Query 026974
Match_columns 230
No_of_seqs 294 out of 1748
Neff 7.1
Searched_HMMs 46136
Date Fri Mar 29 03:14:06 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/026974.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/026974hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG0483 Transcription factor H 99.8 2.4E-21 5.3E-26 161.7 6.9 109 63-171 49-157 (198)
2 KOG0493 Transcription factor E 99.8 2.3E-20 5E-25 159.0 4.1 92 26-122 212-304 (342)
3 KOG0489 Transcription factor z 99.7 6.2E-19 1.4E-23 154.1 1.2 66 59-124 154-219 (261)
4 KOG0842 Transcription factor t 99.7 3.6E-18 7.9E-23 150.5 5.2 68 63-130 152-219 (307)
5 KOG0487 Transcription factor A 99.7 2.5E-18 5.4E-23 151.6 3.6 66 61-126 232-297 (308)
6 KOG0488 Transcription factor B 99.7 2.9E-18 6.3E-23 152.8 3.8 66 60-125 168-233 (309)
7 KOG0843 Transcription factor E 99.7 2.2E-17 4.8E-22 134.0 4.4 64 63-126 101-164 (197)
8 KOG0492 Transcription factor M 99.7 6.3E-17 1.4E-21 134.0 6.7 62 62-123 142-203 (246)
9 KOG0850 Transcription factor D 99.7 4.7E-17 1E-21 136.7 4.3 70 55-124 113-182 (245)
10 KOG2251 Homeobox transcription 99.7 7.3E-17 1.6E-21 135.0 4.6 63 64-126 37-99 (228)
11 KOG0484 Transcription factor P 99.6 2.8E-17 6.1E-22 122.3 1.4 60 64-123 17-76 (125)
12 KOG0485 Transcription factor N 99.6 8.7E-17 1.9E-21 134.0 2.2 62 62-123 102-163 (268)
13 PF00046 Homeobox: Homeobox do 99.6 1.8E-16 3.9E-21 107.1 1.7 57 65-121 1-57 (57)
14 KOG0848 Transcription factor C 99.6 2.1E-16 4.6E-21 135.3 2.1 61 66-126 201-261 (317)
15 KOG3802 Transcription factor O 99.6 5.7E-16 1.2E-20 139.5 1.5 100 16-123 254-353 (398)
16 KOG0494 Transcription factor C 99.6 1.4E-15 2.9E-20 129.9 3.3 60 66-125 143-202 (332)
17 TIGR01565 homeo_ZF_HD homeobox 99.5 3E-14 6.5E-19 96.7 5.3 52 65-116 2-57 (58)
18 smart00389 HOX Homeodomain. DN 99.5 1.4E-14 3E-19 97.2 2.6 55 66-120 2-56 (56)
19 cd00086 homeodomain Homeodomai 99.5 2E-14 4.3E-19 97.2 2.5 57 66-122 2-58 (59)
20 COG5576 Homeodomain-containing 99.5 4.5E-14 9.8E-19 114.3 4.3 64 62-125 49-112 (156)
21 KOG0844 Transcription factor E 99.4 2.4E-14 5.3E-19 124.7 2.4 64 62-125 179-242 (408)
22 KOG0491 Transcription factor B 99.4 1.3E-14 2.9E-19 116.3 -1.4 61 63-123 99-159 (194)
23 KOG4577 Transcription factor L 99.4 2.3E-13 5E-18 117.9 5.3 66 61-126 164-229 (383)
24 KOG0486 Transcription factor P 99.3 5.3E-13 1.1E-17 116.9 3.6 65 63-127 111-175 (351)
25 KOG0847 Transcription factor, 99.3 6.1E-13 1.3E-17 111.3 1.0 66 61-126 164-229 (288)
26 KOG1168 Transcription factor A 99.2 1.7E-12 3.7E-17 112.6 -0.9 99 16-123 268-368 (385)
27 KOG0490 Transcription factor, 99.1 2.4E-11 5.3E-16 103.4 3.3 62 62-123 58-119 (235)
28 KOG0849 Transcription factor P 98.9 6E-10 1.3E-14 101.5 3.5 64 61-124 173-236 (354)
29 KOG0775 Transcription factor S 98.9 2.1E-09 4.6E-14 92.8 4.5 63 59-121 171-233 (304)
30 KOG0774 Transcription factor P 98.7 2.9E-08 6.2E-13 85.4 7.3 58 65-122 189-249 (334)
31 PF05920 Homeobox_KN: Homeobox 98.2 1.8E-07 4E-12 58.8 -0.6 34 85-118 7-40 (40)
32 KOG2252 CCAAT displacement pro 98.1 2.6E-06 5.6E-11 80.2 3.3 62 59-120 415-476 (558)
33 KOG0490 Transcription factor, 98.0 5.6E-06 1.2E-10 70.3 3.2 62 62-123 151-212 (235)
34 KOG1146 Homeobox protein [Gene 97.4 0.00012 2.7E-09 75.0 4.0 63 62-124 901-963 (1406)
35 PF11569 Homez: Homeodomain le 96.3 0.00053 1.1E-08 46.0 -1.4 41 76-116 10-50 (56)
36 KOG0773 Transcription factor M 96.1 0.0054 1.2E-07 55.6 3.5 61 65-125 240-303 (342)
37 KOG3623 Homeobox transcription 92.6 0.055 1.2E-06 53.3 1.4 47 76-122 568-614 (1007)
38 PF04218 CENP-B_N: CENP-B N-te 91.2 0.17 3.6E-06 33.5 2.1 46 65-115 1-46 (53)
39 PF02183 HALZ: Homeobox associ 87.8 1.2 2.6E-05 28.5 4.1 41 123-163 2-42 (45)
40 KOG4196 bZIP transcription fac 83.7 4.9 0.00011 31.6 6.4 89 69-170 22-111 (135)
41 PF10224 DUF2205: Predicted co 78.4 13 0.00028 26.8 6.6 49 121-169 18-66 (80)
42 KOG4005 Transcription factor X 74.6 34 0.00074 29.8 9.2 41 123-163 108-148 (292)
43 PRK09413 IS2 repressor TnpA; R 68.2 4.9 0.00011 30.8 2.7 41 68-113 10-51 (121)
44 PF04967 HTH_10: HTH DNA bindi 66.4 7 0.00015 25.9 2.7 38 71-108 1-40 (53)
45 smart00340 HALZ homeobox assoc 63.1 11 0.00024 23.8 3.0 29 124-152 3-31 (44)
46 PF04545 Sigma70_r4: Sigma-70, 63.1 3.1 6.6E-05 26.5 0.5 37 71-112 5-41 (50)
47 PF01527 HTH_Tnp_1: Transposas 56.5 2.4 5.1E-05 29.2 -1.0 44 66-113 2-45 (76)
48 cd06171 Sigma70_r4 Sigma70, re 53.6 3.8 8.2E-05 25.3 -0.3 42 70-116 10-51 (55)
49 cd00569 HTH_Hin_like Helix-tur 49.0 16 0.00035 19.8 2.0 36 71-111 6-41 (42)
50 KOG1146 Homeobox protein [Gene 47.0 36 0.00078 36.5 5.3 56 68-123 709-764 (1406)
51 PF10668 Phage_terminase: Phag 46.9 4.6 9.9E-05 27.5 -0.7 18 95-112 26-43 (60)
52 PF00170 bZIP_1: bZIP transcri 43.6 97 0.0021 20.7 5.7 28 133-160 33-60 (64)
53 PRK03975 tfx putative transcri 42.1 21 0.00046 28.4 2.3 47 69-121 5-51 (141)
54 COG3413 Predicted DNA binding 42.0 24 0.00052 29.6 2.8 38 70-107 155-194 (215)
55 KOG3755 SATB1 matrix attachmen 40.6 5.4 0.00012 39.0 -1.6 45 80-124 708-759 (769)
56 KOG0709 CREB/ATF family transc 40.4 3.4E+02 0.0074 26.0 12.2 96 68-170 218-316 (472)
57 PF06005 DUF904: Protein of un 39.8 1.3E+02 0.0027 21.2 5.7 46 123-168 22-67 (72)
58 KOG2391 Vacuolar sorting prote 39.7 84 0.0018 28.8 5.9 56 115-170 221-276 (365)
59 PF13443 HTH_26: Cro/C1-type H 38.4 13 0.00028 24.5 0.4 36 94-129 13-48 (63)
60 KOG1924 RhoA GTPase effector D 37.9 1E+02 0.0022 31.7 6.6 43 127-169 475-517 (1102)
61 KOG3650 Predicted coiled-coil 37.7 1.4E+02 0.0029 22.5 5.8 38 133-170 70-107 (120)
62 PF08281 Sigma70_r4_2: Sigma-7 36.4 16 0.00034 23.3 0.6 39 71-114 11-49 (54)
63 PRK13729 conjugal transfer pil 34.4 1.4E+02 0.0031 28.6 6.8 45 121-165 78-122 (475)
64 PF04880 NUDE_C: NUDE protein, 32.0 34 0.00074 28.1 2.1 26 138-163 22-47 (166)
65 TIGR03752 conj_TIGR03752 integ 30.2 2.7E+02 0.0058 26.8 7.9 32 141-172 110-141 (472)
66 KOG4571 Activating transcripti 29.4 1.6E+02 0.0035 26.4 5.9 34 136-169 251-284 (294)
67 KOG1962 B-cell receptor-associ 29.4 1.5E+02 0.0033 25.4 5.6 32 141-172 180-211 (216)
68 PRK06759 RNA polymerase factor 28.4 34 0.00074 26.4 1.5 44 71-119 107-150 (154)
69 PRK09646 RNA polymerase sigma 27.9 37 0.00081 27.6 1.7 45 71-120 143-187 (194)
70 smart00338 BRLZ basic region l 26.5 2E+02 0.0043 19.1 5.4 18 147-164 40-57 (65)
71 PF06005 DUF904: Protein of un 26.4 2.3E+02 0.005 19.8 5.6 47 123-169 15-61 (72)
72 COG4367 Uncharacterized protei 26.1 38 0.00082 25.0 1.2 36 71-106 3-38 (97)
73 KOG4571 Activating transcripti 25.8 2E+02 0.0044 25.8 5.9 45 122-166 244-288 (294)
74 PF00196 GerE: Bacterial regul 25.5 29 0.00063 22.6 0.5 45 70-120 3-47 (58)
75 PRK11546 zraP zinc resistance 25.2 2.6E+02 0.0056 22.4 5.9 23 142-164 91-113 (143)
76 PRK04217 hypothetical protein; 25.0 40 0.00087 25.7 1.2 39 71-114 43-81 (110)
77 PRK09652 RNA polymerase sigma 24.7 39 0.00084 26.6 1.2 42 70-116 128-169 (182)
78 KOG2008 BTK-associated SH3-dom 24.6 2.8E+02 0.006 25.4 6.5 27 142-168 199-225 (426)
79 KOG3119 Basic region leucine z 24.3 2.1E+02 0.0045 25.2 5.7 26 145-170 227-252 (269)
80 PRK12526 RNA polymerase sigma 23.9 43 0.00093 27.6 1.3 44 71-119 154-197 (206)
81 PF13518 HTH_28: Helix-turn-he 23.8 19 0.00042 22.5 -0.6 21 94-114 15-35 (52)
82 KOG3623 Homeobox transcription 23.6 9 0.0002 38.4 -3.1 57 69-125 631-687 (1007)
83 PRK14127 cell division protein 23.2 2.7E+02 0.0059 21.2 5.4 26 146-171 43-68 (109)
84 cd04766 HTH_HspR Helix-Turn-He 23.1 1.3E+02 0.0029 21.4 3.7 22 94-115 4-25 (91)
85 PF06056 Terminase_5: Putative 23.0 24 0.00052 23.6 -0.3 27 94-122 16-42 (58)
86 PRK10884 SH3 domain-containing 22.9 3.1E+02 0.0066 23.2 6.3 27 140-166 139-165 (206)
87 PF08280 HTH_Mga: M protein tr 22.7 38 0.00082 22.4 0.6 32 74-109 6-37 (59)
88 PRK11924 RNA polymerase sigma 22.7 45 0.00097 26.1 1.2 45 71-120 126-170 (179)
89 cd04761 HTH_MerR-SF Helix-Turn 22.6 19 0.00041 22.2 -0.8 21 95-115 4-24 (49)
90 PRK12514 RNA polymerase sigma 22.4 34 0.00074 27.3 0.4 44 71-119 130-173 (179)
91 PRK09642 RNA polymerase sigma 22.4 51 0.0011 25.7 1.4 45 71-120 107-151 (160)
92 smart00421 HTH_LUXR helix_turn 22.2 64 0.0014 19.8 1.6 37 71-113 4-40 (58)
93 PF06156 DUF972: Protein of un 22.0 1.8E+02 0.004 21.9 4.3 38 124-161 20-57 (107)
94 cd02413 40S_S3_KH K homology R 22.0 94 0.002 22.1 2.6 20 94-113 56-75 (81)
95 TIGR02937 sigma70-ECF RNA poly 21.8 49 0.0011 24.6 1.2 41 71-116 111-151 (158)
96 PRK12512 RNA polymerase sigma 21.8 52 0.0011 26.3 1.4 45 71-120 132-176 (184)
97 PHA02955 hypothetical protein; 21.1 93 0.002 26.6 2.8 43 73-115 60-103 (213)
98 PRK10072 putative transcriptio 21.1 25 0.00054 26.1 -0.6 41 71-118 33-73 (96)
99 PF15058 Speriolin_N: Sperioli 20.5 5.3E+02 0.011 21.8 7.1 18 132-149 11-28 (200)
100 PRK12519 RNA polymerase sigma 20.4 47 0.001 26.8 0.8 45 71-120 142-186 (194)
101 TIGR02989 Sig-70_gvs1 RNA poly 20.2 55 0.0012 25.3 1.2 38 71-113 112-149 (159)
102 PF13936 HTH_38: Helix-turn-he 20.1 61 0.0013 20.1 1.2 37 70-111 4-40 (44)
No 1
>KOG0483 consensus Transcription factor HEX, contains HOX and HALZ domains [Transcription]
Probab=99.84 E-value=2.4e-21 Score=161.73 Aligned_cols=109 Identities=52% Similarity=0.705 Sum_probs=101.1
Q ss_pred cccccccCCCHHHHHHHHHhhccCCCCCHHHHHHHHHHhCCCCcceEEecccchhhhhhhhHHHHHHHHHhhhccchhhh
Q 026974 63 FRALKKRKLTAEQAELLEMHFGNEHKLESDRKDKLAAELGLDPRQVAVWFQNRRARDKTKKIEETYATLKTAHENVVVEK 142 (230)
Q Consensus 63 ~~~r~r~~~t~~Q~~~Le~~F~~~~~p~~~~r~~La~~lgL~~~qV~vWFqNRR~k~kr~~~~~~~~~lk~~~~~~~~~~ 142 (230)
.+..++.+|+.+|+..||..|+...++.+.++..||.+|||.++||+|||||||||||.++++.+++.|+..++.+..++
T Consensus 49 ~~~~kk~Rlt~eQ~~~LE~~F~~~~~L~p~~K~~LAk~LgL~pRQVavWFQNRRARwK~kqlE~d~~~Lk~~~~~l~~~~ 128 (198)
T KOG0483|consen 49 KGKGKKRRLTSEQVKFLEKSFESEKKLEPERKKKLAKELGLQPRQVAVWFQNRRARWKTKQLEKDYESLKRQLESLRSEN 128 (198)
T ss_pred ccccccccccHHHHHHhHHhhccccccChHHHHHHHHhhCCChhHHHHHHhhccccccchhhhhhHHHHHHHHHHHhhhh
Confidence 35567778999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred hhhHHHHHHHHHHHHHHHHHHHHHhhhhc
Q 026974 143 TRLESEVATLKEKLSVAEKEIKKMSELIE 171 (230)
Q Consensus 143 ~~~~~e~~~l~~~~~~~~~e~~~~~~~~~ 171 (230)
+.++.++..|..++..+...++.......
T Consensus 129 ~~Lq~e~~eL~~~~~~~~~~~~~~~~~~~ 157 (198)
T KOG0483|consen 129 DRLQSEVQELVAELSSLKREMQKSPENTL 157 (198)
T ss_pred hHHHHHHHHHHHHHhhhhhhhccCccccc
Confidence 99999999999999999988887544433
No 2
>KOG0493 consensus Transcription factor Engrailed, contains HOX domain [General function prediction only]
Probab=99.80 E-value=2.3e-20 Score=158.98 Aligned_cols=92 Identities=32% Similarity=0.539 Sum_probs=77.1
Q ss_pred cCCCCCCCCCCCCC-CCCCCCCCCccccCCCCCCCCCCcccccccCCCHHHHHHHHHhhccCCCCCHHHHHHHHHHhCCC
Q 026974 26 QFYPSDVLTPTGIV-PQQGEPSKPKRRQRKRNTNGNGGFRALKKRKLTAEQAELLEMHFGNEHKLESDRKDKLAAELGLD 104 (230)
Q Consensus 26 ~~~p~~~~~~~~~~-~~~~~~~~p~~~~~~~~~~~~~~~~~r~r~~~t~~Q~~~Le~~F~~~~~p~~~~r~~La~~lgL~ 104 (230)
.+||+|+||+..+. |+++ |+.++.++.. .+....||.|+.||.+||..|...|+.++|++..+|++||.+|||.
T Consensus 212 ~mwPAWVycTRYSDRPSsG----PR~Rk~kkkk-~~~~eeKRPRTAFtaeQL~RLK~EF~enRYlTEqRRQ~La~ELgLN 286 (342)
T KOG0493|consen 212 SMWPAWVYCTRYSDRPSSG----PRHRKPKKKK-SSSKEEKRPRTAFTAEQLQRLKAEFQENRYLTEQRRQELAQELGLN 286 (342)
T ss_pred cccceeeeeecccCCCCCC----cccccccccC-CccchhcCccccccHHHHHHHHHHHhhhhhHHHHHHHHHHHHhCcC
Confidence 68999999999884 4444 3333322222 2445678999999999999999999999999999999999999999
Q ss_pred CcceEEecccchhhhhhh
Q 026974 105 PRQVAVWFQNRRARDKTK 122 (230)
Q Consensus 105 ~~qV~vWFqNRR~k~kr~ 122 (230)
+.||+|||||+|+|.||.
T Consensus 287 EsQIKIWFQNKRAKiKKs 304 (342)
T KOG0493|consen 287 ESQIKIWFQNKRAKIKKS 304 (342)
T ss_pred HHHhhHHhhhhhhhhhhc
Confidence 999999999999999975
No 3
>KOG0489 consensus Transcription factor zerknullt and related HOX domain proteins [General function prediction only]
Probab=99.73 E-value=6.2e-19 Score=154.11 Aligned_cols=66 Identities=32% Similarity=0.450 Sum_probs=61.3
Q ss_pred CCCCcccccccCCCHHHHHHHHHhhccCCCCCHHHHHHHHHHhCCCCcceEEecccchhhhhhhhH
Q 026974 59 GNGGFRALKKRKLTAEQAELLEMHFGNEHKLESDRKDKLAAELGLDPRQVAVWFQNRRARDKTKKI 124 (230)
Q Consensus 59 ~~~~~~~r~r~~~t~~Q~~~Le~~F~~~~~p~~~~r~~La~~lgL~~~qV~vWFqNRR~k~kr~~~ 124 (230)
..+++.||.|+.||..|+.+||+.|..++|++..+|.+||..|.|+++||||||||||+||||..+
T Consensus 154 ~~~~~~kR~RtayT~~QllELEkEFhfN~YLtR~RRiEiA~~L~LtErQIKIWFQNRRMK~Kk~~k 219 (261)
T KOG0489|consen 154 ETGGKSKRRRTAFTRYQLLELEKEFHFNKYLTRSRRIEIAHALNLTERQIKIWFQNRRMKWKKENK 219 (261)
T ss_pred cccCCCCCCCcccchhhhhhhhhhhccccccchHHHHHHHhhcchhHHHHHHHHHHHHHHHHHhhc
Confidence 345667899999999999999999999999999999999999999999999999999999998753
No 4
>KOG0842 consensus Transcription factor tinman/NKX2-3, contains HOX domain [Transcription]
Probab=99.72 E-value=3.6e-18 Score=150.54 Aligned_cols=68 Identities=28% Similarity=0.494 Sum_probs=61.3
Q ss_pred cccccccCCCHHHHHHHHHhhccCCCCCHHHHHHHHHHhCCCCcceEEecccchhhhhhhhHHHHHHH
Q 026974 63 FRALKKRKLTAEQAELLEMHFGNEHKLESDRKDKLAAELGLDPRQVAVWFQNRRARDKTKKIEETYAT 130 (230)
Q Consensus 63 ~~~r~r~~~t~~Q~~~Le~~F~~~~~p~~~~r~~La~~lgL~~~qV~vWFqNRR~k~kr~~~~~~~~~ 130 (230)
++||+|..|+..|+-+||+.|+.++|++..+|+.||..|+|++.||||||||||-|+||+++.+..+.
T Consensus 152 ~kRKrRVLFSqAQV~ELERRFrqQRYLSAPERE~LA~~LrLT~TQVKIWFQNrRYK~KR~~~dk~~~~ 219 (307)
T KOG0842|consen 152 KKRKRRVLFSQAQVYELERRFRQQRYLSAPEREHLASSLRLTPTQVKIWFQNRRYKTKRQQKDKALEA 219 (307)
T ss_pred cccccccccchhHHHHHHHHHHhhhccccHhHHHHHHhcCCCchheeeeeecchhhhhhhhhhhhhhc
Confidence 34455556999999999999999999999999999999999999999999999999999988776554
No 5
>KOG0487 consensus Transcription factor Abd-B, contains HOX domain [Transcription]
Probab=99.72 E-value=2.5e-18 Score=151.62 Aligned_cols=66 Identities=30% Similarity=0.404 Sum_probs=61.3
Q ss_pred CCcccccccCCCHHHHHHHHHhhccCCCCCHHHHHHHHHHhCCCCcceEEecccchhhhhhhhHHH
Q 026974 61 GGFRALKKRKLTAEQAELLEMHFGNEHKLESDRKDKLAAELGLDPRQVAVWFQNRRARDKTKKIEE 126 (230)
Q Consensus 61 ~~~~~r~r~~~t~~Q~~~Le~~F~~~~~p~~~~r~~La~~lgL~~~qV~vWFqNRR~k~kr~~~~~ 126 (230)
.+.+||||..+|+.|+.+||+.|..|.|++.++|.+|++.|+|++|||+|||||||+|.||...+.
T Consensus 232 ~~~~RKKRcPYTK~QtlELEkEFlfN~YitkeKR~ElSr~lNLTeRQVKIWFQNRRMK~KK~~re~ 297 (308)
T KOG0487|consen 232 ARRGRKKRCPYTKHQTLELEKEFLFNMYITKEKRLELSRTLNLTERQVKIWFQNRRMKEKKVNREN 297 (308)
T ss_pred ccccccccCCchHHHHHHHHHHHHHHHHHhHHHHHHHHHhcccchhheeeeehhhhhHHhhhhhhh
Confidence 467888899999999999999999999999999999999999999999999999999999876433
No 6
>KOG0488 consensus Transcription factor BarH and related HOX domain proteins [General function prediction only]
Probab=99.72 E-value=2.9e-18 Score=152.83 Aligned_cols=66 Identities=33% Similarity=0.427 Sum_probs=61.5
Q ss_pred CCCcccccccCCCHHHHHHHHHhhccCCCCCHHHHHHHHHHhCCCCcceEEecccchhhhhhhhHH
Q 026974 60 NGGFRALKKRKLTAEQAELLEMHFGNEHKLESDRKDKLAAELGLDPRQVAVWFQNRRARDKTKKIE 125 (230)
Q Consensus 60 ~~~~~~r~r~~~t~~Q~~~Le~~F~~~~~p~~~~r~~La~~lgL~~~qV~vWFqNRR~k~kr~~~~ 125 (230)
..+++|+.|+.||..|+..||+.|+..+|++..+|.+||..|||+..||++||||||+||||+..+
T Consensus 168 ~pkK~RksRTaFT~~Ql~~LEkrF~~QKYLS~~DR~~LA~~LgLTdaQVKtWfQNRRtKWKrq~a~ 233 (309)
T KOG0488|consen 168 TPKKRRKSRTAFSDHQLFELEKRFEKQKYLSVADRIELAASLGLTDAQVKTWFQNRRTKWKRQTAE 233 (309)
T ss_pred CCcccccchhhhhHHHHHHHHHHHHHhhcccHHHHHHHHHHcCCchhhHHHHHhhhhHHHHHHHHh
Confidence 346777889999999999999999999999999999999999999999999999999999987654
No 7
>KOG0843 consensus Transcription factor EMX1 and related HOX domain proteins [Transcription]
Probab=99.68 E-value=2.2e-17 Score=134.02 Aligned_cols=64 Identities=33% Similarity=0.457 Sum_probs=60.6
Q ss_pred cccccccCCCHHHHHHHHHhhccCCCCCHHHHHHHHHHhCCCCcceEEecccchhhhhhhhHHH
Q 026974 63 FRALKKRKLTAEQAELLEMHFGNEHKLESDRKDKLAAELGLDPRQVAVWFQNRRARDKTKKIEE 126 (230)
Q Consensus 63 ~~~r~r~~~t~~Q~~~Le~~F~~~~~p~~~~r~~La~~lgL~~~qV~vWFqNRR~k~kr~~~~~ 126 (230)
+.||.||.||.+|+..||..|+.++|....+|+.||..|+|++.||+|||||||.|.||.+.++
T Consensus 101 ~~kr~RT~ft~~Ql~~LE~~F~~~~Yvvg~eR~~LA~~L~LsetQVkvWFQNRRtk~kr~~~e~ 164 (197)
T KOG0843|consen 101 RPKRIRTAFTPEQLLKLEHAFEGNQYVVGAERKQLAQSLSLSETQVKVWFQNRRTKHKRMQQED 164 (197)
T ss_pred CCCccccccCHHHHHHHHHHHhcCCeeechHHHHHHHHcCCChhHhhhhhhhhhHHHHHHHHHh
Confidence 5678899999999999999999999999999999999999999999999999999999987664
No 8
>KOG0492 consensus Transcription factor MSH, contains HOX domain [General function prediction only]
Probab=99.68 E-value=6.3e-17 Score=134.02 Aligned_cols=62 Identities=29% Similarity=0.442 Sum_probs=58.1
Q ss_pred CcccccccCCCHHHHHHHHHhhccCCCCCHHHHHHHHHHhCCCCcceEEecccchhhhhhhh
Q 026974 62 GFRALKKRKLTAEQAELLEMHFGNEHKLESDRKDKLAAELGLDPRQVAVWFQNRRARDKTKK 123 (230)
Q Consensus 62 ~~~~r~r~~~t~~Q~~~Le~~F~~~~~p~~~~r~~La~~lgL~~~qV~vWFqNRR~k~kr~~ 123 (230)
...|+.|+.||.+||..||+.|+..+|+++.+|.+++..|.|++.||+|||||||+|.||.+
T Consensus 142 k~nRkPRtPFTtqQLlaLErkfrekqYLSiaEraefSsSL~LTeTqVKIWFQNRRAKaKRlQ 203 (246)
T KOG0492|consen 142 KPNRKPRTPFTTQQLLALERKFREKQYLSIAERAEFSSSLELTETQVKIWFQNRRAKAKRLQ 203 (246)
T ss_pred CCCCCCCCCCCHHHHHHHHHHHhHhhhhhHHHHHhhhhhhhhhhhheehhhhhhhHHHHHHH
Confidence 34578899999999999999999999999999999999999999999999999999999754
No 9
>KOG0850 consensus Transcription factor DLX and related proteins with LIM Zn-binding and HOX domains [Transcription]
Probab=99.66 E-value=4.7e-17 Score=136.75 Aligned_cols=70 Identities=34% Similarity=0.481 Sum_probs=64.5
Q ss_pred CCCCCCCCcccccccCCCHHHHHHHHHhhccCCCCCHHHHHHHHHHhCCCCcceEEecccchhhhhhhhH
Q 026974 55 RNTNGNGGFRALKKRKLTAEQAELLEMHFGNEHKLESDRKDKLAAELGLDPRQVAVWFQNRRARDKTKKI 124 (230)
Q Consensus 55 ~~~~~~~~~~~r~r~~~t~~Q~~~Le~~F~~~~~p~~~~r~~La~~lgL~~~qV~vWFqNRR~k~kr~~~ 124 (230)
++.++++.|-||.||.|+.-||..|.+.|++++|+-..+|.+||..|||+..||||||||||.|.||...
T Consensus 113 ~~~Ngk~KK~RKPRTIYSS~QLqaL~rRFQkTQYLALPERAeLAAsLGLTQTQVKIWFQNrRSK~KKl~k 182 (245)
T KOG0850|consen 113 RRPNGKGKKVRKPRTIYSSLQLQALNRRFQQTQYLALPERAELAASLGLTQTQVKIWFQNRRSKFKKLKK 182 (245)
T ss_pred eccCCCcccccCCcccccHHHHHHHHHHHhhcchhcCcHHHHHHHHhCCchhHhhhhhhhhHHHHHHHHh
Confidence 4455778888899999999999999999999999999999999999999999999999999999997643
No 10
>KOG2251 consensus Homeobox transcription factor [Transcription]
Probab=99.65 E-value=7.3e-17 Score=134.97 Aligned_cols=63 Identities=29% Similarity=0.492 Sum_probs=58.3
Q ss_pred ccccccCCCHHHHHHHHHhhccCCCCCHHHHHHHHHHhCCCCcceEEecccchhhhhhhhHHH
Q 026974 64 RALKKRKLTAEQAELLEMHFGNEHKLESDRKDKLAAELGLDPRQVAVWFQNRRARDKTKKIEE 126 (230)
Q Consensus 64 ~~r~r~~~t~~Q~~~Le~~F~~~~~p~~~~r~~La~~lgL~~~qV~vWFqNRR~k~kr~~~~~ 126 (230)
++|.||+|+..|+.+||..|.+.+||+...|++||.+|+|.+.+|+|||+|||+|+|+++..+
T Consensus 37 qRRERTtFtr~QlevLe~LF~kTqYPDv~~rEelAlklnLpeSrVqVWFKNRRAK~r~qq~qq 99 (228)
T KOG2251|consen 37 QRRERTTFTRKQLEVLEALFAKTQYPDVFMREELALKLNLPESRVQVWFKNRRAKCRRQQQQQ 99 (228)
T ss_pred cccccceecHHHHHHHHHHHHhhcCccHHHHHHHHHHhCCchhhhhhhhccccchhhHhhhhh
Confidence 446778899999999999999999999999999999999999999999999999999876543
No 11
>KOG0484 consensus Transcription factor PHOX2/ARIX, contains HOX domain [Transcription]
Probab=99.65 E-value=2.8e-17 Score=122.25 Aligned_cols=60 Identities=28% Similarity=0.475 Sum_probs=56.3
Q ss_pred ccccccCCCHHHHHHHHHhhccCCCCCHHHHHHHHHHhCCCCcceEEecccchhhhhhhh
Q 026974 64 RALKKRKLTAEQAELLEMHFGNEHKLESDRKDKLAAELGLDPRQVAVWFQNRRARDKTKK 123 (230)
Q Consensus 64 ~~r~r~~~t~~Q~~~Le~~F~~~~~p~~~~r~~La~~lgL~~~qV~vWFqNRR~k~kr~~ 123 (230)
.+|-|+.||..||..||+.|...|||+.-.|++||.++.|++..|||||||||+|.|++.
T Consensus 17 QRRIRTTFTS~QLkELErvF~ETHYPDIYTREEiA~kidLTEARVQVWFQNRRAKfRKQE 76 (125)
T KOG0484|consen 17 QRRIRTTFTSAQLKELERVFAETHYPDIYTREEIALKIDLTEARVQVWFQNRRAKFRKQE 76 (125)
T ss_pred hhhhhhhhhHHHHHHHHHHHHhhcCCcchhHHHHHHhhhhhHHHHHHHHHhhHHHHHHHH
Confidence 446678899999999999999999999999999999999999999999999999999764
No 12
>KOG0485 consensus Transcription factor NKX-5.1/HMX1, contains HOX domain [Transcription]
Probab=99.63 E-value=8.7e-17 Score=134.03 Aligned_cols=62 Identities=32% Similarity=0.408 Sum_probs=58.1
Q ss_pred CcccccccCCCHHHHHHHHHhhccCCCCCHHHHHHHHHHhCCCCcceEEecccchhhhhhhh
Q 026974 62 GFRALKKRKLTAEQAELLEMHFGNEHKLESDRKDKLAAELGLDPRQVAVWFQNRRARDKTKK 123 (230)
Q Consensus 62 ~~~~r~r~~~t~~Q~~~Le~~F~~~~~p~~~~r~~La~~lgL~~~qV~vWFqNRR~k~kr~~ 123 (230)
.++||.||+|+..|+..||..|+..+|++..+|.-||.+|.|++.||||||||||.||||+-
T Consensus 102 ~RKKktRTvFSraQV~qLEs~Fe~krYLSsaeRa~LA~sLqLTETQVKIWFQNRRnKwKRq~ 163 (268)
T KOG0485|consen 102 DRKKKTRTVFSRAQVFQLESTFELKRYLSSAERAGLAASLQLTETQVKIWFQNRRNKWKRQY 163 (268)
T ss_pred cccccchhhhhHHHHHHHHHHHHHHhhhhHHHHhHHHHhhhhhhhhhhhhhhhhhHHHHHHH
Confidence 35567788999999999999999999999999999999999999999999999999999874
No 13
>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=1.8e-16 Score=107.12 Aligned_cols=57 Identities=40% Similarity=0.648 Sum_probs=54.2
Q ss_pred cccccCCCHHHHHHHHHhhccCCCCCHHHHHHHHHHhCCCCcceEEecccchhhhhh
Q 026974 65 ALKKRKLTAEQAELLEMHFGNEHKLESDRKDKLAAELGLDPRQVAVWFQNRRARDKT 121 (230)
Q Consensus 65 ~r~r~~~t~~Q~~~Le~~F~~~~~p~~~~r~~La~~lgL~~~qV~vWFqNRR~k~kr 121 (230)
|++|+.||.+|+.+|+..|..++||+..+++.||..|||+..+|++||+|||+++|+
T Consensus 1 kr~r~~~t~~q~~~L~~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrR~k~kk 57 (57)
T PF00046_consen 1 KRKRTRFTKEQLKVLEEYFQENPYPSKEEREELAKELGLTERQVKNWFQNRRRKEKK 57 (57)
T ss_dssp SSSSSSSSHHHHHHHHHHHHHSSSCHHHHHHHHHHHHTSSHHHHHHHHHHHHHHHHH
T ss_pred CcCCCCCCHHHHHHHHHHHHHhccccccccccccccccccccccccCHHHhHHHhCc
Confidence 466788999999999999999999999999999999999999999999999999985
No 14
>KOG0848 consensus Transcription factor Caudal, contains HOX domain [Transcription]
Probab=99.60 E-value=2.1e-16 Score=135.29 Aligned_cols=61 Identities=38% Similarity=0.556 Sum_probs=56.2
Q ss_pred ccccCCCHHHHHHHHHhhccCCCCCHHHHHHHHHHhCCCCcceEEecccchhhhhhhhHHH
Q 026974 66 LKKRKLTAEQAELLEMHFGNEHKLESDRKDKLAAELGLDPRQVAVWFQNRRARDKTKKIEE 126 (230)
Q Consensus 66 r~r~~~t~~Q~~~Le~~F~~~~~p~~~~r~~La~~lgL~~~qV~vWFqNRR~k~kr~~~~~ 126 (230)
|-|.++|+.|..+||+.|...+|+++.++.+||..|||++|||||||||||+|+||.++.+
T Consensus 201 KYRvVYTDhQRLELEKEfh~SryITirRKSELA~~LgLsERQVKIWFQNRRAKERK~nKKk 261 (317)
T KOG0848|consen 201 KYRVVYTDHQRLELEKEFHTSRYITIRRKSELAATLGLSERQVKIWFQNRRAKERKDNKKK 261 (317)
T ss_pred ceeEEecchhhhhhhhhhccccceeeehhHHHHHhhCccHhhhhHhhhhhhHHHHHHHHHH
Confidence 4467899999999999999999999999999999999999999999999999999875433
No 15
>KOG3802 consensus Transcription factor OCT-1, contains POU and HOX domains [Transcription]
Probab=99.57 E-value=5.7e-16 Score=139.51 Aligned_cols=100 Identities=23% Similarity=0.290 Sum_probs=76.3
Q ss_pred CCCCcccccccCCCCCCCCCCCCCCCCCCCCCCccccCCCCCCCCCCcccccccCCCHHHHHHHHHhhccCCCCCHHHHH
Q 026974 16 DNKSNMVLLSQFYPSDVLTPTGIVPQQGEPSKPKRRQRKRNTNGNGGFRALKKRKLTAEQAELLEMHFGNEHKLESDRKD 95 (230)
Q Consensus 16 ~~~~~m~~ls~~~p~~~~~~~~~~~~~~~~~~p~~~~~~~~~~~~~~~~~r~r~~~t~~Q~~~Le~~F~~~~~p~~~~r~ 95 (230)
-+=-|||.|.+++-.|+-.........+ ..++..- +..+++|||||.|....+..||++|..|++|+.+++.
T Consensus 254 LSFKNMCKLKPLL~KWLeEAes~~~~~~-~~~~e~i-------~a~~RkRKKRTSie~~vr~aLE~~F~~npKPt~qEIt 325 (398)
T KOG3802|consen 254 LSFKNMCKLKPLLEKWLEEAESRESTGS-PNSIEKI-------GAQSRKRKKRTSIEVNVRGALEKHFLKNPKPTSQEIT 325 (398)
T ss_pred cCHHHHhhhHHHHHHHHHHHhcccccCC-CCCHHHh-------hccccccccccceeHHHHHHHHHHHHhCCCCCHHHHH
Confidence 3445899999999999866544211111 1111100 0111445677889999999999999999999999999
Q ss_pred HHHHHhCCCCcceEEecccchhhhhhhh
Q 026974 96 KLAAELGLDPRQVAVWFQNRRARDKTKK 123 (230)
Q Consensus 96 ~La~~lgL~~~qV~vWFqNRR~k~kr~~ 123 (230)
.||.+|+|.+.+|+|||||||.|.||..
T Consensus 326 ~iA~~L~leKEVVRVWFCNRRQkeKR~~ 353 (398)
T KOG3802|consen 326 HIAESLQLEKEVVRVWFCNRRQKEKRIT 353 (398)
T ss_pred HHHHHhccccceEEEEeeccccccccCC
Confidence 9999999999999999999999999864
No 16
>KOG0494 consensus Transcription factor CHX10 and related HOX domain proteins [General function prediction only]
Probab=99.56 E-value=1.4e-15 Score=129.87 Aligned_cols=60 Identities=30% Similarity=0.398 Sum_probs=56.2
Q ss_pred ccccCCCHHHHHHHHHhhccCCCCCHHHHHHHHHHhCCCCcceEEecccchhhhhhhhHH
Q 026974 66 LKKRKLTAEQAELLEMHFGNEHKLESDRKDKLAAELGLDPRQVAVWFQNRRARDKTKKIE 125 (230)
Q Consensus 66 r~r~~~t~~Q~~~Le~~F~~~~~p~~~~r~~La~~lgL~~~qV~vWFqNRR~k~kr~~~~ 125 (230)
+-||.||..|+..||+.|+..+||+...|+.||.++.|.+.+|+|||||||+||||...+
T Consensus 143 h~RTiFT~~Qle~LEkaFkeaHYPDv~Are~la~ktelpEDRIqVWfQNRRAKWRk~Ek~ 202 (332)
T KOG0494|consen 143 HFRTIFTSYQLEELEKAFKEAHYPDVYAREMLADKTELPEDRIQVWFQNRRAKWRKTEKR 202 (332)
T ss_pred cccchhhHHHHHHHHHHHhhccCccHHHHHHHhhhccCchhhhhHHhhhhhHHhhhhhhh
Confidence 347889999999999999999999999999999999999999999999999999987544
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=99.50 E-value=3e-14 Score=96.68 Aligned_cols=52 Identities=21% Similarity=0.355 Sum_probs=49.5
Q ss_pred cccccCCCHHHHHHHHHhhccCCC----CCHHHHHHHHHHhCCCCcceEEecccch
Q 026974 65 ALKKRKLTAEQAELLEMHFGNEHK----LESDRKDKLAAELGLDPRQVAVWFQNRR 116 (230)
Q Consensus 65 ~r~r~~~t~~Q~~~Le~~F~~~~~----p~~~~r~~La~~lgL~~~qV~vWFqNRR 116 (230)
+|.||.||.+|+..||..|..++| |+...+++||..|||++++|+|||||-+
T Consensus 2 kR~RT~Ft~~Q~~~Le~~fe~~~y~~~~~~~~~r~~la~~lgl~~~vvKVWfqN~k 57 (58)
T TIGR01565 2 KRRRTKFTAEQKEKMRDFAEKLGWKLKDKRREEVREFCEEIGVTRKVFKVWMHNNK 57 (58)
T ss_pred CCCCCCCCHHHHHHHHHHHHHcCCCCCCCCHHHHHHHHHHhCCCHHHeeeecccCC
Confidence 577888999999999999999999 9999999999999999999999999964
No 18
>smart00389 HOX Homeodomain. DNA-binding factors that are involved in the transcriptional regulation of key developmental processes
Probab=99.48 E-value=1.4e-14 Score=97.17 Aligned_cols=55 Identities=47% Similarity=0.675 Sum_probs=51.4
Q ss_pred ccccCCCHHHHHHHHHhhccCCCCCHHHHHHHHHHhCCCCcceEEecccchhhhh
Q 026974 66 LKKRKLTAEQAELLEMHFGNEHKLESDRKDKLAAELGLDPRQVAVWFQNRRARDK 120 (230)
Q Consensus 66 r~r~~~t~~Q~~~Le~~F~~~~~p~~~~r~~La~~lgL~~~qV~vWFqNRR~k~k 120 (230)
+.|+.|+.+|+.+|+..|..++||+..++..||..+||+..+|+.||+|||++.+
T Consensus 2 k~r~~~~~~~~~~L~~~f~~~~~P~~~~~~~la~~~~l~~~qV~~WF~nrR~~~~ 56 (56)
T smart00389 2 RKRTSFTPEQLEELEKEFQKNPYPSREEREELAAKLGLSERQVKVWFQNRRAKWK 56 (56)
T ss_pred CCCCcCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHHCcCHHHHHHhHHHHhhccC
Confidence 4456699999999999999999999999999999999999999999999998864
No 19
>cd00086 homeodomain Homeodomain; DNA binding domains involved in the transcriptional regulation of key eukaryotic developmental processes; may bind to DNA as monomers or as homo- and/or heterodimers, in a sequence-specific manner.
Probab=99.47 E-value=2e-14 Score=97.17 Aligned_cols=57 Identities=44% Similarity=0.668 Sum_probs=53.2
Q ss_pred ccccCCCHHHHHHHHHhhccCCCCCHHHHHHHHHHhCCCCcceEEecccchhhhhhh
Q 026974 66 LKKRKLTAEQAELLEMHFGNEHKLESDRKDKLAAELGLDPRQVAVWFQNRRARDKTK 122 (230)
Q Consensus 66 r~r~~~t~~Q~~~Le~~F~~~~~p~~~~r~~La~~lgL~~~qV~vWFqNRR~k~kr~ 122 (230)
+.+..++..|+.+|+..|..++||+..+++.||..+||+..+|+.||+|||++.++.
T Consensus 2 ~~r~~~~~~~~~~Le~~f~~~~~P~~~~~~~la~~~~l~~~qV~~WF~nrR~~~~~~ 58 (59)
T cd00086 2 RKRTRFTPEQLEELEKEFEKNPYPSREEREELAKELGLTERQVKIWFQNRRAKLKRS 58 (59)
T ss_pred CCCCcCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHHCcCHHHHHHHHHHHHHHHhcc
Confidence 445679999999999999999999999999999999999999999999999998863
No 20
>COG5576 Homeodomain-containing transcription factor [Transcription]
Probab=99.46 E-value=4.5e-14 Score=114.30 Aligned_cols=64 Identities=34% Similarity=0.479 Sum_probs=58.1
Q ss_pred CcccccccCCCHHHHHHHHHhhccCCCCCHHHHHHHHHHhCCCCcceEEecccchhhhhhhhHH
Q 026974 62 GFRALKKRKLTAEQAELLEMHFGNEHKLESDRKDKLAAELGLDPRQVAVWFQNRRARDKTKKIE 125 (230)
Q Consensus 62 ~~~~r~r~~~t~~Q~~~Le~~F~~~~~p~~~~r~~La~~lgL~~~qV~vWFqNRR~k~kr~~~~ 125 (230)
...+++|++.|..|+.+|++.|..++||+...|..|+..|+|+++-|++||||||++.|+....
T Consensus 49 ~~~~~~r~R~t~~Q~~vL~~~F~i~p~Ps~~~r~~L~~~lnm~~ksVqIWFQNkR~~~k~~~~~ 112 (156)
T COG5576 49 SPPKSKRRRTTDEQLMVLEREFEINPYPSSITRIKLSLLLNMPPKSVQIWFQNKRAKEKKKRSG 112 (156)
T ss_pred CcCcccceechHHHHHHHHHHhccCCCCCHHHHHHHHHhcCCChhhhhhhhchHHHHHHHhccc
Confidence 4455667779999999999999999999999999999999999999999999999999987544
No 21
>KOG0844 consensus Transcription factor EVX1, contains HOX domain [Transcription]
Probab=99.45 E-value=2.4e-14 Score=124.69 Aligned_cols=64 Identities=34% Similarity=0.496 Sum_probs=59.8
Q ss_pred CcccccccCCCHHHHHHHHHhhccCCCCCHHHHHHHHHHhCCCCcceEEecccchhhhhhhhHH
Q 026974 62 GFRALKKRKLTAEQAELLEMHFGNEHKLESDRKDKLAAELGLDPRQVAVWFQNRRARDKTKKIE 125 (230)
Q Consensus 62 ~~~~r~r~~~t~~Q~~~Le~~F~~~~~p~~~~r~~La~~lgL~~~qV~vWFqNRR~k~kr~~~~ 125 (230)
..-||-||.||.+|+..||+.|-+..|.+..+|.+||..|+|++..|||||||||+|+||+++.
T Consensus 179 dqmRRYRTAFTReQIaRLEKEFyrENYVSRprRcELAAaLNLPEtTIKVWFQNRRMKDKRQRla 242 (408)
T KOG0844|consen 179 DQMRRYRTAFTREQIARLEKEFYRENYVSRPRRCELAAALNLPETTIKVWFQNRRMKDKRQRLA 242 (408)
T ss_pred HHHHHHHhhhhHHHHHHHHHHHHHhccccCchhhhHHHhhCCCcceeehhhhhchhhhhhhhhh
Confidence 3446779999999999999999999999999999999999999999999999999999998765
No 22
>KOG0491 consensus Transcription factor BSH, contains HOX domain [General function prediction only]
Probab=99.42 E-value=1.3e-14 Score=116.30 Aligned_cols=61 Identities=31% Similarity=0.486 Sum_probs=57.4
Q ss_pred cccccccCCCHHHHHHHHHhhccCCCCCHHHHHHHHHHhCCCCcceEEecccchhhhhhhh
Q 026974 63 FRALKKRKLTAEQAELLEMHFGNEHKLESDRKDKLAAELGLDPRQVAVWFQNRRARDKTKK 123 (230)
Q Consensus 63 ~~~r~r~~~t~~Q~~~Le~~F~~~~~p~~~~r~~La~~lgL~~~qV~vWFqNRR~k~kr~~ 123 (230)
++++-|++|+..|+..||+.|+..+|++..++.+||..|+|++.||+.||||||+|.||..
T Consensus 99 ~r~K~Rtvfs~~ql~~l~~rFe~QrYLS~~e~~ELan~L~LS~~QVKTWFQNrRMK~Kk~~ 159 (194)
T KOG0491|consen 99 RRRKARTVFSDPQLSGLEKRFERQRYLSTPERQELANALSLSETQVKTWFQNRRMKHKKQQ 159 (194)
T ss_pred HhhhhcccccCccccccHHHHhhhhhcccHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHHH
Confidence 4567789999999999999999999999999999999999999999999999999999764
No 23
>KOG4577 consensus Transcription factor LIM3, contains LIM and HOX domains [Transcription]
Probab=99.40 E-value=2.3e-13 Score=117.89 Aligned_cols=66 Identities=35% Similarity=0.534 Sum_probs=60.8
Q ss_pred CCcccccccCCCHHHHHHHHHhhccCCCCCHHHHHHHHHHhCCCCcceEEecccchhhhhhhhHHH
Q 026974 61 GGFRALKKRKLTAEQAELLEMHFGNEHKLESDRKDKLAAELGLDPRQVAVWFQNRRARDKTKKIEE 126 (230)
Q Consensus 61 ~~~~~r~r~~~t~~Q~~~Le~~F~~~~~p~~~~r~~La~~lgL~~~qV~vWFqNRR~k~kr~~~~~ 126 (230)
....||.||++|..||+.|...|+..+.|-...|++|+.++||.-+.|||||||||||+||.++..
T Consensus 164 d~~nKRPRTTItAKqLETLK~AYn~SpKPARHVREQLsseTGLDMRVVQVWFQNRRAKEKRLKKDA 229 (383)
T KOG4577|consen 164 DASNKRPRTTITAKQLETLKQAYNTSPKPARHVREQLSSETGLDMRVVQVWFQNRRAKEKRLKKDA 229 (383)
T ss_pred ccccCCCcceeeHHHHHHHHHHhcCCCchhHHHHHHhhhccCcceeehhhhhhhhhHHHHhhhhhc
Confidence 445678899999999999999999999999999999999999999999999999999999876554
No 24
>KOG0486 consensus Transcription factor PTX1, contains HOX domain [Transcription]
Probab=99.34 E-value=5.3e-13 Score=116.87 Aligned_cols=65 Identities=23% Similarity=0.408 Sum_probs=59.5
Q ss_pred cccccccCCCHHHHHHHHHhhccCCCCCHHHHHHHHHHhCCCCcceEEecccchhhhhhhhHHHH
Q 026974 63 FRALKKRKLTAEQAELLEMHFGNEHKLESDRKDKLAAELGLDPRQVAVWFQNRRARDKTKKIEET 127 (230)
Q Consensus 63 ~~~r~r~~~t~~Q~~~Le~~F~~~~~p~~~~r~~La~~lgL~~~qV~vWFqNRR~k~kr~~~~~~ 127 (230)
+++|.|+.||.+|+..||..|.+++||+...|++||.-++|++..|+|||.|||+|||++..-..
T Consensus 111 KqrrQrthFtSqqlqele~tF~rNrypdMstrEEIavwtNlTE~rvrvwfknrrakwrkrErN~~ 175 (351)
T KOG0486|consen 111 KQRRQRTHFTSQQLQELEATFQRNRYPDMSTREEIAVWTNLTEARVRVWFKNRRAKWRKRERNQQ 175 (351)
T ss_pred hhhhhhhhhHHHHHHHHHHHHhhccCCccchhhHHHhhccccchhhhhhcccchhhhhhhhhhHH
Confidence 45677888999999999999999999999999999999999999999999999999998754444
No 25
>KOG0847 consensus Transcription factor, contains HOX domain [Transcription]
Probab=99.29 E-value=6.1e-13 Score=111.32 Aligned_cols=66 Identities=35% Similarity=0.514 Sum_probs=59.2
Q ss_pred CCcccccccCCCHHHHHHHHHhhccCCCCCHHHHHHHHHHhCCCCcceEEecccchhhhhhhhHHH
Q 026974 61 GGFRALKKRKLTAEQAELLEMHFGNEHKLESDRKDKLAAELGLDPRQVAVWFQNRRARDKTKKIEE 126 (230)
Q Consensus 61 ~~~~~r~r~~~t~~Q~~~Le~~F~~~~~p~~~~r~~La~~lgL~~~qV~vWFqNRR~k~kr~~~~~ 126 (230)
+++++..|.+|+-.|+..||..|...+|+-..++.+||..+|+++.||+|||||||+||||+...+
T Consensus 164 dG~rk~srPTf~g~qi~~le~~feqtkylaG~~ra~lA~~lgmteSqvkVWFQNRRTKWRKkhAaE 229 (288)
T KOG0847|consen 164 NGQRKQSRPTFTGHQIYQLERKFEQTKYLAGADRAQLAQELNMTESQVKVWFQNRRTKWRKKHAAE 229 (288)
T ss_pred CccccccCCCccchhhhhhhhhhhhhhcccchhHHHhhccccccHHHHHHHHhcchhhhhhhhccc
Confidence 355556677899999999999999999999999999999999999999999999999999875443
No 26
>KOG1168 consensus Transcription factor ACJ6/BRN-3, contains POU and HOX domains [Transcription]
Probab=99.20 E-value=1.7e-12 Score=112.58 Aligned_cols=99 Identities=23% Similarity=0.335 Sum_probs=77.7
Q ss_pred CCCCcccccccCCCCCCCCCCCCCCCCCCCCCCccccCCCC--CCCCCCcccccccCCCHHHHHHHHHhhccCCCCCHHH
Q 026974 16 DNKSNMVLLSQFYPSDVLTPTGIVPQQGEPSKPKRRQRKRN--TNGNGGFRALKKRKLTAEQAELLEMHFGNEHKLESDR 93 (230)
Q Consensus 16 ~~~~~m~~ls~~~p~~~~~~~~~~~~~~~~~~p~~~~~~~~--~~~~~~~~~r~r~~~t~~Q~~~Le~~F~~~~~p~~~~ 93 (230)
-+.+||+-+.+++.+|....... -+.+.++.- .--.++.+||+||.+...+.+.||.+|..++.|+.+.
T Consensus 268 LSHNNMiALKPILqaWLEeAE~a---------~keK~~~pd~~~l~~~~ekKRKRTSIAAPEKRsLEayFavQPRPS~Ek 338 (385)
T KOG1168|consen 268 LSHNNMIALKPILQAWLEEAEAA---------MKEKDTKPDINELLPGGEKKRKRTSIAAPEKRSLEAYFAVQPRPSGEK 338 (385)
T ss_pred cccCcchhhhHHHHHHHHHHHHH---------HHhhccCCchhhccCccccccccccccCcccccHHHHhccCCCCchhH
Confidence 46778999999998887653211 111211111 1124567788888899999999999999999999999
Q ss_pred HHHHHHHhCCCCcceEEecccchhhhhhhh
Q 026974 94 KDKLAAELGLDPRQVAVWFQNRRARDKTKK 123 (230)
Q Consensus 94 r~~La~~lgL~~~qV~vWFqNRR~k~kr~~ 123 (230)
+..||++|.|.+..|+|||||.|.|.||.+
T Consensus 339 IAaIAekLDLKKNVVRVWFCNQRQKQKRm~ 368 (385)
T KOG1168|consen 339 IAAIAEKLDLKKNVVRVWFCNQRQKQKRMK 368 (385)
T ss_pred HHHHHHhhhhhhceEEEEeeccHHHHHHhh
Confidence 999999999999999999999999999854
No 27
>KOG0490 consensus Transcription factor, contains HOX domain [General function prediction only]
Probab=99.14 E-value=2.4e-11 Score=103.36 Aligned_cols=62 Identities=34% Similarity=0.374 Sum_probs=57.5
Q ss_pred CcccccccCCCHHHHHHHHHhhccCCCCCHHHHHHHHHHhCCCCcceEEecccchhhhhhhh
Q 026974 62 GFRALKKRKLTAEQAELLEMHFGNEHKLESDRKDKLAAELGLDPRQVAVWFQNRRARDKTKK 123 (230)
Q Consensus 62 ~~~~r~r~~~t~~Q~~~Le~~F~~~~~p~~~~r~~La~~lgL~~~qV~vWFqNRR~k~kr~~ 123 (230)
.++++.|+.|+..|+.+||+.|...|||+...++.||..+++++..|++||||||++|+++.
T Consensus 58 ~~~rr~rt~~~~~ql~~ler~f~~~h~Pd~~~r~~la~~~~~~e~rVqvwFqnrrak~r~~~ 119 (235)
T KOG0490|consen 58 FSKRCARCKFTISQLDELERAFEKVHLPCFACRECLALLLTGDEFRVQVWFQNRRAKDRKEE 119 (235)
T ss_pred ccccccCCCCCcCHHHHHHHhhcCCCcCccchHHHHhhcCCCCeeeeehhhhhhcHhhhhhh
Confidence 34556778899999999999999999999999999999999999999999999999999765
No 28
>KOG0849 consensus Transcription factor PRD and related proteins, contain PAX and HOX domains [Transcription]
Probab=98.92 E-value=6e-10 Score=101.46 Aligned_cols=64 Identities=30% Similarity=0.376 Sum_probs=59.1
Q ss_pred CCcccccccCCCHHHHHHHHHhhccCCCCCHHHHHHHHHHhCCCCcceEEecccchhhhhhhhH
Q 026974 61 GGFRALKKRKLTAEQAELLEMHFGNEHKLESDRKDKLAAELGLDPRQVAVWFQNRRARDKTKKI 124 (230)
Q Consensus 61 ~~~~~r~r~~~t~~Q~~~Le~~F~~~~~p~~~~r~~La~~lgL~~~qV~vWFqNRR~k~kr~~~ 124 (230)
+.++++.|++|+..|+..||+.|+.++||+...|+.||.++++++..|++||+|||++++|...
T Consensus 173 ~~~~rr~rtsft~~Q~~~le~~f~rt~yP~i~~Re~La~~i~l~e~riqvwf~nrra~~rr~~~ 236 (354)
T KOG0849|consen 173 QRGGRRNRTSFSPSQLEALEECFQRTPYPDIVGRETLAKETGLPEPRVQVWFQNRRAKWRRQHR 236 (354)
T ss_pred cccccccccccccchHHHHHHHhcCCCCCchhhHHHHhhhccCCchHHHHHHhhhhhhhhhccc
Confidence 4455677889999999999999999999999999999999999999999999999999998754
No 29
>KOG0775 consensus Transcription factor SIX and related HOX domain proteins [Transcription]
Probab=98.86 E-value=2.1e-09 Score=92.85 Aligned_cols=63 Identities=25% Similarity=0.283 Sum_probs=55.0
Q ss_pred CCCCcccccccCCCHHHHHHHHHhhccCCCCCHHHHHHHHHHhCCCCcceEEecccchhhhhh
Q 026974 59 GNGGFRALKKRKLTAEQAELLEMHFGNEHKLESDRKDKLAAELGLDPRQVAVWFQNRRARDKT 121 (230)
Q Consensus 59 ~~~~~~~r~r~~~t~~Q~~~Le~~F~~~~~p~~~~r~~La~~lgL~~~qV~vWFqNRR~k~kr 121 (230)
.+-++|--.--.|...-..+|..+|..++||++.++.+||+.+||+..||-.||+|||+|+|.
T Consensus 171 rTIWDGEet~yCFKekSR~~LrewY~~~~YPsp~eKReLA~aTgLt~tQVsNWFKNRRQRDRa 233 (304)
T KOG0775|consen 171 RTIWDGEETVYCFKEKSRSLLREWYLQNPYPSPREKRELAEATGLTITQVSNWFKNRRQRDRA 233 (304)
T ss_pred CccccCceeeeehhHhhHHHHHHHHhcCCCCChHHHHHHHHHhCCchhhhhhhhhhhhhhhhh
Confidence 344555555556788888999999999999999999999999999999999999999999993
No 30
>KOG0774 consensus Transcription factor PBX and related HOX domain proteins [Transcription]
Probab=98.74 E-value=2.9e-08 Score=85.42 Aligned_cols=58 Identities=28% Similarity=0.454 Sum_probs=53.9
Q ss_pred cccccCCCHHHHHHHHHhhc---cCCCCCHHHHHHHHHHhCCCCcceEEecccchhhhhhh
Q 026974 65 ALKKRKLTAEQAELLEMHFG---NEHKLESDRKDKLAAELGLDPRQVAVWFQNRRARDKTK 122 (230)
Q Consensus 65 ~r~r~~~t~~Q~~~Le~~F~---~~~~p~~~~r~~La~~lgL~~~qV~vWFqNRR~k~kr~ 122 (230)
+|+|+.|+..-.++|..+|. .++||+.+.+++||.++|++..||-.||.|+|.+.||.
T Consensus 189 rRKRRNFsK~aTeiLneyF~~h~~nPYPSee~K~eLAkqCnItvsQvsnwfgnkrIrykK~ 249 (334)
T KOG0774|consen 189 RRKRRNFSKQATEILNEYFYSHLSNPYPSEEAKEELAKQCNITVSQVSNWFGNKRIRYKKN 249 (334)
T ss_pred HHhhcccchhHHHHHHHHHHHhcCCCCCcHHHHHHHHHHcCceehhhccccccceeehhhh
Confidence 46777899999999999996 59999999999999999999999999999999999975
No 31
>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=98.21 E-value=1.8e-07 Score=58.80 Aligned_cols=34 Identities=32% Similarity=0.612 Sum_probs=28.9
Q ss_pred cCCCCCHHHHHHHHHHhCCCCcceEEecccchhh
Q 026974 85 NEHKLESDRKDKLAAELGLDPRQVAVWFQNRRAR 118 (230)
Q Consensus 85 ~~~~p~~~~r~~La~~lgL~~~qV~vWFqNRR~k 118 (230)
.++||+.++++.||.++||+..||..||-|.|.|
T Consensus 7 ~nPYPs~~ek~~L~~~tgls~~Qi~~WF~NaRrR 40 (40)
T PF05920_consen 7 HNPYPSKEEKEELAKQTGLSRKQISNWFINARRR 40 (40)
T ss_dssp TSGS--HHHHHHHHHHHTS-HHHHHHHHHHHHHH
T ss_pred CCCCCCHHHHHHHHHHcCCCHHHHHHHHHHhHcc
Confidence 4799999999999999999999999999998865
No 32
>KOG2252 consensus CCAAT displacement protein and related homeoproteins [Transcription]
Probab=98.06 E-value=2.6e-06 Score=80.21 Aligned_cols=62 Identities=18% Similarity=0.217 Sum_probs=56.0
Q ss_pred CCCCcccccccCCCHHHHHHHHHhhccCCCCCHHHHHHHHHHhCCCCcceEEecccchhhhh
Q 026974 59 GNGGFRALKKRKLTAEQAELLEMHFGNEHKLESDRKDKLAAELGLDPRQVAVWFQNRRARDK 120 (230)
Q Consensus 59 ~~~~~~~r~r~~~t~~Q~~~Le~~F~~~~~p~~~~r~~La~~lgL~~~qV~vWFqNRR~k~k 120 (230)
......||.|.+||..|+..|..+|+.+++|+.+..+.|+.+|||...-|..||-|-|.|.+
T Consensus 415 d~~~~~KKPRlVfTd~QkrTL~aiFke~~RPS~Emq~tIS~qL~L~~sTV~NfFmNaRRRsl 476 (558)
T KOG2252|consen 415 DKMLQTKKPRLVFTDIQKRTLQAIFKENKRPSREMQETISQQLNLELSTVINFFMNARRRSL 476 (558)
T ss_pred cccccCCCceeeecHHHHHHHHHHHhcCCCCCHHHHHHHHHHhCCcHHHHHHHHHhhhhhcc
Confidence 33455678899999999999999999999999999999999999999999999999887753
No 33
>KOG0490 consensus Transcription factor, contains HOX domain [General function prediction only]
Probab=97.95 E-value=5.6e-06 Score=70.31 Aligned_cols=62 Identities=37% Similarity=0.567 Sum_probs=56.8
Q ss_pred CcccccccCCCHHHHHHHHHhhccCCCCCHHHHHHHHHHhCCCCcceEEecccchhhhhhhh
Q 026974 62 GFRALKKRKLTAEQAELLEMHFGNEHKLESDRKDKLAAELGLDPRQVAVWFQNRRARDKTKK 123 (230)
Q Consensus 62 ~~~~r~r~~~t~~Q~~~Le~~F~~~~~p~~~~r~~La~~lgL~~~qV~vWFqNRR~k~kr~~ 123 (230)
.+.++.++.+...|+..|+..|...++|+...++.|+..+|++.+.|++||+|+|++.++..
T Consensus 151 ~~~~~~~~~~~~~~~~~~~~~~~~~~~P~~~~~~~l~~~~~~~~~~~q~~~~~~~~~~~~~~ 212 (235)
T KOG0490|consen 151 KKPRRPRTTFTENQLEVLETVFRATPKPDADDREQLAEETGLSERVIQVWFQNRRAKLRKHK 212 (235)
T ss_pred cccCCCccccccchhHhhhhcccCCCCCchhhHHHHHHhcCCChhhhhhhcccHHHHHHhhc
Confidence 44556677899999999999999999999999999999999999999999999999999764
No 34
>KOG1146 consensus Homeobox protein [General function prediction only]
Probab=97.42 E-value=0.00012 Score=75.02 Aligned_cols=63 Identities=24% Similarity=0.386 Sum_probs=58.1
Q ss_pred CcccccccCCCHHHHHHHHHhhccCCCCCHHHHHHHHHHhCCCCcceEEecccchhhhhhhhH
Q 026974 62 GFRALKKRKLTAEQAELLEMHFGNEHKLESDRKDKLAAELGLDPRQVAVWFQNRRARDKTKKI 124 (230)
Q Consensus 62 ~~~~r~r~~~t~~Q~~~Le~~F~~~~~p~~~~r~~La~~lgL~~~qV~vWFqNRR~k~kr~~~ 124 (230)
-.+++.|+.++..|+..|..+|....+|..++.+.|...++|..+.|++||||-|++.|+..+
T Consensus 901 ~~r~a~~~~~~d~qlk~i~~~~~~q~~~~~~~~E~l~~~~~~~~~~i~vw~qna~~~s~k~~~ 963 (1406)
T KOG1146|consen 901 MGRRAYRTQESDLQLKIIKACYEAQRTPTMQECEVLEEPIGLPKRVIQVWFQNARAKSKKAKL 963 (1406)
T ss_pred hhhhhhccchhHHHHHHHHHHHhhccCChHHHHHhhcccccCCcchhHHhhhhhhhhhhhhhh
Confidence 345677889999999999999999999999999999999999999999999999999998755
No 35
>PF11569 Homez: Homeodomain leucine-zipper encoding, Homez; PDB: 2YS9_A.
Probab=96.28 E-value=0.00053 Score=46.04 Aligned_cols=41 Identities=24% Similarity=0.396 Sum_probs=31.1
Q ss_pred HHHHHHhhccCCCCCHHHHHHHHHHhCCCCcceEEecccch
Q 026974 76 AELLEMHFGNEHKLESDRKDKLAAELGLDPRQVAVWFQNRR 116 (230)
Q Consensus 76 ~~~Le~~F~~~~~p~~~~r~~La~~lgL~~~qV~vWFqNRR 116 (230)
+..|+++|...+++.......|..+.+|+..||+.||-.|+
T Consensus 10 ~~pL~~Yy~~h~~L~E~DL~~L~~kS~ms~qqVr~WFa~~~ 50 (56)
T PF11569_consen 10 IQPLEDYYLKHKQLQEEDLDELCDKSRMSYQQVRDWFAERM 50 (56)
T ss_dssp -HHHHHHHHHT----TTHHHHHHHHTT--HHHHHHHHHHHS
T ss_pred hHHHHHHHHHcCCccHhhHHHHHHHHCCCHHHHHHHHHHhc
Confidence 56799999999999999999999999999999999997553
No 36
>KOG0773 consensus Transcription factor MEIS1 and related HOX domain proteins [Transcription]
Probab=96.07 E-value=0.0054 Score=55.60 Aligned_cols=61 Identities=31% Similarity=0.302 Sum_probs=50.2
Q ss_pred cccccCCCHHHHHHHHHhhc---cCCCCCHHHHHHHHHHhCCCCcceEEecccchhhhhhhhHH
Q 026974 65 ALKKRKLTAEQAELLEMHFG---NEHKLESDRKDKLAAELGLDPRQVAVWFQNRRARDKTKKIE 125 (230)
Q Consensus 65 ~r~r~~~t~~Q~~~Le~~F~---~~~~p~~~~r~~La~~lgL~~~qV~vWFqNRR~k~kr~~~~ 125 (230)
.+++..+......+|+.+.. ..+||+...+..||.++||+..||..||-|.|-|..+-...
T Consensus 240 ~r~~~~lP~~a~~ilr~Wl~~h~~~PYPse~~K~~La~~TGLs~~Qv~NWFINaR~R~w~p~~~ 303 (342)
T KOG0773|consen 240 WRPQRGLPKEAVSILRAWLFEHLLHPYPSDDEKLMLAKQTGLSRPQVSNWFINARVRLWKPMIE 303 (342)
T ss_pred CCCCCCCCHHHHHHHHHHHHHhccCCCCcchhccccchhcCCCcccCCchhhhcccccCCchHH
Confidence 34455799999999997743 25799999999999999999999999999998887765443
No 37
>KOG3623 consensus Homeobox transcription factor SIP1 [Transcription]
Probab=92.58 E-value=0.055 Score=53.28 Aligned_cols=47 Identities=21% Similarity=0.393 Sum_probs=43.9
Q ss_pred HHHHHHhhccCCCCCHHHHHHHHHHhCCCCcceEEecccchhhhhhh
Q 026974 76 AELLEMHFGNEHKLESDRKDKLAAELGLDPRQVAVWFQNRRARDKTK 122 (230)
Q Consensus 76 ~~~Le~~F~~~~~p~~~~r~~La~~lgL~~~qV~vWFqNRR~k~kr~ 122 (230)
+.+|..+|..|..|+..+...+|.+.||..+.|+.||+++++.....
T Consensus 568 ~sllkayyaln~~ps~eelskia~qvglp~~vvk~wfE~~~a~e~sv 614 (1007)
T KOG3623|consen 568 TSLLKAYYALNGLPSEEELSKIAQQVGLPFAVVKAWFEDEEAEEMSV 614 (1007)
T ss_pred HHHHHHHHHhcCCCCHHHHHHHHHHhcccHHHHHHHHHhhhhhhhhh
Confidence 77899999999999999999999999999999999999999887754
No 38
>PF04218 CENP-B_N: CENP-B N-terminal DNA-binding domain; InterPro: IPR006695 Centromere Protein B (CENP-B) is a DNA-binding protein localized to the centromere. Within the N-terminal 125 residues, there is a DNA-binding region, which binds to a corresponding 17bp CENP-B box sequence. CENP-B dimers either bind two separate DNA molecules or alternatively, they may bind two CENP-B boxes on one DNA molecule, with the intervening stretch of DNA forming a loop structure. The CENP-B DNA-binding domain consists of two repeating domains, RP1 and RP2. This family corresponds to RP1 has been shown to consist of four helices in a helix-turn-helix structure [].; GO: 0003677 DNA binding, 0000775 chromosome, centromeric region; PDB: 1BW6_A 1HLV_A 2ELH_A.
Probab=91.19 E-value=0.17 Score=33.48 Aligned_cols=46 Identities=22% Similarity=0.332 Sum_probs=32.8
Q ss_pred cccccCCCHHHHHHHHHhhccCCCCCHHHHHHHHHHhCCCCcceEEecccc
Q 026974 65 ALKKRKLTAEQAELLEMHFGNEHKLESDRKDKLAAELGLDPRQVAVWFQNR 115 (230)
Q Consensus 65 ~r~r~~~t~~Q~~~Le~~F~~~~~p~~~~r~~La~~lgL~~~qV~vWFqNR 115 (230)
+++|..+|.++...+-..++... ....||.++|++..+|..|..|+
T Consensus 1 krkR~~LTl~eK~~iI~~~e~g~-----s~~~ia~~fgv~~sTv~~I~K~k 46 (53)
T PF04218_consen 1 KRKRKSLTLEEKLEIIKRLEEGE-----SKRDIAREFGVSRSTVSTILKNK 46 (53)
T ss_dssp SSSSSS--HHHHHHHHHHHHCTT------HHHHHHHHT--CCHHHHHHHCH
T ss_pred CCCCccCCHHHHHHHHHHHHcCC-----CHHHHHHHhCCCHHHHHHHHHhH
Confidence 35677799988877777777665 45679999999999999999874
No 39
>PF02183 HALZ: Homeobox associated leucine zipper; InterPro: IPR003106 This region is a plant specific leucine zipper that is always found associated with a homeobox []. ; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent, 0005634 nucleus
Probab=87.84 E-value=1.2 Score=28.53 Aligned_cols=41 Identities=20% Similarity=0.393 Sum_probs=32.9
Q ss_pred hHHHHHHHHHhhhccchhhhhhhHHHHHHHHHHHHHHHHHH
Q 026974 123 KIEETYATLKTAHENVVVEKTRLESEVATLKEKLSVAEKEI 163 (230)
Q Consensus 123 ~~~~~~~~lk~~~~~~~~~~~~~~~e~~~l~~~~~~~~~e~ 163 (230)
+++..++.|+...+....+...+..|++.|+.++..+...+
T Consensus 2 QlE~Dy~~LK~~yd~Lk~~~~~L~~E~~~L~aev~~L~~kl 42 (45)
T PF02183_consen 2 QLERDYDALKASYDSLKAEYDSLKKENEKLRAEVQELKEKL 42 (45)
T ss_pred chHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Confidence 57788899999998888888888888888887777766544
No 40
>KOG4196 consensus bZIP transcription factor MafK [Transcription]
Probab=83.67 E-value=4.9 Score=31.57 Aligned_cols=89 Identities=19% Similarity=0.215 Sum_probs=48.9
Q ss_pred cCCCHHHHHHHHHhhccCCCCCHHHHHHHH-HHhCCCCcceEEecccchhhhhhhhHHHHHHHHHhhhccchhhhhhhHH
Q 026974 69 RKLTAEQAELLEMHFGNEHKLESDRKDKLA-AELGLDPRQVAVWFQNRRARDKTKKIEETYATLKTAHENVVVEKTRLES 147 (230)
Q Consensus 69 ~~~t~~Q~~~Le~~F~~~~~p~~~~r~~La-~~lgL~~~qV~vWFqNRR~k~kr~~~~~~~~~lk~~~~~~~~~~~~~~~ 147 (230)
..|++++|..+- -| +|= .--|++...|-.|=|.||+-.-|-=...-.-+.-.....+..++..+..
T Consensus 22 d~lsDd~LvsmS------------VR-eLNr~LrG~~reEVvrlKQrRRTLKNRGYA~sCR~KRv~Qk~eLE~~k~~L~q 88 (135)
T KOG4196|consen 22 DRLSDDELVSMS------------VR-ELNRHLRGLSREEVVRLKQRRRTLKNRGYAQSCRVKRVQQKHELEKEKAELQQ 88 (135)
T ss_pred CCcCHHHHHHhh------------HH-HHHHHhcCCCHHHHHHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 349998887662 22 233 3337888888888787765322210000000000111122234555677
Q ss_pred HHHHHHHHHHHHHHHHHHHhhhh
Q 026974 148 EVATLKEKLSVAEKEIKKMSELI 170 (230)
Q Consensus 148 e~~~l~~~~~~~~~e~~~~~~~~ 170 (230)
|+++|+++++++..|++......
T Consensus 89 qv~~L~~e~s~~~~E~da~k~k~ 111 (135)
T KOG4196|consen 89 QVEKLKEENSRLRRELDAYKSKY 111 (135)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHH
Confidence 88888888888887777665554
No 41
>PF10224 DUF2205: Predicted coiled-coil protein (DUF2205); InterPro: IPR019357 This entry represents a highly conserved 100 residue region which is likely to have a coiled-coil structure. The exact function is unknown.
Probab=78.39 E-value=13 Score=26.85 Aligned_cols=49 Identities=10% Similarity=0.118 Sum_probs=39.3
Q ss_pred hhhHHHHHHHHHhhhccchhhhhhhHHHHHHHHHHHHHHHHHHHHHhhh
Q 026974 121 TKKIEETYATLKTAHENVVVEKTRLESEVATLKEKLSVAEKEIKKMSEL 169 (230)
Q Consensus 121 r~~~~~~~~~lk~~~~~~~~~~~~~~~e~~~l~~~~~~~~~e~~~~~~~ 169 (230)
+..+.++...|+...............|+.+|+.++..++..|..+...
T Consensus 18 k~~Li~ei~~LQ~sL~~L~~Rve~Vk~E~~kL~~EN~~Lq~YI~nLm~~ 66 (80)
T PF10224_consen 18 KEELIQEILELQDSLEALSDRVEEVKEENEKLESENEYLQQYIGNLMSS 66 (80)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 4455666667777777777777888899999999999999999988654
No 42
>KOG4005 consensus Transcription factor XBP-1 [Transcription]
Probab=74.59 E-value=34 Score=29.80 Aligned_cols=41 Identities=17% Similarity=0.392 Sum_probs=26.3
Q ss_pred hHHHHHHHHHhhhccchhhhhhhHHHHHHHHHHHHHHHHHH
Q 026974 123 KIEETYATLKTAHENVVVEKTRLESEVATLKEKLSVAEKEI 163 (230)
Q Consensus 123 ~~~~~~~~lk~~~~~~~~~~~~~~~e~~~l~~~~~~~~~e~ 163 (230)
+++.+++.|+..+..+..+++.+..+++.+++++.+++++-
T Consensus 108 ~L~~en~~Lr~~n~~L~~~n~el~~~le~~~~~l~~~~~~~ 148 (292)
T KOG4005|consen 108 ILQNENDSLRAINESLLAKNHELDSELELLRQELAELKQQQ 148 (292)
T ss_pred HHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHHhhHHHH
Confidence 34445556666666666777777777777777777666543
No 43
>PRK09413 IS2 repressor TnpA; Reviewed
Probab=68.18 E-value=4.9 Score=30.81 Aligned_cols=41 Identities=17% Similarity=0.347 Sum_probs=27.0
Q ss_pred ccCCCHHHHH-HHHHhhccCCCCCHHHHHHHHHHhCCCCcceEEecc
Q 026974 68 KRKLTAEQAE-LLEMHFGNEHKLESDRKDKLAAELGLDPRQVAVWFQ 113 (230)
Q Consensus 68 r~~~t~~Q~~-~Le~~F~~~~~p~~~~r~~La~~lgL~~~qV~vWFq 113 (230)
|++|+.++.. ++...+... ....++|.++|+++.+|..|.+
T Consensus 10 rr~ys~EfK~~aV~~~~~~g-----~sv~evA~e~gIs~~tl~~W~r 51 (121)
T PRK09413 10 RRRRTTQEKIAIVQQSFEPG-----MTVSLVARQHGVAASQLFLWRK 51 (121)
T ss_pred CCCCCHHHHHHHHHHHHcCC-----CCHHHHHHHHCcCHHHHHHHHH
Confidence 3447777644 444444432 1244689999999999999954
No 44
>PF04967 HTH_10: HTH DNA binding domain; InterPro: IPR007050 Numerous bacterial transcription regulatory proteins bind DNA via a helix-turn-helix (HTH) motif. This entry represents the HTH DNA binding domain found in Halobacterium salinarium (Halobacterium halobium) and described as a putative bacterio-opsin activator.
Probab=66.42 E-value=7 Score=25.86 Aligned_cols=38 Identities=29% Similarity=0.317 Sum_probs=29.2
Q ss_pred CCHHHHHHHHHhhccCCC--CCHHHHHHHHHHhCCCCcce
Q 026974 71 LTAEQAELLEMHFGNEHK--LESDRKDKLAAELGLDPRQV 108 (230)
Q Consensus 71 ~t~~Q~~~Le~~F~~~~~--p~~~~r~~La~~lgL~~~qV 108 (230)
+|+.|..+|...|...-| |-.....+||.+||+++.-|
T Consensus 1 LT~~Q~e~L~~A~~~GYfd~PR~~tl~elA~~lgis~st~ 40 (53)
T PF04967_consen 1 LTDRQREILKAAYELGYFDVPRRITLEELAEELGISKSTV 40 (53)
T ss_pred CCHHHHHHHHHHHHcCCCCCCCcCCHHHHHHHhCCCHHHH
Confidence 578899999999886554 44455678999999987543
No 45
>smart00340 HALZ homeobox associated leucin zipper.
Probab=63.12 E-value=11 Score=23.77 Aligned_cols=29 Identities=34% Similarity=0.407 Sum_probs=16.1
Q ss_pred HHHHHHHHHhhhccchhhhhhhHHHHHHH
Q 026974 124 IEETYATLKTAHENVVVEKTRLESEVATL 152 (230)
Q Consensus 124 ~~~~~~~lk~~~~~~~~~~~~~~~e~~~l 152 (230)
.+-..+.||...+....+|.+++.|++.|
T Consensus 3 TEvdCe~LKrcce~LteeNrRL~ke~~eL 31 (44)
T smart00340 3 TEVDCELLKRCCESLTEENRRLQKEVQEL 31 (44)
T ss_pred hHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 34456666766665555555555554443
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=63.07 E-value=3.1 Score=26.52 Aligned_cols=37 Identities=16% Similarity=0.316 Sum_probs=27.5
Q ss_pred CCHHHHHHHHHhhccCCCCCHHHHHHHHHHhCCCCcceEEec
Q 026974 71 LTAEQAELLEMHFGNEHKLESDRKDKLAAELGLDPRQVAVWF 112 (230)
Q Consensus 71 ~t~~Q~~~Le~~F~~~~~p~~~~r~~La~~lgL~~~qV~vWF 112 (230)
+++.+..+|...|-.. ..-.++|..+|++...|+.+.
T Consensus 5 L~~~er~vi~~~y~~~-----~t~~eIa~~lg~s~~~V~~~~ 41 (50)
T PF04545_consen 5 LPPREREVIRLRYFEG-----LTLEEIAERLGISRSTVRRIL 41 (50)
T ss_dssp S-HHHHHHHHHHHTST------SHHHHHHHHTSCHHHHHHHH
T ss_pred CCHHHHHHHHHHhcCC-----CCHHHHHHHHCCcHHHHHHHH
Confidence 7889999999999332 234578999999998876544
No 47
>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=56.50 E-value=2.4 Score=29.23 Aligned_cols=44 Identities=18% Similarity=0.305 Sum_probs=26.1
Q ss_pred ccccCCCHHHHHHHHHhhccCCCCCHHHHHHHHHHhCCCCcceEEecc
Q 026974 66 LKKRKLTAEQAELLEMHFGNEHKLESDRKDKLAAELGLDPRQVAVWFQ 113 (230)
Q Consensus 66 r~r~~~t~~Q~~~Le~~F~~~~~p~~~~r~~La~~lgL~~~qV~vWFq 113 (230)
++|+.||+++...+-..+. ........+|.++|+++.++..|-.
T Consensus 2 ~~r~~ys~e~K~~~v~~~~----~~g~sv~~va~~~gi~~~~l~~W~~ 45 (76)
T PF01527_consen 2 RKRRRYSPEFKLQAVREYL----ESGESVSEVAREYGISPSTLYNWRK 45 (76)
T ss_dssp -SS----HHHHHHHHHHHH----HHHCHHHHHHHHHTS-HHHHHHHHH
T ss_pred CCCCCCCHHHHHHHHHHHH----HCCCceEeeecccccccccccHHHH
Confidence 3456699988766555541 1124566899999999999888763
No 48
>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=53.64 E-value=3.8 Score=25.25 Aligned_cols=42 Identities=21% Similarity=0.355 Sum_probs=30.6
Q ss_pred CCCHHHHHHHHHhhccCCCCCHHHHHHHHHHhCCCCcceEEecccch
Q 026974 70 KLTAEQAELLEMHFGNEHKLESDRKDKLAAELGLDPRQVAVWFQNRR 116 (230)
Q Consensus 70 ~~t~~Q~~~Le~~F~~~~~p~~~~r~~La~~lgL~~~qV~vWFqNRR 116 (230)
.++..+..++...|... .....+|..+|++...|..|...-+
T Consensus 10 ~l~~~~~~~~~~~~~~~-----~~~~~ia~~~~~s~~~i~~~~~~~~ 51 (55)
T cd06171 10 KLPEREREVILLRFGEG-----LSYEEIAEILGISRSTVRQRLHRAL 51 (55)
T ss_pred hCCHHHHHHHHHHHhcC-----CCHHHHHHHHCcCHHHHHHHHHHHH
Confidence 37788888888877433 2345789999999999988775433
No 49
>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=48.97 E-value=16 Score=19.81 Aligned_cols=36 Identities=22% Similarity=0.261 Sum_probs=23.7
Q ss_pred CCHHHHHHHHHhhccCCCCCHHHHHHHHHHhCCCCcceEEe
Q 026974 71 LTAEQAELLEMHFGNEHKLESDRKDKLAAELGLDPRQVAVW 111 (230)
Q Consensus 71 ~t~~Q~~~Le~~F~~~~~p~~~~r~~La~~lgL~~~qV~vW 111 (230)
++..+...+...|.... ....+|..+|++...|..|
T Consensus 6 ~~~~~~~~i~~~~~~~~-----s~~~ia~~~~is~~tv~~~ 41 (42)
T cd00569 6 LTPEQIEEARRLLAAGE-----SVAEIARRLGVSRSTLYRY 41 (42)
T ss_pred CCHHHHHHHHHHHHcCC-----CHHHHHHHHCCCHHHHHHh
Confidence 66666666666665322 3447889999888777655
No 50
>KOG1146 consensus Homeobox protein [General function prediction only]
Probab=47.04 E-value=36 Score=36.46 Aligned_cols=56 Identities=18% Similarity=0.311 Sum_probs=50.5
Q ss_pred ccCCCHHHHHHHHHhhccCCCCCHHHHHHHHHHhCCCCcceEEecccchhhhhhhh
Q 026974 68 KRKLTAEQAELLEMHFGNEHKLESDRKDKLAAELGLDPRQVAVWFQNRRARDKTKK 123 (230)
Q Consensus 68 r~~~t~~Q~~~Le~~F~~~~~p~~~~r~~La~~lgL~~~qV~vWFqNRR~k~kr~~ 123 (230)
+..+-.+++..|-.+|-.+.-|+...+..|....+.+.+++.+||+|-|.|.++..
T Consensus 709 ~~~~~~~aa~~l~~a~~~~~sps~k~~~civcd~~st~~l~~l~~h~~~~rs~ke~ 764 (1406)
T KOG1146|consen 709 RLTILPEAAMILGRAYMQDNSPSLKVFDCIVCDVFSTDRLDQLWFHNTRERSRKEQ 764 (1406)
T ss_pred cccccHHHHhhhhhcccCCCCHHHHHHHHhhhhhhhhhhHHHHhhcchhhhhhhhc
Confidence 34467799999999999999999999999999999999999999999999988654
No 51
>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=46.87 E-value=4.6 Score=27.54 Aligned_cols=18 Identities=22% Similarity=0.580 Sum_probs=15.9
Q ss_pred HHHHHHhCCCCcceEEec
Q 026974 95 DKLAAELGLDPRQVAVWF 112 (230)
Q Consensus 95 ~~La~~lgL~~~qV~vWF 112 (230)
..||.+||+++.+|+.|=
T Consensus 26 kdIA~~Lgvs~~tIr~WK 43 (60)
T PF10668_consen 26 KDIAEKLGVSESTIRKWK 43 (60)
T ss_pred HHHHHHHCCCHHHHHHHh
Confidence 468999999999999885
No 52
>PF00170 bZIP_1: bZIP transcription factor cAMP response element binding (CREB) protein signature fos transforming protein signature jun transcription factor signature; InterPro: IPR011616 The basic-leucine zipper (bZIP) transcription factors [, ] of eukaryotic are proteins that contain a basic region mediating sequence-specific DNA-binding followed by a leucine zipper region (see IPR002158 from INTERPRO) required for dimerization.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0043565 sequence-specific DNA binding, 0046983 protein dimerization activity, 0006355 regulation of transcription, DNA-dependent; PDB: 2H7H_B 2OQQ_B 1S9K_E 1JNM_A 1JUN_A 1FOS_H 1A02_J 1T2K_C 1CI6_A 1DH3_C ....
Probab=43.59 E-value=97 Score=20.66 Aligned_cols=28 Identities=21% Similarity=0.334 Sum_probs=11.3
Q ss_pred hhhccchhhhhhhHHHHHHHHHHHHHHH
Q 026974 133 TAHENVVVEKTRLESEVATLKEKLSVAE 160 (230)
Q Consensus 133 ~~~~~~~~~~~~~~~e~~~l~~~~~~~~ 160 (230)
........++..+..++..|..++..+.
T Consensus 33 ~~~~~L~~en~~L~~~~~~L~~~~~~L~ 60 (64)
T PF00170_consen 33 EKVEELESENEELKKELEQLKKEIQSLK 60 (64)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3333333334444444444444444433
No 53
>PRK03975 tfx putative transcriptional regulator; Provisional
Probab=42.15 E-value=21 Score=28.44 Aligned_cols=47 Identities=23% Similarity=0.235 Sum_probs=35.0
Q ss_pred cCCCHHHHHHHHHhhccCCCCCHHHHHHHHHHhCCCCcceEEecccchhhhhh
Q 026974 69 RKLTAEQAELLEMHFGNEHKLESDRKDKLAAELGLDPRQVAVWFQNRRARDKT 121 (230)
Q Consensus 69 ~~~t~~Q~~~Le~~F~~~~~p~~~~r~~La~~lgL~~~qV~vWFqNRR~k~kr 121 (230)
..+++.|..+|...++ . . ...++|..||++...|..|-.+.+.+.++
T Consensus 5 ~~Lt~rqreVL~lr~~-G--l---Tq~EIAe~LGiS~~tVs~ie~ra~kkLr~ 51 (141)
T PRK03975 5 SFLTERQIEVLRLRER-G--L---TQQEIADILGTSRANVSSIEKRARENIEK 51 (141)
T ss_pred cCCCHHHHHHHHHHHc-C--C---CHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 4589999999988432 2 1 24478999999999999998865555553
No 54
>COG3413 Predicted DNA binding protein [General function prediction only]
Probab=41.95 E-value=24 Score=29.62 Aligned_cols=38 Identities=26% Similarity=0.285 Sum_probs=30.5
Q ss_pred CCCHHHHHHHHHhhccCCC--CCHHHHHHHHHHhCCCCcc
Q 026974 70 KLTAEQAELLEMHFGNEHK--LESDRKDKLAAELGLDPRQ 107 (230)
Q Consensus 70 ~~t~~Q~~~Le~~F~~~~~--p~~~~r~~La~~lgL~~~q 107 (230)
.+|..|+.+|...|...-| |-.....+||+++|+++.-
T Consensus 155 ~LTdrQ~~vL~~A~~~GYFd~PR~~~l~dLA~~lGISkst 194 (215)
T COG3413 155 DLTDRQLEVLRLAYKMGYFDYPRRVSLKDLAKELGISKST 194 (215)
T ss_pred cCCHHHHHHHHHHHHcCCCCCCccCCHHHHHHHhCCCHHH
Confidence 4999999999999986554 4444557899999998864
No 55
>KOG3755 consensus SATB1 matrix attachment region binding protein [Transcription]
Probab=40.60 E-value=5.4 Score=39.01 Aligned_cols=45 Identities=18% Similarity=0.208 Sum_probs=30.7
Q ss_pred HHhhccCCCCCHHHHHHHHHHhC-------CCCcceEEecccchhhhhhhhH
Q 026974 80 EMHFGNEHKLESDRKDKLAAELG-------LDPRQVAVWFQNRRARDKTKKI 124 (230)
Q Consensus 80 e~~F~~~~~p~~~~r~~La~~lg-------L~~~qV~vWFqNRR~k~kr~~~ 124 (230)
+.+|..++.++.....+-.+++. ...+-|+.||.|||+++|+.+.
T Consensus 708 ~~w~~k~~s~s~~~v~eYkee~~~~~~~e~~~~kn~~~~fk~~~ee~~~~k~ 759 (769)
T KOG3755|consen 708 HHWKLKTRSGSWVDVAEYKEEELLMPYEEKFESKNVQFWFKVRREEEKRLKM 759 (769)
T ss_pred hhheecccCchhHHHHHhhHHhhcchhhhhhhhcchHHHHHHHHHHHhhhhc
Confidence 44455666666665555444444 3567899999999999997643
No 56
>KOG0709 consensus CREB/ATF family transcription factor [Transcription]
Probab=40.35 E-value=3.4e+02 Score=26.00 Aligned_cols=96 Identities=18% Similarity=0.249 Sum_probs=53.9
Q ss_pred ccCCCHHHHHHHHHh-hcc-CCCCCHHHHHHHHHHhCCCCcceEEecccchhh-hhhhhHHHHHHHHHhhhccchhhhhh
Q 026974 68 KRKLTAEQAELLEMH-FGN-EHKLESDRKDKLAAELGLDPRQVAVWFQNRRAR-DKTKKIEETYATLKTAHENVVVEKTR 144 (230)
Q Consensus 68 r~~~t~~Q~~~Le~~-F~~-~~~p~~~~r~~La~~lgL~~~qV~vWFqNRR~k-~kr~~~~~~~~~lk~~~~~~~~~~~~ 144 (230)
--+++.+....|.+. +.. ..+|-...-+++.++. +.=.+|+|.. ++|++..+=.+.|-........++..
T Consensus 218 ~L~LteeEkrLL~kEG~slPs~lPLTKaEEriLKrv-------RRKIrNK~SAQESRrkKkeYid~LE~rv~~~taeNqe 290 (472)
T KOG0709|consen 218 PLVLTEEEKRLLTKEGYSLPSKLPLTKAEERILKRV-------RRKIRNKRSAQESRRKKKEYIDGLESRVSAFTAENQE 290 (472)
T ss_pred ceeccHHHHHHHHhccCcCcccCCchHHHHHHHHHH-------HHHHHhhhhhHHHHHhHhhHHHHHhhhhhhcccCcHH
Confidence 345788888888766 332 3455555445555444 1111233322 22222222223344444555668888
Q ss_pred hHHHHHHHHHHHHHHHHHHHHHhhhh
Q 026974 145 LESEVATLKEKLSVAEKEIKKMSELI 170 (230)
Q Consensus 145 ~~~e~~~l~~~~~~~~~e~~~~~~~~ 170 (230)
+..+++.|..++..+-+++.++...+
T Consensus 291 L~kkV~~Le~~N~sLl~qL~klQt~v 316 (472)
T KOG0709|consen 291 LQKKVEELELSNRSLLAQLKKLQTLV 316 (472)
T ss_pred HHHHHHHHhhccHHHHHHHHHHHHHH
Confidence 88888888888888777777666553
No 57
>PF06005 DUF904: Protein of unknown function (DUF904); InterPro: IPR009252 Cell division protein ZapB is a non-essential, abundant cell division factor that is required for proper Z-ring formation. It is recruited early to the divisome by direct interaction with FtsZ, stimulating Z-ring assembly and thereby promoting cell division earlier in the cell cycle. Its recruitment to the Z-ring requires functional FtsA or ZipA.; GO: 0000917 barrier septum formation, 0043093 cytokinesis by binary fission, 0005737 cytoplasm; PDB: 2JEE_A.
Probab=39.79 E-value=1.3e+02 Score=21.15 Aligned_cols=46 Identities=15% Similarity=0.236 Sum_probs=25.4
Q ss_pred hHHHHHHHHHhhhccchhhhhhhHHHHHHHHHHHHHHHHHHHHHhh
Q 026974 123 KIEETYATLKTAHENVVVEKTRLESEVATLKEKLSVAEKEIKKMSE 168 (230)
Q Consensus 123 ~~~~~~~~lk~~~~~~~~~~~~~~~e~~~l~~~~~~~~~e~~~~~~ 168 (230)
.++.+.+.|+........++..+..++++|+.+....+..+..+-+
T Consensus 22 ~Lq~e~eeLke~n~~L~~e~~~L~~en~~L~~e~~~~~~rl~~LL~ 67 (72)
T PF06005_consen 22 LLQMENEELKEKNNELKEENEELKEENEQLKQERNAWQERLRSLLG 67 (72)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3344455555555444455555666666666666666555555443
No 58
>KOG2391 consensus Vacuolar sorting protein/ubiquitin receptor VPS23 [Posttranslational modification, protein turnover, chaperones; Intracellular trafficking, secretion, and vesicular transport]
Probab=39.65 E-value=84 Score=28.82 Aligned_cols=56 Identities=21% Similarity=0.392 Sum_probs=39.8
Q ss_pred chhhhhhhhHHHHHHHHHhhhccchhhhhhhHHHHHHHHHHHHHHHHHHHHHhhhh
Q 026974 115 RRARDKTKKIEETYATLKTAHENVVVEKTRLESEVATLKEKLSVAEKEIKKMSELI 170 (230)
Q Consensus 115 RR~k~kr~~~~~~~~~lk~~~~~~~~~~~~~~~e~~~l~~~~~~~~~e~~~~~~~~ 170 (230)
+|.+.+-.+...+.+.+|...+........++.+.+.|+.++..++..++-+..-.
T Consensus 221 ~r~eeeme~~~aeq~slkRt~EeL~~G~~kL~~~~etLEqq~~~L~~niDIL~~k~ 276 (365)
T KOG2391|consen 221 RRREEEMERLQAEQESLKRTEEELNIGKQKLVAMKETLEQQLQSLQKNIDILKSKV 276 (365)
T ss_pred HHHHHHHHHHHHHHHHHHhhHHHHHhhHHHHHHHHHHHHHHHHHHHhhhHHHHHHH
Confidence 34444445566677777877777777777888888888888888887777665543
No 59
>PF13443 HTH_26: Cro/C1-type HTH DNA-binding domain; PDB: 3TYR_A 3TYS_A 3B7H_A.
Probab=38.37 E-value=13 Score=24.50 Aligned_cols=36 Identities=11% Similarity=0.238 Sum_probs=20.5
Q ss_pred HHHHHHHhCCCCcceEEecccchhhhhhhhHHHHHH
Q 026974 94 KDKLAAELGLDPRQVAVWFQNRRARDKTKKIEETYA 129 (230)
Q Consensus 94 r~~La~~lgL~~~qV~vWFqNRR~k~kr~~~~~~~~ 129 (230)
...||+.+|++...|..|+.++.....-..+..-..
T Consensus 13 ~~~La~~~gis~~tl~~~~~~~~~~~~~~~l~~ia~ 48 (63)
T PF13443_consen 13 QKDLARKTGISRSTLSRILNGKPSNPSLDTLEKIAK 48 (63)
T ss_dssp HHHHHHHHT--HHHHHHHHTTT-----HHHHHHHHH
T ss_pred HHHHHHHHCcCHHHHHHHHhcccccccHHHHHHHHH
Confidence 457899999999999999987755555444444333
No 60
>KOG1924 consensus RhoA GTPase effector DIA/Diaphanous [Signal transduction mechanisms; Cytoskeleton]
Probab=37.86 E-value=1e+02 Score=31.65 Aligned_cols=43 Identities=19% Similarity=0.286 Sum_probs=29.6
Q ss_pred HHHHHHhhhccchhhhhhhHHHHHHHHHHHHHHHHHHHHHhhh
Q 026974 127 TYATLKTAHENVVVEKTRLESEVATLKEKLSVAEKEIKKMSEL 169 (230)
Q Consensus 127 ~~~~lk~~~~~~~~~~~~~~~e~~~l~~~~~~~~~e~~~~~~~ 169 (230)
....+....+...|..+..+.|+++..+....++.+.+.+.+.
T Consensus 475 kA~e~~kk~~ke~ta~qe~qael~k~e~Ki~~l~ae~~al~s~ 517 (1102)
T KOG1924|consen 475 KAAELEKKFDKELTARQEAQAELQKHEEKIKLLEAEKQALSSP 517 (1102)
T ss_pred HHHHHHHHHHHHHhHHHHHHHHHHHhhhhcccCchhhhhccCc
Confidence 4444555556666777777788888887777777777766654
No 61
>KOG3650 consensus Predicted coiled-coil protein [General function prediction only]
Probab=37.72 E-value=1.4e+02 Score=22.55 Aligned_cols=38 Identities=11% Similarity=0.138 Sum_probs=23.6
Q ss_pred hhhccchhhhhhhHHHHHHHHHHHHHHHHHHHHHhhhh
Q 026974 133 TAHENVVVEKTRLESEVATLKEKLSVAEKEIKKMSELI 170 (230)
Q Consensus 133 ~~~~~~~~~~~~~~~e~~~l~~~~~~~~~e~~~~~~~~ 170 (230)
...+....--.....|..+|+.++..+-+.|+.+.+..
T Consensus 70 nTLdDLSqRVdsVKEEnLKLrSENQVLGQYIeNLMSaS 107 (120)
T KOG3650|consen 70 NTLDDLSQRVDSVKEENLKLRSENQVLGQYIENLMSAS 107 (120)
T ss_pred HHHHHHHHHHHHHHHhhhhhhhhhHHHHHHHHHHHhhh
Confidence 33333333334455666777888888888888876543
No 62
>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=36.37 E-value=16 Score=23.33 Aligned_cols=39 Identities=18% Similarity=0.257 Sum_probs=27.1
Q ss_pred CCHHHHHHHHHhhccCCCCCHHHHHHHHHHhCCCCcceEEeccc
Q 026974 71 LTAEQAELLEMHFGNEHKLESDRKDKLAAELGLDPRQVAVWFQN 114 (230)
Q Consensus 71 ~t~~Q~~~Le~~F~~~~~p~~~~r~~La~~lgL~~~qV~vWFqN 114 (230)
+++.+..++...|-.. ....++|..+|+++..|+.|.+.
T Consensus 11 L~~~~r~i~~l~~~~g-----~s~~eIa~~l~~s~~~v~~~l~r 49 (54)
T PF08281_consen 11 LPERQREIFLLRYFQG-----MSYAEIAEILGISESTVKRRLRR 49 (54)
T ss_dssp S-HHHHHHHHHHHTS--------HHHHHHHCTS-HHHHHHHHHH
T ss_pred CCHHHHHHHHHHHHHC-----cCHHHHHHHHCcCHHHHHHHHHH
Confidence 6777778877766443 34568999999999999988863
No 63
>PRK13729 conjugal transfer pilus assembly protein TraB; Provisional
Probab=34.45 E-value=1.4e+02 Score=28.56 Aligned_cols=45 Identities=7% Similarity=0.236 Sum_probs=27.8
Q ss_pred hhhHHHHHHHHHhhhccchhhhhhhHHHHHHHHHHHHHHHHHHHH
Q 026974 121 TKKIEETYATLKTAHENVVVEKTRLESEVATLKEKLSVAEKEIKK 165 (230)
Q Consensus 121 r~~~~~~~~~lk~~~~~~~~~~~~~~~e~~~l~~~~~~~~~e~~~ 165 (230)
...++++++.+++..+........++..++.++.++..++.+++.
T Consensus 78 asELEKqLaaLrqElq~~saq~~dle~KIkeLEaE~~~Lk~Ql~a 122 (475)
T PRK13729 78 AAQMQKQYEEIRRELDVLNKQRGDDQRRIEKLGQDNAALAEQVKA 122 (475)
T ss_pred HHHHHHHHHHHHHHHHHHhhhhhhHHHHHHHHHHHHHHHHHHHHh
Confidence 345555566665555544445555666777777777777777743
No 64
>PF04880 NUDE_C: NUDE protein, C-terminal conserved region; InterPro: IPR006964 This domain represents the C-terminal conserved region of NUDE proteins. Emericella nidulans (Aspergillus nidulans) NUDE, acts in the cytoplasmic dynein/dynactin pathway and is required for distribution of nuclei []. It is a homologue of the nuclear distribution protein RO11 of Neurospora crassa. NUDE interacts with the NUDF via an N-terminal coiled coil domain; this is the only domain which is absolutely required for NUDE function.; PDB: 2V66_B 2V71_B.
Probab=32.03 E-value=34 Score=28.07 Aligned_cols=26 Identities=35% Similarity=0.451 Sum_probs=8.9
Q ss_pred chhhhhhhHHHHHHHHHHHHHHHHHH
Q 026974 138 VVVEKTRLESEVATLKEKLSVAEKEI 163 (230)
Q Consensus 138 ~~~~~~~~~~e~~~l~~~~~~~~~e~ 163 (230)
-+.|+..|..++++|++|+.++++|+
T Consensus 22 ELdEKE~L~~~~QRLkDE~RDLKqEl 47 (166)
T PF04880_consen 22 ELDEKENLREEVQRLKDELRDLKQEL 47 (166)
T ss_dssp HHHHHHHHHHCH--------------
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 33677888889999999999999988
No 65
>TIGR03752 conj_TIGR03752 integrating conjugative element protein, PFL_4705 family. Members of this protein family are found occasionally on plasmids such as the Pseudomonas putida toluene catabolic TOL plasmid pWWO_p085. Usually, however, they are found on the bacterial main chromosome in regions flanked by markers of conjugative transfer and/or transposition.
Probab=30.20 E-value=2.7e+02 Score=26.77 Aligned_cols=32 Identities=22% Similarity=0.346 Sum_probs=22.0
Q ss_pred hhhhhHHHHHHHHHHHHHHHHHHHHHhhhhcC
Q 026974 141 EKTRLESEVATLKEKLSVAEKEIKKMSELIEG 172 (230)
Q Consensus 141 ~~~~~~~e~~~l~~~~~~~~~e~~~~~~~~~~ 172 (230)
+...+..+.++|+++...++..++.+..+.++
T Consensus 110 ~~~~~~~~~~ql~~~~~~~~~~l~~l~~~l~~ 141 (472)
T TIGR03752 110 ETQELTKEIEQLKSERQQLQGLIDQLQRRLAG 141 (472)
T ss_pred hhHHHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Confidence 34445567777777777777777777776654
No 66
>KOG4571 consensus Activating transcription factor 4 [Transcription]
Probab=29.41 E-value=1.6e+02 Score=26.41 Aligned_cols=34 Identities=32% Similarity=0.415 Sum_probs=24.1
Q ss_pred ccchhhhhhhHHHHHHHHHHHHHHHHHHHHHhhh
Q 026974 136 ENVVVEKTRLESEVATLKEKLSVAEKEIKKMSEL 169 (230)
Q Consensus 136 ~~~~~~~~~~~~e~~~l~~~~~~~~~e~~~~~~~ 169 (230)
+++.-+-..++..+++|+++..+++.||+.+..-
T Consensus 251 E~l~ge~~~Le~rN~~LK~qa~~lerEI~ylKql 284 (294)
T KOG4571|consen 251 EALLGELEGLEKRNEELKDQASELEREIRYLKQL 284 (294)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3444455567777888888888888888876554
No 67
>KOG1962 consensus B-cell receptor-associated protein and related proteins [Defense mechanisms]
Probab=29.35 E-value=1.5e+02 Score=25.37 Aligned_cols=32 Identities=22% Similarity=0.294 Sum_probs=15.0
Q ss_pred hhhhhHHHHHHHHHHHHHHHHHHHHHhhhhcC
Q 026974 141 EKTRLESEVATLKEKLSVAEKEIKKMSELIEG 172 (230)
Q Consensus 141 ~~~~~~~e~~~l~~~~~~~~~e~~~~~~~~~~ 172 (230)
....+..+.+.+..|..++.++.+.+..++++
T Consensus 180 ~~~al~Kq~e~~~~EydrLlee~~~Lq~~i~~ 211 (216)
T KOG1962|consen 180 KVDALKKQSEGLQDEYDRLLEEYSKLQEQIES 211 (216)
T ss_pred HHHHHHHHHHHcccHHHHHHHHHHHHHHHHhc
Confidence 33334444444445555555555555444443
No 68
>PRK06759 RNA polymerase factor sigma-70; Validated
Probab=28.42 E-value=34 Score=26.37 Aligned_cols=44 Identities=14% Similarity=0.092 Sum_probs=31.0
Q ss_pred CCHHHHHHHHHhhccCCCCCHHHHHHHHHHhCCCCcceEEecccchhhh
Q 026974 71 LTAEQAELLEMHFGNEHKLESDRKDKLAAELGLDPRQVAVWFQNRRARD 119 (230)
Q Consensus 71 ~t~~Q~~~Le~~F~~~~~p~~~~r~~La~~lgL~~~qV~vWFqNRR~k~ 119 (230)
+++.+..++...|-.. ....++|..+|++...|+.|...-|.+.
T Consensus 107 L~~~~r~ii~l~~~~~-----~s~~EIA~~l~is~~tV~~~~~ra~~~L 150 (154)
T PRK06759 107 LDEKEKYIIFERFFVG-----KTMGEIALETEMTYYQVRWIYRQALEKM 150 (154)
T ss_pred CCHHHHHHHHHHHhcC-----CCHHHHHHHHCCCHHHHHHHHHHHHHHH
Confidence 6777777777665433 2356899999999999998775444333
No 69
>PRK09646 RNA polymerase sigma factor SigK; Reviewed
Probab=27.91 E-value=37 Score=27.60 Aligned_cols=45 Identities=18% Similarity=0.163 Sum_probs=30.7
Q ss_pred CCHHHHHHHHHhhccCCCCCHHHHHHHHHHhCCCCcceEEecccchhhhh
Q 026974 71 LTAEQAELLEMHFGNEHKLESDRKDKLAAELGLDPRQVAVWFQNRRARDK 120 (230)
Q Consensus 71 ~t~~Q~~~Le~~F~~~~~p~~~~r~~La~~lgL~~~qV~vWFqNRR~k~k 120 (230)
++..+..+|...|-.. ....++|..||++...|+.+...-|.+.|
T Consensus 143 L~~~~r~vl~l~~~~~-----~s~~EIA~~Lgis~~tVk~~l~ra~~~Lr 187 (194)
T PRK09646 143 LTDTQRESVTLAYYGG-----LTYREVAERLAVPLGTVKTRMRDGLIRLR 187 (194)
T ss_pred CCHHHHHHHHHHHHcC-----CCHHHHHHHhCCChHhHHHHHHHHHHHHH
Confidence 7777777776655332 23567899999999999877754333333
No 70
>smart00338 BRLZ basic region leucin zipper.
Probab=26.53 E-value=2e+02 Score=19.12 Aligned_cols=18 Identities=22% Similarity=0.416 Sum_probs=7.3
Q ss_pred HHHHHHHHHHHHHHHHHH
Q 026974 147 SEVATLKEKLSVAEKEIK 164 (230)
Q Consensus 147 ~e~~~l~~~~~~~~~e~~ 164 (230)
.++..|..++..+..++.
T Consensus 40 ~en~~L~~~~~~l~~e~~ 57 (65)
T smart00338 40 AENERLKKEIERLRRELE 57 (65)
T ss_pred HHHHHHHHHHHHHHHHHH
Confidence 333334444444444443
No 71
>PF06005 DUF904: Protein of unknown function (DUF904); InterPro: IPR009252 Cell division protein ZapB is a non-essential, abundant cell division factor that is required for proper Z-ring formation. It is recruited early to the divisome by direct interaction with FtsZ, stimulating Z-ring assembly and thereby promoting cell division earlier in the cell cycle. Its recruitment to the Z-ring requires functional FtsA or ZipA.; GO: 0000917 barrier septum formation, 0043093 cytokinesis by binary fission, 0005737 cytoplasm; PDB: 2JEE_A.
Probab=26.42 E-value=2.3e+02 Score=19.80 Aligned_cols=47 Identities=26% Similarity=0.251 Sum_probs=27.6
Q ss_pred hHHHHHHHHHhhhccchhhhhhhHHHHHHHHHHHHHHHHHHHHHhhh
Q 026974 123 KIEETYATLKTAHENVVVEKTRLESEVATLKEKLSVAEKEIKKMSEL 169 (230)
Q Consensus 123 ~~~~~~~~lk~~~~~~~~~~~~~~~e~~~l~~~~~~~~~e~~~~~~~ 169 (230)
+.-.....|+........++..+..+...|+.++..++.+.......
T Consensus 15 ~aveti~~Lq~e~eeLke~n~~L~~e~~~L~~en~~L~~e~~~~~~r 61 (72)
T PF06005_consen 15 QAVETIALLQMENEELKEKNNELKEENEELKEENEQLKQERNAWQER 61 (72)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 34445555555555555666666666666666666666665544433
No 72
>COG4367 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=26.12 E-value=38 Score=24.96 Aligned_cols=36 Identities=17% Similarity=0.195 Sum_probs=28.5
Q ss_pred CCHHHHHHHHHhhccCCCCCHHHHHHHHHHhCCCCc
Q 026974 71 LTAEQAELLEMHFGNEHKLESDRKDKLAAELGLDPR 106 (230)
Q Consensus 71 ~t~~Q~~~Le~~F~~~~~p~~~~r~~La~~lgL~~~ 106 (230)
+.++|...-...|+.+--.+....+++|..||+++.
T Consensus 3 Ln~eq~~~Tk~elqan~el~~LS~~~iA~~Ln~t~~ 38 (97)
T COG4367 3 LNPEQKQRTKQELQANFELCPLSDEEIATALNWTEV 38 (97)
T ss_pred CCHHHHHHHHHHHHHhhhhccccHHHHHHHhCCCHH
Confidence 667788777777777777777778889999998874
No 73
>KOG4571 consensus Activating transcription factor 4 [Transcription]
Probab=25.79 E-value=2e+02 Score=25.76 Aligned_cols=45 Identities=13% Similarity=0.181 Sum_probs=31.9
Q ss_pred hhHHHHHHHHHhhhccchhhhhhhHHHHHHHHHHHHHHHHHHHHH
Q 026974 122 KKIEETYATLKTAHENVVVEKTRLESEVATLKEKLSVAEKEIKKM 166 (230)
Q Consensus 122 ~~~~~~~~~lk~~~~~~~~~~~~~~~e~~~l~~~~~~~~~e~~~~ 166 (230)
++++.+.+.+-...+.....|..|..++..+..|...+++-+...
T Consensus 244 qKkRae~E~l~ge~~~Le~rN~~LK~qa~~lerEI~ylKqli~e~ 288 (294)
T KOG4571|consen 244 QKKRAEKEALLGELEGLEKRNEELKDQASELEREIRYLKQLILEV 288 (294)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 344556666777777777788888888888888887777766543
No 74
>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=25.51 E-value=29 Score=22.59 Aligned_cols=45 Identities=20% Similarity=0.249 Sum_probs=32.2
Q ss_pred CCCHHHHHHHHHhhccCCCCCHHHHHHHHHHhCCCCcceEEecccchhhhh
Q 026974 70 KLTAEQAELLEMHFGNEHKLESDRKDKLAAELGLDPRQVAVWFQNRRARDK 120 (230)
Q Consensus 70 ~~t~~Q~~~Le~~F~~~~~p~~~~r~~La~~lgL~~~qV~vWFqNRR~k~k 120 (230)
.||..++.+|.....-. ...++|..+|++++.|..+..+=+.|..
T Consensus 3 ~LT~~E~~vl~~l~~G~------~~~eIA~~l~is~~tV~~~~~~i~~Kl~ 47 (58)
T PF00196_consen 3 SLTERELEVLRLLAQGM------SNKEIAEELGISEKTVKSHRRRIMKKLG 47 (58)
T ss_dssp SS-HHHHHHHHHHHTTS-------HHHHHHHHTSHHHHHHHHHHHHHHHHT
T ss_pred ccCHHHHHHHHHHHhcC------CcchhHHhcCcchhhHHHHHHHHHHHhC
Confidence 48899999998876533 3567999999999998877665444443
No 75
>PRK11546 zraP zinc resistance protein; Provisional
Probab=25.24 E-value=2.6e+02 Score=22.37 Aligned_cols=23 Identities=13% Similarity=0.195 Sum_probs=15.1
Q ss_pred hhhhHHHHHHHHHHHHHHHHHHH
Q 026974 142 KTRLESEVATLKEKLSVAEKEIK 164 (230)
Q Consensus 142 ~~~~~~e~~~l~~~~~~~~~e~~ 164 (230)
-..+..|+..|+.++.+...+.+
T Consensus 91 I~aL~kEI~~Lr~kL~e~r~~~~ 113 (143)
T PRK11546 91 INAVAKEMENLRQSLDELRVKRD 113 (143)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHH
Confidence 45566788888877776655444
No 76
>PRK04217 hypothetical protein; Provisional
Probab=24.96 E-value=40 Score=25.71 Aligned_cols=39 Identities=15% Similarity=0.129 Sum_probs=29.9
Q ss_pred CCHHHHHHHHHhhccCCCCCHHHHHHHHHHhCCCCcceEEeccc
Q 026974 71 LTAEQAELLEMHFGNEHKLESDRKDKLAAELGLDPRQVAVWFQN 114 (230)
Q Consensus 71 ~t~~Q~~~Le~~F~~~~~p~~~~r~~La~~lgL~~~qV~vWFqN 114 (230)
++.+|..++...|.... ...+||+.+|++...|...+..
T Consensus 43 Lt~eereai~l~~~eGl-----S~~EIAk~LGIS~sTV~r~L~R 81 (110)
T PRK04217 43 MTYEEFEALRLVDYEGL-----TQEEAGKRMGVSRGTVWRALTS 81 (110)
T ss_pred CCHHHHHHHHHHHHcCC-----CHHHHHHHHCcCHHHHHHHHHH
Confidence 88899888887774432 4567999999999988766543
No 77
>PRK09652 RNA polymerase sigma factor RpoE; Provisional
Probab=24.69 E-value=39 Score=26.56 Aligned_cols=42 Identities=14% Similarity=0.072 Sum_probs=30.0
Q ss_pred CCCHHHHHHHHHhhccCCCCCHHHHHHHHHHhCCCCcceEEecccch
Q 026974 70 KLTAEQAELLEMHFGNEHKLESDRKDKLAAELGLDPRQVAVWFQNRR 116 (230)
Q Consensus 70 ~~t~~Q~~~Le~~F~~~~~p~~~~r~~La~~lgL~~~qV~vWFqNRR 116 (230)
.+++.+..+|...|-.. ....++|..+|++...|+.|...-+
T Consensus 128 ~L~~~~r~vl~l~~~~~-----~s~~eIA~~lgis~~tV~~~l~ra~ 169 (182)
T PRK09652 128 SLPEELRTAITLREIEG-----LSYEEIAEIMGCPIGTVRSRIFRAR 169 (182)
T ss_pred hCCHHHHHHHHHHHHcC-----CCHHHHHHHHCCCHHHHHHHHHHHH
Confidence 37788888887765322 1345789999999999988776333
No 78
>KOG2008 consensus BTK-associated SH3-domain binding protein SAB [Signal transduction mechanisms]
Probab=24.61 E-value=2.8e+02 Score=25.42 Aligned_cols=27 Identities=22% Similarity=0.359 Sum_probs=13.2
Q ss_pred hhhhHHHHHHHHHHHHHHHHHHHHHhh
Q 026974 142 KTRLESEVATLKEKLSVAEKEIKKMSE 168 (230)
Q Consensus 142 ~~~~~~e~~~l~~~~~~~~~e~~~~~~ 168 (230)
-..++.++..-+.++...-..+++++.
T Consensus 199 v~~Leaev~~~K~~Y~~slrnLE~ISd 225 (426)
T KOG2008|consen 199 VDDLEAEVTLAKGEYKMSLRNLEMISD 225 (426)
T ss_pred HHHHHHHHHHhhccHHHHHHHHHHHHH
Confidence 344566666555555443333333333
No 79
>KOG3119 consensus Basic region leucine zipper transcription factor [Transcription]
Probab=24.27 E-value=2.1e+02 Score=25.19 Aligned_cols=26 Identities=27% Similarity=0.457 Sum_probs=14.2
Q ss_pred hHHHHHHHHHHHHHHHHHHHHHhhhh
Q 026974 145 LESEVATLKEKLSVAEKEIKKMSELI 170 (230)
Q Consensus 145 ~~~e~~~l~~~~~~~~~e~~~~~~~~ 170 (230)
++.|.+.|+.++..++.++..+....
T Consensus 227 leken~~lr~~v~~l~~el~~~~~~~ 252 (269)
T KOG3119|consen 227 LEKENEALRTQVEQLKKELATLRRLF 252 (269)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 34555555555666666665554443
No 80
>PRK12526 RNA polymerase sigma factor; Provisional
Probab=23.92 E-value=43 Score=27.65 Aligned_cols=44 Identities=18% Similarity=0.160 Sum_probs=28.4
Q ss_pred CCHHHHHHHHHhhccCCCCCHHHHHHHHHHhCCCCcceEEecccchhhh
Q 026974 71 LTAEQAELLEMHFGNEHKLESDRKDKLAAELGLDPRQVAVWFQNRRARD 119 (230)
Q Consensus 71 ~t~~Q~~~Le~~F~~~~~p~~~~r~~La~~lgL~~~qV~vWFqNRR~k~ 119 (230)
++..+..+|...|-.. ....+||..+|++...|+.+...-+.+.
T Consensus 154 L~~~~r~vl~l~~~~g-----~s~~EIA~~lgis~~tV~~~l~Ra~~~L 197 (206)
T PRK12526 154 LPEAQQTVVKGVYFQE-----LSQEQLAQQLNVPLGTVKSRLRLALAKL 197 (206)
T ss_pred CCHHHHHHHHHHHHcC-----CCHHHHHHHHCCCHHHHHHHHHHHHHHH
Confidence 5666666666543222 2356789999999999977665433333
No 81
>PF13518 HTH_28: Helix-turn-helix domain
Probab=23.78 E-value=19 Score=22.47 Aligned_cols=21 Identities=24% Similarity=0.547 Sum_probs=17.7
Q ss_pred HHHHHHHhCCCCcceEEeccc
Q 026974 94 KDKLAAELGLDPRQVAVWFQN 114 (230)
Q Consensus 94 r~~La~~lgL~~~qV~vWFqN 114 (230)
..++|.++|++..+|..|.+.
T Consensus 15 ~~~~a~~~gis~~tv~~w~~~ 35 (52)
T PF13518_consen 15 VREIAREFGISRSTVYRWIKR 35 (52)
T ss_pred HHHHHHHHCCCHhHHHHHHHH
Confidence 346899999999999999863
No 82
>KOG3623 consensus Homeobox transcription factor SIP1 [Transcription]
Probab=23.63 E-value=9 Score=38.41 Aligned_cols=57 Identities=19% Similarity=0.274 Sum_probs=38.6
Q ss_pred cCCCHHHHHHHHHhhccCCCCCHHHHHHHHHHhCCCCcceEEecccchhhhhhhhHH
Q 026974 69 RKLTAEQAELLEMHFGNEHKLESDRKDKLAAELGLDPRQVAVWFQNRRARDKTKKIE 125 (230)
Q Consensus 69 ~~~t~~Q~~~Le~~F~~~~~p~~~~r~~La~~lgL~~~qV~vWFqNRR~k~kr~~~~ 125 (230)
+....++-..|...+..+-.++..+-..++.+|...+..|.+||++|+..-+...+.
T Consensus 631 sp~k~~dq~ql~~a~elq~s~~n~~~pl~~t~~~n~~pv~ev~dhsrsstpsp~pl~ 687 (1007)
T KOG3623|consen 631 SPIKEEDQQQLKQAYELQASPSNDEFPLIATRLQNDPPVVEVWDHSRSSTPSPMPLF 687 (1007)
T ss_pred CCCCccchhhhHhhhhcccCccCcccchhhhhccCCCcchhhcccCCCCCCCCCccc
Confidence 334444555566666655555544444556668888999999999999998876543
No 83
>PRK14127 cell division protein GpsB; Provisional
Probab=23.16 E-value=2.7e+02 Score=21.18 Aligned_cols=26 Identities=8% Similarity=0.337 Sum_probs=14.2
Q ss_pred HHHHHHHHHHHHHHHHHHHHHhhhhc
Q 026974 146 ESEVATLKEKLSVAEKEIKKMSELIE 171 (230)
Q Consensus 146 ~~e~~~l~~~~~~~~~e~~~~~~~~~ 171 (230)
..++..|++++..++.++........
T Consensus 43 ~~e~~~Lk~e~~~l~~~l~e~~~~~~ 68 (109)
T PRK14127 43 QKEIEELQQENARLKAQVDELTKQVS 68 (109)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHhhc
Confidence 34455555555555555555555444
No 84
>cd04766 HTH_HspR Helix-Turn-Helix DNA binding domain of the HspR transcription regulator. Helix-turn-helix (HTH) transcription regulator HspR, N-terminal domain. Heat shock protein regulators (HspR) have been shown to regulate expression of specific regulons in response to high temperature or high osmolarity in Streptomyces and Helicobacter, respectively. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules.
Probab=23.06 E-value=1.3e+02 Score=21.43 Aligned_cols=22 Identities=14% Similarity=0.193 Sum_probs=17.7
Q ss_pred HHHHHHHhCCCCcceEEecccc
Q 026974 94 KDKLAAELGLDPRQVAVWFQNR 115 (230)
Q Consensus 94 r~~La~~lgL~~~qV~vWFqNR 115 (230)
..++|..+|++.+.|+.|-+..
T Consensus 4 i~e~A~~~gvs~~tLr~ye~~G 25 (91)
T cd04766 4 ISVAAELSGMHPQTLRLYERLG 25 (91)
T ss_pred HHHHHHHHCcCHHHHHHHHHCC
Confidence 3468999999999999997543
No 85
>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=23.03 E-value=24 Score=23.62 Aligned_cols=27 Identities=26% Similarity=0.363 Sum_probs=21.3
Q ss_pred HHHHHHHhCCCCcceEEecccchhhhhhh
Q 026974 94 KDKLAAELGLDPRQVAVWFQNRRARDKTK 122 (230)
Q Consensus 94 r~~La~~lgL~~~qV~vWFqNRR~k~kr~ 122 (230)
..+||..||++.+.|..|-+ |.+|...
T Consensus 16 ~~eIA~~Lg~~~~TV~~W~~--r~~W~~~ 42 (58)
T PF06056_consen 16 IKEIAEELGVPRSTVYSWKD--RYKWDEL 42 (58)
T ss_pred HHHHHHHHCCChHHHHHHHH--hhCcccc
Confidence 45789999999999999975 5665543
No 86
>PRK10884 SH3 domain-containing protein; Provisional
Probab=22.89 E-value=3.1e+02 Score=23.20 Aligned_cols=27 Identities=15% Similarity=0.327 Sum_probs=11.7
Q ss_pred hhhhhhHHHHHHHHHHHHHHHHHHHHH
Q 026974 140 VEKTRLESEVATLKEKLSVAEKEIKKM 166 (230)
Q Consensus 140 ~~~~~~~~e~~~l~~~~~~~~~e~~~~ 166 (230)
.++..+..++..++.++..++.+.+.+
T Consensus 139 ~~n~~L~~~l~~~~~~~~~l~~~~~~~ 165 (206)
T PRK10884 139 EENQKLKNQLIVAQKKVDAANLQLDDK 165 (206)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 344444444444444444444444433
No 87
>PF08280 HTH_Mga: M protein trans-acting positive regulator (MGA) HTH domain; InterPro: IPR013199 Mga is a DNA-binding protein that activates the expression of several important virulence genes in group A streptococcus in response to changing environmental conditions [].; PDB: 2WTE_A 3SQN_A.
Probab=22.73 E-value=38 Score=22.39 Aligned_cols=32 Identities=25% Similarity=0.403 Sum_probs=23.8
Q ss_pred HHHHHHHHhhccCCCCCHHHHHHHHHHhCCCCcceE
Q 026974 74 EQAELLEMHFGNEHKLESDRKDKLAAELGLDPRQVA 109 (230)
Q Consensus 74 ~Q~~~Le~~F~~~~~p~~~~r~~La~~lgL~~~qV~ 109 (230)
.|+..|+-.+. +...+.. +||..+|++.+.|+
T Consensus 6 rq~~Ll~~L~~-~~~~~~~---ela~~l~~S~rti~ 37 (59)
T PF08280_consen 6 RQLKLLELLLK-NKWITLK---ELAKKLNISERTIK 37 (59)
T ss_dssp HHHHHHHHHHH-HTSBBHH---HHHHHCTS-HHHHH
T ss_pred HHHHHHHHHHc-CCCCcHH---HHHHHHCCCHHHHH
Confidence 57888888888 6666655 78999999987654
No 88
>PRK11924 RNA polymerase sigma factor; Provisional
Probab=22.72 E-value=45 Score=26.11 Aligned_cols=45 Identities=18% Similarity=0.209 Sum_probs=29.5
Q ss_pred CCHHHHHHHHHhhccCCCCCHHHHHHHHHHhCCCCcceEEecccchhhhh
Q 026974 71 LTAEQAELLEMHFGNEHKLESDRKDKLAAELGLDPRQVAVWFQNRRARDK 120 (230)
Q Consensus 71 ~t~~Q~~~Le~~F~~~~~p~~~~r~~La~~lgL~~~qV~vWFqNRR~k~k 120 (230)
+++.+..++...|-.. ....+||..+|++...|..|...-|.+.|
T Consensus 126 L~~~~r~i~~l~~~~~-----~~~~eIA~~lgis~~tv~~~~~ra~~~lr 170 (179)
T PRK11924 126 LPVKQREVFLLRYVEG-----LSYREIAEILGVPVGTVKSRLRRARQLLR 170 (179)
T ss_pred CCHHHHHHhhHHHHcC-----CCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Confidence 5555666665544322 23468999999999999988764444444
No 89
>cd04761 HTH_MerR-SF Helix-Turn-Helix DNA binding domain of transcription regulators from the MerR superfamily. Helix-turn-helix (HTH) transcription regulator MerR superfamily, N-terminal domain. The MerR family transcription regulators have been shown to mediate responses to stress including exposure to heavy metals, drugs, or oxygen radicals in eubacterial and some archaeal species. They regulate transcription of multidrug/metal ion transporter genes and oxidative stress regulons by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.
Probab=22.65 E-value=19 Score=22.20 Aligned_cols=21 Identities=19% Similarity=0.279 Sum_probs=17.7
Q ss_pred HHHHHHhCCCCcceEEecccc
Q 026974 95 DKLAAELGLDPRQVAVWFQNR 115 (230)
Q Consensus 95 ~~La~~lgL~~~qV~vWFqNR 115 (230)
.++|+.+|+++..|+.|.+.-
T Consensus 4 ~e~a~~~gv~~~tlr~~~~~g 24 (49)
T cd04761 4 GELAKLTGVSPSTLRYYERIG 24 (49)
T ss_pred HHHHHHHCcCHHHHHHHHHCC
Confidence 478999999999999997554
No 90
>PRK12514 RNA polymerase sigma factor; Provisional
Probab=22.37 E-value=34 Score=27.28 Aligned_cols=44 Identities=11% Similarity=0.176 Sum_probs=28.9
Q ss_pred CCHHHHHHHHHhhccCCCCCHHHHHHHHHHhCCCCcceEEecccchhhh
Q 026974 71 LTAEQAELLEMHFGNEHKLESDRKDKLAAELGLDPRQVAVWFQNRRARD 119 (230)
Q Consensus 71 ~t~~Q~~~Le~~F~~~~~p~~~~r~~La~~lgL~~~qV~vWFqNRR~k~ 119 (230)
+++.+..++...|-.. ...++||..+|++...|+.+...-|.+.
T Consensus 130 L~~~~r~i~~l~~~~g-----~s~~eIA~~lgis~~tV~~~l~Rar~~L 173 (179)
T PRK12514 130 LEKDRAAAVRRAYLEG-----LSYKELAERHDVPLNTMRTWLRRSLLKL 173 (179)
T ss_pred CCHHHHHHHHHHHHcC-----CCHHHHHHHHCCChHHHHHHHHHHHHHH
Confidence 5666666666555221 2356789999999999987765444433
No 91
>PRK09642 RNA polymerase sigma factor SigW; Reviewed
Probab=22.37 E-value=51 Score=25.67 Aligned_cols=45 Identities=16% Similarity=0.215 Sum_probs=29.4
Q ss_pred CCHHHHHHHHHhhccCCCCCHHHHHHHHHHhCCCCcceEEecccchhhhh
Q 026974 71 LTAEQAELLEMHFGNEHKLESDRKDKLAAELGLDPRQVAVWFQNRRARDK 120 (230)
Q Consensus 71 ~t~~Q~~~Le~~F~~~~~p~~~~r~~La~~lgL~~~qV~vWFqNRR~k~k 120 (230)
+++.+..++...|-.. ....++|..+|++...|+.....-|.+.|
T Consensus 107 Lp~~~r~v~~l~~~~g-----~s~~EIA~~lgis~~tV~~~l~Rar~~Lr 151 (160)
T PRK09642 107 LPENYRDVVLAHYLEE-----KSYQEIALQEKIEVKTVEMKLYRARKWIK 151 (160)
T ss_pred CCHHHHHHHHHHHHhC-----CCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Confidence 5666666665554322 13457899999999999987764444444
No 92
>smart00421 HTH_LUXR helix_turn_helix, Lux Regulon. lux regulon (activates the bioluminescence operon
Probab=22.19 E-value=64 Score=19.81 Aligned_cols=37 Identities=22% Similarity=0.368 Sum_probs=26.9
Q ss_pred CCHHHHHHHHHhhccCCCCCHHHHHHHHHHhCCCCcceEEecc
Q 026974 71 LTAEQAELLEMHFGNEHKLESDRKDKLAAELGLDPRQVAVWFQ 113 (230)
Q Consensus 71 ~t~~Q~~~Le~~F~~~~~p~~~~r~~La~~lgL~~~qV~vWFq 113 (230)
++..+..++...+.. ....++|..+|++...|..|..
T Consensus 4 l~~~e~~i~~~~~~g------~s~~eia~~l~is~~tv~~~~~ 40 (58)
T smart00421 4 LTPREREVLRLLAEG------LTNKEIAERLGISEKTVKTHLS 40 (58)
T ss_pred CCHHHHHHHHHHHcC------CCHHHHHHHHCCCHHHHHHHHH
Confidence 778888888664422 1345789999999998877665
No 93
>PF06156 DUF972: Protein of unknown function (DUF972); InterPro: IPR010377 FUNCTION: Involved in initiation control of chromosome replication. SUBUNIT: Interacts with both DnaA and DnaN, acting as a bridge between these two proteins. SIMILARITY: Belongs to the YabA family.
Probab=22.05 E-value=1.8e+02 Score=21.92 Aligned_cols=38 Identities=29% Similarity=0.400 Sum_probs=19.7
Q ss_pred HHHHHHHHHhhhccchhhhhhhHHHHHHHHHHHHHHHH
Q 026974 124 IEETYATLKTAHENVVVEKTRLESEVATLKEKLSVAEK 161 (230)
Q Consensus 124 ~~~~~~~lk~~~~~~~~~~~~~~~e~~~l~~~~~~~~~ 161 (230)
+..+...||.....++.++..+.-|++.|++.+.....
T Consensus 20 l~~~~~~LK~~~~~l~EEN~~L~~EN~~Lr~~l~~~~~ 57 (107)
T PF06156_consen 20 LLEELEELKKQLQELLEENARLRIENEHLRERLEELEQ 57 (107)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhc
Confidence 33445555555555555555555555555555444433
No 94
>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=22.00 E-value=94 Score=22.14 Aligned_cols=20 Identities=5% Similarity=0.189 Sum_probs=17.2
Q ss_pred HHHHHHHhCCCCcceEEecc
Q 026974 94 KDKLAAELGLDPRQVAVWFQ 113 (230)
Q Consensus 94 r~~La~~lgL~~~qV~vWFq 113 (230)
+..|...++|...|+.+|+.
T Consensus 56 ~~~L~k~~~~~~~~i~v~~~ 75 (81)
T cd02413 56 TSLVQKRFNFPEGSVELYAE 75 (81)
T ss_pred HHHHHHHhCCCCCeEEEEEE
Confidence 45688889999999999985
No 95
>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=21.83 E-value=49 Score=24.61 Aligned_cols=41 Identities=20% Similarity=0.275 Sum_probs=27.2
Q ss_pred CCHHHHHHHHHhhccCCCCCHHHHHHHHHHhCCCCcceEEecccch
Q 026974 71 LTAEQAELLEMHFGNEHKLESDRKDKLAAELGLDPRQVAVWFQNRR 116 (230)
Q Consensus 71 ~t~~Q~~~Le~~F~~~~~p~~~~r~~La~~lgL~~~qV~vWFqNRR 116 (230)
+++.+..++...|-.. ....+||..+|+++..|..|...-+
T Consensus 111 L~~~~~~ii~~~~~~g-----~s~~eIA~~l~~s~~~v~~~~~~~~ 151 (158)
T TIGR02937 111 LPEREREVLVLRYLEG-----LSYKEIAEILGISVGTVKRRLKRAR 151 (158)
T ss_pred CCHHHHHHHhhHHhcC-----CCHHHHHHHHCCCHHHHHHHHHHHH
Confidence 6667777766554321 2345789999999998887665433
No 96
>PRK12512 RNA polymerase sigma factor; Provisional
Probab=21.77 E-value=52 Score=26.33 Aligned_cols=45 Identities=18% Similarity=0.116 Sum_probs=31.9
Q ss_pred CCHHHHHHHHHhhccCCCCCHHHHHHHHHHhCCCCcceEEecccchhhhh
Q 026974 71 LTAEQAELLEMHFGNEHKLESDRKDKLAAELGLDPRQVAVWFQNRRARDK 120 (230)
Q Consensus 71 ~t~~Q~~~Le~~F~~~~~p~~~~r~~La~~lgL~~~qV~vWFqNRR~k~k 120 (230)
+++.+..+|...|-.. ....+||..+|++...|+.++..-|.+.|
T Consensus 132 L~~~~r~v~~l~~~~g-----~s~~eIA~~l~is~~tV~~~l~ra~~~Lr 176 (184)
T PRK12512 132 LPPRQRDVVQSISVEG-----ASIKETAAKLSMSEGAVRVALHRGLAALA 176 (184)
T ss_pred CCHHHHHHHHHHHHcC-----CCHHHHHHHhCCCHHHHHHHHHHHHHHHH
Confidence 6777777777765332 23567899999999999987765444444
No 97
>PHA02955 hypothetical protein; Provisional
Probab=21.14 E-value=93 Score=26.58 Aligned_cols=43 Identities=12% Similarity=0.194 Sum_probs=33.5
Q ss_pred HHHHHHHHHhhccC-CCCCHHHHHHHHHHhCCCCcceEEecccc
Q 026974 73 AEQAELLEMHFGNE-HKLESDRKDKLAAELGLDPRQVAVWFQNR 115 (230)
Q Consensus 73 ~~Q~~~Le~~F~~~-~~p~~~~r~~La~~lgL~~~qV~vWFqNR 115 (230)
..++..|-+.|... .-+..+++.+++.+||+....|..||.+.
T Consensus 60 ~~sf~lli~a~~Et~~~Lp~~qk~~ia~~lgI~~~~~~~d~~t~ 103 (213)
T PHA02955 60 EKNFQLLIEALIETIENFPEKEQKEIAADIGINIDDYKAGKKTD 103 (213)
T ss_pred HHHHHHHHHHHHHHHHhCCHHHHHHHHHHhCCChhhccCcccch
Confidence 45666666666654 56778889999999999998889999874
No 98
>PRK10072 putative transcriptional regulator; Provisional
Probab=21.06 E-value=25 Score=26.12 Aligned_cols=41 Identities=24% Similarity=0.255 Sum_probs=29.7
Q ss_pred CCHHHHHHHHHhhccCCCCCHHHHHHHHHHhCCCCcceEEecccchhh
Q 026974 71 LTAEQAELLEMHFGNEHKLESDRKDKLAAELGLDPRQVAVWFQNRRAR 118 (230)
Q Consensus 71 ~t~~Q~~~Le~~F~~~~~p~~~~r~~La~~lgL~~~qV~vWFqNRR~k 118 (230)
.+...+..|...-..+ ..+||..+|++...|..|.+.+|.-
T Consensus 33 ~~~~eik~LR~~~glT-------Q~elA~~lGvS~~TVs~WE~G~r~P 73 (96)
T PRK10072 33 TSFTEFEQLRKGTGLK-------IDDFARVLGVSVAMVKEWESRRVKP 73 (96)
T ss_pred CChHHHHHHHHHcCCC-------HHHHHHHhCCCHHHHHHHHcCCCCC
Confidence 4666666664433222 4579999999999999999987654
No 99
>PF15058 Speriolin_N: Speriolin N terminus
Probab=20.46 E-value=5.3e+02 Score=21.80 Aligned_cols=18 Identities=28% Similarity=0.329 Sum_probs=7.6
Q ss_pred HhhhccchhhhhhhHHHH
Q 026974 132 KTAHENVVVEKTRLESEV 149 (230)
Q Consensus 132 k~~~~~~~~~~~~~~~e~ 149 (230)
.+.++..+-||..++..|
T Consensus 11 rhqierLv~ENeeLKKlV 28 (200)
T PF15058_consen 11 RHQIERLVRENEELKKLV 28 (200)
T ss_pred HHHHHHHHhhhHHHHHHH
Confidence 333333444444444444
No 100
>PRK12519 RNA polymerase sigma factor; Provisional
Probab=20.35 E-value=47 Score=26.83 Aligned_cols=45 Identities=20% Similarity=0.273 Sum_probs=29.2
Q ss_pred CCHHHHHHHHHhhccCCCCCHHHHHHHHHHhCCCCcceEEecccchhhhh
Q 026974 71 LTAEQAELLEMHFGNEHKLESDRKDKLAAELGLDPRQVAVWFQNRRARDK 120 (230)
Q Consensus 71 ~t~~Q~~~Le~~F~~~~~p~~~~r~~La~~lgL~~~qV~vWFqNRR~k~k 120 (230)
+++.+..+|...|- ......++|..+|++...|+.|+..-|.+.|
T Consensus 142 L~~~~~~v~~l~~~-----~g~s~~EIA~~lgis~~tV~~~l~Ra~~~Lr 186 (194)
T PRK12519 142 LPESQRQVLELAYY-----EGLSQSEIAKRLGIPLGTVKARARQGLLKLR 186 (194)
T ss_pred CCHHHhhhhhhhhh-----cCCCHHHHHHHhCCCHHHHHHHHHHHHHHHH
Confidence 45555555555432 2234567899999999999998864444444
No 101
>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=20.19 E-value=55 Score=25.27 Aligned_cols=38 Identities=26% Similarity=0.301 Sum_probs=27.4
Q ss_pred CCHHHHHHHHHhhccCCCCCHHHHHHHHHHhCCCCcceEEecc
Q 026974 71 LTAEQAELLEMHFGNEHKLESDRKDKLAAELGLDPRQVAVWFQ 113 (230)
Q Consensus 71 ~t~~Q~~~Le~~F~~~~~p~~~~r~~La~~lgL~~~qV~vWFq 113 (230)
+++.+..++...|-.. ....++|..+|++...|+.+..
T Consensus 112 L~~~~r~v~~l~~~~g-----~~~~eIA~~l~is~~tv~~~l~ 149 (159)
T TIGR02989 112 LPERQRELLQLRYQRG-----VSLTALAEQLGRTVNAVYKALS 149 (159)
T ss_pred CCHHHHHHHHHHHhcC-----CCHHHHHHHhCCCHHHHHHHHH
Confidence 7777777777754322 2356789999999999987654
No 102
>PF13936 HTH_38: Helix-turn-helix domain; PDB: 2W48_A.
Probab=20.11 E-value=61 Score=20.08 Aligned_cols=37 Identities=22% Similarity=0.210 Sum_probs=17.6
Q ss_pred CCCHHHHHHHHHhhccCCCCCHHHHHHHHHHhCCCCcceEEe
Q 026974 70 KLTAEQAELLEMHFGNEHKLESDRKDKLAAELGLDPRQVAVW 111 (230)
Q Consensus 70 ~~t~~Q~~~Le~~F~~~~~p~~~~r~~La~~lgL~~~qV~vW 111 (230)
.+|.+|...++..+... .-..+||..||.+..-|..|
T Consensus 4 ~Lt~~eR~~I~~l~~~G-----~s~~~IA~~lg~s~sTV~re 40 (44)
T PF13936_consen 4 HLTPEERNQIEALLEQG-----MSIREIAKRLGRSRSTVSRE 40 (44)
T ss_dssp --------HHHHHHCS--------HHHHHHHTT--HHHHHHH
T ss_pred chhhhHHHHHHHHHHcC-----CCHHHHHHHHCcCcHHHHHH
Confidence 48889999999887644 23446899999887666443
Done!