Query 046813
Match_columns 250
No_of_seqs 195 out of 837
Neff 4.0
Searched_HMMs 46136
Date Fri Mar 29 04:42:24 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/046813.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/046813hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG0489 Transcription factor z 99.8 6.9E-21 1.5E-25 171.9 2.6 85 5-96 138-222 (261)
2 KOG0842 Transcription factor t 99.8 4.1E-19 8.9E-24 164.9 6.8 71 24-99 149-219 (307)
3 KOG0843 Transcription factor E 99.8 4E-19 8.7E-24 155.1 6.2 89 2-95 67-164 (197)
4 KOG0487 Transcription factor A 99.8 2.7E-19 5.9E-24 166.2 5.4 71 23-98 230-300 (308)
5 KOG0484 Transcription factor P 99.8 3.7E-19 8.1E-24 144.6 5.4 70 23-97 12-81 (125)
6 KOG0485 Transcription factor N 99.8 7E-19 1.5E-23 157.8 5.5 85 4-95 82-166 (268)
7 KOG0848 Transcription factor C 99.7 7.2E-19 1.6E-23 161.3 4.2 86 6-97 178-263 (317)
8 KOG0488 Transcription factor B 99.7 9.1E-19 2E-23 162.4 4.5 66 24-94 168-233 (309)
9 PF00046 Homeobox: Homeobox do 99.7 2E-18 4.3E-23 120.7 2.8 57 29-90 1-57 (57)
10 KOG0483 Transcription factor H 99.7 3.2E-18 7E-23 150.7 4.1 69 31-104 53-121 (198)
11 KOG0494 Transcription factor C 99.7 8E-18 1.7E-22 154.2 4.7 69 22-95 134-203 (332)
12 KOG0492 Transcription factor M 99.7 2.9E-17 6.4E-22 146.5 5.7 67 24-95 140-206 (246)
13 KOG2251 Homeobox transcription 99.7 8.3E-17 1.8E-21 143.9 7.1 82 9-95 17-99 (228)
14 KOG0850 Transcription factor D 99.7 5.1E-17 1.1E-21 146.2 5.0 69 22-95 116-184 (245)
15 smart00389 HOX Homeodomain. DN 99.6 2.2E-16 4.9E-21 109.0 2.7 56 29-89 1-56 (56)
16 cd00086 homeodomain Homeodomai 99.6 4.3E-16 9.4E-21 107.9 3.1 58 29-91 1-58 (59)
17 KOG0493 Transcription factor E 99.6 6E-16 1.3E-20 142.2 3.2 61 27-92 245-305 (342)
18 TIGR01565 homeo_ZF_HD homeobox 99.6 4.6E-15 1E-19 108.2 5.7 52 29-85 2-57 (58)
19 KOG0844 Transcription factor E 99.6 1.7E-15 3.6E-20 141.7 4.1 64 27-95 180-243 (408)
20 COG5576 Homeodomain-containing 99.5 5.2E-15 1.1E-19 126.1 5.6 66 25-95 48-113 (156)
21 KOG0486 Transcription factor P 99.5 5.6E-15 1.2E-19 138.0 6.2 67 25-96 109-175 (351)
22 KOG0491 Transcription factor B 99.4 2E-14 4.4E-19 124.7 -1.9 68 25-97 97-164 (194)
23 KOG0490 Transcription factor, 99.4 1.4E-13 3E-18 117.6 3.1 64 25-93 57-120 (235)
24 KOG4577 Transcription factor L 99.4 2.3E-13 5.1E-18 126.6 4.3 63 28-95 167-229 (383)
25 KOG3802 Transcription factor O 99.4 5.5E-13 1.2E-17 127.5 5.5 61 27-92 293-353 (398)
26 KOG0847 Transcription factor, 99.3 6.2E-13 1.3E-17 120.1 2.1 65 26-95 165-229 (288)
27 KOG0849 Transcription factor P 99.2 6.4E-12 1.4E-16 118.5 3.8 69 23-96 171-239 (354)
28 KOG1168 Transcription factor A 98.9 1.5E-09 3.2E-14 101.7 3.8 60 28-92 309-368 (385)
29 KOG0490 Transcription factor, 98.3 3.5E-07 7.7E-12 78.2 3.6 63 26-93 151-213 (235)
30 KOG0774 Transcription factor P 98.3 1.4E-06 3E-11 81.0 7.5 63 28-94 188-252 (334)
31 KOG0775 Transcription factor S 98.3 3.9E-07 8.5E-12 84.7 3.8 51 35-90 183-233 (304)
32 KOG2252 CCAAT displacement pro 98.3 4.6E-07 1E-11 90.2 3.0 59 25-88 417-475 (558)
33 PF05920 Homeobox_KN: Homeobox 97.9 1.5E-06 3.2E-11 59.1 -0.6 32 52-87 9-40 (40)
34 KOG1146 Homeobox protein [Gene 97.5 7.8E-05 1.7E-09 80.6 4.3 63 26-93 901-963 (1406)
35 KOG0773 Transcription factor M 96.5 0.0024 5.2E-08 59.3 3.7 70 26-99 237-308 (342)
36 KOG3623 Homeobox transcription 93.8 0.03 6.6E-07 58.7 1.7 50 40-94 568-617 (1007)
37 PF11569 Homez: Homeodomain le 91.5 0.044 9.6E-07 40.3 -0.5 41 40-85 10-50 (56)
38 PF04218 CENP-B_N: CENP-B N-te 91.1 0.26 5.5E-06 34.9 3.1 47 29-85 1-47 (53)
39 KOG1146 Homeobox protein [Gene 86.4 0.69 1.5E-05 51.3 3.8 67 21-92 698-764 (1406)
40 cd06171 Sigma70_r4 Sigma70, re 76.9 1.4 3E-05 28.2 1.2 43 34-86 10-52 (55)
41 KOG3755 SATB1 matrix attachmen 68.5 1.2 2.6E-05 46.3 -0.9 70 21-93 684-759 (769)
42 PRK09652 RNA polymerase sigma 66.4 8 0.00017 31.1 3.7 45 34-90 128-172 (182)
43 PRK03975 tfx putative transcri 66.3 10 0.00022 32.3 4.4 55 33-100 5-59 (141)
44 PF04967 HTH_10: HTH DNA bindi 65.6 9.1 0.0002 27.6 3.4 38 35-77 1-40 (53)
45 PF01527 HTH_Tnp_1: Transposas 64.7 2.7 5.9E-05 30.2 0.5 42 30-81 2-44 (76)
46 PF04545 Sigma70_r4: Sigma-70, 61.6 6.7 0.00015 26.5 2.0 37 34-80 4-40 (50)
47 PRK09642 RNA polymerase sigma 58.8 9 0.0002 30.9 2.7 47 35-91 107-153 (160)
48 cd00569 HTH_Hin_like Helix-tur 57.2 17 0.00038 20.3 3.1 37 35-81 6-42 (42)
49 COG3413 Predicted DNA binding 54.2 15 0.00032 32.1 3.4 39 34-77 155-195 (215)
50 TIGR02937 sigma70-ECF RNA poly 54.2 11 0.00024 28.5 2.4 44 34-87 110-153 (158)
51 PF08281 Sigma70_r4_2: Sigma-7 52.4 6.7 0.00015 26.6 0.8 39 35-83 11-49 (54)
52 PRK09646 RNA polymerase sigma 50.1 17 0.00037 30.6 3.1 37 35-81 143-179 (194)
53 PRK12515 RNA polymerase sigma 45.8 21 0.00045 29.8 2.9 45 34-88 131-175 (189)
54 PF10925 DUF2680: Protein of u 45.6 14 0.0003 27.1 1.6 38 35-77 1-38 (59)
55 PRK12519 RNA polymerase sigma 44.5 20 0.00043 29.9 2.6 42 35-86 142-183 (194)
56 PRK06759 RNA polymerase factor 44.0 18 0.00039 28.7 2.2 40 34-83 106-145 (154)
57 PRK04217 hypothetical protein; 43.9 41 0.00089 27.5 4.2 48 30-87 38-85 (110)
58 PRK12526 RNA polymerase sigma 43.7 22 0.00047 30.5 2.8 38 35-82 154-191 (206)
59 PRK12514 RNA polymerase sigma 43.5 27 0.00058 28.7 3.2 43 35-87 130-172 (179)
60 KOG3623 Homeobox transcription 43.0 87 0.0019 34.0 7.4 57 29-90 627-683 (1007)
61 PF12824 MRP-L20: Mitochondria 43.0 53 0.0011 28.6 5.0 48 31-85 82-129 (164)
62 PF10668 Phage_terminase: Phag 42.5 6.8 0.00015 29.1 -0.4 17 60-80 26-42 (60)
63 PRK11924 RNA polymerase sigma 42.2 31 0.00066 27.7 3.3 45 35-89 126-170 (179)
64 TIGR02948 SigW_bacill RNA poly 42.1 21 0.00045 29.3 2.3 45 34-88 136-180 (187)
65 TIGR02985 Sig70_bacteroi1 RNA 41.8 23 0.0005 27.8 2.5 39 35-83 114-152 (161)
66 PLN02705 beta-amylase 41.4 49 0.0011 34.9 5.3 19 58-76 94-116 (681)
67 PF13936 HTH_38: Helix-turn-he 41.0 8.4 0.00018 26.1 -0.1 37 33-79 3-39 (44)
68 TIGR02959 SigZ RNA polymerase 40.9 23 0.00051 29.2 2.5 39 34-82 100-138 (170)
69 PRK09637 RNA polymerase sigma 40.0 31 0.00068 28.9 3.1 45 34-90 106-150 (181)
70 PRK12512 RNA polymerase sigma 39.4 28 0.00062 28.7 2.7 47 34-90 131-177 (184)
71 PRK09644 RNA polymerase sigma 39.1 30 0.00064 28.2 2.8 43 35-87 109-151 (165)
72 PF02796 HTH_7: Helix-turn-hel 39.1 11 0.00023 25.5 0.2 37 34-80 5-41 (45)
73 PF00196 GerE: Bacterial regul 38.8 14 0.00031 25.6 0.8 44 34-88 3-46 (58)
74 PRK10100 DNA-binding transcrip 38.5 22 0.00047 31.4 2.0 51 34-95 155-205 (216)
75 TIGR02989 Sig-70_gvs1 RNA poly 38.4 26 0.00055 28.0 2.3 37 35-81 112-148 (159)
76 PRK12537 RNA polymerase sigma 38.1 36 0.00079 28.2 3.2 38 35-82 134-171 (182)
77 cd06170 LuxR_C_like C-terminal 38.0 31 0.00067 22.5 2.3 36 36-82 2-37 (57)
78 PRK09047 RNA polymerase factor 38.0 27 0.00058 27.9 2.3 38 35-82 107-144 (161)
79 PRK12541 RNA polymerase sigma 37.8 23 0.0005 28.6 1.9 39 34-82 112-150 (161)
80 PHA02955 hypothetical protein; 37.7 32 0.00069 31.6 2.9 44 37-84 60-103 (213)
81 PRK09639 RNA polymerase sigma 37.7 37 0.00081 27.3 3.1 44 34-90 112-155 (166)
82 TIGR02952 Sig70_famx2 RNA poly 37.6 37 0.00081 27.2 3.1 37 35-81 123-159 (170)
83 smart00421 HTH_LUXR helix_turn 36.5 26 0.00056 22.6 1.7 37 35-82 4-40 (58)
84 PRK12532 RNA polymerase sigma 36.5 26 0.00057 29.3 2.1 47 34-90 136-182 (195)
85 PRK12531 RNA polymerase sigma 35.4 31 0.00067 29.0 2.4 37 35-81 142-178 (194)
86 TIGR02999 Sig-70_X6 RNA polyme 34.8 34 0.00074 28.1 2.5 41 35-85 135-175 (183)
87 smart00027 EH Eps15 homology d 34.7 33 0.00071 26.0 2.2 46 33-82 2-51 (96)
88 TIGR02983 SigE-fam_strep RNA p 33.8 35 0.00076 27.4 2.4 42 36-87 112-153 (162)
89 PF12323 HTH_OrfB_IS605: Helix 33.4 29 0.00062 23.3 1.5 23 28-50 4-26 (46)
90 PRK05602 RNA polymerase sigma 33.1 35 0.00076 28.3 2.3 38 35-82 129-166 (186)
91 PRK09648 RNA polymerase sigma 33.0 38 0.00083 28.1 2.6 44 34-89 139-182 (189)
92 PRK09413 IS2 repressor TnpA; R 32.5 38 0.00083 27.2 2.4 41 33-83 11-52 (121)
93 TIGR02943 Sig70_famx1 RNA poly 32.3 42 0.00092 28.3 2.7 45 35-89 132-176 (188)
94 PRK00118 putative DNA-binding 32.2 40 0.00086 27.4 2.4 46 35-90 18-63 (104)
95 PRK12538 RNA polymerase sigma 32.1 44 0.00095 29.7 2.9 44 36-89 173-216 (233)
96 PRK09651 RNA polymerase sigma 31.3 49 0.0011 27.3 2.9 38 34-81 119-156 (172)
97 PRK12530 RNA polymerase sigma 30.9 58 0.0012 27.4 3.3 38 35-82 135-172 (189)
98 PRK06930 positive control sigm 30.8 53 0.0011 28.3 3.1 47 34-90 114-160 (170)
99 PRK06811 RNA polymerase factor 30.8 43 0.00093 28.1 2.5 38 34-81 131-168 (189)
100 PF13443 HTH_26: Cro/C1-type H 30.5 23 0.00051 24.4 0.7 37 59-99 13-49 (63)
101 PRK12546 RNA polymerase sigma 30.4 41 0.00088 28.7 2.3 45 35-89 114-158 (188)
102 PRK12536 RNA polymerase sigma 29.9 46 0.00099 27.6 2.5 25 59-87 148-172 (181)
103 PRK07037 extracytoplasmic-func 29.0 51 0.0011 26.5 2.6 36 35-80 110-145 (163)
104 TIGR02939 RpoE_Sigma70 RNA pol 28.8 37 0.00081 27.8 1.8 25 59-89 157-181 (190)
105 PRK09645 RNA polymerase sigma 27.9 46 0.001 27.1 2.2 38 35-82 119-156 (173)
106 PRK12545 RNA polymerase sigma 27.5 61 0.0013 27.6 2.9 43 35-89 140-182 (201)
107 TIGR02954 Sig70_famx3 RNA poly 27.2 62 0.0013 26.3 2.8 39 34-82 119-157 (169)
108 PF13518 HTH_28: Helix-turn-he 26.8 43 0.00093 22.0 1.5 31 41-82 4-34 (52)
109 PRK12513 RNA polymerase sigma 26.5 31 0.00067 28.8 0.9 27 59-89 158-184 (194)
110 TIGR00721 tfx DNA-binding prot 26.5 88 0.0019 26.6 3.6 47 32-91 4-50 (137)
111 PRK12524 RNA polymerase sigma 26.2 58 0.0013 27.4 2.5 38 35-82 137-174 (196)
112 PRK12516 RNA polymerase sigma 26.1 70 0.0015 27.0 3.0 39 35-83 117-155 (187)
113 PF08280 HTH_Mga: M protein tr 25.9 34 0.00075 24.2 0.9 46 37-107 5-50 (59)
114 PRK12520 RNA polymerase sigma 25.8 77 0.0017 26.4 3.2 39 35-83 132-170 (191)
115 PRK11923 algU RNA polymerase s 25.5 68 0.0015 26.7 2.8 20 60-83 158-177 (193)
116 PRK12543 RNA polymerase sigma 25.4 1E+02 0.0022 25.5 3.8 46 35-90 118-163 (179)
117 PLN03105 TCP24 transcription f 25.4 2.8E+02 0.0061 26.5 7.0 26 184-210 233-263 (324)
118 PF06056 Terminase_5: Putative 25.3 23 0.0005 25.7 -0.1 29 44-82 7-35 (58)
119 PRK09647 RNA polymerase sigma 24.9 81 0.0018 27.2 3.2 39 35-83 139-177 (203)
120 PF07750 GcrA: GcrA cell cycle 24.6 1.2E+02 0.0027 26.1 4.3 35 34-77 2-36 (162)
121 COG4566 TtrR Response regulato 24.4 1.3E+02 0.0028 27.5 4.4 54 34-102 142-195 (202)
122 PF07638 Sigma70_ECF: ECF sigm 24.3 64 0.0014 27.4 2.5 42 37-88 138-179 (185)
123 PRK12539 RNA polymerase sigma 24.1 72 0.0016 26.5 2.7 39 34-82 131-169 (184)
124 PRK13919 putative RNA polymera 24.0 66 0.0014 26.5 2.4 39 34-82 135-173 (186)
125 PRK09643 RNA polymerase sigma 23.4 1.3E+02 0.0028 25.4 4.1 44 35-90 135-178 (192)
126 PRK12544 RNA polymerase sigma 23.3 97 0.0021 26.8 3.4 46 35-90 149-194 (206)
127 PRK12547 RNA polymerase sigma 23.3 73 0.0016 26.0 2.5 39 34-82 112-150 (164)
128 PRK12533 RNA polymerase sigma 23.2 56 0.0012 28.7 1.9 39 35-83 135-173 (216)
129 PRK08295 RNA polymerase factor 23.1 72 0.0016 26.7 2.5 38 34-82 155-192 (208)
130 PRK12529 RNA polymerase sigma 22.8 73 0.0016 26.4 2.5 39 34-82 127-165 (178)
131 PF08880 QLQ: QLQ; InterPro: 22.4 67 0.0014 21.6 1.8 13 34-46 2-14 (37)
132 PRK12542 RNA polymerase sigma 22.2 95 0.0021 25.7 3.1 43 35-89 123-165 (185)
133 COG4367 Uncharacterized protei 21.7 61 0.0013 26.4 1.7 69 34-114 2-74 (97)
134 cd00131 PAX Paired Box domain 21.3 89 0.0019 25.6 2.7 44 35-83 76-126 (128)
135 PRK12522 RNA polymerase sigma 21.2 1.1E+02 0.0024 25.0 3.2 19 60-82 139-157 (173)
136 PRK06986 fliA flagellar biosyn 20.7 82 0.0018 27.5 2.5 45 36-90 186-230 (236)
137 PRK10360 DNA-binding transcrip 20.3 65 0.0014 25.7 1.6 43 34-87 137-179 (196)
138 PRK09636 RNA polymerase sigma 20.1 78 0.0017 28.6 2.3 46 35-90 116-161 (293)
139 PRK10651 transcriptional regul 20.1 59 0.0013 25.9 1.3 48 34-92 155-202 (216)
No 1
>KOG0489 consensus Transcription factor zerknullt and related HOX domain proteins [General function prediction only]
Probab=99.81 E-value=6.9e-21 Score=171.89 Aligned_cols=85 Identities=15% Similarity=0.137 Sum_probs=69.1
Q ss_pred CCCCCCcccccCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhHhcCCCCCCceeeecccc
Q 046813 5 GDNNNNMGMVSGGGGGGGGGTTLSSSSRWNPTKEQINMLESLYAQGIRTPSAEQIQQITTRLRAYGHIEGKNVFYWFQNH 84 (250)
Q Consensus 5 ~~~~~~~~~~s~gg~~g~g~~~~~rR~Rt~fT~eQL~~LE~~F~~~~~yPs~e~R~qLA~~L~~~G~L~erqVqvWFQNR 84 (250)
..++||...-.+.. ..+.....||.|+.||..||.+||.+|+.| +|.++.+|.+||..| +|+|+|||||||||
T Consensus 138 ~~~p~~~~~~~~~~--~~~~~~~~kR~RtayT~~QllELEkEFhfN-~YLtR~RRiEiA~~L----~LtErQIKIWFQNR 210 (261)
T KOG0489|consen 138 QIYPWMKSTANYLS--SSETGGKSKRRRTAFTRYQLLELEKEFHFN-KYLTRSRRIEIAHAL----NLTERQIKIWFQNR 210 (261)
T ss_pred ccccchhhhhcccc--cccccCCCCCCCcccchhhhhhhhhhhccc-cccchHHHHHHHhhc----chhHHHHHHHHHHH
Confidence 46777776542111 111122278999999999999999999999 599999999999999 79999999999999
Q ss_pred hhHHHHHHHHHH
Q 046813 85 KARQRQKQKQER 96 (250)
Q Consensus 85 RAR~Krkq~~~~ 96 (250)
|+||||..+...
T Consensus 211 RMK~Kk~~k~~~ 222 (261)
T KOG0489|consen 211 RMKWKKENKAKS 222 (261)
T ss_pred HHHHHHhhcccc
Confidence 999999877654
No 2
>KOG0842 consensus Transcription factor tinman/NKX2-3, contains HOX domain [Transcription]
Probab=99.77 E-value=4.1e-19 Score=164.95 Aligned_cols=71 Identities=24% Similarity=0.352 Sum_probs=65.7
Q ss_pred CCCCCCCCCCCCCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhHhcCCCCCCceeeecccchhHHHHHHHHHHHHH
Q 046813 24 GTTLSSSSRWNPTKEQINMLESLYAQGIRTPSAEQIQQITTRLRAYGHIEGKNVFYWFQNHKARQRQKQKQERTAF 99 (250)
Q Consensus 24 ~~~~~rR~Rt~fT~eQL~~LE~~F~~~~~yPs~e~R~qLA~~L~~~G~L~erqVqvWFQNRRAR~Krkq~~~~~a~ 99 (250)
+..++||+|.-||+.|+.+||+.|++. +|.+..+|++||..| +||+.||||||||||.|.||+++++.+..
T Consensus 149 ~~~~kRKrRVLFSqAQV~ELERRFrqQ-RYLSAPERE~LA~~L----rLT~TQVKIWFQNrRYK~KR~~~dk~~~~ 219 (307)
T KOG0842|consen 149 GKRKKRKRRVLFSQAQVYELERRFRQQ-RYLSAPEREHLASSL----RLTPTQVKIWFQNRRYKTKRQQKDKALEA 219 (307)
T ss_pred ccccccccccccchhHHHHHHHHHHhh-hccccHhHHHHHHhc----CCCchheeeeeecchhhhhhhhhhhhhhc
Confidence 355778899999999999999999999 699999999999999 69999999999999999999999987664
No 3
>KOG0843 consensus Transcription factor EMX1 and related HOX domain proteins [Transcription]
Probab=99.77 E-value=4e-19 Score=155.11 Aligned_cols=89 Identities=18% Similarity=0.197 Sum_probs=73.4
Q ss_pred CCCCCCCCCcccccCC-CCC--CC------CCCCCCCCCCCCCCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhHhcCCC
Q 046813 2 EGDGDNNNNMGMVSGG-GGG--GG------GGTTLSSSSRWNPTKEQINMLESLYAQGIRTPSAEQIQQITTRLRAYGHI 72 (250)
Q Consensus 2 ~~~~~~~~~~~~~s~g-g~~--g~------g~~~~~rR~Rt~fT~eQL~~LE~~F~~~~~yPs~e~R~qLA~~L~~~G~L 72 (250)
.++...+|++..++.- +-+ -. =...+++|.||.||.+||..||..|+.+. |....+|++||+.| + |
T Consensus 67 ~~~~~~p~~~~~~~~~~~~~~~~~~~l~~~~~~~~~kr~RT~ft~~Ql~~LE~~F~~~~-Yvvg~eR~~LA~~L---~-L 141 (197)
T KOG0843|consen 67 PPTTQYPWLIRIYSRHGGKDTMLEGFLLLPLRSMRPKRIRTAFTPEQLLKLEHAFEGNQ-YVVGAERKQLAQSL---S-L 141 (197)
T ss_pred CCcccCCcceeeeecccccchhhhhhccccccccCCCccccccCHHHHHHHHHHHhcCC-eeechHHHHHHHHc---C-C
Confidence 3466778888877762 221 11 12238899999999999999999999996 88889999999999 5 9
Q ss_pred CCCceeeecccchhHHHHHHHHH
Q 046813 73 EGKNVFYWFQNHKARQRQKQKQE 95 (250)
Q Consensus 73 ~erqVqvWFQNRRAR~Krkq~~~ 95 (250)
+|.||+|||||||.|.||++.+.
T Consensus 142 setQVkvWFQNRRtk~kr~~~e~ 164 (197)
T KOG0843|consen 142 SETQVKVWFQNRRTKHKRMQQED 164 (197)
T ss_pred ChhHhhhhhhhhhHHHHHHHHHh
Confidence 99999999999999999998774
No 4
>KOG0487 consensus Transcription factor Abd-B, contains HOX domain [Transcription]
Probab=99.77 E-value=2.7e-19 Score=166.22 Aligned_cols=71 Identities=20% Similarity=0.334 Sum_probs=64.8
Q ss_pred CCCCCCCCCCCCCCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhHhcCCCCCCceeeecccchhHHHHHHHHHHHH
Q 046813 23 GGTTLSSSSRWNPTKEQINMLESLYAQGIRTPSAEQIQQITTRLRAYGHIEGKNVFYWFQNHKARQRQKQKQERTA 98 (250)
Q Consensus 23 g~~~~~rR~Rt~fT~eQL~~LE~~F~~~~~yPs~e~R~qLA~~L~~~G~L~erqVqvWFQNRRAR~Krkq~~~~~a 98 (250)
...++-|+||.-||+.|+.+||++|--|. |.+.++|.+|++.| ||+||||+|||||||+|+||..++..+.
T Consensus 230 ~~~~~~RKKRcPYTK~QtlELEkEFlfN~-YitkeKR~ElSr~l----NLTeRQVKIWFQNRRMK~KK~~re~r~~ 300 (308)
T KOG0487|consen 230 SSARRGRKKRCPYTKHQTLELEKEFLFNM-YITKEKRLELSRTL----NLTERQVKIWFQNRRMKEKKVNRENRLK 300 (308)
T ss_pred ccccccccccCCchHHHHHHHHHHHHHHH-HHhHHHHHHHHHhc----ccchhheeeeehhhhhHHhhhhhhhhcc
Confidence 34478899999999999999999999995 99999999999999 7999999999999999999988776544
No 5
>KOG0484 consensus Transcription factor PHOX2/ARIX, contains HOX domain [Transcription]
Probab=99.77 E-value=3.7e-19 Score=144.59 Aligned_cols=70 Identities=21% Similarity=0.343 Sum_probs=63.9
Q ss_pred CCCCCCCCCCCCCCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhHhcCCCCCCceeeecccchhHHHHHHHHHHH
Q 046813 23 GGTTLSSSSRWNPTKEQINMLESLYAQGIRTPSAEQIQQITTRLRAYGHIEGKNVFYWFQNHKARQRQKQKQERT 97 (250)
Q Consensus 23 g~~~~~rR~Rt~fT~eQL~~LE~~F~~~~~yPs~e~R~qLA~~L~~~G~L~erqVqvWFQNRRAR~Krkq~~~~~ 97 (250)
...+..+|.|++||..||..||++|...+ ||+.-.|++||.+| .|+|.+|||||||||||-|++++....
T Consensus 12 ~ekrKQRRIRTTFTS~QLkELErvF~ETH-YPDIYTREEiA~ki----dLTEARVQVWFQNRRAKfRKQEr~a~~ 81 (125)
T KOG0484|consen 12 TEKRKQRRIRTTFTSAQLKELERVFAETH-YPDIYTREEIALKI----DLTEARVQVWFQNRRAKFRKQERAAIA 81 (125)
T ss_pred hHHHHhhhhhhhhhHHHHHHHHHHHHhhc-CCcchhHHHHHHhh----hhhHHHHHHHHHhhHHHHHHHHHHHHH
Confidence 45566889999999999999999999995 99999999999999 699999999999999999998877643
No 6
>KOG0485 consensus Transcription factor NKX-5.1/HMX1, contains HOX domain [Transcription]
Probab=99.75 E-value=7e-19 Score=157.83 Aligned_cols=85 Identities=21% Similarity=0.375 Sum_probs=71.4
Q ss_pred CCCCCCCcccccCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhHhcCCCCCCceeeeccc
Q 046813 4 DGDNNNNMGMVSGGGGGGGGGTTLSSSSRWNPTKEQINMLESLYAQGIRTPSAEQIQQITTRLRAYGHIEGKNVFYWFQN 83 (250)
Q Consensus 4 ~~~~~~~~~~~s~gg~~g~g~~~~~rR~Rt~fT~eQL~~LE~~F~~~~~yPs~e~R~qLA~~L~~~G~L~erqVqvWFQN 83 (250)
.|+.|-+++.+|.-|++.|+ .|+||+||.|+..|+..||..|+.. +|.+..+|..||++| .|+|.||+|||||
T Consensus 82 sd~~e~~~~~~ssdg~~~g~--~RKKktRTvFSraQV~qLEs~Fe~k-rYLSsaeRa~LA~sL----qLTETQVKIWFQN 154 (268)
T KOG0485|consen 82 SDDGESDIDLASSDGNGLGD--DRKKKTRTVFSRAQVFQLESTFELK-RYLSSAERAGLAASL----QLTETQVKIWFQN 154 (268)
T ss_pred cccccccccccccCCCcccc--cccccchhhhhHHHHHHHHHHHHHH-hhhhHHHHhHHHHhh----hhhhhhhhhhhhh
Confidence 44456666766665554444 3578999999999999999999999 699999999999999 6999999999999
Q ss_pred chhHHHHHHHHH
Q 046813 84 HKARQRQKQKQE 95 (250)
Q Consensus 84 RRAR~Krkq~~~ 95 (250)
||.||||+-...
T Consensus 155 RRnKwKRq~aad 166 (268)
T KOG0485|consen 155 RRNKWKRQYAAD 166 (268)
T ss_pred hhHHHHHHHhhh
Confidence 999999986543
No 7
>KOG0848 consensus Transcription factor Caudal, contains HOX domain [Transcription]
Probab=99.74 E-value=7.2e-19 Score=161.30 Aligned_cols=86 Identities=23% Similarity=0.297 Sum_probs=75.3
Q ss_pred CCCCCcccccCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhHhcCCCCCCceeeecccch
Q 046813 6 DNNNNMGMVSGGGGGGGGGTTLSSSSRWNPTKEQINMLESLYAQGIRTPSAEQIQQITTRLRAYGHIEGKNVFYWFQNHK 85 (250)
Q Consensus 6 ~~~~~~~~~s~gg~~g~g~~~~~rR~Rt~fT~eQL~~LE~~F~~~~~yPs~e~R~qLA~~L~~~G~L~erqVqvWFQNRR 85 (250)
.++||.-.+.- |.|+.++.+-.-+-|..||+.|.-+||++|..+ +|.++.+|.|||..| | |+||||+|||||||
T Consensus 178 ~~dwmrkpa~~-~~g~~~KtRTkDKYRvVYTDhQRLELEKEfh~S-ryITirRKSELA~~L---g-LsERQVKIWFQNRR 251 (317)
T KOG0848|consen 178 PYDWMRKPAQP-GTGQNVKTRTKDKYRVVYTDHQRLELEKEFHTS-RYITIRRKSELAATL---G-LSERQVKIWFQNRR 251 (317)
T ss_pred hhhhhhccccc-CCCCCceeecccceeEEecchhhhhhhhhhccc-cceeeehhHHHHHhh---C-ccHhhhhHhhhhhh
Confidence 46888886544 444677888888999999999999999999999 699999999999999 7 99999999999999
Q ss_pred hHHHHHHHHHHH
Q 046813 86 ARQRQKQKQERT 97 (250)
Q Consensus 86 AR~Krkq~~~~~ 97 (250)
||+||..++..+
T Consensus 252 AKERK~nKKk~~ 263 (317)
T KOG0848|consen 252 AKERKDNKKKRL 263 (317)
T ss_pred HHHHHHHHHHHH
Confidence 999998877653
No 8
>KOG0488 consensus Transcription factor BarH and related HOX domain proteins [General function prediction only]
Probab=99.74 E-value=9.1e-19 Score=162.40 Aligned_cols=66 Identities=20% Similarity=0.321 Sum_probs=61.6
Q ss_pred CCCCCCCCCCCCCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhHhcCCCCCCceeeecccchhHHHHHHHH
Q 046813 24 GTTLSSSSRWNPTKEQINMLESLYAQGIRTPSAEQIQQITTRLRAYGHIEGKNVFYWFQNHKARQRQKQKQ 94 (250)
Q Consensus 24 ~~~~~rR~Rt~fT~eQL~~LE~~F~~~~~yPs~e~R~qLA~~L~~~G~L~erqVqvWFQNRRAR~Krkq~~ 94 (250)
..++.|+.|+.||..||..||+.|+.. +|.+..+|.+||+.| | |++.||++||||||+||||+..+
T Consensus 168 ~pkK~RksRTaFT~~Ql~~LEkrF~~Q-KYLS~~DR~~LA~~L---g-LTdaQVKtWfQNRRtKWKrq~a~ 233 (309)
T KOG0488|consen 168 TPKKRRKSRTAFSDHQLFELEKRFEKQ-KYLSVADRIELAASL---G-LTDAQVKTWFQNRRTKWKRQTAE 233 (309)
T ss_pred CCcccccchhhhhHHHHHHHHHHHHHh-hcccHHHHHHHHHHc---C-CchhhHHHHHhhhhHHHHHHHHh
Confidence 447788899999999999999999999 699999999999999 5 99999999999999999998766
No 9
>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=99.72 E-value=2e-18 Score=120.71 Aligned_cols=57 Identities=30% Similarity=0.586 Sum_probs=54.5
Q ss_pred CCCCCCCCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhHhcCCCCCCceeeecccchhHHHH
Q 046813 29 SSSRWNPTKEQINMLESLYAQGIRTPSAEQIQQITTRLRAYGHIEGKNVFYWFQNHKARQRQ 90 (250)
Q Consensus 29 rR~Rt~fT~eQL~~LE~~F~~~~~yPs~e~R~qLA~~L~~~G~L~erqVqvWFQNRRAR~Kr 90 (250)
+|+|+.||++|+.+||.+|..+ .||+.++++.||.+| | |++.+|++||||||+|+|+
T Consensus 1 kr~r~~~t~~q~~~L~~~f~~~-~~p~~~~~~~la~~l---~-l~~~~V~~WF~nrR~k~kk 57 (57)
T PF00046_consen 1 KRKRTRFTKEQLKVLEEYFQEN-PYPSKEEREELAKEL---G-LTERQVKNWFQNRRRKEKK 57 (57)
T ss_dssp SSSSSSSSHHHHHHHHHHHHHS-SSCHHHHHHHHHHHH---T-SSHHHHHHHHHHHHHHHHH
T ss_pred CcCCCCCCHHHHHHHHHHHHHh-ccccccccccccccc---c-ccccccccCHHHhHHHhCc
Confidence 5899999999999999999999 499999999999999 6 9999999999999999986
No 10
>KOG0483 consensus Transcription factor HEX, contains HOX and HALZ domains [Transcription]
Probab=99.72 E-value=3.2e-18 Score=150.70 Aligned_cols=69 Identities=28% Similarity=0.470 Sum_probs=61.4
Q ss_pred CCCCCCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhHhcCCCCCCceeeecccchhHHHHHHHHHHHHHHHHhh
Q 046813 31 SRWNPTKEQINMLESLYAQGIRTPSAEQIQQITTRLRAYGHIEGKNVFYWFQNHKARQRQKQKQERTAFINRYL 104 (250)
Q Consensus 31 ~Rt~fT~eQL~~LE~~F~~~~~yPs~e~R~qLA~~L~~~G~L~erqVqvWFQNRRAR~Krkq~~~~~a~~N~~L 104 (250)
+..+||.+|+..||..|+.+. +..+++|.+||++| | |.++||.|||||||||||.++.+.++.++.+.+
T Consensus 53 kk~Rlt~eQ~~~LE~~F~~~~-~L~p~~K~~LAk~L---g-L~pRQVavWFQNRRARwK~kqlE~d~~~Lk~~~ 121 (198)
T KOG0483|consen 53 KKRRLTSEQVKFLEKSFESEK-KLEPERKKKLAKEL---G-LQPRQVAVWFQNRRARWKTKQLEKDYESLKRQL 121 (198)
T ss_pred ccccccHHHHHHhHHhhcccc-ccChHHHHHHHHhh---C-CChhHHHHHHhhccccccchhhhhhHHHHHHHH
Confidence 444566999999999999995 88999999999999 7 999999999999999999999999888764443
No 11
>KOG0494 consensus Transcription factor CHX10 and related HOX domain proteins [General function prediction only]
Probab=99.70 E-value=8e-18 Score=154.23 Aligned_cols=69 Identities=19% Similarity=0.281 Sum_probs=61.0
Q ss_pred CCCCCCCCCC-CCCCCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhHhcCCCCCCceeeecccchhHHHHHHHHH
Q 046813 22 GGGTTLSSSS-RWNPTKEQINMLESLYAQGIRTPSAEQIQQITTRLRAYGHIEGKNVFYWFQNHKARQRQKQKQE 95 (250)
Q Consensus 22 ~g~~~~~rR~-Rt~fT~eQL~~LE~~F~~~~~yPs~e~R~qLA~~L~~~G~L~erqVqvWFQNRRAR~Krkq~~~ 95 (250)
+++.+..||. ||.||..||+.||+.|++.+ ||+...|+-||..+ .|.|.+|+||||||||||||+++.-
T Consensus 134 ~~kkk~kRRh~RTiFT~~Qle~LEkaFkeaH-YPDv~Are~la~kt----elpEDRIqVWfQNRRAKWRk~Ek~w 203 (332)
T KOG0494|consen 134 NAKKKKKRRHFRTIFTSYQLEELEKAFKEAH-YPDVYAREMLADKT----ELPEDRIQVWFQNRRAKWRKTEKRW 203 (332)
T ss_pred ccccccccccccchhhHHHHHHHHHHHhhcc-CccHHHHHHHhhhc----cCchhhhhHHhhhhhHHhhhhhhhc
Confidence 3444445555 99999999999999999995 99999999999999 5999999999999999999988764
No 12
>KOG0492 consensus Transcription factor MSH, contains HOX domain [General function prediction only]
Probab=99.68 E-value=2.9e-17 Score=146.49 Aligned_cols=67 Identities=22% Similarity=0.311 Sum_probs=61.8
Q ss_pred CCCCCCCCCCCCCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhHhcCCCCCCceeeecccchhHHHHHHHHH
Q 046813 24 GTTLSSSSRWNPTKEQINMLESLYAQGIRTPSAEQIQQITTRLRAYGHIEGKNVFYWFQNHKARQRQKQKQE 95 (250)
Q Consensus 24 ~~~~~rR~Rt~fT~eQL~~LE~~F~~~~~yPs~e~R~qLA~~L~~~G~L~erqVqvWFQNRRAR~Krkq~~~ 95 (250)
+++-.|++|+-||..||..||+.|.+.+ |.++++|.+++..| +|++.||+|||||||||.||.|+++
T Consensus 140 Khk~nRkPRtPFTtqQLlaLErkfrekq-YLSiaEraefSsSL----~LTeTqVKIWFQNRRAKaKRlQeae 206 (246)
T KOG0492|consen 140 KHKPNRKPRTPFTTQQLLALERKFREKQ-YLSIAERAEFSSSL----ELTETQVKIWFQNRRAKAKRLQEAE 206 (246)
T ss_pred ccCCCCCCCCCCCHHHHHHHHHHHhHhh-hhhHHHHHhhhhhh----hhhhhheehhhhhhhHHHHHHHHHH
Confidence 4455678999999999999999999995 99999999999999 6999999999999999999988775
No 13
>KOG2251 consensus Homeobox transcription factor [Transcription]
Probab=99.67 E-value=8.3e-17 Score=143.90 Aligned_cols=82 Identities=24% Similarity=0.412 Sum_probs=71.5
Q ss_pred CCcccc-cCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhHhcCCCCCCceeeecccchhH
Q 046813 9 NNMGMV-SGGGGGGGGGTTLSSSSRWNPTKEQINMLESLYAQGIRTPSAEQIQQITTRLRAYGHIEGKNVFYWFQNHKAR 87 (250)
Q Consensus 9 ~~~~~~-s~gg~~g~g~~~~~rR~Rt~fT~eQL~~LE~~F~~~~~yPs~e~R~qLA~~L~~~G~L~erqVqvWFQNRRAR 87 (250)
.+|++. .-.+.+-.++.++.||-||+||..|+++||.+|.+.. ||+...|++||.+| +|.|.+|+|||.|||||
T Consensus 17 p~~d~~h~~~~vP~~~~pRkqRRERTtFtr~QlevLe~LF~kTq-YPDv~~rEelAlkl----nLpeSrVqVWFKNRRAK 91 (228)
T KOG2251|consen 17 PYMDLLHPKPGVPYSSGPRKQRRERTTFTRKQLEVLEALFAKTQ-YPDVFMREELALKL----NLPESRVQVWFKNRRAK 91 (228)
T ss_pred ccccccccCCCCCcCccchhcccccceecHHHHHHHHHHHHhhc-CccHHHHHHHHHHh----CCchhhhhhhhccccch
Confidence 444433 2245556678899999999999999999999999995 99999999999999 79999999999999999
Q ss_pred HHHHHHHH
Q 046813 88 QRQKQKQE 95 (250)
Q Consensus 88 ~Krkq~~~ 95 (250)
+|+++++.
T Consensus 92 ~r~qq~qq 99 (228)
T KOG2251|consen 92 CRRQQQQQ 99 (228)
T ss_pred hhHhhhhh
Confidence 99988775
No 14
>KOG0850 consensus Transcription factor DLX and related proteins with LIM Zn-binding and HOX domains [Transcription]
Probab=99.66 E-value=5.1e-17 Score=146.15 Aligned_cols=69 Identities=20% Similarity=0.301 Sum_probs=63.3
Q ss_pred CCCCCCCCCCCCCCCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhHhcCCCCCCceeeecccchhHHHHHHHHH
Q 046813 22 GGGTTLSSSSRWNPTKEQINMLESLYAQGIRTPSAEQIQQITTRLRAYGHIEGKNVFYWFQNHKARQRQKQKQE 95 (250)
Q Consensus 22 ~g~~~~~rR~Rt~fT~eQL~~LE~~F~~~~~yPs~e~R~qLA~~L~~~G~L~erqVqvWFQNRRAR~Krkq~~~ 95 (250)
+|..+..|++||.|+.-||+.|.+.|++.+ |.-..+|.+||+.| | |+..||+|||||||.|.||..+..
T Consensus 116 Ngk~KK~RKPRTIYSS~QLqaL~rRFQkTQ-YLALPERAeLAAsL---G-LTQTQVKIWFQNrRSK~KKl~k~g 184 (245)
T KOG0850|consen 116 NGKGKKVRKPRTIYSSLQLQALNRRFQQTQ-YLALPERAELAASL---G-LTQTQVKIWFQNRRSKFKKLKKQG 184 (245)
T ss_pred CCCcccccCCcccccHHHHHHHHHHHhhcc-hhcCcHHHHHHHHh---C-CchhHhhhhhhhhHHHHHHHHhcC
Confidence 456677889999999999999999999995 99999999999999 8 999999999999999999988743
No 15
>smart00389 HOX Homeodomain. DNA-binding factors that are involved in the transcriptional regulation of key developmental processes
Probab=99.61 E-value=2.2e-16 Score=109.03 Aligned_cols=56 Identities=30% Similarity=0.528 Sum_probs=52.1
Q ss_pred CCCCCCCCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhHhcCCCCCCceeeecccchhHHH
Q 046813 29 SSSRWNPTKEQINMLESLYAQGIRTPSAEQIQQITTRLRAYGHIEGKNVFYWFQNHKARQR 89 (250)
Q Consensus 29 rR~Rt~fT~eQL~~LE~~F~~~~~yPs~e~R~qLA~~L~~~G~L~erqVqvWFQNRRAR~K 89 (250)
++.|+.||++|+.+||..|..++ ||+.+++.+||.+| | |+..+|++||+|||++.|
T Consensus 1 ~k~r~~~~~~~~~~L~~~f~~~~-~P~~~~~~~la~~~---~-l~~~qV~~WF~nrR~~~~ 56 (56)
T smart00389 1 RRKRTSFTPEQLEELEKEFQKNP-YPSREEREELAAKL---G-LSERQVKVWFQNRRAKWK 56 (56)
T ss_pred CCCCCcCCHHHHHHHHHHHHhCC-CCCHHHHHHHHHHH---C-cCHHHHHHhHHHHhhccC
Confidence 36788899999999999999995 99999999999999 6 999999999999999864
No 16
>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=99.60 E-value=4.3e-16 Score=107.90 Aligned_cols=58 Identities=29% Similarity=0.508 Sum_probs=53.9
Q ss_pred CCCCCCCCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhHhcCCCCCCceeeecccchhHHHHH
Q 046813 29 SSSRWNPTKEQINMLESLYAQGIRTPSAEQIQQITTRLRAYGHIEGKNVFYWFQNHKARQRQK 91 (250)
Q Consensus 29 rR~Rt~fT~eQL~~LE~~F~~~~~yPs~e~R~qLA~~L~~~G~L~erqVqvWFQNRRAR~Krk 91 (250)
++.|..|+++|+.+||..|..++ ||+.+++..||.+| | |++++|++||+|||++.|+.
T Consensus 1 ~~~r~~~~~~~~~~Le~~f~~~~-~P~~~~~~~la~~~---~-l~~~qV~~WF~nrR~~~~~~ 58 (59)
T cd00086 1 RRKRTRFTPEQLEELEKEFEKNP-YPSREEREELAKEL---G-LTERQVKIWFQNRRAKLKRS 58 (59)
T ss_pred CCCCCcCCHHHHHHHHHHHHhCC-CCCHHHHHHHHHHH---C-cCHHHHHHHHHHHHHHHhcc
Confidence 36788999999999999999995 99999999999999 6 99999999999999998863
No 17
>KOG0493 consensus Transcription factor Engrailed, contains HOX domain [General function prediction only]
Probab=99.58 E-value=6e-16 Score=142.21 Aligned_cols=61 Identities=23% Similarity=0.430 Sum_probs=56.9
Q ss_pred CCCCCCCCCCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhHhcCCCCCCceeeecccchhHHHHHH
Q 046813 27 LSSSSRWNPTKEQINMLESLYAQGIRTPSAEQIQQITTRLRAYGHIEGKNVFYWFQNHKARQRQKQ 92 (250)
Q Consensus 27 ~~rR~Rt~fT~eQL~~LE~~F~~~~~yPs~e~R~qLA~~L~~~G~L~erqVqvWFQNRRAR~Krkq 92 (250)
..+|+||.||.|||+.|...|..| +|....+|++||.+| | |.|.||+|||||+|||.||.-
T Consensus 245 eeKRPRTAFtaeQL~RLK~EF~en-RYlTEqRRQ~La~EL---g-LNEsQIKIWFQNKRAKiKKsT 305 (342)
T KOG0493|consen 245 EEKRPRTAFTAEQLQRLKAEFQEN-RYLTEQRRQELAQEL---G-LNESQIKIWFQNKRAKIKKST 305 (342)
T ss_pred hhcCccccccHHHHHHHHHHHhhh-hhHHHHHHHHHHHHh---C-cCHHHhhHHhhhhhhhhhhcc
Confidence 457899999999999999999999 699999999999999 7 999999999999999998743
No 18
>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=99.56 E-value=4.6e-15 Score=108.23 Aligned_cols=52 Identities=19% Similarity=0.284 Sum_probs=49.7
Q ss_pred CCCCCCCCHHHHHHHHHHHhcCCCC----CCHHHHHHHHHHhHhcCCCCCCceeeecccch
Q 046813 29 SSSRWNPTKEQINMLESLYAQGIRT----PSAEQIQQITTRLRAYGHIEGKNVFYWFQNHK 85 (250)
Q Consensus 29 rR~Rt~fT~eQL~~LE~~F~~~~~y----Ps~e~R~qLA~~L~~~G~L~erqVqvWFQNRR 85 (250)
+|.||.||++|+..||..|+.+ .| |+...|.+||.+| | |++++|+|||||-+
T Consensus 2 kR~RT~Ft~~Q~~~Le~~fe~~-~y~~~~~~~~~r~~la~~l---g-l~~~vvKVWfqN~k 57 (58)
T TIGR01565 2 KRRRTKFTAEQKEKMRDFAEKL-GWKLKDKRREEVREFCEEI---G-VTRKVFKVWMHNNK 57 (58)
T ss_pred CCCCCCCCHHHHHHHHHHHHHc-CCCCCCCCHHHHHHHHHHh---C-CCHHHeeeecccCC
Confidence 7899999999999999999999 59 9999999999999 7 99999999999965
No 19
>KOG0844 consensus Transcription factor EVX1, contains HOX domain [Transcription]
Probab=99.56 E-value=1.7e-15 Score=141.65 Aligned_cols=64 Identities=20% Similarity=0.278 Sum_probs=58.7
Q ss_pred CCCCCCCCCCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhHhcCCCCCCceeeecccchhHHHHHHHHH
Q 046813 27 LSSSSRWNPTKEQINMLESLYAQGIRTPSAEQIQQITTRLRAYGHIEGKNVFYWFQNHKARQRQKQKQE 95 (250)
Q Consensus 27 ~~rR~Rt~fT~eQL~~LE~~F~~~~~yPs~e~R~qLA~~L~~~G~L~erqVqvWFQNRRAR~Krkq~~~ 95 (250)
.-||-||.||.|||..||+.|-+.. |.++.+|-+||..| ||.|..|+|||||||+|.||+....
T Consensus 180 qmRRYRTAFTReQIaRLEKEFyrEN-YVSRprRcELAAaL----NLPEtTIKVWFQNRRMKDKRQRlam 243 (408)
T KOG0844|consen 180 QMRRYRTAFTREQIARLEKEFYREN-YVSRPRRCELAAAL----NLPETTIKVWFQNRRMKDKRQRLAM 243 (408)
T ss_pred HHHHHHhhhhHHHHHHHHHHHHHhc-cccCchhhhHHHhh----CCCcceeehhhhhchhhhhhhhhhc
Confidence 3478999999999999999998875 99999999999999 7999999999999999999987653
No 20
>COG5576 Homeodomain-containing transcription factor [Transcription]
Probab=99.55 E-value=5.2e-15 Score=126.10 Aligned_cols=66 Identities=27% Similarity=0.431 Sum_probs=57.8
Q ss_pred CCCCCCCCCCCCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhHhcCCCCCCceeeecccchhHHHHHHHHH
Q 046813 25 TTLSSSSRWNPTKEQINMLESLYAQGIRTPSAEQIQQITTRLRAYGHIEGKNVFYWFQNHKARQRQKQKQE 95 (250)
Q Consensus 25 ~~~~rR~Rt~fT~eQL~~LE~~F~~~~~yPs~e~R~qLA~~L~~~G~L~erqVqvWFQNRRAR~Krkq~~~ 95 (250)
....+++|.+.|.+|+.+||+.|+.++ ||+...|..|+..| +|+++.|||||||||++.|++....
T Consensus 48 s~~~~~~r~R~t~~Q~~vL~~~F~i~p-~Ps~~~r~~L~~~l----nm~~ksVqIWFQNkR~~~k~~~~~~ 113 (156)
T COG5576 48 SSPPKSKRRRTTDEQLMVLEREFEINP-YPSSITRIKLSLLL----NMPPKSVQIWFQNKRAKEKKKRSGK 113 (156)
T ss_pred CCcCcccceechHHHHHHHHHHhccCC-CCCHHHHHHHHHhc----CCChhhhhhhhchHHHHHHHhcccc
Confidence 344556666667999999999999995 99999999999999 5999999999999999999876553
No 21
>KOG0486 consensus Transcription factor PTX1, contains HOX domain [Transcription]
Probab=99.55 E-value=5.6e-15 Score=138.01 Aligned_cols=67 Identities=21% Similarity=0.423 Sum_probs=62.8
Q ss_pred CCCCCCCCCCCCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhHhcCCCCCCceeeecccchhHHHHHHHHHH
Q 046813 25 TTLSSSSRWNPTKEQINMLESLYAQGIRTPSAEQIQQITTRLRAYGHIEGKNVFYWFQNHKARQRQKQKQER 96 (250)
Q Consensus 25 ~~~~rR~Rt~fT~eQL~~LE~~F~~~~~yPs~e~R~qLA~~L~~~G~L~erqVqvWFQNRRAR~Krkq~~~~ 96 (250)
.+++||.|+.||..||+.||..|.++ +||+.+.|++||--. +|+|.+|.|||.|||||||+.++-.+
T Consensus 109 i~KqrrQrthFtSqqlqele~tF~rN-rypdMstrEEIavwt----NlTE~rvrvwfknrrakwrkrErN~~ 175 (351)
T KOG0486|consen 109 ISKQRRQRTHFTSQQLQELEATFQRN-RYPDMSTREEIAVWT----NLTEARVRVWFKNRRAKWRKRERNQQ 175 (351)
T ss_pred hhhhhhhhhhhHHHHHHHHHHHHhhc-cCCccchhhHHHhhc----cccchhhhhhcccchhhhhhhhhhHH
Confidence 34788999999999999999999999 699999999999999 79999999999999999999887766
No 22
>KOG0491 consensus Transcription factor BSH, contains HOX domain [General function prediction only]
Probab=99.39 E-value=2e-14 Score=124.75 Aligned_cols=68 Identities=21% Similarity=0.353 Sum_probs=62.4
Q ss_pred CCCCCCCCCCCCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhHhcCCCCCCceeeecccchhHHHHHHHHHHH
Q 046813 25 TTLSSSSRWNPTKEQINMLESLYAQGIRTPSAEQIQQITTRLRAYGHIEGKNVFYWFQNHKARQRQKQKQERT 97 (250)
Q Consensus 25 ~~~~rR~Rt~fT~eQL~~LE~~F~~~~~yPs~e~R~qLA~~L~~~G~L~erqVqvWFQNRRAR~Krkq~~~~~ 97 (250)
.++.++.|+.|+..|+..||+.|+.. +|.+..+|++||..| +|+++||+.||||||+|.||.++..+-
T Consensus 97 ~~~r~K~Rtvfs~~ql~~l~~rFe~Q-rYLS~~e~~ELan~L----~LS~~QVKTWFQNrRMK~Kk~~r~~~p 164 (194)
T KOG0491|consen 97 HCRRRKARTVFSDPQLSGLEKRFERQ-RYLSTPERQELANAL----SLSETQVKTWFQNRRMKHKKQQRNNQP 164 (194)
T ss_pred HHHhhhhcccccCccccccHHHHhhh-hhcccHHHHHHHHHh----hhhHHHHHHHHHHHHHHHHHHHhccCC
Confidence 35678899999999999999999998 699999999999999 599999999999999999999887663
No 23
>KOG0490 consensus Transcription factor, contains HOX domain [General function prediction only]
Probab=99.39 E-value=1.4e-13 Score=117.58 Aligned_cols=64 Identities=22% Similarity=0.309 Sum_probs=59.4
Q ss_pred CCCCCCCCCCCCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhHhcCCCCCCceeeecccchhHHHHHHH
Q 046813 25 TTLSSSSRWNPTKEQINMLESLYAQGIRTPSAEQIQQITTRLRAYGHIEGKNVFYWFQNHKARQRQKQK 93 (250)
Q Consensus 25 ~~~~rR~Rt~fT~eQL~~LE~~F~~~~~yPs~e~R~qLA~~L~~~G~L~erqVqvWFQNRRAR~Krkq~ 93 (250)
....+|.|+.||..|+++||+.|... .||+...|+.||..+ +++|..|+||||||||||+++++
T Consensus 57 ~~~~rr~rt~~~~~ql~~ler~f~~~-h~Pd~~~r~~la~~~----~~~e~rVqvwFqnrrak~r~~~~ 120 (235)
T KOG0490|consen 57 KFSKRCARCKFTISQLDELERAFEKV-HLPCFACRECLALLL----TGDEFRVQVWFQNRRAKDRKEER 120 (235)
T ss_pred hccccccCCCCCcCHHHHHHHhhcCC-CcCccchHHHHhhcC----CCCeeeeehhhhhhcHhhhhhhc
Confidence 34578999999999999999999999 499999999999999 59999999999999999998875
No 24
>KOG4577 consensus Transcription factor LIM3, contains LIM and HOX domains [Transcription]
Probab=99.38 E-value=2.3e-13 Score=126.65 Aligned_cols=63 Identities=24% Similarity=0.462 Sum_probs=59.0
Q ss_pred CCCCCCCCCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhHhcCCCCCCceeeecccchhHHHHHHHHH
Q 046813 28 SSSSRWNPTKEQINMLESLYAQGIRTPSAEQIQQITTRLRAYGHIEGKNVFYWFQNHKARQRQKQKQE 95 (250)
Q Consensus 28 ~rR~Rt~fT~eQL~~LE~~F~~~~~yPs~e~R~qLA~~L~~~G~L~erqVqvWFQNRRAR~Krkq~~~ 95 (250)
.+|+||++|+.||+.|...|...+ .|-+--|+||+.+. | |.-+.|||||||||||+||.++..
T Consensus 167 nKRPRTTItAKqLETLK~AYn~Sp-KPARHVREQLsseT---G-LDMRVVQVWFQNRRAKEKRLKKDA 229 (383)
T KOG4577|consen 167 NKRPRTTITAKQLETLKQAYNTSP-KPARHVREQLSSET---G-LDMRVVQVWFQNRRAKEKRLKKDA 229 (383)
T ss_pred cCCCcceeeHHHHHHHHHHhcCCC-chhHHHHHHhhhcc---C-cceeehhhhhhhhhHHHHhhhhhc
Confidence 678999999999999999999995 89999999999999 8 999999999999999999987764
No 25
>KOG3802 consensus Transcription factor OCT-1, contains POU and HOX domains [Transcription]
Probab=99.36 E-value=5.5e-13 Score=127.50 Aligned_cols=61 Identities=20% Similarity=0.358 Sum_probs=57.7
Q ss_pred CCCCCCCCCCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhHhcCCCCCCceeeecccchhHHHHHH
Q 046813 27 LSSSSRWNPTKEQINMLESLYAQGIRTPSAEQIQQITTRLRAYGHIEGKNVFYWFQNHKARQRQKQ 92 (250)
Q Consensus 27 ~~rR~Rt~fT~eQL~~LE~~F~~~~~yPs~e~R~qLA~~L~~~G~L~erqVqvWFQNRRAR~Krkq 92 (250)
|+||+||+++...+..||..|..|+ .|+.++|.+||.+| +|+..+|+|||+|||-|+||-.
T Consensus 293 RkRKKRTSie~~vr~aLE~~F~~np-KPt~qEIt~iA~~L----~leKEVVRVWFCNRRQkeKR~~ 353 (398)
T KOG3802|consen 293 RKRKKRTSIEVNVRGALEKHFLKNP-KPTSQEITHIAESL----QLEKEVVRVWFCNRRQKEKRIT 353 (398)
T ss_pred cccccccceeHHHHHHHHHHHHhCC-CCCHHHHHHHHHHh----ccccceEEEEeeccccccccCC
Confidence 7889999999999999999999995 99999999999999 6999999999999999999844
No 26
>KOG0847 consensus Transcription factor, contains HOX domain [Transcription]
Probab=99.31 E-value=6.2e-13 Score=120.15 Aligned_cols=65 Identities=28% Similarity=0.360 Sum_probs=58.1
Q ss_pred CCCCCCCCCCCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhHhcCCCCCCceeeecccchhHHHHHHHHH
Q 046813 26 TLSSSSRWNPTKEQINMLESLYAQGIRTPSAEQIQQITTRLRAYGHIEGKNVFYWFQNHKARQRQKQKQE 95 (250)
Q Consensus 26 ~~~rR~Rt~fT~eQL~~LE~~F~~~~~yPs~e~R~qLA~~L~~~G~L~erqVqvWFQNRRAR~Krkq~~~ 95 (250)
..++-.|-+|+-.||..||..|++. +|+-.++|.+||..| | +++.||+|||||||.|||+|...+
T Consensus 165 G~rk~srPTf~g~qi~~le~~feqt-kylaG~~ra~lA~~l---g-mteSqvkVWFQNRRTKWRKkhAaE 229 (288)
T KOG0847|consen 165 GQRKQSRPTFTGHQIYQLERKFEQT-KYLAGADRAQLAQEL---N-MTESQVKVWFQNRRTKWRKKHAAE 229 (288)
T ss_pred ccccccCCCccchhhhhhhhhhhhh-hcccchhHHHhhccc---c-ccHHHHHHHHhcchhhhhhhhccc
Confidence 3455678889999999999999999 599999999999999 6 999999999999999999987554
No 27
>KOG0849 consensus Transcription factor PRD and related proteins, contain PAX and HOX domains [Transcription]
Probab=99.22 E-value=6.4e-12 Score=118.55 Aligned_cols=69 Identities=19% Similarity=0.297 Sum_probs=62.1
Q ss_pred CCCCCCCCCCCCCCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhHhcCCCCCCceeeecccchhHHHHHHHHHH
Q 046813 23 GGTTLSSSSRWNPTKEQINMLESLYAQGIRTPSAEQIQQITTRLRAYGHIEGKNVFYWFQNHKARQRQKQKQER 96 (250)
Q Consensus 23 g~~~~~rR~Rt~fT~eQL~~LE~~F~~~~~yPs~e~R~qLA~~L~~~G~L~erqVqvWFQNRRAR~Krkq~~~~ 96 (250)
...+..+|.|++||.+|++.||+.|+.++ ||+...|++||.++ | |++.+|+||||||||||||.....+
T Consensus 171 ~~~~~~rr~rtsft~~Q~~~le~~f~rt~-yP~i~~Re~La~~i---~-l~e~riqvwf~nrra~~rr~~~~~s 239 (354)
T KOG0849|consen 171 ALQRGGRRNRTSFSPSQLEALEECFQRTP-YPDIVGRETLAKET---G-LPEPRVQVWFQNRRAKWRRQHRDCS 239 (354)
T ss_pred cccccccccccccccchHHHHHHHhcCCC-CCchhhHHHHhhhc---c-CCchHHHHHHhhhhhhhhhcccccc
Confidence 34555667799999999999999999996 99999999999999 6 9999999999999999999886644
No 28
>KOG1168 consensus Transcription factor ACJ6/BRN-3, contains POU and HOX domains [Transcription]
Probab=98.86 E-value=1.5e-09 Score=101.67 Aligned_cols=60 Identities=25% Similarity=0.423 Sum_probs=56.1
Q ss_pred CCCCCCCCCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhHhcCCCCCCceeeecccchhHHHHHH
Q 046813 28 SSSSRWNPTKEQINMLESLYAQGIRTPSAEQIQQITTRLRAYGHIEGKNVFYWFQNHKARQRQKQ 92 (250)
Q Consensus 28 ~rR~Rt~fT~eQL~~LE~~F~~~~~yPs~e~R~qLA~~L~~~G~L~erqVqvWFQNRRAR~Krkq 92 (250)
.+|+||++-.-..+.||.+|...+ -|+.|.|..||++| .|....|+|||.|.|.|+||.+
T Consensus 309 kKRKRTSIAAPEKRsLEayFavQP-RPS~EkIAaIAekL----DLKKNVVRVWFCNQRQKQKRm~ 368 (385)
T KOG1168|consen 309 KKRKRTSIAAPEKRSLEAYFAVQP-RPSGEKIAAIAEKL----DLKKNVVRVWFCNQRQKQKRMK 368 (385)
T ss_pred cccccccccCcccccHHHHhccCC-CCchhHHHHHHHhh----hhhhceEEEEeeccHHHHHHhh
Confidence 678999999999999999999995 89999999999999 6999999999999999999843
No 29
>KOG0490 consensus Transcription factor, contains HOX domain [General function prediction only]
Probab=98.34 E-value=3.5e-07 Score=78.18 Aligned_cols=63 Identities=24% Similarity=0.494 Sum_probs=58.0
Q ss_pred CCCCCCCCCCCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhHhcCCCCCCceeeecccchhHHHHHHH
Q 046813 26 TLSSSSRWNPTKEQINMLESLYAQGIRTPSAEQIQQITTRLRAYGHIEGKNVFYWFQNHKARQRQKQK 93 (250)
Q Consensus 26 ~~~rR~Rt~fT~eQL~~LE~~F~~~~~yPs~e~R~qLA~~L~~~G~L~erqVqvWFQNRRAR~Krkq~ 93 (250)
...++.|+.++..|+..|+..|.... +|+...+.+|+..+ | ++++.|++||||+|++.++...
T Consensus 151 ~~~~~~~~~~~~~~~~~~~~~~~~~~-~P~~~~~~~l~~~~---~-~~~~~~q~~~~~~~~~~~~~~~ 213 (235)
T KOG0490|consen 151 KKPRRPRTTFTENQLEVLETVFRATP-KPDADDREQLAEET---G-LSERVIQVWFQNRRAKLRKHKR 213 (235)
T ss_pred cccCCCccccccchhHhhhhcccCCC-CCchhhHHHHHHhc---C-CChhhhhhhcccHHHHHHhhcc
Confidence 44678999999999999999999995 99999999999999 6 9999999999999999998765
No 30
>KOG0774 consensus Transcription factor PBX and related HOX domain proteins [Transcription]
Probab=98.33 E-value=1.4e-06 Score=81.00 Aligned_cols=63 Identities=21% Similarity=0.360 Sum_probs=55.7
Q ss_pred CCCCCCCCCHHHHHHHHHHHhcC--CCCCCHHHHHHHHHHhHhcCCCCCCceeeecccchhHHHHHHHH
Q 046813 28 SSSSRWNPTKEQINMLESLYAQG--IRTPSAEQIQQITTRLRAYGHIEGKNVFYWFQNHKARQRQKQKQ 94 (250)
Q Consensus 28 ~rR~Rt~fT~eQL~~LE~~F~~~--~~yPs~e~R~qLA~~L~~~G~L~erqVqvWFQNRRAR~Krkq~~ 94 (250)
.+|+|-.|++.-.++|.++|..+ .+||+.+.+++||++. +|+-.||-.||-|+|-|.|+--..
T Consensus 188 arRKRRNFsK~aTeiLneyF~~h~~nPYPSee~K~eLAkqC----nItvsQvsnwfgnkrIrykK~~~k 252 (334)
T KOG0774|consen 188 ARRKRRNFSKQATEILNEYFYSHLSNPYPSEEAKEELAKQC----NITVSQVSNWFGNKRIRYKKNMGK 252 (334)
T ss_pred HHHhhcccchhHHHHHHHHHHHhcCCCCCcHHHHHHHHHHc----Cceehhhccccccceeehhhhhhh
Confidence 46899999999999999999653 4699999999999999 599999999999999999986433
No 31
>KOG0775 consensus Transcription factor SIX and related HOX domain proteins [Transcription]
Probab=98.33 E-value=3.9e-07 Score=84.66 Aligned_cols=51 Identities=24% Similarity=0.449 Sum_probs=45.6
Q ss_pred CCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhHhcCCCCCCceeeecccchhHHHH
Q 046813 35 PTKEQINMLESLYAQGIRTPSAEQIQQITTRLRAYGHIEGKNVFYWFQNHKARQRQ 90 (250)
Q Consensus 35 fT~eQL~~LE~~F~~~~~yPs~e~R~qLA~~L~~~G~L~erqVqvWFQNRRAR~Kr 90 (250)
|...-...|.+.|.+++ ||+.+++.+||+.. | |+..||-+||.|||.|.|-
T Consensus 183 FKekSR~~LrewY~~~~-YPsp~eKReLA~aT---g-Lt~tQVsNWFKNRRQRDRa 233 (304)
T KOG0775|consen 183 FKEKSRSLLREWYLQNP-YPSPREKRELAEAT---G-LTITQVSNWFKNRRQRDRA 233 (304)
T ss_pred hhHhhHHHHHHHHhcCC-CCChHHHHHHHHHh---C-Cchhhhhhhhhhhhhhhhh
Confidence 34445678999999994 99999999999999 7 9999999999999999983
No 32
>KOG2252 consensus CCAAT displacement protein and related homeoproteins [Transcription]
Probab=98.27 E-value=4.6e-07 Score=90.22 Aligned_cols=59 Identities=24% Similarity=0.369 Sum_probs=54.6
Q ss_pred CCCCCCCCCCCCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhHhcCCCCCCceeeecccchhHH
Q 046813 25 TTLSSSSRWNPTKEQINMLESLYAQGIRTPSAEQIQQITTRLRAYGHIEGKNVFYWFQNHKARQ 88 (250)
Q Consensus 25 ~~~~rR~Rt~fT~eQL~~LE~~F~~~~~yPs~e~R~qLA~~L~~~G~L~erqVqvWFQNRRAR~ 88 (250)
.-.++|+|+.||+.|++.|-.+|+.+ ++|+.+..+.|+.+| +|...-|.+||.|-|.|.
T Consensus 417 ~~~~KKPRlVfTd~QkrTL~aiFke~-~RPS~Emq~tIS~qL----~L~~sTV~NfFmNaRRRs 475 (558)
T KOG2252|consen 417 MLQTKKPRLVFTDIQKRTLQAIFKEN-KRPSREMQETISQQL----NLELSTVINFFMNARRRS 475 (558)
T ss_pred cccCCCceeeecHHHHHHHHHHHhcC-CCCCHHHHHHHHHHh----CCcHHHHHHHHHhhhhhc
Confidence 34578999999999999999999999 599999999999999 599999999999999876
No 33
>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=97.93 E-value=1.5e-06 Score=59.09 Aligned_cols=32 Identities=28% Similarity=0.598 Sum_probs=27.3
Q ss_pred CCCCHHHHHHHHHHhHhcCCCCCCceeeecccchhH
Q 046813 52 RTPSAEQIQQITTRLRAYGHIEGKNVFYWFQNHKAR 87 (250)
Q Consensus 52 ~yPs~e~R~qLA~~L~~~G~L~erqVqvWFQNRRAR 87 (250)
+||+.++|.+||++. | |+.+||..||-|.|.|
T Consensus 9 PYPs~~ek~~L~~~t---g-ls~~Qi~~WF~NaRrR 40 (40)
T PF05920_consen 9 PYPSKEEKEELAKQT---G-LSRKQISNWFINARRR 40 (40)
T ss_dssp GS--HHHHHHHHHHH---T-S-HHHHHHHHHHHHHH
T ss_pred CCCCHHHHHHHHHHc---C-CCHHHHHHHHHHhHcc
Confidence 599999999999999 7 9999999999999976
No 34
>KOG1146 consensus Homeobox protein [General function prediction only]
Probab=97.52 E-value=7.8e-05 Score=80.62 Aligned_cols=63 Identities=19% Similarity=0.434 Sum_probs=56.8
Q ss_pred CCCCCCCCCCCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhHhcCCCCCCceeeecccchhHHHHHHH
Q 046813 26 TLSSSSRWNPTKEQINMLESLYAQGIRTPSAEQIQQITTRLRAYGHIEGKNVFYWFQNHKARQRQKQK 93 (250)
Q Consensus 26 ~~~rR~Rt~fT~eQL~~LE~~F~~~~~yPs~e~R~qLA~~L~~~G~L~erqVqvWFQNRRAR~Krkq~ 93 (250)
...++.|+.++..||.+|..+|... .||..++.+.|-..+ + +..+.|++||||-|+|.|+...
T Consensus 901 ~~r~a~~~~~~d~qlk~i~~~~~~q-~~~~~~~~E~l~~~~---~-~~~~~i~vw~qna~~~s~k~~~ 963 (1406)
T KOG1146|consen 901 MGRRAYRTQESDLQLKIIKACYEAQ-RTPTMQECEVLEEPI---G-LPKRVIQVWFQNARAKSKKAKL 963 (1406)
T ss_pred hhhhhhccchhHHHHHHHHHHHhhc-cCChHHHHHhhcccc---c-CCcchhHHhhhhhhhhhhhhhh
Confidence 3457789999999999999999998 599999999999999 6 9999999999999999998655
No 35
>KOG0773 consensus Transcription factor MEIS1 and related HOX domain proteins [Transcription]
Probab=96.49 E-value=0.0024 Score=59.26 Aligned_cols=70 Identities=17% Similarity=0.247 Sum_probs=57.6
Q ss_pred CCCCCCCCCCCHHHHHHHHHHHhcC--CCCCCHHHHHHHHHHhHhcCCCCCCceeeecccchhHHHHHHHHHHHHH
Q 046813 26 TLSSSSRWNPTKEQINMLESLYAQG--IRTPSAEQIQQITTRLRAYGHIEGKNVFYWFQNHKARQRQKQKQERTAF 99 (250)
Q Consensus 26 ~~~rR~Rt~fT~eQL~~LE~~F~~~--~~yPs~e~R~qLA~~L~~~G~L~erqVqvWFQNRRAR~Krkq~~~~~a~ 99 (250)
....|++..+-++...+|+.....+ .+||+..++..||++. | |+..||.+||-|.|-|.++-.....+..
T Consensus 237 ~~~~r~~~~lP~~a~~ilr~Wl~~h~~~PYPse~~K~~La~~T---G-Ls~~Qv~NWFINaR~R~w~p~~~~~~~~ 308 (342)
T KOG0773|consen 237 QSKWRPQRGLPKEAVSILRAWLFEHLLHPYPSDDEKLMLAKQT---G-LSRPQVSNWFINARVRLWKPMIEEMYLL 308 (342)
T ss_pred cCCCCCCCCCCHHHHHHHHHHHHHhccCCCCcchhccccchhc---C-CCcccCCchhhhcccccCCchHHHHHHH
Confidence 3355667788899999999877664 2499999999999999 7 9999999999999999998777665544
No 36
>KOG3623 consensus Homeobox transcription factor SIP1 [Transcription]
Probab=93.78 E-value=0.03 Score=58.67 Aligned_cols=50 Identities=24% Similarity=0.479 Sum_probs=45.3
Q ss_pred HHHHHHHHhcCCCCCCHHHHHHHHHHhHhcCCCCCCceeeecccchhHHHHHHHH
Q 046813 40 INMLESLYAQGIRTPSAEQIQQITTRLRAYGHIEGKNVFYWFQNHKARQRQKQKQ 94 (250)
Q Consensus 40 L~~LE~~F~~~~~yPs~e~R~qLA~~L~~~G~L~erqVqvWFQNRRAR~Krkq~~ 94 (250)
+..|..+|..|. .|+.++-..||.++ | |.-+.|+.||+|+++.+..-++.
T Consensus 568 ~sllkayyaln~-~ps~eelskia~qv---g-lp~~vvk~wfE~~~a~e~sv~rs 617 (1007)
T KOG3623|consen 568 TSLLKAYYALNG-LPSEEELSKIAQQV---G-LPFAVVKAWFEDEEAEEMSVERS 617 (1007)
T ss_pred HHHHHHHHHhcC-CCCHHHHHHHHHHh---c-ccHHHHHHHHHhhhhhhhhhccC
Confidence 789999999995 99999999999999 6 99999999999999999876643
No 37
>PF11569 Homez: Homeodomain leucine-zipper encoding, Homez; PDB: 2YS9_A.
Probab=91.48 E-value=0.044 Score=40.27 Aligned_cols=41 Identities=20% Similarity=0.399 Sum_probs=29.9
Q ss_pred HHHHHHHHhcCCCCCCHHHHHHHHHHhHhcCCCCCCceeeecccch
Q 046813 40 INMLESLYAQGIRTPSAEQIQQITTRLRAYGHIEGKNVFYWFQNHK 85 (250)
Q Consensus 40 L~~LE~~F~~~~~yPs~e~R~qLA~~L~~~G~L~erqVqvWFQNRR 85 (250)
++-|+.+|..+ +.+.......|..+- | |+..||+.||--|+
T Consensus 10 ~~pL~~Yy~~h-~~L~E~DL~~L~~kS---~-ms~qqVr~WFa~~~ 50 (56)
T PF11569_consen 10 IQPLEDYYLKH-KQLQEEDLDELCDKS---R-MSYQQVRDWFAERM 50 (56)
T ss_dssp -HHHHHHHHHT-----TTHHHHHHHHT---T---HHHHHHHHHHHS
T ss_pred hHHHHHHHHHc-CCccHhhHHHHHHHH---C-CCHHHHHHHHHHhc
Confidence 56699999998 488888899999998 6 99999999997554
No 38
>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=91.14 E-value=0.26 Score=34.95 Aligned_cols=47 Identities=19% Similarity=0.187 Sum_probs=36.4
Q ss_pred CCCCCCCCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhHhcCCCCCCceeeecccch
Q 046813 29 SSSRWNPTKEQINMLESLYAQGIRTPSAEQIQQITTRLRAYGHIEGKNVFYWFQNHK 85 (250)
Q Consensus 29 rR~Rt~fT~eQL~~LE~~F~~~~~yPs~e~R~qLA~~L~~~G~L~erqVqvWFQNRR 85 (250)
+|+|..+|-+|...+=..++.+. + ..+||+++ | +...+|..|..||.
T Consensus 1 krkR~~LTl~eK~~iI~~~e~g~---s---~~~ia~~f---g-v~~sTv~~I~K~k~ 47 (53)
T PF04218_consen 1 KRKRKSLTLEEKLEIIKRLEEGE---S---KRDIAREF---G-VSRSTVSTILKNKD 47 (53)
T ss_dssp SSSSSS--HHHHHHHHHHHHCTT-------HHHHHHHH---T---CCHHHHHHHCHH
T ss_pred CCCCccCCHHHHHHHHHHHHcCC---C---HHHHHHHh---C-CCHHHHHHHHHhHH
Confidence 57899999999998888899883 3 56999999 7 99999999998864
No 39
>KOG1146 consensus Homeobox protein [General function prediction only]
Probab=86.39 E-value=0.69 Score=51.34 Aligned_cols=67 Identities=22% Similarity=0.273 Sum_probs=60.6
Q ss_pred CCCCCCCCCCCCCCCCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhHhcCCCCCCceeeecccchhHHHHHH
Q 046813 21 GGGGTTLSSSSRWNPTKEQINMLESLYAQGIRTPSAEQIQQITTRLRAYGHIEGKNVFYWFQNHKARQRQKQ 92 (250)
Q Consensus 21 g~g~~~~~rR~Rt~fT~eQL~~LE~~F~~~~~yPs~e~R~qLA~~L~~~G~L~erqVqvWFQNRRAR~Krkq 92 (250)
|++...+.++.|+..-.+++.+|=+.|..+. -|+.+.+..|.-.. + .+.+++++||+|=|.|.++.+
T Consensus 698 ~~~~~~~~~~~~~~~~~~aa~~l~~a~~~~~-sps~k~~~civcd~---~-st~~l~~l~~h~~~~rs~ke~ 764 (1406)
T KOG1146|consen 698 GESLSPRDKLLRLTILPEAAMILGRAYMQDN-SPSLKVFDCIVCDV---F-STDRLDQLWFHNTRERSRKEQ 764 (1406)
T ss_pred CCCCCcccccCcccccHHHHhhhhhcccCCC-CHHHHHHHHhhhhh---h-hhhhHHHHhhcchhhhhhhhc
Confidence 7778888888999888899999999999996 89999999999887 5 889999999999999999876
No 40
>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=76.87 E-value=1.4 Score=28.19 Aligned_cols=43 Identities=16% Similarity=0.225 Sum_probs=32.7
Q ss_pred CCCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhHhcCCCCCCceeeecccchh
Q 046813 34 NPTKEQINMLESLYAQGIRTPSAEQIQQITTRLRAYGHIEGKNVFYWFQNHKA 86 (250)
Q Consensus 34 ~fT~eQL~~LE~~F~~~~~yPs~e~R~qLA~~L~~~G~L~erqVqvWFQNRRA 86 (250)
.+++++..+++..|..+ + + ..+||.+| | ++...|..|.+.-+.
T Consensus 10 ~l~~~~~~~~~~~~~~~--~-~---~~~ia~~~---~-~s~~~i~~~~~~~~~ 52 (55)
T cd06171 10 KLPEREREVILLRFGEG--L-S---YEEIAEIL---G-ISRSTVRQRLHRALK 52 (55)
T ss_pred hCCHHHHHHHHHHHhcC--C-C---HHHHHHHH---C-cCHHHHHHHHHHHHH
Confidence 35688999999998766 3 2 35889999 6 999999887755443
No 41
>KOG3755 consensus SATB1 matrix attachment region binding protein [Transcription]
Probab=68.51 E-value=1.2 Score=46.31 Aligned_cols=70 Identities=14% Similarity=0.187 Sum_probs=44.8
Q ss_pred CCCCCCCCCCCCCCCCHHHHHHHHHH-HhcCCCCCCHHHHHHHHHHh-----HhcCCCCCCceeeecccchhHHHHHHH
Q 046813 21 GGGGTTLSSSSRWNPTKEQINMLESL-YAQGIRTPSAEQIQQITTRL-----RAYGHIEGKNVFYWFQNHKARQRQKQK 93 (250)
Q Consensus 21 g~g~~~~~rR~Rt~fT~eQL~~LE~~-F~~~~~yPs~e~R~qLA~~L-----~~~G~L~erqVqvWFQNRRAR~Krkq~ 93 (250)
.+.-...+|++|..|=.+|...+... |-.+ ..++--.+.+..+++ ++ +.+.++|+.||.|||+++|+.+.
T Consensus 684 LSa~~~~pk~~~~k~f~~~~~ev~~~w~~k~-~s~s~~~v~eYkee~~~~~~~e--~~~~kn~~~~fk~~~ee~~~~k~ 759 (769)
T KOG3755|consen 684 LSAQLDLPKKTIIKFFQNQRYEVKHHWKLKT-RSGSWVDVAEYKEEELLMPYEE--KFESKNVQFWFKVRREEEKRLKM 759 (769)
T ss_pred hhhhhcccHHHHHHhhhcceeecchhheecc-cCchhHHHHHhhHHhhcchhhh--hhhhcchHHHHHHHHHHHhhhhc
Confidence 34455667777777767776665443 3444 356555554444444 11 24678999999999999998653
No 42
>PRK09652 RNA polymerase sigma factor RpoE; Provisional
Probab=66.38 E-value=8 Score=31.14 Aligned_cols=45 Identities=16% Similarity=0.102 Sum_probs=33.3
Q ss_pred CCCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhHhcCCCCCCceeeecccchhHHHH
Q 046813 34 NPTKEQINMLESLYAQGIRTPSAEQIQQITTRLRAYGHIEGKNVFYWFQNHKARQRQ 90 (250)
Q Consensus 34 ~fT~eQL~~LE~~F~~~~~yPs~e~R~qLA~~L~~~G~L~erqVqvWFQNRRAR~Kr 90 (250)
.+++.|.++|...|-.+ ++ -.+||+.| | +++..|..|.+ ||+.|-
T Consensus 128 ~L~~~~r~vl~l~~~~~--~s----~~eIA~~l---g-is~~tV~~~l~--ra~~~L 172 (182)
T PRK09652 128 SLPEELRTAITLREIEG--LS----YEEIAEIM---G-CPIGTVRSRIF--RAREAL 172 (182)
T ss_pred hCCHHHHHHHHHHHHcC--CC----HHHHHHHH---C-CCHHHHHHHHH--HHHHHH
Confidence 46678888888877666 32 35889999 6 99999998877 454443
No 43
>PRK03975 tfx putative transcriptional regulator; Provisional
Probab=66.33 E-value=10 Score=32.32 Aligned_cols=55 Identities=25% Similarity=0.241 Sum_probs=39.3
Q ss_pred CCCCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhHhcCCCCCCceeeecccchhHHHHHHHHHHHHHH
Q 046813 33 WNPTKEQINMLESLYAQGIRTPSAEQIQQITTRLRAYGHIEGKNVFYWFQNHKARQRQKQKQERTAFI 100 (250)
Q Consensus 33 t~fT~eQL~~LE~~F~~~~~yPs~e~R~qLA~~L~~~G~L~erqVqvWFQNRRAR~Krkq~~~~~a~~ 100 (250)
..+|+.|.++|+. +..+ + + ..+||+.| | ++...|..|-++.+.|.| +....+++.
T Consensus 5 ~~Lt~rqreVL~l-r~~G--l-T---q~EIAe~L---G-iS~~tVs~ie~ra~kkLr--~~~~tl~~~ 59 (141)
T PRK03975 5 SFLTERQIEVLRL-RERG--L-T---QQEIADIL---G-TSRANVSSIEKRARENIE--KARETLAFA 59 (141)
T ss_pred cCCCHHHHHHHHH-HHcC--C-C---HHHHHHHH---C-CCHHHHHHHHHHHHHHHH--HHHHHHHHH
Confidence 4578999999988 5455 2 2 36999999 6 999999999985444444 444445543
No 44
>PF04967 HTH_10: HTH DNA binding domain; InterPro: IPR007050 Numerous bacterial transcription regulatory proteins bind DNA via a helix-turn-helix (HTH) motif. This entry represents the HTH DNA binding domain found in Halobacterium salinarium (Halobacterium halobium) and described as a putative bacterio-opsin activator.
Probab=65.59 E-value=9.1 Score=27.55 Aligned_cols=38 Identities=26% Similarity=0.443 Sum_probs=30.1
Q ss_pred CCHHHHHHHHHHHhcCCCC--CCHHHHHHHHHHhHhcCCCCCCce
Q 046813 35 PTKEQINMLESLYAQGIRT--PSAEQIQQITTRLRAYGHIEGKNV 77 (250)
Q Consensus 35 fT~eQL~~LE~~F~~~~~y--Ps~e~R~qLA~~L~~~G~L~erqV 77 (250)
+|+.|.++|...|+.+ +| |-...-.+||++| | |+..-|
T Consensus 1 LT~~Q~e~L~~A~~~G-Yfd~PR~~tl~elA~~l---g-is~st~ 40 (53)
T PF04967_consen 1 LTDRQREILKAAYELG-YFDVPRRITLEELAEEL---G-ISKSTV 40 (53)
T ss_pred CCHHHHHHHHHHHHcC-CCCCCCcCCHHHHHHHh---C-CCHHHH
Confidence 5899999999999998 44 4445568999999 6 887543
No 45
>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=64.68 E-value=2.7 Score=30.19 Aligned_cols=42 Identities=19% Similarity=0.347 Sum_probs=26.4
Q ss_pred CCCCCCCHHHHHHHHHHH-hcCCCCCCHHHHHHHHHHhHhcCCCCCCceeeec
Q 046813 30 SSRWNPTKEQINMLESLY-AQGIRTPSAEQIQQITTRLRAYGHIEGKNVFYWF 81 (250)
Q Consensus 30 R~Rt~fT~eQL~~LE~~F-~~~~~yPs~e~R~qLA~~L~~~G~L~erqVqvWF 81 (250)
++|..||+++...+=..+ ..+ ..+.+||+++ | |++..|..|=
T Consensus 2 ~~r~~ys~e~K~~~v~~~~~~g------~sv~~va~~~---g-i~~~~l~~W~ 44 (76)
T PF01527_consen 2 RKRRRYSPEFKLQAVREYLESG------ESVSEVAREY---G-ISPSTLYNWR 44 (76)
T ss_dssp -SS----HHHHHHHHHHHHHHH------CHHHHHHHHH---T-S-HHHHHHHH
T ss_pred CCCCCCCHHHHHHHHHHHHHCC------CceEeeeccc---c-cccccccHHH
Confidence 456777898877666666 444 2367999999 7 9999998774
No 46
>PF04545 Sigma70_r4: Sigma-70, region 4; InterPro: IPR007630 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognised by the major sigma factors [, ]. Region 4 of sigma-70 like sigma-factors is involved in binding to the -35 promoter element via a helix-turn-helix motif []. Due to the way Pfam works, the threshold has been set artificially high to prevent overlaps with other helix-turn-helix families. Therefore there are many false negatives.; GO: 0003677 DNA binding, 0003700 sequence-specific DNA binding transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, DNA-dependent, 0006355 regulation of transcription, DNA-dependent; PDB: 2P7V_B 3IYD_F 1TLH_B 1KU7_A 1RIO_H 3N97_A 1KU3_A 1RP3_C 1SC5_A 1NR3_A ....
Probab=61.56 E-value=6.7 Score=26.48 Aligned_cols=37 Identities=22% Similarity=0.393 Sum_probs=28.1
Q ss_pred CCCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhHhcCCCCCCceeee
Q 046813 34 NPTKEQINMLESLYAQGIRTPSAEQIQQITTRLRAYGHIEGKNVFYW 80 (250)
Q Consensus 34 ~fT~eQL~~LE~~F~~~~~yPs~e~R~qLA~~L~~~G~L~erqVqvW 80 (250)
.++++|.++|...|-.+. + -.+||+.| | ++...|..+
T Consensus 4 ~L~~~er~vi~~~y~~~~---t---~~eIa~~l---g-~s~~~V~~~ 40 (50)
T PF04545_consen 4 QLPPREREVIRLRYFEGL---T---LEEIAERL---G-ISRSTVRRI 40 (50)
T ss_dssp TS-HHHHHHHHHHHTST----S---HHHHHHHH---T-SCHHHHHHH
T ss_pred hCCHHHHHHHHHHhcCCC---C---HHHHHHHH---C-CcHHHHHHH
Confidence 367999999999997662 2 36899999 6 998877644
No 47
>PRK09642 RNA polymerase sigma factor SigW; Reviewed
Probab=58.81 E-value=9 Score=30.88 Aligned_cols=47 Identities=15% Similarity=0.111 Sum_probs=31.3
Q ss_pred CCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhHhcCCCCCCceeeecccchhHHHHH
Q 046813 35 PTKEQINMLESLYAQGIRTPSAEQIQQITTRLRAYGHIEGKNVFYWFQNHKARQRQK 91 (250)
Q Consensus 35 fT~eQL~~LE~~F~~~~~yPs~e~R~qLA~~L~~~G~L~erqVqvWFQNRRAR~Krk 91 (250)
+++.|..++...|-.+. + -.+||+.| | +++..|+++...=|.+.|+.
T Consensus 107 Lp~~~r~v~~l~~~~g~--s----~~EIA~~l---g-is~~tV~~~l~Rar~~Lr~~ 153 (160)
T PRK09642 107 LPENYRDVVLAHYLEEK--S----YQEIALQE---K-IEVKTVEMKLYRARKWIKKH 153 (160)
T ss_pred CCHHHHHHHHHHHHhCC--C----HHHHHHHH---C-CCHHHHHHHHHHHHHHHHHH
Confidence 44566666666666652 2 35889999 6 99999998876444444443
No 48
>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=57.21 E-value=17 Score=20.29 Aligned_cols=37 Identities=32% Similarity=0.551 Sum_probs=26.9
Q ss_pred CCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhHhcCCCCCCceeeec
Q 046813 35 PTKEQINMLESLYAQGIRTPSAEQIQQITTRLRAYGHIEGKNVFYWF 81 (250)
Q Consensus 35 fT~eQL~~LE~~F~~~~~yPs~e~R~qLA~~L~~~G~L~erqVqvWF 81 (250)
++.++...+...|..+ + + ..+||+.+ | ++...|..|.
T Consensus 6 ~~~~~~~~i~~~~~~~--~-s---~~~ia~~~---~-is~~tv~~~~ 42 (42)
T cd00569 6 LTPEQIEEARRLLAAG--E-S---VAEIARRL---G-VSRSTLYRYL 42 (42)
T ss_pred CCHHHHHHHHHHHHcC--C-C---HHHHHHHH---C-CCHHHHHHhC
Confidence 5577787777778765 3 2 46889999 6 9888787763
No 49
>COG3413 Predicted DNA binding protein [General function prediction only]
Probab=54.21 E-value=15 Score=32.13 Aligned_cols=39 Identities=23% Similarity=0.445 Sum_probs=31.8
Q ss_pred CCCHHHHHHHHHHHhcCCC--CCCHHHHHHHHHHhHhcCCCCCCce
Q 046813 34 NPTKEQINMLESLYAQGIR--TPSAEQIQQITTRLRAYGHIEGKNV 77 (250)
Q Consensus 34 ~fT~eQL~~LE~~F~~~~~--yPs~e~R~qLA~~L~~~G~L~erqV 77 (250)
.+|+.|+++|...|+.+ + ||-.-...+||++| | |+..-+
T Consensus 155 ~LTdrQ~~vL~~A~~~G-YFd~PR~~~l~dLA~~l---G-ISkst~ 195 (215)
T COG3413 155 DLTDRQLEVLRLAYKMG-YFDYPRRVSLKDLAKEL---G-ISKSTL 195 (215)
T ss_pred cCCHHHHHHHHHHHHcC-CCCCCccCCHHHHHHHh---C-CCHHHH
Confidence 78999999999999999 3 35555568999999 8 987643
No 50
>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=54.19 E-value=11 Score=28.51 Aligned_cols=44 Identities=18% Similarity=0.259 Sum_probs=31.1
Q ss_pred CCCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhHhcCCCCCCceeeecccchhH
Q 046813 34 NPTKEQINMLESLYAQGIRTPSAEQIQQITTRLRAYGHIEGKNVFYWFQNHKAR 87 (250)
Q Consensus 34 ~fT~eQL~~LE~~F~~~~~yPs~e~R~qLA~~L~~~G~L~erqVqvWFQNRRAR 87 (250)
.+++.|..+|...|-.+ ++ ..+||+.| | +++..|..|.+.=+.|
T Consensus 110 ~L~~~~~~ii~~~~~~g--~s----~~eIA~~l---~-~s~~~v~~~~~~~~~k 153 (158)
T TIGR02937 110 KLPEREREVLVLRYLEG--LS----YKEIAEIL---G-ISVGTVKRRLKRARKK 153 (158)
T ss_pred hCCHHHHHHHhhHHhcC--CC----HHHHHHHH---C-CCHHHHHHHHHHHHHH
Confidence 35688888888776655 33 35899999 6 9999998766543333
No 51
>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=52.42 E-value=6.7 Score=26.61 Aligned_cols=39 Identities=23% Similarity=0.263 Sum_probs=28.6
Q ss_pred CCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhHhcCCCCCCceeeeccc
Q 046813 35 PTKEQINMLESLYAQGIRTPSAEQIQQITTRLRAYGHIEGKNVFYWFQN 83 (250)
Q Consensus 35 fT~eQL~~LE~~F~~~~~yPs~e~R~qLA~~L~~~G~L~erqVqvWFQN 83 (250)
+++.|..++...|-.+ ++ -.+||+.| | +++..|+.|.+.
T Consensus 11 L~~~~r~i~~l~~~~g--~s----~~eIa~~l---~-~s~~~v~~~l~r 49 (54)
T PF08281_consen 11 LPERQREIFLLRYFQG--MS----YAEIAEIL---G-ISESTVKRRLRR 49 (54)
T ss_dssp S-HHHHHHHHHHHTS---------HHHHHHHC---T-S-HHHHHHHHHH
T ss_pred CCHHHHHHHHHHHHHC--cC----HHHHHHHH---C-cCHHHHHHHHHH
Confidence 5688889999988888 33 36899999 6 999999988763
No 52
>PRK09646 RNA polymerase sigma factor SigK; Reviewed
Probab=50.14 E-value=17 Score=30.59 Aligned_cols=37 Identities=19% Similarity=0.194 Sum_probs=27.4
Q ss_pred CCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhHhcCCCCCCceeeec
Q 046813 35 PTKEQINMLESLYAQGIRTPSAEQIQQITTRLRAYGHIEGKNVFYWF 81 (250)
Q Consensus 35 fT~eQL~~LE~~F~~~~~yPs~e~R~qLA~~L~~~G~L~erqVqvWF 81 (250)
+++.|..+|...|-.+ + + ..+||+.| | ++...|+++.
T Consensus 143 L~~~~r~vl~l~~~~~--~-s---~~EIA~~L---g-is~~tVk~~l 179 (194)
T PRK09646 143 LTDTQRESVTLAYYGG--L-T---YREVAERL---A-VPLGTVKTRM 179 (194)
T ss_pred CCHHHHHHHHHHHHcC--C-C---HHHHHHHh---C-CChHhHHHHH
Confidence 5567777777766665 2 2 36889999 6 9999997776
No 53
>PRK12515 RNA polymerase sigma factor; Provisional
Probab=45.79 E-value=21 Score=29.78 Aligned_cols=45 Identities=11% Similarity=0.221 Sum_probs=30.4
Q ss_pred CCCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhHhcCCCCCCceeeecccchhHH
Q 046813 34 NPTKEQINMLESLYAQGIRTPSAEQIQQITTRLRAYGHIEGKNVFYWFQNHKARQ 88 (250)
Q Consensus 34 ~fT~eQL~~LE~~F~~~~~yPs~e~R~qLA~~L~~~G~L~erqVqvWFQNRRAR~ 88 (250)
.++++|.++|+-.|-.+ + + -.+||+.| | +++..|++-...=|.+.
T Consensus 131 ~L~~~~r~vl~l~~~~~--~-s---~~eIA~~l---g-is~~tV~~~l~Rar~~L 175 (189)
T PRK12515 131 KLSPAHREIIDLVYYHE--K-S---VEEVGEIV---G-IPESTVKTRMFYARKKL 175 (189)
T ss_pred hCCHHHHHHHHHHHHcC--C-C---HHHHHHHH---C-cCHHHHHHHHHHHHHHH
Confidence 45667777777766665 2 2 36889999 6 99999987664333333
No 54
>PF10925 DUF2680: Protein of unknown function (DUF2680); InterPro: IPR024485 Members in this family of proteins are annotated as YckD however currently no function is known.
Probab=45.59 E-value=14 Score=27.14 Aligned_cols=38 Identities=29% Similarity=0.291 Sum_probs=30.5
Q ss_pred CCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhHhcCCCCCCce
Q 046813 35 PTKEQINMLESLYAQGIRTPSAEQIQQITTRLRAYGHIEGKNV 77 (250)
Q Consensus 35 fT~eQL~~LE~~F~~~~~yPs~e~R~qLA~~L~~~G~L~erqV 77 (250)
+|.+|+..|+.+|..= .+.|.+|-.+.-.+|.|+..|=
T Consensus 1 lT~~Qk~el~~l~~qm-----~e~kK~~idk~Ve~G~iTqeqA 38 (59)
T PF10925_consen 1 LTDQQKKELKALYKQM-----LELKKQIIDKYVEAGVITQEQA 38 (59)
T ss_pred CCHHHHHHHHHHHHHH-----HHHHHHHHHHHHHcCCCCHHHH
Confidence 5899999999999885 3456677777778998887663
No 55
>PRK12519 RNA polymerase sigma factor; Provisional
Probab=44.54 E-value=20 Score=29.88 Aligned_cols=42 Identities=26% Similarity=0.233 Sum_probs=29.1
Q ss_pred CCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhHhcCCCCCCceeeecccchh
Q 046813 35 PTKEQINMLESLYAQGIRTPSAEQIQQITTRLRAYGHIEGKNVFYWFQNHKA 86 (250)
Q Consensus 35 fT~eQL~~LE~~F~~~~~yPs~e~R~qLA~~L~~~G~L~erqVqvWFQNRRA 86 (250)
+++++..+|+..|-.+ ++ ..+||+.| | +++..|+.|.+.=|.
T Consensus 142 L~~~~~~v~~l~~~~g--~s----~~EIA~~l---g-is~~tV~~~l~Ra~~ 183 (194)
T PRK12519 142 LPESQRQVLELAYYEG--LS----QSEIAKRL---G-IPLGTVKARARQGLL 183 (194)
T ss_pred CCHHHhhhhhhhhhcC--CC----HHHHHHHh---C-CCHHHHHHHHHHHHH
Confidence 4566666666666555 22 36899999 7 999999999853333
No 56
>PRK06759 RNA polymerase factor sigma-70; Validated
Probab=44.02 E-value=18 Score=28.75 Aligned_cols=40 Identities=8% Similarity=0.122 Sum_probs=29.4
Q ss_pred CCCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhHhcCCCCCCceeeeccc
Q 046813 34 NPTKEQINMLESLYAQGIRTPSAEQIQQITTRLRAYGHIEGKNVFYWFQN 83 (250)
Q Consensus 34 ~fT~eQL~~LE~~F~~~~~yPs~e~R~qLA~~L~~~G~L~erqVqvWFQN 83 (250)
.+++.|.+++...|-.+. + ..+||..| | +++..|+.|...
T Consensus 106 ~L~~~~r~ii~l~~~~~~---s---~~EIA~~l---~-is~~tV~~~~~r 145 (154)
T PRK06759 106 VLDEKEKYIIFERFFVGK---T---MGEIALET---E-MTYYQVRWIYRQ 145 (154)
T ss_pred hCCHHHHHHHHHHHhcCC---C---HHHHHHHH---C-CCHHHHHHHHHH
Confidence 345677777777776662 2 46899999 6 999999977653
No 57
>PRK04217 hypothetical protein; Provisional
Probab=43.86 E-value=41 Score=27.53 Aligned_cols=48 Identities=15% Similarity=0.245 Sum_probs=35.7
Q ss_pred CCCCCCCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhHhcCCCCCCceeeecccchhH
Q 046813 30 SSRWNPTKEQINMLESLYAQGIRTPSAEQIQQITTRLRAYGHIEGKNVFYWFQNHKAR 87 (250)
Q Consensus 30 R~Rt~fT~eQL~~LE~~F~~~~~yPs~e~R~qLA~~L~~~G~L~erqVqvWFQNRRAR 87 (250)
..=-.+|++|.++++..|..+. + .++||+.| | |+...|+...+.-|.+
T Consensus 38 ~p~~~Lt~eereai~l~~~eGl---S---~~EIAk~L---G-IS~sTV~r~L~RArkk 85 (110)
T PRK04217 38 KPPIFMTYEEFEALRLVDYEGL---T---QEEAGKRM---G-VSRGTVWRALTSARKK 85 (110)
T ss_pred CCcccCCHHHHHHHHHHHHcCC---C---HHHHHHHH---C-cCHHHHHHHHHHHHHH
Confidence 3345677999999999988772 3 46899999 6 9999988766543333
No 58
>PRK12526 RNA polymerase sigma factor; Provisional
Probab=43.68 E-value=22 Score=30.48 Aligned_cols=38 Identities=18% Similarity=0.220 Sum_probs=26.4
Q ss_pred CCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhHhcCCCCCCceeeecc
Q 046813 35 PTKEQINMLESLYAQGIRTPSAEQIQQITTRLRAYGHIEGKNVFYWFQ 82 (250)
Q Consensus 35 fT~eQL~~LE~~F~~~~~yPs~e~R~qLA~~L~~~G~L~erqVqvWFQ 82 (250)
+++.|..+|...|-.+ + + .++||..| | +++..|+++..
T Consensus 154 L~~~~r~vl~l~~~~g--~-s---~~EIA~~l---g-is~~tV~~~l~ 191 (206)
T PRK12526 154 LPEAQQTVVKGVYFQE--L-S---QEQLAQQL---N-VPLGTVKSRLR 191 (206)
T ss_pred CCHHHHHHHHHHHHcC--C-C---HHHHHHHH---C-CCHHHHHHHHH
Confidence 4456666676666555 2 2 36899999 6 99999976663
No 59
>PRK12514 RNA polymerase sigma factor; Provisional
Probab=43.50 E-value=27 Score=28.74 Aligned_cols=43 Identities=14% Similarity=0.325 Sum_probs=28.1
Q ss_pred CCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhHhcCCCCCCceeeecccchhH
Q 046813 35 PTKEQINMLESLYAQGIRTPSAEQIQQITTRLRAYGHIEGKNVFYWFQNHKAR 87 (250)
Q Consensus 35 fT~eQL~~LE~~F~~~~~yPs~e~R~qLA~~L~~~G~L~erqVqvWFQNRRAR 87 (250)
++++|..+|.-.|-.+ + + .++||+.| | +++..|+++.+.=|.+
T Consensus 130 L~~~~r~i~~l~~~~g--~-s---~~eIA~~l---g-is~~tV~~~l~Rar~~ 172 (179)
T PRK12514 130 LEKDRAAAVRRAYLEG--L-S---YKELAERH---D-VPLNTMRTWLRRSLLK 172 (179)
T ss_pred CCHHHHHHHHHHHHcC--C-C---HHHHHHHH---C-CChHHHHHHHHHHHHH
Confidence 3455656666665554 2 2 46899999 7 9999998776533333
No 60
>KOG3623 consensus Homeobox transcription factor SIP1 [Transcription]
Probab=42.97 E-value=87 Score=34.04 Aligned_cols=57 Identities=21% Similarity=0.274 Sum_probs=37.9
Q ss_pred CCCCCCCCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhHhcCCCCCCceeeecccchhHHHH
Q 046813 29 SSSRWNPTKEQINMLESLYAQGIRTPSAEQIQQITTRLRAYGHIEGKNVFYWFQNHKARQRQ 90 (250)
Q Consensus 29 rR~Rt~fT~eQL~~LE~~F~~~~~yPs~e~R~qLA~~L~~~G~L~erqVqvWFQNRRAR~Kr 90 (250)
.+-|+-...++-..|-..++-+. -++..+-.-++.+| ...+..|.+||++|+.+-+.
T Consensus 627 ~kv~sp~k~~dq~ql~~a~elq~-s~~n~~~pl~~t~~----~n~~pv~ev~dhsrsstpsp 683 (1007)
T KOG3623|consen 627 VKVRSPIKEEDQQQLKQAYELQA-SPSNDEFPLIATRL----QNDPPVVEVWDHSRSSTPSP 683 (1007)
T ss_pred ccccCCCCccchhhhHhhhhccc-CccCcccchhhhhc----cCCCcchhhcccCCCCCCCC
Confidence 34445555667777888887763 34433334556666 36788899999999987664
No 61
>PF12824 MRP-L20: Mitochondrial ribosomal protein subunit L20; InterPro: IPR024388 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. This entry represents the essential mitochondrial ribosomal protein L20 family from fungi [].
Probab=42.96 E-value=53 Score=28.62 Aligned_cols=48 Identities=17% Similarity=0.183 Sum_probs=39.2
Q ss_pred CCCCCCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhHhcCCCCCCceeeecccch
Q 046813 31 SRWNPTKEQINMLESLYAQGIRTPSAEQIQQITTRLRAYGHIEGKNVFYWFQNHK 85 (250)
Q Consensus 31 ~Rt~fT~eQL~~LE~~F~~~~~yPs~e~R~qLA~~L~~~G~L~erqVqvWFQNRR 85 (250)
+..++|+|+++.+-++-..+ |....+..||++. | ++.--|.+=-+--+
T Consensus 82 k~y~Lt~e~i~Eir~LR~~D---P~~wTr~~LAkkF---~-~S~~fV~~v~~~~~ 129 (164)
T PF12824_consen 82 KKYHLTPEDIQEIRRLRAED---PEKWTRKKLAKKF---N-CSPLFVSMVAPAPK 129 (164)
T ss_pred ccccCCHHHHHHHHHHHHcC---chHhhHHHHHHHh---C-CCHHHHHHhcCCCH
Confidence 55899999999999999998 5788899999998 5 98877765554433
No 62
>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=42.53 E-value=6.8 Score=29.11 Aligned_cols=17 Identities=24% Similarity=0.692 Sum_probs=15.4
Q ss_pred HHHHHHhHhcCCCCCCceeee
Q 046813 60 QQITTRLRAYGHIEGKNVFYW 80 (250)
Q Consensus 60 ~qLA~~L~~~G~L~erqVqvW 80 (250)
.+||++| | +++.+|..|
T Consensus 26 kdIA~~L---g-vs~~tIr~W 42 (60)
T PF10668_consen 26 KDIAEKL---G-VSESTIRKW 42 (60)
T ss_pred HHHHHHH---C-CCHHHHHHH
Confidence 5899999 6 999999977
No 63
>PRK11924 RNA polymerase sigma factor; Provisional
Probab=42.23 E-value=31 Score=27.66 Aligned_cols=45 Identities=18% Similarity=0.203 Sum_probs=30.1
Q ss_pred CCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhHhcCCCCCCceeeecccchhHHH
Q 046813 35 PTKEQINMLESLYAQGIRTPSAEQIQQITTRLRAYGHIEGKNVFYWFQNHKARQR 89 (250)
Q Consensus 35 fT~eQL~~LE~~F~~~~~yPs~e~R~qLA~~L~~~G~L~erqVqvWFQNRRAR~K 89 (250)
+++.+..+|...|-.+ +. -.+||+.| | +++..|..|..-=|.|.|
T Consensus 126 L~~~~r~i~~l~~~~~--~~----~~eIA~~l---g-is~~tv~~~~~ra~~~lr 170 (179)
T PRK11924 126 LPVKQREVFLLRYVEG--LS----YREIAEIL---G-VPVGTVKSRLRRARQLLR 170 (179)
T ss_pred CCHHHHHHhhHHHHcC--CC----HHHHHHHH---C-CCHHHHHHHHHHHHHHHH
Confidence 4456666666666555 22 36899999 6 999999988764444433
No 64
>TIGR02948 SigW_bacill RNA polymerase sigma-W factor. This sigma factor is restricted to certain lineages of the order Bacillales.
Probab=42.07 E-value=21 Score=29.26 Aligned_cols=45 Identities=9% Similarity=0.060 Sum_probs=29.2
Q ss_pred CCCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhHhcCCCCCCceeeecccchhHH
Q 046813 34 NPTKEQINMLESLYAQGIRTPSAEQIQQITTRLRAYGHIEGKNVFYWFQNHKARQ 88 (250)
Q Consensus 34 ~fT~eQL~~LE~~F~~~~~yPs~e~R~qLA~~L~~~G~L~erqVqvWFQNRRAR~ 88 (250)
.+++.|..+|+..|-.+ ++ -++||+.| | +++..|+++.+.=|.+.
T Consensus 136 ~L~~~~r~v~~l~~~~g--~s----~~eIA~~l---g-is~~~v~~~l~Rar~~L 180 (187)
T TIGR02948 136 ALPPKYRMVIVLKYMED--LS----LKEISEIL---D-LPVGTVKTRIHRGREAL 180 (187)
T ss_pred hCCHHHhHHhhhHHhcC--CC----HHHHHHHH---C-CCHHHHHHHHHHHHHHH
Confidence 34556666666655444 22 36889999 6 99999998885333333
No 65
>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=41.80 E-value=23 Score=27.78 Aligned_cols=39 Identities=21% Similarity=0.259 Sum_probs=26.8
Q ss_pred CCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhHhcCCCCCCceeeeccc
Q 046813 35 PTKEQINMLESLYAQGIRTPSAEQIQQITTRLRAYGHIEGKNVFYWFQN 83 (250)
Q Consensus 35 fT~eQL~~LE~~F~~~~~yPs~e~R~qLA~~L~~~G~L~erqVqvWFQN 83 (250)
++..+.++|.-.|-.+ ++ ..+||+.| | +++..|+.+...
T Consensus 114 L~~~~r~il~l~~~~~--~~----~~eIA~~l---g-is~~tv~~~~~r 152 (161)
T TIGR02985 114 LPEQCRKIFILSRFEG--KS----YKEIAEEL---G-ISVKTVEYHISK 152 (161)
T ss_pred CCHHHHHHHHHHHHcC--CC----HHHHHHHH---C-CCHHHHHHHHHH
Confidence 4566667777656554 33 35889999 6 999998866543
No 66
>PLN02705 beta-amylase
Probab=41.45 E-value=49 Score=34.93 Aligned_cols=19 Identities=37% Similarity=0.564 Sum_probs=11.0
Q ss_pred HHHHHHHH----hHhcCCCCCCc
Q 046813 58 QIQQITTR----LRAYGHIEGKN 76 (250)
Q Consensus 58 ~R~qLA~~----L~~~G~L~erq 76 (250)
+|..||.+ |++||++...+
T Consensus 94 ~rrai~~ki~aglr~~g~~~lp~ 116 (681)
T PLN02705 94 HRRAITSRMLAGLRQYGNFPLPA 116 (681)
T ss_pred HHHHHHHHHHHHHHhccCCCCCc
Confidence 34555554 57778765543
No 67
>PF13936 HTH_38: Helix-turn-helix domain; PDB: 2W48_A.
Probab=41.02 E-value=8.4 Score=26.05 Aligned_cols=37 Identities=38% Similarity=0.469 Sum_probs=18.1
Q ss_pred CCCCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhHhcCCCCCCceee
Q 046813 33 WNPTKEQINMLESLYAQGIRTPSAEQIQQITTRLRAYGHIEGKNVFY 79 (250)
Q Consensus 33 t~fT~eQL~~LE~~F~~~~~yPs~e~R~qLA~~L~~~G~L~erqVqv 79 (250)
..+|.+|...++..+..+. + ..+||+.| | ++..-|..
T Consensus 3 ~~Lt~~eR~~I~~l~~~G~---s---~~~IA~~l---g-~s~sTV~r 39 (44)
T PF13936_consen 3 KHLTPEERNQIEALLEQGM---S---IREIAKRL---G-RSRSTVSR 39 (44)
T ss_dssp ---------HHHHHHCS---------HHHHHHHT---T---HHHHHH
T ss_pred cchhhhHHHHHHHHHHcCC---C---HHHHHHHH---C-cCcHHHHH
Confidence 3577999999999998773 3 45899999 6 77766543
No 68
>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=40.87 E-value=23 Score=29.21 Aligned_cols=39 Identities=18% Similarity=0.153 Sum_probs=30.0
Q ss_pred CCCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhHhcCCCCCCceeeecc
Q 046813 34 NPTKEQINMLESLYAQGIRTPSAEQIQQITTRLRAYGHIEGKNVFYWFQ 82 (250)
Q Consensus 34 ~fT~eQL~~LE~~F~~~~~yPs~e~R~qLA~~L~~~G~L~erqVqvWFQ 82 (250)
.+++.|..+|+-.|-.+ ++ ..+||+.| | +++..|+++-+
T Consensus 100 ~L~~~~r~v~~l~~~~g--~s----~~eIA~~l---g-is~~tV~~~l~ 138 (170)
T TIGR02959 100 ELPDEYREAIRLTELEG--LS----QQEIAEKL---G-LSLSGAKSRVQ 138 (170)
T ss_pred hCCHHHHHHHHHHHHcC--CC----HHHHHHHH---C-CCHHHHHHHHH
Confidence 56678888888877776 33 36899999 6 99999987663
No 69
>PRK09637 RNA polymerase sigma factor SigZ; Provisional
Probab=40.02 E-value=31 Score=28.95 Aligned_cols=45 Identities=16% Similarity=0.179 Sum_probs=32.0
Q ss_pred CCCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhHhcCCCCCCceeeecccchhHHHH
Q 046813 34 NPTKEQINMLESLYAQGIRTPSAEQIQQITTRLRAYGHIEGKNVFYWFQNHKARQRQ 90 (250)
Q Consensus 34 ~fT~eQL~~LE~~F~~~~~yPs~e~R~qLA~~L~~~G~L~erqVqvWFQNRRAR~Kr 90 (250)
.+++.|..+|...|-.+ ++ ..+||..| | +++..|+..+. |||.+-
T Consensus 106 ~L~~~~r~i~~l~~~~g--~~----~~EIA~~l---g-is~~tV~~~l~--Rar~~L 150 (181)
T PRK09637 106 ALPEKYAEALRLTELEG--LS----QKEIAEKL---G-LSLSGAKSRVQ--RGRVKL 150 (181)
T ss_pred hCCHHHHHHHHHHHhcC--CC----HHHHHHHh---C-CCHHHHHHHHH--HHHHHH
Confidence 45677777777777666 33 36889999 6 99998887774 555443
No 70
>PRK12512 RNA polymerase sigma factor; Provisional
Probab=39.35 E-value=28 Score=28.71 Aligned_cols=47 Identities=17% Similarity=0.207 Sum_probs=32.3
Q ss_pred CCCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhHhcCCCCCCceeeecccchhHHHH
Q 046813 34 NPTKEQINMLESLYAQGIRTPSAEQIQQITTRLRAYGHIEGKNVFYWFQNHKARQRQ 90 (250)
Q Consensus 34 ~fT~eQL~~LE~~F~~~~~yPs~e~R~qLA~~L~~~G~L~erqVqvWFQNRRAR~Kr 90 (250)
.+++.+.++|...|-.+. + -.+||..| | ++...|+.+...=|.+.|.
T Consensus 131 ~L~~~~r~v~~l~~~~g~---s---~~eIA~~l---~-is~~tV~~~l~ra~~~Lr~ 177 (184)
T PRK12512 131 TLPPRQRDVVQSISVEGA---S---IKETAAKL---S-MSEGAVRVALHRGLAALAA 177 (184)
T ss_pred hCCHHHHHHHHHHHHcCC---C---HHHHHHHh---C-CCHHHHHHHHHHHHHHHHH
Confidence 355667777777766652 2 35889999 6 9999999877654444443
No 71
>PRK09644 RNA polymerase sigma factor SigM; Provisional
Probab=39.13 E-value=30 Score=28.16 Aligned_cols=43 Identities=5% Similarity=-0.056 Sum_probs=28.2
Q ss_pred CCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhHhcCCCCCCceeeecccchhH
Q 046813 35 PTKEQINMLESLYAQGIRTPSAEQIQQITTRLRAYGHIEGKNVFYWFQNHKAR 87 (250)
Q Consensus 35 fT~eQL~~LE~~F~~~~~yPs~e~R~qLA~~L~~~G~L~erqVqvWFQNRRAR 87 (250)
+++.|.++|...|-.+ ++ .++||..| | +++..|++|.+-=|.|
T Consensus 109 L~~~~r~v~~l~~~~g--~s----~~eIA~~l---g-is~~tv~~~l~Rar~~ 151 (165)
T PRK09644 109 LPVIEAQAILLCDVHE--LT----YEEAASVL---D-LKLNTYKSHLFRGRKR 151 (165)
T ss_pred CCHHHHHHHHhHHHhc--CC----HHHHHHHH---C-CCHHHHHHHHHHHHHH
Confidence 4566666666555444 22 36889999 6 9999998776533333
No 72
>PF02796 HTH_7: Helix-turn-helix domain of resolvase; InterPro: IPR006120 Site-specific recombination plays an important role in DNA rearrangement in prokaryotic organisms. Two types of site-specific recombination are known to occur: Recombination between inverted repeats resulting in the reversal of a DNA segment. Recombination between repeat sequences on two DNA molecules resulting in their cointegration, or between repeats on one DNA molecule resulting in the excision of a DNA fragment. Site-specific recombination is characterised by a strand exchange mechanism that requires no DNA synthesis or high energy cofactor; the phosphodiester bond energy is conserved in a phospho-protein linkage during strand cleavage and re-ligation. Two unrelated families of recombinases are currently known []. The first, called the 'phage integrase' family, groups a number of bacterial phage and yeast plasmid enzymes. The second [], called the 'resolvase' family, groups enzymes which share the following structural characteristics: an N-terminal catalytic and dimerization domain that contains a conserved serine residue involved in the transient covalent attachment to DNA IPR006119 from INTERPRO, and a C-terminal helix-turn-helix DNA-binding domain. ; GO: 0000150 recombinase activity, 0003677 DNA binding, 0006310 DNA recombination; PDB: 1ZR2_A 2GM4_B 1RES_A 1ZR4_A 1RET_A 1GDT_B 2R0Q_C 1JKP_C 1IJW_C 1JJ6_C ....
Probab=39.09 E-value=11 Score=25.46 Aligned_cols=37 Identities=32% Similarity=0.657 Sum_probs=27.2
Q ss_pred CCCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhHhcCCCCCCceeee
Q 046813 34 NPTKEQINMLESLYAQGIRTPSAEQIQQITTRLRAYGHIEGKNVFYW 80 (250)
Q Consensus 34 ~fT~eQL~~LE~~F~~~~~yPs~e~R~qLA~~L~~~G~L~erqVqvW 80 (250)
.++++|++.+-+++..+ ++ +.+||+++ | |+...|.-+
T Consensus 5 ~~~~~~~~~i~~l~~~G--~s----i~~IA~~~---g-vsr~TvyR~ 41 (45)
T PF02796_consen 5 KLSKEQIEEIKELYAEG--MS----IAEIAKQF---G-VSRSTVYRY 41 (45)
T ss_dssp SSSHCCHHHHHHHHHTT--------HHHHHHHT---T-S-HHHHHHH
T ss_pred CCCHHHHHHHHHHHHCC--CC----HHHHHHHH---C-cCHHHHHHH
Confidence 46788899999999988 33 57999999 6 987776543
No 73
>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=38.77 E-value=14 Score=25.58 Aligned_cols=44 Identities=20% Similarity=0.179 Sum_probs=32.4
Q ss_pred CCCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhHhcCCCCCCceeeecccchhHH
Q 046813 34 NPTKEQINMLESLYAQGIRTPSAEQIQQITTRLRAYGHIEGKNVFYWFQNHKARQ 88 (250)
Q Consensus 34 ~fT~eQL~~LE~~F~~~~~yPs~e~R~qLA~~L~~~G~L~erqVqvWFQNRRAR~ 88 (250)
.+|+.|+++|.-+..... ..+||..| | ++++.|..+..|=+.|.
T Consensus 3 ~LT~~E~~vl~~l~~G~~-------~~eIA~~l---~-is~~tV~~~~~~i~~Kl 46 (58)
T PF00196_consen 3 SLTERELEVLRLLAQGMS-------NKEIAEEL---G-ISEKTVKSHRRRIMKKL 46 (58)
T ss_dssp SS-HHHHHHHHHHHTTS--------HHHHHHHH---T-SHHHHHHHHHHHHHHHH
T ss_pred ccCHHHHHHHHHHHhcCC-------cchhHHhc---C-cchhhHHHHHHHHHHHh
Confidence 478999999998877652 36899999 5 99999987665544443
No 74
>PRK10100 DNA-binding transcriptional regulator CsgD; Provisional
Probab=38.54 E-value=22 Score=31.38 Aligned_cols=51 Identities=20% Similarity=0.168 Sum_probs=39.5
Q ss_pred CCCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhHhcCCCCCCceeeecccchhHHHHHHHHH
Q 046813 34 NPTKEQINMLESLYAQGIRTPSAEQIQQITTRLRAYGHIEGKNVFYWFQNHKARQRQKQKQE 95 (250)
Q Consensus 34 ~fT~eQL~~LE~~F~~~~~yPs~e~R~qLA~~L~~~G~L~erqVqvWFQNRRAR~Krkq~~~ 95 (250)
.+|+-|+++|+-... + +. .++||++| + ++++.|+.+..|=..|..-+.+.+
T Consensus 155 ~Lt~rE~~Vl~l~~~-G--~s----~~eIA~~L---~-iS~~TVk~~~~~i~~Kl~v~nr~e 205 (216)
T PRK10100 155 LLTHREKEILNKLRI-G--AS----NNEIARSL---F-ISENTVKTHLYNLFKKIAVKNRTQ 205 (216)
T ss_pred CCCHHHHHHHHHHHc-C--CC----HHHHHHHh---C-CCHHHHHHHHHHHHHHhCCCCHHH
Confidence 488999999999988 4 22 36899999 5 999999998887777666544433
No 75
>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=38.41 E-value=26 Score=27.96 Aligned_cols=37 Identities=19% Similarity=0.347 Sum_probs=27.1
Q ss_pred CCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhHhcCCCCCCceeeec
Q 046813 35 PTKEQINMLESLYAQGIRTPSAEQIQQITTRLRAYGHIEGKNVFYWF 81 (250)
Q Consensus 35 fT~eQL~~LE~~F~~~~~yPs~e~R~qLA~~L~~~G~L~erqVqvWF 81 (250)
+++.|..++...|-.+ ++ ..+||+.| | |+...|+++.
T Consensus 112 L~~~~r~v~~l~~~~g--~~----~~eIA~~l---~-is~~tv~~~l 148 (159)
T TIGR02989 112 LPERQRELLQLRYQRG--VS----LTALAEQL---G-RTVNAVYKAL 148 (159)
T ss_pred CCHHHHHHHHHHHhcC--CC----HHHHHHHh---C-CCHHHHHHHH
Confidence 5677777777766555 22 36889999 6 9999998653
No 76
>PRK12537 RNA polymerase sigma factor; Provisional
Probab=38.07 E-value=36 Score=28.25 Aligned_cols=38 Identities=24% Similarity=0.356 Sum_probs=26.6
Q ss_pred CCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhHhcCCCCCCceeeecc
Q 046813 35 PTKEQINMLESLYAQGIRTPSAEQIQQITTRLRAYGHIEGKNVFYWFQ 82 (250)
Q Consensus 35 fT~eQL~~LE~~F~~~~~yPs~e~R~qLA~~L~~~G~L~erqVqvWFQ 82 (250)
+++.|..++...|-.+ ++ ..+||+.| | +++..|++|-+
T Consensus 134 L~~~~r~i~~l~~~~~--~s----~~eIA~~l---g-is~~tV~~~l~ 171 (182)
T PRK12537 134 LEPARRNCILHAYVDG--CS----HAEIAQRL---G-APLGTVKAWIK 171 (182)
T ss_pred CCHHHHHHHHHHHHcC--CC----HHHHHHHH---C-CChhhHHHHHH
Confidence 3455566666666555 22 46899999 6 99999987654
No 77
>cd06170 LuxR_C_like C-terminal DNA-binding domain of LuxR-like proteins. This domain contains a helix-turn-helix motif and binds DNA. Proteins belonging to this group are response regulators; some act as transcriptional activators, others as transcriptional repressors. Many are active as homodimers. Many are two domain proteins in which the DNA binding property of the C-terminal DNA binding domain is modulated by modifications of the N-terminal domain. For example in the case of Lux R which participates in the regulation of gene expression in response to fluctuations in cell-population density (quorum-sensing), a signaling molecule, the pheromone Acyl HSL (N-acyl derivatives of homoserine lactone), binds to the N-terminal domain and leads to LuxR dimerization. For others phophorylation of the N-terminal domain leads to multimerization, for example Escherichia coli NarL and Sinorhizobium melilot FixJ. NarL controls gene expression of many respiratory-related operons when environmental
Probab=38.03 E-value=31 Score=22.51 Aligned_cols=36 Identities=28% Similarity=0.365 Sum_probs=25.8
Q ss_pred CHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhHhcCCCCCCceeeecc
Q 046813 36 TKEQINMLESLYAQGIRTPSAEQIQQITTRLRAYGHIEGKNVFYWFQ 82 (250)
Q Consensus 36 T~eQL~~LE~~F~~~~~yPs~e~R~qLA~~L~~~G~L~erqVqvWFQ 82 (250)
+..|.++++..+ .+ + + ..+||+.| | ++...|..|..
T Consensus 2 ~~~e~~i~~~~~-~~--~-s---~~eia~~l---~-~s~~tv~~~~~ 37 (57)
T cd06170 2 TPREREVLRLLA-EG--K-T---NKEIADIL---G-ISEKTVKTHLR 37 (57)
T ss_pred CHHHHHHHHHHH-cC--C-C---HHHHHHHH---C-CCHHHHHHHHH
Confidence 567788887644 33 2 2 46899999 5 99998887764
No 78
>PRK09047 RNA polymerase factor sigma-70; Validated
Probab=37.97 E-value=27 Score=27.90 Aligned_cols=38 Identities=11% Similarity=0.062 Sum_probs=26.7
Q ss_pred CCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhHhcCCCCCCceeeecc
Q 046813 35 PTKEQINMLESLYAQGIRTPSAEQIQQITTRLRAYGHIEGKNVFYWFQ 82 (250)
Q Consensus 35 fT~eQL~~LE~~F~~~~~yPs~e~R~qLA~~L~~~G~L~erqVqvWFQ 82 (250)
+++.|.+++.-.|-.+ ++ ..+||+.| | +++..|++...
T Consensus 107 Lp~~~r~v~~l~~~~g--~s----~~EIA~~l---g-is~~tV~~~l~ 144 (161)
T PRK09047 107 LPARQREAFLLRYWED--MD----VAETAAAM---G-CSEGSVKTHCS 144 (161)
T ss_pred CCHHHHHHHHHHHHhc--CC----HHHHHHHH---C-CCHHHHHHHHH
Confidence 4466666777666665 22 36899999 6 99999886554
No 79
>PRK12541 RNA polymerase sigma factor; Provisional
Probab=37.77 E-value=23 Score=28.61 Aligned_cols=39 Identities=18% Similarity=0.067 Sum_probs=29.0
Q ss_pred CCCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhHhcCCCCCCceeeecc
Q 046813 34 NPTKEQINMLESLYAQGIRTPSAEQIQQITTRLRAYGHIEGKNVFYWFQ 82 (250)
Q Consensus 34 ~fT~eQL~~LE~~F~~~~~yPs~e~R~qLA~~L~~~G~L~erqVqvWFQ 82 (250)
.+++.|..+|+-.|-.+ ++ ..+||..| | +++..|+++..
T Consensus 112 ~L~~~~r~v~~l~~~~~--~s----~~eIA~~l---g-is~~tv~~~l~ 150 (161)
T PRK12541 112 SLPLERRNVLLLRDYYG--FS----YKEIAEMT---G-LSLAKVKIELH 150 (161)
T ss_pred HCCHHHHHHhhhHHhcC--CC----HHHHHHHH---C-CCHHHHHHHHH
Confidence 36677777777777666 33 36889999 7 99998887665
No 80
>PHA02955 hypothetical protein; Provisional
Probab=37.68 E-value=32 Score=31.56 Aligned_cols=44 Identities=11% Similarity=0.148 Sum_probs=31.7
Q ss_pred HHHHHHHHHHHhcCCCCCCHHHHHHHHHHhHhcCCCCCCceeeecccc
Q 046813 37 KEQINMLESLYAQGIRTPSAEQIQQITTRLRAYGHIEGKNVFYWFQNH 84 (250)
Q Consensus 37 ~eQL~~LE~~F~~~~~yPs~e~R~qLA~~L~~~G~L~erqVqvWFQNR 84 (250)
..|+..|-+.|.+.--....++|.++|++| | +....|..||++.
T Consensus 60 ~~sf~lli~a~~Et~~~Lp~~qk~~ia~~l---g-I~~~~~~~d~~t~ 103 (213)
T PHA02955 60 EKNFQLLIEALIETIENFPEKEQKEIAADI---G-INIDDYKAGKKTD 103 (213)
T ss_pred HHHHHHHHHHHHHHHHhCCHHHHHHHHHHh---C-CChhhccCcccch
Confidence 356666666665541134578999999999 7 9987788999874
No 81
>PRK09639 RNA polymerase sigma factor SigX; Provisional
Probab=37.68 E-value=37 Score=27.28 Aligned_cols=44 Identities=20% Similarity=0.276 Sum_probs=31.7
Q ss_pred CCCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhHhcCCCCCCceeeecccchhHHHH
Q 046813 34 NPTKEQINMLESLYAQGIRTPSAEQIQQITTRLRAYGHIEGKNVFYWFQNHKARQRQ 90 (250)
Q Consensus 34 ~fT~eQL~~LE~~F~~~~~yPs~e~R~qLA~~L~~~G~L~erqVqvWFQNRRAR~Kr 90 (250)
.+++.|..+|.-.| .+ ++ -.+||..| | +++..|+.+. +||+.+-
T Consensus 112 ~L~~~~r~il~l~~-~g--~s----~~eIA~~l---g-is~~tV~~~i--~ra~~~L 155 (166)
T PRK09639 112 KMTERDRTVLLLRF-SG--YS----YKEIAEAL---G-IKESSVGTTL--ARAKKKF 155 (166)
T ss_pred cCCHHHHHHHHHHH-cC--CC----HHHHHHHH---C-CCHHHHHHHH--HHHHHHH
Confidence 35677778888888 65 33 36889999 6 9999999887 4555443
No 82
>TIGR02952 Sig70_famx2 RNA polymerase sigma-70 factor, TIGR02952 family. This group of sigma factors are members of the sigma-70 family (TIGR02937). They and appear by homology, tree building, bidirectional best hits and one-to-a-genome distribution, to represent a conserved family. This family is found in a limited number of Gram-positive bacterial lineages.
Probab=37.63 E-value=37 Score=27.25 Aligned_cols=37 Identities=22% Similarity=0.243 Sum_probs=23.9
Q ss_pred CCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhHhcCCCCCCceeeec
Q 046813 35 PTKEQINMLESLYAQGIRTPSAEQIQQITTRLRAYGHIEGKNVFYWF 81 (250)
Q Consensus 35 fT~eQL~~LE~~F~~~~~yPs~e~R~qLA~~L~~~G~L~erqVqvWF 81 (250)
+++.|..+|.-.|-.+ ++ -.+||+.| | +++..|+...
T Consensus 123 L~~~~r~vl~l~~~~g--~s----~~eIA~~l---~-is~~tv~~~l 159 (170)
T TIGR02952 123 LTPKQQHVIALRFGQN--LP----IAEVARIL---G-KTEGAVKILQ 159 (170)
T ss_pred CCHHHHHHHHHHHhcC--CC----HHHHHHHH---C-CCHHHHHHHH
Confidence 4455556666655444 22 36889999 6 9998887543
No 83
>smart00421 HTH_LUXR helix_turn_helix, Lux Regulon. lux regulon (activates the bioluminescence operon
Probab=36.54 E-value=26 Score=22.64 Aligned_cols=37 Identities=30% Similarity=0.379 Sum_probs=27.3
Q ss_pred CCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhHhcCCCCCCceeeecc
Q 046813 35 PTKEQINMLESLYAQGIRTPSAEQIQQITTRLRAYGHIEGKNVFYWFQ 82 (250)
Q Consensus 35 fT~eQL~~LE~~F~~~~~yPs~e~R~qLA~~L~~~G~L~erqVqvWFQ 82 (250)
+++.|.++++. +..+ + + ..+||+.| | ++...|..|.+
T Consensus 4 l~~~e~~i~~~-~~~g--~-s---~~eia~~l---~-is~~tv~~~~~ 40 (58)
T smart00421 4 LTPREREVLRL-LAEG--L-T---NKEIAERL---G-ISEKTVKTHLS 40 (58)
T ss_pred CCHHHHHHHHH-HHcC--C-C---HHHHHHHH---C-CCHHHHHHHHH
Confidence 57888998876 4444 2 2 36899999 6 99999876655
No 84
>PRK12532 RNA polymerase sigma factor; Provisional
Probab=36.48 E-value=26 Score=29.34 Aligned_cols=47 Identities=19% Similarity=0.179 Sum_probs=31.5
Q ss_pred CCCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhHhcCCCCCCceeeecccchhHHHH
Q 046813 34 NPTKEQINMLESLYAQGIRTPSAEQIQQITTRLRAYGHIEGKNVFYWFQNHKARQRQ 90 (250)
Q Consensus 34 ~fT~eQL~~LE~~F~~~~~yPs~e~R~qLA~~L~~~G~L~erqVqvWFQNRRAR~Kr 90 (250)
.+++.|.++++-.|-.+ + + -.+||+.| | ++...|+.+...=|.+.|+
T Consensus 136 ~L~~~~r~i~~L~~~~g--~-s---~~EIA~~l---g-is~~tVk~~l~Rar~~Lr~ 182 (195)
T PRK12532 136 NLPENTARVFTLKEILG--F-S---SDEIQQMC---G-ISTSNYHTIMHRARESLRQ 182 (195)
T ss_pred hCCHHHHHHhhhHHHhC--C-C---HHHHHHHH---C-CCHHHHHHHHHHHHHHHHH
Confidence 34566777777666555 2 2 36889999 6 9999999877544444444
No 85
>PRK12531 RNA polymerase sigma factor; Provisional
Probab=35.37 E-value=31 Score=29.04 Aligned_cols=37 Identities=24% Similarity=0.288 Sum_probs=25.1
Q ss_pred CCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhHhcCCCCCCceeeec
Q 046813 35 PTKEQINMLESLYAQGIRTPSAEQIQQITTRLRAYGHIEGKNVFYWF 81 (250)
Q Consensus 35 fT~eQL~~LE~~F~~~~~yPs~e~R~qLA~~L~~~G~L~erqVqvWF 81 (250)
+++.|.++|.-.|-.+ ++ -++||+.| | ++...|++..
T Consensus 142 Lp~~~r~v~~l~~~eg--~s----~~EIA~~l---g-is~~tVk~rl 178 (194)
T PRK12531 142 LPKAQRDVLQAVYLEE--LP----HQQVAEMF---D-IPLGTVKSRL 178 (194)
T ss_pred CCHHHHHHHHHHHHcC--CC----HHHHHHHh---C-cCHHHHHHHH
Confidence 3455666666655555 22 36889999 6 9999996544
No 86
>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=34.82 E-value=34 Score=28.06 Aligned_cols=41 Identities=17% Similarity=0.261 Sum_probs=28.7
Q ss_pred CCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhHhcCCCCCCceeeecccch
Q 046813 35 PTKEQINMLESLYAQGIRTPSAEQIQQITTRLRAYGHIEGKNVFYWFQNHK 85 (250)
Q Consensus 35 fT~eQL~~LE~~F~~~~~yPs~e~R~qLA~~L~~~G~L~erqVqvWFQNRR 85 (250)
+.+.|..+++-.|-.+ + + .++||+.| | +++..|++..+.=|
T Consensus 135 Lp~~~r~v~~l~~~~g--~-s---~~EIA~~l---g-is~~tVk~~l~Rar 175 (183)
T TIGR02999 135 VDPRQAEVVELRFFAG--L-T---VEEIAELL---G-VSVRTVERDWRFAR 175 (183)
T ss_pred CCHHHHHHHHHHHHcC--C-C---HHHHHHHh---C-CCHHHHHHHHHHHH
Confidence 5566666666666665 2 2 36889999 6 99999987765433
No 87
>smart00027 EH Eps15 homology domain. Pair of EF hand motifs that recognise proteins containing Asn-Pro-Phe (NPF) sequences.
Probab=34.67 E-value=33 Score=26.00 Aligned_cols=46 Identities=15% Similarity=0.160 Sum_probs=30.2
Q ss_pred CCCCHHHHHHHHHHHhcC----CCCCCHHHHHHHHHHhHhcCCCCCCceeeecc
Q 046813 33 WNPTKEQINMLESLYAQG----IRTPSAEQIQQITTRLRAYGHIEGKNVFYWFQ 82 (250)
Q Consensus 33 t~fT~eQL~~LE~~F~~~----~~yPs~e~R~qLA~~L~~~G~L~erqVqvWFQ 82 (250)
|-+|.+|+..|...|..- ..+.+.+ +|.+-|+..| +++..|..+|.
T Consensus 2 ~~ls~~~~~~l~~~F~~~D~d~~G~Is~~---el~~~l~~~~-~~~~ev~~i~~ 51 (96)
T smart00027 2 WAISPEDKAKYEQIFRSLDKNQDGTVTGA---QAKPILLKSG-LPQTLLAKIWN 51 (96)
T ss_pred CCCCHHHHHHHHHHHHHhCCCCCCeEeHH---HHHHHHHHcC-CCHHHHHHHHH
Confidence 678999999999999763 2244544 4444444446 77766665553
No 88
>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=33.77 E-value=35 Score=27.41 Aligned_cols=42 Identities=21% Similarity=0.167 Sum_probs=28.9
Q ss_pred CHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhHhcCCCCCCceeeecccchhH
Q 046813 36 TKEQINMLESLYAQGIRTPSAEQIQQITTRLRAYGHIEGKNVFYWFQNHKAR 87 (250)
Q Consensus 36 T~eQL~~LE~~F~~~~~yPs~e~R~qLA~~L~~~G~L~erqVqvWFQNRRAR 87 (250)
++.|..+|+..|-.+ +. -++||..| | +++..|+++-..=|.+
T Consensus 112 ~~~~r~i~~l~~~~g--~s----~~eIA~~l---g-is~~tV~~~l~ra~~~ 153 (162)
T TIGR02983 112 PARQRAVVVLRYYED--LS----EAQVAEAL---G-ISVGTVKSRLSRALAR 153 (162)
T ss_pred CHHHHHHhhhHHHhc--CC----HHHHHHHh---C-CCHHHHHHHHHHHHHH
Confidence 466777777777555 32 35889999 6 9999998765433333
No 89
>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=33.43 E-value=29 Score=23.35 Aligned_cols=23 Identities=35% Similarity=0.385 Sum_probs=18.9
Q ss_pred CCCCCCCCCHHHHHHHHHHHhcC
Q 046813 28 SSSSRWNPTKEQINMLESLYAQG 50 (250)
Q Consensus 28 ~rR~Rt~fT~eQL~~LE~~F~~~ 50 (250)
..+-|..+|++|...|+..|..+
T Consensus 4 ~~k~rl~Pt~~Q~~~L~~~~~~~ 26 (46)
T PF12323_consen 4 AYKYRLYPTKEQEEKLERWFGAC 26 (46)
T ss_pred ceEEEEecCHHHHHHHHHHHHHH
Confidence 34678888999999999998876
No 90
>PRK05602 RNA polymerase sigma factor; Reviewed
Probab=33.09 E-value=35 Score=28.28 Aligned_cols=38 Identities=13% Similarity=0.105 Sum_probs=26.5
Q ss_pred CCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhHhcCCCCCCceeeecc
Q 046813 35 PTKEQINMLESLYAQGIRTPSAEQIQQITTRLRAYGHIEGKNVFYWFQ 82 (250)
Q Consensus 35 fT~eQL~~LE~~F~~~~~yPs~e~R~qLA~~L~~~G~L~erqVqvWFQ 82 (250)
+++.+..+|+..|-.+. . -.+||+.| | ++...|+.+..
T Consensus 129 L~~~~r~i~~l~~~~g~--s----~~EIA~~l---g-is~~tV~~~l~ 166 (186)
T PRK05602 129 LPERQREAIVLQYYQGL--S----NIEAAAVM---D-ISVDALESLLA 166 (186)
T ss_pred CCHHHHHHhhHHHhcCC--C----HHHHHHHh---C-cCHHHHHHHHH
Confidence 35666666666655552 2 35889999 6 99999987763
No 91
>PRK09648 RNA polymerase sigma factor SigD; Reviewed
Probab=32.99 E-value=38 Score=28.13 Aligned_cols=44 Identities=20% Similarity=0.139 Sum_probs=30.0
Q ss_pred CCCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhHhcCCCCCCceeeecccchhHHH
Q 046813 34 NPTKEQINMLESLYAQGIRTPSAEQIQQITTRLRAYGHIEGKNVFYWFQNHKARQR 89 (250)
Q Consensus 34 ~fT~eQL~~LE~~F~~~~~yPs~e~R~qLA~~L~~~G~L~erqVqvWFQNRRAR~K 89 (250)
.+++.|.++++..|-.+ + + .++||..| | ++...|+.+. +||+.+
T Consensus 139 ~L~~~~r~i~~l~~~~g--~-s---~~EIA~~l---g-is~~tV~~~l--~Ra~~~ 182 (189)
T PRK09648 139 TLPEKQREILILRVVVG--L-S---AEETAEAV---G-STPGAVRVAQ--HRALAR 182 (189)
T ss_pred hCCHHHHHHHHHHHHcC--C-C---HHHHHHHH---C-CCHHHHHHHH--HHHHHH
Confidence 34566777777766655 2 2 46899999 6 9999998776 344444
No 92
>PRK09413 IS2 repressor TnpA; Reviewed
Probab=32.47 E-value=38 Score=27.18 Aligned_cols=41 Identities=15% Similarity=0.492 Sum_probs=29.4
Q ss_pred CCCCHHH-HHHHHHHHhcCCCCCCHHHHHHHHHHhHhcCCCCCCceeeeccc
Q 046813 33 WNPTKEQ-INMLESLYAQGIRTPSAEQIQQITTRLRAYGHIEGKNVFYWFQN 83 (250)
Q Consensus 33 t~fT~eQ-L~~LE~~F~~~~~yPs~e~R~qLA~~L~~~G~L~erqVqvWFQN 83 (250)
-.||.|. ++++..++..+ .+ ..+||+++ | |++..|..|-+-
T Consensus 11 r~ys~EfK~~aV~~~~~~g--~s----v~evA~e~---g-Is~~tl~~W~r~ 52 (121)
T PRK09413 11 RRRTTQEKIAIVQQSFEPG--MT----VSLVARQH---G-VAASQLFLWRKQ 52 (121)
T ss_pred CCCCHHHHHHHHHHHHcCC--CC----HHHHHHHH---C-cCHHHHHHHHHH
Confidence 3355665 55677777766 32 45889999 7 999999999543
No 93
>TIGR02943 Sig70_famx1 RNA polymerase sigma-70 factor, TIGR02943 family. This group of sigma factors are members of the sigma-70 family (TIGR02937). They and appear by homology, tree building, bidirectional best hits and one-to-a-genome distribution, to represent a conserved family.
Probab=32.32 E-value=42 Score=28.28 Aligned_cols=45 Identities=13% Similarity=0.143 Sum_probs=29.4
Q ss_pred CCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhHhcCCCCCCceeeecccchhHHH
Q 046813 35 PTKEQINMLESLYAQGIRTPSAEQIQQITTRLRAYGHIEGKNVFYWFQNHKARQR 89 (250)
Q Consensus 35 fT~eQL~~LE~~F~~~~~yPs~e~R~qLA~~L~~~G~L~erqVqvWFQNRRAR~K 89 (250)
+.+.|.++|.-.|-.+. + .++||+.| | ++...|+.+..-=|.+.|
T Consensus 132 L~~~~r~v~~l~~~~g~---s---~~EIA~~l---g-is~~tvk~rl~Rar~~Lr 176 (188)
T TIGR02943 132 LPEQTARVFMMREVLGF---E---SDEICQEL---E-ISTSNCHVLLYRARLSLR 176 (188)
T ss_pred CCHHHHHHHHHHHHhCC---C---HHHHHHHh---C-CCHHHHHHHHHHHHHHHH
Confidence 44566667777665552 2 46899999 6 999999766553333333
No 94
>PRK00118 putative DNA-binding protein; Validated
Probab=32.25 E-value=40 Score=27.37 Aligned_cols=46 Identities=17% Similarity=0.270 Sum_probs=35.2
Q ss_pred CCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhHhcCCCCCCceeeecccchhHHHH
Q 046813 35 PTKEQINMLESLYAQGIRTPSAEQIQQITTRLRAYGHIEGKNVFYWFQNHKARQRQ 90 (250)
Q Consensus 35 fT~eQL~~LE~~F~~~~~yPs~e~R~qLA~~L~~~G~L~erqVqvWFQNRRAR~Kr 90 (250)
+++.|.+++...|..+. + ..+||+.+ | +++..|..|...-|.+.|.
T Consensus 18 L~ekqRevl~L~y~eg~---S---~~EIAe~l---G-IS~~TV~r~L~RArkkLr~ 63 (104)
T PRK00118 18 LTEKQRNYMELYYLDDY---S---LGEIAEEF---N-VSRQAVYDNIKRTEKLLED 63 (104)
T ss_pred CCHHHHHHHHHHHHcCC---C---HHHHHHHH---C-cCHHHHHHHHHHHHHHHHH
Confidence 46788889988888873 2 36899999 6 9999999998755555543
No 95
>PRK12538 RNA polymerase sigma factor; Provisional
Probab=32.06 E-value=44 Score=29.67 Aligned_cols=44 Identities=11% Similarity=0.067 Sum_probs=28.5
Q ss_pred CHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhHhcCCCCCCceeeecccchhHHH
Q 046813 36 TKEQINMLESLYAQGIRTPSAEQIQQITTRLRAYGHIEGKNVFYWFQNHKARQR 89 (250)
Q Consensus 36 T~eQL~~LE~~F~~~~~yPs~e~R~qLA~~L~~~G~L~erqVqvWFQNRRAR~K 89 (250)
++.|.++|.-.|-.+ +. -++||+.| | +++..|+++.+.=|.+.|
T Consensus 173 p~~~R~v~~L~~~eg--~s----~~EIA~~L---g-is~~tVk~~l~RAr~kLr 216 (233)
T PRK12538 173 PEQQRIAVILSYHEN--MS----NGEIAEVM---D-TTVAAVESLLKRGRQQLR 216 (233)
T ss_pred CHHHHHHhhhHHhcC--CC----HHHHHHHH---C-cCHHHHHHHHHHHHHHHH
Confidence 345555555555555 22 36899999 6 999999887754444443
No 96
>PRK09651 RNA polymerase sigma factor FecI; Provisional
Probab=31.25 E-value=49 Score=27.26 Aligned_cols=38 Identities=13% Similarity=0.186 Sum_probs=26.4
Q ss_pred CCCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhHhcCCCCCCceeeec
Q 046813 34 NPTKEQINMLESLYAQGIRTPSAEQIQQITTRLRAYGHIEGKNVFYWF 81 (250)
Q Consensus 34 ~fT~eQL~~LE~~F~~~~~yPs~e~R~qLA~~L~~~G~L~erqVqvWF 81 (250)
.++++|.+++.-.|-.+. + ..+||+.| | ++...|+++.
T Consensus 119 ~L~~~~r~i~~l~~~~g~--s----~~EIA~~l---g-is~~tV~~~l 156 (172)
T PRK09651 119 GLNGKTREAFLLSQLDGL--T----YSEIAHKL---G-VSVSSVKKYV 156 (172)
T ss_pred hCCHHHhHHhhhhhccCC--C----HHHHHHHh---C-CCHHHHHHHH
Confidence 345666666666655552 2 46899999 7 9999988765
No 97
>PRK12530 RNA polymerase sigma factor; Provisional
Probab=30.86 E-value=58 Score=27.41 Aligned_cols=38 Identities=16% Similarity=0.048 Sum_probs=27.9
Q ss_pred CCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhHhcCCCCCCceeeecc
Q 046813 35 PTKEQINMLESLYAQGIRTPSAEQIQQITTRLRAYGHIEGKNVFYWFQ 82 (250)
Q Consensus 35 fT~eQL~~LE~~F~~~~~yPs~e~R~qLA~~L~~~G~L~erqVqvWFQ 82 (250)
+++.|.++|.-.|-.+ + + .++||..| | +++..|+++..
T Consensus 135 Lp~~~R~v~~L~~~~g--~-s---~~EIA~~l---g-is~~tVk~~l~ 172 (189)
T PRK12530 135 LPAQQARVFMMREYLE--L-S---SEQICQEC---D-ISTSNLHVLLY 172 (189)
T ss_pred CCHHHHHHHhHHHHcC--C-C---HHHHHHHH---C-CCHHHHHHHHH
Confidence 4456667777766655 2 2 36899999 6 99999998865
No 98
>PRK06930 positive control sigma-like factor; Validated
Probab=30.84 E-value=53 Score=28.30 Aligned_cols=47 Identities=13% Similarity=0.130 Sum_probs=34.4
Q ss_pred CCCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhHhcCCCCCCceeeecccchhHHHH
Q 046813 34 NPTKEQINMLESLYAQGIRTPSAEQIQQITTRLRAYGHIEGKNVFYWFQNHKARQRQ 90 (250)
Q Consensus 34 ~fT~eQL~~LE~~F~~~~~yPs~e~R~qLA~~L~~~G~L~erqVqvWFQNRRAR~Kr 90 (250)
.+++.+..+|...|..+. . -.+||..| | ++...|+.+...=|.|.++
T Consensus 114 ~L~~rer~V~~L~~~eg~--s----~~EIA~~l---g-iS~~tVk~~l~Ra~~kLr~ 160 (170)
T PRK06930 114 VLTEREKEVYLMHRGYGL--S----YSEIADYL---N-IKKSTVQSMIERAEKKIAR 160 (170)
T ss_pred hCCHHHHHHHHHHHHcCC--C----HHHHHHHH---C-cCHHHHHHHHHHHHHHHHH
Confidence 567888888888776662 2 35899999 6 9999999887755555444
No 99
>PRK06811 RNA polymerase factor sigma-70; Validated
Probab=30.81 E-value=43 Score=28.07 Aligned_cols=38 Identities=18% Similarity=0.303 Sum_probs=25.8
Q ss_pred CCCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhHhcCCCCCCceeeec
Q 046813 34 NPTKEQINMLESLYAQGIRTPSAEQIQQITTRLRAYGHIEGKNVFYWF 81 (250)
Q Consensus 34 ~fT~eQL~~LE~~F~~~~~yPs~e~R~qLA~~L~~~G~L~erqVqvWF 81 (250)
.++++|..+|.-.|-.+ ++ ..+||+.| | ++...|+..-
T Consensus 131 ~L~~~~r~i~~l~~~~g--~s----~~EIAe~l---g-is~~~V~~~l 168 (189)
T PRK06811 131 DLEKLDREIFIRRYLLG--EK----IEEIAKKL---G-LTRSAIDNRL 168 (189)
T ss_pred hCCHHHHHHHHHHHHcc--CC----HHHHHHHH---C-CCHHHHHHHH
Confidence 34567777777666555 22 36889999 6 9998876443
No 100
>PF13443 HTH_26: Cro/C1-type HTH DNA-binding domain; PDB: 3TYR_A 3TYS_A 3B7H_A.
Probab=30.46 E-value=23 Score=24.44 Aligned_cols=37 Identities=5% Similarity=0.094 Sum_probs=22.0
Q ss_pred HHHHHHHhHhcCCCCCCceeeecccchhHHHHHHHHHHHHH
Q 046813 59 IQQITTRLRAYGHIEGKNVFYWFQNHKARQRQKQKQERTAF 99 (250)
Q Consensus 59 R~qLA~~L~~~G~L~erqVqvWFQNRRAR~Krkq~~~~~a~ 99 (250)
..+||+.+ | |+...|..|+.++..+..-.....=..+
T Consensus 13 ~~~La~~~---g-is~~tl~~~~~~~~~~~~~~~l~~ia~~ 49 (63)
T PF13443_consen 13 QKDLARKT---G-ISRSTLSRILNGKPSNPSLDTLEKIAKA 49 (63)
T ss_dssp HHHHHHHH---T---HHHHHHHHTTT-----HHHHHHHHHH
T ss_pred HHHHHHHH---C-cCHHHHHHHHhcccccccHHHHHHHHHH
Confidence 56899999 7 9999999999988666655444433333
No 101
>PRK12546 RNA polymerase sigma factor; Provisional
Probab=30.41 E-value=41 Score=28.66 Aligned_cols=45 Identities=20% Similarity=0.105 Sum_probs=30.1
Q ss_pred CCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhHhcCCCCCCceeeecccchhHHH
Q 046813 35 PTKEQINMLESLYAQGIRTPSAEQIQQITTRLRAYGHIEGKNVFYWFQNHKARQR 89 (250)
Q Consensus 35 fT~eQL~~LE~~F~~~~~yPs~e~R~qLA~~L~~~G~L~erqVqvWFQNRRAR~K 89 (250)
+++.|.++|.-.|-.+ ++ ..+||..| | +++..|+++.+-=|.+.|
T Consensus 114 Lp~~~r~v~~L~~~~g--~s----~~EIA~~L---g-iS~~tVk~~l~Rar~~Lr 158 (188)
T PRK12546 114 LPDEQREALILVGASG--FS----YEEAAEMC---G-VAVGTVKSRANRARARLA 158 (188)
T ss_pred CCHHHhHHhhhHHhcC--CC----HHHHHHHH---C-CCHHHHHHHHHHHHHHHH
Confidence 4566666666665555 32 36889999 6 999999988764333333
No 102
>PRK12536 RNA polymerase sigma factor; Provisional
Probab=29.92 E-value=46 Score=27.63 Aligned_cols=25 Identities=8% Similarity=0.038 Sum_probs=18.7
Q ss_pred HHHHHHHhHhcCCCCCCceeeecccchhH
Q 046813 59 IQQITTRLRAYGHIEGKNVFYWFQNHKAR 87 (250)
Q Consensus 59 R~qLA~~L~~~G~L~erqVqvWFQNRRAR 87 (250)
.++||+.| | +++..|++....=|.+
T Consensus 148 ~~EIA~~l---~-is~~tV~~~l~rar~~ 172 (181)
T PRK12536 148 VAETAQLT---G-LSESAVKVGIHRGLKA 172 (181)
T ss_pred HHHHHHHH---C-CCHHHHHHHHHHHHHH
Confidence 46899999 6 9999999877443333
No 103
>PRK07037 extracytoplasmic-function sigma-70 factor; Validated
Probab=28.97 E-value=51 Score=26.46 Aligned_cols=36 Identities=17% Similarity=0.200 Sum_probs=24.3
Q ss_pred CCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhHhcCCCCCCceeee
Q 046813 35 PTKEQINMLESLYAQGIRTPSAEQIQQITTRLRAYGHIEGKNVFYW 80 (250)
Q Consensus 35 fT~eQL~~LE~~F~~~~~yPs~e~R~qLA~~L~~~G~L~erqVqvW 80 (250)
+++.+..+|+-.|-.+ +. ..+||+.| | ++...|+..
T Consensus 110 L~~~~r~v~~l~~~~~--~s----~~EIA~~l---g-is~~tV~~~ 145 (163)
T PRK07037 110 LPARTRYAFEMYRLHG--ET----QKDIAREL---G-VSPTLVNFM 145 (163)
T ss_pred CCHHHHHHHHHHHHcC--CC----HHHHHHHH---C-CCHHHHHHH
Confidence 3455555666555555 22 46899999 6 999999864
No 104
>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=28.83 E-value=37 Score=27.83 Aligned_cols=25 Identities=16% Similarity=0.133 Sum_probs=18.9
Q ss_pred HHHHHHHhHhcCCCCCCceeeecccchhHHH
Q 046813 59 IQQITTRLRAYGHIEGKNVFYWFQNHKARQR 89 (250)
Q Consensus 59 R~qLA~~L~~~G~L~erqVqvWFQNRRAR~K 89 (250)
-.+||+.| | +++..|+++. +|||.+
T Consensus 157 ~~EIA~~l---g-is~~tv~~~l--~rar~~ 181 (190)
T TIGR02939 157 YEDIARIM---D-CPVGTVRSRI--FRAREA 181 (190)
T ss_pred HHHHHHHH---C-cCHHHHHHHH--HHHHHH
Confidence 36899999 6 9999998777 344444
No 105
>PRK09645 RNA polymerase sigma factor SigL; Provisional
Probab=27.95 E-value=46 Score=27.10 Aligned_cols=38 Identities=26% Similarity=0.282 Sum_probs=26.9
Q ss_pred CCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhHhcCCCCCCceeeecc
Q 046813 35 PTKEQINMLESLYAQGIRTPSAEQIQQITTRLRAYGHIEGKNVFYWFQ 82 (250)
Q Consensus 35 fT~eQL~~LE~~F~~~~~yPs~e~R~qLA~~L~~~G~L~erqVqvWFQ 82 (250)
+++.|.++|+-.|-.+ ++ .++||+.| | +++..|+.+..
T Consensus 119 L~~~~r~vl~L~~~~g--~s----~~EIA~~l---g-is~~tV~~~l~ 156 (173)
T PRK09645 119 LSPEHRAVLVRSYYRG--WS----TAQIAADL---G-IPEGTVKSRLH 156 (173)
T ss_pred CCHHHHHHHHHHHHcC--CC----HHHHHHHH---C-cCHHHHHHHHH
Confidence 4566677777766665 32 36899999 6 99999886553
No 106
>PRK12545 RNA polymerase sigma factor; Provisional
Probab=27.50 E-value=61 Score=27.60 Aligned_cols=43 Identities=16% Similarity=0.110 Sum_probs=28.0
Q ss_pred CCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhHhcCCCCCCceeeecccchhHHH
Q 046813 35 PTKEQINMLESLYAQGIRTPSAEQIQQITTRLRAYGHIEGKNVFYWFQNHKARQR 89 (250)
Q Consensus 35 fT~eQL~~LE~~F~~~~~yPs~e~R~qLA~~L~~~G~L~erqVqvWFQNRRAR~K 89 (250)
+++.|..++.-.|-.+ ++ -.+||..| | +++..|++... |||.+
T Consensus 140 Lp~~~r~v~~L~~~eg--~s----~~EIA~~l---g-is~~tVk~~l~--RAr~~ 182 (201)
T PRK12545 140 LPEQIGRVFMMREFLD--FE----IDDICTEL---T-LTANHCSVLLY--RARTR 182 (201)
T ss_pred CCHHHHHHHHHHHHcC--CC----HHHHHHHH---C-cCHHHHHHHHH--HHHHH
Confidence 3455555666555555 22 36899999 6 99999987765 44443
No 107
>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=27.24 E-value=62 Score=26.31 Aligned_cols=39 Identities=10% Similarity=0.156 Sum_probs=27.9
Q ss_pred CCCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhHhcCCCCCCceeeecc
Q 046813 34 NPTKEQINMLESLYAQGIRTPSAEQIQQITTRLRAYGHIEGKNVFYWFQ 82 (250)
Q Consensus 34 ~fT~eQL~~LE~~F~~~~~yPs~e~R~qLA~~L~~~G~L~erqVqvWFQ 82 (250)
.+++.|.+++...|-.+. + .++||+.| | +++..|+++..
T Consensus 119 ~L~~~~r~i~~l~~~~g~---s---~~eiA~~l---g-is~~tv~~~l~ 157 (169)
T TIGR02954 119 TLNDKYQTAIILRYYHDL---T---IKEIAEVM---N-KPEGTVKTYLH 157 (169)
T ss_pred hCCHHHhHHHHHHHHcCC---C---HHHHHHHH---C-CCHHHHHHHHH
Confidence 355677777777776662 2 36899999 7 99999875543
No 108
>PF13518 HTH_28: Helix-turn-helix domain
Probab=26.82 E-value=43 Score=22.04 Aligned_cols=31 Identities=26% Similarity=0.686 Sum_probs=22.1
Q ss_pred HHHHHHHhcCCCCCCHHHHHHHHHHhHhcCCCCCCceeeecc
Q 046813 41 NMLESLYAQGIRTPSAEQIQQITTRLRAYGHIEGKNVFYWFQ 82 (250)
Q Consensus 41 ~~LE~~F~~~~~yPs~e~R~qLA~~L~~~G~L~erqVqvWFQ 82 (250)
++++.+. .+ . + ..++|+++ | |+..+|..|-+
T Consensus 4 ~iv~~~~-~g--~-s---~~~~a~~~---g-is~~tv~~w~~ 34 (52)
T PF13518_consen 4 QIVELYL-EG--E-S---VREIAREF---G-ISRSTVYRWIK 34 (52)
T ss_pred HHHHHHH-cC--C-C---HHHHHHHH---C-CCHhHHHHHHH
Confidence 4555555 44 2 3 46899999 6 99999998865
No 109
>PRK12513 RNA polymerase sigma factor; Provisional
Probab=26.53 E-value=31 Score=28.83 Aligned_cols=27 Identities=15% Similarity=0.233 Sum_probs=18.9
Q ss_pred HHHHHHHhHhcCCCCCCceeeecccchhHHH
Q 046813 59 IQQITTRLRAYGHIEGKNVFYWFQNHKARQR 89 (250)
Q Consensus 59 R~qLA~~L~~~G~L~erqVqvWFQNRRAR~K 89 (250)
..+||+.| | |+...|+.+...=|.+.|
T Consensus 158 ~~EIA~~l---g-is~~tV~~~l~ra~~~Lr 184 (194)
T PRK12513 158 LEEIAELT---G-VPEETVKSRLRYALQKLR 184 (194)
T ss_pred HHHHHHHH---C-CCHHHHHHHHHHHHHHHH
Confidence 46899999 7 999999865543333333
No 110
>TIGR00721 tfx DNA-binding protein, Tfx family. Tfx from Methanobacterium thermoautotrophicum is associated with the operon for molybdenum formyl-methanofuran dehydrogenase and binds a DNA sequence near its promoter.
Probab=26.48 E-value=88 Score=26.57 Aligned_cols=47 Identities=26% Similarity=0.209 Sum_probs=33.2
Q ss_pred CCCCCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhHhcCCCCCCceeeecccchhHHHHH
Q 046813 32 RWNPTKEQINMLESLYAQGIRTPSAEQIQQITTRLRAYGHIEGKNVFYWFQNHKARQRQK 91 (250)
Q Consensus 32 Rt~fT~eQL~~LE~~F~~~~~yPs~e~R~qLA~~L~~~G~L~erqVqvWFQNRRAR~Krk 91 (250)
...+|+.|+++|+.. ..+ + + .++||+.| | ++...|..|-+ |++.|-+
T Consensus 4 ~~~Lte~qr~VL~Lr-~~G--l-T---q~EIAe~L---g-iS~stV~~~e~--ra~kkLr 50 (137)
T TIGR00721 4 KTFLTERQIKVLELR-EKG--L-S---QKEIAKEL---K-TTRANVSAIEK--RAMENIE 50 (137)
T ss_pred cCCCCHHHHHHHHHH-HcC--C-C---HHHHHHHH---C-cCHHHHHHHHH--hHHHHHH
Confidence 356889999999884 455 2 2 36899999 6 99988876654 4444443
No 111
>PRK12524 RNA polymerase sigma factor; Provisional
Probab=26.16 E-value=58 Score=27.42 Aligned_cols=38 Identities=13% Similarity=-0.013 Sum_probs=26.1
Q ss_pred CCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhHhcCCCCCCceeeecc
Q 046813 35 PTKEQINMLESLYAQGIRTPSAEQIQQITTRLRAYGHIEGKNVFYWFQ 82 (250)
Q Consensus 35 fT~eQL~~LE~~F~~~~~yPs~e~R~qLA~~L~~~G~L~erqVqvWFQ 82 (250)
+++.|..+|.-.|-.+ ++ -.+||+.| | ++...|+.+..
T Consensus 137 L~~~~r~i~~L~~~~g--~s----~~eIA~~l---g-is~~tV~~~l~ 174 (196)
T PRK12524 137 LPERQRQAVVLRHIEG--LS----NPEIAEVM---E-IGVEAVESLTA 174 (196)
T ss_pred CCHHHHHHHHHHHHcC--CC----HHHHHHHH---C-cCHHHHHHHHH
Confidence 4455555666655554 22 35889999 6 99999988775
No 112
>PRK12516 RNA polymerase sigma factor; Provisional
Probab=26.07 E-value=70 Score=27.05 Aligned_cols=39 Identities=10% Similarity=0.020 Sum_probs=27.8
Q ss_pred CCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhHhcCCCCCCceeeeccc
Q 046813 35 PTKEQINMLESLYAQGIRTPSAEQIQQITTRLRAYGHIEGKNVFYWFQN 83 (250)
Q Consensus 35 fT~eQL~~LE~~F~~~~~yPs~e~R~qLA~~L~~~G~L~erqVqvWFQN 83 (250)
+++.|.+++.-.|-.+ ++ -.+||+.| | +++..|+++...
T Consensus 117 Lp~~~r~i~~L~~~~g--~s----~~EIA~~L---g-is~~tVk~~l~R 155 (187)
T PRK12516 117 LPDDQREAIILVGASG--FA----YEEAAEIC---G-CAVGTIKSRVNR 155 (187)
T ss_pred CCHHHHHHHHHHHHcC--CC----HHHHHHHH---C-CCHHHHHHHHHH
Confidence 4566777777766665 33 35899999 6 999999876643
No 113
>PF08280 HTH_Mga: M protein trans-acting positive regulator (MGA) HTH domain; InterPro: IPR013199 Mga is a DNA-binding protein that activates the expression of several important virulence genes in group A streptococcus in response to changing environmental conditions [].; PDB: 2WTE_A 3SQN_A.
Probab=25.85 E-value=34 Score=24.23 Aligned_cols=46 Identities=17% Similarity=0.403 Sum_probs=31.0
Q ss_pred HHHHHHHHHHHhcCCCCCCHHHHHHHHHHhHhcCCCCCCceeeecccchhHHHHHHHHHHHHHHHHhhhhc
Q 046813 37 KEQINMLESLYAQGIRTPSAEQIQQITTRLRAYGHIEGKNVFYWFQNHKARQRQKQKQERTAFINRYLHKS 107 (250)
Q Consensus 37 ~eQL~~LE~~F~~~~~yPs~e~R~qLA~~L~~~G~L~erqVqvWFQNRRAR~Krkq~~~~~a~~N~~L~~~ 107 (250)
..|+++|+-.+... ..+ ..+||..| | ++++.| ...+..+|..|+..
T Consensus 5 ~rq~~Ll~~L~~~~--~~~---~~ela~~l---~-~S~rti----------------~~~i~~L~~~f~~~ 50 (59)
T PF08280_consen 5 KRQLKLLELLLKNK--WIT---LKELAKKL---N-ISERTI----------------KNDINELNEFFPEN 50 (59)
T ss_dssp HHHHHHHHHHHHHT--SBB---HHHHHHHC---T-S-HHHH----------------HHHHHHHHTT--TC
T ss_pred HHHHHHHHHHHcCC--CCc---HHHHHHHH---C-CCHHHH----------------HHHHHHHHHHhhhh
Confidence 46899999999944 555 45899999 5 998764 35566666666543
No 114
>PRK12520 RNA polymerase sigma factor; Provisional
Probab=25.79 E-value=77 Score=26.42 Aligned_cols=39 Identities=10% Similarity=0.014 Sum_probs=28.1
Q ss_pred CCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhHhcCCCCCCceeeeccc
Q 046813 35 PTKEQINMLESLYAQGIRTPSAEQIQQITTRLRAYGHIEGKNVFYWFQN 83 (250)
Q Consensus 35 fT~eQL~~LE~~F~~~~~yPs~e~R~qLA~~L~~~G~L~erqVqvWFQN 83 (250)
+++.|..++.-.|-.+ ++ .++||..| | +++..|++....
T Consensus 132 Lp~~~r~v~~l~~~~g--~s----~~EIA~~l---g-is~~tV~~~l~R 170 (191)
T PRK12520 132 LPPRTGRVFMMREWLE--LE----TEEICQEL---Q-ITATNAWVLLYR 170 (191)
T ss_pred CCHHHHHHHHHHHHcC--CC----HHHHHHHH---C-CCHHHHHHHHHH
Confidence 5566777777766555 22 36899999 6 999999876643
No 115
>PRK11923 algU RNA polymerase sigma factor AlgU; Provisional
Probab=25.51 E-value=68 Score=26.66 Aligned_cols=20 Identities=10% Similarity=-0.024 Sum_probs=16.2
Q ss_pred HHHHHHhHhcCCCCCCceeeeccc
Q 046813 60 QQITTRLRAYGHIEGKNVFYWFQN 83 (250)
Q Consensus 60 ~qLA~~L~~~G~L~erqVqvWFQN 83 (250)
++||+.| | +++..|++..+.
T Consensus 158 ~eIA~~l---g-is~~tv~~~l~R 177 (193)
T PRK11923 158 EDIASVM---Q-CPVGTVRSRIFR 177 (193)
T ss_pred HHHHHHH---C-CCHHHHHHHHHH
Confidence 6899999 6 999999766653
No 116
>PRK12543 RNA polymerase sigma factor; Provisional
Probab=25.45 E-value=1e+02 Score=25.54 Aligned_cols=46 Identities=17% Similarity=0.070 Sum_probs=28.3
Q ss_pred CCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhHhcCCCCCCceeeecccchhHHHH
Q 046813 35 PTKEQINMLESLYAQGIRTPSAEQIQQITTRLRAYGHIEGKNVFYWFQNHKARQRQ 90 (250)
Q Consensus 35 fT~eQL~~LE~~F~~~~~yPs~e~R~qLA~~L~~~G~L~erqVqvWFQNRRAR~Kr 90 (250)
+++.|..++.-.|-.+. + ..+||+.| | +++..|++....=|.+.|+
T Consensus 118 Lp~~~r~i~~l~~~e~~---s---~~EIA~~l---g-is~~tV~~~l~ra~~~Lr~ 163 (179)
T PRK12543 118 LPYKLRQVIILRYLHDY---S---QEEIAQLL---Q-IPIGTVKSRIHAALKKLRQ 163 (179)
T ss_pred CCHHHHHHHHHHHHccC---C---HHHHHHHH---C-CCHHHHHHHHHHHHHHHHH
Confidence 34555555555554441 2 35889999 6 9999988766544444443
No 117
>PLN03105 TCP24 transcription factor TCP24 (TEOSINTE BRANCHED1, CYCLOIDEA, AND PCF FAMILY 24); Provisional
Probab=25.39 E-value=2.8e+02 Score=26.50 Aligned_cols=26 Identities=35% Similarity=0.376 Sum_probs=19.0
Q ss_pred CCCCCCCCCccccc-----cccCCCCcccccc
Q 046813 184 NINNSDISNQETLP-----LFPLHPTGILQAK 210 (250)
Q Consensus 184 ~~~~~~~~~~etl~-----lfpl~pt~~~~~~ 210 (250)
.+| ++++.|-||+ |||-.+..|++--
T Consensus 233 ~~~-~~~~~rgtlqsns~sl~~~~~~~~~qr~ 263 (324)
T PLN03105 233 AIN-GGYSSRGTLQSNSQSLFLNNNNNITQRS 263 (324)
T ss_pred ccc-CccccccccccCChhhcccCCcchhhhc
Confidence 355 6778899986 8888787886543
No 118
>PF06056 Terminase_5: Putative ATPase subunit of terminase (gpP-like); InterPro: IPR010332 This family of proteins are annotated as ATPase subunits of phage terminase after []. Terminases are viral proteins that are involved in packaging viral DNA into the capsid.; GO: 0005524 ATP binding, 0019069 viral capsid assembly
Probab=25.28 E-value=23 Score=25.68 Aligned_cols=29 Identities=38% Similarity=0.721 Sum_probs=21.6
Q ss_pred HHHHhcCCCCCCHHHHHHHHHHhHhcCCCCCCceeeecc
Q 046813 44 ESLYAQGIRTPSAEQIQQITTRLRAYGHIEGKNVFYWFQ 82 (250)
Q Consensus 44 E~~F~~~~~yPs~e~R~qLA~~L~~~G~L~erqVqvWFQ 82 (250)
..+|-++ |. ..+||+.| | |+.+.|+.|=+
T Consensus 7 ~~LY~~G--~~----~~eIA~~L---g-~~~~TV~~W~~ 35 (58)
T PF06056_consen 7 RSLYLQG--WS----IKEIAEEL---G-VPRSTVYSWKD 35 (58)
T ss_pred HHHHHcC--CC----HHHHHHHH---C-CChHHHHHHHH
Confidence 3456666 43 36899999 6 99999999953
No 119
>PRK09647 RNA polymerase sigma factor SigE; Reviewed
Probab=24.86 E-value=81 Score=27.20 Aligned_cols=39 Identities=15% Similarity=0.102 Sum_probs=26.0
Q ss_pred CCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhHhcCCCCCCceeeeccc
Q 046813 35 PTKEQINMLESLYAQGIRTPSAEQIQQITTRLRAYGHIEGKNVFYWFQN 83 (250)
Q Consensus 35 fT~eQL~~LE~~F~~~~~yPs~e~R~qLA~~L~~~G~L~erqVqvWFQN 83 (250)
+++.|.+++.-.|-.+ ++ -.+||+.| | +++..|+++..-
T Consensus 139 L~~~~r~v~~L~~~~g--~s----~~EIA~~L---g-is~~tV~~~l~R 177 (203)
T PRK09647 139 LPPEFRAAVVLCDIEG--LS----YEEIAATL---G-VKLGTVRSRIHR 177 (203)
T ss_pred CCHHHHHHHHHHHHcC--CC----HHHHHHHH---C-CCHHHHHHHHHH
Confidence 3455555555555554 22 36889999 6 999999987753
No 120
>PF07750 GcrA: GcrA cell cycle regulator; InterPro: IPR011681 GcrA, together with CtrA (see IPR001789 from INTERPRO and IPR001867 from INTERPRO), form a master cell cycle regulator. These bacterial regulators are involved in controlling the progression and asymmetric polar morphogenesis []. During this process, there are temporal and spatial variations in the concentrations of GcrA and CtrA. The variation in concentration produces time and space dependent transcriptional regulation of modular functions that implement cell-cycle processes []. More specifically, GcrA acts as an activator of components of the replisome and the segregation machinery [].
Probab=24.60 E-value=1.2e+02 Score=26.11 Aligned_cols=35 Identities=37% Similarity=0.583 Sum_probs=26.9
Q ss_pred CCCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhHhcCCCCCCce
Q 046813 34 NPTKEQINMLESLYAQGIRTPSAEQIQQITTRLRAYGHIEGKNV 77 (250)
Q Consensus 34 ~fT~eQL~~LE~~F~~~~~yPs~e~R~qLA~~L~~~G~L~erqV 77 (250)
..|+|+++.|.+++..+. +. .+||++| |.++-.-|
T Consensus 2 ~Wtde~~~~L~~lw~~G~---Sa---sqIA~~l---g~vsRnAV 36 (162)
T PF07750_consen 2 SWTDERVERLRKLWAEGL---SA---SQIARQL---GGVSRNAV 36 (162)
T ss_pred CCCHHHHHHHHHHHHcCC---CH---HHHHHHh---CCcchhhh
Confidence 467999999999999984 43 5889999 63665444
No 121
>COG4566 TtrR Response regulator [Signal transduction mechanisms]
Probab=24.40 E-value=1.3e+02 Score=27.55 Aligned_cols=54 Identities=24% Similarity=0.243 Sum_probs=42.3
Q ss_pred CCCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhHhcCCCCCCceeeecccchhHHHHHHHHHHHHHHHH
Q 046813 34 NPTKEQINMLESLYAQGIRTPSAEQIQQITTRLRAYGHIEGKNVFYWFQNHKARQRQKQKQERTAFINR 102 (250)
Q Consensus 34 ~fT~eQL~~LE~~F~~~~~yPs~e~R~qLA~~L~~~G~L~erqVqvWFQNRRAR~Krkq~~~~~a~~N~ 102 (250)
++|+-+.++|+.+-.- +++ ++||..| | ++++.|+ ++||+-=+|.+..+++.+-+
T Consensus 142 tLT~RERqVl~~vV~G---~~N----KqIA~dL---g-iS~rTVe----~HRanvM~Km~a~SlaeLvr 195 (202)
T COG4566 142 TLTPRERQVLDLVVRG---LMN----KQIAFDL---G-ISERTVE----LHRANVMEKMQARSLAELVR 195 (202)
T ss_pred hcCHHHHHHHHHHHcC---ccc----HHHHHHc---C-CchhhHH----HHHHHHHHHHhhccHHHHHH
Confidence 5788888899888743 355 4899999 6 9999998 46998888888877776544
No 122
>PF07638 Sigma70_ECF: ECF sigma factor
Probab=24.34 E-value=64 Score=27.37 Aligned_cols=42 Identities=26% Similarity=0.396 Sum_probs=26.8
Q ss_pred HHHHHHHHHHHhcCCCCCCHHHHHHHHHHhHhcCCCCCCceeeecccchhHH
Q 046813 37 KEQINMLESLYAQGIRTPSAEQIQQITTRLRAYGHIEGKNVFYWFQNHKARQ 88 (250)
Q Consensus 37 ~eQL~~LE~~F~~~~~yPs~e~R~qLA~~L~~~G~L~erqVqvWFQNRRAR~ 88 (250)
++|.+++|-.|-.+ | + .++||+.| | |+++.|+...+.=|++.
T Consensus 138 ~~~~~~v~l~~~~G--l-s---~~EIA~~l---g-iS~~tV~r~l~~aR~~l 179 (185)
T PF07638_consen 138 PRQRRVVELRFFEG--L-S---VEEIAERL---G-ISERTVRRRLRRARAWL 179 (185)
T ss_pred HHHHHHHHHHHHCC--C-C---HHHHHHHH---C-cCHHHHHHHHHHHHHHH
Confidence 44555555555444 2 2 36889999 6 99999986665544333
No 123
>PRK12539 RNA polymerase sigma factor; Provisional
Probab=24.11 E-value=72 Score=26.50 Aligned_cols=39 Identities=15% Similarity=0.186 Sum_probs=28.1
Q ss_pred CCCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhHhcCCCCCCceeeecc
Q 046813 34 NPTKEQINMLESLYAQGIRTPSAEQIQQITTRLRAYGHIEGKNVFYWFQ 82 (250)
Q Consensus 34 ~fT~eQL~~LE~~F~~~~~yPs~e~R~qLA~~L~~~G~L~erqVqvWFQ 82 (250)
.+++.|.++|+-.|-.+ + + ..+||+.| | ++...|+.+..
T Consensus 131 ~L~~~~r~v~~l~~~~g--~-s---~~eIA~~l---g-is~~tV~~~l~ 169 (184)
T PRK12539 131 RLPEKMRLAIQAVKLEG--L-S---VAEAATRS---G-MSESAVKVSVH 169 (184)
T ss_pred hCCHHHHHHHHHHHHcC--C-c---HHHHHHHH---C-cCHHHHHHHHH
Confidence 45677777777666555 2 2 36889999 6 99999987763
No 124
>PRK13919 putative RNA polymerase sigma E protein; Provisional
Probab=23.97 E-value=66 Score=26.50 Aligned_cols=39 Identities=21% Similarity=0.249 Sum_probs=26.4
Q ss_pred CCCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhHhcCCCCCCceeeecc
Q 046813 34 NPTKEQINMLESLYAQGIRTPSAEQIQQITTRLRAYGHIEGKNVFYWFQ 82 (250)
Q Consensus 34 ~fT~eQL~~LE~~F~~~~~yPs~e~R~qLA~~L~~~G~L~erqVqvWFQ 82 (250)
.+++.|.++|.-.|-.+. + -++||+.| | +++..|+.+-+
T Consensus 135 ~L~~~~r~vl~l~~~~~~---s---~~eIA~~l---g-is~~~V~~~l~ 173 (186)
T PRK13919 135 ALSPEERRVIEVLYYQGY---T---HREAAQLL---G-LPLGTLKTRAR 173 (186)
T ss_pred hCCHHHHHHHHHHHHcCC---C---HHHHHHHH---C-cCHHHHHHHHH
Confidence 355666677766655552 2 25889999 7 99988876543
No 125
>PRK09643 RNA polymerase sigma factor SigM; Reviewed
Probab=23.35 E-value=1.3e+02 Score=25.36 Aligned_cols=44 Identities=25% Similarity=0.246 Sum_probs=28.4
Q ss_pred CCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhHhcCCCCCCceeeecccchhHHHH
Q 046813 35 PTKEQINMLESLYAQGIRTPSAEQIQQITTRLRAYGHIEGKNVFYWFQNHKARQRQ 90 (250)
Q Consensus 35 fT~eQL~~LE~~F~~~~~yPs~e~R~qLA~~L~~~G~L~erqVqvWFQNRRAR~Kr 90 (250)
+.+.|.++|+-.|-.+. + -.+||..| | ++...|+ -.-+|||.+-
T Consensus 135 Lp~~~r~i~~l~~~~g~---s---~~EIA~~l---g-~s~~tV~--~rl~rar~~L 178 (192)
T PRK09643 135 LPVEQRAALVAVDMQGY---S---VADAARML---G-VAEGTVK--SRCARGRARL 178 (192)
T ss_pred CCHHHHHHHHHHHHcCC---C---HHHHHHHH---C-cCHHHHH--HHHHHHHHHH
Confidence 45667777776666652 2 35889999 6 9998884 3345555443
No 126
>PRK12544 RNA polymerase sigma factor; Provisional
Probab=23.29 E-value=97 Score=26.79 Aligned_cols=46 Identities=9% Similarity=0.021 Sum_probs=29.8
Q ss_pred CCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhHhcCCCCCCceeeecccchhHHHH
Q 046813 35 PTKEQINMLESLYAQGIRTPSAEQIQQITTRLRAYGHIEGKNVFYWFQNHKARQRQ 90 (250)
Q Consensus 35 fT~eQL~~LE~~F~~~~~yPs~e~R~qLA~~L~~~G~L~erqVqvWFQNRRAR~Kr 90 (250)
+++.|..++.-.|-.+ ++ ..+||+.| | ++...|+++.+-=|.+.|+
T Consensus 149 L~~~~r~v~~L~~~~g--~s----~~EIAe~l---g-is~~tV~~~l~RAr~~Lr~ 194 (206)
T PRK12544 149 LPAKYARVFMMREFIE--LE----TNEICHAV---D-LSVSNLNVLLYRARLRLRE 194 (206)
T ss_pred CCHHHHHHHHHHHHcC--CC----HHHHHHHH---C-cCHHHHHHHHHHHHHHHHH
Confidence 4456666666666555 22 36899999 6 9999998776543333333
No 127
>PRK12547 RNA polymerase sigma factor; Provisional
Probab=23.27 E-value=73 Score=25.97 Aligned_cols=39 Identities=13% Similarity=0.016 Sum_probs=27.7
Q ss_pred CCCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhHhcCCCCCCceeeecc
Q 046813 34 NPTKEQINMLESLYAQGIRTPSAEQIQQITTRLRAYGHIEGKNVFYWFQ 82 (250)
Q Consensus 34 ~fT~eQL~~LE~~F~~~~~yPs~e~R~qLA~~L~~~G~L~erqVqvWFQ 82 (250)
.+++.|.++|.-.|-.+ + + ..+||+.| | +++..|+++..
T Consensus 112 ~L~~~~r~v~~l~~~~g--~-s---~~eIA~~l---g-is~~tV~~~l~ 150 (164)
T PRK12547 112 LLSADQREAIILIGASG--F-S---YEDAAAIC---G-CAVGTIKSRVS 150 (164)
T ss_pred hCCHHHHHHHHHHHHcC--C-C---HHHHHHHh---C-CCHHHHHHHHH
Confidence 34566777777766655 2 2 36889999 6 99999987664
No 128
>PRK12533 RNA polymerase sigma factor; Provisional
Probab=23.25 E-value=56 Score=28.74 Aligned_cols=39 Identities=10% Similarity=0.003 Sum_probs=26.5
Q ss_pred CCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhHhcCCCCCCceeeeccc
Q 046813 35 PTKEQINMLESLYAQGIRTPSAEQIQQITTRLRAYGHIEGKNVFYWFQN 83 (250)
Q Consensus 35 fT~eQL~~LE~~F~~~~~yPs~e~R~qLA~~L~~~G~L~erqVqvWFQN 83 (250)
+++.|..+|...|-.+ ++ -++||+.| | |++..|+++-..
T Consensus 135 Lp~~~R~v~~L~y~eg--~s----~~EIAe~L---g-iS~~tVk~~L~R 173 (216)
T PRK12533 135 LPVEYREVLVLRELED--MS----YREIAAIA---D-VPVGTVMSRLAR 173 (216)
T ss_pred CCHHHHhHhhhHHhcC--CC----HHHHHHHH---C-CCHHHHHHHHHH
Confidence 3455666666655555 32 36899999 6 999999876653
No 129
>PRK08295 RNA polymerase factor sigma-70; Validated
Probab=23.08 E-value=72 Score=26.69 Aligned_cols=38 Identities=26% Similarity=0.253 Sum_probs=23.9
Q ss_pred CCCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhHhcCCCCCCceeeecc
Q 046813 34 NPTKEQINMLESLYAQGIRTPSAEQIQQITTRLRAYGHIEGKNVFYWFQ 82 (250)
Q Consensus 34 ~fT~eQL~~LE~~F~~~~~yPs~e~R~qLA~~L~~~G~L~erqVqvWFQ 82 (250)
.+++.+..+|.. |-.+ + + -.+||..| | +++..|++...
T Consensus 155 ~L~~~~r~vl~l-~~e~--~-s---~~EIA~~l---g-is~~tV~~~l~ 192 (208)
T PRK08295 155 LLSELEKEVLEL-YLDG--K-S---YQEIAEEL---N-RHVKSIDNALQ 192 (208)
T ss_pred hCCHHHHHHHHH-HHcc--C-C---HHHHHHHH---C-CCHHHHHHHHH
Confidence 344555556655 4333 2 2 35889999 6 99999975443
No 130
>PRK12529 RNA polymerase sigma factor; Provisional
Probab=22.84 E-value=73 Score=26.45 Aligned_cols=39 Identities=13% Similarity=0.063 Sum_probs=28.0
Q ss_pred CCCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhHhcCCCCCCceeeecc
Q 046813 34 NPTKEQINMLESLYAQGIRTPSAEQIQQITTRLRAYGHIEGKNVFYWFQ 82 (250)
Q Consensus 34 ~fT~eQL~~LE~~F~~~~~yPs~e~R~qLA~~L~~~G~L~erqVqvWFQ 82 (250)
.+++.|..++.-.|-.+ + + .++||+.| | +++..|+....
T Consensus 127 ~Lp~~~R~v~~L~~~~g--~-s---~~EIA~~l---g-is~~tVk~~l~ 165 (178)
T PRK12529 127 TLRPRVKQAFLMATLDG--M-K---QKDIAQAL---D-IALPTVKKYIH 165 (178)
T ss_pred hCCHHHHHHHHHHHHcC--C-C---HHHHHHHH---C-CCHHHHHHHHH
Confidence 34567777777766665 2 2 36889999 6 99999887665
No 131
>PF08880 QLQ: QLQ; InterPro: IPR014978 QLQ is named after the conserved Gln, Leu, Gln motif. QLQ is found at the N terminus of SWI2/SNF2 protein, which has been shown to be involved in protein-protein interactions. QLQ has been postulated to be involved in mediating protein interactions []. ; GO: 0005524 ATP binding, 0016818 hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides, 0006355 regulation of transcription, DNA-dependent, 0005634 nucleus
Probab=22.42 E-value=67 Score=21.61 Aligned_cols=13 Identities=23% Similarity=0.138 Sum_probs=11.0
Q ss_pred CCCHHHHHHHHHH
Q 046813 34 NPTKEQINMLESL 46 (250)
Q Consensus 34 ~fT~eQL~~LE~~ 46 (250)
.||++|+..||.-
T Consensus 2 ~FT~~Ql~~L~~Q 14 (37)
T PF08880_consen 2 PFTPAQLQELRAQ 14 (37)
T ss_pred CCCHHHHHHHHHH
Confidence 5899999999963
No 132
>PRK12542 RNA polymerase sigma factor; Provisional
Probab=22.19 E-value=95 Score=25.72 Aligned_cols=43 Identities=23% Similarity=0.298 Sum_probs=28.7
Q ss_pred CCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhHhcCCCCCCceeeecccchhHHH
Q 046813 35 PTKEQINMLESLYAQGIRTPSAEQIQQITTRLRAYGHIEGKNVFYWFQNHKARQR 89 (250)
Q Consensus 35 fT~eQL~~LE~~F~~~~~yPs~e~R~qLA~~L~~~G~L~erqVqvWFQNRRAR~K 89 (250)
+++.|.+++.-.|-.+ + + ..+||..| | +++..|++.. .|||.+
T Consensus 123 L~~~~r~i~~l~~~~g--~-s---~~EIA~~l---g-is~~tVk~~l--~Rar~~ 165 (185)
T PRK12542 123 LNESNRQVFKYKVFYN--L-T---YQEISSVM---G-ITEANVRKQF--ERARKR 165 (185)
T ss_pred CCHHHHHHHHHHHHcC--C-C---HHHHHHHH---C-CCHHHHHHHH--HHHHHH
Confidence 4456666666655555 2 2 36889999 6 9999999865 344444
No 133
>COG4367 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=21.66 E-value=61 Score=26.37 Aligned_cols=69 Identities=16% Similarity=0.169 Sum_probs=38.0
Q ss_pred CCCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhHhcCCCCCCceeeecccchhHHHHHHHHH----HHHHHHHhhhhcCC
Q 046813 34 NPTKEQINMLESLYAQGIRTPSAEQIQQITTRLRAYGHIEGKNVFYWFQNHKARQRQKQKQE----RTAFINRYLHKSAH 109 (250)
Q Consensus 34 ~fT~eQL~~LE~~F~~~~~yPs~e~R~qLA~~L~~~G~L~erqVqvWFQNRRAR~Krkq~~~----~~a~~N~~L~~~~h 109 (250)
+++++|+++-...|..|- -...-..++||..| +.++-.|+-=.|-. ++-. -..++++.++..++
T Consensus 2 SLn~eq~~~Tk~elqan~-el~~LS~~~iA~~L----n~t~~~lekil~~t-------qr~~dvW~lRd~l~~~i~e~Gq 69 (97)
T COG4367 2 SLNPEQKQRTKQELQANF-ELCPLSDEEIATAL----NWTEVKLEKILQVT-------QRPADVWRLRDFLVQAIRESGQ 69 (97)
T ss_pred CCCHHHHHHHHHHHHHhh-hhccccHHHHHHHh----CCCHHHHHHHHHHh-------hccchhHHHHHHHHHHHHhcCC
Confidence 467888877666555551 22333367899999 58876543111100 0000 02356777777666
Q ss_pred CCCCC
Q 046813 110 QPAPL 114 (250)
Q Consensus 110 ~p~~~ 114 (250)
-|.+|
T Consensus 70 tP~Pf 74 (97)
T COG4367 70 TPVPF 74 (97)
T ss_pred CCCCe
Confidence 65544
No 134
>cd00131 PAX Paired Box domain
Probab=21.34 E-value=89 Score=25.61 Aligned_cols=44 Identities=20% Similarity=0.245 Sum_probs=25.9
Q ss_pred CCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhHhcCCC-------CCCceeeeccc
Q 046813 35 PTKEQINMLESLYAQGIRTPSAEQIQQITTRLRAYGHI-------EGKNVFYWFQN 83 (250)
Q Consensus 35 fT~eQL~~LE~~F~~~~~yPs~e~R~qLA~~L~~~G~L-------~erqVqvWFQN 83 (250)
.+.++...|+..-..+ |+... .+|+++|...| + +...|-.||+|
T Consensus 76 ~~~~~~~~i~~~v~~~---p~~Tl-~El~~~L~~~g-v~~~~~~~s~stI~R~L~~ 126 (128)
T cd00131 76 ATPEVVKKIEIYKQEN---PGMFA-WEIRDRLLQEG-VCDKSNVPSVSSINRILRN 126 (128)
T ss_pred CCHHHHHHHHHHHHHC---CCCCH-HHHHHHHHHcC-CcccCCCCCHHHHHHHHHh
Confidence 3567777777766665 34333 46677775545 4 55555555544
No 135
>PRK12522 RNA polymerase sigma factor; Provisional
Probab=21.19 E-value=1.1e+02 Score=25.01 Aligned_cols=19 Identities=21% Similarity=0.291 Sum_probs=15.7
Q ss_pred HHHHHHhHhcCCCCCCceeeecc
Q 046813 60 QQITTRLRAYGHIEGKNVFYWFQ 82 (250)
Q Consensus 60 ~qLA~~L~~~G~L~erqVqvWFQ 82 (250)
++||+.| | +++..|+++..
T Consensus 139 ~EIA~~l---g-is~~tV~~~l~ 157 (173)
T PRK12522 139 KEMSEIL---N-IPIGTVKYRLN 157 (173)
T ss_pred HHHHHHh---C-CCHHHHHHHHH
Confidence 6889999 6 99999986654
No 136
>PRK06986 fliA flagellar biosynthesis sigma factor; Validated
Probab=20.70 E-value=82 Score=27.51 Aligned_cols=45 Identities=18% Similarity=0.280 Sum_probs=30.3
Q ss_pred CHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhHhcCCCCCCceeeecccchhHHHH
Q 046813 36 TKEQINMLESLYAQGIRTPSAEQIQQITTRLRAYGHIEGKNVFYWFQNHKARQRQ 90 (250)
Q Consensus 36 T~eQL~~LE~~F~~~~~yPs~e~R~qLA~~L~~~G~L~erqVqvWFQNRRAR~Kr 90 (250)
.+.|.++|...|-.+. + -.+||+.| | ++...|+.+...=|.+.|+
T Consensus 186 ~~~~r~vl~l~~~~g~---s---~~EIA~~l---g-is~~tV~~~~~ra~~~Lr~ 230 (236)
T PRK06986 186 PEREQLVLSLYYQEEL---N---LKEIGAVL---G-VSESRVSQIHSQAIKRLRA 230 (236)
T ss_pred CHHHHHHHHhHhccCC---C---HHHHHHHH---C-CCHHHHHHHHHHHHHHHHH
Confidence 4555566666665542 2 36899999 6 9999999887655555554
No 137
>PRK10360 DNA-binding transcriptional activator UhpA; Provisional
Probab=20.35 E-value=65 Score=25.67 Aligned_cols=43 Identities=23% Similarity=0.288 Sum_probs=31.4
Q ss_pred CCCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhHhcCCCCCCceeeecccchhH
Q 046813 34 NPTKEQINMLESLYAQGIRTPSAEQIQQITTRLRAYGHIEGKNVFYWFQNHKAR 87 (250)
Q Consensus 34 ~fT~eQL~~LE~~F~~~~~yPs~e~R~qLA~~L~~~G~L~erqVqvWFQNRRAR 87 (250)
.+|+.+.++|+-+... + + +++||++| + ++++.|++..+|=|.|
T Consensus 137 ~Lt~~E~~il~~l~~g---~-~---~~~Ia~~l---~-~s~~tv~~~~~~l~~K 179 (196)
T PRK10360 137 PLTKRERQVAEKLAQG---M-A---VKEIAAEL---G-LSPKTVHVHRANLMEK 179 (196)
T ss_pred CCCHHHHHHHHHHHCC---C-C---HHHHHHHh---C-CCHHHHHHHHHHHHHH
Confidence 5889999998886653 3 2 67999999 4 9999997655544443
No 138
>PRK09636 RNA polymerase sigma factor SigJ; Provisional
Probab=20.06 E-value=78 Score=28.65 Aligned_cols=46 Identities=13% Similarity=0.086 Sum_probs=29.4
Q ss_pred CCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhHhcCCCCCCceeeecccchhHHHH
Q 046813 35 PTKEQINMLESLYAQGIRTPSAEQIQQITTRLRAYGHIEGKNVFYWFQNHKARQRQ 90 (250)
Q Consensus 35 fT~eQL~~LE~~F~~~~~yPs~e~R~qLA~~L~~~G~L~erqVqvWFQNRRAR~Kr 90 (250)
+++.|..++.-.|-.+ ++ .++||+.| | +++..|+...+.=|.+.|+
T Consensus 116 L~~~~R~v~~L~~~~g--~s----~~EIA~~l---g-~s~~tVk~~l~RAr~~Lr~ 161 (293)
T PRK09636 116 LSPLERAAFLLHDVFG--VP----FDEIASTL---G-RSPAACRQLASRARKHVRA 161 (293)
T ss_pred CCHHHHHHHHHHHHhC--CC----HHHHHHHH---C-CCHHHHHHHHHHHHHHHHh
Confidence 3455555555554444 22 35889999 6 9999999888754444443
No 139
>PRK10651 transcriptional regulator NarL; Provisional
Probab=20.05 E-value=59 Score=25.94 Aligned_cols=48 Identities=23% Similarity=0.293 Sum_probs=35.5
Q ss_pred CCCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhHhcCCCCCCceeeecccchhHHHHHH
Q 046813 34 NPTKEQINMLESLYAQGIRTPSAEQIQQITTRLRAYGHIEGKNVFYWFQNHKARQRQKQ 92 (250)
Q Consensus 34 ~fT~eQL~~LE~~F~~~~~yPs~e~R~qLA~~L~~~G~L~erqVqvWFQNRRAR~Krkq 92 (250)
.+|+.+.++|+-+. .+ ++ .++||++| + ++++.|++..+|=|.|..-+.
T Consensus 155 ~Lt~rE~~vl~~l~-~g--~~----~~~ia~~l---~-is~~tV~~~~~~l~~Kl~~~~ 202 (216)
T PRK10651 155 QLTPRERDILKLIA-QG--LP----NKMIARRL---D-ITESTVKVHVKHMLKKMKLKS 202 (216)
T ss_pred cCCHHHHHHHHHHH-cC--CC----HHHHHHHc---C-CCHHHHHHHHHHHHHHcCCCC
Confidence 48999999998765 33 23 35889999 5 999999887777666655433
Done!