Query psy16978
Match_columns 154
No_of_seqs 169 out of 1441
Neff 7.8
Searched_HMMs 46136
Date Fri Aug 16 18:34:50 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy16978.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/16978hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG0488|consensus 99.8 1.9E-19 4E-24 145.6 4.1 70 35-104 169-238 (309)
2 KOG0843|consensus 99.8 2.1E-19 4.6E-24 132.9 2.5 63 37-99 101-163 (197)
3 KOG3802|consensus 99.7 2.1E-18 4.5E-23 141.1 7.1 97 1-97 246-353 (398)
4 KOG0489|consensus 99.7 4.7E-19 1E-23 140.6 2.7 67 33-99 154-220 (261)
5 KOG0842|consensus 99.7 2E-18 4.3E-23 138.3 5.9 64 35-98 150-213 (307)
6 KOG0484|consensus 99.7 1.7E-18 3.6E-23 117.7 3.8 65 35-99 14-78 (125)
7 KOG0850|consensus 99.7 2.9E-18 6.4E-23 131.1 4.9 65 34-98 118-182 (245)
8 KOG0487|consensus 99.7 8.2E-18 1.8E-22 134.8 4.9 64 36-99 233-296 (308)
9 KOG2251|consensus 99.7 1.5E-17 3.3E-22 126.6 5.3 68 33-100 32-99 (228)
10 KOG0485|consensus 99.7 1E-17 2.3E-22 127.2 4.1 65 34-98 100-164 (268)
11 KOG0492|consensus 99.7 3.1E-17 6.8E-22 123.8 6.0 62 38-99 144-205 (246)
12 PF00046 Homeobox: Homeobox do 99.7 1.4E-17 3.1E-22 102.8 3.4 57 39-95 1-57 (57)
13 KOG1168|consensus 99.7 2.9E-17 6.2E-22 129.5 3.5 96 1-96 260-367 (385)
14 KOG0494|consensus 99.6 2.5E-16 5.4E-21 122.5 4.1 62 38-99 140-202 (332)
15 KOG0483|consensus 99.6 1.9E-15 4.2E-20 114.9 7.9 63 38-100 50-112 (198)
16 KOG0848|consensus 99.6 2E-16 4.4E-21 123.4 2.1 61 39-99 200-260 (317)
17 KOG4577|consensus 99.6 1.4E-15 2.9E-20 120.1 6.1 87 14-100 143-229 (383)
18 COG5576 Homeodomain-containing 99.6 1.6E-15 3.5E-20 111.7 6.1 67 32-98 45-111 (156)
19 TIGR01565 homeo_ZF_HD homeobox 99.6 3.6E-15 7.9E-20 92.3 5.7 53 38-90 1-57 (58)
20 smart00389 HOX Homeodomain. DN 99.6 1.8E-15 3.9E-20 92.7 3.5 56 39-94 1-56 (56)
21 KOG0493|consensus 99.6 1.3E-15 2.8E-20 118.7 3.3 58 39-96 247-304 (342)
22 KOG0491|consensus 99.6 3E-16 6.5E-21 114.7 -0.2 64 36-99 98-161 (194)
23 cd00086 homeodomain Homeodomai 99.6 2.8E-15 6.1E-20 92.6 3.8 57 39-95 1-57 (59)
24 KOG0486|consensus 99.5 2E-14 4.4E-19 114.5 3.5 64 37-100 111-174 (351)
25 KOG0844|consensus 99.5 1.7E-14 3.6E-19 114.7 2.2 62 39-100 182-243 (408)
26 KOG0847|consensus 99.4 5.1E-14 1.1E-18 107.5 1.0 64 35-98 164-227 (288)
27 KOG0490|consensus 99.2 5.1E-12 1.1E-16 97.7 3.1 64 35-98 57-120 (235)
28 KOG0775|consensus 99.1 8E-11 1.7E-15 92.5 3.7 50 45-94 183-232 (304)
29 KOG0849|consensus 99.1 9.9E-11 2.1E-15 96.7 3.2 65 34-98 172-236 (354)
30 KOG0774|consensus 99.0 4.3E-10 9.2E-15 88.1 6.5 95 3-97 145-250 (334)
31 PF05920 Homeobox_KN: Homeobox 98.6 8.3E-09 1.8E-13 59.3 0.1 34 59-92 7-40 (40)
32 KOG2252|consensus 98.4 1.8E-07 3.8E-12 80.0 3.8 59 35-93 417-475 (558)
33 KOG0490|consensus 98.1 2.4E-06 5.3E-11 65.9 3.8 62 35-96 150-211 (235)
34 KOG1146|consensus 97.5 6.4E-05 1.4E-09 70.1 2.7 60 37-96 902-961 (1406)
35 PF11569 Homez: Homeodomain le 97.1 0.00013 2.8E-09 44.7 0.2 41 50-90 10-50 (56)
36 KOG0773|consensus 97.0 0.00078 1.7E-08 55.4 4.3 61 38-98 239-302 (342)
37 KOG3623|consensus 95.5 0.0089 1.9E-07 53.5 2.3 48 50-97 568-615 (1007)
38 PF04218 CENP-B_N: CENP-B N-te 94.8 0.033 7E-07 33.6 2.8 46 39-89 1-46 (53)
39 PF04967 HTH_10: HTH DNA bindi 78.1 2.6 5.6E-05 25.4 2.5 39 45-83 1-41 (53)
40 PF04545 Sigma70_r4: Sigma-70, 74.6 2.1 4.7E-05 24.8 1.5 39 44-87 4-42 (50)
41 PF01527 HTH_Tnp_1: Transposas 72.9 1.2 2.5E-05 28.0 0.0 44 40-87 2-45 (76)
42 PF10668 Phage_terminase: Phag 69.4 1.7 3.7E-05 27.0 0.2 20 67-86 24-43 (60)
43 PF09607 BrkDBD: Brinker DNA-b 69.1 5 0.00011 24.7 2.2 44 42-87 3-47 (58)
44 cd00569 HTH_Hin_like Helix-tur 62.1 13 0.00028 18.3 2.9 37 45-86 6-42 (42)
45 cd06171 Sigma70_r4 Sigma70, re 58.3 3.8 8.2E-05 22.9 0.3 39 45-88 11-49 (55)
46 COG3413 Predicted DNA binding 55.3 11 0.00025 28.7 2.6 39 44-82 155-195 (215)
47 KOG3623|consensus 51.0 18 0.00039 33.3 3.3 62 34-95 622-683 (1007)
48 PRK03975 tfx putative transcri 50.8 34 0.00074 24.8 4.3 49 42-96 4-52 (141)
49 PF08281 Sigma70_r4_2: Sigma-7 48.8 9.9 0.00021 22.1 1.1 38 45-87 11-48 (54)
50 KOG1146|consensus 48.1 17 0.00038 35.3 3.0 60 38-97 705-764 (1406)
51 PRK10072 putative transcriptio 47.3 50 0.0011 22.2 4.4 42 44-92 32-73 (96)
52 PF06056 Terminase_5: Putative 45.5 8.5 0.00018 23.5 0.4 25 68-94 16-40 (58)
53 cd04761 HTH_MerR-SF Helix-Turn 45.3 6.9 0.00015 22.1 -0.0 22 68-89 3-24 (49)
54 PF13411 MerR_1: MerR HTH fami 43.0 9 0.0002 23.3 0.2 21 68-88 3-23 (69)
55 PF13518 HTH_28: Helix-turn-he 42.9 9.9 0.00022 21.7 0.4 20 68-87 15-34 (52)
56 TIGR03879 near_KaiC_dom probab 41.3 4.9 0.00011 25.9 -1.2 32 57-88 24-55 (73)
57 PF13384 HTH_23: Homeodomain-l 39.3 9.1 0.0002 21.8 -0.2 22 66-87 18-39 (50)
58 PRK09413 IS2 repressor TnpA; R 37.4 1.4E+02 0.003 20.6 7.5 43 42-88 10-52 (121)
59 PF00424 REV: REV protein (ant 37.4 96 0.0021 20.8 4.5 39 50-102 14-52 (91)
60 PRK09646 RNA polymerase sigma 37.3 27 0.00058 25.9 2.1 29 67-95 160-188 (194)
61 PF00376 MerR: MerR family reg 36.4 12 0.00026 20.7 0.0 18 69-86 3-20 (38)
62 PRK06759 RNA polymerase factor 36.2 34 0.00074 23.9 2.4 27 66-92 123-149 (154)
63 PF13443 HTH_26: Cro/C1-type H 36.2 11 0.00024 22.5 -0.2 26 67-92 12-37 (63)
64 PHA02955 hypothetical protein; 35.3 61 0.0013 25.2 3.7 42 48-89 61-103 (213)
65 PF13936 HTH_38: Helix-turn-he 34.9 20 0.00043 20.3 0.8 39 43-86 3-41 (44)
66 cd04764 HTH_MlrA-like_sg1 Heli 34.7 14 0.00031 22.4 0.2 21 68-88 3-23 (67)
67 PRK09652 RNA polymerase sigma 33.9 28 0.00061 24.8 1.7 29 67-95 146-174 (182)
68 PRK11924 RNA polymerase sigma 33.6 28 0.0006 24.8 1.6 29 67-95 143-171 (179)
69 PRK12514 RNA polymerase sigma 33.1 20 0.00044 26.0 0.8 28 67-94 147-174 (179)
70 PF08280 HTH_Mga: M protein tr 32.7 41 0.00088 20.2 2.0 33 48-84 6-38 (59)
71 PRK12512 RNA polymerase sigma 32.6 26 0.00056 25.5 1.3 30 67-96 149-178 (184)
72 PF00196 GerE: Bacterial regul 32.5 27 0.00059 20.6 1.2 45 44-94 3-47 (58)
73 PRK09480 slmA division inhibit 32.4 31 0.00066 25.0 1.7 37 54-91 20-56 (194)
74 PRK12526 RNA polymerase sigma 32.1 44 0.00094 25.1 2.5 29 67-95 171-199 (206)
75 PRK04217 hypothetical protein; 31.8 52 0.0011 22.8 2.6 48 41-93 39-86 (110)
76 COG2963 Transposase and inacti 31.8 68 0.0015 21.7 3.3 42 42-87 5-47 (116)
77 cd04763 HTH_MlrA-like Helix-Tu 31.2 15 0.00033 22.5 -0.1 21 68-88 3-23 (68)
78 PF00157 Pou: Pou domain - N-t 30.9 22 0.00047 23.0 0.6 27 1-27 47-73 (75)
79 cd04762 HTH_MerR-trunc Helix-T 30.7 16 0.00036 20.0 -0.0 24 68-91 3-26 (49)
80 KOG3755|consensus 30.6 8.9 0.00019 34.3 -1.6 61 37-97 691-758 (769)
81 COG4367 Uncharacterized protei 30.4 52 0.0011 22.1 2.3 38 45-82 3-40 (97)
82 PRK09642 RNA polymerase sigma 30.3 22 0.00048 25.2 0.6 28 68-95 125-152 (160)
83 PRK00118 putative DNA-binding 29.7 42 0.00091 23.0 1.9 49 45-98 18-66 (104)
84 TIGR02937 sigma70-ECF RNA poly 28.8 31 0.00067 23.4 1.1 27 67-93 128-154 (158)
85 cd01104 HTH_MlrA-CarA Helix-Tu 28.4 21 0.00045 21.6 0.2 20 68-87 3-22 (68)
86 KOG0773|consensus 28.3 38 0.00083 27.7 1.7 44 55-98 114-157 (342)
87 PF04936 DUF658: Protein of un 27.8 16 0.00035 27.3 -0.5 32 67-98 16-47 (186)
88 PRK09639 RNA polymerase sigma 27.5 54 0.0012 23.2 2.3 29 67-95 129-157 (166)
89 cd00131 PAX Paired Box domain 26.9 2.3E+02 0.0049 19.8 5.5 45 44-88 75-126 (128)
90 COG1905 NuoE NADH:ubiquinone o 26.8 98 0.0021 23.0 3.5 36 47-82 25-60 (160)
91 cd01392 HTH_LacI Helix-turn-he 26.8 16 0.00034 20.9 -0.6 21 70-90 2-22 (52)
92 PRK12518 RNA polymerase sigma 26.3 31 0.00066 24.8 0.8 32 64-95 135-166 (175)
93 PRK06986 fliA flagellar biosyn 26.3 38 0.00081 26.0 1.3 29 67-95 202-230 (236)
94 PRK05602 RNA polymerase sigma 25.6 38 0.00081 24.7 1.1 29 67-95 146-174 (186)
95 PF01381 HTH_3: Helix-turn-hel 25.3 23 0.00051 20.3 -0.0 24 68-91 12-35 (55)
96 cd02413 40S_S3_KH K homology R 25.2 70 0.0015 20.7 2.3 20 68-87 56-75 (81)
97 TIGR02985 Sig70_bacteroi1 RNA 25.0 31 0.00068 24.0 0.6 26 67-92 131-156 (161)
98 PRK12519 RNA polymerase sigma 24.7 37 0.0008 24.9 1.0 31 65-95 157-187 (194)
99 TIGR02939 RpoE_Sigma70 RNA pol 24.6 30 0.00065 25.1 0.4 30 66-95 155-184 (190)
100 PRK09047 RNA polymerase factor 24.5 1E+02 0.0022 21.6 3.2 27 68-94 125-151 (161)
101 PRK12543 RNA polymerase sigma 24.1 51 0.0011 23.9 1.6 32 67-98 135-166 (179)
102 PRK09644 RNA polymerase sigma 24.0 34 0.00074 24.4 0.6 29 67-95 126-154 (165)
103 smart00421 HTH_LUXR helix_turn 23.9 42 0.00092 18.7 1.0 38 44-87 3-40 (58)
104 TIGR02948 SigW_bacill RNA poly 23.6 33 0.00071 24.9 0.5 30 66-95 153-182 (187)
105 PRK12515 RNA polymerase sigma 23.4 89 0.0019 22.8 2.8 29 67-95 149-177 (189)
106 smart00422 HTH_MERR helix_turn 23.1 30 0.00066 20.9 0.2 20 68-87 3-22 (70)
107 PRK09648 RNA polymerase sigma 23.0 48 0.0011 24.2 1.3 29 66-94 156-184 (189)
108 PRK08301 sporulation sigma fac 22.9 66 0.0014 24.5 2.1 30 66-95 199-228 (234)
109 PRK06930 positive control sigm 21.9 92 0.002 23.0 2.6 46 45-95 115-160 (170)
110 smart00595 MADF subfamily of S 21.8 55 0.0012 20.9 1.3 31 69-99 31-61 (89)
111 PRK05988 formate dehydrogenase 21.6 1.4E+02 0.0029 21.9 3.4 35 48-82 24-58 (156)
112 PF08452 DNAP_B_exo_N: DNA pol 21.4 31 0.00067 16.8 -0.0 10 82-91 5-14 (22)
113 TIGR03070 couple_hipB transcri 21.2 35 0.00077 19.4 0.2 23 68-90 18-40 (58)
114 cd00093 HTH_XRE Helix-turn-hel 21.0 35 0.00077 18.4 0.2 22 69-90 16-37 (58)
115 TIGR01764 excise DNA binding d 21.0 33 0.00072 18.8 0.0 23 68-90 4-26 (49)
116 PF08279 HTH_11: HTH domain; 20.4 90 0.002 17.9 1.9 16 68-83 18-33 (55)
117 TIGR02947 SigH_actino RNA poly 20.3 49 0.0011 24.3 0.9 31 65-95 147-177 (193)
118 TIGR02959 SigZ RNA polymerase 20.1 1.1E+02 0.0024 21.9 2.7 28 67-94 118-145 (170)
No 1
>KOG0488|consensus
Probab=99.77 E-value=1.9e-19 Score=145.64 Aligned_cols=70 Identities=41% Similarity=0.636 Sum_probs=63.5
Q ss_pred CCCCCCCCCCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCCcccceeeeccchhhHHHhHHHHHHHH
Q psy16978 35 GCPRRRGRQTYTRFQTLELEKEFHFNHYLTRRRRIEIAHALCLTERQIKIWFQNRRMKLKKELRAVKEIN 104 (154)
Q Consensus 35 ~~~~rr~R~~~t~~q~~~Le~~F~~~~~p~~~~~~~La~~l~l~~~qV~~WFqNrRak~kr~~~~~~~~~ 104 (154)
..++|+.||.||..|+..||+.|++.+|.+..+|.+||..|||+..||++||||||+||||......+..
T Consensus 169 pkK~RksRTaFT~~Ql~~LEkrF~~QKYLS~~DR~~LA~~LgLTdaQVKtWfQNRRtKWKrq~a~g~~~~ 238 (309)
T KOG0488|consen 169 PKKRRKSRTAFSDHQLFELEKRFEKQKYLSVADRIELAASLGLTDAQVKTWFQNRRTKWKRQTAEGGELL 238 (309)
T ss_pred CcccccchhhhhHHHHHHHHHHHHHhhcccHHHHHHHHHHcCCchhhHHHHHhhhhHHHHHHHHhhhccc
Confidence 3567788999999999999999999999999999999999999999999999999999999776644333
No 2
>KOG0843|consensus
Probab=99.76 E-value=2.1e-19 Score=132.87 Aligned_cols=63 Identities=40% Similarity=0.625 Sum_probs=60.1
Q ss_pred CCCCCCCCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCCcccceeeeccchhhHHHhHHH
Q psy16978 37 PRRRGRQTYTRFQTLELEKEFHFNHYLTRRRRIEIAHALCLTERQIKIWFQNRRMKLKKELRA 99 (154)
Q Consensus 37 ~~rr~R~~~t~~q~~~Le~~F~~~~~p~~~~~~~La~~l~l~~~qV~~WFqNrRak~kr~~~~ 99 (154)
++||.||.|+.+|+..||..|+.+.|....+|+.||..|+|++.||+|||||||.|.||...+
T Consensus 101 ~~kr~RT~ft~~Ql~~LE~~F~~~~Yvvg~eR~~LA~~L~LsetQVkvWFQNRRtk~kr~~~e 163 (197)
T KOG0843|consen 101 RPKRIRTAFTPEQLLKLEHAFEGNQYVVGAERKQLAQSLSLSETQVKVWFQNRRTKHKRMQQE 163 (197)
T ss_pred CCCccccccCHHHHHHHHHHHhcCCeeechHHHHHHHHcCCChhHhhhhhhhhhHHHHHHHHH
Confidence 789999999999999999999999999999999999999999999999999999999986544
No 3
>KOG3802|consensus
Probab=99.75 E-value=2.1e-18 Score=141.06 Aligned_cols=97 Identities=24% Similarity=0.291 Sum_probs=82.1
Q ss_pred CCccccccchhhHHHHHhhhHHHHhhhhccC--CC---------CCCCCCCCCCCCCHHHHHHHHHHhhhcCCCCHHHHH
Q psy16978 1 MCFPLEIRFTHQLVIVLNVHFAKMLCQLKQS--GP---------NGCPRRRGRQTYTRFQTLELEKEFHFNHYLTRRRRI 69 (154)
Q Consensus 1 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~--~~---------~~~~~rr~R~~~t~~q~~~Le~~F~~~~~p~~~~~~ 69 (154)
||||+-+....-++-.|.+=+.+|+.+.+.. +. ...++||+||.|....+..||.+|.+|+.|+..++.
T Consensus 246 IcRFEALqLSFKNMCKLKPLL~KWLeEAes~~~~~~~~~~e~i~a~~RkRKKRTSie~~vr~aLE~~F~~npKPt~qEIt 325 (398)
T KOG3802|consen 246 ICRFEALQLSFKNMCKLKPLLEKWLEEAESRESTGSPNSIEKIGAQSRKRKKRTSIEVNVRGALEKHFLKNPKPTSQEIT 325 (398)
T ss_pred hhHhHhhccCHHHHhhhHHHHHHHHHHHhcccccCCCCCHHHhhccccccccccceeHHHHHHHHHHHHhCCCCCHHHHH
Confidence 7999888777777666666666666666552 11 235788999999999999999999999999999999
Q ss_pred HHHHHhCCCcccceeeeccchhhHHHhH
Q psy16978 70 EIAHALCLTERQIKIWFQNRRMKLKKEL 97 (154)
Q Consensus 70 ~La~~l~l~~~qV~~WFqNrRak~kr~~ 97 (154)
.||.+|+|...+|+|||||||.|.||..
T Consensus 326 ~iA~~L~leKEVVRVWFCNRRQkeKR~~ 353 (398)
T KOG3802|consen 326 HIAESLQLEKEVVRVWFCNRRQKEKRIT 353 (398)
T ss_pred HHHHHhccccceEEEEeeccccccccCC
Confidence 9999999999999999999999999853
No 4
>KOG0489|consensus
Probab=99.74 E-value=4.7e-19 Score=140.58 Aligned_cols=67 Identities=73% Similarity=1.084 Sum_probs=61.9
Q ss_pred CCCCCCCCCCCCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCCcccceeeeccchhhHHHhHHH
Q psy16978 33 PNGCPRRRGRQTYTRFQTLELEKEFHFNHYLTRRRRIEIAHALCLTERQIKIWFQNRRMKLKKELRA 99 (154)
Q Consensus 33 ~~~~~~rr~R~~~t~~q~~~Le~~F~~~~~p~~~~~~~La~~l~l~~~qV~~WFqNrRak~kr~~~~ 99 (154)
....+.||.||.||..|+..||+.|..|+|.+...|.+||..|.|+++||+|||||||+||||..+.
T Consensus 154 ~~~~~~kR~RtayT~~QllELEkEFhfN~YLtR~RRiEiA~~L~LtErQIKIWFQNRRMK~Kk~~k~ 220 (261)
T KOG0489|consen 154 ETGGKSKRRRTAFTRYQLLELEKEFHFNKYLTRSRRIEIAHALNLTERQIKIWFQNRRMKWKKENKA 220 (261)
T ss_pred cccCCCCCCCcccchhhhhhhhhhhccccccchHHHHHHHhhcchhHHHHHHHHHHHHHHHHHhhcc
Confidence 3445689999999999999999999999999999999999999999999999999999999986544
No 5
>KOG0842|consensus
Probab=99.74 E-value=2e-18 Score=138.31 Aligned_cols=64 Identities=39% Similarity=0.651 Sum_probs=59.8
Q ss_pred CCCCCCCCCCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCCcccceeeeccchhhHHHhHH
Q psy16978 35 GCPRRRGRQTYTRFQTLELEKEFHFNHYLTRRRRIEIAHALCLTERQIKIWFQNRRMKLKKELR 98 (154)
Q Consensus 35 ~~~~rr~R~~~t~~q~~~Le~~F~~~~~p~~~~~~~La~~l~l~~~qV~~WFqNrRak~kr~~~ 98 (154)
.+++||.|..|+..|+.+||+.|..++|++..||+.||..|+|+++||+|||||||-|.||+.+
T Consensus 150 ~~~kRKrRVLFSqAQV~ELERRFrqQRYLSAPERE~LA~~LrLT~TQVKIWFQNrRYK~KR~~~ 213 (307)
T KOG0842|consen 150 KRKKRKRRVLFSQAQVYELERRFRQQRYLSAPEREHLASSLRLTPTQVKIWFQNRRYKTKRQQK 213 (307)
T ss_pred cccccccccccchhHHHHHHHHHHhhhccccHhHHHHHHhcCCCchheeeeeecchhhhhhhhh
Confidence 4567788889999999999999999999999999999999999999999999999999998643
No 6
>KOG0484|consensus
Probab=99.73 E-value=1.7e-18 Score=117.65 Aligned_cols=65 Identities=45% Similarity=0.603 Sum_probs=60.4
Q ss_pred CCCCCCCCCCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCCcccceeeeccchhhHHHhHHH
Q psy16978 35 GCPRRRGRQTYTRFQTLELEKEFHFNHYLTRRRRIEIAHALCLTERQIKIWFQNRRMKLKKELRA 99 (154)
Q Consensus 35 ~~~~rr~R~~~t~~q~~~Le~~F~~~~~p~~~~~~~La~~l~l~~~qV~~WFqNrRak~kr~~~~ 99 (154)
.++.||-|+.||..||..||+.|....||++-.|++||..+.|++..|+|||||||+|.|++.+.
T Consensus 14 krKQRRIRTTFTS~QLkELErvF~ETHYPDIYTREEiA~kidLTEARVQVWFQNRRAKfRKQEr~ 78 (125)
T KOG0484|consen 14 KRKQRRIRTTFTSAQLKELERVFAETHYPDIYTREEIALKIDLTEARVQVWFQNRRAKFRKQERA 78 (125)
T ss_pred HHHhhhhhhhhhHHHHHHHHHHHHhhcCCcchhHHHHHHhhhhhHHHHHHHHHhhHHHHHHHHHH
Confidence 35667889999999999999999999999999999999999999999999999999999986554
No 7
>KOG0850|consensus
Probab=99.73 E-value=2.9e-18 Score=131.14 Aligned_cols=65 Identities=42% Similarity=0.661 Sum_probs=61.0
Q ss_pred CCCCCCCCCCCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCCcccceeeeccchhhHHHhHH
Q psy16978 34 NGCPRRRGRQTYTRFQTLELEKEFHFNHYLTRRRRIEIAHALCLTERQIKIWFQNRRMKLKKELR 98 (154)
Q Consensus 34 ~~~~~rr~R~~~t~~q~~~Le~~F~~~~~p~~~~~~~La~~l~l~~~qV~~WFqNrRak~kr~~~ 98 (154)
.+.|.|+.||.++.-||..|.+.|++++|+-..||.+||..|||+.+||+|||||||.|.||.++
T Consensus 118 k~KK~RKPRTIYSS~QLqaL~rRFQkTQYLALPERAeLAAsLGLTQTQVKIWFQNrRSK~KKl~k 182 (245)
T KOG0850|consen 118 KGKKVRKPRTIYSSLQLQALNRRFQQTQYLALPERAELAASLGLTQTQVKIWFQNRRSKFKKLKK 182 (245)
T ss_pred CcccccCCcccccHHHHHHHHHHHhhcchhcCcHHHHHHHHhCCchhHhhhhhhhhHHHHHHHHh
Confidence 34566788999999999999999999999999999999999999999999999999999998776
No 8
>KOG0487|consensus
Probab=99.71 E-value=8.2e-18 Score=134.83 Aligned_cols=64 Identities=59% Similarity=0.897 Sum_probs=60.3
Q ss_pred CCCCCCCCCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCCcccceeeeccchhhHHHhHHH
Q psy16978 36 CPRRRGRQTYTRFQTLELEKEFHFNHYLTRRRRIEIAHALCLTERQIKIWFQNRRMKLKKELRA 99 (154)
Q Consensus 36 ~~~rr~R~~~t~~q~~~Le~~F~~~~~p~~~~~~~La~~l~l~~~qV~~WFqNrRak~kr~~~~ 99 (154)
+..||+|..+|..|+..||+.|..|.|.+.+.|.+|++.|+|+++||+|||||||+|.||..++
T Consensus 233 ~~~RKKRcPYTK~QtlELEkEFlfN~YitkeKR~ElSr~lNLTeRQVKIWFQNRRMK~KK~~re 296 (308)
T KOG0487|consen 233 RRGRKKRCPYTKHQTLELEKEFLFNMYITKEKRLELSRTLNLTERQVKIWFQNRRMKEKKVNRE 296 (308)
T ss_pred cccccccCCchHHHHHHHHHHHHHHHHHhHHHHHHHHHhcccchhheeeeehhhhhHHhhhhhh
Confidence 4568889999999999999999999999999999999999999999999999999999997754
No 9
>KOG2251|consensus
Probab=99.70 E-value=1.5e-17 Score=126.63 Aligned_cols=68 Identities=34% Similarity=0.474 Sum_probs=63.3
Q ss_pred CCCCCCCCCCCCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCCcccceeeeccchhhHHHhHHHH
Q psy16978 33 PNGCPRRRGRQTYTRFQTLELEKEFHFNHYLTRRRRIEIAHALCLTERQIKIWFQNRRMKLKKELRAV 100 (154)
Q Consensus 33 ~~~~~~rr~R~~~t~~q~~~Le~~F~~~~~p~~~~~~~La~~l~l~~~qV~~WFqNrRak~kr~~~~~ 100 (154)
...++.||+||.|+..|+.+||..|.+.+||+...+++||.+|+|.+.+|+|||+|||+|+|++++..
T Consensus 32 ~~pRkqRRERTtFtr~QlevLe~LF~kTqYPDv~~rEelAlklnLpeSrVqVWFKNRRAK~r~qq~qq 99 (228)
T KOG2251|consen 32 SGPRKQRRERTTFTRKQLEVLEALFAKTQYPDVFMREELALKLNLPESRVQVWFKNRRAKCRRQQQQQ 99 (228)
T ss_pred ccchhcccccceecHHHHHHHHHHHHhhcCccHHHHHHHHHHhCCchhhhhhhhccccchhhHhhhhh
Confidence 45667889999999999999999999999999999999999999999999999999999999876653
No 10
>KOG0485|consensus
Probab=99.70 E-value=1e-17 Score=127.23 Aligned_cols=65 Identities=38% Similarity=0.679 Sum_probs=61.0
Q ss_pred CCCCCCCCCCCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCCcccceeeeccchhhHHHhHH
Q psy16978 34 NGCPRRRGRQTYTRFQTLELEKEFHFNHYLTRRRRIEIAHALCLTERQIKIWFQNRRMKLKKELR 98 (154)
Q Consensus 34 ~~~~~rr~R~~~t~~q~~~Le~~F~~~~~p~~~~~~~La~~l~l~~~qV~~WFqNrRak~kr~~~ 98 (154)
.+.++||.||+|+..|+..||..|+..+|.+..+|..||.+|.|++.||+|||||||.||||+..
T Consensus 100 g~~RKKktRTvFSraQV~qLEs~Fe~krYLSsaeRa~LA~sLqLTETQVKIWFQNRRnKwKRq~a 164 (268)
T KOG0485|consen 100 GDDRKKKTRTVFSRAQVFQLESTFELKRYLSSAERAGLAASLQLTETQVKIWFQNRRNKWKRQYA 164 (268)
T ss_pred cccccccchhhhhHHHHHHHHHHHHHHhhhhHHHHhHHHHhhhhhhhhhhhhhhhhhHHHHHHHh
Confidence 34578899999999999999999999999999999999999999999999999999999998653
No 11
>KOG0492|consensus
Probab=99.69 E-value=3.1e-17 Score=123.84 Aligned_cols=62 Identities=45% Similarity=0.678 Sum_probs=58.3
Q ss_pred CCCCCCCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCCcccceeeeccchhhHHHhHHH
Q psy16978 38 RRRGRQTYTRFQTLELEKEFHFNHYLTRRRRIEIAHALCLTERQIKIWFQNRRMKLKKELRA 99 (154)
Q Consensus 38 ~rr~R~~~t~~q~~~Le~~F~~~~~p~~~~~~~La~~l~l~~~qV~~WFqNrRak~kr~~~~ 99 (154)
-|+.|+.||..||..||+.|...+|.++.+|.+++..|.|+++||+|||||||+|.||.++.
T Consensus 144 nRkPRtPFTtqQLlaLErkfrekqYLSiaEraefSsSL~LTeTqVKIWFQNRRAKaKRlQea 205 (246)
T KOG0492|consen 144 NRKPRTPFTTQQLLALERKFREKQYLSIAERAEFSSSLELTETQVKIWFQNRRAKAKRLQEA 205 (246)
T ss_pred CCCCCCCCCHHHHHHHHHHHhHhhhhhHHHHHhhhhhhhhhhhheehhhhhhhHHHHHHHHH
Confidence 46789999999999999999999999999999999999999999999999999999986543
No 12
>PF00046 Homeobox: Homeobox domain not present here.; InterPro: IPR001356 The homeobox domain was first identified in a number of drosophila homeotic and segmentation proteins, but is now known to be well-conserved in many other animals, including vertebrates [, , ]. Hox genes encode homeodomain-containing transcriptional regulators that operate differential genetic programs along the anterior-posterior axis of animal bodies []. The domain binds DNA through a helix-turn-helix (HTH) structure. The HTH motif is characterised by two alpha-helices, which make intimate contacts with the DNA and are joined by a short turn. The second helix binds to DNA via a number of hydrogen bonds and hydrophobic interactions, which occur between specific side chains and the exposed bases and thymine methyl groups within the major groove of the DNA []. The first helix helps to stabilise the structure. The motif is very similar in sequence and structure in a wide range of DNA-binding proteins (e.g., cro and repressor proteins, homeotic proteins, etc.). One of the principal differences between HTH motifs in these different proteins arises from the stereo-chemical requirement for glycine in the turn which is needed to avoid steric interference of the beta-carbon with the main chain: for cro and repressor proteins the glycine appears to be mandatory, while for many of the homeotic and other DNA-binding proteins the requirement is relaxed.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0043565 sequence-specific DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 2DA3_A 1LFB_A 2LFB_A 2ECB_A 2DA5_A 3D1N_O 3A03_A 2XSD_C 3CMY_A 1AHD_P ....
Probab=99.69 E-value=1.4e-17 Score=102.82 Aligned_cols=57 Identities=49% Similarity=0.672 Sum_probs=55.0
Q ss_pred CCCCCCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCCcccceeeeccchhhHHH
Q psy16978 39 RRGRQTYTRFQTLELEKEFHFNHYLTRRRRIEIAHALCLTERQIKIWFQNRRMKLKK 95 (154)
Q Consensus 39 rr~R~~~t~~q~~~Le~~F~~~~~p~~~~~~~La~~l~l~~~qV~~WFqNrRak~kr 95 (154)
|++|+.|+.+|+..|+..|..++||+..++..||..+||+..+|++||+|+|+++|+
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 578999999999999999999999999999999999999999999999999999885
No 13
>KOG1168|consensus
Probab=99.67 E-value=2.9e-17 Score=129.51 Aligned_cols=96 Identities=23% Similarity=0.366 Sum_probs=85.4
Q ss_pred CCccccccchhhHHHHHhhhHHHHhhhhccC------CC------CCCCCCCCCCCCCHHHHHHHHHHhhhcCCCCHHHH
Q psy16978 1 MCFPLEIRFTHQLVIVLNVHFAKMLCQLKQS------GP------NGCPRRRGRQTYTRFQTLELEKEFHFNHYLTRRRR 68 (154)
Q Consensus 1 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~------~~------~~~~~rr~R~~~t~~q~~~Le~~F~~~~~p~~~~~ 68 (154)
||||+.++..|++++.|.+.+..|+.+.... .+ ++..+||+||.+.+.+.+.||.+|...+.|+.+.+
T Consensus 260 ICRFESLTLSHNNMiALKPILqaWLEeAE~a~keK~~~pd~~~l~~~~ekKRKRTSIAAPEKRsLEayFavQPRPS~EkI 339 (385)
T KOG1168|consen 260 ICRFESLTLSHNNMIALKPILQAWLEEAEAAMKEKDTKPDINELLPGGEKKRKRTSIAAPEKRSLEAYFAVQPRPSGEKI 339 (385)
T ss_pred eeeeeeeccccCcchhhhHHHHHHHHHHHHHHHhhccCCchhhccCccccccccccccCcccccHHHHhccCCCCchhHH
Confidence 7999999999999999988888888765221 11 34568999999999999999999999999999999
Q ss_pred HHHHHHhCCCcccceeeeccchhhHHHh
Q psy16978 69 IEIAHALCLTERQIKIWFQNRRMKLKKE 96 (154)
Q Consensus 69 ~~La~~l~l~~~qV~~WFqNrRak~kr~ 96 (154)
..||.+|.|.+..|+|||||.|.|.||.
T Consensus 340 AaIAekLDLKKNVVRVWFCNQRQKQKRm 367 (385)
T KOG1168|consen 340 AAIAEKLDLKKNVVRVWFCNQRQKQKRM 367 (385)
T ss_pred HHHHHhhhhhhceEEEEeeccHHHHHHh
Confidence 9999999999999999999999998874
No 14
>KOG0494|consensus
Probab=99.62 E-value=2.5e-16 Score=122.52 Aligned_cols=62 Identities=40% Similarity=0.609 Sum_probs=57.7
Q ss_pred CCCC-CCCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCCcccceeeeccchhhHHHhHHH
Q psy16978 38 RRRG-RQTYTRFQTLELEKEFHFNHYLTRRRRIEIAHALCLTERQIKIWFQNRRMKLKKELRA 99 (154)
Q Consensus 38 ~rr~-R~~~t~~q~~~Le~~F~~~~~p~~~~~~~La~~l~l~~~qV~~WFqNrRak~kr~~~~ 99 (154)
+||. ||.||..|+..||+.|++..||+...|+-||..+.|.+.+|+|||||||+||||..+.
T Consensus 140 kRRh~RTiFT~~Qle~LEkaFkeaHYPDv~Are~la~ktelpEDRIqVWfQNRRAKWRk~Ek~ 202 (332)
T KOG0494|consen 140 KRRHFRTIFTSYQLEELEKAFKEAHYPDVYAREMLADKTELPEDRIQVWFQNRRAKWRKTEKR 202 (332)
T ss_pred ccccccchhhHHHHHHHHHHHhhccCccHHHHHHHhhhccCchhhhhHHhhhhhHHhhhhhhh
Confidence 3444 8999999999999999999999999999999999999999999999999999987664
No 15
>KOG0483|consensus
Probab=99.61 E-value=1.9e-15 Score=114.91 Aligned_cols=63 Identities=32% Similarity=0.453 Sum_probs=57.7
Q ss_pred CCCCCCCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCCcccceeeeccchhhHHHhHHHH
Q psy16978 38 RRRGRQTYTRFQTLELEKEFHFNHYLTRRRRIEIAHALCLTERQIKIWFQNRRMKLKKELRAV 100 (154)
Q Consensus 38 ~rr~R~~~t~~q~~~Le~~F~~~~~p~~~~~~~La~~l~l~~~qV~~WFqNrRak~kr~~~~~ 100 (154)
...++.+|+.+|+..||..|+...+..+..+..||..|||.++||.|||||||||||.++...
T Consensus 50 ~~~kk~Rlt~eQ~~~LE~~F~~~~~L~p~~K~~LAk~LgL~pRQVavWFQNRRARwK~kqlE~ 112 (198)
T KOG0483|consen 50 GKGKKRRLTSEQVKFLEKSFESEKKLEPERKKKLAKELGLQPRQVAVWFQNRRARWKTKQLEK 112 (198)
T ss_pred cccccccccHHHHHHhHHhhccccccChHHHHHHHHhhCCChhHHHHHHhhccccccchhhhh
Confidence 455566799999999999999999999999999999999999999999999999999877655
No 16
>KOG0848|consensus
Probab=99.61 E-value=2e-16 Score=123.43 Aligned_cols=61 Identities=54% Similarity=0.827 Sum_probs=56.6
Q ss_pred CCCCCCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCCcccceeeeccchhhHHHhHHH
Q psy16978 39 RRGRQTYTRFQTLELEKEFHFNHYLTRRRRIEIAHALCLTERQIKIWFQNRRMKLKKELRA 99 (154)
Q Consensus 39 rr~R~~~t~~q~~~Le~~F~~~~~p~~~~~~~La~~l~l~~~qV~~WFqNrRak~kr~~~~ 99 (154)
-+-|.++|..|+..||+.|..++|.++..+.+||..|||+++||+|||||||+|+||.++.
T Consensus 200 DKYRvVYTDhQRLELEKEfh~SryITirRKSELA~~LgLsERQVKIWFQNRRAKERK~nKK 260 (317)
T KOG0848|consen 200 DKYRVVYTDHQRLELEKEFHTSRYITIRRKSELAATLGLSERQVKIWFQNRRAKERKDNKK 260 (317)
T ss_pred cceeEEecchhhhhhhhhhccccceeeehhHHHHHhhCccHhhhhHhhhhhhHHHHHHHHH
Confidence 3458899999999999999999999999999999999999999999999999999986554
No 17
>KOG4577|consensus
Probab=99.60 E-value=1.4e-15 Score=120.05 Aligned_cols=87 Identities=22% Similarity=0.279 Sum_probs=70.1
Q ss_pred HHHHhhhHHHHhhhhccCCCCCCCCCCCCCCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCCcccceeeeccchhhH
Q psy16978 14 VIVLNVHFAKMLCQLKQSGPNGCPRRRGRQTYTRFQTLELEKEFHFNHYLTRRRRIEIAHALCLTERQIKIWFQNRRMKL 93 (154)
Q Consensus 14 ~~~~~~~~~~~~~~~~~~~~~~~~~rr~R~~~t~~q~~~Le~~F~~~~~p~~~~~~~La~~l~l~~~qV~~WFqNrRak~ 93 (154)
..+....++..-.....+-.++..-||+||.+|+.|+..|..+|...+.|....|+.|+..+||.-++|||||||||||.
T Consensus 143 rLvCK~DYE~Ak~k~~~~l~gd~~nKRPRTTItAKqLETLK~AYn~SpKPARHVREQLsseTGLDMRVVQVWFQNRRAKE 222 (383)
T KOG4577|consen 143 RLVCKDDYETAKQKHCNELEGDASNKRPRTTITAKQLETLKQAYNTSPKPARHVREQLSSETGLDMRVVQVWFQNRRAKE 222 (383)
T ss_pred eeehhhhHHHHHhccccccccccccCCCcceeeHHHHHHHHHHhcCCCchhHHHHHHhhhccCcceeehhhhhhhhhHHH
Confidence 34445555433222222223566779999999999999999999999999999999999999999999999999999999
Q ss_pred HHhHHHH
Q psy16978 94 KKELRAV 100 (154)
Q Consensus 94 kr~~~~~ 100 (154)
||.++..
T Consensus 223 KRLKKDA 229 (383)
T KOG4577|consen 223 KRLKKDA 229 (383)
T ss_pred Hhhhhhc
Confidence 9877643
No 18
>COG5576 Homeodomain-containing transcription factor [Transcription]
Probab=99.60 E-value=1.6e-15 Score=111.68 Aligned_cols=67 Identities=33% Similarity=0.538 Sum_probs=60.9
Q ss_pred CCCCCCCCCCCCCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCCcccceeeeccchhhHHHhHH
Q psy16978 32 GPNGCPRRRGRQTYTRFQTLELEKEFHFNHYLTRRRRIEIAHALCLTERQIKIWFQNRRMKLKKELR 98 (154)
Q Consensus 32 ~~~~~~~rr~R~~~t~~q~~~Le~~F~~~~~p~~~~~~~La~~l~l~~~qV~~WFqNrRak~kr~~~ 98 (154)
....+..+++|++.+..|+.+|++.|+.++||+...+..|+..++|+++.|++||||+|++.|+...
T Consensus 45 ~~~s~~~~~~r~R~t~~Q~~vL~~~F~i~p~Ps~~~r~~L~~~lnm~~ksVqIWFQNkR~~~k~~~~ 111 (156)
T COG5576 45 QDGSSPPKSKRRRTTDEQLMVLEREFEINPYPSSITRIKLSLLLNMPPKSVQIWFQNKRAKEKKKRS 111 (156)
T ss_pred ccCCCcCcccceechHHHHHHHHHHhccCCCCCHHHHHHHHHhcCCChhhhhhhhchHHHHHHHhcc
Confidence 3445567888888999999999999999999999999999999999999999999999999997544
No 19
>TIGR01565 homeo_ZF_HD homeobox domain, ZF-HD class. This model represents a class of homoebox domain that differs substantially from the typical homoebox domain described in pfam model pfam00046. It is found in both C4 and C3 plants.
Probab=99.58 E-value=3.6e-15 Score=92.34 Aligned_cols=53 Identities=19% Similarity=0.345 Sum_probs=50.8
Q ss_pred CCCCCCCCCHHHHHHHHHHhhhcCC----CCHHHHHHHHHHhCCCcccceeeeccch
Q psy16978 38 RRRGRQTYTRFQTLELEKEFHFNHY----LTRRRRIEIAHALCLTERQIKIWFQNRR 90 (154)
Q Consensus 38 ~rr~R~~~t~~q~~~Le~~F~~~~~----p~~~~~~~La~~l~l~~~qV~~WFqNrR 90 (154)
+||.||.||.+|+..|+..|+.++| |+..++.+||..+||++++|++||||-+
T Consensus 1 ~kR~RT~Ft~~Q~~~Le~~fe~~~y~~~~~~~~~r~~la~~lgl~~~vvKVWfqN~k 57 (58)
T TIGR01565 1 KKRRRTKFTAEQKEKMRDFAEKLGWKLKDKRREEVREFCEEIGVTRKVFKVWMHNNK 57 (58)
T ss_pred CCCCCCCCCHHHHHHHHHHHHHcCCCCCCCCHHHHHHHHHHhCCCHHHeeeecccCC
Confidence 4789999999999999999999999 9999999999999999999999999964
No 20
>smart00389 HOX Homeodomain. DNA-binding factors that are involved in the transcriptional regulation of key developmental processes
Probab=99.57 E-value=1.8e-15 Score=92.75 Aligned_cols=56 Identities=55% Similarity=0.795 Sum_probs=52.3
Q ss_pred CCCCCCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCCcccceeeeccchhhHH
Q psy16978 39 RRGRQTYTRFQTLELEKEFHFNHYLTRRRRIEIAHALCLTERQIKIWFQNRRMKLK 94 (154)
Q Consensus 39 rr~R~~~t~~q~~~Le~~F~~~~~p~~~~~~~La~~l~l~~~qV~~WFqNrRak~k 94 (154)
++.|+.|+..++..|+..|..++||+..++..||..+||+..+|++||+|+|++.+
T Consensus 1 ~k~r~~~~~~~~~~L~~~f~~~~~P~~~~~~~la~~~~l~~~qV~~WF~nrR~~~~ 56 (56)
T smart00389 1 RRKRTSFTPEQLEELEKEFQKNPYPSREEREELAAKLGLSERQVKVWFQNRRAKWK 56 (56)
T ss_pred CCCCCcCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHHCcCHHHHHHhHHHHhhccC
Confidence 35677899999999999999999999999999999999999999999999998753
No 21
>KOG0493|consensus
Probab=99.57 E-value=1.3e-15 Score=118.73 Aligned_cols=58 Identities=52% Similarity=0.781 Sum_probs=55.4
Q ss_pred CCCCCCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCCcccceeeeccchhhHHHh
Q psy16978 39 RRGRQTYTRFQTLELEKEFHFNHYLTRRRRIEIAHALCLTERQIKIWFQNRRMKLKKE 96 (154)
Q Consensus 39 rr~R~~~t~~q~~~Le~~F~~~~~p~~~~~~~La~~l~l~~~qV~~WFqNrRak~kr~ 96 (154)
||.||.|+.+||..|...|+.++|.+...|.+||.+|+|.+.||+|||||+|+|.||-
T Consensus 247 KRPRTAFtaeQL~RLK~EF~enRYlTEqRRQ~La~ELgLNEsQIKIWFQNKRAKiKKs 304 (342)
T KOG0493|consen 247 KRPRTAFTAEQLQRLKAEFQENRYLTEQRRQELAQELGLNESQIKIWFQNKRAKIKKS 304 (342)
T ss_pred cCccccccHHHHHHHHHHHhhhhhHHHHHHHHHHHHhCcCHHHhhHHhhhhhhhhhhc
Confidence 5679999999999999999999999999999999999999999999999999999863
No 22
>KOG0491|consensus
Probab=99.57 E-value=3e-16 Score=114.69 Aligned_cols=64 Identities=48% Similarity=0.773 Sum_probs=60.0
Q ss_pred CCCCCCCCCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCCcccceeeeccchhhHHHhHHH
Q psy16978 36 CPRRRGRQTYTRFQTLELEKEFHFNHYLTRRRRIEIAHALCLTERQIKIWFQNRRMKLKKELRA 99 (154)
Q Consensus 36 ~~~rr~R~~~t~~q~~~Le~~F~~~~~p~~~~~~~La~~l~l~~~qV~~WFqNrRak~kr~~~~ 99 (154)
.++++.|++|+..|+..|++.|+..+|.+..++.+||..|+|++.||+.||||||+|.||.++.
T Consensus 98 ~~r~K~Rtvfs~~ql~~l~~rFe~QrYLS~~e~~ELan~L~LS~~QVKTWFQNrRMK~Kk~~r~ 161 (194)
T KOG0491|consen 98 CRRRKARTVFSDPQLSGLEKRFERQRYLSTPERQELANALSLSETQVKTWFQNRRMKHKKQQRN 161 (194)
T ss_pred HHhhhhcccccCccccccHHHHhhhhhcccHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHHHhc
Confidence 4567889999999999999999999999999999999999999999999999999999987653
No 23
>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=99.56 E-value=2.8e-15 Score=92.62 Aligned_cols=57 Identities=60% Similarity=0.831 Sum_probs=53.8
Q ss_pred CCCCCCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCCcccceeeeccchhhHHH
Q psy16978 39 RRGRQTYTRFQTLELEKEFHFNHYLTRRRRIEIAHALCLTERQIKIWFQNRRMKLKK 95 (154)
Q Consensus 39 rr~R~~~t~~q~~~Le~~F~~~~~p~~~~~~~La~~l~l~~~qV~~WFqNrRak~kr 95 (154)
++.|..++..++..|+..|..++||+..++..||..+||+..+|++||+|+|++.++
T Consensus 1 ~~~r~~~~~~~~~~Le~~f~~~~~P~~~~~~~la~~~~l~~~qV~~WF~nrR~~~~~ 57 (59)
T cd00086 1 RRKRTRFTPEQLEELEKEFEKNPYPSREEREELAKELGLTERQVKIWFQNRRAKLKR 57 (59)
T ss_pred CCCCCcCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHHCcCHHHHHHHHHHHHHHHhc
Confidence 356788999999999999999999999999999999999999999999999999875
No 24
>KOG0486|consensus
Probab=99.48 E-value=2e-14 Score=114.49 Aligned_cols=64 Identities=41% Similarity=0.569 Sum_probs=60.0
Q ss_pred CCCCCCCCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCCcccceeeeccchhhHHHhHHHH
Q psy16978 37 PRRRGRQTYTRFQTLELEKEFHFNHYLTRRRRIEIAHALCLTERQIKIWFQNRRMKLKKELRAV 100 (154)
Q Consensus 37 ~~rr~R~~~t~~q~~~Le~~F~~~~~p~~~~~~~La~~l~l~~~qV~~WFqNrRak~kr~~~~~ 100 (154)
++||.|+.|+..|+..||..|+++.||+...|++||..++|++..|+|||.|||+||||..+..
T Consensus 111 KqrrQrthFtSqqlqele~tF~rNrypdMstrEEIavwtNlTE~rvrvwfknrrakwrkrErN~ 174 (351)
T KOG0486|consen 111 KQRRQRTHFTSQQLQELEATFQRNRYPDMSTREEIAVWTNLTEARVRVWFKNRRAKWRKRERNQ 174 (351)
T ss_pred hhhhhhhhhHHHHHHHHHHHHhhccCCccchhhHHHhhccccchhhhhhcccchhhhhhhhhhH
Confidence 5678899999999999999999999999999999999999999999999999999999876543
No 25
>KOG0844|consensus
Probab=99.47 E-value=1.7e-14 Score=114.68 Aligned_cols=62 Identities=53% Similarity=0.752 Sum_probs=58.5
Q ss_pred CCCCCCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCCcccceeeeccchhhHHHhHHHH
Q psy16978 39 RRGRQTYTRFQTLELEKEFHFNHYLTRRRRIEIAHALCLTERQIKIWFQNRRMKLKKELRAV 100 (154)
Q Consensus 39 rr~R~~~t~~q~~~Le~~F~~~~~p~~~~~~~La~~l~l~~~qV~~WFqNrRak~kr~~~~~ 100 (154)
||-||.||.+|+..||+.|-+..|.+...|.+||..|+|++..|+|||||||+|+||+.-.+
T Consensus 182 RRYRTAFTReQIaRLEKEFyrENYVSRprRcELAAaLNLPEtTIKVWFQNRRMKDKRQRlam 243 (408)
T KOG0844|consen 182 RRYRTAFTREQIARLEKEFYRENYVSRPRRCELAAALNLPETTIKVWFQNRRMKDKRQRLAM 243 (408)
T ss_pred HHHHhhhhHHHHHHHHHHHHHhccccCchhhhHHHhhCCCcceeehhhhhchhhhhhhhhhc
Confidence 67899999999999999999999999999999999999999999999999999999876544
No 26
>KOG0847|consensus
Probab=99.40 E-value=5.1e-14 Score=107.46 Aligned_cols=64 Identities=39% Similarity=0.684 Sum_probs=59.2
Q ss_pred CCCCCCCCCCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCCcccceeeeccchhhHHHhHH
Q psy16978 35 GCPRRRGRQTYTRFQTLELEKEFHFNHYLTRRRRIEIAHALCLTERQIKIWFQNRRMKLKKELR 98 (154)
Q Consensus 35 ~~~~rr~R~~~t~~q~~~Le~~F~~~~~p~~~~~~~La~~l~l~~~qV~~WFqNrRak~kr~~~ 98 (154)
+++++..|..|+..|+..|+..|+..+|+-..++.+||..+|+++.||+|||||||.||||+..
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 3566777889999999999999999999999999999999999999999999999999998654
No 27
>KOG0490|consensus
Probab=99.23 E-value=5.1e-12 Score=97.70 Aligned_cols=64 Identities=36% Similarity=0.398 Sum_probs=59.8
Q ss_pred CCCCCCCCCCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCCcccceeeeccchhhHHHhHH
Q psy16978 35 GCPRRRGRQTYTRFQTLELEKEFHFNHYLTRRRRIEIAHALCLTERQIKIWFQNRRMKLKKELR 98 (154)
Q Consensus 35 ~~~~rr~R~~~t~~q~~~Le~~F~~~~~p~~~~~~~La~~l~l~~~qV~~WFqNrRak~kr~~~ 98 (154)
..+.|+.|+.|+..|+..|++.|+..+||+...++.||..+++++..|++||||+|++|++..+
T Consensus 57 ~~~~rr~rt~~~~~ql~~ler~f~~~h~Pd~~~r~~la~~~~~~e~rVqvwFqnrrak~r~~~~ 120 (235)
T KOG0490|consen 57 KFSKRCARCKFTISQLDELERAFEKVHLPCFACRECLALLLTGDEFRVQVWFQNRRAKDRKEER 120 (235)
T ss_pred hccccccCCCCCcCHHHHHHHhhcCCCcCccchHHHHhhcCCCCeeeeehhhhhhcHhhhhhhc
Confidence 4567889999999999999999999999999999999999999999999999999999998643
No 28
>KOG0775|consensus
Probab=99.08 E-value=8e-11 Score=92.54 Aligned_cols=50 Identities=30% Similarity=0.433 Sum_probs=46.3
Q ss_pred CCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCCcccceeeeccchhhHH
Q psy16978 45 YTRFQTLELEKEFHFNHYLTRRRRIEIAHALCLTERQIKIWFQNRRMKLK 94 (154)
Q Consensus 45 ~t~~q~~~Le~~F~~~~~p~~~~~~~La~~l~l~~~qV~~WFqNrRak~k 94 (154)
|...-+.+|..+|..++||++.++.+||+.+||+..||-+||.|||.|+|
T Consensus 183 FKekSR~~LrewY~~~~YPsp~eKReLA~aTgLt~tQVsNWFKNRRQRDR 232 (304)
T KOG0775|consen 183 FKEKSRSLLREWYLQNPYPSPREKRELAEATGLTITQVSNWFKNRRQRDR 232 (304)
T ss_pred hhHhhHHHHHHHHhcCCCCChHHHHHHHHHhCCchhhhhhhhhhhhhhhh
Confidence 34445789999999999999999999999999999999999999999998
No 29
>KOG0849|consensus
Probab=99.05 E-value=9.9e-11 Score=96.70 Aligned_cols=65 Identities=31% Similarity=0.453 Sum_probs=60.4
Q ss_pred CCCCCCCCCCCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCCcccceeeeccchhhHHHhHH
Q psy16978 34 NGCPRRRGRQTYTRFQTLELEKEFHFNHYLTRRRRIEIAHALCLTERQIKIWFQNRRMKLKKELR 98 (154)
Q Consensus 34 ~~~~~rr~R~~~t~~q~~~Le~~F~~~~~p~~~~~~~La~~l~l~~~qV~~WFqNrRak~kr~~~ 98 (154)
.+++.+|.|+.|+..|+..|+..|+.++||+...|+.||.++++++..|++||+|||++++|...
T Consensus 172 ~~~~~rr~rtsft~~Q~~~le~~f~rt~yP~i~~Re~La~~i~l~e~riqvwf~nrra~~rr~~~ 236 (354)
T KOG0849|consen 172 LQRGGRRNRTSFSPSQLEALEECFQRTPYPDIVGRETLAKETGLPEPRVQVWFQNRRAKWRRQHR 236 (354)
T ss_pred ccccccccccccccchHHHHHHHhcCCCCCchhhHHHHhhhccCCchHHHHHHhhhhhhhhhccc
Confidence 34566788999999999999999999999999999999999999999999999999999998764
No 30
>KOG0774|consensus
Probab=99.05 E-value=4.3e-10 Score=88.06 Aligned_cols=95 Identities=27% Similarity=0.439 Sum_probs=77.9
Q ss_pred ccccccchhhHHHHHhhhHHHHhhhhccCCCCCC--------CCCCCCCCCCHHHHHHHHHHhh---hcCCCCHHHHHHH
Q psy16978 3 FPLEIRFTHQLVIVLNVHFAKMLCQLKQSGPNGC--------PRRRGRQTYTRFQTLELEKEFH---FNHYLTRRRRIEI 71 (154)
Q Consensus 3 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~--------~~rr~R~~~t~~q~~~Le~~F~---~~~~p~~~~~~~L 71 (154)
||+..+-.++++.++...+..+-..++++.+... ..+|+|..|+.....+|..+|. .++||+...+++|
T Consensus 145 RPi~~ke~e~m~~~i~~kF~~iq~~lkqstce~vmiLr~r~ldarRKRRNFsK~aTeiLneyF~~h~~nPYPSee~K~eL 224 (334)
T KOG0774|consen 145 RPIMPKEIERMVQIISKKFSHIQMQLKQSTCEAVMILRSRFLDARRKRRNFSKQATEILNEYFYSHLSNPYPSEEAKEEL 224 (334)
T ss_pred CCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhcccchhHHHHHHHHHHHhcCCCCCcHHHHHHH
Confidence 5555566678888888887777777777665321 2467777899999999999995 6889999999999
Q ss_pred HHHhCCCcccceeeeccchhhHHHhH
Q psy16978 72 AHALCLTERQIKIWFQNRRMKLKKEL 97 (154)
Q Consensus 72 a~~l~l~~~qV~~WFqNrRak~kr~~ 97 (154)
|+++|++..||.+||.|+|-+.+|..
T Consensus 225 AkqCnItvsQvsnwfgnkrIrykK~~ 250 (334)
T KOG0774|consen 225 AKQCNITVSQVSNWFGNKRIRYKKNM 250 (334)
T ss_pred HHHcCceehhhccccccceeehhhhh
Confidence 99999999999999999999999743
No 31
>PF05920 Homeobox_KN: Homeobox KN domain; InterPro: IPR008422 This entry represents a homeobox transcription factor KN domain conserved from fungi to human and plants [].; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent, 0005634 nucleus; PDB: 3K2A_B 2LK2_A 1X2N_A 2DMN_A.
Probab=98.60 E-value=8.3e-09 Score=59.27 Aligned_cols=34 Identities=32% Similarity=0.587 Sum_probs=28.9
Q ss_pred hcCCCCHHHHHHHHHHhCCCcccceeeeccchhh
Q psy16978 59 FNHYLTRRRRIEIAHALCLTERQIKIWFQNRRMK 92 (154)
Q Consensus 59 ~~~~p~~~~~~~La~~l~l~~~qV~~WFqNrRak 92 (154)
.++||+..++..||..+||+..||..||-|.|.+
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 4799999999999999999999999999998864
No 32
>KOG2252|consensus
Probab=98.43 E-value=1.8e-07 Score=80.01 Aligned_cols=59 Identities=22% Similarity=0.252 Sum_probs=55.0
Q ss_pred CCCCCCCCCCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCCcccceeeeccchhhH
Q psy16978 35 GCPRRRGRQTYTRFQTLELEKEFHFNHYLTRRRRIEIAHALCLTERQIKIWFQNRRMKL 93 (154)
Q Consensus 35 ~~~~rr~R~~~t~~q~~~Le~~F~~~~~p~~~~~~~La~~l~l~~~qV~~WFqNrRak~ 93 (154)
....||.|.+||..|...|..+|+.+++|+.+..+.|+.+|+|....|.+||.|-|.|.
T Consensus 417 ~~~~KKPRlVfTd~QkrTL~aiFke~~RPS~Emq~tIS~qL~L~~sTV~NfFmNaRRRs 475 (558)
T KOG2252|consen 417 MLQTKKPRLVFTDIQKRTLQAIFKENKRPSREMQETISQQLNLELSTVINFFMNARRRS 475 (558)
T ss_pred cccCCCceeeecHHHHHHHHHHHhcCCCCCHHHHHHHHHHhCCcHHHHHHHHHhhhhhc
Confidence 34568889999999999999999999999999999999999999999999999988774
No 33
>KOG0490|consensus
Probab=98.12 E-value=2.4e-06 Score=65.88 Aligned_cols=62 Identities=39% Similarity=0.508 Sum_probs=57.8
Q ss_pred CCCCCCCCCCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCCcccceeeeccchhhHHHh
Q psy16978 35 GCPRRRGRQTYTRFQTLELEKEFHFNHYLTRRRRIEIAHALCLTERQIKIWFQNRRMKLKKE 96 (154)
Q Consensus 35 ~~~~rr~R~~~t~~q~~~Le~~F~~~~~p~~~~~~~La~~l~l~~~qV~~WFqNrRak~kr~ 96 (154)
..+.++.|+.+...++..+...|....+|+...+..|+..+|++...|++||+|+|++.++.
T Consensus 150 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~P~~~~~~~l~~~~~~~~~~~q~~~~~~~~~~~~~ 211 (235)
T KOG0490|consen 150 NKKPRRPRTTFTENQLEVLETVFRATPKPDADDREQLAEETGLSERVIQVWFQNRRAKLRKH 211 (235)
T ss_pred ccccCCCccccccchhHhhhhcccCCCCCchhhHHHHHHhcCCChhhhhhhcccHHHHHHhh
Confidence 35677889999999999999999999999999999999999999999999999999999874
No 34
>KOG1146|consensus
Probab=97.48 E-value=6.4e-05 Score=70.09 Aligned_cols=60 Identities=27% Similarity=0.345 Sum_probs=56.5
Q ss_pred CCCCCCCCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCCcccceeeeccchhhHHHh
Q psy16978 37 PRRRGRQTYTRFQTLELEKEFHFNHYLTRRRRIEIAHALCLTERQIKIWFQNRRMKLKKE 96 (154)
Q Consensus 37 ~~rr~R~~~t~~q~~~Le~~F~~~~~p~~~~~~~La~~l~l~~~qV~~WFqNrRak~kr~ 96 (154)
.++..|+.++..|+..+...|....+|...+.+.|...++++.+.|++||||-|++.++.
T Consensus 902 ~r~a~~~~~~d~qlk~i~~~~~~q~~~~~~~~E~l~~~~~~~~~~i~vw~qna~~~s~k~ 961 (1406)
T KOG1146|consen 902 GRRAYRTQESDLQLKIIKACYEAQRTPTMQECEVLEEPIGLPKRVIQVWFQNARAKSKKA 961 (1406)
T ss_pred hhhhhccchhHHHHHHHHHHHhhccCChHHHHHhhcccccCCcchhHHhhhhhhhhhhhh
Confidence 467889999999999999999999999999999999999999999999999999998864
No 35
>PF11569 Homez: Homeodomain leucine-zipper encoding, Homez; PDB: 2YS9_A.
Probab=97.11 E-value=0.00013 Score=44.66 Aligned_cols=41 Identities=20% Similarity=0.298 Sum_probs=31.0
Q ss_pred HHHHHHHhhhcCCCCHHHHHHHHHHhCCCcccceeeeccch
Q psy16978 50 TLELEKEFHFNHYLTRRRRIEIAHALCLTERQIKIWFQNRR 90 (154)
Q Consensus 50 ~~~Le~~F~~~~~p~~~~~~~La~~l~l~~~qV~~WFqNrR 90 (154)
+..|+++|...+.+...+...|..+.+|+..||+.||-.++
T Consensus 10 ~~pL~~Yy~~h~~L~E~DL~~L~~kS~ms~qqVr~WFa~~~ 50 (56)
T PF11569_consen 10 IQPLEDYYLKHKQLQEEDLDELCDKSRMSYQQVRDWFAERM 50 (56)
T ss_dssp -HHHHHHHHHT----TTHHHHHHHHTT--HHHHHHHHHHHS
T ss_pred hHHHHHHHHHcCCccHhhHHHHHHHHCCCHHHHHHHHHHhc
Confidence 46799999999999999999999999999999999996553
No 36
>KOG0773|consensus
Probab=97.04 E-value=0.00078 Score=55.38 Aligned_cols=61 Identities=20% Similarity=0.327 Sum_probs=50.3
Q ss_pred CCCCCCCCCHHHHHHHHHHhh---hcCCCCHHHHHHHHHHhCCCcccceeeeccchhhHHHhHH
Q psy16978 38 RRRGRQTYTRFQTLELEKEFH---FNHYLTRRRRIEIAHALCLTERQIKIWFQNRRMKLKKELR 98 (154)
Q Consensus 38 ~rr~R~~~t~~q~~~Le~~F~---~~~~p~~~~~~~La~~l~l~~~qV~~WFqNrRak~kr~~~ 98 (154)
..|.+..+......+|+.+.. ..+||+..++..||.++||+..||.+||-|.|.+..+-+.
T Consensus 239 ~~r~~~~lP~~a~~ilr~Wl~~h~~~PYPse~~K~~La~~TGLs~~Qv~NWFINaR~R~w~p~~ 302 (342)
T KOG0773|consen 239 KWRPQRGLPKEAVSILRAWLFEHLLHPYPSDDEKLMLAKQTGLSRPQVSNWFINARVRLWKPMI 302 (342)
T ss_pred CCCCCCCCCHHHHHHHHHHHHHhccCCCCcchhccccchhcCCCcccCCchhhhcccccCCchH
Confidence 445566788888888887743 3579999999999999999999999999999988776544
No 37
>KOG3623|consensus
Probab=95.49 E-value=0.0089 Score=53.50 Aligned_cols=48 Identities=19% Similarity=0.241 Sum_probs=44.7
Q ss_pred HHHHHHHhhhcCCCCHHHHHHHHHHhCCCcccceeeeccchhhHHHhH
Q psy16978 50 TLELEKEFHFNHYLTRRRRIEIAHALCLTERQIKIWFQNRRMKLKKEL 97 (154)
Q Consensus 50 ~~~Le~~F~~~~~p~~~~~~~La~~l~l~~~qV~~WFqNrRak~kr~~ 97 (154)
+.+|..+|..|..|+..+...+|.+.||+.+.|+.||+++++......
T Consensus 568 ~sllkayyaln~~ps~eelskia~qvglp~~vvk~wfE~~~a~e~sv~ 615 (1007)
T KOG3623|consen 568 TSLLKAYYALNGLPSEEELSKIAQQVGLPFAVVKAWFEDEEAEEMSVE 615 (1007)
T ss_pred HHHHHHHHHhcCCCCHHHHHHHHHHhcccHHHHHHHHHhhhhhhhhhc
Confidence 778999999999999999999999999999999999999999877654
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=94.83 E-value=0.033 Score=33.61 Aligned_cols=46 Identities=20% Similarity=0.341 Sum_probs=33.6
Q ss_pred CCCCCCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCCcccceeeeccc
Q psy16978 39 RRGRQTYTRFQTLELEKEFHFNHYLTRRRRIEIAHALCLTERQIKIWFQNR 89 (154)
Q Consensus 39 rr~R~~~t~~q~~~Le~~F~~~~~p~~~~~~~La~~l~l~~~qV~~WFqNr 89 (154)
|++|..+|-++...+-..++... ....||..+|++..+|..|..|+
T Consensus 1 krkR~~LTl~eK~~iI~~~e~g~-----s~~~ia~~fgv~~sTv~~I~K~k 46 (53)
T PF04218_consen 1 KRKRKSLTLEEKLEIIKRLEEGE-----SKRDIAREFGVSRSTVSTILKNK 46 (53)
T ss_dssp SSSSSS--HHHHHHHHHHHHCTT------HHHHHHHHT--CCHHHHHHHCH
T ss_pred CCCCccCCHHHHHHHHHHHHcCC-----CHHHHHHHhCCCHHHHHHHHHhH
Confidence 56788899998777777776655 46789999999999999999875
No 39
>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=78.09 E-value=2.6 Score=25.41 Aligned_cols=39 Identities=18% Similarity=0.224 Sum_probs=31.0
Q ss_pred CCHHHHHHHHHHhhhcCC--CCHHHHHHHHHHhCCCcccce
Q psy16978 45 YTRFQTLELEKEFHFNHY--LTRRRRIEIAHALCLTERQIK 83 (154)
Q Consensus 45 ~t~~q~~~Le~~F~~~~~--p~~~~~~~La~~l~l~~~qV~ 83 (154)
+|..|..+|...|...-| |-.....+||..+|++...|.
T Consensus 1 LT~~Q~e~L~~A~~~GYfd~PR~~tl~elA~~lgis~st~~ 41 (53)
T PF04967_consen 1 LTDRQREILKAAYELGYFDVPRRITLEELAEELGISKSTVS 41 (53)
T ss_pred CCHHHHHHHHHHHHcCCCCCCCcCCHHHHHHHhCCCHHHHH
Confidence 578899999999886654 555667889999999987643
No 40
>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=74.61 E-value=2.1 Score=24.76 Aligned_cols=39 Identities=10% Similarity=0.107 Sum_probs=28.4
Q ss_pred CCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCCcccceeeec
Q psy16978 44 TYTRFQTLELEKEFHFNHYLTRRRRIEIAHALCLTERQIKIWFQ 87 (154)
Q Consensus 44 ~~t~~q~~~Le~~F~~~~~p~~~~~~~La~~l~l~~~qV~~WFq 87 (154)
.+++.+..++...|. ......++|..+|++...|+.+..
T Consensus 4 ~L~~~er~vi~~~y~-----~~~t~~eIa~~lg~s~~~V~~~~~ 42 (50)
T PF04545_consen 4 QLPPREREVIRLRYF-----EGLTLEEIAERLGISRSTVRRILK 42 (50)
T ss_dssp TS-HHHHHHHHHHHT-----ST-SHHHHHHHHTSCHHHHHHHHH
T ss_pred hCCHHHHHHHHHHhc-----CCCCHHHHHHHHCCcHHHHHHHHH
Confidence 467888889988882 223356889999999998877654
No 41
>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=72.93 E-value=1.2 Score=28.03 Aligned_cols=44 Identities=18% Similarity=0.292 Sum_probs=27.6
Q ss_pred CCCCCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCCcccceeeec
Q psy16978 40 RGRQTYTRFQTLELEKEFHFNHYLTRRRRIEIAHALCLTERQIKIWFQ 87 (154)
Q Consensus 40 r~R~~~t~~q~~~Le~~F~~~~~p~~~~~~~La~~l~l~~~qV~~WFq 87 (154)
+.|..|+.++...+-..+.. .......+|..+||++..|..|-.
T Consensus 2 ~~r~~ys~e~K~~~v~~~~~----~g~sv~~va~~~gi~~~~l~~W~~ 45 (76)
T PF01527_consen 2 RKRRRYSPEFKLQAVREYLE----SGESVSEVAREYGISPSTLYNWRK 45 (76)
T ss_dssp -SS----HHHHHHHHHHHHH----HHCHHHHHHHHHTS-HHHHHHHHH
T ss_pred CCCCCCCHHHHHHHHHHHHH----CCCceEeeecccccccccccHHHH
Confidence 45677999887666655522 235567899999999999999864
No 42
>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=69.38 E-value=1.7 Score=26.96 Aligned_cols=20 Identities=30% Similarity=0.529 Sum_probs=17.2
Q ss_pred HHHHHHHHhCCCcccceeee
Q psy16978 67 RRIEIAHALCLTERQIKIWF 86 (154)
Q Consensus 67 ~~~~La~~l~l~~~qV~~WF 86 (154)
....||..||+++.+|+.|=
T Consensus 24 ~lkdIA~~Lgvs~~tIr~WK 43 (60)
T PF10668_consen 24 KLKDIAEKLGVSESTIRKWK 43 (60)
T ss_pred cHHHHHHHHCCCHHHHHHHh
Confidence 34578999999999999985
No 43
>PF09607 BrkDBD: Brinker DNA-binding domain; InterPro: IPR018586 This DNA-binding domain is the first approx. 100 residues of the N-terminal end of Brinker. The structure of this domain in complex with DNA consists of four alpha-helices that contain a helix-turn-helix DNA recognition motif specific for GC-rich DNA. The Brinker nuclear repressor is a major element of the Drosophila Decapentaplegic morphogen signalling pathway []. ; PDB: 2GLO_A.
Probab=69.06 E-value=5 Score=24.70 Aligned_cols=44 Identities=20% Similarity=0.292 Sum_probs=22.3
Q ss_pred CCCCCHHH-HHHHHHHhhhcCCCCHHHHHHHHHHhCCCcccceeeec
Q psy16978 42 RQTYTRFQ-TLELEKEFHFNHYLTRRRRIEIAHALCLTERQIKIWFQ 87 (154)
Q Consensus 42 R~~~t~~q-~~~Le~~F~~~~~p~~~~~~~La~~l~l~~~qV~~WFq 87 (154)
|..|+... |.+++. |.....--...|. .|.++|+++++|+-|-+
T Consensus 3 rrsy~~~FKL~Vv~~-a~~~~nc~~~~RA-aarkf~V~r~~Vr~W~k 47 (58)
T PF09607_consen 3 RRSYTAEFKLKVVEY-AEKDNNCKGNQRA-AARKFNVSRRQVRKWRK 47 (58)
T ss_dssp -----HHHHHHHHHH-HHH-TTTTT-HHH-HHHHTTS-HHHHHHHHT
T ss_pred ccccChHHHHHHHHH-HHHccchhhhHHH-HHHHhCccHHHHHHHHH
Confidence 44566654 444444 4333332233344 49999999999999864
No 44
>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=62.13 E-value=13 Score=18.33 Aligned_cols=37 Identities=19% Similarity=0.105 Sum_probs=24.2
Q ss_pred CCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCCcccceeee
Q psy16978 45 YTRFQTLELEKEFHFNHYLTRRRRIEIAHALCLTERQIKIWF 86 (154)
Q Consensus 45 ~t~~q~~~Le~~F~~~~~p~~~~~~~La~~l~l~~~qV~~WF 86 (154)
++......+...|.. .. ....+|..+|++...|..|.
T Consensus 6 ~~~~~~~~i~~~~~~-~~----s~~~ia~~~~is~~tv~~~~ 42 (42)
T cd00569 6 LTPEQIEEARRLLAA-GE----SVAEIARRLGVSRSTLYRYL 42 (42)
T ss_pred CCHHHHHHHHHHHHc-CC----CHHHHHHHHCCCHHHHHHhC
Confidence 556666555555642 22 35577899999988877763
No 45
>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=58.26 E-value=3.8 Score=22.91 Aligned_cols=39 Identities=13% Similarity=0.083 Sum_probs=27.5
Q ss_pred CCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCCcccceeeecc
Q psy16978 45 YTRFQTLELEKEFHFNHYLTRRRRIEIAHALCLTERQIKIWFQN 88 (154)
Q Consensus 45 ~t~~q~~~Le~~F~~~~~p~~~~~~~La~~l~l~~~qV~~WFqN 88 (154)
++..+..++...|... .....+|..+|++...|..|...
T Consensus 11 l~~~~~~~~~~~~~~~-----~~~~~ia~~~~~s~~~i~~~~~~ 49 (55)
T cd06171 11 LPEREREVILLRFGEG-----LSYEEIAEILGISRSTVRQRLHR 49 (55)
T ss_pred CCHHHHHHHHHHHhcC-----CCHHHHHHHHCcCHHHHHHHHHH
Confidence 5566677777665322 23557799999999999888754
No 46
>COG3413 Predicted DNA binding protein [General function prediction only]
Probab=55.31 E-value=11 Score=28.72 Aligned_cols=39 Identities=18% Similarity=0.221 Sum_probs=32.9
Q ss_pred CCCHHHHHHHHHHhhhcC--CCCHHHHHHHHHHhCCCcccc
Q psy16978 44 TYTRFQTLELEKEFHFNH--YLTRRRRIEIAHALCLTERQI 82 (154)
Q Consensus 44 ~~t~~q~~~Le~~F~~~~--~p~~~~~~~La~~l~l~~~qV 82 (154)
.+|..|+.+|..+|...= +|-.....+||+.+|+++..+
T Consensus 155 ~LTdrQ~~vL~~A~~~GYFd~PR~~~l~dLA~~lGISkst~ 195 (215)
T COG3413 155 DLTDRQLEVLRLAYKMGYFDYPRRVSLKDLAKELGISKSTL 195 (215)
T ss_pred cCCHHHHHHHHHHHHcCCCCCCccCCHHHHHHHhCCCHHHH
Confidence 699999999999998665 366667789999999998763
No 47
>KOG3623|consensus
Probab=50.97 E-value=18 Score=33.32 Aligned_cols=62 Identities=13% Similarity=0.142 Sum_probs=45.7
Q ss_pred CCCCCCCCCCCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCCcccceeeeccchhhHHH
Q psy16978 34 NGCPRRRGRQTYTRFQTLELEKEFHFNHYLTRRRRIEIAHALCLTERQIKIWFQNRRMKLKK 95 (154)
Q Consensus 34 ~~~~~rr~R~~~t~~q~~~Le~~F~~~~~p~~~~~~~La~~l~l~~~qV~~WFqNrRak~kr 95 (154)
++..+-+-++....++-.-|..+++.+-.++-.+-..++..+...+..|.+||++|+..-+.
T Consensus 622 sg~~p~kv~sp~k~~dq~ql~~a~elq~s~~n~~~pl~~t~~~n~~pv~ev~dhsrsstpsp 683 (1007)
T KOG3623|consen 622 SGERPVKVRSPIKEEDQQQLKQAYELQASPSNDEFPLIATRLQNDPPVVEVWDHSRSSTPSP 683 (1007)
T ss_pred CCCCCccccCCCCccchhhhHhhhhcccCccCcccchhhhhccCCCcchhhcccCCCCCCCC
Confidence 34445566677777777888888887776666665555666777888999999999987664
No 48
>PRK03975 tfx putative transcriptional regulator; Provisional
Probab=50.79 E-value=34 Score=24.80 Aligned_cols=49 Identities=18% Similarity=0.072 Sum_probs=36.2
Q ss_pred CCCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCCcccceeeeccchhhHHHh
Q psy16978 42 RQTYTRFQTLELEKEFHFNHYLTRRRRIEIAHALCLTERQIKIWFQNRRMKLKKE 96 (154)
Q Consensus 42 R~~~t~~q~~~Le~~F~~~~~p~~~~~~~La~~l~l~~~qV~~WFqNrRak~kr~ 96 (154)
...+++.|..+|...+ .. ....++|..+|++...|..|-...+.+.++.
T Consensus 4 ~~~Lt~rqreVL~lr~--~G----lTq~EIAe~LGiS~~tVs~ie~ra~kkLr~~ 52 (141)
T PRK03975 4 ESFLTERQIEVLRLRE--RG----LTQQEIADILGTSRANVSSIEKRARENIEKA 52 (141)
T ss_pred ccCCCHHHHHHHHHHH--cC----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 3568889999987732 12 2345789999999999999998666665543
No 49
>PF08281 Sigma70_r4_2: Sigma-70, region 4; InterPro: IPR013249 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognised by the major sigma factors [, ]. Region 4 of sigma-70 like sigma-factors are involved in binding to the -35 promoter element via a helix-turn-helix motif [].; GO: 0003677 DNA binding, 0003700 sequence-specific DNA binding transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, DNA-dependent, 0006355 regulation of transcription, DNA-dependent; PDB: 2LFW_A 1OR7_B 2H27_D 2O8X_B.
Probab=48.82 E-value=9.9 Score=22.07 Aligned_cols=38 Identities=18% Similarity=0.164 Sum_probs=24.4
Q ss_pred CCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCCcccceeeec
Q psy16978 45 YTRFQTLELEKEFHFNHYLTRRRRIEIAHALCLTERQIKIWFQ 87 (154)
Q Consensus 45 ~t~~q~~~Le~~F~~~~~p~~~~~~~La~~l~l~~~qV~~WFq 87 (154)
+++.+..++...| .......++|..+|++...|+.|..
T Consensus 11 L~~~~r~i~~l~~-----~~g~s~~eIa~~l~~s~~~v~~~l~ 48 (54)
T PF08281_consen 11 LPERQREIFLLRY-----FQGMSYAEIAEILGISESTVKRRLR 48 (54)
T ss_dssp S-HHHHHHHHHHH-----TS---HHHHHHHCTS-HHHHHHHHH
T ss_pred CCHHHHHHHHHHH-----HHCcCHHHHHHHHCcCHHHHHHHHH
Confidence 4455556665543 3344567899999999999999886
No 50
>KOG1146|consensus
Probab=48.11 E-value=17 Score=35.33 Aligned_cols=60 Identities=20% Similarity=0.217 Sum_probs=53.3
Q ss_pred CCCCCCCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCCcccceeeeccchhhHHHhH
Q psy16978 38 RRRGRQTYTRFQTLELEKEFHFNHYLTRRRRIEIAHALCLTERQIKIWFQNRRMKLKKEL 97 (154)
Q Consensus 38 ~rr~R~~~t~~q~~~Le~~F~~~~~p~~~~~~~La~~l~l~~~qV~~WFqNrRak~kr~~ 97 (154)
.++-+..+-.++...|-++|-.+..|+...+..|......+.+++.+||+|-|.+.++..
T Consensus 705 ~~~~~~~~~~~aa~~l~~a~~~~~sps~k~~~civcd~~st~~l~~l~~h~~~~rs~ke~ 764 (1406)
T KOG1146|consen 705 DKLLRLTILPEAAMILGRAYMQDNSPSLKVFDCIVCDVFSTDRLDQLWFHNTRERSRKEQ 764 (1406)
T ss_pred cccCcccccHHHHhhhhhcccCCCCHHHHHHHHhhhhhhhhhhHHHHhhcchhhhhhhhc
Confidence 355566777799999999999999999999999999999999999999999999988765
No 51
>PRK10072 putative transcriptional regulator; Provisional
Probab=47.33 E-value=50 Score=22.23 Aligned_cols=42 Identities=21% Similarity=0.180 Sum_probs=30.4
Q ss_pred CCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCCcccceeeeccchhh
Q psy16978 44 TYTRFQTLELEKEFHFNHYLTRRRRIEIAHALCLTERQIKIWFQNRRMK 92 (154)
Q Consensus 44 ~~t~~q~~~Le~~F~~~~~p~~~~~~~La~~l~l~~~qV~~WFqNrRak 92 (154)
..+...+..|...-. . ...+||..+|++...|..|...+|.-
T Consensus 32 ~~~~~eik~LR~~~g----l---TQ~elA~~lGvS~~TVs~WE~G~r~P 73 (96)
T PRK10072 32 TTSFTEFEQLRKGTG----L---KIDDFARVLGVSVAMVKEWESRRVKP 73 (96)
T ss_pred cCChHHHHHHHHHcC----C---CHHHHHHHhCCCHHHHHHHHcCCCCC
Confidence 446666777754322 2 25689999999999999999877653
No 52
>PF06056 Terminase_5: Putative ATPase subunit of terminase (gpP-like); InterPro: IPR010332 This family of proteins are annotated as ATPase subunits of phage terminase after []. Terminases are viral proteins that are involved in packaging viral DNA into the capsid.; GO: 0005524 ATP binding, 0019069 viral capsid assembly
Probab=45.54 E-value=8.5 Score=23.47 Aligned_cols=25 Identities=28% Similarity=0.381 Sum_probs=19.9
Q ss_pred HHHHHHHhCCCcccceeeeccchhhHH
Q psy16978 68 RIEIAHALCLTERQIKIWFQNRRMKLK 94 (154)
Q Consensus 68 ~~~La~~l~l~~~qV~~WFqNrRak~k 94 (154)
..++|..||++...|..|-+ |-+|.
T Consensus 16 ~~eIA~~Lg~~~~TV~~W~~--r~~W~ 40 (58)
T PF06056_consen 16 IKEIAEELGVPRSTVYSWKD--RYKWD 40 (58)
T ss_pred HHHHHHHHCCChHHHHHHHH--hhCcc
Confidence 45789999999999999974 44443
No 53
>cd04761 HTH_MerR-SF Helix-Turn-Helix DNA binding domain of transcription regulators from the MerR superfamily. Helix-turn-helix (HTH) transcription regulator MerR superfamily, N-terminal domain. The MerR family transcription regulators have been shown to mediate responses to stress including exposure to heavy metals, drugs, or oxygen radicals in eubacterial and some archaeal species. They regulate transcription of multidrug/metal ion transporter genes and oxidative stress regulons by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.
Probab=45.31 E-value=6.9 Score=22.05 Aligned_cols=22 Identities=9% Similarity=0.052 Sum_probs=18.3
Q ss_pred HHHHHHHhCCCcccceeeeccc
Q psy16978 68 RIEIAHALCLTERQIKIWFQNR 89 (154)
Q Consensus 68 ~~~La~~l~l~~~qV~~WFqNr 89 (154)
..++|..+|++...|+.|.++.
T Consensus 3 ~~e~a~~~gv~~~tlr~~~~~g 24 (49)
T cd04761 3 IGELAKLTGVSPSTLRYYERIG 24 (49)
T ss_pred HHHHHHHHCcCHHHHHHHHHCC
Confidence 3578999999999999997554
No 54
>PF13411 MerR_1: MerR HTH family regulatory protein; PDB: 2JML_A 3GP4_A 3GPV_B.
Probab=42.96 E-value=9 Score=23.34 Aligned_cols=21 Identities=14% Similarity=0.256 Sum_probs=17.4
Q ss_pred HHHHHHHhCCCcccceeeecc
Q psy16978 68 RIEIAHALCLTERQIKIWFQN 88 (154)
Q Consensus 68 ~~~La~~l~l~~~qV~~WFqN 88 (154)
..++|..+|++...|+.|=..
T Consensus 3 i~eva~~~gvs~~tlr~y~~~ 23 (69)
T PF13411_consen 3 IKEVAKLLGVSPSTLRYYERE 23 (69)
T ss_dssp HHHHHHHTTTTHHHHHHHHHT
T ss_pred HHHHHHHHCcCHHHHHHHHHh
Confidence 357899999999999999643
No 55
>PF13518 HTH_28: Helix-turn-helix domain
Probab=42.89 E-value=9.9 Score=21.66 Aligned_cols=20 Identities=20% Similarity=0.434 Sum_probs=17.5
Q ss_pred HHHHHHHhCCCcccceeeec
Q psy16978 68 RIEIAHALCLTERQIKIWFQ 87 (154)
Q Consensus 68 ~~~La~~l~l~~~qV~~WFq 87 (154)
..++|..+|++..+|..|.+
T Consensus 15 ~~~~a~~~gis~~tv~~w~~ 34 (52)
T PF13518_consen 15 VREIAREFGISRSTVYRWIK 34 (52)
T ss_pred HHHHHHHHCCCHhHHHHHHH
Confidence 45689999999999999985
No 56
>TIGR03879 near_KaiC_dom probable regulatory domain. This model describes a common domain shared by two different families of proteins, each of which occurs regularly next to its corresponding partner family, a probable regulatory with homology to KaiC. By implication, this protein family likely is also involved in sensory transduction and/or regulation.
Probab=41.28 E-value=4.9 Score=25.88 Aligned_cols=32 Identities=19% Similarity=0.182 Sum_probs=23.4
Q ss_pred hhhcCCCCHHHHHHHHHHhCCCcccceeeecc
Q psy16978 57 FHFNHYLTRRRRIEIAHALCLTERQIKIWFQN 88 (154)
Q Consensus 57 F~~~~~p~~~~~~~La~~l~l~~~qV~~WFqN 88 (154)
|....+-......++|..+|+++..|+.|+.+
T Consensus 24 f~L~R~~eGlS~kEIAe~LGIS~~TVk~~l~~ 55 (73)
T TIGR03879 24 AALAREEAGKTASEIAEELGRTEQTVRNHLKG 55 (73)
T ss_pred HHHHHHHcCCCHHHHHHHHCcCHHHHHHHHhc
Confidence 43333333445678999999999999999864
No 57
>PF13384 HTH_23: Homeodomain-like domain; PDB: 2X48_C.
Probab=39.35 E-value=9.1 Score=21.83 Aligned_cols=22 Identities=23% Similarity=0.368 Sum_probs=16.9
Q ss_pred HHHHHHHHHhCCCcccceeeec
Q psy16978 66 RRRIEIAHALCLTERQIKIWFQ 87 (154)
Q Consensus 66 ~~~~~La~~l~l~~~qV~~WFq 87 (154)
....++|..+|++...|..|..
T Consensus 18 ~s~~~ia~~lgvs~~Tv~~w~k 39 (50)
T PF13384_consen 18 WSIREIAKRLGVSRSTVYRWIK 39 (50)
T ss_dssp --HHHHHHHHTS-HHHHHHHHT
T ss_pred CCHHHHHHHHCcCHHHHHHHHH
Confidence 4466789999999999999975
No 58
>PRK09413 IS2 repressor TnpA; Reviewed
Probab=37.44 E-value=1.4e+02 Score=20.57 Aligned_cols=43 Identities=12% Similarity=0.149 Sum_probs=28.5
Q ss_pred CCCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCCcccceeeecc
Q psy16978 42 RQTYTRFQTLELEKEFHFNHYLTRRRRIEIAHALCLTERQIKIWFQN 88 (154)
Q Consensus 42 R~~~t~~q~~~Le~~F~~~~~p~~~~~~~La~~l~l~~~qV~~WFqN 88 (154)
|..++.++....-.....+.. ....+|..+|++...|..|..-
T Consensus 10 rr~ys~EfK~~aV~~~~~~g~----sv~evA~e~gIs~~tl~~W~r~ 52 (121)
T PRK09413 10 RRRRTTQEKIAIVQQSFEPGM----TVSLVARQHGVAASQLFLWRKQ 52 (121)
T ss_pred CCCCCHHHHHHHHHHHHcCCC----CHHHHHHHHCcCHHHHHHHHHH
Confidence 455888765444333333332 3456799999999999999643
No 59
>PF00424 REV: REV protein (anti-repression trans-activator protein); InterPro: IPR000625 REV is a viral anti-repression trans-activator protein, which appears to act post-transcriptionally [] to relieve negative repression of GAG and ENV production. It is a phosphoprotein [, ] whose state of phosphorylation is mediated by a specific serine kinase activity present in the nucleus []. REV accumulates in the nucleoli [].; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0042025 host cell nucleus; PDB: 1ETF_B 1ETG_B 1ULL_B 3LPH_B 2X7L_R.
Probab=37.36 E-value=96 Score=20.83 Aligned_cols=39 Identities=18% Similarity=0.263 Sum_probs=20.2
Q ss_pred HHHHHHHhhhcCCCCHHHHHHHHHHhCCCcccceeeeccchhhHHHhHHHHHH
Q psy16978 50 TLELEKEFHFNHYLTRRRRIEIAHALCLTERQIKIWFQNRRMKLKKELRAVKE 102 (154)
Q Consensus 50 ~~~Le~~F~~~~~p~~~~~~~La~~l~l~~~qV~~WFqNrRak~kr~~~~~~~ 102 (154)
+....-.|+.++||...-... | =.|||.+|++.+++...
T Consensus 14 vRiIk~LyqsnPyP~~~GTr~-a-------------RRnRRRRWR~rq~QI~~ 52 (91)
T PF00424_consen 14 VRIIKILYQSNPYPSPEGTRQ-A-------------RRNRRRRWRARQRQIRA 52 (91)
T ss_dssp HHHHHHHHHTS-S--S-S-HH-H-------------HHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHccccCCCCCCccc-c-------------ccchhhhHHHHHHHHHH
Confidence 344455588899987441111 1 14889999976655433
No 60
>PRK09646 RNA polymerase sigma factor SigK; Reviewed
Probab=37.29 E-value=27 Score=25.86 Aligned_cols=29 Identities=17% Similarity=0.297 Sum_probs=21.7
Q ss_pred HHHHHHHHhCCCcccceeeeccchhhHHH
Q psy16978 67 RRIEIAHALCLTERQIKIWFQNRRMKLKK 95 (154)
Q Consensus 67 ~~~~La~~l~l~~~qV~~WFqNrRak~kr 95 (154)
...++|..+|++...|+++...-|.+.|+
T Consensus 160 s~~EIA~~Lgis~~tVk~~l~ra~~~Lr~ 188 (194)
T PRK09646 160 TYREVAERLAVPLGTVKTRMRDGLIRLRD 188 (194)
T ss_pred CHHHHHHHhCCChHhHHHHHHHHHHHHHH
Confidence 45678999999999999888655554443
No 61
>PF00376 MerR: MerR family regulatory protein; InterPro: IPR000551 The many bacterial transcription regulation proteins which bind DNA through a 'helix-turn-helix' motif can be classified into subfamilies on the basis of sequence similarities. One of these is the MerR subfamily. MerR, which is found in many bacterial species mediates the mercuric-dependent induction of the mercury resistance operon. In the absence of mercury merR represses transcription by binding tightly, as a dimer, to the 'mer' operator region; when mercury is present the dimeric complex binds a single ion and becomes a potent transcriptional activator, while remaining bound to the mer site. Members of the family include the mercuric resistance operon regulatory protein merR; Bacillus subtilis bltR and bmrR; Bacillus glnR; Streptomyces coelicolor hspR; Bradyrhizobium japonicum nolA; Escherichia coli superoxide response regulator soxR; and Streptomyces lividans transcriptional activator tipA [, , , , , ]. Other members include hypothetical proteins from E. coli, B. subtilis and Haemophilus influenzae. Within this family, the HTH motif is situated towards the N terminus.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent; PDB: 3HH0_A 2DG6_A 1R8D_B 1JBG_A 2VZ4_A 2ZHH_A 2ZHG_A 1Q07_A 1Q06_A 1Q05_B ....
Probab=36.38 E-value=12 Score=20.68 Aligned_cols=18 Identities=22% Similarity=0.344 Sum_probs=14.1
Q ss_pred HHHHHHhCCCcccceeee
Q psy16978 69 IEIAHALCLTERQIKIWF 86 (154)
Q Consensus 69 ~~La~~l~l~~~qV~~WF 86 (154)
.++|+.+|++.+.|+.|=
T Consensus 3 ~e~A~~~gvs~~tlR~ye 20 (38)
T PF00376_consen 3 GEVAKLLGVSPRTLRYYE 20 (38)
T ss_dssp HHHHHHHTS-HHHHHHHH
T ss_pred HHHHHHHCCCHHHHHHHH
Confidence 468999999999888874
No 62
>PRK06759 RNA polymerase factor sigma-70; Validated
Probab=36.20 E-value=34 Score=23.94 Aligned_cols=27 Identities=22% Similarity=0.144 Sum_probs=20.5
Q ss_pred HHHHHHHHHhCCCcccceeeeccchhh
Q psy16978 66 RRRIEIAHALCLTERQIKIWFQNRRMK 92 (154)
Q Consensus 66 ~~~~~La~~l~l~~~qV~~WFqNrRak 92 (154)
....++|..+|++...|+.|...-+.+
T Consensus 123 ~s~~EIA~~l~is~~tV~~~~~ra~~~ 149 (154)
T PRK06759 123 KTMGEIALETEMTYYQVRWIYRQALEK 149 (154)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHHH
Confidence 346678999999999999987643433
No 63
>PF13443 HTH_26: Cro/C1-type HTH DNA-binding domain; PDB: 3TYR_A 3TYS_A 3B7H_A.
Probab=36.18 E-value=11 Score=22.53 Aligned_cols=26 Identities=4% Similarity=0.150 Sum_probs=17.9
Q ss_pred HHHHHHHHhCCCcccceeeeccchhh
Q psy16978 67 RRIEIAHALCLTERQIKIWFQNRRMK 92 (154)
Q Consensus 67 ~~~~La~~l~l~~~qV~~WFqNrRak 92 (154)
....||..+|++...|..|+.++...
T Consensus 12 t~~~La~~~gis~~tl~~~~~~~~~~ 37 (63)
T PF13443_consen 12 TQKDLARKTGISRSTLSRILNGKPSN 37 (63)
T ss_dssp -HHHHHHHHT--HHHHHHHHTTT---
T ss_pred CHHHHHHHHCcCHHHHHHHHhccccc
Confidence 35679999999999999999877433
No 64
>PHA02955 hypothetical protein; Provisional
Probab=35.35 E-value=61 Score=25.22 Aligned_cols=42 Identities=12% Similarity=0.008 Sum_probs=33.8
Q ss_pred HHHHHHHHHhhhc-CCCCHHHHHHHHHHhCCCcccceeeeccc
Q psy16978 48 FQTLELEKEFHFN-HYLTRRRRIEIAHALCLTERQIKIWFQNR 89 (154)
Q Consensus 48 ~q~~~Le~~F~~~-~~p~~~~~~~La~~l~l~~~qV~~WFqNr 89 (154)
.++..|-+.|.+. ...+.+++.+++..+|+....|..||.+-
T Consensus 61 ~sf~lli~a~~Et~~~Lp~~qk~~ia~~lgI~~~~~~~d~~t~ 103 (213)
T PHA02955 61 KNFQLLIEALIETIENFPEKEQKEIAADIGINIDDYKAGKKTD 103 (213)
T ss_pred HHHHHHHHHHHHHHHhCCHHHHHHHHHHhCCChhhccCcccch
Confidence 4677777777655 56778899999999999988789999764
No 65
>PF13936 HTH_38: Helix-turn-helix domain; PDB: 2W48_A.
Probab=34.94 E-value=20 Score=20.28 Aligned_cols=39 Identities=15% Similarity=0.062 Sum_probs=18.2
Q ss_pred CCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCCcccceeee
Q psy16978 43 QTYTRFQTLELEKEFHFNHYLTRRRRIEIAHALCLTERQIKIWF 86 (154)
Q Consensus 43 ~~~t~~q~~~Le~~F~~~~~p~~~~~~~La~~l~l~~~qV~~WF 86 (154)
..+|.++...++..+. ......+||..+|.+...|..|.
T Consensus 3 ~~Lt~~eR~~I~~l~~-----~G~s~~~IA~~lg~s~sTV~rel 41 (44)
T PF13936_consen 3 KHLTPEERNQIEALLE-----QGMSIREIAKRLGRSRSTVSREL 41 (44)
T ss_dssp ---------HHHHHHC-----S---HHHHHHHTT--HHHHHHHH
T ss_pred cchhhhHHHHHHHHHH-----cCCCHHHHHHHHCcCcHHHHHHH
Confidence 3577777777777654 22445678999999988876554
No 66
>cd04764 HTH_MlrA-like_sg1 Helix-Turn-Helix DNA binding domain of putative MlrA-like transcription regulators. Putative helix-turn-helix (HTH) MlrA-like transcription regulators (subgroup 1). The MlrA protein, also known as YehV, has been shown to control cell-cell aggregation by co-regulating the expression of curli and extracellular matrix production in Escherichia coli and Salmonella typhimurium. These proteins belong to the MerR superfamily of transcription regulators that promote expression of several stress regulon genes by reconfiguring the spacer between the -35 and -10 promoter elements. Their conserved N-terminal domains contain predicted HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules. Many MlrA-like proteins in this group appear to lack the long dimerization helix seen in the N-terminal domains of typical MerR-like proteins.
Probab=34.66 E-value=14 Score=22.45 Aligned_cols=21 Identities=5% Similarity=0.210 Sum_probs=17.8
Q ss_pred HHHHHHHhCCCcccceeeecc
Q psy16978 68 RIEIAHALCLTERQIKIWFQN 88 (154)
Q Consensus 68 ~~~La~~l~l~~~qV~~WFqN 88 (154)
..++|+.+|++...|+.|-+.
T Consensus 3 i~evA~~~gvs~~tlR~~~~~ 23 (67)
T cd04764 3 IKEVSEIIGVKPHTLRYYEKE 23 (67)
T ss_pred HHHHHHHHCcCHHHHHHHHHh
Confidence 357899999999999999764
No 67
>PRK09652 RNA polymerase sigma factor RpoE; Provisional
Probab=33.92 E-value=28 Score=24.84 Aligned_cols=29 Identities=17% Similarity=0.114 Sum_probs=21.4
Q ss_pred HHHHHHHHhCCCcccceeeeccchhhHHH
Q psy16978 67 RRIEIAHALCLTERQIKIWFQNRRMKLKK 95 (154)
Q Consensus 67 ~~~~La~~l~l~~~qV~~WFqNrRak~kr 95 (154)
...++|..+|++...|+.|...-+.+.++
T Consensus 146 s~~eIA~~lgis~~tV~~~l~ra~~~Lr~ 174 (182)
T PRK09652 146 SYEEIAEIMGCPIGTVRSRIFRAREALRA 174 (182)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 34578999999999999988744444443
No 68
>PRK11924 RNA polymerase sigma factor; Provisional
Probab=33.64 E-value=28 Score=24.81 Aligned_cols=29 Identities=24% Similarity=0.252 Sum_probs=22.2
Q ss_pred HHHHHHHHhCCCcccceeeeccchhhHHH
Q psy16978 67 RRIEIAHALCLTERQIKIWFQNRRMKLKK 95 (154)
Q Consensus 67 ~~~~La~~l~l~~~qV~~WFqNrRak~kr 95 (154)
...++|..+|++...|..|..--|.+.|+
T Consensus 143 ~~~eIA~~lgis~~tv~~~~~ra~~~lr~ 171 (179)
T PRK11924 143 SYREIAEILGVPVGTVKSRLRRARQLLRE 171 (179)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 34679999999999999998755555443
No 69
>PRK12514 RNA polymerase sigma factor; Provisional
Probab=33.08 E-value=20 Score=25.98 Aligned_cols=28 Identities=18% Similarity=0.379 Sum_probs=21.2
Q ss_pred HHHHHHHHhCCCcccceeeeccchhhHH
Q psy16978 67 RRIEIAHALCLTERQIKIWFQNRRMKLK 94 (154)
Q Consensus 67 ~~~~La~~l~l~~~qV~~WFqNrRak~k 94 (154)
...++|..+|++...|+++...-|.+.|
T Consensus 147 s~~eIA~~lgis~~tV~~~l~Rar~~Lr 174 (179)
T PRK12514 147 SYKELAERHDVPLNTMRTWLRRSLLKLR 174 (179)
T ss_pred CHHHHHHHHCCChHHHHHHHHHHHHHHH
Confidence 3567899999999999888764444444
No 70
>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=32.74 E-value=41 Score=20.17 Aligned_cols=33 Identities=36% Similarity=0.416 Sum_probs=23.9
Q ss_pred HHHHHHHHHhhhcCCCCHHHHHHHHHHhCCCccccee
Q psy16978 48 FQTLELEKEFHFNHYLTRRRRIEIAHALCLTERQIKI 84 (154)
Q Consensus 48 ~q~~~Le~~F~~~~~p~~~~~~~La~~l~l~~~qV~~ 84 (154)
.|+..|+-.+. +...+.. +||..+|++++.|+.
T Consensus 6 rq~~Ll~~L~~-~~~~~~~---ela~~l~~S~rti~~ 38 (59)
T PF08280_consen 6 RQLKLLELLLK-NKWITLK---ELAKKLNISERTIKN 38 (59)
T ss_dssp HHHHHHHHHHH-HTSBBHH---HHHHHCTS-HHHHHH
T ss_pred HHHHHHHHHHc-CCCCcHH---HHHHHHCCCHHHHHH
Confidence 46777777777 6666644 899999999987754
No 71
>PRK12512 RNA polymerase sigma factor; Provisional
Probab=32.63 E-value=26 Score=25.52 Aligned_cols=30 Identities=17% Similarity=0.215 Sum_probs=23.3
Q ss_pred HHHHHHHHhCCCcccceeeeccchhhHHHh
Q psy16978 67 RRIEIAHALCLTERQIKIWFQNRRMKLKKE 96 (154)
Q Consensus 67 ~~~~La~~l~l~~~qV~~WFqNrRak~kr~ 96 (154)
...++|..+|++...|+.++..-|.+.|..
T Consensus 149 s~~eIA~~l~is~~tV~~~l~ra~~~Lr~~ 178 (184)
T PRK12512 149 SIKETAAKLSMSEGAVRVALHRGLAALAAK 178 (184)
T ss_pred CHHHHHHHhCCCHHHHHHHHHHHHHHHHHH
Confidence 455789999999999999887666665543
No 72
>PF00196 GerE: Bacterial regulatory proteins, luxR family; InterPro: IPR000792 This domain is a DNA-binding, helix-turn-helix (HTH) domain of about 65 amino acids, present in transcription regulators of the LuxR/FixJ family of response regulators. The domain is named after Vibrio fischeri luxR, a transcriptional activator for quorum-sensing control of luminescence. LuxR-type HTH domain proteins occur in a variety of organisms. The DNA-binding HTH domain is usually located in the C-terminal region; the N-terminal region often containing an autoinducer-binding domain or a response regulatory domain. Most luxR-type regulators act as transcription activators, but some can be repressors or have a dual role for different sites. LuxR-type HTH regulators control a wide variety of activities in various biological processes. The luxR-type, DNA-binding HTH domain forms a four-helical bundle structure. The HTH motif comprises the second and third helices, known as the scaffold and recognition helix, respectively. The HTH binds DNA in the major groove, where the N-terminal part of the recognition helix makes most of the DNA contacts. The fourth helix is involved in dimerisation of gerE and traR. Signalling events by one of the four activation mechanisms described below lead to multimerisation of the regulator. The regulators bind DNA as multimers [, , ]. LuxR-type HTH proteins can be activated by one of four different mechanisms: 1) Regulators which belong to a two-component sensory transduction system where the protein is activated by its phosphorylation, generally on an aspartate residue, by a transmembrane kinase [, ]. Some proteins that belong to this category are: Rhizobiaceae fixJ (global regulator inducing expression of nitrogen-fixation genes in microaerobiosis) Escherichia coli and Salmonella typhimurium uhpA (activates hexose phosphate transport gene uhpT) E. coli narL and narP (activate nitrate reductase operon) Enterobacteria rcsB (regulation of exopolysaccharide biosynthesis in enteric and plant pathogenesis) Bordetella pertussis bvgA (virulence factor) Bacillus subtilis coma (involved in expression of late-expressing competence genes) 2) Regulators which are activated, or in very rare cases repressed, when bound to N-acyl homoserine lactones, which are used as quorum sensing molecules in a variety of Gram-negative bacteria []: V. fischeri luxR (activates bioluminescence operon) Agrobacterium tumefaciens traR (regulation of Ti plasmid transfer) Erwinia carotovora carR (control of carbapenem antibiotics biosynthesis) E. carotovora expR (virulence factor for soft rot disease; activates plant tissue macerating enzyme genes) Pseudomonas aeruginosa lasR (activates elastase gene lasB) Erwinia chrysanthemi echR and Erwinia stewartii esaR Pseudomonas chlororaphis phzR (positive regulator of phenazine antibiotic production) Pseudomonas aeruginosa rhlR (activates rhlAB operon and lasB gene) 3) Autonomous effector domain regulators, without a regulatory domain, represented by gerE []. B. subtilis gerE (transcription activator and repressor for the regulation of spore formation) 4) Multiple ligand-binding regulators, exemplified by malT []. E. coli malT (activates maltose operon; MalT binds ATP and maltotriose); GO: 0003700 sequence-specific DNA binding transcription factor activity, 0043565 sequence-specific DNA binding, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 3SZT_A 3CLO_A 1H0M_A 1L3L_A 3C57_B 1ZLK_B 1ZLJ_H 3C3W_B 1RNL_A 1ZG1_A ....
Probab=32.46 E-value=27 Score=20.60 Aligned_cols=45 Identities=22% Similarity=0.124 Sum_probs=30.9
Q ss_pred CCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCCcccceeeeccchhhHH
Q psy16978 44 TYTRFQTLELEKEFHFNHYLTRRRRIEIAHALCLTERQIKIWFQNRRMKLK 94 (154)
Q Consensus 44 ~~t~~q~~~Le~~F~~~~~p~~~~~~~La~~l~l~~~qV~~WFqNrRak~k 94 (154)
.+|..+..+|.-... .....++|..+|+++..|..+..+=+.|..
T Consensus 3 ~LT~~E~~vl~~l~~------G~~~~eIA~~l~is~~tV~~~~~~i~~Kl~ 47 (58)
T PF00196_consen 3 SLTERELEVLRLLAQ------GMSNKEIAEELGISEKTVKSHRRRIMKKLG 47 (58)
T ss_dssp SS-HHHHHHHHHHHT------TS-HHHHHHHHTSHHHHHHHHHHHHHHHHT
T ss_pred ccCHHHHHHHHHHHh------cCCcchhHHhcCcchhhHHHHHHHHHHHhC
Confidence 477778777765542 233567899999999999988766555543
No 73
>PRK09480 slmA division inhibitor protein; Provisional
Probab=32.43 E-value=31 Score=25.05 Aligned_cols=37 Identities=11% Similarity=0.098 Sum_probs=29.5
Q ss_pred HHHhhhcCCCCHHHHHHHHHHhCCCcccceeeeccchh
Q psy16978 54 EKEFHFNHYLTRRRRIEIAHALCLTERQIKIWFQNRRM 91 (154)
Q Consensus 54 e~~F~~~~~p~~~~~~~La~~l~l~~~qV~~WFqNrRa 91 (154)
...|...+. .......||...|++...+-.+|.|+-.
T Consensus 20 ~~l~~~~~G-~~~ti~~Ia~~agvs~gt~Y~~F~~K~~ 56 (194)
T PRK09480 20 AQMLESPPG-ERITTAKLAARVGVSEAALYRHFPSKAR 56 (194)
T ss_pred HHHHHhcCC-CccCHHHHHHHhCCCHhHHHHHCCCHHH
Confidence 344555545 7777889999999999999999999763
No 74
>PRK12526 RNA polymerase sigma factor; Provisional
Probab=32.10 E-value=44 Score=25.07 Aligned_cols=29 Identities=21% Similarity=0.179 Sum_probs=21.5
Q ss_pred HHHHHHHHhCCCcccceeeeccchhhHHH
Q psy16978 67 RRIEIAHALCLTERQIKIWFQNRRMKLKK 95 (154)
Q Consensus 67 ~~~~La~~l~l~~~qV~~WFqNrRak~kr 95 (154)
...++|..+|++...|+++...-+.+.++
T Consensus 171 s~~EIA~~lgis~~tV~~~l~Ra~~~Lr~ 199 (206)
T PRK12526 171 SQEQLAQQLNVPLGTVKSRLRLALAKLKV 199 (206)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 45678999999999998887655554443
No 75
>PRK04217 hypothetical protein; Provisional
Probab=31.83 E-value=52 Score=22.78 Aligned_cols=48 Identities=10% Similarity=-0.104 Sum_probs=33.3
Q ss_pred CCCCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCCcccceeeeccchhhH
Q psy16978 41 GRQTYTRFQTLELEKEFHFNHYLTRRRRIEIAHALCLTERQIKIWFQNRRMKL 93 (154)
Q Consensus 41 ~R~~~t~~q~~~Le~~F~~~~~p~~~~~~~La~~l~l~~~qV~~WFqNrRak~ 93 (154)
.-..++.++..++...|...- ...++|..+|++...|...+..-+.+.
T Consensus 39 p~~~Lt~eereai~l~~~eGl-----S~~EIAk~LGIS~sTV~r~L~RArkkL 86 (110)
T PRK04217 39 PPIFMTYEEFEALRLVDYEGL-----TQEEAGKRMGVSRGTVWRALTSARKKV 86 (110)
T ss_pred CcccCCHHHHHHHHHHHHcCC-----CHHHHHHHHCcCHHHHHHHHHHHHHHH
Confidence 345678888877776654322 456799999999999888775444433
No 76
>COG2963 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=31.76 E-value=68 Score=21.67 Aligned_cols=42 Identities=19% Similarity=0.208 Sum_probs=31.5
Q ss_pred CCCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCC-Ccccceeeec
Q psy16978 42 RQTYTRFQTLELEKEFHFNHYLTRRRRIEIAHALCL-TERQIKIWFQ 87 (154)
Q Consensus 42 R~~~t~~q~~~Le~~F~~~~~p~~~~~~~La~~l~l-~~~qV~~WFq 87 (154)
|..|+.+....+-..+....+ ....+|..+|+ ...++..|-.
T Consensus 5 ~r~~s~EfK~~iv~~~~~~g~----sv~~vAr~~gv~~~~~l~~W~~ 47 (116)
T COG2963 5 RKKYSPEFKLEAVALYLRGGD----TVSEVAREFGIVSATQLYKWRI 47 (116)
T ss_pred cccCCHHHHHHHHHHHHhcCc----cHHHHHHHhCCCChHHHHHHHH
Confidence 677999877666666655554 46788999996 9988887764
No 77
>cd04763 HTH_MlrA-like Helix-Turn-Helix DNA binding domain of MlrA-like transcription regulators. Helix-turn-helix (HTH) transcription regulator MlrA (merR-like regulator A) and related proteins, N-terminal domain. The MlrA protein, also known as YehV, has been shown to control cell-cell aggregation by co-regulating the expression of curli and extracellular matrix production in Escherichia coli and Salmonella typhimurium. Its close homolog, CarA from Myxococcus xanthus, is involved in activation of the carotenoid biosynthesis genes by light. These proteins belong to the MerR superfamily of transcription regulators that promote expression of several stress regulon genes by reconfiguring the spacer between the -35 and -10 promoter elements. Their conserved N-terminal domains contain predicted HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules. Many MlrA-like proteins in this group appear to lack the long dimerization helix seen
Probab=31.15 E-value=15 Score=22.45 Aligned_cols=21 Identities=14% Similarity=0.235 Sum_probs=17.9
Q ss_pred HHHHHHHhCCCcccceeeecc
Q psy16978 68 RIEIAHALCLTERQIKIWFQN 88 (154)
Q Consensus 68 ~~~La~~l~l~~~qV~~WFqN 88 (154)
..++|+.+|++...|+.|.+.
T Consensus 3 i~e~A~~~gVs~~tlr~ye~~ 23 (68)
T cd04763 3 IGEVALLTGIKPHVLRAWERE 23 (68)
T ss_pred HHHHHHHHCcCHHHHHHHHHh
Confidence 357899999999999999764
No 78
>PF00157 Pou: Pou domain - N-terminal to homeobox domain; InterPro: IPR000327 POU proteins are eukaryotic transcription factors containing a bipartite DNA binding domain referred to as the POU domain. The acronym POU (pronounced 'pow') is derived from the names of three mammalian transcription factors, the pituitary-specific Pit-1, the octamer-binding proteins Oct-1 and Oct-2, and the neural Unc-86 from Caenorhabditis elegans. POU domain genes have been identified in diverse organisms including nematodes, flies, amphibians, fish and mammals but have not been yet identified in plants and fungi. The various members of the POU family have a wide variety of functions, all of which are related to the function of the neuroendocrine system [] and the development of an organism []. Some other genes are also regulated, including those for immunoglobulin light and heavy chains (Oct-2) [, ], and trophic hormone genes, such as those for prolactin and growth hormone (Pit-1). The POU domain is a bipartite domain composed of two subunits separated by a non-conserved region of 15-55 aa. The N-terminal subunit is known as the POU-specific (POUs) domain (IPR000327 from INTERPRO), while the C-terminal subunit is a homeobox domain (IPR007103 from INTERPRO). 3D structures of complexes including both POU subdomains bound to DNA are available. Both subdomains contain the structural motif 'helix-turn-helix', which directly associates with the two components of bipartite DNA binding sites, and both are required for high affinity sequence-specific DNA-binding. The domain may also be involved in protein-protein interactions []. The subdomains are connected by a flexible linker [, , ]. In proteins a POU-specific domain is always accompanied by a homeodomain. Despite of the lack of sequence homology, 3D structure of POUs is similar to 3D structure of bacteriophage lambda repressor and other members of HTH_3 family [, ]. This entry represents the POU-specific subunit of the POU domain.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent; PDB: 3D1N_O 1AU7_A 3L1P_A 2XSD_C 1O4X_A 1HF0_B 1GT0_C 1POU_A 1CQT_B 1E3O_C ....
Probab=30.90 E-value=22 Score=23.02 Aligned_cols=27 Identities=15% Similarity=0.214 Sum_probs=21.0
Q ss_pred CCccccccchhhHHHHHhhhHHHHhhh
Q psy16978 1 MCFPLEIRFTHQLVIVLNVHFAKMLCQ 27 (154)
Q Consensus 1 ~~~~~~~~~~~~~~~~~~~~~~~~~~~ 27 (154)
||||..+......+..+.+.+.+++.+
T Consensus 47 I~RFE~L~LS~kn~~klkP~L~kWL~e 73 (75)
T PF00157_consen 47 ICRFEALQLSFKNMCKLKPLLEKWLEE 73 (75)
T ss_dssp HHHHHTTTSCHHHHHHHHHHHHHHHHH
T ss_pred hhhhHhcccCHHHHHHHHHHHHHHHHh
Confidence 688888888887777777777777654
No 79
>cd04762 HTH_MerR-trunc Helix-Turn-Helix DNA binding domain of truncated MerR-like proteins. Proteins in this family mostly have a truncated helix-turn-helix (HTH) MerR-like domain. They lack a portion of the C-terminal region, called Wing 2 and the long dimerization helix that is typically present in MerR-like proteins. These truncated domains are found in response regulator receiver (REC) domain proteins (i.e., CheY), cytosine-C5 specific DNA methylases, IS607 transposase-like proteins, and RacA, a bacterial protein that anchors chromosomes to cell poles.
Probab=30.68 E-value=16 Score=19.95 Aligned_cols=24 Identities=17% Similarity=0.432 Sum_probs=19.4
Q ss_pred HHHHHHHhCCCcccceeeeccchh
Q psy16978 68 RIEIAHALCLTERQIKIWFQNRRM 91 (154)
Q Consensus 68 ~~~La~~l~l~~~qV~~WFqNrRa 91 (154)
..++|..+|++...|..|..+...
T Consensus 3 ~~e~a~~lgvs~~tl~~~~~~g~~ 26 (49)
T cd04762 3 TKEAAELLGVSPSTLRRWVKEGKL 26 (49)
T ss_pred HHHHHHHHCcCHHHHHHHHHcCCC
Confidence 357899999999999999866543
No 80
>KOG3755|consensus
Probab=30.57 E-value=8.9 Score=34.30 Aligned_cols=61 Identities=11% Similarity=0.088 Sum_probs=0.0
Q ss_pred CCCCCCCCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhC-------CCcccceeeeccchhhHHHhH
Q psy16978 37 PRRRGRQTYTRFQTLELEKEFHFNHYLTRRRRIEIAHALC-------LTERQIKIWFQNRRMKLKKEL 97 (154)
Q Consensus 37 ~~rr~R~~~t~~q~~~Le~~F~~~~~p~~~~~~~La~~l~-------l~~~qV~~WFqNrRak~kr~~ 97 (154)
+++..-..|-..-..+-+.+|..+..+......+--.... .....|+.||.|||+++++.+
T Consensus 691 pk~~~~k~f~~~~~ev~~~w~~k~~s~s~~~v~eYkee~~~~~~~e~~~~kn~~~~fk~~~ee~~~~k 758 (769)
T KOG3755|consen 691 PKKTIIKFFQNQRYEVKHHWKLKTRSGSWVDVAEYKEEELLMPYEEKFESKNVQFWFKVRREEEKRLK 758 (769)
T ss_pred cHHHHHHhhhcceeecchhheecccCchhHHHHHhhHHhhcchhhhhhhhcchHHHHHHHHHHHhhhh
No 81
>COG4367 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=30.39 E-value=52 Score=22.06 Aligned_cols=38 Identities=29% Similarity=0.207 Sum_probs=26.6
Q ss_pred CCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCCcccc
Q psy16978 45 YTRFQTLELEKEFHFNHYLTRRRRIEIAHALCLTERQI 82 (154)
Q Consensus 45 ~t~~q~~~Le~~F~~~~~p~~~~~~~La~~l~l~~~qV 82 (154)
++++|...-...|+.+--.+.....++|..|+.++-.|
T Consensus 3 Ln~eq~~~Tk~elqan~el~~LS~~~iA~~Ln~t~~~l 40 (97)
T COG4367 3 LNPEQKQRTKQELQANFELCPLSDEEIATALNWTEVKL 40 (97)
T ss_pred CCHHHHHHHHHHHHHhhhhccccHHHHHHHhCCCHHHH
Confidence 56677666666666666566677788999999887443
No 82
>PRK09642 RNA polymerase sigma factor SigW; Reviewed
Probab=30.32 E-value=22 Score=25.20 Aligned_cols=28 Identities=21% Similarity=0.173 Sum_probs=21.3
Q ss_pred HHHHHHHhCCCcccceeeeccchhhHHH
Q psy16978 68 RIEIAHALCLTERQIKIWFQNRRMKLKK 95 (154)
Q Consensus 68 ~~~La~~l~l~~~qV~~WFqNrRak~kr 95 (154)
..++|..+|++...|++....-|.+.|.
T Consensus 125 ~~EIA~~lgis~~tV~~~l~Rar~~Lr~ 152 (160)
T PRK09642 125 YQEIALQEKIEVKTVEMKLYRARKWIKK 152 (160)
T ss_pred HHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 4568999999999999988655555444
No 83
>PRK00118 putative DNA-binding protein; Validated
Probab=29.71 E-value=42 Score=23.00 Aligned_cols=49 Identities=14% Similarity=-0.001 Sum_probs=32.9
Q ss_pred CCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCCcccceeeeccchhhHHHhHH
Q psy16978 45 YTRFQTLELEKEFHFNHYLTRRRRIEIAHALCLTERQIKIWFQNRRMKLKKELR 98 (154)
Q Consensus 45 ~t~~q~~~Le~~F~~~~~p~~~~~~~La~~l~l~~~qV~~WFqNrRak~kr~~~ 98 (154)
++..+..++...|... ....++|..+|++...|..|...-|.+.+....
T Consensus 18 L~ekqRevl~L~y~eg-----~S~~EIAe~lGIS~~TV~r~L~RArkkLr~~~~ 66 (104)
T PRK00118 18 LTEKQRNYMELYYLDD-----YSLGEIAEEFNVSRQAVYDNIKRTEKLLEDYEE 66 (104)
T ss_pred CCHHHHHHHHHHHHcC-----CCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHH
Confidence 4555666665554432 234578999999999999998766665554433
No 84
>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=28.75 E-value=31 Score=23.39 Aligned_cols=27 Identities=30% Similarity=0.309 Sum_probs=20.0
Q ss_pred HHHHHHHHhCCCcccceeeeccchhhH
Q psy16978 67 RRIEIAHALCLTERQIKIWFQNRRMKL 93 (154)
Q Consensus 67 ~~~~La~~l~l~~~qV~~WFqNrRak~ 93 (154)
...++|..+|+++..|..|...-+.+.
T Consensus 128 s~~eIA~~l~~s~~~v~~~~~~~~~kl 154 (158)
T TIGR02937 128 SYKEIAEILGISVGTVKRRLKRARKKL 154 (158)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHH
Confidence 455789999999999988776444433
No 85
>cd01104 HTH_MlrA-CarA Helix-Turn-Helix DNA binding domain of the transcription regulators MlrA and CarA. Helix-turn-helix (HTH) transcription regulator MlrA (merR-like regulator A), N-terminal domain. The MlrA protein, also known as YehV, has been shown to control cell-cell aggregation by co-regulating the expression of curli and extracellular matrix production in Escherichia coli and Salmonella typhimurium. Its close homolog, CarA from Myxococcus xanthus, is involved in activation of the carotenoid biosynthesis genes by light. These proteins belong to the MerR superfamily of transcription regulators that promote expression of several stress regulon genes by reconfiguring the spacer between the -35 and -10 promoter elements. Their conserved N-terminal domains contain predicted HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules. Many MlrA- and CarA-like proteins in this group appear to lack the long dimerization helix seen i
Probab=28.43 E-value=21 Score=21.58 Aligned_cols=20 Identities=10% Similarity=0.230 Sum_probs=17.3
Q ss_pred HHHHHHHhCCCcccceeeec
Q psy16978 68 RIEIAHALCLTERQIKIWFQ 87 (154)
Q Consensus 68 ~~~La~~l~l~~~qV~~WFq 87 (154)
..++|+.+|++...|+.|-+
T Consensus 3 ~~eva~~~gvs~~tlr~w~~ 22 (68)
T cd01104 3 IGAVARLTGVSPDTLRAWER 22 (68)
T ss_pred HHHHHHHHCcCHHHHHHHHH
Confidence 35789999999999999985
No 86
>KOG0773|consensus
Probab=28.29 E-value=38 Score=27.69 Aligned_cols=44 Identities=39% Similarity=0.603 Sum_probs=36.6
Q ss_pred HHhhhcCCCCHHHHHHHHHHhCCCcccceeeeccchhhHHHhHH
Q psy16978 55 KEFHFNHYLTRRRRIEIAHALCLTERQIKIWFQNRRMKLKKELR 98 (154)
Q Consensus 55 ~~F~~~~~p~~~~~~~La~~l~l~~~qV~~WFqNrRak~kr~~~ 98 (154)
..-..++|++..+...++....++..+|.+||-|-|.+.+....
T Consensus 114 ~~~~~~~~~~k~~~~ll~~~~~~~~~~~~~~~~~a~r~~~~~~~ 157 (342)
T KOG0773|consen 114 EEHRLNPYPSKLEKILLAVITKLTLTQVSTWFANARRRLKKELK 157 (342)
T ss_pred hhhhhccCchHHHHHHHHHHHHhhhhhHHHHHHHHHHHHHhccC
Confidence 33456889999999999999999999999999998877665444
No 87
>PF04936 DUF658: Protein of unknown function (DUF658); InterPro: IPR007020 This entry is represented by Bacteriophage r1t, Orf18. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. These are proteins of unknown function found in Lactococcus lactis and in their associated bacteriophage.
Probab=27.83 E-value=16 Score=27.29 Aligned_cols=32 Identities=13% Similarity=0.312 Sum_probs=27.4
Q ss_pred HHHHHHHHhCCCcccceeeeccchhhHHHhHH
Q psy16978 67 RRIEIAHALCLTERQIKIWFQNRRMKLKKELR 98 (154)
Q Consensus 67 ~~~~La~~l~l~~~qV~~WFqNrRak~kr~~~ 98 (154)
.+.+|+.-++++..+|-.|..|-+...+....
T Consensus 16 t~~e~~~~~~VS~~sv~~WiKNG~~~~~a~~~ 47 (186)
T PF04936_consen 16 TIDELADYFDVSRTSVSVWIKNGKDPKRAKPK 47 (186)
T ss_pred cHHHHHHHHccCHHHHHHHHHcCCCcccccch
Confidence 46789999999999999999999888775544
No 88
>PRK09639 RNA polymerase sigma factor SigX; Provisional
Probab=27.46 E-value=54 Score=23.19 Aligned_cols=29 Identities=28% Similarity=0.335 Sum_probs=21.7
Q ss_pred HHHHHHHHhCCCcccceeeeccchhhHHH
Q psy16978 67 RRIEIAHALCLTERQIKIWFQNRRMKLKK 95 (154)
Q Consensus 67 ~~~~La~~l~l~~~qV~~WFqNrRak~kr 95 (154)
...++|..+|++...|+.+...-|.+.|+
T Consensus 129 s~~eIA~~lgis~~tV~~~i~ra~~~Lr~ 157 (166)
T PRK09639 129 SYKEIAEALGIKESSVGTTLARAKKKFRK 157 (166)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 44578999999999999888655555444
No 89
>cd00131 PAX Paired Box domain
Probab=26.88 E-value=2.3e+02 Score=19.84 Aligned_cols=45 Identities=11% Similarity=-0.124 Sum_probs=27.4
Q ss_pred CCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCC-------Ccccceeeecc
Q psy16978 44 TYTRFQTLELEKEFHFNHYLTRRRRIEIAHALCL-------TERQIKIWFQN 88 (154)
Q Consensus 44 ~~t~~q~~~Le~~F~~~~~p~~~~~~~La~~l~l-------~~~qV~~WFqN 88 (154)
..+..+...++.....++..+..+..++...-|+ +...|--||++
T Consensus 75 ~~~~~~~~~i~~~v~~~p~~Tl~El~~~L~~~gv~~~~~~~s~stI~R~L~~ 126 (128)
T cd00131 75 VATPEVVKKIEIYKQENPGMFAWEIRDRLLQEGVCDKSNVPSVSSINRILRN 126 (128)
T ss_pred cCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHcCCcccCCCCCHHHHHHHHHh
Confidence 3455666666666677887777766544223355 66666666543
No 90
>COG1905 NuoE NADH:ubiquinone oxidoreductase 24 kD subunit [Energy production and conversion]
Probab=26.79 E-value=98 Score=22.96 Aligned_cols=36 Identities=17% Similarity=0.041 Sum_probs=31.0
Q ss_pred HHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCCcccc
Q psy16978 47 RFQTLELEKEFHFNHYLTRRRRIEIAHALCLTERQI 82 (154)
Q Consensus 47 ~~q~~~Le~~F~~~~~p~~~~~~~La~~l~l~~~qV 82 (154)
..-+..|...+....|........+|..||++...|
T Consensus 25 sAlip~L~~aQ~~~G~l~~~ai~~iA~~L~i~~~~v 60 (160)
T COG1905 25 SALIPLLHIAQEQFGWLPPEAIEEIADMLGIPRARV 60 (160)
T ss_pred hHHHHHHHHHHHHhCCCCHHHHHHHHHHhCCCHHHh
Confidence 456788888888888999999999999999997664
No 91
>cd01392 HTH_LacI Helix-turn-helix (HTH) DNA binding domain of the LacI family of transcriptional regulators. HTH-DNA binding domain of the LacI (lactose operon repressor) family of bacterial transcriptional regulators and their putative homologs found in plants. The LacI family has more than 500 members distributed among almost all bacterial species. The monomeric proteins of the LacI family contain common structural features that include a small DNA-binding domain with a helix-turn-helix motif in the N-terminus, a regulatory ligand-binding domain which exhibits the type I periplasmic binding protein fold in the C-terminus for oligomerization and for effector binding, and an approximately 18-amino acid linker connecting these two functional domains. In LacI-like transcriptional regulators, the ligands are monosaccharides including lactose, ribose, fructose, xylose, arabinose, galactose/glucose, and other sugars, with a few exceptions. When the C-terminal domain of the LacI family repre
Probab=26.78 E-value=16 Score=20.87 Aligned_cols=21 Identities=14% Similarity=0.205 Sum_probs=18.9
Q ss_pred HHHHHhCCCcccceeeeccch
Q psy16978 70 EIAHALCLTERQIKIWFQNRR 90 (154)
Q Consensus 70 ~La~~l~l~~~qV~~WFqNrR 90 (154)
+||..+|++...|..|+.++.
T Consensus 2 ~lA~~~gvs~~tvs~~l~g~~ 22 (52)
T cd01392 2 DIARAAGVSVATVSRVLNGKP 22 (52)
T ss_pred cHHHHHCcCHHHHHHHHcCCC
Confidence 589999999999999998874
No 92
>PRK12518 RNA polymerase sigma factor; Provisional
Probab=26.34 E-value=31 Score=24.82 Aligned_cols=32 Identities=25% Similarity=0.235 Sum_probs=24.1
Q ss_pred CHHHHHHHHHHhCCCcccceeeeccchhhHHH
Q psy16978 64 TRRRRIEIAHALCLTERQIKIWFQNRRMKLKK 95 (154)
Q Consensus 64 ~~~~~~~La~~l~l~~~qV~~WFqNrRak~kr 95 (154)
......++|..+|++...|++.+..-|.+.++
T Consensus 135 ~g~s~~eIA~~lg~s~~tv~~~l~Rar~~L~~ 166 (175)
T PRK12518 135 EDLPQKEIAEILNIPVGTVKSRLFYARRQLRK 166 (175)
T ss_pred cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 33446779999999999999988655555554
No 93
>PRK06986 fliA flagellar biosynthesis sigma factor; Validated
Probab=26.27 E-value=38 Score=26.01 Aligned_cols=29 Identities=17% Similarity=0.214 Sum_probs=23.0
Q ss_pred HHHHHHHHhCCCcccceeeeccchhhHHH
Q psy16978 67 RRIEIAHALCLTERQIKIWFQNRRMKLKK 95 (154)
Q Consensus 67 ~~~~La~~l~l~~~qV~~WFqNrRak~kr 95 (154)
...++|..+|++...|+.+...-+.+.|+
T Consensus 202 s~~EIA~~lgis~~tV~~~~~ra~~~Lr~ 230 (236)
T PRK06986 202 NLKEIGAVLGVSESRVSQIHSQAIKRLRA 230 (236)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 45679999999999999988766665554
No 94
>PRK05602 RNA polymerase sigma factor; Reviewed
Probab=25.58 E-value=38 Score=24.74 Aligned_cols=29 Identities=17% Similarity=0.250 Sum_probs=21.8
Q ss_pred HHHHHHHHhCCCcccceeeeccchhhHHH
Q psy16978 67 RRIEIAHALCLTERQIKIWFQNRRMKLKK 95 (154)
Q Consensus 67 ~~~~La~~l~l~~~qV~~WFqNrRak~kr 95 (154)
...++|..+|++...|+.+...-|.+.|+
T Consensus 146 s~~EIA~~lgis~~tV~~~l~Rar~~Lr~ 174 (186)
T PRK05602 146 SNIEAAAVMDISVDALESLLARGRRALRA 174 (186)
T ss_pred CHHHHHHHhCcCHHHHHHHHHHHHHHHHH
Confidence 34568999999999999988655555554
No 95
>PF01381 HTH_3: Helix-turn-helix; InterPro: IPR001387 This is large family of DNA binding helix-turn helix proteins that include a bacterial plasmid copy control protein, bacterial methylases, various bacteriophage transcription control proteins and a vegetative specific protein from Dictyostelium discoideum (Slime mould).; GO: 0043565 sequence-specific DNA binding; PDB: 2AXU_A 2AWI_D 2AXV_D 2AXZ_C 2AW6_A 3KXA_C 3BS3_A 2CRO_A 1ZUG_A 3CRO_R ....
Probab=25.27 E-value=23 Score=20.32 Aligned_cols=24 Identities=21% Similarity=0.238 Sum_probs=19.5
Q ss_pred HHHHHHHhCCCcccceeeeccchh
Q psy16978 68 RIEIAHALCLTERQIKIWFQNRRM 91 (154)
Q Consensus 68 ~~~La~~l~l~~~qV~~WFqNrRa 91 (154)
..+||..+|++...|..|..+.+.
T Consensus 12 ~~~la~~~gis~~~i~~~~~g~~~ 35 (55)
T PF01381_consen 12 QKELAEKLGISRSTISRIENGKRN 35 (55)
T ss_dssp HHHHHHHHTS-HHHHHHHHTTSST
T ss_pred HHHHHHHhCCCcchhHHHhcCCCC
Confidence 367999999999999999988653
No 96
>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=25.24 E-value=70 Score=20.71 Aligned_cols=20 Identities=5% Similarity=0.232 Sum_probs=17.1
Q ss_pred HHHHHHHhCCCcccceeeec
Q psy16978 68 RIEIAHALCLTERQIKIWFQ 87 (154)
Q Consensus 68 ~~~La~~l~l~~~qV~~WFq 87 (154)
+..|...++|..-+|.+|+.
T Consensus 56 ~~~L~k~~~~~~~~i~v~~~ 75 (81)
T cd02413 56 TSLVQKRFNFPEGSVELYAE 75 (81)
T ss_pred HHHHHHHhCCCCCeEEEEEE
Confidence 45688889999999999985
No 97
>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=24.96 E-value=31 Score=23.99 Aligned_cols=26 Identities=15% Similarity=0.197 Sum_probs=18.8
Q ss_pred HHHHHHHHhCCCcccceeeeccchhh
Q psy16978 67 RRIEIAHALCLTERQIKIWFQNRRMK 92 (154)
Q Consensus 67 ~~~~La~~l~l~~~qV~~WFqNrRak 92 (154)
...++|..+|+++..|+.+...-+.+
T Consensus 131 ~~~eIA~~lgis~~tv~~~~~ra~~~ 156 (161)
T TIGR02985 131 SYKEIAEELGISVKTVEYHISKALKE 156 (161)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHH
Confidence 34568999999999988876543333
No 98
>PRK12519 RNA polymerase sigma factor; Provisional
Probab=24.67 E-value=37 Score=24.92 Aligned_cols=31 Identities=23% Similarity=0.237 Sum_probs=23.1
Q ss_pred HHHHHHHHHHhCCCcccceeeeccchhhHHH
Q psy16978 65 RRRRIEIAHALCLTERQIKIWFQNRRMKLKK 95 (154)
Q Consensus 65 ~~~~~~La~~l~l~~~qV~~WFqNrRak~kr 95 (154)
.....++|..+|++...|+.|+..-|.+.++
T Consensus 157 g~s~~EIA~~lgis~~tV~~~l~Ra~~~Lr~ 187 (194)
T PRK12519 157 GLSQSEIAKRLGIPLGTVKARARQGLLKLRE 187 (194)
T ss_pred CCCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Confidence 3445678999999999999998655555443
No 99
>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=24.62 E-value=30 Score=25.15 Aligned_cols=30 Identities=10% Similarity=0.007 Sum_probs=22.2
Q ss_pred HHHHHHHHHhCCCcccceeeeccchhhHHH
Q psy16978 66 RRRIEIAHALCLTERQIKIWFQNRRMKLKK 95 (154)
Q Consensus 66 ~~~~~La~~l~l~~~qV~~WFqNrRak~kr 95 (154)
..-.++|..+|++...|+++...-|.+.|.
T Consensus 155 ~s~~EIA~~lgis~~tv~~~l~rar~~Lr~ 184 (190)
T TIGR02939 155 LSYEDIARIMDCPVGTVRSRIFRAREAIAI 184 (190)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 345678999999999999888654544443
No 100
>PRK09047 RNA polymerase factor sigma-70; Validated
Probab=24.45 E-value=1e+02 Score=21.57 Aligned_cols=27 Identities=22% Similarity=0.169 Sum_probs=19.5
Q ss_pred HHHHHHHhCCCcccceeeeccchhhHH
Q psy16978 68 RIEIAHALCLTERQIKIWFQNRRMKLK 94 (154)
Q Consensus 68 ~~~La~~l~l~~~qV~~WFqNrRak~k 94 (154)
..++|..+|++...|++....-|.+.|
T Consensus 125 ~~EIA~~lgis~~tV~~~l~ra~~~Lr 151 (161)
T PRK09047 125 VAETAAAMGCSEGSVKTHCSRATHALA 151 (161)
T ss_pred HHHHHHHHCCCHHHHHHHHHHHHHHHH
Confidence 457899999999999887654343333
No 101
>PRK12543 RNA polymerase sigma factor; Provisional
Probab=24.12 E-value=51 Score=23.94 Aligned_cols=32 Identities=22% Similarity=0.224 Sum_probs=23.8
Q ss_pred HHHHHHHHhCCCcccceeeeccchhhHHHhHH
Q psy16978 67 RRIEIAHALCLTERQIKIWFQNRRMKLKKELR 98 (154)
Q Consensus 67 ~~~~La~~l~l~~~qV~~WFqNrRak~kr~~~ 98 (154)
...++|..+|++...|++....-|.+.|+...
T Consensus 135 s~~EIA~~lgis~~tV~~~l~ra~~~Lr~~l~ 166 (179)
T PRK12543 135 SQEEIAQLLQIPIGTVKSRIHAALKKLRQKEQ 166 (179)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Confidence 34568999999999999887766666665443
No 102
>PRK09644 RNA polymerase sigma factor SigM; Provisional
Probab=24.00 E-value=34 Score=24.44 Aligned_cols=29 Identities=28% Similarity=0.165 Sum_probs=21.9
Q ss_pred HHHHHHHHhCCCcccceeeeccchhhHHH
Q psy16978 67 RRIEIAHALCLTERQIKIWFQNRRMKLKK 95 (154)
Q Consensus 67 ~~~~La~~l~l~~~qV~~WFqNrRak~kr 95 (154)
...++|..+|++...|++|...-|.+.++
T Consensus 126 s~~eIA~~lgis~~tv~~~l~Rar~~Lr~ 154 (165)
T PRK09644 126 TYEEAASVLDLKLNTYKSHLFRGRKRLKA 154 (165)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 45678999999999999988655555444
No 103
>smart00421 HTH_LUXR helix_turn_helix, Lux Regulon. lux regulon (activates the bioluminescence operon
Probab=23.91 E-value=42 Score=18.74 Aligned_cols=38 Identities=21% Similarity=0.166 Sum_probs=26.4
Q ss_pred CCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCCcccceeeec
Q psy16978 44 TYTRFQTLELEKEFHFNHYLTRRRRIEIAHALCLTERQIKIWFQ 87 (154)
Q Consensus 44 ~~t~~q~~~Le~~F~~~~~p~~~~~~~La~~l~l~~~qV~~WFq 87 (154)
.++..+..++...+ .. ....++|..+|++...|..|..
T Consensus 3 ~l~~~e~~i~~~~~--~g----~s~~eia~~l~is~~tv~~~~~ 40 (58)
T smart00421 3 SLTPREREVLRLLA--EG----LTNKEIAERLGISEKTVKTHLS 40 (58)
T ss_pred CCCHHHHHHHHHHH--cC----CCHHHHHHHHCCCHHHHHHHHH
Confidence 35677777665532 22 2456789999999999988775
No 104
>TIGR02948 SigW_bacill RNA polymerase sigma-W factor. This sigma factor is restricted to certain lineages of the order Bacillales.
Probab=23.57 E-value=33 Score=24.85 Aligned_cols=30 Identities=27% Similarity=0.240 Sum_probs=22.3
Q ss_pred HHHHHHHHHhCCCcccceeeeccchhhHHH
Q psy16978 66 RRRIEIAHALCLTERQIKIWFQNRRMKLKK 95 (154)
Q Consensus 66 ~~~~~La~~l~l~~~qV~~WFqNrRak~kr 95 (154)
....++|..+|++...|+++...-|.+.+.
T Consensus 153 ~s~~eIA~~lgis~~~v~~~l~Rar~~Lr~ 182 (187)
T TIGR02948 153 LSLKEISEILDLPVGTVKTRIHRGREALRK 182 (187)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 345678999999999999988655555443
No 105
>PRK12515 RNA polymerase sigma factor; Provisional
Probab=23.41 E-value=89 Score=22.79 Aligned_cols=29 Identities=21% Similarity=0.236 Sum_probs=21.0
Q ss_pred HHHHHHHHhCCCcccceeeeccchhhHHH
Q psy16978 67 RRIEIAHALCLTERQIKIWFQNRRMKLKK 95 (154)
Q Consensus 67 ~~~~La~~l~l~~~qV~~WFqNrRak~kr 95 (154)
...++|..+|++...|++-...-|.+.+.
T Consensus 149 s~~eIA~~lgis~~tV~~~l~Rar~~Lr~ 177 (189)
T PRK12515 149 SVEEVGEIVGIPESTVKTRMFYARKKLAE 177 (189)
T ss_pred CHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 34568999999999998877655555443
No 106
>smart00422 HTH_MERR helix_turn_helix, mercury resistance.
Probab=23.14 E-value=30 Score=20.87 Aligned_cols=20 Identities=15% Similarity=0.185 Sum_probs=16.4
Q ss_pred HHHHHHHhCCCcccceeeec
Q psy16978 68 RIEIAHALCLTERQIKIWFQ 87 (154)
Q Consensus 68 ~~~La~~l~l~~~qV~~WFq 87 (154)
..++|+.+|++...|+.|-.
T Consensus 3 ~~eva~~~gvs~~tlr~~~~ 22 (70)
T smart00422 3 IGEVAKLAGVSVRTLRYYER 22 (70)
T ss_pred HHHHHHHHCcCHHHHHHHHH
Confidence 35689999999999999854
No 107
>PRK09648 RNA polymerase sigma factor SigD; Reviewed
Probab=22.97 E-value=48 Score=24.20 Aligned_cols=29 Identities=17% Similarity=0.130 Sum_probs=20.4
Q ss_pred HHHHHHHHHhCCCcccceeeeccchhhHH
Q psy16978 66 RRRIEIAHALCLTERQIKIWFQNRRMKLK 94 (154)
Q Consensus 66 ~~~~~La~~l~l~~~qV~~WFqNrRak~k 94 (154)
....++|..+|++...|+.+...-|.+.|
T Consensus 156 ~s~~EIA~~lgis~~tV~~~l~Ra~~~Lr 184 (189)
T PRK09648 156 LSAEETAEAVGSTPGAVRVAQHRALARLR 184 (189)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Confidence 34567899999999999887754343333
No 108
>PRK08301 sporulation sigma factor SigE; Reviewed
Probab=22.87 E-value=66 Score=24.53 Aligned_cols=30 Identities=23% Similarity=0.253 Sum_probs=21.8
Q ss_pred HHHHHHHHHhCCCcccceeeeccchhhHHH
Q psy16978 66 RRRIEIAHALCLTERQIKIWFQNRRMKLKK 95 (154)
Q Consensus 66 ~~~~~La~~l~l~~~qV~~WFqNrRak~kr 95 (154)
....++|..+|++...|+.+...-|.+.|+
T Consensus 199 ~s~~EIA~~lgis~~tVk~~~~rA~~~Lr~ 228 (234)
T PRK08301 199 KTQKEVADMLGISQSYISRLEKRIIKRLKK 228 (234)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 345678999999999998877544444443
No 109
>PRK06930 positive control sigma-like factor; Validated
Probab=21.94 E-value=92 Score=23.04 Aligned_cols=46 Identities=13% Similarity=0.041 Sum_probs=29.7
Q ss_pred CCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCCcccceeeeccchhhHHH
Q psy16978 45 YTRFQTLELEKEFHFNHYLTRRRRIEIAHALCLTERQIKIWFQNRRMKLKK 95 (154)
Q Consensus 45 ~t~~q~~~Le~~F~~~~~p~~~~~~~La~~l~l~~~qV~~WFqNrRak~kr 95 (154)
+++.+..++...|. ....-.++|..+|++...|+.+...-+.+.++
T Consensus 115 L~~rer~V~~L~~~-----eg~s~~EIA~~lgiS~~tVk~~l~Ra~~kLr~ 160 (170)
T PRK06930 115 LTEREKEVYLMHRG-----YGLSYSEIADYLNIKKSTVQSMIERAEKKIAR 160 (170)
T ss_pred CCHHHHHHHHHHHH-----cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 55555555554332 11234578999999999999988755555554
No 110
>smart00595 MADF subfamily of SANT domain.
Probab=21.84 E-value=55 Score=20.87 Aligned_cols=31 Identities=32% Similarity=0.431 Sum_probs=25.7
Q ss_pred HHHHHHhCCCcccceeeeccchhhHHHhHHH
Q psy16978 69 IEIAHALCLTERQIKIWFQNRRMKLKKELRA 99 (154)
Q Consensus 69 ~~La~~l~l~~~qV~~WFqNrRak~kr~~~~ 99 (154)
.+||..+|.+...|+.-+.|-|...++..+.
T Consensus 31 ~~Ia~~l~~~~~~~~~kw~~LR~~y~~e~~r 61 (89)
T smart00595 31 EEIAEELGLSVEECKKRWKNLRDRYRRELKR 61 (89)
T ss_pred HHHHHHHCcCHHHHHHHHHHHHHHHHHHHHH
Confidence 4588999999999999999999888876554
No 111
>PRK05988 formate dehydrogenase subunit gamma; Validated
Probab=21.61 E-value=1.4e+02 Score=21.89 Aligned_cols=35 Identities=20% Similarity=0.047 Sum_probs=27.6
Q ss_pred HHHHHHHHHhhhcCCCCHHHHHHHHHHhCCCcccc
Q psy16978 48 FQTLELEKEFHFNHYLTRRRRIEIAHALCLTERQI 82 (154)
Q Consensus 48 ~q~~~Le~~F~~~~~p~~~~~~~La~~l~l~~~qV 82 (154)
.-+..|...=+...|.+......+|..+|++..+|
T Consensus 24 ~li~~L~~vQ~~~G~Ip~e~~~~iA~~l~v~~~~V 58 (156)
T PRK05988 24 ALLPILHAIQDEFGYVPEDAVPVIAEALNLSRAEV 58 (156)
T ss_pred HHHHHHHHHHHHcCCCCHHHHHHHHHHhCCCHHHH
Confidence 34556655556677999999999999999998776
No 112
>PF08452 DNAP_B_exo_N: DNA polymerase family B exonuclease domain, N-terminal; InterPro: IPR013660 This domain is found in viral DNA polymerases to the N terminus of DNA polymerase family B exonuclease domains (IPR006133 from INTERPRO). ; GO: 0003887 DNA-directed DNA polymerase activity
Probab=21.38 E-value=31 Score=16.78 Aligned_cols=10 Identities=30% Similarity=0.650 Sum_probs=7.0
Q ss_pred ceeeeccchh
Q psy16978 82 IKIWFQNRRM 91 (154)
Q Consensus 82 V~~WFqNrRa 91 (154)
.-+||-|+.-
T Consensus 5 CiNWFE~~ge 14 (22)
T PF08452_consen 5 CINWFESRGE 14 (22)
T ss_pred EeehhhhCCc
Confidence 3479988763
No 113
>TIGR03070 couple_hipB transcriptional regulator, y4mF family. Members of this family belong to a clade of helix-turn-helix DNA-binding proteins, among the larger family pfam01381 (HTH_3; Helix-turn-helix). Members are similar in sequence to the HipB protein of E. coli. Genes for members of the seed alignment for this protein family were found to be closely linked to genes encoding proteins related to HipA. The HibBA operon appears to have some features in common with toxin-antitoxin post-segregational killing systems.
Probab=21.24 E-value=35 Score=19.39 Aligned_cols=23 Identities=13% Similarity=0.059 Sum_probs=19.8
Q ss_pred HHHHHHHhCCCcccceeeeccch
Q psy16978 68 RIEIAHALCLTERQIKIWFQNRR 90 (154)
Q Consensus 68 ~~~La~~l~l~~~qV~~WFqNrR 90 (154)
..+||..+|++...|..|...++
T Consensus 18 q~~lA~~~gvs~~~vs~~e~g~~ 40 (58)
T TIGR03070 18 QADLADLAGVGLRFIRDVENGKP 40 (58)
T ss_pred HHHHHHHhCCCHHHHHHHHCCCC
Confidence 46789999999999999997664
No 114
>cd00093 HTH_XRE Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the xenobiotic response element family of transcriptional regulators.
Probab=21.02 E-value=35 Score=18.40 Aligned_cols=22 Identities=23% Similarity=0.246 Sum_probs=18.8
Q ss_pred HHHHHHhCCCcccceeeeccch
Q psy16978 69 IEIAHALCLTERQIKIWFQNRR 90 (154)
Q Consensus 69 ~~La~~l~l~~~qV~~WFqNrR 90 (154)
..+|..+|++...|..|..+.+
T Consensus 16 ~~~a~~~~~~~~~v~~~~~g~~ 37 (58)
T cd00093 16 EELAEKLGVSRSTISRIENGKR 37 (58)
T ss_pred HHHHHHHCCCHHHHHHHHcCCC
Confidence 4789999999999999987764
No 115
>TIGR01764 excise DNA binding domain, excisionase family. An excisionase, or Xis protein, is a small protein that binds and promotes excisive recombination; it is not enzymatically active. This model represents a number of putative excisionases and related proteins from temperate phage, plasmids, and transposons, as well as DNA binding domains of other proteins, such as a DNA modification methylase. This model identifies mostly small proteins and N-terminal regions of large proteins, but some proteins appear to have two copies. This domain appears similar, in both sequence and predicted secondary structure (PSIPRED) to the MerR family of transcriptional regulators (pfam00376).
Probab=21.00 E-value=33 Score=18.78 Aligned_cols=23 Identities=13% Similarity=0.079 Sum_probs=17.4
Q ss_pred HHHHHHHhCCCcccceeeeccch
Q psy16978 68 RIEIAHALCLTERQIKIWFQNRR 90 (154)
Q Consensus 68 ~~~La~~l~l~~~qV~~WFqNrR 90 (154)
..++|..+|++...|..|..+.+
T Consensus 4 ~~e~a~~lgis~~ti~~~~~~g~ 26 (49)
T TIGR01764 4 VEEAAEYLGVSKDTVYRLIHEGE 26 (49)
T ss_pred HHHHHHHHCCCHHHHHHHHHcCC
Confidence 35678888999888888876543
No 116
>PF08279 HTH_11: HTH domain; InterPro: IPR013196 Winged helix DNA-binding proteins share a related winged helix-turn-helix DNA-binding motif, where the "wings", or loops, are small beta-sheets. The winged helix motif consists of two wings (W1, W2), three alpha helices (H1, H2, H3) and three beta-sheets (S1, S2, S3) arranged in the order H1-S1-H2-H3-S2-W1-S3-W2 []. The DNA-recognition helix makes sequence-specific DNA contacts with the major groove of DNA, while the wings make different DNA contacts, often with the minor groove or the backbone of DNA. Several winged-helix proteins display an exposed patch of hydrophobic residues thought to mediate protein-protein interactions. This entry represents a subset of the winged helix domain superfamily which is predominantly found in bacterial proteins, though there are also some archaeal and eukaryotic examples. This domain is commonly found in the biotin (vitamin H) repressor protein BirA which regulates transcription of the biotin operon []. It is also found in other proteins including regulators of amino acid biosynthsis such as LysM [], and regulators of carbohydrate metabolisms such as LicR and FrvR [, ].; PDB: 1HXD_B 2EWN_B 1BIA_A 1BIB_A 1J5Y_A 3V7S_A 3V7C_A 3RKW_A 3RIR_A 3RKX_A ....
Probab=20.37 E-value=90 Score=17.86 Aligned_cols=16 Identities=31% Similarity=0.493 Sum_probs=11.7
Q ss_pred HHHHHHHhCCCcccce
Q psy16978 68 RIEIAHALCLTERQIK 83 (154)
Q Consensus 68 ~~~La~~l~l~~~qV~ 83 (154)
..+||..++++.+.|.
T Consensus 18 ~~eLa~~l~vS~rTi~ 33 (55)
T PF08279_consen 18 AKELAEELGVSRRTIR 33 (55)
T ss_dssp HHHHHHHCTS-HHHHH
T ss_pred HHHHHHHhCCCHHHHH
Confidence 4578999999987654
No 117
>TIGR02947 SigH_actino RNA polymerase sigma-70 factor, TIGR02947 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 (with the exception of a paralog in Thermobifida fusca YX) one-to-a-genome distribution, to represent a conserved family. This family is restricted to the Actinobacteria and each gene examined is followed by an anti-sigma factor in an apparent operon.
Probab=20.28 E-value=49 Score=24.30 Aligned_cols=31 Identities=19% Similarity=0.134 Sum_probs=23.2
Q ss_pred HHHHHHHHHHhCCCcccceeeeccchhhHHH
Q psy16978 65 RRRRIEIAHALCLTERQIKIWFQNRRMKLKK 95 (154)
Q Consensus 65 ~~~~~~La~~l~l~~~qV~~WFqNrRak~kr 95 (154)
.....++|..+|++...|+++...-|.+.|+
T Consensus 147 g~s~~EIA~~lgis~~tVk~~l~Rar~~Lr~ 177 (193)
T TIGR02947 147 GFAYKEIAEIMGTPIGTVMSRLHRGRKQLRK 177 (193)
T ss_pred CCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 3456679999999999999988655555443
No 118
>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=20.06 E-value=1.1e+02 Score=21.95 Aligned_cols=28 Identities=39% Similarity=0.331 Sum_probs=19.7
Q ss_pred HHHHHHHHhCCCcccceeeeccchhhHH
Q psy16978 67 RRIEIAHALCLTERQIKIWFQNRRMKLK 94 (154)
Q Consensus 67 ~~~~La~~l~l~~~qV~~WFqNrRak~k 94 (154)
...++|..+|++...|+++-..-|.+.+
T Consensus 118 s~~eIA~~lgis~~tV~~~l~Rar~~Lr 145 (170)
T TIGR02959 118 SQQEIAEKLGLSLSGAKSRVQRGRKKLK 145 (170)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHH
Confidence 3456899999999998887754343333
Done!