Query 026809
Match_columns 233
No_of_seqs 305 out of 1509
Neff 6.5
Searched_HMMs 46136
Date Fri Mar 29 13:01:48 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/026809.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/026809hhsearch_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 7.7E-36 1.7E-40 271.8 5.7 141 7-156 214-354 (398)
2 KOG1168 Transcription factor A 99.8 3.9E-20 8.5E-25 162.8 0.2 144 7-158 225-371 (385)
3 KOG0489 Transcription factor z 99.7 8.6E-19 1.9E-23 155.4 3.2 69 88-161 156-224 (261)
4 KOG0484 Transcription factor P 99.7 1.4E-18 3.1E-23 132.2 2.6 66 88-158 14-79 (125)
5 KOG4577 Transcription factor L 99.7 5.2E-18 1.1E-22 149.4 5.8 112 42-158 109-229 (383)
6 KOG0488 Transcription factor B 99.7 5.7E-18 1.2E-22 153.3 5.2 75 85-164 166-240 (309)
7 KOG0843 Transcription factor E 99.7 1E-17 2.2E-22 138.8 5.4 64 90-158 101-164 (197)
8 KOG2251 Homeobox transcription 99.7 1.3E-16 2.8E-21 136.1 8.7 68 86-158 32-99 (228)
9 KOG0487 Transcription factor A 99.7 5.4E-17 1.2E-21 145.7 6.2 67 87-158 231-297 (308)
10 KOG0842 Transcription factor t 99.7 5.5E-17 1.2E-21 145.6 5.2 67 88-159 150-216 (307)
11 KOG0850 Transcription factor D 99.7 8.7E-17 1.9E-21 137.8 5.6 69 85-158 116-184 (245)
12 PF00046 Homeobox: Homeobox do 99.6 4.3E-16 9.3E-21 106.8 3.6 57 92-153 1-57 (57)
13 KOG0485 Transcription factor N 99.6 3.1E-16 6.7E-21 133.5 3.4 67 87-158 100-166 (268)
14 KOG0492 Transcription factor M 99.6 6.3E-16 1.4E-20 130.8 5.1 68 86-158 139-206 (246)
15 KOG0494 Transcription factor C 99.6 2.8E-15 6E-20 130.6 5.0 64 90-158 140-203 (332)
16 KOG0848 Transcription factor C 99.5 2.8E-15 6.2E-20 131.0 1.1 62 93-159 201-262 (317)
17 TIGR01565 homeo_ZF_HD homeobox 99.5 5E-14 1.1E-18 97.6 5.8 52 92-148 2-57 (58)
18 smart00389 HOX Homeodomain. DN 99.5 3.6E-14 7.7E-19 96.5 3.7 55 93-152 2-56 (56)
19 KOG0493 Transcription factor E 99.5 4.2E-14 9.2E-19 123.4 5.0 63 91-158 246-308 (342)
20 cd00086 homeodomain Homeodomai 99.5 5.6E-14 1.2E-18 96.1 4.0 57 93-154 2-58 (59)
21 KOG0491 Transcription factor B 99.4 2.1E-14 4.6E-19 117.6 1.3 68 90-162 99-166 (194)
22 COG5576 Homeodomain-containing 99.4 2.1E-13 4.5E-18 112.4 5.2 64 91-159 51-114 (156)
23 KOG0844 Transcription factor E 99.4 1.1E-13 2.4E-18 123.1 2.4 63 90-157 180-242 (408)
24 KOG0486 Transcription factor P 99.4 3.6E-13 7.8E-18 120.2 4.3 66 89-159 110-175 (351)
25 KOG0490 Transcription factor, 99.4 1.8E-12 3.9E-17 111.3 7.9 104 47-156 17-120 (235)
26 KOG0483 Transcription factor H 99.3 3.2E-13 6.8E-18 115.0 2.6 62 92-158 51-112 (198)
27 KOG0847 Transcription factor, 99.3 2.5E-12 5.5E-17 109.9 4.7 66 89-159 165-230 (288)
28 PF00157 Pou: Pou domain - N-t 99.1 8.3E-12 1.8E-16 90.5 -1.9 60 7-66 15-74 (75)
29 KOG0849 Transcription factor P 98.9 7.6E-10 1.6E-14 102.3 4.1 65 88-157 173-237 (354)
30 KOG0775 Transcription factor S 98.7 2.1E-08 4.5E-13 88.5 7.1 51 98-153 183-233 (304)
31 KOG0774 Transcription factor P 98.7 2.4E-07 5.1E-12 81.5 10.6 64 91-158 188-253 (334)
32 smart00352 POU Found in Pit-Oc 98.3 2E-07 4.2E-12 67.7 0.1 60 7-66 15-74 (75)
33 PF05920 Homeobox_KN: Homeobox 98.2 4.5E-07 9.7E-12 58.3 0.5 33 114-150 8-40 (40)
34 KOG0490 Transcription factor, 98.0 5.3E-06 1.2E-10 71.1 3.9 64 88-156 150-213 (235)
35 KOG2252 CCAAT displacement pro 97.8 1.4E-05 3E-10 76.8 3.5 57 90-151 419-475 (558)
36 KOG1146 Homeobox protein [Gene 97.3 0.00018 4E-09 75.0 3.9 62 90-156 902-963 (1406)
37 PF11569 Homez: Homeodomain le 95.7 0.0029 6.2E-08 43.5 0.2 42 103-149 10-51 (56)
38 KOG0773 Transcription factor M 95.3 0.015 3.3E-07 53.3 3.5 59 91-153 239-299 (342)
39 KOG3623 Homeobox transcription 93.9 0.054 1.2E-06 54.3 3.6 51 103-158 568-618 (1007)
40 PF08880 QLQ: QLQ; InterPro: 88.2 0.63 1.4E-05 29.3 2.9 22 33-54 2-23 (37)
41 PF04218 CENP-B_N: CENP-B N-te 85.2 0.97 2.1E-05 30.4 2.8 46 92-147 1-46 (53)
42 PF04967 HTH_10: HTH DNA bindi 60.4 11 0.00023 25.6 2.8 38 98-140 1-40 (53)
43 PF01527 HTH_Tnp_1: Transposas 53.7 8.5 0.00019 26.7 1.6 43 93-145 2-45 (76)
44 cd06171 Sigma70_r4 Sigma70, re 50.7 9.6 0.00021 23.6 1.3 43 97-149 10-52 (55)
45 KOG3755 SATB1 matrix attachmen 46.9 4.2 9.1E-05 40.4 -1.2 50 107-157 708-760 (769)
46 PF04545 Sigma70_r4: Sigma-70, 45.0 19 0.00041 23.1 2.1 40 97-146 4-43 (50)
47 cd00569 HTH_Hin_like Helix-tur 44.1 36 0.00079 18.5 3.1 38 97-144 5-42 (42)
48 COG3413 Predicted DNA binding 37.0 39 0.00084 28.8 3.3 49 97-152 155-205 (215)
49 PF08281 Sigma70_r4_2: Sigma-7 36.2 22 0.00047 23.1 1.3 39 98-146 11-49 (54)
50 PF10668 Phage_terminase: Phag 32.7 17 0.00036 25.3 0.3 19 122-144 25-43 (60)
51 PRK09413 IS2 repressor TnpA; R 30.3 61 0.0013 25.1 3.2 41 95-145 10-51 (121)
52 PRK03975 tfx putative transcri 28.9 61 0.0013 26.3 3.0 49 96-155 5-53 (141)
53 PRK09652 RNA polymerase sigma 28.7 44 0.00096 26.5 2.2 47 97-153 128-174 (182)
54 PRK09480 slmA division inhibit 26.9 47 0.001 26.8 2.1 35 108-148 21-55 (194)
55 COG4367 Uncharacterized protei 26.4 64 0.0014 24.3 2.5 39 97-140 2-40 (97)
56 PRK09646 RNA polymerase sigma 26.0 59 0.0013 26.8 2.5 47 98-154 143-189 (194)
57 PRK06759 RNA polymerase factor 25.4 47 0.001 25.9 1.8 45 97-151 106-150 (154)
58 PF00196 GerE: Bacterial regul 23.0 70 0.0015 21.1 2.0 43 97-150 3-45 (58)
59 PF13936 HTH_38: Helix-turn-he 22.8 36 0.00079 21.6 0.5 39 96-144 3-41 (44)
60 KOG3623 Homeobox transcription 22.6 1.2E+02 0.0027 31.3 4.4 60 93-157 628-687 (1007)
61 KOG1146 Homeobox protein [Gene 22.6 61 0.0013 35.4 2.4 61 90-155 704-764 (1406)
62 PRK09644 RNA polymerase sigma 22.2 74 0.0016 25.3 2.4 31 122-156 127-157 (165)
63 TIGR02937 sigma70-ECF RNA poly 22.1 66 0.0014 24.1 2.0 45 98-152 111-155 (158)
64 PRK09642 RNA polymerase sigma 21.8 78 0.0017 24.9 2.4 47 98-154 107-153 (160)
65 PF06056 Terminase_5: Putative 21.6 38 0.00082 23.1 0.5 20 122-145 16-35 (58)
66 PRK12516 RNA polymerase sigma 21.6 84 0.0018 25.9 2.7 31 122-156 135-165 (187)
67 PRK12533 RNA polymerase sigma 21.4 78 0.0017 27.0 2.5 33 122-158 153-185 (216)
68 PRK12526 RNA polymerase sigma 21.4 71 0.0015 26.7 2.2 29 122-154 172-200 (206)
69 PRK12541 RNA polymerase sigma 21.0 70 0.0015 25.2 2.0 46 98-153 113-158 (161)
70 cd02413 40S_S3_KH K homology R 20.4 98 0.0021 22.5 2.5 25 121-145 51-75 (81)
71 PF02796 HTH_7: Helix-turn-hel 20.0 51 0.0011 20.9 0.8 38 97-144 5-42 (45)
No 1
>KOG3802 consensus Transcription factor OCT-1, contains POU and HOX domains [Transcription]
Probab=100.00 E-value=7.7e-36 Score=271.79 Aligned_cols=141 Identities=19% Similarity=0.218 Sum_probs=123.7
Q ss_pred CcccccchhhhhhccCCCcCCCcccccCCHHHHHHHHHHHHHHHHHHHHHHHhhhhhccchhhccCCCCCCCCCCCccCC
Q 026809 7 NFQQGGEMERQFQQDGGDTSNGLCVKVMTDEQMELLRKQIAVYAMICEQLVQMHKVFSAQNEIAGMRMGNPYFDPFVASG 86 (233)
Q Consensus 7 ~~~~~~~~~~~~q~~~~~~~~~~~~~~~t~~~~~~lr~qi~~y~~ic~q~~~~~~~l~~~~~~~~~~~~~~~~~p~~~s~ 86 (233)
.|||++++++++|+|||+|+|+|||+|||||+||||+++.++|++||+..++|.|||.+++..... .+..+.+.+ .
T Consensus 214 ~FKqRRIkLGfTQaDVGlALG~lyGn~FSQTTIcRFEALqLSFKNMCKLKPLL~KWLeEAes~~~~-~~~~~~e~i---~ 289 (398)
T KOG3802|consen 214 TFKQRRIKLGFTQADVGLALGALYGNVFSQTTICRFEALQLSFKNMCKLKPLLEKWLEEAESREST-GSPNSIEKI---G 289 (398)
T ss_pred HHHhheeccccchhHHHHHHHhhhCcccchhhhhHhHhhccCHHHHhhhHHHHHHHHHHHhccccc-CCCCCHHHh---h
Confidence 599999999999999999999999999999999999999999999999999999999998763111 111222222 1
Q ss_pred CCCCCCCCCCCCCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHHHhhCCCcccceeeccccchhhHHhhhc
Q 026809 87 SQKLTARQRWTPTPAQLQILEHVYDECKGTPRKQKIQDMTAELAKHGQISETNVYNWFQNRRARLKRKQS 156 (233)
Q Consensus 87 ~~~~~rr~Rt~~t~~Ql~~Le~~F~~~~~~P~~~~r~~LA~~L~~~~gls~~qV~vWFQNRR~k~Kr~~~ 156 (233)
...|+|++||+|....+..||+.|.+| ++|+.++|..||.+| +|+..+|+|||||||+|+||...
T Consensus 290 a~~RkRKKRTSie~~vr~aLE~~F~~n-pKPt~qEIt~iA~~L----~leKEVVRVWFCNRRQkeKR~~~ 354 (398)
T KOG3802|consen 290 AQSRKRKKRTSIEVNVRGALEKHFLKN-PKPTSQEITHIAESL----QLEKEVVRVWFCNRRQKEKRITP 354 (398)
T ss_pred ccccccccccceeHHHHHHHHHHHHhC-CCCCHHHHHHHHHHh----ccccceEEEEeeccccccccCCC
Confidence 222688899999999999999999999 899999999999999 99999999999999999999766
No 2
>KOG1168 consensus Transcription factor ACJ6/BRN-3, contains POU and HOX domains [Transcription]
Probab=99.77 E-value=3.9e-20 Score=162.83 Aligned_cols=144 Identities=17% Similarity=0.204 Sum_probs=120.0
Q ss_pred CcccccchhhhhhccCCCcCCCc---ccccCCHHHHHHHHHHHHHHHHHHHHHHHhhhhhccchhhccCCCCCCCCCCCc
Q 026809 7 NFQQGGEMERQFQQDGGDTSNGL---CVKVMTDEQMELLRKQIAVYAMICEQLVQMHKVFSAQNEIAGMRMGNPYFDPFV 83 (233)
Q Consensus 7 ~~~~~~~~~~~~q~~~~~~~~~~---~~~~~t~~~~~~lr~qi~~y~~ic~q~~~~~~~l~~~~~~~~~~~~~~~~~p~~ 83 (233)
.|+|++++++-+|+|||.|+..| .+..+||.+||+|+-+-++-.+|--..+.++.||..+..-.......+....+
T Consensus 225 rFKQRRIKLGVTQADVG~ALAnLKiPGVGsLSQSTICRFESLTLSHNNMiALKPILqaWLEeAE~a~keK~~~pd~~~l- 303 (385)
T KOG1168|consen 225 RFKQRRIKLGVTQADVGKALANLKIPGVGSLSQSTICRFESLTLSHNNMIALKPILQAWLEEAEAAMKEKDTKPDINEL- 303 (385)
T ss_pred HHHhhhhhhcccHHHHHHHHHhCcCCCcccccccceeeeeeeccccCcchhhhHHHHHHHHHHHHHHHhhccCCchhhc-
Confidence 59999999999999999998888 88999999999999999999999999999999999876532211111111111
Q ss_pred cCCCCCCCCCCCCCCCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHHHhhCCCcccceeeccccchhhHHhhhcCC
Q 026809 84 ASGSQKLTARQRWTPTPAQLQILEHVYDECKGTPRKQKIQDMTAELAKHGQISETNVYNWFQNRRARLKRKQSGV 158 (233)
Q Consensus 84 ~s~~~~~~rr~Rt~~t~~Ql~~Le~~F~~~~~~P~~~~r~~LA~~L~~~~gls~~qV~vWFQNRR~k~Kr~~~~~ 158 (233)
-.++ .++|+||.+..-....||.+|... +.|+.+.+..||++| +|...+|+|||||.|+|-||.+...
T Consensus 304 ~~~~--ekKRKRTSIAAPEKRsLEayFavQ-PRPS~EkIAaIAekL----DLKKNVVRVWFCNQRQKQKRm~~Sa 371 (385)
T KOG1168|consen 304 LPGG--EKKRKRTSIAAPEKRSLEAYFAVQ-PRPSGEKIAAIAEKL----DLKKNVVRVWFCNQRQKQKRMKRSA 371 (385)
T ss_pred cCcc--ccccccccccCcccccHHHHhccC-CCCchhHHHHHHHhh----hhhhceEEEEeeccHHHHHHhhhhh
Confidence 1222 367789999999999999999999 789999999999999 9999999999999999999966544
No 3
>KOG0489 consensus Transcription factor zerknullt and related HOX domain proteins [General function prediction only]
Probab=99.73 E-value=8.6e-19 Score=155.40 Aligned_cols=69 Identities=23% Similarity=0.322 Sum_probs=63.9
Q ss_pred CCCCCCCCCCCCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHHHhhCCCcccceeeccccchhhHHhhhcCCCCC
Q 026809 88 QKLTARQRWTPTPAQLQILEHVYDECKGTPRKQKIQDMTAELAKHGQISETNVYNWFQNRRARLKRKQSGVVPN 161 (233)
Q Consensus 88 ~~~~rr~Rt~~t~~Ql~~Le~~F~~~~~~P~~~~r~~LA~~L~~~~gls~~qV~vWFQNRR~k~Kr~~~~~~~~ 161 (233)
....||.||.||..||.+||+.|+.| +|.++..|.+||..| .|+|+||||||||||+||||..+.....
T Consensus 156 ~~~~kR~RtayT~~QllELEkEFhfN-~YLtR~RRiEiA~~L----~LtErQIKIWFQNRRMK~Kk~~k~~~~~ 224 (261)
T KOG0489|consen 156 GGKSKRRRTAFTRYQLLELEKEFHFN-KYLTRSRRIEIAHAL----NLTERQIKIWFQNRRMKWKKENKAKSSQ 224 (261)
T ss_pred cCCCCCCCcccchhhhhhhhhhhccc-cccchHHHHHHHhhc----chhHHHHHHHHHHHHHHHHHhhcccccc
Confidence 34578999999999999999999999 999999999999999 9999999999999999999988777544
No 4
>KOG0484 consensus Transcription factor PHOX2/ARIX, contains HOX domain [Transcription]
Probab=99.72 E-value=1.4e-18 Score=132.24 Aligned_cols=66 Identities=32% Similarity=0.532 Sum_probs=61.8
Q ss_pred CCCCCCCCCCCCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHHHhhCCCcccceeeccccchhhHHhhhcCC
Q 026809 88 QKLTARQRWTPTPAQLQILEHVYDECKGTPRKQKIQDMTAELAKHGQISETNVYNWFQNRRARLKRKQSGV 158 (233)
Q Consensus 88 ~~~~rr~Rt~~t~~Ql~~Le~~F~~~~~~P~~~~r~~LA~~L~~~~gls~~qV~vWFQNRR~k~Kr~~~~~ 158 (233)
.++.||-||+||..||..||+.|..+ +||++-.|++||.++ .|++..|+|||||||+|.+++.+..
T Consensus 14 krKQRRIRTTFTS~QLkELErvF~ET-HYPDIYTREEiA~ki----dLTEARVQVWFQNRRAKfRKQEr~a 79 (125)
T KOG0484|consen 14 KRKQRRIRTTFTSAQLKELERVFAET-HYPDIYTREEIALKI----DLTEARVQVWFQNRRAKFRKQERAA 79 (125)
T ss_pred HHHhhhhhhhhhHHHHHHHHHHHHhh-cCCcchhHHHHHHhh----hhhHHHHHHHHHhhHHHHHHHHHHH
Confidence 44678899999999999999999999 999999999999999 9999999999999999999987655
No 5
>KOG4577 consensus Transcription factor LIM3, contains LIM and HOX domains [Transcription]
Probab=99.72 E-value=5.2e-18 Score=149.42 Aligned_cols=112 Identities=23% Similarity=0.299 Sum_probs=99.5
Q ss_pred HHHHHHHHHHHHHHHHHhhhhhccchhhccCCCCCCCCCCCccC---------CCCCCCCCCCCCCCHHHHHHHHHHHhh
Q 026809 42 LRKQIAVYAMICEQLVQMHKVFSAQNEIAGMRMGNPYFDPFVAS---------GSQKLTARQRWTPTPAQLQILEHVYDE 112 (233)
Q Consensus 42 lr~qi~~y~~ic~q~~~~~~~l~~~~~~~~~~~~~~~~~p~~~s---------~~~~~~rr~Rt~~t~~Ql~~Le~~F~~ 112 (233)
-++|..||+..|.+++.+.+.|.+.+++.-|..+.+.|.-.+.. .+....+|+||++|..||+.|+.+|..
T Consensus 109 RkAqd~VYHl~CF~C~iC~R~L~TGdEFYLmeD~rLvCK~DYE~Ak~k~~~~l~gd~~nKRPRTTItAKqLETLK~AYn~ 188 (383)
T KOG4577|consen 109 RKAQDFVYHLHCFACFICKRQLATGDEFYLMEDARLVCKDDYETAKQKHCNELEGDASNKRPRTTITAKQLETLKQAYNT 188 (383)
T ss_pred HHhhcceeehhhhhhHhhhcccccCCeeEEeccceeehhhhHHHHHhccccccccccccCCCcceeeHHHHHHHHHHhcC
Confidence 37899999999999999999999999998888877777554432 234457899999999999999999999
Q ss_pred cCCCCCHHHHHHHHHHHHhhCCCcccceeeccccchhhHHhhhcCC
Q 026809 113 CKGTPRKQKIQDMTAELAKHGQISETNVYNWFQNRRARLKRKQSGV 158 (233)
Q Consensus 113 ~~~~P~~~~r~~LA~~L~~~~gls~~qV~vWFQNRR~k~Kr~~~~~ 158 (233)
. ++|.+.-|++|+.++ ||..++|+|||||||+|+||.++.+
T Consensus 189 S-pKPARHVREQLsseT----GLDMRVVQVWFQNRRAKEKRLKKDA 229 (383)
T KOG4577|consen 189 S-PKPARHVREQLSSET----GLDMRVVQVWFQNRRAKEKRLKKDA 229 (383)
T ss_pred C-CchhHHHHHHhhhcc----CcceeehhhhhhhhhHHHHhhhhhc
Confidence 8 899999999999999 9999999999999999999988776
No 6
>KOG0488 consensus Transcription factor BarH and related HOX domain proteins [General function prediction only]
Probab=99.71 E-value=5.7e-18 Score=153.25 Aligned_cols=75 Identities=23% Similarity=0.283 Sum_probs=67.2
Q ss_pred CCCCCCCCCCCCCCCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHHHhhCCCcccceeeccccchhhHHhhhcCCCCCCCC
Q 026809 85 SGSQKLTARQRWTPTPAQLQILEHVYDECKGTPRKQKIQDMTAELAKHGQISETNVYNWFQNRRARLKRKQSGVVPNNAE 164 (233)
Q Consensus 85 s~~~~~~rr~Rt~~t~~Ql~~Le~~F~~~~~~P~~~~r~~LA~~L~~~~gls~~qV~vWFQNRR~k~Kr~~~~~~~~~~~ 164 (233)
....+++|+.||.||..||..||+.|++. +|.+..+|.+||..| ||+..||++||||||+||||...........
T Consensus 166 ~~~pkK~RksRTaFT~~Ql~~LEkrF~~Q-KYLS~~DR~~LA~~L----gLTdaQVKtWfQNRRtKWKrq~a~g~~~~~~ 240 (309)
T KOG0488|consen 166 RSTPKKRRKSRTAFSDHQLFELEKRFEKQ-KYLSVADRIELAASL----GLTDAQVKTWFQNRRTKWKRQTAEGGELLYQ 240 (309)
T ss_pred cCCCcccccchhhhhHHHHHHHHHHHHHh-hcccHHHHHHHHHHc----CCchhhHHHHHhhhhHHHHHHHHhhhccccc
Confidence 34457888999999999999999999999 999999999999999 9999999999999999999988775444333
No 7
>KOG0843 consensus Transcription factor EMX1 and related HOX domain proteins [Transcription]
Probab=99.71 E-value=1e-17 Score=138.84 Aligned_cols=64 Identities=36% Similarity=0.450 Sum_probs=61.6
Q ss_pred CCCCCCCCCCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHHHhhCCCcccceeeccccchhhHHhhhcCC
Q 026809 90 LTARQRWTPTPAQLQILEHVYDECKGTPRKQKIQDMTAELAKHGQISETNVYNWFQNRRARLKRKQSGV 158 (233)
Q Consensus 90 ~~rr~Rt~~t~~Ql~~Le~~F~~~~~~P~~~~r~~LA~~L~~~~gls~~qV~vWFQNRR~k~Kr~~~~~ 158 (233)
+.+|.||.|+++||..||.+|+.+ +|....+|+.||..| +|++.||+|||||||.|.||.+.+.
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 788999999999999999999999 999999999999999 9999999999999999999988775
No 8
>KOG2251 consensus Homeobox transcription factor [Transcription]
Probab=99.68 E-value=1.3e-16 Score=136.12 Aligned_cols=68 Identities=29% Similarity=0.488 Sum_probs=65.0
Q ss_pred CCCCCCCCCCCCCCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHHHhhCCCcccceeeccccchhhHHhhhcCC
Q 026809 86 GSQKLTARQRWTPTPAQLQILEHVYDECKGTPRKQKIQDMTAELAKHGQISETNVYNWFQNRRARLKRKQSGV 158 (233)
Q Consensus 86 ~~~~~~rr~Rt~~t~~Ql~~Le~~F~~~~~~P~~~~r~~LA~~L~~~~gls~~qV~vWFQNRR~k~Kr~~~~~ 158 (233)
.+.++.||.||+|+..||.+||.+|.++ .||+...|++||.+| +|.+.+|+|||+|||+|+|++++..
T Consensus 32 ~~pRkqRRERTtFtr~QlevLe~LF~kT-qYPDv~~rEelAlkl----nLpeSrVqVWFKNRRAK~r~qq~qq 99 (228)
T KOG2251|consen 32 SGPRKQRRERTTFTRKQLEVLEALFAKT-QYPDVFMREELALKL----NLPESRVQVWFKNRRAKCRRQQQQQ 99 (228)
T ss_pred ccchhcccccceecHHHHHHHHHHHHhh-cCccHHHHHHHHHHh----CCchhhhhhhhccccchhhHhhhhh
Confidence 6778899999999999999999999999 999999999999999 9999999999999999999988864
No 9
>KOG0487 consensus Transcription factor Abd-B, contains HOX domain [Transcription]
Probab=99.67 E-value=5.4e-17 Score=145.69 Aligned_cols=67 Identities=27% Similarity=0.287 Sum_probs=62.3
Q ss_pred CCCCCCCCCCCCCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHHHhhCCCcccceeeccccchhhHHhhhcCC
Q 026809 87 SQKLTARQRWTPTPAQLQILEHVYDECKGTPRKQKIQDMTAELAKHGQISETNVYNWFQNRRARLKRKQSGV 158 (233)
Q Consensus 87 ~~~~~rr~Rt~~t~~Ql~~Le~~F~~~~~~P~~~~r~~LA~~L~~~~gls~~qV~vWFQNRR~k~Kr~~~~~ 158 (233)
..++.|++|..+|..|+.+||+.|..| .|.+++.|.+|++.| +|+++||+|||||||+|+||..++.
T Consensus 231 ~~~~~RKKRcPYTK~QtlELEkEFlfN-~YitkeKR~ElSr~l----NLTeRQVKIWFQNRRMK~KK~~re~ 297 (308)
T KOG0487|consen 231 SARRGRKKRCPYTKHQTLELEKEFLFN-MYITKEKRLELSRTL----NLTERQVKIWFQNRRMKEKKVNREN 297 (308)
T ss_pred cccccccccCCchHHHHHHHHHHHHHH-HHHhHHHHHHHHHhc----ccchhheeeeehhhhhHHhhhhhhh
Confidence 346788899999999999999999999 899999999999999 9999999999999999999988644
No 10
>KOG0842 consensus Transcription factor tinman/NKX2-3, contains HOX domain [Transcription]
Probab=99.66 E-value=5.5e-17 Score=145.57 Aligned_cols=67 Identities=25% Similarity=0.372 Sum_probs=62.7
Q ss_pred CCCCCCCCCCCCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHHHhhCCCcccceeeccccchhhHHhhhcCCC
Q 026809 88 QKLTARQRWTPTPAQLQILEHVYDECKGTPRKQKIQDMTAELAKHGQISETNVYNWFQNRRARLKRKQSGVV 159 (233)
Q Consensus 88 ~~~~rr~Rt~~t~~Ql~~Le~~F~~~~~~P~~~~r~~LA~~L~~~~gls~~qV~vWFQNRR~k~Kr~~~~~~ 159 (233)
..++||+|..|+..|..+||+.|.+. +|.+.+||++||..| .|+++||||||||||-|.||++....
T Consensus 150 ~~~kRKrRVLFSqAQV~ELERRFrqQ-RYLSAPERE~LA~~L----rLT~TQVKIWFQNrRYK~KR~~~dk~ 216 (307)
T KOG0842|consen 150 KRKKRKRRVLFSQAQVYELERRFRQQ-RYLSAPEREHLASSL----RLTPTQVKIWFQNRRYKTKRQQKDKA 216 (307)
T ss_pred cccccccccccchhHHHHHHHHHHhh-hccccHhHHHHHHhc----CCCchheeeeeecchhhhhhhhhhhh
Confidence 44677889999999999999999999 999999999999999 99999999999999999999887764
No 11
>KOG0850 consensus Transcription factor DLX and related proteins with LIM Zn-binding and HOX domains [Transcription]
Probab=99.66 E-value=8.7e-17 Score=137.81 Aligned_cols=69 Identities=26% Similarity=0.393 Sum_probs=64.4
Q ss_pred CCCCCCCCCCCCCCCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHHHhhCCCcccceeeccccchhhHHhhhcCC
Q 026809 85 SGSQKLTARQRWTPTPAQLQILEHVYDECKGTPRKQKIQDMTAELAKHGQISETNVYNWFQNRRARLKRKQSGV 158 (233)
Q Consensus 85 s~~~~~~rr~Rt~~t~~Ql~~Le~~F~~~~~~P~~~~r~~LA~~L~~~~gls~~qV~vWFQNRR~k~Kr~~~~~ 158 (233)
.+..+|.|+.||.++.-||..|.+.|+++ .|.-..||.+||..| ||+.+||||||||||.|.||..+..
T Consensus 116 Ngk~KK~RKPRTIYSS~QLqaL~rRFQkT-QYLALPERAeLAAsL----GLTQTQVKIWFQNrRSK~KKl~k~g 184 (245)
T KOG0850|consen 116 NGKGKKVRKPRTIYSSLQLQALNRRFQQT-QYLALPERAELAASL----GLTQTQVKIWFQNRRSKFKKLKKQG 184 (245)
T ss_pred CCCcccccCCcccccHHHHHHHHHHHhhc-chhcCcHHHHHHHHh----CCchhHhhhhhhhhHHHHHHHHhcC
Confidence 35567888999999999999999999999 999999999999999 9999999999999999999998844
No 12
>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=99.61 E-value=4.3e-16 Score=106.77 Aligned_cols=57 Identities=39% Similarity=0.634 Sum_probs=54.8
Q ss_pred CCCCCCCCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHHHhhCCCcccceeeccccchhhHHh
Q 026809 92 ARQRWTPTPAQLQILEHVYDECKGTPRKQKIQDMTAELAKHGQISETNVYNWFQNRRARLKR 153 (233)
Q Consensus 92 rr~Rt~~t~~Ql~~Le~~F~~~~~~P~~~~r~~LA~~L~~~~gls~~qV~vWFQNRR~k~Kr 153 (233)
|++|+.|+..|+.+|+.+|..+ +||+..++..||..| ||+..+|++||+|||+++||
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 5789999999999999999998 999999999999999 99999999999999999986
No 13
>KOG0485 consensus Transcription factor NKX-5.1/HMX1, contains HOX domain [Transcription]
Probab=99.60 E-value=3.1e-16 Score=133.48 Aligned_cols=67 Identities=28% Similarity=0.363 Sum_probs=62.1
Q ss_pred CCCCCCCCCCCCCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHHHhhCCCcccceeeccccchhhHHhhhcCC
Q 026809 87 SQKLTARQRWTPTPAQLQILEHVYDECKGTPRKQKIQDMTAELAKHGQISETNVYNWFQNRRARLKRKQSGV 158 (233)
Q Consensus 87 ~~~~~rr~Rt~~t~~Ql~~Le~~F~~~~~~P~~~~r~~LA~~L~~~~gls~~qV~vWFQNRR~k~Kr~~~~~ 158 (233)
+..++++.||+|+..|+..||..|+.. +|.+..+|..||++| .|+|.||+|||||||.||||+-...
T Consensus 100 g~~RKKktRTvFSraQV~qLEs~Fe~k-rYLSsaeRa~LA~sL----qLTETQVKIWFQNRRnKwKRq~aad 166 (268)
T KOG0485|consen 100 GDDRKKKTRTVFSRAQVFQLESTFELK-RYLSSAERAGLAASL----QLTETQVKIWFQNRRNKWKRQYAAD 166 (268)
T ss_pred cccccccchhhhhHHHHHHHHHHHHHH-hhhhHHHHhHHHHhh----hhhhhhhhhhhhhhhHHHHHHHhhh
Confidence 344788899999999999999999999 999999999999999 9999999999999999999976554
No 14
>KOG0492 consensus Transcription factor MSH, contains HOX domain [General function prediction only]
Probab=99.60 E-value=6.3e-16 Score=130.77 Aligned_cols=68 Identities=32% Similarity=0.401 Sum_probs=62.4
Q ss_pred CCCCCCCCCCCCCCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHHHhhCCCcccceeeccccchhhHHhhhcCC
Q 026809 86 GSQKLTARQRWTPTPAQLQILEHVYDECKGTPRKQKIQDMTAELAKHGQISETNVYNWFQNRRARLKRKQSGV 158 (233)
Q Consensus 86 ~~~~~~rr~Rt~~t~~Ql~~Le~~F~~~~~~P~~~~r~~LA~~L~~~~gls~~qV~vWFQNRR~k~Kr~~~~~ 158 (233)
.+++..|++||.||..||..||+.|... .|.++++|.+++..| .|+++||+|||||||+|.||.+...
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 3456678899999999999999999999 899999999999999 9999999999999999999977554
No 15
>KOG0494 consensus Transcription factor CHX10 and related HOX domain proteins [General function prediction only]
Probab=99.56 E-value=2.8e-15 Score=130.59 Aligned_cols=64 Identities=25% Similarity=0.361 Sum_probs=59.1
Q ss_pred CCCCCCCCCCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHHHhhCCCcccceeeccccchhhHHhhhcCC
Q 026809 90 LTARQRWTPTPAQLQILEHVYDECKGTPRKQKIQDMTAELAKHGQISETNVYNWFQNRRARLKRKQSGV 158 (233)
Q Consensus 90 ~~rr~Rt~~t~~Ql~~Le~~F~~~~~~P~~~~r~~LA~~L~~~~gls~~qV~vWFQNRR~k~Kr~~~~~ 158 (233)
++|+-||.||..|+..||+.|+.. +||+...|+-||.++ .|.+.+|+|||||||+||||..+.-
T Consensus 140 kRRh~RTiFT~~Qle~LEkaFkea-HYPDv~Are~la~kt----elpEDRIqVWfQNRRAKWRk~Ek~w 203 (332)
T KOG0494|consen 140 KRRHFRTIFTSYQLEELEKAFKEA-HYPDVYAREMLADKT----ELPEDRIQVWFQNRRAKWRKTEKRW 203 (332)
T ss_pred ccccccchhhHHHHHHHHHHHhhc-cCccHHHHHHHhhhc----cCchhhhhHHhhhhhHHhhhhhhhc
Confidence 334449999999999999999999 999999999999999 9999999999999999999988764
No 16
>KOG0848 consensus Transcription factor Caudal, contains HOX domain [Transcription]
Probab=99.51 E-value=2.8e-15 Score=130.97 Aligned_cols=62 Identities=27% Similarity=0.344 Sum_probs=57.8
Q ss_pred CCCCCCCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHHHhhCCCcccceeeccccchhhHHhhhcCCC
Q 026809 93 RQRWTPTPAQLQILEHVYDECKGTPRKQKIQDMTAELAKHGQISETNVYNWFQNRRARLKRKQSGVV 159 (233)
Q Consensus 93 r~Rt~~t~~Ql~~Le~~F~~~~~~P~~~~r~~LA~~L~~~~gls~~qV~vWFQNRR~k~Kr~~~~~~ 159 (233)
+-|.++|.-|+.+||+.|..+ +|.++..+.+||.-| +|+|+||+|||||||+|+||..+...
T Consensus 201 KYRvVYTDhQRLELEKEfh~S-ryITirRKSELA~~L----gLsERQVKIWFQNRRAKERK~nKKk~ 262 (317)
T KOG0848|consen 201 KYRVVYTDHQRLELEKEFHTS-RYITIRRKSELAATL----GLSERQVKIWFQNRRAKERKDNKKKR 262 (317)
T ss_pred ceeEEecchhhhhhhhhhccc-cceeeehhHHHHHhh----CccHhhhhHhhhhhhHHHHHHHHHHH
Confidence 447899999999999999999 999999999999999 99999999999999999998877663
No 17
>TIGR01565 homeo_ZF_HD homeobox domain, ZF-HD class. This model represents a class of homoebox domain that differs substantially from the typical homoebox domain described in pfam model pfam00046. It is found in both C4 and C3 plants.
Probab=99.49 E-value=5e-14 Score=97.63 Aligned_cols=52 Identities=17% Similarity=0.381 Sum_probs=50.2
Q ss_pred CCCCCCCCHHHHHHHHHHHhhcCCC----CCHHHHHHHHHHHHhhCCCcccceeeccccch
Q 026809 92 ARQRWTPTPAQLQILEHVYDECKGT----PRKQKIQDMTAELAKHGQISETNVYNWFQNRR 148 (233)
Q Consensus 92 rr~Rt~~t~~Ql~~Le~~F~~~~~~----P~~~~r~~LA~~L~~~~gls~~qV~vWFQNRR 148 (233)
+|.||.||++|+..||.+|+.+ +| |+..+|.+||..| ||++++|+|||||-+
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 7889999999999999999999 99 9999999999999 999999999999964
No 18
>smart00389 HOX Homeodomain. DNA-binding factors that are involved in the transcriptional regulation of key developmental processes
Probab=99.47 E-value=3.6e-14 Score=96.45 Aligned_cols=55 Identities=40% Similarity=0.649 Sum_probs=51.7
Q ss_pred CCCCCCCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHHHhhCCCcccceeeccccchhhHH
Q 026809 93 RQRWTPTPAQLQILEHVYDECKGTPRKQKIQDMTAELAKHGQISETNVYNWFQNRRARLK 152 (233)
Q Consensus 93 r~Rt~~t~~Ql~~Le~~F~~~~~~P~~~~r~~LA~~L~~~~gls~~qV~vWFQNRR~k~K 152 (233)
+.|+.|+..++.+|+..|..+ +||+..++..||..| ||+..+|++||+|||.+.+
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 567789999999999999999 899999999999999 9999999999999998754
No 19
>KOG0493 consensus Transcription factor Engrailed, contains HOX domain [General function prediction only]
Probab=99.47 E-value=4.2e-14 Score=123.37 Aligned_cols=63 Identities=32% Similarity=0.487 Sum_probs=58.2
Q ss_pred CCCCCCCCCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHHHhhCCCcccceeeccccchhhHHhhhcCC
Q 026809 91 TARQRWTPTPAQLQILEHVYDECKGTPRKQKIQDMTAELAKHGQISETNVYNWFQNRRARLKRKQSGV 158 (233)
Q Consensus 91 ~rr~Rt~~t~~Ql~~Le~~F~~~~~~P~~~~r~~LA~~L~~~~gls~~qV~vWFQNRR~k~Kr~~~~~ 158 (233)
-+|+||.||.+||..|+..|..+ +|.+...|.+||.+| +|.+.||+|||||+|+|.||-....
T Consensus 246 eKRPRTAFtaeQL~RLK~EF~en-RYlTEqRRQ~La~EL----gLNEsQIKIWFQNKRAKiKKsTgsk 308 (342)
T KOG0493|consen 246 EKRPRTAFTAEQLQRLKAEFQEN-RYLTEQRRQELAQEL----GLNESQIKIWFQNKRAKIKKSTGSK 308 (342)
T ss_pred hcCccccccHHHHHHHHHHHhhh-hhHHHHHHHHHHHHh----CcCHHHhhHHhhhhhhhhhhccCCC
Confidence 45789999999999999999999 999999999999999 9999999999999999998855433
No 20
>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=99.46 E-value=5.6e-14 Score=96.14 Aligned_cols=57 Identities=40% Similarity=0.672 Sum_probs=53.7
Q ss_pred CCCCCCCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHHHhhCCCcccceeeccccchhhHHhh
Q 026809 93 RQRWTPTPAQLQILEHVYDECKGTPRKQKIQDMTAELAKHGQISETNVYNWFQNRRARLKRK 154 (233)
Q Consensus 93 r~Rt~~t~~Ql~~Le~~F~~~~~~P~~~~r~~LA~~L~~~~gls~~qV~vWFQNRR~k~Kr~ 154 (233)
+.|+.++..++.+||.+|..+ +||+..++..||..| ||++.+|++||+|||.+.++.
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 567889999999999999999 899999999999999 999999999999999998763
No 21
>KOG0491 consensus Transcription factor BSH, contains HOX domain [General function prediction only]
Probab=99.44 E-value=2.1e-14 Score=117.63 Aligned_cols=68 Identities=31% Similarity=0.433 Sum_probs=62.8
Q ss_pred CCCCCCCCCCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHHHhhCCCcccceeeccccchhhHHhhhcCCCCCC
Q 026809 90 LTARQRWTPTPAQLQILEHVYDECKGTPRKQKIQDMTAELAKHGQISETNVYNWFQNRRARLKRKQSGVVPNN 162 (233)
Q Consensus 90 ~~rr~Rt~~t~~Ql~~Le~~F~~~~~~P~~~~r~~LA~~L~~~~gls~~qV~vWFQNRR~k~Kr~~~~~~~~~ 162 (233)
++++.|++|+..||..||+.|+.. +|.+.++|.+||..| +|++.||+.||||||+|.||..+.....+
T Consensus 99 ~r~K~Rtvfs~~ql~~l~~rFe~Q-rYLS~~e~~ELan~L----~LS~~QVKTWFQNrRMK~Kk~~r~~~p~n 166 (194)
T KOG0491|consen 99 RRRKARTVFSDPQLSGLEKRFERQ-RYLSTPERQELANAL----SLSETQVKTWFQNRRMKHKKQQRNNQPKN 166 (194)
T ss_pred HhhhhcccccCccccccHHHHhhh-hhcccHHHHHHHHHh----hhhHHHHHHHHHHHHHHHHHHHhccCCCC
Confidence 567789999999999999999999 999999999999999 99999999999999999999888775433
No 22
>COG5576 Homeodomain-containing transcription factor [Transcription]
Probab=99.41 E-value=2.1e-13 Score=112.36 Aligned_cols=64 Identities=31% Similarity=0.461 Sum_probs=58.4
Q ss_pred CCCCCCCCCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHHHhhCCCcccceeeccccchhhHHhhhcCCC
Q 026809 91 TARQRWTPTPAQLQILEHVYDECKGTPRKQKIQDMTAELAKHGQISETNVYNWFQNRRARLKRKQSGVV 159 (233)
Q Consensus 91 ~rr~Rt~~t~~Ql~~Le~~F~~~~~~P~~~~r~~LA~~L~~~~gls~~qV~vWFQNRR~k~Kr~~~~~~ 159 (233)
.+++|++.+..|+.+|++.|+.+ +||+...|..|+..| +|+++.|+|||||||++.|+......
T Consensus 51 ~~~~r~R~t~~Q~~vL~~~F~i~-p~Ps~~~r~~L~~~l----nm~~ksVqIWFQNkR~~~k~~~~~~~ 114 (156)
T COG5576 51 PKSKRRRTTDEQLMVLEREFEIN-PYPSSITRIKLSLLL----NMPPKSVQIWFQNKRAKEKKKRSGKV 114 (156)
T ss_pred CcccceechHHHHHHHHHHhccC-CCCCHHHHHHHHHhc----CCChhhhhhhhchHHHHHHHhcccch
Confidence 45566667999999999999999 999999999999999 99999999999999999999777654
No 23
>KOG0844 consensus Transcription factor EVX1, contains HOX domain [Transcription]
Probab=99.39 E-value=1.1e-13 Score=123.09 Aligned_cols=63 Identities=29% Similarity=0.381 Sum_probs=58.8
Q ss_pred CCCCCCCCCCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHHHhhCCCcccceeeccccchhhHHhhhcC
Q 026809 90 LTARQRWTPTPAQLQILEHVYDECKGTPRKQKIQDMTAELAKHGQISETNVYNWFQNRRARLKRKQSG 157 (233)
Q Consensus 90 ~~rr~Rt~~t~~Ql~~Le~~F~~~~~~P~~~~r~~LA~~L~~~~gls~~qV~vWFQNRR~k~Kr~~~~ 157 (233)
.-||-||.||.+|+..||+.|-+- -|.+++.|.+||..| +|.+..|+|||||||+|+||++..
T Consensus 180 qmRRYRTAFTReQIaRLEKEFyrE-NYVSRprRcELAAaL----NLPEtTIKVWFQNRRMKDKRQRla 242 (408)
T KOG0844|consen 180 QMRRYRTAFTREQIARLEKEFYRE-NYVSRPRRCELAAAL----NLPETTIKVWFQNRRMKDKRQRLA 242 (408)
T ss_pred HHHHHHhhhhHHHHHHHHHHHHHh-ccccCchhhhHHHhh----CCCcceeehhhhhchhhhhhhhhh
Confidence 467889999999999999999888 599999999999999 999999999999999999998755
No 24
>KOG0486 consensus Transcription factor PTX1, contains HOX domain [Transcription]
Probab=99.37 E-value=3.6e-13 Score=120.18 Aligned_cols=66 Identities=27% Similarity=0.414 Sum_probs=61.8
Q ss_pred CCCCCCCCCCCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHHHhhCCCcccceeeccccchhhHHhhhcCCC
Q 026809 89 KLTARQRWTPTPAQLQILEHVYDECKGTPRKQKIQDMTAELAKHGQISETNVYNWFQNRRARLKRKQSGVV 159 (233)
Q Consensus 89 ~~~rr~Rt~~t~~Ql~~Le~~F~~~~~~P~~~~r~~LA~~L~~~~gls~~qV~vWFQNRR~k~Kr~~~~~~ 159 (233)
+|+||.|+.|+..||..||..|.++ +||+...|++||.-. +|++.+|+|||.|||+||+|+++...
T Consensus 110 ~KqrrQrthFtSqqlqele~tF~rN-rypdMstrEEIavwt----NlTE~rvrvwfknrrakwrkrErN~~ 175 (351)
T KOG0486|consen 110 SKQRRQRTHFTSQQLQELEATFQRN-RYPDMSTREEIAVWT----NLTEARVRVWFKNRRAKWRKRERNQQ 175 (351)
T ss_pred hhhhhhhhhhHHHHHHHHHHHHhhc-cCCccchhhHHHhhc----cccchhhhhhcccchhhhhhhhhhHH
Confidence 3788999999999999999999999 999999999999999 99999999999999999998776543
No 25
>KOG0490 consensus Transcription factor, contains HOX domain [General function prediction only]
Probab=99.36 E-value=1.8e-12 Score=111.29 Aligned_cols=104 Identities=19% Similarity=0.201 Sum_probs=76.0
Q ss_pred HHHHHHHHHHHHhhhhhccchhhccCCCCCCCCCCCccCCCCCCCCCCCCCCCHHHHHHHHHHHhhcCCCCCHHHHHHHH
Q 026809 47 AVYAMICEQLVQMHKVFSAQNEIAGMRMGNPYFDPFVASGSQKLTARQRWTPTPAQLQILEHVYDECKGTPRKQKIQDMT 126 (233)
Q Consensus 47 ~~y~~ic~q~~~~~~~l~~~~~~~~~~~~~~~~~p~~~s~~~~~~rr~Rt~~t~~Ql~~Le~~F~~~~~~P~~~~r~~LA 126 (233)
..|..-|-.+..+...+......... .|..++..........+.|+.|+.|+..|+.+||++|+.+ +||+...|+.||
T Consensus 17 ~~~~~~~~~~~~~~~~~~~~~~~~~~-~g~~~~~~d~~~~~~~~~rr~rt~~~~~ql~~ler~f~~~-h~Pd~~~r~~la 94 (235)
T KOG0490|consen 17 RYWHASCLKCAECDNPLGVGDTCFSK-DGSIYCKRDYQREFKFSKRCARCKFTISQLDELERAFEKV-HLPCFACRECLA 94 (235)
T ss_pred HHHHHHHHhhhhhcchhccCCCcccC-CCcccccccchhhhhccccccCCCCCcCHHHHHHHhhcCC-CcCccchHHHHh
Confidence 33455555555554444411111112 4444444433322244678899999999999999999999 999999999999
Q ss_pred HHHHhhCCCcccceeeccccchhhHHhhhc
Q 026809 127 AELAKHGQISETNVYNWFQNRRARLKRKQS 156 (233)
Q Consensus 127 ~~L~~~~gls~~qV~vWFQNRR~k~Kr~~~ 156 (233)
..+ ++++..|+|||||||+|+++..+
T Consensus 95 ~~~----~~~e~rVqvwFqnrrak~r~~~~ 120 (235)
T KOG0490|consen 95 LLL----TGDEFRVQVWFQNRRAKDRKEER 120 (235)
T ss_pred hcC----CCCeeeeehhhhhhcHhhhhhhc
Confidence 999 99999999999999999998775
No 26
>KOG0483 consensus Transcription factor HEX, contains HOX and HALZ domains [Transcription]
Probab=99.35 E-value=3.2e-13 Score=115.05 Aligned_cols=62 Identities=29% Similarity=0.437 Sum_probs=56.9
Q ss_pred CCCCCCCCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHHHhhCCCcccceeeccccchhhHHhhhcCC
Q 026809 92 ARQRWTPTPAQLQILEHVYDECKGTPRKQKIQDMTAELAKHGQISETNVYNWFQNRRARLKRKQSGV 158 (233)
Q Consensus 92 rr~Rt~~t~~Ql~~Le~~F~~~~~~P~~~~r~~LA~~L~~~~gls~~qV~vWFQNRR~k~Kr~~~~~ 158 (233)
.+++.+++.+|+..||..|+.+ .|....++..||+.| ||.++||.|||||||||||.++...
T Consensus 51 ~~kk~Rlt~eQ~~~LE~~F~~~-~~L~p~~K~~LAk~L----gL~pRQVavWFQNRRARwK~kqlE~ 112 (198)
T KOG0483|consen 51 KGKKRRLTSEQVKFLEKSFESE-KKLEPERKKKLAKEL----GLQPRQVAVWFQNRRARWKTKQLEK 112 (198)
T ss_pred ccccccccHHHHHHhHHhhccc-cccChHHHHHHHHhh----CCChhHHHHHHhhccccccchhhhh
Confidence 3445678999999999999999 899999999999999 9999999999999999999888765
No 27
>KOG0847 consensus Transcription factor, contains HOX domain [Transcription]
Probab=99.29 E-value=2.5e-12 Score=109.90 Aligned_cols=66 Identities=26% Similarity=0.391 Sum_probs=61.0
Q ss_pred CCCCCCCCCCCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHHHhhCCCcccceeeccccchhhHHhhhcCCC
Q 026809 89 KLTARQRWTPTPAQLQILEHVYDECKGTPRKQKIQDMTAELAKHGQISETNVYNWFQNRRARLKRKQSGVV 159 (233)
Q Consensus 89 ~~~rr~Rt~~t~~Ql~~Le~~F~~~~~~P~~~~r~~LA~~L~~~~gls~~qV~vWFQNRR~k~Kr~~~~~~ 159 (233)
.+++..|.+|+-.|+..||+.|+.. +|+-.++|.+||..| |+++.+|+|||||||.||||+.....
T Consensus 165 G~rk~srPTf~g~qi~~le~~feqt-kylaG~~ra~lA~~l----gmteSqvkVWFQNRRTKWRKkhAaEm 230 (288)
T KOG0847|consen 165 GQRKQSRPTFTGHQIYQLERKFEQT-KYLAGADRAQLAQEL----NMTESQVKVWFQNRRTKWRKKHAAEM 230 (288)
T ss_pred ccccccCCCccchhhhhhhhhhhhh-hcccchhHHHhhccc----cccHHHHHHHHhcchhhhhhhhccch
Confidence 4566789999999999999999999 999999999999999 99999999999999999999876653
No 28
>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=99.07 E-value=8.3e-12 Score=90.46 Aligned_cols=60 Identities=15% Similarity=0.123 Sum_probs=55.6
Q ss_pred CcccccchhhhhhccCCCcCCCcccccCCHHHHHHHHHHHHHHHHHHHHHHHhhhhhccc
Q 026809 7 NFQQGGEMERQFQQDGGDTSNGLCVKVMTDEQMELLRKQIAVYAMICEQLVQMHKVFSAQ 66 (233)
Q Consensus 7 ~~~~~~~~~~~~q~~~~~~~~~~~~~~~t~~~~~~lr~qi~~y~~ic~q~~~~~~~l~~~ 66 (233)
.|+|.++..+.+|+|||.++|.+||++||+++||+|+++..+++++|+..|.+.+||.+.
T Consensus 15 ~fk~rRi~LG~TQ~dVg~al~~~~G~~~SQttI~RFE~L~LS~kn~~klkP~L~kWL~ea 74 (75)
T PF00157_consen 15 EFKQRRIKLGYTQADVGAALGRLYGKEFSQTTICRFEALQLSFKNMCKLKPLLEKWLEEA 74 (75)
T ss_dssp HHHHHHHHTT--HHHHHHHHHHHHSSGGSHHHHHHHHTTTSCHHHHHHHHHHHHHHHHHH
T ss_pred HHHHhhhhcccCHHHHhHHHHHhcCccccchhhhhhHhcccCHHHHHHHHHHHHHHHHhc
Confidence 489999999999999999999999999999999999999999999999999999999764
No 29
>KOG0849 consensus Transcription factor PRD and related proteins, contain PAX and HOX domains [Transcription]
Probab=98.92 E-value=7.6e-10 Score=102.28 Aligned_cols=65 Identities=31% Similarity=0.494 Sum_probs=60.2
Q ss_pred CCCCCCCCCCCCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHHHhhCCCcccceeeccccchhhHHhhhcC
Q 026809 88 QKLTARQRWTPTPAQLQILEHVYDECKGTPRKQKIQDMTAELAKHGQISETNVYNWFQNRRARLKRKQSG 157 (233)
Q Consensus 88 ~~~~rr~Rt~~t~~Ql~~Le~~F~~~~~~P~~~~r~~LA~~L~~~~gls~~qV~vWFQNRR~k~Kr~~~~ 157 (233)
.++.+|.||+|++.|+..||+.|+.+ +||+...|++||.++ ++++..|+|||+|||++++|....
T Consensus 173 ~~~~rr~rtsft~~Q~~~le~~f~rt-~yP~i~~Re~La~~i----~l~e~riqvwf~nrra~~rr~~~~ 237 (354)
T KOG0849|consen 173 QRGGRRNRTSFSPSQLEALEECFQRT-PYPDIVGRETLAKET----GLPEPRVQVWFQNRRAKWRRQHRD 237 (354)
T ss_pred cccccccccccccchHHHHHHHhcCC-CCCchhhHHHHhhhc----cCCchHHHHHHhhhhhhhhhcccc
Confidence 44567789999999999999999999 799999999999999 999999999999999999998843
No 30
>KOG0775 consensus Transcription factor SIX and related HOX domain proteins [Transcription]
Probab=98.75 E-value=2.1e-08 Score=88.50 Aligned_cols=51 Identities=24% Similarity=0.394 Sum_probs=46.1
Q ss_pred CCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHHHhhCCCcccceeeccccchhhHHh
Q 026809 98 PTPAQLQILEHVYDECKGTPRKQKIQDMTAELAKHGQISETNVYNWFQNRRARLKR 153 (233)
Q Consensus 98 ~t~~Ql~~Le~~F~~~~~~P~~~~r~~LA~~L~~~~gls~~qV~vWFQNRR~k~Kr 153 (233)
|...-+..|..+|..+ +||+..++.+||+.+ ||+..||-+||+|||+|+|-
T Consensus 183 FKekSR~~LrewY~~~-~YPsp~eKReLA~aT----gLt~tQVsNWFKNRRQRDRa 233 (304)
T KOG0775|consen 183 FKEKSRSLLREWYLQN-PYPSPREKRELAEAT----GLTITQVSNWFKNRRQRDRA 233 (304)
T ss_pred hhHhhHHHHHHHHhcC-CCCChHHHHHHHHHh----CCchhhhhhhhhhhhhhhhh
Confidence 3444567999999999 999999999999999 99999999999999999983
No 31
>KOG0774 consensus Transcription factor PBX and related HOX domain proteins [Transcription]
Probab=98.65 E-value=2.4e-07 Score=81.47 Aligned_cols=64 Identities=22% Similarity=0.412 Sum_probs=57.0
Q ss_pred CCCCCCCCCHHHHHHHHHHHhhc--CCCCCHHHHHHHHHHHHhhCCCcccceeeccccchhhHHhhhcCC
Q 026809 91 TARQRWTPTPAQLQILEHVYDEC--KGTPRKQKIQDMTAELAKHGQISETNVYNWFQNRRARLKRKQSGV 158 (233)
Q Consensus 91 ~rr~Rt~~t~~Ql~~Le~~F~~~--~~~P~~~~r~~LA~~L~~~~gls~~qV~vWFQNRR~k~Kr~~~~~ 158 (233)
.||+|..|+..-..+|..+|..+ |+||+.+.+++||+++ +++..||-.||.|+|-+.||.....
T Consensus 188 arRKRRNFsK~aTeiLneyF~~h~~nPYPSee~K~eLAkqC----nItvsQvsnwfgnkrIrykK~~~k~ 253 (334)
T KOG0774|consen 188 ARRKRRNFSKQATEILNEYFYSHLSNPYPSEEAKEELAKQC----NITVSQVSNWFGNKRIRYKKNMGKN 253 (334)
T ss_pred HHHhhcccchhHHHHHHHHHHHhcCCCCCcHHHHHHHHHHc----Cceehhhccccccceeehhhhhhhh
Confidence 56788899999999999999744 6999999999999999 9999999999999999998855433
No 32
>smart00352 POU Found in Pit-Oct-Unc transcription factors.
Probab=98.26 E-value=2e-07 Score=67.68 Aligned_cols=60 Identities=13% Similarity=0.077 Sum_probs=56.9
Q ss_pred CcccccchhhhhhccCCCcCCCcccccCCHHHHHHHHHHHHHHHHHHHHHHHhhhhhccc
Q 026809 7 NFQQGGEMERQFQQDGGDTSNGLCVKVMTDEQMELLRKQIAVYAMICEQLVQMHKVFSAQ 66 (233)
Q Consensus 7 ~~~~~~~~~~~~q~~~~~~~~~~~~~~~t~~~~~~lr~qi~~y~~ic~q~~~~~~~l~~~ 66 (233)
.|++.+...+-+|+++|-++|.+||..+|+.+|++|+....+++++|+..|.+.+|+.+.
T Consensus 15 ~lk~~R~~lGLTQ~dvA~~lg~~~g~i~SQstISR~Es~~ls~~n~~kl~p~l~~wl~~~ 74 (75)
T smart00352 15 TFKQRRIKLGFTQADVGLALGALYGPDFSQTTICRFEALQLSFKNMCKLKPLLEKWLEEA 74 (75)
T ss_pred HHHHHHHHcCCCHHHHHHHhcccccCcCCHHHHHHHHhcCccHHHHHHHHHHHHHHHHhc
Confidence 577888999999999999999999999999999999999999999999999999999764
No 33
>PF05920 Homeobox_KN: Homeobox KN domain; InterPro: IPR008422 This entry represents a homeobox transcription factor KN domain conserved from fungi to human and plants [].; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent, 0005634 nucleus; PDB: 3K2A_B 2LK2_A 1X2N_A 2DMN_A.
Probab=98.17 E-value=4.5e-07 Score=58.29 Aligned_cols=33 Identities=27% Similarity=0.586 Sum_probs=28.0
Q ss_pred CCCCCHHHHHHHHHHHHhhCCCcccceeeccccchhh
Q 026809 114 KGTPRKQKIQDMTAELAKHGQISETNVYNWFQNRRAR 150 (233)
Q Consensus 114 ~~~P~~~~r~~LA~~L~~~~gls~~qV~vWFQNRR~k 150 (233)
++||+.+++..||..+ ||+..||..||-|.|.|
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 4899999999999999 99999999999998864
No 34
>KOG0490 consensus Transcription factor, contains HOX domain [General function prediction only]
Probab=98.00 E-value=5.3e-06 Score=71.07 Aligned_cols=64 Identities=34% Similarity=0.545 Sum_probs=59.3
Q ss_pred CCCCCCCCCCCCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHHHhhCCCcccceeeccccchhhHHhhhc
Q 026809 88 QKLTARQRWTPTPAQLQILEHVYDECKGTPRKQKIQDMTAELAKHGQISETNVYNWFQNRRARLKRKQS 156 (233)
Q Consensus 88 ~~~~rr~Rt~~t~~Ql~~Le~~F~~~~~~P~~~~r~~LA~~L~~~~gls~~qV~vWFQNRR~k~Kr~~~ 156 (233)
..+.++.|+.+...++..|+..|..+ ++|+...+..|+..+ |++++.|++||+|+|++.++...
T Consensus 150 ~~~~~~~~~~~~~~~~~~~~~~~~~~-~~P~~~~~~~l~~~~----~~~~~~~q~~~~~~~~~~~~~~~ 213 (235)
T KOG0490|consen 150 NKKPRRPRTTFTENQLEVLETVFRAT-PKPDADDREQLAEET----GLSERVIQVWFQNRRAKLRKHKR 213 (235)
T ss_pred ccccCCCccccccchhHhhhhcccCC-CCCchhhHHHHHHhc----CCChhhhhhhcccHHHHHHhhcc
Confidence 34677889999999999999999999 899999999999999 99999999999999999998766
No 35
>KOG2252 consensus CCAAT displacement protein and related homeoproteins [Transcription]
Probab=97.81 E-value=1.4e-05 Score=76.76 Aligned_cols=57 Identities=25% Similarity=0.401 Sum_probs=53.1
Q ss_pred CCCCCCCCCCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHHHhhCCCcccceeeccccchhhH
Q 026809 90 LTARQRWTPTPAQLQILEHVYDECKGTPRKQKIQDMTAELAKHGQISETNVYNWFQNRRARL 151 (233)
Q Consensus 90 ~~rr~Rt~~t~~Ql~~Le~~F~~~~~~P~~~~r~~LA~~L~~~~gls~~qV~vWFQNRR~k~ 151 (233)
..+++|.+||..|+..|..+|+.+ ++|+.+..+.|+.+| +|...-|.+||-|-|.|.
T Consensus 419 ~~KKPRlVfTd~QkrTL~aiFke~-~RPS~Emq~tIS~qL----~L~~sTV~NfFmNaRRRs 475 (558)
T KOG2252|consen 419 QTKKPRLVFTDIQKRTLQAIFKEN-KRPSREMQETISQQL----NLELSTVINFFMNARRRS 475 (558)
T ss_pred cCCCceeeecHHHHHHHHHHHhcC-CCCCHHHHHHHHHHh----CCcHHHHHHHHHhhhhhc
Confidence 466779999999999999999999 899999999999999 999999999999977764
No 36
>KOG1146 consensus Homeobox protein [General function prediction only]
Probab=97.32 E-value=0.00018 Score=74.98 Aligned_cols=62 Identities=24% Similarity=0.379 Sum_probs=57.7
Q ss_pred CCCCCCCCCCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHHHhhCCCcccceeeccccchhhHHhhhc
Q 026809 90 LTARQRWTPTPAQLQILEHVYDECKGTPRKQKIQDMTAELAKHGQISETNVYNWFQNRRARLKRKQS 156 (233)
Q Consensus 90 ~~rr~Rt~~t~~Ql~~Le~~F~~~~~~P~~~~r~~LA~~L~~~~gls~~qV~vWFQNRR~k~Kr~~~ 156 (233)
.+|+.|+.++..||.+|..+|... .||...+.+.|...+ +++.++|++||||-|+|.|+...
T Consensus 902 ~r~a~~~~~~d~qlk~i~~~~~~q-~~~~~~~~E~l~~~~----~~~~~~i~vw~qna~~~s~k~~~ 963 (1406)
T KOG1146|consen 902 GRRAYRTQESDLQLKIIKACYEAQ-RTPTMQECEVLEEPI----GLPKRVIQVWFQNARAKSKKAKL 963 (1406)
T ss_pred hhhhhccchhHHHHHHHHHHHhhc-cCChHHHHHhhcccc----cCCcchhHHhhhhhhhhhhhhhh
Confidence 366789999999999999999999 899999999999999 99999999999999999988665
No 37
>PF11569 Homez: Homeodomain leucine-zipper encoding, Homez; PDB: 2YS9_A.
Probab=95.74 E-value=0.0029 Score=43.50 Aligned_cols=42 Identities=21% Similarity=0.439 Sum_probs=30.8
Q ss_pred HHHHHHHHhhcCCCCCHHHHHHHHHHHHhhCCCcccceeeccccchh
Q 026809 103 LQILEHVYDECKGTPRKQKIQDMTAELAKHGQISETNVYNWFQNRRA 149 (233)
Q Consensus 103 l~~Le~~F~~~~~~P~~~~r~~LA~~L~~~~gls~~qV~vWFQNRR~ 149 (233)
+..|+.+|... +.+...+...|+.+. +|+..+|+.||-.|+.
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 45699999998 889999999999999 9999999999976543
No 38
>KOG0773 consensus Transcription factor MEIS1 and related HOX domain proteins [Transcription]
Probab=95.35 E-value=0.015 Score=53.29 Aligned_cols=59 Identities=24% Similarity=0.290 Sum_probs=47.8
Q ss_pred CCCCCCCCCHHHHHHHHHHHhhc--CCCCCHHHHHHHHHHHHhhCCCcccceeeccccchhhHHh
Q 026809 91 TARQRWTPTPAQLQILEHVYDEC--KGTPRKQKIQDMTAELAKHGQISETNVYNWFQNRRARLKR 153 (233)
Q Consensus 91 ~rr~Rt~~t~~Ql~~Le~~F~~~--~~~P~~~~r~~LA~~L~~~~gls~~qV~vWFQNRR~k~Kr 153 (233)
..|++..+......+|+.+...+ .+||+..+...||+++ ||+..+|-+||-|.|.|..+
T Consensus 239 ~~r~~~~lP~~a~~ilr~Wl~~h~~~PYPse~~K~~La~~T----GLs~~Qv~NWFINaR~R~w~ 299 (342)
T KOG0773|consen 239 KWRPQRGLPKEAVSILRAWLFEHLLHPYPSDDEKLMLAKQT----GLSRPQVSNWFINARVRLWK 299 (342)
T ss_pred CCCCCCCCCHHHHHHHHHHHHHhccCCCCcchhccccchhc----CCCcccCCchhhhcccccCC
Confidence 34455578888888998874432 3799999999999999 99999999999998877544
No 39
>KOG3623 consensus Homeobox transcription factor SIP1 [Transcription]
Probab=93.90 E-value=0.054 Score=54.27 Aligned_cols=51 Identities=16% Similarity=0.361 Sum_probs=46.0
Q ss_pred HHHHHHHHhhcCCCCCHHHHHHHHHHHHhhCCCcccceeeccccchhhHHhhhcCC
Q 026809 103 LQILEHVYDECKGTPRKQKIQDMTAELAKHGQISETNVYNWFQNRRARLKRKQSGV 158 (233)
Q Consensus 103 l~~Le~~F~~~~~~P~~~~r~~LA~~L~~~~gls~~qV~vWFQNRR~k~Kr~~~~~ 158 (233)
+..|..+|..| ..|+..+...||.++ ||+.+.|+.||+++++......+.-
T Consensus 568 ~sllkayyaln-~~ps~eelskia~qv----glp~~vvk~wfE~~~a~e~sv~rsp 618 (1007)
T KOG3623|consen 568 TSLLKAYYALN-GLPSEEELSKIAQQV----GLPFAVVKAWFEDEEAEEMSVERSP 618 (1007)
T ss_pred HHHHHHHHHhc-CCCCHHHHHHHHHHh----cccHHHHHHHHHhhhhhhhhhccCc
Confidence 67889999999 899999999999999 9999999999999999988766443
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=88.24 E-value=0.63 Score=29.29 Aligned_cols=22 Identities=32% Similarity=0.468 Sum_probs=19.6
Q ss_pred cCCHHHHHHHHHHHHHHHHHHH
Q 026809 33 VMTDEQMELLRKQIAVYAMICE 54 (233)
Q Consensus 33 ~~t~~~~~~lr~qi~~y~~ic~ 54 (233)
.||.+|+..||+||.+|.-+.+
T Consensus 2 ~FT~~Ql~~L~~Qi~ayK~l~~ 23 (37)
T PF08880_consen 2 PFTPAQLQELRAQILAYKYLAR 23 (37)
T ss_pred CCCHHHHHHHHHHHHHHHHHHc
Confidence 4899999999999999988664
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=85.21 E-value=0.97 Score=30.38 Aligned_cols=46 Identities=20% Similarity=0.242 Sum_probs=34.3
Q ss_pred CCCCCCCCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHHHhhCCCcccceeeccccc
Q 026809 92 ARQRWTPTPAQLQILEHVYDECKGTPRKQKIQDMTAELAKHGQISETNVYNWFQNR 147 (233)
Q Consensus 92 rr~Rt~~t~~Ql~~Le~~F~~~~~~P~~~~r~~LA~~L~~~~gls~~qV~vWFQNR 147 (233)
+|+|..+|-++...+-..++.+ . ....||+.+ |++...|..|..|+
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 4678899998888888888777 3 356899999 99999999999885
No 42
>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=60.36 E-value=11 Score=25.57 Aligned_cols=38 Identities=32% Similarity=0.479 Sum_probs=30.5
Q ss_pred CCHHHHHHHHHHHhhcCC--CCCHHHHHHHHHHHHhhCCCcccce
Q 026809 98 PTPAQLQILEHVYDECKG--TPRKQKIQDMTAELAKHGQISETNV 140 (233)
Q Consensus 98 ~t~~Ql~~Le~~F~~~~~--~P~~~~r~~LA~~L~~~~gls~~qV 140 (233)
+|+.|+.+|..+|+.. - +|-.....+||+.| |++..-|
T Consensus 1 LT~~Q~e~L~~A~~~G-Yfd~PR~~tl~elA~~l----gis~st~ 40 (53)
T PF04967_consen 1 LTDRQREILKAAYELG-YFDVPRRITLEELAEEL----GISKSTV 40 (53)
T ss_pred CCHHHHHHHHHHHHcC-CCCCCCcCCHHHHHHHh----CCCHHHH
Confidence 4788999999999877 2 26566778899999 9998654
No 43
>PF01527 HTH_Tnp_1: Transposase; InterPro: IPR002514 Transposase proteins are necessary for efficient DNA transposition. This family consists of various Escherichia coli insertion elements and other bacterial transposases some of which are members of the IS3 family. This region includes a helix-turn-helix motif (HTH) at the N terminus followed by a leucine zipper (LZ) motif. The LZ motif has been shown to mediate oligomerisation of the transposase components in IS911 []. More information about these proteins can be found at Protein of the Month: Transposase [].; GO: 0003677 DNA binding, 0004803 transposase activity, 0006313 transposition, DNA-mediated; PDB: 2JN6_A 2RN7_A.
Probab=53.75 E-value=8.5 Score=26.74 Aligned_cols=43 Identities=23% Similarity=0.441 Sum_probs=27.8
Q ss_pred CCCCCCCHHHHHHHHHHH-hhcCCCCCHHHHHHHHHHHHhhCCCcccceeeccc
Q 026809 93 RQRWTPTPAQLQILEHVY-DECKGTPRKQKIQDMTAELAKHGQISETNVYNWFQ 145 (233)
Q Consensus 93 r~Rt~~t~~Ql~~Le~~F-~~~~~~P~~~~r~~LA~~L~~~~gls~~qV~vWFQ 145 (233)
++|..|++++...+-..+ ... ..+..+|..+ ||+...+..|-.
T Consensus 2 ~~r~~ys~e~K~~~v~~~~~~g------~sv~~va~~~----gi~~~~l~~W~~ 45 (76)
T PF01527_consen 2 RKRRRYSPEFKLQAVREYLESG------ESVSEVAREY----GISPSTLYNWRK 45 (76)
T ss_dssp -SS----HHHHHHHHHHHHHHH------CHHHHHHHHH----TS-HHHHHHHHH
T ss_pred CCCCCCCHHHHHHHHHHHHHCC------CceEeeeccc----ccccccccHHHH
Confidence 456788998877666665 333 3567899999 999999999864
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=50.74 E-value=9.6 Score=23.59 Aligned_cols=43 Identities=12% Similarity=0.153 Sum_probs=30.9
Q ss_pred CCCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHHHhhCCCcccceeeccccchh
Q 026809 97 TPTPAQLQILEHVYDECKGTPRKQKIQDMTAELAKHGQISETNVYNWFQNRRA 149 (233)
Q Consensus 97 ~~t~~Ql~~Le~~F~~~~~~P~~~~r~~LA~~L~~~~gls~~qV~vWFQNRR~ 149 (233)
.+++.+..++...|... + ...++|..+ |++...|+.|...-+.
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 35677778887777544 2 244789999 9999999988765443
No 45
>KOG3755 consensus SATB1 matrix attachment region binding protein [Transcription]
Probab=46.86 E-value=4.2 Score=40.40 Aligned_cols=50 Identities=20% Similarity=0.231 Sum_probs=33.1
Q ss_pred HHHHhhcCCCCCHHHHHHHHHHHH---hhCCCcccceeeccccchhhHHhhhcC
Q 026809 107 EHVYDECKGTPRKQKIQDMTAELA---KHGQISETNVYNWFQNRRARLKRKQSG 157 (233)
Q Consensus 107 e~~F~~~~~~P~~~~r~~LA~~L~---~~~gls~~qV~vWFQNRR~k~Kr~~~~ 157 (233)
+.+|.++ +.+....+.+..+.+- -.-..+...|+.||.|||.++|+.+..
T Consensus 708 ~~w~~k~-~s~s~~~v~eYkee~~~~~~~e~~~~kn~~~~fk~~~ee~~~~k~~ 760 (769)
T KOG3755|consen 708 HHWKLKT-RSGSWVDVAEYKEEELLMPYEEKFESKNVQFWFKVRREEEKRLKMS 760 (769)
T ss_pred hhheecc-cCchhHHHHHhhHHhhcchhhhhhhhcchHHHHHHHHHHHhhhhcc
Confidence 4556666 5677766665554440 001235678999999999999987654
No 46
>PF04545 Sigma70_r4: Sigma-70, region 4; InterPro: IPR007630 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognised by the major sigma factors [, ]. Region 4 of sigma-70 like sigma-factors is involved in binding to the -35 promoter element via a helix-turn-helix motif []. Due to the way Pfam works, the threshold has been set artificially high to prevent overlaps with other helix-turn-helix families. Therefore there are many false negatives.; GO: 0003677 DNA binding, 0003700 sequence-specific DNA binding transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, DNA-dependent, 0006355 regulation of transcription, DNA-dependent; PDB: 2P7V_B 3IYD_F 1TLH_B 1KU7_A 1RIO_H 3N97_A 1KU3_A 1RP3_C 1SC5_A 1NR3_A ....
Probab=44.97 E-value=19 Score=23.15 Aligned_cols=40 Identities=18% Similarity=0.312 Sum_probs=29.5
Q ss_pred CCCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHHHhhCCCcccceeecccc
Q 026809 97 TPTPAQLQILEHVYDECKGTPRKQKIQDMTAELAKHGQISETNVYNWFQN 146 (233)
Q Consensus 97 ~~t~~Ql~~Le~~F~~~~~~P~~~~r~~LA~~L~~~~gls~~qV~vWFQN 146 (233)
.+++.+..+|...|-.. - .-.++|..+ |++...|+.+...
T Consensus 4 ~L~~~er~vi~~~y~~~---~---t~~eIa~~l----g~s~~~V~~~~~~ 43 (50)
T PF04545_consen 4 QLPPREREVIRLRYFEG---L---TLEEIAERL----GISRSTVRRILKR 43 (50)
T ss_dssp TS-HHHHHHHHHHHTST-------SHHHHHHHH----TSCHHHHHHHHHH
T ss_pred hCCHHHHHHHHHHhcCC---C---CHHHHHHHH----CCcHHHHHHHHHH
Confidence 46788899999998544 1 245899999 9999988776543
No 47
>cd00569 HTH_Hin_like Helix-turn-helix domain of Hin and related proteins, a family of DNA-binding domains unique to bacteria and represented by the Hin protein of Salmonella. The basic HTH domain is a simple fold comprised of three core helices that form a right-handed helical bundle. The principal DNA-protein interface is formed by the third helix, the recognition helix, inserting itself into the major groove of the DNA. A diverse array of HTH domains participate in a variety of functions that depend on their DNA-binding properties. HTH_Hin represents one of the simplest versions of the HTH domains; the characterization of homologous relationships between various sequence-diverse HTH domain families remains difficult. The Hin recombinase induces the site-specific inversion of a chromosomal DNA segment containing a promoter, which controls the alternate expression of two genes by reversibly switching orientation. The Hin recombinase consists of a single polypeptide chain containing a D
Probab=44.14 E-value=36 Score=18.47 Aligned_cols=38 Identities=16% Similarity=0.413 Sum_probs=25.3
Q ss_pred CCCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHHHhhCCCcccceeecc
Q 026809 97 TPTPAQLQILEHVYDECKGTPRKQKIQDMTAELAKHGQISETNVYNWF 144 (233)
Q Consensus 97 ~~t~~Ql~~Le~~F~~~~~~P~~~~r~~LA~~L~~~~gls~~qV~vWF 144 (233)
.++......+...|... + ....+|+.+ +++...|..|.
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 2 345788899 99988887763
No 48
>COG3413 Predicted DNA binding protein [General function prediction only]
Probab=37.02 E-value=39 Score=28.76 Aligned_cols=49 Identities=33% Similarity=0.403 Sum_probs=35.9
Q ss_pred CCCHHHHHHHHHHHhhcCC--CCCHHHHHHHHHHHHhhCCCcccceeeccccchhhHH
Q 026809 97 TPTPAQLQILEHVYDECKG--TPRKQKIQDMTAELAKHGQISETNVYNWFQNRRARLK 152 (233)
Q Consensus 97 ~~t~~Ql~~Le~~F~~~~~--~P~~~~r~~LA~~L~~~~gls~~qV~vWFQNRR~k~K 152 (233)
.+|+.|+.+|..+|+.. = ||-.....+||+.| |+++.-+ +..=||+..|
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 69999999999999877 2 36666778899999 9998643 3333444433
No 49
>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=36.18 E-value=22 Score=23.05 Aligned_cols=39 Identities=21% Similarity=0.182 Sum_probs=26.4
Q ss_pred CCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHHHhhCCCcccceeecccc
Q 026809 98 PTPAQLQILEHVYDECKGTPRKQKIQDMTAELAKHGQISETNVYNWFQN 146 (233)
Q Consensus 98 ~t~~Ql~~Le~~F~~~~~~P~~~~r~~LA~~L~~~~gls~~qV~vWFQN 146 (233)
+++.+..++.-.|-.+ ....++|..+ |+++..|+.|...
T Consensus 11 L~~~~r~i~~l~~~~g------~s~~eIa~~l----~~s~~~v~~~l~r 49 (54)
T PF08281_consen 11 LPERQREIFLLRYFQG------MSYAEIAEIL----GISESTVKRRLRR 49 (54)
T ss_dssp S-HHHHHHHHHHHTS---------HHHHHHHC----TS-HHHHHHHHHH
T ss_pred CCHHHHHHHHHHHHHC------cCHHHHHHHH----CcCHHHHHHHHHH
Confidence 4566777777766555 2345899999 9999999999864
No 50
>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=32.75 E-value=17 Score=25.33 Aligned_cols=19 Identities=26% Similarity=0.705 Sum_probs=16.6
Q ss_pred HHHHHHHHHhhCCCcccceeecc
Q 026809 122 IQDMTAELAKHGQISETNVYNWF 144 (233)
Q Consensus 122 r~~LA~~L~~~~gls~~qV~vWF 144 (233)
-.+||.+| |+++.+|..|=
T Consensus 25 lkdIA~~L----gvs~~tIr~WK 43 (60)
T PF10668_consen 25 LKDIAEKL----GVSESTIRKWK 43 (60)
T ss_pred HHHHHHHH----CCCHHHHHHHh
Confidence 34799999 99999999984
No 51
>PRK09413 IS2 repressor TnpA; Reviewed
Probab=30.30 E-value=61 Score=25.06 Aligned_cols=41 Identities=10% Similarity=0.303 Sum_probs=27.2
Q ss_pred CCCCCHHHHH-HHHHHHhhcCCCCCHHHHHHHHHHHHhhCCCcccceeeccc
Q 026809 95 RWTPTPAQLQ-ILEHVYDECKGTPRKQKIQDMTAELAKHGQISETNVYNWFQ 145 (233)
Q Consensus 95 Rt~~t~~Ql~-~Le~~F~~~~~~P~~~~r~~LA~~L~~~~gls~~qV~vWFQ 145 (233)
|..|+.+... ++...+..+ .+ ..++|..+ |++...|..|.+
T Consensus 10 rr~ys~EfK~~aV~~~~~~g--~s----v~evA~e~----gIs~~tl~~W~r 51 (121)
T PRK09413 10 RRRRTTQEKIAIVQQSFEPG--MT----VSLVARQH----GVAASQLFLWRK 51 (121)
T ss_pred CCCCCHHHHHHHHHHHHcCC--CC----HHHHHHHH----CcCHHHHHHHHH
Confidence 4456776644 444444433 22 34789999 999999999954
No 52
>PRK03975 tfx putative transcriptional regulator; Provisional
Probab=28.86 E-value=61 Score=26.30 Aligned_cols=49 Identities=18% Similarity=0.186 Sum_probs=37.0
Q ss_pred CCCCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHHHhhCCCcccceeeccccchhhHHhhh
Q 026809 96 WTPTPAQLQILEHVYDECKGTPRKQKIQDMTAELAKHGQISETNVYNWFQNRRARLKRKQ 155 (233)
Q Consensus 96 t~~t~~Ql~~Le~~F~~~~~~P~~~~r~~LA~~L~~~~gls~~qV~vWFQNRR~k~Kr~~ 155 (233)
..+++.|+.+|... ..+ . ...+||..| |++...|..|-.+.+.+.++..
T Consensus 5 ~~Lt~rqreVL~lr-~~G---l---Tq~EIAe~L----GiS~~tVs~ie~ra~kkLr~~~ 53 (141)
T PRK03975 5 SFLTERQIEVLRLR-ERG---L---TQQEIADIL----GTSRANVSSIEKRARENIEKAR 53 (141)
T ss_pred cCCCHHHHHHHHHH-HcC---C---CHHHHHHHH----CCCHHHHHHHHHHHHHHHHHHH
Confidence 46789999999884 333 1 234899999 9999999999987766665543
No 53
>PRK09652 RNA polymerase sigma factor RpoE; Provisional
Probab=28.69 E-value=44 Score=26.49 Aligned_cols=47 Identities=9% Similarity=-0.009 Sum_probs=31.5
Q ss_pred CCCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHHHhhCCCcccceeeccccchhhHHh
Q 026809 97 TPTPAQLQILEHVYDECKGTPRKQKIQDMTAELAKHGQISETNVYNWFQNRRARLKR 153 (233)
Q Consensus 97 ~~t~~Ql~~Le~~F~~~~~~P~~~~r~~LA~~L~~~~gls~~qV~vWFQNRR~k~Kr 153 (233)
.+++.+..+|...|-.+ ++ ..+||..| |++...|+.|...=+.+.|+
T Consensus 128 ~L~~~~r~vl~l~~~~~--~s----~~eIA~~l----gis~~tV~~~l~ra~~~Lr~ 174 (182)
T PRK09652 128 SLPEELRTAITLREIEG--LS----YEEIAEIM----GCPIGTVRSRIFRAREALRA 174 (182)
T ss_pred hCCHHHHHHHHHHHHcC--CC----HHHHHHHH----CCCHHHHHHHHHHHHHHHHH
Confidence 35666666666655433 22 34889999 99999999988754544444
No 54
>PRK09480 slmA division inhibitor protein; Provisional
Probab=26.94 E-value=47 Score=26.77 Aligned_cols=35 Identities=14% Similarity=0.344 Sum_probs=28.3
Q ss_pred HHHhhcCCCCCHHHHHHHHHHHHhhCCCcccceeeccccch
Q 026809 108 HVYDECKGTPRKQKIQDMTAELAKHGQISETNVYNWFQNRR 148 (233)
Q Consensus 108 ~~F~~~~~~P~~~~r~~LA~~L~~~~gls~~qV~vWFQNRR 148 (233)
..|... +. .......||++. |++...++.+|.|+-
T Consensus 21 ~l~~~~-~G-~~~ti~~Ia~~a----gvs~gt~Y~~F~~K~ 55 (194)
T PRK09480 21 QMLESP-PG-ERITTAKLAARV----GVSEAALYRHFPSKA 55 (194)
T ss_pred HHHHhc-CC-CccCHHHHHHHh----CCCHhHHHHHCCCHH
Confidence 335444 45 777888999999 999999999999976
No 55
>COG4367 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=26.42 E-value=64 Score=24.34 Aligned_cols=39 Identities=13% Similarity=0.084 Sum_probs=26.0
Q ss_pred CCCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHHHhhCCCcccce
Q 026809 97 TPTPAQLQILEHVYDECKGTPRKQKIQDMTAELAKHGQISETNV 140 (233)
Q Consensus 97 ~~t~~Ql~~Le~~F~~~~~~P~~~~r~~LA~~L~~~~gls~~qV 140 (233)
+++++|...-...|..+ --.+.-..+++|..| ++++..|
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 35667766666665555 445555667899999 9888644
No 56
>PRK09646 RNA polymerase sigma factor SigK; Reviewed
Probab=26.02 E-value=59 Score=26.76 Aligned_cols=47 Identities=15% Similarity=0.150 Sum_probs=30.7
Q ss_pred CCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHHHhhCCCcccceeeccccchhhHHhh
Q 026809 98 PTPAQLQILEHVYDECKGTPRKQKIQDMTAELAKHGQISETNVYNWFQNRRARLKRK 154 (233)
Q Consensus 98 ~t~~Ql~~Le~~F~~~~~~P~~~~r~~LA~~L~~~~gls~~qV~vWFQNRR~k~Kr~ 154 (233)
+++.+..+|...|-.+ ....+||+.| |++...|+++...-|.+.|+.
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 4555555555444333 2345889999 999999999886555555543
No 57
>PRK06759 RNA polymerase factor sigma-70; Validated
Probab=25.41 E-value=47 Score=25.90 Aligned_cols=45 Identities=7% Similarity=0.082 Sum_probs=29.8
Q ss_pred CCCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHHHhhCCCcccceeeccccchhhH
Q 026809 97 TPTPAQLQILEHVYDECKGTPRKQKIQDMTAELAKHGQISETNVYNWFQNRRARL 151 (233)
Q Consensus 97 ~~t~~Ql~~Le~~F~~~~~~P~~~~r~~LA~~L~~~~gls~~qV~vWFQNRR~k~ 151 (233)
.+++.+..++...|-.+ ....+||..| |++...|+.|...=|.+.
T Consensus 106 ~L~~~~r~ii~l~~~~~------~s~~EIA~~l----~is~~tV~~~~~ra~~~L 150 (154)
T PRK06759 106 VLDEKEKYIIFERFFVG------KTMGEIALET----EMTYYQVRWIYRQALEKM 150 (154)
T ss_pred hCCHHHHHHHHHHHhcC------CCHHHHHHHH----CCCHHHHHHHHHHHHHHH
Confidence 34555666665555444 2356899999 999999999876444443
No 58
>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=22.98 E-value=70 Score=21.07 Aligned_cols=43 Identities=21% Similarity=0.251 Sum_probs=31.1
Q ss_pred CCCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHHHhhCCCcccceeeccccchhh
Q 026809 97 TPTPAQLQILEHVYDECKGTPRKQKIQDMTAELAKHGQISETNVYNWFQNRRAR 150 (233)
Q Consensus 97 ~~t~~Ql~~Le~~F~~~~~~P~~~~r~~LA~~L~~~~gls~~qV~vWFQNRR~k 150 (233)
.+|+.++.+|.-...-. ...+||..+ ++++..|+.+..+=+.|
T Consensus 3 ~LT~~E~~vl~~l~~G~-------~~~eIA~~l----~is~~tV~~~~~~i~~K 45 (58)
T PF00196_consen 3 SLTERELEVLRLLAQGM-------SNKEIAEEL----GISEKTVKSHRRRIMKK 45 (58)
T ss_dssp SS-HHHHHHHHHHHTTS--------HHHHHHHH----TSHHHHHHHHHHHHHHH
T ss_pred ccCHHHHHHHHHHHhcC-------CcchhHHhc----CcchhhHHHHHHHHHHH
Confidence 47888888887766433 245899999 99999999877654444
No 59
>PF13936 HTH_38: Helix-turn-helix domain; PDB: 2W48_A.
Probab=22.80 E-value=36 Score=21.60 Aligned_cols=39 Identities=18% Similarity=0.213 Sum_probs=19.2
Q ss_pred CCCCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHHHhhCCCcccceeecc
Q 026809 96 WTPTPAQLQILEHVYDECKGTPRKQKIQDMTAELAKHGQISETNVYNWF 144 (233)
Q Consensus 96 t~~t~~Ql~~Le~~F~~~~~~P~~~~r~~LA~~L~~~~gls~~qV~vWF 144 (233)
..+|.+++..++..++.+ . ...+||+.| |.+..-|..+.
T Consensus 3 ~~Lt~~eR~~I~~l~~~G-~-----s~~~IA~~l----g~s~sTV~rel 41 (44)
T PF13936_consen 3 KHLTPEERNQIEALLEQG-M-----SIREIAKRL----GRSRSTVSREL 41 (44)
T ss_dssp ---------HHHHHHCS---------HHHHHHHT----T--HHHHHHHH
T ss_pred cchhhhHHHHHHHHHHcC-C-----CHHHHHHHH----CcCcHHHHHHH
Confidence 457888888999888766 2 344799999 99888776543
No 60
>KOG3623 consensus Homeobox transcription factor SIP1 [Transcription]
Probab=22.63 E-value=1.2e+02 Score=31.27 Aligned_cols=60 Identities=17% Similarity=0.170 Sum_probs=42.2
Q ss_pred CCCCCCCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHHHhhCCCcccceeeccccchhhHHhhhcC
Q 026809 93 RQRWTPTPAQLQILEHVYDECKGTPRKQKIQDMTAELAKHGQISETNVYNWFQNRRARLKRKQSG 157 (233)
Q Consensus 93 r~Rt~~t~~Ql~~Le~~F~~~~~~P~~~~r~~LA~~L~~~~gls~~qV~vWFQNRR~k~Kr~~~~ 157 (233)
+.|+....++-..|..+++.+ --++..+-..++.+| ...+.+|.+||++|+...+.....
T Consensus 628 kv~sp~k~~dq~ql~~a~elq-~s~~n~~~pl~~t~~----~n~~pv~ev~dhsrsstpsp~pl~ 687 (1007)
T KOG3623|consen 628 KVRSPIKEEDQQQLKQAYELQ-ASPSNDEFPLIATRL----QNDPPVVEVWDHSRSSTPSPMPLF 687 (1007)
T ss_pred cccCCCCccchhhhHhhhhcc-cCccCcccchhhhhc----cCCCcchhhcccCCCCCCCCCccc
Confidence 344556666667788888777 346555555556667 778889999999999887765443
No 61
>KOG1146 consensus Homeobox protein [General function prediction only]
Probab=22.63 E-value=61 Score=35.38 Aligned_cols=61 Identities=21% Similarity=0.315 Sum_probs=52.6
Q ss_pred CCCCCCCCCCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHHHhhCCCcccceeeccccchhhHHhhh
Q 026809 90 LTARQRWTPTPAQLQILEHVYDECKGTPRKQKIQDMTAELAKHGQISETNVYNWFQNRRARLKRKQ 155 (233)
Q Consensus 90 ~~rr~Rt~~t~~Ql~~Le~~F~~~~~~P~~~~r~~LA~~L~~~~gls~~qV~vWFQNRR~k~Kr~~ 155 (233)
+.++.|..+-++++.+|-.+|-.+ --|+..-+.-|.... ..+.+.+.+||+|-|.|.++..
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 455677888889999999999998 469999999998888 8999999999999999887765
No 62
>PRK09644 RNA polymerase sigma factor SigM; Provisional
Probab=22.17 E-value=74 Score=25.27 Aligned_cols=31 Identities=16% Similarity=0.178 Sum_probs=23.7
Q ss_pred HHHHHHHHHhhCCCcccceeeccccchhhHHhhhc
Q 026809 122 IQDMTAELAKHGQISETNVYNWFQNRRARLKRKQS 156 (233)
Q Consensus 122 r~~LA~~L~~~~gls~~qV~vWFQNRR~k~Kr~~~ 156 (233)
..+||..| |+++..|++|...=|.+.|+.-.
T Consensus 127 ~~eIA~~l----gis~~tv~~~l~Rar~~Lr~~l~ 157 (165)
T PRK09644 127 YEEAASVL----DLKLNTYKSHLFRGRKRLKALLK 157 (165)
T ss_pred HHHHHHHH----CCCHHHHHHHHHHHHHHHHHHHH
Confidence 45888999 99999999998766666555443
No 63
>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=22.08 E-value=66 Score=24.09 Aligned_cols=45 Identities=20% Similarity=0.231 Sum_probs=29.3
Q ss_pred CCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHHHhhCCCcccceeeccccchhhHH
Q 026809 98 PTPAQLQILEHVYDECKGTPRKQKIQDMTAELAKHGQISETNVYNWFQNRRARLK 152 (233)
Q Consensus 98 ~t~~Ql~~Le~~F~~~~~~P~~~~r~~LA~~L~~~~gls~~qV~vWFQNRR~k~K 152 (233)
+++.+..++...|-.. + ...+||+.+ |+++..|+.+...-+.|.|
T Consensus 111 L~~~~~~ii~~~~~~g--~----s~~eIA~~l----~~s~~~v~~~~~~~~~kl~ 155 (158)
T TIGR02937 111 LPEREREVLVLRYLEG--L----SYKEIAEIL----GISVGTVKRRLKRARKKLR 155 (158)
T ss_pred CCHHHHHHHhhHHhcC--C----CHHHHHHHH----CCCHHHHHHHHHHHHHHHH
Confidence 4555666665544332 2 344889999 9999999988865554443
No 64
>PRK09642 RNA polymerase sigma factor SigW; Reviewed
Probab=21.78 E-value=78 Score=24.89 Aligned_cols=47 Identities=15% Similarity=0.117 Sum_probs=30.1
Q ss_pred CCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHHHhhCCCcccceeeccccchhhHHhh
Q 026809 98 PTPAQLQILEHVYDECKGTPRKQKIQDMTAELAKHGQISETNVYNWFQNRRARLKRK 154 (233)
Q Consensus 98 ~t~~Ql~~Le~~F~~~~~~P~~~~r~~LA~~L~~~~gls~~qV~vWFQNRR~k~Kr~ 154 (233)
+++.+..++...|-.. ....+||..| |+++..|++....-|.+.|+.
T Consensus 107 Lp~~~r~v~~l~~~~g------~s~~EIA~~l----gis~~tV~~~l~Rar~~Lr~~ 153 (160)
T PRK09642 107 LPENYRDVVLAHYLEE------KSYQEIALQE----KIEVKTVEMKLYRARKWIKKH 153 (160)
T ss_pred CCHHHHHHHHHHHHhC------CCHHHHHHHH----CCCHHHHHHHHHHHHHHHHHH
Confidence 3444445554444333 1234889999 999999999887655555543
No 65
>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=21.61 E-value=38 Score=23.13 Aligned_cols=20 Identities=30% Similarity=0.795 Sum_probs=17.3
Q ss_pred HHHHHHHHHhhCCCcccceeeccc
Q 026809 122 IQDMTAELAKHGQISETNVYNWFQ 145 (233)
Q Consensus 122 r~~LA~~L~~~~gls~~qV~vWFQ 145 (233)
..+||+.| |++...|+.|-+
T Consensus 16 ~~eIA~~L----g~~~~TV~~W~~ 35 (58)
T PF06056_consen 16 IKEIAEEL----GVPRSTVYSWKD 35 (58)
T ss_pred HHHHHHHH----CCChHHHHHHHH
Confidence 34899999 999999999964
No 66
>PRK12516 RNA polymerase sigma factor; Provisional
Probab=21.55 E-value=84 Score=25.86 Aligned_cols=31 Identities=10% Similarity=0.092 Sum_probs=23.8
Q ss_pred HHHHHHHHHhhCCCcccceeeccccchhhHHhhhc
Q 026809 122 IQDMTAELAKHGQISETNVYNWFQNRRARLKRKQS 156 (233)
Q Consensus 122 r~~LA~~L~~~~gls~~qV~vWFQNRR~k~Kr~~~ 156 (233)
..+||+.| |+++..|++....=|.+.++.-.
T Consensus 135 ~~EIA~~L----gis~~tVk~~l~Rar~~Lr~~l~ 165 (187)
T PRK12516 135 YEEAAEIC----GCAVGTIKSRVNRARQRLQEILQ 165 (187)
T ss_pred HHHHHHHH----CCCHHHHHHHHHHHHHHHHHHHH
Confidence 44889999 99999999988766666555443
No 67
>PRK12533 RNA polymerase sigma factor; Provisional
Probab=21.44 E-value=78 Score=27.00 Aligned_cols=33 Identities=18% Similarity=0.266 Sum_probs=24.7
Q ss_pred HHHHHHHHHhhCCCcccceeeccccchhhHHhhhcCC
Q 026809 122 IQDMTAELAKHGQISETNVYNWFQNRRARLKRKQSGV 158 (233)
Q Consensus 122 r~~LA~~L~~~~gls~~qV~vWFQNRR~k~Kr~~~~~ 158 (233)
..+||..| |+++..|++.-..=|.+.++.-...
T Consensus 153 ~~EIAe~L----giS~~tVk~~L~RAr~~Lr~~l~~~ 185 (216)
T PRK12533 153 YREIAAIA----DVPVGTVMSRLARARRRLAALLGGA 185 (216)
T ss_pred HHHHHHHH----CCCHHHHHHHHHHHHHHHHHHHccc
Confidence 45889999 9999999998876666666554433
No 68
>PRK12526 RNA polymerase sigma factor; Provisional
Probab=21.38 E-value=71 Score=26.67 Aligned_cols=29 Identities=17% Similarity=0.237 Sum_probs=22.3
Q ss_pred HHHHHHHHHhhCCCcccceeeccccchhhHHhh
Q 026809 122 IQDMTAELAKHGQISETNVYNWFQNRRARLKRK 154 (233)
Q Consensus 122 r~~LA~~L~~~~gls~~qV~vWFQNRR~k~Kr~ 154 (233)
..+||..| |+++..|+++...-|.+.++.
T Consensus 172 ~~EIA~~l----gis~~tV~~~l~Ra~~~Lr~~ 200 (206)
T PRK12526 172 QEQLAQQL----NVPLGTVKSRLRLALAKLKVQ 200 (206)
T ss_pred HHHHHHHH----CCCHHHHHHHHHHHHHHHHHH
Confidence 45889999 999999998886655555543
No 69
>PRK12541 RNA polymerase sigma factor; Provisional
Probab=20.96 E-value=70 Score=25.24 Aligned_cols=46 Identities=11% Similarity=-0.052 Sum_probs=29.5
Q ss_pred CCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHHHhhCCCcccceeeccccchhhHHh
Q 026809 98 PTPAQLQILEHVYDECKGTPRKQKIQDMTAELAKHGQISETNVYNWFQNRRARLKR 153 (233)
Q Consensus 98 ~t~~Ql~~Le~~F~~~~~~P~~~~r~~LA~~L~~~~gls~~qV~vWFQNRR~k~Kr 153 (233)
+++.+..+|.-.|-.+ + ...+||..| |++...|+.+...=|.+.|+
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 5555555555554333 2 234889999 99999998887654444443
No 70
>cd02413 40S_S3_KH K homology RNA-binding (KH) domain of the eukaryotic 40S small ribosomal subunit protein S3. S3 is part of the head region of the 40S ribosomal subunit and is believed to interact with mRNA as it threads its way from the latch into the channel. The KH motif is a beta-alpha-alpha-beta-beta unit that folds into an alpha-beta structure with a three stranded beta-sheet interupted by two contiguous helices. In general, KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.
Probab=20.43 E-value=98 Score=22.50 Aligned_cols=25 Identities=20% Similarity=0.287 Sum_probs=17.8
Q ss_pred HHHHHHHHHHhhCCCcccceeeccc
Q 026809 121 KIQDMTAELAKHGQISETNVYNWFQ 145 (233)
Q Consensus 121 ~r~~LA~~L~~~~gls~~qV~vWFQ 145 (233)
.+.+|...|....+|...+|.+|+.
T Consensus 51 ~i~~L~~~L~k~~~~~~~~i~v~~~ 75 (81)
T cd02413 51 RIRELTSLVQKRFNFPEGSVELYAE 75 (81)
T ss_pred hHHHHHHHHHHHhCCCCCeEEEEEE
Confidence 3445555555555999999999985
No 71
>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=20.05 E-value=51 Score=20.90 Aligned_cols=38 Identities=18% Similarity=0.482 Sum_probs=25.6
Q ss_pred CCCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHHHhhCCCcccceeecc
Q 026809 97 TPTPAQLQILEHVYDECKGTPRKQKIQDMTAELAKHGQISETNVYNWF 144 (233)
Q Consensus 97 ~~t~~Ql~~Le~~F~~~~~~P~~~~r~~LA~~L~~~~gls~~qV~vWF 144 (233)
.+++++...+...+... ..+.+||+.+ |++...|+-++
T Consensus 5 ~~~~~~~~~i~~l~~~G------~si~~IA~~~----gvsr~TvyR~l 42 (45)
T PF02796_consen 5 KLSKEQIEEIKELYAEG------MSIAEIAKQF----GVSRSTVYRYL 42 (45)
T ss_dssp SSSHCCHHHHHHHHHTT--------HHHHHHHT----TS-HHHHHHHH
T ss_pred CCCHHHHHHHHHHHHCC------CCHHHHHHHH----CcCHHHHHHHH
Confidence 45665666777777665 2356899999 99998887654
Done!