Query 029573
Match_columns 191
No_of_seqs 243 out of 1108
Neff 5.0
Searched_HMMs 46136
Date Fri Mar 29 15:05:04 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/029573.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/029573hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF04618 HD-ZIP_N: HD-ZIP prot 99.9 1.7E-26 3.7E-31 178.9 6.3 102 1-107 2-110 (111)
2 KOG0483 Transcription factor H 99.7 1.1E-18 2.4E-23 147.2 5.0 61 129-189 48-110 (198)
3 KOG0842 Transcription factor t 99.7 2.5E-18 5.4E-23 153.0 7.1 52 138-189 160-213 (307)
4 KOG0489 Transcription factor z 99.7 6.2E-19 1.3E-23 153.3 2.9 61 129-189 157-219 (261)
5 KOG0487 Transcription factor A 99.7 1.8E-18 4E-23 153.9 4.4 58 129-186 233-292 (308)
6 KOG0488 Transcription factor B 99.7 1.9E-18 4.2E-23 153.9 4.5 60 129-188 170-231 (309)
7 KOG0843 Transcription factor E 99.7 1.1E-17 2.3E-22 139.3 4.6 60 130-189 101-162 (197)
8 KOG0484 Transcription factor P 99.7 1.2E-17 2.6E-22 129.0 1.1 59 130-188 16-76 (125)
9 KOG0485 Transcription factor N 99.7 4.2E-17 9.1E-22 139.5 4.3 58 130-187 101-162 (268)
10 PF00046 Homeobox: Homeobox do 99.7 4.7E-17 1E-21 109.7 3.6 55 132-186 1-57 (57)
11 KOG0492 Transcription factor M 99.6 2.8E-16 6E-21 133.7 4.8 59 130-188 143-203 (246)
12 KOG0850 Transcription factor D 99.6 3E-16 6.5E-21 134.7 4.4 58 131-188 122-181 (245)
13 KOG0494 Transcription factor C 99.6 1.3E-15 2.9E-20 133.2 5.4 54 135-188 145-200 (332)
14 KOG2251 Homeobox transcription 99.6 3.2E-15 6.9E-20 127.7 4.6 62 128-189 34-97 (228)
15 cd00086 homeodomain Homeodomai 99.5 6.3E-15 1.4E-19 98.6 3.9 55 133-187 2-58 (59)
16 COG5576 Homeodomain-containing 99.5 9.5E-15 2.1E-19 119.3 5.6 61 128-188 48-110 (156)
17 smart00389 HOX Homeodomain. DN 99.5 6.8E-15 1.5E-19 98.1 3.5 53 133-185 2-56 (56)
18 KOG0844 Transcription factor E 99.5 5.6E-15 1.2E-19 131.7 4.0 60 131-190 181-242 (408)
19 KOG0848 Transcription factor C 99.5 4.2E-15 9.1E-20 130.3 1.3 51 137-187 205-257 (317)
20 KOG0493 Transcription factor E 99.4 6E-14 1.3E-18 123.0 3.7 57 131-187 246-304 (342)
21 TIGR01565 homeo_ZF_HD homeobox 99.4 2.6E-13 5.6E-18 94.4 5.7 50 132-181 2-57 (58)
22 KOG0491 Transcription factor B 99.3 1.8E-13 3.9E-18 113.1 0.2 57 132-188 101-159 (194)
23 KOG0847 Transcription factor, 99.3 9.8E-13 2.1E-17 113.2 2.4 60 130-189 164-227 (288)
24 KOG0490 Transcription factor, 99.3 1.9E-12 4.1E-17 107.3 3.4 60 129-188 58-119 (235)
25 KOG4577 Transcription factor L 99.3 2.7E-12 5.9E-17 114.0 4.2 60 128-187 164-225 (383)
26 KOG0486 Transcription factor P 99.3 5.2E-12 1.1E-16 112.9 5.0 54 134-187 115-170 (351)
27 KOG3802 Transcription factor O 99.2 1.4E-11 3E-16 112.8 4.8 57 130-186 293-351 (398)
28 KOG0849 Transcription factor P 99.0 1.1E-10 2.3E-15 106.0 3.2 60 129-188 174-235 (354)
29 KOG1168 Transcription factor A 98.7 1.5E-08 3.2E-13 90.5 3.2 59 129-187 307-367 (385)
30 KOG0775 Transcription factor S 98.4 1.6E-07 3.5E-12 83.0 3.8 49 138-186 183-233 (304)
31 KOG0774 Transcription factor P 98.3 4E-07 8.6E-12 80.5 3.5 57 130-186 187-248 (334)
32 KOG0490 Transcription factor, 98.3 7.5E-07 1.6E-11 73.8 4.7 124 64-187 71-211 (235)
33 PF05920 Homeobox_KN: Homeobox 98.0 1E-06 2.2E-11 57.0 0.3 32 152-183 7-40 (40)
34 KOG2252 CCAAT displacement pro 97.6 4.7E-05 1E-09 72.8 4.0 56 129-184 418-475 (558)
35 KOG1146 Homeobox protein [Gene 96.7 0.00099 2.1E-08 69.2 2.5 59 130-188 902-962 (1406)
36 KOG0773 Transcription factor M 96.0 0.0043 9.3E-08 55.4 2.4 55 132-186 240-299 (342)
37 PF11569 Homez: Homeodomain le 95.8 0.0036 7.8E-08 43.5 1.0 40 143-182 10-51 (56)
38 KOG3623 Homeobox transcription 91.9 0.12 2.5E-06 51.9 2.7 44 143-186 568-613 (1007)
39 PF04218 CENP-B_N: CENP-B N-te 88.8 0.42 9E-06 32.2 2.5 45 132-181 1-47 (53)
40 PF04967 HTH_10: HTH DNA bindi 82.6 1.1 2.3E-05 30.6 2.1 48 138-185 1-50 (53)
41 COG3413 Predicted DNA binding 75.8 2 4.3E-05 36.0 2.2 50 137-186 155-206 (215)
42 PF01527 HTH_Tnp_1: Transposas 60.7 8.8 0.00019 26.3 2.5 41 133-178 2-45 (76)
43 cd00569 HTH_Hin_like Helix-tur 58.9 17 0.00037 19.5 3.2 35 137-176 5-41 (42)
44 PRK09646 RNA polymerase sigma 50.3 16 0.00035 29.4 2.9 46 138-190 143-190 (194)
45 COG4367 Uncharacterized protei 49.3 14 0.00031 28.1 2.2 34 138-171 3-36 (97)
46 cd06171 Sigma70_r4 Sigma70, re 47.9 12 0.00027 22.6 1.5 40 138-182 11-52 (55)
47 PRK09648 RNA polymerase sigma 47.3 19 0.0004 28.8 2.7 46 138-190 140-187 (189)
48 PRK12519 RNA polymerase sigma 44.0 16 0.00035 29.2 1.9 45 138-189 142-188 (194)
49 PRK09652 RNA polymerase sigma 43.7 18 0.00039 27.9 2.1 45 137-188 128-174 (182)
50 PRK12526 RNA polymerase sigma 42.4 24 0.00051 29.0 2.7 45 138-189 154-200 (206)
51 PRK09639 RNA polymerase sigma 41.5 24 0.00051 27.3 2.5 44 138-189 113-158 (166)
52 PF04545 Sigma70_r4: Sigma-70, 40.3 22 0.00049 22.6 1.8 43 137-186 4-48 (50)
53 PRK03975 tfx putative transcri 39.4 27 0.00058 28.3 2.5 46 135-186 4-51 (141)
54 TIGR02989 Sig-70_gvs1 RNA poly 37.9 38 0.00082 25.8 3.1 45 138-189 112-158 (159)
55 KOG3755 SATB1 matrix attachmen 36.9 7.4 0.00016 38.7 -1.3 17 172-188 742-758 (769)
56 PRK09413 IS2 repressor TnpA; R 36.0 55 0.0012 25.0 3.7 43 132-179 7-52 (121)
57 TIGR02939 RpoE_Sigma70 RNA pol 35.7 26 0.00057 27.6 1.9 45 138-189 139-185 (190)
58 PF02796 HTH_7: Helix-turn-hel 35.0 31 0.00067 21.9 1.8 35 137-176 5-41 (45)
59 TIGR02948 SigW_bacill RNA poly 34.4 33 0.00071 27.0 2.3 46 137-189 136-183 (187)
60 TIGR02999 Sig-70_X6 RNA polyme 34.4 42 0.00092 26.4 2.9 47 138-191 135-183 (183)
61 PRK05602 RNA polymerase sigma 32.7 37 0.00079 27.0 2.3 45 138-189 129-175 (186)
62 PHA02955 hypothetical protein; 32.5 59 0.0013 28.3 3.6 42 139-180 59-103 (213)
63 PRK09642 RNA polymerase sigma 29.5 47 0.001 25.5 2.4 45 138-189 107-153 (160)
64 PRK12539 RNA polymerase sigma 29.2 52 0.0011 26.2 2.7 46 138-190 132-179 (184)
65 PF10668 Phage_terminase: Phag 28.6 23 0.0005 24.8 0.4 17 160-176 24-42 (60)
66 TIGR02959 SigZ RNA polymerase 27.7 56 0.0012 25.7 2.6 45 137-188 100-146 (170)
67 PRK12511 RNA polymerase sigma 27.2 51 0.0011 26.6 2.3 46 138-190 112-159 (182)
68 PF13936 HTH_38: Helix-turn-he 27.2 48 0.001 21.1 1.7 34 136-174 3-38 (44)
69 KOG3623 Homeobox transcription 26.4 42 0.0009 34.5 1.9 57 132-188 627-685 (1007)
70 PF13551 HTH_29: Winged helix- 26.0 1E+02 0.0022 22.0 3.5 44 134-177 54-108 (112)
71 PRK12535 RNA polymerase sigma 25.2 66 0.0014 26.2 2.7 46 138-190 134-181 (196)
72 PRK12536 RNA polymerase sigma 25.1 70 0.0015 25.3 2.7 45 138-189 130-176 (181)
73 PF08281 Sigma70_r4_2: Sigma-7 25.1 51 0.0011 21.1 1.6 36 138-178 11-48 (54)
74 PF13443 HTH_26: Cro/C1-type H 25.0 26 0.00057 23.0 0.2 21 161-181 13-35 (63)
75 PRK12515 RNA polymerase sigma 24.7 68 0.0015 25.5 2.6 45 138-189 132-178 (189)
76 PRK13558 bacterio-opsin activa 24.6 52 0.0011 31.4 2.2 50 137-186 607-658 (665)
77 PRK12530 RNA polymerase sigma 24.5 67 0.0014 25.8 2.5 45 138-189 135-181 (189)
78 PRK12538 RNA polymerase sigma 24.5 53 0.0012 27.8 2.0 45 138-189 172-218 (233)
79 PRK12531 RNA polymerase sigma 23.0 81 0.0018 25.3 2.7 46 138-190 142-189 (194)
80 PRK09480 slmA division inhibit 22.1 1E+02 0.0022 24.1 3.1 38 144-182 14-56 (194)
81 TIGR00721 tfx DNA-binding prot 21.5 88 0.0019 25.2 2.6 48 135-188 4-51 (137)
82 PF08280 HTH_Mga: M protein tr 21.4 85 0.0018 21.0 2.2 28 140-171 5-32 (59)
83 PRK07037 extracytoplasmic-func 21.1 99 0.0021 23.7 2.8 45 138-189 110-156 (163)
84 PRK10072 putative transcriptio 20.8 38 0.00083 25.5 0.4 23 160-182 48-72 (96)
85 PRK09643 RNA polymerase sigma 20.1 82 0.0018 25.4 2.2 47 138-189 135-181 (192)
No 1
>PF04618 HD-ZIP_N: HD-ZIP protein N terminus; InterPro: IPR006712 Homeodomain leucine zipper (HDZip) genes encode putative transcription factors that are unique to plants. This observation suggests that homeobox-leucine zipper genes evolved after the divergence of plants and animals, perhaps to mediate specific regulatory events []. This domain is the N-terminal of plant homeobox-leucine zipper proteins. Its function is unknown.; GO: 0006351 transcription, DNA-dependent, 0005634 nucleus
Probab=99.93 E-value=1.7e-26 Score=178.89 Aligned_cols=102 Identities=67% Similarity=0.867 Sum_probs=85.3
Q ss_pred CCCcCcccceeecCCCCCC-----CCcccCcCCCCcCCCCCCCCCCCCCCCCcCCCCCCCCCchhhHhhhhhhhcccccC
Q 029573 1 MAEKDDLGLSLSLSFPQNH-----HSLQLNLMPSSACSTSPSGFSLQKTPWNEALFPSSDPNSESCRAETRSFLRGIDVN 75 (191)
Q Consensus 1 ~~~~~~~~~~~~~~~~~~~-----~~~~~~l~p~~~~~~~~~~~~~~~~~w~~~~~~~~~~~~~~c~~~~~~~~rg~dvn 75 (191)
|.+||||||||||+|++++ ||++++|+|+++ |.....+...|+. .|...++.+..|..++++|+||||||
T Consensus 2 ~~~~d~LGLsLSLg~~~~~~~~~~~plql~L~P~s~----p~~~~~~~~s~~~-~~~~~~~~~~~~~~~~~~flRgiDVN 76 (111)
T PF04618_consen 2 MEKKDGLGLSLSLGFAGNRHPSQQPPLQLNLLPSSS----PSNSHPLFSSHNQ-PFWSDDRMMASCDSETRSFLRGIDVN 76 (111)
T ss_pred CCCCCcceeeeeccCCCCCCCccCCCcccccCCccc----cccccCccccccc-cCCccccccccccccccccccceecc
Confidence 3445789999999998765 579999999985 3444455566666 67777788888889999999999999
Q ss_pred CCCCCC--cccccccCCCCCCccccccCCCCCCC
Q 029573 76 RLPSHA--DNEEEVGVSSPNSTISSVSGKRSERE 107 (191)
Q Consensus 76 ~~p~~~--~~ee~~~~ssp~S~~ss~s~~rs~~~ 107 (191)
++|.++ +|||+++++|||||+||++|+|++++
T Consensus 77 r~p~~~~~d~eEe~gvSSPNStiSS~sgkr~~~~ 110 (111)
T PF04618_consen 77 RLPSTVEADCEEEAGVSSPNSTISSVSGKRSERE 110 (111)
T ss_pred CCCccccccccccccccCCCccceeccccccccc
Confidence 999988 89999999999999999999998764
No 2
>KOG0483 consensus Transcription factor HEX, contains HOX and HALZ domains [Transcription]
Probab=99.74 E-value=1.1e-18 Score=147.16 Aligned_cols=61 Identities=26% Similarity=0.292 Sum_probs=57.8
Q ss_pred CCCCCCCccCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCC--cceeeCCchhhhHHhhhc
Q 029573 129 GDTSRKKLRLSKDQSAILEESFKEHNTLNPVSIFLLRLLLVLR--ENEVKLEKKKKKTFLQFL 189 (191)
Q Consensus 129 ~~~~RkR~r~s~~Q~~~LE~~F~~~~~p~~~~r~~LA~qL~Ls--QVqVWFQNRRaK~K~kq~ 189 (191)
....+||.||+.+|+..||+.|+.++++.+.+|..||++|||+ ||.|||||||||||.||+
T Consensus 48 ~~~~~kk~Rlt~eQ~~~LE~~F~~~~~L~p~~K~~LAk~LgL~pRQVavWFQNRRARwK~kql 110 (198)
T KOG0483|consen 48 SKGKGKKRRLTSEQVKFLEKSFESEKKLEPERKKKLAKELGLQPRQVAVWFQNRRARWKTKQL 110 (198)
T ss_pred cccccccccccHHHHHHhHHhhccccccChHHHHHHHHhhCCChhHHHHHHhhccccccchhh
Confidence 3467888899999999999999999999999999999999999 999999999999999986
No 3
>KOG0842 consensus Transcription factor tinman/NKX2-3, contains HOX domain [Transcription]
Probab=99.74 E-value=2.5e-18 Score=152.98 Aligned_cols=52 Identities=23% Similarity=0.180 Sum_probs=50.8
Q ss_pred CCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCC--cceeeCCchhhhHHhhhc
Q 029573 138 LSKDQSAILEESFKEHNTLNPVSIFLLRLLLVLR--ENEVKLEKKKKKTFLQFL 189 (191)
Q Consensus 138 ~s~~Q~~~LE~~F~~~~~p~~~~r~~LA~qL~Ls--QVqVWFQNRRaK~K~kq~ 189 (191)
||..|+.+||+.|+.++|++..+|++||+.|+|| ||||||||||.|.||+++
T Consensus 160 FSqAQV~ELERRFrqQRYLSAPERE~LA~~LrLT~TQVKIWFQNrRYK~KR~~~ 213 (307)
T KOG0842|consen 160 FSQAQVYELERRFRQQRYLSAPEREHLASSLRLTPTQVKIWFQNRRYKTKRQQK 213 (307)
T ss_pred cchhHHHHHHHHHHhhhccccHhHHHHHHhcCCCchheeeeeecchhhhhhhhh
Confidence 9999999999999999999999999999999999 999999999999999874
No 4
>KOG0489 consensus Transcription factor zerknullt and related HOX domain proteins [General function prediction only]
Probab=99.74 E-value=6.2e-19 Score=153.30 Aligned_cols=61 Identities=16% Similarity=0.175 Sum_probs=57.3
Q ss_pred CCCCCCCccCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCC--cceeeCCchhhhHHhhhc
Q 029573 129 GDTSRKKLRLSKDQSAILEESFKEHNTLNPVSIFLLRLLLVLR--ENEVKLEKKKKKTFLQFL 189 (191)
Q Consensus 129 ~~~~RkR~r~s~~Q~~~LE~~F~~~~~p~~~~r~~LA~qL~Ls--QVqVWFQNRRaK~K~kq~ 189 (191)
+..+|.|+.||..|+.+||+.|..|+|++...|.+||..|.|+ |||||||||||||||+.+
T Consensus 157 ~~~kR~RtayT~~QllELEkEFhfN~YLtR~RRiEiA~~L~LtErQIKIWFQNRRMK~Kk~~k 219 (261)
T KOG0489|consen 157 GKSKRRRTAFTRYQLLELEKEFHFNKYLTRSRRIEIAHALNLTERQIKIWFQNRRMKWKKENK 219 (261)
T ss_pred CCCCCCCcccchhhhhhhhhhhccccccchHHHHHHHhhcchhHHHHHHHHHHHHHHHHHhhc
Confidence 4578888889999999999999999999999999999999999 999999999999998654
No 5
>KOG0487 consensus Transcription factor Abd-B, contains HOX domain [Transcription]
Probab=99.73 E-value=1.8e-18 Score=153.90 Aligned_cols=58 Identities=17% Similarity=0.153 Sum_probs=55.8
Q ss_pred CCCCCCCccCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCC--cceeeCCchhhhHHh
Q 029573 129 GDTSRKKLRLSKDQSAILEESFKEHNTLNPVSIFLLRLLLVLR--ENEVKLEKKKKKTFL 186 (191)
Q Consensus 129 ~~~~RkR~r~s~~Q~~~LE~~F~~~~~p~~~~r~~LA~qL~Ls--QVqVWFQNRRaK~K~ 186 (191)
+.++|||..||+.|+.+||+.|-.|.|++.+.|.+|++.|+|+ ||||||||||+|.||
T Consensus 233 ~~~RKKRcPYTK~QtlELEkEFlfN~YitkeKR~ElSr~lNLTeRQVKIWFQNRRMK~KK 292 (308)
T KOG0487|consen 233 RRGRKKRCPYTKHQTLELEKEFLFNMYITKEKRLELSRTLNLTERQVKIWFQNRRMKEKK 292 (308)
T ss_pred cccccccCCchHHHHHHHHHHHHHHHHHhHHHHHHHHHhcccchhheeeeehhhhhHHhh
Confidence 5678889999999999999999999999999999999999999 999999999999998
No 6
>KOG0488 consensus Transcription factor BarH and related HOX domain proteins [General function prediction only]
Probab=99.73 E-value=1.9e-18 Score=153.92 Aligned_cols=60 Identities=18% Similarity=0.154 Sum_probs=54.5
Q ss_pred CCCCCCCccCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCC--cceeeCCchhhhHHhhh
Q 029573 129 GDTSRKKLRLSKDQSAILEESFKEHNTLNPVSIFLLRLLLVLR--ENEVKLEKKKKKTFLQF 188 (191)
Q Consensus 129 ~~~~RkR~r~s~~Q~~~LE~~F~~~~~p~~~~r~~LA~qL~Ls--QVqVWFQNRRaK~K~kq 188 (191)
++.++.|+.||..|+..||+.|++.+|++..+|++||+.|||+ ||++||||||+|||+..
T Consensus 170 kK~RksRTaFT~~Ql~~LEkrF~~QKYLS~~DR~~LA~~LgLTdaQVKtWfQNRRtKWKrq~ 231 (309)
T KOG0488|consen 170 KKRRKSRTAFSDHQLFELEKRFEKQKYLSVADRIELAASLGLTDAQVKTWFQNRRTKWKRQT 231 (309)
T ss_pred cccccchhhhhHHHHHHHHHHHHHhhcccHHHHHHHHHHcCCchhhHHHHHhhhhHHHHHHH
Confidence 3445556669999999999999999999999999999999999 99999999999999953
No 7
>KOG0843 consensus Transcription factor EMX1 and related HOX domain proteins [Transcription]
Probab=99.70 E-value=1.1e-17 Score=139.34 Aligned_cols=60 Identities=17% Similarity=0.130 Sum_probs=57.0
Q ss_pred CCCCCCccCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCC--cceeeCCchhhhHHhhhc
Q 029573 130 DTSRKKLRLSKDQSAILEESFKEHNTLNPVSIFLLRLLLVLR--ENEVKLEKKKKKTFLQFL 189 (191)
Q Consensus 130 ~~~RkR~r~s~~Q~~~LE~~F~~~~~p~~~~r~~LA~qL~Ls--QVqVWFQNRRaK~K~kq~ 189 (191)
..+|.|+.||.+|+..||.+|+.++|....+|++||+.|+|+ ||+|||||||+|.||+|.
T Consensus 101 ~~kr~RT~ft~~Ql~~LE~~F~~~~Yvvg~eR~~LA~~L~LsetQVkvWFQNRRtk~kr~~~ 162 (197)
T KOG0843|consen 101 RPKRIRTAFTPEQLLKLEHAFEGNQYVVGAERKQLAQSLSLSETQVKVWFQNRRTKHKRMQQ 162 (197)
T ss_pred CCCccccccCHHHHHHHHHHHhcCCeeechHHHHHHHHcCCChhHhhhhhhhhhHHHHHHHH
Confidence 567888889999999999999999999999999999999999 999999999999999874
No 8
>KOG0484 consensus Transcription factor PHOX2/ARIX, contains HOX domain [Transcription]
Probab=99.67 E-value=1.2e-17 Score=128.96 Aligned_cols=59 Identities=19% Similarity=0.122 Sum_probs=54.0
Q ss_pred CCCCCCccCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCC--cceeeCCchhhhHHhhh
Q 029573 130 DTSRKKLRLSKDQSAILEESFKEHNTLNPVSIFLLRLLLVLR--ENEVKLEKKKKKTFLQF 188 (191)
Q Consensus 130 ~~~RkR~r~s~~Q~~~LE~~F~~~~~p~~~~r~~LA~qL~Ls--QVqVWFQNRRaK~K~kq 188 (191)
..+|-|+.||..|+.+||++|.+.+||++.+|++||.+++|+ +|||||||||||.+++.
T Consensus 16 KQRRIRTTFTS~QLkELErvF~ETHYPDIYTREEiA~kidLTEARVQVWFQNRRAKfRKQE 76 (125)
T KOG0484|consen 16 KQRRIRTTFTSAQLKELERVFAETHYPDIYTREEIALKIDLTEARVQVWFQNRRAKFRKQE 76 (125)
T ss_pred HhhhhhhhhhHHHHHHHHHHHHhhcCCcchhHHHHHHhhhhhHHHHHHHHHhhHHHHHHHH
Confidence 345556779999999999999999999999999999999999 99999999999998753
No 9
>KOG0485 consensus Transcription factor NKX-5.1/HMX1, contains HOX domain [Transcription]
Probab=99.66 E-value=4.2e-17 Score=139.52 Aligned_cols=58 Identities=24% Similarity=0.225 Sum_probs=52.9
Q ss_pred CCCCCC--ccCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCC--cceeeCCchhhhHHhh
Q 029573 130 DTSRKK--LRLSKDQSAILEESFKEHNTLNPVSIFLLRLLLVLR--ENEVKLEKKKKKTFLQ 187 (191)
Q Consensus 130 ~~~RkR--~r~s~~Q~~~LE~~F~~~~~p~~~~r~~LA~qL~Ls--QVqVWFQNRRaK~K~k 187 (191)
+.+||| +.|+..|+..||..|+.+.|++..+|..||++|.|+ ||||||||||.|||++
T Consensus 101 ~~RKKktRTvFSraQV~qLEs~Fe~krYLSsaeRa~LA~sLqLTETQVKIWFQNRRnKwKRq 162 (268)
T KOG0485|consen 101 DDRKKKTRTVFSRAQVFQLESTFELKRYLSSAERAGLAASLQLTETQVKIWFQNRRNKWKRQ 162 (268)
T ss_pred ccccccchhhhhHHHHHHHHHHHHHHhhhhHHHHhHHHHhhhhhhhhhhhhhhhhhHHHHHH
Confidence 334444 459999999999999999999999999999999999 9999999999999995
No 10
>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=99.66 E-value=4.7e-17 Score=109.67 Aligned_cols=55 Identities=25% Similarity=0.257 Sum_probs=52.8
Q ss_pred CCCCccCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCC--cceeeCCchhhhHHh
Q 029573 132 SRKKLRLSKDQSAILEESFKEHNTLNPVSIFLLRLLLVLR--ENEVKLEKKKKKTFL 186 (191)
Q Consensus 132 ~RkR~r~s~~Q~~~LE~~F~~~~~p~~~~r~~LA~qL~Ls--QVqVWFQNRRaK~K~ 186 (191)
+|+|+.||.+|+.+||..|..++||+..+++.||.+|||+ +|++||||||+|+|+
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 4788899999999999999999999999999999999999 999999999999986
No 11
>KOG0492 consensus Transcription factor MSH, contains HOX domain [General function prediction only]
Probab=99.62 E-value=2.8e-16 Score=133.65 Aligned_cols=59 Identities=15% Similarity=0.164 Sum_probs=55.2
Q ss_pred CCCCCCccCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCC--cceeeCCchhhhHHhhh
Q 029573 130 DTSRKKLRLSKDQSAILEESFKEHNTLNPVSIFLLRLLLVLR--ENEVKLEKKKKKTFLQF 188 (191)
Q Consensus 130 ~~~RkR~r~s~~Q~~~LE~~F~~~~~p~~~~r~~LA~qL~Ls--QVqVWFQNRRaK~K~kq 188 (191)
.+++.|+.||..|+..||+.|+..+|+++.+|.+++..|.|+ ||+|||||||||.||-|
T Consensus 143 ~nRkPRtPFTtqQLlaLErkfrekqYLSiaEraefSsSL~LTeTqVKIWFQNRRAKaKRlQ 203 (246)
T KOG0492|consen 143 PNRKPRTPFTTQQLLALERKFREKQYLSIAERAEFSSSLELTETQVKIWFQNRRAKAKRLQ 203 (246)
T ss_pred CCCCCCCCCCHHHHHHHHHHHhHhhhhhHHHHHhhhhhhhhhhhheehhhhhhhHHHHHHH
Confidence 456667889999999999999999999999999999999999 99999999999999865
No 12
>KOG0850 consensus Transcription factor DLX and related proteins with LIM Zn-binding and HOX domains [Transcription]
Probab=99.62 E-value=3e-16 Score=134.73 Aligned_cols=58 Identities=16% Similarity=0.063 Sum_probs=53.1
Q ss_pred CCCCCccCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCC--cceeeCCchhhhHHhhh
Q 029573 131 TSRKKLRLSKDQSAILEESFKEHNTLNPVSIFLLRLLLVLR--ENEVKLEKKKKKTFLQF 188 (191)
Q Consensus 131 ~~RkR~r~s~~Q~~~LE~~F~~~~~p~~~~r~~LA~qL~Ls--QVqVWFQNRRaK~K~kq 188 (191)
-++.|+.|+.-|++.|.+.|+++.|+-..+|.+||..|||+ ||||||||||.|.||..
T Consensus 122 ~RKPRTIYSS~QLqaL~rRFQkTQYLALPERAeLAAsLGLTQTQVKIWFQNrRSK~KKl~ 181 (245)
T KOG0850|consen 122 VRKPRTIYSSLQLQALNRRFQQTQYLALPERAELAASLGLTQTQVKIWFQNRRSKFKKLK 181 (245)
T ss_pred ccCCcccccHHHHHHHHHHHhhcchhcCcHHHHHHHHhCCchhHhhhhhhhhHHHHHHHH
Confidence 34456779999999999999999999999999999999999 99999999999998843
No 13
>KOG0494 consensus Transcription factor CHX10 and related HOX domain proteins [General function prediction only]
Probab=99.58 E-value=1.3e-15 Score=133.18 Aligned_cols=54 Identities=19% Similarity=0.070 Sum_probs=51.4
Q ss_pred CccCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCC--cceeeCCchhhhHHhhh
Q 029573 135 KLRLSKDQSAILEESFKEHNTLNPVSIFLLRLLLVLR--ENEVKLEKKKKKTFLQF 188 (191)
Q Consensus 135 R~r~s~~Q~~~LE~~F~~~~~p~~~~r~~LA~qL~Ls--QVqVWFQNRRaK~K~kq 188 (191)
|+.||..|+.+||++|++.+||+...|+-||.++.|. +|+||||||||||+|+.
T Consensus 145 RTiFT~~Qle~LEkaFkeaHYPDv~Are~la~ktelpEDRIqVWfQNRRAKWRk~E 200 (332)
T KOG0494|consen 145 RTIFTSYQLEELEKAFKEAHYPDVYAREMLADKTELPEDRIQVWFQNRRAKWRKTE 200 (332)
T ss_pred cchhhHHHHHHHHHHHhhccCccHHHHHHHhhhccCchhhhhHHhhhhhHHhhhhh
Confidence 5569999999999999999999999999999999999 99999999999998865
No 14
>KOG2251 consensus Homeobox transcription factor [Transcription]
Probab=99.55 E-value=3.2e-15 Score=127.68 Aligned_cols=62 Identities=19% Similarity=0.165 Sum_probs=57.8
Q ss_pred CCCCCCCCccCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCC--cceeeCCchhhhHHhhhc
Q 029573 128 DGDTSRKKLRLSKDQSAILEESFKEHNTLNPVSIFLLRLLLVLR--ENEVKLEKKKKKTFLQFL 189 (191)
Q Consensus 128 ~~~~~RkR~r~s~~Q~~~LE~~F~~~~~p~~~~r~~LA~qL~Ls--QVqVWFQNRRaK~K~kq~ 189 (191)
.++.+|-|+.|+..|+.+||..|.+..||+...|++||.+|+|. +|+|||.|||||+|++|.
T Consensus 34 pRkqRRERTtFtr~QlevLe~LF~kTqYPDv~~rEelAlklnLpeSrVqVWFKNRRAK~r~qq~ 97 (228)
T KOG2251|consen 34 PRKQRRERTTFTRKQLEVLEALFAKTQYPDVFMREELALKLNLPESRVQVWFKNRRAKCRRQQQ 97 (228)
T ss_pred chhcccccceecHHHHHHHHHHHHhhcCccHHHHHHHHHHhCCchhhhhhhhccccchhhHhhh
Confidence 35678889999999999999999999999999999999999999 999999999999998663
No 15
>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=99.53 E-value=6.3e-15 Score=98.65 Aligned_cols=55 Identities=20% Similarity=0.187 Sum_probs=51.9
Q ss_pred CCCccCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCC--cceeeCCchhhhHHhh
Q 029573 133 RKKLRLSKDQSAILEESFKEHNTLNPVSIFLLRLLLVLR--ENEVKLEKKKKKTFLQ 187 (191)
Q Consensus 133 RkR~r~s~~Q~~~LE~~F~~~~~p~~~~r~~LA~qL~Ls--QVqVWFQNRRaK~K~k 187 (191)
+++..++.+|+.+||..|..++||+..++..||.++||+ +|++||+|||++.|+.
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 567789999999999999999999999999999999999 9999999999998864
No 16
>COG5576 Homeodomain-containing transcription factor [Transcription]
Probab=99.53 E-value=9.5e-15 Score=119.25 Aligned_cols=61 Identities=20% Similarity=0.264 Sum_probs=57.0
Q ss_pred CCCCCCCCccCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCC--cceeeCCchhhhHHhhh
Q 029573 128 DGDTSRKKLRLSKDQSAILEESFKEHNTLNPVSIFLLRLLLVLR--ENEVKLEKKKKKTFLQF 188 (191)
Q Consensus 128 ~~~~~RkR~r~s~~Q~~~LE~~F~~~~~p~~~~r~~LA~qL~Ls--QVqVWFQNRRaK~K~kq 188 (191)
....+++|+|.|..|+.+|++.|+.++||+...|..|+..|+|+ .|||||||||++.|++.
T Consensus 48 s~~~~~~r~R~t~~Q~~vL~~~F~i~p~Ps~~~r~~L~~~lnm~~ksVqIWFQNkR~~~k~~~ 110 (156)
T COG5576 48 SSPPKSKRRRTTDEQLMVLEREFEINPYPSSITRIKLSLLLNMPPKSVQIWFQNKRAKEKKKR 110 (156)
T ss_pred CCcCcccceechHHHHHHHHHHhccCCCCCHHHHHHHHHhcCCChhhhhhhhchHHHHHHHhc
Confidence 35578889999999999999999999999999999999999999 89999999999998864
No 17
>smart00389 HOX Homeodomain. DNA-binding factors that are involved in the transcriptional regulation of key developmental processes
Probab=99.52 E-value=6.8e-15 Score=98.06 Aligned_cols=53 Identities=21% Similarity=0.176 Sum_probs=49.8
Q ss_pred CCCccCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCC--cceeeCCchhhhHH
Q 029573 133 RKKLRLSKDQSAILEESFKEHNTLNPVSIFLLRLLLVLR--ENEVKLEKKKKKTF 185 (191)
Q Consensus 133 RkR~r~s~~Q~~~LE~~F~~~~~p~~~~r~~LA~qL~Ls--QVqVWFQNRRaK~K 185 (191)
+.|..|+.+|+.+||..|..++||+..++..||..+||+ +|++||+|||++.|
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 456679999999999999999999999999999999999 99999999999864
No 18
>KOG0844 consensus Transcription factor EVX1, contains HOX domain [Transcription]
Probab=99.52 E-value=5.6e-15 Score=131.72 Aligned_cols=60 Identities=23% Similarity=0.201 Sum_probs=56.5
Q ss_pred CCCCCccCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCC--cceeeCCchhhhHHhhhcc
Q 029573 131 TSRKKLRLSKDQSAILEESFKEHNTLNPVSIFLLRLLLVLR--ENEVKLEKKKKKTFLQFLI 190 (191)
Q Consensus 131 ~~RkR~r~s~~Q~~~LE~~F~~~~~p~~~~r~~LA~qL~Ls--QVqVWFQNRRaK~K~kq~~ 190 (191)
-+|-|+-||.+|+..||+.|-+.+|.+...|.+||..|||. .|||||||||+|+|++.|.
T Consensus 181 mRRYRTAFTReQIaRLEKEFyrENYVSRprRcELAAaLNLPEtTIKVWFQNRRMKDKRQRla 242 (408)
T KOG0844|consen 181 MRRYRTAFTREQIARLEKEFYRENYVSRPRRCELAAALNLPETTIKVWFQNRRMKDKRQRLA 242 (408)
T ss_pred HHHHHhhhhHHHHHHHHHHHHHhccccCchhhhHHHhhCCCcceeehhhhhchhhhhhhhhh
Confidence 46778889999999999999999999999999999999999 9999999999999998763
No 19
>KOG0848 consensus Transcription factor Caudal, contains HOX domain [Transcription]
Probab=99.50 E-value=4.2e-15 Score=130.32 Aligned_cols=51 Identities=16% Similarity=0.122 Sum_probs=48.7
Q ss_pred cCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCC--cceeeCCchhhhHHhh
Q 029573 137 RLSKDQSAILEESFKEHNTLNPVSIFLLRLLLVLR--ENEVKLEKKKKKTFLQ 187 (191)
Q Consensus 137 r~s~~Q~~~LE~~F~~~~~p~~~~r~~LA~qL~Ls--QVqVWFQNRRaK~K~k 187 (191)
.||..|..+||+.|...+|+++..|.+||.-|+|+ ||||||||||||+||.
T Consensus 205 VYTDhQRLELEKEfh~SryITirRKSELA~~LgLsERQVKIWFQNRRAKERK~ 257 (317)
T KOG0848|consen 205 VYTDHQRLELEKEFHTSRYITIRRKSELAATLGLSERQVKIWFQNRRAKERKD 257 (317)
T ss_pred EecchhhhhhhhhhccccceeeehhHHHHHhhCccHhhhhHhhhhhhHHHHHH
Confidence 39999999999999999999999999999999999 9999999999998763
No 20
>KOG0493 consensus Transcription factor Engrailed, contains HOX domain [General function prediction only]
Probab=99.43 E-value=6e-14 Score=123.01 Aligned_cols=57 Identities=19% Similarity=0.186 Sum_probs=53.0
Q ss_pred CCCCCccCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCC--cceeeCCchhhhHHhh
Q 029573 131 TSRKKLRLSKDQSAILEESFKEHNTLNPVSIFLLRLLLVLR--ENEVKLEKKKKKTFLQ 187 (191)
Q Consensus 131 ~~RkR~r~s~~Q~~~LE~~F~~~~~p~~~~r~~LA~qL~Ls--QVqVWFQNRRaK~K~k 187 (191)
.+|.|+.||.+|++.|...|+.+.|++...|.+||.+|+|. ||+|||||+|||-||-
T Consensus 246 eKRPRTAFtaeQL~RLK~EF~enRYlTEqRRQ~La~ELgLNEsQIKIWFQNKRAKiKKs 304 (342)
T KOG0493|consen 246 EKRPRTAFTAEQLQRLKAEFQENRYLTEQRRQELAQELGLNESQIKIWFQNKRAKIKKS 304 (342)
T ss_pred hcCccccccHHHHHHHHHHHhhhhhHHHHHHHHHHHHhCcCHHHhhHHhhhhhhhhhhc
Confidence 35666779999999999999999999999999999999999 9999999999999873
No 21
>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=99.43 E-value=2.6e-13 Score=94.42 Aligned_cols=50 Identities=8% Similarity=0.058 Sum_probs=47.8
Q ss_pred CCCCccCCHHHHHHHHHHHhhcCC----CCHHHHHHHHHHcCCC--cceeeCCchh
Q 029573 132 SRKKLRLSKDQSAILEESFKEHNT----LNPVSIFLLRLLLVLR--ENEVKLEKKK 181 (191)
Q Consensus 132 ~RkR~r~s~~Q~~~LE~~F~~~~~----p~~~~r~~LA~qL~Ls--QVqVWFQNRR 181 (191)
+|.|+.||.+|+..||..|..+.| |+..+|.+||..|||+ +|+|||||-+
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 678899999999999999999999 9999999999999999 9999999964
No 22
>KOG0491 consensus Transcription factor BSH, contains HOX domain [General function prediction only]
Probab=99.33 E-value=1.8e-13 Score=113.11 Aligned_cols=57 Identities=19% Similarity=0.145 Sum_probs=53.5
Q ss_pred CCCCccCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCC--cceeeCCchhhhHHhhh
Q 029573 132 SRKKLRLSKDQSAILEESFKEHNTLNPVSIFLLRLLLVLR--ENEVKLEKKKKKTFLQF 188 (191)
Q Consensus 132 ~RkR~r~s~~Q~~~LE~~F~~~~~p~~~~r~~LA~qL~Ls--QVqVWFQNRRaK~K~kq 188 (191)
++.|+.|+..|+..||+.|+...|++..+|.+||..|+|+ ||+.||||||+|.||.+
T Consensus 101 ~K~Rtvfs~~ql~~l~~rFe~QrYLS~~e~~ELan~L~LS~~QVKTWFQNrRMK~Kk~~ 159 (194)
T KOG0491|consen 101 RKARTVFSDPQLSGLEKRFERQRYLSTPERQELANALSLSETQVKTWFQNRRMKHKKQQ 159 (194)
T ss_pred hhhcccccCccccccHHHHhhhhhcccHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHHH
Confidence 4557779999999999999999999999999999999999 99999999999999865
No 23
>KOG0847 consensus Transcription factor, contains HOX domain [Transcription]
Probab=99.29 E-value=9.8e-13 Score=113.16 Aligned_cols=60 Identities=18% Similarity=0.166 Sum_probs=54.1
Q ss_pred CCCCCCc--cCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCC--cceeeCCchhhhHHhhhc
Q 029573 130 DTSRKKL--RLSKDQSAILEESFKEHNTLNPVSIFLLRLLLVLR--ENEVKLEKKKKKTFLQFL 189 (191)
Q Consensus 130 ~~~RkR~--r~s~~Q~~~LE~~F~~~~~p~~~~r~~LA~qL~Ls--QVqVWFQNRRaK~K~kq~ 189 (191)
+++||.. .|+-.|+..||+.|....|+-..+|.+||..+|++ ||+|||||||+||+||..
T Consensus 164 dG~rk~srPTf~g~qi~~le~~feqtkylaG~~ra~lA~~lgmteSqvkVWFQNRRTKWRKkhA 227 (288)
T KOG0847|consen 164 NGQRKQSRPTFTGHQIYQLERKFEQTKYLAGADRAQLAQELNMTESQVKVWFQNRRTKWRKKHA 227 (288)
T ss_pred CccccccCCCccchhhhhhhhhhhhhhcccchhHHHhhccccccHHHHHHHHhcchhhhhhhhc
Confidence 3455544 49999999999999999999999999999999999 999999999999999764
No 24
>KOG0490 consensus Transcription factor, contains HOX domain [General function prediction only]
Probab=99.28 E-value=1.9e-12 Score=107.29 Aligned_cols=60 Identities=17% Similarity=0.072 Sum_probs=55.4
Q ss_pred CCCCCCCccCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCC--cceeeCCchhhhHHhhh
Q 029573 129 GDTSRKKLRLSKDQSAILEESFKEHNTLNPVSIFLLRLLLVLR--ENEVKLEKKKKKTFLQF 188 (191)
Q Consensus 129 ~~~~RkR~r~s~~Q~~~LE~~F~~~~~p~~~~r~~LA~qL~Ls--QVqVWFQNRRaK~K~kq 188 (191)
...++.|+.|+..|+.+||++|+..+||+...|+.||..++++ .|+|||||||+|++++.
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 3457778889999999999999999999999999999999999 99999999999998754
No 25
>KOG4577 consensus Transcription factor LIM3, contains LIM and HOX domains [Transcription]
Probab=99.27 E-value=2.7e-12 Score=114.02 Aligned_cols=60 Identities=13% Similarity=0.088 Sum_probs=56.1
Q ss_pred CCCCCCCCccCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCC--cceeeCCchhhhHHhh
Q 029573 128 DGDTSRKKLRLSKDQSAILEESFKEHNTLNPVSIFLLRLLLVLR--ENEVKLEKKKKKTFLQ 187 (191)
Q Consensus 128 ~~~~~RkR~r~s~~Q~~~LE~~F~~~~~p~~~~r~~LA~qL~Ls--QVqVWFQNRRaK~K~k 187 (191)
++..+|.|+.+|+.|+..|..+|+..+.|-...|++|+..+||. .|||||||||||+|+-
T Consensus 164 d~~nKRPRTTItAKqLETLK~AYn~SpKPARHVREQLsseTGLDMRVVQVWFQNRRAKEKRL 225 (383)
T KOG4577|consen 164 DASNKRPRTTITAKQLETLKQAYNTSPKPARHVREQLSSETGLDMRVVQVWFQNRRAKEKRL 225 (383)
T ss_pred ccccCCCcceeeHHHHHHHHHHhcCCCchhHHHHHHhhhccCcceeehhhhhhhhhHHHHhh
Confidence 35678899999999999999999999999999999999999999 8999999999999874
No 26
>KOG0486 consensus Transcription factor PTX1, contains HOX domain [Transcription]
Probab=99.25 E-value=5.2e-12 Score=112.90 Aligned_cols=54 Identities=13% Similarity=0.121 Sum_probs=50.5
Q ss_pred CCccCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCC--cceeeCCchhhhHHhh
Q 029573 134 KKLRLSKDQSAILEESFKEHNTLNPVSIFLLRLLLVLR--ENEVKLEKKKKKTFLQ 187 (191)
Q Consensus 134 kR~r~s~~Q~~~LE~~F~~~~~p~~~~r~~LA~qL~Ls--QVqVWFQNRRaK~K~k 187 (191)
.|+.|+..|+.+||..|+++.||+...|++||..++|+ +|.|||.||||||++.
T Consensus 115 QrthFtSqqlqele~tF~rNrypdMstrEEIavwtNlTE~rvrvwfknrrakwrkr 170 (351)
T KOG0486|consen 115 QRTHFTSQQLQELEATFQRNRYPDMSTREEIAVWTNLTEARVRVWFKNRRAKWRKR 170 (351)
T ss_pred hhhhhHHHHHHHHHHHHhhccCCccchhhHHHhhccccchhhhhhcccchhhhhhh
Confidence 34459999999999999999999999999999999999 9999999999999774
No 27
>KOG3802 consensus Transcription factor OCT-1, contains POU and HOX domains [Transcription]
Probab=99.20 E-value=1.4e-11 Score=112.85 Aligned_cols=57 Identities=16% Similarity=0.149 Sum_probs=53.3
Q ss_pred CCCCCCccCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCC--cceeeCCchhhhHHh
Q 029573 130 DTSRKKLRLSKDQSAILEESFKEHNTLNPVSIFLLRLLLVLR--ENEVKLEKKKKKTFL 186 (191)
Q Consensus 130 ~~~RkR~r~s~~Q~~~LE~~F~~~~~p~~~~r~~LA~qL~Ls--QVqVWFQNRRaK~K~ 186 (191)
+.+|||+.+....+..||+.|.+|++|+..++..||.+|+|. .|+|||+|||.|+||
T Consensus 293 RkRKKRTSie~~vr~aLE~~F~~npKPt~qEIt~iA~~L~leKEVVRVWFCNRRQkeKR 351 (398)
T KOG3802|consen 293 RKRKKRTSIEVNVRGALEKHFLKNPKPTSQEITHIAESLQLEKEVVRVWFCNRRQKEKR 351 (398)
T ss_pred cccccccceeHHHHHHHHHHHHhCCCCCHHHHHHHHHHhccccceEEEEeecccccccc
Confidence 456667779999999999999999999999999999999999 999999999999998
No 28
>KOG0849 consensus Transcription factor PRD and related proteins, contain PAX and HOX domains [Transcription]
Probab=99.04 E-value=1.1e-10 Score=105.98 Aligned_cols=60 Identities=22% Similarity=0.125 Sum_probs=56.0
Q ss_pred CCCCCCCccCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCC--cceeeCCchhhhHHhhh
Q 029573 129 GDTSRKKLRLSKDQSAILEESFKEHNTLNPVSIFLLRLLLVLR--ENEVKLEKKKKKTFLQF 188 (191)
Q Consensus 129 ~~~~RkR~r~s~~Q~~~LE~~F~~~~~p~~~~r~~LA~qL~Ls--QVqVWFQNRRaK~K~kq 188 (191)
...+|+|+.|+..|+..||+.|+.++||+...|++||++++++ +|+|||+|||+|+++..
T Consensus 174 ~~~rr~rtsft~~Q~~~le~~f~rt~yP~i~~Re~La~~i~l~e~riqvwf~nrra~~rr~~ 235 (354)
T KOG0849|consen 174 RGGRRNRTSFSPSQLEALEECFQRTPYPDIVGRETLAKETGLPEPRVQVWFQNRRAKWRRQH 235 (354)
T ss_pred ccccccccccccchHHHHHHHhcCCCCCchhhHHHHhhhccCCchHHHHHHhhhhhhhhhcc
Confidence 4466777889999999999999999999999999999999999 99999999999999866
No 29
>KOG1168 consensus Transcription factor ACJ6/BRN-3, contains POU and HOX domains [Transcription]
Probab=98.65 E-value=1.5e-08 Score=90.50 Aligned_cols=59 Identities=19% Similarity=0.174 Sum_probs=54.7
Q ss_pred CCCCCCCccCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCC--cceeeCCchhhhHHhh
Q 029573 129 GDTSRKKLRLSKDQSAILEESFKEHNTLNPVSIFLLRLLLVLR--ENEVKLEKKKKKTFLQ 187 (191)
Q Consensus 129 ~~~~RkR~r~s~~Q~~~LE~~F~~~~~p~~~~r~~LA~qL~Ls--QVqVWFQNRRaK~K~k 187 (191)
+..+|||+.+-......||.+|...+.|+.+.+..||.+|+|. .|+|||.|.|.|.||.
T Consensus 307 ~ekKRKRTSIAAPEKRsLEayFavQPRPS~EkIAaIAekLDLKKNVVRVWFCNQRQKQKRm 367 (385)
T KOG1168|consen 307 GEKKRKRTSIAAPEKRSLEAYFAVQPRPSGEKIAAIAEKLDLKKNVVRVWFCNQRQKQKRM 367 (385)
T ss_pred cccccccccccCcccccHHHHhccCCCCchhHHHHHHHhhhhhhceEEEEeeccHHHHHHh
Confidence 4568888888899999999999999999999999999999999 8999999999999984
No 30
>KOG0775 consensus Transcription factor SIX and related HOX domain proteins [Transcription]
Probab=98.43 E-value=1.6e-07 Score=83.04 Aligned_cols=49 Identities=10% Similarity=0.095 Sum_probs=45.6
Q ss_pred CCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCC--cceeeCCchhhhHHh
Q 029573 138 LSKDQSAILEESFKEHNTLNPVSIFLLRLLLVLR--ENEVKLEKKKKKTFL 186 (191)
Q Consensus 138 ~s~~Q~~~LE~~F~~~~~p~~~~r~~LA~qL~Ls--QVqVWFQNRRaK~K~ 186 (191)
|...-..+|-+.|..+.||++.++.+||+.+||+ ||-.||.|||.|+|-
T Consensus 183 FKekSR~~LrewY~~~~YPsp~eKReLA~aTgLt~tQVsNWFKNRRQRDRa 233 (304)
T KOG0775|consen 183 FKEKSRSLLREWYLQNPYPSPREKRELAEATGLTITQVSNWFKNRRQRDRA 233 (304)
T ss_pred hhHhhHHHHHHHHhcCCCCChHHHHHHHHHhCCchhhhhhhhhhhhhhhhh
Confidence 6667778999999999999999999999999999 999999999999884
No 31
>KOG0774 consensus Transcription factor PBX and related HOX domain proteins [Transcription]
Probab=98.32 E-value=4e-07 Score=80.47 Aligned_cols=57 Identities=19% Similarity=0.118 Sum_probs=52.5
Q ss_pred CCCCCCccCCHHHHHHHHHHHh---hcCCCCHHHHHHHHHHcCCC--cceeeCCchhhhHHh
Q 029573 130 DTSRKKLRLSKDQSAILEESFK---EHNTLNPVSIFLLRLLLVLR--ENEVKLEKKKKKTFL 186 (191)
Q Consensus 130 ~~~RkR~r~s~~Q~~~LE~~F~---~~~~p~~~~r~~LA~qL~Ls--QVqVWFQNRRaK~K~ 186 (191)
+.+|||+.|++.-..+|.++|. .|+||+...+++||+++||+ ||-.||-|+|-++||
T Consensus 187 darRKRRNFsK~aTeiLneyF~~h~~nPYPSee~K~eLAkqCnItvsQvsnwfgnkrIrykK 248 (334)
T KOG0774|consen 187 DARRKRRNFSKQATEILNEYFYSHLSNPYPSEEAKEELAKQCNITVSQVSNWFGNKRIRYKK 248 (334)
T ss_pred HHHHhhcccchhHHHHHHHHHHHhcCCCCCcHHHHHHHHHHcCceehhhccccccceeehhh
Confidence 4578888899999999999996 46699999999999999999 999999999999987
No 32
>KOG0490 consensus Transcription factor, contains HOX domain [General function prediction only]
Probab=98.30 E-value=7.5e-07 Score=73.78 Aligned_cols=124 Identities=12% Similarity=0.072 Sum_probs=86.6
Q ss_pred hhhhhhcccccCCCCCCCcccccc-cCCCCCCcccc-ccCCCCCCCCCC--chhhhhhhccC---------C--CCCCcC
Q 029573 64 ETRSFLRGIDVNRLPSHADNEEEV-GVSSPNSTISS-VSGKRSEREPNG--DELEMERACSR---------G--ISDEED 128 (191)
Q Consensus 64 ~~~~~~rg~dvn~~p~~~~~ee~~-~~ssp~S~~ss-~s~~rs~~~~~~--~~~~~er~~s~---------~--~~~~~~ 128 (191)
....+.+.|+.+-||.+..+++.+ ....+...+.. |++.+..-.... -.......... . ......
T Consensus 71 ql~~ler~f~~~h~Pd~~~r~~la~~~~~~e~rVqvwFqnrrak~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 150 (235)
T KOG0490|consen 71 QLDELERAFEKVHLPCFACRECLALLLTGDEFRVQVWFQNRRAKDRKEERPLPEGENLPDLSGTAPPSASRDKLDKGPSN 150 (235)
T ss_pred HHHHHHHhhcCCCcCccchHHHHhhcCCCCeeeeehhhhhhcHhhhhhhccccccccCCCCCCCCCccccccccccCCCc
Confidence 345567899999999988888764 56667777777 688775221110 00000000000 0 001111
Q ss_pred CCCCCCCccCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCC--cceeeCCchhhhHHhh
Q 029573 129 GDTSRKKLRLSKDQSAILEESFKEHNTLNPVSIFLLRLLLVLR--ENEVKLEKKKKKTFLQ 187 (191)
Q Consensus 129 ~~~~RkR~r~s~~Q~~~LE~~F~~~~~p~~~~r~~LA~qL~Ls--QVqVWFQNRRaK~K~k 187 (191)
...++.++.++..|+..++..|...++|+...+..|+..++++ .|+|||||+|++.++.
T Consensus 151 ~~~~~~~~~~~~~~~~~~~~~~~~~~~P~~~~~~~l~~~~~~~~~~~q~~~~~~~~~~~~~ 211 (235)
T KOG0490|consen 151 KKPRRPRTTFTENQLEVLETVFRATPKPDADDREQLAEETGLSERVIQVWFQNRRAKLRKH 211 (235)
T ss_pred cccCCCccccccchhHhhhhcccCCCCCchhhHHHHHHhcCCChhhhhhhcccHHHHHHhh
Confidence 3455566779999999999999999999999999999999999 7899999999999874
No 33
>PF05920 Homeobox_KN: Homeobox KN domain; InterPro: IPR008422 This entry represents a homeobox transcription factor KN domain conserved from fungi to human and plants [].; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent, 0005634 nucleus; PDB: 3K2A_B 2LK2_A 1X2N_A 2DMN_A.
Probab=98.05 E-value=1e-06 Score=56.95 Aligned_cols=32 Identities=6% Similarity=-0.139 Sum_probs=27.0
Q ss_pred hcCCCCHHHHHHHHHHcCCC--cceeeCCchhhh
Q 029573 152 EHNTLNPVSIFLLRLLLVLR--ENEVKLEKKKKK 183 (191)
Q Consensus 152 ~~~~p~~~~r~~LA~qL~Ls--QVqVWFQNRRaK 183 (191)
.++||+..++..||+++||+ ||..||-|.|.|
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 56899999999999999999 999999999975
No 34
>KOG2252 consensus CCAAT displacement protein and related homeoproteins [Transcription]
Probab=97.63 E-value=4.7e-05 Score=72.80 Aligned_cols=56 Identities=16% Similarity=0.119 Sum_probs=51.3
Q ss_pred CCCCCCCccCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCC--cceeeCCchhhhH
Q 029573 129 GDTSRKKLRLSKDQSAILEESFKEHNTLNPVSIFLLRLLLVLR--ENEVKLEKKKKKT 184 (191)
Q Consensus 129 ~~~~RkR~r~s~~Q~~~LE~~F~~~~~p~~~~r~~LA~qL~Ls--QVqVWFQNRRaK~ 184 (191)
-..+|.|+.||..|+..|..+|+.+++|+....+.|+.+|+|. .|..||-|-|.|.
T Consensus 418 ~~~KKPRlVfTd~QkrTL~aiFke~~RPS~Emq~tIS~qL~L~~sTV~NfFmNaRRRs 475 (558)
T KOG2252|consen 418 LQTKKPRLVFTDIQKRTLQAIFKENKRPSREMQETISQQLNLELSTVINFFMNARRRS 475 (558)
T ss_pred ccCCCceeeecHHHHHHHHHHHhcCCCCCHHHHHHHHHHhCCcHHHHHHHHHhhhhhc
Confidence 3456777789999999999999999999999999999999999 9999999988874
No 35
>KOG1146 consensus Homeobox protein [General function prediction only]
Probab=96.67 E-value=0.00099 Score=69.22 Aligned_cols=59 Identities=14% Similarity=0.040 Sum_probs=53.8
Q ss_pred CCCCCCccCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCC--cceeeCCchhhhHHhhh
Q 029573 130 DTSRKKLRLSKDQSAILEESFKEHNTLNPVSIFLLRLLLVLR--ENEVKLEKKKKKTFLQF 188 (191)
Q Consensus 130 ~~~RkR~r~s~~Q~~~LE~~F~~~~~p~~~~r~~LA~qL~Ls--QVqVWFQNRRaK~K~kq 188 (191)
+.+++|++++..|+.++...|....|+...+-+.|...+++. .|+|||||-|+|.|+..
T Consensus 902 ~r~a~~~~~~d~qlk~i~~~~~~q~~~~~~~~E~l~~~~~~~~~~i~vw~qna~~~s~k~~ 962 (1406)
T KOG1146|consen 902 GRRAYRTQESDLQLKIIKACYEAQRTPTMQECEVLEEPIGLPKRVIQVWFQNARAKSKKAK 962 (1406)
T ss_pred hhhhhccchhHHHHHHHHHHHhhccCChHHHHHhhcccccCCcchhHHhhhhhhhhhhhhh
Confidence 356778899999999999999999999999999999999999 89999999999998754
No 36
>KOG0773 consensus Transcription factor MEIS1 and related HOX domain proteins [Transcription]
Probab=95.98 E-value=0.0043 Score=55.43 Aligned_cols=55 Identities=16% Similarity=0.108 Sum_probs=44.5
Q ss_pred CCCCccCCHHHHHHHHHH-Hh--hcCCCCHHHHHHHHHHcCCC--cceeeCCchhhhHHh
Q 029573 132 SRKKLRLSKDQSAILEES-FK--EHNTLNPVSIFLLRLLLVLR--ENEVKLEKKKKKTFL 186 (191)
Q Consensus 132 ~RkR~r~s~~Q~~~LE~~-F~--~~~~p~~~~r~~LA~qL~Ls--QVqVWFQNRRaK~K~ 186 (191)
+|.+..+......+|..- |+ .++||+..++..||+++||+ ||..||-|.|-|..+
T Consensus 240 ~r~~~~lP~~a~~ilr~Wl~~h~~~PYPse~~K~~La~~TGLs~~Qv~NWFINaR~R~w~ 299 (342)
T KOG0773|consen 240 WRPQRGLPKEAVSILRAWLFEHLLHPYPSDDEKLMLAKQTGLSRPQVSNWFINARVRLWK 299 (342)
T ss_pred CCCCCCCCHHHHHHHHHHHHHhccCCCCcchhccccchhcCCCcccCCchhhhcccccCC
Confidence 344445889999999866 43 24589999999999999999 999999999987543
No 37
>PF11569 Homez: Homeodomain leucine-zipper encoding, Homez; PDB: 2YS9_A.
Probab=95.85 E-value=0.0036 Score=43.49 Aligned_cols=40 Identities=13% Similarity=0.059 Sum_probs=29.3
Q ss_pred HHHHHHHHhhcCCCCHHHHHHHHHHcCCC--cceeeCCchhh
Q 029573 143 SAILEESFKEHNTLNPVSIFLLRLLLVLR--ENEVKLEKKKK 182 (191)
Q Consensus 143 ~~~LE~~F~~~~~p~~~~r~~LA~qL~Ls--QVqVWFQNRRa 182 (191)
+.-|+++|..++.+...+...|..+.+|+ ||+.||--|+.
T Consensus 10 ~~pL~~Yy~~h~~L~E~DL~~L~~kS~ms~qqVr~WFa~~~~ 51 (56)
T PF11569_consen 10 IQPLEDYYLKHKQLQEEDLDELCDKSRMSYQQVRDWFAERMQ 51 (56)
T ss_dssp -HHHHHHHHHT----TTHHHHHHHHTT--HHHHHHHHHHHS-
T ss_pred hHHHHHHHHHcCCccHhhHHHHHHHHCCCHHHHHHHHHHhcc
Confidence 34599999999999999999999999999 99999976654
No 38
>KOG3623 consensus Homeobox transcription factor SIP1 [Transcription]
Probab=91.93 E-value=0.12 Score=51.95 Aligned_cols=44 Identities=7% Similarity=0.065 Sum_probs=40.5
Q ss_pred HHHHHHHHhhcCCCCHHHHHHHHHHcCCC--cceeeCCchhhhHHh
Q 029573 143 SAILEESFKEHNTLNPVSIFLLRLLLVLR--ENEVKLEKKKKKTFL 186 (191)
Q Consensus 143 ~~~LE~~F~~~~~p~~~~r~~LA~qL~Ls--QVqVWFQNRRaK~K~ 186 (191)
..+|..+|..|..|+..+-..+|.+.||. -|++||+++++++..
T Consensus 568 ~sllkayyaln~~ps~eelskia~qvglp~~vvk~wfE~~~a~e~s 613 (1007)
T KOG3623|consen 568 TSLLKAYYALNGLPSEEELSKIAQQVGLPFAVVKAWFEDEEAEEMS 613 (1007)
T ss_pred HHHHHHHHHhcCCCCHHHHHHHHHHhcccHHHHHHHHHhhhhhhhh
Confidence 67788889999999999999999999999 899999999998754
No 39
>PF04218 CENP-B_N: CENP-B N-terminal DNA-binding domain; InterPro: IPR006695 Centromere Protein B (CENP-B) is a DNA-binding protein localized to the centromere. Within the N-terminal 125 residues, there is a DNA-binding region, which binds to a corresponding 17bp CENP-B box sequence. CENP-B dimers either bind two separate DNA molecules or alternatively, they may bind two CENP-B boxes on one DNA molecule, with the intervening stretch of DNA forming a loop structure. The CENP-B DNA-binding domain consists of two repeating domains, RP1 and RP2. This family corresponds to RP1 has been shown to consist of four helices in a helix-turn-helix structure [].; GO: 0003677 DNA binding, 0000775 chromosome, centromeric region; PDB: 1BW6_A 1HLV_A 2ELH_A.
Probab=88.75 E-value=0.42 Score=32.15 Aligned_cols=45 Identities=16% Similarity=0.118 Sum_probs=33.4
Q ss_pred CCCCccCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCC--cceeeCCchh
Q 029573 132 SRKKLRLSKDQSAILEESFKEHNTLNPVSIFLLRLLLVLR--ENEVKLEKKK 181 (191)
Q Consensus 132 ~RkR~r~s~~Q~~~LE~~F~~~~~p~~~~r~~LA~qL~Ls--QVqVWFQNRR 181 (191)
+|+|..+|-++...+-+.++.+. ...+||+++|+. +|.-|..||.
T Consensus 1 krkR~~LTl~eK~~iI~~~e~g~-----s~~~ia~~fgv~~sTv~~I~K~k~ 47 (53)
T PF04218_consen 1 KRKRKSLTLEEKLEIIKRLEEGE-----SKRDIAREFGVSRSTVSTILKNKD 47 (53)
T ss_dssp SSSSSS--HHHHHHHHHHHHCTT------HHHHHHHHT--CCHHHHHHHCHH
T ss_pred CCCCccCCHHHHHHHHHHHHcCC-----CHHHHHHHhCCCHHHHHHHHHhHH
Confidence 46788899999988888887776 578999999999 8999988854
No 40
>PF04967 HTH_10: HTH DNA binding domain; InterPro: IPR007050 Numerous bacterial transcription regulatory proteins bind DNA via a helix-turn-helix (HTH) motif. This entry represents the HTH DNA binding domain found in Halobacterium salinarium (Halobacterium halobium) and described as a putative bacterio-opsin activator.
Probab=82.61 E-value=1.1 Score=30.63 Aligned_cols=48 Identities=15% Similarity=0.138 Sum_probs=36.3
Q ss_pred CCHHHHHHHHHHHhhcCC--CCHHHHHHHHHHcCCCcceeeCCchhhhHH
Q 029573 138 LSKDQSAILEESFKEHNT--LNPVSIFLLRLLLVLRENEVKLEKKKKKTF 185 (191)
Q Consensus 138 ~s~~Q~~~LE~~F~~~~~--p~~~~r~~LA~qL~LsQVqVWFQNRRaK~K 185 (191)
+|..|..+|..+|....| |-...-.+||..||++.--+...=||+-.|
T Consensus 1 LT~~Q~e~L~~A~~~GYfd~PR~~tl~elA~~lgis~st~~~~LRrae~k 50 (53)
T PF04967_consen 1 LTDRQREILKAAYELGYFDVPRRITLEELAEELGISKSTVSEHLRRAERK 50 (53)
T ss_pred CCHHHHHHHHHHHHcCCCCCCCcCCHHHHHHHhCCCHHHHHHHHHHHHHH
Confidence 588999999999998887 666677899999999933344445555443
No 41
>COG3413 Predicted DNA binding protein [General function prediction only]
Probab=75.81 E-value=2 Score=36.02 Aligned_cols=50 Identities=18% Similarity=0.130 Sum_probs=41.5
Q ss_pred cCCHHHHHHHHHHHhhcCC--CCHHHHHHHHHHcCCCcceeeCCchhhhHHh
Q 029573 137 RLSKDQSAILEESFKEHNT--LNPVSIFLLRLLLVLRENEVKLEKKKKKTFL 186 (191)
Q Consensus 137 r~s~~Q~~~LE~~F~~~~~--p~~~~r~~LA~qL~LsQVqVWFQNRRaK~K~ 186 (191)
.+|..|+.+|..+|+..-| |-...-.+||++||++..-+|.-=|||..|.
T Consensus 155 ~LTdrQ~~vL~~A~~~GYFd~PR~~~l~dLA~~lGISkst~~ehLRrAe~Kl 206 (215)
T COG3413 155 DLTDRQLEVLRLAYKMGYFDYPRRVSLKDLAKELGISKSTLSEHLRRAERKL 206 (215)
T ss_pred cCCHHHHHHHHHHHHcCCCCCCccCCHHHHHHHhCCCHHHHHHHHHHHHHHH
Confidence 5999999999999999886 6666778999999999445666678887665
No 42
>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=60.70 E-value=8.8 Score=26.25 Aligned_cols=41 Identities=12% Similarity=-0.036 Sum_probs=25.7
Q ss_pred CCCccCCHHHHHHHHHHH-hhcCCCCHHHHHHHHHHcCCC--cceeeCC
Q 029573 133 RKKLRLSKDQSAILEESF-KEHNTLNPVSIFLLRLLLVLR--ENEVKLE 178 (191)
Q Consensus 133 RkR~r~s~~Q~~~LE~~F-~~~~~p~~~~r~~LA~qL~Ls--QVqVWFQ 178 (191)
+++.+||+++...+-..+ ... ....++|+++||+ +|..|-.
T Consensus 2 ~~r~~ys~e~K~~~v~~~~~~g-----~sv~~va~~~gi~~~~l~~W~~ 45 (76)
T PF01527_consen 2 RKRRRYSPEFKLQAVREYLESG-----ESVSEVAREYGISPSTLYNWRK 45 (76)
T ss_dssp -SS----HHHHHHHHHHHHHHH-----CHHHHHHHHHTS-HHHHHHHHH
T ss_pred CCCCCCCHHHHHHHHHHHHHCC-----CceEeeecccccccccccHHHH
Confidence 456779999888655555 433 4778999999999 8888743
No 43
>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=58.86 E-value=17 Score=19.45 Aligned_cols=35 Identities=11% Similarity=-0.021 Sum_probs=23.5
Q ss_pred cCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCC--cceee
Q 029573 137 RLSKDQSAILEESFKEHNTLNPVSIFLLRLLLVLR--ENEVK 176 (191)
Q Consensus 137 r~s~~Q~~~LE~~F~~~~~p~~~~r~~LA~qL~Ls--QVqVW 176 (191)
.++.++...+...|.... ...++|+.++++ .|..|
T Consensus 5 ~~~~~~~~~i~~~~~~~~-----s~~~ia~~~~is~~tv~~~ 41 (42)
T cd00569 5 KLTPEQIEEARRLLAAGE-----SVAEIARRLGVSRSTLYRY 41 (42)
T ss_pred cCCHHHHHHHHHHHHcCC-----CHHHHHHHHCCCHHHHHHh
Confidence 466677766666665332 456888999998 56655
No 44
>PRK09646 RNA polymerase sigma factor SigK; Reviewed
Probab=50.27 E-value=16 Score=29.44 Aligned_cols=46 Identities=9% Similarity=0.062 Sum_probs=32.5
Q ss_pred CCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCC--cceeeCCchhhhHHhhhcc
Q 029573 138 LSKDQSAILEESFKEHNTLNPVSIFLLRLLLVLR--ENEVKLEKKKKKTFLQFLI 190 (191)
Q Consensus 138 ~s~~Q~~~LE~~F~~~~~p~~~~r~~LA~qL~Ls--QVqVWFQNRRaK~K~kq~~ 190 (191)
++..+..+|.-.|-.+ ..-.++|..||++ .|+.+. .|++.|.+..+
T Consensus 143 L~~~~r~vl~l~~~~~-----~s~~EIA~~Lgis~~tVk~~l--~ra~~~Lr~~l 190 (194)
T PRK09646 143 LTDTQRESVTLAYYGG-----LTYREVAERLAVPLGTVKTRM--RDGLIRLRDCL 190 (194)
T ss_pred CCHHHHHHHHHHHHcC-----CCHHHHHHHhCCChHhHHHHH--HHHHHHHHHHh
Confidence 7777877777665333 2456899999999 777665 67777766543
No 45
>COG4367 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=49.34 E-value=14 Score=28.13 Aligned_cols=34 Identities=18% Similarity=0.143 Sum_probs=30.9
Q ss_pred CCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCC
Q 029573 138 LSKDQSAILEESFKEHNTLNPVSIFLLRLLLVLR 171 (191)
Q Consensus 138 ~s~~Q~~~LE~~F~~~~~p~~~~r~~LA~qL~Ls 171 (191)
++++|...-.+.|+.|.-+..-..+++|..||++
T Consensus 3 Ln~eq~~~Tk~elqan~el~~LS~~~iA~~Ln~t 36 (97)
T COG4367 3 LNPEQKQRTKQELQANFELCPLSDEEIATALNWT 36 (97)
T ss_pred CCHHHHHHHHHHHHHhhhhccccHHHHHHHhCCC
Confidence 6789999988999999888888999999999998
No 46
>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=47.90 E-value=12 Score=22.56 Aligned_cols=40 Identities=18% Similarity=0.203 Sum_probs=28.3
Q ss_pred CCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCC--cceeeCCchhh
Q 029573 138 LSKDQSAILEESFKEHNTLNPVSIFLLRLLLVLR--ENEVKLEKKKK 182 (191)
Q Consensus 138 ~s~~Q~~~LE~~F~~~~~p~~~~r~~LA~qL~Ls--QVqVWFQNRRa 182 (191)
++..+..+++..|... ..-.++|..+|++ +|..|...-+.
T Consensus 11 l~~~~~~~~~~~~~~~-----~~~~~ia~~~~~s~~~i~~~~~~~~~ 52 (55)
T cd06171 11 LPEREREVILLRFGEG-----LSYEEIAEILGISRSTVRQRLHRALK 52 (55)
T ss_pred CCHHHHHHHHHHHhcC-----CCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 6777778887776433 2456789999999 88877755443
No 47
>PRK09648 RNA polymerase sigma factor SigD; Reviewed
Probab=47.25 E-value=19 Score=28.79 Aligned_cols=46 Identities=17% Similarity=-0.068 Sum_probs=33.6
Q ss_pred CCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCC--cceeeCCchhhhHHhhhcc
Q 029573 138 LSKDQSAILEESFKEHNTLNPVSIFLLRLLLVLR--ENEVKLEKKKKKTFLQFLI 190 (191)
Q Consensus 138 ~s~~Q~~~LE~~F~~~~~p~~~~r~~LA~qL~Ls--QVqVWFQNRRaK~K~kq~~ 190 (191)
+++.|..+++..|-... .-.++|..+|++ .|+.+. +|++.|.++.+
T Consensus 140 L~~~~r~i~~l~~~~g~-----s~~EIA~~lgis~~tV~~~l--~Ra~~~Lr~~l 187 (189)
T PRK09648 140 LPEKQREILILRVVVGL-----SAEETAEAVGSTPGAVRVAQ--HRALARLRAEI 187 (189)
T ss_pred CCHHHHHHHHHHHHcCC-----CHHHHHHHHCCCHHHHHHHH--HHHHHHHHHHh
Confidence 77778888877654432 456899999999 777755 67877776654
No 48
>PRK12519 RNA polymerase sigma factor; Provisional
Probab=43.97 E-value=16 Score=29.23 Aligned_cols=45 Identities=20% Similarity=0.166 Sum_probs=29.8
Q ss_pred CCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCC--cceeeCCchhhhHHhhhc
Q 029573 138 LSKDQSAILEESFKEHNTLNPVSIFLLRLLLVLR--ENEVKLEKKKKKTFLQFL 189 (191)
Q Consensus 138 ~s~~Q~~~LE~~F~~~~~p~~~~r~~LA~qL~Ls--QVqVWFQNRRaK~K~kq~ 189 (191)
+++.+..++...|-.. ....++|..+|++ .|+.|+ +|++.|.++.
T Consensus 142 L~~~~~~v~~l~~~~g-----~s~~EIA~~lgis~~tV~~~l--~Ra~~~Lr~~ 188 (194)
T PRK12519 142 LPESQRQVLELAYYEG-----LSQSEIAKRLGIPLGTVKARA--RQGLLKLREL 188 (194)
T ss_pred CCHHHhhhhhhhhhcC-----CCHHHHHHHhCCCHHHHHHHH--HHHHHHHHHH
Confidence 5566666665544222 2456899999999 888887 5666666553
No 49
>PRK09652 RNA polymerase sigma factor RpoE; Provisional
Probab=43.73 E-value=18 Score=27.93 Aligned_cols=45 Identities=9% Similarity=-0.015 Sum_probs=32.1
Q ss_pred cCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCC--cceeeCCchhhhHHhhh
Q 029573 137 RLSKDQSAILEESFKEHNTLNPVSIFLLRLLLVLR--ENEVKLEKKKKKTFLQF 188 (191)
Q Consensus 137 r~s~~Q~~~LE~~F~~~~~p~~~~r~~LA~qL~Ls--QVqVWFQNRRaK~K~kq 188 (191)
.+++.+..+|...|-.+. .-.++|+.||++ .|+.|.. |++.|.+.
T Consensus 128 ~L~~~~r~vl~l~~~~~~-----s~~eIA~~lgis~~tV~~~l~--ra~~~Lr~ 174 (182)
T PRK09652 128 SLPEELRTAITLREIEGL-----SYEEIAEIMGCPIGTVRSRIF--RAREALRA 174 (182)
T ss_pred hCCHHHHHHHHHHHHcCC-----CHHHHHHHHCCCHHHHHHHHH--HHHHHHHH
Confidence 377888888877653322 345899999999 8888776 66666654
No 50
>PRK12526 RNA polymerase sigma factor; Provisional
Probab=42.36 E-value=24 Score=28.96 Aligned_cols=45 Identities=16% Similarity=0.118 Sum_probs=29.9
Q ss_pred CCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCC--cceeeCCchhhhHHhhhc
Q 029573 138 LSKDQSAILEESFKEHNTLNPVSIFLLRLLLVLR--ENEVKLEKKKKKTFLQFL 189 (191)
Q Consensus 138 ~s~~Q~~~LE~~F~~~~~p~~~~r~~LA~qL~Ls--QVqVWFQNRRaK~K~kq~ 189 (191)
++..+..+|...|-.+. ...++|..+|++ .|+++. +|++.+.++.
T Consensus 154 L~~~~r~vl~l~~~~g~-----s~~EIA~~lgis~~tV~~~l--~Ra~~~Lr~~ 200 (206)
T PRK12526 154 LPEAQQTVVKGVYFQEL-----SQEQLAQQLNVPLGTVKSRL--RLALAKLKVQ 200 (206)
T ss_pred CCHHHHHHHHHHHHcCC-----CHHHHHHHHCCCHHHHHHHH--HHHHHHHHHH
Confidence 66777777765443332 456899999999 676554 6777666543
No 51
>PRK09639 RNA polymerase sigma factor SigX; Provisional
Probab=41.53 E-value=24 Score=27.28 Aligned_cols=44 Identities=14% Similarity=0.140 Sum_probs=32.3
Q ss_pred CCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCC--cceeeCCchhhhHHhhhc
Q 029573 138 LSKDQSAILEESFKEHNTLNPVSIFLLRLLLVLR--ENEVKLEKKKKKTFLQFL 189 (191)
Q Consensus 138 ~s~~Q~~~LE~~F~~~~~p~~~~r~~LA~qL~Ls--QVqVWFQNRRaK~K~kq~ 189 (191)
++..+..+|.-.| .+. .-.++|..+|++ .|+.+. .|++.+.++.
T Consensus 113 L~~~~r~il~l~~-~g~-----s~~eIA~~lgis~~tV~~~i--~ra~~~Lr~~ 158 (166)
T PRK09639 113 MTERDRTVLLLRF-SGY-----SYKEIAEALGIKESSVGTTL--ARAKKKFRKI 158 (166)
T ss_pred CCHHHHHHHHHHH-cCC-----CHHHHHHHHCCCHHHHHHHH--HHHHHHHHHH
Confidence 6777777777777 333 456899999999 777765 6777777654
No 52
>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=40.34 E-value=22 Score=22.64 Aligned_cols=43 Identities=12% Similarity=0.078 Sum_probs=28.4
Q ss_pred cCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCC--cceeeCCchhhhHHh
Q 029573 137 RLSKDQSAILEESFKEHNTLNPVSIFLLRLLLVLR--ENEVKLEKKKKKTFL 186 (191)
Q Consensus 137 r~s~~Q~~~LE~~F~~~~~p~~~~r~~LA~qL~Ls--QVqVWFQNRRaK~K~ 186 (191)
.+++.+..+|...|... ..-.++|..+|++ .|..+ -+|+-.|.
T Consensus 4 ~L~~~er~vi~~~y~~~-----~t~~eIa~~lg~s~~~V~~~--~~~al~kL 48 (50)
T PF04545_consen 4 QLPPREREVIRLRYFEG-----LTLEEIAERLGISRSTVRRI--LKRALKKL 48 (50)
T ss_dssp TS-HHHHHHHHHHHTST------SHHHHHHHHTSCHHHHHHH--HHHHHHHH
T ss_pred hCCHHHHHHHHHHhcCC-----CCHHHHHHHHCCcHHHHHHH--HHHHHHHh
Confidence 47888999999999333 3457899999999 55543 34444443
No 53
>PRK03975 tfx putative transcriptional regulator; Provisional
Probab=39.37 E-value=27 Score=28.28 Aligned_cols=46 Identities=9% Similarity=-0.044 Sum_probs=33.5
Q ss_pred CccCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCC--cceeeCCchhhhHHh
Q 029573 135 KLRLSKDQSAILEESFKEHNTLNPVSIFLLRLLLVLR--ENEVKLEKKKKKTFL 186 (191)
Q Consensus 135 R~r~s~~Q~~~LE~~F~~~~~p~~~~r~~LA~qL~Ls--QVqVWFQNRRaK~K~ 186 (191)
...+++.|..+|...+ .. ....++|..||++ .|..|-++-+.|.++
T Consensus 4 ~~~Lt~rqreVL~lr~-~G-----lTq~EIAe~LGiS~~tVs~ie~ra~kkLr~ 51 (141)
T PRK03975 4 ESFLTERQIEVLRLRE-RG-----LTQQEIADILGTSRANVSSIEKRARENIEK 51 (141)
T ss_pred ccCCCHHHHHHHHHHH-cC-----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 3468999999998732 22 2456999999999 788888765555443
No 54
>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=37.86 E-value=38 Score=25.84 Aligned_cols=45 Identities=18% Similarity=0.090 Sum_probs=31.3
Q ss_pred CCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCC--cceeeCCchhhhHHhhhc
Q 029573 138 LSKDQSAILEESFKEHNTLNPVSIFLLRLLLVLR--ENEVKLEKKKKKTFLQFL 189 (191)
Q Consensus 138 ~s~~Q~~~LE~~F~~~~~p~~~~r~~LA~qL~Ls--QVqVWFQNRRaK~K~kq~ 189 (191)
+++.+..++...|-.. ..-.++|..+|++ .|+++ -.|+|.|.+..
T Consensus 112 L~~~~r~v~~l~~~~g-----~~~~eIA~~l~is~~tv~~~--l~Rar~~Lr~~ 158 (159)
T TIGR02989 112 LPERQRELLQLRYQRG-----VSLTALAEQLGRTVNAVYKA--LSRLRVRLRDC 158 (159)
T ss_pred CCHHHHHHHHHHHhcC-----CCHHHHHHHhCCCHHHHHHH--HHHHHHHHHhc
Confidence 7777777777754332 2456899999999 66654 67777776643
No 55
>KOG3755 consensus SATB1 matrix attachment region binding protein [Transcription]
Probab=36.89 E-value=7.4 Score=38.75 Aligned_cols=17 Identities=0% Similarity=-0.079 Sum_probs=15.2
Q ss_pred cceeeCCchhhhHHhhh
Q 029573 172 ENEVKLEKKKKKTFLQF 188 (191)
Q Consensus 172 QVqVWFQNRRaK~K~kq 188 (191)
.|+.||.|||+++|+.+
T Consensus 742 n~~~~fk~~~ee~~~~k 758 (769)
T KOG3755|consen 742 NVQFWFKVRREEEKRLK 758 (769)
T ss_pred chHHHHHHHHHHHhhhh
Confidence 79999999999998853
No 56
>PRK09413 IS2 repressor TnpA; Reviewed
Probab=35.97 E-value=55 Score=24.99 Aligned_cols=43 Identities=14% Similarity=0.177 Sum_probs=29.0
Q ss_pred CCCCccCCHHHHH-HHHHHHhhcCCCCHHHHHHHHHHcCCC--cceeeCCc
Q 029573 132 SRKKLRLSKDQSA-ILEESFKEHNTLNPVSIFLLRLLLVLR--ENEVKLEK 179 (191)
Q Consensus 132 ~RkR~r~s~~Q~~-~LE~~F~~~~~p~~~~r~~LA~qL~Ls--QVqVWFQN 179 (191)
.+++.+||.+... ++..++... ....++|+.+|++ +|..|.+-
T Consensus 7 ~~~rr~ys~EfK~~aV~~~~~~g-----~sv~evA~e~gIs~~tl~~W~r~ 52 (121)
T PRK09413 7 PEKRRRRTTQEKIAIVQQSFEPG-----MTVSLVARQHGVAASQLFLWRKQ 52 (121)
T ss_pred CCCCCCCCHHHHHHHHHHHHcCC-----CCHHHHHHHHCcCHHHHHHHHHH
Confidence 3456678888766 444444432 2456899999999 89999543
No 57
>TIGR02939 RpoE_Sigma70 RNA polymerase sigma factor RpoE. A sigma factor is a DNA-binding protein protein that binds to the DNA-directed RNA polymerase core to produce the holoenzyme capable of initiating transcription at specific sites. Different sigma factors act in vegetative growth, heat shock, extracytoplasmic functions (ECF), etc. This model represents the clade of sigma factors called RpoE. This protein may be called sigma-24, sigma-E factor, sigma-H factor, fecI-like sigma factor or alternative sigma factor AlgU.
Probab=35.67 E-value=26 Score=27.58 Aligned_cols=45 Identities=9% Similarity=0.025 Sum_probs=28.5
Q ss_pred CCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCC--cceeeCCchhhhHHhhhc
Q 029573 138 LSKDQSAILEESFKEHNTLNPVSIFLLRLLLVLR--ENEVKLEKKKKKTFLQFL 189 (191)
Q Consensus 138 ~s~~Q~~~LE~~F~~~~~p~~~~r~~LA~qL~Ls--QVqVWFQNRRaK~K~kq~ 189 (191)
++..+..++.-.|-. ...-.++|..||++ .|+++. .|+|.|+++.
T Consensus 139 L~~~~r~v~~l~~~~-----~~s~~EIA~~lgis~~tv~~~l--~rar~~Lr~~ 185 (190)
T TIGR02939 139 LPEDLRTAITLRELE-----GLSYEDIARIMDCPVGTVRSRI--FRAREAIAIR 185 (190)
T ss_pred CCHHHhhhhhhhhhc-----CCCHHHHHHHHCcCHHHHHHHH--HHHHHHHHHH
Confidence 455555555444322 22456899999999 777665 6777777654
No 58
>PF02796 HTH_7: Helix-turn-helix domain of resolvase; InterPro: IPR006120 Site-specific recombination plays an important role in DNA rearrangement in prokaryotic organisms. Two types of site-specific recombination are known to occur: Recombination between inverted repeats resulting in the reversal of a DNA segment. Recombination between repeat sequences on two DNA molecules resulting in their cointegration, or between repeats on one DNA molecule resulting in the excision of a DNA fragment. Site-specific recombination is characterised by a strand exchange mechanism that requires no DNA synthesis or high energy cofactor; the phosphodiester bond energy is conserved in a phospho-protein linkage during strand cleavage and re-ligation. Two unrelated families of recombinases are currently known []. The first, called the 'phage integrase' family, groups a number of bacterial phage and yeast plasmid enzymes. The second [], called the 'resolvase' family, groups enzymes which share the following structural characteristics: an N-terminal catalytic and dimerization domain that contains a conserved serine residue involved in the transient covalent attachment to DNA IPR006119 from INTERPRO, and a C-terminal helix-turn-helix DNA-binding domain. ; GO: 0000150 recombinase activity, 0003677 DNA binding, 0006310 DNA recombination; PDB: 1ZR2_A 2GM4_B 1RES_A 1ZR4_A 1RET_A 1GDT_B 2R0Q_C 1JKP_C 1IJW_C 1JJ6_C ....
Probab=34.96 E-value=31 Score=21.95 Aligned_cols=35 Identities=23% Similarity=0.135 Sum_probs=23.5
Q ss_pred cCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCC--cceee
Q 029573 137 RLSKDQSAILEESFKEHNTLNPVSIFLLRLLLVLR--ENEVK 176 (191)
Q Consensus 137 r~s~~Q~~~LE~~F~~~~~p~~~~r~~LA~qL~Ls--QVqVW 176 (191)
.++.+|...+-+.+.... ...++|+.+|++ .|..+
T Consensus 5 ~~~~~~~~~i~~l~~~G~-----si~~IA~~~gvsr~TvyR~ 41 (45)
T PF02796_consen 5 KLSKEQIEEIKELYAEGM-----SIAEIAKQFGVSRSTVYRY 41 (45)
T ss_dssp SSSHCCHHHHHHHHHTT-------HHHHHHHTTS-HHHHHHH
T ss_pred CCCHHHHHHHHHHHHCCC-----CHHHHHHHHCcCHHHHHHH
Confidence 467777777777776662 577999999999 56543
No 59
>TIGR02948 SigW_bacill RNA polymerase sigma-W factor. This sigma factor is restricted to certain lineages of the order Bacillales.
Probab=34.43 E-value=33 Score=26.95 Aligned_cols=46 Identities=13% Similarity=0.184 Sum_probs=30.9
Q ss_pred cCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCC--cceeeCCchhhhHHhhhc
Q 029573 137 RLSKDQSAILEESFKEHNTLNPVSIFLLRLLLVLR--ENEVKLEKKKKKTFLQFL 189 (191)
Q Consensus 137 r~s~~Q~~~LE~~F~~~~~p~~~~r~~LA~qL~Ls--QVqVWFQNRRaK~K~kq~ 189 (191)
.+++.+..+++..|-.. ..-.++|..||++ .|++++ .|+|.|.++.
T Consensus 136 ~L~~~~r~v~~l~~~~g-----~s~~eIA~~lgis~~~v~~~l--~Rar~~Lr~~ 183 (187)
T TIGR02948 136 ALPPKYRMVIVLKYMED-----LSLKEISEILDLPVGTVKTRI--HRGREALRKQ 183 (187)
T ss_pred hCCHHHhHHhhhHHhcC-----CCHHHHHHHHCCCHHHHHHHH--HHHHHHHHHH
Confidence 36777777777654322 2456899999999 788776 5666665543
No 60
>TIGR02999 Sig-70_X6 RNA polymerase sigma factor, TIGR02999 family. This group of sigma factors are members of the sigma-70 family (TIGR02937) and are found in a variety of species including Rhodopirellula baltica which encodes a paralogous group of five.
Probab=34.37 E-value=42 Score=26.35 Aligned_cols=47 Identities=17% Similarity=0.145 Sum_probs=30.3
Q ss_pred CCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCC--cceeeCCchhhhHHhhhccC
Q 029573 138 LSKDQSAILEESFKEHNTLNPVSIFLLRLLLVLR--ENEVKLEKKKKKTFLQFLIS 191 (191)
Q Consensus 138 ~s~~Q~~~LE~~F~~~~~p~~~~r~~LA~qL~Ls--QVqVWFQNRRaK~K~kq~~s 191 (191)
+++.|..++.-.|-... .-.++|..||++ .|++.. +|++.+.++.++
T Consensus 135 Lp~~~r~v~~l~~~~g~-----s~~EIA~~lgis~~tVk~~l--~Rar~~Lr~~l~ 183 (183)
T TIGR02999 135 VDPRQAEVVELRFFAGL-----TVEEIAELLGVSVRTVERDW--RFARAWLADELS 183 (183)
T ss_pred CCHHHHHHHHHHHHcCC-----CHHHHHHHhCCCHHHHHHHH--HHHHHHHHHHhC
Confidence 55666666665543332 345899999999 777654 567777666553
No 61
>PRK05602 RNA polymerase sigma factor; Reviewed
Probab=32.70 E-value=37 Score=26.99 Aligned_cols=45 Identities=13% Similarity=0.069 Sum_probs=30.5
Q ss_pred CCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCC--cceeeCCchhhhHHhhhc
Q 029573 138 LSKDQSAILEESFKEHNTLNPVSIFLLRLLLVLR--ENEVKLEKKKKKTFLQFL 189 (191)
Q Consensus 138 ~s~~Q~~~LE~~F~~~~~p~~~~r~~LA~qL~Ls--QVqVWFQNRRaK~K~kq~ 189 (191)
+++.+..++...|-... .-.++|..||++ .|+.+. +|++.|.++.
T Consensus 129 L~~~~r~i~~l~~~~g~-----s~~EIA~~lgis~~tV~~~l--~Rar~~Lr~~ 175 (186)
T PRK05602 129 LPERQREAIVLQYYQGL-----SNIEAAAVMDISVDALESLL--ARGRRALRAQ 175 (186)
T ss_pred CCHHHHHHhhHHHhcCC-----CHHHHHHHhCcCHHHHHHHH--HHHHHHHHHH
Confidence 66777777766553322 346899999999 787755 6676666543
No 62
>PHA02955 hypothetical protein; Provisional
Probab=32.54 E-value=59 Score=28.30 Aligned_cols=42 Identities=7% Similarity=0.041 Sum_probs=34.2
Q ss_pred CHHHHHHHHHHHhhc-CCCCHHHHHHHHHHcCCC--cceeeCCch
Q 029573 139 SKDQSAILEESFKEH-NTLNPVSIFLLRLLLVLR--ENEVKLEKK 180 (191)
Q Consensus 139 s~~Q~~~LE~~F~~~-~~p~~~~r~~LA~qL~Ls--QVqVWFQNR 180 (191)
...|+..|-++|.+. ..++.++|.++|+.||+. .|.-||.+-
T Consensus 59 a~~sf~lli~a~~Et~~~Lp~~qk~~ia~~lgI~~~~~~~d~~t~ 103 (213)
T PHA02955 59 EEKNFQLLIEALIETIENFPEKEQKEIAADIGINIDDYKAGKKTD 103 (213)
T ss_pred HHHHHHHHHHHHHHHHHhCCHHHHHHHHHHhCCChhhccCcccch
Confidence 355778888888776 568999999999999998 568888874
No 63
>PRK09642 RNA polymerase sigma factor SigW; Reviewed
Probab=29.48 E-value=47 Score=25.54 Aligned_cols=45 Identities=16% Similarity=0.228 Sum_probs=30.2
Q ss_pred CCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCC--cceeeCCchhhhHHhhhc
Q 029573 138 LSKDQSAILEESFKEHNTLNPVSIFLLRLLLVLR--ENEVKLEKKKKKTFLQFL 189 (191)
Q Consensus 138 ~s~~Q~~~LE~~F~~~~~p~~~~r~~LA~qL~Ls--QVqVWFQNRRaK~K~kq~ 189 (191)
+++.+..++.-.|-... .-.++|..||++ .|+... .|++.+.++.
T Consensus 107 Lp~~~r~v~~l~~~~g~-----s~~EIA~~lgis~~tV~~~l--~Rar~~Lr~~ 153 (160)
T PRK09642 107 LPENYRDVVLAHYLEEK-----SYQEIALQEKIEVKTVEMKL--YRARKWIKKH 153 (160)
T ss_pred CCHHHHHHHHHHHHhCC-----CHHHHHHHHCCCHHHHHHHH--HHHHHHHHHH
Confidence 67777777776654333 345899999999 777654 4666665543
No 64
>PRK12539 RNA polymerase sigma factor; Provisional
Probab=29.24 E-value=52 Score=26.16 Aligned_cols=46 Identities=15% Similarity=0.066 Sum_probs=31.2
Q ss_pred CCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCC--cceeeCCchhhhHHhhhcc
Q 029573 138 LSKDQSAILEESFKEHNTLNPVSIFLLRLLLVLR--ENEVKLEKKKKKTFLQFLI 190 (191)
Q Consensus 138 ~s~~Q~~~LE~~F~~~~~p~~~~r~~LA~qL~Ls--QVqVWFQNRRaK~K~kq~~ 190 (191)
++..+..+++-.|-.+ ..-.++|..||++ .|+.+. .|++.+.++.+
T Consensus 132 L~~~~r~v~~l~~~~g-----~s~~eIA~~lgis~~tV~~~l--~ra~~~Lr~~l 179 (184)
T PRK12539 132 LPEKMRLAIQAVKLEG-----LSVAEAATRSGMSESAVKVSV--HRGLKALAALI 179 (184)
T ss_pred CCHHHHHHHHHHHHcC-----CcHHHHHHHHCcCHHHHHHHH--HHHHHHHHHHH
Confidence 6777777777554322 2456899999999 777655 66766666544
No 65
>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=28.57 E-value=23 Score=24.82 Aligned_cols=17 Identities=6% Similarity=-0.242 Sum_probs=14.4
Q ss_pred HHHHHHHHcCCC--cceee
Q 029573 160 SIFLLRLLLVLR--ENEVK 176 (191)
Q Consensus 160 ~r~~LA~qL~Ls--QVqVW 176 (191)
.-.+||.+||++ +|..|
T Consensus 24 ~lkdIA~~Lgvs~~tIr~W 42 (60)
T PF10668_consen 24 KLKDIAEKLGVSESTIRKW 42 (60)
T ss_pred cHHHHHHHHCCCHHHHHHH
Confidence 345799999999 99988
No 66
>TIGR02959 SigZ RNA polymerase sigma factor, SigZ family. This family of RNA polymerase sigma factors is a member of the Sigma-70 subfamily (TIGR02937). One of these is designated as SigZ in B. subtilis (Swiss_Prot: SIGZ_BACSU). Interestingly, this group has a very sporatic distribution, B. subtilis, for instance, being the only sequenced strain of Bacilli with a member. Dechloromonas aromatica RCB appears to have two of these sigma factors. A member appears on a plasmid found in Photobacterium profundum SS9 and Vibrio fischeri ES114 (where a second one is chromosomally encoded).
Probab=27.72 E-value=56 Score=25.74 Aligned_cols=45 Identities=13% Similarity=0.039 Sum_probs=31.4
Q ss_pred cCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCC--cceeeCCchhhhHHhhh
Q 029573 137 RLSKDQSAILEESFKEHNTLNPVSIFLLRLLLVLR--ENEVKLEKKKKKTFLQF 188 (191)
Q Consensus 137 r~s~~Q~~~LE~~F~~~~~p~~~~r~~LA~qL~Ls--QVqVWFQNRRaK~K~kq 188 (191)
.+++.+..+|+-.|-.+. .-.++|..+|++ .|+++. .|++.+.++
T Consensus 100 ~L~~~~r~v~~l~~~~g~-----s~~eIA~~lgis~~tV~~~l--~Rar~~Lr~ 146 (170)
T TIGR02959 100 ELPDEYREAIRLTELEGL-----SQQEIAEKLGLSLSGAKSRV--QRGRKKLKE 146 (170)
T ss_pred hCCHHHHHHHHHHHHcCC-----CHHHHHHHHCCCHHHHHHHH--HHHHHHHHH
Confidence 477788888887664433 456899999999 676654 566666554
No 67
>PRK12511 RNA polymerase sigma factor; Provisional
Probab=27.20 E-value=51 Score=26.59 Aligned_cols=46 Identities=17% Similarity=0.070 Sum_probs=31.3
Q ss_pred CCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCC--cceeeCCchhhhHHhhhcc
Q 029573 138 LSKDQSAILEESFKEHNTLNPVSIFLLRLLLVLR--ENEVKLEKKKKKTFLQFLI 190 (191)
Q Consensus 138 ~s~~Q~~~LE~~F~~~~~p~~~~r~~LA~qL~Ls--QVqVWFQNRRaK~K~kq~~ 190 (191)
++..+..+++-.|-... .-.++|..||++ .|+++. .|++.+.+..+
T Consensus 112 Lp~~~R~v~~L~~~eg~-----s~~EIA~~lgis~~tV~~~l--~Rar~~Lr~~~ 159 (182)
T PRK12511 112 LPEEQRAALHLVAIEGL-----SYQEAAAVLGIPIGTLMSRI--GRARAALRAFE 159 (182)
T ss_pred CCHHHHHHHHHHHHcCC-----CHHHHHHHhCcCHHHHHHHH--HHHHHHHHHHH
Confidence 67777777776543322 356899999999 677654 67777765543
No 68
>PF13936 HTH_38: Helix-turn-helix domain; PDB: 2W48_A.
Probab=27.17 E-value=48 Score=21.07 Aligned_cols=34 Identities=15% Similarity=0.091 Sum_probs=15.5
Q ss_pred ccCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCC--cce
Q 029573 136 LRLSKDQSAILEESFKEHNTLNPVSIFLLRLLLVLR--ENE 174 (191)
Q Consensus 136 ~r~s~~Q~~~LE~~F~~~~~p~~~~r~~LA~qL~Ls--QVq 174 (191)
..||.+|...++..+..+ ....+||+.||.+ .|.
T Consensus 3 ~~Lt~~eR~~I~~l~~~G-----~s~~~IA~~lg~s~sTV~ 38 (44)
T PF13936_consen 3 KHLTPEERNQIEALLEQG-----MSIREIAKRLGRSRSTVS 38 (44)
T ss_dssp ---------HHHHHHCS--------HHHHHHHTT--HHHHH
T ss_pred cchhhhHHHHHHHHHHcC-----CCHHHHHHHHCcCcHHHH
Confidence 468889999999887644 3556799999988 454
No 69
>KOG3623 consensus Homeobox transcription factor SIP1 [Transcription]
Probab=26.37 E-value=42 Score=34.52 Aligned_cols=57 Identities=7% Similarity=-0.013 Sum_probs=33.5
Q ss_pred CCCCccCCHHHHHHHHHHHhhcCCCCHHH-HHHHHHHcCCC-cceeeCCchhhhHHhhh
Q 029573 132 SRKKLRLSKDQSAILEESFKEHNTLNPVS-IFLLRLLLVLR-ENEVKLEKKKKKTFLQF 188 (191)
Q Consensus 132 ~RkR~r~s~~Q~~~LE~~F~~~~~p~~~~-r~~LA~qL~Ls-QVqVWFQNRRaK~K~kq 188 (191)
.+.+......+-..|-.++.-+..+.-.+ ++.+++-.+.. .|+|||++|+..-+.-+
T Consensus 627 ~kv~sp~k~~dq~ql~~a~elq~s~~n~~~pl~~t~~~n~~pv~ev~dhsrsstpsp~p 685 (1007)
T KOG3623|consen 627 VKVRSPIKEEDQQQLKQAYELQASPSNDEFPLIATRLQNDPPVVEVWDHSRSSTPSPMP 685 (1007)
T ss_pred ccccCCCCccchhhhHhhhhcccCccCcccchhhhhccCCCcchhhcccCCCCCCCCCc
Confidence 33444455566666777777666543333 33344412223 77999999998766544
No 70
>PF13551 HTH_29: Winged helix-turn helix
Probab=25.96 E-value=1e+02 Score=21.99 Aligned_cols=44 Identities=23% Similarity=0.155 Sum_probs=27.5
Q ss_pred CCccCCHHHHHHHHHHHhhcCC-----CCHHHHHH-H-HHHcCCC----cceeeC
Q 029573 134 KKLRLSKDQSAILEESFKEHNT-----LNPVSIFL-L-RLLLVLR----ENEVKL 177 (191)
Q Consensus 134 kR~r~s~~Q~~~LE~~F~~~~~-----p~~~~r~~-L-A~qL~Ls----QVqVWF 177 (191)
.+.+++.++...|.+.+..++. .+...... | .+..++. .|..|+
T Consensus 54 ~~~~l~~~~~~~l~~~~~~~p~~g~~~~t~~~l~~~l~~~~~~~~~s~~ti~r~L 108 (112)
T PF13551_consen 54 PRKRLSEEQRAQLIELLRENPPEGRSRWTLEELAEWLIEEEFGIDVSPSTIRRIL 108 (112)
T ss_pred CCCCCCHHHHHHHHHHHHHCCCCCCCcccHHHHHHHHHHhccCccCCHHHHHHHH
Confidence 3333899999999999998762 34444433 4 4444544 555544
No 71
>PRK12535 RNA polymerase sigma factor; Provisional
Probab=25.20 E-value=66 Score=26.24 Aligned_cols=46 Identities=9% Similarity=-0.054 Sum_probs=30.7
Q ss_pred CCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCC--cceeeCCchhhhHHhhhcc
Q 029573 138 LSKDQSAILEESFKEHNTLNPVSIFLLRLLLVLR--ENEVKLEKKKKKTFLQFLI 190 (191)
Q Consensus 138 ~s~~Q~~~LE~~F~~~~~p~~~~r~~LA~qL~Ls--QVqVWFQNRRaK~K~kq~~ 190 (191)
+++.+..++.-.|-.+. .-.++|..||++ .|+++. .|++.++++++
T Consensus 134 Lp~~~r~v~~l~~~~g~-----s~~EIAe~lgis~~tV~~~l--~Rar~~Lr~~l 181 (196)
T PRK12535 134 LPPERREALILTQVLGY-----TYEEAAKIADVRVGTIRSRV--ARARADLIAAT 181 (196)
T ss_pred CCHHHHHHhhhHHHhCC-----CHHHHHHHhCCCHHHHHHHH--HHHHHHHHHHh
Confidence 56666666655543332 346899999999 777655 67777776554
No 72
>PRK12536 RNA polymerase sigma factor; Provisional
Probab=25.10 E-value=70 Score=25.34 Aligned_cols=45 Identities=18% Similarity=0.027 Sum_probs=27.3
Q ss_pred CCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCC--cceeeCCchhhhHHhhhc
Q 029573 138 LSKDQSAILEESFKEHNTLNPVSIFLLRLLLVLR--ENEVKLEKKKKKTFLQFL 189 (191)
Q Consensus 138 ~s~~Q~~~LE~~F~~~~~p~~~~r~~LA~qL~Ls--QVqVWFQNRRaK~K~kq~ 189 (191)
+++.+..++...|-. .....++|..||++ .|++.. .|++.|.++.
T Consensus 130 L~~~~r~v~~l~~~~-----g~s~~EIA~~l~is~~tV~~~l--~rar~~Lr~~ 176 (181)
T PRK12536 130 LPDRQRLPIVHVKLE-----GLSVAETAQLTGLSESAVKVGI--HRGLKALAAK 176 (181)
T ss_pred CCHHHHHHHHHHHHc-----CCCHHHHHHHHCCCHHHHHHHH--HHHHHHHHHH
Confidence 455555544443322 22456899999999 666655 5666666543
No 73
>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=25.09 E-value=51 Score=21.07 Aligned_cols=36 Identities=17% Similarity=0.165 Sum_probs=22.7
Q ss_pred CCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCC--cceeeCC
Q 029573 138 LSKDQSAILEESFKEHNTLNPVSIFLLRLLLVLR--ENEVKLE 178 (191)
Q Consensus 138 ~s~~Q~~~LE~~F~~~~~p~~~~r~~LA~qL~Ls--QVqVWFQ 178 (191)
+++.+..++.-.|-.+ ..-.++|..+|++ .|+.|.+
T Consensus 11 L~~~~r~i~~l~~~~g-----~s~~eIa~~l~~s~~~v~~~l~ 48 (54)
T PF08281_consen 11 LPERQREIFLLRYFQG-----MSYAEIAEILGISESTVKRRLR 48 (54)
T ss_dssp S-HHHHHHHHHHHTS--------HHHHHHHCTS-HHHHHHHHH
T ss_pred CCHHHHHHHHHHHHHC-----cCHHHHHHHHCcCHHHHHHHHH
Confidence 5666777776665433 3667999999999 7777654
No 74
>PF13443 HTH_26: Cro/C1-type HTH DNA-binding domain; PDB: 3TYR_A 3TYS_A 3B7H_A.
Probab=25.00 E-value=26 Score=23.02 Aligned_cols=21 Identities=14% Similarity=-0.198 Sum_probs=10.6
Q ss_pred HHHHHHHcCCC--cceeeCCchh
Q 029573 161 IFLLRLLLVLR--ENEVKLEKKK 181 (191)
Q Consensus 161 r~~LA~qL~Ls--QVqVWFQNRR 181 (191)
...||+.+|++ +|..|+.++.
T Consensus 13 ~~~La~~~gis~~tl~~~~~~~~ 35 (63)
T PF13443_consen 13 QKDLARKTGISRSTLSRILNGKP 35 (63)
T ss_dssp HHHHHHHHT--HHHHHHHHTTT-
T ss_pred HHHHHHHHCcCHHHHHHHHhccc
Confidence 44566666666 5666666553
No 75
>PRK12515 RNA polymerase sigma factor; Provisional
Probab=24.68 E-value=68 Score=25.54 Aligned_cols=45 Identities=13% Similarity=0.138 Sum_probs=30.5
Q ss_pred CCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCC--cceeeCCchhhhHHhhhc
Q 029573 138 LSKDQSAILEESFKEHNTLNPVSIFLLRLLLVLR--ENEVKLEKKKKKTFLQFL 189 (191)
Q Consensus 138 ~s~~Q~~~LE~~F~~~~~p~~~~r~~LA~qL~Ls--QVqVWFQNRRaK~K~kq~ 189 (191)
+++.+..+|+-.|-... .-.++|..+|++ .|++-. .|+|.|.++.
T Consensus 132 L~~~~r~vl~l~~~~~~-----s~~eIA~~lgis~~tV~~~l--~Rar~~Lr~~ 178 (189)
T PRK12515 132 LSPAHREIIDLVYYHEK-----SVEEVGEIVGIPESTVKTRM--FYARKKLAEL 178 (189)
T ss_pred CCHHHHHHHHHHHHcCC-----CHHHHHHHHCcCHHHHHHHH--HHHHHHHHHH
Confidence 77778887776653332 346899999999 666543 5677666543
No 76
>PRK13558 bacterio-opsin activator; Provisional
Probab=24.59 E-value=52 Score=31.43 Aligned_cols=50 Identities=12% Similarity=0.034 Sum_probs=38.4
Q ss_pred cCCHHHHHHHHHHHhhcCC--CCHHHHHHHHHHcCCCcceeeCCchhhhHHh
Q 029573 137 RLSKDQSAILEESFKEHNT--LNPVSIFLLRLLLVLRENEVKLEKKKKKTFL 186 (191)
Q Consensus 137 r~s~~Q~~~LE~~F~~~~~--p~~~~r~~LA~qL~LsQVqVWFQNRRaK~K~ 186 (191)
.+|..|...|+.+|....| |-...-.+||..||+++=-++-.=||+-.|.
T Consensus 607 ~lt~~q~e~l~~a~~~gyf~~pr~~~~~e~a~~l~is~~t~~~~lr~a~~~l 658 (665)
T PRK13558 607 DLTDRQLTALQKAYVSGYFEWPRRVEGEELAESMGISRSTFHQHLRAAERKL 658 (665)
T ss_pred hCCHHHHHHHHHHHHcCCCCCCccCCHHHHHHHhCCCHHHHHHHHHHHHHHH
Confidence 5999999999999999997 7666888999999999223333345555443
No 77
>PRK12530 RNA polymerase sigma factor; Provisional
Probab=24.52 E-value=67 Score=25.84 Aligned_cols=45 Identities=16% Similarity=-0.054 Sum_probs=30.5
Q ss_pred CCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCC--cceeeCCchhhhHHhhhc
Q 029573 138 LSKDQSAILEESFKEHNTLNPVSIFLLRLLLVLR--ENEVKLEKKKKKTFLQFL 189 (191)
Q Consensus 138 ~s~~Q~~~LE~~F~~~~~p~~~~r~~LA~qL~Ls--QVqVWFQNRRaK~K~kq~ 189 (191)
++..+..++.-.|-... ...++|..||++ .|+++. +||+.+.+..
T Consensus 135 Lp~~~R~v~~L~~~~g~-----s~~EIA~~lgis~~tVk~~l--~RAr~~Lr~~ 181 (189)
T PRK12530 135 LPAQQARVFMMREYLEL-----SSEQICQECDISTSNLHVLL--YRARLQLQAC 181 (189)
T ss_pred CCHHHHHHHhHHHHcCC-----CHHHHHHHHCCCHHHHHHHH--HHHHHHHHHH
Confidence 66677776666653322 356899999999 888764 5666666543
No 78
>PRK12538 RNA polymerase sigma factor; Provisional
Probab=24.47 E-value=53 Score=27.81 Aligned_cols=45 Identities=22% Similarity=0.159 Sum_probs=27.3
Q ss_pred CCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCC--cceeeCCchhhhHHhhhc
Q 029573 138 LSKDQSAILEESFKEHNTLNPVSIFLLRLLLVLR--ENEVKLEKKKKKTFLQFL 189 (191)
Q Consensus 138 ~s~~Q~~~LE~~F~~~~~p~~~~r~~LA~qL~Ls--QVqVWFQNRRaK~K~kq~ 189 (191)
++..|..++.-.|-.. ..-.++|..||++ .|++.. .|++.|+++.
T Consensus 172 Lp~~~R~v~~L~~~eg-----~s~~EIA~~Lgis~~tVk~~l--~RAr~kLr~~ 218 (233)
T PRK12538 172 LPEQQRIAVILSYHEN-----MSNGEIAEVMDTTVAAVESLL--KRGRQQLRDL 218 (233)
T ss_pred CCHHHHHHhhhHHhcC-----CCHHHHHHHHCcCHHHHHHHH--HHHHHHHHHH
Confidence 4555555544443222 2345899999999 777655 5666666543
No 79
>PRK12531 RNA polymerase sigma factor; Provisional
Probab=22.99 E-value=81 Score=25.34 Aligned_cols=46 Identities=15% Similarity=0.169 Sum_probs=29.3
Q ss_pred CCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCC--cceeeCCchhhhHHhhhcc
Q 029573 138 LSKDQSAILEESFKEHNTLNPVSIFLLRLLLVLR--ENEVKLEKKKKKTFLQFLI 190 (191)
Q Consensus 138 ~s~~Q~~~LE~~F~~~~~p~~~~r~~LA~qL~Ls--QVqVWFQNRRaK~K~kq~~ 190 (191)
++..+..++.-.|-... .-.++|..||++ .|++-. +|++.+.++.+
T Consensus 142 Lp~~~r~v~~l~~~eg~-----s~~EIA~~lgis~~tVk~rl--~ra~~~Lr~~l 189 (194)
T PRK12531 142 LPKAQRDVLQAVYLEEL-----PHQQVAEMFDIPLGTVKSRL--RLAVEKLRHSM 189 (194)
T ss_pred CCHHHHHHHHHHHHcCC-----CHHHHHHHhCcCHHHHHHHH--HHHHHHHHHHh
Confidence 56666666665443322 345899999999 675533 67777666543
No 80
>PRK09480 slmA division inhibitor protein; Provisional
Probab=22.14 E-value=1e+02 Score=24.06 Aligned_cols=38 Identities=11% Similarity=0.067 Sum_probs=29.5
Q ss_pred HHHHHH---HhhcCCCCHHHHHHHHHHcCCC--cceeeCCchhh
Q 029573 144 AILEES---FKEHNTLNPVSIFLLRLLLVLR--ENEVKLEKKKK 182 (191)
Q Consensus 144 ~~LE~~---F~~~~~p~~~~r~~LA~qL~Ls--QVqVWFQNRRa 182 (191)
.+|+.+ |..++. .......||++.|++ .+..+|.|+-.
T Consensus 14 ~Il~aa~~l~~~~~G-~~~ti~~Ia~~agvs~gt~Y~~F~~K~~ 56 (194)
T PRK09480 14 QILQALAQMLESPPG-ERITTAKLAARVGVSEAALYRHFPSKAR 56 (194)
T ss_pred HHHHHHHHHHHhcCC-CccCHHHHHHHhCCCHhHHHHHCCCHHH
Confidence 444443 555556 788899999999999 89999999763
No 81
>TIGR00721 tfx DNA-binding protein, Tfx family. Tfx from Methanobacterium thermoautotrophicum is associated with the operon for molybdenum formyl-methanofuran dehydrogenase and binds a DNA sequence near its promoter.
Probab=21.54 E-value=88 Score=25.16 Aligned_cols=48 Identities=19% Similarity=0.052 Sum_probs=32.7
Q ss_pred CccCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCCcceeeCCchhhhHHhhh
Q 029573 135 KLRLSKDQSAILEESFKEHNTLNPVSIFLLRLLLVLRENEVKLEKKKKKTFLQF 188 (191)
Q Consensus 135 R~r~s~~Q~~~LE~~F~~~~~p~~~~r~~LA~qL~LsQVqVWFQNRRaK~K~kq 188 (191)
..-++..|..+|+-.+ .. ....++|..||+++-.|+-.-+|++.|.++
T Consensus 4 ~~~Lte~qr~VL~Lr~-~G-----lTq~EIAe~LgiS~stV~~~e~ra~kkLr~ 51 (137)
T TIGR00721 4 KTFLTERQIKVLELRE-KG-----LSQKEIAKELKTTRANVSAIEKRAMENIEK 51 (137)
T ss_pred cCCCCHHHHHHHHHHH-cC-----CCHHHHHHHHCcCHHHHHHHHHhHHHHHHH
Confidence 4458899999998742 22 256799999999943444455666666654
No 82
>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=21.36 E-value=85 Score=20.99 Aligned_cols=28 Identities=25% Similarity=0.150 Sum_probs=21.1
Q ss_pred HHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCC
Q 029573 140 KDQSAILEESFKEHNTLNPVSIFLLRLLLVLR 171 (191)
Q Consensus 140 ~~Q~~~LE~~F~~~~~p~~~~r~~LA~qL~Ls 171 (191)
..|+..|+-.+. +.+.+.. +||.+||++
T Consensus 5 ~rq~~Ll~~L~~-~~~~~~~---ela~~l~~S 32 (59)
T PF08280_consen 5 KRQLKLLELLLK-NKWITLK---ELAKKLNIS 32 (59)
T ss_dssp HHHHHHHHHHHH-HTSBBHH---HHHHHCTS-
T ss_pred HHHHHHHHHHHc-CCCCcHH---HHHHHHCCC
Confidence 357788888888 6666544 899999998
No 83
>PRK07037 extracytoplasmic-function sigma-70 factor; Validated
Probab=21.09 E-value=99 Score=23.72 Aligned_cols=45 Identities=7% Similarity=-0.168 Sum_probs=30.0
Q ss_pred CCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCC--cceeeCCchhhhHHhhhc
Q 029573 138 LSKDQSAILEESFKEHNTLNPVSIFLLRLLLVLR--ENEVKLEKKKKKTFLQFL 189 (191)
Q Consensus 138 ~s~~Q~~~LE~~F~~~~~p~~~~r~~LA~qL~Ls--QVqVWFQNRRaK~K~kq~ 189 (191)
+++.+..++.-.|-... ...++|..+|++ .|+.. -+|++.+.++.
T Consensus 110 L~~~~r~v~~l~~~~~~-----s~~EIA~~lgis~~tV~~~--l~ra~~~lr~~ 156 (163)
T PRK07037 110 LPARTRYAFEMYRLHGE-----TQKDIARELGVSPTLVNFM--IRDALVHCRKC 156 (163)
T ss_pred CCHHHHHHHHHHHHcCC-----CHHHHHHHHCCCHHHHHHH--HHHHHHHHHHH
Confidence 66777777766553332 356899999999 77764 45666655543
No 84
>PRK10072 putative transcriptional regulator; Provisional
Probab=20.77 E-value=38 Score=25.53 Aligned_cols=23 Identities=13% Similarity=-0.073 Sum_probs=20.1
Q ss_pred HHHHHHHHcCCC--cceeeCCchhh
Q 029573 160 SIFLLRLLLVLR--ENEVKLEKKKK 182 (191)
Q Consensus 160 ~r~~LA~qL~Ls--QVqVWFQNRRa 182 (191)
...+||+.+|++ .|.-|.+.+|.
T Consensus 48 TQ~elA~~lGvS~~TVs~WE~G~r~ 72 (96)
T PRK10072 48 KIDDFARVLGVSVAMVKEWESRRVK 72 (96)
T ss_pred CHHHHHHHhCCCHHHHHHHHcCCCC
Confidence 367899999999 89999998874
No 85
>PRK09643 RNA polymerase sigma factor SigM; Reviewed
Probab=20.10 E-value=82 Score=25.38 Aligned_cols=47 Identities=23% Similarity=0.105 Sum_probs=31.2
Q ss_pred CCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCCcceeeCCchhhhHHhhhc
Q 029573 138 LSKDQSAILEESFKEHNTLNPVSIFLLRLLLVLRENEVKLEKKKKKTFLQFL 189 (191)
Q Consensus 138 ~s~~Q~~~LE~~F~~~~~p~~~~r~~LA~qL~LsQVqVWFQNRRaK~K~kq~ 189 (191)
+++.+..+|+-.|-... .-.++|..+|++.-.|.-+-+|+|.|.+..
T Consensus 135 Lp~~~r~i~~l~~~~g~-----s~~EIA~~lg~s~~tV~~rl~rar~~Lr~~ 181 (192)
T PRK09643 135 LPVEQRAALVAVDMQGY-----SVADAARMLGVAEGTVKSRCARGRARLAEL 181 (192)
T ss_pred CCHHHHHHHHHHHHcCC-----CHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence 67777777776543332 345899999999223344668888877654
Done!