Query 043602
Match_columns 352
No_of_seqs 124 out of 343
Neff 2.9
Searched_HMMs 46136
Date Fri Mar 29 06:32:46 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/043602.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/043602hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG0489 Transcription factor z 99.7 2.1E-19 4.6E-24 166.8 1.5 66 70-140 159-224 (261)
2 KOG0488 Transcription factor B 99.7 1E-18 2.2E-23 167.0 4.2 69 66-139 168-236 (309)
3 KOG0484 Transcription factor P 99.7 9.2E-19 2E-23 148.8 2.5 66 70-140 17-82 (125)
4 KOG0487 Transcription factor A 99.7 3.5E-18 7.7E-23 164.2 4.2 64 70-138 235-298 (308)
5 KOG0842 Transcription factor t 99.7 2.4E-17 5.1E-22 158.5 9.2 70 68-142 151-220 (307)
6 KOG0492 Transcription factor M 99.7 3.6E-17 7.9E-22 151.8 5.0 66 70-140 144-209 (246)
7 PF00046 Homeobox: Homeobox do 99.7 2.2E-17 4.7E-22 118.6 2.7 57 71-132 1-57 (57)
8 KOG0843 Transcription factor E 99.7 4.7E-17 1E-21 148.0 4.4 63 70-137 102-164 (197)
9 KOG2251 Homeobox transcription 99.6 4.3E-16 9.3E-21 144.7 4.8 64 69-137 36-99 (228)
10 KOG0494 Transcription factor C 99.6 7E-16 1.5E-20 147.3 3.5 66 70-140 141-206 (332)
11 KOG0850 Transcription factor D 99.6 2.7E-15 5.8E-20 140.4 6.1 72 59-135 111-182 (245)
12 smart00389 HOX Homeodomain. DN 99.5 2.5E-15 5.5E-20 106.5 2.7 55 72-131 2-56 (56)
13 cd00086 homeodomain Homeodomai 99.5 3.8E-15 8.2E-20 105.8 2.9 57 72-133 2-58 (59)
14 KOG0485 Transcription factor N 99.5 4.9E-15 1.1E-19 138.7 3.0 69 70-143 104-172 (268)
15 TIGR01565 homeo_ZF_HD homeobox 99.5 5.6E-14 1.2E-18 106.8 5.3 52 71-127 2-57 (58)
16 KOG0848 Transcription factor C 99.5 9.9E-15 2.1E-19 139.6 1.1 60 72-136 201-260 (317)
17 KOG0493 Transcription factor E 99.4 3.1E-14 6.8E-19 136.3 2.9 60 69-133 245-304 (342)
18 KOG0844 Transcription factor E 99.4 3.2E-14 6.9E-19 138.4 2.1 63 68-135 179-241 (408)
19 KOG0491 Transcription factor B 99.4 1.7E-14 3.7E-19 130.5 -0.0 66 70-140 100-165 (194)
20 KOG0486 Transcription factor P 99.4 1E-13 2.2E-18 134.6 3.0 64 70-138 112-175 (351)
21 COG5576 Homeodomain-containing 99.4 2.6E-13 5.5E-18 119.7 4.7 67 70-141 51-117 (156)
22 KOG0483 Transcription factor H 99.3 2.8E-13 6.1E-18 123.7 2.3 61 71-136 51-111 (198)
23 KOG0490 Transcription factor, 99.3 3.7E-13 8.1E-18 117.1 2.8 62 69-135 59-120 (235)
24 KOG4577 Transcription factor L 99.2 1.8E-11 3.9E-16 118.8 4.2 62 70-136 167-228 (383)
25 KOG0849 Transcription factor P 99.1 3.4E-11 7.4E-16 117.1 5.4 63 69-136 175-237 (354)
26 KOG0847 Transcription factor, 99.1 1.2E-11 2.6E-16 116.5 1.3 66 72-142 169-234 (288)
27 KOG3802 Transcription factor O 98.7 1.2E-08 2.5E-13 101.9 4.8 62 69-135 293-354 (398)
28 KOG0490 Transcription factor, 98.1 1.9E-06 4.1E-11 75.4 3.6 62 69-135 152-213 (235)
29 KOG0775 Transcription factor S 98.0 4.1E-06 8.9E-11 81.2 4.3 54 73-131 170-232 (304)
30 KOG2252 CCAAT displacement pro 97.7 1.7E-05 3.7E-10 82.3 3.0 57 69-130 419-475 (558)
31 KOG1168 Transcription factor A 97.6 5.1E-05 1.1E-09 74.8 4.1 62 69-135 308-369 (385)
32 KOG0774 Transcription factor P 97.6 3.8E-05 8.1E-10 74.7 3.0 107 17-141 143-257 (334)
33 PF05920 Homeobox_KN: Homeobox 97.5 1.6E-05 3.5E-10 56.4 -0.7 33 92-129 8-40 (40)
34 KOG1146 Homeobox protein [Gene 96.3 0.0021 4.6E-08 72.5 2.7 61 70-135 903-963 (1406)
35 KOG0773 Transcription factor M 91.6 0.13 2.8E-06 49.3 2.6 61 70-135 239-302 (342)
36 KOG3623 Homeobox transcription 89.5 0.18 3.9E-06 55.3 1.7 49 82-135 568-616 (1007)
37 PF11569 Homez: Homeodomain le 84.8 0.26 5.6E-06 38.2 -0.2 41 82-127 10-50 (56)
38 PF04218 CENP-B_N: CENP-B N-te 71.9 4.4 9.6E-05 30.0 2.9 47 71-127 1-47 (53)
39 cd06171 Sigma70_r4 Sigma70, re 64.1 2.8 6.1E-05 27.6 0.5 42 76-127 10-51 (55)
40 PF04967 HTH_10: HTH DNA bindi 51.1 13 0.00027 28.3 2.1 40 77-120 1-41 (53)
41 cd00569 HTH_Hin_like Helix-tur 49.9 19 0.00041 20.9 2.4 40 74-123 3-42 (42)
42 PF01527 HTH_Tnp_1: Transposas 48.3 10 0.00023 28.1 1.3 41 72-122 2-43 (76)
43 smart00027 EH Eps15 homology d 42.4 20 0.00043 28.3 2.2 45 75-123 2-50 (96)
44 KOG3755 SATB1 matrix attachmen 41.1 7.3 0.00016 42.6 -0.6 63 71-134 692-758 (769)
45 PF02796 HTH_7: Helix-turn-hel 40.3 11 0.00024 26.7 0.4 39 74-122 3-41 (45)
46 PRK03975 tfx putative transcri 39.4 20 0.00043 32.0 1.9 49 75-134 5-53 (141)
47 PRK09652 RNA polymerase sigma 37.5 23 0.00049 29.4 1.9 39 76-124 128-166 (182)
48 PRK12519 RNA polymerase sigma 35.6 23 0.0005 30.5 1.7 46 77-132 142-187 (194)
49 PF04545 Sigma70_r4: Sigma-70, 34.5 20 0.00044 25.2 1.0 37 76-122 4-40 (50)
50 smart00421 HTH_LUXR helix_turn 34.2 28 0.00061 23.4 1.6 38 76-124 3-40 (58)
51 PRK11924 RNA polymerase sigma 33.7 34 0.00074 28.3 2.3 46 77-132 126-171 (179)
52 TIGR02989 Sig-70_gvs1 RNA poly 33.5 42 0.00091 27.6 2.8 37 76-122 111-147 (159)
53 PRK09646 RNA polymerase sigma 33.5 32 0.0007 30.0 2.2 49 76-138 142-190 (194)
54 PRK09413 IS2 repressor TnpA; R 33.0 39 0.00084 28.3 2.6 41 72-122 8-49 (121)
55 TIGR02937 sigma70-ECF RNA poly 32.2 26 0.00057 27.2 1.4 41 76-126 110-150 (158)
56 COG3413 Predicted DNA binding 32.2 49 0.0011 30.0 3.3 41 76-120 155-196 (215)
57 PRK09642 RNA polymerase sigma 31.6 34 0.00074 28.5 2.0 41 77-127 107-147 (160)
58 PRK12533 RNA polymerase sigma 31.5 45 0.00097 30.5 2.9 54 77-144 135-188 (216)
59 PF13936 HTH_38: Helix-turn-he 31.5 15 0.00033 26.1 -0.1 38 75-122 3-40 (44)
60 TIGR02952 Sig70_famx2 RNA poly 30.6 53 0.0011 27.3 3.0 47 76-136 122-168 (170)
61 PRK12526 RNA polymerase sigma 30.6 35 0.00076 30.3 2.0 38 76-123 153-190 (206)
62 TIGR02948 SigW_bacill RNA poly 30.3 31 0.00067 29.2 1.6 42 76-127 136-177 (187)
63 PRK12514 RNA polymerase sigma 29.8 77 0.0017 26.9 3.9 38 77-124 130-167 (179)
64 PF08880 QLQ: QLQ; InterPro: 29.2 43 0.00093 23.9 1.9 14 76-89 2-15 (37)
65 PF13565 HTH_32: Homeodomain-l 29.2 1E+02 0.0022 22.9 4.1 47 70-122 26-76 (77)
66 PF12824 MRP-L20: Mitochondria 28.5 2E+02 0.0043 26.3 6.4 40 74-120 83-122 (164)
67 PRK12512 RNA polymerase sigma 27.3 41 0.0009 28.7 1.8 47 76-132 131-177 (184)
68 PRK12531 RNA polymerase sigma 27.0 75 0.0016 27.7 3.4 49 77-139 142-190 (194)
69 PF08281 Sigma70_r4_2: Sigma-7 26.7 20 0.00042 25.4 -0.2 38 77-124 11-48 (54)
70 PF10925 DUF2680: Protein of u 25.4 74 0.0016 24.6 2.7 42 77-123 1-42 (59)
71 PRK09639 RNA polymerase sigma 24.2 57 0.0012 27.1 2.1 38 76-124 112-149 (166)
72 PRK07037 extracytoplasmic-func 23.9 85 0.0018 26.1 3.0 50 76-139 109-158 (163)
73 PRK06759 RNA polymerase factor 23.6 44 0.00096 27.4 1.3 39 76-124 106-144 (154)
74 PRK04217 hypothetical protein; 23.5 87 0.0019 26.9 3.1 45 73-127 39-83 (110)
75 TIGR02985 Sig70_bacteroi1 RNA 23.2 54 0.0012 26.5 1.7 39 76-124 113-151 (161)
76 cd02413 40S_S3_KH K homology R 22.6 71 0.0015 25.7 2.2 27 98-124 49-75 (81)
77 PRK09643 RNA polymerase sigma 22.5 71 0.0015 27.9 2.4 35 77-121 135-169 (192)
78 PF13873 Myb_DNA-bind_5: Myb/S 22.3 1.2E+02 0.0026 23.0 3.4 58 75-133 3-75 (78)
79 PF13551 HTH_29: Winged helix- 20.9 2.5E+02 0.0054 21.7 5.0 52 71-123 52-108 (112)
80 PRK09637 RNA polymerase sigma 20.8 71 0.0015 27.8 2.1 39 76-124 106-144 (181)
81 TIGR02983 SigE-fam_strep RNA p 20.5 60 0.0013 27.0 1.5 48 77-138 111-158 (162)
82 PRK09480 slmA division inhibit 20.3 61 0.0013 27.3 1.5 36 86-127 20-55 (194)
83 PRK12515 RNA polymerase sigma 20.1 79 0.0017 27.3 2.2 40 75-124 130-169 (189)
No 1
>KOG0489 consensus Transcription factor zerknullt and related HOX domain proteins [General function prediction only]
Probab=99.75 E-value=2.1e-19 Score=166.82 Aligned_cols=66 Identities=18% Similarity=0.253 Sum_probs=61.7
Q ss_pred CCCCCCCCCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHhcCCCCCCceeeccccchhhHHHHHHhhhcC
Q 043602 70 VVSSRWNPTPEQLRTLEDLYRRGTRTPSADQIQHITAQLRRFGKIEGKNVFYWFQNHKARERQKRRRQMES 140 (352)
Q Consensus 70 ~rR~Rw~FT~eQLqiLE~lF~~~~~YPs~e~RqqIA~qL~~~G~LsEsqVqvWFQNRRAReKRKrRrq~e~ 140 (352)
.+|.|++||.+||.+||+.|..++ |++..+|.+||..|. |+|+|||||||||||||||..+.....
T Consensus 159 ~kR~RtayT~~QllELEkEFhfN~-YLtR~RRiEiA~~L~----LtErQIKIWFQNRRMK~Kk~~k~~~~~ 224 (261)
T KOG0489|consen 159 SKRRRTAFTRYQLLELEKEFHFNK-YLTRSRRIEIAHALN----LTERQIKIWFQNRRMKWKKENKAKSSQ 224 (261)
T ss_pred CCCCCcccchhhhhhhhhhhcccc-ccchHHHHHHHhhcc----hhHHHHHHHHHHHHHHHHHhhcccccc
Confidence 799999999999999999999999 999999999999996 999999999999999999877755544
No 2
>KOG0488 consensus Transcription factor BarH and related HOX domain proteins [General function prediction only]
Probab=99.74 E-value=1e-18 Score=167.02 Aligned_cols=69 Identities=25% Similarity=0.294 Sum_probs=63.4
Q ss_pred CCCCCCCCCCCCCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHhcCCCCCCceeeccccchhhHHHHHHhhhc
Q 043602 66 TPPVVVSSRWNPTPEQLRTLEDLYRRGTRTPSADQIQHITAQLRRFGKIEGKNVFYWFQNHKARERQKRRRQME 139 (352)
Q Consensus 66 ~~p~~rR~Rw~FT~eQLqiLE~lF~~~~~YPs~e~RqqIA~qL~~~G~LsEsqVqvWFQNRRAReKRKrRrq~e 139 (352)
.|...|+.||.||..||..||+.|++++ |++..+|.+||+.|+ |++.|||+||||||+||||+..+..+
T Consensus 168 ~pkK~RksRTaFT~~Ql~~LEkrF~~QK-YLS~~DR~~LA~~Lg----LTdaQVKtWfQNRRtKWKrq~a~g~~ 236 (309)
T KOG0488|consen 168 TPKKRRKSRTAFSDHQLFELEKRFEKQK-YLSVADRIELAASLG----LTDAQVKTWFQNRRTKWKRQTAEGGE 236 (309)
T ss_pred CCcccccchhhhhHHHHHHHHHHHHHhh-cccHHHHHHHHHHcC----CchhhHHHHHhhhhHHHHHHHHhhhc
Confidence 4456999999999999999999999999 999999999999996 99999999999999999998776433
No 3
>KOG0484 consensus Transcription factor PHOX2/ARIX, contains HOX domain [Transcription]
Probab=99.73 E-value=9.2e-19 Score=148.79 Aligned_cols=66 Identities=24% Similarity=0.381 Sum_probs=60.9
Q ss_pred CCCCCCCCCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHhcCCCCCCceeeccccchhhHHHHHHhhhcC
Q 043602 70 VVSSRWNPTPEQLRTLEDLYRRGTRTPSADQIQHITAQLRRFGKIEGKNVFYWFQNHKARERQKRRRQMES 140 (352)
Q Consensus 70 ~rR~Rw~FT~eQLqiLE~lF~~~~~YPs~e~RqqIA~qL~~~G~LsEsqVqvWFQNRRAReKRKrRrq~e~ 140 (352)
.||-||+||..||.+||++|...+ ||++..|++||..|. |+|.+|||||||||||-||+.|-....
T Consensus 17 QRRIRTTFTS~QLkELErvF~ETH-YPDIYTREEiA~kid----LTEARVQVWFQNRRAKfRKQEr~a~~~ 82 (125)
T KOG0484|consen 17 QRRIRTTFTSAQLKELERVFAETH-YPDIYTREEIALKID----LTEARVQVWFQNRRAKFRKQERAAIAK 82 (125)
T ss_pred hhhhhhhhhHHHHHHHHHHHHhhc-CCcchhHHHHHHhhh----hhHHHHHHHHHhhHHHHHHHHHHHHHH
Confidence 678999999999999999999999 999999999999996 999999999999999999887744433
No 4
>KOG0487 consensus Transcription factor Abd-B, contains HOX domain [Transcription]
Probab=99.71 E-value=3.5e-18 Score=164.22 Aligned_cols=64 Identities=20% Similarity=0.284 Sum_probs=60.6
Q ss_pred CCCCCCCCCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHhcCCCCCCceeeccccchhhHHHHHHhhh
Q 043602 70 VVSSRWNPTPEQLRTLEDLYRRGTRTPSADQIQHITAQLRRFGKIEGKNVFYWFQNHKARERQKRRRQM 138 (352)
Q Consensus 70 ~rR~Rw~FT~eQLqiLE~lF~~~~~YPs~e~RqqIA~qL~~~G~LsEsqVqvWFQNRRAReKRKrRrq~ 138 (352)
.|++|..+|+.|+.+||+.|..++ |++.+.|.+|++.|+ |||+||||||||||||+||-.|+.-
T Consensus 235 ~RKKRcPYTK~QtlELEkEFlfN~-YitkeKR~ElSr~lN----LTeRQVKIWFQNRRMK~KK~~re~r 298 (308)
T KOG0487|consen 235 GRKKRCPYTKHQTLELEKEFLFNM-YITKEKRLELSRTLN----LTERQVKIWFQNRRMKEKKVNRENR 298 (308)
T ss_pred cccccCCchHHHHHHHHHHHHHHH-HHhHHHHHHHHHhcc----cchhheeeeehhhhhHHhhhhhhhh
Confidence 899999999999999999999999 999999999999995 9999999999999999999887443
No 5
>KOG0842 consensus Transcription factor tinman/NKX2-3, contains HOX domain [Transcription]
Probab=99.71 E-value=2.4e-17 Score=158.51 Aligned_cols=70 Identities=21% Similarity=0.322 Sum_probs=63.5
Q ss_pred CCCCCCCCCCCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHhcCCCCCCceeeccccchhhHHHHHHhhhcCCC
Q 043602 68 PVVVSSRWNPTPEQLRTLEDLYRRGTRTPSADQIQHITAQLRRFGKIEGKNVFYWFQNHKARERQKRRRQMESSP 142 (352)
Q Consensus 68 p~~rR~Rw~FT~eQLqiLE~lF~~~~~YPs~e~RqqIA~qL~~~G~LsEsqVqvWFQNRRAReKRKrRrq~e~a~ 142 (352)
.-.||+|..||+.|+-+||+.|..++ |++..||++||..|+ ||++||||||||||+|.||++..+...+.
T Consensus 151 ~~kRKrRVLFSqAQV~ELERRFrqQR-YLSAPERE~LA~~Lr----LT~TQVKIWFQNrRYK~KR~~~dk~~~~~ 220 (307)
T KOG0842|consen 151 RKKRKRRVLFSQAQVYELERRFRQQR-YLSAPEREHLASSLR----LTPTQVKIWFQNRRYKTKRQQKDKALEAL 220 (307)
T ss_pred ccccccccccchhHHHHHHHHHHhhh-ccccHhHHHHHHhcC----CCchheeeeeecchhhhhhhhhhhhhhcc
Confidence 34899999999999999999999999 999999999999996 99999999999999999988776554443
No 6
>KOG0492 consensus Transcription factor MSH, contains HOX domain [General function prediction only]
Probab=99.67 E-value=3.6e-17 Score=151.83 Aligned_cols=66 Identities=24% Similarity=0.359 Sum_probs=62.6
Q ss_pred CCCCCCCCCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHhcCCCCCCceeeccccchhhHHHHHHhhhcC
Q 043602 70 VVSSRWNPTPEQLRTLEDLYRRGTRTPSADQIQHITAQLRRFGKIEGKNVFYWFQNHKARERQKRRRQMES 140 (352)
Q Consensus 70 ~rR~Rw~FT~eQLqiLE~lF~~~~~YPs~e~RqqIA~qL~~~G~LsEsqVqvWFQNRRAReKRKrRrq~e~ 140 (352)
-|++||.||..||..||+.|+... |+++++|.+++..|. |+|.|||+||||||||.||.++.+.|.
T Consensus 144 nRkPRtPFTtqQLlaLErkfrekq-YLSiaEraefSsSL~----LTeTqVKIWFQNRRAKaKRlQeae~Ek 209 (246)
T KOG0492|consen 144 NRKPRTPFTTQQLLALERKFREKQ-YLSIAERAEFSSSLE----LTETQVKIWFQNRRAKAKRLQEAELEK 209 (246)
T ss_pred CCCCCCCCCHHHHHHHHHHHhHhh-hhhHHHHHhhhhhhh----hhhhheehhhhhhhHHHHHHHHHHHHH
Confidence 588999999999999999999999 999999999999997 999999999999999999998877765
No 7
>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=99.67 E-value=2.2e-17 Score=118.61 Aligned_cols=57 Identities=28% Similarity=0.543 Sum_probs=54.8
Q ss_pred CCCCCCCCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHhcCCCCCCceeeccccchhhHHH
Q 043602 71 VSSRWNPTPEQLRTLEDLYRRGTRTPSADQIQHITAQLRRFGKIEGKNVFYWFQNHKARERQ 132 (352)
Q Consensus 71 rR~Rw~FT~eQLqiLE~lF~~~~~YPs~e~RqqIA~qL~~~G~LsEsqVqvWFQNRRAReKR 132 (352)
+++|+.||++|+.+||+.|..++ ||+.++++.||..|+ |+..+|++||||||+|+||
T Consensus 1 kr~r~~~t~~q~~~L~~~f~~~~-~p~~~~~~~la~~l~----l~~~~V~~WF~nrR~k~kk 57 (57)
T PF00046_consen 1 KRKRTRFTKEQLKVLEEYFQENP-YPSKEEREELAKELG----LTERQVKNWFQNRRRKEKK 57 (57)
T ss_dssp SSSSSSSSHHHHHHHHHHHHHSS-SCHHHHHHHHHHHHT----SSHHHHHHHHHHHHHHHHH
T ss_pred CcCCCCCCHHHHHHHHHHHHHhc-ccccccccccccccc----ccccccccCHHHhHHHhCc
Confidence 57999999999999999999999 999999999999995 9999999999999999986
No 8
>KOG0843 consensus Transcription factor EMX1 and related HOX domain proteins [Transcription]
Probab=99.66 E-value=4.7e-17 Score=148.03 Aligned_cols=63 Identities=22% Similarity=0.372 Sum_probs=59.8
Q ss_pred CCCCCCCCCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHhcCCCCCCceeeccccchhhHHHHHHhh
Q 043602 70 VVSSRWNPTPEQLRTLEDLYRRGTRTPSADQIQHITAQLRRFGKIEGKNVFYWFQNHKARERQKRRRQ 137 (352)
Q Consensus 70 ~rR~Rw~FT~eQLqiLE~lF~~~~~YPs~e~RqqIA~qL~~~G~LsEsqVqvWFQNRRAReKRKrRrq 137 (352)
.+|.||.||++||..||..|+.+. |....+|++||+.|+ |+|.||||||||||.|.||++.+.
T Consensus 102 ~kr~RT~ft~~Ql~~LE~~F~~~~-Yvvg~eR~~LA~~L~----LsetQVkvWFQNRRtk~kr~~~e~ 164 (197)
T KOG0843|consen 102 PKRIRTAFTPEQLLKLEHAFEGNQ-YVVGAERKQLAQSLS----LSETQVKVWFQNRRTKHKRMQQED 164 (197)
T ss_pred CCccccccCHHHHHHHHHHHhcCC-eeechHHHHHHHHcC----CChhHhhhhhhhhhHHHHHHHHHh
Confidence 579999999999999999999999 999999999999996 999999999999999999887765
No 9
>KOG2251 consensus Homeobox transcription factor [Transcription]
Probab=99.61 E-value=4.3e-16 Score=144.74 Aligned_cols=64 Identities=25% Similarity=0.402 Sum_probs=61.0
Q ss_pred CCCCCCCCCCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHhcCCCCCCceeeccccchhhHHHHHHhh
Q 043602 69 VVVSSRWNPTPEQLRTLEDLYRRGTRTPSADQIQHITAQLRRFGKIEGKNVFYWFQNHKARERQKRRRQ 137 (352)
Q Consensus 69 ~~rR~Rw~FT~eQLqiLE~lF~~~~~YPs~e~RqqIA~qL~~~G~LsEsqVqvWFQNRRAReKRKrRrq 137 (352)
..||.||+||..||.+||.+|.+.. ||++..|++||.+|+ |.|.+|||||.|||||+|++++.+
T Consensus 36 kqRRERTtFtr~QlevLe~LF~kTq-YPDv~~rEelAlkln----LpeSrVqVWFKNRRAK~r~qq~qq 99 (228)
T KOG2251|consen 36 KQRRERTTFTRKQLEVLEALFAKTQ-YPDVFMREELALKLN----LPESRVQVWFKNRRAKCRRQQQQQ 99 (228)
T ss_pred hcccccceecHHHHHHHHHHHHhhc-CccHHHHHHHHHHhC----CchhhhhhhhccccchhhHhhhhh
Confidence 4789999999999999999999999 999999999999995 999999999999999999988876
No 10
>KOG0494 consensus Transcription factor CHX10 and related HOX domain proteins [General function prediction only]
Probab=99.58 E-value=7e-16 Score=147.26 Aligned_cols=66 Identities=23% Similarity=0.294 Sum_probs=59.6
Q ss_pred CCCCCCCCCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHhcCCCCCCceeeccccchhhHHHHHHhhhcC
Q 043602 70 VVSSRWNPTPEQLRTLEDLYRRGTRTPSADQIQHITAQLRRFGKIEGKNVFYWFQNHKARERQKRRRQMES 140 (352)
Q Consensus 70 ~rR~Rw~FT~eQLqiLE~lF~~~~~YPs~e~RqqIA~qL~~~G~LsEsqVqvWFQNRRAReKRKrRrq~e~ 140 (352)
+|+-||.||..||.+||+.|...+ ||+...|+-||..+. |.|.+|+||||||||||||+.++.--+
T Consensus 141 RRh~RTiFT~~Qle~LEkaFkeaH-YPDv~Are~la~kte----lpEDRIqVWfQNRRAKWRk~Ek~wg~s 206 (332)
T KOG0494|consen 141 RRHFRTIFTSYQLEELEKAFKEAH-YPDVYAREMLADKTE----LPEDRIQVWFQNRRAKWRKTEKRWGGS 206 (332)
T ss_pred cccccchhhHHHHHHHHHHHhhcc-CccHHHHHHHhhhcc----CchhhhhHHhhhhhHHhhhhhhhcCcc
Confidence 455599999999999999999999 999999999998885 999999999999999999988765443
No 11
>KOG0850 consensus Transcription factor DLX and related proteins with LIM Zn-binding and HOX domains [Transcription]
Probab=99.57 E-value=2.7e-15 Score=140.43 Aligned_cols=72 Identities=18% Similarity=0.276 Sum_probs=63.7
Q ss_pred cccCCCCCCCCCCCCCCCCCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHhcCCCCCCceeeccccchhhHHHHHH
Q 043602 59 NKREFSSTPPVVVSSRWNPTPEQLRTLEDLYRRGTRTPSADQIQHITAQLRRFGKIEGKNVFYWFQNHKARERQKRR 135 (352)
Q Consensus 59 ~kre~~~~~p~~rR~Rw~FT~eQLqiLE~lF~~~~~YPs~e~RqqIA~qL~~~G~LsEsqVqvWFQNRRAReKRKrR 135 (352)
..|-++..+--+|++||.++.-||+.|.+.|++.. |+-..||.+||+.|+ |+..||||||||||.|-||..+
T Consensus 111 ~e~~~Ngk~KK~RKPRTIYSS~QLqaL~rRFQkTQ-YLALPERAeLAAsLG----LTQTQVKIWFQNrRSK~KKl~k 182 (245)
T KOG0850|consen 111 SERRPNGKGKKVRKPRTIYSSLQLQALNRRFQQTQ-YLALPERAELAASLG----LTQTQVKIWFQNRRSKFKKLKK 182 (245)
T ss_pred ceeccCCCcccccCCcccccHHHHHHHHHHHhhcc-hhcCcHHHHHHHHhC----CchhHhhhhhhhhHHHHHHHHh
Confidence 33444433334899999999999999999999999 999999999999996 9999999999999999999887
No 12
>smart00389 HOX Homeodomain. DNA-binding factors that are involved in the transcriptional regulation of key developmental processes
Probab=99.54 E-value=2.5e-15 Score=106.52 Aligned_cols=55 Identities=33% Similarity=0.575 Sum_probs=52.2
Q ss_pred CCCCCCCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHhcCCCCCCceeeccccchhhHH
Q 043602 72 SSRWNPTPEQLRTLEDLYRRGTRTPSADQIQHITAQLRRFGKIEGKNVFYWFQNHKARER 131 (352)
Q Consensus 72 R~Rw~FT~eQLqiLE~lF~~~~~YPs~e~RqqIA~qL~~~G~LsEsqVqvWFQNRRAReK 131 (352)
+.|+.||++|+.+||+.|..++ ||+.+++++||..|+ |+..+|++||+|||+|.|
T Consensus 2 k~r~~~~~~~~~~L~~~f~~~~-~P~~~~~~~la~~~~----l~~~qV~~WF~nrR~~~~ 56 (56)
T smart00389 2 RKRTSFTPEQLEELEKEFQKNP-YPSREEREELAAKLG----LSERQVKVWFQNRRAKWK 56 (56)
T ss_pred CCCCcCCHHHHHHHHHHHHhCC-CCCHHHHHHHHHHHC----cCHHHHHHhHHHHhhccC
Confidence 6788999999999999999999 999999999999996 999999999999999864
No 13
>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=3.8e-15 Score=105.77 Aligned_cols=57 Identities=30% Similarity=0.549 Sum_probs=54.0
Q ss_pred CCCCCCCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHhcCCCCCCceeeccccchhhHHHH
Q 043602 72 SSRWNPTPEQLRTLEDLYRRGTRTPSADQIQHITAQLRRFGKIEGKNVFYWFQNHKARERQK 133 (352)
Q Consensus 72 R~Rw~FT~eQLqiLE~lF~~~~~YPs~e~RqqIA~qL~~~G~LsEsqVqvWFQNRRAReKRK 133 (352)
+.|..|+++|+.+||..|..++ ||+.++++.||.+|+ |++.+|++||+|||++.++.
T Consensus 2 ~~r~~~~~~~~~~Le~~f~~~~-~P~~~~~~~la~~~~----l~~~qV~~WF~nrR~~~~~~ 58 (59)
T cd00086 2 RKRTRFTPEQLEELEKEFEKNP-YPSREEREELAKELG----LTERQVKIWFQNRRAKLKRS 58 (59)
T ss_pred CCCCcCCHHHHHHHHHHHHhCC-CCCHHHHHHHHHHHC----cCHHHHHHHHHHHHHHHhcc
Confidence 6789999999999999999999 999999999999996 99999999999999998763
No 14
>KOG0485 consensus Transcription factor NKX-5.1/HMX1, contains HOX domain [Transcription]
Probab=99.51 E-value=4.9e-15 Score=138.71 Aligned_cols=69 Identities=19% Similarity=0.266 Sum_probs=64.7
Q ss_pred CCCCCCCCCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHhcCCCCCCceeeccccchhhHHHHHHhhhcCCCC
Q 043602 70 VVSSRWNPTPEQLRTLEDLYRRGTRTPSADQIQHITAQLRRFGKIEGKNVFYWFQNHKARERQKRRRQMESSPA 143 (352)
Q Consensus 70 ~rR~Rw~FT~eQLqiLE~lF~~~~~YPs~e~RqqIA~qL~~~G~LsEsqVqvWFQNRRAReKRKrRrq~e~a~~ 143 (352)
-.+.||.|+..|+..||..|+..+ |++..+|.-||++|+ |+|.|||+||||||-||||+-.-.+|.++.
T Consensus 104 KKktRTvFSraQV~qLEs~Fe~kr-YLSsaeRa~LA~sLq----LTETQVKIWFQNRRnKwKRq~aad~ea~sl 172 (268)
T KOG0485|consen 104 KKKTRTVFSRAQVFQLESTFELKR-YLSSAERAGLAASLQ----LTETQVKIWFQNRRNKWKRQYAADLEAASL 172 (268)
T ss_pred cccchhhhhHHHHHHHHHHHHHHh-hhhHHHHhHHHHhhh----hhhhhhhhhhhhhhHHHHHHHhhhhhhhhc
Confidence 457899999999999999999999 999999999999997 999999999999999999999888887764
No 15
>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=99.47 E-value=5.6e-14 Score=106.76 Aligned_cols=52 Identities=17% Similarity=0.266 Sum_probs=50.1
Q ss_pred CCCCCCCCHHHHHHHHHHHhcCCCC----CCHHHHHHHHHHHHhcCCCCCCceeeccccch
Q 043602 71 VSSRWNPTPEQLRTLEDLYRRGTRT----PSADQIQHITAQLRRFGKIEGKNVFYWFQNHK 127 (352)
Q Consensus 71 rR~Rw~FT~eQLqiLE~lF~~~~~Y----Ps~e~RqqIA~qL~~~G~LsEsqVqvWFQNRR 127 (352)
+|.||.||++|++.||+.|+... | |+..+|++||..|+ |++.+|+|||||-|
T Consensus 2 kR~RT~Ft~~Q~~~Le~~fe~~~-y~~~~~~~~~r~~la~~lg----l~~~vvKVWfqN~k 57 (58)
T TIGR01565 2 KRRRTKFTAEQKEKMRDFAEKLG-WKLKDKRREEVREFCEEIG----VTRKVFKVWMHNNK 57 (58)
T ss_pred CCCCCCCCHHHHHHHHHHHHHcC-CCCCCCCHHHHHHHHHHhC----CCHHHeeeecccCC
Confidence 68999999999999999999999 9 99999999999996 99999999999975
No 16
>KOG0848 consensus Transcription factor Caudal, contains HOX domain [Transcription]
Probab=99.47 E-value=9.9e-15 Score=139.60 Aligned_cols=60 Identities=25% Similarity=0.380 Sum_probs=55.0
Q ss_pred CCCCCCCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHhcCCCCCCceeeccccchhhHHHHHHh
Q 043602 72 SSRWNPTPEQLRTLEDLYRRGTRTPSADQIQHITAQLRRFGKIEGKNVFYWFQNHKARERQKRRR 136 (352)
Q Consensus 72 R~Rw~FT~eQLqiLE~lF~~~~~YPs~e~RqqIA~qL~~~G~LsEsqVqvWFQNRRAReKRKrRr 136 (352)
+-|..+|..|..+||+.|...+ |.++.++.+||..|+ |+|+||||||||||||+||..+.
T Consensus 201 KYRvVYTDhQRLELEKEfh~Sr-yITirRKSELA~~Lg----LsERQVKIWFQNRRAKERK~nKK 260 (317)
T KOG0848|consen 201 KYRVVYTDHQRLELEKEFHTSR-YITIRRKSELAATLG----LSERQVKIWFQNRRAKERKDNKK 260 (317)
T ss_pred ceeEEecchhhhhhhhhhcccc-ceeeehhHHHHHhhC----ccHhhhhHhhhhhhHHHHHHHHH
Confidence 4467899999999999999999 999999999999996 99999999999999999985443
No 17
>KOG0493 consensus Transcription factor Engrailed, contains HOX domain [General function prediction only]
Probab=99.44 E-value=3.1e-14 Score=136.26 Aligned_cols=60 Identities=22% Similarity=0.359 Sum_probs=57.4
Q ss_pred CCCCCCCCCCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHhcCCCCCCceeeccccchhhHHHH
Q 043602 69 VVVSSRWNPTPEQLRTLEDLYRRGTRTPSADQIQHITAQLRRFGKIEGKNVFYWFQNHKARERQK 133 (352)
Q Consensus 69 ~~rR~Rw~FT~eQLqiLE~lF~~~~~YPs~e~RqqIA~qL~~~G~LsEsqVqvWFQNRRAReKRK 133 (352)
...|+||.||.|||+.|...|+.++ |++...|++||.+|+ |.|+|||+||||+|||-||.
T Consensus 245 eeKRPRTAFtaeQL~RLK~EF~enR-YlTEqRRQ~La~ELg----LNEsQIKIWFQNKRAKiKKs 304 (342)
T KOG0493|consen 245 EEKRPRTAFTAEQLQRLKAEFQENR-YLTEQRRQELAQELG----LNESQIKIWFQNKRAKIKKS 304 (342)
T ss_pred hhcCccccccHHHHHHHHHHHhhhh-hHHHHHHHHHHHHhC----cCHHHhhHHhhhhhhhhhhc
Confidence 4789999999999999999999999 999999999999996 99999999999999999874
No 18
>KOG0844 consensus Transcription factor EVX1, contains HOX domain [Transcription]
Probab=99.43 E-value=3.2e-14 Score=138.43 Aligned_cols=63 Identities=24% Similarity=0.341 Sum_probs=59.1
Q ss_pred CCCCCCCCCCCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHhcCCCCCCceeeccccchhhHHHHHH
Q 043602 68 PVVVSSRWNPTPEQLRTLEDLYRRGTRTPSADQIQHITAQLRRFGKIEGKNVFYWFQNHKARERQKRR 135 (352)
Q Consensus 68 p~~rR~Rw~FT~eQLqiLE~lF~~~~~YPs~e~RqqIA~qL~~~G~LsEsqVqvWFQNRRAReKRKrR 135 (352)
+..||-||.||.|||..||+.|-+.. |.+...|=+||..|+ |+|.-|||||||||||.||+|-
T Consensus 179 dqmRRYRTAFTReQIaRLEKEFyrEN-YVSRprRcELAAaLN----LPEtTIKVWFQNRRMKDKRQRl 241 (408)
T KOG0844|consen 179 DQMRRYRTAFTREQIARLEKEFYREN-YVSRPRRCELAAALN----LPETTIKVWFQNRRMKDKRQRL 241 (408)
T ss_pred HHHHHHHhhhhHHHHHHHHHHHHHhc-cccCchhhhHHHhhC----CCcceeehhhhhchhhhhhhhh
Confidence 34899999999999999999999999 999999999999995 9999999999999999998654
No 19
>KOG0491 consensus Transcription factor BSH, contains HOX domain [General function prediction only]
Probab=99.43 E-value=1.7e-14 Score=130.48 Aligned_cols=66 Identities=23% Similarity=0.335 Sum_probs=61.8
Q ss_pred CCCCCCCCCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHhcCCCCCCceeeccccchhhHHHHHHhhhcC
Q 043602 70 VVSSRWNPTPEQLRTLEDLYRRGTRTPSADQIQHITAQLRRFGKIEGKNVFYWFQNHKARERQKRRRQMES 140 (352)
Q Consensus 70 ~rR~Rw~FT~eQLqiLE~lF~~~~~YPs~e~RqqIA~qL~~~G~LsEsqVqvWFQNRRAReKRKrRrq~e~ 140 (352)
.++.|+.|+.-||..||+.|+.++ |++..+|++||..|+ |+++|||.||||||||.||..|...-.
T Consensus 100 r~K~Rtvfs~~ql~~l~~rFe~Qr-YLS~~e~~ELan~L~----LS~~QVKTWFQNrRMK~Kk~~r~~~p~ 165 (194)
T KOG0491|consen 100 RRKARTVFSDPQLSGLEKRFERQR-YLSTPERQELANALS----LSETQVKTWFQNRRMKHKKQQRNNQPK 165 (194)
T ss_pred hhhhcccccCccccccHHHHhhhh-hcccHHHHHHHHHhh----hhHHHHHHHHHHHHHHHHHHHhccCCC
Confidence 788999999999999999999999 999999999999996 999999999999999999988865533
No 20
>KOG0486 consensus Transcription factor PTX1, contains HOX domain [Transcription]
Probab=99.40 E-value=1e-13 Score=134.60 Aligned_cols=64 Identities=27% Similarity=0.415 Sum_probs=61.6
Q ss_pred CCCCCCCCCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHhcCCCCCCceeeccccchhhHHHHHHhhh
Q 043602 70 VVSSRWNPTPEQLRTLEDLYRRGTRTPSADQIQHITAQLRRFGKIEGKNVFYWFQNHKARERQKRRRQM 138 (352)
Q Consensus 70 ~rR~Rw~FT~eQLqiLE~lF~~~~~YPs~e~RqqIA~qL~~~G~LsEsqVqvWFQNRRAReKRKrRrq~ 138 (352)
.||.|+-||..||++||..|+.++ ||+.+.|++||.... |+|++|.|||.||||||||..|.++
T Consensus 112 qrrQrthFtSqqlqele~tF~rNr-ypdMstrEEIavwtN----lTE~rvrvwfknrrakwrkrErN~~ 175 (351)
T KOG0486|consen 112 QRRQRTHFTSQQLQELEATFQRNR-YPDMSTREEIAVWTN----LTEARVRVWFKNRRAKWRKRERNQQ 175 (351)
T ss_pred hhhhhhhhHHHHHHHHHHHHhhcc-CCccchhhHHHhhcc----ccchhhhhhcccchhhhhhhhhhHH
Confidence 789999999999999999999999 999999999999995 9999999999999999999888777
No 21
>COG5576 Homeodomain-containing transcription factor [Transcription]
Probab=99.39 E-value=2.6e-13 Score=119.73 Aligned_cols=67 Identities=33% Similarity=0.449 Sum_probs=61.9
Q ss_pred CCCCCCCCCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHhcCCCCCCceeeccccchhhHHHHHHhhhcCC
Q 043602 70 VVSSRWNPTPEQLRTLEDLYRRGTRTPSADQIQHITAQLRRFGKIEGKNVFYWFQNHKARERQKRRRQMESS 141 (352)
Q Consensus 70 ~rR~Rw~FT~eQLqiLE~lF~~~~~YPs~e~RqqIA~qL~~~G~LsEsqVqvWFQNRRAReKRKrRrq~e~a 141 (352)
.++.|..-|.+|+.+||+.|..++ ||+...|..|+..|+ |+++.||+||||||++.|++++...+..
T Consensus 51 ~~~~r~R~t~~Q~~vL~~~F~i~p-~Ps~~~r~~L~~~ln----m~~ksVqIWFQNkR~~~k~~~~~~~~~~ 117 (156)
T COG5576 51 PKSKRRRTTDEQLMVLEREFEINP-YPSSITRIKLSLLLN----MPPKSVQIWFQNKRAKEKKKRSGKVEQR 117 (156)
T ss_pred CcccceechHHHHHHHHHHhccCC-CCCHHHHHHHHHhcC----CChhhhhhhhchHHHHHHHhcccchhcc
Confidence 668899999999999999999999 999999999999995 9999999999999999999888765554
No 22
>KOG0483 consensus Transcription factor HEX, contains HOX and HALZ domains [Transcription]
Probab=99.35 E-value=2.8e-13 Score=123.68 Aligned_cols=61 Identities=23% Similarity=0.416 Sum_probs=56.1
Q ss_pred CCCCCCCCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHhcCCCCCCceeeccccchhhHHHHHHh
Q 043602 71 VSSRWNPTPEQLRTLEDLYRRGTRTPSADQIQHITAQLRRFGKIEGKNVFYWFQNHKARERQKRRR 136 (352)
Q Consensus 71 rR~Rw~FT~eQLqiLE~lF~~~~~YPs~e~RqqIA~qL~~~G~LsEsqVqvWFQNRRAReKRKrRr 136 (352)
.++.-.||.+|+..||+.|+.+. |...+++.+||.+|+ |..+||.+||||||||||.|+-.
T Consensus 51 ~~kk~Rlt~eQ~~~LE~~F~~~~-~L~p~~K~~LAk~Lg----L~pRQVavWFQNRRARwK~kqlE 111 (198)
T KOG0483|consen 51 KGKKRRLTSEQVKFLEKSFESEK-KLEPERKKKLAKELG----LQPRQVAVWFQNRRARWKTKQLE 111 (198)
T ss_pred ccccccccHHHHHHhHHhhcccc-ccChHHHHHHHHhhC----CChhHHHHHHhhccccccchhhh
Confidence 45667899999999999999999 999999999999996 99999999999999999987653
No 23
>KOG0490 consensus Transcription factor, contains HOX domain [General function prediction only]
Probab=99.34 E-value=3.7e-13 Score=117.15 Aligned_cols=62 Identities=26% Similarity=0.343 Sum_probs=58.2
Q ss_pred CCCCCCCCCCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHhcCCCCCCceeeccccchhhHHHHHH
Q 043602 69 VVVSSRWNPTPEQLRTLEDLYRRGTRTPSADQIQHITAQLRRFGKIEGKNVFYWFQNHKARERQKRR 135 (352)
Q Consensus 69 ~~rR~Rw~FT~eQLqiLE~lF~~~~~YPs~e~RqqIA~qL~~~G~LsEsqVqvWFQNRRAReKRKrR 135 (352)
..++.|+.||..|+.+||++|...+ ||+..-|+.+|..+. ++|.+|++||||||+|++++.+
T Consensus 59 ~~rr~rt~~~~~ql~~ler~f~~~h-~Pd~~~r~~la~~~~----~~e~rVqvwFqnrrak~r~~~~ 120 (235)
T KOG0490|consen 59 SKRCARCKFTISQLDELERAFEKVH-LPCFACRECLALLLT----GDEFRVQVWFQNRRAKDRKEER 120 (235)
T ss_pred cccccCCCCCcCHHHHHHHhhcCCC-cCccchHHHHhhcCC----CCeeeeehhhhhhcHhhhhhhc
Confidence 3789999999999999999999998 999999998888885 9999999999999999998776
No 24
>KOG4577 consensus Transcription factor LIM3, contains LIM and HOX domains [Transcription]
Probab=99.16 E-value=1.8e-11 Score=118.83 Aligned_cols=62 Identities=24% Similarity=0.452 Sum_probs=58.2
Q ss_pred CCCCCCCCCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHhcCCCCCCceeeccccchhhHHHHHHh
Q 043602 70 VVSSRWNPTPEQLRTLEDLYRRGTRTPSADQIQHITAQLRRFGKIEGKNVFYWFQNHKARERQKRRR 136 (352)
Q Consensus 70 ~rR~Rw~FT~eQLqiLE~lF~~~~~YPs~e~RqqIA~qL~~~G~LsEsqVqvWFQNRRAReKRKrRr 136 (352)
..|+||+.|.-||+.|..+|...+ .|..--|++|+.+.+ |..+.|||||||||||+||.++.
T Consensus 167 nKRPRTTItAKqLETLK~AYn~Sp-KPARHVREQLsseTG----LDMRVVQVWFQNRRAKEKRLKKD 228 (383)
T KOG4577|consen 167 NKRPRTTITAKQLETLKQAYNTSP-KPARHVREQLSSETG----LDMRVVQVWFQNRRAKEKRLKKD 228 (383)
T ss_pred cCCCcceeeHHHHHHHHHHhcCCC-chhHHHHHHhhhccC----cceeehhhhhhhhhHHHHhhhhh
Confidence 779999999999999999999999 899999999999885 99999999999999999998773
No 25
>KOG0849 consensus Transcription factor PRD and related proteins, contain PAX and HOX domains [Transcription]
Probab=99.15 E-value=3.4e-11 Score=117.08 Aligned_cols=63 Identities=25% Similarity=0.397 Sum_probs=59.3
Q ss_pred CCCCCCCCCCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHhcCCCCCCceeeccccchhhHHHHHHh
Q 043602 69 VVVSSRWNPTPEQLRTLEDLYRRGTRTPSADQIQHITAQLRRFGKIEGKNVFYWFQNHKARERQKRRR 136 (352)
Q Consensus 69 ~~rR~Rw~FT~eQLqiLE~lF~~~~~YPs~e~RqqIA~qL~~~G~LsEsqVqvWFQNRRAReKRKrRr 136 (352)
..+|.|+.||++|+..||+.|..++ ||++..|++||.+++ ++|.+|++||||||+|++|..+.
T Consensus 175 ~~rr~rtsft~~Q~~~le~~f~rt~-yP~i~~Re~La~~i~----l~e~riqvwf~nrra~~rr~~~~ 237 (354)
T KOG0849|consen 175 GGRRNRTSFSPSQLEALEECFQRTP-YPDIVGRETLAKETG----LPEPRVQVWFQNRRAKWRRQHRD 237 (354)
T ss_pred cccccccccccchHHHHHHHhcCCC-CCchhhHHHHhhhcc----CCchHHHHHHhhhhhhhhhcccc
Confidence 3788899999999999999999999 999999999999996 99999999999999999987764
No 26
>KOG0847 consensus Transcription factor, contains HOX domain [Transcription]
Probab=99.13 E-value=1.2e-11 Score=116.53 Aligned_cols=66 Identities=24% Similarity=0.353 Sum_probs=59.7
Q ss_pred CCCCCCCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHhcCCCCCCceeeccccchhhHHHHHHhhhcCCC
Q 043602 72 SSRWNPTPEQLRTLEDLYRRGTRTPSADQIQHITAQLRRFGKIEGKNVFYWFQNHKARERQKRRRQMESSP 142 (352)
Q Consensus 72 R~Rw~FT~eQLqiLE~lF~~~~~YPs~e~RqqIA~qL~~~G~LsEsqVqvWFQNRRAReKRKrRrq~e~a~ 142 (352)
-.|-+|+-.||..||+-|+..+ ||-.++|.++|..|+ ++|++|+|||||||.|||||-..+|.++.
T Consensus 169 ~srPTf~g~qi~~le~~feqtk-ylaG~~ra~lA~~lg----mteSqvkVWFQNRRTKWRKkhAaEmasak 234 (288)
T KOG0847|consen 169 QSRPTFTGHQIYQLERKFEQTK-YLAGADRAQLAQELN----MTESQVKVWFQNRRTKWRKKHAAEMASAK 234 (288)
T ss_pred ccCCCccchhhhhhhhhhhhhh-cccchhHHHhhcccc----ccHHHHHHHHhcchhhhhhhhccchhhcc
Confidence 3577899999999999999999 999999999999996 99999999999999999998776666553
No 27
>KOG3802 consensus Transcription factor OCT-1, contains POU and HOX domains [Transcription]
Probab=98.71 E-value=1.2e-08 Score=101.86 Aligned_cols=62 Identities=23% Similarity=0.382 Sum_probs=57.3
Q ss_pred CCCCCCCCCCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHhcCCCCCCceeeccccchhhHHHHHH
Q 043602 69 VVVSSRWNPTPEQLRTLEDLYRRGTRTPSADQIQHITAQLRRFGKIEGKNVFYWFQNHKARERQKRR 135 (352)
Q Consensus 69 ~~rR~Rw~FT~eQLqiLE~lF~~~~~YPs~e~RqqIA~qL~~~G~LsEsqVqvWFQNRRAReKRKrR 135 (352)
-.||+||.+..-...+||+.|.+++ .|+.++|-+||++|+ |+-..|.|||=|||=|+||-.-
T Consensus 293 RkRKKRTSie~~vr~aLE~~F~~np-KPt~qEIt~iA~~L~----leKEVVRVWFCNRRQkeKR~~~ 354 (398)
T KOG3802|consen 293 RKRKKRTSIEVNVRGALEKHFLKNP-KPTSQEITHIAESLQ----LEKEVVRVWFCNRRQKEKRITP 354 (398)
T ss_pred cccccccceeHHHHHHHHHHHHhCC-CCCHHHHHHHHHHhc----cccceEEEEeeccccccccCCC
Confidence 3689999999999999999999999 899999999999996 8888899999999999987544
No 28
>KOG0490 consensus Transcription factor, contains HOX domain [General function prediction only]
Probab=98.13 E-value=1.9e-06 Score=75.35 Aligned_cols=62 Identities=27% Similarity=0.481 Sum_probs=57.8
Q ss_pred CCCCCCCCCCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHhcCCCCCCceeeccccchhhHHHHHH
Q 043602 69 VVVSSRWNPTPEQLRTLEDLYRRGTRTPSADQIQHITAQLRRFGKIEGKNVFYWFQNHKARERQKRR 135 (352)
Q Consensus 69 ~~rR~Rw~FT~eQLqiLE~lF~~~~~YPs~e~RqqIA~qL~~~G~LsEsqVqvWFQNRRAReKRKrR 135 (352)
..++.|+.++..|+..|+..|.... ||+...+.+|+..++ +++..|++||||+|++.++...
T Consensus 152 ~~~~~~~~~~~~~~~~~~~~~~~~~-~P~~~~~~~l~~~~~----~~~~~~q~~~~~~~~~~~~~~~ 213 (235)
T KOG0490|consen 152 KPRRPRTTFTENQLEVLETVFRATP-KPDADDREQLAEETG----LSERVIQVWFQNRRAKLRKHKR 213 (235)
T ss_pred ccCCCccccccchhHhhhhcccCCC-CCchhhHHHHHHhcC----CChhhhhhhcccHHHHHHhhcc
Confidence 3678899999999999999999999 999999999999995 9999999999999999998776
No 29
>KOG0775 consensus Transcription factor SIX and related HOX domain proteins [Transcription]
Probab=98.04 E-value=4.1e-06 Score=81.22 Aligned_cols=54 Identities=22% Similarity=0.359 Sum_probs=47.3
Q ss_pred CCCCCCHHH---------HHHHHHHHhcCCCCCCHHHHHHHHHHHHhcCCCCCCceeeccccchhhHH
Q 043602 73 SRWNPTPEQ---------LRTLEDLYRRGTRTPSADQIQHITAQLRRFGKIEGKNVFYWFQNHKARER 131 (352)
Q Consensus 73 ~Rw~FT~eQ---------LqiLE~lF~~~~~YPs~e~RqqIA~qL~~~G~LsEsqVqvWFQNRRAReK 131 (352)
+||...-|| ...|.+.|..++ ||+.++..+||+..+ |+-.||-+||.|||-|.|
T Consensus 170 PrTIWDGEet~yCFKekSR~~LrewY~~~~-YPsp~eKReLA~aTg----Lt~tQVsNWFKNRRQRDR 232 (304)
T KOG0775|consen 170 PRTIWDGEETVYCFKEKSRSLLREWYLQNP-YPSPREKRELAEATG----LTITQVSNWFKNRRQRDR 232 (304)
T ss_pred CCccccCceeeeehhHhhHHHHHHHHhcCC-CCChHHHHHHHHHhC----Cchhhhhhhhhhhhhhhh
Confidence 566655555 578999999999 999999999999996 999999999999997775
No 30
>KOG2252 consensus CCAAT displacement protein and related homeoproteins [Transcription]
Probab=97.74 E-value=1.7e-05 Score=82.28 Aligned_cols=57 Identities=28% Similarity=0.392 Sum_probs=53.4
Q ss_pred CCCCCCCCCCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHhcCCCCCCceeeccccchhhH
Q 043602 69 VVVSSRWNPTPEQLRTLEDLYRRGTRTPSADQIQHITAQLRRFGKIEGKNVFYWFQNHKARE 130 (352)
Q Consensus 69 ~~rR~Rw~FT~eQLqiLE~lF~~~~~YPs~e~RqqIA~qL~~~G~LsEsqVqvWFQNRRARe 130 (352)
+..++|..||..|...|-.+|..++ +|+.+..+.|+.+|+ |.-+-|.+||-|-|-|.
T Consensus 419 ~~KKPRlVfTd~QkrTL~aiFke~~-RPS~Emq~tIS~qL~----L~~sTV~NfFmNaRRRs 475 (558)
T KOG2252|consen 419 QTKKPRLVFTDIQKRTLQAIFKENK-RPSREMQETISQQLN----LELSTVINFFMNARRRS 475 (558)
T ss_pred cCCCceeeecHHHHHHHHHHHhcCC-CCCHHHHHHHHHHhC----CcHHHHHHHHHhhhhhc
Confidence 5788999999999999999999999 999999999999996 99999999999988665
No 31
>KOG1168 consensus Transcription factor ACJ6/BRN-3, contains POU and HOX domains [Transcription]
Probab=97.62 E-value=5.1e-05 Score=74.75 Aligned_cols=62 Identities=23% Similarity=0.419 Sum_probs=55.1
Q ss_pred CCCCCCCCCCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHhcCCCCCCceeeccccchhhHHHHHH
Q 043602 69 VVVSSRWNPTPEQLRTLEDLYRRGTRTPSADQIQHITAQLRRFGKIEGKNVFYWFQNHKARERQKRR 135 (352)
Q Consensus 69 ~~rR~Rw~FT~eQLqiLE~lF~~~~~YPs~e~RqqIA~qL~~~G~LsEsqVqvWFQNRRAReKRKrR 135 (352)
...|+||..-.-.-+.||..|..++ -|+.|.|..||++|. |-...|.|||=|.|-|.||-++
T Consensus 308 ekKRKRTSIAAPEKRsLEayFavQP-RPS~EkIAaIAekLD----LKKNVVRVWFCNQRQKQKRm~~ 369 (385)
T KOG1168|consen 308 EKKRKRTSIAAPEKRSLEAYFAVQP-RPSGEKIAAIAEKLD----LKKNVVRVWFCNQRQKQKRMKR 369 (385)
T ss_pred ccccccccccCcccccHHHHhccCC-CCchhHHHHHHHhhh----hhhceEEEEeeccHHHHHHhhh
Confidence 4788999999999999999999999 699999999999997 7777799999999988877443
No 32
>KOG0774 consensus Transcription factor PBX and related HOX domain proteins [Transcription]
Probab=97.60 E-value=3.8e-05 Score=74.72 Aligned_cols=107 Identities=20% Similarity=0.331 Sum_probs=76.3
Q ss_pred ccccCCCCCCCCCCCCCCC-CCccccCCccccccCCCCccccc----cccCCCCCCCCCCCCCCCCCHHHHHHHHHHHhc
Q 043602 17 KLRPLIPRPLPTTTAINNN-PSRIHGADFFGLNHHLGSHFGEQ----NKREFSSTPPVVVSSRWNPTPEQLRTLEDLYRR 91 (352)
Q Consensus 17 ~lrPl~p~~~~~~~~~~t~-l~~~~~~~~~~~~~~l~~~~~e~----~kre~~~~~p~~rR~Rw~FT~eQLqiLE~lF~~ 91 (352)
++||++|+- -.. ...|| .-|-.++..|....+|. ++|-+. .||+|.+|++.=..+|.+.|-.
T Consensus 143 r~RPi~~ke-------~e~m~~~i~-~kF~~iq~~lkqstce~vmiLr~r~ld-----arRKRRNFsK~aTeiLneyF~~ 209 (334)
T KOG0774|consen 143 RTRPIMPKE-------IERMVQIIS-KKFSHIQMQLKQSTCEAVMILRSRFLD-----ARRKRRNFSKQATEILNEYFYS 209 (334)
T ss_pred ccCCCCHHH-------HHHHHHHHH-HHHHHHHHHHHHHHHHHHHHHHHHHHH-----HHHhhcccchhHHHHHHHHHHH
Confidence 567777764 111 22334 33545555554433433 233333 7899999999999999999965
Q ss_pred ---CCCCCCHHHHHHHHHHHHhcCCCCCCceeeccccchhhHHHHHHhhhcCC
Q 043602 92 ---GTRTPSADQIQHITAQLRRFGKIEGKNVFYWFQNHKARERQKRRRQMESS 141 (352)
Q Consensus 92 ---~~~YPs~e~RqqIA~qL~~~G~LsEsqVqvWFQNRRAReKRKrRrq~e~a 141 (352)
++ ||+.+..++||.+.+ |+-+||-.||-|+|.|.||---.-++.+
T Consensus 210 h~~nP-YPSee~K~eLAkqCn----ItvsQvsnwfgnkrIrykK~~~k~~ee~ 257 (334)
T KOG0774|consen 210 HLSNP-YPSEEAKEELAKQCN----ITVSQVSNWFGNKRIRYKKNMGKNQEEA 257 (334)
T ss_pred hcCCC-CCcHHHHHHHHHHcC----ceehhhccccccceeehhhhhhhhhhhh
Confidence 55 999999999999885 9999999999999999998655444433
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=97.50 E-value=1.6e-05 Score=56.42 Aligned_cols=33 Identities=24% Similarity=0.503 Sum_probs=27.3
Q ss_pred CCCCCCHHHHHHHHHHHHhcCCCCCCceeeccccchhh
Q 043602 92 GTRTPSADQIQHITAQLRRFGKIEGKNVFYWFQNHKAR 129 (352)
Q Consensus 92 ~~~YPs~e~RqqIA~qL~~~G~LsEsqVqvWFQNRRAR 129 (352)
++ ||+.+++++||.+.+ |+..||..||-|.|.|
T Consensus 8 nP-YPs~~ek~~L~~~tg----ls~~Qi~~WF~NaRrR 40 (40)
T PF05920_consen 8 NP-YPSKEEKEELAKQTG----LSRKQISNWFINARRR 40 (40)
T ss_dssp SG-S--HHHHHHHHHHHT----S-HHHHHHHHHHHHHH
T ss_pred CC-CCCHHHHHHHHHHcC----CCHHHHHHHHHHhHcc
Confidence 45 999999999999995 9999999999999865
No 34
>KOG1146 consensus Homeobox protein [General function prediction only]
Probab=96.33 E-value=0.0021 Score=72.53 Aligned_cols=61 Identities=18% Similarity=0.377 Sum_probs=56.3
Q ss_pred CCCCCCCCCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHhcCCCCCCceeeccccchhhHHHHHH
Q 043602 70 VVSSRWNPTPEQLRTLEDLYRRGTRTPSADQIQHITAQLRRFGKIEGKNVFYWFQNHKARERQKRR 135 (352)
Q Consensus 70 ~rR~Rw~FT~eQLqiLE~lF~~~~~YPs~e~RqqIA~qL~~~G~LsEsqVqvWFQNRRAReKRKrR 135 (352)
+|+.|+.++..||.+|..+|.... ||..++++.+-..+. ++-..|++||||-|+|.|+..-
T Consensus 903 r~a~~~~~~d~qlk~i~~~~~~q~-~~~~~~~E~l~~~~~----~~~~~i~vw~qna~~~s~k~~~ 963 (1406)
T KOG1146|consen 903 RRAYRTQESDLQLKIIKACYEAQR-TPTMQECEVLEEPIG----LPKRVIQVWFQNARAKSKKAKL 963 (1406)
T ss_pred hhhhccchhHHHHHHHHHHHhhcc-CChHHHHHhhccccc----CCcchhHHhhhhhhhhhhhhhh
Confidence 889999999999999999999999 999999999999885 7777799999999999988665
No 35
>KOG0773 consensus Transcription factor MEIS1 and related HOX domain proteins [Transcription]
Probab=91.61 E-value=0.13 Score=49.30 Aligned_cols=61 Identities=18% Similarity=0.182 Sum_probs=49.7
Q ss_pred CCCCCCCCCHHHHHHHHHHHhc---CCCCCCHHHHHHHHHHHHhcCCCCCCceeeccccchhhHHHHHH
Q 043602 70 VVSSRWNPTPEQLRTLEDLYRR---GTRTPSADQIQHITAQLRRFGKIEGKNVFYWFQNHKARERQKRR 135 (352)
Q Consensus 70 ~rR~Rw~FT~eQLqiLE~lF~~---~~~YPs~e~RqqIA~qL~~~G~LsEsqVqvWFQNRRAReKRKrR 135 (352)
..|++..+-++...+|+.-... .+ ||+..+...||.+.+ |+-.+|.+||-|.|-|..+-.-
T Consensus 239 ~~r~~~~lP~~a~~ilr~Wl~~h~~~P-YPse~~K~~La~~TG----Ls~~Qv~NWFINaR~R~w~p~~ 302 (342)
T KOG0773|consen 239 KWRPQRGLPKEAVSILRAWLFEHLLHP-YPSDDEKLMLAKQTG----LSRPQVSNWFINARVRLWKPMI 302 (342)
T ss_pred CCCCCCCCCHHHHHHHHHHHHHhccCC-CCcchhccccchhcC----CCcccCCchhhhcccccCCchH
Confidence 5567778889999999865544 35 999999999999985 9999999999999977765443
No 36
>KOG3623 consensus Homeobox transcription factor SIP1 [Transcription]
Probab=89.53 E-value=0.18 Score=55.34 Aligned_cols=49 Identities=24% Similarity=0.397 Sum_probs=45.2
Q ss_pred HHHHHHHHhcCCCCCCHHHHHHHHHHHHhcCCCCCCceeeccccchhhHHHHHH
Q 043602 82 LRTLEDLYRRGTRTPSADQIQHITAQLRRFGKIEGKNVFYWFQNHKARERQKRR 135 (352)
Q Consensus 82 LqiLE~lF~~~~~YPs~e~RqqIA~qL~~~G~LsEsqVqvWFQNRRAReKRKrR 135 (352)
+..|...|..+. .|+.++...||.+++ |+-.-|+.||+++++++..-.|
T Consensus 568 ~sllkayyaln~-~ps~eelskia~qvg----lp~~vvk~wfE~~~a~e~sv~r 616 (1007)
T KOG3623|consen 568 TSLLKAYYALNG-LPSEEELSKIAQQVG----LPFAVVKAWFEDEEAEEMSVER 616 (1007)
T ss_pred HHHHHHHHHhcC-CCCHHHHHHHHHHhc----ccHHHHHHHHHhhhhhhhhhcc
Confidence 788999999999 999999999999996 9999999999999999987665
No 37
>PF11569 Homez: Homeodomain leucine-zipper encoding, Homez; PDB: 2YS9_A.
Probab=84.80 E-value=0.26 Score=38.21 Aligned_cols=41 Identities=20% Similarity=0.447 Sum_probs=30.4
Q ss_pred HHHHHHHHhcCCCCCCHHHHHHHHHHHHhcCCCCCCceeeccccch
Q 043602 82 LRTLEDLYRRGTRTPSADQIQHITAQLRRFGKIEGKNVFYWFQNHK 127 (352)
Q Consensus 82 LqiLE~lF~~~~~YPs~e~RqqIA~qL~~~G~LsEsqVqvWFQNRR 127 (352)
++-|++.|.... ++...+...|..+-+ |+..+|+.||--|.
T Consensus 10 ~~pL~~Yy~~h~-~L~E~DL~~L~~kS~----ms~qqVr~WFa~~~ 50 (56)
T PF11569_consen 10 IQPLEDYYLKHK-QLQEEDLDELCDKSR----MSYQQVRDWFAERM 50 (56)
T ss_dssp -HHHHHHHHHT-----TTHHHHHHHHTT------HHHHHHHHHHHS
T ss_pred hHHHHHHHHHcC-CccHhhHHHHHHHHC----CCHHHHHHHHHHhc
Confidence 456999999999 899999999999996 99999999997554
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=71.86 E-value=4.4 Score=29.98 Aligned_cols=47 Identities=15% Similarity=0.142 Sum_probs=35.0
Q ss_pred CCCCCCCCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHhcCCCCCCceeeccccch
Q 043602 71 VSSRWNPTPEQLRTLEDLYRRGTRTPSADQIQHITAQLRRFGKIEGKNVFYWFQNHK 127 (352)
Q Consensus 71 rR~Rw~FT~eQLqiLE~lF~~~~~YPs~e~RqqIA~qL~~~G~LsEsqVqvWFQNRR 127 (352)
+|+|..+|-+|-..+=+.++.|. ...+||..++ |+.+.|..|..||.
T Consensus 1 krkR~~LTl~eK~~iI~~~e~g~------s~~~ia~~fg----v~~sTv~~I~K~k~ 47 (53)
T PF04218_consen 1 KRKRKSLTLEEKLEIIKRLEEGE------SKRDIAREFG----VSRSTVSTILKNKD 47 (53)
T ss_dssp SSSSSS--HHHHHHHHHHHHCTT-------HHHHHHHHT------CCHHHHHHHCHH
T ss_pred CCCCccCCHHHHHHHHHHHHcCC------CHHHHHHHhC----CCHHHHHHHHHhHH
Confidence 47899999999888878888888 2456999996 99999999988864
No 39
>cd06171 Sigma70_r4 Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in Escherichia coli (Ec) sigma70, the main housekeeping sigma, and related sigma-factors (SFs). A SF is a dissociable subunit of RNA polymerase, it directs bacterial or plastid core RNA polymerase to specific promoter elements located upstream of transcription initiation points. The SR4 of Ec sigma70 and other essential primary SFs contact promoter sequences located 35 base-pairs upstream of the initiation point, recognizing a 6-base-pair -35 consensus TTGACA. Sigma70 related SFs also include SFs which are dispensable for bacterial cell growth for example Ec sigmaS, SFs which activate regulons in response to a specific signal for example heat-shock Ec sigmaH, and a group of SFs which includes the extracytoplasmic function (ECF) SFs and is typified by Ec sigmaE which contains SR2 and -4 only. ECF SFs direct the transcription of genes that regulate various responses including periplas
Probab=64.07 E-value=2.8 Score=27.57 Aligned_cols=42 Identities=12% Similarity=0.088 Sum_probs=31.8
Q ss_pred CCCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHhcCCCCCCceeeccccch
Q 043602 76 NPTPEQLRTLEDLYRRGTRTPSADQIQHITAQLRRFGKIEGKNVFYWFQNHK 127 (352)
Q Consensus 76 ~FT~eQLqiLE~lF~~~~~YPs~e~RqqIA~qL~~~G~LsEsqVqvWFQNRR 127 (352)
.+++.|..+++..|..+. + ..+||..|+ ++...|+.|.+.-+
T Consensus 10 ~l~~~~~~~~~~~~~~~~--~----~~~ia~~~~----~s~~~i~~~~~~~~ 51 (55)
T cd06171 10 KLPEREREVILLRFGEGL--S----YEEIAEILG----ISRSTVRQRLHRAL 51 (55)
T ss_pred hCCHHHHHHHHHHHhcCC--C----HHHHHHHHC----cCHHHHHHHHHHHH
Confidence 357889999999987665 3 335899995 99999988875443
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=51.13 E-value=13 Score=28.26 Aligned_cols=40 Identities=23% Similarity=0.266 Sum_probs=32.1
Q ss_pred CCHHHHHHHHHHHhcCCC-CCCHHHHHHHHHHHHhcCCCCCCcee
Q 043602 77 PTPEQLRTLEDLYRRGTR-TPSADQIQHITAQLRRFGKIEGKNVF 120 (352)
Q Consensus 77 FT~eQLqiLE~lF~~~~~-YPs~e~RqqIA~qL~~~G~LsEsqVq 120 (352)
+|+.|.++|..+|..|=. +|-.....+||+.|+ |+..-|.
T Consensus 1 LT~~Q~e~L~~A~~~GYfd~PR~~tl~elA~~lg----is~st~~ 41 (53)
T PF04967_consen 1 LTDRQREILKAAYELGYFDVPRRITLEELAEELG----ISKSTVS 41 (53)
T ss_pred CCHHHHHHHHHHHHcCCCCCCCcCCHHHHHHHhC----CCHHHHH
Confidence 589999999999999751 377778889999996 8776553
No 41
>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=49.92 E-value=19 Score=20.86 Aligned_cols=40 Identities=20% Similarity=0.388 Sum_probs=27.2
Q ss_pred CCCCCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHhcCCCCCCceeecc
Q 043602 74 RWNPTPEQLRTLEDLYRRGTRTPSADQIQHITAQLRRFGKIEGKNVFYWF 123 (352)
Q Consensus 74 Rw~FT~eQLqiLE~lF~~~~~YPs~e~RqqIA~qL~~~G~LsEsqVqvWF 123 (352)
+..++.++...+...|..+. ...+||..++ ++...|+.|.
T Consensus 3 ~~~~~~~~~~~i~~~~~~~~------s~~~ia~~~~----is~~tv~~~~ 42 (42)
T cd00569 3 PPKLTPEQIEEARRLLAAGE------SVAEIARRLG----VSRSTLYRYL 42 (42)
T ss_pred CCcCCHHHHHHHHHHHHcCC------CHHHHHHHHC----CCHHHHHHhC
Confidence 34467777777777787544 2345888885 8887787773
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=48.29 E-value=10 Score=28.15 Aligned_cols=41 Identities=17% Similarity=0.366 Sum_probs=26.1
Q ss_pred CCCCCCCHHHHHHHHHHH-hcCCCCCCHHHHHHHHHHHHhcCCCCCCceeec
Q 043602 72 SSRWNPTPEQLRTLEDLY-RRGTRTPSADQIQHITAQLRRFGKIEGKNVFYW 122 (352)
Q Consensus 72 R~Rw~FT~eQLqiLE~lF-~~~~~YPs~e~RqqIA~qL~~~G~LsEsqVqvW 122 (352)
+.|..||+++-..+=..+ ..+. .+.+||.+++ |+...++.|
T Consensus 2 ~~r~~ys~e~K~~~v~~~~~~g~------sv~~va~~~g----i~~~~l~~W 43 (76)
T PF01527_consen 2 RKRRRYSPEFKLQAVREYLESGE------SVSEVAREYG----ISPSTLYNW 43 (76)
T ss_dssp -SS----HHHHHHHHHHHHHHHC------HHHHHHHHHT----S-HHHHHHH
T ss_pred CCCCCCCHHHHHHHHHHHHHCCC------ceEeeecccc----cccccccHH
Confidence 567889998876665555 5554 5667999995 999999887
No 43
>smart00027 EH Eps15 homology domain. Pair of EF hand motifs that recognise proteins containing Asn-Pro-Phe (NPF) sequences.
Probab=42.45 E-value=20 Score=28.33 Aligned_cols=45 Identities=18% Similarity=0.293 Sum_probs=29.5
Q ss_pred CCCCHHHHHHHHHHHhc----CCCCCCHHHHHHHHHHHHhcCCCCCCceeecc
Q 043602 75 WNPTPEQLRTLEDLYRR----GTRTPSADQIQHITAQLRRFGKIEGKNVFYWF 123 (352)
Q Consensus 75 w~FT~eQLqiLE~lF~~----~~~YPs~e~RqqIA~qL~~~G~LsEsqVqvWF 123 (352)
|-+|++|+..|.++|.. +..+.+..+..++-..+ ++++..|...|
T Consensus 2 ~~ls~~~~~~l~~~F~~~D~d~~G~Is~~el~~~l~~~----~~~~~ev~~i~ 50 (96)
T smart00027 2 WAISPEDKAKYEQIFRSLDKNQDGTVTGAQAKPILLKS----GLPQTLLAKIW 50 (96)
T ss_pred CCCCHHHHHHHHHHHHHhCCCCCCeEeHHHHHHHHHHc----CCCHHHHHHHH
Confidence 78899999999999987 34456666555543333 36655554443
No 44
>KOG3755 consensus SATB1 matrix attachment region binding protein [Transcription]
Probab=41.09 E-value=7.3 Score=42.56 Aligned_cols=63 Identities=16% Similarity=0.173 Sum_probs=35.2
Q ss_pred CCCCCCCCHHHHHHHHH-HHhcCCCCCCHHHHHHHHHHHHh---cCCCCCCceeeccccchhhHHHHH
Q 043602 71 VSSRWNPTPEQLRTLED-LYRRGTRTPSADQIQHITAQLRR---FGKIEGKNVFYWFQNHKARERQKR 134 (352)
Q Consensus 71 rR~Rw~FT~eQLqiLE~-lF~~~~~YPs~e~RqqIA~qL~~---~G~LsEsqVqvWFQNRRAReKRKr 134 (352)
++.|..|=.+|.-++.+ -|.+++ -++--++.+-.+.+.. .-+..+++|+.||.|||+++|+.+
T Consensus 692 k~~~~k~f~~~~~ev~~~w~~k~~-s~s~~~v~eYkee~~~~~~~e~~~~kn~~~~fk~~~ee~~~~k 758 (769)
T KOG3755|consen 692 KKTIIKFFQNQRYEVKHHWKLKTR-SGSWVDVAEYKEEELLMPYEEKFESKNVQFWFKVRREEEKRLK 758 (769)
T ss_pred HHHHHHhhhcceeecchhheeccc-CchhHHHHHhhHHhhcchhhhhhhhcchHHHHHHHHHHHhhhh
Confidence 34444444444433332 233333 4555555554444320 013578899999999999998754
No 45
>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=40.26 E-value=11 Score=26.67 Aligned_cols=39 Identities=23% Similarity=0.457 Sum_probs=28.6
Q ss_pred CCCCCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHhcCCCCCCceeec
Q 043602 74 RWNPTPEQLRTLEDLYRRGTRTPSADQIQHITAQLRRFGKIEGKNVFYW 122 (352)
Q Consensus 74 Rw~FT~eQLqiLE~lF~~~~~YPs~e~RqqIA~qL~~~G~LsEsqVqvW 122 (352)
+..++++|++.+-+++..+. + +.+||+.++ |+-+-|+.+
T Consensus 3 p~~~~~~~~~~i~~l~~~G~--s----i~~IA~~~g----vsr~TvyR~ 41 (45)
T PF02796_consen 3 PPKLSKEQIEEIKELYAEGM--S----IAEIAKQFG----VSRSTVYRY 41 (45)
T ss_dssp SSSSSHCCHHHHHHHHHTT--------HHHHHHHTT----S-HHHHHHH
T ss_pred CCCCCHHHHHHHHHHHHCCC--C----HHHHHHHHC----cCHHHHHHH
Confidence 34588889999999999996 3 456999995 888777744
No 46
>PRK03975 tfx putative transcriptional regulator; Provisional
Probab=39.39 E-value=20 Score=32.02 Aligned_cols=49 Identities=22% Similarity=0.133 Sum_probs=36.6
Q ss_pred CCCCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHhcCCCCCCceeeccccchhhHHHHH
Q 043602 75 WNPTPEQLRTLEDLYRRGTRTPSADQIQHITAQLRRFGKIEGKNVFYWFQNHKARERQKR 134 (352)
Q Consensus 75 w~FT~eQLqiLE~lF~~~~~YPs~e~RqqIA~qL~~~G~LsEsqVqvWFQNRRAReKRKr 134 (352)
..+|+-|.++|+. +..+. + .++||+.|+ ++...|..|-+..+-|.|+.+
T Consensus 5 ~~Lt~rqreVL~l-r~~Gl---T---q~EIAe~LG----iS~~tVs~ie~ra~kkLr~~~ 53 (141)
T PRK03975 5 SFLTERQIEVLRL-RERGL---T---QQEIADILG----TSRANVSSIEKRARENIEKAR 53 (141)
T ss_pred cCCCHHHHHHHHH-HHcCC---C---HHHHHHHHC----CCHHHHHHHHHHHHHHHHHHH
Confidence 4679999999988 55555 2 236999996 999999999986665555433
No 47
>PRK09652 RNA polymerase sigma factor RpoE; Provisional
Probab=37.45 E-value=23 Score=29.39 Aligned_cols=39 Identities=10% Similarity=-0.106 Sum_probs=31.2
Q ss_pred CCCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHhcCCCCCCceeeccc
Q 043602 76 NPTPEQLRTLEDLYRRGTRTPSADQIQHITAQLRRFGKIEGKNVFYWFQ 124 (352)
Q Consensus 76 ~FT~eQLqiLE~lF~~~~~YPs~e~RqqIA~qL~~~G~LsEsqVqvWFQ 124 (352)
.+++.|.++|.-.|-.+. +-. +||..|+ +++..|+.|.+
T Consensus 128 ~L~~~~r~vl~l~~~~~~--s~~----eIA~~lg----is~~tV~~~l~ 166 (182)
T PRK09652 128 SLPEELRTAITLREIEGL--SYE----EIAEIMG----CPIGTVRSRIF 166 (182)
T ss_pred hCCHHHHHHHHHHHHcCC--CHH----HHHHHHC----CCHHHHHHHHH
Confidence 578888999988877666 333 4999996 99999988876
No 48
>PRK12519 RNA polymerase sigma factor; Provisional
Probab=35.64 E-value=23 Score=30.49 Aligned_cols=46 Identities=22% Similarity=0.130 Sum_probs=31.9
Q ss_pred CCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHhcCCCCCCceeeccccchhhHHH
Q 043602 77 PTPEQLRTLEDLYRRGTRTPSADQIQHITAQLRRFGKIEGKNVFYWFQNHKARERQ 132 (352)
Q Consensus 77 FT~eQLqiLE~lF~~~~~YPs~e~RqqIA~qL~~~G~LsEsqVqvWFQNRRAReKR 132 (352)
+++.|..+|+-.|-.+. + .++||+.|+ ++...|+.|.+.=|.+-|+
T Consensus 142 L~~~~~~v~~l~~~~g~--s----~~EIA~~lg----is~~tV~~~l~Ra~~~Lr~ 187 (194)
T PRK12519 142 LPESQRQVLELAYYEGL--S----QSEIAKRLG----IPLGTVKARARQGLLKLRE 187 (194)
T ss_pred CCHHHhhhhhhhhhcCC--C----HHHHHHHhC----CCHHHHHHHHHHHHHHHHH
Confidence 56677777777766665 2 345999996 9999999988544434333
No 49
>PF04545 Sigma70_r4: Sigma-70, region 4; InterPro: IPR007630 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognised by the major sigma factors [, ]. Region 4 of sigma-70 like sigma-factors is involved in binding to the -35 promoter element via a helix-turn-helix motif []. Due to the way Pfam works, the threshold has been set artificially high to prevent overlaps with other helix-turn-helix families. Therefore there are many false negatives.; GO: 0003677 DNA binding, 0003700 sequence-specific DNA binding transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, DNA-dependent, 0006355 regulation of transcription, DNA-dependent; PDB: 2P7V_B 3IYD_F 1TLH_B 1KU7_A 1RIO_H 3N97_A 1KU3_A 1RP3_C 1SC5_A 1NR3_A ....
Probab=34.49 E-value=20 Score=25.18 Aligned_cols=37 Identities=19% Similarity=0.256 Sum_probs=27.9
Q ss_pred CCCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHhcCCCCCCceeec
Q 043602 76 NPTPEQLRTLEDLYRRGTRTPSADQIQHITAQLRRFGKIEGKNVFYW 122 (352)
Q Consensus 76 ~FT~eQLqiLE~lF~~~~~YPs~e~RqqIA~qL~~~G~LsEsqVqvW 122 (352)
.+++.|.++|...|..+. + .++||+.|+ ++...|..+
T Consensus 4 ~L~~~er~vi~~~y~~~~--t----~~eIa~~lg----~s~~~V~~~ 40 (50)
T PF04545_consen 4 QLPPREREVIRLRYFEGL--T----LEEIAERLG----ISRSTVRRI 40 (50)
T ss_dssp TS-HHHHHHHHHHHTST---S----HHHHHHHHT----SCHHHHHHH
T ss_pred hCCHHHHHHHHHHhcCCC--C----HHHHHHHHC----CcHHHHHHH
Confidence 468999999999996666 2 346999996 999888754
No 50
>smart00421 HTH_LUXR helix_turn_helix, Lux Regulon. lux regulon (activates the bioluminescence operon
Probab=34.18 E-value=28 Score=23.35 Aligned_cols=38 Identities=24% Similarity=0.260 Sum_probs=27.6
Q ss_pred CCCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHhcCCCCCCceeeccc
Q 043602 76 NPTPEQLRTLEDLYRRGTRTPSADQIQHITAQLRRFGKIEGKNVFYWFQ 124 (352)
Q Consensus 76 ~FT~eQLqiLE~lF~~~~~YPs~e~RqqIA~qL~~~G~LsEsqVqvWFQ 124 (352)
.+++.|.++++. +..+. . ..+||..|+ ++...|+.|.+
T Consensus 3 ~l~~~e~~i~~~-~~~g~--s----~~eia~~l~----is~~tv~~~~~ 40 (58)
T smart00421 3 SLTPREREVLRL-LAEGL--T----NKEIAERLG----ISEKTVKTHLS 40 (58)
T ss_pred CCCHHHHHHHHH-HHcCC--C----HHHHHHHHC----CCHHHHHHHHH
Confidence 468889999876 44444 2 345999995 99999987655
No 51
>PRK11924 RNA polymerase sigma factor; Provisional
Probab=33.72 E-value=34 Score=28.28 Aligned_cols=46 Identities=15% Similarity=0.081 Sum_probs=31.0
Q ss_pred CCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHhcCCCCCCceeeccccchhhHHH
Q 043602 77 PTPEQLRTLEDLYRRGTRTPSADQIQHITAQLRRFGKIEGKNVFYWFQNHKARERQ 132 (352)
Q Consensus 77 FT~eQLqiLE~lF~~~~~YPs~e~RqqIA~qL~~~G~LsEsqVqvWFQNRRAReKR 132 (352)
.++.+..+|...|..+. +- ++||+.|+ ++...|+.|..-=|.|.|+
T Consensus 126 L~~~~r~i~~l~~~~~~--~~----~eIA~~lg----is~~tv~~~~~ra~~~lr~ 171 (179)
T PRK11924 126 LPVKQREVFLLRYVEGL--SY----REIAEILG----VPVGTVKSRLRRARQLLRE 171 (179)
T ss_pred CCHHHHHHhhHHHHcCC--CH----HHHHHHHC----CCHHHHHHHHHHHHHHHHH
Confidence 55666677776666555 22 45999996 9999999887644444433
No 52
>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=33.53 E-value=42 Score=27.63 Aligned_cols=37 Identities=22% Similarity=0.203 Sum_probs=28.3
Q ss_pred CCCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHhcCCCCCCceeec
Q 043602 76 NPTPEQLRTLEDLYRRGTRTPSADQIQHITAQLRRFGKIEGKNVFYW 122 (352)
Q Consensus 76 ~FT~eQLqiLE~lF~~~~~YPs~e~RqqIA~qL~~~G~LsEsqVqvW 122 (352)
.+++.|.+++.-.|-.+. +. ++||+.|+ |+...|+++
T Consensus 111 ~L~~~~r~v~~l~~~~g~--~~----~eIA~~l~----is~~tv~~~ 147 (159)
T TIGR02989 111 KLPERQRELLQLRYQRGV--SL----TALAEQLG----RTVNAVYKA 147 (159)
T ss_pred HCCHHHHHHHHHHHhcCC--CH----HHHHHHhC----CCHHHHHHH
Confidence 477888888888776665 33 45999996 999999965
No 53
>PRK09646 RNA polymerase sigma factor SigK; Reviewed
Probab=33.52 E-value=32 Score=29.96 Aligned_cols=49 Identities=14% Similarity=0.094 Sum_probs=33.4
Q ss_pred CCCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHhcCCCCCCceeeccccchhhHHHHHHhhh
Q 043602 76 NPTPEQLRTLEDLYRRGTRTPSADQIQHITAQLRRFGKIEGKNVFYWFQNHKARERQKRRRQM 138 (352)
Q Consensus 76 ~FT~eQLqiLE~lF~~~~~YPs~e~RqqIA~qL~~~G~LsEsqVqvWFQNRRAReKRKrRrq~ 138 (352)
.+++.|..+|.-.|-.+. . .++||+.|+ +++..|+.+. .|.|++-|..+
T Consensus 142 ~L~~~~r~vl~l~~~~~~--s----~~EIA~~Lg----is~~tVk~~l----~ra~~~Lr~~l 190 (194)
T PRK09646 142 ALTDTQRESVTLAYYGGL--T----YREVAERLA----VPLGTVKTRM----RDGLIRLRDCL 190 (194)
T ss_pred hCCHHHHHHHHHHHHcCC--C----HHHHHHHhC----CChHhHHHHH----HHHHHHHHHHh
Confidence 467778888887776666 2 345999996 9999997766 34444444433
No 54
>PRK09413 IS2 repressor TnpA; Reviewed
Probab=33.01 E-value=39 Score=28.30 Aligned_cols=41 Identities=15% Similarity=0.423 Sum_probs=30.1
Q ss_pred CCCCCCCHHH-HHHHHHHHhcCCCCCCHHHHHHHHHHHHhcCCCCCCceeec
Q 043602 72 SSRWNPTPEQ-LRTLEDLYRRGTRTPSADQIQHITAQLRRFGKIEGKNVFYW 122 (352)
Q Consensus 72 R~Rw~FT~eQ-LqiLE~lF~~~~~YPs~e~RqqIA~qL~~~G~LsEsqVqvW 122 (352)
.+|..||+++ ++++...+..+. +-. +||..++ |+...|+.|
T Consensus 8 ~~rr~ys~EfK~~aV~~~~~~g~--sv~----evA~e~g----Is~~tl~~W 49 (121)
T PRK09413 8 EKRRRRTTQEKIAIVQQSFEPGM--TVS----LVARQHG----VAASQLFLW 49 (121)
T ss_pred CCCCCCCHHHHHHHHHHHHcCCC--CHH----HHHHHHC----cCHHHHHHH
Confidence 4566677776 556677777665 333 4899995 999999999
No 55
>TIGR02937 sigma70-ECF RNA polymerase sigma factor, sigma-70 family. Several PFAM models hit segments of these sequences including Sigma-70 region 2 (pfam04542) and Sigma-70, region 4 (pfam04545), but not always above their respective trusted cutoffs.
Probab=32.25 E-value=26 Score=27.22 Aligned_cols=41 Identities=17% Similarity=0.082 Sum_probs=30.0
Q ss_pred CCCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHhcCCCCCCceeeccccc
Q 043602 76 NPTPEQLRTLEDLYRRGTRTPSADQIQHITAQLRRFGKIEGKNVFYWFQNH 126 (352)
Q Consensus 76 ~FT~eQLqiLE~lF~~~~~YPs~e~RqqIA~qL~~~G~LsEsqVqvWFQNR 126 (352)
.+++.|.++|...|-.+. +.. +||+.|+ ++...|..+.+.=
T Consensus 110 ~L~~~~~~ii~~~~~~g~--s~~----eIA~~l~----~s~~~v~~~~~~~ 150 (158)
T TIGR02937 110 KLPEREREVLVLRYLEGL--SYK----EIAEILG----ISVGTVKRRLKRA 150 (158)
T ss_pred hCCHHHHHHHhhHHhcCC--CHH----HHHHHHC----CCHHHHHHHHHHH
Confidence 567888888887766554 444 5999995 9999998776543
No 56
>COG3413 Predicted DNA binding protein [General function prediction only]
Probab=32.18 E-value=49 Score=30.00 Aligned_cols=41 Identities=22% Similarity=0.318 Sum_probs=34.3
Q ss_pred CCCHHHHHHHHHHHhcCC-CCCCHHHHHHHHHHHHhcCCCCCCcee
Q 043602 76 NPTPEQLRTLEDLYRRGT-RTPSADQIQHITAQLRRFGKIEGKNVF 120 (352)
Q Consensus 76 ~FT~eQLqiLE~lF~~~~-~YPs~e~RqqIA~qL~~~G~LsEsqVq 120 (352)
.+|+-|+++|..+|..|= -||-.-..++||++|+ |+..-+.
T Consensus 155 ~LTdrQ~~vL~~A~~~GYFd~PR~~~l~dLA~~lG----ISkst~~ 196 (215)
T COG3413 155 DLTDRQLEVLRLAYKMGYFDYPRRVSLKDLAKELG----ISKSTLS 196 (215)
T ss_pred cCCHHHHHHHHHHHHcCCCCCCccCCHHHHHHHhC----CCHHHHH
Confidence 899999999999999973 1688888899999996 8876553
No 57
>PRK09642 RNA polymerase sigma factor SigW; Reviewed
Probab=31.59 E-value=34 Score=28.47 Aligned_cols=41 Identities=20% Similarity=0.084 Sum_probs=29.0
Q ss_pred CCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHhcCCCCCCceeeccccch
Q 043602 77 PTPEQLRTLEDLYRRGTRTPSADQIQHITAQLRRFGKIEGKNVFYWFQNHK 127 (352)
Q Consensus 77 FT~eQLqiLE~lF~~~~~YPs~e~RqqIA~qL~~~G~LsEsqVqvWFQNRR 127 (352)
+++.|.+++.-.|-.+. +- ++||+.|+ +++..|++...-=|
T Consensus 107 Lp~~~r~v~~l~~~~g~--s~----~EIA~~lg----is~~tV~~~l~Rar 147 (160)
T PRK09642 107 LPENYRDVVLAHYLEEK--SY----QEIALQEK----IEVKTVEMKLYRAR 147 (160)
T ss_pred CCHHHHHHHHHHHHhCC--CH----HHHHHHHC----CCHHHHHHHHHHHH
Confidence 45667777777776666 22 35999995 99999998765333
No 58
>PRK12533 RNA polymerase sigma factor; Provisional
Probab=31.51 E-value=45 Score=30.49 Aligned_cols=54 Identities=17% Similarity=0.052 Sum_probs=36.3
Q ss_pred CCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHhcCCCCCCceeeccccchhhHHHHHHhhhcCCCCc
Q 043602 77 PTPEQLRTLEDLYRRGTRTPSADQIQHITAQLRRFGKIEGKNVFYWFQNHKARERQKRRRQMESSPAD 144 (352)
Q Consensus 77 FT~eQLqiLE~lF~~~~~YPs~e~RqqIA~qL~~~G~LsEsqVqvWFQNRRAReKRKrRrq~e~a~~~ 144 (352)
+++.|.++|.-.|-.+. +-. +||+.|+ |++..|+++- .|-|++.|..++.++++
T Consensus 135 Lp~~~R~v~~L~y~eg~--s~~----EIAe~Lg----iS~~tVk~~L----~RAr~~Lr~~l~~~~~~ 188 (216)
T PRK12533 135 LPVEYREVLVLRELEDM--SYR----EIAAIAD----VPVGTVMSRL----ARARRRLAALLGGASAA 188 (216)
T ss_pred CCHHHHhHhhhHHhcCC--CHH----HHHHHHC----CCHHHHHHHH----HHHHHHHHHHHcccchh
Confidence 44556666666666554 333 5999995 9999997654 35566677777777665
No 59
>PF13936 HTH_38: Helix-turn-helix domain; PDB: 2W48_A.
Probab=31.45 E-value=15 Score=26.06 Aligned_cols=38 Identities=29% Similarity=0.314 Sum_probs=17.8
Q ss_pred CCCCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHhcCCCCCCceeec
Q 043602 75 WNPTPEQLRTLEDLYRRGTRTPSADQIQHITAQLRRFGKIEGKNVFYW 122 (352)
Q Consensus 75 w~FT~eQLqiLE~lF~~~~~YPs~e~RqqIA~qL~~~G~LsEsqVqvW 122 (352)
..+|.+|...++.++..+. + ..+||+.|+ ++.+-|..+
T Consensus 3 ~~Lt~~eR~~I~~l~~~G~---s---~~~IA~~lg----~s~sTV~re 40 (44)
T PF13936_consen 3 KHLTPEERNQIEALLEQGM---S---IREIAKRLG----RSRSTVSRE 40 (44)
T ss_dssp ---------HHHHHHCS---------HHHHHHHTT------HHHHHHH
T ss_pred cchhhhHHHHHHHHHHcCC---C---HHHHHHHHC----cCcHHHHHH
Confidence 4589999999999998877 2 335999996 666666543
No 60
>TIGR02952 Sig70_famx2 RNA polymerase sigma-70 factor, TIGR02952 family. This group of sigma factors are members of the sigma-70 family (TIGR02937). They and appear by homology, tree building, bidirectional best hits and one-to-a-genome distribution, to represent a conserved family. This family is found in a limited number of Gram-positive bacterial lineages.
Probab=30.63 E-value=53 Score=27.28 Aligned_cols=47 Identities=19% Similarity=0.157 Sum_probs=31.2
Q ss_pred CCCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHhcCCCCCCceeeccccchhhHHHHHHh
Q 043602 76 NPTPEQLRTLEDLYRRGTRTPSADQIQHITAQLRRFGKIEGKNVFYWFQNHKARERQKRRR 136 (352)
Q Consensus 76 ~FT~eQLqiLE~lF~~~~~YPs~e~RqqIA~qL~~~G~LsEsqVqvWFQNRRAReKRKrRr 136 (352)
.+++.|.++|.-.|-.+. +. ++||+.|+ +++..|+.. ..|-+++-|.
T Consensus 122 ~L~~~~r~vl~l~~~~g~--s~----~eIA~~l~----is~~tv~~~----l~ra~~~Lr~ 168 (170)
T TIGR02952 122 ILTPKQQHVIALRFGQNL--PI----AEVARILG----KTEGAVKIL----QFRAIKKLAR 168 (170)
T ss_pred hCCHHHHHHHHHHHhcCC--CH----HHHHHHHC----CCHHHHHHH----HHHHHHHHHH
Confidence 456677777777666665 33 35999996 999999864 3444445543
No 61
>PRK12526 RNA polymerase sigma factor; Provisional
Probab=30.63 E-value=35 Score=30.27 Aligned_cols=38 Identities=13% Similarity=0.138 Sum_probs=27.3
Q ss_pred CCCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHhcCCCCCCceeecc
Q 043602 76 NPTPEQLRTLEDLYRRGTRTPSADQIQHITAQLRRFGKIEGKNVFYWF 123 (352)
Q Consensus 76 ~FT~eQLqiLE~lF~~~~~YPs~e~RqqIA~qL~~~G~LsEsqVqvWF 123 (352)
.+++.|.++|.-.|-.+. ..++||+.|+ +++..|+++.
T Consensus 153 ~L~~~~r~vl~l~~~~g~------s~~EIA~~lg----is~~tV~~~l 190 (206)
T PRK12526 153 KLPEAQQTVVKGVYFQEL------SQEQLAQQLN----VPLGTVKSRL 190 (206)
T ss_pred hCCHHHHHHHHHHHHcCC------CHHHHHHHHC----CCHHHHHHHH
Confidence 356677777776666666 2345999996 9999997665
No 62
>TIGR02948 SigW_bacill RNA polymerase sigma-W factor. This sigma factor is restricted to certain lineages of the order Bacillales.
Probab=30.26 E-value=31 Score=29.19 Aligned_cols=42 Identities=12% Similarity=0.059 Sum_probs=29.1
Q ss_pred CCCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHhcCCCCCCceeeccccch
Q 043602 76 NPTPEQLRTLEDLYRRGTRTPSADQIQHITAQLRRFGKIEGKNVFYWFQNHK 127 (352)
Q Consensus 76 ~FT~eQLqiLE~lF~~~~~YPs~e~RqqIA~qL~~~G~LsEsqVqvWFQNRR 127 (352)
.+++.|..+|+-.|-.+. +- ++||+.|+ ++...|+++.+.=|
T Consensus 136 ~L~~~~r~v~~l~~~~g~--s~----~eIA~~lg----is~~~v~~~l~Rar 177 (187)
T TIGR02948 136 ALPPKYRMVIVLKYMEDL--SL----KEISEILD----LPVGTVKTRIHRGR 177 (187)
T ss_pred hCCHHHhHHhhhHHhcCC--CH----HHHHHHHC----CCHHHHHHHHHHHH
Confidence 456667777777666555 33 45999996 99999998775333
No 63
>PRK12514 RNA polymerase sigma factor; Provisional
Probab=29.81 E-value=77 Score=26.95 Aligned_cols=38 Identities=8% Similarity=0.265 Sum_probs=26.9
Q ss_pred CCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHhcCCCCCCceeeccc
Q 043602 77 PTPEQLRTLEDLYRRGTRTPSADQIQHITAQLRRFGKIEGKNVFYWFQ 124 (352)
Q Consensus 77 FT~eQLqiLE~lF~~~~~YPs~e~RqqIA~qL~~~G~LsEsqVqvWFQ 124 (352)
.++.|-.+|.-.|-.+. + .++||+.|+ +++..|+++.+
T Consensus 130 L~~~~r~i~~l~~~~g~--s----~~eIA~~lg----is~~tV~~~l~ 167 (179)
T PRK12514 130 LEKDRAAAVRRAYLEGL--S----YKELAERHD----VPLNTMRTWLR 167 (179)
T ss_pred CCHHHHHHHHHHHHcCC--C----HHHHHHHHC----CChHHHHHHHH
Confidence 45566666776766555 2 456999996 99999976654
No 64
>PF08880 QLQ: QLQ; InterPro: IPR014978 QLQ is named after the conserved Gln, Leu, Gln motif. QLQ is found at the N terminus of SWI2/SNF2 protein, which has been shown to be involved in protein-protein interactions. QLQ has been postulated to be involved in mediating protein interactions []. ; GO: 0005524 ATP binding, 0016818 hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides, 0006355 regulation of transcription, DNA-dependent, 0005634 nucleus
Probab=29.22 E-value=43 Score=23.89 Aligned_cols=14 Identities=36% Similarity=0.366 Sum_probs=12.0
Q ss_pred CCCHHHHHHHHHHH
Q 043602 76 NPTPEQLRTLEDLY 89 (352)
Q Consensus 76 ~FT~eQLqiLE~lF 89 (352)
.||++|+.+||.--
T Consensus 2 ~FT~~Ql~~L~~Qi 15 (37)
T PF08880_consen 2 PFTPAQLQELRAQI 15 (37)
T ss_pred CCCHHHHHHHHHHH
Confidence 59999999999754
No 65
>PF13565 HTH_32: Homeodomain-like domain
Probab=29.20 E-value=1e+02 Score=22.93 Aligned_cols=47 Identities=17% Similarity=0.093 Sum_probs=30.1
Q ss_pred CCCCCCCCCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHhcCC----CCCCceeec
Q 043602 70 VVSSRWNPTPEQLRTLEDLYRRGTRTPSADQIQHITAQLRRFGK----IEGKNVFYW 122 (352)
Q Consensus 70 ~rR~Rw~FT~eQLqiLE~lF~~~~~YPs~e~RqqIA~qL~~~G~----LsEsqVqvW 122 (352)
..++|. +++|.+.|.++....+ .-+.. +|+..|....+ ++.+.|+.|
T Consensus 26 ~Grp~~--~~e~~~~i~~~~~~~p-~wt~~---~i~~~L~~~~g~~~~~S~~tv~R~ 76 (77)
T PF13565_consen 26 PGRPRK--DPEQRERIIALIEEHP-RWTPR---EIAEYLEEEFGISVRVSRSTVYRI 76 (77)
T ss_pred CCCCCC--cHHHHHHHHHHHHhCC-CCCHH---HHHHHHHHHhCCCCCccHhHHHHh
Confidence 445555 8888899999999887 34444 46666664433 365556543
No 66
>PF12824 MRP-L20: Mitochondrial ribosomal protein subunit L20; InterPro: IPR024388 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. This entry represents the essential mitochondrial ribosomal protein L20 family from fungi [].
Probab=28.47 E-value=2e+02 Score=26.29 Aligned_cols=40 Identities=13% Similarity=0.199 Sum_probs=32.0
Q ss_pred CCCCCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHhcCCCCCCcee
Q 043602 74 RWNPTPEQLRTLEDLYRRGTRTPSADQIQHITAQLRRFGKIEGKNVF 120 (352)
Q Consensus 74 Rw~FT~eQLqiLE~lF~~~~~YPs~e~RqqIA~qL~~~G~LsEsqVq 120 (352)
.-.+|+++++++-++=..++ ..-.|..||++.+ ++.--|.
T Consensus 83 ~y~Lt~e~i~Eir~LR~~DP---~~wTr~~LAkkF~----~S~~fV~ 122 (164)
T PF12824_consen 83 KYHLTPEDIQEIRRLRAEDP---EKWTRKKLAKKFN----CSPLFVS 122 (164)
T ss_pred cccCCHHHHHHHHHHHHcCc---hHhhHHHHHHHhC----CCHHHHH
Confidence 36899999999999988776 7788889999885 5554444
No 67
>PRK12512 RNA polymerase sigma factor; Provisional
Probab=27.30 E-value=41 Score=28.70 Aligned_cols=47 Identities=17% Similarity=0.181 Sum_probs=31.5
Q ss_pred CCCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHhcCCCCCCceeeccccchhhHHH
Q 043602 76 NPTPEQLRTLEDLYRRGTRTPSADQIQHITAQLRRFGKIEGKNVFYWFQNHKARERQ 132 (352)
Q Consensus 76 ~FT~eQLqiLE~lF~~~~~YPs~e~RqqIA~qL~~~G~LsEsqVqvWFQNRRAReKR 132 (352)
.+++.|.++|.-.|-.+. . .++||..|+ |+...|+.+...=|.+-|+
T Consensus 131 ~L~~~~r~v~~l~~~~g~--s----~~eIA~~l~----is~~tV~~~l~ra~~~Lr~ 177 (184)
T PRK12512 131 TLPPRQRDVVQSISVEGA--S----IKETAAKLS----MSEGAVRVALHRGLAALAA 177 (184)
T ss_pred hCCHHHHHHHHHHHHcCC--C----HHHHHHHhC----CCHHHHHHHHHHHHHHHHH
Confidence 456667777777766666 2 245999995 9999999776544433333
No 68
>PRK12531 RNA polymerase sigma factor; Provisional
Probab=27.04 E-value=75 Score=27.69 Aligned_cols=49 Identities=20% Similarity=0.217 Sum_probs=31.9
Q ss_pred CCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHhcCCCCCCceeeccccchhhHHHHHHhhhc
Q 043602 77 PTPEQLRTLEDLYRRGTRTPSADQIQHITAQLRRFGKIEGKNVFYWFQNHKARERQKRRRQME 139 (352)
Q Consensus 77 FT~eQLqiLE~lF~~~~~YPs~e~RqqIA~qL~~~G~LsEsqVqvWFQNRRAReKRKrRrq~e 139 (352)
+++.|.++|.-.|-.+. +- ++||+.|+ ++...|++.. .|.+++-|..++
T Consensus 142 Lp~~~r~v~~l~~~eg~--s~----~EIA~~lg----is~~tVk~rl----~ra~~~Lr~~l~ 190 (194)
T PRK12531 142 LPKAQRDVLQAVYLEEL--PH----QQVAEMFD----IPLGTVKSRL----RLAVEKLRHSMD 190 (194)
T ss_pred CCHHHHHHHHHHHHcCC--CH----HHHHHHhC----cCHHHHHHHH----HHHHHHHHHHhh
Confidence 45667777777776666 23 45999996 9999996443 344445554444
No 69
>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=26.66 E-value=20 Score=25.35 Aligned_cols=38 Identities=18% Similarity=0.105 Sum_probs=27.0
Q ss_pred CCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHhcCCCCCCceeeccc
Q 043602 77 PTPEQLRTLEDLYRRGTRTPSADQIQHITAQLRRFGKIEGKNVFYWFQ 124 (352)
Q Consensus 77 FT~eQLqiLE~lF~~~~~YPs~e~RqqIA~qL~~~G~LsEsqVqvWFQ 124 (352)
.++.|-.++.-.|-.+. +- ++||+.|+ ++++.|+.|.+
T Consensus 11 L~~~~r~i~~l~~~~g~--s~----~eIa~~l~----~s~~~v~~~l~ 48 (54)
T PF08281_consen 11 LPERQREIFLLRYFQGM--SY----AEIAEILG----ISESTVKRRLR 48 (54)
T ss_dssp S-HHHHHHHHHHHTS-----H----HHHHHHCT----S-HHHHHHHHH
T ss_pred CCHHHHHHHHHHHHHCc--CH----HHHHHHHC----cCHHHHHHHHH
Confidence 56788888998888887 33 45999995 99999998875
No 70
>PF10925 DUF2680: Protein of unknown function (DUF2680); InterPro: IPR024485 Members in this family of proteins are annotated as YckD however currently no function is known.
Probab=25.39 E-value=74 Score=24.65 Aligned_cols=42 Identities=19% Similarity=0.168 Sum_probs=33.6
Q ss_pred CCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHhcCCCCCCceeecc
Q 043602 77 PTPEQLRTLEDLYRRGTRTPSADQIQHITAQLRRFGKIEGKNVFYWF 123 (352)
Q Consensus 77 FT~eQLqiLE~lF~~~~~YPs~e~RqqIA~qL~~~G~LsEsqVqvWF 123 (352)
+|++|+.+|+.+|..=- +.+++|-...-.+|-||..+=..|-
T Consensus 1 lT~~Qk~el~~l~~qm~-----e~kK~~idk~Ve~G~iTqeqAd~ik 42 (59)
T PF10925_consen 1 LTDQQKKELKALYKQML-----ELKKQIIDKYVEAGVITQEQADAIK 42 (59)
T ss_pred CCHHHHHHHHHHHHHHH-----HHHHHHHHHHHHcCCCCHHHHHHHH
Confidence 58999999999998744 6677788888889999988855443
No 71
>PRK09639 RNA polymerase sigma factor SigX; Provisional
Probab=24.18 E-value=57 Score=27.14 Aligned_cols=38 Identities=18% Similarity=0.088 Sum_probs=28.9
Q ss_pred CCCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHhcCCCCCCceeeccc
Q 043602 76 NPTPEQLRTLEDLYRRGTRTPSADQIQHITAQLRRFGKIEGKNVFYWFQ 124 (352)
Q Consensus 76 ~FT~eQLqiLE~lF~~~~~YPs~e~RqqIA~qL~~~G~LsEsqVqvWFQ 124 (352)
.+++.|..+|.-.| .+. +-. +||..|+ +++..|+++..
T Consensus 112 ~L~~~~r~il~l~~-~g~--s~~----eIA~~lg----is~~tV~~~i~ 149 (166)
T PRK09639 112 KMTERDRTVLLLRF-SGY--SYK----EIAEALG----IKESSVGTTLA 149 (166)
T ss_pred cCCHHHHHHHHHHH-cCC--CHH----HHHHHHC----CCHHHHHHHHH
Confidence 36677888888888 555 444 4999995 99999998774
No 72
>PRK07037 extracytoplasmic-function sigma-70 factor; Validated
Probab=23.87 E-value=85 Score=26.11 Aligned_cols=50 Identities=12% Similarity=0.108 Sum_probs=32.2
Q ss_pred CCCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHhcCCCCCCceeeccccchhhHHHHHHhhhc
Q 043602 76 NPTPEQLRTLEDLYRRGTRTPSADQIQHITAQLRRFGKIEGKNVFYWFQNHKARERQKRRRQME 139 (352)
Q Consensus 76 ~FT~eQLqiLE~lF~~~~~YPs~e~RqqIA~qL~~~G~LsEsqVqvWFQNRRAReKRKrRrq~e 139 (352)
.+++.|-++|+-.|-.+. + .++||+.|+ ++...|+.. -.|.+++-|..++
T Consensus 109 ~L~~~~r~v~~l~~~~~~--s----~~EIA~~lg----is~~tV~~~----l~ra~~~lr~~l~ 158 (163)
T PRK07037 109 ELPARTRYAFEMYRLHGE--T----QKDIARELG----VSPTLVNFM----IRDALVHCRKCLD 158 (163)
T ss_pred hCCHHHHHHHHHHHHcCC--C----HHHHHHHHC----CCHHHHHHH----HHHHHHHHHHHHh
Confidence 445666667766666665 2 345999996 999999964 3444445554443
No 73
>PRK06759 RNA polymerase factor sigma-70; Validated
Probab=23.63 E-value=44 Score=27.43 Aligned_cols=39 Identities=8% Similarity=0.102 Sum_probs=29.8
Q ss_pred CCCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHhcCCCCCCceeeccc
Q 043602 76 NPTPEQLRTLEDLYRRGTRTPSADQIQHITAQLRRFGKIEGKNVFYWFQ 124 (352)
Q Consensus 76 ~FT~eQLqiLE~lF~~~~~YPs~e~RqqIA~qL~~~G~LsEsqVqvWFQ 124 (352)
.+++.|.+++.-.|-.+. . .++||+.|+ +++..|+.|..
T Consensus 106 ~L~~~~r~ii~l~~~~~~--s----~~EIA~~l~----is~~tV~~~~~ 144 (154)
T PRK06759 106 VLDEKEKYIIFERFFVGK--T----MGEIALETE----MTYYQVRWIYR 144 (154)
T ss_pred hCCHHHHHHHHHHHhcCC--C----HHHHHHHHC----CCHHHHHHHHH
Confidence 456777888888777776 2 456999996 99999998754
No 74
>PRK04217 hypothetical protein; Provisional
Probab=23.52 E-value=87 Score=26.91 Aligned_cols=45 Identities=11% Similarity=0.095 Sum_probs=34.6
Q ss_pred CCCCCCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHhcCCCCCCceeeccccch
Q 043602 73 SRWNPTPEQLRTLEDLYRRGTRTPSADQIQHITAQLRRFGKIEGKNVFYWFQNHK 127 (352)
Q Consensus 73 ~Rw~FT~eQLqiLE~lF~~~~~YPs~e~RqqIA~qL~~~G~LsEsqVqvWFQNRR 127 (352)
+=-.+|++|.++++..|..+. ..++||+.|+ |+...|+...+.-+
T Consensus 39 p~~~Lt~eereai~l~~~eGl------S~~EIAk~LG----IS~sTV~r~L~RAr 83 (110)
T PRK04217 39 PPIFMTYEEFEALRLVDYEGL------TQEEAGKRMG----VSRGTVWRALTSAR 83 (110)
T ss_pred CcccCCHHHHHHHHHHHHcCC------CHHHHHHHHC----cCHHHHHHHHHHHH
Confidence 345789999999998887777 3446999995 99999997665433
No 75
>TIGR02985 Sig70_bacteroi1 RNA polymerase sigma-70 factor, Bacteroides expansion family 1. This group of sigma factors are members of the sigma-70 family (TIGR02937) and are found primarily in the genus Bacteroides. This family appears to have resulted from a lineage-specific expansion as B. thetaiotaomicron VPI-5482, Bacteroides forsythus ATCC 43037, Bacteroides fragilis YCH46 and Bacteroides fragilis NCTC 9343 contain 25, 12, 24 and 23 members, respectively. There are currentlyonly two known members of this family outside of the Bacteroides, in Rhodopseudomonas and Bradyrhizobium.
Probab=23.16 E-value=54 Score=26.49 Aligned_cols=39 Identities=18% Similarity=0.111 Sum_probs=27.1
Q ss_pred CCCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHhcCCCCCCceeeccc
Q 043602 76 NPTPEQLRTLEDLYRRGTRTPSADQIQHITAQLRRFGKIEGKNVFYWFQ 124 (352)
Q Consensus 76 ~FT~eQLqiLE~lF~~~~~YPs~e~RqqIA~qL~~~G~LsEsqVqvWFQ 124 (352)
.+++.+.++|.-.|-.+. +-. +||..|+ +++..|+.+..
T Consensus 113 ~L~~~~r~il~l~~~~~~--~~~----eIA~~lg----is~~tv~~~~~ 151 (161)
T TIGR02985 113 KLPEQCRKIFILSRFEGK--SYK----EIAEELG----ISVKTVEYHIS 151 (161)
T ss_pred HCCHHHHHHHHHHHHcCC--CHH----HHHHHHC----CCHHHHHHHHH
Confidence 456677777777665544 344 4999995 99999986554
No 76
>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=22.56 E-value=71 Score=25.73 Aligned_cols=27 Identities=11% Similarity=0.166 Sum_probs=23.5
Q ss_pred HHHHHHHHHHHHhcCCCCCCceeeccc
Q 043602 98 ADQIQHITAQLRRFGKIEGKNVFYWFQ 124 (352)
Q Consensus 98 ~e~RqqIA~qL~~~G~LsEsqVqvWFQ 124 (352)
...+++|+..|....+|.+.+|.+|+.
T Consensus 49 G~~i~~L~~~L~k~~~~~~~~i~v~~~ 75 (81)
T cd02413 49 GRRIRELTSLVQKRFNFPEGSVELYAE 75 (81)
T ss_pred chhHHHHHHHHHHHhCCCCCeEEEEEE
Confidence 467888999999888999999999985
No 77
>PRK09643 RNA polymerase sigma factor SigM; Reviewed
Probab=22.47 E-value=71 Score=27.94 Aligned_cols=35 Identities=17% Similarity=0.099 Sum_probs=26.1
Q ss_pred CCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHhcCCCCCCceee
Q 043602 77 PTPEQLRTLEDLYRRGTRTPSADQIQHITAQLRRFGKIEGKNVFY 121 (352)
Q Consensus 77 FT~eQLqiLE~lF~~~~~YPs~e~RqqIA~qL~~~G~LsEsqVqv 121 (352)
+.+.|.++|+-.|-.+. + .++||..|+ ++...|++
T Consensus 135 Lp~~~r~i~~l~~~~g~--s----~~EIA~~lg----~s~~tV~~ 169 (192)
T PRK09643 135 LPVEQRAALVAVDMQGY--S----VADAARMLG----VAEGTVKS 169 (192)
T ss_pred CCHHHHHHHHHHHHcCC--C----HHHHHHHHC----cCHHHHHH
Confidence 56778888887777766 2 345999996 99999953
No 78
>PF13873 Myb_DNA-bind_5: Myb/SANT-like DNA-binding domain
Probab=22.27 E-value=1.2e+02 Score=23.00 Aligned_cols=58 Identities=17% Similarity=0.217 Sum_probs=37.1
Q ss_pred CCCCHHHHHHHHHHHhcCCC-----CCCHH---H----HHHHHHHHHhcCCCCCCc---eeeccccchhhHHHH
Q 043602 75 WNPTPEQLRTLEDLYRRGTR-----TPSAD---Q----IQHITAQLRRFGKIEGKN---VFYWFQNHKARERQK 133 (352)
Q Consensus 75 w~FT~eQLqiLE~lF~~~~~-----YPs~e---~----RqqIA~qL~~~G~LsEsq---VqvWFQNRRAReKRK 133 (352)
-.||++|+.+|-+++..... ..+.. . =++||..|+..|+. .+. |+..++|=+.+.|++
T Consensus 3 ~~fs~~E~~~Lv~~v~~~~~il~~k~~~~~~~~~k~~~W~~I~~~lN~~~~~-~Rs~~~lkkkW~nlk~~~Kk~ 75 (78)
T PF13873_consen 3 PNFSEEEKEILVELVEKHKDILENKFSDSVSNKEKRKAWEEIAEELNALGPG-KRSWKQLKKKWKNLKSKAKKK 75 (78)
T ss_pred CCCCHHHHHHHHHHHHHhHHHHhcccccHHHHHHHHHHHHHHHHHHHhcCCC-CCCHHHHHHHHHHHHHHHHHH
Confidence 46999999999998776431 11111 1 24799999876664 333 555666766666654
No 79
>PF13551 HTH_29: Winged helix-turn helix
Probab=20.94 E-value=2.5e+02 Score=21.69 Aligned_cols=52 Identities=13% Similarity=0.068 Sum_probs=31.8
Q ss_pred CCCCCCCCHHHHHHHHHHHhcCCCCCC--HHHHHHHHHHH-HhcC--CCCCCceeecc
Q 043602 71 VSSRWNPTPEQLRTLEDLYRRGTRTPS--ADQIQHITAQL-RRFG--KIEGKNVFYWF 123 (352)
Q Consensus 71 rR~Rw~FT~eQLqiLE~lF~~~~~YPs--~e~RqqIA~qL-~~~G--~LsEsqVqvWF 123 (352)
.+++..++++|.+.|.+++...+.+ . .-....|+..| ...+ .++...|..|+
T Consensus 52 g~~~~~l~~~~~~~l~~~~~~~p~~-g~~~~t~~~l~~~l~~~~~~~~~s~~ti~r~L 108 (112)
T PF13551_consen 52 GRPRKRLSEEQRAQLIELLRENPPE-GRSRWTLEELAEWLIEEEFGIDVSPSTIRRIL 108 (112)
T ss_pred CCCCCCCCHHHHHHHHHHHHHCCCC-CCCcccHHHHHHHHHHhccCccCCHHHHHHHH
Confidence 4455559999999999999987622 1 12244566655 3322 35555565554
No 80
>PRK09637 RNA polymerase sigma factor SigZ; Provisional
Probab=20.84 E-value=71 Score=27.82 Aligned_cols=39 Identities=13% Similarity=0.028 Sum_probs=29.2
Q ss_pred CCCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHhcCCCCCCceeeccc
Q 043602 76 NPTPEQLRTLEDLYRRGTRTPSADQIQHITAQLRRFGKIEGKNVFYWFQ 124 (352)
Q Consensus 76 ~FT~eQLqiLE~lF~~~~~YPs~e~RqqIA~qL~~~G~LsEsqVqvWFQ 124 (352)
.+++.|.++|.-.|-.+. +- ++||..|+ ++...|+..+.
T Consensus 106 ~L~~~~r~i~~l~~~~g~--~~----~EIA~~lg----is~~tV~~~l~ 144 (181)
T PRK09637 106 ALPEKYAEALRLTELEGL--SQ----KEIAEKLG----LSLSGAKSRVQ 144 (181)
T ss_pred hCCHHHHHHHHHHHhcCC--CH----HHHHHHhC----CCHHHHHHHHH
Confidence 567777788877776666 33 35999996 99999987774
No 81
>TIGR02983 SigE-fam_strep RNA polymerase sigma-70 factor, sigma-E family. This group of similar sigma-70 factors includes the sigE factor from Streptomyces coelicolor. The family appears to include a paralagous expansion in the Streptomycetes lineage, while related Actinomycetales have at most two representatives.
Probab=20.51 E-value=60 Score=26.97 Aligned_cols=48 Identities=17% Similarity=0.115 Sum_probs=32.2
Q ss_pred CCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHhcCCCCCCceeeccccchhhHHHHHHhhh
Q 043602 77 PTPEQLRTLEDLYRRGTRTPSADQIQHITAQLRRFGKIEGKNVFYWFQNHKARERQKRRRQM 138 (352)
Q Consensus 77 FT~eQLqiLE~lF~~~~~YPs~e~RqqIA~qL~~~G~LsEsqVqvWFQNRRAReKRKrRrq~ 138 (352)
+++.|..+|+-.|-.+. +.. +||+.|+ +++..|+++-. |-+++-|..+
T Consensus 111 L~~~~r~i~~l~~~~g~--s~~----eIA~~lg----is~~tV~~~l~----ra~~~Lr~~l 158 (162)
T TIGR02983 111 LPARQRAVVVLRYYEDL--SEA----QVAEALG----ISVGTVKSRLS----RALARLRELL 158 (162)
T ss_pred CCHHHHHHhhhHHHhcC--CHH----HHHHHhC----CCHHHHHHHHH----HHHHHHHHHh
Confidence 46777788877776655 333 4999995 99999986543 4444444443
No 82
>PRK09480 slmA division inhibitor protein; Provisional
Probab=20.27 E-value=61 Score=27.32 Aligned_cols=36 Identities=6% Similarity=0.178 Sum_probs=28.8
Q ss_pred HHHHhcCCCCCCHHHHHHHHHHHHhcCCCCCCceeeccccch
Q 043602 86 EDLYRRGTRTPSADQIQHITAQLRRFGKIEGKNVFYWFQNHK 127 (352)
Q Consensus 86 E~lF~~~~~YPs~e~RqqIA~qL~~~G~LsEsqVqvWFQNRR 127 (352)
.++|.... . ....+.+||+..+ |+..-++++|.|+.
T Consensus 20 ~~l~~~~~-G-~~~ti~~Ia~~ag----vs~gt~Y~~F~~K~ 55 (194)
T PRK09480 20 AQMLESPP-G-ERITTAKLAARVG----VSEAALYRHFPSKA 55 (194)
T ss_pred HHHHHhcC-C-CccCHHHHHHHhC----CCHhHHHHHCCCHH
Confidence 44565554 4 6777889999995 99999999999977
No 83
>PRK12515 RNA polymerase sigma factor; Provisional
Probab=20.10 E-value=79 Score=27.26 Aligned_cols=40 Identities=10% Similarity=0.147 Sum_probs=29.5
Q ss_pred CCCCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHhcCCCCCCceeeccc
Q 043602 75 WNPTPEQLRTLEDLYRRGTRTPSADQIQHITAQLRRFGKIEGKNVFYWFQ 124 (352)
Q Consensus 75 w~FT~eQLqiLE~lF~~~~~YPs~e~RqqIA~qL~~~G~LsEsqVqvWFQ 124 (352)
-.+++.|.++|+-.|-.+. + .++||+.|+ |+...|++-..
T Consensus 130 ~~L~~~~r~vl~l~~~~~~--s----~~eIA~~lg----is~~tV~~~l~ 169 (189)
T PRK12515 130 AKLSPAHREIIDLVYYHEK--S----VEEVGEIVG----IPESTVKTRMF 169 (189)
T ss_pred HhCCHHHHHHHHHHHHcCC--C----HHHHHHHHC----cCHHHHHHHHH
Confidence 3567778888887777666 2 345999996 99999986653
Done!