Query 019151
Match_columns 345
No_of_seqs 242 out of 1079
Neff 4.9
Searched_HMMs 46136
Date Fri Mar 29 07:07:02 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/019151.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/019151hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG0774 Transcription factor P 100.0 1.1E-31 2.4E-36 252.3 17.9 209 68-321 26-251 (334)
2 KOG0773 Transcription factor M 99.9 4.6E-29 1E-33 243.0 0.7 254 66-327 45-308 (342)
3 PF03791 KNOX2: KNOX2 domain ; 99.9 2.7E-23 5.9E-28 153.2 6.8 50 126-179 3-52 (52)
4 PF03790 KNOX1: KNOX1 domain ; 99.8 1.5E-20 3.1E-25 134.6 2.9 43 71-113 1-43 (45)
5 PF05920 Homeobox_KN: Homeobox 99.6 1.9E-16 4.1E-21 111.2 4.2 40 276-315 1-40 (40)
6 cd00086 homeodomain Homeodomai 99.5 1.2E-13 2.6E-18 101.0 6.8 57 260-319 2-58 (59)
7 smart00389 HOX Homeodomain. DN 99.4 2.9E-13 6.4E-18 98.4 6.6 55 260-317 2-56 (56)
8 PF00046 Homeobox: Homeobox do 99.4 2.7E-13 5.8E-18 99.6 5.6 57 259-318 1-57 (57)
9 PF03792 PBC: PBC domain; Int 99.3 1.1E-11 2.5E-16 113.0 12.9 148 68-257 24-190 (191)
10 KOG0775 Transcription factor S 99.3 5.1E-12 1.1E-16 120.6 6.2 50 265-317 183-232 (304)
11 TIGR01565 homeo_ZF_HD homeobox 98.8 5.8E-09 1.3E-13 79.0 5.1 53 258-313 1-57 (58)
12 KOG0843 Transcription factor E 98.8 3.1E-09 6.6E-14 96.6 4.3 62 257-321 101-162 (197)
13 KOG0487 Transcription factor A 98.8 2.5E-09 5.4E-14 104.4 3.0 60 259-321 236-295 (308)
14 KOG0489 Transcription factor z 98.8 3.8E-09 8.2E-14 100.9 3.8 66 258-326 159-224 (261)
15 KOG0493 Transcription factor E 98.7 1.9E-08 4.1E-13 96.1 5.0 62 258-322 246-307 (342)
16 KOG3802 Transcription factor O 98.6 1.8E-08 4E-13 100.7 3.8 67 252-321 288-354 (398)
17 KOG0485 Transcription factor N 98.6 6E-08 1.3E-12 90.6 6.3 62 258-322 104-165 (268)
18 KOG0850 Transcription factor D 98.6 4.5E-08 9.8E-13 91.9 4.0 58 261-321 125-182 (245)
19 KOG0842 Transcription factor t 98.6 3.7E-08 8E-13 96.2 3.2 60 258-320 153-212 (307)
20 KOG0483 Transcription factor H 98.5 6.7E-08 1.5E-12 89.4 4.2 58 258-318 50-107 (198)
21 KOG0488 Transcription factor B 98.5 7.1E-08 1.5E-12 94.6 4.6 58 260-320 174-231 (309)
22 COG5576 Homeodomain-containing 98.5 9.6E-08 2.1E-12 85.4 4.4 63 257-322 50-112 (156)
23 KOG0491 Transcription factor B 98.4 1.6E-07 3.5E-12 84.5 2.5 58 258-318 100-157 (194)
24 KOG0492 Transcription factor M 98.2 6.8E-07 1.5E-11 83.1 3.2 65 251-318 137-201 (246)
25 KOG2251 Homeobox transcription 98.2 1.8E-06 4E-11 80.8 4.3 58 259-319 38-95 (228)
26 KOG0484 Transcription factor P 98.1 1.7E-06 3.7E-11 72.9 3.0 61 256-319 15-75 (125)
27 KOG0848 Transcription factor C 98.1 7.6E-07 1.6E-11 85.5 1.0 56 263-321 204-259 (317)
28 KOG0494 Transcription factor C 98.1 3.2E-06 7E-11 81.0 4.2 55 262-319 145-199 (332)
29 KOG4577 Transcription factor L 98.1 2.5E-06 5.3E-11 82.8 3.1 66 252-320 161-226 (383)
30 KOG0486 Transcription factor P 98.0 2.6E-06 5.6E-11 83.4 2.5 59 260-321 114-172 (351)
31 KOG2252 CCAAT displacement pro 97.9 2.7E-05 5.8E-10 81.0 7.5 56 259-317 421-476 (558)
32 KOG1168 Transcription factor A 97.8 5.8E-06 1.3E-10 80.3 0.6 69 256-327 307-375 (385)
33 KOG0847 Transcription factor, 97.7 1.7E-05 3.7E-10 74.6 3.0 61 258-321 167-227 (288)
34 KOG0844 Transcription factor E 97.6 2.6E-05 5.7E-10 76.3 1.7 54 262-318 185-238 (408)
35 KOG0490 Transcription factor, 97.5 3.8E-05 8.2E-10 70.1 1.9 62 256-320 58-119 (235)
36 KOG0849 Transcription factor P 97.4 0.00018 3.8E-09 72.0 5.0 60 259-321 177-236 (354)
37 KOG0773 Transcription factor M 97.4 0.0001 2.2E-09 72.4 2.7 68 258-326 95-162 (342)
38 PF11569 Homez: Homeodomain le 97.1 0.00046 9.9E-09 52.2 3.2 43 270-315 10-52 (56)
39 PF03789 ELK: ELK domain ; In 97.0 0.00047 1E-08 42.9 2.2 22 236-257 1-22 (22)
40 KOG0490 Transcription factor, 94.8 0.038 8.2E-07 50.4 4.5 60 259-321 154-213 (235)
41 KOG3623 Homeobox transcription 86.3 1.4 3.1E-05 48.4 6.0 52 270-324 568-619 (1007)
42 KOG1146 Homeobox protein [Gene 85.0 1.1 2.4E-05 51.8 4.7 61 258-321 903-963 (1406)
43 PF04218 CENP-B_N: CENP-B N-te 82.7 2.6 5.6E-05 31.0 4.3 47 259-313 1-47 (53)
44 PF01527 HTH_Tnp_1: Transposas 71.8 5.7 0.00012 30.0 3.7 45 261-313 3-48 (76)
45 cd00569 HTH_Hin_like Helix-tur 70.0 13 0.00028 22.2 4.5 40 262-309 3-42 (42)
46 cd06171 Sigma70_r4 Sigma70, re 63.7 14 0.0003 24.8 4.0 46 264-317 10-55 (55)
47 PF08281 Sigma70_r4_2: Sigma-7 59.0 17 0.00036 25.8 3.9 44 264-315 10-53 (54)
48 PF04545 Sigma70_r4: Sigma-70, 52.3 21 0.00045 25.2 3.4 46 264-317 4-49 (50)
49 PRK06759 RNA polymerase factor 50.6 21 0.00045 30.1 3.7 47 264-318 106-152 (154)
50 PRK12533 RNA polymerase sigma 46.8 26 0.00057 32.4 4.0 63 264-334 134-196 (216)
51 PF13443 HTH_26: Cro/C1-type H 44.5 18 0.0004 26.3 2.2 23 290-312 12-34 (63)
52 PRK09642 RNA polymerase sigma 44.0 28 0.00061 29.7 3.5 48 264-319 106-153 (160)
53 TIGR02937 sigma70-ECF RNA poly 43.5 36 0.00079 27.4 4.0 47 264-318 110-156 (158)
54 PF13518 HTH_28: Helix-turn-he 40.8 29 0.00062 24.1 2.6 24 291-314 15-38 (52)
55 TIGR02985 Sig70_bacteroi1 RNA 39.8 52 0.0011 27.4 4.5 47 264-318 113-159 (161)
56 PF11288 DUF3089: Protein of u 39.5 8 0.00017 36.4 -0.6 38 58-101 100-137 (207)
57 PRK11924 RNA polymerase sigma 38.6 33 0.00072 29.2 3.2 48 264-319 125-172 (179)
58 PRK09646 RNA polymerase sigma 38.5 34 0.00075 30.4 3.4 50 264-321 142-191 (194)
59 KOG4040 NADH:ubiquinone oxidor 38.1 20 0.00044 32.9 1.7 41 264-304 20-61 (186)
60 PRK09652 RNA polymerase sigma 38.0 36 0.00079 29.0 3.3 48 264-319 128-175 (182)
61 KOG2070 Guanine nucleotide exc 37.4 63 0.0014 34.7 5.4 26 129-154 182-214 (661)
62 TIGR02983 SigE-fam_strep RNA p 37.4 39 0.00085 28.8 3.4 51 264-322 110-160 (162)
63 PRK12516 RNA polymerase sigma 37.2 30 0.00064 31.0 2.7 51 264-322 116-166 (187)
64 PRK12514 RNA polymerase sigma 36.4 63 0.0014 28.1 4.7 48 264-319 129-176 (179)
65 PRK12541 RNA polymerase sigma 36.3 39 0.00084 28.9 3.2 49 263-319 111-159 (161)
66 TIGR02939 RpoE_Sigma70 RNA pol 35.7 32 0.0007 30.0 2.7 49 264-320 138-186 (190)
67 PRK09644 RNA polymerase sigma 35.4 47 0.001 28.6 3.6 50 263-320 107-156 (165)
68 PF05190 MutS_IV: MutS family 34.7 67 0.0015 24.7 4.1 26 129-154 1-26 (92)
69 smart00421 HTH_LUXR helix_turn 34.4 91 0.002 21.1 4.4 47 264-319 3-49 (58)
70 PRK12547 RNA polymerase sigma 34.1 46 0.00099 28.7 3.3 48 264-319 112-159 (164)
71 PRK00118 putative DNA-binding 34.1 53 0.0012 27.7 3.6 47 264-318 17-63 (104)
72 PRK06811 RNA polymerase factor 34.0 48 0.001 29.4 3.5 48 264-319 131-178 (189)
73 PF12022 DUF3510: Domain of un 33.9 1.7E+02 0.0037 25.0 6.8 43 130-180 56-99 (125)
74 PF13097 CENP-U: CENP-A nucleo 33.9 1E+02 0.0022 28.6 5.6 47 130-179 102-149 (175)
75 TIGR02999 Sig-70_X6 RNA polyme 33.6 50 0.0011 28.7 3.5 48 264-319 134-181 (183)
76 TIGR02989 Sig-70_gvs1 RNA poly 32.7 54 0.0012 27.6 3.5 47 264-318 111-157 (159)
77 PRK03975 tfx putative transcri 32.6 53 0.0011 29.2 3.5 48 262-318 4-51 (141)
78 KOG4445 Uncharacterized conser 31.7 96 0.0021 31.4 5.4 46 132-179 134-179 (368)
79 PRK12526 RNA polymerase sigma 31.4 52 0.0011 29.7 3.4 49 264-320 153-201 (206)
80 PF07425 Pardaxin: Pardaxin; 30.8 33 0.00071 22.9 1.4 22 73-94 5-26 (33)
81 PRK12512 RNA polymerase sigma 30.6 58 0.0013 28.5 3.4 51 264-322 131-181 (184)
82 PF10668 Phage_terminase: Phag 30.5 41 0.00088 25.9 2.1 20 290-309 24-43 (60)
83 PF01381 HTH_3: Helix-turn-hel 29.0 43 0.00093 23.5 1.9 21 292-312 13-33 (55)
84 PRK13919 putative RNA polymera 28.2 72 0.0016 27.8 3.6 50 264-321 135-184 (186)
85 PF15500 Toxin_39: Putative RN 28.2 1.3E+02 0.0029 25.1 4.8 39 128-173 44-82 (96)
86 PRK05602 RNA polymerase sigma 28.0 60 0.0013 28.5 3.1 50 264-321 128-177 (186)
87 PRK12523 RNA polymerase sigma 27.9 72 0.0016 27.6 3.6 49 264-320 119-167 (172)
88 PRK09648 RNA polymerase sigma 27.4 72 0.0016 28.0 3.5 48 264-319 139-186 (189)
89 PRK12532 RNA polymerase sigma 27.0 69 0.0015 28.4 3.3 49 264-320 136-184 (195)
90 PRK12546 RNA polymerase sigma 26.5 66 0.0014 28.9 3.1 50 264-321 113-162 (188)
91 TIGR02954 Sig70_famx3 RNA poly 26.5 75 0.0016 27.3 3.4 48 264-319 119-166 (169)
92 TIGR03070 couple_hipB transcri 26.3 47 0.001 23.0 1.7 22 292-313 19-40 (58)
93 PRK09047 RNA polymerase factor 26.1 1.4E+02 0.003 25.2 4.9 49 264-320 106-154 (161)
94 PRK12531 RNA polymerase sigma 25.9 69 0.0015 28.5 3.1 51 263-321 140-190 (194)
95 PRK12530 RNA polymerase sigma 25.8 75 0.0016 28.2 3.4 48 264-319 134-181 (189)
96 cd01392 HTH_LacI Helix-turn-he 25.7 39 0.00084 23.5 1.2 20 293-312 2-21 (52)
97 cd00131 PAX Paired Box domain 25.6 2.1E+02 0.0047 24.5 6.0 46 264-312 75-127 (128)
98 PRK09649 RNA polymerase sigma 25.6 76 0.0017 28.1 3.3 47 264-318 130-176 (185)
99 PRK12524 RNA polymerase sigma 25.5 76 0.0017 28.2 3.3 49 264-320 136-184 (196)
100 PRK09413 IS2 repressor TnpA; R 25.0 1.1E+02 0.0023 25.8 3.9 48 260-314 8-55 (121)
101 PRK12520 RNA polymerase sigma 24.8 86 0.0019 27.7 3.5 48 264-319 131-178 (191)
102 PRK10072 putative transcriptio 24.5 50 0.0011 27.4 1.8 23 291-313 49-71 (96)
103 PRK09639 RNA polymerase sigma 24.3 92 0.002 26.5 3.5 47 264-319 112-158 (166)
104 cd00093 HTH_XRE Helix-turn-hel 24.2 63 0.0014 21.0 2.0 21 292-312 16-36 (58)
105 PF13384 HTH_23: Homeodomain-l 24.2 65 0.0014 22.3 2.1 23 291-313 20-42 (50)
106 PRK15369 two component system 23.9 1.9E+02 0.0041 24.1 5.3 48 264-320 149-196 (211)
107 PF12362 DUF3646: DNA polymera 23.8 56 0.0012 28.1 2.0 24 67-90 85-108 (117)
108 PRK12536 RNA polymerase sigma 23.8 92 0.002 27.3 3.5 48 264-319 129-176 (181)
109 PRK12542 RNA polymerase sigma 23.5 90 0.0019 27.4 3.4 48 264-319 122-169 (185)
110 PRK12519 RNA polymerase sigma 23.5 69 0.0015 28.2 2.6 47 264-318 141-187 (194)
111 TIGR02959 SigZ RNA polymerase 23.4 96 0.0021 27.0 3.5 50 264-321 100-149 (170)
112 PRK11511 DNA-binding transcrip 23.3 2.1E+02 0.0046 24.0 5.5 42 267-312 8-49 (127)
113 PRK12537 RNA polymerase sigma 22.4 1.1E+02 0.0023 26.9 3.6 48 264-319 133-180 (182)
114 PRK09645 RNA polymerase sigma 22.0 1E+02 0.0023 26.5 3.4 49 264-320 118-166 (173)
115 TIGR02948 SigW_bacill RNA poly 21.9 94 0.002 26.9 3.1 48 264-319 136-183 (187)
116 PF00196 GerE: Bacterial regul 21.8 1.3E+02 0.0028 21.7 3.4 48 264-320 3-50 (58)
117 PRK08583 RNA polymerase sigma 21.7 1.2E+02 0.0026 28.4 4.0 48 264-319 205-252 (257)
118 PF13551 HTH_29: Winged helix- 21.7 4E+02 0.0086 20.9 6.5 46 265-310 58-109 (112)
119 PRK12529 RNA polymerase sigma 21.4 1.3E+02 0.0029 26.3 4.0 49 264-320 127-175 (178)
120 PRK09415 RNA polymerase factor 21.3 91 0.002 27.3 3.0 47 264-318 127-173 (179)
121 PF12323 HTH_OrfB_IS605: Helix 21.3 70 0.0015 22.3 1.8 35 284-319 9-43 (46)
122 smart00530 HTH_XRE Helix-turn- 21.2 77 0.0017 20.4 1.9 22 291-312 13-34 (56)
123 PF06729 CENP-R: Kinetochore c 21.2 6E+02 0.013 22.8 8.7 33 130-171 54-86 (139)
124 TIGR02947 SigH_actino RNA poly 21.1 50 0.0011 29.2 1.3 49 264-320 131-179 (193)
125 PRK12515 RNA polymerase sigma 20.9 1.1E+02 0.0025 26.8 3.5 48 264-319 131-178 (189)
126 PF13411 MerR_1: MerR HTH fami 20.9 72 0.0016 23.5 1.9 18 292-309 4-21 (69)
127 PRK09647 RNA polymerase sigma 20.9 1.3E+02 0.0029 27.3 4.0 48 264-319 138-185 (203)
128 PRK06986 fliA flagellar biosyn 20.8 94 0.002 28.7 3.1 48 264-319 184-231 (236)
129 PRK07037 extracytoplasmic-func 20.7 1.1E+02 0.0024 25.9 3.3 48 264-319 109-156 (163)
130 PRK12535 RNA polymerase sigma 20.7 1.1E+02 0.0023 27.6 3.4 50 264-321 133-182 (196)
131 PF13865 FoP_duplication: C-te 20.1 99 0.0022 24.3 2.6 9 133-141 44-52 (74)
No 1
>KOG0774 consensus Transcription factor PBX and related HOX domain proteins [Transcription]
Probab=99.98 E-value=1.1e-31 Score=252.26 Aligned_cols=209 Identities=23% Similarity=0.364 Sum_probs=179.5
Q ss_pred hhhHHHHHHHhhCCChHHHHHHHHhh-----hcccCCCcchhhhHHHHHHHHHHHHhhhcccCC---------CCCCChH
Q 019151 68 WETVKCKAEIVGHPLYEQLLSAHVSC-----LRIATPVDQLPKIDAQLSRSRDVLAKYSAVANG---------RVLDDKE 133 (345)
Q Consensus 68 ~e~~~lKakI~sHPlYp~Ll~A~idC-----~KVGaP~e~~~~ld~~l~~~~~~~~k~~~~~~~---------~~g~dpE 133 (345)
+|+++.|.+|-+||+||.|.+++++. +.|....|.-|. |.++.++++|+...+++|+. ..|+..+
T Consensus 26 Deaqa~K~~lnch~mk~AlfsVLcE~KeKt~lsir~~qdeep~-dpqlmRLDnML~AEGVagPekgga~~~~Asgg~hsd 104 (334)
T KOG0774|consen 26 DEAQARKHALNCHRMKPALFSVLCEIKEKTVLSIRGMQDEEPP-DPQLMRLDNMLLAEGVAGPEKGGARAAAASGGDHSD 104 (334)
T ss_pred chHHhhhhccccccchHHHHHHHHHhhhhheeeeccccccCCC-ChHHHHHHHHHHHhcccCccccchhhhhccCCChHH
Confidence 45568999999999999999999995 555544443222 56777888998888888763 2446788
Q ss_pred HHHHHHHHHHHHHHHHHHHhHHHhhhhHHHHHHHhHHHHHhhhhhCCCCCCCCCCCCCCccccccCCCCCcCCCCCCCCC
Q 019151 134 LDQFMTHYVLLLYSFKEQLQQHVRVHAMEAVMACWDLEQSLQSLTGVSPGESTGATMSDDDEDQVDSDTNFFDGSLDGPD 213 (345)
Q Consensus 134 LDqFMeaYc~vL~kykEEL~kP~~~~~~EA~~fc~~iE~QL~sL~~~s~~~~~~~~~S~de~e~~~s~~~~~~g~~~~~d 213 (345)
+.+-+.+ +.+.|++||++ +...|+++.+.+.+|.. +
T Consensus 105 YR~kL~q---iR~iy~~Elek--------yeqaCneftthV~nlL~---------------------------------e 140 (334)
T KOG0774|consen 105 YRAKLLQ---IRQIYHNELEK--------YEQACNEFTTHVMNLLR---------------------------------E 140 (334)
T ss_pred HHHHHHH---HHHHHHHHHHH--------HHHHHHHHHHHHHHHHH---------------------------------H
Confidence 8887766 99999999987 66689999999999995 3
Q ss_pred CCCCCCCCCChhhhh--hHHHHHHHHHHHHhhhhhHHHHHHHHHHhh-hcCCCCCChhHHHHHHHHHHHccCCCCCCHHH
Q 019151 214 SMGFGPLVPTESERS--LMERVRHELKHELKQGYKEKIVDIREEILR-KRRAGKLPGDTTSLLKAWWLSHAKWPYPTEED 290 (345)
Q Consensus 214 ~~~f~~~~~~~~e~~--~~~~~~~eLk~~L~~~y~~~i~~l~~e~~k-krkr~~lpk~a~~~L~~wf~~h~~~PYPS~~e 290 (345)
++.|+||.+.++|+. .|.+.|.-++..|++..|..+..||.+|.. +|||++|+|.++.+|.+||+.|..||||+++.
T Consensus 141 Qsr~RPi~~ke~e~m~~~i~~kF~~iq~~lkqstce~vmiLr~r~ldarRKRRNFsK~aTeiLneyF~~h~~nPYPSee~ 220 (334)
T KOG0774|consen 141 QSRTRPIMPKEIERMVQIISKKFSHIQMQLKQSTCEAVMILRSRFLDARRKRRNFSKQATEILNEYFYSHLSNPYPSEEA 220 (334)
T ss_pred hcccCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhcccchhHHHHHHHHHHHhcCCCCCcHHH
Confidence 356999999999985 488889999999999999999999999987 46788999999999999999999999999999
Q ss_pred HHHHHHHhCCChhhhhhhhhhhhhhcccCCC
Q 019151 291 KARLVQETGLQLKQINNWFINQRKRNWHANP 321 (345)
Q Consensus 291 K~~LA~~TgLs~kQV~NWFiN~RkR~kk~~~ 321 (345)
|+.||++||++..||+|||.|+|.|.||...
T Consensus 221 K~eLAkqCnItvsQvsnwfgnkrIrykK~~~ 251 (334)
T KOG0774|consen 221 KEELAKQCNITVSQVSNWFGNKRIRYKKNMG 251 (334)
T ss_pred HHHHHHHcCceehhhccccccceeehhhhhh
Confidence 9999999999999999999999999998543
No 2
>KOG0773 consensus Transcription factor MEIS1 and related HOX domain proteins [Transcription]
Probab=99.95 E-value=4.6e-29 Score=242.98 Aligned_cols=254 Identities=22% Similarity=0.287 Sum_probs=178.3
Q ss_pred hhhhhHHHHHHHhhCCChHHHHHHHHhhhcccCCCcchhhhHHHHHHHHHHHHhhhcccC-----CCCCCChHHHHHHHH
Q 019151 66 EDWETVKCKAEIVGHPLYEQLLSAHVSCLRIATPVDQLPKIDAQLSRSRDVLAKYSAVAN-----GRVLDDKELDQFMTH 140 (345)
Q Consensus 66 ~~~e~~~lKakI~sHPlYp~Ll~A~idC~KVGaP~e~~~~ld~~l~~~~~~~~k~~~~~~-----~~~g~dpELDqFMea 140 (345)
..+....+|..+.+||+|..++.||++|+++++|.+.+.+.++...........+...+. ...+.+++|+.||..
T Consensus 45 ~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~n~~~~s~~~~~~~~~~~~~~~~~k 124 (342)
T KOG0773|consen 45 IMVSLASSKYLTAAQELLDEFCSAGLDCLKGKMPYDPVPRSPASLSPPEDKGARRGNATRESATLKAWLEEHRLNPYPSK 124 (342)
T ss_pred cccccccccccccchhHHhHHhhccccccccccCcCccccccccccCccccccccccccccccccccchhhhhhccCchH
Confidence 345566789999999999999999999999999999888865543322222122221111 135688999999999
Q ss_pred HHHHHHHHHHHHhHHHhhhhHHHHHHHhHHHHHhhhhhCCCCCCCCCCCCCCcccccc---CCCCCcCCCCCCCCCCCCC
Q 019151 141 YVLLLYSFKEQLQQHVRVHAMEAVMACWDLEQSLQSLTGVSPGESTGATMSDDDEDQV---DSDTNFFDGSLDGPDSMGF 217 (345)
Q Consensus 141 Yc~vL~kykEEL~kP~~~~~~EA~~fc~~iE~QL~sL~~~s~~~~~~~~~S~de~e~~---~s~~~~~~g~~~~~d~~~f 217 (345)
|+.+|..+...|+..+. -++++.++++++..+.+.+..++....+.+...+.++.. .+...... +..++
T Consensus 125 ~~~~ll~~~~~~~~~~~--~~~~~~a~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~q~~~~~------~~~~~ 196 (342)
T KOG0773|consen 125 LEKILLAVITKLTLTQV--STWFANARRRLKKELKMTWGPTPLALDGISRHFSDLEKEKAIGGQLSSSE------ELLGE 196 (342)
T ss_pred HHHHHHHHHHHhhhhhH--HHHHHHHHHHHHhccCCCCCCccccccchhhhhhhhhhcccccccccccc------ccccc
Confidence 99999999999999863 389999999999999999876665444332222211110 00000000 11111
Q ss_pred CCCCCChhhhhhH--HHHHHHHHHHHhhhhhHHHHHHHHHHhhhcCCCCCChhHHHHHHHHHHHccCCCCCCHHHHHHHH
Q 019151 218 GPLVPTESERSLM--ERVRHELKHELKQGYKEKIVDIREEILRKRRAGKLPGDTTSLLKAWWLSHAKWPYPTEEDKARLV 295 (345)
Q Consensus 218 ~~~~~~~~e~~~~--~~~~~eLk~~L~~~y~~~i~~l~~e~~kkrkr~~lpk~a~~~L~~wf~~h~~~PYPS~~eK~~LA 295 (345)
++......+...+ ......++..+.+.+..++.....+..++|+++.||+.++.+|+.||.+|+.||||++.+|..||
T Consensus 197 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~r~~~~lP~~a~~ilr~Wl~~h~~~PYPse~~K~~La 276 (342)
T KOG0773|consen 197 SEQDDSEDESGPSGSEPPLRLAKQSLRQQRSAYDGSGGKKQSKWRPQRGLPKEAVSILRAWLFEHLLHPYPSDDEKLMLA 276 (342)
T ss_pred ccccccccccCcccccCCcccccccccccccccccccccccCCCCCCCCCCHHHHHHHHHHHHHhccCCCCcchhccccc
Confidence 1111111111100 11234555566666665666666667788889999999999999999999999999999999999
Q ss_pred HHhCCChhhhhhhhhhhhhhcccCCCCCCccc
Q 019151 296 QETGLQLKQINNWFINQRKRNWHANPSSSTAS 327 (345)
Q Consensus 296 ~~TgLs~kQV~NWFiN~RkR~kk~~~s~~~~~ 327 (345)
++|||+..||+|||||+|+|.|+++...+...
T Consensus 277 ~~TGLs~~Qv~NWFINaR~R~w~p~~~~~~~~ 308 (342)
T KOG0773|consen 277 KQTGLSRPQVSNWFINARVRLWKPMIEEMYLL 308 (342)
T ss_pred hhcCCCcccCCchhhhcccccCCchHHHHHHH
Confidence 99999999999999999999999998444333
No 3
>PF03791 KNOX2: KNOX2 domain ; InterPro: IPR005541 The MEINOX region is comprised of two domains, KNOX1 and KNOX2. KNOX1 plays a role in suppressing target gene expression. KNOX2, essential for function, is thought to be necessary for homo-dimerization [].; GO: 0003677 DNA binding, 0005634 nucleus
Probab=99.89 E-value=2.7e-23 Score=153.16 Aligned_cols=50 Identities=46% Similarity=0.698 Sum_probs=47.4
Q ss_pred CCCCCChHHHHHHHHHHHHHHHHHHHHhHHHhhhhHHHHHHHhHHHHHhhhhhC
Q 019151 126 GRVLDDKELDQFMTHYVLLLYSFKEQLQQHVRVHAMEAVMACWDLEQSLQSLTG 179 (345)
Q Consensus 126 ~~~g~dpELDqFMeaYc~vL~kykEEL~kP~~~~~~EA~~fc~~iE~QL~sL~~ 179 (345)
.++|+||||||||++||.||+||||||++||+ ||++|||+||+||++||+
T Consensus 3 ~~~~~dpELDqFMeaYc~~L~kykeeL~~p~~----EA~~f~~~ie~qL~~Lt~ 52 (52)
T PF03791_consen 3 SSIGADPELDQFMEAYCDMLVKYKEELQRPFQ----EAMEFCREIEQQLSSLTG 52 (52)
T ss_pred CCCCCCccHHHHHHHHHHHHHHHHHHHHHHHH----HHHHHHHHHHHHHHHHhC
Confidence 46899999999999999999999999999984 999999999999999985
No 4
>PF03790 KNOX1: KNOX1 domain ; InterPro: IPR005540 The MEINOX region is comprised of two domains, KNOX1 and KNOX2. KNOX1 plays a role in suppressing target gene expression. KNOX2, essential for function, is thought to be necessary for homo-dimerization [].; GO: 0003677 DNA binding, 0005634 nucleus
Probab=99.80 E-value=1.5e-20 Score=134.64 Aligned_cols=43 Identities=35% Similarity=0.691 Sum_probs=40.0
Q ss_pred HHHHHHHhhCCChHHHHHHHHhhhcccCCCcchhhhHHHHHHH
Q 019151 71 VKCKAEIVGHPLYEQLLSAHVSCLRIATPVDQLPKIDAQLSRS 113 (345)
Q Consensus 71 ~~lKakI~sHPlYp~Ll~A~idC~KVGaP~e~~~~ld~~l~~~ 113 (345)
+.|||+|++||+||+||+|||+|+|||||||++++|++++.+.
T Consensus 1 e~iKA~I~~HP~Y~~Ll~Ayi~C~KVGAP~e~~~~L~e~~~~~ 43 (45)
T PF03790_consen 1 EAIKAKIASHPLYPRLLAAYIDCQKVGAPPEVVARLDEILAES 43 (45)
T ss_pred ChHHHHHHcCCCcHHHHHHHHHHHhcCCCHHHHHHHHHHHHHh
Confidence 4799999999999999999999999999999999999987654
No 5
>PF05920 Homeobox_KN: Homeobox KN domain; InterPro: IPR008422 This entry represents a homeobox transcription factor KN domain conserved from fungi to human and plants [].; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent, 0005634 nucleus; PDB: 3K2A_B 2LK2_A 1X2N_A 2DMN_A.
Probab=99.63 E-value=1.9e-16 Score=111.16 Aligned_cols=40 Identities=55% Similarity=1.074 Sum_probs=36.4
Q ss_pred HHHHccCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhh
Q 019151 276 WWLSHAKWPYPTEEDKARLVQETGLQLKQINNWFINQRKR 315 (345)
Q Consensus 276 wf~~h~~~PYPS~~eK~~LA~~TgLs~kQV~NWFiN~RkR 315 (345)
||..|+.+||||+++|..||..|||+.+||+|||+|+|+|
T Consensus 1 Wl~~h~~nPYPs~~ek~~L~~~tgls~~Qi~~WF~NaRrR 40 (40)
T PF05920_consen 1 WLLEHLHNPYPSKEEKEELAKQTGLSRKQISNWFINARRR 40 (40)
T ss_dssp HHHHTTTSGS--HHHHHHHHHHHTS-HHHHHHHHHHHHHH
T ss_pred CHHHHCCCCCCCHHHHHHHHHHcCCCHHHHHHHHHHhHcc
Confidence 8999999999999999999999999999999999999998
No 6
>cd00086 homeodomain Homeodomain; DNA binding domains involved in the transcriptional regulation of key eukaryotic developmental processes; may bind to DNA as monomers or as homo- and/or heterodimers, in a sequence-specific manner.
Probab=99.47 E-value=1.2e-13 Score=101.01 Aligned_cols=57 Identities=26% Similarity=0.520 Sum_probs=53.6
Q ss_pred cCCCCCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhcccC
Q 019151 260 RRAGKLPGDTTSLLKAWWLSHAKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHA 319 (345)
Q Consensus 260 rkr~~lpk~a~~~L~~wf~~h~~~PYPS~~eK~~LA~~TgLs~kQV~NWFiN~RkR~kk~ 319 (345)
+++..|++++..+|+.||.. +|||+.+++..||..|||+..||.+||.|+|.+.++.
T Consensus 2 ~~r~~~~~~~~~~Le~~f~~---~~~P~~~~~~~la~~~~l~~~qV~~WF~nrR~~~~~~ 58 (59)
T cd00086 2 RKRTRFTPEQLEELEKEFEK---NPYPSREEREELAKELGLTERQVKIWFQNRRAKLKRS 58 (59)
T ss_pred CCCCcCCHHHHHHHHHHHHh---CCCCCHHHHHHHHHHHCcCHHHHHHHHHHHHHHHhcc
Confidence 45679999999999999999 7999999999999999999999999999999998764
No 7
>smart00389 HOX Homeodomain. DNA-binding factors that are involved in the transcriptional regulation of key developmental processes
Probab=99.43 E-value=2.9e-13 Score=98.44 Aligned_cols=55 Identities=25% Similarity=0.497 Sum_probs=51.1
Q ss_pred cCCCCCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhcc
Q 019151 260 RRAGKLPGDTTSLLKAWWLSHAKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNW 317 (345)
Q Consensus 260 rkr~~lpk~a~~~L~~wf~~h~~~PYPS~~eK~~LA~~TgLs~kQV~NWFiN~RkR~k 317 (345)
+.+..|++++..+|+.||.. +|||+.+++..||..+||+..||.+||+|+|.|.+
T Consensus 2 k~r~~~~~~~~~~L~~~f~~---~~~P~~~~~~~la~~~~l~~~qV~~WF~nrR~~~~ 56 (56)
T smart00389 2 RKRTSFTPEQLEELEKEFQK---NPYPSREEREELAAKLGLSERQVKVWFQNRRAKWK 56 (56)
T ss_pred CCCCcCCHHHHHHHHHHHHh---CCCCCHHHHHHHHHHHCcCHHHHHHhHHHHhhccC
Confidence 44567999999999999999 69999999999999999999999999999999864
No 8
>PF00046 Homeobox: Homeobox domain not present here.; InterPro: IPR001356 The homeobox domain was first identified in a number of drosophila homeotic and segmentation proteins, but is now known to be well-conserved in many other animals, including vertebrates [, , ]. Hox genes encode homeodomain-containing transcriptional regulators that operate differential genetic programs along the anterior-posterior axis of animal bodies []. The domain binds DNA through a helix-turn-helix (HTH) structure. The HTH motif is characterised by two alpha-helices, which make intimate contacts with the DNA and are joined by a short turn. The second helix binds to DNA via a number of hydrogen bonds and hydrophobic interactions, which occur between specific side chains and the exposed bases and thymine methyl groups within the major groove of the DNA []. The first helix helps to stabilise the structure. The motif is very similar in sequence and structure in a wide range of DNA-binding proteins (e.g., cro and repressor proteins, homeotic proteins, etc.). One of the principal differences between HTH motifs in these different proteins arises from the stereo-chemical requirement for glycine in the turn which is needed to avoid steric interference of the beta-carbon with the main chain: for cro and repressor proteins the glycine appears to be mandatory, while for many of the homeotic and other DNA-binding proteins the requirement is relaxed.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0043565 sequence-specific DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 2DA3_A 1LFB_A 2LFB_A 2ECB_A 2DA5_A 3D1N_O 3A03_A 2XSD_C 3CMY_A 1AHD_P ....
Probab=99.42 E-value=2.7e-13 Score=99.61 Aligned_cols=57 Identities=30% Similarity=0.704 Sum_probs=53.7
Q ss_pred hcCCCCCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhccc
Q 019151 259 KRRAGKLPGDTTSLLKAWWLSHAKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWH 318 (345)
Q Consensus 259 krkr~~lpk~a~~~L~~wf~~h~~~PYPS~~eK~~LA~~TgLs~kQV~NWFiN~RkR~kk 318 (345)
||++..|+.++..+|+.+|.. +|||+.+++..||..+||+..||.+||.|+|.+.|+
T Consensus 1 kr~r~~~t~~q~~~L~~~f~~---~~~p~~~~~~~la~~l~l~~~~V~~WF~nrR~k~kk 57 (57)
T PF00046_consen 1 KRKRTRFTKEQLKVLEEYFQE---NPYPSKEEREELAKELGLTERQVKNWFQNRRRKEKK 57 (57)
T ss_dssp SSSSSSSSHHHHHHHHHHHHH---SSSCHHHHHHHHHHHHTSSHHHHHHHHHHHHHHHHH
T ss_pred CcCCCCCCHHHHHHHHHHHHH---hccccccccccccccccccccccccCHHHhHHHhCc
Confidence 467789999999999999999 799999999999999999999999999999999764
No 9
>PF03792 PBC: PBC domain; InterPro: IPR005542 Pbx proteins are members of the TALE (three-amino-acid loop extension) family of atypical homeodomain proteins, whose members are characterised by a three-residue insertion in the first helix of the homeodomain involved in their interaction with Hox proteins. Examination of Pbx1 has shown that, in addition to the homeodomain, a short 16-residue C-terminal tail is essential for maximal cooperative interactions with Hox partners as well as for maximal monomeric binding of Pbx1 to DNA. The PBX domain is a bipartite acidic domain [].; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0005634 nucleus
Probab=99.35 E-value=1.1e-11 Score=112.97 Aligned_cols=148 Identities=21% Similarity=0.296 Sum_probs=114.0
Q ss_pred hhhHHHHHHHhhCCChHHHHHHHHhh-----hcccCCCcchhhhHHHHHHHHHHHHhhhcccCCCCC--------C--Ch
Q 019151 68 WETVKCKAEIVGHPLYEQLLSAHVSC-----LRIATPVDQLPKIDAQLSRSRDVLAKYSAVANGRVL--------D--DK 132 (345)
Q Consensus 68 ~e~~~lKakI~sHPlYp~Ll~A~idC-----~KVGaP~e~~~~ld~~l~~~~~~~~k~~~~~~~~~g--------~--dp 132 (345)
+|++.+|.+|.+||+||.|.+++|+- +++..+.+..+. |+++.++++|+.+.++.|+...| . |-
T Consensus 24 Deaqa~K~~l~~hr~k~ALfsVLcE~KEkt~LSir~~qee~p~-dpQl~RLDNML~AEGV~gPe~~~~~~~~~~~~~~~~ 102 (191)
T PF03792_consen 24 DEAQARKHALNCHRMKPALFSVLCEIKEKTVLSIRNIQEEDPP-DPQLMRLDNMLLAEGVAGPEKGGRAAAAAAGTAADN 102 (191)
T ss_pred hHHHHhchhhcCCCCchhhHHHHHHHHhhcCccccccCCcCCC-chhhhhhhcchhhhcCcCCCCcccchhhhhccCccc
Confidence 36689999999999999999999995 455555433222 56777889999888888765322 1 11
Q ss_pred --HHHHHHHHHHHHHHHHHHHHhHHHhhhhHHHHHHHhHHHHHhhhhhCCCCCCCCCCCCCCccccccCCCCCcCCCCCC
Q 019151 133 --ELDQFMTHYVLLLYSFKEQLQQHVRVHAMEAVMACWDLEQSLQSLTGVSPGESTGATMSDDDEDQVDSDTNFFDGSLD 210 (345)
Q Consensus 133 --ELDqFMeaYc~vL~kykEEL~kP~~~~~~EA~~fc~~iE~QL~sL~~~s~~~~~~~~~S~de~e~~~s~~~~~~g~~~ 210 (345)
|-+.|-...-++...|++||++ +...|+++...+.+|..
T Consensus 103 ~~d~~dYr~kL~~ir~~y~~el~k--------ye~ac~eF~~hV~~lLr------------------------------- 143 (191)
T PF03792_consen 103 SIDHSDYRAKLSQIRQIYHSELEK--------YEQACNEFTEHVMNLLR------------------------------- 143 (191)
T ss_pred ccchHHHHHHHHHHHHHHHHHHHH--------HHHHhhhhHHHHHHHHH-------------------------------
Confidence 2234444555588899999987 55678999999999885
Q ss_pred CCCCCCCCCCCCChhhhh--hHHHHHHHHHHHHhhhhhHHHHHHHHHHh
Q 019151 211 GPDSMGFGPLVPTESERS--LMERVRHELKHELKQGYKEKIVDIREEIL 257 (345)
Q Consensus 211 ~~d~~~f~~~~~~~~e~~--~~~~~~~eLk~~L~~~y~~~i~~l~~e~~ 257 (345)
+++.|+||++.++|+. .+++.+.-+..+||+..|+.+..||.+|.
T Consensus 144 --eQs~~RPIs~keiE~m~~~i~~Kf~~iq~qLKQstCEaVm~LRsRfl 190 (191)
T PF03792_consen 144 --EQSEFRPISPKEIERMVNIIHRKFSKIQMQLKQSTCEAVMILRSRFL 190 (191)
T ss_pred --HhcccCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhc
Confidence 2346999999999985 57899999999999999999999998875
No 10
>KOG0775 consensus Transcription factor SIX and related HOX domain proteins [Transcription]
Probab=99.27 E-value=5.1e-12 Score=120.61 Aligned_cols=50 Identities=40% Similarity=0.883 Sum_probs=46.7
Q ss_pred CChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhcc
Q 019151 265 LPGDTTSLLKAWWLSHAKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNW 317 (345)
Q Consensus 265 lpk~a~~~L~~wf~~h~~~PYPS~~eK~~LA~~TgLs~kQV~NWFiN~RkR~k 317 (345)
|....+..|++||.. +|||++++|..||+.|||+..||.|||.|+|.|.+
T Consensus 183 FKekSR~~LrewY~~---~~YPsp~eKReLA~aTgLt~tQVsNWFKNRRQRDR 232 (304)
T KOG0775|consen 183 FKEKSRSLLREWYLQ---NPYPSPREKRELAEATGLTITQVSNWFKNRRQRDR 232 (304)
T ss_pred hhHhhHHHHHHHHhc---CCCCChHHHHHHHHHhCCchhhhhhhhhhhhhhhh
Confidence 345789999999997 89999999999999999999999999999999988
No 11
>TIGR01565 homeo_ZF_HD homeobox domain, ZF-HD class. This model represents a class of homoebox domain that differs substantially from the typical homoebox domain described in pfam model pfam00046. It is found in both C4 and C3 plants.
Probab=98.82 E-value=5.8e-09 Score=78.99 Aligned_cols=53 Identities=19% Similarity=0.401 Sum_probs=49.8
Q ss_pred hhcCCCCCChhHHHHHHHHHHHccCCCC----CCHHHHHHHHHHhCCChhhhhhhhhhhh
Q 019151 258 RKRRAGKLPGDTTSLLKAWWLSHAKWPY----PTEEDKARLVQETGLQLKQINNWFINQR 313 (345)
Q Consensus 258 kkrkr~~lpk~a~~~L~~wf~~h~~~PY----PS~~eK~~LA~~TgLs~kQV~NWFiN~R 313 (345)
+||.|++|+.++...|+..|.. ++| |+..++..||..+||+..+|.+||+|-+
T Consensus 1 ~kR~RT~Ft~~Q~~~Le~~fe~---~~y~~~~~~~~~r~~la~~lgl~~~vvKVWfqN~k 57 (58)
T TIGR01565 1 KKRRRTKFTAEQKEKMRDFAEK---LGWKLKDKRREEVREFCEEIGVTRKVFKVWMHNNK 57 (58)
T ss_pred CCCCCCCCCHHHHHHHHHHHHH---cCCCCCCCCHHHHHHHHHHhCCCHHHeeeecccCC
Confidence 4678899999999999999999 799 9999999999999999999999999954
No 12
>KOG0843 consensus Transcription factor EMX1 and related HOX domain proteins [Transcription]
Probab=98.82 E-value=3.1e-09 Score=96.60 Aligned_cols=62 Identities=19% Similarity=0.271 Sum_probs=57.3
Q ss_pred hhhcCCCCCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhcccCCC
Q 019151 257 LRKRRAGKLPGDTTSLLKAWWLSHAKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHANP 321 (345)
Q Consensus 257 ~kkrkr~~lpk~a~~~L~~wf~~h~~~PYPS~~eK~~LA~~TgLs~kQV~NWFiN~RkR~kk~~~ 321 (345)
..||.|+.|+.++...|+..|.. +.|-.-.+|..||+.++|+..||..||+|+|.|+|+...
T Consensus 101 ~~kr~RT~ft~~Ql~~LE~~F~~---~~Yvvg~eR~~LA~~L~LsetQVkvWFQNRRtk~kr~~~ 162 (197)
T KOG0843|consen 101 RPKRIRTAFTPEQLLKLEHAFEG---NQYVVGAERKQLAQSLSLSETQVKVWFQNRRTKHKRMQQ 162 (197)
T ss_pred CCCccccccCHHHHHHHHHHHhc---CCeeechHHHHHHHHcCCChhHhhhhhhhhhHHHHHHHH
Confidence 35677889999999999999999 799999999999999999999999999999999997554
No 13
>KOG0487 consensus Transcription factor Abd-B, contains HOX domain [Transcription]
Probab=98.79 E-value=2.5e-09 Score=104.37 Aligned_cols=60 Identities=23% Similarity=0.329 Sum_probs=54.8
Q ss_pred hcCCCCCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhcccCCC
Q 019151 259 KRRAGKLPGDTTSLLKAWWLSHAKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHANP 321 (345)
Q Consensus 259 krkr~~lpk~a~~~L~~wf~~h~~~PYPS~~eK~~LA~~TgLs~kQV~NWFiN~RkR~kk~~~ 321 (345)
+|||..++|.++.-|+.-|.- |-|.|++-|.+|++.++|+..||..||||||++.||-+.
T Consensus 236 RKKRcPYTK~QtlELEkEFlf---N~YitkeKR~ElSr~lNLTeRQVKIWFQNRRMK~KK~~r 295 (308)
T KOG0487|consen 236 RKKRCPYTKHQTLELEKEFLF---NMYITKEKRLELSRTLNLTERQVKIWFQNRRMKEKKVNR 295 (308)
T ss_pred ccccCCchHHHHHHHHHHHHH---HHHHhHHHHHHHHHhcccchhheeeeehhhhhHHhhhhh
Confidence 344568999999999999988 699999999999999999999999999999999998764
No 14
>KOG0489 consensus Transcription factor zerknullt and related HOX domain proteins [General function prediction only]
Probab=98.78 E-value=3.8e-09 Score=100.94 Aligned_cols=66 Identities=23% Similarity=0.264 Sum_probs=60.1
Q ss_pred hhcCCCCCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhcccCCCCCCcc
Q 019151 258 RKRRAGKLPGDTTSLLKAWWLSHAKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHANPSSSTA 326 (345)
Q Consensus 258 kkrkr~~lpk~a~~~L~~wf~~h~~~PYPS~~eK~~LA~~TgLs~kQV~NWFiN~RkR~kk~~~s~~~~ 326 (345)
.||.|..|+..++..|+.-|.- |.|.|...|.+||..+.|+..||.+||+|+|++.||.+......
T Consensus 159 ~kR~RtayT~~QllELEkEFhf---N~YLtR~RRiEiA~~L~LtErQIKIWFQNRRMK~Kk~~k~~~~~ 224 (261)
T KOG0489|consen 159 SKRRRTAFTRYQLLELEKEFHF---NKYLTRSRRIEIAHALNLTERQIKIWFQNRRMKWKKENKAKSSQ 224 (261)
T ss_pred CCCCCcccchhhhhhhhhhhcc---ccccchHHHHHHHhhcchhHHHHHHHHHHHHHHHHHhhcccccc
Confidence 5777889999999999999999 69999999999999999999999999999999999887754443
No 15
>KOG0493 consensus Transcription factor Engrailed, contains HOX domain [General function prediction only]
Probab=98.68 E-value=1.9e-08 Score=96.09 Aligned_cols=62 Identities=32% Similarity=0.414 Sum_probs=57.4
Q ss_pred hhcCCCCCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhcccCCCC
Q 019151 258 RKRRAGKLPGDTTSLLKAWWLSHAKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHANPS 322 (345)
Q Consensus 258 kkrkr~~lpk~a~~~L~~wf~~h~~~PYPS~~eK~~LA~~TgLs~kQV~NWFiN~RkR~kk~~~s 322 (345)
.||.|+-|+.++.+.|+.-|+. |-|.|+..|+.||.++||...||..||+|+|.+.||...+
T Consensus 246 eKRPRTAFtaeQL~RLK~EF~e---nRYlTEqRRQ~La~ELgLNEsQIKIWFQNKRAKiKKsTgs 307 (342)
T KOG0493|consen 246 EKRPRTAFTAEQLQRLKAEFQE---NRYLTEQRRQELAQELGLNESQIKIWFQNKRAKIKKSTGS 307 (342)
T ss_pred hcCccccccHHHHHHHHHHHhh---hhhHHHHHHHHHHHHhCcCHHHhhHHhhhhhhhhhhccCC
Confidence 3666788999999999999999 6999999999999999999999999999999999987654
No 16
>KOG3802 consensus Transcription factor OCT-1, contains POU and HOX domains [Transcription]
Probab=98.64 E-value=1.8e-08 Score=100.72 Aligned_cols=67 Identities=18% Similarity=0.420 Sum_probs=61.0
Q ss_pred HHHHHhhhcCCCCCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhcccCCC
Q 019151 252 IREEILRKRRAGKLPGDTTSLLKAWWLSHAKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHANP 321 (345)
Q Consensus 252 l~~e~~kkrkr~~lpk~a~~~L~~wf~~h~~~PYPS~~eK~~LA~~TgLs~kQV~NWFiN~RkR~kk~~~ 321 (345)
+-.+-+|||||+.+...++..|+..|.. ||-||-+|.-.||+.++|....|++||+|||.+.|+.++
T Consensus 288 i~a~~RkRKKRTSie~~vr~aLE~~F~~---npKPt~qEIt~iA~~L~leKEVVRVWFCNRRQkeKR~~~ 354 (398)
T KOG3802|consen 288 IGAQSRKRKKRTSIEVNVRGALEKHFLK---NPKPTSQEITHIAESLQLEKEVVRVWFCNRRQKEKRITP 354 (398)
T ss_pred hhccccccccccceeHHHHHHHHHHHHh---CCCCCHHHHHHHHHHhccccceEEEEeeccccccccCCC
Confidence 3344456777889999999999999999 799999999999999999999999999999999999888
No 17
>KOG0485 consensus Transcription factor NKX-5.1/HMX1, contains HOX domain [Transcription]
Probab=98.62 E-value=6e-08 Score=90.61 Aligned_cols=62 Identities=18% Similarity=0.270 Sum_probs=56.8
Q ss_pred hhcCCCCCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhcccCCCC
Q 019151 258 RKRRAGKLPGDTTSLLKAWWLSHAKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHANPS 322 (345)
Q Consensus 258 kkrkr~~lpk~a~~~L~~wf~~h~~~PYPS~~eK~~LA~~TgLs~kQV~NWFiN~RkR~kk~~~s 322 (345)
|||.|+-|+..++..|+.-|... -|.+-++|..||.++-|+..||..||||+|.+.|+.-..
T Consensus 104 KKktRTvFSraQV~qLEs~Fe~k---rYLSsaeRa~LA~sLqLTETQVKIWFQNRRnKwKRq~aa 165 (268)
T KOG0485|consen 104 KKKTRTVFSRAQVFQLESTFELK---RYLSSAERAGLAASLQLTETQVKIWFQNRRNKWKRQYAA 165 (268)
T ss_pred cccchhhhhHHHHHHHHHHHHHH---hhhhHHHHhHHHHhhhhhhhhhhhhhhhhhHHHHHHHhh
Confidence 67778899999999999999994 999999999999999999999999999999998875543
No 18
>KOG0850 consensus Transcription factor DLX and related proteins with LIM Zn-binding and HOX domains [Transcription]
Probab=98.57 E-value=4.5e-08 Score=91.94 Aligned_cols=58 Identities=19% Similarity=0.247 Sum_probs=53.5
Q ss_pred CCCCCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhcccCCC
Q 019151 261 RAGKLPGDTTSLLKAWWLSHAKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHANP 321 (345)
Q Consensus 261 kr~~lpk~a~~~L~~wf~~h~~~PYPS~~eK~~LA~~TgLs~kQV~NWFiN~RkR~kk~~~ 321 (345)
.|+.++.-+.+.|..-|++ ..|..-.||.+||..+||+++||..||+|+|-+.||...
T Consensus 125 PRTIYSS~QLqaL~rRFQk---TQYLALPERAeLAAsLGLTQTQVKIWFQNrRSK~KKl~k 182 (245)
T KOG0850|consen 125 PRTIYSSLQLQALNRRFQQ---TQYLALPERAELAASLGLTQTQVKIWFQNRRSKFKKLKK 182 (245)
T ss_pred CcccccHHHHHHHHHHHhh---cchhcCcHHHHHHHHhCCchhHhhhhhhhhHHHHHHHHh
Confidence 4568999999999999999 899999999999999999999999999999999887554
No 19
>KOG0842 consensus Transcription factor tinman/NKX2-3, contains HOX domain [Transcription]
Probab=98.55 E-value=3.7e-08 Score=96.24 Aligned_cols=60 Identities=17% Similarity=0.293 Sum_probs=53.8
Q ss_pred hhcCCCCCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhcccCC
Q 019151 258 RKRRAGKLPGDTTSLLKAWWLSHAKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHAN 320 (345)
Q Consensus 258 kkrkr~~lpk~a~~~L~~wf~~h~~~PYPS~~eK~~LA~~TgLs~kQV~NWFiN~RkR~kk~~ 320 (345)
|||+|--|++.++-.|+.-|.+ .-|.|..||+.||...+||.+||..||||+|-+-|+..
T Consensus 153 kRKrRVLFSqAQV~ELERRFrq---QRYLSAPERE~LA~~LrLT~TQVKIWFQNrRYK~KR~~ 212 (307)
T KOG0842|consen 153 KRKRRVLFSQAQVYELERRFRQ---QRYLSAPEREHLASSLRLTPTQVKIWFQNRRYKTKRQQ 212 (307)
T ss_pred ccccccccchhHHHHHHHHHHh---hhccccHhHHHHHHhcCCCchheeeeeecchhhhhhhh
Confidence 4444558999999999999999 69999999999999999999999999999999988643
No 20
>KOG0483 consensus Transcription factor HEX, contains HOX and HALZ domains [Transcription]
Probab=98.53 E-value=6.7e-08 Score=89.39 Aligned_cols=58 Identities=29% Similarity=0.425 Sum_probs=52.8
Q ss_pred hhcCCCCCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhccc
Q 019151 258 RKRRAGKLPGDTTSLLKAWWLSHAKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWH 318 (345)
Q Consensus 258 kkrkr~~lpk~a~~~L~~wf~~h~~~PYPS~~eK~~LA~~TgLs~kQV~NWFiN~RkR~kk 318 (345)
.++|+.+|+.++...|+.=|..| -|..+.+|..||+..||.+.||..||+|+|.|.|.
T Consensus 50 ~~~kk~Rlt~eQ~~~LE~~F~~~---~~L~p~~K~~LAk~LgL~pRQVavWFQNRRARwK~ 107 (198)
T KOG0483|consen 50 GKGKKRRLTSEQVKFLEKSFESE---KKLEPERKKKLAKELGLQPRQVAVWFQNRRARWKT 107 (198)
T ss_pred cccccccccHHHHHHhHHhhccc---cccChHHHHHHHHhhCCChhHHHHHHhhccccccc
Confidence 34566789999999999999995 88899999999999999999999999999999874
No 21
>KOG0488 consensus Transcription factor BarH and related HOX domain proteins [General function prediction only]
Probab=98.53 E-value=7.1e-08 Score=94.56 Aligned_cols=58 Identities=19% Similarity=0.296 Sum_probs=52.5
Q ss_pred cCCCCCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhcccCC
Q 019151 260 RRAGKLPGDTTSLLKAWWLSHAKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHAN 320 (345)
Q Consensus 260 rkr~~lpk~a~~~L~~wf~~h~~~PYPS~~eK~~LA~~TgLs~kQV~NWFiN~RkR~kk~~ 320 (345)
|.|.-|+..++..|+.-|.. --|.+..||..||...||+-.||..||+|||++.|+..
T Consensus 174 ksRTaFT~~Ql~~LEkrF~~---QKYLS~~DR~~LA~~LgLTdaQVKtWfQNRRtKWKrq~ 231 (309)
T KOG0488|consen 174 KSRTAFSDHQLFELEKRFEK---QKYLSVADRIELAASLGLTDAQVKTWFQNRRTKWKRQT 231 (309)
T ss_pred cchhhhhHHHHHHHHHHHHH---hhcccHHHHHHHHHHcCCchhhHHHHHhhhhHHHHHHH
Confidence 34568999999999999998 59999999999999999999999999999999887644
No 22
>COG5576 Homeodomain-containing transcription factor [Transcription]
Probab=98.51 E-value=9.6e-08 Score=85.38 Aligned_cols=63 Identities=17% Similarity=0.315 Sum_probs=57.3
Q ss_pred hhhcCCCCCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhcccCCCC
Q 019151 257 LRKRRAGKLPGDTTSLLKAWWLSHAKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHANPS 322 (345)
Q Consensus 257 ~kkrkr~~lpk~a~~~L~~wf~~h~~~PYPS~~eK~~LA~~TgLs~kQV~NWFiN~RkR~kk~~~s 322 (345)
..++++.+.+..++.+|+..|.. +|||+...|..|+..+|++++-|..||+|+|.+.|+...-
T Consensus 50 ~~~~~r~R~t~~Q~~vL~~~F~i---~p~Ps~~~r~~L~~~lnm~~ksVqIWFQNkR~~~k~~~~~ 112 (156)
T COG5576 50 PPKSKRRRTTDEQLMVLEREFEI---NPYPSSITRIKLSLLLNMPPKSVQIWFQNKRAKEKKKRSG 112 (156)
T ss_pred cCcccceechHHHHHHHHHHhcc---CCCCCHHHHHHHHHhcCCChhhhhhhhchHHHHHHHhccc
Confidence 35667778999999999999999 7999999999999999999999999999999999876653
No 23
>KOG0491 consensus Transcription factor BSH, contains HOX domain [General function prediction only]
Probab=98.38 E-value=1.6e-07 Score=84.55 Aligned_cols=58 Identities=19% Similarity=0.335 Sum_probs=52.8
Q ss_pred hhcCCCCCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhccc
Q 019151 258 RKRRAGKLPGDTTSLLKAWWLSHAKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWH 318 (345)
Q Consensus 258 kkrkr~~lpk~a~~~L~~wf~~h~~~PYPS~~eK~~LA~~TgLs~kQV~NWFiN~RkR~kk 318 (345)
++|.|..|+..+...|+.-|+. --|.+-.++.+||...+|+++||..||+|+|+++||
T Consensus 100 r~K~Rtvfs~~ql~~l~~rFe~---QrYLS~~e~~ELan~L~LS~~QVKTWFQNrRMK~Kk 157 (194)
T KOG0491|consen 100 RRKARTVFSDPQLSGLEKRFER---QRYLSTPERQELANALSLSETQVKTWFQNRRMKHKK 157 (194)
T ss_pred hhhhcccccCccccccHHHHhh---hhhcccHHHHHHHHHhhhhHHHHHHHHHHHHHHHHH
Confidence 3445668999999999999998 489999999999999999999999999999999986
No 24
>KOG0492 consensus Transcription factor MSH, contains HOX domain [General function prediction only]
Probab=98.23 E-value=6.8e-07 Score=83.15 Aligned_cols=65 Identities=15% Similarity=0.252 Sum_probs=57.3
Q ss_pred HHHHHHhhhcCCCCCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhccc
Q 019151 251 DIREEILRKRRAGKLPGDTTSLLKAWWLSHAKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWH 318 (345)
Q Consensus 251 ~l~~e~~kkrkr~~lpk~a~~~L~~wf~~h~~~PYPS~~eK~~LA~~TgLs~kQV~NWFiN~RkR~kk 318 (345)
.||+....++.|..|+..+...|++=|.+ -.|.+.+|+..++..+.|+..||..||+|+|.|.|+
T Consensus 137 ~LrKhk~nRkPRtPFTtqQLlaLErkfre---kqYLSiaEraefSsSL~LTeTqVKIWFQNRRAKaKR 201 (246)
T KOG0492|consen 137 TLRKHKPNRKPRTPFTTQQLLALERKFRE---KQYLSIAERAEFSSSLELTETQVKIWFQNRRAKAKR 201 (246)
T ss_pred hhcccCCCCCCCCCCCHHHHHHHHHHHhH---hhhhhHHHHHhhhhhhhhhhhheehhhhhhhHHHHH
Confidence 45555555666778999999999999999 599999999999999999999999999999999775
No 25
>KOG2251 consensus Homeobox transcription factor [Transcription]
Probab=98.15 E-value=1.8e-06 Score=80.78 Aligned_cols=58 Identities=19% Similarity=0.342 Sum_probs=53.3
Q ss_pred hcCCCCCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhcccC
Q 019151 259 KRRAGKLPGDTTSLLKAWWLSHAKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHA 319 (345)
Q Consensus 259 krkr~~lpk~a~~~L~~wf~~h~~~PYPS~~eK~~LA~~TgLs~kQV~NWFiN~RkR~kk~ 319 (345)
+|-|+.|+..+..+|+..|.+ .-||+...+++||.+.+|...+|.+||.|+|.+.++.
T Consensus 38 RRERTtFtr~QlevLe~LF~k---TqYPDv~~rEelAlklnLpeSrVqVWFKNRRAK~r~q 95 (228)
T KOG2251|consen 38 RRERTTFTRKQLEVLEALFAK---TQYPDVFMREELALKLNLPESRVQVWFKNRRAKCRRQ 95 (228)
T ss_pred ccccceecHHHHHHHHHHHHh---hcCccHHHHHHHHHHhCCchhhhhhhhccccchhhHh
Confidence 455789999999999999999 7999999999999999999999999999999886643
No 26
>KOG0484 consensus Transcription factor PHOX2/ARIX, contains HOX domain [Transcription]
Probab=98.12 E-value=1.7e-06 Score=72.92 Aligned_cols=61 Identities=15% Similarity=0.247 Sum_probs=54.4
Q ss_pred HhhhcCCCCCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhcccC
Q 019151 256 ILRKRRAGKLPGDTTSLLKAWWLSHAKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHA 319 (345)
Q Consensus 256 ~~kkrkr~~lpk~a~~~L~~wf~~h~~~PYPS~~eK~~LA~~TgLs~kQV~NWFiN~RkR~kk~ 319 (345)
.+.+|=|..|+..+..-|+..|.+ ..||..=.|+.||.+..|+...|.+||+|+|.+.+|.
T Consensus 15 rKQRRIRTTFTS~QLkELErvF~E---THYPDIYTREEiA~kidLTEARVQVWFQNRRAKfRKQ 75 (125)
T KOG0484|consen 15 RKQRRIRTTFTSAQLKELERVFAE---THYPDIYTREEIALKIDLTEARVQVWFQNRRAKFRKQ 75 (125)
T ss_pred HHhhhhhhhhhHHHHHHHHHHHHh---hcCCcchhHHHHHHhhhhhHHHHHHHHHhhHHHHHHH
Confidence 334445679999999999999999 6999999999999999999999999999999998764
No 27
>KOG0848 consensus Transcription factor Caudal, contains HOX domain [Transcription]
Probab=98.12 E-value=7.6e-07 Score=85.48 Aligned_cols=56 Identities=23% Similarity=0.306 Sum_probs=50.7
Q ss_pred CCCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhcccCCC
Q 019151 263 GKLPGDTTSLLKAWWLSHAKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHANP 321 (345)
Q Consensus 263 ~~lpk~a~~~L~~wf~~h~~~PYPS~~eK~~LA~~TgLs~kQV~NWFiN~RkR~kk~~~ 321 (345)
--++..+|-.|+.-|.- .+|.|...|.+||..+||++.||..||+|+|.+.+|-+.
T Consensus 204 vVYTDhQRLELEKEfh~---SryITirRKSELA~~LgLsERQVKIWFQNRRAKERK~nK 259 (317)
T KOG0848|consen 204 VVYTDHQRLELEKEFHT---SRYITIRRKSELAATLGLSERQVKIWFQNRRAKERKDNK 259 (317)
T ss_pred EEecchhhhhhhhhhcc---ccceeeehhHHHHHhhCccHhhhhHhhhhhhHHHHHHHH
Confidence 35788999999999988 799999999999999999999999999999999886543
No 28
>KOG0494 consensus Transcription factor CHX10 and related HOX domain proteins [General function prediction only]
Probab=98.07 E-value=3.2e-06 Score=80.97 Aligned_cols=55 Identities=20% Similarity=0.261 Sum_probs=51.3
Q ss_pred CCCCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhcccC
Q 019151 262 AGKLPGDTTSLLKAWWLSHAKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHA 319 (345)
Q Consensus 262 r~~lpk~a~~~L~~wf~~h~~~PYPS~~eK~~LA~~TgLs~kQV~NWFiN~RkR~kk~ 319 (345)
|+.|+..+...|+.-|.+ --||.--.|+.||.+|+|....|.+||+|+|.+.+|.
T Consensus 145 RTiFT~~Qle~LEkaFke---aHYPDv~Are~la~ktelpEDRIqVWfQNRRAKWRk~ 199 (332)
T KOG0494|consen 145 RTIFTSYQLEELEKAFKE---AHYPDVYAREMLADKTELPEDRIQVWFQNRRAKWRKT 199 (332)
T ss_pred cchhhHHHHHHHHHHHhh---ccCccHHHHHHHhhhccCchhhhhHHhhhhhHHhhhh
Confidence 568999999999999999 5999999999999999999999999999999987654
No 29
>KOG4577 consensus Transcription factor LIM3, contains LIM and HOX domains [Transcription]
Probab=98.05 E-value=2.5e-06 Score=82.81 Aligned_cols=66 Identities=23% Similarity=0.423 Sum_probs=58.3
Q ss_pred HHHHHhhhcCCCCCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhcccCC
Q 019151 252 IREEILRKRRAGKLPGDTTSLLKAWWLSHAKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHAN 320 (345)
Q Consensus 252 l~~e~~kkrkr~~lpk~a~~~L~~wf~~h~~~PYPS~~eK~~LA~~TgLs~kQV~NWFiN~RkR~kk~~ 320 (345)
|--+-..||.|++++.++...|+.-|.. .|-|..--|++|+..|||+...|++||+|+|.+.|+-.
T Consensus 161 l~gd~~nKRPRTTItAKqLETLK~AYn~---SpKPARHVREQLsseTGLDMRVVQVWFQNRRAKEKRLK 226 (383)
T KOG4577|consen 161 LEGDASNKRPRTTITAKQLETLKQAYNT---SPKPARHVREQLSSETGLDMRVVQVWFQNRRAKEKRLK 226 (383)
T ss_pred cccccccCCCcceeeHHHHHHHHHHhcC---CCchhHHHHHHhhhccCcceeehhhhhhhhhHHHHhhh
Confidence 3345567888999999999999999887 79999999999999999999999999999998876533
No 30
>KOG0486 consensus Transcription factor PTX1, contains HOX domain [Transcription]
Probab=98.02 E-value=2.6e-06 Score=83.37 Aligned_cols=59 Identities=19% Similarity=0.298 Sum_probs=53.5
Q ss_pred cCCCCCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhcccCCC
Q 019151 260 RRAGKLPGDTTSLLKAWWLSHAKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHANP 321 (345)
Q Consensus 260 rkr~~lpk~a~~~L~~wf~~h~~~PYPS~~eK~~LA~~TgLs~kQV~NWFiN~RkR~kk~~~ 321 (345)
|-|.-|+..+.+-|+.||+. |-||+.+.|+.||--|+|+...|.+||.|+|.+.+|+..
T Consensus 114 rQrthFtSqqlqele~tF~r---NrypdMstrEEIavwtNlTE~rvrvwfknrrakwrkrEr 172 (351)
T KOG0486|consen 114 RQRTHFTSQQLQELEATFQR---NRYPDMSTREEIAVWTNLTEARVRVWFKNRRAKWRKRER 172 (351)
T ss_pred hhhhhhHHHHHHHHHHHHhh---ccCCccchhhHHHhhccccchhhhhhcccchhhhhhhhh
Confidence 33557999999999999999 799999999999999999999999999999998876544
No 31
>KOG2252 consensus CCAAT displacement protein and related homeoproteins [Transcription]
Probab=97.90 E-value=2.7e-05 Score=81.00 Aligned_cols=56 Identities=23% Similarity=0.339 Sum_probs=52.0
Q ss_pred hcCCCCCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhcc
Q 019151 259 KRRAGKLPGDTTSLLKAWWLSHAKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNW 317 (345)
Q Consensus 259 krkr~~lpk~a~~~L~~wf~~h~~~PYPS~~eK~~LA~~TgLs~kQV~NWFiN~RkR~k 317 (345)
||.|-.|+..+++.|...|.+ ++||+.+.-+.|+.++||...-|.|||-|+|+|.+
T Consensus 421 KKPRlVfTd~QkrTL~aiFke---~~RPS~Emq~tIS~qL~L~~sTV~NfFmNaRRRsl 476 (558)
T KOG2252|consen 421 KKPRLVFTDIQKRTLQAIFKE---NKRPSREMQETISQQLNLELSTVINFFMNARRRSL 476 (558)
T ss_pred CCceeeecHHHHHHHHHHHhc---CCCCCHHHHHHHHHHhCCcHHHHHHHHHhhhhhcc
Confidence 555668999999999999999 79999999999999999999999999999999943
No 32
>KOG1168 consensus Transcription factor ACJ6/BRN-3, contains POU and HOX domains [Transcription]
Probab=97.79 E-value=5.8e-06 Score=80.32 Aligned_cols=69 Identities=22% Similarity=0.380 Sum_probs=60.6
Q ss_pred HhhhcCCCCCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhcccCCCCCCccc
Q 019151 256 ILRKRRAGKLPGDTTSLLKAWWLSHAKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHANPSSSTAS 327 (345)
Q Consensus 256 ~~kkrkr~~lpk~a~~~L~~wf~~h~~~PYPS~~eK~~LA~~TgLs~kQV~NWFiN~RkR~kk~~~s~~~~~ 327 (345)
--|||||+.+-..-++-|+.+|.. -|-|+-+-...+|+++.|....|.+||+|+|.+.|+...|...++
T Consensus 307 ~ekKRKRTSIAAPEKRsLEayFav---QPRPS~EkIAaIAekLDLKKNVVRVWFCNQRQKQKRm~~Sa~~~m 375 (385)
T KOG1168|consen 307 GEKKRKRTSIAAPEKRSLEAYFAV---QPRPSGEKIAAIAEKLDLKKNVVRVWFCNQRQKQKRMKRSATAVM 375 (385)
T ss_pred cccccccccccCcccccHHHHhcc---CCCCchhHHHHHHHhhhhhhceEEEEeeccHHHHHHhhhhhceee
Confidence 347888888877788999999998 699999999999999999999999999999999998766666555
No 33
>KOG0847 consensus Transcription factor, contains HOX domain [Transcription]
Probab=97.75 E-value=1.7e-05 Score=74.58 Aligned_cols=61 Identities=25% Similarity=0.380 Sum_probs=54.4
Q ss_pred hhcCCCCCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhcccCCC
Q 019151 258 RKRRAGKLPGDTTSLLKAWWLSHAKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHANP 321 (345)
Q Consensus 258 kkrkr~~lpk~a~~~L~~wf~~h~~~PYPS~~eK~~LA~~TgLs~kQV~NWFiN~RkR~kk~~~ 321 (345)
+|..+.+|+..++..|+.-|.+ ..||--.++.+||...|++..||.+||+|+|.+.+|...
T Consensus 167 rk~srPTf~g~qi~~le~~feq---tkylaG~~ra~lA~~lgmteSqvkVWFQNRRTKWRKkhA 227 (288)
T KOG0847|consen 167 RKQSRPTFTGHQIYQLERKFEQ---TKYLAGADRAQLAQELNMTESQVKVWFQNRRTKWRKKHA 227 (288)
T ss_pred ccccCCCccchhhhhhhhhhhh---hhcccchhHHHhhccccccHHHHHHHHhcchhhhhhhhc
Confidence 4445668999999999999999 699999999999999999999999999999998877654
No 34
>KOG0844 consensus Transcription factor EVX1, contains HOX domain [Transcription]
Probab=97.58 E-value=2.6e-05 Score=76.30 Aligned_cols=54 Identities=17% Similarity=0.286 Sum_probs=49.1
Q ss_pred CCCCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhccc
Q 019151 262 AGKLPGDTTSLLKAWWLSHAKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWH 318 (345)
Q Consensus 262 r~~lpk~a~~~L~~wf~~h~~~PYPS~~eK~~LA~~TgLs~kQV~NWFiN~RkR~kk 318 (345)
|+-|+.+++-.|+.-|++ --|-+.-.|.+||..++|....|.+||||+|++.|+
T Consensus 185 RTAFTReQIaRLEKEFyr---ENYVSRprRcELAAaLNLPEtTIKVWFQNRRMKDKR 238 (408)
T KOG0844|consen 185 RTAFTREQIARLEKEFYR---ENYVSRPRRCELAAALNLPETTIKVWFQNRRMKDKR 238 (408)
T ss_pred HhhhhHHHHHHHHHHHHH---hccccCchhhhHHHhhCCCcceeehhhhhchhhhhh
Confidence 467999999999887777 489999999999999999999999999999999885
No 35
>KOG0490 consensus Transcription factor, contains HOX domain [General function prediction only]
Probab=97.53 E-value=3.8e-05 Score=70.05 Aligned_cols=62 Identities=13% Similarity=0.109 Sum_probs=56.4
Q ss_pred HhhhcCCCCCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhcccCC
Q 019151 256 ILRKRRAGKLPGDTTSLLKAWWLSHAKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHAN 320 (345)
Q Consensus 256 ~~kkrkr~~lpk~a~~~L~~wf~~h~~~PYPS~~eK~~LA~~TgLs~kQV~NWFiN~RkR~kk~~ 320 (345)
+.++|.+.+|+..+.+.|+.-|.. .+||.-..++.||..++++...|.+||+|+|.++++..
T Consensus 58 ~~~rr~rt~~~~~ql~~ler~f~~---~h~Pd~~~r~~la~~~~~~e~rVqvwFqnrrak~r~~~ 119 (235)
T KOG0490|consen 58 FSKRCARCKFTISQLDELERAFEK---VHLPCFACRECLALLLTGDEFRVQVWFQNRRAKDRKEE 119 (235)
T ss_pred ccccccCCCCCcCHHHHHHHhhcC---CCcCccchHHHHhhcCCCCeeeeehhhhhhcHhhhhhh
Confidence 446677789999999999999999 59999999999999999999999999999999988755
No 36
>KOG0849 consensus Transcription factor PRD and related proteins, contain PAX and HOX domains [Transcription]
Probab=97.41 E-value=0.00018 Score=72.03 Aligned_cols=60 Identities=23% Similarity=0.432 Sum_probs=54.4
Q ss_pred hcCCCCCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhcccCCC
Q 019151 259 KRRAGKLPGDTTSLLKAWWLSHAKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHANP 321 (345)
Q Consensus 259 krkr~~lpk~a~~~L~~wf~~h~~~PYPS~~eK~~LA~~TgLs~kQV~NWFiN~RkR~kk~~~ 321 (345)
+|.|..|+..+...|..+|.. +|||.-..++.||.++||....|..||.|+|.|.++...
T Consensus 177 rr~rtsft~~Q~~~le~~f~r---t~yP~i~~Re~La~~i~l~e~riqvwf~nrra~~rr~~~ 236 (354)
T KOG0849|consen 177 RRNRTSFSPSQLEALEECFQR---TPYPDIVGRETLAKETGLPEPRVQVWFQNRRAKWRRQHR 236 (354)
T ss_pred cccccccccchHHHHHHHhcC---CCCCchhhHHHHhhhccCCchHHHHHHhhhhhhhhhccc
Confidence 344578999999999999999 689999999999999999999999999999998887663
No 37
>KOG0773 consensus Transcription factor MEIS1 and related HOX domain proteins [Transcription]
Probab=97.36 E-value=0.0001 Score=72.36 Aligned_cols=68 Identities=31% Similarity=0.489 Sum_probs=60.8
Q ss_pred hhcCCCCCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhcccCCCCCCcc
Q 019151 258 RKRRAGKLPGDTTSLLKAWWLSHAKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHANPSSSTA 326 (345)
Q Consensus 258 kkrkr~~lpk~a~~~L~~wf~~h~~~PYPS~~eK~~LA~~TgLs~kQV~NWFiN~RkR~kk~~~s~~~~ 326 (345)
..+++++.+.+. ..|+.|...|..+|||++-++..|+-.++++..||++||+|.|+|.++.+......
T Consensus 95 ~~~~~~n~~~~s-~~~~~~~~~~~~~~~~~k~~~~ll~~~~~~~~~~~~~~~~~a~r~~~~~~~~~~~~ 162 (342)
T KOG0773|consen 95 KGARRGNATRES-ATLKAWLEEHRLNPYPSKLEKILLAVITKLTLTQVSTWFANARRRLKKELKMTWGP 162 (342)
T ss_pred cccccccccccc-cccccchhhhhhccCchHHHHHHHHHHHHhhhhhHHHHHHHHHHHHHhccCCCCCC
Confidence 345577899999 99999999999999999999999999999999999999999999999877754443
No 38
>PF11569 Homez: Homeodomain leucine-zipper encoding, Homez; PDB: 2YS9_A.
Probab=97.11 E-value=0.00046 Score=52.16 Aligned_cols=43 Identities=23% Similarity=0.529 Sum_probs=31.4
Q ss_pred HHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhh
Q 019151 270 TSLLKAWWLSHAKWPYPTEEDKARLVQETGLQLKQINNWFINQRKR 315 (345)
Q Consensus 270 ~~~L~~wf~~h~~~PYPS~~eK~~LA~~TgLs~kQV~NWFiN~RkR 315 (345)
++.|+.+|..| .++.+.+...|+.++||+..||.+||.-++.+
T Consensus 10 ~~pL~~Yy~~h---~~L~E~DL~~L~~kS~ms~qqVr~WFa~~~~e 52 (56)
T PF11569_consen 10 IQPLEDYYLKH---KQLQEEDLDELCDKSRMSYQQVRDWFAERMQE 52 (56)
T ss_dssp -HHHHHHHHHT-------TTHHHHHHHHTT--HHHHHHHHHHHS--
T ss_pred hHHHHHHHHHc---CCccHhhHHHHHHHHCCCHHHHHHHHHHhccc
Confidence 45699999995 99999999999999999999999999877543
No 39
>PF03789 ELK: ELK domain ; InterPro: IPR005539 This domain is required for the nuclear localisation of these proteins []. All of these proteins are members of the Tale/Knox homeodomain family, a subfamily, containing homeobox IPR001356 from INTERPRO.; GO: 0003677 DNA binding, 0005634 nucleus
Probab=97.03 E-value=0.00047 Score=42.86 Aligned_cols=22 Identities=41% Similarity=0.622 Sum_probs=20.5
Q ss_pred HHHHHHhhhhhHHHHHHHHHHh
Q 019151 236 ELKHELKQGYKEKIVDIREEIL 257 (345)
Q Consensus 236 eLk~~L~~~y~~~i~~l~~e~~ 257 (345)
|||.+|+++|+++|.+||+||+
T Consensus 1 ELK~~LlrkY~g~i~~Lr~Ef~ 22 (22)
T PF03789_consen 1 ELKHQLLRKYSGYISSLRQEFS 22 (22)
T ss_pred CHHHHHHHHHhHhHHHHHHHhC
Confidence 6899999999999999999984
No 40
>KOG0490 consensus Transcription factor, contains HOX domain [General function prediction only]
Probab=94.80 E-value=0.038 Score=50.35 Aligned_cols=60 Identities=25% Similarity=0.480 Sum_probs=51.7
Q ss_pred hcCCCCCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhcccCCC
Q 019151 259 KRRAGKLPGDTTSLLKAWWLSHAKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHANP 321 (345)
Q Consensus 259 krkr~~lpk~a~~~L~~wf~~h~~~PYPS~~eK~~LA~~TgLs~kQV~NWFiN~RkR~kk~~~ 321 (345)
++.+..+.......+..-|.. .+||....+..|+..+|++...|.+||+|+|.+.++...
T Consensus 154 ~~~~~~~~~~~~~~~~~~~~~---~~~P~~~~~~~l~~~~~~~~~~~q~~~~~~~~~~~~~~~ 213 (235)
T KOG0490|consen 154 RRPRTTFTENQLEVLETVFRA---TPKPDADDREQLAEETGLSERVIQVWFQNRRAKLRKHKR 213 (235)
T ss_pred CCCccccccchhHhhhhcccC---CCCCchhhHHHHHHhcCCChhhhhhhcccHHHHHHhhcc
Confidence 344557777788888887777 799999999999999999999999999999999987655
No 41
>KOG3623 consensus Homeobox transcription factor SIP1 [Transcription]
Probab=86.26 E-value=1.4 Score=48.36 Aligned_cols=52 Identities=31% Similarity=0.562 Sum_probs=46.8
Q ss_pred HHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhcccCCCCCC
Q 019151 270 TSLLKAWWLSHAKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHANPSSS 324 (345)
Q Consensus 270 ~~~L~~wf~~h~~~PYPS~~eK~~LA~~TgLs~kQV~NWFiN~RkR~kk~~~s~~ 324 (345)
+.+|+.+|.. |+.|++++...+|..-||...-|..||.+.+........+++
T Consensus 568 ~sllkayyal---n~~ps~eelskia~qvglp~~vvk~wfE~~~a~e~sv~rsps 619 (1007)
T KOG3623|consen 568 TSLLKAYYAL---NGLPSEEELSKIAQQVGLPFAVVKAWFEDEEAEEMSVERSPS 619 (1007)
T ss_pred HHHHHHHHHh---cCCCCHHHHHHHHHHhcccHHHHHHHHHhhhhhhhhhccCcc
Confidence 7788889888 799999999999999999999999999999998887665554
No 42
>KOG1146 consensus Homeobox protein [General function prediction only]
Probab=84.97 E-value=1.1 Score=51.77 Aligned_cols=61 Identities=23% Similarity=0.305 Sum_probs=53.1
Q ss_pred hhcCCCCCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhcccCCC
Q 019151 258 RKRRAGKLPGDTTSLLKAWWLSHAKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHANP 321 (345)
Q Consensus 258 kkrkr~~lpk~a~~~L~~wf~~h~~~PYPS~~eK~~LA~~TgLs~kQV~NWFiN~RkR~kk~~~ 321 (345)
+++.+..+...+..+++..|.. --||+.++-+.|.+..+|...-|..||+|.|.+.++..-
T Consensus 903 r~a~~~~~~d~qlk~i~~~~~~---q~~~~~~~~E~l~~~~~~~~~~i~vw~qna~~~s~k~~~ 963 (1406)
T KOG1146|consen 903 RRAYRTQESDLQLKIIKACYEA---QRTPTMQECEVLEEPIGLPKRVIQVWFQNARAKSKKAKL 963 (1406)
T ss_pred hhhhccchhHHHHHHHHHHHhh---ccCChHHHHHhhcccccCCcchhHHhhhhhhhhhhhhhh
Confidence 3445567888889999999988 689999999999999999999999999999999887543
No 43
>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=82.68 E-value=2.6 Score=31.04 Aligned_cols=47 Identities=15% Similarity=0.163 Sum_probs=31.1
Q ss_pred hcCCCCCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhh
Q 019151 259 KRRAGKLPGDTTSLLKAWWLSHAKWPYPTEEDKARLVQETGLQLKQINNWFINQR 313 (345)
Q Consensus 259 krkr~~lpk~a~~~L~~wf~~h~~~PYPS~~eK~~LA~~TgLs~kQV~NWFiN~R 313 (345)
||+|..|+-+..-.+-.-+... + -...||+.+|++..+|.+|..|+.
T Consensus 1 krkR~~LTl~eK~~iI~~~e~g---~-----s~~~ia~~fgv~~sTv~~I~K~k~ 47 (53)
T PF04218_consen 1 KRKRKSLTLEEKLEIIKRLEEG---E-----SKRDIAREFGVSRSTVSTILKNKD 47 (53)
T ss_dssp SSSSSS--HHHHHHHHHHHHCT---T------HHHHHHHHT--CCHHHHHHHCHH
T ss_pred CCCCccCCHHHHHHHHHHHHcC---C-----CHHHHHHHhCCCHHHHHHHHHhHH
Confidence 4566678777755555555552 2 578999999999999999999864
No 44
>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=71.76 E-value=5.7 Score=30.00 Aligned_cols=45 Identities=16% Similarity=0.214 Sum_probs=30.1
Q ss_pred CCCCCChhHHHHHHHHH-HHccCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhh
Q 019151 261 RAGKLPGDTTSLLKAWW-LSHAKWPYPTEEDKARLVQETGLQLKQINNWFINQR 313 (345)
Q Consensus 261 kr~~lpk~a~~~L~~wf-~~h~~~PYPS~~eK~~LA~~TgLs~kQV~NWFiN~R 313 (345)
+++.||.+.+..+-.-. .. ......+|+..|+++.+|.+|-.-.+
T Consensus 3 ~r~~ys~e~K~~~v~~~~~~--------g~sv~~va~~~gi~~~~l~~W~~~~~ 48 (76)
T PF01527_consen 3 KRRRYSPEFKLQAVREYLES--------GESVSEVAREYGISPSTLYNWRKQYR 48 (76)
T ss_dssp SS----HHHHHHHHHHHHHH--------HCHHHHHHHHHTS-HHHHHHHHHHHH
T ss_pred CCCCCCHHHHHHHHHHHHHC--------CCceEeeecccccccccccHHHHHHh
Confidence 45678888865554333 33 36678999999999999999987777
No 45
>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=70.00 E-value=13 Score=22.15 Aligned_cols=40 Identities=10% Similarity=0.155 Sum_probs=28.2
Q ss_pred CCCCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhhhhhh
Q 019151 262 AGKLPGDTTSLLKAWWLSHAKWPYPTEEDKARLVQETGLQLKQINNWF 309 (345)
Q Consensus 262 r~~lpk~a~~~L~~wf~~h~~~PYPS~~eK~~LA~~TgLs~kQV~NWF 309 (345)
+..++.+.+..+...+.. ++ ....+|+.+|++...|.+|.
T Consensus 3 ~~~~~~~~~~~i~~~~~~----~~----s~~~ia~~~~is~~tv~~~~ 42 (42)
T cd00569 3 PPKLTPEQIEEARRLLAA----GE----SVAEIARRLGVSRSTLYRYL 42 (42)
T ss_pred CCcCCHHHHHHHHHHHHc----CC----CHHHHHHHHCCCHHHHHHhC
Confidence 345666666666666543 33 34578899999999999985
No 46
>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=63.69 E-value=14 Score=24.75 Aligned_cols=46 Identities=11% Similarity=0.145 Sum_probs=34.8
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhcc
Q 019151 264 KLPGDTTSLLKAWWLSHAKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNW 317 (345)
Q Consensus 264 ~lpk~a~~~L~~wf~~h~~~PYPS~~eK~~LA~~TgLs~kQV~NWFiN~RkR~k 317 (345)
.++...+.++...+... + .-..+|+.+|++...|..|....+.+.+
T Consensus 10 ~l~~~~~~~~~~~~~~~----~----~~~~ia~~~~~s~~~i~~~~~~~~~~l~ 55 (55)
T cd06171 10 KLPEREREVILLRFGEG----L----SYEEIAEILGISRSTVRQRLHRALKKLR 55 (55)
T ss_pred hCCHHHHHHHHHHHhcC----C----CHHHHHHHHCcCHHHHHHHHHHHHHHcC
Confidence 46777788887766442 2 2457899999999999999988877653
No 47
>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=59.01 E-value=17 Score=25.83 Aligned_cols=44 Identities=14% Similarity=0.291 Sum_probs=32.5
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhh
Q 019151 264 KLPGDTTSLLKAWWLSHAKWPYPTEEDKARLVQETGLQLKQINNWFINQRKR 315 (345)
Q Consensus 264 ~lpk~a~~~L~~wf~~h~~~PYPS~~eK~~LA~~TgLs~kQV~NWFiN~RkR 315 (345)
.+|+..+.++.-.+... + .-..+|+.+|++...|.+|....|++
T Consensus 10 ~L~~~~r~i~~l~~~~g----~----s~~eIa~~l~~s~~~v~~~l~ra~~~ 53 (54)
T PF08281_consen 10 QLPERQREIFLLRYFQG----M----SYAEIAEILGISESTVKRRLRRARKK 53 (54)
T ss_dssp CS-HHHHHHHHHHHTS-----------HHHHHHHCTS-HHHHHHHHHHHHHH
T ss_pred CCCHHHHHHHHHHHHHC----c----CHHHHHHHHCcCHHHHHHHHHHHHhh
Confidence 57888888887665553 2 34589999999999999999998876
No 48
>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=52.26 E-value=21 Score=25.17 Aligned_cols=46 Identities=9% Similarity=0.225 Sum_probs=35.9
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhcc
Q 019151 264 KLPGDTTSLLKAWWLSHAKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNW 317 (345)
Q Consensus 264 ~lpk~a~~~L~~wf~~h~~~PYPS~~eK~~LA~~TgLs~kQV~NWFiN~RkR~k 317 (345)
.||+..+.+|...|.. ++ .-..+|+..|++...|..+.....++.+
T Consensus 4 ~L~~~er~vi~~~y~~----~~----t~~eIa~~lg~s~~~V~~~~~~al~kLR 49 (50)
T PF04545_consen 4 QLPPREREVIRLRYFE----GL----TLEEIAERLGISRSTVRRILKRALKKLR 49 (50)
T ss_dssp TS-HHHHHHHHHHHTS----T-----SHHHHHHHHTSCHHHHHHHHHHHHHHHH
T ss_pred hCCHHHHHHHHHHhcC----CC----CHHHHHHHHCCcHHHHHHHHHHHHHHhc
Confidence 5788888998877744 32 2457999999999999999998888765
No 49
>PRK06759 RNA polymerase factor sigma-70; Validated
Probab=50.64 E-value=21 Score=30.15 Aligned_cols=47 Identities=9% Similarity=0.071 Sum_probs=37.7
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhccc
Q 019151 264 KLPGDTTSLLKAWWLSHAKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWH 318 (345)
Q Consensus 264 ~lpk~a~~~L~~wf~~h~~~PYPS~~eK~~LA~~TgLs~kQV~NWFiN~RkR~kk 318 (345)
.||+..+.++...|... .+ -..+|+.+|++...|.+|....|++.++
T Consensus 106 ~L~~~~r~ii~l~~~~~--~s------~~EIA~~l~is~~tV~~~~~ra~~~Lr~ 152 (154)
T PRK06759 106 VLDEKEKYIIFERFFVG--KT------MGEIALETEMTYYQVRWIYRQALEKMRN 152 (154)
T ss_pred hCCHHHHHHHHHHHhcC--CC------HHHHHHHHCCCHHHHHHHHHHHHHHHhh
Confidence 68888999886655552 12 4579999999999999999999998875
No 50
>PRK12533 RNA polymerase sigma factor; Provisional
Probab=46.82 E-value=26 Score=32.43 Aligned_cols=63 Identities=16% Similarity=0.149 Sum_probs=47.4
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhcccCCCCCCcccccccccc
Q 019151 264 KLPGDTTSLLKAWWLSHAKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHANPSSSTASKSKRKSW 334 (345)
Q Consensus 264 ~lpk~a~~~L~~wf~~h~~~PYPS~~eK~~LA~~TgLs~kQV~NWFiN~RkR~kk~~~s~~~~~~~~~k~~ 334 (345)
.||...+.++.-.+..+ .+| ..+|+.+|++...|.++....|++.++.....+..--.+..+-
T Consensus 134 ~Lp~~~R~v~~L~y~eg--~s~------~EIAe~LgiS~~tVk~~L~RAr~~Lr~~l~~~~~~~~~~~~~~ 196 (216)
T PRK12533 134 KLPVEYREVLVLRELED--MSY------REIAAIADVPVGTVMSRLARARRRLAALLGGASAAQAAPGERA 196 (216)
T ss_pred cCCHHHHhHhhhHHhcC--CCH------HHHHHHHCCCHHHHHHHHHHHHHHHHHHHcccchhhcCCcccc
Confidence 68888999998877664 222 4789999999999999999999999987665554444444333
No 51
>PF13443 HTH_26: Cro/C1-type HTH DNA-binding domain; PDB: 3TYR_A 3TYS_A 3B7H_A.
Probab=44.54 E-value=18 Score=26.28 Aligned_cols=23 Identities=13% Similarity=0.304 Sum_probs=18.1
Q ss_pred HHHHHHHHhCCChhhhhhhhhhh
Q 019151 290 DKARLVQETGLQLKQINNWFINQ 312 (345)
Q Consensus 290 eK~~LA~~TgLs~kQV~NWFiN~ 312 (345)
....||+.+|++..+|+.|+.+.
T Consensus 12 t~~~La~~~gis~~tl~~~~~~~ 34 (63)
T PF13443_consen 12 TQKDLARKTGISRSTLSRILNGK 34 (63)
T ss_dssp -HHHHHHHHT--HHHHHHHHTTT
T ss_pred CHHHHHHHHCcCHHHHHHHHhcc
Confidence 35689999999999999999976
No 52
>PRK09642 RNA polymerase sigma factor SigW; Reviewed
Probab=43.96 E-value=28 Score=29.66 Aligned_cols=48 Identities=17% Similarity=0.280 Sum_probs=38.5
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhcccC
Q 019151 264 KLPGDTTSLLKAWWLSHAKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHA 319 (345)
Q Consensus 264 ~lpk~a~~~L~~wf~~h~~~PYPS~~eK~~LA~~TgLs~kQV~NWFiN~RkR~kk~ 319 (345)
+||+..+.++.-.+... .+| ..+|+.+|++...|.+.+.-.|++.++.
T Consensus 106 ~Lp~~~r~v~~l~~~~g--~s~------~EIA~~lgis~~tV~~~l~Rar~~Lr~~ 153 (160)
T PRK09642 106 ELPENYRDVVLAHYLEE--KSY------QEIALQEKIEVKTVEMKLYRARKWIKKH 153 (160)
T ss_pred hCCHHHHHHHHHHHHhC--CCH------HHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 48999999987666553 222 4799999999999999999999988764
No 53
>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=43.46 E-value=36 Score=27.41 Aligned_cols=47 Identities=17% Similarity=0.284 Sum_probs=35.9
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhccc
Q 019151 264 KLPGDTTSLLKAWWLSHAKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWH 318 (345)
Q Consensus 264 ~lpk~a~~~L~~wf~~h~~~PYPS~~eK~~LA~~TgLs~kQV~NWFiN~RkR~kk 318 (345)
.||+..+.++...+.. .++ -..+|+.+|+++..|.+|....+++.++
T Consensus 110 ~L~~~~~~ii~~~~~~----g~s----~~eIA~~l~~s~~~v~~~~~~~~~kl~~ 156 (158)
T TIGR02937 110 KLPEREREVLVLRYLE----GLS----YKEIAEILGISVGTVKRRLKRARKKLRE 156 (158)
T ss_pred hCCHHHHHHHhhHHhc----CCC----HHHHHHHHCCCHHHHHHHHHHHHHHHHh
Confidence 4677777777544333 332 3489999999999999999999988775
No 54
>PF13518 HTH_28: Helix-turn-helix domain
Probab=40.83 E-value=29 Score=24.07 Aligned_cols=24 Identities=17% Similarity=0.432 Sum_probs=20.8
Q ss_pred HHHHHHHhCCChhhhhhhhhhhhh
Q 019151 291 KARLVQETGLQLKQINNWFINQRK 314 (345)
Q Consensus 291 K~~LA~~TgLs~kQV~NWFiN~Rk 314 (345)
...+|..+|++..+|.+|....+.
T Consensus 15 ~~~~a~~~gis~~tv~~w~~~y~~ 38 (52)
T PF13518_consen 15 VREIAREFGISRSTVYRWIKRYRE 38 (52)
T ss_pred HHHHHHHHCCCHhHHHHHHHHHHh
Confidence 446999999999999999987765
No 55
>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=39.79 E-value=52 Score=27.38 Aligned_cols=47 Identities=15% Similarity=0.203 Sum_probs=37.0
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhccc
Q 019151 264 KLPGDTTSLLKAWWLSHAKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWH 318 (345)
Q Consensus 264 ~lpk~a~~~L~~wf~~h~~~PYPS~~eK~~LA~~TgLs~kQV~NWFiN~RkR~kk 318 (345)
.||...+.++.-.+.. .++- ..+|+.+|++...|.++....|++.++
T Consensus 113 ~L~~~~r~il~l~~~~----~~~~----~eIA~~lgis~~tv~~~~~ra~~~Lr~ 159 (161)
T TIGR02985 113 KLPEQCRKIFILSRFE----GKSY----KEIAEELGISVKTVEYHISKALKELRK 159 (161)
T ss_pred HCCHHHHHHHHHHHHc----CCCH----HHHHHHHCCCHHHHHHHHHHHHHHHHh
Confidence 5788888888765544 3332 358999999999999999999998875
No 56
>PF11288 DUF3089: Protein of unknown function (DUF3089); InterPro: IPR021440 This family of proteins has no known function.
Probab=39.50 E-value=8 Score=36.41 Aligned_cols=38 Identities=34% Similarity=0.468 Sum_probs=30.4
Q ss_pred CCCCCcchhhhhhHHHHHHHhhCCChHHHHHHHHhhhcccCCCc
Q 019151 58 ASNDNGRAEDWETVKCKAEIVGHPLYEQLLSAHVSCLRIATPVD 101 (345)
Q Consensus 58 ~~~~~~~~~~~e~~~lKakI~sHPlYp~Ll~A~idC~KVGaP~e 101 (345)
+||+-|...- ...||..|..||++.+||.||+ ||.|.-
T Consensus 100 aGHSQGs~~l--~~LL~e~~~~~pl~~rLVAAYl----iG~~v~ 137 (207)
T PF11288_consen 100 AGHSQGSMHL--LRLLKEEIAGDPLRKRLVAAYL----IGYPVT 137 (207)
T ss_pred EEeChHHHHH--HHHHHHHhcCchHHhhhheeee----cCcccc
Confidence 5566666553 3589999999999999999999 887743
No 57
>PRK11924 RNA polymerase sigma factor; Provisional
Probab=38.57 E-value=33 Score=29.20 Aligned_cols=48 Identities=8% Similarity=0.160 Sum_probs=37.3
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhcccC
Q 019151 264 KLPGDTTSLLKAWWLSHAKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHA 319 (345)
Q Consensus 264 ~lpk~a~~~L~~wf~~h~~~PYPS~~eK~~LA~~TgLs~kQV~NWFiN~RkR~kk~ 319 (345)
.||+..+.++...+.. .+ .-..+|+..|++...|.+|..-.|++.++.
T Consensus 125 ~L~~~~r~i~~l~~~~----~~----~~~eIA~~lgis~~tv~~~~~ra~~~lr~~ 172 (179)
T PRK11924 125 ALPVKQREVFLLRYVE----GL----SYREIAEILGVPVGTVKSRLRRARQLLREC 172 (179)
T ss_pred hCCHHHHHHhhHHHHc----CC----CHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 4777788887665544 22 235899999999999999999999998753
No 58
>PRK09646 RNA polymerase sigma factor SigK; Reviewed
Probab=38.55 E-value=34 Score=30.43 Aligned_cols=50 Identities=6% Similarity=0.016 Sum_probs=39.9
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhcccCCC
Q 019151 264 KLPGDTTSLLKAWWLSHAKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHANP 321 (345)
Q Consensus 264 ~lpk~a~~~L~~wf~~h~~~PYPS~~eK~~LA~~TgLs~kQV~NWFiN~RkR~kk~~~ 321 (345)
.||+..+.+|.-.+... .+ -..+|+.+|++...|.+++...|++.++...
T Consensus 142 ~L~~~~r~vl~l~~~~~--~s------~~EIA~~Lgis~~tVk~~l~ra~~~Lr~~l~ 191 (194)
T PRK09646 142 ALTDTQRESVTLAYYGG--LT------YREVAERLAVPLGTVKTRMRDGLIRLRDCLG 191 (194)
T ss_pred hCCHHHHHHHHHHHHcC--CC------HHHHHHHhCCChHhHHHHHHHHHHHHHHHhc
Confidence 58888999887665553 22 3579999999999999999999999887653
No 59
>KOG4040 consensus NADH:ubiquinone oxidoreductase, NDUFB8/ASHI subunit [Energy production and conversion]
Probab=38.06 E-value=20 Score=32.88 Aligned_cols=41 Identities=24% Similarity=0.529 Sum_probs=32.4
Q ss_pred CCChhHHHHHHHHHHHccCCCCCC-HHHHHHHHHHhCCChhh
Q 019151 264 KLPGDTTSLLKAWWLSHAKWPYPT-EEDKARLVQETGLQLKQ 304 (345)
Q Consensus 264 ~lpk~a~~~L~~wf~~h~~~PYPS-~~eK~~LA~~TgLs~kQ 304 (345)
+.........-.|...|.-.|||+ ++||.+-|++.||-+..
T Consensus 20 ~v~~~g~rt~~gw~kD~kPgpyP~teeER~AAAkKY~lrpEd 61 (186)
T KOG4040|consen 20 NVMPRGPRTFDGWYKDHKPGPYPTTEEERRAAAKKYGLRPED 61 (186)
T ss_pred cccccccccccccccccCCCCCCCCHHHHHHHHHHhCCCHhh
Confidence 444555666778999999999995 78899999999987764
No 60
>PRK09652 RNA polymerase sigma factor RpoE; Provisional
Probab=38.03 E-value=36 Score=29.04 Aligned_cols=48 Identities=8% Similarity=0.145 Sum_probs=37.3
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhcccC
Q 019151 264 KLPGDTTSLLKAWWLSHAKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHA 319 (345)
Q Consensus 264 ~lpk~a~~~L~~wf~~h~~~PYPS~~eK~~LA~~TgLs~kQV~NWFiN~RkR~kk~ 319 (345)
.||+..+.++.-.+.. .++ -..+|+.+|++...|.+|....|++.++.
T Consensus 128 ~L~~~~r~vl~l~~~~----~~s----~~eIA~~lgis~~tV~~~l~ra~~~Lr~~ 175 (182)
T PRK09652 128 SLPEELRTAITLREIE----GLS----YEEIAEIMGCPIGTVRSRIFRAREALRAK 175 (182)
T ss_pred hCCHHHHHHHHHHHHc----CCC----HHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 5788888888665444 222 24789999999999999999999988764
No 61
>KOG2070 consensus Guanine nucleotide exchange factor [Nucleotide transport and metabolism]
Probab=37.45 E-value=63 Score=34.66 Aligned_cols=26 Identities=12% Similarity=0.222 Sum_probs=14.6
Q ss_pred CCChHHHHHHHHHH-------HHHHHHHHHHhH
Q 019151 129 LDDKELDQFMTHYV-------LLLYSFKEQLQQ 154 (345)
Q Consensus 129 g~dpELDqFMeaYc-------~vL~kykEEL~k 154 (345)
..-|++.-..-+|| .||.+|++||++
T Consensus 182 n~ap~mkt~~~aYcanHP~AV~VL~k~~dELek 214 (661)
T KOG2070|consen 182 NLAPQMKTLYLAYCANHPSAVNVLTKHSDELEK 214 (661)
T ss_pred hhhHHHHHHHHHHHhcCchhhhHHHHhHHHHHH
Confidence 34555555555555 356666666554
No 62
>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=37.44 E-value=39 Score=28.75 Aligned_cols=51 Identities=10% Similarity=0.218 Sum_probs=39.8
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhcccCCCC
Q 019151 264 KLPGDTTSLLKAWWLSHAKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHANPS 322 (345)
Q Consensus 264 ~lpk~a~~~L~~wf~~h~~~PYPS~~eK~~LA~~TgLs~kQV~NWFiN~RkR~kk~~~s 322 (345)
.||...+.++.-.+.. .++ -..+|+.+|++...|.++....|++.++....
T Consensus 110 ~L~~~~r~i~~l~~~~----g~s----~~eIA~~lgis~~tV~~~l~ra~~~Lr~~l~~ 160 (162)
T TIGR02983 110 RLPARQRAVVVLRYYE----DLS----EAQVAEALGISVGTVKSRLSRALARLRELLEE 160 (162)
T ss_pred hCCHHHHHHhhhHHHh----cCC----HHHHHHHhCCCHHHHHHHHHHHHHHHHHHhcC
Confidence 5788888888666555 222 24789999999999999999999998875543
No 63
>PRK12516 RNA polymerase sigma factor; Provisional
Probab=37.18 E-value=30 Score=30.97 Aligned_cols=51 Identities=18% Similarity=0.169 Sum_probs=40.2
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhcccCCCC
Q 019151 264 KLPGDTTSLLKAWWLSHAKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHANPS 322 (345)
Q Consensus 264 ~lpk~a~~~L~~wf~~h~~~PYPS~~eK~~LA~~TgLs~kQV~NWFiN~RkR~kk~~~s 322 (345)
.||...+.++.-.+... .+| ..+|+.+|++...|.++....|++.++....
T Consensus 116 ~Lp~~~r~i~~L~~~~g--~s~------~EIA~~Lgis~~tVk~~l~Rar~~Lr~~l~~ 166 (187)
T PRK12516 116 QLPDDQREAIILVGASG--FAY------EEAAEICGCAVGTIKSRVNRARQRLQEILQI 166 (187)
T ss_pred hCCHHHHHHHHHHHHcC--CCH------HHHHHHHCCCHHHHHHHHHHHHHHHHHHHHh
Confidence 47888888887665552 232 3789999999999999999999998876553
No 64
>PRK12514 RNA polymerase sigma factor; Provisional
Probab=36.43 E-value=63 Score=28.07 Aligned_cols=48 Identities=13% Similarity=0.270 Sum_probs=38.8
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhcccC
Q 019151 264 KLPGDTTSLLKAWWLSHAKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHA 319 (345)
Q Consensus 264 ~lpk~a~~~L~~wf~~h~~~PYPS~~eK~~LA~~TgLs~kQV~NWFiN~RkR~kk~ 319 (345)
.||+..+.++...+.. .++ -..+|+.+|++...|.+++...|++.++.
T Consensus 129 ~L~~~~r~i~~l~~~~----g~s----~~eIA~~lgis~~tV~~~l~Rar~~Lr~~ 176 (179)
T PRK12514 129 ELEKDRAAAVRRAYLE----GLS----YKELAERHDVPLNTMRTWLRRSLLKLREC 176 (179)
T ss_pred hCCHHHHHHHHHHHHc----CCC----HHHHHHHHCCChHHHHHHHHHHHHHHHHH
Confidence 5788888888777665 332 35799999999999999999999998764
No 65
>PRK12541 RNA polymerase sigma factor; Provisional
Probab=36.25 E-value=39 Score=28.90 Aligned_cols=49 Identities=18% Similarity=0.182 Sum_probs=39.2
Q ss_pred CCCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhcccC
Q 019151 263 GKLPGDTTSLLKAWWLSHAKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHA 319 (345)
Q Consensus 263 ~~lpk~a~~~L~~wf~~h~~~PYPS~~eK~~LA~~TgLs~kQV~NWFiN~RkR~kk~ 319 (345)
..||..++.++.-.+... .+ -..+|..+|++...|..+....|++.++.
T Consensus 111 ~~L~~~~r~v~~l~~~~~--~s------~~eIA~~lgis~~tv~~~l~Rar~~L~~~ 159 (161)
T PRK12541 111 SSLPLERRNVLLLRDYYG--FS------YKEIAEMTGLSLAKVKIELHRGRKETKSI 159 (161)
T ss_pred HHCCHHHHHHhhhHHhcC--CC------HHHHHHHHCCCHHHHHHHHHHHHHHHHhh
Confidence 368999999987766553 23 24799999999999999999999998753
No 66
>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=35.75 E-value=32 Score=29.96 Aligned_cols=49 Identities=10% Similarity=0.062 Sum_probs=37.9
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhcccCC
Q 019151 264 KLPGDTTSLLKAWWLSHAKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHAN 320 (345)
Q Consensus 264 ~lpk~a~~~L~~wf~~h~~~PYPS~~eK~~LA~~TgLs~kQV~NWFiN~RkR~kk~~ 320 (345)
.||+..+.++.-.+..+ + .-..+|+.+|++...|.++.-..|++.++..
T Consensus 138 ~L~~~~r~v~~l~~~~~----~----s~~EIA~~lgis~~tv~~~l~rar~~Lr~~l 186 (190)
T TIGR02939 138 ALPEDLRTAITLRELEG----L----SYEDIARIMDCPVGTVRSRIFRAREAIAIRL 186 (190)
T ss_pred cCCHHHhhhhhhhhhcC----C----CHHHHHHHHCcCHHHHHHHHHHHHHHHHHHh
Confidence 46777888876554442 2 2357999999999999999999999988654
No 67
>PRK09644 RNA polymerase sigma factor SigM; Provisional
Probab=35.38 E-value=47 Score=28.57 Aligned_cols=50 Identities=14% Similarity=0.040 Sum_probs=40.4
Q ss_pred CCCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhcccCC
Q 019151 263 GKLPGDTTSLLKAWWLSHAKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHAN 320 (345)
Q Consensus 263 ~~lpk~a~~~L~~wf~~h~~~PYPS~~eK~~LA~~TgLs~kQV~NWFiN~RkR~kk~~ 320 (345)
..||...++++.-++..+ .+ -..+|..+|++...|.+|..-.|++.++..
T Consensus 107 ~~L~~~~r~v~~l~~~~g--~s------~~eIA~~lgis~~tv~~~l~Rar~~Lr~~l 156 (165)
T PRK09644 107 HTLPVIEAQAILLCDVHE--LT------YEEAASVLDLKLNTYKSHLFRGRKRLKALL 156 (165)
T ss_pred HhCCHHHHHHHHhHHHhc--CC------HHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 368888999998776664 33 357999999999999999999999987643
No 68
>PF05190 MutS_IV: MutS family domain IV C-terminus.; InterPro: IPR007861 Mismatch repair contributes to the overall fidelity of DNA replication and is essential for combating the adverse effects of damage to the genome. It involves the correction of mismatched base pairs that have been missed by the proofreading element of the DNA polymerase complex. The post-replicative Mismatch Repair System (MMRS) of Escherichia coli involves MutS (Mutator S), MutL and MutH proteins, and acts to correct point mutations or small insertion/deletion loops produced during DNA replication []. MutS and MutL are involved in preventing recombination between partially homologous DNA sequences. The assembly of MMRS is initiated by MutS, which recognises and binds to mispaired nucleotides and allows further action of MutL and MutH to eliminate a portion of newly synthesized DNA strand containing the mispaired base []. MutS can also collaborate with methyltransferases in the repair of O(6)-methylguanine damage, which would otherwise pair with thymine during replication to create an O(6)mG:T mismatch []. MutS exists as a dimer, where the two monomers have different conformations and form a heterodimer at the structural level []. Only one monomer recognises the mismatch specifically and has ADP bound. Non-specific major groove DNA-binding domains from both monomers embrace the DNA in a clamp-like structure. Mismatch binding induces ATP uptake and a conformational change in the MutS protein, resulting in a clamp that translocates on DNA. MutS is a modular protein with a complex structure [], and is composed of: N-terminal mismatch-recognition domain, which is similar in structure to tRNA endonuclease. Connector domain, which is similar in structure to Holliday junction resolvase ruvC. Core domain, which is composed of two separate subdomains that join together to form a helical bundle; from within the core domain, two helices act as levers that extend towards (but do not touch) the DNA. Clamp domain, which is inserted between the two subdomains of the core domain at the top of the lever helices; the clamp domain has a beta-sheet structure. ATPase domain (connected to the core domain), which has a classical Walker A motif. HTH (helix-turn-helix) domain, which is involved in dimer contacts. The MutS family of proteins is named after the Salmonella typhimurium MutS protein involved in mismatch repair. Homologues of MutS have been found in many species including eukaryotes (MSH 1, 2, 3, 4, 5, and 6 proteins), archaea and bacteria, and together these proteins have been grouped into the MutS family. Although many of these proteins have similar activities to the E. coli MutS, there is significant diversity of function among the MutS family members. Human MSH has been implicated in non-polyposis colorectal carcinoma (HNPCC) and is a mismatch binding protein [].This diversity is even seen within species, where many species encode multiple MutS homologues with distinct functions []. Inter-species homologues may have arisen through frequent ancient horizontal gene transfer of MutS (and MutL) from bacteria to archaea and eukaryotes via endosymbiotic ancestors of mitochondria and chloroplasts []. This entry represents the clamp domain (domain 4) found in proteins of the MutS family. The clamp domain is inserted within the core domain at the top of the lever helices. It has a beta-sheet structure [].; GO: 0005524 ATP binding, 0030983 mismatched DNA binding, 0006298 mismatch repair; PDB: 2WTU_A 1OH7_A 1OH5_B 1W7A_B 1NG9_A 1OH8_B 1WBD_A 1WB9_A 3K0S_A 1OH6_A ....
Probab=34.74 E-value=67 Score=24.71 Aligned_cols=26 Identities=27% Similarity=0.319 Sum_probs=21.0
Q ss_pred CCChHHHHHHHHHHHHHHHHHHHHhH
Q 019151 129 LDDKELDQFMTHYVLLLYSFKEQLQQ 154 (345)
Q Consensus 129 g~dpELDqFMeaYc~vL~kykEEL~k 154 (345)
|-|+|||.....|..+.....+.+.+
T Consensus 1 g~d~~Ld~~~~~~~~~~~~l~~~~~~ 26 (92)
T PF05190_consen 1 GFDEELDELREEYEEIEEELEELLEE 26 (92)
T ss_dssp TSSHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred CCCHHHHHHHHHHHHHHHHHHHHHHH
Confidence 56999999999999888776666543
No 69
>smart00421 HTH_LUXR helix_turn_helix, Lux Regulon. lux regulon (activates the bioluminescence operon
Probab=34.38 E-value=91 Score=21.10 Aligned_cols=47 Identities=11% Similarity=0.147 Sum_probs=34.4
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhcccC
Q 019151 264 KLPGDTTSLLKAWWLSHAKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHA 319 (345)
Q Consensus 264 ~lpk~a~~~L~~wf~~h~~~PYPS~~eK~~LA~~TgLs~kQV~NWFiN~RkR~kk~ 319 (345)
.|+.....++..+ .. .+ ....+|+.+|++...|..|....+.+..-.
T Consensus 3 ~l~~~e~~i~~~~-~~----g~----s~~eia~~l~is~~tv~~~~~~~~~kl~~~ 49 (58)
T smart00421 3 SLTPREREVLRLL-AE----GL----TNKEIAERLGISEKTVKTHLSNIMRKLGVR 49 (58)
T ss_pred CCCHHHHHHHHHH-Hc----CC----CHHHHHHHHCCCHHHHHHHHHHHHHHHCCC
Confidence 4677777777543 32 22 346889999999999999999888776543
No 70
>PRK12547 RNA polymerase sigma factor; Provisional
Probab=34.09 E-value=46 Score=28.74 Aligned_cols=48 Identities=15% Similarity=0.072 Sum_probs=38.8
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhcccC
Q 019151 264 KLPGDTTSLLKAWWLSHAKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHA 319 (345)
Q Consensus 264 ~lpk~a~~~L~~wf~~h~~~PYPS~~eK~~LA~~TgLs~kQV~NWFiN~RkR~kk~ 319 (345)
.||+..++++.-.+... +. -..+|+.+|++...|.++..-.|++.+..
T Consensus 112 ~L~~~~r~v~~l~~~~g----~s----~~eIA~~lgis~~tV~~~l~Rar~~Lr~~ 159 (164)
T PRK12547 112 LLSADQREAIILIGASG----FS----YEDAAAICGCAVGTIKSRVSRARNRLQEL 159 (164)
T ss_pred hCCHHHHHHHHHHHHcC----CC----HHHHHHHhCCCHHHHHHHHHHHHHHHHHH
Confidence 58899999887766653 21 34799999999999999999999988753
No 71
>PRK00118 putative DNA-binding protein; Validated
Probab=34.07 E-value=53 Score=27.72 Aligned_cols=47 Identities=11% Similarity=0.193 Sum_probs=37.7
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhccc
Q 019151 264 KLPGDTTSLLKAWWLSHAKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWH 318 (345)
Q Consensus 264 ~lpk~a~~~L~~wf~~h~~~PYPS~~eK~~LA~~TgLs~kQV~NWFiN~RkR~kk 318 (345)
.+|...+.++..++... + .-..+|+.+|++..-|.+|+...|++.++
T Consensus 17 ~L~ekqRevl~L~y~eg----~----S~~EIAe~lGIS~~TV~r~L~RArkkLr~ 63 (104)
T PRK00118 17 LLTEKQRNYMELYYLDD----Y----SLGEIAEEFNVSRQAVYDNIKRTEKLLED 63 (104)
T ss_pred cCCHHHHHHHHHHHHcC----C----CHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 57888889987776663 2 23469999999999999999998888764
No 72
>PRK06811 RNA polymerase factor sigma-70; Validated
Probab=34.00 E-value=48 Score=29.36 Aligned_cols=48 Identities=17% Similarity=0.163 Sum_probs=39.1
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhcccC
Q 019151 264 KLPGDTTSLLKAWWLSHAKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHA 319 (345)
Q Consensus 264 ~lpk~a~~~L~~wf~~h~~~PYPS~~eK~~LA~~TgLs~kQV~NWFiN~RkR~kk~ 319 (345)
+||+..+.++.-.|... .+ -..+|+.+|++...|.+...-.|++.++.
T Consensus 131 ~L~~~~r~i~~l~~~~g--~s------~~EIAe~lgis~~~V~~~l~Ra~~~Lr~~ 178 (189)
T PRK06811 131 DLEKLDREIFIRRYLLG--EK------IEEIAKKLGLTRSAIDNRLSRGRKKLQKN 178 (189)
T ss_pred hCCHHHHHHHHHHHHcc--CC------HHHHHHHHCCCHHHHHHHHHHHHHHHHHc
Confidence 68999999987665552 23 34799999999999999999999998764
No 73
>PF12022 DUF3510: Domain of unknown function (DUF3510); InterPro: IPR024603 The COG complex comprises eight proteins (COG1-8) and plays critical roles in Golgi structure and function []. This uncharacterised domain is found in the C-terminal of COG complex subunit 2 proteins.
Probab=33.93 E-value=1.7e+02 Score=25.03 Aligned_cols=43 Identities=16% Similarity=0.265 Sum_probs=25.2
Q ss_pred CChHHHHHHHHHHH-HHHHHHHHHhHHHhhhhHHHHHHHhHHHHHhhhhhCC
Q 019151 130 DDKELDQFMTHYVL-LLYSFKEQLQQHVRVHAMEAVMACWDLEQSLQSLTGV 180 (345)
Q Consensus 130 ~dpELDqFMeaYc~-vL~kykEEL~kP~~~~~~EA~~fc~~iE~QL~sL~~~ 180 (345)
.+....+++...+. +...|.+. +.|...-++++|..|+-|-..
T Consensus 56 ~~~~~~~~~~~v~~~v~~~y~~~--------~~evL~sv~KtEeSL~rlkk~ 99 (125)
T PF12022_consen 56 SPEIIEEWLQKVITEVTERYYEI--------ASEVLTSVRKTEESLKRLKKR 99 (125)
T ss_pred CHHHHHHHHHHHHHHHHHHHHHH--------HHHHHHHHHHHHHHHHHHHHh
Confidence 34555555554222 33334333 346667778999999988653
No 74
>PF13097 CENP-U: CENP-A nucleosome associated complex (NAC) subunit
Probab=33.91 E-value=1e+02 Score=28.59 Aligned_cols=47 Identities=15% Similarity=0.239 Sum_probs=37.6
Q ss_pred CChHHHHHHHHHHHHHHHHHHHHhHHHhhhhHHH-HHHHhHHHHHhhhhhC
Q 019151 130 DDKELDQFMTHYVLLLYSFKEQLQQHVRVHAMEA-VMACWDLEQSLQSLTG 179 (345)
Q Consensus 130 ~dpELDqFMeaYc~vL~kykEEL~kP~~~~~~EA-~~fc~~iE~QL~sL~~ 179 (345)
+=-|||-.+.++-.++..|++.++-.+= .+| ..||..|..||-.+..
T Consensus 102 DItELDVvL~~FEk~~~eYkq~ieS~~c---r~AI~~F~~~~keqL~~~i~ 149 (175)
T PF13097_consen 102 DITELDVVLSAFEKTALEYKQSIESKIC---RKAINKFYSNFKEQLIEMIK 149 (175)
T ss_pred cchHHHHHHHHHHHHHHHHHHhhccHHH---HHHHHHHHHHHHHHHHHHHH
Confidence 4489999999999999999999976552 233 3588999999987663
No 75
>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=33.62 E-value=50 Score=28.71 Aligned_cols=48 Identities=4% Similarity=0.104 Sum_probs=38.7
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhcccC
Q 019151 264 KLPGDTTSLLKAWWLSHAKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHA 319 (345)
Q Consensus 264 ~lpk~a~~~L~~wf~~h~~~PYPS~~eK~~LA~~TgLs~kQV~NWFiN~RkR~kk~ 319 (345)
.||+..+.++.-.+... ++ -..+|+.+|++...|.+.+...|++.++.
T Consensus 134 ~Lp~~~r~v~~l~~~~g----~s----~~EIA~~lgis~~tVk~~l~Rar~~Lr~~ 181 (183)
T TIGR02999 134 QVDPRQAEVVELRFFAG----LT----VEEIAELLGVSVRTVERDWRFARAWLADE 181 (183)
T ss_pred cCCHHHHHHHHHHHHcC----CC----HHHHHHHhCCCHHHHHHHHHHHHHHHHHH
Confidence 48899999987776653 21 24799999999999999999999988753
No 76
>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=32.71 E-value=54 Score=27.63 Aligned_cols=47 Identities=19% Similarity=0.233 Sum_probs=37.3
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhccc
Q 019151 264 KLPGDTTSLLKAWWLSHAKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWH 318 (345)
Q Consensus 264 ~lpk~a~~~L~~wf~~h~~~PYPS~~eK~~LA~~TgLs~kQV~NWFiN~RkR~kk 318 (345)
.||+..+.++...+.. .++ -..+|+.+|++...|.++..-.|++.+.
T Consensus 111 ~L~~~~r~v~~l~~~~----g~~----~~eIA~~l~is~~tv~~~l~Rar~~Lr~ 157 (159)
T TIGR02989 111 KLPERQRELLQLRYQR----GVS----LTALAEQLGRTVNAVYKALSRLRVRLRD 157 (159)
T ss_pred HCCHHHHHHHHHHHhc----CCC----HHHHHHHhCCCHHHHHHHHHHHHHHHHh
Confidence 5888888888775554 332 3478999999999999999999988765
No 77
>PRK03975 tfx putative transcriptional regulator; Provisional
Probab=32.64 E-value=53 Score=29.20 Aligned_cols=48 Identities=8% Similarity=0.022 Sum_probs=37.7
Q ss_pred CCCCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhccc
Q 019151 262 AGKLPGDTTSLLKAWWLSHAKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWH 318 (345)
Q Consensus 262 r~~lpk~a~~~L~~wf~~h~~~PYPS~~eK~~LA~~TgLs~kQV~NWFiN~RkR~kk 318 (345)
...|++..+.+|... .. .+ .-..+|+.+|++...|.+|....+++.++
T Consensus 4 ~~~Lt~rqreVL~lr-~~----Gl----Tq~EIAe~LGiS~~tVs~ie~ra~kkLr~ 51 (141)
T PRK03975 4 ESFLTERQIEVLRLR-ER----GL----TQQEIADILGTSRANVSSIEKRARENIEK 51 (141)
T ss_pred ccCCCHHHHHHHHHH-Hc----CC----CHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 457899999998763 33 32 23489999999999999999999888664
No 78
>KOG4445 consensus Uncharacterized conserved protein, contains RWD domain [Function unknown]
Probab=31.71 E-value=96 Score=31.35 Aligned_cols=46 Identities=11% Similarity=0.179 Sum_probs=37.6
Q ss_pred hHHHHHHHHHHHHHHHHHHHHhHHHhhhhHHHHHHHhHHHHHhhhhhC
Q 019151 132 KELDQFMTHYVLLLYSFKEQLQQHVRVHAMEAVMACWDLEQSLQSLTG 179 (345)
Q Consensus 132 pELDqFMeaYc~vL~kykEEL~kP~~~~~~EA~~fc~~iE~QL~sL~~ 179 (345)
-+-|.||--|| |.+|-.+|.+=+|..+.++..-+..+-.|+..+|.
T Consensus 134 T~C~Hy~H~~C--laRyl~~~~~~lrqe~q~~~~~~qh~~~~~eavcp 179 (368)
T KOG4445|consen 134 TACDHYMHFAC--LARYLTECLTGLRQEIQDAQKERQHMKEQVEAVCP 179 (368)
T ss_pred ehhHHHHHHHH--HHHHHHHHHHHHHHHHHHHHHHHHHhhhhHhhhhh
Confidence 36899999998 55677777777777778888888899999999985
No 79
>PRK12526 RNA polymerase sigma factor; Provisional
Probab=31.36 E-value=52 Score=29.74 Aligned_cols=49 Identities=14% Similarity=0.213 Sum_probs=38.6
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhcccCC
Q 019151 264 KLPGDTTSLLKAWWLSHAKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHAN 320 (345)
Q Consensus 264 ~lpk~a~~~L~~wf~~h~~~PYPS~~eK~~LA~~TgLs~kQV~NWFiN~RkR~kk~~ 320 (345)
.||+..+.++...+... + .-..+|+.+|++...|.+++...|++.++..
T Consensus 153 ~L~~~~r~vl~l~~~~g----~----s~~EIA~~lgis~~tV~~~l~Ra~~~Lr~~l 201 (206)
T PRK12526 153 KLPEAQQTVVKGVYFQE----L----SQEQLAQQLNVPLGTVKSRLRLALAKLKVQM 201 (206)
T ss_pred hCCHHHHHHHHHHHHcC----C----CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 58888988887655542 2 2357999999999999999999999887643
No 80
>PF07425 Pardaxin: Pardaxin; InterPro: IPR009990 This family consists of several Pardaxin proteins. Pardaxin, a 33-amino-acid pore-forming polypeptide toxin isolated from the Red Sea Moses sole Pardachirus marmoratus, has a helix-hinge-helix structure. This is a common structural motif found both in antibacterial peptides that can act selectively on bacterial membranes (e.g., cecropin), and in cytotoxic peptides that can lyse both mammalian and bacterial cells (e.g., melittin). Pardaxin possesses a high antibacterial activity with a significantly reduced haemolytic activity towards human red blood cells compared with melittin []. Pardaxin has also been found to have a shark repellent action [].; GO: 0005576 extracellular region; PDB: 1XC0_A 2KNS_A.
Probab=30.80 E-value=33 Score=22.94 Aligned_cols=22 Identities=41% Similarity=0.563 Sum_probs=17.5
Q ss_pred HHHHHhhCCChHHHHHHHHhhh
Q 019151 73 CKAEIVGHPLYEQLLSAHVSCL 94 (345)
Q Consensus 73 lKakI~sHPlYp~Ll~A~idC~ 94 (345)
+-.+|++.|||.-||+|--..+
T Consensus 5 lipkiissplfktllsavgsal 26 (33)
T PF07425_consen 5 LIPKIISSPLFKTLLSAVGSAL 26 (33)
T ss_dssp CHHHHCCTTTCHHHHHHHHHHC
T ss_pred hhhHHHccHHHHHHHHHHHHHH
Confidence 3468999999999998865544
No 81
>PRK12512 RNA polymerase sigma factor; Provisional
Probab=30.56 E-value=58 Score=28.46 Aligned_cols=51 Identities=6% Similarity=-0.074 Sum_probs=40.8
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhcccCCCC
Q 019151 264 KLPGDTTSLLKAWWLSHAKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHANPS 322 (345)
Q Consensus 264 ~lpk~a~~~L~~wf~~h~~~PYPS~~eK~~LA~~TgLs~kQV~NWFiN~RkR~kk~~~s 322 (345)
.||+..+.++...+... .+ -..+|+.+|++...|.+++...|++.+....+
T Consensus 131 ~L~~~~r~v~~l~~~~g--~s------~~eIA~~l~is~~tV~~~l~ra~~~Lr~~l~~ 181 (184)
T PRK12512 131 TLPPRQRDVVQSISVEG--AS------IKETAAKLSMSEGAVRVALHRGLAALAAKFRS 181 (184)
T ss_pred hCCHHHHHHHHHHHHcC--CC------HHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhc
Confidence 68888999988765553 22 35799999999999999999999998865543
No 82
>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=30.54 E-value=41 Score=25.88 Aligned_cols=20 Identities=15% Similarity=0.403 Sum_probs=17.5
Q ss_pred HHHHHHHHhCCChhhhhhhh
Q 019151 290 DKARLVQETGLQLKQINNWF 309 (345)
Q Consensus 290 eK~~LA~~TgLs~kQV~NWF 309 (345)
.-..||++.|++..+|..|=
T Consensus 24 ~lkdIA~~Lgvs~~tIr~WK 43 (60)
T PF10668_consen 24 KLKDIAEKLGVSESTIRKWK 43 (60)
T ss_pred cHHHHHHHHCCCHHHHHHHh
Confidence 45689999999999999994
No 83
>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=29.03 E-value=43 Score=23.51 Aligned_cols=21 Identities=14% Similarity=0.189 Sum_probs=18.3
Q ss_pred HHHHHHhCCChhhhhhhhhhh
Q 019151 292 ARLVQETGLQLKQINNWFINQ 312 (345)
Q Consensus 292 ~~LA~~TgLs~kQV~NWFiN~ 312 (345)
..||+.+|+++..|+.|..+.
T Consensus 13 ~~la~~~gis~~~i~~~~~g~ 33 (55)
T PF01381_consen 13 KELAEKLGISRSTISRIENGK 33 (55)
T ss_dssp HHHHHHHTS-HHHHHHHHTTS
T ss_pred HHHHHHhCCCcchhHHHhcCC
Confidence 689999999999999999883
No 84
>PRK13919 putative RNA polymerase sigma E protein; Provisional
Probab=28.18 E-value=72 Score=27.85 Aligned_cols=50 Identities=14% Similarity=0.151 Sum_probs=39.3
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhcccCCC
Q 019151 264 KLPGDTTSLLKAWWLSHAKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHANP 321 (345)
Q Consensus 264 ~lpk~a~~~L~~wf~~h~~~PYPS~~eK~~LA~~TgLs~kQV~NWFiN~RkR~kk~~~ 321 (345)
.||...+.++.-.+... + .-..+|+.+|++...|.++....|++.++...
T Consensus 135 ~L~~~~r~vl~l~~~~~----~----s~~eIA~~lgis~~~V~~~l~ra~~~Lr~~l~ 184 (186)
T PRK13919 135 ALSPEERRVIEVLYYQG----Y----THREAAQLLGLPLGTLKTRARRALSRLKEVLR 184 (186)
T ss_pred hCCHHHHHHHHHHHHcC----C----CHHHHHHHHCcCHHHHHHHHHHHHHHHHHHhc
Confidence 48888999987665552 2 23579999999999999999999999876543
No 85
>PF15500 Toxin_39: Putative RNase-like toxin
Probab=28.16 E-value=1.3e+02 Score=25.08 Aligned_cols=39 Identities=21% Similarity=0.162 Sum_probs=27.6
Q ss_pred CCCChHHHHHHHHHHHHHHHHHHHHhHHHhhhhHHHHHHHhHHHHH
Q 019151 128 VLDDKELDQFMTHYVLLLYSFKEQLQQHVRVHAMEAVMACWDLEQS 173 (345)
Q Consensus 128 ~g~dpELDqFMeaYc~vL~kykEEL~kP~~~~~~EA~~fc~~iE~Q 173 (345)
++++|+|.+.|+. ++-+++.--++ .++||...+..+|.-
T Consensus 44 l~a~p~lk~wne~-vq~~Rk~dp~~------aAdeaakLi~alE~a 82 (96)
T PF15500_consen 44 LAADPALKAWNET-VQAKRKLDPKF------AADEAAKLIQALETA 82 (96)
T ss_pred hccCHHHHHHHHH-HHHHHhhchhh------hHHHHHHHHHHHHHH
Confidence 6799999999998 44455554444 357888777777653
No 86
>PRK05602 RNA polymerase sigma factor; Reviewed
Probab=28.04 E-value=60 Score=28.50 Aligned_cols=50 Identities=6% Similarity=0.097 Sum_probs=38.2
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhcccCCC
Q 019151 264 KLPGDTTSLLKAWWLSHAKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHANP 321 (345)
Q Consensus 264 ~lpk~a~~~L~~wf~~h~~~PYPS~~eK~~LA~~TgLs~kQV~NWFiN~RkR~kk~~~ 321 (345)
.||+..+.++...+... + .-..+|+.+|++...|.++....|++.++...
T Consensus 128 ~L~~~~r~i~~l~~~~g----~----s~~EIA~~lgis~~tV~~~l~Rar~~Lr~~l~ 177 (186)
T PRK05602 128 ALPERQREAIVLQYYQG----L----SNIEAAAVMDISVDALESLLARGRRALRAQLA 177 (186)
T ss_pred hCCHHHHHHhhHHHhcC----C----CHHHHHHHhCcCHHHHHHHHHHHHHHHHHHHH
Confidence 46788888876544442 2 23479999999999999999999999887544
No 87
>PRK12523 RNA polymerase sigma factor; Reviewed
Probab=27.87 E-value=72 Score=27.64 Aligned_cols=49 Identities=12% Similarity=0.197 Sum_probs=38.5
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhcccCC
Q 019151 264 KLPGDTTSLLKAWWLSHAKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHAN 320 (345)
Q Consensus 264 ~lpk~a~~~L~~wf~~h~~~PYPS~~eK~~LA~~TgLs~kQV~NWFiN~RkR~kk~~ 320 (345)
.||++.+.++.-.+... .+| ..+|+.+|++..-|.++....|++.+...
T Consensus 119 ~Lp~~~r~v~~L~~~~g--~s~------~EIA~~lgis~~tV~~~l~ra~~~~~~~l 167 (172)
T PRK12523 119 KLSSKARAAFLYNRLDG--MGH------AEIAERLGVSVSRVRQYLAQGLRQCYIAL 167 (172)
T ss_pred hCCHHHHHHHHHHHHcC--CCH------HHHHHHHCCCHHHHHHHHHHHHHHHHHHh
Confidence 58888888887665553 233 47999999999999999999999876543
No 88
>PRK09648 RNA polymerase sigma factor SigD; Reviewed
Probab=27.35 E-value=72 Score=28.04 Aligned_cols=48 Identities=10% Similarity=0.014 Sum_probs=38.4
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhcccC
Q 019151 264 KLPGDTTSLLKAWWLSHAKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHA 319 (345)
Q Consensus 264 ~lpk~a~~~L~~wf~~h~~~PYPS~~eK~~LA~~TgLs~kQV~NWFiN~RkR~kk~ 319 (345)
.||+..+.++..-+... + .-..+|+.+|++...|.++....|++.++.
T Consensus 139 ~L~~~~r~i~~l~~~~g----~----s~~EIA~~lgis~~tV~~~l~Ra~~~Lr~~ 186 (189)
T PRK09648 139 TLPEKQREILILRVVVG----L----SAEETAEAVGSTPGAVRVAQHRALARLRAE 186 (189)
T ss_pred hCCHHHHHHHHHHHHcC----C----CHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 58888888887655552 2 245899999999999999999999988764
No 89
>PRK12532 RNA polymerase sigma factor; Provisional
Probab=26.97 E-value=69 Score=28.37 Aligned_cols=49 Identities=12% Similarity=0.177 Sum_probs=38.7
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhcccCC
Q 019151 264 KLPGDTTSLLKAWWLSHAKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHAN 320 (345)
Q Consensus 264 ~lpk~a~~~L~~wf~~h~~~PYPS~~eK~~LA~~TgLs~kQV~NWFiN~RkR~kk~~ 320 (345)
.||+..+.++.-.+... +. -..+|+.+|++...|.+.....|++.++..
T Consensus 136 ~L~~~~r~i~~L~~~~g----~s----~~EIA~~lgis~~tVk~~l~Rar~~Lr~~l 184 (195)
T PRK12532 136 NLPENTARVFTLKEILG----FS----SDEIQQMCGISTSNYHTIMHRARESLRQCL 184 (195)
T ss_pred hCCHHHHHHhhhHHHhC----CC----HHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 58888888887655542 22 357999999999999999999999988644
No 90
>PRK12546 RNA polymerase sigma factor; Provisional
Probab=26.55 E-value=66 Score=28.86 Aligned_cols=50 Identities=14% Similarity=0.106 Sum_probs=39.9
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhcccCCC
Q 019151 264 KLPGDTTSLLKAWWLSHAKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHANP 321 (345)
Q Consensus 264 ~lpk~a~~~L~~wf~~h~~~PYPS~~eK~~LA~~TgLs~kQV~NWFiN~RkR~kk~~~ 321 (345)
.||+..+.++.-.+.. .++ -..+|+.+|++...|.+++.-.|++.++...
T Consensus 113 ~Lp~~~r~v~~L~~~~----g~s----~~EIA~~LgiS~~tVk~~l~Rar~~Lr~~l~ 162 (188)
T PRK12546 113 QLPDEQREALILVGAS----GFS----YEEAAEMCGVAVGTVKSRANRARARLAELLQ 162 (188)
T ss_pred hCCHHHhHHhhhHHhc----CCC----HHHHHHHHCCCHHHHHHHHHHHHHHHHHHHh
Confidence 6888999998776555 332 2478999999999999999999999886443
No 91
>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=26.47 E-value=75 Score=27.34 Aligned_cols=48 Identities=4% Similarity=0.028 Sum_probs=37.4
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhcccC
Q 019151 264 KLPGDTTSLLKAWWLSHAKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHA 319 (345)
Q Consensus 264 ~lpk~a~~~L~~wf~~h~~~PYPS~~eK~~LA~~TgLs~kQV~NWFiN~RkR~kk~ 319 (345)
.||...+.++..-+... .+ -..+|+.+|++...|.++..-.|++.++.
T Consensus 119 ~L~~~~r~i~~l~~~~g--~s------~~eiA~~lgis~~tv~~~l~Ra~~~Lr~~ 166 (169)
T TIGR02954 119 TLNDKYQTAIILRYYHD--LT------IKEIAEVMNKPEGTVKTYLHRALKKLKKR 166 (169)
T ss_pred hCCHHHhHHHHHHHHcC--CC------HHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 57888888886655552 12 34789999999999999999999988753
No 92
>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=26.29 E-value=47 Score=23.03 Aligned_cols=22 Identities=23% Similarity=0.223 Sum_probs=19.0
Q ss_pred HHHHHHhCCChhhhhhhhhhhh
Q 019151 292 ARLVQETGLQLKQINNWFINQR 313 (345)
Q Consensus 292 ~~LA~~TgLs~kQV~NWFiN~R 313 (345)
..||+.+|+++..|+.|...++
T Consensus 19 ~~lA~~~gvs~~~vs~~e~g~~ 40 (58)
T TIGR03070 19 ADLADLAGVGLRFIRDVENGKP 40 (58)
T ss_pred HHHHHHhCCCHHHHHHHHCCCC
Confidence 5799999999999999986653
No 93
>PRK09047 RNA polymerase factor sigma-70; Validated
Probab=26.13 E-value=1.4e+02 Score=25.18 Aligned_cols=49 Identities=12% Similarity=0.056 Sum_probs=39.1
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhcccCC
Q 019151 264 KLPGDTTSLLKAWWLSHAKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHAN 320 (345)
Q Consensus 264 ~lpk~a~~~L~~wf~~h~~~PYPS~~eK~~LA~~TgLs~kQV~NWFiN~RkR~kk~~ 320 (345)
+||+..+.++.-.+.. .++ -..+|+.+|++...|.+...-.|++.++..
T Consensus 106 ~Lp~~~r~v~~l~~~~----g~s----~~EIA~~lgis~~tV~~~l~ra~~~Lr~~l 154 (161)
T PRK09047 106 KLPARQREAFLLRYWE----DMD----VAETAAAMGCSEGSVKTHCSRATHALAKAL 154 (161)
T ss_pred hCCHHHHHHHHHHHHh----cCC----HHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 6889999998775555 222 357999999999999999999999887543
No 94
>PRK12531 RNA polymerase sigma factor; Provisional
Probab=25.85 E-value=69 Score=28.49 Aligned_cols=51 Identities=16% Similarity=0.271 Sum_probs=39.8
Q ss_pred CCCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhcccCCC
Q 019151 263 GKLPGDTTSLLKAWWLSHAKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHANP 321 (345)
Q Consensus 263 ~~lpk~a~~~L~~wf~~h~~~PYPS~~eK~~LA~~TgLs~kQV~NWFiN~RkR~kk~~~ 321 (345)
..||+..+.++.-.+... .+| ..+|+.+|++...|.+-+...|++.++...
T Consensus 140 ~~Lp~~~r~v~~l~~~eg--~s~------~EIA~~lgis~~tVk~rl~ra~~~Lr~~l~ 190 (194)
T PRK12531 140 DRLPKAQRDVLQAVYLEE--LPH------QQVAEMFDIPLGTVKSRLRLAVEKLRHSMD 190 (194)
T ss_pred HhCCHHHHHHHHHHHHcC--CCH------HHHHHHhCcCHHHHHHHHHHHHHHHHHHhh
Confidence 368888999987654442 333 479999999999999999999998876543
No 95
>PRK12530 RNA polymerase sigma factor; Provisional
Probab=25.84 E-value=75 Score=28.23 Aligned_cols=48 Identities=10% Similarity=0.149 Sum_probs=38.5
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhcccC
Q 019151 264 KLPGDTTSLLKAWWLSHAKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHA 319 (345)
Q Consensus 264 ~lpk~a~~~L~~wf~~h~~~PYPS~~eK~~LA~~TgLs~kQV~NWFiN~RkR~kk~ 319 (345)
.||...+.++.-.+... .+ -..+|+.+|+++..|.++..-.|++.++.
T Consensus 134 ~Lp~~~R~v~~L~~~~g--~s------~~EIA~~lgis~~tVk~~l~RAr~~Lr~~ 181 (189)
T PRK12530 134 HLPAQQARVFMMREYLE--LS------SEQICQECDISTSNLHVLLYRARLQLQAC 181 (189)
T ss_pred hCCHHHHHHHhHHHHcC--CC------HHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 58888888887766552 22 35799999999999999999999988753
No 96
>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=25.69 E-value=39 Score=23.52 Aligned_cols=20 Identities=5% Similarity=0.293 Sum_probs=18.4
Q ss_pred HHHHHhCCChhhhhhhhhhh
Q 019151 293 RLVQETGLQLKQINNWFINQ 312 (345)
Q Consensus 293 ~LA~~TgLs~kQV~NWFiN~ 312 (345)
.||+.+|++...|+.|+.+.
T Consensus 2 ~lA~~~gvs~~tvs~~l~g~ 21 (52)
T cd01392 2 DIARAAGVSVATVSRVLNGK 21 (52)
T ss_pred cHHHHHCcCHHHHHHHHcCC
Confidence 58999999999999999876
No 97
>cd00131 PAX Paired Box domain
Probab=25.63 E-value=2.1e+02 Score=24.47 Aligned_cols=46 Identities=11% Similarity=0.082 Sum_probs=32.3
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCC-------Chhhhhhhhhhh
Q 019151 264 KLPGDTTSLLKAWWLSHAKWPYPTEEDKARLVQETGL-------QLKQINNWFINQ 312 (345)
Q Consensus 264 ~lpk~a~~~L~~wf~~h~~~PYPS~~eK~~LA~~TgL-------s~kQV~NWFiN~ 312 (345)
++.......+..+... +|..|..|-..+-...|+ +..+|+.||.++
T Consensus 75 ~~~~~~~~~i~~~v~~---~p~~Tl~El~~~L~~~gv~~~~~~~s~stI~R~L~~~ 127 (128)
T cd00131 75 VATPEVVKKIEIYKQE---NPGMFAWEIRDRLLQEGVCDKSNVPSVSSINRILRNK 127 (128)
T ss_pred cCCHHHHHHHHHHHHH---CCCCCHHHHHHHHHHcCCcccCCCCCHHHHHHHHHhc
Confidence 3445555666667677 698888887666335576 999999998764
No 98
>PRK09649 RNA polymerase sigma factor SigC; Reviewed
Probab=25.62 E-value=76 Score=28.09 Aligned_cols=47 Identities=17% Similarity=0.055 Sum_probs=38.3
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhccc
Q 019151 264 KLPGDTTSLLKAWWLSHAKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWH 318 (345)
Q Consensus 264 ~lpk~a~~~L~~wf~~h~~~PYPS~~eK~~LA~~TgLs~kQV~NWFiN~RkR~kk 318 (345)
.||...+.++.-.+... ++ -..+|+.+|+++..|.++..-.|++.++
T Consensus 130 ~Lp~~~r~v~~L~~~~g----~s----~~EIA~~lgis~~tVk~~l~Rar~~Lr~ 176 (185)
T PRK09649 130 DLTTDQREALLLTQLLG----LS----YADAAAVCGCPVGTIRSRVARARDALLA 176 (185)
T ss_pred hCCHHHhHHhhhHHHcC----CC----HHHHHHHHCCCHHHHHHHHHHHHHHHHh
Confidence 68888988887665553 22 3479999999999999999999999887
No 99
>PRK12524 RNA polymerase sigma factor; Provisional
Probab=25.54 E-value=76 Score=28.25 Aligned_cols=49 Identities=4% Similarity=0.059 Sum_probs=38.5
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhcccCC
Q 019151 264 KLPGDTTSLLKAWWLSHAKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHAN 320 (345)
Q Consensus 264 ~lpk~a~~~L~~wf~~h~~~PYPS~~eK~~LA~~TgLs~kQV~NWFiN~RkR~kk~~ 320 (345)
.||+..+.++.-.+.. .|+ -..+|+.+|++...|.+++.-.|++.++..
T Consensus 136 ~L~~~~r~i~~L~~~~----g~s----~~eIA~~lgis~~tV~~~l~Ra~~~Lr~~l 184 (196)
T PRK12524 136 ALPERQRQAVVLRHIE----GLS----NPEIAEVMEIGVEAVESLTARGKRALAALL 184 (196)
T ss_pred hCCHHHHHHHHHHHHc----CCC----HHHHHHHHCcCHHHHHHHHHHHHHHHHHHH
Confidence 5888888887665444 332 347999999999999999999999988643
No 100
>PRK09413 IS2 repressor TnpA; Reviewed
Probab=24.96 E-value=1.1e+02 Score=25.83 Aligned_cols=48 Identities=6% Similarity=0.060 Sum_probs=31.7
Q ss_pred cCCCCCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhh
Q 019151 260 RRAGKLPGDTTSLLKAWWLSHAKWPYPTEEDKARLVQETGLQLKQINNWFINQRK 314 (345)
Q Consensus 260 rkr~~lpk~a~~~L~~wf~~h~~~PYPS~~eK~~LA~~TgLs~kQV~NWFiN~Rk 314 (345)
+++++++.+-+...-..... ..+ ....+|+..|++..+|.+|..-.+.
T Consensus 8 ~~rr~ys~EfK~~aV~~~~~---~g~----sv~evA~e~gIs~~tl~~W~r~y~~ 55 (121)
T PRK09413 8 EKRRRRTTQEKIAIVQQSFE---PGM----TVSLVARQHGVAASQLFLWRKQYQE 55 (121)
T ss_pred CCCCCCCHHHHHHHHHHHHc---CCC----CHHHHHHHHCcCHHHHHHHHHHHhh
Confidence 34567888775543333333 232 2457899999999999999766654
No 101
>PRK12520 RNA polymerase sigma factor; Provisional
Probab=24.79 E-value=86 Score=27.66 Aligned_cols=48 Identities=15% Similarity=0.085 Sum_probs=38.0
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhcccC
Q 019151 264 KLPGDTTSLLKAWWLSHAKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHA 319 (345)
Q Consensus 264 ~lpk~a~~~L~~wf~~h~~~PYPS~~eK~~LA~~TgLs~kQV~NWFiN~RkR~kk~ 319 (345)
.||+..+.++.-.+... .+| ..+|+.+|++..-|.+.....|++.++-
T Consensus 131 ~Lp~~~r~v~~l~~~~g--~s~------~EIA~~lgis~~tV~~~l~Rar~~Lr~~ 178 (191)
T PRK12520 131 RLPPRTGRVFMMREWLE--LET------EEICQELQITATNAWVLLYRARMRLREC 178 (191)
T ss_pred hCCHHHHHHHHHHHHcC--CCH------HHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 58888888887665552 232 5799999999999999999999988753
No 102
>PRK10072 putative transcriptional regulator; Provisional
Probab=24.54 E-value=50 Score=27.42 Aligned_cols=23 Identities=9% Similarity=0.289 Sum_probs=20.3
Q ss_pred HHHHHHHhCCChhhhhhhhhhhh
Q 019151 291 KARLVQETGLQLKQINNWFINQR 313 (345)
Q Consensus 291 K~~LA~~TgLs~kQV~NWFiN~R 313 (345)
...||+.+|++...|++|...+|
T Consensus 49 Q~elA~~lGvS~~TVs~WE~G~r 71 (96)
T PRK10072 49 IDDFARVLGVSVAMVKEWESRRV 71 (96)
T ss_pred HHHHHHHhCCCHHHHHHHHcCCC
Confidence 45899999999999999998765
No 103
>PRK09639 RNA polymerase sigma factor SigX; Provisional
Probab=24.27 E-value=92 Score=26.50 Aligned_cols=47 Identities=13% Similarity=0.248 Sum_probs=37.5
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhcccC
Q 019151 264 KLPGDTTSLLKAWWLSHAKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHA 319 (345)
Q Consensus 264 ~lpk~a~~~L~~wf~~h~~~PYPS~~eK~~LA~~TgLs~kQV~NWFiN~RkR~kk~ 319 (345)
.||...+.+|.-.+ . .++ -..+|..+|++...|.++....|++.++-
T Consensus 112 ~L~~~~r~il~l~~-~----g~s----~~eIA~~lgis~~tV~~~i~ra~~~Lr~~ 158 (166)
T PRK09639 112 KMTERDRTVLLLRF-S----GYS----YKEIAEALGIKESSVGTTLARAKKKFRKI 158 (166)
T ss_pred cCCHHHHHHHHHHH-c----CCC----HHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 57888888887666 4 332 35799999999999999999999988764
No 104
>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=24.15 E-value=63 Score=20.98 Aligned_cols=21 Identities=14% Similarity=0.180 Sum_probs=18.6
Q ss_pred HHHHHHhCCChhhhhhhhhhh
Q 019151 292 ARLVQETGLQLKQINNWFINQ 312 (345)
Q Consensus 292 ~~LA~~TgLs~kQV~NWFiN~ 312 (345)
..+|+.+|++...|++|..+.
T Consensus 16 ~~~a~~~~~~~~~v~~~~~g~ 36 (58)
T cd00093 16 EELAEKLGVSRSTISRIENGK 36 (58)
T ss_pred HHHHHHHCCCHHHHHHHHcCC
Confidence 488999999999999998775
No 105
>PF13384 HTH_23: Homeodomain-like domain; PDB: 2X48_C.
Probab=24.15 E-value=65 Score=22.33 Aligned_cols=23 Identities=13% Similarity=0.379 Sum_probs=16.9
Q ss_pred HHHHHHHhCCChhhhhhhhhhhh
Q 019151 291 KARLVQETGLQLKQINNWFINQR 313 (345)
Q Consensus 291 K~~LA~~TgLs~kQV~NWFiN~R 313 (345)
...+|+.+|++...|.+|....+
T Consensus 20 ~~~ia~~lgvs~~Tv~~w~kr~~ 42 (50)
T PF13384_consen 20 IREIAKRLGVSRSTVYRWIKRYR 42 (50)
T ss_dssp HHHHHHHHTS-HHHHHHHHT---
T ss_pred HHHHHHHHCcCHHHHHHHHHHcc
Confidence 45899999999999999976544
No 106
>PRK15369 two component system sensor kinase SsrB; Provisional
Probab=23.87 E-value=1.9e+02 Score=24.11 Aligned_cols=48 Identities=13% Similarity=0.185 Sum_probs=38.4
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhcccCC
Q 019151 264 KLPGDTTSLLKAWWLSHAKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHAN 320 (345)
Q Consensus 264 ~lpk~a~~~L~~wf~~h~~~PYPS~~eK~~LA~~TgLs~kQV~NWFiN~RkR~kk~~ 320 (345)
.|++..+++|.-+ ..+ |. ...+|+..+++.+.|.++..+.|++..-.+
T Consensus 149 ~lt~~e~~vl~l~-~~g----~~----~~~Ia~~l~~s~~tv~~~~~~~~~kl~~~~ 196 (211)
T PRK15369 149 LLTPRERQILKLI-TEG----YT----NRDIAEQLSISIKTVETHRLNMMRKLDVHK 196 (211)
T ss_pred CCCHHHHHHHHHH-HCC----CC----HHHHHHHhCCCHHHHHHHHHHHHHHhCCCC
Confidence 5888888888774 442 32 468899999999999999999999987544
No 107
>PF12362 DUF3646: DNA polymerase III gamma and tau subunits C terminal; InterPro: IPR022107 This domain family is found in bacteria, and is approximately 120 amino acids in length. The family is found in association with PF00004 from PFAM. The proteins in this family are frequently annotated as the gamma and tau subunits of DNA polymerase III, however there is little accompanying literature to back this up.
Probab=23.79 E-value=56 Score=28.11 Aligned_cols=24 Identities=25% Similarity=0.296 Sum_probs=20.3
Q ss_pred hhhhHHHHHHHhhCCChHHHHHHH
Q 019151 67 DWETVKCKAEIVGHPLYEQLLSAH 90 (345)
Q Consensus 67 ~~e~~~lKakI~sHPlYp~Ll~A~ 90 (345)
..+.+..++.+..||++-..|.+|
T Consensus 85 ~~~~~~~~~~a~~~P~V~avL~~F 108 (117)
T PF12362_consen 85 AAAKEARRAAARAHPLVKAVLAAF 108 (117)
T ss_pred HHHHHHHHHHHHhCcHHHHHHHHC
Confidence 345567899999999999999887
No 108
>PRK12536 RNA polymerase sigma factor; Provisional
Probab=23.76 E-value=92 Score=27.29 Aligned_cols=48 Identities=19% Similarity=0.033 Sum_probs=37.4
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhcccC
Q 019151 264 KLPGDTTSLLKAWWLSHAKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHA 319 (345)
Q Consensus 264 ~lpk~a~~~L~~wf~~h~~~PYPS~~eK~~LA~~TgLs~kQV~NWFiN~RkR~kk~ 319 (345)
.||+..+.++.-.+... + .-..+|+.+|++...|.+.+...|++.++.
T Consensus 129 ~L~~~~r~v~~l~~~~g----~----s~~EIA~~l~is~~tV~~~l~rar~~Lr~~ 176 (181)
T PRK12536 129 QLPDRQRLPIVHVKLEG----L----SVAETAQLTGLSESAVKVGIHRGLKALAAK 176 (181)
T ss_pred HCCHHHHHHHHHHHHcC----C----CHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 46887888776555553 2 235799999999999999999999998864
No 109
>PRK12542 RNA polymerase sigma factor; Provisional
Probab=23.51 E-value=90 Score=27.40 Aligned_cols=48 Identities=15% Similarity=0.158 Sum_probs=37.6
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhcccC
Q 019151 264 KLPGDTTSLLKAWWLSHAKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHA 319 (345)
Q Consensus 264 ~lpk~a~~~L~~wf~~h~~~PYPS~~eK~~LA~~TgLs~kQV~NWFiN~RkR~kk~ 319 (345)
.||+..+.++.-.+... .+ -..+|+.+|++...|.+.....|++.++.
T Consensus 122 ~L~~~~r~i~~l~~~~g--~s------~~EIA~~lgis~~tVk~~l~Rar~~Lr~~ 169 (185)
T PRK12542 122 ELNESNRQVFKYKVFYN--LT------YQEISSVMGITEANVRKQFERARKRVQNM 169 (185)
T ss_pred hCCHHHHHHHHHHHHcC--CC------HHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 58888888887654442 12 24799999999999999999999988764
No 110
>PRK12519 RNA polymerase sigma factor; Provisional
Probab=23.46 E-value=69 Score=28.25 Aligned_cols=47 Identities=11% Similarity=0.202 Sum_probs=36.4
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhccc
Q 019151 264 KLPGDTTSLLKAWWLSHAKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWH 318 (345)
Q Consensus 264 ~lpk~a~~~L~~wf~~h~~~PYPS~~eK~~LA~~TgLs~kQV~NWFiN~RkR~kk 318 (345)
.||++.+.++.--+... + .-..+|+.+|++...|.+|+...|++.++
T Consensus 141 ~L~~~~~~v~~l~~~~g----~----s~~EIA~~lgis~~tV~~~l~Ra~~~Lr~ 187 (194)
T PRK12519 141 QLPESQRQVLELAYYEG----L----SQSEIAKRLGIPLGTVKARARQGLLKLRE 187 (194)
T ss_pred hCCHHHhhhhhhhhhcC----C----CHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Confidence 57888888886554442 2 23579999999999999999999988775
No 111
>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=23.37 E-value=96 Score=26.99 Aligned_cols=50 Identities=16% Similarity=0.195 Sum_probs=39.7
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhcccCCC
Q 019151 264 KLPGDTTSLLKAWWLSHAKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHANP 321 (345)
Q Consensus 264 ~lpk~a~~~L~~wf~~h~~~PYPS~~eK~~LA~~TgLs~kQV~NWFiN~RkR~kk~~~ 321 (345)
+||+..+.++.-.+... |+ -..+|+.+|++...|.++..-.|++.++...
T Consensus 100 ~L~~~~r~v~~l~~~~g----~s----~~eIA~~lgis~~tV~~~l~Rar~~Lr~~l~ 149 (170)
T TIGR02959 100 ELPDEYREAIRLTELEG----LS----QQEIAEKLGLSLSGAKSRVQRGRKKLKELLE 149 (170)
T ss_pred hCCHHHHHHHHHHHHcC----CC----HHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Confidence 58888888887766553 32 3479999999999999999999999886543
No 112
>PRK11511 DNA-binding transcriptional activator MarA; Provisional
Probab=23.26 E-value=2.1e+02 Score=24.03 Aligned_cols=42 Identities=12% Similarity=0.227 Sum_probs=31.6
Q ss_pred hhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhhhhhhhhh
Q 019151 267 GDTTSLLKAWWLSHAKWPYPTEEDKARLVQETGLQLKQINNWFINQ 312 (345)
Q Consensus 267 k~a~~~L~~wf~~h~~~PYPS~~eK~~LA~~TgLs~kQV~NWFiN~ 312 (345)
......+..|...|+..| ++- ..||+.+|+++.++..+|...
T Consensus 8 ~~~i~~~~~~I~~~~~~~-~sl---~~lA~~~g~S~~~l~r~Fk~~ 49 (127)
T PRK11511 8 AITIHSILDWIEDNLESP-LSL---EKVSERSGYSKWHLQRMFKKE 49 (127)
T ss_pred HHHHHHHHHHHHHhcCCC-CCH---HHHHHHHCcCHHHHHHHHHHH
Confidence 345567778888987666 454 568888999999998888754
No 113
>PRK12537 RNA polymerase sigma factor; Provisional
Probab=22.37 E-value=1.1e+02 Score=26.93 Aligned_cols=48 Identities=15% Similarity=0.230 Sum_probs=37.0
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhcccC
Q 019151 264 KLPGDTTSLLKAWWLSHAKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHA 319 (345)
Q Consensus 264 ~lpk~a~~~L~~wf~~h~~~PYPS~~eK~~LA~~TgLs~kQV~NWFiN~RkR~kk~ 319 (345)
.||+..+.++..-+... .+ -..+|+.+|++...|.+|....|++.++.
T Consensus 133 ~L~~~~r~i~~l~~~~~--~s------~~eIA~~lgis~~tV~~~l~ra~~~Lr~~ 180 (182)
T PRK12537 133 QLEPARRNCILHAYVDG--CS------HAEIAQRLGAPLGTVKAWIKRSLKALREC 180 (182)
T ss_pred hCCHHHHHHHHHHHHcC--CC------HHHHHHHHCCChhhHHHHHHHHHHHHHHH
Confidence 57888888766555442 23 35799999999999999999999887753
No 114
>PRK09645 RNA polymerase sigma factor SigL; Provisional
Probab=21.95 E-value=1e+02 Score=26.48 Aligned_cols=49 Identities=10% Similarity=0.153 Sum_probs=39.1
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhcccCC
Q 019151 264 KLPGDTTSLLKAWWLSHAKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHAN 320 (345)
Q Consensus 264 ~lpk~a~~~L~~wf~~h~~~PYPS~~eK~~LA~~TgLs~kQV~NWFiN~RkR~kk~~ 320 (345)
.||+..+.+|.--+.. .++ -..+|+.+|++...|.+..--.|++.++..
T Consensus 118 ~L~~~~r~vl~L~~~~----g~s----~~EIA~~lgis~~tV~~~l~ra~~~Lr~~l 166 (173)
T PRK09645 118 QLSPEHRAVLVRSYYR----GWS----TAQIAADLGIPEGTVKSRLHYALRALRLAL 166 (173)
T ss_pred hCCHHHHHHHHHHHHc----CCC----HHHHHHHHCcCHHHHHHHHHHHHHHHHHHh
Confidence 4888999988776555 232 347999999999999999999999888654
No 115
>TIGR02948 SigW_bacill RNA polymerase sigma-W factor. This sigma factor is restricted to certain lineages of the order Bacillales.
Probab=21.92 E-value=94 Score=26.94 Aligned_cols=48 Identities=8% Similarity=0.111 Sum_probs=37.2
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhcccC
Q 019151 264 KLPGDTTSLLKAWWLSHAKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHA 319 (345)
Q Consensus 264 ~lpk~a~~~L~~wf~~h~~~PYPS~~eK~~LA~~TgLs~kQV~NWFiN~RkR~kk~ 319 (345)
.||+..+.++.-.+.. .++ -..+|+.+|++...|.+++...|++.+..
T Consensus 136 ~L~~~~r~v~~l~~~~----g~s----~~eIA~~lgis~~~v~~~l~Rar~~Lr~~ 183 (187)
T TIGR02948 136 ALPPKYRMVIVLKYME----DLS----LKEISEILDLPVGTVKTRIHRGREALRKQ 183 (187)
T ss_pred hCCHHHhHHhhhHHhc----CCC----HHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 5788888888664444 222 35789999999999999999999988754
No 116
>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=21.82 E-value=1.3e+02 Score=21.67 Aligned_cols=48 Identities=15% Similarity=0.121 Sum_probs=34.5
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhcccCC
Q 019151 264 KLPGDTTSLLKAWWLSHAKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHAN 320 (345)
Q Consensus 264 ~lpk~a~~~L~~wf~~h~~~PYPS~~eK~~LA~~TgLs~kQV~NWFiN~RkR~kk~~ 320 (345)
.|++.-..+|.-+..- + ....+|...|++++.|.++..+.++|..-.+
T Consensus 3 ~LT~~E~~vl~~l~~G-----~----~~~eIA~~l~is~~tV~~~~~~i~~Kl~~~~ 50 (58)
T PF00196_consen 3 SLTERELEVLRLLAQG-----M----SNKEIAEELGISEKTVKSHRRRIMKKLGVKN 50 (58)
T ss_dssp SS-HHHHHHHHHHHTT-----S-----HHHHHHHHTSHHHHHHHHHHHHHHHHT-SS
T ss_pred ccCHHHHHHHHHHHhc-----C----CcchhHHhcCcchhhHHHHHHHHHHHhCCCC
Confidence 4666677777655433 2 3457899999999999999999999876543
No 117
>PRK08583 RNA polymerase sigma factor SigB; Validated
Probab=21.70 E-value=1.2e+02 Score=28.40 Aligned_cols=48 Identities=10% Similarity=0.159 Sum_probs=38.8
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhcccC
Q 019151 264 KLPGDTTSLLKAWWLSHAKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHA 319 (345)
Q Consensus 264 ~lpk~a~~~L~~wf~~h~~~PYPS~~eK~~LA~~TgLs~kQV~NWFiN~RkR~kk~ 319 (345)
.||+..+.+|.-.|... .+ -..+|+.+|++...|.+|....+++.++.
T Consensus 205 ~L~~~~r~vl~l~~~~g--~s------~~eIA~~l~is~~tV~~~~~ra~~kLr~~ 252 (257)
T PRK08583 205 VLSDREKSIIQCTFIEN--LS------QKETGERLGISQMHVSRLQRQAIKKLREA 252 (257)
T ss_pred hCCHHHHHHHHHHHhCC--CC------HHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 58888999988766552 12 36899999999999999999999988754
No 118
>PF13551 HTH_29: Winged helix-turn helix
Probab=21.69 E-value=4e+02 Score=20.88 Aligned_cols=46 Identities=17% Similarity=0.052 Sum_probs=29.4
Q ss_pred CChhHHHHHHHHHHHccCCC--CCCHHHHHH-H-HHHh--CCChhhhhhhhh
Q 019151 265 LPGDTTSLLKAWWLSHAKWP--YPTEEDKAR-L-VQET--GLQLKQINNWFI 310 (345)
Q Consensus 265 lpk~a~~~L~~wf~~h~~~P--YPS~~eK~~-L-A~~T--gLs~kQV~NWFi 310 (345)
++.+....|.+++.++.... ..+...-.. | .+.+ .++...|..|+.
T Consensus 58 l~~~~~~~l~~~~~~~p~~g~~~~t~~~l~~~l~~~~~~~~~s~~ti~r~L~ 109 (112)
T PF13551_consen 58 LSEEQRAQLIELLRENPPEGRSRWTLEELAEWLIEEEFGIDVSPSTIRRILK 109 (112)
T ss_pred CCHHHHHHHHHHHHHCCCCCCCcccHHHHHHHHHHhccCccCCHHHHHHHHH
Confidence 89999999999999952221 233343333 4 3333 377788888764
No 119
>PRK12529 RNA polymerase sigma factor; Provisional
Probab=21.40 E-value=1.3e+02 Score=26.33 Aligned_cols=49 Identities=8% Similarity=0.026 Sum_probs=38.8
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhcccCC
Q 019151 264 KLPGDTTSLLKAWWLSHAKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHAN 320 (345)
Q Consensus 264 ~lpk~a~~~L~~wf~~h~~~PYPS~~eK~~LA~~TgLs~kQV~NWFiN~RkR~kk~~ 320 (345)
.||++.+.++.-.+... .+ -..+|+.+|++..-|.+.+...+.+.....
T Consensus 127 ~Lp~~~R~v~~L~~~~g--~s------~~EIA~~lgis~~tVk~~l~rAl~~~~~~~ 175 (178)
T PRK12529 127 TLRPRVKQAFLMATLDG--MK------QKDIAQALDIALPTVKKYIHQAYVTCLSLM 175 (178)
T ss_pred hCCHHHHHHHHHHHHcC--CC------HHHHHHHHCCCHHHHHHHHHHHHHHHHHhC
Confidence 58999999887766653 22 247999999999999999999888876543
No 120
>PRK09415 RNA polymerase factor sigma C; Reviewed
Probab=21.34 E-value=91 Score=27.31 Aligned_cols=47 Identities=9% Similarity=0.175 Sum_probs=37.5
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhccc
Q 019151 264 KLPGDTTSLLKAWWLSHAKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWH 318 (345)
Q Consensus 264 ~lpk~a~~~L~~wf~~h~~~PYPS~~eK~~LA~~TgLs~kQV~NWFiN~RkR~kk 318 (345)
+||+..+.++.-.+... .+ -..+|+.+|++...|.++..-.|++.++
T Consensus 127 ~L~~~~r~v~~l~~~~g--~s------~~EIA~~l~is~~tv~~~l~Ra~~~Lr~ 173 (179)
T PRK09415 127 SLPIKYREVIYLFYYEE--LS------IKEIAEVTGVNENTVKTRLKKAKELLKK 173 (179)
T ss_pred hCCHHHhhHhHhHHhcC--CC------HHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 58888988876655553 22 2479999999999999999999988775
No 121
>PF12323 HTH_OrfB_IS605: Helix-turn-helix domain; InterPro: IPR021027 This entry represents an N-terminal helix-turn-helix domain found in a variety of putative transposases [, , ]. It is usually associated with PF01385 from PFAM and PF07282 from PFAM.
Probab=21.31 E-value=70 Score=22.35 Aligned_cols=35 Identities=29% Similarity=0.567 Sum_probs=25.8
Q ss_pred CCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhcccC
Q 019151 284 PYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHA 319 (345)
Q Consensus 284 PYPS~~eK~~LA~~TgLs~kQV~NWFiN~RkR~kk~ 319 (345)
=|||.+++..|.+..|.. ..|-||....|...++.
T Consensus 9 l~Pt~~Q~~~L~~~~~~~-R~vyN~~L~~~~~~y~~ 43 (46)
T PF12323_consen 9 LYPTKEQEEKLERWFGAC-RFVYNWALAERKEAYKQ 43 (46)
T ss_pred EecCHHHHHHHHHHHHHH-HHHHHHHHHHHHHHHHH
Confidence 378888888888777653 56788888888776543
No 122
>smart00530 HTH_XRE Helix-turn-helix XRE-family like proteins.
Probab=21.25 E-value=77 Score=20.38 Aligned_cols=22 Identities=9% Similarity=0.176 Sum_probs=18.4
Q ss_pred HHHHHHHhCCChhhhhhhhhhh
Q 019151 291 KARLVQETGLQLKQINNWFINQ 312 (345)
Q Consensus 291 K~~LA~~TgLs~kQV~NWFiN~ 312 (345)
...+|+.+|++...|..|..+.
T Consensus 13 ~~~la~~~~i~~~~i~~~~~~~ 34 (56)
T smart00530 13 QEELAEKLGVSRSTLSRIENGK 34 (56)
T ss_pred HHHHHHHhCCCHHHHHHHHCCC
Confidence 4488999999999999997654
No 123
>PF06729 CENP-R: Kinetochore component, CENP-R; InterPro: IPR009601 This family consists of mammalian nuclear receptor co-activator NRIF3 proteins. NRIF3 exhibits a distinct receptor specificity in interacting with and potentiating the activity of only TRs and RXRs but not other examined nuclear receptors. NRIF3 as a coregulator that possesses both transactivation and transrepression domains and/or functions. Collectively, the NRIF3 family of coregulators may play dual roles in mediating both positive and negative regulatory effects on gene expression [].
Probab=21.23 E-value=6e+02 Score=22.76 Aligned_cols=33 Identities=27% Similarity=0.329 Sum_probs=20.5
Q ss_pred CChHHHHHHHHHHHHHHHHHHHHhHHHhhhhHHHHHHHhHHH
Q 019151 130 DDKELDQFMTHYVLLLYSFKEQLQQHVRVHAMEAVMACWDLE 171 (345)
Q Consensus 130 ~dpELDqFMeaYc~vL~kykEEL~kP~~~~~~EA~~fc~~iE 171 (345)
...+.|.||.- |-+-+.-+.+ |||++.-+.+|.
T Consensus 54 p~t~dD~fm~L----~SkvekS~ee-----ime~~qnL~slQ 86 (139)
T PF06729_consen 54 PQTEDDEFMVL----LSKVEKSLEE-----IMEIRQNLSSLQ 86 (139)
T ss_pred CCcchhHHHHH----HHHHHHHHHH-----HHHHHHHHHHHH
Confidence 45677999964 5555555554 577776665554
No 124
>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=21.05 E-value=50 Score=29.22 Aligned_cols=49 Identities=10% Similarity=0.080 Sum_probs=37.0
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhcccCC
Q 019151 264 KLPGDTTSLLKAWWLSHAKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHAN 320 (345)
Q Consensus 264 ~lpk~a~~~L~~wf~~h~~~PYPS~~eK~~LA~~TgLs~kQV~NWFiN~RkR~kk~~ 320 (345)
.||...+.++.-.+.. .+ .-..+|+.+|++...|.++..-.|++.++..
T Consensus 131 ~Lp~~~r~i~~L~~~~----g~----s~~EIA~~lgis~~tVk~~l~Rar~~Lr~~l 179 (193)
T TIGR02947 131 GLPEEFRQAVYLADVE----GF----AYKEIAEIMGTPIGTVMSRLHRGRKQLRKQL 179 (193)
T ss_pred hCCHHHhhheeehhhc----CC----CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 5777787777544444 22 2357999999999999999999999988643
No 125
>PRK12515 RNA polymerase sigma factor; Provisional
Probab=20.92 E-value=1.1e+02 Score=26.81 Aligned_cols=48 Identities=10% Similarity=0.135 Sum_probs=38.0
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhcccC
Q 019151 264 KLPGDTTSLLKAWWLSHAKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHA 319 (345)
Q Consensus 264 ~lpk~a~~~L~~wf~~h~~~PYPS~~eK~~LA~~TgLs~kQV~NWFiN~RkR~kk~ 319 (345)
.||+..+.+|.--+.. .+ .-..+|+.+|++...|.+-+...|++.++.
T Consensus 131 ~L~~~~r~vl~l~~~~----~~----s~~eIA~~lgis~~tV~~~l~Rar~~Lr~~ 178 (189)
T PRK12515 131 KLSPAHREIIDLVYYH----EK----SVEEVGEIVGIPESTVKTRMFYARKKLAEL 178 (189)
T ss_pred hCCHHHHHHHHHHHHc----CC----CHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence 5788898888665544 22 235799999999999999999999988764
No 126
>PF13411 MerR_1: MerR HTH family regulatory protein; PDB: 2JML_A 3GP4_A 3GPV_B.
Probab=20.91 E-value=72 Score=23.45 Aligned_cols=18 Identities=6% Similarity=0.143 Sum_probs=16.2
Q ss_pred HHHHHHhCCChhhhhhhh
Q 019151 292 ARLVQETGLQLKQINNWF 309 (345)
Q Consensus 292 ~~LA~~TgLs~kQV~NWF 309 (345)
..+|+.+|++..+|..|-
T Consensus 4 ~eva~~~gvs~~tlr~y~ 21 (69)
T PF13411_consen 4 KEVAKLLGVSPSTLRYYE 21 (69)
T ss_dssp HHHHHHTTTTHHHHHHHH
T ss_pred HHHHHHHCcCHHHHHHHH
Confidence 478999999999999993
No 127
>PRK09647 RNA polymerase sigma factor SigE; Reviewed
Probab=20.90 E-value=1.3e+02 Score=27.26 Aligned_cols=48 Identities=15% Similarity=0.225 Sum_probs=36.7
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhcccC
Q 019151 264 KLPGDTTSLLKAWWLSHAKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHA 319 (345)
Q Consensus 264 ~lpk~a~~~L~~wf~~h~~~PYPS~~eK~~LA~~TgLs~kQV~NWFiN~RkR~kk~ 319 (345)
.||...+.++.--+... .+| ..+|+.+|++...|.++..-.|++.++.
T Consensus 138 ~L~~~~r~v~~L~~~~g--~s~------~EIA~~Lgis~~tV~~~l~RArk~Lr~~ 185 (203)
T PRK09647 138 SLPPEFRAAVVLCDIEG--LSY------EEIAATLGVKLGTVRSRIHRGRQQLRAA 185 (203)
T ss_pred hCCHHHHHHHHHHHHcC--CCH------HHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 57777777665544442 333 4799999999999999999999998864
No 128
>PRK06986 fliA flagellar biosynthesis sigma factor; Validated
Probab=20.79 E-value=94 Score=28.69 Aligned_cols=48 Identities=13% Similarity=0.169 Sum_probs=38.3
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhcccC
Q 019151 264 KLPGDTTSLLKAWWLSHAKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHA 319 (345)
Q Consensus 264 ~lpk~a~~~L~~wf~~h~~~PYPS~~eK~~LA~~TgLs~kQV~NWFiN~RkR~kk~ 319 (345)
.||...+.++..-|.. .+ .-..+|+.+|++...|.++....|++.++.
T Consensus 184 ~L~~~~r~vl~l~~~~----g~----s~~EIA~~lgis~~tV~~~~~ra~~~Lr~~ 231 (236)
T PRK06986 184 SLPEREQLVLSLYYQE----EL----NLKEIGAVLGVSESRVSQIHSQAIKRLRAR 231 (236)
T ss_pred hCCHHHHHHHHhHhcc----CC----CHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 4788888888766544 22 346899999999999999999999998764
No 129
>PRK07037 extracytoplasmic-function sigma-70 factor; Validated
Probab=20.72 E-value=1.1e+02 Score=25.91 Aligned_cols=48 Identities=15% Similarity=0.179 Sum_probs=37.3
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhcccC
Q 019151 264 KLPGDTTSLLKAWWLSHAKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHA 319 (345)
Q Consensus 264 ~lpk~a~~~L~~wf~~h~~~PYPS~~eK~~LA~~TgLs~kQV~NWFiN~RkR~kk~ 319 (345)
.||+..+.++.-.|... .+ -..+|+.+|++...|.....-.|++.++.
T Consensus 109 ~L~~~~r~v~~l~~~~~--~s------~~EIA~~lgis~~tV~~~l~ra~~~lr~~ 156 (163)
T PRK07037 109 ELPARTRYAFEMYRLHG--ET------QKDIARELGVSPTLVNFMIRDALVHCRKC 156 (163)
T ss_pred hCCHHHHHHHHHHHHcC--CC------HHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 58888988886655442 22 35799999999999999988888887754
No 130
>PRK12535 RNA polymerase sigma factor; Provisional
Probab=20.67 E-value=1.1e+02 Score=27.61 Aligned_cols=50 Identities=12% Similarity=0.090 Sum_probs=39.8
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhcccCCC
Q 019151 264 KLPGDTTSLLKAWWLSHAKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHANP 321 (345)
Q Consensus 264 ~lpk~a~~~L~~wf~~h~~~PYPS~~eK~~LA~~TgLs~kQV~NWFiN~RkR~kk~~~ 321 (345)
+||+..+.++.--+... .+ -..+|+.+|++...|.++....|++.++...
T Consensus 133 ~Lp~~~r~v~~l~~~~g--~s------~~EIAe~lgis~~tV~~~l~Rar~~Lr~~l~ 182 (196)
T PRK12535 133 ALPPERREALILTQVLG--YT------YEEAAKIADVRVGTIRSRVARARADLIAATA 182 (196)
T ss_pred cCCHHHHHHhhhHHHhC--CC------HHHHHHHhCCCHHHHHHHHHHHHHHHHHHhc
Confidence 58888888886665553 22 3579999999999999999999999887554
No 131
>PF13865 FoP_duplication: C-terminal duplication domain of Friend of PRMT1
Probab=20.12 E-value=99 Score=24.31 Aligned_cols=9 Identities=44% Similarity=0.667 Sum_probs=3.4
Q ss_pred HHHHHHHHH
Q 019151 133 ELDQFMTHY 141 (345)
Q Consensus 133 ELDqFMeaY 141 (345)
|||.-|++|
T Consensus 44 eLDaELD~Y 52 (74)
T PF13865_consen 44 ELDAELDAY 52 (74)
T ss_pred HHHHHHHHH
Confidence 333333333
Done!