Query 023479
Match_columns 281
No_of_seqs 350 out of 1606
Neff 6.1
Searched_HMMs 46136
Date Fri Mar 29 04:21:03 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/023479.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/023479hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG3802 Transcription factor O 100.0 9.4E-43 2E-47 328.7 7.1 151 6-168 204-354 (398)
2 KOG1168 Transcription factor A 99.9 5.2E-23 1.1E-27 187.6 3.2 153 7-170 216-371 (385)
3 KOG0489 Transcription factor z 99.8 6.4E-19 1.4E-23 162.0 5.5 67 101-172 157-223 (261)
4 KOG0484 Transcription factor P 99.7 1.4E-18 3E-23 137.4 5.2 69 99-172 13-81 (125)
5 KOG0842 Transcription factor t 99.7 2E-17 4.3E-22 154.0 6.7 69 99-172 149-217 (307)
6 KOG0488 Transcription factor B 99.7 1.9E-17 4.2E-22 155.4 5.1 67 99-170 168-234 (309)
7 KOG0843 Transcription factor E 99.7 5.7E-17 1.2E-21 139.5 6.7 64 102-170 101-164 (197)
8 KOG2251 Homeobox transcription 99.7 3.6E-16 7.7E-21 138.5 11.2 68 98-170 32-99 (228)
9 KOG0487 Transcription factor A 99.7 3.4E-17 7.4E-22 152.5 4.4 66 101-171 233-298 (308)
10 PF00157 Pou: Pou domain - N-t 99.6 2.7E-17 5.9E-22 123.5 1.1 71 5-75 4-74 (75)
11 KOG0492 Transcription factor M 99.6 2.1E-16 4.6E-21 138.7 5.3 68 98-170 139-206 (246)
12 KOG0850 Transcription factor D 99.6 4.6E-16 9.9E-21 138.4 6.9 67 98-169 117-183 (245)
13 KOG0485 Transcription factor N 99.6 3.6E-16 7.8E-21 138.0 3.7 72 99-175 100-171 (268)
14 PF00046 Homeobox: Homeobox do 99.6 9.2E-16 2E-20 108.9 4.1 57 104-165 1-57 (57)
15 KOG0494 Transcription factor C 99.6 1.5E-15 3.2E-20 137.2 5.4 68 100-172 137-205 (332)
16 KOG0848 Transcription factor C 99.5 1.6E-15 3.4E-20 137.5 2.8 61 105-170 201-261 (317)
17 KOG0844 Transcription factor E 99.5 9E-15 2E-19 134.7 3.1 65 100-169 178-242 (408)
18 KOG4577 Transcription factor L 99.5 1.6E-13 3.4E-18 125.8 10.4 114 52-172 110-231 (383)
19 TIGR01565 homeo_ZF_HD homeobox 99.4 1.1E-13 2.4E-18 99.6 5.3 52 104-160 2-57 (58)
20 smart00389 HOX Homeodomain. DN 99.4 7.5E-14 1.6E-18 98.2 3.8 55 105-164 2-56 (56)
21 KOG0847 Transcription factor, 99.4 6.9E-14 1.5E-18 123.9 3.8 69 101-174 165-233 (288)
22 cd00086 homeodomain Homeodomai 99.4 1.2E-13 2.7E-18 97.7 4.4 57 105-166 2-58 (59)
23 KOG0486 Transcription factor P 99.4 1.2E-13 2.6E-18 127.8 5.0 68 99-171 108-175 (351)
24 KOG0493 Transcription factor E 99.4 1.1E-13 2.3E-18 125.3 3.6 59 104-167 247-305 (342)
25 KOG0483 Transcription factor H 99.4 1.5E-13 3.4E-18 121.3 3.0 61 104-169 51-111 (198)
26 KOG0491 Transcription factor B 99.4 9.6E-14 2.1E-18 118.1 1.6 66 102-172 99-164 (194)
27 COG5576 Homeodomain-containing 99.4 6.8E-13 1.5E-17 113.4 5.4 64 101-169 49-112 (156)
28 KOG0490 Transcription factor, 99.1 2.2E-11 4.8E-16 108.2 3.4 64 100-168 57-120 (235)
29 smart00352 POU Found in Pit-Oc 99.1 6E-11 1.3E-15 89.2 3.6 71 5-75 4-74 (75)
30 KOG0849 Transcription factor P 98.9 1.1E-09 2.4E-14 104.9 3.8 66 99-169 172-237 (354)
31 KOG0775 Transcription factor S 98.8 1.6E-08 3.4E-13 92.6 7.6 50 110-164 183-232 (304)
32 KOG0774 Transcription factor P 98.4 5.3E-06 1.1E-10 75.8 12.3 62 103-168 188-251 (334)
33 KOG2252 CCAAT displacement pro 98.2 2.4E-06 5.2E-11 84.9 6.7 58 101-163 418-475 (558)
34 PF05920 Homeobox_KN: Homeobox 98.1 8E-07 1.7E-11 59.3 0.8 33 126-162 8-40 (40)
35 KOG0490 Transcription factor, 97.9 9.5E-06 2.1E-10 72.0 3.6 64 100-168 150-213 (235)
36 KOG1146 Homeobox protein [Gene 97.3 0.00019 4.2E-09 77.6 4.4 64 102-170 902-965 (1406)
37 PF11569 Homez: Homeodomain le 95.1 0.0092 2E-07 42.7 1.1 42 115-161 10-51 (56)
38 KOG0773 Transcription factor M 94.6 0.028 6.1E-07 53.4 3.3 62 103-168 239-302 (342)
39 KOG3623 Homeobox transcription 94.2 0.042 9.1E-07 57.0 3.6 52 115-171 568-619 (1007)
40 PF08880 QLQ: QLQ; InterPro: 90.1 0.4 8.6E-06 31.5 3.1 22 42-63 2-23 (37)
41 PF04218 CENP-B_N: CENP-B N-te 88.0 0.68 1.5E-05 32.4 3.3 46 104-159 1-46 (53)
42 KOG3623 Homeobox transcription 86.6 4.6 0.0001 42.6 9.6 108 43-170 581-688 (1007)
43 PF04545 Sigma70_r4: Sigma-70, 55.6 14 0.0003 24.8 2.8 44 109-162 4-47 (50)
44 cd06171 Sigma70_r4 Sigma70, re 53.4 10 0.00022 24.4 1.8 43 109-161 10-52 (55)
45 PF01527 HTH_Tnp_1: Transposas 52.9 13 0.00028 26.8 2.5 44 105-157 2-45 (76)
46 PF08281 Sigma70_r4_2: Sigma-7 51.7 11 0.00024 25.5 1.9 41 110-160 11-51 (54)
47 PF04967 HTH_10: HTH DNA bindi 47.7 26 0.00056 24.7 3.2 38 110-153 1-41 (53)
48 cd00569 HTH_Hin_like Helix-tur 45.9 38 0.00083 19.2 3.5 38 109-156 5-42 (42)
49 PF11336 DUF3138: Protein of u 42.8 1.2E+02 0.0026 30.5 8.0 83 33-124 12-94 (514)
50 KOG3755 SATB1 matrix attachmen 41.2 7 0.00015 40.4 -0.7 64 104-168 692-759 (769)
51 KOG1146 Homeobox protein [Gene 37.0 42 0.00091 37.9 4.2 61 102-167 704-764 (1406)
52 PF00424 REV: REV protein (ant 37.0 32 0.00069 27.1 2.5 37 115-170 14-50 (91)
53 PRK09646 RNA polymerase sigma 36.6 39 0.00085 28.9 3.3 47 110-166 143-189 (194)
54 PRK09652 RNA polymerase sigma 34.0 39 0.00084 27.9 2.8 48 109-166 128-175 (182)
55 PRK03975 tfx putative transcri 33.9 46 0.001 28.1 3.2 51 108-169 5-55 (141)
56 PF10668 Phage_terminase: Phag 33.6 17 0.00037 26.3 0.5 20 133-156 24-43 (60)
57 PRK06759 RNA polymerase factor 33.0 39 0.00084 27.4 2.6 46 109-164 106-151 (154)
58 PRK12526 RNA polymerase sigma 31.7 50 0.0011 28.7 3.2 31 133-167 171-201 (206)
59 PF13936 HTH_38: Helix-turn-he 31.4 23 0.0005 23.5 0.8 39 108-156 3-41 (44)
60 COG3413 Predicted DNA binding 30.9 54 0.0012 28.9 3.4 48 109-164 155-205 (215)
61 PRK12512 RNA polymerase sigma 30.7 55 0.0012 27.5 3.2 49 110-168 132-180 (184)
62 PRK09642 RNA polymerase sigma 28.5 64 0.0014 26.4 3.2 48 110-167 107-154 (160)
63 PRK11924 RNA polymerase sigma 28.3 57 0.0012 26.8 2.9 31 133-167 143-173 (179)
64 PRK12519 RNA polymerase sigma 28.3 45 0.00098 28.3 2.3 32 131-166 157-188 (194)
65 PRK12515 RNA polymerase sigma 26.8 72 0.0015 27.0 3.3 50 109-168 131-180 (189)
66 PRK04217 hypothetical protein; 26.5 72 0.0016 25.8 3.0 50 108-167 41-90 (110)
67 TIGR02937 sigma70-ECF RNA poly 26.4 60 0.0013 25.3 2.6 46 109-164 110-155 (158)
68 TIGR02959 SigZ RNA polymerase 26.2 93 0.002 26.0 3.8 50 109-168 100-149 (170)
69 PRK09413 IS2 repressor TnpA; R 26.2 81 0.0018 25.3 3.3 40 107-156 10-50 (121)
70 PRK12514 RNA polymerase sigma 25.7 76 0.0016 26.5 3.2 29 133-165 147-175 (179)
71 PRK00118 putative DNA-binding 25.5 74 0.0016 25.5 2.9 47 110-166 18-64 (104)
72 TIGR02999 Sig-70_X6 RNA polyme 25.4 69 0.0015 26.8 2.9 46 110-165 135-180 (183)
73 PF02796 HTH_7: Helix-turn-hel 25.2 49 0.0011 21.9 1.6 38 109-156 5-42 (45)
74 PRK12533 RNA polymerase sigma 24.9 80 0.0017 28.0 3.4 31 133-167 152-182 (216)
75 TIGR02948 SigW_bacill RNA poly 24.4 69 0.0015 26.8 2.7 31 132-166 153-183 (187)
76 PF00196 GerE: Bacterial regul 23.8 72 0.0016 21.9 2.3 44 109-163 3-46 (58)
77 PRK09644 RNA polymerase sigma 23.8 79 0.0017 26.1 3.0 49 110-168 109-157 (165)
78 TIGR02985 Sig70_bacteroi1 RNA 23.4 80 0.0017 25.3 2.9 45 110-164 114-158 (161)
79 PRK09648 RNA polymerase sigma 23.2 81 0.0017 26.7 2.9 47 109-165 139-185 (189)
80 PF06056 Terminase_5: Putative 22.7 23 0.00049 25.3 -0.5 26 134-165 16-41 (58)
81 PRK09637 RNA polymerase sigma 22.5 79 0.0017 26.9 2.7 48 110-167 107-154 (181)
82 TIGR03879 near_KaiC_dom probab 22.3 28 0.00061 26.2 -0.1 25 130-158 31-55 (73)
83 PRK09480 slmA division inhibit 22.1 73 0.0016 26.6 2.4 37 119-161 20-56 (194)
84 TIGR02983 SigE-fam_strep RNA p 21.7 92 0.002 25.4 2.9 46 111-166 112-157 (162)
85 PRK12537 RNA polymerase sigma 21.7 99 0.0021 26.0 3.2 28 133-164 151-178 (182)
86 PRK09639 RNA polymerase sigma 21.3 1E+02 0.0022 25.2 3.1 48 109-167 112-159 (166)
87 COG4367 Uncharacterized protei 21.2 98 0.0021 24.4 2.7 39 109-152 2-40 (97)
88 PRK12541 RNA polymerase sigma 21.2 79 0.0017 25.9 2.4 46 110-165 113-158 (161)
89 PRK05602 RNA polymerase sigma 21.1 95 0.0021 26.1 3.0 31 134-168 147-177 (186)
90 TIGR02989 Sig-70_gvs1 RNA poly 21.1 88 0.0019 25.3 2.7 40 109-158 111-150 (159)
91 PRK12530 RNA polymerase sigma 20.6 97 0.0021 26.4 2.9 30 133-166 152-181 (189)
92 PRK06930 positive control sigm 20.4 1.1E+02 0.0023 26.4 3.1 50 109-168 114-163 (170)
93 TIGR02939 RpoE_Sigma70 RNA pol 20.4 81 0.0018 26.4 2.4 32 130-165 153-184 (190)
No 1
>KOG3802 consensus Transcription factor OCT-1, contains POU and HOX domains [Transcription]
Probab=100.00 E-value=9.4e-43 Score=328.74 Aligned_cols=151 Identities=20% Similarity=0.247 Sum_probs=133.3
Q ss_pred HHHHHHHHHHhhhhhhhhcCCCCCCCcccCcccccccCCHHHHHHHHHHHHHHHHHHHHHHHhhhhhhhhhhhhhcCCCC
Q 023479 6 IREAAQQETQTQNQNQNQRGGENDNNNVVNGVMYVKVMTDEQLETLRKQIAVYATICEQLVEMHKSLSAHQDLAAAGGRL 85 (281)
Q Consensus 6 ~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~g~~~~~~~t~~~~~~lr~qi~~~~~~c~~~~~~~k~ls~~~~~~~~g~~~ 85 (281)
..||||||||+||||||||||||+|||+|+|+|||+|||+++||||+++..+|++||++++++.|||.+++.....+
T Consensus 204 ~leELEqFAK~FKqRRIkLGfTQaDVGlALG~lyGn~FSQTTIcRFEALqLSFKNMCKLKPLL~KWLeEAes~~~~~--- 280 (398)
T KOG3802|consen 204 DLEELEQFAKTFKQRRIKLGFTQADVGLALGALYGNVFSQTTICRFEALQLSFKNMCKLKPLLEKWLEEAESRESTG--- 280 (398)
T ss_pred CHHHHHHHHHHHHhheeccccchhHHHHHHHhhhCcccchhhhhHhHhhccCHHHHhhhHHHHHHHHHHHhcccccC---
Confidence 36899999999999999999999999999999999999999999999999999999999999999999988753111
Q ss_pred CCccCCCCCcCCCCCCCCCCCCCCCChHHHHHHHHHHhhcCCCCCHhHHHHHHHHHHhcCCCccccccccccchhhHHHH
Q 023479 86 GNIYCDPLMTSGGGHKISARQRWTPTPVQLQILESIFDQGTGTPSKQKIKEITVELSQHGQISETNVYNWFQNRRARSKR 165 (281)
Q Consensus 86 g~~~~~p~~~s~~~~~~~rr~Rt~ft~~Ql~~LE~~F~~~~~~Ps~~~r~~LA~~L~~~~gLse~qV~vWFQNRRaK~Kr 165 (281)
+....+-+. ...++||+||.|+...+..||+.|..| ++|+.++|..||.+| +|.+.+|+|||||||.|+||
T Consensus 281 ~~~~~e~i~----a~~RkRKKRTSie~~vr~aLE~~F~~n-pKPt~qEIt~iA~~L----~leKEVVRVWFCNRRQkeKR 351 (398)
T KOG3802|consen 281 SPNSIEKIG----AQSRKRKKRTSIEVNVRGALEKHFLKN-PKPTSQEITHIAESL----QLEKEVVRVWFCNRRQKEKR 351 (398)
T ss_pred CCCCHHHhh----ccccccccccceeHHHHHHHHHHHHhC-CCCCHHHHHHHHHHh----ccccceEEEEeecccccccc
Confidence 111122111 122678889999999999999999998 999999999999999 99999999999999999999
Q ss_pred Hhh
Q 023479 166 KQL 168 (281)
Q Consensus 166 ~~~ 168 (281)
...
T Consensus 352 ~~~ 354 (398)
T KOG3802|consen 352 ITP 354 (398)
T ss_pred CCC
Confidence 876
No 2
>KOG1168 consensus Transcription factor ACJ6/BRN-3, contains POU and HOX domains [Transcription]
Probab=99.86 E-value=5.2e-23 Score=187.57 Aligned_cols=153 Identities=16% Similarity=0.181 Sum_probs=125.1
Q ss_pred HHHHHHHHHhhhhhhhhcCCCCCCCcccCccc---ccccCCHHHHHHHHHHHHHHHHHHHHHHHhhhhhhhhhhhhhcCC
Q 023479 7 REAAQQETQTQNQNQNQRGGENDNNNVVNGVM---YVKVMTDEQLETLRKQIAVYATICEQLVEMHKSLSAHQDLAAAGG 83 (281)
Q Consensus 7 ~~~~~~~~~~~~~~~~~~g~~~~~~~~~~g~~---~~~~~t~~~~~~lr~qi~~~~~~c~~~~~~~k~ls~~~~~~~~g~ 83 (281)
-.+||-||.-|||||||||.||+|||-|+--| -+..+|+.+||||+.+..+-.+|.-+++.++.||..+......-.
T Consensus 216 PReLEaFAErFKQRRIKLGVTQADVG~ALAnLKiPGVGsLSQSTICRFESLTLSHNNMiALKPILqaWLEeAE~a~keK~ 295 (385)
T KOG1168|consen 216 PRELEAFAERFKQRRIKLGVTQADVGKALANLKIPGVGSLSQSTICRFESLTLSHNNMIALKPILQAWLEEAEAAMKEKD 295 (385)
T ss_pred HHHHHHHHHHHHhhhhhhcccHHHHHHHHHhCcCCCcccccccceeeeeeeccccCcchhhhHHHHHHHHHHHHHHHhhc
Confidence 45899999999999999999999999665433 677899999999999999999999999999999988754331111
Q ss_pred CCCCccCCCCCcCCCCCCCCCCCCCCCChHHHHHHHHHHhhcCCCCCHhHHHHHHHHHHhcCCCccccccccccchhhHH
Q 023479 84 RLGNIYCDPLMTSGGGHKISARQRWTPTPVQLQILESIFDQGTGTPSKQKIKEITVELSQHGQISETNVYNWFQNRRARS 163 (281)
Q Consensus 84 ~~g~~~~~p~~~s~~~~~~~rr~Rt~ft~~Ql~~LE~~F~~~~~~Ps~~~r~~LA~~L~~~~gLse~qV~vWFQNRRaK~ 163 (281)
..+ ....+.+ ++ -+||+||.+.....+.||.+|... +.|+.+.+..||++| .|.+.+|+|||||.|+|.
T Consensus 296 ~~p--d~~~l~~--~~--ekKRKRTSIAAPEKRsLEayFavQ-PRPS~EkIAaIAekL----DLKKNVVRVWFCNQRQKQ 364 (385)
T KOG1168|consen 296 TKP--DINELLP--GG--EKKRKRTSIAAPEKRSLEAYFAVQ-PRPSGEKIAAIAEKL----DLKKNVVRVWFCNQRQKQ 364 (385)
T ss_pred cCC--chhhccC--cc--ccccccccccCcccccHHHHhccC-CCCchhHHHHHHHhh----hhhhceEEEEeeccHHHH
Confidence 111 0001111 12 357789999999999999999997 999999999999999 999999999999999999
Q ss_pred HHHhhhh
Q 023479 164 KRKQLVS 170 (281)
Q Consensus 164 Kr~~~~~ 170 (281)
||.....
T Consensus 365 KRm~~Sa 371 (385)
T KOG1168|consen 365 KRMKRSA 371 (385)
T ss_pred HHhhhhh
Confidence 9966543
No 3
>KOG0489 consensus Transcription factor zerknullt and related HOX domain proteins [General function prediction only]
Probab=99.75 E-value=6.4e-19 Score=162.01 Aligned_cols=67 Identities=33% Similarity=0.383 Sum_probs=63.2
Q ss_pred CCCCCCCCCCChHHHHHHHHHHhhcCCCCCHhHHHHHHHHHHhcCCCccccccccccchhhHHHHHhhhhcc
Q 023479 101 KISARQRWTPTPVQLQILESIFDQGTGTPSKQKIKEITVELSQHGQISETNVYNWFQNRRARSKRKQLVSSS 172 (281)
Q Consensus 101 ~~~rr~Rt~ft~~Ql~~LE~~F~~~~~~Ps~~~r~~LA~~L~~~~gLse~qV~vWFQNRRaK~Kr~~~~~~~ 172 (281)
...||.||.||..||.+||+.|+.| +|+++.+|.|||..| +|+|+||+||||||||||||..+....
T Consensus 157 ~~~kR~RtayT~~QllELEkEFhfN-~YLtR~RRiEiA~~L----~LtErQIKIWFQNRRMK~Kk~~k~~~~ 223 (261)
T KOG0489|consen 157 GKSKRRRTAFTRYQLLELEKEFHFN-KYLTRSRRIEIAHAL----NLTERQIKIWFQNRRMKWKKENKAKSS 223 (261)
T ss_pred CCCCCCCcccchhhhhhhhhhhccc-cccchHHHHHHHhhc----chhHHHHHHHHHHHHHHHHHhhccccc
Confidence 4578999999999999999999998 999999999999999 999999999999999999999887655
No 4
>KOG0484 consensus Transcription factor PHOX2/ARIX, contains HOX domain [Transcription]
Probab=99.74 E-value=1.4e-18 Score=137.36 Aligned_cols=69 Identities=32% Similarity=0.494 Sum_probs=63.5
Q ss_pred CCCCCCCCCCCCChHHHHHHHHHHhhcCCCCCHhHHHHHHHHHHhcCCCccccccccccchhhHHHHHhhhhcc
Q 023479 99 GHKISARQRWTPTPVQLQILESIFDQGTGTPSKQKIKEITVELSQHGQISETNVYNWFQNRRARSKRKQLVSSS 172 (281)
Q Consensus 99 ~~~~~rr~Rt~ft~~Ql~~LE~~F~~~~~~Ps~~~r~~LA~~L~~~~gLse~qV~vWFQNRRaK~Kr~~~~~~~ 172 (281)
..++.||-||+||..||.+||+.|.. ++||++-.|++||.++ .|++..|+|||||||+|.||+.+....
T Consensus 13 ekrKQRRIRTTFTS~QLkELErvF~E-THYPDIYTREEiA~ki----dLTEARVQVWFQNRRAKfRKQEr~a~~ 81 (125)
T KOG0484|consen 13 EKRKQRRIRTTFTSAQLKELERVFAE-THYPDIYTREEIALKI----DLTEARVQVWFQNRRAKFRKQERAAIA 81 (125)
T ss_pred HHHHhhhhhhhhhHHHHHHHHHHHHh-hcCCcchhHHHHHHhh----hhhHHHHHHHHHhhHHHHHHHHHHHHH
Confidence 44567889999999999999999999 5999999999999999 999999999999999999999887544
No 5
>KOG0842 consensus Transcription factor tinman/NKX2-3, contains HOX domain [Transcription]
Probab=99.70 E-value=2e-17 Score=154.00 Aligned_cols=69 Identities=29% Similarity=0.383 Sum_probs=64.2
Q ss_pred CCCCCCCCCCCCChHHHHHHHHHHhhcCCCCCHhHHHHHHHHHHhcCCCccccccccccchhhHHHHHhhhhcc
Q 023479 99 GHKISARQRWTPTPVQLQILESIFDQGTGTPSKQKIKEITVELSQHGQISETNVYNWFQNRRARSKRKQLVSSS 172 (281)
Q Consensus 99 ~~~~~rr~Rt~ft~~Ql~~LE~~F~~~~~~Ps~~~r~~LA~~L~~~~gLse~qV~vWFQNRRaK~Kr~~~~~~~ 172 (281)
+..++||+|..|+..|+.+||+.|..+ +|++.+||+.||..| .|+++||||||||||.|.||+++....
T Consensus 149 ~~~~kRKrRVLFSqAQV~ELERRFrqQ-RYLSAPERE~LA~~L----rLT~TQVKIWFQNrRYK~KR~~~dk~~ 217 (307)
T KOG0842|consen 149 GKRKKRKRRVLFSQAQVYELERRFRQQ-RYLSAPEREHLASSL----RLTPTQVKIWFQNRRYKTKRQQKDKAL 217 (307)
T ss_pred ccccccccccccchhHHHHHHHHHHhh-hccccHhHHHHHHhc----CCCchheeeeeecchhhhhhhhhhhhh
Confidence 455677889999999999999999998 999999999999999 999999999999999999999988665
No 6
>KOG0488 consensus Transcription factor BarH and related HOX domain proteins [General function prediction only]
Probab=99.68 E-value=1.9e-17 Score=155.39 Aligned_cols=67 Identities=28% Similarity=0.349 Sum_probs=63.2
Q ss_pred CCCCCCCCCCCCChHHHHHHHHHHhhcCCCCCHhHHHHHHHHHHhcCCCccccccccccchhhHHHHHhhhh
Q 023479 99 GHKISARQRWTPTPVQLQILESIFDQGTGTPSKQKIKEITVELSQHGQISETNVYNWFQNRRARSKRKQLVS 170 (281)
Q Consensus 99 ~~~~~rr~Rt~ft~~Ql~~LE~~F~~~~~~Ps~~~r~~LA~~L~~~~gLse~qV~vWFQNRRaK~Kr~~~~~ 170 (281)
..+++|+.||.||..||..||+.|++. +|.+..+|.+||..| ||+..||++||||||+||||.....
T Consensus 168 ~pkK~RksRTaFT~~Ql~~LEkrF~~Q-KYLS~~DR~~LA~~L----gLTdaQVKtWfQNRRtKWKrq~a~g 234 (309)
T KOG0488|consen 168 TPKKRRKSRTAFSDHQLFELEKRFEKQ-KYLSVADRIELAASL----GLTDAQVKTWFQNRRTKWKRQTAEG 234 (309)
T ss_pred CCcccccchhhhhHHHHHHHHHHHHHh-hcccHHHHHHHHHHc----CCchhhHHHHHhhhhHHHHHHHHhh
Confidence 457888899999999999999999998 999999999999999 9999999999999999999988763
No 7
>KOG0843 consensus Transcription factor EMX1 and related HOX domain proteins [Transcription]
Probab=99.68 E-value=5.7e-17 Score=139.50 Aligned_cols=64 Identities=38% Similarity=0.447 Sum_probs=61.3
Q ss_pred CCCCCCCCCChHHHHHHHHHHhhcCCCCCHhHHHHHHHHHHhcCCCccccccccccchhhHHHHHhhhh
Q 023479 102 ISARQRWTPTPVQLQILESIFDQGTGTPSKQKIKEITVELSQHGQISETNVYNWFQNRRARSKRKQLVS 170 (281)
Q Consensus 102 ~~rr~Rt~ft~~Ql~~LE~~F~~~~~~Ps~~~r~~LA~~L~~~~gLse~qV~vWFQNRRaK~Kr~~~~~ 170 (281)
+.||.||.|+++||..||.+|+.+ +|....+|+.||..| +|++.||+|||||||.|.||++.+.
T Consensus 101 ~~kr~RT~ft~~Ql~~LE~~F~~~-~Yvvg~eR~~LA~~L----~LsetQVkvWFQNRRtk~kr~~~e~ 164 (197)
T KOG0843|consen 101 RPKRIRTAFTPEQLLKLEHAFEGN-QYVVGAERKQLAQSL----SLSETQVKVWFQNRRTKHKRMQQED 164 (197)
T ss_pred CCCccccccCHHHHHHHHHHHhcC-CeeechHHHHHHHHc----CCChhHhhhhhhhhhHHHHHHHHHh
Confidence 678899999999999999999998 999999999999999 9999999999999999999988774
No 8
>KOG2251 consensus Homeobox transcription factor [Transcription]
Probab=99.67 E-value=3.6e-16 Score=138.47 Aligned_cols=68 Identities=35% Similarity=0.574 Sum_probs=64.5
Q ss_pred CCCCCCCCCCCCCChHHHHHHHHHHhhcCCCCCHhHHHHHHHHHHhcCCCccccccccccchhhHHHHHhhhh
Q 023479 98 GGHKISARQRWTPTPVQLQILESIFDQGTGTPSKQKIKEITVELSQHGQISETNVYNWFQNRRARSKRKQLVS 170 (281)
Q Consensus 98 ~~~~~~rr~Rt~ft~~Ql~~LE~~F~~~~~~Ps~~~r~~LA~~L~~~~gLse~qV~vWFQNRRaK~Kr~~~~~ 170 (281)
.+.++.||.||+|+..||.+||.+|.+ |.||+...|++||.+| +|.+.+|+|||+|||+|+|++++..
T Consensus 32 ~~pRkqRRERTtFtr~QlevLe~LF~k-TqYPDv~~rEelAlkl----nLpeSrVqVWFKNRRAK~r~qq~qq 99 (228)
T KOG2251|consen 32 SGPRKQRRERTTFTRKQLEVLEALFAK-TQYPDVFMREELALKL----NLPESRVQVWFKNRRAKCRRQQQQQ 99 (228)
T ss_pred ccchhcccccceecHHHHHHHHHHHHh-hcCccHHHHHHHHHHh----CCchhhhhhhhccccchhhHhhhhh
Confidence 377889999999999999999999999 5999999999999999 9999999999999999999998875
No 9
>KOG0487 consensus Transcription factor Abd-B, contains HOX domain [Transcription]
Probab=99.67 E-value=3.4e-17 Score=152.50 Aligned_cols=66 Identities=29% Similarity=0.320 Sum_probs=61.7
Q ss_pred CCCCCCCCCCChHHHHHHHHHHhhcCCCCCHhHHHHHHHHHHhcCCCccccccccccchhhHHHHHhhhhc
Q 023479 101 KISARQRWTPTPVQLQILESIFDQGTGTPSKQKIKEITVELSQHGQISETNVYNWFQNRRARSKRKQLVSS 171 (281)
Q Consensus 101 ~~~rr~Rt~ft~~Ql~~LE~~F~~~~~~Ps~~~r~~LA~~L~~~~gLse~qV~vWFQNRRaK~Kr~~~~~~ 171 (281)
+..|++|..+|+.|+.+||+.|..| .|+++++|.+|++.| +|+++||+|||||||+|.||..++..
T Consensus 233 ~~~RKKRcPYTK~QtlELEkEFlfN-~YitkeKR~ElSr~l----NLTeRQVKIWFQNRRMK~KK~~re~r 298 (308)
T KOG0487|consen 233 RRGRKKRCPYTKHQTLELEKEFLFN-MYITKEKRLELSRTL----NLTERQVKIWFQNRRMKEKKVNRENR 298 (308)
T ss_pred cccccccCCchHHHHHHHHHHHHHH-HHHhHHHHHHHHHhc----ccchhheeeeehhhhhHHhhhhhhhh
Confidence 5678899999999999999999998 899999999999999 99999999999999999999987543
No 10
>PF00157 Pou: Pou domain - N-terminal to homeobox domain; InterPro: IPR000327 POU proteins are eukaryotic transcription factors containing a bipartite DNA binding domain referred to as the POU domain. The acronym POU (pronounced 'pow') is derived from the names of three mammalian transcription factors, the pituitary-specific Pit-1, the octamer-binding proteins Oct-1 and Oct-2, and the neural Unc-86 from Caenorhabditis elegans. POU domain genes have been identified in diverse organisms including nematodes, flies, amphibians, fish and mammals but have not been yet identified in plants and fungi. The various members of the POU family have a wide variety of functions, all of which are related to the function of the neuroendocrine system [] and the development of an organism []. Some other genes are also regulated, including those for immunoglobulin light and heavy chains (Oct-2) [, ], and trophic hormone genes, such as those for prolactin and growth hormone (Pit-1). The POU domain is a bipartite domain composed of two subunits separated by a non-conserved region of 15-55 aa. The N-terminal subunit is known as the POU-specific (POUs) domain (IPR000327 from INTERPRO), while the C-terminal subunit is a homeobox domain (IPR007103 from INTERPRO). 3D structures of complexes including both POU subdomains bound to DNA are available. Both subdomains contain the structural motif 'helix-turn-helix', which directly associates with the two components of bipartite DNA binding sites, and both are required for high affinity sequence-specific DNA-binding. The domain may also be involved in protein-protein interactions []. The subdomains are connected by a flexible linker [, , ]. In proteins a POU-specific domain is always accompanied by a homeodomain. Despite of the lack of sequence homology, 3D structure of POUs is similar to 3D structure of bacteriophage lambda repressor and other members of HTH_3 family [, ]. This entry represents the POU-specific subunit of the POU domain.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent; PDB: 3D1N_O 1AU7_A 3L1P_A 2XSD_C 1O4X_A 1HF0_B 1GT0_C 1POU_A 1CQT_B 1E3O_C ....
Probab=99.65 E-value=2.7e-17 Score=123.50 Aligned_cols=71 Identities=13% Similarity=0.128 Sum_probs=65.9
Q ss_pred hHHHHHHHHHHhhhhhhhhcCCCCCCCcccCcccccccCCHHHHHHHHHHHHHHHHHHHHHHHhhhhhhhh
Q 023479 5 NIREAAQQETQTQNQNQNQRGGENDNNNVVNGVMYVKVMTDEQLETLRKQIAVYATICEQLVEMHKSLSAH 75 (281)
Q Consensus 5 ~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~g~~~~~~~t~~~~~~lr~qi~~~~~~c~~~~~~~k~ls~~ 75 (281)
...+++++||+.||||||++||+|.|||.++|.+||++||+++|+||+++..++++||+.++.+.+||...
T Consensus 4 ~~~~ele~Fa~~fk~rRi~LG~TQ~dVg~al~~~~G~~~SQttI~RFE~L~LS~kn~~klkP~L~kWL~ea 74 (75)
T PF00157_consen 4 PDLKELEQFAKEFKQRRIKLGYTQADVGAALGRLYGKEFSQTTICRFEALQLSFKNMCKLKPLLEKWLEEA 74 (75)
T ss_dssp HHHHHHHHHHHHHHHHHHHTT--HHHHHHHHHHHHSSGGSHHHHHHHHTTTSCHHHHHHHHHHHHHHHHHH
T ss_pred cCHHHHHHHHHHHHHhhhhcccCHHHHhHHHHHhcCccccchhhhhhHhcccCHHHHHHHHHHHHHHHHhc
Confidence 35789999999999999999999999999999999999999999999999999999999999999998764
No 11
>KOG0492 consensus Transcription factor MSH, contains HOX domain [General function prediction only]
Probab=99.63 E-value=2.1e-16 Score=138.65 Aligned_cols=68 Identities=37% Similarity=0.422 Sum_probs=63.4
Q ss_pred CCCCCCCCCCCCCChHHHHHHHHHHhhcCCCCCHhHHHHHHHHHHhcCCCccccccccccchhhHHHHHhhhh
Q 023479 98 GGHKISARQRWTPTPVQLQILESIFDQGTGTPSKQKIKEITVELSQHGQISETNVYNWFQNRRARSKRKQLVS 170 (281)
Q Consensus 98 ~~~~~~rr~Rt~ft~~Ql~~LE~~F~~~~~~Ps~~~r~~LA~~L~~~~gLse~qV~vWFQNRRaK~Kr~~~~~ 170 (281)
.+|+..|++||.||..||..||+.|... +|.++.+|.+++..| .|+++||+|||||||+|.||.+...
T Consensus 139 rKhk~nRkPRtPFTtqQLlaLErkfrek-qYLSiaEraefSsSL----~LTeTqVKIWFQNRRAKaKRlQeae 206 (246)
T KOG0492|consen 139 RKHKPNRKPRTPFTTQQLLALERKFREK-QYLSIAERAEFSSSL----ELTETQVKIWFQNRRAKAKRLQEAE 206 (246)
T ss_pred cccCCCCCCCCCCCHHHHHHHHHHHhHh-hhhhHHHHHhhhhhh----hhhhhheehhhhhhhHHHHHHHHHH
Confidence 3777788999999999999999999997 999999999999999 9999999999999999999987653
No 12
>KOG0850 consensus Transcription factor DLX and related proteins with LIM Zn-binding and HOX domains [Transcription]
Probab=99.63 E-value=4.6e-16 Score=138.44 Aligned_cols=67 Identities=30% Similarity=0.387 Sum_probs=63.5
Q ss_pred CCCCCCCCCCCCCChHHHHHHHHHHhhcCCCCCHhHHHHHHHHHHhcCCCccccccccccchhhHHHHHhhh
Q 023479 98 GGHKISARQRWTPTPVQLQILESIFDQGTGTPSKQKIKEITVELSQHGQISETNVYNWFQNRRARSKRKQLV 169 (281)
Q Consensus 98 ~~~~~~rr~Rt~ft~~Ql~~LE~~F~~~~~~Ps~~~r~~LA~~L~~~~gLse~qV~vWFQNRRaK~Kr~~~~ 169 (281)
|..+|.|++||.++.-||..|.+.|++. .|+-.+||.+||..| ||+.+||+|||||||.|.||..+.
T Consensus 117 gk~KK~RKPRTIYSS~QLqaL~rRFQkT-QYLALPERAeLAAsL----GLTQTQVKIWFQNrRSK~KKl~k~ 183 (245)
T KOG0850|consen 117 GKGKKVRKPRTIYSSLQLQALNRRFQQT-QYLALPERAELAASL----GLTQTQVKIWFQNRRSKFKKLKKQ 183 (245)
T ss_pred CCcccccCCcccccHHHHHHHHHHHhhc-chhcCcHHHHHHHHh----CCchhHhhhhhhhhHHHHHHHHhc
Confidence 4677889999999999999999999995 999999999999999 999999999999999999999884
No 13
>KOG0485 consensus Transcription factor NKX-5.1/HMX1, contains HOX domain [Transcription]
Probab=99.60 E-value=3.6e-16 Score=138.04 Aligned_cols=72 Identities=31% Similarity=0.378 Sum_probs=64.5
Q ss_pred CCCCCCCCCCCCChHHHHHHHHHHhhcCCCCCHhHHHHHHHHHHhcCCCccccccccccchhhHHHHHhhhhccccc
Q 023479 99 GHKISARQRWTPTPVQLQILESIFDQGTGTPSKQKIKEITVELSQHGQISETNVYNWFQNRRARSKRKQLVSSSANT 175 (281)
Q Consensus 99 ~~~~~rr~Rt~ft~~Ql~~LE~~F~~~~~~Ps~~~r~~LA~~L~~~~gLse~qV~vWFQNRRaK~Kr~~~~~~~~~~ 175 (281)
+..++|+.||+|+..|+..||..|+.. +|++..+|..||.+| .|+|+||+|||||||.||||+....-.+..
T Consensus 100 g~~RKKktRTvFSraQV~qLEs~Fe~k-rYLSsaeRa~LA~sL----qLTETQVKIWFQNRRnKwKRq~aad~ea~s 171 (268)
T KOG0485|consen 100 GDDRKKKTRTVFSRAQVFQLESTFELK-RYLSSAERAGLAASL----QLTETQVKIWFQNRRNKWKRQYAADLEAAS 171 (268)
T ss_pred cccccccchhhhhHHHHHHHHHHHHHH-hhhhHHHHhHHHHhh----hhhhhhhhhhhhhhhHHHHHHHhhhhhhhh
Confidence 344678899999999999999999997 999999999999999 999999999999999999998876554443
No 14
>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=99.59 E-value=9.2e-16 Score=108.88 Aligned_cols=57 Identities=42% Similarity=0.663 Sum_probs=54.8
Q ss_pred CCCCCCCChHHHHHHHHHHhhcCCCCCHhHHHHHHHHHHhcCCCccccccccccchhhHHHH
Q 023479 104 ARQRWTPTPVQLQILESIFDQGTGTPSKQKIKEITVELSQHGQISETNVYNWFQNRRARSKR 165 (281)
Q Consensus 104 rr~Rt~ft~~Ql~~LE~~F~~~~~~Ps~~~r~~LA~~L~~~~gLse~qV~vWFQNRRaK~Kr 165 (281)
||+|+.|+.+|+.+||.+|..+ +||+..++..||..| ||+..+|++||+|||+++||
T Consensus 1 kr~r~~~t~~q~~~L~~~f~~~-~~p~~~~~~~la~~l----~l~~~~V~~WF~nrR~k~kk 57 (57)
T PF00046_consen 1 KRKRTRFTKEQLKVLEEYFQEN-PYPSKEEREELAKEL----GLTERQVKNWFQNRRRKEKK 57 (57)
T ss_dssp SSSSSSSSHHHHHHHHHHHHHS-SSCHHHHHHHHHHHH----TSSHHHHHHHHHHHHHHHHH
T ss_pred CcCCCCCCHHHHHHHHHHHHHh-ccccccccccccccc----cccccccccCHHHhHHHhCc
Confidence 5789999999999999999997 999999999999999 99999999999999999986
No 15
>KOG0494 consensus Transcription factor CHX10 and related HOX domain proteins [General function prediction only]
Probab=99.58 E-value=1.5e-15 Score=137.23 Aligned_cols=68 Identities=26% Similarity=0.363 Sum_probs=60.7
Q ss_pred CCCCCCC-CCCCChHHHHHHHHHHhhcCCCCCHhHHHHHHHHHHhcCCCccccccccccchhhHHHHHhhhhcc
Q 023479 100 HKISARQ-RWTPTPVQLQILESIFDQGTGTPSKQKIKEITVELSQHGQISETNVYNWFQNRRARSKRKQLVSSS 172 (281)
Q Consensus 100 ~~~~rr~-Rt~ft~~Ql~~LE~~F~~~~~~Ps~~~r~~LA~~L~~~~gLse~qV~vWFQNRRaK~Kr~~~~~~~ 172 (281)
.+++||. ||.||..|+..||+.|... +||+..-|+-||.++ .|.|.+|+|||||||+||||.++.-..
T Consensus 137 kk~kRRh~RTiFT~~Qle~LEkaFkea-HYPDv~Are~la~kt----elpEDRIqVWfQNRRAKWRk~Ek~wg~ 205 (332)
T KOG0494|consen 137 KKKKRRHFRTIFTSYQLEELEKAFKEA-HYPDVYAREMLADKT----ELPEDRIQVWFQNRRAKWRKTEKRWGG 205 (332)
T ss_pred cccccccccchhhHHHHHHHHHHHhhc-cCccHHHHHHHhhhc----cCchhhhhHHhhhhhHHhhhhhhhcCc
Confidence 3334444 9999999999999999997 999999999999999 999999999999999999999887543
No 16
>KOG0848 consensus Transcription factor Caudal, contains HOX domain [Transcription]
Probab=99.55 E-value=1.6e-15 Score=137.50 Aligned_cols=61 Identities=30% Similarity=0.372 Sum_probs=57.7
Q ss_pred CCCCCCChHHHHHHHHHHhhcCCCCCHhHHHHHHHHHHhcCCCccccccccccchhhHHHHHhhhh
Q 023479 105 RQRWTPTPVQLQILESIFDQGTGTPSKQKIKEITVELSQHGQISETNVYNWFQNRRARSKRKQLVS 170 (281)
Q Consensus 105 r~Rt~ft~~Ql~~LE~~F~~~~~~Ps~~~r~~LA~~L~~~~gLse~qV~vWFQNRRaK~Kr~~~~~ 170 (281)
+-|.++|.-|+.+||+.|..+ +|.++.++.+||..| +|+||||+|||||||+|+||.++..
T Consensus 201 KYRvVYTDhQRLELEKEfh~S-ryITirRKSELA~~L----gLsERQVKIWFQNRRAKERK~nKKk 261 (317)
T KOG0848|consen 201 KYRVVYTDHQRLELEKEFHTS-RYITIRRKSELAATL----GLSERQVKIWFQNRRAKERKDNKKK 261 (317)
T ss_pred ceeEEecchhhhhhhhhhccc-cceeeehhHHHHHhh----CccHhhhhHhhhhhhHHHHHHHHHH
Confidence 458899999999999999997 999999999999999 9999999999999999999988765
No 17
>KOG0844 consensus Transcription factor EVX1, contains HOX domain [Transcription]
Probab=99.49 E-value=9e-15 Score=134.72 Aligned_cols=65 Identities=32% Similarity=0.434 Sum_probs=60.4
Q ss_pred CCCCCCCCCCCChHHHHHHHHHHhhcCCCCCHhHHHHHHHHHHhcCCCccccccccccchhhHHHHHhhh
Q 023479 100 HKISARQRWTPTPVQLQILESIFDQGTGTPSKQKIKEITVELSQHGQISETNVYNWFQNRRARSKRKQLV 169 (281)
Q Consensus 100 ~~~~rr~Rt~ft~~Ql~~LE~~F~~~~~~Ps~~~r~~LA~~L~~~~gLse~qV~vWFQNRRaK~Kr~~~~ 169 (281)
...-||-||.||.+|+..||+.|-+. -|.+++.|.|||..| +|.|+.|+|||||||+|+||+...
T Consensus 178 ~dqmRRYRTAFTReQIaRLEKEFyrE-NYVSRprRcELAAaL----NLPEtTIKVWFQNRRMKDKRQRla 242 (408)
T KOG0844|consen 178 DDQMRRYRTAFTREQIARLEKEFYRE-NYVSRPRRCELAAAL----NLPETTIKVWFQNRRMKDKRQRLA 242 (408)
T ss_pred cHHHHHHHhhhhHHHHHHHHHHHHHh-ccccCchhhhHHHhh----CCCcceeehhhhhchhhhhhhhhh
Confidence 34568899999999999999999987 599999999999999 999999999999999999998766
No 18
>KOG4577 consensus Transcription factor LIM3, contains LIM and HOX domains [Transcription]
Probab=99.48 E-value=1.6e-13 Score=125.76 Aligned_cols=114 Identities=23% Similarity=0.304 Sum_probs=85.4
Q ss_pred HHHHHHHHHHHHHHHHhhhhhhhhhhhhhcCCCCCCccCCCC--------CcCCCCCCCCCCCCCCCChHHHHHHHHHHh
Q 023479 52 RKQIAVYATICEQLVEMHKSLSAHQDLAAAGGRLGNIYCDPL--------MTSGGGHKISARQRWTPTPVQLQILESIFD 123 (281)
Q Consensus 52 r~qi~~~~~~c~~~~~~~k~ls~~~~~~~~g~~~g~~~~~p~--------~~s~~~~~~~rr~Rt~ft~~Ql~~LE~~F~ 123 (281)
++|--+|..-|-+.+...+.|...+.+. -+.-+-+.|-.- .....+....||+||++|..||+.|+.+|.
T Consensus 110 kAqd~VYHl~CF~C~iC~R~L~TGdEFY--LmeD~rLvCK~DYE~Ak~k~~~~l~gd~~nKRPRTTItAKqLETLK~AYn 187 (383)
T KOG4577|consen 110 KAQDFVYHLHCFACFICKRQLATGDEFY--LMEDARLVCKDDYETAKQKHCNELEGDASNKRPRTTITAKQLETLKQAYN 187 (383)
T ss_pred HhhcceeehhhhhhHhhhcccccCCeeE--EeccceeehhhhHHHHHhccccccccccccCCCcceeeHHHHHHHHHHhc
Confidence 7788899999999888777766554432 111111111100 001114445789999999999999999999
Q ss_pred hcCCCCCHhHHHHHHHHHHhcCCCccccccccccchhhHHHHHhhhhcc
Q 023479 124 QGTGTPSKQKIKEITVELSQHGQISETNVYNWFQNRRARSKRKQLVSSS 172 (281)
Q Consensus 124 ~~~~~Ps~~~r~~LA~~L~~~~gLse~qV~vWFQNRRaK~Kr~~~~~~~ 172 (281)
.. +.|-+..|++|+..+ ||..++|+|||||||||+||.++....
T Consensus 188 ~S-pKPARHVREQLsseT----GLDMRVVQVWFQNRRAKEKRLKKDAGR 231 (383)
T KOG4577|consen 188 TS-PKPARHVREQLSSET----GLDMRVVQVWFQNRRAKEKRLKKDAGR 231 (383)
T ss_pred CC-CchhHHHHHHhhhcc----CcceeehhhhhhhhhHHHHhhhhhcch
Confidence 97 999999999999998 999999999999999999998876543
No 19
>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=99.45 E-value=1.1e-13 Score=99.55 Aligned_cols=52 Identities=17% Similarity=0.325 Sum_probs=50.0
Q ss_pred CCCCCCCChHHHHHHHHHHhhcCCC----CCHhHHHHHHHHHHhcCCCccccccccccchh
Q 023479 104 ARQRWTPTPVQLQILESIFDQGTGT----PSKQKIKEITVELSQHGQISETNVYNWFQNRR 160 (281)
Q Consensus 104 rr~Rt~ft~~Ql~~LE~~F~~~~~~----Ps~~~r~~LA~~L~~~~gLse~qV~vWFQNRR 160 (281)
||.||.||.+|+..||..|+.+ +| |+..+|.+||..| ||++++|+|||||-+
T Consensus 2 kR~RT~Ft~~Q~~~Le~~fe~~-~y~~~~~~~~~r~~la~~l----gl~~~vvKVWfqN~k 57 (58)
T TIGR01565 2 KRRRTKFTAEQKEKMRDFAEKL-GWKLKDKRREEVREFCEEI----GVTRKVFKVWMHNNK 57 (58)
T ss_pred CCCCCCCCHHHHHHHHHHHHHc-CCCCCCCCHHHHHHHHHHh----CCCHHHeeeecccCC
Confidence 7899999999999999999997 99 9999999999999 999999999999965
No 20
>smart00389 HOX Homeodomain. DNA-binding factors that are involved in the transcriptional regulation of key developmental processes
Probab=99.44 E-value=7.5e-14 Score=98.21 Aligned_cols=55 Identities=44% Similarity=0.643 Sum_probs=51.7
Q ss_pred CCCCCCChHHHHHHHHHHhhcCCCCCHhHHHHHHHHHHhcCCCccccccccccchhhHHH
Q 023479 105 RQRWTPTPVQLQILESIFDQGTGTPSKQKIKEITVELSQHGQISETNVYNWFQNRRARSK 164 (281)
Q Consensus 105 r~Rt~ft~~Ql~~LE~~F~~~~~~Ps~~~r~~LA~~L~~~~gLse~qV~vWFQNRRaK~K 164 (281)
+.|+.|+.+++.+||..|..+ +||+..++..||..| ||+..+|++||+|||++.+
T Consensus 2 k~r~~~~~~~~~~L~~~f~~~-~~P~~~~~~~la~~~----~l~~~qV~~WF~nrR~~~~ 56 (56)
T smart00389 2 RKRTSFTPEQLEELEKEFQKN-PYPSREEREELAAKL----GLSERQVKVWFQNRRAKWK 56 (56)
T ss_pred CCCCcCCHHHHHHHHHHHHhC-CCCCHHHHHHHHHHH----CcCHHHHHHhHHHHhhccC
Confidence 567889999999999999997 899999999999999 9999999999999998864
No 21
>KOG0847 consensus Transcription factor, contains HOX domain [Transcription]
Probab=99.43 E-value=6.9e-14 Score=123.89 Aligned_cols=69 Identities=29% Similarity=0.373 Sum_probs=62.1
Q ss_pred CCCCCCCCCCChHHHHHHHHHHhhcCCCCCHhHHHHHHHHHHhcCCCccccccccccchhhHHHHHhhhhcccc
Q 023479 101 KISARQRWTPTPVQLQILESIFDQGTGTPSKQKIKEITVELSQHGQISETNVYNWFQNRRARSKRKQLVSSSAN 174 (281)
Q Consensus 101 ~~~rr~Rt~ft~~Ql~~LE~~F~~~~~~Ps~~~r~~LA~~L~~~~gLse~qV~vWFQNRRaK~Kr~~~~~~~~~ 174 (281)
.+++..|.+|+..|+..||+.|+. ++||-.++|.+||..| |+++.+|+|||||||.||||+.......+
T Consensus 165 G~rk~srPTf~g~qi~~le~~feq-tkylaG~~ra~lA~~l----gmteSqvkVWFQNRRTKWRKkhAaEmasa 233 (288)
T KOG0847|consen 165 GQRKQSRPTFTGHQIYQLERKFEQ-TKYLAGADRAQLAQEL----NMTESQVKVWFQNRRTKWRKKHAAEMASA 233 (288)
T ss_pred ccccccCCCccchhhhhhhhhhhh-hhcccchhHHHhhccc----cccHHHHHHHHhcchhhhhhhhccchhhc
Confidence 456667899999999999999999 5999999999999999 99999999999999999999987765444
No 22
>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=99.43 E-value=1.2e-13 Score=97.71 Aligned_cols=57 Identities=44% Similarity=0.652 Sum_probs=53.7
Q ss_pred CCCCCCChHHHHHHHHHHhhcCCCCCHhHHHHHHHHHHhcCCCccccccccccchhhHHHHH
Q 023479 105 RQRWTPTPVQLQILESIFDQGTGTPSKQKIKEITVELSQHGQISETNVYNWFQNRRARSKRK 166 (281)
Q Consensus 105 r~Rt~ft~~Ql~~LE~~F~~~~~~Ps~~~r~~LA~~L~~~~gLse~qV~vWFQNRRaK~Kr~ 166 (281)
+.|+.|+..++.+||.+|..+ +||+..++..||..| ||++.+|++||+|||++.++.
T Consensus 2 ~~r~~~~~~~~~~Le~~f~~~-~~P~~~~~~~la~~~----~l~~~qV~~WF~nrR~~~~~~ 58 (59)
T cd00086 2 RKRTRFTPEQLEELEKEFEKN-PYPSREEREELAKEL----GLTERQVKIWFQNRRAKLKRS 58 (59)
T ss_pred CCCCcCCHHHHHHHHHHHHhC-CCCCHHHHHHHHHHH----CcCHHHHHHHHHHHHHHHhcc
Confidence 467899999999999999997 999999999999999 999999999999999998864
No 23
>KOG0486 consensus Transcription factor PTX1, contains HOX domain [Transcription]
Probab=99.42 E-value=1.2e-13 Score=127.77 Aligned_cols=68 Identities=32% Similarity=0.423 Sum_probs=64.0
Q ss_pred CCCCCCCCCCCCChHHHHHHHHHHhhcCCCCCHhHHHHHHHHHHhcCCCccccccccccchhhHHHHHhhhhc
Q 023479 99 GHKISARQRWTPTPVQLQILESIFDQGTGTPSKQKIKEITVELSQHGQISETNVYNWFQNRRARSKRKQLVSS 171 (281)
Q Consensus 99 ~~~~~rr~Rt~ft~~Ql~~LE~~F~~~~~~Ps~~~r~~LA~~L~~~~gLse~qV~vWFQNRRaK~Kr~~~~~~ 171 (281)
..++.||.|+.|+..||.+||..|.+| +||+-..|++||.-. +|++..|+|||.|||+||||+++...
T Consensus 108 ki~KqrrQrthFtSqqlqele~tF~rN-rypdMstrEEIavwt----NlTE~rvrvwfknrrakwrkrErN~~ 175 (351)
T KOG0486|consen 108 KISKQRRQRTHFTSQQLQELEATFQRN-RYPDMSTREEIAVWT----NLTEARVRVWFKNRRAKWRKRERNQQ 175 (351)
T ss_pred hhhhhhhhhhhhHHHHHHHHHHHHhhc-cCCccchhhHHHhhc----cccchhhhhhcccchhhhhhhhhhHH
Confidence 445788999999999999999999997 999999999999999 99999999999999999999988766
No 24
>KOG0493 consensus Transcription factor Engrailed, contains HOX domain [General function prediction only]
Probab=99.41 E-value=1.1e-13 Score=125.33 Aligned_cols=59 Identities=34% Similarity=0.508 Sum_probs=56.0
Q ss_pred CCCCCCCChHHHHHHHHHHhhcCCCCCHhHHHHHHHHHHhcCCCccccccccccchhhHHHHHh
Q 023479 104 ARQRWTPTPVQLQILESIFDQGTGTPSKQKIKEITVELSQHGQISETNVYNWFQNRRARSKRKQ 167 (281)
Q Consensus 104 rr~Rt~ft~~Ql~~LE~~F~~~~~~Ps~~~r~~LA~~L~~~~gLse~qV~vWFQNRRaK~Kr~~ 167 (281)
||+||.||.+||..|+..|..| +|.+..+|.+||.+| +|.|.||+|||||+|+|-||..
T Consensus 247 KRPRTAFtaeQL~RLK~EF~en-RYlTEqRRQ~La~EL----gLNEsQIKIWFQNKRAKiKKsT 305 (342)
T KOG0493|consen 247 KRPRTAFTAEQLQRLKAEFQEN-RYLTEQRRQELAQEL----GLNESQIKIWFQNKRAKIKKST 305 (342)
T ss_pred cCccccccHHHHHHHHHHHhhh-hhHHHHHHHHHHHHh----CcCHHHhhHHhhhhhhhhhhcc
Confidence 5789999999999999999997 999999999999999 9999999999999999998843
No 25
>KOG0483 consensus Transcription factor HEX, contains HOX and HALZ domains [Transcription]
Probab=99.38 E-value=1.5e-13 Score=121.34 Aligned_cols=61 Identities=34% Similarity=0.476 Sum_probs=56.1
Q ss_pred CCCCCCCChHHHHHHHHHHhhcCCCCCHhHHHHHHHHHHhcCCCccccccccccchhhHHHHHhhh
Q 023479 104 ARQRWTPTPVQLQILESIFDQGTGTPSKQKIKEITVELSQHGQISETNVYNWFQNRRARSKRKQLV 169 (281)
Q Consensus 104 rr~Rt~ft~~Ql~~LE~~F~~~~~~Ps~~~r~~LA~~L~~~~gLse~qV~vWFQNRRaK~Kr~~~~ 169 (281)
.+++.+|+.+|+..||+.|+.+ .|..+.++..||+.| ||.++||.|||||||||||.++..
T Consensus 51 ~~kk~Rlt~eQ~~~LE~~F~~~-~~L~p~~K~~LAk~L----gL~pRQVavWFQNRRARwK~kqlE 111 (198)
T KOG0483|consen 51 KGKKRRLTSEQVKFLEKSFESE-KKLEPERKKKLAKEL----GLQPRQVAVWFQNRRARWKTKQLE 111 (198)
T ss_pred ccccccccHHHHHHhHHhhccc-cccChHHHHHHHHhh----CCChhHHHHHHhhccccccchhhh
Confidence 3445579999999999999997 899999999999999 999999999999999999998766
No 26
>KOG0491 consensus Transcription factor BSH, contains HOX domain [General function prediction only]
Probab=99.38 E-value=9.6e-14 Score=118.12 Aligned_cols=66 Identities=32% Similarity=0.403 Sum_probs=61.2
Q ss_pred CCCCCCCCCChHHHHHHHHHHhhcCCCCCHhHHHHHHHHHHhcCCCccccccccccchhhHHHHHhhhhcc
Q 023479 102 ISARQRWTPTPVQLQILESIFDQGTGTPSKQKIKEITVELSQHGQISETNVYNWFQNRRARSKRKQLVSSS 172 (281)
Q Consensus 102 ~~rr~Rt~ft~~Ql~~LE~~F~~~~~~Ps~~~r~~LA~~L~~~~gLse~qV~vWFQNRRaK~Kr~~~~~~~ 172 (281)
++++.|+.|+..||..||+.|+.. +|.+.++|.+||..| +|+++||+.||||||+|.||.++....
T Consensus 99 ~r~K~Rtvfs~~ql~~l~~rFe~Q-rYLS~~e~~ELan~L----~LS~~QVKTWFQNrRMK~Kk~~r~~~p 164 (194)
T KOG0491|consen 99 RRRKARTVFSDPQLSGLEKRFERQ-RYLSTPERQELANAL----SLSETQVKTWFQNRRMKHKKQQRNNQP 164 (194)
T ss_pred HhhhhcccccCccccccHHHHhhh-hhcccHHHHHHHHHh----hhhHHHHHHHHHHHHHHHHHHHhccCC
Confidence 456779999999999999999997 999999999999999 999999999999999999999886543
No 27
>COG5576 Homeodomain-containing transcription factor [Transcription]
Probab=99.36 E-value=6.8e-13 Score=113.43 Aligned_cols=64 Identities=30% Similarity=0.421 Sum_probs=58.3
Q ss_pred CCCCCCCCCCChHHHHHHHHHHhhcCCCCCHhHHHHHHHHHHhcCCCccccccccccchhhHHHHHhhh
Q 023479 101 KISARQRWTPTPVQLQILESIFDQGTGTPSKQKIKEITVELSQHGQISETNVYNWFQNRRARSKRKQLV 169 (281)
Q Consensus 101 ~~~rr~Rt~ft~~Ql~~LE~~F~~~~~~Ps~~~r~~LA~~L~~~~gLse~qV~vWFQNRRaK~Kr~~~~ 169 (281)
...+++|++.+..|+.+|++.|+.+ +||+...|..|+..| +|+++.|+|||||||++.|+....
T Consensus 49 ~~~~~~r~R~t~~Q~~vL~~~F~i~-p~Ps~~~r~~L~~~l----nm~~ksVqIWFQNkR~~~k~~~~~ 112 (156)
T COG5576 49 SPPKSKRRRTTDEQLMVLEREFEIN-PYPSSITRIKLSLLL----NMPPKSVQIWFQNKRAKEKKKRSG 112 (156)
T ss_pred CcCcccceechHHHHHHHHHHhccC-CCCCHHHHHHHHHhc----CCChhhhhhhhchHHHHHHHhccc
Confidence 3456677788899999999999997 999999999999999 999999999999999999997664
No 28
>KOG0490 consensus Transcription factor, contains HOX domain [General function prediction only]
Probab=99.14 E-value=2.2e-11 Score=108.23 Aligned_cols=64 Identities=28% Similarity=0.303 Sum_probs=60.1
Q ss_pred CCCCCCCCCCCChHHHHHHHHHHhhcCCCCCHhHHHHHHHHHHhcCCCccccccccccchhhHHHHHhh
Q 023479 100 HKISARQRWTPTPVQLQILESIFDQGTGTPSKQKIKEITVELSQHGQISETNVYNWFQNRRARSKRKQL 168 (281)
Q Consensus 100 ~~~~rr~Rt~ft~~Ql~~LE~~F~~~~~~Ps~~~r~~LA~~L~~~~gLse~qV~vWFQNRRaK~Kr~~~ 168 (281)
..+.||.|+.|+..|+.+||++|+.. +||+...|+.||..+ ++++..|+|||||||+||++..+
T Consensus 57 ~~~~rr~rt~~~~~ql~~ler~f~~~-h~Pd~~~r~~la~~~----~~~e~rVqvwFqnrrak~r~~~~ 120 (235)
T KOG0490|consen 57 KFSKRCARCKFTISQLDELERAFEKV-HLPCFACRECLALLL----TGDEFRVQVWFQNRRAKDRKEER 120 (235)
T ss_pred hccccccCCCCCcCHHHHHHHhhcCC-CcCccchHHHHhhcC----CCCeeeeehhhhhhcHhhhhhhc
Confidence 44678899999999999999999996 999999999999999 99999999999999999999875
No 29
>smart00352 POU Found in Pit-Oct-Unc transcription factors.
Probab=99.10 E-value=6e-11 Score=89.24 Aligned_cols=71 Identities=11% Similarity=0.126 Sum_probs=67.3
Q ss_pred hHHHHHHHHHHhhhhhhhhcCCCCCCCcccCcccccccCCHHHHHHHHHHHHHHHHHHHHHHHhhhhhhhh
Q 023479 5 NIREAAQQETQTQNQNQNQRGGENDNNNVVNGVMYVKVMTDEQLETLRKQIAVYATICEQLVEMHKSLSAH 75 (281)
Q Consensus 5 ~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~g~~~~~~~t~~~~~~lr~qi~~~~~~c~~~~~~~k~ls~~ 75 (281)
....|+|.++..++++|+++|+||.+++-++|++||..+|+.+|++|+....+++++|+..+.+.+|+...
T Consensus 4 ~~~~ele~~~~~lk~~R~~lGLTQ~dvA~~lg~~~g~i~SQstISR~Es~~ls~~n~~kl~p~l~~wl~~~ 74 (75)
T smart00352 4 TDPRELEAFAKTFKQRRIKLGFTQADVGLALGALYGPDFSQTTICRFEALQLSFKNMCKLKPLLEKWLEEA 74 (75)
T ss_pred CCHHHHHHHHHHHHHHHHHcCCCHHHHHHHhcccccCcCCHHHHHHHHhcCccHHHHHHHHHHHHHHHHhc
Confidence 44678999999999999999999999999999999999999999999999999999999999999998753
No 30
>KOG0849 consensus Transcription factor PRD and related proteins, contain PAX and HOX domains [Transcription]
Probab=98.88 E-value=1.1e-09 Score=104.92 Aligned_cols=66 Identities=30% Similarity=0.415 Sum_probs=60.9
Q ss_pred CCCCCCCCCCCCChHHHHHHHHHHhhcCCCCCHhHHHHHHHHHHhcCCCccccccccccchhhHHHHHhhh
Q 023479 99 GHKISARQRWTPTPVQLQILESIFDQGTGTPSKQKIKEITVELSQHGQISETNVYNWFQNRRARSKRKQLV 169 (281)
Q Consensus 99 ~~~~~rr~Rt~ft~~Ql~~LE~~F~~~~~~Ps~~~r~~LA~~L~~~~gLse~qV~vWFQNRRaK~Kr~~~~ 169 (281)
..++.+|.|++|+..|+..||+.|+.+ +||+...|+.||.++ ++++..|+|||+|||++++|....
T Consensus 172 ~~~~~rr~rtsft~~Q~~~le~~f~rt-~yP~i~~Re~La~~i----~l~e~riqvwf~nrra~~rr~~~~ 237 (354)
T KOG0849|consen 172 LQRGGRRNRTSFSPSQLEALEECFQRT-PYPDIVGRETLAKET----GLPEPRVQVWFQNRRAKWRRQHRD 237 (354)
T ss_pred ccccccccccccccchHHHHHHHhcCC-CCCchhhHHHHhhhc----cCCchHHHHHHhhhhhhhhhcccc
Confidence 445667789999999999999999997 899999999999999 999999999999999999998854
No 31
>KOG0775 consensus Transcription factor SIX and related HOX domain proteins [Transcription]
Probab=98.78 E-value=1.6e-08 Score=92.63 Aligned_cols=50 Identities=28% Similarity=0.452 Sum_probs=46.1
Q ss_pred CChHHHHHHHHHHhhcCCCCCHhHHHHHHHHHHhcCCCccccccccccchhhHHH
Q 023479 110 PTPVQLQILESIFDQGTGTPSKQKIKEITVELSQHGQISETNVYNWFQNRRARSK 164 (281)
Q Consensus 110 ft~~Ql~~LE~~F~~~~~~Ps~~~r~~LA~~L~~~~gLse~qV~vWFQNRRaK~K 164 (281)
|...-+..|..+|..+ +||+..++.+||+.+ ||+..||-+||+|||+|+|
T Consensus 183 FKekSR~~LrewY~~~-~YPsp~eKReLA~aT----gLt~tQVsNWFKNRRQRDR 232 (304)
T KOG0775|consen 183 FKEKSRSLLREWYLQN-PYPSPREKRELAEAT----GLTITQVSNWFKNRRQRDR 232 (304)
T ss_pred hhHhhHHHHHHHHhcC-CCCChHHHHHHHHHh----CCchhhhhhhhhhhhhhhh
Confidence 4445578999999997 999999999999999 9999999999999999998
No 32
>KOG0774 consensus Transcription factor PBX and related HOX domain proteins [Transcription]
Probab=98.38 E-value=5.3e-06 Score=75.85 Aligned_cols=62 Identities=27% Similarity=0.430 Sum_probs=55.5
Q ss_pred CCCCCCCCChHHHHHHHHHHhh--cCCCCCHhHHHHHHHHHHhcCCCccccccccccchhhHHHHHhh
Q 023479 103 SARQRWTPTPVQLQILESIFDQ--GTGTPSKQKIKEITVELSQHGQISETNVYNWFQNRRARSKRKQL 168 (281)
Q Consensus 103 ~rr~Rt~ft~~Ql~~LE~~F~~--~~~~Ps~~~r~~LA~~L~~~~gLse~qV~vWFQNRRaK~Kr~~~ 168 (281)
.||+|..|+..-..+|..+|.. +++||+.+.+++||+++ +++..||.+||.|+|-+.||...
T Consensus 188 arRKRRNFsK~aTeiLneyF~~h~~nPYPSee~K~eLAkqC----nItvsQvsnwfgnkrIrykK~~~ 251 (334)
T KOG0774|consen 188 ARRKRRNFSKQATEILNEYFYSHLSNPYPSEEAKEELAKQC----NITVSQVSNWFGNKRIRYKKNMG 251 (334)
T ss_pred HHHhhcccchhHHHHHHHHHHHhcCCCCCcHHHHHHHHHHc----Cceehhhccccccceeehhhhhh
Confidence 3677889999999999999965 34999999999999999 99999999999999999998543
No 33
>KOG2252 consensus CCAAT displacement protein and related homeoproteins [Transcription]
Probab=98.21 E-value=2.4e-06 Score=84.92 Aligned_cols=58 Identities=29% Similarity=0.462 Sum_probs=54.0
Q ss_pred CCCCCCCCCCChHHHHHHHHHHhhcCCCCCHhHHHHHHHHHHhcCCCccccccccccchhhHH
Q 023479 101 KISARQRWTPTPVQLQILESIFDQGTGTPSKQKIKEITVELSQHGQISETNVYNWFQNRRARS 163 (281)
Q Consensus 101 ~~~rr~Rt~ft~~Ql~~LE~~F~~~~~~Ps~~~r~~LA~~L~~~~gLse~qV~vWFQNRRaK~ 163 (281)
-..||+|.+||..|+..|-.+|+.+ ++|+.+..+.|+.+| +|..+.|.+||-|.|.|.
T Consensus 418 ~~~KKPRlVfTd~QkrTL~aiFke~-~RPS~Emq~tIS~qL----~L~~sTV~NfFmNaRRRs 475 (558)
T KOG2252|consen 418 LQTKKPRLVFTDIQKRTLQAIFKEN-KRPSREMQETISQQL----NLELSTVINFFMNARRRS 475 (558)
T ss_pred ccCCCceeeecHHHHHHHHHHHhcC-CCCCHHHHHHHHHHh----CCcHHHHHHHHHhhhhhc
Confidence 3567789999999999999999996 999999999999999 999999999999988775
No 34
>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=98.12 E-value=8e-07 Score=59.34 Aligned_cols=33 Identities=33% Similarity=0.598 Sum_probs=28.0
Q ss_pred CCCCCHhHHHHHHHHHHhcCCCccccccccccchhhH
Q 023479 126 TGTPSKQKIKEITVELSQHGQISETNVYNWFQNRRAR 162 (281)
Q Consensus 126 ~~~Ps~~~r~~LA~~L~~~~gLse~qV~vWFQNRRaK 162 (281)
+|||+.+++..||..+ ||+..||..||-|.|.|
T Consensus 8 nPYPs~~ek~~L~~~t----gls~~Qi~~WF~NaRrR 40 (40)
T PF05920_consen 8 NPYPSKEEKEELAKQT----GLSRKQISNWFINARRR 40 (40)
T ss_dssp SGS--HHHHHHHHHHH----TS-HHHHHHHHHHHHHH
T ss_pred CCCCCHHHHHHHHHHc----CCCHHHHHHHHHHhHcc
Confidence 3899999999999999 99999999999999875
No 35
>KOG0490 consensus Transcription factor, contains HOX domain [General function prediction only]
Probab=97.89 E-value=9.5e-06 Score=72.00 Aligned_cols=64 Identities=33% Similarity=0.507 Sum_probs=58.9
Q ss_pred CCCCCCCCCCCChHHHHHHHHHHhhcCCCCCHhHHHHHHHHHHhcCCCccccccccccchhhHHHHHhh
Q 023479 100 HKISARQRWTPTPVQLQILESIFDQGTGTPSKQKIKEITVELSQHGQISETNVYNWFQNRRARSKRKQL 168 (281)
Q Consensus 100 ~~~~rr~Rt~ft~~Ql~~LE~~F~~~~~~Ps~~~r~~LA~~L~~~~gLse~qV~vWFQNRRaK~Kr~~~ 168 (281)
..+.++.|+.+...|+..|+..|... ++|+...+..|+..+ +++++.|++||+|+|++.++...
T Consensus 150 ~~~~~~~~~~~~~~~~~~~~~~~~~~-~~P~~~~~~~l~~~~----~~~~~~~q~~~~~~~~~~~~~~~ 213 (235)
T KOG0490|consen 150 NKKPRRPRTTFTENQLEVLETVFRAT-PKPDADDREQLAEET----GLSERVIQVWFQNRRAKLRKHKR 213 (235)
T ss_pred ccccCCCccccccchhHhhhhcccCC-CCCchhhHHHHHHhc----CCChhhhhhhcccHHHHHHhhcc
Confidence 34677889999999999999999996 999999999999999 99999999999999999998765
No 36
>KOG1146 consensus Homeobox protein [General function prediction only]
Probab=97.33 E-value=0.00019 Score=77.57 Aligned_cols=64 Identities=25% Similarity=0.425 Sum_probs=58.4
Q ss_pred CCCCCCCCCChHHHHHHHHHHhhcCCCCCHhHHHHHHHHHHhcCCCccccccccccchhhHHHHHhhhh
Q 023479 102 ISARQRWTPTPVQLQILESIFDQGTGTPSKQKIKEITVELSQHGQISETNVYNWFQNRRARSKRKQLVS 170 (281)
Q Consensus 102 ~~rr~Rt~ft~~Ql~~LE~~F~~~~~~Ps~~~r~~LA~~L~~~~gLse~qV~vWFQNRRaK~Kr~~~~~ 170 (281)
.+|+.|+.++..||..|..+|... .||.-.+.+-|-..+ +++.++|.+||||-|+|.|+.....
T Consensus 902 ~r~a~~~~~~d~qlk~i~~~~~~q-~~~~~~~~E~l~~~~----~~~~~~i~vw~qna~~~s~k~~~n~ 965 (1406)
T KOG1146|consen 902 GRRAYRTQESDLQLKIIKACYEAQ-RTPTMQECEVLEEPI----GLPKRVIQVWFQNARAKSKKAKLNG 965 (1406)
T ss_pred hhhhhccchhHHHHHHHHHHHhhc-cCChHHHHHhhcccc----cCCcchhHHhhhhhhhhhhhhhhcc
Confidence 367789999999999999999997 899999998899999 9999999999999999999987744
No 37
>PF11569 Homez: Homeodomain leucine-zipper encoding, Homez; PDB: 2YS9_A.
Probab=95.13 E-value=0.0092 Score=42.70 Aligned_cols=42 Identities=21% Similarity=0.396 Sum_probs=30.2
Q ss_pred HHHHHHHHhhcCCCCCHhHHHHHHHHHHhcCCCccccccccccchhh
Q 023479 115 LQILESIFDQGTGTPSKQKIKEITVELSQHGQISETNVYNWFQNRRA 161 (281)
Q Consensus 115 l~~LE~~F~~~~~~Ps~~~r~~LA~~L~~~~gLse~qV~vWFQNRRa 161 (281)
+..|+.+|... +++...+...|..+. +|+..+|+.||--|+.
T Consensus 10 ~~pL~~Yy~~h-~~L~E~DL~~L~~kS----~ms~qqVr~WFa~~~~ 51 (56)
T PF11569_consen 10 IQPLEDYYLKH-KQLQEEDLDELCDKS----RMSYQQVRDWFAERMQ 51 (56)
T ss_dssp -HHHHHHHHHT-----TTHHHHHHHHT----T--HHHHHHHHHHHS-
T ss_pred hHHHHHHHHHc-CCccHhhHHHHHHHH----CCCHHHHHHHHHHhcc
Confidence 45699999995 899999999999999 9999999999966543
No 38
>KOG0773 consensus Transcription factor MEIS1 and related HOX domain proteins [Transcription]
Probab=94.63 E-value=0.028 Score=53.44 Aligned_cols=62 Identities=21% Similarity=0.242 Sum_probs=48.9
Q ss_pred CCCCCCCCChHHHHHHHHHHhh-c-CCCCCHhHHHHHHHHHHhcCCCccccccccccchhhHHHHHhh
Q 023479 103 SARQRWTPTPVQLQILESIFDQ-G-TGTPSKQKIKEITVELSQHGQISETNVYNWFQNRRARSKRKQL 168 (281)
Q Consensus 103 ~rr~Rt~ft~~Ql~~LE~~F~~-~-~~~Ps~~~r~~LA~~L~~~~gLse~qV~vWFQNRRaK~Kr~~~ 168 (281)
..|++..+......+|+.+... - .+||+..++..||.++ ||+..||.+||-|.|-|..+-..
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 4455567888888888877333 1 2799999999999999 99999999999999887665443
No 39
>KOG3623 consensus Homeobox transcription factor SIP1 [Transcription]
Probab=94.21 E-value=0.042 Score=57.04 Aligned_cols=52 Identities=19% Similarity=0.419 Sum_probs=47.7
Q ss_pred HHHHHHHHhhcCCCCCHhHHHHHHHHHHhcCCCccccccccccchhhHHHHHhhhhc
Q 023479 115 LQILESIFDQGTGTPSKQKIKEITVELSQHGQISETNVYNWFQNRRARSKRKQLVSS 171 (281)
Q Consensus 115 l~~LE~~F~~~~~~Ps~~~r~~LA~~L~~~~gLse~qV~vWFQNRRaK~Kr~~~~~~ 171 (281)
+.+|..+|..| ..|+..+...||.+. ||+.+.|+.||++++++..+..+...
T Consensus 568 ~sllkayyaln-~~ps~eelskia~qv----glp~~vvk~wfE~~~a~e~sv~rsps 619 (1007)
T KOG3623|consen 568 TSLLKAYYALN-GLPSEEELSKIAQQV----GLPFAVVKAWFEDEEAEEMSVERSPS 619 (1007)
T ss_pred HHHHHHHHHhc-CCCCHHHHHHHHHHh----cccHHHHHHHHHhhhhhhhhhccCcc
Confidence 77899999998 999999999999999 99999999999999999998876654
No 40
>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=90.09 E-value=0.4 Score=31.45 Aligned_cols=22 Identities=36% Similarity=0.501 Sum_probs=20.0
Q ss_pred cCCHHHHHHHHHHHHHHHHHHH
Q 023479 42 VMTDEQLETLRKQIAVYATICE 63 (281)
Q Consensus 42 ~~t~~~~~~lr~qi~~~~~~c~ 63 (281)
.||.+|+..||+||.+|+-|..
T Consensus 2 ~FT~~Ql~~L~~Qi~ayK~l~~ 23 (37)
T PF08880_consen 2 PFTPAQLQELRAQILAYKYLAR 23 (37)
T ss_pred CCCHHHHHHHHHHHHHHHHHHc
Confidence 5999999999999999998765
No 41
>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=88.00 E-value=0.68 Score=32.40 Aligned_cols=46 Identities=20% Similarity=0.279 Sum_probs=34.3
Q ss_pred CCCCCCCChHHHHHHHHHHhhcCCCCCHhHHHHHHHHHHhcCCCccccccccccch
Q 023479 104 ARQRWTPTPVQLQILESIFDQGTGTPSKQKIKEITVELSQHGQISETNVYNWFQNR 159 (281)
Q Consensus 104 rr~Rt~ft~~Ql~~LE~~F~~~~~~Ps~~~r~~LA~~L~~~~gLse~qV~vWFQNR 159 (281)
||+|..+|.++...+-..++.+ . ....||..+ |++..+|..|..|+
T Consensus 1 krkR~~LTl~eK~~iI~~~e~g-~-----s~~~ia~~f----gv~~sTv~~I~K~k 46 (53)
T PF04218_consen 1 KRKRKSLTLEEKLEIIKRLEEG-E-----SKRDIAREF----GVSRSTVSTILKNK 46 (53)
T ss_dssp SSSSSS--HHHHHHHHHHHHCT-T------HHHHHHHH----T--CCHHHHHHHCH
T ss_pred CCCCccCCHHHHHHHHHHHHcC-C-----CHHHHHHHh----CCCHHHHHHHHHhH
Confidence 4678899998888888888875 3 456889999 99999999999885
No 42
>KOG3623 consensus Homeobox transcription factor SIP1 [Transcription]
Probab=86.56 E-value=4.6 Score=42.58 Aligned_cols=108 Identities=18% Similarity=0.231 Sum_probs=70.3
Q ss_pred CCHHHHHHHHHHHHHHHHHHHHHHHhhhhhhhhhhhhhcCCCCCCccCCCCCcCCCCCCCCCCCCCCCChHHHHHHHHHH
Q 023479 43 MTDEQLETLRKQIAVYATICEQLVEMHKSLSAHQDLAAAGGRLGNIYCDPLMTSGGGHKISARQRWTPTPVQLQILESIF 122 (281)
Q Consensus 43 ~t~~~~~~lr~qi~~~~~~c~~~~~~~k~ls~~~~~~~~g~~~g~~~~~p~~~s~~~~~~~rr~Rt~ft~~Ql~~LE~~F 122 (281)
-+.+++..+..|+.+-....+.|++-.+.-.-... -.|..+++ . ..-+.|+....++-..|..++
T Consensus 581 ps~eelskia~qvglp~~vvk~wfE~~~a~e~sv~------------rsps~psg-~--~p~kv~sp~k~~dq~ql~~a~ 645 (1007)
T KOG3623|consen 581 PSEEELSKIAQQVGLPFAVVKAWFEDEEAEEMSVE------------RSPSQPSG-E--RPVKVRSPIKEEDQQQLKQAY 645 (1007)
T ss_pred CCHHHHHHHHHHhcccHHHHHHHHHhhhhhhhhhc------------cCccCCCC-C--CCccccCCCCccchhhhHhhh
Confidence 47788888899998888888888876543111100 00111111 1 123345666666667788888
Q ss_pred hhcCCCCCHhHHHHHHHHHHhcCCCccccccccccchhhHHHHHhhhh
Q 023479 123 DQGTGTPSKQKIKEITVELSQHGQISETNVYNWFQNRRARSKRKQLVS 170 (281)
Q Consensus 123 ~~~~~~Ps~~~r~~LA~~L~~~~gLse~qV~vWFQNRRaK~Kr~~~~~ 170 (281)
+.+ -.++..+-..++.+| ...+.+|.+||++|+...+......
T Consensus 646 elq-~s~~n~~~pl~~t~~----~n~~pv~ev~dhsrsstpsp~pl~l 688 (1007)
T KOG3623|consen 646 ELQ-ASPSNDEFPLIATRL----QNDPPVVEVWDHSRSSTPSPMPLFL 688 (1007)
T ss_pred hcc-cCccCcccchhhhhc----cCCCcchhhcccCCCCCCCCCcccc
Confidence 875 566666666667777 7888999999999998877765543
No 43
>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=55.56 E-value=14 Score=24.83 Aligned_cols=44 Identities=18% Similarity=0.303 Sum_probs=31.8
Q ss_pred CCChHHHHHHHHHHhhcCCCCCHhHHHHHHHHHHhcCCCccccccccccchhhH
Q 023479 109 TPTPVQLQILESIFDQGTGTPSKQKIKEITVELSQHGQISETNVYNWFQNRRAR 162 (281)
Q Consensus 109 ~ft~~Ql~~LE~~F~~~~~~Ps~~~r~~LA~~L~~~~gLse~qV~vWFQNRRaK 162 (281)
.+++.+..+|...|..+ + ...++|..| |++...|+.+...-..|
T Consensus 4 ~L~~~er~vi~~~y~~~--~----t~~eIa~~l----g~s~~~V~~~~~~al~k 47 (50)
T PF04545_consen 4 QLPPREREVIRLRYFEG--L----TLEEIAERL----GISRSTVRRILKRALKK 47 (50)
T ss_dssp TS-HHHHHHHHHHHTST-------SHHHHHHHH----TSCHHHHHHHHHHHHHH
T ss_pred hCCHHHHHHHHHHhcCC--C----CHHHHHHHH----CCcHHHHHHHHHHHHHH
Confidence 46788999999998553 2 345889999 99999988776544333
No 44
>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=53.43 E-value=10 Score=24.42 Aligned_cols=43 Identities=19% Similarity=0.204 Sum_probs=31.0
Q ss_pred CCChHHHHHHHHHHhhcCCCCCHhHHHHHHHHHHhcCCCccccccccccchhh
Q 023479 109 TPTPVQLQILESIFDQGTGTPSKQKIKEITVELSQHGQISETNVYNWFQNRRA 161 (281)
Q Consensus 109 ~ft~~Ql~~LE~~F~~~~~~Ps~~~r~~LA~~L~~~~gLse~qV~vWFQNRRa 161 (281)
.+++.+..+++..|..+ + ...++|..+ |++...|+.|....+.
T Consensus 10 ~l~~~~~~~~~~~~~~~--~----~~~~ia~~~----~~s~~~i~~~~~~~~~ 52 (55)
T cd06171 10 KLPEREREVILLRFGEG--L----SYEEIAEIL----GISRSTVRQRLHRALK 52 (55)
T ss_pred hCCHHHHHHHHHHHhcC--C----CHHHHHHHH----CcCHHHHHHHHHHHHH
Confidence 35677778887777543 2 345789999 9999999998865443
No 45
>PF01527 HTH_Tnp_1: Transposase; InterPro: IPR002514 Transposase proteins are necessary for efficient DNA transposition. This family consists of various Escherichia coli insertion elements and other bacterial transposases some of which are members of the IS3 family. This region includes a helix-turn-helix motif (HTH) at the N terminus followed by a leucine zipper (LZ) motif. The LZ motif has been shown to mediate oligomerisation of the transposase components in IS911 []. More information about these proteins can be found at Protein of the Month: Transposase [].; GO: 0003677 DNA binding, 0004803 transposase activity, 0006313 transposition, DNA-mediated; PDB: 2JN6_A 2RN7_A.
Probab=52.87 E-value=13 Score=26.84 Aligned_cols=44 Identities=23% Similarity=0.362 Sum_probs=27.7
Q ss_pred CCCCCCChHHHHHHHHHHhhcCCCCCHhHHHHHHHHHHhcCCCcccccccccc
Q 023479 105 RQRWTPTPVQLQILESIFDQGTGTPSKQKIKEITVELSQHGQISETNVYNWFQ 157 (281)
Q Consensus 105 r~Rt~ft~~Ql~~LE~~F~~~~~~Ps~~~r~~LA~~L~~~~gLse~qV~vWFQ 157 (281)
+.|..|++++...+-..+... ...+.++|..+ ||+...|..|-.
T Consensus 2 ~~r~~ys~e~K~~~v~~~~~~-----g~sv~~va~~~----gi~~~~l~~W~~ 45 (76)
T PF01527_consen 2 RKRRRYSPEFKLQAVREYLES-----GESVSEVAREY----GISPSTLYNWRK 45 (76)
T ss_dssp -SS----HHHHHHHHHHHHHH-----HCHHHHHHHHH----TS-HHHHHHHHH
T ss_pred CCCCCCCHHHHHHHHHHHHHC-----CCceEeeeccc----ccccccccHHHH
Confidence 356788888777666655332 24567899999 999999999963
No 46
>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=51.75 E-value=11 Score=25.51 Aligned_cols=41 Identities=29% Similarity=0.249 Sum_probs=27.7
Q ss_pred CChHHHHHHHHHHhhcCCCCCHhHHHHHHHHHHhcCCCccccccccccchh
Q 023479 110 PTPVQLQILESIFDQGTGTPSKQKIKEITVELSQHGQISETNVYNWFQNRR 160 (281)
Q Consensus 110 ft~~Ql~~LE~~F~~~~~~Ps~~~r~~LA~~L~~~~gLse~qV~vWFQNRR 160 (281)
+++.+..++.-.|..+ ....+||..+ |+++..|+.|...-|
T Consensus 11 L~~~~r~i~~l~~~~g------~s~~eIa~~l----~~s~~~v~~~l~ra~ 51 (54)
T PF08281_consen 11 LPERQREIFLLRYFQG------MSYAEIAEIL----GISESTVKRRLRRAR 51 (54)
T ss_dssp S-HHHHHHHHHHHTS---------HHHHHHHC----TS-HHHHHHHHHHHH
T ss_pred CCHHHHHHHHHHHHHC------cCHHHHHHHH----CcCHHHHHHHHHHHH
Confidence 4566777777766664 3355889999 999999999986443
No 47
>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=47.71 E-value=26 Score=24.67 Aligned_cols=38 Identities=29% Similarity=0.390 Sum_probs=29.3
Q ss_pred CChHHHHHHHHHHhhcCCCCC---HhHHHHHHHHHHhcCCCcccccc
Q 023479 110 PTPVQLQILESIFDQGTGTPS---KQKIKEITVELSQHGQISETNVY 153 (281)
Q Consensus 110 ft~~Ql~~LE~~F~~~~~~Ps---~~~r~~LA~~L~~~~gLse~qV~ 153 (281)
+|+.|+.+|..+|+.. |-+ .....+||..| |++...|.
T Consensus 1 LT~~Q~e~L~~A~~~G--Yfd~PR~~tl~elA~~l----gis~st~~ 41 (53)
T PF04967_consen 1 LTDRQREILKAAYELG--YFDVPRRITLEELAEEL----GISKSTVS 41 (53)
T ss_pred CCHHHHHHHHHHHHcC--CCCCCCcCCHHHHHHHh----CCCHHHHH
Confidence 5788999999999984 544 34557889999 99987653
No 48
>cd00569 HTH_Hin_like Helix-turn-helix domain of Hin and related proteins, a family of DNA-binding domains unique to bacteria and represented by the Hin protein of Salmonella. The basic HTH domain is a simple fold comprised of three core helices that form a right-handed helical bundle. The principal DNA-protein interface is formed by the third helix, the recognition helix, inserting itself into the major groove of the DNA. A diverse array of HTH domains participate in a variety of functions that depend on their DNA-binding properties. HTH_Hin represents one of the simplest versions of the HTH domains; the characterization of homologous relationships between various sequence-diverse HTH domain families remains difficult. The Hin recombinase induces the site-specific inversion of a chromosomal DNA segment containing a promoter, which controls the alternate expression of two genes by reversibly switching orientation. The Hin recombinase consists of a single polypeptide chain containing a D
Probab=45.93 E-value=38 Score=19.15 Aligned_cols=38 Identities=24% Similarity=0.496 Sum_probs=26.0
Q ss_pred CCChHHHHHHHHHHhhcCCCCCHhHHHHHHHHHHhcCCCccccccccc
Q 023479 109 TPTPVQLQILESIFDQGTGTPSKQKIKEITVELSQHGQISETNVYNWF 156 (281)
Q Consensus 109 ~ft~~Ql~~LE~~F~~~~~~Ps~~~r~~LA~~L~~~~gLse~qV~vWF 156 (281)
.++......+...|... + ...++|..+ +++...|..|.
T Consensus 5 ~~~~~~~~~i~~~~~~~--~----s~~~ia~~~----~is~~tv~~~~ 42 (42)
T cd00569 5 KLTPEQIEEARRLLAAG--E----SVAEIARRL----GVSRSTLYRYL 42 (42)
T ss_pred cCCHHHHHHHHHHHHcC--C----CHHHHHHHH----CCCHHHHHHhC
Confidence 35566666666666543 3 345788888 99998888774
No 49
>PF11336 DUF3138: Protein of unknown function (DUF3138); InterPro: IPR021485 This family of proteins with unknown function appear to be restricted to Proteobacteria.
Probab=42.82 E-value=1.2e+02 Score=30.47 Aligned_cols=83 Identities=14% Similarity=0.143 Sum_probs=52.6
Q ss_pred ccCcccccccCCHHHHHHHHHHHHHHHHHHHHHHHhhhhhhhhhhhhhcCCCCCCccCCCCCcCCCCCCCCCCCCCCCCh
Q 023479 33 VVNGVMYVKVMTDEQLETLRKQIAVYATICEQLVEMHKSLSAHQDLAAAGGRLGNIYCDPLMTSGGGHKISARQRWTPTP 112 (281)
Q Consensus 33 ~~~g~~~~~~~t~~~~~~lr~qi~~~~~~c~~~~~~~k~ls~~~~~~~~g~~~g~~~~~p~~~s~~~~~~~rr~Rt~ft~ 112 (281)
+|++++....-+..+|+.|.+|+.... ++.-+|.+.+.+++..+..+...+....-+...+. ...++.+|+
T Consensus 12 ~al~~~a~a~a~a~~i~~L~~ql~aLq---~~v~eL~~~laa~~~aa~~gA~~~~~~~a~~~aP~------~~a~~~~T~ 82 (514)
T PF11336_consen 12 GALPGAAMAAATADQIKALQAQLQALQ---DQVNELRAKLAAKPAAAPGGAAIGPAATAAAAAPS------SDAQAGLTN 82 (514)
T ss_pred hhccccccccCCHHHHHHHHHHHHHHH---HHHHHHHHHHhcCCCCCCccccccccccccccCCC------cccccccCh
Confidence 466666677788899999999987654 45557777777666654333333333322222111 125789999
Q ss_pred HHHHHHHHHHhh
Q 023479 113 VQLQILESIFDQ 124 (281)
Q Consensus 113 ~Ql~~LE~~F~~ 124 (281)
+++..+..-+..
T Consensus 83 d~~~~~~qqiAn 94 (514)
T PF11336_consen 83 DDATEMRQQIAN 94 (514)
T ss_pred HHHHHHHHHHHh
Confidence 999777766655
No 50
>KOG3755 consensus SATB1 matrix attachment region binding protein [Transcription]
Probab=41.25 E-value=7 Score=40.36 Aligned_cols=64 Identities=19% Similarity=0.098 Sum_probs=37.2
Q ss_pred CCCCCCCChHHHHH-HHHHHhhcCCCCCHhHHHHHHHHHH---hcCCCccccccccccchhhHHHHHhh
Q 023479 104 ARQRWTPTPVQLQI-LESIFDQGTGTPSKQKIKEITVELS---QHGQISETNVYNWFQNRRARSKRKQL 168 (281)
Q Consensus 104 rr~Rt~ft~~Ql~~-LE~~F~~~~~~Ps~~~r~~LA~~L~---~~~gLse~qV~vWFQNRRaK~Kr~~~ 168 (281)
|+.+..|-..++.. -+..|..+ ..++.-.+.+....+- -.-......|+.||.|||+++|+.+-
T Consensus 692 k~~~~k~f~~~~~ev~~~w~~k~-~s~s~~~v~eYkee~~~~~~~e~~~~kn~~~~fk~~~ee~~~~k~ 759 (769)
T KOG3755|consen 692 KKTIIKFFQNQRYEVKHHWKLKT-RSGSWVDVAEYKEEELLMPYEEKFESKNVQFWFKVRREEEKRLKM 759 (769)
T ss_pred HHHHHHhhhcceeecchhheecc-cCchhHHHHHhhHHhhcchhhhhhhhcchHHHHHHHHHHHhhhhc
Confidence 33333333333333 34556664 6777666655554440 00023457899999999999998654
No 51
>KOG1146 consensus Homeobox protein [General function prediction only]
Probab=37.04 E-value=42 Score=37.88 Aligned_cols=61 Identities=26% Similarity=0.347 Sum_probs=53.1
Q ss_pred CCCCCCCCCChHHHHHHHHHHhhcCCCCCHhHHHHHHHHHHhcCCCccccccccccchhhHHHHHh
Q 023479 102 ISARQRWTPTPVQLQILESIFDQGTGTPSKQKIKEITVELSQHGQISETNVYNWFQNRRARSKRKQ 167 (281)
Q Consensus 102 ~~rr~Rt~ft~~Ql~~LE~~F~~~~~~Ps~~~r~~LA~~L~~~~gLse~qV~vWFQNRRaK~Kr~~ 167 (281)
+.++.|..+-++++..|-++|-.+ --|+...+.-|.... ..+.+++.+||+|-|.|.++..
T Consensus 704 ~~~~~~~~~~~~aa~~l~~a~~~~-~sps~k~~~civcd~----~st~~l~~l~~h~~~~rs~ke~ 764 (1406)
T KOG1146|consen 704 RDKLLRLTILPEAAMILGRAYMQD-NSPSLKVFDCIVCDV----FSTDRLDQLWFHNTRERSRKEQ 764 (1406)
T ss_pred ccccCcccccHHHHhhhhhcccCC-CCHHHHHHHHhhhhh----hhhhhHHHHhhcchhhhhhhhc
Confidence 345667888889999999999997 689999888888888 8999999999999999988866
No 52
>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=37.02 E-value=32 Score=27.06 Aligned_cols=37 Identities=22% Similarity=0.321 Sum_probs=21.1
Q ss_pred HHHHHHHHhhcCCCCCHhHHHHHHHHHHhcCCCccccccccccchhhHHHHHhhhh
Q 023479 115 LQILESIFDQGTGTPSKQKIKEITVELSQHGQISETNVYNWFQNRRARSKRKQLVS 170 (281)
Q Consensus 115 l~~LE~~F~~~~~~Ps~~~r~~LA~~L~~~~gLse~qV~vWFQNRRaK~Kr~~~~~ 170 (281)
+.+..-.|+.| +||... .. +..= .|||.+|++.+..-
T Consensus 14 vRiIk~Lyqsn-PyP~~~-GT--r~aR---------------RnRRRRWR~rq~QI 50 (91)
T PF00424_consen 14 VRIIKILYQSN-PYPSPE-GT--RQAR---------------RNRRRRWRARQRQI 50 (91)
T ss_dssp HHHHHHHHHTS--S--S--S---HHHH---------------HHHHHHHHHHHHHH
T ss_pred HHHHHHHHccc-cCCCCC-Cc--cccc---------------cchhhhHHHHHHHH
Confidence 44556668887 999753 11 1111 58999999887763
No 53
>PRK09646 RNA polymerase sigma factor SigK; Reviewed
Probab=36.62 E-value=39 Score=28.93 Aligned_cols=47 Identities=15% Similarity=0.148 Sum_probs=31.1
Q ss_pred CChHHHHHHHHHHhhcCCCCCHhHHHHHHHHHHhcCCCccccccccccchhhHHHHH
Q 023479 110 PTPVQLQILESIFDQGTGTPSKQKIKEITVELSQHGQISETNVYNWFQNRRARSKRK 166 (281)
Q Consensus 110 ft~~Ql~~LE~~F~~~~~~Ps~~~r~~LA~~L~~~~gLse~qV~vWFQNRRaK~Kr~ 166 (281)
+++.+..+|...|..+ ....+||..| |++...|+++...-|.+-|+.
T Consensus 143 L~~~~r~vl~l~~~~~------~s~~EIA~~L----gis~~tVk~~l~ra~~~Lr~~ 189 (194)
T PRK09646 143 LTDTQRESVTLAYYGG------LTYREVAERL----AVPLGTVKTRMRDGLIRLRDC 189 (194)
T ss_pred CCHHHHHHHHHHHHcC------CCHHHHHHHh----CCChHhHHHHHHHHHHHHHHH
Confidence 4455555555444332 3355889999 999999999986555555544
No 54
>PRK09652 RNA polymerase sigma factor RpoE; Provisional
Probab=34.03 E-value=39 Score=27.87 Aligned_cols=48 Identities=13% Similarity=-0.011 Sum_probs=32.4
Q ss_pred CCChHHHHHHHHHHhhcCCCCCHhHHHHHHHHHHhcCCCccccccccccchhhHHHHH
Q 023479 109 TPTPVQLQILESIFDQGTGTPSKQKIKEITVELSQHGQISETNVYNWFQNRRARSKRK 166 (281)
Q Consensus 109 ~ft~~Ql~~LE~~F~~~~~~Ps~~~r~~LA~~L~~~~gLse~qV~vWFQNRRaK~Kr~ 166 (281)
.+++.+..+|...|..+ + ...+||..| |+++..|+.|...-+.+-|+.
T Consensus 128 ~L~~~~r~vl~l~~~~~--~----s~~eIA~~l----gis~~tV~~~l~ra~~~Lr~~ 175 (182)
T PRK09652 128 SLPEELRTAITLREIEG--L----SYEEIAEIM----GCPIGTVRSRIFRAREALRAK 175 (182)
T ss_pred hCCHHHHHHHHHHHHcC--C----CHHHHHHHH----CCCHHHHHHHHHHHHHHHHHH
Confidence 35566666666655443 2 244889999 999999999987555555543
No 55
>PRK03975 tfx putative transcriptional regulator; Provisional
Probab=33.90 E-value=46 Score=28.12 Aligned_cols=51 Identities=22% Similarity=0.173 Sum_probs=38.5
Q ss_pred CCCChHHHHHHHHHHhhcCCCCCHhHHHHHHHHHHhcCCCccccccccccchhhHHHHHhhh
Q 023479 108 WTPTPVQLQILESIFDQGTGTPSKQKIKEITVELSQHGQISETNVYNWFQNRRARSKRKQLV 169 (281)
Q Consensus 108 t~ft~~Ql~~LE~~F~~~~~~Ps~~~r~~LA~~L~~~~gLse~qV~vWFQNRRaK~Kr~~~~ 169 (281)
..+++.|+.+|.. +..+ + ...+||..| |++...|..|-.+.+.+-|+....
T Consensus 5 ~~Lt~rqreVL~l-r~~G--l----Tq~EIAe~L----GiS~~tVs~ie~ra~kkLr~~~~t 55 (141)
T PRK03975 5 SFLTERQIEVLRL-RERG--L----TQQEIADIL----GTSRANVSSIEKRARENIEKARET 55 (141)
T ss_pred cCCCHHHHHHHHH-HHcC--C----CHHHHHHHH----CCCHHHHHHHHHHHHHHHHHHHHH
Confidence 4678999999988 4332 2 244899999 999999999998777776655443
No 56
>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=33.59 E-value=17 Score=26.32 Aligned_cols=20 Identities=35% Similarity=0.712 Sum_probs=17.2
Q ss_pred HHHHHHHHHHhcCCCccccccccc
Q 023479 133 KIKEITVELSQHGQISETNVYNWF 156 (281)
Q Consensus 133 ~r~~LA~~L~~~~gLse~qV~vWF 156 (281)
.-.+||.+| |+++.+|+.|=
T Consensus 24 ~lkdIA~~L----gvs~~tIr~WK 43 (60)
T PF10668_consen 24 KLKDIAEKL----GVSESTIRKWK 43 (60)
T ss_pred cHHHHHHHH----CCCHHHHHHHh
Confidence 345889999 99999999995
No 57
>PRK06759 RNA polymerase factor sigma-70; Validated
Probab=33.01 E-value=39 Score=27.39 Aligned_cols=46 Identities=15% Similarity=0.172 Sum_probs=30.2
Q ss_pred CCChHHHHHHHHHHhhcCCCCCHhHHHHHHHHHHhcCCCccccccccccchhhHHH
Q 023479 109 TPTPVQLQILESIFDQGTGTPSKQKIKEITVELSQHGQISETNVYNWFQNRRARSK 164 (281)
Q Consensus 109 ~ft~~Ql~~LE~~F~~~~~~Ps~~~r~~LA~~L~~~~gLse~qV~vWFQNRRaK~K 164 (281)
.+++.+..++...|-.+ ....+||..| |+++..|+.|...-|.+-|
T Consensus 106 ~L~~~~r~ii~l~~~~~------~s~~EIA~~l----~is~~tV~~~~~ra~~~Lr 151 (154)
T PRK06759 106 VLDEKEKYIIFERFFVG------KTMGEIALET----EMTYYQVRWIYRQALEKMR 151 (154)
T ss_pred hCCHHHHHHHHHHHhcC------CCHHHHHHHH----CCCHHHHHHHHHHHHHHHh
Confidence 34455555655554443 2356889999 9999999999865444433
No 58
>PRK12526 RNA polymerase sigma factor; Provisional
Probab=31.72 E-value=50 Score=28.69 Aligned_cols=31 Identities=13% Similarity=0.137 Sum_probs=23.4
Q ss_pred HHHHHHHHHHhcCCCccccccccccchhhHHHHHh
Q 023479 133 KIKEITVELSQHGQISETNVYNWFQNRRARSKRKQ 167 (281)
Q Consensus 133 ~r~~LA~~L~~~~gLse~qV~vWFQNRRaK~Kr~~ 167 (281)
...+||..| |+++..|+++...-|.+-++..
T Consensus 171 s~~EIA~~l----gis~~tV~~~l~Ra~~~Lr~~l 201 (206)
T PRK12526 171 SQEQLAQQL----NVPLGTVKSRLRLALAKLKVQM 201 (206)
T ss_pred CHHHHHHHH----CCCHHHHHHHHHHHHHHHHHHH
Confidence 455889999 9999999988866555555543
No 59
>PF13936 HTH_38: Helix-turn-helix domain; PDB: 2W48_A.
Probab=31.36 E-value=23 Score=23.52 Aligned_cols=39 Identities=28% Similarity=0.361 Sum_probs=20.0
Q ss_pred CCCChHHHHHHHHHHhhcCCCCCHhHHHHHHHHHHhcCCCccccccccc
Q 023479 108 WTPTPVQLQILESIFDQGTGTPSKQKIKEITVELSQHGQISETNVYNWF 156 (281)
Q Consensus 108 t~ft~~Ql~~LE~~F~~~~~~Ps~~~r~~LA~~L~~~~gLse~qV~vWF 156 (281)
..+|.+++..++..+..+ ....+||..| |.+...|..|.
T Consensus 3 ~~Lt~~eR~~I~~l~~~G------~s~~~IA~~l----g~s~sTV~rel 41 (44)
T PF13936_consen 3 KHLTPEERNQIEALLEQG------MSIREIAKRL----GRSRSTVSREL 41 (44)
T ss_dssp ---------HHHHHHCS---------HHHHHHHT----T--HHHHHHHH
T ss_pred cchhhhHHHHHHHHHHcC------CCHHHHHHHH----CcCcHHHHHHH
Confidence 467888899999887764 2345789999 99998887665
No 60
>COG3413 Predicted DNA binding protein [General function prediction only]
Probab=30.90 E-value=54 Score=28.94 Aligned_cols=48 Identities=29% Similarity=0.358 Sum_probs=34.9
Q ss_pred CCChHHHHHHHHHHhhcCCCCCHhH---HHHHHHHHHhcCCCccccccccccchhhHHH
Q 023479 109 TPTPVQLQILESIFDQGTGTPSKQK---IKEITVELSQHGQISETNVYNWFQNRRARSK 164 (281)
Q Consensus 109 ~ft~~Ql~~LE~~F~~~~~~Ps~~~---r~~LA~~L~~~~gLse~qV~vWFQNRRaK~K 164 (281)
.+|+.|+.+|..+|... |-+.++ ..+||+.| |+++..+ |..=|||..|
T Consensus 155 ~LTdrQ~~vL~~A~~~G--YFd~PR~~~l~dLA~~l----GISkst~--~ehLRrAe~K 205 (215)
T COG3413 155 DLTDRQLEVLRLAYKMG--YFDYPRRVSLKDLAKEL----GISKSTL--SEHLRRAERK 205 (215)
T ss_pred cCCHHHHHHHHHHHHcC--CCCCCccCCHHHHHHHh----CCCHHHH--HHHHHHHHHH
Confidence 79999999999999983 655554 46788888 9998763 3333455443
No 61
>PRK12512 RNA polymerase sigma factor; Provisional
Probab=30.67 E-value=55 Score=27.53 Aligned_cols=49 Identities=29% Similarity=0.250 Sum_probs=32.3
Q ss_pred CChHHHHHHHHHHhhcCCCCCHhHHHHHHHHHHhcCCCccccccccccchhhHHHHHhh
Q 023479 110 PTPVQLQILESIFDQGTGTPSKQKIKEITVELSQHGQISETNVYNWFQNRRARSKRKQL 168 (281)
Q Consensus 110 ft~~Ql~~LE~~F~~~~~~Ps~~~r~~LA~~L~~~~gLse~qV~vWFQNRRaK~Kr~~~ 168 (281)
+++.+..+|...|..+ ....+||..| |++...|++++..-|.+-|+...
T Consensus 132 L~~~~r~v~~l~~~~g------~s~~eIA~~l----~is~~tV~~~l~ra~~~Lr~~l~ 180 (184)
T PRK12512 132 LPPRQRDVVQSISVEG------ASIKETAAKL----SMSEGAVRVALHRGLAALAAKFR 180 (184)
T ss_pred CCHHHHHHHHHHHHcC------CCHHHHHHHh----CCCHHHHHHHHHHHHHHHHHHhh
Confidence 3444444554444332 3345888999 99999999999776766665543
No 62
>PRK09642 RNA polymerase sigma factor SigW; Reviewed
Probab=28.52 E-value=64 Score=26.39 Aligned_cols=48 Identities=13% Similarity=0.075 Sum_probs=31.3
Q ss_pred CChHHHHHHHHHHhhcCCCCCHhHHHHHHHHHHhcCCCccccccccccchhhHHHHHh
Q 023479 110 PTPVQLQILESIFDQGTGTPSKQKIKEITVELSQHGQISETNVYNWFQNRRARSKRKQ 167 (281)
Q Consensus 110 ft~~Ql~~LE~~F~~~~~~Ps~~~r~~LA~~L~~~~gLse~qV~vWFQNRRaK~Kr~~ 167 (281)
+++.+..++...|..+ ....+||..| |+++..|++....-|.+-|+..
T Consensus 107 Lp~~~r~v~~l~~~~g------~s~~EIA~~l----gis~~tV~~~l~Rar~~Lr~~l 154 (160)
T PRK09642 107 LPENYRDVVLAHYLEE------KSYQEIALQE----KIEVKTVEMKLYRARKWIKKHW 154 (160)
T ss_pred CCHHHHHHHHHHHHhC------CCHHHHHHHH----CCCHHHHHHHHHHHHHHHHHHH
Confidence 3444455555444442 2345889999 9999999999876666655544
No 63
>PRK11924 RNA polymerase sigma factor; Provisional
Probab=28.30 E-value=57 Score=26.76 Aligned_cols=31 Identities=16% Similarity=0.135 Sum_probs=23.9
Q ss_pred HHHHHHHHHHhcCCCccccccccccchhhHHHHHh
Q 023479 133 KIKEITVELSQHGQISETNVYNWFQNRRARSKRKQ 167 (281)
Q Consensus 133 ~r~~LA~~L~~~~gLse~qV~vWFQNRRaK~Kr~~ 167 (281)
...+||..| |+++..|+.|...-|.+.|+.-
T Consensus 143 ~~~eIA~~l----gis~~tv~~~~~ra~~~lr~~l 173 (179)
T PRK11924 143 SYREIAEIL----GVPVGTVKSRLRRARQLLRECL 173 (179)
T ss_pred CHHHHHHHH----CCCHHHHHHHHHHHHHHHHHHH
Confidence 346888999 9999999999976666665543
No 64
>PRK12519 RNA polymerase sigma factor; Provisional
Probab=28.27 E-value=45 Score=28.31 Aligned_cols=32 Identities=16% Similarity=0.034 Sum_probs=24.4
Q ss_pred HhHHHHHHHHHHhcCCCccccccccccchhhHHHHH
Q 023479 131 KQKIKEITVELSQHGQISETNVYNWFQNRRARSKRK 166 (281)
Q Consensus 131 ~~~r~~LA~~L~~~~gLse~qV~vWFQNRRaK~Kr~ 166 (281)
.....+||..| |++...|++|+..-|.+-|+.
T Consensus 157 g~s~~EIA~~l----gis~~tV~~~l~Ra~~~Lr~~ 188 (194)
T PRK12519 157 GLSQSEIAKRL----GIPLGTVKARARQGLLKLREL 188 (194)
T ss_pred CCCHHHHHHHh----CCCHHHHHHHHHHHHHHHHHH
Confidence 34466889999 999999999997655555543
No 65
>PRK12515 RNA polymerase sigma factor; Provisional
Probab=26.82 E-value=72 Score=27.05 Aligned_cols=50 Identities=14% Similarity=0.234 Sum_probs=32.8
Q ss_pred CCChHHHHHHHHHHhhcCCCCCHhHHHHHHHHHHhcCCCccccccccccchhhHHHHHhh
Q 023479 109 TPTPVQLQILESIFDQGTGTPSKQKIKEITVELSQHGQISETNVYNWFQNRRARSKRKQL 168 (281)
Q Consensus 109 ~ft~~Ql~~LE~~F~~~~~~Ps~~~r~~LA~~L~~~~gLse~qV~vWFQNRRaK~Kr~~~ 168 (281)
.+++.+..+|+..|..+ ....+||..| |+++..|++-...-|.+.|+...
T Consensus 131 ~L~~~~r~vl~l~~~~~------~s~~eIA~~l----gis~~tV~~~l~Rar~~Lr~~l~ 180 (189)
T PRK12515 131 KLSPAHREIIDLVYYHE------KSVEEVGEIV----GIPESTVKTRMFYARKKLAELLK 180 (189)
T ss_pred hCCHHHHHHHHHHHHcC------CCHHHHHHHH----CcCHHHHHHHHHHHHHHHHHHHH
Confidence 34455555555544432 2345788889 99999999888766666666544
No 66
>PRK04217 hypothetical protein; Provisional
Probab=26.47 E-value=72 Score=25.80 Aligned_cols=50 Identities=14% Similarity=0.123 Sum_probs=37.8
Q ss_pred CCCChHHHHHHHHHHhhcCCCCCHhHHHHHHHHHHhcCCCccccccccccchhhHHHHHh
Q 023479 108 WTPTPVQLQILESIFDQGTGTPSKQKIKEITVELSQHGQISETNVYNWFQNRRARSKRKQ 167 (281)
Q Consensus 108 t~ft~~Ql~~LE~~F~~~~~~Ps~~~r~~LA~~L~~~~gLse~qV~vWFQNRRaK~Kr~~ 167 (281)
..++.+++.++...|... + ...+||+.| |++...|+..+..-+.+-+...
T Consensus 41 ~~Lt~eereai~l~~~eG--l----S~~EIAk~L----GIS~sTV~r~L~RArkkLre~L 90 (110)
T PRK04217 41 IFMTYEEFEALRLVDYEG--L----TQEEAGKRM----GVSRGTVWRALTSARKKVAQML 90 (110)
T ss_pred ccCCHHHHHHHHHHHHcC--C----CHHHHHHHH----CcCHHHHHHHHHHHHHHHHHHH
Confidence 467888888888777664 2 456889999 9999999998876666655543
No 67
>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=26.37 E-value=60 Score=25.28 Aligned_cols=46 Identities=22% Similarity=0.211 Sum_probs=30.0
Q ss_pred CCChHHHHHHHHHHhhcCCCCCHhHHHHHHHHHHhcCCCccccccccccchhhHHH
Q 023479 109 TPTPVQLQILESIFDQGTGTPSKQKIKEITVELSQHGQISETNVYNWFQNRRARSK 164 (281)
Q Consensus 109 ~ft~~Ql~~LE~~F~~~~~~Ps~~~r~~LA~~L~~~~gLse~qV~vWFQNRRaK~K 164 (281)
.+++.+..++...|... ....+||..+ |+++..|+.|...-+.|-|
T Consensus 110 ~L~~~~~~ii~~~~~~g------~s~~eIA~~l----~~s~~~v~~~~~~~~~kl~ 155 (158)
T TIGR02937 110 KLPEREREVLVLRYLEG------LSYKEIAEIL----GISVGTVKRRLKRARKKLR 155 (158)
T ss_pred hCCHHHHHHHhhHHhcC------CCHHHHHHHH----CCCHHHHHHHHHHHHHHHH
Confidence 34455556655544332 2345889999 9999999998865555544
No 68
>TIGR02959 SigZ RNA polymerase sigma factor, SigZ family. This family of RNA polymerase sigma factors is a member of the Sigma-70 subfamily (TIGR02937). One of these is designated as SigZ in B. subtilis (Swiss_Prot: SIGZ_BACSU). Interestingly, this group has a very sporatic distribution, B. subtilis, for instance, being the only sequenced strain of Bacilli with a member. Dechloromonas aromatica RCB appears to have two of these sigma factors. A member appears on a plasmid found in Photobacterium profundum SS9 and Vibrio fischeri ES114 (where a second one is chromosomally encoded).
Probab=26.18 E-value=93 Score=26.00 Aligned_cols=50 Identities=16% Similarity=0.050 Sum_probs=34.0
Q ss_pred CCChHHHHHHHHHHhhcCCCCCHhHHHHHHHHHHhcCCCccccccccccchhhHHHHHhh
Q 023479 109 TPTPVQLQILESIFDQGTGTPSKQKIKEITVELSQHGQISETNVYNWFQNRRARSKRKQL 168 (281)
Q Consensus 109 ~ft~~Ql~~LE~~F~~~~~~Ps~~~r~~LA~~L~~~~gLse~qV~vWFQNRRaK~Kr~~~ 168 (281)
.+++.+..+|.-.|..+ ....+||..| |+++..|+++-..-|.+.++...
T Consensus 100 ~L~~~~r~v~~l~~~~g------~s~~eIA~~l----gis~~tV~~~l~Rar~~Lr~~l~ 149 (170)
T TIGR02959 100 ELPDEYREAIRLTELEG------LSQQEIAEKL----GLSLSGAKSRVQRGRKKLKELLE 149 (170)
T ss_pred hCCHHHHHHHHHHHHcC------CCHHHHHHHH----CCCHHHHHHHHHHHHHHHHHHHH
Confidence 45566666666655443 2355889999 99999999988766666555443
No 69
>PRK09413 IS2 repressor TnpA; Reviewed
Probab=26.18 E-value=81 Score=25.33 Aligned_cols=40 Identities=15% Similarity=0.372 Sum_probs=26.4
Q ss_pred CCCCChHHHH-HHHHHHhhcCCCCCHhHHHHHHHHHHhcCCCccccccccc
Q 023479 107 RWTPTPVQLQ-ILESIFDQGTGTPSKQKIKEITVELSQHGQISETNVYNWF 156 (281)
Q Consensus 107 Rt~ft~~Ql~-~LE~~F~~~~~~Ps~~~r~~LA~~L~~~~gLse~qV~vWF 156 (281)
|..++.+... ++...+.. .++ ..++|..+ |++...|..|.
T Consensus 10 rr~ys~EfK~~aV~~~~~~--g~s----v~evA~e~----gIs~~tl~~W~ 50 (121)
T PRK09413 10 RRRRTTQEKIAIVQQSFEP--GMT----VSLVARQH----GVAASQLFLWR 50 (121)
T ss_pred CCCCCHHHHHHHHHHHHcC--CCC----HHHHHHHH----CcCHHHHHHHH
Confidence 3456676544 44444443 233 44789999 99999999995
No 70
>PRK12514 RNA polymerase sigma factor; Provisional
Probab=25.72 E-value=76 Score=26.53 Aligned_cols=29 Identities=10% Similarity=0.314 Sum_probs=22.4
Q ss_pred HHHHHHHHHHhcCCCccccccccccchhhHHHH
Q 023479 133 KIKEITVELSQHGQISETNVYNWFQNRRARSKR 165 (281)
Q Consensus 133 ~r~~LA~~L~~~~gLse~qV~vWFQNRRaK~Kr 165 (281)
...+||..| |+++..|+++...-|.+-|+
T Consensus 147 s~~eIA~~l----gis~~tV~~~l~Rar~~Lr~ 175 (179)
T PRK12514 147 SYKELAERH----DVPLNTMRTWLRRSLLKLRE 175 (179)
T ss_pred CHHHHHHHH----CCChHHHHHHHHHHHHHHHH
Confidence 356889999 99999999988755555544
No 71
>PRK00118 putative DNA-binding protein; Validated
Probab=25.50 E-value=74 Score=25.46 Aligned_cols=47 Identities=19% Similarity=0.208 Sum_probs=33.4
Q ss_pred CChHHHHHHHHHHhhcCCCCCHhHHHHHHHHHHhcCCCccccccccccchhhHHHHH
Q 023479 110 PTPVQLQILESIFDQGTGTPSKQKIKEITVELSQHGQISETNVYNWFQNRRARSKRK 166 (281)
Q Consensus 110 ft~~Ql~~LE~~F~~~~~~Ps~~~r~~LA~~L~~~~gLse~qV~vWFQNRRaK~Kr~ 166 (281)
+++.|..++...|..+ + ...+||..+ |+++..|..|....|.+-|..
T Consensus 18 L~ekqRevl~L~y~eg--~----S~~EIAe~l----GIS~~TV~r~L~RArkkLr~~ 64 (104)
T PRK00118 18 LTEKQRNYMELYYLDD--Y----SLGEIAEEF----NVSRQAVYDNIKRTEKLLEDY 64 (104)
T ss_pred CCHHHHHHHHHHHHcC--C----CHHHHHHHH----CcCHHHHHHHHHHHHHHHHHH
Confidence 4566677776666554 2 345789999 999999999997666655543
No 72
>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=25.41 E-value=69 Score=26.75 Aligned_cols=46 Identities=26% Similarity=0.240 Sum_probs=30.8
Q ss_pred CChHHHHHHHHHHhhcCCCCCHhHHHHHHHHHHhcCCCccccccccccchhhHHHH
Q 023479 110 PTPVQLQILESIFDQGTGTPSKQKIKEITVELSQHGQISETNVYNWFQNRRARSKR 165 (281)
Q Consensus 110 ft~~Ql~~LE~~F~~~~~~Ps~~~r~~LA~~L~~~~gLse~qV~vWFQNRRaK~Kr 165 (281)
+++.+..++.-.|..+ ....+||..| |+++..|++....-|.+-|+
T Consensus 135 Lp~~~r~v~~l~~~~g------~s~~EIA~~l----gis~~tVk~~l~Rar~~Lr~ 180 (183)
T TIGR02999 135 VDPRQAEVVELRFFAG------LTVEEIAELL----GVSVRTVERDWRFARAWLAD 180 (183)
T ss_pred CCHHHHHHHHHHHHcC------CCHHHHHHHh----CCCHHHHHHHHHHHHHHHHH
Confidence 4555555555555443 2345888999 99999999998765555544
No 73
>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=25.16 E-value=49 Score=21.89 Aligned_cols=38 Identities=21% Similarity=0.518 Sum_probs=26.1
Q ss_pred CCChHHHHHHHHHHhhcCCCCCHhHHHHHHHHHHhcCCCccccccccc
Q 023479 109 TPTPVQLQILESIFDQGTGTPSKQKIKEITVELSQHGQISETNVYNWF 156 (281)
Q Consensus 109 ~ft~~Ql~~LE~~F~~~~~~Ps~~~r~~LA~~L~~~~gLse~qV~vWF 156 (281)
.++.+++..+-..+... + .+.+||+.+ |++...|+.++
T Consensus 5 ~~~~~~~~~i~~l~~~G--~----si~~IA~~~----gvsr~TvyR~l 42 (45)
T PF02796_consen 5 KLSKEQIEEIKELYAEG--M----SIAEIAKQF----GVSRSTVYRYL 42 (45)
T ss_dssp SSSHCCHHHHHHHHHTT--------HHHHHHHT----TS-HHHHHHHH
T ss_pred CCCHHHHHHHHHHHHCC--C----CHHHHHHHH----CcCHHHHHHHH
Confidence 46666677777777663 2 356889999 99999887765
No 74
>PRK12533 RNA polymerase sigma factor; Provisional
Probab=24.88 E-value=80 Score=27.98 Aligned_cols=31 Identities=16% Similarity=0.157 Sum_probs=23.9
Q ss_pred HHHHHHHHHHhcCCCccccccccccchhhHHHHHh
Q 023479 133 KIKEITVELSQHGQISETNVYNWFQNRRARSKRKQ 167 (281)
Q Consensus 133 ~r~~LA~~L~~~~gLse~qV~vWFQNRRaK~Kr~~ 167 (281)
...+||..| |+++..|+++...-|.+-++..
T Consensus 152 s~~EIAe~L----giS~~tVk~~L~RAr~~Lr~~l 182 (216)
T PRK12533 152 SYREIAAIA----DVPVGTVMSRLARARRRLAALL 182 (216)
T ss_pred CHHHHHHHH----CCCHHHHHHHHHHHHHHHHHHH
Confidence 345889999 9999999998876666655554
No 75
>TIGR02948 SigW_bacill RNA polymerase sigma-W factor. This sigma factor is restricted to certain lineages of the order Bacillales.
Probab=24.37 E-value=69 Score=26.76 Aligned_cols=31 Identities=19% Similarity=0.273 Sum_probs=23.3
Q ss_pred hHHHHHHHHHHhcCCCccccccccccchhhHHHHH
Q 023479 132 QKIKEITVELSQHGQISETNVYNWFQNRRARSKRK 166 (281)
Q Consensus 132 ~~r~~LA~~L~~~~gLse~qV~vWFQNRRaK~Kr~ 166 (281)
....+||..| |+++..|+++...-|.+-|..
T Consensus 153 ~s~~eIA~~l----gis~~~v~~~l~Rar~~Lr~~ 183 (187)
T TIGR02948 153 LSLKEISEIL----DLPVGTVKTRIHRGREALRKQ 183 (187)
T ss_pred CCHHHHHHHH----CCCHHHHHHHHHHHHHHHHHH
Confidence 3456888999 999999999997655555543
No 76
>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=23.84 E-value=72 Score=21.90 Aligned_cols=44 Identities=27% Similarity=0.220 Sum_probs=32.0
Q ss_pred CCChHHHHHHHHHHhhcCCCCCHhHHHHHHHHHHhcCCCccccccccccchhhHH
Q 023479 109 TPTPVQLQILESIFDQGTGTPSKQKIKEITVELSQHGQISETNVYNWFQNRRARS 163 (281)
Q Consensus 109 ~ft~~Ql~~LE~~F~~~~~~Ps~~~r~~LA~~L~~~~gLse~qV~vWFQNRRaK~ 163 (281)
.||+.++.+|.-...-. ...+||..| ++++..|+.+..+=+.|.
T Consensus 3 ~LT~~E~~vl~~l~~G~-------~~~eIA~~l----~is~~tV~~~~~~i~~Kl 46 (58)
T PF00196_consen 3 SLTERELEVLRLLAQGM-------SNKEIAEEL----GISEKTVKSHRRRIMKKL 46 (58)
T ss_dssp SS-HHHHHHHHHHHTTS--------HHHHHHHH----TSHHHHHHHHHHHHHHHH
T ss_pred ccCHHHHHHHHHHHhcC-------CcchhHHhc----CcchhhHHHHHHHHHHHh
Confidence 57888888887765442 245899999 999999998887655553
No 77
>PRK09644 RNA polymerase sigma factor SigM; Provisional
Probab=23.83 E-value=79 Score=26.06 Aligned_cols=49 Identities=12% Similarity=-0.024 Sum_probs=31.7
Q ss_pred CChHHHHHHHHHHhhcCCCCCHhHHHHHHHHHHhcCCCccccccccccchhhHHHHHhh
Q 023479 110 PTPVQLQILESIFDQGTGTPSKQKIKEITVELSQHGQISETNVYNWFQNRRARSKRKQL 168 (281)
Q Consensus 110 ft~~Ql~~LE~~F~~~~~~Ps~~~r~~LA~~L~~~~gLse~qV~vWFQNRRaK~Kr~~~ 168 (281)
+++.+..++...|-.+ ....+||..| |+++..|++|...-|.+-|+...
T Consensus 109 L~~~~r~v~~l~~~~g------~s~~eIA~~l----gis~~tv~~~l~Rar~~Lr~~l~ 157 (165)
T PRK09644 109 LPVIEAQAILLCDVHE------LTYEEAASVL----DLKLNTYKSHLFRGRKRLKALLK 157 (165)
T ss_pred CCHHHHHHHHhHHHhc------CCHHHHHHHH----CCCHHHHHHHHHHHHHHHHHHHH
Confidence 4445555554443332 2355889999 99999999999766666655443
No 78
>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=23.40 E-value=80 Score=25.28 Aligned_cols=45 Identities=22% Similarity=0.098 Sum_probs=27.6
Q ss_pred CChHHHHHHHHHHhhcCCCCCHhHHHHHHHHHHhcCCCccccccccccchhhHHH
Q 023479 110 PTPVQLQILESIFDQGTGTPSKQKIKEITVELSQHGQISETNVYNWFQNRRARSK 164 (281)
Q Consensus 110 ft~~Ql~~LE~~F~~~~~~Ps~~~r~~LA~~L~~~~gLse~qV~vWFQNRRaK~K 164 (281)
+++.+..+|.-.|..+ ....+||..| |+++..|+.+...-|.+.|
T Consensus 114 L~~~~r~il~l~~~~~------~~~~eIA~~l----gis~~tv~~~~~ra~~~Lr 158 (161)
T TIGR02985 114 LPEQCRKIFILSRFEG------KSYKEIAEEL----GISVKTVEYHISKALKELR 158 (161)
T ss_pred CCHHHHHHHHHHHHcC------CCHHHHHHHH----CCCHHHHHHHHHHHHHHHH
Confidence 3444455555444332 2345788999 9999999988754444443
No 79
>PRK09648 RNA polymerase sigma factor SigD; Reviewed
Probab=23.25 E-value=81 Score=26.67 Aligned_cols=47 Identities=19% Similarity=0.014 Sum_probs=29.7
Q ss_pred CCChHHHHHHHHHHhhcCCCCCHhHHHHHHHHHHhcCCCccccccccccchhhHHHH
Q 023479 109 TPTPVQLQILESIFDQGTGTPSKQKIKEITVELSQHGQISETNVYNWFQNRRARSKR 165 (281)
Q Consensus 109 ~ft~~Ql~~LE~~F~~~~~~Ps~~~r~~LA~~L~~~~gLse~qV~vWFQNRRaK~Kr 165 (281)
.+++.+..++...|-.+ ....+||..| |++...|+++...-|.+-|+
T Consensus 139 ~L~~~~r~i~~l~~~~g------~s~~EIA~~l----gis~~tV~~~l~Ra~~~Lr~ 185 (189)
T PRK09648 139 TLPEKQREILILRVVVG------LSAEETAEAV----GSTPGAVRVAQHRALARLRA 185 (189)
T ss_pred hCCHHHHHHHHHHHHcC------CCHHHHHHHH----CCCHHHHHHHHHHHHHHHHH
Confidence 34445555555544332 3456889999 99999999888544444443
No 80
>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=22.66 E-value=23 Score=25.29 Aligned_cols=26 Identities=38% Similarity=0.676 Sum_probs=20.1
Q ss_pred HHHHHHHHHhcCCCccccccccccchhhHHHH
Q 023479 134 IKEITVELSQHGQISETNVYNWFQNRRARSKR 165 (281)
Q Consensus 134 r~~LA~~L~~~~gLse~qV~vWFQNRRaK~Kr 165 (281)
..+||..| |++...|+.|-+ |.+|..
T Consensus 16 ~~eIA~~L----g~~~~TV~~W~~--r~~W~~ 41 (58)
T PF06056_consen 16 IKEIAEEL----GVPRSTVYSWKD--RYKWDE 41 (58)
T ss_pred HHHHHHHH----CCChHHHHHHHH--hhCccc
Confidence 45899999 999999999974 444433
No 81
>PRK09637 RNA polymerase sigma factor SigZ; Provisional
Probab=22.47 E-value=79 Score=26.87 Aligned_cols=48 Identities=19% Similarity=0.052 Sum_probs=30.4
Q ss_pred CChHHHHHHHHHHhhcCCCCCHhHHHHHHHHHHhcCCCccccccccccchhhHHHHHh
Q 023479 110 PTPVQLQILESIFDQGTGTPSKQKIKEITVELSQHGQISETNVYNWFQNRRARSKRKQ 167 (281)
Q Consensus 110 ft~~Ql~~LE~~F~~~~~~Ps~~~r~~LA~~L~~~~gLse~qV~vWFQNRRaK~Kr~~ 167 (281)
+++.+..+|...|-. .....+||..| |+++..|+..+..-|.+.|+..
T Consensus 107 L~~~~r~i~~l~~~~------g~~~~EIA~~l----gis~~tV~~~l~Rar~~Lr~~l 154 (181)
T PRK09637 107 LPEKYAEALRLTELE------GLSQKEIAEKL----GLSLSGAKSRVQRGRVKLKELL 154 (181)
T ss_pred CCHHHHHHHHHHHhc------CCCHHHHHHHh----CCCHHHHHHHHHHHHHHHHHHH
Confidence 344444444444333 23355889999 9999999998875555555443
No 82
>TIGR03879 near_KaiC_dom probable regulatory domain. This model describes a common domain shared by two different families of proteins, each of which occurs regularly next to its corresponding partner family, a probable regulatory with homology to KaiC. By implication, this protein family likely is also involved in sensory transduction and/or regulation.
Probab=22.35 E-value=28 Score=26.21 Aligned_cols=25 Identities=28% Similarity=0.341 Sum_probs=20.6
Q ss_pred CHhHHHHHHHHHHhcCCCccccccccccc
Q 023479 130 SKQKIKEITVELSQHGQISETNVYNWFQN 158 (281)
Q Consensus 130 s~~~r~~LA~~L~~~~gLse~qV~vWFQN 158 (281)
......+||..| |+++..|++|+.+
T Consensus 31 eGlS~kEIAe~L----GIS~~TVk~~l~~ 55 (73)
T TIGR03879 31 AGKTASEIAEEL----GRTEQTVRNHLKG 55 (73)
T ss_pred cCCCHHHHHHHH----CcCHHHHHHHHhc
Confidence 334567999999 9999999999864
No 83
>PRK09480 slmA division inhibitor protein; Provisional
Probab=22.09 E-value=73 Score=26.63 Aligned_cols=37 Identities=11% Similarity=0.333 Sum_probs=28.9
Q ss_pred HHHHhhcCCCCCHhHHHHHHHHHHhcCCCccccccccccchhh
Q 023479 119 ESIFDQGTGTPSKQKIKEITVELSQHGQISETNVYNWFQNRRA 161 (281)
Q Consensus 119 E~~F~~~~~~Ps~~~r~~LA~~L~~~~gLse~qV~vWFQNRRa 161 (281)
...|... +. .......||+.. |++...+..+|.|+-.
T Consensus 20 ~~l~~~~-~G-~~~ti~~Ia~~a----gvs~gt~Y~~F~~K~~ 56 (194)
T PRK09480 20 AQMLESP-PG-ERITTAKLAARV----GVSEAALYRHFPSKAR 56 (194)
T ss_pred HHHHHhc-CC-CccCHHHHHHHh----CCCHhHHHHHCCCHHH
Confidence 3345443 45 777888999999 9999999999999763
No 84
>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=21.74 E-value=92 Score=25.42 Aligned_cols=46 Identities=15% Similarity=0.098 Sum_probs=30.4
Q ss_pred ChHHHHHHHHHHhhcCCCCCHhHHHHHHHHHHhcCCCccccccccccchhhHHHHH
Q 023479 111 TPVQLQILESIFDQGTGTPSKQKIKEITVELSQHGQISETNVYNWFQNRRARSKRK 166 (281)
Q Consensus 111 t~~Ql~~LE~~F~~~~~~Ps~~~r~~LA~~L~~~~gLse~qV~vWFQNRRaK~Kr~ 166 (281)
++.+..+|...|..+ ....+||..| |++...|+++-..-|.+-|+.
T Consensus 112 ~~~~r~i~~l~~~~g------~s~~eIA~~l----gis~~tV~~~l~ra~~~Lr~~ 157 (162)
T TIGR02983 112 PARQRAVVVLRYYED------LSEAQVAEAL----GISVGTVKSRLSRALARLREL 157 (162)
T ss_pred CHHHHHHhhhHHHhc------CCHHHHHHHh----CCCHHHHHHHHHHHHHHHHHH
Confidence 445555555544332 2345888999 999999999887666665554
No 85
>PRK12537 RNA polymerase sigma factor; Provisional
Probab=21.73 E-value=99 Score=26.04 Aligned_cols=28 Identities=18% Similarity=0.228 Sum_probs=21.2
Q ss_pred HHHHHHHHHHhcCCCccccccccccchhhHHH
Q 023479 133 KIKEITVELSQHGQISETNVYNWFQNRRARSK 164 (281)
Q Consensus 133 ~r~~LA~~L~~~~gLse~qV~vWFQNRRaK~K 164 (281)
...+||..| |+++..|++|-..-|.+-|
T Consensus 151 s~~eIA~~l----gis~~tV~~~l~ra~~~Lr 178 (182)
T PRK12537 151 SHAEIAQRL----GAPLGTVKAWIKRSLKALR 178 (182)
T ss_pred CHHHHHHHH----CCChhhHHHHHHHHHHHHH
Confidence 355889999 9999999998865444444
No 86
>PRK09639 RNA polymerase sigma factor SigX; Provisional
Probab=21.28 E-value=1e+02 Score=25.24 Aligned_cols=48 Identities=23% Similarity=0.224 Sum_probs=33.1
Q ss_pred CCChHHHHHHHHHHhhcCCCCCHhHHHHHHHHHHhcCCCccccccccccchhhHHHHHh
Q 023479 109 TPTPVQLQILESIFDQGTGTPSKQKIKEITVELSQHGQISETNVYNWFQNRRARSKRKQ 167 (281)
Q Consensus 109 ~ft~~Ql~~LE~~F~~~~~~Ps~~~r~~LA~~L~~~~gLse~qV~vWFQNRRaK~Kr~~ 167 (281)
.+++.+..+|.-.| .+ ....+||..| |+++..|+++...-|.+.|+..
T Consensus 112 ~L~~~~r~il~l~~-~g------~s~~eIA~~l----gis~~tV~~~i~ra~~~Lr~~l 159 (166)
T PRK09639 112 KMTERDRTVLLLRF-SG------YSYKEIAEAL----GIKESSVGTTLARAKKKFRKIY 159 (166)
T ss_pred cCCHHHHHHHHHHH-cC------CCHHHHHHHH----CCCHHHHHHHHHHHHHHHHHHH
Confidence 35556666666666 42 2355889999 9999999999866566655543
No 87
>COG4367 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=21.22 E-value=98 Score=24.36 Aligned_cols=39 Identities=18% Similarity=0.117 Sum_probs=27.2
Q ss_pred CCChHHHHHHHHHHhhcCCCCCHhHHHHHHHHHHhcCCCccccc
Q 023479 109 TPTPVQLQILESIFDQGTGTPSKQKIKEITVELSQHGQISETNV 152 (281)
Q Consensus 109 ~ft~~Ql~~LE~~F~~~~~~Ps~~~r~~LA~~L~~~~gLse~qV 152 (281)
+++++|+..-...|..| --.+.-...+||..| ++++.-|
T Consensus 2 SLn~eq~~~Tk~elqan-~el~~LS~~~iA~~L----n~t~~~l 40 (97)
T COG4367 2 SLNPEQKQRTKQELQAN-FELCPLSDEEIATAL----NWTEVKL 40 (97)
T ss_pred CCCHHHHHHHHHHHHHh-hhhccccHHHHHHHh----CCCHHHH
Confidence 35677777766666665 555566677899999 8887543
No 88
>PRK12541 RNA polymerase sigma factor; Provisional
Probab=21.19 E-value=79 Score=25.91 Aligned_cols=46 Identities=20% Similarity=0.023 Sum_probs=30.2
Q ss_pred CChHHHHHHHHHHhhcCCCCCHhHHHHHHHHHHhcCCCccccccccccchhhHHHH
Q 023479 110 PTPVQLQILESIFDQGTGTPSKQKIKEITVELSQHGQISETNVYNWFQNRRARSKR 165 (281)
Q Consensus 110 ft~~Ql~~LE~~F~~~~~~Ps~~~r~~LA~~L~~~~gLse~qV~vWFQNRRaK~Kr 165 (281)
+++.|..+|.-.|..+ + ...+||..| |++...|+++...-|.+-|+
T Consensus 113 L~~~~r~v~~l~~~~~--~----s~~eIA~~l----gis~~tv~~~l~Rar~~L~~ 158 (161)
T PRK12541 113 LPLERRNVLLLRDYYG--F----SYKEIAEMT----GLSLAKVKIELHRGRKETKS 158 (161)
T ss_pred CCHHHHHHhhhHHhcC--C----CHHHHHHHH----CCCHHHHHHHHHHHHHHHHh
Confidence 5555556665555443 2 345889999 99999999888654544443
No 89
>PRK05602 RNA polymerase sigma factor; Reviewed
Probab=21.13 E-value=95 Score=26.14 Aligned_cols=31 Identities=13% Similarity=0.078 Sum_probs=23.5
Q ss_pred HHHHHHHHHhcCCCccccccccccchhhHHHHHhh
Q 023479 134 IKEITVELSQHGQISETNVYNWFQNRRARSKRKQL 168 (281)
Q Consensus 134 r~~LA~~L~~~~gLse~qV~vWFQNRRaK~Kr~~~ 168 (281)
..+||..| |++...|+++...-|.+-|+...
T Consensus 147 ~~EIA~~l----gis~~tV~~~l~Rar~~Lr~~l~ 177 (186)
T PRK05602 147 NIEAAAVM----DISVDALESLLARGRRALRAQLA 177 (186)
T ss_pred HHHHHHHh----CcCHHHHHHHHHHHHHHHHHHHH
Confidence 45788889 99999999998665655555443
No 90
>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=21.10 E-value=88 Score=25.35 Aligned_cols=40 Identities=15% Similarity=0.266 Sum_probs=26.9
Q ss_pred CCChHHHHHHHHHHhhcCCCCCHhHHHHHHHHHHhcCCCccccccccccc
Q 023479 109 TPTPVQLQILESIFDQGTGTPSKQKIKEITVELSQHGQISETNVYNWFQN 158 (281)
Q Consensus 109 ~ft~~Ql~~LE~~F~~~~~~Ps~~~r~~LA~~L~~~~gLse~qV~vWFQN 158 (281)
.+++.+..++...|-.. ....+||..| |++...|+++...
T Consensus 111 ~L~~~~r~v~~l~~~~g------~~~~eIA~~l----~is~~tv~~~l~R 150 (159)
T TIGR02989 111 KLPERQRELLQLRYQRG------VSLTALAEQL----GRTVNAVYKALSR 150 (159)
T ss_pred HCCHHHHHHHHHHHhcC------CCHHHHHHHh----CCCHHHHHHHHHH
Confidence 35555666665544432 3356889999 9999999987643
No 91
>PRK12530 RNA polymerase sigma factor; Provisional
Probab=20.56 E-value=97 Score=26.41 Aligned_cols=30 Identities=20% Similarity=0.172 Sum_probs=23.0
Q ss_pred HHHHHHHHHHhcCCCccccccccccchhhHHHHH
Q 023479 133 KIKEITVELSQHGQISETNVYNWFQNRRARSKRK 166 (281)
Q Consensus 133 ~r~~LA~~L~~~~gLse~qV~vWFQNRRaK~Kr~ 166 (281)
...+||..| |+++..|+++...-|.+-|+.
T Consensus 152 s~~EIA~~l----gis~~tVk~~l~RAr~~Lr~~ 181 (189)
T PRK12530 152 SSEQICQEC----DISTSNLHVLLYRARLQLQAC 181 (189)
T ss_pred CHHHHHHHH----CCCHHHHHHHHHHHHHHHHHH
Confidence 356889999 999999999986555555544
No 92
>PRK06930 positive control sigma-like factor; Validated
Probab=20.43 E-value=1.1e+02 Score=26.41 Aligned_cols=50 Identities=16% Similarity=0.108 Sum_probs=34.8
Q ss_pred CCChHHHHHHHHHHhhcCCCCCHhHHHHHHHHHHhcCCCccccccccccchhhHHHHHhh
Q 023479 109 TPTPVQLQILESIFDQGTGTPSKQKIKEITVELSQHGQISETNVYNWFQNRRARSKRKQL 168 (281)
Q Consensus 109 ~ft~~Ql~~LE~~F~~~~~~Ps~~~r~~LA~~L~~~~gLse~qV~vWFQNRRaK~Kr~~~ 168 (281)
.+++.++.++.-.|..+ ....+||..| |++...|+.+...-|.+-++...
T Consensus 114 ~L~~rer~V~~L~~~eg------~s~~EIA~~l----giS~~tVk~~l~Ra~~kLr~~l~ 163 (170)
T PRK06930 114 VLTEREKEVYLMHRGYG------LSYSEIADYL----NIKKSTVQSMIERAEKKIARQIN 163 (170)
T ss_pred hCCHHHHHHHHHHHHcC------CCHHHHHHHH----CcCHHHHHHHHHHHHHHHHHHHH
Confidence 45666666666555443 2345889999 99999999999877776666543
No 93
>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=20.36 E-value=81 Score=26.40 Aligned_cols=32 Identities=9% Similarity=-0.000 Sum_probs=23.2
Q ss_pred CHhHHHHHHHHHHhcCCCccccccccccchhhHHHH
Q 023479 130 SKQKIKEITVELSQHGQISETNVYNWFQNRRARSKR 165 (281)
Q Consensus 130 s~~~r~~LA~~L~~~~gLse~qV~vWFQNRRaK~Kr 165 (281)
......+||..| |+++..|+++...-|.+-|+
T Consensus 153 ~~~s~~EIA~~l----gis~~tv~~~l~rar~~Lr~ 184 (190)
T TIGR02939 153 EGLSYEDIARIM----DCPVGTVRSRIFRAREAIAI 184 (190)
T ss_pred cCCCHHHHHHHH----CcCHHHHHHHHHHHHHHHHH
Confidence 334566889999 99999999988544444444
Done!