexA acts as a homodimer to repress a number of genes involved in the response to DNA damage (SOS response), including itself and RecA. RecA, in the presence of single-stranded DNA, acts as a co-protease to activate a latent autolytic protease activity (EC 3.4.21.88) of LexA, where the active site Ser is part of LexA. The autolytic cleavage site is an Ala-Gly bond in LexA (at position 84-85 in E. coli LexA; this sequence is replaced by Gly-Gly in Synechocystis). The cleavage leads to derepression of the SOS regulon and eventually to DNA repair. LexA in Bacillus subtilis is called DinR. LexA is much less broadly distributed than RecA.
Probab=36.44 E-value=46 Score=30.55 Aligned_cols=33 Identities=21% Similarity=0.225 Sum_probs=30.4
Q ss_pred ccHHhHHHHcCCC-hHHHHHHHHHHHHcCccceE
Q 013559 353 VDLHMMANAFKTS-VAGIEKELEALITDNQIQAR 385 (441)
Q Consensus 353 I~L~~mA~~fg~s-~~~~E~~L~~LI~~g~L~ak 385 (441)
.++..||+.+|++ ...+-+.|..|...|-|...
T Consensus 26 ~~~~ela~~~~~~s~~tv~~~l~~L~~~g~i~~~ 59 (199)
T TIGR00498 26 PSIREIARAVGLRSPSAAEEHLKALERKGYIERD 59 (199)
T ss_pred CcHHHHHHHhCCCChHHHHHHHHHHHHCCCEecC
Confidence 8899999999998 99999999999999988654
No 351
>PF07079 DUF1347: Protein of unknown function (DUF1347); InterPro: IPR010764 This family consists of several hypothetical bacterial proteins of around 610 residues in length. Members of this family are highly conserved and seem to be specific to Chlamydia species. The function of this family is unknown.
Probab=36.43 E-value=2.5e+02 Score=29.70 Aligned_cols=92 Identities=12% Similarity=0.049 Sum_probs=70.7
Q ss_pred HHHHHHHcCCHHHHHHHHHHHHhhhcCch--hHHHHHHHHHHHHHHhcCHHHHHhHHHHHhcccccCChhhhhhHHHHHH
Q 013559 145 FGDFYYAHGALGDAFKSYVRTRDYCTTSK--HIIHMCMSAILVSIEMGQFTHVTSYVSKAEQTPEALEPVTIAKLRCAAG 222 (441)
Q Consensus 145 la~~~~~~Gd~~~A~~~~~~~r~~~~~~~--~~~~~~l~~i~~~i~~~~~~~~~~~~~ka~~~~~~~d~~~~~~l~~~~g 222 (441)
-|-..-+.|+.++|-+.+.++.+..+++. -+-+++.+.|--+.+.+|.+.+...+...+.....+. -+-.+.|
T Consensus 12 Qgf~Lqkq~~~~esEkifskI~~e~~~~~f~lkeEvl~grilnAffl~nld~Me~~l~~l~~~~~~s~-----~l~LF~~ 86 (549)
T PF07079_consen 12 QGFILQKQKKFQESEKIFSKIYDEKESSPFLLKEEVLGGRILNAFFLNNLDLMEKQLMELRQQFGKSA-----YLPLFKA 86 (549)
T ss_pred hhHHHHHHhhhhHHHHHHHHHHHHhhcchHHHHHHHHhhHHHHHHHHhhHHHHHHHHHHHHHhcCCch-----HHHHHHH
Confidence 35567788999999999999977665442 2336788888889999999999988887776543333 3556789
Q ss_pred HHhcccccHHHHHHHHHhc
Q 013559 223 LAHLEARKYKLAARKFLEV 241 (441)
Q Consensus 223 l~~l~~r~y~~Aa~~Fl~~ 241 (441)
+.+-.++.|.+|.+.|---
T Consensus 87 L~~Y~~k~~~kal~~ls~w 105 (549)
T PF07079_consen 87 LVAYKQKEYRKALQALSVW 105 (549)
T ss_pred HHHHHhhhHHHHHHHHHHH
Confidence 9999999999998877643
No 352
>COG4565 CitB Response regulator of citrate/malate metabolism [Transcription / Signal transduction mechanisms]
Probab=36.40 E-value=2.9e+02 Score=26.16 Aligned_cols=39 Identities=23% Similarity=0.297 Sum_probs=35.3
Q ss_pred ccccccHHhHHHHcCCChHHHHHHHHHHHHcCccceEec
Q 013559 349 PFVSVDLHMMANAFKTSVAGIEKELEALITDNQIQARID 387 (441)
Q Consensus 349 pYs~I~L~~mA~~fg~s~~~~E~~L~~LI~~g~L~akID 387 (441)
|=...|-+.+|++.|+|--.+-+.|.-|+..|.|.+.|-
T Consensus 170 ~~~~~Taeela~~~giSRvTaRRYLeyl~~~~~l~a~i~ 208 (224)
T COG4565 170 PDQELTAEELAQALGISRVTARRYLEYLVSNGILEAEIH 208 (224)
T ss_pred cCCccCHHHHHHHhCccHHHHHHHHHHHHhcCeeeEEee
Confidence 457788999999999999999999999999999988764
No 353
>TIGR02018 his_ut_repres histidine utilization repressor, proteobacterial. This model represents a proteobacterial histidine utilization repressor. It is usually found clustered with the enzymes HutUHIG so that it can regulate its own expression as well. A number of species have several paralogs and may fine-tune the regulation according to levels of degradation intermediates such as urocanate. This family belongs to the larger GntR family of transcriptional regulators.
Probab=35.97 E-value=99 Score=28.94 Aligned_cols=63 Identities=13% Similarity=0.139 Sum_probs=49.9
Q ss_pred HHHHHHHHHHHHHHhccccccc-cHHhHHHHcCCChHHHHHHHHHHHHcCccceEecCCCCeEEEe
Q 013559 332 ETLYDQIRNKALIQYTHPFVSV-DLHMMANAFKTSVAGIEKELEALITDNQIQARIDSHNKILYAR 396 (441)
Q Consensus 332 ~~l~~~iR~~~i~qy~~pYs~I-~L~~mA~~fg~s~~~~E~~L~~LI~~g~L~akID~~~gvv~~~ 396 (441)
..+.+.++.++..--+.|=..+ +-..||+.||+|-..+-+-|..|+.+|-|.-+ +-.|+.+..
T Consensus 4 ~qi~~~l~~~I~~g~~~~g~~LPsE~eLa~~~~VSR~TVR~Al~~L~~eGli~r~--~G~GtfV~~ 67 (230)
T TIGR02018 4 QRIKQDILERIRSGEWPPGHRIPSEHELVAQYGCSRMTVNRALRELTDAGLLERR--QGVGTFVAE 67 (230)
T ss_pred HHHHHHHHHHHHhCCCCCCCcCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEe--cCCEEEEcc
Confidence 3456677777777677888888 89999999999999999999999999988532 334666654
No 354
>PF07106 TBPIP: Tat binding protein 1(TBP-1)-interacting protein (TBPIP); InterPro: IPR010776 This family consists of several eukaryotic TBP-1 interacting protein (TBPIP) sequences. TBP-1 has been demonstrated to interact with the human immunodeficiency virus type 1 (HIV-1) viral protein Tat, then modulate the essential replication process of HIV. In addition, TBP-1 has been shown to be a component of the 26S proteasome, a basic multiprotein complex that degrades ubiquitinated proteins in an ATP-dependent fashion. Human TBPIP interacts with human TBP-1 then modulates the inhibitory action of human TBP-1 on HIV-Tat-mediated transactivation [].
Probab=35.42 E-value=3.2e+02 Score=24.30 Aligned_cols=48 Identities=21% Similarity=0.422 Sum_probs=35.4
Q ss_pred cccccccHHhHHHHcCCChHHHHHHHHHHHHcCccceEecCCCCeEEEe
Q 013559 348 HPFVSVDLHMMANAFKTSVAGIEKELEALITDNQIQARIDSHNKILYAR 396 (441)
Q Consensus 348 ~pYs~I~L~~mA~~fg~s~~~~E~~L~~LI~~g~L~akID~~~gvv~~~ 396 (441)
+||+..++..-=.. +++-..+.+-|-.|..+|+|.+|.=....+-..+
T Consensus 15 RPys~~di~~nL~~-~~~K~~v~k~Ld~L~~~g~i~~K~~GKqkiY~~~ 62 (169)
T PF07106_consen 15 RPYSAQDIFDNLHN-KVGKTAVQKALDSLVEEGKIVEKEYGKQKIYFAN 62 (169)
T ss_pred CCCcHHHHHHHHHh-hccHHHHHHHHHHHHhCCCeeeeeecceEEEeeC
Confidence 79998887432222 5788899999999999999999965555443333
No 355
>COG2976 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=35.41 E-value=3.8e+02 Score=25.09 Aligned_cols=24 Identities=8% Similarity=-0.017 Sum_probs=13.7
Q ss_pred HhHHHHHHHHcCCHHHHHHHHHHH
Q 013559 142 YNDFGDFYYAHGALGDAFKSYVRT 165 (441)
Q Consensus 142 ~~~la~~~~~~Gd~~~A~~~~~~~ 165 (441)
..+||+..++.|.+++|++.+.-.
T Consensus 129 ~lRLArvq~q~~k~D~AL~~L~t~ 152 (207)
T COG2976 129 ALRLARVQLQQKKADAALKTLDTI 152 (207)
T ss_pred HHHHHHHHHHhhhHHHHHHHHhcc
Confidence 355566666666666666655543
No 356
>TIGR03697 NtcA_cyano global nitrogen regulator NtcA, cyanobacterial. Members of this protein family, found in the cyanobacteria, are the global nitrogen regulator NtcA. This DNA-binding transcriptional regulator is required for expressing many different ammonia-repressible genes. The consensus NtcA-binding site is G T A N(8)T A C.
Probab=34.78 E-value=1.6e+02 Score=26.11 Aligned_cols=41 Identities=20% Similarity=0.244 Sum_probs=33.9
Q ss_pred cccHHhHHHHcCCChHHHHHHHHHHHHcCccceEecCCCCeEEEe
Q 013559 352 SVDLHMMANAFKTSVAGIEKELEALITDNQIQARIDSHNKILYAR 396 (441)
Q Consensus 352 ~I~L~~mA~~fg~s~~~~E~~L~~LI~~g~L~akID~~~gvv~~~ 396 (441)
.++-..||..+|++.+.+-+.|.+|-.+|-|.. ..|.|+..
T Consensus 143 ~~t~~~iA~~lG~tretvsR~l~~l~~~g~I~~----~~~~i~I~ 183 (193)
T TIGR03697 143 RLSHQAIAEAIGSTRVTITRLLGDLRKKKLISI----HKKKITVH 183 (193)
T ss_pred CCCHHHHHHHhCCcHHHHHHHHHHHHHCCCEEe----cCCEEEEe
Confidence 578899999999999999999999999998854 24555555
No 357
>PF01710 HTH_Tnp_IS630: Transposase; InterPro: IPR002622 Transposase proteins are necessary for efficient DNA transposition. This entry includes insertion sequences from Synechocystis sp. (strain PCC 6803) three of which are characterised as homologous to bacterial IS5- and IS4- and to several members of the IS630-Tc1-mariner superfamily []. More information about these proteins can be found at Protein of the Month: Transposase [].
Probab=34.78 E-value=51 Score=27.80 Aligned_cols=43 Identities=16% Similarity=0.271 Sum_probs=34.4
Q ss_pred HHHHHHHHHhccccccccHHhHHHHcCCChHHHHHHHHHHHHcCccc
Q 013559 337 QIRNKALIQYTHPFVSVDLHMMANAFKTSVAGIEKELEALITDNQIQ 383 (441)
Q Consensus 337 ~iR~~~i~qy~~pYs~I~L~~mA~~fg~s~~~~E~~L~~LI~~g~L~ 383 (441)
.+|.+++. |++- .-++...|..||||...+..|+. -...|.+.
T Consensus 6 DlR~rVl~-~~~~--g~s~~eaa~~F~VS~~Tv~~W~k-~~~~G~~~ 48 (119)
T PF01710_consen 6 DLRQRVLA-YIEK--GKSIREAAKRFGVSRNTVYRWLK-RKETGDLE 48 (119)
T ss_pred HHHHHHHH-HHHc--cchHHHHHHHhCcHHHHHHHHHH-hccccccc
Confidence 36778886 5443 45899999999999999999999 77777663
No 358
>PF14493 HTH_40: Helix-turn-helix domain
Probab=34.75 E-value=55 Score=26.08 Aligned_cols=33 Identities=15% Similarity=0.189 Sum_probs=30.8
Q ss_pred ccccHHhHHHHcCCChHHHHHHHHHHHHcCc-cc
Q 013559 351 VSVDLHMMANAFKTSVAGIEKELEALITDNQ-IQ 383 (441)
Q Consensus 351 s~I~L~~mA~~fg~s~~~~E~~L~~LI~~g~-L~ 383 (441)
+..+++.+|+.-|+++..+...|++++..|. ++
T Consensus 12 ~G~si~eIA~~R~L~~sTI~~HL~~~~~~g~~~~ 45 (91)
T PF14493_consen 12 KGLSIEEIAKIRGLKESTIYGHLAELIESGEPLD 45 (91)
T ss_pred cCCCHHHHHHHcCCCHHHHHHHHHHHHHhCCCCC
Confidence 5789999999999999999999999999998 54
No 359
>cd06171 Sigma70_r4 Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in Escherichia coli (Ec) sigma70, the main housekeeping sigma, and related sigma-factors (SFs). A SF is a dissociable subunit of RNA polymerase, it directs bacterial or plastid core RNA polymerase to specific promoter elements located upstream of transcription initiation points. The SR4 of Ec sigma70 and other essential primary SFs contact promoter sequences located 35 base-pairs upstream of the initiation point, recognizing a 6-base-pair -35 consensus TTGACA. Sigma70 related SFs also include SFs which are dispensable for bacterial cell growth for example Ec sigmaS, SFs which activate regulons in response to a specific signal for example heat-shock Ec sigmaH, and a group of SFs which includes the extracytoplasmic function (ECF) SFs and is typified by Ec sigmaE which contains SR2 and -4 only. ECF SFs direct the transcription of genes that regulate various responses including periplas
Probab=34.43 E-value=99 Score=20.59 Aligned_cols=27 Identities=11% Similarity=0.193 Sum_probs=23.7
Q ss_pred ccccHHhHHHHcCCChHHHHHHHHHHH
Q 013559 351 VSVDLHMMANAFKTSVAGIEKELEALI 377 (441)
Q Consensus 351 s~I~L~~mA~~fg~s~~~~E~~L~~LI 377 (441)
...+...+|+.+|++...+-+++....
T Consensus 25 ~~~~~~~ia~~~~~s~~~i~~~~~~~~ 51 (55)
T cd06171 25 EGLSYEEIAEILGISRSTVRQRLHRAL 51 (55)
T ss_pred cCCCHHHHHHHHCcCHHHHHHHHHHHH
Confidence 778999999999999999988887654
No 360
>PRK14999 histidine utilization repressor; Provisional
Probab=34.40 E-value=99 Score=29.22 Aligned_cols=65 Identities=15% Similarity=0.096 Sum_probs=52.1
Q ss_pred HHHHHHHHHHHHHHHhccccccc-cHHhHHHHcCCChHHHHHHHHHHHHcCccceEecCCCCeEEEec
Q 013559 331 VETLYDQIRNKALIQYTHPFVSV-DLHMMANAFKTSVAGIEKELEALITDNQIQARIDSHNKILYARH 397 (441)
Q Consensus 331 ~~~l~~~iR~~~i~qy~~pYs~I-~L~~mA~~fg~s~~~~E~~L~~LI~~g~L~akID~~~gvv~~~~ 397 (441)
...+.+.|+.++...-+.|=..+ +=..||+.||+|-..+-+-|..|+.+|-|.-+ +-.|+.+...
T Consensus 14 y~qi~~~i~~~I~~g~~~~G~~LPsE~eLa~~~gVSR~TVR~Al~~L~~eGli~r~--~GkGTfV~~~ 79 (241)
T PRK14999 14 YETVKQDICKKIAGGVWQPHDRIPSEAELVAQYGFSRMTINRALRELTDEGWLVRL--QGVGTFVAEP 79 (241)
T ss_pred HHHHHHHHHHHHHcCCCCCCCcCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEe--cCcEEEECCC
Confidence 34566777777777677888889 89999999999999999999999999998432 4457776543
No 361
>PF14561 TPR_20: Tetratricopeptide repeat; PDB: 3QOU_A 2R5S_A 3QDN_B.
Probab=34.36 E-value=1.8e+02 Score=23.16 Aligned_cols=44 Identities=20% Similarity=0.141 Sum_probs=30.4
Q ss_pred HHHHHHHHHHHHHhhhhHHHHHhHHhHHHHHHHHcCCHHHHHHHHHHHHh
Q 013559 118 RKEKLENELNAYRTNLIKESIRMGYNDFGDFYYAHGALGDAFKSYVRTRD 167 (441)
Q Consensus 118 ~~~~Le~el~~~~~n~~~esir~~~~~la~~~~~~Gd~~~A~~~~~~~r~ 167 (441)
.++.|+..+.. |-... .+.+.+|..+...|++++|++.+-.+..
T Consensus 7 ~~~al~~~~a~---~P~D~---~ar~~lA~~~~~~g~~e~Al~~Ll~~v~ 50 (90)
T PF14561_consen 7 DIAALEAALAA---NPDDL---DARYALADALLAAGDYEEALDQLLELVR 50 (90)
T ss_dssp HHHHHHHHHHH---STT-H---HHHHHHHHHHHHTT-HHHHHHHHHHHHC
T ss_pred cHHHHHHHHHc---CCCCH---HHHHHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 34555555542 22222 4779999999999999999999988743
No 362
>smart00421 HTH_LUXR helix_turn_helix, Lux Regulon. lux regulon (activates the bioluminescence operon
Probab=34.33 E-value=90 Score=21.32 Aligned_cols=29 Identities=10% Similarity=0.137 Sum_probs=25.0
Q ss_pred cccccHHhHHHHcCCChHHHHHHHHHHHH
Q 013559 350 FVSVDLHMMANAFKTSVAGIEKELEALIT 378 (441)
Q Consensus 350 Ys~I~L~~mA~~fg~s~~~~E~~L~~LI~ 378 (441)
+...+...+|+.+|+|...+..++.++..
T Consensus 16 ~~g~s~~eia~~l~is~~tv~~~~~~~~~ 44 (58)
T smart00421 16 AEGLTNKEIAERLGISEKTVKTHLSNIMR 44 (58)
T ss_pred HcCCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 45679999999999999999999987744
No 363
>PRK09764 DNA-binding transcriptional repressor MngR; Provisional
Probab=34.24 E-value=1e+02 Score=29.06 Aligned_cols=63 Identities=13% Similarity=0.173 Sum_probs=51.2
Q ss_pred HHHHHHHHHHHHHHhccccccc-cHHhHHHHcCCChHHHHHHHHHHHHcCccceEecCCCCeEEEe
Q 013559 332 ETLYDQIRNKALIQYTHPFVSV-DLHMMANAFKTSVAGIEKELEALITDNQIQARIDSHNKILYAR 396 (441)
Q Consensus 332 ~~l~~~iR~~~i~qy~~pYs~I-~L~~mA~~fg~s~~~~E~~L~~LI~~g~L~akID~~~gvv~~~ 396 (441)
..+.+.|+.++..--+.|=..+ +=..||+.||+|...+-+-|..|+.+|-|.-+ +-.|+.+..
T Consensus 8 ~qi~~~L~~~I~~g~~~~G~~LPsE~eL~~~~~VSR~TvR~Al~~L~~eGli~r~--~G~GtfV~~ 71 (240)
T PRK09764 8 RQIADRIREQIARGELKPGDALPTESALQTEFGVSRVTVRQALRQLVEQQILESI--QGSGTYVKE 71 (240)
T ss_pred HHHHHHHHHHHHcCCCCCCCcCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEe--cCceeEEcc
Confidence 4566777777777777888888 78999999999999999999999999998543 345776654
No 364
>cd06170 LuxR_C_like C-terminal DNA-binding domain of LuxR-like proteins. This domain contains a helix-turn-helix motif and binds DNA. Proteins belonging to this group are response regulators; some act as transcriptional activators, others as transcriptional repressors. Many are active as homodimers. Many are two domain proteins in which the DNA binding property of the C-terminal DNA binding domain is modulated by modifications of the N-terminal domain. For example in the case of Lux R which participates in the regulation of gene expression in response to fluctuations in cell-population density (quorum-sensing), a signaling molecule, the pheromone Acyl HSL (N-acyl derivatives of homoserine lactone), binds to the N-terminal domain and leads to LuxR dimerization. For others phophorylation of the N-terminal domain leads to multimerization, for example Escherichia coli NarL and Sinorhizobium melilot FixJ. NarL controls gene expression of many respiratory-related operons when environmental
Probab=34.01 E-value=93 Score=21.38 Aligned_cols=29 Identities=10% Similarity=0.111 Sum_probs=24.8
Q ss_pred cccccHHhHHHHcCCChHHHHHHHHHHHH
Q 013559 350 FVSVDLHMMANAFKTSVAGIEKELEALIT 378 (441)
Q Consensus 350 Ys~I~L~~mA~~fg~s~~~~E~~L~~LI~ 378 (441)
+.-.+...+|+.+|+|+..+..++.++..
T Consensus 13 ~~~~s~~eia~~l~~s~~tv~~~~~~~~~ 41 (57)
T cd06170 13 AEGKTNKEIADILGISEKTVKTHLRNIMR 41 (57)
T ss_pred HcCCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 35679999999999999999999887644
No 365
>PRK11161 fumarate/nitrate reduction transcriptional regulator; Provisional
Probab=33.87 E-value=1.3e+02 Score=28.05 Aligned_cols=41 Identities=12% Similarity=0.139 Sum_probs=32.9
Q ss_pred cccHHhHHHHcCCChHHHHHHHHHHHHcCccceEecCCCCeEEEe
Q 013559 352 SVDLHMMANAFKTSVAGIEKELEALITDNQIQARIDSHNKILYAR 396 (441)
Q Consensus 352 ~I~L~~mA~~fg~s~~~~E~~L~~LI~~g~L~akID~~~gvv~~~ 396 (441)
.++-+.+|+.+|++.+.+-+.+.+|-.+|-|. ...+.+...
T Consensus 184 ~lt~~~iA~~lG~sr~tvsR~l~~l~~~g~I~----~~~~~i~i~ 224 (235)
T PRK11161 184 TMTRGDIGNYLGLTVETISRLLGRFQKSGMLA----VKGKYITIE 224 (235)
T ss_pred cccHHHHHHHhCCcHHHHHHHHHHHHHCCCEE----ecCCEEEEc
Confidence 47889999999999999999999999988774 333455554
No 366
>cd04761 HTH_MerR-SF Helix-Turn-Helix DNA binding domain of transcription regulators from the MerR superfamily. Helix-turn-helix (HTH) transcription regulator MerR superfamily, 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=33.77 E-value=77 Score=21.42 Aligned_cols=28 Identities=7% Similarity=-0.063 Sum_probs=22.8
Q ss_pred cHHhHHHHcCCChHHHHHHHHHHHHcCccceE
Q 013559 354 DLHMMANAFKTSVAGIEKELEALITDNQIQAR 385 (441)
Q Consensus 354 ~L~~mA~~fg~s~~~~E~~L~~LI~~g~L~ak 385 (441)
+++.+|+.+|+++..+..| +..|.|.+.
T Consensus 2 ~~~e~a~~~gv~~~tlr~~----~~~g~l~~~ 29 (49)
T cd04761 2 TIGELAKLTGVSPSTLRYY----ERIGLLSPA 29 (49)
T ss_pred cHHHHHHHHCcCHHHHHHH----HHCCCCCCC
Confidence 6789999999999987776 677777643
No 367
>PF12324 HTH_15: Helix-turn-helix domain of alkylmercury lyase; InterPro: IPR024259 Alkylmercury lyase (EC:4.99.1.2) cleaves the carbon-mercury bond of organomercurials such as phenylmercuric acetate. This entry represents the N-terminal helix-turn-helix domain.; PDB: 3FN8_B 3F2G_B 3F0P_A 3F2F_B 3F2H_A 3F0O_B 1S6L_A.
Probab=33.52 E-value=73 Score=24.96 Aligned_cols=36 Identities=19% Similarity=0.251 Sum_probs=25.7
Q ss_pred HHHHHhccccccccHHhHHHHcCCChHHHHHHHHHH
Q 013559 341 KALIQYTHPFVSVDLHMMANAFKTSVAGIEKELEAL 376 (441)
Q Consensus 341 ~~i~qy~~pYs~I~L~~mA~~fg~s~~~~E~~L~~L 376 (441)
+.+.+.+.-=.-|+...||.++|.+++++..-|..+
T Consensus 27 r~LLr~LA~G~PVt~~~LA~a~g~~~e~v~~~L~~~ 62 (77)
T PF12324_consen 27 RPLLRLLAKGQPVTVEQLAAALGWPVEEVRAALAAM 62 (77)
T ss_dssp HHHHHHHTTTS-B-HHHHHHHHT--HHHHHHHHHH-
T ss_pred HHHHHHHHcCCCcCHHHHHHHHCCCHHHHHHHHHhC
Confidence 345555666788999999999999999999999876
No 368
>PF01710 HTH_Tnp_IS630: Transposase; InterPro: IPR002622 Transposase proteins are necessary for efficient DNA transposition. This entry includes insertion sequences from Synechocystis sp. (strain PCC 6803) three of which are characterised as homologous to bacterial IS5- and IS4- and to several members of the IS630-Tc1-mariner superfamily []. More information about these proteins can be found at Protein of the Month: Transposase [].
Probab=33.45 E-value=47 Score=27.98 Aligned_cols=36 Identities=19% Similarity=0.171 Sum_probs=30.1
Q ss_pred HHHHHhccccccccHHhHHHHcCCChHHHHHHHHHH
Q 013559 341 KALIQYTHPFVSVDLHMMANAFKTSVAGIEKELEAL 376 (441)
Q Consensus 341 ~~i~qy~~pYs~I~L~~mA~~fg~s~~~~E~~L~~L 376 (441)
..+.+++.-+..+++..+|+.||++...+-..|-+|
T Consensus 60 ~~L~~~v~~~pd~tl~Ela~~l~Vs~~ti~~~Lkrl 95 (119)
T PF01710_consen 60 DELKALVEENPDATLRELAERLGVSPSTIWRALKRL 95 (119)
T ss_pred HHHHHHHHHCCCcCHHHHHHHcCCCHHHHHHHHHHc
Confidence 345666777999999999999999999988887665
No 369
>PF07720 TPR_3: Tetratricopeptide repeat; InterPro: IPR011716 This entry includes tetratricopeptide-like repeats found in the LcrH/SycD-like chaperones [].; PDB: 3KS2_O 3GZ2_A 3GZ1_A 3GYZ_A 4AM9_A 2VGX_A 2VGY_A.
Probab=33.37 E-value=75 Score=20.86 Aligned_cols=23 Identities=13% Similarity=0.268 Sum_probs=18.9
Q ss_pred HHhHHHHHHHHcCCHHHHHHHHH
Q 013559 141 GYNDFGDFYYAHGALGDAFKSYV 163 (441)
Q Consensus 141 ~~~~la~~~~~~Gd~~~A~~~~~ 163 (441)
..+.+|-.++..|++++|.+.|.
T Consensus 3 ~~y~~a~~~y~~~ky~~A~~~~~ 25 (36)
T PF07720_consen 3 YLYGLAYNFYQKGKYDEAIHFFQ 25 (36)
T ss_dssp HHHHHHHHHHHTT-HHHHHHHHH
T ss_pred HHHHHHHHHHHHhhHHHHHHHHH
Confidence 45788999999999999999944
No 370
>PF12728 HTH_17: Helix-turn-helix domain
Probab=33.27 E-value=63 Score=22.40 Aligned_cols=38 Identities=11% Similarity=0.050 Sum_probs=27.7
Q ss_pred ccHHhHHHHcCCChHHHHHHHHHHHHcCccceEecCCCCeEEEe
Q 013559 353 VDLHMMANAFKTSVAGIEKELEALITDNQIQARIDSHNKILYAR 396 (441)
Q Consensus 353 I~L~~mA~~fg~s~~~~E~~L~~LI~~g~L~akID~~~gvv~~~ 396 (441)
+|.+.+|+.||+|...+. ++|..|.|.+- .+.+.....
T Consensus 2 lt~~e~a~~l~is~~tv~----~~~~~g~i~~~--~~g~~~~~~ 39 (51)
T PF12728_consen 2 LTVKEAAELLGISRSTVY----RWIRQGKIPPF--KIGRKWRIP 39 (51)
T ss_pred CCHHHHHHHHCcCHHHHH----HHHHcCCCCeE--EeCCEEEEe
Confidence 477899999999988855 55678999775 344545444
No 371
>TIGR02675 tape_meas_nterm tape measure domain. Proteins containing this domain are strictly bacterial, including bacteriophage and prophage regions of bacterial genomes. Most members are 800 to 1800 amino acids long, making them among the longest predicted proteins of their respective phage genomes, where they are encoded in tail protein regions. This roughly 80-residue domain described here usually begins between residue 100 and 250. Many members are known or predicted to act as phage tail tape measure proteins, a minor tail component that regulates tail length.
Probab=33.26 E-value=48 Score=25.64 Aligned_cols=27 Identities=22% Similarity=0.436 Sum_probs=22.1
Q ss_pred HHhHHHHcCCChHHHHHHHHHHHHcCccceE
Q 013559 355 LHMMANAFKTSVAGIEKELEALITDNQIQAR 385 (441)
Q Consensus 355 L~~mA~~fg~s~~~~E~~L~~LI~~g~L~ak 385 (441)
+..+|+.+|++..+ +.+|+.+|+|.+.
T Consensus 47 ~~~lAk~~G~t~~~----l~~~~~~Gkit~~ 73 (75)
T TIGR02675 47 LQALAKAMGVTRGE----LRKMLSDGKLTAD 73 (75)
T ss_pred HHHHHHHhCCCHHH----HHHHHHCCCCccc
Confidence 46889999999775 6889999999763
No 372
>TIGR00373 conserved hypothetical protein TIGR00373. This family of proteins is, so far, restricted to archaeal genomes. The family appears to be distantly related to the N-terminal region of the eukaryotic transcription initiation factor IIE alpha chain.
Probab=32.93 E-value=3.5e+02 Score=24.01 Aligned_cols=46 Identities=11% Similarity=-0.011 Sum_probs=36.8
Q ss_pred ccccccHHhHHHHcCCChHHHHHHHHHHHHcCccceEe--cCCCCeEE
Q 013559 349 PFVSVDLHMMANAFKTSVAGIEKELEALITDNQIQARI--DSHNKILY 394 (441)
Q Consensus 349 pYs~I~L~~mA~~fg~s~~~~E~~L~~LI~~g~L~akI--D~~~gvv~ 394 (441)
.++.++-+.||+.+|++...+-+-|-.|-.+|-+.-+- |..+|...
T Consensus 25 ~~~~~tdEeLa~~Lgi~~~~VRk~L~~L~e~~Lv~~~r~r~~~~gw~~ 72 (158)
T TIGR00373 25 IKGEFTDEEISLELGIKLNEVRKALYALYDAGLADYKRRKDDETGWYE 72 (158)
T ss_pred ccCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCceeeeeeecCCCcEE
Confidence 46889999999999999999999999999999884322 34445433
No 373
>PRK05626 rpsO 30S ribosomal protein S15; Reviewed
Probab=32.79 E-value=64 Score=26.00 Aligned_cols=55 Identities=11% Similarity=0.122 Sum_probs=32.5
Q ss_pred HHHHhhccCchhhHHHHHHHHhcCCCchhHHHHHHHHHHHHHhcCChHHHHHHHHHhh
Q 013559 37 VEAYASLYQGRTKITRLMFIADHCDIASMQLEALRMAYDEIKKGENTQLFREVVKKID 94 (441)
Q Consensus 37 l~~y~~~y~g~~~i~rL~fi~~~~~~~~~~~~a~~~~~~~lk~t~~~~~Y~~~~~~l~ 94 (441)
||..|.+++.|....+-.|-...+ --.-..--+.++.+++++ |.+.|..+++.|+
T Consensus 32 LT~rI~~L~~Hlk~~~KD~~srrg--L~~lv~kRkrlL~YL~~~-d~~~Y~~li~~Lg 86 (89)
T PRK05626 32 LTERINHLTEHLKEHKKDHHSRRG--LLKMVGQRRKLLDYLKKK-DVERYRALIERLG 86 (89)
T ss_pred HHHHHHHHHHHHHHcccchhhHHH--HHHHHHhHHHHHHHHHhc-CHHHHHHHHHHhC
Confidence 455555555555444444444433 222233344677788766 6788999999875
No 374
>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=32.63 E-value=73 Score=23.39 Aligned_cols=35 Identities=9% Similarity=0.107 Sum_probs=28.7
Q ss_pred HHHHHHHHhccccccccHHhHHHHcCCChHHHHHHHHH
Q 013559 338 IRNKALIQYTHPFVSVDLHMMANAFKTSVAGIEKELEA 375 (441)
Q Consensus 338 iR~~~i~qy~~pYs~I~L~~mA~~fg~s~~~~E~~L~~ 375 (441)
+|..|..=|+ +-.++..+|+.+|++...+-.|..+
T Consensus 2 ~k~~A~~LY~---~G~~~~eIA~~Lg~~~~TV~~W~~r 36 (58)
T PF06056_consen 2 VKEQARSLYL---QGWSIKEIAEELGVPRSTVYSWKDR 36 (58)
T ss_pred HHHHHHHHHH---cCCCHHHHHHHHCCChHHHHHHHHh
Confidence 4667777784 5678999999999999999999866
No 375
>PF10771 DUF2582: Protein of unknown function (DUF2582); InterPro: IPR019707 This entry represents conserved proteins found in bacteria and archaea. The function is not known. ; PDB: 2L02_B 2L01_A.
Probab=32.13 E-value=1e+02 Score=23.28 Aligned_cols=51 Identities=18% Similarity=0.148 Sum_probs=41.2
Q ss_pred HHHhccccccccHHhHHHHcCCChHHHHHHHHHHHHcCccceEecCCCCeEEE
Q 013559 343 LIQYTHPFVSVDLHMMANAFKTSVAGIEKELEALITDNQIQARIDSHNKILYA 395 (441)
Q Consensus 343 i~qy~~pYs~I~L~~mA~~fg~s~~~~E~~L~~LI~~g~L~akID~~~gvv~~ 395 (441)
+=+++......+++.+++..|++..++-.-|-=|.++++|. |+..++.+++
T Consensus 13 Vw~~L~~~~~~s~~el~k~~~l~~~~~~~AiGWLarE~KI~--~~~~~~~~~v 63 (65)
T PF10771_consen 13 VWQLLNENGEWSVSELKKATGLSDKEVYLAIGWLARENKIE--FEEKNGELYV 63 (65)
T ss_dssp HHHHHCCSSSEEHHHHHHHCT-SCHHHHHHHHHHHCTTSEE--EEEETTEEEE
T ss_pred HHHHHhhCCCcCHHHHHHHhCcCHHHHHHHHHHHhccCcee--EEeeCCEEEE
Confidence 45677778899999999999999999999999999999994 5566666554
No 376
>KOG0495 consensus HAT repeat protein [RNA processing and modification]
Probab=31.76 E-value=7.7e+02 Score=27.57 Aligned_cols=68 Identities=16% Similarity=0.157 Sum_probs=48.0
Q ss_pred HHHHHHHHHHHHHhcCHHHHHhHHHHHhcc-cc-c----------CChhhh-------------hhHHHHHHHHhccccc
Q 013559 176 IHMCMSAILVSIEMGQFTHVTSYVSKAEQT-PE-A----------LEPVTI-------------AKLRCAAGLAHLEARK 230 (441)
Q Consensus 176 ~~~~l~~i~~~i~~~~~~~~~~~~~ka~~~-~~-~----------~d~~~~-------------~~l~~~~gl~~l~~r~ 230 (441)
..+.+..||+.+..|+.+.+...+.||-+- +. + ..+.++ ..+-+.-|...-.+++
T Consensus 753 ~~lwle~Ir~ElR~gn~~~a~~lmakALQecp~sg~LWaEaI~le~~~~rkTks~DALkkce~dphVllaia~lfw~e~k 832 (913)
T KOG0495|consen 753 ALLWLESIRMELRAGNKEQAELLMAKALQECPSSGLLWAEAIWLEPRPQRKTKSIDALKKCEHDPHVLLAIAKLFWSEKK 832 (913)
T ss_pred chhHHHHHHHHHHcCCHHHHHHHHHHHHHhCCccchhHHHHHHhccCcccchHHHHHHHhccCCchhHHHHHHHHHHHHH
Confidence 456788999999999999999999988543 22 1 112222 1233444556667899
Q ss_pred HHHHHHHHHhcCc
Q 013559 231 YKLAARKFLEVGP 243 (441)
Q Consensus 231 y~~Aa~~Fl~~~~ 243 (441)
|.+|.+.|.-+..
T Consensus 833 ~~kar~Wf~Ravk 845 (913)
T KOG0495|consen 833 IEKAREWFERAVK 845 (913)
T ss_pred HHHHHHHHHHHHc
Confidence 9999999998875
No 377
>PF14502 HTH_41: Helix-turn-helix domain
Probab=31.52 E-value=75 Score=22.53 Aligned_cols=30 Identities=20% Similarity=0.290 Sum_probs=26.9
Q ss_pred cHHhHHHHcCCChHHHHHHHHHHHHcCccc
Q 013559 354 DLHMMANAFKTSVAGIEKELEALITDNQIQ 383 (441)
Q Consensus 354 ~L~~mA~~fg~s~~~~E~~L~~LI~~g~L~ 383 (441)
+++.+++.|+++.-.++.-|.-|-.+|-+.
T Consensus 8 tI~e~~~~~~vs~GtiQ~Alk~Le~~gaI~ 37 (48)
T PF14502_consen 8 TISEYSEKFGVSRGTIQNALKFLEENGAIK 37 (48)
T ss_pred CHHHHHHHhCcchhHHHHHHHHHHHCCcEE
Confidence 688999999999999999999998888664
No 378
>COG1497 Predicted transcriptional regulator [Transcription]
Probab=31.44 E-value=86 Score=30.10 Aligned_cols=44 Identities=11% Similarity=0.229 Sum_probs=35.0
Q ss_pred HHHHHhccccccccHHhHHHHcCCChHHHHHHHHHHHHcCccce
Q 013559 341 KALIQYTHPFVSVDLHMMANAFKTSVAGIEKELEALITDNQIQA 384 (441)
Q Consensus 341 ~~i~qy~~pYs~I~L~~mA~~fg~s~~~~E~~L~~LI~~g~L~a 384 (441)
++++-...-+-.+.-+.+|+.+|+++..+-..+-+||.+|-++-
T Consensus 14 qIL~ei~~~qp~v~q~eIA~~lgiT~QaVsehiK~Lv~eG~i~~ 57 (260)
T COG1497 14 QILSEIAVRQPRVKQKEIAKKLGITLQAVSEHIKELVKEGLIEK 57 (260)
T ss_pred HHHHHHHHhCCCCCHHHHHHHcCCCHHHHHHHHHHHHhccceee
Confidence 33333333356889999999999999999999999999997643
No 379
>PF12739 TRAPPC-Trs85: ER-Golgi trafficking TRAPP I complex 85 kDa subunit; InterPro: IPR024420 This entry represents Trs85, a subunit of the TRAPP III complex []. Trs85 is a multimeric guanine nucleotide-exchange factor for Ypt1, required for membrane expansion during autophagy and the CVT pathway. It directs Ypt1 to the phagophore assembly site [, , , ].
Probab=31.18 E-value=2.4e+02 Score=29.25 Aligned_cols=59 Identities=10% Similarity=0.090 Sum_probs=42.6
Q ss_pred HHHHHhHHhHHHHHHHHcCCHHHHHHHHHHHHhhh-cCch-hHHHHHHHHHHHHHHhcCHH
Q 013559 135 KESIRMGYNDFGDFYYAHGALGDAFKSYVRTRDYC-TTSK-HIIHMCMSAILVSIEMGQFT 193 (441)
Q Consensus 135 ~esir~~~~~la~~~~~~Gd~~~A~~~~~~~r~~~-~~~~-~~~~~~l~~i~~~i~~~~~~ 193 (441)
.+++...+..||++.+=.|||+-|...|.-++... .+.. ..+.-+.+++.++++++.-.
T Consensus 204 ~~S~E~q~R~LAD~aFml~Dy~~A~s~Y~~~k~Df~~Dkaw~~~A~~~Em~alsl~~~~~~ 264 (414)
T PF12739_consen 204 ADSPEAQMRRLADLAFMLRDYELAYSTYRLLKKDFKNDKAWKYLAGAQEMAALSLLMQGQS 264 (414)
T ss_pred CCChHHHHHHHHHHHHHHccHHHHHHHHHHHHHHHhhchhHHHHHhHHHHHHHHHHhcCCC
Confidence 35666778899999999999999999999885444 2221 12345667777887776543
No 380
>PF12688 TPR_5: Tetratrico peptide repeat
Probab=30.96 E-value=3.3e+02 Score=23.02 Aligned_cols=62 Identities=6% Similarity=0.113 Sum_probs=39.3
Q ss_pred HHHHhHHhHHHHHHHHcCCHHHHHHHHHHHHhhhcCc--hhHHHHHHHHHHHHHHhcCHHHHHhHH
Q 013559 136 ESIRMGYNDFGDFYYAHGALGDAFKSYVRTRDYCTTS--KHIIHMCMSAILVSIEMGQFTHVTSYV 199 (441)
Q Consensus 136 esir~~~~~la~~~~~~Gd~~~A~~~~~~~r~~~~~~--~~~~~~~l~~i~~~i~~~~~~~~~~~~ 199 (441)
+.-++++..+|.-+...|++++|...+........+. ...+...+.. +-...|.+..+...+
T Consensus 35 ~~~~~a~i~lastlr~LG~~deA~~~L~~~~~~~p~~~~~~~l~~f~Al--~L~~~gr~~eAl~~~ 98 (120)
T PF12688_consen 35 ADRRRALIQLASTLRNLGRYDEALALLEEALEEFPDDELNAALRVFLAL--ALYNLGRPKEALEWL 98 (120)
T ss_pred hHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHCCCccccHHHHHHHHH--HHHHCCCHHHHHHHH
Confidence 3345689999999999999999999999886544321 1122222111 223446777666543
No 381
>PRK00215 LexA repressor; Validated
Probab=30.79 E-value=67 Score=29.59 Aligned_cols=34 Identities=21% Similarity=0.230 Sum_probs=30.8
Q ss_pred cccHHhHHHHcCC-ChHHHHHHHHHHHHcCccceE
Q 013559 352 SVDLHMMANAFKT-SVAGIEKELEALITDNQIQAR 385 (441)
Q Consensus 352 ~I~L~~mA~~fg~-s~~~~E~~L~~LI~~g~L~ak 385 (441)
..++..||+.+|+ +...+-+.|..|...|-|.-.
T Consensus 23 ~~s~~ela~~~~~~~~~tv~~~l~~L~~~g~i~~~ 57 (205)
T PRK00215 23 PPSRREIADALGLRSPSAVHEHLKALERKGFIRRD 57 (205)
T ss_pred CCCHHHHHHHhCCCChHHHHHHHHHHHHCCCEEeC
Confidence 4799999999999 999999999999999999543
No 382
>TIGR00635 ruvB Holliday junction DNA helicase, RuvB subunit. RuvA specifically binds Holliday junctions as a sandwich of two tetramers and maintains the configuration of the junction. It forms a complex with two hexameric rings of RuvB, the subunit that contains helicase activity. The complex drives ATP-dependent branch migration of the Holliday junction recombination intermediate. The endonuclease RuvC resolves junctions.
Probab=30.78 E-value=3.6e+02 Score=26.11 Aligned_cols=32 Identities=28% Similarity=0.305 Sum_probs=28.8
Q ss_pred cccHHhHHHHcCCChHHHHHHHH-HHHHcCccc
Q 013559 352 SVDLHMMANAFKTSVAGIEKELE-ALITDNQIQ 383 (441)
Q Consensus 352 ~I~L~~mA~~fg~s~~~~E~~L~-~LI~~g~L~ 383 (441)
.++++.+|+.+|+++..++..+. .||..|-|.
T Consensus 255 ~~~~~~ia~~lg~~~~~~~~~~e~~Li~~~li~ 287 (305)
T TIGR00635 255 PVGLKTLAAALGEDADTIEDVYEPYLLQIGFLQ 287 (305)
T ss_pred cccHHHHHHHhCCCcchHHHhhhHHHHHcCCcc
Confidence 47899999999999999999999 699988883
No 383
>CHL00027 rps15 ribosomal protein S15
Probab=30.61 E-value=54 Score=26.51 Aligned_cols=55 Identities=5% Similarity=0.088 Sum_probs=33.3
Q ss_pred HHHHhhccCchhhHHHHHHHHhcCCCchhHHHHHHHHHHHHHhcCChHHHHHHHHHhh
Q 013559 37 VEAYASLYQGRTKITRLMFIADHCDIASMQLEALRMAYDEIKKGENTQLFREVVKKID 94 (441)
Q Consensus 37 l~~y~~~y~g~~~i~rL~fi~~~~~~~~~~~~a~~~~~~~lk~t~~~~~Y~~~~~~l~ 94 (441)
||..|.+++.|....+-.|-...+ -..-..--+.++.+++++ |.+.|..+++.|+
T Consensus 29 LT~rI~~Lt~Hlk~hkKD~~s~Rg--L~~lv~kRkrLL~YL~r~-d~~~Y~~li~~Lg 83 (90)
T CHL00027 29 FTNKIRRLTSHLELHKKDYSSQRG--LRKILGKRQRLLAYLSKK-NRVRYKKLISQLG 83 (90)
T ss_pred HHHHHHHHHHHHHHCCCcchhHHH--HHHHHHHHHHHHHHHHhC-CHHHHHHHHHHhC
Confidence 455566666555444444444433 222233345678888776 7799999999876
No 384
>COG4783 Putative Zn-dependent protease, contains TPR repeats [General function prediction only]
Probab=30.50 E-value=6.8e+02 Score=26.58 Aligned_cols=170 Identities=14% Similarity=0.024 Sum_probs=112.6
Q ss_pred hHHhHHHHHHHHcCCHHHHHHHHHHHHhhhcCchhHHHHHHHHHHHHHHhcCHHHHHhHHHHHhcccccCChhhhhhHHH
Q 013559 140 MGYNDFGDFYYAHGALGDAFKSYVRTRDYCTTSKHIIHMCMSAILVSIEMGQFTHVTSYVSKAEQTPEALEPVTIAKLRC 219 (441)
Q Consensus 140 ~~~~~la~~~~~~Gd~~~A~~~~~~~r~~~~~~~~~~~~~l~~i~~~i~~~~~~~~~~~~~ka~~~~~~~d~~~~~~l~~ 219 (441)
.+.|..|--++..|++.+|.+.+..+.....++- . +.-....+.+..+....+.+.+.|+-...- .. .-+..
T Consensus 307 aa~YG~A~~~~~~~~~d~A~~~l~~L~~~~P~N~-~--~~~~~~~i~~~~nk~~~A~e~~~kal~l~P----~~-~~l~~ 378 (484)
T COG4783 307 AAQYGRALQTYLAGQYDEALKLLQPLIAAQPDNP-Y--YLELAGDILLEANKAKEAIERLKKALALDP----NS-PLLQL 378 (484)
T ss_pred HHHHHHHHHHHHhcccchHHHHHHHHHHhCCCCH-H--HHHHHHHHHHHcCChHHHHHHHHHHHhcCC----Cc-cHHHH
Confidence 3778899999999999999999998755543221 1 112244566788899999988888877532 11 33556
Q ss_pred HHHHHhcccccHHHHHHHHHhcCcCCCCCchhhhcHHHHHHHHHHHHHhcCChHHHHHhcccCHhhHhhhccchHHHHHH
Q 013559 220 AAGLAHLEARKYKLAARKFLEVGPDLGNSYNEVIAAQDVATYGGLCALASFDRAELKSKVIDNVNFRNFLELVPEVRELI 299 (441)
Q Consensus 220 ~~gl~~l~~r~y~~Aa~~Fl~~~~t~~~~~~el~s~~d~~~Y~~l~al~s~~R~eLk~~vl~~~~~~~~le~~p~~~~ll 299 (441)
..|-.++..|++.+|...+-+.....+++ + . .|=.|+- ...++.+.. +-+.-..-
T Consensus 379 ~~a~all~~g~~~eai~~L~~~~~~~p~d-p--~------~w~~LAq----ay~~~g~~~------------~a~~A~AE 433 (484)
T COG4783 379 NLAQALLKGGKPQEAIRILNRYLFNDPED-P--N------GWDLLAQ----AYAELGNRA------------EALLARAE 433 (484)
T ss_pred HHHHHHHhcCChHHHHHHHHHHhhcCCCC-c--h------HHHHHHH----HHHHhCchH------------HHHHHHHH
Confidence 67888999999999988877765433221 1 1 2211111 111111100 00111222
Q ss_pred HHHhcCCHHHHHHHHHHhHHhhhhchhHHHHHHHHHHHHHHHH
Q 013559 300 NDFYSSRYASCLDYLGNLKANLLLDIHLHDHVETLYDQIRNKA 342 (441)
Q Consensus 300 ~~f~~~~y~~~~~~L~~~~~~l~~D~~L~~h~~~l~~~iR~~~ 342 (441)
.-|+.++|......+....+....++.-+.-++..+..+|...
T Consensus 434 ~~~~~G~~~~A~~~l~~A~~~~~~~~~~~aR~dari~~~~~~~ 476 (484)
T COG4783 434 GYALAGRLEQAIIFLMRASQQVKLGFPDWARADARIDQLRQQN 476 (484)
T ss_pred HHHhCCCHHHHHHHHHHHHHhccCCcHHHHHHHHHHHHHHHHH
Confidence 3578999999999999999999999999999999988887554
No 385
>cd02680 MIT_calpain7_2 MIT: domain contained within Microtubule Interacting and Trafficking molecules. This sub-family of MIT domains is found in the nuclear thiol protease PalBH. The molecular function of the MIT domain is unclear.
Probab=30.08 E-value=42 Score=26.11 Aligned_cols=27 Identities=15% Similarity=0.180 Sum_probs=21.4
Q ss_pred HHHHHHHcCCHHHHHHHHHHHHhhhcC
Q 013559 145 FGDFYYAHGALGDAFKSYVRTRDYCTT 171 (441)
Q Consensus 145 la~~~~~~Gd~~~A~~~~~~~r~~~~~ 171 (441)
-|---=..|+|++|+++|....++|..
T Consensus 12 ~A~~eD~~gny~eA~~lY~~ale~~~~ 38 (75)
T cd02680 12 QAFDEDEKGNAEEAIELYTEAVELCIN 38 (75)
T ss_pred HHHHhhHhhhHHHHHHHHHHHHHHHHH
Confidence 334445789999999999999998853
No 386
>PF13551 HTH_29: Winged helix-turn helix
Probab=30.02 E-value=83 Score=25.35 Aligned_cols=36 Identities=14% Similarity=0.121 Sum_probs=29.3
Q ss_pred ccc-cHHhHHHHcCCChHHHHHHHHHHHHcCccceEec
Q 013559 351 VSV-DLHMMANAFKTSVAGIEKELEALITDNQIQARID 387 (441)
Q Consensus 351 s~I-~L~~mA~~fg~s~~~~E~~L~~LI~~g~L~akID 387 (441)
.-. +...+|+.||+|...+-+|+.++=.+| +.+-.+
T Consensus 10 ~g~~~~~~ia~~lg~s~~Tv~r~~~~~~~~G-~~~l~~ 46 (112)
T PF13551_consen 10 EGVSTIAEIARRLGISRRTVYRWLKRYREGG-IEGLLP 46 (112)
T ss_pred cCCCcHHHHHHHHCcCHHHHHHHHHHHHccc-HHHHHh
Confidence 344 699999999999999999999988777 444444
No 387
>PRK10219 DNA-binding transcriptional regulator SoxS; Provisional
Probab=30.00 E-value=1.3e+02 Score=24.32 Aligned_cols=38 Identities=5% Similarity=-0.061 Sum_probs=26.7
Q ss_pred HHHHHHHHHHHhccccccccHHhHHHHcCCChHHHHHHHHH
Q 013559 335 YDQIRNKALIQYTHPFVSVDLHMMANAFKTSVAGIEKELEA 375 (441)
Q Consensus 335 ~~~iR~~~i~qy~~pYs~I~L~~mA~~fg~s~~~~E~~L~~ 375 (441)
+..+...+-..+ ...++++.||+.+|+|...+.+...+
T Consensus 7 ~~~~~~~i~~~~---~~~~~~~~lA~~~~~S~~~l~r~f~~ 44 (107)
T PRK10219 7 IQTLIAWIDEHI---DQPLNIDVVAKKSGYSKWYLQRMFRT 44 (107)
T ss_pred HHHHHHHHHHhc---CCCCCHHHHHHHHCCCHHHHHHHHHH
Confidence 344433334444 56699999999999999887766655
No 388
>PF10516 SHNi-TPR: SHNi-TPR; InterPro: IPR019544 The tetratrico peptide repeat region (TPR) is a structural motif present in a wide range of proteins [, , ]. It mediates protein-protein interactions and the assembly of multiprotein complexes []. The TPR motif consists of 3-16 tandem-repeats of 34 amino acids residues, although individual TPR motifs can be dispersed in the protein sequence. Sequence alignment of the TPR domains reveals a consensus sequence defined by a pattern of small and large amino acids. TPR motifs have been identified in various different organisms, ranging from bacteria to humans. Proteins containing TPRs are involved in a variety of biological processes, such as cell cycle regulation, transcriptional control, mitochondrial and peroxisomal protein transport, neurogenesis and protein folding. The X-ray structure of a domain containing three TPRs from protein phosphatase 5 revealed that TPR adopts a helix-turn-helix arrangement, with adjacent TPR motifs packing in a parallel fashion, resulting in a spiral of repeating anti-parallel alpha-helices []. The two helices are denoted helix A and helix B. The packing angle between helix A and helix B is ~24 degrees within a single TPR and generates a right-handed superhelical shape. Helix A interacts with helix B and with helix A' of the next TPR. Two protein surfaces are generated: the inner concave surface is contributed to mainly by residue on helices A, and the other surface presents residues from both helices A and B. This entry represents SHNi-TPR (Sim3-Hif1-NASP interrupted TPR), a sequence that is an interrupted form of TPR repeat [].
Probab=29.90 E-value=1.1e+02 Score=20.41 Aligned_cols=27 Identities=15% Similarity=0.373 Sum_probs=21.4
Q ss_pred HHhHHHHHHHHcCCHHHHHHHHHHHHh
Q 013559 141 GYNDFGDFYYAHGALGDAFKSYVRTRD 167 (441)
Q Consensus 141 ~~~~la~~~~~~Gd~~~A~~~~~~~r~ 167 (441)
.+..||++-...++|+.|.+=|.+..+
T Consensus 3 v~~~Lgeisle~e~f~qA~~D~~~aL~ 29 (38)
T PF10516_consen 3 VYDLLGEISLENENFEQAIEDYEKALE 29 (38)
T ss_pred HHHHHHHHHHHhccHHHHHHHHHHHHH
Confidence 567888888899999888887776533
No 389
>PF00376 MerR: MerR family regulatory protein; InterPro: IPR000551 The many bacterial transcription regulation proteins which bind DNA through a 'helix-turn-helix' motif can be classified into subfamilies on the basis of sequence similarities. One of these is the MerR subfamily. MerR, which is found in many bacterial species mediates the mercuric-dependent induction of the mercury resistance operon. In the absence of mercury merR represses transcription by binding tightly, as a dimer, to the 'mer' operator region; when mercury is present the dimeric complex binds a single ion and becomes a potent transcriptional activator, while remaining bound to the mer site. Members of the family include the mercuric resistance operon regulatory protein merR; Bacillus subtilis bltR and bmrR; Bacillus glnR; Streptomyces coelicolor hspR; Bradyrhizobium japonicum nolA; Escherichia coli superoxide response regulator soxR; and Streptomyces lividans transcriptional activator tipA [, , , , , ]. Other members include hypothetical proteins from E. coli, B. subtilis and Haemophilus influenzae. 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; PDB: 3HH0_A 2DG6_A 1R8D_B 1JBG_A 2VZ4_A 2ZHH_A 2ZHG_A 1Q07_A 1Q06_A 1Q05_B ....
Probab=29.89 E-value=51 Score=21.90 Aligned_cols=20 Identities=10% Similarity=-0.027 Sum_probs=15.6
Q ss_pred cHHhHHHHcCCChHHHHHHH
Q 013559 354 DLHMMANAFKTSVAGIEKEL 373 (441)
Q Consensus 354 ~L~~mA~~fg~s~~~~E~~L 373 (441)
+|+.+|+.+|+|+..+-.|=
T Consensus 1 ti~e~A~~~gvs~~tlR~ye 20 (38)
T PF00376_consen 1 TIGEVAKLLGVSPRTLRYYE 20 (38)
T ss_dssp EHHHHHHHHTS-HHHHHHHH
T ss_pred CHHHHHHHHCCCHHHHHHHH
Confidence 57899999999999876553
No 390
>COG3413 Predicted DNA binding protein [General function prediction only]
Probab=29.73 E-value=62 Score=30.22 Aligned_cols=39 Identities=18% Similarity=0.129 Sum_probs=30.6
Q ss_pred HHHHHHHH-hccccccccHHhHHHHcCCChHHHHHHHHHH
Q 013559 338 IRNKALIQ-YTHPFVSVDLHMMANAFKTSVAGIEKELEAL 376 (441)
Q Consensus 338 iR~~~i~q-y~~pYs~I~L~~mA~~fg~s~~~~E~~L~~L 376 (441)
+-..|+.+ |+..=+++++..||+.||+|...+...|.+-
T Consensus 163 vL~~A~~~GYFd~PR~~~l~dLA~~lGISkst~~ehLRrA 202 (215)
T COG3413 163 VLRLAYKMGYFDYPRRVSLKDLAKELGISKSTLSEHLRRA 202 (215)
T ss_pred HHHHHHHcCCCCCCccCCHHHHHHHhCCCHHHHHHHHHHH
Confidence 33455554 8887799999999999999998887777653
No 391
>PF01527 HTH_Tnp_1: Transposase; InterPro: IPR002514 Transposase proteins are necessary for efficient DNA transposition. This family consists of various Escherichia coli insertion elements and other bacterial transposases some of which are members of the IS3 family. This region includes a helix-turn-helix motif (HTH) at the N terminus followed by a leucine zipper (LZ) motif. The LZ motif has been shown to mediate oligomerisation of the transposase components in IS911 []. 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; PDB: 2JN6_A 2RN7_A.
Probab=29.69 E-value=92 Score=23.36 Aligned_cols=41 Identities=10% Similarity=0.087 Sum_probs=31.4
Q ss_pred HHHHHHHHHHHhccccccccHHhHHHHcCCChHHHHHHHHHHH
Q 013559 335 YDQIRNKALIQYTHPFVSVDLHMMANAFKTSVAGIEKELEALI 377 (441)
Q Consensus 335 ~~~iR~~~i~qy~~pYs~I~L~~mA~~fg~s~~~~E~~L~~LI 377 (441)
-.+.+..++..++. .-.++..+|..+|+++..+=+|+.++-
T Consensus 8 s~e~K~~~v~~~~~--~g~sv~~va~~~gi~~~~l~~W~~~~~ 48 (76)
T PF01527_consen 8 SPEFKLQAVREYLE--SGESVSEVAREYGISPSTLYNWRKQYR 48 (76)
T ss_dssp -HHHHHHHHHHHHH--HHCHHHHHHHHHTS-HHHHHHHHHHHH
T ss_pred CHHHHHHHHHHHHH--CCCceEeeecccccccccccHHHHHHh
Confidence 34455566666644 468999999999999999999999987
No 392
>PF13936 HTH_38: Helix-turn-helix domain; PDB: 2W48_A.
Probab=29.60 E-value=63 Score=22.05 Aligned_cols=25 Identities=16% Similarity=0.303 Sum_probs=17.5
Q ss_pred ccccHHhHHHHcCCChHHHHHHHHH
Q 013559 351 VSVDLHMMANAFKTSVAGIEKELEA 375 (441)
Q Consensus 351 s~I~L~~mA~~fg~s~~~~E~~L~~ 375 (441)
.-.++..+|+.||++...|-++|-+
T Consensus 19 ~G~s~~~IA~~lg~s~sTV~relkR 43 (44)
T PF13936_consen 19 QGMSIREIAKRLGRSRSTVSRELKR 43 (44)
T ss_dssp S---HHHHHHHTT--HHHHHHHHHH
T ss_pred cCCCHHHHHHHHCcCcHHHHHHHhc
Confidence 6789999999999999999888753
No 393
>TIGR02997 Sig70-cyanoRpoD RNA polymerase sigma factor, cyanobacterial RpoD-like family. This family includes a number of closely related sigma-70 (TIGR02937) factors in the cyanobacteria. All appear most closely related to the essential sigma-70 factor RpoD, and some score above trusted to the RpoD C-terminal domain model (TIGR02393).
Probab=29.57 E-value=5.5e+02 Score=25.14 Aligned_cols=36 Identities=11% Similarity=0.106 Sum_probs=26.4
Q ss_pred cccHHhHHHHcCCChHHHHHHHHHHHHcCccceEec
Q 013559 352 SVDLHMMANAFKTSVAGIEKELEALITDNQIQARID 387 (441)
Q Consensus 352 ~I~L~~mA~~fg~s~~~~E~~L~~LI~~g~L~akID 387 (441)
..+...+|+.+|++++.++..+...-..-.|++.++
T Consensus 177 ~pt~~eia~~l~~~~~~v~~~~~~~~~~~SLd~~~~ 212 (298)
T TIGR02997 177 TPSEAEIAEALELEPEQVRELLQRARQPVSLDAPVG 212 (298)
T ss_pred CCCHHHHHHHhCCCHHHHHHHHHHcccCcccCCCcC
Confidence 357899999999999999988765444444555553
No 394
>PF06971 Put_DNA-bind_N: Putative DNA-binding protein N-terminus; InterPro: IPR009718 This entry represents the C terminus (approximately 30 residues) of a number of Rex proteins. These are redox-sensing repressors that appear to be widespread among Gram-positive bacteria []. They modulate transcription in response to changes in cellular NADH/NAD(+) redox state. Rex is predicted to include a pyridine nucleotide-binding domain (Rossmann fold), and residues that might play key structural and nucleotide binding roles are highly conserved.; GO: 0045892 negative regulation of transcription, DNA-dependent, 0051775 response to redox state, 0005737 cytoplasm; PDB: 3IL2_B 3IKT_A 3IKV_B 1XCB_F 2DT5_A 2VT3_A 2VT2_A 3KEO_B 3KET_A 3KEQ_A ....
Probab=29.48 E-value=69 Score=22.85 Aligned_cols=25 Identities=24% Similarity=0.302 Sum_probs=19.5
Q ss_pred cccccHHhHHHHcCCChHHHHHHHH
Q 013559 350 FVSVDLHMMANAFKTSVAGIEKELE 374 (441)
Q Consensus 350 Ys~I~L~~mA~~fg~s~~~~E~~L~ 374 (441)
...|+=..||+.+|+++..+-+.+.
T Consensus 26 ~~~vSS~~La~~~gi~~~qVRKDlS 50 (50)
T PF06971_consen 26 VERVSSQELAEALGITPAQVRKDLS 50 (50)
T ss_dssp -SEE-HHHHHHHHTS-HHHHHHHHH
T ss_pred CeeECHHHHHHHHCCCHHHhcccCC
Confidence 4689999999999999999988763
No 395
>PF14549 P22_Cro: DNA-binding transcriptional regulator Cro; PDB: 1RZS_A 3BD1_A 3QWS_A 2HIN_B.
Probab=29.45 E-value=73 Score=23.63 Aligned_cols=19 Identities=16% Similarity=0.132 Sum_probs=16.2
Q ss_pred cHHhHHHHcCCChHHHHHH
Q 013559 354 DLHMMANAFKTSVAGIEKE 372 (441)
Q Consensus 354 ~L~~mA~~fg~s~~~~E~~ 372 (441)
+...||++||+|...+-.|
T Consensus 11 ~~~~lAkalGVs~~aVs~W 29 (60)
T PF14549_consen 11 GQSKLAKALGVSPQAVSQW 29 (60)
T ss_dssp SHHHHHHHHTS-HHHHHHH
T ss_pred CHHHHHHHHCCCHHHHHHh
Confidence 4568999999999999999
No 396
>TIGR02404 trehalos_R_Bsub trehalose operon repressor, B. subtilis-type. This family consists of repressors of the GntR family typically associated with trehalose utilization operons. Trehalose is imported as trehalose-6-phosphate and then hydrolyzed by alpha,alpha-phosphotrehalase to glucose and glucose-6-P. This family includes repressors mostly from Gram-positive lineages and does not include the TreR from E. coli.
Probab=29.41 E-value=1.5e+02 Score=27.78 Aligned_cols=62 Identities=15% Similarity=0.139 Sum_probs=48.0
Q ss_pred HHHHHHHHHHHHHhccccccc-cHHhHHHHcCCChHHHHHHHHHHHHcCccceEecCCCCeEEEe
Q 013559 333 TLYDQIRNKALIQYTHPFVSV-DLHMMANAFKTSVAGIEKELEALITDNQIQARIDSHNKILYAR 396 (441)
Q Consensus 333 ~l~~~iR~~~i~qy~~pYs~I-~L~~mA~~fg~s~~~~E~~L~~LI~~g~L~akID~~~gvv~~~ 396 (441)
.+.+.|+.++...-+.|=..+ +-..||+.||+|-..+-+-|..|+.+|-|.-+ +-.|+.+..
T Consensus 4 qi~~~l~~~I~~g~~~~G~~LPsE~eLa~~~gVSR~TVR~Al~~L~~eGli~r~--~G~GTfV~~ 66 (233)
T TIGR02404 4 QIYQDLEQKITHGQYKEGDYLPSEHELMDQYGASRETVRKALNLLTEAGYIQKI--QGKGSIVLN 66 (233)
T ss_pred HHHHHHHHHHHhCCCCCCCCCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEe--CCceEEEec
Confidence 455666666666666777777 78999999999999999999999999988654 445666543
No 397
>PRK09334 30S ribosomal protein S25e; Provisional
Probab=29.35 E-value=1.4e+02 Score=23.98 Aligned_cols=38 Identities=13% Similarity=0.050 Sum_probs=34.4
Q ss_pred cccccccHHhHHHHcCCChHHHHHHHHHHHHcCccceE
Q 013559 348 HPFVSVDLHMMANAFKTSVAGIEKELEALITDNQIQAR 385 (441)
Q Consensus 348 ~pYs~I~L~~mA~~fg~s~~~~E~~L~~LI~~g~L~ak 385 (441)
..|+-||-..+|+.|+++..-+-+-|..|-..|-|..-
T Consensus 37 ~~~K~ITps~lserlkI~~SlAr~~Lr~L~~kG~Ik~V 74 (86)
T PRK09334 37 KKEKIVTPYTLASKYGIKISVAKKVLRELEKRGVLVLY 74 (86)
T ss_pred ccCcEEcHHHHHHHhcchHHHHHHHHHHHHHCCCEEEE
Confidence 34899999999999999999999999999999988654
No 398
>PF08672 APC2: Anaphase promoting complex (APC) subunit 2; InterPro: IPR014786 The anaphase-promoting complex (APC) or cyclosome is a multi-subunit E3 protein ubiquitin ligase that regulates important events in mitosis such as the initiation of anaphase and exit from telophase. The APC, in conjunction with other enzymes, assembles multi-ubiquitin chains on a variety of regulatory proteins, thereby targeting them for proteolysis by the 26S proteasome. Anaphase is initiated when the APC triggers the destruction of securin, thereby allowing the protease, separase, to disrupt sister-chromatid cohesion. Securin ubiquitination by the APC is inhibited by cyclin-dependent kinase 1 (Cdk1)-dependent phosphorylation []. Forkhead Box M1 (FoxM1), which is a transcription factor that is over-expressed in many cancers, is degraded in late mitosis and early G1 phase by the APC/cyclosome (APC/C) E3 ubiquitin ligase []. The APC/C targets mitotic cyclins for destruction in mitosis and G1 phase and is then inactivated at S phase. It thereby generates alternating states of high and low cyclin-Cdk activity, which is required for the alternation of mitosis and DNA replication []. The APC/C is composed of at least 13 subunits that stay tightly associated throughout the cell cycle: APC1, APC2, APC4, APC5, APC9, APC11, CDC16, CDC23, CDC26, CDC27, DOC1, MND2 and SWM1[], []. In fission yeast the 13 subunits are known as: Apc1, Apc2, Nuc2, Apc4, Apc5, Cut9, Apc8, Apc10, Apc11, Hcn1, Apc13, Apc14 and Apc15 []. This entry represents a C-terminal domain found in APC subunit 2. ; PDB: 1LDD_A.
Probab=29.33 E-value=60 Score=24.07 Aligned_cols=26 Identities=12% Similarity=0.429 Sum_probs=18.6
Q ss_pred HHcCCChHHHHHHHHHHHHcCccceE
Q 013559 360 NAFKTSVAGIEKELEALITDNQIQAR 385 (441)
Q Consensus 360 ~~fg~s~~~~E~~L~~LI~~g~L~ak 385 (441)
..++.|.++++..|.+++.+|+|.+.
T Consensus 29 ~~~~~s~~eL~~fL~~lv~e~~L~~~ 54 (60)
T PF08672_consen 29 GGYDISLEELQEFLDRLVEEGKLECS 54 (60)
T ss_dssp --TT--HHHHHHHHHHHHHTTSEE--
T ss_pred CCCCCCHHHHHHHHHHHHHCCcEEec
Confidence 34567889999999999999999764
No 399
>smart00342 HTH_ARAC helix_turn_helix, arabinose operon control protein.
Probab=29.10 E-value=1.8e+02 Score=21.42 Aligned_cols=40 Identities=8% Similarity=0.000 Sum_probs=27.8
Q ss_pred HHHHHHHHHHHhccccccccHHhHHHHcCC-ChHHHHHHHHH
Q 013559 335 YDQIRNKALIQYTHPFVSVDLHMMANAFKT-SVAGIEKELEA 375 (441)
Q Consensus 335 ~~~iR~~~i~qy~~pYs~I~L~~mA~~fg~-s~~~~E~~L~~ 375 (441)
....|..-+..|+... .+++..+|..+|+ ++..+-+...+
T Consensus 34 ~~~~r~~~a~~~l~~~-~~~~~~ia~~~g~~s~~~f~r~Fk~ 74 (84)
T smart00342 34 LRDRRLERARRLLRDT-DLSVTEIALRVGFSSQSYFSRAFKK 74 (84)
T ss_pred HHHHHHHHHHHHHHcC-CCCHHHHHHHhCCCChHHHHHHHHH
Confidence 3444555555665554 8999999999999 88776655433
No 400
>smart00668 CTLH C-terminal to LisH motif. Alpha-helical motif of unknown function.
Probab=28.96 E-value=1.1e+02 Score=21.55 Aligned_cols=28 Identities=14% Similarity=0.108 Sum_probs=20.6
Q ss_pred HHHHHHHHHhcCHHHHHhHHHHHhcccc
Q 013559 180 MSAILVSIEMGQFTHVTSYVSKAEQTPE 207 (441)
Q Consensus 180 l~~i~~~i~~~~~~~~~~~~~ka~~~~~ 207 (441)
...++-.|..|+|+.|...++.......
T Consensus 5 ~~~i~~~i~~g~~~~a~~~~~~~~~~l~ 32 (58)
T smart00668 5 RKRIRELILKGDWDEALEWLSSLKPPLL 32 (58)
T ss_pred HHHHHHHHHcCCHHHHHHHHHHcCHHHh
Confidence 3456778889999999888877665443
No 401
>COG1516 FliS Flagellin-specific chaperone FliS [Cell motility and secretion / Intracellular trafficking and secretion / Posttranslational modification, protein turnover, chaperones]
Probab=28.68 E-value=1.4e+02 Score=25.91 Aligned_cols=52 Identities=15% Similarity=0.220 Sum_probs=35.2
Q ss_pred HHHHHHHHHHHhhhcCchhHHHHHH-------HHHHHHHHhcCHHHHHhHHHHHhcccc
Q 013559 156 GDAFKSYVRTRDYCTTSKHIIHMCM-------SAILVSIEMGQFTHVTSYVSKAEQTPE 207 (441)
Q Consensus 156 ~~A~~~~~~~r~~~~~~~~~~~~~l-------~~i~~~i~~~~~~~~~~~~~ka~~~~~ 207 (441)
.+|.+.|.+..-...+|.+.+.|++ ...+.++..+||.+...++.|+..++.
T Consensus 4 ~~~~~aY~qn~V~taSP~~Li~MLyeg~l~~l~~A~~aie~~~i~~k~~~i~ka~~Ii~ 62 (132)
T COG1516 4 ANAYQAYQQNQVNTASPHKLILMLYEGALKFLKRAKEAIEQEDIEEKNESIDKAIDIIT 62 (132)
T ss_pred cHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHHHHHHHHHHhccHHHHHHHHHHHHHHHH
Confidence 3477778777555556776666653 344566778888888888888777654
No 402
>PF09182 PuR_N: Bacterial purine repressor, N-terminal; InterPro: IPR015265 The N-terminal domain of the bacterial purine repressor PuR is a winged-helix domain, a subdivision of the HTH structural family. It consists of a canonical arrangement of secondary structures: a1-b1-a2-T-a3-b2-W-b3, where a2-T-a3 is the HTH motif, a3 is the recognition helix, and W is the wing. The domain allows for recognition of a conserved CGAA sequence in the centre of a DNA PurBox, resulting in binding to the major groove of DNA []. ; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 1O57_B 1P4A_D.
Probab=28.32 E-value=1.2e+02 Score=23.33 Aligned_cols=37 Identities=24% Similarity=0.388 Sum_probs=24.7
Q ss_pred HHHHHHHHHhc--cccccccHHhHHHHcCCChHHHHHHH
Q 013559 337 QIRNKALIQYT--HPFVSVDLHMMANAFKTSVAGIEKEL 373 (441)
Q Consensus 337 ~iR~~~i~qy~--~pYs~I~L~~mA~~fg~s~~~~E~~L 373 (441)
+=|.-++.+|+ .|++-|+|...|+.|+..-.-+-+.|
T Consensus 3 seRlv~it~~L~~~P~~lisL~~Fae~f~~AKSsISEDl 41 (70)
T PF09182_consen 3 SERLVAITKYLLENPNKLISLTYFAERFGAAKSSISEDL 41 (70)
T ss_dssp HHHHHHHHHHHHTSTT--EEHHHHHHHHT--HHHHHHHH
T ss_pred hhHHHHHHHHHHcCCcceEcHHHHHHHhcccccchHHHH
Confidence 34566777775 59999999999999999766554444
No 403
>KOG1941 consensus Acetylcholine receptor-associated protein of the synapse (rapsyn) [Extracellular structures]
Probab=28.21 E-value=3.8e+02 Score=27.68 Aligned_cols=100 Identities=13% Similarity=0.140 Sum_probs=52.0
Q ss_pred HHhHHHHHHHHcCCHHHHHHHHHHHHhhhcCchhH---HHHHHHHHHHHHHhcCH-----HHHHhHHHHHhcccc-cCCh
Q 013559 141 GYNDFGDFYYAHGALGDAFKSYVRTRDYCTTSKHI---IHMCMSAILVSIEMGQF-----THVTSYVSKAEQTPE-ALEP 211 (441)
Q Consensus 141 ~~~~la~~~~~~Gd~~~A~~~~~~~r~~~~~~~~~---~~~~l~~i~~~i~~~~~-----~~~~~~~~ka~~~~~-~~d~ 211 (441)
.+.-+|++|...||.+.|+.-|....-...+.+.+ ++...+..++.-..+-. =.+.....|+-+.-+ -+..
T Consensus 248 c~~~~aDIyR~~gd~e~af~rYe~Am~~m~~~gdrmgqv~al~g~Akc~~~~r~~~k~~~Crale~n~r~levA~~IG~K 327 (518)
T KOG1941|consen 248 CLLCFADIYRSRGDLERAFRRYEQAMGTMASLGDRMGQVEALDGAAKCLETLRLQNKICNCRALEFNTRLLEVASSIGAK 327 (518)
T ss_pred HHHHHHHHHHhcccHhHHHHHHHHHHHHHhhhhhhHHHHHHHHHHHHHHHHHHHhhcccccchhHHHHHHHHHHHHhhhh
Confidence 46678999999999999999998865444333332 33444444443322211 224455555544433 1222
Q ss_pred hhhhhHHHHHHHHhccc---ccHHHHHHHHHh
Q 013559 212 VTIAKLRCAAGLAHLEA---RKYKLAARKFLE 240 (441)
Q Consensus 212 ~~~~~l~~~~gl~~l~~---r~y~~Aa~~Fl~ 240 (441)
-..-|+.+-.+..+-.. +++.+....|-+
T Consensus 328 ~~vlK~hcrla~iYrs~gl~d~~~~h~~ra~~ 359 (518)
T KOG1941|consen 328 LSVLKLHCRLASIYRSKGLQDELRAHVVRAHE 359 (518)
T ss_pred HHHHHHHHHHHHHHHhccchhHHHHHHHHHHH
Confidence 23334444444444333 344444444333
No 404
>COG3415 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=28.15 E-value=1e+02 Score=26.96 Aligned_cols=45 Identities=9% Similarity=0.074 Sum_probs=35.7
Q ss_pred HHHHHHHHHHhccccccccHHhHHHHcCCChHHHHHHHHHHHHcCcc
Q 013559 336 DQIRNKALIQYTHPFVSVDLHMMANAFKTSVAGIEKELEALITDNQI 382 (441)
Q Consensus 336 ~~iR~~~i~qy~~pYs~I~L~~mA~~fg~s~~~~E~~L~~LI~~g~L 382 (441)
+..|.+++.-|. |.-.+...+|+.||+|...+.+|+.+.=..|-+
T Consensus 7 ~~~R~~~~~~~~--~~G~S~re~Ak~~gvs~sTvy~wv~r~~e~G~~ 51 (138)
T COG3415 7 NDLRERVVDAVV--GEGLSCREAAKRFGVSISTVYRWVRRYRETGLD 51 (138)
T ss_pred HHHHHHHHHHHH--HcCccHHHHHHHhCccHHHHHHHHHHhcccccc
Confidence 445555555542 678899999999999999999999998766655
No 405
>PF13959 DUF4217: Domain of unknown function (DUF4217)
Probab=28.08 E-value=2.3e+02 Score=21.05 Aligned_cols=49 Identities=18% Similarity=0.200 Sum_probs=27.0
Q ss_pred hHHhhhhchhHHHH-HHHHHHHHHHHH---HHHhccccccccHHhHHHHcCCC
Q 013559 317 LKANLLLDIHLHDH-VETLYDQIRNKA---LIQYTHPFVSVDLHMMANAFKTS 365 (441)
Q Consensus 317 ~~~~l~~D~~L~~h-~~~l~~~iR~~~---i~qy~~pYs~I~L~~mA~~fg~s 365 (441)
++..+..|..|... .+.|..=+|.-. -...+-..+.+++..+|..||+.
T Consensus 6 l~~~~~~d~~l~~lA~~Af~SyvraY~~~~~~k~iF~~~~L~l~~~A~sfGL~ 58 (65)
T PF13959_consen 6 LEKLVAKDRELKELAQKAFVSYVRAYASHKELKDIFNVKKLDLGHLAKSFGLL 58 (65)
T ss_pred HHHHHHhCHHHHHHHHHHHHHHHHHHHHHhhhhhhCCcccCCHHHHHHHcCCC
Confidence 34445556555443 223333332222 11234456888999999999985
No 406
>KOG4626 consensus O-linked N-acetylglucosamine transferase OGT [Carbohydrate transport and metabolism; Posttranslational modification, protein turnover, chaperones; Signal transduction mechanisms]
Probab=28.01 E-value=8e+02 Score=27.33 Aligned_cols=67 Identities=19% Similarity=0.203 Sum_probs=44.4
Q ss_pred hHHHHHhHHhHHHHHHHHcCCHHHHHHHHHHH-HhhhcCchhHHHHHHHHHHHHHHhcCHHHHHhHHHHHhc
Q 013559 134 IKESIRMGYNDFGDFYYAHGALGDAFKSYVRT-RDYCTTSKHIIHMCMSAILVSIEMGQFTHVTSYVSKAEQ 204 (441)
Q Consensus 134 ~~esir~~~~~la~~~~~~Gd~~~A~~~~~~~-r~~~~~~~~~~~~~l~~i~~~i~~~~~~~~~~~~~ka~~ 204 (441)
+.++.-.++..||-+|-+.|++++|+.+|... |..- .-.+.+-+.-.+.-+.|+.+.+...+.||-.
T Consensus 383 v~p~~aaa~nNLa~i~kqqgnl~~Ai~~YkealrI~P----~fAda~~NmGnt~ke~g~v~~A~q~y~rAI~ 450 (966)
T KOG4626|consen 383 VFPEFAAAHNNLASIYKQQGNLDDAIMCYKEALRIKP----TFADALSNMGNTYKEMGDVSAAIQCYTRAIQ 450 (966)
T ss_pred hChhhhhhhhhHHHHHHhcccHHHHHHHHHHHHhcCc----hHHHHHHhcchHHHHhhhHHHHHHHHHHHHh
Confidence 44555667888888888888888888888775 3322 1244445555566677777777777776644
No 407
>TIGR02859 spore_sigH RNA polymerase sigma-H factor. Members of this protein family are RNA polymerase sigma-H factor for sporulation in endospore-forming bacteria. This protein is also called Sigma-30 and SigH. Although rather close homologs are detected in Listeria, Listeria does not form spores and the role of the related sigma factor in that genus is in doubt.
Probab=27.98 E-value=1.3e+02 Score=27.01 Aligned_cols=45 Identities=18% Similarity=0.316 Sum_probs=31.6
Q ss_pred HHHHHHHHHHHHHHHHHhccccccccHHhHHHHcCCChHHHHHHHHHH
Q 013559 329 DHVETLYDQIRNKALIQYTHPFVSVDLHMMANAFKTSVAGIEKELEAL 376 (441)
Q Consensus 329 ~h~~~l~~~iR~~~i~qy~~pYs~I~L~~mA~~fg~s~~~~E~~L~~L 376 (441)
..++.+...-+..++..| |.-.++..+|+.+|+|+..+...+.+.
T Consensus 145 ~~l~~Ll~~~~~~i~~~~---~~~~s~~eIA~~l~~s~~tV~~~l~r~ 189 (198)
T TIGR02859 145 SKMNELLSDLEWKVLQSY---LDGKSYQEIACDLNRHVKSIDNALQRV 189 (198)
T ss_pred HHHHHhcCHHHHHHHHHH---HcCCCHHHHHHHHCCCHHHHHHHHHHH
Confidence 344444433344455545 788999999999999999988776654
No 408
>KOG1585 consensus Protein required for fusion of vesicles in vesicular transport, gamma-SNAP [Intracellular trafficking, secretion, and vesicular transport]
Probab=27.86 E-value=5.8e+02 Score=24.93 Aligned_cols=28 Identities=29% Similarity=0.246 Sum_probs=22.0
Q ss_pred hhHHHHHHHHhcccccHHHHHHHHHhcC
Q 013559 215 AKLRCAAGLAHLEARKYKLAARKFLEVG 242 (441)
Q Consensus 215 ~~l~~~~gl~~l~~r~y~~Aa~~Fl~~~ 242 (441)
-+..+..-|.+|...+|..|-..|-++.
T Consensus 190 ~k~~va~ilv~L~~~Dyv~aekc~r~~~ 217 (308)
T KOG1585|consen 190 CKAYVAAILVYLYAHDYVQAEKCYRDCS 217 (308)
T ss_pred HHHHHHHHHHHhhHHHHHHHHHHhcchh
Confidence 3445556678899999999999999864
No 409
>PRK05472 redox-sensing transcriptional repressor Rex; Provisional
Probab=27.65 E-value=1.4e+02 Score=27.73 Aligned_cols=46 Identities=15% Similarity=-0.023 Sum_probs=37.5
Q ss_pred HHHHHHHHHHHhccccc--cccHHhHHHHcCCChHHHHHHHHHHHHcC
Q 013559 335 YDQIRNKALIQYTHPFV--SVDLHMMANAFKTSVAGIEKELEALITDN 380 (441)
Q Consensus 335 ~~~iR~~~i~qy~~pYs--~I~L~~mA~~fg~s~~~~E~~L~~LI~~g 380 (441)
-+.-|...+.+++.... .|+...||+.||+++..+-+.|..+=..|
T Consensus 13 ~r~~~~~~il~~l~~~~~~~vs~~~L~~~~~v~~~tirrDl~~l~~~G 60 (213)
T PRK05472 13 KRLPLYYRYLKELKEEGVERVSSKELAEALGVDSAQIRKDLSYFGEFG 60 (213)
T ss_pred HHhHHHHHHHHHHHHcCCcEEeHHHHHHHhCcCHHHHHHHHHHHHhcC
Confidence 34556677777788887 99999999999999999999988884444
No 410
>KOG1538 consensus Uncharacterized conserved protein WDR10, contains WD40 repeats [General function prediction only]
Probab=27.58 E-value=4.2e+02 Score=29.42 Aligned_cols=86 Identities=13% Similarity=0.129 Sum_probs=56.9
Q ss_pred HHHhHHhHHHHHHHHcCCHHHHHHHHHHHHhhhcCchhHHHHHHHHHHHHHHhcCHHHHHhHHHHHhcccccCChhhhhh
Q 013559 137 SIRMGYNDFGDFYYAHGALGDAFKSYVRTRDYCTTSKHIIHMCMSAILVSIEMGQFTHVTSYVSKAEQTPEALEPVTIAK 216 (441)
Q Consensus 137 sir~~~~~la~~~~~~Gd~~~A~~~~~~~r~~~~~~~~~~~~~l~~i~~~i~~~~~~~~~~~~~ka~~~~~~~d~~~~~~ 216 (441)
+-|+.+..+|.++-+...+.-|++.|.++-+. -.++.+.+..++|..+-....+. |+....
T Consensus 745 ~ere~l~~~a~ylk~l~~~gLAaeIF~k~gD~-----------ksiVqlHve~~~W~eAFalAe~h--------Pe~~~d 805 (1081)
T KOG1538|consen 745 AEREPLLLCATYLKKLDSPGLAAEIFLKMGDL-----------KSLVQLHVETQRWDEAFALAEKH--------PEFKDD 805 (1081)
T ss_pred hhhhHHHHHHHHHhhccccchHHHHHHHhccH-----------HHHhhheeecccchHhHhhhhhC--------cccccc
Confidence 34566778888888888899999988776443 24667789999999886554442 222223
Q ss_pred HHHHHHHHhcccccHHHHHHHHHhc
Q 013559 217 LRCAAGLAHLEARKYKLAARKFLEV 241 (441)
Q Consensus 217 l~~~~gl~~l~~r~y~~Aa~~Fl~~ 241 (441)
...-.|-+.-...+|.+|.+-|..+
T Consensus 806 Vy~pyaqwLAE~DrFeEAqkAfhkA 830 (1081)
T KOG1538|consen 806 VYMPYAQWLAENDRFEEAQKAFHKA 830 (1081)
T ss_pred ccchHHHHhhhhhhHHHHHHHHHHh
Confidence 3333455555566677777777654
No 411
>PF02259 FAT: FAT domain; InterPro: IPR003151 The FAT domain is a domain present in the PIK-related kinases. Members of the family of PIK-related kinases may act as intracellular sensors that govern radial and horizontal pathways [].; GO: 0005515 protein binding
Probab=27.32 E-value=5.6e+02 Score=24.90 Aligned_cols=68 Identities=10% Similarity=0.106 Sum_probs=45.0
Q ss_pred HHHHHhHHhHHHHHHHHcCCHHHHHHHHHHHHhhhcCchh-HHHHHHHHHHHHHHhcCHHHHHhHHHHH
Q 013559 135 KESIRMGYNDFGDFYYAHGALGDAFKSYVRTRDYCTTSKH-IIHMCMSAILVSIEMGQFTHVTSYVSKA 202 (441)
Q Consensus 135 ~esir~~~~~la~~~~~~Gd~~~A~~~~~~~r~~~~~~~~-~~~~~l~~i~~~i~~~~~~~~~~~~~ka 202 (441)
..++...+.++++...+.|.++-|..++.++......... ...+.+...++--..|+...+...+...
T Consensus 142 ~~~~~~~~l~~a~~aRk~g~~~~A~~~l~~~~~~~~~~~~~~~~v~~e~akllw~~g~~~~Ai~~L~~~ 210 (352)
T PF02259_consen 142 PEELAETWLKFAKLARKAGNFQLALSALNRLFQLNPSSESLLPRVFLEYAKLLWAQGEQEEAIQKLREL 210 (352)
T ss_pred hhHHHHHHHHHHHHHHHCCCcHHHHHHHHHHhccCCcccCCCcchHHHHHHHHHHcCCHHHHHHHHHHH
Confidence 3466668899999999999999999999998765422111 3344455555555556665555444333
No 412
>cd00086 homeodomain Homeodomain; DNA binding domains involved in the transcriptional regulation of key eukaryotic developmental processes; may bind to DNA as monomers or as homo- and/or heterodimers, in a sequence-specific manner.
Probab=27.22 E-value=1.2e+02 Score=21.18 Aligned_cols=28 Identities=7% Similarity=0.176 Sum_probs=23.8
Q ss_pred ccc-ccccHHhHHHHcCCChHHHHHHHHH
Q 013559 348 HPF-VSVDLHMMANAFKTSVAGIEKELEA 375 (441)
Q Consensus 348 ~pY-s~I~L~~mA~~fg~s~~~~E~~L~~ 375 (441)
.|| +.-.+..||..+|++...|..|..+
T Consensus 22 ~~~P~~~~~~~la~~~~l~~~qV~~WF~n 50 (59)
T cd00086 22 NPYPSREEREELAKELGLTERQVKIWFQN 50 (59)
T ss_pred CCCCCHHHHHHHHHHHCcCHHHHHHHHHH
Confidence 345 6777999999999999999999765
No 413
>TIGR02325 C_P_lyase_phnF phosphonates metabolism transcriptional regulator PhnF. All members of the seed alignment for this family are predicted helix-turn-helix transcriptional regulatory proteins of the broader gntR and are found associated with genes for the import and degradation of phosphonates and/or related compounds (e.g. phosphonites) with a direct C-P bond.
Probab=26.94 E-value=1.7e+02 Score=27.40 Aligned_cols=64 Identities=13% Similarity=0.124 Sum_probs=50.0
Q ss_pred HHHHHHHHHHHHHHHhccccccc-cHHhHHHHcCCChHHHHHHHHHHHHcCccceEecCCCCeEEEe
Q 013559 331 VETLYDQIRNKALIQYTHPFVSV-DLHMMANAFKTSVAGIEKELEALITDNQIQARIDSHNKILYAR 396 (441)
Q Consensus 331 ~~~l~~~iR~~~i~qy~~pYs~I-~L~~mA~~fg~s~~~~E~~L~~LI~~g~L~akID~~~gvv~~~ 396 (441)
...+.+.|+.++..--+.|=+.+ +-..||+.||+|-..+-+-|..|+.+|-|..+ +-.|+.+..
T Consensus 10 y~~i~~~l~~~I~~g~~~~G~~LPsE~eLa~~~~VSR~TvR~Al~~L~~eGli~r~--~G~GtfV~~ 74 (238)
T TIGR02325 10 WRQIADKIEQEIAAGHLRAGDYLPAEMQLAERFGVNRHTVRRAIAALVERGLLRAE--QGRGTFVAA 74 (238)
T ss_pred HHHHHHHHHHHHHcCCCCCCCcCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEe--cCCEEEECC
Confidence 34556667777766555666777 88899999999999999999999999998665 556666653
No 414
>cd04762 HTH_MerR-trunc Helix-Turn-Helix DNA binding domain of truncated MerR-like proteins. Proteins in this family mostly have a truncated helix-turn-helix (HTH) MerR-like domain. They lack a portion of the C-terminal region, called Wing 2 and the long dimerization helix that is typically present in MerR-like proteins. These truncated domains are found in response regulator receiver (REC) domain proteins (i.e., CheY), cytosine-C5 specific DNA methylases, IS607 transposase-like proteins, and RacA, a bacterial protein that anchors chromosomes to cell poles.
Probab=26.57 E-value=68 Score=21.26 Aligned_cols=28 Identities=11% Similarity=0.165 Sum_probs=21.9
Q ss_pred cHHhHHHHcCCChHHHHHHHHHHHHcCccceE
Q 013559 354 DLHMMANAFKTSVAGIEKELEALITDNQIQAR 385 (441)
Q Consensus 354 ~L~~mA~~fg~s~~~~E~~L~~LI~~g~L~ak 385 (441)
++..+|+.||++...+-+| +..|.+.+.
T Consensus 2 s~~e~a~~lgvs~~tl~~~----~~~g~~~~~ 29 (49)
T cd04762 2 TTKEAAELLGVSPSTLRRW----VKEGKLKAI 29 (49)
T ss_pred CHHHHHHHHCcCHHHHHHH----HHcCCCCce
Confidence 6788999999999886655 456887664
No 415
>PRK03902 manganese transport transcriptional regulator; Provisional
Probab=26.35 E-value=4.1e+02 Score=22.72 Aligned_cols=43 Identities=12% Similarity=0.076 Sum_probs=35.4
Q ss_pred HHHHhccccccccHHhHHHHcCCChHHHHHHHHHHHHcCccce
Q 013559 342 ALIQYTHPFVSVDLHMMANAFKTSVAGIEKELEALITDNQIQA 384 (441)
Q Consensus 342 ~i~qy~~pYs~I~L~~mA~~fg~s~~~~E~~L~~LI~~g~L~a 384 (441)
+|-.+......++++.+|+.+|++...+-..|.+|...|-|.-
T Consensus 12 ~I~~l~~~~~~~~~~ela~~l~vs~~svs~~l~~L~~~Gli~~ 54 (142)
T PRK03902 12 QIYLLIEEKGYARVSDIAEALSVHPSSVTKMVQKLDKDEYLIY 54 (142)
T ss_pred HHHHHHhcCCCcCHHHHHHHhCCChhHHHHHHHHHHHCCCEEE
Confidence 3334445556779999999999999999999999999998863
No 416
>PRK03573 transcriptional regulator SlyA; Provisional
Probab=26.34 E-value=3.7e+02 Score=22.92 Aligned_cols=43 Identities=12% Similarity=0.106 Sum_probs=37.4
Q ss_pred cccHHhHHHHcCCChHHHHHHHHHHHHcCccceEecCCCCeEE
Q 013559 352 SVDLHMMANAFKTSVAGIEKELEALITDNQIQARIDSHNKILY 394 (441)
Q Consensus 352 ~I~L~~mA~~fg~s~~~~E~~L~~LI~~g~L~akID~~~gvv~ 394 (441)
.++...+|+.+|++...+=+.+.+|...|-|.-.-|..++-..
T Consensus 46 ~~t~~eLa~~l~~~~~tvt~~v~~Le~~GlV~r~~~~~DrR~~ 88 (144)
T PRK03573 46 EQSQIQLAKAIGIEQPSLVRTLDQLEEKGLISRQTCASDRRAK 88 (144)
T ss_pred CCCHHHHHHHhCCChhhHHHHHHHHHHCCCEeeecCCCCcCee
Confidence 4678999999999999999999999999999888777766433
No 417
>PF13542 HTH_Tnp_ISL3: Helix-turn-helix domain of transposase family ISL3
Probab=26.33 E-value=1.7e+02 Score=20.09 Aligned_cols=25 Identities=12% Similarity=0.171 Sum_probs=21.1
Q ss_pred cccHHhHHHHcCCChHHHHHHHHHH
Q 013559 352 SVDLHMMANAFKTSVAGIEKELEAL 376 (441)
Q Consensus 352 ~I~L~~mA~~fg~s~~~~E~~L~~L 376 (441)
..++..+|+.+|+|...+.+.+-+.
T Consensus 27 ~~s~~~vA~~~~vs~~TV~ri~~~~ 51 (52)
T PF13542_consen 27 SRSFKDVARELGVSWSTVRRIFDRY 51 (52)
T ss_pred cCCHHHHHHHHCCCHHHHHHHHHhh
Confidence 3799999999999999988876543
No 418
>PRK10153 DNA-binding transcriptional activator CadC; Provisional
Probab=26.16 E-value=4.3e+02 Score=28.39 Aligned_cols=51 Identities=14% Similarity=-0.023 Sum_probs=38.0
Q ss_pred HHHhcCHHHHHhHHHHHhcccccCChhhhhhHHHHHHHHhcccccHHHHHHHHHhcC
Q 013559 186 SIEMGQFTHVTSYVSKAEQTPEALEPVTIAKLRCAAGLAHLEARKYKLAARKFLEVG 242 (441)
Q Consensus 186 ~i~~~~~~~~~~~~~ka~~~~~~~d~~~~~~l~~~~gl~~l~~r~y~~Aa~~Fl~~~ 242 (441)
.+..|+|+.+...+++|-.+-. +| --..+.|..+...|++.+|...|..++
T Consensus 430 ~~~~g~~~~A~~~l~rAl~L~p--s~----~a~~~lG~~~~~~G~~~eA~~~~~~A~ 480 (517)
T PRK10153 430 ALVKGKTDEAYQAINKAIDLEM--SW----LNYVLLGKVYELKGDNRLAADAYSTAF 480 (517)
T ss_pred HHhcCCHHHHHHHHHHHHHcCC--CH----HHHHHHHHHHHHcCCHHHHHHHHHHHH
Confidence 4456888888888888777642 22 235667888888899999888888765
No 419
>PF04184 ST7: ST7 protein; InterPro: IPR007311 The ST7 (for suppression of tumorigenicity 7) protein is thought to be a tumour suppressor gene. The molecular function of this protein is uncertain.
Probab=25.82 E-value=2.6e+02 Score=29.85 Aligned_cols=63 Identities=13% Similarity=0.149 Sum_probs=50.7
Q ss_pred HHhHHHHHHHHcCCHHHHHHHHHHHHhhhcCchhHHHHHHHHHHHHHHhcCHHHHHhHHHHHhc
Q 013559 141 GYNDFGDFYYAHGALGDAFKSYVRTRDYCTTSKHIIHMCMSAILVSIEMGQFTHVTSYVSKAEQ 204 (441)
Q Consensus 141 ~~~~la~~~~~~Gd~~~A~~~~~~~r~~~~~~~~~~~~~l~~i~~~i~~~~~~~~~~~~~ka~~ 204 (441)
+...||....+.|...+|.+.+..+..... ....+.+--+++.+-++.+.+..++..+.|=.+
T Consensus 261 ~KrRLAmCarklGr~~EAIk~~rdLlke~p-~~~~l~IrenLie~LLelq~Yad~q~lL~kYdD 323 (539)
T PF04184_consen 261 AKRRLAMCARKLGRLREAIKMFRDLLKEFP-NLDNLNIRENLIEALLELQAYADVQALLAKYDD 323 (539)
T ss_pred hHHHHHHHHHHhCChHHHHHHHHHHHhhCC-ccchhhHHHHHHHHHHhcCCHHHHHHHHHHhcc
Confidence 457799999999999999999999843322 334466777888899999999999999988654
No 420
>PRK11512 DNA-binding transcriptional repressor MarR; Provisional
Probab=25.70 E-value=1.4e+02 Score=25.67 Aligned_cols=46 Identities=7% Similarity=0.127 Sum_probs=40.2
Q ss_pred cccccHHhHHHHcCCChHHHHHHHHHHHHcCccceEecCCCCeEEE
Q 013559 350 FVSVDLHMMANAFKTSVAGIEKELEALITDNQIQARIDSHNKILYA 395 (441)
Q Consensus 350 Ys~I~L~~mA~~fg~s~~~~E~~L~~LI~~g~L~akID~~~gvv~~ 395 (441)
...++...+|+.+|++...+=+.|.+|+..|-|.-..|..++-...
T Consensus 52 ~~~~t~~eLa~~l~i~~~tvsr~l~~Le~~GlI~R~~~~~DrR~~~ 97 (144)
T PRK11512 52 AACITPVELKKVLSVDLGALTRMLDRLVCKGWVERLPNPNDKRGVL 97 (144)
T ss_pred cCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEeccCcccCCeeE
Confidence 4579999999999999999999999999999998888877774433
No 421
>TIGR00331 hrcA heat shock gene repressor HrcA. In Bacillus subtilis, hrcA is the first gene of the dnaK operon and so is itself a heat shock gene.
Probab=25.59 E-value=1.3e+02 Score=30.41 Aligned_cols=44 Identities=16% Similarity=0.145 Sum_probs=39.6
Q ss_pred HHHHHHhccccccccHHhHHHH--cCCChHHHHHHHHHHHHcCccc
Q 013559 340 NKALIQYTHPFVSVDLHMMANA--FKTSVAGIEKELEALITDNQIQ 383 (441)
Q Consensus 340 ~~~i~qy~~pYs~I~L~~mA~~--fg~s~~~~E~~L~~LI~~g~L~ 383 (441)
.-++..|+..-..|+...||+. ||+|.+.+-+++.+|-..|.|.
T Consensus 9 ~aIV~~~l~~~~pv~s~~l~~~~~~~vS~aTiR~d~~~Le~~G~l~ 54 (337)
T TIGR00331 9 KAIVEEYIKTGQPVGSKTLLEKYNLGLSSATIRNDMADLEDLGFIE 54 (337)
T ss_pred HHHHHHHHhcCCCcCHHHHHhhcCCCCChHHHHHHHHHHHHCCCcc
Confidence 3456679999999999999999 9999999999999999999883
No 422
>TIGR03362 VI_chp_7 type VI secretion-associated protein, VC_A0119 family. This protein family is one of two related families in type VI secretion systems that contain an ImpA-related N-terminal domain (pfam06812).
Probab=25.57 E-value=1.8e+02 Score=28.85 Aligned_cols=64 Identities=11% Similarity=0.081 Sum_probs=56.5
Q ss_pred HHHHHHHHcCCHHHHHHHHHHHHhhhcCchhHHHHHHHHHHHHHHhcCHHHHHhHHHHHhcccc
Q 013559 144 DFGDFYYAHGALGDAFKSYVRTRDYCTTSKHIIHMCMSAILVSIEMGQFTHVTSYVSKAEQTPE 207 (441)
Q Consensus 144 ~la~~~~~~Gd~~~A~~~~~~~r~~~~~~~~~~~~~l~~i~~~i~~~~~~~~~~~~~ka~~~~~ 207 (441)
.=|.-..+.|.++.|+..+...+..++++.+++-.-+...+++...|....+...+..+...++
T Consensus 218 ~eA~~l~~~~gl~~Al~~L~~~~~~~~s~R~rf~~rL~~A~l~~~~g~~~lA~~ll~~L~~~~~ 281 (301)
T TIGR03362 218 EEARALAAEGGLEAALQRLQQRLAQAREPRERFHWRLLLARLLEQAGKAELAQQLYAALDQQIQ 281 (301)
T ss_pred HHHHHHHHcCCHHHHHHHHHhhcccCCChHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHH
Confidence 3466778899999999999988888889999999999999999999999999999988877655
No 423
>PRK10870 transcriptional repressor MprA; Provisional
Probab=25.18 E-value=3.7e+02 Score=24.19 Aligned_cols=43 Identities=14% Similarity=0.138 Sum_probs=38.5
Q ss_pred ccccHHhHHHHcCCChHHHHHHHHHHHHcCccceEecCCCCeE
Q 013559 351 VSVDLHMMANAFKTSVAGIEKELEALITDNQIQARIDSHNKIL 393 (441)
Q Consensus 351 s~I~L~~mA~~fg~s~~~~E~~L~~LI~~g~L~akID~~~gvv 393 (441)
..++...||+.+|++...+-+.|.+|+..|-|.-.-|..++-.
T Consensus 70 ~~it~~eLa~~l~l~~~tvsr~v~rLe~kGlV~R~~~~~DrR~ 112 (176)
T PRK10870 70 HSIQPSELSCALGSSRTNATRIADELEKRGWIERRESDNDRRC 112 (176)
T ss_pred CCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEecCCCCCCCe
Confidence 4689999999999999999999999999999988888877644
No 424
>KOG4648 consensus Uncharacterized conserved protein, contains LRR repeats [Function unknown]
Probab=25.01 E-value=1.1e+02 Score=31.10 Aligned_cols=26 Identities=19% Similarity=0.464 Sum_probs=22.1
Q ss_pred hHHHHHHHHcCCHHHHHHHHHHHHhh
Q 013559 143 NDFGDFYYAHGALGDAFKSYVRTRDY 168 (441)
Q Consensus 143 ~~la~~~~~~Gd~~~A~~~~~~~r~~ 168 (441)
-..|+-|++.|.|++|+.||++....
T Consensus 101 KE~GN~yFKQgKy~EAIDCYs~~ia~ 126 (536)
T KOG4648|consen 101 KERGNTYFKQGKYEEAIDCYSTAIAV 126 (536)
T ss_pred HHhhhhhhhccchhHHHHHhhhhhcc
Confidence 35688999999999999999987543
No 425
>PRK06759 RNA polymerase factor sigma-70; Validated
Probab=24.82 E-value=1.7e+02 Score=25.01 Aligned_cols=45 Identities=9% Similarity=0.104 Sum_probs=32.1
Q ss_pred HHHHHHHHHHHHHHHHhccccccccHHhHHHHcCCChHHHHHHHHHHH
Q 013559 330 HVETLYDQIRNKALIQYTHPFVSVDLHMMANAFKTSVAGIEKELEALI 377 (441)
Q Consensus 330 h~~~l~~~iR~~~i~qy~~pYs~I~L~~mA~~fg~s~~~~E~~L~~LI 377 (441)
.+..|=..-|.-+...| +.-.+...+|+.+|+|+..+...+.+.+
T Consensus 103 ~l~~L~~~~r~ii~l~~---~~~~s~~EIA~~l~is~~tV~~~~~ra~ 147 (154)
T PRK06759 103 FMSVLDEKEKYIIFERF---FVGKTMGEIALETEMTYYQVRWIYRQAL 147 (154)
T ss_pred HHHhCCHHHHHHHHHHH---hcCCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence 33344344444444556 6778899999999999999999887754
No 426
>KOG3617 consensus WD40 and TPR repeat-containing protein [General function prediction only]
Probab=24.70 E-value=1.8e+02 Score=33.19 Aligned_cols=88 Identities=17% Similarity=0.250 Sum_probs=54.0
Q ss_pred HHhHHHHHHHHcCCHHHHHHHHHHHHhhhcCchhHHHHHHHHHHHHHHhcCHHHHHhHHH-HHhcccccCChhh--hhhH
Q 013559 141 GYNDFGDFYYAHGALGDAFKSYVRTRDYCTTSKHIIHMCMSAILVSIEMGQFTHVTSYVS-KAEQTPEALEPVT--IAKL 217 (441)
Q Consensus 141 ~~~~la~~~~~~Gd~~~A~~~~~~~r~~~~~~~~~~~~~l~~i~~~i~~~~~~~~~~~~~-ka~~~~~~~d~~~--~~~l 217 (441)
.+.+-|+||+...+|++|...+...|++.. .+.+| .+.--.+.+.+. +....-| +++.- +..+
T Consensus 1082 ll~RcadFF~~~~qyekAV~lL~~ar~~~~----AlqlC---------~~~nv~vtee~aE~mTp~Kd-~~~~e~~R~~v 1147 (1416)
T KOG3617|consen 1082 LLRRCADFFENNQQYEKAVNLLCLAREFSG----ALQLC---------KNRNVRVTEEFAELMTPTKD-DMPNEQERKQV 1147 (1416)
T ss_pred HHHHHHHHHHhHHHHHHHHHHHHHHHHHHH----HHHHH---------hcCCCchhHHHHHhcCcCcC-CCccHHHHHHH
Confidence 346789999999999999999999988842 22222 222223332222 1111222 23322 2234
Q ss_pred HHHHHHHhcccccHHHHHHHHHhcC
Q 013559 218 RCAAGLAHLEARKYKLAARKFLEVG 242 (441)
Q Consensus 218 ~~~~gl~~l~~r~y~~Aa~~Fl~~~ 242 (441)
-..-|=.++.+|.|..|...|.++-
T Consensus 1148 Leqvae~c~qQG~Yh~AtKKfTQAG 1172 (1416)
T KOG3617|consen 1148 LEQVAELCLQQGAYHAATKKFTQAG 1172 (1416)
T ss_pred HHHHHHHHHhccchHHHHHHHhhhh
Confidence 4444567889999999999998763
No 427
>smart00745 MIT Microtubule Interacting and Trafficking molecule domain.
Probab=24.67 E-value=2.5e+02 Score=21.17 Aligned_cols=26 Identities=15% Similarity=0.160 Sum_probs=19.2
Q ss_pred HHHHHHHHcCCHHHHHHHHHHHHhhh
Q 013559 144 DFGDFYYAHGALGDAFKSYVRTRDYC 169 (441)
Q Consensus 144 ~la~~~~~~Gd~~~A~~~~~~~r~~~ 169 (441)
..|--+-+.|++++|+.+|....+.+
T Consensus 13 ~~Av~~d~~g~~~eAl~~Y~~a~e~l 38 (77)
T smart00745 13 SKALKADEAGDYEEALELYKKAIEYL 38 (77)
T ss_pred HHHHHHHHcCCHHHHHHHHHHHHHHH
Confidence 34455666899999999999865544
No 428
>PF13613 HTH_Tnp_4: Helix-turn-helix of DDE superfamily endonuclease
Probab=24.67 E-value=1.1e+02 Score=21.58 Aligned_cols=27 Identities=15% Similarity=0.284 Sum_probs=21.9
Q ss_pred ccccHHhHHHHcCCChHHHHHHHHHHH
Q 013559 351 VSVDLHMMANAFKTSVAGIEKELEALI 377 (441)
Q Consensus 351 s~I~L~~mA~~fg~s~~~~E~~L~~LI 377 (441)
...+...+|..||+|...+-+.+...+
T Consensus 18 ~~~~~~~La~~FgIs~stvsri~~~~~ 44 (53)
T PF13613_consen 18 LNLTFQDLAYRFGISQSTVSRIFHEWI 44 (53)
T ss_pred cCCcHhHHhhheeecHHHHHHHHHHHH
Confidence 457889999999999988877766554
No 429
>PF10345 Cohesin_load: Cohesin loading factor; InterPro: IPR019440 Cohesin loading factor is a conserved protein that has been characterised in fungi. It is associated with the cohesin complex and is required in G1 for cohesin binding to chromosomes, but is dispensable in G2 when cohesion has been established. It is often referred to as Ssl3 in Schizosaccharomyces pombe (Fission yeast), and Scc4 in Saccharomyces cerevisiae (Baker's yeast). It complexes with Mis4 [].
Probab=24.55 E-value=9.4e+02 Score=26.20 Aligned_cols=100 Identities=10% Similarity=0.003 Sum_probs=63.7
Q ss_pred HHhHHHHHHH-HcCCHHHHHHHHHHHHhhhcCc---hhHHHHHHHHHHHHHHhcCHHHHHhHHHHHhccccc---CChhh
Q 013559 141 GYNDFGDFYY-AHGALGDAFKSYVRTRDYCTTS---KHIIHMCMSAILVSIEMGQFTHVTSYVSKAEQTPEA---LEPVT 213 (441)
Q Consensus 141 ~~~~la~~~~-~~Gd~~~A~~~~~~~r~~~~~~---~~~~~~~l~~i~~~i~~~~~~~~~~~~~ka~~~~~~---~d~~~ 213 (441)
.++++|.+++ ++.+++.|-.++.+.+..|..+ +.++.+-+-.+++... .+...+..+++++-+..+. ..|..
T Consensus 61 ~~l~la~iL~~eT~n~~~Ae~~L~k~~~l~~~~~~~d~k~~~~~ll~~i~~~-~~~~~a~~~l~~~I~~~~~~~~~~w~~ 139 (608)
T PF10345_consen 61 VRLRLASILLEETENLDLAETYLEKAILLCERHRLTDLKFRCQFLLARIYFK-TNPKAALKNLDKAIEDSETYGHSAWYY 139 (608)
T ss_pred HHHHHHHHHHHHcCCHHHHHHHHHHHHHhccccchHHHHHHHHHHHHHHHHh-cCHHHHHHHHHHHHHHHhccCchhHHH
Confidence 6789999988 7889999999999998888542 1233333434444433 3444588888887665542 34544
Q ss_pred hhhHHHHHHHHhcccccHHHHHHHHHhcCc
Q 013559 214 IAKLRCAAGLAHLEARKYKLAARKFLEVGP 243 (441)
Q Consensus 214 ~~~l~~~~gl~~l~~r~y~~Aa~~Fl~~~~ 243 (441)
.-++ ...-..+..+++..|.+.+-....
T Consensus 140 ~frl--l~~~l~~~~~d~~~Al~~L~~~~~ 167 (608)
T PF10345_consen 140 AFRL--LKIQLALQHKDYNAALENLQSIAQ 167 (608)
T ss_pred HHHH--HHHHHHHhcccHHHHHHHHHHHHH
Confidence 4443 222223333899998888866643
No 430
>TIGR01716 RGG_Cterm transcriptional activator, Rgg/GadR/MutR family, C-terminal domain. This model describes the whole, except for a 60 residue N-terminal helix-turn-helix DNA-binding domain (PFAM pfam01381) of the family of proteins related to the transcriptional regulator Rgg, also called RopB. Rgg is required for secretion of several proteins, including a cysteine proteinase associated with virulence. GadR is a positive regulator of a glutamate-dependent acid resistance mechanism. MutR is a transcriptional activator for mutacin biosynthesis genes in Streptococcus mutans. This family appears restricted to the low-GC Gram-positive bacteria, including at least eight members in Lactococcus lactis.
Probab=24.04 E-value=4.6e+02 Score=23.91 Aligned_cols=60 Identities=12% Similarity=0.236 Sum_probs=44.4
Q ss_pred hhHHHHHHHHHHHHHHhcCHHHHHhHHHHHhcccccC-ChhhhhhHHHHHHHHhcccccHH
Q 013559 173 KHIIHMCMSAILVSIEMGQFTHVTSYVSKAEQTPEAL-EPVTIAKLRCAAGLAHLEARKYK 232 (441)
Q Consensus 173 ~~~~~~~l~~i~~~i~~~~~~~~~~~~~ka~~~~~~~-d~~~~~~l~~~~gl~~l~~r~y~ 232 (441)
.-.+.++.+.+-.+|..++...+...+++++..+... +--.+..+..+.|++....|+-.
T Consensus 125 ~~i~~il~N~~~~~i~~~~~~~a~~~l~~l~~l~~~~~~~~~ki~~~f~~~l~~y~~g~~~ 185 (220)
T TIGR01716 125 RRVIQLLLNIAVLLIEKNEFSYAQYFLEKLEKILDPEDDLYERILFNFLKGIILYKEGQKE 185 (220)
T ss_pred HHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHhchhhhHHHHHHHHHHHHHHHHHcCCCc
Confidence 3456678888888999999999999999998876521 22245667788888877777633
No 431
>KOG1258 consensus mRNA processing protein [RNA processing and modification]
Probab=24.02 E-value=9.6e+02 Score=26.15 Aligned_cols=101 Identities=15% Similarity=0.024 Sum_probs=62.2
Q ss_pred HhHHHHHHHHcCCHHHHHHHHHHHHhhhcCchhHHHHHHHHHHHHHHhcCHHHHHhHHHHHhc-ccc-cCChhhhhhHHH
Q 013559 142 YNDFGDFYYAHGALGDAFKSYVRTRDYCTTSKHIIHMCMSAILVSIEMGQFTHVTSYVSKAEQ-TPE-ALEPVTIAKLRC 219 (441)
Q Consensus 142 ~~~la~~~~~~Gd~~~A~~~~~~~r~~~~~~~~~~~~~l~~i~~~i~~~~~~~~~~~~~ka~~-~~~-~~d~~~~~~l~~ 219 (441)
+.-.|.|-...||+..|..+|.++..-+ ++ .+++.+..+-+....|+...+.. .+.+.. ..+ ..+..+.+++.+
T Consensus 369 ~L~~a~f~e~~~n~~~A~~~lq~i~~e~--pg-~v~~~l~~~~~e~r~~~~~~~~~-~~~l~s~~~~~~~~~~i~~~l~~ 444 (577)
T KOG1258|consen 369 HLLEARFEESNGNFDDAKVILQRIESEY--PG-LVEVVLRKINWERRKGNLEDANY-KNELYSSIYEGKENNGILEKLYV 444 (577)
T ss_pred HHHHHHHHHhhccHHHHHHHHHHHHhhC--Cc-hhhhHHHHHhHHHHhcchhhhhH-HHHHHHHhcccccCcchhHHHHH
Confidence 3555777888899999999999887766 23 45666666666666666666553 222222 222 244455555555
Q ss_pred HHHH-HhcccccHHHHHHHHHhcCcCCC
Q 013559 220 AAGL-AHLEARKYKLAARKFLEVGPDLG 246 (441)
Q Consensus 220 ~~gl-~~l~~r~y~~Aa~~Fl~~~~t~~ 246 (441)
-... .+...++=..|...+.++....+
T Consensus 445 ~~~r~~~~i~~d~~~a~~~l~~~~~~~~ 472 (577)
T KOG1258|consen 445 KFARLRYKIREDADLARIILLEANDILP 472 (577)
T ss_pred HHHHHHHHHhcCHHHHHHHHHHhhhcCC
Confidence 4443 33446677777888888766443
No 432
>TIGR00122 birA_repr_reg BirA biotin operon repressor domain. This model may recognize some other putative repressor proteins, such as DnrO of Streptomyces peucetius with scores below the noise cutoff but with significance shown by low E-value.
Probab=23.91 E-value=1.9e+02 Score=21.45 Aligned_cols=29 Identities=14% Similarity=0.132 Sum_probs=25.9
Q ss_pred ccHHhHHHHcCCChHHHHHHHHHHHHcCc
Q 013559 353 VDLHMMANAFKTSVAGIEKELEALITDNQ 381 (441)
Q Consensus 353 I~L~~mA~~fg~s~~~~E~~L~~LI~~g~ 381 (441)
++.+.+|+.||+|...+.+.+..|-..|-
T Consensus 14 ~~~~eLa~~l~vS~~tv~~~l~~L~~~g~ 42 (69)
T TIGR00122 14 FSGEKLGEALGMSRTAVNKHIQTLREWGV 42 (69)
T ss_pred cCHHHHHHHHCCCHHHHHHHHHHHHHCCC
Confidence 45899999999999999999999977665
No 433
>PF10078 DUF2316: Uncharacterized protein conserved in bacteria (DUF2316); InterPro: IPR018757 Members of this family of hypothetical bacterial proteins have no known function.
Probab=23.66 E-value=79 Score=25.49 Aligned_cols=23 Identities=26% Similarity=0.317 Sum_probs=21.0
Q ss_pred ccccHHhHHHHcCCChHHHHHHH
Q 013559 351 VSVDLHMMANAFKTSVAGIEKEL 373 (441)
Q Consensus 351 s~I~L~~mA~~fg~s~~~~E~~L 373 (441)
+.++++.+|..||+|++.+|+-|
T Consensus 22 ~~ls~~~ia~dL~~s~~~le~vL 44 (89)
T PF10078_consen 22 SGLSLEQIAADLGTSPEHLEQVL 44 (89)
T ss_pred cCCCHHHHHHHhCCCHHHHHHHH
Confidence 68899999999999999998766
No 434
>PF07304 SRA1: Steroid receptor RNA activator (SRA1); InterPro: IPR009917 This entry consists of several hypothetical mammalian steroid receptor RNA activator proteins. The SRA-RNAs encode stable proteins that are widely expressed and upregulated in breast cancer cell lines. SRA-RNA is a steroid receptor co-activator which acts as a functional RNA. This domain is also found at the C terminus of Sec31, a component of the coat protein complex II (COPII, which promotes the formation of transport vesicles from the endoplasmic reticulum (ER). COPII has two main functions, the physical deformation of the endoplasmic reticulum membrane into vesicles and the selection of cargo molecules. ; PDB: 2YRU_A.
Probab=23.55 E-value=3.8e+02 Score=23.80 Aligned_cols=49 Identities=14% Similarity=0.095 Sum_probs=34.6
Q ss_pred HHHHHHHHHHHHHHHHHHhhhhHHHHHhHHhHHHHHHHHcCCHHHHHHHHHHH
Q 013559 113 RRAEQRKEKLENELNAYRTNLIKESIRMGYNDFGDFYYAHGALGDAFKSYVRT 165 (441)
Q Consensus 113 ~~~~~~~~~Le~el~~~~~n~~~esir~~~~~la~~~~~~Gd~~~A~~~~~~~ 165 (441)
.+..+++..|...++ ++.+...++..+..|+. .++.|||+.|.+....+
T Consensus 68 ~D~~KRL~iLfd~ln---~g~Ls~~v~~~L~~L~~-aL~~~d~~~A~~Ih~~L 116 (157)
T PF07304_consen 68 DDIEKRLNILFDHLN---NGKLSKPVVDKLHQLAQ-ALQARDYDAADEIHVDL 116 (157)
T ss_dssp HHHHHHHHHHHHHHH---HT-S-HHHHHHHHHHHH-HHHHT-HHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHh---cCCCCHHHHHHHHHHHH-HHHcCCHHHHHHHHHHH
Confidence 455666777777775 44456668888899988 67889999999987664
No 435
>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=23.48 E-value=85 Score=21.43 Aligned_cols=21 Identities=19% Similarity=0.289 Sum_probs=15.9
Q ss_pred ccHHhHHHHcCCChHHHHHHH
Q 013559 353 VDLHMMANAFKTSVAGIEKEL 373 (441)
Q Consensus 353 I~L~~mA~~fg~s~~~~E~~L 373 (441)
.++..+|+.||+|...+-+.+
T Consensus 22 ~si~~IA~~~gvsr~TvyR~l 42 (45)
T PF02796_consen 22 MSIAEIAKQFGVSRSTVYRYL 42 (45)
T ss_dssp --HHHHHHHTTS-HHHHHHHH
T ss_pred CCHHHHHHHHCcCHHHHHHHH
Confidence 889999999999999887665
No 436
>PF04760 IF2_N: Translation initiation factor IF-2, N-terminal region; InterPro: IPR006847 This region is found in the N-terminal half of translation initiation factor IF-2. It is found in two copies in IF-2 alpha isoforms, and in only one copy in the N-terminally truncated beta and gamma isoforms []. Its function is unknown.; GO: 0003743 translation initiation factor activity, 0006413 translational initiation; PDB: 1ND9_A.
Probab=23.34 E-value=62 Score=22.98 Aligned_cols=22 Identities=18% Similarity=0.264 Sum_probs=18.5
Q ss_pred cccHHhHHHHcCCChHHHHHHH
Q 013559 352 SVDLHMMANAFKTSVAGIEKEL 373 (441)
Q Consensus 352 ~I~L~~mA~~fg~s~~~~E~~L 373 (441)
.+++..+|+.+|+++.++-+.|
T Consensus 3 ~i~V~elAk~l~v~~~~ii~~l 24 (54)
T PF04760_consen 3 KIRVSELAKELGVPSKEIIKKL 24 (54)
T ss_dssp EE-TTHHHHHHSSSHHHHHHHH
T ss_pred ceEHHHHHHHHCcCHHHHHHHH
Confidence 5788999999999999987666
No 437
>PF04348 LppC: LppC putative lipoprotein; InterPro: IPR007443 This entry includes several bacterial outer membrane antigens, whose molecular function is unknown.; PDB: 3CKM_A.
Probab=23.33 E-value=27 Score=37.64 Aligned_cols=251 Identities=12% Similarity=0.070 Sum_probs=30.9
Q ss_pred hHHhHHHHHHHHcCCHHHHHHHHHHHHhhhcCchhHHHHHHHHHHHHHHhcCHHHHHhHHHHHhcccccCChhhhhhHHH
Q 013559 140 MGYNDFGDFYYAHGALGDAFKSYVRTRDYCTTSKHIIHMCMSAILVSIEMGQFTHVTSYVSKAEQTPEALEPVTIAKLRC 219 (441)
Q Consensus 140 ~~~~~la~~~~~~Gd~~~A~~~~~~~r~~~~~~~~~~~~~l~~i~~~i~~~~~~~~~~~~~ka~~~~~~~d~~~~~~l~~ 219 (441)
.-++.-++.+.+.|++..|...+.++...--++.+..+..+...++.+..|++..+...++.... ..-......++..
T Consensus 25 ~~~L~Aa~a~l~~g~~~~A~~ll~~l~~~~L~~~q~~~~~Ll~A~lal~~~~~~~Al~~L~~~~~--~~l~~~~~~~~~~ 102 (536)
T PF04348_consen 25 QLLLLAARALLQEGDWAQAQALLNQLDPQQLSPSQQARYQLLRARLALAQGDPEQALSLLNAQDL--WQLPPEQQARYHQ 102 (536)
T ss_dssp --------------------------------------------------------------------------------
T ss_pred HHHHHHHHHHHhCCCHHHHHHHHHhcccccCChHHHHHHHHHHHHHHHhcCCHHHHHHHhccCCc--ccCCHHHHHHHHH
Confidence 35567788999999999999999998644335677788888899999999999999988875222 1112334455555
Q ss_pred HHHHHhcccccHHHHHHHHHhcCcCCCCCchhhhcHHHHHHHHHHHHHhcCChHHHHH-hcccCHhhHhhhccchHHHHH
Q 013559 220 AAGLAHLEARKYKLAARKFLEVGPDLGNSYNEVIAAQDVATYGGLCALASFDRAELKS-KVIDNVNFRNFLELVPEVREL 298 (441)
Q Consensus 220 ~~gl~~l~~r~y~~Aa~~Fl~~~~t~~~~~~el~s~~d~~~Y~~l~al~s~~R~eLk~-~vl~~~~~~~~le~~p~~~~l 298 (441)
..+-++-..+++..|++..+....-..+ +.-...+.-.+. ..|..++..+|.. .--.++.++..++. ..+
T Consensus 103 l~A~a~~~~~~~l~Aa~~~i~l~~lL~d--~~~~~~N~~~iW---~~L~~l~~~~L~~~~~~~~~~l~GWl~L----a~i 173 (536)
T PF04348_consen 103 LRAQAYEQQGDPLAAARERIALDPLLPD--PQERQENQDQIW---QALSQLPPEQLQQLRRASEPDLQGWLEL----ALI 173 (536)
T ss_dssp --------------------------------------------------------------------------------
T ss_pred HHHHHHHhcCCHHHHHHHHHHHhhhcCC--hHHHHHHHHHHH---HHHHcCCHHHHHhhhcCCCHHHHHHHHH----HHH
Confidence 5666677788999988877765543221 011112222222 2344445555554 11122222222211 111
Q ss_pred HHHHhcCCHHHHHHHHHHhHHhhhhchhHHHHHHHHHHHHHHHHHHHhccccccccHHhHHHHcCCChHHHHHHHHHHHH
Q 013559 299 INDFYSSRYASCLDYLGNLKANLLLDIHLHDHVETLYDQIRNKALIQYTHPFVSVDLHMMANAFKTSVAGIEKELEALIT 378 (441)
Q Consensus 299 l~~f~~~~y~~~~~~L~~~~~~l~~D~~L~~h~~~l~~~iR~~~i~qy~~pYs~I~L~~mA~~fg~s~~~~E~~L~~LI~ 378 (441)
.+.+. .+=......|......+...|- ...+-..+... ..........+|-.|-+|..+. ...+-|+
T Consensus 174 ~~~~~-~~p~~l~~al~~Wq~~yP~HPA----~~~lP~~l~~~------~~~~~~~~~~IavLLPlsG~~a--~~~~aI~ 240 (536)
T PF04348_consen 174 YRQYQ-QDPAQLKQALNQWQQRYPNHPA----AQYLPAALQQL------LALQPAPPQRIAVLLPLSGRLA--RAGQAIR 240 (536)
T ss_dssp -----------------------------------------------------------EEEEE--SSTTH--HHHHHHH
T ss_pred HHhcc-CCHHHHHHHHHHHHHhCcCCcc----cccCCHHHHHH------HhhccCCccCEEEEeCCCCchh--HHHHHHH
Confidence 11110 1111222233333333222221 11222222111 1112233456777888887654 4688899
Q ss_pred cCccceE--ecCCCCeEEEecCC--chhHHHHHHHHHHhh
Q 013559 379 DNQIQAR--IDSHNKILYARHAD--QRNATFQRVLQTGSE 414 (441)
Q Consensus 379 ~g~L~ak--ID~~~gvv~~~~~d--~r~~~~~~~i~~~~~ 414 (441)
+|-+.|. -....-.|.+.+.+ .-...|++++..|-+
T Consensus 241 ~G~~aA~~~~~~~~~~l~~~Dt~~~~~~~~~~~a~~~ga~ 280 (536)
T PF04348_consen 241 DGFLAAYYADADSRPELRFYDTNADSADALYQQAVADGAD 280 (536)
T ss_dssp HHHHHHH---TT--S-EEEEETTTS-HHHHHHHHHHTT--
T ss_pred HHHHHhhcccccCCCceEEecCCCCCHHHHHHHHHHcCCC
Confidence 9988887 22223355555443 234667777776543
No 438
>KOG1127 consensus TPR repeat-containing protein [RNA processing and modification]
Probab=23.31 E-value=1e+03 Score=28.04 Aligned_cols=108 Identities=15% Similarity=0.068 Sum_probs=64.7
Q ss_pred HHHHHHHHHHHHhhhhHHHHHhHHhHHHHHHHHcCCHHHHHHHHHHHHhhhcCchhHHHHHHHHHHHHHHhcCHHHHHhH
Q 013559 119 KEKLENELNAYRTNLIKESIRMGYNDFGDFYYAHGALGDAFKSYVRTRDYCTTSKHIIHMCMSAILVSIEMGQFTHVTSY 198 (441)
Q Consensus 119 ~~~Le~el~~~~~n~~~esir~~~~~la~~~~~~Gd~~~A~~~~~~~r~~~~~~~~~~~~~l~~i~~~i~~~~~~~~~~~ 198 (441)
..-|+.++..-+.|. +--++|++++..|++++|-...... +....+-..+.--..++.++|....+.
T Consensus 994 iglLe~k~d~sqynv-------ak~~~gRL~lslgefe~A~~a~~~~------~~evdEdi~gt~l~lFfkndf~~sl~~ 1060 (1238)
T KOG1127|consen 994 IGLLELKLDESQYNV-------AKPDAGRLELSLGEFESAKKASWKE------WMEVDEDIRGTDLTLFFKNDFFSSLEF 1060 (1238)
T ss_pred HHHHHHHHhhhhhhh-------hhhhhhhhhhhhcchhhHhhhhccc------chhHHHHHhhhhHHHHHHhHHHHHHHH
Confidence 334555555555554 3468899999999999988876543 112222222222223788999999999
Q ss_pred HHHHhccccc-CChhhhhhHHHHHHHHhccc-ccHHHHHHHHHhcCc
Q 013559 199 VSKAEQTPEA-LEPVTIAKLRCAAGLAHLEA-RKYKLAARKFLEVGP 243 (441)
Q Consensus 199 ~~ka~~~~~~-~d~~~~~~l~~~~gl~~l~~-r~y~~Aa~~Fl~~~~ 243 (441)
..+|-.+.+. .|- .+-++.+++.+.. |.=..|.....++..
T Consensus 1061 fe~aLsis~se~d~----vvLl~kva~~~g~~~~k~~A~~lLfe~~~ 1103 (1238)
T KOG1127|consen 1061 FEQALSISNSESDK----VVLLCKVAVCMGLARQKNDAQFLLFEVKS 1103 (1238)
T ss_pred HHHHhhhcccccch----hhhhHHHHHHHhhcccchHHHHHHHHHHH
Confidence 9999888763 221 1224455555553 333444556666543
No 439
>PF05402 PqqD: Coenzyme PQQ synthesis protein D (PqqD); InterPro: IPR008792 This family contains several bacterial coenzyme PQQ synthesis protein D (PqqD) sequences. This protein is required for coenzyme pyrrolo-quinoline-quinone (PQQ) biosynthesis.; PDB: 3G2B_A.
Probab=23.30 E-value=1e+02 Score=22.73 Aligned_cols=24 Identities=13% Similarity=0.389 Sum_probs=17.1
Q ss_pred HHhHHHHcCCChHHHHHHHHHHHH
Q 013559 355 LHMMANAFKTSVAGIEKELEALIT 378 (441)
Q Consensus 355 L~~mA~~fg~s~~~~E~~L~~LI~ 378 (441)
.+.+++.|+++++.+++.+..+|.
T Consensus 36 ~~~l~~~y~~~~~~~~~dv~~fl~ 59 (68)
T PF05402_consen 36 VDALAEEYDVDPEEAEEDVEEFLE 59 (68)
T ss_dssp HHHHHHHTT--HHHHHHHHHHHHH
T ss_pred HHHHHHHcCCCHHHHHHHHHHHHH
Confidence 356778899999988888887775
No 440
>cd00569 HTH_Hin_like Helix-turn-helix domain of Hin and related proteins, a family of DNA-binding domains unique to bacteria and represented by the Hin protein of Salmonella. The basic HTH domain is a simple fold comprised of three core helices that form a right-handed helical bundle. The principal DNA-protein interface is formed by the third helix, the recognition helix, inserting itself into the major groove of the DNA. A diverse array of HTH domains participate in a variety of functions that depend on their DNA-binding properties. HTH_Hin represents one of the simplest versions of the HTH domains; the characterization of homologous relationships between various sequence-diverse HTH domain families remains difficult. The Hin recombinase induces the site-specific inversion of a chromosomal DNA segment containing a promoter, which controls the alternate expression of two genes by reversibly switching orientation. The Hin recombinase consists of a single polypeptide chain containing a D
Probab=22.75 E-value=1.6e+02 Score=17.20 Aligned_cols=21 Identities=10% Similarity=0.063 Sum_probs=17.2
Q ss_pred cccHHhHHHHcCCChHHHHHH
Q 013559 352 SVDLHMMANAFKTSVAGIEKE 372 (441)
Q Consensus 352 ~I~L~~mA~~fg~s~~~~E~~ 372 (441)
..+...+|+.||++...+-+|
T Consensus 21 ~~s~~~ia~~~~is~~tv~~~ 41 (42)
T cd00569 21 GESVAEIARRLGVSRSTLYRY 41 (42)
T ss_pred CCCHHHHHHHHCCCHHHHHHh
Confidence 348999999999998877665
No 441
>PF10007 DUF2250: Uncharacterized protein conserved in archaea (DUF2250); InterPro: IPR019254 Members of this family of hypothetical archaeal proteins have no known function.
Probab=22.32 E-value=1.3e+02 Score=24.34 Aligned_cols=77 Identities=12% Similarity=0.154 Sum_probs=47.7
Q ss_pred HHHHHhccccccccHHhHHHHcCCChHHHHHHHHHHHHcCcc---ceEecCCCCe-EEEecCCchhHHHHHHHHHHhhHH
Q 013559 341 KALIQYTHPFVSVDLHMMANAFKTSVAGIEKELEALITDNQI---QARIDSHNKI-LYARHADQRNATFQRVLQTGSEFD 416 (441)
Q Consensus 341 ~~i~qy~~pYs~I~L~~mA~~fg~s~~~~E~~L~~LI~~g~L---~akID~~~gv-v~~~~~d~r~~~~~~~i~~~~~~~ 416 (441)
.-|.+++.-+-.=.-..||..++++.++++..+..|..-|-| ++++-..... .-......++.+|=+.-+.|+.+.
T Consensus 10 ~~IL~hl~~~~~Dy~k~ia~~l~~~~~~v~~~l~~Le~~GLler~~g~~iK~~~~k~K~~~e~~~hHtYY~LTr~G~~ll 89 (92)
T PF10007_consen 10 LKILQHLKKAGPDYAKSIARRLKIPLEEVREALEKLEEMGLLERVEGKTIKRSEAKFKPKKEVHKHHTYYRLTREGELLL 89 (92)
T ss_pred HHHHHHHHHHCCCcHHHHHHHHCCCHHHHHHHHHHHHHCCCeEEecCcccchhhhhcccchhhhcCCceeeecHhHHHHH
Confidence 345556666666667889999999999999999999999976 3442222111 000112224455655666666544
Q ss_pred H
Q 013559 417 Q 417 (441)
Q Consensus 417 ~ 417 (441)
+
T Consensus 90 R 90 (92)
T PF10007_consen 90 R 90 (92)
T ss_pred h
Confidence 3
No 442
>PHA00738 putative HTH transcription regulator
Probab=22.20 E-value=4.3e+02 Score=22.11 Aligned_cols=60 Identities=13% Similarity=0.122 Sum_probs=44.8
Q ss_pred HHHHHHHHhccccccccHHhHHHHcCCChHHHHHHHHHHHHcCccceEecCCCCeEEEecC
Q 013559 338 IRNKALIQYTHPFVSVDLHMMANAFKTSVAGIEKELEALITDNQIQARIDSHNKILYARHA 398 (441)
Q Consensus 338 iR~~~i~qy~~pYs~I~L~~mA~~fg~s~~~~E~~L~~LI~~g~L~akID~~~gvv~~~~~ 398 (441)
.|.+++.. +......+...+++.|+++...+=+-|.-|=..|-|..+-+...-....++.
T Consensus 13 tRr~IL~l-L~~~e~~~V~eLae~l~lSQptVS~HLKvLreAGLV~srK~Gr~vyY~Ln~~ 72 (108)
T PHA00738 13 LRRKILEL-IAENYILSASLISHTLLLSYTTVLRHLKILNEQGYIELYKEGRTLYAKIREN 72 (108)
T ss_pred HHHHHHHH-HHHcCCccHHHHHHhhCCCHHHHHHHHHHHHHCCceEEEEECCEEEEEECCC
Confidence 45444444 4444457888999999999999999999999999998877665555555444
No 443
>PF08221 HTH_9: RNA polymerase III subunit RPC82 helix-turn-helix domain; InterPro: IPR013197 DNA-directed RNA polymerases 2.7.7.6 from EC (also known as DNA-dependent RNA polymerases) are responsible for the polymerisation of ribonucleotides into a sequence complementary to the template DNA. In eukaryotes, there are three different forms of DNA-directed RNA polymerases transcribing different sets of genes. Most RNA polymerases are multimeric enzymes and are composed of a variable number of subunits. The core RNA polymerase complex consists of five subunits (two alpha, one beta, one beta-prime and one omega) and is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. The core RNA polymerase complex forms a "crab claw"-like structure with an internal channel running along the full length []. The key functional sites of the enzyme, as defined by mutational and cross-linking analysis, are located on the inner wall of this channel. RNA synthesis follows after the attachment of RNA polymerase to a specific site, the promoter, on the template DNA strand. The RNA synthesis process continues until a termination sequence is reached. The RNA product, which is synthesised in the 5' to 3'direction, is known as the primary transcript. Eukaryotic nuclei contain three distinct types of RNA polymerases that differ in the RNA they synthesise: RNA polymerase I: located in the nucleoli, synthesises precursors of most ribosomal RNAs. RNA polymerase II: occurs in the nucleoplasm, synthesises mRNA precursors. RNA polymerase III: also occurs in the nucleoplasm, synthesises the precursors of 5S ribosomal RNA, the tRNAs, and a variety of other small nuclear and cytosolic RNAs. Eukaryotic cells are also known to contain separate mitochondrial and chloroplast RNA polymerases. Eukaryotic RNA polymerases, whose molecular masses vary in size from 500 to 700 kDa, contain two non-identical large (>100 kDa) subunits and an array of up to 12 different small (less than 50 kDa) subunits. This family consists of several DNA-directed RNA polymerase III polypeptides which are related to the Saccharomyces cerevisiae (Baker's yeast) RPC82 protein. RNA polymerase C (III) promotes the transcription of tRNA and 5S RNA genes. In S. cerevisiae, the enzyme is composed of 15 subunits, ranging from 10 kDa to about 160 kDa []. This region is probably a DNA-binding helix-turn-helix.; PDB: 2XV4_S 2XUB_A.
Probab=22.15 E-value=1.8e+02 Score=21.49 Aligned_cols=39 Identities=21% Similarity=0.158 Sum_probs=30.7
Q ss_pred HhccccccccHHhHHHHcCCChHHHHHHHHHHHHcCccc
Q 013559 345 QYTHPFVSVDLHMMANAFKTSVAGIEKELEALITDNQIQ 383 (441)
Q Consensus 345 qy~~pYs~I~L~~mA~~fg~s~~~~E~~L~~LI~~g~L~ 383 (441)
.++-.+-+.++..+++.-++|...+-+-|+-||.-+-+.
T Consensus 20 ~~Ll~~G~ltl~~i~~~t~l~~~~Vk~~L~~LiQh~~v~ 58 (62)
T PF08221_consen 20 EVLLSRGRLTLREIVRRTGLSPKQVKKALVVLIQHNLVQ 58 (62)
T ss_dssp HHHHHC-SEEHHHHHHHHT--HHHHHHHHHHHHHTTSEE
T ss_pred HHHHHcCCcCHHHHHHHhCCCHHHHHHHHHHHHHcCCee
Confidence 344567899999999999999999999999999877543
No 444
>PRK00080 ruvB Holliday junction DNA helicase RuvB; Reviewed
Probab=22.07 E-value=4.1e+02 Score=26.27 Aligned_cols=33 Identities=33% Similarity=0.308 Sum_probs=29.9
Q ss_pred ccccHHhHHHHcCCChHHHHHHHH-HHHHcCccc
Q 013559 351 VSVDLHMMANAFKTSVAGIEKELE-ALITDNQIQ 383 (441)
Q Consensus 351 s~I~L~~mA~~fg~s~~~~E~~L~-~LI~~g~L~ 383 (441)
..++++.+|..+|.+++.+|..+. .||..|-|.
T Consensus 275 ~~~~~~~~a~~lg~~~~~~~~~~e~~Li~~~li~ 308 (328)
T PRK00080 275 GPVGLDTLAAALGEERDTIEDVYEPYLIQQGFIQ 308 (328)
T ss_pred CceeHHHHHHHHCCCcchHHHHhhHHHHHcCCcc
Confidence 469999999999999999999998 999988873
No 445
>PRK12537 RNA polymerase sigma factor; Provisional
Probab=22.07 E-value=1.8e+02 Score=25.96 Aligned_cols=45 Identities=16% Similarity=0.162 Sum_probs=32.8
Q ss_pred HHHHHHHHHHHHHHHHhccccccccHHhHHHHcCCChHHHHHHHHHHH
Q 013559 330 HVETLYDQIRNKALIQYTHPFVSVDLHMMANAFKTSVAGIEKELEALI 377 (441)
Q Consensus 330 h~~~l~~~iR~~~i~qy~~pYs~I~L~~mA~~fg~s~~~~E~~L~~LI 377 (441)
.++.|=..-|.-+...| +...+.+.+|+.+|+|+..+...+.+..
T Consensus 130 ~l~~L~~~~r~i~~l~~---~~~~s~~eIA~~lgis~~tV~~~l~ra~ 174 (182)
T PRK12537 130 CLEQLEPARRNCILHAY---VDGCSHAEIAQRLGAPLGTVKAWIKRSL 174 (182)
T ss_pred HHHhCCHHHHHHHHHHH---HcCCCHHHHHHHHCCChhhHHHHHHHHH
Confidence 34444444444444445 7889999999999999999999887754
No 446
>TIGR01889 Staph_reg_Sar staphylococcal accessory regulator family. This model represents a family of transcriptional regulatory proteins in Staphylococcus aureus and Staphylococcus epidermidis. Some members contain two tandem copies of this region. This family is related to the MarR transcriptional regulator family described by pfam model pfam01047.
Probab=21.69 E-value=4.4e+02 Score=21.41 Aligned_cols=65 Identities=5% Similarity=0.040 Sum_probs=46.4
Q ss_pred ccccccHHhHHHHcCCChHHHHHHHHHHHHcCccceEecCCCCeEEEecC-CchhHHHHHHHHHHh
Q 013559 349 PFVSVDLHMMANAFKTSVAGIEKELEALITDNQIQARIDSHNKILYARHA-DQRNATFQRVLQTGS 413 (441)
Q Consensus 349 pYs~I~L~~mA~~fg~s~~~~E~~L~~LI~~g~L~akID~~~gvv~~~~~-d~r~~~~~~~i~~~~ 413 (441)
+-..+++..||+.++++...+-+.|.+|...|-|.-.-|..++-...-.. +.....++++.....
T Consensus 40 ~~~~~t~~eL~~~l~~~~stvs~~i~~Le~kg~I~r~~~~~D~R~~~i~lT~~G~~~~~~~~~~~~ 105 (109)
T TIGR01889 40 NEGKLTLKEIIKEILIKQSALVKIIKKLSKKGYLSKERSEDDERKVIISINKEQRSKIESLISEIE 105 (109)
T ss_pred cCCcCcHHHHHHHHCCCHHHHHHHHHHHHHCCCEeccCCcccCCeEEEEECHHHHHHHHHHHHHHH
Confidence 34679999999999999999999999999999997666666653333322 223344555544433
No 447
>PRK12534 RNA polymerase sigma factor; Provisional
Probab=21.57 E-value=1.6e+02 Score=26.28 Aligned_cols=43 Identities=9% Similarity=0.102 Sum_probs=30.4
Q ss_pred HHHHHHHHHHHHHHHhccccccccHHhHHHHcCCChHHHHHHHHHH
Q 013559 331 VETLYDQIRNKALIQYTHPFVSVDLHMMANAFKTSVAGIEKELEAL 376 (441)
Q Consensus 331 ~~~l~~~iR~~~i~qy~~pYs~I~L~~mA~~fg~s~~~~E~~L~~L 376 (441)
+..|-..-|.-....| +.-.+.+.+|+.||+|+..+...|.+.
T Consensus 135 l~~L~~~~r~i~~l~~---~~g~s~~eIA~~lgis~~~v~~~l~Ra 177 (187)
T PRK12534 135 LAELEPPRSELIRTAF---FEGITYEELAARTDTPIGTVKSWIRRG 177 (187)
T ss_pred HHhCCHHHHHHHHHHH---HcCCCHHHHHHHhCCChhHHHHHHHHH
Confidence 3344344443444445 688899999999999999998877653
No 448
>PF03444 HrcA_DNA-bdg: Winged helix-turn-helix transcription repressor, HrcA DNA-binding; InterPro: IPR005104 Prokaryotic cells have a defence mechanism against a sudden heat-shock stress. Commonly, they induce a set of proteins that protect cellular proteins from being denatured by heat. Among such proteins are the GroE and DnaK chaperones whose transcription is regulated by a heat-shock repressor protein HrcA. HrcA is a winged helix-turn-helix repressor that negatively regulates the transcription of dnaK and groE operons by binding the upstream CIRCE (controlling inverted repeat of chaperone expression) element. In Bacillus subtilis this element is a perfect 9 base pair inverted repeat separated by a 9 base pair spacer. The crystal structure of a heat-inducible transcriptional repressor, HrcA, from Thermotoga maritima has been reported at 2.2A resolution. HrcA is composed of three domains: an N-terminal winged helix-turn-helix domain (WHTH), a GAF-like domain, and an inserted dimerizing domain (IDD). The IDD shows a unique structural fold with an anti-parallel beta-sheet composed of three beta-strands sided by four alpha-helices. HrcA crystallises as a dimer, which is formed through hydrophobic contact between the IDDs and a limited contact that involves conserved residues between the GAF-like domains []. The structural studies suggest that the inactive form of HrcA is the dimer and this is converted to its DNA-binding form by interaction with GroEL, which binds to a conserved C-terminal sequence region [, ]. Comparison of the HrcA-CIRCE complexes from B. subtilis and Bacillus thermoglucosidasius (Geobacillus thermoglucosidasius), which grow at vastly different ranges of temperature shows that the thermostability profiles were consistent with the difference in the growth temperatures suggesting that HrcA can function as a thermosensor to detect temperature changes in cells []. Any increase in temperature causes the dissociation of the HrcA from the CIRCE complex with the concomitant activation of transcription of the groE and dnaK operons. This domain represents the winged helix-turn-helix DNA-binding domain which is located close to the N terminus of HrcA. This domain is also found at the N terminus of a set of uncharacterised proteins that have two C-terminal CBS domains. ; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent
Probab=21.38 E-value=2.8e+02 Score=21.76 Aligned_cols=49 Identities=18% Similarity=0.163 Sum_probs=40.9
Q ss_pred HHHHHHHHHHhccccccccHHhHHHHcCCChHHHHHHHHHHHHcCccce
Q 013559 336 DQIRNKALIQYTHPFVSVDLHMMANAFKTSVAGIEKELEALITDNQIQA 384 (441)
Q Consensus 336 ~~iR~~~i~qy~~pYs~I~L~~mA~~fg~s~~~~E~~L~~LI~~g~L~a 384 (441)
++|-.-++..|.+.=+-|.=+.+|+.+|+|+..+-.+++.|-.-|-|.+
T Consensus 7 ~~IL~alV~~Y~~~~~PVgSk~ia~~l~~s~aTIRN~M~~Le~lGlve~ 55 (78)
T PF03444_consen 7 REILKALVELYIETGEPVGSKTIAEELGRSPATIRNEMADLEELGLVES 55 (78)
T ss_pred HHHHHHHHHHHHhcCCCcCHHHHHHHHCCChHHHHHHHHHHHHCCCccC
Confidence 3444556677888888999999999999999999999999998887754
No 449
>KOG4162 consensus Predicted calmodulin-binding protein [Signal transduction mechanisms]
Probab=21.16 E-value=5.1e+02 Score=29.14 Aligned_cols=99 Identities=16% Similarity=0.119 Sum_probs=58.2
Q ss_pred HHHhHHhHHHHHHHHcCCHHHHHHHHHHHHhhhcCchhHHHHHHHHHHHHHHhcCHHHHHh--HHHHHhcccccCChhhh
Q 013559 137 SIRMGYNDFGDFYYAHGALGDAFKSYVRTRDYCTTSKHIIHMCMSAILVSIEMGQFTHVTS--YVSKAEQTPEALEPVTI 214 (441)
Q Consensus 137 sir~~~~~la~~~~~~Gd~~~A~~~~~~~r~~~~~~~~~~~~~l~~i~~~i~~~~~~~~~~--~~~ka~~~~~~~d~~~~ 214 (441)
..-..++..|..+...|...+|..+|...... +|+|.-. .-.+..+....|+-..+.. .+.-+-.. ||...
T Consensus 682 l~~~~~~~~G~~~~~~~~~~EA~~af~~Al~l--dP~hv~s-~~Ala~~lle~G~~~la~~~~~L~dalr~----dp~n~ 754 (799)
T KOG4162|consen 682 LSASVYYLRGLLLEVKGQLEEAKEAFLVALAL--DPDHVPS-MTALAELLLELGSPRLAEKRSLLSDALRL----DPLNH 754 (799)
T ss_pred hhHHHHHHhhHHHHHHHhhHHHHHHHHHHHhc--CCCCcHH-HHHHHHHHHHhCCcchHHHHHHHHHHHhh----CCCCH
Confidence 33346677778888888888888877765443 4444322 2244445556665544443 22222111 22111
Q ss_pred hhHHHHHHHHhcccccHHHHHHHHHhcCc
Q 013559 215 AKLRCAAGLAHLEARKYKLAARKFLEVGP 243 (441)
Q Consensus 215 ~~l~~~~gl~~l~~r~y~~Aa~~Fl~~~~ 243 (441)
..-.+-|-....+|+...|+.+|.-+..
T Consensus 755 -eaW~~LG~v~k~~Gd~~~Aaecf~aa~q 782 (799)
T KOG4162|consen 755 -EAWYYLGEVFKKLGDSKQAAECFQAALQ 782 (799)
T ss_pred -HHHHHHHHHHHHccchHHHHHHHHHHHh
Confidence 2235678888899999999999987653
No 450
>PRK10046 dpiA two-component response regulator DpiA; Provisional
Probab=21.03 E-value=1.9e+02 Score=26.68 Aligned_cols=41 Identities=24% Similarity=0.169 Sum_probs=35.8
Q ss_pred cccccccHHhHHHHcCCChHHHHHHHHHHHHcCccceEecC
Q 013559 348 HPFVSVDLHMMANAFKTSVAGIEKELEALITDNQIQARIDS 388 (441)
Q Consensus 348 ~pYs~I~L~~mA~~fg~s~~~~E~~L~~LI~~g~L~akID~ 388 (441)
+-++-.+.+.+|+.+|+|+..+++.+..|...|.+...|+-
T Consensus 173 ~g~~g~s~~eIa~~l~iS~~Tv~~~~~~~~~~~~~~~~~~~ 213 (225)
T PRK10046 173 EPGVQHTAETVAQALTISRTTARRYLEYCASRHLIIAEIVH 213 (225)
T ss_pred cCCCCcCHHHHHHHhCccHHHHHHHHHHHHhCCeEEEEeec
Confidence 33445789999999999999999999999999999888765
No 451
>KOG3877 consensus NADH:ubiquinone oxidoreductase, NDUFA10/42kDa subunit [Energy production and conversion]
Probab=20.92 E-value=2.3e+02 Score=28.14 Aligned_cols=68 Identities=19% Similarity=0.361 Sum_probs=50.2
Q ss_pred HHHhcCCHHHHHHHHHHhHH---------hhhhchhH----------HHHHHHHHHHHHHHHHHHhccccccccHHhHHH
Q 013559 300 NDFYSSRYASCLDYLGNLKA---------NLLLDIHL----------HDHVETLYDQIRNKALIQYTHPFVSVDLHMMAN 360 (441)
Q Consensus 300 ~~f~~~~y~~~~~~L~~~~~---------~l~~D~~L----------~~h~~~l~~~iR~~~i~qy~~pYs~I~L~~mA~ 360 (441)
.-.|+|+|.++..+|+.+-+ ..-.||.+ ......-+.++|...|-||+-||-.|-|
T Consensus 150 ~r~y~~R~~QY~dAL~HiL~TGQGVVLERsp~SDFVF~eAM~~qgyi~~~~~~hYnevr~nti~~ll~PHLViYl----- 224 (393)
T KOG3877|consen 150 DRIYNCRFDQYLDALAHILNTGQGVVLERSPHSDFVFAEAMRDQGYIGHEYFKHYNEVRKNTIPQLLWPHLVIYL----- 224 (393)
T ss_pred HHHHHhHHHHHHHHHHHHHhcCCeEEEecCcchhHHHHHHHHhcCcchhHHHHHHHHHHhhhhhhhcCccEEEEE-----
Confidence 34689999999999988743 12245544 3345566788999999999999999865
Q ss_pred HcCCChHHHHHHHH
Q 013559 361 AFKTSVAGIEKELE 374 (441)
Q Consensus 361 ~fg~s~~~~E~~L~ 374 (441)
+++++.+.+.|-
T Consensus 225 --d~Pv~~v~~~Ik 236 (393)
T KOG3877|consen 225 --DTPVNKVLENIK 236 (393)
T ss_pred --cCCcHHHHHHHH
Confidence 678887766554
No 452
>PF04492 Phage_rep_O: Bacteriophage replication protein O ; InterPro: IPR006497 This entry is represented by the N-terminal domain of Bacteriophage lambda, GpO. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches.; GO: 0006260 DNA replication
Probab=20.82 E-value=2.6e+02 Score=22.96 Aligned_cols=36 Identities=19% Similarity=0.180 Sum_probs=34.1
Q ss_pred ccccccccHHhHHHHcCCChHHHHHHHHHHHHcCcc
Q 013559 347 THPFVSVDLHMMANAFKTSVAGIEKELEALITDNQI 382 (441)
Q Consensus 347 ~~pYs~I~L~~mA~~fg~s~~~~E~~L~~LI~~g~L 382 (441)
=++...|+.+.+|+.-|++...+.+.+-.||..|-|
T Consensus 49 nKk~d~Is~sq~~e~tg~~~~~V~~al~~Li~~~vI 84 (100)
T PF04492_consen 49 NKKMDRISNSQIAEMTGLSRDHVSKALNELIRRGVI 84 (100)
T ss_pred CCccceeeHHHHHHHHCcCHHHHHHHHHHHHHCCCE
Confidence 377889999999999999999999999999999998
No 453
>smart00342 HTH_ARAC helix_turn_helix, arabinose operon control protein.
Probab=20.79 E-value=1.2e+02 Score=22.43 Aligned_cols=24 Identities=17% Similarity=0.207 Sum_probs=20.5
Q ss_pred ccHHhHHHHcCCChHHHHHHHHHH
Q 013559 353 VDLHMMANAFKTSVAGIEKELEAL 376 (441)
Q Consensus 353 I~L~~mA~~fg~s~~~~E~~L~~L 376 (441)
++++.||+.+|+|...+.+.+.+.
T Consensus 2 ~~~~~la~~~~~s~~~l~~~f~~~ 25 (84)
T smart00342 2 LTLEDLAEALGMSPRHLQRLFKKE 25 (84)
T ss_pred CCHHHHHHHhCCCHHHHHHHHHHH
Confidence 689999999999999888777664
No 454
>PRK11511 DNA-binding transcriptional activator MarA; Provisional
Probab=20.58 E-value=2.4e+02 Score=23.84 Aligned_cols=26 Identities=8% Similarity=0.022 Sum_probs=21.7
Q ss_pred cccccHHhHHHHcCCChHHHHHHHHH
Q 013559 350 FVSVDLHMMANAFKTSVAGIEKELEA 375 (441)
Q Consensus 350 Ys~I~L~~mA~~fg~s~~~~E~~L~~ 375 (441)
...++++.+|+.+|+|+..+.+...+
T Consensus 23 ~~~~sl~~lA~~~g~S~~~l~r~Fk~ 48 (127)
T PRK11511 23 ESPLSLEKVSERSGYSKWHLQRMFKK 48 (127)
T ss_pred CCCCCHHHHHHHHCcCHHHHHHHHHH
Confidence 45699999999999999988776654
No 455
>PRK09413 IS2 repressor TnpA; Reviewed
Probab=20.54 E-value=5.1e+02 Score=21.64 Aligned_cols=41 Identities=7% Similarity=0.030 Sum_probs=32.3
Q ss_pred HHHHHHHHhccccccccHHhHHHHcCCChHHHHHHHHHHHHcC
Q 013559 338 IRNKALIQYTHPFVSVDLHMMANAFKTSVAGIEKELEALITDN 380 (441)
Q Consensus 338 iR~~~i~qy~~pYs~I~L~~mA~~fg~s~~~~E~~L~~LI~~g 380 (441)
-+..++.+++.+ ..+...+|..||++...+-+|+.++-..|
T Consensus 17 fK~~aV~~~~~~--g~sv~evA~e~gIs~~tl~~W~r~y~~~~ 57 (121)
T PRK09413 17 EKIAIVQQSFEP--GMTVSLVARQHGVAASQLFLWRKQYQEGS 57 (121)
T ss_pred HHHHHHHHHHcC--CCCHHHHHHHHCcCHHHHHHHHHHHhhcc
Confidence 345666666554 66899999999999999999999986543
No 456
>PF00046 Homeobox: Homeobox domain not present here.; InterPro: IPR001356 The homeobox domain was first identified in a number of drosophila homeotic and segmentation proteins, but is now known to be well-conserved in many other animals, including vertebrates [, , ]. Hox genes encode homeodomain-containing transcriptional regulators that operate differential genetic programs along the anterior-posterior axis of animal bodies []. The domain binds DNA through a helix-turn-helix (HTH) structure. The HTH motif is characterised by two alpha-helices, which make intimate contacts with the DNA and are joined by a short turn. The second helix binds to DNA via a number of hydrogen bonds and hydrophobic interactions, which occur between specific side chains and the exposed bases and thymine methyl groups within the major groove of the DNA []. The first helix helps to stabilise the structure. The motif is very similar in sequence and structure in a wide range of DNA-binding proteins (e.g., cro and repressor proteins, homeotic proteins, etc.). One of the principal differences between HTH motifs in these different proteins arises from the stereo-chemical requirement for glycine in the turn which is needed to avoid steric interference of the beta-carbon with the main chain: for cro and repressor proteins the glycine appears to be mandatory, while for many of the homeotic and other DNA-binding proteins the requirement is relaxed.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0043565 sequence-specific DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 2DA3_A 1LFB_A 2LFB_A 2ECB_A 2DA5_A 3D1N_O 3A03_A 2XSD_C 3CMY_A 1AHD_P ....
Probab=20.49 E-value=1.1e+02 Score=21.61 Aligned_cols=25 Identities=4% Similarity=0.055 Sum_probs=21.3
Q ss_pred ccccHHhHHHHcCCChHHHHHHHHH
Q 013559 351 VSVDLHMMANAFKTSVAGIEKELEA 375 (441)
Q Consensus 351 s~I~L~~mA~~fg~s~~~~E~~L~~ 375 (441)
+.-.+..||..+|++...|..|..+
T Consensus 26 ~~~~~~~la~~l~l~~~~V~~WF~n 50 (57)
T PF00046_consen 26 SKEEREELAKELGLTERQVKNWFQN 50 (57)
T ss_dssp HHHHHHHHHHHHTSSHHHHHHHHHH
T ss_pred cccccccccccccccccccccCHHH
Confidence 5567889999999999999999754
No 457
>PF10579 Rapsyn_N: Rapsyn N-terminal myristoylation and linker region; InterPro: IPR019568 Neuromuscular junction formation relies upon the clustering of acetylcholine receptors and other proteins in the muscle membrane. Rapsyn is a peripheral membrane protein that is selectively concentrated at the neuromuscular junction and is essential for the formation of synaptic acetylcholine receptor aggregates. Acetylcholine receptors fail to aggregate beneath nerve terminals in mice where rapsyn has been knocked out. The N-terminal six amino acids of rapsyn are its myristoylation site, and myristoylation is necessary for the targeting of the protein to the membrane []. ; GO: 0008270 zinc ion binding, 0033130 acetylcholine receptor binding, 0007268 synaptic transmission, 0005856 cytoskeleton, 0030054 cell junction, 0045211 postsynaptic membrane
Probab=20.30 E-value=4.4e+02 Score=20.82 Aligned_cols=53 Identities=13% Similarity=0.248 Sum_probs=43.1
Q ss_pred HHHHHHcCCHHHHHHHHHHHHhhhcCchhHHHHHHHHHHHHHHhcCHHHHHhH
Q 013559 146 GDFYYAHGALGDAFKSYVRTRDYCTTSKHIIHMCMSAILVSIEMGQFTHVTSY 198 (441)
Q Consensus 146 a~~~~~~Gd~~~A~~~~~~~r~~~~~~~~~~~~~l~~i~~~i~~~~~~~~~~~ 198 (441)
|--+|+..+.++|+....++.+..+.+..++..+-..++..-.+|++..+..+
T Consensus 13 GlkLY~~~~~~~Al~~W~~aL~k~~~~~~rf~~lG~l~qA~~e~Gkyr~~L~f 65 (80)
T PF10579_consen 13 GLKLYHQNETQQALQKWRKALEKITDREDRFRVLGYLIQAHMEWGKYREMLAF 65 (80)
T ss_pred HHHHhccchHHHHHHHHHHHHhhcCChHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 33366889999999999999888877778888887788888888888877765
No 458
>PRK12547 RNA polymerase sigma factor; Provisional
Probab=20.30 E-value=2.2e+02 Score=24.78 Aligned_cols=47 Identities=11% Similarity=0.054 Sum_probs=35.4
Q ss_pred HHHHHHHHHHHHHHHHHHhccccccccHHhHHHHcCCChHHHHHHHHHHH
Q 013559 328 HDHVETLYDQIRNKALIQYTHPFVSVDLHMMANAFKTSVAGIEKELEALI 377 (441)
Q Consensus 328 ~~h~~~l~~~iR~~~i~qy~~pYs~I~L~~mA~~fg~s~~~~E~~L~~LI 377 (441)
...+..|=..-|.-....| +.-.+.+.+|+.||+|+..+...|.+..
T Consensus 107 ~~~l~~L~~~~r~v~~l~~---~~g~s~~eIA~~lgis~~tV~~~l~Rar 153 (164)
T PRK12547 107 KKALNLLSADQREAIILIG---ASGFSYEDAAAICGCAVGTIKSRVSRAR 153 (164)
T ss_pred HHHHHhCCHHHHHHHHHHH---HcCCCHHHHHHHhCCCHHHHHHHHHHHH
Confidence 3455555555565666667 6788899999999999999998887654
No 459
>PRK09642 RNA polymerase sigma factor SigW; Reviewed
Probab=20.24 E-value=1.9e+02 Score=25.06 Aligned_cols=46 Identities=20% Similarity=0.224 Sum_probs=33.3
Q ss_pred HHHHHHHHHHHHHHHHHHhccccccccHHhHHHHcCCChHHHHHHHHHH
Q 013559 328 HDHVETLYDQIRNKALIQYTHPFVSVDLHMMANAFKTSVAGIEKELEAL 376 (441)
Q Consensus 328 ~~h~~~l~~~iR~~~i~qy~~pYs~I~L~~mA~~fg~s~~~~E~~L~~L 376 (441)
...+..|=..-|.-....| |.-.+...+|+.+|+|+..+...+.+.
T Consensus 101 ~~~l~~Lp~~~r~v~~l~~---~~g~s~~EIA~~lgis~~tV~~~l~Ra 146 (160)
T PRK09642 101 AQKLRELPENYRDVVLAHY---LEEKSYQEIALQEKIEVKTVEMKLYRA 146 (160)
T ss_pred HHHHHhCCHHHHHHHHHHH---HhCCCHHHHHHHHCCCHHHHHHHHHHH
Confidence 3344444445555555556 788999999999999999998877653
No 460
>TIGR02899 spore_safA spore coat assembly protein SafA. in which one of which is found in most examples of endospore-forming bacteria. Lysin motifs are repeated in many proteins.
Probab=20.16 E-value=98 Score=20.01 Aligned_cols=17 Identities=12% Similarity=0.212 Sum_probs=14.2
Q ss_pred cHHhHHHHcCCChHHHH
Q 013559 354 DLHMMANAFKTSVAGIE 370 (441)
Q Consensus 354 ~L~~mA~~fg~s~~~~E 370 (441)
++..+|+.||++.+.+.
T Consensus 6 tl~~IA~~~~~~~~~l~ 22 (44)
T TIGR02899 6 TLWKIAKKYGVDFDELI 22 (44)
T ss_pred CHHHHHHHHCcCHHHHH
Confidence 68899999999977653
No 461
>KOG1125 consensus TPR repeat-containing protein [General function prediction only]
Probab=20.09 E-value=8.7e+02 Score=26.41 Aligned_cols=51 Identities=18% Similarity=0.171 Sum_probs=32.9
Q ss_pred hHHHHHHHHhcccccHHHHHHHHHhcCcCCCCCchhhhcHHHHHHHHHHHHHhcCChHH
Q 013559 216 KLRCAAGLAHLEARKYKLAARKFLEVGPDLGNSYNEVIAAQDVATYGGLCALASFDRAE 274 (441)
Q Consensus 216 ~l~~~~gl~~l~~r~y~~Aa~~Fl~~~~t~~~~~~el~s~~d~~~Y~~l~al~s~~R~e 274 (441)
.+.+.-|+.+-..|.|..|..+|-.+...-++ .+++ .+ ++| +.|+.-+|++
T Consensus 431 dvQ~~LGVLy~ls~efdraiDcf~~AL~v~Pn--d~~l-WN---RLG--AtLAN~~~s~ 481 (579)
T KOG1125|consen 431 DVQSGLGVLYNLSGEFDRAVDCFEAALQVKPN--DYLL-WN---RLG--ATLANGNRSE 481 (579)
T ss_pred hHHhhhHHHHhcchHHHHHHHHHHHHHhcCCc--hHHH-HH---Hhh--HHhcCCcccH
Confidence 34577788888899999999999988754332 1222 22 333 4566666653
No 462
>KOG2908 consensus 26S proteasome regulatory complex, subunit RPN9/PSMD13 [Posttranslational modification, protein turnover, chaperones]
Probab=20.02 E-value=8.8e+02 Score=24.73 Aligned_cols=84 Identities=14% Similarity=0.214 Sum_probs=48.1
Q ss_pred cCChHHHHHHHHHhhccCCCCCcCCH---HHHHHHH--HHHHHHHHHHHHHHHHHHhhhhHHHHHhHHhHHHHHHHHcCC
Q 013559 80 GENTQLFREVVKKIDGRLGPNYAMDE---AWCDSVD--RRAEQRKEKLENELNAYRTNLIKESIRMGYNDFGDFYYAHGA 154 (441)
Q Consensus 80 t~~~~~Y~~~~~~l~~~~~~~~~~D~---~~~~~~~--~~~~~~~~~Le~el~~~~~n~~~esir~~~~~la~~~~~~Gd 154 (441)
+-+.++|...+.++.....| ..+=+ ...++.. .+.-+-++++..+++.++ .++.|.......|+++..+||
T Consensus 55 ~~~l~lY~NFvsefe~kINp-lslvei~l~~~~~~~D~~~al~~Le~i~~~~~~~~---e~~av~~~~t~~~r~~L~i~D 130 (380)
T KOG2908|consen 55 DLLLQLYLNFVSEFETKINP-LSLVEILLVVSEQISDKDEALEFLEKIIEKLKEYK---EPDAVIYILTEIARLKLEIND 130 (380)
T ss_pred hHHHHHHHHHHHHHhhccCh-HHHHHHHHHHHHHhccHHHHHHHHHHHHHHHHhhc---cchhHHHHHHHHHHHHHhccc
Confidence 45678888888877643322 00000 1111121 112223334444444333 335666677788899999999
Q ss_pred HHHHHHHHHHHHh
Q 013559 155 LGDAFKSYVRTRD 167 (441)
Q Consensus 155 ~~~A~~~~~~~r~ 167 (441)
+.++.+.+.....
T Consensus 131 Lk~~kk~ldd~~~ 143 (380)
T KOG2908|consen 131 LKEIKKLLDDLKS 143 (380)
T ss_pred HHHHHHHHHHHHH
Confidence 9999999988754
Done!