Query psy14871
Match_columns 238
No_of_seqs 305 out of 1592
Neff 6.6
Searched_HMMs 46136
Date Fri Aug 16 22:56:38 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy14871.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/14871hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG0775|consensus 100.0 1.6E-71 3.4E-76 483.0 17.8 194 24-217 46-239 (304)
2 KOG3802|consensus 99.7 8.4E-18 1.8E-22 154.2 11.4 133 52-214 200-354 (398)
3 KOG0850|consensus 99.5 8.8E-15 1.9E-19 125.7 6.6 73 143-224 120-192 (245)
4 PF00046 Homeobox: Homeobox do 99.5 1.2E-14 2.7E-19 99.7 4.2 55 157-211 3-57 (57)
5 KOG0484|consensus 99.5 1.1E-14 2.4E-19 111.1 3.1 57 159-215 22-78 (125)
6 KOG0843|consensus 99.5 3.6E-14 7.8E-19 117.9 5.8 60 157-216 105-164 (197)
7 KOG0489|consensus 99.5 3E-14 6.5E-19 126.8 4.6 65 155-219 160-224 (261)
8 KOG0488|consensus 99.5 5.9E-14 1.3E-18 127.5 6.6 60 159-218 177-236 (309)
9 KOG0842|consensus 99.5 7.5E-14 1.6E-18 125.7 6.0 62 160-221 159-220 (307)
10 KOG2251|consensus 99.4 1.4E-13 3E-18 117.8 6.6 61 156-216 39-99 (228)
11 KOG0492|consensus 99.4 1.2E-13 2.6E-18 117.2 5.2 73 138-219 137-209 (246)
12 KOG0848|consensus 99.4 7.9E-14 1.7E-18 122.2 4.1 60 159-218 204-263 (317)
13 KOG0487|consensus 99.4 9.3E-14 2E-18 125.2 4.5 64 154-217 235-298 (308)
14 cd00086 homeodomain Homeodomai 99.4 1.5E-13 3.3E-18 94.2 4.5 54 158-211 4-57 (59)
15 KOG0485|consensus 99.4 1.2E-13 2.5E-18 118.0 3.5 61 157-217 107-167 (268)
16 smart00389 HOX Homeodomain. DN 99.4 2.2E-13 4.9E-18 92.7 4.2 52 159-210 5-56 (56)
17 KOG0494|consensus 99.3 1.4E-12 3.1E-17 113.9 5.1 59 159-217 146-204 (332)
18 KOG4577|consensus 99.3 2E-12 4.3E-17 114.5 5.1 121 77-216 106-229 (383)
19 KOG0493|consensus 99.3 5.3E-12 1.2E-16 110.5 5.1 63 153-215 245-307 (342)
20 KOG0483|consensus 99.2 6E-12 1.3E-16 107.4 3.2 58 159-216 55-112 (198)
21 TIGR01565 homeo_ZF_HD homeobox 99.2 2E-11 4.3E-16 84.7 4.9 49 158-206 5-57 (58)
22 KOG0491|consensus 99.2 1E-11 2.2E-16 102.0 1.8 60 158-217 104-163 (194)
23 COG5576 Homeodomain-containing 99.1 6.9E-11 1.5E-15 97.6 6.2 59 160-218 57-115 (156)
24 KOG0486|consensus 99.1 5.2E-11 1.1E-15 106.7 3.3 58 159-216 117-174 (351)
25 KOG0844|consensus 99.1 6.3E-11 1.4E-15 105.8 3.2 61 158-218 185-245 (408)
26 KOG0847|consensus 99.0 1.1E-10 2.5E-15 100.0 3.2 62 158-219 171-232 (288)
27 KOG1168|consensus 98.9 2E-09 4.3E-14 95.7 6.6 49 166-214 321-369 (385)
28 PF05920 Homeobox_KN: Homeobox 98.8 1.4E-09 3.1E-14 70.0 1.3 34 175-208 7-40 (40)
29 KOG0774|consensus 98.8 2.7E-09 5.8E-14 93.6 2.9 65 152-216 186-253 (334)
30 KOG0490|consensus 98.7 9.2E-09 2E-13 88.5 3.3 58 157-214 63-120 (235)
31 KOG0849|consensus 98.5 1.5E-07 3.4E-12 87.2 4.9 58 158-215 180-237 (354)
32 KOG2252|consensus 98.4 3.9E-07 8.5E-12 87.3 7.0 53 158-210 424-476 (558)
33 KOG0773|consensus 97.6 2.8E-05 6.1E-10 71.5 2.5 56 159-214 244-302 (342)
34 KOG0490|consensus 97.6 7.6E-05 1.7E-09 64.1 4.6 57 158-214 157-213 (235)
35 PF11569 Homez: Homeodomain le 96.9 0.00036 7.8E-09 48.0 1.2 43 166-208 10-52 (56)
36 KOG1146|consensus 96.3 0.0044 9.6E-08 65.2 4.8 57 158-214 907-963 (1406)
37 KOG3623|consensus 92.7 0.15 3.2E-06 51.4 4.5 48 166-213 568-615 (1007)
38 PF04218 CENP-B_N: CENP-B N-te 84.1 1.4 3.1E-05 29.6 3.2 41 160-205 6-46 (53)
39 PF04545 Sigma70_r4: Sigma-70, 63.8 7.6 0.00016 25.1 2.5 46 160-210 4-49 (50)
40 KOG4330|consensus 63.8 8.5 0.00018 32.6 3.4 36 28-63 135-170 (206)
41 PF14559 TPR_19: Tetratricopep 63.0 18 0.0004 24.0 4.5 43 75-117 23-65 (68)
42 PF04967 HTH_10: HTH DNA bindi 58.1 12 0.00026 25.3 2.8 40 161-200 1-42 (53)
43 cd06171 Sigma70_r4 Sigma70, re 54.5 8.3 0.00018 24.0 1.5 44 160-208 10-53 (55)
44 KOG0773|consensus 54.2 8.4 0.00018 35.3 2.0 38 175-212 118-155 (342)
45 PF00424 REV: REV protein (ant 53.9 17 0.00038 27.4 3.3 37 166-216 14-50 (91)
46 PF08281 Sigma70_r4_2: Sigma-7 51.5 16 0.00034 23.8 2.5 43 160-207 10-52 (54)
47 PF10668 Phage_terminase: Phag 45.1 9.9 0.00021 26.5 0.7 19 184-202 25-43 (60)
48 cd00569 HTH_Hin_like Helix-tur 42.7 40 0.00086 18.4 3.1 37 161-202 6-42 (42)
49 PF11791 Aconitase_B_N: Aconit 41.1 29 0.00062 28.7 3.0 38 32-69 12-52 (154)
50 COG3413 Predicted DNA binding 37.6 31 0.00067 29.4 2.8 40 160-199 155-196 (215)
51 PRK09646 RNA polymerase sigma 37.0 42 0.00092 27.7 3.5 49 160-213 142-190 (194)
52 PF01527 HTH_Tnp_1: Transposas 36.7 15 0.00032 25.6 0.6 41 160-204 6-46 (76)
53 PRK12540 RNA polymerase sigma 36.7 78 0.0017 26.0 5.1 53 160-217 111-163 (182)
54 PF07035 Mic1: Colon cancer-as 36.6 67 0.0015 26.8 4.6 27 45-71 93-119 (167)
55 PRK06759 RNA polymerase factor 35.9 38 0.00083 26.5 3.0 46 160-210 106-151 (154)
56 PF13936 HTH_38: Helix-turn-he 34.7 23 0.00051 22.5 1.2 39 160-203 4-42 (44)
57 PRK12526 RNA polymerase sigma 34.3 53 0.0012 27.5 3.7 49 160-213 153-201 (206)
58 PF13518 HTH_28: Helix-turn-he 34.3 20 0.00043 22.9 0.9 25 183-207 14-38 (52)
59 PF13384 HTH_23: Homeodomain-l 33.3 18 0.0004 23.1 0.5 24 182-205 18-41 (50)
60 PRK03975 tfx putative transcri 33.1 60 0.0013 26.4 3.6 49 160-214 6-54 (141)
61 PRK09642 RNA polymerase sigma 32.8 60 0.0013 25.6 3.6 48 161-213 107-154 (160)
62 PF13443 HTH_26: Cro/C1-type H 32.7 19 0.00041 24.1 0.6 26 183-208 12-37 (63)
63 PRK09644 RNA polymerase sigma 32.0 60 0.0013 25.9 3.5 50 160-214 108-157 (165)
64 PRK00118 putative DNA-binding 30.8 74 0.0016 24.5 3.6 50 160-214 17-66 (104)
65 PRK09652 RNA polymerase sigma 30.3 58 0.0013 25.9 3.2 49 160-213 128-176 (182)
66 PRK10072 putative transcriptio 29.9 24 0.00051 26.8 0.7 24 184-207 49-72 (96)
67 KOG2274|consensus 29.7 55 0.0012 34.4 3.5 61 52-116 778-847 (1005)
68 PRK12512 RNA polymerase sigma 29.0 70 0.0015 25.9 3.5 50 160-214 131-180 (184)
69 PF13429 TPR_15: Tetratricopep 28.7 61 0.0013 28.2 3.3 56 46-101 115-170 (280)
70 KOG1146|consensus 28.1 22 0.00047 38.6 0.3 55 158-212 448-502 (1406)
71 PF06056 Terminase_5: Putative 28.0 30 0.00064 23.7 0.9 20 184-203 16-35 (58)
72 KOG3623|consensus 27.7 1.8E+02 0.0039 30.2 6.6 49 164-212 636-684 (1007)
73 TIGR02937 sigma70-ECF RNA poly 27.6 64 0.0014 24.2 2.9 46 160-210 110-155 (158)
74 PRK04217 hypothetical protein; 27.5 95 0.0021 24.1 3.8 51 159-214 41-91 (110)
75 PRK12532 RNA polymerase sigma 26.8 92 0.002 25.6 3.9 51 161-216 137-187 (195)
76 PRK05602 RNA polymerase sigma 26.6 93 0.002 25.3 3.8 49 161-214 129-177 (186)
77 PF13432 TPR_16: Tetratricopep 26.5 1.3E+02 0.0028 19.6 3.9 50 50-101 6-55 (65)
78 PRK12514 RNA polymerase sigma 26.3 86 0.0019 25.3 3.6 30 183-212 147-176 (179)
79 TIGR02989 Sig-70_gvs1 RNA poly 26.2 71 0.0015 25.0 3.0 46 160-210 111-156 (159)
80 PRK12515 RNA polymerase sigma 26.1 91 0.002 25.5 3.7 50 160-214 131-180 (189)
81 cd04761 HTH_MerR-SF Helix-Turn 25.8 29 0.00064 21.7 0.5 21 184-204 3-23 (49)
82 smart00421 HTH_LUXR helix_turn 25.6 75 0.0016 19.8 2.5 40 161-206 4-43 (58)
83 PRK11924 RNA polymerase sigma 25.4 90 0.002 24.7 3.5 31 183-213 143-173 (179)
84 PF00196 GerE: Bacterial regul 25.3 66 0.0014 21.3 2.2 45 160-210 3-47 (58)
85 PRK09648 RNA polymerase sigma 25.2 83 0.0018 25.6 3.3 47 160-211 139-185 (189)
86 TIGR02948 SigW_bacill RNA poly 25.1 72 0.0016 25.7 2.9 48 160-212 136-183 (187)
87 TIGR02999 Sig-70_X6 RNA polyme 25.0 87 0.0019 25.2 3.3 46 161-211 135-180 (183)
88 PRK12530 RNA polymerase sigma 24.7 93 0.002 25.6 3.5 49 160-213 134-182 (189)
89 PRK09639 RNA polymerase sigma 24.7 1E+02 0.0022 24.3 3.7 49 160-214 112-160 (166)
90 PRK12524 RNA polymerase sigma 24.5 1.3E+02 0.0029 24.7 4.4 50 161-215 137-186 (196)
91 TIGR02939 RpoE_Sigma70 RNA pol 24.5 66 0.0014 26.0 2.6 35 178-212 151-185 (190)
92 TIGR02985 Sig70_bacteroi1 RNA 24.4 86 0.0019 24.2 3.1 45 161-210 114-158 (161)
93 cd01392 HTH_LacI Helix-turn-he 24.4 24 0.00052 22.6 -0.1 21 186-206 2-22 (52)
94 PF01381 HTH_3: Helix-turn-hel 23.8 33 0.00071 22.1 0.5 23 184-206 12-34 (55)
95 PRK12519 RNA polymerase sigma 23.8 73 0.0016 26.1 2.7 31 182-212 158-188 (194)
96 PRK12516 RNA polymerase sigma 23.2 1.3E+02 0.0028 24.8 4.1 52 160-216 116-167 (187)
97 TIGR02959 SigZ RNA polymerase 22.9 95 0.0021 25.0 3.2 50 160-214 100-149 (170)
98 PRK09047 RNA polymerase factor 22.6 1.2E+02 0.0026 23.7 3.7 49 160-213 106-154 (161)
99 PF13411 MerR_1: MerR HTH fami 22.3 41 0.00089 22.8 0.8 19 184-202 3-21 (69)
100 TIGR02508 type_III_yscG type I 22.2 2.3E+02 0.005 22.2 4.9 45 42-104 22-66 (115)
101 PRK12541 RNA polymerase sigma 22.0 86 0.0019 24.8 2.7 47 160-211 112-158 (161)
102 PRK12536 RNA polymerase sigma 21.8 1.1E+02 0.0024 24.8 3.4 30 183-212 147-176 (181)
103 KOG3755|consensus 21.6 41 0.00089 33.8 0.9 46 170-215 708-760 (769)
104 PRK09413 IS2 repressor TnpA; R 21.2 1.2E+02 0.0026 23.4 3.3 22 183-204 31-52 (121)
105 TIGR03070 couple_hipB transcri 21.1 40 0.00088 21.5 0.5 23 184-206 18-40 (58)
106 PRK12537 RNA polymerase sigma 21.0 1.3E+02 0.0027 24.5 3.6 29 183-211 151-179 (182)
107 TIGR02954 Sig70_famx3 RNA poly 20.9 1.1E+02 0.0025 24.2 3.3 47 160-211 119-165 (169)
108 PF13371 TPR_9: Tetratricopept 20.8 2E+02 0.0042 19.1 4.0 50 51-102 5-54 (73)
109 PRK12547 RNA polymerase sigma 20.3 1.2E+02 0.0026 24.1 3.3 48 160-212 112-159 (164)
110 PRK06930 positive control sigm 20.2 1.3E+02 0.0029 24.8 3.6 50 160-214 114-163 (170)
No 1
>KOG0775|consensus
Probab=100.00 E-value=1.6e-71 Score=483.04 Aligned_cols=194 Identities=81% Similarity=1.353 Sum_probs=186.4
Q ss_pred CCCCCCCCCCCCCCCCChhhHhHHhhhhhccCchhHHHHHHhcCCCcccCCcchHHHHHHHHHHhhhccHHHHHHHHhcC
Q psy14871 24 STSTASISPILPSFGFTQEQVACVCEVLQQSGNIERLGRFLWSLPACEKLHKNESVLKAKAMVAFHRGNFKDLYRILESH 103 (238)
Q Consensus 24 ~~~~~~~~~~~~~~~~~~~q~~~vc~~l~~~gd~~~l~~f~~~lp~~~~~~~~e~vlra~a~v~~h~~~f~e~~~lLe~~ 103 (238)
.......|+++|++.||+|||+||||+|+|.||||||.+|||+||.++.+.+||+||||||+|+||.|+|+|||+|||++
T Consensus 46 ~~~~~~s~~~~pt~~fS~eQvacvCe~L~q~Gd~erL~rFlwsLp~~~~~~~nEsvLkArA~vafH~gnf~eLY~iLE~h 125 (304)
T KOG0775|consen 46 SASASASMSALPTFGFSEEQVACVCESLQQGGDIERLGRFLWSLPVCEELLKNESVLKARAVVAFHSGNFRELYHILENH 125 (304)
T ss_pred CCCcccccccCCCcCCCHHHHHHHHHHHHhccCHHHHHHHHHcCchHHHHhhhHHHHHHHHHHHHhcccHHHHHHHHHhc
Confidence 33445568899999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CCCCCChhHHHHHHHhhhhhHHHHhcCCCCCCCCccccCCCCCCCCcccCCCCcccccCHHHHHHHHHHHhhCCCCCHHH
Q psy14871 104 QFSPHNHPKLQALWLKAHYVEAEKLRGRPLGAVGKYRVRRKFPLPRTIWDGEETSYCFKEKSRSVLRDWYTHNPYPSPRE 183 (238)
Q Consensus 104 ~f~~~~h~~lq~lw~~a~y~~~e~~~grpl~~~~k~r~Rkk~p~P~ti~~~~~t~~~fs~~q~~~Le~~F~~~~yPs~~~ 183 (238)
.|++.+|++||+||++|||.|+|+.||||||+|+|||+|||+|.|+|||||++|.|||+++.+.+|++||.+++||++.+
T Consensus 126 ~Fs~~~h~~LQ~lWl~AhY~EAek~RGR~LgaV~KYRvRrKfPlPrTIWDGEet~yCFKekSR~~LrewY~~~~YPsp~e 205 (304)
T KOG0775|consen 126 KFSPHNHPKLQALWLKAHYKEAEKLRGRPLGAVDKYRVRRKFPLPRTIWDGEETVYCFKEKSRSLLREWYLQNPYPSPRE 205 (304)
T ss_pred cCChhhhHHHHHHHHHHHHHHHHHhcCCcCCccccceeeccCCCCCccccCceeeeehhHhhHHHHHHHHhcCCCCChHH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHhCCCccccccccchhhhhhhHHHhhcc
Q psy14871 184 KRELAEATGLTTTQVSNWFKNRRQRDRAAEQKDG 217 (238)
Q Consensus 184 r~~LA~~lgLs~~qV~~WFqNRR~R~k~~~~~~~ 217 (238)
|.+||+.|||+.+||.|||+|||+|+|....+..
T Consensus 206 KReLA~aTgLt~tQVsNWFKNRRQRDRa~~ak~~ 239 (304)
T KOG0775|consen 206 KRELAEATGLTITQVSNWFKNRRQRDRAAAAKNS 239 (304)
T ss_pred HHHHHHHhCCchhhhhhhhhhhhhhhhhcccccc
Confidence 9999999999999999999999999996655544
No 2
>KOG3802|consensus
Probab=99.75 E-value=8.4e-18 Score=154.25 Aligned_cols=133 Identities=26% Similarity=0.450 Sum_probs=98.9
Q ss_pred hccCchhHHHHHHhcCCCcccCCcchHHHHHHHHHHhhhccHHHHHHHHhcCCCCCCC-----------------hhHHH
Q psy14871 52 QQSGNIERLGRFLWSLPACEKLHKNESVLKAKAMVAFHRGNFKDLYRILESHQFSPHN-----------------HPKLQ 114 (238)
Q Consensus 52 ~~~gd~~~l~~f~~~lp~~~~~~~~e~vlra~a~v~~h~~~f~e~~~lLe~~~f~~~~-----------------h~~lq 114 (238)
.++.|+|+|+.|...+... |..+-|.++|...++.-|++..|+... .+.|+
T Consensus 200 ed~~~leELEqFAK~FKqR------------RIkLGfTQaDVGlALG~lyGn~FSQTTIcRFEALqLSFKNMCKLKPLL~ 267 (398)
T KOG3802|consen 200 EDTPDLEELEQFAKTFKQR------------RIKLGFTQADVGLALGALYGNVFSQTTICRFEALQLSFKNMCKLKPLLE 267 (398)
T ss_pred ccccCHHHHHHHHHHHHhh------------eeccccchhHHHHHHHhhhCcccchhhhhHhHhhccCHHHHhhhHHHHH
Confidence 5688999999995444432 334448899999999999998888744 34444
Q ss_pred HHHHhhhhhHHHH--hcCCCCCC---CCccccCCCCCCCCcccCCCCcccccCHHHHHHHHHHHhhCCCCCHHHHHHHHH
Q psy14871 115 ALWLKAHYVEAEK--LRGRPLGA---VGKYRVRRKFPLPRTIWDGEETSYCFKEKSRSVLRDWYTHNPYPSPREKRELAE 189 (238)
Q Consensus 115 ~lw~~a~y~~~e~--~~grpl~~---~~k~r~Rkk~p~P~ti~~~~~t~~~fs~~q~~~Le~~F~~~~yPs~~~r~~LA~ 189 (238)
+ |++ ++|. ..|.+... ....|+|||+. .|....+..||.+|..|+.|+.+++..||.
T Consensus 268 K-WLe----EAes~~~~~~~~~~e~i~a~~RkRKKRT-------------Sie~~vr~aLE~~F~~npKPt~qEIt~iA~ 329 (398)
T KOG3802|consen 268 K-WLE----EAESRESTGSPNSIEKIGAQSRKRKKRT-------------SIEVNVRGALEKHFLKNPKPTSQEITHIAE 329 (398)
T ss_pred H-HHH----HHhcccccCCCCCHHHhhcccccccccc-------------ceeHHHHHHHHHHHHhCCCCCHHHHHHHHH
Confidence 4 544 3443 22222111 11125555553 788889999999999999999999999999
Q ss_pred HhCCCccccccccchhhhhhhHHHh
Q psy14871 190 ATGLTTTQVSNWFKNRRQRDRAAEQ 214 (238)
Q Consensus 190 ~lgLs~~qV~~WFqNRR~R~k~~~~ 214 (238)
+++|.+.+|+|||||||+|.||...
T Consensus 330 ~L~leKEVVRVWFCNRRQkeKR~~~ 354 (398)
T KOG3802|consen 330 SLQLEKEVVRVWFCNRRQKEKRITP 354 (398)
T ss_pred HhccccceEEEEeeccccccccCCC
Confidence 9999999999999999999998776
No 3
>KOG0850|consensus
Probab=99.54 E-value=8.8e-15 Score=125.72 Aligned_cols=73 Identities=30% Similarity=0.484 Sum_probs=63.3
Q ss_pred CCCCCCCcccCCCCcccccCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCccccccccchhhhhhhHHHhhccccccC
Q psy14871 143 RKFPLPRTIWDGEETSYCFKEKSRSVLRDWYTHNPYPSPREKRELAEATGLTTTQVSNWFKNRRQRDRAAEQKDGSVTRS 222 (238)
Q Consensus 143 kk~p~P~ti~~~~~t~~~fs~~q~~~Le~~F~~~~yPs~~~r~~LA~~lgLs~~qV~~WFqNRR~R~k~~~~~~~~~~~~ 222 (238)
||.+.|||| |+.-|+..|.+.|++..|.-..||.+||..|||+.+||+|||||||.|.||.++......+.
T Consensus 120 KK~RKPRTI---------YSS~QLqaL~rRFQkTQYLALPERAeLAAsLGLTQTQVKIWFQNrRSK~KKl~k~g~~~~e~ 190 (245)
T KOG0850|consen 120 KKVRKPRTI---------YSSLQLQALNRRFQQTQYLALPERAELAASLGLTQTQVKIWFQNRRSKFKKLKKQGSGPVEG 190 (245)
T ss_pred ccccCCccc---------ccHHHHHHHHHHHhhcchhcCcHHHHHHHHhCCchhHhhhhhhhhHHHHHHHHhcCCCcccc
Confidence 555668885 68889999999999999999999999999999999999999999999999998865544444
Q ss_pred CC
Q psy14871 223 VH 224 (238)
Q Consensus 223 ~~ 224 (238)
..
T Consensus 191 ~p 192 (245)
T KOG0850|consen 191 DP 192 (245)
T ss_pred Cc
Confidence 43
No 4
>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=99.51 E-value=1.2e-14 Score=99.73 Aligned_cols=55 Identities=42% Similarity=0.829 Sum_probs=52.2
Q ss_pred cccccCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCccccccccchhhhhhhH
Q psy14871 157 TSYCFKEKSRSVLRDWYTHNPYPSPREKRELAEATGLTTTQVSNWFKNRRQRDRA 211 (238)
Q Consensus 157 t~~~fs~~q~~~Le~~F~~~~yPs~~~r~~LA~~lgLs~~qV~~WFqNRR~R~k~ 211 (238)
++..|+..|+.+|+.+|..++||+..+++.||..+||+..+|.+||+|+|+++|+
T Consensus 3 ~r~~~t~~q~~~L~~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrR~k~kk 57 (57)
T PF00046_consen 3 KRTRFTKEQLKVLEEYFQENPYPSKEEREELAKELGLTERQVKNWFQNRRRKEKK 57 (57)
T ss_dssp SSSSSSHHHHHHHHHHHHHSSSCHHHHHHHHHHHHTSSHHHHHHHHHHHHHHHHH
T ss_pred CCCCCCHHHHHHHHHHHHHhccccccccccccccccccccccccCHHHhHHHhCc
Confidence 3458999999999999999999999999999999999999999999999999985
No 5
>KOG0484|consensus
Probab=99.49 E-value=1.1e-14 Score=111.11 Aligned_cols=57 Identities=28% Similarity=0.468 Sum_probs=54.2
Q ss_pred cccCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCccccccccchhhhhhhHHHhh
Q psy14871 159 YCFKEKSRSVLRDWYTHNPYPSPREKRELAEATGLTTTQVSNWFKNRRQRDRAAEQK 215 (238)
Q Consensus 159 ~~fs~~q~~~Le~~F~~~~yPs~~~r~~LA~~lgLs~~qV~~WFqNRR~R~k~~~~~ 215 (238)
+.|+..|+..|++.|...+||++-.|++||..+.|++..|+|||||||+|.|++...
T Consensus 22 TTFTS~QLkELErvF~ETHYPDIYTREEiA~kidLTEARVQVWFQNRRAKfRKQEr~ 78 (125)
T KOG0484|consen 22 TTFTSAQLKELERVFAETHYPDIYTREEIALKIDLTEARVQVWFQNRRAKFRKQERA 78 (125)
T ss_pred hhhhHHHHHHHHHHHHhhcCCcchhHHHHHHhhhhhHHHHHHHHHhhHHHHHHHHHH
Confidence 489999999999999999999999999999999999999999999999999997654
No 6
>KOG0843|consensus
Probab=99.49 E-value=3.6e-14 Score=117.95 Aligned_cols=60 Identities=30% Similarity=0.515 Sum_probs=56.5
Q ss_pred cccccCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCccccccccchhhhhhhHHHhhc
Q psy14871 157 TSYCFKEKSRSVLRDWYTHNPYPSPREKRELAEATGLTTTQVSNWFKNRRQRDRAAEQKD 216 (238)
Q Consensus 157 t~~~fs~~q~~~Le~~F~~~~yPs~~~r~~LA~~lgLs~~qV~~WFqNRR~R~k~~~~~~ 216 (238)
.++.|+.+|+..||..|+.+.|....+|+.||..++|+++||+|||||||.|.|+.+.++
T Consensus 105 ~RT~ft~~Ql~~LE~~F~~~~Yvvg~eR~~LA~~L~LsetQVkvWFQNRRtk~kr~~~e~ 164 (197)
T KOG0843|consen 105 IRTAFTPEQLLKLEHAFEGNQYVVGAERKQLAQSLSLSETQVKVWFQNRRTKHKRMQQED 164 (197)
T ss_pred cccccCHHHHHHHHHHHhcCCeeechHHHHHHHHcCCChhHhhhhhhhhhHHHHHHHHHh
Confidence 345899999999999999999999999999999999999999999999999999987774
No 7
>KOG0489|consensus
Probab=99.47 E-value=3e-14 Score=126.75 Aligned_cols=65 Identities=25% Similarity=0.374 Sum_probs=59.4
Q ss_pred CCcccccCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCccccccccchhhhhhhHHHhhcccc
Q psy14871 155 EETSYCFKEKSRSVLRDWYTHNPYPSPREKRELAEATGLTTTQVSNWFKNRRQRDRAAEQKDGSV 219 (238)
Q Consensus 155 ~~t~~~fs~~q~~~Le~~F~~~~yPs~~~r~~LA~~lgLs~~qV~~WFqNRR~R~k~~~~~~~~~ 219 (238)
++.|+.||..|+..||+.|..|+|.+...|.+||..|.|+++||+|||||||+||||..+.....
T Consensus 160 kR~RtayT~~QllELEkEFhfN~YLtR~RRiEiA~~L~LtErQIKIWFQNRRMK~Kk~~k~~~~~ 224 (261)
T KOG0489|consen 160 KRRRTAFTRYQLLELEKEFHFNKYLTRSRRIEIAHALNLTERQIKIWFQNRRMKWKKENKAKSSQ 224 (261)
T ss_pred CCCCcccchhhhhhhhhhhccccccchHHHHHHHhhcchhHHHHHHHHHHHHHHHHHhhcccccc
Confidence 34556999999999999999999999999999999999999999999999999999987766544
No 8
>KOG0488|consensus
Probab=99.47 E-value=5.9e-14 Score=127.48 Aligned_cols=60 Identities=30% Similarity=0.517 Sum_probs=56.4
Q ss_pred cccCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCccccccccchhhhhhhHHHhhccc
Q psy14871 159 YCFKEKSRSVLRDWYTHNPYPSPREKRELAEATGLTTTQVSNWFKNRRQRDRAAEQKDGS 218 (238)
Q Consensus 159 ~~fs~~q~~~Le~~F~~~~yPs~~~r~~LA~~lgLs~~qV~~WFqNRR~R~k~~~~~~~~ 218 (238)
+.||..|+..||+.|+..+|.+..+|.+||..+||+..||++||||||+|||++......
T Consensus 177 TaFT~~Ql~~LEkrF~~QKYLS~~DR~~LA~~LgLTdaQVKtWfQNRRtKWKrq~a~g~~ 236 (309)
T KOG0488|consen 177 TAFSDHQLFELEKRFEKQKYLSVADRIELAASLGLTDAQVKTWFQNRRTKWKRQTAEGGE 236 (309)
T ss_pred hhhhHHHHHHHHHHHHHhhcccHHHHHHHHHHcCCchhhHHHHHhhhhHHHHHHHHhhhc
Confidence 389999999999999999999999999999999999999999999999999998877443
No 9
>KOG0842|consensus
Probab=99.46 E-value=7.5e-14 Score=125.69 Aligned_cols=62 Identities=27% Similarity=0.430 Sum_probs=58.1
Q ss_pred ccCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCccccccccchhhhhhhHHHhhcccccc
Q psy14871 160 CFKEKSRSVLRDWYTHNPYPSPREKRELAEATGLTTTQVSNWFKNRRQRDRAAEQKDGSVTR 221 (238)
Q Consensus 160 ~fs~~q~~~Le~~F~~~~yPs~~~r~~LA~~lgLs~~qV~~WFqNRR~R~k~~~~~~~~~~~ 221 (238)
-|+..|...||+.|.+.+|.+..||++||..++||++||+|||||||=|.||+...+.....
T Consensus 159 LFSqAQV~ELERRFrqQRYLSAPERE~LA~~LrLT~TQVKIWFQNrRYK~KR~~~dk~~~~~ 220 (307)
T KOG0842|consen 159 LFSQAQVYELERRFRQQRYLSAPEREHLASSLRLTPTQVKIWFQNRRYKTKRQQKDKALEAL 220 (307)
T ss_pred ccchhHHHHHHHHHHhhhccccHhHHHHHHhcCCCchheeeeeecchhhhhhhhhhhhhhcc
Confidence 79999999999999999999999999999999999999999999999999999887765543
No 10
>KOG2251|consensus
Probab=99.45 E-value=1.4e-13 Score=117.82 Aligned_cols=61 Identities=31% Similarity=0.514 Sum_probs=56.9
Q ss_pred CcccccCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCccccccccchhhhhhhHHHhhc
Q psy14871 156 ETSYCFKEKSRSVLRDWYTHNPYPSPREKRELAEATGLTTTQVSNWFKNRRQRDRAAEQKD 216 (238)
Q Consensus 156 ~t~~~fs~~q~~~Le~~F~~~~yPs~~~r~~LA~~lgLs~~qV~~WFqNRR~R~k~~~~~~ 216 (238)
+-|+.|+..|+.+||..|.+..||+...+++||.+++|.+.+|+|||+|||+|+|+++...
T Consensus 39 RERTtFtr~QlevLe~LF~kTqYPDv~~rEelAlklnLpeSrVqVWFKNRRAK~r~qq~qq 99 (228)
T KOG2251|consen 39 RERTTFTRKQLEVLEALFAKTQYPDVFMREELALKLNLPESRVQVWFKNRRAKCRRQQQQQ 99 (228)
T ss_pred cccceecHHHHHHHHHHHHhhcCccHHHHHHHHHHhCCchhhhhhhhccccchhhHhhhhh
Confidence 3445899999999999999999999999999999999999999999999999999988764
No 11
>KOG0492|consensus
Probab=99.43 E-value=1.2e-13 Score=117.19 Aligned_cols=73 Identities=27% Similarity=0.410 Sum_probs=65.4
Q ss_pred ccccCCCCCCCCcccCCCCcccccCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCccccccccchhhhhhhHHHhhcc
Q psy14871 138 KYRVRRKFPLPRTIWDGEETSYCFKEKSRSVLRDWYTHNPYPSPREKRELAEATGLTTTQVSNWFKNRRQRDRAAEQKDG 217 (238)
Q Consensus 138 k~r~Rkk~p~P~ti~~~~~t~~~fs~~q~~~Le~~F~~~~yPs~~~r~~LA~~lgLs~~qV~~WFqNRR~R~k~~~~~~~ 217 (238)
..|++|..+.||| -|+..|+..||+-|.+.+|.++.++.+++..+.|+++||++||||||+|.|+.+..+-
T Consensus 137 ~LrKhk~nRkPRt---------PFTtqQLlaLErkfrekqYLSiaEraefSsSL~LTeTqVKIWFQNRRAKaKRlQeae~ 207 (246)
T KOG0492|consen 137 TLRKHKPNRKPRT---------PFTTQQLLALERKFREKQYLSIAERAEFSSSLELTETQVKIWFQNRRAKAKRLQEAEL 207 (246)
T ss_pred hhcccCCCCCCCC---------CCCHHHHHHHHHHHhHhhhhhHHHHHhhhhhhhhhhhheehhhhhhhHHHHHHHHHHH
Confidence 4477777777877 8999999999999999999999999999999999999999999999999999877654
Q ss_pred cc
Q psy14871 218 SV 219 (238)
Q Consensus 218 ~~ 219 (238)
..
T Consensus 208 Ek 209 (246)
T KOG0492|consen 208 EK 209 (246)
T ss_pred HH
Confidence 43
No 12
>KOG0848|consensus
Probab=99.43 E-value=7.9e-14 Score=122.16 Aligned_cols=60 Identities=32% Similarity=0.546 Sum_probs=56.9
Q ss_pred cccCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCccccccccchhhhhhhHHHhhccc
Q psy14871 159 YCFKEKSRSVLRDWYTHNPYPSPREKRELAEATGLTTTQVSNWFKNRRQRDRAAEQKDGS 218 (238)
Q Consensus 159 ~~fs~~q~~~Le~~F~~~~yPs~~~r~~LA~~lgLs~~qV~~WFqNRR~R~k~~~~~~~~ 218 (238)
-+++..|+-.||+.|..++|.++..|.+||..|||+++||+|||||||+|+||..+++..
T Consensus 204 vVYTDhQRLELEKEfh~SryITirRKSELA~~LgLsERQVKIWFQNRRAKERK~nKKk~~ 263 (317)
T KOG0848|consen 204 VVYTDHQRLELEKEFHTSRYITIRRKSELAATLGLSERQVKIWFQNRRAKERKDNKKKRL 263 (317)
T ss_pred EEecchhhhhhhhhhccccceeeehhHHHHHhhCccHhhhhHhhhhhhHHHHHHHHHHHH
Confidence 478999999999999999999999999999999999999999999999999999888743
No 13
>KOG0487|consensus
Probab=99.43 E-value=9.3e-14 Score=125.16 Aligned_cols=64 Identities=23% Similarity=0.456 Sum_probs=57.3
Q ss_pred CCCcccccCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCccccccccchhhhhhhHHHhhcc
Q psy14871 154 GEETSYCFKEKSRSVLRDWYTHNPYPSPREKRELAEATGLTTTQVSNWFKNRRQRDRAAEQKDG 217 (238)
Q Consensus 154 ~~~t~~~fs~~q~~~Le~~F~~~~yPs~~~r~~LA~~lgLs~~qV~~WFqNRR~R~k~~~~~~~ 217 (238)
+.++|--+|+.|+..||+.|..|.|.+.+.|.+|+..|+||++||+|||||||+|+||...+.+
T Consensus 235 ~RKKRcPYTK~QtlELEkEFlfN~YitkeKR~ElSr~lNLTeRQVKIWFQNRRMK~KK~~re~r 298 (308)
T KOG0487|consen 235 GRKKRCPYTKHQTLELEKEFLFNMYITKEKRLELSRTLNLTERQVKIWFQNRRMKEKKVNRENR 298 (308)
T ss_pred cccccCCchHHHHHHHHHHHHHHHHHhHHHHHHHHHhcccchhheeeeehhhhhHHhhhhhhhh
Confidence 3344446899999999999999999999999999999999999999999999999999886443
No 14
>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=99.42 E-value=1.5e-13 Score=94.21 Aligned_cols=54 Identities=39% Similarity=0.641 Sum_probs=51.1
Q ss_pred ccccCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCccccccccchhhhhhhH
Q psy14871 158 SYCFKEKSRSVLRDWYTHNPYPSPREKRELAEATGLTTTQVSNWFKNRRQRDRA 211 (238)
Q Consensus 158 ~~~fs~~q~~~Le~~F~~~~yPs~~~r~~LA~~lgLs~~qV~~WFqNRR~R~k~ 211 (238)
+..|+..++.+|+.+|..++||+..++..||..+||+..+|++||+|+|.+.++
T Consensus 4 r~~~~~~~~~~Le~~f~~~~~P~~~~~~~la~~~~l~~~qV~~WF~nrR~~~~~ 57 (59)
T cd00086 4 RTRFTPEQLEELEKEFEKNPYPSREEREELAKELGLTERQVKIWFQNRRAKLKR 57 (59)
T ss_pred CCcCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHHCcCHHHHHHHHHHHHHHHhc
Confidence 347899999999999999999999999999999999999999999999999875
No 15
>KOG0485|consensus
Probab=99.41 E-value=1.2e-13 Score=117.97 Aligned_cols=61 Identities=31% Similarity=0.377 Sum_probs=56.6
Q ss_pred cccccCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCccccccccchhhhhhhHHHhhcc
Q psy14871 157 TSYCFKEKSRSVLRDWYTHNPYPSPREKRELAEATGLTTTQVSNWFKNRRQRDRAAEQKDG 217 (238)
Q Consensus 157 t~~~fs~~q~~~Le~~F~~~~yPs~~~r~~LA~~lgLs~~qV~~WFqNRR~R~k~~~~~~~ 217 (238)
+++.|+..|...||..|+..+|.+..+|..||.++.|+++||++||||||.|||++...+-
T Consensus 107 tRTvFSraQV~qLEs~Fe~krYLSsaeRa~LA~sLqLTETQVKIWFQNRRnKwKRq~aad~ 167 (268)
T KOG0485|consen 107 TRTVFSRAQVFQLESTFELKRYLSSAERAGLAASLQLTETQVKIWFQNRRNKWKRQYAADL 167 (268)
T ss_pred chhhhhHHHHHHHHHHHHHHhhhhHHHHhHHHHhhhhhhhhhhhhhhhhhHHHHHHHhhhh
Confidence 3459999999999999999999999999999999999999999999999999999876543
No 16
>smart00389 HOX Homeodomain. DNA-binding factors that are involved in the transcriptional regulation of key developmental processes
Probab=99.40 E-value=2.2e-13 Score=92.70 Aligned_cols=52 Identities=38% Similarity=0.666 Sum_probs=49.3
Q ss_pred cccCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCccccccccchhhhhhh
Q psy14871 159 YCFKEKSRSVLRDWYTHNPYPSPREKRELAEATGLTTTQVSNWFKNRRQRDR 210 (238)
Q Consensus 159 ~~fs~~q~~~Le~~F~~~~yPs~~~r~~LA~~lgLs~~qV~~WFqNRR~R~k 210 (238)
..|+..++.+|+.+|..++||+..++..||..+||+..+|++||+|+|.+.+
T Consensus 5 ~~~~~~~~~~L~~~f~~~~~P~~~~~~~la~~~~l~~~qV~~WF~nrR~~~~ 56 (56)
T smart00389 5 TSFTPEQLEELEKEFQKNPYPSREEREELAAKLGLSERQVKVWFQNRRAKWK 56 (56)
T ss_pred CcCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHHCcCHHHHHHhHHHHhhccC
Confidence 3689999999999999999999999999999999999999999999998864
No 17
>KOG0494|consensus
Probab=99.32 E-value=1.4e-12 Score=113.94 Aligned_cols=59 Identities=27% Similarity=0.463 Sum_probs=55.3
Q ss_pred cccCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCccccccccchhhhhhhHHHhhcc
Q psy14871 159 YCFKEKSRSVLRDWYTHNPYPSPREKRELAEATGLTTTQVSNWFKNRRQRDRAAEQKDG 217 (238)
Q Consensus 159 ~~fs~~q~~~Le~~F~~~~yPs~~~r~~LA~~lgLs~~qV~~WFqNRR~R~k~~~~~~~ 217 (238)
+.|+..|+..||+.|...+||+...|+.||..|.|.+..|+|||||||+|||+..+.-.
T Consensus 146 TiFT~~Qle~LEkaFkeaHYPDv~Are~la~ktelpEDRIqVWfQNRRAKWRk~Ek~wg 204 (332)
T KOG0494|consen 146 TIFTSYQLEELEKAFKEAHYPDVYAREMLADKTELPEDRIQVWFQNRRAKWRKTEKRWG 204 (332)
T ss_pred chhhHHHHHHHHHHHhhccCccHHHHHHHhhhccCchhhhhHHhhhhhHHhhhhhhhcC
Confidence 47999999999999999999999999999999999999999999999999999776543
No 18
>KOG4577|consensus
Probab=99.30 E-value=2e-12 Score=114.51 Aligned_cols=121 Identities=26% Similarity=0.364 Sum_probs=84.2
Q ss_pred hHHHHHHHHHHhhhccHHHHHHH--Hh-cCCCCCCChhHHHHHHHhhhhhHHHHhcCCCCCCCCccccCCCCCCCCcccC
Q psy14871 77 ESVLKAKAMVAFHRGNFKDLYRI--LE-SHQFSPHNHPKLQALWLKAHYVEAEKLRGRPLGAVGKYRVRRKFPLPRTIWD 153 (238)
Q Consensus 77 e~vlra~a~v~~h~~~f~e~~~l--Le-~~~f~~~~h~~lq~lw~~a~y~~~e~~~grpl~~~~k~r~Rkk~p~P~ti~~ 153 (238)
.-|-||...|| |-.||..+..- |+ +..|--- .=..|..+..|.++...-.-.|.... ...+|||
T Consensus 106 qVVRkAqd~VY-Hl~CF~C~iC~R~L~TGdEFYLm---eD~rLvCK~DYE~Ak~k~~~~l~gd~------~nKRPRT--- 172 (383)
T KOG4577|consen 106 QVVRKAQDFVY-HLHCFACFICKRQLATGDEFYLM---EDARLVCKDDYETAKQKHCNELEGDA------SNKRPRT--- 172 (383)
T ss_pred HHHHHhhccee-ehhhhhhHhhhcccccCCeeEEe---ccceeehhhhHHHHHhcccccccccc------ccCCCcc---
Confidence 45566888888 99999866322 22 2223111 11234456666655432222232211 1123444
Q ss_pred CCCcccccCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCccccccccchhhhhhhHHHhhc
Q psy14871 154 GEETSYCFKEKSRSVLRDWYTHNPYPSPREKRELAEATGLTTTQVSNWFKNRRQRDRAAEQKD 216 (238)
Q Consensus 154 ~~~t~~~fs~~q~~~Le~~F~~~~yPs~~~r~~LA~~lgLs~~qV~~WFqNRR~R~k~~~~~~ 216 (238)
.++.+|+..|+..|...+.|....|+.|+..+||.-+.|+|||||||+|+|+.++..
T Consensus 173 ------TItAKqLETLK~AYn~SpKPARHVREQLsseTGLDMRVVQVWFQNRRAKEKRLKKDA 229 (383)
T KOG4577|consen 173 ------TITAKQLETLKQAYNTSPKPARHVREQLSSETGLDMRVVQVWFQNRRAKEKRLKKDA 229 (383)
T ss_pred ------eeeHHHHHHHHHHhcCCCchhHHHHHHhhhccCcceeehhhhhhhhhHHHHhhhhhc
Confidence 789999999999999999999999999999999999999999999999999977653
No 19
>KOG0493|consensus
Probab=99.26 E-value=5.3e-12 Score=110.46 Aligned_cols=63 Identities=22% Similarity=0.480 Sum_probs=57.6
Q ss_pred CCCCcccccCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCccccccccchhhhhhhHHHhh
Q psy14871 153 DGEETSYCFKEKSRSVLRDWYTHNPYPSPREKRELAEATGLTTTQVSNWFKNRRQRDRAAEQK 215 (238)
Q Consensus 153 ~~~~t~~~fs~~q~~~Le~~F~~~~yPs~~~r~~LA~~lgLs~~qV~~WFqNRR~R~k~~~~~ 215 (238)
+.++.++.|+.+|+..|+..|+.|+|.+...|.+||.++||.+.||++||||+|+|.|+....
T Consensus 245 eeKRPRTAFtaeQL~RLK~EF~enRYlTEqRRQ~La~ELgLNEsQIKIWFQNKRAKiKKsTgs 307 (342)
T KOG0493|consen 245 EEKRPRTAFTAEQLQRLKAEFQENRYLTEQRRQELAQELGLNESQIKIWFQNKRAKIKKSTGS 307 (342)
T ss_pred hhcCccccccHHHHHHHHHHHhhhhhHHHHHHHHHHHHhCcCHHHhhHHhhhhhhhhhhccCC
Confidence 455567799999999999999999999999999999999999999999999999999986543
No 20
>KOG0483|consensus
Probab=99.21 E-value=6e-12 Score=107.44 Aligned_cols=58 Identities=26% Similarity=0.447 Sum_probs=54.5
Q ss_pred cccCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCccccccccchhhhhhhHHHhhc
Q psy14871 159 YCFKEKSRSVLRDWYTHNPYPSPREKRELAEATGLTTTQVSNWFKNRRQRDRAAEQKD 216 (238)
Q Consensus 159 ~~fs~~q~~~Le~~F~~~~yPs~~~r~~LA~~lgLs~~qV~~WFqNRR~R~k~~~~~~ 216 (238)
..|+.+|...|+..|+.+.|..+..|..||..+||.++||.+||||||+|||.++...
T Consensus 55 ~Rlt~eQ~~~LE~~F~~~~~L~p~~K~~LAk~LgL~pRQVavWFQNRRARwK~kqlE~ 112 (198)
T KOG0483|consen 55 RRLTSEQVKFLEKSFESEKKLEPERKKKLAKELGLQPRQVAVWFQNRRARWKTKQLEK 112 (198)
T ss_pred ccccHHHHHHhHHhhccccccChHHHHHHHHhhCCChhHHHHHHhhccccccchhhhh
Confidence 4789999999999999999999999999999999999999999999999999876654
No 21
>TIGR01565 homeo_ZF_HD homeobox domain, ZF-HD class. This model represents a class of homoebox domain that differs substantially from the typical homoebox domain described in pfam model pfam00046. It is found in both C4 and C3 plants.
Probab=99.21 E-value=2e-11 Score=84.72 Aligned_cols=49 Identities=22% Similarity=0.432 Sum_probs=46.8
Q ss_pred ccccCHHHHHHHHHHHhhCCC----CCHHHHHHHHHHhCCCccccccccchhh
Q psy14871 158 SYCFKEKSRSVLRDWYTHNPY----PSPREKRELAEATGLTTTQVSNWFKNRR 206 (238)
Q Consensus 158 ~~~fs~~q~~~Le~~F~~~~y----Ps~~~r~~LA~~lgLs~~qV~~WFqNRR 206 (238)
++.|+.+|+..|+..|+.++| |+..++.+||..+||++.+|++||+|.+
T Consensus 5 RT~Ft~~Q~~~Le~~fe~~~y~~~~~~~~~r~~la~~lgl~~~vvKVWfqN~k 57 (58)
T TIGR01565 5 RTKFTAEQKEKMRDFAEKLGWKLKDKRREEVREFCEEIGVTRKVFKVWMHNNK 57 (58)
T ss_pred CCCCCHHHHHHHHHHHHHcCCCCCCCCHHHHHHHHHHhCCCHHHeeeecccCC
Confidence 458999999999999999999 9999999999999999999999999965
No 22
>KOG0491|consensus
Probab=99.16 E-value=1e-11 Score=102.04 Aligned_cols=60 Identities=32% Similarity=0.555 Sum_probs=55.8
Q ss_pred ccccCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCccccccccchhhhhhhHHHhhcc
Q psy14871 158 SYCFKEKSRSVLRDWYTHNPYPSPREKRELAEATGLTTTQVSNWFKNRRQRDRAAEQKDG 217 (238)
Q Consensus 158 ~~~fs~~q~~~Le~~F~~~~yPs~~~r~~LA~~lgLs~~qV~~WFqNRR~R~k~~~~~~~ 217 (238)
++.|+..|+..|++.|+..+|.+..++.+||..++|+++||+.||||||+|.|+......
T Consensus 104 Rtvfs~~ql~~l~~rFe~QrYLS~~e~~ELan~L~LS~~QVKTWFQNrRMK~Kk~~r~~~ 163 (194)
T KOG0491|consen 104 RTVFSDPQLSGLEKRFERQRYLSTPERQELANALSLSETQVKTWFQNRRMKHKKQQRNNQ 163 (194)
T ss_pred cccccCccccccHHHHhhhhhcccHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHHHhccC
Confidence 358999999999999999999999999999999999999999999999999998877653
No 23
>COG5576 Homeodomain-containing transcription factor [Transcription]
Probab=99.14 E-value=6.9e-11 Score=97.63 Aligned_cols=59 Identities=22% Similarity=0.412 Sum_probs=54.1
Q ss_pred ccCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCccccccccchhhhhhhHHHhhccc
Q psy14871 160 CFKEKSRSVLRDWYTHNPYPSPREKRELAEATGLTTTQVSNWFKNRRQRDRAAEQKDGS 218 (238)
Q Consensus 160 ~fs~~q~~~Le~~F~~~~yPs~~~r~~LA~~lgLs~~qV~~WFqNRR~R~k~~~~~~~~ 218 (238)
..+..|+.+|++.|..++||+...|..|+..++|+++-|++||||+|++.|+.......
T Consensus 57 R~t~~Q~~vL~~~F~i~p~Ps~~~r~~L~~~lnm~~ksVqIWFQNkR~~~k~~~~~~~~ 115 (156)
T COG5576 57 RTTDEQLMVLEREFEINPYPSSITRIKLSLLLNMPPKSVQIWFQNKRAKEKKKRSGKVE 115 (156)
T ss_pred echHHHHHHHHHHhccCCCCCHHHHHHHHHhcCCChhhhhhhhchHHHHHHHhcccchh
Confidence 45788999999999999999999999999999999999999999999999987666433
No 24
>KOG0486|consensus
Probab=99.09 E-value=5.2e-11 Score=106.65 Aligned_cols=58 Identities=33% Similarity=0.509 Sum_probs=54.9
Q ss_pred cccCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCccccccccchhhhhhhHHHhhc
Q psy14871 159 YCFKEKSRSVLRDWYTHNPYPSPREKRELAEATGLTTTQVSNWFKNRRQRDRAAEQKD 216 (238)
Q Consensus 159 ~~fs~~q~~~Le~~F~~~~yPs~~~r~~LA~~lgLs~~qV~~WFqNRR~R~k~~~~~~ 216 (238)
+.|+..|+..||.+|++|.||+...|++||.-++|++..|+|||+|||+|||+.+.-.
T Consensus 117 thFtSqqlqele~tF~rNrypdMstrEEIavwtNlTE~rvrvwfknrrakwrkrErN~ 174 (351)
T KOG0486|consen 117 THFTSQQLQELEATFQRNRYPDMSTREEIAVWTNLTEARVRVWFKNRRAKWRKRERNQ 174 (351)
T ss_pred hhhHHHHHHHHHHHHhhccCCccchhhHHHhhccccchhhhhhcccchhhhhhhhhhH
Confidence 4899999999999999999999999999999999999999999999999999876543
No 25
>KOG0844|consensus
Probab=99.07 E-value=6.3e-11 Score=105.78 Aligned_cols=61 Identities=26% Similarity=0.392 Sum_probs=56.3
Q ss_pred ccccCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCccccccccchhhhhhhHHHhhccc
Q psy14871 158 SYCFKEKSRSVLRDWYTHNPYPSPREKRELAEATGLTTTQVSNWFKNRRQRDRAAEQKDGS 218 (238)
Q Consensus 158 ~~~fs~~q~~~Le~~F~~~~yPs~~~r~~LA~~lgLs~~qV~~WFqNRR~R~k~~~~~~~~ 218 (238)
++.|+.+|+..||+.|.+..|.+...|.+||..++|.++.|+|||||||+|+|++......
T Consensus 185 RTAFTReQIaRLEKEFyrENYVSRprRcELAAaLNLPEtTIKVWFQNRRMKDKRQRlamaW 245 (408)
T KOG0844|consen 185 RTAFTREQIARLEKEFYRENYVSRPRRCELAAALNLPETTIKVWFQNRRMKDKRQRLAMAW 245 (408)
T ss_pred HhhhhHHHHHHHHHHHHHhccccCchhhhHHHhhCCCcceeehhhhhchhhhhhhhhhccC
Confidence 4589999999999999999999999999999999999999999999999999998766433
No 26
>KOG0847|consensus
Probab=99.04 E-value=1.1e-10 Score=99.96 Aligned_cols=62 Identities=23% Similarity=0.374 Sum_probs=56.7
Q ss_pred ccccCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCccccccccchhhhhhhHHHhhcccc
Q psy14871 158 SYCFKEKSRSVLRDWYTHNPYPSPREKRELAEATGLTTTQVSNWFKNRRQRDRAAEQKDGSV 219 (238)
Q Consensus 158 ~~~fs~~q~~~Le~~F~~~~yPs~~~r~~LA~~lgLs~~qV~~WFqNRR~R~k~~~~~~~~~ 219 (238)
+..|+..|+..|+..|++.+|+-..++.+||..+|+++.||+|||||||.|||++...+...
T Consensus 171 rPTf~g~qi~~le~~feqtkylaG~~ra~lA~~lgmteSqvkVWFQNRRTKWRKkhAaEmas 232 (288)
T KOG0847|consen 171 RPTFTGHQIYQLERKFEQTKYLAGADRAQLAQELNMTESQVKVWFQNRRTKWRKKHAAEMAS 232 (288)
T ss_pred CCCccchhhhhhhhhhhhhhcccchhHHHhhccccccHHHHHHHHhcchhhhhhhhccchhh
Confidence 34789999999999999999999999999999999999999999999999999987765443
No 27
>KOG1168|consensus
Probab=98.92 E-value=2e-09 Score=95.69 Aligned_cols=49 Identities=27% Similarity=0.526 Sum_probs=46.1
Q ss_pred HHHHHHHHhhCCCCCHHHHHHHHHHhCCCccccccccchhhhhhhHHHh
Q psy14871 166 RSVLRDWYTHNPYPSPREKRELAEATGLTTTQVSNWFKNRRQRDRAAEQ 214 (238)
Q Consensus 166 ~~~Le~~F~~~~yPs~~~r~~LA~~lgLs~~qV~~WFqNRR~R~k~~~~ 214 (238)
.+.||.+|...|.|+.+.+..||++++|.+..|+|||+|.|+|.|+.+.
T Consensus 321 KRsLEayFavQPRPS~EkIAaIAekLDLKKNVVRVWFCNQRQKQKRm~~ 369 (385)
T KOG1168|consen 321 KRSLEAYFAVQPRPSGEKIAAIAEKLDLKKNVVRVWFCNQRQKQKRMKR 369 (385)
T ss_pred cccHHHHhccCCCCchhHHHHHHHhhhhhhceEEEEeeccHHHHHHhhh
Confidence 5889999999999999999999999999999999999999999998544
No 28
>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=98.81 E-value=1.4e-09 Score=69.98 Aligned_cols=34 Identities=65% Similarity=1.102 Sum_probs=29.4
Q ss_pred hCCCCCHHHHHHHHHHhCCCccccccccchhhhh
Q psy14871 175 HNPYPSPREKRELAEATGLTTTQVSNWFKNRRQR 208 (238)
Q Consensus 175 ~~~yPs~~~r~~LA~~lgLs~~qV~~WFqNRR~R 208 (238)
.+|||+.++|..||..+||+..||.+||-|.|.|
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 4899999999999999999999999999999986
No 29
>KOG0774|consensus
Probab=98.79 E-value=2.7e-09 Score=93.65 Aligned_cols=65 Identities=35% Similarity=0.655 Sum_probs=56.8
Q ss_pred cCCCCcccccCHHHHHHHHHHHh---hCCCCCHHHHHHHHHHhCCCccccccccchhhhhhhHHHhhc
Q psy14871 152 WDGEETSYCFKEKSRSVLRDWYT---HNPYPSPREKRELAEATGLTTTQVSNWFKNRRQRDRAAEQKD 216 (238)
Q Consensus 152 ~~~~~t~~~fs~~q~~~Le~~F~---~~~yPs~~~r~~LA~~lgLs~~qV~~WFqNRR~R~k~~~~~~ 216 (238)
.+..+++++|+.....+|..||. .||||+.+.|++||+++|++..||.+||.|+|-|.|+...+.
T Consensus 186 ldarRKRRNFsK~aTeiLneyF~~h~~nPYPSee~K~eLAkqCnItvsQvsnwfgnkrIrykK~~~k~ 253 (334)
T KOG0774|consen 186 LDARRKRRNFSKQATEILNEYFYSHLSNPYPSEEAKEELAKQCNITVSQVSNWFGNKRIRYKKNMGKN 253 (334)
T ss_pred HHHHHhhcccchhHHHHHHHHHHHhcCCCCCcHHHHHHHHHHcCceehhhccccccceeehhhhhhhh
Confidence 34445566899999999999996 489999999999999999999999999999999999865543
No 30
>KOG0490|consensus
Probab=98.70 E-value=9.2e-09 Score=88.54 Aligned_cols=58 Identities=24% Similarity=0.289 Sum_probs=54.2
Q ss_pred cccccCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCccccccccchhhhhhhHHHh
Q psy14871 157 TSYCFKEKSRSVLRDWYTHNPYPSPREKRELAEATGLTTTQVSNWFKNRRQRDRAAEQ 214 (238)
Q Consensus 157 t~~~fs~~q~~~Le~~F~~~~yPs~~~r~~LA~~lgLs~~qV~~WFqNRR~R~k~~~~ 214 (238)
.++.|+..|+..|++.|+.++||+...++.||..+++++..|++||||+|+++++...
T Consensus 63 ~rt~~~~~ql~~ler~f~~~h~Pd~~~r~~la~~~~~~e~rVqvwFqnrrak~r~~~~ 120 (235)
T KOG0490|consen 63 ARCKFTISQLDELERAFEKVHLPCFACRECLALLLTGDEFRVQVWFQNRRAKDRKEER 120 (235)
T ss_pred cCCCCCcCHHHHHHHhhcCCCcCccchHHHHhhcCCCCeeeeehhhhhhcHhhhhhhc
Confidence 3457888999999999999999999999999999999999999999999999998774
No 31
>KOG0849|consensus
Probab=98.47 E-value=1.5e-07 Score=87.22 Aligned_cols=58 Identities=29% Similarity=0.573 Sum_probs=54.6
Q ss_pred ccccCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCccccccccchhhhhhhHHHhh
Q psy14871 158 SYCFKEKSRSVLRDWYTHNPYPSPREKRELAEATGLTTTQVSNWFKNRRQRDRAAEQK 215 (238)
Q Consensus 158 ~~~fs~~q~~~Le~~F~~~~yPs~~~r~~LA~~lgLs~~qV~~WFqNRR~R~k~~~~~ 215 (238)
++.|+..|...|+++|+.++||+...++.||.++++++..|++||+|||+|+++....
T Consensus 180 rtsft~~Q~~~le~~f~rt~yP~i~~Re~La~~i~l~e~riqvwf~nrra~~rr~~~~ 237 (354)
T KOG0849|consen 180 RTSFSPSQLEALEECFQRTPYPDIVGRETLAKETGLPEPRVQVWFQNRRAKWRRQHRD 237 (354)
T ss_pred ccccccchHHHHHHHhcCCCCCchhhHHHHhhhccCCchHHHHHHhhhhhhhhhcccc
Confidence 4589999999999999999999999999999999999999999999999999987743
No 32
>KOG2252|consensus
Probab=98.44 E-value=3.9e-07 Score=87.30 Aligned_cols=53 Identities=23% Similarity=0.412 Sum_probs=50.6
Q ss_pred ccccCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCccccccccchhhhhhh
Q psy14871 158 SYCFKEKSRSVLRDWYTHNPYPSPREKRELAEATGLTTTQVSNWFKNRRQRDR 210 (238)
Q Consensus 158 ~~~fs~~q~~~Le~~F~~~~yPs~~~r~~LA~~lgLs~~qV~~WFqNRR~R~k 210 (238)
|.+|+..|+..|...|+.+++|+.++.+.|+.+|+|..+.|.|||-|.|+|.+
T Consensus 424 RlVfTd~QkrTL~aiFke~~RPS~Emq~tIS~qL~L~~sTV~NfFmNaRRRsl 476 (558)
T KOG2252|consen 424 RLVFTDIQKRTLQAIFKENKRPSREMQETISQQLNLELSTVINFFMNARRRSL 476 (558)
T ss_pred eeeecHHHHHHHHHHHhcCCCCCHHHHHHHHHHhCCcHHHHHHHHHhhhhhcc
Confidence 55999999999999999999999999999999999999999999999999863
No 33
>KOG0773|consensus
Probab=97.63 E-value=2.8e-05 Score=71.47 Aligned_cols=56 Identities=43% Similarity=0.642 Sum_probs=49.9
Q ss_pred cccCHHHHHHHHHHHhh---CCCCCHHHHHHHHHHhCCCccccccccchhhhhhhHHHh
Q psy14871 159 YCFKEKSRSVLRDWYTH---NPYPSPREKRELAEATGLTTTQVSNWFKNRRQRDRAAEQ 214 (238)
Q Consensus 159 ~~fs~~q~~~Le~~F~~---~~yPs~~~r~~LA~~lgLs~~qV~~WFqNRR~R~k~~~~ 214 (238)
..|.+....+|+.|... .+||+..++..||.++||+..||.|||.|.|.|..+...
T Consensus 244 ~~lP~~a~~ilr~Wl~~h~~~PYPse~~K~~La~~TGLs~~Qv~NWFINaR~R~w~p~~ 302 (342)
T KOG0773|consen 244 RGLPKEAVSILRAWLFEHLLHPYPSDDEKLMLAKQTGLSRPQVSNWFINARVRLWKPMI 302 (342)
T ss_pred CCCCHHHHHHHHHHHHHhccCCCCcchhccccchhcCCCcccCCchhhhcccccCCchH
Confidence 37889999999999754 689999999999999999999999999999999776544
No 34
>KOG0490|consensus
Probab=97.60 E-value=7.6e-05 Score=64.10 Aligned_cols=57 Identities=32% Similarity=0.600 Sum_probs=53.2
Q ss_pred ccccCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCccccccccchhhhhhhHHHh
Q psy14871 158 SYCFKEKSRSVLRDWYTHNPYPSPREKRELAEATGLTTTQVSNWFKNRRQRDRAAEQ 214 (238)
Q Consensus 158 ~~~fs~~q~~~Le~~F~~~~yPs~~~r~~LA~~lgLs~~qV~~WFqNRR~R~k~~~~ 214 (238)
+..|...+...+...|..+++|+...+..|+..+|++...|++||+|+|.+.++...
T Consensus 157 ~~~~~~~~~~~~~~~~~~~~~P~~~~~~~l~~~~~~~~~~~q~~~~~~~~~~~~~~~ 213 (235)
T KOG0490|consen 157 RTTFTENQLEVLETVFRATPKPDADDREQLAEETGLSERVIQVWFQNRRAKLRKHKR 213 (235)
T ss_pred ccccccchhHhhhhcccCCCCCchhhHHHHHHhcCCChhhhhhhcccHHHHHHhhcc
Confidence 347888899999999999999999999999999999999999999999999998766
No 35
>PF11569 Homez: Homeodomain leucine-zipper encoding, Homez; PDB: 2YS9_A.
Probab=96.93 E-value=0.00036 Score=47.98 Aligned_cols=43 Identities=26% Similarity=0.485 Sum_probs=31.6
Q ss_pred HHHHHHHHhhCCCCCHHHHHHHHHHhCCCccccccccchhhhh
Q psy14871 166 RSVLRDWYTHNPYPSPREKRELAEATGLTTTQVSNWFKNRRQR 208 (238)
Q Consensus 166 ~~~Le~~F~~~~yPs~~~r~~LA~~lgLs~~qV~~WFqNRR~R 208 (238)
...|+++|..++++...+...|..+++|+..||+.||-.++.+
T Consensus 10 ~~pL~~Yy~~h~~L~E~DL~~L~~kS~ms~qqVr~WFa~~~~e 52 (56)
T PF11569_consen 10 IQPLEDYYLKHKQLQEEDLDELCDKSRMSYQQVRDWFAERMQE 52 (56)
T ss_dssp -HHHHHHHHHT----TTHHHHHHHHTT--HHHHHHHHHHHS--
T ss_pred hHHHHHHHHHcCCccHhhHHHHHHHHCCCHHHHHHHHHHhccc
Confidence 4669999999999999999999999999999999999766543
No 36
>KOG1146|consensus
Probab=96.33 E-value=0.0044 Score=65.18 Aligned_cols=57 Identities=21% Similarity=0.384 Sum_probs=53.5
Q ss_pred ccccCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCccccccccchhhhhhhHHHh
Q psy14871 158 SYCFKEKSRSVLRDWYTHNPYPSPREKRELAEATGLTTTQVSNWFKNRRQRDRAAEQ 214 (238)
Q Consensus 158 ~~~fs~~q~~~Le~~F~~~~yPs~~~r~~LA~~lgLs~~qV~~WFqNRR~R~k~~~~ 214 (238)
++.++..++.+++..|....||...+.+.|-..+++..+.|.+||+|.|++.++...
T Consensus 907 ~~~~~d~qlk~i~~~~~~q~~~~~~~~E~l~~~~~~~~~~i~vw~qna~~~s~k~~~ 963 (1406)
T KOG1146|consen 907 RTQESDLQLKIIKACYEAQRTPTMQECEVLEEPIGLPKRVIQVWFQNARAKSKKAKL 963 (1406)
T ss_pred ccchhHHHHHHHHHHHhhccCChHHHHHhhcccccCCcchhHHhhhhhhhhhhhhhh
Confidence 457899999999999999999999999999999999999999999999999988766
No 37
>KOG3623|consensus
Probab=92.73 E-value=0.15 Score=51.41 Aligned_cols=48 Identities=29% Similarity=0.585 Sum_probs=44.7
Q ss_pred HHHHHHHHhhCCCCCHHHHHHHHHHhCCCccccccccchhhhhhhHHH
Q psy14871 166 RSVLRDWYTHNPYPSPREKRELAEATGLTTTQVSNWFKNRRQRDRAAE 213 (238)
Q Consensus 166 ~~~Le~~F~~~~yPs~~~r~~LA~~lgLs~~qV~~WFqNRR~R~k~~~ 213 (238)
..+|+.+|..|..|+..+-..+|.+.||....|+.||.+++.......
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 689999999999999999999999999999999999999998877654
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=84.14 E-value=1.4 Score=29.59 Aligned_cols=41 Identities=20% Similarity=0.330 Sum_probs=28.1
Q ss_pred ccCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCccccccccchh
Q psy14871 160 CFKEKSRSVLRDWYTHNPYPSPREKRELAEATGLTTTQVSNWFKNR 205 (238)
Q Consensus 160 ~fs~~q~~~Le~~F~~~~yPs~~~r~~LA~~lgLs~~qV~~WFqNR 205 (238)
.++-++...+-..++... ....||..+|++..+|..|.+|+
T Consensus 6 ~LTl~eK~~iI~~~e~g~-----s~~~ia~~fgv~~sTv~~I~K~k 46 (53)
T PF04218_consen 6 SLTLEEKLEIIKRLEEGE-----SKRDIAREFGVSRSTVSTILKNK 46 (53)
T ss_dssp S--HHHHHHHHHHHHCTT------HHHHHHHHT--CCHHHHHHHCH
T ss_pred cCCHHHHHHHHHHHHcCC-----CHHHHHHHhCCCHHHHHHHHHhH
Confidence 566666555556666655 57789999999999999999885
No 39
>PF04545 Sigma70_r4: Sigma-70, region 4; InterPro: IPR007630 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognised by the major sigma factors [, ]. Region 4 of sigma-70 like sigma-factors is involved in binding to the -35 promoter element via a helix-turn-helix motif []. Due to the way Pfam works, the threshold has been set artificially high to prevent overlaps with other helix-turn-helix families. Therefore there are many false negatives.; GO: 0003677 DNA binding, 0003700 sequence-specific DNA binding transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, DNA-dependent, 0006355 regulation of transcription, DNA-dependent; PDB: 2P7V_B 3IYD_F 1TLH_B 1KU7_A 1RIO_H 3N97_A 1KU3_A 1RP3_C 1SC5_A 1NR3_A ....
Probab=63.79 E-value=7.6 Score=25.14 Aligned_cols=46 Identities=24% Similarity=0.335 Sum_probs=33.3
Q ss_pred ccCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCccccccccchhhhhhh
Q psy14871 160 CFKEKSRSVLRDWYTHNPYPSPREKRELAEATGLTTTQVSNWFKNRRQRDR 210 (238)
Q Consensus 160 ~fs~~q~~~Le~~F~~~~yPs~~~r~~LA~~lgLs~~qV~~WFqNRR~R~k 210 (238)
.+++.++.+|...|..+ ..-.++|..+|++...|+.+...-..|-|
T Consensus 4 ~L~~~er~vi~~~y~~~-----~t~~eIa~~lg~s~~~V~~~~~~al~kLR 49 (50)
T PF04545_consen 4 QLPPREREVIRLRYFEG-----LTLEEIAERLGISRSTVRRILKRALKKLR 49 (50)
T ss_dssp TS-HHHHHHHHHHHTST------SHHHHHHHHTSCHHHHHHHHHHHHHHHH
T ss_pred hCCHHHHHHHHHHhcCC-----CCHHHHHHHHCCcHHHHHHHHHHHHHHhc
Confidence 46788899999988332 24678899999999999888765554443
No 40
>KOG4330|consensus
Probab=63.78 E-value=8.5 Score=32.64 Aligned_cols=36 Identities=25% Similarity=0.248 Sum_probs=26.0
Q ss_pred CCCCCCCCCCCCChhhHhHHhhhhhccCchhHHHHH
Q psy14871 28 ASISPILPSFGFTQEQVACVCEVLQQSGNIERLGRF 63 (238)
Q Consensus 28 ~~~~~~~~~~~~~~~q~~~vc~~l~~~gd~~~l~~f 63 (238)
.+.|-...---||..||--|||.|+...++.--++|
T Consensus 135 s~~mr~~ek~~FTlrqVqmICErllKerE~klReey 170 (206)
T KOG4330|consen 135 SSTMRKSEKPLFTLRQVQMICERLLKEREIKLREEY 170 (206)
T ss_pred cchhhccccchhhHHHHHHHHHHHHHHHHHHHHHHH
Confidence 344443233349999999999999987776666777
No 41
>PF14559 TPR_19: Tetratricopeptide repeat; PDB: 2R5S_A 3QDN_B 3QOU_A 3ASG_A 3ASD_A 3AS5_A 3AS4_A 3ASH_B 3FP3_A 3LCA_A ....
Probab=63.01 E-value=18 Score=24.00 Aligned_cols=43 Identities=19% Similarity=0.247 Sum_probs=30.3
Q ss_pred cchHHHHHHHHHHhhhccHHHHHHHHhcCCCCCCChhHHHHHH
Q psy14871 75 KNESVLKAKAMVAFHRGNFKDLYRILESHQFSPHNHPKLQALW 117 (238)
Q Consensus 75 ~~e~vlra~a~v~~h~~~f~e~~~lLe~~~f~~~~h~~lq~lw 117 (238)
+|..+.-.-+.+++..|+|.++..+|+.-.-...+++....++
T Consensus 23 ~~~~~~~~la~~~~~~g~~~~A~~~l~~~~~~~~~~~~~~~l~ 65 (68)
T PF14559_consen 23 DNPEARLLLAQCYLKQGQYDEAEELLERLLKQDPDNPEYQQLL 65 (68)
T ss_dssp TSHHHHHHHHHHHHHTT-HHHHHHHHHCCHGGGTTHHHHHHHH
T ss_pred CCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHCcCHHHHHHHH
Confidence 3567777788888889999999999987654444445555554
No 42
>PF04967 HTH_10: HTH DNA binding domain; InterPro: IPR007050 Numerous bacterial transcription regulatory proteins bind DNA via a helix-turn-helix (HTH) motif. This entry represents the HTH DNA binding domain found in Halobacterium salinarium (Halobacterium halobium) and described as a putative bacterio-opsin activator.
Probab=58.12 E-value=12 Score=25.31 Aligned_cols=40 Identities=28% Similarity=0.452 Sum_probs=32.5
Q ss_pred cCHHHHHHHHHHHhhCC--CCCHHHHHHHHHHhCCCcccccc
Q psy14871 161 FKEKSRSVLRDWYTHNP--YPSPREKRELAEATGLTTTQVSN 200 (238)
Q Consensus 161 fs~~q~~~Le~~F~~~~--yPs~~~r~~LA~~lgLs~~qV~~ 200 (238)
+|+.|+.+|...|...- +|-.....+||..+|++..-|..
T Consensus 1 LT~~Q~e~L~~A~~~GYfd~PR~~tl~elA~~lgis~st~~~ 42 (53)
T PF04967_consen 1 LTDRQREILKAAYELGYFDVPRRITLEELAEELGISKSTVSE 42 (53)
T ss_pred CCHHHHHHHHHHHHcCCCCCCCcCCHHHHHHHhCCCHHHHHH
Confidence 47789999999998764 47777788999999999977654
No 43
>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=54.47 E-value=8.3 Score=23.98 Aligned_cols=44 Identities=18% Similarity=0.294 Sum_probs=31.6
Q ss_pred ccCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCccccccccchhhhh
Q psy14871 160 CFKEKSRSVLRDWYTHNPYPSPREKRELAEATGLTTTQVSNWFKNRRQR 208 (238)
Q Consensus 160 ~fs~~q~~~Le~~F~~~~yPs~~~r~~LA~~lgLs~~qV~~WFqNRR~R 208 (238)
.++..++.++...|... .....+|..+|++...|..|....+.+
T Consensus 10 ~l~~~~~~~~~~~~~~~-----~~~~~ia~~~~~s~~~i~~~~~~~~~~ 53 (55)
T cd06171 10 KLPEREREVILLRFGEG-----LSYEEIAEILGISRSTVRQRLHRALKK 53 (55)
T ss_pred hCCHHHHHHHHHHHhcC-----CCHHHHHHHHCcCHHHHHHHHHHHHHH
Confidence 45666778887776433 235678999999999999998655443
No 44
>KOG0773|consensus
Probab=54.16 E-value=8.4 Score=35.31 Aligned_cols=38 Identities=55% Similarity=0.708 Sum_probs=35.0
Q ss_pred hCCCCCHHHHHHHHHHhCCCccccccccchhhhhhhHH
Q psy14871 175 HNPYPSPREKRELAEATGLTTTQVSNWFKNRRQRDRAA 212 (238)
Q Consensus 175 ~~~yPs~~~r~~LA~~lgLs~~qV~~WFqNRR~R~k~~ 212 (238)
.++||+..++..++..++++..+|.+||-|.|.+.+..
T Consensus 118 ~~~~~~k~~~~ll~~~~~~~~~~~~~~~~~a~r~~~~~ 155 (342)
T KOG0773|consen 118 LNPYPSKLEKILLAVITKLTLTQVSTWFANARRRLKKE 155 (342)
T ss_pred hccCchHHHHHHHHHHHHhhhhhHHHHHHHHHHHHHhc
Confidence 48999999999999999999999999999999887764
No 45
>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=53.94 E-value=17 Score=27.42 Aligned_cols=37 Identities=41% Similarity=0.682 Sum_probs=20.9
Q ss_pred HHHHHHHHhhCCCCCHHHHHHHHHHhCCCccccccccchhhhhhhHHHhhc
Q psy14871 166 RSVLRDWYTHNPYPSPREKRELAEATGLTTTQVSNWFKNRRQRDRAAEQKD 216 (238)
Q Consensus 166 ~~~Le~~F~~~~yPs~~~r~~LA~~lgLs~~qV~~WFqNRR~R~k~~~~~~ 216 (238)
+.+.+-.|+.||||+..-... | =.|||.|||+.+.+-
T Consensus 14 vRiIk~LyqsnPyP~~~GTr~-a-------------RRnRRRRWR~rq~QI 50 (91)
T PF00424_consen 14 VRIIKILYQSNPYPSPEGTRQ-A-------------RRNRRRRWRARQRQI 50 (91)
T ss_dssp HHHHHHHHHTS-S--S-S-HH-H-------------HHHHHHHHHHHHHHH
T ss_pred HHHHHHHHccccCCCCCCccc-c-------------ccchhhhHHHHHHHH
Confidence 455566688899998542111 1 158999999876654
No 46
>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=51.49 E-value=16 Score=23.82 Aligned_cols=43 Identities=21% Similarity=0.359 Sum_probs=29.1
Q ss_pred ccCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCccccccccchhhh
Q psy14871 160 CFKEKSRSVLRDWYTHNPYPSPREKRELAEATGLTTTQVSNWFKNRRQ 207 (238)
Q Consensus 160 ~fs~~q~~~Le~~F~~~~yPs~~~r~~LA~~lgLs~~qV~~WFqNRR~ 207 (238)
.+++.++.++...|..+ ..-.++|..+|++...|++|...-|.
T Consensus 10 ~L~~~~r~i~~l~~~~g-----~s~~eIa~~l~~s~~~v~~~l~ra~~ 52 (54)
T PF08281_consen 10 QLPERQREIFLLRYFQG-----MSYAEIAEILGISESTVKRRLRRARK 52 (54)
T ss_dssp CS-HHHHHHHHHHHTS--------HHHHHHHCTS-HHHHHHHHHHHHH
T ss_pred CCCHHHHHHHHHHHHHC-----cCHHHHHHHHCcCHHHHHHHHHHHHh
Confidence 45667777777765443 45678999999999999999865444
No 47
>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=45.10 E-value=9.9 Score=26.50 Aligned_cols=19 Identities=21% Similarity=0.637 Sum_probs=16.6
Q ss_pred HHHHHHHhCCCcccccccc
Q psy14871 184 KRELAEATGLTTTQVSNWF 202 (238)
Q Consensus 184 r~~LA~~lgLs~~qV~~WF 202 (238)
-..||.++|+++.+|+.|=
T Consensus 25 lkdIA~~Lgvs~~tIr~WK 43 (60)
T PF10668_consen 25 LKDIAEKLGVSESTIRKWK 43 (60)
T ss_pred HHHHHHHHCCCHHHHHHHh
Confidence 4568999999999999993
No 48
>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=42.74 E-value=40 Score=18.36 Aligned_cols=37 Identities=11% Similarity=0.178 Sum_probs=24.3
Q ss_pred cCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCcccccccc
Q psy14871 161 FKEKSRSVLRDWYTHNPYPSPREKRELAEATGLTTTQVSNWF 202 (238)
Q Consensus 161 fs~~q~~~Le~~F~~~~yPs~~~r~~LA~~lgLs~~qV~~WF 202 (238)
++...+..+...+.. .+ ....+|..+|++...|..|.
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 344445555555543 22 45678899999999888874
No 49
>PF11791 Aconitase_B_N: Aconitate B N-terminal domain; InterPro: IPR015933 Aconitase (aconitate hydratase; 4.2.1.3 from EC) is an iron-sulphur protein that contains a [4Fe-4S]-cluster and catalyses the interconversion of isocitrate and citrate via a cis-aconitate intermediate. Aconitase functions in both the TCA and glyoxylate cycles, however unlike the majority of iron-sulphur proteins that function as electron carriers, the [4Fe-4S]-cluster of aconitase reacts directly with an enzyme substrate. In eukaryotes there is a cytosolic form (cAcn) and a mitochondrial form (mAcn) of the enzyme. In bacteria there are also 2 forms, aconitase A (AcnA) and B (AcnB). Several aconitases are known to be multi-functional enzymes with a second non-catalytic, but essential function that arises when the cellular environment changes, such as when iron levels drop [, ]. Eukaryotic cAcn and mAcn, and bacterial AcnA have the same domain organisation, consisting of three N-terminal alpha/beta/alpha domains, a linker region, followed by a C-terminal 'swivel' domain with a beta/beta/alpha structure (1-2-3-linker-4), although mAcn is small than cAcn. However, bacterial AcnB has a different organisation: it contains an N-terminal HEAT-like domain, followed by the 'swivel' domain, then the three alpha/beta/alpha domains (HEAT-4-1-2-3) []. Below is a description of some of the multi-functional activities associated with different aconitases. Eukaryotic mAcn catalyses the second step of the mitochondrial TCA cycle, which is important for energy production, providing high energy electrons in the form of NADH and FADH2 to the mitochondrial oxidative phosphorylation pathway []. The TCA cycle also provides precursors for haem and amino acid production. This enzyme has a second, non-catalytic but essential role in mitochondrial DNA (mtDNA) maintenance: mAcn acts to stabilise mtDNA, forming part of mtDNA protein-DNA complexes known as nucleoids. mAcn is thought to reversibly model nucleoids to directly influence mitochondrial gene expression in response to changes in the cellular environment. Therefore, mAcn can influence the expression of components of the oxidative phosphorylation pathway encoded in mtDNA. Eukaryotic cAcn enzyme balances the amount of citrate and isocitrate in the cytoplasm, which in turn creates a balance between the amount of NADPH generated from isocitrate by isocitrate dehydrogenase with the amount of acetyl-CoA generated from citrate by citrate lyase. Fatty acid synthesis requires both NADPH and acetyl-CoA, as do other metabolic processes, including the need for NADPH to combat oxidative stress. The enzymatic form of cAcn predominates when iron levels are normal, but if they drop sufficiently to cause the disassembly of the [4Fe-4S]-cluster, then cAcn undergoes a conformational change from a compact enzyme to a more open L-shaped protein known as iron regulatory protein 1 (IRP1; or IRE-binding protein 1, IREBP1) [, ]. As IRP1, the catalytic site and the [4Fe-4S]-cluster are lost, and two new RNA-binding sites appear. IRP1 functions in the post-transcriptional regulation of genes involved in iron metabolism - it binds to mRNA iron-responsive elements (IRE), 30-nucleotide stem-loop structures at the 3' or 5' end of specific transcripts. Transcripts containing an IRE include ferritin L and H subunits (iron storage), transferrin (iron plasma chaperone), transferrin receptor (iron uptake into cells), ferroportin (iron exporter), mAcn, succinate dehydrogenase, erythroid aminolevulinic acid synthetase (tetrapyrrole biosynthesis), among others. If the IRE is in the 5'-UTR of the transcript (e.g. in ferritin mRNA), then IRP1-binding prevents its translation by blocking the transcript from binding to the ribosome. If the IRE is in the 3'-UTR of the transcript (e.g. transferrin receptor), then IRP1-binding protects it from endonuclease degradation, thereby prolonging the half-life of the transcript and enabling it to be translated []. IRP2 is another IRE-binding protein that binds to the same transcripts as IRP1. However, since IRP1 is predominantly in the enzymatic cAcn form, it is IRP2 that acts as the major metabolic regulator that maintains iron homeostasis []. Although IRP2 is homologous to IRP1, IRP2 lacks aconitase activity, and is known only to have a single function in the post-transcriptional regulation of iron metabolism genes []. In iron-replete cells, IRP2 activity is regulated primarily by iron-dependent degradation through the ubiquitin-proteasomal system. Bacterial AcnB is also known to be multi-functional. In addition to its role in the TCA cycle, AcnB was shown to be a post-transcriptional regulator of gene expression in Escherichia coli and Salmonella enterica [, ]. In S. enterica, AcnB initiates a regulatory cascade controlling flagella biosynthesis through an interaction with the ftsH transcript, an alternative RNA polymerase sigma factor. This binding lowers the intracellular concentration of FtsH protease, which in turn enhances the amount of RNA polymerase sigma32 factor (normally degraded by FtsH protease), and sigma32 then increases the synthesis of chaperone DnaK, which in turn promotes the synthesis of the flagellar protein FliC. AcnB regulates the synthesis of other proteins as well, such as superoxide dismutase (SodA) and other enzymes involved in oxidative stress. This entry represents the N-terminal HEAT-like domain, which is present in bacterial aconitase (AcnB), but not in AcnA or eukaryotic cAcn/IRP2 or mAcn. This domain is multi-helical, forming two curved layers in a right-handed alpha-alpha superhelix. HEAT-like domains are usually implicated in protein-protein interactions. The HEAT-like domain and the 'swivel' domain that follows it were shown to be sufficient for dimerisation and for AcnB binding to mRNA. An iron-mediated dimerisation mechanism may be responsible for switching AcnB between its catalytic and regulatory roles, as dimerisation requires iron while mRNA binding is inhibited by iron. More information about these proteins can be found at Protein of the Month: Aconitase [].; GO: 0003994 aconitate hydratase activity, 0006099 tricarboxylic acid cycle; PDB: 1L5J_B.
Probab=41.08 E-value=29 Score=28.75 Aligned_cols=38 Identities=26% Similarity=0.341 Sum_probs=19.9
Q ss_pred CCCCCCCCChhhHhHHhhhhhc--cCchhHHHHHHh-cCCC
Q psy14871 32 PILPSFGFTQEQVACVCEVLQQ--SGNIERLGRFLW-SLPA 69 (238)
Q Consensus 32 ~~~~~~~~~~~q~~~vc~~l~~--~gd~~~l~~f~~-~lp~ 69 (238)
.++|.++++.+|++.+||-|.. .|+-+.|..+|- .+|+
T Consensus 12 ~GipPlPL~a~Qt~~lielLk~~~~~~~~~lldLL~~RV~P 52 (154)
T PF11791_consen 12 LGIPPLPLNAEQTAELIELLKNPPAGEEAFLLDLLTNRVPP 52 (154)
T ss_dssp TT-------HHHHHHHHHHHHS--TT-HHHHHHHHHHSS--
T ss_pred CCCCCCCCCHHHHHHHHHHHhCCCCccHHHHHHHHHhcCCC
Confidence 3789999999999999997776 345555665554 4665
No 50
>COG3413 Predicted DNA binding protein [General function prediction only]
Probab=37.57 E-value=31 Score=29.43 Aligned_cols=40 Identities=25% Similarity=0.434 Sum_probs=34.4
Q ss_pred ccCHHHHHHHHHHHhhC--CCCCHHHHHHHHHHhCCCccccc
Q psy14871 160 CFKEKSRSVLRDWYTHN--PYPSPREKRELAEATGLTTTQVS 199 (238)
Q Consensus 160 ~fs~~q~~~Le~~F~~~--~yPs~~~r~~LA~~lgLs~~qV~ 199 (238)
.+|+.|+.+|+..|... -||-.....+||+.+|+++.-+.
T Consensus 155 ~LTdrQ~~vL~~A~~~GYFd~PR~~~l~dLA~~lGISkst~~ 196 (215)
T COG3413 155 DLTDRQLEVLRLAYKMGYFDYPRRVSLKDLAKELGISKSTLS 196 (215)
T ss_pred cCCHHHHHHHHHHHHcCCCCCCccCCHHHHHHHhCCCHHHHH
Confidence 58999999999999875 45888888999999999997644
No 51
>PRK09646 RNA polymerase sigma factor SigK; Reviewed
Probab=36.99 E-value=42 Score=27.70 Aligned_cols=49 Identities=18% Similarity=0.171 Sum_probs=34.5
Q ss_pred ccCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCccccccccchhhhhhhHHH
Q psy14871 160 CFKEKSRSVLRDWYTHNPYPSPREKRELAEATGLTTTQVSNWFKNRRQRDRAAE 213 (238)
Q Consensus 160 ~fs~~q~~~Le~~F~~~~yPs~~~r~~LA~~lgLs~~qV~~WFqNRR~R~k~~~ 213 (238)
.+++.++.+|...|..+ ..-.++|..+|++...|+++...-|++.|..-
T Consensus 142 ~L~~~~r~vl~l~~~~~-----~s~~EIA~~Lgis~~tVk~~l~ra~~~Lr~~l 190 (194)
T PRK09646 142 ALTDTQRESVTLAYYGG-----LTYREVAERLAVPLGTVKTRMRDGLIRLRDCL 190 (194)
T ss_pred hCCHHHHHHHHHHHHcC-----CCHHHHHHHhCCChHhHHHHHHHHHHHHHHHh
Confidence 45666666665554332 34578999999999999999877776666543
No 52
>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=36.72 E-value=15 Score=25.55 Aligned_cols=41 Identities=20% Similarity=0.293 Sum_probs=25.4
Q ss_pred ccCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCccccccccch
Q psy14871 160 CFKEKSRSVLRDWYTHNPYPSPREKRELAEATGLTTTQVSNWFKN 204 (238)
Q Consensus 160 ~fs~~q~~~Le~~F~~~~yPs~~~r~~LA~~lgLs~~qV~~WFqN 204 (238)
.|+.+....+-..+.. .......+|..+|+++.++.+|-+-
T Consensus 6 ~ys~e~K~~~v~~~~~----~g~sv~~va~~~gi~~~~l~~W~~~ 46 (76)
T PF01527_consen 6 RYSPEFKLQAVREYLE----SGESVSEVAREYGISPSTLYNWRKQ 46 (76)
T ss_dssp ---HHHHHHHHHHHHH----HHCHHHHHHHHHTS-HHHHHHHHHH
T ss_pred CCCHHHHHHHHHHHHH----CCCceEeeecccccccccccHHHHH
Confidence 5666665544444411 2246788999999999999999643
No 53
>PRK12540 RNA polymerase sigma factor; Provisional
Probab=36.68 E-value=78 Score=26.00 Aligned_cols=53 Identities=15% Similarity=0.072 Sum_probs=35.3
Q ss_pred ccCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCccccccccchhhhhhhHHHhhcc
Q psy14871 160 CFKEKSRSVLRDWYTHNPYPSPREKRELAEATGLTTTQVSNWFKNRRQRDRAAEQKDG 217 (238)
Q Consensus 160 ~fs~~q~~~Le~~F~~~~yPs~~~r~~LA~~lgLs~~qV~~WFqNRR~R~k~~~~~~~ 217 (238)
.+++.++.++...|.. ...-.++|..+|++...|++....-|.+.|+......
T Consensus 111 ~Lp~~~R~v~~L~~~~-----g~s~~EIA~~Lgis~~tV~~~l~RAr~~Lr~~l~~~~ 163 (182)
T PRK12540 111 KLPQDQREALILVGAS-----GFSYEDAAAICGCAVGTIKSRVNRARSKLSALLYVDG 163 (182)
T ss_pred hCCHHHHHHhhHHHHc-----CCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHhcc
Confidence 3455555555554422 2245789999999999999998777777666555433
No 54
>PF07035 Mic1: Colon cancer-associated protein Mic1-like; InterPro: IPR009755 This entry represents the C terminus (approximately 160 residues) of a number of proteins that resemble colon cancer-associated protein Mic1.
Probab=36.64 E-value=67 Score=26.84 Aligned_cols=27 Identities=19% Similarity=0.243 Sum_probs=21.4
Q ss_pred hHHhhhhhccCchhHHHHHHhcCCCcc
Q psy14871 45 ACVCEVLQQSGNIERLGRFLWSLPACE 71 (238)
Q Consensus 45 ~~vc~~l~~~gd~~~l~~f~~~lp~~~ 71 (238)
+-|||+|++.|++-.=.+|+++....+
T Consensus 93 ~~iievLL~~g~vl~ALr~ar~~~~~~ 119 (167)
T PF07035_consen 93 EEIIEVLLSKGQVLEALRYARQYHKVD 119 (167)
T ss_pred HHHHHHHHhCCCHHHHHHHHHHcCCcc
Confidence 457888999999999999998765433
No 55
>PRK06759 RNA polymerase factor sigma-70; Validated
Probab=35.92 E-value=38 Score=26.47 Aligned_cols=46 Identities=20% Similarity=0.271 Sum_probs=32.6
Q ss_pred ccCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCccccccccchhhhhhh
Q psy14871 160 CFKEKSRSVLRDWYTHNPYPSPREKRELAEATGLTTTQVSNWFKNRRQRDR 210 (238)
Q Consensus 160 ~fs~~q~~~Le~~F~~~~yPs~~~r~~LA~~lgLs~~qV~~WFqNRR~R~k 210 (238)
.+++.++.++...|..+ ....++|..+|++...|++|...-+.+.|
T Consensus 106 ~L~~~~r~ii~l~~~~~-----~s~~EIA~~l~is~~tV~~~~~ra~~~Lr 151 (154)
T PRK06759 106 VLDEKEKYIIFERFFVG-----KTMGEIALETEMTYYQVRWIYRQALEKMR 151 (154)
T ss_pred hCCHHHHHHHHHHHhcC-----CCHHHHHHHHCCCHHHHHHHHHHHHHHHh
Confidence 45666667666554332 34678999999999999999876555544
No 56
>PF13936 HTH_38: Helix-turn-helix domain; PDB: 2W48_A.
Probab=34.70 E-value=23 Score=22.55 Aligned_cols=39 Identities=21% Similarity=0.281 Sum_probs=21.3
Q ss_pred ccCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCccccccccc
Q psy14871 160 CFKEKSRSVLRDWYTHNPYPSPREKRELAEATGLTTTQVSNWFK 203 (238)
Q Consensus 160 ~fs~~q~~~Le~~F~~~~yPs~~~r~~LA~~lgLs~~qV~~WFq 203 (238)
.++.+++..++.++... ....+||..+|.+...|..+.+
T Consensus 4 ~Lt~~eR~~I~~l~~~G-----~s~~~IA~~lg~s~sTV~relk 42 (44)
T PF13936_consen 4 HLTPEERNQIEALLEQG-----MSIREIAKRLGRSRSTVSRELK 42 (44)
T ss_dssp --------HHHHHHCS--------HHHHHHHTT--HHHHHHHHH
T ss_pred chhhhHHHHHHHHHHcC-----CCHHHHHHHHCcCcHHHHHHHh
Confidence 56777888888887643 3566799999999999988764
No 57
>PRK12526 RNA polymerase sigma factor; Provisional
Probab=34.34 E-value=53 Score=27.52 Aligned_cols=49 Identities=12% Similarity=0.176 Sum_probs=32.9
Q ss_pred ccCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCccccccccchhhhhhhHHH
Q psy14871 160 CFKEKSRSVLRDWYTHNPYPSPREKRELAEATGLTTTQVSNWFKNRRQRDRAAE 213 (238)
Q Consensus 160 ~fs~~q~~~Le~~F~~~~yPs~~~r~~LA~~lgLs~~qV~~WFqNRR~R~k~~~ 213 (238)
.+++.++.++...|.. .....++|..+|++...|+++...-+.+.++..
T Consensus 153 ~L~~~~r~vl~l~~~~-----g~s~~EIA~~lgis~~tV~~~l~Ra~~~Lr~~l 201 (206)
T PRK12526 153 KLPEAQQTVVKGVYFQ-----ELSQEQLAQQLNVPLGTVKSRLRLALAKLKVQM 201 (206)
T ss_pred hCCHHHHHHHHHHHHc-----CCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 3445555555543322 234678999999999999999877666666544
No 58
>PF13518 HTH_28: Helix-turn-helix domain
Probab=34.32 E-value=20 Score=22.85 Aligned_cols=25 Identities=32% Similarity=0.634 Sum_probs=20.3
Q ss_pred HHHHHHHHhCCCccccccccchhhh
Q psy14871 183 EKRELAEATGLTTTQVSNWFKNRRQ 207 (238)
Q Consensus 183 ~r~~LA~~lgLs~~qV~~WFqNRR~ 207 (238)
...++|..+|++..+|..|.+..+.
T Consensus 14 s~~~~a~~~gis~~tv~~w~~~y~~ 38 (52)
T PF13518_consen 14 SVREIAREFGISRSTVYRWIKRYRE 38 (52)
T ss_pred CHHHHHHHHCCCHhHHHHHHHHHHh
Confidence 3456899999999999999865544
No 59
>PF13384 HTH_23: Homeodomain-like domain; PDB: 2X48_C.
Probab=33.28 E-value=18 Score=23.08 Aligned_cols=24 Identities=29% Similarity=0.545 Sum_probs=17.3
Q ss_pred HHHHHHHHHhCCCccccccccchh
Q psy14871 182 REKRELAEATGLTTTQVSNWFKNR 205 (238)
Q Consensus 182 ~~r~~LA~~lgLs~~qV~~WFqNR 205 (238)
....++|..+|++...|..|.+.-
T Consensus 18 ~s~~~ia~~lgvs~~Tv~~w~kr~ 41 (50)
T PF13384_consen 18 WSIREIAKRLGVSRSTVYRWIKRY 41 (50)
T ss_dssp --HHHHHHHHTS-HHHHHHHHT--
T ss_pred CCHHHHHHHHCcCHHHHHHHHHHc
Confidence 356789999999999999997643
No 60
>PRK03975 tfx putative transcriptional regulator; Provisional
Probab=33.06 E-value=60 Score=26.41 Aligned_cols=49 Identities=24% Similarity=0.270 Sum_probs=37.7
Q ss_pred ccCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCccccccccchhhhhhhHHHh
Q psy14871 160 CFKEKSRSVLRDWYTHNPYPSPREKRELAEATGLTTTQVSNWFKNRRQRDRAAEQ 214 (238)
Q Consensus 160 ~fs~~q~~~Le~~F~~~~yPs~~~r~~LA~~lgLs~~qV~~WFqNRR~R~k~~~~ 214 (238)
.+++.++.+|...+ .. ....++|..+|++...|+.|-++.+.+.++...
T Consensus 6 ~Lt~rqreVL~lr~-~G-----lTq~EIAe~LGiS~~tVs~ie~ra~kkLr~~~~ 54 (141)
T PRK03975 6 FLTERQIEVLRLRE-RG-----LTQQEIADILGTSRANVSSIEKRARENIEKARE 54 (141)
T ss_pred CCCHHHHHHHHHHH-cC-----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Confidence 57888899987742 22 235689999999999999999988887776543
No 61
>PRK09642 RNA polymerase sigma factor SigW; Reviewed
Probab=32.80 E-value=60 Score=25.64 Aligned_cols=48 Identities=17% Similarity=0.169 Sum_probs=32.9
Q ss_pred cCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCccccccccchhhhhhhHHH
Q psy14871 161 FKEKSRSVLRDWYTHNPYPSPREKRELAEATGLTTTQVSNWFKNRRQRDRAAE 213 (238)
Q Consensus 161 fs~~q~~~Le~~F~~~~yPs~~~r~~LA~~lgLs~~qV~~WFqNRR~R~k~~~ 213 (238)
+++.++.++...|... ..-.++|..+|++...|++....-|.+.|..-
T Consensus 107 Lp~~~r~v~~l~~~~g-----~s~~EIA~~lgis~~tV~~~l~Rar~~Lr~~l 154 (160)
T PRK09642 107 LPENYRDVVLAHYLEE-----KSYQEIALQEKIEVKTVEMKLYRARKWIKKHW 154 (160)
T ss_pred CCHHHHHHHHHHHHhC-----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 4555555555544322 23568999999999999999887777766554
No 62
>PF13443 HTH_26: Cro/C1-type HTH DNA-binding domain; PDB: 3TYR_A 3TYS_A 3B7H_A.
Probab=32.75 E-value=19 Score=24.11 Aligned_cols=26 Identities=19% Similarity=0.461 Sum_probs=18.2
Q ss_pred HHHHHHHHhCCCccccccccchhhhh
Q psy14871 183 EKRELAEATGLTTTQVSNWFKNRRQR 208 (238)
Q Consensus 183 ~r~~LA~~lgLs~~qV~~WFqNRR~R 208 (238)
....||..+|++...|..|+.++..+
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 45689999999999999999887433
No 63
>PRK09644 RNA polymerase sigma factor SigM; Provisional
Probab=31.96 E-value=60 Score=25.88 Aligned_cols=50 Identities=14% Similarity=0.035 Sum_probs=34.2
Q ss_pred ccCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCccccccccchhhhhhhHHHh
Q psy14871 160 CFKEKSRSVLRDWYTHNPYPSPREKRELAEATGLTTTQVSNWFKNRRQRDRAAEQ 214 (238)
Q Consensus 160 ~fs~~q~~~Le~~F~~~~yPs~~~r~~LA~~lgLs~~qV~~WFqNRR~R~k~~~~ 214 (238)
.+++.++.++...|-. .....++|..+|++...|++|...-|.+.|+.-.
T Consensus 108 ~L~~~~r~v~~l~~~~-----g~s~~eIA~~lgis~~tv~~~l~Rar~~Lr~~l~ 157 (165)
T PRK09644 108 TLPVIEAQAILLCDVH-----ELTYEEAASVLDLKLNTYKSHLFRGRKRLKALLK 157 (165)
T ss_pred hCCHHHHHHHHhHHHh-----cCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Confidence 4455555555544322 2246789999999999999998877777666544
No 64
>PRK00118 putative DNA-binding protein; Validated
Probab=30.82 E-value=74 Score=24.50 Aligned_cols=50 Identities=20% Similarity=0.246 Sum_probs=36.5
Q ss_pred ccCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCccccccccchhhhhhhHHHh
Q psy14871 160 CFKEKSRSVLRDWYTHNPYPSPREKRELAEATGLTTTQVSNWFKNRRQRDRAAEQ 214 (238)
Q Consensus 160 ~fs~~q~~~Le~~F~~~~yPs~~~r~~LA~~lgLs~~qV~~WFqNRR~R~k~~~~ 214 (238)
.+++.++.++..+|... ....++|..+|++...|..|....|.+.+....
T Consensus 17 ~L~ekqRevl~L~y~eg-----~S~~EIAe~lGIS~~TV~r~L~RArkkLr~~~~ 66 (104)
T PRK00118 17 LLTEKQRNYMELYYLDD-----YSLGEIAEEFNVSRQAVYDNIKRTEKLLEDYEE 66 (104)
T ss_pred cCCHHHHHHHHHHHHcC-----CCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHH
Confidence 45666777777666543 245679999999999999999877777665433
No 65
>PRK09652 RNA polymerase sigma factor RpoE; Provisional
Probab=30.25 E-value=58 Score=25.86 Aligned_cols=49 Identities=20% Similarity=0.148 Sum_probs=34.0
Q ss_pred ccCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCccccccccchhhhhhhHHH
Q psy14871 160 CFKEKSRSVLRDWYTHNPYPSPREKRELAEATGLTTTQVSNWFKNRRQRDRAAE 213 (238)
Q Consensus 160 ~fs~~q~~~Le~~F~~~~yPs~~~r~~LA~~lgLs~~qV~~WFqNRR~R~k~~~ 213 (238)
.+++.++.++...|..+ ..-.++|..+|++...|++|...-+.+.++..
T Consensus 128 ~L~~~~r~vl~l~~~~~-----~s~~eIA~~lgis~~tV~~~l~ra~~~Lr~~l 176 (182)
T PRK09652 128 SLPEELRTAITLREIEG-----LSYEEIAEIMGCPIGTVRSRIFRAREALRAKL 176 (182)
T ss_pred hCCHHHHHHHHHHHHcC-----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 45666666666554322 23567899999999999999986666666543
No 66
>PRK10072 putative transcriptional regulator; Provisional
Probab=29.88 E-value=24 Score=26.80 Aligned_cols=24 Identities=21% Similarity=0.455 Sum_probs=21.2
Q ss_pred HHHHHHHhCCCccccccccchhhh
Q psy14871 184 KRELAEATGLTTTQVSNWFKNRRQ 207 (238)
Q Consensus 184 r~~LA~~lgLs~~qV~~WFqNRR~ 207 (238)
..+||..+|++...|+.|...+|.
T Consensus 49 Q~elA~~lGvS~~TVs~WE~G~r~ 72 (96)
T PRK10072 49 IDDFARVLGVSVAMVKEWESRRVK 72 (96)
T ss_pred HHHHHHHhCCCHHHHHHHHcCCCC
Confidence 578999999999999999987764
No 67
>KOG2274|consensus
Probab=29.67 E-value=55 Score=34.40 Aligned_cols=61 Identities=21% Similarity=0.281 Sum_probs=44.2
Q ss_pred hccCchhHHHHHHhcCCCcccCCcchHHHH---HHHHHHhhhccHH------HHHHHHhcCCCCCCChhHHHHH
Q psy14871 52 QQSGNIERLGRFLWSLPACEKLHKNESVLK---AKAMVAFHRGNFK------DLYRILESHQFSPHNHPKLQAL 116 (238)
Q Consensus 52 ~~~gd~~~l~~f~~~lp~~~~~~~~e~vlr---a~a~v~~h~~~f~------e~~~lLe~~~f~~~~h~~lq~l 116 (238)
+--.|.|.+..||.|||.......-|+||+ .|..++ .|+|+ .++.+|+..-+ .++..||+.
T Consensus 778 L~~t~~~~~l~FL~Slp~~~g~~AlefVMteW~srqhl~--~g~ye~kv~i~alc~al~~~~~--~ddkrLq~V 847 (1005)
T KOG2274|consen 778 LVHTDLDQLLNFLSSLPGPTGEPALEFVMTEWTSRQHLY--FGEYEGKVSIKALCKALQHLIS--TDDKRLQKV 847 (1005)
T ss_pred HhhCCHHHHHHHHHhCCCCCCCcHHHHHHHHHHhhhhhh--hhhhhchhhHHHHHHHHHhhhc--cCChhhcee
Confidence 345689999999999999888778899998 566677 57777 55666654432 345666654
No 68
>PRK12512 RNA polymerase sigma factor; Provisional
Probab=28.99 E-value=70 Score=25.94 Aligned_cols=50 Identities=12% Similarity=0.060 Sum_probs=35.1
Q ss_pred ccCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCccccccccchhhhhhhHHHh
Q psy14871 160 CFKEKSRSVLRDWYTHNPYPSPREKRELAEATGLTTTQVSNWFKNRRQRDRAAEQ 214 (238)
Q Consensus 160 ~fs~~q~~~Le~~F~~~~yPs~~~r~~LA~~lgLs~~qV~~WFqNRR~R~k~~~~ 214 (238)
.+++.++.++...|.. ...-.++|..+|++...|++++..-|.+.|....
T Consensus 131 ~L~~~~r~v~~l~~~~-----g~s~~eIA~~l~is~~tV~~~l~ra~~~Lr~~l~ 180 (184)
T PRK12512 131 TLPPRQRDVVQSISVE-----GASIKETAAKLSMSEGAVRVALHRGLAALAAKFR 180 (184)
T ss_pred hCCHHHHHHHHHHHHc-----CCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhh
Confidence 4555556666555433 2345789999999999999999877777765443
No 69
>PF13429 TPR_15: Tetratricopeptide repeat; PDB: 2VQ2_A 2PL2_B.
Probab=28.68 E-value=61 Score=28.15 Aligned_cols=56 Identities=13% Similarity=0.070 Sum_probs=38.4
Q ss_pred HHhhhhhccCchhHHHHHHhcCCCcccCCcchHHHHHHHHHHhhhccHHHHHHHHh
Q psy14871 46 CVCEVLQQSGNIERLGRFLWSLPACEKLHKNESVLKAKAMVAFHRGNFKDLYRILE 101 (238)
Q Consensus 46 ~vc~~l~~~gd~~~l~~f~~~lp~~~~~~~~e~vlra~a~v~~h~~~f~e~~~lLe 101 (238)
..-+...+.|+.+++..+|..+........+..++.+.+.++...|++.+....++
T Consensus 115 ~~l~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~a~~~~~~G~~~~A~~~~~ 170 (280)
T PF13429_consen 115 SALQLYYRLGDYDEAEELLEKLEELPAAPDSARFWLALAEIYEQLGDPDKALRDYR 170 (280)
T ss_dssp ---H-HHHTT-HHHHHHHHHHHHH-T---T-HHHHHHHHHHHHHCCHHHHHHHHHH
T ss_pred HHHHHHHHHhHHHHHHHHHHHHHhccCCCCCHHHHHHHHHHHHHcCCHHHHHHHHH
Confidence 34445677899999999999877555556778889999999988999998877665
No 70
>KOG1146|consensus
Probab=28.09 E-value=22 Score=38.65 Aligned_cols=55 Identities=15% Similarity=0.072 Sum_probs=47.0
Q ss_pred ccccCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCccccccccchhhhhhhHH
Q psy14871 158 SYCFKEKSRSVLRDWYTHNPYPSPREKRELAEATGLTTTQVSNWFKNRRQRDRAA 212 (238)
Q Consensus 158 ~~~fs~~q~~~Le~~F~~~~yPs~~~r~~LA~~lgLs~~qV~~WFqNRR~R~k~~ 212 (238)
+..+...+...|..+|....||.-.+...++..+++..+.+-.||+++++++...
T Consensus 448 s~r~~~~~t~~L~S~~kt~~cpkc~~~yk~a~~L~vhmRskhp~~~~~~c~~gq~ 502 (1406)
T KOG1146|consen 448 SKRSLEGQTVVLHSFFKTLKCPKCNWHYKLAQTLGVHMRSKHPESQSAYCKAGQN 502 (1406)
T ss_pred hhcccccceeeeecccccccCCccchhhhhHHHhhhcccccccccchhHhHhccc
Confidence 3466777788888889889999999999999999999999999999977776543
No 71
>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=28.03 E-value=30 Score=23.70 Aligned_cols=20 Identities=30% Similarity=0.589 Sum_probs=17.5
Q ss_pred HHHHHHHhCCCccccccccc
Q psy14871 184 KRELAEATGLTTTQVSNWFK 203 (238)
Q Consensus 184 r~~LA~~lgLs~~qV~~WFq 203 (238)
..++|..+|++...|..|-+
T Consensus 16 ~~eIA~~Lg~~~~TV~~W~~ 35 (58)
T PF06056_consen 16 IKEIAEELGVPRSTVYSWKD 35 (58)
T ss_pred HHHHHHHHCCChHHHHHHHH
Confidence 56789999999999999953
No 72
>KOG3623|consensus
Probab=27.70 E-value=1.8e+02 Score=30.20 Aligned_cols=49 Identities=18% Similarity=0.204 Sum_probs=36.2
Q ss_pred HHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCccccccccchhhhhhhHH
Q psy14871 164 KSRSVLRDWYTHNPYPSPREKRELAEATGLTTTQVSNWFKNRRQRDRAA 212 (238)
Q Consensus 164 ~q~~~Le~~F~~~~yPs~~~r~~LA~~lgLs~~qV~~WFqNRR~R~k~~ 212 (238)
.+-..|...|..+-.++..+-..++..+...+..|.+||.+|+...+..
T Consensus 636 ~dq~ql~~a~elq~s~~n~~~pl~~t~~~n~~pv~ev~dhsrsstpsp~ 684 (1007)
T KOG3623|consen 636 EDQQQLKQAYELQASPSNDEFPLIATRLQNDPPVVEVWDHSRSSTPSPM 684 (1007)
T ss_pred cchhhhHhhhhcccCccCcccchhhhhccCCCcchhhcccCCCCCCCCC
Confidence 3346677777766666666666666677888889999999999887654
No 73
>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=27.56 E-value=64 Score=24.24 Aligned_cols=46 Identities=28% Similarity=0.367 Sum_probs=31.2
Q ss_pred ccCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCccccccccchhhhhhh
Q psy14871 160 CFKEKSRSVLRDWYTHNPYPSPREKRELAEATGLTTTQVSNWFKNRRQRDR 210 (238)
Q Consensus 160 ~fs~~q~~~Le~~F~~~~yPs~~~r~~LA~~lgLs~~qV~~WFqNRR~R~k 210 (238)
.+++.++.++...|.. .....++|..+|+++..|+.+...-+.+.|
T Consensus 110 ~L~~~~~~ii~~~~~~-----g~s~~eIA~~l~~s~~~v~~~~~~~~~kl~ 155 (158)
T TIGR02937 110 KLPEREREVLVLRYLE-----GLSYKEIAEILGISVGTVKRRLKRARKKLR 155 (158)
T ss_pred hCCHHHHHHHhhHHhc-----CCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Confidence 3455556666544332 224568999999999999999876665554
No 74
>PRK04217 hypothetical protein; Provisional
Probab=27.45 E-value=95 Score=24.14 Aligned_cols=51 Identities=12% Similarity=0.032 Sum_probs=39.1
Q ss_pred cccCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCccccccccchhhhhhhHHHh
Q psy14871 159 YCFKEKSRSVLRDWYTHNPYPSPREKRELAEATGLTTTQVSNWFKNRRQRDRAAEQ 214 (238)
Q Consensus 159 ~~fs~~q~~~Le~~F~~~~yPs~~~r~~LA~~lgLs~~qV~~WFqNRR~R~k~~~~ 214 (238)
-.++.+++.++...|...- ...++|+.+|++...|.+.+..-+.+.+....
T Consensus 41 ~~Lt~eereai~l~~~eGl-----S~~EIAk~LGIS~sTV~r~L~RArkkLre~L~ 91 (110)
T PRK04217 41 IFMTYEEFEALRLVDYEGL-----TQEEAGKRMGVSRGTVWRALTSARKKVAQMLV 91 (110)
T ss_pred ccCCHHHHHHHHHHHHcCC-----CHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHH
Confidence 3678888888877764432 46789999999999999999877777766544
No 75
>PRK12532 RNA polymerase sigma factor; Provisional
Probab=26.77 E-value=92 Score=25.57 Aligned_cols=51 Identities=16% Similarity=0.141 Sum_probs=34.0
Q ss_pred cCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCccccccccchhhhhhhHHHhhc
Q psy14871 161 FKEKSRSVLRDWYTHNPYPSPREKRELAEATGLTTTQVSNWFKNRRQRDRAAEQKD 216 (238)
Q Consensus 161 fs~~q~~~Le~~F~~~~yPs~~~r~~LA~~lgLs~~qV~~WFqNRR~R~k~~~~~~ 216 (238)
+++.++.++.-.|.. ...-.++|..+|++...|++....-|.+.|+.....
T Consensus 137 L~~~~r~i~~L~~~~-----g~s~~EIA~~lgis~~tVk~~l~Rar~~Lr~~l~~~ 187 (195)
T PRK12532 137 LPENTARVFTLKEIL-----GFSSDEIQQMCGISTSNYHTIMHRARESLRQCLQIK 187 (195)
T ss_pred CCHHHHHHhhhHHHh-----CCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHh
Confidence 444445555433322 223578999999999999999887777777665433
No 76
>PRK05602 RNA polymerase sigma factor; Reviewed
Probab=26.57 E-value=93 Score=25.28 Aligned_cols=49 Identities=16% Similarity=0.179 Sum_probs=32.6
Q ss_pred cCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCccccccccchhhhhhhHHHh
Q psy14871 161 FKEKSRSVLRDWYTHNPYPSPREKRELAEATGLTTTQVSNWFKNRRQRDRAAEQ 214 (238)
Q Consensus 161 fs~~q~~~Le~~F~~~~yPs~~~r~~LA~~lgLs~~qV~~WFqNRR~R~k~~~~ 214 (238)
+++.++.++...|.. ...-.++|..+|++...|+++...-|.+.|+...
T Consensus 129 L~~~~r~i~~l~~~~-----g~s~~EIA~~lgis~~tV~~~l~Rar~~Lr~~l~ 177 (186)
T PRK05602 129 LPERQREAIVLQYYQ-----GLSNIEAAAVMDISVDALESLLARGRRALRAQLA 177 (186)
T ss_pred CCHHHHHHhhHHHhc-----CCCHHHHHHHhCcCHHHHHHHHHHHHHHHHHHHH
Confidence 455555555443322 2235688999999999999998777766666544
No 77
>PF13432 TPR_16: Tetratricopeptide repeat; PDB: 3CVP_A 3CVL_A 3CVQ_A 3CV0_A 2GW1_B 3CVN_A 3QKY_A 2PL2_B.
Probab=26.47 E-value=1.3e+02 Score=19.64 Aligned_cols=50 Identities=12% Similarity=0.161 Sum_probs=29.7
Q ss_pred hhhccCchhHHHHHHhcCCCcccCCcchHHHHHHHHHHhhhccHHHHHHHHh
Q psy14871 50 VLQQSGNIERLGRFLWSLPACEKLHKNESVLKAKAMVAFHRGNFKDLYRILE 101 (238)
Q Consensus 50 ~l~~~gd~~~l~~f~~~lp~~~~~~~~e~vlra~a~v~~h~~~f~e~~~lLe 101 (238)
.+++.||++.=...+..+-... ..+..+....+.+++.+|++.+....++
T Consensus 6 ~~~~~g~~~~A~~~~~~~l~~~--P~~~~a~~~lg~~~~~~g~~~~A~~~~~ 55 (65)
T PF13432_consen 6 ALYQQGDYDEAIAAFEQALKQD--PDNPEAWYLLGRILYQQGRYDEALAYYE 55 (65)
T ss_dssp HHHHCTHHHHHHHHHHHHHCCS--TTHHHHHHHHHHHHHHTT-HHHHHHHHH
T ss_pred HHHHcCCHHHHHHHHHHHHHHC--CCCHHHHHHHHHHHHHcCCHHHHHHHHH
Confidence 4567777666555444332211 2356677777777788888887755543
No 78
>PRK12514 RNA polymerase sigma factor; Provisional
Probab=26.26 E-value=86 Score=25.26 Aligned_cols=30 Identities=20% Similarity=0.398 Sum_probs=24.0
Q ss_pred HHHHHHHHhCCCccccccccchhhhhhhHH
Q psy14871 183 EKRELAEATGLTTTQVSNWFKNRRQRDRAA 212 (238)
Q Consensus 183 ~r~~LA~~lgLs~~qV~~WFqNRR~R~k~~ 212 (238)
..+++|..+|++...|+++...-|.+.|+.
T Consensus 147 s~~eIA~~lgis~~tV~~~l~Rar~~Lr~~ 176 (179)
T PRK12514 147 SYKELAERHDVPLNTMRTWLRRSLLKLREC 176 (179)
T ss_pred CHHHHHHHHCCChHHHHHHHHHHHHHHHHH
Confidence 367899999999999999887666666543
No 79
>TIGR02989 Sig-70_gvs1 RNA polymerase sigma-70 factor, Rhodopirellula/Verrucomicrobium family. This group of sigma factors are members of the sigma-70 family (TIGR02937) and are abundantly found in the species Rhodopirellula baltica (11), and Verrucomicrobium spinosum (16) and to a lesser extent in Gemmata obscuriglobus (2).
Probab=26.17 E-value=71 Score=25.01 Aligned_cols=46 Identities=28% Similarity=0.274 Sum_probs=31.3
Q ss_pred ccCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCccccccccchhhhhhh
Q psy14871 160 CFKEKSRSVLRDWYTHNPYPSPREKRELAEATGLTTTQVSNWFKNRRQRDR 210 (238)
Q Consensus 160 ~fs~~q~~~Le~~F~~~~yPs~~~r~~LA~~lgLs~~qV~~WFqNRR~R~k 210 (238)
.+++.++.++...|.. .....++|..+|++...|.++...-|.+.+
T Consensus 111 ~L~~~~r~v~~l~~~~-----g~~~~eIA~~l~is~~tv~~~l~Rar~~Lr 156 (159)
T TIGR02989 111 KLPERQRELLQLRYQR-----GVSLTALAEQLGRTVNAVYKALSRLRVRLR 156 (159)
T ss_pred HCCHHHHHHHHHHHhc-----CCCHHHHHHHhCCCHHHHHHHHHHHHHHHH
Confidence 4666667777664432 234678999999999999988655444433
No 80
>PRK12515 RNA polymerase sigma factor; Provisional
Probab=26.05 E-value=91 Score=25.47 Aligned_cols=50 Identities=16% Similarity=0.246 Sum_probs=34.3
Q ss_pred ccCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCccccccccchhhhhhhHHHh
Q psy14871 160 CFKEKSRSVLRDWYTHNPYPSPREKRELAEATGLTTTQVSNWFKNRRQRDRAAEQ 214 (238)
Q Consensus 160 ~fs~~q~~~Le~~F~~~~yPs~~~r~~LA~~lgLs~~qV~~WFqNRR~R~k~~~~ 214 (238)
.+++.++.+|...|... ..-.++|..+|++...|++-...-|.+.+....
T Consensus 131 ~L~~~~r~vl~l~~~~~-----~s~~eIA~~lgis~~tV~~~l~Rar~~Lr~~l~ 180 (189)
T PRK12515 131 KLSPAHREIIDLVYYHE-----KSVEEVGEIVGIPESTVKTRMFYARKKLAELLK 180 (189)
T ss_pred hCCHHHHHHHHHHHHcC-----CCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHH
Confidence 45555666665544322 245678999999999999988777777666543
No 81
>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=25.78 E-value=29 Score=21.71 Aligned_cols=21 Identities=24% Similarity=0.338 Sum_probs=17.6
Q ss_pred HHHHHHHhCCCccccccccch
Q psy14871 184 KRELAEATGLTTTQVSNWFKN 204 (238)
Q Consensus 184 r~~LA~~lgLs~~qV~~WFqN 204 (238)
..++|+.+|++...|+.|.++
T Consensus 3 ~~e~a~~~gv~~~tlr~~~~~ 23 (49)
T cd04761 3 IGELAKLTGVSPSTLRYYERI 23 (49)
T ss_pred HHHHHHHHCcCHHHHHHHHHC
Confidence 357899999999999999643
No 82
>smart00421 HTH_LUXR helix_turn_helix, Lux Regulon. lux regulon (activates the bioluminescence operon
Probab=25.60 E-value=75 Score=19.83 Aligned_cols=40 Identities=25% Similarity=0.357 Sum_probs=27.8
Q ss_pred cCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCccccccccchhh
Q psy14871 161 FKEKSRSVLRDWYTHNPYPSPREKRELAEATGLTTTQVSNWFKNRR 206 (238)
Q Consensus 161 fs~~q~~~Le~~F~~~~yPs~~~r~~LA~~lgLs~~qV~~WFqNRR 206 (238)
+++.++.++..++. .+ ...++|..+|++...|..|...-+
T Consensus 4 l~~~e~~i~~~~~~--g~----s~~eia~~l~is~~tv~~~~~~~~ 43 (58)
T smart00421 4 LTPREREVLRLLAE--GL----TNKEIAERLGISEKTVKTHLSNIM 43 (58)
T ss_pred CCHHHHHHHHHHHc--CC----CHHHHHHHHCCCHHHHHHHHHHHH
Confidence 56666777755432 22 457889999999999998876433
No 83
>PRK11924 RNA polymerase sigma factor; Provisional
Probab=25.37 E-value=90 Score=24.65 Aligned_cols=31 Identities=29% Similarity=0.338 Sum_probs=25.2
Q ss_pred HHHHHHHHhCCCccccccccchhhhhhhHHH
Q psy14871 183 EKRELAEATGLTTTQVSNWFKNRRQRDRAAE 213 (238)
Q Consensus 183 ~r~~LA~~lgLs~~qV~~WFqNRR~R~k~~~ 213 (238)
.-.++|..+|++...|.+|...-|.+.|+.-
T Consensus 143 ~~~eIA~~lgis~~tv~~~~~ra~~~lr~~l 173 (179)
T PRK11924 143 SYREIAEILGVPVGTVKSRLRRARQLLRECL 173 (179)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 4578999999999999999987777766543
No 84
>PF00196 GerE: Bacterial regulatory proteins, luxR family; InterPro: IPR000792 This domain is a DNA-binding, helix-turn-helix (HTH) domain of about 65 amino acids, present in transcription regulators of the LuxR/FixJ family of response regulators. The domain is named after Vibrio fischeri luxR, a transcriptional activator for quorum-sensing control of luminescence. LuxR-type HTH domain proteins occur in a variety of organisms. The DNA-binding HTH domain is usually located in the C-terminal region; the N-terminal region often containing an autoinducer-binding domain or a response regulatory domain. Most luxR-type regulators act as transcription activators, but some can be repressors or have a dual role for different sites. LuxR-type HTH regulators control a wide variety of activities in various biological processes. The luxR-type, DNA-binding HTH domain forms a four-helical bundle structure. The HTH motif comprises the second and third helices, known as the scaffold and recognition helix, respectively. The HTH binds DNA in the major groove, where the N-terminal part of the recognition helix makes most of the DNA contacts. The fourth helix is involved in dimerisation of gerE and traR. Signalling events by one of the four activation mechanisms described below lead to multimerisation of the regulator. The regulators bind DNA as multimers [, , ]. LuxR-type HTH proteins can be activated by one of four different mechanisms: 1) Regulators which belong to a two-component sensory transduction system where the protein is activated by its phosphorylation, generally on an aspartate residue, by a transmembrane kinase [, ]. Some proteins that belong to this category are: Rhizobiaceae fixJ (global regulator inducing expression of nitrogen-fixation genes in microaerobiosis) Escherichia coli and Salmonella typhimurium uhpA (activates hexose phosphate transport gene uhpT) E. coli narL and narP (activate nitrate reductase operon) Enterobacteria rcsB (regulation of exopolysaccharide biosynthesis in enteric and plant pathogenesis) Bordetella pertussis bvgA (virulence factor) Bacillus subtilis coma (involved in expression of late-expressing competence genes) 2) Regulators which are activated, or in very rare cases repressed, when bound to N-acyl homoserine lactones, which are used as quorum sensing molecules in a variety of Gram-negative bacteria []: V. fischeri luxR (activates bioluminescence operon) Agrobacterium tumefaciens traR (regulation of Ti plasmid transfer) Erwinia carotovora carR (control of carbapenem antibiotics biosynthesis) E. carotovora expR (virulence factor for soft rot disease; activates plant tissue macerating enzyme genes) Pseudomonas aeruginosa lasR (activates elastase gene lasB) Erwinia chrysanthemi echR and Erwinia stewartii esaR Pseudomonas chlororaphis phzR (positive regulator of phenazine antibiotic production) Pseudomonas aeruginosa rhlR (activates rhlAB operon and lasB gene) 3) Autonomous effector domain regulators, without a regulatory domain, represented by gerE []. B. subtilis gerE (transcription activator and repressor for the regulation of spore formation) 4) Multiple ligand-binding regulators, exemplified by malT []. E. coli malT (activates maltose operon; MalT binds ATP and maltotriose); GO: 0003700 sequence-specific DNA binding transcription factor activity, 0043565 sequence-specific DNA binding, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 3SZT_A 3CLO_A 1H0M_A 1L3L_A 3C57_B 1ZLK_B 1ZLJ_H 3C3W_B 1RNL_A 1ZG1_A ....
Probab=25.34 E-value=66 Score=21.26 Aligned_cols=45 Identities=20% Similarity=0.243 Sum_probs=33.2
Q ss_pred ccCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCccccccccchhhhhhh
Q psy14871 160 CFKEKSRSVLRDWYTHNPYPSPREKRELAEATGLTTTQVSNWFKNRRQRDR 210 (238)
Q Consensus 160 ~fs~~q~~~Le~~F~~~~yPs~~~r~~LA~~lgLs~~qV~~WFqNRR~R~k 210 (238)
.||+.+..+|.-...-. ...++|..+|+++..|..+..+=+.|..
T Consensus 3 ~LT~~E~~vl~~l~~G~------~~~eIA~~l~is~~tV~~~~~~i~~Kl~ 47 (58)
T PF00196_consen 3 SLTERELEVLRLLAQGM------SNKEIAEELGISEKTVKSHRRRIMKKLG 47 (58)
T ss_dssp SS-HHHHHHHHHHHTTS-------HHHHHHHHTSHHHHHHHHHHHHHHHHT
T ss_pred ccCHHHHHHHHHHHhcC------CcchhHHhcCcchhhHHHHHHHHHHHhC
Confidence 57788888887665432 3678899999999999998877666643
No 85
>PRK09648 RNA polymerase sigma factor SigD; Reviewed
Probab=25.23 E-value=83 Score=25.64 Aligned_cols=47 Identities=30% Similarity=0.174 Sum_probs=32.5
Q ss_pred ccCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCccccccccchhhhhhhH
Q psy14871 160 CFKEKSRSVLRDWYTHNPYPSPREKRELAEATGLTTTQVSNWFKNRRQRDRA 211 (238)
Q Consensus 160 ~fs~~q~~~Le~~F~~~~yPs~~~r~~LA~~lgLs~~qV~~WFqNRR~R~k~ 211 (238)
.+++.++.++...|..+ ....++|..+|++...|+++...-|.+.|+
T Consensus 139 ~L~~~~r~i~~l~~~~g-----~s~~EIA~~lgis~~tV~~~l~Ra~~~Lr~ 185 (189)
T PRK09648 139 TLPEKQREILILRVVVG-----LSAEETAEAVGSTPGAVRVAQHRALARLRA 185 (189)
T ss_pred hCCHHHHHHHHHHHHcC-----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 45566666666544332 346789999999999999988665555554
No 86
>TIGR02948 SigW_bacill RNA polymerase sigma-W factor. This sigma factor is restricted to certain lineages of the order Bacillales.
Probab=25.06 E-value=72 Score=25.70 Aligned_cols=48 Identities=21% Similarity=0.193 Sum_probs=31.7
Q ss_pred ccCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCccccccccchhhhhhhHH
Q psy14871 160 CFKEKSRSVLRDWYTHNPYPSPREKRELAEATGLTTTQVSNWFKNRRQRDRAA 212 (238)
Q Consensus 160 ~fs~~q~~~Le~~F~~~~yPs~~~r~~LA~~lgLs~~qV~~WFqNRR~R~k~~ 212 (238)
.+++.++.++...| -....-.++|..+|++...|++++..-|.+.+..
T Consensus 136 ~L~~~~r~v~~l~~-----~~g~s~~eIA~~lgis~~~v~~~l~Rar~~Lr~~ 183 (187)
T TIGR02948 136 ALPPKYRMVIVLKY-----MEDLSLKEISEILDLPVGTVKTRIHRGREALRKQ 183 (187)
T ss_pred hCCHHHhHHhhhHH-----hcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 34444444444432 2234467899999999999999987666666543
No 87
>TIGR02999 Sig-70_X6 RNA polymerase sigma factor, TIGR02999 family. This group of sigma factors are members of the sigma-70 family (TIGR02937) and are found in a variety of species including Rhodopirellula baltica which encodes a paralogous group of five.
Probab=24.98 E-value=87 Score=25.25 Aligned_cols=46 Identities=15% Similarity=0.150 Sum_probs=32.1
Q ss_pred cCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCccccccccchhhhhhhH
Q psy14871 161 FKEKSRSVLRDWYTHNPYPSPREKRELAEATGLTTTQVSNWFKNRRQRDRA 211 (238)
Q Consensus 161 fs~~q~~~Le~~F~~~~yPs~~~r~~LA~~lgLs~~qV~~WFqNRR~R~k~ 211 (238)
+++.++.++.-.|..+ ..-.++|..+|+++..|++....-|.+.|+
T Consensus 135 Lp~~~r~v~~l~~~~g-----~s~~EIA~~lgis~~tVk~~l~Rar~~Lr~ 180 (183)
T TIGR02999 135 VDPRQAEVVELRFFAG-----LTVEEIAELLGVSVRTVERDWRFARAWLAD 180 (183)
T ss_pred CCHHHHHHHHHHHHcC-----CCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Confidence 5566666665554332 235688999999999999988766666554
No 88
>PRK12530 RNA polymerase sigma factor; Provisional
Probab=24.73 E-value=93 Score=25.60 Aligned_cols=49 Identities=8% Similarity=0.062 Sum_probs=34.0
Q ss_pred ccCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCccccccccchhhhhhhHHH
Q psy14871 160 CFKEKSRSVLRDWYTHNPYPSPREKRELAEATGLTTTQVSNWFKNRRQRDRAAE 213 (238)
Q Consensus 160 ~fs~~q~~~Le~~F~~~~yPs~~~r~~LA~~lgLs~~qV~~WFqNRR~R~k~~~ 213 (238)
.+++.++.++.-.|... ..-.++|..+|+++..|+++...-|.+.|...
T Consensus 134 ~Lp~~~R~v~~L~~~~g-----~s~~EIA~~lgis~~tVk~~l~RAr~~Lr~~l 182 (189)
T PRK12530 134 HLPAQQARVFMMREYLE-----LSSEQICQECDISTSNLHVLLYRARLQLQACL 182 (189)
T ss_pred hCCHHHHHHHhHHHHcC-----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 34555566655554332 23578999999999999999877776666544
No 89
>PRK09639 RNA polymerase sigma factor SigX; Provisional
Probab=24.66 E-value=1e+02 Score=24.33 Aligned_cols=49 Identities=22% Similarity=0.310 Sum_probs=34.5
Q ss_pred ccCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCccccccccchhhhhhhHHHh
Q psy14871 160 CFKEKSRSVLRDWYTHNPYPSPREKRELAEATGLTTTQVSNWFKNRRQRDRAAEQ 214 (238)
Q Consensus 160 ~fs~~q~~~Le~~F~~~~yPs~~~r~~LA~~lgLs~~qV~~WFqNRR~R~k~~~~ 214 (238)
.+++.++.+|.-.| . ...-.++|..+|++...|+++...-|.+.|....
T Consensus 112 ~L~~~~r~il~l~~-~-----g~s~~eIA~~lgis~~tV~~~i~ra~~~Lr~~l~ 160 (166)
T PRK09639 112 KMTERDRTVLLLRF-S-----GYSYKEIAEALGIKESSVGTTLARAKKKFRKIYE 160 (166)
T ss_pred cCCHHHHHHHHHHH-c-----CCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Confidence 35555566665555 2 2345688999999999999999777777666543
No 90
>PRK12524 RNA polymerase sigma factor; Provisional
Probab=24.55 E-value=1.3e+02 Score=24.73 Aligned_cols=50 Identities=14% Similarity=0.070 Sum_probs=33.5
Q ss_pred cCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCccccccccchhhhhhhHHHhh
Q psy14871 161 FKEKSRSVLRDWYTHNPYPSPREKRELAEATGLTTTQVSNWFKNRRQRDRAAEQK 215 (238)
Q Consensus 161 fs~~q~~~Le~~F~~~~yPs~~~r~~LA~~lgLs~~qV~~WFqNRR~R~k~~~~~ 215 (238)
+++.++.++.-.|.. ...-.++|..+|++...|+++..--|.+.|+....
T Consensus 137 L~~~~r~i~~L~~~~-----g~s~~eIA~~lgis~~tV~~~l~Ra~~~Lr~~l~~ 186 (196)
T PRK12524 137 LPERQRQAVVLRHIE-----GLSNPEIAEVMEIGVEAVESLTARGKRALAALLAG 186 (196)
T ss_pred CCHHHHHHHHHHHHc-----CCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHh
Confidence 445555454443322 22356889999999999999998777777765443
No 91
>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=24.47 E-value=66 Score=26.01 Aligned_cols=35 Identities=9% Similarity=-0.052 Sum_probs=26.1
Q ss_pred CCCHHHHHHHHHHhCCCccccccccchhhhhhhHH
Q psy14871 178 YPSPREKRELAEATGLTTTQVSNWFKNRRQRDRAA 212 (238)
Q Consensus 178 yPs~~~r~~LA~~lgLs~~qV~~WFqNRR~R~k~~ 212 (238)
|.....-.++|..+|++...|+++...-|.+.|..
T Consensus 151 ~~~~~s~~EIA~~lgis~~tv~~~l~rar~~Lr~~ 185 (190)
T TIGR02939 151 ELEGLSYEDIARIMDCPVGTVRSRIFRAREAIAIR 185 (190)
T ss_pred hhcCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence 33344567899999999999999987666665544
No 92
>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=24.39 E-value=86 Score=24.24 Aligned_cols=45 Identities=18% Similarity=0.226 Sum_probs=29.7
Q ss_pred cCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCccccccccchhhhhhh
Q psy14871 161 FKEKSRSVLRDWYTHNPYPSPREKRELAEATGLTTTQVSNWFKNRRQRDR 210 (238)
Q Consensus 161 fs~~q~~~Le~~F~~~~yPs~~~r~~LA~~lgLs~~qV~~WFqNRR~R~k 210 (238)
+++.++.++...|.. . ....++|..+|++...|+++...-+.+.|
T Consensus 114 L~~~~r~il~l~~~~-~----~~~~eIA~~lgis~~tv~~~~~ra~~~Lr 158 (161)
T TIGR02985 114 LPEQCRKIFILSRFE-G----KSYKEIAEELGISVKTVEYHISKALKELR 158 (161)
T ss_pred CCHHHHHHHHHHHHc-C----CCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Confidence 455556666654432 2 23567899999999999988765555544
No 93
>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=24.37 E-value=24 Score=22.56 Aligned_cols=21 Identities=24% Similarity=0.479 Sum_probs=19.1
Q ss_pred HHHHHhCCCccccccccchhh
Q psy14871 186 ELAEATGLTTTQVSNWFKNRR 206 (238)
Q Consensus 186 ~LA~~lgLs~~qV~~WFqNRR 206 (238)
+||..+|++...|..|+.++.
T Consensus 2 ~lA~~~gvs~~tvs~~l~g~~ 22 (52)
T cd01392 2 DIARAAGVSVATVSRVLNGKP 22 (52)
T ss_pred cHHHHHCcCHHHHHHHHcCCC
Confidence 589999999999999999884
No 94
>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=23.84 E-value=33 Score=22.12 Aligned_cols=23 Identities=30% Similarity=0.534 Sum_probs=19.2
Q ss_pred HHHHHHHhCCCccccccccchhh
Q psy14871 184 KRELAEATGLTTTQVSNWFKNRR 206 (238)
Q Consensus 184 r~~LA~~lgLs~~qV~~WFqNRR 206 (238)
..+||..+|++...|..|..+.+
T Consensus 12 ~~~la~~~gis~~~i~~~~~g~~ 34 (55)
T PF01381_consen 12 QKELAEKLGISRSTISRIENGKR 34 (55)
T ss_dssp HHHHHHHHTS-HHHHHHHHTTSS
T ss_pred HHHHHHHhCCCcchhHHHhcCCC
Confidence 46899999999999999998854
No 95
>PRK12519 RNA polymerase sigma factor; Provisional
Probab=23.77 E-value=73 Score=26.07 Aligned_cols=31 Identities=16% Similarity=0.159 Sum_probs=25.4
Q ss_pred HHHHHHHHHhCCCccccccccchhhhhhhHH
Q psy14871 182 REKRELAEATGLTTTQVSNWFKNRRQRDRAA 212 (238)
Q Consensus 182 ~~r~~LA~~lgLs~~qV~~WFqNRR~R~k~~ 212 (238)
....++|..+|++...|++|+..-|.+.|+.
T Consensus 158 ~s~~EIA~~lgis~~tV~~~l~Ra~~~Lr~~ 188 (194)
T PRK12519 158 LSQSEIAKRLGIPLGTVKARARQGLLKLREL 188 (194)
T ss_pred CCHHHHHHHhCCCHHHHHHHHHHHHHHHHHH
Confidence 4567899999999999999997777766654
No 96
>PRK12516 RNA polymerase sigma factor; Provisional
Probab=23.19 E-value=1.3e+02 Score=24.84 Aligned_cols=52 Identities=17% Similarity=0.113 Sum_probs=35.3
Q ss_pred ccCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCccccccccchhhhhhhHHHhhc
Q psy14871 160 CFKEKSRSVLRDWYTHNPYPSPREKRELAEATGLTTTQVSNWFKNRRQRDRAAEQKD 216 (238)
Q Consensus 160 ~fs~~q~~~Le~~F~~~~yPs~~~r~~LA~~lgLs~~qV~~WFqNRR~R~k~~~~~~ 216 (238)
.+++.++.++.-.|... ..-.++|..+|++...|+++...-|.+.++.....
T Consensus 116 ~Lp~~~r~i~~L~~~~g-----~s~~EIA~~Lgis~~tVk~~l~Rar~~Lr~~l~~~ 167 (187)
T PRK12516 116 QLPDDQREAIILVGASG-----FAYEEAAEICGCAVGTIKSRVNRARQRLQEILQIE 167 (187)
T ss_pred hCCHHHHHHHHHHHHcC-----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHhh
Confidence 34555555555443221 23568899999999999999988887777765543
No 97
>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=22.94 E-value=95 Score=25.01 Aligned_cols=50 Identities=16% Similarity=0.208 Sum_probs=35.8
Q ss_pred ccCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCccccccccchhhhhhhHHHh
Q psy14871 160 CFKEKSRSVLRDWYTHNPYPSPREKRELAEATGLTTTQVSNWFKNRRQRDRAAEQ 214 (238)
Q Consensus 160 ~fs~~q~~~Le~~F~~~~yPs~~~r~~LA~~lgLs~~qV~~WFqNRR~R~k~~~~ 214 (238)
.+++.++.+|.-.|..+ ....++|..+|++...|+++...-|.+.+....
T Consensus 100 ~L~~~~r~v~~l~~~~g-----~s~~eIA~~lgis~~tV~~~l~Rar~~Lr~~l~ 149 (170)
T TIGR02959 100 ELPDEYREAIRLTELEG-----LSQQEIAEKLGLSLSGAKSRVQRGRKKLKELLE 149 (170)
T ss_pred hCCHHHHHHHHHHHHcC-----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Confidence 45666666666654332 246789999999999999998777777666544
No 98
>PRK09047 RNA polymerase factor sigma-70; Validated
Probab=22.59 E-value=1.2e+02 Score=23.68 Aligned_cols=49 Identities=16% Similarity=0.108 Sum_probs=33.8
Q ss_pred ccCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCccccccccchhhhhhhHHH
Q psy14871 160 CFKEKSRSVLRDWYTHNPYPSPREKRELAEATGLTTTQVSNWFKNRRQRDRAAE 213 (238)
Q Consensus 160 ~fs~~q~~~Le~~F~~~~yPs~~~r~~LA~~lgLs~~qV~~WFqNRR~R~k~~~ 213 (238)
.+++.++.++.-.|... ..-.++|..+|++...|++....-|.+.|..-
T Consensus 106 ~Lp~~~r~v~~l~~~~g-----~s~~EIA~~lgis~~tV~~~l~ra~~~Lr~~l 154 (161)
T PRK09047 106 KLPARQREAFLLRYWED-----MDVAETAAAMGCSEGSVKTHCSRATHALAKAL 154 (161)
T ss_pred hCCHHHHHHHHHHHHhc-----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 45556666666654332 23578999999999999998876666666543
No 99
>PF13411 MerR_1: MerR HTH family regulatory protein; PDB: 2JML_A 3GP4_A 3GPV_B.
Probab=22.29 E-value=41 Score=22.78 Aligned_cols=19 Identities=16% Similarity=0.335 Sum_probs=16.6
Q ss_pred HHHHHHHhCCCcccccccc
Q psy14871 184 KRELAEATGLTTTQVSNWF 202 (238)
Q Consensus 184 r~~LA~~lgLs~~qV~~WF 202 (238)
..++|+.+|++...|+.|=
T Consensus 3 i~eva~~~gvs~~tlr~y~ 21 (69)
T PF13411_consen 3 IKEVAKLLGVSPSTLRYYE 21 (69)
T ss_dssp HHHHHHHTTTTHHHHHHHH
T ss_pred HHHHHHHHCcCHHHHHHHH
Confidence 3578999999999999993
No 100
>TIGR02508 type_III_yscG type III secretion protein, YscG family. YscG is a molecular chaperone for YscE, where both are part of the type III secretion system that in Yersinia is designated Ysc (Yersinia secretion). The secretion system delivers effector proteins, designate Yops (Yersinia outer proteins) in Yersinia. This family consists of YscG of Yersinia, and functionally equivalent type III secretion machinery protein in other species: AscG in Aeromonas, LscG in Photorhabdus luminescens, etc.
Probab=22.24 E-value=2.3e+02 Score=22.16 Aligned_cols=45 Identities=13% Similarity=0.276 Sum_probs=33.2
Q ss_pred hhHhHHhhhhhccCchhHHHHHHhcCCCcccCCcchHHHHHHHHHHhhhccHHHHHHHHhcCC
Q psy14871 42 EQVACVCEVLQQSGNIERLGRFLWSLPACEKLHKNESVLKAKAMVAFHRGNFKDLYRILESHQ 104 (238)
Q Consensus 42 ~q~~~vc~~l~~~gd~~~l~~f~~~lp~~~~~~~~e~vlra~a~v~~h~~~f~e~~~lLe~~~ 104 (238)
++-.||-+.|...|+. .|.|.--|..-.+.+|+|.++..+++...
T Consensus 22 qEA~tIAdwL~~~~~~------------------~E~v~lIRlsSLmNrG~Yq~Al~l~~~~~ 66 (115)
T TIGR02508 22 QEANTIADWLHLKGES------------------EEAVQLIRLSSLMNRGDYQSALQLGNKLC 66 (115)
T ss_pred HHHHHHHHHHhcCCch------------------HHHHHHHHHHHHHccchHHHHHHhcCCCC
Confidence 3455666666666541 27777778888888999999999998773
No 101
>PRK12541 RNA polymerase sigma factor; Provisional
Probab=22.02 E-value=86 Score=24.77 Aligned_cols=47 Identities=23% Similarity=0.227 Sum_probs=31.4
Q ss_pred ccCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCccccccccchhhhhhhH
Q psy14871 160 CFKEKSRSVLRDWYTHNPYPSPREKRELAEATGLTTTQVSNWFKNRRQRDRA 211 (238)
Q Consensus 160 ~fs~~q~~~Le~~F~~~~yPs~~~r~~LA~~lgLs~~qV~~WFqNRR~R~k~ 211 (238)
.+++.++.++.-.|..+ ..-.++|..+|++...|+.+...-|.+.++
T Consensus 112 ~L~~~~r~v~~l~~~~~-----~s~~eIA~~lgis~~tv~~~l~Rar~~L~~ 158 (161)
T PRK12541 112 SLPLERRNVLLLRDYYG-----FSYKEIAEMTGLSLAKVKIELHRGRKETKS 158 (161)
T ss_pred HCCHHHHHHhhhHHhcC-----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Confidence 35566666665544322 235688999999999999987665555543
No 102
>PRK12536 RNA polymerase sigma factor; Provisional
Probab=21.79 E-value=1.1e+02 Score=24.77 Aligned_cols=30 Identities=23% Similarity=0.149 Sum_probs=24.6
Q ss_pred HHHHHHHHhCCCccccccccchhhhhhhHH
Q psy14871 183 EKRELAEATGLTTTQVSNWFKNRRQRDRAA 212 (238)
Q Consensus 183 ~r~~LA~~lgLs~~qV~~WFqNRR~R~k~~ 212 (238)
...++|..+|++...|++....-|.+.|..
T Consensus 147 s~~EIA~~l~is~~tV~~~l~rar~~Lr~~ 176 (181)
T PRK12536 147 SVAETAQLTGLSESAVKVGIHRGLKALAAK 176 (181)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 467899999999999999987777766653
No 103
>KOG3755|consensus
Probab=21.63 E-value=41 Score=33.80 Aligned_cols=46 Identities=22% Similarity=0.354 Sum_probs=30.6
Q ss_pred HHHHhhCCCCCHHHHHHHHHHhC-------CCccccccccchhhhhhhHHHhh
Q psy14871 170 RDWYTHNPYPSPREKRELAEATG-------LTTTQVSNWFKNRRQRDRAAEQK 215 (238)
Q Consensus 170 e~~F~~~~yPs~~~r~~LA~~lg-------Ls~~qV~~WFqNRR~R~k~~~~~ 215 (238)
+.||..+..++.....+--+... ....-|+-||+|||.++++.+..
T Consensus 708 ~~w~~k~~s~s~~~v~eYkee~~~~~~~e~~~~kn~~~~fk~~~ee~~~~k~~ 760 (769)
T KOG3755|consen 708 HHWKLKTRSGSWVDVAEYKEEELLMPYEEKFESKNVQFWFKVRREEEKRLKMS 760 (769)
T ss_pred hhheecccCchhHHHHHhhHHhhcchhhhhhhhcchHHHHHHHHHHHhhhhcc
Confidence 44555566666655544443333 34457899999999999987764
No 104
>PRK09413 IS2 repressor TnpA; Reviewed
Probab=21.23 E-value=1.2e+02 Score=23.43 Aligned_cols=22 Identities=23% Similarity=0.365 Sum_probs=18.1
Q ss_pred HHHHHHHHhCCCccccccccch
Q psy14871 183 EKRELAEATGLTTTQVSNWFKN 204 (238)
Q Consensus 183 ~r~~LA~~lgLs~~qV~~WFqN 204 (238)
....+|..+|++..+|.+|.+-
T Consensus 31 sv~evA~e~gIs~~tl~~W~r~ 52 (121)
T PRK09413 31 TVSLVARQHGVAASQLFLWRKQ 52 (121)
T ss_pred CHHHHHHHHCcCHHHHHHHHHH
Confidence 3557899999999999999543
No 105
>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=21.15 E-value=40 Score=21.51 Aligned_cols=23 Identities=13% Similarity=0.247 Sum_probs=20.0
Q ss_pred HHHHHHHhCCCccccccccchhh
Q psy14871 184 KRELAEATGLTTTQVSNWFKNRR 206 (238)
Q Consensus 184 r~~LA~~lgLs~~qV~~WFqNRR 206 (238)
..+||..+|++...|..|..+++
T Consensus 18 q~~lA~~~gvs~~~vs~~e~g~~ 40 (58)
T TIGR03070 18 QADLADLAGVGLRFIRDVENGKP 40 (58)
T ss_pred HHHHHHHhCCCHHHHHHHHCCCC
Confidence 46789999999999999997764
No 106
>PRK12537 RNA polymerase sigma factor; Provisional
Probab=20.97 E-value=1.3e+02 Score=24.48 Aligned_cols=29 Identities=24% Similarity=0.381 Sum_probs=22.9
Q ss_pred HHHHHHHHhCCCccccccccchhhhhhhH
Q psy14871 183 EKRELAEATGLTTTQVSNWFKNRRQRDRA 211 (238)
Q Consensus 183 ~r~~LA~~lgLs~~qV~~WFqNRR~R~k~ 211 (238)
...++|..+|++...|++|...-+.+.|.
T Consensus 151 s~~eIA~~lgis~~tV~~~l~ra~~~Lr~ 179 (182)
T PRK12537 151 SHAEIAQRLGAPLGTVKAWIKRSLKALRE 179 (182)
T ss_pred CHHHHHHHHCCChhhHHHHHHHHHHHHHH
Confidence 45788999999999999998766655543
No 107
>TIGR02954 Sig70_famx3 RNA polymerase sigma-70 factor, TIGR02954 family. This group of sigma factors are members of the sigma-70 family (TIGR02937). They and appear by homology, tree building, bidirectional best hits and one-to-a-genome distribution, to represent a conserved family. This family is found in certain Bacillus and Clostridium species.
Probab=20.87 E-value=1.1e+02 Score=24.25 Aligned_cols=47 Identities=15% Similarity=0.260 Sum_probs=31.3
Q ss_pred ccCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCccccccccchhhhhhhH
Q psy14871 160 CFKEKSRSVLRDWYTHNPYPSPREKRELAEATGLTTTQVSNWFKNRRQRDRA 211 (238)
Q Consensus 160 ~fs~~q~~~Le~~F~~~~yPs~~~r~~LA~~lgLs~~qV~~WFqNRR~R~k~ 211 (238)
.+++.++.++...|..+ ....++|..+|++...|+++...-|.+.++
T Consensus 119 ~L~~~~r~i~~l~~~~g-----~s~~eiA~~lgis~~tv~~~l~Ra~~~Lr~ 165 (169)
T TIGR02954 119 TLNDKYQTAIILRYYHD-----LTIKEIAEVMNKPEGTVKTYLHRALKKLKK 165 (169)
T ss_pred hCCHHHhHHHHHHHHcC-----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 35555555555544332 345688999999999999887665555554
No 108
>PF13371 TPR_9: Tetratricopeptide repeat
Probab=20.76 E-value=2e+02 Score=19.05 Aligned_cols=50 Identities=16% Similarity=0.125 Sum_probs=31.6
Q ss_pred hhccCchhHHHHHHhcCCCcccCCcchHHHHHHHHHHhhhccHHHHHHHHhc
Q psy14871 51 LQQSGNIERLGRFLWSLPACEKLHKNESVLKAKAMVAFHRGNFKDLYRILES 102 (238)
Q Consensus 51 l~~~gd~~~l~~f~~~lp~~~~~~~~e~vlra~a~v~~h~~~f~e~~~lLe~ 102 (238)
.++.+|++.....+..+-.. ...+-.....++.+++..|+|.+....++.
T Consensus 5 ~~~~~~~~~A~~~~~~~l~~--~p~~~~~~~~~a~~~~~~g~~~~A~~~l~~ 54 (73)
T PF13371_consen 5 YLQQEDYEEALEVLERALEL--DPDDPELWLQRARCLFQLGRYEEALEDLER 54 (73)
T ss_pred HHhCCCHHHHHHHHHHHHHh--CcccchhhHHHHHHHHHhccHHHHHHHHHH
Confidence 45566766665555432211 112456677788888889999988777654
No 109
>PRK12547 RNA polymerase sigma factor; Provisional
Probab=20.31 E-value=1.2e+02 Score=24.12 Aligned_cols=48 Identities=10% Similarity=0.051 Sum_probs=32.1
Q ss_pred ccCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCccccccccchhhhhhhHH
Q psy14871 160 CFKEKSRSVLRDWYTHNPYPSPREKRELAEATGLTTTQVSNWFKNRRQRDRAA 212 (238)
Q Consensus 160 ~fs~~q~~~Le~~F~~~~yPs~~~r~~LA~~lgLs~~qV~~WFqNRR~R~k~~ 212 (238)
.+++.++.++.-.|.. ...-.++|..+|++...|+++...-|.+.|..
T Consensus 112 ~L~~~~r~v~~l~~~~-----g~s~~eIA~~lgis~~tV~~~l~Rar~~Lr~~ 159 (164)
T PRK12547 112 LLSADQREAIILIGAS-----GFSYEDAAAICGCAVGTIKSRVSRARNRLQEL 159 (164)
T ss_pred hCCHHHHHHHHHHHHc-----CCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHH
Confidence 3455555555554332 22467899999999999999987666665543
No 110
>PRK06930 positive control sigma-like factor; Validated
Probab=20.19 E-value=1.3e+02 Score=24.85 Aligned_cols=50 Identities=10% Similarity=0.106 Sum_probs=36.2
Q ss_pred ccCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCccccccccchhhhhhhHHHh
Q psy14871 160 CFKEKSRSVLRDWYTHNPYPSPREKRELAEATGLTTTQVSNWFKNRRQRDRAAEQ 214 (238)
Q Consensus 160 ~fs~~q~~~Le~~F~~~~yPs~~~r~~LA~~lgLs~~qV~~WFqNRR~R~k~~~~ 214 (238)
.+++.++.++...|... ..-.++|..+|++...|+++...-+.+.++...
T Consensus 114 ~L~~rer~V~~L~~~eg-----~s~~EIA~~lgiS~~tVk~~l~Ra~~kLr~~l~ 163 (170)
T PRK06930 114 VLTEREKEVYLMHRGYG-----LSYSEIADYLNIKKSTVQSMIERAEKKIARQIN 163 (170)
T ss_pred hCCHHHHHHHHHHHHcC-----CCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHH
Confidence 46666677776654322 235678999999999999999887777776544
Done!