Query 046372
Match_columns 266
No_of_seqs 150 out of 527
Neff 3.6
Searched_HMMs 46136
Date Fri Mar 29 11:27:06 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/046372.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/046372hhsearch_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 1.1E-20 2.4E-25 171.1 2.2 65 28-98 158-222 (261)
2 KOG0484 Transcription factor P 99.8 1E-19 2.2E-24 149.5 1.4 67 26-98 14-80 (125)
3 KOG0842 Transcription factor t 99.8 6.3E-19 1.4E-23 164.8 6.0 69 23-97 147-215 (307)
4 KOG0843 Transcription factor E 99.8 4.5E-19 9.7E-24 156.3 4.7 64 27-96 100-163 (197)
5 KOG0487 Transcription factor A 99.7 9E-19 2E-23 163.8 4.4 67 23-95 229-295 (308)
6 KOG0488 Transcription factor B 99.7 1.5E-18 3.2E-23 161.7 5.2 68 24-97 167-234 (309)
7 KOG2251 Homeobox transcription 99.7 1.8E-17 4E-22 149.3 8.8 68 24-97 32-99 (228)
8 KOG0844 Transcription factor E 99.7 4.8E-18 1.1E-22 159.9 4.2 80 12-97 160-243 (408)
9 PF00046 Homeobox: Homeobox do 99.7 5.4E-18 1.2E-22 118.9 2.3 57 30-92 1-57 (57)
10 KOG0494 Transcription factor C 99.7 1.2E-17 2.6E-22 154.5 5.0 73 23-101 134-207 (332)
11 KOG0485 Transcription factor N 99.7 2.8E-17 6E-22 149.0 3.8 70 23-98 98-167 (268)
12 KOG0492 Transcription factor M 99.7 5E-17 1.1E-21 146.4 4.7 63 30-98 145-207 (246)
13 KOG0850 Transcription factor D 99.6 4.7E-16 1E-20 141.2 7.0 64 28-97 121-184 (245)
14 KOG0848 Transcription factor C 99.6 2.2E-16 4.9E-21 146.3 2.1 63 29-97 199-261 (317)
15 smart00389 HOX Homeodomain. DN 99.6 5.3E-16 1.1E-20 107.5 3.2 56 30-91 1-56 (56)
16 cd00086 homeodomain Homeodomai 99.6 8.6E-16 1.9E-20 106.7 3.4 58 30-93 1-58 (59)
17 TIGR01565 homeo_ZF_HD homeobox 99.6 3.3E-15 7.1E-20 110.0 5.6 52 30-87 2-57 (58)
18 KOG0493 Transcription factor E 99.6 1.3E-15 2.9E-20 141.2 3.2 58 30-93 247-304 (342)
19 COG5576 Homeodomain-containing 99.5 6.8E-15 1.5E-19 126.2 5.4 67 23-97 47-113 (156)
20 KOG0491 Transcription factor B 99.5 7.5E-16 1.6E-20 134.9 -0.6 70 23-98 94-163 (194)
21 KOG0483 Transcription factor H 99.5 5.2E-15 1.1E-19 131.3 2.6 60 32-97 53-112 (198)
22 KOG0486 Transcription factor P 99.5 3.3E-14 7.2E-19 134.0 4.2 67 26-98 109-175 (351)
23 KOG3802 Transcription factor O 99.4 8.5E-14 1.8E-18 134.0 5.0 62 28-95 293-354 (398)
24 KOG0490 Transcription factor, 99.4 6.5E-14 1.4E-18 119.6 3.3 64 26-95 57-120 (235)
25 KOG4577 Transcription factor L 99.4 9.1E-14 2E-18 130.6 3.9 65 28-98 166-230 (383)
26 KOG0847 Transcription factor, 99.3 8.3E-13 1.8E-17 120.5 1.4 67 28-100 166-232 (288)
27 KOG0849 Transcription factor P 99.2 4.4E-11 9.6E-16 113.4 7.0 67 25-97 172-238 (354)
28 KOG1168 Transcription factor A 98.9 7.8E-10 1.7E-14 104.4 3.3 64 28-97 308-371 (385)
29 KOG0490 Transcription factor, 98.3 3.4E-07 7.4E-12 78.3 3.7 65 25-95 149-213 (235)
30 KOG0775 Transcription factor S 98.2 9.7E-07 2.1E-11 82.9 4.0 56 31-92 169-233 (304)
31 KOG2252 CCAAT displacement pro 98.2 9.9E-07 2.1E-11 88.6 2.9 59 27-91 418-476 (558)
32 PF05920 Homeobox_KN: Homeobox 98.0 1E-06 2.2E-11 60.5 -0.3 34 52-89 7-40 (40)
33 KOG0774 Transcription factor P 97.8 1.6E-05 3.5E-10 74.8 3.5 61 30-94 189-250 (334)
34 KOG1146 Homeobox protein [Gene 97.8 2E-05 4.3E-10 85.7 3.9 66 26-97 900-965 (1406)
35 KOG0773 Transcription factor M 96.0 0.0051 1.1E-07 57.3 3.0 63 29-95 239-302 (342)
36 KOG3623 Homeobox transcription 94.2 0.026 5.7E-07 59.7 2.2 52 41-98 568-619 (1007)
37 PF11569 Homez: Homeodomain le 86.3 0.12 2.5E-06 38.6 -1.4 42 41-88 10-51 (56)
38 PF04218 CENP-B_N: CENP-B N-te 83.6 1.1 2.3E-05 32.1 2.6 47 30-87 1-47 (53)
39 KOG3755 SATB1 matrix attachmen 75.1 0.69 1.5E-05 48.5 -0.9 70 23-95 685-759 (769)
40 PF04967 HTH_10: HTH DNA bindi 72.0 3.8 8.2E-05 29.9 2.5 40 36-79 1-40 (53)
41 KOG1146 Homeobox protein [Gene 70.9 5.6 0.00012 45.0 4.6 67 22-94 698-764 (1406)
42 cd06171 Sigma70_r4 Sigma70, re 64.3 2.9 6.3E-05 26.7 0.6 44 35-89 10-53 (55)
43 PF01527 HTH_Tnp_1: Transposas 62.9 2.7 5.9E-05 30.4 0.2 43 31-83 2-44 (76)
44 PRK09646 RNA polymerase sigma 62.0 8.2 0.00018 32.7 3.0 43 36-91 143-185 (194)
45 KOG0048 Transcription factor, 60.2 11 0.00023 34.1 3.6 55 31-97 60-114 (238)
46 PRK03975 tfx putative transcri 54.5 8 0.00017 33.3 1.7 47 34-92 5-51 (141)
47 cd00569 HTH_Hin_like Helix-tur 53.8 20 0.00043 20.1 2.9 38 35-83 5-42 (42)
48 COG3413 Predicted DNA binding 52.9 17 0.00037 31.9 3.6 50 35-90 155-204 (215)
49 PF04545 Sigma70_r4: Sigma-70, 51.6 9.6 0.00021 25.9 1.5 39 35-84 4-42 (50)
50 PF00196 GerE: Bacterial regul 46.5 7.7 0.00017 27.2 0.4 44 35-90 3-46 (58)
51 smart00027 EH Eps15 homology d 46.5 21 0.00046 27.3 2.8 46 34-83 2-50 (96)
52 PRK06759 RNA polymerase factor 43.9 12 0.00027 29.9 1.2 46 35-91 106-151 (154)
53 smart00421 HTH_LUXR helix_turn 42.5 13 0.00029 24.2 1.0 38 35-84 3-40 (58)
54 cd06170 LuxR_C_like C-terminal 41.8 16 0.00036 24.0 1.4 37 36-84 1-37 (57)
55 TIGR02937 sigma70-ECF RNA poly 41.0 20 0.00042 27.2 1.9 46 35-91 110-155 (158)
56 PF13873 Myb_DNA-bind_5: Myb/S 40.9 23 0.00051 26.0 2.2 61 34-94 3-76 (78)
57 PF08281 Sigma70_r4_2: Sigma-7 40.4 16 0.00034 24.9 1.2 39 36-85 11-49 (54)
58 cd02413 40S_S3_KH K homology R 40.2 26 0.00056 27.2 2.4 26 59-84 50-75 (81)
59 PRK09652 RNA polymerase sigma 39.3 22 0.00047 28.7 2.0 46 35-93 128-173 (182)
60 PRK12519 RNA polymerase sigma 39.0 16 0.00034 30.6 1.2 45 36-91 142-186 (194)
61 PF13551 HTH_29: Winged helix- 38.3 29 0.00063 26.2 2.4 52 30-83 52-108 (112)
62 PF00424 REV: REV protein (ant 37.9 27 0.00059 28.4 2.3 38 41-98 14-51 (91)
63 PRK12526 RNA polymerase sigma 36.4 21 0.00047 30.7 1.6 22 62-87 173-194 (206)
64 PF10668 Phage_terminase: Phag 36.1 11 0.00025 28.3 -0.1 17 62-82 26-42 (60)
65 PF10925 DUF2680: Protein of u 35.6 54 0.0012 24.4 3.4 43 36-84 1-43 (59)
66 PF13565 HTH_32: Homeodomain-l 34.5 1E+02 0.0022 22.2 4.7 39 29-74 26-64 (77)
67 PRK09642 RNA polymerase sigma 33.7 33 0.00072 27.7 2.3 27 62-92 126-152 (160)
68 COG4367 Uncharacterized protei 33.4 28 0.00061 28.7 1.7 39 35-79 2-40 (97)
69 KOG3623 Homeobox transcription 32.5 17 0.00037 39.5 0.4 62 28-95 625-686 (1007)
70 PRK12541 RNA polymerase sigma 31.9 30 0.00064 28.1 1.7 47 35-92 112-158 (161)
71 TIGR02948 SigW_bacill RNA poly 31.8 31 0.00067 28.4 1.8 26 62-91 156-181 (187)
72 PF12323 HTH_OrfB_IS605: Helix 31.4 27 0.00059 23.7 1.2 20 30-49 5-24 (46)
73 PRK12514 RNA polymerase sigma 31.3 38 0.00082 28.0 2.2 27 61-91 148-174 (179)
74 PRK12512 RNA polymerase sigma 31.0 36 0.00078 28.2 2.1 48 36-94 132-179 (184)
75 PRK04217 hypothetical protein; 31.0 44 0.00095 27.7 2.5 54 27-91 34-87 (110)
76 PF08880 QLQ: QLQ; InterPro: 30.4 41 0.00088 23.0 1.9 14 35-48 2-15 (37)
77 PRK11924 RNA polymerase sigma 29.7 35 0.00076 27.4 1.7 45 36-91 126-170 (179)
78 PHA02955 hypothetical protein; 29.3 72 0.0016 29.6 3.8 44 38-86 60-103 (213)
79 TIGR02999 Sig-70_X6 RNA polyme 28.7 36 0.00078 28.1 1.7 45 36-91 135-179 (183)
80 PRK12537 RNA polymerase sigma 28.5 46 0.00099 27.8 2.3 39 36-85 134-172 (182)
81 PF08144 CPL: CPL (NUC119) dom 28.5 89 0.0019 26.7 4.0 40 30-69 16-55 (148)
82 TIGR02952 Sig70_famx2 RNA poly 28.4 55 0.0012 26.4 2.7 43 36-91 123-165 (170)
83 COG4829 CatC1 Muconolactone de 28.2 46 0.00099 27.4 2.1 45 197-258 50-94 (98)
84 TIGR02989 Sig-70_gvs1 RNA poly 27.5 44 0.00095 26.7 1.9 38 35-83 111-148 (159)
85 PRK10100 DNA-binding transcrip 26.3 29 0.00062 30.8 0.7 47 35-93 155-201 (216)
86 TIGR02985 Sig70_bacteroi1 RNA 26.2 55 0.0012 25.7 2.3 39 36-85 114-152 (161)
87 PRK09648 RNA polymerase sigma 26.2 42 0.00091 28.1 1.6 44 35-91 139-182 (189)
88 PRK05602 RNA polymerase sigma 26.1 38 0.00083 28.2 1.4 45 37-94 130-174 (186)
89 TIGR02983 SigE-fam_strep RNA p 25.6 49 0.0011 26.7 1.9 44 37-91 112-155 (162)
90 PF13936 HTH_38: Helix-turn-he 25.4 26 0.00057 23.9 0.3 38 34-82 3-40 (44)
91 PRK09413 IS2 repressor TnpA; R 25.2 70 0.0015 25.9 2.7 41 32-83 9-50 (121)
92 TIGR02959 SigZ RNA polymerase 25.1 54 0.0012 27.2 2.1 44 35-91 100-143 (170)
93 PRK10651 transcriptional regul 24.8 26 0.00056 28.1 0.2 45 35-91 155-199 (216)
94 TIGR02939 RpoE_Sigma70 RNA pol 24.7 37 0.0008 28.0 1.1 25 61-91 157-181 (190)
95 PF06056 Terminase_5: Putative 24.3 28 0.00062 25.5 0.3 18 62-83 17-34 (58)
96 PF02796 HTH_7: Helix-turn-hel 24.0 32 0.00069 23.4 0.5 38 34-82 4-41 (45)
97 PRK12515 RNA polymerase sigma 24.0 62 0.0013 27.1 2.3 44 35-91 131-174 (189)
98 PRK00118 putative DNA-binding 23.1 51 0.0011 27.0 1.6 46 36-92 18-63 (104)
99 TIGR02954 Sig70_famx3 RNA poly 23.0 56 0.0012 26.7 1.8 39 35-84 119-157 (169)
100 PRK10360 DNA-binding transcrip 22.9 41 0.00089 26.9 1.0 43 35-89 137-179 (196)
101 PRK09644 RNA polymerase sigma 22.8 49 0.0011 27.0 1.4 46 36-92 109-154 (165)
102 PRK07037 extracytoplasmic-func 22.8 54 0.0012 26.5 1.6 36 36-82 110-145 (163)
103 PRK09637 RNA polymerase sigma 22.4 61 0.0013 27.4 1.9 47 35-94 106-152 (181)
104 PRK09047 RNA polymerase factor 22.2 64 0.0014 25.8 2.0 38 36-84 107-144 (161)
105 PRK05657 RNA polymerase sigma 22.1 56 0.0012 30.9 1.9 50 35-91 262-311 (325)
106 PRK12538 RNA polymerase sigma 22.1 42 0.00092 30.0 1.0 27 62-92 191-217 (233)
107 PF07638 Sigma70_ECF: ECF sigm 22.1 55 0.0012 28.0 1.6 27 62-92 155-181 (185)
108 PTZ00183 centrin; Provisional 21.5 2.9E+02 0.0064 21.6 5.6 40 29-68 4-46 (158)
109 PRK12530 RNA polymerase sigma 21.2 57 0.0012 27.6 1.5 43 37-90 136-178 (189)
110 PRK12536 RNA polymerase sigma 21.0 60 0.0013 27.0 1.6 27 61-91 148-174 (181)
111 PRK06930 positive control sigm 20.9 66 0.0014 27.9 1.9 49 35-94 114-162 (170)
112 PRK13919 putative RNA polymera 20.8 70 0.0015 26.5 2.0 43 36-91 136-178 (186)
113 TIGR00721 tfx DNA-binding prot 20.8 63 0.0014 27.7 1.7 47 33-91 4-50 (137)
114 PRK12546 RNA polymerase sigma 20.5 68 0.0015 27.5 1.9 46 36-92 114-159 (188)
115 PRK09651 RNA polymerase sigma 20.4 60 0.0013 26.9 1.5 44 35-91 119-162 (172)
116 PRK08295 RNA polymerase factor 20.4 57 0.0012 27.5 1.4 20 62-85 174-193 (208)
No 1
>KOG0489 consensus Transcription factor zerknullt and related HOX domain proteins [General function prediction only]
Probab=99.80 E-value=1.1e-20 Score=171.13 Aligned_cols=65 Identities=18% Similarity=0.218 Sum_probs=60.7
Q ss_pred CCCCCCCCCCHHHHHHHHHHHhhCCCCCCCHHHHHHHHHHHhhcCCCCCCceeeccccchhHHHHhhhhcc
Q 046372 28 RPTCPRWTPTTDQIRILKELYYNNGVRSPTAEQIQKISARLRQYGKIEGKNVFYWFQNYKARERLKKKIEG 98 (266)
Q Consensus 28 R~rR~Rt~FT~eQL~iLE~~F~~~~n~yPs~e~R~eIA~~L~~~g~LsE~qVqvWFQNRRAKeKRkkr~~~ 98 (266)
..||.||.||..||.+||++|. .|+|+++.+|.|||..| .|+|+||||||||||+||||..+...
T Consensus 158 ~~kR~RtayT~~QllELEkEFh--fN~YLtR~RRiEiA~~L----~LtErQIKIWFQNRRMK~Kk~~k~~~ 222 (261)
T KOG0489|consen 158 KSKRRRTAFTRYQLLELEKEFH--FNKYLTRSRRIEIAHAL----NLTERQIKIWFQNRRMKWKKENKAKS 222 (261)
T ss_pred CCCCCCcccchhhhhhhhhhhc--cccccchHHHHHHHhhc----chhHHHHHHHHHHHHHHHHHhhcccc
Confidence 4788999999999999999997 68999999999999999 69999999999999999998887763
No 2
>KOG0484 consensus Transcription factor PHOX2/ARIX, contains HOX domain [Transcription]
Probab=99.76 E-value=1e-19 Score=149.53 Aligned_cols=67 Identities=21% Similarity=0.308 Sum_probs=61.8
Q ss_pred cCCCCCCCCCCCHHHHHHHHHHHhhCCCCCCCHHHHHHHHHHHhhcCCCCCCceeeccccchhHHHHhhhhcc
Q 046372 26 HCRPTCPRWTPTTDQIRILKELYYNNGVRSPTAEQIQKISARLRQYGKIEGKNVFYWFQNYKARERLKKKIEG 98 (266)
Q Consensus 26 ~~R~rR~Rt~FT~eQL~iLE~~F~~~~n~yPs~e~R~eIA~~L~~~g~LsE~qVqvWFQNRRAKeKRkkr~~~ 98 (266)
..++||.||+||..||.+||++|. ..+||+...|++||.+| +|+|.+|+|||||||||-|++.|...
T Consensus 14 krKQRRIRTTFTS~QLkELErvF~--ETHYPDIYTREEiA~ki----dLTEARVQVWFQNRRAKfRKQEr~a~ 80 (125)
T KOG0484|consen 14 KRKQRRIRTTFTSAQLKELERVFA--ETHYPDIYTREEIALKI----DLTEARVQVWFQNRRAKFRKQERAAI 80 (125)
T ss_pred HHHhhhhhhhhhHHHHHHHHHHHH--hhcCCcchhHHHHHHhh----hhhHHHHHHHHHhhHHHHHHHHHHHH
Confidence 455689999999999999999997 57999999999999999 59999999999999999999888764
No 3
>KOG0842 consensus Transcription factor tinman/NKX2-3, contains HOX domain [Transcription]
Probab=99.76 E-value=6.3e-19 Score=164.78 Aligned_cols=69 Identities=17% Similarity=0.248 Sum_probs=63.2
Q ss_pred CcccCCCCCCCCCCCHHHHHHHHHHHhhCCCCCCCHHHHHHHHHHHhhcCCCCCCceeeccccchhHHHHhhhhc
Q 046372 23 NNCHCRPTCPRWTPTTDQIRILKELYYNNGVRSPTAEQIQKISARLRQYGKIEGKNVFYWFQNYKARERLKKKIE 97 (266)
Q Consensus 23 g~~~~R~rR~Rt~FT~eQL~iLE~~F~~~~n~yPs~e~R~eIA~~L~~~g~LsE~qVqvWFQNRRAKeKRkkr~~ 97 (266)
++...++||+|..||+.|+.+||+.|. .++|++..+|++||..| +|+++||||||||||.|.||++...
T Consensus 147 ~t~~~~kRKrRVLFSqAQV~ELERRFr--qQRYLSAPERE~LA~~L----rLT~TQVKIWFQNrRYK~KR~~~dk 215 (307)
T KOG0842|consen 147 QTGKRKKRKRRVLFSQAQVYELERRFR--QQRYLSAPEREHLASSL----RLTPTQVKIWFQNRRYKTKRQQKDK 215 (307)
T ss_pred ccccccccccccccchhHHHHHHHHHH--hhhccccHhHHHHHHhc----CCCchheeeeeecchhhhhhhhhhh
Confidence 445668899999999999999999996 57999999999999999 5999999999999999999988766
No 4
>KOG0843 consensus Transcription factor EMX1 and related HOX domain proteins [Transcription]
Probab=99.76 E-value=4.5e-19 Score=156.25 Aligned_cols=64 Identities=20% Similarity=0.336 Sum_probs=60.4
Q ss_pred CCCCCCCCCCCHHHHHHHHHHHhhCCCCCCCHHHHHHHHHHHhhcCCCCCCceeeccccchhHHHHhhhh
Q 046372 27 CRPTCPRWTPTTDQIRILKELYYNNGVRSPTAEQIQKISARLRQYGKIEGKNVFYWFQNYKARERLKKKI 96 (266)
Q Consensus 27 ~R~rR~Rt~FT~eQL~iLE~~F~~~~n~yPs~e~R~eIA~~L~~~g~LsE~qVqvWFQNRRAKeKRkkr~ 96 (266)
.|++|.||.||++||..||..|+ ++.|....+|++||..| +|+|.||||||||||.|.||++..
T Consensus 100 ~~~kr~RT~ft~~Ql~~LE~~F~--~~~Yvvg~eR~~LA~~L----~LsetQVkvWFQNRRtk~kr~~~e 163 (197)
T KOG0843|consen 100 MRPKRIRTAFTPEQLLKLEHAFE--GNQYVVGAERKQLAQSL----SLSETQVKVWFQNRRTKHKRMQQE 163 (197)
T ss_pred cCCCccccccCHHHHHHHHHHHh--cCCeeechHHHHHHHHc----CCChhHhhhhhhhhhHHHHHHHHH
Confidence 38999999999999999999998 68999999999999999 699999999999999999998766
No 5
>KOG0487 consensus Transcription factor Abd-B, contains HOX domain [Transcription]
Probab=99.74 E-value=9e-19 Score=163.80 Aligned_cols=67 Identities=22% Similarity=0.240 Sum_probs=61.5
Q ss_pred CcccCCCCCCCCCCCHHHHHHHHHHHhhCCCCCCCHHHHHHHHHHHhhcCCCCCCceeeccccchhHHHHhhh
Q 046372 23 NNCHCRPTCPRWTPTTDQIRILKELYYNNGVRSPTAEQIQKISARLRQYGKIEGKNVFYWFQNYKARERLKKK 95 (266)
Q Consensus 23 g~~~~R~rR~Rt~FT~eQL~iLE~~F~~~~n~yPs~e~R~eIA~~L~~~g~LsE~qVqvWFQNRRAKeKRkkr 95 (266)
.+...|-|++|..+|+.||.+||++|. -|.|+++++|.||++.| +|+|+||||||||||+|+||--|
T Consensus 229 ~~~~~~~RKKRcPYTK~QtlELEkEFl--fN~YitkeKR~ElSr~l----NLTeRQVKIWFQNRRMK~KK~~r 295 (308)
T KOG0487|consen 229 ASSARRGRKKRCPYTKHQTLELEKEFL--FNMYITKEKRLELSRTL----NLTERQVKIWFQNRRMKEKKVNR 295 (308)
T ss_pred cccccccccccCCchHHHHHHHHHHHH--HHHHHhHHHHHHHHHhc----ccchhheeeeehhhhhHHhhhhh
Confidence 345567789999999999999999998 57899999999999999 79999999999999999998776
No 6
>KOG0488 consensus Transcription factor BarH and related HOX domain proteins [General function prediction only]
Probab=99.74 E-value=1.5e-18 Score=161.72 Aligned_cols=68 Identities=15% Similarity=0.174 Sum_probs=61.7
Q ss_pred cccCCCCCCCCCCCHHHHHHHHHHHhhCCCCCCCHHHHHHHHHHHhhcCCCCCCceeeccccchhHHHHhhhhc
Q 046372 24 NCHCRPTCPRWTPTTDQIRILKELYYNNGVRSPTAEQIQKISARLRQYGKIEGKNVFYWFQNYKARERLKKKIE 97 (266)
Q Consensus 24 ~~~~R~rR~Rt~FT~eQL~iLE~~F~~~~n~yPs~e~R~eIA~~L~~~g~LsE~qVqvWFQNRRAKeKRkkr~~ 97 (266)
....++|+.||.||..||..||+.|++ .+|++..+|.+||+.| ||++.|||+||||||+||||.....
T Consensus 167 ~~pkK~RksRTaFT~~Ql~~LEkrF~~--QKYLS~~DR~~LA~~L----gLTdaQVKtWfQNRRtKWKrq~a~g 234 (309)
T KOG0488|consen 167 STPKKRRKSRTAFSDHQLFELEKRFEK--QKYLSVADRIELAASL----GLTDAQVKTWFQNRRTKWKRQTAEG 234 (309)
T ss_pred CCCcccccchhhhhHHHHHHHHHHHHH--hhcccHHHHHHHHHHc----CCchhhHHHHHhhhhHHHHHHHHhh
Confidence 334677889999999999999999985 6899999999999999 7999999999999999999987664
No 7
>KOG2251 consensus Homeobox transcription factor [Transcription]
Probab=99.71 E-value=1.8e-17 Score=149.33 Aligned_cols=68 Identities=21% Similarity=0.339 Sum_probs=63.3
Q ss_pred cccCCCCCCCCCCCHHHHHHHHHHHhhCCCCCCCHHHHHHHHHHHhhcCCCCCCceeeccccchhHHHHhhhhc
Q 046372 24 NCHCRPTCPRWTPTTDQIRILKELYYNNGVRSPTAEQIQKISARLRQYGKIEGKNVFYWFQNYKARERLKKKIE 97 (266)
Q Consensus 24 ~~~~R~rR~Rt~FT~eQL~iLE~~F~~~~n~yPs~e~R~eIA~~L~~~g~LsE~qVqvWFQNRRAKeKRkkr~~ 97 (266)
...+|.||.||+||-.||.+||.+|. +..||+...|++||.+| +|+|.+|+|||.|||||.|+++++.
T Consensus 32 ~~pRkqRRERTtFtr~QlevLe~LF~--kTqYPDv~~rEelAlkl----nLpeSrVqVWFKNRRAK~r~qq~qq 99 (228)
T KOG2251|consen 32 SGPRKQRRERTTFTRKQLEVLEALFA--KTQYPDVFMREELALKL----NLPESRVQVWFKNRRAKCRRQQQQQ 99 (228)
T ss_pred ccchhcccccceecHHHHHHHHHHHH--hhcCccHHHHHHHHHHh----CCchhhhhhhhccccchhhHhhhhh
Confidence 55678899999999999999999997 57999999999999999 7999999999999999999988875
No 8
>KOG0844 consensus Transcription factor EVX1, contains HOX domain [Transcription]
Probab=99.71 E-value=4.8e-18 Score=159.93 Aligned_cols=80 Identities=20% Similarity=0.347 Sum_probs=67.5
Q ss_pred CCCCCCCCCCCCcccCCC----CCCCCCCCHHHHHHHHHHHhhCCCCCCCHHHHHHHHHHHhhcCCCCCCceeeccccch
Q 046372 12 GNGACGSSGKGNNCHCRP----TCPRWTPTTDQIRILKELYYNNGVRSPTAEQIQKISARLRQYGKIEGKNVFYWFQNYK 87 (266)
Q Consensus 12 ~~~~~~g~~~~g~~~~R~----rR~Rt~FT~eQL~iLE~~F~~~~n~yPs~e~R~eIA~~L~~~g~LsE~qVqvWFQNRR 87 (266)
.++.+|++|+||.+.|+. ||-||.||.|||.+||+.|+++ -|.++.+|-|||..| +|+|..|||||||||
T Consensus 160 ~~g~sg~ggs~g~~a~sa~dqmRRYRTAFTReQIaRLEKEFyrE--NYVSRprRcELAAaL----NLPEtTIKVWFQNRR 233 (408)
T KOG0844|consen 160 ASGLSGAGGSGGPYANSADDQMRRYRTAFTREQIARLEKEFYRE--NYVSRPRRCELAAAL----NLPETTIKVWFQNRR 233 (408)
T ss_pred ccCCCcCCCCCCccccCccHHHHHHHhhhhHHHHHHHHHHHHHh--ccccCchhhhHHHhh----CCCcceeehhhhhch
Confidence 334455556666766654 7999999999999999999973 699999999999999 799999999999999
Q ss_pred hHHHHhhhhc
Q 046372 88 ARERLKKKIE 97 (266)
Q Consensus 88 AKeKRkkr~~ 97 (266)
+|.||++--+
T Consensus 234 MKDKRQRlam 243 (408)
T KOG0844|consen 234 MKDKRQRLAM 243 (408)
T ss_pred hhhhhhhhhc
Confidence 9999866544
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=99.70 E-value=5.4e-18 Score=118.89 Aligned_cols=57 Identities=25% Similarity=0.465 Sum_probs=53.9
Q ss_pred CCCCCCCCHHHHHHHHHHHhhCCCCCCCHHHHHHHHHHHhhcCCCCCCceeeccccchhHHHH
Q 046372 30 TCPRWTPTTDQIRILKELYYNNGVRSPTAEQIQKISARLRQYGKIEGKNVFYWFQNYKARERL 92 (266)
Q Consensus 30 rR~Rt~FT~eQL~iLE~~F~~~~n~yPs~e~R~eIA~~L~~~g~LsE~qVqvWFQNRRAKeKR 92 (266)
+|+|+.||++|+.+||..|.. ++||+.+++++||..| +|++.+|++||||||+|+||
T Consensus 1 kr~r~~~t~~q~~~L~~~f~~--~~~p~~~~~~~la~~l----~l~~~~V~~WF~nrR~k~kk 57 (57)
T PF00046_consen 1 KRKRTRFTKEQLKVLEEYFQE--NPYPSKEEREELAKEL----GLTERQVKNWFQNRRRKEKK 57 (57)
T ss_dssp SSSSSSSSHHHHHHHHHHHHH--SSSCHHHHHHHHHHHH----TSSHHHHHHHHHHHHHHHHH
T ss_pred CcCCCCCCHHHHHHHHHHHHH--hccccccccccccccc----cccccccccCHHHhHHHhCc
Confidence 578999999999999999984 7999999999999999 69999999999999999986
No 10
>KOG0494 consensus Transcription factor CHX10 and related HOX domain proteins [General function prediction only]
Probab=99.69 E-value=1.2e-17 Score=154.55 Aligned_cols=73 Identities=22% Similarity=0.260 Sum_probs=61.9
Q ss_pred CcccCCCCCC-CCCCCHHHHHHHHHHHhhCCCCCCCHHHHHHHHHHHhhcCCCCCCceeeccccchhHHHHhhhhccCCC
Q 046372 23 NNCHCRPTCP-RWTPTTDQIRILKELYYNNGVRSPTAEQIQKISARLRQYGKIEGKNVFYWFQNYKARERLKKKIEGSST 101 (266)
Q Consensus 23 g~~~~R~rR~-Rt~FT~eQL~iLE~~F~~~~n~yPs~e~R~eIA~~L~~~g~LsE~qVqvWFQNRRAKeKRkkr~~~~~~ 101 (266)
+...|.+||. ||.||..||..||+.|. ..+||+...|+-||.++ +|+|.+|+||||||||||||+++.-.-++
T Consensus 134 ~~kkk~kRRh~RTiFT~~Qle~LEkaFk--eaHYPDv~Are~la~kt----elpEDRIqVWfQNRRAKWRk~Ek~wg~sT 207 (332)
T KOG0494|consen 134 NAKKKKKRRHFRTIFTSYQLEELEKAFK--EAHYPDVYAREMLADKT----ELPEDRIQVWFQNRRAKWRKTEKRWGGST 207 (332)
T ss_pred ccccccccccccchhhHHHHHHHHHHHh--hccCccHHHHHHHhhhc----cCchhhhhHHhhhhhHHhhhhhhhcCcch
Confidence 4445555666 99999999999999996 56999999999888888 69999999999999999999877664433
No 11
>KOG0485 consensus Transcription factor NKX-5.1/HMX1, contains HOX domain [Transcription]
Probab=99.67 E-value=2.8e-17 Score=149.02 Aligned_cols=70 Identities=17% Similarity=0.162 Sum_probs=63.2
Q ss_pred CcccCCCCCCCCCCCHHHHHHHHHHHhhCCCCCCCHHHHHHHHHHHhhcCCCCCCceeeccccchhHHHHhhhhcc
Q 046372 23 NNCHCRPTCPRWTPTTDQIRILKELYYNNGVRSPTAEQIQKISARLRQYGKIEGKNVFYWFQNYKARERLKKKIEG 98 (266)
Q Consensus 23 g~~~~R~rR~Rt~FT~eQL~iLE~~F~~~~n~yPs~e~R~eIA~~L~~~g~LsE~qVqvWFQNRRAKeKRkkr~~~ 98 (266)
|....|++|+||.|+..|+..||..|+. .+|++..+|..||+.|. |+|.|||+||||||-||||+-.-..
T Consensus 98 ~~g~~RKKktRTvFSraQV~qLEs~Fe~--krYLSsaeRa~LA~sLq----LTETQVKIWFQNRRnKwKRq~aad~ 167 (268)
T KOG0485|consen 98 GLGDDRKKKTRTVFSRAQVFQLESTFEL--KRYLSSAERAGLAASLQ----LTETQVKIWFQNRRNKWKRQYAADL 167 (268)
T ss_pred cccccccccchhhhhHHHHHHHHHHHHH--HhhhhHHHHhHHHHhhh----hhhhhhhhhhhhhhHHHHHHHhhhh
Confidence 4566799999999999999999999984 58999999999999995 9999999999999999999775544
No 12
>KOG0492 consensus Transcription factor MSH, contains HOX domain [General function prediction only]
Probab=99.66 E-value=5e-17 Score=146.39 Aligned_cols=63 Identities=24% Similarity=0.307 Sum_probs=58.1
Q ss_pred CCCCCCCCHHHHHHHHHHHhhCCCCCCCHHHHHHHHHHHhhcCCCCCCceeeccccchhHHHHhhhhcc
Q 046372 30 TCPRWTPTTDQIRILKELYYNNGVRSPTAEQIQKISARLRQYGKIEGKNVFYWFQNYKARERLKKKIEG 98 (266)
Q Consensus 30 rR~Rt~FT~eQL~iLE~~F~~~~n~yPs~e~R~eIA~~L~~~g~LsE~qVqvWFQNRRAKeKRkkr~~~ 98 (266)
|++||.||+.||..||+.|. ...|+++++|.+++.-| .|+|.||||||||||||.||.++...
T Consensus 145 RkPRtPFTtqQLlaLErkfr--ekqYLSiaEraefSsSL----~LTeTqVKIWFQNRRAKaKRlQeae~ 207 (246)
T KOG0492|consen 145 RKPRTPFTTQQLLALERKFR--EKQYLSIAERAEFSSSL----ELTETQVKIWFQNRRAKAKRLQEAEL 207 (246)
T ss_pred CCCCCCCCHHHHHHHHHHHh--HhhhhhHHHHHhhhhhh----hhhhhheehhhhhhhHHHHHHHHHHH
Confidence 68999999999999999996 35899999999999999 59999999999999999999887763
No 13
>KOG0850 consensus Transcription factor DLX and related proteins with LIM Zn-binding and HOX domains [Transcription]
Probab=99.63 E-value=4.7e-16 Score=141.19 Aligned_cols=64 Identities=20% Similarity=0.280 Sum_probs=59.4
Q ss_pred CCCCCCCCCCHHHHHHHHHHHhhCCCCCCCHHHHHHHHHHHhhcCCCCCCceeeccccchhHHHHhhhhc
Q 046372 28 RPTCPRWTPTTDQIRILKELYYNNGVRSPTAEQIQKISARLRQYGKIEGKNVFYWFQNYKARERLKKKIE 97 (266)
Q Consensus 28 R~rR~Rt~FT~eQL~iLE~~F~~~~n~yPs~e~R~eIA~~L~~~g~LsE~qVqvWFQNRRAKeKRkkr~~ 97 (266)
+.|++||.|+.-||+.|.+.|++ ..|+-..+|.+||+.| ||+..||||||||||.|.||.+++.
T Consensus 121 K~RKPRTIYSS~QLqaL~rRFQk--TQYLALPERAeLAAsL----GLTQTQVKIWFQNrRSK~KKl~k~g 184 (245)
T KOG0850|consen 121 KVRKPRTIYSSLQLQALNRRFQQ--TQYLALPERAELAASL----GLTQTQVKIWFQNRRSKFKKLKKQG 184 (245)
T ss_pred cccCCcccccHHHHHHHHHHHhh--cchhcCcHHHHHHHHh----CCchhHhhhhhhhhHHHHHHHHhcC
Confidence 56789999999999999999984 6899999999999999 6999999999999999999988854
No 14
>KOG0848 consensus Transcription factor Caudal, contains HOX domain [Transcription]
Probab=99.60 E-value=2.2e-16 Score=146.30 Aligned_cols=63 Identities=27% Similarity=0.297 Sum_probs=57.0
Q ss_pred CCCCCCCCCHHHHHHHHHHHhhCCCCCCCHHHHHHHHHHHhhcCCCCCCceeeccccchhHHHHhhhhc
Q 046372 29 PTCPRWTPTTDQIRILKELYYNNGVRSPTAEQIQKISARLRQYGKIEGKNVFYWFQNYKARERLKKKIE 97 (266)
Q Consensus 29 ~rR~Rt~FT~eQL~iLE~~F~~~~n~yPs~e~R~eIA~~L~~~g~LsE~qVqvWFQNRRAKeKRkkr~~ 97 (266)
+-+-|..+|..|.-+||++|. .++|.++.++.|||..| +|+|+||||||||||||+||..+.+
T Consensus 199 kDKYRvVYTDhQRLELEKEfh--~SryITirRKSELA~~L----gLsERQVKIWFQNRRAKERK~nKKk 261 (317)
T KOG0848|consen 199 KDKYRVVYTDHQRLELEKEFH--TSRYITIRRKSELAATL----GLSERQVKIWFQNRRAKERKDNKKK 261 (317)
T ss_pred ccceeEEecchhhhhhhhhhc--cccceeeehhHHHHHhh----CccHhhhhHhhhhhhHHHHHHHHHH
Confidence 346799999999999999996 78999999999999999 6999999999999999999855544
No 15
>smart00389 HOX Homeodomain. DNA-binding factors that are involved in the transcriptional regulation of key developmental processes
Probab=99.60 E-value=5.3e-16 Score=107.46 Aligned_cols=56 Identities=25% Similarity=0.407 Sum_probs=51.6
Q ss_pred CCCCCCCCHHHHHHHHHHHhhCCCCCCCHHHHHHHHHHHhhcCCCCCCceeeccccchhHHH
Q 046372 30 TCPRWTPTTDQIRILKELYYNNGVRSPTAEQIQKISARLRQYGKIEGKNVFYWFQNYKARER 91 (266)
Q Consensus 30 rR~Rt~FT~eQL~iLE~~F~~~~n~yPs~e~R~eIA~~L~~~g~LsE~qVqvWFQNRRAKeK 91 (266)
++.|+.||++|+.+||+.|. .++||+.+++.+||..| +|+..+|++||+|||+|.|
T Consensus 1 ~k~r~~~~~~~~~~L~~~f~--~~~~P~~~~~~~la~~~----~l~~~qV~~WF~nrR~~~~ 56 (56)
T smart00389 1 RRKRTSFTPEQLEELEKEFQ--KNPYPSREEREELAAKL----GLSERQVKVWFQNRRAKWK 56 (56)
T ss_pred CCCCCcCCHHHHHHHHHHHH--hCCCCCHHHHHHHHHHH----CcCHHHHHHhHHHHhhccC
Confidence 35788899999999999998 46899999999999999 6999999999999999864
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=99.58 E-value=8.6e-16 Score=106.65 Aligned_cols=58 Identities=22% Similarity=0.357 Sum_probs=53.6
Q ss_pred CCCCCCCCHHHHHHHHHHHhhCCCCCCCHHHHHHHHHHHhhcCCCCCCceeeccccchhHHHHh
Q 046372 30 TCPRWTPTTDQIRILKELYYNNGVRSPTAEQIQKISARLRQYGKIEGKNVFYWFQNYKARERLK 93 (266)
Q Consensus 30 rR~Rt~FT~eQL~iLE~~F~~~~n~yPs~e~R~eIA~~L~~~g~LsE~qVqvWFQNRRAKeKRk 93 (266)
++.|..|+.+|+.+||..|.. ++||+.+++++||.+| +|++++|++||+|||++.|+.
T Consensus 1 ~~~r~~~~~~~~~~Le~~f~~--~~~P~~~~~~~la~~~----~l~~~qV~~WF~nrR~~~~~~ 58 (59)
T cd00086 1 RRKRTRFTPEQLEELEKEFEK--NPYPSREEREELAKEL----GLTERQVKIWFQNRRAKLKRS 58 (59)
T ss_pred CCCCCcCCHHHHHHHHHHHHh--CCCCCHHHHHHHHHHH----CcCHHHHHHHHHHHHHHHhcc
Confidence 357889999999999999984 7999999999999999 699999999999999999864
No 17
>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=99.57 E-value=3.3e-15 Score=109.99 Aligned_cols=52 Identities=15% Similarity=0.239 Sum_probs=49.2
Q ss_pred CCCCCCCCHHHHHHHHHHHhhCCCCC----CCHHHHHHHHHHHhhcCCCCCCceeeccccch
Q 046372 30 TCPRWTPTTDQIRILKELYYNNGVRS----PTAEQIQKISARLRQYGKIEGKNVFYWFQNYK 87 (266)
Q Consensus 30 rR~Rt~FT~eQL~iLE~~F~~~~n~y----Ps~e~R~eIA~~L~~~g~LsE~qVqvWFQNRR 87 (266)
+|.||.||++|+..||+.|++ ++| |+..+|++||..| ||++++|+|||||-+
T Consensus 2 kR~RT~Ft~~Q~~~Le~~fe~--~~y~~~~~~~~~r~~la~~l----gl~~~vvKVWfqN~k 57 (58)
T TIGR01565 2 KRRRTKFTAEQKEKMRDFAEK--LGWKLKDKRREEVREFCEEI----GVTRKVFKVWMHNNK 57 (58)
T ss_pred CCCCCCCCHHHHHHHHHHHHH--cCCCCCCCCHHHHHHHHHHh----CCCHHHeeeecccCC
Confidence 689999999999999999984 689 9999999999999 799999999999976
No 18
>KOG0493 consensus Transcription factor Engrailed, contains HOX domain [General function prediction only]
Probab=99.56 E-value=1.3e-15 Score=141.20 Aligned_cols=58 Identities=26% Similarity=0.390 Sum_probs=54.9
Q ss_pred CCCCCCCCHHHHHHHHHHHhhCCCCCCCHHHHHHHHHHHhhcCCCCCCceeeccccchhHHHHh
Q 046372 30 TCPRWTPTTDQIRILKELYYNNGVRSPTAEQIQKISARLRQYGKIEGKNVFYWFQNYKARERLK 93 (266)
Q Consensus 30 rR~Rt~FT~eQL~iLE~~F~~~~n~yPs~e~R~eIA~~L~~~g~LsE~qVqvWFQNRRAKeKRk 93 (266)
+|+||.||.|||++|+..|. .|+|++..+|++||.+| +|.|.|||+||||+|||.||.
T Consensus 247 KRPRTAFtaeQL~RLK~EF~--enRYlTEqRRQ~La~EL----gLNEsQIKIWFQNKRAKiKKs 304 (342)
T KOG0493|consen 247 KRPRTAFTAEQLQRLKAEFQ--ENRYLTEQRRQELAQEL----GLNESQIKIWFQNKRAKIKKS 304 (342)
T ss_pred cCccccccHHHHHHHHHHHh--hhhhHHHHHHHHHHHHh----CcCHHHhhHHhhhhhhhhhhc
Confidence 58999999999999999997 68999999999999999 699999999999999999874
No 19
>COG5576 Homeodomain-containing transcription factor [Transcription]
Probab=99.53 E-value=6.8e-15 Score=126.15 Aligned_cols=67 Identities=25% Similarity=0.320 Sum_probs=58.3
Q ss_pred CcccCCCCCCCCCCCHHHHHHHHHHHhhCCCCCCCHHHHHHHHHHHhhcCCCCCCceeeccccchhHHHHhhhhc
Q 046372 23 NNCHCRPTCPRWTPTTDQIRILKELYYNNGVRSPTAEQIQKISARLRQYGKIEGKNVFYWFQNYKARERLKKKIE 97 (266)
Q Consensus 23 g~~~~R~rR~Rt~FT~eQL~iLE~~F~~~~n~yPs~e~R~eIA~~L~~~g~LsE~qVqvWFQNRRAKeKRkkr~~ 97 (266)
+...++.+|.|+ |.+|+.+||+.|. .++||+...|.+|+..| +|+++.|++||||||+|+|++.+..
T Consensus 47 ~s~~~~~~r~R~--t~~Q~~vL~~~F~--i~p~Ps~~~r~~L~~~l----nm~~ksVqIWFQNkR~~~k~~~~~~ 113 (156)
T COG5576 47 GSSPPKSKRRRT--TDEQLMVLEREFE--INPYPSSITRIKLSLLL----NMPPKSVQIWFQNKRAKEKKKRSGK 113 (156)
T ss_pred CCCcCcccceec--hHHHHHHHHHHhc--cCCCCCHHHHHHHHHhc----CCChhhhhhhhchHHHHHHHhcccc
Confidence 344555555555 9999999999998 68999999999999999 6999999999999999999888775
No 20
>KOG0491 consensus Transcription factor BSH, contains HOX domain [General function prediction only]
Probab=99.53 E-value=7.5e-16 Score=134.92 Aligned_cols=70 Identities=20% Similarity=0.326 Sum_probs=64.3
Q ss_pred CcccCCCCCCCCCCCHHHHHHHHHHHhhCCCCCCCHHHHHHHHHHHhhcCCCCCCceeeccccchhHHHHhhhhcc
Q 046372 23 NNCHCRPTCPRWTPTTDQIRILKELYYNNGVRSPTAEQIQKISARLRQYGKIEGKNVFYWFQNYKARERLKKKIEG 98 (266)
Q Consensus 23 g~~~~R~rR~Rt~FT~eQL~iLE~~F~~~~n~yPs~e~R~eIA~~L~~~g~LsE~qVqvWFQNRRAKeKRkkr~~~ 98 (266)
--..||+++.|+.|+..||..||+.|+ ..+|++..+|+|||..| +|+++|||.||||||+|-||..|...
T Consensus 94 ~~~~~~r~K~Rtvfs~~ql~~l~~rFe--~QrYLS~~e~~ELan~L----~LS~~QVKTWFQNrRMK~Kk~~r~~~ 163 (194)
T KOG0491|consen 94 ARLHCRRRKARTVFSDPQLSGLEKRFE--RQRYLSTPERQELANAL----SLSETQVKTWFQNRRMKHKKQQRNNQ 163 (194)
T ss_pred hhHHHHhhhhcccccCccccccHHHHh--hhhhcccHHHHHHHHHh----hhhHHHHHHHHHHHHHHHHHHHhccC
Confidence 456789999999999999999999998 46899999999999999 69999999999999999999887763
No 21
>KOG0483 consensus Transcription factor HEX, contains HOX and HALZ domains [Transcription]
Probab=99.51 E-value=5.2e-15 Score=131.33 Aligned_cols=60 Identities=23% Similarity=0.417 Sum_probs=54.5
Q ss_pred CCCCCCHHHHHHHHHHHhhCCCCCCCHHHHHHHHHHHhhcCCCCCCceeeccccchhHHHHhhhhc
Q 046372 32 PRWTPTTDQIRILKELYYNNGVRSPTAEQIQKISARLRQYGKIEGKNVFYWFQNYKARERLKKKIE 97 (266)
Q Consensus 32 ~Rt~FT~eQL~iLE~~F~~~~n~yPs~e~R~eIA~~L~~~g~LsE~qVqvWFQNRRAKeKRkkr~~ 97 (266)
+..+||.+|+..||+.|+ .+.++.++++..||.+| ||.++||.|||||||||||.|+...
T Consensus 53 kk~Rlt~eQ~~~LE~~F~--~~~~L~p~~K~~LAk~L----gL~pRQVavWFQNRRARwK~kqlE~ 112 (198)
T KOG0483|consen 53 KKRRLTSEQVKFLEKSFE--SEKKLEPERKKKLAKEL----GLQPRQVAVWFQNRRARWKTKQLEK 112 (198)
T ss_pred ccccccHHHHHHhHHhhc--cccccChHHHHHHHHhh----CCChhHHHHHHhhccccccchhhhh
Confidence 445689999999999997 57899999999999999 7999999999999999999987665
No 22
>KOG0486 consensus Transcription factor PTX1, contains HOX domain [Transcription]
Probab=99.46 E-value=3.3e-14 Score=134.00 Aligned_cols=67 Identities=19% Similarity=0.296 Sum_probs=62.7
Q ss_pred cCCCCCCCCCCCHHHHHHHHHHHhhCCCCCCCHHHHHHHHHHHhhcCCCCCCceeeccccchhHHHHhhhhcc
Q 046372 26 HCRPTCPRWTPTTDQIRILKELYYNNGVRSPTAEQIQKISARLRQYGKIEGKNVFYWFQNYKARERLKKKIEG 98 (266)
Q Consensus 26 ~~R~rR~Rt~FT~eQL~iLE~~F~~~~n~yPs~e~R~eIA~~L~~~g~LsE~qVqvWFQNRRAKeKRkkr~~~ 98 (266)
..|+||.|+.||..||++||..|.+ |+||+-+.|++||.-. +|+|++|.|||.||||||||++|-.+
T Consensus 109 i~KqrrQrthFtSqqlqele~tF~r--NrypdMstrEEIavwt----NlTE~rvrvwfknrrakwrkrErN~~ 175 (351)
T KOG0486|consen 109 ISKQRRQRTHFTSQQLQELEATFQR--NRYPDMSTREEIAVWT----NLTEARVRVWFKNRRAKWRKRERNQQ 175 (351)
T ss_pred hhhhhhhhhhhHHHHHHHHHHHHhh--ccCCccchhhHHHhhc----cccchhhhhhcccchhhhhhhhhhHH
Confidence 3488999999999999999999985 7999999999999998 79999999999999999999988776
No 23
>KOG3802 consensus Transcription factor OCT-1, contains POU and HOX domains [Transcription]
Probab=99.43 E-value=8.5e-14 Score=134.01 Aligned_cols=62 Identities=23% Similarity=0.340 Sum_probs=58.3
Q ss_pred CCCCCCCCCCHHHHHHHHHHHhhCCCCCCCHHHHHHHHHHHhhcCCCCCCceeeccccchhHHHHhhh
Q 046372 28 RPTCPRWTPTTDQIRILKELYYNNGVRSPTAEQIQKISARLRQYGKIEGKNVFYWFQNYKARERLKKK 95 (266)
Q Consensus 28 R~rR~Rt~FT~eQL~iLE~~F~~~~n~yPs~e~R~eIA~~L~~~g~LsE~qVqvWFQNRRAKeKRkkr 95 (266)
|+||+||.++.-.+.+||+.|. .++.|+.++|.+||++| +|+..+|+|||+|||.|+||-..
T Consensus 293 RkRKKRTSie~~vr~aLE~~F~--~npKPt~qEIt~iA~~L----~leKEVVRVWFCNRRQkeKR~~~ 354 (398)
T KOG3802|consen 293 RKRKKRTSIEVNVRGALEKHFL--KNPKPTSQEITHIAESL----QLEKEVVRVWFCNRRQKEKRITP 354 (398)
T ss_pred cccccccceeHHHHHHHHHHHH--hCCCCCHHHHHHHHHHh----ccccceEEEEeeccccccccCCC
Confidence 8899999999999999999998 57999999999999999 69999999999999999988655
No 24
>KOG0490 consensus Transcription factor, contains HOX domain [General function prediction only]
Probab=99.43 E-value=6.5e-14 Score=119.56 Aligned_cols=64 Identities=23% Similarity=0.339 Sum_probs=58.8
Q ss_pred cCCCCCCCCCCCHHHHHHHHHHHhhCCCCCCCHHHHHHHHHHHhhcCCCCCCceeeccccchhHHHHhhh
Q 046372 26 HCRPTCPRWTPTTDQIRILKELYYNNGVRSPTAEQIQKISARLRQYGKIEGKNVFYWFQNYKARERLKKK 95 (266)
Q Consensus 26 ~~R~rR~Rt~FT~eQL~iLE~~F~~~~n~yPs~e~R~eIA~~L~~~g~LsE~qVqvWFQNRRAKeKRkkr 95 (266)
..+++|.|++||..|+.+||+.|+ .++||+..-|+.+|..+ +++|.+|+|||||||+|++++++
T Consensus 57 ~~~~rr~rt~~~~~ql~~ler~f~--~~h~Pd~~~r~~la~~~----~~~e~rVqvwFqnrrak~r~~~~ 120 (235)
T KOG0490|consen 57 KFSKRCARCKFTISQLDELERAFE--KVHLPCFACRECLALLL----TGDEFRVQVWFQNRRAKDRKEER 120 (235)
T ss_pred hccccccCCCCCcCHHHHHHHhhc--CCCcCccchHHHHhhcC----CCCeeeeehhhhhhcHhhhhhhc
Confidence 456789999999999999999998 46999999999888888 79999999999999999999887
No 25
>KOG4577 consensus Transcription factor LIM3, contains LIM and HOX domains [Transcription]
Probab=99.42 E-value=9.1e-14 Score=130.57 Aligned_cols=65 Identities=31% Similarity=0.407 Sum_probs=52.3
Q ss_pred CCCCCCCCCCHHHHHHHHHHHhhCCCCCCCHHHHHHHHHHHhhcCCCCCCceeeccccchhHHHHhhhhcc
Q 046372 28 RPTCPRWTPTTDQIRILKELYYNNGVRSPTAEQIQKISARLRQYGKIEGKNVFYWFQNYKARERLKKKIEG 98 (266)
Q Consensus 28 R~rR~Rt~FT~eQL~iLE~~F~~~~n~yPs~e~R~eIA~~L~~~g~LsE~qVqvWFQNRRAKeKRkkr~~~ 98 (266)
..+|+||++|..||+.|+..|. ..+.|-+-.|+ +|+..+||+-++|||||||||||+||.|+...
T Consensus 166 ~nKRPRTTItAKqLETLK~AYn--~SpKPARHVRE----QLsseTGLDMRVVQVWFQNRRAKEKRLKKDAG 230 (383)
T KOG4577|consen 166 SNKRPRTTITAKQLETLKQAYN--TSPKPARHVRE----QLSSETGLDMRVVQVWFQNRRAKEKRLKKDAG 230 (383)
T ss_pred ccCCCcceeeHHHHHHHHHHhc--CCCchhHHHHH----HhhhccCcceeehhhhhhhhhHHHHhhhhhcc
Confidence 3468999999999999999995 34566555454 45555589999999999999999999887653
No 26
>KOG0847 consensus Transcription factor, contains HOX domain [Transcription]
Probab=99.28 E-value=8.3e-13 Score=120.52 Aligned_cols=67 Identities=24% Similarity=0.264 Sum_probs=59.7
Q ss_pred CCCCCCCCCCHHHHHHHHHHHhhCCCCCCCHHHHHHHHHHHhhcCCCCCCceeeccccchhHHHHhhhhccCC
Q 046372 28 RPTCPRWTPTTDQIRILKELYYNNGVRSPTAEQIQKISARLRQYGKIEGKNVFYWFQNYKARERLKKKIEGSS 100 (266)
Q Consensus 28 R~rR~Rt~FT~eQL~iLE~~F~~~~n~yPs~e~R~eIA~~L~~~g~LsE~qVqvWFQNRRAKeKRkkr~~~~~ 100 (266)
.++..|.+|+-.||..||+.|+ ..+||-.++|.++|..| ++.|.+|+|||||||.|||||......+
T Consensus 166 ~rk~srPTf~g~qi~~le~~fe--qtkylaG~~ra~lA~~l----gmteSqvkVWFQNRRTKWRKkhAaEmas 232 (288)
T KOG0847|consen 166 QRKQSRPTFTGHQIYQLERKFE--QTKYLAGADRAQLAQEL----NMTESQVKVWFQNRRTKWRKKHAAEMAS 232 (288)
T ss_pred cccccCCCccchhhhhhhhhhh--hhhcccchhHHHhhccc----cccHHHHHHHHhcchhhhhhhhccchhh
Confidence 4456889999999999999998 57899999999999999 6999999999999999999988776543
No 27
>KOG0849 consensus Transcription factor PRD and related proteins, contain PAX and HOX domains [Transcription]
Probab=99.17 E-value=4.4e-11 Score=113.39 Aligned_cols=67 Identities=18% Similarity=0.208 Sum_probs=59.6
Q ss_pred ccCCCCCCCCCCCHHHHHHHHHHHhhCCCCCCCHHHHHHHHHHHhhcCCCCCCceeeccccchhHHHHhhhhc
Q 046372 25 CHCRPTCPRWTPTTDQIRILKELYYNNGVRSPTAEQIQKISARLRQYGKIEGKNVFYWFQNYKARERLKKKIE 97 (266)
Q Consensus 25 ~~~R~rR~Rt~FT~eQL~iLE~~F~~~~n~yPs~e~R~eIA~~L~~~g~LsE~qVqvWFQNRRAKeKRkkr~~ 97 (266)
...+.+|.||+||++|+..||+.|++ ++||+...|++||.++ +|+|.+|+|||+|||+|+||..+..
T Consensus 172 ~~~~~rr~rtsft~~Q~~~le~~f~r--t~yP~i~~Re~La~~i----~l~e~riqvwf~nrra~~rr~~~~~ 238 (354)
T KOG0849|consen 172 LQRGGRRNRTSFSPSQLEALEECFQR--TPYPDIVGRETLAKET----GLPEPRVQVWFQNRRAKWRRQHRDC 238 (354)
T ss_pred ccccccccccccccchHHHHHHHhcC--CCCCchhhHHHHhhhc----cCCchHHHHHHhhhhhhhhhccccc
Confidence 34455677999999999999999984 6799999999999999 6999999999999999999988664
No 28
>KOG1168 consensus Transcription factor ACJ6/BRN-3, contains POU and HOX domains [Transcription]
Probab=98.90 E-value=7.8e-10 Score=104.45 Aligned_cols=64 Identities=20% Similarity=0.337 Sum_probs=58.4
Q ss_pred CCCCCCCCCCHHHHHHHHHHHhhCCCCCCCHHHHHHHHHHHhhcCCCCCCceeeccccchhHHHHhhhhc
Q 046372 28 RPTCPRWTPTTDQIRILKELYYNNGVRSPTAEQIQKISARLRQYGKIEGKNVFYWFQNYKARERLKKKIE 97 (266)
Q Consensus 28 R~rR~Rt~FT~eQL~iLE~~F~~~~n~yPs~e~R~eIA~~L~~~g~LsE~qVqvWFQNRRAKeKRkkr~~ 97 (266)
.++|+||.+-....+.||.+|. .++-|+.++|..||++| +|...+|+|||+|.|.|+||.++..
T Consensus 308 ekKRKRTSIAAPEKRsLEayFa--vQPRPS~EkIAaIAekL----DLKKNVVRVWFCNQRQKQKRm~~Sa 371 (385)
T KOG1168|consen 308 EKKRKRTSIAAPEKRSLEAYFA--VQPRPSGEKIAAIAEKL----DLKKNVVRVWFCNQRQKQKRMKRSA 371 (385)
T ss_pred ccccccccccCcccccHHHHhc--cCCCCchhHHHHHHHhh----hhhhceEEEEeeccHHHHHHhhhhh
Confidence 4578999999999999999997 57999999999999999 5999999999999999999977655
No 29
>KOG0490 consensus Transcription factor, contains HOX domain [General function prediction only]
Probab=98.35 E-value=3.4e-07 Score=78.33 Aligned_cols=65 Identities=25% Similarity=0.492 Sum_probs=57.8
Q ss_pred ccCCCCCCCCCCCHHHHHHHHHHHhhCCCCCCCHHHHHHHHHHHhhcCCCCCCceeeccccchhHHHHhhh
Q 046372 25 CHCRPTCPRWTPTTDQIRILKELYYNNGVRSPTAEQIQKISARLRQYGKIEGKNVFYWFQNYKARERLKKK 95 (266)
Q Consensus 25 ~~~R~rR~Rt~FT~eQL~iLE~~F~~~~n~yPs~e~R~eIA~~L~~~g~LsE~qVqvWFQNRRAKeKRkkr 95 (266)
...+.++.|+.++..|+..|+..|. ..++|+...+.+|+..+ ++++..|++||||+|++.|+.+.
T Consensus 149 ~~~~~~~~~~~~~~~~~~~~~~~~~--~~~~P~~~~~~~l~~~~----~~~~~~~q~~~~~~~~~~~~~~~ 213 (235)
T KOG0490|consen 149 SNKKPRRPRTTFTENQLEVLETVFR--ATPKPDADDREQLAEET----GLSERVIQVWFQNRRAKLRKHKR 213 (235)
T ss_pred CccccCCCccccccchhHhhhhccc--CCCCCchhhHHHHHHhc----CCChhhhhhhcccHHHHHHhhcc
Confidence 3346678999999999999999997 57899998888888888 69999999999999999998776
No 30
>KOG0775 consensus Transcription factor SIX and related HOX domain proteins [Transcription]
Probab=98.22 E-value=9.7e-07 Score=82.87 Aligned_cols=56 Identities=21% Similarity=0.393 Sum_probs=47.4
Q ss_pred CCCCCCCHHH---------HHHHHHHHhhCCCCCCCHHHHHHHHHHHhhcCCCCCCceeeccccchhHHHH
Q 046372 31 CPRWTPTTDQ---------IRILKELYYNNGVRSPTAEQIQKISARLRQYGKIEGKNVFYWFQNYKARERL 92 (266)
Q Consensus 31 R~Rt~FT~eQ---------L~iLE~~F~~~~n~yPs~e~R~eIA~~L~~~g~LsE~qVqvWFQNRRAKeKR 92 (266)
-+||...-|| ...|.+.|. .++||+++++.+||+.. ||+..||-+||.|||.|.|-
T Consensus 169 lPrTIWDGEet~yCFKekSR~~LrewY~--~~~YPsp~eKReLA~aT----gLt~tQVsNWFKNRRQRDRa 233 (304)
T KOG0775|consen 169 LPRTIWDGEETVYCFKEKSRSLLREWYL--QNPYPSPREKRELAEAT----GLTITQVSNWFKNRRQRDRA 233 (304)
T ss_pred CCCccccCceeeeehhHhhHHHHHHHHh--cCCCCChHHHHHHHHHh----CCchhhhhhhhhhhhhhhhh
Confidence 4677655554 578888885 68999999999999998 79999999999999999983
No 31
>KOG2252 consensus CCAAT displacement protein and related homeoproteins [Transcription]
Probab=98.16 E-value=9.9e-07 Score=88.60 Aligned_cols=59 Identities=27% Similarity=0.365 Sum_probs=53.9
Q ss_pred CCCCCCCCCCCHHHHHHHHHHHhhCCCCCCCHHHHHHHHHHHhhcCCCCCCceeeccccchhHHH
Q 046372 27 CRPTCPRWTPTTDQIRILKELYYNNGVRSPTAEQIQKISARLRQYGKIEGKNVFYWFQNYKARER 91 (266)
Q Consensus 27 ~R~rR~Rt~FT~eQL~iLE~~F~~~~n~yPs~e~R~eIA~~L~~~g~LsE~qVqvWFQNRRAKeK 91 (266)
-+++|+|++||..|++.|-.+|. .+++|+.+..+.|+.+| +|....|.+||.|-|.|.+
T Consensus 418 ~~~KKPRlVfTd~QkrTL~aiFk--e~~RPS~Emq~tIS~qL----~L~~sTV~NfFmNaRRRsl 476 (558)
T KOG2252|consen 418 LQTKKPRLVFTDIQKRTLQAIFK--ENKRPSREMQETISQQL----NLELSTVINFFMNARRRSL 476 (558)
T ss_pred ccCCCceeeecHHHHHHHHHHHh--cCCCCCHHHHHHHHHHh----CCcHHHHHHHHHhhhhhcc
Confidence 36678999999999999999997 57999999999999999 7999999999999997764
No 32
>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=98.01 E-value=1e-06 Score=60.47 Aligned_cols=34 Identities=21% Similarity=0.428 Sum_probs=28.5
Q ss_pred CCCCCCHHHHHHHHHHHhhcCCCCCCceeeccccchhH
Q 046372 52 GVRSPTAEQIQKISARLRQYGKIEGKNVFYWFQNYKAR 89 (266)
Q Consensus 52 ~n~yPs~e~R~eIA~~L~~~g~LsE~qVqvWFQNRRAK 89 (266)
.+|||+.+++++||.+. ||+.+||..||-|.|.|
T Consensus 7 ~nPYPs~~ek~~L~~~t----gls~~Qi~~WF~NaRrR 40 (40)
T PF05920_consen 7 HNPYPSKEEKEELAKQT----GLSRKQISNWFINARRR 40 (40)
T ss_dssp TSGS--HHHHHHHHHHH----TS-HHHHHHHHHHHHHH
T ss_pred CCCCCCHHHHHHHHHHc----CCCHHHHHHHHHHhHcc
Confidence 47999999999999998 79999999999999975
No 33
>KOG0774 consensus Transcription factor PBX and related HOX domain proteins [Transcription]
Probab=97.79 E-value=1.6e-05 Score=74.78 Aligned_cols=61 Identities=21% Similarity=0.360 Sum_probs=54.2
Q ss_pred CCCCCCCCHHHHHHHHHHHhhC-CCCCCCHHHHHHHHHHHhhcCCCCCCceeeccccchhHHHHhh
Q 046372 30 TCPRWTPTTDQIRILKELYYNN-GVRSPTAEQIQKISARLRQYGKIEGKNVFYWFQNYKARERLKK 94 (266)
Q Consensus 30 rR~Rt~FT~eQL~iLE~~F~~~-~n~yPs~e~R~eIA~~L~~~g~LsE~qVqvWFQNRRAKeKRkk 94 (266)
+|+|-.|++.-..+|.+.|..+ .++||+.+.+++||++. +|+-.||-.||-|+|.|-||--
T Consensus 189 rRKRRNFsK~aTeiLneyF~~h~~nPYPSee~K~eLAkqC----nItvsQvsnwfgnkrIrykK~~ 250 (334)
T KOG0774|consen 189 RRKRRNFSKQATEILNEYFYSHLSNPYPSEEAKEELAKQC----NITVSQVSNWFGNKRIRYKKNM 250 (334)
T ss_pred HHhhcccchhHHHHHHHHHHHhcCCCCCcHHHHHHHHHHc----Cceehhhccccccceeehhhhh
Confidence 5788899999999999999732 47999999999999998 7999999999999999998743
No 34
>KOG1146 consensus Homeobox protein [General function prediction only]
Probab=97.75 E-value=2e-05 Score=85.67 Aligned_cols=66 Identities=21% Similarity=0.335 Sum_probs=57.0
Q ss_pred cCCCCCCCCCCCHHHHHHHHHHHhhCCCCCCCHHHHHHHHHHHhhcCCCCCCceeeccccchhHHHHhhhhc
Q 046372 26 HCRPTCPRWTPTTDQIRILKELYYNNGVRSPTAEQIQKISARLRQYGKIEGKNVFYWFQNYKARERLKKKIE 97 (266)
Q Consensus 26 ~~R~rR~Rt~FT~eQL~iLE~~F~~~~n~yPs~e~R~eIA~~L~~~g~LsE~qVqvWFQNRRAKeKRkkr~~ 97 (266)
.+-+++.|+.++..||++|..+|. ...||.-++.+.|-..+ +|+.++|.|||||-|+|.|+.+-..
T Consensus 900 ~~~r~a~~~~~~d~qlk~i~~~~~--~q~~~~~~~~E~l~~~~----~~~~~~i~vw~qna~~~s~k~~~n~ 965 (1406)
T KOG1146|consen 900 GMGRRAYRTQESDLQLKIIKACYE--AQRTPTMQECEVLEEPI----GLPKRVIQVWFQNARAKSKKAKLNG 965 (1406)
T ss_pred hhhhhhhccchhHHHHHHHHHHHh--hccCChHHHHHhhcccc----cCCcchhHHhhhhhhhhhhhhhhcc
Confidence 344578999999999999999997 56899998888888887 6999999999999999999876643
No 35
>KOG0773 consensus Transcription factor MEIS1 and related HOX domain proteins [Transcription]
Probab=95.99 E-value=0.0051 Score=57.32 Aligned_cols=63 Identities=14% Similarity=0.220 Sum_probs=48.5
Q ss_pred CCCCCCCCCHHHHHHHHHHHhhCC-CCCCCHHHHHHHHHHHhhcCCCCCCceeeccccchhHHHHhhh
Q 046372 29 PTCPRWTPTTDQIRILKELYYNNG-VRSPTAEQIQKISARLRQYGKIEGKNVFYWFQNYKARERLKKK 95 (266)
Q Consensus 29 ~rR~Rt~FT~eQL~iLE~~F~~~~-n~yPs~e~R~eIA~~L~~~g~LsE~qVqvWFQNRRAKeKRkkr 95 (266)
..|++..|-.+...+|+.-...+- .+||+..++..||.+. ||+-.||.+||-|.|-|.++--.
T Consensus 239 ~~r~~~~lP~~a~~ilr~Wl~~h~~~PYPse~~K~~La~~T----GLs~~Qv~NWFINaR~R~w~p~~ 302 (342)
T KOG0773|consen 239 KWRPQRGLPKEAVSILRAWLFEHLLHPYPSDDEKLMLAKQT----GLSRPQVSNWFINARVRLWKPMI 302 (342)
T ss_pred CCCCCCCCCHHHHHHHHHHHHHhccCCCCcchhccccchhc----CCCcccCCchhhhcccccCCchH
Confidence 456677888888888886544322 4899998887777766 79999999999999988775443
No 36
>KOG3623 consensus Homeobox transcription factor SIP1 [Transcription]
Probab=94.20 E-value=0.026 Score=59.68 Aligned_cols=52 Identities=23% Similarity=0.333 Sum_probs=46.6
Q ss_pred HHHHHHHHhhCCCCCCCHHHHHHHHHHHhhcCCCCCCceeeccccchhHHHHhhhhcc
Q 046372 41 IRILKELYYNNGVRSPTAEQIQKISARLRQYGKIEGKNVFYWFQNYKARERLKKKIEG 98 (266)
Q Consensus 41 L~iLE~~F~~~~n~yPs~e~R~eIA~~L~~~g~LsE~qVqvWFQNRRAKeKRkkr~~~ 98 (266)
+.+|+..|. .+..|+.++...||..+ +|+-+.|++||+++|+++.+-.|.-.
T Consensus 568 ~sllkayya--ln~~ps~eelskia~qv----glp~~vvk~wfE~~~a~e~sv~rsps 619 (1007)
T KOG3623|consen 568 TSLLKAYYA--LNGLPSEEELSKIAQQV----GLPFAVVKAWFEDEEAEEMSVERSPS 619 (1007)
T ss_pred HHHHHHHHH--hcCCCCHHHHHHHHHHh----cccHHHHHHHHHhhhhhhhhhccCcc
Confidence 788999997 47899999999999999 69999999999999999998887654
No 37
>PF11569 Homez: Homeodomain leucine-zipper encoding, Homez; PDB: 2YS9_A.
Probab=86.32 E-value=0.12 Score=38.59 Aligned_cols=42 Identities=17% Similarity=0.399 Sum_probs=28.2
Q ss_pred HHHHHHHHhhCCCCCCCHHHHHHHHHHHhhcCCCCCCceeeccccchh
Q 046372 41 IRILKELYYNNGVRSPTAEQIQKISARLRQYGKIEGKNVFYWFQNYKA 88 (266)
Q Consensus 41 L~iLE~~F~~~~n~yPs~e~R~eIA~~L~~~g~LsE~qVqvWFQNRRA 88 (266)
++-|++.|.. .+.+...+...|..+- +|+..||+.||--|+.
T Consensus 10 ~~pL~~Yy~~--h~~L~E~DL~~L~~kS----~ms~qqVr~WFa~~~~ 51 (56)
T PF11569_consen 10 IQPLEDYYLK--HKQLQEEDLDELCDKS----RMSYQQVRDWFAERMQ 51 (56)
T ss_dssp -HHHHHHHHH--T----TTHHHHHHHHT----T--HHHHHHHHHHHS-
T ss_pred hHHHHHHHHH--cCCccHhhHHHHHHHH----CCCHHHHHHHHHHhcc
Confidence 5669999984 5788888888888887 6999999999976643
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=83.62 E-value=1.1 Score=32.05 Aligned_cols=47 Identities=13% Similarity=0.085 Sum_probs=33.3
Q ss_pred CCCCCCCCHHHHHHHHHHHhhCCCCCCCHHHHHHHHHHHhhcCCCCCCceeeccccch
Q 046372 30 TCPRWTPTTDQIRILKELYYNNGVRSPTAEQIQKISARLRQYGKIEGKNVFYWFQNYK 87 (266)
Q Consensus 30 rR~Rt~FT~eQL~iLE~~F~~~~n~yPs~e~R~eIA~~L~~~g~LsE~qVqvWFQNRR 87 (266)
+|+|..+|-+|...+=+.++. + + ...+||.++ ||+..+|..|..||.
T Consensus 1 krkR~~LTl~eK~~iI~~~e~-g---~---s~~~ia~~f----gv~~sTv~~I~K~k~ 47 (53)
T PF04218_consen 1 KRKRKSLTLEEKLEIIKRLEE-G---E---SKRDIAREF----GVSRSTVSTILKNKD 47 (53)
T ss_dssp SSSSSS--HHHHHHHHHHHHC-T---T----HHHHHHHH----T--CCHHHHHHHCHH
T ss_pred CCCCccCCHHHHHHHHHHHHc-C---C---CHHHHHHHh----CCCHHHHHHHHHhHH
Confidence 478999999998877778873 3 2 345789999 699999999998864
No 39
>KOG3755 consensus SATB1 matrix attachment region binding protein [Transcription]
Probab=75.12 E-value=0.69 Score=48.47 Aligned_cols=70 Identities=20% Similarity=0.180 Sum_probs=49.6
Q ss_pred CcccCCCCCCCCCCCHHHHHHHHHHHhhCCCCCCCHHHHHHHHHHH-----hhcCCCCCCceeeccccchhHHHHhhh
Q 046372 23 NNCHCRPTCPRWTPTTDQIRILKELYYNNGVRSPTAEQIQKISARL-----RQYGKIEGKNVFYWFQNYKARERLKKK 95 (266)
Q Consensus 23 g~~~~R~rR~Rt~FT~eQL~iLE~~F~~~~n~yPs~e~R~eIA~~L-----~~~g~LsE~qVqvWFQNRRAKeKRkkr 95 (266)
...+.-+||+|.+|=.+|...+..... .+++.+.--.+.+-.+++ .+ +.++++|+.||.|||+++||.+-
T Consensus 685 Sa~~~~pk~~~~k~f~~~~~ev~~~w~-~k~~s~s~~~v~eYkee~~~~~~~e--~~~~kn~~~~fk~~~ee~~~~k~ 759 (769)
T KOG3755|consen 685 SAQLDLPKKTIIKFFQNQRYEVKHHWK-LKTRSGSWVDVAEYKEEELLMPYEE--KFESKNVQFWFKVRREEEKRLKM 759 (769)
T ss_pred hhhhcccHHHHHHhhhcceeecchhhe-ecccCchhHHHHHhhHHhhcchhhh--hhhhcchHHHHHHHHHHHhhhhc
Confidence 456667788888888888888876653 356677665554444333 32 34778999999999999988663
No 40
>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=71.98 E-value=3.8 Score=29.88 Aligned_cols=40 Identities=25% Similarity=0.268 Sum_probs=31.1
Q ss_pred CCHHHHHHHHHHHhhCCCCCCCHHHHHHHHHHHhhcCCCCCCce
Q 046372 36 PTTDQIRILKELYYNNGVRSPTAEQIQKISARLRQYGKIEGKNV 79 (266)
Q Consensus 36 FT~eQL~iLE~~F~~~~n~yPs~e~R~eIA~~L~~~g~LsE~qV 79 (266)
+|+.|.++|...|+...--+|-.....+||++| ||+..-|
T Consensus 1 LT~~Q~e~L~~A~~~GYfd~PR~~tl~elA~~l----gis~st~ 40 (53)
T PF04967_consen 1 LTDRQREILKAAYELGYFDVPRRITLEELAEEL----GISKSTV 40 (53)
T ss_pred CCHHHHHHHHHHHHcCCCCCCCcCCHHHHHHHh----CCCHHHH
Confidence 589999999999985444456667778899999 6887654
No 41
>KOG1146 consensus Homeobox protein [General function prediction only]
Probab=70.87 E-value=5.6 Score=44.98 Aligned_cols=67 Identities=22% Similarity=0.285 Sum_probs=55.5
Q ss_pred CCcccCCCCCCCCCCCHHHHHHHHHHHhhCCCCCCCHHHHHHHHHHHhhcCCCCCCceeeccccchhHHHHhh
Q 046372 22 GNNCHCRPTCPRWTPTTDQIRILKELYYNNGVRSPTAEQIQKISARLRQYGKIEGKNVFYWFQNYKARERLKK 94 (266)
Q Consensus 22 ~g~~~~R~rR~Rt~FT~eQL~iLE~~F~~~~n~yPs~e~R~eIA~~L~~~g~LsE~qVqvWFQNRRAKeKRkk 94 (266)
|.+.-=|.++.|+..=++++.+|=+.|. .+-.|+...+.-|.... ..+.+++++||+|-|.|.++..
T Consensus 698 ~~~~~~~~~~~~~~~~~~aa~~l~~a~~--~~~sps~k~~~civcd~----~st~~l~~l~~h~~~~rs~ke~ 764 (1406)
T KOG1146|consen 698 GESLSPRDKLLRLTILPEAAMILGRAYM--QDNSPSLKVFDCIVCDV----FSTDRLDQLWFHNTRERSRKEQ 764 (1406)
T ss_pred CCCCCcccccCcccccHHHHhhhhhccc--CCCCHHHHHHHHhhhhh----hhhhhHHHHhhcchhhhhhhhc
Confidence 4677778888899888899999999997 46788887776666665 4788889999999999998876
No 42
>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=64.30 E-value=2.9 Score=26.73 Aligned_cols=44 Identities=11% Similarity=0.100 Sum_probs=31.6
Q ss_pred CCCHHHHHHHHHHHhhCCCCCCCHHHHHHHHHHHhhcCCCCCCceeeccccchhH
Q 046372 35 TPTTDQIRILKELYYNNGVRSPTAEQIQKISARLRQYGKIEGKNVFYWFQNYKAR 89 (266)
Q Consensus 35 ~FT~eQL~iLE~~F~~~~n~yPs~e~R~eIA~~L~~~g~LsE~qVqvWFQNRRAK 89 (266)
.+++++..+|+..|. .+ +. ..+||..| +++...|+.|...-|.+
T Consensus 10 ~l~~~~~~~~~~~~~-~~--~~----~~~ia~~~----~~s~~~i~~~~~~~~~~ 53 (55)
T cd06171 10 KLPEREREVILLRFG-EG--LS----YEEIAEIL----GISRSTVRQRLHRALKK 53 (55)
T ss_pred hCCHHHHHHHHHHHh-cC--CC----HHHHHHHH----CcCHHHHHHHHHHHHHH
Confidence 358889999998874 12 22 34689999 69999998887654443
No 43
>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=62.86 E-value=2.7 Score=30.37 Aligned_cols=43 Identities=12% Similarity=0.220 Sum_probs=26.5
Q ss_pred CCCCCCCHHHHHHHHHHHhhCCCCCCCHHHHHHHHHHHhhcCCCCCCceeecc
Q 046372 31 CPRWTPTTDQIRILKELYYNNGVRSPTAEQIQKISARLRQYGKIEGKNVFYWF 83 (266)
Q Consensus 31 R~Rt~FT~eQL~iLE~~F~~~~n~yPs~e~R~eIA~~L~~~g~LsE~qVqvWF 83 (266)
++|..||+++...+=..+... ...+.+||.++ ||+...|..|-
T Consensus 2 ~~r~~ys~e~K~~~v~~~~~~------g~sv~~va~~~----gi~~~~l~~W~ 44 (76)
T PF01527_consen 2 RKRRRYSPEFKLQAVREYLES------GESVSEVAREY----GISPSTLYNWR 44 (76)
T ss_dssp -SS----HHHHHHHHHHHHHH------HCHHHHHHHHH----TS-HHHHHHHH
T ss_pred CCCCCCCHHHHHHHHHHHHHC------CCceEeeeccc----ccccccccHHH
Confidence 467778999877666555211 35566899999 69999999883
No 44
>PRK09646 RNA polymerase sigma factor SigK; Reviewed
Probab=62.04 E-value=8.2 Score=32.71 Aligned_cols=43 Identities=21% Similarity=0.210 Sum_probs=28.5
Q ss_pred CCHHHHHHHHHHHhhCCCCCCCHHHHHHHHHHHhhcCCCCCCceeeccccchhHHH
Q 046372 36 PTTDQIRILKELYYNNGVRSPTAEQIQKISARLRQYGKIEGKNVFYWFQNYKARER 91 (266)
Q Consensus 36 FT~eQL~iLE~~F~~~~n~yPs~e~R~eIA~~L~~~g~LsE~qVqvWFQNRRAKeK 91 (266)
+++.|..+|...|.. + + ..++||+.| ||++..|+++. +|||.+
T Consensus 143 L~~~~r~vl~l~~~~-~--~----s~~EIA~~L----gis~~tVk~~l--~ra~~~ 185 (194)
T PRK09646 143 LTDTQRESVTLAYYG-G--L----TYREVAERL----AVPLGTVKTRM--RDGLIR 185 (194)
T ss_pred CCHHHHHHHHHHHHc-C--C----CHHHHHHHh----CCChHhHHHHH--HHHHHH
Confidence 566677777665531 2 2 234789999 69999998887 444444
No 45
>KOG0048 consensus Transcription factor, Myb superfamily [Transcription]
Probab=60.19 E-value=11 Score=34.12 Aligned_cols=55 Identities=16% Similarity=0.061 Sum_probs=40.7
Q ss_pred CCCCCCCHHHHHHHHHHHhhCCCCCCCHHHHHHHHHHHhhcCCCCCCceeeccccchhHHHHhhhhc
Q 046372 31 CPRWTPTTDQIRILKELYYNNGVRSPTAEQIQKISARLRQYGKIEGKNVFYWFQNYKARERLKKKIE 97 (266)
Q Consensus 31 R~Rt~FT~eQL~iLE~~F~~~~n~yPs~e~R~eIA~~L~~~g~LsE~qVqvWFQNRRAKeKRkkr~~ 97 (266)
-+|-.||+|.-.+|-++...-+|+ -..||..|. |=++..||++. ..+.|||.+..
T Consensus 60 ikrg~fT~eEe~~Ii~lH~~~GNr------Ws~IA~~LP---GRTDNeIKN~W---nt~lkkkl~~~ 114 (238)
T KOG0048|consen 60 LKRGNFSDEEEDLIIKLHALLGNR------WSLIAGRLP---GRTDNEVKNHW---NTHLKKKLLKM 114 (238)
T ss_pred ccCCCCCHHHHHHHHHHHHHHCcH------HHHHHhhCC---CcCHHHHHHHH---HHHHHHHHHHc
Confidence 456689999999988888765654 567999996 78888899443 56666666555
No 46
>PRK03975 tfx putative transcriptional regulator; Provisional
Probab=54.51 E-value=8 Score=33.28 Aligned_cols=47 Identities=21% Similarity=0.051 Sum_probs=35.7
Q ss_pred CCCCHHHHHHHHHHHhhCCCCCCCHHHHHHHHHHHhhcCCCCCCceeeccccchhHHHH
Q 046372 34 WTPTTDQIRILKELYYNNGVRSPTAEQIQKISARLRQYGKIEGKNVFYWFQNYKARERL 92 (266)
Q Consensus 34 t~FT~eQL~iLE~~F~~~~n~yPs~e~R~eIA~~L~~~g~LsE~qVqvWFQNRRAKeKR 92 (266)
..+|+.|+++|+..+. + +. .++||+.| +++...|..|-+..|.|.|+
T Consensus 5 ~~Lt~rqreVL~lr~~--G--lT----q~EIAe~L----GiS~~tVs~ie~ra~kkLr~ 51 (141)
T PRK03975 5 SFLTERQIEVLRLRER--G--LT----QQEIADIL----GTSRANVSSIEKRARENIEK 51 (141)
T ss_pred cCCCHHHHHHHHHHHc--C--CC----HHHHHHHH----CCCHHHHHHHHHHHHHHHHH
Confidence 5689999999998542 2 22 24799999 69999999999876666554
No 47
>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=53.83 E-value=20 Score=20.13 Aligned_cols=38 Identities=18% Similarity=0.357 Sum_probs=25.8
Q ss_pred CCCHHHHHHHHHHHhhCCCCCCCHHHHHHHHHHHhhcCCCCCCceeecc
Q 046372 35 TPTTDQIRILKELYYNNGVRSPTAEQIQKISARLRQYGKIEGKNVFYWF 83 (266)
Q Consensus 35 ~FT~eQL~iLE~~F~~~~n~yPs~e~R~eIA~~L~~~g~LsE~qVqvWF 83 (266)
.++.++...+...|.. .. ...+||+.+ +++...|..|.
T Consensus 5 ~~~~~~~~~i~~~~~~---~~----s~~~ia~~~----~is~~tv~~~~ 42 (42)
T cd00569 5 KLTPEQIEEARRLLAA---GE----SVAEIARRL----GVSRSTLYRYL 42 (42)
T ss_pred cCCHHHHHHHHHHHHc---CC----CHHHHHHHH----CCCHHHHHHhC
Confidence 3677888777777752 22 234688888 68888787763
No 48
>COG3413 Predicted DNA binding protein [General function prediction only]
Probab=52.94 E-value=17 Score=31.92 Aligned_cols=50 Identities=16% Similarity=0.180 Sum_probs=36.0
Q ss_pred CCCHHHHHHHHHHHhhCCCCCCCHHHHHHHHHHHhhcCCCCCCceeeccccchhHH
Q 046372 35 TPTTDQIRILKELYYNNGVRSPTAEQIQKISARLRQYGKIEGKNVFYWFQNYKARE 90 (266)
Q Consensus 35 ~FT~eQL~iLE~~F~~~~n~yPs~e~R~eIA~~L~~~g~LsE~qVqvWFQNRRAKe 90 (266)
.+|+.|+++|...|....--||-.....+||++| ||+..-+ |..=|||-.
T Consensus 155 ~LTdrQ~~vL~~A~~~GYFd~PR~~~l~dLA~~l----GISkst~--~ehLRrAe~ 204 (215)
T COG3413 155 DLTDRQLEVLRLAYKMGYFDYPRRVSLKDLAKEL----GISKSTL--SEHLRRAER 204 (215)
T ss_pred cCCHHHHHHHHHHHHcCCCCCCccCCHHHHHHHh----CCCHHHH--HHHHHHHHH
Confidence 6999999999999975444466667778889998 6887654 333344433
No 49
>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=51.57 E-value=9.6 Score=25.93 Aligned_cols=39 Identities=15% Similarity=0.292 Sum_probs=28.2
Q ss_pred CCCHHHHHHHHHHHhhCCCCCCCHHHHHHHHHHHhhcCCCCCCceeeccc
Q 046372 35 TPTTDQIRILKELYYNNGVRSPTAEQIQKISARLRQYGKIEGKNVFYWFQ 84 (266)
Q Consensus 35 ~FT~eQL~iLE~~F~~~~n~yPs~e~R~eIA~~L~~~g~LsE~qVqvWFQ 84 (266)
.++++|..+|...|.. ..+ -.+||+.| |++...|+.+..
T Consensus 4 ~L~~~er~vi~~~y~~---~~t----~~eIa~~l----g~s~~~V~~~~~ 42 (50)
T PF04545_consen 4 QLPPREREVIRLRYFE---GLT----LEEIAERL----GISRSTVRRILK 42 (50)
T ss_dssp TS-HHHHHHHHHHHTS---T-S----HHHHHHHH----TSCHHHHHHHHH
T ss_pred hCCHHHHHHHHHHhcC---CCC----HHHHHHHH----CCcHHHHHHHHH
Confidence 4689999999999952 222 34789999 699998876543
No 50
>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=46.49 E-value=7.7 Score=27.21 Aligned_cols=44 Identities=20% Similarity=0.210 Sum_probs=32.2
Q ss_pred CCCHHHHHHHHHHHhhCCCCCCCHHHHHHHHHHHhhcCCCCCCceeeccccchhHH
Q 046372 35 TPTTDQIRILKELYYNNGVRSPTAEQIQKISARLRQYGKIEGKNVFYWFQNYKARE 90 (266)
Q Consensus 35 ~FT~eQL~iLE~~F~~~~n~yPs~e~R~eIA~~L~~~g~LsE~qVqvWFQNRRAKe 90 (266)
.||+.++++|+-+.. + + ...+||+.| +|+++.|+.+..+=+.|.
T Consensus 3 ~LT~~E~~vl~~l~~--G--~----~~~eIA~~l----~is~~tV~~~~~~i~~Kl 46 (58)
T PF00196_consen 3 SLTERELEVLRLLAQ--G--M----SNKEIAEEL----GISEKTVKSHRRRIMKKL 46 (58)
T ss_dssp SS-HHHHHHHHHHHT--T--S-----HHHHHHHH----TSHHHHHHHHHHHHHHHH
T ss_pred ccCHHHHHHHHHHHh--c--C----CcchhHHhc----CcchhhHHHHHHHHHHHh
Confidence 589999999998875 3 2 334799999 699999998766554443
No 51
>smart00027 EH Eps15 homology domain. Pair of EF hand motifs that recognise proteins containing Asn-Pro-Phe (NPF) sequences.
Probab=46.46 E-value=21 Score=27.28 Aligned_cols=46 Identities=9% Similarity=0.112 Sum_probs=29.8
Q ss_pred CCCCHHHHHHHHHHHhhC---CCCCCCHHHHHHHHHHHhhcCCCCCCceeecc
Q 046372 34 WTPTTDQIRILKELYYNN---GVRSPTAEQIQKISARLRQYGKIEGKNVFYWF 83 (266)
Q Consensus 34 t~FT~eQL~iLE~~F~~~---~n~yPs~e~R~eIA~~L~~~g~LsE~qVqvWF 83 (266)
|-+|.+|+..|.+.|..- +..+.+.++ |...|... ++++..|..+|
T Consensus 2 ~~ls~~~~~~l~~~F~~~D~d~~G~Is~~e---l~~~l~~~-~~~~~ev~~i~ 50 (96)
T smart00027 2 WAISPEDKAKYEQIFRSLDKNQDGTVTGAQ---AKPILLKS-GLPQTLLAKIW 50 (96)
T ss_pred CCCCHHHHHHHHHHHHHhCCCCCCeEeHHH---HHHHHHHc-CCCHHHHHHHH
Confidence 678999999999999752 223445554 44444432 57776666555
No 52
>PRK06759 RNA polymerase factor sigma-70; Validated
Probab=43.92 E-value=12 Score=29.86 Aligned_cols=46 Identities=13% Similarity=0.221 Sum_probs=29.7
Q ss_pred CCCHHHHHHHHHHHhhCCCCCCCHHHHHHHHHHHhhcCCCCCCceeeccccchhHHH
Q 046372 35 TPTTDQIRILKELYYNNGVRSPTAEQIQKISARLRQYGKIEGKNVFYWFQNYKARER 91 (266)
Q Consensus 35 ~FT~eQL~iLE~~F~~~~n~yPs~e~R~eIA~~L~~~g~LsE~qVqvWFQNRRAKeK 91 (266)
.+++.|..+|...|.. + . ...+||+.| |+++..|++|...=|.|.|
T Consensus 106 ~L~~~~r~ii~l~~~~-~--~----s~~EIA~~l----~is~~tV~~~~~ra~~~Lr 151 (154)
T PRK06759 106 VLDEKEKYIIFERFFV-G--K----TMGEIALET----EMTYYQVRWIYRQALEKMR 151 (154)
T ss_pred hCCHHHHHHHHHHHhc-C--C----CHHHHHHHH----CCCHHHHHHHHHHHHHHHh
Confidence 3466677777666542 2 2 235789999 6999999988754443333
No 53
>smart00421 HTH_LUXR helix_turn_helix, Lux Regulon. lux regulon (activates the bioluminescence operon
Probab=42.54 E-value=13 Score=24.22 Aligned_cols=38 Identities=26% Similarity=0.274 Sum_probs=28.2
Q ss_pred CCCHHHHHHHHHHHhhCCCCCCCHHHHHHHHHHHhhcCCCCCCceeeccc
Q 046372 35 TPTTDQIRILKELYYNNGVRSPTAEQIQKISARLRQYGKIEGKNVFYWFQ 84 (266)
Q Consensus 35 ~FT~eQL~iLE~~F~~~~n~yPs~e~R~eIA~~L~~~g~LsE~qVqvWFQ 84 (266)
.+|+.+.++++..+. + . ...+||..| +|+...|+.|.+
T Consensus 3 ~l~~~e~~i~~~~~~--g--~----s~~eia~~l----~is~~tv~~~~~ 40 (58)
T smart00421 3 SLTPREREVLRLLAE--G--L----TNKEIAERL----GISEKTVKTHLS 40 (58)
T ss_pred CCCHHHHHHHHHHHc--C--C----CHHHHHHHH----CCCHHHHHHHHH
Confidence 468899999977543 3 2 235789999 699999987765
No 54
>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=41.79 E-value=16 Score=24.01 Aligned_cols=37 Identities=24% Similarity=0.233 Sum_probs=26.3
Q ss_pred CCHHHHHHHHHHHhhCCCCCCCHHHHHHHHHHHhhcCCCCCCceeeccc
Q 046372 36 PTTDQIRILKELYYNNGVRSPTAEQIQKISARLRQYGKIEGKNVFYWFQ 84 (266)
Q Consensus 36 FT~eQL~iLE~~F~~~~n~yPs~e~R~eIA~~L~~~g~LsE~qVqvWFQ 84 (266)
+++.|..++...+. + . ...+||+.| +|+...|+.|..
T Consensus 1 l~~~e~~i~~~~~~--~--~----s~~eia~~l----~~s~~tv~~~~~ 37 (57)
T cd06170 1 LTPREREVLRLLAE--G--K----TNKEIADIL----GISEKTVKTHLR 37 (57)
T ss_pred CCHHHHHHHHHHHc--C--C----CHHHHHHHH----CCCHHHHHHHHH
Confidence 36778888876542 2 2 335789998 699999988764
No 55
>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=41.03 E-value=20 Score=27.24 Aligned_cols=46 Identities=15% Similarity=0.123 Sum_probs=31.2
Q ss_pred CCCHHHHHHHHHHHhhCCCCCCCHHHHHHHHHHHhhcCCCCCCceeeccccchhHHH
Q 046372 35 TPTTDQIRILKELYYNNGVRSPTAEQIQKISARLRQYGKIEGKNVFYWFQNYKARER 91 (266)
Q Consensus 35 ~FT~eQL~iLE~~F~~~~n~yPs~e~R~eIA~~L~~~g~LsE~qVqvWFQNRRAKeK 91 (266)
.+++.|..+|...|.. .++ ..+||+.| |+++..|..+.+.=|.|.|
T Consensus 110 ~L~~~~~~ii~~~~~~---g~s----~~eIA~~l----~~s~~~v~~~~~~~~~kl~ 155 (158)
T TIGR02937 110 KLPEREREVLVLRYLE---GLS----YKEIAEIL----GISVGTVKRRLKRARKKLR 155 (158)
T ss_pred hCCHHHHHHHhhHHhc---CCC----HHHHHHHH----CCCHHHHHHHHHHHHHHHH
Confidence 4578888888776531 233 34689999 6999999987765444443
No 56
>PF13873 Myb_DNA-bind_5: Myb/SANT-like DNA-binding domain
Probab=40.87 E-value=23 Score=26.00 Aligned_cols=61 Identities=18% Similarity=0.157 Sum_probs=36.7
Q ss_pred CCCCHHHHHHHHHHHhhCC----CCCCCHH---HH----HHHHHHHhhcCCC--CCCceeeccccchhHHHHhh
Q 046372 34 WTPTTDQIRILKELYYNNG----VRSPTAE---QI----QKISARLRQYGKI--EGKNVFYWFQNYKARERLKK 94 (266)
Q Consensus 34 t~FT~eQL~iLE~~F~~~~----n~yPs~e---~R----~eIA~~L~~~g~L--sE~qVqvWFQNRRAKeKRkk 94 (266)
-.||.+|+.+|-+++.... ++..+.. .+ ++||..|...++. +..+|+..+.|-+.+.|++.
T Consensus 3 ~~fs~~E~~~Lv~~v~~~~~il~~k~~~~~~~~~k~~~W~~I~~~lN~~~~~~Rs~~~lkkkW~nlk~~~Kk~~ 76 (78)
T PF13873_consen 3 PNFSEEEKEILVELVEKHKDILENKFSDSVSNKEKRKAWEEIAEELNALGPGKRSWKQLKKKWKNLKSKAKKKL 76 (78)
T ss_pred CCCCHHHHHHHHHHHHHhHHHHhcccccHHHHHHHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHHHHHHHh
Confidence 3579999999998876310 1111111 11 4688888766553 22346667777777777653
No 57
>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=40.41 E-value=16 Score=24.94 Aligned_cols=39 Identities=21% Similarity=0.229 Sum_probs=26.6
Q ss_pred CCHHHHHHHHHHHhhCCCCCCCHHHHHHHHHHHhhcCCCCCCceeecccc
Q 046372 36 PTTDQIRILKELYYNNGVRSPTAEQIQKISARLRQYGKIEGKNVFYWFQN 85 (266)
Q Consensus 36 FT~eQL~iLE~~F~~~~n~yPs~e~R~eIA~~L~~~g~LsE~qVqvWFQN 85 (266)
+++.+..++...|.. + ++ ..+||+.| ++++..|++|.+.
T Consensus 11 L~~~~r~i~~l~~~~-g--~s----~~eIa~~l----~~s~~~v~~~l~r 49 (54)
T PF08281_consen 11 LPERQREIFLLRYFQ-G--MS----YAEIAEIL----GISESTVKRRLRR 49 (54)
T ss_dssp S-HHHHHHHHHHHTS----------HHHHHHHC----TS-HHHHHHHHHH
T ss_pred CCHHHHHHHHHHHHH-C--cC----HHHHHHHH----CcCHHHHHHHHHH
Confidence 577888888887752 2 33 34789999 6999999998753
No 58
>cd02413 40S_S3_KH K homology RNA-binding (KH) domain of the eukaryotic 40S small ribosomal subunit protein S3. S3 is part of the head region of the 40S ribosomal subunit and is believed to interact with mRNA as it threads its way from the latch into the channel. The KH motif is a beta-alpha-alpha-beta-beta unit that folds into an alpha-beta structure with a three stranded beta-sheet interupted by two contiguous helices. In general, KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.
Probab=40.21 E-value=26 Score=27.20 Aligned_cols=26 Identities=8% Similarity=0.167 Sum_probs=22.9
Q ss_pred HHHHHHHHHHhhcCCCCCCceeeccc
Q 046372 59 EQIQKISARLRQYGKIEGKNVFYWFQ 84 (266)
Q Consensus 59 e~R~eIA~~L~~~g~LsE~qVqvWFQ 84 (266)
..+.+|...|.+..+|++.+|.+|+.
T Consensus 50 ~~i~~L~~~L~k~~~~~~~~i~v~~~ 75 (81)
T cd02413 50 RRIRELTSLVQKRFNFPEGSVELYAE 75 (81)
T ss_pred hhHHHHHHHHHHHhCCCCCeEEEEEE
Confidence 56778999999888999999999985
No 59
>PRK09652 RNA polymerase sigma factor RpoE; Provisional
Probab=39.30 E-value=22 Score=28.72 Aligned_cols=46 Identities=15% Similarity=0.087 Sum_probs=31.7
Q ss_pred CCCHHHHHHHHHHHhhCCCCCCCHHHHHHHHHHHhhcCCCCCCceeeccccchhHHHHh
Q 046372 35 TPTTDQIRILKELYYNNGVRSPTAEQIQKISARLRQYGKIEGKNVFYWFQNYKARERLK 93 (266)
Q Consensus 35 ~FT~eQL~iLE~~F~~~~n~yPs~e~R~eIA~~L~~~g~LsE~qVqvWFQNRRAKeKRk 93 (266)
.+++.+..+|...|.. + ++ ..+||..| ||++..|+.|.. |||.|=+
T Consensus 128 ~L~~~~r~vl~l~~~~-~--~s----~~eIA~~l----gis~~tV~~~l~--ra~~~Lr 173 (182)
T PRK09652 128 SLPEELRTAITLREIE-G--LS----YEEIAEIM----GCPIGTVRSRIF--RAREALR 173 (182)
T ss_pred hCCHHHHHHHHHHHHc-C--CC----HHHHHHHH----CCCHHHHHHHHH--HHHHHHH
Confidence 4677888888776541 2 32 23689999 699999999887 4554433
No 60
>PRK12519 RNA polymerase sigma factor; Provisional
Probab=38.95 E-value=16 Score=30.62 Aligned_cols=45 Identities=24% Similarity=0.214 Sum_probs=27.8
Q ss_pred CCHHHHHHHHHHHhhCCCCCCCHHHHHHHHHHHhhcCCCCCCceeeccccchhHHH
Q 046372 36 PTTDQIRILKELYYNNGVRSPTAEQIQKISARLRQYGKIEGKNVFYWFQNYKARER 91 (266)
Q Consensus 36 FT~eQL~iLE~~F~~~~n~yPs~e~R~eIA~~L~~~g~LsE~qVqvWFQNRRAKeK 91 (266)
+++++..+|+..|.. + -...+||+.| ||++..|++|...=|.|.|
T Consensus 142 L~~~~~~v~~l~~~~-g------~s~~EIA~~l----gis~~tV~~~l~Ra~~~Lr 186 (194)
T PRK12519 142 LPESQRQVLELAYYE-G------LSQSEIAKRL----GIPLGTVKARARQGLLKLR 186 (194)
T ss_pred CCHHHhhhhhhhhhc-C------CCHHHHHHHh----CCCHHHHHHHHHHHHHHHH
Confidence 345555555554421 1 2234789999 6999999999954444443
No 61
>PF13551 HTH_29: Winged helix-turn helix
Probab=38.28 E-value=29 Score=26.16 Aligned_cols=52 Identities=13% Similarity=0.077 Sum_probs=29.3
Q ss_pred CCCCCCCCHHHHHHHHHHHhhCCCCCCC--HHHHHHHHHHH-hhcC--CCCCCceeecc
Q 046372 30 TCPRWTPTTDQIRILKELYYNNGVRSPT--AEQIQKISARL-RQYG--KIEGKNVFYWF 83 (266)
Q Consensus 30 rR~Rt~FT~eQL~iLE~~F~~~~n~yPs--~e~R~eIA~~L-~~~g--~LsE~qVqvWF 83 (266)
.+++..+|++|+..|.+.+.. .+.-+ .-....|+..| .+.. .++...|..|+
T Consensus 52 g~~~~~l~~~~~~~l~~~~~~--~p~~g~~~~t~~~l~~~l~~~~~~~~~s~~ti~r~L 108 (112)
T PF13551_consen 52 GRPRKRLSEEQRAQLIELLRE--NPPEGRSRWTLEELAEWLIEEEFGIDVSPSTIRRIL 108 (112)
T ss_pred CCCCCCCCHHHHHHHHHHHHH--CCCCCCCcccHHHHHHHHHHhccCccCCHHHHHHHH
Confidence 445555899999999999963 22111 11233566654 3222 35555566554
No 62
>PF00424 REV: REV protein (anti-repression trans-activator protein); InterPro: IPR000625 REV is a viral anti-repression trans-activator protein, which appears to act post-transcriptionally [] to relieve negative repression of GAG and ENV production. It is a phosphoprotein [, ] whose state of phosphorylation is mediated by a specific serine kinase activity present in the nucleus []. REV accumulates in the nucleoli [].; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0042025 host cell nucleus; PDB: 1ETF_B 1ETG_B 1ULL_B 3LPH_B 2X7L_R.
Probab=37.88 E-value=27 Score=28.44 Aligned_cols=38 Identities=26% Similarity=0.349 Sum_probs=21.5
Q ss_pred HHHHHHHHhhCCCCCCCHHHHHHHHHHHhhcCCCCCCceeeccccchhHHHHhhhhcc
Q 046372 41 IRILKELYYNNGVRSPTAEQIQKISARLRQYGKIEGKNVFYWFQNYKARERLKKKIEG 98 (266)
Q Consensus 41 L~iLE~~F~~~~n~yPs~e~R~eIA~~L~~~g~LsE~qVqvWFQNRRAKeKRkkr~~~ 98 (266)
+++.+-+|+ .|+||..+-- |..= -|||-|||+.+++..
T Consensus 14 vRiIk~Lyq--snPyP~~~GT---r~aR---------------RnRRRRWR~rq~QI~ 51 (91)
T PF00424_consen 14 VRIIKILYQ--SNPYPSPEGT---RQAR---------------RNRRRRWRARQRQIR 51 (91)
T ss_dssp HHHHHHHHH--TS-S--S-S----HHHH---------------HHHHHHHHHHHHHHH
T ss_pred HHHHHHHHc--cccCCCCCCc---cccc---------------cchhhhHHHHHHHHH
Confidence 456667776 5899976422 1121 278989998888763
No 63
>PRK12526 RNA polymerase sigma factor; Provisional
Probab=36.41 E-value=21 Score=30.67 Aligned_cols=22 Identities=9% Similarity=0.057 Sum_probs=16.7
Q ss_pred HHHHHHHhhcCCCCCCceeeccccch
Q 046372 62 QKISARLRQYGKIEGKNVFYWFQNYK 87 (266)
Q Consensus 62 ~eIA~~L~~~g~LsE~qVqvWFQNRR 87 (266)
++||+.| |+++..|+++...=|
T Consensus 173 ~EIA~~l----gis~~tV~~~l~Ra~ 194 (206)
T PRK12526 173 EQLAQQL----NVPLGTVKSRLRLAL 194 (206)
T ss_pred HHHHHHH----CCCHHHHHHHHHHHH
Confidence 4789999 799999987774333
No 64
>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=36.09 E-value=11 Score=28.28 Aligned_cols=17 Identities=18% Similarity=0.546 Sum_probs=15.3
Q ss_pred HHHHHHHhhcCCCCCCceeec
Q 046372 62 QKISARLRQYGKIEGKNVFYW 82 (266)
Q Consensus 62 ~eIA~~L~~~g~LsE~qVqvW 82 (266)
.+||++| ++++.+|..|
T Consensus 26 kdIA~~L----gvs~~tIr~W 42 (60)
T PF10668_consen 26 KDIAEKL----GVSESTIRKW 42 (60)
T ss_pred HHHHHHH----CCCHHHHHHH
Confidence 4789999 6999999988
No 65
>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=35.58 E-value=54 Score=24.38 Aligned_cols=43 Identities=23% Similarity=0.150 Sum_probs=33.9
Q ss_pred CCHHHHHHHHHHHhhCCCCCCCHHHHHHHHHHHhhcCCCCCCceeeccc
Q 046372 36 PTTDQIRILKELYYNNGVRSPTAEQIQKISARLRQYGKIEGKNVFYWFQ 84 (266)
Q Consensus 36 FT~eQL~iLE~~F~~~~n~yPs~e~R~eIA~~L~~~g~LsE~qVqvWFQ 84 (266)
+|++|+..|+.+|.. . .+.|.+|-.+.-..|-|+..+=..|-+
T Consensus 1 lT~~Qk~el~~l~~q-m-----~e~kK~~idk~Ve~G~iTqeqAd~ik~ 43 (59)
T PF10925_consen 1 LTDQQKKELKALYKQ-M-----LELKKQIIDKYVEAGVITQEQADAIKK 43 (59)
T ss_pred CCHHHHHHHHHHHHH-H-----HHHHHHHHHHHHHcCCCCHHHHHHHHH
Confidence 599999999999963 2 477778888888899999887555543
No 66
>PF13565 HTH_32: Homeodomain-like domain
Probab=34.54 E-value=1e+02 Score=22.19 Aligned_cols=39 Identities=23% Similarity=0.134 Sum_probs=24.6
Q ss_pred CCCCCCCCCHHHHHHHHHHHhhCCCCCCCHHHHHHHHHHHhhcCCC
Q 046372 29 PTCPRWTPTTDQIRILKELYYNNGVRSPTAEQIQKISARLRQYGKI 74 (266)
Q Consensus 29 ~rR~Rt~FT~eQL~iLE~~F~~~~n~yPs~e~R~eIA~~L~~~g~L 74 (266)
+.|+|. ++++.+.|.+++. .++.-+.. +|+..|....++
T Consensus 26 ~Grp~~--~~e~~~~i~~~~~--~~p~wt~~---~i~~~L~~~~g~ 64 (77)
T PF13565_consen 26 PGRPRK--DPEQRERIIALIE--EHPRWTPR---EIAEYLEEEFGI 64 (77)
T ss_pred CCCCCC--cHHHHHHHHHHHH--hCCCCCHH---HHHHHHHHHhCC
Confidence 344555 7888788888886 33444543 567777765553
No 67
>PRK09642 RNA polymerase sigma factor SigW; Reviewed
Probab=33.73 E-value=33 Score=27.69 Aligned_cols=27 Identities=26% Similarity=0.132 Sum_probs=19.7
Q ss_pred HHHHHHHhhcCCCCCCceeeccccchhHHHH
Q 046372 62 QKISARLRQYGKIEGKNVFYWFQNYKARERL 92 (266)
Q Consensus 62 ~eIA~~L~~~g~LsE~qVqvWFQNRRAKeKR 92 (266)
++||+.| ||++..|++...-=|.+.|+
T Consensus 126 ~EIA~~l----gis~~tV~~~l~Rar~~Lr~ 152 (160)
T PRK09642 126 QEIALQE----KIEVKTVEMKLYRARKWIKK 152 (160)
T ss_pred HHHHHHH----CCCHHHHHHHHHHHHHHHHH
Confidence 4688998 79999999887644444443
No 68
>COG4367 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=33.42 E-value=28 Score=28.66 Aligned_cols=39 Identities=10% Similarity=-0.009 Sum_probs=29.1
Q ss_pred CCCHHHHHHHHHHHhhCCCCCCCHHHHHHHHHHHhhcCCCCCCce
Q 046372 35 TPTTDQIRILKELYYNNGVRSPTAEQIQKISARLRQYGKIEGKNV 79 (266)
Q Consensus 35 ~FT~eQL~iLE~~F~~~~n~yPs~e~R~eIA~~L~~~g~LsE~qV 79 (266)
+++++|+++-.+.|+ .+.-...-..++||.+| ++++..|
T Consensus 2 SLn~eq~~~Tk~elq--an~el~~LS~~~iA~~L----n~t~~~l 40 (97)
T COG4367 2 SLNPEQKQRTKQELQ--ANFELCPLSDEEIATAL----NWTEVKL 40 (97)
T ss_pred CCCHHHHHHHHHHHH--HhhhhccccHHHHHHHh----CCCHHHH
Confidence 578999998888886 34555666677899999 5777544
No 69
>KOG3623 consensus Homeobox transcription factor SIP1 [Transcription]
Probab=32.52 E-value=17 Score=39.48 Aligned_cols=62 Identities=21% Similarity=0.235 Sum_probs=43.0
Q ss_pred CCCCCCCCCCHHHHHHHHHHHhhCCCCCCCHHHHHHHHHHHhhcCCCCCCceeeccccchhHHHHhhh
Q 046372 28 RPTCPRWTPTTDQIRILKELYYNNGVRSPTAEQIQKISARLRQYGKIEGKNVFYWFQNYKARERLKKK 95 (266)
Q Consensus 28 R~rR~Rt~FT~eQL~iLE~~F~~~~n~yPs~e~R~eIA~~L~~~g~LsE~qVqvWFQNRRAKeKRkkr 95 (266)
++.+.|+....++-..|...++- +-.|+..+-.-|+.+|. ..+.+|.|||++|+.+.+.-.-
T Consensus 625 ~p~kv~sp~k~~dq~ql~~a~el--q~s~~n~~~pl~~t~~~----n~~pv~ev~dhsrsstpsp~pl 686 (1007)
T KOG3623|consen 625 RPVKVRSPIKEEDQQQLKQAYEL--QASPSNDEFPLIATRLQ----NDPPVVEVWDHSRSSTPSPMPL 686 (1007)
T ss_pred CCccccCCCCccchhhhHhhhhc--ccCccCcccchhhhhcc----CCCcchhhcccCCCCCCCCCcc
Confidence 55556676777777778888873 34555544445666664 6778889999999988875443
No 70
>PRK12541 RNA polymerase sigma factor; Provisional
Probab=31.95 E-value=30 Score=28.11 Aligned_cols=47 Identities=9% Similarity=-0.005 Sum_probs=30.4
Q ss_pred CCCHHHHHHHHHHHhhCCCCCCCHHHHHHHHHHHhhcCCCCCCceeeccccchhHHHH
Q 046372 35 TPTTDQIRILKELYYNNGVRSPTAEQIQKISARLRQYGKIEGKNVFYWFQNYKARERL 92 (266)
Q Consensus 35 ~FT~eQL~iLE~~F~~~~n~yPs~e~R~eIA~~L~~~g~LsE~qVqvWFQNRRAKeKR 92 (266)
.+++.|..+|+-.|.. .++. ++||..| |+++..|+++...=|.|.|+
T Consensus 112 ~L~~~~r~v~~l~~~~---~~s~----~eIA~~l----gis~~tv~~~l~Rar~~L~~ 158 (161)
T PRK12541 112 SLPLERRNVLLLRDYY---GFSY----KEIAEMT----GLSLAKVKIELHRGRKETKS 158 (161)
T ss_pred HCCHHHHHHhhhHHhc---CCCH----HHHHHHH----CCCHHHHHHHHHHHHHHHHh
Confidence 3667777777765531 2332 4689999 69999998877654444443
No 71
>TIGR02948 SigW_bacill RNA polymerase sigma-W factor. This sigma factor is restricted to certain lineages of the order Bacillales.
Probab=31.77 E-value=31 Score=28.38 Aligned_cols=26 Identities=19% Similarity=0.111 Sum_probs=19.4
Q ss_pred HHHHHHHhhcCCCCCCceeeccccchhHHH
Q 046372 62 QKISARLRQYGKIEGKNVFYWFQNYKARER 91 (266)
Q Consensus 62 ~eIA~~L~~~g~LsE~qVqvWFQNRRAKeK 91 (266)
++||+.| |+++..|+++.+.=|.|.|
T Consensus 156 ~eIA~~l----gis~~~v~~~l~Rar~~Lr 181 (187)
T TIGR02948 156 KEISEIL----DLPVGTVKTRIHRGREALR 181 (187)
T ss_pred HHHHHHH----CCCHHHHHHHHHHHHHHHH
Confidence 4789999 6999999998854444443
No 72
>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=31.41 E-value=27 Score=23.72 Aligned_cols=20 Identities=25% Similarity=0.194 Sum_probs=16.9
Q ss_pred CCCCCCCCHHHHHHHHHHHh
Q 046372 30 TCPRWTPTTDQIRILKELYY 49 (266)
Q Consensus 30 rR~Rt~FT~eQL~iLE~~F~ 49 (266)
.+-|..||++|...|++.|.
T Consensus 5 ~k~rl~Pt~~Q~~~L~~~~~ 24 (46)
T PF12323_consen 5 YKYRLYPTKEQEEKLERWFG 24 (46)
T ss_pred eEEEEecCHHHHHHHHHHHH
Confidence 45688899999999999985
No 73
>PRK12514 RNA polymerase sigma factor; Provisional
Probab=31.29 E-value=38 Score=27.97 Aligned_cols=27 Identities=11% Similarity=0.281 Sum_probs=19.5
Q ss_pred HHHHHHHHhhcCCCCCCceeeccccchhHHH
Q 046372 61 IQKISARLRQYGKIEGKNVFYWFQNYKARER 91 (266)
Q Consensus 61 R~eIA~~L~~~g~LsE~qVqvWFQNRRAKeK 91 (266)
.++||+.| |+++..|+++.+.=|.+.|
T Consensus 148 ~~eIA~~l----gis~~tV~~~l~Rar~~Lr 174 (179)
T PRK12514 148 YKELAERH----DVPLNTMRTWLRRSLLKLR 174 (179)
T ss_pred HHHHHHHH----CCChHHHHHHHHHHHHHHH
Confidence 35789999 6999999887764444443
No 74
>PRK12512 RNA polymerase sigma factor; Provisional
Probab=30.98 E-value=36 Score=28.23 Aligned_cols=48 Identities=17% Similarity=0.139 Sum_probs=30.4
Q ss_pred CCHHHHHHHHHHHhhCCCCCCCHHHHHHHHHHHhhcCCCCCCceeeccccchhHHHHhh
Q 046372 36 PTTDQIRILKELYYNNGVRSPTAEQIQKISARLRQYGKIEGKNVFYWFQNYKARERLKK 94 (266)
Q Consensus 36 FT~eQL~iLE~~F~~~~n~yPs~e~R~eIA~~L~~~g~LsE~qVqvWFQNRRAKeKRkk 94 (266)
+++.+..+|...|.. + . .-++||..| ||+...|+++...=|.|.|++-
T Consensus 132 L~~~~r~v~~l~~~~-g--~----s~~eIA~~l----~is~~tV~~~l~ra~~~Lr~~l 179 (184)
T PRK12512 132 LPPRQRDVVQSISVE-G--A----SIKETAAKL----SMSEGAVRVALHRGLAALAAKF 179 (184)
T ss_pred CCHHHHHHHHHHHHc-C--C----CHHHHHHHh----CCCHHHHHHHHHHHHHHHHHHh
Confidence 455555666655431 1 1 124689999 7999999988866555555443
No 75
>PRK04217 hypothetical protein; Provisional
Probab=30.96 E-value=44 Score=27.67 Aligned_cols=54 Identities=15% Similarity=0.242 Sum_probs=38.1
Q ss_pred CCCCCCCCCCCHHHHHHHHHHHhhCCCCCCCHHHHHHHHHHHhhcCCCCCCceeeccccchhHHH
Q 046372 27 CRPTCPRWTPTTDQIRILKELYYNNGVRSPTAEQIQKISARLRQYGKIEGKNVFYWFQNYKARER 91 (266)
Q Consensus 27 ~R~rR~Rt~FT~eQL~iLE~~F~~~~n~yPs~e~R~eIA~~L~~~g~LsE~qVqvWFQNRRAKeK 91 (266)
|-+.-+=-.+|.+|+.+|...|.. + . ..++||+.| +|+...|+..+..-|.+.|
T Consensus 34 ~~~~~p~~~Lt~eereai~l~~~e-G--l----S~~EIAk~L----GIS~sTV~r~L~RArkkLr 87 (110)
T PRK04217 34 VGPPKPPIFMTYEEFEALRLVDYE-G--L----TQEEAGKRM----GVSRGTVWRALTSARKKVA 87 (110)
T ss_pred ccCCCCcccCCHHHHHHHHHHHHc-C--C----CHHHHHHHH----CcCHHHHHHHHHHHHHHHH
Confidence 333444556799999999988852 2 2 345789999 6999999987765554444
No 76
>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=30.44 E-value=41 Score=22.98 Aligned_cols=14 Identities=21% Similarity=0.176 Sum_probs=11.8
Q ss_pred CCCHHHHHHHHHHH
Q 046372 35 TPTTDQIRILKELY 48 (266)
Q Consensus 35 ~FT~eQL~iLE~~F 48 (266)
.||++|+..||.--
T Consensus 2 ~FT~~Ql~~L~~Qi 15 (37)
T PF08880_consen 2 PFTPAQLQELRAQI 15 (37)
T ss_pred CCCHHHHHHHHHHH
Confidence 59999999999643
No 77
>PRK11924 RNA polymerase sigma factor; Provisional
Probab=29.66 E-value=35 Score=27.41 Aligned_cols=45 Identities=16% Similarity=0.121 Sum_probs=27.4
Q ss_pred CCHHHHHHHHHHHhhCCCCCCCHHHHHHHHHHHhhcCCCCCCceeeccccchhHHH
Q 046372 36 PTTDQIRILKELYYNNGVRSPTAEQIQKISARLRQYGKIEGKNVFYWFQNYKARER 91 (266)
Q Consensus 36 FT~eQL~iLE~~F~~~~n~yPs~e~R~eIA~~L~~~g~LsE~qVqvWFQNRRAKeK 91 (266)
+++.+..+|...|.. + + ...+||+.| ||++..|+.|..-=|.|.|
T Consensus 126 L~~~~r~i~~l~~~~-~--~----~~~eIA~~l----gis~~tv~~~~~ra~~~lr 170 (179)
T PRK11924 126 LPVKQREVFLLRYVE-G--L----SYREIAEIL----GVPVGTVKSRLRRARQLLR 170 (179)
T ss_pred CCHHHHHHhhHHHHc-C--C----CHHHHHHHH----CCCHHHHHHHHHHHHHHHH
Confidence 344555555554431 1 1 224689998 6999999998765444444
No 78
>PHA02955 hypothetical protein; Provisional
Probab=29.28 E-value=72 Score=29.64 Aligned_cols=44 Identities=11% Similarity=0.089 Sum_probs=30.2
Q ss_pred HHHHHHHHHHHhhCCCCCCCHHHHHHHHHHHhhcCCCCCCceeeccccc
Q 046372 38 TDQIRILKELYYNNGVRSPTAEQIQKISARLRQYGKIEGKNVFYWFQNY 86 (266)
Q Consensus 38 ~eQL~iLE~~F~~~~n~yPs~e~R~eIA~~L~~~g~LsE~qVqvWFQNR 86 (266)
..|+.+|=+.|.. ..-...+++|.+||++| |+.-..|..||++.
T Consensus 60 ~~sf~lli~a~~E-t~~~Lp~~qk~~ia~~l----gI~~~~~~~d~~t~ 103 (213)
T PHA02955 60 EKNFQLLIEALIE-TIENFPEKEQKEIAADI----GINIDDYKAGKKTD 103 (213)
T ss_pred HHHHHHHHHHHHH-HHHhCCHHHHHHHHHHh----CCChhhccCcccch
Confidence 3455555555432 22356788999999999 57776689999874
No 79
>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=28.71 E-value=36 Score=28.05 Aligned_cols=45 Identities=13% Similarity=0.174 Sum_probs=28.0
Q ss_pred CCHHHHHHHHHHHhhCCCCCCCHHHHHHHHHHHhhcCCCCCCceeeccccchhHHH
Q 046372 36 PTTDQIRILKELYYNNGVRSPTAEQIQKISARLRQYGKIEGKNVFYWFQNYKARER 91 (266)
Q Consensus 36 FT~eQL~iLE~~F~~~~n~yPs~e~R~eIA~~L~~~g~LsE~qVqvWFQNRRAKeK 91 (266)
+.+.|..+|.-.|.. + + ..++||+.| ||++..|++....=|.+.|
T Consensus 135 Lp~~~r~v~~l~~~~-g--~----s~~EIA~~l----gis~~tVk~~l~Rar~~Lr 179 (183)
T TIGR02999 135 VDPRQAEVVELRFFA-G--L----TVEEIAELL----GVSVRTVERDWRFARAWLA 179 (183)
T ss_pred CCHHHHHHHHHHHHc-C--C----CHHHHHHHh----CCCHHHHHHHHHHHHHHHH
Confidence 455555566555531 2 2 224789999 6999999988754444433
No 80
>PRK12537 RNA polymerase sigma factor; Provisional
Probab=28.51 E-value=46 Score=27.80 Aligned_cols=39 Identities=18% Similarity=0.269 Sum_probs=24.4
Q ss_pred CCHHHHHHHHHHHhhCCCCCCCHHHHHHHHHHHhhcCCCCCCceeecccc
Q 046372 36 PTTDQIRILKELYYNNGVRSPTAEQIQKISARLRQYGKIEGKNVFYWFQN 85 (266)
Q Consensus 36 FT~eQL~iLE~~F~~~~n~yPs~e~R~eIA~~L~~~g~LsE~qVqvWFQN 85 (266)
+++.|..++...|.. + . ..++||+.| ||++..|++|-..
T Consensus 134 L~~~~r~i~~l~~~~-~--~----s~~eIA~~l----gis~~tV~~~l~r 172 (182)
T PRK12537 134 LEPARRNCILHAYVD-G--C----SHAEIAQRL----GAPLGTVKAWIKR 172 (182)
T ss_pred CCHHHHHHHHHHHHc-C--C----CHHHHHHHH----CCChhhHHHHHHH
Confidence 344555555555531 2 2 234789999 6999999987643
No 81
>PF08144 CPL: CPL (NUC119) domain; InterPro: IPR012959 This C-terminal domain is found in Penguin-like proteins (CPL) and is associated with Pumilio like repeats [].; GO: 0003723 RNA binding
Probab=28.49 E-value=89 Score=26.75 Aligned_cols=40 Identities=13% Similarity=0.076 Sum_probs=30.4
Q ss_pred CCCCCCCCHHHHHHHHHHHhhCCCCCCCHHHHHHHHHHHh
Q 046372 30 TCPRWTPTTDQIRILKELYYNNGVRSPTAEQIQKISARLR 69 (266)
Q Consensus 30 rR~Rt~FT~eQL~iLE~~F~~~~n~yPs~e~R~eIA~~L~ 69 (266)
+|-+..|+++++++|++.=.+...+.+...+|+||.+.+.
T Consensus 16 ~~d~~~f~p~~i~~L~~~d~~~tSKKd~~~Rr~ELl~~~s 55 (148)
T PF08144_consen 16 PRDPRYFSPEIIKLLKEGDRNATSKKDPEVRRKELLEAIS 55 (148)
T ss_pred CCCcccCCHHHHHHHhhhcccccccCCHHHHHHHHHHHhh
Confidence 3566779999999999886444556777788888888764
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=28.36 E-value=55 Score=26.39 Aligned_cols=43 Identities=16% Similarity=0.179 Sum_probs=25.5
Q ss_pred CCHHHHHHHHHHHhhCCCCCCCHHHHHHHHHHHhhcCCCCCCceeeccccchhHHH
Q 046372 36 PTTDQIRILKELYYNNGVRSPTAEQIQKISARLRQYGKIEGKNVFYWFQNYKARER 91 (266)
Q Consensus 36 FT~eQL~iLE~~F~~~~n~yPs~e~R~eIA~~L~~~g~LsE~qVqvWFQNRRAKeK 91 (266)
+++.|..+|.-.|.. + ++ .++||+.| +|++..|++.. +|+|.|
T Consensus 123 L~~~~r~vl~l~~~~-g--~s----~~eIA~~l----~is~~tv~~~l--~ra~~~ 165 (170)
T TIGR02952 123 LTPKQQHVIALRFGQ-N--LP----IAEVARIL----GKTEGAVKILQ--FRAIKK 165 (170)
T ss_pred CCHHHHHHHHHHHhc-C--CC----HHHHHHHH----CCCHHHHHHHH--HHHHHH
Confidence 455555555554431 2 22 24689999 69999998654 444444
No 83
>COG4829 CatC1 Muconolactone delta-isomerase [Secondary metabolites biosynthesis, transport, and catabolism]
Probab=28.17 E-value=46 Score=27.45 Aligned_cols=45 Identities=20% Similarity=0.349 Sum_probs=30.5
Q ss_pred CCcceeccccCCCCCCCCCCchhhhhhhcCCCCcccccCcccCCCCccccccCCCCCCCCCC
Q 046372 197 TSSYIFFGQKNSADGNQGNDKEDEEEEENGHPGIETLPLFPMHGEDSINNYCNSKPNSSSYY 258 (266)
Q Consensus 197 ~s~y~~~~~~~~~~~~~e~~ee~e~~~e~~~~~~etlplfpmh~ed~~~~~~~~~~~~~~~~ 258 (266)
+..|++|+-.+. +|-+ .-+-.||+||--+.| |+..|- +||+..||
T Consensus 50 yanyslFd~dd~--------~eLh-------~~L~~~P~f~ym~~~-itpL~~-HPn~~~~~ 94 (98)
T COG4829 50 YANYSLFDADDN--------GELH-------QLLASMPPFSYMTDD-ITPLGA-HPNQGITI 94 (98)
T ss_pred ccceeeecCCch--------HHHH-------HHHhcCCCccccccc-cchhcc-CCCcceee
Confidence 345999987321 2222 125779999999888 999887 77766554
No 84
>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=27.49 E-value=44 Score=26.72 Aligned_cols=38 Identities=16% Similarity=0.213 Sum_probs=25.7
Q ss_pred CCCHHHHHHHHHHHhhCCCCCCCHHHHHHHHHHHhhcCCCCCCceeecc
Q 046372 35 TPTTDQIRILKELYYNNGVRSPTAEQIQKISARLRQYGKIEGKNVFYWF 83 (266)
Q Consensus 35 ~FT~eQL~iLE~~F~~~~n~yPs~e~R~eIA~~L~~~g~LsE~qVqvWF 83 (266)
.+++.|..+|...|.. + ++ .++||+.| ||+...|+++.
T Consensus 111 ~L~~~~r~v~~l~~~~-g--~~----~~eIA~~l----~is~~tv~~~l 148 (159)
T TIGR02989 111 KLPERQRELLQLRYQR-G--VS----LTALAEQL----GRTVNAVYKAL 148 (159)
T ss_pred HCCHHHHHHHHHHHhc-C--CC----HHHHHHHh----CCCHHHHHHHH
Confidence 3667777777765531 2 22 34689999 69999999663
No 85
>PRK10100 DNA-binding transcriptional regulator CsgD; Provisional
Probab=26.26 E-value=29 Score=30.82 Aligned_cols=47 Identities=23% Similarity=0.230 Sum_probs=36.6
Q ss_pred CCCHHHHHHHHHHHhhCCCCCCCHHHHHHHHHHHhhcCCCCCCceeeccccchhHHHHh
Q 046372 35 TPTTDQIRILKELYYNNGVRSPTAEQIQKISARLRQYGKIEGKNVFYWFQNYKARERLK 93 (266)
Q Consensus 35 ~FT~eQL~iLE~~F~~~~n~yPs~e~R~eIA~~L~~~g~LsE~qVqvWFQNRRAKeKRk 93 (266)
.+|+.|+++|+-+.. + +.+ ++||++| +|+++.|+.+..+=..|..-+
T Consensus 155 ~Lt~rE~~Vl~l~~~--G--~s~----~eIA~~L----~iS~~TVk~~~~~i~~Kl~v~ 201 (216)
T PRK10100 155 LLTHREKEILNKLRI--G--ASN----NEIARSL----FISENTVKTHLYNLFKKIAVK 201 (216)
T ss_pred CCCHHHHHHHHHHHc--C--CCH----HHHHHHh----CCCHHHHHHHHHHHHHHhCCC
Confidence 489999999998874 3 333 4799999 699999999887776665543
No 86
>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=26.21 E-value=55 Score=25.72 Aligned_cols=39 Identities=18% Similarity=0.196 Sum_probs=25.2
Q ss_pred CCHHHHHHHHHHHhhCCCCCCCHHHHHHHHHHHhhcCCCCCCceeecccc
Q 046372 36 PTTDQIRILKELYYNNGVRSPTAEQIQKISARLRQYGKIEGKNVFYWFQN 85 (266)
Q Consensus 36 FT~eQL~iLE~~F~~~~n~yPs~e~R~eIA~~L~~~g~LsE~qVqvWFQN 85 (266)
+++.+..+|.-.|.. .++ ..+||..| ||++..|+.+...
T Consensus 114 L~~~~r~il~l~~~~---~~~----~~eIA~~l----gis~~tv~~~~~r 152 (161)
T TIGR02985 114 LPEQCRKIFILSRFE---GKS----YKEIAEEL----GISVKTVEYHISK 152 (161)
T ss_pred CCHHHHHHHHHHHHc---CCC----HHHHHHHH----CCCHHHHHHHHHH
Confidence 456666666665531 232 23688888 6999999876643
No 87
>PRK09648 RNA polymerase sigma factor SigD; Reviewed
Probab=26.16 E-value=42 Score=28.05 Aligned_cols=44 Identities=18% Similarity=-0.013 Sum_probs=28.2
Q ss_pred CCCHHHHHHHHHHHhhCCCCCCCHHHHHHHHHHHhhcCCCCCCceeeccccchhHHH
Q 046372 35 TPTTDQIRILKELYYNNGVRSPTAEQIQKISARLRQYGKIEGKNVFYWFQNYKARER 91 (266)
Q Consensus 35 ~FT~eQL~iLE~~F~~~~n~yPs~e~R~eIA~~L~~~g~LsE~qVqvWFQNRRAKeK 91 (266)
.+++.|.++|+..|.. + ...++||+.| ||++..|+++. +||+.|
T Consensus 139 ~L~~~~r~i~~l~~~~-g------~s~~EIA~~l----gis~~tV~~~l--~Ra~~~ 182 (189)
T PRK09648 139 TLPEKQREILILRVVV-G------LSAEETAEAV----GSTPGAVRVAQ--HRALAR 182 (189)
T ss_pred hCCHHHHHHHHHHHHc-C------CCHHHHHHHH----CCCHHHHHHHH--HHHHHH
Confidence 3455666666655431 2 2235789999 69999999877 455554
No 88
>PRK05602 RNA polymerase sigma factor; Reviewed
Probab=26.07 E-value=38 Score=28.20 Aligned_cols=45 Identities=18% Similarity=0.224 Sum_probs=27.0
Q ss_pred CHHHHHHHHHHHhhCCCCCCCHHHHHHHHHHHhhcCCCCCCceeeccccchhHHHHhh
Q 046372 37 TTDQIRILKELYYNNGVRSPTAEQIQKISARLRQYGKIEGKNVFYWFQNYKARERLKK 94 (266)
Q Consensus 37 T~eQL~iLE~~F~~~~n~yPs~e~R~eIA~~L~~~g~LsE~qVqvWFQNRRAKeKRkk 94 (266)
++.+..+|...|.. + . ...+||+.| ||+...|+++.. |||.+=++
T Consensus 130 ~~~~r~i~~l~~~~-g--~----s~~EIA~~l----gis~~tV~~~l~--Rar~~Lr~ 174 (186)
T PRK05602 130 PERQREAIVLQYYQ-G--L----SNIEAAAVM----DISVDALESLLA--RGRRALRA 174 (186)
T ss_pred CHHHHHHhhHHHhc-C--C----CHHHHHHHh----CcCHHHHHHHHH--HHHHHHHH
Confidence 45555555554431 1 1 224689998 799999998874 44444333
No 89
>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=25.60 E-value=49 Score=26.68 Aligned_cols=44 Identities=20% Similarity=0.172 Sum_probs=28.4
Q ss_pred CHHHHHHHHHHHhhCCCCCCCHHHHHHHHHHHhhcCCCCCCceeeccccchhHHH
Q 046372 37 TTDQIRILKELYYNNGVRSPTAEQIQKISARLRQYGKIEGKNVFYWFQNYKARER 91 (266)
Q Consensus 37 T~eQL~iLE~~F~~~~n~yPs~e~R~eIA~~L~~~g~LsE~qVqvWFQNRRAKeK 91 (266)
++.|..+|+..|.. + ++ .++||..| ||++..|+++-..=|.+.|
T Consensus 112 ~~~~r~i~~l~~~~-g--~s----~~eIA~~l----gis~~tV~~~l~ra~~~Lr 155 (162)
T TIGR02983 112 PARQRAVVVLRYYE-D--LS----EAQVAEAL----GISVGTVKSRLSRALARLR 155 (162)
T ss_pred CHHHHHHhhhHHHh-c--CC----HHHHHHHh----CCCHHHHHHHHHHHHHHHH
Confidence 56666677665531 2 22 24689999 6999999987654444444
No 90
>PF13936 HTH_38: Helix-turn-helix domain; PDB: 2W48_A.
Probab=25.40 E-value=26 Score=23.86 Aligned_cols=38 Identities=21% Similarity=0.165 Sum_probs=17.0
Q ss_pred CCCCHHHHHHHHHHHhhCCCCCCCHHHHHHHHHHHhhcCCCCCCceeec
Q 046372 34 WTPTTDQIRILKELYYNNGVRSPTAEQIQKISARLRQYGKIEGKNVFYW 82 (266)
Q Consensus 34 t~FT~eQL~iLE~~F~~~~n~yPs~e~R~eIA~~L~~~g~LsE~qVqvW 82 (266)
..+|.+|...++.++. .+ ....+||+.| |++..-|..+
T Consensus 3 ~~Lt~~eR~~I~~l~~-~G------~s~~~IA~~l----g~s~sTV~re 40 (44)
T PF13936_consen 3 KHLTPEERNQIEALLE-QG------MSIREIAKRL----GRSRSTVSRE 40 (44)
T ss_dssp ---------HHHHHHC-S---------HHHHHHHT----T--HHHHHHH
T ss_pred cchhhhHHHHHHHHHH-cC------CCHHHHHHHH----CcCcHHHHHH
Confidence 4579999999998875 22 2334799999 5776666543
No 91
>PRK09413 IS2 repressor TnpA; Reviewed
Probab=25.15 E-value=70 Score=25.87 Aligned_cols=41 Identities=17% Similarity=0.375 Sum_probs=27.4
Q ss_pred CCCCCCHHH-HHHHHHHHhhCCCCCCCHHHHHHHHHHHhhcCCCCCCceeecc
Q 046372 32 PRWTPTTDQ-IRILKELYYNNGVRSPTAEQIQKISARLRQYGKIEGKNVFYWF 83 (266)
Q Consensus 32 ~Rt~FT~eQ-L~iLE~~F~~~~n~yPs~e~R~eIA~~L~~~g~LsE~qVqvWF 83 (266)
+|-.||.+. +.++...+. . ..+ ..+||+++ +|+...|..|-
T Consensus 9 ~rr~ys~EfK~~aV~~~~~-~--g~s----v~evA~e~----gIs~~tl~~W~ 50 (121)
T PRK09413 9 KRRRRTTQEKIAIVQQSFE-P--GMT----VSLVARQH----GVAASQLFLWR 50 (121)
T ss_pred CCCCCCHHHHHHHHHHHHc-C--CCC----HHHHHHHH----CcCHHHHHHHH
Confidence 344467776 456666664 2 232 33689999 69999999993
No 92
>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=25.06 E-value=54 Score=27.22 Aligned_cols=44 Identities=14% Similarity=0.154 Sum_probs=29.6
Q ss_pred CCCHHHHHHHHHHHhhCCCCCCCHHHHHHHHHHHhhcCCCCCCceeeccccchhHHH
Q 046372 35 TPTTDQIRILKELYYNNGVRSPTAEQIQKISARLRQYGKIEGKNVFYWFQNYKARER 91 (266)
Q Consensus 35 ~FT~eQL~iLE~~F~~~~n~yPs~e~R~eIA~~L~~~g~LsE~qVqvWFQNRRAKeK 91 (266)
.+++.|..+|+-.|.. + ++ .++||+.| +|++..|+++-+ |+|.+
T Consensus 100 ~L~~~~r~v~~l~~~~-g--~s----~~eIA~~l----gis~~tV~~~l~--Rar~~ 143 (170)
T TIGR02959 100 ELPDEYREAIRLTELE-G--LS----QQEIAEKL----GLSLSGAKSRVQ--RGRKK 143 (170)
T ss_pred hCCHHHHHHHHHHHHc-C--CC----HHHHHHHH----CCCHHHHHHHHH--HHHHH
Confidence 5677777777766641 2 32 24689999 699999998764 44444
No 93
>PRK10651 transcriptional regulator NarL; Provisional
Probab=24.81 E-value=26 Score=28.06 Aligned_cols=45 Identities=24% Similarity=0.284 Sum_probs=34.0
Q ss_pred CCCHHHHHHHHHHHhhCCCCCCCHHHHHHHHHHHhhcCCCCCCceeeccccchhHHH
Q 046372 35 TPTTDQIRILKELYYNNGVRSPTAEQIQKISARLRQYGKIEGKNVFYWFQNYKARER 91 (266)
Q Consensus 35 ~FT~eQL~iLE~~F~~~~n~yPs~e~R~eIA~~L~~~g~LsE~qVqvWFQNRRAKeK 91 (266)
.+|+.+.++|+-+.. + ++. ++||++| +++++.|++..+|=|.|..
T Consensus 155 ~Lt~rE~~vl~~l~~--g--~~~----~~ia~~l----~is~~tV~~~~~~l~~Kl~ 199 (216)
T PRK10651 155 QLTPRERDILKLIAQ--G--LPN----KMIARRL----DITESTVKVHVKHMLKKMK 199 (216)
T ss_pred cCCHHHHHHHHHHHc--C--CCH----HHHHHHc----CCCHHHHHHHHHHHHHHcC
Confidence 499999999998764 2 333 4689998 6999999887776665554
No 94
>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=24.74 E-value=37 Score=27.99 Aligned_cols=25 Identities=20% Similarity=0.228 Sum_probs=18.8
Q ss_pred HHHHHHHHhhcCCCCCCceeeccccchhHHH
Q 046372 61 IQKISARLRQYGKIEGKNVFYWFQNYKARER 91 (266)
Q Consensus 61 R~eIA~~L~~~g~LsE~qVqvWFQNRRAKeK 91 (266)
-++||+.| ||++..|+++. +|||.|
T Consensus 157 ~~EIA~~l----gis~~tv~~~l--~rar~~ 181 (190)
T TIGR02939 157 YEDIARIM----DCPVGTVRSRI--FRAREA 181 (190)
T ss_pred HHHHHHHH----CcCHHHHHHHH--HHHHHH
Confidence 35789998 79999999887 455444
No 95
>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=24.31 E-value=28 Score=25.49 Aligned_cols=18 Identities=22% Similarity=0.571 Sum_probs=15.6
Q ss_pred HHHHHHHhhcCCCCCCceeecc
Q 046372 62 QKISARLRQYGKIEGKNVFYWF 83 (266)
Q Consensus 62 ~eIA~~L~~~g~LsE~qVqvWF 83 (266)
.+||+.| ||+.+.|+.|=
T Consensus 17 ~eIA~~L----g~~~~TV~~W~ 34 (58)
T PF06056_consen 17 KEIAEEL----GVPRSTVYSWK 34 (58)
T ss_pred HHHHHHH----CCChHHHHHHH
Confidence 4699999 69999999994
No 96
>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=24.02 E-value=32 Score=23.39 Aligned_cols=38 Identities=26% Similarity=0.459 Sum_probs=26.1
Q ss_pred CCCCHHHHHHHHHHHhhCCCCCCCHHHHHHHHHHHhhcCCCCCCceeec
Q 046372 34 WTPTTDQIRILKELYYNNGVRSPTAEQIQKISARLRQYGKIEGKNVFYW 82 (266)
Q Consensus 34 t~FT~eQL~iLE~~F~~~~n~yPs~e~R~eIA~~L~~~g~LsE~qVqvW 82 (266)
..++++|++.+-+++. .+ ..+.+||+.+ +|+...|+.+
T Consensus 4 ~~~~~~~~~~i~~l~~-~G------~si~~IA~~~----gvsr~TvyR~ 41 (45)
T PF02796_consen 4 PKLSKEQIEEIKELYA-EG------MSIAEIAKQF----GVSRSTVYRY 41 (45)
T ss_dssp SSSSHCCHHHHHHHHH-TT--------HHHHHHHT----TS-HHHHHHH
T ss_pred CCCCHHHHHHHHHHHH-CC------CCHHHHHHHH----CcCHHHHHHH
Confidence 3478888888888986 23 3345789999 6888777644
No 97
>PRK12515 RNA polymerase sigma factor; Provisional
Probab=24.00 E-value=62 Score=27.11 Aligned_cols=44 Identities=16% Similarity=0.280 Sum_probs=27.6
Q ss_pred CCCHHHHHHHHHHHhhCCCCCCCHHHHHHHHHHHhhcCCCCCCceeeccccchhHHH
Q 046372 35 TPTTDQIRILKELYYNNGVRSPTAEQIQKISARLRQYGKIEGKNVFYWFQNYKARER 91 (266)
Q Consensus 35 ~FT~eQL~iLE~~F~~~~n~yPs~e~R~eIA~~L~~~g~LsE~qVqvWFQNRRAKeK 91 (266)
.++++|..+|+-.|.. + ++ .++||+.| ||++..|++-.. |||.+
T Consensus 131 ~L~~~~r~vl~l~~~~-~--~s----~~eIA~~l----gis~~tV~~~l~--Rar~~ 174 (189)
T PRK12515 131 KLSPAHREIIDLVYYH-E--KS----VEEVGEIV----GIPESTVKTRMF--YARKK 174 (189)
T ss_pred hCCHHHHHHHHHHHHc-C--CC----HHHHHHHH----CcCHHHHHHHHH--HHHHH
Confidence 4556666666655431 1 22 24689999 699999998764 44444
No 98
>PRK00118 putative DNA-binding protein; Validated
Probab=23.13 E-value=51 Score=27.02 Aligned_cols=46 Identities=11% Similarity=0.149 Sum_probs=32.6
Q ss_pred CCHHHHHHHHHHHhhCCCCCCCHHHHHHHHHHHhhcCCCCCCceeeccccchhHHHH
Q 046372 36 PTTDQIRILKELYYNNGVRSPTAEQIQKISARLRQYGKIEGKNVFYWFQNYKARERL 92 (266)
Q Consensus 36 FT~eQL~iLE~~F~~~~n~yPs~e~R~eIA~~L~~~g~LsE~qVqvWFQNRRAKeKR 92 (266)
+++.|..++...|.. + +. ..+||+.+ |+++..|+.|...-|.+.|+
T Consensus 18 L~ekqRevl~L~y~e-g--~S----~~EIAe~l----GIS~~TV~r~L~RArkkLr~ 63 (104)
T PRK00118 18 LTEKQRNYMELYYLD-D--YS----LGEIAEEF----NVSRQAVYDNIKRTEKLLED 63 (104)
T ss_pred CCHHHHHHHHHHHHc-C--CC----HHHHHHHH----CcCHHHHHHHHHHHHHHHHH
Confidence 577888888777752 2 22 34689999 69999999988755554443
No 99
>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=23.04 E-value=56 Score=26.68 Aligned_cols=39 Identities=15% Similarity=0.190 Sum_probs=26.0
Q ss_pred CCCHHHHHHHHHHHhhCCCCCCCHHHHHHHHHHHhhcCCCCCCceeeccc
Q 046372 35 TPTTDQIRILKELYYNNGVRSPTAEQIQKISARLRQYGKIEGKNVFYWFQ 84 (266)
Q Consensus 35 ~FT~eQL~iLE~~F~~~~n~yPs~e~R~eIA~~L~~~g~LsE~qVqvWFQ 84 (266)
.+++.|.++|...|.. + . ..++||+.| ||++..|+++..
T Consensus 119 ~L~~~~r~i~~l~~~~-g--~----s~~eiA~~l----gis~~tv~~~l~ 157 (169)
T TIGR02954 119 TLNDKYQTAIILRYYH-D--L----TIKEIAEVM----NKPEGTVKTYLH 157 (169)
T ss_pred hCCHHHhHHHHHHHHc-C--C----CHHHHHHHH----CCCHHHHHHHHH
Confidence 3566677777666542 2 2 234789999 699999987653
No 100
>PRK10360 DNA-binding transcriptional activator UhpA; Provisional
Probab=22.93 E-value=41 Score=26.91 Aligned_cols=43 Identities=21% Similarity=0.274 Sum_probs=32.1
Q ss_pred CCCHHHHHHHHHHHhhCCCCCCCHHHHHHHHHHHhhcCCCCCCceeeccccchhH
Q 046372 35 TPTTDQIRILKELYYNNGVRSPTAEQIQKISARLRQYGKIEGKNVFYWFQNYKAR 89 (266)
Q Consensus 35 ~FT~eQL~iLE~~F~~~~n~yPs~e~R~eIA~~L~~~g~LsE~qVqvWFQNRRAK 89 (266)
.+|+.+.++|+-+.. + + .+++||.+| +++++.|++..++=|.|
T Consensus 137 ~Lt~~E~~il~~l~~--g--~----~~~~Ia~~l----~~s~~tv~~~~~~l~~K 179 (196)
T PRK10360 137 PLTKRERQVAEKLAQ--G--M----AVKEIAAEL----GLSPKTVHVHRANLMEK 179 (196)
T ss_pred CCCHHHHHHHHHHHC--C--C----CHHHHHHHh----CCCHHHHHHHHHHHHHH
Confidence 589999999997764 2 3 456899999 69999997766554444
No 101
>PRK09644 RNA polymerase sigma factor SigM; Provisional
Probab=22.82 E-value=49 Score=27.00 Aligned_cols=46 Identities=4% Similarity=-0.086 Sum_probs=27.6
Q ss_pred CCHHHHHHHHHHHhhCCCCCCCHHHHHHHHHHHhhcCCCCCCceeeccccchhHHHH
Q 046372 36 PTTDQIRILKELYYNNGVRSPTAEQIQKISARLRQYGKIEGKNVFYWFQNYKARERL 92 (266)
Q Consensus 36 FT~eQL~iLE~~F~~~~n~yPs~e~R~eIA~~L~~~g~LsE~qVqvWFQNRRAKeKR 92 (266)
++++|..+|...|-. + + ..++||..| ++++..|++|.+-=|.|.|+
T Consensus 109 L~~~~r~v~~l~~~~-g--~----s~~eIA~~l----gis~~tv~~~l~Rar~~Lr~ 154 (165)
T PRK09644 109 LPVIEAQAILLCDVH-E--L----TYEEAASVL----DLKLNTYKSHLFRGRKRLKA 154 (165)
T ss_pred CCHHHHHHHHhHHHh-c--C----CHHHHHHHH----CCCHHHHHHHHHHHHHHHHH
Confidence 455555555543321 1 2 234688888 69999999887644444443
No 102
>PRK07037 extracytoplasmic-function sigma-70 factor; Validated
Probab=22.76 E-value=54 Score=26.49 Aligned_cols=36 Identities=11% Similarity=0.110 Sum_probs=22.8
Q ss_pred CCHHHHHHHHHHHhhCCCCCCCHHHHHHHHHHHhhcCCCCCCceeec
Q 046372 36 PTTDQIRILKELYYNNGVRSPTAEQIQKISARLRQYGKIEGKNVFYW 82 (266)
Q Consensus 36 FT~eQL~iLE~~F~~~~n~yPs~e~R~eIA~~L~~~g~LsE~qVqvW 82 (266)
+++.+..+|.-.|.. + + ..++||+.| ||++..|+..
T Consensus 110 L~~~~r~v~~l~~~~-~--~----s~~EIA~~l----gis~~tV~~~ 145 (163)
T PRK07037 110 LPARTRYAFEMYRLH-G--E----TQKDIAREL----GVSPTLVNFM 145 (163)
T ss_pred CCHHHHHHHHHHHHc-C--C----CHHHHHHHH----CCCHHHHHHH
Confidence 345555555544431 2 2 234789999 6999999975
No 103
>PRK09637 RNA polymerase sigma factor SigZ; Provisional
Probab=22.39 E-value=61 Score=27.39 Aligned_cols=47 Identities=17% Similarity=0.182 Sum_probs=29.9
Q ss_pred CCCHHHHHHHHHHHhhCCCCCCCHHHHHHHHHHHhhcCCCCCCceeeccccchhHHHHhh
Q 046372 35 TPTTDQIRILKELYYNNGVRSPTAEQIQKISARLRQYGKIEGKNVFYWFQNYKARERLKK 94 (266)
Q Consensus 35 ~FT~eQL~iLE~~F~~~~n~yPs~e~R~eIA~~L~~~g~LsE~qVqvWFQNRRAKeKRkk 94 (266)
.+++.|..+|...|.. + ++ ..+||..| ||++..|+..+. |||.+=++
T Consensus 106 ~L~~~~r~i~~l~~~~-g--~~----~~EIA~~l----gis~~tV~~~l~--Rar~~Lr~ 152 (181)
T PRK09637 106 ALPEKYAEALRLTELE-G--LS----QKEIAEKL----GLSLSGAKSRVQ--RGRVKLKE 152 (181)
T ss_pred hCCHHHHHHHHHHHhc-C--CC----HHHHHHHh----CCCHHHHHHHHH--HHHHHHHH
Confidence 4566666677665431 2 22 24689999 699999998885 55554333
No 104
>PRK09047 RNA polymerase factor sigma-70; Validated
Probab=22.16 E-value=64 Score=25.82 Aligned_cols=38 Identities=11% Similarity=0.061 Sum_probs=23.5
Q ss_pred CCHHHHHHHHHHHhhCCCCCCCHHHHHHHHHHHhhcCCCCCCceeeccc
Q 046372 36 PTTDQIRILKELYYNNGVRSPTAEQIQKISARLRQYGKIEGKNVFYWFQ 84 (266)
Q Consensus 36 FT~eQL~iLE~~F~~~~n~yPs~e~R~eIA~~L~~~g~LsE~qVqvWFQ 84 (266)
+++.|..+|.-.|.. + ++ .++||+.| ||++..|++...
T Consensus 107 Lp~~~r~v~~l~~~~-g--~s----~~EIA~~l----gis~~tV~~~l~ 144 (161)
T PRK09047 107 LPARQREAFLLRYWE-D--MD----VAETAAAM----GCSEGSVKTHCS 144 (161)
T ss_pred CCHHHHHHHHHHHHh-c--CC----HHHHHHHH----CCCHHHHHHHHH
Confidence 344555555554431 2 22 24789999 699999987654
No 105
>PRK05657 RNA polymerase sigma factor RpoS; Validated
Probab=22.13 E-value=56 Score=30.94 Aligned_cols=50 Identities=12% Similarity=0.093 Sum_probs=32.5
Q ss_pred CCCHHHHHHHHHHHhhCCCCCCCHHHHHHHHHHHhhcCCCCCCceeeccccchhHHH
Q 046372 35 TPTTDQIRILKELYYNNGVRSPTAEQIQKISARLRQYGKIEGKNVFYWFQNYKARER 91 (266)
Q Consensus 35 ~FT~eQL~iLE~~F~~~~n~yPs~e~R~eIA~~L~~~g~LsE~qVqvWFQNRRAKeK 91 (266)
.+++.|..+|+..|. -.+-..-..++||+.| ||+...|+.+...=|.|.|
T Consensus 262 ~L~~~~R~vl~lryg---L~~~e~~s~~EIA~~L----gis~~tV~~~~~rAl~kLr 311 (325)
T PRK05657 262 ELNDKQREVLARRFG---LLGYEAATLEDVAREI----GLTRERVRQIQVEALRRLR 311 (325)
T ss_pred cCCHHHHHHHHHHhc---cCCCCCcCHHHHHHHH----CcCHHHHHHHHHHHHHHHH
Confidence 457777777777662 1222233445789999 7999999998764444444
No 106
>PRK12538 RNA polymerase sigma factor; Provisional
Probab=22.10 E-value=42 Score=29.96 Aligned_cols=27 Identities=11% Similarity=0.009 Sum_probs=20.1
Q ss_pred HHHHHHHhhcCCCCCCceeeccccchhHHHH
Q 046372 62 QKISARLRQYGKIEGKNVFYWFQNYKARERL 92 (266)
Q Consensus 62 ~eIA~~L~~~g~LsE~qVqvWFQNRRAKeKR 92 (266)
++||+.| ||++..|++..+.=|.|.|+
T Consensus 191 ~EIA~~L----gis~~tVk~~l~RAr~kLr~ 217 (233)
T PRK12538 191 GEIAEVM----DTTVAAVESLLKRGRQQLRD 217 (233)
T ss_pred HHHHHHH----CcCHHHHHHHHHHHHHHHHH
Confidence 4789999 79999999888654444443
No 107
>PF07638 Sigma70_ECF: ECF sigma factor
Probab=22.05 E-value=55 Score=27.96 Aligned_cols=27 Identities=26% Similarity=0.296 Sum_probs=19.8
Q ss_pred HHHHHHHhhcCCCCCCceeeccccchhHHHH
Q 046372 62 QKISARLRQYGKIEGKNVFYWFQNYKARERL 92 (266)
Q Consensus 62 ~eIA~~L~~~g~LsE~qVqvWFQNRRAKeKR 92 (266)
++||+.| ||+++.|+..++-=|++.++
T Consensus 155 ~EIA~~l----giS~~tV~r~l~~aR~~l~~ 181 (185)
T PF07638_consen 155 EEIAERL----GISERTVRRRLRRARAWLRR 181 (185)
T ss_pred HHHHHHH----CcCHHHHHHHHHHHHHHHHH
Confidence 4678888 79999999777655554443
No 108
>PTZ00183 centrin; Provisional
Probab=21.46 E-value=2.9e+02 Score=21.62 Aligned_cols=40 Identities=18% Similarity=0.187 Sum_probs=27.0
Q ss_pred CCCCCCCCCHHHHHHHHHHHhh---CCCCCCCHHHHHHHHHHH
Q 046372 29 PTCPRWTPTTDQIRILKELYYN---NGVRSPTAEQIQKISARL 68 (266)
Q Consensus 29 ~rR~Rt~FT~eQL~iLE~~F~~---~~n~yPs~e~R~eIA~~L 68 (266)
++-.|..++++|++.|++.|.. ..+.+.+..+-..+...+
T Consensus 4 ~~~~~~~~~~~~~~~~~~~F~~~D~~~~G~i~~~e~~~~l~~~ 46 (158)
T PTZ00183 4 RRSERPGLTEDQKKEIREAFDLFDTDGSGTIDPKELKVAMRSL 46 (158)
T ss_pred cccccCCCCHHHHHHHHHHHHHhCCCCCCcccHHHHHHHHHHh
Confidence 3456888999999999999963 233556665554444443
No 109
>PRK12530 RNA polymerase sigma factor; Provisional
Probab=21.17 E-value=57 Score=27.60 Aligned_cols=43 Identities=14% Similarity=0.136 Sum_probs=26.7
Q ss_pred CHHHHHHHHHHHhhCCCCCCCHHHHHHHHHHHhhcCCCCCCceeeccccchhHH
Q 046372 37 TTDQIRILKELYYNNGVRSPTAEQIQKISARLRQYGKIEGKNVFYWFQNYKARE 90 (266)
Q Consensus 37 T~eQL~iLE~~F~~~~n~yPs~e~R~eIA~~L~~~g~LsE~qVqvWFQNRRAKe 90 (266)
++.|..+|.-.|.. + + ..++||+.| ||++..|+++..-=|.+.
T Consensus 136 p~~~R~v~~L~~~~-g--~----s~~EIA~~l----gis~~tVk~~l~RAr~~L 178 (189)
T PRK12530 136 PAQQARVFMMREYL-E--L----SSEQICQEC----DISTSNLHVLLYRARLQL 178 (189)
T ss_pred CHHHHHHHhHHHHc-C--C----CHHHHHHHH----CCCHHHHHHHHHHHHHHH
Confidence 44555555555431 2 2 234789999 799999999874333333
No 110
>PRK12536 RNA polymerase sigma factor; Provisional
Probab=20.97 E-value=60 Score=27.04 Aligned_cols=27 Identities=4% Similarity=-0.135 Sum_probs=19.4
Q ss_pred HHHHHHHHhhcCCCCCCceeeccccchhHHH
Q 046372 61 IQKISARLRQYGKIEGKNVFYWFQNYKARER 91 (266)
Q Consensus 61 R~eIA~~L~~~g~LsE~qVqvWFQNRRAKeK 91 (266)
.++||+.| +|++..|++....-|.|.|
T Consensus 148 ~~EIA~~l----~is~~tV~~~l~rar~~Lr 174 (181)
T PRK12536 148 VAETAQLT----GLSESAVKVGIHRGLKALA 174 (181)
T ss_pred HHHHHHHH----CCCHHHHHHHHHHHHHHHH
Confidence 35789999 6999999988844443333
No 111
>PRK06930 positive control sigma-like factor; Validated
Probab=20.88 E-value=66 Score=27.95 Aligned_cols=49 Identities=12% Similarity=0.029 Sum_probs=33.6
Q ss_pred CCCHHHHHHHHHHHhhCCCCCCCHHHHHHHHHHHhhcCCCCCCceeeccccchhHHHHhh
Q 046372 35 TPTTDQIRILKELYYNNGVRSPTAEQIQKISARLRQYGKIEGKNVFYWFQNYKARERLKK 94 (266)
Q Consensus 35 ~FT~eQL~iLE~~F~~~~n~yPs~e~R~eIA~~L~~~g~LsE~qVqvWFQNRRAKeKRkk 94 (266)
.+++.+..+|.-.|.. + .+ ..+||+.| +|++..|+++...-|.|.++.-
T Consensus 114 ~L~~rer~V~~L~~~e-g--~s----~~EIA~~l----giS~~tVk~~l~Ra~~kLr~~l 162 (170)
T PRK06930 114 VLTEREKEVYLMHRGY-G--LS----YSEIADYL----NIKKSTVQSMIERAEKKIARQI 162 (170)
T ss_pred hCCHHHHHHHHHHHHc-C--CC----HHHHHHHH----CcCHHHHHHHHHHHHHHHHHHH
Confidence 4677777877765531 2 22 24689999 6999999999876665555433
No 112
>PRK13919 putative RNA polymerase sigma E protein; Provisional
Probab=20.81 E-value=70 Score=26.50 Aligned_cols=43 Identities=19% Similarity=0.287 Sum_probs=25.5
Q ss_pred CCHHHHHHHHHHHhhCCCCCCCHHHHHHHHHHHhhcCCCCCCceeeccccchhHHH
Q 046372 36 PTTDQIRILKELYYNNGVRSPTAEQIQKISARLRQYGKIEGKNVFYWFQNYKARER 91 (266)
Q Consensus 36 FT~eQL~iLE~~F~~~~n~yPs~e~R~eIA~~L~~~g~LsE~qVqvWFQNRRAKeK 91 (266)
+++.+..+|.-.|.. + + .-++||+.| ||++..|+++-+ |||.|
T Consensus 136 L~~~~r~vl~l~~~~-~--~----s~~eIA~~l----gis~~~V~~~l~--ra~~~ 178 (186)
T PRK13919 136 LSPEERRVIEVLYYQ-G--Y----THREAAQLL----GLPLGTLKTRAR--RALSR 178 (186)
T ss_pred CCHHHHHHHHHHHHc-C--C----CHHHHHHHH----CcCHHHHHHHHH--HHHHH
Confidence 455555555544321 1 1 124688888 699999987654 44444
No 113
>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=20.78 E-value=63 Score=27.72 Aligned_cols=47 Identities=21% Similarity=0.095 Sum_probs=34.0
Q ss_pred CCCCCHHHHHHHHHHHhhCCCCCCCHHHHHHHHHHHhhcCCCCCCceeeccccchhHHH
Q 046372 33 RWTPTTDQIRILKELYYNNGVRSPTAEQIQKISARLRQYGKIEGKNVFYWFQNYKARER 91 (266)
Q Consensus 33 Rt~FT~eQL~iLE~~F~~~~n~yPs~e~R~eIA~~L~~~g~LsE~qVqvWFQNRRAKeK 91 (266)
.+.+|+.|+.+|+-.+. + + ..++||+.| +++...|..+-..-|-|.|
T Consensus 4 ~~~Lte~qr~VL~Lr~~--G--l----Tq~EIAe~L----giS~stV~~~e~ra~kkLr 50 (137)
T TIGR00721 4 KTFLTERQIKVLELREK--G--L----SQKEIAKEL----KTTRANVSAIEKRAMENIE 50 (137)
T ss_pred cCCCCHHHHHHHHHHHc--C--C----CHHHHHHHH----CcCHHHHHHHHHhHHHHHH
Confidence 46789999999998542 3 2 234799999 6999999887655444444
No 114
>PRK12546 RNA polymerase sigma factor; Provisional
Probab=20.52 E-value=68 Score=27.46 Aligned_cols=46 Identities=13% Similarity=-0.039 Sum_probs=28.5
Q ss_pred CCHHHHHHHHHHHhhCCCCCCCHHHHHHHHHHHhhcCCCCCCceeeccccchhHHHH
Q 046372 36 PTTDQIRILKELYYNNGVRSPTAEQIQKISARLRQYGKIEGKNVFYWFQNYKARERL 92 (266)
Q Consensus 36 FT~eQL~iLE~~F~~~~n~yPs~e~R~eIA~~L~~~g~LsE~qVqvWFQNRRAKeKR 92 (266)
+++.|..+|.-.|.. + ++ ..+||..| ||++..|+++.+-=|.+.|+
T Consensus 114 Lp~~~r~v~~L~~~~-g--~s----~~EIA~~L----giS~~tVk~~l~Rar~~Lr~ 159 (188)
T PRK12546 114 LPDEQREALILVGAS-G--FS----YEEAAEMC----GVAVGTVKSRANRARARLAE 159 (188)
T ss_pred CCHHHhHHhhhHHhc-C--CC----HHHHHHHH----CCCHHHHHHHHHHHHHHHHH
Confidence 455555555554421 1 22 24689999 79999999988654444443
No 115
>PRK09651 RNA polymerase sigma factor FecI; Provisional
Probab=20.41 E-value=60 Score=26.91 Aligned_cols=44 Identities=16% Similarity=0.115 Sum_probs=27.6
Q ss_pred CCCHHHHHHHHHHHhhCCCCCCCHHHHHHHHHHHhhcCCCCCCceeeccccchhHHH
Q 046372 35 TPTTDQIRILKELYYNNGVRSPTAEQIQKISARLRQYGKIEGKNVFYWFQNYKARER 91 (266)
Q Consensus 35 ~FT~eQL~iLE~~F~~~~n~yPs~e~R~eIA~~L~~~g~LsE~qVqvWFQNRRAKeK 91 (266)
.++++|..+|.-.|.. + . ..++||+.| ||++..|+++. +||+.+
T Consensus 119 ~L~~~~r~i~~l~~~~-g--~----s~~EIA~~l----gis~~tV~~~l--~Ra~~~ 162 (172)
T PRK09651 119 GLNGKTREAFLLSQLD-G--L----TYSEIAHKL----GVSVSSVKKYV--AKATEH 162 (172)
T ss_pred hCCHHHhHHhhhhhcc-C--C----CHHHHHHHh----CCCHHHHHHHH--HHHHHH
Confidence 3455566665554421 1 2 234789999 69999999876 455554
No 116
>PRK08295 RNA polymerase factor sigma-70; Validated
Probab=20.41 E-value=57 Score=27.45 Aligned_cols=20 Identities=25% Similarity=0.195 Sum_probs=15.3
Q ss_pred HHHHHHHhhcCCCCCCceeecccc
Q 046372 62 QKISARLRQYGKIEGKNVFYWFQN 85 (266)
Q Consensus 62 ~eIA~~L~~~g~LsE~qVqvWFQN 85 (266)
.+||..| ||++..|++....
T Consensus 174 ~EIA~~l----gis~~tV~~~l~r 193 (208)
T PRK08295 174 QEIAEEL----NRHVKSIDNALQR 193 (208)
T ss_pred HHHHHHH----CCCHHHHHHHHHH
Confidence 4689999 6999999864443
Done!