Query 013640
Match_columns 439
No_of_seqs 155 out of 294
Neff 5.8
Searched_HMMs 46136
Date Fri Mar 29 05:54:47 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/013640.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/013640hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG2758 Translation initiation 100.0 1E-141 2E-146 1039.4 40.4 423 1-436 1-428 (432)
2 KOG0687 26S proteasome regulat 100.0 2.1E-59 4.5E-64 460.7 32.6 359 16-430 17-392 (393)
3 COG5187 RPN7 26S proteasome re 100.0 1.1E-41 2.4E-46 331.6 29.2 361 17-430 22-406 (412)
4 PF09440 eIF3_N: eIF3 subunit 100.0 1.4E-42 2.9E-47 308.4 12.4 133 5-138 1-133 (133)
5 KOG1464 COP9 signalosome, subu 100.0 3.3E-37 7.2E-42 299.1 21.7 292 111-432 118-438 (440)
6 KOG0686 COP9 signalosome, subu 99.7 9.9E-16 2.1E-20 155.9 25.7 344 35-431 64-448 (466)
7 PF10602 RPN7: 26S proteasome 99.6 6.5E-15 1.4E-19 137.3 13.6 161 68-267 5-172 (177)
8 PF01399 PCI: PCI domain; Int 99.6 4.4E-15 9.6E-20 124.1 9.6 104 286-401 1-104 (105)
9 smart00088 PINT motif in prote 99.5 3.3E-13 7.2E-18 110.8 9.7 73 334-406 1-73 (88)
10 smart00753 PAM PCI/PINT associ 99.5 3.3E-13 7.2E-18 110.8 9.7 73 334-406 1-73 (88)
11 KOG1463 26S proteasome regulat 99.2 4.4E-08 9.5E-13 98.8 28.7 251 132-418 132-408 (411)
12 KOG2908 26S proteasome regulat 98.7 0.00015 3.3E-09 73.6 32.3 340 49-422 3-361 (380)
13 COG5159 RPN6 26S proteasome re 98.5 2.4E-06 5.2E-11 85.1 15.1 269 132-419 129-407 (421)
14 KOG1498 26S proteasome regulat 98.0 0.00083 1.8E-08 69.5 21.1 276 132-431 135-432 (439)
15 KOG2753 Uncharacterized conser 97.7 0.0038 8.2E-08 63.5 19.1 82 338-419 275-361 (378)
16 COG5071 RPN5 26S proteasome re 97.6 0.036 7.7E-07 56.2 23.3 259 125-417 128-412 (439)
17 KOG2581 26S proteasome regulat 97.1 0.092 2E-06 55.1 20.9 145 240-401 254-422 (493)
18 KOG1076 Translation initiation 96.8 0.47 1E-05 52.8 24.3 72 335-407 696-768 (843)
19 PF10075 PCI_Csn8: COP9 signal 96.5 0.0079 1.7E-07 53.9 7.1 78 288-381 44-121 (143)
20 KOG2072 Translation initiation 96.5 0.73 1.6E-05 52.1 23.0 256 132-402 184-493 (988)
21 KOG2582 COP9 signalosome, subu 96.1 0.12 2.5E-06 53.7 13.6 155 252-424 225-387 (422)
22 PF09012 FeoC: FeoC like trans 95.7 0.015 3.2E-07 46.0 4.0 49 346-395 3-51 (69)
23 PF09756 DDRGK: DDRGK domain; 94.4 0.088 1.9E-06 50.0 6.1 73 344-417 100-174 (188)
24 KOG1497 COP9 signalosome, subu 94.2 7.9 0.00017 40.0 28.6 93 336-434 300-392 (399)
25 PF12569 NARP1: NMDA receptor- 94.0 3 6.4E-05 45.6 17.4 231 114-360 24-293 (517)
26 PF09976 TPR_21: Tetratricopep 93.9 0.84 1.8E-05 40.4 11.1 76 115-190 35-110 (145)
27 PRK15331 chaperone protein Sic 93.5 0.29 6.3E-06 45.6 7.5 69 117-188 26-94 (165)
28 PRK15431 ferrous iron transpor 93.3 0.23 5E-06 40.7 5.7 53 345-398 4-57 (78)
29 PF13424 TPR_12: Tetratricopep 92.8 0.65 1.4E-05 36.3 7.6 71 125-195 2-76 (78)
30 PF13174 TPR_6: Tetratricopept 92.4 0.21 4.7E-06 32.3 3.7 32 129-160 1-32 (33)
31 PF13432 TPR_16: Tetratricopep 92.4 0.72 1.6E-05 34.7 7.2 59 132-193 1-59 (65)
32 KOG2688 Transcription-associat 91.9 0.8 1.7E-05 48.1 9.0 128 252-405 246-387 (394)
33 PF14559 TPR_19: Tetratricopep 91.7 0.23 4.9E-06 37.7 3.6 55 116-171 13-67 (68)
34 PF10255 Paf67: RNA polymerase 91.5 14 0.00031 39.2 17.8 199 130-379 124-343 (404)
35 TIGR02795 tol_pal_ybgF tol-pal 91.4 3.3 7.2E-05 33.8 10.7 67 129-195 3-69 (119)
36 PF08220 HTH_DeoR: DeoR-like h 90.6 0.87 1.9E-05 34.6 5.9 54 344-401 1-54 (57)
37 PF13414 TPR_11: TPR repeat; P 90.6 1.2 2.5E-05 33.9 6.7 63 128-193 3-66 (69)
38 TIGR02917 PEP_TPR_lipo putativ 90.4 31 0.00067 37.8 22.4 62 129-193 737-798 (899)
39 PF07719 TPR_2: Tetratricopept 90.3 0.63 1.4E-05 30.3 4.3 32 129-160 2-33 (34)
40 TIGR02521 type_IV_pilW type IV 90.2 13 0.00028 33.2 14.7 64 128-194 135-198 (234)
41 PF12895 Apc3: Anaphase-promot 90.1 0.83 1.8E-05 36.5 5.8 59 128-190 25-83 (84)
42 PRK10803 tol-pal system protei 89.7 2.9 6.3E-05 41.6 10.4 71 127-197 179-249 (263)
43 PRK15363 pathogenicity island 89.6 1.7 3.6E-05 40.3 7.9 75 111-191 20-95 (157)
44 cd00189 TPR Tetratricopeptide 89.4 2.5 5.4E-05 31.2 7.7 63 126-191 32-94 (100)
45 TIGR02795 tol_pal_ybgF tol-pal 89.3 4.3 9.2E-05 33.2 9.6 70 127-196 38-107 (119)
46 KOG3060 Uncharacterized conser 88.6 11 0.00025 37.8 13.3 72 115-197 145-216 (289)
47 PF08279 HTH_11: HTH domain; 88.5 1.5 3.3E-05 32.4 5.7 47 347-396 5-51 (55)
48 PF13176 TPR_7: Tetratricopept 88.4 0.73 1.6E-05 31.4 3.6 32 130-161 1-32 (36)
49 PF13525 YfiO: Outer membrane 88.3 2.9 6.3E-05 39.4 8.9 70 128-197 5-74 (203)
50 PF10668 Phage_terminase: Phag 88.2 0.82 1.8E-05 35.7 4.2 37 344-380 9-45 (60)
51 PF14938 SNAP: Soluble NSF att 87.5 27 0.00058 34.6 15.7 33 288-321 238-270 (282)
52 PF13371 TPR_9: Tetratricopept 87.2 1.1 2.4E-05 34.3 4.5 48 114-161 15-62 (73)
53 cd00189 TPR Tetratricopeptide 87.2 2.6 5.6E-05 31.1 6.5 61 130-193 2-62 (100)
54 TIGR02552 LcrH_SycD type III s 85.7 6.2 0.00014 33.5 8.9 73 117-193 6-79 (135)
55 TIGR03504 FimV_Cterm FimV C-te 85.4 0.97 2.1E-05 33.0 3.0 27 131-157 2-28 (44)
56 PF13432 TPR_16: Tetratricopep 85.1 3.1 6.7E-05 31.2 5.9 45 116-160 19-63 (65)
57 PF09295 ChAPs: ChAPs (Chs5p-A 84.4 7.4 0.00016 41.2 10.3 125 35-191 169-294 (395)
58 PF13181 TPR_8: Tetratricopept 83.9 2.5 5.4E-05 27.6 4.3 31 129-159 2-32 (34)
59 smart00345 HTH_GNTR helix_turn 83.8 2.4 5.2E-05 31.1 4.7 48 341-388 3-51 (60)
60 PRK11788 tetratricopeptide rep 83.8 48 0.001 33.3 15.7 76 116-194 202-278 (389)
61 TIGR02552 LcrH_SycD type III s 83.5 19 0.00042 30.5 11.0 66 128-196 51-116 (135)
62 PF13428 TPR_14: Tetratricopep 82.6 2.7 5.8E-05 29.7 4.3 33 129-161 2-34 (44)
63 PRK10866 outer membrane biogen 82.1 23 0.0005 34.6 12.2 83 115-197 56-153 (243)
64 TIGR02917 PEP_TPR_lipo putativ 82.1 84 0.0018 34.4 22.5 66 123-191 154-219 (899)
65 PRK10049 pgaA outer membrane p 81.6 1E+02 0.0022 35.2 18.7 96 115-218 380-475 (765)
66 PRK11014 transcriptional repre 80.6 4.8 0.0001 35.9 6.3 62 342-404 10-71 (141)
67 PF13412 HTH_24: Winged helix- 80.0 5.7 0.00012 28.6 5.4 44 343-387 4-47 (48)
68 TIGR03302 OM_YfiO outer membra 79.9 10 0.00022 35.7 8.6 63 131-193 169-231 (235)
69 PF09743 DUF2042: Uncharacteri 79.6 15 0.00033 36.9 10.0 98 285-394 70-167 (272)
70 PF00515 TPR_1: Tetratricopept 79.4 4.3 9.4E-05 26.5 4.3 31 129-159 2-32 (34)
71 smart00420 HTH_DEOR helix_turn 79.4 4.9 0.00011 28.5 4.9 34 355-388 12-45 (53)
72 cd05804 StaR_like StaR_like; a 79.4 30 0.00066 34.4 12.3 77 115-191 135-212 (355)
73 PF14853 Fis1_TPR_C: Fis1 C-te 79.2 4.9 0.00011 30.4 4.9 34 128-161 1-34 (53)
74 PF02082 Rrf2: Transcriptional 78.9 13 0.00028 30.1 7.7 67 338-405 6-72 (83)
75 PF13374 TPR_10: Tetratricopep 78.7 4.3 9.3E-05 27.2 4.2 32 128-159 2-33 (42)
76 COG5600 Transcription-associat 78.4 96 0.0021 32.9 16.8 240 142-405 144-406 (413)
77 PF13431 TPR_17: Tetratricopep 78.3 1.4 2.9E-05 30.0 1.5 27 122-148 7-33 (34)
78 TIGR02521 type_IV_pilW type IV 78.0 50 0.0011 29.4 17.7 66 126-194 29-94 (234)
79 TIGR00990 3a0801s09 mitochondr 77.6 1E+02 0.0022 33.9 16.6 75 116-193 353-427 (615)
80 TIGR03826 YvyF flagellar opero 77.2 2.8 6.2E-05 37.9 3.7 42 347-392 34-77 (137)
81 TIGR02944 suf_reg_Xantho FeS a 76.3 10 0.00022 33.2 6.9 79 334-417 6-85 (130)
82 PF13518 HTH_28: Helix-turn-he 76.2 6.8 0.00015 28.2 4.9 39 344-385 2-40 (52)
83 TIGR03302 OM_YfiO outer membra 76.0 15 0.00033 34.5 8.5 74 124-197 29-102 (235)
84 COG2976 Uncharacterized protei 75.6 15 0.00032 35.5 8.1 92 114-210 75-166 (207)
85 TIGR03879 near_KaiC_dom probab 75.1 4.6 0.0001 32.7 4.0 35 353-387 28-62 (73)
86 PF13384 HTH_23: Homeodomain-l 74.4 4.1 8.8E-05 29.4 3.3 40 343-385 6-45 (50)
87 smart00550 Zalpha Z-DNA-bindin 74.1 5.8 0.00013 31.2 4.3 38 351-388 14-53 (68)
88 PF13371 TPR_9: Tetratricopept 74.0 12 0.00026 28.4 6.0 58 135-195 2-59 (73)
89 cd00090 HTH_ARSR Arsenical Res 73.4 23 0.00051 26.3 7.6 45 358-402 21-65 (78)
90 PF00392 GntR: Bacterial regul 73.2 13 0.00029 28.4 6.1 52 337-388 3-55 (64)
91 PF13525 YfiO: Outer membrane 73.0 61 0.0013 30.4 11.8 54 114-167 28-81 (203)
92 PF01047 MarR: MarR family; I 72.8 8.9 0.00019 28.5 4.9 47 350-396 10-56 (59)
93 PRK10747 putative protoheme IX 72.6 1.3E+02 0.0027 31.4 16.8 97 112-214 136-233 (398)
94 PRK15359 type III secretion sy 72.6 26 0.00055 31.1 8.7 78 115-195 45-122 (144)
95 PRK11189 lipoprotein NlpI; Pro 72.5 62 0.0013 32.2 12.3 75 114-192 118-192 (296)
96 smart00419 HTH_CRP helix_turn_ 71.4 11 0.00025 26.3 5.0 33 356-388 7-39 (48)
97 COG1849 Uncharacterized protei 71.2 30 0.00065 29.2 8.0 33 125-157 38-70 (90)
98 PRK11189 lipoprotein NlpI; Pro 70.9 46 0.00099 33.2 11.0 76 115-193 85-160 (296)
99 PF08784 RPA_C: Replication pr 70.6 6.3 0.00014 33.1 4.0 41 352-392 60-100 (102)
100 KOG1861 Leucine permease trans 70.4 31 0.00068 37.3 9.8 109 251-384 388-502 (540)
101 PRK02603 photosystem I assembl 69.8 32 0.0007 31.1 8.9 69 125-193 32-100 (172)
102 TIGR02010 IscR iron-sulfur clu 69.1 18 0.00039 32.0 6.8 61 343-404 11-71 (135)
103 PRK04424 fatty acid biosynthes 69.0 6.6 0.00014 37.0 4.2 46 342-387 6-51 (185)
104 PF13424 TPR_12: Tetratricopep 69.0 8.2 0.00018 29.9 4.2 40 118-157 35-75 (78)
105 PRK10857 DNA-binding transcrip 68.9 16 0.00034 33.9 6.6 62 342-404 10-71 (164)
106 PF13414 TPR_11: TPR repeat; P 68.8 20 0.00044 26.8 6.3 44 115-158 24-68 (69)
107 KOG2796 Uncharacterized conser 68.6 1.4E+02 0.0031 30.5 17.0 121 47-189 116-236 (366)
108 TIGR00990 3a0801s09 mitochondr 68.6 98 0.0021 34.0 13.9 82 112-196 417-498 (615)
109 PF10475 DUF2450: Protein of u 68.5 1.3E+02 0.0029 30.1 13.9 49 110-159 110-158 (291)
110 PF14559 TPR_19: Tetratricopep 68.4 12 0.00025 28.0 4.8 52 139-193 2-53 (68)
111 PF11972 HTH_13: HTH DNA bindi 67.5 10 0.00022 29.1 4.1 34 349-382 5-38 (54)
112 PLN03088 SGT1, suppressor of 67.5 27 0.00058 36.1 8.7 76 117-195 25-100 (356)
113 PRK09802 DNA-binding transcrip 67.4 13 0.00027 37.1 6.0 55 334-388 8-62 (269)
114 cd00092 HTH_CRP helix_turn_hel 67.4 17 0.00036 27.4 5.5 35 354-388 22-56 (67)
115 PRK11447 cellulose synthase su 67.1 2.5E+02 0.0055 33.6 17.7 181 114-313 481-665 (1157)
116 PF13512 TPR_18: Tetratricopep 66.9 37 0.0008 31.0 8.4 68 130-197 12-79 (142)
117 smart00028 TPR Tetratricopepti 66.7 11 0.00023 22.1 3.6 29 129-157 2-30 (34)
118 KOG3054 Uncharacterized conser 65.9 13 0.00027 37.0 5.4 55 348-402 205-259 (299)
119 cd07377 WHTH_GntR Winged helix 65.8 17 0.00036 27.0 5.1 50 338-387 5-55 (66)
120 PF12862 Apc5: Anaphase-promot 65.8 22 0.00048 29.3 6.3 59 139-197 9-73 (94)
121 PRK06266 transcription initiat 65.3 29 0.00064 32.6 7.7 92 333-431 11-107 (178)
122 PLN03088 SGT1, suppressor of 65.1 66 0.0014 33.2 11.0 46 115-160 57-102 (356)
123 PRK10906 DNA-binding transcrip 65.1 11 0.00025 37.0 5.2 47 342-388 4-50 (252)
124 PRK11920 rirA iron-responsive 65.0 23 0.0005 32.3 6.8 61 342-404 10-70 (153)
125 PF04703 FaeA: FaeA-like prote 65.0 11 0.00025 29.5 4.1 34 355-388 13-46 (62)
126 KOG2376 Signal recognition par 64.8 73 0.0016 35.5 11.5 108 47-157 91-204 (652)
127 PF12895 Apc3: Anaphase-promot 64.7 8 0.00017 30.7 3.3 38 115-153 46-83 (84)
128 PRK10434 srlR DNA-bindng trans 64.4 44 0.00095 32.9 9.2 47 342-388 4-50 (256)
129 PRK10411 DNA-binding transcrip 64.0 15 0.00031 36.0 5.7 54 342-399 3-56 (240)
130 smart00346 HTH_ICLR helix_turn 63.5 42 0.00092 26.8 7.5 56 344-401 6-62 (91)
131 COG4105 ComL DNA uptake lipopr 63.3 34 0.00074 34.2 8.1 84 114-197 57-145 (254)
132 TIGR00540 hemY_coli hemY prote 63.1 2E+02 0.0042 30.0 14.7 74 115-190 320-395 (409)
133 TIGR00540 hemY_coli hemY prote 62.8 81 0.0017 32.9 11.3 78 114-194 138-216 (409)
134 PF12688 TPR_5: Tetratrico pep 62.7 1.1E+02 0.0023 26.9 10.7 110 130-246 3-114 (120)
135 PRK10866 outer membrane biogen 62.4 43 0.00094 32.7 8.7 70 128-197 32-101 (243)
136 PF01022 HTH_5: Bacterial regu 62.4 26 0.00055 25.2 5.4 43 342-386 2-44 (47)
137 PRK15359 type III secretion sy 61.9 73 0.0016 28.2 9.4 47 115-161 79-125 (144)
138 PF04545 Sigma70_r4: Sigma-70, 61.1 25 0.00053 25.4 5.1 37 344-383 10-46 (50)
139 PRK10370 formate-dependent nit 61.0 25 0.00054 33.1 6.5 83 112-197 91-176 (198)
140 PRK12370 invasion protein regu 61.0 2.5E+02 0.0055 30.6 18.2 78 114-194 324-401 (553)
141 PF12569 NARP1: NMDA receptor- 60.6 2.6E+02 0.0057 30.7 22.3 64 128-194 194-257 (517)
142 PRK13509 transcriptional repre 60.6 16 0.00035 35.9 5.3 45 343-387 5-49 (251)
143 KOG4414 COP9 signalosome, subu 60.5 16 0.00035 33.7 4.8 46 335-380 110-155 (197)
144 KOG2114 Vacuolar assembly/sort 60.0 67 0.0015 37.2 10.4 121 117-237 356-504 (933)
145 cd00131 PAX Paired Box domain 59.6 23 0.00051 31.3 5.7 47 341-390 20-66 (128)
146 COG1349 GlpR Transcriptional r 59.6 15 0.00033 36.1 5.0 59 343-405 5-63 (253)
147 PF09339 HTH_IclR: IclR helix- 59.3 17 0.00036 26.7 4.0 42 346-387 7-48 (52)
148 KOG2003 TPR repeat-containing 58.9 1.1E+02 0.0024 33.3 11.3 37 217-258 662-702 (840)
149 PF13512 TPR_18: Tetratricopep 58.7 70 0.0015 29.2 8.7 50 114-163 33-82 (142)
150 PRK11447 cellulose synthase su 58.5 1.4E+02 0.003 35.8 13.5 64 130-195 114-177 (1157)
151 KOG1155 Anaphase-promoting com 57.6 1.3E+02 0.0028 32.9 11.5 104 35-156 432-535 (559)
152 smart00351 PAX Paired Box doma 56.8 28 0.00062 30.6 5.7 47 341-390 20-66 (125)
153 PF13545 HTH_Crp_2: Crp-like h 56.8 22 0.00047 27.6 4.5 44 356-403 27-70 (76)
154 PRK02603 photosystem I assembl 56.5 1.4E+02 0.0031 26.8 10.5 34 127-160 71-104 (172)
155 TIGR01610 phage_O_Nterm phage 56.3 53 0.0011 27.4 7.0 49 354-404 44-92 (95)
156 PRK10747 putative protoheme IX 55.7 1.2E+02 0.0026 31.5 11.1 46 114-159 314-359 (398)
157 PLN03098 LPA1 LOW PSII ACCUMUL 55.6 52 0.0011 35.5 8.3 72 122-194 69-141 (453)
158 PRK10681 DNA-binding transcrip 55.5 22 0.00048 34.9 5.3 42 341-382 5-46 (252)
159 cd06171 Sigma70_r4 Sigma70, re 55.5 36 0.00079 23.4 5.2 28 356-383 25-52 (55)
160 PRK03837 transcriptional regul 54.9 45 0.00096 31.8 7.2 67 334-402 13-80 (241)
161 KOG1840 Kinesin light chain [C 54.6 3.2E+02 0.0069 30.1 14.3 84 114-197 268-357 (508)
162 PF04733 Coatomer_E: Coatomer 54.5 41 0.00088 33.9 7.1 67 121-190 158-226 (290)
163 PRK09954 putative kinase; Prov 54.1 37 0.00081 34.6 7.0 52 350-401 10-64 (362)
164 PRK12370 invasion protein regu 54.1 1.4E+02 0.0031 32.5 11.8 77 114-193 358-434 (553)
165 PF03374 ANT: Phage antirepres 53.9 28 0.0006 29.5 5.0 36 345-380 12-47 (111)
166 PF03399 SAC3_GANP: SAC3/GANP/ 53.8 19 0.00042 33.4 4.4 61 294-369 143-204 (204)
167 TIGR00738 rrf2_super rrf2 fami 53.8 37 0.0008 29.4 5.9 62 342-404 10-71 (132)
168 COG2345 Predicted transcriptio 53.6 19 0.0004 35.2 4.3 52 349-404 17-68 (218)
169 TIGR02844 spore_III_D sporulat 52.6 25 0.00055 28.9 4.3 34 344-378 7-40 (80)
170 COG3063 PilF Tfp pilus assembl 52.6 66 0.0014 32.0 7.9 81 114-197 159-239 (250)
171 CHL00033 ycf3 photosystem I as 52.6 1E+02 0.0022 27.6 8.8 69 126-194 33-101 (168)
172 PF01978 TrmB: Sugar-specific 52.0 32 0.0007 26.5 4.7 41 347-388 13-53 (68)
173 PRK15179 Vi polysaccharide bio 51.1 2E+02 0.0042 32.9 12.5 54 124-177 184-237 (694)
174 PF08280 HTH_Mga: M protein tr 50.1 43 0.00093 25.4 5.0 36 345-381 8-43 (59)
175 PF12802 MarR_2: MarR family; 50.0 38 0.00083 25.1 4.7 37 357-393 21-57 (62)
176 PF07720 TPR_3: Tetratricopept 49.9 42 0.0009 23.3 4.5 24 129-152 2-25 (36)
177 KOG2047 mRNA splicing factor [ 49.4 94 0.002 35.2 9.2 85 75-159 175-279 (835)
178 PRK10049 pgaA outer membrane p 49.3 1.4E+02 0.0031 34.0 11.3 47 114-161 103-149 (765)
179 KOG1126 DNA-binding cell divis 49.0 57 0.0012 36.5 7.6 80 116-198 511-590 (638)
180 TIGR01764 excise DNA binding d 49.0 26 0.00056 24.3 3.5 29 358-390 2-30 (49)
181 COG1959 Predicted transcriptio 48.8 48 0.001 30.1 6.0 62 342-404 10-71 (150)
182 PF08281 Sigma70_r4_2: Sigma-7 48.6 30 0.00064 25.2 3.9 39 341-382 13-51 (54)
183 PF09976 TPR_21: Tetratricopep 48.6 72 0.0016 28.0 7.0 53 130-188 87-141 (145)
184 smart00344 HTH_ASNC helix_turn 48.4 30 0.00064 28.9 4.3 42 352-393 12-56 (108)
185 smart00418 HTH_ARSR helix_turn 48.3 54 0.0012 23.5 5.3 36 355-390 8-43 (66)
186 PF07721 TPR_4: Tetratricopept 48.3 27 0.00058 22.0 3.1 23 130-152 3-25 (26)
187 KOG0495 HAT repeat protein [RN 48.2 99 0.0021 35.2 9.1 79 111-193 553-646 (913)
188 TIGR03338 phnR_burk phosphonat 48.1 83 0.0018 29.4 7.8 67 335-403 12-78 (212)
189 PF13011 LZ_Tnp_IS481: leucine 47.7 28 0.0006 29.1 3.9 31 355-385 23-53 (85)
190 PRK10141 DNA-binding transcrip 47.5 1.8E+02 0.0038 25.6 9.1 93 337-432 11-103 (117)
191 cd00086 homeodomain Homeodomai 47.4 20 0.00043 26.2 2.8 23 358-380 28-50 (59)
192 COG3118 Thioredoxin domain-con 46.9 1.1E+02 0.0024 31.4 8.6 44 113-156 221-264 (304)
193 PF13463 HTH_27: Winged helix 45.7 89 0.0019 23.4 6.3 44 347-390 8-51 (68)
194 PRK01773 hscB co-chaperone Hsc 45.4 2.2E+02 0.0048 26.6 10.0 32 161-192 123-154 (173)
195 smart00421 HTH_LUXR helix_turn 45.0 49 0.0011 23.3 4.5 29 355-383 16-44 (58)
196 PRK10803 tol-pal system protei 44.7 3.2E+02 0.007 27.1 11.7 43 119-161 208-250 (263)
197 PF06163 DUF977: Bacterial pro 44.6 41 0.00088 30.2 4.6 38 350-387 19-56 (127)
198 COG1536 FliG Flagellar motor s 44.3 3.9E+02 0.0085 27.8 13.2 146 87-258 27-184 (339)
199 PF13730 HTH_36: Helix-turn-he 43.7 38 0.00082 24.8 3.8 28 359-386 27-54 (55)
200 PF10771 DUF2582: Protein of u 43.5 45 0.00098 26.4 4.3 51 347-400 13-63 (65)
201 PF01325 Fe_dep_repress: Iron 43.3 39 0.00085 25.9 3.9 34 354-387 19-52 (60)
202 TIGR00714 hscB Fe-S protein as 43.2 2.4E+02 0.0051 25.9 9.7 33 161-193 109-141 (157)
203 PF06971 Put_DNA-bind_N: Putat 43.1 47 0.001 24.9 4.1 37 343-379 9-50 (50)
204 PF00046 Homeobox: Homeobox do 43.0 29 0.00062 25.6 3.1 23 358-380 28-50 (57)
205 smart00389 HOX Homeodomain. DN 42.5 26 0.00056 25.5 2.7 22 359-380 29-50 (56)
206 PF14938 SNAP: Soluble NSF att 42.3 1.2E+02 0.0027 29.9 8.3 71 122-192 149-223 (282)
207 PF11817 Foie-gras_1: Foie gra 42.2 1E+02 0.0022 30.1 7.6 57 130-186 180-239 (247)
208 PRK11050 manganese transport r 42.0 1.2E+02 0.0026 27.4 7.6 36 355-390 49-84 (152)
209 PF09743 DUF2042: Uncharacteri 41.8 71 0.0015 32.1 6.5 59 335-393 170-228 (272)
210 PF13281 DUF4071: Domain of un 41.8 1.9E+02 0.004 30.6 9.8 68 130-197 181-251 (374)
211 COG2956 Predicted N-acetylgluc 41.6 3.9E+02 0.0084 28.1 11.7 33 121-153 207-239 (389)
212 PRK10225 DNA-binding transcrip 41.1 93 0.002 30.1 7.1 69 334-404 9-78 (257)
213 COG1729 Uncharacterized protei 41.0 1.2E+02 0.0027 30.4 8.0 60 130-189 180-239 (262)
214 PF04967 HTH_10: HTH DNA bindi 40.8 60 0.0013 24.6 4.4 39 344-382 10-48 (53)
215 PRK10370 formate-dependent nit 40.8 3.1E+02 0.0068 25.7 12.2 73 118-194 63-139 (198)
216 COG3415 Transposase and inacti 40.3 61 0.0013 29.4 5.2 47 338-386 4-50 (138)
217 PRK03902 manganese transport t 39.6 1.7E+02 0.0036 25.9 8.0 63 351-416 16-78 (142)
218 TIGR00373 conserved hypothetic 39.4 1.6E+02 0.0034 27.1 7.9 92 335-432 7-100 (158)
219 PF06160 EzrA: Septation ring 39.3 2.6E+02 0.0057 30.9 11.0 41 120-160 507-548 (560)
220 PF12840 HTH_20: Helix-turn-he 39.2 98 0.0021 23.3 5.6 49 339-388 7-55 (61)
221 PF14561 TPR_20: Tetratricopep 39.1 39 0.00084 28.1 3.5 45 115-159 9-53 (90)
222 KOG4056 Translocase of outer m 38.9 80 0.0017 28.8 5.6 46 132-177 85-130 (143)
223 PRK11534 DNA-binding transcrip 38.9 91 0.002 29.5 6.6 67 334-402 7-73 (224)
224 PRK15174 Vi polysaccharide exp 38.9 6E+02 0.013 28.5 14.6 77 114-193 270-346 (656)
225 PF01476 LysM: LysM domain; I 38.7 32 0.00069 23.8 2.6 19 359-377 8-26 (44)
226 cd06170 LuxR_C_like C-terminal 38.6 71 0.0015 22.6 4.6 29 355-383 13-41 (57)
227 PRK15481 transcriptional regul 38.4 81 0.0018 32.9 6.7 65 334-400 5-70 (431)
228 COG5484 Uncharacterized conser 38.0 45 0.00097 33.4 4.2 34 344-380 9-42 (279)
229 CHL00033 ycf3 photosystem I as 38.0 2.2E+02 0.0047 25.4 8.6 71 127-197 71-145 (168)
230 PF14276 DUF4363: Domain of un 37.6 2.4E+02 0.0051 24.3 8.4 73 125-197 25-109 (121)
231 KOG0550 Molecular chaperone (D 37.5 1.9E+02 0.004 31.3 8.9 60 118-179 311-370 (486)
232 PRK10046 dpiA two-component re 37.3 66 0.0014 30.2 5.3 48 346-393 166-213 (225)
233 KOG3252 Uncharacterized conser 37.3 86 0.0019 30.1 5.8 86 295-405 107-193 (217)
234 KOG4234 TPR repeat-containing 37.2 1.4E+02 0.0031 29.4 7.4 66 128-193 95-162 (271)
235 TIGR02812 fadR_gamma fatty aci 36.9 99 0.0021 29.5 6.5 65 335-401 7-72 (235)
236 PRK09464 pdhR transcriptional 36.8 1.4E+02 0.0031 28.7 7.7 67 334-402 10-77 (254)
237 PF04049 APC8: Anaphase promot 36.4 98 0.0021 28.0 6.0 27 129-155 75-101 (142)
238 PLN03083 E3 UFM1-protein ligas 36.3 1.4E+02 0.0029 34.7 8.2 102 284-400 73-174 (803)
239 TIGR02337 HpaR homoprotocatech 35.5 2.1E+02 0.0045 24.2 7.7 43 354-396 39-81 (118)
240 KOG0624 dsRNA-activated protei 35.4 3.7E+02 0.008 28.6 10.5 46 116-161 211-256 (504)
241 cd04762 HTH_MerR-trunc Helix-T 34.8 44 0.00096 22.9 2.8 28 359-390 2-29 (49)
242 COG4367 Uncharacterized protei 34.3 41 0.0009 28.4 2.9 23 356-378 22-44 (97)
243 PF13551 HTH_29: Winged helix- 34.2 65 0.0014 26.5 4.2 31 355-385 9-40 (112)
244 PF02064 MAS20: MAS20 protein 33.9 1.1E+02 0.0023 27.2 5.7 44 132-175 67-110 (121)
245 PF04539 Sigma70_r3: Sigma-70 33.9 92 0.002 24.3 4.8 37 356-392 19-55 (78)
246 PRK14999 histidine utilization 33.8 2.2E+02 0.0049 27.2 8.5 69 333-403 11-80 (241)
247 PF04010 DUF357: Protein of un 33.7 88 0.0019 25.3 4.7 33 125-157 32-64 (75)
248 COG1497 Predicted transcriptio 33.0 87 0.0019 31.2 5.3 67 343-413 11-79 (260)
249 PF12487 DUF3703: Protein of u 32.9 3.3E+02 0.0071 23.9 8.4 65 128-192 9-74 (112)
250 COG2378 Predicted transcriptio 32.9 77 0.0017 32.3 5.3 60 339-401 4-67 (311)
251 PRK05472 redox-sensing transcr 32.6 91 0.002 29.6 5.4 43 339-381 12-56 (213)
252 PF00440 TetR_N: Bacterial reg 32.6 99 0.0021 22.0 4.4 32 340-374 2-33 (47)
253 PF13404 HTH_AsnC-type: AsnC-t 32.3 63 0.0014 23.1 3.3 25 356-380 16-40 (42)
254 COG3355 Predicted transcriptio 32.2 3.8E+02 0.0081 24.1 9.3 88 343-430 28-119 (126)
255 KOG4747 Two-component phosphor 31.9 3E+02 0.0066 25.4 8.3 114 51-177 13-143 (150)
256 PRK14165 winged helix-turn-hel 31.8 1.9E+02 0.0042 28.1 7.5 52 351-402 15-66 (217)
257 KOG1126 DNA-binding cell divis 31.8 82 0.0018 35.4 5.5 77 109-188 538-614 (638)
258 cd01020 TroA_b Metal binding p 31.4 81 0.0017 31.0 5.0 74 45-124 99-173 (264)
259 PF05043 Mga: Mga helix-turn-h 31.2 1.2E+02 0.0026 24.3 5.2 64 337-403 10-76 (87)
260 PRK15179 Vi polysaccharide bio 31.0 8.5E+02 0.018 27.8 14.9 42 115-156 141-182 (694)
261 PF13182 DUF4007: Protein of u 30.6 1E+02 0.0022 31.1 5.6 58 353-413 216-283 (286)
262 cd01145 TroA_c Periplasmic bin 30.5 82 0.0018 29.7 4.7 74 45-124 112-186 (203)
263 smart00342 HTH_ARAC helix_turn 30.3 1E+02 0.0022 23.3 4.5 41 337-378 31-72 (84)
264 KOG2076 RNA polymerase III tra 30.2 9.7E+02 0.021 28.3 19.7 116 15-155 392-510 (895)
265 PF03704 BTAD: Bacterial trans 30.1 3.6E+02 0.0078 23.2 8.6 77 125-204 59-136 (146)
266 PF09182 PuR_N: Bacterial puri 30.1 1.1E+02 0.0024 24.7 4.6 38 341-378 2-41 (70)
267 PF09295 ChAPs: ChAPs (Chs5p-A 29.9 4.7E+02 0.01 27.8 10.6 62 130-196 202-265 (395)
268 PRK11179 DNA-binding transcrip 29.7 1.4E+02 0.0029 26.9 5.8 42 352-393 18-62 (153)
269 TIGR01636 phage_rinA phage tra 29.3 1E+02 0.0022 27.3 4.9 47 335-382 79-125 (134)
270 PF05559 DUF763: Protein of un 29.3 25 0.00054 36.2 1.0 29 359-394 101-129 (319)
271 KOG2114 Vacuolar assembly/sort 29.3 2E+02 0.0044 33.5 8.0 112 38-150 337-453 (933)
272 KOG4340 Uncharacterized conser 29.0 5.4E+02 0.012 27.0 10.3 182 117-310 33-266 (459)
273 smart00530 HTH_XRE Helix-turn- 29.0 67 0.0015 21.5 3.0 24 355-378 8-31 (56)
274 cd04761 HTH_MerR-SF Helix-Turn 28.9 62 0.0013 22.7 2.8 27 359-389 2-28 (49)
275 PF10141 ssDNA-exonuc_C: Singl 28.8 2E+02 0.0044 27.1 7.1 73 333-415 94-177 (195)
276 COG1802 GntR Transcriptional r 28.6 1.2E+02 0.0027 28.8 5.7 70 333-404 15-84 (230)
277 cd00569 HTH_Hin_like Helix-tur 28.5 1.2E+02 0.0026 18.3 3.9 23 356-378 20-42 (42)
278 PRK03578 hscB co-chaperone Hsc 28.4 5E+02 0.011 24.3 9.5 31 162-192 127-158 (176)
279 PF04100 Vps53_N: Vps53-like, 28.4 4.6E+02 0.01 27.6 10.3 97 69-173 60-167 (383)
280 KOG0553 TPR repeat-containing 28.4 2.1E+02 0.0045 29.4 7.3 45 115-159 136-180 (304)
281 PF03962 Mnd1: Mnd1 family; I 28.1 1.8E+02 0.0039 27.5 6.5 35 73-107 103-142 (188)
282 KOG0547 Translocase of outer m 28.1 1.3E+02 0.0029 33.1 6.1 57 130-190 117-174 (606)
283 PF14493 HTH_40: Helix-turn-he 28.0 1.2E+02 0.0026 24.9 4.7 39 350-388 6-45 (91)
284 PF08672 APC2: Anaphase promot 28.0 64 0.0014 25.1 2.8 27 364-390 28-54 (60)
285 PF13429 TPR_15: Tetratricopep 27.7 2.2E+02 0.0047 27.6 7.3 68 126-197 144-212 (280)
286 PF12728 HTH_17: Helix-turn-he 27.7 67 0.0014 23.1 2.8 29 358-390 2-30 (51)
287 PRK03573 transcriptional regul 27.6 3.8E+02 0.0082 23.4 8.2 45 356-400 45-89 (144)
288 COG5499 Predicted transcriptio 27.5 1.3E+02 0.0028 26.5 4.9 49 116-173 67-115 (120)
289 PF13542 HTH_Tnp_ISL3: Helix-t 27.0 2E+02 0.0042 20.6 5.3 24 358-381 28-51 (52)
290 PF13936 HTH_38: Helix-turn-he 26.9 80 0.0017 22.6 3.0 25 356-380 19-43 (44)
291 PRK11523 DNA-binding transcrip 26.9 2E+02 0.0043 27.8 6.8 69 334-404 8-77 (253)
292 KOG2115 Vacuolar sorting prote 26.8 4E+02 0.0086 31.4 9.8 88 70-160 279-367 (951)
293 PF02002 TFIIE_alpha: TFIIE al 26.7 1.3E+02 0.0028 25.2 4.8 45 345-390 16-60 (105)
294 PRK04984 fatty acid metabolism 26.6 2E+02 0.0044 27.3 6.8 66 335-402 8-74 (239)
295 PF00325 Crp: Bacterial regula 26.6 1.2E+02 0.0025 20.8 3.6 28 358-385 3-30 (32)
296 PF01710 HTH_Tnp_IS630: Transp 26.5 93 0.002 27.0 4.0 34 348-381 62-95 (119)
297 KOG0551 Hsp90 co-chaperone CNS 26.5 2.4E+02 0.0051 29.7 7.3 72 122-193 75-147 (390)
298 PF00165 HTH_AraC: Bacterial r 26.3 48 0.001 23.0 1.8 20 355-374 6-25 (42)
299 cd04749 Commd1_MURR1 COMM_Doma 26.3 2.6E+02 0.0057 26.4 7.1 38 20-73 2-39 (174)
300 PF05402 PqqD: Coenzyme PQQ sy 26.1 83 0.0018 23.9 3.2 25 360-384 36-60 (68)
301 PLN03081 pentatricopeptide (PP 26.1 3.7E+02 0.0081 30.0 9.7 137 21-157 412-557 (697)
302 PRK10421 DNA-binding transcrip 26.0 2E+02 0.0044 27.7 6.7 65 336-402 4-69 (253)
303 PF08831 MHCassoc_trimer: Clas 26.0 87 0.0019 25.4 3.3 35 183-224 26-60 (72)
304 PF06056 Terminase_5: Putative 25.9 1.3E+02 0.0029 23.0 4.2 35 344-381 3-37 (58)
305 smart00422 HTH_MERR helix_turn 25.7 1.6E+02 0.0035 22.1 4.9 28 359-390 2-29 (70)
306 PRK10219 DNA-binding transcrip 25.7 1.5E+02 0.0032 24.6 5.0 40 337-379 4-43 (107)
307 PRK11414 colanic acid/biofilm 25.4 2.1E+02 0.0046 26.9 6.6 65 334-400 11-75 (221)
308 PRK11511 DNA-binding transcrip 25.2 1.4E+02 0.0031 25.9 5.0 40 337-379 8-47 (127)
309 PRK15174 Vi polysaccharide exp 25.0 1E+03 0.022 26.7 20.6 74 114-191 130-203 (656)
310 KOG2076 RNA polymerase III tra 24.7 1.2E+03 0.026 27.5 17.2 97 118-220 615-715 (895)
311 PF08765 Mor: Mor transcriptio 24.6 1.6E+02 0.0035 25.1 5.0 39 334-376 52-91 (108)
312 PF13411 MerR_1: MerR HTH fami 24.6 1.9E+02 0.0042 21.8 5.1 65 359-429 2-66 (69)
313 PRK06759 RNA polymerase factor 24.5 1.1E+02 0.0023 26.8 4.0 44 337-383 105-148 (154)
314 TIGR00985 3a0801s04tom mitocho 24.4 2.6E+02 0.0055 25.8 6.5 45 132-176 94-139 (148)
315 PF01527 HTH_Tnp_1: Transposas 24.4 1.5E+02 0.0033 22.8 4.5 42 339-382 7-48 (76)
316 KOG3364 Membrane protein invol 24.3 1.4E+02 0.0029 27.5 4.6 44 114-157 55-100 (149)
317 PF12862 Apc5: Anaphase-promot 24.2 2.1E+02 0.0045 23.5 5.5 35 127-161 40-74 (94)
318 PRK09990 DNA-binding transcrip 24.2 2.5E+02 0.0055 26.9 7.0 68 335-404 8-76 (251)
319 PF04760 IF2_N: Translation in 24.0 45 0.00097 24.7 1.3 22 357-378 3-24 (54)
320 PF04695 Pex14_N: Peroxisomal 23.5 91 0.002 27.9 3.4 44 88-136 5-48 (136)
321 PF14394 DUF4423: Domain of un 23.5 3.6E+02 0.0078 25.0 7.5 59 338-398 19-80 (171)
322 smart00347 HTH_MARR helix_turn 23.5 3.7E+02 0.0079 21.1 7.4 40 354-393 21-60 (101)
323 PF05843 Suf: Suppressor of fo 23.4 3E+02 0.0065 27.3 7.5 75 119-197 64-139 (280)
324 KOG4234 TPR repeat-containing 23.4 7.3E+02 0.016 24.6 9.6 80 112-194 152-233 (271)
325 PRK11169 leucine-responsive tr 23.3 1.1E+02 0.0023 28.0 3.9 49 345-394 17-68 (164)
326 PRK09782 bacteriophage N4 rece 22.7 4.3E+02 0.0094 31.5 9.6 45 115-159 664-708 (987)
327 PRK11788 tetratricopeptide rep 22.7 7.7E+02 0.017 24.5 24.9 27 130-156 109-135 (389)
328 COG4103 Uncharacterized protei 22.6 1.9E+02 0.0041 26.7 5.2 24 115-138 55-78 (148)
329 smart00342 HTH_ARAC helix_turn 22.5 1.1E+02 0.0025 23.0 3.5 24 358-381 2-25 (84)
330 PRK11512 DNA-binding transcrip 22.4 1.5E+02 0.0032 26.2 4.5 47 355-401 52-98 (144)
331 PF12983 DUF3867: Protein of u 22.3 2.5E+02 0.0055 26.6 6.1 61 52-134 23-84 (186)
332 PF10078 DUF2316: Uncharacteri 22.2 89 0.0019 26.4 2.9 23 356-378 22-44 (89)
333 TIGR02018 his_ut_repres histid 22.1 3.3E+02 0.0071 25.8 7.2 65 337-403 4-69 (230)
334 TIGR01889 Staph_reg_Sar staphy 22.0 4.5E+02 0.0098 22.0 7.3 46 355-400 41-86 (109)
335 cd01018 ZntC Metal binding pro 21.9 1.1E+02 0.0023 30.1 3.9 75 45-125 116-191 (266)
336 cd00155 RasGEF Guanine nucleot 21.9 2.5E+02 0.0054 26.7 6.4 63 125-198 75-137 (237)
337 TIGR02985 Sig70_bacteroi1 RNA 21.9 1.3E+02 0.0028 26.1 4.0 30 354-383 126-155 (161)
338 PF13429 TPR_15: Tetratricopep 21.8 6.2E+02 0.013 24.3 9.3 79 111-193 163-242 (280)
339 COG1309 AcrR Transcriptional r 21.7 1.2E+02 0.0026 25.7 3.8 35 336-373 14-48 (201)
340 PRK14574 hmsH outer membrane p 21.7 5.1E+02 0.011 30.2 9.8 92 121-220 443-534 (822)
341 PRK04778 septation ring format 21.6 1.1E+03 0.024 26.0 12.1 41 119-159 510-550 (569)
342 PF00126 HTH_1: Bacterial regu 21.4 1.6E+02 0.0035 22.1 4.0 34 348-381 4-37 (60)
343 PF02438 Adeno_100: Late 100kD 21.4 8E+02 0.017 27.4 10.5 40 67-107 213-252 (583)
344 PRK09545 znuA high-affinity zi 21.3 1.1E+02 0.0024 31.1 3.9 74 45-124 149-223 (311)
345 smart00653 eIF2B_5 domain pres 21.3 2.3E+02 0.0051 24.6 5.4 54 358-414 22-75 (110)
346 TIGR02431 pcaR_pcaU beta-ketoa 21.3 1.6E+02 0.0035 28.5 4.9 42 347-388 14-55 (248)
347 COG3160 Rsd Regulator of sigma 21.3 2.4E+02 0.0053 25.9 5.6 72 343-435 25-100 (162)
348 PRK09764 DNA-binding transcrip 21.1 4E+02 0.0087 25.5 7.7 68 334-403 5-73 (240)
349 PF05920 Homeobox_KN: Homeobox 20.9 1.1E+02 0.0025 21.6 2.8 31 351-381 6-37 (40)
350 KOG0548 Molecular co-chaperone 20.8 1.2E+03 0.026 26.0 12.1 24 134-157 364-387 (539)
351 PF04733 Coatomer_E: Coatomer 20.6 8.7E+02 0.019 24.3 11.8 159 132-321 106-272 (290)
352 KOG1174 Anaphase-promoting com 20.5 9.6E+02 0.021 26.2 10.6 114 39-160 352-470 (564)
353 COG3413 Predicted DNA binding 20.4 1.5E+02 0.0032 28.2 4.4 48 335-382 156-203 (215)
354 PF06969 HemN_C: HemN C-termin 20.4 2.4E+02 0.0051 21.3 4.8 46 353-402 16-62 (66)
355 TIGR00331 hrcA heat shock gene 20.3 1.6E+02 0.0034 30.5 4.8 43 346-388 10-54 (337)
356 COG1516 FliS Flagellin-specifi 20.3 5.4E+02 0.012 23.3 7.6 85 181-279 28-112 (132)
357 PRK12537 RNA polymerase sigma 20.2 1.3E+02 0.0028 27.3 3.9 46 335-383 130-175 (182)
358 PRK09782 bacteriophage N4 rece 20.1 1.5E+03 0.033 27.0 14.7 77 115-194 630-706 (987)
359 COG1522 Lrp Transcriptional re 20.0 1.6E+02 0.0035 25.8 4.3 39 355-393 20-61 (154)
No 1
>KOG2758 consensus Translation initiation factor 3, subunit e (eIF-3e) [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=1e-141 Score=1039.39 Aligned_cols=423 Identities=62% Similarity=1.023 Sum_probs=414.2
Q ss_pred CCcccchhhhccccccccchhhHHHHhhcCCCCHHHHHHHHHHHHccCCCchHHHHHHHHhCCCCCChhHHHHHHHHHHH
Q 013640 1 MATYDLTQRIAPNLDRHLVFPLLEFLQERQMYPDEQILKSKIELLNKTNMVDYAMDIHKSLYHTEDVPQDMVERRVEVVA 80 (439)
Q Consensus 1 ~~~~dlt~~~~~~LD~hl~lpll~fl~~~~~y~~~~l~~a~~~llk~TnM~dy~~~~~~~l~~~~~~p~e~~~k~~ev~~ 80 (439)
|++||||++|+|||||||+|||||||+.+++|++++++++++++|++|||+||+|++|+.+|.++++|++|.+||.+|++
T Consensus 1 m~~yDLT~~ia~fLDrHLifPLlEFl~~r~iy~~keLle~k~~ll~~TNMiDy~md~~k~l~~sed~p~a~~ekr~~Vla 80 (432)
T KOG2758|consen 1 MANYDLTQRIAQFLDRHLIFPLLEFLSLRQIYDEKELLEAKLQLLNKTNMIDYVMDTYKNLHTSEDMPNALVEKRTEVLA 80 (432)
T ss_pred CCccchhHHHHHhHhhHHHHHHHHHhhhhccCCHHHHHHHHHHHHcccchHHHHHHHHhcccccccchHHHHHHHHHHHH
Confidence 89999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHHHHHhhCChhHHHHhhhcchh--ccHHHHHHhcCCChhHHHHHHHHHHHHHhcCChhhHHHHHHHHHhhc
Q 013640 81 RLKALEERAAPIVSFLQNPNSFQDLRANDQH--YNLQMLHDRYQIGPDQIEALYQYAKFQFECGNYSGAADYLYQYRALC 158 (439)
Q Consensus 81 ~l~~l~~~~~~~~~~~~~~e~~~~l~~~dk~--~n~~~l~~~~g~t~e~~~al~~~ak~~y~~Gdy~~A~~~L~~~~~~~ 158 (439)
++++|+++++|++.+++||+++++|++ ||. .|+++|+++|+||+|.++++|+||||+|+||||++|+++||+||.++
T Consensus 81 ~lkeLe~ev~piv~~le~Pd~~~~~~~-~k~~~~~l~~L~e~ynf~~e~i~~lykyakfqyeCGNY~gAs~yLY~~r~l~ 159 (432)
T KOG2758|consen 81 ELKELEEEVAPIVKVLENPDLIAALRS-DKDRVQNLQHLQEHYNFTPERIETLYKYAKFQYECGNYSGASDYLYFYRALV 159 (432)
T ss_pred HHHHHHHHHHHHHHHHcCHHHHHHHHh-hhhHHHHHHHHHHhcCCCHHHHHHHHHHHHHHHhccCcccHHHHHHHHHHhc
Confidence 999999999999999999999999999 555 99999999999999999999999999999999999999999999999
Q ss_pred cccch-hHHHHHHHHHHHHhhcCHHHHHHHHHHHHHHhcCCCCCCChHHHHHHHHHHHHHHHHHHhcCccchHHHHHHhc
Q 013640 159 TNSER-RLSALWGKMAAEILMQNWDIALEELNQLKEKVDDPKSFTSPLNQMQSRIWLMHWSLFIFFNHDNGRTLIIDLFN 237 (439)
Q Consensus 159 ~~~~~-k~~~lwg~la~eIl~~~w~~a~~~l~klke~id~~~~~~~~l~~l~~R~WllHwsLf~~fn~~~~~~~l~d~F~ 237 (439)
.+.++ .++++|||+|+||+++|||.|++++.|||+.||+ +.|.+|..+++|||||+||||||||||++|++.++|+|+
T Consensus 160 ~~~d~n~lsalwGKlASEIL~qnWd~A~edL~rLre~IDs-~~f~~~~~~l~qRtWLiHWslfv~fnhpkgrd~iid~fl 238 (432)
T KOG2758|consen 160 SDPDRNYLSALWGKLASEILTQNWDGALEDLTRLREYIDS-KSFSTSAQQLQQRTWLIHWSLFVFFNHPKGRDTIIDMFL 238 (432)
T ss_pred CCcchhhHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHcc-cccccHHHHHHHHHHHHHHHHHhhccCCChhhHHHHHHc
Confidence 98877 7999999999999999999999999999999999 899999999999999999999999999999999999999
Q ss_pred -cccchhHHHhhchhHHHHHHHHHHHh-cccccchHHHHHHHhhhccCCcchHHHHHHHhhhcCChhHHHHHHHHHHHHh
Q 013640 238 -QDKYLNAIQTNAPHLLRYLATAFIVN-KRRRPQFKDFIKVIQQEQNSYKDPITEFLACVYVNYDFDGAQKKMKECEEVI 315 (439)
Q Consensus 238 -~~~yl~~Iqt~~p~lLrYlvva~il~-~~r~~~l~~i~~vi~qe~~~Y~Dpit~f~~~lY~~fdF~~aq~~L~~~e~~i 315 (439)
.|.|+|+|||+|||+||||++|+|+| ++|++.+||+|+||+||.|+|+||+|+|++|+|++|||++||++|.+||+||
T Consensus 239 y~p~YLNaIQt~cPhllRYLatAvvtnk~~rr~~lkdlvkVIqqE~ysYkDPiteFl~clyvn~DFdgAq~kl~eCeeVl 318 (432)
T KOG2758|consen 239 YQPPYLNAIQTSCPHLLRYLATAVVTNKRRRRNRLKDLVKVIQQESYSYKDPITEFLECLYVNYDFDGAQKKLRECEEVL 318 (432)
T ss_pred cCHHHHHHHHhhCHHHHHHHHHHhhcchHhhHHHHHHHHHHHHHhccccCCcHHHHHHHHhhccchHHHHHHHHHHHHHH
Confidence 67899999999999999999999999 5668889999999999999999999999999999999999999999999999
Q ss_pred cCCcccccccccccccccccHHHHHHHHHHHHHHHhhhhhccccHHHHHHHcCCCHHHHHHHHHHHhhcCccceeecccC
Q 013640 316 LNDPFLGKRVEDSNFATVPLRDEFLENARLFIFETYCRIHQRIDMAVLAEKLNLNYEEAQRWIVNLIRNSKLDAKIDAKS 395 (439)
Q Consensus 316 ~~D~FL~~~~~~~~~~~~~~~~~f~e~aR~~ife~ycriy~~I~I~~lA~~l~~s~~~~E~wiv~lI~~~rL~aKID~~~ 395 (439)
.+|||| .++.++|+|+||++|||+|||||+||+|+|||++|||+++++|+||||+||++||+|||||+.
T Consensus 319 ~nDfFL-----------va~l~~F~E~ARl~ifEtfCRIHqcIti~mLA~kLnm~~eeaErwivnlIr~~rl~AkidSkl 387 (432)
T KOG2758|consen 319 VNDFFL-----------VALLDEFLENARLLIFETFCRIHQCITIDMLADKLNMDPEEAERWIVNLIRTARLDAKIDSKL 387 (432)
T ss_pred hcchhH-----------HHHHHHHHHHHHHHHHHHHHHHHHheeHHHHHHHhcCCHHHHHHHHHHHHHHhhhhhhhcccc
Confidence 999999 899999999999999999999999999999999999999999999999999999999999999
Q ss_pred CEEEeCCCCchhHHHHHHhhhhhhhHHHHHHHHHHhhhhhh
Q 013640 396 GTVIMEPTHPNVYEQLIDHTKGLSGRTYKLVGQLLEHAQTQ 436 (439)
Q Consensus 396 g~V~~~~~~~~~yqqvi~kt~~L~~R~q~L~~~i~~~~~~~ 436 (439)
|+|+|++|+.|+|||+|++||+|++|+|.|+..+++..+.+
T Consensus 388 g~Vvmg~~~~s~~qQ~ie~tksLS~rsq~la~~lek~~~~~ 428 (432)
T KOG2758|consen 388 GHVVMGHPTVSPHQQLIEKTKSLSFRSQNLAQQLEKKIQQK 428 (432)
T ss_pred CceeecCCCCCHHHHHHHhccccchhHHHHHHHHHHHHHHh
Confidence 99999999999999999999999999999999999987663
No 2
>KOG0687 consensus 26S proteasome regulatory complex, subunit RPN7/PSMD6 [Posttranslational modification, protein turnover, chaperones]
Probab=100.00 E-value=2.1e-59 Score=460.68 Aligned_cols=359 Identities=15% Similarity=0.250 Sum_probs=328.1
Q ss_pred cccchhhHHHHhhcCCCC--HHHHHHHHHHHHccCCCchHHHHHHHHhC--CCCCChhHHHHHHHHHHHHHHHHHHHHHH
Q 013640 16 RHLVFPLLEFLQERQMYP--DEQILKSKIELLNKTNMVDYAMDIHKSLY--HTEDVPQDMVERRVEVVARLKALEERAAP 91 (439)
Q Consensus 16 ~hl~lpll~fl~~~~~y~--~~~l~~a~~~llk~TnM~dy~~~~~~~l~--~~~~~p~e~~~k~~ev~~~l~~l~~~~~~ 91 (439)
+||.+.++.|+..++.++ ..+.++-.++.++..+|+|||..+|+++. .|.+..++|.+++++.+++ |++++
T Consensus 17 p~le~sq~~FlLt~p~~~~~~~~~~e~l~~~Ird~~Map~Ye~lce~~~i~~D~~~l~~m~~~neeki~e---ld~~i-- 91 (393)
T KOG0687|consen 17 PDLELSQLRFLLTHPEVLGQKAAAREKLLAAIRDEDMAPLYEYLCESLVIKLDQDLLNSMKKANEEKIKE---LDEKI-- 91 (393)
T ss_pred cchhHHHHHHHHcCccccCcCHHHHHHHHHHHHhcccchHHHHHHhhcceeccHHHHHHHHHhhHHHHHH---HHHHH--
Confidence 788999999999998888 37778888899999999999999999876 7788899999999997777 77777
Q ss_pred HHHhhCChhHHHHhhhcchhccHHHHHHhcCCChhHHHHHHHHHHHHHhcCChhhHHHHHHHHHhhccccchhHHHHHHH
Q 013640 92 IVSFLQNPNSFQDLRANDQHYNLQMLHDRYQIGPDQIEALYQYAKFQFECGNYSGAADYLYQYRALCTNSERRLSALWGK 171 (439)
Q Consensus 92 ~~~~~~~~e~~~~l~~~dk~~n~~~l~~~~g~t~e~~~al~~~ak~~y~~Gdy~~A~~~L~~~~~~~~~~~~k~~~lwg~ 171 (439)
+.+++|.| +.|++++..+.|.||+++||.++|.+++.....++++.|.|++.++.+
T Consensus 92 -----------------------edaeenlG-E~ev~ea~~~kaeYycqigDkena~~~~~~t~~ktvs~g~kiDVvf~~ 147 (393)
T KOG0687|consen 92 -----------------------EDAEENLG-ESEVREAMLRKAEYYCQIGDKENALEALRKTYEKTVSLGHKIDVVFYK 147 (393)
T ss_pred -----------------------HHHHHhcc-hHHHHHHHHHHHHHHHHhccHHHHHHHHHHHHHHHhhcccchhhHHHH
Confidence 66789999 999999999999999999999999999999999999999999999999
Q ss_pred HHHHHhhcCHHHHHHHHHHHHHHhcCCCCC--CChHHHHHHHHHHHHHHHHH--HhcCccchHHHHHHhccccchhHHHh
Q 013640 172 MAAEILMQNWDIALEELNQLKEKVDDPKSF--TSPLNQMQSRIWLMHWSLFI--FFNHDNGRTLIIDLFNQDKYLNAIQT 247 (439)
Q Consensus 172 la~eIl~~~w~~a~~~l~klke~id~~~~~--~~~l~~l~~R~WllHwsLf~--~fn~~~~~~~l~d~F~~~~yl~~Iqt 247 (439)
++++++..|.+...+.++|+|.+|++|||| +|++++|+ ++|. .+||+.|.++|+|+.. +|.+.-.+
T Consensus 148 iRlglfy~D~~lV~~~iekak~liE~GgDWeRrNRlKvY~--------Gly~msvR~Fk~Aa~Lfld~vs--TFtS~El~ 217 (393)
T KOG0687|consen 148 IRLGLFYLDHDLVTESIEKAKSLIEEGGDWERRNRLKVYQ--------GLYCMSVRNFKEAADLFLDSVS--TFTSYELM 217 (393)
T ss_pred HHHHHhhccHHHHHHHHHHHHHHHHhCCChhhhhhHHHHH--------HHHHHHHHhHHHHHHHHHHHcc--cccceecc
Confidence 999999999999999999999999999999 89999999 7884 8999999999999655 55555677
Q ss_pred hchhHHHHHHHHHHHhcccc----cch--HHHHHHHhhhccCCcchHHHHHHHhhhcCChhHHHHHHHHH-HHHhcCCcc
Q 013640 248 NAPHLLRYLATAFIVNKRRR----PQF--KDFIKVIQQEQNSYKDPITEFLACVYVNYDFDGAQKKMKEC-EEVILNDPF 320 (439)
Q Consensus 248 ~~p~lLrYlvva~il~~~r~----~~l--~~i~~vi~qe~~~Y~Dpit~f~~~lY~~fdF~~aq~~L~~~-e~~i~~D~F 320 (439)
+++.++||+|++++++..|. +++ |||+.++.+- .|+.+|+.++|. +|+.+|...|... ...++.|.|
T Consensus 218 ~Y~~~v~Ytv~~g~i~leR~dlktKVi~~~Evl~vl~~l-----~~~~q~l~SLY~-C~Y~~Ff~~L~~~~~~~lk~D~~ 291 (393)
T KOG0687|consen 218 SYETFVRYTVITGLIALERVDLKTKVIKCPEVLEVLHKL-----PSVSQLLNSLYE-CDYSDFFNDLAAVEAKQLKDDRY 291 (393)
T ss_pred cHHHHHHHHHHHhhheeccchHHhhhcCcHHHHHHhhcC-----chHHHHHHHHHh-ccHHHHHHHHHHHHHHhhccchh
Confidence 88889999999999999984 445 8999988883 457788888877 7788888999665 778999999
Q ss_pred cccccccccccccccHHHHHHHHHHHHHHHhhhhhccccHHHHHHHcCCCHHHHHHHHHHHhhcCccceeecccCCEEEe
Q 013640 321 LGKRVEDSNFATVPLRDEFLENARLFIFETYCRIHQRIDMAVLAEKLNLNYEEAQRWIVNLIRNSKLDAKIDAKSGTVIM 400 (439)
Q Consensus 321 L~~~~~~~~~~~~~~~~~f~e~aR~~ife~ycriy~~I~I~~lA~~l~~s~~~~E~wiv~lI~~~rL~aKID~~~g~V~~ 400 (439)
| .||.++|+|++|+.+|.|++++|++++|++||+.||||.+++|+.|++||.+|||+||||.|||+|++
T Consensus 292 l-----------~~h~~yyvREMR~rvY~QlLESYrsl~l~~MA~aFgVSVefiDreL~rFI~~grL~ckIDrVnGVVEt 360 (393)
T KOG0687|consen 292 L-----------GPHYRYYVREMRRRVYAQLLESYRSLTLESMAKAFGVSVEFIDRELGRFIAAGRLHCKIDRVNGVVET 360 (393)
T ss_pred c-----------chHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCchHHHHHhHHHHhhccCceeeeeecccceeec
Confidence 9 89999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CCCC--chhHHHHHHhhhhhhhHHHHHHHHHH
Q 013640 401 EPTH--PNVYEQLIDHTKGLSGRTYKLVGQLL 430 (439)
Q Consensus 401 ~~~~--~~~yqqvi~kt~~L~~R~q~L~~~i~ 430 (439)
|+|+ +.+||.||++||.|+||+||++++|.
T Consensus 361 NrpD~KN~qyq~vikqGd~LLnriQK~~rvi~ 392 (393)
T KOG0687|consen 361 NRPDEKNAQYQAVIKQGDLLLNRIQKLSRVIN 392 (393)
T ss_pred CCccccchHHHHHHhhhHHHHHHHHHHHHHhc
Confidence 9999 45899999999999999999999884
No 3
>COG5187 RPN7 26S proteasome regulatory complex component, contains PCI domain [Posttranslational modification, protein turnover, chaperones]
Probab=100.00 E-value=1.1e-41 Score=331.61 Aligned_cols=361 Identities=13% Similarity=0.207 Sum_probs=298.3
Q ss_pred ccchhhHHHHhhcCCCCH--HHHHHHHHHHHccCCCchHHHHHHHHhC---------CCCCChhHHHHHHHHHHHHHHHH
Q 013640 17 HLVFPLLEFLQERQMYPD--EQILKSKIELLNKTNMVDYAMDIHKSLY---------HTEDVPQDMVERRVEVVARLKAL 85 (439)
Q Consensus 17 hl~lpll~fl~~~~~y~~--~~l~~a~~~llk~TnM~dy~~~~~~~l~---------~~~~~p~e~~~k~~ev~~~l~~l 85 (439)
.|....--|+....-... ...++-...+++...|+|+|..++++-+ .|.....+|-+++++-+++ |
T Consensus 22 ~l~vs~~~fll~~~kl~n~~~ka~e~l~~~i~d~~maplYkyL~E~~n~kt~a~~ikfD~~~~n~l~kkneeki~E---l 98 (412)
T COG5187 22 TLLVSDAIFLLHGTKLGNPESKALEHLERLIIDKCMAPLYKYLAEKGNPKTSASVIKFDRGRMNTLLKKNEEKIEE---L 98 (412)
T ss_pred ceehhhHHHHhcccccCChhhHHHHHHHHHHHHhhhhHHHHHHHhccCCcccchheehhhHHHHHHHHhhHHHHHH---H
Confidence 344444455554432222 3345666778899999999999999654 3344457788888886666 7
Q ss_pred HHHHHHHHHhhCChhHHHHhhhcchhccHHHHHHhcCCChhHHHHHHHHHHHHHhcCChhhHHHHHHHHHhhccccchhH
Q 013640 86 EERAAPIVSFLQNPNSFQDLRANDQHYNLQMLHDRYQIGPDQIEALYQYAKFQFECGNYSGAADYLYQYRALCTNSERRL 165 (439)
Q Consensus 86 ~~~~~~~~~~~~~~e~~~~l~~~dk~~n~~~l~~~~g~t~e~~~al~~~ak~~y~~Gdy~~A~~~L~~~~~~~~~~~~k~ 165 (439)
.+++ +.+++.-| +.|..++.-..|.||+.+||.+++.+++.......+.+|.|+
T Consensus 99 de~i-------------------------~~~eedng-E~e~~ea~~n~aeyY~qi~D~~ng~~~~~~~~~~a~stg~Ki 152 (412)
T COG5187 99 DERI-------------------------REKEEDNG-ETEGSEADRNIAEYYCQIMDIQNGFEWMRRLMRDAMSTGLKI 152 (412)
T ss_pred HHHH-------------------------HHHhhccc-chHHHHHHHHHHHHHHHHhhhhhHHHHHHHHHHHHHhcccch
Confidence 6666 34455557 889999999999999999999999999999998888999999
Q ss_pred HHHHHHHHHHHhhcCHHHHHHHHHHHHHHhcCCCCC--CChHHHHHHHHHHHHHHHHH--HhcCccchHHHHHHhccccc
Q 013640 166 SALWGKMAAEILMQNWDIALEELNQLKEKVDDPKSF--TSPLNQMQSRIWLMHWSLFI--FFNHDNGRTLIIDLFNQDKY 241 (439)
Q Consensus 166 ~~lwg~la~eIl~~~w~~a~~~l~klke~id~~~~~--~~~l~~l~~R~WllHwsLf~--~fn~~~~~~~l~d~F~~~~y 241 (439)
+.++.+++++.+.+|--...+-+++++.+|++|++| +|+.++|+ ++|. .+||+.|..+|.|... +|
T Consensus 153 Dv~l~kiRlg~~y~d~~vV~e~lE~~~~~iEkGgDWeRrNRyK~Y~--------Gi~~m~~RnFkeAa~Ll~d~l~--tF 222 (412)
T COG5187 153 DVFLCKIRLGLIYGDRKVVEESLEVADDIIEKGGDWERRNRYKVYK--------GIFKMMRRNFKEAAILLSDILP--TF 222 (412)
T ss_pred hhHHHHHHHHHhhccHHHHHHHHHHHHHHHHhCCCHHhhhhHHHHH--------HHHHHHHHhhHHHHHHHHHHhc--cc
Confidence 999999999999999888889999999999999999 89999888 6664 8899999999999544 44
Q ss_pred hhHHHhhchhHHHHHHHHHHHhcccccc----h--HHHHHHHhhhccCCcchHHHHHHHhhhcCChhHHHHHHHHHH-HH
Q 013640 242 LNAIQTNAPHLLRYLATAFIVNKRRRPQ----F--KDFIKVIQQEQNSYKDPITEFLACVYVNYDFDGAQKKMKECE-EV 314 (439)
Q Consensus 242 l~~Iqt~~p~lLrYlvva~il~~~r~~~----l--~~i~~vi~qe~~~Y~Dpit~f~~~lY~~fdF~~aq~~L~~~e-~~ 314 (439)
.++-.+++....||.+++++++..|+++ + |+++.||++...- ..+.++..+||. +|+.+.+..|.... .+
T Consensus 223 ~S~El~sY~~~vrYa~~~Gl~~leR~diktki~dspevl~vi~~~e~l--~sl~~l~~SLy~-cdY~~~F~~ll~~~~n~ 299 (412)
T COG5187 223 ESSELISYSRAVRYAIFCGLLRLERRDIKTKILDSPEVLDVIGSSEKL--GSLVQLATSLYE-CDYGGDFMNLLYLFCNS 299 (412)
T ss_pred cccccccHHHHHHHHHHhhhheeehhhhhhhhcCCHHHHHhccchhhh--hhHHHHHHHHHH-hccchhhHHHHHHHHhh
Confidence 4555566666779999999999988544 4 9999999985332 234455555555 55555557766654 48
Q ss_pred hcCCcccccccccccccccccHHHHHHHHHHHHHHHhhhhhccccHHHHHHHcCCCHHHHHHHHHHHhhcCccceeeccc
Q 013640 315 ILNDPFLGKRVEDSNFATVPLRDEFLENARLFIFETYCRIHQRIDMAVLAEKLNLNYEEAQRWIVNLIRNSKLDAKIDAK 394 (439)
Q Consensus 315 i~~D~FL~~~~~~~~~~~~~~~~~f~e~aR~~ife~ycriy~~I~I~~lA~~l~~s~~~~E~wiv~lI~~~rL~aKID~~ 394 (439)
+..|.|| ..|.|+|+|++|..+|.|.+++|+.++|++||+.||||.+.+|+.|..||.+|||+|+||.+
T Consensus 300 L~~d~fl-----------~rh~d~fvREMRrrvYaQlLESYr~lsl~sMA~tFgVSV~yvdrDLg~FIp~~~LncvIDRv 368 (412)
T COG5187 300 LQDDVFL-----------GRHVDLFVREMRRRVYAQLLESYRLLSLESMAQTFGVSVEYVDRDLGEFIPEGRLNCVIDRV 368 (412)
T ss_pred ccchHHH-----------HHHHHHHHHHHHHHHHHHHHHHHHHhhHHHHHHHhCccHHHHhhhHHhhCCCCceeeeeecc
Confidence 9999999 79999999999999999999999999999999999999999999999999999999999999
Q ss_pred CCEEEeCCCC--chhHHHHHHhhhhhhhHHHHHHHHHH
Q 013640 395 SGTVIMEPTH--PNVYEQLIDHTKGLSGRTYKLVGQLL 430 (439)
Q Consensus 395 ~g~V~~~~~~--~~~yqqvi~kt~~L~~R~q~L~~~i~ 430 (439)
||+|++|+|+ +.+|+.|+++|++|++|+|+-...+-
T Consensus 369 nGvVetnrpdekn~qy~~vVkqGd~ll~klqKy~atvm 406 (412)
T COG5187 369 NGVVETNRPDEKNQQYSSVVKQGDDLLRKLQKYVATVM 406 (412)
T ss_pred cceEeccCcchhhhhHHHHHhcchHHHHHHHHHHHHHH
Confidence 9999999999 48999999999999999999988773
No 4
>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=100.00 E-value=1.4e-42 Score=308.41 Aligned_cols=133 Identities=53% Similarity=0.948 Sum_probs=132.0
Q ss_pred cchhhhccccccccchhhHHHHhhcCCCCHHHHHHHHHHHHccCCCchHHHHHHHHhCCCCCChhHHHHHHHHHHHHHHH
Q 013640 5 DLTQRIAPNLDRHLVFPLLEFLQERQMYPDEQILKSKIELLNKTNMVDYAMDIHKSLYHTEDVPQDMVERRVEVVARLKA 84 (439)
Q Consensus 5 dlt~~~~~~LD~hl~lpll~fl~~~~~y~~~~l~~a~~~llk~TnM~dy~~~~~~~l~~~~~~p~e~~~k~~ev~~~l~~ 84 (439)
|||+||+||||||||||||+|++++++|++++|++||++||++|||+||++++|+++|+++++|+|+.+||++|++++++
T Consensus 1 DLT~ki~~~LDrHLvfPLLeFl~~~~iy~~~dl~~akl~LL~~TnMvDy~~d~~~~l~~~~e~p~e~~~kr~~Vl~~l~~ 80 (133)
T PF09440_consen 1 DLTSKIAPYLDRHLVFPLLEFLSDKGIYDEEDLLKAKLDLLKKTNMVDYAMDLYKELYPDDEVPAELAEKREEVLAELKE 80 (133)
T ss_pred ChHHHHHHHhhHHHHHHHHHHHhhcccccHHHHHHHHHHHHHhccchHHHHHHHHHhcCCCCCcHHHHHHHHHHHHHHHH
Confidence 89999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHhhCChhHHHHhhhcchhccHHHHHHhcCCChhHHHHHHHHHHHH
Q 013640 85 LEERAAPIVSFLQNPNSFQDLRANDQHYNLQMLHDRYQIGPDQIEALYQYAKFQ 138 (439)
Q Consensus 85 l~~~~~~~~~~~~~~e~~~~l~~~dk~~n~~~l~~~~g~t~e~~~al~~~ak~~ 138 (439)
++++++|++++++||+|+++|++ ||.+|+++|+++||||+|+++++|+||+|+
T Consensus 81 l~~~~~~v~~~~~~~ev~~~l~~-dk~~nl~~L~~~h~it~e~id~LY~~akfq 133 (133)
T PF09440_consen 81 LEEETEPVLELLEDPEVVKNLRS-DKKQNLEYLEENHGITPEMIDALYKYAKFQ 133 (133)
T ss_pred HHHHHHHHHHHHcCHHHHHHHHc-cHHHHHHHHHHhcCCCHHHHHHHHHHhCcC
Confidence 99999999999999999999999 999999999999999999999999999986
No 5
>KOG1464 consensus COP9 signalosome, subunit CSN2 [Posttranslational modification, protein turnover, chaperones; Signal transduction mechanisms]
Probab=100.00 E-value=3.3e-37 Score=299.06 Aligned_cols=292 Identities=20% Similarity=0.315 Sum_probs=254.7
Q ss_pred hccHHHHHHhcCCChhHHHH----------HHHHHHHHHhcCChhhHHHHHHHHHhhccc-----cchhHHHHHHHHHHH
Q 013640 111 HYNLQMLHDRYQIGPDQIEA----------LYQYAKFQFECGNYSGAADYLYQYRALCTN-----SERRLSALWGKMAAE 175 (439)
Q Consensus 111 ~~n~~~l~~~~g~t~e~~~a----------l~~~ak~~y~~Gdy~~A~~~L~~~~~~~~~-----~~~k~~~lwg~la~e 175 (439)
..|...||+.|..|.+.+.. -.++|++|++.|+|....++|.+++..|.. +.+|++.|++++|+|
T Consensus 118 S~~m~LLQ~FYeTTL~ALkdAKNeRLWFKTNtKLgkl~fd~~e~~kl~KIlkqLh~SCq~edGedD~kKGtQLLEiYAlE 197 (440)
T KOG1464|consen 118 SKNMDLLQEFYETTLDALKDAKNERLWFKTNTKLGKLYFDRGEYTKLQKILKQLHQSCQTEDGEDDQKKGTQLLEIYALE 197 (440)
T ss_pred hhhhHHHHHHHHHHHHHHHhhhcceeeeeccchHhhhheeHHHHHHHHHHHHHHHHHhccccCchhhhccchhhhhHhhH
Confidence 45667899999988877663 389999999999999999999999999975 457899999999999
Q ss_pred HhhcCHHHHHHHHHHHHHHhcCC----CCCCChH--HHHHHHHHHHHHHHHHHhcCccchHHHHHHhcc---ccchhHHH
Q 013640 176 ILMQNWDIALEELNQLKEKVDDP----KSFTSPL--NQMQSRIWLMHWSLFIFFNHDNGRTLIIDLFNQ---DKYLNAIQ 246 (439)
Q Consensus 176 Il~~~w~~a~~~l~klke~id~~----~~~~~~l--~~l~~R~WllHwsLf~~fn~~~~~~~l~d~F~~---~~yl~~Iq 246 (439)
|+|+ ++.++.++||.++++. +.+++|+ .+++++.-.+|-.-- .+.+|...|||.|++ ++....++
T Consensus 198 IQmY---T~qKnNKkLK~lYeqalhiKSAIPHPlImGvIRECGGKMHlreg---~fe~AhTDFFEAFKNYDEsGspRRtt 271 (440)
T KOG1464|consen 198 IQMY---TEQKNNKKLKALYEQALHIKSAIPHPLIMGVIRECGGKMHLREG---EFEKAHTDFFEAFKNYDESGSPRRTT 271 (440)
T ss_pred hhhh---hhhcccHHHHHHHHHHHHhhccCCchHHHhHHHHcCCccccccc---hHHHHHhHHHHHHhcccccCCcchhH
Confidence 9999 7999999999999975 6789996 233333333332110 022789999999994 47777776
Q ss_pred hhchhHHHHHHHHHHHhcccccchHHHHHHHhhhccCCc-ch----HHHHHHHhhhcCChhHHHHHHHHHHHHhcCCccc
Q 013640 247 TNAPHLLRYLATAFIVNKRRRPQFKDFIKVIQQEQNSYK-DP----ITEFLACVYVNYDFDGAQKKMKECEEVILNDPFL 321 (439)
Q Consensus 247 t~~p~lLrYlvva~il~~~r~~~l~~i~~vi~qe~~~Y~-Dp----it~f~~~lY~~fdF~~aq~~L~~~e~~i~~D~FL 321 (439)
||+|||+|.|++++..++| .+||+++|+ || ||+++ +.|++.|+.+|++.|+...+.|+.|+|+
T Consensus 272 -----CLKYLVLANMLmkS~iNPF------DsQEAKPyKNdPEIlAMTnlv-~aYQ~NdI~eFE~Il~~~~~~IM~DpFI 339 (440)
T KOG1464|consen 272 -----CLKYLVLANMLMKSGINPF------DSQEAKPYKNDPEILAMTNLV-AAYQNNDIIEFERILKSNRSNIMDDPFI 339 (440)
T ss_pred -----HHHHHHHHHHHHHcCCCCC------cccccCCCCCCHHHHHHHHHH-HHHhcccHHHHHHHHHhhhccccccHHH
Confidence 9999999999999999999 999999999 89 99999 7799999999999999999999999999
Q ss_pred ccccccccccccccHHHHHHHHHHHHHHHhhhhhccccHHHHHHHcCCCHHHHHHHHHHHhhcCccceeecccCCEEEeC
Q 013640 322 GKRVEDSNFATVPLRDEFLENARLFIFETYCRIHQRIDMAVLAEKLNLNYEEAQRWIVNLIRNSKLDAKIDAKSGTVIME 401 (439)
Q Consensus 322 ~~~~~~~~~~~~~~~~~f~e~aR~~ife~ycriy~~I~I~~lA~~l~~s~~~~E~wiv~lI~~~rL~aKID~~~g~V~~~ 401 (439)
..|.+++++++|+.+.-..++||+.|.|+.+|++|||++.+++..+|.+|.+.+++++||.+|+.+++.
T Consensus 340 -----------Reh~EdLl~niRTQVLlkLIkPYt~i~Ipfis~~Lnv~~~dV~~LLV~~ILD~~i~g~Ide~n~~l~~~ 408 (440)
T KOG1464|consen 340 -----------REHIEDLLRNIRTQVLLKLIKPYTNIGIPFISKELNVPEADVESLLVSCILDDTIDGRIDEVNQYLELD 408 (440)
T ss_pred -----------HHHHHHHHHHHHHHHHHHHhccccccCchhhHhhcCCCHHHHHHHHHHHHhccccccchHHhhhHhccC
Confidence 899999999999999999999999999999999999999999999999999999999999999999998
Q ss_pred CCCchhHHHHHHhhhhhhhHHHHHHHHHHhh
Q 013640 402 PTHPNVYEQLIDHTKGLSGRTYKLVGQLLEH 432 (439)
Q Consensus 402 ~~~~~~yqqvi~kt~~L~~R~q~L~~~i~~~ 432 (439)
...++- ....+..+.+.++++.|..+|...
T Consensus 409 ~~~~s~-~k~~~al~kW~~ql~Sl~~~i~sr 438 (440)
T KOG1464|consen 409 KSKNSG-SKLYKALDKWNNQLKSLQSNIVSR 438 (440)
T ss_pred ccCCcc-hHHHHHHHHHHHHHHHHHHHHHhh
Confidence 877543 235667788999999999988643
No 6
>KOG0686 consensus COP9 signalosome, subunit CSN1 [Posttranslational modification, protein turnover, chaperones; Signal transduction mechanisms]
Probab=99.73 E-value=9.9e-16 Score=155.95 Aligned_cols=344 Identities=17% Similarity=0.225 Sum_probs=236.7
Q ss_pred HHHHHHHHHHHcc-CCCchHHHHHHH--HhCCC-C-----------CCh----hHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 013640 35 EQILKSKIELLNK-TNMVDYAMDIHK--SLYHT-E-----------DVP----QDMVERRVEVVARLKALEERAAPIVSF 95 (439)
Q Consensus 35 ~~l~~a~~~llk~-TnM~dy~~~~~~--~l~~~-~-----------~~p----~e~~~k~~ev~~~l~~l~~~~~~~~~~ 95 (439)
-+.++.-++.+|. |-=++-+..+|+ ++.+. + +.| +=.+.++.+-..++++|+.+.
T Consensus 64 ~~Al~~Ai~~vk~~t~nv~ly~~l~~~~k~~~~L~~~~~~~~~~~~e~~~~D~~WvE~~~~~a~~~le~L~~eL------ 137 (466)
T KOG0686|consen 64 VEALRMAIDEVKEDTYNVDLYQELFNASKIQGELGRAPFKNPQLGFEGYLLDEKWVETNNKKAVLKLEKLDNEL------ 137 (466)
T ss_pred HHHHHHHHHHHHhcCcchhHHHHHHHHHHhcchhhcCCCCCccccccccccchHHHHHhhHHHHHHHHHHHHHH------
Confidence 4666777788887 888888888888 44311 0 111 112333334344444444443
Q ss_pred hCChhHHHHhhhcchhccHHHHHHhcCCChhHHHHHHHHHHHHHhcCChhhHHHHHHHHHhhccccchhHHHHHHHHHHH
Q 013640 96 LQNPNSFQDLRANDQHYNLQMLHDRYQIGPDQIEALYQYAKFQFECGNYSGAADYLYQYRALCTNSERRLSALWGKMAAE 175 (439)
Q Consensus 96 ~~~~e~~~~l~~~dk~~n~~~l~~~~g~t~e~~~al~~~ak~~y~~Gdy~~A~~~L~~~~~~~~~~~~k~~~lwg~la~e 175 (439)
++ -++-++...++.++-++|.+|++||+.+.|.+.....|.-||+.+..++.....+..-
T Consensus 138 ----------k~----------yK~n~iKEsiRra~~Dl~dhy~~cG~l~~Alr~YsR~RdYCTs~khvInm~ln~i~VS 197 (466)
T KOG0686|consen 138 ----------KS----------YKDNLIKESIRRALEDLGDHYLDCGQLDNALRCYSRARDYCTSAKHVINMCLNLILVS 197 (466)
T ss_pred ----------HH----------hhcchhhHHHHHHHHHHHHHHHHhccHHHHHhhhhhhhhhhcchHHHHHHHHHHHHHH
Confidence 11 2344557778899999999999999999999999999999999999999999999999
Q ss_pred HhhcCHHHHHHHHHHHHHHhcCC----CCCCChHHHHHHHHHHHHHHHHHHhcCccchHHHHHHhc-cccchhHHHhhch
Q 013640 176 ILMQNWDIALEELNQLKEKVDDP----KSFTSPLNQMQSRIWLMHWSLFIFFNHDNGRTLIIDLFN-QDKYLNAIQTNAP 250 (439)
Q Consensus 176 Il~~~w~~a~~~l~klke~id~~----~~~~~~l~~l~~R~WllHwsLf~~fn~~~~~~~l~d~F~-~~~yl~~Iqt~~p 250 (439)
|.++||....-...+++..-+.. ...+.|+.-+- -|.|..| .....+..-|+..=+ ...|...|. -.
T Consensus 198 I~~~nw~hv~sy~~~A~st~~~~~~~~q~v~~kl~C~a---gLa~L~l---kkyk~aa~~fL~~~~~~~d~~~ivt--ps 269 (466)
T KOG0686|consen 198 IYMGNWGHVLSYISKAESTPDANENLAQEVPAKLKCAA---GLANLLL---KKYKSAAKYFLLAEFDHCDYPEIVT--PS 269 (466)
T ss_pred HhhcchhhhhhHHHHHHhCchhhhhHHHhcCcchHHHH---HHHHHHH---HHHHHHHHHHHhCCCCccCccceec--ch
Confidence 99999999999999998875321 11244433222 1111111 111223333322111 111111110 01
Q ss_pred hHHHHHHHHHHHhcccccchHHHHHHHhhhccC-Cc--ch-----HHHHHHHhhhcCChhHHHHHHHHHHHHhcCCcccc
Q 013640 251 HLLRYLATAFIVNKRRRPQFKDFIKVIQQEQNS-YK--DP-----ITEFLACVYVNYDFDGAQKKMKECEEVILNDPFLG 322 (439)
Q Consensus 251 ~lLrYlvva~il~~~r~~~l~~i~~vi~qe~~~-Y~--Dp-----it~f~~~lY~~fdF~~aq~~L~~~e~~i~~D~FL~ 322 (439)
.+-=|--++++-+-+|.+.. +.||..+... +. +| +..|+++-| ..-.+.|.+++.-+.-|+||
T Consensus 270 dv~iYggLcALAtfdr~~Lk---~~vi~n~~Fk~flel~Pqlr~il~~fy~sky-----~~cl~~L~~~k~~llLD~yL- 340 (466)
T KOG0686|consen 270 DVAIYGGLCALATFDRQDLK---LNVIKNESFKLFLELEPQLREILFKFYSSKY-----ASCLELLREIKPRLLLDMYL- 340 (466)
T ss_pred hhHHHHhhHhhccCCHHHHH---HHHHcchhhhhHHhcChHHHHHHHHHhhhhH-----HHHHHHHHHhccceeechhc-
Confidence 23358888888888885554 2344444321 11 33 444554444 44458999999999999999
Q ss_pred cccccccccccccHHHHHHHHHHHHHHHhhhhhccccHHHHHHHcCCCHHHHHHHHHHHhhcCccceeecccCCEEEeCC
Q 013640 323 KRVEDSNFATVPLRDEFLENARLFIFETYCRIHQRIDMAVLAEKLNLNYEEAQRWIVNLIRNSKLDAKIDAKSGTVIMEP 402 (439)
Q Consensus 323 ~~~~~~~~~~~~~~~~f~e~aR~~ife~ycriy~~I~I~~lA~~l~~s~~~~E~wiv~lI~~~rL~aKID~~~g~V~~~~ 402 (439)
++|++.+..-+|-...-+|..||.++++.-||..||+|..+.|+.+-.||.+|++.||||+-+++|-+..
T Consensus 341 ----------aphVd~Ly~~IR~r~llqy~~py~s~~m~~mA~af~~sv~~le~~l~~LI~~~~i~~rIDs~~ki~~~~~ 410 (466)
T KOG0686|consen 341 ----------APHVDNLYSLIRNRALLQYLSPYSSADMSKMAEAFNTSVAILESELLELILEGKISGRIDSHNKILYARD 410 (466)
T ss_pred ----------chhHHHHHHHHHHhhHHHhcCccccchHHHHHHHhcccHHHHHHHHHHHHHccchheeeccccceeeecc
Confidence 8999999999999999999999999999999999999999999999999999999999999999999876
Q ss_pred CC--chhH-------HHHHHhhhhhhhHHHHHHHHHHh
Q 013640 403 TH--PNVY-------EQLIDHTKGLSGRTYKLVGQLLE 431 (439)
Q Consensus 403 ~~--~~~y-------qqvi~kt~~L~~R~q~L~~~i~~ 431 (439)
.+ +..+ ++---+++.++-|+.++.+.+.-
T Consensus 411 ~~~en~~fe~~~~~~~~~~~~~kal~lr~~~~~~~~ht 448 (466)
T KOG0686|consen 411 ADSENATFERVLPMGKRSQLEAKALLLRAALLKNKIHT 448 (466)
T ss_pred cccccchhhhcchhhHHHHHHHHHHHHHHHHHhccccC
Confidence 54 3333 33345667778888777766654
No 7
>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=99.61 E-value=6.5e-15 Score=137.27 Aligned_cols=161 Identities=13% Similarity=0.190 Sum_probs=134.8
Q ss_pred hhHHHHHHHHHHHHHHHHHHHHHHHHHhhCChhHHHHhhhcchhccHHHHHHhcCCChhHHHHHHHHHHHHHhcCChhhH
Q 013640 68 PQDMVERRVEVVARLKALEERAAPIVSFLQNPNSFQDLRANDQHYNLQMLHDRYQIGPDQIEALYQYAKFQFECGNYSGA 147 (439)
Q Consensus 68 p~e~~~k~~ev~~~l~~l~~~~~~~~~~~~~~e~~~~l~~~dk~~n~~~l~~~~g~t~e~~~al~~~ak~~y~~Gdy~~A 147 (439)
-+++.+++++.+++ |+.++ ...++|.| ..++++++.++|.||+++||+++|
T Consensus 5 ~~~~~~~~~~~~~~---Le~el-------------------------k~~~~n~~-kesir~~~~~l~~~~~~~Gd~~~A 55 (177)
T PF10602_consen 5 IEETKAKNAEELEK---LEAEL-------------------------KDAKSNLG-KESIRMALEDLADHYCKIGDLEEA 55 (177)
T ss_pred HHHHHHHHHHHHHH---HHHHH-------------------------HHHHhccc-hHHHHHHHHHHHHHHHHhhhHHHH
Confidence 35666666665555 77776 44567777 999999999999999999999999
Q ss_pred HHHHHHHHhhccccchhHHHHHHHHHHHHhhcCHHHHHHHHHHHHHHhcCCCCC--CChHHHHHHHHHHHHHHHHH--Hh
Q 013640 148 ADYLYQYRALCTNSERRLSALWGKMAAEILMQNWDIALEELNQLKEKVDDPKSF--TSPLNQMQSRIWLMHWSLFI--FF 223 (439)
Q Consensus 148 ~~~L~~~~~~~~~~~~k~~~lwg~la~eIl~~~w~~a~~~l~klke~id~~~~~--~~~l~~l~~R~WllHwsLf~--~f 223 (439)
.+.+...+..|++.+.+++..+..++..|+.+||..+...+.|++.+++.+++| +|++++++ +|+. ..
T Consensus 56 ~k~y~~~~~~~~~~~~~id~~l~~irv~i~~~d~~~v~~~i~ka~~~~~~~~d~~~~nrlk~~~--------gL~~l~~r 127 (177)
T PF10602_consen 56 LKAYSRARDYCTSPGHKIDMCLNVIRVAIFFGDWSHVEKYIEKAESLIEKGGDWERRNRLKVYE--------GLANLAQR 127 (177)
T ss_pred HHHHHHHhhhcCCHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHhccchHHHHHHHHHHH--------HHHHHHhc
Confidence 999999999999999999999999999999999999999999999999999888 78888888 6664 55
Q ss_pred cCccchHHHHHH---hccccchhHHHhhchhHHHHHHHHHHHhcccc
Q 013640 224 NHDNGRTLIIDL---FNQDKYLNAIQTNAPHLLRYLATAFIVNKRRR 267 (439)
Q Consensus 224 n~~~~~~~l~d~---F~~~~yl~~Iqt~~p~lLrYlvva~il~~~r~ 267 (439)
++..+...|+|. |.+..| .--.++..+..|.+++++++.+|.
T Consensus 128 ~f~~AA~~fl~~~~t~~~~~~--~el~s~~d~a~Y~~l~aLat~~R~ 172 (177)
T PF10602_consen 128 DFKEAAELFLDSLSTFTSLQY--TELISYNDFAIYGGLCALATLDRS 172 (177)
T ss_pred hHHHHHHHHHccCcCCCCCch--hhhcCHHHHHHHHHHHHHHhCCHH
Confidence 578888999884 332222 233467789999999999999984
No 8
>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=99.60 E-value=4.4e-15 Score=124.07 Aligned_cols=104 Identities=25% Similarity=0.433 Sum_probs=93.6
Q ss_pred chHHHHHHHhhhcCChhHHHHHHHHHHHHhcCCcccccccccccccccccHHHHHHHHHHHHHHHhhhhhccccHHHHHH
Q 013640 286 DPITEFLACVYVNYDFDGAQKKMKECEEVILNDPFLGKRVEDSNFATVPLRDEFLENARLFIFETYCRIHQRIDMAVLAE 365 (439)
Q Consensus 286 Dpit~f~~~lY~~fdF~~aq~~L~~~e~~i~~D~FL~~~~~~~~~~~~~~~~~f~e~aR~~ife~ycriy~~I~I~~lA~ 365 (439)
+|+++++++ |...|+.++.+.+...++.+..|.++ ..+.+.+.+.+|...+.+++++|++|+++.||+
T Consensus 1 ~~~~~l~~~-~~~~~~~~~~~~l~~~~~~~~~~~~l-----------~~~~~~l~~~i~~~~l~~l~~~y~~i~~~~ia~ 68 (105)
T PF01399_consen 1 PPYSELLRA-FRSGDLQEFEEFLEKHSESLFKDPFL-----------AEYVEQLKEKIRRRNLRQLSKPYSSISISEIAK 68 (105)
T ss_dssp HHHHHHHHH-HHCT-HHHHHHHHHHTCHHHHHCTTH-----------HHHHHHHHHHHHHHHHHHHHHC-SEEEHHHHHH
T ss_pred CHHHHHHHH-HHhCCHHHHHHHHHHHHHHHHcCccH-----------HHHHHHHHHHHHHHHHHHHHHHhcccchHHHHH
Confidence 468899955 66688999999999996667778888 689999999999999999999999999999999
Q ss_pred HcCCCHHHHHHHHHHHhhcCccceeecccCCEEEeC
Q 013640 366 KLNLNYEEAQRWIVNLIRNSKLDAKIDAKSGTVIME 401 (439)
Q Consensus 366 ~l~~s~~~~E~wiv~lI~~~rL~aKID~~~g~V~~~ 401 (439)
.|+++.+++|.|++++|++|+|+||||.++|+|+++
T Consensus 69 ~l~~~~~~vE~~l~~~I~~~~i~~~ID~~~~~v~~~ 104 (105)
T PF01399_consen 69 ALQLSEEEVESILIDLISNGLIKAKIDQVNGVVVFS 104 (105)
T ss_dssp HHTCCHHHHHHHHHHHHHTTSSEEEEETTTTEEEE-
T ss_pred HhccchHHHHHHHHHHHHCCCEEEEEECCCCEEEec
Confidence 999999999999999999999999999999999986
No 9
>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=99.46 E-value=3.3e-13 Score=110.84 Aligned_cols=73 Identities=26% Similarity=0.371 Sum_probs=69.9
Q ss_pred ccHHHHHHHHHHHHHHHhhhhhccccHHHHHHHcCCCHHHHHHHHHHHhhcCccceeecccCCEEEeCCCCch
Q 013640 334 PLRDEFLENARLFIFETYCRIHQRIDMAVLAEKLNLNYEEAQRWIVNLIRNSKLDAKIDAKSGTVIMEPTHPN 406 (439)
Q Consensus 334 ~~~~~f~e~aR~~ife~ycriy~~I~I~~lA~~l~~s~~~~E~wiv~lI~~~rL~aKID~~~g~V~~~~~~~~ 406 (439)
+|.+.+.+.+|...+.+||++|++|+++.||+.|+++.+++|.||+++|++|.|+||||+.+|+|.+++.++.
T Consensus 1 ~~~~~l~~~~~~~~l~~l~~~y~~i~~~~i~~~~~l~~~~vE~~i~~~i~~~~l~~~ID~~~~~v~~~~~~~r 73 (88)
T smart00088 1 QLVERLQRKIRLTNLLQLSEPYSSISLSDLAKLLGLSVPEVEKLVSKAIRDGEISAKIDQVNGIVEFEEVDPR 73 (88)
T ss_pred ChHHHHHHHHHHHHHHHHhHHhceeeHHHHHHHhCcCHHHHHHHHHHHHHCCCeEEEEcCcCCEEEECCCchh
Confidence 4788999999999999999999999999999999999999999999999999999999999999999988753
No 10
>smart00753 PAM PCI/PINT associated module.
Probab=99.46 E-value=3.3e-13 Score=110.84 Aligned_cols=73 Identities=26% Similarity=0.371 Sum_probs=69.9
Q ss_pred ccHHHHHHHHHHHHHHHhhhhhccccHHHHHHHcCCCHHHHHHHHHHHhhcCccceeecccCCEEEeCCCCch
Q 013640 334 PLRDEFLENARLFIFETYCRIHQRIDMAVLAEKLNLNYEEAQRWIVNLIRNSKLDAKIDAKSGTVIMEPTHPN 406 (439)
Q Consensus 334 ~~~~~f~e~aR~~ife~ycriy~~I~I~~lA~~l~~s~~~~E~wiv~lI~~~rL~aKID~~~g~V~~~~~~~~ 406 (439)
+|.+.+.+.+|...+.+||++|++|+++.||+.|+++.+++|.||+++|++|.|+||||+.+|+|.+++.++.
T Consensus 1 ~~~~~l~~~~~~~~l~~l~~~y~~i~~~~i~~~~~l~~~~vE~~i~~~i~~~~l~~~ID~~~~~v~~~~~~~r 73 (88)
T smart00753 1 QLVERLQRKIRLTNLLQLSEPYSSISLSDLAKLLGLSVPEVEKLVSKAIRDGEISAKIDQVNGIVEFEEVDPR 73 (88)
T ss_pred ChHHHHHHHHHHHHHHHHhHHhceeeHHHHHHHhCcCHHHHHHHHHHHHHCCCeEEEEcCcCCEEEECCCchh
Confidence 4788999999999999999999999999999999999999999999999999999999999999999988753
No 11
>KOG1463 consensus 26S proteasome regulatory complex, subunit RPN6/PSMD11 [Posttranslational modification, protein turnover, chaperones]
Probab=99.17 E-value=4.4e-08 Score=98.84 Aligned_cols=251 Identities=13% Similarity=0.205 Sum_probs=169.5
Q ss_pred HHHHHHHHhcCChhhHHHHHHHHH-hhccccchhHHHHHHHHHHHHhhcCHHHHHHHHHHHHHHhcCC-----CCCCChH
Q 013640 132 YQYAKFQFECGNYSGAADYLYQYR-ALCTNSERRLSALWGKMAAEILMQNWDIALEELNQLKEKVDDP-----KSFTSPL 205 (439)
Q Consensus 132 ~~~ak~~y~~Gdy~~A~~~L~~~~-~~~~~~~~k~~~lwg~la~eIl~~~w~~a~~~l~klke~id~~-----~~~~~~l 205 (439)
-+++.+|++.|+|.+|..+...+. ++-.-+++.+=.--..+-+-.. -+..++.|.|.-+-+. ..+-+|.
T Consensus 132 arli~Ly~d~~~YteAlaL~~~L~rElKKlDDK~lLvev~llESK~y-----~~l~Nl~KakasLTsART~AnaiYcpPq 206 (411)
T KOG1463|consen 132 ARLIRLYNDTKRYTEALALINDLLRELKKLDDKILLVEVHLLESKAY-----HALRNLPKAKASLTSARTTANAIYCPPQ 206 (411)
T ss_pred HHHHHHHHhhHHHHHHHHHHHHHHHHHHhcccccceeeehhhhhHHH-----HHHhcchhHHHHHHHHHHhhcccccCHH
Confidence 578999999999999998776543 3222222221111111111111 1344455555544432 1234554
Q ss_pred HH----H-------HHHHHHHHHHHHHHhcCccchHHHHHHhc---ccc-chhHHHhhchhHHHHHHHHHHHhcccccch
Q 013640 206 NQ----M-------QSRIWLMHWSLFIFFNHDNGRTLIIDLFN---QDK-YLNAIQTNAPHLLRYLATAFIVNKRRRPQF 270 (439)
Q Consensus 206 ~~----l-------~~R~WllHwsLf~~fn~~~~~~~l~d~F~---~~~-yl~~Iqt~~p~lLrYlvva~il~~~r~~~l 270 (439)
.| | .+|.|.. |+.=|+|.|- +-+ -.++.+ -|||..++-|.- ++.+-+
T Consensus 207 lQa~lDLqSGIlha~ekDykT------------afSYFyEAfEgf~s~~~~v~A~~-----sLKYMlLcKIMl-n~~ddv 268 (411)
T KOG1463|consen 207 LQATLDLQSGILHAAEKDYKT------------AFSYFYEAFEGFDSLDDDVKALT-----SLKYMLLCKIML-NLPDDV 268 (411)
T ss_pred HHHHHHHhccceeecccccch------------HHHHHHHHHccccccCCcHHHHH-----HHHHHHHHHHHh-cCHHHH
Confidence 32 1 1344443 4444444443 222 145555 899998876643 222323
Q ss_pred HHHHHHHhhhccCCcchHHH---HHHHhhhcCChhHHHHHHHHHHHHhcCCcccccccccccccccccHHHHHHHHHHHH
Q 013640 271 KDFIKVIQQEQNSYKDPITE---FLACVYVNYDFDGAQKKMKECEEVILNDPFLGKRVEDSNFATVPLRDEFLENARLFI 347 (439)
Q Consensus 271 ~~i~~vi~qe~~~Y~Dpit~---f~~~lY~~fdF~~aq~~L~~~e~~i~~D~FL~~~~~~~~~~~~~~~~~f~e~aR~~i 347 (439)
.-+++ ...+-.|.+|..+ =+...|.+-+-.+|+..|++....+..|++. +.|...+-+++=-.=
T Consensus 269 ~~lls--~K~~l~y~g~~i~AmkavAeA~~nRSLkdF~~AL~~yk~eL~~D~iv-----------r~Hl~~Lyd~lLEkn 335 (411)
T KOG1463|consen 269 AALLS--AKLALKYAGRDIDAMKAVAEAFGNRSLKDFEKALADYKKELAEDPIV-----------RSHLQSLYDNLLEKN 335 (411)
T ss_pred HHHHh--hHHHHhccCcchHHHHHHHHHhcCCcHHHHHHHHHHhHHHHhcChHH-----------HHHHHHHHHHHHHHh
Confidence 33333 2233347776332 2345688899999999999999999999999 899999999988777
Q ss_pred HHHhhhhhccccHHHHHHHcCCCHHHHHHHHHHHhhcCccceeecccCCEEEeCCCC--chhHHHHHHhhhhh
Q 013640 348 FETYCRIHQRIDMAVLAEKLNLNYEEAQRWIVNLIRNSKLDAKIDAKSGTVIMEPTH--PNVYEQLIDHTKGL 418 (439)
Q Consensus 348 fe~ycriy~~I~I~~lA~~l~~s~~~~E~wiv~lI~~~rL~aKID~~~g~V~~~~~~--~~~yqqvi~kt~~L 418 (439)
.-..++||++|.|..+|+-.|++...+|+-|+..|.+.++.+-+|+-+|+++.-..+ .+.|+..+|.-.++
T Consensus 336 l~riIEPyS~Vei~hIA~~IGl~~~~VEkKLsqMILDKkf~G~LDQg~g~Liv~~e~~~d~~y~~aLetI~~m 408 (411)
T KOG1463|consen 336 LCRIIEPYSRVEISHIAEVIGLDVPQVEKKLSQMILDKKFYGTLDQGEGCLIVFEEPPADNTYDAALETIQNM 408 (411)
T ss_pred HHHHcCchhhhhHHHHHHHHCCCcHHHHHHHHHHHHHHHhhcccccCCCeEEEeCCCCcchHHHHHHHHHHhc
Confidence 778889999999999999999999999999999999999999999999999986544 58999988876554
No 12
>KOG2908 consensus 26S proteasome regulatory complex, subunit RPN9/PSMD13 [Posttranslational modification, protein turnover, chaperones]
Probab=98.66 E-value=0.00015 Score=73.62 Aligned_cols=340 Identities=14% Similarity=0.164 Sum_probs=202.2
Q ss_pred CCchHHHHHHHHhCCCCCChhHHHHHHHHHHHHHHHHHHHHHHHHHhhCChhHHH-HhhhcchhccHHHHHHhcCCChhH
Q 013640 49 NMVDYAMDIHKSLYHTEDVPQDMVERRVEVVARLKALEERAAPIVSFLQNPNSFQ-DLRANDQHYNLQMLHDRYQIGPDQ 127 (439)
Q Consensus 49 nM~dy~~~~~~~l~~~~~~p~e~~~k~~ev~~~l~~l~~~~~~~~~~~~~~e~~~-~l~~~dk~~n~~~l~~~~g~t~e~ 127 (439)
||.||+.+--++-+ ++++++... =+.+-+-+-+.+=+-.+.+++.+|-... -++- +.-. .+..+.++ ....
T Consensus 3 ~~~~~L~~~~~~a~--~~l~~ew~~--leeLy~eKLW~QLt~~l~~fvd~~~f~~~~~~l-~lY~--NFvsefe~-kINp 74 (380)
T KOG2908|consen 3 NAPDYLQTQLKSAN--PSLAAEWDR--LEELYEEKLWHQLTLALVDFVDDPPFQAGDLLL-QLYL--NFVSEFET-KINP 74 (380)
T ss_pred cHHHHHHHHHhhcC--cchhhHHHH--HHHHHHHHHHHHHHHHHHHHHhccccccchHHH-HHHH--HHHHHHhh-ccCh
Confidence 56777775444333 457767665 3334444667777878888888885321 1111 1111 23334444 3444
Q ss_pred HHHHHHHHHHHHhcCChhhHHHHHHHHHhhccccc---hhHHHHHHHHHHHHhhcCHHHHHHHHHHHHHHhcCCCCCCCh
Q 013640 128 IEALYQYAKFQFECGNYSGAADYLYQYRALCTNSE---RRLSALWGKMAAEILMQNWDIALEELNQLKEKVDDPKSFTSP 204 (439)
Q Consensus 128 ~~al~~~ak~~y~~Gdy~~A~~~L~~~~~~~~~~~---~k~~~lwg~la~eIl~~~w~~a~~~l~klke~id~~~~~~~~ 204 (439)
+....=+-.+-=+++|...|.++|........... -..-+.-++-+|-...+|-..+.+-+..++..+|+-.+.+..
T Consensus 75 lslvei~l~~~~~~~D~~~al~~Le~i~~~~~~~~e~~av~~~~t~~~r~~L~i~DLk~~kk~ldd~~~~ld~~~~v~~~ 154 (380)
T KOG2908|consen 75 LSLVEILLVVSEQISDKDEALEFLEKIIEKLKEYKEPDAVIYILTEIARLKLEINDLKEIKKLLDDLKSMLDSLDGVTSN 154 (380)
T ss_pred HHHHHHHHHHHHHhccHHHHHHHHHHHHHHHHhhccchhHHHHHHHHHHHHHhcccHHHHHHHHHHHHHHHhcccCCChh
Confidence 44444444555678899999999999888765433 344555566666667788889999999999999984333221
Q ss_pred HHHHHHHHHHHHHHHHHHhcCccchHHHHHHhccc-cchhHH-Hhhch-----hHHHHHHHHHHHhcccccchHHHHH--
Q 013640 205 LNQMQSRIWLMHWSLFIFFNHDNGRTLIIDLFNQD-KYLNAI-QTNAP-----HLLRYLATAFIVNKRRRPQFKDFIK-- 275 (439)
Q Consensus 205 l~~l~~R~WllHwsLf~~fn~~~~~~~l~d~F~~~-~yl~~I-qt~~p-----~lLrYlvva~il~~~r~~~l~~i~~-- 275 (439)
....- .|+ =+-|+.... .+-+.|+.. .|++++ .+.|| ..-.-|.+|+++... .-.|-+++.
T Consensus 155 Vh~~f--Y~l----ssqYyk~~~---d~a~yYr~~L~YL~~~d~~~l~~se~~~lA~~L~~aALLGe~-iyNfGELL~HP 224 (380)
T KOG2908|consen 155 VHSSF--YSL----SSQYYKKIG---DFASYYRHALLYLGCSDIDDLSESEKQDLAFDLSLAALLGEN-IYNFGELLAHP 224 (380)
T ss_pred hhhhH--HHH----HHHHHHHHH---hHHHHHHHHHHHhccccccccCHHHHHHHHHHHHHHHHhccc-cccHHHHHhhH
Confidence 11000 011 011222111 111112211 344443 22333 233445556666431 111222221
Q ss_pred HHhhhccCCcchHHHHHHHhhhcCChhHHHHHHHHHHHHhcCCcccccccccccccccccHHHHHHHHHHHHHH--Hhhh
Q 013640 276 VIQQEQNSYKDPITEFLACVYVNYDFDGAQKKMKECEEVILNDPFLGKRVEDSNFATVPLRDEFLENARLFIFE--TYCR 353 (439)
Q Consensus 276 vi~qe~~~Y~Dpit~f~~~lY~~fdF~~aq~~L~~~e~~i~~D~FL~~~~~~~~~~~~~~~~~f~e~aR~~ife--~ycr 353 (439)
+...-..+=.+=+.+++ -+|..-|++++++.-. +...=+-| .++.+...+-+|+++.- .|.|
T Consensus 225 ilesL~gT~~eWL~dll-~Afn~Gdl~~f~~l~~----~~~~~p~L-----------~~~e~~L~qKI~LmaLiEi~F~r 288 (380)
T KOG2908|consen 225 ILESLKGTNREWLKDLL-IAFNSGDLKRFESLKG----VWGKQPDL-----------ASNEDFLLQKIRLLALIEITFSR 288 (380)
T ss_pred HHHHhcCCcHHHHHHHH-HHhccCCHHHHHHHHH----HhccCchH-----------HHHHHHHHHHHHHHHHHHHHhcC
Confidence 22211110012244555 4577788877776433 33445666 57889999999998775 5667
Q ss_pred --hhccccHHHHHHHcCCCHHHHHHHHHHHhhcCccceeecccCCEEEeCCCC--chhHHHHHHhhhhhhhHH
Q 013640 354 --IHQRIDMAVLAEKLNLNYEEAQRWIVNLIRNSKLDAKIDAKSGTVIMEPTH--PNVYEQLIDHTKGLSGRT 422 (439)
Q Consensus 354 --iy~~I~I~~lA~~l~~s~~~~E~wiv~lI~~~rL~aKID~~~g~V~~~~~~--~~~yqqvi~kt~~L~~R~ 422 (439)
..+.|+.+.+|++..+|.+++|-.+.+.++.|-+.+.||.|+|+|.|+.-- ....+|+.+=.+.+..+-
T Consensus 289 pa~~R~lsf~~Ia~~tkip~~eVE~LVMKAlslgLikG~Idqv~~~v~~swvqPRvl~~~qI~~Mk~rl~~W~ 361 (380)
T KOG2908|consen 289 PANERTLSFKEIAEATKIPNKEVELLVMKALSLGLIKGSIDQVEGVVYMSWVQPRVLDRSQIVKMKDRLDEWN 361 (380)
T ss_pred cchhccccHHHHHHHhCCCHHHHHHHHHHHHhccceeeeecccccEEEEecccccccCHHHHHhHHHHHHHHH
Confidence 789999999999999999999999999999999999999999999998533 355567766555444443
No 13
>COG5159 RPN6 26S proteasome regulatory complex component [Posttranslational modification, protein turnover, chaperones]
Probab=98.53 E-value=2.4e-06 Score=85.06 Aligned_cols=269 Identities=12% Similarity=0.201 Sum_probs=170.6
Q ss_pred HHHHHHHHhcCChhhHHHHHHHHH-hhccccchhHHHHHHHHHHHHhh--cCHHHHHHHHHHHHHHhcCCCCCCChHHHH
Q 013640 132 YQYAKFQFECGNYSGAADYLYQYR-ALCTNSERRLSALWGKMAAEILM--QNWDIALEELNQLKEKVDDPKSFTSPLNQM 208 (439)
Q Consensus 132 ~~~ak~~y~~Gdy~~A~~~L~~~~-~~~~~~~~k~~~lwg~la~eIl~--~~w~~a~~~l~klke~id~~~~~~~~l~~l 208 (439)
.+++.++|+.|.|.+|...+..+. ++-.-+++..-.....+-+-.+. .|..-++.-+..+|-.-.+ ..-+|. +
T Consensus 129 ~Kli~l~y~~~~YsdalalIn~ll~ElKk~DDK~~Li~vhllESKvyh~irnv~KskaSLTaArt~Ans--~YCPpq--l 204 (421)
T COG5159 129 CKLIYLLYKTGKYSDALALINPLLHELKKYDDKINLITVHLLESKVYHEIRNVSKSKASLTAARTLANS--AYCPPQ--L 204 (421)
T ss_pred HHHHHHHHhcccHHHHHHHHHHHHHHHHhhcCccceeehhhhhHHHHHHHHhhhhhhhHHHHHHHHhhc--cCCCHH--H
Confidence 678899999999999998887643 33222333222222222222221 1222233333334333322 233332 2
Q ss_pred HHHHHHHHHHHHH--HhcCccchHHHHHHhccccchhHHHhhchhHHHHHHHHHHHhcccccchHHHHHHHhhhccCCcc
Q 013640 209 QSRIWLMHWSLFI--FFNHDNGRTLIIDLFNQDKYLNAIQTNAPHLLRYLATAFIVNKRRRPQFKDFIKVIQQEQNSYKD 286 (439)
Q Consensus 209 ~~R~WllHwsLf~--~fn~~~~~~~l~d~F~~~~yl~~Iqt~~p~lLrYlvva~il~~~r~~~l~~i~~vi~qe~~~Y~D 286 (439)
|..--|+. +++. =.+++-|+.-|+|.|-+-+.+..-.-.| -.|||..+.-|.-.+| .-++.+++-=.. ...|.|
T Consensus 205 qa~lDL~s-GIlhcdd~dyktA~SYF~Ea~Egft~l~~d~kAc-~sLkYmlLSkIMlN~~-~evk~vl~~K~t-~~~y~~ 280 (421)
T COG5159 205 QAQLDLLS-GILHCDDRDYKTASSYFIEALEGFTLLKMDVKAC-VSLKYMLLSKIMLNRR-EEVKAVLRNKNT-LKHYDD 280 (421)
T ss_pred HHHHHHhc-cceeeccccchhHHHHHHHHHhccccccchHHHH-HHHHHHHHHHHHHhhH-HHHHHHHccchh-Hhhhhh
Confidence 22111111 1111 2334556666777554322222111112 2789998877654333 333333331111 123555
Q ss_pred hHH---HHHHHhhhcCChhHHHHHHHHHHHHhcCCcccccccccccccccccHHHHHHHHHHHHHHHhhhhhccccHHHH
Q 013640 287 PIT---EFLACVYVNYDFDGAQKKMKECEEVILNDPFLGKRVEDSNFATVPLRDEFLENARLFIFETYCRIHQRIDMAVL 363 (439)
Q Consensus 287 pit---~f~~~lY~~fdF~~aq~~L~~~e~~i~~D~FL~~~~~~~~~~~~~~~~~f~e~aR~~ife~ycriy~~I~I~~l 363 (439)
.+. -=+...|.+-+..+|...|++.+..+..|.|+ .+|..++-.+.=-.=.-..++||.+|.|..+
T Consensus 281 r~I~am~avaea~~NRsL~df~~aL~qY~~el~~D~~i-----------RsHl~~LYD~LLe~Nl~kiiEPfs~VeishI 349 (421)
T COG5159 281 RMIRAMLAVAEAFGNRSLKDFSDALAQYSDELHQDSFI-----------RSHLQYLYDVLLEKNLVKIIEPFSVVEISHI 349 (421)
T ss_pred hhHHHHHHHHHHhCCCcHhhHHHHHHHhhHHhccCHHH-----------HHHHHHHHHHHHHhhhhhhcCcceeeehhHH
Confidence 422 22345688888899999999999999999999 8999999888777777788899999999999
Q ss_pred HHHcCCCHHHHHHHHHHHhhcCccceeecccCCEEEeCCCC--chhHHHHHHhhhhhh
Q 013640 364 AEKLNLNYEEAQRWIVNLIRNSKLDAKIDAKSGTVIMEPTH--PNVYEQLIDHTKGLS 419 (439)
Q Consensus 364 A~~l~~s~~~~E~wiv~lI~~~rL~aKID~~~g~V~~~~~~--~~~yqqvi~kt~~L~ 419 (439)
|+-+|.+...+|.-++..|.+.-..+..|+-+|+++....+ .+.|..-++..+.|.
T Consensus 350 a~viGldt~qvEgKLsqMILDKifyG~LDqg~gcLivy~ep~qd~tyd~ale~v~~l~ 407 (421)
T COG5159 350 ADVIGLDTNQVEGKLSQMILDKIFYGTLDQGDGCLIVYGEPAQDNTYDEALEQVEALD 407 (421)
T ss_pred HHHhcccHHHHHHHHHHHHHHHHHHhhhccCCceEEEeCCccccchHHHHHHHHHHhh
Confidence 99999999999999999999999999999999999886555 578988888776554
No 14
>KOG1498 consensus 26S proteasome regulatory complex, subunit RPN5/PSMD12 [Posttranslational modification, protein turnover, chaperones]
Probab=98.03 E-value=0.00083 Score=69.52 Aligned_cols=276 Identities=19% Similarity=0.231 Sum_probs=162.6
Q ss_pred HHHHHHHHhcCChhhHHHHHHHHHhhcccc---chhHHHHHHHHHHHHhhcCHHHHHHHHHHHHHHhcCCCCCC-ChHHH
Q 013640 132 YQYAKFQFECGNYSGAADYLYQYRALCTNS---ERRLSALWGKMAAEILMQNWDIALEELNQLKEKVDDPKSFT-SPLNQ 207 (439)
Q Consensus 132 ~~~ak~~y~~Gdy~~A~~~L~~~~~~~~~~---~~k~~~lwg~la~eIl~~~w~~a~~~l~klke~id~~~~~~-~~l~~ 207 (439)
-.+|+..=++||-.+|++.+-.+..-+-++ .-+....++.++..++-.||-.|.--.+|+.--+-+..+.. =.++.
T Consensus 135 k~L~~ike~~Gdi~~Aa~il~el~VETygsm~~~ekV~fiLEQmrKOG~~~D~vra~i~skKI~~K~F~~~~~~~lKlky 214 (439)
T KOG1498|consen 135 KMLAKIKEEQGDIAEAADILCELQVETYGSMEKSEKVAFILEQMRLCLLRLDYVRAQIISKKINKKFFEKPDVQELKLKY 214 (439)
T ss_pred HHHHHHHHHcCCHHHHHHHHHhcchhhhhhhHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHhhHHhcCCccHHHHHHHH
Confidence 457999999999999999998888766553 34689999999999999999888777777655333312210 01122
Q ss_pred HHHHHHHHHHHHHH-HhcCccchHHHHHHhc---cccchhHHHhhc--hhHHHHHHHHHHHhcccccchHHHHHHHhhhc
Q 013640 208 MQSRIWLMHWSLFI-FFNHDNGRTLIIDLFN---QDKYLNAIQTNA--PHLLRYLATAFIVNKRRRPQFKDFIKVIQQEQ 281 (439)
Q Consensus 208 l~~R~WllHwsLf~-~fn~~~~~~~l~d~F~---~~~yl~~Iqt~~--p~lLrYlvva~il~~~r~~~l~~i~~vi~qe~ 281 (439)
|. |-+ .--|..++-.....+. .++...+- +. -..|+=.|..++++.- .+.-.+++.-++..
T Consensus 215 Y~---------lmI~l~lh~~~Yl~v~~~Yraiy~t~~vk~d--~~kw~~vL~~iv~f~~LAp~-dneQsdll~~is~d- 281 (439)
T KOG1498|consen 215 YE---------LMIRLGLHDRAYLNVCRSYRAIYDTGNVKED--PEKWIEVLRSIVSFCVLAPH-DNEQSDLLARISND- 281 (439)
T ss_pred HH---------HHHHhcccccchhhHHHHHHHHhcccccccC--hhhhhhhhhhheeEEeecCC-CcHHHHHHHHHhcc-
Confidence 22 111 1112222222222222 11111110 00 0122222233333221 12224555555533
Q ss_pred cCCc-chHH-HHHHHhhhcCChhHHHHHHHHHHHHhc-CCcccccccccccccccccHHHHHHHHHHHHHHHhhh----h
Q 013640 282 NSYK-DPIT-EFLACVYVNYDFDGAQKKMKECEEVIL-NDPFLGKRVEDSNFATVPLRDEFLENARLFIFETYCR----I 354 (439)
Q Consensus 282 ~~Y~-Dpit-~f~~~lY~~fdF~~aq~~L~~~e~~i~-~D~FL~~~~~~~~~~~~~~~~~f~e~aR~~ife~ycr----i 354 (439)
+..+ .|-+ +++ -+|++-.--..-..-+.-..++. +|+|-+ ..+-+--...++..|+|-=+| -
T Consensus 282 KkL~e~p~~k~lL-klfv~~EL~rw~s~~~~yg~~l~~~~~~~~----------~~~gek~~~dL~~RIiEHNiRiiA~y 350 (439)
T KOG1498|consen 282 KKLSELPDYKELL-KLFVTMELIRWVSLVESYGDELRTNDFFDG----------GEEGEKRWSDLKLRIIEHNIRIIAKY 350 (439)
T ss_pred cccccCccHHHHH-HHHHhcceeeehhHhhhhHHHHhhcccccc----------cchhhhHHHHHHHHHHHHHHHHHHHH
Confidence 3343 5522 222 22222211000011112223333 356653 456667777777777775444 5
Q ss_pred hccccHHHHHHHcCCCHHHHHHHHHHHhhcCccceeecccCCEEEeCCCCch-----hHHHHHHhhhhhhhHHHHHHHHH
Q 013640 355 HQRIDMAVLAEKLNLNYEEAQRWIVNLIRNSKLDAKIDAKSGTVIMEPTHPN-----VYEQLIDHTKGLSGRTYKLVGQL 429 (439)
Q Consensus 355 y~~I~I~~lA~~l~~s~~~~E~wiv~lI~~~rL~aKID~~~g~V~~~~~~~~-----~yqqvi~kt~~L~~R~q~L~~~i 429 (439)
|+||+...||+.|++++++.|+.|++++.+|-+-||||.-+|+|.-..+-++ ..-+-+++.=++++|+.-|-..-
T Consensus 351 YSrIt~~rl~eLLdl~~ee~E~~LS~lv~t~ti~aKidrpsgII~F~k~K~~~~~LneW~~nve~L~~ll~K~~HLI~KE 430 (439)
T KOG1498|consen 351 YSRITLKRLAELLDLPVEEMEKFLSDLVVTGTIYAKIDRPSGIINFQKVKDSNEILNEWASNVEKLLGLLEKVSHLIHKE 430 (439)
T ss_pred HhhccHHHHHHHhCCCHHHHHHHHHHHHhccceEEEecCCCceEEEEecccHHHHHHHHHhhHHHHHHHHHHHHHHHHHH
Confidence 9999999999999999999999999999999999999999999998877743 45566777777777776665544
Q ss_pred Hh
Q 013640 430 LE 431 (439)
Q Consensus 430 ~~ 431 (439)
..
T Consensus 431 em 432 (439)
T KOG1498|consen 431 EM 432 (439)
T ss_pred HH
Confidence 33
No 15
>KOG2753 consensus Uncharacterized conserved protein, contains PCI domain [General function prediction only]
Probab=97.71 E-value=0.0038 Score=63.47 Aligned_cols=82 Identities=23% Similarity=0.398 Sum_probs=74.6
Q ss_pred HHHHHHHHHHHHHhhhhhccccHHHHHHHcCCCHHHHHHHHHHHhhcCccceeecccCCEEEeCCCC-----chhHHHHH
Q 013640 338 EFLENARLFIFETYCRIHQRIDMAVLAEKLNLNYEEAQRWIVNLIRNSKLDAKIDAKSGTVIMEPTH-----PNVYEQLI 412 (439)
Q Consensus 338 ~f~e~aR~~ife~ycriy~~I~I~~lA~~l~~s~~~~E~wiv~lI~~~rL~aKID~~~g~V~~~~~~-----~~~yqqvi 412 (439)
..++-||++-+-+....-..|+.+.|++.|.+.++++|-|++..|+.+-+.||||+.+.+|+..+.. ..+.||+-
T Consensus 275 ~~~~KMRLLTlm~LA~es~eisy~~l~k~LqI~edeVE~fVIdaI~aklV~~kidq~~~~viVs~~~hR~FG~~qW~~L~ 354 (378)
T KOG2753|consen 275 QNMAKMRLLTLMSLAEESNEISYDTLAKELQINEDEVELFVIDAIRAKLVEGKIDQMNRTVIVSSSTHRTFGKQQWQQLR 354 (378)
T ss_pred HHHHHHHHHHHHHHhccCCCCCHHHHHHHhccCHHHHHHHHHHHHHHHHHHhhHHhhcceEEeehhhhhhcccHHHHHHH
Confidence 5678899999999999999999999999999999999999999999999999999999999987644 45888988
Q ss_pred Hhhhhhh
Q 013640 413 DHTKGLS 419 (439)
Q Consensus 413 ~kt~~L~ 419 (439)
++...|.
T Consensus 355 ~kL~aw~ 361 (378)
T KOG2753|consen 355 DKLAAWG 361 (378)
T ss_pred HHHHHHH
Confidence 8887775
No 16
>COG5071 RPN5 26S proteasome regulatory complex component [Posttranslational modification, protein turnover, chaperones]
Probab=97.56 E-value=0.036 Score=56.20 Aligned_cols=259 Identities=14% Similarity=0.183 Sum_probs=146.8
Q ss_pred hhHHHHHHHHHHHHHhcCChhhHHHHHHHHHhhccc---cchhHHHHHHHHHHHHhhcCHHHHHHHHHHHHHHhcCCCCC
Q 013640 125 PDQIEALYQYAKFQFECGNYSGAADYLYQYRALCTN---SERRLSALWGKMAAEILMQNWDIALEELNQLKEKVDDPKSF 201 (439)
Q Consensus 125 ~e~~~al~~~ak~~y~~Gdy~~A~~~L~~~~~~~~~---~~~k~~~lwg~la~eIl~~~w~~a~~~l~klke~id~~~~~ 201 (439)
.|-..---.+.+.+-+|||-..|.+.+-....-+-+ -.-+..-.++.+++-++-+||-.|.-..+|++.-+-+..+.
T Consensus 128 vERariT~~L~~ikee~Gdi~sA~Dilcn~pVETygs~~~Sekv~fiLEQ~rL~vl~~Dy~~A~~~~kKI~KK~Fe~~d~ 207 (439)
T COG5071 128 VERARLTQLLSQIKEEQGDIKSAQDILCNEPVETYGSFDLSEKVAFILEQVRLFLLRSDYYMASTYTKKINKKFFEKEDV 207 (439)
T ss_pred hhHHHHHHHHHHHHHHhcchhHHHHHHhcCchhhccchhHHHHHHHHHHHHHHHHhccchHHHHHHHHHHHHHHhccccH
Confidence 333333456788899999999999988655544333 23468889999999999999999988888877644432222
Q ss_pred C-ChHHH--------HHHHHHHHHHHHHHHhcCccchHHHHHHhccccchhHH-Hh------hchhHHHHHHHH-----H
Q 013640 202 T-SPLNQ--------MQSRIWLMHWSLFIFFNHDNGRTLIIDLFNQDKYLNAI-QT------NAPHLLRYLATA-----F 260 (439)
Q Consensus 202 ~-~~l~~--------l~~R~WllHwsLf~~fn~~~~~~~l~d~F~~~~yl~~I-qt------~~p~lLrYlvva-----~ 260 (439)
. -.++. +.+|.++ +- ..|++.| +| .+.| |-|++ +
T Consensus 208 ~slKlkyYeL~V~i~Lh~R~Yl---------~v-------------~~y~~~vY~t~~~~~d~Akw---k~VLS~~v~F~ 262 (439)
T COG5071 208 QSLKLKYYELKVRIGLHDRAYL---------DV-------------CKYYRAVYDTAVVQEDPAKW---KEVLSNVVCFA 262 (439)
T ss_pred HHHHHHHHHHhheeecccHHHH---------HH-------------HHHHHHHHHHHHhccCcccc---cchhhcceeeE
Confidence 1 11222 2223222 11 1122222 00 1111 11222 1
Q ss_pred HHhcccccchHHHHHHHhhhccCCc-chHHHHHHHhhhcCChhHHHHHHHHHHHHhcCCcc-cccccccccccccccHHH
Q 013640 261 IVNKRRRPQFKDFIKVIQQEQNSYK-DPITEFLACVYVNYDFDGAQKKMKECEEVILNDPF-LGKRVEDSNFATVPLRDE 338 (439)
Q Consensus 261 il~~~r~~~l~~i~~vi~qe~~~Y~-Dpit~f~~~lY~~fdF~~aq~~L~~~e~~i~~D~F-L~~~~~~~~~~~~~~~~~ 338 (439)
+++. =.+...+++--++...+--+ |...+++.|.-+ ..|=.--..=...+.++..|.| .+ +-++..|.++
T Consensus 263 iLtp-y~neq~dlvhKi~~d~kl~sl~~~~~lVk~f~v-Nelmrwp~V~~~y~~~l~~~~faF~------~e~~~~~w~D 334 (439)
T COG5071 263 LLTP-YDNEQADLLHKINADHKLNSLPLLQQLVKCFIV-NELMRWPKVAEIYGSALRSNVFAFN------DEKGEKRWSD 334 (439)
T ss_pred Eecc-cccHHHHHHHHhhhhhhhccchhhhhHHHHHHH-HHHHhhhHHHHHhHHHHHhhhhhhc------cchhhhhHHH
Confidence 1111 01222344444444433333 335555644322 2221111111223445666644 31 1111234444
Q ss_pred HHHHHHHHHHHHhhhhhccccHHHHHHHcCCCHHHHHHHHHHHhhcCccceeecccCCEEEeCCCCchhHHHHHHhhhh
Q 013640 339 FLENARLFIFETYCRIHQRIDMAVLAEKLNLNYEEAQRWIVNLIRNSKLDAKIDAKSGTVIMEPTHPNVYEQLIDHTKG 417 (439)
Q Consensus 339 f~e~aR~~ife~ycriy~~I~I~~lA~~l~~s~~~~E~wiv~lI~~~rL~aKID~~~g~V~~~~~~~~~yqqvi~kt~~ 417 (439)
+....=--=|...-+-|+||+...|+.-+.+|+++.|+.|+.++-+|-.-|||+..+|+|.-..|.++. |++-+=+++
T Consensus 335 L~krviEHN~RvI~~yYSrI~~~rl~~lld~~~s~te~~ISdlVN~G~~yaKiNrpa~Ii~FEK~~n~~-~~lneW~~N 412 (439)
T COG5071 335 LRKRVIEHNIRVIANYYSRIHCSRLGVLLDMSPSETEQFISDLVNKGHFYAKINRPAQIISFEKSQNVQ-EQLNEWGSN 412 (439)
T ss_pred HHHHHHHhhHhHHHHHhhhhhHHHHHHHHcCCHHHHHHHHHHHHhcCcEEEEecCccceEEeeccccHH-HHHHHhccc
Confidence 433222222233445599999999999999999999999999999999999999999999988876543 555554443
No 17
>KOG2581 consensus 26S proteasome regulatory complex, subunit RPN3/PSMD3 [Posttranslational modification, protein turnover, chaperones]
Probab=97.10 E-value=0.092 Score=55.07 Aligned_cols=145 Identities=21% Similarity=0.264 Sum_probs=95.5
Q ss_pred cchhHHHhhchhHHHHHHHHHHHhccc------ccch--HHHHHHHhhhcc---CCcch--------HHHHHHHhhhcCC
Q 013640 240 KYLNAIQTNAPHLLRYLATAFIVNKRR------RPQF--KDFIKVIQQEQN---SYKDP--------ITEFLACVYVNYD 300 (439)
Q Consensus 240 ~yl~~Iqt~~p~lLrYlvva~il~~~r------~~~l--~~i~~vi~qe~~---~Y~Dp--------it~f~~~lY~~fd 300 (439)
+-+.+||-.+..-.+|++.|...+..- +.+. --+++...-+.+ .+..| --.|- ..-..-|
T Consensus 254 GrIkaiqldYssA~~~~~qa~rkapq~~alGf~q~v~k~~ivv~ll~geiPers~F~Qp~~~ksL~~Yf~Lt-~AVr~gd 332 (493)
T KOG2581|consen 254 GRIKAIQLDYSSALEYFLQALRKAPQHAALGFRQQVNKLMIVVELLLGEIPERSVFRQPGMRKSLRPYFKLT-QAVRLGD 332 (493)
T ss_pred hhHHHhhcchhHHHHHHHHHHHhCcchhhhhHHHHHHHHHHHHHHHcCCCcchhhhcCccHHHHHHHHHHHH-HHHHHhh
Confidence 556778888888888888887766531 1110 112222222212 11222 11222 2335567
Q ss_pred hhHHHHHHHHHHHHhcCCcccccccccccccccccHHHHHHHHHHHHHHHhhh----hhccccHHHHHHHcCCCHHH-HH
Q 013640 301 FDGAQKKMKECEEVILNDPFLGKRVEDSNFATVPLRDEFLENARLFIFETYCR----IHQRIDMAVLAEKLNLNYEE-AQ 375 (439)
Q Consensus 301 F~~aq~~L~~~e~~i~~D~FL~~~~~~~~~~~~~~~~~f~e~aR~~ife~ycr----iy~~I~I~~lA~~l~~s~~~-~E 375 (439)
.+.|...|....+.+..|--. .++--.|+-+..+=+| +|++|++..+|++||++.++ +|
T Consensus 333 lkkF~~~leq~k~~f~~D~ty----------------~LivRLR~NVIkTgIR~ISlsYSRISl~DIA~kL~l~Seed~E 396 (493)
T KOG2581|consen 333 LKKFNETLEQFKDKFQADGTY----------------TLIVRLRHNVIKTGIRKISLSYSRISLQDIAKKLGLNSEEDAE 396 (493)
T ss_pred HHHHHHHHHHHHHHHhhCCcc----------------hHHHHHHHHHHHHhhhheeeeeeeccHHHHHHHhcCCCchhHH
Confidence 777777777776665555322 2444566666666555 69999999999999998776 99
Q ss_pred HHHHHHhhcCccceeecccCCEEEeC
Q 013640 376 RWIVNLIRNSKLDAKIDAKSGTVIME 401 (439)
Q Consensus 376 ~wiv~lI~~~rL~aKID~~~g~V~~~ 401 (439)
-..++.||+|-++||||..+|.++..
T Consensus 397 yiVakAIRDGvIea~Id~~~g~m~sk 422 (493)
T KOG2581|consen 397 YIVAKAIRDGVIEAKIDHEDGFMQSK 422 (493)
T ss_pred HHHHHHHHhccceeeeccccCceehh
Confidence 99999999999999999999988764
No 18
>KOG1076 consensus Translation initiation factor 3, subunit c (eIF-3c) [Translation, ribosomal structure and biogenesis]
Probab=96.83 E-value=0.47 Score=52.75 Aligned_cols=72 Identities=25% Similarity=0.478 Sum_probs=60.6
Q ss_pred cHHHHHH-HHHHHHHHHhhhhhccccHHHHHHHcCCCHHHHHHHHHHHhhcCccceeecccCCEEEeCCCCchh
Q 013640 335 LRDEFLE-NARLFIFETYCRIHQRIDMAVLAEKLNLNYEEAQRWIVNLIRNSKLDAKIDAKSGTVIMEPTHPNV 407 (439)
Q Consensus 335 ~~~~f~e-~aR~~ife~ycriy~~I~I~~lA~~l~~s~~~~E~wiv~lI~~~rL~aKID~~~g~V~~~~~~~~~ 407 (439)
..+.+-+ ..|+..| +|-..|.||+++.||+-|.++...+-..|+..|.+--|.|+.|..+++|+|.+..++-
T Consensus 696 l~~rIqEEsLRTYLf-tYss~Y~SvSl~~LA~mFdLp~~~VhsIiSkmiineEl~AslDqpt~~iv~hrvE~sr 768 (843)
T KOG1076|consen 696 LTERIQEESLRTYLF-TYSSVYDSVSLAKLADMFDLPEPKVHSIISKMIINEELHASLDQPTQCIVMHRVEPSR 768 (843)
T ss_pred HHHHHHHHHHHHHHH-HhhhhhhhccHHHHHHHhCCCchhHHHHHHHHHHHHHhhhccCCCcceEEEeeccchH
Confidence 3334433 3455444 7889999999999999999999999999999999999999999999999999866543
No 19
>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=96.52 E-value=0.0079 Score=53.93 Aligned_cols=78 Identities=19% Similarity=0.253 Sum_probs=55.9
Q ss_pred HHHHHHHhhhcCChhHHHHHHHHHHHHhcCCcccccccccccccccccHHHHHHHHHHHHHHHhhhhhccccHHHHHHHc
Q 013640 288 ITEFLACVYVNYDFDGAQKKMKECEEVILNDPFLGKRVEDSNFATVPLRDEFLENARLFIFETYCRIHQRIDMAVLAEKL 367 (439)
Q Consensus 288 it~f~~~lY~~fdF~~aq~~L~~~e~~i~~D~FL~~~~~~~~~~~~~~~~~f~e~aR~~ife~ycriy~~I~I~~lA~~l 367 (439)
+..+...+. ..||.++-..++... -.+.+. +.+..|.+++|..++...-+.|++|+++.+|+-|
T Consensus 44 i~~l~~~L~-~~~~~~~~~~~~~~~---~~~~~~------------~~v~~~~~~iR~~i~~~i~~aY~sIs~~~la~~L 107 (143)
T PF10075_consen 44 IWSLGQALW-EGDYSKFWQALRSNP---WSPDYK------------PFVPGFEDTIRERIAHLISKAYSSISLSDLAEML 107 (143)
T ss_dssp HHHHHHHHH-TT-HHHHHHHS-TT-------HHH------------HTSTTHHHHHHHHHHHHHHHH-SEE-HHHHHHHT
T ss_pred HHHHHHHHH-CCCHHHHHHHHHhcc---chHHHH------------HHHHHHHHHHHHHHHHHHHHHHhHcCHHHHHHHh
Confidence 555554444 478988776554431 123333 6778899999999999999999999999999999
Q ss_pred CCCHHHHHHHHHHH
Q 013640 368 NLNYEEAQRWIVNL 381 (439)
Q Consensus 368 ~~s~~~~E~wiv~l 381 (439)
|++.+++++++.+.
T Consensus 108 g~~~~el~~~~~~~ 121 (143)
T PF10075_consen 108 GLSEEELEKFIKSR 121 (143)
T ss_dssp TS-HHHHHHHHHHH
T ss_pred CCCHHHHHHHHHHc
Confidence 99999999999875
No 20
>KOG2072 consensus Translation initiation factor 3, subunit a (eIF-3a) [Translation, ribosomal structure and biogenesis]
Probab=96.48 E-value=0.73 Score=52.07 Aligned_cols=256 Identities=14% Similarity=0.179 Sum_probs=159.9
Q ss_pred HHHHHHHHhcCChhhHHHHHHHHHhh-------ccc--------cchhHHHHHHHHHHHHhhcCHHHHHHHHHHHHHHhc
Q 013640 132 YQYAKFQFECGNYSGAADYLYQYRAL-------CTN--------SERRLSALWGKMAAEILMQNWDIALEELNQLKEKVD 196 (439)
Q Consensus 132 ~~~ak~~y~~Gdy~~A~~~L~~~~~~-------~~~--------~~~k~~~lwg~la~eIl~~~w~~a~~~l~klke~id 196 (439)
++|+.=|-+...+-..-+.|...... ++. -+..++.-|-.|-..|.+.-|..|-+-++-+.-++.
T Consensus 184 FqFCLkYqRktEFRrLCe~LR~HL~~i~k~~nq~~~v~Ln~~Etlql~LDtRf~QLdvAi~lELWQEAyrSiEDIhgLm~ 263 (988)
T KOG2072|consen 184 FQFCLKYQRKTEFRRLCELLRMHLDNINKHQNQSTRVDLNDPETLQLYLDTRFQQLDVAIELELWQEAYRSIEDIHGLMK 263 (988)
T ss_pred HHHHHHHhhhHHHHHHHHHHHHHHHHHHHhhccCcCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 55665555666666666665432221 111 134588888999999999999999888777666665
Q ss_pred CCCCC--CChHHH----------------HHHHHHHHHHHHHHHhcCccchHHHHHHhccccchhHHHhh----------
Q 013640 197 DPKSF--TSPLNQ----------------MQSRIWLMHWSLFIFFNHDNGRTLIIDLFNQDKYLNAIQTN---------- 248 (439)
Q Consensus 197 ~~~~~--~~~l~~----------------l~~R~WllHwsLf~~fn~~~~~~~l~d~F~~~~yl~~Iqt~---------- 248 (439)
=.+-- +.-++. ++.=+|+-.+.|+--+|-+--.+.+- ...+.-.|.++++.
T Consensus 264 lSKrtPkp~~laNYY~KL~~VF~~sgn~LfHAaAw~k~f~l~k~~~K~~Tqde~q-~~as~VlLaaLSIP~~~~~~~~~r 342 (988)
T KOG2072|consen 264 LSKRTPKPSTLANYYEKLAKVFWKSGNPLFHAAAWLKLFKLYKNMNKNLTQDELQ-RMASRVLLAALSIPIPDARSDSAR 342 (988)
T ss_pred HhcCCCchhHHHHHHHHHHHHHHhcCcHHHHHHHHHHHHHHHHHhcccccHHHHH-HHHHHHHHHHhcCCCCCccccccc
Confidence 32111 111222 44455663333222122111112221 11122233333322
Q ss_pred -----chhHHHHHHHHHHHhcc----cccchHHHHHHHhhhccCCcch-HHHHHHHhhhcCChhHHHHHHHHHHHHhcCC
Q 013640 249 -----APHLLRYLATAFIVNKR----RRPQFKDFIKVIQQEQNSYKDP-ITEFLACVYVNYDFDGAQKKMKECEEVILND 318 (439)
Q Consensus 249 -----~p~lLrYlvva~il~~~----r~~~l~~i~~vi~qe~~~Y~Dp-it~f~~~lY~~fdF~~aq~~L~~~e~~i~~D 318 (439)
--+.=+=+-+|.+|+.+ |..+|+++++ ...+.+-|+ +.+||+-|=++|+--.--+.|..+-.-|.+-
T Consensus 343 ~~e~e~~~~ek~~rla~LL~L~~~PTR~~ll~e~v~---~gV~~~v~qe~kdLY~iLEveF~PL~l~k~lq~ll~~ls~~ 419 (988)
T KOG2072|consen 343 LIEIEDIGKEKNLRLANLLGLPAPPTRKGLLKEAVR---EGVLSKVDQEVKDLYNILEVEFHPLKLCKKLQPLLDKLSES 419 (988)
T ss_pred ccccccchhhHHHHHHHHhCCCCCccHHHHHHHHHH---hccHhhhhHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHHcC
Confidence 11233444456677663 3445577666 333445565 9999999999998655555555555555554
Q ss_pred cccccccccccccccccHHHHHHHHHHHHHHHhhhhhccccHHHHHHHcC-CCHHHHHHHHHHHhhcCccceeecccCCE
Q 013640 319 PFLGKRVEDSNFATVPLRDEFLENARLFIFETYCRIHQRIDMAVLAEKLN-LNYEEAQRWIVNLIRNSKLDAKIDAKSGT 397 (439)
Q Consensus 319 ~FL~~~~~~~~~~~~~~~~~f~e~aR~~ife~ycriy~~I~I~~lA~~l~-~s~~~~E~wiv~lI~~~rL~aKID~~~g~ 397 (439)
+.- ++++..+-..+=+.+|.|.-.||.+|++..|.+--- +|.-++|+.||+..+++-+..+||..+|+
T Consensus 420 ~~~-----------~QYI~sLq~v~~~RllqQvSqiY~sIs~~~l~~La~F~~~~~lEk~~v~a~k~~~v~iriDH~~~~ 488 (988)
T KOG2072|consen 420 PDK-----------SQYIPSLQDVIILRLLQQVSQIYESISFERLYKLAPFFSAFELEKLLVEAAKHNDVSIRIDHESNS 488 (988)
T ss_pred CCc-----------cccchhHHHHHHHHHHHHHHHHHHHHhHHHHHHHHhhcCHHHHHHHHHHHHhccceeEEeccccce
Confidence 544 578888888888999999999999999887765322 77889999999999999999999999999
Q ss_pred EEeCC
Q 013640 398 VIMEP 402 (439)
Q Consensus 398 V~~~~ 402 (439)
|.-++
T Consensus 489 v~Fgs 493 (988)
T KOG2072|consen 489 VSFGS 493 (988)
T ss_pred eeecc
Confidence 98873
No 21
>KOG2582 consensus COP9 signalosome, subunit CSN3 [Posttranslational modification, protein turnover, chaperones; Signal transduction mechanisms]
Probab=96.13 E-value=0.12 Score=53.68 Aligned_cols=155 Identities=17% Similarity=0.243 Sum_probs=104.1
Q ss_pred HHHHHHHHHHHhcccccchHH-HHHHHhhhccCCcchHHHHHHHhhhcCChhHHHHHHHHHHHHhcCCcccccccccccc
Q 013640 252 LLRYLATAFIVNKRRRPQFKD-FIKVIQQEQNSYKDPITEFLACVYVNYDFDGAQKKMKECEEVILNDPFLGKRVEDSNF 330 (439)
Q Consensus 252 lLrYlvva~il~~~r~~~l~~-i~~vi~qe~~~Y~Dpit~f~~~lY~~fdF~~aq~~L~~~e~~i~~D~FL~~~~~~~~~ 330 (439)
.=+|+.+..|+++.-. .+|. --+.+..--+++..|-.+|.++ |-+-.-.+-+....+..+.+..|-=+
T Consensus 225 YkkylLvsLI~~GK~~-ql~k~ts~~~~r~~K~ms~pY~ef~~~-Y~~~~~~eLr~lVk~~~~rF~kDnnt--------- 293 (422)
T KOG2582|consen 225 YKKYLLVSLILTGKVF-QLPKNTSQNAGRFFKPMSNPYHEFLNV-YLKDSSTELRTLVKKHSERFTKDNNT--------- 293 (422)
T ss_pred HHHHHHHHhhhcCcee-eccccchhhhHHhcccCCchHHHHHHH-HhcCCcHHHHHHHHHHHHHHhhcCcH---------
Confidence 3478888888876442 3322 2233444446677888899966 55444444555555555556666433
Q ss_pred cccccHHHHHHHHHHHHHHHhhhhhccccHHHHHH--HcCCCHHHHHHHHHHHhhcCccceeecccCCEEEeCCCC----
Q 013640 331 ATVPLRDEFLENARLFIFETYCRIHQRIDMAVLAE--KLNLNYEEAQRWIVNLIRNSKLDAKIDAKSGTVIMEPTH---- 404 (439)
Q Consensus 331 ~~~~~~~~f~e~aR~~ife~ycriy~~I~I~~lA~--~l~~s~~~~E~wiv~lI~~~rL~aKID~~~g~V~~~~~~---- 404 (439)
..+.+-++..-..=....-+-|.+++|..||+ +|+ ++.++|+.|-+.|-+|++-|.|| |.|.-...+
T Consensus 294 ---~l~k~av~sl~k~nI~rltktF~sLsL~dIA~~vQLa-~~qevek~Ilqmie~~~i~a~iN---G~v~f~~n~e~~~ 366 (422)
T KOG2582|consen 294 ---GLAKQAVSSLYKKNIQRLTKTFLSLSLSDIASRVQLA-SAQEVEKYILQMIEDGEIFASIN---GMVFFTDNPEKYN 366 (422)
T ss_pred ---HHHHHHHHHHHHHHHHHHHHHHHHhhHHHHHHHHHhc-chHHHHHHHHHHhccCceEEEec---ceEEEecCcccCC
Confidence 46677777777777777889999999999999 565 45689999999999999999999 888765433
Q ss_pred -chhHHHHHHhhhhhhhHHHH
Q 013640 405 -PNVYEQLIDHTKGLSGRTYK 424 (439)
Q Consensus 405 -~~~yqqvi~kt~~L~~R~q~ 424 (439)
+..+..-|+.+..|..++..
T Consensus 367 SpeM~~nk~~~~~~L~e~l~~ 387 (422)
T KOG2582|consen 367 SPEMHENKIDLCIQLIEALKA 387 (422)
T ss_pred CHHHHhhHHHHHHHHHHHHHh
Confidence 33445445555544444433
No 22
>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=95.67 E-value=0.015 Score=45.96 Aligned_cols=49 Identities=27% Similarity=0.402 Sum_probs=39.6
Q ss_pred HHHHHhhhhhccccHHHHHHHcCCCHHHHHHHHHHHhhcCccceeecccC
Q 013640 346 FIFETYCRIHQRIDMAVLAEKLNLNYEEAQRWIVNLIRNSKLDAKIDAKS 395 (439)
Q Consensus 346 ~ife~ycriy~~I~I~~lA~~l~~s~~~~E~wiv~lI~~~rL~aKID~~~ 395 (439)
....+|++-+.++++..||..||+|++.+|..|-.+|+-|++. |++..+
T Consensus 3 ~~i~~~l~~~~~~S~~eLa~~~~~s~~~ve~mL~~l~~kG~I~-~~~~~~ 51 (69)
T PF09012_consen 3 QEIRDYLRERGRVSLAELAREFGISPEAVEAMLEQLIRKGYIR-KVDMSS 51 (69)
T ss_dssp HHHHHHHHHS-SEEHHHHHHHTT--HHHHHHHHHHHHCCTSCE-EEEEE-
T ss_pred HHHHHHHHHcCCcCHHHHHHHHCcCHHHHHHHHHHHHHCCcEE-EecCCC
Confidence 3467899999999999999999999999999999999999998 444443
No 23
>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=94.41 E-value=0.088 Score=50.01 Aligned_cols=73 Identities=21% Similarity=0.274 Sum_probs=43.7
Q ss_pred HHHHHHHhhhhhccccHHHHHHHcCCCHHHHHHHHHHHhhcCccceeecccCCEEEeCCCC--chhHHHHHHhhhh
Q 013640 344 RLFIFETYCRIHQRIDMAVLAEKLNLNYEEAQRWIVNLIRNSKLDAKIDAKSGTVIMEPTH--PNVYEQLIDHTKG 417 (439)
Q Consensus 344 R~~ife~ycriy~~I~I~~lA~~l~~s~~~~E~wiv~lI~~~rL~aKID~~~g~V~~~~~~--~~~yqqvi~kt~~ 417 (439)
-+.-|..|++-++.|.|..||..|||+..++-.-|-.|..+|+|.+-||- .|..+.-+|. ..+=+-|-.+|+.
T Consensus 100 lL~~Fi~yIK~~Kvv~ledla~~f~l~t~~~i~ri~~L~~~g~ltGv~Dd-rGkfIyIs~eE~~~va~fi~~rGRv 174 (188)
T PF09756_consen 100 LLQEFINYIKEHKVVNLEDLAAEFGLRTQDVINRIQELEAEGRLTGVIDD-RGKFIYISEEEMEAVAKFIKQRGRV 174 (188)
T ss_dssp HHHHHHHHHHH-SEE-HHHHHHHH-S-HHHHHHHHHHHHHHSSS-EEE-T-T--EEE-------------------
T ss_pred HHHHHHHHHHHcceeeHHHHHHHcCCCHHHHHHHHHHHHHCCCceeeEcC-CCCeEEecHHHHHHHHHHHHHcCCc
Confidence 45668899999999999999999999999999999999999999999997 5555555544 4555555555553
No 24
>KOG1497 consensus COP9 signalosome, subunit CSN4 [Posttranslational modification, protein turnover, chaperones; Signal transduction mechanisms]
Probab=94.20 E-value=7.9 Score=40.00 Aligned_cols=93 Identities=16% Similarity=0.277 Sum_probs=75.4
Q ss_pred HHHHHHHHHHHHHHHhhhhhccccHHHHHHHcCCCHHHHHHHHHHHhhcCccceeecccCCEEEeCCCCchhHHHHHHhh
Q 013640 336 RDEFLENARLFIFETYCRIHQRIDMAVLAEKLNLNYEEAQRWIVNLIRNSKLDAKIDAKSGTVIMEPTHPNVYEQLIDHT 415 (439)
Q Consensus 336 ~~~f~e~aR~~ife~ycriy~~I~I~~lA~~l~~s~~~~E~wiv~lI~~~rL~aKID~~~g~V~~~~~~~~~yqqvi~kt 415 (439)
.+.|+|.==+.+. +.|..|+.+.|+.-|+++++.+|+.-++.|..+|++|-||+.+|+|+-.. .+.|+|-=++-
T Consensus 300 ~ra~~EhNlls~S----kly~nisf~~Lg~ll~i~~ekaekiaa~MI~qeRmng~IDQ~egiihFe~--~e~l~~wdkqi 373 (399)
T KOG1497|consen 300 DRAVIEHNLLSAS----KLYNNISFEELGALLKIDAEKAEKIAAQMITQERMNGSIDQIEGIIHFED--REELPQWDKQI 373 (399)
T ss_pred hhHHHHHhHHHHH----HHHHhccHHHHHHHhCCCHHHHHHHHHHHHhHHHhccchHhhcceEeecc--hhhhhhhhHHH
Confidence 3455655444444 45788999999999999999999999999999999999999999998765 56677766777
Q ss_pred hhhhhHHHHHHHHHHhhhh
Q 013640 416 KGLSGRTYKLVGQLLEHAQ 434 (439)
Q Consensus 416 ~~L~~R~q~L~~~i~~~~~ 434 (439)
.+|.+-+++++-.|...++
T Consensus 374 ~sl~~qvNki~~~i~~~~s 392 (399)
T KOG1497|consen 374 QSLCNQVNKILDKISHYGS 392 (399)
T ss_pred HHHHHHHHHHHHHHHHhCc
Confidence 7889999998887765443
No 25
>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=93.98 E-value=3 Score=45.59 Aligned_cols=231 Identities=16% Similarity=0.195 Sum_probs=131.6
Q ss_pred HHHHHHhcCCChhHHHHHHHHHHHHHhcCChhhHHHHHHHHHhhccccchhHHHHHHHHHHHHh--hcCHHHHHHHHHHH
Q 013640 114 LQMLHDRYQIGPDQIEALYQYAKFQFECGNYSGAADYLYQYRALCTNSERRLSALWGKMAAEIL--MQNWDIALEELNQL 191 (439)
Q Consensus 114 ~~~l~~~~g~t~e~~~al~~~ak~~y~~Gdy~~A~~~L~~~~~~~~~~~~k~~~lwg~la~eIl--~~~w~~a~~~l~kl 191 (439)
++.|+++-+.-++....+-..|.++...|++++|...+..+....++.......++..+....- ..+.+....-...+
T Consensus 24 L~~L~~~~~~I~Dk~~~~E~rA~ll~kLg~~~eA~~~y~~Li~rNPdn~~Yy~~L~~~~g~~~~~~~~~~~~~~~~y~~l 103 (517)
T PF12569_consen 24 LEHLEKNEKQILDKLAVLEKRAELLLKLGRKEEAEKIYRELIDRNPDNYDYYRGLEEALGLQLQLSDEDVEKLLELYDEL 103 (517)
T ss_pred HHHHHhhhhhCCCHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHCCCcHHHHHHHHHHHhhhcccccccHHHHHHHHHHH
Confidence 4677777777788888889999999999999999999999998888776666666666544431 11122222223333
Q ss_pred HHHhcCCCCC--CChHHHHH-----H--HHHH---HHH---HHHH----HhcCccchH---HHHHHhcc----ccchhH-
Q 013640 192 KEKVDDPKSF--TSPLNQMQ-----S--RIWL---MHW---SLFI----FFNHDNGRT---LIIDLFNQ----DKYLNA- 244 (439)
Q Consensus 192 ke~id~~~~~--~~~l~~l~-----~--R~Wl---lHw---sLf~----~fn~~~~~~---~l~d~F~~----~~yl~~- 244 (439)
.+.+.. ++. +-||..+. . ..++ ++- |||. ++..+.-.. .+++.+.+ .+..+.
T Consensus 104 ~~~yp~-s~~~~rl~L~~~~g~~F~~~~~~yl~~~l~KgvPslF~~lk~Ly~d~~K~~~i~~l~~~~~~~l~~~~~~~~~ 182 (517)
T PF12569_consen 104 AEKYPR-SDAPRRLPLDFLEGDEFKERLDEYLRPQLRKGVPSLFSNLKPLYKDPEKAAIIESLVEEYVNSLESNGSFSNG 182 (517)
T ss_pred HHhCcc-ccchhHhhcccCCHHHHHHHHHHHHHHHHhcCCchHHHHHHHHHcChhHHHHHHHHHHHHHHhhcccCCCCCc
Confidence 333333 222 12221111 0 0111 122 3332 222221112 22222221 111111
Q ss_pred ------HHhhchhHHHHHHHHHHHhcccccchHHHHHHHhhhccCCcchHHHHH----HHhhhcCChhHHHHHHHHHHHH
Q 013640 245 ------IQTNAPHLLRYLATAFIVNKRRRPQFKDFIKVIQQEQNSYKDPITEFL----ACVYVNYDFDGAQKKMKECEEV 314 (439)
Q Consensus 245 ------Iqt~~p~lLrYlvva~il~~~r~~~l~~i~~vi~qe~~~Y~Dpit~f~----~~lY~~fdF~~aq~~L~~~e~~ 314 (439)
..+...|++.|++-.---.++..+.+.-|-+.|... +. +.+|+ ..+=...||++|-+.+..+.+.
T Consensus 183 ~~~~~~~p~~~lw~~~~lAqhyd~~g~~~~Al~~Id~aI~ht-Pt----~~ely~~KarilKh~G~~~~Aa~~~~~Ar~L 257 (517)
T PF12569_consen 183 DDEEKEPPSTLLWTLYFLAQHYDYLGDYEKALEYIDKAIEHT-PT----LVELYMTKARILKHAGDLKEAAEAMDEAREL 257 (517)
T ss_pred cccccCCchHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHhcC-CC----cHHHHHHHHHHHHHCCCHHHHHHHHHHHHhC
Confidence 112224776666443323333344444455555552 22 23333 2334568999999999999999
Q ss_pred hcCCcccccccccccccccccHHHHHHHHHHHHHHHhhhhhccccH
Q 013640 315 ILNDPFLGKRVEDSNFATVPLRDEFLENARLFIFETYCRIHQRIDM 360 (439)
Q Consensus 315 i~~D~FL~~~~~~~~~~~~~~~~~f~e~aR~~ife~ycriy~~I~I 360 (439)
=..|+||. +.|..+.+|+-+.--=+.-|..+.+-+-
T Consensus 258 D~~DRyiN----------sK~aKy~LRa~~~e~A~~~~~~Ftr~~~ 293 (517)
T PF12569_consen 258 DLADRYIN----------SKCAKYLLRAGRIEEAEKTASLFTREDV 293 (517)
T ss_pred ChhhHHHH----------HHHHHHHHHCCCHHHHHHHHHhhcCCCC
Confidence 99999995 6899999999888777777777777664
No 26
>PF09976 TPR_21: Tetratricopeptide repeat; InterPro: IPR018704 This domain, found in various hypothetical prokaryotic proteins, has no known function.
Probab=93.90 E-value=0.84 Score=40.45 Aligned_cols=76 Identities=26% Similarity=0.231 Sum_probs=60.4
Q ss_pred HHHHHhcCCChhHHHHHHHHHHHHHhcCChhhHHHHHHHHHhhccccchhHHHHHHHHHHHHhhcCHHHHHHHHHH
Q 013640 115 QMLHDRYQIGPDQIEALYQYAKFQFECGNYSGAADYLYQYRALCTNSERRLSALWGKMAAEILMQNWDIALEELNQ 190 (439)
Q Consensus 115 ~~l~~~~g~t~e~~~al~~~ak~~y~~Gdy~~A~~~L~~~~~~~~~~~~k~~~lwg~la~eIl~~~w~~a~~~l~k 190 (439)
+.+.+.++=++-...+.+.+|+.+++.|+|++|.+.|..+....+++..+--+.+..-.+.+..++++.|++.+..
T Consensus 35 ~~l~~~~~~s~ya~~A~l~lA~~~~~~g~~~~A~~~l~~~~~~~~d~~l~~~a~l~LA~~~~~~~~~d~Al~~L~~ 110 (145)
T PF09976_consen 35 EQLAKDYPSSPYAALAALQLAKAAYEQGDYDEAKAALEKALANAPDPELKPLARLRLARILLQQGQYDEALATLQQ 110 (145)
T ss_pred HHHHHHCCCChHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHhhCCCHHHHHHHHHHHHHHHHHcCCHHHHHHHHHh
Confidence 4556667757677889999999999999999999999999997755555555566666677778899999888754
No 27
>PRK15331 chaperone protein SicA; Provisional
Probab=93.50 E-value=0.29 Score=45.61 Aligned_cols=69 Identities=19% Similarity=0.137 Sum_probs=51.9
Q ss_pred HHHhcCCChhHHHHHHHHHHHHHhcCChhhHHHHHHHHHhhccccchhHHHHHHHHHHHHhhcCHHHHHHHH
Q 013640 117 LHDRYQIGPDQIEALYQYAKFQFECGNYSGAADYLYQYRALCTNSERRLSALWGKMAAEILMQNWDIALEEL 188 (439)
Q Consensus 117 l~~~~g~t~e~~~al~~~ak~~y~~Gdy~~A~~~L~~~~~~~~~~~~k~~~lwg~la~eIl~~~w~~a~~~l 188 (439)
++.-+|++.+.++.+|.+|.-+|..|+|++|..++..+.. -+...-+-..|.=+|-=+.++|+.|..--
T Consensus 26 lk~l~gis~~~le~iY~~Ay~~y~~Gk~~eA~~~F~~L~~---~d~~n~~Y~~GLaa~~Q~~k~y~~Ai~~Y 94 (165)
T PRK15331 26 LKDVHGIPQDMMDGLYAHAYEFYNQGRLDEAETFFRFLCI---YDFYNPDYTMGLAAVCQLKKQFQKACDLY 94 (165)
T ss_pred HHHHhCCCHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHH---hCcCcHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 4556899999999999999999999999999986655444 33333445566666666677887776643
No 28
>PRK15431 ferrous iron transport protein FeoC; Provisional
Probab=93.29 E-value=0.23 Score=40.72 Aligned_cols=53 Identities=17% Similarity=0.223 Sum_probs=45.5
Q ss_pred HHHHHHhhhhhccccHHHHHHHcCCCHHHHHHHHHHHhhcCccceeec-ccCCEE
Q 013640 345 LFIFETYCRIHQRIDMAVLAEKLNLNYEEAQRWIVNLIRNSKLDAKID-AKSGTV 398 (439)
Q Consensus 345 ~~ife~ycriy~~I~I~~lA~~l~~s~~~~E~wiv~lI~~~rL~aKID-~~~g~V 398 (439)
+.-...|++-|.+++...||..|++|++-+|..|..+++-||+. ||+ ...|+.
T Consensus 4 L~qlRd~l~~~gr~s~~~Ls~~~~~p~~~VeaMLe~l~~kGkve-rv~~~~~gC~ 57 (78)
T PRK15431 4 LIQVRDLLALRGRMEAAQISQTLNTPQPMINAMLQQLESMGKAV-RIQEEPDGCL 57 (78)
T ss_pred HHHHHHHHHHcCcccHHHHHHHHCcCHHHHHHHHHHHHHCCCeE-eeccCCCCCC
Confidence 45567899999999999999999999999999999999999996 665 334544
No 29
>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=92.75 E-value=0.65 Score=36.27 Aligned_cols=71 Identities=20% Similarity=0.199 Sum_probs=49.9
Q ss_pred hhHHHHHHHHHHHHHhcCChhhHHHHHHHHHhhccccc-hh---HHHHHHHHHHHHhhcCHHHHHHHHHHHHHHh
Q 013640 125 PDQIEALYQYAKFQFECGNYSGAADYLYQYRALCTNSE-RR---LSALWGKMAAEILMQNWDIALEELNQLKEKV 195 (439)
Q Consensus 125 ~e~~~al~~~ak~~y~~Gdy~~A~~~L~~~~~~~~~~~-~k---~~~lwg~la~eIl~~~w~~a~~~l~klke~i 195 (439)
|++...+..+|..+++.|+|+.|.+++..........+ .. ..++.+.=.+--..++++.|.+-..+.-++.
T Consensus 2 ~~~a~~~~~la~~~~~~~~~~~A~~~~~~al~~~~~~~~~~~~~a~~~~~lg~~~~~~g~~~~A~~~~~~al~i~ 76 (78)
T PF13424_consen 2 PDTANAYNNLARVYRELGRYDEALDYYEKALDIEEQLGDDHPDTANTLNNLGECYYRLGDYEEALEYYQKALDIF 76 (78)
T ss_dssp HHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHTTTHHHHHHHHHHHHHHHHHHTTHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHhhh
Confidence 56778899999999999999999999998887743222 22 3333333334444678888888888776654
No 30
>PF13174 TPR_6: Tetratricopeptide repeat; PDB: 3QKY_A 2XEV_A 3URZ_B 2Q7F_A.
Probab=92.44 E-value=0.21 Score=32.33 Aligned_cols=32 Identities=25% Similarity=0.551 Sum_probs=28.6
Q ss_pred HHHHHHHHHHHhcCChhhHHHHHHHHHhhccc
Q 013640 129 EALYQYAKFQFECGNYSGAADYLYQYRALCTN 160 (439)
Q Consensus 129 ~al~~~ak~~y~~Gdy~~A~~~L~~~~~~~~~ 160 (439)
+++|..|..+++.|++++|.+++..+...-++
T Consensus 1 ~a~~~~a~~~~~~g~~~~A~~~~~~~~~~~P~ 32 (33)
T PF13174_consen 1 DALYRLARCYYKLGDYDEAIEYFQRLIKRYPD 32 (33)
T ss_dssp HHHHHHHHHHHHHCHHHHHHHHHHHHHHHSTT
T ss_pred CHHHHHHHHHHHccCHHHHHHHHHHHHHHCcC
Confidence 58999999999999999999999998876554
No 31
>PF13432 TPR_16: Tetratricopeptide repeat; PDB: 3CVP_A 3CVL_A 3CVQ_A 3CV0_A 2GW1_B 3CVN_A 3QKY_A 2PL2_B.
Probab=92.41 E-value=0.72 Score=34.74 Aligned_cols=59 Identities=19% Similarity=0.107 Sum_probs=40.7
Q ss_pred HHHHHHHHhcCChhhHHHHHHHHHhhccccchhHHHHHHHHHHHHhhcCHHHHHHHHHHHHH
Q 013640 132 YQYAKFQFECGNYSGAADYLYQYRALCTNSERRLSALWGKMAAEILMQNWDIALEELNQLKE 193 (439)
Q Consensus 132 ~~~ak~~y~~Gdy~~A~~~L~~~~~~~~~~~~k~~~lwg~la~eIl~~~w~~a~~~l~klke 193 (439)
|.+|..+++.|+|+.|.+.+..+...- .....+.++.=.+-...++|+.|.....++-+
T Consensus 1 ~~~a~~~~~~g~~~~A~~~~~~~l~~~---P~~~~a~~~lg~~~~~~g~~~~A~~~~~~a~~ 59 (65)
T PF13432_consen 1 YALARALYQQGDYDEAIAAFEQALKQD---PDNPEAWYLLGRILYQQGRYDEALAYYERALE 59 (65)
T ss_dssp HHHHHHHHHCTHHHHHHHHHHHHHCCS---TTHHHHHHHHHHHHHHTT-HHHHHHHHHHHHH
T ss_pred ChHHHHHHHcCCHHHHHHHHHHHHHHC---CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHH
Confidence 567888888888888888877776644 23555666666666677888888776666544
No 32
>KOG2688 consensus Transcription-associated recombination protein - Thp1p [Cell cycle control, cell division, chromosome partitioning]
Probab=91.91 E-value=0.8 Score=48.15 Aligned_cols=128 Identities=16% Similarity=0.265 Sum_probs=82.7
Q ss_pred HHHHHHHHHHHhcccccchHHHHHHHhhhccCCcchHHHHHHHhhhcCChhHHHHHHHHHHHH-hcCCcccccccccccc
Q 013640 252 LLRYLATAFIVNKRRRPQFKDFIKVIQQEQNSYKDPITEFLACVYVNYDFDGAQKKMKECEEV-ILNDPFLGKRVEDSNF 330 (439)
Q Consensus 252 lLrYlvva~il~~~r~~~l~~i~~vi~qe~~~Y~Dpit~f~~~lY~~fdF~~aq~~L~~~e~~-i~~D~FL~~~~~~~~~ 330 (439)
++-|++.+.++.++ -+-+.++ ...+ .|-+..++.+ -..-+...+...|+..|.. ++.--|+
T Consensus 246 iliylip~~~llg~--~Pt~~lL---~~~~---~~~~~~lv~a-Vr~Gnl~~f~~al~~~E~~f~~~gi~l--------- 307 (394)
T KOG2688|consen 246 ILIYLIPTGLLLGR--IPTKELL---DFYT---LDKYSPLVQA-VRSGNLRLFDLALADNERFFIRSGIYL--------- 307 (394)
T ss_pred HHHHHhHHHHHhcc--CcchhhH---hHhh---HHhHHHHHHH-HHhccHHHHHHHHhhhHHHHHHhccHH---------
Confidence 67899999988765 2222222 2211 1222223312 1334455555888888853 3444444
Q ss_pred cccccHHHHHHHHHHHHHHH----hhhhh---ccccHHHHHHHcCCC------HHHHHHHHHHHhhcCccceeecccCCE
Q 013640 331 ATVPLRDEFLENARLFIFET----YCRIH---QRIDMAVLAEKLNLN------YEEAQRWIVNLIRNSKLDAKIDAKSGT 397 (439)
Q Consensus 331 ~~~~~~~~f~e~aR~~ife~----ycriy---~~I~I~~lA~~l~~s------~~~~E~wiv~lI~~~rL~aKID~~~g~ 397 (439)
.++..|...|.. -.+++ ++++++.+-..+-.+ .+++|.-||++|..|+|.|-|+-+...
T Consensus 308 --------~l~~l~lv~yrnL~kkv~~~~~~~~~lpls~~~~al~~~~~~~~~~deveciLa~lI~~G~ikgYish~~~~ 379 (394)
T KOG2688|consen 308 --------TLEKLPLVVYRNLFKKVIQLWGKTSQLPLSRFLTALQFSGVTDVDLDEVECILANLIDLGRIKGYISHQLQT 379 (394)
T ss_pred --------HhhhhhHHHHHHHHHHHHHHhCCCCCCCHHHHHHHHhhcCCCCCchhhHHHHHHhhhhhccccchhchhhhe
Confidence 233355554433 23566 788888888887644 589999999999999999999999999
Q ss_pred EEeCCCCc
Q 013640 398 VIMEPTHP 405 (439)
Q Consensus 398 V~~~~~~~ 405 (439)
++....++
T Consensus 380 ~V~sK~~p 387 (394)
T KOG2688|consen 380 LVFSKKDP 387 (394)
T ss_pred EEEecCCC
Confidence 99988774
No 33
>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=91.68 E-value=0.23 Score=37.69 Aligned_cols=55 Identities=22% Similarity=0.280 Sum_probs=39.8
Q ss_pred HHHHhcCCChhHHHHHHHHHHHHHhcCChhhHHHHHHHHHhhccccchhHHHHHHH
Q 013640 116 MLHDRYQIGPDQIEALYQYAKFQFECGNYSGAADYLYQYRALCTNSERRLSALWGK 171 (439)
Q Consensus 116 ~l~~~~g~t~e~~~al~~~ak~~y~~Gdy~~A~~~L~~~~~~~~~~~~k~~~lwg~ 171 (439)
.+++-....|+..+..+.+|+.+++.|++++|.+.|..+....+++ .....+|.+
T Consensus 13 ~~~~~l~~~p~~~~~~~~la~~~~~~g~~~~A~~~l~~~~~~~~~~-~~~~~l~a~ 67 (68)
T PF14559_consen 13 LLEKALQRNPDNPEARLLLAQCYLKQGQYDEAEELLERLLKQDPDN-PEYQQLLAQ 67 (68)
T ss_dssp HHHHHHHHTTTSHHHHHHHHHHHHHTT-HHHHHHHHHCCHGGGTTH-HHHHHHHHH
T ss_pred HHHHHHHHCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHCcCH-HHHHHHHhc
Confidence 3444444567778899999999999999999999998888866542 444444443
No 34
>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=91.45 E-value=14 Score=39.17 Aligned_cols=199 Identities=16% Similarity=0.216 Sum_probs=106.4
Q ss_pred HHHHHHHHHHhcCChhhHHHHHHHHHhhccccchhHHHHHHHHHHHHhh-----------cCHHHHHHHHHHHHHHhcCC
Q 013640 130 ALYQYAKFQFECGNYSGAADYLYQYRALCTNSERRLSALWGKMAAEILM-----------QNWDIALEELNQLKEKVDDP 198 (439)
Q Consensus 130 al~~~ak~~y~~Gdy~~A~~~L~~~~~~~~~~~~k~~~lwg~la~eIl~-----------~~w~~a~~~l~klke~id~~ 198 (439)
++.-+.++++=-|||..|.+.|...-. +++. .+|.+.+|-|-. ..+..|.+-+..+=-.+.++
T Consensus 124 SligLlRvh~LLGDY~~Alk~l~~idl-----~~~~-l~~~V~~~~is~~YyvGFaylMlrRY~DAir~f~~iL~yi~r~ 197 (404)
T PF10255_consen 124 SLIGLLRVHCLLGDYYQALKVLENIDL-----NKKG-LYTKVPACHISTYYYVGFAYLMLRRYADAIRTFSQILLYIQRT 197 (404)
T ss_pred HHHHHHHHHHhccCHHHHHHHhhccCc-----ccch-hhccCcchheehHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 557788999999999999998876533 2222 666666665432 23333433333332222221
Q ss_pred CCCCChHHHHHHHHHHHHHHHHHHhcCccchHHHHHHhccccchhHHHhhchhHHHHHHHHHHHhcccccchHH-HHHHH
Q 013640 199 KSFTSPLNQMQSRIWLMHWSLFIFFNHDNGRTLIIDLFNQDKYLNAIQTNAPHLLRYLATAFIVNKRRRPQFKD-FIKVI 277 (439)
Q Consensus 199 ~~~~~~l~~l~~R~WllHwsLf~~fn~~~~~~~l~d~F~~~~yl~~Iqt~~p~lLrYlvva~il~~~r~~~l~~-i~~vi 277 (439)
+ .++++| +..| ..|.-.+....--++++..++..| ++| |...+
T Consensus 198 k------~~~~~~--------------------------~~q~-d~i~K~~eqMyaLlAic~~l~p~~---lde~i~~~l 241 (404)
T PF10255_consen 198 K------NQYHQR--------------------------SYQY-DQINKKNEQMYALLAICLSLCPQR---LDESISSQL 241 (404)
T ss_pred h------hhhccc--------------------------cchh-hHHHhHHHHHHHHHHHHHHhCCCC---CCHHHHHHH
Confidence 1 001100 1111 122222333334455555555444 544 44444
Q ss_pred hhhccCCcchHHHHHHHhhhcCChhHHHHHHHHHHH-HhcCC---ccccccccccc-ccccccHHHHHHHHH----HHHH
Q 013640 278 QQEQNSYKDPITEFLACVYVNYDFDGAQKKMKECEE-VILND---PFLGKRVEDSN-FATVPLRDEFLENAR----LFIF 348 (439)
Q Consensus 278 ~qe~~~Y~Dpit~f~~~lY~~fdF~~aq~~L~~~e~-~i~~D---~FL~~~~~~~~-~~~~~~~~~f~e~aR----~~if 348 (439)
.. . |.|-+..+-. .|.+.+.+.+..|.- -|..- .+- ......| -....+.+-|+++++ +-..
T Consensus 242 ke-k--y~ek~~kmq~-----gd~~~f~elF~~acPKFIsp~~pp~~~-~~~~~~~~e~~~~Ql~~Fl~eV~~q~~l~~l 312 (404)
T PF10255_consen 242 KE-K--YGEKMEKMQR-----GDEEAFEELFSFACPKFISPVSPPDYD-GPSQNKNKEPYRRQLKLFLDEVKQQQKLPTL 312 (404)
T ss_pred HH-H--HHHHHHHHHc-----cCHHHHHHHHHhhCCCccCCCCCCCcc-cccchhhhhHHHHHHHHHHHHHHHhhhhhHH
Confidence 43 2 6666655442 366666666665543 22211 110 0000000 011135556666655 4468
Q ss_pred HHhhhhhccccHHHHHHHcCCCHHHHHHHHH
Q 013640 349 ETYCRIHQRIDMAVLAEKLNLNYEEAQRWIV 379 (439)
Q Consensus 349 e~ycriy~~I~I~~lA~~l~~s~~~~E~wiv 379 (439)
..|++.|++|+++-||.-++|+++++-.+|.
T Consensus 313 RSyLKLYtti~l~KLA~fl~vd~~~lr~~Ll 343 (404)
T PF10255_consen 313 RSYLKLYTTIPLEKLASFLDVDEEELRSQLL 343 (404)
T ss_pred HHHHHhhcCCCHHHHHHHcCCCHHHHHHHHH
Confidence 8999999999999999999999999888885
No 35
>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=91.35 E-value=3.3 Score=33.85 Aligned_cols=67 Identities=18% Similarity=0.154 Sum_probs=46.7
Q ss_pred HHHHHHHHHHHhcCChhhHHHHHHHHHhhccccchhHHHHHHHHHHHHhhcCHHHHHHHHHHHHHHh
Q 013640 129 EALYQYAKFQFECGNYSGAADYLYQYRALCTNSERRLSALWGKMAAEILMQNWDIALEELNQLKEKV 195 (439)
Q Consensus 129 ~al~~~ak~~y~~Gdy~~A~~~L~~~~~~~~~~~~k~~~lwg~la~eIl~~~w~~a~~~l~klke~i 195 (439)
+.+|..|..+++.|+|+.|.+.+..+....++......+.+..-.+-.-.++++.|.+...++-...
T Consensus 3 ~~~~~~~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~ 69 (119)
T TIGR02795 3 EAYYDAALLVLKAGDYADAIQAFQAFLKKYPKSTYAPNAHYWLGEAYYAQGKYADAAKAFLAVVKKY 69 (119)
T ss_pred HHHHHHHHHHHHcCCHHHHHHHHHHHHHHCCCccccHHHHHHHHHHHHhhccHHHHHHHHHHHHHHC
Confidence 5678888888888888888888888877655443334455545555555677888877777765544
No 36
>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=90.62 E-value=0.87 Score=34.65 Aligned_cols=54 Identities=15% Similarity=0.204 Sum_probs=44.0
Q ss_pred HHHHHHHhhhhhccccHHHHHHHcCCCHHHHHHHHHHHhhcCccceeecccCCEEEeC
Q 013640 344 RLFIFETYCRIHQRIDMAVLAEKLNLNYEEAQRWIVNLIRNSKLDAKIDAKSGTVIME 401 (439)
Q Consensus 344 R~~ife~ycriy~~I~I~~lA~~l~~s~~~~E~wiv~lI~~~rL~aKID~~~g~V~~~ 401 (439)
|......|++-+..++++.||+.||+|+.-+-+.|..|-..|. |..+.|-++..
T Consensus 1 R~~~Il~~l~~~~~~s~~ela~~~~VS~~TiRRDl~~L~~~g~----i~r~~GG~~~~ 54 (57)
T PF08220_consen 1 RQQQILELLKEKGKVSVKELAEEFGVSEMTIRRDLNKLEKQGL----IKRTHGGAVLN 54 (57)
T ss_pred CHHHHHHHHHHcCCEEHHHHHHHHCcCHHHHHHHHHHHHHCCC----EEEEcCEEEeC
Confidence 4455667889999999999999999999999999999988775 44556655544
No 37
>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=90.61 E-value=1.2 Score=33.85 Aligned_cols=63 Identities=22% Similarity=0.380 Sum_probs=45.9
Q ss_pred HHHHHHHHHHHHhcCChhhHHHHHHHHHhhccccchhHHHHHHHHHHHHhhc-CHHHHHHHHHHHHH
Q 013640 128 IEALYQYAKFQFECGNYSGAADYLYQYRALCTNSERRLSALWGKMAAEILMQ-NWDIALEELNQLKE 193 (439)
Q Consensus 128 ~~al~~~ak~~y~~Gdy~~A~~~L~~~~~~~~~~~~k~~~lwg~la~eIl~~-~w~~a~~~l~klke 193 (439)
-+.++.+|..+++.|+|+.|.+++.......++. ..++.++=.+-...+ +|+.|.+...+.-+
T Consensus 3 a~~~~~~g~~~~~~~~~~~A~~~~~~ai~~~p~~---~~~~~~~g~~~~~~~~~~~~A~~~~~~al~ 66 (69)
T PF13414_consen 3 AEAWYNLGQIYFQQGDYEEAIEYFEKAIELDPNN---AEAYYNLGLAYMKLGKDYEEAIEDFEKALK 66 (69)
T ss_dssp HHHHHHHHHHHHHTTHHHHHHHHHHHHHHHSTTH---HHHHHHHHHHHHHTTTHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHcCCHHHHHHHHHHHHHcCCCC---HHHHHHHHHHHHHhCccHHHHHHHHHHHHH
Confidence 3578899999999999999999999988875442 223333333444456 68999988887654
No 38
>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=90.41 E-value=31 Score=37.79 Aligned_cols=62 Identities=11% Similarity=0.113 Sum_probs=37.2
Q ss_pred HHHHHHHHHHHhcCChhhHHHHHHHHHhhccccchhHHHHHHHHHHHHhhcCHHHHHHHHHHHHH
Q 013640 129 EALYQYAKFQFECGNYSGAADYLYQYRALCTNSERRLSALWGKMAAEILMQNWDIALEELNQLKE 193 (439)
Q Consensus 129 ~al~~~ak~~y~~Gdy~~A~~~L~~~~~~~~~~~~k~~~lwg~la~eIl~~~w~~a~~~l~klke 193 (439)
..++.+|..++..|+++.|.+.+..+....+++. ......-.+-...++|+.|.+.+.++-+
T Consensus 737 ~~~~~l~~~~~~~g~~~~A~~~~~~~l~~~~~~~---~~~~~la~~~~~~g~~~~A~~~~~~~~~ 798 (899)
T TIGR02917 737 QNAIKLHRALLASGNTAEAVKTLEAWLKTHPNDA---VLRTALAELYLAQKDYDKAIKHYRTVVK 798 (899)
T ss_pred hHHHHHHHHHHHCCCHHHHHHHHHHHHHhCCCCH---HHHHHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 5667778888888888888887777776544321 1111111222235777777776666543
No 39
>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=90.29 E-value=0.63 Score=30.32 Aligned_cols=32 Identities=31% Similarity=0.475 Sum_probs=27.2
Q ss_pred HHHHHHHHHHHhcCChhhHHHHHHHHHhhccc
Q 013640 129 EALYQYAKFQFECGNYSGAADYLYQYRALCTN 160 (439)
Q Consensus 129 ~al~~~ak~~y~~Gdy~~A~~~L~~~~~~~~~ 160 (439)
+.++.+|..++..|+|++|.+.+.....+.++
T Consensus 2 ~~~~~lg~~~~~~~~~~~A~~~~~~al~l~p~ 33 (34)
T PF07719_consen 2 EAWYYLGQAYYQLGNYEEAIEYFEKALELDPN 33 (34)
T ss_dssp HHHHHHHHHHHHTT-HHHHHHHHHHHHHHSTT
T ss_pred HHHHHHHHHHHHhCCHHHHHHHHHHHHHHCcC
Confidence 46889999999999999999999988877654
No 40
>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=90.22 E-value=13 Score=33.18 Aligned_cols=64 Identities=14% Similarity=0.153 Sum_probs=39.0
Q ss_pred HHHHHHHHHHHHhcCChhhHHHHHHHHHhhccccchhHHHHHHHHHHHHhhcCHHHHHHHHHHHHHH
Q 013640 128 IEALYQYAKFQFECGNYSGAADYLYQYRALCTNSERRLSALWGKMAAEILMQNWDIALEELNQLKEK 194 (439)
Q Consensus 128 ~~al~~~ak~~y~~Gdy~~A~~~L~~~~~~~~~~~~k~~~lwg~la~eIl~~~w~~a~~~l~klke~ 194 (439)
...++.+|..+++.|+++.|.+++.......++. ....+..-.+-...++++.|...+.+..+.
T Consensus 135 ~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~---~~~~~~la~~~~~~~~~~~A~~~~~~~~~~ 198 (234)
T TIGR02521 135 ARSLENAGLCALKAGDFDKAEKYLTRALQIDPQR---PESLLELAELYYLRGQYKDARAYLERYQQT 198 (234)
T ss_pred hHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCcCC---hHHHHHHHHHHHHcCCHHHHHHHHHHHHHh
Confidence 3456667777777777777777777666544332 223333334444466777777777766665
No 41
>PF12895 Apc3: Anaphase-promoting complex, cyclosome, subunit 3; PDB: 3KAE_D 3Q4A_B 2C2L_D 3Q47_B 3Q49_B 2XPI_A 3ULQ_A.
Probab=90.13 E-value=0.83 Score=36.48 Aligned_cols=59 Identities=17% Similarity=0.255 Sum_probs=43.3
Q ss_pred HHHHHHHHHHHHhcCChhhHHHHHHHHHhhccccchhHHHHHHHHHHHHhhcCHHHHHHHHHH
Q 013640 128 IEALYQYAKFQFECGNYSGAADYLYQYRALCTNSERRLSALWGKMAAEILMQNWDIALEELNQ 190 (439)
Q Consensus 128 ~~al~~~ak~~y~~Gdy~~A~~~L~~~~~~~~~~~~k~~~lwg~la~eIl~~~w~~a~~~l~k 190 (439)
-..++.+|..+|+.|+|++|.+++.. .. . .+...++.|-.=.|=+..++|+.|.+-+.+
T Consensus 25 ~~~~~~la~~~~~~~~y~~A~~~~~~-~~--~-~~~~~~~~~l~a~~~~~l~~y~eAi~~l~~ 83 (84)
T PF12895_consen 25 SAYLYNLAQCYFQQGKYEEAIELLQK-LK--L-DPSNPDIHYLLARCLLKLGKYEEAIKALEK 83 (84)
T ss_dssp HHHHHHHHHHHHHTTHHHHHHHHHHC-HT--H-HHCHHHHHHHHHHHHHHTT-HHHHHHHHHH
T ss_pred HHHHHHHHHHHHHCCCHHHHHHHHHH-hC--C-CCCCHHHHHHHHHHHHHhCCHHHHHHHHhc
Confidence 44677789999999999999999987 22 1 223355666555677778999999887765
No 42
>PRK10803 tol-pal system protein YbgF; Provisional
Probab=89.71 E-value=2.9 Score=41.61 Aligned_cols=71 Identities=17% Similarity=0.087 Sum_probs=58.8
Q ss_pred HHHHHHHHHHHHHhcCChhhHHHHHHHHHhhccccchhHHHHHHHHHHHHhhcCHHHHHHHHHHHHHHhcC
Q 013640 127 QIEALYQYAKFQFECGNYSGAADYLYQYRALCTNSERRLSALWGKMAAEILMQNWDIALEELNQLKEKVDD 197 (439)
Q Consensus 127 ~~~al~~~ak~~y~~Gdy~~A~~~L~~~~~~~~~~~~k~~~lwg~la~eIl~~~w~~a~~~l~klke~id~ 197 (439)
.-+++|.+|..||..|+|+.|...+..+...-+++.+.-++++-.-.+-.-.++++.|.+.++++-+.+.+
T Consensus 179 a~~A~y~LG~~y~~~g~~~~A~~~f~~vv~~yP~s~~~~dAl~klg~~~~~~g~~~~A~~~~~~vi~~yP~ 249 (263)
T PRK10803 179 QPNANYWLGQLNYNKGKKDDAAYYFASVVKNYPKSPKAADAMFKVGVIMQDKGDTAKAKAVYQQVIKKYPG 249 (263)
T ss_pred hHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHCCCCcchhHHHHHHHHHHHHcCCHHHHHHHHHHHHHHCcC
Confidence 35799999999999999999999999988877877778888876655556678999999888877666554
No 43
>PRK15363 pathogenicity island 2 chaperone protein SscA; Provisional
Probab=89.59 E-value=1.7 Score=40.32 Aligned_cols=75 Identities=19% Similarity=0.260 Sum_probs=52.1
Q ss_pred hccHHHHHHhcCCC-hhHHHHHHHHHHHHHhcCChhhHHHHHHHHHhhccccchhHHHHHHHHHHHHhhcCHHHHHHHHH
Q 013640 111 HYNLQMLHDRYQIG-PDQIEALYQYAKFQFECGNYSGAADYLYQYRALCTNSERRLSALWGKMAAEILMQNWDIALEELN 189 (439)
Q Consensus 111 ~~n~~~l~~~~g~t-~e~~~al~~~ak~~y~~Gdy~~A~~~L~~~~~~~~~~~~k~~~lwg~la~eIl~~~w~~a~~~l~ 189 (439)
.-++..| .+++ +|.++.+|.+|..+|+.|+|++|..++.. +|.-+.....-..|.=+|-=.+++|+.|.+--.
T Consensus 20 Ggsl~~l---~~~~~~~~l~~lY~~A~~ly~~G~l~~A~~~f~~---L~~~Dp~~~~y~~gLG~~~Q~~g~~~~AI~aY~ 93 (157)
T PRK15363 20 GGSLRML---LDDDVTQPLNTLYRYAMQLMEVKEFAGAARLFQL---LTIYDAWSFDYWFRLGECCQAQKHWGEAIYAYG 93 (157)
T ss_pred CCcHHHH---HCCChHHHHHHHHHHHHHHHHCCCHHHHHHHHHH---HHHhCcccHHHHHHHHHHHHHHhhHHHHHHHHH
Confidence 3344454 3688 99999999999999999999999976544 444344445555555555555677777776555
Q ss_pred HH
Q 013640 190 QL 191 (439)
Q Consensus 190 kl 191 (439)
++
T Consensus 94 ~A 95 (157)
T PRK15363 94 RA 95 (157)
T ss_pred HH
Confidence 44
No 44
>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=89.36 E-value=2.5 Score=31.19 Aligned_cols=63 Identities=21% Similarity=0.267 Sum_probs=41.3
Q ss_pred hHHHHHHHHHHHHHhcCChhhHHHHHHHHHhhccccchhHHHHHHHHHHHHhhcCHHHHHHHHHHH
Q 013640 126 DQIEALYQYAKFQFECGNYSGAADYLYQYRALCTNSERRLSALWGKMAAEILMQNWDIALEELNQL 191 (439)
Q Consensus 126 e~~~al~~~ak~~y~~Gdy~~A~~~L~~~~~~~~~~~~k~~~lwg~la~eIl~~~w~~a~~~l~kl 191 (439)
..-...+.+|..++..|+++.|.+++.......+... ...+..-.+-...++++.|.+.+.++
T Consensus 32 ~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~---~~~~~~~~~~~~~~~~~~a~~~~~~~ 94 (100)
T cd00189 32 DNADAYYNLAAAYYKLGKYEEALEDYEKALELDPDNA---KAYYNLGLAYYKLGKYEEALEAYEKA 94 (100)
T ss_pred ccHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCcch---hHHHHHHHHHHHHHhHHHHHHHHHHH
Confidence 3336788889999999999999988887776544333 33333333444456677776665554
No 45
>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=89.28 E-value=4.3 Score=33.21 Aligned_cols=70 Identities=17% Similarity=0.119 Sum_probs=51.4
Q ss_pred HHHHHHHHHHHHHhcCChhhHHHHHHHHHhhccccchhHHHHHHHHHHHHhhcCHHHHHHHHHHHHHHhc
Q 013640 127 QIEALYQYAKFQFECGNYSGAADYLYQYRALCTNSERRLSALWGKMAAEILMQNWDIALEELNQLKEKVD 196 (439)
Q Consensus 127 ~~~al~~~ak~~y~~Gdy~~A~~~L~~~~~~~~~~~~k~~~lwg~la~eIl~~~w~~a~~~l~klke~id 196 (439)
..++.+.+|..++..|+|+.|.+++..+....++......+++..-.+-.-.++++.|.+.+.++.+...
T Consensus 38 ~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~A~~~~~~~~~~~p 107 (119)
T TIGR02795 38 APNAHYWLGEAYYAQGKYADAAKAFLAVVKKYPKSPKAPDALLKLGMSLQELGDKEKAKATLQQVIKRYP 107 (119)
T ss_pred cHHHHHHHHHHHHhhccHHHHHHHHHHHHHHCCCCCcccHHHHHHHHHHHHhCChHHHHHHHHHHHHHCc
Confidence 3568899999999999999999999999887665433334444444444557888888888777766543
No 46
>KOG3060 consensus Uncharacterized conserved protein [Function unknown]
Probab=88.62 E-value=11 Score=37.76 Aligned_cols=72 Identities=15% Similarity=0.158 Sum_probs=49.5
Q ss_pred HHHHHhcCCChhHHHHHHHHHHHHHhcCChhhHHHHHHHHHhhccccchhHHHHHHHHHHHHhhcCHHHHHHHHHHHHHH
Q 013640 115 QMLHDRYQIGPDQIEALYQYAKFQFECGNYSGAADYLYQYRALCTNSERRLSALWGKMAAEILMQNWDIALEELNQLKEK 194 (439)
Q Consensus 115 ~~l~~~~g~t~e~~~al~~~ak~~y~~Gdy~~A~~~L~~~~~~~~~~~~k~~~lwg~la~eIl~~~w~~a~~~l~klke~ 194 (439)
++|....+ ++| +.-.+|.+|...|+|++|.=++.++....+. ...+++.||==..+. +-.+++.-.+..
T Consensus 145 ~YL~~F~~-D~E---AW~eLaeiY~~~~~f~kA~fClEE~ll~~P~----n~l~f~rlae~~Yt~---gg~eN~~~arky 213 (289)
T KOG3060|consen 145 EYLDKFMN-DQE---AWHELAEIYLSEGDFEKAAFCLEELLLIQPF----NPLYFQRLAEVLYTQ---GGAENLELARKY 213 (289)
T ss_pred HHHHHhcC-cHH---HHHHHHHHHHhHhHHHHHHHHHHHHHHcCCC----cHHHHHHHHHHHHHH---hhHHHHHHHHHH
Confidence 57777777 655 8999999999999999999999888774443 345666665333332 234445555555
Q ss_pred hcC
Q 013640 195 VDD 197 (439)
Q Consensus 195 id~ 197 (439)
+.+
T Consensus 214 y~~ 216 (289)
T KOG3060|consen 214 YER 216 (289)
T ss_pred HHH
Confidence 554
No 47
>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=88.53 E-value=1.5 Score=32.43 Aligned_cols=47 Identities=26% Similarity=0.288 Sum_probs=35.3
Q ss_pred HHHHhhhhhccccHHHHHHHcCCCHHHHHHHHHHHhhcCccceeecccCC
Q 013640 347 IFETYCRIHQRIDMAVLAEKLNLNYEEAQRWIVNLIRNSKLDAKIDAKSG 396 (439)
Q Consensus 347 ife~ycriy~~I~I~~lA~~l~~s~~~~E~wiv~lI~~~rL~aKID~~~g 396 (439)
+...++.-...|+.+.||+.||||..-+.+.|..+-..+ +.|.++.|
T Consensus 5 il~~L~~~~~~it~~eLa~~l~vS~rTi~~~i~~L~~~~---~~I~~~~~ 51 (55)
T PF08279_consen 5 ILKLLLESKEPITAKELAEELGVSRRTIRRDIKELREWG---IPIESKRG 51 (55)
T ss_dssp HHHHHHHTTTSBEHHHHHHHCTS-HHHHHHHHHHHHHTT----EEEEETT
T ss_pred HHHHHHHcCCCcCHHHHHHHhCCCHHHHHHHHHHHHHCC---CeEEeeCC
Confidence 344444666669999999999999999999999997766 56666554
No 48
>PF13176 TPR_7: Tetratricopeptide repeat; PDB: 3SF4_C 3RO3_A 3RO2_A.
Probab=88.40 E-value=0.73 Score=31.42 Aligned_cols=32 Identities=28% Similarity=0.387 Sum_probs=25.9
Q ss_pred HHHHHHHHHHhcCChhhHHHHHHHHHhhcccc
Q 013640 130 ALYQYAKFQFECGNYSGAADYLYQYRALCTNS 161 (439)
Q Consensus 130 al~~~ak~~y~~Gdy~~A~~~L~~~~~~~~~~ 161 (439)
++..+|.+|.+.|+|++|.+++.....+..+.
T Consensus 1 al~~Lg~~~~~~g~~~~Ai~~y~~aL~l~~~~ 32 (36)
T PF13176_consen 1 ALNNLGRIYRQQGDYEKAIEYYEQALALARDP 32 (36)
T ss_dssp HHHHHHHHHHHCT-HHHHHHHHHHHHHHHHHC
T ss_pred CHHHHHHHHHHcCCHHHHHHHHHHHHHhcccc
Confidence 46789999999999999999999877665443
No 49
>PF13525 YfiO: Outer membrane lipoprotein; PDB: 3TGO_A 3Q5M_A 2YHC_A.
Probab=88.31 E-value=2.9 Score=39.41 Aligned_cols=70 Identities=20% Similarity=0.142 Sum_probs=58.0
Q ss_pred HHHHHHHHHHHHhcCChhhHHHHHHHHHhhccccchhHHHHHHHHHHHHhhcCHHHHHHHHHHHHHHhcC
Q 013640 128 IEALYQYAKFQFECGNYSGAADYLYQYRALCTNSERRLSALWGKMAAEILMQNWDIALEELNQLKEKVDD 197 (439)
Q Consensus 128 ~~al~~~ak~~y~~Gdy~~A~~~L~~~~~~~~~~~~k~~~lwg~la~eIl~~~w~~a~~~l~klke~id~ 197 (439)
-+++|..|.-.++.|+|+.|.+.|..+...-+++...-++.+...-+-.-.++++.|....+++-+.+-+
T Consensus 5 ~~~lY~~a~~~~~~g~y~~Ai~~f~~l~~~~P~s~~a~~A~l~la~a~y~~~~y~~A~~~~~~fi~~yP~ 74 (203)
T PF13525_consen 5 AEALYQKALEALQQGDYEEAIKLFEKLIDRYPNSPYAPQAQLMLAYAYYKQGDYEEAIAAYERFIKLYPN 74 (203)
T ss_dssp HHHHHHHHHHHHHCT-HHHHHHHHHHHHHH-TTSTTHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHH-TT
T ss_pred HHHHHHHHHHHHHCCCHHHHHHHHHHHHHHCCCChHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHCCC
Confidence 3589999999999999999999999999988887777888888888888899999999888888776665
No 50
>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=88.20 E-value=0.82 Score=35.68 Aligned_cols=37 Identities=27% Similarity=0.437 Sum_probs=33.7
Q ss_pred HHHHHHHhhhhhccccHHHHHHHcCCCHHHHHHHHHH
Q 013640 344 RLFIFETYCRIHQRIDMAVLAEKLNLNYEEAQRWIVN 380 (439)
Q Consensus 344 R~~ife~ycriy~~I~I~~lA~~l~~s~~~~E~wiv~ 380 (439)
|-.+|+-|.+.=..|++..||++||||+.-+-+|=+.
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 5678999999888999999999999999999999765
No 51
>PF14938 SNAP: Soluble NSF attachment protein, SNAP; PDB: 1QQE_A 2IFU_A.
Probab=87.53 E-value=27 Score=34.56 Aligned_cols=33 Identities=15% Similarity=0.268 Sum_probs=24.4
Q ss_pred HHHHHHHhhhcCChhHHHHHHHHHHHHhcCCccc
Q 013640 288 ITEFLACVYVNYDFDGAQKKMKECEEVILNDPFL 321 (439)
Q Consensus 288 it~f~~~lY~~fdF~~aq~~L~~~e~~i~~D~FL 321 (439)
+.+++ ..|.+.|-+.+...+.+-..+-+-|.+.
T Consensus 238 ~~~l~-~A~~~~D~e~f~~av~~~d~~~~ld~w~ 270 (282)
T PF14938_consen 238 LEDLL-EAYEEGDVEAFTEAVAEYDSISRLDNWK 270 (282)
T ss_dssp HHHHH-HHHHTT-CCCHHHHCHHHTTSS---HHH
T ss_pred HHHHH-HHHHhCCHHHHHHHHHHHcccCccHHHH
Confidence 66777 4589999999999999999888888887
No 52
>PF13371 TPR_9: Tetratricopeptide repeat
Probab=87.24 E-value=1.1 Score=34.32 Aligned_cols=48 Identities=27% Similarity=0.411 Sum_probs=40.3
Q ss_pred HHHHHHhcCCChhHHHHHHHHHHHHHhcCChhhHHHHHHHHHhhcccc
Q 013640 114 LQMLHDRYQIGPDQIEALYQYAKFQFECGNYSGAADYLYQYRALCTNS 161 (439)
Q Consensus 114 ~~~l~~~~g~t~e~~~al~~~ak~~y~~Gdy~~A~~~L~~~~~~~~~~ 161 (439)
++.++.-..+.|+....++.+|.+++..|+|+.|.+.|..+...++++
T Consensus 15 ~~~~~~~l~~~p~~~~~~~~~a~~~~~~g~~~~A~~~l~~~l~~~p~~ 62 (73)
T PF13371_consen 15 LEVLERALELDPDDPELWLQRARCLFQLGRYEEALEDLERALELSPDD 62 (73)
T ss_pred HHHHHHHHHhCcccchhhHHHHHHHHHhccHHHHHHHHHHHHHHCCCc
Confidence 345566666788888899999999999999999999999999888753
No 53
>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=87.24 E-value=2.6 Score=31.11 Aligned_cols=61 Identities=23% Similarity=0.361 Sum_probs=42.5
Q ss_pred HHHHHHHHHHhcCChhhHHHHHHHHHhhccccchhHHHHHHHHHHHHhhcCHHHHHHHHHHHHH
Q 013640 130 ALYQYAKFQFECGNYSGAADYLYQYRALCTNSERRLSALWGKMAAEILMQNWDIALEELNQLKE 193 (439)
Q Consensus 130 al~~~ak~~y~~Gdy~~A~~~L~~~~~~~~~~~~k~~~lwg~la~eIl~~~w~~a~~~l~klke 193 (439)
+++..|..++..|+++.|.+.+.......+... ...+..-.+-...++++.|.+.+.++-.
T Consensus 2 ~~~~~a~~~~~~~~~~~A~~~~~~~~~~~~~~~---~~~~~~~~~~~~~~~~~~a~~~~~~~~~ 62 (100)
T cd00189 2 ALLNLGNLYYKLGDYDEALEYYEKALELDPDNA---DAYYNLAAAYYKLGKYEEALEDYEKALE 62 (100)
T ss_pred HHHHHHHHHHHHhcHHHHHHHHHHHHhcCCccH---HHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 578899999999999999999988877655432 2333333333444778888776666544
No 54
>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=85.68 E-value=6.2 Score=33.55 Aligned_cols=73 Identities=19% Similarity=0.330 Sum_probs=51.3
Q ss_pred HHHhcCCChhHHHHHHHHHHHHHhcCChhhHHHHHHHHHhhccccchhHHHHHHHHH-HHHhhcCHHHHHHHHHHHHH
Q 013640 117 LHDRYQIGPDQIEALYQYAKFQFECGNYSGAADYLYQYRALCTNSERRLSALWGKMA-AEILMQNWDIALEELNQLKE 193 (439)
Q Consensus 117 l~~~~g~t~e~~~al~~~ak~~y~~Gdy~~A~~~L~~~~~~~~~~~~k~~~lwg~la-~eIl~~~w~~a~~~l~klke 193 (439)
+++-....|+...+++.+|..++..|+|+.|.+.+..+....++. ...|..++ +-...++++.|.+.+.++-+
T Consensus 6 ~~~~l~~~p~~~~~~~~~a~~~~~~~~~~~A~~~~~~~~~~~p~~----~~~~~~la~~~~~~~~~~~A~~~~~~~~~ 79 (135)
T TIGR02552 6 LKDLLGLDSEQLEQIYALAYNLYQQGRYDEALKLFQLLAAYDPYN----SRYWLGLAACCQMLKEYEEAIDAYALAAA 79 (135)
T ss_pred HHHHHcCChhhHHHHHHHHHHHHHcccHHHHHHHHHHHHHhCCCc----HHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 344455688888899999999999999999999988877654332 23333333 33446788888877776544
No 55
>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=85.40 E-value=0.97 Score=33.01 Aligned_cols=27 Identities=22% Similarity=0.253 Sum_probs=24.3
Q ss_pred HHHHHHHHHhcCChhhHHHHHHHHHhh
Q 013640 131 LYQYAKFQFECGNYSGAADYLYQYRAL 157 (439)
Q Consensus 131 l~~~ak~~y~~Gdy~~A~~~L~~~~~~ 157 (439)
-|++|+-|.+.||+++|.+.|..+...
T Consensus 2 kLdLA~ayie~Gd~e~Ar~lL~evl~~ 28 (44)
T TIGR03504 2 KLDLARAYIEMGDLEGARELLEEVIEE 28 (44)
T ss_pred chHHHHHHHHcCChHHHHHHHHHHHHc
Confidence 378999999999999999999998853
No 56
>PF13432 TPR_16: Tetratricopeptide repeat; PDB: 3CVP_A 3CVL_A 3CVQ_A 3CV0_A 2GW1_B 3CVN_A 3QKY_A 2PL2_B.
Probab=85.13 E-value=3.1 Score=31.21 Aligned_cols=45 Identities=22% Similarity=0.380 Sum_probs=36.5
Q ss_pred HHHHhcCCChhHHHHHHHHHHHHHhcCChhhHHHHHHHHHhhccc
Q 013640 116 MLHDRYQIGPDQIEALYQYAKFQFECGNYSGAADYLYQYRALCTN 160 (439)
Q Consensus 116 ~l~~~~g~t~e~~~al~~~ak~~y~~Gdy~~A~~~L~~~~~~~~~ 160 (439)
.+++-....|+..++++.+|..++..|+|++|.+++..+....++
T Consensus 19 ~~~~~l~~~P~~~~a~~~lg~~~~~~g~~~~A~~~~~~a~~~~P~ 63 (65)
T PF13432_consen 19 AFEQALKQDPDNPEAWYLLGRILYQQGRYDEALAYYERALELDPD 63 (65)
T ss_dssp HHHHHHCCSTTHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHSTT
T ss_pred HHHHHHHHCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHCcC
Confidence 344444556889999999999999999999999999988876654
No 57
>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=84.38 E-value=7.4 Score=41.16 Aligned_cols=125 Identities=21% Similarity=0.336 Sum_probs=77.6
Q ss_pred HHHHHHHHHHHccCCCchHHHHHHHHhCCCCCChhHHHHHHHHHHHHHHHHHHHHHHHHHhhCChhHHHHhhhcchhccH
Q 013640 35 EQILKSKIELLNKTNMVDYAMDIHKSLYHTEDVPQDMVERRVEVVARLKALEERAAPIVSFLQNPNSFQDLRANDQHYNL 114 (439)
Q Consensus 35 ~~l~~a~~~llk~TnM~dy~~~~~~~l~~~~~~p~e~~~k~~ev~~~l~~l~~~~~~~~~~~~~~e~~~~l~~~dk~~n~ 114 (439)
+-|..+.+.+++.|+..+++.+++++|...+ |+ ..- +++++ . +..|.| ++.+
T Consensus 169 NyLv~~Ll~~l~~t~~~~~ai~lle~L~~~~--pe-v~~----~LA~v----------~-l~~~~E-~~AI--------- 220 (395)
T PF09295_consen 169 NYLVDTLLKYLSLTQRYDEAIELLEKLRERD--PE-VAV----LLARV----------Y-LLMNEE-VEAI--------- 220 (395)
T ss_pred hHHHHHHHHHHhhcccHHHHHHHHHHHHhcC--Cc-HHH----HHHHH----------H-HhcCcH-HHHH---------
Confidence 7888999999999999999999999998543 21 111 11111 0 011211 1111
Q ss_pred HHHHHhcCCChhHHHHHHHHHHHHHhcCChhhHHHHHHHHHhhccccchhHHHHHHHHH-HHHhhcCHHHHHHHHHHH
Q 013640 115 QMLHDRYQIGPDQIEALYQYAKFQFECGNYSGAADYLYQYRALCTNSERRLSALWGKMA-AEILMQNWDIALEELNQL 191 (439)
Q Consensus 115 ~~l~~~~g~t~e~~~al~~~ak~~y~~Gdy~~A~~~L~~~~~~~~~~~~k~~~lwg~la-~eIl~~~w~~a~~~l~kl 191 (439)
..+++...-.+..-+.|.-.|+|+.+.|+|+.|.++....-.++++.- -.|..|| |=|..++|+.|+--++.+
T Consensus 221 ~ll~~aL~~~p~d~~LL~~Qa~fLl~k~~~~lAL~iAk~av~lsP~~f----~~W~~La~~Yi~~~d~e~ALlaLNs~ 294 (395)
T PF09295_consen 221 RLLNEALKENPQDSELLNLQAEFLLSKKKYELALEIAKKAVELSPSEF----ETWYQLAECYIQLGDFENALLALNSC 294 (395)
T ss_pred HHHHHHHHhCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHhCchhH----HHHHHHHHHHHhcCCHHHHHHHHhcC
Confidence 112222122333366777889999999999888888877777555432 2455554 456678888888877654
No 58
>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=83.89 E-value=2.5 Score=27.60 Aligned_cols=31 Identities=29% Similarity=0.433 Sum_probs=27.4
Q ss_pred HHHHHHHHHHHhcCChhhHHHHHHHHHhhcc
Q 013640 129 EALYQYAKFQFECGNYSGAADYLYQYRALCT 159 (439)
Q Consensus 129 ~al~~~ak~~y~~Gdy~~A~~~L~~~~~~~~ 159 (439)
+.++.+|.++.+.|+++.|.+++..+....+
T Consensus 2 ~~~~~lg~~y~~~~~~~~A~~~~~~a~~~~~ 32 (34)
T PF13181_consen 2 EAYYNLGKIYEQLGDYEEALEYFEKALELNP 32 (34)
T ss_dssp HHHHHHHHHHHHTTSHHHHHHHHHHHHHHHT
T ss_pred HHHHHHHHHHHHcCCHHHHHHHHHHHHhhCC
Confidence 4678999999999999999999998887654
No 59
>smart00345 HTH_GNTR helix_turn_helix gluconate operon transcriptional repressor.
Probab=83.82 E-value=2.4 Score=31.08 Aligned_cols=48 Identities=17% Similarity=0.129 Sum_probs=39.5
Q ss_pred HHHHHHHHHHhhhhhccc-cHHHHHHHcCCCHHHHHHHHHHHhhcCccc
Q 013640 341 ENARLFIFETYCRIHQRI-DMAVLAEKLNLNYEEAQRWIVNLIRNSKLD 388 (439)
Q Consensus 341 e~aR~~ife~ycriy~~I-~I~~lA~~l~~s~~~~E~wiv~lI~~~rL~ 388 (439)
+..+..+....+.+...+ ++..||+.||+|..-+.+.+-.|...|-+.
T Consensus 3 ~~l~~~i~~~~~~~~~~l~s~~~la~~~~vs~~tv~~~l~~L~~~g~i~ 51 (60)
T smart00345 3 ERLREDIVSGELRPGDKLPSERELAAQLGVSRTTVREALSRLEAEGLVQ 51 (60)
T ss_pred HHHHHHHHcCCCCCCCcCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCEE
Confidence 345556666666778888 899999999999999999999999888653
No 60
>PRK11788 tetratricopeptide repeat protein; Provisional
Probab=83.78 E-value=48 Score=33.35 Aligned_cols=76 Identities=18% Similarity=0.211 Sum_probs=44.6
Q ss_pred HHHHhcCCChhHHHHHHHHHHHHHhcCChhhHHHHHHHHHhhccccchhHHHHHHHH-HHHHhhcCHHHHHHHHHHHHHH
Q 013640 116 MLHDRYQIGPDQIEALYQYAKFQFECGNYSGAADYLYQYRALCTNSERRLSALWGKM-AAEILMQNWDIALEELNQLKEK 194 (439)
Q Consensus 116 ~l~~~~g~t~e~~~al~~~ak~~y~~Gdy~~A~~~L~~~~~~~~~~~~k~~~lwg~l-a~eIl~~~w~~a~~~l~klke~ 194 (439)
.+++-....++...+.+.+|.++...|++++|.+++.......++. ....|..+ .+-.-.++++.|...++++.+.
T Consensus 202 ~~~~al~~~p~~~~~~~~la~~~~~~g~~~~A~~~~~~~~~~~p~~---~~~~~~~l~~~~~~~g~~~~A~~~l~~~~~~ 278 (389)
T PRK11788 202 LLKKALAADPQCVRASILLGDLALAQGDYAAAIEALERVEEQDPEY---LSEVLPKLMECYQALGDEAEGLEFLRRALEE 278 (389)
T ss_pred HHHHHHhHCcCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHChhh---HHHHHHHHHHHHHHcCCHHHHHHHHHHHHHh
Confidence 4444444455566677778888888888888888777766543221 11222222 2233456777777766666554
No 61
>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=83.49 E-value=19 Score=30.47 Aligned_cols=66 Identities=15% Similarity=0.029 Sum_probs=31.3
Q ss_pred HHHHHHHHHHHHhcCChhhHHHHHHHHHhhccccchhHHHHHHHHHHHHhhcCHHHHHHHHHHHHHHhc
Q 013640 128 IEALYQYAKFQFECGNYSGAADYLYQYRALCTNSERRLSALWGKMAAEILMQNWDIALEELNQLKEKVD 196 (439)
Q Consensus 128 ~~al~~~ak~~y~~Gdy~~A~~~L~~~~~~~~~~~~k~~~lwg~la~eIl~~~w~~a~~~l~klke~id 196 (439)
.+..+.+|.+++..|+|+.|.+++.......+.+ ....+..=-+-...++++.|.+.++++-++..
T Consensus 51 ~~~~~~la~~~~~~~~~~~A~~~~~~~~~~~p~~---~~~~~~la~~~~~~g~~~~A~~~~~~al~~~p 116 (135)
T TIGR02552 51 SRYWLGLAACCQMLKEYEEAIDAYALAAALDPDD---PRPYFHAAECLLALGEPESALKALDLAIEICG 116 (135)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCC---hHHHHHHHHHHHHcCCHHHHHHHHHHHHHhcc
Confidence 4455556666666666666666555544432221 11111111233334556666655555554433
No 62
>PF13428 TPR_14: Tetratricopeptide repeat
Probab=82.59 E-value=2.7 Score=29.74 Aligned_cols=33 Identities=21% Similarity=0.099 Sum_probs=29.4
Q ss_pred HHHHHHHHHHHhcCChhhHHHHHHHHHhhcccc
Q 013640 129 EALYQYAKFQFECGNYSGAADYLYQYRALCTNS 161 (439)
Q Consensus 129 ~al~~~ak~~y~~Gdy~~A~~~L~~~~~~~~~~ 161 (439)
++++.+|..|.+.|++++|.+.+.......+++
T Consensus 2 ~~~~~la~~~~~~G~~~~A~~~~~~~l~~~P~~ 34 (44)
T PF13428_consen 2 AAWLALARAYRRLGQPDEAERLLRRALALDPDD 34 (44)
T ss_pred HHHHHHHHHHHHcCCHHHHHHHHHHHHHHCcCC
Confidence 367899999999999999999999999987754
No 63
>PRK10866 outer membrane biogenesis protein BamD; Provisional
Probab=82.15 E-value=23 Score=34.59 Aligned_cols=83 Identities=12% Similarity=0.112 Sum_probs=57.5
Q ss_pred HHHHHhcCCChhHHHHHHHHHHHHHhcCChhhHHHHHHHHHhhccccchhHHHHHHHHHHH---------------Hhhc
Q 013640 115 QMLHDRYQIGPDQIEALYQYAKFQFECGNYSGAADYLYQYRALCTNSERRLSALWGKMAAE---------------ILMQ 179 (439)
Q Consensus 115 ~~l~~~~g~t~e~~~al~~~ak~~y~~Gdy~~A~~~L~~~~~~~~~~~~k~~~lwg~la~e---------------Il~~ 179 (439)
+.+...|-.++....+.+.+|..+|+.|+|+.|...+..+...-+++...-.++.-+--|. --..
T Consensus 56 ~~l~~~yP~s~~a~~a~l~la~ayy~~~~y~~A~~~~e~fi~~~P~~~~~~~a~Y~~g~~~~~~~~~~~~~~~~~~~~~r 135 (243)
T PRK10866 56 EALDNRYPFGPYSQQVQLDLIYAYYKNADLPLAQAAIDRFIRLNPTHPNIDYVLYMRGLTNMALDDSALQGFFGVDRSDR 135 (243)
T ss_pred HHHHHhCCCChHHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHhCcCCCchHHHHHHHHHhhhhcchhhhhhccCCCcccc
Confidence 4455666668888889999999999999999999999999998777655443333332221 1112
Q ss_pred CHHHHHHHHHHHHHHhcC
Q 013640 180 NWDIALEELNQLKEKVDD 197 (439)
Q Consensus 180 ~w~~a~~~l~klke~id~ 197 (439)
|...+.+-++.++++++.
T Consensus 136 D~~~~~~A~~~~~~li~~ 153 (243)
T PRK10866 136 DPQHARAAFRDFSKLVRG 153 (243)
T ss_pred CHHHHHHHHHHHHHHHHH
Confidence 445556566666666665
No 64
>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=82.13 E-value=84 Score=34.44 Aligned_cols=66 Identities=17% Similarity=0.177 Sum_probs=32.5
Q ss_pred CChhHHHHHHHHHHHHHhcCChhhHHHHHHHHHhhccccchhHHHHHHHHHHHHhhcCHHHHHHHHHHH
Q 013640 123 IGPDQIEALYQYAKFQFECGNYSGAADYLYQYRALCTNSERRLSALWGKMAAEILMQNWDIALEELNQL 191 (439)
Q Consensus 123 ~t~e~~~al~~~ak~~y~~Gdy~~A~~~L~~~~~~~~~~~~k~~~lwg~la~eIl~~~w~~a~~~l~kl 191 (439)
..|...++++.+|..++..|+|+.|.+.+.......++. ..+...+-.+....++++.|.+...++
T Consensus 154 ~~~~~~~~~~~la~~~~~~~~~~~A~~~~~~~~~~~~~~---~~~~~~~~~~~~~~g~~~~A~~~~~~a 219 (899)
T TIGR02917 154 IDPRSLYAKLGLAQLALAENRFDEARALIDEVLTADPGN---VDALLLKGDLLLSLGNIELALAAYRKA 219 (899)
T ss_pred cCCCChhhHHHHHHHHHHCCCHHHHHHHHHHHHHhCCCC---hHHHHHHHHHHHhcCCHHHHHHHHHHH
Confidence 344445566666666666666666666666555433221 112222222333345565555555544
No 65
>PRK10049 pgaA outer membrane protein PgaA; Provisional
Probab=81.58 E-value=1e+02 Score=35.19 Aligned_cols=96 Identities=14% Similarity=0.030 Sum_probs=63.9
Q ss_pred HHHHHhcCCChhHHHHHHHHHHHHHhcCChhhHHHHHHHHHhhccccchhHHHHHHHHHHHHhhcCHHHHHHHHHHHHHH
Q 013640 115 QMLHDRYQIGPDQIEALYQYAKFQFECGNYSGAADYLYQYRALCTNSERRLSALWGKMAAEILMQNWDIALEELNQLKEK 194 (439)
Q Consensus 115 ~~l~~~~g~t~e~~~al~~~ak~~y~~Gdy~~A~~~L~~~~~~~~~~~~k~~~lwg~la~eIl~~~w~~a~~~l~klke~ 194 (439)
+.+++-....|+..+.++.+|..+...|++..|.+.|.....+-+++.. .....--+.+-.++|+.|.+.+.++-+.
T Consensus 380 ~~l~~al~~~P~n~~l~~~lA~l~~~~g~~~~A~~~l~~al~l~Pd~~~---l~~~~a~~al~~~~~~~A~~~~~~ll~~ 456 (765)
T PRK10049 380 MRARELAYNAPGNQGLRIDYASVLQARGWPRAAENELKKAEVLEPRNIN---LEVEQAWTALDLQEWRQMDVLTDDVVAR 456 (765)
T ss_pred HHHHHHHHhCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhhCCCChH---HHHHHHHHHHHhCCHHHHHHHHHHHHHh
Confidence 3444444456666778888888888999998888888887776543221 3333333455567899998888777664
Q ss_pred hcCCCCCCChHHHHHHHHHHHHHH
Q 013640 195 VDDPKSFTSPLNQMQSRIWLMHWS 218 (439)
Q Consensus 195 id~~~~~~~~l~~l~~R~WllHws 218 (439)
... +|..+--.|.|-+|-+
T Consensus 457 ~Pd-----~~~~~~~~~~~~~~~~ 475 (765)
T PRK10049 457 EPQ-----DPGVQRLARARDVHHM 475 (765)
T ss_pred CCC-----CHHHHHHHHHHHhccC
Confidence 443 5566666777776544
No 66
>PRK11014 transcriptional repressor NsrR; Provisional
Probab=80.57 E-value=4.8 Score=35.90 Aligned_cols=62 Identities=13% Similarity=0.130 Sum_probs=47.8
Q ss_pred HHHHHHHHHhhhhhccccHHHHHHHcCCCHHHHHHHHHHHhhcCccceeecccCCEEEeCCCC
Q 013640 342 NARLFIFETYCRIHQRIDMAVLAEKLNLNYEEAQRWIVNLIRNSKLDAKIDAKSGTVIMEPTH 404 (439)
Q Consensus 342 ~aR~~ife~ycriy~~I~I~~lA~~l~~s~~~~E~wiv~lI~~~rL~aKID~~~g~V~~~~~~ 404 (439)
..|.+++.....+-+.++++.||+.+|+|+..+.+-+..|-+.|=+..+=-...|. ...+++
T Consensus 10 Al~~~i~la~~~~g~~~s~~~ia~~~~is~~~vrk~l~~L~~~Glv~s~~G~~GG~-~l~~~~ 71 (141)
T PRK11014 10 GLRALIYMASLPEGRMTSISEVTEVYGVSRNHMVKIINQLSRAGYVTAVRGKNGGI-RLGKPA 71 (141)
T ss_pred HHHHHHHHhcCCCCCccCHHHHHHHHCcCHHHHHHHHHHHHhCCEEEEecCCCCCe-eecCCH
Confidence 46777887777787889999999999999999999999999998776543333344 334444
No 67
>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=79.99 E-value=5.7 Score=28.55 Aligned_cols=44 Identities=27% Similarity=0.399 Sum_probs=34.3
Q ss_pred HHHHHHHHhhhhhccccHHHHHHHcCCCHHHHHHHHHHHhhcCcc
Q 013640 343 ARLFIFETYCRIHQRIDMAVLAEKLNLNYEEAQRWIVNLIRNSKL 387 (439)
Q Consensus 343 aR~~ife~ycriy~~I~I~~lA~~l~~s~~~~E~wiv~lI~~~rL 387 (439)
.+..|+ .++.-...++...||+.+|+|..-+-+-|-.|+..|-+
T Consensus 4 ~~~~Il-~~l~~~~~~t~~ela~~~~is~~tv~~~l~~L~~~g~I 47 (48)
T PF13412_consen 4 TQRKIL-NYLRENPRITQKELAEKLGISRSTVNRYLKKLEEKGLI 47 (48)
T ss_dssp HHHHHH-HHHHHCTTS-HHHHHHHHTS-HHHHHHHHHHHHHTTSE
T ss_pred HHHHHH-HHHHHcCCCCHHHHHHHhCCCHHHHHHHHHHHHHCcCc
Confidence 344455 56666899999999999999999999999999887754
No 68
>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=79.94 E-value=10 Score=35.70 Aligned_cols=63 Identities=17% Similarity=0.118 Sum_probs=54.3
Q ss_pred HHHHHHHHHhcCChhhHHHHHHHHHhhccccchhHHHHHHHHHHHHhhcCHHHHHHHHHHHHH
Q 013640 131 LYQYAKFQFECGNYSGAADYLYQYRALCTNSERRLSALWGKMAAEILMQNWDIALEELNQLKE 193 (439)
Q Consensus 131 l~~~ak~~y~~Gdy~~A~~~L~~~~~~~~~~~~k~~~lwg~la~eIl~~~w~~a~~~l~klke 193 (439)
.+..|.++++.|+|..|...+..+....++......+++..-.+-...++++.|.+....|..
T Consensus 169 ~~~~a~~~~~~g~~~~A~~~~~~al~~~p~~~~~~~a~~~l~~~~~~lg~~~~A~~~~~~l~~ 231 (235)
T TIGR03302 169 ELYVARFYLKRGAYVAAINRFETVVENYPDTPATEEALARLVEAYLKLGLKDLAQDAAAVLGA 231 (235)
T ss_pred HHHHHHHHHHcCChHHHHHHHHHHHHHCCCCcchHHHHHHHHHHHHHcCCHHHHHHHHHHHHh
Confidence 357899999999999999999999988887666778888888888889999999987777654
No 69
>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=79.60 E-value=15 Score=36.91 Aligned_cols=98 Identities=13% Similarity=0.231 Sum_probs=69.6
Q ss_pred cchHHHHHHHhhhcCChhHHHHHHHHHHHHhcCCcccccccccccccccccHHHHHHHHHHHHHHHhhhhhccccHHHHH
Q 013640 285 KDPITEFLACVYVNYDFDGAQKKMKECEEVILNDPFLGKRVEDSNFATVPLRDEFLENARLFIFETYCRIHQRIDMAVLA 364 (439)
Q Consensus 285 ~Dpit~f~~~lY~~fdF~~aq~~L~~~e~~i~~D~FL~~~~~~~~~~~~~~~~~f~e~aR~~ife~ycriy~~I~I~~lA 364 (439)
+-+++++=..+=|+++ ..=+.+..+++.|.=+ .+..+.-++..+.|...++++-.. +-...|+|..+|
T Consensus 70 Rv~~~dL~~~LnVd~~-----~ie~~~~~i~~~~~~~--~l~~gelit~~Yld~l~~Eine~L-----qe~G~vsi~eLa 137 (272)
T PF09743_consen 70 RVNLVDLAQALNVDLD-----HIERRAQEIVKSDKSL--QLVQGELITDSYLDSLAEEINEKL-----QESGQVSISELA 137 (272)
T ss_pred ceEHHHHHHhcCcCHH-----HHHHHHHHHHhCCCcE--EEECCEEccHHHHHHHHHHHHHHH-----HHcCeEeHHHHH
Confidence 4567777766655554 2334455566677422 234555666677777777766543 445899999999
Q ss_pred HHcCCCHHHHHHHHHHHhhcCccceeeccc
Q 013640 365 EKLNLNYEEAQRWIVNLIRNSKLDAKIDAK 394 (439)
Q Consensus 365 ~~l~~s~~~~E~wiv~lI~~~rL~aKID~~ 394 (439)
++++++.+++-..++.-...+.++|++|..
T Consensus 138 ~~~~Lp~efl~~~li~~~lg~~I~g~~d~~ 167 (272)
T PF09743_consen 138 KQYDLPSEFLKEELISKRLGKIIKGRLDGD 167 (272)
T ss_pred HhcCCcHHHHHHHHhhhhcCcceeEEEeCC
Confidence 999999999998888888888999999976
No 70
>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=79.45 E-value=4.3 Score=26.52 Aligned_cols=31 Identities=29% Similarity=0.463 Sum_probs=26.2
Q ss_pred HHHHHHHHHHHhcCChhhHHHHHHHHHhhcc
Q 013640 129 EALYQYAKFQFECGNYSGAADYLYQYRALCT 159 (439)
Q Consensus 129 ~al~~~ak~~y~~Gdy~~A~~~L~~~~~~~~ 159 (439)
++++.+|..++..|+|+.|.+.+.....+.+
T Consensus 2 ~~~~~~g~~~~~~~~~~~A~~~~~~al~~~p 32 (34)
T PF00515_consen 2 EAYYNLGNAYFQLGDYEEALEYYQRALELDP 32 (34)
T ss_dssp HHHHHHHHHHHHTT-HHHHHHHHHHHHHHST
T ss_pred HHHHHHHHHHHHhCCchHHHHHHHHHHHHCc
Confidence 4788999999999999999999998877654
No 71
>smart00420 HTH_DEOR helix_turn_helix, Deoxyribose operon repressor.
Probab=79.44 E-value=4.9 Score=28.54 Aligned_cols=34 Identities=21% Similarity=0.224 Sum_probs=31.0
Q ss_pred hccccHHHHHHHcCCCHHHHHHHHHHHhhcCccc
Q 013640 355 HQRIDMAVLAEKLNLNYEEAQRWIVNLIRNSKLD 388 (439)
Q Consensus 355 y~~I~I~~lA~~l~~s~~~~E~wiv~lI~~~rL~ 388 (439)
+..+++..||+.||+|+.-+.+.|.+|...|.+.
T Consensus 12 ~~~~s~~~l~~~l~~s~~tv~~~l~~L~~~g~i~ 45 (53)
T smart00420 12 QGKVSVEELAELLGVSEMTIRRDLNKLEEQGLLT 45 (53)
T ss_pred cCCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCEE
Confidence 5679999999999999999999999999987765
No 72
>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=79.42 E-value=30 Score=34.39 Aligned_cols=77 Identities=14% Similarity=0.164 Sum_probs=60.4
Q ss_pred HHHHHhcCCChhHHHHHHHHHHHHHhcCChhhHHHHHHHHHhhccc-cchhHHHHHHHHHHHHhhcCHHHHHHHHHHH
Q 013640 115 QMLHDRYQIGPDQIEALYQYAKFQFECGNYSGAADYLYQYRALCTN-SERRLSALWGKMAAEILMQNWDIALEELNQL 191 (439)
Q Consensus 115 ~~l~~~~g~t~e~~~al~~~ak~~y~~Gdy~~A~~~L~~~~~~~~~-~~~k~~~lwg~la~eIl~~~w~~a~~~l~kl 191 (439)
..+++-....|+.......+|..+++.|++++|..++.......+. +.......|..-.+-+..++++.|...++++
T Consensus 135 ~~~~~al~~~p~~~~~~~~la~i~~~~g~~~eA~~~l~~~l~~~~~~~~~~~~~~~~la~~~~~~G~~~~A~~~~~~~ 212 (355)
T cd05804 135 EAARRALELNPDDAWAVHAVAHVLEMQGRFKEGIAFMESWRDTWDCSSMLRGHNWWHLALFYLERGDYEAALAIYDTH 212 (355)
T ss_pred HHHHHHHhhCCCCcHHHHHHHHHHHHcCCHHHHHHHHHhhhhccCCCcchhHHHHHHHHHHHHHCCCHHHHHHHHHHH
Confidence 3445555566666778899999999999999999999988876553 3344566777878888899999998888776
No 73
>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=79.22 E-value=4.9 Score=30.41 Aligned_cols=34 Identities=21% Similarity=0.315 Sum_probs=28.5
Q ss_pred HHHHHHHHHHHHhcCChhhHHHHHHHHHhhcccc
Q 013640 128 IEALYQYAKFQFECGNYSGAADYLYQYRALCTNS 161 (439)
Q Consensus 128 ~~al~~~ak~~y~~Gdy~~A~~~L~~~~~~~~~~ 161 (439)
+|.+|-+|--+|+.|||++|.+++..+...-++.
T Consensus 1 Rd~lY~lAig~ykl~~Y~~A~~~~~~lL~~eP~N 34 (53)
T PF14853_consen 1 RDCLYYLAIGHYKLGEYEKARRYCDALLEIEPDN 34 (53)
T ss_dssp HHHHHHHHHHHHHTT-HHHHHHHHHHHHHHTTS-
T ss_pred ChhHHHHHHHHHHhhhHHHHHHHHHHHHhhCCCc
Confidence 4788999999999999999999999998866654
No 74
>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=78.86 E-value=13 Score=30.09 Aligned_cols=67 Identities=9% Similarity=0.135 Sum_probs=46.4
Q ss_pred HHHHHHHHHHHHHhhhhhccccHHHHHHHcCCCHHHHHHHHHHHhhcCccceeecccCCEEEeCCCCc
Q 013640 338 EFLENARLFIFETYCRIHQRIDMAVLAEKLNLNYEEAQRWIVNLIRNSKLDAKIDAKSGTVIMEPTHP 405 (439)
Q Consensus 338 ~f~e~aR~~ife~ycriy~~I~I~~lA~~l~~s~~~~E~wiv~lI~~~rL~aKID~~~g~V~~~~~~~ 405 (439)
.+--..|.+++-.--.--+.++++.||+++|+|+..+++-+..|.+.|=+.++= -.+|-....+++.
T Consensus 6 ~~~~Al~~l~~la~~~~~~~~s~~eiA~~~~i~~~~l~kil~~L~~~Gli~s~~-G~~GGy~L~~~~~ 72 (83)
T PF02082_consen 6 RTDYALRILLYLARHPDGKPVSSKEIAERLGISPSYLRKILQKLKKAGLIESSR-GRGGGYRLARPPE 72 (83)
T ss_dssp HHHHHHHHHHHHHCTTTSC-BEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEET-STTSEEEESS-CC
T ss_pred HHHHHHHHHHHHHhCCCCCCCCHHHHHHHHCcCHHHHHHHHHHHhhCCeeEecC-CCCCceeecCCHH
Confidence 344455666655443333349999999999999999999999999999765431 3367777777773
No 75
>PF13374 TPR_10: Tetratricopeptide repeat; PDB: 3CEQ_B 3EDT_H 3NF1_A.
Probab=78.73 E-value=4.3 Score=27.25 Aligned_cols=32 Identities=22% Similarity=0.167 Sum_probs=26.1
Q ss_pred HHHHHHHHHHHHhcCChhhHHHHHHHHHhhcc
Q 013640 128 IEALYQYAKFQFECGNYSGAADYLYQYRALCT 159 (439)
Q Consensus 128 ~~al~~~ak~~y~~Gdy~~A~~~L~~~~~~~~ 159 (439)
..++..+|.+|+..|+|++|.+++......+.
T Consensus 2 a~~~~~la~~~~~~g~~~~A~~~~~~al~~~~ 33 (42)
T PF13374_consen 2 ASALNNLANAYRAQGRYEEALELLEEALEIRE 33 (42)
T ss_dssp HHHHHHHHHHHHHCT-HHHHHHHHHHHHHHH-
T ss_pred HHHHHHHHHHHHhhhhcchhhHHHHHHHHHHH
Confidence 45788999999999999999999988776543
No 76
>COG5600 Transcription-associated recombination protein [DNA replication, recombination, and repair]
Probab=78.44 E-value=96 Score=32.87 Aligned_cols=240 Identities=16% Similarity=0.175 Sum_probs=123.5
Q ss_pred CChhhHHHHHHHHHhhccccchh---HHHHHHHH-----HHHHh--hcCHHHHHHHHHHHHHHhcCCCCCC-ChH-HHHH
Q 013640 142 GNYSGAADYLYQYRALCTNSERR---LSALWGKM-----AAEIL--MQNWDIALEELNQLKEKVDDPKSFT-SPL-NQMQ 209 (439)
Q Consensus 142 Gdy~~A~~~L~~~~~~~~~~~~k---~~~lwg~l-----a~eIl--~~~w~~a~~~l~klke~id~~~~~~-~~l-~~l~ 209 (439)
..-+.++..+......|.++... -+.-||.+ -+-|. +...+.+..-++-.++ -++.|++ -++ .+..
T Consensus 144 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 144 DNLSKISRLLTRMFNSILNDRSPALNPSKKVGLYYIANLLFQIYLRLGRFKLCENFLKASKE--VSMPDISEYQKSQVVV 221 (413)
T ss_pred hhHHHHHHHHHHHHHHhcCCcCccCChhhHHHHHHHHHHHHHHHHHhccHHHHHHHHHhccc--ccccccchhhhcceee
Confidence 35677888888888888765333 55556632 22222 2344444333333322 1222332 111 1111
Q ss_pred HHHHHHHHHHHHHhc--CccchHHHHHHhccccchhHHHhhchhHHHHHHHHHHHhcccccchHHHHHHHhhhc-cCCcc
Q 013640 210 SRIWLMHWSLFIFFN--HDNGRTLIIDLFNQDKYLNAIQTNAPHLLRYLATAFIVNKRRRPQFKDFIKVIQQEQ-NSYKD 286 (439)
Q Consensus 210 ~R~WllHwsLf~~fn--~~~~~~~l~d~F~~~~yl~~Iqt~~p~lLrYlvva~il~~~r~~~l~~i~~vi~qe~-~~Y~D 286 (439)
.|-+| |.+.+.| ..+|...|-+.|.+-+.+ ++-.=.-++=|.+.++++..+- -+.++ ++++.+ -.+-.
T Consensus 222 f~YYL---G~~~l~~en~heA~~~L~~aFl~c~~l--~~~n~~rIl~~~ipt~Llv~~~-~Ptk~---~L~r~~~~s~~~ 292 (413)
T COG5600 222 FHYYL---GIYYLLNENFHEAFLHLNEAFLQCPWL--ITRNRKRILPYYIPTSLLVNKF-PPTKD---LLERFKRCSVYS 292 (413)
T ss_pred hhhHH---HHHHHHHHhHHHHHHHHHHHHHhChhh--hhcchheehhHHhhHHHHhCCC-CCchH---HHHhccccchhH
Confidence 11122 3333333 334666676677632211 1111111455666666665432 24444 455643 22224
Q ss_pred hHHHHHHHhhhcCChhHHHHHHHHHHHH-hcCCcccccccccccccccc-cHHHHHHHHHHHHH-HHhhhhhccccHHHH
Q 013640 287 PITEFLACVYVNYDFDGAQKKMKECEEV-ILNDPFLGKRVEDSNFATVP-LRDEFLENARLFIF-ETYCRIHQRIDMAVL 363 (439)
Q Consensus 287 pit~f~~~lY~~fdF~~aq~~L~~~e~~-i~~D~FL~~~~~~~~~~~~~-~~~~f~e~aR~~if-e~ycriy~~I~I~~l 363 (439)
|++.=+ .--+.+++...|+..|.. +..--++- . .. +-.=+.||.-..++ -..|.+-=.++|-..
T Consensus 293 ~Lvkav----rsGni~~~~~~l~~ner~~~~~~l~lt--------l-~~~~~~V~~RNL~rk~w~~~~~qsrlp~sil~~ 359 (413)
T COG5600 293 PLVKAV----RSGNIEDFDLALSRNERKFAKRGLYLT--------L-LAHYPLVCFRNLFRKIWRLHGKQSRLPLSILLI 359 (413)
T ss_pred HHHHHH----HcCCHHHHHHHHHHhHHHHHHcchHHH--------H-HhhccHHHHHHHHHHHHhhccccccCcHHHHHH
Confidence 444333 225566666889888863 23333320 0 01 11123344322222 223333225677778
Q ss_pred HHHcCCC-----HHHHHHHHHHHhhcCccceeecccCCEEEeCCCCc
Q 013640 364 AEKLNLN-----YEEAQRWIVNLIRNSKLDAKIDAKSGTVIMEPTHP 405 (439)
Q Consensus 364 A~~l~~s-----~~~~E~wiv~lI~~~rL~aKID~~~g~V~~~~~~~ 405 (439)
+.++..+ .+++|.-+|++|.-|.|.|-|=....+|+....++
T Consensus 360 ~~qls~~dn~~~~~~VEciL~tlI~~G~lrgYis~s~~~vV~sk~~p 406 (413)
T COG5600 360 VLQLSAIDNFHSFKEVECILVTLIGLGLLRGYISHSRRTVVFSKKDP 406 (413)
T ss_pred HHHccCCCcccChHHHHHHHHHHHhhhhhhheecccceEEEEecCCC
Confidence 8888755 48999999999999999999999999999987764
No 77
>PF13431 TPR_17: Tetratricopeptide repeat
Probab=78.31 E-value=1.4 Score=29.99 Aligned_cols=27 Identities=26% Similarity=0.513 Sum_probs=24.1
Q ss_pred CCChhHHHHHHHHHHHHHhcCChhhHH
Q 013640 122 QIGPDQIEALYQYAKFQFECGNYSGAA 148 (439)
Q Consensus 122 g~t~e~~~al~~~ak~~y~~Gdy~~A~ 148 (439)
.+.|+.-++++.+|.+++..|++++|.
T Consensus 7 e~~P~n~~a~~nla~~~~~~g~~~~A~ 33 (34)
T PF13431_consen 7 ELNPNNAEAYNNLANLYLNQGDYEEAI 33 (34)
T ss_pred HHCCCCHHHHHHHHHHHHHCcCHHhhc
Confidence 457888899999999999999999985
No 78
>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=78.04 E-value=50 Score=29.36 Aligned_cols=66 Identities=12% Similarity=-0.038 Sum_probs=47.1
Q ss_pred hHHHHHHHHHHHHHhcCChhhHHHHHHHHHhhccccchhHHHHHHHHHHHHhhcCHHHHHHHHHHHHHH
Q 013640 126 DQIEALYQYAKFQFECGNYSGAADYLYQYRALCTNSERRLSALWGKMAAEILMQNWDIALEELNQLKEK 194 (439)
Q Consensus 126 e~~~al~~~ak~~y~~Gdy~~A~~~L~~~~~~~~~~~~k~~~lwg~la~eIl~~~w~~a~~~l~klke~ 194 (439)
...+..+.+|..++..|+|+.|.+.+.......++. ..+....-.+-+..++++.|.+...++-+.
T Consensus 29 ~~~~~~~~la~~~~~~~~~~~A~~~~~~~l~~~p~~---~~~~~~la~~~~~~~~~~~A~~~~~~al~~ 94 (234)
T TIGR02521 29 KAAKIRVQLALGYLEQGDLEVAKENLDKALEHDPDD---YLAYLALALYYQQLGELEKAEDSFRRALTL 94 (234)
T ss_pred cHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhCccc---HHHHHHHHHHHHHcCCHHHHHHHHHHHHhh
Confidence 346688899999999999999999998877654332 233333444445568888888887777654
No 79
>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=77.62 E-value=1e+02 Score=33.95 Aligned_cols=75 Identities=11% Similarity=0.165 Sum_probs=33.7
Q ss_pred HHHHhcCCChhHHHHHHHHHHHHHhcCChhhHHHHHHHHHhhccccchhHHHHHHHHHHHHhhcCHHHHHHHHHHHHH
Q 013640 116 MLHDRYQIGPDQIEALYQYAKFQFECGNYSGAADYLYQYRALCTNSERRLSALWGKMAAEILMQNWDIALEELNQLKE 193 (439)
Q Consensus 116 ~l~~~~g~t~e~~~al~~~ak~~y~~Gdy~~A~~~L~~~~~~~~~~~~k~~~lwg~la~eIl~~~w~~a~~~l~klke 193 (439)
.+++-..+.|...++++.+|..+...|+|+.|.+++......-++. .+++..+-.+-...++++.|.+...++-+
T Consensus 353 ~~~kal~l~P~~~~~~~~la~~~~~~g~~~eA~~~~~~al~~~p~~---~~~~~~lg~~~~~~g~~~~A~~~~~kal~ 427 (615)
T TIGR00990 353 DLSKSIELDPRVTQSYIKRASMNLELGDPDKAEEDFDKALKLNSED---PDIYYHRAQLHFIKGEFAQAGKDYQKSID 427 (615)
T ss_pred HHHHHHHcCCCcHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhCCCC---HHHHHHHHHHHHHcCCHHHHHHHHHHHHH
Confidence 3333344444445555555555555555555555555544432211 12222222223334555555555554433
No 80
>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=77.19 E-value=2.8 Score=37.93 Aligned_cols=42 Identities=17% Similarity=0.252 Sum_probs=33.3
Q ss_pred HHHHhhhhhcc--ccHHHHHHHcCCCHHHHHHHHHHHhhcCccceeec
Q 013640 347 IFETYCRIHQR--IDMAVLAEKLNLNYEEAQRWIVNLIRNSKLDAKID 392 (439)
Q Consensus 347 ife~ycriy~~--I~I~~lA~~l~~s~~~~E~wiv~lI~~~rL~aKID 392 (439)
....|++-|+. -++..+|+.+|||++.+ -.||++|||.-.-+
T Consensus 34 kV~~yLr~~p~~~ati~eV~e~tgVs~~~I----~~~IreGRL~~~~~ 77 (137)
T TIGR03826 34 KVYKFLRKHENRQATVSEIVEETGVSEKLI----LKFIREGRLQLKHF 77 (137)
T ss_pred HHHHHHHHCCCCCCCHHHHHHHHCcCHHHH----HHHHHcCCeeccCC
Confidence 45678898877 99999999999998765 55578899865433
No 81
>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=76.34 E-value=10 Score=33.16 Aligned_cols=79 Identities=15% Similarity=0.098 Sum_probs=54.4
Q ss_pred ccHHHHHHHHHHHHHHHhhhhhccccHHHHHHHcCCCHHHHHHHHHHHhhcCccceeecccCCEEEeCCCC-chhHHHHH
Q 013640 334 PLRDEFLENARLFIFETYCRIHQRIDMAVLAEKLNLNYEEAQRWIVNLIRNSKLDAKIDAKSGTVIMEPTH-PNVYEQLI 412 (439)
Q Consensus 334 ~~~~~f~e~aR~~ife~ycriy~~I~I~~lA~~l~~s~~~~E~wiv~lI~~~rL~aKID~~~g~V~~~~~~-~~~yqqvi 412 (439)
...++-++-+..++- ..-..+++..||+++|+|+..+.+-+..|.+.|=+...-. .+|-...++++ .-...+++
T Consensus 6 ~~~~yal~~l~~la~----~~~~~~s~~eia~~l~is~~~v~~~l~~L~~~Gli~~~~g-~~ggy~l~~~~~~it~~~v~ 80 (130)
T TIGR02944 6 KLTDYATLVLTTLAQ----NDSQPYSAAEIAEQTGLNAPTVSKILKQLSLAGIVTSKRG-VEGGYTLARAPRDITVADIV 80 (130)
T ss_pred hHHhHHHHHHHHHHh----CCCCCccHHHHHHHHCcCHHHHHHHHHHHHHCCcEEecCC-CCCChhhcCCccccCHHHHH
Confidence 445555555555542 2346799999999999999999999999999998865433 34445555555 33456666
Q ss_pred Hhhhh
Q 013640 413 DHTKG 417 (439)
Q Consensus 413 ~kt~~ 417 (439)
+..+.
T Consensus 81 ~~l~~ 85 (130)
T TIGR02944 81 KAVEG 85 (130)
T ss_pred HHHcC
Confidence 65543
No 82
>PF13518 HTH_28: Helix-turn-helix domain
Probab=76.21 E-value=6.8 Score=28.20 Aligned_cols=39 Identities=23% Similarity=0.386 Sum_probs=32.0
Q ss_pred HHHHHHHhhhhhccccHHHHHHHcCCCHHHHHHHHHHHhhcC
Q 013640 344 RLFIFETYCRIHQRIDMAVLAEKLNLNYEEAQRWIVNLIRNS 385 (439)
Q Consensus 344 R~~ife~ycriy~~I~I~~lA~~l~~s~~~~E~wiv~lI~~~ 385 (439)
|..|.+.|.+ ..++..+|+.||||..-+.+|+-.+=..|
T Consensus 2 r~~iv~~~~~---g~s~~~~a~~~gis~~tv~~w~~~y~~~G 40 (52)
T PF13518_consen 2 RLQIVELYLE---GESVREIAREFGISRSTVYRWIKRYREGG 40 (52)
T ss_pred HHHHHHHHHc---CCCHHHHHHHHCCCHhHHHHHHHHHHhcC
Confidence 4556666664 44999999999999999999999987666
No 83
>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=75.97 E-value=15 Score=34.50 Aligned_cols=74 Identities=18% Similarity=0.139 Sum_probs=54.2
Q ss_pred ChhHHHHHHHHHHHHHhcCChhhHHHHHHHHHhhccccchhHHHHHHHHHHHHhhcCHHHHHHHHHHHHHHhcC
Q 013640 124 GPDQIEALYQYAKFQFECGNYSGAADYLYQYRALCTNSERRLSALWGKMAAEILMQNWDIALEELNQLKEKVDD 197 (439)
Q Consensus 124 t~e~~~al~~~ak~~y~~Gdy~~A~~~L~~~~~~~~~~~~k~~~lwg~la~eIl~~~w~~a~~~l~klke~id~ 197 (439)
.....+.++..|..++..|+|+.|...+..+...-+++.....+....-.+-...++|+.|.+...++-+...+
T Consensus 29 ~~~~~~~~~~~g~~~~~~~~~~~A~~~~~~~~~~~p~~~~~~~a~~~la~~~~~~~~~~~A~~~~~~~l~~~p~ 102 (235)
T TIGR03302 29 EEWPAEELYEEAKEALDSGDYTEAIKYFEALESRYPFSPYAEQAQLDLAYAYYKSGDYAEAIAAADRFIRLHPN 102 (235)
T ss_pred ccCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCchhHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHCcC
Confidence 34456689999999999999999999999887766554333344444444555568999998888887665554
No 84
>COG2976 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=75.61 E-value=15 Score=35.52 Aligned_cols=92 Identities=18% Similarity=0.160 Sum_probs=60.5
Q ss_pred HHHHHHhcCCChhHHHHHHHHHHHHHhcCChhhHHHHHHHHHhhccccchhHHHHHHHHHHHHhhcCHHHHHHHHHHHHH
Q 013640 114 LQMLHDRYQIGPDQIEALYQYAKFQFECGNYSGAADYLYQYRALCTNSERRLSALWGKMAAEILMQNWDIALEELNQLKE 193 (439)
Q Consensus 114 ~~~l~~~~g~t~e~~~al~~~ak~~y~~Gdy~~A~~~L~~~~~~~~~~~~k~~~lwg~la~eIl~~~w~~a~~~l~klke 193 (439)
++.+...+|-|.=-.-+.+.+||-++++|+++.|...|......+.+...+.=+-.-.=+.-+..+-.|.|++-+.-.++
T Consensus 75 ~ekf~~~n~~t~Ya~laaL~lAk~~ve~~~~d~A~aqL~~~l~~t~De~lk~l~~lRLArvq~q~~k~D~AL~~L~t~~~ 154 (207)
T COG2976 75 AEKFVQANGKTIYAVLAALELAKAEVEANNLDKAEAQLKQALAQTKDENLKALAALRLARVQLQQKKADAALKTLDTIKE 154 (207)
T ss_pred HHHHHhhccccHHHHHHHHHHHHHHHhhccHHHHHHHHHHHHccchhHHHHHHHHHHHHHHHHHhhhHHHHHHHHhcccc
Confidence 34444444434444567789999999999999999999988887776555543444444455556667777665543322
Q ss_pred HhcCCCCCCChHHHHHH
Q 013640 194 KVDDPKSFTSPLNQMQS 210 (439)
Q Consensus 194 ~id~~~~~~~~l~~l~~ 210 (439)
.+|.+....+++
T Consensus 155 -----~~w~~~~~elrG 166 (207)
T COG2976 155 -----ESWAAIVAELRG 166 (207)
T ss_pred -----ccHHHHHHHHhh
Confidence 567666665554
No 85
>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=75.13 E-value=4.6 Score=32.75 Aligned_cols=35 Identities=14% Similarity=0.136 Sum_probs=32.1
Q ss_pred hhhccccHHHHHHHcCCCHHHHHHHHHHHhhcCcc
Q 013640 353 RIHQRIDMAVLAEKLNLNYEEAQRWIVNLIRNSKL 387 (439)
Q Consensus 353 riy~~I~I~~lA~~l~~s~~~~E~wiv~lI~~~rL 387 (439)
+-++..++..||+.+|+|+.-+..++.++.++|.|
T Consensus 28 R~~eGlS~kEIAe~LGIS~~TVk~~l~~~~~~~~~ 62 (73)
T TIGR03879 28 REEAGKTASEIAEELGRTEQTVRNHLKGETKAGGL 62 (73)
T ss_pred HHHcCCCHHHHHHHHCcCHHHHHHHHhcCcccchH
Confidence 66799999999999999999999999998888866
No 86
>PF13384 HTH_23: Homeodomain-like domain; PDB: 2X48_C.
Probab=74.37 E-value=4.1 Score=29.45 Aligned_cols=40 Identities=18% Similarity=0.285 Sum_probs=24.0
Q ss_pred HHHHHHHHhhhhhccccHHHHHHHcCCCHHHHHHHHHHHhhcC
Q 013640 343 ARLFIFETYCRIHQRIDMAVLAEKLNLNYEEAQRWIVNLIRNS 385 (439)
Q Consensus 343 aR~~ife~ycriy~~I~I~~lA~~l~~s~~~~E~wiv~lI~~~ 385 (439)
-|..|..-+.. ..+...+|+.||+|+.-+-+|+-++-..|
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 45666666665 88999999999999999999998875544
No 87
>smart00550 Zalpha Z-DNA-binding domain in adenosine deaminases. Helix-turn-helix-containing domain. Also known as Zab.
Probab=74.13 E-value=5.8 Score=31.18 Aligned_cols=38 Identities=21% Similarity=0.226 Sum_probs=33.0
Q ss_pred hhhhhcc--ccHHHHHHHcCCCHHHHHHHHHHHhhcCccc
Q 013640 351 YCRIHQR--IDMAVLAEKLNLNYEEAQRWIVNLIRNSKLD 388 (439)
Q Consensus 351 ycriy~~--I~I~~lA~~l~~s~~~~E~wiv~lI~~~rL~ 388 (439)
+++-... ++...||++||++...+.+-|.+|...|.+.
T Consensus 14 ~L~~~g~~~~ta~eLa~~lgl~~~~v~r~L~~L~~~G~V~ 53 (68)
T smart00550 14 FLENSGDETSTALQLAKNLGLPKKEVNRVLYSLEKKGKVC 53 (68)
T ss_pred HHHHCCCCCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCEE
Confidence 3445555 9999999999999999999999999998774
No 88
>PF13371 TPR_9: Tetratricopeptide repeat
Probab=73.98 E-value=12 Score=28.44 Aligned_cols=58 Identities=16% Similarity=0.172 Sum_probs=45.1
Q ss_pred HHHHHhcCChhhHHHHHHHHHhhccccchhHHHHHHHHHHHHhhcCHHHHHHHHHHHHHHh
Q 013640 135 AKFQFECGNYSGAADYLYQYRALCTNSERRLSALWGKMAAEILMQNWDIALEELNQLKEKV 195 (439)
Q Consensus 135 ak~~y~~Gdy~~A~~~L~~~~~~~~~~~~k~~~lwg~la~eIl~~~w~~a~~~l~klke~i 195 (439)
+..+...|+|+.|.+++.....+-++ .....+.+=.|-...++|+.|.+.+.+.=+.-
T Consensus 2 ~~~~~~~~~~~~A~~~~~~~l~~~p~---~~~~~~~~a~~~~~~g~~~~A~~~l~~~l~~~ 59 (73)
T PF13371_consen 2 KQIYLQQEDYEEALEVLERALELDPD---DPELWLQRARCLFQLGRYEEALEDLERALELS 59 (73)
T ss_pred HHHHHhCCCHHHHHHHHHHHHHhCcc---cchhhHHHHHHHHHhccHHHHHHHHHHHHHHC
Confidence 56789999999999999998887554 44555556666777899999999988875433
No 89
>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=73.41 E-value=23 Score=26.26 Aligned_cols=45 Identities=16% Similarity=0.263 Sum_probs=36.4
Q ss_pred ccHHHHHHHcCCCHHHHHHHHHHHhhcCccceeecccCCEEEeCC
Q 013640 358 IDMAVLAEKLNLNYEEAQRWIVNLIRNSKLDAKIDAKSGTVIMEP 402 (439)
Q Consensus 358 I~I~~lA~~l~~s~~~~E~wiv~lI~~~rL~aKID~~~g~V~~~~ 402 (439)
++.+.+|+.+|++...+-+.+-.|...|-+.+.-+...+....+.
T Consensus 21 ~~~~ei~~~~~i~~~~i~~~l~~L~~~g~i~~~~~~~~~~~~~~~ 65 (78)
T cd00090 21 LTVSELAERLGLSQSTVSRHLKKLEEAGLVESRREGRRVYYSLTD 65 (78)
T ss_pred cCHHHHHHHHCcCHhHHHHHHHHHHHCCCeEEEEeccEEEEEeCC
Confidence 999999999999999999999999999988876554334444433
No 90
>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=73.24 E-value=13 Score=28.37 Aligned_cols=52 Identities=13% Similarity=0.184 Sum_probs=42.4
Q ss_pred HHHHHHHHHHHHHHhhhhhccc-cHHHHHHHcCCCHHHHHHHHHHHhhcCccc
Q 013640 337 DEFLENARLFIFETYCRIHQRI-DMAVLAEKLNLNYEEAQRWIVNLIRNSKLD 388 (439)
Q Consensus 337 ~~f~e~aR~~ife~ycriy~~I-~I~~lA~~l~~s~~~~E~wiv~lI~~~rL~ 388 (439)
+...+..+..|...-..+-+.+ +...||+.||+|..-+-+-+-.|...|-+.
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 4556677777888788899999 999999999999999999999999988773
No 91
>PF13525 YfiO: Outer membrane lipoprotein; PDB: 3TGO_A 3Q5M_A 2YHC_A.
Probab=73.00 E-value=61 Score=30.43 Aligned_cols=54 Identities=26% Similarity=0.287 Sum_probs=41.9
Q ss_pred HHHHHHhcCCChhHHHHHHHHHHHHHhcCChhhHHHHHHHHHhhccccchhHHH
Q 013640 114 LQMLHDRYQIGPDQIEALYQYAKFQFECGNYSGAADYLYQYRALCTNSERRLSA 167 (439)
Q Consensus 114 ~~~l~~~~g~t~e~~~al~~~ak~~y~~Gdy~~A~~~L~~~~~~~~~~~~k~~~ 167 (439)
++.+...|-.++-.-++.+.+|..+|..|||..|...+..+...-+++...-.+
T Consensus 28 f~~l~~~~P~s~~a~~A~l~la~a~y~~~~y~~A~~~~~~fi~~yP~~~~~~~A 81 (203)
T PF13525_consen 28 FEKLIDRYPNSPYAPQAQLMLAYAYYKQGDYEEAIAAYERFIKLYPNSPKADYA 81 (203)
T ss_dssp HHHHHHH-TTSTTHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHH-TT-TTHHHH
T ss_pred HHHHHHHCCCChHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHCCCCcchhhH
Confidence 456667777788889999999999999999999999999999987775544333
No 92
>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=72.75 E-value=8.9 Score=28.46 Aligned_cols=47 Identities=21% Similarity=0.225 Sum_probs=39.4
Q ss_pred HhhhhhccccHHHHHHHcCCCHHHHHHHHHHHhhcCccceeecccCC
Q 013640 350 TYCRIHQRIDMAVLAEKLNLNYEEAQRWIVNLIRNSKLDAKIDAKSG 396 (439)
Q Consensus 350 ~ycriy~~I~I~~lA~~l~~s~~~~E~wiv~lI~~~rL~aKID~~~g 396 (439)
.++.-+..+++..||+.+|++..-+=+.+-+|+..|-+.-..|..++
T Consensus 10 ~~l~~~~~~~~~~la~~~~~~~~~~t~~i~~L~~~g~I~r~~~~~D~ 56 (59)
T PF01047_consen 10 RILYENGGITQSELAEKLGISRSTVTRIIKRLEKKGLIERERDPDDR 56 (59)
T ss_dssp HHHHHHSSEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEEEETTET
T ss_pred HHHHHcCCCCHHHHHHHHCCChhHHHHHHHHHHHCCCEEeccCCCCC
Confidence 34566888999999999999999999999999999988877776544
No 93
>PRK10747 putative protoheme IX biogenesis protein; Provisional
Probab=72.59 E-value=1.3e+02 Score=31.39 Aligned_cols=97 Identities=11% Similarity=0.136 Sum_probs=63.4
Q ss_pred ccHHHHHHhcCCChhH-HHHHHHHHHHHHhcCChhhHHHHHHHHHhhccccchhHHHHHHHHHHHHhhcCHHHHHHHHHH
Q 013640 112 YNLQMLHDRYQIGPDQ-IEALYQYAKFQFECGNYSGAADYLYQYRALCTNSERRLSALWGKMAAEILMQNWDIALEELNQ 190 (439)
Q Consensus 112 ~n~~~l~~~~g~t~e~-~~al~~~ak~~y~~Gdy~~A~~~L~~~~~~~~~~~~k~~~lwg~la~eIl~~~w~~a~~~l~k 190 (439)
.-.+++++-...+++. +-..+-.|.++...|+|+.|.+.+.......+++......+ ..+-...++|+.|.+-+.+
T Consensus 136 ~A~~~l~~A~~~~~~~~~~~~l~~a~l~l~~g~~~~Al~~l~~~~~~~P~~~~al~ll---~~~~~~~gdw~~a~~~l~~ 212 (398)
T PRK10747 136 RANQHLERAAELADNDQLPVEITRVRIQLARNENHAARHGVDKLLEVAPRHPEVLRLA---EQAYIRTGAWSSLLDILPS 212 (398)
T ss_pred HHHHHHHHHHhcCCcchHHHHHHHHHHHHHCCCHHHHHHHHHHHHhcCCCCHHHHHHH---HHHHHHHHhHHHHHHHHHH
Confidence 3345666655556554 33434459999999999999999999988776554333333 3333556999999988888
Q ss_pred HHHHhcCCCCCCChHHHHHHHHHH
Q 013640 191 LKEKVDDPKSFTSPLNQMQSRIWL 214 (439)
Q Consensus 191 lke~id~~~~~~~~l~~l~~R~Wl 214 (439)
++.....+ +.....+++++|.
T Consensus 213 l~k~~~~~---~~~~~~l~~~a~~ 233 (398)
T PRK10747 213 MAKAHVGD---EEHRAMLEQQAWI 233 (398)
T ss_pred HHHcCCCC---HHHHHHHHHHHHH
Confidence 87643321 1224556667775
No 94
>PRK15359 type III secretion system chaperone protein SscB; Provisional
Probab=72.55 E-value=26 Score=31.14 Aligned_cols=78 Identities=12% Similarity=-0.022 Sum_probs=58.3
Q ss_pred HHHHHhcCCChhHHHHHHHHHHHHHhcCChhhHHHHHHHHHhhccccchhHHHHHHHHHHHHhhcCHHHHHHHHHHHHHH
Q 013640 115 QMLHDRYQIGPDQIEALYQYAKFQFECGNYSGAADYLYQYRALCTNSERRLSALWGKMAAEILMQNWDIALEELNQLKEK 194 (439)
Q Consensus 115 ~~l~~~~g~t~e~~~al~~~ak~~y~~Gdy~~A~~~L~~~~~~~~~~~~k~~~lwg~la~eIl~~~w~~a~~~l~klke~ 194 (439)
..++.-..++|...++++.+|..+...|+|++|.+.+.....+.+++ ...+++.=.|=...++.+.|.+...++-++
T Consensus 45 ~~~~~al~~~P~~~~a~~~lg~~~~~~g~~~~A~~~y~~Al~l~p~~---~~a~~~lg~~l~~~g~~~eAi~~~~~Al~~ 121 (144)
T PRK15359 45 IDFSWLVMAQPWSWRAHIALAGTWMMLKEYTTAINFYGHALMLDASH---PEPVYQTGVCLKMMGEPGLAREAFQTAIKM 121 (144)
T ss_pred HHHHHHHHcCCCcHHHHHHHHHHHHHHhhHHHHHHHHHHHHhcCCCC---cHHHHHHHHHHHHcCCHHHHHHHHHHHHHh
Confidence 44455556788888999999999999999999999999988865532 344444444556678999998888777553
Q ss_pred h
Q 013640 195 V 195 (439)
Q Consensus 195 i 195 (439)
-
T Consensus 122 ~ 122 (144)
T PRK15359 122 S 122 (144)
T ss_pred C
Confidence 3
No 95
>PRK11189 lipoprotein NlpI; Provisional
Probab=72.53 E-value=62 Score=32.22 Aligned_cols=75 Identities=21% Similarity=0.156 Sum_probs=56.5
Q ss_pred HHHHHHhcCCChhHHHHHHHHHHHHHhcCChhhHHHHHHHHHhhccccchhHHHHHHHHHHHHhhcCHHHHHHHHHHHH
Q 013640 114 LQMLHDRYQIGPDQIEALYQYAKFQFECGNYSGAADYLYQYRALCTNSERRLSALWGKMAAEILMQNWDIALEELNQLK 192 (439)
Q Consensus 114 ~~~l~~~~g~t~e~~~al~~~ak~~y~~Gdy~~A~~~L~~~~~~~~~~~~k~~~lwg~la~eIl~~~w~~a~~~l~klk 192 (439)
.+.+++-..+.|+...+++.+|..++..|+|+.|.+.+..+....+++.. -.+|..+. -..++.+.|.+.+.+..
T Consensus 118 ~~~~~~Al~l~P~~~~a~~~lg~~l~~~g~~~eA~~~~~~al~~~P~~~~--~~~~~~l~--~~~~~~~~A~~~l~~~~ 192 (296)
T PRK11189 118 YEAFDSVLELDPTYNYAYLNRGIALYYGGRYELAQDDLLAFYQDDPNDPY--RALWLYLA--ESKLDPKQAKENLKQRY 192 (296)
T ss_pred HHHHHHHHHhCCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhCCCCHH--HHHHHHHH--HccCCHHHHHHHHHHHH
Confidence 44556666778888889999999999999999999999999987776542 45666443 23567788888776543
No 96
>smart00419 HTH_CRP helix_turn_helix, cAMP Regulatory protein.
Probab=71.45 E-value=11 Score=26.31 Aligned_cols=33 Identities=21% Similarity=0.236 Sum_probs=29.8
Q ss_pred ccccHHHHHHHcCCCHHHHHHHHHHHhhcCccc
Q 013640 356 QRIDMAVLAEKLNLNYEEAQRWIVNLIRNSKLD 388 (439)
Q Consensus 356 ~~I~I~~lA~~l~~s~~~~E~wiv~lI~~~rL~ 388 (439)
-.++...||+.+|+|...+-+-|..|...|-+.
T Consensus 7 ~~~s~~~la~~l~~s~~tv~~~l~~L~~~g~l~ 39 (48)
T smart00419 7 LPLTRQEIAELLGLTRETVSRTLKRLEKEGLIS 39 (48)
T ss_pred eccCHHHHHHHHCCCHHHHHHHHHHHHHCCCEE
Confidence 357889999999999999999999999988774
No 97
>COG1849 Uncharacterized protein conserved in archaea [Function unknown]
Probab=71.23 E-value=30 Score=29.22 Aligned_cols=33 Identities=27% Similarity=0.319 Sum_probs=27.6
Q ss_pred hhHHHHHHHHHHHHHhcCChhhHHHHHHHHHhh
Q 013640 125 PDQIEALYQYAKFQFECGNYSGAADYLYQYRAL 157 (439)
Q Consensus 125 ~e~~~al~~~ak~~y~~Gdy~~A~~~L~~~~~~ 157 (439)
.++..+.+.=|++|++.|||..|...+.....+
T Consensus 38 ~~ma~~Y~~Dakyf~ekGD~vtAfa~~sYa~g~ 70 (90)
T COG1849 38 VDMAESYFEDAKYFLEKGDYVTAFAALSYAHGW 70 (90)
T ss_pred HHHHHHHHHHHHHHHHcCcHHHHHHHHHHHHHH
Confidence 357888999999999999999999887665554
No 98
>PRK11189 lipoprotein NlpI; Provisional
Probab=70.90 E-value=46 Score=33.16 Aligned_cols=76 Identities=14% Similarity=0.165 Sum_probs=58.2
Q ss_pred HHHHHhcCCChhHHHHHHHHHHHHHhcCChhhHHHHHHHHHhhccccchhHHHHHHHHHHHHhhcCHHHHHHHHHHHHH
Q 013640 115 QMLHDRYQIGPDQIEALYQYAKFQFECGNYSGAADYLYQYRALCTNSERRLSALWGKMAAEILMQNWDIALEELNQLKE 193 (439)
Q Consensus 115 ~~l~~~~g~t~e~~~al~~~ak~~y~~Gdy~~A~~~L~~~~~~~~~~~~k~~~lwg~la~eIl~~~w~~a~~~l~klke 193 (439)
..+++-....|+..++++.+|..+...|+|+.|.+.+.....+.++. ..+.+.+-.+-...++++.|.+.+.++-+
T Consensus 85 ~~~~~Al~l~P~~~~a~~~lg~~~~~~g~~~~A~~~~~~Al~l~P~~---~~a~~~lg~~l~~~g~~~eA~~~~~~al~ 160 (296)
T PRK11189 85 NDFSQALALRPDMADAYNYLGIYLTQAGNFDAAYEAFDSVLELDPTY---NYAYLNRGIALYYGGRYELAQDDLLAFYQ 160 (296)
T ss_pred HHHHHHHHcCCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhCCCC---HHHHHHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 34455566678888999999999999999999999998888866543 23444444445567899999998888755
No 99
>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=70.57 E-value=6.3 Score=33.09 Aligned_cols=41 Identities=15% Similarity=0.242 Sum_probs=34.6
Q ss_pred hhhhccccHHHHHHHcCCCHHHHHHHHHHHhhcCccceeec
Q 013640 352 CRIHQRIDMAVLAEKLNLNYEEAQRWIVNLIRNSKLDAKID 392 (439)
Q Consensus 352 criy~~I~I~~lA~~l~~s~~~~E~wiv~lI~~~rL~aKID 392 (439)
|..=.-|+++.|+++||++.++++.-|-.|+.+|.|=..||
T Consensus 60 ~~~~~Gv~v~~I~~~l~~~~~~v~~al~~L~~eG~IYsTiD 100 (102)
T PF08784_consen 60 PNSEEGVHVDEIAQQLGMSENEVRKALDFLSNEGHIYSTID 100 (102)
T ss_dssp ---TTTEEHHHHHHHSTS-HHHHHHHHHHHHHTTSEEESSS
T ss_pred CCCCCcccHHHHHHHhCcCHHHHHHHHHHHHhCCeEecccC
Confidence 44556799999999999999999999999999999988887
No 100
>KOG1861 consensus Leucine permease transcriptional regulator [Transcription]
Probab=70.40 E-value=31 Score=37.33 Aligned_cols=109 Identities=19% Similarity=0.253 Sum_probs=67.4
Q ss_pred hHHHHHHHHHHHhcccccchHHHHHHHhhhccCCc-chHH----HHHHHhhhcCChhHHHHHHHHHHHHhcCCccccccc
Q 013640 251 HLLRYLATAFIVNKRRRPQFKDFIKVIQQEQNSYK-DPIT----EFLACVYVNYDFDGAQKKMKECEEVILNDPFLGKRV 325 (439)
Q Consensus 251 ~lLrYlvva~il~~~r~~~l~~i~~vi~qe~~~Y~-Dpit----~f~~~lY~~fdF~~aq~~L~~~e~~i~~D~FL~~~~ 325 (439)
.|+-|-++..|+++.+- |+...+...+.+-+ ||.. ++-. ..---++-.|++.-. .=+=++
T Consensus 388 EF~AYriLY~i~tkN~~----di~sll~~lt~E~ked~~V~hAL~vR~-A~~~GNY~kFFrLY~-------~AP~M~--- 452 (540)
T KOG1861|consen 388 EFTAYRILYYIFTKNYP----DILSLLRDLTEEDKEDEAVAHALEVRS-AVTLGNYHKFFRLYL-------TAPNMS--- 452 (540)
T ss_pred hHHHHHHHHHHHhcCch----HHHHHHHhccHhhccCHHHHHHHHHHH-HHHhccHHHHHHHHh-------hcccch---
Confidence 35579999999998763 55555555444444 7732 2221 111122222223211 111221
Q ss_pred ccccccccccHHHHHHHHHHHHHHHhhhhhc-cccHHHHHHHcCCCHHHHHHHHHHHhhc
Q 013640 326 EDSNFATVPLRDEFLENARLFIFETYCRIHQ-RIDMAVLAEKLNLNYEEAQRWIVNLIRN 384 (439)
Q Consensus 326 ~~~~~~~~~~~~~f~e~aR~~ife~ycriy~-~I~I~~lA~~l~~s~~~~E~wiv~lI~~ 384 (439)
.-..|-|++-.|..+..-.|+.|. +|+++.|++.|.+..-+ .++++...
T Consensus 453 -------~yLmdlF~erER~~Al~ii~KsyrP~i~~~fi~~~laf~~~e---~c~~~l~~ 502 (540)
T KOG1861|consen 453 -------GYLMDLFLERERKKALTIICKSYRPTITVDFIASELAFDSME---DCVNFLNE 502 (540)
T ss_pred -------hHHHHHHHHHHHHHHHHHHHHHcCCCccHHHHhhhhhhchHH---HHHHHHhc
Confidence 124589999999999999999999 99999999999987655 34444443
No 101
>PRK02603 photosystem I assembly protein Ycf3; Provisional
Probab=69.80 E-value=32 Score=31.08 Aligned_cols=69 Identities=19% Similarity=0.091 Sum_probs=46.1
Q ss_pred hhHHHHHHHHHHHHHhcCChhhHHHHHHHHHhhccccchhHHHHHHHHHHHHhhcCHHHHHHHHHHHHH
Q 013640 125 PDQIEALYQYAKFQFECGNYSGAADYLYQYRALCTNSERRLSALWGKMAAEILMQNWDIALEELNQLKE 193 (439)
Q Consensus 125 ~e~~~al~~~ak~~y~~Gdy~~A~~~L~~~~~~~~~~~~k~~~lwg~la~eIl~~~w~~a~~~l~klke 193 (439)
+.....++.+|..+...|+|+.|.+++........+......++...-.+-.-.++++.|.+.+.+.-+
T Consensus 32 ~~~a~~~~~lg~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~ 100 (172)
T PRK02603 32 AKEAFVYYRDGMSAQADGEYAEALENYEEALKLEEDPNDRSYILYNMGIIYASNGEHDKALEYYHQALE 100 (172)
T ss_pred hhhHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHhhccchHHHHHHHHHHHHHHcCCHHHHHHHHHHHHH
Confidence 344557899999999999999999999888765544322223322222233335788888887666544
No 102
>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=69.06 E-value=18 Score=32.00 Aligned_cols=61 Identities=7% Similarity=0.070 Sum_probs=44.3
Q ss_pred HHHHHHHHhhhhhccccHHHHHHHcCCCHHHHHHHHHHHhhcCccceeecccCCEEEeCCCC
Q 013640 343 ARLFIFETYCRIHQRIDMAVLAEKLNLNYEEAQRWIVNLIRNSKLDAKIDAKSGTVIMEPTH 404 (439)
Q Consensus 343 aR~~ife~ycriy~~I~I~~lA~~l~~s~~~~E~wiv~lI~~~rL~aKID~~~g~V~~~~~~ 404 (439)
+|.+++-....-.+.++++.||+.+|+|+.++++-+..|-+.|=+..+=. ..|-....+++
T Consensus 11 l~~l~~La~~~~~~~~s~~~ia~~~~ip~~~l~kil~~L~~~glv~s~~G-~~Ggy~l~~~~ 71 (135)
T TIGR02010 11 VTAMLDLALNAETGPVTLADISERQGISLSYLEQLFAKLRKAGLVKSVRG-PGGGYQLGRPA 71 (135)
T ss_pred HHHHHHHHhCCCCCcCcHHHHHHHHCcCHHHHHHHHHHHHHCCceEEEeC-CCCCEeccCCH
Confidence 34444444444445799999999999999999999999999998765333 34445555555
No 103
>PRK04424 fatty acid biosynthesis transcriptional regulator; Provisional
Probab=68.97 E-value=6.6 Score=36.97 Aligned_cols=46 Identities=15% Similarity=0.014 Sum_probs=40.5
Q ss_pred HHHHHHHHHhhhhhccccHHHHHHHcCCCHHHHHHHHHHHhhcCcc
Q 013640 342 NARLFIFETYCRIHQRIDMAVLAEKLNLNYEEAQRWIVNLIRNSKL 387 (439)
Q Consensus 342 ~aR~~ife~ycriy~~I~I~~lA~~l~~s~~~~E~wiv~lI~~~rL 387 (439)
.-|......+++-+..++++.||+.||+|..=+-+.|..|-..|++
T Consensus 6 ~~R~~~Il~~l~~~~~~~~~~La~~~~vS~~TiRRDl~~L~~~g~~ 51 (185)
T PRK04424 6 KERQKALQELIEENPFITDEELAEKFGVSIQTIRLDRMELGIPELR 51 (185)
T ss_pred HHHHHHHHHHHHHCCCEEHHHHHHHHCcCHHHHHHHHHHHhcchHH
Confidence 3488888999999999999999999999999999999877776654
No 104
>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=68.96 E-value=8.2 Score=29.90 Aligned_cols=40 Identities=18% Similarity=0.364 Sum_probs=32.3
Q ss_pred HHhcCC-ChhHHHHHHHHHHHHHhcCChhhHHHHHHHHHhh
Q 013640 118 HDRYQI-GPDQIEALYQYAKFQFECGNYSGAADYLYQYRAL 157 (439)
Q Consensus 118 ~~~~g~-t~e~~~al~~~ak~~y~~Gdy~~A~~~L~~~~~~ 157 (439)
.+.+|= .+++..++..+|..++..|+|+.|.+++......
T Consensus 35 ~~~~~~~~~~~a~~~~~lg~~~~~~g~~~~A~~~~~~al~i 75 (78)
T PF13424_consen 35 EEQLGDDHPDTANTLNNLGECYYRLGDYEEALEYYQKALDI 75 (78)
T ss_dssp HHHTTTHHHHHHHHHHHHHHHHHHTTHHHHHHHHHHHHHHH
T ss_pred HHHHCCCCHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHhh
Confidence 445552 2457889999999999999999999999887654
No 105
>PRK10857 DNA-binding transcriptional regulator IscR; Provisional
Probab=68.92 E-value=16 Score=33.92 Aligned_cols=62 Identities=8% Similarity=0.112 Sum_probs=46.7
Q ss_pred HHHHHHHHHhhhhhccccHHHHHHHcCCCHHHHHHHHHHHhhcCccceeecccCCEEEeCCCC
Q 013640 342 NARLFIFETYCRIHQRIDMAVLAEKLNLNYEEAQRWIVNLIRNSKLDAKIDAKSGTVIMEPTH 404 (439)
Q Consensus 342 ~aR~~ife~ycriy~~I~I~~lA~~l~~s~~~~E~wiv~lI~~~rL~aKID~~~g~V~~~~~~ 404 (439)
..|.+++-.+..-.+.++++.||+++|+|+.++++-+..|-+.|=+...=.. .|-....+++
T Consensus 10 Al~~l~~lA~~~~~~~vs~~eIA~~~~ip~~~l~kIl~~L~~aGLv~s~rG~-~GGy~Lar~p 71 (164)
T PRK10857 10 AVTAMLDVALNSEAGPVPLADISERQGISLSYLEQLFSRLRKNGLVSSVRGP-GGGYLLGKDA 71 (164)
T ss_pred HHHHHHHHHhCCCCCcCcHHHHHHHHCcCHHHHHHHHHHHHHCCCEEeCCCC-CCCeeccCCH
Confidence 3455555556666678999999999999999999999999999988764333 4445555555
No 106
>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=68.84 E-value=20 Score=26.82 Aligned_cols=44 Identities=18% Similarity=0.319 Sum_probs=35.6
Q ss_pred HHHHHhcCCChhHHHHHHHHHHHHHhcC-ChhhHHHHHHHHHhhc
Q 013640 115 QMLHDRYQIGPDQIEALYQYAKFQFECG-NYSGAADYLYQYRALC 158 (439)
Q Consensus 115 ~~l~~~~g~t~e~~~al~~~ak~~y~~G-dy~~A~~~L~~~~~~~ 158 (439)
...++-..+.++...+++.+|..++..| +|++|.+.+.....+-
T Consensus 24 ~~~~~ai~~~p~~~~~~~~~g~~~~~~~~~~~~A~~~~~~al~l~ 68 (69)
T PF13414_consen 24 EYFEKAIELDPNNAEAYYNLGLAYMKLGKDYEEAIEDFEKALKLD 68 (69)
T ss_dssp HHHHHHHHHSTTHHHHHHHHHHHHHHTTTHHHHHHHHHHHHHHHS
T ss_pred HHHHHHHHcCCCCHHHHHHHHHHHHHhCccHHHHHHHHHHHHHcC
Confidence 3444555557788889999999999999 7999999998877653
No 107
>KOG2796 consensus Uncharacterized conserved protein [Function unknown]
Probab=68.62 E-value=1.4e+02 Score=30.47 Aligned_cols=121 Identities=16% Similarity=0.232 Sum_probs=76.2
Q ss_pred cCCCchHHHHHHHHhCCCCCChhHHHHHHHHHHHHHHHHHHHHHHHHHhhCChhHHHHhhhcchhccHHHHHHhcCCChh
Q 013640 47 KTNMVDYAMDIHKSLYHTEDVPQDMVERRVEVVARLKALEERAAPIVSFLQNPNSFQDLRANDQHYNLQMLHDRYQIGPD 126 (439)
Q Consensus 47 ~TnM~dy~~~~~~~l~~~~~~p~e~~~k~~ev~~~l~~l~~~~~~~~~~~~~~e~~~~l~~~dk~~n~~~l~~~~g~t~e 126 (439)
.-.||||.+.+-...-+. +.--+.+-+.++..|+.-++.++..++... ...+.+..-++..|+
T Consensus 116 rGSmVPFsmR~lhAe~~~------~lgnpqesLdRl~~L~~~V~~ii~~~e~~~--------~~ESsv~lW~KRl~~--- 178 (366)
T KOG2796|consen 116 RGSMVPFSMRILHAELQQ------YLGNPQESLDRLHKLKTVVSKILANLEQGL--------AEESSIRLWRKRLGR--- 178 (366)
T ss_pred cCccccHHHHHHHHHHHH------hcCCcHHHHHHHHHHHHHHHHHHHHHHhcc--------chhhHHHHHHHHHHH---
Confidence 456888887753332111 111244556677778877777666554321 223344444555552
Q ss_pred HHHHHHHHHHHHHhcCChhhHHHHHHHHHhhccccchhHHHHHHHHHHHHhhcCHHHHHHHHH
Q 013640 127 QIEALYQYAKFQFECGNYSGAADYLYQYRALCTNSERRLSALWGKMAAEILMQNWDIALEELN 189 (439)
Q Consensus 127 ~~~al~~~ak~~y~~Gdy~~A~~~L~~~~~~~~~~~~k~~~lwg~la~eIl~~~w~~a~~~l~ 189 (439)
..|-++.+..-.|+|.-+.+.+..++..-+..+..+..-+|.++ .+.+|-.+|.....
T Consensus 179 ---Vmy~~~~~llG~kEy~iS~d~~~~vi~~~~e~~p~L~s~Lgr~~--MQ~GD~k~a~~yf~ 236 (366)
T KOG2796|consen 179 ---VMYSMANCLLGMKEYVLSVDAYHSVIKYYPEQEPQLLSGLGRIS--MQIGDIKTAEKYFQ 236 (366)
T ss_pred ---HHHHHHHHHhcchhhhhhHHHHHHHHHhCCcccHHHHHHHHHHH--HhcccHHHHHHHHH
Confidence 56888999999999999999999999965544555555555554 56678777766554
No 108
>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=68.59 E-value=98 Score=34.02 Aligned_cols=82 Identities=13% Similarity=0.192 Sum_probs=56.5
Q ss_pred ccHHHHHHhcCCChhHHHHHHHHHHHHHhcCChhhHHHHHHHHHhhccccchhHHHHHHHHHHHHhhcCHHHHHHHHHHH
Q 013640 112 YNLQMLHDRYQIGPDQIEALYQYAKFQFECGNYSGAADYLYQYRALCTNSERRLSALWGKMAAEILMQNWDIALEELNQL 191 (439)
Q Consensus 112 ~n~~~l~~~~g~t~e~~~al~~~ak~~y~~Gdy~~A~~~L~~~~~~~~~~~~k~~~lwg~la~eIl~~~w~~a~~~l~kl 191 (439)
.-+..+++-..+.|+....++.+|..++..|+|+.|...+.......+.... .-..+|.+- .-.++|+.|.+...++
T Consensus 417 ~A~~~~~kal~l~P~~~~~~~~la~~~~~~g~~~eA~~~~~~al~~~P~~~~-~~~~lg~~~--~~~g~~~~A~~~~~~A 493 (615)
T TIGR00990 417 QAGKDYQKSIDLDPDFIFSHIQLGVTQYKEGSIASSMATFRRCKKNFPEAPD-VYNYYGELL--LDQNKFDEAIEKFDTA 493 (615)
T ss_pred HHHHHHHHHHHcCccCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhCCCChH-HHHHHHHHH--HHccCHHHHHHHHHHH
Confidence 3345666667778888888999999999999999999999888775543221 111223222 3367888998888887
Q ss_pred HHHhc
Q 013640 192 KEKVD 196 (439)
Q Consensus 192 ke~id 196 (439)
-++-.
T Consensus 494 l~l~p 498 (615)
T TIGR00990 494 IELEK 498 (615)
T ss_pred HhcCC
Confidence 66543
No 109
>PF10475 DUF2450: Protein of unknown function N-terminal domain (DUF2450) ; InterPro: IPR019515 This entry represents Vacuolar protein sorting-associated protein 54, and is thought to be involved in retrograde transport from early and late endosomes to late Golgi found in eukaryotes, but its function is not known.
Probab=68.55 E-value=1.3e+02 Score=30.06 Aligned_cols=49 Identities=20% Similarity=0.316 Sum_probs=31.4
Q ss_pred hhccHHHHHHhcCCChhHHHHHHHHHHHHHhcCChhhHHHHHHHHHhhcc
Q 013640 110 QHYNLQMLHDRYQIGPDQIEALYQYAKFQFECGNYSGAADYLYQYRALCT 159 (439)
Q Consensus 110 k~~n~~~l~~~~g~t~e~~~al~~~ak~~y~~Gdy~~A~~~L~~~~~~~~ 159 (439)
|..|+..+.+... ....+...-...+-..+.|||.+|.+++..++....
T Consensus 110 kr~~l~~ll~~L~-~i~~v~~~~~~l~~ll~~~dy~~Al~li~~~~~~l~ 158 (291)
T PF10475_consen 110 KRQNLKKLLEKLE-QIKTVQQTQSRLQELLEEGDYPGALDLIEECQQLLE 158 (291)
T ss_pred HHHHHHHHHHHHH-HHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHH
Confidence 3444444443333 333333445556677899999999999999888754
No 110
>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=68.43 E-value=12 Score=28.04 Aligned_cols=52 Identities=19% Similarity=0.139 Sum_probs=38.9
Q ss_pred HhcCChhhHHHHHHHHHhhccccchhHHHHHHHHHHHHhhcCHHHHHHHHHHHHH
Q 013640 139 FECGNYSGAADYLYQYRALCTNSERRLSALWGKMAAEILMQNWDIALEELNQLKE 193 (439)
Q Consensus 139 y~~Gdy~~A~~~L~~~~~~~~~~~~k~~~lwg~la~eIl~~~w~~a~~~l~klke 193 (439)
++.|+|+.|.+.+.......++ ...+..+.-.|-+-.++++.|.+.+.++..
T Consensus 2 l~~~~~~~A~~~~~~~l~~~p~---~~~~~~~la~~~~~~g~~~~A~~~l~~~~~ 53 (68)
T PF14559_consen 2 LKQGDYDEAIELLEKALQRNPD---NPEARLLLAQCYLKQGQYDEAEELLERLLK 53 (68)
T ss_dssp HHTTHHHHHHHHHHHHHHHTTT---SHHHHHHHHHHHHHTT-HHHHHHHHHCCHG
T ss_pred hhccCHHHHHHHHHHHHHHCCC---CHHHHHHHHHHHHHcCCHHHHHHHHHHHHH
Confidence 5789999999999998886554 455555666777888999998877776644
No 111
>PF11972 HTH_13: HTH DNA binding domain; InterPro: IPR021068 The proteins in this entry have not been characterised. They contain a C-terminal helix-turn-helix DNA binding domain.
Probab=67.54 E-value=10 Score=29.10 Aligned_cols=34 Identities=21% Similarity=0.201 Sum_probs=29.4
Q ss_pred HHhhhhhccccHHHHHHHcCCCHHHHHHHHHHHh
Q 013640 349 ETYCRIHQRIDMAVLAEKLNLNYEEAQRWIVNLI 382 (439)
Q Consensus 349 e~ycriy~~I~I~~lA~~l~~s~~~~E~wiv~lI 382 (439)
-..+-.++-||.+++|+.||+|+.-+.+.+..|-
T Consensus 5 idll~~~P~Vsa~mva~~L~vT~~~A~~li~eLg 38 (54)
T PF11972_consen 5 IDLLLSRPLVSAPMVAKELGVTPQAAQRLIAELG 38 (54)
T ss_pred HHHHHhCccccHHHHHHHhCCCHHHHHHHHHHhh
Confidence 3456778999999999999999999999987763
No 112
>PLN03088 SGT1, suppressor of G2 allele of SKP1; Provisional
Probab=67.50 E-value=27 Score=36.07 Aligned_cols=76 Identities=16% Similarity=0.158 Sum_probs=53.2
Q ss_pred HHHhcCCChhHHHHHHHHHHHHHhcCChhhHHHHHHHHHhhccccchhHHHHHHHHHHHHhhcCHHHHHHHHHHHHHHh
Q 013640 117 LHDRYQIGPDQIEALYQYAKFQFECGNYSGAADYLYQYRALCTNSERRLSALWGKMAAEILMQNWDIALEELNQLKEKV 195 (439)
Q Consensus 117 l~~~~g~t~e~~~al~~~ak~~y~~Gdy~~A~~~L~~~~~~~~~~~~k~~~lwg~la~eIl~~~w~~a~~~l~klke~i 195 (439)
+.+-....+....+++.+|..+...|+|+.|...+.....+.++.. .+++.+=.+-...++++.|...+.++-++-
T Consensus 25 ~~~Al~~~P~~~~a~~~~a~~~~~~g~~~eAl~~~~~Al~l~P~~~---~a~~~lg~~~~~lg~~~eA~~~~~~al~l~ 100 (356)
T PLN03088 25 YTQAIDLDPNNAELYADRAQANIKLGNFTEAVADANKAIELDPSLA---KAYLRKGTACMKLEEYQTAKAALEKGASLA 100 (356)
T ss_pred HHHHHHhCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCcCCH---HHHHHHHHHHHHhCCHHHHHHHHHHHHHhC
Confidence 3344445666677889999999999999999999988888765432 223333334455688999988888776643
No 113
>PRK09802 DNA-binding transcriptional regulator AgaR; Provisional
Probab=67.39 E-value=13 Score=37.11 Aligned_cols=55 Identities=7% Similarity=-0.095 Sum_probs=47.7
Q ss_pred ccHHHHHHHHHHHHHHHhhhhhccccHHHHHHHcCCCHHHHHHHHHHHhhcCccc
Q 013640 334 PLRDEFLENARLFIFETYCRIHQRIDMAVLAEKLNLNYEEAQRWIVNLIRNSKLD 388 (439)
Q Consensus 334 ~~~~~f~e~aR~~ife~ycriy~~I~I~~lA~~l~~s~~~~E~wiv~lI~~~rL~ 388 (439)
.-.+.--+.-|+...-.+++-+.+|+++.||+.||+|..=+-|.|..|=..|.+.
T Consensus 8 ~~~~~~~~~eR~~~Il~~L~~~~~vtv~eLa~~l~VS~~TIRRDL~~Le~~G~l~ 62 (269)
T PRK09802 8 GEKRVTGTSERREQIIQRLRQQGSVQVNDLSALYGVSTVTIRNDLAFLEKQGIAV 62 (269)
T ss_pred chhhhccHHHHHHHHHHHHHHcCCEeHHHHHHHHCCCHHHHHHHHHHHHhCCCeE
Confidence 3445555567999999999999999999999999999999999999998877764
No 114
>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=67.36 E-value=17 Score=27.37 Aligned_cols=35 Identities=17% Similarity=0.239 Sum_probs=31.3
Q ss_pred hhccccHHHHHHHcCCCHHHHHHHHHHHhhcCccc
Q 013640 354 IHQRIDMAVLAEKLNLNYEEAQRWIVNLIRNSKLD 388 (439)
Q Consensus 354 iy~~I~I~~lA~~l~~s~~~~E~wiv~lI~~~rL~ 388 (439)
....++...||+.+|+|..-+.+.|..|...|-+.
T Consensus 22 ~~~~~s~~ela~~~g~s~~tv~r~l~~L~~~g~i~ 56 (67)
T cd00092 22 VQLPLTRQEIADYLGLTRETVSRTLKELEEEGLIS 56 (67)
T ss_pred ccCCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCEE
Confidence 44579999999999999999999999999988764
No 115
>PRK11447 cellulose synthase subunit BcsC; Provisional
Probab=67.05 E-value=2.5e+02 Score=33.63 Aligned_cols=181 Identities=14% Similarity=0.140 Sum_probs=95.3
Q ss_pred HHHHHHhcCCChhHHHHHHHHHHHHHhcCChhhHHHHHHHHHhhccccchhHHHHHHHHHHHHhhcCHHHHHHHHHHHHH
Q 013640 114 LQMLHDRYQIGPDQIEALYQYAKFQFECGNYSGAADYLYQYRALCTNSERRLSALWGKMAAEILMQNWDIALEELNQLKE 193 (439)
Q Consensus 114 ~~~l~~~~g~t~e~~~al~~~ak~~y~~Gdy~~A~~~L~~~~~~~~~~~~k~~~lwg~la~eIl~~~w~~a~~~l~klke 193 (439)
++.+++-..+.|+.....+.+|..+++.|+++.|.+.+..+....+++... -...+.+ -...++|+.|.+.++++..
T Consensus 481 ~~~~~~Al~~~P~~~~~~~~LA~~~~~~G~~~~A~~~l~~al~~~P~~~~~-~~a~al~--l~~~~~~~~Al~~l~~l~~ 557 (1157)
T PRK11447 481 AELQRQRLALDPGSVWLTYRLAQDLRQAGQRSQADALMRRLAQQKPNDPEQ-VYAYGLY--LSGSDRDRAALAHLNTLPR 557 (1157)
T ss_pred HHHHHHHHHhCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHcCCCCHHH-HHHHHHH--HHhCCCHHHHHHHHHhCCc
Confidence 345556666677778899999999999999999999999987755433211 1111222 2235788888887766532
Q ss_pred HhcCCCCCCChHHHHHHHHHHHHH-HHH-HHhcCccchHHHHHHhccccchhHHHhhchhHHHHHHHHHHHhcc-c-ccc
Q 013640 194 KVDDPKSFTSPLNQMQSRIWLMHW-SLF-IFFNHDNGRTLIIDLFNQDKYLNAIQTNAPHLLRYLATAFIVNKR-R-RPQ 269 (439)
Q Consensus 194 ~id~~~~~~~~l~~l~~R~WllHw-sLf-~~fn~~~~~~~l~d~F~~~~yl~~Iqt~~p~lLrYlvva~il~~~-r-~~~ 269 (439)
..|......+..|-+.-+. .+- .+.... ..+..+..+.. + -..|... +.+|.+.... + ...
T Consensus 558 -----~~~~~~~~~l~~~l~~~~~l~~a~~l~~~G-~~~eA~~~l~~--~-----p~~~~~~--~~La~~~~~~g~~~~A 622 (1157)
T PRK11447 558 -----AQWNSNIQELAQRLQSDQVLETANRLRDSG-KEAEAEALLRQ--Q-----PPSTRID--LTLADWAQQRGDYAAA 622 (1157)
T ss_pred -----hhcChhHHHHHHHHhhhHHHHHHHHHHHCC-CHHHHHHHHHh--C-----CCCchHH--HHHHHHHHHcCCHHHH
Confidence 2343333333333222110 000 011111 11122222220 0 0112222 3334443322 2 333
Q ss_pred hHHHHHHHhhhccCCcchHHHHHHHhhhcCChhHHHHHHHHHHH
Q 013640 270 FKDFIKVIQQEQNSYKDPITEFLACVYVNYDFDGAQKKMKECEE 313 (439)
Q Consensus 270 l~~i~~vi~qe~~~Y~Dpit~f~~~lY~~fdF~~aq~~L~~~e~ 313 (439)
+..+-+++... +...+....+...+...-++++|.+.+..+.+
T Consensus 623 ~~~y~~al~~~-P~~~~a~~~la~~~~~~g~~~eA~~~l~~ll~ 665 (1157)
T PRK11447 623 RAAYQRVLTRE-PGNADARLGLIEVDIAQGDLAAARAQLAKLPA 665 (1157)
T ss_pred HHHHHHHHHhC-CCCHHHHHHHHHHHHHCCCHHHHHHHHHHHhc
Confidence 44444555553 33335577777777788888888888876544
No 116
>PF13512 TPR_18: Tetratricopeptide repeat
Probab=66.91 E-value=37 Score=30.97 Aligned_cols=68 Identities=19% Similarity=0.130 Sum_probs=43.9
Q ss_pred HHHHHHHHHHhcCChhhHHHHHHHHHhhccccchhHHHHHHHHHHHHhhcCHHHHHHHHHHHHHHhcC
Q 013640 130 ALYQYAKFQFECGNYSGAADYLYQYRALCTNSERRLSALWGKMAAEILMQNWDIALEELNQLKEKVDD 197 (439)
Q Consensus 130 al~~~ak~~y~~Gdy~~A~~~L~~~~~~~~~~~~k~~~lwg~la~eIl~~~w~~a~~~l~klke~id~ 197 (439)
.+|+-|.--++.|+|..|.+.|..+...-+..+-.-.+.+...=+=...++|+.|.....+.-.+--.
T Consensus 12 ~ly~~a~~~l~~~~Y~~A~~~le~L~~ryP~g~ya~qAqL~l~yayy~~~~y~~A~a~~~rFirLhP~ 79 (142)
T PF13512_consen 12 ELYQEAQEALQKGNYEEAIKQLEALDTRYPFGEYAEQAQLDLAYAYYKQGDYEEAIAAYDRFIRLHPT 79 (142)
T ss_pred HHHHHHHHHHHhCCHHHHHHHHHHHHhcCCCCcccHHHHHHHHHHHHHccCHHHHHHHHHHHHHhCCC
Confidence 66777777777777777777777777665554444444455555556666777777776666655544
No 117
>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=66.67 E-value=11 Score=22.14 Aligned_cols=29 Identities=31% Similarity=0.505 Sum_probs=24.3
Q ss_pred HHHHHHHHHHHhcCChhhHHHHHHHHHhh
Q 013640 129 EALYQYAKFQFECGNYSGAADYLYQYRAL 157 (439)
Q Consensus 129 ~al~~~ak~~y~~Gdy~~A~~~L~~~~~~ 157 (439)
+..+.+|..++..|+|+.|...+......
T Consensus 2 ~~~~~~a~~~~~~~~~~~a~~~~~~~~~~ 30 (34)
T smart00028 2 EALYNLGNAYLKLGDYDEALEYYEKALEL 30 (34)
T ss_pred hHHHHHHHHHHHHhhHHHHHHHHHHHHcc
Confidence 36788999999999999999988776553
No 118
>KOG3054 consensus Uncharacterized conserved protein [Function unknown]
Probab=65.88 E-value=13 Score=37.01 Aligned_cols=55 Identities=16% Similarity=0.312 Sum_probs=47.7
Q ss_pred HHHhhhhhccccHHHHHHHcCCCHHHHHHHHHHHhhcCccceeecccCCEEEeCC
Q 013640 348 FETYCRIHQRIDMAVLAEKLNLNYEEAQRWIVNLIRNSKLDAKIDAKSGTVIMEP 402 (439)
Q Consensus 348 fe~ycriy~~I~I~~lA~~l~~s~~~~E~wiv~lI~~~rL~aKID~~~g~V~~~~ 402 (439)
|.+|++--++|.|..||..||+-..++=.-|-+|+.+|-|.+-||--.--|-++.
T Consensus 205 Fv~YIk~nKvV~ledLas~f~Lrtqd~inriq~~l~eg~ltGVmDDRGKfIYIS~ 259 (299)
T KOG3054|consen 205 FVEYIKKNKVVPLEDLASEFGLRTQDSINRIQELLAEGLLTGVMDDRGKFIYISM 259 (299)
T ss_pred HHHHHHhcCeeeHHHHHHHhCccHHHHHHHHHHHHHhhhheeeecCCCceEEecH
Confidence 5679999999999999999999999888899999999999999996655555543
No 119
>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=65.78 E-value=17 Score=27.01 Aligned_cols=50 Identities=16% Similarity=0.163 Sum_probs=36.1
Q ss_pred HHHHHHHHHHHHHhhhhhcccc-HHHHHHHcCCCHHHHHHHHHHHhhcCcc
Q 013640 338 EFLENARLFIFETYCRIHQRID-MAVLAEKLNLNYEEAQRWIVNLIRNSKL 387 (439)
Q Consensus 338 ~f~e~aR~~ife~ycriy~~I~-I~~lA~~l~~s~~~~E~wiv~lI~~~rL 387 (439)
++.+..+..+...-..+...+. ...||+.+|+|..-+.+.|..|-..|=+
T Consensus 5 ~~~~~i~~~i~~~~~~~~~~~~~~~~la~~~~is~~~v~~~l~~L~~~G~i 55 (66)
T cd07377 5 QIADQLREAILSGELKPGDRLPSERELAEELGVSRTTVREALRELEAEGLV 55 (66)
T ss_pred HHHHHHHHHHHcCCCCCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCE
Confidence 3344444444444334555555 9999999999999999999999887754
No 120
>PF12862 Apc5: Anaphase-promoting complex subunit 5
Probab=65.75 E-value=22 Score=29.33 Aligned_cols=59 Identities=22% Similarity=0.280 Sum_probs=42.2
Q ss_pred HhcCChhhHHHHHHHHHhhccccchh------HHHHHHHHHHHHhhcCHHHHHHHHHHHHHHhcC
Q 013640 139 FECGNYSGAADYLYQYRALCTNSERR------LSALWGKMAAEILMQNWDIALEELNQLKEKVDD 197 (439)
Q Consensus 139 y~~Gdy~~A~~~L~~~~~~~~~~~~k------~~~lwg~la~eIl~~~w~~a~~~l~klke~id~ 197 (439)
.++|||.+|.+.|..+...+...... -.++...-..-..+++++.|.+.++.+=.+-.+
T Consensus 9 ~~~~dy~~A~d~L~~~fD~~~~~~~~~~~~~~~~all~lA~~~~~~G~~~~A~~~l~eAi~~Are 73 (94)
T PF12862_consen 9 LRSGDYSEALDALHRYFDYAKQSNNSSSNSGLAYALLNLAELHRRFGHYEEALQALEEAIRLARE 73 (94)
T ss_pred HHcCCHHHHHHHHHHHHHHHhhcccchhhHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHH
Confidence 57899999999999988877653322 344555555666789999998877766555554
No 121
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=65.27 E-value=29 Score=32.60 Aligned_cols=92 Identities=11% Similarity=0.105 Sum_probs=62.7
Q ss_pred cccHHHHH--HHHHHHHHHHhhhhhccccHHHHHHHcCCCHHHHHHHHHHHhhcCccceeecccCCEEEeCCCCc---hh
Q 013640 333 VPLRDEFL--ENARLFIFETYCRIHQRIDMAVLAEKLNLNYEEAQRWIVNLIRNSKLDAKIDAKSGTVIMEPTHP---NV 407 (439)
Q Consensus 333 ~~~~~~f~--e~aR~~ife~ycriy~~I~I~~lA~~l~~s~~~~E~wiv~lI~~~rL~aKID~~~g~V~~~~~~~---~~ 407 (439)
..+..+++ ...+..|+.. +..|..++-+.||+.|||+..++-+-|..|-.+|-+..+-=+..| +++|.- -.
T Consensus 11 ~~~l~~~~~~~~~~~~Vl~~-L~~~g~~tdeeLA~~Lgi~~~~VRk~L~~L~e~gLv~~~r~r~~~---~Gr~~y~w~l~ 86 (178)
T PRK06266 11 QKVLFEIMEGDEEGFEVLKA-LIKKGEVTDEEIAEQTGIKLNTVRKILYKLYDARLADYKREKDEE---TNWYTYTWKPE 86 (178)
T ss_pred HHHHHHHhcCCccHhHHHHH-HHHcCCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCeEEeeeeccC---CCcEEEEEEeC
Confidence 45666677 4446666665 557889999999999999999999999999888866543322222 255552 34
Q ss_pred HHHHHHhhhhhhhHHHHHHHHHHh
Q 013640 408 YEQLIDHTKGLSGRTYKLVGQLLE 431 (439)
Q Consensus 408 yqqvi~kt~~L~~R~q~L~~~i~~ 431 (439)
|.++++. +..|..++...+..
T Consensus 87 ~~~i~d~---ik~~~~~~~~klk~ 107 (178)
T PRK06266 87 LEKLPEI---IKKKKMEELKKLKE 107 (178)
T ss_pred HHHHHHH---HHHHHHHHHHHHHH
Confidence 5666644 55566666555554
No 122
>PLN03088 SGT1, suppressor of G2 allele of SKP1; Provisional
Probab=65.13 E-value=66 Score=33.19 Aligned_cols=46 Identities=13% Similarity=0.127 Sum_probs=38.3
Q ss_pred HHHHHhcCCChhHHHHHHHHHHHHHhcCChhhHHHHHHHHHhhccc
Q 013640 115 QMLHDRYQIGPDQIEALYQYAKFQFECGNYSGAADYLYQYRALCTN 160 (439)
Q Consensus 115 ~~l~~~~g~t~e~~~al~~~ak~~y~~Gdy~~A~~~L~~~~~~~~~ 160 (439)
..+++-..+.++...+++.+|..++..|+|+.|...+..+..+.++
T Consensus 57 ~~~~~Al~l~P~~~~a~~~lg~~~~~lg~~~eA~~~~~~al~l~P~ 102 (356)
T PLN03088 57 ADANKAIELDPSLAKAYLRKGTACMKLEEYQTAKAALEKGASLAPG 102 (356)
T ss_pred HHHHHHHHhCcCCHHHHHHHHHHHHHhCCHHHHHHHHHHHHHhCCC
Confidence 4455555567777889999999999999999999999998887654
No 123
>PRK10906 DNA-binding transcriptional repressor GlpR; Provisional
Probab=65.11 E-value=11 Score=37.02 Aligned_cols=47 Identities=13% Similarity=0.136 Sum_probs=42.2
Q ss_pred HHHHHHHHHhhhhhccccHHHHHHHcCCCHHHHHHHHHHHhhcCccc
Q 013640 342 NARLFIFETYCRIHQRIDMAVLAEKLNLNYEEAQRWIVNLIRNSKLD 388 (439)
Q Consensus 342 ~aR~~ife~ycriy~~I~I~~lA~~l~~s~~~~E~wiv~lI~~~rL~ 388 (439)
.-|....-.+++-++.+++..||+.||||++-+-|.|..|-..|.+.
T Consensus 4 ~~R~~~Il~~l~~~~~~~~~ela~~l~vS~~TiRRdL~~Le~~g~l~ 50 (252)
T PRK10906 4 TQRHDAIIELVKQQGYVSTEELVEHFSVSPQTIRRDLNDLAEQNKIL 50 (252)
T ss_pred HHHHHHHHHHHHHcCCEeHHHHHHHhCCCHHHHHHHHHHHHHCCCEE
Confidence 35777788888999999999999999999999999999999888763
No 124
>PRK11920 rirA iron-responsive transcriptional regulator; Reviewed
Probab=65.03 E-value=23 Score=32.27 Aligned_cols=61 Identities=8% Similarity=0.072 Sum_probs=44.6
Q ss_pred HHHHHHHHHhhhhhccccHHHHHHHcCCCHHHHHHHHHHHhhcCccceeecccCCEEEeCCCC
Q 013640 342 NARLFIFETYCRIHQRIDMAVLAEKLNLNYEEAQRWIVNLIRNSKLDAKIDAKSGTVIMEPTH 404 (439)
Q Consensus 342 ~aR~~ife~ycriy~~I~I~~lA~~l~~s~~~~E~wiv~lI~~~rL~aKID~~~g~V~~~~~~ 404 (439)
..|.+++-... .-..++++.||++.|+|+.++++.+..|.+.|=+..+=-. +|=....+++
T Consensus 10 Alr~L~~LA~~-~~~~~s~~eIA~~~~is~~~L~kIl~~L~~aGlv~S~rG~-~GGy~La~~p 70 (153)
T PRK11920 10 AIRMLMYCAAN-DGKLSRIPEIARAYGVSELFLFKILQPLVEAGLVETVRGR-NGGVRLGRPA 70 (153)
T ss_pred HHHHHHHHHhC-CCCcCcHHHHHHHHCcCHHHHHHHHHHHHHCCCEEeecCC-CCCeeecCCH
Confidence 45666665533 3456899999999999999999999999999977655433 4444555544
No 125
>PF04703 FaeA: FaeA-like protein; PDB: 2JT1_A 2HTJ_A.
Probab=64.96 E-value=11 Score=29.47 Aligned_cols=34 Identities=18% Similarity=0.349 Sum_probs=30.2
Q ss_pred hccccHHHHHHHcCCCHHHHHHHHHHHhhcCccc
Q 013640 355 HQRIDMAVLAEKLNLNYEEAQRWIVNLIRNSKLD 388 (439)
Q Consensus 355 y~~I~I~~lA~~l~~s~~~~E~wiv~lI~~~rL~ 388 (439)
+..++-..+|+.+|+|.-.+..+|..|-.+|++.
T Consensus 13 ~~p~~T~eiA~~~gls~~~aR~yL~~Le~eG~V~ 46 (62)
T PF04703_consen 13 NGPLKTREIADALGLSIYQARYYLEKLEKEGKVE 46 (62)
T ss_dssp TS-EEHHHHHHHHTS-HHHHHHHHHHHHHCTSEE
T ss_pred CCCCCHHHHHHHhCCCHHHHHHHHHHHHHCCCEE
Confidence 8999999999999999999999999999999774
No 126
>KOG2376 consensus Signal recognition particle, subunit Srp72 [Intracellular trafficking, secretion, and vesicular transport]
Probab=64.80 E-value=73 Score=35.53 Aligned_cols=108 Identities=24% Similarity=0.319 Sum_probs=72.0
Q ss_pred cCCCchHHHHHHHHhCCCCCChhHHHHHHHHHHHHHHHHHHHHHHHHHhhCChh------HHHHhhhcchhccHHHHHHh
Q 013640 47 KTNMVDYAMDIHKSLYHTEDVPQDMVERRVEVVARLKALEERAAPIVSFLQNPN------SFQDLRANDQHYNLQMLHDR 120 (439)
Q Consensus 47 ~TnM~dy~~~~~~~l~~~~~~p~e~~~k~~ev~~~l~~l~~~~~~~~~~~~~~e------~~~~l~~~dk~~n~~~l~~~ 120 (439)
.-||.|.+....+.+ +..+..+.+-|..|+=+++..++..+.--.+.+|.. ...+|-.+-+....+.++..
T Consensus 91 rlnk~Dealk~~~~~---~~~~~~ll~L~AQvlYrl~~ydealdiY~~L~kn~~dd~d~~~r~nl~a~~a~l~~~~~q~v 167 (652)
T KOG2376|consen 91 RLNKLDEALKTLKGL---DRLDDKLLELRAQVLYRLERYDEALDIYQHLAKNNSDDQDEERRANLLAVAAALQVQLLQSV 167 (652)
T ss_pred HcccHHHHHHHHhcc---cccchHHHHHHHHHHHHHhhHHHHHHHHHHHHhcCCchHHHHHHHHHHHHHHhhhHHHHHhc
Confidence 446677777665533 344566888899999999999988866555644431 12222212223333344444
Q ss_pred cCCChhHHHHHHHHHHHHHhcCChhhHHHHHHHHHhh
Q 013640 121 YQIGPDQIEALYQYAKFQFECGNYSGAADYLYQYRAL 157 (439)
Q Consensus 121 ~g~t~e~~~al~~~ak~~y~~Gdy~~A~~~L~~~~~~ 157 (439)
-..+.+.-+-+|..|-.+.+.|+|..|.+.|.-.+..
T Consensus 168 ~~v~e~syel~yN~Ac~~i~~gky~qA~elL~kA~~~ 204 (652)
T KOG2376|consen 168 PEVPEDSYELLYNTACILIENGKYNQAIELLEKALRI 204 (652)
T ss_pred cCCCcchHHHHHHHHHHHHhcccHHHHHHHHHHHHHH
Confidence 4445557889999999999999999999999887433
No 127
>PF12895 Apc3: Anaphase-promoting complex, cyclosome, subunit 3; PDB: 3KAE_D 3Q4A_B 2C2L_D 3Q47_B 3Q49_B 2XPI_A 3ULQ_A.
Probab=64.67 E-value=8 Score=30.70 Aligned_cols=38 Identities=21% Similarity=0.428 Sum_probs=28.6
Q ss_pred HHHHHhcCCChhHHHHHHHHHHHHHhcCChhhHHHHHHH
Q 013640 115 QMLHDRYQIGPDQIEALYQYAKFQFECGNYSGAADYLYQ 153 (439)
Q Consensus 115 ~~l~~~~g~t~e~~~al~~~ak~~y~~Gdy~~A~~~L~~ 153 (439)
+.+++ .++.+...+..+-+|+.+++.|+|++|.+.|..
T Consensus 46 ~~~~~-~~~~~~~~~~~~l~a~~~~~l~~y~eAi~~l~~ 83 (84)
T PF12895_consen 46 ELLQK-LKLDPSNPDIHYLLARCLLKLGKYEEAIKALEK 83 (84)
T ss_dssp HHHHC-HTHHHCHHHHHHHHHHHHHHTT-HHHHHHHHHH
T ss_pred HHHHH-hCCCCCCHHHHHHHHHHHHHhCCHHHHHHHHhc
Confidence 34444 444555677888889999999999999998865
No 128
>PRK10434 srlR DNA-bindng transcriptional repressor SrlR; Provisional
Probab=64.41 E-value=44 Score=32.93 Aligned_cols=47 Identities=13% Similarity=0.097 Sum_probs=42.6
Q ss_pred HHHHHHHHHhhhhhccccHHHHHHHcCCCHHHHHHHHHHHhhcCccc
Q 013640 342 NARLFIFETYCRIHQRIDMAVLAEKLNLNYEEAQRWIVNLIRNSKLD 388 (439)
Q Consensus 342 ~aR~~ife~ycriy~~I~I~~lA~~l~~s~~~~E~wiv~lI~~~rL~ 388 (439)
+-|....-.+++-+.+|+++.||+.||||++=+-+-|..|-..|.+.
T Consensus 4 ~eR~~~Il~~L~~~~~v~v~eLa~~l~VS~~TIRRDL~~Le~~g~l~ 50 (256)
T PRK10434 4 RQRQAAILEYLQKQGKTSVEELAQYFDTTGTTIRKDLVILEHAGTVI 50 (256)
T ss_pred HHHHHHHHHHHHHcCCEEHHHHHHHHCCCHHHHHHHHHHHHHCCCEE
Confidence 34888889999999999999999999999999999999998888653
No 129
>PRK10411 DNA-binding transcriptional activator FucR; Provisional
Probab=64.00 E-value=15 Score=36.03 Aligned_cols=54 Identities=24% Similarity=0.230 Sum_probs=45.0
Q ss_pred HHHHHHHHHhhhhhccccHHHHHHHcCCCHHHHHHHHHHHhhcCccceeecccCCEEE
Q 013640 342 NARLFIFETYCRIHQRIDMAVLAEKLNLNYEEAQRWIVNLIRNSKLDAKIDAKSGTVI 399 (439)
Q Consensus 342 ~aR~~ife~ycriy~~I~I~~lA~~l~~s~~~~E~wiv~lI~~~rL~aKID~~~g~V~ 399 (439)
+.|....-.+++-++.++.+.||+.||+|+.=+.+.|..|-..|++. ...|..+
T Consensus 3 ~~R~~~Il~~l~~~~~~~~~eLa~~l~VS~~TiRRdL~~L~~~~~l~----r~~Gga~ 56 (240)
T PRK10411 3 AARQQAIVDLLLNHTSLTTEALAEQLNVSKETIRRDLNELQTQGKIL----RNHGRAK 56 (240)
T ss_pred hHHHHHHHHHHHHcCCCcHHHHHHHHCcCHHHHHHHHHHHHHCCCEE----EecCeEE
Confidence 45788888889999999999999999999999999999998877653 3455543
No 130
>smart00346 HTH_ICLR helix_turn_helix isocitrate lyase regulation.
Probab=63.51 E-value=42 Score=26.80 Aligned_cols=56 Identities=21% Similarity=0.236 Sum_probs=40.0
Q ss_pred HHHHHHHhhhhh-ccccHHHHHHHcCCCHHHHHHHHHHHhhcCccceeecccCCEEEeC
Q 013640 344 RLFIFETYCRIH-QRIDMAVLAEKLNLNYEEAQRWIVNLIRNSKLDAKIDAKSGTVIME 401 (439)
Q Consensus 344 R~~ife~ycriy-~~I~I~~lA~~l~~s~~~~E~wiv~lI~~~rL~aKID~~~g~V~~~ 401 (439)
|.+..-.++.-+ ..+++..||+.+|++..-+-+.|..|...|-+.. +...|....+
T Consensus 6 r~~~Il~~l~~~~~~~t~~~ia~~l~i~~~tv~r~l~~L~~~g~l~~--~~~~~~y~l~ 62 (91)
T smart00346 6 RGLAVLRALAEEPGGLTLAELAERLGLSKSTAHRLLNTLQELGYVEQ--DGQNGRYRLG 62 (91)
T ss_pred HHHHHHHHHHhCCCCcCHHHHHHHhCCCHHHHHHHHHHHHHCCCeee--cCCCCceeec
Confidence 333333344444 6799999999999999999999999999887753 2234544443
No 131
>COG4105 ComL DNA uptake lipoprotein [General function prediction only]
Probab=63.27 E-value=34 Score=34.15 Aligned_cols=84 Identities=19% Similarity=0.214 Sum_probs=58.2
Q ss_pred HHHHHHhcCCChhHHHHHHHHHHHHHhcCChhhHHHHHHHHHhhccccchhHHHHHHHHHHHHh-----hcCHHHHHHHH
Q 013640 114 LQMLHDRYQIGPDQIEALYQYAKFQFECGNYSGAADYLYQYRALCTNSERRLSALWGKMAAEIL-----MQNWDIALEEL 188 (439)
Q Consensus 114 ~~~l~~~~g~t~e~~~al~~~ak~~y~~Gdy~~A~~~L~~~~~~~~~~~~k~~~lwg~la~eIl-----~~~w~~a~~~l 188 (439)
++-+...|-+++-.-.+++.+|.-+|+.|+|+.|...+..|..+-++....-=++.-+.-+.++ ..|-..+..-+
T Consensus 57 fe~l~~~~p~s~~~~qa~l~l~yA~Yk~~~y~~A~~~~drFi~lyP~~~n~dY~~YlkgLs~~~~i~~~~rDq~~~~~A~ 136 (254)
T COG4105 57 FEALDSRHPFSPYSEQAQLDLAYAYYKNGEYDLALAYIDRFIRLYPTHPNADYAYYLKGLSYFFQIDDVTRDQSAARAAF 136 (254)
T ss_pred HHHHHHcCCCCcccHHHHHHHHHHHHhcccHHHHHHHHHHHHHhCCCCCChhHHHHHHHHHHhccCCccccCHHHHHHHH
Confidence 3456677888999999999999999999999999999999999877644321111111111222 23445566666
Q ss_pred HHHHHHhcC
Q 013640 189 NQLKEKVDD 197 (439)
Q Consensus 189 ~klke~id~ 197 (439)
..++++|++
T Consensus 137 ~~f~~~i~r 145 (254)
T COG4105 137 AAFKELVQR 145 (254)
T ss_pred HHHHHHHHH
Confidence 777777765
No 132
>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=63.06 E-value=2e+02 Score=30.00 Aligned_cols=74 Identities=11% Similarity=-0.013 Sum_probs=42.5
Q ss_pred HHHHHhcCCChhHH--HHHHHHHHHHHhcCChhhHHHHHHHHHhhccccchhHHHHHHHHHHHHhhcCHHHHHHHHHH
Q 013640 115 QMLHDRYQIGPDQI--EALYQYAKFQFECGNYSGAADYLYQYRALCTNSERRLSALWGKMAAEILMQNWDIALEELNQ 190 (439)
Q Consensus 115 ~~l~~~~g~t~e~~--~al~~~ak~~y~~Gdy~~A~~~L~~~~~~~~~~~~k~~~lwg~la~eIl~~~w~~a~~~l~k 190 (439)
+.+++-....|+.- ..+.-+|.++++.|+|++|.++|.....+...++...-..+|.+. ...++.+.|.+--.+
T Consensus 320 ~~~e~~lk~~p~~~~~~ll~sLg~l~~~~~~~~~A~~~le~a~a~~~~p~~~~~~~La~ll--~~~g~~~~A~~~~~~ 395 (409)
T TIGR00540 320 KLIEKQAKNVDDKPKCCINRALGQLLMKHGEFIEAADAFKNVAACKEQLDANDLAMAADAF--DQAGDKAEAAAMRQD 395 (409)
T ss_pred HHHHHHHHhCCCChhHHHHHHHHHHHHHcccHHHHHHHHHHhHHhhcCCCHHHHHHHHHHH--HHcCCHHHHHHHHHH
Confidence 34444444444444 677789999999999999999998655544333332222333322 234555555444433
No 133
>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=62.81 E-value=81 Score=32.87 Aligned_cols=78 Identities=10% Similarity=0.092 Sum_probs=51.9
Q ss_pred HHHHHHhcCCChhH-HHHHHHHHHHHHhcCChhhHHHHHHHHHhhccccchhHHHHHHHHHHHHhhcCHHHHHHHHHHHH
Q 013640 114 LQMLHDRYQIGPDQ-IEALYQYAKFQFECGNYSGAADYLYQYRALCTNSERRLSALWGKMAAEILMQNWDIALEELNQLK 192 (439)
Q Consensus 114 ~~~l~~~~g~t~e~-~~al~~~ak~~y~~Gdy~~A~~~L~~~~~~~~~~~~k~~~lwg~la~eIl~~~w~~a~~~l~klk 192 (439)
.+++++.....++. +..-..+|+++.+.|+|+.|.+.+.......+++.. ++--...+-+..+||+.|.+.+.++.
T Consensus 138 ~~~l~~a~~~~p~~~l~~~~~~a~l~l~~~~~~~Al~~l~~l~~~~P~~~~---~l~ll~~~~~~~~d~~~a~~~l~~l~ 214 (409)
T TIGR00540 138 NQHLEEAAELAGNDNILVEIARTRILLAQNELHAARHGVDKLLEMAPRHKE---VLKLAEEAYIRSGAWQALDDIIDNMA 214 (409)
T ss_pred HHHHHHHHHhCCcCchHHHHHHHHHHHHCCCHHHHHHHHHHHHHhCCCCHH---HHHHHHHHHHHHhhHHHHHHHHHHHH
Confidence 34554433323332 334455699999999999999999998887654432 22233334466889999998888877
Q ss_pred HH
Q 013640 193 EK 194 (439)
Q Consensus 193 e~ 194 (439)
+.
T Consensus 215 k~ 216 (409)
T TIGR00540 215 KA 216 (409)
T ss_pred Hc
Confidence 65
No 134
>PF12688 TPR_5: Tetratrico peptide repeat
Probab=62.71 E-value=1.1e+02 Score=26.88 Aligned_cols=110 Identities=19% Similarity=0.205 Sum_probs=69.9
Q ss_pred HHHHHHHHHHhcCChhhHHHHHHHHHhhccccchhHHHHHHHHHHHHhhcCHHHHHHHHHHHHHHhcCCCCCCChHHHHH
Q 013640 130 ALYQYAKFQFECGNYSGAADYLYQYRALCTNSERRLSALWGKMAAEILMQNWDIALEELNQLKEKVDDPKSFTSPLNQMQ 209 (439)
Q Consensus 130 al~~~ak~~y~~Gdy~~A~~~L~~~~~~~~~~~~k~~~lwg~la~eIl~~~w~~a~~~l~klke~id~~~~~~~~l~~l~ 209 (439)
++|..|-.+-..|+.+.|..++........+....-.++++.=.+---.+.-+.|..-+.+..+-... ..|..++....
T Consensus 3 ~~~~~A~a~d~~G~~~~Ai~~Y~~Al~~gL~~~~~~~a~i~lastlr~LG~~deA~~~L~~~~~~~p~-~~~~~~l~~f~ 81 (120)
T PF12688_consen 3 ALYELAWAHDSLGREEEAIPLYRRALAAGLSGADRRRALIQLASTLRNLGRYDEALALLEEALEEFPD-DELNAALRVFL 81 (120)
T ss_pred hHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCchHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHCCC-ccccHHHHHHH
Confidence 67888999999999999999888887765555555667777766666778888888877766554433 34555554333
Q ss_pred HHHHHHHHHHHHHhcCccchHHHHHHhcc--ccchhHHH
Q 013640 210 SRIWLMHWSLFIFFNHDNGRTLIIDLFNQ--DKYLNAIQ 246 (439)
Q Consensus 210 ~R~WllHwsLf~~fn~~~~~~~l~d~F~~--~~yl~~Iq 246 (439)
. + +|+-.-++.++-..++..... +.|-.+|.
T Consensus 82 A----l--~L~~~gr~~eAl~~~l~~la~~~~~y~ra~~ 114 (120)
T PF12688_consen 82 A----L--ALYNLGRPKEALEWLLEALAETLPRYRRAIR 114 (120)
T ss_pred H----H--HHHHCCCHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 1 0 222222344555555555542 35555553
No 135
>PRK10866 outer membrane biogenesis protein BamD; Provisional
Probab=62.41 E-value=43 Score=32.70 Aligned_cols=70 Identities=11% Similarity=0.055 Sum_probs=57.3
Q ss_pred HHHHHHHHHHHHhcCChhhHHHHHHHHHhhccccchhHHHHHHHHHHHHhhcCHHHHHHHHHHHHHHhcC
Q 013640 128 IEALYQYAKFQFECGNYSGAADYLYQYRALCTNSERRLSALWGKMAAEILMQNWDIALEELNQLKEKVDD 197 (439)
Q Consensus 128 ~~al~~~ak~~y~~Gdy~~A~~~L~~~~~~~~~~~~k~~~lwg~la~eIl~~~w~~a~~~l~klke~id~ 197 (439)
-+.+|..|.-.++.|+|+.|.+.+..+...-+++.....+....--+-....+++.|....+++-+..-+
T Consensus 32 ~~~~Y~~A~~~~~~g~y~~Ai~~f~~l~~~yP~s~~a~~a~l~la~ayy~~~~y~~A~~~~e~fi~~~P~ 101 (243)
T PRK10866 32 PSEIYATAQQKLQDGNWKQAITQLEALDNRYPFGPYSQQVQLDLIYAYYKNADLPLAQAAIDRFIRLNPT 101 (243)
T ss_pred HHHHHHHHHHHHHCCCHHHHHHHHHHHHHhCCCChHHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHhCcC
Confidence 4479999999999999999999999999988877666666666666777788999998888777665554
No 136
>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=62.35 E-value=26 Score=25.24 Aligned_cols=43 Identities=21% Similarity=0.267 Sum_probs=35.9
Q ss_pred HHHHHHHHHhhhhhccccHHHHHHHcCCCHHHHHHHHHHHhhcCc
Q 013640 342 NARLFIFETYCRIHQRIDMAVLAEKLNLNYEEAQRWIVNLIRNSK 386 (439)
Q Consensus 342 ~aR~~ife~ycriy~~I~I~~lA~~l~~s~~~~E~wiv~lI~~~r 386 (439)
..|..|....+. ...+...||+.+|+|+..+-+-|-.|...|=
T Consensus 2 ~~R~~Il~~L~~--~~~~~~el~~~l~~s~~~vs~hL~~L~~~gl 44 (47)
T PF01022_consen 2 PTRLRILKLLSE--GPLTVSELAEELGLSQSTVSHHLKKLREAGL 44 (47)
T ss_dssp HHHHHHHHHHTT--SSEEHHHHHHHHTS-HHHHHHHHHHHHHTTS
T ss_pred HHHHHHHHHHHh--CCCchhhHHHhccccchHHHHHHHHHHHCcC
Confidence 357788877777 8899999999999999999999999877664
No 137
>PRK15359 type III secretion system chaperone protein SscB; Provisional
Probab=61.95 E-value=73 Score=28.18 Aligned_cols=47 Identities=11% Similarity=0.043 Sum_probs=39.6
Q ss_pred HHHHHhcCCChhHHHHHHHHHHHHHhcCChhhHHHHHHHHHhhcccc
Q 013640 115 QMLHDRYQIGPDQIEALYQYAKFQFECGNYSGAADYLYQYRALCTNS 161 (439)
Q Consensus 115 ~~l~~~~g~t~e~~~al~~~ak~~y~~Gdy~~A~~~L~~~~~~~~~~ 161 (439)
...++-..+.|+..++++.+|..+...|++++|.+.+.......+++
T Consensus 79 ~~y~~Al~l~p~~~~a~~~lg~~l~~~g~~~eAi~~~~~Al~~~p~~ 125 (144)
T PRK15359 79 NFYGHALMLDASHPEPVYQTGVCLKMMGEPGLAREAFQTAIKMSYAD 125 (144)
T ss_pred HHHHHHHhcCCCCcHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCC
Confidence 34455556678888899999999999999999999999998887764
No 138
>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=61.09 E-value=25 Score=25.44 Aligned_cols=37 Identities=19% Similarity=0.362 Sum_probs=28.6
Q ss_pred HHHHHHHhhhhhccccHHHHHHHcCCCHHHHHHHHHHHhh
Q 013640 344 RLFIFETYCRIHQRIDMAVLAEKLNLNYEEAQRWIVNLIR 383 (439)
Q Consensus 344 R~~ife~ycriy~~I~I~~lA~~l~~s~~~~E~wiv~lI~ 383 (439)
|..+..-| +...++..+|+.+|+|..-+-++..+.|.
T Consensus 10 r~vi~~~y---~~~~t~~eIa~~lg~s~~~V~~~~~~al~ 46 (50)
T PF04545_consen 10 REVIRLRY---FEGLTLEEIAERLGISRSTVRRILKRALK 46 (50)
T ss_dssp HHHHHHHH---TST-SHHHHHHHHTSCHHHHHHHHHHHHH
T ss_pred HHHHHHHh---cCCCCHHHHHHHHCCcHHHHHHHHHHHHH
Confidence 33444444 78899999999999999999998887764
No 139
>PRK10370 formate-dependent nitrite reductase complex subunit NrfG; Provisional
Probab=60.97 E-value=25 Score=33.14 Aligned_cols=83 Identities=14% Similarity=0.153 Sum_probs=59.7
Q ss_pred ccHHHHHHhcCCChhHHHHHHHHHHH-HHhcCC--hhhHHHHHHHHHhhccccchhHHHHHHHHHHHHhhcCHHHHHHHH
Q 013640 112 YNLQMLHDRYQIGPDQIEALYQYAKF-QFECGN--YSGAADYLYQYRALCTNSERRLSALWGKMAAEILMQNWDIALEEL 188 (439)
Q Consensus 112 ~n~~~l~~~~g~t~e~~~al~~~ak~-~y~~Gd--y~~A~~~L~~~~~~~~~~~~k~~~lwg~la~eIl~~~w~~a~~~l 188 (439)
.-...+++-+.+.++..+.++.+|.. ++..|+ +++|.+.+......-++.. .+++..=.+....++|+.|....
T Consensus 91 ~A~~a~~~Al~l~P~~~~~~~~lA~aL~~~~g~~~~~~A~~~l~~al~~dP~~~---~al~~LA~~~~~~g~~~~Ai~~~ 167 (198)
T PRK10370 91 NALLAYRQALQLRGENAELYAALATVLYYQAGQHMTPQTREMIDKALALDANEV---TALMLLASDAFMQADYAQAIELW 167 (198)
T ss_pred HHHHHHHHHHHhCCCCHHHHHHHHHHHHHhcCCCCcHHHHHHHHHHHHhCCCCh---hHHHHHHHHHHHcCCHHHHHHHH
Confidence 33456667777888888999999995 578887 5899999988888655432 23333333344578999999999
Q ss_pred HHHHHHhcC
Q 013640 189 NQLKEKVDD 197 (439)
Q Consensus 189 ~klke~id~ 197 (439)
.++-++...
T Consensus 168 ~~aL~l~~~ 176 (198)
T PRK10370 168 QKVLDLNSP 176 (198)
T ss_pred HHHHhhCCC
Confidence 888877776
No 140
>PRK12370 invasion protein regulator; Provisional
Probab=60.95 E-value=2.5e+02 Score=30.59 Aligned_cols=78 Identities=12% Similarity=-0.013 Sum_probs=58.2
Q ss_pred HHHHHHhcCCChhHHHHHHHHHHHHHhcCChhhHHHHHHHHHhhccccchhHHHHHHHHHHHHhhcCHHHHHHHHHHHHH
Q 013640 114 LQMLHDRYQIGPDQIEALYQYAKFQFECGNYSGAADYLYQYRALCTNSERRLSALWGKMAAEILMQNWDIALEELNQLKE 193 (439)
Q Consensus 114 ~~~l~~~~g~t~e~~~al~~~ak~~y~~Gdy~~A~~~L~~~~~~~~~~~~k~~~lwg~la~eIl~~~w~~a~~~l~klke 193 (439)
...+++-..+.|+.-+++..+|..+...|+++.|.+++.....+.++... +....=.+-...++++.|...+.++-+
T Consensus 324 ~~~~~~Al~ldP~~~~a~~~lg~~~~~~g~~~~A~~~~~~Al~l~P~~~~---a~~~lg~~l~~~G~~~eAi~~~~~Al~ 400 (553)
T PRK12370 324 KEHAIKATELDHNNPQALGLLGLINTIHSEYIVGSLLFKQANLLSPISAD---IKYYYGWNLFMAGQLEEALQTINECLK 400 (553)
T ss_pred HHHHHHHHhcCCCCHHHHHHHHHHHHHccCHHHHHHHHHHHHHhCCCCHH---HHHHHHHHHHHCCCHHHHHHHHHHHHh
Confidence 34556667778888889999999999999999999999999887765432 222222234456899999888888765
Q ss_pred H
Q 013640 194 K 194 (439)
Q Consensus 194 ~ 194 (439)
+
T Consensus 401 l 401 (553)
T PRK12370 401 L 401 (553)
T ss_pred c
Confidence 4
No 141
>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=60.65 E-value=2.6e+02 Score=30.71 Aligned_cols=64 Identities=17% Similarity=0.143 Sum_probs=52.1
Q ss_pred HHHHHHHHHHHHhcCChhhHHHHHHHHHhhccccchhHHHHHHHHHHHHhhcCHHHHHHHHHHHHHH
Q 013640 128 IEALYQYAKFQFECGNYSGAADYLYQYRALCTNSERRLSALWGKMAAEILMQNWDIALEELNQLKEK 194 (439)
Q Consensus 128 ~~al~~~ak~~y~~Gdy~~A~~~L~~~~~~~~~~~~k~~~lwg~la~eIl~~~w~~a~~~l~klke~ 194 (439)
+=++|=+|++|...|+|+.|.+++......++. ..+.+..|-++=--.++...|.+.++.+|++
T Consensus 194 lw~~~~lAqhyd~~g~~~~Al~~Id~aI~htPt---~~ely~~KarilKh~G~~~~Aa~~~~~Ar~L 257 (517)
T PF12569_consen 194 LWTLYFLAQHYDYLGDYEKALEYIDKAIEHTPT---LVELYMTKARILKHAGDLKEAAEAMDEAREL 257 (517)
T ss_pred HHHHHHHHHHHHHhCCHHHHHHHHHHHHhcCCC---cHHHHHHHHHHHHHCCCHHHHHHHHHHHHhC
Confidence 457788999999999999999999999887643 3556666666555679999999999999874
No 142
>PRK13509 transcriptional repressor UlaR; Provisional
Probab=60.59 E-value=16 Score=35.86 Aligned_cols=45 Identities=22% Similarity=0.175 Sum_probs=40.5
Q ss_pred HHHHHHHHhhhhhccccHHHHHHHcCCCHHHHHHHHHHHhhcCcc
Q 013640 343 ARLFIFETYCRIHQRIDMAVLAEKLNLNYEEAQRWIVNLIRNSKL 387 (439)
Q Consensus 343 aR~~ife~ycriy~~I~I~~lA~~l~~s~~~~E~wiv~lI~~~rL 387 (439)
-|....-.+++-+..++++.||+.||+|+.=+.+.|..|-..|.+
T Consensus 5 ~R~~~Il~~l~~~~~~~~~ela~~l~vS~~TirRdL~~Le~~g~i 49 (251)
T PRK13509 5 QRHQILLELLAQLGFVTVEKVIERLGISPATARRDINKLDESGKL 49 (251)
T ss_pred HHHHHHHHHHHHcCCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCE
Confidence 477778888999999999999999999999999999999777765
No 143
>KOG4414 consensus COP9 signalosome, subunit CSN8 [Posttranslational modification, protein turnover, chaperones; Signal transduction mechanisms]
Probab=60.55 E-value=16 Score=33.68 Aligned_cols=46 Identities=20% Similarity=0.185 Sum_probs=39.6
Q ss_pred cHHHHHHHHHHHHHHHhhhhhccccHHHHHHHcCCCHHHHHHHHHH
Q 013640 335 LRDEFLENARLFIFETYCRIHQRIDMAVLAEKLNLNYEEAQRWIVN 380 (439)
Q Consensus 335 ~~~~f~e~aR~~ife~ycriy~~I~I~~lA~~l~~s~~~~E~wiv~ 380 (439)
....|-..-|..+|.-.+..|++|.++.+|--+||+++++-+-|+.
T Consensus 110 imaAf~D~~~kR~FaLl~qAYssI~~~D~A~FlGl~~ddAtk~ilE 155 (197)
T KOG4414|consen 110 IMAAFRDATRKRAFALLLQAYSSIIADDFAAFLGLPEDDATKGILE 155 (197)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCHHHHHHHHHH
Confidence 3456677778889999999999999999999999999998877763
No 144
>KOG2114 consensus Vacuolar assembly/sorting protein PEP5/VPS11 [Intracellular trafficking, secretion, and vesicular transport]
Probab=60.00 E-value=67 Score=37.18 Aligned_cols=121 Identities=14% Similarity=0.234 Sum_probs=78.0
Q ss_pred HHHhcCCChhHHHH-HHHHHHHHHhcCChhhHHHHHHHHHhhcccc--------ch----hHHHHHHHHHHHHhhcCHHH
Q 013640 117 LHDRYQIGPDQIEA-LYQYAKFQFECGNYSGAADYLYQYRALCTNS--------ER----RLSALWGKMAAEILMQNWDI 183 (439)
Q Consensus 117 l~~~~g~t~e~~~a-l~~~ak~~y~~Gdy~~A~~~L~~~~~~~~~~--------~~----k~~~lwg~la~eIl~~~w~~ 183 (439)
|.+.++.+++.+.. ..+||.+.|..|||++|....-......-++ .+ -.+.||...+-++-..|.-+
T Consensus 356 LAk~~~~d~d~~~~i~~kYgd~Ly~Kgdf~~A~~qYI~tI~~le~s~Vi~kfLdaq~IknLt~YLe~L~~~gla~~dhtt 435 (933)
T KOG2114|consen 356 LAKSQHLDEDTLAEIHRKYGDYLYGKGDFDEATDQYIETIGFLEPSEVIKKFLDAQRIKNLTSYLEALHKKGLANSDHTT 435 (933)
T ss_pred HHHhcCCCHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHcccCChHHHHHHhcCHHHHHHHHHHHHHHHHcccccchhHH
Confidence 45667777777665 4899999999999999998665554433221 11 15677888787776655333
Q ss_pred -------HHHHHHHHHHHhcCC--CCC----CChHHHHHHHHHHHHHHHHH--HhcCccchHHHHHHhc
Q 013640 184 -------ALEELNQLKEKVDDP--KSF----TSPLNQMQSRIWLMHWSLFI--FFNHDNGRTLIIDLFN 237 (439)
Q Consensus 184 -------a~~~l~klke~id~~--~~~----~~~l~~l~~R~WllHwsLf~--~fn~~~~~~~l~d~F~ 237 (439)
-+++..||.+.|+.+ |.| ...++.+.+-..+-|-.+-. |=+|+..-+-+++...
T Consensus 436 lLLncYiKlkd~~kL~efI~~~~~g~~~fd~e~al~Ilr~snyl~~a~~LA~k~~~he~vl~ille~~~ 504 (933)
T KOG2114|consen 436 LLLNCYIKLKDVEKLTEFISKCDKGEWFFDVETALEILRKSNYLDEAELLATKFKKHEWVLDILLEDLH 504 (933)
T ss_pred HHHHHHHHhcchHHHHHHHhcCCCcceeeeHHHHHHHHHHhChHHHHHHHHHHhccCHHHHHHHHHHhc
Confidence 346679999999985 334 23356666666666555443 3335666666666544
No 145
>cd00131 PAX Paired Box domain
Probab=59.61 E-value=23 Score=31.33 Aligned_cols=47 Identities=11% Similarity=0.126 Sum_probs=39.4
Q ss_pred HHHHHHHHHHhhhhhccccHHHHHHHcCCCHHHHHHHHHHHhhcCcccee
Q 013640 341 ENARLFIFETYCRIHQRIDMAVLAEKLNLNYEEAQRWIVNLIRNSKLDAK 390 (439)
Q Consensus 341 e~aR~~ife~ycriy~~I~I~~lA~~l~~s~~~~E~wiv~lI~~~rL~aK 390 (439)
...|..|..-| ....+...+|+.||+|...+-+|+-++-..|.+..|
T Consensus 20 ~d~R~rIv~~~---~~G~s~~~iA~~~~Vs~~tV~r~i~r~~e~G~v~pk 66 (128)
T cd00131 20 DSIRQRIVELA---QSGIRPCDISRQLRVSHGCVSKILNRYYETGSIRPG 66 (128)
T ss_pred HHHHHHHHHHH---HcCCCHHHHHHHHCcCHHHHHHHHHHHHHcCCcCCC
Confidence 34677777655 478899999999999999999999999999987654
No 146
>COG1349 GlpR Transcriptional regulators of sugar metabolism [Transcription / Carbohydrate transport and metabolism]
Probab=59.58 E-value=15 Score=36.14 Aligned_cols=59 Identities=14% Similarity=0.121 Sum_probs=50.0
Q ss_pred HHHHHHHHhhhhhccccHHHHHHHcCCCHHHHHHHHHHHhhcCccceeecccCCEEEeCCCCc
Q 013640 343 ARLFIFETYCRIHQRIDMAVLAEKLNLNYEEAQRWIVNLIRNSKLDAKIDAKSGTVIMEPTHP 405 (439)
Q Consensus 343 aR~~ife~ycriy~~I~I~~lA~~l~~s~~~~E~wiv~lI~~~rL~aKID~~~g~V~~~~~~~ 405 (439)
-|+.....+++-+.+|+++.||+.||||+.=+-|.|..|=..|.|. .+-|-++...+..
T Consensus 5 eR~~~Il~~l~~~g~v~v~eLa~~~~VS~~TIRRDL~~Le~~g~l~----R~hGGa~~~~~~~ 63 (253)
T COG1349 5 ERHQKILELLKEKGKVSVEELAELFGVSEMTIRRDLNELEEQGLLL----RVHGGAVLPDSES 63 (253)
T ss_pred HHHHHHHHHHHHcCcEEHHHHHHHhCCCHHHHHHhHHHHHHCCcEE----EEeCCEecCCCcc
Confidence 4899999999999999999999999999999999999998888664 4566666655553
No 147
>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=59.28 E-value=17 Score=26.74 Aligned_cols=42 Identities=17% Similarity=0.271 Sum_probs=33.6
Q ss_pred HHHHHhhhhhccccHHHHHHHcCCCHHHHHHHHHHHhhcCcc
Q 013640 346 FIFETYCRIHQRIDMAVLAEKLNLNYEEAQRWIVNLIRNSKL 387 (439)
Q Consensus 346 ~ife~ycriy~~I~I~~lA~~l~~s~~~~E~wiv~lI~~~rL 387 (439)
.|++.+.+.-..+++..||+++|++..-+-+.+..|...|=+
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 345555566666899999999999999999999999887754
No 148
>KOG2003 consensus TPR repeat-containing protein [General function prediction only]
Probab=58.88 E-value=1.1e+02 Score=33.33 Aligned_cols=37 Identities=24% Similarity=0.617 Sum_probs=23.4
Q ss_pred HHHHH--HhcCccchHHHHHHhcc--ccchhHHHhhchhHHHHHHH
Q 013640 217 WSLFI--FFNHDNGRTLIIDLFNQ--DKYLNAIQTNAPHLLRYLAT 258 (439)
Q Consensus 217 wsLf~--~fn~~~~~~~l~d~F~~--~~yl~~Iqt~~p~lLrYlvv 258 (439)
|.|.+ +|.....+...+|++.+ -.|.+-+. |||+||-
T Consensus 662 wqlmiasc~rrsgnyqka~d~yk~~hrkfpedld-----clkflvr 702 (840)
T KOG2003|consen 662 WQLMIASCFRRSGNYQKAFDLYKDIHRKFPEDLD-----CLKFLVR 702 (840)
T ss_pred HHHHHHHHHHhcccHHHHHHHHHHHHHhCccchH-----HHHHHHH
Confidence 44443 66666566677787774 25555554 8899873
No 149
>PF13512 TPR_18: Tetratricopeptide repeat
Probab=58.73 E-value=70 Score=29.18 Aligned_cols=50 Identities=22% Similarity=0.305 Sum_probs=42.3
Q ss_pred HHHHHHhcCCChhHHHHHHHHHHHHHhcCChhhHHHHHHHHHhhccccch
Q 013640 114 LQMLHDRYQIGPDQIEALYQYAKFQFECGNYSGAADYLYQYRALCTNSER 163 (439)
Q Consensus 114 ~~~l~~~~g~t~e~~~al~~~ak~~y~~Gdy~~A~~~L~~~~~~~~~~~~ 163 (439)
++.|...|-+++=.-.+-+++|..||..|+|+.|...+..|..+-+...+
T Consensus 33 le~L~~ryP~g~ya~qAqL~l~yayy~~~~y~~A~a~~~rFirLhP~hp~ 82 (142)
T PF13512_consen 33 LEALDTRYPFGEYAEQAQLDLAYAYYKQGDYEEAIAAYDRFIRLHPTHPN 82 (142)
T ss_pred HHHHHhcCCCCcccHHHHHHHHHHHHHccCHHHHHHHHHHHHHhCCCCCC
Confidence 45666777776666789999999999999999999999999999876543
No 150
>PRK11447 cellulose synthase subunit BcsC; Provisional
Probab=58.51 E-value=1.4e+02 Score=35.82 Aligned_cols=64 Identities=16% Similarity=0.100 Sum_probs=44.8
Q ss_pred HHHHHHHHHHhcCChhhHHHHHHHHHhhccccchhHHHHHHHHHHHHhhcCHHHHHHHHHHHHHHh
Q 013640 130 ALYQYAKFQFECGNYSGAADYLYQYRALCTNSERRLSALWGKMAAEILMQNWDIALEELNQLKEKV 195 (439)
Q Consensus 130 al~~~ak~~y~~Gdy~~A~~~L~~~~~~~~~~~~k~~~lwg~la~eIl~~~w~~a~~~l~klke~i 195 (439)
..+..|+++...|+|++|.+.+..+....++.......+|+.++. ..++|+.|.+.++++-+..
T Consensus 114 ~~l~~A~ll~~~g~~~eA~~~~~~~l~~~p~~~~la~~y~~~~~~--~~g~~~~A~~~L~~ll~~~ 177 (1157)
T PRK11447 114 QALQQARLLATTGRTEEALASYDKLFNGAPPELDLAVEYWRLVAK--LPAQRPEAINQLQRLNADY 177 (1157)
T ss_pred hHHHHHHHHHhCCCHHHHHHHHHHHccCCCCChHHHHHHHHHHhh--CCccHHHHHHHHHHHHHhC
Confidence 458889999999999999998888776554433323345665542 3577888888887776543
No 151
>KOG1155 consensus Anaphase-promoting complex (APC), Cdc23 subunit [Cell cycle control, cell division, chromosome partitioning; Posttranslational modification, protein turnover, chaperones]
Probab=57.65 E-value=1.3e+02 Score=32.91 Aligned_cols=104 Identities=18% Similarity=0.157 Sum_probs=68.3
Q ss_pred HHHHHHHHHHHccCCCchHHHHHHHHhCCCCCChhHHHHHHHHHHHHHHHHHHHHHHHHHhhCChhHHHHhhhcchhccH
Q 013640 35 EQILKSKIELLNKTNMVDYAMDIHKSLYHTEDVPQDMVERRVEVVARLKALEERAAPIVSFLQNPNSFQDLRANDQHYNL 114 (439)
Q Consensus 35 ~~l~~a~~~llk~TnM~dy~~~~~~~l~~~~~~p~e~~~k~~ev~~~l~~l~~~~~~~~~~~~~~e~~~~l~~~dk~~n~ 114 (439)
.-+..|.=+--.++|+.+=++..|+....-.++...---+-.+.-++++.++++++-..+.++.
T Consensus 432 sRlw~aLG~CY~kl~~~~eAiKCykrai~~~dte~~~l~~LakLye~l~d~~eAa~~yek~v~~---------------- 495 (559)
T KOG1155|consen 432 SRLWVALGECYEKLNRLEEAIKCYKRAILLGDTEGSALVRLAKLYEELKDLNEAAQYYEKYVEV---------------- 495 (559)
T ss_pred hHHHHHHHHHHHHhccHHHHHHHHHHHHhccccchHHHHHHHHHHHHHHhHHHHHHHHHHHHHH----------------
Confidence 3456666666678888888888888765333343334444555556666676666443333322
Q ss_pred HHHHHhcCCChhHHHHHHHHHHHHHhcCChhhHHHHHHHHHh
Q 013640 115 QMLHDRYQIGPDQIEALYQYAKFQFECGNYSGAADYLYQYRA 156 (439)
Q Consensus 115 ~~l~~~~g~t~e~~~al~~~ak~~y~~Gdy~~A~~~L~~~~~ 156 (439)
..+ .-.++++++.+..=+|.++..++||+.|+.+...+..
T Consensus 496 ~~~--eg~~~~~t~ka~~fLA~~f~k~~~~~~As~Ya~~~~~ 535 (559)
T KOG1155|consen 496 SEL--EGEIDDETIKARLFLAEYFKKMKDFDEASYYATLVLK 535 (559)
T ss_pred HHh--hcccchHHHHHHHHHHHHHHhhcchHHHHHHHHHHhc
Confidence 111 1124888999999999999999999999987655544
No 152
>smart00351 PAX Paired Box domain.
Probab=56.81 E-value=28 Score=30.55 Aligned_cols=47 Identities=9% Similarity=0.081 Sum_probs=37.3
Q ss_pred HHHHHHHHHHhhhhhccccHHHHHHHcCCCHHHHHHHHHHHhhcCcccee
Q 013640 341 ENARLFIFETYCRIHQRIDMAVLAEKLNLNYEEAQRWIVNLIRNSKLDAK 390 (439)
Q Consensus 341 e~aR~~ife~ycriy~~I~I~~lA~~l~~s~~~~E~wiv~lI~~~rL~aK 390 (439)
...|..|..-|- ...+...+|+.||+|..-+-+|+-++-..|.+..|
T Consensus 20 ~~~R~riv~~~~---~G~s~~~iA~~~gvs~~tV~kwi~r~~~~G~~~pk 66 (125)
T smart00351 20 DEERQRIVELAQ---NGVRPCDISRQLCVSHGCVSKILGRYYETGSIRPG 66 (125)
T ss_pred HHHHHHHHHHHH---cCCCHHHHHHHHCcCHHHHHHHHHHHHHcCCcCCc
Confidence 346666665552 56789999999999999999999999888865543
No 153
>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=56.80 E-value=22 Score=27.61 Aligned_cols=44 Identities=18% Similarity=0.302 Sum_probs=35.9
Q ss_pred ccccHHHHHHHcCCCHHHHHHHHHHHhhcCccceeecccCCEEEeCCC
Q 013640 356 QRIDMAVLAEKLNLNYEEAQRWIVNLIRNSKLDAKIDAKSGTVIMEPT 403 (439)
Q Consensus 356 ~~I~I~~lA~~l~~s~~~~E~wiv~lI~~~rL~aKID~~~g~V~~~~~ 403 (439)
-.++.+.||+.+|+|.+-+-+-+..|...|-+ +...|.|++..+
T Consensus 27 ~~lt~~~iA~~~g~sr~tv~r~l~~l~~~g~I----~~~~~~i~I~d~ 70 (76)
T PF13545_consen 27 LPLTQEEIADMLGVSRETVSRILKRLKDEGII----EVKRGKIIILDP 70 (76)
T ss_dssp EESSHHHHHHHHTSCHHHHHHHHHHHHHTTSE----EEETTEEEESSH
T ss_pred ecCCHHHHHHHHCCCHHHHHHHHHHHHHCCCE----EEcCCEEEECCH
Confidence 34789999999999999999999999998855 456777766543
No 154
>PRK02603 photosystem I assembly protein Ycf3; Provisional
Probab=56.46 E-value=1.4e+02 Score=26.81 Aligned_cols=34 Identities=21% Similarity=0.177 Sum_probs=28.9
Q ss_pred HHHHHHHHHHHHHhcCChhhHHHHHHHHHhhccc
Q 013640 127 QIEALYQYAKFQFECGNYSGAADYLYQYRALCTN 160 (439)
Q Consensus 127 ~~~al~~~ak~~y~~Gdy~~A~~~L~~~~~~~~~ 160 (439)
....++.+|..++..|+|+.|.+++.......+.
T Consensus 71 ~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~p~ 104 (172)
T PRK02603 71 RSYILYNMGIIYASNGEHDKALEYYHQALELNPK 104 (172)
T ss_pred HHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCcc
Confidence 4568899999999999999999999887776543
No 155
>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=56.29 E-value=53 Score=27.41 Aligned_cols=49 Identities=20% Similarity=0.187 Sum_probs=42.7
Q ss_pred hhccccHHHHHHHcCCCHHHHHHHHHHHhhcCccceeecccCCEEEeCCCC
Q 013640 354 IHQRIDMAVLAEKLNLNYEEAQRWIVNLIRNSKLDAKIDAKSGTVIMEPTH 404 (439)
Q Consensus 354 iy~~I~I~~lA~~l~~s~~~~E~wiv~lI~~~rL~aKID~~~g~V~~~~~~ 404 (439)
....++-..||+.+|+|.+-+-+-|..|...|-| +.+...|++-+|.+.
T Consensus 44 ~~~~is~~eLa~~~g~sr~tVsr~L~~Le~~GlI--~r~~~~~~~~~n~~~ 92 (95)
T TIGR01610 44 KQDRVTATVIAELTGLSRTHVSDAIKSLARRRII--FRQGMMGIVGVNTPL 92 (95)
T ss_pred cCCccCHHHHHHHHCcCHHHHHHHHHHHHHCCCe--eeecCCceeecCCCc
Confidence 7789999999999999999999999999999988 445667888888653
No 156
>PRK10747 putative protoheme IX biogenesis protein; Provisional
Probab=55.72 E-value=1.2e+02 Score=31.55 Aligned_cols=46 Identities=9% Similarity=0.020 Sum_probs=32.2
Q ss_pred HHHHHHhcCCChhHHHHHHHHHHHHHhcCChhhHHHHHHHHHhhcc
Q 013640 114 LQMLHDRYQIGPDQIEALYQYAKFQFECGNYSGAADYLYQYRALCT 159 (439)
Q Consensus 114 ~~~l~~~~g~t~e~~~al~~~ak~~y~~Gdy~~A~~~L~~~~~~~~ 159 (439)
++.+++-..-.|+.-+.++-+|++++..|+|++|.+++.......+
T Consensus 314 l~~~e~~lk~~P~~~~l~l~lgrl~~~~~~~~~A~~~le~al~~~P 359 (398)
T PRK10747 314 EKVLRQQIKQHGDTPLLWSTLGQLLMKHGEWQEASLAFRAALKQRP 359 (398)
T ss_pred HHHHHHHHhhCCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHhcCC
Confidence 4444444444556666788888888888888888888877776543
No 157
>PLN03098 LPA1 LOW PSII ACCUMULATION1; Provisional
Probab=55.59 E-value=52 Score=35.53 Aligned_cols=72 Identities=14% Similarity=0.016 Sum_probs=53.0
Q ss_pred CCChhHHHHHHHHHHHHHhcCChhhHHHHHHHHHhhccccchhHHHHHHHHHHHHh-hcCHHHHHHHHHHHHHH
Q 013640 122 QIGPDQIEALYQYAKFQFECGNYSGAADYLYQYRALCTNSERRLSALWGKMAAEIL-MQNWDIALEELNQLKEK 194 (439)
Q Consensus 122 g~t~e~~~al~~~ak~~y~~Gdy~~A~~~L~~~~~~~~~~~~k~~~lwg~la~eIl-~~~w~~a~~~l~klke~ 194 (439)
...|+..++.+.+|..++..|+|++|...+.....+-+++. .....|.-++|-.. .++.+.|.+.+.++-++
T Consensus 69 ~~dP~~a~a~~NLG~AL~~lGryeEAIa~f~rALeL~Pd~a-eA~~A~yNLAcaya~LGr~dEAla~LrrALel 141 (453)
T PLN03098 69 EADVKTAEDAVNLGLSLFSKGRVKDALAQFETALELNPNPD-EAQAAYYNKACCHAYREEGKKAADCLRTALRD 141 (453)
T ss_pred cCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHhhCCCch-HHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHh
Confidence 34778888999999999999999999999998888766532 12234555555544 46778888887776664
No 158
>PRK10681 DNA-binding transcriptional repressor DeoR; Provisional
Probab=55.55 E-value=22 Score=34.92 Aligned_cols=42 Identities=10% Similarity=0.027 Sum_probs=37.6
Q ss_pred HHHHHHHHHHhhhhhccccHHHHHHHcCCCHHHHHHHHHHHh
Q 013640 341 ENARLFIFETYCRIHQRIDMAVLAEKLNLNYEEAQRWIVNLI 382 (439)
Q Consensus 341 e~aR~~ife~ycriy~~I~I~~lA~~l~~s~~~~E~wiv~lI 382 (439)
.+-|....-.+++-|.+|++..||+.||||++=+-|.|-.|=
T Consensus 5 ~~eR~~~I~~~l~~~~~v~v~eLa~~~~VS~~TIRRDL~~Le 46 (252)
T PRK10681 5 RDERIGQLLQALKRSDKLHLKDAAALLGVSEMTIRRDLNAHS 46 (252)
T ss_pred HHHHHHHHHHHHHHcCCCcHHHHHHHhCCCHHHHHHHHHHhh
Confidence 345889999999999999999999999999999999998753
No 159
>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=55.46 E-value=36 Score=23.45 Aligned_cols=28 Identities=11% Similarity=0.262 Sum_probs=25.1
Q ss_pred ccccHHHHHHHcCCCHHHHHHHHHHHhh
Q 013640 356 QRIDMAVLAEKLNLNYEEAQRWIVNLIR 383 (439)
Q Consensus 356 ~~I~I~~lA~~l~~s~~~~E~wiv~lI~ 383 (439)
...+...+|+.+|+|..-+-+|+.+...
T Consensus 25 ~~~~~~~ia~~~~~s~~~i~~~~~~~~~ 52 (55)
T cd06171 25 EGLSYEEIAEILGISRSTVRQRLHRALK 52 (55)
T ss_pred cCCCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 7789999999999999999999987654
No 160
>PRK03837 transcriptional regulator NanR; Provisional
Probab=54.85 E-value=45 Score=31.83 Aligned_cols=67 Identities=13% Similarity=0.115 Sum_probs=58.7
Q ss_pred ccHHHHHHHHHHHHHHHhhhhhccc-cHHHHHHHcCCCHHHHHHHHHHHhhcCccceeecccCCEEEeCC
Q 013640 334 PLRDEFLENARLFIFETYCRIHQRI-DMAVLAEKLNLNYEEAQRWIVNLIRNSKLDAKIDAKSGTVIMEP 402 (439)
Q Consensus 334 ~~~~~f~e~aR~~ife~ycriy~~I-~I~~lA~~l~~s~~~~E~wiv~lI~~~rL~aKID~~~g~V~~~~ 402 (439)
...+...+..|..|....++|=.++ +...||++||||..=+-.-|..|-..|=+. +-...|+++...
T Consensus 13 ~~~~~v~~~l~~~I~~g~l~pG~~Lp~E~~Lae~~gVSRt~VREAL~~L~~eGlv~--~~~~~G~~V~~~ 80 (241)
T PRK03837 13 KLSEEVEERLEQMIRSGEFGPGDQLPSERELMAFFGVGRPAVREALQALKRKGLVQ--ISHGERARVSRP 80 (241)
T ss_pred cHHHHHHHHHHHHHHhCCCCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHCCCEE--EecCCceeEecC
Confidence 4567899999999999999999999 999999999999999999999999999874 446678877653
No 161
>KOG1840 consensus Kinesin light chain [Cytoskeleton]
Probab=54.57 E-value=3.2e+02 Score=30.09 Aligned_cols=84 Identities=14% Similarity=0.134 Sum_probs=64.1
Q ss_pred HHHHHHhcCCCh-hHHHHHHHHHHHHHhcCChhhHHHHHHHHHhhcc-----ccchhHHHHHHHHHHHHhhcCHHHHHHH
Q 013640 114 LQMLHDRYQIGP-DQIEALYQYAKFQFECGNYSGAADYLYQYRALCT-----NSERRLSALWGKMAAEILMQNWDIALEE 187 (439)
Q Consensus 114 ~~~l~~~~g~t~-e~~~al~~~ak~~y~~Gdy~~A~~~L~~~~~~~~-----~~~~k~~~lwg~la~eIl~~~w~~a~~~ 187 (439)
++.+++.+|-+. .+...+-.+|..|+..|+|.+|..++........ ..+..-+.+-...+..-.+...+.|.+.
T Consensus 268 L~i~e~~~G~~h~~va~~l~nLa~ly~~~GKf~EA~~~~e~Al~I~~~~~~~~~~~v~~~l~~~~~~~~~~~~~Eea~~l 347 (508)
T KOG1840|consen 268 LTIREEVFGEDHPAVAATLNNLAVLYYKQGKFAEAEEYCERALEIYEKLLGASHPEVAAQLSELAAILQSMNEYEEAKKL 347 (508)
T ss_pred HHHHHHhcCCCCHHHHHHHHHHHHHHhccCChHHHHHHHHHHHHHHHHhhccChHHHHHHHHHHHHHHHHhcchhHHHHH
Confidence 456678888654 4555778899999999999999998877655432 2344566666666777778889999999
Q ss_pred HHHHHHHhcC
Q 013640 188 LNQLKEKVDD 197 (439)
Q Consensus 188 l~klke~id~ 197 (439)
+.++-+++.+
T Consensus 348 ~q~al~i~~~ 357 (508)
T KOG1840|consen 348 LQKALKIYLD 357 (508)
T ss_pred HHHHHHHHHh
Confidence 9999888884
No 162
>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=54.48 E-value=41 Score=33.90 Aligned_cols=67 Identities=24% Similarity=0.309 Sum_probs=39.0
Q ss_pred cCCChhHHHHHHHHHH--HHHhcCChhhHHHHHHHHHhhccccchhHHHHHHHHHHHHhhcCHHHHHHHHHH
Q 013640 121 YQIGPDQIEALYQYAK--FQFECGNYSGAADYLYQYRALCTNSERRLSALWGKMAAEILMQNWDIALEELNQ 190 (439)
Q Consensus 121 ~g~t~e~~~al~~~ak--~~y~~Gdy~~A~~~L~~~~~~~~~~~~k~~~lwg~la~eIl~~~w~~a~~~l~k 190 (439)
-.+..|.+ ++++|. +.+-.|. ++..+.++.|.+++...+.....+-|+..|.|+.++|+.|.+.+..
T Consensus 158 ~~~~eD~~--l~qLa~awv~l~~g~-e~~~~A~y~f~El~~~~~~t~~~lng~A~~~l~~~~~~eAe~~L~~ 226 (290)
T PF04733_consen 158 QQIDEDSI--LTQLAEAWVNLATGG-EKYQDAFYIFEELSDKFGSTPKLLNGLAVCHLQLGHYEEAEELLEE 226 (290)
T ss_dssp HCCSCCHH--HHHHHHHHHHHHHTT-TCCCHHHHHHHHHHCCS--SHHHHHHHHHHHHHCT-HHHHHHHHHH
T ss_pred HhcCCcHH--HHHHHHHHHHHHhCc-hhHHHHHHHHHHHHhccCCCHHHHHHHHHHHHHhCCHHHHHHHHHH
Confidence 33444433 444444 4444664 3333344555555554455667788999999999999999876554
No 163
>PRK09954 putative kinase; Provisional
Probab=54.12 E-value=37 Score=34.64 Aligned_cols=52 Identities=15% Similarity=0.270 Sum_probs=43.5
Q ss_pred HhhhhhccccHHHHHHHcCCCHHHHHHHHHHHhhcCccc---eeecccCCEEEeC
Q 013640 350 TYCRIHQRIDMAVLAEKLNLNYEEAQRWIVNLIRNSKLD---AKIDAKSGTVIME 401 (439)
Q Consensus 350 ~ycriy~~I~I~~lA~~l~~s~~~~E~wiv~lI~~~rL~---aKID~~~g~V~~~ 401 (439)
.+++=+.+++...||+.||||..-+-+.|.+|...|.+. ..+|...++++.+
T Consensus 10 ~~l~~~~~~s~~~la~~l~~s~~~v~~~i~~L~~~g~i~~~~~~l~~~~~v~viG 64 (362)
T PRK09954 10 AILRRNPLIQQNEIADILQISRSRVAAHIMDLMRKGRIKGKGYILTEQEYCVVVG 64 (362)
T ss_pred HHHHHCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCcCCcEEEEcCCccEEEEE
Confidence 445566899999999999999999999999999999774 5677777777665
No 164
>PRK12370 invasion protein regulator; Provisional
Probab=54.06 E-value=1.4e+02 Score=32.50 Aligned_cols=77 Identities=14% Similarity=0.109 Sum_probs=54.9
Q ss_pred HHHHHHhcCCChhHHHHHHHHHHHHHhcCChhhHHHHHHHHHhhccccchhHHHHHHHHHHHHhhcCHHHHHHHHHHHHH
Q 013640 114 LQMLHDRYQIGPDQIEALYQYAKFQFECGNYSGAADYLYQYRALCTNSERRLSALWGKMAAEILMQNWDIALEELNQLKE 193 (439)
Q Consensus 114 ~~~l~~~~g~t~e~~~al~~~ak~~y~~Gdy~~A~~~L~~~~~~~~~~~~k~~~lwg~la~eIl~~~w~~a~~~l~klke 193 (439)
...+++-....|+..++++.+|..++..|++++|.+.+.....+.+....- .+.....-...++++.|.+...++-+
T Consensus 358 ~~~~~~Al~l~P~~~~a~~~lg~~l~~~G~~~eAi~~~~~Al~l~P~~~~~---~~~~~~~~~~~g~~eeA~~~~~~~l~ 434 (553)
T PRK12370 358 SLLFKQANLLSPISADIKYYYGWNLFMAGQLEEALQTINECLKLDPTRAAA---GITKLWITYYHTGIDDAIRLGDELRS 434 (553)
T ss_pred HHHHHHHHHhCCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHhcCCCChhh---HHHHHHHHHhccCHHHHHHHHHHHHH
Confidence 345556666778888899999999999999999999999998887653221 11222234446788888777666533
No 165
>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=53.94 E-value=28 Score=29.49 Aligned_cols=36 Identities=8% Similarity=0.239 Sum_probs=31.6
Q ss_pred HHHHHHhhhhhccccHHHHHHHcCCCHHHHHHHHHH
Q 013640 345 LFIFETYCRIHQRIDMAVLAEKLNLNYEEAQRWIVN 380 (439)
Q Consensus 345 ~~ife~ycriy~~I~I~~lA~~l~~s~~~~E~wiv~ 380 (439)
.-++++|...-.++++...|+.|||++...=+||..
T Consensus 12 a~~~d~~~~~~~~~ti~~~AK~L~i~~~~l~~~Lr~ 47 (111)
T PF03374_consen 12 AEFYDAFVDSDGLYTIREAAKLLGIGRNKLFQWLRE 47 (111)
T ss_pred hHHHHHHHcCCCCccHHHHHHHhCCCHHHHHHHHHh
Confidence 356788999999999999999999999988888864
No 166
>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=53.84 E-value=19 Score=33.41 Aligned_cols=61 Identities=18% Similarity=0.285 Sum_probs=40.9
Q ss_pred HhhhcCChhHHHHHHHHHHHHhcCCcccccccccccccccccHHHHHHHHHHHHHHHhhhhhcc-ccHHHHHHHcCC
Q 013640 294 CVYVNYDFDGAQKKMKECEEVILNDPFLGKRVEDSNFATVPLRDEFLENARLFIFETYCRIHQR-IDMAVLAEKLNL 369 (439)
Q Consensus 294 ~lY~~fdF~~aq~~L~~~e~~i~~D~FL~~~~~~~~~~~~~~~~~f~e~aR~~ife~ycriy~~-I~I~~lA~~l~~ 369 (439)
..+...+|..+.+.+.. ...+++. ....+-|+..+|..+....++.|++ |+++.+++-||.
T Consensus 143 ~a~~~gny~~ff~l~~~-----~~~~~l~----------~~l~~~~~~~iR~~al~~i~~ay~~~i~l~~l~~~L~F 204 (204)
T PF03399_consen 143 RALMEGNYVRFFRLYRS-----KSAPYLF----------ACLMERFFNRIRLRALQSISKAYRSSIPLSFLAELLGF 204 (204)
T ss_dssp HHH--TTHHHHHHHHT------TTS-HHH----------HHHHGGGHHHHHHHHHHHHHHHS-T-EEHHHHHHHTT-
T ss_pred HHHHcCCHHHHHHHHhc-----cCCChHH----------HHHHHHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHcCC
Confidence 44556667666665511 3555552 2333459999999999999999999 999999998873
No 167
>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=53.75 E-value=37 Score=29.37 Aligned_cols=62 Identities=10% Similarity=0.090 Sum_probs=43.6
Q ss_pred HHHHHHHHHhhhhhccccHHHHHHHcCCCHHHHHHHHHHHhhcCccceeecccCCEEEeCCCC
Q 013640 342 NARLFIFETYCRIHQRIDMAVLAEKLNLNYEEAQRWIVNLIRNSKLDAKIDAKSGTVIMEPTH 404 (439)
Q Consensus 342 ~aR~~ife~ycriy~~I~I~~lA~~l~~s~~~~E~wiv~lI~~~rL~aKID~~~g~V~~~~~~ 404 (439)
..|.+++-.--.-.+.+++..||+.+|+++..+.+-+..|.+.|=+...- ...|-...++++
T Consensus 10 al~~l~~la~~~~~~~~s~~eia~~~~i~~~~v~~il~~L~~~gli~~~~-g~~ggy~l~~~~ 71 (132)
T TIGR00738 10 ALRALLDLALNPDEGPVSVKEIAERQGISRSYLEKILRTLRRAGLVESVR-GPGGGYRLARPP 71 (132)
T ss_pred HHHHHHHHHhCCCCCcCcHHHHHHHHCcCHHHHHHHHHHHHHCCcEEecc-CCCCCccCCCCH
Confidence 34444444322223479999999999999999999999999999776532 234555566655
No 168
>COG2345 Predicted transcriptional regulator [Transcription]
Probab=53.57 E-value=19 Score=35.20 Aligned_cols=52 Identities=12% Similarity=0.061 Sum_probs=43.2
Q ss_pred HHhhhhhccccHHHHHHHcCCCHHHHHHHHHHHhhcCccceeecccCCEEEeCCCC
Q 013640 349 ETYCRIHQRIDMAVLAEKLNLNYEEAQRWIVNLIRNSKLDAKIDAKSGTVIMEPTH 404 (439)
Q Consensus 349 e~ycriy~~I~I~~lA~~l~~s~~~~E~wiv~lI~~~rL~aKID~~~g~V~~~~~~ 404 (439)
--+|.-+..++.+.||++||+|+..+-+-+-+|...|-+... ....=|+||.
T Consensus 17 l~lL~~~g~~sa~elA~~Lgis~~avR~HL~~Le~~Glv~~~----~~~~g~GRP~ 68 (218)
T COG2345 17 LELLKKSGPVSADELAEELGISPMAVRRHLDDLEAEGLVEVE----RQQGGRGRPA 68 (218)
T ss_pred HHHHhccCCccHHHHHHHhCCCHHHHHHHHHHHHhCcceeee----eccCCCCCCc
Confidence 346788899999999999999999999999999999988776 3334456665
No 169
>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=52.62 E-value=25 Score=28.92 Aligned_cols=34 Identities=9% Similarity=0.146 Sum_probs=29.6
Q ss_pred HHHHHHHhhhhhccccHHHHHHHcCCCHHHHHHHH
Q 013640 344 RLFIFETYCRIHQRIDMAVLAEKLNLNYEEAQRWI 378 (439)
Q Consensus 344 R~~ife~ycriy~~I~I~~lA~~l~~s~~~~E~wi 378 (439)
|+...-.+++- ++++|..+|+.+|+|..-+-+-|
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 88888888888 99999999999999998776633
No 170
>COG3063 PilF Tfp pilus assembly protein PilF [Cell motility and secretion / Intracellular trafficking and secretion]
Probab=52.61 E-value=66 Score=31.99 Aligned_cols=81 Identities=19% Similarity=0.241 Sum_probs=67.0
Q ss_pred HHHHHHhcCCChhHHHHHHHHHHHHHhcCChhhHHHHHHHHHhhccccchhHHHHHHHHHHHHhhcCHHHHHHHHHHHHH
Q 013640 114 LQMLHDRYQIGPDQIEALYQYAKFQFECGNYSGAADYLYQYRALCTNSERRLSALWGKMAAEILMQNWDIALEELNQLKE 193 (439)
Q Consensus 114 ~~~l~~~~g~t~e~~~al~~~ak~~y~~Gdy~~A~~~L~~~~~~~~~~~~k~~~lwg~la~eIl~~~w~~a~~~l~klke 193 (439)
-+++++....++..--++..+|+..|+.|||..|.-++..+..-. +..-+.||--++++=..+|-+.+.+.-..|..
T Consensus 159 ~~~l~raL~~dp~~~~~~l~~a~~~~~~~~y~~Ar~~~~~~~~~~---~~~A~sL~L~iriak~~gd~~~a~~Y~~qL~r 235 (250)
T COG3063 159 EEYLKRALELDPQFPPALLELARLHYKAGDYAPARLYLERYQQRG---GAQAESLLLGIRIAKRLGDRAAAQRYQAQLQR 235 (250)
T ss_pred HHHHHHHHHhCcCCChHHHHHHHHHHhcccchHHHHHHHHHHhcc---cccHHHHHHHHHHHHHhccHHHHHHHHHHHHH
Confidence 357788888888888899999999999999999999998887622 36678888889999999999888888777776
Q ss_pred HhcC
Q 013640 194 KVDD 197 (439)
Q Consensus 194 ~id~ 197 (439)
.+-.
T Consensus 236 ~fP~ 239 (250)
T COG3063 236 LFPY 239 (250)
T ss_pred hCCC
Confidence 5554
No 171
>CHL00033 ycf3 photosystem I assembly protein Ycf3
Probab=52.57 E-value=1e+02 Score=27.59 Aligned_cols=69 Identities=19% Similarity=0.098 Sum_probs=47.7
Q ss_pred hHHHHHHHHHHHHHhcCChhhHHHHHHHHHhhccccchhHHHHHHHHHHHHhhcCHHHHHHHHHHHHHH
Q 013640 126 DQIEALYQYAKFQFECGNYSGAADYLYQYRALCTNSERRLSALWGKMAAEILMQNWDIALEELNQLKEK 194 (439)
Q Consensus 126 e~~~al~~~ak~~y~~Gdy~~A~~~L~~~~~~~~~~~~k~~~lwg~la~eIl~~~w~~a~~~l~klke~ 194 (439)
.....++..|..+...|+|+.|...+.......+++.....++...=.+-.-.++.+.|.+...++-.+
T Consensus 33 ~~a~~~~~~g~~~~~~g~~~~A~~~~~~al~l~~~~~~~~~~~~~lg~~~~~~g~~~eA~~~~~~Al~~ 101 (168)
T CHL00033 33 KEAFTYYRDGMSAQSEGEYAEALQNYYEAMRLEIDPYDRSYILYNIGLIHTSNGEHTKALEYYFQALER 101 (168)
T ss_pred HHHHHHHHHHHHHHHcCCHHHHHHHHHHHHhccccchhhHHHHHHHHHHHHHcCCHHHHHHHHHHHHHh
Confidence 345677999999999999999999999888765443222233333323344467888888887777654
No 172
>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=51.98 E-value=32 Score=26.45 Aligned_cols=41 Identities=12% Similarity=0.177 Sum_probs=35.4
Q ss_pred HHHHhhhhhccccHHHHHHHcCCCHHHHHHHHHHHhhcCccc
Q 013640 347 IFETYCRIHQRIDMAVLAEKLNLNYEEAQRWIVNLIRNSKLD 388 (439)
Q Consensus 347 ife~ycriy~~I~I~~lA~~l~~s~~~~E~wiv~lI~~~rL~ 388 (439)
+|...+ .+...+...||+.+|++...+-+.|-+|.+.|-+.
T Consensus 13 vy~~Ll-~~~~~t~~eIa~~l~i~~~~v~~~L~~L~~~GlV~ 53 (68)
T PF01978_consen 13 VYLALL-KNGPATAEEIAEELGISRSTVYRALKSLEEKGLVE 53 (68)
T ss_dssp HHHHHH-HHCHEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEE
T ss_pred HHHHHH-HcCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCEE
Confidence 444444 78999999999999999999999999999988764
No 173
>PRK15179 Vi polysaccharide biosynthesis protein TviE; Provisional
Probab=51.14 E-value=2e+02 Score=32.89 Aligned_cols=54 Identities=17% Similarity=0.129 Sum_probs=44.7
Q ss_pred ChhHHHHHHHHHHHHHhcCChhhHHHHHHHHHhhccccchhHHHHHHHHHHHHh
Q 013640 124 GPDQIEALYQYAKFQFECGNYSGAADYLYQYRALCTNSERRLSALWGKMAAEIL 177 (439)
Q Consensus 124 t~e~~~al~~~ak~~y~~Gdy~~A~~~L~~~~~~~~~~~~k~~~lwg~la~eIl 177 (439)
.++.-++++.+|+.+.+.|+.++|...+........+..++++-+.++|..+.-
T Consensus 184 ~p~~~~~~~~~a~~l~~~G~~~~A~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~ 237 (694)
T PRK15179 184 HPEFENGYVGWAQSLTRRGALWRARDVLQAGLDAIGDGARKLTRRLVDLNADLA 237 (694)
T ss_pred CCCcHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhhCcchHHHHHHHHHHHHHHH
Confidence 345567999999999999999999999998888766555888999999987654
No 174
>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=50.14 E-value=43 Score=25.43 Aligned_cols=36 Identities=28% Similarity=0.344 Sum_probs=28.8
Q ss_pred HHHHHHhhhhhccccHHHHHHHcCCCHHHHHHHHHHH
Q 013640 345 LFIFETYCRIHQRIDMAVLAEKLNLNYEEAQRWIVNL 381 (439)
Q Consensus 345 ~~ife~ycriy~~I~I~~lA~~l~~s~~~~E~wiv~l 381 (439)
+.+++-... -+.++++.||+.+|+|.--+-..|..+
T Consensus 8 ~~Ll~~L~~-~~~~~~~ela~~l~~S~rti~~~i~~L 43 (59)
T PF08280_consen 8 LKLLELLLK-NKWITLKELAKKLNISERTIKNDINEL 43 (59)
T ss_dssp HHHHHHHHH-HTSBBHHHHHHHCTS-HHHHHHHHHHH
T ss_pred HHHHHHHHc-CCCCcHHHHHHHHCCCHHHHHHHHHHH
Confidence 344555556 899999999999999999998888876
No 175
>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=49.99 E-value=38 Score=25.07 Aligned_cols=37 Identities=19% Similarity=0.325 Sum_probs=30.9
Q ss_pred cccHHHHHHHcCCCHHHHHHHHHHHhhcCccceeecc
Q 013640 357 RIDMAVLAEKLNLNYEEAQRWIVNLIRNSKLDAKIDA 393 (439)
Q Consensus 357 ~I~I~~lA~~l~~s~~~~E~wiv~lI~~~rL~aKID~ 393 (439)
.+++..||+.+|+++.-+-+-|.+|+..|=+.-.-|.
T Consensus 21 ~~t~~~la~~l~~~~~~vs~~v~~L~~~Glv~r~~~~ 57 (62)
T PF12802_consen 21 ELTQSELAERLGISKSTVSRIVKRLEKKGLVERERDP 57 (62)
T ss_dssp GEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEEE-S
T ss_pred CcCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEeCCC
Confidence 3999999999999999999999999999977655443
No 176
>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=49.94 E-value=42 Score=23.28 Aligned_cols=24 Identities=29% Similarity=0.461 Sum_probs=20.5
Q ss_pred HHHHHHHHHHHhcCChhhHHHHHH
Q 013640 129 EALYQYAKFQFECGNYSGAADYLY 152 (439)
Q Consensus 129 ~al~~~ak~~y~~Gdy~~A~~~L~ 152 (439)
+.++.+|-.++..|+|++|.+++.
T Consensus 2 e~~y~~a~~~y~~~ky~~A~~~~~ 25 (36)
T PF07720_consen 2 EYLYGLAYNFYQKGKYDEAIHFFQ 25 (36)
T ss_dssp HHHHHHHHHHHHTT-HHHHHHHHH
T ss_pred cHHHHHHHHHHHHhhHHHHHHHHH
Confidence 578899999999999999999854
No 177
>KOG2047 consensus mRNA splicing factor [RNA processing and modification]
Probab=49.40 E-value=94 Score=35.25 Aligned_cols=85 Identities=14% Similarity=0.127 Sum_probs=58.1
Q ss_pred HHHHHHHHHHHHHHHHHHHHhhCChhHHH-Hhhh---------------cchhccH--H--HHHHhcCCChhHHHHHHHH
Q 013640 75 RVEVVARLKALEERAAPIVSFLQNPNSFQ-DLRA---------------NDQHYNL--Q--MLHDRYQIGPDQIEALYQY 134 (439)
Q Consensus 75 ~~ev~~~l~~l~~~~~~~~~~~~~~e~~~-~l~~---------------~dk~~n~--~--~l~~~~g~t~e~~~al~~~ 134 (439)
=-+.+.+...+.+.++.+-.++.+++.+. ..++ -|+.+++ + .-+-...+|...---...+
T Consensus 175 yie~L~~~d~~~eaa~~la~vln~d~f~sk~gkSn~qlw~elcdlis~~p~~~~slnvdaiiR~gi~rftDq~g~Lw~SL 254 (835)
T KOG2047|consen 175 YIEYLAKSDRLDEAAQRLATVLNQDEFVSKKGKSNHQLWLELCDLISQNPDKVQSLNVDAIIRGGIRRFTDQLGFLWCSL 254 (835)
T ss_pred HHHHHHhccchHHHHHHHHHhcCchhhhhhcccchhhHHHHHHHHHHhCcchhcccCHHHHHHhhcccCcHHHHHHHHHH
Confidence 44667777888999999999998887543 2222 1222222 1 1122344566655666899
Q ss_pred HHHHHhcCChhhHHHHHHHHHhhcc
Q 013640 135 AKFQFECGNYSGAADYLYQYRALCT 159 (439)
Q Consensus 135 ak~~y~~Gdy~~A~~~L~~~~~~~~ 159 (439)
|++|-+.|.+++|.+.++.....+.
T Consensus 255 AdYYIr~g~~ekarDvyeeai~~v~ 279 (835)
T KOG2047|consen 255 ADYYIRSGLFEKARDVYEEAIQTVM 279 (835)
T ss_pred HHHHHHhhhhHHHHHHHHHHHHhhe
Confidence 9999999999999999998777654
No 178
>PRK10049 pgaA outer membrane protein PgaA; Provisional
Probab=49.34 E-value=1.4e+02 Score=33.95 Aligned_cols=47 Identities=15% Similarity=0.046 Sum_probs=33.5
Q ss_pred HHHHHHhcCCChhHHHHHHHHHHHHHhcCChhhHHHHHHHHHhhcccc
Q 013640 114 LQMLHDRYQIGPDQIEALYQYAKFQFECGNYSGAADYLYQYRALCTNS 161 (439)
Q Consensus 114 ~~~l~~~~g~t~e~~~al~~~ak~~y~~Gdy~~A~~~L~~~~~~~~~~ 161 (439)
+..+++-....|+..+ ++.+|..+...|+++.|...+......-++.
T Consensus 103 ~~~l~~~l~~~P~~~~-~~~la~~l~~~g~~~~Al~~l~~al~~~P~~ 149 (765)
T PRK10049 103 LVKAKQLVSGAPDKAN-LLALAYVYKRAGRHWDELRAMTQALPRAPQT 149 (765)
T ss_pred HHHHHHHHHhCCCCHH-HHHHHHHHHHCCCHHHHHHHHHHHHHhCCCC
Confidence 4455555555666666 7788888888888888888888877765543
No 179
>KOG1126 consensus DNA-binding cell division cycle control protein [Cell cycle control, cell division, chromosome partitioning]
Probab=49.01 E-value=57 Score=36.53 Aligned_cols=80 Identities=18% Similarity=0.197 Sum_probs=61.5
Q ss_pred HHHHhcCCChhHHHHHHHHHHHHHhcCChhhHHHHHHHHHhhccccchhHHHHHHHHHHHHhhcCHHHHHHHHHHHHHHh
Q 013640 116 MLHDRYQIGPDQIEALYQYAKFQFECGNYSGAADYLYQYRALCTNSERRLSALWGKMAAEILMQNWDIALEELNQLKEKV 195 (439)
Q Consensus 116 ~l~~~~g~t~e~~~al~~~ak~~y~~Gdy~~A~~~L~~~~~~~~~~~~k~~~lwg~la~eIl~~~w~~a~~~l~klke~i 195 (439)
++++-..|.|--.--+...|.+|.++|.++.|..++.....+ +.+..-+-+.+..+-+.+.+.+.|..++++||++.
T Consensus 511 ~fqkA~~INP~nsvi~~~~g~~~~~~k~~d~AL~~~~~A~~l---d~kn~l~~~~~~~il~~~~~~~eal~~LEeLk~~v 587 (638)
T KOG1126|consen 511 HFQKAVEINPSNSVILCHIGRIQHQLKRKDKALQLYEKAIHL---DPKNPLCKYHRASILFSLGRYVEALQELEELKELV 587 (638)
T ss_pred HHHhhhcCCccchhHHhhhhHHHHHhhhhhHHHHHHHHHHhc---CCCCchhHHHHHHHHHhhcchHHHHHHHHHHHHhC
Confidence 356667777777778888899999999999998888766543 33444455666666677788899999999999998
Q ss_pred cCC
Q 013640 196 DDP 198 (439)
Q Consensus 196 d~~ 198 (439)
-+.
T Consensus 588 P~e 590 (638)
T KOG1126|consen 588 PQE 590 (638)
T ss_pred cch
Confidence 873
No 180
>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=48.96 E-value=26 Score=24.35 Aligned_cols=29 Identities=24% Similarity=0.299 Sum_probs=23.9
Q ss_pred ccHHHHHHHcCCCHHHHHHHHHHHhhcCcccee
Q 013640 358 IDMAVLAEKLNLNYEEAQRWIVNLIRNSKLDAK 390 (439)
Q Consensus 358 I~I~~lA~~l~~s~~~~E~wiv~lI~~~rL~aK 390 (439)
++++.+|+.||+|..-+.+|+ ++|++.+.
T Consensus 2 lt~~e~a~~lgis~~ti~~~~----~~g~i~~~ 30 (49)
T TIGR01764 2 LTVEEAAEYLGVSKDTVYRLI----HEGELPAY 30 (49)
T ss_pred CCHHHHHHHHCCCHHHHHHHH----HcCCCCeE
Confidence 578999999999999877775 67888764
No 181
>COG1959 Predicted transcriptional regulator [Transcription]
Probab=48.77 E-value=48 Score=30.15 Aligned_cols=62 Identities=10% Similarity=0.105 Sum_probs=43.5
Q ss_pred HHHHHHHHHhhhhhccccHHHHHHHcCCCHHHHHHHHHHHhhcCccceeecccCCEEEeCCCC
Q 013640 342 NARLFIFETYCRIHQRIDMAVLAEKLNLNYEEAQRWIVNLIRNSKLDAKIDAKSGTVIMEPTH 404 (439)
Q Consensus 342 ~aR~~ife~ycriy~~I~I~~lA~~l~~s~~~~E~wiv~lI~~~rL~aKID~~~g~V~~~~~~ 404 (439)
..|.+++-.--..-..++++.||+..|+|+.++++.+..|-++|=+...=-+ +|=...++|+
T Consensus 10 al~~L~~LA~~~~~~~~s~~~IA~~~~is~~~L~kil~~L~kaGlV~S~rG~-~GGy~Lar~~ 71 (150)
T COG1959 10 ALRALLYLALLPGGGPVSSAEIAERQGISPSYLEKILSKLRKAGLVKSVRGK-GGGYRLARPP 71 (150)
T ss_pred HHHHHHHHHhCCCCCcccHHHHHHHhCcCHHHHHHHHHHHHHcCCEEeecCC-CCCccCCCCh
Confidence 4455555444334346899999999999999999999999998877654333 3334444444
No 182
>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=48.57 E-value=30 Score=25.23 Aligned_cols=39 Identities=23% Similarity=0.290 Sum_probs=26.4
Q ss_pred HHHHHHHHHHhhhhhccccHHHHHHHcCCCHHHHHHHHHHHh
Q 013640 341 ENARLFIFETYCRIHQRIDMAVLAEKLNLNYEEAQRWIVNLI 382 (439)
Q Consensus 341 e~aR~~ife~ycriy~~I~I~~lA~~l~~s~~~~E~wiv~lI 382 (439)
+.-|..+.-.| +...+.+.+|+.+|+|+.-+..++.+..
T Consensus 13 ~~~r~i~~l~~---~~g~s~~eIa~~l~~s~~~v~~~l~ra~ 51 (54)
T PF08281_consen 13 ERQREIFLLRY---FQGMSYAEIAEILGISESTVKRRLRRAR 51 (54)
T ss_dssp HHHHHHHHHHH---TS---HHHHHHHCTS-HHHHHHHHHHHH
T ss_pred HHHHHHHHHHH---HHCcCHHHHHHHHCcCHHHHHHHHHHHH
Confidence 34444444434 4678899999999999999999998764
No 183
>PF09976 TPR_21: Tetratricopeptide repeat; InterPro: IPR018704 This domain, found in various hypothetical prokaryotic proteins, has no known function.
Probab=48.56 E-value=72 Score=27.98 Aligned_cols=53 Identities=23% Similarity=0.311 Sum_probs=35.0
Q ss_pred HHHHHHHHHHhcCChhhHHHHHHHHHhhccccchhHHHHHHHHHHHHh--hcCHHHHHHHH
Q 013640 130 ALYQYAKFQFECGNYSGAADYLYQYRALCTNSERRLSALWGKMAAEIL--MQNWDIALEEL 188 (439)
Q Consensus 130 al~~~ak~~y~~Gdy~~A~~~L~~~~~~~~~~~~k~~~lwg~la~eIl--~~~w~~a~~~l 188 (439)
+.+.+|++++..|+|+.|.+.|.. ..+ ........-+.-+|+ .++|+.|...-
T Consensus 87 a~l~LA~~~~~~~~~d~Al~~L~~----~~~--~~~~~~~~~~~Gdi~~~~g~~~~A~~~y 141 (145)
T PF09976_consen 87 ARLRLARILLQQGQYDEALATLQQ----IPD--EAFKALAAELLGDIYLAQGDYDEARAAY 141 (145)
T ss_pred HHHHHHHHHHHcCCHHHHHHHHHh----ccC--cchHHHHHHHHHHHHHHCCCHHHHHHHH
Confidence 668899999999999999999855 122 222233333455555 46777776543
No 184
>smart00344 HTH_ASNC helix_turn_helix ASNC type. AsnC: an autogenously regulated activator of asparagine synthetase A transcription in Escherichia coli
Probab=48.35 E-value=30 Score=28.87 Aligned_cols=42 Identities=24% Similarity=0.311 Sum_probs=35.1
Q ss_pred hhhhccccHHHHHHHcCCCHHHHHHHHHHHhhcCccc---eeecc
Q 013640 352 CRIHQRIDMAVLAEKLNLNYEEAQRWIVNLIRNSKLD---AKIDA 393 (439)
Q Consensus 352 criy~~I~I~~lA~~l~~s~~~~E~wiv~lI~~~rL~---aKID~ 393 (439)
+.-..+++...||+.+|+|+.-+-+.|-+|..+|-+. +.+|.
T Consensus 12 L~~~~~~~~~~la~~l~~s~~tv~~~l~~L~~~g~i~~~~~~~~~ 56 (108)
T smart00344 12 LQKDARISLAELAKKVGLSPSTVHNRVKRLEEEGVIKGYTAVINP 56 (108)
T ss_pred HHHhCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCeeceEEEeCH
Confidence 3446789999999999999999999999999999553 55553
No 185
>smart00418 HTH_ARSR helix_turn_helix, Arsenical Resistance Operon Repressor.
Probab=48.29 E-value=54 Score=23.49 Aligned_cols=36 Identities=17% Similarity=0.238 Sum_probs=32.1
Q ss_pred hccccHHHHHHHcCCCHHHHHHHHHHHhhcCcccee
Q 013640 355 HQRIDMAVLAEKLNLNYEEAQRWIVNLIRNSKLDAK 390 (439)
Q Consensus 355 y~~I~I~~lA~~l~~s~~~~E~wiv~lI~~~rL~aK 390 (439)
...+++..||+.||+|...+-+-|-+|...|-+...
T Consensus 8 ~~~~~~~~i~~~l~is~~~v~~~l~~L~~~g~i~~~ 43 (66)
T smart00418 8 EGELCVCELAEILGLSQSTVSHHLKKLREAGLVESR 43 (66)
T ss_pred cCCccHHHHHHHHCCCHHHHHHHHHHHHHCCCeeee
Confidence 578899999999999999999999999998877643
No 186
>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=48.26 E-value=27 Score=21.95 Aligned_cols=23 Identities=22% Similarity=0.154 Sum_probs=20.1
Q ss_pred HHHHHHHHHHhcCChhhHHHHHH
Q 013640 130 ALYQYAKFQFECGNYSGAADYLY 152 (439)
Q Consensus 130 al~~~ak~~y~~Gdy~~A~~~L~ 152 (439)
+.+.+|..+...||.+.|...+.
T Consensus 3 a~~~la~~~~~~G~~~eA~~~l~ 25 (26)
T PF07721_consen 3 ARLALARALLAQGDPDEAERLLR 25 (26)
T ss_pred HHHHHHHHHHHcCCHHHHHHHHh
Confidence 56789999999999999998764
No 187
>KOG0495 consensus HAT repeat protein [RNA processing and modification]
Probab=48.16 E-value=99 Score=35.21 Aligned_cols=79 Identities=19% Similarity=0.172 Sum_probs=62.8
Q ss_pred hccHHHHHHhcCCChhHHHHHH---------------HHHHHHHhcCChhhHHHHHHHHHhhccccchhHHHHHHHHHHH
Q 013640 111 HYNLQMLHDRYQIGPDQIEALY---------------QYAKFQFECGNYSGAADYLYQYRALCTNSERRLSALWGKMAAE 175 (439)
Q Consensus 111 ~~n~~~l~~~~g~t~e~~~al~---------------~~ak~~y~~Gdy~~A~~~L~~~~~~~~~~~~k~~~lwg~la~e 175 (439)
|.-+.+++++|| |.|-+++++ -+|+-+...||-..|..+|......-++ ..++-+..+.+|
T Consensus 553 Wlra~~~ek~hg-t~Esl~Allqkav~~~pkae~lwlM~ake~w~agdv~~ar~il~~af~~~pn---seeiwlaavKle 628 (913)
T KOG0495|consen 553 WLRAAMFEKSHG-TRESLEALLQKAVEQCPKAEILWLMYAKEKWKAGDVPAARVILDQAFEANPN---SEEIWLAAVKLE 628 (913)
T ss_pred HHHHHHHHHhcC-cHHHHHHHHHHHHHhCCcchhHHHHHHHHHHhcCCcHHHHHHHHHHHHhCCC---cHHHHHHHHHHh
Confidence 344678899999 889899874 4667777889999999999988875544 556677788888
Q ss_pred HhhcCHHHHHHHHHHHHH
Q 013640 176 ILMQNWDIALEELNQLKE 193 (439)
Q Consensus 176 Il~~~w~~a~~~l~klke 193 (439)
+-....+.|..-+.|.+.
T Consensus 629 ~en~e~eraR~llakar~ 646 (913)
T KOG0495|consen 629 FENDELERARDLLAKARS 646 (913)
T ss_pred hccccHHHHHHHHHHHhc
Confidence 888888888887777776
No 188
>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=48.10 E-value=83 Score=29.38 Aligned_cols=67 Identities=10% Similarity=0.096 Sum_probs=58.5
Q ss_pred cHHHHHHHHHHHHHHHhhhhhccccHHHHHHHcCCCHHHHHHHHHHHhhcCccceeecccCCEEEeCCC
Q 013640 335 LRDEFLENARLFIFETYCRIHQRIDMAVLAEKLNLNYEEAQRWIVNLIRNSKLDAKIDAKSGTVIMEPT 403 (439)
Q Consensus 335 ~~~~f~e~aR~~ife~ycriy~~I~I~~lA~~l~~s~~~~E~wiv~lI~~~rL~aKID~~~g~V~~~~~ 403 (439)
..+...+..|-.|...-++|=.+++-..||+.||||..=+-.-|..|-..|=+. +-...|+++..-.
T Consensus 12 ~~~~v~~~l~~~I~~g~l~pG~~L~e~~La~~lgVSRtpVReAL~~L~~eGlv~--~~~~~G~~V~~~~ 78 (212)
T TIGR03338 12 LTTLVQDEIERAILSGELPPGAKLNESDIAARLGVSRGPVREAFRALEEAGLVR--NEKNRGVFVREIS 78 (212)
T ss_pred HHHHHHHHHHHHHHcCCCCCCCEecHHHHHHHhCCChHHHHHHHHHHHHCCCEE--EecCCCeEEecCC
Confidence 457788999999999999999999999999999999999999999999999884 4466788887643
No 189
>PF13011 LZ_Tnp_IS481: leucine-zipper of insertion element IS481
Probab=47.69 E-value=28 Score=29.12 Aligned_cols=31 Identities=16% Similarity=0.289 Sum_probs=28.0
Q ss_pred hccccHHHHHHHcCCCHHHHHHHHHHHhhcC
Q 013640 355 HQRIDMAVLAEKLNLNYEEAQRWIVNLIRNS 385 (439)
Q Consensus 355 y~~I~I~~lA~~l~~s~~~~E~wiv~lI~~~ 385 (439)
-...++...|+.||||..-+.+|+.++-.+|
T Consensus 23 ~~g~~~a~aA~~~gVS~~Ta~kW~~Ryra~G 53 (85)
T PF13011_consen 23 EQGWPVAHAAAEFGVSRRTAYKWLARYRAEG 53 (85)
T ss_pred HcCCcHHHHHHHhCCCHHHHHHHHHHHHHcC
Confidence 3567899999999999999999999998776
No 190
>PRK10141 DNA-binding transcriptional repressor ArsR; Provisional
Probab=47.49 E-value=1.8e+02 Score=25.58 Aligned_cols=93 Identities=13% Similarity=0.085 Sum_probs=61.8
Q ss_pred HHHHHHHHHHHHHHhhhhhccccHHHHHHHcCCCHHHHHHHHHHHhhcCccceeecccCCEEEeCCCCchhHHHHHHhhh
Q 013640 337 DEFLENARLFIFETYCRIHQRIDMAVLAEKLNLNYEEAQRWIVNLIRNSKLDAKIDAKSGTVIMEPTHPNVYEQLIDHTK 416 (439)
Q Consensus 337 ~~f~e~aR~~ife~ycriy~~I~I~~lA~~l~~s~~~~E~wiv~lI~~~rL~aKID~~~g~V~~~~~~~~~yqqvi~kt~ 416 (439)
.-+-...|+.|+..... ....+...||+.||+++.-+-+-|.-|-..|=+..+-+...-....+...+..-+++++.
T Consensus 11 kaLadptRl~IL~~L~~-~~~~~v~ela~~l~lsqstvS~HL~~L~~AGLV~~~r~Gr~~~Y~l~~~~~~~~~~~~~~-- 87 (117)
T PRK10141 11 KILSDETRLGIVLLLRE-SGELCVCDLCTALDQSQPKISRHLALLRESGLLLDRKQGKWVHYRLSPHIPAWAAKIIEQ-- 87 (117)
T ss_pred HHhCCHHHHHHHHHHHH-cCCcCHHHHHHHHCcCHHHHHHHHHHHHHCCceEEEEEcCEEEEEECchHHHHHHHHHHH--
Confidence 44556788888886543 457999999999999999999999999888888776554433334432212222333433
Q ss_pred hhhhHHHHHHHHHHhh
Q 013640 417 GLSGRTYKLVGQLLEH 432 (439)
Q Consensus 417 ~L~~R~q~L~~~i~~~ 432 (439)
.+..+...+.+.+++.
T Consensus 88 ~w~~~~~~l~~~l~~l 103 (117)
T PRK10141 88 AWLCEQEDVQAIVRNL 103 (117)
T ss_pred HHHHHHHHHHHHHHHH
Confidence 4555666666666554
No 191
>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=47.39 E-value=20 Score=26.23 Aligned_cols=23 Identities=26% Similarity=0.439 Sum_probs=20.7
Q ss_pred ccHHHHHHHcCCCHHHHHHHHHH
Q 013640 358 IDMAVLAEKLNLNYEEAQRWIVN 380 (439)
Q Consensus 358 I~I~~lA~~l~~s~~~~E~wiv~ 380 (439)
=.+..||..+||+...|..|..|
T Consensus 28 ~~~~~la~~~~l~~~qV~~WF~n 50 (59)
T cd00086 28 EEREELAKELGLTERQVKIWFQN 50 (59)
T ss_pred HHHHHHHHHHCcCHHHHHHHHHH
Confidence 34899999999999999999876
No 192
>COG3118 Thioredoxin domain-containing protein [Posttranslational modification, protein turnover, chaperones]
Probab=46.86 E-value=1.1e+02 Score=31.42 Aligned_cols=44 Identities=25% Similarity=0.287 Sum_probs=34.1
Q ss_pred cHHHHHHhcCCChhHHHHHHHHHHHHHhcCChhhHHHHHHHHHh
Q 013640 113 NLQMLHDRYQIGPDQIEALYQYAKFQFECGNYSGAADYLYQYRA 156 (439)
Q Consensus 113 n~~~l~~~~g~t~e~~~al~~~ak~~y~~Gdy~~A~~~L~~~~~ 156 (439)
....|+...--.|+..++-+++|+.+--.|+++.|.+.|-.+..
T Consensus 221 ~~~~l~~~~aadPdd~~aa~~lA~~~~~~g~~e~Ale~Ll~~l~ 264 (304)
T COG3118 221 EIQDLQRRLAADPDDVEAALALADQLHLVGRNEAALEHLLALLR 264 (304)
T ss_pred CHHHHHHHHHhCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHH
Confidence 33556666666888899999999999999999999876644333
No 193
>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=45.72 E-value=89 Score=23.43 Aligned_cols=44 Identities=16% Similarity=0.265 Sum_probs=32.4
Q ss_pred HHHHhhhhhccccHHHHHHHcCCCHHHHHHHHHHHhhcCcccee
Q 013640 347 IFETYCRIHQRIDMAVLAEKLNLNYEEAQRWIVNLIRNSKLDAK 390 (439)
Q Consensus 347 ife~ycriy~~I~I~~lA~~l~~s~~~~E~wiv~lI~~~rL~aK 390 (439)
+....+..+..+++..||+.+|++..-+-+.|-+|+..|=+.=.
T Consensus 8 vL~~l~~~~~~~t~~~l~~~~~~~~~~vs~~i~~L~~~glv~~~ 51 (68)
T PF13463_consen 8 VLRALAHSDGPMTQSDLAERLGISKSTVSRIIKKLEEKGLVEKE 51 (68)
T ss_dssp HHHHHT--TS-BEHHHHHHHTT--HHHHHHHHHHHHHTTSEEEE
T ss_pred HHHHHHccCCCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEec
Confidence 33344457899999999999999999999999999999977433
No 194
>PRK01773 hscB co-chaperone HscB; Provisional
Probab=45.43 E-value=2.2e+02 Score=26.64 Aligned_cols=32 Identities=16% Similarity=0.321 Sum_probs=23.0
Q ss_pred cchhHHHHHHHHHHHHhhcCHHHHHHHHHHHH
Q 013640 161 SERRLSALWGKMAAEILMQNWDIALEELNQLK 192 (439)
Q Consensus 161 ~~~k~~~lwg~la~eIl~~~w~~a~~~l~klk 192 (439)
...+...+-..++..+-..||+.|...+.|||
T Consensus 123 v~~~~~~~~~~l~~~~~~~d~~~A~~~~~rL~ 154 (173)
T PRK01773 123 IKQEQQAILTELSTALNSQQWQQASQINDRLR 154 (173)
T ss_pred HHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHH
Confidence 34556666667776677788998888877775
No 195
>smart00421 HTH_LUXR helix_turn_helix, Lux Regulon. lux regulon (activates the bioluminescence operon
Probab=45.00 E-value=49 Score=23.32 Aligned_cols=29 Identities=17% Similarity=0.374 Sum_probs=25.9
Q ss_pred hccccHHHHHHHcCCCHHHHHHHHHHHhh
Q 013640 355 HQRIDMAVLAEKLNLNYEEAQRWIVNLIR 383 (439)
Q Consensus 355 y~~I~I~~lA~~l~~s~~~~E~wiv~lI~ 383 (439)
....+.+.+|+.+|+|+.-+.+++.++..
T Consensus 16 ~~g~s~~eia~~l~is~~tv~~~~~~~~~ 44 (58)
T smart00421 16 AEGLTNKEIAERLGISEKTVKTHLSNIMR 44 (58)
T ss_pred HcCCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 36779999999999999999999998755
No 196
>PRK10803 tol-pal system protein YbgF; Provisional
Probab=44.73 E-value=3.2e+02 Score=27.12 Aligned_cols=43 Identities=14% Similarity=0.213 Sum_probs=36.7
Q ss_pred HhcCCChhHHHHHHHHHHHHHhcCChhhHHHHHHHHHhhcccc
Q 013640 119 DRYQIGPDQIEALYQYAKFQFECGNYSGAADYLYQYRALCTNS 161 (439)
Q Consensus 119 ~~~g~t~e~~~al~~~ak~~y~~Gdy~~A~~~L~~~~~~~~~~ 161 (439)
+.|--++..-+++++.|..+.+.|+++.|.+++..+...-+++
T Consensus 208 ~~yP~s~~~~dAl~klg~~~~~~g~~~~A~~~~~~vi~~yP~s 250 (263)
T PRK10803 208 KNYPKSPKAADAMFKVGVIMQDKGDTAKAKAVYQQVIKKYPGT 250 (263)
T ss_pred HHCCCCcchhHHHHHHHHHHHHcCCHHHHHHHHHHHHHHCcCC
Confidence 4555577889999999999999999999999999888776653
No 197
>PF06163 DUF977: Bacterial protein of unknown function (DUF977); InterPro: IPR010382 This entry consists of several hypothetical bacterial proteins of unknown function.
Probab=44.56 E-value=41 Score=30.20 Aligned_cols=38 Identities=24% Similarity=0.397 Sum_probs=35.8
Q ss_pred HhhhhhccccHHHHHHHcCCCHHHHHHHHHHHhhcCcc
Q 013640 350 TYCRIHQRIDMAVLAEKLNLNYEEAQRWIVNLIRNSKL 387 (439)
Q Consensus 350 ~ycriy~~I~I~~lA~~l~~s~~~~E~wiv~lI~~~rL 387 (439)
.++|-|.++|++.|+..+|+|..-+.+.+-.|+..|.|
T Consensus 19 ElVRe~GRiTi~ql~~~TGasR~Tvk~~lreLVa~G~l 56 (127)
T PF06163_consen 19 ELVREHGRITIKQLVAKTGASRNTVKRYLRELVARGDL 56 (127)
T ss_pred HHHHHcCCccHHHHHHHHCCCHHHHHHHHHHHHHcCCe
Confidence 47899999999999999999999999999999998877
No 198
>COG1536 FliG Flagellar motor switch protein [Cell motility and secretion]
Probab=44.33 E-value=3.9e+02 Score=27.84 Aligned_cols=146 Identities=16% Similarity=0.244 Sum_probs=80.4
Q ss_pred HHHHHHHHhhCChhHHHHhhhcchhccHHHHHHhcCCChhHHHHHHHHHHHHHhcCChh----hHHHHHHHHHhhccccc
Q 013640 87 ERAAPIVSFLQNPNSFQDLRANDQHYNLQMLHDRYQIGPDQIEALYQYAKFQFECGNYS----GAADYLYQYRALCTNSE 162 (439)
Q Consensus 87 ~~~~~~~~~~~~~e~~~~l~~~dk~~n~~~l~~~~g~t~e~~~al~~~ak~~y~~Gdy~----~A~~~L~~~~~~~~~~~ 162 (439)
+.+..|++.+++.|++.-. .....-.+++++..+..+. .|+-.+...+ ++.++......++.+.+
T Consensus 27 ~~aa~vlk~l~~~eiq~l~---------~~~a~lk~v~~~~~~~il~--eF~~~~~~~~~i~~~~~~~~~~lL~kalg~~ 95 (339)
T COG1536 27 EIAAEVLKHLSPEEIQRLS---------TEMATLKTVSPEEKEQVLE--EFEELFTEQAGINKGADEYARELLEKALGEE 95 (339)
T ss_pred HHHHHHHHhCCHHHHHHHH---------HHHHhccCCCHHHHHHHHH--HHHHHHHhccccccChHHHHHHHHHHhCcHh
Confidence 3344566666555432211 2233344566666666553 5555555554 55666777777666544
Q ss_pred hhHHHHHHHHHH-HHhhcCHHHHHHHHHH-HHHHhcCCCCCCChHHHHHHHHHHHHHHHHHHhcCccchHHHHHHhccc-
Q 013640 163 RRLSALWGKMAA-EILMQNWDIALEELNQ-LKEKVDDPKSFTSPLNQMQSRIWLMHWSLFIFFNHDNGRTLIIDLFNQD- 239 (439)
Q Consensus 163 ~k~~~lwg~la~-eIl~~~w~~a~~~l~k-lke~id~~~~~~~~l~~l~~R~WllHwsLf~~fn~~~~~~~l~d~F~~~- 239 (439)
+-+.+..++.. .+....|+.....--. +-.+|.+. || |.. +++..+..++....++..|...
T Consensus 96 -~a~~i~~~i~~~~~~~~~~~~l~~~~p~~l~~~i~~E----hP--Qti--------a~iLs~L~~~~aa~vL~~l~~e~ 160 (339)
T COG1536 96 -KAESLLERITGSAIQTSPFDLLRKLDPSQLADLIKNE----HP--QTI--------ALILSYLPPDQAAEILSTLPEEL 160 (339)
T ss_pred -HHHHHHHHhhhccccccHHHHhhhCCHHHHHHHHHcc----cc--HHH--------HHHHHhcCHHHHHHHHHhCCHHH
Confidence 33444444444 5555567665554333 66777762 55 222 4556666666666666665532
Q ss_pred -----cchhHHHhhchhHHHHHHH
Q 013640 240 -----KYLNAIQTNAPHLLRYLAT 258 (439)
Q Consensus 240 -----~yl~~Iqt~~p~lLrYlvv 258 (439)
..+..+.-..|..|+|+--
T Consensus 161 r~~v~~Ria~l~~v~p~al~~i~~ 184 (339)
T COG1536 161 RADVVKRIATLEGVSPEALAELEN 184 (339)
T ss_pred HHHHHHHHHhhccCCHHHHHHHHH
Confidence 3444444577888888754
No 199
>PF13730 HTH_36: Helix-turn-helix domain
Probab=43.71 E-value=38 Score=24.75 Aligned_cols=28 Identities=25% Similarity=0.253 Sum_probs=25.6
Q ss_pred cHHHHHHHcCCCHHHHHHHHHHHhhcCc
Q 013640 359 DMAVLAEKLNLNYEEAQRWIVNLIRNSK 386 (439)
Q Consensus 359 ~I~~lA~~l~~s~~~~E~wiv~lI~~~r 386 (439)
+++.||+.+|+|..-+.+.|-.|+..|=
T Consensus 27 S~~~la~~~g~s~~Tv~~~i~~L~~~G~ 54 (55)
T PF13730_consen 27 SQETLAKDLGVSRRTVQRAIKELEEKGL 54 (55)
T ss_pred CHHHHHHHHCcCHHHHHHHHHHHHHCcC
Confidence 7999999999999999999999987663
No 200
>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=43.50 E-value=45 Score=26.42 Aligned_cols=51 Identities=18% Similarity=0.255 Sum_probs=40.8
Q ss_pred HHHHhhhhhccccHHHHHHHcCCCHHHHHHHHHHHhhcCccceeecccCCEEEe
Q 013640 347 IFETYCRIHQRIDMAVLAEKLNLNYEEAQRWIVNLIRNSKLDAKIDAKSGTVIM 400 (439)
Q Consensus 347 ife~ycriy~~I~I~~lA~~l~~s~~~~E~wiv~lI~~~rL~aKID~~~g~V~~ 400 (439)
|+... .-....+++.|++..|++..++-.-|.=|-|++|+ .|+.++|.+..
T Consensus 13 Vw~~L-~~~~~~s~~el~k~~~l~~~~~~~AiGWLarE~KI--~~~~~~~~~~v 63 (65)
T PF10771_consen 13 VWQLL-NENGEWSVSELKKATGLSDKEVYLAIGWLARENKI--EFEEKNGELYV 63 (65)
T ss_dssp HHHHH-CCSSSEEHHHHHHHCT-SCHHHHHHHHHHHCTTSE--EEEEETTEEEE
T ss_pred HHHHH-hhCCCcCHHHHHHHhCcCHHHHHHHHHHHhccCce--eEEeeCCEEEE
Confidence 34433 44789999999999999999999999999999999 67777777653
No 201
>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=43.27 E-value=39 Score=25.94 Aligned_cols=34 Identities=12% Similarity=0.131 Sum_probs=29.4
Q ss_pred hhccccHHHHHHHcCCCHHHHHHHHHHHhhcCcc
Q 013640 354 IHQRIDMAVLAEKLNLNYEEAQRWIVNLIRNSKL 387 (439)
Q Consensus 354 iy~~I~I~~lA~~l~~s~~~~E~wiv~lI~~~rL 387 (439)
--..|+...||+.||+|+.-+=.-+-+|-..|-+
T Consensus 19 ~~~~v~~~~iA~~L~vs~~tvt~ml~~L~~~GlV 52 (60)
T PF01325_consen 19 EGGPVRTKDIAERLGVSPPTVTEMLKRLAEKGLV 52 (60)
T ss_dssp CTSSBBHHHHHHHHTS-HHHHHHHHHHHHHTTSE
T ss_pred CCCCccHHHHHHHHCCChHHHHHHHHHHHHCCCE
Confidence 4588999999999999999999999999887755
No 202
>TIGR00714 hscB Fe-S protein assembly co-chaperone HscB. This model describes the small subunit, Hsc20 (20K heat shock cognate protein) of a pair of proteins Hsc66-Hsc20, related to the DnaK-DnaJ heat shock proteins, which also serve as molecular chaperones. Hsc20, unlike DnaJ, appears not to have chaperone activity on its own, but to act solely as a regulatory subunit for Hsc66 (i.e., to be a co-chaperone). The gene for Hsc20 in E. coli, hscB, is not induced by heat shock.
Probab=43.18 E-value=2.4e+02 Score=25.88 Aligned_cols=33 Identities=12% Similarity=0.203 Sum_probs=24.6
Q ss_pred cchhHHHHHHHHHHHHhhcCHHHHHHHHHHHHH
Q 013640 161 SERRLSALWGKMAAEILMQNWDIALEELNQLKE 193 (439)
Q Consensus 161 ~~~k~~~lwg~la~eIl~~~w~~a~~~l~klke 193 (439)
...++..+...+...+-.+||+.|...+.+||=
T Consensus 109 ~~~~~~~~~~~l~~~~~~~d~~~A~~~~~kLky 141 (157)
T TIGR00714 109 VKKMFQTRHQLLVEQLDNQTWAAAADYTRKLRF 141 (157)
T ss_pred HHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHHH
Confidence 455667777777777777899999888877753
No 203
>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=43.08 E-value=47 Score=24.94 Aligned_cols=37 Identities=22% Similarity=0.320 Sum_probs=27.0
Q ss_pred HHHHHHHHhhhhh-----ccccHHHHHHHcCCCHHHHHHHHH
Q 013640 343 ARLFIFETYCRIH-----QRIDMAVLAEKLNLNYEEAQRWIV 379 (439)
Q Consensus 343 aR~~ife~ycriy-----~~I~I~~lA~~l~~s~~~~E~wiv 379 (439)
-|+-.|-.+++-. ..|+=..||+.+|+++..+-+.++
T Consensus 9 ~RL~~Y~r~L~~l~~~G~~~vSS~~La~~~gi~~~qVRKDlS 50 (50)
T PF06971_consen 9 RRLPLYLRYLEQLKEEGVERVSSQELAEALGITPAQVRKDLS 50 (50)
T ss_dssp HHHHHHHHHHHHHHHTT-SEE-HHHHHHHHTS-HHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHcCCeeECHHHHHHHHCCCHHHhcccCC
Confidence 3666666666654 479999999999999999888764
No 204
>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=43.05 E-value=29 Score=25.56 Aligned_cols=23 Identities=26% Similarity=0.478 Sum_probs=20.3
Q ss_pred ccHHHHHHHcCCCHHHHHHHHHH
Q 013640 358 IDMAVLAEKLNLNYEEAQRWIVN 380 (439)
Q Consensus 358 I~I~~lA~~l~~s~~~~E~wiv~ 380 (439)
-.+..||..+||++..|..|.-|
T Consensus 28 ~~~~~la~~l~l~~~~V~~WF~n 50 (57)
T PF00046_consen 28 EEREELAKELGLTERQVKNWFQN 50 (57)
T ss_dssp HHHHHHHHHHTSSHHHHHHHHHH
T ss_pred cccccccccccccccccccCHHH
Confidence 34789999999999999999875
No 205
>smart00389 HOX Homeodomain. DNA-binding factors that are involved in the transcriptional regulation of key developmental processes
Probab=42.50 E-value=26 Score=25.51 Aligned_cols=22 Identities=32% Similarity=0.524 Sum_probs=20.3
Q ss_pred cHHHHHHHcCCCHHHHHHHHHH
Q 013640 359 DMAVLAEKLNLNYEEAQRWIVN 380 (439)
Q Consensus 359 ~I~~lA~~l~~s~~~~E~wiv~ 380 (439)
.+..||+.+|++...|..|..|
T Consensus 29 ~~~~la~~~~l~~~qV~~WF~n 50 (56)
T smart00389 29 EREELAAKLGLSERQVKVWFQN 50 (56)
T ss_pred HHHHHHHHHCcCHHHHHHhHHH
Confidence 4889999999999999999886
No 206
>PF14938 SNAP: Soluble NSF attachment protein, SNAP; PDB: 1QQE_A 2IFU_A.
Probab=42.32 E-value=1.2e+02 Score=29.85 Aligned_cols=71 Identities=14% Similarity=0.178 Sum_probs=49.7
Q ss_pred CCChhHHHHHHHHHHHHHhcCChhhHHHHHHHHHhhccccc-hh---HHHHHHHHHHHHhhcCHHHHHHHHHHHH
Q 013640 122 QIGPDQIEALYQYAKFQFECGNYSGAADYLYQYRALCTNSE-RR---LSALWGKMAAEILMQNWDIALEELNQLK 192 (439)
Q Consensus 122 g~t~e~~~al~~~ak~~y~~Gdy~~A~~~L~~~~~~~~~~~-~k---~~~lwg~la~eIl~~~w~~a~~~l~klk 192 (439)
|-+....+.+.+.|.++.+.|+|++|.+.+...-..+.+.. .+ -+.++..+-|-+.++|...|.+.+++..
T Consensus 149 ~~~~~a~~~~~~~A~l~~~l~~y~~A~~~~e~~~~~~l~~~l~~~~~~~~~l~a~l~~L~~~D~v~A~~~~~~~~ 223 (282)
T PF14938_consen 149 GSPHSAAECLLKAADLYARLGRYEEAIEIYEEVAKKCLENNLLKYSAKEYFLKAILCHLAMGDYVAARKALERYC 223 (282)
T ss_dssp T-HHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHTCCCHCTTGHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHG
T ss_pred CChhhHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHhhcccccchhHHHHHHHHHHHHHHcCCHHHHHHHHHHHH
Confidence 33555667889999999999999999999998887765432 22 3445666667777888777766666553
No 207
>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=42.17 E-value=1e+02 Score=30.09 Aligned_cols=57 Identities=16% Similarity=0.144 Sum_probs=43.4
Q ss_pred HHHHHHHHHHhcCChhhHHHHHHHHHhhccc---cchhHHHHHHHHHHHHhhcCHHHHHH
Q 013640 130 ALYQYAKFQFECGNYSGAADYLYQYRALCTN---SERRLSALWGKMAAEILMQNWDIALE 186 (439)
Q Consensus 130 al~~~ak~~y~~Gdy~~A~~~L~~~~~~~~~---~~~k~~~lwg~la~eIl~~~w~~a~~ 186 (439)
-..+.|..|+..|||++|.++|..+...-.. ...--+.+|..+.|-...+|.+....
T Consensus 180 l~~~~A~ey~~~g~~~~A~~~l~~~~~~yr~egW~~l~~~~l~~l~~Ca~~~~~~~~~l~ 239 (247)
T PF11817_consen 180 LSLEMAEEYFRLGDYDKALKLLEPAASSYRREGWWSLLTEVLWRLLECAKRLGDVEDYLT 239 (247)
T ss_pred HHHHHHHHHHHCCCHHHHHHHHHHHHHHHHhCCcHHHHHHHHHHHHHHHHHhCCHHHHHH
Confidence 4479999999999999999999988433222 23457888888889888888665544
No 208
>PRK11050 manganese transport regulator MntR; Provisional
Probab=41.96 E-value=1.2e+02 Score=27.40 Aligned_cols=36 Identities=11% Similarity=0.216 Sum_probs=31.9
Q ss_pred hccccHHHHHHHcCCCHHHHHHHHHHHhhcCcccee
Q 013640 355 HQRIDMAVLAEKLNLNYEEAQRWIVNLIRNSKLDAK 390 (439)
Q Consensus 355 y~~I~I~~lA~~l~~s~~~~E~wiv~lI~~~rL~aK 390 (439)
...+++..||+.||+|+.-+-++|..|...|-+..+
T Consensus 49 ~~~~t~~eLA~~l~is~stVsr~l~~Le~~GlI~r~ 84 (152)
T PRK11050 49 VGEARQVDIAARLGVSQPTVAKMLKRLARDGLVEMR 84 (152)
T ss_pred cCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEe
Confidence 467899999999999999999999999999866543
No 209
>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=41.79 E-value=71 Score=32.14 Aligned_cols=59 Identities=14% Similarity=0.219 Sum_probs=55.2
Q ss_pred cHHHHHHHHHHHHHHHhhhhhccccHHHHHHHcCCCHHHHHHHHHHHhhcCccceeecc
Q 013640 335 LRDEFLENARLFIFETYCRIHQRIDMAVLAEKLNLNYEEAQRWIVNLIRNSKLDAKIDA 393 (439)
Q Consensus 335 ~~~~f~e~aR~~ife~ycriy~~I~I~~lA~~l~~s~~~~E~wiv~lI~~~rL~aKID~ 393 (439)
+...|+...|..+=..++.+=+.+.+..+.+..|++...+-.-+-+||..|++.++|-.
T Consensus 170 yT~ayv~r~ka~iRG~l~a~T~Pt~l~~l~~~~~~~~~l~~~il~~Li~~~~l~G~i~G 228 (272)
T PF09743_consen 170 YTEAYVARQKARIRGALSAITRPTPLSSLLKRYGFEEKLFQSILEELIKSGELPGSIVG 228 (272)
T ss_pred ecHHHHHHHHHHHHHHHhcCccceEHHHHHHHhCCcHHHHHHHHHHHHhcCcceEEEEC
Confidence 77899999999999999999999999999999999999999999999999999988654
No 210
>PF13281 DUF4071: Domain of unknown function (DUF4071)
Probab=41.77 E-value=1.9e+02 Score=30.64 Aligned_cols=68 Identities=18% Similarity=0.145 Sum_probs=51.5
Q ss_pred HHHHHHHHHHh---cCChhhHHHHHHHHHhhccccchhHHHHHHHHHHHHhhcCHHHHHHHHHHHHHHhcC
Q 013640 130 ALYQYAKFQFE---CGNYSGAADYLYQYRALCTNSERRLSALWGKMAAEILMQNWDIALEELNQLKEKVDD 197 (439)
Q Consensus 130 al~~~ak~~y~---~Gdy~~A~~~L~~~~~~~~~~~~k~~~lwg~la~eIl~~~w~~a~~~l~klke~id~ 197 (439)
--+.||-.+.+ .||.++|.+.+......+.+...-+=+++|.+=-+++...|..-.+.+.++-+.|.+
T Consensus 181 i~~~yafALnRrn~~gdre~Al~il~~~l~~~~~~~~d~~gL~GRIyKD~~~~s~~~d~~~ldkAi~~Y~k 251 (374)
T PF13281_consen 181 IKFQYAFALNRRNKPGDREKALQILLPVLESDENPDPDTLGLLGRIYKDLFLESNFTDRESLDKAIEWYRK 251 (374)
T ss_pred HHHHHHHHHhhcccCCCHHHHHHHHHHHHhccCCCChHHHHHHHHHHHHHHHHcCccchHHHHHHHHHHHH
Confidence 34677888888 999999999999977767777777899999999999876554444555555555544
No 211
>COG2956 Predicted N-acetylglucosaminyl transferase [Carbohydrate transport and metabolism]
Probab=41.58 E-value=3.9e+02 Score=28.14 Aligned_cols=33 Identities=18% Similarity=0.268 Sum_probs=14.3
Q ss_pred cCCChhHHHHHHHHHHHHHhcCChhhHHHHHHH
Q 013640 121 YQIGPDQIEALYQYAKFQFECGNYSGAADYLYQ 153 (439)
Q Consensus 121 ~g~t~e~~~al~~~ak~~y~~Gdy~~A~~~L~~ 153 (439)
+..++.-..+-.-+|++...-|+|+.|.+.+..
T Consensus 207 lqa~~~cvRAsi~lG~v~~~~g~y~~AV~~~e~ 239 (389)
T COG2956 207 LQADKKCVRASIILGRVELAKGDYQKAVEALER 239 (389)
T ss_pred HhhCccceehhhhhhHHHHhccchHHHHHHHHH
Confidence 333333333444444444444444444444433
No 212
>PRK10225 DNA-binding transcriptional repressor UxuR; Provisional
Probab=41.07 E-value=93 Score=30.14 Aligned_cols=69 Identities=14% Similarity=0.162 Sum_probs=60.1
Q ss_pred ccHHHHHHHHHHHHHHHhhhhhccc-cHHHHHHHcCCCHHHHHHHHHHHhhcCccceeecccCCEEEeCCCC
Q 013640 334 PLRDEFLENARLFIFETYCRIHQRI-DMAVLAEKLNLNYEEAQRWIVNLIRNSKLDAKIDAKSGTVIMEPTH 404 (439)
Q Consensus 334 ~~~~~f~e~aR~~ife~ycriy~~I-~I~~lA~~l~~s~~~~E~wiv~lI~~~rL~aKID~~~g~V~~~~~~ 404 (439)
+-.+...+..|..|...-++|=.++ +-..||+.||||..=+-.-|..|-..|=+. +-.-.|+++.....
T Consensus 9 ~~~~~v~~~l~~~I~~g~l~pG~~LpsE~eLa~~~gVSRtpVREAL~~L~~eGlV~--~~~~~G~~V~~~~~ 78 (257)
T PRK10225 9 RPYQEVGAMIRDLIIKTPYNPGERLPPEREIAEMLDVTRTVVREALIMLEIKGLVE--VRRGAGIYVLDSSG 78 (257)
T ss_pred cHHHHHHHHHHHHHHhCCCCCCCcCcCHHHHHHHhCCCHHHHHHHHHHHHHCCCEE--EecCCEEEEeCCCc
Confidence 4568899999999999999999999 699999999999999999999999999884 45667888876443
No 213
>COG1729 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=40.96 E-value=1.2e+02 Score=30.37 Aligned_cols=60 Identities=22% Similarity=0.125 Sum_probs=25.4
Q ss_pred HHHHHHHHHHhcCChhhHHHHHHHHHhhccccchhHHHHHHHHHHHHhhcCHHHHHHHHH
Q 013640 130 ALYQYAKFQFECGNYSGAADYLYQYRALCTNSERRLSALWGKMAAEILMQNWDIALEELN 189 (439)
Q Consensus 130 al~~~ak~~y~~Gdy~~A~~~L~~~~~~~~~~~~k~~~lwg~la~eIl~~~w~~a~~~l~ 189 (439)
|.|=+|+.+|..|||++|...+-.+..--+...+--++++-.=.|.-=.++-|.|..-+.
T Consensus 180 A~yWLGe~~y~qg~y~~Aa~~f~~~~k~~P~s~KApdallKlg~~~~~l~~~d~A~atl~ 239 (262)
T COG1729 180 AYYWLGESLYAQGDYEDAAYIFARVVKDYPKSPKAPDALLKLGVSLGRLGNTDEACATLQ 239 (262)
T ss_pred hHHHHHHHHHhcccchHHHHHHHHHHHhCCCCCCChHHHHHHHHHHHHhcCHHHHHHHHH
Confidence 445555555555555555544444443332222223444333333333344444444333
No 214
>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=40.79 E-value=60 Score=24.65 Aligned_cols=39 Identities=18% Similarity=0.215 Sum_probs=29.1
Q ss_pred HHHHHHHhhhhhccccHHHHHHHcCCCHHHHHHHHHHHh
Q 013640 344 RLFIFETYCRIHQRIDMAVLAEKLNLNYEEAQRWIVNLI 382 (439)
Q Consensus 344 R~~ife~ycriy~~I~I~~lA~~l~~s~~~~E~wiv~lI 382 (439)
+...-.-|-..=+.++++.||+.||||..-+..-|-+-+
T Consensus 10 ~~A~~~GYfd~PR~~tl~elA~~lgis~st~~~~LRrae 48 (53)
T PF04967_consen 10 KAAYELGYFDVPRRITLEELAEELGISKSTVSEHLRRAE 48 (53)
T ss_pred HHHHHcCCCCCCCcCCHHHHHHHhCCCHHHHHHHHHHHH
Confidence 334444566666899999999999999998776665543
No 215
>PRK10370 formate-dependent nitrite reductase complex subunit NrfG; Provisional
Probab=40.77 E-value=3.1e+02 Score=25.68 Aligned_cols=73 Identities=14% Similarity=0.155 Sum_probs=43.7
Q ss_pred HHhcCCChhHHHHHHHHHHHHHhcCChhhHHHHHHHHHhhccccchhHHHHHHHHHHHH-hh-cCH--HHHHHHHHHHHH
Q 013640 118 HDRYQIGPDQIEALYQYAKFQFECGNYSGAADYLYQYRALCTNSERRLSALWGKMAAEI-LM-QNW--DIALEELNQLKE 193 (439)
Q Consensus 118 ~~~~g~t~e~~~al~~~ak~~y~~Gdy~~A~~~L~~~~~~~~~~~~k~~~lwg~la~eI-l~-~~w--~~a~~~l~klke 193 (439)
++.....|+..++.+.+|..+...|+|+.|.+.+.....+.+++ ..+|.-++.-. .. +++ +.|.+-+.++-+
T Consensus 63 ~~~L~~~P~~~~~w~~Lg~~~~~~g~~~~A~~a~~~Al~l~P~~----~~~~~~lA~aL~~~~g~~~~~~A~~~l~~al~ 138 (198)
T PRK10370 63 QDKIRANPQNSEQWALLGEYYLWRNDYDNALLAYRQALQLRGEN----AELYAALATVLYYQAGQHMTPQTREMIDKALA 138 (198)
T ss_pred HHHHHHCCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhCCCC----HHHHHHHHHHHHHhcCCCCcHHHHHHHHHHHH
Confidence 33334466667788888888888888888888888777765542 22333333322 12 222 566666665544
Q ss_pred H
Q 013640 194 K 194 (439)
Q Consensus 194 ~ 194 (439)
.
T Consensus 139 ~ 139 (198)
T PRK10370 139 L 139 (198)
T ss_pred h
Confidence 3
No 216
>COG3415 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=40.26 E-value=61 Score=29.42 Aligned_cols=47 Identities=11% Similarity=0.248 Sum_probs=39.6
Q ss_pred HHHHHHHHHHHHHhhhhhccccHHHHHHHcCCCHHHHHHHHHHHhhcCc
Q 013640 338 EFLENARLFIFETYCRIHQRIDMAVLAEKLNLNYEEAQRWIVNLIRNSK 386 (439)
Q Consensus 338 ~f~e~aR~~ife~ycriy~~I~I~~lA~~l~~s~~~~E~wiv~lI~~~r 386 (439)
.+-+..|..++..|. +.-.|+..+|+.||+|..-+.+|+-++=.+|-
T Consensus 4 ~~s~~~R~~~~~~~~--~~G~S~re~Ak~~gvs~sTvy~wv~r~~e~G~ 50 (138)
T COG3415 4 PFSNDLRERVVDAVV--GEGLSCREAAKRFGVSISTVYRWVRRYRETGL 50 (138)
T ss_pred hhhHHHHHHHHHHHH--HcCccHHHHHHHhCccHHHHHHHHHHhccccc
Confidence 456778888888774 68999999999999999999999999855443
No 217
>PRK03902 manganese transport transcriptional regulator; Provisional
Probab=39.56 E-value=1.7e+02 Score=25.89 Aligned_cols=63 Identities=13% Similarity=0.183 Sum_probs=43.5
Q ss_pred hhhhhccccHHHHHHHcCCCHHHHHHHHHHHhhcCccceeecccCCEEEeCCCCchhHHHHHHhhh
Q 013640 351 YCRIHQRIDMAVLAEKLNLNYEEAQRWIVNLIRNSKLDAKIDAKSGTVIMEPTHPNVYEQLIDHTK 416 (439)
Q Consensus 351 ycriy~~I~I~~lA~~l~~s~~~~E~wiv~lI~~~rL~aKID~~~g~V~~~~~~~~~yqqvi~kt~ 416 (439)
+..-...++++.||+.||+|+.-+=+.|-+|...|-+.-. ..+.|..+..-....+.++.+-+
T Consensus 16 l~~~~~~~~~~ela~~l~vs~~svs~~l~~L~~~Gli~~~---~~~~i~LT~~G~~~a~~~~~~h~ 78 (142)
T PRK03902 16 LIEEKGYARVSDIAEALSVHPSSVTKMVQKLDKDEYLIYE---KYRGLVLTPKGKKIGKRLVYRHE 78 (142)
T ss_pred HHhcCCCcCHHHHHHHhCCChhHHHHHHHHHHHCCCEEEe---cCceEEECHHHHHHHHHHHHHHH
Confidence 3455677899999999999999999999999999876522 22445544333344555544443
No 218
>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=39.38 E-value=1.6e+02 Score=27.11 Aligned_cols=92 Identities=16% Similarity=0.141 Sum_probs=56.8
Q ss_pred cHHHHHHHHHHHHHHHhhhhhccccHHHHHHHcCCCHHHHHHHHHHHhhcCccceee--cccCCEEEeCCCCchhHHHHH
Q 013640 335 LRDEFLENARLFIFETYCRIHQRIDMAVLAEKLNLNYEEAQRWIVNLIRNSKLDAKI--DAKSGTVIMEPTHPNVYEQLI 412 (439)
Q Consensus 335 ~~~~f~e~aR~~ife~ycriy~~I~I~~lA~~l~~s~~~~E~wiv~lI~~~rL~aKI--D~~~g~V~~~~~~~~~yqqvi 412 (439)
+...|+..-=..++...+ .|.-++-+.||+.|||+..++-+-|-.|-.+|=+.-+- |..+|-..--= .--|.+++
T Consensus 7 ~~~~~~g~~~v~Vl~aL~-~~~~~tdEeLa~~Lgi~~~~VRk~L~~L~e~~Lv~~~r~r~~~~gw~~Y~w--~i~~~~i~ 83 (158)
T TIGR00373 7 VVGRAAEEEVGLVLFSLG-IKGEFTDEEISLELGIKLNEVRKALYALYDAGLADYKRRKDDETGWYEYTW--RINYEKAL 83 (158)
T ss_pred HHHHHcChhHHHHHHHHh-ccCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCceeeeeeecCCCcEEEEE--EeCHHHHH
Confidence 344455444466666654 67889999999999999999999999998877653221 22333321110 12455666
Q ss_pred HhhhhhhhHHHHHHHHHHhh
Q 013640 413 DHTKGLSGRTYKLVGQLLEH 432 (439)
Q Consensus 413 ~kt~~L~~R~q~L~~~i~~~ 432 (439)
+. +..|..++...+.+.
T Consensus 84 d~---Ik~~~~~~~~~lk~~ 100 (158)
T TIGR00373 84 DV---LKRKLEETAKKLREK 100 (158)
T ss_pred HH---HHHHHHHHHHHHHHH
Confidence 43 445665555555443
No 219
>PF06160 EzrA: Septation ring formation regulator, EzrA ; InterPro: IPR010379 During the bacterial cell cycle, the tubulin-like cell-division protein FtsZ polymerises into a ring structure that establishes the location of the nascent division site. EzrA modulates the frequency and position of FtsZ ring formation [].; GO: 0000921 septin ring assembly, 0005940 septin ring, 0016021 integral to membrane
Probab=39.31 E-value=2.6e+02 Score=30.85 Aligned_cols=41 Identities=15% Similarity=0.145 Sum_probs=31.9
Q ss_pred hcCCChhHHHHHHHHHHHHHhc-CChhhHHHHHHHHHhhccc
Q 013640 120 RYQIGPDQIEALYQYAKFQFEC-GNYSGAADYLYQYRALCTN 160 (439)
Q Consensus 120 ~~g~t~e~~~al~~~ak~~y~~-Gdy~~A~~~L~~~~~~~~~ 160 (439)
.|.-+...++.-+.-|...|+. |+|.+|.+....+....-+
T Consensus 507 RYR~~~~~v~~al~~Ae~~F~~~~~Y~~ALe~i~~alE~veP 548 (560)
T PF06160_consen 507 RYRSDNPEVDEALTEAEDLFRNEYDYEKALETIATALEKVEP 548 (560)
T ss_pred cccCCCHHHHHHHHHHHHHHHhhCCHHHHHHHHHHHHHHhCC
Confidence 4533555677778889999999 9999999999888876643
No 220
>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=39.23 E-value=98 Score=23.27 Aligned_cols=49 Identities=16% Similarity=0.244 Sum_probs=38.9
Q ss_pred HHHHHHHHHHHHhhhhhccccHHHHHHHcCCCHHHHHHHHHHHhhcCccc
Q 013640 339 FLENARLFIFETYCRIHQRIDMAVLAEKLNLNYEEAQRWIVNLIRNSKLD 388 (439)
Q Consensus 339 f~e~aR~~ife~ycriy~~I~I~~lA~~l~~s~~~~E~wiv~lI~~~rL~ 388 (439)
+-...|..|+... ......++..||+.||+++.-+-.-|-.|...|=+.
T Consensus 7 L~~p~R~~Il~~L-~~~~~~t~~ela~~l~~~~~t~s~hL~~L~~aGli~ 55 (61)
T PF12840_consen 7 LSDPTRLRILRLL-ASNGPMTVSELAEELGISQSTVSYHLKKLEEAGLIE 55 (61)
T ss_dssp HTSHHHHHHHHHH-HHCSTBEHHHHHHHHTS-HHHHHHHHHHHHHTTSEE
T ss_pred hCCHHHHHHHHHH-hcCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCeE
Confidence 3445677777666 778999999999999999999999999888777553
No 221
>PF14561 TPR_20: Tetratricopeptide repeat; PDB: 3QOU_A 2R5S_A 3QDN_B.
Probab=39.08 E-value=39 Score=28.08 Aligned_cols=45 Identities=24% Similarity=0.355 Sum_probs=32.0
Q ss_pred HHHHHhcCCChhHHHHHHHHHHHHHhcCChhhHHHHHHHHHhhcc
Q 013640 115 QMLHDRYQIGPDQIEALYQYAKFQFECGNYSGAADYLYQYRALCT 159 (439)
Q Consensus 115 ~~l~~~~g~t~e~~~al~~~ak~~y~~Gdy~~A~~~L~~~~~~~~ 159 (439)
+.|++...-.|+..++.|.+|..+...|+|+.|.+.|-.+.....
T Consensus 9 ~al~~~~a~~P~D~~ar~~lA~~~~~~g~~e~Al~~Ll~~v~~dr 53 (90)
T PF14561_consen 9 AALEAALAANPDDLDARYALADALLAAGDYEEALDQLLELVRRDR 53 (90)
T ss_dssp HHHHHHHHHSTT-HHHHHHHHHHHHHTT-HHHHHHHHHHHHCC-T
T ss_pred HHHHHHHHcCCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhCc
Confidence 334444444777889999999999999999999998766655443
No 222
>KOG4056 consensus Translocase of outer mitochondrial membrane complex, subunit TOM20 [Intracellular trafficking, secretion, and vesicular transport]
Probab=38.94 E-value=80 Score=28.85 Aligned_cols=46 Identities=20% Similarity=0.236 Sum_probs=36.6
Q ss_pred HHHHHHHHhcCChhhHHHHHHHHHhhccccchhHHHHHHHHHHHHh
Q 013640 132 YQYAKFQFECGNYSGAADYLYQYRALCTNSERRLSALWGKMAAEIL 177 (439)
Q Consensus 132 ~~~ak~~y~~Gdy~~A~~~L~~~~~~~~~~~~k~~~lwg~la~eIl 177 (439)
.++|.=+...|+++.+.+.++.....|..+..-+..+=+.|.-.|+
T Consensus 85 v~lGE~L~~qg~~e~ga~h~~nAi~vcgqpaqLL~vlq~tlp~~if 130 (143)
T KOG4056|consen 85 VQLGEELLAQGNEEEGAEHLANAIVVCGQPAQLLQVLQQTLPEAIF 130 (143)
T ss_pred HHhHHHHHHccCHHHHHHHHHHHHhhcCCHHHHHHHHHhhCCHHHH
Confidence 5789999999999999999999999998766656655555555554
No 223
>PRK11534 DNA-binding transcriptional regulator CsiR; Provisional
Probab=38.93 E-value=91 Score=29.48 Aligned_cols=67 Identities=9% Similarity=0.079 Sum_probs=58.2
Q ss_pred ccHHHHHHHHHHHHHHHhhhhhccccHHHHHHHcCCCHHHHHHHHHHHhhcCccceeecccCCEEEeCC
Q 013640 334 PLRDEFLENARLFIFETYCRIHQRIDMAVLAEKLNLNYEEAQRWIVNLIRNSKLDAKIDAKSGTVIMEP 402 (439)
Q Consensus 334 ~~~~~f~e~aR~~ife~ycriy~~I~I~~lA~~l~~s~~~~E~wiv~lI~~~rL~aKID~~~g~V~~~~ 402 (439)
+..+...+..|-.|...-++|=.+++...||+.||||..=+-.-|..|...|=+. +-...|.++..-
T Consensus 7 ~~~~~vy~~i~~~I~~g~l~pG~~L~e~eLae~lgVSRtpVREAL~~L~~eGlv~--~~~~~G~~V~~~ 73 (224)
T PRK11534 7 ITALDGYRWLKNDIIRGNFQPDEKLRMSLLTSRYALGVGPLREALSQLVAERLVT--VVNQKGYRVASM 73 (224)
T ss_pred hhhHHHHHHHHHHHHhCCCCCCCcCCHHHHHHHHCCChHHHHHHHHHHHHCCCEE--EeCCCceEeCCC
Confidence 3557888999999999999999999999999999999999999999999999884 456778777643
No 224
>PRK15174 Vi polysaccharide export protein VexE; Provisional
Probab=38.93 E-value=6e+02 Score=28.46 Aligned_cols=77 Identities=18% Similarity=0.202 Sum_probs=55.5
Q ss_pred HHHHHHhcCCChhHHHHHHHHHHHHHhcCChhhHHHHHHHHHhhccccchhHHHHHHHHHHHHhhcCHHHHHHHHHHHHH
Q 013640 114 LQMLHDRYQIGPDQIEALYQYAKFQFECGNYSGAADYLYQYRALCTNSERRLSALWGKMAAEILMQNWDIALEELNQLKE 193 (439)
Q Consensus 114 ~~~l~~~~g~t~e~~~al~~~ak~~y~~Gdy~~A~~~L~~~~~~~~~~~~k~~~lwg~la~eIl~~~w~~a~~~l~klke 193 (439)
...+++-..+.|+...++..+|..+...|+++.|..++.....+.++... .-..+|.+ -...++++.|.+.+.++-+
T Consensus 270 ~~~~~~Al~l~P~~~~a~~~lg~~l~~~g~~~eA~~~l~~al~l~P~~~~-a~~~La~~--l~~~G~~~eA~~~l~~al~ 346 (656)
T PRK15174 270 AEHWRHALQFNSDNVRIVTLYADALIRTGQNEKAIPLLQQSLATHPDLPY-VRAMYARA--LRQVGQYTAASDEFVQLAR 346 (656)
T ss_pred HHHHHHHHhhCCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhCCCCHH-HHHHHHHH--HHHCCCHHHHHHHHHHHHH
Confidence 45566667778888889999999999999999999999998887654332 22223332 2236889999887765543
No 225
>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=38.67 E-value=32 Score=23.82 Aligned_cols=19 Identities=11% Similarity=0.249 Sum_probs=15.2
Q ss_pred cHHHHHHHcCCCHHHHHHH
Q 013640 359 DMAVLAEKLNLNYEEAQRW 377 (439)
Q Consensus 359 ~I~~lA~~l~~s~~~~E~w 377 (439)
++..||+++|++.+++.+|
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 5789999999999998776
No 226
>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=38.57 E-value=71 Score=22.63 Aligned_cols=29 Identities=14% Similarity=0.241 Sum_probs=25.7
Q ss_pred hccccHHHHHHHcCCCHHHHHHHHHHHhh
Q 013640 355 HQRIDMAVLAEKLNLNYEEAQRWIVNLIR 383 (439)
Q Consensus 355 y~~I~I~~lA~~l~~s~~~~E~wiv~lI~ 383 (439)
....+...+|+.+|+|+.-+..++-++..
T Consensus 13 ~~~~s~~eia~~l~~s~~tv~~~~~~~~~ 41 (57)
T cd06170 13 AEGKTNKEIADILGISEKTVKTHLRNIMR 41 (57)
T ss_pred HcCCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 36789999999999999999999987755
No 227
>PRK15481 transcriptional regulatory protein PtsJ; Provisional
Probab=38.38 E-value=81 Score=32.92 Aligned_cols=65 Identities=20% Similarity=0.260 Sum_probs=55.7
Q ss_pred ccHHHHHHHHHHHHHHHhhhhhccc-cHHHHHHHcCCCHHHHHHHHHHHhhcCccceeecccCCEEEe
Q 013640 334 PLRDEFLENARLFIFETYCRIHQRI-DMAVLAEKLNLNYEEAQRWIVNLIRNSKLDAKIDAKSGTVIM 400 (439)
Q Consensus 334 ~~~~~f~e~aR~~ife~ycriy~~I-~I~~lA~~l~~s~~~~E~wiv~lI~~~rL~aKID~~~g~V~~ 400 (439)
.-.+.+.+..+..|.+-.+++=.++ ++..||+.||+|..-+.+-+..|..+|-+.++ ...|+.+.
T Consensus 5 ~~~~~~~~~i~~~i~~g~l~~g~~lps~r~la~~~~vsr~tv~~a~~~L~~~g~i~~~--~~~G~~v~ 70 (431)
T PRK15481 5 KTANEIFDSIRQLIQAGRLRPGDSLPPVRELASELGVNRNTVAAAYKRLVTAGLAQSQ--GRNGTVIR 70 (431)
T ss_pred cHHHHHHHHHHHHHHcCCCCCCCcCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEe--CCCceEEc
Confidence 4557788889999999999999999 89999999999999999999999999988654 44666664
No 228
>COG5484 Uncharacterized conserved protein [Function unknown]
Probab=38.03 E-value=45 Score=33.41 Aligned_cols=34 Identities=21% Similarity=0.359 Sum_probs=28.5
Q ss_pred HHHHHHHhhhhhccccHHHHHHHcCCCHHHHHHHHHH
Q 013640 344 RLFIFETYCRIHQRIDMAVLAEKLNLNYEEAQRWIVN 380 (439)
Q Consensus 344 R~~ife~ycriy~~I~I~~lA~~l~~s~~~~E~wiv~ 380 (439)
|..+...|++.+ .+..||++||||+.-+-+|..+
T Consensus 9 r~~Akk~yl~gm---k~~dIAeklGvspntiksWKrr 42 (279)
T COG5484 9 RIIAKKDYLKGM---KLKDIAEKLGVSPNTIKSWKRR 42 (279)
T ss_pred HHHHHHHHHhhc---cHHHHHHHhCCChHHHHHHHHh
Confidence 667788888874 5677899999999999999964
No 229
>CHL00033 ycf3 photosystem I assembly protein Ycf3
Probab=37.99 E-value=2.2e+02 Score=25.36 Aligned_cols=71 Identities=15% Similarity=0.060 Sum_probs=48.1
Q ss_pred HHHHHHHHHHHHHhcCChhhHHHHHHHHHhhccccchh----HHHHHHHHHHHHhhcCHHHHHHHHHHHHHHhcC
Q 013640 127 QIEALYQYAKFQFECGNYSGAADYLYQYRALCTNSERR----LSALWGKMAAEILMQNWDIALEELNQLKEKVDD 197 (439)
Q Consensus 127 ~~~al~~~ak~~y~~Gdy~~A~~~L~~~~~~~~~~~~k----~~~lwg~la~eIl~~~w~~a~~~l~klke~id~ 197 (439)
...+++.+|..+...|+++.|.+++......-+..... ..+++..=+..+..++++.|.....+..+.+.+
T Consensus 71 ~~~~~~~lg~~~~~~g~~~eA~~~~~~Al~~~~~~~~~~~~la~i~~~~~~~~~~~g~~~~A~~~~~~a~~~~~~ 145 (168)
T CHL00033 71 RSYILYNIGLIHTSNGEHTKALEYYFQALERNPFLPQALNNMAVICHYRGEQAIEQGDSEIAEAWFDQAAEYWKQ 145 (168)
T ss_pred hHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCcCcHHHHHHHHHHHHHhhHHHHHcccHHHHHHHHHHHHHHHHH
Confidence 44588999999999999999999998887764432211 111111111223567888888888877777665
No 230
>PF14276 DUF4363: Domain of unknown function (DUF4363)
Probab=37.63 E-value=2.4e+02 Score=24.25 Aligned_cols=73 Identities=16% Similarity=0.185 Sum_probs=55.1
Q ss_pred hhHHHHHHHHHHHHHhcCChhhHHHHHHHHHhhccccc------------hhHHHHHHHHHHHHhhcCHHHHHHHHHHHH
Q 013640 125 PDQIEALYQYAKFQFECGNYSGAADYLYQYRALCTNSE------------RRLSALWGKMAAEILMQNWDIALEELNQLK 192 (439)
Q Consensus 125 ~e~~~al~~~ak~~y~~Gdy~~A~~~L~~~~~~~~~~~------------~k~~~lwg~la~eIl~~~w~~a~~~l~klk 192 (439)
.+.+.....-+.-..+.+||++|.+.+..+........ -.++.-..++..-|..+|-+.++.++..+|
T Consensus 25 ~~~i~~~l~~i~~~i~~~dW~~A~~~~~~l~~~W~k~~~~~~~~~~h~eid~i~~sl~rl~~~i~~~dk~~~l~el~~lk 104 (121)
T PF14276_consen 25 TDSIEEQLEQIEEAIENEDWEKAYKETEELEKEWDKNKKRWSILIEHQEIDNIDISLARLKGYIEAKDKSESLAELAELK 104 (121)
T ss_pred HHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHhhchheeeeecHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHH
Confidence 45566777778888889999999998877766543211 137777888888888888888888888888
Q ss_pred HHhcC
Q 013640 193 EKVDD 197 (439)
Q Consensus 193 e~id~ 197 (439)
.+++.
T Consensus 105 ~~i~~ 109 (121)
T PF14276_consen 105 ELIEH 109 (121)
T ss_pred HHHHH
Confidence 88764
No 231
>KOG0550 consensus Molecular chaperone (DnaJ superfamily) [Posttranslational modification, protein turnover, chaperones]
Probab=37.48 E-value=1.9e+02 Score=31.31 Aligned_cols=60 Identities=12% Similarity=0.131 Sum_probs=49.8
Q ss_pred HHhcCCChhHHHHHHHHHHHHHhcCChhhHHHHHHHHHhhccccchhHHHHHHHHHHHHhhc
Q 013640 118 HDRYQIGPDQIEALYQYAKFQFECGNYSGAADYLYQYRALCTNSERRLSALWGKMAAEILMQ 179 (439)
Q Consensus 118 ~~~~g~t~e~~~al~~~ak~~y~~Gdy~~A~~~L~~~~~~~~~~~~k~~~lwg~la~eIl~~ 179 (439)
.+-..|++..+.+++..|+.+..-|+|+.|.+.+..+..+..+ .-.-..|+....++...
T Consensus 311 ~~Al~iD~syikall~ra~c~l~le~~e~AV~d~~~a~q~~~s--~e~r~~l~~A~~aLkkS 370 (486)
T KOG0550|consen 311 NEALKIDSSYIKALLRRANCHLALEKWEEAVEDYEKAMQLEKD--CEIRRTLREAQLALKKS 370 (486)
T ss_pred hhhhhcCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhccc--cchHHHHHHHHHHHHHh
Confidence 3456689999999999999999999999999999999887655 44667788887777754
No 232
>PRK10046 dpiA two-component response regulator DpiA; Provisional
Probab=37.32 E-value=66 Score=30.22 Aligned_cols=48 Identities=13% Similarity=0.111 Sum_probs=40.4
Q ss_pred HHHHHhhhhhccccHHHHHHHcCCCHHHHHHHHHHHhhcCccceeecc
Q 013640 346 FIFETYCRIHQRIDMAVLAEKLNLNYEEAQRWIVNLIRNSKLDAKIDA 393 (439)
Q Consensus 346 ~ife~ycriy~~I~I~~lA~~l~~s~~~~E~wiv~lI~~~rL~aKID~ 393 (439)
.|..-+.+-+...+.+.+|++||+|+.=+++-+..+-++|-+...|+.
T Consensus 166 ~Vl~~~~~g~~g~s~~eIa~~l~iS~~Tv~~~~~~~~~~~~~~~~~~~ 213 (225)
T PRK10046 166 AVRKLFKEPGVQHTAETVAQALTISRTTARRYLEYCASRHLIIAEIVH 213 (225)
T ss_pred HHHHHHHcCCCCcCHHHHHHHhCccHHHHHHHHHHHHhCCeEEEEeec
Confidence 455555555556789999999999999999999999999999887776
No 233
>KOG3252 consensus Uncharacterized conserved protein [Function unknown]
Probab=37.27 E-value=86 Score=30.14 Aligned_cols=86 Identities=19% Similarity=0.256 Sum_probs=64.2
Q ss_pred hhhcCChhHHHHHHHHHHHHhcCCcccccccccccccccccHHHHHHHHHHHHHHHhhhhhccccHHHHHHHcC-CCHHH
Q 013640 295 VYVNYDFDGAQKKMKECEEVILNDPFLGKRVEDSNFATVPLRDEFLENARLFIFETYCRIHQRIDMAVLAEKLN-LNYEE 373 (439)
Q Consensus 295 lY~~fdF~~aq~~L~~~e~~i~~D~FL~~~~~~~~~~~~~~~~~f~e~aR~~ife~ycriy~~I~I~~lA~~l~-~s~~~ 373 (439)
....++|..|=+.+.+....++ +.-=|-.+.|..+.-..--.|+.|+=..||+.+| .|-.+
T Consensus 107 ~LEt~~Fq~FW~~~~~N~~mle------------------~itGFedsvr~yachvv~iTyQkI~k~lLaellG~~sDs~ 168 (217)
T KOG3252|consen 107 YLETCRFQQFWQEADENRDMLE------------------GITGFEDSVRKYACHVVGITYQKIDKWLLAELLGGLSDSQ 168 (217)
T ss_pred HHhhchHHHHhhhhccchHHhc------------------CCCcHHHHHHHHHHHheechHhhchHHHHHHhhCcccHHH
Confidence 3456788777766666544333 4445788889888888888899999999999999 55559
Q ss_pred HHHHHHHHhhcCccceeecccCCEEEeCCCCc
Q 013640 374 AQRWIVNLIRNSKLDAKIDAKSGTVIMEPTHP 405 (439)
Q Consensus 374 ~E~wiv~lI~~~rL~aKID~~~g~V~~~~~~~ 405 (439)
+|.|+.+. +=|-.++|.|..-.+.-
T Consensus 169 le~~~~~~-------GW~a~e~G~ifv~~qE~ 193 (217)
T KOG3252|consen 169 LEVWMTKY-------GWIADESGQIFVASQEE 193 (217)
T ss_pred HHHHHHHc-------cceecCCceEEEecccc
Confidence 99999884 55666888887766553
No 234
>KOG4234 consensus TPR repeat-containing protein [General function prediction only]
Probab=37.23 E-value=1.4e+02 Score=29.39 Aligned_cols=66 Identities=23% Similarity=0.389 Sum_probs=47.9
Q ss_pred HHHHHHHHHHHHhcCChhhHHHHHHHHHhhccccchh-HHHHHH-HHHHHHhhcCHHHHHHHHHHHHH
Q 013640 128 IEALYQYAKFQFECGNYSGAADYLYQYRALCTNSERR-LSALWG-KMAAEILMQNWDIALEELNQLKE 193 (439)
Q Consensus 128 ~~al~~~ak~~y~~Gdy~~A~~~L~~~~~~~~~~~~k-~~~lwg-~la~eIl~~~w~~a~~~l~klke 193 (439)
.+.+-+=|+=+|.-|+|+.|.+-+......|++...+ -++|++ .-||-|-..-|+.|.++-.|.=+
T Consensus 95 ad~lK~EGN~~F~ngdyeeA~skY~~Ale~cp~~~~e~rsIly~Nraaa~iKl~k~e~aI~dcsKaie 162 (271)
T KOG4234|consen 95 ADSLKKEGNELFKNGDYEEANSKYQEALESCPSTSTEERSILYSNRAAALIKLRKWESAIEDCSKAIE 162 (271)
T ss_pred HHHHHHHHHHhhhcccHHHHHHHHHHHHHhCccccHHHHHHHHhhhHHHHHHhhhHHHHHHHHHhhHh
Confidence 4456666888999999999999999999999885443 444444 44445556678888887766533
No 235
>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=36.93 E-value=99 Score=29.46 Aligned_cols=65 Identities=14% Similarity=0.024 Sum_probs=57.0
Q ss_pred cHHHHHHHHHHHHHHHhhhhhccc-cHHHHHHHcCCCHHHHHHHHHHHhhcCccceeecccCCEEEeC
Q 013640 335 LRDEFLENARLFIFETYCRIHQRI-DMAVLAEKLNLNYEEAQRWIVNLIRNSKLDAKIDAKSGTVIME 401 (439)
Q Consensus 335 ~~~~f~e~aR~~ife~ycriy~~I-~I~~lA~~l~~s~~~~E~wiv~lI~~~rL~aKID~~~g~V~~~ 401 (439)
-.+...+..|-.|..--++|=.++ +-..||+.||||..=+-.-|..|-..|=+. +-.-.|+++..
T Consensus 7 ~~~~v~~~l~~~I~~g~l~pG~~LpsE~~La~~lgVSRtpVREAL~~Le~eGlV~--~~~~~G~~V~~ 72 (235)
T TIGR02812 7 PAGFAEEYIVESIWNNRFPPGSILPAERELSELIGVTRTTLREVLQRLARDGWLT--IQHGKPTKVNN 72 (235)
T ss_pred hHHHHHHHHHHHHHcCCCCCCCcCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCEE--EeCCCccEecC
Confidence 346677889999999999999999 899999999999999999999999999884 55677888866
No 236
>PRK09464 pdhR transcriptional regulator PdhR; Reviewed
Probab=36.84 E-value=1.4e+02 Score=28.67 Aligned_cols=67 Identities=18% Similarity=0.222 Sum_probs=58.6
Q ss_pred ccHHHHHHHHHHHHHHHhhhhhccc-cHHHHHHHcCCCHHHHHHHHHHHhhcCccceeecccCCEEEeCC
Q 013640 334 PLRDEFLENARLFIFETYCRIHQRI-DMAVLAEKLNLNYEEAQRWIVNLIRNSKLDAKIDAKSGTVIMEP 402 (439)
Q Consensus 334 ~~~~~f~e~aR~~ife~ycriy~~I-~I~~lA~~l~~s~~~~E~wiv~lI~~~rL~aKID~~~g~V~~~~ 402 (439)
...+...+..|-.|...-++|=.++ +-..||+.||||..=+-.-|..|-..|=+..+ +-.|+.+...
T Consensus 10 ~~~~~v~~~l~~~I~~g~l~pG~~LpsE~eLa~~lgVSRtpVREAL~~L~~eGlv~~~--~~~G~~V~~~ 77 (254)
T PRK09464 10 KLSDVIEQQLEFLILEGTLRPGEKLPPERELAKQFDVSRPSLREAIQRLEAKGLLLRR--QGGGTFVQSS 77 (254)
T ss_pred cHHHHHHHHHHHHHHcCCCCCCCcCCCHHHHHHHhCCCHHHHHHHHHHHHHCCCEEEe--cCceeEEecC
Confidence 3457889999999999999999999 89999999999999999999999999988543 5678887663
No 237
>PF04049 APC8: Anaphase promoting complex subunit 8 / Cdc23 ; InterPro: IPR007192 The anaphase-promoting complex is composed of eight protein subunits, including BimE (APC1), CDC27 (APC3), CDC16 (APC6), and CDC23 (APC8). This entry is for CDC23.; GO: 0030071 regulation of mitotic metaphase/anaphase transition, 0005680 anaphase-promoting complex
Probab=36.43 E-value=98 Score=27.95 Aligned_cols=27 Identities=33% Similarity=0.490 Sum_probs=22.8
Q ss_pred HHHHHHHHHHHhcCChhhHHHHHHHHH
Q 013640 129 EALYQYAKFQFECGNYSGAADYLYQYR 155 (439)
Q Consensus 129 ~al~~~ak~~y~~Gdy~~A~~~L~~~~ 155 (439)
...|-+|+-||+|++|..|+-+|..+.
T Consensus 75 ~d~yllAksyFD~kEy~RaA~~L~~~~ 101 (142)
T PF04049_consen 75 YDKYLLAKSYFDCKEYDRAAHVLKDCK 101 (142)
T ss_pred HHHHHHHHHHhchhHHHHHHHHHccCC
Confidence 367889999999999999998776533
No 238
>PLN03083 E3 UFM1-protein ligase 1 homolog; Provisional
Probab=36.31 E-value=1.4e+02 Score=34.70 Aligned_cols=102 Identities=15% Similarity=0.225 Sum_probs=64.9
Q ss_pred CcchHHHHHHHhhhcCChhHHHHHHHHHHHHhcCCcccccccccccccccccHHHHHHHHHHHHHHHhhhhhccccHHHH
Q 013640 284 YKDPITEFLACVYVNYDFDGAQKKMKECEEVILNDPFLGKRVEDSNFATVPLRDEFLENARLFIFETYCRIHQRIDMAVL 363 (439)
Q Consensus 284 Y~Dpit~f~~~lY~~fdF~~aq~~L~~~e~~i~~D~FL~~~~~~~~~~~~~~~~~f~e~aR~~ife~ycriy~~I~I~~l 363 (439)
-+-+++++=..|=|++ ...+ +.++.++.+|+=+. ...|.-++ +.|+.+...-|=+...+ -..|+|..+
T Consensus 73 GRvnlvdLa~~LnVD~--~hiE---r~~~~iv~~d~~~~--l~~GeLit----~~Yld~iaeEIne~LqE-~G~isI~eL 140 (803)
T PLN03083 73 GRVSLVDLADTIGVDL--YHVE---RQAQQVVSDDPGLM--LVQGEIIS----QSYWDSIAEEINERLQE-CSQIALAEL 140 (803)
T ss_pred CCeeHHHHhhhcCCCH--HHHH---HHHHHHhcCCCceE--EecCEecc----hHHHHHHHHHHHHHHHH-cCcChHHHH
Confidence 4567777776655544 3333 44556667775541 22333333 34555555555555544 488999999
Q ss_pred HHHcCCCHHHHHHHHHHHhhcCccceeecccCCEEEe
Q 013640 364 AEKLNLNYEEAQRWIVNLIRNSKLDAKIDAKSGTVIM 400 (439)
Q Consensus 364 A~~l~~s~~~~E~wiv~lI~~~rL~aKID~~~g~V~~ 400 (439)
|++++++.+++-..|..- ..+.++|++ ..|++.+
T Consensus 141 a~~~~Lpsefl~~~l~~r-lG~iI~g~~--~g~~lyT 174 (803)
T PLN03083 141 ARQLQVGSELVTSMLEPR-LGTIVKARL--EGGQLYT 174 (803)
T ss_pred HHhcCChHHHHHHHHHHH-hccceEEEe--cCCEEec
Confidence 999999999999888754 456778887 3566654
No 239
>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=35.52 E-value=2.1e+02 Score=24.21 Aligned_cols=43 Identities=9% Similarity=0.084 Sum_probs=36.7
Q ss_pred hhccccHHHHHHHcCCCHHHHHHHHHHHhhcCccceeecccCC
Q 013640 354 IHQRIDMAVLAEKLNLNYEEAQRWIVNLIRNSKLDAKIDAKSG 396 (439)
Q Consensus 354 iy~~I~I~~lA~~l~~s~~~~E~wiv~lI~~~rL~aKID~~~g 396 (439)
-+..+++..||+.+|++..-+=+-|-+|...|=+...-|...+
T Consensus 39 ~~~~~t~~ela~~~~~~~~tvs~~l~~Le~~GlI~r~~~~~D~ 81 (118)
T TIGR02337 39 EQGSMEFTQLANQACILRPSLTGILARLERDGLVTRLKASNDQ 81 (118)
T ss_pred HcCCcCHHHHHHHhCCCchhHHHHHHHHHHCCCEEeccCCCCC
Confidence 3678999999999999999999999999999887766655544
No 240
>KOG0624 consensus dsRNA-activated protein kinase inhibitor P58, contains TPR and DnaJ domains [Defense mechanisms]
Probab=35.36 E-value=3.7e+02 Score=28.63 Aligned_cols=46 Identities=13% Similarity=0.259 Sum_probs=36.7
Q ss_pred HHHHhcCCChhHHHHHHHHHHHHHhcCChhhHHHHHHHHHhhcccc
Q 013640 116 MLHDRYQIGPDQIEALYQYAKFQFECGNYSGAADYLYQYRALCTNS 161 (439)
Q Consensus 116 ~l~~~~g~t~e~~~al~~~ak~~y~~Gdy~~A~~~L~~~~~~~~~~ 161 (439)
.|..--.++.+.-+.+|+.++++|..||-+.++..+..|..+-++.
T Consensus 211 Dlk~askLs~DnTe~~ykis~L~Y~vgd~~~sL~~iRECLKldpdH 256 (504)
T KOG0624|consen 211 DLKQASKLSQDNTEGHYKISQLLYTVGDAENSLKEIRECLKLDPDH 256 (504)
T ss_pred HHHHHHhccccchHHHHHHHHHHHhhhhHHHHHHHHHHHHccCcch
Confidence 3333334566677899999999999999999999999998876653
No 241
>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=34.78 E-value=44 Score=22.92 Aligned_cols=28 Identities=29% Similarity=0.404 Sum_probs=22.4
Q ss_pred cHHHHHHHcCCCHHHHHHHHHHHhhcCcccee
Q 013640 359 DMAVLAEKLNLNYEEAQRWIVNLIRNSKLDAK 390 (439)
Q Consensus 359 ~I~~lA~~l~~s~~~~E~wiv~lI~~~rL~aK 390 (439)
++..+|+.||+|+.-+-+|+. .|.+.++
T Consensus 2 s~~e~a~~lgvs~~tl~~~~~----~g~~~~~ 29 (49)
T cd04762 2 TTKEAAELLGVSPSTLRRWVK----EGKLKAI 29 (49)
T ss_pred CHHHHHHHHCcCHHHHHHHHH----cCCCCce
Confidence 678999999999998888865 4666553
No 242
>COG4367 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=34.26 E-value=41 Score=28.40 Aligned_cols=23 Identities=13% Similarity=0.121 Sum_probs=20.6
Q ss_pred ccccHHHHHHHcCCCHHHHHHHH
Q 013640 356 QRIDMAVLAEKLNLNYEEAQRWI 378 (439)
Q Consensus 356 ~~I~I~~lA~~l~~s~~~~E~wi 378 (439)
..+++.++|++||+|+..+|+-+
T Consensus 22 ~~LS~~~iA~~Ln~t~~~lekil 44 (97)
T COG4367 22 CPLSDEEIATALNWTEVKLEKIL 44 (97)
T ss_pred ccccHHHHHHHhCCCHHHHHHHH
Confidence 46899999999999999999876
No 243
>PF13551 HTH_29: Winged helix-turn helix
Probab=34.15 E-value=65 Score=26.48 Aligned_cols=31 Identities=16% Similarity=0.414 Sum_probs=27.0
Q ss_pred hccc-cHHHHHHHcCCCHHHHHHHHHHHhhcC
Q 013640 355 HQRI-DMAVLAEKLNLNYEEAQRWIVNLIRNS 385 (439)
Q Consensus 355 y~~I-~I~~lA~~l~~s~~~~E~wiv~lI~~~ 385 (439)
.... ++..+|+.+|+|+.-+-+|+-++=..|
T Consensus 9 ~~g~~~~~~ia~~lg~s~~Tv~r~~~~~~~~G 40 (112)
T PF13551_consen 9 AEGVSTIAEIARRLGISRRTVYRWLKRYREGG 40 (112)
T ss_pred HcCCCcHHHHHHHHCcCHHHHHHHHHHHHccc
Confidence 3455 599999999999999999999987666
No 244
>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=33.94 E-value=1.1e+02 Score=27.21 Aligned_cols=44 Identities=18% Similarity=0.312 Sum_probs=32.1
Q ss_pred HHHHHHHHhcCChhhHHHHHHHHHhhccccchhHHHHHHHHHHH
Q 013640 132 YQYAKFQFECGNYSGAADYLYQYRALCTNSERRLSALWGKMAAE 175 (439)
Q Consensus 132 ~~~ak~~y~~Gdy~~A~~~L~~~~~~~~~~~~k~~~lwg~la~e 175 (439)
.++|.-+...|++++|...++.....|+.+..-+..+=..+--+
T Consensus 67 V~lGE~L~~~G~~~~aa~hf~nAl~V~~qP~~LL~i~q~tlP~~ 110 (121)
T PF02064_consen 67 VQLGEQLLAQGDYEEAAEHFYNALKVCPQPAELLQIYQKTLPPP 110 (121)
T ss_dssp HHHHHHHHHTT-HHHHHHHHHHHHHTSSSHHHHHHHHHHHS-HH
T ss_pred HHHHHHHHhCCCHHHHHHHHHHHHHhCCCHHHHHHHHHhhCCHH
Confidence 67788888899999999999999999988765555444333333
No 245
>PF04539 Sigma70_r3: Sigma-70 region 3; InterPro: IPR007624 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 3 forms a discrete compact three helical domain within the sigma-factor. Region is not normally involved in the recognition of promoter DNA, but in some specific bacterial promoters containing an extended -10 promoter element, residues within region 3 play an important role. Region 3 primarily is involved in binding the core RNA polymerase in the holoenzyme [].; 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: 1L0O_C 1KU2_B 1RP3_C 1SC5_A 1TTY_A 2BE5_F 2A6E_F 2CW0_F 2A69_P 2A6H_P ....
Probab=33.85 E-value=92 Score=24.32 Aligned_cols=37 Identities=22% Similarity=0.267 Sum_probs=25.2
Q ss_pred ccccHHHHHHHcCCCHHHHHHHHHHHhhcCccceeec
Q 013640 356 QRIDMAVLAEKLNLNYEEAQRWIVNLIRNSKLDAKID 392 (439)
Q Consensus 356 ~~I~I~~lA~~l~~s~~~~E~wiv~lI~~~rL~aKID 392 (439)
..-+...||+.+|||.+++...+.-.-+-.-|++.+.
T Consensus 19 r~Pt~eEiA~~lgis~~~v~~~l~~~~~~~Sl~~~~~ 55 (78)
T PF04539_consen 19 REPTDEEIAEELGISVEEVRELLQASRRPVSLDLPVG 55 (78)
T ss_dssp S--BHHHHHHHHTS-HHHHHHHHHHHSCCEESSHCCS
T ss_pred CCCCHHHHHHHHcccHHHHHHHHHhCCCCeEEeeeec
Confidence 3578999999999999999988875443334555443
No 246
>PRK14999 histidine utilization repressor; Provisional
Probab=33.82 E-value=2.2e+02 Score=27.24 Aligned_cols=69 Identities=20% Similarity=0.209 Sum_probs=57.9
Q ss_pred cccHHHHHHHHHHHHHHHhhhhhccc-cHHHHHHHcCCCHHHHHHHHHHHhhcCccceeecccCCEEEeCCC
Q 013640 333 VPLRDEFLENARLFIFETYCRIHQRI-DMAVLAEKLNLNYEEAQRWIVNLIRNSKLDAKIDAKSGTVIMEPT 403 (439)
Q Consensus 333 ~~~~~~f~e~aR~~ife~ycriy~~I-~I~~lA~~l~~s~~~~E~wiv~lI~~~rL~aKID~~~g~V~~~~~ 403 (439)
.+....+-+..|..|-.--..+-..+ +-..||+.||||..=+-+-|..|..+|.|.-+ +-.|+.+....
T Consensus 11 ~ply~qi~~~i~~~I~~g~~~~G~~LPsE~eLa~~~gVSR~TVR~Al~~L~~eGli~r~--~GkGTfV~~~~ 80 (241)
T PRK14999 11 APFYETVKQDICKKIAGGVWQPHDRIPSEAELVAQYGFSRMTINRALRELTDEGWLVRL--QGVGTFVAEPK 80 (241)
T ss_pred CcHHHHHHHHHHHHHHcCCCCCCCcCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEe--cCcEEEECCCC
Confidence 35667777888888888777888889 89999999999999999999999999988544 45799987544
No 247
>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=33.69 E-value=88 Score=25.35 Aligned_cols=33 Identities=18% Similarity=0.246 Sum_probs=26.7
Q ss_pred hhHHHHHHHHHHHHHhcCChhhHHHHHHHHHhh
Q 013640 125 PDQIEALYQYAKFQFECGNYSGAADYLYQYRAL 157 (439)
Q Consensus 125 ~e~~~al~~~ak~~y~~Gdy~~A~~~L~~~~~~ 157 (439)
.++..+.++=|++|++.||+.+|...+.....+
T Consensus 32 ~~mA~~Y~~D~~~fl~~gD~v~Ala~~sYa~Gw 64 (75)
T PF04010_consen 32 LEMAESYLEDGKYFLEKGDYVNALACFSYAHGW 64 (75)
T ss_dssp HHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHH
Confidence 467789999999999999999999887665544
No 248
>COG1497 Predicted transcriptional regulator [Transcription]
Probab=33.05 E-value=87 Score=31.25 Aligned_cols=67 Identities=18% Similarity=0.283 Sum_probs=47.7
Q ss_pred HHHHHHHHhhhhhccccHHHHHHHcCCCHHHHHHHHHHHhhcCccceeecccCC-EEEeCCCC-chhHHHHHH
Q 013640 343 ARLFIFETYCRIHQRIDMAVLAEKLNLNYEEAQRWIVNLIRNSKLDAKIDAKSG-TVIMEPTH-PNVYEQLID 413 (439)
Q Consensus 343 aR~~ife~ycriy~~I~I~~lA~~l~~s~~~~E~wiv~lI~~~rL~aKID~~~g-~V~~~~~~-~~~yqqvi~ 413 (439)
.|.+|..-...=|+.+.-+.+|+++|+|+..+-..|-+|+.+|-++ +.++ .-+.++.- .-+|.|+.+
T Consensus 11 t~fqIL~ei~~~qp~v~q~eIA~~lgiT~QaVsehiK~Lv~eG~i~----~~gR~~Y~iTkkG~e~l~~~~~d 79 (260)
T COG1497 11 TRFQILSEIAVRQPRVKQKEIAKKLGITLQAVSEHIKELVKEGLIE----KEGRGEYEITKKGAEWLLEQLSD 79 (260)
T ss_pred hHHHHHHHHHHhCCCCCHHHHHHHcCCCHHHHHHHHHHHHhcccee----ecCCeeEEEehhHHHHHHHHHHH
Confidence 4556666666667999999999999999999999999999988654 3222 33333322 345555554
No 249
>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=32.93 E-value=3.3e+02 Score=23.95 Aligned_cols=65 Identities=15% Similarity=0.108 Sum_probs=55.3
Q ss_pred HHHHHHHHHHHHhcCChhhHHHHHHHHHhhcccc-chhHHHHHHHHHHHHhhcCHHHHHHHHHHHH
Q 013640 128 IEALYQYAKFQFECGNYSGAADYLYQYRALCTNS-ERRLSALWGKMAAEILMQNWDIALEELNQLK 192 (439)
Q Consensus 128 ~~al~~~ak~~y~~Gdy~~A~~~L~~~~~~~~~~-~~k~~~lwg~la~eIl~~~w~~a~~~l~klk 192 (439)
.+.-+..|+-.+..||+..|-..|...+.+++.. ..-.-.-|--|+..+-..||.++.-++-+|-
T Consensus 9 ~~~el~~a~~a~~~~~~~~aw~hLErAHIlgQ~~~~~H~~~H~~ML~~a~r~rd~rEv~GQ~~Rl~ 74 (112)
T PF12487_consen 9 YDAELEAAREALAAGDLQQAWRHLERAHILGQPYPWLHTRVHWAMLRFALRQRDRREVLGQLLRLI 74 (112)
T ss_pred HHHHHHHHHHHHHcCCHHHHHHHHHhhHHhcCCchhHHHHHHHHHHHHHHHccCHHHHHHHHHHHH
Confidence 3455777888899999999999999999998764 5568889999999999999988888876663
No 250
>COG2378 Predicted transcriptional regulator [Transcription]
Probab=32.93 E-value=77 Score=32.30 Aligned_cols=60 Identities=18% Similarity=0.240 Sum_probs=49.6
Q ss_pred HHHHHHHHHHHHhhhhhccccHHHHHHHcCCCHHHHHHHHHHHhhcCccceeecccCC----EEEeC
Q 013640 339 FLENARLFIFETYCRIHQRIDMAVLAEKLNLNYEEAQRWIVNLIRNSKLDAKIDAKSG----TVIME 401 (439)
Q Consensus 339 f~e~aR~~ife~ycriy~~I~I~~lA~~l~~s~~~~E~wiv~lI~~~rL~aKID~~~g----~V~~~ 401 (439)
-.+.-|++-.-+|++-+++++...||+.||||.--+.+.|..|=..| ..|+...| .+.+.
T Consensus 4 ~~ka~RL~~ii~~L~~~~~vta~~lA~~~~VS~RTi~RDi~~L~~~g---vPI~~e~G~~~gy~~~~ 67 (311)
T COG2378 4 MRKAERLLQIIQILRAKETVTAAELADEFEVSVRTIYRDIATLRAAG---VPIEGERGKGGGYRLRP 67 (311)
T ss_pred hhHHHHHHHHHHHHHhCccchHHHHHHhcCCCHHHHHHHHHHHHHCC---CCeEeecCCCccEEEcc
Confidence 35678999999999999999999999999999999999999874443 34777777 55544
No 251
>PRK05472 redox-sensing transcriptional repressor Rex; Provisional
Probab=32.63 E-value=91 Score=29.59 Aligned_cols=43 Identities=12% Similarity=0.139 Sum_probs=37.2
Q ss_pred HHHHHHHHHHHHhhhhhc--cccHHHHHHHcCCCHHHHHHHHHHH
Q 013640 339 FLENARLFIFETYCRIHQ--RIDMAVLAEKLNLNYEEAQRWIVNL 381 (439)
Q Consensus 339 f~e~aR~~ife~ycriy~--~I~I~~lA~~l~~s~~~~E~wiv~l 381 (439)
..|.-|..-+-.++.-.. .|+.+.||+.+|+|+.-+.+.|.-+
T Consensus 12 ~~r~~~~~~il~~l~~~~~~~vs~~~L~~~~~v~~~tirrDl~~l 56 (213)
T PRK05472 12 IKRLPLYYRYLKELKEEGVERVSSKELAEALGVDSAQIRKDLSYF 56 (213)
T ss_pred HHHhHHHHHHHHHHHHcCCcEEeHHHHHHHhCcCHHHHHHHHHHH
Confidence 346778888888888898 9999999999999999998888766
No 252
>PF00440 TetR_N: Bacterial regulatory proteins, tetR family; InterPro: IPR001647 This entry represents a DNA-binding domain with a helix-turn-helix (HTH) structure that is found in several bacterial and archaeal transcriptional regulators, such as TetR, the tetracycline resistance repressor. Numerous other transcriptional regulatory proteins also contain HTH-type DNA-binding domains, and can be grouped into subfamiles based on sequence similarity. The domain represented by this entry is found in a subfamily of proteins that includes the transcriptional regulators TetR, TetC, AcrR, BetI, Bm3R1, EnvR, QacR, MtrR, TcmR, Ttk, YbiH, and YhgD [, , ]. Many of these proteins function as repressors that control the level of susceptibility to hydrophobic antibiotics and detergents. They all have similar molecular weights, ranging from 21 to 25 kDa. The helix-turn-helix motif is located in the initial third of the protein. The 3D structure of the homodimeric TetR protein complexed with 7-chloro-tetracycline-magnesium has been determined to 2.1 A resolution []. TetR folds into ten alpha-helices with connecting turns and loops. The three N-terminal alpha-helices of the repressor form the DNA-binding domain: this structural motif encompasses an HTH fold with an inverse orientation compared with that of other DNA-binding proteins.; GO: 0003677 DNA binding; PDB: 3NPI_B 3IUV_A 3CCY_A 2JK3_A 2FX0_A 2JJ7_A 2WV1_B 3BTI_D 3BR6_E 3BR5_A ....
Probab=32.59 E-value=99 Score=22.03 Aligned_cols=32 Identities=16% Similarity=0.147 Sum_probs=24.1
Q ss_pred HHHHHHHHHHHhhhhhccccHHHHHHHcCCCHHHH
Q 013640 340 LENARLFIFETYCRIHQRIDMAVLAEKLNLNYEEA 374 (439)
Q Consensus 340 ~e~aR~~ife~ycriy~~I~I~~lA~~l~~s~~~~ 374 (439)
++.+..++.+ +.|..+++..+|++.|+|..-+
T Consensus 2 l~aa~~l~~~---~G~~~~s~~~Ia~~~gvs~~~~ 33 (47)
T PF00440_consen 2 LEAALELFAE---KGYEAVSIRDIARRAGVSKGSF 33 (47)
T ss_dssp HHHHHHHHHH---HHTTTSSHHHHHHHHTSCHHHH
T ss_pred HHHHHHHHHH---hCHHhCCHHHHHHHHccchhhH
Confidence 3444444443 6899999999999999998754
No 253
>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=32.33 E-value=63 Score=23.07 Aligned_cols=25 Identities=36% Similarity=0.361 Sum_probs=19.1
Q ss_pred ccccHHHHHHHcCCCHHHHHHHHHH
Q 013640 356 QRIDMAVLAEKLNLNYEEAQRWIVN 380 (439)
Q Consensus 356 ~~I~I~~lA~~l~~s~~~~E~wiv~ 380 (439)
.+.+...||+.+|+|+..+-+=|-+
T Consensus 16 ~r~s~~~la~~lglS~~~v~~Ri~r 40 (42)
T PF13404_consen 16 GRRSYAELAEELGLSESTVRRRIRR 40 (42)
T ss_dssp TTS-HHHHHHHHTS-HHHHHHHHHH
T ss_pred CCccHHHHHHHHCcCHHHHHHHHHH
Confidence 7889999999999999987665544
No 254
>COG3355 Predicted transcriptional regulator [Transcription]
Probab=32.15 E-value=3.8e+02 Score=24.07 Aligned_cols=88 Identities=13% Similarity=0.207 Sum_probs=61.5
Q ss_pred HHHHHHHHhhhhhccccHHHHHHHcCCCHHHHHHHHHHHhhcCccc-eeec-ccCCEEEeCCCC--chhHHHHHHhhhhh
Q 013640 343 ARLFIFETYCRIHQRIDMAVLAEKLNLNYEEAQRWIVNLIRNSKLD-AKID-AKSGTVIMEPTH--PNVYEQLIDHTKGL 418 (439)
Q Consensus 343 aR~~ife~ycriy~~I~I~~lA~~l~~s~~~~E~wiv~lI~~~rL~-aKID-~~~g~V~~~~~~--~~~yqqvi~kt~~L 418 (439)
+=.-+|...+..+.-.+.+.||+.||.|..-|.+-+=||+..|=+. -|+- ...|-...-.|. ..+.+-+.+..+.+
T Consensus 28 ~Dv~v~~~LL~~~~~~tvdelae~lnr~rStv~rsl~~L~~~GlV~Rek~~~~~Ggy~yiY~~i~~ee~k~~i~~~l~~w 107 (126)
T COG3355 28 LDVEVYKALLEENGPLTVDELAEILNRSRSTVYRSLQNLLEAGLVEREKVNLKGGGYYYLYKPIDPEEIKKKILKDLDEW 107 (126)
T ss_pred HHHHHHHHHHhhcCCcCHHHHHHHHCccHHHHHHHHHHHHHcCCeeeeeeccCCCceeEEEecCCHHHHHHHHHHHHHHH
Confidence 3456778888899999999999999999999999999999999653 2322 233444444333 23555566666667
Q ss_pred hhHHHHHHHHHH
Q 013640 419 SGRTYKLVGQLL 430 (439)
Q Consensus 419 ~~R~q~L~~~i~ 430 (439)
..+..++.+...
T Consensus 108 ~~~~~~~i~~~~ 119 (126)
T COG3355 108 YDKMKQLIEEFE 119 (126)
T ss_pred HHHHHHHHHHHh
Confidence 666665554443
No 255
>KOG4747 consensus Two-component phosphorelay intermediate involved in MAP kinase cascade regulation [Signal transduction mechanisms]
Probab=31.94 E-value=3e+02 Score=25.40 Aligned_cols=114 Identities=20% Similarity=0.275 Sum_probs=63.1
Q ss_pred chHHHHHHHHhCCCCCChhHHHHHHHHHHHHHHHHHHHHHH-----HHH-hhCChhH-HHHhhh-----cchhccHHHHH
Q 013640 51 VDYAMDIHKSLYHTEDVPQDMVERRVEVVARLKALEERAAP-----IVS-FLQNPNS-FQDLRA-----NDQHYNLQMLH 118 (439)
Q Consensus 51 ~dy~~~~~~~l~~~~~~p~e~~~k~~ev~~~l~~l~~~~~~-----~~~-~~~~~e~-~~~l~~-----~dk~~n~~~l~ 118 (439)
.||-+.++.+...| +...+|+++++...| ++. +|++-+. ...++. +|-..--....
T Consensus 13 ~d~~~sl~~qgild------------~qF~qlq~lqD~~~p~fv~ev~~~fF~~s~~~i~~~r~ald~~~d~k~~~~~~h 80 (150)
T KOG4747|consen 13 SDYTKSLFDQGILD------------SQFLQLQELQDDSSPDFVEEVVGLFFEDSERLINNLRLALDCERDFKKLGSHVH 80 (150)
T ss_pred HHHHHHHHHHHhhH------------HHHHHHHHHhcccCccHHHHHHHHHHHHHHHHHHHHHHHHhhHhHHHHHHHHHH
Confidence 46666666554432 566677777777766 222 3333332 333332 22222223344
Q ss_pred HhcCCChhHHH-----HHHHHHHHHHhcCChhhHHHHHHHHHhhccccchhHHHHHHHHHHHHh
Q 013640 119 DRYQIGPDQIE-----ALYQYAKFQFECGNYSGAADYLYQYRALCTNSERRLSALWGKMAAEIL 177 (439)
Q Consensus 119 ~~~g~t~e~~~-----al~~~ak~~y~~Gdy~~A~~~L~~~~~~~~~~~~k~~~lwg~la~eIl 177 (439)
...| ..+.+. ....-.+-+++.||++.+...|.....--.-..++++.++-.-+.+|.
T Consensus 81 qlkg-ssssIGa~kvk~~c~~~~~~~~~~n~egcvr~l~~v~ie~~~lkkkL~~~f~L~rq~i~ 143 (150)
T KOG4747|consen 81 QLKG-SSSSIGALKVKKVCVGFNEFCEAGNIEGCVRCLQQVKIEYSLLKKKLETLFQLERQEIL 143 (150)
T ss_pred HccC-chhhhhHHHHHHHHHHHHHHHhhccchhHhhchHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 4556 444444 457788999999999998887766544333344566666664444443
No 256
>PRK14165 winged helix-turn-helix domain-containing protein/riboflavin kinase; Provisional
Probab=31.82 E-value=1.9e+02 Score=28.13 Aligned_cols=52 Identities=12% Similarity=0.119 Sum_probs=42.1
Q ss_pred hhhhhccccHHHHHHHcCCCHHHHHHHHHHHhhcCccceeecccCCEEEeCC
Q 013640 351 YCRIHQRIDMAVLAEKLNLNYEEAQRWIVNLIRNSKLDAKIDAKSGTVIMEP 402 (439)
Q Consensus 351 ycriy~~I~I~~lA~~l~~s~~~~E~wiv~lI~~~rL~aKID~~~g~V~~~~ 402 (439)
.+.=...|+...||+.+|+|..-+=+.|-+|-..|=+.-++|.....|.++.
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 3444556899999999999999999999999999999888877555555443
No 257
>KOG1126 consensus DNA-binding cell division cycle control protein [Cell cycle control, cell division, chromosome partitioning]
Probab=31.77 E-value=82 Score=35.37 Aligned_cols=77 Identities=26% Similarity=0.354 Sum_probs=56.8
Q ss_pred chhccHHHHHHhcCCChhHHHHHHHHHHHHHhcCChhhHHHHHHHHHhhccccchhHHHHHHHHHHHHhhcCHHHHHHHH
Q 013640 109 DQHYNLQMLHDRYQIGPDQIEALYQYAKFQFECGNYSGAADYLYQYRALCTNSERRLSALWGKMAAEILMQNWDIALEEL 188 (439)
Q Consensus 109 dk~~n~~~l~~~~g~t~e~~~al~~~ak~~y~~Gdy~~A~~~L~~~~~~~~~~~~k~~~lwg~la~eIl~~~w~~a~~~l 188 (439)
.+...+.++++..-+++-..-..|+.|++++..|+|++|...|.++.++++ ++...=++.|++=-..- +-+.|++..
T Consensus 538 ~~d~AL~~~~~A~~ld~kn~l~~~~~~~il~~~~~~~eal~~LEeLk~~vP-~es~v~~llgki~k~~~--~~~~Al~~f 614 (638)
T KOG1126|consen 538 RKDKALQLYEKAIHLDPKNPLCKYHRASILFSLGRYVEALQELEELKELVP-QESSVFALLGKIYKRLG--NTDLALLHF 614 (638)
T ss_pred hhhHHHHHHHHHHhcCCCCchhHHHHHHHHHhhcchHHHHHHHHHHHHhCc-chHHHHHHHHHHHHHHc--cchHHHHhh
Confidence 455667777777777776677889999999999999999999999999665 56666677777654433 333454443
No 258
>cd01020 TroA_b Metal binding protein TroA_b. These proteins are predicted to function as initial receptors in ABC transport of metal ions. They belong to the TroA superfamily of helical backbone metal receptor proteins that share a distinct fold and ligand binding mechanism. A typical TroA protein is comprised of two globular subdomains connected by a single helix and can bind the metal ion in the cleft between these domains. In addition, these proteins sometimes have a low complexity region containing a metal-binding histidine-rich motif (repetitive HDH sequence).
Probab=31.45 E-value=81 Score=31.01 Aligned_cols=74 Identities=16% Similarity=0.140 Sum_probs=49.3
Q ss_pred HccCCCchHHHHHHHHhC-CCCCChhHHHHHHHHHHHHHHHHHHHHHHHHHhhCChhHHHHhhhcchhccHHHHHHhcCC
Q 013640 45 LNKTNMVDYAMDIHKSLY-HTEDVPQDMVERRVEVVARLKALEERAAPIVSFLQNPNSFQDLRANDQHYNLQMLHDRYQI 123 (439)
Q Consensus 45 lk~TnM~dy~~~~~~~l~-~~~~~p~e~~~k~~ev~~~l~~l~~~~~~~~~~~~~~e~~~~l~~~dk~~n~~~l~~~~g~ 123 (439)
+.+.||.-++..|.+.|- .+.+-.+.+++.-++.+++|+.++++.+..+.-+.+..++. -...+.|+.+.||+
T Consensus 99 ldp~n~~~~a~~I~~~L~~~dP~~~~~y~~N~~~~~~~l~~l~~~~~~~~~~~~~~~~v~------~H~af~Y~~~~yGl 172 (264)
T cd01020 99 YDPETMSKVANALADALVKADPDNKKYYQANAKKFVASLKPLAAKIAELSAKYKGAPVAA------TEPVFDYLLDALGM 172 (264)
T ss_pred cCHhHHHHHHHHHHHHHHHhCcccHHHHHHHHHHHHHHHHHHHHHHHHHHhhCCCCeEEE------eCchHHHHHHHCCC
Confidence 345667777777777775 33344567888888999999999988866655443322221 12346788888887
Q ss_pred C
Q 013640 124 G 124 (439)
Q Consensus 124 t 124 (439)
.
T Consensus 173 ~ 173 (264)
T cd01020 173 K 173 (264)
T ss_pred c
Confidence 5
No 259
>PF05043 Mga: Mga helix-turn-helix domain; InterPro: IPR007737 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 []. The family also contains VirR like proteins which match only at the C terminus of the alignment.; PDB: 3SQN_A.
Probab=31.15 E-value=1.2e+02 Score=24.31 Aligned_cols=64 Identities=22% Similarity=0.248 Sum_probs=38.5
Q ss_pred HHHHHHHHHHHHHHhhhhhccccHHHHHHHcCCCHHHHHHHHHHH---hhcCccceeecccCCEEEeCCC
Q 013640 337 DEFLENARLFIFETYCRIHQRIDMAVLAEKLNLNYEEAQRWIVNL---IRNSKLDAKIDAKSGTVIMEPT 403 (439)
Q Consensus 337 ~~f~e~aR~~ife~ycriy~~I~I~~lA~~l~~s~~~~E~wiv~l---I~~~rL~aKID~~~g~V~~~~~ 403 (439)
.++.++-+...+-.++=-++.+++..+|+++++|..-+-+.|..+ ++ +-+.+| +..|....|..
T Consensus 10 ~~~~~~s~~~~ll~~ll~~~~~s~~~la~~~~iS~sti~~~i~~l~~~l~--~~~l~i-~~~~~~l~G~E 76 (87)
T PF05043_consen 10 QYYLEESLNYQLLKLLLNNEYVSIEDLAEELFISRSTIYRDIKKLNKYLK--KYGLKI-SKKGYRLEGDE 76 (87)
T ss_dssp HHHGGGSHHHHHHHHHHH-SEEEHHHHHHHHT--HHHHHHHHHHHHHHHH--CCT-EE--SSEEEEES-H
T ss_pred HHHHHhhHHHHHHHHHHcCCCcCHHHHHHHHCCCHHHHHHHHHHHHHHHH--HcCeEE-eCCCeEEEeCH
Confidence 344444444444444447899999999999999999887777533 33 456788 66777666643
No 260
>PRK15179 Vi polysaccharide biosynthesis protein TviE; Provisional
Probab=31.00 E-value=8.5e+02 Score=27.85 Aligned_cols=42 Identities=14% Similarity=0.048 Sum_probs=36.9
Q ss_pred HHHHHhcCCChhHHHHHHHHHHHHHhcCChhhHHHHHHHHHh
Q 013640 115 QMLHDRYQIGPDQIEALYQYAKFQFECGNYSGAADYLYQYRA 156 (439)
Q Consensus 115 ~~l~~~~g~t~e~~~al~~~ak~~y~~Gdy~~A~~~L~~~~~ 156 (439)
...++-+..+|+..++++.+|..+-+.|+|++|.+++..+..
T Consensus 141 ~~~~~~l~~~p~~~~~~~~~a~~l~~~g~~~~A~~~y~~~~~ 182 (694)
T PRK15179 141 AEIELYFSGGSSSAREILLEAKSWDEIGQSEQADACFERLSR 182 (694)
T ss_pred HHHHHHhhcCCCCHHHHHHHHHHHHHhcchHHHHHHHHHHHh
Confidence 444566677999999999999999999999999999998887
No 261
>PF13182 DUF4007: Protein of unknown function (DUF4007)
Probab=30.58 E-value=1e+02 Score=31.13 Aligned_cols=58 Identities=12% Similarity=0.082 Sum_probs=41.2
Q ss_pred hhhccccHHHHH-------HHcCCCHHHHHHHHHHHhhc-CccceeecccCC--EEEeCCCCchhHHHHHH
Q 013640 353 RIHQRIDMAVLA-------EKLNLNYEEAQRWIVNLIRN-SKLDAKIDAKSG--TVIMEPTHPNVYEQLID 413 (439)
Q Consensus 353 riy~~I~I~~lA-------~~l~~s~~~~E~wiv~lI~~-~rL~aKID~~~g--~V~~~~~~~~~yqqvi~ 413 (439)
.-..+|+++.|+ .-||++++.+..-|.++-.. |.+ ++.-.+| +|..... .-...++++
T Consensus 216 ~~~~sis~~~L~~~~~sPGriF~L~~~~l~~~L~~l~~~~g~i--~~~~TaGl~qv~~~~~-~~~~~~~L~ 283 (286)
T PF13182_consen 216 PGRNSISFDELLNEPGSPGRIFKLDEESLAERLEQLEEIYGFI--SWSDTAGLDQVYLKDE-ELDAWDVLK 283 (286)
T ss_pred CCCcEEEHHHHhcCCCCcceEeccCHHHHHHHHHHHHhhcCcE--EEEEcCCCeEEEeccc-cCCHHHHHH
Confidence 466889999985 68999999999999999888 666 5666777 4444432 333345554
No 262
>cd01145 TroA_c Periplasmic binding protein TroA_c. These proteins are predicted to function as initial receptors in the ABC metal ion uptake in eubacteria and archaea. They belong to the TroA superfamily of helical backbone metal receptor proteins that share a distinct fold and ligand binding mechanism. A typical TroA protein is comprised of two globular subdomains connected by a single helix and can bind their ligands in the cleft between these domains.
Probab=30.52 E-value=82 Score=29.68 Aligned_cols=74 Identities=19% Similarity=0.133 Sum_probs=47.6
Q ss_pred HccCCCchHHHHHHHHhC-CCCCChhHHHHHHHHHHHHHHHHHHHHHHHHHhhCChhHHHHhhhcchhccHHHHHHhcCC
Q 013640 45 LNKTNMVDYAMDIHKSLY-HTEDVPQDMVERRVEVVARLKALEERAAPIVSFLQNPNSFQDLRANDQHYNLQMLHDRYQI 123 (439)
Q Consensus 45 lk~TnM~dy~~~~~~~l~-~~~~~p~e~~~k~~ev~~~l~~l~~~~~~~~~~~~~~e~~~~l~~~dk~~n~~~l~~~~g~ 123 (439)
+...||.-++..|...|. .+.+-.+.+++.-++.+++|++|+++++..++-+.+..++ --...+.|+.+.||+
T Consensus 112 ldp~~~~~~a~~I~~~L~~~dP~~~~~y~~N~~~~~~~l~~l~~~~~~~l~~~~~~~~v------~~H~af~Y~~~~yGl 185 (203)
T cd01145 112 LDPNNAPALAKALADALIELDPSEQEEYKENLRVFLAKLNKLLREWERQFEGLKGIQVV------AYHPSYQYLADWLGI 185 (203)
T ss_pred cCHHHHHHHHHHHHHHHHHhCcccHHHHHHHHHHHHHHHHHHHHHHHHHhhccCCCeEE------EecccHHHHHHHcCC
Confidence 345566777777777775 2323456688888888999999988886555433221111 123456789999997
Q ss_pred C
Q 013640 124 G 124 (439)
Q Consensus 124 t 124 (439)
.
T Consensus 186 ~ 186 (203)
T cd01145 186 E 186 (203)
T ss_pred c
Confidence 5
No 263
>smart00342 HTH_ARAC helix_turn_helix, arabinose operon control protein.
Probab=30.25 E-value=1e+02 Score=23.31 Aligned_cols=41 Identities=15% Similarity=0.181 Sum_probs=31.4
Q ss_pred HHHHHHHHHHHHHHhhhhhccccHHHHHHHcCC-CHHHHHHHH
Q 013640 337 DEFLENARLFIFETYCRIHQRIDMAVLAEKLNL-NYEEAQRWI 378 (439)
Q Consensus 337 ~~f~e~aR~~ife~ycriy~~I~I~~lA~~l~~-s~~~~E~wi 378 (439)
..++...|+.-...|+.-+ .++++.+|..+|+ |+.-.-+..
T Consensus 31 ~~~~~~~r~~~a~~~l~~~-~~~~~~ia~~~g~~s~~~f~r~F 72 (84)
T smart00342 31 KQYLRDRRLERARRLLRDT-DLSVTEIALRVGFSSQSYFSRAF 72 (84)
T ss_pred HHHHHHHHHHHHHHHHHcC-CCCHHHHHHHhCCCChHHHHHHH
Confidence 4566777877777887766 8999999999999 876554433
No 264
>KOG2076 consensus RNA polymerase III transcription factor TFIIIC [Transcription]
Probab=30.22 E-value=9.7e+02 Score=28.27 Aligned_cols=116 Identities=20% Similarity=0.224 Sum_probs=77.1
Q ss_pred ccccchhhHHHHhhcC--CCCHHHHHHHHHHHHccCCCchHHHHHHHHhCCCCCCh-hHHHHHHHHHHHHHHHHHHHHHH
Q 013640 15 DRHLVFPLLEFLQERQ--MYPDEQILKSKIELLNKTNMVDYAMDIHKSLYHTEDVP-QDMVERRVEVVARLKALEERAAP 91 (439)
Q Consensus 15 D~hl~lpll~fl~~~~--~y~~~~l~~a~~~llk~TnM~dy~~~~~~~l~~~~~~p-~e~~~k~~ev~~~l~~l~~~~~~ 91 (439)
+.|+.=+++.|+...+ ..+..++..-.-+++..-.|.+-++.++..+-..+..- ...=-+..+-+.+++..++++
T Consensus 392 ~~e~~e~ll~~l~~~n~~~~d~~dL~~d~a~al~~~~~~~~Al~~l~~i~~~~~~~~~~vw~~~a~c~~~l~e~e~A~-- 469 (895)
T KOG2076|consen 392 ERELLEALLHFLVEDNVWVSDDVDLYLDLADALTNIGKYKEALRLLSPITNREGYQNAFVWYKLARCYMELGEYEEAI-- 469 (895)
T ss_pred ccchHHHHHHHHHHhcCChhhhHHHHHHHHHHHHhcccHHHHHHHHHHHhcCccccchhhhHHHHHHHHHHhhHHHHH--
Confidence 5677778888888877 44446777777777778888888888777764221111 112223334444444455554
Q ss_pred HHHhhCChhHHHHhhhcchhccHHHHHHhcCCChhHHHHHHHHHHHHHhcCChhhHHHHHHHHH
Q 013640 92 IVSFLQNPNSFQDLRANDQHYNLQMLHDRYQIGPDQIEALYQYAKFQFECGNYSGAADYLYQYR 155 (439)
Q Consensus 92 ~~~~~~~~e~~~~l~~~dk~~n~~~l~~~~g~t~e~~~al~~~ak~~y~~Gdy~~A~~~L~~~~ 155 (439)
++-++-....|+.+|+...+|.+|...|+.++|.+.|....
T Consensus 470 -----------------------e~y~kvl~~~p~~~D~Ri~Lasl~~~~g~~EkalEtL~~~~ 510 (895)
T KOG2076|consen 470 -----------------------EFYEKVLILAPDNLDARITLASLYQQLGNHEKALETLEQII 510 (895)
T ss_pred -----------------------HHHHHHHhcCCCchhhhhhHHHHHHhcCCHHHHHHHHhccc
Confidence 33344455678888899999999999999999998887644
No 265
>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=30.10 E-value=3.6e+02 Score=23.21 Aligned_cols=77 Identities=23% Similarity=0.184 Sum_probs=54.2
Q ss_pred hhHHHHHHHHHHHHHhcCChhhHHHHHHHHHhhccccchhHHHHHHHHHHHHhhcCHHHHHHHHHHHHHHhcCC-CCCCC
Q 013640 125 PDQIEALYQYAKFQFECGNYSGAADYLYQYRALCTNSERRLSALWGKMAAEILMQNWDIALEELNQLKEKVDDP-KSFTS 203 (439)
Q Consensus 125 ~e~~~al~~~ak~~y~~Gdy~~A~~~L~~~~~~~~~~~~k~~~lwg~la~eIl~~~w~~a~~~l~klke~id~~-~~~~~ 203 (439)
...++++.+++..+.+.|+|+.|...+......-+.++ .+.-..+++-...++...|.+.-.+++..+.+. |.-++
T Consensus 59 ~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~l~~dP~~E---~~~~~lm~~~~~~g~~~~A~~~Y~~~~~~l~~elg~~Ps 135 (146)
T PF03704_consen 59 ELYLDALERLAEALLEAGDYEEALRLLQRALALDPYDE---EAYRLLMRALAAQGRRAEALRVYERYRRRLREELGIEPS 135 (146)
T ss_dssp HHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHSTT-H---HHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHHHS----
T ss_pred HHHHHHHHHHHHHHHhccCHHHHHHHHHHHHhcCCCCH---HHHHHHHHHHHHCcCHHHHHHHHHHHHHHHHHHhCcCcC
Confidence 34567899999999999999999998888777554433 344455777778899999999999988888753 33344
Q ss_pred h
Q 013640 204 P 204 (439)
Q Consensus 204 ~ 204 (439)
|
T Consensus 136 ~ 136 (146)
T PF03704_consen 136 P 136 (146)
T ss_dssp H
T ss_pred H
Confidence 4
No 266
>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=30.05 E-value=1.1e+02 Score=24.71 Aligned_cols=38 Identities=16% Similarity=0.255 Sum_probs=27.4
Q ss_pred HHHHHHHHHHhh--hhhccccHHHHHHHcCCCHHHHHHHH
Q 013640 341 ENARLFIFETYC--RIHQRIDMAVLAEKLNLNYEEAQRWI 378 (439)
Q Consensus 341 e~aR~~ife~yc--riy~~I~I~~lA~~l~~s~~~~E~wi 378 (439)
|+-|+....+|+ .|++-|++...|++||....-+-..|
T Consensus 2 RseRlv~it~~L~~~P~~lisL~~Fae~f~~AKSsISEDl 41 (70)
T PF09182_consen 2 RSERLVAITKYLLENPNKLISLTYFAERFGAAKSSISEDL 41 (70)
T ss_dssp HHHHHHHHHHHHHTSTT--EEHHHHHHHHT--HHHHHHHH
T ss_pred chhHHHHHHHHHHcCCcceEcHHHHHHHhcccccchHHHH
Confidence 567888888887 78999999999999999877554443
No 267
>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=29.93 E-value=4.7e+02 Score=27.81 Aligned_cols=62 Identities=19% Similarity=0.173 Sum_probs=40.5
Q ss_pred HHHHHHHHHHhcCChhhHHHHHHHHHhhccccchhHHHHHHHHHHHHhh--cCHHHHHHHHHHHHHHhc
Q 013640 130 ALYQYAKFQFECGNYSGAADYLYQYRALCTNSERRLSALWGKMAAEILM--QNWDIALEELNQLKEKVD 196 (439)
Q Consensus 130 al~~~ak~~y~~Gdy~~A~~~L~~~~~~~~~~~~k~~~lwg~la~eIl~--~~w~~a~~~l~klke~id 196 (439)
..+-+|+++..+++..+|..++.......+.+ ..++. +.++++. ++.+.|.+-.+++=++--
T Consensus 202 v~~~LA~v~l~~~~E~~AI~ll~~aL~~~p~d----~~LL~-~Qa~fLl~k~~~~lAL~iAk~av~lsP 265 (395)
T PF09295_consen 202 VAVLLARVYLLMNEEVEAIRLLNEALKENPQD----SELLN-LQAEFLLSKKKYELALEIAKKAVELSP 265 (395)
T ss_pred HHHHHHHHHHhcCcHHHHHHHHHHHHHhCCCC----HHHHH-HHHHHHHhcCCHHHHHHHHHHHHHhCc
Confidence 45568999999999999999999888654433 33333 3444443 456777666655544433
No 268
>PRK11179 DNA-binding transcriptional regulator AsnC; Provisional
Probab=29.68 E-value=1.4e+02 Score=26.91 Aligned_cols=42 Identities=10% Similarity=0.137 Sum_probs=36.1
Q ss_pred hhhhccccHHHHHHHcCCCHHHHHHHHHHHhhcCccc---eeecc
Q 013640 352 CRIHQRIDMAVLAEKLNLNYEEAQRWIVNLIRNSKLD---AKIDA 393 (439)
Q Consensus 352 criy~~I~I~~lA~~l~~s~~~~E~wiv~lI~~~rL~---aKID~ 393 (439)
++--.+++...||+++|+|+..+-+=|-+|..+|-+. |-+|.
T Consensus 18 Lq~d~R~s~~eiA~~lglS~~tV~~Ri~rL~~~GvI~~~~~~v~~ 62 (153)
T PRK11179 18 LMENARTPYAELAKQFGVSPGTIHVRVEKMKQAGIITGTRVDVNP 62 (153)
T ss_pred HHHcCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCeeeEEEEECH
Confidence 3444889999999999999999999999999999774 66774
No 269
>TIGR01636 phage_rinA phage transcriptional activator, RinA family. This model represents a family of phage proteins, including RinA, a transcriptional activator in staphylococcal phage phi 11. This family shows similarity to ArpU, a phage-related putative autolysin regulator, and to some sporulation-specific sigma factors.
Probab=29.34 E-value=1e+02 Score=27.34 Aligned_cols=47 Identities=26% Similarity=0.303 Sum_probs=38.0
Q ss_pred cHHHHHHHHHHHHHHHhhhhhccccHHHHHHHcCCCHHHHHHHHHHHh
Q 013640 335 LRDEFLENARLFIFETYCRIHQRIDMAVLAEKLNLNYEEAQRWIVNLI 382 (439)
Q Consensus 335 ~~~~f~e~aR~~ife~ycriy~~I~I~~lA~~l~~s~~~~E~wiv~lI 382 (439)
..+.+-+.-|..|...|++..+ .+...+|..||||..-+-++--+++
T Consensus 79 ~l~~Ld~~er~II~~rY~~~~~-~t~~~Ia~~l~iS~~t~~r~r~~~l 125 (134)
T TIGR01636 79 CLNEADEQTRVIIQELYMKKRP-LTLVGLAQQLFISKSTAYRLRNHII 125 (134)
T ss_pred HHHhCCHHHHHHHHHHHccCCC-CCHHHHHHHhCCCHHHHHHHHHHHH
Confidence 3455666788899999998877 8999999999999998877765554
No 270
>PF05559 DUF763: Protein of unknown function (DUF763); InterPro: IPR008482 This family consists of several uncharacterised bacterial and archaeal proteins of unknown function.
Probab=29.27 E-value=25 Score=36.18 Aligned_cols=29 Identities=34% Similarity=0.583 Sum_probs=25.2
Q ss_pred cHHHHHHHcCCCHHHHHHHHHHHhhcCccceeeccc
Q 013640 359 DMAVLAEKLNLNYEEAQRWIVNLIRNSKLDAKIDAK 394 (439)
Q Consensus 359 ~I~~lA~~l~~s~~~~E~wiv~lI~~~rL~aKID~~ 394 (439)
.|..+|+++|++. -.|++.+||-||+|++
T Consensus 101 El~~~~~~~gld~-------~~L~~~SRL~AKVDn~ 129 (319)
T PF05559_consen 101 ELEEIAERFGLDA-------EELVRASRLVAKVDNA 129 (319)
T ss_pred HHHHHHHHhCCCH-------HHHHHHHHHHHhhhhH
Confidence 4788999999998 4578889999999987
No 271
>KOG2114 consensus Vacuolar assembly/sorting protein PEP5/VPS11 [Intracellular trafficking, secretion, and vesicular transport]
Probab=29.27 E-value=2e+02 Score=33.53 Aligned_cols=112 Identities=16% Similarity=0.236 Sum_probs=61.4
Q ss_pred HHHHHHHHccCCCchHHHHHHHHhCCCCCChhHHHHHHHHHHHHHHHHHHHHHH---HHHhhCChhHHHHh-hhcchhcc
Q 013640 38 LKSKIELLNKTNMVDYAMDIHKSLYHTEDVPQDMVERRVEVVARLKALEERAAP---IVSFLQNPNSFQDL-RANDQHYN 113 (439)
Q Consensus 38 ~~a~~~llk~TnM~dy~~~~~~~l~~~~~~p~e~~~k~~ev~~~l~~l~~~~~~---~~~~~~~~e~~~~l-~~~dk~~n 113 (439)
++.++++|.+-||.+.|..+-+..+.+.+.-++.-.+=..-+=.-...++++.. .+..++-++|++.- .. .+-.|
T Consensus 337 le~kL~iL~kK~ly~~Ai~LAk~~~~d~d~~~~i~~kYgd~Ly~Kgdf~~A~~qYI~tI~~le~s~Vi~kfLda-q~Ikn 415 (933)
T KOG2114|consen 337 LETKLDILFKKNLYKVAINLAKSQHLDEDTLAEIHRKYGDYLYGKGDFDEATDQYIETIGFLEPSEVIKKFLDA-QRIKN 415 (933)
T ss_pred HHHHHHHHHHhhhHHHHHHHHHhcCCCHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHcccCChHHHHHHhcCH-HHHHH
Confidence 678999999999999999999999877665556555544444433445555544 22233444443322 11 12222
Q ss_pred H-HHHHHhcCCChhHHHHHHHHHHHHHhcCChhhHHHH
Q 013640 114 L-QMLHDRYQIGPDQIEALYQYAKFQFECGNYSGAADY 150 (439)
Q Consensus 114 ~-~~l~~~~g~t~e~~~al~~~ak~~y~~Gdy~~A~~~ 150 (439)
+ .||+.-+.-.....|-..=+-..|-+.+|-++..++
T Consensus 416 Lt~YLe~L~~~gla~~dhttlLLncYiKlkd~~kL~ef 453 (933)
T KOG2114|consen 416 LTSYLEALHKKGLANSDHTTLLLNCYIKLKDVEKLTEF 453 (933)
T ss_pred HHHHHHHHHHcccccchhHHHHHHHHHHhcchHHHHHH
Confidence 2 266554433333333333334445555555544443
No 272
>KOG4340 consensus Uncharacterized conserved protein [Function unknown]
Probab=29.01 E-value=5.4e+02 Score=26.95 Aligned_cols=182 Identities=15% Similarity=0.216 Sum_probs=105.7
Q ss_pred HHHhcCCChhHHHHHHHHHHHHHhcCChhhHHHHHHHHHhhccccch-h---HHHH------HHHHHHHHhhcCHHHHHH
Q 013640 117 LHDRYQIGPDQIEALYQYAKFQFECGNYSGAADYLYQYRALCTNSER-R---LSAL------WGKMAAEILMQNWDIALE 186 (439)
Q Consensus 117 l~~~~g~t~e~~~al~~~ak~~y~~Gdy~~A~~~L~~~~~~~~~~~~-k---~~~l------wg~la~eIl~~~w~~a~~ 186 (439)
++-.+.-.+-.+.+|--+|..||...+|..|+++..++..+.+...+ + -..| =.-||.-.+++|-+.-..
T Consensus 33 l~s~~Er~p~~rAgLSlLgyCYY~~Q~f~~AA~CYeQL~ql~P~~~qYrlY~AQSLY~A~i~ADALrV~~~~~D~~~L~~ 112 (459)
T KOG4340|consen 33 LGSELERSPRSRAGLSLLGYCYYRLQEFALAAECYEQLGQLHPELEQYRLYQAQSLYKACIYADALRVAFLLLDNPALHS 112 (459)
T ss_pred HHHHHhcCccchHHHHHHHHHHHHHHHHHHHHHHHHHHHhhChHHHHHHHHHHHHHHHhcccHHHHHHHHHhcCCHHHHH
Confidence 33344445667778888999999999999999998887776654222 1 1111 123566667777777777
Q ss_pred HHHHHHHHhcC-CCCCCChHHHHHHHHHHHHHHHHHHhcCccchHHHHH----HhccccchhHHHh--------hchhHH
Q 013640 187 ELNQLKEKVDD-PKSFTSPLNQMQSRIWLMHWSLFIFFNHDNGRTLIID----LFNQDKYLNAIQT--------NAPHLL 253 (439)
Q Consensus 187 ~l~klke~id~-~~~~~~~l~~l~~R~WllHwsLf~~fn~~~~~~~l~d----~F~~~~yl~~Iqt--------~~p~lL 253 (439)
+--+|...|.= .+++.+....++||. .++..+.+++ .|....|..++|- ++.-+|
T Consensus 113 ~~lqLqaAIkYse~Dl~g~rsLveQlp------------~en~Ad~~in~gCllykegqyEaAvqkFqaAlqvsGyqpll 180 (459)
T KOG4340|consen 113 RVLQLQAAIKYSEGDLPGSRSLVEQLP------------SENEADGQINLGCLLYKEGQYEAAVQKFQAALQVSGYQPLL 180 (459)
T ss_pred HHHHHHHHHhcccccCcchHHHHHhcc------------CCCccchhccchheeeccccHHHHHHHHHHHHhhcCCCchh
Confidence 77777777763 367766655555422 1233344444 3444455555543 556677
Q ss_pred HHHHHHHHHhcc-cccchHHHHHHHhhhc---cCC--------------cchH----HHHHHH-------hhhcCChhHH
Q 013640 254 RYLATAFIVNKR-RRPQFKDFIKVIQQEQ---NSY--------------KDPI----TEFLAC-------VYVNYDFDGA 304 (439)
Q Consensus 254 rYlvva~il~~~-r~~~l~~i~~vi~qe~---~~Y--------------~Dpi----t~f~~~-------lY~~fdF~~a 304 (439)
-|-++.+=.+++ +...++-+..||...- ++. ..|+ ..++++ -|++-||+.|
T Consensus 181 AYniALaHy~~~qyasALk~iSEIieRG~r~HPElgIGm~tegiDvrsvgNt~~lh~Sal~eAfNLKaAIeyq~~n~eAA 260 (459)
T KOG4340|consen 181 AYNLALAHYSSRQYASALKHISEIIERGIRQHPELGIGMTTEGIDVRSVGNTLVLHQSALVEAFNLKAAIEYQLRNYEAA 260 (459)
T ss_pred HHHHHHHHHhhhhHHHHHHHHHHHHHhhhhcCCccCccceeccCchhcccchHHHHHHHHHHHhhhhhhhhhhcccHHHH
Confidence 787665555443 3333444444443321 111 1222 233333 2778899999
Q ss_pred HHHHHH
Q 013640 305 QKKMKE 310 (439)
Q Consensus 305 q~~L~~ 310 (439)
++.|-.
T Consensus 261 ~eaLtD 266 (459)
T KOG4340|consen 261 QEALTD 266 (459)
T ss_pred HHHhhc
Confidence 999854
No 273
>smart00530 HTH_XRE Helix-turn-helix XRE-family like proteins.
Probab=28.98 E-value=67 Score=21.50 Aligned_cols=24 Identities=25% Similarity=0.260 Sum_probs=20.6
Q ss_pred hccccHHHHHHHcCCCHHHHHHHH
Q 013640 355 HQRIDMAVLAEKLNLNYEEAQRWI 378 (439)
Q Consensus 355 y~~I~I~~lA~~l~~s~~~~E~wi 378 (439)
...++...+|+.+|+++..+.+|.
T Consensus 8 ~~~~s~~~la~~~~i~~~~i~~~~ 31 (56)
T smart00530 8 EKGLTQEELAEKLGVSRSTLSRIE 31 (56)
T ss_pred HcCCCHHHHHHHhCCCHHHHHHHH
Confidence 367899999999999998887764
No 274
>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=28.90 E-value=62 Score=22.70 Aligned_cols=27 Identities=15% Similarity=0.129 Sum_probs=22.5
Q ss_pred cHHHHHHHcCCCHHHHHHHHHHHhhcCccce
Q 013640 359 DMAVLAEKLNLNYEEAQRWIVNLIRNSKLDA 389 (439)
Q Consensus 359 ~I~~lA~~l~~s~~~~E~wiv~lI~~~rL~a 389 (439)
++..+|+.+|+|+.-+..| +..|.+.+
T Consensus 2 ~~~e~a~~~gv~~~tlr~~----~~~g~l~~ 28 (49)
T cd04761 2 TIGELAKLTGVSPSTLRYY----ERIGLLSP 28 (49)
T ss_pred cHHHHHHHHCcCHHHHHHH----HHCCCCCC
Confidence 6889999999999999988 46666653
No 275
>PF10141 ssDNA-exonuc_C: Single-strand DNA-specific exonuclease, C terminal domain; InterPro: IPR018779 This entry represents a domain found at the C terminus of a set of single-stranded DNA-specific exonucleases, including RecJ. Its function has not, as yet, been determined.
Probab=28.79 E-value=2e+02 Score=27.10 Aligned_cols=73 Identities=15% Similarity=0.356 Sum_probs=49.7
Q ss_pred cccHHHHHHHHHHHHHHHhhhhhccccH----HHHHHHcCCCHHHHHHHHHHHhhcCccceeecccCCEEEeCCCC----
Q 013640 333 VPLRDEFLENARLFIFETYCRIHQRIDM----AVLAEKLNLNYEEAQRWIVNLIRNSKLDAKIDAKSGTVIMEPTH---- 404 (439)
Q Consensus 333 ~~~~~~f~e~aR~~ife~ycriy~~I~I----~~lA~~l~~s~~~~E~wiv~lI~~~rL~aKID~~~g~V~~~~~~---- 404 (439)
.|..+.|-. +=+|++-|+.+++ ..||+.+|++++-+.-.|-=|---|= |--++|++..+..+
T Consensus 94 ~P~Re~F~~------~Y~~l~~~~~~~l~~~~~~La~~l~i~~~~l~fml~VF~EL~F----Vti~~g~i~~~~~p~k~~ 163 (195)
T PF10141_consen 94 MPTREQFKK------LYKFLKQHPNFDLKEQLQALAKYLGISPDTLKFMLKVFFELGF----VTIEDGVISLNPNPEKRD 163 (195)
T ss_pred CCCHHHHHH------HHHHHHhCCCCCHHHHHHHHHHHHCcCHHHHHHHHHHHHHcCc----EEEeCCEEEeCCCCCCcC
Confidence 577777753 3356677888876 68999999999988766644432222 22357998887665
Q ss_pred ---chhHHHHHHhh
Q 013640 405 ---PNVYEQLIDHT 415 (439)
Q Consensus 405 ---~~~yqqvi~kt 415 (439)
+..||+..++-
T Consensus 164 L~~S~~Yq~~~~~~ 177 (195)
T PF10141_consen 164 LTESPTYQERQQQI 177 (195)
T ss_pred hhhhHHHHHHHHHH
Confidence 35788776554
No 276
>COG1802 GntR Transcriptional regulators [Transcription]
Probab=28.62 E-value=1.2e+02 Score=28.76 Aligned_cols=70 Identities=19% Similarity=0.214 Sum_probs=60.9
Q ss_pred cccHHHHHHHHHHHHHHHhhhhhccccHHHHHHHcCCCHHHHHHHHHHHhhcCccceeecccCCEEEeCCCC
Q 013640 333 VPLRDEFLENARLFIFETYCRIHQRIDMAVLAEKLNLNYEEAQRWIVNLIRNSKLDAKIDAKSGTVIMEPTH 404 (439)
Q Consensus 333 ~~~~~~f~e~aR~~ife~ycriy~~I~I~~lA~~l~~s~~~~E~wiv~lI~~~rL~aKID~~~g~V~~~~~~ 404 (439)
.+..+...+..|-.|..--++|=+.++...||+.||||.-=+-.-|.+|-.+|=+ .+....|.++.....
T Consensus 15 ~~~~~~vy~~Lr~~Il~g~l~pG~~l~e~~La~~~gvSrtPVReAL~rL~~eGlv--~~~p~rG~~V~~~~~ 84 (230)
T COG1802 15 DTLADQVYEELREAILSGELAPGERLSEEELAEELGVSRTPVREALRRLEAEGLV--EIEPNRGAFVAPLSL 84 (230)
T ss_pred ccHHHHHHHHHHHHHHhCCCCCCCCccHHHHHHHhCCCCccHHHHHHHHHHCCCe--EecCCCCCeeCCCCH
Confidence 3566788899999999999999999999999999999999999999999999988 445778888865444
No 277
>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=28.51 E-value=1.2e+02 Score=18.35 Aligned_cols=23 Identities=17% Similarity=0.307 Sum_probs=19.1
Q ss_pred ccccHHHHHHHcCCCHHHHHHHH
Q 013640 356 QRIDMAVLAEKLNLNYEEAQRWI 378 (439)
Q Consensus 356 ~~I~I~~lA~~l~~s~~~~E~wi 378 (439)
...++..+|+.+|++..-+-+|+
T Consensus 20 ~~~s~~~ia~~~~is~~tv~~~~ 42 (42)
T cd00569 20 AGESVAEIARRLGVSRSTLYRYL 42 (42)
T ss_pred cCCCHHHHHHHHCCCHHHHHHhC
Confidence 45589999999999998877764
No 278
>PRK03578 hscB co-chaperone HscB; Provisional
Probab=28.42 E-value=5e+02 Score=24.33 Aligned_cols=31 Identities=16% Similarity=0.113 Sum_probs=19.9
Q ss_pred chhHHHHHHHHHHHHhh-cCHHHHHHHHHHHH
Q 013640 162 ERRLSALWGKMAAEILM-QNWDIALEELNQLK 192 (439)
Q Consensus 162 ~~k~~~lwg~la~eIl~-~~w~~a~~~l~klk 192 (439)
..++..+-..++..+-. .||+.|...+.+|+
T Consensus 127 ~~~~~~~~~~l~~~~~~~~d~~~A~~~~~kL~ 158 (176)
T PRK03578 127 RDERRERYAELGALLDSRGDDQAAAEAVRQLM 158 (176)
T ss_pred HHHHHHHHHHHHHHHHccccHHHHHHHHHHHH
Confidence 44555555666655545 67888887777665
No 279
>PF04100 Vps53_N: Vps53-like, N-terminal ; InterPro: IPR007234 Vps53 complexes with Vps52 and Vps54 to form a multi-subunit complex involved in regulating membrane trafficking events [].
Probab=28.40 E-value=4.6e+02 Score=27.57 Aligned_cols=97 Identities=12% Similarity=0.151 Sum_probs=56.1
Q ss_pred hHHHHHHHHHHHHHHHHHHHHHHHHHhhCChhHHHHhhhcchhccHHHHHHhcCCChhHHH------HHHHHHHHHHhcC
Q 013640 69 QDMVERRVEVVARLKALEERAAPIVSFLQNPNSFQDLRANDQHYNLQMLHDRYQIGPDQIE------ALYQYAKFQFECG 142 (439)
Q Consensus 69 ~e~~~k~~ev~~~l~~l~~~~~~~~~~~~~~e~~~~l~~~dk~~n~~~l~~~~g~t~e~~~------al~~~ak~~y~~G 142 (439)
++..+.-.+++.++.+.+.+++. .+..+.+|-+ .-+.++.+++|...+.-.+. ..+.-.+-..+.+
T Consensus 60 ~~a~~~i~~L~~~i~~ik~kA~~------sE~~V~~it~--dIk~LD~AKrNLT~SIT~LkrL~MLv~a~~qL~~~~~~r 131 (383)
T PF04100_consen 60 EEAQEAIQELFEKISEIKSKAEE------SEQMVQEITR--DIKQLDNAKRNLTQSITTLKRLQMLVTAVEQLKELAKKR 131 (383)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHH------HHHHHHHHHH--HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcC
Confidence 34444456777777777777743 1122333322 12334555555554443333 3366677788889
Q ss_pred ChhhHHHHHHHHHhhccc-----cchhHHHHHHHHH
Q 013640 143 NYSGAADYLYQYRALCTN-----SERRLSALWGKMA 173 (439)
Q Consensus 143 dy~~A~~~L~~~~~~~~~-----~~~k~~~lwg~la 173 (439)
+|.+++..|.....+... +-..+..|+..+.
T Consensus 132 ~Y~e~a~~L~av~~L~~~F~~yksi~~I~~L~~~i~ 167 (383)
T PF04100_consen 132 QYKEIASLLQAVKELLEHFKPYKSIPQIAELSKRID 167 (383)
T ss_pred CHHHHHHHHHHHHHHHHHHHcccCcHHHHHHHHHHH
Confidence 999999999988888753 1223555555443
No 280
>KOG0553 consensus TPR repeat-containing protein [General function prediction only]
Probab=28.39 E-value=2.1e+02 Score=29.44 Aligned_cols=45 Identities=16% Similarity=0.111 Sum_probs=34.0
Q ss_pred HHHHHhcCCChhHHHHHHHHHHHHHhcCChhhHHHHHHHHHhhcc
Q 013640 115 QMLHDRYQIGPDQIEALYQYAKFQFECGNYSGAADYLYQYRALCT 159 (439)
Q Consensus 115 ~~l~~~~g~t~e~~~al~~~ak~~y~~Gdy~~A~~~L~~~~~~~~ 159 (439)
+..+.-..+++..-+++-.+|..|+..|+|+.|.+.+.....+-+
T Consensus 136 kDce~Al~iDp~yskay~RLG~A~~~~gk~~~A~~aykKaLeldP 180 (304)
T KOG0553|consen 136 KDCESALSIDPHYSKAYGRLGLAYLALGKYEEAIEAYKKALELDP 180 (304)
T ss_pred HHHHHHHhcChHHHHHHHHHHHHHHccCcHHHHHHHHHhhhccCC
Confidence 344555667888888999999999999999999988655555433
No 281
>PF03962 Mnd1: Mnd1 family; InterPro: IPR005647 This family of proteins includes meiotic nuclear division protein 1 (MND1) from Saccharomyces cerevisiae (Baker's yeast). The mnd1 protein forms a complex with hop2 to promote homologous chromosome pairing and meiotic double-strand break repair [].
Probab=28.14 E-value=1.8e+02 Score=27.54 Aligned_cols=35 Identities=23% Similarity=0.449 Sum_probs=19.2
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHhh-----CChhHHHHhhh
Q 013640 73 ERRVEVVARLKALEERAAPIVSFL-----QNPNSFQDLRA 107 (439)
Q Consensus 73 ~k~~ev~~~l~~l~~~~~~~~~~~-----~~~e~~~~l~~ 107 (439)
+.|.+.++++++|+++...+..-+ .||+.+..++.
T Consensus 103 ~eR~~~l~~l~~l~~~~~~l~~el~~~~~~Dp~~i~~~~~ 142 (188)
T PF03962_consen 103 EEREELLEELEELKKELKELKKELEKYSENDPEKIEKLKE 142 (188)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCHHHHHHHHH
Confidence 445556666666666655544333 36666665553
No 282
>KOG0547 consensus Translocase of outer mitochondrial membrane complex, subunit TOM70/TOM72 [Intracellular trafficking, secretion, and vesicular transport]
Probab=28.09 E-value=1.3e+02 Score=33.08 Aligned_cols=57 Identities=21% Similarity=0.385 Sum_probs=39.5
Q ss_pred HHHHHHHHHHhcCChhhHHHHHHHHHhhccccchhHHHHH-HHHHHHHhhcCHHHHHHHHHH
Q 013640 130 ALYQYAKFQFECGNYSGAADYLYQYRALCTNSERRLSALW-GKMAAEILMQNWDIALEELNQ 190 (439)
Q Consensus 130 al~~~ak~~y~~Gdy~~A~~~L~~~~~~~~~~~~k~~~lw-g~la~eIl~~~w~~a~~~l~k 190 (439)
++-..|+-+|+.|.|++|.++......+|++-. ..+ .+-||=+..++|+...++-.+
T Consensus 117 ~lK~~GN~~f~~kkY~eAIkyY~~AI~l~p~ep----iFYsNraAcY~~lgd~~~Vied~Tk 174 (606)
T KOG0547|consen 117 ALKTKGNKFFRNKKYDEAIKYYTQAIELCPDEP----IFYSNRAACYESLGDWEKVIEDCTK 174 (606)
T ss_pred HHHhhhhhhhhcccHHHHHHHHHHHHhcCCCCc----hhhhhHHHHHHHHhhHHHHHHHHHH
Confidence 556789999999999999999999999998731 111 122344555666666655433
No 283
>PF14493 HTH_40: Helix-turn-helix domain
Probab=28.04 E-value=1.2e+02 Score=24.90 Aligned_cols=39 Identities=21% Similarity=0.305 Sum_probs=33.5
Q ss_pred HhhhhhccccHHHHHHHcCCCHHHHHHHHHHHhhcCc-cc
Q 013640 350 TYCRIHQRIDMAVLAEKLNLNYEEAQRWIVNLIRNSK-LD 388 (439)
Q Consensus 350 ~ycriy~~I~I~~lA~~l~~s~~~~E~wiv~lI~~~r-L~ 388 (439)
+|--.-+..+|+.+|+.-|+++.=+..-|+.++..|. ++
T Consensus 6 T~~l~~~G~si~eIA~~R~L~~sTI~~HL~~~~~~g~~~~ 45 (91)
T PF14493_consen 6 TYELFQKGLSIEEIAKIRGLKESTIYGHLAELIESGEPLD 45 (91)
T ss_pred HHHHHHcCCCHHHHHHHcCCCHHHHHHHHHHHHHhCCCCC
Confidence 3434447899999999999999999999999999998 54
No 284
>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=27.96 E-value=64 Score=25.05 Aligned_cols=27 Identities=22% Similarity=0.452 Sum_probs=19.5
Q ss_pred HHHcCCCHHHHHHHHHHHhhcCcccee
Q 013640 364 AEKLNLNYEEAQRWIVNLIRNSKLDAK 390 (439)
Q Consensus 364 A~~l~~s~~~~E~wiv~lI~~~rL~aK 390 (439)
+..+++|.++.+.++..++++++|.|.
T Consensus 28 ~~~~~~s~~eL~~fL~~lv~e~~L~~~ 54 (60)
T PF08672_consen 28 PGGYDISLEELQEFLDRLVEEGKLECS 54 (60)
T ss_dssp G--TT--HHHHHHHHHHHHHTTSEE--
T ss_pred CCCCCCCHHHHHHHHHHHHHCCcEEec
Confidence 356889999999999999999999763
No 285
>PF13429 TPR_15: Tetratricopeptide repeat; PDB: 2VQ2_A 2PL2_B.
Probab=27.68 E-value=2.2e+02 Score=27.56 Aligned_cols=68 Identities=22% Similarity=0.187 Sum_probs=46.9
Q ss_pred hHHHHHHHHHHHHHhcCChhhHHHHHHHHHhhccccch-hHHHHHHHHHHHHhhcCHHHHHHHHHHHHHHhcC
Q 013640 126 DQIEALYQYAKFQFECGNYSGAADYLYQYRALCTNSER-RLSALWGKMAAEILMQNWDIALEELNQLKEKVDD 197 (439)
Q Consensus 126 e~~~al~~~ak~~y~~Gdy~~A~~~L~~~~~~~~~~~~-k~~~lwg~la~eIl~~~w~~a~~~l~klke~id~ 197 (439)
..-..++.+|.++.+.|+++.|.+.+.....+-+++.. .....|- -|-.++.+.+.+-++.+.....+
T Consensus 144 ~~~~~~~~~a~~~~~~G~~~~A~~~~~~al~~~P~~~~~~~~l~~~----li~~~~~~~~~~~l~~~~~~~~~ 212 (280)
T PF13429_consen 144 DSARFWLALAEIYEQLGDPDKALRDYRKALELDPDDPDARNALAWL----LIDMGDYDEAREALKRLLKAAPD 212 (280)
T ss_dssp T-HHHHHHHHHHHHHCCHHHHHHHHHHHHHHH-TT-HHHHHHHHHH----HCTTCHHHHHHHHHHHHHHH-HT
T ss_pred CCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHcCCCCHHHHHHHHHH----HHHCCChHHHHHHHHHHHHHCcC
Confidence 34557789999999999999999999999888776433 3444443 35566777777777777776644
No 286
>PF12728 HTH_17: Helix-turn-helix domain
Probab=27.68 E-value=67 Score=23.12 Aligned_cols=29 Identities=28% Similarity=0.468 Sum_probs=23.5
Q ss_pred ccHHHHHHHcCCCHHHHHHHHHHHhhcCcccee
Q 013640 358 IDMAVLAEKLNLNYEEAQRWIVNLIRNSKLDAK 390 (439)
Q Consensus 358 I~I~~lA~~l~~s~~~~E~wiv~lI~~~rL~aK 390 (439)
++++.+|+.||+|..-+.+|+ +.|++.+-
T Consensus 2 lt~~e~a~~l~is~~tv~~~~----~~g~i~~~ 30 (51)
T PF12728_consen 2 LTVKEAAELLGISRSTVYRWI----RQGKIPPF 30 (51)
T ss_pred CCHHHHHHHHCcCHHHHHHHH----HcCCCCeE
Confidence 478999999999999888776 67777554
No 287
>PRK03573 transcriptional regulator SlyA; Provisional
Probab=27.60 E-value=3.8e+02 Score=23.37 Aligned_cols=45 Identities=11% Similarity=0.047 Sum_probs=37.5
Q ss_pred ccccHHHHHHHcCCCHHHHHHHHHHHhhcCccceeecccCCEEEe
Q 013640 356 QRIDMAVLAEKLNLNYEEAQRWIVNLIRNSKLDAKIDAKSGTVIM 400 (439)
Q Consensus 356 ~~I~I~~lA~~l~~s~~~~E~wiv~lI~~~rL~aKID~~~g~V~~ 400 (439)
..++...||+.+|+++.-+=+-|-+|...|=+.-.-|...+.+..
T Consensus 45 ~~~t~~eLa~~l~~~~~tvt~~v~~Le~~GlV~r~~~~~DrR~~~ 89 (144)
T PRK03573 45 PEQSQIQLAKAIGIEQPSLVRTLDQLEEKGLISRQTCASDRRAKR 89 (144)
T ss_pred CCCCHHHHHHHhCCChhhHHHHHHHHHHCCCEeeecCCCCcCeee
Confidence 467899999999999999999999999999887666666555443
No 288
>COG5499 Predicted transcription regulator containing HTH domain [Transcription]
Probab=27.45 E-value=1.3e+02 Score=26.50 Aligned_cols=49 Identities=27% Similarity=0.319 Sum_probs=38.5
Q ss_pred HHHHhcCCChhHHHHHHHHHHHHHhcCChhhHHHHHHHHHhhccccchhHHHHHHHHH
Q 013640 116 MLHDRYQIGPDQIEALYQYAKFQFECGNYSGAADYLYQYRALCTNSERRLSALWGKMA 173 (439)
Q Consensus 116 ~l~~~~g~t~e~~~al~~~ak~~y~~Gdy~~A~~~L~~~~~~~~~~~~k~~~lwg~la 173 (439)
.+-+.||.+.. -+--.+|..+.+++.|.-=|+++.+.-+++..-||+=+
T Consensus 67 t~Md~~glt~~---------dLa~~iGSks~vS~iL~~rraLTle~ikkL~q~~gIpa 115 (120)
T COG5499 67 TLMDQYGLTLA---------DLANEIGSKSRVSNILSGRRALTLEHIKKLHQRFGIPA 115 (120)
T ss_pred HHHHHhCCcHH---------HHHHHhCchHHHHHHHhhhhHhhHHHHHHHHHHhCcCH
Confidence 44567776544 33346899999999999999999998999999998643
No 289
>PF13542 HTH_Tnp_ISL3: Helix-turn-helix domain of transposase family ISL3
Probab=27.04 E-value=2e+02 Score=20.58 Aligned_cols=24 Identities=13% Similarity=0.230 Sum_probs=21.3
Q ss_pred ccHHHHHHHcCCCHHHHHHHHHHH
Q 013640 358 IDMAVLAEKLNLNYEEAQRWIVNL 381 (439)
Q Consensus 358 I~I~~lA~~l~~s~~~~E~wiv~l 381 (439)
.+++.+|+.+|+|..-+.+.+-++
T Consensus 28 ~s~~~vA~~~~vs~~TV~ri~~~~ 51 (52)
T PF13542_consen 28 RSFKDVARELGVSWSTVRRIFDRY 51 (52)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHhh
Confidence 799999999999999998887654
No 290
>PF13936 HTH_38: Helix-turn-helix domain; PDB: 2W48_A.
Probab=26.88 E-value=80 Score=22.57 Aligned_cols=25 Identities=16% Similarity=0.233 Sum_probs=17.3
Q ss_pred ccccHHHHHHHcCCCHHHHHHHHHH
Q 013640 356 QRIDMAVLAEKLNLNYEEAQRWIVN 380 (439)
Q Consensus 356 ~~I~I~~lA~~l~~s~~~~E~wiv~ 380 (439)
+..++..||+.||+|+.-+-++|-+
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 7789999999999999988888743
No 291
>PRK11523 DNA-binding transcriptional repressor ExuR; Provisional
Probab=26.86 E-value=2e+02 Score=27.77 Aligned_cols=69 Identities=12% Similarity=0.146 Sum_probs=59.1
Q ss_pred ccHHHHHHHHHHHHHHHhhhhhccc-cHHHHHHHcCCCHHHHHHHHHHHhhcCccceeecccCCEEEeCCCC
Q 013640 334 PLRDEFLENARLFIFETYCRIHQRI-DMAVLAEKLNLNYEEAQRWIVNLIRNSKLDAKIDAKSGTVIMEPTH 404 (439)
Q Consensus 334 ~~~~~f~e~aR~~ife~ycriy~~I-~I~~lA~~l~~s~~~~E~wiv~lI~~~rL~aKID~~~g~V~~~~~~ 404 (439)
+..+...+..|..|..--++|=.++ +-..||+.||||..=+-.-|-.|-..|=+. +-.-.|+.+.....
T Consensus 8 ~~~~~v~~~l~~~I~~g~l~pG~~LpsE~eLae~~gVSRtpVREAL~~L~~eGlV~--~~~~~G~~V~~~~~ 77 (253)
T PRK11523 8 RLYQQLAAELKERIEQGVYLVGDKLPAERFIADEKNVSRTVVREAIIMLEVEGYVE--VRKGSGIHVVSNQP 77 (253)
T ss_pred cHHHHHHHHHHHHHHcCCCCCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEE--EecCCeeEEecCCc
Confidence 4567889999999999999999999 589999999999999999999999999884 44667888865443
No 292
>KOG2115 consensus Vacuolar sorting protein VPS45 [Intracellular trafficking, secretion, and vesicular transport]
Probab=26.78 E-value=4e+02 Score=31.39 Aligned_cols=88 Identities=11% Similarity=0.173 Sum_probs=52.0
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHhhCChh-HHHHhhhcchhccHHHHHHhcCCChhHHHHHHHHHHHHHhcCChhhHH
Q 013640 70 DMVERRVEVVARLKALEERAAPIVSFLQNPN-SFQDLRANDQHYNLQMLHDRYQIGPDQIEALYQYAKFQFECGNYSGAA 148 (439)
Q Consensus 70 e~~~k~~ev~~~l~~l~~~~~~~~~~~~~~e-~~~~l~~~dk~~n~~~l~~~~g~t~e~~~al~~~ak~~y~~Gdy~~A~ 148 (439)
++.++-.+-+++.++|.+++..|-...-+.. .+-++.. +..|...|++... +.+.+..-..-.+..+..+||.+|.
T Consensus 279 ~Lq~~~~d~~~~vk~Lre~i~~vd~~~~~~s~~Ile~~~--~r~n~~kL~~kL~-~i~~V~~~q~~vq~ll~~~d~~~AL 355 (951)
T KOG2115|consen 279 NLQKELRDTMSEVKELRENIKEVDAENVRKSIKILELAL--TRKNVEKLLQKLR-LIATVHQAQSTVQLLLSTQDFVGAL 355 (951)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHH--HHHHHHHHHHHHH-HHHHHHhhhHHHHHHHhcccHHHHH
Confidence 4445555556666666666655544433322 1122211 3344445554444 4444555566788899999999999
Q ss_pred HHHHHHHhhccc
Q 013640 149 DYLYQYRALCTN 160 (439)
Q Consensus 149 ~~L~~~~~~~~~ 160 (439)
+.+.-...+..+
T Consensus 356 dlI~t~q~~L~g 367 (951)
T KOG2115|consen 356 DLIKTIQELLKG 367 (951)
T ss_pred HHHHHHHHHHhh
Confidence 998877776654
No 293
>PF02002 TFIIE_alpha: TFIIE alpha subunit; InterPro: IPR024550 The general transcription factor TFIIE has an essential role in eukaryotic transcription initiation, together with RNA polymerase II and other general factors. Human TFIIE consists of two subunits, TFIIE-alpha and TFIIE-beta, and joins the preinitiation complex after RNA polymerase II and TFIIF []. This entry represents a helix-turn-helix (HTH) domain found in eukaryotic TFIIE-alpha []. It is also found in proteins from archaebacteria that are presumed to be TFIIE-alpha subunits [], the transcriptional regulator SarR, and also DNA-directed RNA polymerase III subunit Rpc3.; PDB: 1VD4_A 1Q1H_A.
Probab=26.66 E-value=1.3e+02 Score=25.23 Aligned_cols=45 Identities=20% Similarity=0.310 Sum_probs=31.5
Q ss_pred HHHHHHhhhhhccccHHHHHHHcCCCHHHHHHHHHHHhhcCcccee
Q 013640 345 LFIFETYCRIHQRIDMAVLAEKLNLNYEEAQRWIVNLIRNSKLDAK 390 (439)
Q Consensus 345 ~~ife~ycriy~~I~I~~lA~~l~~s~~~~E~wiv~lI~~~rL~aK 390 (439)
..|+...++ |..++=+.||+.+||++.++-+-|..|-.++=+..+
T Consensus 16 ~~Il~~L~~-~~~l~de~la~~~~l~~~~vRkiL~~L~~~~lv~~~ 60 (105)
T PF02002_consen 16 VRILDALLR-KGELTDEDLAKKLGLKPKEVRKILYKLYEDGLVSYR 60 (105)
T ss_dssp HHHHHHHHH-H--B-HHHHHHTT-S-HHHHHHHHHHHHHHSS-EEE
T ss_pred HHHHHHHHH-cCCcCHHHHHHHhCCCHHHHHHHHHHHHHCCCeEEE
Confidence 345555554 789999999999999999999999999888876544
No 294
>PRK04984 fatty acid metabolism regulator; Provisional
Probab=26.59 E-value=2e+02 Score=27.29 Aligned_cols=66 Identities=14% Similarity=0.003 Sum_probs=56.7
Q ss_pred cHHHHHHHHHHHHHHHhhhhhccc-cHHHHHHHcCCCHHHHHHHHHHHhhcCccceeecccCCEEEeCC
Q 013640 335 LRDEFLENARLFIFETYCRIHQRI-DMAVLAEKLNLNYEEAQRWIVNLIRNSKLDAKIDAKSGTVIMEP 402 (439)
Q Consensus 335 ~~~~f~e~aR~~ife~ycriy~~I-~I~~lA~~l~~s~~~~E~wiv~lI~~~rL~aKID~~~g~V~~~~ 402 (439)
-.+...+..|-.|..--+.|=.++ +-..||++||||..=+-.-|..|...|-+. +-.-.|+++...
T Consensus 8 ~~~~~~~~l~~~I~~g~l~pG~~LPsE~eLae~~gVSRt~VReAL~~L~~eGlv~--~~~g~G~~V~~~ 74 (239)
T PRK04984 8 PAGFAEEYIIESIWNNRFPPGSILPAERELSELIGVTRTTLREVLQRLARDGWLT--IQHGKPTKVNNF 74 (239)
T ss_pred HHHHHHHHHHHHHHcCCCCCCCcCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEE--EeCCCeeEeCCc
Confidence 346677888899999989999999 799999999999999999999999999885 346678888653
No 295
>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=26.59 E-value=1.2e+02 Score=20.78 Aligned_cols=28 Identities=25% Similarity=0.315 Sum_probs=22.4
Q ss_pred ccHHHHHHHcCCCHHHHHHHHHHHhhcC
Q 013640 358 IDMAVLAEKLNLNYEEAQRWIVNLIRNS 385 (439)
Q Consensus 358 I~I~~lA~~l~~s~~~~E~wiv~lI~~~ 385 (439)
++-..||+.+|++++-+=+-+..|-++|
T Consensus 3 mtr~diA~~lG~t~ETVSR~l~~l~~~g 30 (32)
T PF00325_consen 3 MTRQDIADYLGLTRETVSRILKKLERQG 30 (32)
T ss_dssp --HHHHHHHHTS-HHHHHHHHHHHHHTT
T ss_pred cCHHHHHHHhCCcHHHHHHHHHHHHHcC
Confidence 4567899999999999999999987766
No 296
>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=26.54 E-value=93 Score=26.96 Aligned_cols=34 Identities=18% Similarity=0.213 Sum_probs=29.9
Q ss_pred HHHhhhhhccccHHHHHHHcCCCHHHHHHHHHHH
Q 013640 348 FETYCRIHQRIDMAVLAEKLNLNYEEAQRWIVNL 381 (439)
Q Consensus 348 fe~ycriy~~I~I~~lA~~l~~s~~~~E~wiv~l 381 (439)
+..++.-|+.+++..||+.||||..-+-..|-++
T Consensus 62 L~~~v~~~pd~tl~Ela~~l~Vs~~ti~~~Lkrl 95 (119)
T PF01710_consen 62 LKALVEENPDATLRELAERLGVSPSTIWRALKRL 95 (119)
T ss_pred HHHHHHHCCCcCHHHHHHHcCCCHHHHHHHHHHc
Confidence 6777888999999999999999999888877665
No 297
>KOG0551 consensus Hsp90 co-chaperone CNS1 (contains TPR repeats) [Posttranslational modification, protein turnover, chaperones]
Probab=26.53 E-value=2.4e+02 Score=29.74 Aligned_cols=72 Identities=15% Similarity=0.209 Sum_probs=58.5
Q ss_pred CCChhHHHHHHHHHHHHHhcCChhhHHHHHHH-HHhhccccchhHHHHHHHHHHHHhhcCHHHHHHHHHHHHH
Q 013640 122 QIGPDQIEALYQYAKFQFECGNYSGAADYLYQ-YRALCTNSERRLSALWGKMAAEILMQNWDIALEELNQLKE 193 (439)
Q Consensus 122 g~t~e~~~al~~~ak~~y~~Gdy~~A~~~L~~-~~~~~~~~~~k~~~lwg~la~eIl~~~w~~a~~~l~klke 193 (439)
|-+.|+-+-.-+=|+.||...+|..|.+.+.. +..+|.+.+....++..+-||..+.+|+..|+++-.+.+.
T Consensus 75 ~ep~E~Aen~KeeGN~~fK~Kryk~A~~~Yt~Glk~kc~D~dlnavLY~NRAAa~~~l~NyRs~l~Dcs~al~ 147 (390)
T KOG0551|consen 75 GEPHEQAENYKEEGNEYFKEKRYKDAVESYTEGLKKKCADPDLNAVLYTNRAAAQLYLGNYRSALNDCSAALK 147 (390)
T ss_pred CChHHHHHHHHHHhHHHHHhhhHHHHHHHHHHHHhhcCCCccHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHh
Confidence 43444445555679999999999999987765 6667888888899999999999999999999998877754
No 298
>PF00165 HTH_AraC: Bacterial regulatory helix-turn-helix proteins, AraC family; PDB: 1WPK_A 1ZGW_A 1U8B_A.
Probab=26.28 E-value=48 Score=23.03 Aligned_cols=20 Identities=15% Similarity=0.232 Sum_probs=13.6
Q ss_pred hccccHHHHHHHcCCCHHHH
Q 013640 355 HQRIDMAVLAEKLNLNYEEA 374 (439)
Q Consensus 355 y~~I~I~~lA~~l~~s~~~~ 374 (439)
.+.++|+.||+.+|+|+.-.
T Consensus 6 ~~~~~l~~iA~~~g~S~~~f 25 (42)
T PF00165_consen 6 QQKLTLEDIAEQAGFSPSYF 25 (42)
T ss_dssp -SS--HHHHHHHHTS-HHHH
T ss_pred cCCCCHHHHHHHHCCCHHHH
Confidence 46799999999999987643
No 299
>cd04749 Commd1_MURR1 COMM_Domain containing protein 1, also called Murr1. Murr1/Commd1 is a protein involved in copper homeostasis, which has also been identified as a regulator of the human delta epithelial sodium channel. The COMM Domain is found at the C-terminus of a variety of proteins; presumably all COMM_Domain containing proteins are located in the nucleus and the COMM domain plays a role in protein-protein interactions. Several family members have been shown to bind and inhibit NF-kappaB.
Probab=26.27 E-value=2.6e+02 Score=26.40 Aligned_cols=38 Identities=18% Similarity=0.342 Sum_probs=26.0
Q ss_pred hhhHHHHhhcCCCCHHHHHHHHHHHHccCCCchHHHHHHHHhCCCCCChhHHHH
Q 013640 20 FPLLEFLQERQMYPDEQILKSKIELLNKTNMVDYAMDIHKSLYHTEDVPQDMVE 73 (439)
Q Consensus 20 lpll~fl~~~~~y~~~~l~~a~~~llk~TnM~dy~~~~~~~l~~~~~~p~e~~~ 73 (439)
..||.++..+..|.+.+|.+..+ +.+++|+ ..|++++.
T Consensus 2 ~~LL~gl~q~~~~~~~~ite~~l---------------~~~l~~~-~~~ed~ka 39 (174)
T cd04749 2 SGLLNGIAQKEYYGNAEITEELL---------------RSELYPE-DPLEEFRA 39 (174)
T ss_pred hHHHHHHHHHHHccccchHHHHH---------------HHHhcCC-CCHHHHHH
Confidence 56888998888787777766544 4667874 33556554
No 300
>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=26.13 E-value=83 Score=23.95 Aligned_cols=25 Identities=24% Similarity=0.404 Sum_probs=19.0
Q ss_pred HHHHHHHcCCCHHHHHHHHHHHhhc
Q 013640 360 MAVLAEKLNLNYEEAQRWIVNLIRN 384 (439)
Q Consensus 360 I~~lA~~l~~s~~~~E~wiv~lI~~ 384 (439)
++.++++++++++.++..+..||..
T Consensus 36 ~~~l~~~y~~~~~~~~~dv~~fl~~ 60 (68)
T PF05402_consen 36 VDALAEEYDVDPEEAEEDVEEFLEQ 60 (68)
T ss_dssp HHHHHHHTT--HHHHHHHHHHHHHH
T ss_pred HHHHHHHcCCCHHHHHHHHHHHHHH
Confidence 5678889999999999888888763
No 301
>PLN03081 pentatricopeptide (PPR) repeat-containing protein; Provisional
Probab=26.12 E-value=3.7e+02 Score=30.00 Aligned_cols=137 Identities=14% Similarity=0.184 Sum_probs=64.2
Q ss_pred hhHHHHhhcCCCCHHHHHHHHHHHHccCCCchHHHHHHHHhCCC-CCChh-HHHHHHHHHHHHHHHHHHHHHHHHHhhCC
Q 013640 21 PLLEFLQERQMYPDEQILKSKIELLNKTNMVDYAMDIHKSLYHT-EDVPQ-DMVERRVEVVARLKALEERAAPIVSFLQN 98 (439)
Q Consensus 21 pll~fl~~~~~y~~~~l~~a~~~llk~TnM~dy~~~~~~~l~~~-~~~p~-e~~~k~~ev~~~l~~l~~~~~~~~~~~~~ 98 (439)
-+++-+...++-+....--+.+....+...++-+..+++++..+ +-.|. +-=..--..+.+...++++.+-+-++-..
T Consensus 412 ~lf~~M~~~g~~Pd~~T~~~ll~a~~~~g~~~~a~~~f~~m~~~~g~~p~~~~y~~li~~l~r~G~~~eA~~~~~~~~~~ 491 (697)
T PLN03081 412 EMFERMIAEGVAPNHVTFLAVLSACRYSGLSEQGWEIFQSMSENHRIKPRAMHYACMIELLGREGLLDEAYAMIRRAPFK 491 (697)
T ss_pred HHHHHHHHhCCCCCHHHHHHHHHHHhcCCcHHHHHHHHHHHHHhcCCCCCccchHhHHHHHHhcCCHHHHHHHHHHCCCC
Confidence 34444445566666666666777777777777777777665321 11111 00001112222222233333222222222
Q ss_pred hh--HHHHhhh---cchh--ccHHHHHHhcCCChhHHHHHHHHHHHHHhcCChhhHHHHHHHHHhh
Q 013640 99 PN--SFQDLRA---NDQH--YNLQMLHDRYQIGPDQIEALYQYAKFQFECGNYSGAADYLYQYRAL 157 (439)
Q Consensus 99 ~e--~~~~l~~---~dk~--~n~~~l~~~~g~t~e~~~al~~~ak~~y~~Gdy~~A~~~L~~~~~~ 157 (439)
|. ++..|-. +.+. .-...+++-.++.|+....+.-++..|.+.|++++|.+++...+..
T Consensus 492 p~~~~~~~Ll~a~~~~g~~~~a~~~~~~l~~~~p~~~~~y~~L~~~y~~~G~~~~A~~v~~~m~~~ 557 (697)
T PLN03081 492 PTVNMWAALLTACRIHKNLELGRLAAEKLYGMGPEKLNNYVVLLNLYNSSGRQAEAAKVVETLKRK 557 (697)
T ss_pred CCHHHHHHHHHHHHHcCCcHHHHHHHHHHhCCCCCCCcchHHHHHHHHhCCCHHHHHHHHHHHHHc
Confidence 22 1222211 0011 0111233445556655556666677777777777777777666654
No 302
>PRK10421 DNA-binding transcriptional repressor LldR; Provisional
Probab=26.03 E-value=2e+02 Score=27.73 Aligned_cols=65 Identities=20% Similarity=0.208 Sum_probs=56.5
Q ss_pred HHHHHHHHHHHHHHHhhhhhccc-cHHHHHHHcCCCHHHHHHHHHHHhhcCccceeecccCCEEEeCC
Q 013640 336 RDEFLENARLFIFETYCRIHQRI-DMAVLAEKLNLNYEEAQRWIVNLIRNSKLDAKIDAKSGTVIMEP 402 (439)
Q Consensus 336 ~~~f~e~aR~~ife~ycriy~~I-~I~~lA~~l~~s~~~~E~wiv~lI~~~rL~aKID~~~g~V~~~~ 402 (439)
.+...+..|..|...=++|=.++ +-..||++||||..=+-.-|..|-..|=+.. -.-.|+.+...
T Consensus 4 ~~~v~~~L~~~I~~g~l~pG~~LpsE~eLae~~gVSRtpVREAL~~Le~~GlV~~--~~~~G~~V~~~ 69 (253)
T PRK10421 4 SDEVADRVRALIEEKNLEAGMKLPAERQLAMQLGVSRNSLREALAKLVSEGVLLS--RRGGGTFIRWR 69 (253)
T ss_pred HHHHHHHHHHHHHcCCCCCCCcCCCHHHHHHHhCCCHHHHHHHHHHHHHCCCEEE--eCCCeEEEecC
Confidence 46788899999999999999999 7999999999999999999999999998853 35678888764
No 303
>PF08831 MHCassoc_trimer: Class II MHC-associated invariant chain trimerisation domain; InterPro: IPR011988 This entry represents the trimerisation domain of the MHC class II-associated invariant chain (Ii). Ii plays a critical role in the assembly of the MHC, as well as in MHC II antigen processing by stabilising peptide-free class II alpha/beta heterodimers in a complex soon after their synthesis and directing transport of the complex from the endoplasmic reticulum to compartments where peptide loading of class II takes place []. In antigen-presenting cells (APCs), loading of MHC II molecules with peptides is regulated by Ii, which blocks MHC II antigen-binding sites in pre-endosomal compartments []. Several molecules then act upon MHC II molecules in endosomes to facilitate peptide loading: Ii-degrading proteases, the peptide exchange factor, human leukocyte antigen-DM (HLA-DM), and its modulator, HLA-DO (DO). The Invariant chain contains a single transmembrane domain. Ii first assembles into a trimer and then associates with three class II alpha/beta MHC heterodimers. Although the membrane-proximal region of the Ii luminal domain is structurally disordered, the C-terminal segment of the luminal domain is largely alpha-helical and contains a major interaction site for the Ii trimer []. More information about these proteins can be found at Protein of the Month: MHC [].; GO: 0042289 MHC class II protein binding, 0006886 intracellular protein transport, 0006955 immune response, 0019882 antigen processing and presentation, 0016020 membrane; PDB: 1IIE_C.
Probab=26.01 E-value=87 Score=25.44 Aligned_cols=35 Identities=26% Similarity=0.616 Sum_probs=24.8
Q ss_pred HHHHHHHHHHHHhcCCCCCCChHHHHHHHHHHHHHHHHHHhc
Q 013640 183 IALEELNQLKEKVDDPKSFTSPLNQMQSRIWLMHWSLFIFFN 224 (439)
Q Consensus 183 ~a~~~l~klke~id~~~~~~~~l~~l~~R~WllHwsLf~~fn 224 (439)
+-.++++.||..++. .+| -.--+|+-||-||-.-.
T Consensus 26 tf~~NL~~LK~~M~~-~~W------k~FEsWM~~WLlFqMaq 60 (72)
T PF08831_consen 26 TFLENLKHLKNQMNE-SDW------KSFESWMHQWLLFQMAQ 60 (72)
T ss_dssp -HHHHHHHHHHHS-H-HHH------HHHHHHHHHHHHHHHHT
T ss_pred HHHHHHHHHHHhcch-hhH------HHHHHHHHHHHHHHHHh
Confidence 567788999998887 455 23458999999996443
No 304
>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=25.87 E-value=1.3e+02 Score=23.05 Aligned_cols=35 Identities=17% Similarity=0.196 Sum_probs=27.2
Q ss_pred HHHHHHHhhhhhccccHHHHHHHcCCCHHHHHHHHHHH
Q 013640 344 RLFIFETYCRIHQRIDMAVLAEKLNLNYEEAQRWIVNL 381 (439)
Q Consensus 344 R~~ife~ycriy~~I~I~~lA~~l~~s~~~~E~wiv~l 381 (439)
|..+-.=|+ +..+++.||+.||++..-+-.|.-+.
T Consensus 3 k~~A~~LY~---~G~~~~eIA~~Lg~~~~TV~~W~~r~ 37 (58)
T PF06056_consen 3 KEQARSLYL---QGWSIKEIAEELGVPRSTVYSWKDRY 37 (58)
T ss_pred HHHHHHHHH---cCCCHHHHHHHHCCChHHHHHHHHhh
Confidence 334444454 47789999999999999999998764
No 305
>smart00422 HTH_MERR helix_turn_helix, mercury resistance.
Probab=25.74 E-value=1.6e+02 Score=22.14 Aligned_cols=28 Identities=11% Similarity=0.105 Sum_probs=22.7
Q ss_pred cHHHHHHHcCCCHHHHHHHHHHHhhcCcccee
Q 013640 359 DMAVLAEKLNLNYEEAQRWIVNLIRNSKLDAK 390 (439)
Q Consensus 359 ~I~~lA~~l~~s~~~~E~wiv~lI~~~rL~aK 390 (439)
+++.+|+.+|+|+..+-.|. +.|.+...
T Consensus 2 s~~eva~~~gvs~~tlr~~~----~~gli~~~ 29 (70)
T smart00422 2 TIGEVAKLAGVSVRTLRYYE----RIGLLPPP 29 (70)
T ss_pred CHHHHHHHHCcCHHHHHHHH----HCCCCCCC
Confidence 68899999999999988884 46766543
No 306
>PRK10219 DNA-binding transcriptional regulator SoxS; Provisional
Probab=25.65 E-value=1.5e+02 Score=24.62 Aligned_cols=40 Identities=20% Similarity=0.208 Sum_probs=29.8
Q ss_pred HHHHHHHHHHHHHHhhhhhccccHHHHHHHcCCCHHHHHHHHH
Q 013640 337 DEFLENARLFIFETYCRIHQRIDMAVLAEKLNLNYEEAQRWIV 379 (439)
Q Consensus 337 ~~f~e~aR~~ife~ycriy~~I~I~~lA~~l~~s~~~~E~wiv 379 (439)
+..++.+...+-+.+ +..++++.||+.+|||+--..+-.-
T Consensus 4 ~~~~~~~~~~i~~~~---~~~~~~~~lA~~~~~S~~~l~r~f~ 43 (107)
T PRK10219 4 QKIIQTLIAWIDEHI---DQPLNIDVVAKKSGYSKWYLQRMFR 43 (107)
T ss_pred HHHHHHHHHHHHHhc---CCCCCHHHHHHHHCCCHHHHHHHHH
Confidence 345666666666654 5669999999999999987766554
No 307
>PRK11414 colanic acid/biofilm transcriptional regulator; Provisional
Probab=25.40 E-value=2.1e+02 Score=26.91 Aligned_cols=65 Identities=12% Similarity=0.110 Sum_probs=55.8
Q ss_pred ccHHHHHHHHHHHHHHHhhhhhccccHHHHHHHcCCCHHHHHHHHHHHhhcCccceeecccCCEEEe
Q 013640 334 PLRDEFLENARLFIFETYCRIHQRIDMAVLAEKLNLNYEEAQRWIVNLIRNSKLDAKIDAKSGTVIM 400 (439)
Q Consensus 334 ~~~~~f~e~aR~~ife~ycriy~~I~I~~lA~~l~~s~~~~E~wiv~lI~~~rL~aKID~~~g~V~~ 400 (439)
...+...+..|-.|..-=++|=.+++-..||+.||||..=+-.-|..|...|=+.- -+-.|.++.
T Consensus 11 ~~~e~v~~~l~~~I~~g~l~pG~~L~e~~La~~lgVSRtpVREAL~~L~~eGLV~~--~~~~g~~v~ 75 (221)
T PRK11414 11 SLTLQVENDLKHQLSIGALKPGARLITKNLAEQLGMSITPVREALLRLVSVNALSV--APAQAFTVP 75 (221)
T ss_pred CHHHHHHHHHHHHHHhCCCCCCCccCHHHHHHHHCCCchhHHHHHHHHHHCCCEEe--cCCCceeec
Confidence 45678999999999999999999999999999999999999999999999998753 344566553
No 308
>PRK11511 DNA-binding transcriptional activator MarA; Provisional
Probab=25.18 E-value=1.4e+02 Score=25.90 Aligned_cols=40 Identities=10% Similarity=0.056 Sum_probs=31.6
Q ss_pred HHHHHHHHHHHHHHhhhhhccccHHHHHHHcCCCHHHHHHHHH
Q 013640 337 DEFLENARLFIFETYCRIHQRIDMAVLAEKLNLNYEEAQRWIV 379 (439)
Q Consensus 337 ~~f~e~aR~~ife~ycriy~~I~I~~lA~~l~~s~~~~E~wiv 379 (439)
...++.+...|-+.+. ..++++.||+.+|||+.-+.++.-
T Consensus 8 ~~~i~~~~~~I~~~~~---~~~sl~~lA~~~g~S~~~l~r~Fk 47 (127)
T PRK11511 8 AITIHSILDWIEDNLE---SPLSLEKVSERSGYSKWHLQRMFK 47 (127)
T ss_pred HHHHHHHHHHHHHhcC---CCCCHHHHHHHHCcCHHHHHHHHH
Confidence 4566777777777765 459999999999999998887764
No 309
>PRK15174 Vi polysaccharide export protein VexE; Provisional
Probab=25.05 E-value=1e+03 Score=26.72 Aligned_cols=74 Identities=3% Similarity=-0.161 Sum_probs=47.8
Q ss_pred HHHHHHhcCCChhHHHHHHHHHHHHHhcCChhhHHHHHHHHHhhccccchhHHHHHHHHHHHHhhcCHHHHHHHHHHH
Q 013640 114 LQMLHDRYQIGPDQIEALYQYAKFQFECGNYSGAADYLYQYRALCTNSERRLSALWGKMAAEILMQNWDIALEELNQL 191 (439)
Q Consensus 114 ~~~l~~~~g~t~e~~~al~~~ak~~y~~Gdy~~A~~~L~~~~~~~~~~~~k~~~lwg~la~eIl~~~w~~a~~~l~kl 191 (439)
.+.+++-..+.|+...+...+|..+...|+++.|.+.+.......++... ...+ +..-+..++++.|.+...++
T Consensus 130 i~~l~~Al~l~P~~~~a~~~la~~l~~~g~~~eA~~~~~~~~~~~P~~~~---a~~~-~~~l~~~g~~~eA~~~~~~~ 203 (656)
T PRK15174 130 ADLAEQAWLAFSGNSQIFALHLRTLVLMDKELQAISLARTQAQEVPPRGD---MIAT-CLSFLNKSRLPEDHDLARAL 203 (656)
T ss_pred HHHHHHHHHhCCCcHHHHHHHHHHHHHCCChHHHHHHHHHHHHhCCCCHH---HHHH-HHHHHHcCCHHHHHHHHHHH
Confidence 34555566667777778888899999999999998888766554443322 1111 22234567788887665554
No 310
>KOG2076 consensus RNA polymerase III transcription factor TFIIIC [Transcription]
Probab=24.70 E-value=1.2e+03 Score=27.54 Aligned_cols=97 Identities=14% Similarity=0.130 Sum_probs=65.9
Q ss_pred HHhcCCChhHH-HHHHHHHHHHHhcCChhhHHHHHHHHHhhc---cccchhHHHHHHHHHHHHhhcCHHHHHHHHHHHHH
Q 013640 118 HDRYQIGPDQI-EALYQYAKFQFECGNYSGAADYLYQYRALC---TNSERRLSALWGKMAAEILMQNWDIALEELNQLKE 193 (439)
Q Consensus 118 ~~~~g~t~e~~-~al~~~ak~~y~~Gdy~~A~~~L~~~~~~~---~~~~~k~~~lwg~la~eIl~~~w~~a~~~l~klke 193 (439)
.+..|.+.+.. +-..++..-.++.|.+++|..++.-....- .++..+=..-|-.++|-+.+.||..|.. -+|.
T Consensus 615 ~e~~~Lsiddwfel~~e~i~~L~k~~r~qeAl~vv~~a~~~~~f~~~~~~~k~l~~~~l~~s~~~~d~~~a~~---~lR~ 691 (895)
T KOG2076|consen 615 VELRGLSIDDWFELFRELILSLAKLQRVQEALSVVFTALEAYIFFQDSEIRKELQFLGLKASLYARDPGDAFS---YLRS 691 (895)
T ss_pred hhhccCcHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHhhhhhhccHHHHHHHHHHHHHHHHhcCCHHHHHH---HHHH
Confidence 34556655555 555667777888899999998876554432 2345556888999999999999998865 4566
Q ss_pred HhcCCCCCCChHHHHHHHHHHHHHHHH
Q 013640 194 KVDDPKSFTSPLNQMQSRIWLMHWSLF 220 (439)
Q Consensus 194 ~id~~~~~~~~l~~l~~R~WllHwsLf 220 (439)
+|-.. . ..+.+++-+.|-+-.+.|
T Consensus 692 ~i~~~-~--~~~~~~q~~l~n~~~s~~ 715 (895)
T KOG2076|consen 692 VITQF-Q--FYLDVYQLNLWNLDFSYF 715 (895)
T ss_pred HHHHH-h--hhhhhHHHHHHHHHHHHH
Confidence 67652 2 225667777777533333
No 311
>PF08765 Mor: Mor transcription activator family; InterPro: IPR014875 Mor (Middle operon regulator) is a sequence specific DNA binding protein. It mediates transcription activation through its interactions with the C-terminal domains of the alpha and sigma subunits of bacterial RNA polymerase. The N-terminal region of Mor is the dimerisation region, and the C-terminal contains a helix-turn-helix motif which binds DNA []. ; PDB: 1RR7_A.
Probab=24.60 E-value=1.6e+02 Score=25.08 Aligned_cols=39 Identities=26% Similarity=0.302 Sum_probs=23.4
Q ss_pred ccHHHHHHHHHH-HHHHHhhhhhccccHHHHHHHcCCCHHHHHH
Q 013640 334 PLRDEFLENARL-FIFETYCRIHQRIDMAVLAEKLNLNYEEAQR 376 (439)
Q Consensus 334 ~~~~~f~e~aR~-~ife~ycriy~~I~I~~lA~~l~~s~~~~E~ 376 (439)
|-...+.+..|- .|++.|- .-++..||.++|+|.--+-+
T Consensus 52 P~~~~~~~~~R~~~I~~~f~----G~n~~eLA~kyglS~r~I~~ 91 (108)
T PF08765_consen 52 PKCDRLLRALRNREIRREFN----GMNVRELARKYGLSERQIYR 91 (108)
T ss_dssp --SHHHHHHHHHHHHHHH------SS-HHHHHHHHT--HHHHHH
T ss_pred eCccHHHHHHHHHHHHHHhC----CCCHHHHHHHHCcCHHHHHH
Confidence 666667777774 6666665 78899999999999554433
No 312
>PF13411 MerR_1: MerR HTH family regulatory protein; PDB: 2JML_A 3GP4_A 3GPV_B.
Probab=24.57 E-value=1.9e+02 Score=21.76 Aligned_cols=65 Identities=9% Similarity=0.012 Sum_probs=36.6
Q ss_pred cHHHHHHHcCCCHHHHHHHHHHHhhcCccceeecccCCEEEeCCCCchhHHHHHHhhhhhhhHHHHHHHHH
Q 013640 359 DMAVLAEKLNLNYEEAQRWIVNLIRNSKLDAKIDAKSGTVIMEPTHPNVYEQLIDHTKGLSGRTYKLVGQL 429 (439)
Q Consensus 359 ~I~~lA~~l~~s~~~~E~wiv~lI~~~rL~aKID~~~g~V~~~~~~~~~yqqvi~kt~~L~~R~q~L~~~i 429 (439)
+|+.+|+.+|||+.-+-.|.- .|-+.... ..+|.-.-+..+-.. =..|........-++.+.+.+
T Consensus 2 ti~eva~~~gvs~~tlr~y~~----~gll~~~~-~~~g~r~y~~~dv~~-l~~i~~l~~~G~sl~~I~~~l 66 (69)
T PF13411_consen 2 TIKEVAKLLGVSPSTLRYYER----EGLLPPPR-DENGYRYYSEEDVER-LREIKELRKQGMSLEEIKKLL 66 (69)
T ss_dssp EHHHHHHHTTTTHHHHHHHHH----TTSSTTBE-STTSSEEE-HHHHHH-HHHHHHHHHTTTHHHHHHHHH
T ss_pred cHHHHHHHHCcCHHHHHHHHH----hcCccccc-ccCceeeccHHHHHH-HHHHHHHHHCcCCHHHHHHHH
Confidence 689999999999999999955 44566554 455543332222111 133334343444444444433
No 313
>PRK06759 RNA polymerase factor sigma-70; Validated
Probab=24.48 E-value=1.1e+02 Score=26.80 Aligned_cols=44 Identities=16% Similarity=0.258 Sum_probs=33.0
Q ss_pred HHHHHHHHHHHHHHhhhhhccccHHHHHHHcCCCHHHHHHHHHHHhh
Q 013640 337 DEFLENARLFIFETYCRIHQRIDMAVLAEKLNLNYEEAQRWIVNLIR 383 (439)
Q Consensus 337 ~~f~e~aR~~ife~ycriy~~I~I~~lA~~l~~s~~~~E~wiv~lI~ 383 (439)
+.+-..-|..+.-.| +...+++.||+.+|+|+.-+..++.+.+.
T Consensus 105 ~~L~~~~r~ii~l~~---~~~~s~~EIA~~l~is~~tV~~~~~ra~~ 148 (154)
T PRK06759 105 SVLDEKEKYIIFERF---FVGKTMGEIALETEMTYYQVRWIYRQALE 148 (154)
T ss_pred HhCCHHHHHHHHHHH---hcCCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 334444555554444 46788999999999999999999988654
No 314
>TIGR00985 3a0801s04tom mitochondrial import receptor subunit translocase of outer membrane 20 kDa subunit.
Probab=24.44 E-value=2.6e+02 Score=25.80 Aligned_cols=45 Identities=18% Similarity=0.160 Sum_probs=34.4
Q ss_pred HHHHHHHHhcC-ChhhHHHHHHHHHhhccccchhHHHHHHHHHHHH
Q 013640 132 YQYAKFQFECG-NYSGAADYLYQYRALCTNSERRLSALWGKMAAEI 176 (439)
Q Consensus 132 ~~~ak~~y~~G-dy~~A~~~L~~~~~~~~~~~~k~~~lwg~la~eI 176 (439)
.+.|.-+...| ++.+|...|+.....|+.++.-+..+=..+--+|
T Consensus 94 V~~GE~L~~~g~~~~ega~hf~nAl~Vc~qP~~LL~iyq~tlP~~V 139 (148)
T TIGR00985 94 VQLGEELMAQGTNVDEGAVHFYNALKVYPQPQQLLSIYQQTLPEPI 139 (148)
T ss_pred HHHHHHHHhCCCchHHHHHHHHHHHHhCCCHHHHHHHHHhhCCHHH
Confidence 67899999999 9999999999999999887665555444333333
No 315
>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=24.43 E-value=1.5e+02 Score=22.77 Aligned_cols=42 Identities=10% Similarity=0.211 Sum_probs=31.1
Q ss_pred HHHHHHHHHHHHhhhhhccccHHHHHHHcCCCHHHHHHHHHHHh
Q 013640 339 FLENARLFIFETYCRIHQRIDMAVLAEKLNLNYEEAQRWIVNLI 382 (439)
Q Consensus 339 f~e~aR~~ife~ycriy~~I~I~~lA~~l~~s~~~~E~wiv~lI 382 (439)
|-.+-+..+...+ .....++..+|..+||++.-+=+|+-.+-
T Consensus 7 ys~e~K~~~v~~~--~~~g~sv~~va~~~gi~~~~l~~W~~~~~ 48 (76)
T PF01527_consen 7 YSPEFKLQAVREY--LESGESVSEVAREYGISPSTLYNWRKQYR 48 (76)
T ss_dssp --HHHHHHHHHHH--HHHHCHHHHHHHHHTS-HHHHHHHHHHHH
T ss_pred CCHHHHHHHHHHH--HHCCCceEeeecccccccccccHHHHHHh
Confidence 3444455566666 34568899999999999999999999885
No 316
>KOG3364 consensus Membrane protein involved in organellar division [Cell wall/membrane/envelope biogenesis]
Probab=24.25 E-value=1.4e+02 Score=27.54 Aligned_cols=44 Identities=20% Similarity=0.239 Sum_probs=34.7
Q ss_pred HHHHHHhc--CCChhHHHHHHHHHHHHHhcCChhhHHHHHHHHHhh
Q 013640 114 LQMLHDRY--QIGPDQIEALYQYAKFQFECGNYSGAADYLYQYRAL 157 (439)
Q Consensus 114 ~~~l~~~~--g~t~e~~~al~~~ak~~y~~Gdy~~A~~~L~~~~~~ 157 (439)
+..|++-+ +=+.+.++.+|=+|-=+|+.|+|+.|..|+.-+...
T Consensus 55 I~iLe~l~~~~~~~~rRe~lyYLAvg~yRlkeY~~s~~yvd~ll~~ 100 (149)
T KOG3364|consen 55 IVILEDLLKSAHPERRRECLYYLAVGHYRLKEYSKSLRYVDALLET 100 (149)
T ss_pred HHHHHHHhhhcCcccchhhhhhhHHHHHHHhhHHHHHHHHHHHHhh
Confidence 34555544 336677889999999999999999999999887763
No 317
>PF12862 Apc5: Anaphase-promoting complex subunit 5
Probab=24.20 E-value=2.1e+02 Score=23.45 Aligned_cols=35 Identities=23% Similarity=0.230 Sum_probs=29.9
Q ss_pred HHHHHHHHHHHHHhcCChhhHHHHHHHHHhhcccc
Q 013640 127 QIEALYQYAKFQFECGNYSGAADYLYQYRALCTNS 161 (439)
Q Consensus 127 ~~~al~~~ak~~y~~Gdy~~A~~~L~~~~~~~~~~ 161 (439)
..-+++.+|.+++.-|++++|.+.+.....+....
T Consensus 40 ~~~all~lA~~~~~~G~~~~A~~~l~eAi~~Are~ 74 (94)
T PF12862_consen 40 LAYALLNLAELHRRFGHYEEALQALEEAIRLAREN 74 (94)
T ss_pred HHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHH
Confidence 34578999999999999999999999988877543
No 318
>PRK09990 DNA-binding transcriptional regulator GlcC; Provisional
Probab=24.17 E-value=2.5e+02 Score=26.94 Aligned_cols=68 Identities=15% Similarity=0.207 Sum_probs=58.5
Q ss_pred cHHHHHHHHHHHHHHHhhhhhccc-cHHHHHHHcCCCHHHHHHHHHHHhhcCccceeecccCCEEEeCCCC
Q 013640 335 LRDEFLENARLFIFETYCRIHQRI-DMAVLAEKLNLNYEEAQRWIVNLIRNSKLDAKIDAKSGTVIMEPTH 404 (439)
Q Consensus 335 ~~~~f~e~aR~~ife~ycriy~~I-~I~~lA~~l~~s~~~~E~wiv~lI~~~rL~aKID~~~g~V~~~~~~ 404 (439)
..+...+..|-.|..-=++|=.++ +-..||+.||||..=+-.-|..|-..|=+. +-.-.|+.+.....
T Consensus 8 ~~~~v~~~i~~~I~~g~l~pG~~LPsE~eLa~~~gVSRtpVREAL~~L~~eGlV~--~~~~~G~~V~~~~~ 76 (251)
T PRK09990 8 IADVVAERIERLIVDGVLKVGQALPSERRLCEKLGFSRSALREGLTVLRGRGIIE--TAQGRGSFVARLNR 76 (251)
T ss_pred HHHHHHHHHHHHHHcCCCCCCCcCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCEE--EeCCCeeEEecCCc
Confidence 457888899999999999999999 899999999999999999999999999884 44567888876443
No 319
>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=24.02 E-value=45 Score=24.71 Aligned_cols=22 Identities=23% Similarity=0.357 Sum_probs=17.6
Q ss_pred cccHHHHHHHcCCCHHHHHHHH
Q 013640 357 RIDMAVLAEKLNLNYEEAQRWI 378 (439)
Q Consensus 357 ~I~I~~lA~~l~~s~~~~E~wi 378 (439)
.+++..||+.+|+++.++=+-+
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 5789999999999999865555
No 320
>PF04695 Pex14_N: Peroxisomal membrane anchor protein (Pex14p) conserved region; InterPro: IPR006785 This conserved region defines a group of peroxisomal membrane anchor proteins which bind the PTS1 (peroxisomal targeting signal) receptor and are required for the import of PTS1-containing proteins into peroxisomes. Loss of functional Pex14p results in defects in both the PTS1 and PTS2-dependent import pathways. Deletion analysis of this conserved region implicates it in selective peroxisome degradation. In the majority of members this region is situated at the N terminus of the protein [, ].; GO: 0005777 peroxisome, 0016020 membrane; PDB: 2W85_A 2W84_A 3FF5_B.
Probab=23.50 E-value=91 Score=27.90 Aligned_cols=44 Identities=18% Similarity=0.270 Sum_probs=28.3
Q ss_pred HHHHHHHhhCChhHHHHhhhcchhccHHHHHHhcCCChhHHHHHHHHHH
Q 013640 88 RAAPIVSFLQNPNSFQDLRANDQHYNLQMLHDRYQIGPDQIEALYQYAK 136 (439)
Q Consensus 88 ~~~~~~~~~~~~e~~~~l~~~dk~~n~~~l~~~~g~t~e~~~al~~~ak 136 (439)
-++...++|+||+|...=.. .-.+||+.+ |+|.|-|+.+++.+.
T Consensus 5 li~~A~~FL~~p~V~~sp~~----~k~~FL~sK-GLt~~EI~~al~~a~ 48 (136)
T PF04695_consen 5 LIEQAVKFLQDPKVRNSPLE----KKIAFLESK-GLTEEEIDEALGRAG 48 (136)
T ss_dssp HHHHHHHHHCTTTCCCS-HH----HHHHHHHHC-T--HHHHHHHHHHHT
T ss_pred HHHHHHHHhCCcccccCCHH----HHHHHHHcC-CCCHHHHHHHHHhcC
Confidence 34456789999998654322 224688654 999999998887654
No 321
>PF14394 DUF4423: Domain of unknown function (DUF4423)
Probab=23.49 E-value=3.6e+02 Score=25.04 Aligned_cols=59 Identities=17% Similarity=0.126 Sum_probs=45.8
Q ss_pred HHHHHHHHHHHHHhhhhhccc-cHHHHHHHc--CCCHHHHHHHHHHHhhcCccceeecccCCEE
Q 013640 338 EFLENARLFIFETYCRIHQRI-DMAVLAEKL--NLNYEEAQRWIVNLIRNSKLDAKIDAKSGTV 398 (439)
Q Consensus 338 ~f~e~aR~~ife~ycriy~~I-~I~~lA~~l--~~s~~~~E~wiv~lI~~~rL~aKID~~~g~V 398 (439)
+|.++=-..+.-..+....-- +...||+++ ++|.++++.-|.-|.+-|=| |-|...+.+
T Consensus 19 ~~~~~W~~~~ir~l~~l~~~~~d~~~iak~l~p~is~~ev~~sL~~L~~~gli--~k~~~g~y~ 80 (171)
T PF14394_consen 19 EYYSSWYHPAIRELLPLMPFAPDPEWIAKRLRPKISAEEVRDSLEFLEKLGLI--KKDGDGKYV 80 (171)
T ss_pred HHHhhhHHHHHHHHhhcCCCCCCHHHHHHHhcCCCCHHHHHHHHHHHHHCCCe--EECCCCcEE
Confidence 455666666666677777777 999999999 99999999999999999977 444443333
No 322
>smart00347 HTH_MARR helix_turn_helix multiple antibiotic resistance protein.
Probab=23.49 E-value=3.7e+02 Score=21.10 Aligned_cols=40 Identities=13% Similarity=0.150 Sum_probs=34.4
Q ss_pred hhccccHHHHHHHcCCCHHHHHHHHHHHhhcCccceeecc
Q 013640 354 IHQRIDMAVLAEKLNLNYEEAQRWIVNLIRNSKLDAKIDA 393 (439)
Q Consensus 354 iy~~I~I~~lA~~l~~s~~~~E~wiv~lI~~~rL~aKID~ 393 (439)
.+..++.+.||+.+++|..-+-+-|-+|...|-+...-|.
T Consensus 21 ~~~~~~~~~la~~~~~s~~~i~~~l~~L~~~g~v~~~~~~ 60 (101)
T smart00347 21 EEGPLSVSELAKRLGVSPSTVTRVLDRLEKKGLIRRLPSP 60 (101)
T ss_pred HcCCcCHHHHHHHHCCCchhHHHHHHHHHHCCCeEecCCC
Confidence 3567999999999999999999999999999888665443
No 323
>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=23.40 E-value=3e+02 Score=27.25 Aligned_cols=75 Identities=11% Similarity=0.189 Sum_probs=55.1
Q ss_pred HhcCCChhHHHHHHHHHHHHHhcCChhhHHHHHHHHHhhccccchhHHHHHHHH-HHHHhhcCHHHHHHHHHHHHHHhcC
Q 013640 119 DRYQIGPDQIEALYQYAKFQFECGNYSGAADYLYQYRALCTNSERRLSALWGKM-AAEILMQNWDIALEELNQLKEKVDD 197 (439)
Q Consensus 119 ~~~g~t~e~~~al~~~ak~~y~~Gdy~~A~~~L~~~~~~~~~~~~k~~~lwg~l-a~eIl~~~w~~a~~~l~klke~id~ 197 (439)
+.|+-. .+-.+.|..|....||.++|..++..+....+ .+.....+|.++ .-|-..+|++.+.+--++..+++.+
T Consensus 64 k~f~~~---~~~~~~Y~~~l~~~~d~~~aR~lfer~i~~l~-~~~~~~~iw~~~i~fE~~~Gdl~~v~~v~~R~~~~~~~ 139 (280)
T PF05843_consen 64 KKFPSD---PDFWLEYLDFLIKLNDINNARALFERAISSLP-KEKQSKKIWKKFIEFESKYGDLESVRKVEKRAEELFPE 139 (280)
T ss_dssp HHHTT----HHHHHHHHHHHHHTT-HHHHHHHHHHHCCTSS-CHHHCHHHHHHHHHHHHHHS-HHHHHHHHHHHHHHTTT
T ss_pred HHCCCC---HHHHHHHHHHHHHhCcHHHHHHHHHHHHHhcC-chhHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHhhh
Confidence 555533 44678899999999999999999988777643 334377888875 5678888998888877888888776
No 324
>KOG4234 consensus TPR repeat-containing protein [General function prediction only]
Probab=23.36 E-value=7.3e+02 Score=24.61 Aligned_cols=80 Identities=13% Similarity=0.055 Sum_probs=55.1
Q ss_pred ccHHHHHHhcCCChhHHHHHHHHHHHHHhcCChhhHHHHHHHHHhhccccchhHHHHHHHHHHHHhhcCHHHHHHH--HH
Q 013640 112 YNLQMLHDRYQIGPDQIEALYQYAKFQFECGNYSGAADYLYQYRALCTNSERRLSALWGKMAAEILMQNWDIALEE--LN 189 (439)
Q Consensus 112 ~n~~~l~~~~g~t~e~~~al~~~ak~~y~~Gdy~~A~~~L~~~~~~~~~~~~k~~~lwg~la~eIl~~~w~~a~~~--l~ 189 (439)
..++.-.+...+.|-...||.+.|..|-....|+.|.+=+..+..+-++. -.+-=+..++.=+..+-...+++ +.
T Consensus 152 ~aI~dcsKaiel~pty~kAl~RRAeayek~ek~eealeDyKki~E~dPs~---~ear~~i~rl~~~i~ernEkmKee~m~ 228 (271)
T KOG4234|consen 152 SAIEDCSKAIELNPTYEKALERRAEAYEKMEKYEEALEDYKKILESDPSR---REAREAIARLPPKINERNEKMKEEMME 228 (271)
T ss_pred HHHHHHHhhHhcCchhHHHHHHHHHHHHhhhhHHHHHHHHHHHHHhCcch---HHHHHHHHhcCHHHHHHHHHHHHHHHH
Confidence 44556667777888889999999999999999999998877777754432 24444555655555544455544 56
Q ss_pred HHHHH
Q 013640 190 QLKEK 194 (439)
Q Consensus 190 klke~ 194 (439)
|||++
T Consensus 229 kLKdl 233 (271)
T KOG4234|consen 229 KLKDL 233 (271)
T ss_pred HHHHh
Confidence 66654
No 325
>PRK11169 leucine-responsive transcriptional regulator; Provisional
Probab=23.30 E-value=1.1e+02 Score=28.01 Aligned_cols=49 Identities=16% Similarity=0.177 Sum_probs=40.1
Q ss_pred HHHHHHhhhhhccccHHHHHHHcCCCHHHHHHHHHHHhhcCcc---ceeeccc
Q 013640 345 LFIFETYCRIHQRIDMAVLAEKLNLNYEEAQRWIVNLIRNSKL---DAKIDAK 394 (439)
Q Consensus 345 ~~ife~ycriy~~I~I~~lA~~l~~s~~~~E~wiv~lI~~~rL---~aKID~~ 394 (439)
..|.. .++--.+++...||+++|+|+.-+-+=|-+|..+|-+ .|.||..
T Consensus 17 ~~IL~-~Lq~d~R~s~~eiA~~lglS~~tv~~Ri~rL~~~GvI~~~~~~v~p~ 68 (164)
T PRK11169 17 RNILN-ELQKDGRISNVELSKRVGLSPTPCLERVRRLERQGFIQGYTALLNPH 68 (164)
T ss_pred HHHHH-HhccCCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCeEEEEEEECHH
Confidence 34443 5677789999999999999999999999999999976 4666643
No 326
>PRK09782 bacteriophage N4 receptor, outer membrane subunit; Provisional
Probab=22.74 E-value=4.3e+02 Score=31.50 Aligned_cols=45 Identities=16% Similarity=0.070 Sum_probs=30.3
Q ss_pred HHHHHhcCCChhHHHHHHHHHHHHHhcCChhhHHHHHHHHHhhcc
Q 013640 115 QMLHDRYQIGPDQIEALYQYAKFQFECGNYSGAADYLYQYRALCT 159 (439)
Q Consensus 115 ~~l~~~~g~t~e~~~al~~~ak~~y~~Gdy~~A~~~L~~~~~~~~ 159 (439)
+.+++-....|+..++++.+|..+...|+++.|.+++.....+-+
T Consensus 664 ~~l~~AL~l~P~~~~a~~nLA~al~~lGd~~eA~~~l~~Al~l~P 708 (987)
T PRK09782 664 EMLERAHKGLPDDPALIRQLAYVNQRLDDMAATQHYARLVIDDID 708 (987)
T ss_pred HHHHHHHHhCCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHhcCC
Confidence 344444555666667777777777777777777777777766554
No 327
>PRK11788 tetratricopeptide repeat protein; Provisional
Probab=22.66 E-value=7.7e+02 Score=24.54 Aligned_cols=27 Identities=19% Similarity=0.205 Sum_probs=14.1
Q ss_pred HHHHHHHHHHhcCChhhHHHHHHHHHh
Q 013640 130 ALYQYAKFQFECGNYSGAADYLYQYRA 156 (439)
Q Consensus 130 al~~~ak~~y~~Gdy~~A~~~L~~~~~ 156 (439)
.+..+|..++..|+|+.|.+++.....
T Consensus 109 ~~~~La~~~~~~g~~~~A~~~~~~~l~ 135 (389)
T PRK11788 109 ALQELGQDYLKAGLLDRAEELFLQLVD 135 (389)
T ss_pred HHHHHHHHHHHCCCHHHHHHHHHHHHc
Confidence 344555555555555555555555443
No 328
>COG4103 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=22.63 E-value=1.9e+02 Score=26.65 Aligned_cols=24 Identities=17% Similarity=0.407 Sum_probs=20.8
Q ss_pred HHHHHhcCCChhHHHHHHHHHHHH
Q 013640 115 QMLHDRYQIGPDQIEALYQYAKFQ 138 (439)
Q Consensus 115 ~~l~~~~g~t~e~~~al~~~ak~~ 138 (439)
..++++||++.+.++++..+|+=.
T Consensus 55 ~il~~~f~i~~~~l~ali~~~e~~ 78 (148)
T COG4103 55 AILKENFGIDGEELDALIEAGEEA 78 (148)
T ss_pred HHHHHHcCCCHHHHHHHHHHHHHh
Confidence 477899999999999999988743
No 329
>smart00342 HTH_ARAC helix_turn_helix, arabinose operon control protein.
Probab=22.55 E-value=1.1e+02 Score=23.01 Aligned_cols=24 Identities=25% Similarity=0.292 Sum_probs=20.4
Q ss_pred ccHHHHHHHcCCCHHHHHHHHHHH
Q 013640 358 IDMAVLAEKLNLNYEEAQRWIVNL 381 (439)
Q Consensus 358 I~I~~lA~~l~~s~~~~E~wiv~l 381 (439)
++++.||+.+|+|+.-+.+.+...
T Consensus 2 ~~~~~la~~~~~s~~~l~~~f~~~ 25 (84)
T smart00342 2 LTLEDLAEALGMSPRHLQRLFKKE 25 (84)
T ss_pred CCHHHHHHHhCCCHHHHHHHHHHH
Confidence 689999999999999887777654
No 330
>PRK11512 DNA-binding transcriptional repressor MarR; Provisional
Probab=22.41 E-value=1.5e+02 Score=26.20 Aligned_cols=47 Identities=11% Similarity=0.112 Sum_probs=40.6
Q ss_pred hccccHHHHHHHcCCCHHHHHHHHHHHhhcCccceeecccCCEEEeC
Q 013640 355 HQRIDMAVLAEKLNLNYEEAQRWIVNLIRNSKLDAKIDAKSGTVIME 401 (439)
Q Consensus 355 y~~I~I~~lA~~l~~s~~~~E~wiv~lI~~~rL~aKID~~~g~V~~~ 401 (439)
...++...||+.+|+++.-+=+-|-+|...|-+.-..|...+....-
T Consensus 52 ~~~~t~~eLa~~l~i~~~tvsr~l~~Le~~GlI~R~~~~~DrR~~~l 98 (144)
T PRK11512 52 AACITPVELKKVLSVDLGALTRMLDRLVCKGWVERLPNPNDKRGVLV 98 (144)
T ss_pred cCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEeccCcccCCeeEe
Confidence 57899999999999999999999999999998887777766655543
No 331
>PF12983 DUF3867: Protein of unknown function (DUF3867); InterPro: IPR024218 This entry represents a family of functionally uncharacterised proteins that are found in bacteria. Proteins in this family are approximately 190 amino acids in length.
Probab=22.34 E-value=2.5e+02 Score=26.65 Aligned_cols=61 Identities=16% Similarity=0.323 Sum_probs=40.1
Q ss_pred hHHHHHHHHhCCCCCChhHHHHHHHHHHHHHHHHHHHHHHHHHhhCChhHHHHhhhcchhccHH-HHHHhcCCChhHHHH
Q 013640 52 DYAMDIHKSLYHTEDVPQDMVERRVEVVARLKALEERAAPIVSFLQNPNSFQDLRANDQHYNLQ-MLHDRYQIGPDQIEA 130 (439)
Q Consensus 52 dy~~~~~~~l~~~~~~p~e~~~k~~ev~~~l~~l~~~~~~~~~~~~~~e~~~~l~~~dk~~n~~-~l~~~~g~t~e~~~a 130 (439)
+|.-.+|-.+..+.-.+.+|.++-.+-+++- .+-+ +|-.|.+ .+-|.|||+|+.++.
T Consensus 23 ~YiY~ly~~~a~Gklsm~dFsk~I~~YmeeN---------------------NISq-eKf~niQkk~mERYGfd~~~iE~ 80 (186)
T PF12983_consen 23 EYIYSLYYDVAEGKLSMADFSKKIMEYMEEN---------------------NISQ-EKFLNIQKKFMERYGFDPSEIEK 80 (186)
T ss_pred HHHHHHHHHHhcCcccHHHHHHHHHHHHHHc---------------------CCcH-HHHHHHHHHHHHHhCCCHHHHHH
Confidence 5666777777777777888888777765551 2222 3333333 344789999999998
Q ss_pred HHHH
Q 013640 131 LYQY 134 (439)
Q Consensus 131 l~~~ 134 (439)
-++-
T Consensus 81 q~K~ 84 (186)
T PF12983_consen 81 QMKS 84 (186)
T ss_pred HHHH
Confidence 7654
No 332
>PF10078 DUF2316: Uncharacterized protein conserved in bacteria (DUF2316); InterPro: IPR018757 Members of this family of hypothetical bacterial proteins have no known function.
Probab=22.15 E-value=89 Score=26.35 Aligned_cols=23 Identities=13% Similarity=0.242 Sum_probs=20.1
Q ss_pred ccccHHHHHHHcCCCHHHHHHHH
Q 013640 356 QRIDMAVLAEKLNLNYEEAQRWI 378 (439)
Q Consensus 356 ~~I~I~~lA~~l~~s~~~~E~wi 378 (439)
..++++.+|..||+|++.+|+-|
T Consensus 22 ~~ls~~~ia~dL~~s~~~le~vL 44 (89)
T PF10078_consen 22 SGLSLEQIAADLGTSPEHLEQVL 44 (89)
T ss_pred cCCCHHHHHHHhCCCHHHHHHHH
Confidence 47899999999999999988644
No 333
>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=22.07 E-value=3.3e+02 Score=25.83 Aligned_cols=65 Identities=17% Similarity=0.144 Sum_probs=51.6
Q ss_pred HHHHHHHHHHHHHHhhhhhccc-cHHHHHHHcCCCHHHHHHHHHHHhhcCccceeecccCCEEEeCCC
Q 013640 337 DEFLENARLFIFETYCRIHQRI-DMAVLAEKLNLNYEEAQRWIVNLIRNSKLDAKIDAKSGTVIMEPT 403 (439)
Q Consensus 337 ~~f~e~aR~~ife~ycriy~~I-~I~~lA~~l~~s~~~~E~wiv~lI~~~rL~aKID~~~g~V~~~~~ 403 (439)
..+.+..|..|-.--..+-..+ +-..||+.||+|..=+-+-|..|..+|-|.-+ +-.|+.+...+
T Consensus 4 ~qi~~~l~~~I~~g~~~~g~~LPsE~eLa~~~~VSR~TVR~Al~~L~~eGli~r~--~G~GtfV~~~~ 69 (230)
T TIGR02018 4 QRIKQDILERIRSGEWPPGHRIPSEHELVAQYGCSRMTVNRALRELTDAGLLERR--QGVGTFVAEPK 69 (230)
T ss_pred HHHHHHHHHHHHhCCCCCCCcCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEe--cCCEEEEccCc
Confidence 3455666777766666777888 89999999999999999999999999988543 45788886543
No 334
>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=21.96 E-value=4.5e+02 Score=22.04 Aligned_cols=46 Identities=7% Similarity=0.178 Sum_probs=37.4
Q ss_pred hccccHHHHHHHcCCCHHHHHHHHHHHhhcCccceeecccCCEEEe
Q 013640 355 HQRIDMAVLAEKLNLNYEEAQRWIVNLIRNSKLDAKIDAKSGTVIM 400 (439)
Q Consensus 355 y~~I~I~~lA~~l~~s~~~~E~wiv~lI~~~rL~aKID~~~g~V~~ 400 (439)
...++...||+.+++++.-+=+-|-+|...|-+.-.-|...+.++.
T Consensus 41 ~~~~t~~eL~~~l~~~~stvs~~i~~Le~kg~I~r~~~~~D~R~~~ 86 (109)
T TIGR01889 41 EGKLTLKEIIKEILIKQSALVKIIKKLSKKGYLSKERSEDDERKVI 86 (109)
T ss_pred CCcCcHHHHHHHHCCCHHHHHHHHHHHHHCCCEeccCCcccCCeEE
Confidence 4679999999999999999999999999999776555555544443
No 335
>cd01018 ZntC Metal binding protein ZntC. These proteins are predicted to function as initial receptors in ABC transport of metal ions. They belong to the TroA superfamily of helical backbone metal receptor proteins that share a distinct fold and ligand binding mechanism. They are comprised of two globular subdomains connected by a long alpha helix and bind their specific ligands in the cleft between these domains. In addition, many of these proteins possess a metal-binding histidine-rich motif (repetitive HDH sequence).
Probab=21.95 E-value=1.1e+02 Score=30.13 Aligned_cols=75 Identities=19% Similarity=0.146 Sum_probs=48.8
Q ss_pred HccCCCchHHHHHHHHhC-CCCCChhHHHHHHHHHHHHHHHHHHHHHHHHHhhCChhHHHHhhhcchhccHHHHHHhcCC
Q 013640 45 LNKTNMVDYAMDIHKSLY-HTEDVPQDMVERRVEVVARLKALEERAAPIVSFLQNPNSFQDLRANDQHYNLQMLHDRYQI 123 (439)
Q Consensus 45 lk~TnM~dy~~~~~~~l~-~~~~~p~e~~~k~~ev~~~l~~l~~~~~~~~~~~~~~e~~~~l~~~dk~~n~~~l~~~~g~ 123 (439)
+.+.||..++..|.+.|. -+.+--+.+++.-++.+++|++|.++++..++-+.+..++. -...+.|+.+.||+
T Consensus 116 ldp~~~~~~a~~I~~~L~~~dP~~~~~y~~N~~~~~~~L~~l~~~~~~~~~~~~~~~~v~------~H~af~Y~~~~ygl 189 (266)
T cd01018 116 LSPANAKIMAENIYEALAELDPQNATYYQANLDALLAELDALDSEIRTILSKLKQRAFMV------YHPAWGYFARDYGL 189 (266)
T ss_pred cCHHHHHHHHHHHHHHHHHhCcccHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCeEEE------ECchhHHHHHHcCC
Confidence 355677778888888775 22234456777778888888889888866654433222111 12346789999997
Q ss_pred Ch
Q 013640 124 GP 125 (439)
Q Consensus 124 t~ 125 (439)
+.
T Consensus 190 ~~ 191 (266)
T cd01018 190 TQ 191 (266)
T ss_pred EE
Confidence 64
No 336
>cd00155 RasGEF Guanine nucleotide exchange factor for Ras-like small GTPases. Small GTP-binding proteins of the Ras superfamily function as molecular switches in fundamental events such as signal transduction, cytoskeleton dynamics and intracellular trafficking. Guanine-nucleotide-exchange factors (GEFs) positively regulate these GTP-binding proteins in response to a variety of signals. GEFs catalyze the dissociation of GDP from the inactive GTP-binding proteins. GTP can then bind and induce structural changes that allow interaction with effectors.
Probab=21.90 E-value=2.5e+02 Score=26.71 Aligned_cols=63 Identities=19% Similarity=0.278 Sum_probs=46.9
Q ss_pred hhHHHHHHHHHHHHHhcCChhhHHHHHHHHHhhccccchhHHHHHHHHHHHHhhcCHHHHHHHHHHHHHHhcCC
Q 013640 125 PDQIEALYQYAKFQFECGNYSGAADYLYQYRALCTNSERRLSALWGKMAAEILMQNWDIALEELNQLKEKVDDP 198 (439)
Q Consensus 125 ~e~~~al~~~ak~~y~~Gdy~~A~~~L~~~~~~~~~~~~k~~~lwg~la~eIl~~~w~~a~~~l~klke~id~~ 198 (439)
.++++...+.|...++.|||..+..++.-+. .+.-.++...|..+.-+ ..+...+|+++++..
T Consensus 75 ~~~i~~~I~ia~~l~~l~Nfns~~aI~~~L~---~~~I~RL~~tw~~l~~~--------~~~~~~~l~~l~~~~ 137 (237)
T cd00155 75 ARLLSKFIQVAKHCRELNNFNSLMAIVSALS---SSPISRLKKTWEVLSSK--------LKKLFEELEELVDPS 137 (237)
T ss_pred HHHHHHHHHHHHHHHHhCCHHHHHHHHHHhC---CccchhHHHHHHHCCHH--------HHHHHHHHHHHhCcH
Confidence 4577788999999999999999998765544 34456888999987643 445566777777653
No 337
>TIGR02985 Sig70_bacteroi1 RNA polymerase sigma-70 factor, Bacteroides expansion family 1. This group of sigma factors are members of the sigma-70 family (TIGR02937) and are found primarily in the genus Bacteroides. This family appears to have resulted from a lineage-specific expansion as B. thetaiotaomicron VPI-5482, Bacteroides forsythus ATCC 43037, Bacteroides fragilis YCH46 and Bacteroides fragilis NCTC 9343 contain 25, 12, 24 and 23 members, respectively. There are currentlyonly two known members of this family outside of the Bacteroides, in Rhodopseudomonas and Bradyrhizobium.
Probab=21.88 E-value=1.3e+02 Score=26.05 Aligned_cols=30 Identities=13% Similarity=0.218 Sum_probs=26.0
Q ss_pred hhccccHHHHHHHcCCCHHHHHHHHHHHhh
Q 013640 354 IHQRIDMAVLAEKLNLNYEEAQRWIVNLIR 383 (439)
Q Consensus 354 iy~~I~I~~lA~~l~~s~~~~E~wiv~lI~ 383 (439)
.+...+++.+|+.+|+|+.-+...+.+..+
T Consensus 126 ~~~~~~~~eIA~~lgis~~tv~~~~~ra~~ 155 (161)
T TIGR02985 126 RFEGKSYKEIAEELGISVKTVEYHISKALK 155 (161)
T ss_pred HHcCCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 357889999999999999999999987643
No 338
>PF13429 TPR_15: Tetratricopeptide repeat; PDB: 2VQ2_A 2PL2_B.
Probab=21.83 E-value=6.2e+02 Score=24.34 Aligned_cols=79 Identities=22% Similarity=0.359 Sum_probs=53.7
Q ss_pred hccHHHHHHhcCCChhHHHHHHHHHHHHHhcCChhhHHHHHHHHHhhccccchhHHHHHHHHHHH-HhhcCHHHHHHHHH
Q 013640 111 HYNLQMLHDRYQIGPDQIEALYQYAKFQFECGNYSGAADYLYQYRALCTNSERRLSALWGKMAAE-ILMQNWDIALEELN 189 (439)
Q Consensus 111 ~~n~~~l~~~~g~t~e~~~al~~~ak~~y~~Gdy~~A~~~L~~~~~~~~~~~~k~~~lwg~la~e-Il~~~w~~a~~~l~ 189 (439)
..-+..+++-....|+..+....++.++.+.|++..+.++|..+....+++. .+|..++.- ...++-+.|..-+.
T Consensus 163 ~~A~~~~~~al~~~P~~~~~~~~l~~~li~~~~~~~~~~~l~~~~~~~~~~~----~~~~~la~~~~~lg~~~~Al~~~~ 238 (280)
T PF13429_consen 163 DKALRDYRKALELDPDDPDARNALAWLLIDMGDYDEAREALKRLLKAAPDDP----DLWDALAAAYLQLGRYEEALEYLE 238 (280)
T ss_dssp HHHHHHHHHHHHH-TT-HHHHHHHHHHHCTTCHHHHHHHHHHHHHHH-HTSC----CHCHHHHHHHHHHT-HHHHHHHHH
T ss_pred HHHHHHHHHHHHcCCCCHHHHHHHHHHHHHCCChHHHHHHHHHHHHHCcCHH----HHHHHHHHHhcccccccccccccc
Confidence 3445566666667788788889999999999999999999999888763322 244444433 33467778888777
Q ss_pred HHHH
Q 013640 190 QLKE 193 (439)
Q Consensus 190 klke 193 (439)
++..
T Consensus 239 ~~~~ 242 (280)
T PF13429_consen 239 KALK 242 (280)
T ss_dssp HHHH
T ss_pred cccc
Confidence 7655
No 339
>COG1309 AcrR Transcriptional regulator [Transcription]
Probab=21.75 E-value=1.2e+02 Score=25.69 Aligned_cols=35 Identities=14% Similarity=0.158 Sum_probs=28.1
Q ss_pred HHHHHHHHHHHHHHHhhhhhccccHHHHHHHcCCCHHH
Q 013640 336 RDEFLENARLFIFETYCRIHQRIDMAVLAEKLNLNYEE 373 (439)
Q Consensus 336 ~~~f~e~aR~~ife~ycriy~~I~I~~lA~~l~~s~~~ 373 (439)
....+..+.-++.+ +.|..+++..+|++.|+|..-
T Consensus 14 ~~~ii~aa~~l~~~---~G~~~~t~~~Ia~~agvs~~~ 48 (201)
T COG1309 14 RERILDAALRLFAE---KGYAATTVDEIAKAAGVSKGT 48 (201)
T ss_pred HHHHHHHHHHHHHH---cCcCCCCHHHHHHHhCCCcch
Confidence 45666666666666 899999999999999999653
No 340
>PRK14574 hmsH outer membrane protein; Provisional
Probab=21.72 E-value=5.1e+02 Score=30.22 Aligned_cols=92 Identities=13% Similarity=0.107 Sum_probs=57.9
Q ss_pred cCCChhHHHHHHHHHHHHHhcCChhhHHHHHHHHHhhccccchhHHHHHHHHHHHHhhcCHHHHHHHHHHHHHHhcCCCC
Q 013640 121 YQIGPDQIEALYQYAKFQFECGNYSGAADYLYQYRALCTNSERRLSALWGKMAAEILMQNWDIALEELNQLKEKVDDPKS 200 (439)
Q Consensus 121 ~g~t~e~~~al~~~ak~~y~~Gdy~~A~~~L~~~~~~~~~~~~k~~~lwg~la~eIl~~~w~~a~~~l~klke~id~~~~ 200 (439)
..+.|....-...+|.++-..|....|.+.++....+-+ ...+...|...+-.-.++|+.|.+-+.++-+......
T Consensus 443 ~~~aP~n~~l~~~~A~v~~~Rg~p~~A~~~~k~a~~l~P---~~~~~~~~~~~~al~l~e~~~A~~~~~~l~~~~Pe~~- 518 (822)
T PRK14574 443 SSTAPANQNLRIALASIYLARDLPRKAEQELKAVESLAP---RSLILERAQAETAMALQEWHQMELLTDDVISRSPEDI- 518 (822)
T ss_pred HHhCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHhhhCC---ccHHHHHHHHHHHHhhhhHHHHHHHHHHHHhhCCCch-
Confidence 334555555667778888888888888887766666522 2244444555555555899999888888877666521
Q ss_pred CCChHHHHHHHHHHHHHHHH
Q 013640 201 FTSPLNQMQSRIWLMHWSLF 220 (439)
Q Consensus 201 ~~~~l~~l~~R~WllHwsLf 220 (439)
..+.+. |.|-+|-+-+
T Consensus 519 ---~~~~l~-r~~~~h~~~~ 534 (822)
T PRK14574 519 ---PSQELD-RQRKVHNMYE 534 (822)
T ss_pred ---hHHHHH-HHHHHhhhHH
Confidence 233343 7777665544
No 341
>PRK04778 septation ring formation regulator EzrA; Provisional
Probab=21.60 E-value=1.1e+03 Score=25.99 Aligned_cols=41 Identities=15% Similarity=0.204 Sum_probs=34.1
Q ss_pred HhcCCChhHHHHHHHHHHHHHhcCChhhHHHHHHHHHhhcc
Q 013640 119 DRYQIGPDQIEALYQYAKFQFECGNYSGAADYLYQYRALCT 159 (439)
Q Consensus 119 ~~~g~t~e~~~al~~~ak~~y~~Gdy~~A~~~L~~~~~~~~ 159 (439)
..|--+.+.++.-++-|..+|+-|+|..|.+.........-
T Consensus 510 nRfr~~~~~V~~~f~~Ae~lF~~~~Y~~al~~~~~alE~ve 550 (569)
T PRK04778 510 NRYRSDNEEVAEALNEAERLFREYDYKAALEIIATALEKVE 550 (569)
T ss_pred hccCCCCHHHHHHHHHHHHHHHhCChHHHHHHHHHHHHhhC
Confidence 44555788899999999999999999999999977666553
No 342
>PF00126 HTH_1: Bacterial regulatory helix-turn-helix protein, lysR family; InterPro: IPR000847 Numerous bacterial transcription regulatory proteins bind DNA via a helix-turn-helix (HTH) motif. These proteins are very diverse, but for convenience may be grouped into subfamilies on the basis of sequence similarity. One such family, the lysR family, groups together a range of proteins, including ampR, catM, catR, cynR, cysB, gltC, iciA, ilvY, irgB, lysR, metR, mkaC, mleR, nahR, nhaR, nodD, nolR, oxyR, pssR, rbcR, syrM, tcbR, tfdS and trpI [, , , , ]. The majority of these proteins appear to be transcription activators and most are known to negatively regulate their own expression. All possess a potential HTH DNA-binding motif towards their N-termini.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent; PDB: 3T1B_D 3SZP_A 1O7L_C 1B9N_A 1B9M_A 3FZJ_J 3FXR_B 3FXQ_A 3FXU_A 2IJL_B ....
Probab=21.42 E-value=1.6e+02 Score=22.05 Aligned_cols=34 Identities=18% Similarity=0.285 Sum_probs=28.7
Q ss_pred HHHhhhhhccccHHHHHHHcCCCHHHHHHHHHHH
Q 013640 348 FETYCRIHQRIDMAVLAEKLNLNYEEAQRWIVNL 381 (439)
Q Consensus 348 fe~ycriy~~I~I~~lA~~l~~s~~~~E~wiv~l 381 (439)
++.|+.+++.=++..-|+.+|+|+.-+=+.|.++
T Consensus 4 l~~f~~v~~~gs~~~AA~~l~is~~~vs~~i~~L 37 (60)
T PF00126_consen 4 LRYFLAVAETGSISAAAEELGISQSAVSRQIKQL 37 (60)
T ss_dssp HHHHHHHHHHSSHHHHHHHCTSSHHHHHHHHHHH
T ss_pred HHHHHHHHHhCCHHHHHHHhhccchHHHHHHHHH
Confidence 4566777777899999999999999988888765
No 343
>PF02438 Adeno_100: Late 100kD protein; InterPro: IPR003381 The late 100 kDa protein is a non-structural viral protein involved in the transport of hexon from the cytoplasm to the nucleus.; GO: 0019060 intracellular transport of viral proteins in host cell
Probab=21.40 E-value=8e+02 Score=27.43 Aligned_cols=40 Identities=20% Similarity=0.417 Sum_probs=26.8
Q ss_pred ChhHHHHHHHHHHHHHHHHHHHHHHHHHhhCChhHHHHhhh
Q 013640 67 VPQDMVERRVEVVARLKALEERAAPIVSFLQNPNSFQDLRA 107 (439)
Q Consensus 67 ~p~e~~~k~~ev~~~l~~l~~~~~~~~~~~~~~e~~~~l~~ 107 (439)
-|+.++++|+.+++. -..-...+-+-++|.+|.+++.++.
T Consensus 213 d~~~l~~~Rk~~~~a-v~~t~~Le~m~rfF~~~~~ikk~qE 252 (583)
T PF02438_consen 213 DPEALEERRKNVMAA-VLVTAQLECMQRFFRSPDMIKKIQE 252 (583)
T ss_pred CHHHHHHHHHHHHHH-HHHHHHHHHHHHHhcCHHHHHHHHH
Confidence 456778887776654 2233444556778999999888764
No 344
>PRK09545 znuA high-affinity zinc transporter periplasmic component; Reviewed
Probab=21.29 E-value=1.1e+02 Score=31.08 Aligned_cols=74 Identities=14% Similarity=0.145 Sum_probs=48.3
Q ss_pred HccCCCchHHHHHHHHhC-CCCCChhHHHHHHHHHHHHHHHHHHHHHHHHHhhCChhHHHHhhhcchhccHHHHHHhcCC
Q 013640 45 LNKTNMVDYAMDIHKSLY-HTEDVPQDMVERRVEVVARLKALEERAAPIVSFLQNPNSFQDLRANDQHYNLQMLHDRYQI 123 (439)
Q Consensus 45 lk~TnM~dy~~~~~~~l~-~~~~~p~e~~~k~~ev~~~l~~l~~~~~~~~~~~~~~e~~~~l~~~dk~~n~~~l~~~~g~ 123 (439)
+.+.||..++..|.+.|. .+.+-.+.+++.-++..++|+.|+++++..+.-..+..++ --...+.|+.+.||+
T Consensus 149 ldp~~~~~~a~~I~~~L~~~dP~~~~~y~~N~~~~~~~L~~l~~~~~~~l~~~~~~~~i------~~H~af~Yf~~~ygl 222 (311)
T PRK09545 149 LSPEIARATAVAIHDKLVELMPQSKAKLDANLKDFEAQLAQTDKQIGNQLAPVKGKGYF------VFHDAYGYFEKHYGL 222 (311)
T ss_pred CCHHHHHHHHHHHHHHHHHhChhhHHHHHHHHHHHHHHHHHHHHHHHHHhhccCCCcEE------EECchHHHHHHhCCC
Confidence 345678888888888875 3333456677888888888888888886655433222211 123346788888887
Q ss_pred C
Q 013640 124 G 124 (439)
Q Consensus 124 t 124 (439)
+
T Consensus 223 ~ 223 (311)
T PRK09545 223 T 223 (311)
T ss_pred c
Confidence 5
No 345
>smart00653 eIF2B_5 domain present in translation initiation factor eIF2B and eIF5.
Probab=21.28 E-value=2.3e+02 Score=24.61 Aligned_cols=54 Identities=17% Similarity=0.322 Sum_probs=37.3
Q ss_pred ccHHHHHHHcCCCHHHHHHHHHHHhhcCccceeecccCCEEEeCCCCchhHHHHHHh
Q 013640 358 IDMAVLAEKLNLNYEEAQRWIVNLIRNSKLDAKIDAKSGTVIMEPTHPNVYEQLIDH 414 (439)
Q Consensus 358 I~I~~lA~~l~~s~~~~E~wiv~lI~~~rL~aKID~~~g~V~~~~~~~~~yqqvi~k 414 (439)
+.+..+|++||-+++.+-+++..=. -..++||.....|..++-++..-|.++++
T Consensus 22 ~Nf~~I~~~L~R~p~hv~kyl~~EL---gt~g~id~~~rlii~G~~~~~~i~~~l~~ 75 (110)
T smart00653 22 VNFADIAKALNRPPDHVLKFLLAEL---GTQGSIDGKGRLIVNGRFTPKKLQDLLRR 75 (110)
T ss_pred EcHHHHHHHHCCCHHHHHHHHHHHh---CCceeECCCCeEEEEEeeCHHHHHHHHHH
Confidence 4688999999999999888886421 23567776644455555556666666654
No 346
>TIGR02431 pcaR_pcaU beta-ketoadipate pathway transcriptional regulators, PcaR/PcaU/PobR family. Member of this family are IclR-type transcriptional regulators with similar DNA binding sites, able to bind at least three different metabolites related to protocatechuate metabolism. Beta-ketoadipate is the inducer for PcaR, p-hydroxybenzoate for PobR, and protocatechuate for PcaU.
Probab=21.26 E-value=1.6e+02 Score=28.45 Aligned_cols=42 Identities=19% Similarity=0.379 Sum_probs=36.3
Q ss_pred HHHHhhhhhccccHHHHHHHcCCCHHHHHHHHHHHhhcCccc
Q 013640 347 IFETYCRIHQRIDMAVLAEKLNLNYEEAQRWIVNLIRNSKLD 388 (439)
Q Consensus 347 ife~ycriy~~I~I~~lA~~l~~s~~~~E~wiv~lI~~~rL~ 388 (439)
|.+.+.+-...+++..||+.+|++..-+-+.+..|...|=+.
T Consensus 14 IL~~l~~~~~~~~l~eia~~lglpksT~~RlL~tL~~~G~l~ 55 (248)
T TIGR02431 14 VIEAFGAERPRLTLTDVAEATGLTRAAARRFLLTLVELGYVT 55 (248)
T ss_pred HHHHHhcCCCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCEE
Confidence 445555666789999999999999999999999999999775
No 347
>COG3160 Rsd Regulator of sigma D [Transcription]
Probab=21.25 E-value=2.4e+02 Score=25.94 Aligned_cols=72 Identities=15% Similarity=0.395 Sum_probs=43.2
Q ss_pred HHHHHHHHhhhhhccccHHH-HHHHcCCCHHHHH---HHHHHHhhcCccceeecccCCEEEeCCCCchhHHHHHHhhhhh
Q 013640 343 ARLFIFETYCRIHQRIDMAV-LAEKLNLNYEEAQ---RWIVNLIRNSKLDAKIDAKSGTVIMEPTHPNVYEQLIDHTKGL 418 (439)
Q Consensus 343 aR~~ife~ycriy~~I~I~~-lA~~l~~s~~~~E---~wiv~lI~~~rL~aKID~~~g~V~~~~~~~~~yqqvi~kt~~L 418 (439)
.|......||..- .|+- =++-.-.++...+ ..+|+.|+.|.. ++|.++++++++-
T Consensus 25 ~Rk~llvayc~l~---gikp~ke~~~plnakaL~~FCq~LvDYlSaGHF------------------~iYe~i~~k~~~~ 83 (162)
T COG3160 25 VRKHLLVAYCNLV---GIKPGKESYMPLNAKALDDFCQSLVDYLSAGHF------------------SIYERILHKLEGN 83 (162)
T ss_pred HHHHHHHHHHHHh---ccCccccccCCCCHHHHHHHHHHHHHHHhccch------------------HHHHHHHHHHhcc
Confidence 5666667777541 1111 0011112444444 345666666644 7999999999999
Q ss_pred hhHHHHHHHHHHhhhhh
Q 013640 419 SGRTYKLVGQLLEHAQT 435 (439)
Q Consensus 419 ~~R~q~L~~~i~~~~~~ 435 (439)
..|--.++..|-....+
T Consensus 84 g~~~l~la~kI~p~l~a 100 (162)
T COG3160 84 GDRQLALAAKIWPQLEA 100 (162)
T ss_pred CcHHHHHHHHHHHHHHh
Confidence 99887777777654443
No 348
>PRK09764 DNA-binding transcriptional repressor MngR; Provisional
Probab=21.07 E-value=4e+02 Score=25.51 Aligned_cols=68 Identities=16% Similarity=0.213 Sum_probs=55.4
Q ss_pred ccHHHHHHHHHHHHHHHhhhhhccc-cHHHHHHHcCCCHHHHHHHHHHHhhcCccceeecccCCEEEeCCC
Q 013640 334 PLRDEFLENARLFIFETYCRIHQRI-DMAVLAEKLNLNYEEAQRWIVNLIRNSKLDAKIDAKSGTVIMEPT 403 (439)
Q Consensus 334 ~~~~~f~e~aR~~ife~ycriy~~I-~I~~lA~~l~~s~~~~E~wiv~lI~~~rL~aKID~~~g~V~~~~~ 403 (439)
+....+.+..|..|-.--..+-..+ +-..||+.||||..=+-+-|..|..+|-|..+ +-.|+.+....
T Consensus 5 ply~qi~~~L~~~I~~g~~~~G~~LPsE~eL~~~~~VSR~TvR~Al~~L~~eGli~r~--~G~GtfV~~~~ 73 (240)
T PRK09764 5 PLYRQIADRIREQIARGELKPGDALPTESALQTEFGVSRVTVRQALRQLVEQQILESI--QGSGTYVKEER 73 (240)
T ss_pred cHHHHHHHHHHHHHHcCCCCCCCcCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEe--cCceeEEcccc
Confidence 3456677777888877777888888 78999999999999999999999999988644 45788886543
No 349
>PF05920 Homeobox_KN: Homeobox KN domain; InterPro: IPR008422 This entry represents a homeobox transcription factor KN domain conserved from fungi to human and plants [].; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent, 0005634 nucleus; PDB: 3K2A_B 2LK2_A 1X2N_A 2DMN_A.
Probab=20.86 E-value=1.1e+02 Score=21.62 Aligned_cols=31 Identities=16% Similarity=0.280 Sum_probs=22.5
Q ss_pred hhhhhcccc-HHHHHHHcCCCHHHHHHHHHHH
Q 013640 351 YCRIHQRID-MAVLAEKLNLNYEEAQRWIVNL 381 (439)
Q Consensus 351 ycriy~~I~-I~~lA~~l~~s~~~~E~wiv~l 381 (439)
.--||.+-. ..+||+.-|+|...+..|.+|.
T Consensus 6 ~~nPYPs~~ek~~L~~~tgls~~Qi~~WF~Na 37 (40)
T PF05920_consen 6 LHNPYPSKEEKEELAKQTGLSRKQISNWFINA 37 (40)
T ss_dssp TTSGS--HHHHHHHHHHHTS-HHHHHHHHHHH
T ss_pred CCCCCCCHHHHHHHHHHcCCCHHHHHHHHHHh
Confidence 345666655 5679999999999999999984
No 350
>KOG0548 consensus Molecular co-chaperone STI1 [Posttranslational modification, protein turnover, chaperones]
Probab=20.76 E-value=1.2e+03 Score=25.98 Aligned_cols=24 Identities=17% Similarity=0.142 Sum_probs=12.5
Q ss_pred HHHHHHhcCChhhHHHHHHHHHhh
Q 013640 134 YAKFQFECGNYSGAADYLYQYRAL 157 (439)
Q Consensus 134 ~ak~~y~~Gdy~~A~~~L~~~~~~ 157 (439)
.|+-+|..|||..|.+.+......
T Consensus 364 kGne~Fk~gdy~~Av~~YteAIkr 387 (539)
T KOG0548|consen 364 KGNEAFKKGDYPEAVKHYTEAIKR 387 (539)
T ss_pred HHHHHHhccCHHHHHHHHHHHHhc
Confidence 355555555555555555554433
No 351
>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=20.58 E-value=8.7e+02 Score=24.34 Aligned_cols=159 Identities=20% Similarity=0.341 Sum_probs=82.0
Q ss_pred HHHHHHHHhcCChhhHHHHHHHHHhhccccchhHHHHHHHHHHHHhhcCHHHHHHHHHHHHHHhcCCCCCCChHHHHHHH
Q 013640 132 YQYAKFQFECGNYSGAADYLYQYRALCTNSERRLSALWGKMAAEILMQNWDIALEELNQLKEKVDDPKSFTSPLNQMQSR 211 (439)
Q Consensus 132 ~~~ak~~y~~Gdy~~A~~~L~~~~~~~~~~~~k~~~lwg~la~eIl~~~w~~a~~~l~klke~id~~~~~~~~l~~l~~R 211 (439)
+--|..++..|+++.|.+.+.. +..+.++--.+-+-+.++..|.|.+.++++++.-|. +.+.++-+
T Consensus 106 ~~~A~i~~~~~~~~~AL~~l~~--------~~~lE~~al~Vqi~L~~~R~dlA~k~l~~~~~~~eD-----~~l~qLa~- 171 (290)
T PF04733_consen 106 LLAATILFHEGDYEEALKLLHK--------GGSLELLALAVQILLKMNRPDLAEKELKNMQQIDED-----SILTQLAE- 171 (290)
T ss_dssp HHHHHHHCCCCHHHHHHCCCTT--------TTCHHHHHHHHHHHHHTT-HHHHHHHHHHHHCCSCC-----HHHHHHHH-
T ss_pred HHHHHHHHHcCCHHHHHHHHHc--------cCcccHHHHHHHHHHHcCCHHHHHHHHHHHHhcCCc-----HHHHHHHH-
Confidence 4457788999999999986643 234555544555556688899999999998775333 34555543
Q ss_pred HHHHHHHHHHHhcCc----cchHHHHHHhccccchhHHHhhchhHHHHHHHHHHHhcccccchHHHHHHHhhhccC-Ccc
Q 013640 212 IWLMHWSLFIFFNHD----NGRTLIIDLFNQDKYLNAIQTNAPHLLRYLATAFIVNKRRRPQFKDFIKVIQQEQNS-YKD 286 (439)
Q Consensus 212 ~WllHwsLf~~fn~~----~~~~~l~d~F~~~~yl~~Iqt~~p~lLrYlvva~il~~~r~~~l~~i~~vi~qe~~~-Y~D 286 (439)
+|. -+.... ++...|-|+ +.+|-+ .|.+|--.+++.|.. ..+++-.+++.+.-.. =.|
T Consensus 172 awv------~l~~g~e~~~~A~y~f~El--~~~~~~-----t~~~lng~A~~~l~~----~~~~eAe~~L~~al~~~~~~ 234 (290)
T PF04733_consen 172 AWV------NLATGGEKYQDAFYIFEEL--SDKFGS-----TPKLLNGLAVCHLQL----GHYEEAEELLEEALEKDPND 234 (290)
T ss_dssp HHH------HHHHTTTCCCHHHHHHHHH--HCCS-------SHHHHHHHHHHHHHC----T-HHHHHHHHHHHCCC-CCH
T ss_pred HHH------HHHhCchhHHHHHHHHHHH--HhccCC-----CHHHHHHHHHHHHHh----CCHHHHHHHHHHHHHhccCC
Confidence 443 233332 122222221 223322 234555555555553 2344444444442110 013
Q ss_pred h--HHHHHHH-hhhcCChhHHHHHHHHHHHHhcCCccc
Q 013640 287 P--ITEFLAC-VYVNYDFDGAQKKMKECEEVILNDPFL 321 (439)
Q Consensus 287 p--it~f~~~-lY~~fdF~~aq~~L~~~e~~i~~D~FL 321 (439)
| +.+++.| .+..-+=+.+.+.+.+..+.-.+-+|+
T Consensus 235 ~d~LaNliv~~~~~gk~~~~~~~~l~qL~~~~p~h~~~ 272 (290)
T PF04733_consen 235 PDTLANLIVCSLHLGKPTEAAERYLSQLKQSNPNHPLV 272 (290)
T ss_dssp HHHHHHHHHHHHHTT-TCHHHHHHHHHCHHHTTTSHHH
T ss_pred HHHHHHHHHHHHHhCCChhHHHHHHHHHHHhCCCChHH
Confidence 3 5555544 344344345566666666655555555
No 352
>KOG1174 consensus Anaphase-promoting complex (APC), subunit 7 [Cell cycle control, cell division, chromosome partitioning; Posttranslational modification, protein turnover, chaperones]
Probab=20.51 E-value=9.6e+02 Score=26.23 Aligned_cols=114 Identities=12% Similarity=0.190 Sum_probs=71.6
Q ss_pred HHHHHHHccCCCchHHHHHHHHhCCCCCChhHHHHHHHHHHHHHHHHHHHHHHHH-----HhhCChhHHHHhhhcchhcc
Q 013640 39 KSKIELLNKTNMVDYAMDIHKSLYHTEDVPQDMVERRVEVVARLKALEERAAPIV-----SFLQNPNSFQDLRANDQHYN 113 (439)
Q Consensus 39 ~a~~~llk~TnM~dy~~~~~~~l~~~~~~p~e~~~k~~ev~~~l~~l~~~~~~~~-----~~~~~~e~~~~l~~~dk~~n 113 (439)
+|.+.-=...|..||=-++|+.|-..=-....+++...-.-..++.+.+.++.+. -.++||--++.-+
T Consensus 352 ~A~IaFR~Aq~Lap~rL~~Y~GL~hsYLA~~~~kEA~~~An~~~~~~~~sA~~LtL~g~~V~~~dp~~rEKAK------- 424 (564)
T KOG1174|consen 352 QAVIAFRTAQMLAPYRLEIYRGLFHSYLAQKRFKEANALANWTIRLFQNSARSLTLFGTLVLFPDPRMREKAK------- 424 (564)
T ss_pred HHHHHHHHHHhcchhhHHHHHHHHHHHHhhchHHHHHHHHHHHHHHhhcchhhhhhhcceeeccCchhHHHHH-------
Confidence 3444444456777788888877631100112233332222223344555554322 2346665443333
Q ss_pred HHHHHHhcCCChhHHHHHHHHHHHHHhcCChhhHHHHHHHHHhhccc
Q 013640 114 LQMLHDRYQIGPDQIEALYQYAKFQFECGNYSGAADYLYQYRALCTN 160 (439)
Q Consensus 114 ~~~l~~~~g~t~e~~~al~~~ak~~y~~Gdy~~A~~~L~~~~~~~~~ 160 (439)
.++++...+.|..+.|..++|.+...-|.|+++..+|..+...-++
T Consensus 425 -kf~ek~L~~~P~Y~~AV~~~AEL~~~Eg~~~D~i~LLe~~L~~~~D 470 (564)
T KOG1174|consen 425 -KFAEKSLKINPIYTPAVNLIAELCQVEGPTKDIIKLLEKHLIIFPD 470 (564)
T ss_pred -HHHHhhhccCCccHHHHHHHHHHHHhhCccchHHHHHHHHHhhccc
Confidence 4778888899999999999999999999999999999988876544
No 353
>COG3413 Predicted DNA binding protein [General function prediction only]
Probab=20.41 E-value=1.5e+02 Score=28.25 Aligned_cols=48 Identities=23% Similarity=0.243 Sum_probs=36.0
Q ss_pred cHHHHHHHHHHHHHHHhhhhhccccHHHHHHHcCCCHHHHHHHHHHHh
Q 013640 335 LRDEFLENARLFIFETYCRIHQRIDMAVLAEKLNLNYEEAQRWIVNLI 382 (439)
Q Consensus 335 ~~~~f~e~aR~~ife~ycriy~~I~I~~lA~~l~~s~~~~E~wiv~lI 382 (439)
.++.=++-+|...=.-|-..=++++++.||+.||+|+.-+..-|-+..
T Consensus 156 LTdrQ~~vL~~A~~~GYFd~PR~~~l~dLA~~lGISkst~~ehLRrAe 203 (215)
T COG3413 156 LTDRQLEVLRLAYKMGYFDYPRRVSLKDLAKELGISKSTLSEHLRRAE 203 (215)
T ss_pred CCHHHHHHHHHHHHcCCCCCCccCCHHHHHHHhCCCHHHHHHHHHHHH
Confidence 455445555555555677888999999999999999998777665543
No 354
>PF06969 HemN_C: HemN C-terminal domain; InterPro: IPR010723 Proteins containing this domain are all oxygen-independent coproporphyrinogen-III oxidases (HemN). This enzyme catalyses the oxygen-independent conversion of coproporphyrinogen-III to protoporphyrinogen-IX [], one of the last steps in haem biosynthesis. The function of this domain is unclear, but comparison to other proteins containing a radical SAM domain suggest it may be a substrate binding domain.; GO: 0004109 coproporphyrinogen oxidase activity, 0006779 porphyrin-containing compound biosynthetic process, 0055114 oxidation-reduction process, 0005737 cytoplasm; PDB: 1OLT_A.
Probab=20.41 E-value=2.4e+02 Score=21.26 Aligned_cols=46 Identities=17% Similarity=0.432 Sum_probs=32.0
Q ss_pred hhhccccHHHHHHHcCCCHHHH-HHHHHHHhhcCccceeecccCCEEEeCC
Q 013640 353 RIHQRIDMAVLAEKLNLNYEEA-QRWIVNLIRNSKLDAKIDAKSGTVIMEP 402 (439)
Q Consensus 353 riy~~I~I~~lA~~l~~s~~~~-E~wiv~lI~~~rL~aKID~~~g~V~~~~ 402 (439)
|....|+++.+.+++|.+..+. .+-|..++.+|-+. -.+|.+..+.
T Consensus 16 R~~~Gi~~~~~~~~~g~~~~~~~~~~l~~l~~~Gll~----~~~~~l~lT~ 62 (66)
T PF06969_consen 16 RCNEGIDLSEFEQRFGIDFAEEFQKELEELQEDGLLE----IDGGRLRLTE 62 (66)
T ss_dssp HHHSEEEHHHHHHHTT--THHH-HHHHHHHHHTTSEE----E-SSEEEE-T
T ss_pred HhHCCcCHHHHHHHHCcCHHHHHHHHHHHHHHCCCEE----EeCCEEEECc
Confidence 5578999999999999985544 77799999988662 2456666543
No 355
>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=20.35 E-value=1.6e+02 Score=30.48 Aligned_cols=43 Identities=23% Similarity=0.265 Sum_probs=39.4
Q ss_pred HHHHHhhhhhccccHHHHHHH--cCCCHHHHHHHHHHHhhcCccc
Q 013640 346 FIFETYCRIHQRIDMAVLAEK--LNLNYEEAQRWIVNLIRNSKLD 388 (439)
Q Consensus 346 ~ife~ycriy~~I~I~~lA~~--l~~s~~~~E~wiv~lI~~~rL~ 388 (439)
.|.+.|++-.+.|+.+.||+. ||+|++=+-+.+..|-..|-|.
T Consensus 10 aIV~~~l~~~~pv~s~~l~~~~~~~vS~aTiR~d~~~Le~~G~l~ 54 (337)
T TIGR00331 10 AIVEEYIKTGQPVGSKTLLEKYNLGLSSATIRNDMADLEDLGFIE 54 (337)
T ss_pred HHHHHHHhcCCCcCHHHHHhhcCCCCChHHHHHHHHHHHHCCCcc
Confidence 467899999999999999999 9999999999999998888663
No 356
>COG1516 FliS Flagellin-specific chaperone FliS [Cell motility and secretion / Intracellular trafficking and secretion / Posttranslational modification, protein turnover, chaperones]
Probab=20.29 E-value=5.4e+02 Score=23.31 Aligned_cols=85 Identities=14% Similarity=0.237 Sum_probs=48.7
Q ss_pred HHHHHHHHHHHHHHhcCCCCCCChHHHHHHHHHHHHHHHHHHhcCccchHHHHHHhccccchhHHHhhchhHHHHHHHHH
Q 013640 181 WDIALEELNQLKEKVDDPKSFTSPLNQMQSRIWLMHWSLFIFFNHDNGRTLIIDLFNQDKYLNAIQTNAPHLLRYLATAF 260 (439)
Q Consensus 181 w~~a~~~l~klke~id~~~~~~~~l~~l~~R~WllHwsLf~~fn~~~~~~~l~d~F~~~~yl~~Iqt~~p~lLrYlvva~ 260 (439)
+|.|.+.+.+++..|+. ++|......+. |+=-+--+|=..-|+++|-+.- .+ +.+-|.++++=|+-|.
T Consensus 28 yeg~l~~l~~A~~aie~-~~i~~k~~~i~-ka~~Ii~eL~~~Ld~E~Ggeia-------~n---L~~LY~y~~~rL~~AN 95 (132)
T COG1516 28 YEGALKFLKRAKEAIEQ-EDIEEKNESID-KAIDIITELRASLDYEKGGEIA-------QN---LDALYDYMVRRLVQAN 95 (132)
T ss_pred HHHHHHHHHHHHHHHHh-ccHHHHHHHHH-HHHHHHHHHHHhcCHhhcchHH-------HH---HHHHHHHHHHHHHHHH
Confidence 46899999999999999 67743333222 2222222555555666654333 22 3345777888888888
Q ss_pred HHhcccccchHHHHHHHhh
Q 013640 261 IVNKRRRPQFKDFIKVIQQ 279 (439)
Q Consensus 261 il~~~r~~~l~~i~~vi~q 279 (439)
+.+- ...+.++..++.+
T Consensus 96 l~nd--~~~i~eV~~ll~~ 112 (132)
T COG1516 96 LKND--ASKIDEVIGLLRE 112 (132)
T ss_pred hccC--HHHHHHHHHHHHH
Confidence 7642 2334444444443
No 357
>PRK12537 RNA polymerase sigma factor; Provisional
Probab=20.16 E-value=1.3e+02 Score=27.33 Aligned_cols=46 Identities=17% Similarity=0.312 Sum_probs=34.4
Q ss_pred cHHHHHHHHHHHHHHHhhhhhccccHHHHHHHcCCCHHHHHHHHHHHhh
Q 013640 335 LRDEFLENARLFIFETYCRIHQRIDMAVLAEKLNLNYEEAQRWIVNLIR 383 (439)
Q Consensus 335 ~~~~f~e~aR~~ife~ycriy~~I~I~~lA~~l~~s~~~~E~wiv~lI~ 383 (439)
..+.+=+..|..+.-.| +...+++.+|+.+|+|+.-+..++.+...
T Consensus 130 ~l~~L~~~~r~i~~l~~---~~~~s~~eIA~~lgis~~tV~~~l~ra~~ 175 (182)
T PRK12537 130 CLEQLEPARRNCILHAY---VDGCSHAEIAQRLGAPLGTVKAWIKRSLK 175 (182)
T ss_pred HHHhCCHHHHHHHHHHH---HcCCCHHHHHHHHCCChhhHHHHHHHHHH
Confidence 34444455555444433 68899999999999999999999988654
No 358
>PRK09782 bacteriophage N4 receptor, outer membrane subunit; Provisional
Probab=20.06 E-value=1.5e+03 Score=27.01 Aligned_cols=77 Identities=5% Similarity=0.039 Sum_probs=50.4
Q ss_pred HHHHHhcCCChhHHHHHHHHHHHHHhcCChhhHHHHHHHHHhhccccchhHHHHHHHHHHHHhhcCHHHHHHHHHHHHHH
Q 013640 115 QMLHDRYQIGPDQIEALYQYAKFQFECGNYSGAADYLYQYRALCTNSERRLSALWGKMAAEILMQNWDIALEELNQLKEK 194 (439)
Q Consensus 115 ~~l~~~~g~t~e~~~al~~~ak~~y~~Gdy~~A~~~L~~~~~~~~~~~~k~~~lwg~la~eIl~~~w~~a~~~l~klke~ 194 (439)
..+++-....|+...+...+|.++.+.|+++.|.+.+......-+++ ..+.+..=.+-...++.+.|.+.+.++-++
T Consensus 630 ~~l~~AL~l~Pd~~~a~~nLG~aL~~~G~~eeAi~~l~~AL~l~P~~---~~a~~nLA~al~~lGd~~eA~~~l~~Al~l 706 (987)
T PRK09782 630 SDLRAALELEPNNSNYQAALGYALWDSGDIAQSREMLERAHKGLPDD---PALIRQLAYVNQRLDDMAATQHYARLVIDD 706 (987)
T ss_pred HHHHHHHHhCCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhCCCC---HHHHHHHHHHHHHCCCHHHHHHHHHHHHhc
Confidence 34555556677777777888888888888888888777766654432 234444444555667777887766666443
No 359
>COG1522 Lrp Transcriptional regulators [Transcription]
Probab=20.02 E-value=1.6e+02 Score=25.83 Aligned_cols=39 Identities=31% Similarity=0.331 Sum_probs=33.8
Q ss_pred hccccHHHHHHHcCCCHHHHHHHHHHHhhcCc---cceeecc
Q 013640 355 HQRIDMAVLAEKLNLNYEEAQRWIVNLIRNSK---LDAKIDA 393 (439)
Q Consensus 355 y~~I~I~~lA~~l~~s~~~~E~wiv~lI~~~r---L~aKID~ 393 (439)
-.++++..||+++|+|+..+=+-|-+|..+|- ..|.+|.
T Consensus 20 d~r~~~~eia~~lglS~~~v~~Ri~~L~~~GiI~~~~~~v~~ 61 (154)
T COG1522 20 DARISNAELAERVGLSPSTVLRRIKRLEEEGVIKGYTAVLDP 61 (154)
T ss_pred hCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCceeeEEEEECH
Confidence 34489999999999999999999999999994 4577775
Done!