Query 001809
Match_columns 1010
No_of_seqs 244 out of 356
Neff 4.2
Searched_HMMs 46136
Date Fri Mar 29 09:50:06 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/001809.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/001809hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 cd06407 PB1_NLP A PB1 domain i 99.9 3.6E-28 7.7E-33 220.0 9.9 81 903-983 1-82 (82)
2 cd06409 PB1_MUG70 The MUG70 pr 99.9 1.4E-27 2.9E-32 217.9 10.4 81 903-984 3-86 (86)
3 cd06396 PB1_NBR1 The PB1 domai 99.9 6.7E-26 1.4E-30 204.6 10.2 78 903-983 1-80 (81)
4 PF02042 RWP-RK: RWP-RK domain 99.9 2.8E-23 6E-28 173.5 5.4 51 599-649 2-52 (52)
5 cd06398 PB1_Joka2 The PB1 doma 99.8 4.2E-20 9E-25 170.7 9.9 81 903-983 1-88 (91)
6 PF00564 PB1: PB1 domain; Int 99.7 3.6E-16 7.8E-21 139.1 10.0 82 902-983 1-83 (84)
7 smart00666 PB1 PB1 domain. Pho 99.6 2.3E-15 5.1E-20 133.6 9.8 81 902-982 1-81 (81)
8 cd05992 PB1 The PB1 domain is 99.6 1.2E-14 2.5E-19 128.6 9.2 80 903-982 1-81 (81)
9 cd06404 PB1_aPKC PB1 domain is 99.0 8.6E-10 1.9E-14 100.7 9.1 79 903-983 1-80 (83)
10 cd06408 PB1_NoxR The PB1 domai 98.8 1.4E-08 3E-13 93.8 8.4 68 902-971 2-69 (86)
11 cd06402 PB1_p62 The PB1 domain 98.7 3.1E-08 6.8E-13 91.7 8.5 78 903-983 1-86 (87)
12 cd06401 PB1_TFG The PB1 domain 98.7 5.6E-08 1.2E-12 88.7 8.4 75 904-981 2-80 (81)
13 cd06397 PB1_UP1 Uncharacterize 98.7 6.1E-08 1.3E-12 88.2 8.3 81 903-983 1-81 (82)
14 cd06403 PB1_Par6 The PB1 domai 98.0 1.6E-05 3.4E-10 72.6 7.8 75 904-982 2-78 (80)
15 cd06406 PB1_P67 A PB1 domain i 97.6 0.00012 2.6E-09 67.3 6.6 68 902-971 2-70 (80)
16 PF14215 bHLH-MYC_N: bHLH-MYC 96.9 0.0018 3.8E-08 66.5 6.2 67 217-298 81-147 (163)
17 cd06411 PB1_p51 The PB1 domain 96.7 0.0043 9.3E-08 57.0 6.5 58 913-970 8-67 (78)
18 PF14215 bHLH-MYC_N: bHLH-MYC 96.4 0.0023 5E-08 65.6 3.5 71 409-488 79-149 (163)
19 KOG0695 Serine/threonine prote 96.4 0.017 3.6E-07 65.6 9.9 83 900-982 13-96 (593)
20 cd06410 PB1_UP2 Uncharacterize 96.0 0.039 8.4E-07 52.6 8.9 74 907-981 17-96 (97)
21 PRK15429 formate hydrogenlyase 95.9 0.12 2.6E-06 63.4 14.7 236 234-506 77-338 (686)
22 cd06405 PB1_Mekk2_3 The PB1 do 95.4 0.078 1.7E-06 48.7 8.0 76 903-982 1-77 (79)
23 PF13185 GAF_2: GAF domain; PD 94.4 0.2 4.3E-06 47.1 8.4 137 164-314 3-139 (148)
24 PF01418 HTH_6: Helix-turn-hel 93.0 0.1 2.2E-06 47.1 3.6 40 604-643 26-65 (77)
25 PF02796 HTH_7: Helix-turn-hel 92.9 0.1 2.3E-06 42.7 3.2 32 604-635 11-44 (45)
26 TIGR01764 excise DNA binding d 91.5 0.19 4.1E-06 39.9 3.1 28 613-640 2-29 (49)
27 PF02954 HTH_8: Bacterial regu 91.4 0.29 6.2E-06 39.6 4.0 29 608-636 14-42 (42)
28 PF11470 TUG-UBL1: GLUT4 regul 90.7 0.39 8.4E-06 42.9 4.6 42 907-948 2-43 (65)
29 cd04762 HTH_MerR-trunc Helix-T 90.6 0.31 6.8E-06 38.3 3.5 27 613-639 1-27 (49)
30 cd01812 BAG1_N Ubiquitin-like 90.2 0.68 1.5E-05 40.1 5.6 46 903-948 1-46 (71)
31 smart00213 UBQ Ubiquitin homol 90.0 1 2.2E-05 37.6 6.3 56 903-965 3-58 (64)
32 PF12728 HTH_17: Helix-turn-he 89.7 0.33 7.1E-06 40.0 3.1 29 613-641 2-30 (51)
33 PF01590 GAF: GAF domain; Int 89.0 2 4.4E-05 40.6 8.3 132 165-314 2-146 (154)
34 PF13542 HTH_Tnp_ISL3: Helix-t 88.9 0.39 8.6E-06 39.5 3.0 41 596-636 10-51 (52)
35 PRK00430 fis global DNA-bindin 88.9 0.57 1.2E-05 44.6 4.4 33 606-638 62-94 (95)
36 PF01527 HTH_Tnp_1: Transposas 88.1 0.47 1E-05 41.6 3.1 67 594-660 3-74 (76)
37 PRK09413 IS2 repressor TnpA; R 87.7 1.4 3.1E-05 43.0 6.4 42 596-637 11-54 (121)
38 PF09379 FERM_N: FERM N-termin 86.9 1.5 3.3E-05 38.9 5.7 53 912-964 7-61 (80)
39 cd01809 Scythe_N Ubiquitin-lik 86.7 2 4.3E-05 37.2 6.1 57 903-965 3-59 (72)
40 PRK11061 fused phosphoenolpyru 86.6 5.3 0.00011 50.4 12.1 126 162-309 15-141 (748)
41 smart00065 GAF Domain present 86.4 13 0.00028 33.0 11.4 122 165-309 2-126 (149)
42 PF13936 HTH_38: Helix-turn-he 86.1 0.65 1.4E-05 38.0 2.7 26 611-636 19-44 (44)
43 PF02001 DUF134: Protein of un 85.7 0.97 2.1E-05 44.1 4.1 36 599-634 39-79 (106)
44 cd04761 HTH_MerR-SF Helix-Turn 85.2 0.9 1.9E-05 36.5 3.1 31 613-645 1-31 (49)
45 PRK01905 DNA-binding protein F 85.2 1.3 2.7E-05 40.4 4.3 30 609-638 47-76 (77)
46 smart00342 HTH_ARAC helix_turn 84.9 1.2 2.5E-05 38.4 3.9 35 612-646 1-36 (84)
47 smart00295 B41 Band 4.1 homolo 84.9 4 8.6E-05 41.6 8.3 65 902-966 3-70 (207)
48 PF13384 HTH_23: Homeodomain-l 84.7 0.99 2.2E-05 36.9 3.1 25 612-636 17-41 (50)
49 PF13185 GAF_2: GAF domain; PD 84.6 2.3 5E-05 40.0 6.0 77 423-505 67-143 (148)
50 PF03472 Autoind_bind: Autoind 84.4 3.4 7.4E-05 39.5 7.2 98 408-507 44-147 (149)
51 PRK11302 DNA-binding transcrip 84.4 0.79 1.7E-05 49.7 3.2 36 607-642 29-64 (284)
52 PRK11608 pspF phage shock prot 84.3 1.1 2.5E-05 50.4 4.4 30 609-638 296-325 (326)
53 cd01763 Sumo Small ubiquitin-r 83.8 4.5 9.9E-05 37.4 7.4 75 900-983 9-84 (87)
54 cd04763 HTH_MlrA-like Helix-Tu 83.8 1.1 2.3E-05 39.1 3.2 27 613-639 1-27 (68)
55 PRK11361 acetoacetate metaboli 83.8 1.1 2.5E-05 51.5 4.3 31 609-639 427-457 (457)
56 cd01806 Nedd8 Nebb8-like ubiq 83.7 7 0.00015 34.1 8.2 71 903-983 3-73 (76)
57 PF14560 Ubiquitin_2: Ubiquiti 83.6 5.4 0.00012 36.6 7.8 79 904-985 3-84 (87)
58 PRK15115 response regulator Gl 83.2 1.3 2.8E-05 51.1 4.4 31 609-639 408-438 (444)
59 PRK15482 transcriptional regul 83.1 0.94 2E-05 49.6 3.1 41 604-644 26-66 (285)
60 TIGR01817 nifA Nif-specific re 83.1 8.1 0.00018 46.4 11.1 125 162-307 17-141 (534)
61 cd04764 HTH_MlrA-like_sg1 Heli 81.8 1.5 3.3E-05 38.0 3.3 27 613-639 1-27 (67)
62 COG3284 AcoR Transcriptional a 81.7 1.2 2.6E-05 54.4 3.5 32 609-640 575-606 (606)
63 TIGR02915 PEP_resp_reg putativ 81.5 1.7 3.6E-05 50.2 4.5 31 609-639 415-445 (445)
64 PRK10820 DNA-binding transcrip 81.2 1.7 3.7E-05 52.2 4.6 26 614-639 488-513 (520)
65 PRK05022 anaerobic nitric oxid 81.1 1.7 3.8E-05 51.8 4.6 123 162-307 16-141 (509)
66 TIGR01817 nifA Nif-specific re 80.9 2.6 5.7E-05 50.4 6.0 89 417-509 67-156 (534)
67 PF11543 UN_NPL4: Nuclear pore 80.8 2.9 6.2E-05 38.7 4.9 48 902-950 4-51 (80)
68 cd01104 HTH_MlrA-CarA Helix-Tu 80.8 1.8 4E-05 37.2 3.5 26 613-638 1-26 (68)
69 COG1737 RpiR Transcriptional r 80.6 1.1 2.3E-05 49.7 2.4 38 609-646 33-70 (281)
70 PF11976 Rad60-SLD: Ubiquitin- 80.1 4.6 0.0001 35.3 5.8 44 904-947 2-47 (72)
71 PRK10923 glnG nitrogen regulat 80.0 2 4.3E-05 50.0 4.5 31 609-639 439-469 (469)
72 PRK11557 putative DNA-binding 79.8 1.4 3E-05 47.9 3.0 36 609-644 27-62 (278)
73 TIGR03070 couple_hipB transcri 79.7 4.6 0.0001 33.0 5.4 31 604-634 7-37 (58)
74 PRK10219 DNA-binding transcrip 79.2 3.2 6.8E-05 39.0 4.8 35 605-639 12-49 (107)
75 PF01381 HTH_3: Helix-turn-hel 79.1 3.9 8.4E-05 33.7 4.7 37 604-643 1-37 (55)
76 PRK11337 DNA-binding transcrip 78.1 1.7 3.7E-05 47.6 3.0 35 608-642 42-76 (292)
77 PF04967 HTH_10: HTH DNA bindi 78.0 2.3 5E-05 36.8 3.1 28 608-635 15-46 (53)
78 PF04545 Sigma70_r4: Sigma-70, 77.1 3.5 7.5E-05 34.0 3.9 30 606-635 12-43 (50)
79 PRK13413 mpi multiple promoter 77.0 2.2 4.8E-05 44.6 3.4 28 612-639 172-199 (200)
80 PF13492 GAF_3: GAF domain; PD 76.9 20 0.00042 32.9 9.2 118 165-314 2-119 (129)
81 cd01789 Alp11_N Ubiquitin-like 76.7 12 0.00026 34.6 7.6 52 903-954 4-55 (84)
82 PRK11388 DNA-binding transcrip 75.8 3.1 6.8E-05 50.8 4.7 35 609-643 601-635 (638)
83 cd01796 DDI1_N DNA damage indu 75.5 5.9 0.00013 35.2 5.1 49 903-951 1-53 (71)
84 PF01710 HTH_Tnp_IS630: Transp 74.7 3.9 8.4E-05 39.9 4.1 33 607-639 66-98 (119)
85 PF00356 LacI: Bacterial regul 74.6 4.9 0.00011 33.6 4.1 23 614-636 1-23 (46)
86 cd01803 Ubiquitin Ubiquitin. U 73.3 6.7 0.00014 34.2 4.9 70 903-982 3-72 (76)
87 COG1342 Predicted DNA-binding 73.0 3.5 7.6E-05 39.8 3.2 35 598-632 30-69 (99)
88 cd01808 hPLIC_N Ubiquitin-like 72.9 16 0.00035 32.1 7.2 42 903-946 3-44 (71)
89 cd01792 ISG15_repeat1 ISG15 ub 72.8 8.2 0.00018 35.0 5.5 75 902-984 4-78 (80)
90 PF13443 HTH_26: Cro/C1-type H 72.7 5.4 0.00012 33.9 4.0 45 605-650 3-47 (63)
91 PRK12515 RNA polymerase sigma 72.2 4.6 0.0001 41.3 4.2 28 606-633 141-168 (189)
92 PRK13182 racA polar chromosome 71.7 3.5 7.6E-05 43.4 3.3 27 613-639 1-27 (175)
93 COG1476 Predicted transcriptio 71.5 4.9 0.00011 36.6 3.6 31 604-634 6-36 (68)
94 smart00422 HTH_MERR helix_turn 71.3 7.6 0.00017 33.4 4.7 26 613-638 1-26 (70)
95 PF13518 HTH_28: Helix-turn-he 71.0 4.3 9.4E-05 33.0 3.0 25 612-636 12-36 (52)
96 KOG3606 Cell polarity protein 70.6 6.3 0.00014 44.3 4.9 81 900-984 16-98 (358)
97 TIGR02431 pcaR_pcaU beta-ketoa 70.5 24 0.00053 38.0 9.4 45 270-316 195-239 (248)
98 KOG0251 Clathrin assembly prot 70.4 5.3 0.00012 48.1 4.7 65 605-669 222-297 (491)
99 PF00165 HTH_AraC: Bacterial r 70.4 4.6 0.0001 32.2 2.9 28 612-639 8-36 (42)
100 smart00497 IENR1 Intron encode 70.3 4.2 9E-05 33.5 2.8 25 610-635 16-40 (53)
101 TIGR02531 yecD_yerC TrpR-relat 70.3 3.9 8.6E-05 38.6 2.9 24 612-635 50-73 (88)
102 PF13492 GAF_3: GAF domain; PD 70.0 58 0.0013 29.7 10.6 75 418-505 49-123 (129)
103 PF13404 HTH_AsnC-type: AsnC-t 69.8 6.8 0.00015 32.1 3.8 33 604-636 9-41 (42)
104 KOG0010 Ubiquitin-like protein 69.4 6.5 0.00014 47.1 5.0 74 902-984 15-88 (493)
105 PRK11061 fused phosphoenolpyru 69.3 9.3 0.0002 48.2 6.7 86 416-505 65-150 (748)
106 cd01805 RAD23_N Ubiquitin-like 69.2 36 0.00077 30.1 8.6 71 903-983 3-75 (77)
107 cd01769 UBL Ubiquitin-like dom 69.2 9 0.0002 32.3 4.7 37 911-947 7-43 (69)
108 smart00421 HTH_LUXR helix_turn 69.2 4.7 0.0001 32.4 2.8 25 611-635 17-41 (58)
109 PF13411 MerR_1: MerR HTH fami 68.9 4.6 0.0001 34.8 2.9 26 613-638 1-26 (69)
110 PF07453 NUMOD1: NUMOD1 domain 68.4 3.6 7.9E-05 32.2 1.9 21 613-633 17-37 (37)
111 cd01799 Hoil1_N Ubiquitin-like 68.0 10 0.00022 34.5 5.0 44 905-950 7-50 (75)
112 cd01813 UBP_N UBP ubiquitin pr 67.7 12 0.00026 33.9 5.3 44 903-946 1-44 (74)
113 PF13412 HTH_24: Winged helix- 66.7 8.2 0.00018 31.4 3.8 33 604-636 9-41 (48)
114 PF13560 HTH_31: Helix-turn-he 66.5 4.6 0.0001 34.8 2.4 34 604-637 6-39 (64)
115 COG1522 Lrp Transcriptional re 66.3 7 0.00015 38.6 4.0 33 604-636 14-46 (154)
116 cd04774 HTH_YfmP Helix-Turn-He 65.9 5.9 0.00013 37.5 3.2 30 613-644 1-30 (96)
117 cd01807 GDX_N ubiquitin-like d 65.6 16 0.00034 32.4 5.7 66 903-982 3-72 (74)
118 COG3829 RocR Transcriptional r 65.2 5.5 0.00012 48.4 3.4 43 596-639 518-560 (560)
119 PF05225 HTH_psq: helix-turn-h 64.6 6.6 0.00014 32.6 2.8 23 613-635 17-39 (45)
120 PRK15429 formate hydrogenlyase 64.4 39 0.00084 42.1 10.6 128 162-307 197-326 (686)
121 PF00240 ubiquitin: Ubiquitin 64.2 14 0.00029 31.9 4.9 39 909-947 3-41 (69)
122 PRK11511 DNA-binding transcrip 64.2 11 0.00023 37.1 4.7 35 605-639 16-53 (127)
123 cd06399 PB1_P40 The PB1 domain 63.8 16 0.00035 35.0 5.4 51 923-975 29-79 (92)
124 PRK11569 transcriptional repre 63.8 46 0.001 36.7 10.0 40 274-315 221-260 (274)
125 cd04765 HTH_MlrA-like_sg2 Heli 63.2 7.2 0.00016 37.2 3.2 26 613-638 1-26 (99)
126 PF11112 PyocinActivator: Pyoc 63.1 11 0.00024 34.8 4.3 60 604-664 3-72 (76)
127 PF08281 Sigma70_r4_2: Sigma-7 63.0 9.6 0.00021 31.6 3.6 29 606-634 20-48 (54)
128 cd01802 AN1_N ubiquitin-like d 62.8 26 0.00057 33.8 6.9 67 902-982 29-99 (103)
129 PHA01976 helix-turn-helix prot 62.1 11 0.00024 32.4 3.9 32 604-635 7-38 (67)
130 PRK09726 antitoxin HipB; Provi 62.0 15 0.00033 33.9 5.0 31 604-634 17-47 (88)
131 cd01794 DC_UbP_C dendritic cel 62.0 31 0.00066 30.9 6.8 68 905-982 3-70 (70)
132 TIGR02607 antidote_HigA addict 61.8 16 0.00034 32.2 4.9 43 606-650 12-54 (78)
133 PF03374 ANT: Phage antirepres 61.7 7.6 0.00016 36.9 3.1 27 612-638 24-50 (111)
134 PRK15424 propionate catabolism 61.6 9.5 0.00021 46.5 4.6 31 609-639 507-537 (538)
135 smart00065 GAF Domain present 61.4 22 0.00049 31.4 5.9 84 417-505 50-135 (149)
136 TIGR03830 CxxCG_CxxCG_HTH puta 60.3 14 0.0003 35.5 4.7 32 603-634 69-100 (127)
137 PRK04217 hypothetical protein; 60.0 10 0.00023 37.3 3.7 28 608-635 54-81 (110)
138 TIGR02974 phageshock_pspF psp 59.6 10 0.00022 43.2 4.1 28 609-636 302-329 (329)
139 TIGR02040 PpsR-CrtJ transcript 59.2 11 0.00023 43.6 4.3 33 606-638 410-442 (442)
140 PRK15418 transcriptional regul 58.9 8.5 0.00018 43.7 3.4 35 606-640 21-60 (318)
141 COG2204 AtoC Response regulato 58.9 12 0.00025 45.1 4.6 38 607-644 425-462 (464)
142 PRK09393 ftrA transcriptional 58.0 13 0.00028 41.5 4.6 37 604-640 224-263 (322)
143 PRK14101 bifunctional glucokin 56.3 8.8 0.00019 47.2 3.2 34 609-642 371-404 (638)
144 COG1595 RpoE DNA-directed RNA 55.9 12 0.00026 38.2 3.6 30 606-635 137-166 (182)
145 TIGR01818 ntrC nitrogen regula 55.7 12 0.00027 43.3 4.1 28 609-636 436-463 (463)
146 smart00354 HTH_LACI helix_turn 55.1 9.5 0.00021 33.8 2.4 24 613-636 1-24 (70)
147 cd01804 midnolin_N Ubiquitin-l 55.0 28 0.00061 31.6 5.4 70 902-982 3-72 (78)
148 PF05930 Phage_AlpA: Prophage 54.9 11 0.00023 31.7 2.5 24 613-636 4-27 (51)
149 PF03683 UPF0175: Uncharacteri 54.6 16 0.00035 33.3 3.8 32 612-644 34-65 (76)
150 cd01791 Ubl5 UBL5 ubiquitin-li 54.5 37 0.0008 30.8 6.0 37 911-947 11-47 (73)
151 PRK10163 DNA-binding transcrip 54.0 1.1E+02 0.0023 33.9 10.8 39 274-314 216-254 (271)
152 TIGR02989 Sig-70_gvs1 RNA poly 53.9 15 0.00033 36.0 3.8 29 606-634 121-149 (159)
153 smart00419 HTH_CRP helix_turn_ 53.7 14 0.0003 29.3 2.9 28 610-637 6-33 (48)
154 PRK11169 leucine-responsive tr 53.5 13 0.00028 38.1 3.4 33 604-636 20-52 (164)
155 PRK09685 DNA-binding transcrip 53.5 19 0.00042 39.2 5.0 52 605-660 204-258 (302)
156 cd01105 HTH_GlnR-like Helix-Tu 53.4 13 0.00029 34.5 3.1 25 613-638 2-26 (88)
157 cd00093 HTH_XRE Helix-turn-hel 53.0 38 0.00083 25.9 5.3 42 606-649 6-47 (58)
158 cd00592 HTH_MerR-like Helix-Tu 52.4 16 0.00034 34.1 3.5 30 613-644 1-30 (100)
159 PF12844 HTH_19: Helix-turn-he 52.3 17 0.00036 31.0 3.4 31 604-634 4-34 (64)
160 PF06056 Terminase_5: Putative 51.9 16 0.00034 32.1 3.1 27 612-638 13-39 (58)
161 PRK12536 RNA polymerase sigma 51.9 18 0.00039 36.8 4.1 28 607-634 140-167 (181)
162 cd04766 HTH_HspR Helix-Turn-He 51.8 16 0.00035 33.9 3.4 27 613-640 2-28 (91)
163 PRK09643 RNA polymerase sigma 51.7 19 0.00041 37.2 4.3 29 606-634 144-172 (192)
164 PRK15186 AraC family transcrip 51.6 10 0.00023 42.6 2.6 40 606-645 189-230 (291)
165 PRK00118 putative DNA-binding 51.6 25 0.00053 34.4 4.7 29 606-634 27-55 (104)
166 PF04218 CENP-B_N: CENP-B N-te 51.6 13 0.00027 31.8 2.5 24 612-635 22-45 (53)
167 PRK05022 anaerobic nitric oxid 51.4 75 0.0016 38.3 9.8 31 609-639 478-508 (509)
168 PRK05602 RNA polymerase sigma 51.4 20 0.00044 36.5 4.4 28 606-633 138-165 (186)
169 PRK10072 putative transcriptio 51.3 20 0.00043 34.5 4.0 33 604-636 38-70 (96)
170 PRK12538 RNA polymerase sigma 51.3 23 0.00051 38.2 5.1 43 606-657 181-223 (233)
171 TIGR02947 SigH_actino RNA poly 51.3 22 0.00047 36.6 4.6 28 607-634 142-169 (193)
172 PF13011 LZ_Tnp_IS481: leucine 51.0 15 0.00032 34.9 3.0 25 612-636 25-49 (85)
173 PRK09646 RNA polymerase sigma 50.7 19 0.00041 37.2 4.1 28 606-633 152-179 (194)
174 cd04773 HTH_TioE_rpt2 Second H 50.5 15 0.00033 35.3 3.1 25 613-638 1-25 (108)
175 TIGR01321 TrpR trp operon repr 50.2 14 0.0003 35.7 2.8 26 612-637 55-80 (94)
176 PF01498 HTH_Tnp_Tc3_2: Transp 50.2 8.4 0.00018 33.9 1.2 37 613-649 14-55 (72)
177 PF10668 Phage_terminase: Phag 49.9 14 0.00029 33.1 2.4 29 612-643 22-50 (60)
178 PRK15043 transcriptional regul 49.6 16 0.00035 40.5 3.5 32 612-644 3-34 (243)
179 PF07638 Sigma70_ECF: ECF sigm 49.3 19 0.0004 37.4 3.8 31 606-636 145-175 (185)
180 PRK09649 RNA polymerase sigma 49.3 18 0.0004 37.1 3.7 29 606-634 140-168 (185)
181 smart00530 HTH_XRE Helix-turn- 49.1 46 0.001 25.2 5.2 30 605-634 3-32 (56)
182 PRK12545 RNA polymerase sigma 48.7 29 0.00064 36.2 5.2 28 606-633 149-176 (201)
183 PRK15090 DNA-binding transcrip 48.6 91 0.002 34.0 9.1 137 162-316 83-244 (257)
184 PRK09645 RNA polymerase sigma 48.5 20 0.00043 35.9 3.8 29 606-634 128-156 (173)
185 cd01106 HTH_TipAL-Mta Helix-Tu 48.2 30 0.00064 32.8 4.6 25 613-638 1-25 (103)
186 cd00196 UBQ Ubiquitin-like pro 48.1 36 0.00077 26.1 4.4 38 910-947 6-43 (69)
187 cd00569 HTH_Hin_like Helix-tur 48.0 18 0.0004 25.2 2.6 21 612-632 21-41 (42)
188 cd04789 HTH_Cfa Helix-Turn-Hel 47.6 19 0.00041 34.4 3.2 27 613-640 2-28 (102)
189 cd04775 HTH_Cfa-like Helix-Tur 47.5 18 0.0004 34.4 3.2 26 613-639 2-27 (102)
190 PRK12533 RNA polymerase sigma 47.3 19 0.00041 38.5 3.6 30 606-635 144-173 (216)
191 PF02309 AUX_IAA: AUX/IAA fami 47.2 6.3 0.00014 42.2 0.0 68 902-970 109-198 (215)
192 cd01279 HTH_HspR-like Helix-Tu 47.1 18 0.00039 34.3 3.1 25 613-638 2-26 (98)
193 smart00344 HTH_ASNC helix_turn 47.1 25 0.00054 32.9 3.9 33 604-636 9-41 (108)
194 PRK12529 RNA polymerase sigma 46.8 22 0.00048 36.2 3.8 29 606-634 137-165 (178)
195 PF09339 HTH_IclR: IclR helix- 46.7 16 0.00036 30.4 2.4 24 613-636 19-42 (52)
196 PRK12543 RNA polymerase sigma 46.7 45 0.00097 33.9 6.0 48 606-662 127-174 (179)
197 TIGR02999 Sig-70_X6 RNA polyme 46.7 22 0.00049 35.8 3.8 30 606-635 144-173 (183)
198 PRK09642 RNA polymerase sigma 46.6 23 0.00049 35.1 3.8 29 606-634 116-144 (160)
199 TIGR02392 rpoH_proteo alternat 46.5 21 0.00046 39.2 3.9 30 606-635 226-259 (270)
200 smart00351 PAX Paired Box doma 46.4 18 0.00039 35.8 3.0 25 612-636 33-57 (125)
201 COG2207 AraC AraC-type DNA-bin 46.0 36 0.00079 31.4 4.9 34 606-639 28-64 (127)
202 cd06571 Bac_DnaA_C C-terminal 45.6 23 0.0005 33.0 3.4 41 597-637 29-70 (90)
203 cd06170 LuxR_C_like C-terminal 45.6 24 0.00052 28.5 3.2 24 612-635 15-38 (57)
204 cd01800 SF3a120_C Ubiquitin-li 45.5 48 0.001 29.8 5.3 66 909-983 5-70 (76)
205 TIGR02293 TAS_TIGR02293 putati 45.2 39 0.00085 33.8 5.2 33 604-636 28-60 (133)
206 PF04760 IF2_N: Translation in 45.0 13 0.00028 31.4 1.5 27 613-639 4-31 (54)
207 KOG4639 RNase P/RNase MRP subu 44.8 53 0.0011 34.3 6.0 39 923-961 28-72 (154)
208 PF01371 Trp_repressor: Trp re 44.8 21 0.00046 33.9 3.1 26 612-637 49-74 (87)
209 PF10078 DUF2316: Uncharacteri 44.3 16 0.00035 34.9 2.2 35 599-633 7-44 (89)
210 PRK06596 RNA polymerase factor 44.3 24 0.00052 39.3 3.9 31 605-635 237-271 (284)
211 PRK11303 DNA-binding transcrip 44.2 28 0.00061 37.9 4.4 25 613-637 1-25 (328)
212 PRK08301 sporulation sigma fac 44.2 35 0.00076 36.3 5.0 23 612-634 198-220 (234)
213 PRK12511 RNA polymerase sigma 44.0 25 0.00054 36.3 3.8 28 606-633 121-148 (182)
214 PRK09637 RNA polymerase sigma 43.9 25 0.00055 36.1 3.8 28 606-633 116-143 (181)
215 PHA00542 putative Cro-like pro 43.9 19 0.00041 33.2 2.6 28 609-636 28-55 (82)
216 PF13551 HTH_29: Winged helix- 43.8 22 0.00047 32.9 3.0 23 614-636 14-36 (112)
217 PRK03975 tfx putative transcri 43.6 45 0.00097 34.3 5.4 26 610-635 19-44 (141)
218 PF00126 HTH_1: Bacterial regu 43.6 21 0.00045 30.7 2.6 23 612-634 13-35 (60)
219 COG5484 Uncharacterized conser 43.6 19 0.0004 40.4 2.9 26 612-637 19-44 (279)
220 PRK07037 extracytoplasmic-func 43.6 27 0.00059 34.5 3.8 27 606-632 119-145 (163)
221 PRK09978 DNA-binding transcrip 43.5 33 0.00072 38.6 4.8 34 605-638 149-184 (274)
222 PRK12519 RNA polymerase sigma 43.5 31 0.00067 35.3 4.3 28 606-633 151-178 (194)
223 smart00342 HTH_ARAC helix_turn 43.5 32 0.00069 29.4 3.8 32 606-638 45-78 (84)
224 PF06970 RepA_N: Replication i 43.2 18 0.00038 33.4 2.2 28 609-636 49-76 (76)
225 PF01590 GAF: GAF domain; Int 43.0 73 0.0016 30.1 6.5 91 413-505 46-150 (154)
226 PRK12530 RNA polymerase sigma 43.0 26 0.00057 36.1 3.8 29 606-634 144-172 (189)
227 PRK12532 RNA polymerase sigma 42.7 26 0.00057 36.0 3.7 29 606-634 146-174 (195)
228 cd01798 parkin_N amino-termina 42.7 41 0.00089 29.5 4.4 41 904-945 2-42 (70)
229 PRK12535 RNA polymerase sigma 42.7 28 0.00061 36.4 3.9 28 606-633 143-170 (196)
230 PRK10365 transcriptional regul 42.5 23 0.00051 40.7 3.6 26 609-634 415-440 (441)
231 PRK15411 rcsA colanic acid cap 42.4 25 0.00055 37.1 3.6 27 612-638 152-182 (207)
232 cd06171 Sigma70_r4 Sigma70, re 42.2 29 0.00063 27.0 3.1 25 611-635 25-49 (55)
233 PRK12527 RNA polymerase sigma 42.2 44 0.00095 33.1 5.1 29 606-634 115-143 (159)
234 smart00345 HTH_GNTR helix_turn 42.1 25 0.00054 28.7 2.8 23 614-636 22-44 (60)
235 cd00092 HTH_CRP helix_turn_hel 42.1 27 0.00057 29.6 3.0 28 609-636 22-49 (67)
236 COG3413 Predicted DNA binding 41.8 21 0.00046 38.0 2.9 27 609-635 171-201 (215)
237 PRK09641 RNA polymerase sigma 41.7 28 0.00062 35.1 3.7 29 606-634 146-174 (187)
238 PF13556 HTH_30: PucR C-termin 41.6 33 0.00072 29.6 3.6 31 604-634 2-34 (59)
239 TIGR03879 near_KaiC_dom probab 41.3 35 0.00075 31.6 3.8 27 609-635 29-55 (73)
240 PRK12547 RNA polymerase sigma 41.2 31 0.00067 34.5 3.9 30 606-635 122-151 (164)
241 PLN02560 enoyl-CoA reductase 41.1 1E+02 0.0023 35.3 8.3 81 903-989 3-88 (308)
242 TIGR02954 Sig70_famx3 RNA poly 40.6 31 0.00066 34.5 3.7 28 606-633 129-156 (169)
243 TIGR02939 RpoE_Sigma70 RNA pol 40.4 35 0.00076 34.5 4.1 28 607-634 149-176 (190)
244 smart00418 HTH_ARSR helix_turn 40.4 29 0.00063 28.1 2.9 31 612-642 10-40 (66)
245 PRK09047 RNA polymerase factor 40.2 33 0.00071 33.7 3.8 29 606-634 116-144 (161)
246 PTZ00044 ubiquitin; Provisiona 40.1 52 0.0011 29.0 4.7 70 903-982 3-72 (76)
247 cd01110 HTH_SoxR Helix-Turn-He 40.0 28 0.00061 35.1 3.3 28 612-640 1-28 (139)
248 PRK10840 transcriptional regul 39.8 30 0.00064 35.8 3.5 35 605-639 157-196 (216)
249 PRK08241 RNA polymerase factor 39.6 28 0.00061 39.1 3.6 29 606-634 163-191 (339)
250 cd01793 Fubi Fubi ubiquitin-li 39.4 60 0.0013 28.9 5.0 68 903-982 3-70 (74)
251 PF07022 Phage_CI_repr: Bacter 39.4 16 0.00034 32.3 1.2 44 604-650 3-48 (66)
252 PRK09635 sigI RNA polymerase s 39.4 29 0.00063 38.9 3.7 29 606-634 128-156 (290)
253 PF08220 HTH_DeoR: DeoR-like h 39.4 38 0.00082 29.1 3.5 33 604-636 6-38 (57)
254 cd01282 HTH_MerR-like_sg3 Heli 39.3 30 0.00064 33.5 3.3 30 613-644 1-30 (112)
255 PRK15044 transcriptional regul 39.3 33 0.00071 39.2 4.0 35 605-639 199-235 (295)
256 PRK10703 DNA-binding transcrip 39.2 35 0.00077 37.4 4.2 24 613-636 2-25 (341)
257 PF03472 Autoind_bind: Autoind 38.9 67 0.0015 30.6 5.6 46 257-304 84-129 (149)
258 PRK01381 Trp operon repressor; 38.8 18 0.00039 35.2 1.7 27 613-639 56-82 (99)
259 PRK15340 transcriptional regul 38.7 29 0.00064 37.9 3.4 28 612-639 125-153 (216)
260 PRK12542 RNA polymerase sigma 38.6 34 0.00075 34.8 3.8 28 606-633 132-159 (185)
261 TIGR02952 Sig70_famx2 RNA poly 38.5 36 0.00078 33.7 3.8 28 607-634 133-160 (170)
262 PRK09636 RNA polymerase sigma 38.4 32 0.0007 38.0 3.8 29 606-634 125-153 (293)
263 PRK12541 RNA polymerase sigma 38.3 35 0.00076 33.9 3.7 29 606-634 122-150 (161)
264 PRK09638 RNA polymerase sigma 38.1 28 0.0006 35.0 2.9 28 607-634 137-164 (176)
265 PRK12520 RNA polymerase sigma 37.9 36 0.00078 34.9 3.8 29 606-634 141-169 (191)
266 PRK10572 DNA-binding transcrip 37.3 48 0.001 36.1 4.8 47 605-651 190-239 (290)
267 TIGR02959 SigZ RNA polymerase 37.2 39 0.00084 34.2 3.8 28 606-633 110-137 (170)
268 TIGR02957 SigX4 RNA polymerase 37.1 35 0.00075 37.7 3.8 30 605-634 117-146 (281)
269 TIGR03209 P21_Cbot clostridium 37.1 24 0.00053 34.3 2.3 26 606-631 117-142 (142)
270 PF08279 HTH_11: HTH domain; 36.8 51 0.0011 27.4 3.9 24 613-636 16-39 (55)
271 TIGR02943 Sig70_famx1 RNA poly 36.8 38 0.00083 35.0 3.8 29 606-634 141-169 (188)
272 PRK13890 conjugal transfer pro 36.8 37 0.00081 33.5 3.5 33 604-636 10-42 (120)
273 PRK10371 DNA-binding transcrip 36.7 46 0.00099 37.2 4.7 34 612-645 207-241 (302)
274 TIGR02329 propionate_PrpR prop 36.7 32 0.00068 42.0 3.6 26 609-634 500-525 (526)
275 PF13744 HTH_37: Helix-turn-he 36.4 38 0.00081 30.9 3.3 31 604-634 23-53 (80)
276 TIGR02960 SigX5 RNA polymerase 36.4 35 0.00076 37.9 3.7 29 606-634 152-180 (324)
277 PRK12516 RNA polymerase sigma 36.3 39 0.00085 35.0 3.8 29 606-634 126-154 (187)
278 PRK09526 lacI lac repressor; R 36.2 42 0.0009 36.8 4.2 24 613-636 6-29 (342)
279 PHA00675 hypothetical protein 36.1 28 0.0006 32.7 2.3 26 610-635 37-62 (78)
280 PRK11753 DNA-binding transcrip 36.0 26 0.00056 35.9 2.4 37 611-647 167-206 (211)
281 PRK09415 RNA polymerase factor 36.0 39 0.00085 34.4 3.7 29 606-634 137-165 (179)
282 TIGR02985 Sig70_bacteroi1 RNA 36.0 43 0.00093 32.4 3.8 29 607-635 124-152 (161)
283 PRK12523 RNA polymerase sigma 35.7 42 0.00092 33.8 3.8 29 606-634 129-157 (172)
284 TIGR02859 spore_sigH RNA polym 35.5 44 0.00095 34.1 4.0 22 610-631 163-184 (198)
285 PF08280 HTH_Mga: M protein tr 35.4 38 0.00082 29.3 2.9 26 612-637 19-44 (59)
286 PRK12540 RNA polymerase sigma 35.3 41 0.00089 34.7 3.8 29 606-634 121-149 (182)
287 cd01107 HTH_BmrR Helix-Turn-He 35.3 34 0.00073 32.9 2.9 25 613-638 1-25 (108)
288 PRK15185 transcriptional regul 35.1 41 0.00089 38.6 4.0 27 612-638 222-248 (309)
289 cd01810 ISG15_repeat2 ISG15 ub 35.0 61 0.0013 28.8 4.3 38 909-946 6-43 (74)
290 PRK11179 DNA-binding transcrip 34.8 46 0.001 33.7 3.9 33 604-636 15-47 (153)
291 cd01109 HTH_YyaN Helix-Turn-He 34.5 64 0.0014 31.1 4.7 26 613-638 1-26 (113)
292 PF00196 GerE: Bacterial regul 34.5 31 0.00068 29.2 2.3 27 612-638 18-48 (58)
293 PF07750 GcrA: GcrA cell cycle 34.3 37 0.00081 35.4 3.2 37 604-640 8-47 (162)
294 TIGR02297 HpaA 4-hydroxyphenyl 34.3 35 0.00075 36.9 3.2 40 606-647 194-236 (287)
295 PRK13870 transcriptional regul 34.3 1.8E+02 0.0039 31.7 8.6 51 258-310 96-146 (234)
296 COG3283 TyrR Transcriptional r 34.3 49 0.0011 39.2 4.4 34 606-639 473-508 (511)
297 PRK10339 DNA-binding transcrip 34.3 42 0.00091 36.8 3.8 25 613-637 2-26 (327)
298 TIGR02983 SigE-fam_strep RNA p 34.1 44 0.00096 33.0 3.6 29 606-634 120-148 (162)
299 PRK12531 RNA polymerase sigma 34.0 45 0.00098 34.4 3.8 24 610-633 155-178 (194)
300 PRK12513 RNA polymerase sigma 33.9 33 0.00071 35.2 2.8 26 607-632 150-175 (194)
301 PRK12518 RNA polymerase sigma 33.5 37 0.00081 34.0 3.1 27 607-633 131-157 (175)
302 COG4367 Uncharacterized protei 33.5 33 0.00071 33.0 2.4 35 599-633 7-44 (97)
303 PF01614 IclR: Bacterial trans 33.3 82 0.0018 30.1 5.2 40 274-314 80-119 (129)
304 COG2963 Transposase and inacti 33.2 43 0.00094 32.1 3.3 51 595-645 5-60 (116)
305 PHA00689 hypothetical protein 33.1 28 0.0006 30.3 1.7 20 941-960 25-44 (62)
306 PRK12528 RNA polymerase sigma 33.0 51 0.0011 32.7 3.8 29 606-634 123-151 (161)
307 PRK09706 transcriptional repre 32.6 48 0.001 32.8 3.6 33 604-636 10-42 (135)
308 PF00440 TetR_N: Bacterial reg 32.6 46 0.001 27.2 2.9 25 608-632 12-36 (47)
309 PRK09648 RNA polymerase sigma 32.6 50 0.0011 33.7 3.9 28 606-633 149-176 (189)
310 TIGR02937 sigma70-ECF RNA poly 32.5 44 0.00094 31.4 3.1 26 611-636 125-150 (158)
311 PRK09940 transcriptional regul 32.4 49 0.0011 36.9 4.0 28 612-639 150-177 (253)
312 TIGR02948 SigW_bacill RNA poly 32.4 47 0.001 33.5 3.6 29 606-634 146-174 (187)
313 PF13613 HTH_Tnp_4: Helix-turn 32.4 39 0.00084 28.6 2.5 25 612-636 19-43 (53)
314 PRK09652 RNA polymerase sigma 32.3 51 0.0011 32.7 3.8 25 609-633 141-165 (182)
315 PRK12522 RNA polymerase sigma 32.1 51 0.0011 33.2 3.8 29 606-634 129-157 (173)
316 TIGR03541 reg_near_HchA LuxR f 31.9 1.9E+02 0.0042 31.2 8.3 51 244-298 84-135 (232)
317 smart00346 HTH_ICLR helix_turn 31.7 62 0.0013 29.1 3.9 31 606-636 13-44 (91)
318 PF12802 MarR_2: MarR family; 31.6 58 0.0013 27.3 3.5 25 613-637 22-46 (62)
319 PRK08295 RNA polymerase factor 31.6 71 0.0015 32.9 4.8 24 609-632 167-190 (208)
320 cd01818 TIAM1_RBD Ubiquitin do 31.5 1.9E+02 0.0041 27.4 6.8 44 912-955 10-56 (77)
321 PRK09651 RNA polymerase sigma 31.5 49 0.0011 33.5 3.5 28 606-633 129-156 (172)
322 cd00131 PAX Paired Box domain 31.4 42 0.00092 33.5 3.0 25 612-636 33-57 (128)
323 COG3093 VapI Plasmid maintenan 31.4 49 0.0011 32.6 3.3 37 600-636 11-47 (104)
324 PRK13869 plasmid-partitioning 31.3 83 0.0018 37.0 5.8 62 613-674 49-113 (405)
325 TIGR03541 reg_near_HchA LuxR f 31.3 5.2E+02 0.011 28.0 11.4 69 412-483 64-132 (232)
326 cd01392 HTH_LacI Helix-turn-he 31.3 25 0.00054 28.7 1.1 21 616-636 1-21 (52)
327 TIGR02984 Sig-70_plancto1 RNA 31.1 55 0.0012 33.0 3.8 29 606-634 150-178 (189)
328 PF02017 CIDE-N: CIDE-N domain 30.9 1.1E+02 0.0024 28.8 5.3 49 904-954 4-52 (78)
329 PRK09647 RNA polymerase sigma 30.9 54 0.0012 34.6 3.8 31 606-636 148-178 (203)
330 PRK10403 transcriptional regul 30.5 57 0.0012 32.2 3.7 27 612-638 168-198 (215)
331 PF00788 RA: Ras association ( 30.4 4E+02 0.0087 23.9 9.9 78 903-983 3-90 (93)
332 TIGR02417 fruct_sucro_rep D-fr 30.3 51 0.0011 36.0 3.7 24 614-637 1-24 (327)
333 PRK13919 putative RNA polymera 30.3 57 0.0012 33.1 3.8 29 607-635 146-174 (186)
334 PRK09191 two-component respons 30.1 55 0.0012 34.4 3.7 29 606-634 98-126 (261)
335 COG3415 Transposase and inacti 30.1 45 0.00097 34.2 2.9 28 610-637 19-46 (138)
336 TIGR01950 SoxR redox-sensitive 29.9 49 0.0011 33.7 3.2 26 613-639 2-27 (142)
337 PRK14987 gluconate operon tran 29.7 52 0.0011 36.1 3.6 25 613-637 6-30 (331)
338 COG2452 Predicted site-specifi 29.7 47 0.001 35.9 3.1 35 612-647 1-35 (193)
339 PRK12546 RNA polymerase sigma 29.6 57 0.0012 34.0 3.7 29 606-634 123-151 (188)
340 PF13545 HTH_Crp_2: Crp-like h 29.6 48 0.001 29.0 2.7 39 610-648 26-67 (76)
341 PRK11161 fumarate/nitrate redu 29.6 35 0.00075 35.9 2.1 39 612-650 184-225 (235)
342 cd04768 HTH_BmrR-like Helix-Tu 29.5 56 0.0012 30.8 3.3 26 613-639 1-26 (96)
343 TIGR02846 spore_sigmaK RNA pol 29.5 55 0.0012 35.0 3.6 23 612-634 194-216 (227)
344 PRK13502 transcriptional activ 29.4 79 0.0017 34.3 4.9 34 606-639 184-220 (282)
345 PRK13503 transcriptional activ 29.3 82 0.0018 33.9 5.0 35 605-639 178-215 (278)
346 PRK10651 transcriptional regul 29.2 82 0.0018 31.2 4.6 34 605-638 162-200 (216)
347 cd00090 HTH_ARSR Arsenical Res 29.0 76 0.0016 26.3 3.7 31 613-643 21-51 (78)
348 PRK06704 RNA polymerase factor 28.7 55 0.0012 35.8 3.5 28 606-633 126-153 (228)
349 PF00392 GntR: Bacterial regul 28.5 47 0.001 28.7 2.4 25 612-636 23-48 (64)
350 PRK12537 RNA polymerase sigma 28.5 63 0.0014 33.0 3.7 28 606-633 143-170 (182)
351 PRK08359 transcription factor; 28.5 62 0.0013 34.5 3.7 28 608-637 94-121 (176)
352 PRK10082 cell density-dependen 28.5 60 0.0013 35.4 3.8 38 600-638 9-55 (303)
353 PRK15092 DNA-binding transcrip 28.2 60 0.0013 36.1 3.8 43 595-638 4-55 (310)
354 PRK11923 algU RNA polymerase s 28.2 62 0.0014 33.1 3.7 29 607-635 149-177 (193)
355 PRK12539 RNA polymerase sigma 28.2 64 0.0014 33.0 3.7 28 606-633 141-168 (184)
356 PRK10130 transcriptional regul 28.1 77 0.0017 36.7 4.7 34 607-640 249-285 (350)
357 PRK06759 RNA polymerase factor 28.0 70 0.0015 31.3 3.8 26 609-634 119-144 (154)
358 cd04782 HTH_BltR Helix-Turn-He 27.7 59 0.0013 30.7 3.1 25 613-638 1-25 (97)
359 TIGR01453 grpIintron_endo grou 27.7 38 0.00083 36.4 2.1 26 612-637 179-204 (214)
360 PRK09943 DNA-binding transcrip 27.4 65 0.0014 33.4 3.7 32 604-635 12-43 (185)
361 TIGR01481 ccpA catabolite cont 27.4 74 0.0016 34.7 4.3 25 613-637 2-26 (329)
362 TIGR02036 dsdC D-serine deamin 27.3 77 0.0017 34.7 4.4 39 597-635 3-45 (302)
363 PRK09492 treR trehalose repres 27.2 69 0.0015 34.7 4.0 24 613-636 5-28 (315)
364 PF09048 Cro: Cro; InterPro: 27.2 58 0.0012 29.2 2.7 32 601-634 3-34 (59)
365 TIGR02393 RpoD_Cterm RNA polym 27.2 68 0.0015 34.5 3.9 31 605-635 183-219 (238)
366 PRK12514 RNA polymerase sigma 27.1 70 0.0015 32.3 3.8 24 610-633 143-166 (179)
367 PRK11924 RNA polymerase sigma 27.0 71 0.0015 31.6 3.7 27 608-634 137-163 (179)
368 TIGR02612 mob_myst_A mobile my 26.8 70 0.0015 33.2 3.7 32 604-635 30-61 (150)
369 TIGR00637 ModE_repress ModE mo 26.8 56 0.0012 31.3 2.8 24 612-635 16-39 (99)
370 TIGR02047 CadR-PbrR Cd(II)/Pb( 26.7 1E+02 0.0022 30.6 4.7 25 613-638 1-25 (127)
371 PF01325 Fe_dep_repress: Iron 26.6 61 0.0013 28.4 2.8 26 611-636 21-46 (60)
372 PF01047 MarR: MarR family; I 26.6 84 0.0018 26.3 3.5 38 604-641 9-46 (59)
373 TIGR02405 trehalos_R_Ecol treh 26.2 48 0.001 36.1 2.6 23 613-635 2-24 (311)
374 COG2522 Predicted transcriptio 26.1 1.5E+02 0.0032 29.9 5.7 31 606-637 17-47 (119)
375 smart00352 POU Found in Pit-Oc 26.0 83 0.0018 29.4 3.6 31 604-634 16-52 (75)
376 COG1709 Predicted transcriptio 25.6 41 0.00089 37.1 1.8 28 604-631 32-59 (241)
377 PRK13500 transcriptional activ 25.6 80 0.0017 35.3 4.2 36 604-639 212-250 (312)
378 cd04767 HTH_HspR-like_MBC Heli 25.1 62 0.0013 32.5 2.8 25 613-638 2-26 (120)
379 PRK12534 RNA polymerase sigma 24.9 88 0.0019 31.8 4.0 28 607-634 148-175 (187)
380 PF13730 HTH_36: Helix-turn-he 24.8 70 0.0015 26.6 2.7 23 614-636 27-49 (55)
381 PRK11475 DNA-binding transcrip 24.8 77 0.0017 33.9 3.7 27 612-638 149-179 (207)
382 PRK12524 RNA polymerase sigma 24.8 80 0.0017 32.6 3.8 28 606-633 146-173 (196)
383 PF13022 HTH_Tnp_1_2: Helix-tu 24.7 64 0.0014 33.4 2.9 24 613-636 35-58 (142)
384 COG1609 PurR Transcriptional r 24.6 83 0.0018 35.7 4.1 24 614-637 2-25 (333)
385 cd08804 Death_ank2 Death domai 24.6 84 0.0018 29.4 3.5 37 600-636 3-39 (84)
386 PRK10094 DNA-binding transcrip 24.6 78 0.0017 34.9 3.9 72 602-674 2-98 (308)
387 PRK05949 RNA polymerase sigma 24.5 1.5E+02 0.0032 34.2 6.1 30 606-635 274-309 (327)
388 COG2944 Predicted transcriptio 24.5 81 0.0018 31.2 3.4 29 604-632 49-77 (104)
389 PF14549 P22_Cro: DNA-binding 24.4 1E+02 0.0022 27.5 3.7 27 605-632 3-29 (60)
390 PRK06986 fliA flagellar biosyn 24.4 78 0.0017 33.9 3.7 26 609-634 197-222 (236)
391 COG2901 Fis Factor for inversi 24.3 1E+02 0.0023 29.8 4.0 35 604-638 63-97 (98)
392 PRK13348 chromosome replicatio 24.1 80 0.0017 34.1 3.8 27 612-638 16-46 (294)
393 PRK10086 DNA-binding transcrip 24.1 76 0.0016 34.9 3.6 45 594-638 6-58 (311)
394 PF14533 USP7_C2: Ubiquitin-sp 24.1 81 0.0018 34.0 3.7 45 915-959 136-194 (213)
395 PF00376 MerR: MerR family reg 24.0 81 0.0017 25.4 2.8 25 614-639 1-25 (38)
396 cd01111 HTH_MerD Helix-Turn-He 24.0 82 0.0018 30.5 3.4 27 613-640 1-27 (107)
397 PRK11922 RNA polymerase sigma 23.9 58 0.0012 34.8 2.6 28 606-633 159-186 (231)
398 TIGR02844 spore_III_D sporulat 23.8 88 0.0019 29.4 3.4 31 604-635 12-42 (80)
399 PRK09508 leuO leucine transcri 23.5 86 0.0019 34.5 3.9 38 600-638 20-66 (314)
400 PHA02591 hypothetical protein; 23.4 78 0.0017 30.0 2.9 24 611-634 58-81 (83)
401 cd04785 HTH_CadR-PbrR-like Hel 23.4 1.2E+02 0.0026 29.9 4.5 23 613-635 1-23 (126)
402 CHL00180 rbcR LysR transcripti 23.3 85 0.0018 34.3 3.8 35 600-635 3-42 (305)
403 PRK10014 DNA-binding transcrip 23.3 59 0.0013 35.7 2.6 23 613-635 7-29 (342)
404 COG2197 CitB Response regulato 23.3 82 0.0018 33.6 3.6 30 611-640 162-195 (211)
405 PRK12526 RNA polymerase sigma 23.3 90 0.002 32.7 3.8 24 609-632 166-189 (206)
406 PF12833 HTH_18: Helix-turn-he 23.0 83 0.0018 27.8 3.0 22 618-639 1-23 (81)
407 COG3604 FhlA Transcriptional r 23.0 76 0.0016 38.9 3.5 75 235-311 103-181 (550)
408 PRK12512 RNA polymerase sigma 23.0 95 0.0021 31.5 3.8 28 607-634 142-169 (184)
409 cd04787 HTH_HMRTR_unk Helix-Tu 22.9 88 0.0019 31.2 3.5 30 613-644 1-30 (133)
410 PRK05572 sporulation sigma fac 22.8 92 0.002 33.8 3.9 23 612-634 218-240 (252)
411 PRK09644 RNA polymerase sigma 22.5 93 0.002 31.1 3.6 27 606-632 118-144 (165)
412 PHA03043 hypothetical protein; 22.5 27 0.00058 35.5 -0.2 60 32-91 19-86 (130)
413 cd04772 HTH_TioE_rpt1 First He 22.5 99 0.0022 29.4 3.6 25 613-638 1-25 (99)
414 PF01710 HTH_Tnp_IS630: Transp 22.5 1.1E+02 0.0025 29.8 4.1 25 612-636 18-42 (119)
415 PRK13719 conjugal transfer tra 22.3 90 0.002 34.4 3.7 28 611-638 157-188 (217)
416 smart00530 HTH_XRE Helix-turn- 22.3 1.2E+02 0.0026 22.9 3.4 40 600-639 9-52 (56)
417 PRK08215 sporulation sigma fac 22.0 97 0.0021 33.8 3.9 24 612-635 225-248 (258)
418 PF05043 Mga: Mga helix-turn-h 21.9 72 0.0016 29.0 2.5 24 612-635 30-53 (87)
419 COG4565 CitB Response regulato 21.9 83 0.0018 34.8 3.3 39 596-634 152-195 (224)
420 PF08965 DUF1870: Domain of un 21.9 2E+02 0.0042 29.2 5.5 58 601-660 3-62 (118)
421 cd04779 HTH_MerR-like_sg4 Heli 21.8 83 0.0018 31.9 3.1 31 613-645 1-31 (134)
422 PRK10727 DNA-binding transcrip 21.8 62 0.0013 35.8 2.4 23 614-636 3-25 (343)
423 PRK06811 RNA polymerase factor 21.8 1E+02 0.0022 31.7 3.8 27 608-634 143-169 (189)
424 TIGR02950 SigM_subfam RNA poly 21.7 83 0.0018 30.7 3.0 26 609-634 118-143 (154)
425 PRK10430 DNA-binding transcrip 21.7 1.1E+02 0.0023 32.4 4.0 26 611-636 177-202 (239)
426 PF05344 DUF746: Domain of Unk 21.7 88 0.0019 28.6 2.8 25 612-636 13-37 (65)
427 PRK06424 transcription factor; 21.7 1E+02 0.0022 31.8 3.7 32 605-636 90-121 (144)
428 PRK10423 transcriptional repre 21.6 51 0.0011 35.9 1.7 22 615-636 1-22 (327)
429 PRK10401 DNA-binding transcrip 21.4 67 0.0015 35.5 2.6 24 613-636 2-25 (346)
430 PRK12517 RNA polymerase sigma 21.4 1E+02 0.0023 31.9 3.8 28 607-634 139-166 (188)
431 PRK11074 putative DNA-binding 21.4 98 0.0021 33.8 3.8 32 602-634 2-38 (300)
432 PRK09935 transcriptional regul 21.4 1.4E+02 0.003 29.6 4.5 34 605-638 156-194 (210)
433 PRK09834 DNA-binding transcrip 21.2 1.4E+02 0.0031 32.7 5.0 40 274-315 206-245 (263)
434 PF05932 CesT: Tir chaperone p 21.2 1.3E+02 0.0028 27.7 4.1 33 926-958 1-47 (119)
435 cd04781 HTH_MerR-like_sg6 Heli 21.1 92 0.002 30.4 3.2 27 613-640 1-27 (120)
436 smart00513 SAP Putative DNA-bi 21.0 97 0.0021 24.2 2.7 20 624-643 4-23 (35)
437 PRK05911 RNA polymerase sigma 21.0 1E+02 0.0022 33.8 3.9 24 612-635 221-244 (257)
438 PRK15121 right oriC-binding tr 21.0 1.1E+02 0.0023 33.9 4.0 42 612-653 21-63 (289)
439 PRK08583 RNA polymerase sigma 20.9 1E+02 0.0022 33.4 3.8 27 608-634 217-243 (257)
440 PF08783 DWNN: DWNN domain; I 20.9 2E+02 0.0042 26.8 5.0 39 912-950 10-50 (74)
441 PRK14997 LysR family transcrip 20.9 1E+02 0.0022 33.4 3.8 24 612-635 16-39 (301)
442 TIGR00270 conserved hypothetic 20.8 1.1E+02 0.0023 31.9 3.7 28 607-634 77-104 (154)
443 PF09035 Tn916-Xis: Excisionas 20.8 81 0.0017 28.8 2.5 29 609-637 10-38 (67)
444 PRK10597 DNA damage-inducible 20.7 2.5E+02 0.0053 26.7 5.6 62 903-968 1-66 (81)
445 PRK07405 RNA polymerase sigma 20.7 1.9E+02 0.004 33.1 5.9 30 605-634 263-298 (317)
446 TIGR03453 partition_RepA plasm 20.6 86 0.0019 36.3 3.3 26 613-638 34-59 (387)
447 smart00550 Zalpha Z-DNA-bindin 20.5 1.4E+02 0.003 26.7 3.8 31 604-634 12-44 (68)
448 TIGR02850 spore_sigG RNA polym 20.5 1.1E+02 0.0024 33.3 3.9 29 606-634 214-244 (254)
449 PF02082 Rrf2: Transcriptional 20.5 86 0.0019 28.5 2.6 44 613-674 26-69 (83)
450 TIGR02479 FliA_WhiG RNA polyme 20.5 1.1E+02 0.0024 32.5 3.8 24 611-634 190-213 (224)
451 PF07860 CCD: WisP family C-Te 20.2 40 0.00087 33.2 0.5 15 630-647 49-63 (141)
452 cd04776 HTH_GnyR Helix-Turn-He 20.2 1E+02 0.0022 30.3 3.2 27 613-640 1-27 (118)
No 1
>cd06407 PB1_NLP A PB1 domain is present in NIN like proteins (NLP), a key enzyme in a process of establishment of symbiosis betweeen legumes and nitrogen fixing bacteria (Rhizobium). The PB1 domain is a modular domain mediating specific protein-protein interaction which play a role in many critical cell processes like osteoclastogenesis, angiogenesis, early cardiovascular development, and cell polarity. A canonical PB1-PB1 interaction, which involves heterodimerization of two PB1 domains, is required for the formation of macromolecular signaling complexes ensuring specificity and fidelity during cellular signaling. The interaction between two PB1 domain depends on the type of PB1. There are three types of PB1 domains: type I which contains an OPCA motif, acidic aminoacid cluster, type II which contains a basic cluster, and type I/II which contains both an OPCA motif and a basic cluster. Interactions of PB1 domains with other protein domains have been described as noncanonical PB1-inte
Probab=99.95 E-value=3.6e-28 Score=220.01 Aligned_cols=81 Identities=51% Similarity=0.927 Sum_probs=79.2
Q ss_pred EEEEEEcCCCeEEEEeCCCcChHHHHHHHHHHcCccc-ceeeeEeecCCCCeEEEecCCcHHHHHHHHhHhCCCeEEEEE
Q 001809 903 IIVKATYKEDIIRFKFDPSAGCFQLYEEVARRLKLQN-GTFQLKYLDDEEEWVMLVSDSDLQECFDILESLGKRSVRFLV 981 (1010)
Q Consensus 903 ~~vKaty~~d~iRF~~~~s~g~~~L~~EIakRf~l~~-~~f~lKYlDDd~EWVlLtcDaDL~EC~di~~~~~~~~vkl~V 981 (1010)
|+|||+|++|+|||+|+|++||.+|++||++||++++ +.|+|||+|||||||+||||+||+||++|++.+++++|||+|
T Consensus 1 ~~vK~~~~~d~~r~~l~~~~~~~~L~~~i~~r~~~~~~~~f~LkY~Ddegd~v~ltsd~DL~eai~i~~~~~~~~v~l~v 80 (82)
T cd06407 1 VRVKATYGEEKIRFRLPPSWGFTELKQEIAKRFKLDDMSAFDLKYLDDDEEWVLLTCDADLEECIDVYRSSGSHTIRLLV 80 (82)
T ss_pred CEEEEEeCCeEEEEEcCCCCCHHHHHHHHHHHhCCCCCCeeEEEEECCCCCeEEeecHHHHHHHHHHHHHCCCCeEEEEe
Confidence 5899999999999999999999999999999999998 789999999999999999999999999999999999999999
Q ss_pred ee
Q 001809 982 RD 983 (1010)
Q Consensus 982 ~d 983 (1010)
|+
T Consensus 81 ~~ 82 (82)
T cd06407 81 HA 82 (82)
T ss_pred eC
Confidence 96
No 2
>cd06409 PB1_MUG70 The MUG70 protein is a product of the meiotically up-regulated gene 70 which has a role in meiosis and harbors a PB1 domain. The PB1 domain is a modular domain mediating specific protein-protein interactions which play a role in many critical cell processes such as osteoclastogenesis, angiogenesis, early cardiovascular development, and cell polarity. A canonical PB1-PB1 interaction, which involves heterodimerization of two PB1 domains, is required for the formation of macromolecular signaling complexes ensuring specificity and fidelity during cellular signaling. The interaction between two PB1 domains depends on the type of PB1. There are three types of PB1 domains: type I which contains an OPCA motif, acidic amino acid cluster, type II which contains a basic cluster, and type I/II which contains both an OPCA motif and a basic cluster. Interactions of PB1 domains with other protein domains have been described as noncanonical PB1-interactions. The PB1 domain module is
Probab=99.95 E-value=1.4e-27 Score=217.87 Aligned_cols=81 Identities=27% Similarity=0.410 Sum_probs=75.8
Q ss_pred EEEEEEcCCCeEEEEeCCCcChHHHHHHHHHHcCccc---ceeeeEeecCCCCeEEEecCCcHHHHHHHHhHhCCCeEEE
Q 001809 903 IIVKATYKEDIIRFKFDPSAGCFQLYEEVARRLKLQN---GTFQLKYLDDEEEWVMLVSDSDLQECFDILESLGKRSVRF 979 (1010)
Q Consensus 903 ~~vKaty~~d~iRF~~~~s~g~~~L~~EIakRf~l~~---~~f~lKYlDDd~EWVlLtcDaDL~EC~di~~~~~~~~vkl 979 (1010)
|.+|+. .+++|||++.|+||+.+|++||++|||+++ +.|+|||+|||+|||+||||+||+|||+|+|.+|.++|||
T Consensus 3 FK~~~~-~GrvhRf~~~~s~~~~~L~~~I~~Rl~~d~~~~~~~~L~YlDDEgD~VllT~D~DL~e~v~iar~~g~~~v~L 81 (86)
T cd06409 3 FKFKDP-KGRVHRFRLRPSESLEELRTLISQRLGDDDFETHLYALSYVDDEGDIVLITSDSDLVAAVLVARSAGLKKLDL 81 (86)
T ss_pred EEeeCC-CCCEEEEEecCCCCHHHHHHHHHHHhCCccccCCcccEEEEcCCCCEEEEeccchHHHHHHHHHHcCCCEEEE
Confidence 566654 669999999999999999999999999998 5799999999999999999999999999999999999999
Q ss_pred EEeec
Q 001809 980 LVRDI 984 (1010)
Q Consensus 980 ~V~d~ 984 (1010)
+||++
T Consensus 82 ~v~~~ 86 (86)
T cd06409 82 HLHYP 86 (86)
T ss_pred EEeCC
Confidence 99974
No 3
>cd06396 PB1_NBR1 The PB1 domain is an essential part of NBR1 protein, next to BRCA1, a scaffold protein mediating specific protein-protein interaction with both titin protein kinase and with another scaffold protein p62. A canonical PB1-PB1 interaction, which involves heterodimerization of two PB1 domain, is required for the formation of macromolecular signaling complexes ensuring specificity and fidelity during cellular signaling. The interaction between two PB1 domain depends on the type of PB1. There are three types of PB1 domains: type I which contains an OPCA motif, acidic aminoacid cluster, type II which contains a basic cluster, and type I/II which contains both an OPCA motif and a basic cluster. The NBR1 protein contains a type I PB1 domain.
Probab=99.93 E-value=6.7e-26 Score=204.55 Aligned_cols=78 Identities=22% Similarity=0.305 Sum_probs=75.8
Q ss_pred EEEEEEcCCCeEEEEeCC--CcChHHHHHHHHHHcCcccceeeeEeecCCCCeEEEecCCcHHHHHHHHhHhCCCeEEEE
Q 001809 903 IIVKATYKEDIIRFKFDP--SAGCFQLYEEVARRLKLQNGTFQLKYLDDEEEWVMLVSDSDLQECFDILESLGKRSVRFL 980 (1010)
Q Consensus 903 ~~vKaty~~d~iRF~~~~--s~g~~~L~~EIakRf~l~~~~f~lKYlDDd~EWVlLtcDaDL~EC~di~~~~~~~~vkl~ 980 (1010)
+||||+|++|++||+|+| +|||.+|++||++||+|+ .|+|||||||+|||+|+||+||+||++++..++ +.+++.
T Consensus 1 V~vKaty~~d~~rf~~~~~~~~~~~~L~~ev~~rf~l~--~f~lKYlDde~e~v~lssd~eLeE~~rl~~~~~-~~l~~~ 77 (81)
T cd06396 1 VNLKVTYNGESQSFLVSDSENTTWASVEAMVKVSFGLN--DIQIKYVDEENEEVSVNSQGEYEEALKSAVRQG-NLLQMN 77 (81)
T ss_pred CEEEEEECCeEEEEEecCCCCCCHHHHHHHHHHHhCCC--cceeEEEcCCCCEEEEEchhhHHHHHHHHHhCC-CEEEEE
Confidence 589999999999999999 889999999999999999 999999999999999999999999999999988 999999
Q ss_pred Eee
Q 001809 981 VRD 983 (1010)
Q Consensus 981 V~d 983 (1010)
|++
T Consensus 78 v~~ 80 (81)
T cd06396 78 VYE 80 (81)
T ss_pred Eec
Confidence 986
No 4
>PF02042 RWP-RK: RWP-RK domain; InterPro: IPR003035 This domain is named RWP-RK after a conserved motif at the C terminus of the domain. The domain is found in algal minus dominance proteins as well as plant proteins involved in nitrogen-controlled development [].
Probab=99.88 E-value=2.8e-23 Score=173.50 Aligned_cols=51 Identities=51% Similarity=0.871 Sum_probs=49.4
Q ss_pred ccccCHHHHHhhcCCcHHHHHHHcCCChhHHHHHHHHcCCCCCcchhhhhh
Q 001809 599 EKNVSLSVLQQYFSGSLKDAAKSIGVCPTTLKRICRQHGISRWPSRKINKV 649 (1010)
Q Consensus 599 ~~~itl~~L~~yF~~pl~eAAk~LGV~~TtLKRiCR~~GI~RWP~Rki~sl 649 (1010)
.++||+++|++|||+|++|||++||||.|+|||+||++||.|||||||+||
T Consensus 2 ~~~lt~~~L~~~fhlp~~eAA~~Lgv~~T~LKr~CR~~GI~RWP~Rkl~Sl 52 (52)
T PF02042_consen 2 TKSLTLEDLSQYFHLPIKEAAKELGVSVTTLKRRCRRLGIPRWPYRKLKSL 52 (52)
T ss_pred CCccCHHHHHHHhCCCHHHHHHHhCCCHHHHHHHHHHcCCCCCCchhhccC
Confidence 478999999999999999999999999999999999999999999999986
No 5
>cd06398 PB1_Joka2 The PB1 domain is present in the Nicotiana plumbaginifolia Joka2 protein which interacts with sulfur stress inducible UP9 protein. The PB1 domain is a modular domain mediating specific protein-protein interactions which play a role in many critical cell processes, such as osteoclastogenesis, angiogenesis, early cardiovascular development and cell polarity. A canonical PB1-PB1 interaction, which involves heterodimerization of two PB1 domain, is required for the formation of macromolecular signaling complexes ensuring specificity and fidelity during cellular signaling. The interaction between two PB1 domain depends on the type of PB1. There are three types of PB1 domains: type I which contains an OPCA motif, acidic aminoacid cluster, type II which contains a basic cluster, and type I/II which contains both an OPCA motif and a basic cluster. Interactions of PB1 domains with other protein domains have been described as noncanonical PB1-interactions. The PB1 domain module
Probab=99.82 E-value=4.2e-20 Score=170.67 Aligned_cols=81 Identities=26% Similarity=0.384 Sum_probs=76.1
Q ss_pred EEEEEEcCCCeEEEEeCC-----CcChHHHHHHHHHHcCccc-ceeeeEeecCCCCeEEEecCCcHHHHHHH-HhHhCCC
Q 001809 903 IIVKATYKEDIIRFKFDP-----SAGCFQLYEEVARRLKLQN-GTFQLKYLDDEEEWVMLVSDSDLQECFDI-LESLGKR 975 (1010)
Q Consensus 903 ~~vKaty~~d~iRF~~~~-----s~g~~~L~~EIakRf~l~~-~~f~lKYlDDd~EWVlLtcDaDL~EC~di-~~~~~~~ 975 (1010)
++||++|+++++||+++. +++|.+|+++|++||+|.. ..|+|+|+|+|||||.|+||+||+||+++ ++.++.+
T Consensus 1 l~vKv~y~~~~rRf~l~~~~~~~d~~~~~L~~kI~~~f~l~~~~~~~l~Y~Dedgd~V~l~~D~DL~~a~~~~~~~~~~~ 80 (91)
T cd06398 1 LVVKVKYGGTLRRFTFPVAENQLDLNMDGLREKVEELFSLSPDADLSLTYTDEDGDVVTLVDDNDLTDAIQYFCSGSRLN 80 (91)
T ss_pred CEEEEEeCCEEEEEEeccccccCCCCHHHHHHHHHHHhCCCCCCcEEEEEECCCCCEEEEccHHHHHHHHHHHhccCCCc
Confidence 479999999999999985 7999999999999999987 57999999999999999999999999999 5888999
Q ss_pred eEEEEEee
Q 001809 976 SVRFLVRD 983 (1010)
Q Consensus 976 ~vkl~V~d 983 (1010)
++||+|.-
T Consensus 81 ~lrl~v~~ 88 (91)
T cd06398 81 PLRIDVTV 88 (91)
T ss_pred eEEEEEEE
Confidence 99999974
No 6
>PF00564 PB1: PB1 domain; InterPro: IPR000270 The Phox and Bem1p domain, is present in many eukaryotic cytoplasmic signalling proteins. The domain adopts a beta-grasp fold, similar to that found in ubiquitin and Ras-binding domains. A motif, variously termed OPR, PC and AID, represents the most conserved region of the majority of PB1 domains, and is necessary for PB1 domain function. This function is the formation of PB1 domain heterodimers, although not all PB1 domain pairs associate.; GO: 0005515 protein binding; PDB: 1IPG_A 1IP9_A 2KFK_A 1WMH_A 1VD2_A 1WI0_A 1OEY_C 1PQS_A 1Q1O_A 1TZ1_A ....
Probab=99.66 E-value=3.6e-16 Score=139.07 Aligned_cols=82 Identities=30% Similarity=0.527 Sum_probs=79.5
Q ss_pred eEEEEEEcCCCeEE-EEeCCCcChHHHHHHHHHHcCcccceeeeEeecCCCCeEEEecCCcHHHHHHHHhHhCCCeEEEE
Q 001809 902 KIIVKATYKEDIIR-FKFDPSAGCFQLYEEVARRLKLQNGTFQLKYLDDEEEWVMLVSDSDLQECFDILESLGKRSVRFL 980 (1010)
Q Consensus 902 ~~~vKaty~~d~iR-F~~~~s~g~~~L~~EIakRf~l~~~~f~lKYlDDd~EWVlLtcDaDL~EC~di~~~~~~~~vkl~ 980 (1010)
+++||+.|+++++| |.+.+...|.+|+.+|+++|++.+..|.|+|.|+|||||.|++|.||++|++.++.++.+++||.
T Consensus 1 t~~vK~~~~~~~~~~~~~~~~~s~~~L~~~i~~~~~~~~~~~~l~Y~D~dgD~V~i~sd~Dl~~a~~~~~~~~~~~lrl~ 80 (84)
T PF00564_consen 1 TVRVKVRYGGDIRRIISLPSDVSFDDLRSKIREKFGLLDEDFQLKYKDEDGDLVTISSDEDLQEAIEQAKESGSKTLRLF 80 (84)
T ss_dssp SEEEEEEETTEEEEEEEECSTSHHHHHHHHHHHHHTTSTSSEEEEEEETTSSEEEESSHHHHHHHHHHHHHCTTSCEEEE
T ss_pred CEEEEEEECCeeEEEEEcCCCCCHHHHHHHHHHHhCCCCccEEEEeeCCCCCEEEeCCHHHHHHHHHHHHhcCCCcEEEE
Confidence 58999999999999 99999999999999999999999889999999999999999999999999999999999999999
Q ss_pred Eee
Q 001809 981 VRD 983 (1010)
Q Consensus 981 V~d 983 (1010)
|++
T Consensus 81 v~~ 83 (84)
T PF00564_consen 81 VQD 83 (84)
T ss_dssp EEE
T ss_pred EEe
Confidence 986
No 7
>smart00666 PB1 PB1 domain. Phox and Bem1p domain, present in many eukaryotic cytoplasmic signalling proteins. The domain adopts a beta-grasp fold, similar to that found in ubiquitin and Ras-binding domains. A motif, variously termed OPR, PC and AID, represents the most conserved region of the majority of PB1 domains, and is necessary for PB1 domain function. This function is the formation of PB1 domain heterodimers, although not all PB1 domain pairs associate.
Probab=99.61 E-value=2.3e-15 Score=133.65 Aligned_cols=81 Identities=33% Similarity=0.512 Sum_probs=77.5
Q ss_pred eEEEEEEcCCCeEEEEeCCCcChHHHHHHHHHHcCcccceeeeEeecCCCCeEEEecCCcHHHHHHHHhHhCCCeEEEEE
Q 001809 902 KIIVKATYKEDIIRFKFDPSAGCFQLYEEVARRLKLQNGTFQLKYLDDEEEWVMLVSDSDLQECFDILESLGKRSVRFLV 981 (1010)
Q Consensus 902 ~~~vKaty~~d~iRF~~~~s~g~~~L~~EIakRf~l~~~~f~lKYlDDd~EWVlLtcDaDL~EC~di~~~~~~~~vkl~V 981 (1010)
+++||+.|++|++||++++...|.+|++.|+++|++....|.|||.|+|++||.|++|.||++|++.++.++...+||.|
T Consensus 1 ~~~vK~~~~~~~~~~~~~~~~s~~dL~~~i~~~~~~~~~~~~l~Y~Dedgd~v~l~sd~Dl~~a~~~~~~~~~~~l~l~v 80 (81)
T smart00666 1 TVDVKLRYGGETRRLSVPRDISFEDLRSKVAKRFGLDNQSFTLKYQDEDGDLVSLTSDEDLEEAIEEYDSLGSKKLRLHV 80 (81)
T ss_pred CccEEEEECCEEEEEEECCCCCHHHHHHHHHHHhCCCCCCeEEEEECCCCCEEEecCHHHHHHHHHHHHHcCCceEEEEe
Confidence 37899999999999999999999999999999999988889999999999999999999999999999999989999987
Q ss_pred e
Q 001809 982 R 982 (1010)
Q Consensus 982 ~ 982 (1010)
+
T Consensus 81 ~ 81 (81)
T smart00666 81 F 81 (81)
T ss_pred C
Confidence 4
No 8
>cd05992 PB1 The PB1 domain is a modular domain mediating specific protein-protein interactions which play a role in many critical cell processes, such as osteoclastogenesis, angiogenesis, early cardiovascular development, and cell polarity. A canonical PB1-PB1 interaction, which involves heterodimerization of two PB1 domain, is required for the formation of macromolecular signaling complexes ensuring specificity and fidelity during cellular signaling. The interaction between two PB1 domain depends on the type of PB1. There are three types of PB1 domains: type I which contains an OPCA motif, acidic aminoacid cluster, type II which contains a basic cluster, and type I/II which contains both an OPCA motif and a basic cluster. Interactions of PB1 domains with other protein domains have been described as a noncanonical PB1-interactions. The PB1 domain module is conserved in amoebas, fungi, animals, and plants.
Probab=99.56 E-value=1.2e-14 Score=128.57 Aligned_cols=80 Identities=30% Similarity=0.479 Sum_probs=76.4
Q ss_pred EEEEEEcCCCeEEEEeC-CCcChHHHHHHHHHHcCcccceeeeEeecCCCCeEEEecCCcHHHHHHHHhHhCCCeEEEEE
Q 001809 903 IIVKATYKEDIIRFKFD-PSAGCFQLYEEVARRLKLQNGTFQLKYLDDEEEWVMLVSDSDLQECFDILESLGKRSVRFLV 981 (1010)
Q Consensus 903 ~~vKaty~~d~iRF~~~-~s~g~~~L~~EIakRf~l~~~~f~lKYlDDd~EWVlLtcDaDL~EC~di~~~~~~~~vkl~V 981 (1010)
++||+.|+++++||+++ .+.+|.+|++.|+++|++....|.|||.|+|++||.|++|.||++|+..++..+..+++|.|
T Consensus 1 ~~vK~~~~~~~~~~~~~~~~~s~~~L~~~i~~~~~~~~~~~~l~y~D~e~d~v~l~sd~Dl~~a~~~~~~~~~~~l~l~v 80 (81)
T cd05992 1 VRVKVKYGGEIRRFVVVSRSISFEDLRSKIAEKFGLDAVSFKLKYPDEDGDLVTISSDEDLEEAIEEARRSGSKKLRLFV 80 (81)
T ss_pred CcEEEEecCCCEEEEEecCCCCHHHHHHHHHHHhCCCCCcEEEEeeCCCCCEEEeCCHHHHHHHHHHHhhcCCccEEEEe
Confidence 47999999999999999 99999999999999999988889999999999999999999999999999998999999987
Q ss_pred e
Q 001809 982 R 982 (1010)
Q Consensus 982 ~ 982 (1010)
+
T Consensus 81 ~ 81 (81)
T cd05992 81 F 81 (81)
T ss_pred C
Confidence 4
No 9
>cd06404 PB1_aPKC PB1 domain is an essential modular domain of the atypical protein kinase C (aPKC) which in complex with Par6 and Par3 proteins is crucial for establishment of apical-basal polarity of animal cells. PB1 domain is a modular domain mediating specific protein-protein interaction which play roles in many critical cell processes. A canonical PB1-PB1 interaction, which involves heterodimerization of two PB1 domains, is required for the formation of macromolecular signaling complexes ensuring specificity and fidelity during cellular signaling. The interaction between two PB1 domain depends on the type of PB1. There are three types of PB1 domains: type I which contains an OPCA motif, acidic aminoacid cluster, type II which contains a basic cluster, and type I/II which contains both an OPCA motif and a basic cluster. Interactions of PB1 domains with other protein domains have been described as noncanonical PB1-interactions. The PB1 domain module is conserved in amoebas, fungi,
Probab=99.04 E-value=8.6e-10 Score=100.73 Aligned_cols=79 Identities=29% Similarity=0.445 Sum_probs=72.3
Q ss_pred EEEEEEcCCCeEEEEeCCCcChHHHHHHHHHHcCcccc-eeeeEeecCCCCeEEEecCCcHHHHHHHHhHhCCCeEEEEE
Q 001809 903 IIVKATYKEDIIRFKFDPSAGCFQLYEEVARRLKLQNG-TFQLKYLDDEEEWVMLVSDSDLQECFDILESLGKRSVRFLV 981 (1010)
Q Consensus 903 ~~vKaty~~d~iRF~~~~s~g~~~L~~EIakRf~l~~~-~f~lKYlDDd~EWVlLtcDaDL~EC~di~~~~~~~~vkl~V 981 (1010)
++|||.|++|++++.+.++-.|.+|.+||+.-+++..+ .|++||+|+||+-|.+++|.+|+|++.++...... -|.+
T Consensus 1 i~~K~~y~gdi~it~~d~~~s~e~L~~~v~~~c~~~~~q~ft~kw~DEEGDp~tiSS~~EL~EA~rl~~~n~~~--~l~i 78 (83)
T cd06404 1 VRVKAAYNGDIMITSIDPSISLEELCNEVRDMCRFHNDQPFTLKWIDEEGDPCTISSQMELEEAFRLYELNKDS--ELNI 78 (83)
T ss_pred CeEEEEecCcEEEEEcCCCcCHHHHHHHHHHHhCCCCCCcEEEEEECCCCCceeecCHHHHHHHHHHHHhcCcc--cEEE
Confidence 58999999999999999999999999999999998875 79999999999999999999999999999977655 4555
Q ss_pred ee
Q 001809 982 RD 983 (1010)
Q Consensus 982 ~d 983 (1010)
|-
T Consensus 79 hv 80 (83)
T cd06404 79 HV 80 (83)
T ss_pred Ee
Confidence 54
No 10
>cd06408 PB1_NoxR The PB1 domain is present in the Epichloe festucae NoxR protein (NADPH oxidase regulator), a key regulator of NADPH oxidase isoform, NoxA. NoxA is essential for growth control of the fungal endophyte in plant tissue in the process of symbiotic interaction between a fungi and its plant host. The Epichloe festucae p67(phox)-like regulator, NoxR, dispensable in culture but essential in plants for the symbiotic interaction. Plants infected with a noxR deletion mutant show severe stunting and premature senescence, whereas hyphae in the meristematic tissues show increased branching leading to increased fungal colonization of pseudostem and leaf blade tissue. The PB1 domain is a modular domain mediating specific protein-protein interactions which a play role in many critical cell processes such as osteoclastogenesis, angiogenesis, early cardiovascular development, and cell polarity. A canonical PB1-PB1 interaction, which involves heterodimerization of two PB1 domains, is
Probab=98.81 E-value=1.4e-08 Score=93.75 Aligned_cols=68 Identities=21% Similarity=0.365 Sum_probs=65.3
Q ss_pred eEEEEEEcCCCeEEEEeCCCcChHHHHHHHHHHcCcccceeeeEeecCCCCeEEEecCCcHHHHHHHHhH
Q 001809 902 KIIVKATYKEDIIRFKFDPSAGCFQLYEEVARRLKLQNGTFQLKYLDDEEEWVMLVSDSDLQECFDILES 971 (1010)
Q Consensus 902 ~~~vKaty~~d~iRF~~~~s~g~~~L~~EIakRf~l~~~~f~lKYlDDd~EWVlLtcDaDL~EC~di~~~ 971 (1010)
.|+||+.|.+|++-++++|+-.|.+|.++|..||++. ..|.|||.|+ |+-|.|+.|.||+++|..++.
T Consensus 2 ~ikVKv~~~~Dv~~i~v~~~i~f~dL~~kIrdkf~~~-~~~~iKykDE-GD~iti~sq~DLd~Ai~~a~~ 69 (86)
T cd06408 2 KIRVKVHAQDDTRYIMIGPDTGFADFEDKIRDKFGFK-RRLKIKMKDD-GDMITMGDQDDLDMAIDTARS 69 (86)
T ss_pred cEEEEEEecCcEEEEEcCCCCCHHHHHHHHHHHhCCC-CceEEEEEcC-CCCccccCHHHHHHHHHHHHH
Confidence 5899999999999999999999999999999999995 6899999999 999999999999999999985
No 11
>cd06402 PB1_p62 The PB1 domain is an essential part of p62 scaffold protein (alias sequestosome 1,SQSTM) involved in cell signaling, receptor internalization, and protein turnover. The PB1 domain is a modular domain mediating specific protein-protein interaction which play roles in many critical cell processes. A canonical PB1-PB1 interaction, which involves heterodimerization of two PB1 domains, is required for the formation of macromolecular signaling complexes ensuring specificity and fidelity during cellular signaling. The interaction between two PB1 domain depends on the type of PB1. There are three types of PB1 domains: type I which contains an OPCA motif, acidic aminoacid cluster, type II which contains a basic cluster, and type I/II which contains both an OPCA motif and a basic cluster. Interactions of PB1 domains with other protein domains have been described as noncanonical PB1-interactions. The PB1 domain module is conserved in amoebas, fungi, animals, and plants.
Probab=98.75 E-value=3.1e-08 Score=91.69 Aligned_cols=78 Identities=31% Similarity=0.448 Sum_probs=67.6
Q ss_pred EEEEEEc-----CCCeEEEEe--CCCcChHHHHHHHHHHcC-cccceeeeEeecCCCCeEEEecCCcHHHHHHHHhHhCC
Q 001809 903 IIVKATY-----KEDIIRFKF--DPSAGCFQLYEEVARRLK-LQNGTFQLKYLDDEEEWVMLVSDSDLQECFDILESLGK 974 (1010)
Q Consensus 903 ~~vKaty-----~~d~iRF~~--~~s~g~~~L~~EIakRf~-l~~~~f~lKYlDDd~EWVlLtcDaDL~EC~di~~~~~~ 974 (1010)
++|||-- ..|+.||.+ ..+..|.+|+++|.++|. +.+..|.|||.|+||+=|.|++|.||++++.-+. .
T Consensus 1 ~~vkayl~~~~~~~EIRRf~l~~~~~~s~~~L~~~V~~~f~~l~~~~ftlky~DeeGDlvtIssdeEL~~A~~~~~---~ 77 (87)
T cd06402 1 LTVKAYLLGKDANAEIRRFAIDEDVSTSYEYLVEKVAAVFPSLRGKNFQLFWKDEEGDLVAFSSDEELVMALGSLN---D 77 (87)
T ss_pred CeEEEeecCCCCccceEEEEecCCCCcCHHHHHHHHHHHccccCCCcEEEEEECCCCCEEeecCHHHHHHHHHcCC---C
Confidence 4788866 359999999 556789999999999995 6567899999999999999999999999998776 4
Q ss_pred CeEEEEEee
Q 001809 975 RSVRFLVRD 983 (1010)
Q Consensus 975 ~~vkl~V~d 983 (1010)
.++||+|..
T Consensus 78 ~~~RlyI~~ 86 (87)
T cd06402 78 DTFRIYIKE 86 (87)
T ss_pred CcEEEEEEe
Confidence 899999864
No 12
>cd06401 PB1_TFG The PB1 domain found in TFG protein, an oncogenic gene product and fusion partner to nerve growth factor tyrosine kinase receptor TrkA and to the tyrosine kinase ALK. The PB1 domain is a modular domain mediating specific protein-protein interaction in many critical cell processes, such as osteoclastogenesis, angiogenesis, early cardiovascular development and cell polarity. A canonical PB1-PB1 interaction, which involves heterodimerization of two PB1 domains, is required for the formation of macromolecular signaling complexes ensuring specificity and fidelity during cellular signaling. The interaction between two PB1 domain depends on the type of PB1. There are three types of PB1 domains: type I which contains an OPCA motif, acidic aminoacid cluster, type II which contains a basic cluster, and type I/II which contains both an OPCA motif and a basic cluster. The PB1 domains of TFG represent a type I/II PB1 domain. The physiological function of TFG remains unknown.
Probab=98.70 E-value=5.6e-08 Score=88.73 Aligned_cols=75 Identities=20% Similarity=0.277 Sum_probs=63.4
Q ss_pred EEEEEcCCCeEEEEeCC-CcChHHHHHHHHHHcCccc---ceeeeEeecCCCCeEEEecCCcHHHHHHHHhHhCCCeEEE
Q 001809 904 IVKATYKEDIIRFKFDP-SAGCFQLYEEVARRLKLQN---GTFQLKYLDDEEEWVMLVSDSDLQECFDILESLGKRSVRF 979 (1010)
Q Consensus 904 ~vKaty~~d~iRF~~~~-s~g~~~L~~EIakRf~l~~---~~f~lKYlDDd~EWVlLtcDaDL~EC~di~~~~~~~~vkl 979 (1010)
.||+.|++|+.||.+.. ...|.+|.+-|++.|+..- ..|-+||.|.||+||-||++.||..++...+ ..+++|
T Consensus 2 iiK~~~g~DiR~~~~~~~~~t~~~L~~~v~~~F~~~~~~~~~flIKYkD~dGDlVTIts~~dL~~A~~~~~---~~~l~~ 78 (81)
T cd06401 2 ILKAQLGDDIRRIPIHNEDITYDELLLMMQRVFRGKLGSSDDVLIKYKDEDGDLITIFDSSDLSFAIQCSR---ILKLTL 78 (81)
T ss_pred eEEEEeCCeEEEEeccCccccHHHHHHHHHHHhccccCCcccEEEEEECCCCCEEEeccHHHHHHHHhcCc---ceEEEE
Confidence 68999999999999986 4799999999999999553 3699999999999999999999999965543 445555
Q ss_pred EE
Q 001809 980 LV 981 (1010)
Q Consensus 980 ~V 981 (1010)
.|
T Consensus 79 ~~ 80 (81)
T cd06401 79 FV 80 (81)
T ss_pred ec
Confidence 44
No 13
>cd06397 PB1_UP1 Uncharacterized protein 1. The PB1 domain is a modular domain mediating specific protein-protein interaction which play a role in many critical cell processes, such as osteoclastogenesis, angiogenesis, early cardiovascular development, and cell polarity. A canonical PB1-PB1 interaction, which involves heterodimerization of two PB1 domain, is required for the formation of macromolecular signaling complexes ensuring specificity and fidelity during cellular signaling. The interaction between two PB1 domain depends on the type of PB1. There are three types of PB1 domains: type I which contains an OPCA motif, acidic aminoacid cluster, type II which contains a basic cluster, and type I/II which contains both an OPCA motif and a basic cluster. Interactions of PB1 domains with other protein domains have been described as noncanonical PB1-interactions.
Probab=98.69 E-value=6.1e-08 Score=88.16 Aligned_cols=81 Identities=17% Similarity=0.295 Sum_probs=74.5
Q ss_pred EEEEEEcCCCeEEEEeCCCcChHHHHHHHHHHcCcccceeeeEeecCCCCeEEEecCCcHHHHHHHHhHhCCCeEEEEEe
Q 001809 903 IIVKATYKEDIIRFKFDPSAGCFQLYEEVARRLKLQNGTFQLKYLDDEEEWVMLVSDSDLQECFDILESLGKRSVRFLVR 982 (1010)
Q Consensus 903 ~~vKaty~~d~iRF~~~~s~g~~~L~~EIakRf~l~~~~f~lKYlDDd~EWVlLtcDaDL~EC~di~~~~~~~~vkl~V~ 982 (1010)
+++|++|++++.||.++---.+..|.+-|..-|+|....|.|+|.|+|++=|.|+.|.||+|.+-+...+...++||-|.
T Consensus 1 ~~fKv~~~g~~RRf~~~~~pt~~~L~~kl~~Lf~lp~~~~~vtYiDeD~D~ITlssd~eL~d~~~~~~~~~~~v~k~~~~ 80 (82)
T cd06397 1 TQFKSSFLGDTRRIVFPDIPTWEALASKLENLYNLPEIKVGVTYIDNDNDEITLSSNKELQDFYRLSHRESTEVIKLNVN 80 (82)
T ss_pred CeEEEEeCCceEEEecCCCccHHHHHHHHHHHhCCChhHeEEEEEcCCCCEEEecchHHHHHHHHhcccccCceeEeecc
Confidence 36899999999999998777888999999999999977799999999999999999999999999888877789999887
Q ss_pred e
Q 001809 983 D 983 (1010)
Q Consensus 983 d 983 (1010)
|
T Consensus 81 d 81 (82)
T cd06397 81 D 81 (82)
T ss_pred c
Confidence 6
No 14
>cd06403 PB1_Par6 The PB1 domain is an essential part of Par6 protein which in complex with Par3 and aPKC proteins is crucial for establishment of apical-basal polarity of animal cells. The PB1 domain is a modular domain mediating specific protein-protein interactions which play a role in many critical cell processes. A canonical PB1-PB1 interaction, which involves heterodimerization of two PB1 domains, is required for the formation of macromolecular signaling complexes ensuring specificity and fidelity during cellular signaling. The interaction between two PB1 domain depends on the type of PB1. There are three types of PB1 domains: type I which contains an OPCA motif, acidic aminoacid cluster, type II which contains a basic cluster, and type I/II which contains both an OPCA motif and a basic cluster. Interactions of PB1 domains with other protein domains have been described as noncanonical PB1-interactions. The PB1 domain module is conserved in amoebas, fungi, animals, and plants. The
Probab=98.04 E-value=1.6e-05 Score=72.65 Aligned_cols=75 Identities=16% Similarity=0.345 Sum_probs=70.8
Q ss_pred EEEEEcCCCeEEEEeCCC--cChHHHHHHHHHHcCcccceeeeEeecCCCCeEEEecCCcHHHHHHHHhHhCCCeEEEEE
Q 001809 904 IVKATYKEDIIRFKFDPS--AGCFQLYEEVARRLKLQNGTFQLKYLDDEEEWVMLVSDSDLQECFDILESLGKRSVRFLV 981 (1010)
Q Consensus 904 ~vKaty~~d~iRF~~~~s--~g~~~L~~EIakRf~l~~~~f~lKYlDDd~EWVlLtcDaDL~EC~di~~~~~~~~vkl~V 981 (1010)
-||.+|+.|..||.|..+ .+|.+++.=|.+.++|.+..|.|+|-|.+|+-.-|++|..+.+++..+ ...+||.|
T Consensus 2 eVKSkfdaEfRRFsl~r~~~~~f~ef~~ll~~lH~l~~~~f~i~Y~D~~gDLLPInNDdNf~kAlssa----~plLRl~i 77 (80)
T cd06403 2 EVKSKFDAEFRRFSLDRNKPGKFEDFYKLLEHLHHIPNVDFLIGYTDPHGDLLPINNDDNFLKALSSA----NPLLRIFI 77 (80)
T ss_pred ceecccCCeEEEEEeccccCcCHHHHHHHHHHHhCCCCCcEEEEEeCCCCCEecccCcHHHHHHHHcC----CCceEEEE
Confidence 599999999999999987 899999999999999999999999999999999999999999999866 58999998
Q ss_pred e
Q 001809 982 R 982 (1010)
Q Consensus 982 ~ 982 (1010)
+
T Consensus 78 q 78 (80)
T cd06403 78 Q 78 (80)
T ss_pred E
Confidence 7
No 15
>cd06406 PB1_P67 A PB1 domain is present in p67 proteins which forms a signaling complex with p40, a crucial step for activation of NADPH oxidase during phagocytosis. PB1 domain is a modular domain mediating specific protein-protein interactions which play a role in many critical cell processes . A canonical PB1-PB1 interaction, which involves heterodimerization of two PB1 domains, is required for the formation of macromolecular signaling complexes ensuring specificity and fidelity during cellular signaling. The interaction between two PB1 domain depends on the type of PB1. There are three types of PB1 domains: type I which contains an OPCA motif, acidic aminoacid cluster, type II which contains a basic cluster, and type I/II which contains both an OPCA motif and a basic cluster. Interactions of PB1 domains with other protein domains have been described as noncanonical PB1-interactions. The PB1 domain module is conserved in amoebas, fungi, animals, and plants. The p67 proteins contain
Probab=97.64 E-value=0.00012 Score=67.26 Aligned_cols=68 Identities=19% Similarity=0.388 Sum_probs=61.2
Q ss_pred eEEEEEEcCCCeEEEEeCCCcChHHHHHHHHHHcCcccceeeeEeecCCC-CeEEEecCCcHHHHHHHHhH
Q 001809 902 KIIVKATYKEDIIRFKFDPSAGCFQLYEEVARRLKLQNGTFQLKYLDDEE-EWVMLVSDSDLQECFDILES 971 (1010)
Q Consensus 902 ~~~vKaty~~d~iRF~~~~s~g~~~L~~EIakRf~l~~~~f~lKYlDDd~-EWVlLtcDaDL~EC~di~~~ 971 (1010)
+..||+.|.. +|-.|+++.-.|.+|++-|++||+|......|.|.|++. |-|.| .|.||++++--.+.
T Consensus 2 ~~vvKV~f~~-tIaIrvp~~~~y~~L~~ki~~kLkl~~e~i~LsYkde~s~~~v~l-~d~dle~aws~~~~ 70 (80)
T cd06406 2 SYVVKVHFKY-TVAIQVARGLSYATLLQKISSKLELPAEHITLSYKSEASGEDVIL-SDTNMEDVWSQAKD 70 (80)
T ss_pred CeEEEEEEEE-EEEEEcCCCCCHHHHHHHHHHHhCCCchhcEEEeccCCCCCccCc-ChHHHHHHHHhhcC
Confidence 3689999996 999999999999999999999999987789999999875 88888 99999999877664
No 16
>PF14215 bHLH-MYC_N: bHLH-MYC and R2R3-MYB transcription factors N-terminal
Probab=96.88 E-value=0.0018 Score=66.49 Aligned_cols=67 Identities=25% Similarity=0.378 Sum_probs=56.4
Q ss_pred hhccceeeeccCCCCCCCCCCCcccccCCCCcccccccccCcccccchhhHHhcCCceEEEEeeecCCCCceEEEEEEee
Q 001809 217 REVSRKFTFSAEAKPGTFLGLPGRVFSSKVPEWTSNVAYYNEAEYARVTHAVNHAVRSCIALPVFQFPEISCSAVLEIVS 296 (1010)
Q Consensus 217 R~vS~~f~Fs~~~~~~~~~GLPGRVF~s~~PEWTpnV~~y~~~EYpR~~~A~~~~VrGsLAlPVf~~~s~~ClAVlElV~ 296 (1010)
-.+|..|.|. .|+|||||.++.|.|..+...-....|+|...|+.+++...+-||| + -|||||=.
T Consensus 81 ~~~s~~~sfg--------~G~~G~a~~sg~~~Wi~~~~~~~~~~~~r~~~aq~~~~~Tiv~IPv--~-----~GVvELGS 145 (163)
T PF14215_consen 81 YLVSMSYSFG--------EGIPGRAAASGQHIWISGANELDSSYCERAWLAQFAGIQTIVCIPV--P-----NGVVELGS 145 (163)
T ss_pred hhceeeEEec--------CCccEEEeecCccEEEeCCCccccccchhhhhhcccccceEEEEEe--c-----CCEEEeee
Confidence 3457778882 3999999999999999999998999999999999999997778999 2 25888855
Q ss_pred ec
Q 001809 297 VK 298 (1010)
Q Consensus 297 t~ 298 (1010)
|+
T Consensus 146 t~ 147 (163)
T PF14215_consen 146 TE 147 (163)
T ss_pred ee
Confidence 54
No 17
>cd06411 PB1_p51 The PB1 domain is present in the p51 protein, a homolog of the p67 protein. p51 plays an important role in NADPH oxidase activation during phagosytosis. The PB1 domain is a modular domain mediating specific protein-protein interaction in many critical cell processes such as osteoclastogenesis, angiogenesis, early cardiovascular development, and cell polarity. A canonical PB1-PB1 interaction, which involves heterodimerization of two PB1 domains, is required for the formation of macromolecular signaling complexes ensuring specificity and fidelity during cellular signaling. The interaction between two PB1 domain depends on the type of PB1. There are three types of PB1 domains: type I which contains an OPCA motif, acidic aminoacid cluster, type II which contains a basic cluster, and type I/II which contains both an OPCA motif and a basic cluster. Interactions of PB1 domains with other protein domains have been described as noncanonical PB1-interactions. The PB1 domain mo
Probab=96.69 E-value=0.0043 Score=57.04 Aligned_cols=58 Identities=21% Similarity=0.286 Sum_probs=51.4
Q ss_pred eEEEEeCCCcChHHHHHHHHHHcCcccceeeeEeecCCC--CeEEEecCCcHHHHHHHHh
Q 001809 913 IIRFKFDPSAGCFQLYEEVARRLKLQNGTFQLKYLDDEE--EWVMLVSDSDLQECFDILE 970 (1010)
Q Consensus 913 ~iRF~~~~s~g~~~L~~EIakRf~l~~~~f~lKYlDDd~--EWVlLtcDaDL~EC~di~~ 970 (1010)
+|-.++++-..+.+|.+=|+++|++.....+|.|.+.++ |||.|+.|.|+|+.-.-.+
T Consensus 8 TVai~v~~g~~y~~L~~~ls~kL~l~~~~~~LSY~~~~~~~~~v~l~~e~~me~aW~~v~ 67 (78)
T cd06411 8 TVALRAPRGADVSSLRALLSQALPQQAQRGQLSYRAPGEDGHWVPISGEESLQRAWQDVA 67 (78)
T ss_pred EEEEEccCCCCHHHHHHHHHHHhcCChhhcEEEecCCCCCccEeecCcchHHHHHHHhcc
Confidence 456889999999999999999999999999999998776 7999999999998765444
No 18
>PF14215 bHLH-MYC_N: bHLH-MYC and R2R3-MYB transcription factors N-terminal
Probab=96.44 E-value=0.0023 Score=65.63 Aligned_cols=71 Identities=20% Similarity=0.270 Sum_probs=60.4
Q ss_pred hHHHHhhhcccccCCCcchhhhhcCCCcccccccccCccccchhhHHHHhCCceeEEEEecccccCCCcEEEEeecCCCC
Q 001809 409 GFVHACSEHYLEEGQGVAGKALQSNHPFFFPDVKLYDITEFPLVHHARKFGLNAAVAIRLRSTYTGDDDYILEFFLPVTI 488 (1010)
Q Consensus 409 gFr~AC~EhhL~~GQGvaGkAf~sn~P~F~~DV~~fsk~EYPL~HhAr~fgL~aAvAIrLrS~~tG~ddyVLEFFLP~~c 488 (1010)
=|...|.-+.| |+|++||||.++.|.|..+........++++..|+..|+..-|-||+.. | ||||+--..+
T Consensus 79 ~f~~~s~~~sf--g~G~~G~a~~sg~~~Wi~~~~~~~~~~~~r~~~aq~~~~~Tiv~IPv~~---G----VvELGSt~~I 149 (163)
T PF14215_consen 79 WFYLVSMSYSF--GEGIPGRAAASGQHIWISGANELDSSYCERAWLAQFAGIQTIVCIPVPN---G----VVELGSTEKI 149 (163)
T ss_pred HHhhceeeEEe--cCCccEEEeecCccEEEeCCCccccccchhhhhhcccccceEEEEEecC---C----EEEeeeeeee
Confidence 34555666666 9999999999999999999999888899999999999999888899954 4 9999865444
No 19
>KOG0695 consensus Serine/threonine protein kinase [Signal transduction mechanisms]
Probab=96.38 E-value=0.017 Score=65.58 Aligned_cols=83 Identities=27% Similarity=0.406 Sum_probs=73.6
Q ss_pred CCeEEEEEEcCCCeEEEEeCCCcChHHHHHHHHHHcCcccc-eeeeEeecCCCCeEEEecCCcHHHHHHHHhHhCCCeEE
Q 001809 900 GSKIIVKATYKEDIIRFKFDPSAGCFQLYEEVARRLKLQNG-TFQLKYLDDEEEWVMLVSDSDLQECFDILESLGKRSVR 978 (1010)
Q Consensus 900 ~~~~~vKaty~~d~iRF~~~~s~g~~~L~~EIakRf~l~~~-~f~lKYlDDd~EWVlLtcDaDL~EC~di~~~~~~~~vk 978 (1010)
+..+++||.|++|++-..+.|+--|.+|++||-.--+++.. -|.+|+.|.|++-+.+..--.|+|++.+++.+.-..+-
T Consensus 13 ~~~vrlka~y~g~i~i~~~~p~~~~e~~~~~vrd~c~~h~~q~~t~kwideegdp~tv~sqmeleea~r~~~~~~d~el~ 92 (593)
T KOG0695|consen 13 GGRVRLKAHYGGDIFITSVDPATTFEELCEEVRDMCRLHQQQPLTLKWIDEEGDPCTVSSQMELEEAFRLARQCRDEELI 92 (593)
T ss_pred CccEEEEEeecCcEEEEeccCcccHHHHHHHHHHHHHHhhcCCceeEeecCCCCcceechhhhHHHHHHHHHhccccceE
Confidence 45799999999999999999999999999999988888875 59999999999999999999999999999987665544
Q ss_pred EEEe
Q 001809 979 FLVR 982 (1010)
Q Consensus 979 l~V~ 982 (1010)
|-|.
T Consensus 93 ihvf 96 (593)
T KOG0695|consen 93 IHVF 96 (593)
T ss_pred EEEc
Confidence 4443
No 20
>cd06410 PB1_UP2 Uncharacterized protein 2. The PB1 domain is a modular domain mediating specific protein-protein interaction which play a role in many critical cell processes such as osteoclastogenesis, angiogenesis, early cardiovascular development, and cell polarity. A canonical PB1-PB1 interaction, which involves heterodimerization of two PB1 domains, is required for the formation of macromolecular signaling complexes ensuring specificity and fidelity during cellular signaling. The interaction between two PB1 domain depends on the type of PB1. There are three types of PB1 domains: type I which contains an OPCA motif, acidic aminoacid cluster, type II which contains a basic cluster, and type I/II which contains both an OPCA motif and a basic cluster. Interactions of PB1 domains with other protein domains have been described as noncanonical PB1-interactions.
Probab=95.99 E-value=0.039 Score=52.63 Aligned_cols=74 Identities=18% Similarity=0.277 Sum_probs=60.3
Q ss_pred EEc-CCCeEEEEeCCCcChHHHHHHHHHHcCcccceeeeEee--cCCCC-eEEEecCCcHHHHHHHHhH--hCCCeEEEE
Q 001809 907 ATY-KEDIIRFKFDPSAGCFQLYEEVARRLKLQNGTFQLKYL--DDEEE-WVMLVSDSDLQECFDILES--LGKRSVRFL 980 (1010)
Q Consensus 907 aty-~~d~iRF~~~~s~g~~~L~~EIakRf~l~~~~f~lKYl--DDd~E-WVlLtcDaDL~EC~di~~~--~~~~~vkl~ 980 (1010)
..| |+++.-..+.-+..|.||...++..+++... +.|||. ++|-+ =|.|++|.||+.=++-+.. .+..+||++
T Consensus 17 l~Y~GG~tr~i~V~r~~s~~el~~kl~~~~~~~~~-~~lky~Lp~edld~Lisv~~DeDl~~M~~e~~~~~~~~~rirvf 95 (97)
T cd06410 17 LRYVGGETRIVSVDRSISFKELVSKLSELFGAGVV-VTLKYQLPDEDLDALISVSNDEDLKNMMEEYDRLSGGSARLRVF 95 (97)
T ss_pred EEEcCCceEEEEEcCCCCHHHHHHHHHHHhCCCCc-eEEEEEcCCCCcceeEEecCcHHHHHHHHhhccccCCCceEEEE
Confidence 445 4588888999999999999999999999877 999998 77767 8899999999987777663 345567666
Q ss_pred E
Q 001809 981 V 981 (1010)
Q Consensus 981 V 981 (1010)
+
T Consensus 96 l 96 (97)
T cd06410 96 L 96 (97)
T ss_pred E
Confidence 4
No 21
>PRK15429 formate hydrogenlyase transcriptional activator FhlA; Provisional
Probab=95.85 E-value=0.12 Score=63.41 Aligned_cols=236 Identities=11% Similarity=0.082 Sum_probs=131.0
Q ss_pred CCCCCcccccCCCCcccccccccCcccccchh-hHHhcCCceEEEEeeecCCCCceEEEEEEeeecccCCchHHHHHHHH
Q 001809 234 FLGLPGRVFSSKVPEWTSNVAYYNEAEYARVT-HAVNHAVRSCIALPVFQFPEISCSAVLEIVSVKEKPNFDAEIENICN 312 (1010)
Q Consensus 234 ~~GLPGRVF~s~~PEWTpnV~~y~~~EYpR~~-~A~~~~VrGsLAlPVf~~~s~~ClAVlElV~t~ek~~f~~E~e~vc~ 312 (1010)
..|+-|+|+.++.|.--++..++.. ||.+. +-.+..++.-++|||...+. -+|+|+|.-.. ...|..+-+.+-+
T Consensus 77 ~~g~~g~vl~~~~~l~~~~~~~~~~--~~~l~~~~~~~~~~~~lgvPl~~~~~--v~G~l~l~~~~-~~~Ft~~d~~ll~ 151 (686)
T PRK15429 77 AHGPVRRILSRPDTLHCSYEEFCET--WPQLAAGGLYPKFGHYCLMPLAAEGH--IFGGCEFIRYD-DRPWSEKEFNRLQ 151 (686)
T ss_pred ccCcceEEeecCceEEEchHHhhhc--cHHHhhcccccCccceEEeceeeCCe--eEEEEEEEEcC-CCCCCHHHHHHHH
Confidence 4599999999999996655555442 22122 22234455566799999664 49999998776 6899988766654
Q ss_pred Hhh--------hccccccCCCCCCcccc--chHHHHHHHHHHH--------------HHHHHHHhcCCcceeeeeccccC
Q 001809 313 ALQ--------AVNLRTTAPPRLLPQNI--SRNQKAALAEITD--------------VLRAVCHAHRLPLALTWIPCNYD 368 (1010)
Q Consensus 313 ALq--------aVnLrss~~~~~~pq~~--~~~~~aAl~EI~e--------------VL~~VC~~h~LPLAqTWvPc~~~ 368 (1010)
+|- .+-++-..-.+ -.-+ ......++.||.+ |++.+.+......+-+|++-..
T Consensus 152 ~la~~a~~aie~~~~~e~~~~~--~~~L~~~r~~~~~L~eIs~~l~s~~dl~ell~~I~~~i~~~~~a~~~~I~L~d~~- 228 (686)
T PRK15429 152 TFTQIVSVVTEQIQSRVVNNVD--YELLCRERDNFRILVAITNAVLSRLDMDELVSEVAKEIHYYFDIDAISIVLRSHR- 228 (686)
T ss_pred HHHHHHHHHHHHHHHHHHHHHH--HHHHHhhHHHHHHHHHHHHHHccCCCHHHHHHHHHHHHHHHhCCCEEEEEEEECC-
Confidence 442 21111000000 0000 0112344555532 2344445555555555555221
Q ss_pred ccchhhhhhhhhccCCcCCCCCeEEEeeCccccccCcchhhHHHHhhhcccccCCCcchhhhhcCCCcccccccccCccc
Q 001809 369 EEAVDEVIKVRVRHSNTSSDGKSVLCIEGTACYVNDSDMQGFVHACSEHYLEEGQGVAGKALQSNHPFFFPDVKLYDITE 448 (1010)
Q Consensus 369 ~~~~d~~~~~~~k~g~~~~~gk~~Lci~dsAcYV~D~~m~gFr~AC~EhhL~~GQGvaGkAf~sn~P~F~~DV~~fsk~E 448 (1010)
.+ .|.+. .+.|+.+.. .......+..+.|++|+||.++.|.++.|+..-....
T Consensus 229 -------------------~~--~L~~~-aa~g~~~~~-----~~~~~~~~~~~~~l~g~V~~~~~p~lv~~~~~d~~~~ 281 (686)
T PRK15429 229 -------------------KN--KLNIY-STHYLDKQH-----PAHEQSEVDEAGTLTERVFKSKEMLLINLHERDDLAP 281 (686)
T ss_pred -------------------CC--cEEEE-EecccChhh-----cccccccCCcccchHHHHHhcCceEEEECccCcccch
Confidence 01 12211 123332111 1112334556679999999999999998876432222
Q ss_pred cchhhHH-HHhCCceeEEEEecccccCCCcEEEEeecCCCCCCcHHHHHHHHHHHHHHH
Q 001809 449 FPLVHHA-RKFGLNAAVAIRLRSTYTGDDDYILEFFLPVTIKGSSEQQLLLNNLSGTMQ 506 (1010)
Q Consensus 449 YPL~HhA-r~fgL~aAvAIrLrS~~tG~ddyVLEFFLP~~ck~~~EQq~ll~sLs~Tmq 506 (1010)
|+-.... ...+++.++++||... |..--||.+.-+..-.=.++...||..+...+-
T Consensus 282 ~~~~~~~~~~~~~~s~l~vPL~~~--~~v~GvL~l~~~~~~~F~~~dl~lL~~iA~~~A 338 (686)
T PRK15429 282 YERMLFDTWGNQIQTLCLLPLMSG--DTMLGVLKLAQCEEKVFTTTNLKLLRQIAERVA 338 (686)
T ss_pred hhhhhhhcccccceEEEEEeEEEC--CEEEEEEEEeeCCCCcCCHHHHHHHHHHHHHHH
Confidence 3322111 1247899999999863 567788998755444445566677766655443
No 22
>cd06405 PB1_Mekk2_3 The PB1 domain is present in the two mitogen-activated protein kinase kinases MEKK2 and MEKK3 which are two members of the signaling kinase cascade involved in angiogenesis and early cardiovascular development. The PB1 domain of MEKK2 (and/or MEKK3) interacts with the PB1 domain of another member of the kinase cascade Map2k5. A canonical PB1-PB1 interaction, which involves heterodimerization of two PB1 domains, is required for the formation of macromolecular signaling complexes ensuring specificity and fidelity during cellular signaling. The interaction between two PB1 domain depends on the type of PB1. There are three types of PB1 domains: type I which contains an OPCA motif, acidic aminoacid cluster, type II which contains a basic cluster, and type I/II which contains both an OPCA motif and a basic cluster. Interactions of PB1 domains with other protein domains have been described as noncanonical PB1-interactions. The PB1 domain module is conserved in amoebas, f
Probab=95.40 E-value=0.078 Score=48.67 Aligned_cols=76 Identities=18% Similarity=0.309 Sum_probs=65.7
Q ss_pred EEEEEEcCCCeEEEEeCCCcChHHHHHHHHHHcCcccceeeeEeecCCCCeEEEecCCcHHHHHHHHhHhC-CCeEEEEE
Q 001809 903 IIVKATYKEDIIRFKFDPSAGCFQLYEEVARRLKLQNGTFQLKYLDDEEEWVMLVSDSDLQECFDILESLG-KRSVRFLV 981 (1010)
Q Consensus 903 ~~vKaty~~d~iRF~~~~s~g~~~L~~EIakRf~l~~~~f~lKYlDDd~EWVlLtcDaDL~EC~di~~~~~-~~~vkl~V 981 (1010)
+|||+-|.+++--+.|+----|.||++-+--+|| ...+|-|+-+| =-|-|.|-.||.-+|+++..++ .+.+||++
T Consensus 1 vRiKfE~~gEKRIi~f~RPvkf~dl~~kv~~afG---q~mdl~ytn~e-L~iPl~~Q~DLDkAie~ld~s~~~ksLRilL 76 (79)
T cd06405 1 VRIKFEHNGEKRIIQFPRPVKFKDLQQKVTTAFG---QPMDLHYTNNE-LLIPLKNQEDLDRAIELLDRSPHMKSLRILL 76 (79)
T ss_pred CeEEEEecCceEEEecCCCccHHHHHHHHHHHhC---CeeeEEEeccc-EEEeccCHHHHHHHHHHHccCccccceeEeE
Confidence 5899999999999999999999999999999997 36788898877 5677899999999999998765 45677765
Q ss_pred e
Q 001809 982 R 982 (1010)
Q Consensus 982 ~ 982 (1010)
-
T Consensus 77 ~ 77 (79)
T cd06405 77 S 77 (79)
T ss_pred e
Confidence 3
No 23
>PF13185 GAF_2: GAF domain; PDB: 2QYB_A 3KSG_B 3KSF_C 3KSI_A 3KSH_A 3MMH_A 3RFB_B 1F5M_A 3KO6_B 3HCY_A ....
Probab=94.40 E-value=0.2 Score=47.12 Aligned_cols=137 Identities=18% Similarity=0.213 Sum_probs=75.5
Q ss_pred CHHHHHHHHHHHHHHhcCCCeeEEEEeeeccCCeeeeeeCCCCcccchhhhHHhhccceeeeccCCCCCCCCCCCccccc
Q 001809 164 SLDEKMLRALSFFKLSSGGGILAQVWVPRKQGDDYILSTSDQPYLLDQMLAGYREVSRKFTFSAEAKPGTFLGLPGRVFS 243 (1010)
Q Consensus 164 svkerm~~AL~~~kes~~~~~L~QVWvP~~~g~~~vLsT~~qP~~ld~~L~~yR~vS~~f~Fs~~~~~~~~~GLPGRVF~ 243 (1010)
++.|=+..++..+.+.++.+ .+-||+=..++....+...+.+- ..+..-+.......+..... . .|+.++++.
T Consensus 3 ~~~ell~~~~~~~~~~~~~~-~~~i~l~d~~~~~~~~~~~~~~~---~~~~~~~~~~~~~~~~~~~~--~-~~~~~~~~~ 75 (148)
T PF13185_consen 3 DLEELLQQILDALLELTGAD-AGAIYLYDPDGQLLPVAASGDPS---EFLKEEIPLPPPPDEPPAYA--A-VGLWEGVLR 75 (148)
T ss_dssp HHHHHHHHHHHHHHHHHS-S-EEEEEEEETTSEEEEEEEESSSC---TSTCCECCCCCCCESCHHHC--C-EETTSHHHH
T ss_pred CHHHHHHHHHHHHHHHhCCC-EEEEEEEECCCcEEEEEEeCCch---hhhhhhcccCcccccccchh--h-hhHHHHHHh
Confidence 35666677788888877755 44466665554333333333220 00000001111111110000 0 467778899
Q ss_pred CCCCcccccccccCcccccchhhHHhcCCceEEEEeeecCCCCceEEEEEEeeecccCCchHHHHHHHHHh
Q 001809 244 SKVPEWTSNVAYYNEAEYARVTHAVNHAVRSCIALPVFQFPEISCSAVLEIVSVKEKPNFDAEIENICNAL 314 (1010)
Q Consensus 244 s~~PEWTpnV~~y~~~EYpR~~~A~~~~VrGsLAlPVf~~~s~~ClAVlElV~t~ek~~f~~E~e~vc~AL 314 (1010)
.+.|.|.+ +....+.+...+.+.++++.|++||+..+ ..+|||-|.. .+...|..+-..+..+|
T Consensus 76 ~~~~~~~~----~~~~~~~~~~~~~~~~~~s~l~vPl~~~~--~~~Gvl~l~~-~~~~~f~~~~~~~l~~l 139 (148)
T PF13185_consen 76 TGEPIIIN----DDDSSFPPWELARHPGIRSILCVPLRSGG--EVIGVLSLYS-KEPNAFSEEDLELLEAL 139 (148)
T ss_dssp HTS-EEES----CCCGGGSTTHHHCCTT-SEEEEEEEEETT--EEEEEEEEEE-SSTT---HHHHHHHHHH
T ss_pred cCceEEEe----CccccccchhhhccccCCEEEEEEEeECC--EEEEEEEEee-CCCCCcCHHHHHHHHHH
Confidence 99999998 33344444678889999999999999777 4499997655 44467777765555544
No 24
>PF01418 HTH_6: Helix-turn-helix domain, rpiR family; InterPro: IPR000281 This domain contains a helix-turn-helix motif []. Every member of this family is N-terminal to a SIS domain IPR001347 from INTERPRO. Members of this family are probably regulators of genes involved in phosphosugar metobolism.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent; PDB: 2O3F_B 3IWF_B.
Probab=93.01 E-value=0.1 Score=47.14 Aligned_cols=40 Identities=28% Similarity=0.474 Sum_probs=30.3
Q ss_pred HHHHHhhcCCcHHHHHHHcCCChhHHHHHHHHcCCCCCcc
Q 001809 604 LSVLQQYFSGSLKDAAKSIGVCPTTLKRICRQHGISRWPS 643 (1010)
Q Consensus 604 l~~L~~yF~~pl~eAAk~LGV~~TtLKRiCR~~GI~RWP~ 643 (1010)
++.....-.+++.|.|+.+|||++|+-|.||++|-..|+-
T Consensus 26 l~~~~~~~~~si~elA~~~~vS~sti~Rf~kkLG~~gf~e 65 (77)
T PF01418_consen 26 LENPDEIAFMSISELAEKAGVSPSTIVRFCKKLGFSGFKE 65 (77)
T ss_dssp HH-HHHHCT--HHHHHHHCTS-HHHHHHHHHHCTTTCHHH
T ss_pred HhCHHHHHHccHHHHHHHcCCCHHHHHHHHHHhCCCCHHH
Confidence 3344456689999999999999999999999999877654
No 25
>PF02796 HTH_7: Helix-turn-helix domain of resolvase; InterPro: IPR006120 Site-specific recombination plays an important role in DNA rearrangement in prokaryotic organisms. Two types of site-specific recombination are known to occur: Recombination between inverted repeats resulting in the reversal of a DNA segment. Recombination between repeat sequences on two DNA molecules resulting in their cointegration, or between repeats on one DNA molecule resulting in the excision of a DNA fragment. Site-specific recombination is characterised by a strand exchange mechanism that requires no DNA synthesis or high energy cofactor; the phosphodiester bond energy is conserved in a phospho-protein linkage during strand cleavage and re-ligation. Two unrelated families of recombinases are currently known []. The first, called the 'phage integrase' family, groups a number of bacterial phage and yeast plasmid enzymes. The second [], called the 'resolvase' family, groups enzymes which share the following structural characteristics: an N-terminal catalytic and dimerization domain that contains a conserved serine residue involved in the transient covalent attachment to DNA IPR006119 from INTERPRO, and a C-terminal helix-turn-helix DNA-binding domain. ; GO: 0000150 recombinase activity, 0003677 DNA binding, 0006310 DNA recombination; PDB: 1ZR2_A 2GM4_B 1RES_A 1ZR4_A 1RET_A 1GDT_B 2R0Q_C 1JKP_C 1IJW_C 1JJ6_C ....
Probab=92.87 E-value=0.1 Score=42.66 Aligned_cols=32 Identities=22% Similarity=0.414 Sum_probs=23.8
Q ss_pred HHHHHhhc--CCcHHHHHHHcCCChhHHHHHHHH
Q 001809 604 LSVLQQYF--SGSLKDAAKSIGVCPTTLKRICRQ 635 (1010)
Q Consensus 604 l~~L~~yF--~~pl~eAAk~LGV~~TtLKRiCR~ 635 (1010)
.+++.+.+ ++++.++|+.+|||.+|++|+.++
T Consensus 11 ~~~i~~l~~~G~si~~IA~~~gvsr~TvyR~l~~ 44 (45)
T PF02796_consen 11 IEEIKELYAEGMSIAEIAKQFGVSRSTVYRYLNK 44 (45)
T ss_dssp HHHHHHHHHTT--HHHHHHHTTS-HHHHHHHHCC
T ss_pred HHHHHHHHHCCCCHHHHHHHHCcCHHHHHHHHhc
Confidence 55565555 599999999999999999999764
No 26
>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=91.53 E-value=0.19 Score=39.85 Aligned_cols=28 Identities=21% Similarity=0.364 Sum_probs=25.2
Q ss_pred CcHHHHHHHcCCChhHHHHHHHHcCCCC
Q 001809 613 GSLKDAAKSIGVCPTTLKRICRQHGISR 640 (1010)
Q Consensus 613 ~pl~eAAk~LGV~~TtLKRiCR~~GI~R 640 (1010)
++++|||+.|||+.+||++.+++..|+.
T Consensus 2 lt~~e~a~~lgis~~ti~~~~~~g~i~~ 29 (49)
T TIGR01764 2 LTVEEAAEYLGVSKDTVYRLIHEGELPA 29 (49)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHcCCCCe
Confidence 6889999999999999999999877753
No 27
>PF02954 HTH_8: Bacterial regulatory protein, Fis family; InterPro: IPR002197 The Factor for Inversion Stimulation (FIS) protein is a regulator of bacterial functions, and binds specifically to weakly related DNA sequences [,]. It activates ribosomal RNA transcription, and is involved in upstream activation of rRNA promoters. The protein has been shown to play a role in the regulation of virulence factors in both Salmonella typhimurium and Escherichia coli []. Some of its functions include inhibition of the initiation of DNA replication from the OriC site, and promotion of Hin-mediated DNA inversion. In its C-terminal extremity, FIS encodes a helix-turn-helix (HTH) DNA- binding motif, which shares a high degree of similarity with other HTH motifs of more primitive bacterial transcriptional regulators, such as the nitrogen assimilation regulatory proteins (NtrC) from species like Azobacter, Rhodobacter and Rhizobium. This has led to speculation that both evolved from a single common ancestor []. The 3-dimensional structure of the E. coli FIS DNA-binding protein has been determined by means of X-ray diffraction to 2.0A resolution [,]. FIS is composed of four alpha-helices tightly intertwined to form a globular dimer with two protruding HTH motifs. The 24 N-terminal amino acids are poorly defined, indicating that they might act as `feelers' suitable for DNA or protein (invertase) recognition []. Other proteins belonging to this subfamily include: E. coli: atoC, hydG, ntrC, fhlA, tyrR, Rhizobium spp.: ntrC, nifA, dctD ; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent; PDB: 1NTC_A 3JRH_A 3JRB_A 3IV5_A 3JRI_A 1ETQ_A 1ETW_B 1ETY_A 3JRF_A 3JRA_A ....
Probab=91.44 E-value=0.29 Score=39.61 Aligned_cols=29 Identities=24% Similarity=0.371 Sum_probs=23.9
Q ss_pred HhhcCCcHHHHHHHcCCChhHHHHHHHHc
Q 001809 608 QQYFSGSLKDAAKSIGVCPTTLKRICRQH 636 (1010)
Q Consensus 608 ~~yF~~pl~eAAk~LGV~~TtLKRiCR~~ 636 (1010)
-..++..+.+||+.|||+++||.|..++|
T Consensus 14 L~~~~gn~~~aA~~Lgisr~tL~~klkk~ 42 (42)
T PF02954_consen 14 LERCGGNVSKAARLLGISRRTLYRKLKKY 42 (42)
T ss_dssp HHHTTT-HHHHHHHHTS-HHHHHHHHHHC
T ss_pred HHHhCCCHHHHHHHHCCCHHHHHHHHHhC
Confidence 36778999999999999999999998875
No 28
>PF11470 TUG-UBL1: GLUT4 regulating protein TUG; InterPro: IPR021569 TUG is a GLUT4 regulating protein and functions to retain membrane vesicles containing GLUT4 intracellularly. TUG releases the GLUT4 containing vesicles to the cellular exocytic machinery in response to insulin stimulation which allows translocation to the plasma membrane []. TUG has an N-terminal ubiquitin-like domain (UBL1) which in similar proteins appears to participate in protein-protein interactions []. The region does have a area of negative electrostatic potential and increased backbone motility which leads to suggestions of a potential protein-protein interaction site []. ; PDB: 2AL3_A.
Probab=90.74 E-value=0.39 Score=42.95 Aligned_cols=42 Identities=21% Similarity=0.366 Sum_probs=30.9
Q ss_pred EEcCCCeEEEEeCCCcChHHHHHHHHHHcCcccceeeeEeec
Q 001809 907 ATYKEDIIRFKFDPSAGCFQLYEEVARRLKLQNGTFQLKYLD 948 (1010)
Q Consensus 907 aty~~d~iRF~~~~s~g~~~L~~EIakRf~l~~~~f~lKYlD 948 (1010)
+.|+.++.++++.|+.-+.++++|.-++|||+...++|||-.
T Consensus 2 i~~~~rr~~vkvtp~~~l~~VL~eac~k~~l~~~~~~L~h~~ 43 (65)
T PF11470_consen 2 ICYNFRRFKVKVTPNTTLNQVLEEACKKFGLDPSSYDLKHNN 43 (65)
T ss_dssp E-TTS-EEEE---TTSBHHHHHHHHHHHTT--GGG-EEEETT
T ss_pred CccCCcEEEEEECCCCCHHHHHHHHHHHcCCCccceEEEECC
Confidence 468889999999999999999999999999999999998844
No 29
>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=90.59 E-value=0.31 Score=38.32 Aligned_cols=27 Identities=33% Similarity=0.550 Sum_probs=23.9
Q ss_pred CcHHHHHHHcCCChhHHHHHHHHcCCC
Q 001809 613 GSLKDAAKSIGVCPTTLKRICRQHGIS 639 (1010)
Q Consensus 613 ~pl~eAAk~LGV~~TtLKRiCR~~GI~ 639 (1010)
+++.|||+.|||+++||++.+++-.|+
T Consensus 1 ~s~~e~a~~lgvs~~tl~~~~~~g~~~ 27 (49)
T cd04762 1 LTTKEAAELLGVSPSTLRRWVKEGKLK 27 (49)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHcCCCC
Confidence 478999999999999999999986664
No 30
>cd01812 BAG1_N Ubiquitin-like domain of BAG1. BAG1_N N-terminal ubiquitin-like (Ubl) domain of the BAG1 protein. This domain occurs together with the BAG domain and is closely related to the Ubl domain of a family of deubiquitinases that includes Rpn11, UBP6 (USP14), USP7 (HAUSP).
Probab=90.20 E-value=0.68 Score=40.13 Aligned_cols=46 Identities=13% Similarity=0.061 Sum_probs=39.8
Q ss_pred EEEEEEcCCCeEEEEeCCCcChHHHHHHHHHHcCcccceeeeEeec
Q 001809 903 IIVKATYKEDIIRFKFDPSAGCFQLYEEVARRLKLQNGTFQLKYLD 948 (1010)
Q Consensus 903 ~~vKaty~~d~iRF~~~~s~g~~~L~~EIakRf~l~~~~f~lKYlD 948 (1010)
|+|+++++++.+-+++.+++-+.+|++.|+++.++......|.|-.
T Consensus 1 i~i~vk~~g~~~~i~v~~~~tv~~lK~~i~~~~gi~~~~q~L~~~g 46 (71)
T cd01812 1 IRVRVKHGGESHDLSISSQATFGDLKKMLAPVTGVEPRDQKLIFKG 46 (71)
T ss_pred CEEEEEECCEEEEEEECCCCcHHHHHHHHHHhhCCChHHeEEeeCC
Confidence 4567777788888999999999999999999999988888887753
No 31
>smart00213 UBQ Ubiquitin homologues. Ubiquitin-mediated proteolysis is involved in the regulated turnover of proteins required for controlling cell cycle progression
Probab=90.04 E-value=1 Score=37.64 Aligned_cols=56 Identities=23% Similarity=0.281 Sum_probs=41.8
Q ss_pred EEEEEEcCCCeEEEEeCCCcChHHHHHHHHHHcCcccceeeeEeecCCCCeEEEecCCcHHHH
Q 001809 903 IIVKATYKEDIIRFKFDPSAGCFQLYEEVARRLKLQNGTFQLKYLDDEEEWVMLVSDSDLQEC 965 (1010)
Q Consensus 903 ~~vKaty~~d~iRF~~~~s~g~~~L~~EIakRf~l~~~~f~lKYlDDd~EWVlLtcDaDL~EC 965 (1010)
++||-.. .++.|++.++.-+.+|++.|++++++....+.|-|-+ -.|..|..|.+|
T Consensus 3 i~vk~~~--~~~~~~v~~~~tv~~lk~~i~~~~~~~~~~~~L~~~g-----~~L~d~~tL~~~ 58 (64)
T smart00213 3 LTVKTLD--GTITLEVKPSDTVSELKEKIAELTGIPVEQQRLIYKG-----KVLEDDRTLADY 58 (64)
T ss_pred EEEEECC--ceEEEEECCCCcHHHHHHHHHHHHCCCHHHEEEEECC-----EECCCCCCHHHc
Confidence 4555554 6889999999999999999999999988777776642 134445556554
No 32
>PF12728 HTH_17: Helix-turn-helix domain
Probab=89.73 E-value=0.33 Score=40.02 Aligned_cols=29 Identities=31% Similarity=0.437 Sum_probs=25.9
Q ss_pred CcHHHHHHHcCCChhHHHHHHHHcCCCCC
Q 001809 613 GSLKDAAKSIGVCPTTLKRICRQHGISRW 641 (1010)
Q Consensus 613 ~pl~eAAk~LGV~~TtLKRiCR~~GI~RW 641 (1010)
++.+|||+.|||+.+|+.+.+++-+|+.-
T Consensus 2 lt~~e~a~~l~is~~tv~~~~~~g~i~~~ 30 (51)
T PF12728_consen 2 LTVKEAAELLGISRSTVYRWIRQGKIPPF 30 (51)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHcCCCCeE
Confidence 67899999999999999999999988433
No 33
>PF01590 GAF: GAF domain; InterPro: IPR003018 This domain is present in phytochromes and cGMP-specific phosphodiesterases. cGMP-dependent 3',5'-cyclic phosphodiesterase (3.1.4.17 from EC) catalyses the conversion of guanosine 3',5'-cyclic phosphate to guanosine 5'-phosphate. A phytochrome is a regulatory photoreceptor which exists in 2 forms that are reversibly interconvertible by light, the PR form that absorbs maximally in the red region of the spectrum, and the PFR form that absorbs maximally in the far-red region. This domain is also found in NifA, a transcriptional activator which is required for activation of most Nif operons which are directly involved in nitrogen fixation. NifA interacts with sigma-54.; GO: 0005515 protein binding; PDB: 2Y8H_A 3DBA_B 3CI6_A 3E0Y_B 2W3G_B 2W3D_A 2W3E_A 2Y79_B 2W3H_A 2W3F_A ....
Probab=88.98 E-value=2 Score=40.59 Aligned_cols=132 Identities=18% Similarity=0.150 Sum_probs=81.6
Q ss_pred HHHHHHHHHHHHHHhcCCCeeEEEEeeeccCCeeeeeeCCCCcccchhhhHHhhccceeeeccCCCCCCCCCCCcccccC
Q 001809 165 LDEKMLRALSFFKLSSGGGILAQVWVPRKQGDDYILSTSDQPYLLDQMLAGYREVSRKFTFSAEAKPGTFLGLPGRVFSS 244 (1010)
Q Consensus 165 vkerm~~AL~~~kes~~~~~L~QVWvP~~~g~~~vLsT~~qP~~ld~~L~~yR~vS~~f~Fs~~~~~~~~~GLPGRVF~s 244 (1010)
+.+-|..+++.+.+.++.+ .+=|++...++....+.+....... ......+..+ .++.|++..+
T Consensus 2 l~~~l~~~~~~l~~~l~~~-~~~i~~~d~~~~~~~~~~~~~~~~~---------~~~~~~~~~~------~~~~~~~~~~ 65 (154)
T PF01590_consen 2 LDELLQRILRELAELLGAD-RASIFLLDPDGNRLYSVAGVGLPDP---------PPGGRRLSMD------ESICGQVLQS 65 (154)
T ss_dssp HHHHHHHHHHHHHHHHTES-EEEEEEEETTTTEEEEEEEEEGGGS---------EHHHEEEETT------SSHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHCCC-EEEEEEEecCCCeEEEEEeeccccc---------cccccccccc------ccHHHHHHhC
Confidence 4567778899999998844 3344666666665444332211110 1111222221 2567889999
Q ss_pred CCCcccccccccCcccccchh-------------hHHhcCCceEEEEeeecCCCCceEEEEEEeeecccCCchHHHHHHH
Q 001809 245 KVPEWTSNVAYYNEAEYARVT-------------HAVNHAVRSCIALPVFQFPEISCSAVLEIVSVKEKPNFDAEIENIC 311 (1010)
Q Consensus 245 ~~PEWTpnV~~y~~~EYpR~~-------------~A~~~~VrGsLAlPVf~~~s~~ClAVlElV~t~ek~~f~~E~e~vc 311 (1010)
+.|...+|+............ +...+++++.|.+||...+ ..+|||.+..+...-.|..+-..+.
T Consensus 66 ~~~~~i~d~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~s~l~vPi~~~g--~~~G~l~l~~~~~~~~~~~~d~~ll 143 (154)
T PF01590_consen 66 REPIVISDVAADPRFAPQIAAQSALRALSSAERPFLAEYGVRSYLCVPIISGG--RLIGVLSLYRTRPGRPFTEEDLALL 143 (154)
T ss_dssp TSCEEESSSGGSTTSSCHHHHHHTTBTTTHHHHHHHHTTTESEEEEEEEEETT--EEEEEEEEEEESSSSS--HHHHHHH
T ss_pred CCeEeeccccccccccccccccccccccccccccccccccCceeeEeeeeccc--CcEEEEEEEECCCCCCcCHHHHHHH
Confidence 999998888544332222111 1227899999999987765 5699999999998777877766655
Q ss_pred HHh
Q 001809 312 NAL 314 (1010)
Q Consensus 312 ~AL 314 (1010)
+++
T Consensus 144 ~~~ 146 (154)
T PF01590_consen 144 ESF 146 (154)
T ss_dssp HHH
T ss_pred HHH
Confidence 544
No 34
>PF13542 HTH_Tnp_ISL3: Helix-turn-helix domain of transposase family ISL3
Probab=88.93 E-value=0.39 Score=39.52 Aligned_cols=41 Identities=27% Similarity=0.377 Sum_probs=32.2
Q ss_pred cccccccCHHHHHhhcCC-cHHHHHHHcCCChhHHHHHHHHc
Q 001809 596 STAEKNVSLSVLQQYFSG-SLKDAAKSIGVCPTTLKRICRQH 636 (1010)
Q Consensus 596 ~~~~~~itl~~L~~yF~~-pl~eAAk~LGV~~TtLKRiCR~~ 636 (1010)
.+..+.+....+...... +++++|+.+||+.+|++||-.++
T Consensus 10 ~r~T~~~~~~i~~~~~~~~s~~~vA~~~~vs~~TV~ri~~~~ 51 (52)
T PF13542_consen 10 CRITKRLEQYILKLLRESRSFKDVARELGVSWSTVRRIFDRY 51 (52)
T ss_pred CcHHHHHHHHHHHHHhhcCCHHHHHHHHCCCHHHHHHHHHhh
Confidence 334445555667777777 99999999999999999998764
No 35
>PRK00430 fis global DNA-binding transcriptional dual regulator Fis; Provisional
Probab=88.89 E-value=0.57 Score=44.55 Aligned_cols=33 Identities=27% Similarity=0.462 Sum_probs=29.2
Q ss_pred HHHhhcCCcHHHHHHHcCCChhHHHHHHHHcCC
Q 001809 606 VLQQYFSGSLKDAAKSIGVCPTTLKRICRQHGI 638 (1010)
Q Consensus 606 ~L~~yF~~pl~eAAk~LGV~~TtLKRiCR~~GI 638 (1010)
..-..++..+.+||+.|||+++||+|..|++||
T Consensus 62 ~aL~~~~gn~s~AAr~LGIsRsTL~rKLkr~gi 94 (95)
T PRK00430 62 MVMQYTRGNQTRAALMLGINRGTLRKKLKKYGM 94 (95)
T ss_pred HHHHHcCCCHHHHHHHhCCCHHHHHHHHHHhCC
Confidence 344556889999999999999999999999998
No 36
>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=88.08 E-value=0.47 Score=41.63 Aligned_cols=67 Identities=24% Similarity=0.482 Sum_probs=47.3
Q ss_pred cccccccccCHHHHHhh--cCCcHHHHHHHcCCChhHHHHHHHHc--CCCCCcch-hhhhhHHHHHHHHHHH
Q 001809 594 KRSTAEKNVSLSVLQQY--FSGSLKDAAKSIGVCPTTLKRICRQH--GISRWPSR-KINKVNRSLKKIQTVL 660 (1010)
Q Consensus 594 ~r~~~~~~itl~~L~~y--F~~pl~eAAk~LGV~~TtLKRiCR~~--GI~RWP~R-ki~sl~~~i~~l~~~i 660 (1010)
+|.+-...+-+..|..| =+.++.++|+++||++.||.+-.+++ |...=|.. ++..+...|..|+..+
T Consensus 3 ~r~~ys~e~K~~~v~~~~~~g~sv~~va~~~gi~~~~l~~W~~~~~~~~~~~~~~~~~~~~~~e~~~L~~~~ 74 (76)
T PF01527_consen 3 KRRRYSPEFKLQAVREYLESGESVSEVAREYGISPSTLYNWRKQYREGQSAFPAKFKPKELEKEIRELRREL 74 (76)
T ss_dssp SS----HHHHHHHHHHHHHHHCHHHHHHHHHTS-HHHHHHHHHHHH--STT-SSSSHHHHTHCHHHHHCH-G
T ss_pred CCCCCCHHHHHHHHHHHHHCCCceEeeecccccccccccHHHHHHhcCCCCCCcccccHhHHHHHHHHHHHh
Confidence 34445556666777777 48999999999999999999999999 66666766 6777777787777654
No 37
>PRK09413 IS2 repressor TnpA; Reviewed
Probab=87.66 E-value=1.4 Score=42.99 Aligned_cols=42 Identities=19% Similarity=0.206 Sum_probs=33.7
Q ss_pred cccccccCHHHHHhhc--CCcHHHHHHHcCCChhHHHHHHHHcC
Q 001809 596 STAEKNVSLSVLQQYF--SGSLKDAAKSIGVCPTTLKRICRQHG 637 (1010)
Q Consensus 596 ~~~~~~itl~~L~~yF--~~pl~eAAk~LGV~~TtLKRiCR~~G 637 (1010)
++....+-++.++.++ +.+..++|+++||+.+||.+..|++.
T Consensus 11 r~ys~EfK~~aV~~~~~~g~sv~evA~e~gIs~~tl~~W~r~y~ 54 (121)
T PRK09413 11 RRRTTQEKIAIVQQSFEPGMTVSLVARQHGVAASQLFLWRKQYQ 54 (121)
T ss_pred CCCCHHHHHHHHHHHHcCCCCHHHHHHHHCcCHHHHHHHHHHHh
Confidence 3444555566777666 68999999999999999999999974
No 38
>PF09379 FERM_N: FERM N-terminal domain ; InterPro: IPR018979 This domain is the N-terminal ubiquitin-like structural domain of the FERM domain. The FERM domain (F for 4.1 protein, E for ezrin, R for radixin and M for moesin) is a widespread protein module involved in localising proteins to the plasma membrane []. FERM domains are found in a number of cytoskeletal-associated proteins that associate with various proteins at the interface between the plasma membrane and the cytoskeleton. The FERM domain is located at the N terminus of the majority of FERM-containing proteins [, ], which includes: Band 4.1, which links the spectrin-actin cytoskeleton of erythrocytes to the plasma membrane. Ezrin, a component of the undercoat of the microvilli plasma membrane. Moesin, which is probably involved in binding major cytoskeletal structures to the plasma membrane. Radixin, which is involved in the binding of the barbed end of actin filaments to the plasma membrane in the undercoat of the cell- to-cell adherens junction. Talin, a cytoskeletal protein concentrated in regions of cell-substratum contact and, in lymphocytes, of cell-cell contacts. Filopodin, a slime mold protein that binds actin and which is involved in the control of cell motility and chemotaxis. Merlin (or schwannomin). Protein NBL4. Unconventional myosins X, VIIa and XV, which are mutated in congenital deafness. Focal-adhesion kinases (FAKs), cytoplasmic protein tyrosine kinases involved in signalling through integrins. Janus tyrosine kinases (JAKs), cytoplasmic tyrosine kinases that are non-covalently associated with the cytoplasmic tails of receptors for cytokines or polypeptidic hormones. Non-receptor tyrosine-protein kinase TYK2. Protein-tyrosine phosphatases PTPN3 and PTPN4, enzyme that appear to act at junctions between the membrane and the cytoskeleton. Protein-tyrosine phosphatases PTPN14 and PTP-D1, PTP-RL10 and PTP2E. Caenorhabditis elegans protein phosphatase ptp-1. Ezrin, moesin, and radixin are highly related proteins (ERM protein family), but the other proteins in which the FERM domain is found do not share any region of similarity outside of this domain. ERM proteins are made of three domains, the FERM domain, a central helical domain and a C-terminal tail domain, which binds F-actin. The amino-acid sequence of the FERM domain is highly conserved among ERM proteins and is responsible for membrane association by direct binding to the cytoplasmic domain or tail of integral membrane proteins. ERM proteins are regulated by an intramolecular association of the FERM and C-terminal tail domains that masks their binding sites for other molecules. For cytoskeleton-membrane cross-linking, the dormant molecules becomes activated and the FERM domain attaches to the membrane by binding specific membrane proteins, while the last 34 residues of the tail bind actin filaments. Aside from binding to membranes, the activated FERM domain of ERM proteins can also bind the guanine nucleotide dissociation inhibitor of Rho GTPase (RhoDGI), which suggests that in addition to functioning as a cross-linker, ERM proteins may influence Rho signalling pathways. The crystal structure of the FERM domain reveals that it is composed of three structural modules (F1, F2, and F3) that together form a compact clover-shaped structure []. The FERM domain has also been called the amino-terminal domain, the 30kDa domain, 4.1N30, the membrane-cytoskeletal-linking domain, the ERM-like domain, the ezrin-like domain of the band 4.1 superfamily, the conserved N-terminal region, and the membrane attachment domain [].; PDB: 1EF1_B 1SGH_A 1E5W_A 2KC2_A 2KMA_A 3IVF_A 1H4R_B 3U8Z_A 1ISN_A 3BIN_A ....
Probab=86.90 E-value=1.5 Score=38.90 Aligned_cols=53 Identities=30% Similarity=0.470 Sum_probs=44.8
Q ss_pred CeEEEEeCCCcChHHHHHHHHHHcCcccc-eeeeEe-ecCCCCeEEEecCCcHHH
Q 001809 912 DIIRFKFDPSAGCFQLYEEVARRLKLQNG-TFQLKY-LDDEEEWVMLVSDSDLQE 964 (1010)
Q Consensus 912 d~iRF~~~~s~g~~~L~~EIakRf~l~~~-~f~lKY-lDDd~EWVlLtcDaDL~E 964 (1010)
.++.|.+.++.-.++|+++|+++++|.+. .|.|.| .|.+++++-|--|.-|.+
T Consensus 7 ~~~~~~v~~~~t~~~l~~~v~~~l~l~e~~~FgL~~~~~~~~~~~wL~~~k~l~~ 61 (80)
T PF09379_consen 7 TTKTFEVDPKTTGQDLLEQVCDKLGLKEKEYFGLQYQVDKDGEHHWLDLDKKLKK 61 (80)
T ss_dssp EEEEEEEETTSBHHHHHHHHHHHHTTSSGGGEEEEE-EBTTSSEEEE-SSSBGGG
T ss_pred CcEEEEEcCCCcHHHHHHHHHHHcCCCCccEEEEEEeecCCCcceeccCcccHHH
Confidence 46889999999999999999999999875 599999 888899888877766543
No 39
>cd01809 Scythe_N Ubiquitin-like domain of Scythe protein. Scythe protein (also known as Bat3) is an apoptotic regulator that is highly conserved in eukaryotes and contains a ubiquitin-like domain near its N-terminus. Scythe binds reaper, a potent apoptotic inducer, and Scythe/Reaper are thought to signal apoptosis, in part through regulating the folding and activity of apoptotic signaling molecules.
Probab=86.68 E-value=2 Score=37.17 Aligned_cols=57 Identities=23% Similarity=0.292 Sum_probs=43.3
Q ss_pred EEEEEEcCCCeEEEEeCCCcChHHHHHHHHHHcCcccceeeeEeecCCCCeEEEecCCcHHHH
Q 001809 903 IIVKATYKEDIIRFKFDPSAGCFQLYEEVARRLKLQNGTFQLKYLDDEEEWVMLVSDSDLQEC 965 (1010)
Q Consensus 903 ~~vKaty~~d~iRF~~~~s~g~~~L~~EIakRf~l~~~~f~lKYlDDd~EWVlLtcDaDL~EC 965 (1010)
+.||.-. ++++.|++.++.-+.+|++.|+++.++......|-|- +. +|.-|..|.++
T Consensus 3 i~vk~~~-g~~~~~~v~~~~tv~~lK~~i~~~~gi~~~~q~L~~~---g~--~L~d~~~L~~~ 59 (72)
T cd01809 3 IKVKTLD-SQTHTFTVEEEITVLDLKEKIAEEVGIPVEQQRLIYS---GR--VLKDDETLSEY 59 (72)
T ss_pred EEEEeCC-CCEEEEEECCCCcHHHHHHHHHHHHCcCHHHeEEEEC---CE--ECCCcCcHHHC
Confidence 5666544 4789999999999999999999999998887888772 22 44445555553
No 40
>PRK11061 fused phosphoenolpyruvate-protein phosphotransferase PtsP/GAF domain; Provisional
Probab=86.59 E-value=5.3 Score=50.36 Aligned_cols=126 Identities=17% Similarity=0.214 Sum_probs=83.0
Q ss_pred CCCHHHHHHHHHHHHHHhcCCCeeEEEEeeeccCCeeeee-eCCCCcccchhhhHHhhccceeeeccCCCCCCCCCCCcc
Q 001809 162 PPSLDEKMLRALSFFKLSSGGGILAQVWVPRKQGDDYILS-TSDQPYLLDQMLAGYREVSRKFTFSAEAKPGTFLGLPGR 240 (1010)
Q Consensus 162 ~~svkerm~~AL~~~kes~~~~~L~QVWvP~~~g~~~vLs-T~~qP~~ld~~L~~yR~vS~~f~Fs~~~~~~~~~GLPGR 240 (1010)
...+.+-|...+..+++..+.+ -+=||+...++....+. +.| ++.. + -....|+.+ .|+-|+
T Consensus 15 ~~dL~e~L~~Iv~~~~~~l~~d-~~sI~L~D~~~~~L~~~as~G----l~~~---~---~~~~~l~~g------eGi~G~ 77 (748)
T PRK11061 15 APRLNEALDILVTETCLAMDTE-VCSVYLADHDRRCYYLMATRG----LKKP---R---GRTVTLAFD------EGIVGL 77 (748)
T ss_pred cCCHHHHHHHHHHHHHHHhCCC-EEEEEEEECCCCEEEEEEeeC----CChH---h---ccceeccCC------cchHHH
Confidence 4568888999999999998643 45677776655443332 222 1111 1 012334443 399999
Q ss_pred cccCCCCcccccccccCcccccchhhHHhcCCceEEEEeeecCCCCceEEEEEEeeecccCCchHHHHH
Q 001809 241 VFSSKVPEWTSNVAYYNEAEYARVTHAVNHAVRSCIALPVFQFPEISCSAVLEIVSVKEKPNFDAEIEN 309 (1010)
Q Consensus 241 VF~s~~PEWTpnV~~y~~~EYpR~~~A~~~~VrGsLAlPVf~~~s~~ClAVlElV~t~ek~~f~~E~e~ 309 (1010)
|+.++.|-+.+|+.-. ..|.....+...++++-|++||...+ .++|||.+..... -.|+.+-..
T Consensus 78 Va~tg~pV~V~Dv~~d--prf~~~~~~~~~~~~S~L~VPL~~~g--eVIGVL~v~~~~~-~~Fs~~d~~ 141 (748)
T PRK11061 78 VGRLAEPINLADAQKH--PSFKYIPSVKEERFRAFLGVPIIYRR--QLLGVLVVQQREL-RQFDESEES 141 (748)
T ss_pred HhccCceEEECCcccC--cccccCccccCccceEEEEEEEeeCC--EEEEEEEEeeCCC-CCCCHHHHH
Confidence 9999999999999643 33433333447899999999999654 5799999855544 557775544
No 41
>smart00065 GAF Domain present in phytochromes and cGMP-specific phosphodiesterases. Mutations within these domains in PDE6B result in autosomal recessive inheritance of retinitis pigmentosa.
Probab=86.38 E-value=13 Score=32.96 Aligned_cols=122 Identities=18% Similarity=0.192 Sum_probs=71.2
Q ss_pred HHHHHHHHHHHHHHhcCCCeeEEEEeeecc-CCeeee-eeCCCCcccchhhhHHhhccceeeeccCCCCCCCCCCCcccc
Q 001809 165 LDEKMLRALSFFKLSSGGGILAQVWVPRKQ-GDDYIL-STSDQPYLLDQMLAGYREVSRKFTFSAEAKPGTFLGLPGRVF 242 (1010)
Q Consensus 165 vkerm~~AL~~~kes~~~~~L~QVWvP~~~-g~~~vL-sT~~qP~~ld~~L~~yR~vS~~f~Fs~~~~~~~~~GLPGRVF 242 (1010)
+++-+..++..+.+.++.+ .+-||.-..+ ...... ...+.. .. .....|... .++-++++
T Consensus 2 ~~~~~~~~~~~l~~~~~~~-~~~i~~~~~~~~~~~~~~~~~~~~----~~-------~~~~~~~~~------~~~~~~~~ 63 (149)
T smart00065 2 LEELLQTILEELRQLLGAD-RVLIYLVDEDDRGELVLVAADGLT----LP-------LLGLRYPLG------EGLAGRVA 63 (149)
T ss_pred HHHHHHHHHHHHHHHhCCc-eEEEEEEecCCCCcEEEEEecCCC----cc-------cceEEecCC------CChHHHHH
Confidence 5677788888888888754 4455555542 222111 111110 00 122233332 26778888
Q ss_pred cCCCCcccccccccCcccccchhhHHhcC-CceEEEEeeecCCCCceEEEEEEeeecccCCchHHHHH
Q 001809 243 SSKVPEWTSNVAYYNEAEYARVTHAVNHA-VRSCIALPVFQFPEISCSAVLEIVSVKEKPNFDAEIEN 309 (1010)
Q Consensus 243 ~s~~PEWTpnV~~y~~~EYpR~~~A~~~~-VrGsLAlPVf~~~s~~ClAVlElV~t~ek~~f~~E~e~ 309 (1010)
..+.|-..+++.... +.......... +++.+.+||+..+ ..+|+|.+......-.|..+-..
T Consensus 64 ~~~~~~~~~~~~~~~---~~~~~~~~~~~~~~s~~~~Pl~~~~--~~~G~l~~~~~~~~~~~~~~~~~ 126 (149)
T smart00065 64 ETGRPLNIPDVEADP---VFALDLLGRYQGVRSFLAVPLVADG--ELVGVLALHNKDSPRPFTEEDEE 126 (149)
T ss_pred HcCCeEEeechhhCC---ccccccccceeceeeEEEeeeeecC--EEEEEEEEEecCCCCCCCHHHHH
Confidence 888888888776433 12222222334 9999999999954 45999999887444556665433
No 42
>PF13936 HTH_38: Helix-turn-helix domain; PDB: 2W48_A.
Probab=86.08 E-value=0.65 Score=38.03 Aligned_cols=26 Identities=23% Similarity=0.356 Sum_probs=19.4
Q ss_pred cCCcHHHHHHHcCCChhHHHHHHHHc
Q 001809 611 FSGSLKDAAKSIGVCPTTLKRICRQH 636 (1010)
Q Consensus 611 F~~pl~eAAk~LGV~~TtLKRiCR~~ 636 (1010)
-++++.++|+.||++++|+.|.+|++
T Consensus 19 ~G~s~~~IA~~lg~s~sTV~relkR~ 44 (44)
T PF13936_consen 19 QGMSIREIAKRLGRSRSTVSRELKRN 44 (44)
T ss_dssp S---HHHHHHHTT--HHHHHHHHHHH
T ss_pred cCCCHHHHHHHHCcCcHHHHHHHhcC
Confidence 47999999999999999999999974
No 43
>PF02001 DUF134: Protein of unknown function DUF134; InterPro: IPR002852 The bacterial and archaeal proteins in this family have no known function.
Probab=85.73 E-value=0.97 Score=44.13 Aligned_cols=36 Identities=28% Similarity=0.385 Sum_probs=30.8
Q ss_pred ccccCHHHHH-----hhcCCcHHHHHHHcCCChhHHHHHHH
Q 001809 599 EKNVSLSVLQ-----QYFSGSLKDAAKSIGVCPTTLKRICR 634 (1010)
Q Consensus 599 ~~~itl~~L~-----~yF~~pl~eAAk~LGV~~TtLKRiCR 634 (1010)
.-.|++|+|. .|-++++.|||+.+|||.+|+-|+-.
T Consensus 39 ~V~L~~dElEAiRL~D~egl~QeeaA~~MgVSR~T~~ril~ 79 (106)
T PF02001_consen 39 PVVLTVDELEAIRLVDYEGLSQEEAAERMGVSRPTFQRILE 79 (106)
T ss_pred eEEeeHHHHHHHHHHHHcCCCHHHHHHHcCCcHHHHHHHHH
Confidence 4577777765 78899999999999999999998854
No 44
>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=85.23 E-value=0.9 Score=36.54 Aligned_cols=31 Identities=35% Similarity=0.453 Sum_probs=24.9
Q ss_pred CcHHHHHHHcCCChhHHHHHHHHcCCCCCcchh
Q 001809 613 GSLKDAAKSIGVCPTTLKRICRQHGISRWPSRK 645 (1010)
Q Consensus 613 ~pl~eAAk~LGV~~TtLKRiCR~~GI~RWP~Rk 645 (1010)
+++.|+|+.|||++.||++..++--|. |.|.
T Consensus 1 ~~~~e~a~~~gv~~~tlr~~~~~g~l~--~~~~ 31 (49)
T cd04761 1 YTIGELAKLTGVSPSTLRYYERIGLLS--PART 31 (49)
T ss_pred CcHHHHHHHHCcCHHHHHHHHHCCCCC--CCcC
Confidence 578999999999999999887665554 6554
No 45
>PRK01905 DNA-binding protein Fis; Provisional
Probab=85.19 E-value=1.3 Score=40.40 Aligned_cols=30 Identities=30% Similarity=0.472 Sum_probs=27.1
Q ss_pred hhcCCcHHHHHHHcCCChhHHHHHHHHcCC
Q 001809 609 QYFSGSLKDAAKSIGVCPTTLKRICRQHGI 638 (1010)
Q Consensus 609 ~yF~~pl~eAAk~LGV~~TtLKRiCR~~GI 638 (1010)
...+....+||+.|||+++||.|.-|++||
T Consensus 47 ~~~~gn~s~aAr~LGIsrstL~rklkk~gi 76 (77)
T PRK01905 47 EQAGGNQSLAAEYLGINRNTLRKKLQQHGL 76 (77)
T ss_pred HHcCCCHHHHHHHHCCCHHHHHHHHHHhCC
Confidence 445678999999999999999999999997
No 46
>smart00342 HTH_ARAC helix_turn_helix, arabinose operon control protein.
Probab=84.95 E-value=1.2 Score=38.36 Aligned_cols=35 Identities=23% Similarity=0.416 Sum_probs=27.6
Q ss_pred CCcHHHHHHHcCCChhHHHHHHHHc-CCCCCcchhh
Q 001809 612 SGSLKDAAKSIGVCPTTLKRICRQH-GISRWPSRKI 646 (1010)
Q Consensus 612 ~~pl~eAAk~LGV~~TtLKRiCR~~-GI~RWP~Rki 646 (1010)
.++++++|+.+|++...|.|+++++ |+....|.+.
T Consensus 1 ~~~~~~la~~~~~s~~~l~~~f~~~~~~s~~~~~~~ 36 (84)
T smart00342 1 PLTLEDLAEALGMSPRHLQRLFKKETGTTPKQYLRD 36 (84)
T ss_pred CCCHHHHHHHhCCCHHHHHHHHHHHhCcCHHHHHHH
Confidence 3689999999999999999999987 4654444333
No 47
>smart00295 B41 Band 4.1 homologues. Also known as ezrin/radixin/moesin (ERM) protein domains. Present in myosins, ezrin, radixin, moesin, protein tyrosine phosphatases. Plasma membrane-binding domain. These proteins play structural and regulatory roles in the assembly and stabilization of specialized plasmamembrane domains. Some PDZ domain containing proteins bind one or more of this family. Now includes JAKs.
Probab=84.92 E-value=4 Score=41.65 Aligned_cols=65 Identities=23% Similarity=0.350 Sum_probs=50.0
Q ss_pred eEEEEEEcCC-CeEEEEeCCCcChHHHHHHHHHHcCcccc-eeeeEeecCCCCe-EEEecCCcHHHHH
Q 001809 902 KIIVKATYKE-DIIRFKFDPSAGCFQLYEEVARRLKLQNG-TFQLKYLDDEEEW-VMLVSDSDLQECF 966 (1010)
Q Consensus 902 ~~~vKaty~~-d~iRF~~~~s~g~~~L~~EIakRf~l~~~-~f~lKYlDDd~EW-VlLtcDaDL~EC~ 966 (1010)
++.|++.+.+ ..+.+++.++.-..|++++|++++||... .|.|.|.|++++. .-|..+..|.+-.
T Consensus 3 ~~~~~V~l~dg~~~~~~~~~~~t~~ev~~~v~~~~~l~~~~~F~L~~~~~~~~~~~~l~~~~~l~~~~ 70 (207)
T smart00295 3 PRVLKVYLLDGTTLEFEVDSSTTAEELLETVCRKLGIRESEYFGLQFEDPDEDLSHWLDPAKTLLDQD 70 (207)
T ss_pred cEEEEEEecCCCEEEEEECCCCCHHHHHHHHHHHhCCCccceeEEEEEcCCCCcCeeCCCccCHHHhc
Confidence 4677777776 55689999999999999999999999764 6999999988744 3344455555443
No 48
>PF13384 HTH_23: Homeodomain-like domain; PDB: 2X48_C.
Probab=84.68 E-value=0.99 Score=36.86 Aligned_cols=25 Identities=28% Similarity=0.413 Sum_probs=19.2
Q ss_pred CCcHHHHHHHcCCChhHHHHHHHHc
Q 001809 612 SGSLKDAAKSIGVCPTTLKRICRQH 636 (1010)
Q Consensus 612 ~~pl~eAAk~LGV~~TtLKRiCR~~ 636 (1010)
+++.+++|+.|||+.+|+.|+.+++
T Consensus 17 G~s~~~ia~~lgvs~~Tv~~w~kr~ 41 (50)
T PF13384_consen 17 GWSIREIAKRLGVSRSTVYRWIKRY 41 (50)
T ss_dssp T--HHHHHHHHTS-HHHHHHHHT--
T ss_pred CCCHHHHHHHHCcCHHHHHHHHHHc
Confidence 8999999999999999999997764
No 49
>PF13185 GAF_2: GAF domain; PDB: 2QYB_A 3KSG_B 3KSF_C 3KSI_A 3KSH_A 3MMH_A 3RFB_B 1F5M_A 3KO6_B 3HCY_A ....
Probab=84.64 E-value=2.3 Score=39.95 Aligned_cols=77 Identities=25% Similarity=0.322 Sum_probs=53.8
Q ss_pred CCcchhhhhcCCCcccccccccCccccchhhHHHHhCCceeEEEEecccccCCCcEEEEeecCCCCCCcHHHHHHHHHHH
Q 001809 423 QGVAGKALQSNHPFFFPDVKLYDITEFPLVHHARKFGLNAAVAIRLRSTYTGDDDYILEFFLPVTIKGSSEQQLLLNNLS 502 (1010)
Q Consensus 423 QGvaGkAf~sn~P~F~~DV~~fsk~EYPL~HhAr~fgL~aAvAIrLrS~~tG~ddyVLEFFLP~~ck~~~EQq~ll~sLs 502 (1010)
.|+.++++.+++|.|.+ .....++..+.++..|+++++++||+.. |..--||-++-+....=++++..+|..|.
T Consensus 67 ~~~~~~~~~~~~~~~~~----~~~~~~~~~~~~~~~~~~s~l~vPl~~~--~~~~Gvl~l~~~~~~~f~~~~~~~l~~la 140 (148)
T PF13185_consen 67 VGLWEGVLRTGEPIIIN----DDDSSFPPWELARHPGIRSILCVPLRSG--GEVIGVLSLYSKEPNAFSEEDLELLEALA 140 (148)
T ss_dssp EETTSHHHHHTS-EEES----CCCGGGSTTHHHCCTT-SEEEEEEEEET--TEEEEEEEEEESSTT---HHHHHHHHHHH
T ss_pred hhHHHHHHhcCceEEEe----CccccccchhhhccccCCEEEEEEEeEC--CEEEEEEEEeeCCCCCcCHHHHHHHHHHH
Confidence 45556669999999999 2122233368999999999999999863 45567788888776667788888888877
Q ss_pred HHH
Q 001809 503 GTM 505 (1010)
Q Consensus 503 ~Tm 505 (1010)
..+
T Consensus 141 ~~~ 143 (148)
T PF13185_consen 141 DQI 143 (148)
T ss_dssp HHH
T ss_pred HHH
Confidence 655
No 50
>PF03472 Autoind_bind: Autoinducer binding domain; InterPro: IPR005143 This domain binds N-acyl homoserine lactones (AHLs), which are also known as autoinducers. These are small, diffusible molecules used as communication signals in a large variety of proteobacteria. It is almost always found in association with the DNA-binding LuxR domain (IPR000792 from INTERPRO). The autoinducer binding domain forms the N-terminal region of the protein, while the DNA-binding domain forms the C-terminal region. In most cases, binding of AHL by this N-terminal domain leads to unmasking of the DNA-binding domain, allowing it to bind DNA and activate transcription []. In rare cases, some LuxR proteins such as EsaR, act as repressors []. In these proteins binding of AHL to this domain leads to inactivation of the protein as a transcriptional regulator. A large number of processes have been shown to be regulated by LuxR proteins, including bioluminescence, production of virulence factors in plant and animal pathogens, antibiotic production and plasmid transfer. Structural studies of TraR from Agrobacterium tumefaciens [, ] show that the functional protein is a homodimer. Binding of the cognate AHL is required for protein folding, resistance to proteases and dimerisation. The autoinducer binding domain binds its cognate AHL in an alpha/beta/alpha sandwich and provides an extensive dimerisation surface, though residues from the C-terminal region also make some contribution to dimerisation. The autoinducer binding domain is also required for interaction with RpoA, allowing transcription to occur []. There are some proteins which consist solely of the autoinducer binding domain. The function of these is not known, but TrlR from Agrobacterium has been shown to inhibit the activity of TraR by the formation of inactive heterodimers [].; PDB: 3SZT_A 1H0M_A 1L3L_B 2Q0O_B 2UV0_F 3IX8_A 3IX4_C 3IX3_A 3JPU_D 3QP8_A ....
Probab=84.44 E-value=3.4 Score=39.50 Aligned_cols=98 Identities=21% Similarity=0.221 Sum_probs=72.8
Q ss_pred hhHHHHhhhcccccCCCcchhhhhcCCCccccccccc---CccccchhhHHHHhCCceeEEEEecccccCCCcEEEEeec
Q 001809 408 QGFVHACSEHYLEEGQGVAGKALQSNHPFFFPDVKLY---DITEFPLVHHARKFGLNAAVAIRLRSTYTGDDDYILEFFL 484 (1010)
Q Consensus 408 ~gFr~AC~EhhL~~GQGvaGkAf~sn~P~F~~DV~~f---sk~EYPL~HhAr~fgL~aAvAIrLrS~~tG~ddyVLEFFL 484 (1010)
.+|.+...+..+..--=+.-.+..+..|+.-.|+..- ++.+.-+...|+.|||+..++||++... | ...+|=|.-
T Consensus 44 ~~w~~~Y~~~~~~~~DPv~~~~~~~~~p~~W~~~~~~~~~~~~~~~~~~~a~~~Gl~~G~~~p~~~~~-g-~~~~~s~~~ 121 (149)
T PF03472_consen 44 DEWLEHYEERGYFRIDPVVRHARRSSGPFFWSDLFERDALSPEQRRFFDEARDFGLRSGVSVPLHGPD-G-RFGALSFAG 121 (149)
T ss_dssp HHHHHHHHHTTGGGT-HHHHHHCHTSSEEEEECHCTSSSSSHHHHHHHHHHHHTTTSEEEEEEEEECC-G-CEEEEEEEE
T ss_pred HHHHHHHHHcCCcCCCHHHHHHHhCCCCEEEccchhhhhhhHHHHHHHHHHHHcCCCceEEEEeEcCC-C-CEEEEEEEC
Confidence 3677777766666555567778888899999998888 7888899999999999999999998752 3 337776665
Q ss_pred CCCCCCcHH---HHHHHHHHHHHHHH
Q 001809 485 PVTIKGSSE---QQLLLNNLSGTMQR 507 (1010)
Q Consensus 485 P~~ck~~~E---Qq~ll~sLs~Tmqq 507 (1010)
+..-.+.++ +...|..|...+.+
T Consensus 122 ~~~~~~~~~~~~~~~~l~~la~~~h~ 147 (149)
T PF03472_consen 122 DERDPDAEELLWHRADLRLLAHYFHE 147 (149)
T ss_dssp SSSSCCHHHHHHHHHHHHHHHHHHHH
T ss_pred CCCCCChHHHHHHHHHHHHHHHHHhh
Confidence 555555444 67777777766654
No 51
>PRK11302 DNA-binding transcriptional regulator HexR; Provisional
Probab=84.38 E-value=0.79 Score=49.68 Aligned_cols=36 Identities=28% Similarity=0.416 Sum_probs=31.8
Q ss_pred HHhhcCCcHHHHHHHcCCChhHHHHHHHHcCCCCCc
Q 001809 607 LQQYFSGSLKDAAKSIGVCPTTLKRICRQHGISRWP 642 (1010)
Q Consensus 607 L~~yF~~pl~eAAk~LGV~~TtLKRiCR~~GI~RWP 642 (1010)
......+++++.|++.|||++|+-|.||++|..-|+
T Consensus 29 ~~~v~~~si~~lA~~~~vS~aTv~Rf~kklG~~gf~ 64 (284)
T PRK11302 29 PQTAIHSSIATLAKMANVSEPTVNRFCRSLDTKGFP 64 (284)
T ss_pred HHHHHhcCHHHHHHHhCCCHHHHHHHHHHcCCCCHH
Confidence 335568999999999999999999999999988774
No 52
>PRK11608 pspF phage shock protein operon transcriptional activator; Provisional
Probab=84.29 E-value=1.1 Score=50.45 Aligned_cols=30 Identities=27% Similarity=0.308 Sum_probs=28.0
Q ss_pred hhcCCcHHHHHHHcCCChhHHHHHHHHcCC
Q 001809 609 QYFSGSLKDAAKSIGVCPTTLKRICRQHGI 638 (1010)
Q Consensus 609 ~yF~~pl~eAAk~LGV~~TtLKRiCR~~GI 638 (1010)
+..++-..+||+.|||+.+||+|..|+|||
T Consensus 296 ~~~~gn~~~aA~~LGIsR~tLyrklk~~gi 325 (326)
T PRK11608 296 QQAKFNQKRAAELLGLTYHQLRALLKKHQI 325 (326)
T ss_pred HHhCCCHHHHHHHhCCCHHHHHHHHHHcCC
Confidence 456888999999999999999999999998
No 53
>cd01763 Sumo Small ubiquitin-related modifier (SUMO). Small ubiquitin-related modifier (SUMO) proteins are conjugated to numerous intracellular targets and serve to modulate protein interaction, localization, activity or stability. SUMO (also known as "Smt3" and "sentrin" in other organisms) is linked to several different pathways, including nucleocytoplasmic transport. Attachment of SUMO to targets proteins is stimulated by PIAS (Protein inhibitor of activated STATs) proteins which serve as E3-like ligases.
Probab=83.85 E-value=4.5 Score=37.36 Aligned_cols=75 Identities=16% Similarity=0.182 Sum_probs=53.3
Q ss_pred CCeEEEEEEcC-CCeEEEEeCCCcChHHHHHHHHHHcCcccceeeeEeecCCCCeEEEecCCcHHHHHHHHhHhCCCeEE
Q 001809 900 GSKIIVKATYK-EDIIRFKFDPSAGCFQLYEEVARRLKLQNGTFQLKYLDDEEEWVMLVSDSDLQECFDILESLGKRSVR 978 (1010)
Q Consensus 900 ~~~~~vKaty~-~d~iRF~~~~s~g~~~L~~EIakRf~l~~~~f~lKYlDDd~EWVlLtcDaDL~EC~di~~~~~~~~vk 978 (1010)
...|+||+... +.+++|++.++.-+..|++.+++|.+|+...+.|-|- |+= |- | .+..+-+.--...+|.
T Consensus 9 ~~~i~I~v~~~~g~~~~~~v~~~~~l~~l~~~y~~~~gi~~~~~rf~f~---G~~--L~-~---~~T~~~l~m~d~d~I~ 79 (87)
T cd01763 9 SEHINLKVKGQDGNEVFFKIKRSTPLKKLMEAYCQRQGLSMNSVRFLFD---GQR--IR-D---NQTPDDLGMEDGDEIE 79 (87)
T ss_pred CCeEEEEEECCCCCEEEEEEcCCCHHHHHHHHHHHHhCCCccceEEEEC---CeE--CC-C---CCCHHHcCCCCCCEEE
Confidence 45688888777 5889999999999999999999999999887877773 211 11 1 1233333444456777
Q ss_pred EEEee
Q 001809 979 FLVRD 983 (1010)
Q Consensus 979 l~V~d 983 (1010)
+.++.
T Consensus 80 v~l~l 84 (87)
T cd01763 80 VMLEQ 84 (87)
T ss_pred EEEec
Confidence 66653
No 54
>cd04763 HTH_MlrA-like Helix-Turn-Helix DNA binding domain of MlrA-like transcription regulators. Helix-turn-helix (HTH) transcription regulator MlrA (merR-like regulator A) and related proteins, N-terminal domain. The MlrA protein, also known as YehV, has been shown to control cell-cell aggregation by co-regulating the expression of curli and extracellular matrix production in Escherichia coli and Salmonella typhimurium. Its close homolog, CarA from Myxococcus xanthus, is involved in activation of the carotenoid biosynthesis genes by light. These proteins belong to the MerR superfamily of transcription regulators that promote expression of several stress regulon genes by reconfiguring the spacer between the -35 and -10 promoter elements. Their conserved N-terminal domains contain predicted HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules. Many MlrA-like proteins in this group appear to lack the long dimerization helix seen
Probab=83.84 E-value=1.1 Score=39.13 Aligned_cols=27 Identities=22% Similarity=0.356 Sum_probs=24.1
Q ss_pred CcHHHHHHHcCCChhHHHHHHHHcCCC
Q 001809 613 GSLKDAAKSIGVCPTTLKRICRQHGIS 639 (1010)
Q Consensus 613 ~pl~eAAk~LGV~~TtLKRiCR~~GI~ 639 (1010)
+++.|+|+.+||++.||+..+++.|+.
T Consensus 1 ~~i~e~A~~~gVs~~tlr~ye~~~gl~ 27 (68)
T cd04763 1 YTIGEVALLTGIKPHVLRAWEREFGLL 27 (68)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHhcCCC
Confidence 478999999999999999999987753
No 55
>PRK11361 acetoacetate metabolism regulatory protein AtoC; Provisional
Probab=83.77 E-value=1.1 Score=51.50 Aligned_cols=31 Identities=19% Similarity=0.255 Sum_probs=28.2
Q ss_pred hhcCCcHHHHHHHcCCChhHHHHHHHHcCCC
Q 001809 609 QYFSGSLKDAAKSIGVCPTTLKRICRQHGIS 639 (1010)
Q Consensus 609 ~yF~~pl~eAAk~LGV~~TtLKRiCR~~GI~ 639 (1010)
..+++-..+||+.|||+.+||+|..|++||.
T Consensus 427 ~~~~gn~~~aA~~LGisr~tL~rkl~~~~i~ 457 (457)
T PRK11361 427 EQQEGNRTRTALMLGISRRALMYKLQEYGID 457 (457)
T ss_pred HHhCCCHHHHHHHHCCCHHHHHHHHHHhCCC
Confidence 4567899999999999999999999999983
No 56
>cd01806 Nedd8 Nebb8-like ubiquitin protein. Nedd8 (also known as Rub1) has a single conserved ubiquitin-like domain that is part of a protein modification pathway similar to that of ubiquitin. Nedd8 modifies a family of molecular scaffold proteins called cullins that are responsible for assembling the ROC1/Rbx1 RING-based E3 ubiquitin ligases, of which several play a direct role in tumorigenesis.
Probab=83.66 E-value=7 Score=34.13 Aligned_cols=71 Identities=15% Similarity=0.201 Sum_probs=52.3
Q ss_pred EEEEEEcCCCeEEEEeCCCcChHHHHHHHHHHcCcccceeeeEeecCCCCeEEEecCCcHHHHHHHHhHhCCCeEEEEEe
Q 001809 903 IIVKATYKEDIIRFKFDPSAGCFQLYEEVARRLKLQNGTFQLKYLDDEEEWVMLVSDSDLQECFDILESLGKRSVRFLVR 982 (1010)
Q Consensus 903 ~~vKaty~~d~iRF~~~~s~g~~~L~~EIakRf~l~~~~f~lKYlDDd~EWVlLtcDaDL~EC~di~~~~~~~~vkl~V~ 982 (1010)
++||... ++++.+++.++.-+.+|++.|+++.++......|-|- +. .|..|..|.+| .-....+|.|.+.
T Consensus 3 i~v~~~~-g~~~~~~v~~~~tv~~lK~~i~~~~g~~~~~qrL~~~---g~--~L~d~~tl~~~----~i~~g~~i~l~~~ 72 (76)
T cd01806 3 IKVKTLT-GKEIEIDIEPTDKVERIKERVEEKEGIPPQQQRLIYS---GK--QMNDDKTAADY----KLEGGSVLHLVLA 72 (76)
T ss_pred EEEEeCC-CCEEEEEECCCCCHHHHHHHHhHhhCCChhhEEEEEC---Ce--EccCCCCHHHc----CCCCCCEEEEEEE
Confidence 5666654 4788999999999999999999999999888888763 22 34555566665 3344567777765
Q ss_pred e
Q 001809 983 D 983 (1010)
Q Consensus 983 d 983 (1010)
.
T Consensus 73 ~ 73 (76)
T cd01806 73 L 73 (76)
T ss_pred c
Confidence 3
No 57
>PF14560 Ubiquitin_2: Ubiquitin-like domain; PDB: 1WJN_A 2KJ6_A 2KJR_A 1V6E_A 1T0Y_A.
Probab=83.65 E-value=5.4 Score=36.61 Aligned_cols=79 Identities=15% Similarity=0.117 Sum_probs=50.8
Q ss_pred EEEEEcCC---CeEEEEeCCCcChHHHHHHHHHHcCcccceeeeEeecCCCCeEEEecCCcHHHHHHHHhHhCCCeEEEE
Q 001809 904 IVKATYKE---DIIRFKFDPSAGCFQLYEEVARRLKLQNGTFQLKYLDDEEEWVMLVSDSDLQECFDILESLGKRSVRFL 980 (1010)
Q Consensus 904 ~vKaty~~---d~iRF~~~~s~g~~~L~~EIakRf~l~~~~f~lKYlDDd~EWVlLtcDaDL~EC~di~~~~~~~~vkl~ 980 (1010)
.|-+|-.. ..+..|++++|-+.+|++-|.+.+|+......|.|.|+++.-.....|.|.. .+....-.+-.+|.
T Consensus 3 ~l~It~~~~~~~~~ekr~~~~~Tv~eLK~kl~~~~Gi~~~~m~L~l~~~~~~~~~~~~~dd~~---~L~~y~~~dg~~i~ 79 (87)
T PF14560_consen 3 KLFITSSNSKQRSVEKRFPKSITVSELKQKLEKLTGIPPSDMRLQLKSDKDDSKIEELDDDDA---TLGSYGIKDGMRIH 79 (87)
T ss_dssp EEEEEESSSSSSEEEEEEETTSBHHHHHHHHHHHHTS-TTTEEEEEE-TSSSSEEEESSGSSS---BCCHHT-STTEEEE
T ss_pred EEEEEeCCCCCeeEEEEcCCCCCHHHHHHHHHHHhCCCcccEEEEEEecCCCccccccCCCcc---EeecCCCCCCCEEE
Confidence 34444444 3788999999999999999999999999999999994443333333333321 11122224567788
Q ss_pred EeecC
Q 001809 981 VRDIS 985 (1010)
Q Consensus 981 V~d~~ 985 (1010)
|+|..
T Consensus 80 V~D~~ 84 (87)
T PF14560_consen 80 VVDTN 84 (87)
T ss_dssp EEE-T
T ss_pred EEeCC
Confidence 88754
No 58
>PRK15115 response regulator GlrR; Provisional
Probab=83.16 E-value=1.3 Score=51.07 Aligned_cols=31 Identities=23% Similarity=0.356 Sum_probs=28.5
Q ss_pred hhcCCcHHHHHHHcCCChhHHHHHHHHcCCC
Q 001809 609 QYFSGSLKDAAKSIGVCPTTLKRICRQHGIS 639 (1010)
Q Consensus 609 ~yF~~pl~eAAk~LGV~~TtLKRiCR~~GI~ 639 (1010)
..+++-..+||+.|||+++||+|..|+|||.
T Consensus 408 ~~~~gn~~~aA~~Lgisr~tL~rkl~~~~~~ 438 (444)
T PRK15115 408 QITKGNVTHAARMAGRNRTEFYKLLSRHELD 438 (444)
T ss_pred HHhCCCHHHHHHHhCCCHHHHHHHHHHhCCC
Confidence 4568889999999999999999999999996
No 59
>PRK15482 transcriptional regulator MurR; Provisional
Probab=83.12 E-value=0.94 Score=49.64 Aligned_cols=41 Identities=15% Similarity=0.269 Sum_probs=34.3
Q ss_pred HHHHHhhcCCcHHHHHHHcCCChhHHHHHHHHcCCCCCcch
Q 001809 604 LSVLQQYFSGSLKDAAKSIGVCPTTLKRICRQHGISRWPSR 644 (1010)
Q Consensus 604 l~~L~~yF~~pl~eAAk~LGV~~TtLKRiCR~~GI~RWP~R 644 (1010)
++.....-.+++.|.|++.|||++|+-|.||++|-.-|+-=
T Consensus 26 l~n~~~v~~~si~elA~~~~vS~aTv~Rf~kkLGf~Gf~ef 66 (285)
T PRK15482 26 RANVSELKSVSSRKMAKQLGISQSSIVKFAQKLGAQGFTEL 66 (285)
T ss_pred HhCHHHHHhcCHHHHHHHhCCCHHHHHHHHHHhCCCCHHHH
Confidence 33444556899999999999999999999999999888543
No 60
>TIGR01817 nifA Nif-specific regulatory protein. This model represents NifA, a DNA-binding regulatory protein for nitrogen fixation. The model produces scores between the trusted and noise cutoffs for a well-described NifA homolog in Aquifex aeolicus (which lacks nitrogenase), for transcriptional activators of alternative nitrogenases (VFe or FeFe instead of MoFe), and truncated forms.
Probab=83.05 E-value=8.1 Score=46.37 Aligned_cols=125 Identities=11% Similarity=0.068 Sum_probs=76.2
Q ss_pred CCCHHHHHHHHHHHHHHhcCCCeeEEEEeeeccCCeeeeeeCCCCcccchhhhHHhhccceeeeccCCCCCCCCCCCccc
Q 001809 162 PPSLDEKMLRALSFFKLSSGGGILAQVWVPRKQGDDYILSTSDQPYLLDQMLAGYREVSRKFTFSAEAKPGTFLGLPGRV 241 (1010)
Q Consensus 162 ~~svkerm~~AL~~~kes~~~~~L~QVWvP~~~g~~~vLsT~~qP~~ld~~L~~yR~vS~~f~Fs~~~~~~~~~GLPGRV 241 (1010)
...+.+=|..++..+.+.++-+ -+=||+...++...++.+.+. ...... ...+.. ..|+-|+|
T Consensus 17 ~~dl~~lL~~il~~l~~~l~a~-~~~I~L~d~~~~~l~~aa~g~----~~~~~~------~~~~~~------~~gi~g~v 79 (534)
T TIGR01817 17 PTRLEKTLANVLNVLSNDLGMR-HGLITLSDSEGEPLLVAAIGW----SEEGFA------PIRYRV------GEGAIGQI 79 (534)
T ss_pred cCCHHHHHHHHHHHHHHhcCCC-EEEEEEECCCCCEEEEEEeCC----Chhhcc------cccccC------CccHHHHH
Confidence 4568888889999999988732 223344444444333333221 111000 011222 24899999
Q ss_pred ccCCCCcccccccccCcccccchhhHHhcCCceEEEEeeecCCCCceEEEEEEeeecccCCchHHH
Q 001809 242 FSSKVPEWTSNVAYYNEAEYARVTHAVNHAVRSCIALPVFQFPEISCSAVLEIVSVKEKPNFDAEI 307 (1010)
Q Consensus 242 F~s~~PEWTpnV~~y~~~EYpR~~~A~~~~VrGsLAlPVf~~~s~~ClAVlElV~t~ek~~f~~E~ 307 (1010)
+..+.|.+.+||..-. -|.....+...++++.|++||... +.++|||.+......-.|..+-
T Consensus 80 ~~~~~pvii~Dv~~d~--~~~~~~~~~~~~~~S~l~VPL~~~--g~viGvL~v~s~~~~~~ft~~d 141 (534)
T TIGR01817 80 VATGNSLVVPDVAAEP--LFLDRLSLYDPGPVPFIGVPIKAD--SETIGVLAADRDFRSRERLEEE 141 (534)
T ss_pred HhcCCeEEecccccCc--hhhhccccccCCcceEEEEEEcCC--CEEEEEEEEEeccccccccHHH
Confidence 9999999999996421 221111134578899999999843 4579999998776555555444
No 61
>cd04764 HTH_MlrA-like_sg1 Helix-Turn-Helix DNA binding domain of putative MlrA-like transcription regulators. Putative helix-turn-helix (HTH) MlrA-like transcription regulators (subgroup 1). The MlrA protein, also known as YehV, has been shown to control cell-cell aggregation by co-regulating the expression of curli and extracellular matrix production in Escherichia coli and Salmonella typhimurium. These proteins belong to the MerR superfamily of transcription regulators that promote expression of several stress regulon genes by reconfiguring the spacer between the -35 and -10 promoter elements. Their conserved N-terminal domains contain predicted HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules. Many MlrA-like proteins in this group appear to lack the long dimerization helix seen in the N-terminal domains of typical MerR-like proteins.
Probab=81.82 E-value=1.5 Score=37.99 Aligned_cols=27 Identities=26% Similarity=0.428 Sum_probs=24.6
Q ss_pred CcHHHHHHHcCCChhHHHHHHHHcCCC
Q 001809 613 GSLKDAAKSIGVCPTTLKRICRQHGIS 639 (1010)
Q Consensus 613 ~pl~eAAk~LGV~~TtLKRiCR~~GI~ 639 (1010)
+++.|+|+.+||++.||.+.+++.+|.
T Consensus 1 ~~i~evA~~~gvs~~tlR~~~~~g~l~ 27 (67)
T cd04764 1 YTIKEVSEIIGVKPHTLRYYEKEFNLY 27 (67)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHhcCCC
Confidence 478999999999999999999997775
No 62
>COG3284 AcoR Transcriptional activator of acetoin/glycerol metabolism [Secondary metabolites biosynthesis, transport, and catabolism / Transcription]
Probab=81.72 E-value=1.2 Score=54.41 Aligned_cols=32 Identities=38% Similarity=0.647 Sum_probs=28.5
Q ss_pred hhcCCcHHHHHHHcCCChhHHHHHHHHcCCCC
Q 001809 609 QYFSGSLKDAAKSIGVCPTTLKRICRQHGISR 640 (1010)
Q Consensus 609 ~yF~~pl~eAAk~LGV~~TtLKRiCR~~GI~R 640 (1010)
+-=..-+.+|||.|||+.+||+|.-|+|||.+
T Consensus 575 ~~~~~~is~aa~~lgi~R~T~yrklk~~gi~~ 606 (606)
T COG3284 575 QATNGNISEAARLLGISRSTLYRKLKRHGISK 606 (606)
T ss_pred HHcCCCHHHHHHHhCCCHHHHHHHHHHhCCCC
Confidence 34478899999999999999999999999964
No 63
>TIGR02915 PEP_resp_reg putative PEP-CTERM system response regulator. Members of this protein family share full-length homology with (but do not include) the acetoacetate metabolism regulatory protein AtoC. These proteins have a Fis family DNA binding sequence (pfam02954), a response regulator receiver domain (pfam00072), and sigma-54 interaction domain (pfam00158).
Probab=81.55 E-value=1.7 Score=50.20 Aligned_cols=31 Identities=29% Similarity=0.540 Sum_probs=28.2
Q ss_pred hhcCCcHHHHHHHcCCChhHHHHHHHHcCCC
Q 001809 609 QYFSGSLKDAAKSIGVCPTTLKRICRQHGIS 639 (1010)
Q Consensus 609 ~yF~~pl~eAAk~LGV~~TtLKRiCR~~GI~ 639 (1010)
..++.-..+||+.|||+++||+|.-|++||.
T Consensus 415 ~~~~gn~~~aA~~Lgisr~tl~rkl~~~~i~ 445 (445)
T TIGR02915 415 ARVDGNIARAAELLGITRPTLYDLMKKHGIK 445 (445)
T ss_pred HHhCCCHHHHHHHhCCCHHHHHHHHHHhCCC
Confidence 5568889999999999999999999999983
No 64
>PRK10820 DNA-binding transcriptional regulator TyrR; Provisional
Probab=81.24 E-value=1.7 Score=52.18 Aligned_cols=26 Identities=35% Similarity=0.489 Sum_probs=24.7
Q ss_pred cHHHHHHHcCCChhHHHHHHHHcCCC
Q 001809 614 SLKDAAKSIGVCPTTLKRICRQHGIS 639 (1010)
Q Consensus 614 pl~eAAk~LGV~~TtLKRiCR~~GI~ 639 (1010)
...+|||.|||+.|||.|.-|+|||.
T Consensus 488 ~~~~aA~~LGisr~tL~rkl~~~gi~ 513 (520)
T PRK10820 488 STRKLAKRLGVSHTAIANKLREYGLS 513 (520)
T ss_pred CHHHHHHHhCCCHHHHHHHHHHcCCC
Confidence 78899999999999999999999994
No 65
>PRK05022 anaerobic nitric oxide reductase transcription regulator; Provisional
Probab=81.09 E-value=1.7 Score=51.82 Aligned_cols=123 Identities=14% Similarity=0.137 Sum_probs=72.0
Q ss_pred CCCHHHHHHHHHHHHHHhcCCCeeEEEEeeeccCCeeeeeeCCCCcccchhhhHHhhccceeeeccCCCCCCCCC-CCcc
Q 001809 162 PPSLDEKMLRALSFFKLSSGGGILAQVWVPRKQGDDYILSTSDQPYLLDQMLAGYREVSRKFTFSAEAKPGTFLG-LPGR 240 (1010)
Q Consensus 162 ~~svkerm~~AL~~~kes~~~~~L~QVWvP~~~g~~~vLsT~~qP~~ld~~L~~yR~vS~~f~Fs~~~~~~~~~G-LPGR 240 (1010)
+..+.|-|...+..+++....+ .+-|.++.. +.-.+..+.+.. ..+ ... .|...+ | .-|.
T Consensus 16 s~d~~e~L~~vl~~l~~~l~~~-~~~l~l~~~-~~l~~~as~gl~----~~~-----~~~--~~~~ge------GP~l~a 76 (509)
T PRK05022 16 GLPHQDRFQRLLTTLRQVLPCD-ASALLRLDG-DQLVPLAIDGLS----PDV-----LGR--RFALEE------HPRLEA 76 (509)
T ss_pred CCCHHHHHHHHHHHHHHHcCCC-EEEEEecCC-CcEEEEEEcCCC----hHh-----hCC--ccCCCc------chHHHH
Confidence 4468899999999999998633 444554432 222222333321 111 111 233322 3 2366
Q ss_pred cccCCCCcccccccccCcccccchh--hHHhcCCceEEEEeeecCCCCceEEEEEEeeecccCCchHHH
Q 001809 241 VFSSKVPEWTSNVAYYNEAEYARVT--HAVNHAVRSCIALPVFQFPEISCSAVLEIVSVKEKPNFDAEI 307 (1010)
Q Consensus 241 VF~s~~PEWTpnV~~y~~~EYpR~~--~A~~~~VrGsLAlPVf~~~s~~ClAVlElV~t~ek~~f~~E~ 307 (1010)
|+.++.|-..+++.-. +..|.|.- .|...||++.|+||++..+ .++|||-+-..... .|..+-
T Consensus 77 v~~~g~~v~v~~~~~~-p~~~~~~~~~~~~~~gi~S~l~vPL~~~~--~~~GvL~l~~~~~~-~f~~~~ 141 (509)
T PRK05022 77 ILRAGDPVRFPADSEL-PDPYDGLIPGVQESLPVHDCMGLPLFVDG--RLIGALTLDALDPG-QFDAFS 141 (509)
T ss_pred HHhcCCeEEEecCCCC-CcccccccccccccCCcceEEEEEEEECC--EEEEEEEEeeCCCC-cCCHHH
Confidence 7766777666655332 22243332 3567899999999999865 57999998665444 566664
No 66
>TIGR01817 nifA Nif-specific regulatory protein. This model represents NifA, a DNA-binding regulatory protein for nitrogen fixation. The model produces scores between the trusted and noise cutoffs for a well-described NifA homolog in Aquifex aeolicus (which lacks nitrogenase), for transcriptional activators of alternative nitrogenases (VFe or FeFe instead of MoFe), and truncated forms.
Probab=80.92 E-value=2.6 Score=50.42 Aligned_cols=89 Identities=11% Similarity=0.121 Sum_probs=61.2
Q ss_pred cccccCCCcchhhhhcCCCcccccccccCccccchhhHHHHhCCceeEEEEecccccCCCcEEEEeecCCCCC-CcHHHH
Q 001809 417 HYLEEGQGVAGKALQSNHPFFFPDVKLYDITEFPLVHHARKFGLNAAVAIRLRSTYTGDDDYILEFFLPVTIK-GSSEQQ 495 (1010)
Q Consensus 417 hhL~~GQGvaGkAf~sn~P~F~~DV~~fsk~EYPL~HhAr~fgL~aAvAIrLrS~~tG~ddyVLEFFLP~~ck-~~~EQq 495 (1010)
..+..|+|+.|+|+.++.|.+++||..-..-.++ ..+...+.++.+++||+. .|..--||..+-+..=. -.+++.
T Consensus 67 ~~~~~~~gi~g~v~~~~~pvii~Dv~~d~~~~~~--~~~~~~~~~S~l~VPL~~--~g~viGvL~v~s~~~~~~ft~~d~ 142 (534)
T TIGR01817 67 IRYRVGEGAIGQIVATGNSLVVPDVAAEPLFLDR--LSLYDPGPVPFIGVPIKA--DSETIGVLAADRDFRSRERLEEEV 142 (534)
T ss_pred ccccCCccHHHHHHhcCCeEEecccccCchhhhc--cccccCCcceEEEEEEcC--CCEEEEEEEEEeccccccccHHHH
Confidence 3456699999999999999999999752111011 113457889999999984 46677788887663322 256777
Q ss_pred HHHHHHHHHHHHhh
Q 001809 496 LLLNNLSGTMQRMC 509 (1010)
Q Consensus 496 ~ll~sLs~Tmqq~c 509 (1010)
.+|..|..-+-..-
T Consensus 143 ~lL~~lA~~ia~aI 156 (534)
T TIGR01817 143 RFLEMVANLIGQTV 156 (534)
T ss_pred HHHHHHHHHHHHHH
Confidence 77777776655443
No 67
>PF11543 UN_NPL4: Nuclear pore localisation protein NPL4; InterPro: IPR024682 Npl4, along with Ufd1, forms the heterodimer adaptor complex UN, which is involved in the recruitment of p97, an AAA ATPase, for tasks involving the ubiquitin pathway. Npl4 has a N-terminal ubiquitin-like domain which has within its structure a beta-grasp fold with a helical insert []. This entry represents the ubiquitin-like domain.; PDB: 2PJH_A 1WF9_A.
Probab=80.80 E-value=2.9 Score=38.68 Aligned_cols=48 Identities=21% Similarity=0.389 Sum_probs=33.7
Q ss_pred eEEEEEEcCCCeEEEEeCCCcChHHHHHHHHHHcCcccceeeeEeecCC
Q 001809 902 KIIVKATYKEDIIRFKFDPSAGCFQLYEEVARRLKLQNGTFQLKYLDDE 950 (1010)
Q Consensus 902 ~~~vKaty~~d~iRF~~~~s~g~~~L~~EIakRf~l~~~~f~lKYlDDd 950 (1010)
.+.|.+.=++.+.|+.+.|+.-+.+|++.|+..|++.+..|.| |+|..
T Consensus 4 ~milRvrS~dG~~Rie~~~~~t~~~L~~kI~~~l~~~~~~~~L-~~~~~ 51 (80)
T PF11543_consen 4 SMILRVRSKDGMKRIEVSPSSTLSDLKEKISEQLSIPDSSQSL-SKDRN 51 (80)
T ss_dssp --EEEEE-SSEEEEEEE-TTSBHHHHHHHHHHHS---TTT----BSSGG
T ss_pred cEEEEEECCCCCEEEEcCCcccHHHHHHHHHHHcCCCCcceEE-EecCC
Confidence 4777778888999999999999999999999999999888777 66653
No 68
>cd01104 HTH_MlrA-CarA Helix-Turn-Helix DNA binding domain of the transcription regulators MlrA and CarA. Helix-turn-helix (HTH) transcription regulator MlrA (merR-like regulator A), N-terminal domain. The MlrA protein, also known as YehV, has been shown to control cell-cell aggregation by co-regulating the expression of curli and extracellular matrix production in Escherichia coli and Salmonella typhimurium. Its close homolog, CarA from Myxococcus xanthus, is involved in activation of the carotenoid biosynthesis genes by light. These proteins belong to the MerR superfamily of transcription regulators that promote expression of several stress regulon genes by reconfiguring the spacer between the -35 and -10 promoter elements. Their conserved N-terminal domains contain predicted HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules. Many MlrA- and CarA-like proteins in this group appear to lack the long dimerization helix seen i
Probab=80.76 E-value=1.8 Score=37.21 Aligned_cols=26 Identities=31% Similarity=0.466 Sum_probs=23.7
Q ss_pred CcHHHHHHHcCCChhHHHHHHHHcCC
Q 001809 613 GSLKDAAKSIGVCPTTLKRICRQHGI 638 (1010)
Q Consensus 613 ~pl~eAAk~LGV~~TtLKRiCR~~GI 638 (1010)
+++.|+|+.+||++.||.+..++.|+
T Consensus 1 ~s~~eva~~~gvs~~tlr~w~~~~g~ 26 (68)
T cd01104 1 YTIGAVARLTGVSPDTLRAWERRYGL 26 (68)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHhCCC
Confidence 47899999999999999999988776
No 69
>COG1737 RpiR Transcriptional regulators [Transcription]
Probab=80.59 E-value=1.1 Score=49.66 Aligned_cols=38 Identities=26% Similarity=0.402 Sum_probs=33.4
Q ss_pred hhcCCcHHHHHHHcCCChhHHHHHHHHcCCCCCcchhh
Q 001809 609 QYFSGSLKDAAKSIGVCPTTLKRICRQHGISRWPSRKI 646 (1010)
Q Consensus 609 ~yF~~pl~eAAk~LGV~~TtLKRiCR~~GI~RWP~Rki 646 (1010)
..-+++++|.|+..|||++|+-|.||++|-.-||==|+
T Consensus 33 ~~~~~si~elA~~a~VS~aTv~Rf~~kLGf~Gf~efk~ 70 (281)
T COG1737 33 EVALLSIAELAERAGVSPATVVRFARKLGFEGFSEFKL 70 (281)
T ss_pred HHHHHHHHHHHHHhCCCHHHHHHHHHHcCCCCHHHHHH
Confidence 44578999999999999999999999999988875554
No 70
>PF11976 Rad60-SLD: Ubiquitin-2 like Rad60 SUMO-like; InterPro: IPR022617 This entry includes small ubiquitin-related modifier (SUMO) proteins. SUMOs are small proteins that are covalently attached to lysines as post-translational modifications and are used to control multiple cellular process including signal transduction, nuclear transport and DNA replication and repair []. Unlike ubiquitin, they are not involved in protein degradation. This entry also contains the C-terminal Rad60 DNA repair protein SUMO-like domain.; PDB: 3RD2_A 2JXX_A 3RCZ_A 3GOE_A 3A4S_D 3A4R_B 2IO1_D 1U4A_A 2K1F_A 1WZ0_A ....
Probab=80.09 E-value=4.6 Score=35.27 Aligned_cols=44 Identities=18% Similarity=0.322 Sum_probs=36.8
Q ss_pred EEEEEcC-CCeEEEEeCCCcChHHHHHHHHHHcCccc-ceeeeEee
Q 001809 904 IVKATYK-EDIIRFKFDPSAGCFQLYEEVARRLKLQN-GTFQLKYL 947 (1010)
Q Consensus 904 ~vKaty~-~d~iRF~~~~s~g~~~L~~EIakRf~l~~-~~f~lKYl 947 (1010)
+||+... +..++|++.++.-+..|.+.++++.+++. ..+.|.|-
T Consensus 2 ~i~v~~~~~~~~~~~v~~~~~~~~l~~~~~~~~~i~~~~~~~l~fd 47 (72)
T PF11976_consen 2 TIKVRSQDGKEIKFKVKPTTTVSKLIEKYCEKKGIPPEESIRLIFD 47 (72)
T ss_dssp EEEEEETTSEEEEEEEETTSCCHHHHHHHHHHHTTTT-TTEEEEET
T ss_pred EEEEEeCCCCEEEEEECCCCcHHHHHHHHHHhhCCCccceEEEEEC
Confidence 4444444 35999999999999999999999999999 78888873
No 71
>PRK10923 glnG nitrogen regulation protein NR(I); Provisional
Probab=79.99 E-value=2 Score=49.99 Aligned_cols=31 Identities=26% Similarity=0.379 Sum_probs=28.5
Q ss_pred hhcCCcHHHHHHHcCCChhHHHHHHHHcCCC
Q 001809 609 QYFSGSLKDAAKSIGVCPTTLKRICRQHGIS 639 (1010)
Q Consensus 609 ~yF~~pl~eAAk~LGV~~TtLKRiCR~~GI~ 639 (1010)
..+++-..+||+.|||+++||+|..|++||.
T Consensus 439 ~~~~gn~~~aA~~Lgisr~tL~rkl~~~~i~ 469 (469)
T PRK10923 439 RHTQGHKQEAARLLGWGRNTLTRKLKELGME 469 (469)
T ss_pred HHhCCCHHHHHHHhCCCHHHHHHHHHHhCCC
Confidence 4578899999999999999999999999984
No 72
>PRK11557 putative DNA-binding transcriptional regulator; Provisional
Probab=79.81 E-value=1.4 Score=47.90 Aligned_cols=36 Identities=17% Similarity=0.254 Sum_probs=31.5
Q ss_pred hhcCCcHHHHHHHcCCChhHHHHHHHHcCCCCCcch
Q 001809 609 QYFSGSLKDAAKSIGVCPTTLKRICRQHGISRWPSR 644 (1010)
Q Consensus 609 ~yF~~pl~eAAk~LGV~~TtLKRiCR~~GI~RWP~R 644 (1010)
..-.++++|.|++.|||++|+-|.||++|-..|+-=
T Consensus 27 ~v~~~si~elA~~~~vS~aTv~Rf~kklG~~Gf~ef 62 (278)
T PRK11557 27 TARHLSSQQLANEAGVSQSSVVKFAQKLGYKGFPAL 62 (278)
T ss_pred HHHhcCHHHHHHHhCCCHHHHHHHHHHcCCCCHHHH
Confidence 444799999999999999999999999998887443
No 73
>TIGR03070 couple_hipB transcriptional regulator, y4mF family. Members of this family belong to a clade of helix-turn-helix DNA-binding proteins, among the larger family pfam01381 (HTH_3; Helix-turn-helix). Members are similar in sequence to the HipB protein of E. coli. Genes for members of the seed alignment for this protein family were found to be closely linked to genes encoding proteins related to HipA. The HibBA operon appears to have some features in common with toxin-antitoxin post-segregational killing systems.
Probab=79.68 E-value=4.6 Score=32.96 Aligned_cols=31 Identities=13% Similarity=0.112 Sum_probs=28.1
Q ss_pred HHHHHhhcCCcHHHHHHHcCCChhHHHHHHH
Q 001809 604 LSVLQQYFSGSLKDAAKSIGVCPTTLKRICR 634 (1010)
Q Consensus 604 l~~L~~yF~~pl~eAAk~LGV~~TtLKRiCR 634 (1010)
+..++...+++++++|+.+||+++++.++.+
T Consensus 7 l~~~r~~~gltq~~lA~~~gvs~~~vs~~e~ 37 (58)
T TIGR03070 7 VRARRKALGLTQADLADLAGVGLRFIRDVEN 37 (58)
T ss_pred HHHHHHHcCCCHHHHHHHhCCCHHHHHHHHC
Confidence 5677888899999999999999999999965
No 74
>PRK10219 DNA-binding transcriptional regulator SoxS; Provisional
Probab=79.23 E-value=3.2 Score=38.99 Aligned_cols=35 Identities=17% Similarity=0.159 Sum_probs=29.1
Q ss_pred HHHHhhcC--CcHHHHHHHcCCChhHHHHHHHHc-CCC
Q 001809 605 SVLQQYFS--GSLKDAAKSIGVCPTTLKRICRQH-GIS 639 (1010)
Q Consensus 605 ~~L~~yF~--~pl~eAAk~LGV~~TtLKRiCR~~-GI~ 639 (1010)
.-|...++ +++.++|+.+|+++.+|.|+++++ |+.
T Consensus 12 ~~i~~~~~~~~~~~~lA~~~~~S~~~l~r~f~~~~g~s 49 (107)
T PRK10219 12 AWIDEHIDQPLNIDVVAKKSGYSKWYLQRMFRTVTHQT 49 (107)
T ss_pred HHHHHhcCCCCCHHHHHHHHCCCHHHHHHHHHHHHCcC
Confidence 34455554 899999999999999999999997 763
No 75
>PF01381 HTH_3: Helix-turn-helix; InterPro: IPR001387 This is large family of DNA binding helix-turn helix proteins that include a bacterial plasmid copy control protein, bacterial methylases, various bacteriophage transcription control proteins and a vegetative specific protein from Dictyostelium discoideum (Slime mould).; GO: 0043565 sequence-specific DNA binding; PDB: 2AXU_A 2AWI_D 2AXV_D 2AXZ_C 2AW6_A 3KXA_C 3BS3_A 2CRO_A 1ZUG_A 3CRO_R ....
Probab=79.09 E-value=3.9 Score=33.74 Aligned_cols=37 Identities=30% Similarity=0.376 Sum_probs=28.6
Q ss_pred HHHHHhhcCCcHHHHHHHcCCChhHHHHHHHHcCCCCCcc
Q 001809 604 LSVLQQYFSGSLKDAAKSIGVCPTTLKRICRQHGISRWPS 643 (1010)
Q Consensus 604 l~~L~~yF~~pl~eAAk~LGV~~TtLKRiCR~~GI~RWP~ 643 (1010)
+..++.--+++++|.|+.+||+++++.|+.+. .+.|.
T Consensus 1 ik~~r~~~gls~~~la~~~gis~~~i~~~~~g---~~~~~ 37 (55)
T PF01381_consen 1 IKELRKEKGLSQKELAEKLGISRSTISRIENG---KRNPS 37 (55)
T ss_dssp HHHHHHHTTS-HHHHHHHHTS-HHHHHHHHTT---SSTSB
T ss_pred CHHHHHHcCCCHHHHHHHhCCCcchhHHHhcC---CCCCC
Confidence 34667778999999999999999999999876 45454
No 76
>PRK11337 DNA-binding transcriptional repressor RpiR; Provisional
Probab=78.15 E-value=1.7 Score=47.65 Aligned_cols=35 Identities=20% Similarity=0.362 Sum_probs=30.8
Q ss_pred HhhcCCcHHHHHHHcCCChhHHHHHHHHcCCCCCc
Q 001809 608 QQYFSGSLKDAAKSIGVCPTTLKRICRQHGISRWP 642 (1010)
Q Consensus 608 ~~yF~~pl~eAAk~LGV~~TtLKRiCR~~GI~RWP 642 (1010)
.....+++++.|++.|||++|+-|.||++|-..|+
T Consensus 42 ~~v~~~si~~lA~~~~vS~aTi~Rf~kkLGf~gf~ 76 (292)
T PRK11337 42 DLSEATALKDIAEALAVSEAMIVKVAKKLGFSGFR 76 (292)
T ss_pred HHHHhcCHHHHHHHhCCChHHHHHHHHHcCCCCHH
Confidence 34557899999999999999999999999987764
No 77
>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=78.00 E-value=2.3 Score=36.78 Aligned_cols=28 Identities=25% Similarity=0.490 Sum_probs=24.2
Q ss_pred HhhcCCc----HHHHHHHcCCChhHHHHHHHH
Q 001809 608 QQYFSGS----LKDAAKSIGVCPTTLKRICRQ 635 (1010)
Q Consensus 608 ~~yF~~p----l~eAAk~LGV~~TtLKRiCR~ 635 (1010)
..||+.| ++|.|+.|||+.+|+-..-|+
T Consensus 15 ~GYfd~PR~~tl~elA~~lgis~st~~~~LRr 46 (53)
T PF04967_consen 15 LGYFDVPRRITLEELAEELGISKSTVSEHLRR 46 (53)
T ss_pred cCCCCCCCcCCHHHHHHHhCCCHHHHHHHHHH
Confidence 3799876 899999999999999887765
No 78
>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=77.10 E-value=3.5 Score=33.97 Aligned_cols=30 Identities=23% Similarity=0.545 Sum_probs=23.7
Q ss_pred HHHhhc--CCcHHHHHHHcCCChhHHHHHHHH
Q 001809 606 VLQQYF--SGSLKDAAKSIGVCPTTLKRICRQ 635 (1010)
Q Consensus 606 ~L~~yF--~~pl~eAAk~LGV~~TtLKRiCR~ 635 (1010)
.|.-+| +++++|+|+.|||+..+++++.++
T Consensus 12 vi~~~y~~~~t~~eIa~~lg~s~~~V~~~~~~ 43 (50)
T PF04545_consen 12 VIRLRYFEGLTLEEIAERLGISRSTVRRILKR 43 (50)
T ss_dssp HHHHHHTST-SHHHHHHHHTSCHHHHHHHHHH
T ss_pred HHHHHhcCCCCHHHHHHHHCCcHHHHHHHHHH
Confidence 344444 789999999999999999998764
No 79
>PRK13413 mpi multiple promoter invertase; Provisional
Probab=77.01 E-value=2.2 Score=44.57 Aligned_cols=28 Identities=32% Similarity=0.523 Sum_probs=25.8
Q ss_pred CCcHHHHHHHcCCChhHHHHHHHHcCCC
Q 001809 612 SGSLKDAAKSIGVCPTTLKRICRQHGIS 639 (1010)
Q Consensus 612 ~~pl~eAAk~LGV~~TtLKRiCR~~GI~ 639 (1010)
++++.++|+.|||+.+|++|++++.|+.
T Consensus 172 g~s~~~iak~lgis~~Tv~r~~k~~~~~ 199 (200)
T PRK13413 172 GTSKSEIARKLGVSRTTLARFLKTRGLR 199 (200)
T ss_pred CCCHHHHHHHHCCCHHHHHHHHHhcccC
Confidence 4699999999999999999999998873
No 80
>PF13492 GAF_3: GAF domain; PDB: 3EEA_A 4DMZ_A 4DN0_A 1VHM_A.
Probab=76.90 E-value=20 Score=32.86 Aligned_cols=118 Identities=19% Similarity=0.222 Sum_probs=65.3
Q ss_pred HHHHHHHHHHHHHHhcCCCeeEEEEeeeccCCeeeeeeCCCCcccchhhhHHhhccceeeeccCCCCCCCCCCCcccccC
Q 001809 165 LDEKMLRALSFFKLSSGGGILAQVWVPRKQGDDYILSTSDQPYLLDQMLAGYREVSRKFTFSAEAKPGTFLGLPGRVFSS 244 (1010)
Q Consensus 165 vkerm~~AL~~~kes~~~~~L~QVWvP~~~g~~~vLsT~~qP~~ld~~L~~yR~vS~~f~Fs~~~~~~~~~GLPGRVF~s 244 (1010)
++|-+.++++.+++.++-+ -+=||+...++....+.....+ +..+.. .++. ..++-++++..
T Consensus 2 l~~l~~~i~~~l~~~~~~~-~~~l~~~d~~~~~~~~~~~~~~---~~~~~~--------~l~~------~~~~~~~~~~~ 63 (129)
T PF13492_consen 2 LDELLERILELLRELLGAD-RAALFLLDEDGNRLRVVAGWGG---DPRLSE--------SLPE------DDPLIGRALET 63 (129)
T ss_dssp HHHHHHHHHHHHHHHST-S-EEEEEEEETTCECEEEEEEESS----GCGHH--------CEET------TSHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHhCCC-EEEEEEEECCCCEEEEEEEeCC---Cccccc--------cCCC------CccHHHHHHhh
Confidence 5677788999999999865 3447887766544333322111 111111 2221 12455566666
Q ss_pred CCCcccccccccCcccccchhhHHhcCCceEEEEeeecCCCCceEEEEEEeeecccCCchHHHHHHHHHh
Q 001809 245 KVPEWTSNVAYYNEAEYARVTHAVNHAVRSCIALPVFQFPEISCSAVLEIVSVKEKPNFDAEIENICNAL 314 (1010)
Q Consensus 245 ~~PEWTpnV~~y~~~EYpR~~~A~~~~VrGsLAlPVf~~~s~~ClAVlElV~t~ek~~f~~E~e~vc~AL 314 (1010)
+.|--.+++... ...+.+..+++||..++ .++|||.+- ..++-.|..+-..+-+.+
T Consensus 64 ~~~~~~~~~~~~-----------~~~~~~s~~~vPl~~~~--~~~Gvl~~~-~~~~~~~~~~d~~~l~~~ 119 (129)
T PF13492_consen 64 GEPVSVPDIDER-----------DFLGIRSLLVVPLRSRD--RVIGVLCLD-SREPEEFSDEDLQLLESL 119 (129)
T ss_dssp TS-EEESTCCC------------TTTTTCEEEEEEEEETT--EEEEEEEEE-ECTTCG-SHHHHHHHHHH
T ss_pred CCeEEecccccc-----------cCCCCCEEEEEEEeECC--EEEEEEEEE-ECCCCCCCHHHHHHHHHH
Confidence 655222332111 11677899999999988 669999984 444446766655444433
No 81
>cd01789 Alp11_N Ubiquitin-like domain of Alp11 tubulin-folding cofactor B. Alp11, also known as tubulin-folding cofactor B, is one of at least three proteins required for the proper folding of tubulins prior to their incorporation into microtubules. These cofactors are necessary for the biogenesis of microtubules and for cell viability. Alp11 has three domains including an N-terminal ubiquitin-like domain (represented by this CD) which executes the essential function, a central coiled-coil domain necessary for maintenance of cellular alpha-tubulin levels, and a C-terminal CLIP-170 domain is required for efficient binding to alpha-tubulin.
Probab=76.73 E-value=12 Score=34.58 Aligned_cols=52 Identities=10% Similarity=0.182 Sum_probs=43.3
Q ss_pred EEEEEEcCCCeEEEEeCCCcChHHHHHHHHHHcCcccceeeeEeecCCCCeE
Q 001809 903 IIVKATYKEDIIRFKFDPSAGCFQLYEEVARRLKLQNGTFQLKYLDDEEEWV 954 (1010)
Q Consensus 903 ~~vKaty~~d~iRF~~~~s~g~~~L~~EIakRf~l~~~~f~lKYlDDd~EWV 954 (1010)
+.|+.+.....+.-|++++|.+.+|++-+.+.+|++...-.|-|.|+++.-|
T Consensus 4 v~i~~~~~~~~~ekr~~~~~Tv~~lK~kl~~~~G~~~~~mrL~l~~~~~~~~ 55 (84)
T cd01789 4 VNITSSADSFSFEKKYSRGLTIAELKKKLELVVGTPASSMRLQLFDGDDKLV 55 (84)
T ss_pred EEEEeCCCceeeeEecCCCCcHHHHHHHHHHHHCCCccceEEEEEcCCCCeE
Confidence 5566665456677789999999999999999999999999998888887644
No 82
>PRK11388 DNA-binding transcriptional regulator DhaR; Provisional
Probab=75.77 E-value=3.1 Score=50.83 Aligned_cols=35 Identities=34% Similarity=0.434 Sum_probs=30.6
Q ss_pred hhcCCcHHHHHHHcCCChhHHHHHHHHcCCCCCcc
Q 001809 609 QYFSGSLKDAAKSIGVCPTTLKRICRQHGISRWPS 643 (1010)
Q Consensus 609 ~yF~~pl~eAAk~LGV~~TtLKRiCR~~GI~RWP~ 643 (1010)
..++.-..+||+.|||+.+||+|.-|++||..=|+
T Consensus 601 ~~~~gn~~~aA~~LGisR~TLyrklk~~~i~~~~~ 635 (638)
T PRK11388 601 QVCGGRIQEMAALLGIGRTTLWRKMKQHGIDAGQF 635 (638)
T ss_pred HHhCCCHHHHHHHHCCCHHHHHHHHHHcCCCcccc
Confidence 55688999999999999999999999999955443
No 83
>cd01796 DDI1_N DNA damage inducible protein 1 ubiquitin-like domain. DDI1_N DDI1 (DNA damage inducible protein 1) has an amino-terminal ubiquitin-like domain, an retroviral protease-like (RVP-like) domain, and a UBA (ubiquitin-associated) domain. This CD represents the amino-terminal ubiquitin-like domain of DDI1.
Probab=75.46 E-value=5.9 Score=35.23 Aligned_cols=49 Identities=14% Similarity=0.154 Sum_probs=39.4
Q ss_pred EEEEEEcCCCeEEEEeCCCcChHHHHHHHHHHcCcccce----eeeEeecCCC
Q 001809 903 IIVKATYKEDIIRFKFDPSAGCFQLYEEVARRLKLQNGT----FQLKYLDDEE 951 (1010)
Q Consensus 903 ~~vKaty~~d~iRF~~~~s~g~~~L~~EIakRf~l~~~~----f~lKYlDDd~ 951 (1010)
++||-.-+++++-+.+.|+.-+.+|++.|+.+.|+.... |.-|.|+||.
T Consensus 1 l~v~~~~~g~~~~l~v~~~~TV~~lK~~I~~~~gip~~~q~Li~~Gk~L~D~~ 53 (71)
T cd01796 1 ITVYTARSETTFSLDVDPDLELENFKALCEAESGIPASQQQLIYNGRELVDNK 53 (71)
T ss_pred CEEEECCCCCEEEEEECCcCCHHHHHHHHHHHhCCCHHHeEEEECCeEccCCc
Confidence 467777466889999999999999999999999998753 5556676653
No 84
>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=74.71 E-value=3.9 Score=39.92 Aligned_cols=33 Identities=27% Similarity=0.553 Sum_probs=29.9
Q ss_pred HHhhcCCcHHHHHHHcCCChhHHHHHHHHcCCC
Q 001809 607 LQQYFSGSLKDAAKSIGVCPTTLKRICRQHGIS 639 (1010)
Q Consensus 607 L~~yF~~pl~eAAk~LGV~~TtLKRiCR~~GI~ 639 (1010)
+..+=++++.|.|+.|||+..||-+..+++||.
T Consensus 66 v~~~pd~tl~Ela~~l~Vs~~ti~~~Lkrlg~t 98 (119)
T PF01710_consen 66 VEENPDATLRELAERLGVSPSTIWRALKRLGIT 98 (119)
T ss_pred HHHCCCcCHHHHHHHcCCCHHHHHHHHHHcCch
Confidence 346679999999999999999999999999984
No 85
>PF00356 LacI: Bacterial regulatory proteins, lacI family; InterPro: IPR000843 Numerous bacterial transcription regulatory proteins bind DNA via a helix-turn-helix (HTH) motif. These proteins are very diverse, but for convenience may be grouped into subfamilies on the basis of sequence similarity. One such family groups together a range of proteins, including ascG, ccpA, cytR, ebgR, fruR, galR, galS, lacI, malI, opnR, purF, rafR, rbtR and scrR [, ]. Within this family, the HTH motif is situated towards the N terminus.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 3KJX_C 1ZAY_A 1VPW_A 2PUA_A 1QQA_A 1PNR_A 1JFT_A 1QP4_A 2PUD_A 1JH9_A ....
Probab=74.63 E-value=4.9 Score=33.65 Aligned_cols=23 Identities=30% Similarity=0.520 Sum_probs=20.9
Q ss_pred cHHHHHHHcCCChhHHHHHHHHc
Q 001809 614 SLKDAAKSIGVCPTTLKRICRQH 636 (1010)
Q Consensus 614 pl~eAAk~LGV~~TtLKRiCR~~ 636 (1010)
+++|+|+.+|||++|+-|+-...
T Consensus 1 Ti~dIA~~agvS~~TVSr~ln~~ 23 (46)
T PF00356_consen 1 TIKDIAREAGVSKSTVSRVLNGP 23 (46)
T ss_dssp CHHHHHHHHTSSHHHHHHHHTTC
T ss_pred CHHHHHHHHCcCHHHHHHHHhCC
Confidence 58999999999999999998765
No 86
>cd01803 Ubiquitin Ubiquitin. Ubiquitin (includes Ubq/RPL40e and Ubq/RPS27a fusions as well as homopolymeric multiubiquitin protein chains)
Probab=73.31 E-value=6.7 Score=34.24 Aligned_cols=70 Identities=14% Similarity=0.244 Sum_probs=50.1
Q ss_pred EEEEEEcCCCeEEEEeCCCcChHHHHHHHHHHcCcccceeeeEeecCCCCeEEEecCCcHHHHHHHHhHhCCCeEEEEEe
Q 001809 903 IIVKATYKEDIIRFKFDPSAGCFQLYEEVARRLKLQNGTFQLKYLDDEEEWVMLVSDSDLQECFDILESLGKRSVRFLVR 982 (1010)
Q Consensus 903 ~~vKaty~~d~iRF~~~~s~g~~~L~~EIakRf~l~~~~f~lKYlDDd~EWVlLtcDaDL~EC~di~~~~~~~~vkl~V~ 982 (1010)
+.||... +.++.+.+.+++-+.+|++.|+++.++......|.|-.. .|..|..|.+| .-....+|.|.++
T Consensus 3 i~v~~~~-g~~~~~~v~~~~tV~~lK~~i~~~~g~~~~~q~L~~~g~-----~L~d~~~L~~~----~i~~~~~i~l~~~ 72 (76)
T cd01803 3 IFVKTLT-GKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGK-----QLEDGRTLSDY----NIQKESTLHLVLR 72 (76)
T ss_pred EEEEcCC-CCEEEEEECCcCcHHHHHHHHHHHhCCCHHHeEEEECCE-----ECCCCCcHHHc----CCCCCCEEEEEEE
Confidence 4555443 467889999999999999999999999888788877321 24445555553 3344567777776
No 87
>COG1342 Predicted DNA-binding proteins [General function prediction only]
Probab=73.01 E-value=3.5 Score=39.82 Aligned_cols=35 Identities=20% Similarity=0.307 Sum_probs=29.2
Q ss_pred cccccCHHHHH-----hhcCCcHHHHHHHcCCChhHHHHH
Q 001809 598 AEKNVSLSVLQ-----QYFSGSLKDAAKSIGVCPTTLKRI 632 (1010)
Q Consensus 598 ~~~~itl~~L~-----~yF~~pl~eAAk~LGV~~TtLKRi 632 (1010)
..-.||+++|. .|-++.++|||..+|||..||-|.
T Consensus 30 ~~V~lt~eElEAlRLvD~~~l~QeeAA~rMgISr~Tfwr~ 69 (99)
T COG1342 30 EPVILTIEELEALRLVDYEGLTQEEAALRMGISRQTFWRL 69 (99)
T ss_pred cceeecHHHHHHHHHHhHhhccHHHHHHHhcccHHHHHHH
Confidence 34567777654 899999999999999999999765
No 88
>cd01808 hPLIC_N Ubiquitin-like domain of hPLIC-1 and hPLIC2. hPLIC-1 and hPLIC-2 (human homologs of the yeast ubiquitin-like Dsk2 protein) are type2 UBL's (ubiquitin-like) proteins that are thought to serve as adaptors that link the ubiquitination machinery to the proteasome. The hPLIC's have an N-terminal UBL domain that binds the S5a subunit of the proteasome and a C-terminal UBA (ubiquitin-associated) domain that binds a ubiquitylated protein.
Probab=72.85 E-value=16 Score=32.14 Aligned_cols=42 Identities=17% Similarity=0.281 Sum_probs=33.6
Q ss_pred EEEEEEcCCCeEEEEeCCCcChHHHHHHHHHHcCcccceeeeEe
Q 001809 903 IIVKATYKEDIIRFKFDPSAGCFQLYEEVARRLKLQNGTFQLKY 946 (1010)
Q Consensus 903 ~~vKaty~~d~iRF~~~~s~g~~~L~~EIakRf~l~~~~f~lKY 946 (1010)
++||...+ . .-+.+.+++-+.+|++.|++++++....+.|-|
T Consensus 3 i~vk~~~g-~-~~l~v~~~~TV~~lK~~I~~~~~i~~~~~~Li~ 44 (71)
T cd01808 3 VTVKTPKD-K-EEIEIAEDASVKDFKEAVSKKFKANQEQLVLIF 44 (71)
T ss_pred EEEEcCCC-C-EEEEECCCChHHHHHHHHHHHhCCCHHHEEEEE
Confidence 67774433 3 478899999999999999999998777666666
No 89
>cd01792 ISG15_repeat1 ISG15 ubiquitin-like protein, first repeat of 2. ISG15 is a ubiquitin-like protein containing two ubiquitin homology domains that becomes conjugated to a variety of proteins when cells are treated with type I interferon or lipopolysaccharide. Although ISG15 has properties similar to those of other ubiquitin-like molecules, it is a unique member of the ubiquitin-like superfamily, whose expression and conjugation to target proteins are tightly regulated by specific signaling pathways, indicating it may have specialized functions in the immune system.
Probab=72.81 E-value=8.2 Score=34.98 Aligned_cols=75 Identities=17% Similarity=0.144 Sum_probs=49.7
Q ss_pred eEEEEEEcCCCeEEEEeCCCcChHHHHHHHHHHcCcccceeeeEeecCCCCeEEEecCCcHHHHHHHHhHhCCCeEEEEE
Q 001809 902 KIIVKATYKEDIIRFKFDPSAGCFQLYEEVARRLKLQNGTFQLKYLDDEEEWVMLVSDSDLQECFDILESLGKRSVRFLV 981 (1010)
Q Consensus 902 ~~~vKaty~~d~iRF~~~~s~g~~~L~~EIakRf~l~~~~f~lKYlDDd~EWVlLtcDaDL~EC~di~~~~~~~~vkl~V 981 (1010)
.++||...| .++-+.+.++.-+.+|+++|++++++....+.|.|.. .+. .|.-|.-|.+ +......+|.|.+
T Consensus 4 ~i~Vk~~~G-~~~~~~v~~~~TV~~lK~~I~~~~~i~~~~qrL~~~~-~G~--~L~D~~tL~~----~gi~~gs~l~l~~ 75 (80)
T cd01792 4 DLKVKMLGG-NEFLVSLRDSMTVSELKQQIAQKIGVPAFQQRLAHLD-SRE--VLQDGVPLVS----QGLGPGSTVLLVV 75 (80)
T ss_pred EEEEEeCCC-CEEEEEcCCCCcHHHHHHHHHHHhCCCHHHEEEEecc-CCC--CCCCCCCHHH----cCCCCCCEEEEEE
Confidence 477777555 6677889999999999999999999988777774322 222 2222222333 3334567788877
Q ss_pred eec
Q 001809 982 RDI 984 (1010)
Q Consensus 982 ~d~ 984 (1010)
+..
T Consensus 76 ~~~ 78 (80)
T cd01792 76 QNC 78 (80)
T ss_pred Ecc
Confidence 643
No 90
>PF13443 HTH_26: Cro/C1-type HTH DNA-binding domain; PDB: 3TYR_A 3TYS_A 3B7H_A.
Probab=72.66 E-value=5.4 Score=33.89 Aligned_cols=45 Identities=24% Similarity=0.217 Sum_probs=27.6
Q ss_pred HHHHhhcCCcHHHHHHHcCCChhHHHHHHHHcCCCCCcchhhhhhH
Q 001809 605 SVLQQYFSGSLKDAAKSIGVCPTTLKRICRQHGISRWPSRKINKVN 650 (1010)
Q Consensus 605 ~~L~~yF~~pl~eAAk~LGV~~TtLKRiCR~~GI~RWP~Rki~sl~ 650 (1010)
.++-+--++++.+.|+..||+.+||.|+++.- +.+|+.-.+.++=
T Consensus 3 ~~~m~~~~it~~~La~~~gis~~tl~~~~~~~-~~~~~~~~l~~ia 47 (63)
T PF13443_consen 3 KELMAERGITQKDLARKTGISRSTLSRILNGK-PSNPSLDTLEKIA 47 (63)
T ss_dssp HHHHHHTT--HHHHHHHHT--HHHHHHHHTTT------HHHHHHHH
T ss_pred HHHHHHcCCCHHHHHHHHCcCHHHHHHHHhcc-cccccHHHHHHHH
Confidence 44555567899999999999999999999843 4577776665553
No 91
>PRK12515 RNA polymerase sigma factor; Provisional
Probab=72.23 E-value=4.6 Score=41.27 Aligned_cols=28 Identities=21% Similarity=0.326 Sum_probs=23.6
Q ss_pred HHHhhcCCcHHHHHHHcCCChhHHHHHH
Q 001809 606 VLQQYFSGSLKDAAKSIGVCPTTLKRIC 633 (1010)
Q Consensus 606 ~L~~yF~~pl~eAAk~LGV~~TtLKRiC 633 (1010)
.|+-+.+++.+|+|+.|||++.|+|.+-
T Consensus 141 ~l~~~~~~s~~eIA~~lgis~~tV~~~l 168 (189)
T PRK12515 141 DLVYYHEKSVEEVGEIVGIPESTVKTRM 168 (189)
T ss_pred HHHHHcCCCHHHHHHHHCcCHHHHHHHH
Confidence 4556679999999999999999997653
No 92
>PRK13182 racA polar chromosome segregation protein; Reviewed
Probab=71.74 E-value=3.5 Score=43.38 Aligned_cols=27 Identities=30% Similarity=0.401 Sum_probs=25.1
Q ss_pred CcHHHHHHHcCCChhHHHHHHHHcCCC
Q 001809 613 GSLKDAAKSIGVCPTTLKRICRQHGIS 639 (1010)
Q Consensus 613 ~pl~eAAk~LGV~~TtLKRiCR~~GI~ 639 (1010)
|.+.++|+.+||++.||.|..++.||+
T Consensus 1 mti~evA~~lGVS~~TLRrw~k~g~L~ 27 (175)
T PRK13182 1 MKTPFVAKKLGVSPKTVQRWVKQLNLP 27 (175)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHcCCCC
Confidence 478999999999999999999999985
No 93
>COG1476 Predicted transcriptional regulators [Transcription]
Probab=71.46 E-value=4.9 Score=36.58 Aligned_cols=31 Identities=26% Similarity=0.297 Sum_probs=27.5
Q ss_pred HHHHHhhcCCcHHHHHHHcCCChhHHHHHHH
Q 001809 604 LSVLQQYFSGSLKDAAKSIGVCPTTLKRICR 634 (1010)
Q Consensus 604 l~~L~~yF~~pl~eAAk~LGV~~TtLKRiCR 634 (1010)
+.++|..+++++.|.|+.+||++.|+-.|=+
T Consensus 6 ~k~~R~~~~ltQ~elA~~vgVsRQTi~~iEk 36 (68)
T COG1476 6 LKELRAELGLTQEELAKLVGVSRQTIIAIEK 36 (68)
T ss_pred HHHHHHHhCcCHHHHHHHcCcCHHHHHHHHc
Confidence 6789999999999999999999999876543
No 94
>smart00422 HTH_MERR helix_turn_helix, mercury resistance.
Probab=71.26 E-value=7.6 Score=33.43 Aligned_cols=26 Identities=27% Similarity=0.211 Sum_probs=21.8
Q ss_pred CcHHHHHHHcCCChhHHHHHHHHcCC
Q 001809 613 GSLKDAAKSIGVCPTTLKRICRQHGI 638 (1010)
Q Consensus 613 ~pl~eAAk~LGV~~TtLKRiCR~~GI 638 (1010)
++++|+|+.+||++.||++..++--|
T Consensus 1 ~s~~eva~~~gvs~~tlr~~~~~gli 26 (70)
T smart00422 1 YTIGEVAKLAGVSVRTLRYYERIGLL 26 (70)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHCCCC
Confidence 47899999999999999998874433
No 95
>PF13518 HTH_28: Helix-turn-helix domain
Probab=70.98 E-value=4.3 Score=32.98 Aligned_cols=25 Identities=20% Similarity=0.413 Sum_probs=22.3
Q ss_pred CCcHHHHHHHcCCChhHHHHHHHHc
Q 001809 612 SGSLKDAAKSIGVCPTTLKRICRQH 636 (1010)
Q Consensus 612 ~~pl~eAAk~LGV~~TtLKRiCR~~ 636 (1010)
+.++.++|+.+||+.+||.+..+++
T Consensus 12 g~s~~~~a~~~gis~~tv~~w~~~y 36 (52)
T PF13518_consen 12 GESVREIAREFGISRSTVYRWIKRY 36 (52)
T ss_pred CCCHHHHHHHHCCCHhHHHHHHHHH
Confidence 4599999999999999999998765
No 96
>KOG3606 consensus Cell polarity protein PAR6 [Signal transduction mechanisms]
Probab=70.62 E-value=6.3 Score=44.30 Aligned_cols=81 Identities=19% Similarity=0.331 Sum_probs=68.3
Q ss_pred CCeEEEEEEcCCCeEEEEeCCCc--ChHHHHHHHHHHcCcccceeeeEeecCCCCeEEEecCCcHHHHHHHHhHhCCCeE
Q 001809 900 GSKIIVKATYKEDIIRFKFDPSA--GCFQLYEEVARRLKLQNGTFQLKYLDDEEEWVMLVSDSDLQECFDILESLGKRSV 977 (1010)
Q Consensus 900 ~~~~~vKaty~~d~iRF~~~~s~--g~~~L~~EIakRf~l~~~~f~lKYlDDd~EWVlLtcDaDL~EC~di~~~~~~~~v 977 (1010)
.+++-||-+|+.+--||.|+.+. +|.+++.=|-+--+|.+--|-|-|-|--++-.=|++|..|.-++.-++ --+
T Consensus 16 ~~~veVKSKFdaEfRRfsl~r~~~~~f~~F~~Lv~~~H~i~nvdvllgY~d~hgDLLPinNDDn~~ka~~sa~----PlL 91 (358)
T KOG3606|consen 16 SSTVEVKSKFDAEFRRFSLPRHSASSFDEFYSLVEHLHHIPNVDVLLGYADTHGDLLPINNDDNLHKALSSAR----PLL 91 (358)
T ss_pred cceEEeeccccchhheecccccCcccHHHHHHHHHHHhcCCCceEEEEEecCCCceecccCchhHHHHhhccC----chh
Confidence 45899999999999999995432 888888888888899988999999999999999999999988776544 567
Q ss_pred EEEEeec
Q 001809 978 RFLVRDI 984 (1010)
Q Consensus 978 kl~V~d~ 984 (1010)
||+|+.-
T Consensus 92 R~~iQkr 98 (358)
T KOG3606|consen 92 RLLIQKR 98 (358)
T ss_pred hhhhhhh
Confidence 7777653
No 97
>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=70.52 E-value=24 Score=38.04 Aligned_cols=45 Identities=18% Similarity=0.206 Sum_probs=29.0
Q ss_pred cCCceEEEEeeecCCCCceEEEEEEeeecccCCchHHHHHHHHHhhh
Q 001809 270 HAVRSCIALPVFQFPEISCSAVLEIVSVKEKPNFDAEIENICNALQA 316 (1010)
Q Consensus 270 ~~VrGsLAlPVf~~~s~~ClAVlElV~t~ek~~f~~E~e~vc~ALqa 316 (1010)
-|+ .+||+|||++... ++|.|-+.......+.....+.+..+|.+
T Consensus 195 ~g~-~~vA~Pv~~~~g~-~~aalsv~~p~~r~~~~~~~~~~~~~l~~ 239 (248)
T TIGR02431 195 LGL-RSIAVPIRNARGQ-VVAALNVSTHAARTTPEELVERILPLLLE 239 (248)
T ss_pred cCC-eEEEEEEECCCCC-EEEEEEEeeecccCCHHHHHHHHHHHHHH
Confidence 344 7899999997654 48888887666554433334555555543
No 98
>KOG0251 consensus Clathrin assembly protein AP180 and related proteins, contain ENTH domain [Signal transduction mechanisms; Intracellular trafficking, secretion, and vesicular transport]
Probab=70.41 E-value=5.3 Score=48.13 Aligned_cols=65 Identities=22% Similarity=0.443 Sum_probs=53.1
Q ss_pred HHHHhhcCCcHHHHHHHcCCChhHHH---------HHHHHcCCCCC-cchhhhhh-HHHHHHHHHHHhhcccccCc
Q 001809 605 SVLQQYFSGSLKDAAKSIGVCPTTLK---------RICRQHGISRW-PSRKINKV-NRSLKKIQTVLNSVQGVEGG 669 (1010)
Q Consensus 605 ~~L~~yF~~pl~eAAk~LGV~~TtLK---------RiCR~~GI~RW-P~Rki~sl-~~~i~~l~~~i~s~qg~e~~ 669 (1010)
..|.+||+|...+|.+.|.+-.+.++ ++||..||.|| .|=.|+++ .+.|+.|++.|..+.+....
T Consensus 222 ~Llekffem~~~~a~~al~iykr~~~q~e~L~~f~~~ck~~g~~r~~~iP~l~~i~~s~l~~lEe~l~~~~~~~~~ 297 (491)
T KOG0251|consen 222 NLLEKFFEMSKHDAIKALDIYKRFLSQTEKLSEFLKVCKSVGVDRGFEIPVLKRIPISLLEALEEHLRDVEGGKAK 297 (491)
T ss_pred HHHHHHhhcchHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcccccccCcchhhcCHHHHHHHHHHHhhccccccc
Confidence 35668999999999999999988877 68999999999 78777764 45577888888877665544
No 99
>PF00165 HTH_AraC: Bacterial regulatory helix-turn-helix proteins, AraC family; PDB: 1WPK_A 1ZGW_A 1U8B_A.
Probab=70.36 E-value=4.6 Score=32.18 Aligned_cols=28 Identities=25% Similarity=0.564 Sum_probs=22.2
Q ss_pred CCcHHHHHHHcCCChhHHHHHHHHc-CCC
Q 001809 612 SGSLKDAAKSIGVCPTTLKRICRQH-GIS 639 (1010)
Q Consensus 612 ~~pl~eAAk~LGV~~TtLKRiCR~~-GI~ 639 (1010)
.++++|+|..+|+++..|+|+.|+. |+.
T Consensus 8 ~~~l~~iA~~~g~S~~~f~r~Fk~~~g~t 36 (42)
T PF00165_consen 8 KLTLEDIAEQAGFSPSYFSRLFKKETGMT 36 (42)
T ss_dssp S--HHHHHHHHTS-HHHHHHHHHHHTSS-
T ss_pred CCCHHHHHHHHCCCHHHHHHHHHHHHCcC
Confidence 4789999999999999999999988 763
No 100
>smart00497 IENR1 Intron encoded nuclease repeat motif. Repeat of unknown function, but possibly DNA-binding via helix-turn-helix motif (Ponting, unpublished).
Probab=70.31 E-value=4.2 Score=33.46 Aligned_cols=25 Identities=24% Similarity=0.526 Sum_probs=22.2
Q ss_pred hcCCcHHHHHHHcCCChhHHHHHHHH
Q 001809 610 YFSGSLKDAAKSIGVCPTTLKRICRQ 635 (1010)
Q Consensus 610 yF~~pl~eAAk~LGV~~TtLKRiCR~ 635 (1010)
.| -++.||||.||++.+++.+.|+.
T Consensus 16 ~f-~S~~eAa~~lg~~~~~I~~~~~~ 40 (53)
T smart00497 16 EF-SSIREAAKYLGISHSSISKYLNT 40 (53)
T ss_pred Ee-cCHHHHHHHhCCCHHHHHHHHhC
Confidence 44 38999999999999999999985
No 101
>TIGR02531 yecD_yerC TrpR-related protein YerC/YecD. This model represents a protein subfamily found mostly in the Firmicutes (Bacillus and allies). This family is similar in sequence to the trp operon repressor TrpR described by TIGR01321, and represents a distinct clade within the broader family described by pfam01371. At least one species, Xylella fastidiosa, in the Proteobacteria, has a member of both this family and TIGR01321. Several genomes with a member of this family do not synthesize tryptophan, and members of this family should not be considered trp operon repressors without new evidence.
Probab=70.29 E-value=3.9 Score=38.62 Aligned_cols=24 Identities=21% Similarity=0.338 Sum_probs=21.8
Q ss_pred CCcHHHHHHHcCCChhHHHHHHHH
Q 001809 612 SGSLKDAAKSIGVCPTTLKRICRQ 635 (1010)
Q Consensus 612 ~~pl~eAAk~LGV~~TtLKRiCR~ 635 (1010)
+.+.+++|+.|||+.+|++|++|=
T Consensus 50 G~S~~eIA~~LgISrsTIyRi~R~ 73 (88)
T TIGR02531 50 GKTYSDIEAETGASTATISRVKRC 73 (88)
T ss_pred CCCHHHHHHHHCcCHHHHHHHHHh
Confidence 469999999999999999999873
No 102
>PF13492 GAF_3: GAF domain; PDB: 3EEA_A 4DMZ_A 4DN0_A 1VHM_A.
Probab=69.99 E-value=58 Score=29.74 Aligned_cols=75 Identities=25% Similarity=0.335 Sum_probs=53.4
Q ss_pred ccccCCCcchhhhhcCCCcccccccccCccccchhhHHHHhCCceeEEEEecccccCCCcEEEEeecCCCCCCcHHHHHH
Q 001809 418 YLEEGQGVAGKALQSNHPFFFPDVKLYDITEFPLVHHARKFGLNAAVAIRLRSTYTGDDDYILEFFLPVTIKGSSEQQLL 497 (1010)
Q Consensus 418 hL~~GQGvaGkAf~sn~P~F~~DV~~fsk~EYPL~HhAr~fgL~aAvAIrLrS~~tG~ddyVLEFFLP~~ck~~~EQq~l 497 (1010)
.|..+.++.++++.++.|...+|+..... .+.+..+++||+.. +..-.||.+.-+..-.=+.++..+
T Consensus 49 ~l~~~~~~~~~~~~~~~~~~~~~~~~~~~-----------~~~~s~~~vPl~~~--~~~~Gvl~~~~~~~~~~~~~d~~~ 115 (129)
T PF13492_consen 49 SLPEDDPLIGRALETGEPVSVPDIDERDF-----------LGIRSLLVVPLRSR--DRVIGVLCLDSREPEEFSDEDLQL 115 (129)
T ss_dssp CEETTSHHHHHHHHHTS-EEESTCCC-TT-----------TTTCEEEEEEEEET--TEEEEEEEEEECTTCG-SHHHHHH
T ss_pred cCCCCccHHHHHHhhCCeEEecccccccC-----------CCCCEEEEEEEeEC--CEEEEEEEEEECCCCCCCHHHHHH
Confidence 77799999999999999988888655322 66789999999885 245566777666544455677777
Q ss_pred HHHHHHHH
Q 001809 498 LNNLSGTM 505 (1010)
Q Consensus 498 l~sLs~Tm 505 (1010)
|..+...+
T Consensus 116 l~~~a~~~ 123 (129)
T PF13492_consen 116 LESLANQL 123 (129)
T ss_dssp HHHHHHHH
T ss_pred HHHHHHHH
Confidence 77766554
No 103
>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=69.79 E-value=6.8 Score=32.10 Aligned_cols=33 Identities=27% Similarity=0.372 Sum_probs=25.2
Q ss_pred HHHHHhhcCCcHHHHHHHcCCChhHHHHHHHHc
Q 001809 604 LSVLQQYFSGSLKDAAKSIGVCPTTLKRICRQH 636 (1010)
Q Consensus 604 l~~L~~yF~~pl~eAAk~LGV~~TtLKRiCR~~ 636 (1010)
+..|+.-=-.|..+.|+.+||+.+++.++-+++
T Consensus 9 l~~Lq~d~r~s~~~la~~lglS~~~v~~Ri~rL 41 (42)
T PF13404_consen 9 LRLLQEDGRRSYAELAEELGLSESTVRRRIRRL 41 (42)
T ss_dssp HHHHHH-TTS-HHHHHHHHTS-HHHHHHHHHHH
T ss_pred HHHHHHcCCccHHHHHHHHCcCHHHHHHHHHHh
Confidence 456677777899999999999999999887764
No 104
>KOG0010 consensus Ubiquitin-like protein [Posttranslational modification, protein turnover, chaperones; General function prediction only]
Probab=69.35 E-value=6.5 Score=47.14 Aligned_cols=74 Identities=19% Similarity=0.262 Sum_probs=54.7
Q ss_pred eEEEEEEcCCCeEEEEeCCCcChHHHHHHHHHHcCcccceeeeEeecCCCCeEEEecCCcHHHHHHHHhHhCCCeEEEEE
Q 001809 902 KIIVKATYKEDIIRFKFDPSAGCFQLYEEVARRLKLQNGTFQLKYLDDEEEWVMLVSDSDLQECFDILESLGKRSVRFLV 981 (1010)
Q Consensus 902 ~~~vKaty~~d~iRF~~~~s~g~~~L~~EIakRf~l~~~~f~lKYlDDd~EWVlLtcDaDL~EC~di~~~~~~~~vkl~V 981 (1010)
.++|-+++.+||.-|.+.....+.+|||+|++||+....-..|=|..- +|- |.| -+.-|.-...+||-|..
T Consensus 15 ~irV~Vkt~~dk~~~~V~~~ssV~qlKE~I~~~f~a~~dqlvLIfaGr-----ILK-D~d---TL~~~gI~Dg~TvHLVi 85 (493)
T KOG0010|consen 15 LIRVTVKTPKDKYEVNVASDSSVLQLKELIAQRFGAPPDQLVLIYAGR-----ILK-DDD---TLKQYGIQDGHTVHLVI 85 (493)
T ss_pred eeEEEEecCCcceeEecccchHHHHHHHHHHHhcCCChhHeeeeecCc-----ccc-Chh---hHHHcCCCCCcEEEEEe
Confidence 588888899999999999999999999999999998877665555431 111 222 24455556678888876
Q ss_pred eec
Q 001809 982 RDI 984 (1010)
Q Consensus 982 ~d~ 984 (1010)
--.
T Consensus 86 k~~ 88 (493)
T KOG0010|consen 86 KSQ 88 (493)
T ss_pred ccC
Confidence 554
No 105
>PRK11061 fused phosphoenolpyruvate-protein phosphotransferase PtsP/GAF domain; Provisional
Probab=69.33 E-value=9.3 Score=48.25 Aligned_cols=86 Identities=12% Similarity=0.077 Sum_probs=60.5
Q ss_pred hcccccCCCcchhhhhcCCCcccccccccCccccchhhHHHHhCCceeEEEEecccccCCCcEEEEeecCCCCCCcHHHH
Q 001809 416 EHYLEEGQGVAGKALQSNHPFFFPDVKLYDITEFPLVHHARKFGLNAAVAIRLRSTYTGDDDYILEFFLPVTIKGSSEQQ 495 (1010)
Q Consensus 416 EhhL~~GQGvaGkAf~sn~P~F~~DV~~fsk~EYPL~HhAr~fgL~aAvAIrLrS~~tG~ddyVLEFFLP~~ck~~~EQq 495 (1010)
..++..|+|++|+|+.++.|...+|+..-.. |...-.+..+++++.+++||+. .|..--||-++-...-.=+++..
T Consensus 65 ~~~l~~geGi~G~Va~tg~pV~V~Dv~~dpr--f~~~~~~~~~~~~S~L~VPL~~--~geVIGVL~v~~~~~~~Fs~~d~ 140 (748)
T PRK11061 65 TVTLAFDEGIVGLVGRLAEPINLADAQKHPS--FKYIPSVKEERFRAFLGVPIIY--RRQLLGVLVVQQRELRQFDESEE 140 (748)
T ss_pred ceeccCCcchHHHHhccCceEEECCcccCcc--cccCccccCccceEEEEEEEee--CCEEEEEEEEeeCCCCCCCHHHH
Confidence 3567789999999999999999999987332 2111122357899999999984 36566688887775544455555
Q ss_pred HHHHHHHHHH
Q 001809 496 LLLNNLSGTM 505 (1010)
Q Consensus 496 ~ll~sLs~Tm 505 (1010)
.+|..|...+
T Consensus 141 ~lL~~LA~~a 150 (748)
T PRK11061 141 SFLVTLATQL 150 (748)
T ss_pred HHHHHHHHHH
Confidence 6555555444
No 106
>cd01805 RAD23_N Ubiquitin-like domain of RAD23. RAD23 belongs to a family of adaptor molecules having affinity for both the proteasome and ubiquitinylated proteins and thought to shuttle these ubiquitinylated proteins to the proteasome for destruction. RAD23 interacts with ubiquitin through its C-terminal ubiquitin-associated domains (UBA) and with the proteasome through its N-terminal ubiquitin-like domain (UBL).
Probab=69.25 E-value=36 Score=30.06 Aligned_cols=71 Identities=21% Similarity=0.251 Sum_probs=49.6
Q ss_pred EEEEEEcCCCeEEEEeCCCcChHHHHHHHHHHcCc--ccceeeeEeecCCCCeEEEecCCcHHHHHHHHhHhCCCeEEEE
Q 001809 903 IIVKATYKEDIIRFKFDPSAGCFQLYEEVARRLKL--QNGTFQLKYLDDEEEWVMLVSDSDLQECFDILESLGKRSVRFL 980 (1010)
Q Consensus 903 ~~vKaty~~d~iRF~~~~s~g~~~L~~EIakRf~l--~~~~f~lKYlDDd~EWVlLtcDaDL~EC~di~~~~~~~~vkl~ 980 (1010)
++||..- ++++-|.+.++..+.+|++.|+.+.++ ......|-|- |. .|.-|..|.+| .-....+|-+.
T Consensus 3 i~vk~~~-g~~~~l~v~~~~TV~~lK~~i~~~~~i~~~~~~q~L~~~---G~--~L~d~~~L~~~----~i~~~~~i~~~ 72 (77)
T cd01805 3 ITFKTLK-QQTFPIEVDPDDTVAELKEKIEEEKGCDYPPEQQKLIYS---GK--ILKDDTTLEEY----KIDEKDFVVVM 72 (77)
T ss_pred EEEEeCC-CCEEEEEECCCCcHHHHHHHHHHhhCCCCChhHeEEEEC---CE--EccCCCCHHHc----CCCCCCEEEEE
Confidence 5676644 478889999999999999999999998 6666666662 22 33445556664 33345677777
Q ss_pred Eee
Q 001809 981 VRD 983 (1010)
Q Consensus 981 V~d 983 (1010)
|+.
T Consensus 73 ~~~ 75 (77)
T cd01805 73 VSK 75 (77)
T ss_pred Eec
Confidence 664
No 107
>cd01769 UBL Ubiquitin-like domain of UBL. UBLs function by remodeling the surface of their target proteins, changing their target's half-life, enzymatic activity, protein-protein interactions, subcellular localization or other properties. At least 10 different ubiquitin-like modifications exist in mammals, and attachment of different ubls to a target leads to different biological consequences. Ubl-conjugation cascades are initiated by activating enzymes, which also coordinate the ubls with their downstream pathways.
Probab=69.20 E-value=9 Score=32.28 Aligned_cols=37 Identities=14% Similarity=0.223 Sum_probs=32.0
Q ss_pred CCeEEEEeCCCcChHHHHHHHHHHcCcccceeeeEee
Q 001809 911 EDIIRFKFDPSAGCFQLYEEVARRLKLQNGTFQLKYL 947 (1010)
Q Consensus 911 ~d~iRF~~~~s~g~~~L~~EIakRf~l~~~~f~lKYl 947 (1010)
+..+.|++.+++-+.+|++.|+++++++.....|.|-
T Consensus 7 ~~~~~~~~~~~~ti~~lK~~i~~~~~~~~~~~~l~~~ 43 (69)
T cd01769 7 GKTFELEVSPDDTVAELKAKIAAKEGVPPEQQRLIYA 43 (69)
T ss_pred CCEEEEEECCCChHHHHHHHHHHHHCcChHHEEEEEC
Confidence 4677889999999999999999999998877777663
No 108
>smart00421 HTH_LUXR helix_turn_helix, Lux Regulon. lux regulon (activates the bioluminescence operon
Probab=69.16 E-value=4.7 Score=32.38 Aligned_cols=25 Identities=20% Similarity=0.207 Sum_probs=21.4
Q ss_pred cCCcHHHHHHHcCCChhHHHHHHHH
Q 001809 611 FSGSLKDAAKSIGVCPTTLKRICRQ 635 (1010)
Q Consensus 611 F~~pl~eAAk~LGV~~TtLKRiCR~ 635 (1010)
-+++.+++|+.|||+..|+++.-++
T Consensus 17 ~g~s~~eia~~l~is~~tv~~~~~~ 41 (58)
T smart00421 17 EGLTNKEIAERLGISEKTVKTHLSN 41 (58)
T ss_pred cCCCHHHHHHHHCCCHHHHHHHHHH
Confidence 3789999999999999999877553
No 109
>PF13411 MerR_1: MerR HTH family regulatory protein; PDB: 2JML_A 3GP4_A 3GPV_B.
Probab=68.95 E-value=4.6 Score=34.83 Aligned_cols=26 Identities=35% Similarity=0.499 Sum_probs=23.2
Q ss_pred CcHHHHHHHcCCChhHHHHHHHHcCC
Q 001809 613 GSLKDAAKSIGVCPTTLKRICRQHGI 638 (1010)
Q Consensus 613 ~pl~eAAk~LGV~~TtLKRiCR~~GI 638 (1010)
++++|+|+.+||++.||+...++.-|
T Consensus 1 yti~eva~~~gvs~~tlr~y~~~gll 26 (69)
T PF13411_consen 1 YTIKEVAKLLGVSPSTLRYYEREGLL 26 (69)
T ss_dssp EEHHHHHHHTTTTHHHHHHHHHTTSS
T ss_pred CcHHHHHHHHCcCHHHHHHHHHhcCc
Confidence 47899999999999999999987664
No 110
>PF07453 NUMOD1: NUMOD1 domain; InterPro: IPR010896 This helix-turn-helix-containing DNA-binding domain is found associated in homing nucleases [].
Probab=68.37 E-value=3.6 Score=32.21 Aligned_cols=21 Identities=24% Similarity=0.556 Sum_probs=18.7
Q ss_pred CcHHHHHHHcCCChhHHHHHH
Q 001809 613 GSLKDAAKSIGVCPTTLKRIC 633 (1010)
Q Consensus 613 ~pl~eAAk~LGV~~TtLKRiC 633 (1010)
-++.|||+.||++.+++.+.|
T Consensus 17 ~Si~eAa~~l~i~~~~I~~~l 37 (37)
T PF07453_consen 17 DSIREAARYLGISHSTISKYL 37 (37)
T ss_pred cCHHHHHHHhCCCHHHHHHhC
Confidence 478999999999999998864
No 111
>cd01799 Hoil1_N Ubiquitin-like domain of HOIL1. HOIL1_N HOIL-1 (heme-oxidized IRP2 ubiquitin ligase-1) is an E3 ubiquitin-protein ligase that recognizes heme-oxidized IRP2 (iron regulatory protein2) and is thought to affect the turnover of oxidatively damaged proteins. Hoil-1 has an amino-terminal ubiquitin-like domain as well as an RBR signature consisting of two RING finger domains separated by an IBR/DRIL domain.
Probab=67.96 E-value=10 Score=34.49 Aligned_cols=44 Identities=11% Similarity=0.074 Sum_probs=37.1
Q ss_pred EEEEcCCCeEEEEeCCCcChHHHHHHHHHHcCcccceeeeEeecCC
Q 001809 905 VKATYKEDIIRFKFDPSAGCFQLYEEVARRLKLQNGTFQLKYLDDE 950 (1010)
Q Consensus 905 vKaty~~d~iRF~~~~s~g~~~L~~EIakRf~l~~~~f~lKYlDDd 950 (1010)
=|.+++ .++.+.+.|++-+.+|++-|..++|+......| |-...
T Consensus 7 ~~~~~~-~t~~l~v~~~~TV~~lK~kI~~~~gip~~~QrL-~~G~~ 50 (75)
T cd01799 7 DAQSHT-VTIWLTVRPDMTVAQLKDKVFLDYGFPPAVQRW-VIGQR 50 (75)
T ss_pred ccccCC-CeEEEEECCCCcHHHHHHHHHHHHCcCHHHEEE-EcCCe
Confidence 366766 778899999999999999999999999888888 75433
No 112
>cd01813 UBP_N UBP ubiquitin processing protease. The UBP (ubiquitin processing protease) domain (also referred to as USP which stands for "ubiquitin-specific protease") is present at in a large family of cysteine proteases that specifically cleave ubiquitin conjugates. This family includes Rpn11, UBP6 (USP14), USP7 (HAUSP). This domain is closely related to the amino-terminal ubiquitin-like domain of BAG1 (Bcl2-associated anthanogene1) protein and is found only in eukaryotes.
Probab=67.70 E-value=12 Score=33.86 Aligned_cols=44 Identities=7% Similarity=-0.071 Sum_probs=38.1
Q ss_pred EEEEEEcCCCeEEEEeCCCcChHHHHHHHHHHcCcccceeeeEe
Q 001809 903 IIVKATYKEDIIRFKFDPSAGCFQLYEEVARRLKLQNGTFQLKY 946 (1010)
Q Consensus 903 ~~vKaty~~d~iRF~~~~s~g~~~L~~EIakRf~l~~~~f~lKY 946 (1010)
++|.+.++..++-+.+.++..+.+|++.|+.+.++....--|=|
T Consensus 1 ~~i~vk~~g~~~~v~v~~~~Tv~~lK~~i~~~tgvp~~~QKLi~ 44 (74)
T cd01813 1 VPVIVKWGGQEYSVTTLSEDTVLDLKQFIKTLTGVLPERQKLLG 44 (74)
T ss_pred CEEEEEECCEEEEEEECCCCCHHHHHHHHHHHHCCCHHHEEEEe
Confidence 46777789999999999999999999999999998877666665
No 113
>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=66.70 E-value=8.2 Score=31.43 Aligned_cols=33 Identities=21% Similarity=0.330 Sum_probs=26.1
Q ss_pred HHHHHhhcCCcHHHHHHHcCCChhHHHHHHHHc
Q 001809 604 LSVLQQYFSGSLKDAAKSIGVCPTTLKRICRQH 636 (1010)
Q Consensus 604 l~~L~~yF~~pl~eAAk~LGV~~TtLKRiCR~~ 636 (1010)
|..|...=.++.+|+|+.+|++.+|+.++.+++
T Consensus 9 l~~l~~~~~~t~~ela~~~~is~~tv~~~l~~L 41 (48)
T PF13412_consen 9 LNYLRENPRITQKELAEKLGISRSTVNRYLKKL 41 (48)
T ss_dssp HHHHHHCTTS-HHHHHHHHTS-HHHHHHHHHHH
T ss_pred HHHHHHcCCCCHHHHHHHhCCCHHHHHHHHHHH
Confidence 455666667999999999999999999998875
No 114
>PF13560 HTH_31: Helix-turn-helix domain; PDB: 3F51_C 3F52_A 3PXP_A 2OFY_A.
Probab=66.48 E-value=4.6 Score=34.77 Aligned_cols=34 Identities=29% Similarity=0.306 Sum_probs=26.7
Q ss_pred HHHHHhhcCCcHHHHHHHcCCChhHHHHHHHHcC
Q 001809 604 LSVLQQYFSGSLKDAAKSIGVCPTTLKRICRQHG 637 (1010)
Q Consensus 604 l~~L~~yF~~pl~eAAk~LGV~~TtLKRiCR~~G 637 (1010)
+..++..=++++.++|+.+||+.+++.++.+--.
T Consensus 6 lr~~R~~~gls~~~lA~~~g~s~s~v~~iE~G~~ 39 (64)
T PF13560_consen 6 LRRLRERAGLSQAQLADRLGVSQSTVSRIERGRR 39 (64)
T ss_dssp HHHHHHCHTS-HHHHHHHHTS-HHHHHHHHTTSS
T ss_pred HHHHHHHcCCCHHHHHHHHCcCHHHHHHHHCCCC
Confidence 4456677789999999999999999999987443
No 115
>COG1522 Lrp Transcriptional regulators [Transcription]
Probab=66.29 E-value=7 Score=38.56 Aligned_cols=33 Identities=27% Similarity=0.348 Sum_probs=29.8
Q ss_pred HHHHHhhcCCcHHHHHHHcCCChhHHHHHHHHc
Q 001809 604 LSVLQQYFSGSLKDAAKSIGVCPTTLKRICRQH 636 (1010)
Q Consensus 604 l~~L~~yF~~pl~eAAk~LGV~~TtLKRiCR~~ 636 (1010)
|..|+.-.-.|+++.|++||+|++++.++-+++
T Consensus 14 L~~L~~d~r~~~~eia~~lglS~~~v~~Ri~~L 46 (154)
T COG1522 14 LRLLQEDARISNAELAERVGLSPSTVLRRIKRL 46 (154)
T ss_pred HHHHHHhCCCCHHHHHHHHCCCHHHHHHHHHHH
Confidence 678899999999999999999999998887765
No 116
>cd04774 HTH_YfmP Helix-Turn-Helix DNA binding domain of the YfmP transcription regulator. Helix-turn-helix (HTH) transcription regulator, YfmP, and related proteins; N-terminal domain. YfmP regulates the multidrug efflux protein, YfmO, and indirectly regulates the expression of the Bacillus subtilis copZA operon encoding a metallochaperone, CopZ, and a CPx-type ATPase efflux protein, CopA. These proteins belong to the MerR superfamily of transcription regulators that promote expression of several stress regulon genes by reconfiguring the spacer between the -35 and -10 promoter elements. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules.
Probab=65.88 E-value=5.9 Score=37.48 Aligned_cols=30 Identities=30% Similarity=0.444 Sum_probs=25.4
Q ss_pred CcHHHHHHHcCCChhHHHHHHHHcCCCCCcch
Q 001809 613 GSLKDAAKSIGVCPTTLKRICRQHGISRWPSR 644 (1010)
Q Consensus 613 ~pl~eAAk~LGV~~TtLKRiCR~~GI~RWP~R 644 (1010)
+++.|+|+.+||++.||+...|. |+-. |-|
T Consensus 1 ~~I~e~a~~~gvs~~tLR~ye~~-Gll~-p~r 30 (96)
T cd04774 1 YKVDEVAKRLGLTKRTLKYYEEI-GLVS-PER 30 (96)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHC-CCCC-CCc
Confidence 47899999999999999999985 8765 644
No 117
>cd01807 GDX_N ubiquitin-like domain of GDX. GDX contains an N-terminal ubiquitin-like domain as well as an uncharacterized c-terminal domain. The function of GDX is unknown.
Probab=65.59 E-value=16 Score=32.45 Aligned_cols=66 Identities=18% Similarity=0.209 Sum_probs=46.4
Q ss_pred EEEEEEcCCCeEEEEeCCCcChHHHHHHHHHHcCcccceeee----EeecCCCCeEEEecCCcHHHHHHHHhHhCCCeEE
Q 001809 903 IIVKATYKEDIIRFKFDPSAGCFQLYEEVARRLKLQNGTFQL----KYLDDEEEWVMLVSDSDLQECFDILESLGKRSVR 978 (1010)
Q Consensus 903 ~~vKaty~~d~iRF~~~~s~g~~~L~~EIakRf~l~~~~f~l----KYlDDd~EWVlLtcDaDL~EC~di~~~~~~~~vk 978 (1010)
+.||..- +.++.+.+.++.-+.+|++.|+.+.|+......| |-|+|+ ..|.+| .-....+|.
T Consensus 3 i~vk~~~-G~~~~l~v~~~~tV~~lK~~i~~~~gi~~~~q~L~~~G~~L~d~---------~~L~~~----~i~~~~~l~ 68 (74)
T cd01807 3 LTVKLLQ-GRECSLQVSEKESVSTLKKLVSEHLNVPEEQQRLLFKGKALADD---------KRLSDY----SIGPNAKLN 68 (74)
T ss_pred EEEEeCC-CCEEEEEECCCCcHHHHHHHHHHHHCCCHHHeEEEECCEECCCC---------CCHHHC----CCCCCCEEE
Confidence 5666554 4788899999999999999999999998876555 445443 334333 333456776
Q ss_pred EEEe
Q 001809 979 FLVR 982 (1010)
Q Consensus 979 l~V~ 982 (1010)
|.++
T Consensus 69 l~~~ 72 (74)
T cd01807 69 LVVR 72 (74)
T ss_pred EEEc
Confidence 6665
No 118
>COG3829 RocR Transcriptional regulator containing PAS, AAA-type ATPase, and DNA-binding domains [Transcription / Signal transduction mechanisms]
Probab=65.15 E-value=5.5 Score=48.45 Aligned_cols=43 Identities=30% Similarity=0.424 Sum_probs=33.3
Q ss_pred cccccccCHHHHHhhcCCcHHHHHHHcCCChhHHHHHHHHcCCC
Q 001809 596 STAEKNVSLSVLQQYFSGSLKDAAKSIGVCPTTLKRICRQHGIS 639 (1010)
Q Consensus 596 ~~~~~~itl~~L~~yF~~pl~eAAk~LGV~~TtLKRiCR~~GI~ 639 (1010)
...++.+=.+.|.+| +.....||+.|||+.|||.|.++++||.
T Consensus 518 e~~Ek~~I~~aL~~~-~gn~~~aAk~LgIsrttL~rKlkk~~l~ 560 (560)
T COG3829 518 EEYEKHLIREALERH-GGNKSKAAKELGISRTTLYRKLKKYGLR 560 (560)
T ss_pred HHHHHHHHHHHHHHh-CCCHHHHHHHhCCCHHHHHHHHHHhcCC
Confidence 344555545555554 4578899999999999999999999984
No 119
>PF05225 HTH_psq: helix-turn-helix, Psq domain; InterPro: IPR007889 This DNA-binding motif is found in four copies in the pipsqueak protein of Drosophila melanogaster []. In pipsqueak this domain binds to GAGA sequence []. The pipsqueak family, which includes proteins from fungi, sea urchins, nematodes, insects, and vertebrates appear to be proteins essential for sequence-specific targeting of a polycomb group protein complex [].; GO: 0003677 DNA binding; PDB: 2COB_A.
Probab=64.59 E-value=6.6 Score=32.59 Aligned_cols=23 Identities=43% Similarity=0.483 Sum_probs=17.8
Q ss_pred CcHHHHHHHcCCChhHHHHHHHH
Q 001809 613 GSLKDAAKSIGVCPTTLKRICRQ 635 (1010)
Q Consensus 613 ~pl~eAAk~LGV~~TtLKRiCR~ 635 (1010)
+++.+||+..||..+||.++-+.
T Consensus 17 ~S~r~AA~~ygVp~sTL~~r~~g 39 (45)
T PF05225_consen 17 MSIRKAAKKYGVPRSTLRRRLRG 39 (45)
T ss_dssp S-HHHHHHHHT--HHHHHHHHHH
T ss_pred CCHHHHHHHHCcCHHHHHHHHcC
Confidence 89999999999999999976654
No 120
>PRK15429 formate hydrogenlyase transcriptional activator FhlA; Provisional
Probab=64.40 E-value=39 Score=42.11 Aligned_cols=128 Identities=16% Similarity=0.115 Sum_probs=75.1
Q ss_pred CCCHHHHHHHHHHHHHHhcCCCeeEEEEeeeccCCeeee-eeCCCCcccchhhhHHhhccceeeeccCCCCCCCCCCCcc
Q 001809 162 PPSLDEKMLRALSFFKLSSGGGILAQVWVPRKQGDDYIL-STSDQPYLLDQMLAGYREVSRKFTFSAEAKPGTFLGLPGR 240 (1010)
Q Consensus 162 ~~svkerm~~AL~~~kes~~~~~L~QVWvP~~~g~~~vL-sT~~qP~~ld~~L~~yR~vS~~f~Fs~~~~~~~~~GLPGR 240 (1010)
+.++.+=+...++.+++.++-+ .+=||++..+++...+ .+.+ ++..-. . -....... .-|+-|+
T Consensus 197 ~~dl~ell~~I~~~i~~~~~a~-~~~I~L~d~~~~~L~~~aa~g----~~~~~~---~-~~~~~~~~------~~~l~g~ 261 (686)
T PRK15429 197 RLDMDELVSEVAKEIHYYFDID-AISIVLRSHRKNKLNIYSTHY----LDKQHP---A-HEQSEVDE------AGTLTER 261 (686)
T ss_pred CCCHHHHHHHHHHHHHHHhCCC-EEEEEEEECCCCcEEEEEecc----cChhhc---c-cccccCCc------ccchHHH
Confidence 4467777777788888887754 4556777666554332 2222 111000 0 00011111 1279999
Q ss_pred cccCCCCcccccccccCcccccchhhH-HhcCCceEEEEeeecCCCCceEEEEEEeeecccCCchHHH
Q 001809 241 VFSSKVPEWTSNVAYYNEAEYARVTHA-VNHAVRSCIALPVFQFPEISCSAVLEIVSVKEKPNFDAEI 307 (1010)
Q Consensus 241 VF~s~~PEWTpnV~~y~~~EYpR~~~A-~~~~VrGsLAlPVf~~~s~~ClAVlElV~t~ek~~f~~E~ 307 (1010)
||.++.|.-..++.--.-..|.+.-.. ...+++..++||++..+ ..+|||.+.. .+...|..+-
T Consensus 262 V~~~~~p~lv~~~~~d~~~~~~~~~~~~~~~~~~s~l~vPL~~~~--~v~GvL~l~~-~~~~~F~~~d 326 (686)
T PRK15429 262 VFKSKEMLLINLHERDDLAPYERMLFDTWGNQIQTLCLLPLMSGD--TMLGVLKLAQ-CEEKVFTTTN 326 (686)
T ss_pred HHhcCceEEEECccCcccchhhhhhhhcccccceEEEEEeEEECC--EEEEEEEEee-CCCCcCCHHH
Confidence 999999998866642222223332211 12468899999999765 4699999984 4566777553
No 121
>PF00240 ubiquitin: Ubiquitin family; InterPro: IPR000626 Ubiquitinylation is an ATP-dependent process that involves the action of at least three enzymes: a ubiquitin-activating enzyme (E1, IPR000011 from INTERPRO), a ubiquitin-conjugating enzyme (E2, IPR000608 from INTERPRO), and a ubiquitin ligase (E3, IPR000569 from INTERPRO, IPR003613 from INTERPRO), which work sequentially in a cascade. There are many different E3 ligases, which are responsible for the type of ubiquitin chain formed, the specificity of the target protein, and the regulation of the ubiquitinylation process []. Ubiquitinylation is an important regulatory tool that controls the concentration of key signalling proteins, such as those involved in cell cycle control, as well as removing misfolded, damaged or mutant proteins that could be harmful to the cell. Several ubiquitin-like molecules have been discovered, such as Ufm1 (IPR005375 from INTERPRO), SUMO1 (IPR003653 from INTERPRO), NEDD8, Rad23 (IPR004806 from INTERPRO), Elongin B and Parkin (IPR003977 from INTERPRO), the latter being involved in Parkinson's disease []. Ubiquitin is a protein of 76 amino acid residues, found in all eukaryotic cells and whose sequence is extremely well conserved from protozoan to vertebrates. Ubiquitin acts through its post-translational attachment (ubiquitinylation) to other proteins, where these modifications alter the function, location or trafficking of the protein, or targets it for destruction by the 26S proteasome []. The terminal glycine in the C-terminal 4-residue tail of ubiquitin can form an isopeptide bond with a lysine residue in the target protein, or with a lysine in another ubiquitin molecule to form a ubiquitin chain that attaches itself to a target protein. Ubiquitin has seven lysine residues, any one of which can be used to link ubiquitin molecules together, resulting in different structures that alter the target protein in different ways. It appears that Lys(11)-, Lys(29) and Lys(48)-linked poly-ubiquitin chains target the protein to the proteasome for degradation, while mono-ubiquitinylated and Lys(6)- or Lys(63)-linked poly-ubiquitin chains signal reversible modifications in protein activity, location or trafficking []. For example, Lys(63)-linked poly-ubiquitinylation is known to be involved in DNA damage tolerance, inflammatory response, protein trafficking and signal transduction through kinase activation []. In addition, the length of the ubiquitin chain alters the fate of the target protein. Regulatory proteins such as transcription factors and histones are frequent targets of ubquitinylation [].; GO: 0005515 protein binding; PDB: 2DZI_A 2XEW_E 3NOB_E 2KWU_B 2Y5B_F 3PHD_G 2KWV_B 2KOX_A 2XK5_B 3NHE_B ....
Probab=64.21 E-value=14 Score=31.94 Aligned_cols=39 Identities=15% Similarity=0.245 Sum_probs=34.7
Q ss_pred cCCCeEEEEeCCCcChHHHHHHHHHHcCcccceeeeEee
Q 001809 909 YKEDIIRFKFDPSAGCFQLYEEVARRLKLQNGTFQLKYL 947 (1010)
Q Consensus 909 y~~d~iRF~~~~s~g~~~L~~EIakRf~l~~~~f~lKYl 947 (1010)
..+..+.|.+.+++-+.+|++.|+.++++....+.|-|-
T Consensus 3 ~~g~~~~~~v~~~~tV~~lK~~i~~~~~~~~~~~~L~~~ 41 (69)
T PF00240_consen 3 LSGKTFTLEVDPDDTVADLKQKIAEETGIPPEQQRLIYN 41 (69)
T ss_dssp TTSEEEEEEEETTSBHHHHHHHHHHHHTSTGGGEEEEET
T ss_pred CCCcEEEEEECCCCCHHHhhhhcccccccccccceeeee
Confidence 456788999999999999999999999999988888773
No 122
>PRK11511 DNA-binding transcriptional activator MarA; Provisional
Probab=64.18 E-value=11 Score=37.06 Aligned_cols=35 Identities=20% Similarity=0.309 Sum_probs=29.1
Q ss_pred HHHHhhcC--CcHHHHHHHcCCChhHHHHHHHHc-CCC
Q 001809 605 SVLQQYFS--GSLKDAAKSIGVCPTTLKRICRQH-GIS 639 (1010)
Q Consensus 605 ~~L~~yF~--~pl~eAAk~LGV~~TtLKRiCR~~-GI~ 639 (1010)
+-|..+++ +++.++|+.+||++.+|.|++++. |+.
T Consensus 16 ~~I~~~~~~~~sl~~lA~~~g~S~~~l~r~Fk~~~G~s 53 (127)
T PRK11511 16 DWIEDNLESPLSLEKVSERSGYSKWHLQRMFKKETGHS 53 (127)
T ss_pred HHHHHhcCCCCCHHHHHHHHCcCHHHHHHHHHHHHCcC
Confidence 34555554 799999999999999999999988 873
No 123
>cd06399 PB1_P40 The PB1 domain is essential part of the p40 adaptor protein which plays an important role in activating phagocyte NADPH oxidase during phagocytosis. The PB1 domain is a modular domain mediating specific protein-protein interaction which play a role in many critical cell processes , such as osteoclastogenesis, angiogenesis, early cardiovascular development and cell polarity. A canonical PB1-PB1 interaction, which involves heterodimerization of two PB1 domain, is required for the formation of macromolecular signaling complexes ensuring specificity and fidelity during cellular signaling. The interaction between two PB1 domain depends on the type of PB1. There are three types of PB1 domains: type I which contains an OPCA motif, acidic aminoacid cluster, type II which contains a basic cluster, and type I/II which contains both an OPCA motif and a basic cluster. The PB1 domain of p40 represents a type I PB1 domain which interacts with the PB1 domain of oxidase activator p67 w
Probab=63.78 E-value=16 Score=35.01 Aligned_cols=51 Identities=24% Similarity=0.275 Sum_probs=43.1
Q ss_pred ChHHHHHHHHHHcCcccceeeeEeecCCCCeEEEecCCcHHHHHHHHhHhCCC
Q 001809 923 GCFQLYEEVARRLKLQNGTFQLKYLDDEEEWVMLVSDSDLQECFDILESLGKR 975 (1010)
Q Consensus 923 g~~~L~~EIakRf~l~~~~f~lKYlDDd~EWVlLtcDaDL~EC~di~~~~~~~ 975 (1010)
.|.+|+.=|-+.|+-+ -+.|.|.|-||+-|-|-.|.|++==|.-.+...+.
T Consensus 29 ~~kdLl~lmr~~f~~~--dIaLNYrD~EGDLIRllddeDv~LMV~~~r~~~~~ 79 (92)
T cd06399 29 LLKDLLELTRREFQRE--DIALNYRDAEGDLIRLLSDEDVALMVRQSRGLPSQ 79 (92)
T ss_pred cHHHHHHHHHHHhchh--heeeeeecCCCCEEEEcchhhHHHHHHHHhcCCCc
Confidence 4689999999999976 57899999999999999999998777766655444
No 124
>PRK11569 transcriptional repressor IclR; Provisional
Probab=63.76 E-value=46 Score=36.72 Aligned_cols=40 Identities=13% Similarity=0.130 Sum_probs=25.8
Q ss_pred eEEEEeeecCCCCceEEEEEEeeecccCCchHHHHHHHHHhh
Q 001809 274 SCIALPVFQFPEISCSAVLEIVSVKEKPNFDAEIENICNALQ 315 (1010)
Q Consensus 274 GsLAlPVf~~~s~~ClAVlElV~t~ek~~f~~E~e~vc~ALq 315 (1010)
.+||+|||++... ++|.|=+.......+- ..++.+..+|.
T Consensus 221 ~~iA~Pi~~~~g~-~~aalsvs~p~~r~~~-~~~~~~~~~l~ 260 (274)
T PRK11569 221 RCVAACIFDEHRE-PFAAISISGPISRITD-DRVTELGAMVI 260 (274)
T ss_pred EEEEEEEECCCCC-EEEEEEEEeehhhCCH-HHHHHHHHHHH
Confidence 6899999998655 4777777666555432 23455666553
No 125
>cd04765 HTH_MlrA-like_sg2 Helix-Turn-Helix DNA binding domain of putative MlrA-like transcription regulators. Putative helix-turn-helix (HTH) MlrA-like transcription regulators (subgroup 2), N-terminal domain. The MlrA protein, also known as YehV, has been shown to control cell-cell aggregation by co-regulating the expression of curli and extracellular matrix production in Escherichia coli and Salmonella typhimurium. These proteins belong to the MerR superfamily of transcription regulators that promote expression of several stress regulon genes by reconfiguring the spacer between the -35 and -10 promoter elements. Their conserved N-terminal domains contain predicted HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules.
Probab=63.25 E-value=7.2 Score=37.18 Aligned_cols=26 Identities=19% Similarity=0.216 Sum_probs=23.6
Q ss_pred CcHHHHHHHcCCChhHHHHHHHHcCC
Q 001809 613 GSLKDAAKSIGVCPTTLKRICRQHGI 638 (1010)
Q Consensus 613 ~pl~eAAk~LGV~~TtLKRiCR~~GI 638 (1010)
+++.|+|+.+||+++||...+++.|+
T Consensus 1 yti~EvA~~~gVs~~tLR~ye~~~gl 26 (99)
T cd04765 1 FSIGEVAEILGLPPHVLRYWETEFPQ 26 (99)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHHcCC
Confidence 47899999999999999999999765
No 126
>PF11112 PyocinActivator: Pyocin activator protein PrtN
Probab=63.06 E-value=11 Score=34.83 Aligned_cols=60 Identities=17% Similarity=0.375 Sum_probs=47.7
Q ss_pred HHHHHhhc---CCcHHHHHHHc--CCChhHHHHHHHHcCCCCCcchhhhhhHHH-----HHHHHHHHhhcc
Q 001809 604 LSVLQQYF---SGSLKDAAKSI--GVCPTTLKRICRQHGISRWPSRKINKVNRS-----LKKIQTVLNSVQ 664 (1010)
Q Consensus 604 l~~L~~yF---~~pl~eAAk~L--GV~~TtLKRiCR~~GI~RWP~Rki~sl~~~-----i~~l~~~i~s~q 664 (1010)
+.-|.+|| ..|+.++++.. |+++.+++|..+...| .||.=|+..-++. |.+|-.+||...
T Consensus 3 flLma~~~~~~~IpL~~v~~~yf~~lt~~~a~rk~~~g~l-plPv~rl~~SqKs~~~V~v~dLA~yiD~~~ 72 (76)
T PF11112_consen 3 FLLMAQYFGDPVIPLEEVCEDYFPHLTPKTAKRKANAGEL-PLPVFRLDDSQKSPKFVHVQDLAAYIDKRR 72 (76)
T ss_pred HHHHHHHcCCCCCcHHHHHHHHHccCCHHHHHHHHHCCCC-CCceeecCCcccCCceeeHHHHHHHHHHHH
Confidence 55677886 57889998766 9999999999999999 9999888643343 788888888654
No 127
>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=62.98 E-value=9.6 Score=31.57 Aligned_cols=29 Identities=28% Similarity=0.427 Sum_probs=20.6
Q ss_pred HHHhhcCCcHHHHHHHcCCChhHHHHHHH
Q 001809 606 VLQQYFSGSLKDAAKSIGVCPTTLKRICR 634 (1010)
Q Consensus 606 ~L~~yF~~pl~eAAk~LGV~~TtLKRiCR 634 (1010)
.+.-+.+++.+|+|+.|||++.++++.-+
T Consensus 20 ~l~~~~g~s~~eIa~~l~~s~~~v~~~l~ 48 (54)
T PF08281_consen 20 LLRYFQGMSYAEIAEILGISESTVKRRLR 48 (54)
T ss_dssp HHHHTS---HHHHHHHCTS-HHHHHHHHH
T ss_pred HHHHHHCcCHHHHHHHHCcCHHHHHHHHH
Confidence 45567799999999999999999987654
No 128
>cd01802 AN1_N ubiquitin-like domain of AN1. AN1 (also known as ANUBL1 and RSD-7) is ubiquitin-like protein with a testis-specific expression in rats that has an N-terminal ubiquitin-like domain and a C-terminal zinc-binding domain. Unlike ubiquitin polyproteins and most ubiquitin fusion proteins, the N-terminal ubiquitin-like domain of An1 does not undergo proteolytic processing. The function of AN1 is unknown.
Probab=62.80 E-value=26 Score=33.80 Aligned_cols=67 Identities=10% Similarity=0.210 Sum_probs=46.7
Q ss_pred eEEEEEEcCCCeEEEEeCCCcChHHHHHHHHHHcCcccceeee----EeecCCCCeEEEecCCcHHHHHHHHhHhCCCeE
Q 001809 902 KIIVKATYKEDIIRFKFDPSAGCFQLYEEVARRLKLQNGTFQL----KYLDDEEEWVMLVSDSDLQECFDILESLGKRSV 977 (1010)
Q Consensus 902 ~~~vKaty~~d~iRF~~~~s~g~~~L~~EIakRf~l~~~~f~l----KYlDDd~EWVlLtcDaDL~EC~di~~~~~~~~v 977 (1010)
.+.||- ..++++-+.+.++.-+.+|++.|+.+.|+......| |-|+|+. -|.+ |.-....+|
T Consensus 29 ~I~Vk~-l~G~~~~leV~~~~TV~~lK~kI~~~~gip~~~QrLi~~Gk~L~D~~---------tL~d----y~I~~~stL 94 (103)
T cd01802 29 ELFIET-LTGTCFELRVSPFETVISVKAKIQRLEGIPVAQQHLIWNNMELEDEY---------CLND----YNISEGCTL 94 (103)
T ss_pred EEEEEc-CCCCEEEEEeCCCCcHHHHHHHHHHHhCCChHHEEEEECCEECCCCC---------cHHH----cCCCCCCEE
Confidence 344443 345788899999999999999999999998876555 5566653 2333 233345677
Q ss_pred EEEEe
Q 001809 978 RFLVR 982 (1010)
Q Consensus 978 kl~V~ 982 (1010)
.|.+.
T Consensus 95 ~l~~~ 99 (103)
T cd01802 95 KLVLA 99 (103)
T ss_pred EEEEe
Confidence 77665
No 129
>PHA01976 helix-turn-helix protein
Probab=62.11 E-value=11 Score=32.39 Aligned_cols=32 Identities=13% Similarity=0.039 Sum_probs=28.3
Q ss_pred HHHHHhhcCCcHHHHHHHcCCChhHHHHHHHH
Q 001809 604 LSVLQQYFSGSLKDAAKSIGVCPTTLKRICRQ 635 (1010)
Q Consensus 604 l~~L~~yF~~pl~eAAk~LGV~~TtLKRiCR~ 635 (1010)
+..++..-+++++++|+.+||+.+++.++-+.
T Consensus 7 l~~~R~~~glt~~~lA~~~gvs~~~v~~~e~g 38 (67)
T PHA01976 7 LIKARNARAWSAPELSRRAGVRHSLIYDFEAD 38 (67)
T ss_pred HHHHHHHcCCCHHHHHHHhCCCHHHHHHHHcC
Confidence 56788889999999999999999999998553
No 130
>PRK09726 antitoxin HipB; Provisional
Probab=61.98 E-value=15 Score=33.89 Aligned_cols=31 Identities=19% Similarity=0.268 Sum_probs=28.5
Q ss_pred HHHHHhhcCCcHHHHHHHcCCChhHHHHHHH
Q 001809 604 LSVLQQYFSGSLKDAAKSIGVCPTTLKRICR 634 (1010)
Q Consensus 604 l~~L~~yF~~pl~eAAk~LGV~~TtLKRiCR 634 (1010)
+..++.--+++++++|+.+||++.++.++.+
T Consensus 17 lk~~R~~~gltq~elA~~~gvs~~tis~~e~ 47 (88)
T PRK09726 17 MKLVRQQNGWTQSELAKKIGIKQATISNFEN 47 (88)
T ss_pred HHHHHHHcCCCHHHHHHHHCcCHHHHHHHHC
Confidence 5677888899999999999999999999988
No 131
>cd01794 DC_UbP_C dendritic cell derived ubiquitin-like protein. DC_UbP (dendritic cell derived ubiquitin-like protein) is a ubiquitin-like protein from human dendritic cells that is expressed in the mitochondrion. The ubiquitin-like domain of this protein is found at the C-terminus and lacks the canonical gly-gly motif of ubiquitin required for ubiquitinization. DC_UbP is expressed in tumor cells but not in normal human adult tissue suggesting a role for DC_UbP in tumorogenesis.
Probab=61.96 E-value=31 Score=30.91 Aligned_cols=68 Identities=13% Similarity=0.126 Sum_probs=47.2
Q ss_pred EEEEcCCCeEEEEeCCCcChHHHHHHHHHHcCcccceeeeEeecCCCCeEEEecCCcHHHHHHHHhHhCCCeEEEEEe
Q 001809 905 VKATYKEDIIRFKFDPSAGCFQLYEEVARRLKLQNGTFQLKYLDDEEEWVMLVSDSDLQECFDILESLGKRSVRFLVR 982 (1010)
Q Consensus 905 vKaty~~d~iRF~~~~s~g~~~L~~EIakRf~l~~~~f~lKYlDDd~EWVlLtcDaDL~EC~di~~~~~~~~vkl~V~ 982 (1010)
||..- ++++-+.+.|+.-+.+|++.|+.+.|+......|-| ....|.-|.-|.+| .-.+..+|-|.||
T Consensus 3 vk~~~-G~~~~l~v~~~~TV~~lK~~I~~~~gi~~~~q~Li~-----~G~~L~D~~~l~~~----~i~~~~tv~~~~~ 70 (70)
T cd01794 3 VRLST-GKDVKLSVSSKDTVGQLKKQLQAAEGVDPCCQRWFF-----SGKLLTDKTRLQET----KIQKDYVVQVIVN 70 (70)
T ss_pred EEcCC-CCEEEEEECCcChHHHHHHHHHHHhCCCHHHeEEEE-----CCeECCCCCCHHHc----CCCCCCEEEEEeC
Confidence 44443 477889999999999999999999999876555544 12234444566653 3335678888776
No 132
>TIGR02607 antidote_HigA addiction module antidote protein, HigA family. Members of this family form a distinct clade within the larger family HTH_3 of helix-turn-helix proteins, described by Pfam model pfam01381. Members of this clade are strictly bacterial and nearly always shorter than 110 amino acids. This family includes the characterized member HigA, without which the killer protein HigB cannot be cloned. The hig (host inhibition of growth) system is noted to be unusual in that killer protein is uncoded by the upstream member of the gene pair.
Probab=61.77 E-value=16 Score=32.23 Aligned_cols=43 Identities=23% Similarity=0.298 Sum_probs=32.2
Q ss_pred HHHhhcCCcHHHHHHHcCCChhHHHHHHHHcCCCCCcchhhhhhH
Q 001809 606 VLQQYFSGSLKDAAKSIGVCPTTLKRICRQHGISRWPSRKINKVN 650 (1010)
Q Consensus 606 ~L~~yF~~pl~eAAk~LGV~~TtLKRiCR~~GI~RWP~Rki~sl~ 650 (1010)
.++.--++++.++|+.+||+.+++-++.. |-.+.+...+.++-
T Consensus 12 ~~~~~~~~t~~~lA~~~gis~~tis~~~~--g~~~~~~~~~~~l~ 54 (78)
T TIGR02607 12 EFLEPLGLSIRALAKALGVSRSTLSRIVN--GRRGITADMALRLA 54 (78)
T ss_pred HHHHHcCCCHHHHHHHhCCCHHHHHHHHc--CCCCCCHHHHHHHH
Confidence 56677789999999999999999999986 43444545544443
No 133
>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=61.74 E-value=7.6 Score=36.92 Aligned_cols=27 Identities=26% Similarity=0.377 Sum_probs=25.3
Q ss_pred CCcHHHHHHHcCCChhHHHHHHHHcCC
Q 001809 612 SGSLKDAAKSIGVCPTTLKRICRQHGI 638 (1010)
Q Consensus 612 ~~pl~eAAk~LGV~~TtLKRiCR~~GI 638 (1010)
.+.+.++||.|||++..|.+..|++||
T Consensus 24 ~~ti~~~AK~L~i~~~~l~~~Lr~~g~ 50 (111)
T PF03374_consen 24 LYTIREAAKLLGIGRNKLFQWLREKGW 50 (111)
T ss_pred CccHHHHHHHhCCCHHHHHHHHHhCCc
Confidence 478999999999999999999999986
No 134
>PRK15424 propionate catabolism operon regulatory protein PrpR; Provisional
Probab=61.61 E-value=9.5 Score=46.49 Aligned_cols=31 Identities=29% Similarity=0.396 Sum_probs=27.9
Q ss_pred hhcCCcHHHHHHHcCCChhHHHHHHHHcCCC
Q 001809 609 QYFSGSLKDAAKSIGVCPTTLKRICRQHGIS 639 (1010)
Q Consensus 609 ~yF~~pl~eAAk~LGV~~TtLKRiCR~~GI~ 639 (1010)
..+++-..+||+.|||++|||+|.-+++|-.
T Consensus 507 ~~~~Gn~~~aA~~LGIsRtTL~RkLk~~g~~ 537 (538)
T PRK15424 507 ERFNGDKTAAANYLGISRTTLWRRLKAEAKA 537 (538)
T ss_pred HHhCCCHHHHHHHhCCCHHHHHHHHHHhCCC
Confidence 5568899999999999999999999999853
No 135
>smart00065 GAF Domain present in phytochromes and cGMP-specific phosphodiesterases. Mutations within these domains in PDE6B result in autosomal recessive inheritance of retinitis pigmentosa.
Probab=61.41 E-value=22 Score=31.40 Aligned_cols=84 Identities=20% Similarity=0.314 Sum_probs=55.2
Q ss_pred cccccCCCcchhhhhcCCCcccccccccCccccchhhHHHHh-CCceeEEEEecccccCCCcEEEEeecC-CCCCCcHHH
Q 001809 417 HYLEEGQGVAGKALQSNHPFFFPDVKLYDITEFPLVHHARKF-GLNAAVAIRLRSTYTGDDDYILEFFLP-VTIKGSSEQ 494 (1010)
Q Consensus 417 hhL~~GQGvaGkAf~sn~P~F~~DV~~fsk~EYPL~HhAr~f-gL~aAvAIrLrS~~tG~ddyVLEFFLP-~~ck~~~EQ 494 (1010)
..+..+.+..++++.++.|...+|+.... ++...+...+ ++++.+.+||+.. |..-.+|.+.-+ ..-.-..+.
T Consensus 50 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---~~~~~~~~~~~~~~s~~~~Pl~~~--~~~~G~l~~~~~~~~~~~~~~~ 124 (149)
T smart00065 50 LRYPLGEGLAGRVAETGRPLNIPDVEADP---VFALDLLGRYQGVRSFLAVPLVAD--GELVGVLALHNKDSPRPFTEED 124 (149)
T ss_pred EEecCCCChHHHHHHcCCeEEeechhhCC---ccccccccceeceeeEEEeeeeec--CEEEEEEEEEecCCCCCCCHHH
Confidence 34556679999999999999999987643 2222333333 3899999999873 555667888876 333444455
Q ss_pred HHHHHHHHHHH
Q 001809 495 QLLLNNLSGTM 505 (1010)
Q Consensus 495 q~ll~sLs~Tm 505 (1010)
..+|..+...+
T Consensus 125 ~~~l~~~~~~i 135 (149)
T smart00065 125 EELLQALANQL 135 (149)
T ss_pred HHHHHHHHHHH
Confidence 55555554443
No 136
>TIGR03830 CxxCG_CxxCG_HTH putative zinc finger/helix-turn-helix protein, YgiT family. This model describes a family of predicted regulatory proteins with a conserved zinc finger/HTH architecture. The amino-terminal region contains a novel domain, featuring two CXXC motifs and occuring in a number of small bacterial proteins as well as in the present family. The carboxyl-terminal region consists of a helix-turn-helix domain, modeled by pfam01381. The predicted function is DNA binding and transcriptional regulation.
Probab=60.26 E-value=14 Score=35.51 Aligned_cols=32 Identities=19% Similarity=0.248 Sum_probs=28.4
Q ss_pred CHHHHHhhcCCcHHHHHHHcCCChhHHHHHHH
Q 001809 603 SLSVLQQYFSGSLKDAAKSIGVCPTTLKRICR 634 (1010)
Q Consensus 603 tl~~L~~yF~~pl~eAAk~LGV~~TtLKRiCR 634 (1010)
.+..+++..+++++++|+.||++..|+.|+-+
T Consensus 69 ~i~~~r~~~gltq~~lA~~lg~~~~tis~~e~ 100 (127)
T TIGR03830 69 EIRRIRKKLGLSQREAAELLGGGVNAFSRYER 100 (127)
T ss_pred HHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHC
Confidence 36678899999999999999999999999854
No 137
>PRK04217 hypothetical protein; Provisional
Probab=60.04 E-value=10 Score=37.29 Aligned_cols=28 Identities=25% Similarity=0.273 Sum_probs=24.0
Q ss_pred HhhcCCcHHHHHHHcCCChhHHHHHHHH
Q 001809 608 QQYFSGSLKDAAKSIGVCPTTLKRICRQ 635 (1010)
Q Consensus 608 ~~yF~~pl~eAAk~LGV~~TtLKRiCR~ 635 (1010)
..+-+++++|+|+.|||+..|++++.++
T Consensus 54 ~~~eGlS~~EIAk~LGIS~sTV~r~L~R 81 (110)
T PRK04217 54 VDYEGLTQEEAGKRMGVSRGTVWRALTS 81 (110)
T ss_pred HHHcCCCHHHHHHHHCcCHHHHHHHHHH
Confidence 3344789999999999999999998774
No 138
>TIGR02974 phageshock_pspF psp operon transcriptional activator PspF. Members of this protein family are PspF, the sigma-54-dependent transcriptional activator of the phage shock protein (psp) operon, in Escherichia coli and numerous other species. The psp operon is induced by a number of stress conditions, including heat shock, ethanol, and filamentous phage infection. Changed com_name to adhere to TIGR role notes conventions. 09/15/06 - DMH
Probab=59.64 E-value=10 Score=43.21 Aligned_cols=28 Identities=21% Similarity=0.272 Sum_probs=25.0
Q ss_pred hhcCCcHHHHHHHcCCChhHHHHHHHHc
Q 001809 609 QYFSGSLKDAAKSIGVCPTTLKRICRQH 636 (1010)
Q Consensus 609 ~yF~~pl~eAAk~LGV~~TtLKRiCR~~ 636 (1010)
..+++-+.+||+.|||+.+||+|..++|
T Consensus 302 ~~~~gn~~~aA~~LGisr~tL~rklkk~ 329 (329)
T TIGR02974 302 AEAQFNQRKAAELLGLTYHQLRGLLRKH 329 (329)
T ss_pred HHhCCCHHHHHHHhCCCHHHHHHHHHhC
Confidence 5568899999999999999999998875
No 139
>TIGR02040 PpsR-CrtJ transcriptional regulator PpsR. This model represents the transcriptional regulator PpsR which is strictly associated with photosynthetic proteobacteria and found in photosynthetic operons. PpsR has been reported to be a repressor. These proteins contain a Helix-Turn_Helix motif of the "fis" type (pfam02954).
Probab=59.23 E-value=11 Score=43.57 Aligned_cols=33 Identities=18% Similarity=0.217 Sum_probs=29.0
Q ss_pred HHHhhcCCcHHHHHHHcCCChhHHHHHHHHcCC
Q 001809 606 VLQQYFSGSLKDAAKSIGVCPTTLKRICRQHGI 638 (1010)
Q Consensus 606 ~L~~yF~~pl~eAAk~LGV~~TtLKRiCR~~GI 638 (1010)
.+-..++.....||+.|||+++||+|..|++||
T Consensus 410 ~~l~~~~~n~~~aa~~lgi~r~~l~~~l~~~~~ 442 (442)
T TIGR02040 410 AALELTRDNRASAAEILGLSRQSLYVKLRRYGL 442 (442)
T ss_pred HHHHHcCCCHHHHHHHhCCCHHHHHHHHHHhCc
Confidence 344567888999999999999999999999986
No 140
>PRK15418 transcriptional regulator LsrR; Provisional
Probab=58.94 E-value=8.5 Score=43.73 Aligned_cols=35 Identities=23% Similarity=0.435 Sum_probs=28.6
Q ss_pred HHHhhc--CCcHHHHHHHcCCChhHHHHH---HHHcCCCC
Q 001809 606 VLQQYF--SGSLKDAAKSIGVCPTTLKRI---CRQHGISR 640 (1010)
Q Consensus 606 ~L~~yF--~~pl~eAAk~LGV~~TtLKRi---CR~~GI~R 640 (1010)
.-+-|| +++++|+|++||||++++-|+ ||+.||-+
T Consensus 21 vA~lYY~~g~tQ~eIA~~lgiSR~~VsRlL~~Ar~~GiV~ 60 (318)
T PRK15418 21 IAWFYYHDGLTQSEIGERLGLTRLKVSRLLEKGRQSGIIR 60 (318)
T ss_pred HHHHHHhcCCCHHHHHHHhCCCHHHHHHHHHHHHHcCcEE
Confidence 344566 899999999999999988775 89999743
No 141
>COG2204 AtoC Response regulator containing CheY-like receiver, AAA-type ATPase, and DNA-binding domains [Signal transduction mechanisms]
Probab=58.88 E-value=12 Score=45.11 Aligned_cols=38 Identities=26% Similarity=0.352 Sum_probs=33.4
Q ss_pred HHhhcCCcHHHHHHHcCCChhHHHHHHHHcCCCCCcch
Q 001809 607 LQQYFSGSLKDAAKSIGVCPTTLKRICRQHGISRWPSR 644 (1010)
Q Consensus 607 L~~yF~~pl~eAAk~LGV~~TtLKRiCR~~GI~RWP~R 644 (1010)
.-..+++-+++||+.|||+++||+|.-++|||.+=++.
T Consensus 425 aL~~~~g~~~~aA~~LGi~R~tLy~Klk~~g~~~~~~~ 462 (464)
T COG2204 425 ALERTGGNKSEAAERLGISRKTLYRKLKEYGIDRSDVE 462 (464)
T ss_pred HHHHhCCCHHHHHHHHCCCHHHHHHHHHHhCCCccccC
Confidence 33678999999999999999999999999999876553
No 142
>PRK09393 ftrA transcriptional activator FtrA; Provisional
Probab=58.01 E-value=13 Score=41.48 Aligned_cols=37 Identities=14% Similarity=0.273 Sum_probs=30.4
Q ss_pred HHHHHhhcC--CcHHHHHHHcCCChhHHHHHHHHc-CCCC
Q 001809 604 LSVLQQYFS--GSLKDAAKSIGVCPTTLKRICRQH-GISR 640 (1010)
Q Consensus 604 l~~L~~yF~--~pl~eAAk~LGV~~TtLKRiCR~~-GI~R 640 (1010)
++-|..+++ +++.++|+.+|+++.+|.|++++. |+.-
T Consensus 224 ~~~i~~~~~~~~sl~~lA~~~~~S~~~l~r~fk~~~g~s~ 263 (322)
T PRK09393 224 IDWMRAHLAEPHTVASLAARAAMSPRTFLRRFEAATGMTP 263 (322)
T ss_pred HHHHHhccCCCCCHHHHHHHHCcCHHHHHHHHHHHHCcCH
Confidence 345556554 889999999999999999999997 8853
No 143
>PRK14101 bifunctional glucokinase/RpiR family transcriptional regulator; Provisional
Probab=56.25 E-value=8.8 Score=47.22 Aligned_cols=34 Identities=24% Similarity=0.409 Sum_probs=30.0
Q ss_pred hhcCCcHHHHHHHcCCChhHHHHHHHHcCCCCCc
Q 001809 609 QYFSGSLKDAAKSIGVCPTTLKRICRQHGISRWP 642 (1010)
Q Consensus 609 ~yF~~pl~eAAk~LGV~~TtLKRiCR~~GI~RWP 642 (1010)
..-.++++|.|++.|||++|+-|.||++|-.-|+
T Consensus 371 ~v~~~si~eLA~~~~vS~aTV~Rf~kkLGf~Gf~ 404 (638)
T PRK14101 371 SIINDPIVDIARKADVSQPTVIRFCRSLGCQGLS 404 (638)
T ss_pred HHHhccHHHHHHHhCCCHHHHHHHHHHhCCCCHH
Confidence 4447899999999999999999999999976653
No 144
>COG1595 RpoE DNA-directed RNA polymerase specialized sigma subunit, sigma24 homolog [Transcription]
Probab=55.88 E-value=12 Score=38.23 Aligned_cols=30 Identities=20% Similarity=0.224 Sum_probs=26.1
Q ss_pred HHHhhcCCcHHHHHHHcCCChhHHHHHHHH
Q 001809 606 VLQQYFSGSLKDAAKSIGVCPTTLKRICRQ 635 (1010)
Q Consensus 606 ~L~~yF~~pl~eAAk~LGV~~TtLKRiCR~ 635 (1010)
.|..+.+++.+|+|+.|||+..|+|.+.++
T Consensus 137 ~l~~~~gls~~EIA~~l~i~~~tVks~l~r 166 (182)
T COG1595 137 LLRYLEGLSYEEIAEILGISVGTVKSRLHR 166 (182)
T ss_pred hhHhhcCCCHHHHHHHHCCCHHHHHHHHHH
Confidence 566777999999999999999999987653
No 145
>TIGR01818 ntrC nitrogen regulation protein NR(I). This model represents NtrC, a DNA-binding response regulator that is phosphorylated by NtrB and interacts with sigma-54. NtrC usually controls the expression of glutamine synthase, GlnA, and may be called GlnL, GlnG, etc.
Probab=55.69 E-value=12 Score=43.32 Aligned_cols=28 Identities=29% Similarity=0.281 Sum_probs=24.6
Q ss_pred hhcCCcHHHHHHHcCCChhHHHHHHHHc
Q 001809 609 QYFSGSLKDAAKSIGVCPTTLKRICRQH 636 (1010)
Q Consensus 609 ~yF~~pl~eAAk~LGV~~TtLKRiCR~~ 636 (1010)
..+++...+||+.|||+++||+|..+++
T Consensus 436 ~~~~gn~~~aA~~Lgisr~tL~rkl~~~ 463 (463)
T TIGR01818 436 QHTRGHKQEAAALLGWGRNTLTRKLKEL 463 (463)
T ss_pred HHcCCCHHHHHHHhCCCHHHHHHHHHhC
Confidence 4568899999999999999999987764
No 146
>smart00354 HTH_LACI helix_turn _helix lactose operon repressor.
Probab=55.09 E-value=9.5 Score=33.82 Aligned_cols=24 Identities=29% Similarity=0.505 Sum_probs=21.6
Q ss_pred CcHHHHHHHcCCChhHHHHHHHHc
Q 001809 613 GSLKDAAKSIGVCPTTLKRICRQH 636 (1010)
Q Consensus 613 ~pl~eAAk~LGV~~TtLKRiCR~~ 636 (1010)
++++|.|+.+||+..|+-|+|+..
T Consensus 1 ~t~~~iA~~~gvS~~TVSr~ln~~ 24 (70)
T smart00354 1 ATIKDVARLAGVSKATVSRVLNGN 24 (70)
T ss_pred CCHHHHHHHHCCCHHHHHHHHCCC
Confidence 368899999999999999999865
No 147
>cd01804 midnolin_N Ubiquitin-like domain of midnolin. midnolin_N Midnolin (midbrain nucleolar protein) is expressed in the nucleolus and is thought to regulate genes involved in neurogenesis. Midnolin contains an amino-terminal ubiquitin-like domain.
Probab=55.01 E-value=28 Score=31.56 Aligned_cols=70 Identities=17% Similarity=0.189 Sum_probs=47.0
Q ss_pred eEEEEEEcCCCeEEEEeCCCcChHHHHHHHHHHcCcccceeeeEeecCCCCeEEEecCCcHHHHHHHHhHhCCCeEEEEE
Q 001809 902 KIIVKATYKEDIIRFKFDPSAGCFQLYEEVARRLKLQNGTFQLKYLDDEEEWVMLVSDSDLQECFDILESLGKRSVRFLV 981 (1010)
Q Consensus 902 ~~~vKaty~~d~iRF~~~~s~g~~~L~~EIakRf~l~~~~f~lKYlDDd~EWVlLtcDaDL~EC~di~~~~~~~~vkl~V 981 (1010)
.++||-..| ..+-+.+.|+..+.+|++.|++++++......|-|- +. .|..+ -|.+| .-....+|-|.+
T Consensus 3 ~I~Vk~~~G-~~~~l~v~~~~TV~~LK~~I~~~~~~~~~~qrL~~~---Gk--~L~d~-~L~~~----gi~~~~~i~l~~ 71 (78)
T cd01804 3 NLNIHSTTG-TRFDLSVPPDETVEGLKKRISQRLKVPKERLALLHR---ET--RLSSG-KLQDL----GLGDGSKLTLVP 71 (78)
T ss_pred EEEEEECCC-CEEEEEECCcCHHHHHHHHHHHHhCCChHHEEEEEC---Cc--CCCCC-cHHHc----CCCCCCEEEEEe
Confidence 367776655 567789999999999999999999998776666554 21 23322 34443 333456666654
Q ss_pred e
Q 001809 982 R 982 (1010)
Q Consensus 982 ~ 982 (1010)
.
T Consensus 72 ~ 72 (78)
T cd01804 72 T 72 (78)
T ss_pred e
Confidence 3
No 148
>PF05930 Phage_AlpA: Prophage CP4-57 regulatory protein (AlpA); InterPro: IPR010260 This entry is represents phage P4, Orf88. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. In Escherichia coli phage P4 Orf 88 is similar to AlpA of the CP4-57 cryptic prophage []. AlpA acts as a positive transcriptional regulator of slpA, a gene linked to alpA and necessary for suppression of lon mutants [, ]. The sequence of slpA suggests that it encodes an integrase gene closely related to phage P4 int and that both alpA and slpA are part of a cryptic P4-like prophage. Increase in alpA expression increases SlpA synthesis. Increased SlpA leads, in turn, to the excision and loss of the cryptic prophage. ; PDB: 1Z4H_A.
Probab=54.88 E-value=11 Score=31.69 Aligned_cols=24 Identities=25% Similarity=0.432 Sum_probs=19.7
Q ss_pred CcHHHHHHHcCCChhHHHHHHHHc
Q 001809 613 GSLKDAAKSIGVCPTTLKRICRQH 636 (1010)
Q Consensus 613 ~pl~eAAk~LGV~~TtLKRiCR~~ 636 (1010)
+.++|+|+.+|||.+|+.+..++-
T Consensus 4 l~~~ev~~~~g~s~~ti~~~~k~g 27 (51)
T PF05930_consen 4 LRIKEVAELLGVSRSTIYRLIKDG 27 (51)
T ss_dssp E-HHHHHHHHSS-HHHHHHHHHHH
T ss_pred ccHHHHHHHHCCCHHHHHHHHhcc
Confidence 468999999999999999999853
No 149
>PF03683 UPF0175: Uncharacterised protein family (UPF0175); InterPro: IPR005368 This entry contains small proteins of unknown function.
Probab=54.63 E-value=16 Score=33.30 Aligned_cols=32 Identities=22% Similarity=0.219 Sum_probs=29.2
Q ss_pred CCcHHHHHHHcCCChhHHHHHHHHcCCCCCcch
Q 001809 612 SGSLKDAAKSIGVCPTTLKRICRQHGISRWPSR 644 (1010)
Q Consensus 612 ~~pl~eAAk~LGV~~TtLKRiCR~~GI~RWP~R 644 (1010)
.+++-.||+.+|++.-.+..+++++||. +.|-
T Consensus 34 ~iS~gkAAelag~s~~eF~~~L~~~gI~-~~~~ 65 (76)
T PF03683_consen 34 KISLGKAAELAGMSRWEFLELLKERGIP-INYD 65 (76)
T ss_pred CCCHHHHHHHhCCCHHHHHHHHHHCCCC-CCCC
Confidence 7899999999999999999999999998 5553
No 150
>cd01791 Ubl5 UBL5 ubiquitin-like modifier. UBL5 (also known as HUB1) is a ubiquitin-like modifier that is both widely expressed and highly phylogenetically conserved. At the C-terminal end of the ubiquitin-like fold of UBL5 is a di-tyrosine motif followed by a single variable residue instead of the characteristic di-glycine found in all other ubiquitin-like modifiers. ULB5 interacts with a cyclin-like kinase called CLK4 but not with other cyclin-like kinase family members.
Probab=54.46 E-value=37 Score=30.79 Aligned_cols=37 Identities=19% Similarity=0.166 Sum_probs=32.3
Q ss_pred CCeEEEEeCCCcChHHHHHHHHHHcCcccceeeeEee
Q 001809 911 EDIIRFKFDPSAGCFQLYEEVARRLKLQNGTFQLKYL 947 (1010)
Q Consensus 911 ~d~iRF~~~~s~g~~~L~~EIakRf~l~~~~f~lKYl 947 (1010)
+.++.+.+.|+.-+.+|++.|++++++......|-|-
T Consensus 11 Gk~~~~~v~~~~TV~~LK~~I~~~~~~~~~~qrLi~~ 47 (73)
T cd01791 11 GKKVRVKCNPDDTIGDLKKLIAAQTGTRPEKIVLKKW 47 (73)
T ss_pred CCEEEEEeCCCCcHHHHHHHHHHHhCCChHHEEEEeC
Confidence 4788889999999999999999999998877666664
No 151
>PRK10163 DNA-binding transcriptional repressor AllR; Provisional
Probab=54.02 E-value=1.1e+02 Score=33.87 Aligned_cols=39 Identities=15% Similarity=0.201 Sum_probs=25.8
Q ss_pred eEEEEeeecCCCCceEEEEEEeeecccCCchHHHHHHHHHh
Q 001809 274 SCIALPVFQFPEISCSAVLEIVSVKEKPNFDAEIENICNAL 314 (1010)
Q Consensus 274 GsLAlPVf~~~s~~ClAVlElV~t~ek~~f~~E~e~vc~AL 314 (1010)
.+||+|||++... ++|.|-+........-. +++.+..+|
T Consensus 216 ~~vAvPI~~~~g~-~~aalsvs~p~~r~~~~-~~~~~~~~l 254 (271)
T PRK10163 216 NCIASAIYDDVGS-VVAAISISGPSSRLTED-RFVSQGELV 254 (271)
T ss_pred eEEEEEEECCCCC-EEEEEEEEEecccCCHH-HHHHHHHHH
Confidence 6899999997544 58888887776654322 234444444
No 152
>TIGR02989 Sig-70_gvs1 RNA polymerase sigma-70 factor, Rhodopirellula/Verrucomicrobium family. This group of sigma factors are members of the sigma-70 family (TIGR02937) and are abundantly found in the species Rhodopirellula baltica (11), and Verrucomicrobium spinosum (16) and to a lesser extent in Gemmata obscuriglobus (2).
Probab=53.91 E-value=15 Score=36.03 Aligned_cols=29 Identities=17% Similarity=0.108 Sum_probs=24.6
Q ss_pred HHHhhcCCcHHHHHHHcCCChhHHHHHHH
Q 001809 606 VLQQYFSGSLKDAAKSIGVCPTTLKRICR 634 (1010)
Q Consensus 606 ~L~~yF~~pl~eAAk~LGV~~TtLKRiCR 634 (1010)
.|.-+.+++.+|+|+.|||++.|+|....
T Consensus 121 ~l~~~~g~~~~eIA~~l~is~~tv~~~l~ 149 (159)
T TIGR02989 121 QLRYQRGVSLTALAEQLGRTVNAVYKALS 149 (159)
T ss_pred HHHHhcCCCHHHHHHHhCCCHHHHHHHHH
Confidence 45566799999999999999999997644
No 153
>smart00419 HTH_CRP helix_turn_helix, cAMP Regulatory protein.
Probab=53.75 E-value=14 Score=29.29 Aligned_cols=28 Identities=14% Similarity=0.223 Sum_probs=24.5
Q ss_pred hcCCcHHHHHHHcCCChhHHHHHHHHcC
Q 001809 610 YFSGSLKDAAKSIGVCPTTLKRICRQHG 637 (1010)
Q Consensus 610 yF~~pl~eAAk~LGV~~TtLKRiCR~~G 637 (1010)
.|.++.+|+|+.+|+++.++.|..+++-
T Consensus 6 ~~~~s~~~la~~l~~s~~tv~~~l~~L~ 33 (48)
T smart00419 6 RLPLTRQEIAELLGLTRETVSRTLKRLE 33 (48)
T ss_pred EeccCHHHHHHHHCCCHHHHHHHHHHHH
Confidence 4678899999999999999999888764
No 154
>PRK11169 leucine-responsive transcriptional regulator; Provisional
Probab=53.52 E-value=13 Score=38.07 Aligned_cols=33 Identities=27% Similarity=0.225 Sum_probs=28.7
Q ss_pred HHHHHhhcCCcHHHHHHHcCCChhHHHHHHHHc
Q 001809 604 LSVLQQYFSGSLKDAAKSIGVCPTTLKRICRQH 636 (1010)
Q Consensus 604 l~~L~~yF~~pl~eAAk~LGV~~TtLKRiCR~~ 636 (1010)
|..|++-.-++..|.|++||++++|+.|+-+++
T Consensus 20 L~~Lq~d~R~s~~eiA~~lglS~~tv~~Ri~rL 52 (164)
T PRK11169 20 LNELQKDGRISNVELSKRVGLSPTPCLERVRRL 52 (164)
T ss_pred HHHhccCCCCCHHHHHHHHCcCHHHHHHHHHHH
Confidence 557888999999999999999999998876654
No 155
>PRK09685 DNA-binding transcriptional activator FeaR; Provisional
Probab=53.48 E-value=19 Score=39.22 Aligned_cols=52 Identities=17% Similarity=0.248 Sum_probs=37.4
Q ss_pred HHHHhhcC---CcHHHHHHHcCCChhHHHHHHHHcCCCCCcchhhhhhHHHHHHHHHHH
Q 001809 605 SVLQQYFS---GSLKDAAKSIGVCPTTLKRICRQHGISRWPSRKINKVNRSLKKIQTVL 660 (1010)
Q Consensus 605 ~~L~~yF~---~pl~eAAk~LGV~~TtLKRiCR~~GI~RWP~Rki~sl~~~i~~l~~~i 660 (1010)
+-|.++++ +++.++|+.+|||+.+|.|++++.|.. |.+=|... .|++.+++|
T Consensus 204 ~~I~~~l~~~~ls~~~lA~~~giS~r~L~r~Fk~~G~T--~~~yi~~~--RL~~A~~lL 258 (302)
T PRK09685 204 ALIDQSIQEEILRPEWIAGELGISVRSLYRLFAEQGLV--VAQYIRNR--RLDRCADDL 258 (302)
T ss_pred HHHHHhcCCCCCCHHHHHHHHCCCHHHHHHHHHHcCCC--HHHHHHHH--HHHHHHHHh
Confidence 45667773 789999999999999999999999975 44444322 334444444
No 156
>cd01105 HTH_GlnR-like Helix-Turn-Helix DNA binding domain of GlnR-like transcription regulators. Helix-turn-helix (HTH) transcription regulator GlnR and related proteins, N-terminal domain. The GlnR and TnrA (also known as ScgR) proteins have been shown to regulate expression of glutamine synthetase as well as several genes involved in nitrogen metabolism. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules.
Probab=53.38 E-value=13 Score=34.46 Aligned_cols=25 Identities=24% Similarity=0.413 Sum_probs=22.2
Q ss_pred CcHHHHHHHcCCChhHHHHHHHHcCC
Q 001809 613 GSLKDAAKSIGVCPTTLKRICRQHGI 638 (1010)
Q Consensus 613 ~pl~eAAk~LGV~~TtLKRiCR~~GI 638 (1010)
+++.|+|+.+||++.||+...|+ |+
T Consensus 2 ~ti~evA~~~gvs~~tLR~ye~~-Gl 26 (88)
T cd01105 2 IGIGEVSKLTGVSPRQLRYWEEK-GL 26 (88)
T ss_pred cCHHHHHHHHCcCHHHHHHHHHC-CC
Confidence 58999999999999999999876 54
No 157
>cd00093 HTH_XRE Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the xenobiotic response element family of transcriptional regulators.
Probab=52.98 E-value=38 Score=25.89 Aligned_cols=42 Identities=21% Similarity=0.267 Sum_probs=30.0
Q ss_pred HHHhhcCCcHHHHHHHcCCChhHHHHHHHHcCCCCCcchhhhhh
Q 001809 606 VLQQYFSGSLKDAAKSIGVCPTTLKRICRQHGISRWPSRKINKV 649 (1010)
Q Consensus 606 ~L~~yF~~pl~eAAk~LGV~~TtLKRiCR~~GI~RWP~Rki~sl 649 (1010)
.++..-.++..++|+.+|+++.++.+... |-...+...+..+
T Consensus 6 ~~~~~~~~s~~~~a~~~~~~~~~v~~~~~--g~~~~~~~~~~~i 47 (58)
T cd00093 6 ELRKEKGLTQEELAEKLGVSRSTISRIEN--GKRNPSLETLEKL 47 (58)
T ss_pred HHHHHcCCCHHHHHHHHCCCHHHHHHHHc--CCCCCCHHHHHHH
Confidence 34455688999999999999999988765 4345555554443
No 158
>cd00592 HTH_MerR-like Helix-Turn-Helix DNA binding domain of MerR-like transcription regulators. Helix-turn-helix (HTH) MerR-like transcription regulator, N-terminal domain. The MerR family transcription regulators have been shown to mediate responses to stress including exposure to heavy metals, drugs, or oxygen radicals in eubacterial and some archaeal species. They regulate transcription of multidrug/metal ion transporter genes and oxidative stress regulons by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.
Probab=52.38 E-value=16 Score=34.09 Aligned_cols=30 Identities=30% Similarity=0.455 Sum_probs=23.8
Q ss_pred CcHHHHHHHcCCChhHHHHHHHHcCCCCCcch
Q 001809 613 GSLKDAAKSIGVCPTTLKRICRQHGISRWPSR 644 (1010)
Q Consensus 613 ~pl~eAAk~LGV~~TtLKRiCR~~GI~RWP~R 644 (1010)
++++|+|+.+||+++||+...++ |+-. |.|
T Consensus 1 ~~~~eva~~~gi~~~tlr~~~~~-Gll~-~~~ 30 (100)
T cd00592 1 YTIGEVAKLLGVSVRTLRYYEEK-GLLP-PER 30 (100)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHC-CCcC-CCc
Confidence 47899999999999999998874 6533 433
No 159
>PF12844 HTH_19: Helix-turn-helix domain; PDB: 3LIS_B 3LFP_A 2XIU_B 2GZU_B 2XJ3_A 1UTX_A 2XI8_B 3F6W_C 3EUS_B.
Probab=52.30 E-value=17 Score=30.98 Aligned_cols=31 Identities=26% Similarity=0.349 Sum_probs=23.9
Q ss_pred HHHHHhhcCCcHHHHHHHcCCChhHHHHHHH
Q 001809 604 LSVLQQYFSGSLKDAAKSIGVCPTTLKRICR 634 (1010)
Q Consensus 604 l~~L~~yF~~pl~eAAk~LGV~~TtLKRiCR 634 (1010)
|..++..-+++++++|+.+||+++++.++=.
T Consensus 4 lk~~r~~~~lt~~~~a~~~~i~~~~i~~~e~ 34 (64)
T PF12844_consen 4 LKELREEKGLTQKDLAEKLGISRSTISKIEN 34 (64)
T ss_dssp HHHHHHHCT--HHHHHHHHTS-HHHHHHHHT
T ss_pred HHHHHHHcCCCHHHHHHHHCcCHHHHHHHHC
Confidence 5678888999999999999999988888743
No 160
>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=51.94 E-value=16 Score=32.10 Aligned_cols=27 Identities=22% Similarity=0.176 Sum_probs=25.3
Q ss_pred CCcHHHHHHHcCCChhHHHHHHHHcCC
Q 001809 612 SGSLKDAAKSIGVCPTTLKRICRQHGI 638 (1010)
Q Consensus 612 ~~pl~eAAk~LGV~~TtLKRiCR~~GI 638 (1010)
+++++|+|+.|||...|++.-.++.+=
T Consensus 13 G~~~~eIA~~Lg~~~~TV~~W~~r~~W 39 (58)
T PF06056_consen 13 GWSIKEIAEELGVPRSTVYSWKDRYKW 39 (58)
T ss_pred CCCHHHHHHHHCCChHHHHHHHHhhCc
Confidence 789999999999999999999999873
No 161
>PRK12536 RNA polymerase sigma factor; Provisional
Probab=51.87 E-value=18 Score=36.81 Aligned_cols=28 Identities=14% Similarity=0.078 Sum_probs=24.1
Q ss_pred HHhhcCCcHHHHHHHcCCChhHHHHHHH
Q 001809 607 LQQYFSGSLKDAAKSIGVCPTTLKRICR 634 (1010)
Q Consensus 607 L~~yF~~pl~eAAk~LGV~~TtLKRiCR 634 (1010)
|.-+.+++.+|+|+.|||++.|+|....
T Consensus 140 l~~~~g~s~~EIA~~l~is~~tV~~~l~ 167 (181)
T PRK12536 140 HVKLEGLSVAETAQLTGLSESAVKVGIH 167 (181)
T ss_pred HHHHcCCCHHHHHHHHCCCHHHHHHHHH
Confidence 3456799999999999999999998763
No 162
>cd04766 HTH_HspR Helix-Turn-Helix DNA binding domain of the HspR transcription regulator. Helix-turn-helix (HTH) transcription regulator HspR, N-terminal domain. Heat shock protein regulators (HspR) have been shown to regulate expression of specific regulons in response to high temperature or high osmolarity in Streptomyces and Helicobacter, respectively. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules.
Probab=51.77 E-value=16 Score=33.88 Aligned_cols=27 Identities=30% Similarity=0.308 Sum_probs=23.2
Q ss_pred CcHHHHHHHcCCChhHHHHHHHHcCCCC
Q 001809 613 GSLKDAAKSIGVCPTTLKRICRQHGISR 640 (1010)
Q Consensus 613 ~pl~eAAk~LGV~~TtLKRiCR~~GI~R 640 (1010)
+++.++|+.+||++.||+...+ .|+-.
T Consensus 2 ~~i~e~A~~~gvs~~tLr~ye~-~Gli~ 28 (91)
T cd04766 2 YVISVAAELSGMHPQTLRLYER-LGLLS 28 (91)
T ss_pred cCHHHHHHHHCcCHHHHHHHHH-CCCcC
Confidence 5899999999999999999987 47533
No 163
>PRK09643 RNA polymerase sigma factor SigM; Reviewed
Probab=51.72 E-value=19 Score=37.21 Aligned_cols=29 Identities=34% Similarity=0.428 Sum_probs=24.3
Q ss_pred HHHhhcCCcHHHHHHHcCCChhHHHHHHH
Q 001809 606 VLQQYFSGSLKDAAKSIGVCPTTLKRICR 634 (1010)
Q Consensus 606 ~L~~yF~~pl~eAAk~LGV~~TtLKRiCR 634 (1010)
.|+-+-+++.+|+|+.|||+..|+|...+
T Consensus 144 ~l~~~~g~s~~EIA~~lg~s~~tV~~rl~ 172 (192)
T PRK09643 144 VAVDMQGYSVADAARMLGVAEGTVKSRCA 172 (192)
T ss_pred HHHHHcCCCHHHHHHHHCcCHHHHHHHHH
Confidence 34445689999999999999999998773
No 164
>PRK15186 AraC family transcriptional regulator; Provisional
Probab=51.63 E-value=10 Score=42.59 Aligned_cols=40 Identities=25% Similarity=0.169 Sum_probs=31.1
Q ss_pred HHHhhc--CCcHHHHHHHcCCChhHHHHHHHHcCCCCCcchh
Q 001809 606 VLQQYF--SGSLKDAAKSIGVCPTTLKRICRQHGISRWPSRK 645 (1010)
Q Consensus 606 ~L~~yF--~~pl~eAAk~LGV~~TtLKRiCR~~GI~RWP~Rk 645 (1010)
.|...+ .+++++.|+.+|+|+++|+|+.|+.|..=-+|.+
T Consensus 189 ~I~~~~~~~~sl~~lA~~~gmS~stl~R~Fk~~g~s~~~~~~ 230 (291)
T PRK15186 189 IIISDISRKWALKDISDSLYMSCSTLKRKLKQENTSFSEVYL 230 (291)
T ss_pred HHHhCccCCCCHHHHHHHHCcCHHHHHHHHHHcCCCHHHHHH
Confidence 344444 5889999999999999999999998865444443
No 165
>PRK00118 putative DNA-binding protein; Validated
Probab=51.61 E-value=25 Score=34.43 Aligned_cols=29 Identities=17% Similarity=0.052 Sum_probs=24.2
Q ss_pred HHHhhcCCcHHHHHHHcCCChhHHHHHHH
Q 001809 606 VLQQYFSGSLKDAAKSIGVCPTTLKRICR 634 (1010)
Q Consensus 606 ~L~~yF~~pl~eAAk~LGV~~TtLKRiCR 634 (1010)
.+.-+-+++.+|+|+.+||++.|++++-+
T Consensus 27 ~L~y~eg~S~~EIAe~lGIS~~TV~r~L~ 55 (104)
T PRK00118 27 ELYYLDDYSLGEIAEEFNVSRQAVYDNIK 55 (104)
T ss_pred HHHHHcCCCHHHHHHHHCcCHHHHHHHHH
Confidence 34456689999999999999999987755
No 166
>PF04218 CENP-B_N: CENP-B N-terminal DNA-binding domain; InterPro: IPR006695 Centromere Protein B (CENP-B) is a DNA-binding protein localized to the centromere. Within the N-terminal 125 residues, there is a DNA-binding region, which binds to a corresponding 17bp CENP-B box sequence. CENP-B dimers either bind two separate DNA molecules or alternatively, they may bind two CENP-B boxes on one DNA molecule, with the intervening stretch of DNA forming a loop structure. The CENP-B DNA-binding domain consists of two repeating domains, RP1 and RP2. This family corresponds to RP1 has been shown to consist of four helices in a helix-turn-helix structure [].; GO: 0003677 DNA binding, 0000775 chromosome, centromeric region; PDB: 1BW6_A 1HLV_A 2ELH_A.
Probab=51.56 E-value=13 Score=31.85 Aligned_cols=24 Identities=29% Similarity=0.465 Sum_probs=18.0
Q ss_pred CCcHHHHHHHcCCChhHHHHHHHH
Q 001809 612 SGSLKDAAKSIGVCPTTLKRICRQ 635 (1010)
Q Consensus 612 ~~pl~eAAk~LGV~~TtLKRiCR~ 635 (1010)
+.+..++|+.+||+.||+..|.+.
T Consensus 22 g~s~~~ia~~fgv~~sTv~~I~K~ 45 (53)
T PF04218_consen 22 GESKRDIAREFGVSRSTVSTILKN 45 (53)
T ss_dssp TT-HHHHHHHHT--CCHHHHHHHC
T ss_pred CCCHHHHHHHhCCCHHHHHHHHHh
Confidence 457899999999999999988763
No 167
>PRK05022 anaerobic nitric oxide reductase transcription regulator; Provisional
Probab=51.42 E-value=75 Score=38.29 Aligned_cols=31 Identities=19% Similarity=0.411 Sum_probs=28.5
Q ss_pred hhcCCcHHHHHHHcCCChhHHHHHHHHcCCC
Q 001809 609 QYFSGSLKDAAKSIGVCPTTLKRICRQHGIS 639 (1010)
Q Consensus 609 ~yF~~pl~eAAk~LGV~~TtLKRiCR~~GI~ 639 (1010)
+.+++-+.+||+.|||+++||+|..|+|||.
T Consensus 478 ~~~~gn~~~aA~~LGisr~tL~rklk~~gi~ 508 (509)
T PRK05022 478 AQHQGNWAAAARALELDRANLHRLAKRLGLK 508 (509)
T ss_pred HHcCCCHHHHHHHhCCCHHHHHHHHHHcCCC
Confidence 5568889999999999999999999999995
No 168
>PRK05602 RNA polymerase sigma factor; Reviewed
Probab=51.39 E-value=20 Score=36.46 Aligned_cols=28 Identities=29% Similarity=0.284 Sum_probs=24.4
Q ss_pred HHHhhcCCcHHHHHHHcCCChhHHHHHH
Q 001809 606 VLQQYFSGSLKDAAKSIGVCPTTLKRIC 633 (1010)
Q Consensus 606 ~L~~yF~~pl~eAAk~LGV~~TtLKRiC 633 (1010)
.|+-+.+++.+|+|+.||+++.|+|.+-
T Consensus 138 ~l~~~~g~s~~EIA~~lgis~~tV~~~l 165 (186)
T PRK05602 138 VLQYYQGLSNIEAAAVMDISVDALESLL 165 (186)
T ss_pred hHHHhcCCCHHHHHHHhCcCHHHHHHHH
Confidence 4555679999999999999999999875
No 169
>PRK10072 putative transcriptional regulator; Provisional
Probab=51.34 E-value=20 Score=34.49 Aligned_cols=33 Identities=18% Similarity=0.214 Sum_probs=29.0
Q ss_pred HHHHHhhcCCcHHHHHHHcCCChhHHHHHHHHc
Q 001809 604 LSVLQQYFSGSLKDAAKSIGVCPTTLKRICRQH 636 (1010)
Q Consensus 604 l~~L~~yF~~pl~eAAk~LGV~~TtLKRiCR~~ 636 (1010)
+..|+.--+++++++|+.|||+.+|+.+..+..
T Consensus 38 ik~LR~~~glTQ~elA~~lGvS~~TVs~WE~G~ 70 (96)
T PRK10072 38 FEQLRKGTGLKIDDFARVLGVSVAMVKEWESRR 70 (96)
T ss_pred HHHHHHHcCCCHHHHHHHhCCCHHHHHHHHcCC
Confidence 567778889999999999999999999987743
No 170
>PRK12538 RNA polymerase sigma factor; Provisional
Probab=51.30 E-value=23 Score=38.22 Aligned_cols=43 Identities=12% Similarity=0.155 Sum_probs=31.8
Q ss_pred HHHhhcCCcHHHHHHHcCCChhHHHHHHHHcCCCCCcchhhhhhHHHHHHHH
Q 001809 606 VLQQYFSGSLKDAAKSIGVCPTTLKRICRQHGISRWPSRKINKVNRSLKKIQ 657 (1010)
Q Consensus 606 ~L~~yF~~pl~eAAk~LGV~~TtLKRiCR~~GI~RWP~Rki~sl~~~i~~l~ 657 (1010)
.|+-+-+++.+|+|+.|||+..|+|.+.+ |-+++|.+.+.+.+
T Consensus 181 ~L~~~eg~s~~EIA~~Lgis~~tVk~~l~---------RAr~kLr~~l~~~~ 223 (233)
T PRK12538 181 ILSYHENMSNGEIAEVMDTTVAAVESLLK---------RGRQQLRDLLRRHE 223 (233)
T ss_pred hhHHhcCCCHHHHHHHHCcCHHHHHHHHH---------HHHHHHHHHHHHhh
Confidence 45667899999999999999999998763 34455555444333
No 171
>TIGR02947 SigH_actino RNA polymerase sigma-70 factor, TIGR02947 family. This group of sigma factors are members of the sigma-70 family (TIGR02937). They and appear by homology, tree building, bidirectional best hits and (with the exception of a paralog in Thermobifida fusca YX) one-to-a-genome distribution, to represent a conserved family. This family is restricted to the Actinobacteria and each gene examined is followed by an anti-sigma factor in an apparent operon.
Probab=51.25 E-value=22 Score=36.56 Aligned_cols=28 Identities=18% Similarity=0.057 Sum_probs=24.0
Q ss_pred HHhhcCCcHHHHHHHcCCChhHHHHHHH
Q 001809 607 LQQYFSGSLKDAAKSIGVCPTTLKRICR 634 (1010)
Q Consensus 607 L~~yF~~pl~eAAk~LGV~~TtLKRiCR 634 (1010)
|+-+.+++.+|+|+.|||++.|+|.+..
T Consensus 142 L~~~~g~s~~EIA~~lgis~~tVk~~l~ 169 (193)
T TIGR02947 142 LADVEGFAYKEIAEIMGTPIGTVMSRLH 169 (193)
T ss_pred ehhhcCCCHHHHHHHHCCCHHHHHHHHH
Confidence 4556799999999999999999998743
No 172
>PF13011 LZ_Tnp_IS481: leucine-zipper of insertion element IS481
Probab=51.02 E-value=15 Score=34.88 Aligned_cols=25 Identities=20% Similarity=0.142 Sum_probs=22.5
Q ss_pred CCcHHHHHHHcCCChhHHHHHHHHc
Q 001809 612 SGSLKDAAKSIGVCPTTLKRICRQH 636 (1010)
Q Consensus 612 ~~pl~eAAk~LGV~~TtLKRiCR~~ 636 (1010)
..|+.+||+.+|||..|.+|.-.++
T Consensus 25 g~~~a~aA~~~gVS~~Ta~kW~~Ry 49 (85)
T PF13011_consen 25 GWPVAHAAAEFGVSRRTAYKWLARY 49 (85)
T ss_pred CCcHHHHHHHhCCCHHHHHHHHHHH
Confidence 5899999999999999999987665
No 173
>PRK09646 RNA polymerase sigma factor SigK; Reviewed
Probab=50.72 E-value=19 Score=37.17 Aligned_cols=28 Identities=21% Similarity=0.184 Sum_probs=24.1
Q ss_pred HHHhhcCCcHHHHHHHcCCChhHHHHHH
Q 001809 606 VLQQYFSGSLKDAAKSIGVCPTTLKRIC 633 (1010)
Q Consensus 606 ~L~~yF~~pl~eAAk~LGV~~TtLKRiC 633 (1010)
.|+-+.+++.+|+|+.|||+..++|.+.
T Consensus 152 ~l~~~~~~s~~EIA~~Lgis~~tVk~~l 179 (194)
T PRK09646 152 TLAYYGGLTYREVAERLAVPLGTVKTRM 179 (194)
T ss_pred HHHHHcCCCHHHHHHHhCCChHhHHHHH
Confidence 4556679999999999999999998765
No 174
>cd04773 HTH_TioE_rpt2 Second Helix-Turn-Helix DNA binding domain of the regulatory protein TioE. Putative helix-turn-helix (HTH) regulatory protein, TioE, and related proteins. TioE is part of the thiocoraline gene cluster, which is involved in the biosynthesis of the antitumor thiocoraline from the marine actinomycete, Micromonospora. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements. Proteins in this family are unique within the MerR superfamily in that they are composed of just two adjacent MerR-like N-terminal domains; this CD mainly contains the C-terminal or second repeat (rpt2) of these tandem MerR-like domain proteins.
Probab=50.52 E-value=15 Score=35.34 Aligned_cols=25 Identities=28% Similarity=0.530 Sum_probs=22.4
Q ss_pred CcHHHHHHHcCCChhHHHHHHHHcCC
Q 001809 613 GSLKDAAKSIGVCPTTLKRICRQHGI 638 (1010)
Q Consensus 613 ~pl~eAAk~LGV~~TtLKRiCR~~GI 638 (1010)
|++.|+|+.+||++.||....++ |+
T Consensus 1 ~~i~eva~~~gvs~~tlR~ye~~-Gl 25 (108)
T cd04773 1 MTIGELAHLLGVPPSTLRHWEKE-GL 25 (108)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHC-CC
Confidence 57899999999999999999885 64
No 175
>TIGR01321 TrpR trp operon repressor, proteobacterial. This model represents TrpR, the repressor of the trp operon. It is found so far only in the gamma subdivision of the proteobacteria and in Chlamydia trachomatis. All members belong to species capable of tryptophan biosynthesis.
Probab=50.24 E-value=14 Score=35.67 Aligned_cols=26 Identities=23% Similarity=0.256 Sum_probs=24.0
Q ss_pred CCcHHHHHHHcCCChhHHHHHHHHcC
Q 001809 612 SGSLKDAAKSIGVCPTTLKRICRQHG 637 (1010)
Q Consensus 612 ~~pl~eAAk~LGV~~TtLKRiCR~~G 637 (1010)
.+|++|+|+.||||.+|+-|.-|-+.
T Consensus 55 ~~tQrEIa~~lGiS~atIsR~sn~lk 80 (94)
T TIGR01321 55 NMSQREIASKLGVSIATITRGSNNLK 80 (94)
T ss_pred CCCHHHHHHHhCCChhhhhHHHhhcc
Confidence 58999999999999999999988776
No 176
>PF01498 HTH_Tnp_Tc3_2: Transposase; InterPro: IPR002492 Transposase proteins are necessary for efficient DNA transposition. This family includes the amino-terminal region of Tc1, Tc1A, Tc1B and Tc2B transposases of Caenorhabditis elegans. The region encompasses the specific DNA binding and second DNA recognition domains as well as an amino-terminal region of the catalytic domain of Tc3 as described in []. Tc3 is a member of the Tc1/mariner family of transposable elements. This entry also includes histone-lysine N-methyltransferase SETMAR, which is a SET domain and mariner transposase fusion gene-containing protein. This histone methyltransferase has sequence-specific DNA-binding activity and recognises the 19-mer core of the 5'-terminal inverted repeats (TIRs) of the Hsmar1 element. This protein has DNA nicking activity, and has in vivo end joining activity and may mediate genomic integration of foreign DNA [, , , ]. 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, 0015074 DNA integration; PDB: 3K9K_B 3F2K_B 3K9J_B 1U78_A.
Probab=50.17 E-value=8.4 Score=33.87 Aligned_cols=37 Identities=24% Similarity=0.377 Sum_probs=25.6
Q ss_pred CcHHHHHHHc-----CCChhHHHHHHHHcCCCCCcchhhhhh
Q 001809 613 GSLKDAAKSI-----GVCPTTLKRICRQHGISRWPSRKINKV 649 (1010)
Q Consensus 613 ~pl~eAAk~L-----GV~~TtLKRiCR~~GI~RWP~Rki~sl 649 (1010)
.+.++++.+| +||.+|+.|+.++.|+..|.-++.--|
T Consensus 14 ~s~~~i~~~l~~~~~~vS~~TI~r~L~~~g~~~~~~~~kP~L 55 (72)
T PF01498_consen 14 ISAREIAQELQEAGISVSKSTIRRRLREAGLKKRKARKKPFL 55 (72)
T ss_dssp --HHHHHHHT---T--S-HHHHHHHHHHT-EEEETTEEEES-
T ss_pred CCHHHHHHHHHHccCCcCHHHHHHHHHHcCccccccccCCCC
Confidence 5677777777 899999999999999988877764443
No 177
>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=49.93 E-value=14 Score=33.06 Aligned_cols=29 Identities=28% Similarity=0.559 Sum_probs=23.3
Q ss_pred CCcHHHHHHHcCCChhHHHHHHHHcCCCCCcc
Q 001809 612 SGSLKDAAKSIGVCPTTLKRICRQHGISRWPS 643 (1010)
Q Consensus 612 ~~pl~eAAk~LGV~~TtLKRiCR~~GI~RWP~ 643 (1010)
.++++|+|+.|||+..|+.+--.+. +|..
T Consensus 22 ~i~lkdIA~~Lgvs~~tIr~WK~~d---kW~~ 50 (60)
T PF10668_consen 22 KIKLKDIAEKLGVSESTIRKWKSRD---KWDE 50 (60)
T ss_pred CccHHHHHHHHCCCHHHHHHHhhhc---chhh
Confidence 5899999999999999998765553 3554
No 178
>PRK15043 transcriptional regulator MirA; Provisional
Probab=49.65 E-value=16 Score=40.50 Aligned_cols=32 Identities=25% Similarity=0.386 Sum_probs=27.9
Q ss_pred CCcHHHHHHHcCCChhHHHHHHHHcCCCCCcch
Q 001809 612 SGSLKDAAKSIGVCPTTLKRICRQHGISRWPSR 644 (1010)
Q Consensus 612 ~~pl~eAAk~LGV~~TtLKRiCR~~GI~RWP~R 644 (1010)
.+++.|+|+.+||++.||....|+.|+-. |.|
T Consensus 3 ~ytIgeVA~~~GVs~~TLR~wErr~GLL~-P~R 34 (243)
T PRK15043 3 LYTIGEVALLCDINPVTLRAWQRRYGLLK-PQR 34 (243)
T ss_pred CCCHHHHHHHHCcCHHHHHHHHHhcCCCC-Ccc
Confidence 47899999999999999999999988755 654
No 179
>PF07638 Sigma70_ECF: ECF sigma factor
Probab=49.30 E-value=19 Score=37.40 Aligned_cols=31 Identities=23% Similarity=0.365 Sum_probs=26.7
Q ss_pred HHHhhcCCcHHHHHHHcCCChhHHHHHHHHc
Q 001809 606 VLQQYFSGSLKDAAKSIGVCPTTLKRICRQH 636 (1010)
Q Consensus 606 ~L~~yF~~pl~eAAk~LGV~~TtLKRiCR~~ 636 (1010)
+|+.+=+++.+|+|+.||||+.|++|..+..
T Consensus 145 ~l~~~~Gls~~EIA~~lgiS~~tV~r~l~~a 175 (185)
T PF07638_consen 145 ELRFFEGLSVEEIAERLGISERTVRRRLRRA 175 (185)
T ss_pred HHHHHCCCCHHHHHHHHCcCHHHHHHHHHHH
Confidence 4555568999999999999999999988765
No 180
>PRK09649 RNA polymerase sigma factor SigC; Reviewed
Probab=49.27 E-value=18 Score=37.11 Aligned_cols=29 Identities=28% Similarity=0.240 Sum_probs=25.9
Q ss_pred HHHhhcCCcHHHHHHHcCCChhHHHHHHH
Q 001809 606 VLQQYFSGSLKDAAKSIGVCPTTLKRICR 634 (1010)
Q Consensus 606 ~L~~yF~~pl~eAAk~LGV~~TtLKRiCR 634 (1010)
.|+-+.+++.+|+|+.||+++.|+|...+
T Consensus 140 ~L~~~~g~s~~EIA~~lgis~~tVk~~l~ 168 (185)
T PRK09649 140 LLTQLLGLSYADAAAVCGCPVGTIRSRVA 168 (185)
T ss_pred hhHHHcCCCHHHHHHHHCCCHHHHHHHHH
Confidence 66778899999999999999999998764
No 181
>smart00530 HTH_XRE Helix-turn-helix XRE-family like proteins.
Probab=49.08 E-value=46 Score=25.24 Aligned_cols=30 Identities=27% Similarity=0.310 Sum_probs=24.1
Q ss_pred HHHHhhcCCcHHHHHHHcCCChhHHHHHHH
Q 001809 605 SVLQQYFSGSLKDAAKSIGVCPTTLKRICR 634 (1010)
Q Consensus 605 ~~L~~yF~~pl~eAAk~LGV~~TtLKRiCR 634 (1010)
..++..-+++.++.|+.+||+..++.++.+
T Consensus 3 ~~~~~~~~~s~~~la~~~~i~~~~i~~~~~ 32 (56)
T smart00530 3 KELREEKGLTQEELAEKLGVSRSTLSRIEN 32 (56)
T ss_pred HHHHHHcCCCHHHHHHHhCCCHHHHHHHHC
Confidence 344555678899999999999999988765
No 182
>PRK12545 RNA polymerase sigma factor; Provisional
Probab=48.70 E-value=29 Score=36.16 Aligned_cols=28 Identities=4% Similarity=0.235 Sum_probs=23.7
Q ss_pred HHHhhcCCcHHHHHHHcCCChhHHHHHH
Q 001809 606 VLQQYFSGSLKDAAKSIGVCPTTLKRIC 633 (1010)
Q Consensus 606 ~L~~yF~~pl~eAAk~LGV~~TtLKRiC 633 (1010)
.|+-+.+++.+|+|+.||+++.|+|.+-
T Consensus 149 ~L~~~eg~s~~EIA~~lgis~~tVk~~l 176 (201)
T PRK12545 149 MMREFLDFEIDDICTELTLTANHCSVLL 176 (201)
T ss_pred HHHHHcCCCHHHHHHHHCcCHHHHHHHH
Confidence 4555678999999999999999999763
No 183
>PRK15090 DNA-binding transcriptional regulator KdgR; Provisional
Probab=48.59 E-value=91 Score=33.97 Aligned_cols=137 Identities=12% Similarity=0.071 Sum_probs=0.0
Q ss_pred CCCHHHHHHHHHHHHHHhcCCCeeEEEEeeeccCCeeeeeeCCCCcccchhhhHHhhccceeeeccCCCCCCCCCCCccc
Q 001809 162 PPSLDEKMLRALSFFKLSSGGGILAQVWVPRKQGDDYILSTSDQPYLLDQMLAGYREVSRKFTFSAEAKPGTFLGLPGRV 241 (1010)
Q Consensus 162 ~~svkerm~~AL~~~kes~~~~~L~QVWvP~~~g~~~vLsT~~qP~~ld~~L~~yR~vS~~f~Fs~~~~~~~~~GLPGRV 241 (1010)
...+.+...-.|+-|.+.++.-+.+-||- |+.++....-.+-. ...+.+..........+..|||
T Consensus 83 ~~~l~~~a~p~l~~La~~~~etv~L~v~~----g~~~v~l~~~~~~~-----------~~~~~~~~G~~~Pl~~tA~Gka 147 (257)
T PRK15090 83 NVDLIRSADIQMREISRLTKETIHLGALD----EDSIVYIHKIDSMY-----------NLRMYSRIGRRNPLYSTAIGKV 147 (257)
T ss_pred hCcHHHHHHHHHHHHHHHhCCeEEEEEEE----CCEEEEEEEecCCC-----------ceEEEccCCCccchhhhhHHHH
Q ss_pred ccCCCC-------------------------cccccccccCcccccchhhHHhcCCceEEEEeeecCCCCceEEEEEEee
Q 001809 242 FSSKVP-------------------------EWTSNVAYYNEAEYARVTHAVNHAVRSCIALPVFQFPEISCSAVLEIVS 296 (1010)
Q Consensus 242 F~s~~P-------------------------EWTpnV~~y~~~EYpR~~~A~~~~VrGsLAlPVf~~~s~~ClAVlElV~ 296 (1010)
|+...| ++-..+..-+..-|..-..-...|| .+||+|||++.... +|.|=++.
T Consensus 148 lLA~~~~~~~~~~l~~~~~~~~t~~t~~~~~~l~~~l~~iR~~Gya~~~~e~~~gv-~~vA~Pv~~~~g~~-~aalsv~~ 225 (257)
T PRK15090 148 LLAWRDRDEVREILSGVEFKRSTEKTITSTEALLPVLDQVREQGYGEDNEEQEEGL-RCIAVPVFDRFGVV-IAGLSISF 225 (257)
T ss_pred HHhCCCHHHHHHHHccCCCCcCCCCCCCCHHHHHHHHHHHHHhCCCccccccccCC-EEEEEEEECCCCCE-EEEEEEEe
Q ss_pred ecccCCchHHHHHHHHHhhh
Q 001809 297 VKEKPNFDAEIENICNALQA 316 (1010)
Q Consensus 297 t~ek~~f~~E~e~vc~ALqa 316 (1010)
...... ....+.+..+|++
T Consensus 226 p~~r~~-~~~~~~~~~~l~~ 244 (257)
T PRK15090 226 PTLRFS-EERKQEYVAMLHT 244 (257)
T ss_pred ehhhcC-HHHHHHHHHHHHH
No 184
>PRK09645 RNA polymerase sigma factor SigL; Provisional
Probab=48.46 E-value=20 Score=35.92 Aligned_cols=29 Identities=24% Similarity=0.181 Sum_probs=24.4
Q ss_pred HHHhhcCCcHHHHHHHcCCChhHHHHHHH
Q 001809 606 VLQQYFSGSLKDAAKSIGVCPTTLKRICR 634 (1010)
Q Consensus 606 ~L~~yF~~pl~eAAk~LGV~~TtLKRiCR 634 (1010)
.|+-+-+++.+|+|+.||++..|+|...+
T Consensus 128 ~L~~~~g~s~~EIA~~lgis~~tV~~~l~ 156 (173)
T PRK09645 128 VRSYYRGWSTAQIAADLGIPEGTVKSRLH 156 (173)
T ss_pred HHHHHcCCCHHHHHHHHCcCHHHHHHHHH
Confidence 34455699999999999999999998755
No 185
>cd01106 HTH_TipAL-Mta Helix-Turn-Helix DNA binding domain of the transcription regulators TipAL, Mta, and SkgA. Helix-turn-helix (HTH) TipAL, Mta, and SkgA transcription regulators, and related proteins, N-terminal domain. TipAL regulates resistance to and activation by numerous cyclic thiopeptide antibiotics, such as thiostrepton. Mta is a global transcriptional regulator; the N-terminal DNA-binding domain of Mta interacts directly with the promoters of mta, bmr, blt, and ydfK, and induces transcription of these multidrug-efflux transport genes. SkgA has been shown to control stationary-phase expression of catalase-peroxidase in Caulobacter crescentus. These proteins are comprised of distinct domains that harbor an N-terminal active (DNA-binding) site and a regulatory (effector-binding) site. The conserved N-terminal domain of these transcription regulators contains winged HTH motifs that mediate DNA binding. These proteins share the N-terminal DNA binding domain with other transcrip
Probab=48.16 E-value=30 Score=32.81 Aligned_cols=25 Identities=28% Similarity=0.282 Sum_probs=21.1
Q ss_pred CcHHHHHHHcCCChhHHHHHHHHcCC
Q 001809 613 GSLKDAAKSIGVCPTTLKRICRQHGI 638 (1010)
Q Consensus 613 ~pl~eAAk~LGV~~TtLKRiCR~~GI 638 (1010)
++++|+|+.+||+++||+...+ .|+
T Consensus 1 ~ti~eva~~~gvs~~tlR~ye~-~Gl 25 (103)
T cd01106 1 YTVGEVAKLTGVSVRTLHYYDE-IGL 25 (103)
T ss_pred CCHHHHHHHHCcCHHHHHHHHH-CCC
Confidence 4789999999999999997766 454
No 186
>cd00196 UBQ Ubiquitin-like proteins. Ubiquitin homologs; Includes ubiquitin and ubiquitin-like proteins. Ubiquitin-mediated proteolysis is part of the regulated turnover of proteins required for controlling cell cycle progression. Other family members are protein modifiers that perform a wide range of functions. Ubiquitination usually results in a covalent bond between the C-terminus of ubiquitin and the epsilon-amino group of a substrate lysine. The three-step mechanism requires an activating enzyme (E1) that forms a thiol ester with the C-terminal carboxy group, a conjugating enzyme (E2) that transiently carries the activated ubiquitin molecule as a thiol ester, and a ligase (E3) that transfers the activated ubiquitin from the E2 to the substrate lysine residue. In poly-ubiquitination, ubiquitin itself is the substrate.
Probab=48.11 E-value=36 Score=26.06 Aligned_cols=38 Identities=16% Similarity=0.171 Sum_probs=30.9
Q ss_pred CCCeEEEEeCCCcChHHHHHHHHHHcCcccceeeeEee
Q 001809 910 KEDIIRFKFDPSAGCFQLYEEVARRLKLQNGTFQLKYL 947 (1010)
Q Consensus 910 ~~d~iRF~~~~s~g~~~L~~EIakRf~l~~~~f~lKYl 947 (1010)
+.....+.+.+..-+.+|++.|.+++++....+.|.|-
T Consensus 6 ~~~~~~~~~~~~~tv~~l~~~i~~~~~~~~~~~~l~~~ 43 (69)
T cd00196 6 DGKTVELLVPSGTTVADLKEKLAKKLGLPPEQQRLLVN 43 (69)
T ss_pred CCCEEEEEcCCCCcHHHHHHHHHHHHCcChHHeEEEEC
Confidence 35677788889999999999999999977776777553
No 187
>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=48.04 E-value=18 Score=25.20 Aligned_cols=21 Identities=33% Similarity=0.507 Sum_probs=18.7
Q ss_pred CCcHHHHHHHcCCChhHHHHH
Q 001809 612 SGSLKDAAKSIGVCPTTLKRI 632 (1010)
Q Consensus 612 ~~pl~eAAk~LGV~~TtLKRi 632 (1010)
+.+..++|+.+||+.+|+.++
T Consensus 21 ~~s~~~ia~~~~is~~tv~~~ 41 (42)
T cd00569 21 GESVAEIARRLGVSRSTLYRY 41 (42)
T ss_pred CCCHHHHHHHHCCCHHHHHHh
Confidence 569999999999999999875
No 188
>cd04789 HTH_Cfa Helix-Turn-Helix DNA binding domain of the Cfa transcription regulator. Putative helix-turn-helix (HTH) MerR-like transcription regulator; the N-terminal domain of Cfa, a cyclopropane fatty acid synthase and other related methyltransferases. Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of 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=47.55 E-value=19 Score=34.35 Aligned_cols=27 Identities=19% Similarity=0.281 Sum_probs=23.4
Q ss_pred CcHHHHHHHcCCChhHHHHHHHHcCCCC
Q 001809 613 GSLKDAAKSIGVCPTTLKRICRQHGISR 640 (1010)
Q Consensus 613 ~pl~eAAk~LGV~~TtLKRiCR~~GI~R 640 (1010)
+++.|+|+.+||++.||....++ |+-.
T Consensus 2 ~~i~eva~~~gvs~~tlR~ye~~-Gll~ 28 (102)
T cd04789 2 YTISELAEKAGISRSTLLYYEKL-GLIT 28 (102)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHC-CCCC
Confidence 68999999999999999988886 7543
No 189
>cd04775 HTH_Cfa-like Helix-Turn-Helix DNA binding domain of Cfa-like transcription regulators. Putative helix-turn-helix (HTH) MerR-like transcription regulators; the HTH domain of Cfa, a cyclopropane fatty acid synthase, and other related methyltransferases, as well as, the N-terminal domain of a conserved, uncharacterized ~172 a.a. protein. Based on sequence similarity of the N-terminal domain, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of 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 dissimil
Probab=47.54 E-value=18 Score=34.35 Aligned_cols=26 Identities=19% Similarity=0.250 Sum_probs=22.4
Q ss_pred CcHHHHHHHcCCChhHHHHHHHHcCCC
Q 001809 613 GSLKDAAKSIGVCPTTLKRICRQHGIS 639 (1010)
Q Consensus 613 ~pl~eAAk~LGV~~TtLKRiCR~~GI~ 639 (1010)
+++.|+|+.+||++.||....++ |+-
T Consensus 2 ~~i~eva~~~gvs~~tLR~ye~~-Gll 27 (102)
T cd04775 2 YTIGQMSRKFGVSRSTLLYYESI-GLI 27 (102)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHC-CCC
Confidence 68999999999999999776665 865
No 190
>PRK12533 RNA polymerase sigma factor; Provisional
Probab=47.33 E-value=19 Score=38.50 Aligned_cols=30 Identities=20% Similarity=0.081 Sum_probs=25.8
Q ss_pred HHHhhcCCcHHHHHHHcCCChhHHHHHHHH
Q 001809 606 VLQQYFSGSLKDAAKSIGVCPTTLKRICRQ 635 (1010)
Q Consensus 606 ~L~~yF~~pl~eAAk~LGV~~TtLKRiCR~ 635 (1010)
.|.-+.+++.+|+|+.|||++.|+|.+.++
T Consensus 144 ~L~y~eg~s~~EIAe~LgiS~~tVk~~L~R 173 (216)
T PRK12533 144 VLRELEDMSYREIAAIADVPVGTVMSRLAR 173 (216)
T ss_pred hhHHhcCCCHHHHHHHHCCCHHHHHHHHHH
Confidence 455677999999999999999999987763
No 191
>PF02309 AUX_IAA: AUX/IAA family; InterPro: IPR003311 The Aux/IAA family of genes are key regulators of auxin-modified gene expression []. The plant hormone auxin (indole-3-acetic acid, IAA) regulates diverse cellular and developmental responses in plants, including cell division, expansion, differentiation and patterning of embryo responses []. Auxin can regulate the gene expression of several families, including GH3 and SAUR, as well as Aux/IAA itself. The Aux/IAA proteins act as repressors of auxin-induced gene expression, possibly through modulating the activity of DNA-binding auxin response factors (ARFs) (IPR010525 from INTERPRO). Aux/IAA and ARF are thought to interact through C-terminal protein-protein interaction domains found in both Aux/IAA and ARF. Recent evidence suggests that Aux/IAA proteins can also mediate light responses []. Some members of the AUX/IAA family are longer and contain an N-terminal DNA binding domain [] and may have an early function in the establishment of vascular and body patterns in embryonic and post-embryonic development in some plants.; GO: 0006355 regulation of transcription, DNA-dependent, 0005634 nucleus; PDB: 2P1N_F 2P1Q_C 2P1O_C.
Probab=47.22 E-value=6.3 Score=42.24 Aligned_cols=68 Identities=21% Similarity=0.390 Sum_probs=0.0
Q ss_pred eEEEEEEcCCCeEE--EEeCCCcChHHHHHHHHHHc---Ccc----------------cc-eeeeEeecCCCCeEEEecC
Q 001809 902 KIIVKATYKEDIIR--FKFDPSAGCFQLYEEVARRL---KLQ----------------NG-TFQLKYLDDEEEWVMLVSD 959 (1010)
Q Consensus 902 ~~~vKaty~~d~iR--F~~~~s~g~~~L~~EIakRf---~l~----------------~~-~f~lKYlDDd~EWVlLtcD 959 (1010)
..-||+.--+.-|= +-|..-.||.+|..++.+-| .|. ++ .|.|=|-|.|++|+| +-|
T Consensus 109 ~~~vKV~mdG~~igRkVDL~~~~sY~~L~~~L~~MF~~~~i~~~~~~~~~~~~~~~~~~~~~~~l~Y~D~egd~ml-vGD 187 (215)
T PF02309_consen 109 RSYVKVNMDGVPIGRKVDLSAYSSYEELSSALEKMFSCFSIEQCGSHGLNESGLLDLLNGSEYVLVYEDKEGDWML-VGD 187 (215)
T ss_dssp --------------------------------------------------------------------------------
T ss_pred CceeEEEecCcccceecCHHHhhCHHHHHHHHHHhcCCCCccccccccccchhhccccCCcceeEEEECCCCCEEE-ecC
Confidence 56778766552221 22334559999999999999 554 22 489999999999975 456
Q ss_pred CcHHHHHHHHh
Q 001809 960 SDLQECFDILE 970 (1010)
Q Consensus 960 aDL~EC~di~~ 970 (1010)
---+|=+..+|
T Consensus 188 ~PW~~F~~~vk 198 (215)
T PF02309_consen 188 VPWEEFVKSVK 198 (215)
T ss_dssp -----------
T ss_pred CCHHHHHHHhh
Confidence 66666555554
No 192
>cd01279 HTH_HspR-like Helix-Turn-Helix DNA binding domain of HspR-like transcription regulators. Helix-turn-helix (HTH) transcription regulator HspR and related proteins, N-terminal domain. Heat shock protein regulators (HspR) have been shown to regulate expression of specific regulons in response to high temperature or high osmolarity in Streptomyces and Helicobacter, respectively. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules.
Probab=47.14 E-value=18 Score=34.26 Aligned_cols=25 Identities=32% Similarity=0.462 Sum_probs=22.2
Q ss_pred CcHHHHHHHcCCChhHHHHHHHHcCC
Q 001809 613 GSLKDAAKSIGVCPTTLKRICRQHGI 638 (1010)
Q Consensus 613 ~pl~eAAk~LGV~~TtLKRiCR~~GI 638 (1010)
+++.|+|+.+||++.||....| .|+
T Consensus 2 ~~i~eva~~~gVs~~tLR~ye~-~Gl 26 (98)
T cd01279 2 YPISVAAELLGIHPQTLRVYDR-LGL 26 (98)
T ss_pred cCHHHHHHHHCcCHHHHHHHHH-CCC
Confidence 5899999999999999998876 665
No 193
>smart00344 HTH_ASNC helix_turn_helix ASNC type. AsnC: an autogenously regulated activator of asparagine synthetase A transcription in Escherichia coli
Probab=47.09 E-value=25 Score=32.93 Aligned_cols=33 Identities=30% Similarity=0.400 Sum_probs=28.2
Q ss_pred HHHHHhhcCCcHHHHHHHcCCChhHHHHHHHHc
Q 001809 604 LSVLQQYFSGSLKDAAKSIGVCPTTLKRICRQH 636 (1010)
Q Consensus 604 l~~L~~yF~~pl~eAAk~LGV~~TtLKRiCR~~ 636 (1010)
+..|++.-.+|..++|+.||++++|+.|+.+++
T Consensus 9 l~~L~~~~~~~~~~la~~l~~s~~tv~~~l~~L 41 (108)
T smart00344 9 LEELQKDARISLAELAKKVGLSPSTVHNRVKRL 41 (108)
T ss_pred HHHHHHhCCCCHHHHHHHHCcCHHHHHHHHHHH
Confidence 456667778999999999999999999888766
No 194
>PRK12529 RNA polymerase sigma factor; Provisional
Probab=46.80 E-value=22 Score=36.24 Aligned_cols=29 Identities=17% Similarity=0.240 Sum_probs=24.8
Q ss_pred HHHhhcCCcHHHHHHHcCCChhHHHHHHH
Q 001809 606 VLQQYFSGSLKDAAKSIGVCPTTLKRICR 634 (1010)
Q Consensus 606 ~L~~yF~~pl~eAAk~LGV~~TtLKRiCR 634 (1010)
.|+-+-+++.+|+|+.|||++.|+|.+.+
T Consensus 137 ~L~~~~g~s~~EIA~~lgis~~tVk~~l~ 165 (178)
T PRK12529 137 LMATLDGMKQKDIAQALDIALPTVKKYIH 165 (178)
T ss_pred HHHHHcCCCHHHHHHHHCCCHHHHHHHHH
Confidence 45556689999999999999999998765
No 195
>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=46.72 E-value=16 Score=30.43 Aligned_cols=24 Identities=21% Similarity=0.401 Sum_probs=21.3
Q ss_pred CcHHHHHHHcCCChhHHHHHHHHc
Q 001809 613 GSLKDAAKSIGVCPTTLKRICRQH 636 (1010)
Q Consensus 613 ~pl~eAAk~LGV~~TtLKRiCR~~ 636 (1010)
+++.|+|+.+|+..+|+.|+++.+
T Consensus 19 ~t~~eia~~~gl~~stv~r~L~tL 42 (52)
T PF09339_consen 19 LTLSEIARALGLPKSTVHRLLQTL 42 (52)
T ss_dssp EEHHHHHHHHTS-HHHHHHHHHHH
T ss_pred CCHHHHHHHHCcCHHHHHHHHHHH
Confidence 689999999999999999999865
No 196
>PRK12543 RNA polymerase sigma factor; Provisional
Probab=46.71 E-value=45 Score=33.93 Aligned_cols=48 Identities=15% Similarity=0.144 Sum_probs=33.7
Q ss_pred HHHhhcCCcHHHHHHHcCCChhHHHHHHHHcCCCCCcchhhhhhHHHHHHHHHHHhh
Q 001809 606 VLQQYFSGSLKDAAKSIGVCPTTLKRICRQHGISRWPSRKINKVNRSLKKIQTVLNS 662 (1010)
Q Consensus 606 ~L~~yF~~pl~eAAk~LGV~~TtLKRiCR~~GI~RWP~Rki~sl~~~i~~l~~~i~s 662 (1010)
.|+-+-+++.+|+|+.|||+..|+|..-. |-++.|.+.|.++..-+..
T Consensus 127 ~l~~~e~~s~~EIA~~lgis~~tV~~~l~---------ra~~~Lr~~l~~~~~~~~~ 174 (179)
T PRK12543 127 ILRYLHDYSQEEIAQLLQIPIGTVKSRIH---------AALKKLRQKEQIEEIFLGE 174 (179)
T ss_pred HHHHHccCCHHHHHHHHCCCHHHHHHHHH---------HHHHHHHHHHHHHHHHHhh
Confidence 44455799999999999999999886543 3355566666665555443
No 197
>TIGR02999 Sig-70_X6 RNA polymerase sigma factor, TIGR02999 family. This group of sigma factors are members of the sigma-70 family (TIGR02937) and are found in a variety of species including Rhodopirellula baltica which encodes a paralogous group of five.
Probab=46.67 E-value=22 Score=35.81 Aligned_cols=30 Identities=23% Similarity=0.292 Sum_probs=24.6
Q ss_pred HHHhhcCCcHHHHHHHcCCChhHHHHHHHH
Q 001809 606 VLQQYFSGSLKDAAKSIGVCPTTLKRICRQ 635 (1010)
Q Consensus 606 ~L~~yF~~pl~eAAk~LGV~~TtLKRiCR~ 635 (1010)
.|+-+-+++.+|+|+.|||++.|+|.+.++
T Consensus 144 ~l~~~~g~s~~EIA~~lgis~~tVk~~l~R 173 (183)
T TIGR02999 144 ELRFFAGLTVEEIAELLGVSVRTVERDWRF 173 (183)
T ss_pred HHHHHcCCCHHHHHHHhCCCHHHHHHHHHH
Confidence 344455799999999999999999987654
No 198
>PRK09642 RNA polymerase sigma factor SigW; Reviewed
Probab=46.60 E-value=23 Score=35.06 Aligned_cols=29 Identities=10% Similarity=-0.062 Sum_probs=24.8
Q ss_pred HHHhhcCCcHHHHHHHcCCChhHHHHHHH
Q 001809 606 VLQQYFSGSLKDAAKSIGVCPTTLKRICR 634 (1010)
Q Consensus 606 ~L~~yF~~pl~eAAk~LGV~~TtLKRiCR 634 (1010)
.|.-+.+++.+|+|+.|||+..|+|.+..
T Consensus 116 ~l~~~~g~s~~EIA~~lgis~~tV~~~l~ 144 (160)
T PRK09642 116 LAHYLEEKSYQEIALQEKIEVKTVEMKLY 144 (160)
T ss_pred HHHHHhCCCHHHHHHHHCCCHHHHHHHHH
Confidence 45566799999999999999999997754
No 199
>TIGR02392 rpoH_proteo alternative sigma factor RpoH. A sigma factor is a DNA-binding protein protein that binds to the DNA-directed RNA polymerase core to produce the holoenzyme capable of initiating transcription at specific sites. Different sigma factors act in vegetative growth, heat shock, extracytoplasmic functions (ECF), etc. This model represents the clade of sigma factors called RpoH and further restricted to the Proteobacteria. This protein may be called sigma-32, sigma factor H, heat shock sigma factor, and alternative sigma factor RpoH. Note that in some species the single locus rpoH may be replaced by two or more differentially regulated stress response sigma factors.
Probab=46.48 E-value=21 Score=39.24 Aligned_cols=30 Identities=17% Similarity=0.406 Sum_probs=24.7
Q ss_pred HHHhhc----CCcHHHHHHHcCCChhHHHHHHHH
Q 001809 606 VLQQYF----SGSLKDAAKSIGVCPTTLKRICRQ 635 (1010)
Q Consensus 606 ~L~~yF----~~pl~eAAk~LGV~~TtLKRiCR~ 635 (1010)
.|.-+| .++++|+|+.|||+..+++++.++
T Consensus 226 vl~l~y~~~~~~t~~eIA~~lgvS~~~V~q~~~~ 259 (270)
T TIGR02392 226 IIEARWLDDDKLTLQELAAEYGVSAERIRQIEKN 259 (270)
T ss_pred HHHHHhcCCCCcCHHHHHHHHCCCHHHHHHHHHH
Confidence 555555 489999999999999999988764
No 200
>smart00351 PAX Paired Box domain.
Probab=46.42 E-value=18 Score=35.78 Aligned_cols=25 Identities=12% Similarity=0.092 Sum_probs=22.7
Q ss_pred CCcHHHHHHHcCCChhHHHHHHHHc
Q 001809 612 SGSLKDAAKSIGVCPTTLKRICRQH 636 (1010)
Q Consensus 612 ~~pl~eAAk~LGV~~TtLKRiCR~~ 636 (1010)
+.+..++|+.|||+..|+.|+.+++
T Consensus 33 G~s~~~iA~~~gvs~~tV~kwi~r~ 57 (125)
T smart00351 33 GVRPCDISRQLCVSHGCVSKILGRY 57 (125)
T ss_pred CCCHHHHHHHHCcCHHHHHHHHHHH
Confidence 5699999999999999999998875
No 201
>COG2207 AraC AraC-type DNA-binding domain-containing proteins [Transcription]
Probab=46.02 E-value=36 Score=31.37 Aligned_cols=34 Identities=26% Similarity=0.521 Sum_probs=27.9
Q ss_pred HHHhhcC--CcHHHHHHHcCCChhHHHHHHH-HcCCC
Q 001809 606 VLQQYFS--GSLKDAAKSIGVCPTTLKRICR-QHGIS 639 (1010)
Q Consensus 606 ~L~~yF~--~pl~eAAk~LGV~~TtLKRiCR-~~GI~ 639 (1010)
-|...++ +.+++.|+.+|+++++|.|+++ ..|+.
T Consensus 28 ~i~~~~~~~~~l~~la~~~g~S~~~l~r~f~~~~g~s 64 (127)
T COG2207 28 YIEENLAEPLTLEDLARRLGMSRRTLSRLFKKETGTS 64 (127)
T ss_pred HHHHHhcCCCCHHHHHHHHCCCHHHHHHHHHHHHCCC
Confidence 3344454 7899999999999999999999 66874
No 202
>cd06571 Bac_DnaA_C C-terminal domain of bacterial DnaA proteins. The DNA-binding C-terminal domain of DnaA contains a helix-turn-helix motif that specifically interacts with the DnaA box, a 9-mer motif that occurs repetitively in the replication origin oriC. Multiple copies of DnaA, which is an ATPase, bind to 9-mers at the origin and form an initial complex in which the DNA strands are being separated in an ATP-dependent step.
Probab=45.61 E-value=23 Score=32.98 Aligned_cols=41 Identities=12% Similarity=0.208 Sum_probs=35.1
Q ss_pred ccccccCHHHHHhhcCCcHHHHHHHcC-CChhHHHHHHHHcC
Q 001809 597 TAEKNVSLSVLQQYFSGSLKDAAKSIG-VCPTTLKRICRQHG 637 (1010)
Q Consensus 597 ~~~~~itl~~L~~yF~~pl~eAAk~LG-V~~TtLKRiCR~~G 637 (1010)
.....+-.--++.++++++.++|+.|| .+.||+-..||+.-
T Consensus 29 ~~aR~ia~yl~~~~~~~s~~~Ig~~fg~r~hStV~~a~~ri~ 70 (90)
T cd06571 29 ALARQIAMYLARELTGLSLPEIGRAFGGRDHSTVLHAVRKIE 70 (90)
T ss_pred chHHHHHHHHHHHHhCCCHHHHHHHhCCCCHhHHHHHHHHHH
Confidence 344567777888999999999999999 99999999998764
No 203
>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=45.57 E-value=24 Score=28.45 Aligned_cols=24 Identities=25% Similarity=0.351 Sum_probs=21.0
Q ss_pred CCcHHHHHHHcCCChhHHHHHHHH
Q 001809 612 SGSLKDAAKSIGVCPTTLKRICRQ 635 (1010)
Q Consensus 612 ~~pl~eAAk~LGV~~TtLKRiCR~ 635 (1010)
+++.+++|+.||+++.|+++..++
T Consensus 15 ~~s~~eia~~l~~s~~tv~~~~~~ 38 (57)
T cd06170 15 GKTNKEIADILGISEKTVKTHLRN 38 (57)
T ss_pred CCCHHHHHHHHCCCHHHHHHHHHH
Confidence 579999999999999999887654
No 204
>cd01800 SF3a120_C Ubiquitin-like domain of Mammalian splicing factor SF3a_120. SF3a120_C Mammalian splicing factor SF3a consists of three subunits of 60, 66, and 120 kDa and functions early during pre-mRNA splicing by converting the U2 snRNP to its active form. The 120kDa subunit (SF3a120) has a carboxy-terminal ubiquitin-like domain and two SWAP (suppressor-of-white-apricot) domains, referred to collectively as the SURP module, at its amino-terminus.
Probab=45.47 E-value=48 Score=29.76 Aligned_cols=66 Identities=11% Similarity=0.232 Sum_probs=50.7
Q ss_pred cCCCeEEEEeCCCcChHHHHHHHHHHcCcccceeeeEeecCCCCeEEEecCCcHHHHHHHHhHhCCCeEEEEEee
Q 001809 909 YKEDIIRFKFDPSAGCFQLYEEVARRLKLQNGTFQLKYLDDEEEWVMLVSDSDLQECFDILESLGKRSVRFLVRD 983 (1010)
Q Consensus 909 y~~d~iRF~~~~s~g~~~L~~EIakRf~l~~~~f~lKYlDDd~EWVlLtcDaDL~EC~di~~~~~~~~vkl~V~d 983 (1010)
..++++-+.+.++.-+.+|++.|..+.++......|.|-. -+|.-|..|.+| .-....+|.+.++.
T Consensus 5 l~g~~~~l~v~~~~TV~~lK~~i~~~~gip~~~q~L~~~G-----~~L~d~~tL~~~----~i~~g~~l~v~~~~ 70 (76)
T cd01800 5 LNGQMLNFTLQLSDPVSVLKVKIHEETGMPAGKQKLQYEG-----IFIKDSNSLAYY----NLANGTIIHLQLKE 70 (76)
T ss_pred cCCeEEEEEECCCCcHHHHHHHHHHHHCCCHHHEEEEECC-----EEcCCCCcHHHc----CCCCCCEEEEEEec
Confidence 3567888999999999999999999999988888888864 245555566544 34456788887763
No 205
>TIGR02293 TAS_TIGR02293 putative toxin-antitoxin system antitoxin component, TIGR02293 family. Proteins in this family are found almost exclusively in the Proteobacteria, but also in Gloeobacter violaceus PCC 7421, a cyanobacterium. This family was proposed by Makarova, et al. (2009) to be the antitoxin component of a new class of type 2 toxin-antitoxin system, or addiction module.
Probab=45.24 E-value=39 Score=33.80 Aligned_cols=33 Identities=24% Similarity=0.259 Sum_probs=29.1
Q ss_pred HHHHHhhcCCcHHHHHHHcCCChhHHHHHHHHc
Q 001809 604 LSVLQQYFSGSLKDAAKSIGVCPTTLKRICRQH 636 (1010)
Q Consensus 604 l~~L~~yF~~pl~eAAk~LGV~~TtLKRiCR~~ 636 (1010)
+..+..++.++.+|+|+.|||+.+||+|.-++.
T Consensus 28 ~~~l~~~l~ls~~el~~~lgis~~Tl~R~~~~~ 60 (133)
T TIGR02293 28 LDRLAHLLAIGKAEIFKATGIPKATLQRRKMAH 60 (133)
T ss_pred HHHHHHHHCCCHHHHHHHHCCCHHHHHHHhhcC
Confidence 556789999999999999999999999987754
No 206
>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=45.01 E-value=13 Score=31.44 Aligned_cols=27 Identities=22% Similarity=0.249 Sum_probs=22.1
Q ss_pred CcHHHHHHHcCCChhHHHHHHHH-cCCC
Q 001809 613 GSLKDAAKSIGVCPTTLKRICRQ-HGIS 639 (1010)
Q Consensus 613 ~pl~eAAk~LGV~~TtLKRiCR~-~GI~ 639 (1010)
+.+.|.|++|||.+..|-+.|++ +||.
T Consensus 4 i~V~elAk~l~v~~~~ii~~l~~~~Gi~ 31 (54)
T PF04760_consen 4 IRVSELAKELGVPSKEIIKKLFKELGIM 31 (54)
T ss_dssp E-TTHHHHHHSSSHHHHHHHH-HHHTS-
T ss_pred eEHHHHHHHHCcCHHHHHHHHHHhCCcC
Confidence 45679999999999999999976 9996
No 207
>KOG4639 consensus RNase P/RNase MRP subunit POP5 [Translation, ribosomal structure and biogenesis]
Probab=44.81 E-value=53 Score=34.30 Aligned_cols=39 Identities=15% Similarity=0.269 Sum_probs=29.2
Q ss_pred ChHHHHHH-HHHHcC---cc--cceeeeEeecCCCCeEEEecCCc
Q 001809 923 GCFQLYEE-VARRLK---LQ--NGTFQLKYLDDEEEWVMLVSDSD 961 (1010)
Q Consensus 923 g~~~L~~E-IakRf~---l~--~~~f~lKYlDDd~EWVlLtcDaD 961 (1010)
-+.++... |++-|| +. ...|.+|||+++---++|-|++-
T Consensus 28 iL~~iir~~v~~~~Gd~G~a~~~s~l~VkYl~~~T~v~ilRc~~~ 72 (154)
T KOG4639|consen 28 ILQSIIRSRVSENYGDFGLAKVKSLLSVKYLNENTSVAILRCARE 72 (154)
T ss_pred HHHHHHHHHHHHHhhhHHHHHhhcceEEEEeCCCCcEEEEEEccc
Confidence 34455555 666676 33 35799999999999999999974
No 208
>PF01371 Trp_repressor: Trp repressor protein; InterPro: IPR000831 The Trp repressor (TrpR) binds to at least five operators in the Escherichia coli genome, repressing gene expression. The operators at which it binds vary considerably in DNA sequence and location within the promoter; when bound to the Trp operon it recognises the sequence 5'-ACTAGT-3' and acts to prevent the initiation of transcription. The TrpR controls the trpEDCBA (trpO) operon and the genes for trpR, aroH, mtr and aroL, which are involved in the biosynthesis and uptake of the amino acid tryptophan []. The repressor binds to the operators only in the presence of L-tryptophan, thereby controlling the intracellular level of its effector; the complex also regulates Trp repressor biosynthesis by binding to its own regulatory region. TrpR acts as a dimer that is composed of identical 6-helical subunits, where four of the helices form the core of the protein and intertwine with the corresponding helices from the other subunit.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 3FRW_H 3KOR_A 3SSW_N 1P6Z_N 1CO0_B 1JHG_A 1WRT_S 1WRS_R 1WRP_R 1RCS_B ....
Probab=44.77 E-value=21 Score=33.88 Aligned_cols=26 Identities=27% Similarity=0.386 Sum_probs=23.9
Q ss_pred CCcHHHHHHHcCCChhHHHHHHHHcC
Q 001809 612 SGSLKDAAKSIGVCPTTLKRICRQHG 637 (1010)
Q Consensus 612 ~~pl~eAAk~LGV~~TtLKRiCR~~G 637 (1010)
++|..|+|+.+|||.+|+-|..|.+.
T Consensus 49 g~syreIa~~tgvS~aTItRvsr~Lk 74 (87)
T PF01371_consen 49 GKSYREIAEETGVSIATITRVSRCLK 74 (87)
T ss_dssp TSSHHHHHHHHTSTHHHHHHHHHHHH
T ss_pred CCCHHHHHHHhCCCHHHHHHHHHHHH
Confidence 68999999999999999999998764
No 209
>PF10078 DUF2316: Uncharacterized protein conserved in bacteria (DUF2316); InterPro: IPR018757 Members of this family of hypothetical bacterial proteins have no known function.
Probab=44.30 E-value=16 Score=34.90 Aligned_cols=35 Identities=26% Similarity=0.434 Sum_probs=30.2
Q ss_pred ccccCHHHHHhhc---CCcHHHHHHHcCCChhHHHHHH
Q 001809 599 EKNVSLSVLQQYF---SGSLKDAAKSIGVCPTTLKRIC 633 (1010)
Q Consensus 599 ~~~itl~~L~~yF---~~pl~eAAk~LGV~~TtLKRiC 633 (1010)
.+..|-++|+..| +++++++|+.||+++.-|.++-
T Consensus 7 Q~~~T~~ELq~nf~~~~ls~~~ia~dL~~s~~~le~vL 44 (89)
T PF10078_consen 7 QRRATRQELQANFELSGLSLEQIAADLGTSPEHLEQVL 44 (89)
T ss_pred HHHHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHH
Confidence 3556788999998 7899999999999999888774
No 210
>PRK06596 RNA polymerase factor sigma-32; Reviewed
Probab=44.25 E-value=24 Score=39.32 Aligned_cols=31 Identities=16% Similarity=0.439 Sum_probs=26.2
Q ss_pred HHHHhhc----CCcHHHHHHHcCCChhHHHHHHHH
Q 001809 605 SVLQQYF----SGSLKDAAKSIGVCPTTLKRICRQ 635 (1010)
Q Consensus 605 ~~L~~yF----~~pl~eAAk~LGV~~TtLKRiCR~ 635 (1010)
.+|+-|| .++++|+|+.|||+..+++++.++
T Consensus 237 ~VL~lry~~~~~~Tl~EIA~~lgvS~~rVrqi~~~ 271 (284)
T PRK06596 237 DIIEARWLDDDKSTLQELAAEYGVSAERVRQIEKN 271 (284)
T ss_pred HHHHHHhcCCCCcCHHHHHHHHCCCHHHHHHHHHH
Confidence 4677655 589999999999999999998764
No 211
>PRK11303 DNA-binding transcriptional regulator FruR; Provisional
Probab=44.25 E-value=28 Score=37.89 Aligned_cols=25 Identities=24% Similarity=0.254 Sum_probs=22.1
Q ss_pred CcHHHHHHHcCCChhHHHHHHHHcC
Q 001809 613 GSLKDAAKSIGVCPTTLKRICRQHG 637 (1010)
Q Consensus 613 ~pl~eAAk~LGV~~TtLKRiCR~~G 637 (1010)
++++|+||..|||.+|+.|.....+
T Consensus 1 ~ti~dIA~~aGVS~~TVSrvLn~~~ 25 (328)
T PRK11303 1 MKLDEIARLAGVSRTTASYVINGKA 25 (328)
T ss_pred CCHHHHHHHhCCCHHHHHHHHcCCC
Confidence 4799999999999999999997653
No 212
>PRK08301 sporulation sigma factor SigE; Reviewed
Probab=44.17 E-value=35 Score=36.33 Aligned_cols=23 Identities=17% Similarity=0.416 Sum_probs=20.9
Q ss_pred CCcHHHHHHHcCCChhHHHHHHH
Q 001809 612 SGSLKDAAKSIGVCPTTLKRICR 634 (1010)
Q Consensus 612 ~~pl~eAAk~LGV~~TtLKRiCR 634 (1010)
+++.+|+|+.|||+..|+|++-.
T Consensus 198 g~s~~EIA~~lgis~~tVk~~~~ 220 (234)
T PRK08301 198 EKTQKEVADMLGISQSYISRLEK 220 (234)
T ss_pred CCCHHHHHHHHCCCHHHHHHHHH
Confidence 89999999999999999987654
No 213
>PRK12511 RNA polymerase sigma factor; Provisional
Probab=44.04 E-value=25 Score=36.33 Aligned_cols=28 Identities=25% Similarity=0.104 Sum_probs=24.4
Q ss_pred HHHhhcCCcHHHHHHHcCCChhHHHHHH
Q 001809 606 VLQQYFSGSLKDAAKSIGVCPTTLKRIC 633 (1010)
Q Consensus 606 ~L~~yF~~pl~eAAk~LGV~~TtLKRiC 633 (1010)
.|+-+.+++.+|+|+.|||++.|+|...
T Consensus 121 ~L~~~eg~s~~EIA~~lgis~~tV~~~l 148 (182)
T PRK12511 121 HLVAIEGLSYQEAAAVLGIPIGTLMSRI 148 (182)
T ss_pred HHHHHcCCCHHHHHHHhCcCHHHHHHHH
Confidence 4556679999999999999999999875
No 214
>PRK09637 RNA polymerase sigma factor SigZ; Provisional
Probab=43.93 E-value=25 Score=36.13 Aligned_cols=28 Identities=21% Similarity=0.169 Sum_probs=24.2
Q ss_pred HHHhhcCCcHHHHHHHcCCChhHHHHHH
Q 001809 606 VLQQYFSGSLKDAAKSIGVCPTTLKRIC 633 (1010)
Q Consensus 606 ~L~~yF~~pl~eAAk~LGV~~TtLKRiC 633 (1010)
.|+-+.++++.|+|+.|||++.|+|.+.
T Consensus 116 ~l~~~~g~~~~EIA~~lgis~~tV~~~l 143 (181)
T PRK09637 116 RLTELEGLSQKEIAEKLGLSLSGAKSRV 143 (181)
T ss_pred HHHHhcCCCHHHHHHHhCCCHHHHHHHH
Confidence 3455679999999999999999998876
No 215
>PHA00542 putative Cro-like protein
Probab=43.85 E-value=19 Score=33.16 Aligned_cols=28 Identities=21% Similarity=0.113 Sum_probs=24.6
Q ss_pred hhcCCcHHHHHHHcCCChhHHHHHHHHc
Q 001809 609 QYFSGSLKDAAKSIGVCPTTLKRICRQH 636 (1010)
Q Consensus 609 ~yF~~pl~eAAk~LGV~~TtLKRiCR~~ 636 (1010)
.--++++.++|+.+||+..++.|+++..
T Consensus 28 ~~~glTq~elA~~lgIs~~tIsr~e~g~ 55 (82)
T PHA00542 28 IRAGWSQEQIADATDVSQPTICRIYSGR 55 (82)
T ss_pred HHCCCCHHHHHHHHCcCHHHHHHHHcCC
Confidence 4458999999999999999999998754
No 216
>PF13551 HTH_29: Winged helix-turn helix
Probab=43.81 E-value=22 Score=32.92 Aligned_cols=23 Identities=17% Similarity=0.404 Sum_probs=21.0
Q ss_pred cHHHHHHHcCCChhHHHHHHHHc
Q 001809 614 SLKDAAKSIGVCPTTLKRICRQH 636 (1010)
Q Consensus 614 pl~eAAk~LGV~~TtLKRiCR~~ 636 (1010)
++++||+.|||+..|++|.-+++
T Consensus 14 ~~~~ia~~lg~s~~Tv~r~~~~~ 36 (112)
T PF13551_consen 14 TIAEIARRLGISRRTVYRWLKRY 36 (112)
T ss_pred cHHHHHHHHCcCHHHHHHHHHHH
Confidence 49999999999999999998874
No 217
>PRK03975 tfx putative transcriptional regulator; Provisional
Probab=43.63 E-value=45 Score=34.32 Aligned_cols=26 Identities=12% Similarity=0.144 Sum_probs=23.6
Q ss_pred hcCCcHHHHHHHcCCChhHHHHHHHH
Q 001809 610 YFSGSLKDAAKSIGVCPTTLKRICRQ 635 (1010)
Q Consensus 610 yF~~pl~eAAk~LGV~~TtLKRiCR~ 635 (1010)
+=+++++|+|+.||++..+++++.++
T Consensus 19 ~~GlTq~EIAe~LGiS~~tVs~ie~r 44 (141)
T PRK03975 19 ERGLTQQEIADILGTSRANVSSIEKR 44 (141)
T ss_pred HcCCCHHHHHHHHCCCHHHHHHHHHH
Confidence 46899999999999999999998875
No 218
>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=43.63 E-value=21 Score=30.65 Aligned_cols=23 Identities=26% Similarity=0.579 Sum_probs=19.1
Q ss_pred CCcHHHHHHHcCCChhHHHHHHH
Q 001809 612 SGSLKDAAKSIGVCPTTLKRICR 634 (1010)
Q Consensus 612 ~~pl~eAAk~LGV~~TtLKRiCR 634 (1010)
+.++..||+.|||+.+++.|.-+
T Consensus 13 ~gs~~~AA~~l~is~~~vs~~i~ 35 (60)
T PF00126_consen 13 TGSISAAAEELGISQSAVSRQIK 35 (60)
T ss_dssp HSSHHHHHHHCTSSHHHHHHHHH
T ss_pred hCCHHHHHHHhhccchHHHHHHH
Confidence 56899999999999998866544
No 219
>COG5484 Uncharacterized conserved protein [Function unknown]
Probab=43.58 E-value=19 Score=40.36 Aligned_cols=26 Identities=42% Similarity=0.638 Sum_probs=25.1
Q ss_pred CCcHHHHHHHcCCChhHHHHHHHHcC
Q 001809 612 SGSLKDAAKSIGVCPTTLKRICRQHG 637 (1010)
Q Consensus 612 ~~pl~eAAk~LGV~~TtLKRiCR~~G 637 (1010)
+|+++|+|..|||++.|+|..-|++|
T Consensus 19 gmk~~dIAeklGvspntiksWKrr~g 44 (279)
T COG5484 19 GMKLKDIAEKLGVSPNTIKSWKRRDG 44 (279)
T ss_pred hccHHHHHHHhCCChHHHHHHHHhcC
Confidence 49999999999999999999999998
No 220
>PRK07037 extracytoplasmic-function sigma-70 factor; Validated
Probab=43.57 E-value=27 Score=34.54 Aligned_cols=27 Identities=26% Similarity=0.447 Sum_probs=23.0
Q ss_pred HHHhhcCCcHHHHHHHcCCChhHHHHH
Q 001809 606 VLQQYFSGSLKDAAKSIGVCPTTLKRI 632 (1010)
Q Consensus 606 ~L~~yF~~pl~eAAk~LGV~~TtLKRi 632 (1010)
.|+-+.+++.+|+|+.|||+..|+|+.
T Consensus 119 ~l~~~~~~s~~EIA~~lgis~~tV~~~ 145 (163)
T PRK07037 119 EMYRLHGETQKDIARELGVSPTLVNFM 145 (163)
T ss_pred HHHHHcCCCHHHHHHHHCCCHHHHHHH
Confidence 344557899999999999999999974
No 221
>PRK09978 DNA-binding transcriptional regulator GadX; Provisional
Probab=43.54 E-value=33 Score=38.64 Aligned_cols=34 Identities=21% Similarity=0.307 Sum_probs=28.5
Q ss_pred HHHHhhc--CCcHHHHHHHcCCChhHHHHHHHHcCC
Q 001809 605 SVLQQYF--SGSLKDAAKSIGVCPTTLKRICRQHGI 638 (1010)
Q Consensus 605 ~~L~~yF--~~pl~eAAk~LGV~~TtLKRiCR~~GI 638 (1010)
+-|.+++ .+++.++|+.+||++.+|+|++++.|.
T Consensus 149 ~yI~~~~~~~lsl~~lA~~~g~S~~~L~R~Fk~~G~ 184 (274)
T PRK09978 149 TVINNNIAHEWTLARIASELLMSPSLLKKKLREEET 184 (274)
T ss_pred HHHHhcccCCCCHHHHHHHHCcCHHHHHHHHHhcCC
Confidence 3455555 478999999999999999999999885
No 222
>PRK12519 RNA polymerase sigma factor; Provisional
Probab=43.50 E-value=31 Score=35.30 Aligned_cols=28 Identities=29% Similarity=0.229 Sum_probs=23.6
Q ss_pred HHHhhcCCcHHHHHHHcCCChhHHHHHH
Q 001809 606 VLQQYFSGSLKDAAKSIGVCPTTLKRIC 633 (1010)
Q Consensus 606 ~L~~yF~~pl~eAAk~LGV~~TtLKRiC 633 (1010)
.|+-+.+++.+|+|+.||++..|+|.+-
T Consensus 151 ~l~~~~g~s~~EIA~~lgis~~tV~~~l 178 (194)
T PRK12519 151 ELAYYEGLSQSEIAKRLGIPLGTVKARA 178 (194)
T ss_pred hhhhhcCCCHHHHHHHhCCCHHHHHHHH
Confidence 3444579999999999999999999764
No 223
>smart00342 HTH_ARAC helix_turn_helix, arabinose operon control protein.
Probab=43.46 E-value=32 Score=29.42 Aligned_cols=32 Identities=19% Similarity=0.366 Sum_probs=26.6
Q ss_pred HHHhhcCCcHHHHHHHcCC-ChhHHHHHHHHc-CC
Q 001809 606 VLQQYFSGSLKDAAKSIGV-CPTTLKRICRQH-GI 638 (1010)
Q Consensus 606 ~L~~yF~~pl~eAAk~LGV-~~TtLKRiCR~~-GI 638 (1010)
.|... .++++++|..+|+ +++.|-|.++++ |+
T Consensus 45 ~l~~~-~~~~~~ia~~~g~~s~~~f~r~Fk~~~g~ 78 (84)
T smart00342 45 LLRDT-DLSVTEIALRVGFSSQSYFSRAFKKLFGV 78 (84)
T ss_pred HHHcC-CCCHHHHHHHhCCCChHHHHHHHHHHHCc
Confidence 44444 6999999999999 999999999776 65
No 224
>PF06970 RepA_N: Replication initiator protein A (RepA) N-terminus; InterPro: IPR010724 This entry represents the N terminus (approximately 80 residues) of replication initiator protein A (RepA), a DNA replication initiator in plasmids []. Most proteins in this entry are bacterial, but archaeal and eukaryotic members are also included.
Probab=43.18 E-value=18 Score=33.40 Aligned_cols=28 Identities=11% Similarity=0.173 Sum_probs=25.6
Q ss_pred hhcCCcHHHHHHHcCCChhHHHHHHHHc
Q 001809 609 QYFSGSLKDAAKSIGVCPTTLKRICRQH 636 (1010)
Q Consensus 609 ~yF~~pl~eAAk~LGV~~TtLKRiCR~~ 636 (1010)
-||..|++|+|+.||+|..|+.|+-+++
T Consensus 49 vYi~~s~eel~~~L~~s~~tv~~~~keL 76 (76)
T PF06970_consen 49 VYIIFSIEELMELLNCSKSTVIKAKKEL 76 (76)
T ss_pred EEEEeeHHHHHHHHCCCHHHHHHHHHcC
Confidence 4899999999999999999999988764
No 225
>PF01590 GAF: GAF domain; InterPro: IPR003018 This domain is present in phytochromes and cGMP-specific phosphodiesterases. cGMP-dependent 3',5'-cyclic phosphodiesterase (3.1.4.17 from EC) catalyses the conversion of guanosine 3',5'-cyclic phosphate to guanosine 5'-phosphate. A phytochrome is a regulatory photoreceptor which exists in 2 forms that are reversibly interconvertible by light, the PR form that absorbs maximally in the red region of the spectrum, and the PFR form that absorbs maximally in the far-red region. This domain is also found in NifA, a transcriptional activator which is required for activation of most Nif operons which are directly involved in nitrogen fixation. NifA interacts with sigma-54.; GO: 0005515 protein binding; PDB: 2Y8H_A 3DBA_B 3CI6_A 3E0Y_B 2W3G_B 2W3D_A 2W3E_A 2Y79_B 2W3H_A 2W3F_A ....
Probab=43.02 E-value=73 Score=30.06 Aligned_cols=91 Identities=16% Similarity=0.223 Sum_probs=62.3
Q ss_pred HhhhcccccCCCcchhhhhcCCCcccccccccCccccchh-------------hHHHHhCCceeEEEEecccccCCCcEE
Q 001809 413 ACSEHYLEEGQGVAGKALQSNHPFFFPDVKLYDITEFPLV-------------HHARKFGLNAAVAIRLRSTYTGDDDYI 479 (1010)
Q Consensus 413 AC~EhhL~~GQGvaGkAf~sn~P~F~~DV~~fsk~EYPL~-------------HhAr~fgL~aAvAIrLrS~~tG~ddyV 479 (1010)
...+.-+..+.++.|+++.++.|...+|+........... |+...+|+++.+.+||... |..--|
T Consensus 46 ~~~~~~~~~~~~~~~~~~~~~~~~~i~d~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~s~l~vPi~~~--g~~~G~ 123 (154)
T PF01590_consen 46 PPGGRRLSMDESICGQVLQSREPIVISDVAADPRFAPQIAAQSALRALSSAERPFLAEYGVRSYLCVPIISG--GRLIGV 123 (154)
T ss_dssp EHHHEEEETTSSHHHHHHHHTSCEEESSSGGSTTSSCHHHHHHTTBTTTHHHHHHHHTTTESEEEEEEEEET--TEEEEE
T ss_pred ccccccccccccHHHHHHhCCCeEeeccccccccccccccccccccccccccccccccccCceeeEeeeecc--cCcEEE
Confidence 3445566677889999999999999999877443222111 2334789999999998764 666677
Q ss_pred EEeecCCC-CCCcHHHHHHHHHHHHHH
Q 001809 480 LEFFLPVT-IKGSSEQQLLLNNLSGTM 505 (1010)
Q Consensus 480 LEFFLP~~-ck~~~EQq~ll~sLs~Tm 505 (1010)
|.|.-+.. -.=.++...+|..+...+
T Consensus 124 l~l~~~~~~~~~~~~d~~ll~~~a~~~ 150 (154)
T PF01590_consen 124 LSLYRTRPGRPFTEEDLALLESFAQQL 150 (154)
T ss_dssp EEEEEESSSSS--HHHHHHHHHHHHHH
T ss_pred EEEEECCCCCCcCHHHHHHHHHHHHHH
Confidence 77777766 444455666777666554
No 226
>PRK12530 RNA polymerase sigma factor; Provisional
Probab=43.00 E-value=26 Score=36.08 Aligned_cols=29 Identities=10% Similarity=0.268 Sum_probs=24.5
Q ss_pred HHHhhcCCcHHHHHHHcCCChhHHHHHHH
Q 001809 606 VLQQYFSGSLKDAAKSIGVCPTTLKRICR 634 (1010)
Q Consensus 606 ~L~~yF~~pl~eAAk~LGV~~TtLKRiCR 634 (1010)
.|+-+.+++.+|+|+.||+++.|+|.+.+
T Consensus 144 ~L~~~~g~s~~EIA~~lgis~~tVk~~l~ 172 (189)
T PRK12530 144 MMREYLELSSEQICQECDISTSNLHVLLY 172 (189)
T ss_pred hHHHHcCCCHHHHHHHHCCCHHHHHHHHH
Confidence 44556799999999999999999998744
No 227
>PRK12532 RNA polymerase sigma factor; Provisional
Probab=42.69 E-value=26 Score=36.02 Aligned_cols=29 Identities=14% Similarity=0.243 Sum_probs=24.8
Q ss_pred HHHhhcCCcHHHHHHHcCCChhHHHHHHH
Q 001809 606 VLQQYFSGSLKDAAKSIGVCPTTLKRICR 634 (1010)
Q Consensus 606 ~L~~yF~~pl~eAAk~LGV~~TtLKRiCR 634 (1010)
.|+-+.+++.+|+|+.||+++.|+|.+..
T Consensus 146 ~L~~~~g~s~~EIA~~lgis~~tVk~~l~ 174 (195)
T PRK12532 146 TLKEILGFSSDEIQQMCGISTSNYHTIMH 174 (195)
T ss_pred hhHHHhCCCHHHHHHHHCCCHHHHHHHHH
Confidence 45677899999999999999999997643
No 228
>cd01798 parkin_N amino-terminal ubiquitin-like of parkin protein. parkin_N parkin protein is a RING-type E3 ubiquitin ligase with an amino-terminal ubiquitin-like (Ubl) domain and an RBR signature consisting of two RING finger domains separated by an IBR/DRIL domain. Naturally occurring mutations in parkin are thought to cause the disease AR_JP (autosomal-recessive juvenile parkinsonism). Parkin binds the Rpn10 subunit of 26S proteasomes through its Ubl domain.
Probab=42.66 E-value=41 Score=29.45 Aligned_cols=41 Identities=22% Similarity=0.302 Sum_probs=32.7
Q ss_pred EEEEEcCCCeEEEEeCCCcChHHHHHHHHHHcCcccceeeeE
Q 001809 904 IVKATYKEDIIRFKFDPSAGCFQLYEEVARRLKLQNGTFQLK 945 (1010)
Q Consensus 904 ~vKaty~~d~iRF~~~~s~g~~~L~~EIakRf~l~~~~f~lK 945 (1010)
.||.. .++++-+.+.|+.-+.+|++.|+++.|++.....|-
T Consensus 2 ~vk~~-~g~~~~~~v~~~~tV~~lK~~i~~~~gi~~~~q~Li 42 (70)
T cd01798 2 YVRTN-TGHTFPVEVDPDTDIKQLKEVVAKRQGVPPDQLRVI 42 (70)
T ss_pred EEEcC-CCCEEEEEECCCChHHHHHHHHHHHHCCCHHHeEEE
Confidence 34544 457888999999999999999999999987654443
No 229
>PRK12535 RNA polymerase sigma factor; Provisional
Probab=42.65 E-value=28 Score=36.37 Aligned_cols=28 Identities=25% Similarity=0.260 Sum_probs=24.6
Q ss_pred HHHhhcCCcHHHHHHHcCCChhHHHHHH
Q 001809 606 VLQQYFSGSLKDAAKSIGVCPTTLKRIC 633 (1010)
Q Consensus 606 ~L~~yF~~pl~eAAk~LGV~~TtLKRiC 633 (1010)
.|+-+.+++.+|+|+.|||++.|+|...
T Consensus 143 ~l~~~~g~s~~EIAe~lgis~~tV~~~l 170 (196)
T PRK12535 143 ILTQVLGYTYEEAAKIADVRVGTIRSRV 170 (196)
T ss_pred hhHHHhCCCHHHHHHHhCCCHHHHHHHH
Confidence 4566789999999999999999999765
No 230
>PRK10365 transcriptional regulatory protein ZraR; Provisional
Probab=42.45 E-value=23 Score=40.70 Aligned_cols=26 Identities=23% Similarity=0.321 Sum_probs=22.7
Q ss_pred hhcCCcHHHHHHHcCCChhHHHHHHH
Q 001809 609 QYFSGSLKDAAKSIGVCPTTLKRICR 634 (1010)
Q Consensus 609 ~yF~~pl~eAAk~LGV~~TtLKRiCR 634 (1010)
..+++-..+||+.|||+++||+|.-+
T Consensus 415 ~~~~gn~~~aa~~Lgisr~tl~rk~~ 440 (441)
T PRK10365 415 EKTGGNKTEAARQLGITRKTLLAKLS 440 (441)
T ss_pred HHhCCCHHHHHHHhCCCHHHHHHHhh
Confidence 45688999999999999999988755
No 231
>PRK15411 rcsA colanic acid capsular biosynthesis activation protein A; Provisional
Probab=42.40 E-value=25 Score=37.15 Aligned_cols=27 Identities=11% Similarity=0.127 Sum_probs=22.9
Q ss_pred CCcHHHHHHHcCCChhHHH----HHHHHcCC
Q 001809 612 SGSLKDAAKSIGVCPTTLK----RICRQHGI 638 (1010)
Q Consensus 612 ~~pl~eAAk~LGV~~TtLK----RiCR~~GI 638 (1010)
+++.+|+|++||||..|+| ++++++|+
T Consensus 152 G~snkeIA~~L~iS~~TVk~h~~~I~~KL~v 182 (207)
T PRK15411 152 GQGTIQISDQMNIKAKTVSSHKGNIKRKIKT 182 (207)
T ss_pred CCCHHHHHHHcCCCHHHHHHHHHHHHHHhCC
Confidence 7899999999999999876 56667776
No 232
>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=42.21 E-value=29 Score=27.03 Aligned_cols=25 Identities=16% Similarity=0.256 Sum_probs=21.7
Q ss_pred cCCcHHHHHHHcCCChhHHHHHHHH
Q 001809 611 FSGSLKDAAKSIGVCPTTLKRICRQ 635 (1010)
Q Consensus 611 F~~pl~eAAk~LGV~~TtLKRiCR~ 635 (1010)
-+++.+++|+.||++..+++++-++
T Consensus 25 ~~~~~~~ia~~~~~s~~~i~~~~~~ 49 (55)
T cd06171 25 EGLSYEEIAEILGISRSTVRQRLHR 49 (55)
T ss_pred cCCCHHHHHHHHCcCHHHHHHHHHH
Confidence 5889999999999999999877554
No 233
>PRK12527 RNA polymerase sigma factor; Reviewed
Probab=42.21 E-value=44 Score=33.09 Aligned_cols=29 Identities=14% Similarity=0.214 Sum_probs=23.9
Q ss_pred HHHhhcCCcHHHHHHHcCCChhHHHHHHH
Q 001809 606 VLQQYFSGSLKDAAKSIGVCPTTLKRICR 634 (1010)
Q Consensus 606 ~L~~yF~~pl~eAAk~LGV~~TtLKRiCR 634 (1010)
.|.-+=+++.+|+|+.||++.+|+|..-+
T Consensus 115 ~l~~~~~~s~~eIA~~lgis~~tv~~~l~ 143 (159)
T PRK12527 115 LLRKLEGLSHQQIAEHLGISRSLVEKHIV 143 (159)
T ss_pred HHHHHcCCCHHHHHHHhCCCHHHHHHHHH
Confidence 44455588999999999999999997654
No 234
>smart00345 HTH_GNTR helix_turn_helix gluconate operon transcriptional repressor.
Probab=42.11 E-value=25 Score=28.74 Aligned_cols=23 Identities=26% Similarity=0.361 Sum_probs=20.8
Q ss_pred cHHHHHHHcCCChhHHHHHHHHc
Q 001809 614 SLKDAAKSIGVCPTTLKRICRQH 636 (1010)
Q Consensus 614 pl~eAAk~LGV~~TtLKRiCR~~ 636 (1010)
+.++.|+.+||+.+|+.|..+++
T Consensus 22 s~~~la~~~~vs~~tv~~~l~~L 44 (60)
T smart00345 22 SERELAAQLGVSRTTVREALSRL 44 (60)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHH
Confidence 68999999999999999988876
No 235
>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=42.10 E-value=27 Score=29.58 Aligned_cols=28 Identities=14% Similarity=0.213 Sum_probs=23.9
Q ss_pred hhcCCcHHHHHHHcCCChhHHHHHHHHc
Q 001809 609 QYFSGSLKDAAKSIGVCPTTLKRICRQH 636 (1010)
Q Consensus 609 ~yF~~pl~eAAk~LGV~~TtLKRiCR~~ 636 (1010)
..+.+++.|+|+.+|++..|+.|+.+++
T Consensus 22 ~~~~~s~~ela~~~g~s~~tv~r~l~~L 49 (67)
T cd00092 22 VQLPLTRQEIADYLGLTRETVSRTLKEL 49 (67)
T ss_pred ccCCcCHHHHHHHHCCCHHHHHHHHHHH
Confidence 3467899999999999999999888655
No 236
>COG3413 Predicted DNA binding protein [General function prediction only]
Probab=41.78 E-value=21 Score=37.99 Aligned_cols=27 Identities=41% Similarity=0.620 Sum_probs=22.8
Q ss_pred hhcCCc----HHHHHHHcCCChhHHHHHHHH
Q 001809 609 QYFSGS----LKDAAKSIGVCPTTLKRICRQ 635 (1010)
Q Consensus 609 ~yF~~p----l~eAAk~LGV~~TtLKRiCR~ 635 (1010)
.||+.| ++|.|++|||+++|+-..-|+
T Consensus 171 GYFd~PR~~~l~dLA~~lGISkst~~ehLRr 201 (215)
T COG3413 171 GYFDYPRRVSLKDLAKELGISKSTLSEHLRR 201 (215)
T ss_pred CCCCCCccCCHHHHHHHhCCCHHHHHHHHHH
Confidence 899766 899999999999998766553
No 237
>PRK09641 RNA polymerase sigma factor SigW; Provisional
Probab=41.68 E-value=28 Score=35.05 Aligned_cols=29 Identities=24% Similarity=0.158 Sum_probs=24.9
Q ss_pred HHHhhcCCcHHHHHHHcCCChhHHHHHHH
Q 001809 606 VLQQYFSGSLKDAAKSIGVCPTTLKRICR 634 (1010)
Q Consensus 606 ~L~~yF~~pl~eAAk~LGV~~TtLKRiCR 634 (1010)
.|.-+.+++.+|+|+.|||++.+++...+
T Consensus 146 ~l~~~~~~s~~eIA~~lgis~~~v~~~l~ 174 (187)
T PRK09641 146 VLKYIEDLSLKEISEILDLPVGTVKTRIH 174 (187)
T ss_pred hhHHhhCCCHHHHHHHHCCCHHHHHHHHH
Confidence 45667899999999999999999987654
No 238
>PF13556 HTH_30: PucR C-terminal helix-turn-helix domain; PDB: 3ONQ_B.
Probab=41.62 E-value=33 Score=29.58 Aligned_cols=31 Identities=23% Similarity=0.505 Sum_probs=21.6
Q ss_pred HHHHHhhc--CCcHHHHHHHcCCChhHHHHHHH
Q 001809 604 LSVLQQYF--SGSLKDAAKSIGVCPTTLKRICR 634 (1010)
Q Consensus 604 l~~L~~yF--~~pl~eAAk~LGV~~TtLKRiCR 634 (1010)
++.|+.|+ ++.+++||+.|+|.+.||+-+-+
T Consensus 2 ~~TL~~yl~~~~n~~~tA~~L~iHrNTl~yRl~ 34 (59)
T PF13556_consen 2 LETLRAYLENNGNISKTARALHIHRNTLRYRLK 34 (59)
T ss_dssp --HHHHHHHTTT-HHHHHHHHTS-HHHHHHHHH
T ss_pred hhHHHHHHHcCCCHHHHHHHHCCCHHHHHHHHH
Confidence 35677777 58999999999999999765433
No 239
>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=41.28 E-value=35 Score=31.60 Aligned_cols=27 Identities=11% Similarity=0.172 Sum_probs=23.8
Q ss_pred hhcCCcHHHHHHHcCCChhHHHHHHHH
Q 001809 609 QYFSGSLKDAAKSIGVCPTTLKRICRQ 635 (1010)
Q Consensus 609 ~yF~~pl~eAAk~LGV~~TtLKRiCR~ 635 (1010)
.+=+++.+|+|+.|||++.|+|.+-++
T Consensus 29 ~~eGlS~kEIAe~LGIS~~TVk~~l~~ 55 (73)
T TIGR03879 29 EEAGKTASEIAEELGRTEQTVRNHLKG 55 (73)
T ss_pred HHcCCCHHHHHHHHCcCHHHHHHHHhc
Confidence 346899999999999999999998764
No 240
>PRK12547 RNA polymerase sigma factor; Provisional
Probab=41.16 E-value=31 Score=34.55 Aligned_cols=30 Identities=27% Similarity=0.173 Sum_probs=24.6
Q ss_pred HHHhhcCCcHHHHHHHcCCChhHHHHHHHH
Q 001809 606 VLQQYFSGSLKDAAKSIGVCPTTLKRICRQ 635 (1010)
Q Consensus 606 ~L~~yF~~pl~eAAk~LGV~~TtLKRiCR~ 635 (1010)
.|.-+-+++.+|+|+.|||++.|+|...++
T Consensus 122 ~l~~~~g~s~~eIA~~lgis~~tV~~~l~R 151 (164)
T PRK12547 122 ILIGASGFSYEDAAAICGCAVGTIKSRVSR 151 (164)
T ss_pred HHHHHcCCCHHHHHHHhCCCHHHHHHHHHH
Confidence 344566899999999999999999976543
No 241
>PLN02560 enoyl-CoA reductase
Probab=41.07 E-value=1e+02 Score=35.29 Aligned_cols=81 Identities=15% Similarity=0.135 Sum_probs=53.8
Q ss_pred EEEEEEcCCCe--EEEEeCCCcChHHHHHHHHHHcCc-ccceeeeEeecCCCC--eEEEecCCcHHHHHHHHhHhCCCeE
Q 001809 903 IIVKATYKEDI--IRFKFDPSAGCFQLYEEVARRLKL-QNGTFQLKYLDDEEE--WVMLVSDSDLQECFDILESLGKRSV 977 (1010)
Q Consensus 903 ~~vKaty~~d~--iRF~~~~s~g~~~L~~EIakRf~l-~~~~f~lKYlDDd~E--WVlLtcDaDL~EC~di~~~~~~~~v 977 (1010)
++||..-|..+ .-+.+.|+..+.||+++|+++.++ +.....|.|-++++. =+.|.-|.-|+++ .| .+..
T Consensus 3 I~Vk~~~Gk~i~~~~lev~~~aTV~dLK~~Isk~~~~~~~~RqRL~~~~~~gk~~g~~L~d~ktL~d~-gv-----~~gs 76 (308)
T PLN02560 3 VTVVSRSGREIIKGGLEVPDSATVADLKKAIHKRKKKYYPSRQRLTLPLPPGKTRPTVLDDSKSLKDY-GL-----GDGG 76 (308)
T ss_pred EEEEcCCCCeecceeEEcCCCCcHHHHHHHHHHHcCCCChhheEEEEecCCCCcCccccCCCCCHHhc-CC-----CCCc
Confidence 67775555443 257889999999999999999986 556667776544443 3455655557664 22 2333
Q ss_pred EEEEeecCCccc
Q 001809 978 RFLVRDISCNVG 989 (1010)
Q Consensus 978 kl~V~d~~~~lg 989 (1010)
.|.|-|.-.-+|
T Consensus 77 tLy~kDLGpQi~ 88 (308)
T PLN02560 77 TVVFKDLGPQVS 88 (308)
T ss_pred eEEEEeCCCcCc
Confidence 588888765443
No 242
>TIGR02954 Sig70_famx3 RNA polymerase sigma-70 factor, TIGR02954 family. This group of sigma factors are members of the sigma-70 family (TIGR02937). They and appear by homology, tree building, bidirectional best hits and one-to-a-genome distribution, to represent a conserved family. This family is found in certain Bacillus and Clostridium species.
Probab=40.58 E-value=31 Score=34.54 Aligned_cols=28 Identities=21% Similarity=0.291 Sum_probs=23.3
Q ss_pred HHHhhcCCcHHHHHHHcCCChhHHHHHH
Q 001809 606 VLQQYFSGSLKDAAKSIGVCPTTLKRIC 633 (1010)
Q Consensus 606 ~L~~yF~~pl~eAAk~LGV~~TtLKRiC 633 (1010)
.+.-+.+++.+|+|+.|||++.|+|.+-
T Consensus 129 ~l~~~~g~s~~eiA~~lgis~~tv~~~l 156 (169)
T TIGR02954 129 ILRYYHDLTIKEIAEVMNKPEGTVKTYL 156 (169)
T ss_pred HHHHHcCCCHHHHHHHHCCCHHHHHHHH
Confidence 3445668999999999999999998754
No 243
>TIGR02939 RpoE_Sigma70 RNA polymerase sigma factor RpoE. A sigma factor is a DNA-binding protein protein that binds to the DNA-directed RNA polymerase core to produce the holoenzyme capable of initiating transcription at specific sites. Different sigma factors act in vegetative growth, heat shock, extracytoplasmic functions (ECF), etc. This model represents the clade of sigma factors called RpoE. This protein may be called sigma-24, sigma-E factor, sigma-H factor, fecI-like sigma factor or alternative sigma factor AlgU.
Probab=40.42 E-value=35 Score=34.51 Aligned_cols=28 Identities=18% Similarity=0.081 Sum_probs=23.4
Q ss_pred HHhhcCCcHHHHHHHcCCChhHHHHHHH
Q 001809 607 LQQYFSGSLKDAAKSIGVCPTTLKRICR 634 (1010)
Q Consensus 607 L~~yF~~pl~eAAk~LGV~~TtLKRiCR 634 (1010)
|+-+.+++.+|+|+.||++..|+|...+
T Consensus 149 l~~~~~~s~~EIA~~lgis~~tv~~~l~ 176 (190)
T TIGR02939 149 LRELEGLSYEDIARIMDCPVGTVRSRIF 176 (190)
T ss_pred hhhhcCCCHHHHHHHHCcCHHHHHHHHH
Confidence 3345689999999999999999988763
No 244
>smart00418 HTH_ARSR helix_turn_helix, Arsenical Resistance Operon Repressor.
Probab=40.37 E-value=29 Score=28.12 Aligned_cols=31 Identities=10% Similarity=0.092 Sum_probs=24.6
Q ss_pred CCcHHHHHHHcCCChhHHHHHHHHcCCCCCc
Q 001809 612 SGSLKDAAKSIGVCPTTLKRICRQHGISRWP 642 (1010)
Q Consensus 612 ~~pl~eAAk~LGV~~TtLKRiCR~~GI~RWP 642 (1010)
.++..++|+.|||+.+++.++.+++==..|.
T Consensus 10 ~~~~~~i~~~l~is~~~v~~~l~~L~~~g~i 40 (66)
T smart00418 10 ELCVCELAEILGLSQSTVSHHLKKLREAGLV 40 (66)
T ss_pred CccHHHHHHHHCCCHHHHHHHHHHHHHCCCe
Confidence 3578899999999999999999877433444
No 245
>PRK09047 RNA polymerase factor sigma-70; Validated
Probab=40.17 E-value=33 Score=33.74 Aligned_cols=29 Identities=17% Similarity=0.393 Sum_probs=24.2
Q ss_pred HHHhhcCCcHHHHHHHcCCChhHHHHHHH
Q 001809 606 VLQQYFSGSLKDAAKSIGVCPTTLKRICR 634 (1010)
Q Consensus 606 ~L~~yF~~pl~eAAk~LGV~~TtLKRiCR 634 (1010)
.|.-+-+++.+|+|+.|||+..|+|.+-.
T Consensus 116 ~l~~~~g~s~~EIA~~lgis~~tV~~~l~ 144 (161)
T PRK09047 116 LLRYWEDMDVAETAAAMGCSEGSVKTHCS 144 (161)
T ss_pred HHHHHhcCCHHHHHHHHCCCHHHHHHHHH
Confidence 34455699999999999999999998654
No 246
>PTZ00044 ubiquitin; Provisional
Probab=40.08 E-value=52 Score=29.01 Aligned_cols=70 Identities=14% Similarity=0.284 Sum_probs=47.2
Q ss_pred EEEEEEcCCCeEEEEeCCCcChHHHHHHHHHHcCcccceeeeEeecCCCCeEEEecCCcHHHHHHHHhHhCCCeEEEEEe
Q 001809 903 IIVKATYKEDIIRFKFDPSAGCFQLYEEVARRLKLQNGTFQLKYLDDEEEWVMLVSDSDLQECFDILESLGKRSVRFLVR 982 (1010)
Q Consensus 903 ~~vKaty~~d~iRF~~~~s~g~~~L~~EIakRf~l~~~~f~lKYlDDd~EWVlLtcDaDL~EC~di~~~~~~~~vkl~V~ 982 (1010)
+.||-. .+.++.+++.++.-+.+|++-|+.+.|+......|-|-. .+ |..+..|.++ .-....+|.|.+.
T Consensus 3 i~vk~~-~G~~~~l~v~~~~tv~~lK~~i~~~~gi~~~~q~L~~~g----~~-L~d~~~l~~~----~i~~~~~i~l~~~ 72 (76)
T PTZ00044 3 ILIKTL-TGKKQSFNFEPDNTVQQVKMALQEKEGIDVKQIRLIYSG----KQ-MSDDLKLSDY----KVVPGSTIHMVLQ 72 (76)
T ss_pred EEEEeC-CCCEEEEEECCCCcHHHHHHHHHHHHCCCHHHeEEEECC----EE-ccCCCcHHHc----CCCCCCEEEEEEE
Confidence 455544 557888999999999999999999999988766666621 12 3434445444 2233456666655
No 247
>cd01110 HTH_SoxR Helix-Turn-Helix DNA binding domain of the SoxR transcription regulator. Helix-turn-helix (HTH) transcriptional regulator SoxR. The global regulator, SoxR, up-regulates gene expression of another transcription activator, SoxS, which directly stimulates the oxidative stress regulon genes in E. coli. The soxRS response renders the bacterial cell resistant to superoxide-generating agents, macrophage-generated nitric oxide, organic solvents, and antibiotics. The SoxR proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the unusually long spacer between the -35 and -10 promoter elements. They also harbor a regulatory C-terminal domain containing an iron-sulfur center.
Probab=40.04 E-value=28 Score=35.12 Aligned_cols=28 Identities=25% Similarity=0.283 Sum_probs=24.2
Q ss_pred CCcHHHHHHHcCCChhHHHHHHHHcCCCC
Q 001809 612 SGSLKDAAKSIGVCPTTLKRICRQHGISR 640 (1010)
Q Consensus 612 ~~pl~eAAk~LGV~~TtLKRiCR~~GI~R 640 (1010)
.+++.|+|+.+||++.||.-..++ |+-.
T Consensus 1 ~~~I~EvA~~~Gvs~~tLRyYE~~-GLl~ 28 (139)
T cd01110 1 ELSVGEVAKRSGVAVSALHFYEQK-GLIA 28 (139)
T ss_pred CCCHHHHHHHHCcCHHHHHHHHHC-CCCC
Confidence 368999999999999999988887 7644
No 248
>PRK10840 transcriptional regulator RcsB; Provisional
Probab=39.81 E-value=30 Score=35.77 Aligned_cols=35 Identities=17% Similarity=0.221 Sum_probs=27.1
Q ss_pred HHHHhhc-CCcHHHHHHHcCCChhHHH----HHHHHcCCC
Q 001809 605 SVLQQYF-SGSLKDAAKSIGVCPTTLK----RICRQHGIS 639 (1010)
Q Consensus 605 ~~L~~yF-~~pl~eAAk~LGV~~TtLK----RiCR~~GI~ 639 (1010)
+.|+-+. +++.+|+|++|+||..|+| ++.|++|++
T Consensus 157 evl~~~~~G~s~~eIA~~l~iS~~TV~~h~~~i~~Kl~v~ 196 (216)
T PRK10840 157 EVLRLFAEGFLVTEIAKKLNRSIKTISSQKKSAMMKLGVE 196 (216)
T ss_pred HHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHcCCC
Confidence 3444444 7899999999999998865 677788874
No 249
>PRK08241 RNA polymerase factor sigma-70; Validated
Probab=39.63 E-value=28 Score=39.06 Aligned_cols=29 Identities=10% Similarity=0.182 Sum_probs=25.4
Q ss_pred HHHhhcCCcHHHHHHHcCCChhHHHHHHH
Q 001809 606 VLQQYFSGSLKDAAKSIGVCPTTLKRICR 634 (1010)
Q Consensus 606 ~L~~yF~~pl~eAAk~LGV~~TtLKRiCR 634 (1010)
.|+-+++++.+|+|+.||+++.|+|.+-+
T Consensus 163 ~L~~~~g~s~~EIA~~lgis~~tVk~~l~ 191 (339)
T PRK08241 163 ILRDVLGWSAAEVAELLDTSVAAVNSALQ 191 (339)
T ss_pred hhHHhhCCCHHHHHHHhCCCHHHHHHHHH
Confidence 56778899999999999999999987643
No 250
>cd01793 Fubi Fubi ubiquitin-like protein. Fubi is a ubiquitin-like protein encoded by the fau gene which has an N-terminal ubiquitin-like domain (also referred to as FUBI) fused to the ribosomal protein S30. Fubi is thought to be a tumor suppressor protein and the FUBI domain may act as a substitute or an inhibitor of ubiquitin or one of ubiquitin's close relatives UCRP, FAT10, and Nedd8.
Probab=39.45 E-value=60 Score=28.87 Aligned_cols=68 Identities=15% Similarity=0.112 Sum_probs=45.3
Q ss_pred EEEEEEcCCCeEEEEeCCCcChHHHHHHHHHHcCcccceeeeEeecCCCCeEEEecCCcHHHHHHHHhHhCCCeEEEEEe
Q 001809 903 IIVKATYKEDIIRFKFDPSAGCFQLYEEVARRLKLQNGTFQLKYLDDEEEWVMLVSDSDLQECFDILESLGKRSVRFLVR 982 (1010)
Q Consensus 903 ~~vKaty~~d~iRF~~~~s~g~~~L~~EIakRf~l~~~~f~lKYlDDd~EWVlLtcDaDL~EC~di~~~~~~~~vkl~V~ 982 (1010)
+.||. ..++-+.+.|+.-+.+|++.|+.+.++......|-|- + . .|.-|.-|.+| .-....||.|.++
T Consensus 3 i~vk~---~~~~~l~v~~~~tV~~lK~~i~~~~gip~~~q~Li~~---G-k-~L~D~~tL~~~----~i~~~~tl~l~~~ 70 (74)
T cd01793 3 LFVRA---QNTHTLEVTGQETVSDIKAHVAGLEGIDVEDQVLLLA---G-V-PLEDDATLGQC----GVEELCTLEVAGR 70 (74)
T ss_pred EEEEC---CCEEEEEECCcCcHHHHHHHHHhhhCCCHHHEEEEEC---C-e-ECCCCCCHHHc----CCCCCCEEEEEEe
Confidence 56664 3688899999999999999999999998776555552 1 1 12223334442 3334567777665
No 251
>PF07022 Phage_CI_repr: Bacteriophage CI repressor helix-turn-helix domain; InterPro: IPR010744 This family consists of several phage CI repressor proteins and related bacterial sequences. The CI repressor is known to function as a transcriptional switch, determining whether transcription is lytic or lysogenic [].; GO: 0003677 DNA binding, 0045892 negative regulation of transcription, DNA-dependent; PDB: 2FJR_B.
Probab=39.43 E-value=16 Score=32.29 Aligned_cols=44 Identities=20% Similarity=0.348 Sum_probs=26.0
Q ss_pred HHHHHhhcCCcH-HHHHHHcCCChhHHHH-HHHHcCCCCCcchhhhhhH
Q 001809 604 LSVLQQYFSGSL-KDAAKSIGVCPTTLKR-ICRQHGISRWPSRKINKVN 650 (1010)
Q Consensus 604 l~~L~~yF~~pl-~eAAk~LGV~~TtLKR-iCR~~GI~RWP~Rki~sl~ 650 (1010)
++.|...++..- +|.|+.|||+..||-. .-++.-| |+-.+-.+-
T Consensus 3 i~rl~~~~g~~~~~~lA~~lgis~st~s~~~~~r~~~---P~~~l~~ia 48 (66)
T PF07022_consen 3 IERLKEALGVKSDKELAERLGISKSTLSNNWKKRGSI---PAEWLIKIA 48 (66)
T ss_dssp HHHHHHHHT-SSCHHHHCCTT--HHHHH-HHHHSSS-----HHHHHHHH
T ss_pred HHHHHHHhCCCCHHHHHHHhCcCHHHhhHHHHhCCCC---CHHHHHHHH
Confidence 455666666665 5999999999999994 4443334 666665553
No 252
>PRK09635 sigI RNA polymerase sigma factor SigI; Provisional
Probab=39.41 E-value=29 Score=38.87 Aligned_cols=29 Identities=24% Similarity=0.423 Sum_probs=26.1
Q ss_pred HHHhhcCCcHHHHHHHcCCChhHHHHHHH
Q 001809 606 VLQQYFSGSLKDAAKSIGVCPTTLKRICR 634 (1010)
Q Consensus 606 ~L~~yF~~pl~eAAk~LGV~~TtLKRiCR 634 (1010)
.|+.+|+++.+|+|+.||+++.++|.+.+
T Consensus 128 ~L~~~~g~s~~EIA~~Lgis~~tVr~~l~ 156 (290)
T PRK09635 128 VLHEIFGLPYQQIATTIGSQASTCRQLAH 156 (290)
T ss_pred hHHHHhCCCHHHHHHHHCcCHHHHHHHHH
Confidence 67889999999999999999999987654
No 253
>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=39.37 E-value=38 Score=29.14 Aligned_cols=33 Identities=27% Similarity=0.330 Sum_probs=27.1
Q ss_pred HHHHHhhcCCcHHHHHHHcCCChhHHHHHHHHc
Q 001809 604 LSVLQQYFSGSLKDAAKSIGVCPTTLKRICRQH 636 (1010)
Q Consensus 604 l~~L~~yF~~pl~eAAk~LGV~~TtLKRiCR~~ 636 (1010)
++.|++.=.++++|+|+.||||..|+.|=...+
T Consensus 6 l~~l~~~~~~s~~ela~~~~VS~~TiRRDl~~L 38 (57)
T PF08220_consen 6 LELLKEKGKVSVKELAEEFGVSEMTIRRDLNKL 38 (57)
T ss_pred HHHHHHcCCEEHHHHHHHHCcCHHHHHHHHHHH
Confidence 455677778999999999999999998866543
No 254
>cd01282 HTH_MerR-like_sg3 Helix-Turn-Helix DNA binding domain of putative transcription regulators from the MerR superfamily. Putative helix-turn-helix (HTH) MerR-like transcription regulators (subgroup 3). Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.
Probab=39.34 E-value=30 Score=33.51 Aligned_cols=30 Identities=27% Similarity=0.361 Sum_probs=24.5
Q ss_pred CcHHHHHHHcCCChhHHHHHHHHcCCCCCcch
Q 001809 613 GSLKDAAKSIGVCPTTLKRICRQHGISRWPSR 644 (1010)
Q Consensus 613 ~pl~eAAk~LGV~~TtLKRiCR~~GI~RWP~R 644 (1010)
|++.|+|+.+||++.||.-..+. |+-+ |.|
T Consensus 1 m~i~eva~~~gvs~~tlR~Ye~~-GLl~-p~r 30 (112)
T cd01282 1 MRIGELAARTGVSVRSLRYYEEQ-GLLV-PER 30 (112)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHC-CCCC-CCc
Confidence 57899999999999999998885 7644 444
No 255
>PRK15044 transcriptional regulator SirC; Provisional
Probab=39.26 E-value=33 Score=39.18 Aligned_cols=35 Identities=17% Similarity=0.170 Sum_probs=28.4
Q ss_pred HHHHhhc--CCcHHHHHHHcCCChhHHHHHHHHcCCC
Q 001809 605 SVLQQYF--SGSLKDAAKSIGVCPTTLKRICRQHGIS 639 (1010)
Q Consensus 605 ~~L~~yF--~~pl~eAAk~LGV~~TtLKRiCR~~GI~ 639 (1010)
+-|..++ .+++.+.|+.+|+|+++|+|++++.|..
T Consensus 199 ~~I~~nl~~~~SLeeLA~~lgmS~~tL~R~Fk~eg~T 235 (295)
T PRK15044 199 NIIISDLTRKWSQAEVAGKLFMSVSSLKRKLAAEEVS 235 (295)
T ss_pred HHHHhCcccCCCHHHHHHHhCCCHHHHHHHHHHcCCC
Confidence 3344444 4789999999999999999999998753
No 256
>PRK10703 DNA-binding transcriptional repressor PurR; Provisional
Probab=39.15 E-value=35 Score=37.44 Aligned_cols=24 Identities=33% Similarity=0.537 Sum_probs=21.3
Q ss_pred CcHHHHHHHcCCChhHHHHHHHHc
Q 001809 613 GSLKDAAKSIGVCPTTLKRICRQH 636 (1010)
Q Consensus 613 ~pl~eAAk~LGV~~TtLKRiCR~~ 636 (1010)
.+++|+|+.+|||.+|+.|..+..
T Consensus 2 ~Ti~dIA~~agVS~~TVSrvLn~~ 25 (341)
T PRK10703 2 ATIKDVAKRAGVSTTTVSHVINKT 25 (341)
T ss_pred CCHHHHHHHhCCCHHHHHHHHcCC
Confidence 479999999999999999999643
No 257
>PF03472 Autoind_bind: Autoinducer binding domain; InterPro: IPR005143 This domain binds N-acyl homoserine lactones (AHLs), which are also known as autoinducers. These are small, diffusible molecules used as communication signals in a large variety of proteobacteria. It is almost always found in association with the DNA-binding LuxR domain (IPR000792 from INTERPRO). The autoinducer binding domain forms the N-terminal region of the protein, while the DNA-binding domain forms the C-terminal region. In most cases, binding of AHL by this N-terminal domain leads to unmasking of the DNA-binding domain, allowing it to bind DNA and activate transcription []. In rare cases, some LuxR proteins such as EsaR, act as repressors []. In these proteins binding of AHL to this domain leads to inactivation of the protein as a transcriptional regulator. A large number of processes have been shown to be regulated by LuxR proteins, including bioluminescence, production of virulence factors in plant and animal pathogens, antibiotic production and plasmid transfer. Structural studies of TraR from Agrobacterium tumefaciens [, ] show that the functional protein is a homodimer. Binding of the cognate AHL is required for protein folding, resistance to proteases and dimerisation. The autoinducer binding domain binds its cognate AHL in an alpha/beta/alpha sandwich and provides an extensive dimerisation surface, though residues from the C-terminal region also make some contribution to dimerisation. The autoinducer binding domain is also required for interaction with RpoA, allowing transcription to occur []. There are some proteins which consist solely of the autoinducer binding domain. The function of these is not known, but TrlR from Agrobacterium has been shown to inhibit the activity of TraR by the formation of inactive heterodimers [].; PDB: 3SZT_A 1H0M_A 1L3L_B 2Q0O_B 2UV0_F 3IX8_A 3IX4_C 3IX3_A 3JPU_D 3QP8_A ....
Probab=38.93 E-value=67 Score=30.65 Aligned_cols=46 Identities=13% Similarity=0.192 Sum_probs=34.4
Q ss_pred CcccccchhhHHhcCCceEEEEeeecCCCCceEEEEEEeeecccCCch
Q 001809 257 NEAEYARVTHAVNHAVRSCIALPVFQFPEISCSAVLEIVSVKEKPNFD 304 (1010)
Q Consensus 257 ~~~EYpR~~~A~~~~VrGsLAlPVf~~~s~~ClAVlElV~t~ek~~f~ 304 (1010)
.+.+..-+..|.++|++..+.+||+.++.. .|+|=+..........
T Consensus 84 ~~~~~~~~~~a~~~Gl~~G~~~p~~~~~g~--~~~~s~~~~~~~~~~~ 129 (149)
T PF03472_consen 84 SPEQRRFFDEARDFGLRSGVSVPLHGPDGR--FGALSFAGDERDPDAE 129 (149)
T ss_dssp SHHHHHHHHHHHHTTTSEEEEEEEEECCGC--EEEEEEEESSSSCCHH
T ss_pred hHHHHHHHHHHHHcCCCceEEEEeEcCCCC--EEEEEEECCCCCCChH
Confidence 667777889999999999999999998755 4888554444444433
No 258
>PRK01381 Trp operon repressor; Provisional
Probab=38.79 E-value=18 Score=35.22 Aligned_cols=27 Identities=19% Similarity=0.182 Sum_probs=24.8
Q ss_pred CcHHHHHHHcCCChhHHHHHHHHcCCC
Q 001809 613 GSLKDAAKSIGVCPTTLKRICRQHGIS 639 (1010)
Q Consensus 613 ~pl~eAAk~LGV~~TtLKRiCR~~GI~ 639 (1010)
+|+.|+|+.||||.+|+-|..|.+.-.
T Consensus 56 ~sQREIa~~lGvSiaTITRgsn~Lk~~ 82 (99)
T PRK01381 56 LSQREIKQELGVGIATITRGSNSLKTA 82 (99)
T ss_pred cCHHHHHHHhCCceeeehhhHHHhccC
Confidence 799999999999999999999988753
No 259
>PRK15340 transcriptional regulator InvF; Provisional
Probab=38.71 E-value=29 Score=37.85 Aligned_cols=28 Identities=21% Similarity=0.485 Sum_probs=25.8
Q ss_pred CCcHHHHHHHcCCChhHHHHHHHHc-CCC
Q 001809 612 SGSLKDAAKSIGVCPTTLKRICRQH-GIS 639 (1010)
Q Consensus 612 ~~pl~eAAk~LGV~~TtLKRiCR~~-GI~ 639 (1010)
..++++.|+.+|+++++|.|+||++ |+.
T Consensus 125 ~~sleeLA~~~gvS~r~f~RlFk~~~G~t 153 (216)
T PRK15340 125 GNTMRMLGEDYGVSYTHFRRLCSRALGGK 153 (216)
T ss_pred CCCHHHHHHHHCcCHHHHHHHHHHHHCcC
Confidence 6789999999999999999999997 875
No 260
>PRK12542 RNA polymerase sigma factor; Provisional
Probab=38.59 E-value=34 Score=34.85 Aligned_cols=28 Identities=4% Similarity=0.322 Sum_probs=24.1
Q ss_pred HHHhhcCCcHHHHHHHcCCChhHHHHHH
Q 001809 606 VLQQYFSGSLKDAAKSIGVCPTTLKRIC 633 (1010)
Q Consensus 606 ~L~~yF~~pl~eAAk~LGV~~TtLKRiC 633 (1010)
.|+-+.+++.+|+|+.||++..|+|...
T Consensus 132 ~l~~~~g~s~~EIA~~lgis~~tVk~~l 159 (185)
T PRK12542 132 KYKVFYNLTYQEISSVMGITEANVRKQF 159 (185)
T ss_pred HHHHHcCCCHHHHHHHHCCCHHHHHHHH
Confidence 4556678999999999999999999764
No 261
>TIGR02952 Sig70_famx2 RNA polymerase sigma-70 factor, TIGR02952 family. This group of sigma factors are members of the sigma-70 family (TIGR02937). They and appear by homology, tree building, bidirectional best hits and one-to-a-genome distribution, to represent a conserved family. This family is found in a limited number of Gram-positive bacterial lineages.
Probab=38.52 E-value=36 Score=33.70 Aligned_cols=28 Identities=14% Similarity=0.094 Sum_probs=23.2
Q ss_pred HHhhcCCcHHHHHHHcCCChhHHHHHHH
Q 001809 607 LQQYFSGSLKDAAKSIGVCPTTLKRICR 634 (1010)
Q Consensus 607 L~~yF~~pl~eAAk~LGV~~TtLKRiCR 634 (1010)
|+-+.+++.+|+|+.|||+..|+|..-+
T Consensus 133 l~~~~g~s~~eIA~~l~is~~tv~~~l~ 160 (170)
T TIGR02952 133 LRFGQNLPIAEVARILGKTEGAVKILQF 160 (170)
T ss_pred HHHhcCCCHHHHHHHHCCCHHHHHHHHH
Confidence 3345599999999999999999987654
No 262
>PRK09636 RNA polymerase sigma factor SigJ; Provisional
Probab=38.43 E-value=32 Score=38.02 Aligned_cols=29 Identities=17% Similarity=0.481 Sum_probs=25.8
Q ss_pred HHHhhcCCcHHHHHHHcCCChhHHHHHHH
Q 001809 606 VLQQYFSGSLKDAAKSIGVCPTTLKRICR 634 (1010)
Q Consensus 606 ~L~~yF~~pl~eAAk~LGV~~TtLKRiCR 634 (1010)
.|+-+|+++.+|+|+.||++..|+|.+..
T Consensus 125 ~L~~~~g~s~~EIA~~lg~s~~tVk~~l~ 153 (293)
T PRK09636 125 LLHDVFGVPFDEIASTLGRSPAACRQLAS 153 (293)
T ss_pred HHHHHhCCCHHHHHHHHCCCHHHHHHHHH
Confidence 56778999999999999999999987755
No 263
>PRK12541 RNA polymerase sigma factor; Provisional
Probab=38.28 E-value=35 Score=33.87 Aligned_cols=29 Identities=24% Similarity=0.359 Sum_probs=24.6
Q ss_pred HHHhhcCCcHHHHHHHcCCChhHHHHHHH
Q 001809 606 VLQQYFSGSLKDAAKSIGVCPTTLKRICR 634 (1010)
Q Consensus 606 ~L~~yF~~pl~eAAk~LGV~~TtLKRiCR 634 (1010)
.|+-+.+++.+|+|+.||++..|+|....
T Consensus 122 ~l~~~~~~s~~eIA~~lgis~~tv~~~l~ 150 (161)
T PRK12541 122 LLRDYYGFSYKEIAEMTGLSLAKVKIELH 150 (161)
T ss_pred hhHHhcCCCHHHHHHHHCCCHHHHHHHHH
Confidence 55567899999999999999999987644
No 264
>PRK09638 RNA polymerase sigma factor SigY; Reviewed
Probab=38.13 E-value=28 Score=34.96 Aligned_cols=28 Identities=21% Similarity=0.381 Sum_probs=23.8
Q ss_pred HHhhcCCcHHHHHHHcCCChhHHHHHHH
Q 001809 607 LQQYFSGSLKDAAKSIGVCPTTLKRICR 634 (1010)
Q Consensus 607 L~~yF~~pl~eAAk~LGV~~TtLKRiCR 634 (1010)
|+-+++++.+|+|+.||++..++|...+
T Consensus 137 l~~~~g~s~~eIA~~l~is~~~V~~~l~ 164 (176)
T PRK09638 137 LKHYYGYTYEEIAKMLNIPEGTVKSRVH 164 (176)
T ss_pred ehhhcCCCHHHHHHHHCCChhHHHHHHH
Confidence 4456799999999999999999987763
No 265
>PRK12520 RNA polymerase sigma factor; Provisional
Probab=37.93 E-value=36 Score=34.89 Aligned_cols=29 Identities=3% Similarity=0.165 Sum_probs=24.8
Q ss_pred HHHhhcCCcHHHHHHHcCCChhHHHHHHH
Q 001809 606 VLQQYFSGSLKDAAKSIGVCPTTLKRICR 634 (1010)
Q Consensus 606 ~L~~yF~~pl~eAAk~LGV~~TtLKRiCR 634 (1010)
.|+-+.+++.+|+|+.||++..|+|....
T Consensus 141 ~l~~~~g~s~~EIA~~lgis~~tV~~~l~ 169 (191)
T PRK12520 141 MMREWLELETEEICQELQITATNAWVLLY 169 (191)
T ss_pred HHHHHcCCCHHHHHHHHCCCHHHHHHHHH
Confidence 45566799999999999999999997654
No 266
>PRK10572 DNA-binding transcriptional regulator AraC; Provisional
Probab=37.27 E-value=48 Score=36.13 Aligned_cols=47 Identities=21% Similarity=0.380 Sum_probs=34.3
Q ss_pred HHHHhhc--CCcHHHHHHHcCCChhHHHHHHHHc-CCCCCcchhhhhhHH
Q 001809 605 SVLQQYF--SGSLKDAAKSIGVCPTTLKRICRQH-GISRWPSRKINKVNR 651 (1010)
Q Consensus 605 ~~L~~yF--~~pl~eAAk~LGV~~TtLKRiCR~~-GI~RWP~Rki~sl~~ 651 (1010)
+-|.+++ .+++.+.|+.+|+|++.|.|++|+. |+.-==|.+...+.+
T Consensus 190 ~~i~~~~~~~isl~~lA~~~~lS~~~l~r~Fk~~~G~tp~~~l~~~Rl~~ 239 (290)
T PRK10572 190 QYISDHLASEFDIESVAQHVCLSPSRLAHLFRQQLGISVLRWREDQRISR 239 (290)
T ss_pred HHHHhcccCCCCHHHHHHHHCCCHHHHHHHHHHHHCcCHHHHHHHHHHHH
Confidence 3444555 7889999999999999999999997 875333444443433
No 267
>TIGR02959 SigZ RNA polymerase sigma factor, SigZ family. This family of RNA polymerase sigma factors is a member of the Sigma-70 subfamily (TIGR02937). One of these is designated as SigZ in B. subtilis (Swiss_Prot: SIGZ_BACSU). Interestingly, this group has a very sporatic distribution, B. subtilis, for instance, being the only sequenced strain of Bacilli with a member. Dechloromonas aromatica RCB appears to have two of these sigma factors. A member appears on a plasmid found in Photobacterium profundum SS9 and Vibrio fischeri ES114 (where a second one is chromosomally encoded).
Probab=37.24 E-value=39 Score=34.24 Aligned_cols=28 Identities=18% Similarity=0.148 Sum_probs=24.2
Q ss_pred HHHhhcCCcHHHHHHHcCCChhHHHHHH
Q 001809 606 VLQQYFSGSLKDAAKSIGVCPTTLKRIC 633 (1010)
Q Consensus 606 ~L~~yF~~pl~eAAk~LGV~~TtLKRiC 633 (1010)
.|.-+.+++.+|+|+.||+++.|+|..-
T Consensus 110 ~l~~~~g~s~~eIA~~lgis~~tV~~~l 137 (170)
T TIGR02959 110 RLTELEGLSQQEIAEKLGLSLSGAKSRV 137 (170)
T ss_pred HHHHHcCCCHHHHHHHHCCCHHHHHHHH
Confidence 4556789999999999999999998754
No 268
>TIGR02957 SigX4 RNA polymerase sigma-70 factor, TIGR02957 family. This group of sigma factors are members of the sigma-70 family (TIGR02937). They and appear by homology, tree building and bidirectional best hits, to represent a conserved family. This family is found in a limited number of bacterial lineages. This family includes apparent paralogous expansion in Streptomyces coelicolor A3(2), and multiple copies in Mycobacterium smegmatis MC2, Streptomyces avermitilis MA-4680 and Nocardia farcinica IFM10152.
Probab=37.13 E-value=35 Score=37.73 Aligned_cols=30 Identities=17% Similarity=0.317 Sum_probs=25.8
Q ss_pred HHHHhhcCCcHHHHHHHcCCChhHHHHHHH
Q 001809 605 SVLQQYFSGSLKDAAKSIGVCPTTLKRICR 634 (1010)
Q Consensus 605 ~~L~~yF~~pl~eAAk~LGV~~TtLKRiCR 634 (1010)
=.|+-+|+++.+|+|+.||++..++|.+-+
T Consensus 117 ~~L~~~~g~s~~EIA~~lg~s~~tVr~~l~ 146 (281)
T TIGR02957 117 FVLREVFDYPYEEIASIVGKSEANCRQLVS 146 (281)
T ss_pred HHHHHHcCCCHHHHHHHHCCCHHHHHHHHH
Confidence 367788999999999999999999886643
No 269
>TIGR03209 P21_Cbot clostridium toxin-associated regulator BotR. Similarly, tetanus toxin production of Clostridium tetani is regulated by TetR which is a very close relative of BotR. Both BotR and TetR are members of the TIGR02937 subfamily of sigma-70 RNA polymerase sigma factors. Functional complementation experiments have been done for botR and tetR in highly transformable strain of Clostridium perfringens host cells to assess functional interchangeability of sigma factors and it has been confirmed that they are interchangeable in vivo.
Probab=37.07 E-value=24 Score=34.31 Aligned_cols=26 Identities=12% Similarity=0.146 Sum_probs=21.9
Q ss_pred HHHhhcCCcHHHHHHHcCCChhHHHH
Q 001809 606 VLQQYFSGSLKDAAKSIGVCPTTLKR 631 (1010)
Q Consensus 606 ~L~~yF~~pl~eAAk~LGV~~TtLKR 631 (1010)
.|+-|=+++.+|+|+.||+++.|+|+
T Consensus 117 ~l~~~~~~s~~EIA~~l~is~~tV~~ 142 (142)
T TIGR03209 117 YMKFFEDMKEIDIAKKLHISRQSVYK 142 (142)
T ss_pred HHHHHcCCCHHHHHHHHCcCHHhhcC
Confidence 44455678999999999999999985
No 270
>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=36.84 E-value=51 Score=27.39 Aligned_cols=24 Identities=25% Similarity=0.368 Sum_probs=20.1
Q ss_pred CcHHHHHHHcCCChhHHHHHHHHc
Q 001809 613 GSLKDAAKSIGVCPTTLKRICRQH 636 (1010)
Q Consensus 613 ~pl~eAAk~LGV~~TtLKRiCR~~ 636 (1010)
++.++.|+.||||..|++|-...+
T Consensus 16 it~~eLa~~l~vS~rTi~~~i~~L 39 (55)
T PF08279_consen 16 ITAKELAEELGVSRRTIRRDIKEL 39 (55)
T ss_dssp BEHHHHHHHCTS-HHHHHHHHHHH
T ss_pred cCHHHHHHHhCCCHHHHHHHHHHH
Confidence 899999999999999998866544
No 271
>TIGR02943 Sig70_famx1 RNA polymerase sigma-70 factor, TIGR02943 family. This group of sigma factors are members of the sigma-70 family (TIGR02937). They and appear by homology, tree building, bidirectional best hits and one-to-a-genome distribution, to represent a conserved family.
Probab=36.79 E-value=38 Score=34.96 Aligned_cols=29 Identities=0% Similarity=0.120 Sum_probs=24.3
Q ss_pred HHHhhcCCcHHHHHHHcCCChhHHHHHHH
Q 001809 606 VLQQYFSGSLKDAAKSIGVCPTTLKRICR 634 (1010)
Q Consensus 606 ~L~~yF~~pl~eAAk~LGV~~TtLKRiCR 634 (1010)
.|+-+-+++.+|+|+.||++..|+|.+..
T Consensus 141 ~l~~~~g~s~~EIA~~lgis~~tvk~rl~ 169 (188)
T TIGR02943 141 MMREVLGFESDEICQELEISTSNCHVLLY 169 (188)
T ss_pred HHHHHhCCCHHHHHHHhCCCHHHHHHHHH
Confidence 44455689999999999999999987653
No 272
>PRK13890 conjugal transfer protein TrbA; Provisional
Probab=36.76 E-value=37 Score=33.53 Aligned_cols=33 Identities=15% Similarity=0.084 Sum_probs=29.0
Q ss_pred HHHHHhhcCCcHHHHHHHcCCChhHHHHHHHHc
Q 001809 604 LSVLQQYFSGSLKDAAKSIGVCPTTLKRICRQH 636 (1010)
Q Consensus 604 l~~L~~yF~~pl~eAAk~LGV~~TtLKRiCR~~ 636 (1010)
+..+....+++++|.|+.+||+.+++.++.+..
T Consensus 10 l~~ll~~~Glsq~eLA~~~Gis~~~is~iE~g~ 42 (120)
T PRK13890 10 VLRLLDERHMTKKELSERSGVSISFLSDLTTGK 42 (120)
T ss_pred HHHHHHHcCCCHHHHHHHHCcCHHHHHHHHcCC
Confidence 456777889999999999999999999998754
No 273
>PRK10371 DNA-binding transcriptional regulator MelR; Provisional
Probab=36.70 E-value=46 Score=37.20 Aligned_cols=34 Identities=9% Similarity=0.053 Sum_probs=28.1
Q ss_pred CCcHHHHHHHcCCChhHHHHHHHHc-CCCCCcchh
Q 001809 612 SGSLKDAAKSIGVCPTTLKRICRQH-GISRWPSRK 645 (1010)
Q Consensus 612 ~~pl~eAAk~LGV~~TtLKRiCR~~-GI~RWP~Rk 645 (1010)
.+++++.|+.+||++.+|.|++++. |+.--=|.+
T Consensus 207 ~~tl~~lA~~~~~S~~~l~r~Fk~~~G~t~~~~l~ 241 (302)
T PRK10371 207 ALTINDVAEHVKLNANYAMGIFQRVMQLTMKQYIT 241 (302)
T ss_pred CCCHHHHHHHHCcCHHHHHHHHHHHhCCCHHHHHH
Confidence 5899999999999999999999995 875333333
No 274
>TIGR02329 propionate_PrpR propionate catabolism operon regulatory protein PrpR. At least five distinct pathways exists for the catabolism of propionate by way of propionyl-CoA. Members of this family represent the transcriptional regulatory protein PrpR, whose gene is found in most cases divergently transcribed from an operon for the methylcitric acid cycle of propionate catabolism. 2-methylcitric acid, a catabolite by this pathway, is a coactivator of PrpR.
Probab=36.66 E-value=32 Score=41.99 Aligned_cols=26 Identities=38% Similarity=0.542 Sum_probs=22.8
Q ss_pred hhcCCcHHHHHHHcCCChhHHHHHHH
Q 001809 609 QYFSGSLKDAAKSIGVCPTTLKRICR 634 (1010)
Q Consensus 609 ~yF~~pl~eAAk~LGV~~TtLKRiCR 634 (1010)
+..++-..+||+.|||++|||+|.-|
T Consensus 500 ~~~~Gn~~~aA~~LGIsRtTL~Rklk 525 (526)
T TIGR02329 500 ERFGGDRDAAAKALGISRTTLWRRLK 525 (526)
T ss_pred HHcCCCHHHHHHHhCCCHHHHHHHHh
Confidence 45678899999999999999998765
No 275
>PF13744 HTH_37: Helix-turn-helix domain; PDB: 2A6C_B 2O38_A.
Probab=36.40 E-value=38 Score=30.90 Aligned_cols=31 Identities=13% Similarity=0.232 Sum_probs=25.3
Q ss_pred HHHHHhhcCCcHHHHHHHcCCChhHHHHHHH
Q 001809 604 LSVLQQYFSGSLKDAAKSIGVCPTTLKRICR 634 (1010)
Q Consensus 604 l~~L~~yF~~pl~eAAk~LGV~~TtLKRiCR 634 (1010)
+.+++.-=+++++|+|+.|||+.+++-|+=+
T Consensus 23 i~~~~~~~~ltQ~e~A~~lgisq~~vS~l~~ 53 (80)
T PF13744_consen 23 IRELREERGLTQAELAERLGISQPRVSRLEN 53 (80)
T ss_dssp HHHHHHCCT--HHHHHHHHTS-HHHHHHHHT
T ss_pred HHHHHHHcCCCHHHHHHHHCCChhHHHHHHc
Confidence 7778888899999999999999999999874
No 276
>TIGR02960 SigX5 RNA polymerase sigma-70 factor, TIGR02960 family. This group of sigma factors are members of the sigma-70 family (TIGR02937). They and appear by homology, tree building, bidirectional best hits and one-to-a-genome distribution, to represent a conserved family.
Probab=36.39 E-value=35 Score=37.86 Aligned_cols=29 Identities=10% Similarity=0.252 Sum_probs=25.3
Q ss_pred HHHhhcCCcHHHHHHHcCCChhHHHHHHH
Q 001809 606 VLQQYFSGSLKDAAKSIGVCPTTLKRICR 634 (1010)
Q Consensus 606 ~L~~yF~~pl~eAAk~LGV~~TtLKRiCR 634 (1010)
.|+-+++++.+|+|+.|||++.|+|.+-.
T Consensus 152 ~L~~~~g~s~~EIA~~lgis~~tV~~~l~ 180 (324)
T TIGR02960 152 LLRDVLGWRAAETAELLGTSTASVNSALQ 180 (324)
T ss_pred hhHHHhCCCHHHHHHHHCCCHHHHHHHHH
Confidence 56778899999999999999999987643
No 277
>PRK12516 RNA polymerase sigma factor; Provisional
Probab=36.26 E-value=39 Score=34.97 Aligned_cols=29 Identities=21% Similarity=0.155 Sum_probs=24.3
Q ss_pred HHHhhcCCcHHHHHHHcCCChhHHHHHHH
Q 001809 606 VLQQYFSGSLKDAAKSIGVCPTTLKRICR 634 (1010)
Q Consensus 606 ~L~~yF~~pl~eAAk~LGV~~TtLKRiCR 634 (1010)
.|+-+-+++.+|+|+.|||+..|+|..-.
T Consensus 126 ~L~~~~g~s~~EIA~~Lgis~~tVk~~l~ 154 (187)
T PRK12516 126 ILVGASGFAYEEAAEICGCAVGTIKSRVN 154 (187)
T ss_pred HHHHHcCCCHHHHHHHHCCCHHHHHHHHH
Confidence 45566799999999999999999987643
No 278
>PRK09526 lacI lac repressor; Reviewed
Probab=36.16 E-value=42 Score=36.83 Aligned_cols=24 Identities=33% Similarity=0.379 Sum_probs=21.2
Q ss_pred CcHHHHHHHcCCChhHHHHHHHHc
Q 001809 613 GSLKDAAKSIGVCPTTLKRICRQH 636 (1010)
Q Consensus 613 ~pl~eAAk~LGV~~TtLKRiCR~~ 636 (1010)
.+++|+||..|||.+|+.|.-...
T Consensus 6 ~ti~dIA~~aGVS~~TVSrvLn~~ 29 (342)
T PRK09526 6 VTLYDVARYAGVSYQTVSRVLNQA 29 (342)
T ss_pred CcHHHHHHHhCCCHHHHHHHhcCC
Confidence 379999999999999999998654
No 279
>PHA00675 hypothetical protein
Probab=36.07 E-value=28 Score=32.69 Aligned_cols=26 Identities=19% Similarity=0.189 Sum_probs=23.1
Q ss_pred hcCCcHHHHHHHcCCChhHHHHHHHH
Q 001809 610 YFSGSLKDAAKSIGVCPTTLKRICRQ 635 (1010)
Q Consensus 610 yF~~pl~eAAk~LGV~~TtLKRiCR~ 635 (1010)
+-..+..+.|+.+||+.+|+..||+.
T Consensus 37 r~G~s~~~IA~~fGVsrstV~~I~~g 62 (78)
T PHA00675 37 VEGMSYAVLAEKFEQSKGAIAKICRY 62 (78)
T ss_pred hcCccHHHHHHHhCCCHHHHHHHHcc
Confidence 45667889999999999999999985
No 280
>PRK11753 DNA-binding transcriptional dual regulator Crp; Provisional
Probab=36.04 E-value=26 Score=35.95 Aligned_cols=37 Identities=11% Similarity=0.258 Sum_probs=30.4
Q ss_pred cCCcHHHHHHHcCCChhHHHHHHH---HcCCCCCcchhhh
Q 001809 611 FSGSLKDAAKSIGVCPTTLKRICR---QHGISRWPSRKIN 647 (1010)
Q Consensus 611 F~~pl~eAAk~LGV~~TtLKRiCR---~~GI~RWP~Rki~ 647 (1010)
+.++.++.|..||+++.|+-|+-+ +-||-+|..|+|.
T Consensus 167 ~~~t~~~lA~~lG~tr~tvsR~l~~l~~~gii~~~~~~i~ 206 (211)
T PRK11753 167 IKITRQEIGRIVGCSREMVGRVLKMLEDQGLISAHGKTIV 206 (211)
T ss_pred cCCCHHHHHHHhCCCHHHHHHHHHHHHHCCCEEecCCEEE
Confidence 468889999999999999988654 5588888888764
No 281
>PRK09415 RNA polymerase factor sigma C; Reviewed
Probab=36.00 E-value=39 Score=34.39 Aligned_cols=29 Identities=31% Similarity=0.285 Sum_probs=24.3
Q ss_pred HHHhhcCCcHHHHHHHcCCChhHHHHHHH
Q 001809 606 VLQQYFSGSLKDAAKSIGVCPTTLKRICR 634 (1010)
Q Consensus 606 ~L~~yF~~pl~eAAk~LGV~~TtLKRiCR 634 (1010)
.|.-+.+++.+|+|+.|||+..|+|.+..
T Consensus 137 ~l~~~~g~s~~EIA~~l~is~~tv~~~l~ 165 (179)
T PRK09415 137 YLFYYEELSIKEIAEVTGVNENTVKTRLK 165 (179)
T ss_pred HhHHhcCCCHHHHHHHHCCCHHHHHHHHH
Confidence 45566799999999999999999987654
No 282
>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=36.00 E-value=43 Score=32.42 Aligned_cols=29 Identities=21% Similarity=0.345 Sum_probs=23.4
Q ss_pred HHhhcCCcHHHHHHHcCCChhHHHHHHHH
Q 001809 607 LQQYFSGSLKDAAKSIGVCPTTLKRICRQ 635 (1010)
Q Consensus 607 L~~yF~~pl~eAAk~LGV~~TtLKRiCR~ 635 (1010)
|.-+-++|.+|+|+.|||+..|+|.+-++
T Consensus 124 l~~~~~~~~~eIA~~lgis~~tv~~~~~r 152 (161)
T TIGR02985 124 LSRFEGKSYKEIAEELGISVKTVEYHISK 152 (161)
T ss_pred HHHHcCCCHHHHHHHHCCCHHHHHHHHHH
Confidence 33455899999999999999998876543
No 283
>PRK12523 RNA polymerase sigma factor; Reviewed
Probab=35.69 E-value=42 Score=33.80 Aligned_cols=29 Identities=10% Similarity=0.179 Sum_probs=24.5
Q ss_pred HHHhhcCCcHHHHHHHcCCChhHHHHHHH
Q 001809 606 VLQQYFSGSLKDAAKSIGVCPTTLKRICR 634 (1010)
Q Consensus 606 ~L~~yF~~pl~eAAk~LGV~~TtLKRiCR 634 (1010)
.|.-+-+++.+|+|+.|||+..|+|.+-+
T Consensus 129 ~L~~~~g~s~~EIA~~lgis~~tV~~~l~ 157 (172)
T PRK12523 129 LYNRLDGMGHAEIAERLGVSVSRVRQYLA 157 (172)
T ss_pred HHHHHcCCCHHHHHHHHCCCHHHHHHHHH
Confidence 45566799999999999999999987653
No 284
>TIGR02859 spore_sigH RNA polymerase sigma-H factor. Members of this protein family are RNA polymerase sigma-H factor for sporulation in endospore-forming bacteria. This protein is also called Sigma-30 and SigH. Although rather close homologs are detected in Listeria, Listeria does not form spores and the role of the related sigma factor in that genus is in doubt.
Probab=35.47 E-value=44 Score=34.11 Aligned_cols=22 Identities=9% Similarity=0.060 Sum_probs=19.5
Q ss_pred hcCCcHHHHHHHcCCChhHHHH
Q 001809 610 YFSGSLKDAAKSIGVCPTTLKR 631 (1010)
Q Consensus 610 yF~~pl~eAAk~LGV~~TtLKR 631 (1010)
+=+++.+|+|+.||++..|+|.
T Consensus 163 ~~~~s~~eIA~~l~~s~~tV~~ 184 (198)
T TIGR02859 163 LDGKSYQEIACDLNRHVKSIDN 184 (198)
T ss_pred HcCCCHHHHHHHHCCCHHHHHH
Confidence 3389999999999999999984
No 285
>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=35.35 E-value=38 Score=29.30 Aligned_cols=26 Identities=23% Similarity=0.235 Sum_probs=22.4
Q ss_pred CCcHHHHHHHcCCChhHHHHHHHHcC
Q 001809 612 SGSLKDAAKSIGVCPTTLKRICRQHG 637 (1010)
Q Consensus 612 ~~pl~eAAk~LGV~~TtLKRiCR~~G 637 (1010)
.++++|+|+.||+|..||++.+.++.
T Consensus 19 ~~~~~ela~~l~~S~rti~~~i~~L~ 44 (59)
T PF08280_consen 19 WITLKELAKKLNISERTIKNDINELN 44 (59)
T ss_dssp SBBHHHHHHHCTS-HHHHHHHHHHHH
T ss_pred CCcHHHHHHHHCCCHHHHHHHHHHHH
Confidence 57889999999999999999988775
No 286
>PRK12540 RNA polymerase sigma factor; Provisional
Probab=35.35 E-value=41 Score=34.68 Aligned_cols=29 Identities=28% Similarity=0.172 Sum_probs=24.7
Q ss_pred HHHhhcCCcHHHHHHHcCCChhHHHHHHH
Q 001809 606 VLQQYFSGSLKDAAKSIGVCPTTLKRICR 634 (1010)
Q Consensus 606 ~L~~yF~~pl~eAAk~LGV~~TtLKRiCR 634 (1010)
.|+-+.+++.+|+|+.||++..|+|....
T Consensus 121 ~L~~~~g~s~~EIA~~Lgis~~tV~~~l~ 149 (182)
T PRK12540 121 ILVGASGFSYEDAAAICGCAVGTIKSRVN 149 (182)
T ss_pred hHHHHcCCCHHHHHHHHCCCHHHHHHHHH
Confidence 44556799999999999999999998654
No 287
>cd01107 HTH_BmrR Helix-Turn-Helix DNA binding domain of the BmrR transcription regulator. Helix-turn-helix (HTH) multidrug-efflux transporter transcription regulator, BmrR and YdfL of Bacillus subtilis, and related proteins; N-terminal domain. Bmr is a membrane protein which causes the efflux of a variety of toxic substances and antibiotics. BmrR is comprised of two distinct domains that harbor a regulatory (effector-binding) site and an active (DNA-binding) site. The conserved N-terminal domain contains a winged HTH motif that mediates DNA binding, while the C-terminal domain binds coactivating, toxic compounds. BmrR shares the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements.
Probab=35.35 E-value=34 Score=32.87 Aligned_cols=25 Identities=16% Similarity=0.158 Sum_probs=22.8
Q ss_pred CcHHHHHHHcCCChhHHHHHHHHcCC
Q 001809 613 GSLKDAAKSIGVCPTTLKRICRQHGI 638 (1010)
Q Consensus 613 ~pl~eAAk~LGV~~TtLKRiCR~~GI 638 (1010)
+++.|+|+.+||++.||+-.+++ |+
T Consensus 1 ~~i~eva~~~gis~~tlR~ye~~-GL 25 (108)
T cd01107 1 FTIGEFAKLSNLSIKALRYYDKI-GL 25 (108)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHc-CC
Confidence 57899999999999999999997 75
No 288
>PRK15185 transcriptional regulator HilD; Provisional
Probab=35.06 E-value=41 Score=38.62 Aligned_cols=27 Identities=33% Similarity=0.351 Sum_probs=24.9
Q ss_pred CCcHHHHHHHcCCChhHHHHHHHHcCC
Q 001809 612 SGSLKDAAKSIGVCPTTLKRICRQHGI 638 (1010)
Q Consensus 612 ~~pl~eAAk~LGV~~TtLKRiCR~~GI 638 (1010)
.+++.+.|+.+|+++.+|+|+.++.|+
T Consensus 222 ~~SledLA~~lgmS~~tL~R~FK~~G~ 248 (309)
T PRK15185 222 QWKLTDVADHIFMSTSTLKRKLAEEGT 248 (309)
T ss_pred CCCHHHHHHHHCcCHHHHHHHHHHcCC
Confidence 569999999999999999999998776
No 289
>cd01810 ISG15_repeat2 ISG15 ubiquitin-like protein, second repeat of 2. ISG15 is a ubiquitin-like protein containing two ubiquitin homology domains and becomes conjugated to a variety of proteins when cells are treated with type I interferon or lipopolysaccharide. Although ISG15 has properties similar to those of other ubiquitin-like molecules, it is a unique member of the ubiquitin-like superfamily, whose expression and conjugation to target proteins are tightly regulated by specific signaling pathways, indicating it may have specialized functions in the immune system.
Probab=34.99 E-value=61 Score=28.80 Aligned_cols=38 Identities=18% Similarity=0.264 Sum_probs=31.9
Q ss_pred cCCCeEEEEeCCCcChHHHHHHHHHHcCcccceeeeEe
Q 001809 909 YKEDIIRFKFDPSAGCFQLYEEVARRLKLQNGTFQLKY 946 (1010)
Q Consensus 909 y~~d~iRF~~~~s~g~~~L~~EIakRf~l~~~~f~lKY 946 (1010)
..++++-+.+.++.-+.+|++.|+.+.++....+.|-|
T Consensus 6 ~~g~~~~l~v~~~~tV~~lK~~I~~~~gi~~~~q~L~~ 43 (74)
T cd01810 6 DKGRSSIYEVQLTQTVATLKQQVSQRERVQADQFWLSF 43 (74)
T ss_pred CCCCEEEEEECCcChHHHHHHHHHHHhCCCHHHeEEEE
Confidence 44578889999999999999999999999877666655
No 290
>PRK11179 DNA-binding transcriptional regulator AsnC; Provisional
Probab=34.79 E-value=46 Score=33.66 Aligned_cols=33 Identities=24% Similarity=0.315 Sum_probs=27.2
Q ss_pred HHHHHhhcCCcHHHHHHHcCCChhHHHHHHHHc
Q 001809 604 LSVLQQYFSGSLKDAAKSIGVCPTTLKRICRQH 636 (1010)
Q Consensus 604 l~~L~~yF~~pl~eAAk~LGV~~TtLKRiCR~~ 636 (1010)
++.|++-=-.|..+.|++||++++|+.++-+++
T Consensus 15 l~~Lq~d~R~s~~eiA~~lglS~~tV~~Ri~rL 47 (153)
T PRK11179 15 LEALMENARTPYAELAKQFGVSPGTIHVRVEKM 47 (153)
T ss_pred HHHHHHcCCCCHHHHHHHHCcCHHHHHHHHHHH
Confidence 456777778999999999999999998776554
No 291
>cd01109 HTH_YyaN Helix-Turn-Helix DNA binding domain of the MerR-like transcription regulators YyaN and YraB. Putative helix-turn-helix (HTH) MerR-like transcription regulators of Bacillus subtilis, YyaN and YraB, and related proteins; N-terminal domain. Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of 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=34.55 E-value=64 Score=31.07 Aligned_cols=26 Identities=19% Similarity=0.300 Sum_probs=21.9
Q ss_pred CcHHHHHHHcCCChhHHHHHHHHcCC
Q 001809 613 GSLKDAAKSIGVCPTTLKRICRQHGI 638 (1010)
Q Consensus 613 ~pl~eAAk~LGV~~TtLKRiCR~~GI 638 (1010)
+++.|+|+.+||++.||....++--|
T Consensus 1 ~~i~e~a~~~gvs~~tlr~ye~~gll 26 (113)
T cd01109 1 YTIKEVAEKTGLSADTLRYYEKEGLL 26 (113)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHCCCC
Confidence 47899999999999999988775434
No 292
>PF00196 GerE: Bacterial regulatory proteins, luxR family; InterPro: IPR000792 This domain is a DNA-binding, helix-turn-helix (HTH) domain of about 65 amino acids, present in transcription regulators of the LuxR/FixJ family of response regulators. The domain is named after Vibrio fischeri luxR, a transcriptional activator for quorum-sensing control of luminescence. LuxR-type HTH domain proteins occur in a variety of organisms. The DNA-binding HTH domain is usually located in the C-terminal region; the N-terminal region often containing an autoinducer-binding domain or a response regulatory domain. Most luxR-type regulators act as transcription activators, but some can be repressors or have a dual role for different sites. LuxR-type HTH regulators control a wide variety of activities in various biological processes. The luxR-type, DNA-binding HTH domain forms a four-helical bundle structure. The HTH motif comprises the second and third helices, known as the scaffold and recognition helix, respectively. The HTH binds DNA in the major groove, where the N-terminal part of the recognition helix makes most of the DNA contacts. The fourth helix is involved in dimerisation of gerE and traR. Signalling events by one of the four activation mechanisms described below lead to multimerisation of the regulator. The regulators bind DNA as multimers [, , ]. LuxR-type HTH proteins can be activated by one of four different mechanisms: 1) Regulators which belong to a two-component sensory transduction system where the protein is activated by its phosphorylation, generally on an aspartate residue, by a transmembrane kinase [, ]. Some proteins that belong to this category are: Rhizobiaceae fixJ (global regulator inducing expression of nitrogen-fixation genes in microaerobiosis) Escherichia coli and Salmonella typhimurium uhpA (activates hexose phosphate transport gene uhpT) E. coli narL and narP (activate nitrate reductase operon) Enterobacteria rcsB (regulation of exopolysaccharide biosynthesis in enteric and plant pathogenesis) Bordetella pertussis bvgA (virulence factor) Bacillus subtilis coma (involved in expression of late-expressing competence genes) 2) Regulators which are activated, or in very rare cases repressed, when bound to N-acyl homoserine lactones, which are used as quorum sensing molecules in a variety of Gram-negative bacteria []: V. fischeri luxR (activates bioluminescence operon) Agrobacterium tumefaciens traR (regulation of Ti plasmid transfer) Erwinia carotovora carR (control of carbapenem antibiotics biosynthesis) E. carotovora expR (virulence factor for soft rot disease; activates plant tissue macerating enzyme genes) Pseudomonas aeruginosa lasR (activates elastase gene lasB) Erwinia chrysanthemi echR and Erwinia stewartii esaR Pseudomonas chlororaphis phzR (positive regulator of phenazine antibiotic production) Pseudomonas aeruginosa rhlR (activates rhlAB operon and lasB gene) 3) Autonomous effector domain regulators, without a regulatory domain, represented by gerE []. B. subtilis gerE (transcription activator and repressor for the regulation of spore formation) 4) Multiple ligand-binding regulators, exemplified by malT []. E. coli malT (activates maltose operon; MalT binds ATP and maltotriose); GO: 0003700 sequence-specific DNA binding transcription factor activity, 0043565 sequence-specific DNA binding, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 3SZT_A 3CLO_A 1H0M_A 1L3L_A 3C57_B 1ZLK_B 1ZLJ_H 3C3W_B 1RNL_A 1ZG1_A ....
Probab=34.47 E-value=31 Score=29.22 Aligned_cols=27 Identities=30% Similarity=0.490 Sum_probs=20.9
Q ss_pred CCcHHHHHHHcCCChhHHHH----HHHHcCC
Q 001809 612 SGSLKDAAKSIGVCPTTLKR----ICRQHGI 638 (1010)
Q Consensus 612 ~~pl~eAAk~LGV~~TtLKR----iCR~~GI 638 (1010)
+++.+|+|+.|||++.|++. +.+++|+
T Consensus 18 G~~~~eIA~~l~is~~tV~~~~~~i~~Kl~~ 48 (58)
T PF00196_consen 18 GMSNKEIAEELGISEKTVKSHRRRIMKKLGV 48 (58)
T ss_dssp TS-HHHHHHHHTSHHHHHHHHHHHHHHHHT-
T ss_pred cCCcchhHHhcCcchhhHHHHHHHHHHHhCC
Confidence 78999999999999999764 5556665
No 293
>PF07750 GcrA: GcrA cell cycle regulator; InterPro: IPR011681 GcrA, together with CtrA (see IPR001789 from INTERPRO and IPR001867 from INTERPRO), form a master cell cycle regulator. These bacterial regulators are involved in controlling the progression and asymmetric polar morphogenesis []. During this process, there are temporal and spatial variations in the concentrations of GcrA and CtrA. The variation in concentration produces time and space dependent transcriptional regulation of modular functions that implement cell-cycle processes []. More specifically, GcrA acts as an activator of components of the replisome and the segregation machinery [].
Probab=34.34 E-value=37 Score=35.41 Aligned_cols=37 Identities=19% Similarity=0.309 Sum_probs=32.6
Q ss_pred HHHHHhhc--CCcHHHHHHHcC-CChhHHHHHHHHcCCCC
Q 001809 604 LSVLQQYF--SGSLKDAAKSIG-VCPTTLKRICRQHGISR 640 (1010)
Q Consensus 604 l~~L~~yF--~~pl~eAAk~LG-V~~TtLKRiCR~~GI~R 640 (1010)
++.|++.+ +++..++|++|| |+...+--+++++|+..
T Consensus 8 ~~~L~~lw~~G~SasqIA~~lg~vsRnAViGk~hRlgL~~ 47 (162)
T PF07750_consen 8 VERLRKLWAEGLSASQIARQLGGVSRNAVIGKAHRLGLSG 47 (162)
T ss_pred HHHHHHHHHcCCCHHHHHHHhCCcchhhhhhhhhcccccc
Confidence 56778777 799999999999 99999999999999855
No 294
>TIGR02297 HpaA 4-hydroxyphenylacetate catabolism regulatory protein HpaA. This putative transcriptional regulator, which contains both the substrate-binding, dimerization domain (pfam02311) and the helix-turn-helix DNA-binding domain (pfam00165) of the AraC famil, is located proximal to genes of the 4-hydroxyphenylacetate catabolism pathway.
Probab=34.33 E-value=35 Score=36.95 Aligned_cols=40 Identities=28% Similarity=0.583 Sum_probs=31.7
Q ss_pred HHHhhc--CCcHHHHHHHcCCChhHHHHHHHH-cCCCCCcchhhh
Q 001809 606 VLQQYF--SGSLKDAAKSIGVCPTTLKRICRQ-HGISRWPSRKIN 647 (1010)
Q Consensus 606 ~L~~yF--~~pl~eAAk~LGV~~TtLKRiCR~-~GI~RWP~Rki~ 647 (1010)
-|..+| ++++++.|+.+|+|+..|-|++|+ .|+. |..=|.
T Consensus 194 ~I~~~~~~~~sl~~lA~~~~~S~~~l~r~Fk~~~G~t--~~~yi~ 236 (287)
T TIGR02297 194 LIEENYKQHLRLPEYADRLGISESRLNDICRRFSALS--PKRLII 236 (287)
T ss_pred HHHHhhccCCCHHHHHHHHCCCHHHHHHHHHHHhCCC--HHHHHH
Confidence 455555 569999999999999999999999 6886 444443
No 295
>PRK13870 transcriptional regulator TraR; Provisional
Probab=34.33 E-value=1.8e+02 Score=31.67 Aligned_cols=51 Identities=25% Similarity=0.378 Sum_probs=36.1
Q ss_pred cccccchhhHHhcCCceEEEEeeecCCCCceEEEEEEeeecccCCchHHHHHH
Q 001809 258 EAEYARVTHAVNHAVRSCIALPVFQFPEISCSAVLEIVSVKEKPNFDAEIENI 310 (1010)
Q Consensus 258 ~~EYpR~~~A~~~~VrGsLAlPVf~~~s~~ClAVlElV~t~ek~~f~~E~e~v 310 (1010)
+.+-.-...|.++|++-.+.+||.++.. +.|++=+.......++..+++.+
T Consensus 96 ~~~~~~~~~a~~~Gl~~G~tiPi~~~~g--~~~~lS~~~~~~~~~~~~~~~~~ 146 (234)
T PRK13870 96 KDERAFYAHAADFGIRSGITIPIKTANG--SMSMFTLASEKPVIDLDREIDAV 146 (234)
T ss_pred HHHHHHHHHHHHcCCCCceEEEEECCCC--CEEEEEEecCCccccHHHHHHHH
Confidence 4444556889999999999999999764 47877775554444555665433
No 296
>COG3283 TyrR Transcriptional regulator of aromatic amino acids metabolism [Transcription / Amino acid transport and metabolism]
Probab=34.32 E-value=49 Score=39.24 Aligned_cols=34 Identities=35% Similarity=0.481 Sum_probs=27.7
Q ss_pred HHHhhc--CCcHHHHHHHcCCChhHHHHHHHHcCCC
Q 001809 606 VLQQYF--SGSLKDAAKSIGVCPTTLKRICRQHGIS 639 (1010)
Q Consensus 606 ~L~~yF--~~pl~eAAk~LGV~~TtLKRiCR~~GI~ 639 (1010)
+|.+.| +=+-...|++||||-|++-..-|++||.
T Consensus 473 VL~rly~~yPStRkLAkRLgvSHTaIAnKLRqyGi~ 508 (511)
T COG3283 473 VLTRLYRSYPSTRKLAKRLGVSHTAIANKLRQYGIG 508 (511)
T ss_pred HHHHHHHhCCcHHHHHHHhCCcHHHHHHHHHHhCCC
Confidence 444444 3456789999999999999999999995
No 297
>PRK10339 DNA-binding transcriptional repressor EbgR; Provisional
Probab=34.32 E-value=42 Score=36.81 Aligned_cols=25 Identities=32% Similarity=0.426 Sum_probs=21.8
Q ss_pred CcHHHHHHHcCCChhHHHHHHHHcC
Q 001809 613 GSLKDAAKSIGVCPTTLKRICRQHG 637 (1010)
Q Consensus 613 ~pl~eAAk~LGV~~TtLKRiCR~~G 637 (1010)
.+++|+|+..|||++|+.|.....+
T Consensus 2 ~ti~dIA~~agVS~~TVSrvln~~~ 26 (327)
T PRK10339 2 ATLKDIAIEAGVSLATVSRVLNDDP 26 (327)
T ss_pred CCHHHHHHHhCCCHHhhhhhhcCCC
Confidence 3789999999999999999996553
No 298
>TIGR02983 SigE-fam_strep RNA polymerase sigma-70 factor, sigma-E family. This group of similar sigma-70 factors includes the sigE factor from Streptomyces coelicolor. The family appears to include a paralagous expansion in the Streptomycetes lineage, while related Actinomycetales have at most two representatives.
Probab=34.08 E-value=44 Score=33.02 Aligned_cols=29 Identities=28% Similarity=0.287 Sum_probs=24.0
Q ss_pred HHHhhcCCcHHHHHHHcCCChhHHHHHHH
Q 001809 606 VLQQYFSGSLKDAAKSIGVCPTTLKRICR 634 (1010)
Q Consensus 606 ~L~~yF~~pl~eAAk~LGV~~TtLKRiCR 634 (1010)
.|.-+.+++.+|+|+.|||+..|+|....
T Consensus 120 ~l~~~~g~s~~eIA~~lgis~~tV~~~l~ 148 (162)
T TIGR02983 120 VLRYYEDLSEAQVAEALGISVGTVKSRLS 148 (162)
T ss_pred hhHHHhcCCHHHHHHHhCCCHHHHHHHHH
Confidence 34456689999999999999999997643
No 299
>PRK12531 RNA polymerase sigma factor; Provisional
Probab=33.98 E-value=45 Score=34.40 Aligned_cols=24 Identities=13% Similarity=-0.050 Sum_probs=20.8
Q ss_pred hcCCcHHHHHHHcCCChhHHHHHH
Q 001809 610 YFSGSLKDAAKSIGVCPTTLKRIC 633 (1010)
Q Consensus 610 yF~~pl~eAAk~LGV~~TtLKRiC 633 (1010)
+-+++.+|+|+.|||+..|+|.+.
T Consensus 155 ~eg~s~~EIA~~lgis~~tVk~rl 178 (194)
T PRK12531 155 LEELPHQQVAEMFDIPLGTVKSRL 178 (194)
T ss_pred HcCCCHHHHHHHhCcCHHHHHHHH
Confidence 348999999999999999997653
No 300
>PRK12513 RNA polymerase sigma factor; Provisional
Probab=33.94 E-value=33 Score=35.19 Aligned_cols=26 Identities=27% Similarity=0.198 Sum_probs=22.1
Q ss_pred HHhhcCCcHHHHHHHcCCChhHHHHH
Q 001809 607 LQQYFSGSLKDAAKSIGVCPTTLKRI 632 (1010)
Q Consensus 607 L~~yF~~pl~eAAk~LGV~~TtLKRi 632 (1010)
|.-+.+++.+|+|+.||+++.|+|.+
T Consensus 150 l~~~~g~s~~EIA~~lgis~~tV~~~ 175 (194)
T PRK12513 150 LREHGDLELEEIAELTGVPEETVKSR 175 (194)
T ss_pred eehccCCCHHHHHHHHCCCHHHHHHH
Confidence 33456999999999999999999855
No 301
>PRK12518 RNA polymerase sigma factor; Provisional
Probab=33.50 E-value=37 Score=33.97 Aligned_cols=27 Identities=19% Similarity=0.097 Sum_probs=22.7
Q ss_pred HHhhcCCcHHHHHHHcCCChhHHHHHH
Q 001809 607 LQQYFSGSLKDAAKSIGVCPTTLKRIC 633 (1010)
Q Consensus 607 L~~yF~~pl~eAAk~LGV~~TtLKRiC 633 (1010)
|.-+.+++.+|+|+.||+++.|+|..-
T Consensus 131 l~~~~g~s~~eIA~~lg~s~~tv~~~l 157 (175)
T PRK12518 131 LHDLEDLPQKEIAEILNIPVGTVKSRL 157 (175)
T ss_pred ehHhcCCCHHHHHHHHCCCHHHHHHHH
Confidence 344568999999999999999998764
No 302
>COG4367 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=33.46 E-value=33 Score=33.04 Aligned_cols=35 Identities=23% Similarity=0.234 Sum_probs=30.2
Q ss_pred ccccCHHHHHhhc---CCcHHHHHHHcCCChhHHHHHH
Q 001809 599 EKNVSLSVLQQYF---SGSLKDAAKSIGVCPTTLKRIC 633 (1010)
Q Consensus 599 ~~~itl~~L~~yF---~~pl~eAAk~LGV~~TtLKRiC 633 (1010)
.+.+|.++|+..| .++..++|++||+++--|-||-
T Consensus 7 q~~~Tk~elqan~el~~LS~~~iA~~Ln~t~~~lekil 44 (97)
T COG4367 7 QKQRTKQELQANFELCPLSDEEIATALNWTEVKLEKIL 44 (97)
T ss_pred HHHHHHHHHHHhhhhccccHHHHHHHhCCCHHHHHHHH
Confidence 4556788999988 5789999999999999998887
No 303
>PF01614 IclR: Bacterial transcriptional regulator This Pfam family contains some of the members of the iclR family; InterPro: IPR014757 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 [].; PDB: 3MQ0_A 2IA2_D 3OBF_B 2G7U_C 3R4K_A 1TF1_D 1MKM_A 1YSP_A 3BJN_A 1TD5_A ....
Probab=33.28 E-value=82 Score=30.13 Aligned_cols=40 Identities=25% Similarity=0.315 Sum_probs=24.5
Q ss_pred eEEEEeeecCCCCceEEEEEEeeecccCCchHHHHHHHHHh
Q 001809 274 SCIALPVFQFPEISCSAVLEIVSVKEKPNFDAEIENICNAL 314 (1010)
Q Consensus 274 GsLAlPVf~~~s~~ClAVlElV~t~ek~~f~~E~e~vc~AL 314 (1010)
.+||+|||++... ++|+|=++...+.++-...-..+..+|
T Consensus 80 ~~iA~Pi~~~~g~-~~~alsv~~~~~~~~~~~~~~~~~~~l 119 (129)
T PF01614_consen 80 AAIAVPIFDPNGQ-VVAALSVSGPSERFDEERLEERLAPAL 119 (129)
T ss_dssp EEEEEEEEETTSC-EEEEEEEEEEGGGSHHHHHHHHHHHHH
T ss_pred ceEEEEEECCCCC-EEEEEEEeeEhHhCCHHHHHHHHHHHH
Confidence 5799999998544 477777766665443333222245554
No 304
>COG2963 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=33.19 E-value=43 Score=32.06 Aligned_cols=51 Identities=24% Similarity=0.313 Sum_probs=37.3
Q ss_pred ccccccccCHHHHHhhc--CCcHHHHHHHcCC-ChhHHHH--HHHHcCCCCCcchh
Q 001809 595 RSTAEKNVSLSVLQQYF--SGSLKDAAKSIGV-CPTTLKR--ICRQHGISRWPSRK 645 (1010)
Q Consensus 595 r~~~~~~itl~~L~~yF--~~pl~eAAk~LGV-~~TtLKR--iCR~~GI~RWP~Rk 645 (1010)
+.+-...+-++.++.|+ +.++.++|+++|| .+++|++ +.-+.+-..++-.+
T Consensus 5 ~r~~s~EfK~~iv~~~~~~g~sv~~vAr~~gv~~~~~l~~W~~~~~~~~~~~~~~~ 60 (116)
T COG2963 5 RKKYSPEFKLEAVALYLRGGDTVSEVAREFGIVSATQLYKWRIQLQKGGGLAFSGK 60 (116)
T ss_pred cccCCHHHHHHHHHHHHhcCccHHHHHHHhCCCChHHHHHHHHHHHHcccccccCc
Confidence 44555667778888888 5679999999995 9999994 44444455676554
No 305
>PHA00689 hypothetical protein
Probab=33.07 E-value=28 Score=30.29 Aligned_cols=20 Identities=30% Similarity=0.609 Sum_probs=15.7
Q ss_pred eeeeEeecCCCCeEEEecCC
Q 001809 941 TFQLKYLDDEEEWVMLVSDS 960 (1010)
Q Consensus 941 ~f~lKYlDDd~EWVlLtcDa 960 (1010)
.-.|.+-||-+||||+-.--
T Consensus 25 ktglrweddggewvlmeghy 44 (62)
T PHA00689 25 KTGLRWEDDGGEWVLMEGHY 44 (62)
T ss_pred ccCceeecCCCcEEEEecce
Confidence 34678999999999986443
No 306
>PRK12528 RNA polymerase sigma factor; Provisional
Probab=32.98 E-value=51 Score=32.73 Aligned_cols=29 Identities=24% Similarity=0.275 Sum_probs=24.1
Q ss_pred HHHhhcCCcHHHHHHHcCCChhHHHHHHH
Q 001809 606 VLQQYFSGSLKDAAKSIGVCPTTLKRICR 634 (1010)
Q Consensus 606 ~L~~yF~~pl~eAAk~LGV~~TtLKRiCR 634 (1010)
.|.-+-+++.+|+|+.|||+..|+|..-.
T Consensus 123 ~L~~~~g~s~~EIA~~l~is~~tV~~~l~ 151 (161)
T PRK12528 123 LLAQVDGLGYGEIATELGISLATVKRYLN 151 (161)
T ss_pred HHHHHcCCCHHHHHHHHCCCHHHHHHHHH
Confidence 44556799999999999999999987644
No 307
>PRK09706 transcriptional repressor DicA; Reviewed
Probab=32.63 E-value=48 Score=32.77 Aligned_cols=33 Identities=15% Similarity=0.195 Sum_probs=29.2
Q ss_pred HHHHHhhcCCcHHHHHHHcCCChhHHHHHHHHc
Q 001809 604 LSVLQQYFSGSLKDAAKSIGVCPTTLKRICRQH 636 (1010)
Q Consensus 604 l~~L~~yF~~pl~eAAk~LGV~~TtLKRiCR~~ 636 (1010)
+..++..-++++.++|+.+||++.++.++.+.-
T Consensus 10 lk~~R~~~gltq~~lA~~~gvs~~~is~~E~g~ 42 (135)
T PRK09706 10 IRYRRKQLKLSQRSLAKAVKVSHVSISQWERDE 42 (135)
T ss_pred HHHHHHHcCCCHHHHHHHhCCCHHHHHHHHcCC
Confidence 567888899999999999999999999987654
No 308
>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=32.58 E-value=46 Score=27.18 Aligned_cols=25 Identities=28% Similarity=0.424 Sum_probs=19.1
Q ss_pred HhhcCCcHHHHHHHcCCChhHHHHH
Q 001809 608 QQYFSGSLKDAAKSIGVCPTTLKRI 632 (1010)
Q Consensus 608 ~~yF~~pl~eAAk~LGV~~TtLKRi 632 (1010)
..|-..+++++|+++||+++++.+.
T Consensus 12 ~G~~~~s~~~Ia~~~gvs~~~~y~~ 36 (47)
T PF00440_consen 12 KGYEAVSIRDIARRAGVSKGSFYRY 36 (47)
T ss_dssp HHTTTSSHHHHHHHHTSCHHHHHHH
T ss_pred hCHHhCCHHHHHHHHccchhhHHHH
Confidence 4677788888888888888887753
No 309
>PRK09648 RNA polymerase sigma factor SigD; Reviewed
Probab=32.56 E-value=50 Score=33.70 Aligned_cols=28 Identities=18% Similarity=0.322 Sum_probs=23.3
Q ss_pred HHHhhcCCcHHHHHHHcCCChhHHHHHH
Q 001809 606 VLQQYFSGSLKDAAKSIGVCPTTLKRIC 633 (1010)
Q Consensus 606 ~L~~yF~~pl~eAAk~LGV~~TtLKRiC 633 (1010)
.++-+.+++.+|+|+.|||+..|+|..-
T Consensus 149 ~l~~~~g~s~~EIA~~lgis~~tV~~~l 176 (189)
T PRK09648 149 ILRVVVGLSAEETAEAVGSTPGAVRVAQ 176 (189)
T ss_pred HHHHHcCCCHHHHHHHHCCCHHHHHHHH
Confidence 4445569999999999999999998764
No 310
>TIGR02937 sigma70-ECF RNA polymerase sigma factor, sigma-70 family. Several PFAM models hit segments of these sequences including Sigma-70 region 2 (pfam04542) and Sigma-70, region 4 (pfam04545), but not always above their respective trusted cutoffs.
Probab=32.50 E-value=44 Score=31.35 Aligned_cols=26 Identities=27% Similarity=0.291 Sum_probs=22.7
Q ss_pred cCCcHHHHHHHcCCChhHHHHHHHHc
Q 001809 611 FSGSLKDAAKSIGVCPTTLKRICRQH 636 (1010)
Q Consensus 611 F~~pl~eAAk~LGV~~TtLKRiCR~~ 636 (1010)
-+++.+|+|+.|||++.+++++.++.
T Consensus 125 ~g~s~~eIA~~l~~s~~~v~~~~~~~ 150 (158)
T TIGR02937 125 EGLSYKEIAEILGISVGTVKRRLKRA 150 (158)
T ss_pred cCCCHHHHHHHHCCCHHHHHHHHHHH
Confidence 48899999999999999998877653
No 311
>PRK09940 transcriptional regulator YdeO; Provisional
Probab=32.41 E-value=49 Score=36.91 Aligned_cols=28 Identities=21% Similarity=0.268 Sum_probs=25.5
Q ss_pred CCcHHHHHHHcCCChhHHHHHHHHcCCC
Q 001809 612 SGSLKDAAKSIGVCPTTLKRICRQHGIS 639 (1010)
Q Consensus 612 ~~pl~eAAk~LGV~~TtLKRiCR~~GI~ 639 (1010)
.+++++.|+.+|+++++|+|+.++.|..
T Consensus 150 ~~tl~~LA~~~gmS~s~l~R~FK~~G~T 177 (253)
T PRK09940 150 PWKLKDICDCLYISESLLKKKLKQEQTT 177 (253)
T ss_pred CCCHHHHHHHHCcCHHHHHHHHHHcCCC
Confidence 3679999999999999999999999864
No 312
>TIGR02948 SigW_bacill RNA polymerase sigma-W factor. This sigma factor is restricted to certain lineages of the order Bacillales.
Probab=32.38 E-value=47 Score=33.48 Aligned_cols=29 Identities=24% Similarity=0.164 Sum_probs=23.9
Q ss_pred HHHhhcCCcHHHHHHHcCCChhHHHHHHH
Q 001809 606 VLQQYFSGSLKDAAKSIGVCPTTLKRICR 634 (1010)
Q Consensus 606 ~L~~yF~~pl~eAAk~LGV~~TtLKRiCR 634 (1010)
.|+-+.+++.+|+|+.||+++.++|.+..
T Consensus 146 ~l~~~~g~s~~eIA~~lgis~~~v~~~l~ 174 (187)
T TIGR02948 146 VLKYMEDLSLKEISEILDLPVGTVKTRIH 174 (187)
T ss_pred hhHHhcCCCHHHHHHHHCCCHHHHHHHHH
Confidence 34445699999999999999999988753
No 313
>PF13613 HTH_Tnp_4: Helix-turn-helix of DDE superfamily endonuclease
Probab=32.38 E-value=39 Score=28.61 Aligned_cols=25 Identities=24% Similarity=0.414 Sum_probs=22.5
Q ss_pred CCcHHHHHHHcCCChhHHHHHHHHc
Q 001809 612 SGSLKDAAKSIGVCPTTLKRICRQH 636 (1010)
Q Consensus 612 ~~pl~eAAk~LGV~~TtLKRiCR~~ 636 (1010)
+.+..+.|..+||+.+|..|++++.
T Consensus 19 ~~~~~~La~~FgIs~stvsri~~~~ 43 (53)
T PF13613_consen 19 NLTFQDLAYRFGISQSTVSRIFHEW 43 (53)
T ss_pred CCcHhHHhhheeecHHHHHHHHHHH
Confidence 6789999999999999999998753
No 314
>PRK09652 RNA polymerase sigma factor RpoE; Provisional
Probab=32.26 E-value=51 Score=32.67 Aligned_cols=25 Identities=16% Similarity=0.080 Sum_probs=21.2
Q ss_pred hhcCCcHHHHHHHcCCChhHHHHHH
Q 001809 609 QYFSGSLKDAAKSIGVCPTTLKRIC 633 (1010)
Q Consensus 609 ~yF~~pl~eAAk~LGV~~TtLKRiC 633 (1010)
-+-+++.+|+|+.|||+++|++..-
T Consensus 141 ~~~~~s~~eIA~~lgis~~tV~~~l 165 (182)
T PRK09652 141 EIEGLSYEEIAEIMGCPIGTVRSRI 165 (182)
T ss_pred HHcCCCHHHHHHHHCCCHHHHHHHH
Confidence 3458999999999999999997653
No 315
>PRK12522 RNA polymerase sigma factor; Provisional
Probab=32.14 E-value=51 Score=33.17 Aligned_cols=29 Identities=24% Similarity=0.158 Sum_probs=24.1
Q ss_pred HHHhhcCCcHHHHHHHcCCChhHHHHHHH
Q 001809 606 VLQQYFSGSLKDAAKSIGVCPTTLKRICR 634 (1010)
Q Consensus 606 ~L~~yF~~pl~eAAk~LGV~~TtLKRiCR 634 (1010)
.|.-+-+++.+|+|+.|||+..|+|....
T Consensus 129 ~l~~~~~~s~~EIA~~lgis~~tV~~~l~ 157 (173)
T PRK12522 129 VLYYYEQYSYKEMSEILNIPIGTVKYRLN 157 (173)
T ss_pred HHHHHcCCCHHHHHHHhCCCHHHHHHHHH
Confidence 34556799999999999999999987643
No 316
>TIGR03541 reg_near_HchA LuxR family transcriptional regulatory, chaperone HchA-associated. Members of this protein family belong to the LuxR transcriptional regulator family, and contain both autoinducer binding (pfam03472) and transcriptional regulator (pfam00196) domains. Members, however, occur only in a few members of the Gammaproteobacteria that have the chaperone/aminopeptidase HchA, and are always encoded by the adjacent gene.
Probab=31.93 E-value=1.9e+02 Score=31.17 Aligned_cols=51 Identities=18% Similarity=0.329 Sum_probs=33.7
Q ss_pred CCCC-cccccccccCcccccchhhHHhcCCceEEEEeeecCCCCceEEEEEEeeec
Q 001809 244 SKVP-EWTSNVAYYNEAEYARVTHAVNHAVRSCIALPVFQFPEISCSAVLEIVSVK 298 (1010)
Q Consensus 244 s~~P-EWTpnV~~y~~~EYpR~~~A~~~~VrGsLAlPVf~~~s~~ClAVlElV~t~ 298 (1010)
+..| .|+.. ...++.++.-+..|..+|+ -.+.+||+++... .|++-++...
T Consensus 84 ~~~p~~W~~~-~~~~~~~~~~~~~a~~~g~-~G~t~Pv~~~~g~--~~~~s~~~~~ 135 (232)
T TIGR03541 84 ADEPFFWSKT-PNENGERYRVVRNPSGRGV-HGLQVPVFGRTGL--EGAVSLGGKL 135 (232)
T ss_pred CCCCeecccC-cccCchHhHHHHHHHHcCC-CcEEEeEEcCCCC--EEEEEeecCc
Confidence 3344 46532 2234455666789999997 7899999987633 6777776543
No 317
>smart00346 HTH_ICLR helix_turn_helix isocitrate lyase regulation.
Probab=31.74 E-value=62 Score=29.12 Aligned_cols=31 Identities=19% Similarity=0.240 Sum_probs=24.8
Q ss_pred HHHhh-cCCcHHHHHHHcCCChhHHHHHHHHc
Q 001809 606 VLQQY-FSGSLKDAAKSIGVCPTTLKRICRQH 636 (1010)
Q Consensus 606 ~L~~y-F~~pl~eAAk~LGV~~TtLKRiCR~~ 636 (1010)
.|.+. =.+++.|+|+.+||+.+|+.|+.+.+
T Consensus 13 ~l~~~~~~~t~~~ia~~l~i~~~tv~r~l~~L 44 (91)
T smart00346 13 ALAEEPGGLTLAELAERLGLSKSTAHRLLNTL 44 (91)
T ss_pred HHHhCCCCcCHHHHHHHhCCCHHHHHHHHHHH
Confidence 34443 36889999999999999999988754
No 318
>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=31.64 E-value=58 Score=27.29 Aligned_cols=25 Identities=20% Similarity=0.383 Sum_probs=21.9
Q ss_pred CcHHHHHHHcCCChhHHHHHHHHcC
Q 001809 613 GSLKDAAKSIGVCPTTLKRICRQHG 637 (1010)
Q Consensus 613 ~pl~eAAk~LGV~~TtLKRiCR~~G 637 (1010)
+++.|.|+.||+++.++.|+.+++=
T Consensus 22 ~t~~~la~~l~~~~~~vs~~v~~L~ 46 (62)
T PF12802_consen 22 LTQSELAERLGISKSTVSRIVKRLE 46 (62)
T ss_dssp EEHHHHHHHHTS-HHHHHHHHHHHH
T ss_pred cCHHHHHHHHCcCHHHHHHHHHHHH
Confidence 7999999999999999999998773
No 319
>PRK08295 RNA polymerase factor sigma-70; Validated
Probab=31.59 E-value=71 Score=32.93 Aligned_cols=24 Identities=8% Similarity=0.072 Sum_probs=21.3
Q ss_pred hhcCCcHHHHHHHcCCChhHHHHH
Q 001809 609 QYFSGSLKDAAKSIGVCPTTLKRI 632 (1010)
Q Consensus 609 ~yF~~pl~eAAk~LGV~~TtLKRi 632 (1010)
-+.+++.+|+|..|||++.|+|.+
T Consensus 167 ~~e~~s~~EIA~~lgis~~tV~~~ 190 (208)
T PRK08295 167 YLDGKSYQEIAEELNRHVKSIDNA 190 (208)
T ss_pred HHccCCHHHHHHHHCCCHHHHHHH
Confidence 566899999999999999999864
No 320
>cd01818 TIAM1_RBD Ubiquitin domain of Tiam1 guanine nucleotide exchange factor. Tiam1 (T lymphoma invasion and metastasis 1) a guanine nucleotide exchange factor that activates Rac, is an important regulator of Rho GTPase functions in tumor cells including regulation of cell shape and invasiveness in epithelial cells and fibroblasts. TIAM1 has an RBD (Ras-binding domain) similar to that of Raf kinase as well as PH (pleckstrin homology), PDZ, and RhoGEF domains.
Probab=31.47 E-value=1.9e+02 Score=27.36 Aligned_cols=44 Identities=18% Similarity=0.316 Sum_probs=38.4
Q ss_pred CeEEEEeCCCcChHHHHHHHHHHcCcccc--eeeeEee-cCCCCeEE
Q 001809 912 DIIRFKFDPSAGCFQLYEEVARRLKLQNG--TFQLKYL-DDEEEWVM 955 (1010)
Q Consensus 912 d~iRF~~~~s~g~~~L~~EIakRf~l~~~--~f~lKYl-DDd~EWVl 955 (1010)
..+-..+.|.....|+++-+.||-+||.. .++||.+ |+++||..
T Consensus 10 ~~~~v~vrp~~tv~dvLe~aCk~~~ldp~eh~Lrlk~~~~e~~~~~~ 56 (77)
T cd01818 10 QPVLTYLRPGMSVEDFLESACKRKQLDPMEHYLRLKFLRMENHEYFY 56 (77)
T ss_pred ceEEEEECCCCCHHHHHHHHHHhcCCChhHheeEEEEEecCCccEEE
Confidence 44555678999999999999999999986 5999999 89999987
No 321
>PRK09651 RNA polymerase sigma factor FecI; Provisional
Probab=31.45 E-value=49 Score=33.50 Aligned_cols=28 Identities=21% Similarity=0.333 Sum_probs=23.9
Q ss_pred HHHhhcCCcHHHHHHHcCCChhHHHHHH
Q 001809 606 VLQQYFSGSLKDAAKSIGVCPTTLKRIC 633 (1010)
Q Consensus 606 ~L~~yF~~pl~eAAk~LGV~~TtLKRiC 633 (1010)
.|.-+.+++.+|+|+.|||+..|+|..-
T Consensus 129 ~l~~~~g~s~~EIA~~lgis~~tV~~~l 156 (172)
T PRK09651 129 LLSQLDGLTYSEIAHKLGVSVSSVKKYV 156 (172)
T ss_pred hhhhccCCCHHHHHHHhCCCHHHHHHHH
Confidence 4566789999999999999999998653
No 322
>cd00131 PAX Paired Box domain
Probab=31.43 E-value=42 Score=33.46 Aligned_cols=25 Identities=12% Similarity=0.106 Sum_probs=22.5
Q ss_pred CCcHHHHHHHcCCChhHHHHHHHHc
Q 001809 612 SGSLKDAAKSIGVCPTTLKRICRQH 636 (1010)
Q Consensus 612 ~~pl~eAAk~LGV~~TtLKRiCR~~ 636 (1010)
+++..+||+.|||+..|+.|+.+++
T Consensus 33 G~s~~~iA~~~~Vs~~tV~r~i~r~ 57 (128)
T cd00131 33 GIRPCDISRQLRVSHGCVSKILNRY 57 (128)
T ss_pred CCCHHHHHHHHCcCHHHHHHHHHHH
Confidence 7799999999999999999987764
No 323
>COG3093 VapI Plasmid maintenance system antidote protein [General function prediction only]
Probab=31.37 E-value=49 Score=32.65 Aligned_cols=37 Identities=11% Similarity=0.177 Sum_probs=31.1
Q ss_pred cccCHHHHHhhcCCcHHHHHHHcCCChhHHHHHHHHc
Q 001809 600 KNVSLSVLQQYFSGSLKDAAKSIGVCPTTLKRICRQH 636 (1010)
Q Consensus 600 ~~itl~~L~~yF~~pl~eAAk~LGV~~TtLKRiCR~~ 636 (1010)
-+|=.+++-.-|++++.++|+.|||.+.++-++|+--
T Consensus 11 GEiL~eeflep~glt~~~lA~~lgV~r~~is~ling~ 47 (104)
T COG3093 11 GEILREEFLEPLGLTQTELAEALGVTRNTISELINGR 47 (104)
T ss_pred hHHHHHHHhccccCCHHHHHHHhCCCHHHHHHHHcCC
Confidence 4455667777789999999999999999999999743
No 324
>PRK13869 plasmid-partitioning protein RepA; Provisional
Probab=31.32 E-value=83 Score=37.01 Aligned_cols=62 Identities=15% Similarity=0.176 Sum_probs=36.5
Q ss_pred CcHHHHHHHcCCChhHHHHHHHHc-C--CCCCcchhhhhhHHHHHHHHHHHhhcccccCcccccC
Q 001809 613 GSLKDAAKSIGVCPTTLKRICRQH-G--ISRWPSRKINKVNRSLKKIQTVLNSVQGVEGGLKFDP 674 (1010)
Q Consensus 613 ~pl~eAAk~LGV~~TtLKRiCR~~-G--I~RWP~Rki~sl~~~i~~l~~~i~s~qg~e~~~~~~~ 674 (1010)
++..|||+.|||+..||++.+++- + ..|=+..+..=-...|..+++++.........+++-|
T Consensus 49 ft~~e~A~~lgvs~~tlr~~~~~g~~~~~~~~~~grR~yt~~di~~lr~~l~~~~~~~~~~~~~~ 113 (405)
T PRK13869 49 FTSGEAARLMKISDSTLRKMTLAGEGPQPELASNGRRFYTLGQINEIRQMLAGSTRGRESIDFVP 113 (405)
T ss_pred CCHHHHHHHhCcCHHHHHHHHHcCCCCCCccCCCCceeecHHHHHHHHHHHHhhccccccccccC
Confidence 388999999999999999999871 1 1122211111222456666776654222344444433
No 325
>TIGR03541 reg_near_HchA LuxR family transcriptional regulatory, chaperone HchA-associated. Members of this protein family belong to the LuxR transcriptional regulator family, and contain both autoinducer binding (pfam03472) and transcriptional regulator (pfam00196) domains. Members, however, occur only in a few members of the Gammaproteobacteria that have the chaperone/aminopeptidase HchA, and are always encoded by the adjacent gene.
Probab=31.31 E-value=5.2e+02 Score=27.96 Aligned_cols=69 Identities=13% Similarity=0.198 Sum_probs=49.2
Q ss_pred HHhhhcccccCCCcchhhhhcCCCcccccccccCccccchhhHHHHhCCceeEEEEecccccCCCcEEEEee
Q 001809 412 HACSEHYLEEGQGVAGKALQSNHPFFFPDVKLYDITEFPLVHHARKFGLNAAVAIRLRSTYTGDDDYILEFF 483 (1010)
Q Consensus 412 ~AC~EhhL~~GQGvaGkAf~sn~P~F~~DV~~fsk~EYPL~HhAr~fgL~aAvAIrLrS~~tG~ddyVLEFF 483 (1010)
+...+.++...-=|+=.++.+..|++-.++...+..++.+-..|+.||+ ..++||++... | .-.++-|.
T Consensus 64 ~~Y~~~~y~~~DPvv~~~~~~~~p~~W~~~~~~~~~~~~~~~~a~~~g~-~G~t~Pv~~~~-g-~~~~~s~~ 132 (232)
T TIGR03541 64 NAVDAQTYLRHCPVTRHILEADEPFFWSKTPNENGERYRVVRNPSGRGV-HGLQVPVFGRT-G-LEGAVSLG 132 (232)
T ss_pred HHHHHcCCcccCHHHHHHHhCCCCeecccCcccCchHhHHHHHHHHcCC-CcEEEeEEcCC-C-CEEEEEee
Confidence 4555666666666777788888897666766666677788999999998 88999997642 2 22345555
No 326
>cd01392 HTH_LacI Helix-turn-helix (HTH) DNA binding domain of the LacI family of transcriptional regulators. HTH-DNA binding domain of the LacI (lactose operon repressor) family of bacterial transcriptional regulators and their putative homologs found in plants. The LacI family has more than 500 members distributed among almost all bacterial species. The monomeric proteins of the LacI family contain common structural features that include a small DNA-binding domain with a helix-turn-helix motif in the N-terminus, a regulatory ligand-binding domain which exhibits the type I periplasmic binding protein fold in the C-terminus for oligomerization and for effector binding, and an approximately 18-amino acid linker connecting these two functional domains. In LacI-like transcriptional regulators, the ligands are monosaccharides including lactose, ribose, fructose, xylose, arabinose, galactose/glucose, and other sugars, with a few exceptions. When the C-terminal domain of the LacI family repre
Probab=31.28 E-value=25 Score=28.67 Aligned_cols=21 Identities=33% Similarity=0.509 Sum_probs=18.5
Q ss_pred HHHHHHcCCChhHHHHHHHHc
Q 001809 616 KDAAKSIGVCPTTLKRICRQH 636 (1010)
Q Consensus 616 ~eAAk~LGV~~TtLKRiCR~~ 636 (1010)
++.|+.+||+.+|+-|+++..
T Consensus 1 ~~lA~~~gvs~~tvs~~l~g~ 21 (52)
T cd01392 1 KDIARAAGVSVATVSRVLNGK 21 (52)
T ss_pred CcHHHHHCcCHHHHHHHHcCC
Confidence 378999999999999999854
No 327
>TIGR02984 Sig-70_plancto1 RNA polymerase sigma-70 factor, Planctomycetaceae-specific subfamily 1. This group of sigma factors are members of the sigma-70 family (TIGR02937) and are apparently found only in the Planctomycetaceae family including the genuses Gemmata and Pirellula (in which seven sequences are found).
Probab=31.08 E-value=55 Score=32.98 Aligned_cols=29 Identities=10% Similarity=0.120 Sum_probs=24.3
Q ss_pred HHHhhcCCcHHHHHHHcCCChhHHHHHHH
Q 001809 606 VLQQYFSGSLKDAAKSIGVCPTTLKRICR 634 (1010)
Q Consensus 606 ~L~~yF~~pl~eAAk~LGV~~TtLKRiCR 634 (1010)
.+.-+.+++.+|+|..|||+..|+|+...
T Consensus 150 ~l~~~~g~s~~eIA~~lgis~~~v~~~l~ 178 (189)
T TIGR02984 150 LLRHLEGLSFAEVAERMDRSEGAVSMLWV 178 (189)
T ss_pred HHHHhcCCCHHHHHHHHCcCHHHHHHHHH
Confidence 44456799999999999999999987644
No 328
>PF02017 CIDE-N: CIDE-N domain; InterPro: IPR003508 This domain consists of caspase-activated (CAD) nucleases, which induce DNA fragmentation and chromatin condensation during apoptosis, and the cell death activator proteins CIDE-A and CIDE-B, which are inhibitors of CAD nuclease. The two proteins interact through the region defined by the method signatures.; GO: 0006915 apoptosis, 0005622 intracellular; PDB: 1IBX_A 2EEL_A 1F2R_I 1C9F_A 1D4B_A.
Probab=30.93 E-value=1.1e+02 Score=28.79 Aligned_cols=49 Identities=16% Similarity=0.245 Sum_probs=39.2
Q ss_pred EEEEEcCCCeEEEEeCCCcChHHHHHHHHHHcCcccceeeeEeecCCCCeE
Q 001809 904 IVKATYKEDIIRFKFDPSAGCFQLYEEVARRLKLQNGTFQLKYLDDEEEWV 954 (1010)
Q Consensus 904 ~vKaty~~d~iRF~~~~s~g~~~L~~EIakRf~l~~~~f~lKYlDDd~EWV 954 (1010)
.+|++=.++.+|+-+-. ..+.||++-+.++|+|....+.| +|+.||-=|
T Consensus 4 p~kv~~~~r~~k~Gv~A-~sL~eL~~K~~~~l~~~~~~~~l-vL~eDGT~V 52 (78)
T PF02017_consen 4 PFKVRNHDRSVKKGVAA-SSLEELLEKACDKLQLPEEPVRL-VLEEDGTEV 52 (78)
T ss_dssp EEEEEETTSSCEEEEEE-SSHHHHHHHHHHHHT-SSSTCEE-EETTTTCBE
T ss_pred cEEEecCCCCceEeEEc-CCHHHHHHHHHHHhCCCCcCcEE-EEeCCCcEE
Confidence 46777778888998877 67999999999999999766766 788777544
No 329
>PRK09647 RNA polymerase sigma factor SigE; Reviewed
Probab=30.91 E-value=54 Score=34.60 Aligned_cols=31 Identities=23% Similarity=0.182 Sum_probs=25.6
Q ss_pred HHHhhcCCcHHHHHHHcCCChhHHHHHHHHc
Q 001809 606 VLQQYFSGSLKDAAKSIGVCPTTLKRICRQH 636 (1010)
Q Consensus 606 ~L~~yF~~pl~eAAk~LGV~~TtLKRiCR~~ 636 (1010)
.|.-+-+++.+|+|+.|||+..|+|...++-
T Consensus 148 ~L~~~~g~s~~EIA~~Lgis~~tV~~~l~RA 178 (203)
T PRK09647 148 VLCDIEGLSYEEIAATLGVKLGTVRSRIHRG 178 (203)
T ss_pred HHHHHcCCCHHHHHHHHCCCHHHHHHHHHHH
Confidence 3445679999999999999999999876543
No 330
>PRK10403 transcriptional regulator NarP; Provisional
Probab=30.54 E-value=57 Score=32.21 Aligned_cols=27 Identities=19% Similarity=0.289 Sum_probs=23.3
Q ss_pred CCcHHHHHHHcCCChhH----HHHHHHHcCC
Q 001809 612 SGSLKDAAKSIGVCPTT----LKRICRQHGI 638 (1010)
Q Consensus 612 ~~pl~eAAk~LGV~~Tt----LKRiCR~~GI 638 (1010)
+++-+++|+.||++..| ++|+++++|+
T Consensus 168 g~s~~~ia~~l~~s~~tv~~~~~~i~~kl~~ 198 (215)
T PRK10403 168 GLSNKQIASVLNISEQTVKVHIRNLLRKLNV 198 (215)
T ss_pred CCCHHHHHHHcCCCHHHHHHHHHHHHHHcCC
Confidence 58899999999999998 6677888886
No 331
>PF00788 RA: Ras association (RalGDS/AF-6) domain; InterPro: IPR000159 Proteins with this domain are mostly RasGTP effectors and include guanine-nucleotide releasing factor in mammals []. This factor stimulates the dissociation of GDP from the Ras-related RALA and RALB GTPases, which allows GTP binding and activation of the GTPases. It interacts and acts as an effector molecule for R-ras, K-Ras and Rap []. The domain is also present in a number of other proteins among them the sexual differentiation protein in yeast that is essential for mating and meiosis and yeast adenylate cyclase. These proteins contain repeated leucine-rich (LRR) segments.; GO: 0007165 signal transduction; PDB: 3EC8_A 2C5L_D 2BYF_A 2CS4_A 3KH0_A 2B3A_A 1RAX_A 2RGF_A 1WGR_A 1WXA_A ....
Probab=30.42 E-value=4e+02 Score=23.85 Aligned_cols=78 Identities=17% Similarity=0.151 Sum_probs=50.1
Q ss_pred EEEEEEcCCC-----eEEEEeCCCcChHHHHHHHHHHcCcc-c-ceeeeE-eecCCCCeEEEecCCcHHHHHHHHhHhCC
Q 001809 903 IIVKATYKED-----IIRFKFDPSAGCFQLYEEVARRLKLQ-N-GTFQLK-YLDDEEEWVMLVSDSDLQECFDILESLGK 974 (1010)
Q Consensus 903 ~~vKaty~~d-----~iRF~~~~s~g~~~L~~EIakRf~l~-~-~~f~lK-YlDDd~EWVlLtcDaDL~EC~di~~~~~~ 974 (1010)
..||+-.++. ..-+++.+..-..|+.+.++++|+|. + ..|.|- ++-..+..-.|.-|.-.. ++....+.
T Consensus 3 ~~lrVy~~~~~~~~~~k~i~v~~~tTa~evi~~~l~k~~l~~~~~~y~L~~~~~~~~~er~L~~~E~pl---~i~~~~~~ 79 (93)
T PF00788_consen 3 GVLRVYDGDGSPGSTYKTIKVSSSTTAREVIEMALEKFGLAEDPSDYCLVEVEESGGEERPLDDDECPL---QIQLQWPK 79 (93)
T ss_dssp EEEEEEETTSSSCCSEEEEEEETTSBHHHHHHHHHHHTTTSSSGGGEEEEEEECTTTEEEEETTTSBHH---HHHHTTSS
T ss_pred eEEEEEcCCCCCCccEEEEEECCCCCHHHHHHHHHHHhCCCCCCCCEEEEEEEcCCCEEEEcCCCCchH---HHHHhCcc
Confidence 4455555542 67788999999999999999999993 3 359993 554444444554444333 33333333
Q ss_pred --CeEEEEEee
Q 001809 975 --RSVRFLVRD 983 (1010)
Q Consensus 975 --~~vkl~V~d 983 (1010)
...+|.++.
T Consensus 80 ~~~~~~f~lr~ 90 (93)
T PF00788_consen 80 DSQNSRFVLRR 90 (93)
T ss_dssp GTTTEEEEEEE
T ss_pred ccCceEEEEEE
Confidence 367777664
No 332
>TIGR02417 fruct_sucro_rep D-fructose-responsive transcription factor. Members of this family belong the lacI helix-turn-helix family (pfam00356) of DNA-binding transcriptional regulators. All members are from the proteobacteria. Characterized members act as positive and negative transcriptional regulators of fructose and sucrose transport and metabolism. Sucrose is a disaccharide composed of fructose and glucose; D-fructose-1-phosphate rather than an intact sucrose moiety has been shown to act as the inducer.
Probab=30.32 E-value=51 Score=35.97 Aligned_cols=24 Identities=33% Similarity=0.365 Sum_probs=21.1
Q ss_pred cHHHHHHHcCCChhHHHHHHHHcC
Q 001809 614 SLKDAAKSIGVCPTTLKRICRQHG 637 (1010)
Q Consensus 614 pl~eAAk~LGV~~TtLKRiCR~~G 637 (1010)
+++|+||..|||++|+.|.-...+
T Consensus 1 ti~dIA~~aGVS~~TVSrvLn~~~ 24 (327)
T TIGR02417 1 TLSDIAKLAGVSKTTASYVINGKA 24 (327)
T ss_pred CHHHHHHHhCCCHHHHHHHHcCCC
Confidence 589999999999999999996543
No 333
>PRK13919 putative RNA polymerase sigma E protein; Provisional
Probab=30.29 E-value=57 Score=33.07 Aligned_cols=29 Identities=28% Similarity=0.321 Sum_probs=24.0
Q ss_pred HHhhcCCcHHHHHHHcCCChhHHHHHHHH
Q 001809 607 LQQYFSGSLKDAAKSIGVCPTTLKRICRQ 635 (1010)
Q Consensus 607 L~~yF~~pl~eAAk~LGV~~TtLKRiCR~ 635 (1010)
|+-+-+++.+|+|+.|||+..++|...++
T Consensus 146 l~~~~~~s~~eIA~~lgis~~~V~~~l~r 174 (186)
T PRK13919 146 VLYYQGYTHREAAQLLGLPLGTLKTRARR 174 (186)
T ss_pred HHHHcCCCHHHHHHHHCcCHHHHHHHHHH
Confidence 34566999999999999999999976543
No 334
>PRK09191 two-component response regulator; Provisional
Probab=30.10 E-value=55 Score=34.43 Aligned_cols=29 Identities=24% Similarity=0.313 Sum_probs=24.6
Q ss_pred HHHhhcCCcHHHHHHHcCCChhHHHHHHH
Q 001809 606 VLQQYFSGSLKDAAKSIGVCPTTLKRICR 634 (1010)
Q Consensus 606 ~L~~yF~~pl~eAAk~LGV~~TtLKRiCR 634 (1010)
.|+.+-+++.+|+|+.||++..|+|.+.+
T Consensus 98 ~l~~~~~~s~~eIA~~l~~s~~tV~~~l~ 126 (261)
T PRK09191 98 LLTALEGFSVEEAAEILGVDPAEAEALLD 126 (261)
T ss_pred HHHHHhcCCHHHHHHHHCCCHHHHHHHHH
Confidence 34456689999999999999999998875
No 335
>COG3415 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=30.06 E-value=45 Score=34.21 Aligned_cols=28 Identities=32% Similarity=0.241 Sum_probs=24.5
Q ss_pred hcCCcHHHHHHHcCCChhHHHHHHHHcC
Q 001809 610 YFSGSLKDAAKSIGVCPTTLKRICRQHG 637 (1010)
Q Consensus 610 yF~~pl~eAAk~LGV~~TtLKRiCR~~G 637 (1010)
|=++++++||+.+|||..|.++.-++..
T Consensus 19 ~~G~S~re~Ak~~gvs~sTvy~wv~r~~ 46 (138)
T COG3415 19 GEGLSCREAAKRFGVSISTVYRWVRRYR 46 (138)
T ss_pred HcCccHHHHHHHhCccHHHHHHHHHHhc
Confidence 4489999999999999999998887764
No 336
>TIGR01950 SoxR redox-sensitive transcriptional activator SoxR. SoxR is a MerR-family homodimeric transcription factor with a 2Fe-2S cluster in each monomer. The motif CIGCGCxxxxxC is conserved. Oxidation of the iron-sulfur cluster activates SoxR. The physiological role in E. coli is response to oxidative stress. It is activated by superoxide, singlet oxygen, nitric oxide (NO), and hydrogen peroxide. In E. coli, SoxR increases expression of transcription factor SoxS; different downstream targets may exist in other species.
Probab=29.86 E-value=49 Score=33.66 Aligned_cols=26 Identities=23% Similarity=0.262 Sum_probs=22.9
Q ss_pred CcHHHHHHHcCCChhHHHHHHHHcCCC
Q 001809 613 GSLKDAAKSIGVCPTTLKRICRQHGIS 639 (1010)
Q Consensus 613 ~pl~eAAk~LGV~~TtLKRiCR~~GI~ 639 (1010)
|++.|+|+.+||++.||.-..++ |+-
T Consensus 2 ~~IgevA~~~Gvs~~tLRyYE~~-GLl 27 (142)
T TIGR01950 2 LTVGELAKRSGVAVSALHFYESK-GLI 27 (142)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHC-CCC
Confidence 68999999999999999988876 654
No 337
>PRK14987 gluconate operon transcriptional regulator; Provisional
Probab=29.72 E-value=52 Score=36.08 Aligned_cols=25 Identities=32% Similarity=0.453 Sum_probs=21.8
Q ss_pred CcHHHHHHHcCCChhHHHHHHHHcC
Q 001809 613 GSLKDAAKSIGVCPTTLKRICRQHG 637 (1010)
Q Consensus 613 ~pl~eAAk~LGV~~TtLKRiCR~~G 637 (1010)
.+++|+|+..|||++|+-|+.+..+
T Consensus 6 ~ti~dIA~~agVS~~TVSrvLn~~~ 30 (331)
T PRK14987 6 PVLQDVADRVGVTKMTVSRFLRNPE 30 (331)
T ss_pred CcHHHHHHHhCCCHHHhhhhhCCCC
Confidence 4789999999999999999997553
No 338
>COG2452 Predicted site-specific integrase-resolvase [DNA replication, recombination, and repair]
Probab=29.68 E-value=47 Score=35.88 Aligned_cols=35 Identities=26% Similarity=0.221 Sum_probs=27.3
Q ss_pred CCcHHHHHHHcCCChhHHHHHHHHcCCCCCcchhhh
Q 001809 612 SGSLKDAAKSIGVCPTTLKRICRQHGISRWPSRKIN 647 (1010)
Q Consensus 612 ~~pl~eAAk~LGV~~TtLKRiCR~~GI~RWP~Rki~ 647 (1010)
.|.++|||+.|||+..||+|.-|.=-| |-|-++-.
T Consensus 1 ~m~~~e~~~~lgis~~Tl~rw~r~G~i-~~~~~~~g 35 (193)
T COG2452 1 LLRPKEACQLLGISYSTLLRWIREGKI-RVVTTEGG 35 (193)
T ss_pred CCCHHHHHHHhCcCHHHHHHHHHcCcc-cceEecCc
Confidence 477899999999999999999987555 44544433
No 339
>PRK12546 RNA polymerase sigma factor; Provisional
Probab=29.63 E-value=57 Score=33.96 Aligned_cols=29 Identities=28% Similarity=0.205 Sum_probs=24.8
Q ss_pred HHHhhcCCcHHHHHHHcCCChhHHHHHHH
Q 001809 606 VLQQYFSGSLKDAAKSIGVCPTTLKRICR 634 (1010)
Q Consensus 606 ~L~~yF~~pl~eAAk~LGV~~TtLKRiCR 634 (1010)
.|+-+.+++.+|+|+.|||+..|+|..-+
T Consensus 123 ~L~~~~g~s~~EIA~~LgiS~~tVk~~l~ 151 (188)
T PRK12546 123 ILVGASGFSYEEAAEMCGVAVGTVKSRAN 151 (188)
T ss_pred hhHHhcCCCHHHHHHHHCCCHHHHHHHHH
Confidence 45667899999999999999999987654
No 340
>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=29.60 E-value=48 Score=28.96 Aligned_cols=39 Identities=26% Similarity=0.278 Sum_probs=30.7
Q ss_pred hcCCcHHHHHHHcCCChhHHHHHHHHc---CCCCCcchhhhh
Q 001809 610 YFSGSLKDAAKSIGVCPTTLKRICRQH---GISRWPSRKINK 648 (1010)
Q Consensus 610 yF~~pl~eAAk~LGV~~TtLKRiCR~~---GI~RWP~Rki~s 648 (1010)
-+.++.++.|..+|++..|+-|+.+++ ||-++-+++|.=
T Consensus 26 ~~~lt~~~iA~~~g~sr~tv~r~l~~l~~~g~I~~~~~~i~I 67 (76)
T PF13545_consen 26 PLPLTQEEIADMLGVSRETVSRILKRLKDEGIIEVKRGKIII 67 (76)
T ss_dssp EEESSHHHHHHHHTSCHHHHHHHHHHHHHTTSEEEETTEEEE
T ss_pred EecCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEcCCEEEE
Confidence 356889999999999999999888765 776666666543
No 341
>PRK11161 fumarate/nitrate reduction transcriptional regulator; Provisional
Probab=29.55 E-value=35 Score=35.89 Aligned_cols=39 Identities=18% Similarity=0.246 Sum_probs=32.6
Q ss_pred CCcHHHHHHHcCCChhHHHHHHHHc---CCCCCcchhhhhhH
Q 001809 612 SGSLKDAAKSIGVCPTTLKRICRQH---GISRWPSRKINKVN 650 (1010)
Q Consensus 612 ~~pl~eAAk~LGV~~TtLKRiCR~~---GI~RWP~Rki~sl~ 650 (1010)
.++.++.|..|||++.||-|+-+++ |+-+|-+++|.=++
T Consensus 184 ~lt~~~iA~~lG~sr~tvsR~l~~l~~~g~I~~~~~~i~i~d 225 (235)
T PRK11161 184 TMTRGDIGNYLGLTVETISRLLGRFQKSGMLAVKGKYITIEN 225 (235)
T ss_pred cccHHHHHHHhCCcHHHHHHHHHHHHHCCCEEecCCEEEEcC
Confidence 4788999999999999999877654 88899999987554
No 342
>cd04768 HTH_BmrR-like Helix-Turn-Helix DNA binding domain of BmrR-like transcription regulators. Helix-turn-helix (HTH) BmrR-like transcription regulators (TipAL, Mta, SkgA, BmrR, and BltR), N-terminal domain. These proteins have been shown to regulate expression of specific regulons in response to various toxic substances, antibiotics, or oxygen radicals in Bacillus subtilis, Streptomyces, and Caulobacter crescentus. They are comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain HTH motifs that mediate DNA binding, while the C-terminal domains are often unrelated and bind specific coactivator molecules. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements.
Probab=29.53 E-value=56 Score=30.80 Aligned_cols=26 Identities=27% Similarity=0.252 Sum_probs=22.9
Q ss_pred CcHHHHHHHcCCChhHHHHHHHHcCCC
Q 001809 613 GSLKDAAKSIGVCPTTLKRICRQHGIS 639 (1010)
Q Consensus 613 ~pl~eAAk~LGV~~TtLKRiCR~~GI~ 639 (1010)
+++.|+|+.+||++.||+-..++ |+-
T Consensus 1 ~ti~eva~~~gvs~~tLRyye~~-Gll 26 (96)
T cd04768 1 LTIGEFAKLAGVSIRTLRHYDDI-GLF 26 (96)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHC-CCC
Confidence 47899999999999999998887 753
No 343
>TIGR02846 spore_sigmaK RNA polymerase sigma-K factor. The sporulation-specific transcription factor sigma-K (also called sigma-27) is expressed in the mother cell compartment of endospore-forming bacteria such as Bacillus subtilis. Like its close homolog sigma-E (sigma-29) (see TIGR02835), also specific to the mother cell compartment, it must be activated by a proteolytic cleavage. Note that in Bacillus subtilis (and apparently also Clostridium tetani), but not in other endospore forming species such as Bacillus anthracis, the sigK gene is generated by a non-germline (mother cell only) chromosomal rearrangement that recombines coding regions for the N-terminal and C-terminal regions of sigma-K.
Probab=29.51 E-value=55 Score=34.96 Aligned_cols=23 Identities=22% Similarity=0.416 Sum_probs=20.7
Q ss_pred CCcHHHHHHHcCCChhHHHHHHH
Q 001809 612 SGSLKDAAKSIGVCPTTLKRICR 634 (1010)
Q Consensus 612 ~~pl~eAAk~LGV~~TtLKRiCR 634 (1010)
+++.+|+|+.||+++.|+|++.+
T Consensus 194 ~~S~~EIAe~lgis~~tV~~~~~ 216 (227)
T TIGR02846 194 RKTQREIAKILGISRSYVSRIEK 216 (227)
T ss_pred CcCHHHHHHHHCCCHHHHHHHHH
Confidence 68999999999999999988754
No 344
>PRK13502 transcriptional activator RhaR; Provisional
Probab=29.38 E-value=79 Score=34.27 Aligned_cols=34 Identities=15% Similarity=0.209 Sum_probs=27.6
Q ss_pred HHHhhc--CCcHHHHHHHcCCChhHHHHHHHH-cCCC
Q 001809 606 VLQQYF--SGSLKDAAKSIGVCPTTLKRICRQ-HGIS 639 (1010)
Q Consensus 606 ~L~~yF--~~pl~eAAk~LGV~~TtLKRiCR~-~GI~ 639 (1010)
-|.++| .+.++++|+.+||+++.|.|++|+ .|+.
T Consensus 184 ~I~~~~~~~~~~~~lA~~~~iS~~~L~r~fk~~~G~t 220 (282)
T PRK13502 184 ALANSLECPFALDAFCQQEQCSERVLRQQFRAQTGMT 220 (282)
T ss_pred HHHhcccCCCCHHHHHHHHCcCHHHHHHHHHHHHCcC
Confidence 344444 467899999999999999999998 6974
No 345
>PRK13503 transcriptional activator RhaS; Provisional
Probab=29.32 E-value=82 Score=33.85 Aligned_cols=35 Identities=23% Similarity=0.358 Sum_probs=29.2
Q ss_pred HHHHhhcC--CcHHHHHHHcCCChhHHHHHHHHc-CCC
Q 001809 605 SVLQQYFS--GSLKDAAKSIGVCPTTLKRICRQH-GIS 639 (1010)
Q Consensus 605 ~~L~~yF~--~pl~eAAk~LGV~~TtLKRiCR~~-GI~ 639 (1010)
+-|.++|. +++.+.|+.+|+++..|.|++++. |+.
T Consensus 178 ~~I~~~~~~~~tl~~lA~~~~lS~~~l~r~Fk~~~G~S 215 (278)
T PRK13503 178 AWLEDHFAEEVNWEALADQFSLSLRTLHRQLKQQTGLT 215 (278)
T ss_pred HHHHHhhcCCCCHHHHHHHHCCCHHHHHHHHHHHhCcC
Confidence 44556664 778999999999999999999887 874
No 346
>PRK10651 transcriptional regulator NarL; Provisional
Probab=29.15 E-value=82 Score=31.21 Aligned_cols=34 Identities=15% Similarity=0.194 Sum_probs=25.0
Q ss_pred HHHHhhcC-CcHHHHHHHcCCChhHHHH----HHHHcCC
Q 001809 605 SVLQQYFS-GSLKDAAKSIGVCPTTLKR----ICRQHGI 638 (1010)
Q Consensus 605 ~~L~~yF~-~pl~eAAk~LGV~~TtLKR----iCR~~GI 638 (1010)
+.|+-+.. ++.+++|++|+|+..|+|. +.+++|+
T Consensus 162 ~vl~~l~~g~~~~~ia~~l~is~~tV~~~~~~l~~Kl~~ 200 (216)
T PRK10651 162 DILKLIAQGLPNKMIARRLDITESTVKVHVKHMLKKMKL 200 (216)
T ss_pred HHHHHHHcCCCHHHHHHHcCCCHHHHHHHHHHHHHHcCC
Confidence 45555555 5999999999999988664 5555665
No 347
>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=29.00 E-value=76 Score=26.31 Aligned_cols=31 Identities=13% Similarity=0.201 Sum_probs=24.6
Q ss_pred CcHHHHHHHcCCChhHHHHHHHHcCCCCCcc
Q 001809 613 GSLKDAAKSIGVCPTTLKRICRQHGISRWPS 643 (1010)
Q Consensus 613 ~pl~eAAk~LGV~~TtLKRiCR~~GI~RWP~ 643 (1010)
.+..|+|+.||++..++.|.++++-=..|..
T Consensus 21 ~~~~ei~~~~~i~~~~i~~~l~~L~~~g~i~ 51 (78)
T cd00090 21 LTVSELAERLGLSQSTVSRHLKKLEEAGLVE 51 (78)
T ss_pred cCHHHHHHHHCcCHhHHHHHHHHHHHCCCeE
Confidence 7899999999999999999988763233443
No 348
>PRK06704 RNA polymerase factor sigma-70; Validated
Probab=28.71 E-value=55 Score=35.76 Aligned_cols=28 Identities=29% Similarity=0.315 Sum_probs=23.8
Q ss_pred HHHhhcCCcHHHHHHHcCCChhHHHHHH
Q 001809 606 VLQQYFSGSLKDAAKSIGVCPTTLKRIC 633 (1010)
Q Consensus 606 ~L~~yF~~pl~eAAk~LGV~~TtLKRiC 633 (1010)
.|+-+++++.+|+|+.||++..|+|.+-
T Consensus 126 lL~~~eg~S~~EIAe~LgiS~~tVksrL 153 (228)
T PRK06704 126 LLKDVFQYSIADIAKVCSVSEGAVKASL 153 (228)
T ss_pred hhHHhhCCCHHHHHHHHCcCHHHHHHHH
Confidence 4555679999999999999999998754
No 349
>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=28.50 E-value=47 Score=28.70 Aligned_cols=25 Identities=28% Similarity=0.305 Sum_probs=20.5
Q ss_pred CC-cHHHHHHHcCCChhHHHHHHHHc
Q 001809 612 SG-SLKDAAKSIGVCPTTLKRICRQH 636 (1010)
Q Consensus 612 ~~-pl~eAAk~LGV~~TtLKRiCR~~ 636 (1010)
.+ +..+.|+.+||+.+|+++..+++
T Consensus 23 ~lps~~~la~~~~vsr~tvr~al~~L 48 (64)
T PF00392_consen 23 RLPSERELAERYGVSRTTVREALRRL 48 (64)
T ss_dssp BE--HHHHHHHHTS-HHHHHHHHHHH
T ss_pred EeCCHHHHHHHhccCCcHHHHHHHHH
Confidence 45 78899999999999999998877
No 350
>PRK12537 RNA polymerase sigma factor; Provisional
Probab=28.50 E-value=63 Score=32.96 Aligned_cols=28 Identities=18% Similarity=0.042 Sum_probs=23.2
Q ss_pred HHHhhcCCcHHHHHHHcCCChhHHHHHH
Q 001809 606 VLQQYFSGSLKDAAKSIGVCPTTLKRIC 633 (1010)
Q Consensus 606 ~L~~yF~~pl~eAAk~LGV~~TtLKRiC 633 (1010)
.|+-+-+++.+|+|+.|||+..|+|..-
T Consensus 143 ~l~~~~~~s~~eIA~~lgis~~tV~~~l 170 (182)
T PRK12537 143 LHAYVDGCSHAEIAQRLGAPLGTVKAWI 170 (182)
T ss_pred HHHHHcCCCHHHHHHHHCCChhhHHHHH
Confidence 4455568999999999999999998653
No 351
>PRK08359 transcription factor; Validated
Probab=28.49 E-value=62 Score=34.48 Aligned_cols=28 Identities=29% Similarity=0.439 Sum_probs=22.9
Q ss_pred HhhcCCcHHHHHHHcCCChhHHHHHHHHcC
Q 001809 608 QQYFSGSLKDAAKSIGVCPTTLKRICRQHG 637 (1010)
Q Consensus 608 ~~yF~~pl~eAAk~LGV~~TtLKRiCR~~G 637 (1010)
|.--+++++|.|+.|||+.+++.+| +.|
T Consensus 94 Re~kglSQeeLA~~lgvs~stI~~i--E~G 121 (176)
T PRK08359 94 IQKSGLSYEELSHEVGLSVNDLRRI--AHG 121 (176)
T ss_pred HHHcCCCHHHHHHHhCCCHHHHHHH--HCC
Confidence 3445899999999999999999877 445
No 352
>PRK10082 cell density-dependent motility repressor; Provisional
Probab=28.48 E-value=60 Score=35.40 Aligned_cols=38 Identities=26% Similarity=0.317 Sum_probs=29.5
Q ss_pred cccCHHHHHhhc-----CCcHHHHHHHcCCChhHHHHHHH----HcCC
Q 001809 600 KNVSLSVLQQYF-----SGSLKDAAKSIGVCPTTLKRICR----QHGI 638 (1010)
Q Consensus 600 ~~itl~~L~~yF-----~~pl~eAAk~LGV~~TtLKRiCR----~~GI 638 (1010)
+++++..| +|| ++++..||++|||+.+++-|.-+ ++|+
T Consensus 9 ~~m~~~~l-~~F~av~e~gS~t~AA~~L~iSQpavS~~I~~LE~~lG~ 55 (303)
T PRK10082 9 HNIETKWL-YDFLTLEKCRNFSQAAVSRNVSQPAFSRRIRALEQAIGV 55 (303)
T ss_pred cccchHHH-HHHHHHHhcCCHHHHHHHhCCChHHHHHHHHHHHHHcCC
Confidence 55777777 455 79999999999999998766555 5564
No 353
>PRK15092 DNA-binding transcriptional repressor LrhA; Provisional
Probab=28.21 E-value=60 Score=36.09 Aligned_cols=43 Identities=16% Similarity=0.224 Sum_probs=32.3
Q ss_pred ccccccccCHHHHHhhc-----CCcHHHHHHHcCCChhHHHHHHH----HcCC
Q 001809 595 RSTAEKNVSLSVLQQYF-----SGSLKDAAKSIGVCPTTLKRICR----QHGI 638 (1010)
Q Consensus 595 r~~~~~~itl~~L~~yF-----~~pl~eAAk~LGV~~TtLKRiCR----~~GI 638 (1010)
+++...++.+..|+ || +.++..||++|+|+..++-|.-+ ++|.
T Consensus 4 ~~~~~~~m~l~~L~-~F~~v~e~gs~s~AA~~L~iSQpavS~~I~~LE~~lG~ 55 (310)
T PRK15092 4 ANRPIINLDLDLLR-TFVAVADLNTFAAAAAAVCRTQSAVSQQMQRLEQLVGK 55 (310)
T ss_pred hhhhhhcCCHHHHH-HHHHHHHcCCHHHHHHHhCCChHHHHHHHHHHHHHhCc
Confidence 45556678888774 55 88999999999999888755544 5564
No 354
>PRK11923 algU RNA polymerase sigma factor AlgU; Provisional
Probab=28.18 E-value=62 Score=33.07 Aligned_cols=29 Identities=17% Similarity=0.114 Sum_probs=24.2
Q ss_pred HHhhcCCcHHHHHHHcCCChhHHHHHHHH
Q 001809 607 LQQYFSGSLKDAAKSIGVCPTTLKRICRQ 635 (1010)
Q Consensus 607 L~~yF~~pl~eAAk~LGV~~TtLKRiCR~ 635 (1010)
|+-+-+++.+|+|+.|||++.|+|...++
T Consensus 149 l~~~~g~s~~eIA~~lgis~~tv~~~l~R 177 (193)
T PRK11923 149 LREFDGLSYEDIASVMQCPVGTVRSRIFR 177 (193)
T ss_pred hHHhcCCCHHHHHHHHCCCHHHHHHHHHH
Confidence 34456899999999999999999987643
No 355
>PRK12539 RNA polymerase sigma factor; Provisional
Probab=28.18 E-value=64 Score=32.98 Aligned_cols=28 Identities=18% Similarity=0.118 Sum_probs=23.7
Q ss_pred HHHhhcCCcHHHHHHHcCCChhHHHHHH
Q 001809 606 VLQQYFSGSLKDAAKSIGVCPTTLKRIC 633 (1010)
Q Consensus 606 ~L~~yF~~pl~eAAk~LGV~~TtLKRiC 633 (1010)
.|.-+-+++.+|+|+.|||+..|+|.+.
T Consensus 141 ~l~~~~g~s~~eIA~~lgis~~tV~~~l 168 (184)
T PRK12539 141 QAVKLEGLSVAEAATRSGMSESAVKVSV 168 (184)
T ss_pred HHHHHcCCcHHHHHHHHCcCHHHHHHHH
Confidence 3445569999999999999999999875
No 356
>PRK10130 transcriptional regulator EutR; Provisional
Probab=28.10 E-value=77 Score=36.71 Aligned_cols=34 Identities=21% Similarity=0.257 Sum_probs=28.0
Q ss_pred HHhhcC--CcHHHHHHHcCCChhHHHHHHHHc-CCCC
Q 001809 607 LQQYFS--GSLKDAAKSIGVCPTTLKRICRQH-GISR 640 (1010)
Q Consensus 607 L~~yF~--~pl~eAAk~LGV~~TtLKRiCR~~-GI~R 640 (1010)
|..+++ +++.+.|+.+|||+.+|.|.++++ |+.-
T Consensus 249 i~~~~~~~ltv~~lA~~~gvS~r~L~r~Fk~~~G~sp 285 (350)
T PRK10130 249 VLENMSEPVTVLDLCNQLHVSRRTLQNAFHAILGIGP 285 (350)
T ss_pred HHhhhcCCCCHHHHHHHHCCCHHHHHHHHHHHHCcCH
Confidence 344453 789999999999999999999885 8753
No 357
>PRK06759 RNA polymerase factor sigma-70; Validated
Probab=28.00 E-value=70 Score=31.29 Aligned_cols=26 Identities=12% Similarity=0.173 Sum_probs=21.9
Q ss_pred hhcCCcHHHHHHHcCCChhHHHHHHH
Q 001809 609 QYFSGSLKDAAKSIGVCPTTLKRICR 634 (1010)
Q Consensus 609 ~yF~~pl~eAAk~LGV~~TtLKRiCR 634 (1010)
-+-+++.+|+|+.|||+..|+|.+-.
T Consensus 119 ~~~~~s~~EIA~~l~is~~tV~~~~~ 144 (154)
T PRK06759 119 FFVGKTMGEIALETEMTYYQVRWIYR 144 (154)
T ss_pred HhcCCCHHHHHHHHCCCHHHHHHHHH
Confidence 34489999999999999999987643
No 358
>cd04782 HTH_BltR Helix-Turn-Helix DNA binding domain of the BltR transcription regulator. Helix-turn-helix (HTH) multidrug-efflux transporter transcription regulator, BltR (BmrR-like transporter) of Bacillus subtilis, and related proteins; N-terminal domain. Blt, like Bmr, is a membrane protein which causes the efflux of a variety of toxic substances and antibiotics. These regulators are comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the C-terminal domains are often unrelated and bind specific coactivator molecules. They share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements.
Probab=27.74 E-value=59 Score=30.71 Aligned_cols=25 Identities=24% Similarity=0.211 Sum_probs=21.9
Q ss_pred CcHHHHHHHcCCChhHHHHHHHHcCC
Q 001809 613 GSLKDAAKSIGVCPTTLKRICRQHGI 638 (1010)
Q Consensus 613 ~pl~eAAk~LGV~~TtLKRiCR~~GI 638 (1010)
+++.|+|+.+||++.||+...+ .|+
T Consensus 1 ~~i~eva~~~gvs~~tlR~ye~-~Gl 25 (97)
T cd04782 1 FTTGEFAKLCGISKQTLFHYDK-IGL 25 (97)
T ss_pred CCHHHHHHHHCcCHHHHHHHHH-CCC
Confidence 4789999999999999998876 576
No 359
>TIGR01453 grpIintron_endo group I intron endonuclease. This model represents one subfamily of endonucleases containing the endo/excinuclease amino terminal domain, Pfam:PF01541 at its amino end. A distinct subfamily includes excinuclease abc subunit c (uvrC). Members of pfam01541 are often termed GIY-YIG endonucleases after conserved motifs near the amino end. This subfamily in this model is found in open reading frames of group I introns in both phage and mitochondria. The closely related endonucleases of phage T4: segA, segB, segC, segD and segE, score below the trusted cutoff for the family.
Probab=27.69 E-value=38 Score=36.43 Aligned_cols=26 Identities=19% Similarity=0.376 Sum_probs=22.9
Q ss_pred CCcHHHHHHHcCCChhHHHHHHHHcC
Q 001809 612 SGSLKDAAKSIGVCPTTLKRICRQHG 637 (1010)
Q Consensus 612 ~~pl~eAAk~LGV~~TtLKRiCR~~G 637 (1010)
--++.|||+.|||+..|+++.|+.-.
T Consensus 179 F~S~~eAa~~l~i~~~tI~~~l~~~~ 204 (214)
T TIGR01453 179 FDSIAEAARHLGISRGTISKYIKSGK 204 (214)
T ss_pred ecCHHHHHHHhCCCHHHHHHHHcccc
Confidence 46899999999999999999998654
No 360
>PRK09943 DNA-binding transcriptional repressor PuuR; Provisional
Probab=27.41 E-value=65 Score=33.37 Aligned_cols=32 Identities=25% Similarity=0.242 Sum_probs=28.6
Q ss_pred HHHHHhhcCCcHHHHHHHcCCChhHHHHHHHH
Q 001809 604 LSVLQQYFSGSLKDAAKSIGVCPTTLKRICRQ 635 (1010)
Q Consensus 604 l~~L~~yF~~pl~eAAk~LGV~~TtLKRiCR~ 635 (1010)
+..+|+--+++++++|+.+||+.++|.++-+.
T Consensus 12 l~~~R~~~glt~~elA~~~gis~~~is~~E~g 43 (185)
T PRK09943 12 LSEIRQQQGLSQRRAAELSGLTHSAISTIEQD 43 (185)
T ss_pred HHHHHHHcCCCHHHHHHHHCCCHHHHHHHHcC
Confidence 66788888999999999999999999999764
No 361
>TIGR01481 ccpA catabolite control protein A. Catabolite control protein A is a LacI family global transcriptional regulator found in Gram-positive bacteria. CcpA is involved in repressing carbohydrate utilization genes [ex: alpha-amylase (amyE), acetyl-coenzyme A synthase (acsA)] and in activating genes involved in transporting excess carbon from the cell [ex: acetate kinase (ackA), alpha-acetolactate synthase (alsS)]. Additionally, disruption of CcpA in Bacillus megaterium, Staphylococcus xylosus, Lactobacillus casei and Lactocacillus pentosus also decreases growth rate, which suggests CcpA is involved in the regulation of other metabolic pathways.
Probab=27.39 E-value=74 Score=34.71 Aligned_cols=25 Identities=24% Similarity=0.369 Sum_probs=21.9
Q ss_pred CcHHHHHHHcCCChhHHHHHHHHcC
Q 001809 613 GSLKDAAKSIGVCPTTLKRICRQHG 637 (1010)
Q Consensus 613 ~pl~eAAk~LGV~~TtLKRiCR~~G 637 (1010)
.+++|+||..|||++|+-|+-+..+
T Consensus 2 ~ti~dIA~~agvS~~TVSrvLn~~~ 26 (329)
T TIGR01481 2 VTIYDVAREAGVSMATVSRVVNGNP 26 (329)
T ss_pred CcHHHHHHHhCCCHHHHHHHhCCCC
Confidence 4799999999999999999987553
No 362
>TIGR02036 dsdC D-serine deaminase transcriptional activator. This family, part of the LysR family of transcriptional regulators, activates transcription of the gene for D-serine deaminase, dsdA. Trusted members of this family so far are found adjacent to dsdA and only in Gammaproteobacteria, including E. coli, Vibrio cholerae, and Colwellia psychrerythraea.
Probab=27.26 E-value=77 Score=34.72 Aligned_cols=39 Identities=18% Similarity=0.263 Sum_probs=30.0
Q ss_pred ccccccCHHHHHhhc----CCcHHHHHHHcCCChhHHHHHHHH
Q 001809 597 TAEKNVSLSVLQQYF----SGSLKDAAKSIGVCPTTLKRICRQ 635 (1010)
Q Consensus 597 ~~~~~itl~~L~~yF----~~pl~eAAk~LGV~~TtLKRiCR~ 635 (1010)
+.-+.++++.|+-+- +.++..||+.|||+.++|-|.-++
T Consensus 3 ~~~~~~~l~~L~~F~~va~~gs~s~AA~~L~isQpavS~~I~~ 45 (302)
T TIGR02036 3 RRLNSFQLSKMHTFEVAARHQSFSLAAEELSLTPSAISHRINQ 45 (302)
T ss_pred ccccCcCHHHHHHHHHHHHhCCHHHHHHHHCCCHHHHHHHHHH
Confidence 445667787776333 789999999999999998776663
No 363
>PRK09492 treR trehalose repressor; Provisional
Probab=27.21 E-value=69 Score=34.70 Aligned_cols=24 Identities=29% Similarity=0.407 Sum_probs=20.9
Q ss_pred CcHHHHHHHcCCChhHHHHHHHHc
Q 001809 613 GSLKDAAKSIGVCPTTLKRICRQH 636 (1010)
Q Consensus 613 ~pl~eAAk~LGV~~TtLKRiCR~~ 636 (1010)
.+++|+||.+|||.+|+-|.-...
T Consensus 5 ~ti~dIA~~agVS~~TVSrvLn~~ 28 (315)
T PRK09492 5 LTIKDIARLSGVGKSTVSRVLNNE 28 (315)
T ss_pred CcHHHHHHHhCCCHHHHhHHhCCC
Confidence 479999999999999999988643
No 364
>PF09048 Cro: Cro; InterPro: IPR000655 Bacteriophage lambda encodes two repressors: the Cro repressor that acts to turn off early gene transcription during the lytic cycle, and the lambda or cI repressor that is required to maintain lysogenic growth. Together the Cro and cI repressors form a helix-turn-helix (HTH) superfamily. The lambda Cro repressor binds to DNA as a highly flexible dimer. The crystal structure of the lambda Cro repressor [] reveals a HTH DNA-binding protein with an alpha/beta fold that differs from other Cro family members, possibly by an evolutionary fold change []. Most Cro proteins, such as Enterobacteria phage P22 Cro and Bacteriophage 434 Cro, have an all-alpha structure that is thought to be ancestral to lambda Cro, where the fourth and fifth helices are replaced by a beta-sheet, possibly as a result of secondary structure switching rather than by nonhomologous replacement []. This entry represents the lambda-type Cro repressor with an alpha/beta topology.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent; PDB: 5CRO_A 2ECS_A 2OVG_A 6CRO_A 1D1L_A 2ORC_A 1D1M_B 3ORC_A 1ORC_A 2A63_A ....
Probab=27.21 E-value=58 Score=29.24 Aligned_cols=32 Identities=19% Similarity=0.366 Sum_probs=25.0
Q ss_pred ccCHHHHHhhcCCcHHHHHHHcCCChhHHHHHHH
Q 001809 601 NVSLSVLQQYFSGSLKDAAKSIGVCPTTLKRICR 634 (1010)
Q Consensus 601 ~itl~~L~~yF~~pl~eAAk~LGV~~TtLKRiCR 634 (1010)
.|+|.+.-.-.+ +.+||+.|||..+.+-+.-|
T Consensus 3 ~i~L~eyv~~~G--Q~kaA~~lGV~Q~AIsKAlr 34 (59)
T PF09048_consen 3 RITLAEYVKEHG--QAKAARALGVTQSAISKALR 34 (59)
T ss_dssp EEEHHHHHHHHH--HHHHHHHHTS-HHHHHHHHH
T ss_pred eeeHHHHHHHhC--hHHHHHHcCCcHHHHHHHHH
Confidence 567777776666 89999999999999877665
No 365
>TIGR02393 RpoD_Cterm RNA polymerase sigma factor RpoD, C-terminal domain. This model represents the well-conserved C-terminal region of the major, essential sigma factor of most bacteria. Members of this clade show considerable variability in domain architecture and molecular weight, as well as in nomenclature: RpoD in E. coli and other Proteobacteria, SigA in Bacillus subtilis and many other Gram-positive bacteria, HrdB in Streptomyces, MysA in Mycobacterium smegmatis, etc.
Probab=27.16 E-value=68 Score=34.49 Aligned_cols=31 Identities=19% Similarity=0.389 Sum_probs=24.8
Q ss_pred HHHHhhc------CCcHHHHHHHcCCChhHHHHHHHH
Q 001809 605 SVLQQYF------SGSLKDAAKSIGVCPTTLKRICRQ 635 (1010)
Q Consensus 605 ~~L~~yF------~~pl~eAAk~LGV~~TtLKRiCR~ 635 (1010)
+.|.-+| .++++|+|+.|||+..+++++-.+
T Consensus 183 ~vl~l~ygl~~~~~~t~~EIA~~lgis~~~V~q~~~~ 219 (238)
T TIGR02393 183 KVLRMRYGLLDGRPHTLEEVGKEFNVTRERIRQIESK 219 (238)
T ss_pred HHHHHHhCCCCCCCccHHHHHHHHCCCHHHHHHHHHH
Confidence 3555555 489999999999999999988653
No 366
>PRK12514 RNA polymerase sigma factor; Provisional
Probab=27.06 E-value=70 Score=32.30 Aligned_cols=24 Identities=21% Similarity=0.048 Sum_probs=20.6
Q ss_pred hcCCcHHHHHHHcCCChhHHHHHH
Q 001809 610 YFSGSLKDAAKSIGVCPTTLKRIC 633 (1010)
Q Consensus 610 yF~~pl~eAAk~LGV~~TtLKRiC 633 (1010)
+-+++.+|+|+.|||+..++|...
T Consensus 143 ~~g~s~~eIA~~lgis~~tV~~~l 166 (179)
T PRK12514 143 LEGLSYKELAERHDVPLNTMRTWL 166 (179)
T ss_pred HcCCCHHHHHHHHCCChHHHHHHH
Confidence 348899999999999999997653
No 367
>PRK11924 RNA polymerase sigma factor; Provisional
Probab=26.98 E-value=71 Score=31.57 Aligned_cols=27 Identities=26% Similarity=0.178 Sum_probs=22.4
Q ss_pred HhhcCCcHHHHHHHcCCChhHHHHHHH
Q 001809 608 QQYFSGSLKDAAKSIGVCPTTLKRICR 634 (1010)
Q Consensus 608 ~~yF~~pl~eAAk~LGV~~TtLKRiCR 634 (1010)
.-..+++.+|+|+.||+++.|++++-+
T Consensus 137 ~~~~~~~~~eIA~~lgis~~tv~~~~~ 163 (179)
T PRK11924 137 RYVEGLSYREIAEILGVPVGTVKSRLR 163 (179)
T ss_pred HHHcCCCHHHHHHHHCCCHHHHHHHHH
Confidence 344689999999999999999987643
No 368
>TIGR02612 mob_myst_A mobile mystery protein A. Members of this protein family are found in mobization-related contexts more often than not, including within a CRISPR-associated gene region in Geobacter sulfurreducens PCA, and on plasmids in Agrobacterium tumefaciens and Coxiella burnetii, always together with mobile mystery protein B, a member of the Fic protein family (pfam02661). This protein is encoded by the upstream member of the gene pair and belongs to a family of helix-turn-helix DNA binding proteins (pfam01381).
Probab=26.82 E-value=70 Score=33.16 Aligned_cols=32 Identities=16% Similarity=0.285 Sum_probs=29.3
Q ss_pred HHHHHhhcCCcHHHHHHHcCCChhHHHHHHHH
Q 001809 604 LSVLQQYFSGSLKDAAKSIGVCPTTLKRICRQ 635 (1010)
Q Consensus 604 l~~L~~yF~~pl~eAAk~LGV~~TtLKRiCR~ 635 (1010)
+..++.-.++++++.|+.+||++.++.++.+.
T Consensus 30 Ir~~R~~lGmTq~eLAerlGVS~~tIs~iE~G 61 (150)
T TIGR02612 30 VRAIRKALGMSGAQLAGRLGVTPQRVEALEKS 61 (150)
T ss_pred HHHHHHHcCCCHHHHHHHhCCCHHHHHHHHcC
Confidence 56889999999999999999999999999865
No 369
>TIGR00637 ModE_repress ModE molybdate transport repressor domain. ModE is a molybdate-activated repressor of the molybdate transport operon in E. coli. It consists of the domain represented by this model and two tandem copies of mop-like domain, where Mop proteins are a family of 68-residue molybdenum-pterin binding proteins of Clostridium pasteurianum. This model also represents the full length of a pair of archaeal proteins that lack Mop-like domains. PSI-BLAST analysis shows similarity to helix-turn-helix regulatory proteins.
Probab=26.81 E-value=56 Score=31.29 Aligned_cols=24 Identities=29% Similarity=0.347 Sum_probs=20.3
Q ss_pred CCcHHHHHHHcCCChhHHHHHHHH
Q 001809 612 SGSLKDAAKSIGVCPTTLKRICRQ 635 (1010)
Q Consensus 612 ~~pl~eAAk~LGV~~TtLKRiCR~ 635 (1010)
+.++..||+.|||+.+++-|.-++
T Consensus 16 ~gSis~AA~~L~iS~stvs~~I~~ 39 (99)
T TIGR00637 16 MGSISQAAKDAGISYKSAWDYIRA 39 (99)
T ss_pred hCCHHHHHHHHCCCHHHHHHHHHH
Confidence 789999999999999998665553
No 370
>TIGR02047 CadR-PbrR Cd(II)/Pb(II)-responsive transcriptional regulator. This model represents the cadmium(II) and/or lead(II) responsive transcriptional activator of the proteobacterial metal efflux system. This protein is a member of the MerR family of transcriptional activators (pfam00376) and contains a distinctive pattern of cysteine residues in its metal binding loop, Cys-X(6-9)-Cys, as well as a conserved and critical cysteine at the N-terminal end of the dimerization helix.
Probab=26.66 E-value=1e+02 Score=30.57 Aligned_cols=25 Identities=24% Similarity=0.365 Sum_probs=21.0
Q ss_pred CcHHHHHHHcCCChhHHHHHHHHcCC
Q 001809 613 GSLKDAAKSIGVCPTTLKRICRQHGI 638 (1010)
Q Consensus 613 ~pl~eAAk~LGV~~TtLKRiCR~~GI 638 (1010)
|++.|+|+.+||++.||.-..++ |+
T Consensus 1 m~I~e~a~~~gvs~~tlR~Ye~~-GL 25 (127)
T TIGR02047 1 MKIGELAQKTGVSVETIRFYEKQ-GL 25 (127)
T ss_pred CcHHHHHHHHCcCHHHHHHHHHC-CC
Confidence 57899999999999999887663 43
No 371
>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=26.59 E-value=61 Score=28.41 Aligned_cols=26 Identities=27% Similarity=0.381 Sum_probs=20.8
Q ss_pred cCCcHHHHHHHcCCChhHHHHHHHHc
Q 001809 611 FSGSLKDAAKSIGVCPTTLKRICRQH 636 (1010)
Q Consensus 611 F~~pl~eAAk~LGV~~TtLKRiCR~~ 636 (1010)
-....+++|+.|||++.|.-..++++
T Consensus 21 ~~v~~~~iA~~L~vs~~tvt~ml~~L 46 (60)
T PF01325_consen 21 GPVRTKDIAERLGVSPPTVTEMLKRL 46 (60)
T ss_dssp SSBBHHHHHHHHTS-HHHHHHHHHHH
T ss_pred CCccHHHHHHHHCCChHHHHHHHHHH
Confidence 34678999999999999988888766
No 372
>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=26.58 E-value=84 Score=26.27 Aligned_cols=38 Identities=18% Similarity=0.251 Sum_probs=29.0
Q ss_pred HHHHHhhcCCcHHHHHHHcCCChhHHHHHHHHcCCCCC
Q 001809 604 LSVLQQYFSGSLKDAAKSIGVCPTTLKRICRQHGISRW 641 (1010)
Q Consensus 604 l~~L~~yF~~pl~eAAk~LGV~~TtLKRiCR~~GI~RW 641 (1010)
|..|.++=.+++.+.|+.+++..+++-|+.+++-=..|
T Consensus 9 L~~l~~~~~~~~~~la~~~~~~~~~~t~~i~~L~~~g~ 46 (59)
T PF01047_consen 9 LRILYENGGITQSELAEKLGISRSTVTRIIKRLEKKGL 46 (59)
T ss_dssp HHHHHHHSSEEHHHHHHHHTS-HHHHHHHHHHHHHTTS
T ss_pred HHHHHHcCCCCHHHHHHHHCCChhHHHHHHHHHHHCCC
Confidence 44555666789999999999999999999998743333
No 373
>TIGR02405 trehalos_R_Ecol trehalose operon repressor, proteobacterial. This family consists of repressors of the LacI family typically associated with trehalose utilization operons. Trehalose is imported as trehalose-6-phosphate and then hydrolyzed by alpha,alpha-phosphotrehalase to glucose and glucose-6-P. This family includes repressors mostly from Gammaproteobacteria and does not include the GntR family TreR of Bacillus subtilis
Probab=26.20 E-value=48 Score=36.15 Aligned_cols=23 Identities=30% Similarity=0.433 Sum_probs=20.4
Q ss_pred CcHHHHHHHcCCChhHHHHHHHH
Q 001809 613 GSLKDAAKSIGVCPTTLKRICRQ 635 (1010)
Q Consensus 613 ~pl~eAAk~LGV~~TtLKRiCR~ 635 (1010)
.+++|+|+..|||++|+.|.-..
T Consensus 2 ~ti~dIA~~agVS~sTVSr~Ln~ 24 (311)
T TIGR02405 2 LTIKDIARLAGVGKSTVSRVLNN 24 (311)
T ss_pred CcHHHHHHHhCCCHHHHHHHhCC
Confidence 47999999999999999999853
No 374
>COG2522 Predicted transcriptional regulator [General function prediction only]
Probab=26.11 E-value=1.5e+02 Score=29.95 Aligned_cols=31 Identities=16% Similarity=0.082 Sum_probs=26.7
Q ss_pred HHHhhcCCcHHHHHHHcCCChhHHHHHHHHcC
Q 001809 606 VLQQYFSGSLKDAAKSIGVCPTTLKRICRQHG 637 (1010)
Q Consensus 606 ~L~~yF~~pl~eAAk~LGV~~TtLKRiCR~~G 637 (1010)
+|+.- ++++.++|+.|||+++.+.+.-+...
T Consensus 17 ~L~ee-G~Sq~~iA~LLGltqaAVS~Yls~kr 47 (119)
T COG2522 17 ELIEE-GLSQYRIAKLLGLTQAAVSQYLSGKR 47 (119)
T ss_pred HHHHc-CCcHHHHHHHhCCCHHHHHHHHccCC
Confidence 55555 99999999999999999999887654
No 375
>smart00352 POU Found in Pit-Oct-Unc transcription factors.
Probab=25.98 E-value=83 Score=29.44 Aligned_cols=31 Identities=16% Similarity=0.146 Sum_probs=25.1
Q ss_pred HHHHHhhcCCcHHHHHHHcC------CChhHHHHHHH
Q 001809 604 LSVLQQYFSGSLKDAAKSIG------VCPTTLKRICR 634 (1010)
Q Consensus 604 l~~L~~yF~~pl~eAAk~LG------V~~TtLKRiCR 634 (1010)
+...|.-.++++.+.|+.|| ++.+|+-|+=+
T Consensus 16 lk~~R~~lGLTQ~dvA~~lg~~~g~i~SQstISR~Es 52 (75)
T smart00352 16 FKQRRIKLGFTQADVGLALGALYGPDFSQTTICRFEA 52 (75)
T ss_pred HHHHHHHcCCCHHHHHHHhcccccCcCCHHHHHHHHh
Confidence 45667788999999999999 48999877543
No 376
>COG1709 Predicted transcriptional regulator [Transcription]
Probab=25.59 E-value=41 Score=37.14 Aligned_cols=28 Identities=25% Similarity=0.484 Sum_probs=24.4
Q ss_pred HHHHHhhcCCcHHHHHHHcCCChhHHHH
Q 001809 604 LSVLQQYFSGSLKDAAKSIGVCPTTLKR 631 (1010)
Q Consensus 604 l~~L~~yF~~pl~eAAk~LGV~~TtLKR 631 (1010)
+.--|.+|+.++.|.|+.|||+++++--
T Consensus 32 lrKWR~~F~vSQ~elA~~l~vSpSVISD 59 (241)
T COG1709 32 LRKWREIFNVSQTELARELGVSPSVISD 59 (241)
T ss_pred HHHHHHHhCccHHHHHHHhCCCcceeeh
Confidence 4456789999999999999999999865
No 377
>PRK13500 transcriptional activator RhaR; Provisional
Probab=25.58 E-value=80 Score=35.31 Aligned_cols=36 Identities=17% Similarity=0.276 Sum_probs=30.5
Q ss_pred HHHHHhhcC--CcHHHHHHHcCCChhHHHHHHHHc-CCC
Q 001809 604 LSVLQQYFS--GSLKDAAKSIGVCPTTLKRICRQH-GIS 639 (1010)
Q Consensus 604 l~~L~~yF~--~pl~eAAk~LGV~~TtLKRiCR~~-GI~ 639 (1010)
++-|.++|. +++.+.|+.+|+|+.+|.|++|+. |..
T Consensus 212 ~~yI~~~~~e~isl~~lA~~~~iS~~~L~r~FK~~tG~T 250 (312)
T PRK13500 212 ITRLAASLKSPFALDKFCDEASCSERVLRQQFRQQTGMT 250 (312)
T ss_pred HHHHHHcccCCCCHHHHHHHHCcCHHHHHHHHHHHHCcC
Confidence 356667664 789999999999999999999997 864
No 378
>cd04767 HTH_HspR-like_MBC Helix-Turn-Helix DNA binding domain of putative HspR-like transcription regulators. Putative helix-turn-helix (HTH) transcription regulator HspR-like proteins. Unlike the characterized HspR, these proteins have a C-terminal domain with putative metal binding cysteines (MBC). Heat shock protein regulators (HspR) have been shown to regulate expression of specific regulons in response to high temperature or high osmolarity in Streptomyces and Helicobacter, respectively. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind spe
Probab=25.14 E-value=62 Score=32.46 Aligned_cols=25 Identities=24% Similarity=0.356 Sum_probs=22.2
Q ss_pred CcHHHHHHHcCCChhHHHHHHHHcCC
Q 001809 613 GSLKDAAKSIGVCPTTLKRICRQHGI 638 (1010)
Q Consensus 613 ~pl~eAAk~LGV~~TtLKRiCR~~GI 638 (1010)
+++.++|+.+||++.||...-|+ |+
T Consensus 2 ysI~eVA~~~GVs~~TLR~wE~~-GL 26 (120)
T cd04767 2 YPIGVVAELLNIHPETLRIWERH-GL 26 (120)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHC-CC
Confidence 68999999999999999988776 64
No 379
>PRK12534 RNA polymerase sigma factor; Provisional
Probab=24.91 E-value=88 Score=31.82 Aligned_cols=28 Identities=14% Similarity=0.012 Sum_probs=23.2
Q ss_pred HHhhcCCcHHHHHHHcCCChhHHHHHHH
Q 001809 607 LQQYFSGSLKDAAKSIGVCPTTLKRICR 634 (1010)
Q Consensus 607 L~~yF~~pl~eAAk~LGV~~TtLKRiCR 634 (1010)
+.-+-+++.+|+|+.|||++.+++.+..
T Consensus 148 l~~~~g~s~~eIA~~lgis~~~v~~~l~ 175 (187)
T PRK12534 148 TAFFEGITYEELAARTDTPIGTVKSWIR 175 (187)
T ss_pred HHHHcCCCHHHHHHHhCCChhHHHHHHH
Confidence 3334599999999999999999987654
No 380
>PF13730 HTH_36: Helix-turn-helix domain
Probab=24.85 E-value=70 Score=26.56 Aligned_cols=23 Identities=30% Similarity=0.430 Sum_probs=20.5
Q ss_pred cHHHHHHHcCCChhHHHHHHHHc
Q 001809 614 SLKDAAKSIGVCPTTLKRICRQH 636 (1010)
Q Consensus 614 pl~eAAk~LGV~~TtLKRiCR~~ 636 (1010)
+++..|+.+|++..|+.|..+++
T Consensus 27 S~~~la~~~g~s~~Tv~~~i~~L 49 (55)
T PF13730_consen 27 SQETLAKDLGVSRRTVQRAIKEL 49 (55)
T ss_pred CHHHHHHHHCcCHHHHHHHHHHH
Confidence 68999999999999999988766
No 381
>PRK11475 DNA-binding transcriptional activator BglJ; Provisional
Probab=24.82 E-value=77 Score=33.88 Aligned_cols=27 Identities=15% Similarity=0.249 Sum_probs=23.4
Q ss_pred CCcHHHHHHHcCCChhHHH----HHHHHcCC
Q 001809 612 SGSLKDAAKSIGVCPTTLK----RICRQHGI 638 (1010)
Q Consensus 612 ~~pl~eAAk~LGV~~TtLK----RiCR~~GI 638 (1010)
+++.+|+|++|+||..|+| ++.+++|+
T Consensus 149 G~snkeIA~~L~iS~~TV~~h~~~I~~KLgv 179 (207)
T PRK11475 149 GYSMPQIAEQLERNIKTIRAHKFNVMSKLGV 179 (207)
T ss_pred CCCHHHHHHHHCCCHHHHHHHHHHHHHHcCC
Confidence 7899999999999998875 67777886
No 382
>PRK12524 RNA polymerase sigma factor; Provisional
Probab=24.82 E-value=80 Score=32.65 Aligned_cols=28 Identities=14% Similarity=0.135 Sum_probs=23.3
Q ss_pred HHHhhcCCcHHHHHHHcCCChhHHHHHH
Q 001809 606 VLQQYFSGSLKDAAKSIGVCPTTLKRIC 633 (1010)
Q Consensus 606 ~L~~yF~~pl~eAAk~LGV~~TtLKRiC 633 (1010)
.|+-+-+++.+|+|+.|||++.|+|.+-
T Consensus 146 ~L~~~~g~s~~eIA~~lgis~~tV~~~l 173 (196)
T PRK12524 146 VLRHIEGLSNPEIAEVMEIGVEAVESLT 173 (196)
T ss_pred HHHHHcCCCHHHHHHHHCcCHHHHHHHH
Confidence 4444568999999999999999998764
No 383
>PF13022 HTH_Tnp_1_2: Helix-turn-helix of insertion element transposase; PDB: 2AO9_I.
Probab=24.66 E-value=64 Score=33.43 Aligned_cols=24 Identities=25% Similarity=0.393 Sum_probs=18.3
Q ss_pred CcHHHHHHHcCCChhHHHHHHHHc
Q 001809 613 GSLKDAAKSIGVCPTTLKRICRQH 636 (1010)
Q Consensus 613 ~pl~eAAk~LGV~~TtLKRiCR~~ 636 (1010)
.++.+.|+++||+++||+|.-++.
T Consensus 35 ~T~~eiAee~Gis~~tLYrWr~~~ 58 (142)
T PF13022_consen 35 RTQAEIAEEVGISRSTLYRWRQQN 58 (142)
T ss_dssp S-HHHHHHHHTS-HHHHHHHHHH-
T ss_pred chHHHHHHHhCCCHHHHHHHHhcC
Confidence 579999999999999999865443
No 384
>COG1609 PurR Transcriptional regulators [Transcription]
Probab=24.62 E-value=83 Score=35.69 Aligned_cols=24 Identities=33% Similarity=0.463 Sum_probs=22.0
Q ss_pred cHHHHHHHcCCChhHHHHHHHHcC
Q 001809 614 SLKDAAKSIGVCPTTLKRICRQHG 637 (1010)
Q Consensus 614 pl~eAAk~LGV~~TtLKRiCR~~G 637 (1010)
+++|+|+..|||.+|+-|.-+..+
T Consensus 2 TikDVA~~AGVS~sTVSrvln~~~ 25 (333)
T COG1609 2 TIKDVAKLAGVSKATVSRVLNGSP 25 (333)
T ss_pred CHHHHHHHhCCCHHHHHHHHcCCC
Confidence 689999999999999999988776
No 385
>cd08804 Death_ank2 Death domain of Ankyrin-2. Death Domain (DD) of Ankyrin-2 (ANK-2) and related proteins. Ankyrins are modular proteins comprising three conserved domains, an N-terminal membrane-binding domain containing ANK repeats, a spectrin-binding domain and a C-terminal DD. ANK-2, also called ankyrin-B (for broadly expressed), is required for proper function of the Na/Ca ion exchanger-1 in cardiomyocytes, and is thought to function in linking integral membrane proteins to the underlying cytoskeleton. Human ANK-2 is associated with "Ankyrin-B syndrome", an atypical arrythmia disorder with risk of sudden cardiac death. It also plays key roles in the brain and striated muscle. Loss of ANK-2 is associated with significant nervous system defects and sarcomere disorganization. In general, DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other
Probab=24.61 E-value=84 Score=29.36 Aligned_cols=37 Identities=16% Similarity=0.240 Sum_probs=33.5
Q ss_pred cccCHHHHHhhcCCcHHHHHHHcCCChhHHHHHHHHc
Q 001809 600 KNVSLSVLQQYFSGSLKDAAKSIGVCPTTLKRICRQH 636 (1010)
Q Consensus 600 ~~itl~~L~~yF~~pl~eAAk~LGV~~TtLKRiCR~~ 636 (1010)
+++-+.+|....+-.-++.|++|||+.+.+.+|..+|
T Consensus 3 ~~~~l~~ia~~LG~dWk~LAr~Lg~se~dI~~i~~~~ 39 (84)
T cd08804 3 KEERLAVIADHLGFSWTELARELDFTEEQIHQIRIEN 39 (84)
T ss_pred hhhHHHHHHHHHhhhHHHHHHHcCCCHHHHHHHHHHC
Confidence 4567889999999999999999999999999999886
No 386
>PRK10094 DNA-binding transcriptional activator AllS; Provisional
Probab=24.55 E-value=78 Score=34.89 Aligned_cols=72 Identities=21% Similarity=0.255 Sum_probs=43.7
Q ss_pred cCHHHHHhhc-----CCcHHHHHHHcCCChhHHHHHHH----HcCC---CCCc------------chhhhhhHHHHHHHH
Q 001809 602 VSLSVLQQYF-----SGSLKDAAKSIGVCPTTLKRICR----QHGI---SRWP------------SRKINKVNRSLKKIQ 657 (1010)
Q Consensus 602 itl~~L~~yF-----~~pl~eAAk~LGV~~TtLKRiCR----~~GI---~RWP------------~Rki~sl~~~i~~l~ 657 (1010)
+.++.|+ || +.++..||++|||+.+++-|.-+ ++|+ .|=+ |++.+.+-..++.++
T Consensus 2 ~~~~~L~-~f~~v~e~gs~s~AA~~L~iSQpavS~~I~~LE~~lg~~Lf~R~~r~~~lT~~G~~l~~~a~~il~~~~~~~ 80 (308)
T PRK10094 2 FDPETLR-TFIAVAETGSFSKAAERLCKTTATISYRIKLLEENTGVALFFRTTRSVTLTAAGEHLLSQARDWLSWLESMP 80 (308)
T ss_pred CCHHHHH-HHHHHHHhCCHHHHHHHhcCCHHHHHHHHHHHHHHhCCEEEeeCCCceeECHhHHHHHHHHHHHHHHHHHHH
Confidence 4455665 44 78999999999999988766655 4564 2322 344555555555555
Q ss_pred HHHhhc-ccccCcccccC
Q 001809 658 TVLNSV-QGVEGGLKFDP 674 (1010)
Q Consensus 658 ~~i~s~-qg~e~~~~~~~ 674 (1010)
+.+... ++..+.+++..
T Consensus 81 ~~~~~~~~~~~g~l~Ig~ 98 (308)
T PRK10094 81 SELQQVNDGVERQVNIVI 98 (308)
T ss_pred HHHHHhcCCCCccEEEEe
Confidence 444432 44556566543
No 387
>PRK05949 RNA polymerase sigma factor; Validated
Probab=24.51 E-value=1.5e+02 Score=34.16 Aligned_cols=30 Identities=20% Similarity=0.311 Sum_probs=24.2
Q ss_pred HHHhhcC------CcHHHHHHHcCCChhHHHHHHHH
Q 001809 606 VLQQYFS------GSLKDAAKSIGVCPTTLKRICRQ 635 (1010)
Q Consensus 606 ~L~~yF~------~pl~eAAk~LGV~~TtLKRiCR~ 635 (1010)
.|+-+|. ++++|+|+.|||+..++|.+=++
T Consensus 274 Vi~lr~gl~~~e~~Tl~EIa~~lgiS~erVrq~~~r 309 (327)
T PRK05949 274 VLTLRFGLEDGKELSLAKVGERLNLSRERVRQLEHQ 309 (327)
T ss_pred HHHHHhccCCCCCCCHHHHHHHHCcCHHHHHHHHHH
Confidence 5555553 89999999999999999987543
No 388
>COG2944 Predicted transcriptional regulator [Transcription]
Probab=24.48 E-value=81 Score=31.15 Aligned_cols=29 Identities=17% Similarity=0.271 Sum_probs=26.5
Q ss_pred HHHHHhhcCCcHHHHHHHcCCChhHHHHH
Q 001809 604 LSVLQQYFSGSLKDAAKSIGVCPTTLKRI 632 (1010)
Q Consensus 604 l~~L~~yF~~pl~eAAk~LGV~~TtLKRi 632 (1010)
+..||+-+++++.+=|+.|||+..||...
T Consensus 49 Ik~iRe~~~lSQ~vFA~~L~vs~~Tv~~W 77 (104)
T COG2944 49 IKAIREKLGLSQPVFARYLGVSVSTVRKW 77 (104)
T ss_pred HHHHHHHhCCCHHHHHHHHCCCHHHHHHH
Confidence 56788999999999999999999999865
No 389
>PF14549 P22_Cro: DNA-binding transcriptional regulator Cro; PDB: 1RZS_A 3BD1_A 3QWS_A 2HIN_B.
Probab=24.38 E-value=1e+02 Score=27.51 Aligned_cols=27 Identities=26% Similarity=0.475 Sum_probs=22.1
Q ss_pred HHHHhhcCCcHHHHHHHcCCChhHHHHH
Q 001809 605 SVLQQYFSGSLKDAAKSIGVCPTTLKRI 632 (1010)
Q Consensus 605 ~~L~~yF~~pl~eAAk~LGV~~TtLKRi 632 (1010)
+++-.||+ ....+|+.|||++.++.+.
T Consensus 3 ~~aI~~~G-~~~~lAkalGVs~~aVs~W 29 (60)
T PF14549_consen 3 KDAIKYFG-GQSKLAKALGVSPQAVSQW 29 (60)
T ss_dssp HHHHHHHS-SHHHHHHHHTS-HHHHHHH
T ss_pred HHHHHHHC-CHHHHHHHHCCCHHHHHHh
Confidence 46778887 7789999999999998776
No 390
>PRK06986 fliA flagellar biosynthesis sigma factor; Validated
Probab=24.36 E-value=78 Score=33.89 Aligned_cols=26 Identities=19% Similarity=0.222 Sum_probs=22.0
Q ss_pred hhcCCcHHHHHHHcCCChhHHHHHHH
Q 001809 609 QYFSGSLKDAAKSIGVCPTTLKRICR 634 (1010)
Q Consensus 609 ~yF~~pl~eAAk~LGV~~TtLKRiCR 634 (1010)
-+-+++.+|+|+.|||+..|+|++-+
T Consensus 197 ~~~g~s~~EIA~~lgis~~tV~~~~~ 222 (236)
T PRK06986 197 YQEELNLKEIGAVLGVSESRVSQIHS 222 (236)
T ss_pred hccCCCHHHHHHHHCCCHHHHHHHHH
Confidence 34578999999999999999997644
No 391
>COG2901 Fis Factor for inversion stimulation Fis, transcriptional activator [Transcription / DNA replication, recombination, and repair]
Probab=24.30 E-value=1e+02 Score=29.84 Aligned_cols=35 Identities=29% Similarity=0.481 Sum_probs=32.7
Q ss_pred HHHHHhhcCCcHHHHHHHcCCChhHHHHHHHHcCC
Q 001809 604 LSVLQQYFSGSLKDAAKSIGVCPTTLKRICRQHGI 638 (1010)
Q Consensus 604 l~~L~~yF~~pl~eAAk~LGV~~TtLKRiCR~~GI 638 (1010)
|+.+-+|-..-+..||.-|||-+.||.|.-.+||.
T Consensus 63 L~~vM~~~~gNQtrAa~mLGinR~TLRKKLkqygl 97 (98)
T COG2901 63 LDMVMQYTRGNQTRAALMLGINRGTLRKKLKKYGL 97 (98)
T ss_pred HHHHHHHhcccHHHHHHHHcccHHHHHHHHHHhCC
Confidence 67888999999999999999999999999999986
No 392
>PRK13348 chromosome replication initiation inhibitor protein; Provisional
Probab=24.15 E-value=80 Score=34.07 Aligned_cols=27 Identities=26% Similarity=0.496 Sum_probs=21.9
Q ss_pred CCcHHHHHHHcCCChhHHHHHHH----HcCC
Q 001809 612 SGSLKDAAKSIGVCPTTLKRICR----QHGI 638 (1010)
Q Consensus 612 ~~pl~eAAk~LGV~~TtLKRiCR----~~GI 638 (1010)
+.++..||++|||+.+++-|.-+ ++|+
T Consensus 16 ~gs~t~AA~~L~iSQ~avS~~i~~LE~~lg~ 46 (294)
T PRK13348 16 TGSFERAARRLHVTPSAVSQRIKALEESLGQ 46 (294)
T ss_pred cCCHHHHHHHhCCCchHHHHHHHHHHHHhCc
Confidence 78999999999999988766555 4564
No 393
>PRK10086 DNA-binding transcriptional regulator DsdC; Provisional
Probab=24.14 E-value=76 Score=34.93 Aligned_cols=45 Identities=22% Similarity=0.281 Sum_probs=33.9
Q ss_pred cccccccccCHHHHHhhc----CCcHHHHHHHcCCChhHHHHHHH----HcCC
Q 001809 594 KRSTAEKNVSLSVLQQYF----SGSLKDAAKSIGVCPTTLKRICR----QHGI 638 (1010)
Q Consensus 594 ~r~~~~~~itl~~L~~yF----~~pl~eAAk~LGV~~TtLKRiCR----~~GI 638 (1010)
-|++...++++..|+-+- +.++..||+.|||+.+++-|.-+ ++|+
T Consensus 6 ~~~~~~~~~~l~~L~~f~~va~~gs~s~AA~~L~iSQpavS~~I~~LE~~lG~ 58 (311)
T PRK10086 6 MRNRLLNGWQLSKLHTFEVAARHQSFALAADELSLTPSAVSHRINQLEEELGI 58 (311)
T ss_pred HHHhhhcCCcHHHHHHHHHHHHcCCHHHHHHHHCCCHHHHHHHHHHHHHHhCC
Confidence 345666788888876333 78999999999999988766555 5575
No 394
>PF14533 USP7_C2: Ubiquitin-specific protease C-terminal; PDB: 2YLM_A.
Probab=24.06 E-value=81 Score=33.98 Aligned_cols=45 Identities=20% Similarity=0.474 Sum_probs=24.3
Q ss_pred EEEeCCCcChHHHHHHHHHHcCcccc-----eeee---------EeecCCCCeEEEecC
Q 001809 915 RFKFDPSAGCFQLYEEVARRLKLQNG-----TFQL---------KYLDDEEEWVMLVSD 959 (1010)
Q Consensus 915 RF~~~~s~g~~~L~~EIakRf~l~~~-----~f~l---------KYlDDd~EWVlLtcD 959 (1010)
.|.+.|..-|.++++=|.+|+||.+- .|.| .|++||.+-|+-.-+
T Consensus 136 ~f~v~~gE~f~~tK~Rl~~rlgv~~keF~K~Kfaiv~~~~~~~~~yl~d~~~~il~~~~ 194 (213)
T PF14533_consen 136 LFVVKPGETFSDTKERLQKRLGVSDKEFEKWKFAIVQNSRYSKPRYLEDDDDLILFDEI 194 (213)
T ss_dssp EEEEETT--HHHHHHHHHHHH---HHHHTT-EEEEEETTEE---EE--TT-T----GGG
T ss_pred EEEeeCCCcHHHHHHHHHHHhCCChhhheeEEEEEEecCCcccceeccccchhhhhhhh
Confidence 45566778899999999999997652 3554 799998776665433
No 395
>PF00376 MerR: MerR family regulatory protein; InterPro: IPR000551 The many bacterial transcription regulation proteins which bind DNA through a 'helix-turn-helix' motif can be classified into subfamilies on the basis of sequence similarities. One of these is the MerR subfamily. MerR, which is found in many bacterial species mediates the mercuric-dependent induction of the mercury resistance operon. In the absence of mercury merR represses transcription by binding tightly, as a dimer, to the 'mer' operator region; when mercury is present the dimeric complex binds a single ion and becomes a potent transcriptional activator, while remaining bound to the mer site. Members of the family include the mercuric resistance operon regulatory protein merR; Bacillus subtilis bltR and bmrR; Bacillus glnR; Streptomyces coelicolor hspR; Bradyrhizobium japonicum nolA; Escherichia coli superoxide response regulator soxR; and Streptomyces lividans transcriptional activator tipA [, , , , , ]. Other members include hypothetical proteins from E. coli, B. subtilis and Haemophilus influenzae. Within this family, the HTH motif is situated towards the N terminus.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent; PDB: 3HH0_A 2DG6_A 1R8D_B 1JBG_A 2VZ4_A 2ZHH_A 2ZHG_A 1Q07_A 1Q06_A 1Q05_B ....
Probab=24.03 E-value=81 Score=25.45 Aligned_cols=25 Identities=36% Similarity=0.630 Sum_probs=19.5
Q ss_pred cHHHHHHHcCCChhHHHHHHHHcCCC
Q 001809 614 SLKDAAKSIGVCPTTLKRICRQHGIS 639 (1010)
Q Consensus 614 pl~eAAk~LGV~~TtLKRiCR~~GI~ 639 (1010)
++.|+|+.+||++.||...=++ |+-
T Consensus 1 ti~e~A~~~gvs~~tlR~ye~~-Gll 25 (38)
T PF00376_consen 1 TIGEVAKLLGVSPRTLRYYERE-GLL 25 (38)
T ss_dssp EHHHHHHHHTS-HHHHHHHHHT-TSS
T ss_pred CHHHHHHHHCCCHHHHHHHHHC-CCC
Confidence 4789999999999999876665 653
No 396
>cd01111 HTH_MerD Helix-Turn-Helix DNA binding domain of the MerD transcription regulator. Helix-turn-helix (HTH) transcription regulator MerD. The putative secondary regulator of mercury resistance (mer) operons, MerD, has been shown to down-regulate the expression of this operon in gram-negative bacteria. It binds to the same operator DNA as MerR that activates transcription of the operon in the presence of mercury ions. The MerD protein shares the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily, which promote transcription 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 conserved and contain predicted winged HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules such as metal ions, drugs,
Probab=23.99 E-value=82 Score=30.53 Aligned_cols=27 Identities=19% Similarity=0.217 Sum_probs=22.7
Q ss_pred CcHHHHHHHcCCChhHHHHHHHHcCCCC
Q 001809 613 GSLKDAAKSIGVCPTTLKRICRQHGISR 640 (1010)
Q Consensus 613 ~pl~eAAk~LGV~~TtLKRiCR~~GI~R 640 (1010)
+++.|+|+.+||++.||....++ |+-+
T Consensus 1 y~Ige~A~~~gvs~~tlR~ye~~-GLl~ 27 (107)
T cd01111 1 YSISQLALDAGVSVHIVRDYLLR-GLLH 27 (107)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHC-CCCC
Confidence 57899999999999999887776 7543
No 397
>PRK11922 RNA polymerase sigma factor; Provisional
Probab=23.89 E-value=58 Score=34.84 Aligned_cols=28 Identities=25% Similarity=0.271 Sum_probs=23.6
Q ss_pred HHHhhcCCcHHHHHHHcCCChhHHHHHH
Q 001809 606 VLQQYFSGSLKDAAKSIGVCPTTLKRIC 633 (1010)
Q Consensus 606 ~L~~yF~~pl~eAAk~LGV~~TtLKRiC 633 (1010)
.++-+.+++.+|+|+.|||+..|+|.+-
T Consensus 159 ~l~~~~g~s~~EIAe~lgis~~tVk~~l 186 (231)
T PRK11922 159 VLRVVEELSVEETAQALGLPEETVKTRL 186 (231)
T ss_pred eeehhcCCCHHHHHHHHCcCHHHHHHHH
Confidence 3445678999999999999999998764
No 398
>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=23.82 E-value=88 Score=29.36 Aligned_cols=31 Identities=16% Similarity=0.294 Sum_probs=25.6
Q ss_pred HHHHHhhcCCcHHHHHHHcCCChhHHHHHHHH
Q 001809 604 LSVLQQYFSGSLKDAAKSIGVCPTTLKRICRQ 635 (1010)
Q Consensus 604 l~~L~~yF~~pl~eAAk~LGV~~TtLKRiCR~ 635 (1010)
++-|+. =..++++.|+.+|||.+|+-|.-..
T Consensus 12 ~e~l~~-~~~ti~dvA~~~gvS~~TVsr~L~~ 42 (80)
T TIGR02844 12 GKYIVE-TKATVRETAKVFGVSKSTVHKDVTE 42 (80)
T ss_pred HHHHHH-CCCCHHHHHHHhCCCHHHHHHHhcC
Confidence 455666 6789999999999999999996644
No 399
>PRK09508 leuO leucine transcriptional activator; Reviewed
Probab=23.49 E-value=86 Score=34.46 Aligned_cols=38 Identities=18% Similarity=0.334 Sum_probs=29.1
Q ss_pred cccCHHHHHhhc-----CCcHHHHHHHcCCChhHHHHHHH----HcCC
Q 001809 600 KNVSLSVLQQYF-----SGSLKDAAKSIGVCPTTLKRICR----QHGI 638 (1010)
Q Consensus 600 ~~itl~~L~~yF-----~~pl~eAAk~LGV~~TtLKRiCR----~~GI 638 (1010)
..+++..|+ || +.++..||+.|||+.+++-|.-+ ++|+
T Consensus 20 ~~~~l~~L~-~f~avae~gs~s~AA~~L~isQpavS~~I~~LE~~lg~ 66 (314)
T PRK09508 20 RMVDLNLLT-VFDAVMQEQNITRAAHNLGMSQPAVSNAVARLKVMFND 66 (314)
T ss_pred cccChHHHH-HHHHHHhcCCHHHHHHHhCCCHHHHHHHHHHHHHhhCC
Confidence 347788874 55 78999999999999988766555 4564
No 400
>PHA02591 hypothetical protein; Provisional
Probab=23.41 E-value=78 Score=29.99 Aligned_cols=24 Identities=17% Similarity=0.209 Sum_probs=21.5
Q ss_pred cCCcHHHHHHHcCCChhHHHHHHH
Q 001809 611 FSGSLKDAAKSIGVCPTTLKRICR 634 (1010)
Q Consensus 611 F~~pl~eAAk~LGV~~TtLKRiCR 634 (1010)
-++++.++|+.|||+..++++.-+
T Consensus 58 qGlSqeqIA~~LGVsqetVrKYL~ 81 (83)
T PHA02591 58 KGFTVEKIASLLGVSVRKVRRYLE 81 (83)
T ss_pred cCCCHHHHHHHhCCCHHHHHHHHh
Confidence 488999999999999999998765
No 401
>cd04785 HTH_CadR-PbrR-like Helix-Turn-Helix DNA binding domain of the CadR- and PbrR-like transcription regulators. Helix-turn-helix (HTH) CadR- and PbrR-like transcription regulators. CadR and PbrR regulate expression of the cadmium and lead resistance operons, respectively. These proteins are comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the C-terminal domains have three conserved cysteines which comprise a putative metal binding site. Some members in this group have a histidine-rich C-terminal extension. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements.
Probab=23.36 E-value=1.2e+02 Score=29.92 Aligned_cols=23 Identities=22% Similarity=0.176 Sum_probs=19.6
Q ss_pred CcHHHHHHHcCCChhHHHHHHHH
Q 001809 613 GSLKDAAKSIGVCPTTLKRICRQ 635 (1010)
Q Consensus 613 ~pl~eAAk~LGV~~TtLKRiCR~ 635 (1010)
+++.|+|+.+||++.||.-.-++
T Consensus 1 ~~I~e~a~~~gvs~~tlR~Ye~~ 23 (126)
T cd04785 1 LSIGELARRTGVNVETIRYYESI 23 (126)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHC
Confidence 57899999999999999866553
No 402
>CHL00180 rbcR LysR transcriptional regulator; Provisional
Probab=23.31 E-value=85 Score=34.30 Aligned_cols=35 Identities=23% Similarity=0.324 Sum_probs=27.0
Q ss_pred cccCHHHHHhhc-----CCcHHHHHHHcCCChhHHHHHHHH
Q 001809 600 KNVSLSVLQQYF-----SGSLKDAAKSIGVCPTTLKRICRQ 635 (1010)
Q Consensus 600 ~~itl~~L~~yF-----~~pl~eAAk~LGV~~TtLKRiCR~ 635 (1010)
..|++..| +|| ++++..||++|||+..++-|.-++
T Consensus 3 ~~~~l~~L-~~f~~v~e~gs~s~AA~~L~isqpavS~~i~~ 42 (305)
T CHL00180 3 LPFTLDQL-RILKAIATEGSFKKAAESLYISQPAVSLQIKN 42 (305)
T ss_pred CcccHHHH-HHHHHHHHcCCHHHHHHHhcCCChHHHHHHHH
Confidence 34556665 455 789999999999999988777664
No 403
>PRK10014 DNA-binding transcriptional repressor MalI; Provisional
Probab=23.26 E-value=59 Score=35.69 Aligned_cols=23 Identities=22% Similarity=0.265 Sum_probs=20.6
Q ss_pred CcHHHHHHHcCCChhHHHHHHHH
Q 001809 613 GSLKDAAKSIGVCPTTLKRICRQ 635 (1010)
Q Consensus 613 ~pl~eAAk~LGV~~TtLKRiCR~ 635 (1010)
.+++|+|+..|||++|+.|.-..
T Consensus 7 ~Ti~dIA~~agVS~~TVSr~Ln~ 29 (342)
T PRK10014 7 ITIHDVALAAGVSVSTVSLVLSG 29 (342)
T ss_pred CcHHHHHHHhCCCHHHHHHHHCC
Confidence 57999999999999999999764
No 404
>COG2197 CitB Response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain [Signal transduction mechanisms / Transcription]
Probab=23.25 E-value=82 Score=33.62 Aligned_cols=30 Identities=27% Similarity=0.327 Sum_probs=25.8
Q ss_pred cCCcHHHHHHHcCCChhHHH----HHHHHcCCCC
Q 001809 611 FSGSLKDAAKSIGVCPTTLK----RICRQHGISR 640 (1010)
Q Consensus 611 F~~pl~eAAk~LGV~~TtLK----RiCR~~GI~R 640 (1010)
-+++-+|+|++|++|..|+| +|-|++|++.
T Consensus 162 ~G~snkeIA~~L~iS~~TVk~h~~~i~~KL~v~~ 195 (211)
T COG2197 162 EGLSNKEIAEELNLSEKTVKTHVSNILRKLGVRN 195 (211)
T ss_pred CCCCHHHHHHHHCCCHhHHHHHHHHHHHHcCCCC
Confidence 38899999999999999987 5777888855
No 405
>PRK12526 RNA polymerase sigma factor; Provisional
Probab=23.25 E-value=90 Score=32.73 Aligned_cols=24 Identities=21% Similarity=0.102 Sum_probs=20.7
Q ss_pred hhcCCcHHHHHHHcCCChhHHHHH
Q 001809 609 QYFSGSLKDAAKSIGVCPTTLKRI 632 (1010)
Q Consensus 609 ~yF~~pl~eAAk~LGV~~TtLKRi 632 (1010)
-+-+++.+|+|+.|||+..|+|.+
T Consensus 166 ~~~g~s~~EIA~~lgis~~tV~~~ 189 (206)
T PRK12526 166 YFQELSQEQLAQQLNVPLGTVKSR 189 (206)
T ss_pred HHcCCCHHHHHHHHCCCHHHHHHH
Confidence 334999999999999999999754
No 406
>PF12833 HTH_18: Helix-turn-helix domain; PDB: 2K9S_A 3LSG_C 3OIO_A 1D5Y_B 3GBG_A 3OOU_A 1BL0_A 1XS9_A 3MN2_B 3MKL_B ....
Probab=23.01 E-value=83 Score=27.80 Aligned_cols=22 Identities=32% Similarity=0.570 Sum_probs=18.3
Q ss_pred HHHHcCCChhHHHHHHHH-cCCC
Q 001809 618 AAKSIGVCPTTLKRICRQ-HGIS 639 (1010)
Q Consensus 618 AAk~LGV~~TtLKRiCR~-~GI~ 639 (1010)
.|+.|||++..|.|+|++ .|+.
T Consensus 1 lA~~~~~s~~~l~~~f~~~~g~s 23 (81)
T PF12833_consen 1 LADELGMSERYLSRIFKKETGMS 23 (81)
T ss_dssp HHHHCTS-HHHHHHHHHHHHSS-
T ss_pred ChHHhCcCHHHHHHHHHHHHCcC
Confidence 489999999999999999 6873
No 407
>COG3604 FhlA Transcriptional regulator containing GAF, AAA-type ATPase, and DNA binding domains [Transcription / Signal transduction mechanisms]
Probab=22.97 E-value=76 Score=38.95 Aligned_cols=75 Identities=11% Similarity=0.197 Sum_probs=46.7
Q ss_pred CCCCcccccCCCCccc-ccccccCcccccchhhHHhcCCceEEEEeeecCCCCceEEEEEEeeeccc---CCchHHHHHH
Q 001809 235 LGLPGRVFSSKVPEWT-SNVAYYNEAEYARVTHAVNHAVRSCIALPVFQFPEISCSAVLEIVSVKEK---PNFDAEIENI 310 (1010)
Q Consensus 235 ~GLPGRVF~s~~PEWT-pnV~~y~~~EYpR~~~A~~~~VrGsLAlPVf~~~s~~ClAVlElV~t~ek---~~f~~E~e~v 310 (1010)
.++-++||..+.|--. +.=.-|....-..+..-....++.+|++|++-.+.. +|+|-+-.+..+ ..++.++..+
T Consensus 103 ~~~l~~i~~~~~p~~~~~~d~~~~~~~~~l~~~~~~~~~~a~i~~PL~~~~~~--~G~Ltld~~~~~~f~~~~~~~lr~L 180 (550)
T COG3604 103 HPLLEQILKAGRPLVFHPADSLFPDPYDGLLPDTEGNKKHACIGVPLKSGDKL--IGALTLDHTEPDQFDEDLDEELRFL 180 (550)
T ss_pred chHHHHHHhCCCcEEEecCCcccCCcccccccCccCCcceeEEeeeeeeCCee--eeeEEeeeecccccchhHHHHHHHH
Confidence 4677788888887666 222222222222333223346999999999987644 788888777663 4566666666
Q ss_pred H
Q 001809 311 C 311 (1010)
Q Consensus 311 c 311 (1010)
+
T Consensus 181 a 181 (550)
T COG3604 181 A 181 (550)
T ss_pred H
Confidence 5
No 408
>PRK12512 RNA polymerase sigma factor; Provisional
Probab=22.97 E-value=95 Score=31.52 Aligned_cols=28 Identities=11% Similarity=0.126 Sum_probs=23.2
Q ss_pred HHhhcCCcHHHHHHHcCCChhHHHHHHH
Q 001809 607 LQQYFSGSLKDAAKSIGVCPTTLKRICR 634 (1010)
Q Consensus 607 L~~yF~~pl~eAAk~LGV~~TtLKRiCR 634 (1010)
|.-+-+++.+|+|+.||++..|+|....
T Consensus 142 l~~~~g~s~~eIA~~l~is~~tV~~~l~ 169 (184)
T PRK12512 142 SISVEGASIKETAAKLSMSEGAVRVALH 169 (184)
T ss_pred HHHHcCCCHHHHHHHhCCCHHHHHHHHH
Confidence 3344599999999999999999997654
No 409
>cd04787 HTH_HMRTR_unk Helix-Turn-Helix DNA binding domain of putative Heavy Metal Resistance transcription regulators. Putative helix-turn-helix (HTH) heavy metal resistance transcription regulators (HMRTR), unknown subgroup. Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to heavy metal stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules, such as, metal ions, drugs, and organic substrates. This subgroup lacks one of the c
Probab=22.88 E-value=88 Score=31.15 Aligned_cols=30 Identities=37% Similarity=0.646 Sum_probs=23.7
Q ss_pred CcHHHHHHHcCCChhHHHHHHHHcCCCCCcch
Q 001809 613 GSLKDAAKSIGVCPTTLKRICRQHGISRWPSR 644 (1010)
Q Consensus 613 ~pl~eAAk~LGV~~TtLKRiCR~~GI~RWP~R 644 (1010)
|.+.|+|+.+||++.|| |.--+.|+-. |.|
T Consensus 1 m~IgE~A~~~gvs~~TL-RyYE~~GLl~-p~r 30 (133)
T cd04787 1 MKVKELANAAGVTPDTV-RFYTRIGLLR-PTR 30 (133)
T ss_pred CCHHHHHHHHCcCHHHH-HHHHHCCCCC-CCc
Confidence 57899999999999999 5556778744 543
No 410
>PRK05572 sporulation sigma factor SigF; Validated
Probab=22.78 E-value=92 Score=33.83 Aligned_cols=23 Identities=17% Similarity=0.423 Sum_probs=20.4
Q ss_pred CCcHHHHHHHcCCChhHHHHHHH
Q 001809 612 SGSLKDAAKSIGVCPTTLKRICR 634 (1010)
Q Consensus 612 ~~pl~eAAk~LGV~~TtLKRiCR 634 (1010)
+++++|+|+.|||++.+++++=+
T Consensus 218 ~~s~~eIA~~lgis~~~V~~~~~ 240 (252)
T PRK05572 218 DKTQSEVAKRLGISQVQVSRLEK 240 (252)
T ss_pred CCCHHHHHHHHCcCHHHHHHHHH
Confidence 78999999999999999987643
No 411
>PRK09644 RNA polymerase sigma factor SigM; Provisional
Probab=22.53 E-value=93 Score=31.06 Aligned_cols=27 Identities=19% Similarity=0.145 Sum_probs=22.6
Q ss_pred HHHhhcCCcHHHHHHHcCCChhHHHHH
Q 001809 606 VLQQYFSGSLKDAAKSIGVCPTTLKRI 632 (1010)
Q Consensus 606 ~L~~yF~~pl~eAAk~LGV~~TtLKRi 632 (1010)
.|.-+.+++.+|+|+.||++..|+|.+
T Consensus 118 ~l~~~~g~s~~eIA~~lgis~~tv~~~ 144 (165)
T PRK09644 118 LLCDVHELTYEEAASVLDLKLNTYKSH 144 (165)
T ss_pred HhHHHhcCCHHHHHHHHCCCHHHHHHH
Confidence 344567999999999999999999754
No 412
>PHA03043 hypothetical protein; Provisional
Probab=22.52 E-value=27 Score=35.53 Aligned_cols=60 Identities=20% Similarity=0.194 Sum_probs=41.7
Q ss_pred CcCCC---CCCcCcC-hhhhccccccccccCCCchhhhh----hcccCCCccccCCCCCCCCCCcccc
Q 001809 32 TRSSN---SGDLFNN-FSDLLNFDAYAGWCNSPSVTDQM----FASYGFSSFQSTPCASFDTSNVMAS 91 (1010)
Q Consensus 32 ~~n~~---~~d~f~~-~selmnfd~ya~~cn~ps~~dq~----~~~~~~~~~~s~~~~~~~~~~~~~~ 91 (1010)
||+.+ .+++.+- |-|||.||.+|.|==+-.-.|.+ ++..+-|-+|-++.+..+++|..|-
T Consensus 19 wRG~~~~~l~~~~g~~Fkel~kfD~~Ak~kfg~~~~~~~K~m~L~~dDGp~l~k~~~~~~~~~~~~E~ 86 (130)
T PHA03043 19 WRGNSDICEEHPLNIFFEKLMKFDSFAKKKIGESDYDFIKSMKLSLDDGPRLDKLPTNLLDGLNAEEI 86 (130)
T ss_pred hhcCCcccccchHHHHHHHHHHHHHHHHHhcCchhHHHHHhhcCccccCccccccccccccccCHHHH
Confidence 44444 3444443 89999999999988777777766 5555667777777766677766553
No 413
>cd04772 HTH_TioE_rpt1 First Helix-Turn-Helix DNA binding domain of the regulatory protein TioE. Putative helix-turn-helix (HTH) regulatory protein, TioE, and related proteins. TioE is part of the thiocoraline gene cluster, which is involved in the biosynthesis of the antitumor thiocoraline from the marine actinomycete, Micromonospora. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements. Proteins in this family are unique within the MerR superfamily in that they are composed of just two adjacent MerR-like N-terminal domains; this CD contains the N-terminal or first repeat (rpt1) of these tandem MerR-like domain proteins.
Probab=22.49 E-value=99 Score=29.40 Aligned_cols=25 Identities=28% Similarity=0.448 Sum_probs=21.4
Q ss_pred CcHHHHHHHcCCChhHHHHHHHHcCC
Q 001809 613 GSLKDAAKSIGVCPTTLKRICRQHGI 638 (1010)
Q Consensus 613 ~pl~eAAk~LGV~~TtLKRiCR~~GI 638 (1010)
+++.|+|+.+||++.||+...+ -|+
T Consensus 1 y~i~e~A~~~gvs~~tlR~Ye~-~Gl 25 (99)
T cd04772 1 YRTVDLARAIGLSPQTVRNYES-LGL 25 (99)
T ss_pred CCHHHHHHHHCcCHHHHHHHHH-cCC
Confidence 3789999999999999998877 454
No 414
>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=22.47 E-value=1.1e+02 Score=29.83 Aligned_cols=25 Identities=32% Similarity=0.489 Sum_probs=22.2
Q ss_pred CCcHHHHHHHcCCChhHHHHHHHHc
Q 001809 612 SGSLKDAAKSIGVCPTTLKRICRQH 636 (1010)
Q Consensus 612 ~~pl~eAAk~LGV~~TtLKRiCR~~ 636 (1010)
+.++.+||+.++||..|+.|..++.
T Consensus 18 g~s~~eaa~~F~VS~~Tv~~W~k~~ 42 (119)
T PF01710_consen 18 GKSIREAAKRFGVSRNTVYRWLKRK 42 (119)
T ss_pred cchHHHHHHHhCcHHHHHHHHHHhc
Confidence 5689999999999999999998743
No 415
>PRK13719 conjugal transfer transcriptional regulator TraJ; Provisional
Probab=22.34 E-value=90 Score=34.37 Aligned_cols=28 Identities=25% Similarity=0.250 Sum_probs=24.6
Q ss_pred cCCcHHHHHHHcCCChhHHH----HHHHHcCC
Q 001809 611 FSGSLKDAAKSIGVCPTTLK----RICRQHGI 638 (1010)
Q Consensus 611 F~~pl~eAAk~LGV~~TtLK----RiCR~~GI 638 (1010)
-+++.+|+|++|+|++.|+| +|.+++|+
T Consensus 157 ~G~SnkEIA~~L~IS~~TVk~hvs~I~~KLgv 188 (217)
T PRK13719 157 FGFSHEYIAQLLNITVGSSKNKISEILKFFGI 188 (217)
T ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHHHHHhCC
Confidence 38999999999999998865 68888998
No 416
>smart00530 HTH_XRE Helix-turn-helix XRE-family like proteins.
Probab=22.29 E-value=1.2e+02 Score=22.91 Aligned_cols=40 Identities=20% Similarity=0.229 Sum_probs=31.7
Q ss_pred cccCHHHHHhhcCCcHHHHHHHc----CCChhHHHHHHHHcCCC
Q 001809 600 KNVSLSVLQQYFSGSLKDAAKSI----GVCPTTLKRICRQHGIS 639 (1010)
Q Consensus 600 ~~itl~~L~~yF~~pl~eAAk~L----GV~~TtLKRiCR~~GI~ 639 (1010)
..++..+|....+++...+.+-+ .+...++.++|+.+|+.
T Consensus 9 ~~~s~~~la~~~~i~~~~i~~~~~~~~~~~~~~~~~i~~~~~~~ 52 (56)
T smart00530 9 KGLTQEELAEKLGVSRSTLSRIENGKRKPSLETLKKLAKALGVS 52 (56)
T ss_pred cCCCHHHHHHHhCCCHHHHHHHHCCCCCCCHHHHHHHHHHhCCC
Confidence 56788889988888887776633 34788999999999983
No 417
>PRK08215 sporulation sigma factor SigG; Reviewed
Probab=22.03 E-value=97 Score=33.78 Aligned_cols=24 Identities=17% Similarity=0.383 Sum_probs=21.2
Q ss_pred CCcHHHHHHHcCCChhHHHHHHHH
Q 001809 612 SGSLKDAAKSIGVCPTTLKRICRQ 635 (1010)
Q Consensus 612 ~~pl~eAAk~LGV~~TtLKRiCR~ 635 (1010)
+++++|+|+.|||+..+++++=++
T Consensus 225 ~~t~~eIA~~lgis~~~V~~~~~~ 248 (258)
T PRK08215 225 GKTQMEVAEEIGISQAQVSRLEKA 248 (258)
T ss_pred CCCHHHHHHHHCcCHHHHHHHHHH
Confidence 789999999999999999887543
No 418
>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=21.94 E-value=72 Score=28.98 Aligned_cols=24 Identities=21% Similarity=0.236 Sum_probs=18.8
Q ss_pred CCcHHHHHHHcCCChhHHHHHHHH
Q 001809 612 SGSLKDAAKSIGVCPTTLKRICRQ 635 (1010)
Q Consensus 612 ~~pl~eAAk~LGV~~TtLKRiCR~ 635 (1010)
..++.+.|..++||.+|++|..++
T Consensus 30 ~~s~~~la~~~~iS~sti~~~i~~ 53 (87)
T PF05043_consen 30 YVSIEDLAEELFISRSTIYRDIKK 53 (87)
T ss_dssp EEEHHHHHHHHT--HHHHHHHHHH
T ss_pred CcCHHHHHHHHCCCHHHHHHHHHH
Confidence 678999999999999999886554
No 419
>COG4565 CitB Response regulator of citrate/malate metabolism [Transcription / Signal transduction mechanisms]
Probab=21.89 E-value=83 Score=34.76 Aligned_cols=39 Identities=13% Similarity=0.279 Sum_probs=31.8
Q ss_pred cccccccCHHHHHhhcC-----CcHHHHHHHcCCChhHHHHHHH
Q 001809 596 STAEKNVSLSVLQQYFS-----GSLKDAAKSIGVCPTTLKRICR 634 (1010)
Q Consensus 596 ~~~~~~itl~~L~~yF~-----~pl~eAAk~LGV~~TtLKRiCR 634 (1010)
.|.-...||..+.+.|. ++..|+|+.+|+|.||..|.--
T Consensus 152 PkGi~~~Tl~~i~~~~~~~~~~~Taeela~~~giSRvTaRRYLe 195 (224)
T COG4565 152 PKGLDELTLQKVREALKEPDQELTAEELAQALGISRVTARRYLE 195 (224)
T ss_pred CCCcCHHHHHHHHHHHhCcCCccCHHHHHHHhCccHHHHHHHHH
Confidence 35667788888888776 6789999999999999887643
No 420
>PF08965 DUF1870: Domain of unknown function (DUF1870); InterPro: IPR015060 This family consist of hypothetical bacterial proteins. ; PDB: 1S4K_A.
Probab=21.88 E-value=2e+02 Score=29.18 Aligned_cols=58 Identities=21% Similarity=0.275 Sum_probs=36.2
Q ss_pred ccCHHHHHhhcCCcHHHHHHHcC--CChhHHHHHHHHcCCCCCcchhhhhhHHHHHHHHHHH
Q 001809 601 NVSLSVLQQYFSGSLKDAAKSIG--VCPTTLKRICRQHGISRWPSRKINKVNRSLKKIQTVL 660 (1010)
Q Consensus 601 ~itl~~L~~yF~~pl~eAAk~LG--V~~TtLKRiCR~~GI~RWP~Rki~sl~~~i~~l~~~i 660 (1010)
.+.|..||+.|.|++.|||..++ |+..|-.+- +.|=.-=|..=+..+....++-+++|
T Consensus 3 ~~ELqalR~~l~lt~~EaA~~Ia~~v~~~tWq~W--E~G~~~IP~~Vie~l~~m~~~R~~~i 62 (118)
T PF08965_consen 3 NLELQALRQILGLTVEEAAYYIAQDVSSRTWQQW--EKGERPIPDDVIEELLEMKSQRKQRI 62 (118)
T ss_dssp HHHHHHHHHHTT--HHHHHHHTSSS--HHHHHHH--HTTSS---HHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHcCCHHHHHHHHHccCCHHHHHHH--HcCCCCCCHHHHHHHHHHHHHHHHHH
Confidence 45688999999999999999999 988887765 55655557766655554444333333
No 421
>cd04779 HTH_MerR-like_sg4 Helix-Turn-Helix DNA binding domain of putative transcription regulators from the MerR superfamily. Putative helix-turn-helix (HTH) MerR-like transcription regulators (subgroup 4). Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.
Probab=21.84 E-value=83 Score=31.87 Aligned_cols=31 Identities=23% Similarity=0.300 Sum_probs=25.1
Q ss_pred CcHHHHHHHcCCChhHHHHHHHHcCCCCCcchh
Q 001809 613 GSLKDAAKSIGVCPTTLKRICRQHGISRWPSRK 645 (1010)
Q Consensus 613 ~pl~eAAk~LGV~~TtLKRiCR~~GI~RWP~Rk 645 (1010)
+.+.|+|+.+||++.||...-+. |+-. |.|.
T Consensus 1 y~I~e~a~~~gvs~~TLR~Ye~~-GLl~-p~r~ 31 (134)
T cd04779 1 YRIGQLAHLAGVSKRTIDYYTNL-GLLT-PERS 31 (134)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHC-CCCC-CccC
Confidence 46899999999999999998754 7655 7663
No 422
>PRK10727 DNA-binding transcriptional regulator GalR; Provisional
Probab=21.76 E-value=62 Score=35.77 Aligned_cols=23 Identities=30% Similarity=0.512 Sum_probs=20.8
Q ss_pred cHHHHHHHcCCChhHHHHHHHHc
Q 001809 614 SLKDAAKSIGVCPTTLKRICRQH 636 (1010)
Q Consensus 614 pl~eAAk~LGV~~TtLKRiCR~~ 636 (1010)
+++|+||..|||.+|+-|.-...
T Consensus 3 ti~dIA~~aGVS~~TVSrvLn~~ 25 (343)
T PRK10727 3 TIKDVARLAGVSVATVSRVINNS 25 (343)
T ss_pred CHHHHHHHhCCCHHHHHHHhCCC
Confidence 79999999999999999998654
No 423
>PRK06811 RNA polymerase factor sigma-70; Validated
Probab=21.75 E-value=1e+02 Score=31.71 Aligned_cols=27 Identities=11% Similarity=0.304 Sum_probs=22.4
Q ss_pred HhhcCCcHHHHHHHcCCChhHHHHHHH
Q 001809 608 QQYFSGSLKDAAKSIGVCPTTLKRICR 634 (1010)
Q Consensus 608 ~~yF~~pl~eAAk~LGV~~TtLKRiCR 634 (1010)
.-+-+++.+|+|+.||++..++|..-.
T Consensus 143 ~~~~g~s~~EIAe~lgis~~~V~~~l~ 169 (189)
T PRK06811 143 RYLLGEKIEEIAKKLGLTRSAIDNRLS 169 (189)
T ss_pred HHHccCCHHHHHHHHCCCHHHHHHHHH
Confidence 344599999999999999999987533
No 424
>TIGR02950 SigM_subfam RNA polymerase sigma factor, SigM family. This family of RNA polymerase sigma factors is a member of the Sigma-70 subfamily (TIGR02937) and is restricted to certain lineages of the order Bacillales. This family encompasses at least two distinct sigma factors as two proteins are found in each of B. anthracis, B. subtilis subsp. subtilis str. 168, and B. lichiniformis (although these are not apparently the same two in each). One of these is designated as SigM in B. subtilis (Swiss_Prot: SIGM_BACSU) and is activated by various stressors.
Probab=21.73 E-value=83 Score=30.67 Aligned_cols=26 Identities=15% Similarity=0.106 Sum_probs=21.8
Q ss_pred hhcCCcHHHHHHHcCCChhHHHHHHH
Q 001809 609 QYFSGSLKDAAKSIGVCPTTLKRICR 634 (1010)
Q Consensus 609 ~yF~~pl~eAAk~LGV~~TtLKRiCR 634 (1010)
-+-+++.+|+|+.|||++.|+|..-.
T Consensus 118 ~~~g~s~~eIA~~lgis~~tv~~~l~ 143 (154)
T TIGR02950 118 EFKEFSYKEIAELLNLSLAKVKSNLF 143 (154)
T ss_pred hhccCcHHHHHHHHCCCHHHHHHHHH
Confidence 34588999999999999999987543
No 425
>PRK10430 DNA-binding transcriptional activator DcuR; Provisional
Probab=21.73 E-value=1.1e+02 Score=32.45 Aligned_cols=26 Identities=8% Similarity=0.121 Sum_probs=23.4
Q ss_pred cCCcHHHHHHHcCCChhHHHHHHHHc
Q 001809 611 FSGSLKDAAKSIGVCPTTLKRICRQH 636 (1010)
Q Consensus 611 F~~pl~eAAk~LGV~~TtLKRiCR~~ 636 (1010)
-+++.+++|+.||++..|+|+.-+.+
T Consensus 177 ~g~s~~eIA~~l~iS~~Tv~~~~~~~ 202 (239)
T PRK10430 177 YEFSTDELANAVNISRVSCRKYLIWL 202 (239)
T ss_pred CCcCHHHHHHHhCchHHHHHHHHHHH
Confidence 46899999999999999999988855
No 426
>PF05344 DUF746: Domain of Unknown Function (DUF746); InterPro: IPR008008 This is a short conserved region found in some transposons.
Probab=21.68 E-value=88 Score=28.60 Aligned_cols=25 Identities=32% Similarity=0.421 Sum_probs=21.6
Q ss_pred CCcHHHHHHHcCCChhHHHHHHHHc
Q 001809 612 SGSLKDAAKSIGVCPTTLKRICRQH 636 (1010)
Q Consensus 612 ~~pl~eAAk~LGV~~TtLKRiCR~~ 636 (1010)
.+++.+||+.||+...++.+.-|.+
T Consensus 13 ~~s~~~Aa~~lG~~~~~v~~wv~~f 37 (65)
T PF05344_consen 13 QISVAQAADRLGTDPGTVRRWVRMF 37 (65)
T ss_pred cccHHHHHHHHCcCHHHHHHHHHHH
Confidence 4678999999999999998887764
No 427
>PRK06424 transcription factor; Provisional
Probab=21.67 E-value=1e+02 Score=31.82 Aligned_cols=32 Identities=22% Similarity=0.070 Sum_probs=26.9
Q ss_pred HHHHhhcCCcHHHHHHHcCCChhHHHHHHHHc
Q 001809 605 SVLQQYFSGSLKDAAKSIGVCPTTLKRICRQH 636 (1010)
Q Consensus 605 ~~L~~yF~~pl~eAAk~LGV~~TtLKRiCR~~ 636 (1010)
..+|.--++++.+.|+.+||+.+++.++-+-.
T Consensus 90 r~lRe~~GLSQ~eLA~~iGvs~stIskiE~G~ 121 (144)
T PRK06424 90 KNARERLSMSQADLAAKIFERKNVIASIERGD 121 (144)
T ss_pred HHHHHHcCCCHHHHHHHhCCCHHHHHHHHCCC
Confidence 35667779999999999999999999987643
No 428
>PRK10423 transcriptional repressor RbsR; Provisional
Probab=21.60 E-value=51 Score=35.85 Aligned_cols=22 Identities=27% Similarity=0.514 Sum_probs=19.4
Q ss_pred HHHHHHHcCCChhHHHHHHHHc
Q 001809 615 LKDAAKSIGVCPTTLKRICRQH 636 (1010)
Q Consensus 615 l~eAAk~LGV~~TtLKRiCR~~ 636 (1010)
++|+|+.+|||.+|+.|.-...
T Consensus 1 i~dIA~~agVS~~TVSrvLn~~ 22 (327)
T PRK10423 1 MKDVARLAGVSTSTVSHVINKD 22 (327)
T ss_pred ChhHHHHhCCcHHHHHHHhCCC
Confidence 5799999999999999999643
No 429
>PRK10401 DNA-binding transcriptional regulator GalS; Provisional
Probab=21.42 E-value=67 Score=35.53 Aligned_cols=24 Identities=25% Similarity=0.448 Sum_probs=20.9
Q ss_pred CcHHHHHHHcCCChhHHHHHHHHc
Q 001809 613 GSLKDAAKSIGVCPTTLKRICRQH 636 (1010)
Q Consensus 613 ~pl~eAAk~LGV~~TtLKRiCR~~ 636 (1010)
.+++|+|+.+|||.+|+-|.-+..
T Consensus 2 ~ti~dIA~~aGVS~~TVSrvLn~~ 25 (346)
T PRK10401 2 ITIRDVARQAGVSVATVSRVLNNS 25 (346)
T ss_pred CCHHHHHHHhCCCHHHHHHHHCCC
Confidence 479999999999999999988643
No 430
>PRK12517 RNA polymerase sigma factor; Provisional
Probab=21.38 E-value=1e+02 Score=31.86 Aligned_cols=28 Identities=18% Similarity=-0.050 Sum_probs=23.4
Q ss_pred HHhhcCCcHHHHHHHcCCChhHHHHHHH
Q 001809 607 LQQYFSGSLKDAAKSIGVCPTTLKRICR 634 (1010)
Q Consensus 607 L~~yF~~pl~eAAk~LGV~~TtLKRiCR 634 (1010)
|+-+-+++.+|+|+.|||+..|++.+..
T Consensus 139 l~~~~g~s~~EIA~~lgis~~tV~~~l~ 166 (188)
T PRK12517 139 LQVIGGFSGEEIAEILDLNKNTVMTRLF 166 (188)
T ss_pred HHHHhCCCHHHHHHHHCCCHHHHHHHHH
Confidence 4445589999999999999999998754
No 431
>PRK11074 putative DNA-binding transcriptional regulator; Provisional
Probab=21.37 E-value=98 Score=33.75 Aligned_cols=32 Identities=25% Similarity=0.319 Sum_probs=24.2
Q ss_pred cCHHHHHhhc-----CCcHHHHHHHcCCChhHHHHHHH
Q 001809 602 VSLSVLQQYF-----SGSLKDAAKSIGVCPTTLKRICR 634 (1010)
Q Consensus 602 itl~~L~~yF-----~~pl~eAAk~LGV~~TtLKRiCR 634 (1010)
++++.| +|| +.++..||+.|||+.+++-|.-+
T Consensus 2 ~~~~~L-~~f~~v~e~~s~s~AA~~L~isQpavS~~I~ 38 (300)
T PRK11074 2 WSEYSL-EVVDAVARTGSFSAAAQELHRVPSAVSYTVR 38 (300)
T ss_pred CCHHHH-HHHHHHHHhCCHHHHHHHhCCCHHHHHHHHH
Confidence 445555 444 78999999999999998766554
No 432
>PRK09935 transcriptional regulator FimZ; Provisional
Probab=21.36 E-value=1.4e+02 Score=29.62 Aligned_cols=34 Identities=21% Similarity=0.272 Sum_probs=25.3
Q ss_pred HHHHhhc-CCcHHHHHHHcCCChhHHH----HHHHHcCC
Q 001809 605 SVLQQYF-SGSLKDAAKSIGVCPTTLK----RICRQHGI 638 (1010)
Q Consensus 605 ~~L~~yF-~~pl~eAAk~LGV~~TtLK----RiCR~~GI 638 (1010)
+.|+-+. +++-+|+|+.|+++..|+| |+.+++||
T Consensus 156 ~vl~~l~~g~s~~eIa~~l~~s~~tv~~~~~~~~~kl~~ 194 (210)
T PRK09935 156 TILRYLVSGLSNKEIADQLLLSNKTVSAHKSNIYGKLGL 194 (210)
T ss_pred HHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHHHHHcCC
Confidence 3455443 7999999999999998876 45556665
No 433
>PRK09834 DNA-binding transcriptional activator MhpR; Provisional
Probab=21.25 E-value=1.4e+02 Score=32.69 Aligned_cols=40 Identities=23% Similarity=0.244 Sum_probs=27.0
Q ss_pred eEEEEeeecCCCCceEEEEEEeeecccCCchHHHHHHHHHhh
Q 001809 274 SCIALPVFQFPEISCSAVLEIVSVKEKPNFDAEIENICNALQ 315 (1010)
Q Consensus 274 GsLAlPVf~~~s~~ClAVlElV~t~ek~~f~~E~e~vc~ALq 315 (1010)
.+||+|||++ +..+|.|=++.......-....+.+..+|.
T Consensus 206 ~~iA~PV~~~--g~~vaalsv~~p~~r~~~~~~~~~~~~~l~ 245 (263)
T PRK09834 206 ASIAVPVRSG--QRVLGCLNLVYIASAMSIEEAAKRYLPALQ 245 (263)
T ss_pred eEEEeeEecC--CceEEEEEeeehhhcCCHHHHHHHHHHHHH
Confidence 6799999996 456888888777665543333455655553
No 434
>PF05932 CesT: Tir chaperone protein (CesT) family; InterPro: IPR010261 This family consists of a number of bacterial sequences, which are highly similar to the Tir chaperone protein in Escherichia coli. In many Gram-negative bacteria, a key indicator of pathogenic potential is the possession of a specialised type III secretion system, which is utilised to deliver virulence effector proteins directly into the host cell cytosol. Many of the proteins secreted from such systems require small cytosolic chaperones to maintain the secreted substrates in a secretion-competent state. CesT serves a chaperone function for the enteropathogenic E. coli (EPEC) translocated intimin receptor (Tir) protein, which confers upon EPEC the ability to alter host cell morphology following intimate bacterial attachment [].; GO: 0009405 pathogenesis, 0050708 regulation of protein secretion, 0005737 cytoplasm; PDB: 1K3E_A 3KXY_E 1S28_C 1JYA_B 1K6Z_B 2BSH_A 2BSJ_B 2BHO_A 2BSI_B 3EPU_A ....
Probab=21.24 E-value=1.3e+02 Score=27.73 Aligned_cols=33 Identities=33% Similarity=0.767 Sum_probs=22.3
Q ss_pred HHHHHHHHHcCc------ccceeeeEe--------ecCCCCeEEEec
Q 001809 926 QLYEEVARRLKL------QNGTFQLKY--------LDDEEEWVMLVS 958 (1010)
Q Consensus 926 ~L~~EIakRf~l------~~~~f~lKY--------lDDd~EWVlLtc 958 (1010)
.|.+|+++++|| +++.+.|+. .+.+.+|+++.|
T Consensus 1 ~ll~~l~~~lgl~~l~~d~~g~~~l~~~~~~~~~~~~~~~~~l~l~~ 47 (119)
T PF05932_consen 1 QLLAELGERLGLPPLEFDEDGACSLTVDGDFLILEFDEDSDWLLLYA 47 (119)
T ss_dssp HHHHHHHHHHTCSCEESSTTSEEEEEETTTEEEEEEEESTTEEEEEE
T ss_pred CHHHHHHHHhCCCCCCCCCCCEEEEEECCeEEEEEEecCCCEEEEEE
Confidence 478999999998 234566666 444566666644
No 435
>cd04781 HTH_MerR-like_sg6 Helix-Turn-Helix DNA binding domain of putative transcription regulators from the MerR superfamily. Putative helix-turn-helix (HTH) MerR-like transcription regulators (subgroup 6) with at least two conserved cysteines present in the C-terminal portion of the protein. Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, an
Probab=21.14 E-value=92 Score=30.42 Aligned_cols=27 Identities=19% Similarity=0.304 Sum_probs=22.6
Q ss_pred CcHHHHHHHcCCChhHHHHHHHHcCCCC
Q 001809 613 GSLKDAAKSIGVCPTTLKRICRQHGISR 640 (1010)
Q Consensus 613 ~pl~eAAk~LGV~~TtLKRiCR~~GI~R 640 (1010)
|++.|+|+..||++.||.-..++ |+-+
T Consensus 1 m~IgevA~~~gvs~~tlRyYe~~-GLl~ 27 (120)
T cd04781 1 LDIAEVARQSGLPASTLRYYEEK-GLIA 27 (120)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHC-CCCC
Confidence 57899999999999999877775 7544
No 436
>smart00513 SAP Putative DNA-binding (bihelical) motif predicted to be involved in chromosomal organisation.
Probab=21.03 E-value=97 Score=24.20 Aligned_cols=20 Identities=20% Similarity=0.237 Sum_probs=16.7
Q ss_pred CChhHHHHHHHHcCCCCCcc
Q 001809 624 VCPTTLKRICRQHGISRWPS 643 (1010)
Q Consensus 624 V~~TtLKRiCR~~GI~RWP~ 643 (1010)
+....||.+||++|++.+--
T Consensus 4 l~~~~Lk~~l~~~gl~~~G~ 23 (35)
T smart00513 4 LKVSELKDELKKRGLSTSGT 23 (35)
T ss_pred CcHHHHHHHHHHcCCCCCCC
Confidence 56778999999999987664
No 437
>PRK05911 RNA polymerase sigma factor sigma-28; Reviewed
Probab=20.98 E-value=1e+02 Score=33.80 Aligned_cols=24 Identities=25% Similarity=0.375 Sum_probs=21.6
Q ss_pred CCcHHHHHHHcCCChhHHHHHHHH
Q 001809 612 SGSLKDAAKSIGVCPTTLKRICRQ 635 (1010)
Q Consensus 612 ~~pl~eAAk~LGV~~TtLKRiCR~ 635 (1010)
+++++|+|+.|||+..+++++-++
T Consensus 221 ~~t~~EIA~~lgis~~~V~~~~~r 244 (257)
T PRK05911 221 ELVLKEIGKILGVSESRVSQIHSK 244 (257)
T ss_pred CCCHHHHHHHHCcCHHHHHHHHHH
Confidence 889999999999999999987654
No 438
>PRK15121 right oriC-binding transcriptional activator; Provisional
Probab=20.96 E-value=1.1e+02 Score=33.90 Aligned_cols=42 Identities=17% Similarity=0.211 Sum_probs=31.4
Q ss_pred CCcHHHHHHHcCCChhHHHHHHHHc-CCCCCcchhhhhhHHHH
Q 001809 612 SGSLKDAAKSIGVCPTTLKRICRQH-GISRWPSRKINKVNRSL 653 (1010)
Q Consensus 612 ~~pl~eAAk~LGV~~TtLKRiCR~~-GI~RWP~Rki~sl~~~i 653 (1010)
.+++.+.|+.+|+|+.+|.|+.++. |+.-==|.+...|.+..
T Consensus 21 ~~~l~~lA~~~~~S~~~l~r~F~~~~g~s~~~yi~~~Rl~~A~ 63 (289)
T PRK15121 21 PLSLDNVAAKAGYSKWHLQRMFKDVTGHAIGAYIRARRLSKAA 63 (289)
T ss_pred CCCHHHHHHHHCcCHHHHHHHHHHHHCcCHHHHHHHHHHHHHH
Confidence 4789999999999999999999987 98533344444444433
No 439
>PRK08583 RNA polymerase sigma factor SigB; Validated
Probab=20.94 E-value=1e+02 Score=33.41 Aligned_cols=27 Identities=19% Similarity=0.262 Sum_probs=22.4
Q ss_pred HhhcCCcHHHHHHHcCCChhHHHHHHH
Q 001809 608 QQYFSGSLKDAAKSIGVCPTTLKRICR 634 (1010)
Q Consensus 608 ~~yF~~pl~eAAk~LGV~~TtLKRiCR 634 (1010)
+-+-+++++|+|+.|||+..|+|++-+
T Consensus 217 ~~~~g~s~~eIA~~l~is~~tV~~~~~ 243 (257)
T PRK08583 217 TFIENLSQKETGERLGISQMHVSRLQR 243 (257)
T ss_pred HHhCCCCHHHHHHHHCCCHHHHHHHHH
Confidence 334588999999999999999987644
No 440
>PF08783 DWNN: DWNN domain; InterPro: IPR014891 The ~75-residue DWNN (Domain With No Name) domain is highly conserved through eukaryotic species but is absent in prokaryotes. The DWNN domain is found only at the N terminus of the RBBP6 family of proteins which includes: Mammalian RBBP6, a splicing-associated protein that plays a role in the induction of apoptosis and regulation of the cell cycle. Drosophila melanogaster (Fruit fly) SNAMA (something that sticks like glue), a protein that appears to play a role in apoptosis. All of the identified RBBP6 homologues include the DWNN domain, a CCHC-type zinc finger (see PDOC50158 from PROSITEDOC) and a RING-type zinc finger (see PDOC00449 from PROSITEDOC). The three domain form is found in plants, protozoa, fungi and microsporidia. The RBBP6 homologues in vertebrates, insects and worms are longer and include additional domains. In addition to forming part of the full-length RBBP6 protein, the DWNN domain is also expressed in vertebrates as a small protein containing a DWNN domain and a short C-terminal tail (RBBP6 variant 3). The DWNN domain adopts a fold similar to the ubiquitin one, characterised by two alpha-helices and four beta-sheets ordered as beta-beta-alpha-beta-alpha-beta along the sequence. The similarity of DWNN domain to ubiquitin and the presence of the RING finger suggest that the DWNN domain may act as an ubiquitin-like modifier, possibly playing a role in the regulation of the splicing machinery [, ]. ; GO: 0008270 zinc ion binding, 0005634 nucleus; PDB: 2C7H_A.
Probab=20.89 E-value=2e+02 Score=26.85 Aligned_cols=39 Identities=31% Similarity=0.501 Sum_probs=25.9
Q ss_pred CeEEEEeC-CCcChHHHHHHHHHHcCcccc-eeeeEeecCC
Q 001809 912 DIIRFKFD-PSAGCFQLYEEVARRLKLQNG-TFQLKYLDDE 950 (1010)
Q Consensus 912 d~iRF~~~-~s~g~~~L~~EIakRf~l~~~-~f~lKYlDDd 950 (1010)
+.-+..|. ++-.+.||+.||+.+-+|..+ .|+|.-.|.+
T Consensus 10 ~~~~i~fdG~~Isv~dLKr~I~~~~~lg~~~dfdL~i~na~ 50 (74)
T PF08783_consen 10 DYDTITFDGTSISVFDLKREIIEKKKLGKGTDFDLVIYNAQ 50 (74)
T ss_dssp SEEEEEESSSEEEHHHHHHHHHHHHT---TTTEEEEEEESS
T ss_pred CccEEEECCCeeEHHHHHHHHHHHhCCCcCCcCCEEEECCC
Confidence 44444442 344788999999999999665 4999877765
No 441
>PRK14997 LysR family transcriptional regulator; Provisional
Probab=20.86 E-value=1e+02 Score=33.41 Aligned_cols=24 Identities=21% Similarity=0.300 Sum_probs=20.6
Q ss_pred CCcHHHHHHHcCCChhHHHHHHHH
Q 001809 612 SGSLKDAAKSIGVCPTTLKRICRQ 635 (1010)
Q Consensus 612 ~~pl~eAAk~LGV~~TtLKRiCR~ 635 (1010)
++++..||++|||+.+++-|.-++
T Consensus 16 ~gs~s~AA~~L~isQpavS~~I~~ 39 (301)
T PRK14997 16 EGGFAAAGRALDEPKSKLSRRIAQ 39 (301)
T ss_pred cCCHHHHHHHhCCCHHHHHHHHHH
Confidence 889999999999999987666653
No 442
>TIGR00270 conserved hypothetical protein TIGR00270.
Probab=20.85 E-value=1.1e+02 Score=31.88 Aligned_cols=28 Identities=21% Similarity=0.082 Sum_probs=23.7
Q ss_pred HHhhcCCcHHHHHHHcCCChhHHHHHHH
Q 001809 607 LQQYFSGSLKDAAKSIGVCPTTLKRICR 634 (1010)
Q Consensus 607 L~~yF~~pl~eAAk~LGV~~TtLKRiCR 634 (1010)
+|.--++++++.|+.+||+.+++.|+-+
T Consensus 77 ~Re~~glSqeeLA~~lgvs~s~IsriE~ 104 (154)
T TIGR00270 77 EREKRGWSQEQLAKKIQEKESLIKKIEN 104 (154)
T ss_pred HHHHcCCCHHHHHHHhCCCHHHHHHHHC
Confidence 3344589999999999999999999865
No 443
>PF09035 Tn916-Xis: Excisionase from transposon Tn916; InterPro: IPR015122 The phage-encoded excisionase protein Tn916-Xis adopts a winged-helix structure that consists of a three-stranded anti-parallel beta-sheet that packs against a helix-turn-helix (HTH) motif and a third C-terminal alpha-helix. It is encoded for by Tn916, which also codes for the integrase Tn916-Int. The protein interacts with DNA by the insertion of helix alpha-2 into the major groove and the contact of the hairpin that connects strands beta-2 and beta-3 with the adjacent phosphodiester backbone and/or minor groove. Tn916-Xis stimulates phage excision and inhibits viral integration by stabilising distorted DNA structures []. ; PDB: 1Y6U_A.
Probab=20.82 E-value=81 Score=28.81 Aligned_cols=29 Identities=14% Similarity=0.399 Sum_probs=22.3
Q ss_pred hhcCCcHHHHHHHcCCChhHHHHHHHHcC
Q 001809 609 QYFSGSLKDAAKSIGVCPTTLKRICRQHG 637 (1010)
Q Consensus 609 ~yF~~pl~eAAk~LGV~~TtLKRiCR~~G 637 (1010)
.-+.|+++|||+=.||+...|.++++++.
T Consensus 10 eK~~LTi~EAa~Y~gIG~~klr~l~~~~~ 38 (67)
T PF09035_consen 10 EKYTLTIEEAAEYFGIGEKKLRELAEENP 38 (67)
T ss_dssp TSSEEEHHHHHHHT-S-HHHHHHHHHH-T
T ss_pred HhhccCHHHHHHHhCccHHHHHHHHHhCC
Confidence 34678999999999999999999996654
No 444
>PRK10597 DNA damage-inducible protein I; Provisional
Probab=20.68 E-value=2.5e+02 Score=26.73 Aligned_cols=62 Identities=16% Similarity=0.238 Sum_probs=45.7
Q ss_pred EEEEEEcCCCeEEEEeCCCcChHHHHHHHHHHcC--cccce--eeeEeecCCCCeEEEecCCcHHHHHHH
Q 001809 903 IIVKATYKEDIIRFKFDPSAGCFQLYEEVARRLK--LQNGT--FQLKYLDDEEEWVMLVSDSDLQECFDI 968 (1010)
Q Consensus 903 ~~vKaty~~d~iRF~~~~s~g~~~L~~EIakRf~--l~~~~--f~lKYlDDd~EWVlLtcDaDL~EC~di 968 (1010)
++|..+|.-.+ ..|...+.-|.+|+-||+. ..+.. +.+||.=-++=-|+=+.+.|=+.-.+|
T Consensus 1 MrVEi~~dK~~----~lp~ga~~AL~~EL~kRl~~~fPd~~~~v~Vr~~s~n~lsv~g~~k~dK~~i~ei 66 (81)
T PRK10597 1 MRIEVTIAKTS----PLPAGAIDALAGELSRRIQYAFPDNEGHVSVRYAAANNLSVIGATKEDKDRISEI 66 (81)
T ss_pred CeEEEEEecCC----CCChhHHHHHHHHHHHHHHhhCCCCCccEEEeecCCCceEecCCCcchHHHHHHH
Confidence 46778887544 5567788899999999998 44654 999999988877776766664443333
No 445
>PRK07405 RNA polymerase sigma factor SigD; Validated
Probab=20.67 E-value=1.9e+02 Score=33.08 Aligned_cols=30 Identities=17% Similarity=0.324 Sum_probs=24.1
Q ss_pred HHHHhhc------CCcHHHHHHHcCCChhHHHHHHH
Q 001809 605 SVLQQYF------SGSLKDAAKSIGVCPTTLKRICR 634 (1010)
Q Consensus 605 ~~L~~yF------~~pl~eAAk~LGV~~TtLKRiCR 634 (1010)
+.|+-+| .++++|+|+.|||+..+++.+=.
T Consensus 263 ~Vi~lr~gl~~~~~~Tl~EIa~~lgiS~erVRqi~~ 298 (317)
T PRK07405 263 EVIALRFGLEDGQPLTLAKIGERLNISRERVRQIER 298 (317)
T ss_pred HHHHHHhhcCCCCCcCHHHHHHHHCcCHHHHHHHHH
Confidence 3566555 38999999999999999988754
No 446
>TIGR03453 partition_RepA plasmid partitioning protein RepA. Members of this family are the RepA (or ParA) protein involved in replicon partitioning. All known examples occur in bacterial species with two or more replicons, on a plasmid or the smaller chromosome. Note that an apparent exception may be seen as a pseudomolecule from assembly of an incompletely sequenced genome. Members of this family belong to a larger family that also includes the enzyme cobyrinic acid a,c-diamide synthase, but assignment of that name to members of this family would be in error.
Probab=20.56 E-value=86 Score=36.31 Aligned_cols=26 Identities=19% Similarity=0.192 Sum_probs=23.5
Q ss_pred CcHHHHHHHcCCChhHHHHHHHHcCC
Q 001809 613 GSLKDAAKSIGVCPTTLKRICRQHGI 638 (1010)
Q Consensus 613 ~pl~eAAk~LGV~~TtLKRiCR~~GI 638 (1010)
+++.|+|+.+||++.||+...++..+
T Consensus 34 ~~i~eva~~~gv~~~tlr~~e~~~~~ 59 (387)
T TIGR03453 34 FTSGEVAKLLGVSDSYLRQLSLEGKG 59 (387)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHcCCC
Confidence 69999999999999999999887654
No 447
>smart00550 Zalpha Z-DNA-binding domain in adenosine deaminases. Helix-turn-helix-containing domain. Also known as Zab.
Probab=20.55 E-value=1.4e+02 Score=26.67 Aligned_cols=31 Identities=19% Similarity=0.254 Sum_probs=21.7
Q ss_pred HHHHHhhcC--CcHHHHHHHcCCChhHHHHHHH
Q 001809 604 LSVLQQYFS--GSLKDAAKSIGVCPTTLKRICR 634 (1010)
Q Consensus 604 l~~L~~yF~--~pl~eAAk~LGV~~TtLKRiCR 634 (1010)
|+-|...=. +++.|+|+.|||...++.|.-.
T Consensus 12 L~~L~~~g~~~~ta~eLa~~lgl~~~~v~r~L~ 44 (68)
T smart00550 12 LEFLENSGDETSTALQLAKNLGLPKKEVNRVLY 44 (68)
T ss_pred HHHHHHCCCCCcCHHHHHHHHCCCHHHHHHHHH
Confidence 344444434 7889999999999888776644
No 448
>TIGR02850 spore_sigG RNA polymerase sigma-G factor. Members of this family comprise the Firmicutes lineage endospore formation-specific sigma factor SigG. It is also desginated stage III sporulation protein G (SpoIIIG). This protein is rather closely related to sigma-F (SpoIIAC), another sporulation sigma factor.
Probab=20.51 E-value=1.1e+02 Score=33.34 Aligned_cols=29 Identities=21% Similarity=0.457 Sum_probs=23.1
Q ss_pred HHHhhc--CCcHHHHHHHcCCChhHHHHHHH
Q 001809 606 VLQQYF--SGSLKDAAKSIGVCPTTLKRICR 634 (1010)
Q Consensus 606 ~L~~yF--~~pl~eAAk~LGV~~TtLKRiCR 634 (1010)
.|.-+| +++++|+|+.|||+..+++++=+
T Consensus 214 vi~~~~~~~~t~~eIA~~lgis~~~V~~~~~ 244 (254)
T TIGR02850 214 ILNMRFFEGKTQMEVAEEIGISQAQVSRLEK 244 (254)
T ss_pred HHHHHHcCCCCHHHHHHHHCcCHHHHHHHHH
Confidence 444454 68999999999999999887644
No 449
>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=20.49 E-value=86 Score=28.55 Aligned_cols=44 Identities=27% Similarity=0.513 Sum_probs=32.1
Q ss_pred CcHHHHHHHcCCChhHHHHHHHHcCCCCCcchhhhhhHHHHHHHHHHHhhcccccCcccccC
Q 001809 613 GSLKDAAKSIGVCPTTLKRICRQHGISRWPSRKINKVNRSLKKIQTVLNSVQGVEGGLKFDP 674 (1010)
Q Consensus 613 ~pl~eAAk~LGV~~TtLKRiCR~~GI~RWP~Rki~sl~~~i~~l~~~i~s~qg~e~~~~~~~ 674 (1010)
++.+|.|+.+|+++..|.++.+++- + ..++++..|..|++.+..
T Consensus 26 ~s~~eiA~~~~i~~~~l~kil~~L~-----------------~-~Gli~s~~G~~GGy~L~~ 69 (83)
T PF02082_consen 26 VSSKEIAERLGISPSYLRKILQKLK-----------------K-AGLIESSRGRGGGYRLAR 69 (83)
T ss_dssp BEHHHHHHHHTS-HHHHHHHHHHHH-----------------H-TTSEEEETSTTSEEEESS
T ss_pred CCHHHHHHHHCcCHHHHHHHHHHHh-----------------h-CCeeEecCCCCCceeecC
Confidence 7899999999999999998876541 1 234677778888777644
No 450
>TIGR02479 FliA_WhiG RNA polymerase sigma factor, FliA/WhiG family. Most members of this family are the flagellar operon sigma factor FliA, controlling transcription of bacterial flagellar genes by RNA polymerase. An exception is the sigma factor WhiG in the genus Streptomyces, involved in the production of sporulating aerial mycelium.
Probab=20.47 E-value=1.1e+02 Score=32.47 Aligned_cols=24 Identities=17% Similarity=0.279 Sum_probs=21.1
Q ss_pred cCCcHHHHHHHcCCChhHHHHHHH
Q 001809 611 FSGSLKDAAKSIGVCPTTLKRICR 634 (1010)
Q Consensus 611 F~~pl~eAAk~LGV~~TtLKRiCR 634 (1010)
-+++++|+|+.|||+..++|++-+
T Consensus 190 ~~~s~~eIA~~lgis~~tV~~~~~ 213 (224)
T TIGR02479 190 EELNLKEIGEVLGLTESRVSQIHS 213 (224)
T ss_pred CCCCHHHHHHHhCCCHHHHHHHHH
Confidence 388999999999999999998654
No 451
>PF07860 CCD: WisP family C-Terminal Region; InterPro: IPR012421 This entry represents the C-terminal domain found in the Tropheryma whipplei WisP family of proteins [].
Probab=20.24 E-value=40 Score=33.24 Aligned_cols=15 Identities=60% Similarity=1.057 Sum_probs=11.3
Q ss_pred HHHHHHcCCCCCcchhhh
Q 001809 630 KRICRQHGISRWPSRKIN 647 (1010)
Q Consensus 630 KRiCR~~GI~RWP~Rki~ 647 (1010)
|-|. ||| -||+||+-
T Consensus 49 kwiw--hgi-twpfrklf 63 (141)
T PF07860_consen 49 KWIW--HGI-TWPFRKLF 63 (141)
T ss_pred hhhh--hcc-cchHHHHh
Confidence 4443 798 89999974
No 452
>cd04776 HTH_GnyR Helix-Turn-Helix DNA binding domain of the regulatory protein GnyR. Putative helix-turn-helix (HTH) regulatory protein, GnyR, and other related proteins. GnyR belongs to the gnyRDBHAL cluster, which is involved in acyclic isoprenoid degradation in Pseudomonas aeruginosa. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules.
Probab=20.21 E-value=1e+02 Score=30.34 Aligned_cols=27 Identities=22% Similarity=0.362 Sum_probs=22.6
Q ss_pred CcHHHHHHHcCCChhHHHHHHHHcCCCC
Q 001809 613 GSLKDAAKSIGVCPTTLKRICRQHGISR 640 (1010)
Q Consensus 613 ~pl~eAAk~LGV~~TtLKRiCR~~GI~R 640 (1010)
+++.|+|+.+||++.||.-.-++ |+-.
T Consensus 1 ~~Igeva~~~gvs~~tlRyYe~~-GLl~ 27 (118)
T cd04776 1 YTISELAREFDVTPRTLRFYEDK-GLLS 27 (118)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHC-CCCC
Confidence 47899999999999999877775 7643
Done!