Query psy16800
Match_columns 221
No_of_seqs 217 out of 1300
Neff 6.2
Searched_HMMs 46136
Date Fri Aug 16 22:27:24 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy16800.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/16800hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG0484|consensus 99.8 1E-19 2.2E-24 138.9 2.3 68 131-198 13-80 (125)
2 KOG0489|consensus 99.8 2.7E-19 5.9E-24 157.9 3.5 67 134-200 158-224 (261)
3 KOG0488|consensus 99.8 6.1E-18 1.3E-22 152.5 11.4 76 132-207 169-244 (309)
4 KOG0850|consensus 99.7 8.5E-18 1.8E-22 144.0 9.0 71 131-201 118-188 (245)
5 KOG0487|consensus 99.7 3.5E-18 7.6E-23 153.0 5.2 68 133-200 233-300 (308)
6 KOG0842|consensus 99.7 1.2E-17 2.5E-22 149.6 5.9 72 132-203 150-221 (307)
7 KOG0492|consensus 99.7 3.3E-17 7.2E-22 138.6 7.6 72 124-197 135-206 (246)
8 KOG2251|consensus 99.7 7.6E-17 1.7E-21 137.5 9.3 66 132-197 34-99 (228)
9 KOG0843|consensus 99.7 2.2E-17 4.7E-22 137.0 4.7 64 134-197 101-164 (197)
10 KOG0494|consensus 99.7 8.1E-17 1.8E-21 140.2 6.3 62 135-196 141-202 (332)
11 KOG0485|consensus 99.6 5.7E-17 1.2E-21 138.1 3.2 67 133-199 102-168 (268)
12 KOG0848|consensus 99.6 4.7E-16 1E-20 135.9 8.0 65 133-197 197-261 (317)
13 PF00046 Homeobox: Homeobox do 99.6 1.4E-16 3.1E-21 108.8 3.1 57 136-192 1-57 (57)
14 KOG0493|consensus 99.6 1.7E-14 3.7E-19 125.9 10.7 61 135-195 246-306 (342)
15 TIGR01565 homeo_ZF_HD homeobox 99.6 4.3E-15 9.4E-20 103.0 5.6 52 136-187 2-57 (58)
16 KOG0486|consensus 99.5 3.2E-15 6.9E-20 133.2 4.3 89 132-220 109-199 (351)
17 KOG0844|consensus 99.5 1.4E-14 3E-19 128.8 4.8 61 136-196 182-242 (408)
18 smart00389 HOX Homeodomain. DN 99.5 1.9E-14 4E-19 97.4 3.0 55 137-191 2-56 (56)
19 cd00086 homeodomain Homeodomai 99.5 3.5E-14 7.6E-19 96.7 3.5 57 137-193 2-58 (59)
20 KOG0491|consensus 99.5 9.2E-15 2E-19 120.0 0.4 68 134-201 99-166 (194)
21 KOG3802|consensus 99.5 5.5E-14 1.2E-18 128.9 5.1 62 134-195 293-354 (398)
22 COG5576 Homeodomain-containing 99.4 1.2E-13 2.7E-18 113.5 5.3 67 134-200 50-116 (156)
23 KOG0483|consensus 99.4 4.8E-14 1E-18 119.8 2.6 62 135-196 50-111 (198)
24 KOG4577|consensus 99.4 9.3E-14 2E-18 122.8 3.1 70 133-202 165-234 (383)
25 KOG0847|consensus 99.4 4.1E-13 8.8E-18 114.9 4.7 67 133-199 165-231 (288)
26 KOG0490|consensus 99.3 1.9E-12 4E-17 110.3 3.3 63 133-195 58-120 (235)
27 KOG1168|consensus 99.1 1.1E-10 2.3E-15 103.7 3.7 64 134-197 308-371 (385)
28 KOG0849|consensus 99.0 1.3E-10 2.8E-15 106.9 3.8 64 132-195 173-236 (354)
29 KOG0775|consensus 98.7 2.3E-08 5.1E-13 88.2 5.6 55 142-196 183-237 (304)
30 KOG0774|consensus 98.4 3.1E-07 6.7E-12 80.8 5.6 62 134-195 187-251 (334)
31 KOG2252|consensus 98.2 7.6E-07 1.6E-11 85.1 3.7 59 132-190 417-475 (558)
32 PF05920 Homeobox_KN: Homeobox 98.2 2.8E-07 6E-12 59.3 -0.1 34 156-189 7-40 (40)
33 KOG0490|consensus 98.1 2.2E-06 4.8E-11 72.9 3.4 63 133-195 151-213 (235)
34 KOG1146|consensus 98.1 9.7E-06 2.1E-10 84.0 7.7 64 134-197 902-965 (1406)
35 PF11569 Homez: Homeodomain le 96.2 0.0011 2.3E-08 45.7 -0.2 41 147-187 10-50 (56)
36 KOG0773|consensus 96.1 0.0043 9.3E-08 56.6 2.9 61 135-195 239-302 (342)
37 KOG3623|consensus 94.7 0.023 5E-07 56.7 2.8 54 142-196 564-617 (1007)
38 PF04218 CENP-B_N: CENP-B N-te 91.2 0.22 4.7E-06 33.6 2.7 47 136-187 1-47 (53)
39 PF04545 Sigma70_r4: Sigma-70, 67.2 3.1 6.8E-05 26.9 1.2 46 141-191 4-49 (50)
40 KOG1146|consensus 65.2 20 0.00044 38.7 7.1 62 133-194 703-764 (1406)
41 PF04967 HTH_10: HTH DNA bindi 61.3 7.4 0.00016 26.3 2.2 39 142-180 1-41 (53)
42 PF01527 HTH_Tnp_1: Transposas 57.6 3 6.4E-05 29.0 -0.3 44 137-184 2-45 (76)
43 cd00569 HTH_Hin_like Helix-tur 51.5 19 0.00041 19.7 2.6 38 141-183 5-42 (42)
44 cd06171 Sigma70_r4 Sigma70, re 50.3 5.2 0.00011 24.8 -0.0 43 141-188 10-52 (55)
45 PRK03975 tfx putative transcri 49.6 16 0.00034 29.7 2.6 51 139-195 4-54 (141)
46 PRK04217 hypothetical protein; 49.1 16 0.00035 28.4 2.5 53 141-198 42-94 (110)
47 PF10668 Phage_terminase: Phag 42.4 7.7 0.00017 27.0 -0.1 20 164-183 24-43 (60)
48 PF08281 Sigma70_r4_2: Sigma-7 40.4 15 0.00033 23.8 1.1 42 142-188 11-52 (54)
49 PF09607 BrkDBD: Brinker DNA-b 34.8 28 0.00061 24.1 1.7 45 139-184 3-47 (58)
50 COG3413 Predicted DNA binding 33.7 40 0.00087 28.5 2.9 48 141-190 155-204 (215)
51 PF00196 GerE: Bacterial regul 33.4 20 0.00044 23.7 0.8 46 141-192 3-48 (58)
52 PRK12526 RNA polymerase sigma 33.1 36 0.00078 28.3 2.5 49 142-195 154-202 (206)
53 TIGR03879 near_KaiC_dom probab 32.6 7.1 0.00015 28.3 -1.7 35 151-185 21-55 (73)
54 PRK09413 IS2 repressor TnpA; R 31.4 52 0.0011 25.4 2.9 43 138-184 9-51 (121)
55 PRK09646 RNA polymerase sigma 31.3 42 0.00092 27.5 2.6 49 141-194 142-190 (194)
56 PF08280 HTH_Mga: M protein tr 31.1 31 0.00067 23.2 1.4 35 144-182 5-39 (59)
57 KOG3755|consensus 28.9 13 0.00028 37.1 -1.0 60 136-195 692-759 (769)
58 PRK12512 RNA polymerase sigma 28.7 49 0.0011 26.6 2.5 51 141-196 131-181 (184)
59 PRK06759 RNA polymerase factor 28.6 44 0.00095 25.9 2.1 47 141-192 106-152 (154)
60 PRK09642 RNA polymerase sigma 27.9 53 0.0012 25.7 2.5 50 142-196 107-156 (160)
61 KOG3623|consensus 27.2 36 0.00078 34.9 1.6 60 137-196 628-687 (1007)
62 cd04761 HTH_MerR-SF Helix-Turn 26.8 17 0.00038 22.7 -0.4 21 165-185 3-23 (49)
63 COG4367 Uncharacterized protei 26.8 46 0.001 25.2 1.8 39 141-179 2-40 (97)
64 PRK09652 RNA polymerase sigma 26.6 52 0.0011 25.9 2.2 49 141-194 128-176 (182)
65 PRK12533 RNA polymerase sigma 26.5 77 0.0017 26.9 3.4 51 141-196 134-184 (216)
66 TIGR02937 sigma70-ECF RNA poly 25.9 49 0.0011 24.6 1.9 47 141-192 110-156 (158)
67 PRK12515 RNA polymerase sigma 25.8 64 0.0014 26.2 2.7 52 141-197 131-182 (189)
68 smart00421 HTH_LUXR helix_turn 25.8 53 0.0011 20.4 1.8 42 141-188 3-44 (58)
69 PRK12514 RNA polymerase sigma 25.8 35 0.00075 27.4 1.1 47 142-193 130-176 (179)
70 PRK12546 RNA polymerase sigma 24.8 78 0.0017 26.1 3.1 33 164-196 131-163 (188)
71 PF13518 HTH_28: Helix-turn-he 24.5 23 0.00049 22.5 -0.2 22 165-186 15-36 (52)
72 PHA02955 hypothetical protein; 24.4 97 0.0021 27.0 3.6 45 144-188 60-105 (213)
73 PRK12518 RNA polymerase sigma 23.8 37 0.00079 27.0 0.9 38 159-196 133-170 (175)
74 PRK11924 RNA polymerase sigma 23.0 68 0.0015 25.1 2.3 49 142-195 126-174 (179)
75 PRK10072 putative transcriptio 22.9 27 0.00058 26.4 -0.1 41 141-188 32-72 (96)
76 PRK12535 RNA polymerase sigma 22.9 81 0.0017 26.1 2.8 55 142-201 134-188 (196)
77 PRK09639 RNA polymerase sigma 22.9 86 0.0019 24.5 2.9 49 141-195 112-160 (166)
78 PF06056 Terminase_5: Putative 22.8 28 0.00061 23.8 0.0 21 164-184 15-35 (58)
79 KOG0773|consensus 22.7 41 0.00089 30.5 1.1 45 151-195 113-157 (342)
80 TIGR02948 SigW_bacill RNA poly 22.6 67 0.0014 25.7 2.2 49 141-194 136-184 (187)
81 PRK09480 slmA division inhibit 22.5 62 0.0014 25.8 2.0 41 147-188 16-56 (194)
82 PRK00118 putative DNA-binding 21.8 82 0.0018 24.2 2.4 49 141-194 17-65 (104)
83 PRK12519 RNA polymerase sigma 21.8 62 0.0013 26.3 1.9 33 162-194 157-189 (194)
84 KOG3816|consensus 21.8 1.7E+02 0.0037 28.0 4.9 33 18-56 189-221 (526)
85 PRK05657 RNA polymerase sigma 21.6 66 0.0014 29.2 2.2 55 141-196 262-316 (325)
86 PRK09644 RNA polymerase sigma 20.9 75 0.0016 25.1 2.1 32 164-195 126-157 (165)
87 PRK06930 positive control sigm 20.4 82 0.0018 26.0 2.3 51 141-196 114-164 (170)
88 TIGR02959 SigZ RNA polymerase 20.0 86 0.0019 25.1 2.3 51 141-196 100-150 (170)
No 1
>KOG0484|consensus
Probab=99.77 E-value=1e-19 Score=138.93 Aligned_cols=68 Identities=40% Similarity=0.557 Sum_probs=63.3
Q ss_pred ccCCCCCCCcccCHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCCCCceeeccccchhHHHHHhhhcc
Q psy16800 131 QSLLNNSGRTNFTNKQLTELEKEFHFNKYLTRARRIEIASVLQLNETQVKIWFQNRRMKQKKRIKEGI 198 (221)
Q Consensus 131 ~~~~~rr~Rt~ft~~Ql~~Le~~F~~~~yps~~~r~~LA~~L~Lt~~qVqvWFQNRRaK~Kr~~k~g~ 198 (221)
..++++|.||.||..||..||+.|...+||++..|++||..++|++.+|||||||||+|.+|+.+...
T Consensus 13 ekrKQRRIRTTFTS~QLkELErvF~ETHYPDIYTREEiA~kidLTEARVQVWFQNRRAKfRKQEr~a~ 80 (125)
T KOG0484|consen 13 EKRKQRRIRTTFTSAQLKELERVFAETHYPDIYTREEIALKIDLTEARVQVWFQNRRAKFRKQERAAI 80 (125)
T ss_pred HHHHhhhhhhhhhHHHHHHHHHHHHhhcCCcchhHHHHHHhhhhhHHHHHHHHHhhHHHHHHHHHHHH
Confidence 34567889999999999999999999999999999999999999999999999999999999988643
No 2
>KOG0489|consensus
Probab=99.76 E-value=2.7e-19 Score=157.91 Aligned_cols=67 Identities=64% Similarity=0.868 Sum_probs=63.7
Q ss_pred CCCCCCcccCHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCCCCceeeccccchhHHHHHhhhcccc
Q psy16800 134 LNNSGRTNFTNKQLTELEKEFHFNKYLTRARRIEIASVLQLNETQVKIWFQNRRMKQKKRIKEGILI 200 (221)
Q Consensus 134 ~~rr~Rt~ft~~Ql~~Le~~F~~~~yps~~~r~~LA~~L~Lt~~qVqvWFQNRRaK~Kr~~k~g~~~ 200 (221)
..||.||.||..|+.+||+.|+.|+|++...|.+||..|+|+|+||+|||||||+||||..+.....
T Consensus 158 ~~kR~RtayT~~QllELEkEFhfN~YLtR~RRiEiA~~L~LtErQIKIWFQNRRMK~Kk~~k~~~~~ 224 (261)
T KOG0489|consen 158 KSKRRRTAFTRYQLLELEKEFHFNKYLTRSRRIEIAHALNLTERQIKIWFQNRRMKWKKENKAKSSQ 224 (261)
T ss_pred CCCCCCcccchhhhhhhhhhhccccccchHHHHHHHhhcchhHHHHHHHHHHHHHHHHHhhcccccc
Confidence 4689999999999999999999999999999999999999999999999999999999999976655
No 3
>KOG0488|consensus
Probab=99.75 E-value=6.1e-18 Score=152.52 Aligned_cols=76 Identities=45% Similarity=0.620 Sum_probs=68.1
Q ss_pred cCCCCCCCcccCHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCCCCceeeccccchhHHHHHhhhccccCCCCCCC
Q psy16800 132 SLLNNSGRTNFTNKQLTELEKEFHFNKYLTRARRIEIASVLQLNETQVKIWFQNRRMKQKKRIKEGILIGVGEGSL 207 (221)
Q Consensus 132 ~~~~rr~Rt~ft~~Ql~~Le~~F~~~~yps~~~r~~LA~~L~Lt~~qVqvWFQNRRaK~Kr~~k~g~~~~~~~g~~ 207 (221)
.+++|+.||.||..||..||+.|++.+|++..+|.+||..|||+..||++||||||+||||+...+....-..+..
T Consensus 169 pkK~RksRTaFT~~Ql~~LEkrF~~QKYLS~~DR~~LA~~LgLTdaQVKtWfQNRRtKWKrq~a~g~~~~~~~~~~ 244 (309)
T KOG0488|consen 169 PKKRRKSRTAFSDHQLFELEKRFEKQKYLSVADRIELAASLGLTDAQVKTWFQNRRTKWKRQTAEGGELLYQAGNS 244 (309)
T ss_pred CcccccchhhhhHHHHHHHHHHHHHhhcccHHHHHHHHHHcCCchhhHHHHHhhhhHHHHHHHHhhhccccccccc
Confidence 3566777999999999999999999999999999999999999999999999999999999999866665555444
No 4
>KOG0850|consensus
Probab=99.73 E-value=8.5e-18 Score=144.04 Aligned_cols=71 Identities=41% Similarity=0.531 Sum_probs=64.6
Q ss_pred ccCCCCCCCcccCHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCCCCceeeccccchhHHHHHhhhccccC
Q psy16800 131 QSLLNNSGRTNFTNKQLTELEKEFHFNKYLTRARRIEIASVLQLNETQVKIWFQNRRMKQKKRIKEGILIG 201 (221)
Q Consensus 131 ~~~~~rr~Rt~ft~~Ql~~Le~~F~~~~yps~~~r~~LA~~L~Lt~~qVqvWFQNRRaK~Kr~~k~g~~~~ 201 (221)
+.++-|+.||.|+..||..|.+.|++++|+...||.+||..|||+-.||+|||||||.|.||..+.+....
T Consensus 118 k~KK~RKPRTIYSS~QLqaL~rRFQkTQYLALPERAeLAAsLGLTQTQVKIWFQNrRSK~KKl~k~g~~~~ 188 (245)
T KOG0850|consen 118 KGKKVRKPRTIYSSLQLQALNRRFQQTQYLALPERAELAASLGLTQTQVKIWFQNRRSKFKKLKKQGSGPV 188 (245)
T ss_pred CcccccCCcccccHHHHHHHHHHHhhcchhcCcHHHHHHHHhCCchhHhhhhhhhhHHHHHHHHhcCCCcc
Confidence 34456777999999999999999999999999999999999999999999999999999999999765443
No 5
>KOG0487|consensus
Probab=99.72 E-value=3.5e-18 Score=153.03 Aligned_cols=68 Identities=50% Similarity=0.752 Sum_probs=63.3
Q ss_pred CCCCCCCcccCHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCCCCceeeccccchhHHHHHhhhcccc
Q psy16800 133 LLNNSGRTNFTNKQLTELEKEFHFNKYLTRARRIEIASVLQLNETQVKIWFQNRRMKQKKRIKEGILI 200 (221)
Q Consensus 133 ~~~rr~Rt~ft~~Ql~~Le~~F~~~~yps~~~r~~LA~~L~Lt~~qVqvWFQNRRaK~Kr~~k~g~~~ 200 (221)
+..|++|..||+.|+.+||+.|..|.|++.+.|.+|++.|+|+++||+|||||||+|.||..++....
T Consensus 233 ~~~RKKRcPYTK~QtlELEkEFlfN~YitkeKR~ElSr~lNLTeRQVKIWFQNRRMK~KK~~re~r~~ 300 (308)
T KOG0487|consen 233 RRGRKKRCPYTKHQTLELEKEFLFNMYITKEKRLELSRTLNLTERQVKIWFQNRRMKEKKVNRENRLK 300 (308)
T ss_pred cccccccCCchHHHHHHHHHHHHHHHHHhHHHHHHHHHhcccchhheeeeehhhhhHHhhhhhhhhcc
Confidence 45688899999999999999999999999999999999999999999999999999999999765444
No 6
>KOG0842|consensus
Probab=99.70 E-value=1.2e-17 Score=149.64 Aligned_cols=72 Identities=40% Similarity=0.594 Sum_probs=65.2
Q ss_pred cCCCCCCCcccCHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCCCCceeeccccchhHHHHHhhhccccCCC
Q psy16800 132 SLLNNSGRTNFTNKQLTELEKEFHFNKYLTRARRIEIASVLQLNETQVKIWFQNRRMKQKKRIKEGILIGVG 203 (221)
Q Consensus 132 ~~~~rr~Rt~ft~~Ql~~Le~~F~~~~yps~~~r~~LA~~L~Lt~~qVqvWFQNRRaK~Kr~~k~g~~~~~~ 203 (221)
..++||.|..||..|+.+||+.|.+++|++..||++||..|.||+.||||||||||-|.||+.++..+.+..
T Consensus 150 ~~~kRKrRVLFSqAQV~ELERRFrqQRYLSAPERE~LA~~LrLT~TQVKIWFQNrRYK~KR~~~dk~~~~~~ 221 (307)
T KOG0842|consen 150 KRKKRKRRVLFSQAQVYELERRFRQQRYLSAPEREHLASSLRLTPTQVKIWFQNRRYKTKRQQKDKALEALL 221 (307)
T ss_pred cccccccccccchhHHHHHHHHHHhhhccccHhHHHHHHhcCCCchheeeeeecchhhhhhhhhhhhhhccc
Confidence 345677799999999999999999999999999999999999999999999999999999999986555433
No 7
>KOG0492|consensus
Probab=99.70 E-value=3.3e-17 Score=138.63 Aligned_cols=72 Identities=47% Similarity=0.698 Sum_probs=64.1
Q ss_pred CccccccccCCCCCCCcccCHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCCCCceeeccccchhHHHHHhhhc
Q psy16800 124 PAALSQHQSLLNNSGRTNFTNKQLTELEKEFHFNKYLTRARRIEIASVLQLNETQVKIWFQNRRMKQKKRIKEG 197 (221)
Q Consensus 124 ~~~~~~~~~~~~rr~Rt~ft~~Ql~~Le~~F~~~~yps~~~r~~LA~~L~Lt~~qVqvWFQNRRaK~Kr~~k~g 197 (221)
.+.+..|. ..|+.||.||..||..||+.|...+|+++.+|.+++..|.||+.||+|||||||+|.||.+...
T Consensus 135 ~C~LrKhk--~nRkPRtPFTtqQLlaLErkfrekqYLSiaEraefSsSL~LTeTqVKIWFQNRRAKaKRlQeae 206 (246)
T KOG0492|consen 135 TCTLRKHK--PNRKPRTPFTTQQLLALERKFREKQYLSIAERAEFSSSLELTETQVKIWFQNRRAKAKRLQEAE 206 (246)
T ss_pred cchhcccC--CCCCCCCCCCHHHHHHHHHHHhHhhhhhHHHHHhhhhhhhhhhhheehhhhhhhHHHHHHHHHH
Confidence 34445444 3477899999999999999999999999999999999999999999999999999999988753
No 8
>KOG2251|consensus
Probab=99.69 E-value=7.6e-17 Score=137.51 Aligned_cols=66 Identities=36% Similarity=0.520 Sum_probs=62.5
Q ss_pred cCCCCCCCcccCHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCCCCceeeccccchhHHHHHhhhc
Q psy16800 132 SLLNNSGRTNFTNKQLTELEKEFHFNKYLTRARRIEIASVLQLNETQVKIWFQNRRMKQKKRIKEG 197 (221)
Q Consensus 132 ~~~~rr~Rt~ft~~Ql~~Le~~F~~~~yps~~~r~~LA~~L~Lt~~qVqvWFQNRRaK~Kr~~k~g 197 (221)
.++.+|.||.|+..|+.+||.+|.+.+||++..|++||.+|+|.+.+|||||.|||+|+|++++..
T Consensus 34 pRkqRRERTtFtr~QlevLe~LF~kTqYPDv~~rEelAlklnLpeSrVqVWFKNRRAK~r~qq~qq 99 (228)
T KOG2251|consen 34 PRKQRRERTTFTRKQLEVLEALFAKTQYPDVFMREELALKLNLPESRVQVWFKNRRAKCRRQQQQQ 99 (228)
T ss_pred chhcccccceecHHHHHHHHHHHHhhcCccHHHHHHHHHHhCCchhhhhhhhccccchhhHhhhhh
Confidence 456789999999999999999999999999999999999999999999999999999999998863
No 9
>KOG0843|consensus
Probab=99.68 E-value=2.2e-17 Score=136.99 Aligned_cols=64 Identities=47% Similarity=0.667 Sum_probs=61.4
Q ss_pred CCCCCCcccCHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCCCCceeeccccchhHHHHHhhhc
Q psy16800 134 LNNSGRTNFTNKQLTELEKEFHFNKYLTRARRIEIASVLQLNETQVKIWFQNRRMKQKKRIKEG 197 (221)
Q Consensus 134 ~~rr~Rt~ft~~Ql~~Le~~F~~~~yps~~~r~~LA~~L~Lt~~qVqvWFQNRRaK~Kr~~k~g 197 (221)
+.||.||.||.+||..||..|+.++|....+|+.||..|+|++.||+|||||||.|.||...+.
T Consensus 101 ~~kr~RT~ft~~Ql~~LE~~F~~~~Yvvg~eR~~LA~~L~LsetQVkvWFQNRRtk~kr~~~e~ 164 (197)
T KOG0843|consen 101 RPKRIRTAFTPEQLLKLEHAFEGNQYVVGAERKQLAQSLSLSETQVKVWFQNRRTKHKRMQQED 164 (197)
T ss_pred CCCccccccCHHHHHHHHHHHhcCCeeechHHHHHHHHcCCChhHhhhhhhhhhHHHHHHHHHh
Confidence 5688899999999999999999999999999999999999999999999999999999988874
No 10
>KOG0494|consensus
Probab=99.66 E-value=8.1e-17 Score=140.21 Aligned_cols=62 Identities=40% Similarity=0.524 Sum_probs=58.7
Q ss_pred CCCCCcccCHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCCCCceeeccccchhHHHHHhhh
Q psy16800 135 NNSGRTNFTNKQLTELEKEFHFNKYLTRARRIEIASVLQLNETQVKIWFQNRRMKQKKRIKE 196 (221)
Q Consensus 135 ~rr~Rt~ft~~Ql~~Le~~F~~~~yps~~~r~~LA~~L~Lt~~qVqvWFQNRRaK~Kr~~k~ 196 (221)
+|+.||.||..|+..||+.|+..+||+...|+.||..+.|.+.+|+|||||||+||||..+.
T Consensus 141 RRh~RTiFT~~Qle~LEkaFkeaHYPDv~Are~la~ktelpEDRIqVWfQNRRAKWRk~Ek~ 202 (332)
T KOG0494|consen 141 RRHFRTIFTSYQLEELEKAFKEAHYPDVYAREMLADKTELPEDRIQVWFQNRRAKWRKTEKR 202 (332)
T ss_pred cccccchhhHHHHHHHHHHHhhccCccHHHHHHHhhhccCchhhhhHHhhhhhHHhhhhhhh
Confidence 34449999999999999999999999999999999999999999999999999999998886
No 11
>KOG0485|consensus
Probab=99.65 E-value=5.7e-17 Score=138.07 Aligned_cols=67 Identities=43% Similarity=0.642 Sum_probs=62.6
Q ss_pred CCCCCCCcccCHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCCCCceeeccccchhHHHHHhhhccc
Q psy16800 133 LLNNSGRTNFTNKQLTELEKEFHFNKYLTRARRIEIASVLQLNETQVKIWFQNRRMKQKKRIKEGIL 199 (221)
Q Consensus 133 ~~~rr~Rt~ft~~Ql~~Le~~F~~~~yps~~~r~~LA~~L~Lt~~qVqvWFQNRRaK~Kr~~k~g~~ 199 (221)
.++|+.||+|+..|+..||..|+...|++..+|..||.+|.|++.||+|||||||.||||+......
T Consensus 102 ~RKKktRTvFSraQV~qLEs~Fe~krYLSsaeRa~LA~sLqLTETQVKIWFQNRRnKwKRq~aad~e 168 (268)
T KOG0485|consen 102 DRKKKTRTVFSRAQVFQLESTFELKRYLSSAERAGLAASLQLTETQVKIWFQNRRNKWKRQYAADLE 168 (268)
T ss_pred cccccchhhhhHHHHHHHHHHHHHHhhhhHHHHhHHHHhhhhhhhhhhhhhhhhhHHHHHHHhhhhh
Confidence 3578889999999999999999999999999999999999999999999999999999999886433
No 12
>KOG0848|consensus
Probab=99.64 E-value=4.7e-16 Score=135.94 Aligned_cols=65 Identities=48% Similarity=0.706 Sum_probs=60.1
Q ss_pred CCCCCCCcccCHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCCCCceeeccccchhHHHHHhhhc
Q psy16800 133 LLNNSGRTNFTNKQLTELEKEFHFNKYLTRARRIEIASVLQLNETQVKIWFQNRRMKQKKRIKEG 197 (221)
Q Consensus 133 ~~~rr~Rt~ft~~Ql~~Le~~F~~~~yps~~~r~~LA~~L~Lt~~qVqvWFQNRRaK~Kr~~k~g 197 (221)
+.+-+-|.+||..|..+||+.|..++|.++..+.+||..|+|+|+||+|||||||+|+||..++.
T Consensus 197 RTkDKYRvVYTDhQRLELEKEfh~SryITirRKSELA~~LgLsERQVKIWFQNRRAKERK~nKKk 261 (317)
T KOG0848|consen 197 RTKDKYRVVYTDHQRLELEKEFHTSRYITIRRKSELAATLGLSERQVKIWFQNRRAKERKDNKKK 261 (317)
T ss_pred ecccceeEEecchhhhhhhhhhccccceeeehhHHHHHhhCccHhhhhHhhhhhhHHHHHHHHHH
Confidence 34445588999999999999999999999999999999999999999999999999999988875
No 13
>PF00046 Homeobox: Homeobox domain not present here.; InterPro: IPR001356 The homeobox domain was first identified in a number of drosophila homeotic and segmentation proteins, but is now known to be well-conserved in many other animals, including vertebrates [, , ]. Hox genes encode homeodomain-containing transcriptional regulators that operate differential genetic programs along the anterior-posterior axis of animal bodies []. The domain binds DNA through a helix-turn-helix (HTH) structure. The HTH motif is characterised by two alpha-helices, which make intimate contacts with the DNA and are joined by a short turn. The second helix binds to DNA via a number of hydrogen bonds and hydrophobic interactions, which occur between specific side chains and the exposed bases and thymine methyl groups within the major groove of the DNA []. The first helix helps to stabilise the structure. The motif is very similar in sequence and structure in a wide range of DNA-binding proteins (e.g., cro and repressor proteins, homeotic proteins, etc.). One of the principal differences between HTH motifs in these different proteins arises from the stereo-chemical requirement for glycine in the turn which is needed to avoid steric interference of the beta-carbon with the main chain: for cro and repressor proteins the glycine appears to be mandatory, while for many of the homeotic and other DNA-binding proteins the requirement is relaxed.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0043565 sequence-specific DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 2DA3_A 1LFB_A 2LFB_A 2ECB_A 2DA5_A 3D1N_O 3A03_A 2XSD_C 3CMY_A 1AHD_P ....
Probab=99.63 E-value=1.4e-16 Score=108.79 Aligned_cols=57 Identities=51% Similarity=0.703 Sum_probs=55.1
Q ss_pred CCCCcccCHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCCCCceeeccccchhHHHH
Q psy16800 136 NSGRTNFTNKQLTELEKEFHFNKYLTRARRIEIASVLQLNETQVKIWFQNRRMKQKK 192 (221)
Q Consensus 136 rr~Rt~ft~~Ql~~Le~~F~~~~yps~~~r~~LA~~L~Lt~~qVqvWFQNRRaK~Kr 192 (221)
|+.|+.||.+|+..|+.+|..++||+..+++.||..|+|+..+|++||+|+|+++|+
T Consensus 1 kr~r~~~t~~q~~~L~~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrR~k~kk 57 (57)
T PF00046_consen 1 KRKRTRFTKEQLKVLEEYFQENPYPSKEEREELAKELGLTERQVKNWFQNRRRKEKK 57 (57)
T ss_dssp SSSSSSSSHHHHHHHHHHHHHSSSCHHHHHHHHHHHHTSSHHHHHHHHHHHHHHHHH
T ss_pred CcCCCCCCHHHHHHHHHHHHHhccccccccccccccccccccccccCHHHhHHHhCc
Confidence 577999999999999999999999999999999999999999999999999999986
No 14
>KOG0493|consensus
Probab=99.57 E-value=1.7e-14 Score=125.91 Aligned_cols=61 Identities=52% Similarity=0.774 Sum_probs=57.9
Q ss_pred CCCCCcccCHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCCCCceeeccccchhHHHHHhh
Q psy16800 135 NNSGRTNFTNKQLTELEKEFHFNKYLTRARRIEIASVLQLNETQVKIWFQNRRMKQKKRIK 195 (221)
Q Consensus 135 ~rr~Rt~ft~~Ql~~Le~~F~~~~yps~~~r~~LA~~L~Lt~~qVqvWFQNRRaK~Kr~~k 195 (221)
-||.||.||.+||..|+..|+.|.|++...|.+||.+|+|++.||+|||||+|+|.||..-
T Consensus 246 eKRPRTAFtaeQL~RLK~EF~enRYlTEqRRQ~La~ELgLNEsQIKIWFQNKRAKiKKsTg 306 (342)
T KOG0493|consen 246 EKRPRTAFTAEQLQRLKAEFQENRYLTEQRRQELAQELGLNESQIKIWFQNKRAKIKKSTG 306 (342)
T ss_pred hcCccccccHHHHHHHHHHHhhhhhHHHHHHHHHHHHhCcCHHHhhHHhhhhhhhhhhccC
Confidence 4678999999999999999999999999999999999999999999999999999998654
No 15
>TIGR01565 homeo_ZF_HD homeobox domain, ZF-HD class. This model represents a class of homoebox domain that differs substantially from the typical homoebox domain described in pfam model pfam00046. It is found in both C4 and C3 plants.
Probab=99.57 E-value=4.3e-15 Score=103.02 Aligned_cols=52 Identities=19% Similarity=0.318 Sum_probs=50.6
Q ss_pred CCCCcccCHHHHHHHHHHhhhCCC----CCHHHHHHHHHHhCCCCCceeeccccch
Q psy16800 136 NSGRTNFTNKQLTELEKEFHFNKY----LTRARRIEIASVLQLNETQVKIWFQNRR 187 (221)
Q Consensus 136 rr~Rt~ft~~Ql~~Le~~F~~~~y----ps~~~r~~LA~~L~Lt~~qVqvWFQNRR 187 (221)
||.||.||.+|+..|+.+|+.+.| |+..++++||..|||++.+|+|||||.+
T Consensus 2 kR~RT~Ft~~Q~~~Le~~fe~~~y~~~~~~~~~r~~la~~lgl~~~vvKVWfqN~k 57 (58)
T TIGR01565 2 KRRRTKFTAEQKEKMRDFAEKLGWKLKDKRREEVREFCEEIGVTRKVFKVWMHNNK 57 (58)
T ss_pred CCCCCCCCHHHHHHHHHHHHHcCCCCCCCCHHHHHHHHHHhCCCHHHeeeecccCC
Confidence 788999999999999999999999 9999999999999999999999999975
No 16
>KOG0486|consensus
Probab=99.54 E-value=3.2e-15 Score=133.18 Aligned_cols=89 Identities=36% Similarity=0.480 Sum_probs=75.9
Q ss_pred cCCCCCCCcccCHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCCCCceeeccccchhHHHHHhhhcc--ccCCCCCCCCC
Q psy16800 132 SLLNNSGRTNFTNKQLTELEKEFHFNKYLTRARRIEIASVLQLNETQVKIWFQNRRMKQKKRIKEGI--LIGVGEGSLMG 209 (221)
Q Consensus 132 ~~~~rr~Rt~ft~~Ql~~Le~~F~~~~yps~~~r~~LA~~L~Lt~~qVqvWFQNRRaK~Kr~~k~g~--~~~~~~g~~~~ 209 (221)
..+++|.||+||..||..||..|++|.||+...|++||.-.+|++.+|+|||.|||+||+|+++..+ ..-.+-+....
T Consensus 109 i~KqrrQrthFtSqqlqele~tF~rNrypdMstrEEIavwtNlTE~rvrvwfknrrakwrkrErN~~ae~~k~~f~~~~~ 188 (351)
T KOG0486|consen 109 ISKQRRQRTHFTSQQLQELEATFQRNRYPDMSTREEIAVWTNLTEARVRVWFKNRRAKWRKRERNQQAELAKGGFGPQFL 188 (351)
T ss_pred hhhhhhhhhhhHHHHHHHHHHHHhhccCCccchhhHHHhhccccchhhhhhcccchhhhhhhhhhHHHHhhhcCCccccc
Confidence 3467888999999999999999999999999999999999999999999999999999999999766 33334445555
Q ss_pred CCCCCCCCCCC
Q psy16800 210 AQGSSPNGGLY 220 (221)
Q Consensus 210 ~~~~sp~~~~~ 220 (221)
++-|.|.++.|
T Consensus 189 t~~~~P~~~vy 199 (351)
T KOG0486|consen 189 TGLMQPYFDVY 199 (351)
T ss_pred ccccCchhhhc
Confidence 66777777665
No 17
>KOG0844|consensus
Probab=99.50 E-value=1.4e-14 Score=128.80 Aligned_cols=61 Identities=49% Similarity=0.788 Sum_probs=58.8
Q ss_pred CCCCcccCHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCCCCceeeccccchhHHHHHhhh
Q psy16800 136 NSGRTNFTNKQLTELEKEFHFNKYLTRARRIEIASVLQLNETQVKIWFQNRRMKQKKRIKE 196 (221)
Q Consensus 136 rr~Rt~ft~~Ql~~Le~~F~~~~yps~~~r~~LA~~L~Lt~~qVqvWFQNRRaK~Kr~~k~ 196 (221)
||-||.||.+||..||+.|-+.+|.+...|.+||..|+|.+..|+|||||||+|+||+...
T Consensus 182 RRYRTAFTReQIaRLEKEFyrENYVSRprRcELAAaLNLPEtTIKVWFQNRRMKDKRQRla 242 (408)
T KOG0844|consen 182 RRYRTAFTREQIARLEKEFYRENYVSRPRRCELAAALNLPETTIKVWFQNRRMKDKRQRLA 242 (408)
T ss_pred HHHHhhhhHHHHHHHHHHHHHhccccCchhhhHHHhhCCCcceeehhhhhchhhhhhhhhh
Confidence 7889999999999999999999999999999999999999999999999999999998765
No 18
>smart00389 HOX Homeodomain. DNA-binding factors that are involved in the transcriptional regulation of key developmental processes
Probab=99.48 E-value=1.9e-14 Score=97.44 Aligned_cols=55 Identities=58% Similarity=0.820 Sum_probs=52.1
Q ss_pred CCCcccCHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCCCCceeeccccchhHHH
Q psy16800 137 SGRTNFTNKQLTELEKEFHFNKYLTRARRIEIASVLQLNETQVKIWFQNRRMKQK 191 (221)
Q Consensus 137 r~Rt~ft~~Ql~~Le~~F~~~~yps~~~r~~LA~~L~Lt~~qVqvWFQNRRaK~K 191 (221)
+.|+.|+.+|+..|+..|..++||+..++..||..++|+..+|++||+|+|++.+
T Consensus 2 k~r~~~~~~~~~~L~~~f~~~~~P~~~~~~~la~~~~l~~~qV~~WF~nrR~~~~ 56 (56)
T smart00389 2 RKRTSFTPEQLEELEKEFQKNPYPSREEREELAAKLGLSERQVKVWFQNRRAKWK 56 (56)
T ss_pred CCCCcCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHHCcCHHHHHHhHHHHhhccC
Confidence 5678899999999999999999999999999999999999999999999998753
No 19
>cd00086 homeodomain Homeodomain; DNA binding domains involved in the transcriptional regulation of key eukaryotic developmental processes; may bind to DNA as monomers or as homo- and/or heterodimers, in a sequence-specific manner.
Probab=99.46 E-value=3.5e-14 Score=96.67 Aligned_cols=57 Identities=58% Similarity=0.800 Sum_probs=54.0
Q ss_pred CCCcccCHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCCCCceeeccccchhHHHHH
Q psy16800 137 SGRTNFTNKQLTELEKEFHFNKYLTRARRIEIASVLQLNETQVKIWFQNRRMKQKKR 193 (221)
Q Consensus 137 r~Rt~ft~~Ql~~Le~~F~~~~yps~~~r~~LA~~L~Lt~~qVqvWFQNRRaK~Kr~ 193 (221)
+.|+.|+..|+..|+..|..++||+..++..||..+||+..+|++||+|+|++.++.
T Consensus 2 ~~r~~~~~~~~~~Le~~f~~~~~P~~~~~~~la~~~~l~~~qV~~WF~nrR~~~~~~ 58 (59)
T cd00086 2 RKRTRFTPEQLEELEKEFEKNPYPSREEREELAKELGLTERQVKIWFQNRRAKLKRS 58 (59)
T ss_pred CCCCcCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHHCcCHHHHHHHHHHHHHHHhcc
Confidence 457899999999999999999999999999999999999999999999999998763
No 20
>KOG0491|consensus
Probab=99.46 E-value=9.2e-15 Score=119.96 Aligned_cols=68 Identities=46% Similarity=0.689 Sum_probs=62.8
Q ss_pred CCCCCCcccCHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCCCCceeeccccchhHHHHHhhhccccC
Q psy16800 134 LNNSGRTNFTNKQLTELEKEFHFNKYLTRARRIEIASVLQLNETQVKIWFQNRRMKQKKRIKEGILIG 201 (221)
Q Consensus 134 ~~rr~Rt~ft~~Ql~~Le~~F~~~~yps~~~r~~LA~~L~Lt~~qVqvWFQNRRaK~Kr~~k~g~~~~ 201 (221)
.+++.||+|+..|+..|++.|+...|++..++.+||..|+|++.||+.||||||+|.||..+.....+
T Consensus 99 ~r~K~Rtvfs~~ql~~l~~rFe~QrYLS~~e~~ELan~L~LS~~QVKTWFQNrRMK~Kk~~r~~~p~n 166 (194)
T KOG0491|consen 99 RRRKARTVFSDPQLSGLEKRFERQRYLSTPERQELANALSLSETQVKTWFQNRRMKHKKQQRNNQPKN 166 (194)
T ss_pred HhhhhcccccCccccccHHHHhhhhhcccHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHHHhccCCCC
Confidence 45667999999999999999999999999999999999999999999999999999999999865443
No 21
>KOG3802|consensus
Probab=99.45 E-value=5.5e-14 Score=128.87 Aligned_cols=62 Identities=34% Similarity=0.413 Sum_probs=60.3
Q ss_pred CCCCCCcccCHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCCCCceeeccccchhHHHHHhh
Q psy16800 134 LNNSGRTNFTNKQLTELEKEFHFNKYLTRARRIEIASVLQLNETQVKIWFQNRRMKQKKRIK 195 (221)
Q Consensus 134 ~~rr~Rt~ft~~Ql~~Le~~F~~~~yps~~~r~~LA~~L~Lt~~qVqvWFQNRRaK~Kr~~k 195 (221)
++||+||.|.......||++|.+|+.|+..++..||.+|+|.+++|+|||||||+|.||...
T Consensus 293 RkRKKRTSie~~vr~aLE~~F~~npKPt~qEIt~iA~~L~leKEVVRVWFCNRRQkeKR~~~ 354 (398)
T KOG3802|consen 293 RKRKKRTSIEVNVRGALEKHFLKNPKPTSQEITHIAESLQLEKEVVRVWFCNRRQKEKRITP 354 (398)
T ss_pred cccccccceeHHHHHHHHHHHHhCCCCCHHHHHHHHHHhccccceEEEEeeccccccccCCC
Confidence 57888999999999999999999999999999999999999999999999999999999888
No 22
>COG5576 Homeodomain-containing transcription factor [Transcription]
Probab=99.43 E-value=1.2e-13 Score=113.49 Aligned_cols=67 Identities=36% Similarity=0.568 Sum_probs=61.1
Q ss_pred CCCCCCcccCHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCCCCceeeccccchhHHHHHhhhcccc
Q psy16800 134 LNNSGRTNFTNKQLTELEKEFHFNKYLTRARRIEIASVLQLNETQVKIWFQNRRMKQKKRIKEGILI 200 (221)
Q Consensus 134 ~~rr~Rt~ft~~Ql~~Le~~F~~~~yps~~~r~~LA~~L~Lt~~qVqvWFQNRRaK~Kr~~k~g~~~ 200 (221)
..+++|++.|..|+.+|++.|..++||+..+|..|+..|+|+++-|||||||+|++.|+....+...
T Consensus 50 ~~~~~r~R~t~~Q~~vL~~~F~i~p~Ps~~~r~~L~~~lnm~~ksVqIWFQNkR~~~k~~~~~~~~~ 116 (156)
T COG5576 50 PPKSKRRRTTDEQLMVLEREFEINPYPSSITRIKLSLLLNMPPKSVQIWFQNKRAKEKKKRSGKVEQ 116 (156)
T ss_pred cCcccceechHHHHHHHHHHhccCCCCCHHHHHHHHHhcCCChhhhhhhhchHHHHHHHhcccchhc
Confidence 3477899999999999999999999999999999999999999999999999999999887764333
No 23
>KOG0483|consensus
Probab=99.43 E-value=4.8e-14 Score=119.81 Aligned_cols=62 Identities=35% Similarity=0.532 Sum_probs=57.8
Q ss_pred CCCCCcccCHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCCCCceeeccccchhHHHHHhhh
Q psy16800 135 NNSGRTNFTNKQLTELEKEFHFNKYLTRARRIEIASVLQLNETQVKIWFQNRRMKQKKRIKE 196 (221)
Q Consensus 135 ~rr~Rt~ft~~Ql~~Le~~F~~~~yps~~~r~~LA~~L~Lt~~qVqvWFQNRRaK~Kr~~k~ 196 (221)
..+++.+|+.+|+..||..|+.+.++....+..||.+|||.++||.||||||||+||.++.+
T Consensus 50 ~~~kk~Rlt~eQ~~~LE~~F~~~~~L~p~~K~~LAk~LgL~pRQVavWFQNRRARwK~kqlE 111 (198)
T KOG0483|consen 50 GKGKKRRLTSEQVKFLEKSFESEKKLEPERKKKLAKELGLQPRQVAVWFQNRRARWKTKQLE 111 (198)
T ss_pred cccccccccHHHHHHhHHhhccccccChHHHHHHHHhhCCChhHHHHHHhhccccccchhhh
Confidence 35556789999999999999999999999999999999999999999999999999988765
No 24
>KOG4577|consensus
Probab=99.41 E-value=9.3e-14 Score=122.81 Aligned_cols=70 Identities=31% Similarity=0.400 Sum_probs=65.0
Q ss_pred CCCCCCCcccCHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCCCCceeeccccchhHHHHHhhhccccCC
Q psy16800 133 LLNNSGRTNFTNKQLTELEKEFHFNKYLTRARRIEIASVLQLNETQVKIWFQNRRMKQKKRIKEGILIGV 202 (221)
Q Consensus 133 ~~~rr~Rt~ft~~Ql~~Le~~F~~~~yps~~~r~~LA~~L~Lt~~qVqvWFQNRRaK~Kr~~k~g~~~~~ 202 (221)
...||.||.+|..||+.|...|...+.|....|++|+.++||.-++|||||||||||+||.++..-.+.|
T Consensus 165 ~~nKRPRTTItAKqLETLK~AYn~SpKPARHVREQLsseTGLDMRVVQVWFQNRRAKEKRLKKDAGR~RW 234 (383)
T KOG4577|consen 165 ASNKRPRTTITAKQLETLKQAYNTSPKPARHVREQLSSETGLDMRVVQVWFQNRRAKEKRLKKDAGRTRW 234 (383)
T ss_pred cccCCCcceeeHHHHHHHHHHhcCCCchhHHHHHHhhhccCcceeehhhhhhhhhHHHHhhhhhcchhHH
Confidence 3569999999999999999999999999999999999999999999999999999999999998655544
No 25
>KOG0847|consensus
Probab=99.37 E-value=4.1e-13 Score=114.87 Aligned_cols=67 Identities=39% Similarity=0.639 Sum_probs=61.3
Q ss_pred CCCCCCCcccCHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCCCCceeeccccchhHHHHHhhhccc
Q psy16800 133 LLNNSGRTNFTNKQLTELEKEFHFNKYLTRARRIEIASVLQLNETQVKIWFQNRRMKQKKRIKEGIL 199 (221)
Q Consensus 133 ~~~rr~Rt~ft~~Ql~~Le~~F~~~~yps~~~r~~LA~~L~Lt~~qVqvWFQNRRaK~Kr~~k~g~~ 199 (221)
..++..|..|+-.|+..|+..|++.+|+-.++|.+||..++|++.||+|||||||.||||++.....
T Consensus 165 G~rk~srPTf~g~qi~~le~~feqtkylaG~~ra~lA~~lgmteSqvkVWFQNRRTKWRKkhAaEma 231 (288)
T KOG0847|consen 165 GQRKQSRPTFTGHQIYQLERKFEQTKYLAGADRAQLAQELNMTESQVKVWFQNRRTKWRKKHAAEMA 231 (288)
T ss_pred ccccccCCCccchhhhhhhhhhhhhhcccchhHHHhhccccccHHHHHHHHhcchhhhhhhhccchh
Confidence 4455668899999999999999999999999999999999999999999999999999999876543
No 26
>KOG0490|consensus
Probab=99.28 E-value=1.9e-12 Score=110.33 Aligned_cols=63 Identities=37% Similarity=0.499 Sum_probs=60.0
Q ss_pred CCCCCCCcccCHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCCCCceeeccccchhHHHHHhh
Q psy16800 133 LLNNSGRTNFTNKQLTELEKEFHFNKYLTRARRIEIASVLQLNETQVKIWFQNRRMKQKKRIK 195 (221)
Q Consensus 133 ~~~rr~Rt~ft~~Ql~~Le~~F~~~~yps~~~r~~LA~~L~Lt~~qVqvWFQNRRaK~Kr~~k 195 (221)
..+++.||.|+..|+.+|++.|+..+||+...++.||..+++++..|+|||||+|+||+++.+
T Consensus 58 ~~~rr~rt~~~~~ql~~ler~f~~~h~Pd~~~r~~la~~~~~~e~rVqvwFqnrrak~r~~~~ 120 (235)
T KOG0490|consen 58 FSKRCARCKFTISQLDELERAFEKVHLPCFACRECLALLLTGDEFRVQVWFQNRRAKDRKEER 120 (235)
T ss_pred ccccccCCCCCcCHHHHHHHhhcCCCcCccchHHHHhhcCCCCeeeeehhhhhhcHhhhhhhc
Confidence 456888999999999999999999999999999999999999999999999999999999875
No 27
>KOG1168|consensus
Probab=99.05 E-value=1.1e-10 Score=103.67 Aligned_cols=64 Identities=27% Similarity=0.397 Sum_probs=60.2
Q ss_pred CCCCCCcccCHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCCCCceeeccccchhHHHHHhhhc
Q psy16800 134 LNNSGRTNFTNKQLTELEKEFHFNKYLTRARRIEIASVLQLNETQVKIWFQNRRMKQKKRIKEG 197 (221)
Q Consensus 134 ~~rr~Rt~ft~~Ql~~Le~~F~~~~yps~~~r~~LA~~L~Lt~~qVqvWFQNRRaK~Kr~~k~g 197 (221)
.+||+||.+..-....||++|...+.|+.+.+..||.+|+|.+.+|+|||||.|+|.||.....
T Consensus 308 ekKRKRTSIAAPEKRsLEayFavQPRPS~EkIAaIAekLDLKKNVVRVWFCNQRQKQKRm~~Sa 371 (385)
T KOG1168|consen 308 EKKRKRTSIAAPEKRSLEAYFAVQPRPSGEKIAAIAEKLDLKKNVVRVWFCNQRQKQKRMKRSA 371 (385)
T ss_pred ccccccccccCcccccHHHHhccCCCCchhHHHHHHHhhhhhhceEEEEeeccHHHHHHhhhhh
Confidence 4789999999999999999999999999999999999999999999999999999999976653
No 28
>KOG0849|consensus
Probab=99.04 E-value=1.3e-10 Score=106.94 Aligned_cols=64 Identities=33% Similarity=0.487 Sum_probs=60.1
Q ss_pred cCCCCCCCcccCHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCCCCceeeccccchhHHHHHhh
Q psy16800 132 SLLNNSGRTNFTNKQLTELEKEFHFNKYLTRARRIEIASVLQLNETQVKIWFQNRRMKQKKRIK 195 (221)
Q Consensus 132 ~~~~rr~Rt~ft~~Ql~~Le~~F~~~~yps~~~r~~LA~~L~Lt~~qVqvWFQNRRaK~Kr~~k 195 (221)
....+|.||.|+..|+..|++.|+.++||++..|+.||.++++++..|+|||+|||++++|...
T Consensus 173 ~~~~rr~rtsft~~Q~~~le~~f~rt~yP~i~~Re~La~~i~l~e~riqvwf~nrra~~rr~~~ 236 (354)
T KOG0849|consen 173 QRGGRRNRTSFSPSQLEALEECFQRTPYPDIVGRETLAKETGLPEPRVQVWFQNRRAKWRRQHR 236 (354)
T ss_pred cccccccccccccchHHHHHHHhcCCCCCchhhHHHHhhhccCCchHHHHHHhhhhhhhhhccc
Confidence 3455777999999999999999999999999999999999999999999999999999999984
No 29
>KOG0775|consensus
Probab=98.69 E-value=2.3e-08 Score=88.18 Aligned_cols=55 Identities=29% Similarity=0.449 Sum_probs=48.8
Q ss_pred cCHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCCCCceeeccccchhHHHHHhhh
Q psy16800 142 FTNKQLTELEKEFHFNKYLTRARRIEIASVLQLNETQVKIWFQNRRMKQKKRIKE 196 (221)
Q Consensus 142 ft~~Ql~~Le~~F~~~~yps~~~r~~LA~~L~Lt~~qVqvWFQNRRaK~Kr~~k~ 196 (221)
|...-..+|..+|..++||+..++.+||..+||+..||-+||.|||+++|-...+
T Consensus 183 FKekSR~~LrewY~~~~YPsp~eKReLA~aTgLt~tQVsNWFKNRRQRDRa~~ak 237 (304)
T KOG0775|consen 183 FKEKSRSLLREWYLQNPYPSPREKRELAEATGLTITQVSNWFKNRRQRDRAAAAK 237 (304)
T ss_pred hhHhhHHHHHHHHhcCCCCChHHHHHHHHHhCCchhhhhhhhhhhhhhhhhcccc
Confidence 4445567999999999999999999999999999999999999999999955444
No 30
>KOG0774|consensus
Probab=98.44 E-value=3.1e-07 Score=80.82 Aligned_cols=62 Identities=27% Similarity=0.435 Sum_probs=56.6
Q ss_pred CCCCCCcccCHHHHHHHHHHhh---hCCCCCHHHHHHHHHHhCCCCCceeeccccchhHHHHHhh
Q psy16800 134 LNNSGRTNFTNKQLTELEKEFH---FNKYLTRARRIEIASVLQLNETQVKIWFQNRRMKQKKRIK 195 (221)
Q Consensus 134 ~~rr~Rt~ft~~Ql~~Le~~F~---~~~yps~~~r~~LA~~L~Lt~~qVqvWFQNRRaK~Kr~~k 195 (221)
..+|+|..|++.-.++|..+|. .++||+..++++||.+++++..||-.||.|+|-+.||-.-
T Consensus 187 darRKRRNFsK~aTeiLneyF~~h~~nPYPSee~K~eLAkqCnItvsQvsnwfgnkrIrykK~~~ 251 (334)
T KOG0774|consen 187 DARRKRRNFSKQATEILNEYFYSHLSNPYPSEEAKEELAKQCNITVSQVSNWFGNKRIRYKKNMG 251 (334)
T ss_pred HHHHhhcccchhHHHHHHHHHHHhcCCCCCcHHHHHHHHHHcCceehhhccccccceeehhhhhh
Confidence 3578899999999999999995 5889999999999999999999999999999999887544
No 31
>KOG2252|consensus
Probab=98.24 E-value=7.6e-07 Score=85.06 Aligned_cols=59 Identities=29% Similarity=0.304 Sum_probs=55.1
Q ss_pred cCCCCCCCcccCHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCCCCceeeccccchhHH
Q psy16800 132 SLLNNSGRTNFTNKQLTELEKEFHFNKYLTRARRIEIASVLQLNETQVKIWFQNRRMKQ 190 (221)
Q Consensus 132 ~~~~rr~Rt~ft~~Ql~~Le~~F~~~~yps~~~r~~LA~~L~Lt~~qVqvWFQNRRaK~ 190 (221)
....|+.|.+||..|...|..+|+.+++|+.+..+.|+.+|+|....|.+||-|.|.+.
T Consensus 417 ~~~~KKPRlVfTd~QkrTL~aiFke~~RPS~Emq~tIS~qL~L~~sTV~NfFmNaRRRs 475 (558)
T KOG2252|consen 417 MLQTKKPRLVFTDIQKRTLQAIFKENKRPSREMQETISQQLNLELSTVINFFMNARRRS 475 (558)
T ss_pred cccCCCceeeecHHHHHHHHHHHhcCCCCCHHHHHHHHHHhCCcHHHHHHHHHhhhhhc
Confidence 34567889999999999999999999999999999999999999999999999998874
No 32
>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=98.20 E-value=2.8e-07 Score=59.32 Aligned_cols=34 Identities=29% Similarity=0.540 Sum_probs=29.0
Q ss_pred hCCCCCHHHHHHHHHHhCCCCCceeeccccchhH
Q psy16800 156 FNKYLTRARRIEIASVLQLNETQVKIWFQNRRMK 189 (221)
Q Consensus 156 ~~~yps~~~r~~LA~~L~Lt~~qVqvWFQNRRaK 189 (221)
.++||+..+++.||.++||+..||..||-|.|.+
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 4789999999999999999999999999999875
No 33
>KOG0490|consensus
Probab=98.10 E-value=2.2e-06 Score=72.90 Aligned_cols=63 Identities=33% Similarity=0.461 Sum_probs=59.2
Q ss_pred CCCCCCCcccCHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCCCCceeeccccchhHHHHHhh
Q psy16800 133 LLNNSGRTNFTNKQLTELEKEFHFNKYLTRARRIEIASVLQLNETQVKIWFQNRRMKQKKRIK 195 (221)
Q Consensus 133 ~~~rr~Rt~ft~~Ql~~Le~~F~~~~yps~~~r~~LA~~L~Lt~~qVqvWFQNRRaK~Kr~~k 195 (221)
...++.|+.+...|+..|...|..+.+|+...++.|+..++++...|++||||+|++.++...
T Consensus 151 ~~~~~~~~~~~~~~~~~~~~~~~~~~~P~~~~~~~l~~~~~~~~~~~q~~~~~~~~~~~~~~~ 213 (235)
T KOG0490|consen 151 KKPRRPRTTFTENQLEVLETVFRATPKPDADDREQLAEETGLSERVIQVWFQNRRAKLRKHKR 213 (235)
T ss_pred cccCCCccccccchhHhhhhcccCCCCCchhhHHHHHHhcCCChhhhhhhcccHHHHHHhhcc
Confidence 345778999999999999999999999999999999999999999999999999999998766
No 34
>KOG1146|consensus
Probab=98.06 E-value=9.7e-06 Score=83.97 Aligned_cols=64 Identities=23% Similarity=0.299 Sum_probs=60.4
Q ss_pred CCCCCCcccCHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCCCCceeeccccchhHHHHHhhhc
Q psy16800 134 LNNSGRTNFTNKQLTELEKEFHFNKYLTRARRIEIASVLQLNETQVKIWFQNRRMKQKKRIKEG 197 (221)
Q Consensus 134 ~~rr~Rt~ft~~Ql~~Le~~F~~~~yps~~~r~~LA~~L~Lt~~qVqvWFQNRRaK~Kr~~k~g 197 (221)
.+++.|+.++..||..|..+|....|+...+.+.|-..+++..++|++||||.|+|.++....+
T Consensus 902 ~r~a~~~~~~d~qlk~i~~~~~~q~~~~~~~~E~l~~~~~~~~~~i~vw~qna~~~s~k~~~n~ 965 (1406)
T KOG1146|consen 902 GRRAYRTQESDLQLKIIKACYEAQRTPTMQECEVLEEPIGLPKRVIQVWFQNARAKSKKAKLNG 965 (1406)
T ss_pred hhhhhccchhHHHHHHHHHHHhhccCChHHHHHhhcccccCCcchhHHhhhhhhhhhhhhhhcc
Confidence 4577899999999999999999999999999999999999999999999999999999988865
No 35
>PF11569 Homez: Homeodomain leucine-zipper encoding, Homez; PDB: 2YS9_A.
Probab=96.23 E-value=0.0011 Score=45.75 Aligned_cols=41 Identities=24% Similarity=0.362 Sum_probs=31.0
Q ss_pred HHHHHHHhhhCCCCCHHHHHHHHHHhCCCCCceeeccccch
Q psy16800 147 LTELEKEFHFNKYLTRARRIEIASVLQLNETQVKIWFQNRR 187 (221)
Q Consensus 147 l~~Le~~F~~~~yps~~~r~~LA~~L~Lt~~qVqvWFQNRR 187 (221)
+..|+.+|....++...+...|+.+.+|+..||+.||-.+.
T Consensus 10 ~~pL~~Yy~~h~~L~E~DL~~L~~kS~ms~qqVr~WFa~~~ 50 (56)
T PF11569_consen 10 IQPLEDYYLKHKQLQEEDLDELCDKSRMSYQQVRDWFAERM 50 (56)
T ss_dssp -HHHHHHHHHT----TTHHHHHHHHTT--HHHHHHHHHHHS
T ss_pred hHHHHHHHHHcCCccHhhHHHHHHHHCCCHHHHHHHHHHhc
Confidence 45699999999999999999999999999999999996543
No 36
>KOG0773|consensus
Probab=96.07 E-value=0.0043 Score=56.56 Aligned_cols=61 Identities=18% Similarity=0.305 Sum_probs=50.6
Q ss_pred CCCCCcccCHHHHHHHHHHhh---hCCCCCHHHHHHHHHHhCCCCCceeeccccchhHHHHHhh
Q psy16800 135 NNSGRTNFTNKQLTELEKEFH---FNKYLTRARRIEIASVLQLNETQVKIWFQNRRMKQKKRIK 195 (221)
Q Consensus 135 ~rr~Rt~ft~~Ql~~Le~~F~---~~~yps~~~r~~LA~~L~Lt~~qVqvWFQNRRaK~Kr~~k 195 (221)
..|.+..+......+|+.... ..+||+..++..||.++||+..||.+||.|.|.+..+-..
T Consensus 239 ~~r~~~~lP~~a~~ilr~Wl~~h~~~PYPse~~K~~La~~TGLs~~Qv~NWFINaR~R~w~p~~ 302 (342)
T KOG0773|consen 239 KWRPQRGLPKEAVSILRAWLFEHLLHPYPSDDEKLMLAKQTGLSRPQVSNWFINARVRLWKPMI 302 (342)
T ss_pred CCCCCCCCCHHHHHHHHHHHHHhccCCCCcchhccccchhcCCCcccCCchhhhcccccCCchH
Confidence 455667899999999987743 2579999999999999999999999999999987664444
No 37
>KOG3623|consensus
Probab=94.66 E-value=0.023 Score=56.74 Aligned_cols=54 Identities=19% Similarity=0.303 Sum_probs=48.3
Q ss_pred cCHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCCCCceeeccccchhHHHHHhhh
Q psy16800 142 FTNKQLTELEKEFHFNKYLTRARRIEIASVLQLNETQVKIWFQNRRMKQKKRIKE 196 (221)
Q Consensus 142 ft~~Ql~~Le~~F~~~~yps~~~r~~LA~~L~Lt~~qVqvWFQNRRaK~Kr~~k~ 196 (221)
|+.. +..|..+|..|..|+..+...+|.+.+|..+.|+.||+++++......+.
T Consensus 564 ~~~p-~sllkayyaln~~ps~eelskia~qvglp~~vvk~wfE~~~a~e~sv~rs 617 (1007)
T KOG3623|consen 564 FNHP-TSLLKAYYALNGLPSEEELSKIAQQVGLPFAVVKAWFEDEEAEEMSVERS 617 (1007)
T ss_pred cCCc-HHHHHHHHHhcCCCCHHHHHHHHHHhcccHHHHHHHHHhhhhhhhhhccC
Confidence 4433 78999999999999999999999999999999999999999998876654
No 38
>PF04218 CENP-B_N: CENP-B N-terminal DNA-binding domain; InterPro: IPR006695 Centromere Protein B (CENP-B) is a DNA-binding protein localized to the centromere. Within the N-terminal 125 residues, there is a DNA-binding region, which binds to a corresponding 17bp CENP-B box sequence. CENP-B dimers either bind two separate DNA molecules or alternatively, they may bind two CENP-B boxes on one DNA molecule, with the intervening stretch of DNA forming a loop structure. The CENP-B DNA-binding domain consists of two repeating domains, RP1 and RP2. This family corresponds to RP1 has been shown to consist of four helices in a helix-turn-helix structure [].; GO: 0003677 DNA binding, 0000775 chromosome, centromeric region; PDB: 1BW6_A 1HLV_A 2ELH_A.
Probab=91.16 E-value=0.22 Score=33.59 Aligned_cols=47 Identities=17% Similarity=0.265 Sum_probs=36.0
Q ss_pred CCCCcccCHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCCCCceeeccccch
Q psy16800 136 NSGRTNFTNKQLTELEKEFHFNKYLTRARRIEIASVLQLNETQVKIWFQNRR 187 (221)
Q Consensus 136 rr~Rt~ft~~Ql~~Le~~F~~~~yps~~~r~~LA~~L~Lt~~qVqvWFQNRR 187 (221)
+|+|..+|-++-..+-..++... ....||..+|++..+|..|..|+.
T Consensus 1 krkR~~LTl~eK~~iI~~~e~g~-----s~~~ia~~fgv~~sTv~~I~K~k~ 47 (53)
T PF04218_consen 1 KRKRKSLTLEEKLEIIKRLEEGE-----SKRDIAREFGVSRSTVSTILKNKD 47 (53)
T ss_dssp SSSSSS--HHHHHHHHHHHHCTT------HHHHHHHHT--CCHHHHHHHCHH
T ss_pred CCCCccCCHHHHHHHHHHHHcCC-----CHHHHHHHhCCCHHHHHHHHHhHH
Confidence 46789999999888888888776 467899999999999999998753
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=67.25 E-value=3.1 Score=26.90 Aligned_cols=46 Identities=13% Similarity=0.147 Sum_probs=32.7
Q ss_pred ccCHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCCCCceeeccccchhHHH
Q psy16800 141 NFTNKQLTELEKEFHFNKYLTRARRIEIASVLQLNETQVKIWFQNRRMKQK 191 (221)
Q Consensus 141 ~ft~~Ql~~Le~~F~~~~yps~~~r~~LA~~L~Lt~~qVqvWFQNRRaK~K 191 (221)
.++..+..+|...|.. ...-.++|..+|++...|+.+...-..|.|
T Consensus 4 ~L~~~er~vi~~~y~~-----~~t~~eIa~~lg~s~~~V~~~~~~al~kLR 49 (50)
T PF04545_consen 4 QLPPREREVIRLRYFE-----GLTLEEIAERLGISRSTVRRILKRALKKLR 49 (50)
T ss_dssp TS-HHHHHHHHHHHTS-----T-SHHHHHHHHTSCHHHHHHHHHHHHHHHH
T ss_pred hCCHHHHHHHHHHhcC-----CCCHHHHHHHHCCcHHHHHHHHHHHHHHhc
Confidence 4678888999888832 233668899999999999887765444443
No 40
>KOG1146|consensus
Probab=65.19 E-value=20 Score=38.68 Aligned_cols=62 Identities=13% Similarity=0.116 Sum_probs=56.4
Q ss_pred CCCCCCCcccCHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCCCCceeeccccchhHHHHHh
Q psy16800 133 LLNNSGRTNFTNKQLTELEKEFHFNKYLTRARRIEIASVLQLNETQVKIWFQNRRMKQKKRI 194 (221)
Q Consensus 133 ~~~rr~Rt~ft~~Ql~~Le~~F~~~~yps~~~r~~LA~~L~Lt~~qVqvWFQNRRaK~Kr~~ 194 (221)
-+.+..++.+-.+++..|-+.|-.+.-|+...+..|......+.+++++||+|-+.+.++..
T Consensus 703 ~~~~~~~~~~~~~aa~~l~~a~~~~~sps~k~~~civcd~~st~~l~~l~~h~~~~rs~ke~ 764 (1406)
T KOG1146|consen 703 PRDKLLRLTILPEAAMILGRAYMQDNSPSLKVFDCIVCDVFSTDRLDQLWFHNTRERSRKEQ 764 (1406)
T ss_pred cccccCcccccHHHHhhhhhcccCCCCHHHHHHHHhhhhhhhhhhHHHHhhcchhhhhhhhc
Confidence 34577788888999999999999999999999999999999999999999999999988776
No 41
>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=61.26 E-value=7.4 Score=26.34 Aligned_cols=39 Identities=21% Similarity=0.283 Sum_probs=31.6
Q ss_pred cCHHHHHHHHHHhhhCC--CCCHHHHHHHHHHhCCCCCcee
Q psy16800 142 FTNKQLTELEKEFHFNK--YLTRARRIEIASVLQLNETQVK 180 (221)
Q Consensus 142 ft~~Ql~~Le~~F~~~~--yps~~~r~~LA~~L~Lt~~qVq 180 (221)
+|..|..+|...|...= +|-.....+||..||++...|.
T Consensus 1 LT~~Q~e~L~~A~~~GYfd~PR~~tl~elA~~lgis~st~~ 41 (53)
T PF04967_consen 1 LTDRQREILKAAYELGYFDVPRRITLEELAEELGISKSTVS 41 (53)
T ss_pred CCHHHHHHHHHHHHcCCCCCCCcCCHHHHHHHhCCCHHHHH
Confidence 57889999999998754 4767778899999999986543
No 42
>PF01527 HTH_Tnp_1: Transposase; InterPro: IPR002514 Transposase proteins are necessary for efficient DNA transposition. This family consists of various Escherichia coli insertion elements and other bacterial transposases some of which are members of the IS3 family. This region includes a helix-turn-helix motif (HTH) at the N terminus followed by a leucine zipper (LZ) motif. The LZ motif has been shown to mediate oligomerisation of the transposase components in IS911 []. More information about these proteins can be found at Protein of the Month: Transposase [].; GO: 0003677 DNA binding, 0004803 transposase activity, 0006313 transposition, DNA-mediated; PDB: 2JN6_A 2RN7_A.
Probab=57.64 E-value=3 Score=29.04 Aligned_cols=44 Identities=11% Similarity=0.188 Sum_probs=28.1
Q ss_pred CCCcccCHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCCCCceeeccc
Q psy16800 137 SGRTNFTNKQLTELEKEFHFNKYLTRARRIEIASVLQLNETQVKIWFQ 184 (221)
Q Consensus 137 r~Rt~ft~~Ql~~Le~~F~~~~yps~~~r~~LA~~L~Lt~~qVqvWFQ 184 (221)
++|..||.++...+-..+... ......+|..+||+..+|..|-.
T Consensus 2 ~~r~~ys~e~K~~~v~~~~~~----g~sv~~va~~~gi~~~~l~~W~~ 45 (76)
T PF01527_consen 2 RKRRRYSPEFKLQAVREYLES----GESVSEVAREYGISPSTLYNWRK 45 (76)
T ss_dssp -SS----HHHHHHHHHHHHHH----HCHHHHHHHHHTS-HHHHHHHHH
T ss_pred CCCCCCCHHHHHHHHHHHHHC----CCceEeeecccccccccccHHHH
Confidence 346789998888776666222 25677899999999998888753
No 43
>cd00569 HTH_Hin_like Helix-turn-helix domain of Hin and related proteins, a family of DNA-binding domains unique to bacteria and represented by the Hin protein of Salmonella. The basic HTH domain is a simple fold comprised of three core helices that form a right-handed helical bundle. The principal DNA-protein interface is formed by the third helix, the recognition helix, inserting itself into the major groove of the DNA. A diverse array of HTH domains participate in a variety of functions that depend on their DNA-binding properties. HTH_Hin represents one of the simplest versions of the HTH domains; the characterization of homologous relationships between various sequence-diverse HTH domain families remains difficult. The Hin recombinase induces the site-specific inversion of a chromosomal DNA segment containing a promoter, which controls the alternate expression of two genes by reversibly switching orientation. The Hin recombinase consists of a single polypeptide chain containing a D
Probab=51.46 E-value=19 Score=19.66 Aligned_cols=38 Identities=18% Similarity=0.231 Sum_probs=25.7
Q ss_pred ccCHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCCCCceeecc
Q psy16800 141 NFTNKQLTELEKEFHFNKYLTRARRIEIASVLQLNETQVKIWF 183 (221)
Q Consensus 141 ~ft~~Ql~~Le~~F~~~~yps~~~r~~LA~~L~Lt~~qVqvWF 183 (221)
.++..+...+...|... + ....+|..++++...|..|.
T Consensus 5 ~~~~~~~~~i~~~~~~~-~----s~~~ia~~~~is~~tv~~~~ 42 (42)
T cd00569 5 KLTPEQIEEARRLLAAG-E----SVAEIARRLGVSRSTLYRYL 42 (42)
T ss_pred cCCHHHHHHHHHHHHcC-C----CHHHHHHHHCCCHHHHHHhC
Confidence 45666666666666533 2 35578899999888777663
No 44
>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=50.33 E-value=5.2 Score=24.77 Aligned_cols=43 Identities=14% Similarity=0.175 Sum_probs=30.7
Q ss_pred ccCHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCCCCceeeccccchh
Q psy16800 141 NFTNKQLTELEKEFHFNKYLTRARRIEIASVLQLNETQVKIWFQNRRM 188 (221)
Q Consensus 141 ~ft~~Ql~~Le~~F~~~~yps~~~r~~LA~~L~Lt~~qVqvWFQNRRa 188 (221)
.++..+..++...|... ....++|..++++...|..|....+.
T Consensus 10 ~l~~~~~~~~~~~~~~~-----~~~~~ia~~~~~s~~~i~~~~~~~~~ 52 (55)
T cd06171 10 KLPEREREVILLRFGEG-----LSYEEIAEILGISRSTVRQRLHRALK 52 (55)
T ss_pred hCCHHHHHHHHHHHhcC-----CCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 45667777777766422 23567899999999999988865443
No 45
>PRK03975 tfx putative transcriptional regulator; Provisional
Probab=49.58 E-value=16 Score=29.72 Aligned_cols=51 Identities=20% Similarity=0.171 Sum_probs=38.8
Q ss_pred CcccCHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCCCCceeeccccchhHHHHHhh
Q psy16800 139 RTNFTNKQLTELEKEFHFNKYLTRARRIEIASVLQLNETQVKIWFQNRRMKQKKRIK 195 (221)
Q Consensus 139 Rt~ft~~Ql~~Le~~F~~~~yps~~~r~~LA~~L~Lt~~qVqvWFQNRRaK~Kr~~k 195 (221)
...+++.|..+|...+ .. ....++|..|+++...|..|-++.+.+.++...
T Consensus 4 ~~~Lt~rqreVL~lr~--~G----lTq~EIAe~LGiS~~tVs~ie~ra~kkLr~~~~ 54 (141)
T PRK03975 4 ESFLTERQIEVLRLRE--RG----LTQQEIADILGTSRANVSSIEKRARENIEKARE 54 (141)
T ss_pred ccCCCHHHHHHHHHHH--cC----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Confidence 3578899999997742 22 235689999999999999999987777665543
No 46
>PRK04217 hypothetical protein; Provisional
Probab=49.15 E-value=16 Score=28.41 Aligned_cols=53 Identities=15% Similarity=0.039 Sum_probs=39.8
Q ss_pred ccCHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCCCCceeeccccchhHHHHHhhhcc
Q psy16800 141 NFTNKQLTELEKEFHFNKYLTRARRIEIASVLQLNETQVKIWFQNRRMKQKKRIKEGI 198 (221)
Q Consensus 141 ~ft~~Ql~~Le~~F~~~~yps~~~r~~LA~~L~Lt~~qVqvWFQNRRaK~Kr~~k~g~ 198 (221)
.++.+|..++...|...- ...+||..++++...|...+...+.+.+.......
T Consensus 42 ~Lt~eereai~l~~~eGl-----S~~EIAk~LGIS~sTV~r~L~RArkkLre~L~~~~ 94 (110)
T PRK04217 42 FMTYEEFEALRLVDYEGL-----TQEEAGKRMGVSRGTVWRALTSARKKVAQMLVEGR 94 (110)
T ss_pred cCCHHHHHHHHHHHHcCC-----CHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHhcc
Confidence 567788877766664333 46689999999999999999877777776665543
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=42.43 E-value=7.7 Score=27.04 Aligned_cols=20 Identities=25% Similarity=0.524 Sum_probs=17.1
Q ss_pred HHHHHHHHhCCCCCceeecc
Q psy16800 164 RRIEIASVLQLNETQVKIWF 183 (221)
Q Consensus 164 ~r~~LA~~L~Lt~~qVqvWF 183 (221)
.-.+||.+|++++.+|+.|=
T Consensus 24 ~lkdIA~~Lgvs~~tIr~WK 43 (60)
T PF10668_consen 24 KLKDIAEKLGVSESTIRKWK 43 (60)
T ss_pred cHHHHHHHHCCCHHHHHHHh
Confidence 34578999999999999985
No 48
>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=40.38 E-value=15 Score=23.77 Aligned_cols=42 Identities=21% Similarity=0.284 Sum_probs=26.0
Q ss_pred cCHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCCCCceeeccccchh
Q psy16800 142 FTNKQLTELEKEFHFNKYLTRARRIEIASVLQLNETQVKIWFQNRRM 188 (221)
Q Consensus 142 ft~~Ql~~Le~~F~~~~yps~~~r~~LA~~L~Lt~~qVqvWFQNRRa 188 (221)
++..+..++.-.|- ....-.++|..+|++...|+.|.+.-|.
T Consensus 11 L~~~~r~i~~l~~~-----~g~s~~eIa~~l~~s~~~v~~~l~ra~~ 52 (54)
T PF08281_consen 11 LPERQREIFLLRYF-----QGMSYAEIAEILGISESTVKRRLRRARK 52 (54)
T ss_dssp S-HHHHHHHHHHHT-----S---HHHHHHHCTS-HHHHHHHHHHHHH
T ss_pred CCHHHHHHHHHHHH-----HCcCHHHHHHHHCcCHHHHHHHHHHHHh
Confidence 34455555544443 3345678999999999999999875443
No 49
>PF09607 BrkDBD: Brinker DNA-binding domain; InterPro: IPR018586 This DNA-binding domain is the first approx. 100 residues of the N-terminal end of Brinker. The structure of this domain in complex with DNA consists of four alpha-helices that contain a helix-turn-helix DNA recognition motif specific for GC-rich DNA. The Brinker nuclear repressor is a major element of the Drosophila Decapentaplegic morphogen signalling pathway []. ; PDB: 2GLO_A.
Probab=34.76 E-value=28 Score=24.13 Aligned_cols=45 Identities=16% Similarity=0.232 Sum_probs=23.1
Q ss_pred CcccCHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCCCCceeeccc
Q psy16800 139 RTNFTNKQLTELEKEFHFNKYLTRARRIEIASVLQLNETQVKIWFQ 184 (221)
Q Consensus 139 Rt~ft~~Ql~~Le~~F~~~~yps~~~r~~LA~~L~Lt~~qVqvWFQ 184 (221)
|..|+.......-.+|.....--...|. .|.++++++.+|+-|-+
T Consensus 3 rrsy~~~FKL~Vv~~a~~~~nc~~~~RA-aarkf~V~r~~Vr~W~k 47 (58)
T PF09607_consen 3 RRSYTAEFKLKVVEYAEKDNNCKGNQRA-AARKFNVSRRQVRKWRK 47 (58)
T ss_dssp -----HHHHHHHHHHHHH-TTTTT-HHH-HHHHTTS-HHHHHHHHT
T ss_pred ccccChHHHHHHHHHHHHccchhhhHHH-HHHHhCccHHHHHHHHH
Confidence 4456665544444444443322223343 49999999999999975
No 50
>COG3413 Predicted DNA binding protein [General function prediction only]
Probab=33.72 E-value=40 Score=28.51 Aligned_cols=48 Identities=21% Similarity=0.345 Sum_probs=37.4
Q ss_pred ccCHHHHHHHHHHhhhCC--CCCHHHHHHHHHHhCCCCCceeeccccchhHH
Q psy16800 141 NFTNKQLTELEKEFHFNK--YLTRARRIEIASVLQLNETQVKIWFQNRRMKQ 190 (221)
Q Consensus 141 ~ft~~Ql~~Le~~F~~~~--yps~~~r~~LA~~L~Lt~~qVqvWFQNRRaK~ 190 (221)
.+|..|+.+|...|...= ||-.....+||.+||+++..+ |..=||+..
T Consensus 155 ~LTdrQ~~vL~~A~~~GYFd~PR~~~l~dLA~~lGISkst~--~ehLRrAe~ 204 (215)
T COG3413 155 DLTDRQLEVLRLAYKMGYFDYPRRVSLKDLAKELGISKSTL--SEHLRRAER 204 (215)
T ss_pred cCCHHHHHHHHHHHHcCCCCCCccCCHHHHHHHhCCCHHHH--HHHHHHHHH
Confidence 799999999999998754 577888889999999998653 444444443
No 51
>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=33.45 E-value=20 Score=23.73 Aligned_cols=46 Identities=24% Similarity=0.122 Sum_probs=33.9
Q ss_pred ccCHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCCCCceeeccccchhHHHH
Q psy16800 141 NFTNKQLTELEKEFHFNKYLTRARRIEIASVLQLNETQVKIWFQNRRMKQKK 192 (221)
Q Consensus 141 ~ft~~Ql~~Le~~F~~~~yps~~~r~~LA~~L~Lt~~qVqvWFQNRRaK~Kr 192 (221)
.||..++.+|.-...-.. ..++|..+++++..|..+..+=+.|..-
T Consensus 3 ~LT~~E~~vl~~l~~G~~------~~eIA~~l~is~~tV~~~~~~i~~Kl~~ 48 (58)
T PF00196_consen 3 SLTERELEVLRLLAQGMS------NKEIAEELGISEKTVKSHRRRIMKKLGV 48 (58)
T ss_dssp SS-HHHHHHHHHHHTTS-------HHHHHHHHTSHHHHHHHHHHHHHHHHT-
T ss_pred ccCHHHHHHHHHHHhcCC------cchhHHhcCcchhhHHHHHHHHHHHhCC
Confidence 578888888877665433 6789999999999999988776666543
No 52
>PRK12526 RNA polymerase sigma factor; Provisional
Probab=33.11 E-value=36 Score=28.34 Aligned_cols=49 Identities=16% Similarity=0.156 Sum_probs=33.7
Q ss_pred cCHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCCCCceeeccccchhHHHHHhh
Q psy16800 142 FTNKQLTELEKEFHFNKYLTRARRIEIASVLQLNETQVKIWFQNRRMKQKKRIK 195 (221)
Q Consensus 142 ft~~Ql~~Le~~F~~~~yps~~~r~~LA~~L~Lt~~qVqvWFQNRRaK~Kr~~k 195 (221)
++..|..+|...| .......++|..+|++...|+++....+.+.++...
T Consensus 154 L~~~~r~vl~l~~-----~~g~s~~EIA~~lgis~~tV~~~l~Ra~~~Lr~~l~ 202 (206)
T PRK12526 154 LPEAQQTVVKGVY-----FQELSQEQLAQQLNVPLGTVKSRLRLALAKLKVQMG 202 (206)
T ss_pred CCHHHHHHHHHHH-----HcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHh
Confidence 4455555554333 222346789999999999999999877777766654
No 53
>TIGR03879 near_KaiC_dom probable regulatory domain. This model describes a common domain shared by two different families of proteins, each of which occurs regularly next to its corresponding partner family, a probable regulatory with homology to KaiC. By implication, this protein family likely is also involved in sensory transduction and/or regulation.
Probab=32.58 E-value=7.1 Score=28.27 Aligned_cols=35 Identities=20% Similarity=0.147 Sum_probs=26.1
Q ss_pred HHHhhhCCCCCHHHHHHHHHHhCCCCCceeecccc
Q psy16800 151 EKEFHFNKYLTRARRIEIASVLQLNETQVKIWFQN 185 (221)
Q Consensus 151 e~~F~~~~yps~~~r~~LA~~L~Lt~~qVqvWFQN 185 (221)
+..|....|.......+||..+++++..|+.|+.+
T Consensus 21 r~af~L~R~~eGlS~kEIAe~LGIS~~TVk~~l~~ 55 (73)
T TIGR03879 21 EAAAALAREEAGKTASEIAEELGRTEQTVRNHLKG 55 (73)
T ss_pred HHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHhc
Confidence 34455545445556779999999999999999864
No 54
>PRK09413 IS2 repressor TnpA; Reviewed
Probab=31.38 E-value=52 Score=25.36 Aligned_cols=43 Identities=12% Similarity=0.101 Sum_probs=29.2
Q ss_pred CCcccCHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCCCCceeeccc
Q psy16800 138 GRTNFTNKQLTELEKEFHFNKYLTRARRIEIASVLQLNETQVKIWFQ 184 (221)
Q Consensus 138 ~Rt~ft~~Ql~~Le~~F~~~~yps~~~r~~LA~~L~Lt~~qVqvWFQ 184 (221)
+|..|+.++....-.....+.+ ...++|..+|++..+|..|.+
T Consensus 9 ~rr~ys~EfK~~aV~~~~~~g~----sv~evA~e~gIs~~tl~~W~r 51 (121)
T PRK09413 9 KRRRRTTQEKIAIVQQSFEPGM----TVSLVARQHGVAASQLFLWRK 51 (121)
T ss_pred CCCCCCHHHHHHHHHHHHcCCC----CHHHHHHHHCcCHHHHHHHHH
Confidence 3566888876544443333332 355789999999999999953
No 55
>PRK09646 RNA polymerase sigma factor SigK; Reviewed
Probab=31.27 E-value=42 Score=27.47 Aligned_cols=49 Identities=14% Similarity=0.146 Sum_probs=34.5
Q ss_pred ccCHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCCCCceeeccccchhHHHHHh
Q psy16800 141 NFTNKQLTELEKEFHFNKYLTRARRIEIASVLQLNETQVKIWFQNRRMKQKKRI 194 (221)
Q Consensus 141 ~ft~~Ql~~Le~~F~~~~yps~~~r~~LA~~L~Lt~~qVqvWFQNRRaK~Kr~~ 194 (221)
.++..+..+|.-.|-.. ..-.++|..||++...|+++...-|.+.++..
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 45666666665544222 33568899999999999999987777666554
No 56
>PF08280 HTH_Mga: M protein trans-acting positive regulator (MGA) HTH domain; InterPro: IPR013199 Mga is a DNA-binding protein that activates the expression of several important virulence genes in group A streptococcus in response to changing environmental conditions [].; PDB: 2WTE_A 3SQN_A.
Probab=31.05 E-value=31 Score=23.24 Aligned_cols=35 Identities=34% Similarity=0.419 Sum_probs=26.4
Q ss_pred HHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCCCCceeec
Q psy16800 144 NKQLTELEKEFHFNKYLTRARRIEIASVLQLNETQVKIW 182 (221)
Q Consensus 144 ~~Ql~~Le~~F~~~~yps~~~r~~LA~~L~Lt~~qVqvW 182 (221)
..|+..|+-.+. +.+.+.. +||..++++++.|+.-
T Consensus 5 ~rq~~Ll~~L~~-~~~~~~~---ela~~l~~S~rti~~~ 39 (59)
T PF08280_consen 5 KRQLKLLELLLK-NKWITLK---ELAKKLNISERTIKND 39 (59)
T ss_dssp HHHHHHHHHHHH-HTSBBHH---HHHHHCTS-HHHHHHH
T ss_pred HHHHHHHHHHHc-CCCCcHH---HHHHHHCCCHHHHHHH
Confidence 357888888888 6666655 8999999999877643
No 57
>KOG3755|consensus
Probab=28.94 E-value=13 Score=37.10 Aligned_cols=60 Identities=18% Similarity=0.164 Sum_probs=36.5
Q ss_pred CCCCcccCHHHHHHH-HHHhhhCCCCCHHHHHHHHHHhCC-------CCCceeeccccchhHHHHHhh
Q psy16800 136 NSGRTNFTNKQLTEL-EKEFHFNKYLTRARRIEIASVLQL-------NETQVKIWFQNRRMKQKKRIK 195 (221)
Q Consensus 136 rr~Rt~ft~~Ql~~L-e~~F~~~~yps~~~r~~LA~~L~L-------t~~qVqvWFQNRRaK~Kr~~k 195 (221)
|+.+-.|-.+|...+ +..|..+..+......+--..+.| ...-|+.||.|||.++++.+-
T Consensus 692 k~~~~k~f~~~~~ev~~~w~~k~~s~s~~~v~eYkee~~~~~~~e~~~~kn~~~~fk~~~ee~~~~k~ 759 (769)
T KOG3755|consen 692 KKTIIKFFQNQRYEVKHHWKLKTRSGSWVDVAEYKEEELLMPYEEKFESKNVQFWFKVRREEEKRLKM 759 (769)
T ss_pred HHHHHHhhhcceeecchhheecccCchhHHHHHhhHHhhcchhhhhhhhcchHHHHHHHHHHHhhhhc
Confidence 444444444444433 334566666666655554444443 346799999999999887653
No 58
>PRK12512 RNA polymerase sigma factor; Provisional
Probab=28.72 E-value=49 Score=26.61 Aligned_cols=51 Identities=14% Similarity=0.106 Sum_probs=36.5
Q ss_pred ccCHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCCCCceeeccccchhHHHHHhhh
Q psy16800 141 NFTNKQLTELEKEFHFNKYLTRARRIEIASVLQLNETQVKIWFQNRRMKQKKRIKE 196 (221)
Q Consensus 141 ~ft~~Ql~~Le~~F~~~~yps~~~r~~LA~~L~Lt~~qVqvWFQNRRaK~Kr~~k~ 196 (221)
.++..+..+|...|-. ...-.+||..||++...|+.++..-|.+.+.....
T Consensus 131 ~L~~~~r~v~~l~~~~-----g~s~~eIA~~l~is~~tV~~~l~ra~~~Lr~~l~~ 181 (184)
T PRK12512 131 TLPPRQRDVVQSISVE-----GASIKETAAKLSMSEGAVRVALHRGLAALAAKFRS 181 (184)
T ss_pred hCCHHHHHHHHHHHHc-----CCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhc
Confidence 4555666666555433 23356899999999999999998888777766543
No 59
>PRK06759 RNA polymerase factor sigma-70; Validated
Probab=28.60 E-value=44 Score=25.90 Aligned_cols=47 Identities=17% Similarity=0.133 Sum_probs=32.3
Q ss_pred ccCHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCCCCceeeccccchhHHHH
Q psy16800 141 NFTNKQLTELEKEFHFNKYLTRARRIEIASVLQLNETQVKIWFQNRRMKQKK 192 (221)
Q Consensus 141 ~ft~~Ql~~Le~~F~~~~yps~~~r~~LA~~L~Lt~~qVqvWFQNRRaK~Kr 192 (221)
.++..+..++...|-.. ....++|..+|++...|+.|...-+.+.|+
T Consensus 106 ~L~~~~r~ii~l~~~~~-----~s~~EIA~~l~is~~tV~~~~~ra~~~Lr~ 152 (154)
T PRK06759 106 VLDEKEKYIIFERFFVG-----KTMGEIALETEMTYYQVRWIYRQALEKMRN 152 (154)
T ss_pred hCCHHHHHHHHHHHhcC-----CCHHHHHHHHCCCHHHHHHHHHHHHHHHhh
Confidence 45556666665544332 336789999999999999998765555543
No 60
>PRK09642 RNA polymerase sigma factor SigW; Reviewed
Probab=27.90 E-value=53 Score=25.69 Aligned_cols=50 Identities=18% Similarity=0.092 Sum_probs=34.1
Q ss_pred cCHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCCCCceeeccccchhHHHHHhhh
Q psy16800 142 FTNKQLTELEKEFHFNKYLTRARRIEIASVLQLNETQVKIWFQNRRMKQKKRIKE 196 (221)
Q Consensus 142 ft~~Ql~~Le~~F~~~~yps~~~r~~LA~~L~Lt~~qVqvWFQNRRaK~Kr~~k~ 196 (221)
++..+..++.-.|-.. ..-.++|..+|++...|++++..-|.+.|+..+.
T Consensus 107 Lp~~~r~v~~l~~~~g-----~s~~EIA~~lgis~~tV~~~l~Rar~~Lr~~l~~ 156 (160)
T PRK09642 107 LPENYRDVVLAHYLEE-----KSYQEIALQEKIEVKTVEMKLYRARKWIKKHWKE 156 (160)
T ss_pred CCHHHHHHHHHHHHhC-----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHhh
Confidence 4555555554443222 2356889999999999999998777777766543
No 61
>KOG3623|consensus
Probab=27.19 E-value=36 Score=34.93 Aligned_cols=60 Identities=15% Similarity=0.177 Sum_probs=44.1
Q ss_pred CCCcccCHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCCCCceeeccccchhHHHHHhhh
Q psy16800 137 SGRTNFTNKQLTELEKEFHFNKYLTRARRIEIASVLQLNETQVKIWFQNRRMKQKKRIKE 196 (221)
Q Consensus 137 r~Rt~ft~~Ql~~Le~~F~~~~yps~~~r~~LA~~L~Lt~~qVqvWFQNRRaK~Kr~~k~ 196 (221)
+.++.+...+-..|...+..+..++..+-..++..|...+.+|.+||++|+..-+.....
T Consensus 628 kv~sp~k~~dq~ql~~a~elq~s~~n~~~pl~~t~~~n~~pv~ev~dhsrsstpsp~pl~ 687 (1007)
T KOG3623|consen 628 KVRSPIKEEDQQQLKQAYELQASPSNDEFPLIATRLQNDPPVVEVWDHSRSSTPSPMPLF 687 (1007)
T ss_pred cccCCCCccchhhhHhhhhcccCccCcccchhhhhccCCCcchhhcccCCCCCCCCCccc
Confidence 345666666777778888777766666666667778888899999999999876655443
No 62
>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=26.84 E-value=17 Score=22.70 Aligned_cols=21 Identities=10% Similarity=0.127 Sum_probs=17.7
Q ss_pred HHHHHHHhCCCCCceeecccc
Q psy16800 165 RIEIASVLQLNETQVKIWFQN 185 (221)
Q Consensus 165 r~~LA~~L~Lt~~qVqvWFQN 185 (221)
..++|..+|++...|+.|.++
T Consensus 3 ~~e~a~~~gv~~~tlr~~~~~ 23 (49)
T cd04761 3 IGELAKLTGVSPSTLRYYERI 23 (49)
T ss_pred HHHHHHHHCcCHHHHHHHHHC
Confidence 457899999999999999643
No 63
>COG4367 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=26.82 E-value=46 Score=25.16 Aligned_cols=39 Identities=23% Similarity=0.255 Sum_probs=29.5
Q ss_pred ccCHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCCCCce
Q psy16800 141 NFTNKQLTELEKEFHFNKYLTRARRIEIASVLQLNETQV 179 (221)
Q Consensus 141 ~ft~~Ql~~Le~~F~~~~yps~~~r~~LA~~L~Lt~~qV 179 (221)
.++++|...-...|+.|--.+....+++|..|++++..|
T Consensus 2 SLn~eq~~~Tk~elqan~el~~LS~~~iA~~Ln~t~~~l 40 (97)
T COG4367 2 SLNPEQKQRTKQELQANFELCPLSDEEIATALNWTEVKL 40 (97)
T ss_pred CCCHHHHHHHHHHHHHhhhhccccHHHHHHHhCCCHHHH
Confidence 356778777777777777677777889999999887543
No 64
>PRK09652 RNA polymerase sigma factor RpoE; Provisional
Probab=26.55 E-value=52 Score=25.91 Aligned_cols=49 Identities=12% Similarity=0.053 Sum_probs=34.4
Q ss_pred ccCHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCCCCceeeccccchhHHHHHh
Q psy16800 141 NFTNKQLTELEKEFHFNKYLTRARRIEIASVLQLNETQVKIWFQNRRMKQKKRI 194 (221)
Q Consensus 141 ~ft~~Ql~~Le~~F~~~~yps~~~r~~LA~~L~Lt~~qVqvWFQNRRaK~Kr~~ 194 (221)
.+++.+..+|...|-.. ....++|..+|++...|+.|...-+.+.++..
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 46667777776654322 23558899999999999999986666665543
No 65
>PRK12533 RNA polymerase sigma factor; Provisional
Probab=26.51 E-value=77 Score=26.89 Aligned_cols=51 Identities=12% Similarity=-0.029 Sum_probs=34.6
Q ss_pred ccCHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCCCCceeeccccchhHHHHHhhh
Q psy16800 141 NFTNKQLTELEKEFHFNKYLTRARRIEIASVLQLNETQVKIWFQNRRMKQKKRIKE 196 (221)
Q Consensus 141 ~ft~~Ql~~Le~~F~~~~yps~~~r~~LA~~L~Lt~~qVqvWFQNRRaK~Kr~~k~ 196 (221)
.++..+..+|...|-. ...-.++|..||+++..|+++...-|.+.++....
T Consensus 134 ~Lp~~~R~v~~L~y~e-----g~s~~EIAe~LgiS~~tVk~~L~RAr~~Lr~~l~~ 184 (216)
T PRK12533 134 KLPVEYREVLVLRELE-----DMSYREIAAIADVPVGTVMSRLARARRRLAALLGG 184 (216)
T ss_pred cCCHHHHhHhhhHHhc-----CCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHcc
Confidence 3444455555443332 22356889999999999999998777777776654
No 66
>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=25.85 E-value=49 Score=24.62 Aligned_cols=47 Identities=19% Similarity=0.207 Sum_probs=31.5
Q ss_pred ccCHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCCCCceeeccccchhHHHH
Q psy16800 141 NFTNKQLTELEKEFHFNKYLTRARRIEIASVLQLNETQVKIWFQNRRMKQKK 192 (221)
Q Consensus 141 ~ft~~Ql~~Le~~F~~~~yps~~~r~~LA~~L~Lt~~qVqvWFQNRRaK~Kr 192 (221)
.++..|..+|...|-. .....++|..+|+++..|..|...-+.+.++
T Consensus 110 ~L~~~~~~ii~~~~~~-----g~s~~eIA~~l~~s~~~v~~~~~~~~~kl~~ 156 (158)
T TIGR02937 110 KLPEREREVLVLRYLE-----GLSYKEIAEILGISVGTVKRRLKRARKKLRE 156 (158)
T ss_pred hCCHHHHHHHhhHHhc-----CCCHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Confidence 4456666665544332 2345689999999999999988765555443
No 67
>PRK12515 RNA polymerase sigma factor; Provisional
Probab=25.82 E-value=64 Score=26.17 Aligned_cols=52 Identities=13% Similarity=0.183 Sum_probs=36.9
Q ss_pred ccCHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCCCCceeeccccchhHHHHHhhhc
Q psy16800 141 NFTNKQLTELEKEFHFNKYLTRARRIEIASVLQLNETQVKIWFQNRRMKQKKRIKEG 197 (221)
Q Consensus 141 ~ft~~Ql~~Le~~F~~~~yps~~~r~~LA~~L~Lt~~qVqvWFQNRRaK~Kr~~k~g 197 (221)
.++..+..+|.-.|-. ...-.++|..+|++...|++....-|.+.++.....
T Consensus 131 ~L~~~~r~vl~l~~~~-----~~s~~eIA~~lgis~~tV~~~l~Rar~~Lr~~l~~~ 182 (189)
T PRK12515 131 KLSPAHREIIDLVYYH-----EKSVEEVGEIVGIPESTVKTRMFYARKKLAELLKAA 182 (189)
T ss_pred hCCHHHHHHHHHHHHc-----CCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHHh
Confidence 4555666666544332 223568899999999999999988888887776653
No 68
>smart00421 HTH_LUXR helix_turn_helix, Lux Regulon. lux regulon (activates the bioluminescence operon
Probab=25.81 E-value=53 Score=20.44 Aligned_cols=42 Identities=24% Similarity=0.188 Sum_probs=29.1
Q ss_pred ccCHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCCCCceeeccccchh
Q psy16800 141 NFTNKQLTELEKEFHFNKYLTRARRIEIASVLQLNETQVKIWFQNRRM 188 (221)
Q Consensus 141 ~ft~~Ql~~Le~~F~~~~yps~~~r~~LA~~L~Lt~~qVqvWFQNRRa 188 (221)
.++..+..++...+. . ....++|..++++...|..|.+.-+.
T Consensus 3 ~l~~~e~~i~~~~~~-g-----~s~~eia~~l~is~~tv~~~~~~~~~ 44 (58)
T smart00421 3 SLTPREREVLRLLAE-G-----LTNKEIAERLGISEKTVKTHLSNIMR 44 (58)
T ss_pred CCCHHHHHHHHHHHc-C-----CCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 367777777755432 2 24568899999999999888764433
No 69
>PRK12514 RNA polymerase sigma factor; Provisional
Probab=25.77 E-value=35 Score=27.39 Aligned_cols=47 Identities=9% Similarity=0.256 Sum_probs=31.4
Q ss_pred cCHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCCCCceeeccccchhHHHHH
Q psy16800 142 FTNKQLTELEKEFHFNKYLTRARRIEIASVLQLNETQVKIWFQNRRMKQKKR 193 (221)
Q Consensus 142 ft~~Ql~~Le~~F~~~~yps~~~r~~LA~~L~Lt~~qVqvWFQNRRaK~Kr~ 193 (221)
++..+..+|.-.|- .....+++|..+|+++..|+++.+.-|.+.|+.
T Consensus 130 L~~~~r~i~~l~~~-----~g~s~~eIA~~lgis~~tV~~~l~Rar~~Lr~~ 176 (179)
T PRK12514 130 LEKDRAAAVRRAYL-----EGLSYKELAERHDVPLNTMRTWLRRSLLKLREC 176 (179)
T ss_pred CCHHHHHHHHHHHH-----cCCCHHHHHHHHCCChHHHHHHHHHHHHHHHHH
Confidence 44445544444442 223367899999999999999988666666554
No 70
>PRK12546 RNA polymerase sigma factor; Provisional
Probab=24.82 E-value=78 Score=26.05 Aligned_cols=33 Identities=15% Similarity=0.051 Sum_probs=27.4
Q ss_pred HHHHHHHHhCCCCCceeeccccchhHHHHHhhh
Q psy16800 164 RRIEIASVLQLNETQVKIWFQNRRMKQKKRIKE 196 (221)
Q Consensus 164 ~r~~LA~~L~Lt~~qVqvWFQNRRaK~Kr~~k~ 196 (221)
...++|..||++...|+++++.-|.+.|+....
T Consensus 131 s~~EIA~~LgiS~~tVk~~l~Rar~~Lr~~l~~ 163 (188)
T PRK12546 131 SYEEAAEMCGVAVGTVKSRANRARARLAELLQL 163 (188)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHhc
Confidence 356889999999999999999877777766554
No 71
>PF13518 HTH_28: Helix-turn-helix domain
Probab=24.54 E-value=23 Score=22.45 Aligned_cols=22 Identities=23% Similarity=0.368 Sum_probs=18.4
Q ss_pred HHHHHHHhCCCCCceeeccccc
Q psy16800 165 RIEIASVLQLNETQVKIWFQNR 186 (221)
Q Consensus 165 r~~LA~~L~Lt~~qVqvWFQNR 186 (221)
..++|.+++++..+|..|.+.-
T Consensus 15 ~~~~a~~~gis~~tv~~w~~~y 36 (52)
T PF13518_consen 15 VREIAREFGISRSTVYRWIKRY 36 (52)
T ss_pred HHHHHHHHCCCHhHHHHHHHHH
Confidence 4568999999999999998643
No 72
>PHA02955 hypothetical protein; Provisional
Probab=24.36 E-value=97 Score=26.95 Aligned_cols=45 Identities=16% Similarity=0.090 Sum_probs=34.7
Q ss_pred HHHHHHHHHHhhhC-CCCCHHHHHHHHHHhCCCCCceeeccccchh
Q psy16800 144 NKQLTELEKEFHFN-KYLTRARRIEIASVLQLNETQVKIWFQNRRM 188 (221)
Q Consensus 144 ~~Ql~~Le~~F~~~-~yps~~~r~~LA~~L~Lt~~qVqvWFQNRRa 188 (221)
..|+..|-+.|... .-++..++.+++.+||+....|..||.+--.
T Consensus 60 ~~sf~lli~a~~Et~~~Lp~~qk~~ia~~lgI~~~~~~~d~~t~~~ 105 (213)
T PHA02955 60 EKNFQLLIEALIETIENFPEKEQKEIAADIGINIDDYKAGKKTDLQ 105 (213)
T ss_pred HHHHHHHHHHHHHHHHhCCHHHHHHHHHHhCCChhhccCcccchhh
Confidence 35666666666554 6678899999999999998888999987543
No 73
>PRK12518 RNA polymerase sigma factor; Provisional
Probab=23.82 E-value=37 Score=27.03 Aligned_cols=38 Identities=24% Similarity=0.240 Sum_probs=30.2
Q ss_pred CCCHHHHHHHHHHhCCCCCceeeccccchhHHHHHhhh
Q psy16800 159 YLTRARRIEIASVLQLNETQVKIWFQNRRMKQKKRIKE 196 (221)
Q Consensus 159 yps~~~r~~LA~~L~Lt~~qVqvWFQNRRaK~Kr~~k~ 196 (221)
|.....-.++|..+|++...|++.+..-|.+.++....
T Consensus 133 ~~~g~s~~eIA~~lg~s~~tv~~~l~Rar~~L~~~l~~ 170 (175)
T PRK12518 133 DLEDLPQKEIAEILNIPVGTVKSRLFYARRQLRKFLQQ 170 (175)
T ss_pred HhcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHh
Confidence 34444577899999999999999998888887776654
No 74
>PRK11924 RNA polymerase sigma factor; Provisional
Probab=22.98 E-value=68 Score=25.12 Aligned_cols=49 Identities=18% Similarity=0.150 Sum_probs=32.6
Q ss_pred cCHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCCCCceeeccccchhHHHHHhh
Q psy16800 142 FTNKQLTELEKEFHFNKYLTRARRIEIASVLQLNETQVKIWFQNRRMKQKKRIK 195 (221)
Q Consensus 142 ft~~Ql~~Le~~F~~~~yps~~~r~~LA~~L~Lt~~qVqvWFQNRRaK~Kr~~k 195 (221)
++..+..+|...|- ....-.++|..+|++...|..|..--|.+.|+...
T Consensus 126 L~~~~r~i~~l~~~-----~~~~~~eIA~~lgis~~tv~~~~~ra~~~lr~~l~ 174 (179)
T PRK11924 126 LPVKQREVFLLRYV-----EGLSYREIAEILGVPVGTVKSRLRRARQLLRECLE 174 (179)
T ss_pred CCHHHHHHhhHHHH-----cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Confidence 44444444444432 22345789999999999999999877766665443
No 75
>PRK10072 putative transcriptional regulator; Provisional
Probab=22.90 E-value=27 Score=26.41 Aligned_cols=41 Identities=22% Similarity=0.266 Sum_probs=29.5
Q ss_pred ccCHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCCCCceeeccccchh
Q psy16800 141 NFTNKQLTELEKEFHFNKYLTRARRIEIASVLQLNETQVKIWFQNRRM 188 (221)
Q Consensus 141 ~ft~~Ql~~Le~~F~~~~yps~~~r~~LA~~L~Lt~~qVqvWFQNRRa 188 (221)
+.+...+..|...... ...+||..+|++...|..|.+.+|.
T Consensus 32 ~~~~~eik~LR~~~gl-------TQ~elA~~lGvS~~TVs~WE~G~r~ 72 (96)
T PRK10072 32 TTSFTEFEQLRKGTGL-------KIDDFARVLGVSVAMVKEWESRRVK 72 (96)
T ss_pred cCChHHHHHHHHHcCC-------CHHHHHHHhCCCHHHHHHHHcCCCC
Confidence 3456666666443322 2668999999999999999988774
No 76
>PRK12535 RNA polymerase sigma factor; Provisional
Probab=22.89 E-value=81 Score=26.11 Aligned_cols=55 Identities=9% Similarity=0.013 Sum_probs=38.6
Q ss_pred cCHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCCCCceeeccccchhHHHHHhhhccccC
Q psy16800 142 FTNKQLTELEKEFHFNKYLTRARRIEIASVLQLNETQVKIWFQNRRMKQKKRIKEGILIG 201 (221)
Q Consensus 142 ft~~Ql~~Le~~F~~~~yps~~~r~~LA~~L~Lt~~qVqvWFQNRRaK~Kr~~k~g~~~~ 201 (221)
++..+..++.-.|-.. ..-.++|..|+++...|+++...-|.+.|+....+++.+
T Consensus 134 Lp~~~r~v~~l~~~~g-----~s~~EIAe~lgis~~tV~~~l~Rar~~Lr~~l~~~~~~~ 188 (196)
T PRK12535 134 LPPERREALILTQVLG-----YTYEEAAKIADVRVGTIRSRVARARADLIAATATGQASA 188 (196)
T ss_pred CCHHHHHHhhhHHHhC-----CCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhccccchh
Confidence 4455555554443222 235689999999999999999888888887777766554
No 77
>PRK09639 RNA polymerase sigma factor SigX; Provisional
Probab=22.86 E-value=86 Score=24.53 Aligned_cols=49 Identities=24% Similarity=0.244 Sum_probs=35.2
Q ss_pred ccCHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCCCCceeeccccchhHHHHHhh
Q psy16800 141 NFTNKQLTELEKEFHFNKYLTRARRIEIASVLQLNETQVKIWFQNRRMKQKKRIK 195 (221)
Q Consensus 141 ~ft~~Ql~~Le~~F~~~~yps~~~r~~LA~~L~Lt~~qVqvWFQNRRaK~Kr~~k 195 (221)
.++..+..+|.-.| .. ..-.+||..+|++...|+.+...-+.+.|+...
T Consensus 112 ~L~~~~r~il~l~~--~g----~s~~eIA~~lgis~~tV~~~i~ra~~~Lr~~l~ 160 (166)
T PRK09639 112 KMTERDRTVLLLRF--SG----YSYKEIAEALGIKESSVGTTLARAKKKFRKIYE 160 (166)
T ss_pred cCCHHHHHHHHHHH--cC----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Confidence 45666666666666 22 235688999999999999999777776666544
No 78
>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=22.83 E-value=28 Score=23.77 Aligned_cols=21 Identities=29% Similarity=0.330 Sum_probs=18.0
Q ss_pred HHHHHHHHhCCCCCceeeccc
Q psy16800 164 RRIEIASVLQLNETQVKIWFQ 184 (221)
Q Consensus 164 ~r~~LA~~L~Lt~~qVqvWFQ 184 (221)
...+||..||++...|..|-+
T Consensus 15 ~~~eIA~~Lg~~~~TV~~W~~ 35 (58)
T PF06056_consen 15 SIKEIAEELGVPRSTVYSWKD 35 (58)
T ss_pred CHHHHHHHHCCChHHHHHHHH
Confidence 356889999999999999974
No 79
>KOG0773|consensus
Probab=22.75 E-value=41 Score=30.50 Aligned_cols=45 Identities=36% Similarity=0.585 Sum_probs=37.2
Q ss_pred HHHhhhCCCCCHHHHHHHHHHhCCCCCceeeccccchhHHHHHhh
Q psy16800 151 EKEFHFNKYLTRARRIEIASVLQLNETQVKIWFQNRRMKQKKRIK 195 (221)
Q Consensus 151 e~~F~~~~yps~~~r~~LA~~L~Lt~~qVqvWFQNRRaK~Kr~~k 195 (221)
...-..+.|++..+...|+....|+-.+|.+||-|.|.+.+....
T Consensus 113 ~~~~~~~~~~~k~~~~ll~~~~~~~~~~~~~~~~~a~r~~~~~~~ 157 (342)
T KOG0773|consen 113 LEEHRLNPYPSKLEKILLAVITKLTLTQVSTWFANARRRLKKELK 157 (342)
T ss_pred hhhhhhccCchHHHHHHHHHHHHhhhhhHHHHHHHHHHHHHhccC
Confidence 334456889999999999999999999999999998887665444
No 80
>TIGR02948 SigW_bacill RNA polymerase sigma-W factor. This sigma factor is restricted to certain lineages of the order Bacillales.
Probab=22.62 E-value=67 Score=25.68 Aligned_cols=49 Identities=18% Similarity=0.200 Sum_probs=33.6
Q ss_pred ccCHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCCCCceeeccccchhHHHHHh
Q psy16800 141 NFTNKQLTELEKEFHFNKYLTRARRIEIASVLQLNETQVKIWFQNRRMKQKKRI 194 (221)
Q Consensus 141 ~ft~~Ql~~Le~~F~~~~yps~~~r~~LA~~L~Lt~~qVqvWFQNRRaK~Kr~~ 194 (221)
.++..+..+|...|- ....-.++|..+|++...|+++++.-|.+.+...
T Consensus 136 ~L~~~~r~v~~l~~~-----~g~s~~eIA~~lgis~~~v~~~l~Rar~~Lr~~l 184 (187)
T TIGR02948 136 ALPPKYRMVIVLKYM-----EDLSLKEISEILDLPVGTVKTRIHRGREALRKQL 184 (187)
T ss_pred hCCHHHhHHhhhHHh-----cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHh
Confidence 455555555554332 2334678899999999999999987666666543
No 81
>PRK09480 slmA division inhibitor protein; Provisional
Probab=22.52 E-value=62 Score=25.85 Aligned_cols=41 Identities=15% Similarity=0.179 Sum_probs=32.7
Q ss_pred HHHHHHHhhhCCCCCHHHHHHHHHHhCCCCCceeeccccchh
Q psy16800 147 LTELEKEFHFNKYLTRARRIEIASVLQLNETQVKIWFQNRRM 188 (221)
Q Consensus 147 l~~Le~~F~~~~yps~~~r~~LA~~L~Lt~~qVqvWFQNRRa 188 (221)
+......|..+.. .......||...|++...+-.+|.|+-.
T Consensus 16 l~aa~~l~~~~~G-~~~ti~~Ia~~agvs~gt~Y~~F~~K~~ 56 (194)
T PRK09480 16 LQALAQMLESPPG-ERITTAKLAARVGVSEAALYRHFPSKAR 56 (194)
T ss_pred HHHHHHHHHhcCC-CccCHHHHHHHhCCCHhHHHHHCCCHHH
Confidence 3344455666656 7788899999999999999999999874
No 82
>PRK00118 putative DNA-binding protein; Validated
Probab=21.84 E-value=82 Score=24.18 Aligned_cols=49 Identities=16% Similarity=0.005 Sum_probs=34.2
Q ss_pred ccCHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCCCCceeeccccchhHHHHHh
Q psy16800 141 NFTNKQLTELEKEFHFNKYLTRARRIEIASVLQLNETQVKIWFQNRRMKQKKRI 194 (221)
Q Consensus 141 ~ft~~Ql~~Le~~F~~~~yps~~~r~~LA~~L~Lt~~qVqvWFQNRRaK~Kr~~ 194 (221)
.++..|..++...|.... ...+||..+|++...|..|....|.+.+...
T Consensus 17 ~L~ekqRevl~L~y~eg~-----S~~EIAe~lGIS~~TV~r~L~RArkkLr~~~ 65 (104)
T PRK00118 17 LLTEKQRNYMELYYLDDY-----SLGEIAEEFNVSRQAVYDNIKRTEKLLEDYE 65 (104)
T ss_pred cCCHHHHHHHHHHHHcCC-----CHHHHHHHHCcCHHHHHHHHHHHHHHHHHHH
Confidence 345666666655554432 3567899999999999999986666655543
No 83
>PRK12519 RNA polymerase sigma factor; Provisional
Probab=21.79 E-value=62 Score=26.28 Aligned_cols=33 Identities=21% Similarity=0.166 Sum_probs=26.3
Q ss_pred HHHHHHHHHHhCCCCCceeeccccchhHHHHHh
Q psy16800 162 RARRIEIASVLQLNETQVKIWFQNRRMKQKKRI 194 (221)
Q Consensus 162 ~~~r~~LA~~L~Lt~~qVqvWFQNRRaK~Kr~~ 194 (221)
.....++|..+|++...|+.|+...|.+.++..
T Consensus 157 g~s~~EIA~~lgis~~tV~~~l~Ra~~~Lr~~l 189 (194)
T PRK12519 157 GLSQSEIAKRLGIPLGTVKARARQGLLKLRELL 189 (194)
T ss_pred CCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHH
Confidence 344678999999999999999987776666543
No 84
>KOG3816|consensus
Probab=21.79 E-value=1.7e+02 Score=28.01 Aligned_cols=33 Identities=24% Similarity=0.494 Sum_probs=24.6
Q ss_pred cCCCCCCCccccchhHHHHHhhhhcCCCCCCCCCCCCCC
Q psy16800 18 DENKGGVGGEVGKVGEEMKEKEEERLPGEGREGEERDFS 56 (221)
Q Consensus 18 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 56 (221)
..|.||++|+.-++++++ |-|+++-+|..+|+.
T Consensus 189 ~kN~G~~~G~~A~~~~~~------r~P~~~~~G~S~~LP 221 (526)
T KOG3816|consen 189 EKNTGRPPGEAAEEAKKC------RPPNKPQKGPSHDLP 221 (526)
T ss_pred cccCCCCCCcchhhcccC------CCCCCCCCCccccCc
Confidence 346788888776666665 468888899999865
No 85
>PRK05657 RNA polymerase sigma factor RpoS; Validated
Probab=21.63 E-value=66 Score=29.25 Aligned_cols=55 Identities=15% Similarity=0.185 Sum_probs=41.9
Q ss_pred ccCHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCCCCceeeccccchhHHHHHhhh
Q psy16800 141 NFTNKQLTELEKEFHFNKYLTRARRIEIASVLQLNETQVKIWFQNRRMKQKKRIKE 196 (221)
Q Consensus 141 ~ft~~Ql~~Le~~F~~~~yps~~~r~~LA~~L~Lt~~qVqvWFQNRRaK~Kr~~k~ 196 (221)
.++..|..+|...|-... ......++||..+|++...|+.+....+.+.|+....
T Consensus 262 ~L~~~~R~vl~lrygL~~-~e~~s~~EIA~~Lgis~~tV~~~~~rAl~kLr~~l~~ 316 (325)
T PRK05657 262 ELNDKQREVLARRFGLLG-YEAATLEDVAREIGLTRERVRQIQVEALRRLREILQT 316 (325)
T ss_pred cCCHHHHHHHHHHhccCC-CCCcCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHh
Confidence 677788888887773322 2334567899999999999999998888887776654
No 86
>PRK09644 RNA polymerase sigma factor SigM; Provisional
Probab=20.87 E-value=75 Score=25.09 Aligned_cols=32 Identities=31% Similarity=0.238 Sum_probs=25.9
Q ss_pred HHHHHHHHhCCCCCceeeccccchhHHHHHhh
Q psy16800 164 RRIEIASVLQLNETQVKIWFQNRRMKQKKRIK 195 (221)
Q Consensus 164 ~r~~LA~~L~Lt~~qVqvWFQNRRaK~Kr~~k 195 (221)
..+++|..+|++...|++|.+.-|.+.++...
T Consensus 126 s~~eIA~~lgis~~tv~~~l~Rar~~Lr~~l~ 157 (165)
T PRK09644 126 TYEEAASVLDLKLNTYKSHLFRGRKRLKALLK 157 (165)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Confidence 36789999999999999999877766666544
No 87
>PRK06930 positive control sigma-like factor; Validated
Probab=20.42 E-value=82 Score=26.02 Aligned_cols=51 Identities=18% Similarity=0.217 Sum_probs=37.1
Q ss_pred ccCHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCCCCceeeccccchhHHHHHhhh
Q psy16800 141 NFTNKQLTELEKEFHFNKYLTRARRIEIASVLQLNETQVKIWFQNRRMKQKKRIKE 196 (221)
Q Consensus 141 ~ft~~Ql~~Le~~F~~~~yps~~~r~~LA~~L~Lt~~qVqvWFQNRRaK~Kr~~k~ 196 (221)
.++..+..+|.-.|... ..-.++|..++++...|+.+...-+.+.++....
T Consensus 114 ~L~~rer~V~~L~~~eg-----~s~~EIA~~lgiS~~tVk~~l~Ra~~kLr~~l~~ 164 (170)
T PRK06930 114 VLTEREKEVYLMHRGYG-----LSYSEIADYLNIKKSTVQSMIERAEKKIARQINE 164 (170)
T ss_pred hCCHHHHHHHHHHHHcC-----CCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHH
Confidence 46666777666544322 2356889999999999999998888777776554
No 88
>TIGR02959 SigZ RNA polymerase sigma factor, SigZ family. This family of RNA polymerase sigma factors is a member of the Sigma-70 subfamily (TIGR02937). One of these is designated as SigZ in B. subtilis (Swiss_Prot: SIGZ_BACSU). Interestingly, this group has a very sporatic distribution, B. subtilis, for instance, being the only sequenced strain of Bacilli with a member. Dechloromonas aromatica RCB appears to have two of these sigma factors. A member appears on a plasmid found in Photobacterium profundum SS9 and Vibrio fischeri ES114 (where a second one is chromosomally encoded).
Probab=20.01 E-value=86 Score=25.06 Aligned_cols=51 Identities=20% Similarity=0.129 Sum_probs=35.9
Q ss_pred ccCHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCCCCceeeccccchhHHHHHhhh
Q psy16800 141 NFTNKQLTELEKEFHFNKYLTRARRIEIASVLQLNETQVKIWFQNRRMKQKKRIKE 196 (221)
Q Consensus 141 ~ft~~Ql~~Le~~F~~~~yps~~~r~~LA~~L~Lt~~qVqvWFQNRRaK~Kr~~k~ 196 (221)
.++..+..+|.-.|-.. ....++|..+|++...|+++.+.-|.+.+.....
T Consensus 100 ~L~~~~r~v~~l~~~~g-----~s~~eIA~~lgis~~tV~~~l~Rar~~Lr~~l~~ 150 (170)
T TIGR02959 100 ELPDEYREAIRLTELEG-----LSQQEIAEKLGLSLSGAKSRVQRGRKKLKELLET 150 (170)
T ss_pred hCCHHHHHHHHHHHHcC-----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHH
Confidence 45566666665554322 2366889999999999999998777777666553
Done!