Query psy5913
Match_columns 341
No_of_seqs 212 out of 1267
Neff 5.0
Searched_HMMs 46136
Date Fri Aug 16 21:39:33 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy5913.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/5913hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG0489|consensus 99.8 7.7E-19 1.7E-23 166.9 7.2 68 4-71 156-223 (261)
2 KOG0488|consensus 99.7 3.7E-18 8E-23 166.0 4.7 64 5-68 170-233 (309)
3 KOG0843|consensus 99.7 2.1E-17 4.6E-22 148.7 6.7 63 6-68 101-163 (197)
4 KOG0850|consensus 99.6 1.9E-16 4E-21 147.3 6.0 64 5-68 120-183 (245)
5 KOG0487|consensus 99.6 1.1E-16 2.3E-21 155.1 4.0 63 5-67 233-295 (308)
6 KOG0842|consensus 99.6 1.6E-16 3.5E-21 153.9 4.5 63 5-67 151-213 (307)
7 KOG0484|consensus 99.6 4E-16 8.7E-21 129.9 4.0 64 5-68 15-78 (125)
8 KOG0485|consensus 99.6 4.7E-16 1E-20 143.8 3.6 63 5-67 102-164 (268)
9 KOG2251|consensus 99.5 3.2E-14 7E-19 131.7 10.2 66 4-69 34-99 (228)
10 KOG0494|consensus 99.5 5.8E-15 1.3E-19 139.5 4.6 63 6-68 140-202 (332)
11 KOG0492|consensus 99.5 9.3E-15 2E-19 134.4 4.7 66 3-68 140-205 (246)
12 KOG0847|consensus 99.5 1.7E-14 3.7E-19 133.7 4.2 71 2-72 162-232 (288)
13 KOG0491|consensus 99.5 8.8E-15 1.9E-19 130.5 0.6 64 6-69 99-162 (194)
14 PF00046 Homeobox: Homeobox do 99.5 5.7E-14 1.2E-18 103.0 4.4 57 8-64 1-57 (57)
15 KOG0848|consensus 99.5 1.5E-14 3.3E-19 137.1 1.7 63 7-69 199-261 (317)
16 KOG0493|consensus 99.4 2.7E-13 5.9E-18 128.4 4.2 60 8-67 247-306 (342)
17 KOG4577|consensus 99.4 1.1E-11 2.3E-16 119.0 13.7 79 1-79 161-239 (383)
18 smart00389 HOX Homeodomain. DN 99.3 1.4E-12 2.9E-17 94.8 4.6 56 8-63 1-56 (56)
19 KOG0844|consensus 99.3 6.2E-13 1.3E-17 128.2 2.2 66 5-70 179-245 (408)
20 cd00086 homeodomain Homeodomai 99.3 2.6E-12 5.7E-17 93.7 5.0 57 9-65 2-58 (59)
21 KOG0483|consensus 99.3 1.3E-12 2.9E-17 120.1 3.0 61 7-67 50-110 (198)
22 TIGR01565 homeo_ZF_HD homeobox 99.3 5.8E-12 1.3E-16 95.1 5.1 53 7-59 1-57 (58)
23 COG5576 Homeodomain-containing 99.2 1.4E-11 3E-16 109.7 7.0 65 4-68 48-112 (156)
24 KOG0486|consensus 99.2 6.9E-12 1.5E-16 121.4 3.2 64 4-67 109-172 (351)
25 KOG3802|consensus 99.1 3.1E-11 6.8E-16 120.0 4.4 65 3-67 290-354 (398)
26 KOG0490|consensus 99.1 5.1E-11 1.1E-15 108.4 3.2 64 4-67 57-120 (235)
27 PF05920 Homeobox_KN: Homeobox 98.9 6.5E-10 1.4E-14 78.0 2.3 40 22-61 1-40 (40)
28 KOG0849|consensus 98.9 1.6E-09 3.5E-14 107.5 4.9 65 4-68 173-237 (354)
29 KOG0775|consensus 98.8 2.1E-09 4.5E-14 102.8 4.0 49 13-64 185-233 (304)
30 KOG0774|consensus 98.8 3.2E-09 6.9E-14 101.0 2.5 65 4-68 188-252 (334)
31 smart00548 IRO Motif in Iroquo 98.7 5.7E-09 1.2E-13 66.0 1.0 18 192-209 3-20 (26)
32 KOG0773|consensus 98.3 2.4E-07 5.1E-12 90.7 2.4 60 8-67 243-302 (342)
33 KOG1168|consensus 98.1 1.2E-06 2.6E-11 84.8 2.8 63 4-66 306-368 (385)
34 KOG2252|consensus 97.8 2.7E-05 5.9E-10 80.8 4.9 57 6-62 419-475 (558)
35 KOG0490|consensus 97.7 3.8E-05 8.3E-10 69.9 4.2 64 4-67 150-213 (235)
36 KOG1146|consensus 96.9 0.00061 1.3E-08 76.8 3.2 61 7-67 903-963 (1406)
37 KOG0773|consensus 96.9 0.001 2.2E-08 65.3 4.2 76 4-80 95-170 (342)
38 PF11569 Homez: Homeodomain le 94.6 0.011 2.3E-07 44.7 0.3 39 22-60 13-51 (56)
39 PF04218 CENP-B_N: CENP-B N-te 87.2 1.1 2.3E-05 33.0 4.1 47 8-59 1-47 (53)
40 KOG3623|consensus 84.1 1.3 2.8E-05 48.6 4.4 52 19-70 568-619 (1007)
41 PF12522 UL73_N: Cytomegalovir 58.0 6.9 0.00015 25.4 1.4 22 307-328 4-25 (27)
42 KOG0943|consensus 57.7 95 0.0021 37.0 10.9 7 259-265 1930-1936(3015)
43 PF06284 Cytomega_UL84: Cytome 50.9 5.2 0.00011 41.6 0.0 11 244-254 393-404 (530)
44 KOG1924|consensus 42.7 85 0.0018 35.5 7.5 10 242-251 611-622 (1102)
45 cd06171 Sigma70_r4 Sigma70, re 38.5 36 0.00078 22.6 2.8 27 37-63 29-55 (55)
46 PF04545 Sigma70_r4: Sigma-70, 34.7 55 0.0012 22.9 3.3 45 15-64 6-50 (50)
47 PF08281 Sigma70_r4_2: Sigma-7 33.9 52 0.0011 23.2 3.1 28 35-62 27-54 (54)
48 KOG1146|consensus 33.3 13 0.00029 43.4 -0.2 56 10-65 447-502 (1406)
49 PRK03975 tfx putative transcri 33.3 62 0.0013 28.7 4.0 48 13-66 6-53 (141)
50 PF01527 HTH_Tnp_1: Transposas 31.6 22 0.00048 26.7 0.8 46 10-59 3-48 (76)
51 PRK09646 RNA polymerase sigma 29.7 75 0.0016 28.2 4.0 32 36-67 160-191 (194)
52 PF00424 REV: REV protein (ant 29.0 56 0.0012 27.1 2.8 32 22-67 17-48 (91)
53 PF13443 HTH_26: Cro/C1-type H 28.9 22 0.00048 25.8 0.4 26 37-62 13-38 (63)
54 cd00569 HTH_Hin_like Helix-tur 27.7 98 0.0021 18.0 3.2 19 37-55 24-42 (42)
55 PRK06759 RNA polymerase factor 27.3 73 0.0016 26.7 3.4 30 36-65 124-153 (154)
56 PRK13908 putative recombinatio 25.7 22 0.00048 33.4 -0.1 9 243-251 27-35 (204)
57 PRK11924 RNA polymerase sigma 25.2 83 0.0018 26.7 3.4 32 37-68 144-175 (179)
58 PRK09480 slmA division inhibit 24.9 65 0.0014 27.9 2.7 47 13-60 10-56 (194)
59 PRK12512 RNA polymerase sigma 24.6 1.1E+02 0.0023 26.7 4.0 32 36-67 149-180 (184)
60 PRK12515 RNA polymerase sigma 24.0 1E+02 0.0022 27.1 3.8 33 36-68 149-181 (189)
61 PF00196 GerE: Bacterial regul 23.8 87 0.0019 22.6 2.8 47 13-65 3-49 (58)
62 PRK12526 RNA polymerase sigma 23.8 96 0.0021 28.0 3.7 32 36-67 171-202 (206)
63 PRK09642 RNA polymerase sigma 23.7 1E+02 0.0022 26.2 3.6 31 37-67 125-155 (160)
64 PRK12519 RNA polymerase sigma 23.4 78 0.0017 27.8 3.0 32 35-66 158-189 (194)
65 PF01690 PLRV_ORF5: Potato lea 22.4 80 0.0017 33.3 3.2 12 193-204 29-40 (465)
66 PF13518 HTH_28: Helix-turn-he 22.0 48 0.001 22.9 1.1 24 37-60 15-38 (52)
67 PRK09652 RNA polymerase sigma 21.7 1.1E+02 0.0024 25.9 3.5 31 37-67 147-177 (182)
68 PF10668 Phage_terminase: Phag 20.5 42 0.00091 25.7 0.5 20 37-56 25-44 (60)
69 TIGR02959 SigZ RNA polymerase 20.5 1.5E+02 0.0033 25.7 4.1 31 37-67 119-149 (170)
70 TIGR02937 sigma70-ECF RNA poly 20.4 41 0.0009 27.0 0.5 30 36-65 128-157 (158)
71 PRK09644 RNA polymerase sigma 20.1 1.2E+02 0.0027 25.8 3.5 32 36-67 126-157 (165)
No 1
>KOG0489|consensus
Probab=99.76 E-value=7.7e-19 Score=166.87 Aligned_cols=68 Identities=31% Similarity=0.399 Sum_probs=63.5
Q ss_pred CCCCCCCCCcccHHHHHHHHHHHhcCCCCCHHHHHHHHHHhCCCccccccchhhhHHHHhhhhcccCC
Q psy5913 4 NGARRKNATRETTSTLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKKENKMTWE 71 (341)
Q Consensus 4 ~~krRR~Rt~fS~~QL~~Le~~F~~npYPs~~eR~~LA~~lgLsesQVkvWFQNRR~K~KK~~k~~~~ 71 (341)
.++.||.||.||..||.+||++|+.|+|+++..|+++|..|+|+++|||||||||||||||.++....
T Consensus 156 ~~~~kR~RtayT~~QllELEkEFhfN~YLtR~RRiEiA~~L~LtErQIKIWFQNRRMK~Kk~~k~~~~ 223 (261)
T KOG0489|consen 156 GGKSKRRRTAFTRYQLLELEKEFHFNKYLTRSRRIEIAHALNLTERQIKIWFQNRRMKWKKENKAKSS 223 (261)
T ss_pred cCCCCCCCcccchhhhhhhhhhhccccccchHHHHHHHhhcchhHHHHHHHHHHHHHHHHHhhccccc
Confidence 46789999999999999999999999999999999999999999999999999999999998776443
No 2
>KOG0488|consensus
Probab=99.71 E-value=3.7e-18 Score=165.99 Aligned_cols=64 Identities=30% Similarity=0.392 Sum_probs=60.9
Q ss_pred CCCCCCCCcccHHHHHHHHHHHhcCCCCCHHHHHHHHHHhCCCccccccchhhhHHHHhhhhcc
Q psy5913 5 GARRKNATRETTSTLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKKENKM 68 (341)
Q Consensus 5 ~krRR~Rt~fS~~QL~~Le~~F~~npYPs~~eR~~LA~~lgLsesQVkvWFQNRR~K~KK~~k~ 68 (341)
+|+||.||.||..||.+||++|++++|++..+|+.||..|||+..||++|||||||||||+...
T Consensus 170 kK~RksRTaFT~~Ql~~LEkrF~~QKYLS~~DR~~LA~~LgLTdaQVKtWfQNRRtKWKrq~a~ 233 (309)
T KOG0488|consen 170 KKRRKSRTAFSDHQLFELEKRFEKQKYLSVADRIELAASLGLTDAQVKTWFQNRRTKWKRQTAE 233 (309)
T ss_pred cccccchhhhhHHHHHHHHHHHHHhhcccHHHHHHHHHHcCCchhhHHHHHhhhhHHHHHHHHh
Confidence 6788899999999999999999999999999999999999999999999999999999998553
No 3
>KOG0843|consensus
Probab=99.70 E-value=2.1e-17 Score=148.74 Aligned_cols=63 Identities=25% Similarity=0.308 Sum_probs=59.8
Q ss_pred CCCCCCCcccHHHHHHHHHHHhcCCCCCHHHHHHHHHHhCCCccccccchhhhHHHHhhhhcc
Q psy5913 6 ARRKNATRETTSTLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKKENKM 68 (341)
Q Consensus 6 krRR~Rt~fS~~QL~~Le~~F~~npYPs~~eR~~LA~~lgLsesQVkvWFQNRR~K~KK~~k~ 68 (341)
+.||.||.|+..||..||..|+.|+|....+|++||..|+|+++||+|||||||.|.||.+..
T Consensus 101 ~~kr~RT~ft~~Ql~~LE~~F~~~~Yvvg~eR~~LA~~L~LsetQVkvWFQNRRtk~kr~~~e 163 (197)
T KOG0843|consen 101 RPKRIRTAFTPEQLLKLEHAFEGNQYVVGAERKQLAQSLSLSETQVKVWFQNRRTKHKRMQQE 163 (197)
T ss_pred CCCccccccCHHHHHHHHHHHhcCCeeechHHHHHHHHcCCChhHhhhhhhhhhHHHHHHHHH
Confidence 567799999999999999999999999999999999999999999999999999999998654
No 4
>KOG0850|consensus
Probab=99.64 E-value=1.9e-16 Score=147.26 Aligned_cols=64 Identities=31% Similarity=0.358 Sum_probs=60.7
Q ss_pred CCCCCCCCcccHHHHHHHHHHHhcCCCCCHHHHHHHHHHhCCCccccccchhhhHHHHhhhhcc
Q psy5913 5 GARRKNATRETTSTLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKKENKM 68 (341)
Q Consensus 5 ~krRR~Rt~fS~~QL~~Le~~F~~npYPs~~eR~~LA~~lgLsesQVkvWFQNRR~K~KK~~k~ 68 (341)
+|.||.||.++..||..|..+|+++.|+...||.+||..|||+.+||||||||||.|+||.+|.
T Consensus 120 KK~RKPRTIYSS~QLqaL~rRFQkTQYLALPERAeLAAsLGLTQTQVKIWFQNrRSK~KKl~k~ 183 (245)
T KOG0850|consen 120 KKVRKPRTIYSSLQLQALNRRFQQTQYLALPERAELAASLGLTQTQVKIWFQNRRSKFKKLKKQ 183 (245)
T ss_pred ccccCCcccccHHHHHHHHHHHhhcchhcCcHHHHHHHHhCCchhHhhhhhhhhHHHHHHHHhc
Confidence 4567789999999999999999999999999999999999999999999999999999999874
No 5
>KOG0487|consensus
Probab=99.63 E-value=1.1e-16 Score=155.14 Aligned_cols=63 Identities=30% Similarity=0.317 Sum_probs=59.7
Q ss_pred CCCCCCCCcccHHHHHHHHHHHhcCCCCCHHHHHHHHHHhCCCccccccchhhhHHHHhhhhc
Q psy5913 5 GARRKNATRETTSTLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKKENK 67 (341)
Q Consensus 5 ~krRR~Rt~fS~~QL~~Le~~F~~npYPs~~eR~~LA~~lgLsesQVkvWFQNRR~K~KK~~k 67 (341)
+..||+|+-.|..|+.+||++|..|.|+++..|.+|++.|+|+++||||||||||||.||..+
T Consensus 233 ~~~RKKRcPYTK~QtlELEkEFlfN~YitkeKR~ElSr~lNLTeRQVKIWFQNRRMK~KK~~r 295 (308)
T KOG0487|consen 233 RRGRKKRCPYTKHQTLELEKEFLFNMYITKEKRLELSRTLNLTERQVKIWFQNRRMKEKKVNR 295 (308)
T ss_pred cccccccCCchHHHHHHHHHHHHHHHHHhHHHHHHHHHhcccchhheeeeehhhhhHHhhhhh
Confidence 456889999999999999999999999999999999999999999999999999999999864
No 6
>KOG0842|consensus
Probab=99.63 E-value=1.6e-16 Score=153.87 Aligned_cols=63 Identities=25% Similarity=0.365 Sum_probs=59.9
Q ss_pred CCCCCCCCcccHHHHHHHHHHHhcCCCCCHHHHHHHHHHhCCCccccccchhhhHHHHhhhhc
Q psy5913 5 GARRKNATRETTSTLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKKENK 67 (341)
Q Consensus 5 ~krRR~Rt~fS~~QL~~Le~~F~~npYPs~~eR~~LA~~lgLsesQVkvWFQNRR~K~KK~~k 67 (341)
.+|||.|..|+..|+.+||.+|+.++|++..||+.||..|.|+++||||||||||-|.||+.+
T Consensus 151 ~~kRKrRVLFSqAQV~ELERRFrqQRYLSAPERE~LA~~LrLT~TQVKIWFQNrRYK~KR~~~ 213 (307)
T KOG0842|consen 151 RKKRKRRVLFSQAQVYELERRFRQQRYLSAPEREHLASSLRLTPTQVKIWFQNRRYKTKRQQK 213 (307)
T ss_pred ccccccccccchhHHHHHHHHHHhhhccccHhHHHHHHhcCCCchheeeeeecchhhhhhhhh
Confidence 367888999999999999999999999999999999999999999999999999999999855
No 7
>KOG0484|consensus
Probab=99.60 E-value=4e-16 Score=129.90 Aligned_cols=64 Identities=23% Similarity=0.389 Sum_probs=60.6
Q ss_pred CCCCCCCCcccHHHHHHHHHHHhcCCCCCHHHHHHHHHHhCCCccccccchhhhHHHHhhhhcc
Q psy5913 5 GARRKNATRETTSTLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKKENKM 68 (341)
Q Consensus 5 ~krRR~Rt~fS~~QL~~Le~~F~~npYPs~~eR~~LA~~lgLsesQVkvWFQNRR~K~KK~~k~ 68 (341)
+|.||.|+.|+..||++|+..|...+||++-.|++||..+.|++.+|||||||||+|+||+.+.
T Consensus 15 rKQRRIRTTFTS~QLkELErvF~ETHYPDIYTREEiA~kidLTEARVQVWFQNRRAKfRKQEr~ 78 (125)
T KOG0484|consen 15 RKQRRIRTTFTSAQLKELERVFAETHYPDIYTREEIALKIDLTEARVQVWFQNRRAKFRKQERA 78 (125)
T ss_pred HHhhhhhhhhhHHHHHHHHHHHHhhcCCcchhHHHHHHhhhhhHHHHHHHHHhhHHHHHHHHHH
Confidence 4678899999999999999999999999999999999999999999999999999999998654
No 8
>KOG0485|consensus
Probab=99.59 E-value=4.7e-16 Score=143.75 Aligned_cols=63 Identities=24% Similarity=0.333 Sum_probs=59.9
Q ss_pred CCCCCCCCcccHHHHHHHHHHHhcCCCCCHHHHHHHHHHhCCCccccccchhhhHHHHhhhhc
Q psy5913 5 GARRKNATRETTSTLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKKENK 67 (341)
Q Consensus 5 ~krRR~Rt~fS~~QL~~Le~~F~~npYPs~~eR~~LA~~lgLsesQVkvWFQNRR~K~KK~~k 67 (341)
.+|||.||.|+..|+..||..|+..+|++..+|..||.+|.|+++||||||||||.||||+..
T Consensus 102 ~RKKktRTvFSraQV~qLEs~Fe~krYLSsaeRa~LA~sLqLTETQVKIWFQNRRnKwKRq~a 164 (268)
T KOG0485|consen 102 DRKKKTRTVFSRAQVFQLESTFELKRYLSSAERAGLAASLQLTETQVKIWFQNRRNKWKRQYA 164 (268)
T ss_pred cccccchhhhhHHHHHHHHHHHHHHhhhhHHHHhHHHHhhhhhhhhhhhhhhhhhHHHHHHHh
Confidence 367789999999999999999999999999999999999999999999999999999999754
No 9
>KOG2251|consensus
Probab=99.53 E-value=3.2e-14 Score=131.72 Aligned_cols=66 Identities=21% Similarity=0.329 Sum_probs=62.7
Q ss_pred CCCCCCCCCcccHHHHHHHHHHHhcCCCCCHHHHHHHHHHhCCCccccccchhhhHHHHhhhhccc
Q psy5913 4 NGARRKNATRETTSTLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKKENKMT 69 (341)
Q Consensus 4 ~~krRR~Rt~fS~~QL~~Le~~F~~npYPs~~eR~~LA~~lgLsesQVkvWFQNRR~K~KK~~k~~ 69 (341)
-+|.||.||.|+..||+.||..|.+..||+...|++||.+|+|.+.+|+|||+|||+|+|++++..
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 457888999999999999999999999999999999999999999999999999999999998764
No 10
>KOG0494|consensus
Probab=99.53 E-value=5.8e-15 Score=139.52 Aligned_cols=63 Identities=29% Similarity=0.378 Sum_probs=58.2
Q ss_pred CCCCCCCcccHHHHHHHHHHHhcCCCCCHHHHHHHHHHhCCCccccccchhhhHHHHhhhhcc
Q psy5913 6 ARRKNATRETTSTLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKKENKM 68 (341)
Q Consensus 6 krRR~Rt~fS~~QL~~Le~~F~~npYPs~~eR~~LA~~lgLsesQVkvWFQNRR~K~KK~~k~ 68 (341)
|||+-||.||.-||++||+.|+..+||+...|+.||..|+|.+.+|+|||||||+||||..|.
T Consensus 140 kRRh~RTiFT~~Qle~LEkaFkeaHYPDv~Are~la~ktelpEDRIqVWfQNRRAKWRk~Ek~ 202 (332)
T KOG0494|consen 140 KRRHFRTIFTSYQLEELEKAFKEAHYPDVYAREMLADKTELPEDRIQVWFQNRRAKWRKTEKR 202 (332)
T ss_pred ccccccchhhHHHHHHHHHHHhhccCccHHHHHHHhhhccCchhhhhHHhhhhhHHhhhhhhh
Confidence 344448999999999999999999999999999999999999999999999999999998654
No 11
>KOG0492|consensus
Probab=99.51 E-value=9.3e-15 Score=134.40 Aligned_cols=66 Identities=27% Similarity=0.343 Sum_probs=61.1
Q ss_pred CCCCCCCCCCcccHHHHHHHHHHHhcCCCCCHHHHHHHHHHhCCCccccccchhhhHHHHhhhhcc
Q psy5913 3 INGARRKNATRETTSTLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKKENKM 68 (341)
Q Consensus 3 ~~~krRR~Rt~fS~~QL~~Le~~F~~npYPs~~eR~~LA~~lgLsesQVkvWFQNRR~K~KK~~k~ 68 (341)
+++..|+.|+-||.+||..||+.|+..+|+++.+|.+++..|.|+++||+|||||||+|.||.++.
T Consensus 140 Khk~nRkPRtPFTtqQLlaLErkfrekqYLSiaEraefSsSL~LTeTqVKIWFQNRRAKaKRlQea 205 (246)
T KOG0492|consen 140 KHKPNRKPRTPFTTQQLLALERKFREKQYLSIAERAEFSSSLELTETQVKIWFQNRRAKAKRLQEA 205 (246)
T ss_pred ccCCCCCCCCCCCHHHHHHHHHHHhHhhhhhHHHHHhhhhhhhhhhhheehhhhhhhHHHHHHHHH
Confidence 345568889999999999999999999999999999999999999999999999999999997553
No 12
>KOG0847|consensus
Probab=99.48 E-value=1.7e-14 Score=133.70 Aligned_cols=71 Identities=23% Similarity=0.386 Sum_probs=66.0
Q ss_pred CCCCCCCCCCCcccHHHHHHHHHHHhcCCCCCHHHHHHHHHHhCCCccccccchhhhHHHHhhhhcccCCC
Q psy5913 2 DINGARRKNATRETTSTLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKKENKMTWEP 72 (341)
Q Consensus 2 d~~~krRR~Rt~fS~~QL~~Le~~F~~npYPs~~eR~~LA~~lgLsesQVkvWFQNRR~K~KK~~k~~~~~ 72 (341)
+++++|+..|..|+..|+..++..|+..+|+-..+|.+||..+||++.||+|||||||+||||+...+...
T Consensus 162 ~kdG~rk~srPTf~g~qi~~le~~feqtkylaG~~ra~lA~~lgmteSqvkVWFQNRRTKWRKkhAaEmas 232 (288)
T KOG0847|consen 162 NLNGQRKQSRPTFTGHQIYQLERKFEQTKYLAGADRAQLAQELNMTESQVKVWFQNRRTKWRKKHAAEMAS 232 (288)
T ss_pred CcCccccccCCCccchhhhhhhhhhhhhhcccchhHHHhhccccccHHHHHHHHhcchhhhhhhhccchhh
Confidence 57899999999999999999999999999999999999999999999999999999999999986655443
No 13
>KOG0491|consensus
Probab=99.46 E-value=8.8e-15 Score=130.46 Aligned_cols=64 Identities=30% Similarity=0.394 Sum_probs=60.3
Q ss_pred CCCCCCCcccHHHHHHHHHHHhcCCCCCHHHHHHHHHHhCCCccccccchhhhHHHHhhhhccc
Q psy5913 6 ARRKNATRETTSTLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKKENKMT 69 (341)
Q Consensus 6 krRR~Rt~fS~~QL~~Le~~F~~npYPs~~eR~~LA~~lgLsesQVkvWFQNRR~K~KK~~k~~ 69 (341)
++||-|+.|+..||..|+++|+.++|++..+|.+||..|+|+++||+.||||||||.||+.+..
T Consensus 99 ~r~K~Rtvfs~~ql~~l~~rFe~QrYLS~~e~~ELan~L~LS~~QVKTWFQNrRMK~Kk~~r~~ 162 (194)
T KOG0491|consen 99 RRRKARTVFSDPQLSGLEKRFERQRYLSTPERQELANALSLSETQVKTWFQNRRMKHKKQQRNN 162 (194)
T ss_pred HhhhhcccccCccccccHHHHhhhhhcccHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHHHhcc
Confidence 5677899999999999999999999999999999999999999999999999999999987653
No 14
>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=99.46 E-value=5.7e-14 Score=103.03 Aligned_cols=57 Identities=40% Similarity=0.566 Sum_probs=55.1
Q ss_pred CCCCCcccHHHHHHHHHHHhcCCCCCHHHHHHHHHHhCCCccccccchhhhHHHHhh
Q psy5913 8 RKNATRETTSTLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKK 64 (341)
Q Consensus 8 RR~Rt~fS~~QL~~Le~~F~~npYPs~~eR~~LA~~lgLsesQVkvWFQNRR~K~KK 64 (341)
||.|+.++..|+..|+..|..++||+..++..||..+||+..||++||+|+|.++||
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 578999999999999999999999999999999999999999999999999999986
No 15
>KOG0848|consensus
Probab=99.46 E-value=1.5e-14 Score=137.07 Aligned_cols=63 Identities=27% Similarity=0.292 Sum_probs=58.0
Q ss_pred CCCCCCcccHHHHHHHHHHHhcCCCCCHHHHHHHHHHhCCCccccccchhhhHHHHhhhhccc
Q psy5913 7 RRKNATRETTSTLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKKENKMT 69 (341)
Q Consensus 7 rRR~Rt~fS~~QL~~Le~~F~~npYPs~~eR~~LA~~lgLsesQVkvWFQNRR~K~KK~~k~~ 69 (341)
|-|-|...|.-|..+||++|..++|+++..|.+||..|+|+|+||||||||||+|.||.+|++
T Consensus 199 kDKYRvVYTDhQRLELEKEfh~SryITirRKSELA~~LgLsERQVKIWFQNRRAKERK~nKKk 261 (317)
T KOG0848|consen 199 KDKYRVVYTDHQRLELEKEFHTSRYITIRRKSELAATLGLSERQVKIWFQNRRAKERKDNKKK 261 (317)
T ss_pred ccceeEEecchhhhhhhhhhccccceeeehhHHHHHhhCccHhhhhHhhhhhhHHHHHHHHHH
Confidence 344567889999999999999999999999999999999999999999999999999998764
No 16
>KOG0493|consensus
Probab=99.37 E-value=2.7e-13 Score=128.38 Aligned_cols=60 Identities=27% Similarity=0.391 Sum_probs=57.2
Q ss_pred CCCCCcccHHHHHHHHHHHhcCCCCCHHHHHHHHHHhCCCccccccchhhhHHHHhhhhc
Q psy5913 8 RKNATRETTSTLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKKENK 67 (341)
Q Consensus 8 RR~Rt~fS~~QL~~Le~~F~~npYPs~~eR~~LA~~lgLsesQVkvWFQNRR~K~KK~~k 67 (341)
||.||.|+.+||.+|..+|+.|+|++...|..||.+|+|.+.||+|||||+|+|.||.-.
T Consensus 247 KRPRTAFtaeQL~RLK~EF~enRYlTEqRRQ~La~ELgLNEsQIKIWFQNKRAKiKKsTg 306 (342)
T KOG0493|consen 247 KRPRTAFTAEQLQRLKAEFQENRYLTEQRRQELAQELGLNESQIKIWFQNKRAKIKKSTG 306 (342)
T ss_pred cCccccccHHHHHHHHHHHhhhhhHHHHHHHHHHHHhCcCHHHhhHHhhhhhhhhhhccC
Confidence 678999999999999999999999999999999999999999999999999999998743
No 17
>KOG4577|consensus
Probab=99.35 E-value=1.1e-11 Score=119.03 Aligned_cols=79 Identities=19% Similarity=0.246 Sum_probs=69.1
Q ss_pred CCCCCCCCCCCCcccHHHHHHHHHHHhcCCCCCHHHHHHHHHHhCCCccccccchhhhHHHHhhhhcccCCCCCccccc
Q psy5913 1 MDINGARRKNATRETTSTLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKKENKMTWEPRNRVEDE 79 (341)
Q Consensus 1 ~d~~~krRR~Rt~fS~~QL~~Le~~F~~npYPs~~eR~~LA~~lgLsesQVkvWFQNRR~K~KK~~k~~~~~~~~~ee~ 79 (341)
||.+...||.||.++..||+.|...|+..+.|.+..|++|+..+||..+.|||||||||+|.||.+|-....+|.+.-.
T Consensus 161 l~gd~~nKRPRTTItAKqLETLK~AYn~SpKPARHVREQLsseTGLDMRVVQVWFQNRRAKEKRLKKDAGR~RWgqyfr 239 (383)
T KOG4577|consen 161 LEGDASNKRPRTTITAKQLETLKQAYNTSPKPARHVREQLSSETGLDMRVVQVWFQNRRAKEKRLKKDAGRTRWGQYFR 239 (383)
T ss_pred cccccccCCCcceeeHHHHHHHHHHhcCCCchhHHHHHHhhhccCcceeehhhhhhhhhHHHHhhhhhcchhHHHHHHH
Confidence 3556677899999999999999999999999999999999999999999999999999999999877655555544443
No 18
>smart00389 HOX Homeodomain. DNA-binding factors that are involved in the transcriptional regulation of key developmental processes
Probab=99.33 E-value=1.4e-12 Score=94.79 Aligned_cols=56 Identities=36% Similarity=0.557 Sum_probs=52.3
Q ss_pred CCCCCcccHHHHHHHHHHHhcCCCCCHHHHHHHHHHhCCCccccccchhhhHHHHh
Q psy5913 8 RKNATRETTSTLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLK 63 (341)
Q Consensus 8 RR~Rt~fS~~QL~~Le~~F~~npYPs~~eR~~LA~~lgLsesQVkvWFQNRR~K~K 63 (341)
++.|+.++..++..|+..|..++||+..++..||..+||+..||++||+|+|.+.|
T Consensus 1 ~k~r~~~~~~~~~~L~~~f~~~~~P~~~~~~~la~~~~l~~~qV~~WF~nrR~~~~ 56 (56)
T smart00389 1 RRKRTSFTPEQLEELEKEFQKNPYPSREEREELAAKLGLSERQVKVWFQNRRAKWK 56 (56)
T ss_pred CCCCCcCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHHCcCHHHHHHhHHHHhhccC
Confidence 35677899999999999999999999999999999999999999999999998864
No 19
>KOG0844|consensus
Probab=99.31 E-value=6.2e-13 Score=128.23 Aligned_cols=66 Identities=23% Similarity=0.389 Sum_probs=60.5
Q ss_pred CCCCCCCCcccHHHHHHHHHHHhcCCCCCHHHHHHHHHHhCCCccccccchhhhHHHHhhhhc-ccC
Q psy5913 5 GARRKNATRETTSTLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKKENK-MTW 70 (341)
Q Consensus 5 ~krRR~Rt~fS~~QL~~Le~~F~~npYPs~~eR~~LA~~lgLsesQVkvWFQNRR~K~KK~~k-~~~ 70 (341)
..-||-||.|+++|+-+||++|.+-.|.++..|.+||.+|+|.++.|||||||||||.||++- |.|
T Consensus 179 dqmRRYRTAFTReQIaRLEKEFyrENYVSRprRcELAAaLNLPEtTIKVWFQNRRMKDKRQRlamaW 245 (408)
T KOG0844|consen 179 DQMRRYRTAFTREQIARLEKEFYRENYVSRPRRCELAAALNLPETTIKVWFQNRRMKDKRQRLAMAW 245 (408)
T ss_pred HHHHHHHhhhhHHHHHHHHHHHHHhccccCchhhhHHHhhCCCcceeehhhhhchhhhhhhhhhccC
Confidence 345788999999999999999999999999999999999999999999999999999999853 444
No 20
>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=99.31 E-value=2.6e-12 Score=93.72 Aligned_cols=57 Identities=39% Similarity=0.582 Sum_probs=53.6
Q ss_pred CCCCcccHHHHHHHHHHHhcCCCCCHHHHHHHHHHhCCCccccccchhhhHHHHhhh
Q psy5913 9 KNATRETTSTLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKKE 65 (341)
Q Consensus 9 R~Rt~fS~~QL~~Le~~F~~npYPs~~eR~~LA~~lgLsesQVkvWFQNRR~K~KK~ 65 (341)
+.+..++..++..|+..|..++||+..++..||..+||+..||++||+|+|.+.++.
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 567789999999999999999999999999999999999999999999999998864
No 21
>KOG0483|consensus
Probab=99.28 E-value=1.3e-12 Score=120.14 Aligned_cols=61 Identities=23% Similarity=0.247 Sum_probs=56.2
Q ss_pred CCCCCCcccHHHHHHHHHHHhcCCCCCHHHHHHHHHHhCCCccccccchhhhHHHHhhhhc
Q psy5913 7 RRKNATRETTSTLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKKENK 67 (341)
Q Consensus 7 rRR~Rt~fS~~QL~~Le~~F~~npYPs~~eR~~LA~~lgLsesQVkvWFQNRR~K~KK~~k 67 (341)
..++..+++..|+..|+..|+.+.|+.+..|..||++|||.++||.|||||||+|||.++.
T Consensus 50 ~~~kk~Rlt~eQ~~~LE~~F~~~~~L~p~~K~~LAk~LgL~pRQVavWFQNRRARwK~kql 110 (198)
T KOG0483|consen 50 GKGKKRRLTSEQVKFLEKSFESEKKLEPERKKKLAKELGLQPRQVAVWFQNRRARWKTKQL 110 (198)
T ss_pred cccccccccHHHHHHhHHhhccccccChHHHHHHHHhhCCChhHHHHHHhhccccccchhh
Confidence 3455678999999999999999999999999999999999999999999999999998744
No 22
>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=99.27 E-value=5.8e-12 Score=95.06 Aligned_cols=53 Identities=13% Similarity=0.161 Sum_probs=50.6
Q ss_pred CCCCCCcccHHHHHHHHHHHhcCCC----CCHHHHHHHHHHhCCCccccccchhhhH
Q psy5913 7 RRKNATRETTSTLKAWLNEHKKNPY----PTKGEKIMLAIITKMTLTQVSTWFANAR 59 (341)
Q Consensus 7 rRR~Rt~fS~~QL~~Le~~F~~npY----Ps~~eR~~LA~~lgLsesQVkvWFQNRR 59 (341)
+||.||.|+..|++.|+..|.+++| |+..++.+||..+||++.+|+|||||.+
T Consensus 1 ~kR~RT~Ft~~Q~~~Le~~fe~~~y~~~~~~~~~r~~la~~lgl~~~vvKVWfqN~k 57 (58)
T TIGR01565 1 KKRRRTKFTAEQKEKMRDFAEKLGWKLKDKRREEVREFCEEIGVTRKVFKVWMHNNK 57 (58)
T ss_pred CCCCCCCCCHHHHHHHHHHHHHcCCCCCCCCHHHHHHHHHHhCCCHHHeeeecccCC
Confidence 4789999999999999999999999 9999999999999999999999999953
No 23
>COG5576 Homeodomain-containing transcription factor [Transcription]
Probab=99.24 E-value=1.4e-11 Score=109.70 Aligned_cols=65 Identities=28% Similarity=0.465 Sum_probs=60.3
Q ss_pred CCCCCCCCCcccHHHHHHHHHHHhcCCCCCHHHHHHHHHHhCCCccccccchhhhHHHHhhhhcc
Q psy5913 4 NGARRKNATRETTSTLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKKENKM 68 (341)
Q Consensus 4 ~~krRR~Rt~fS~~QL~~Le~~F~~npYPs~~eR~~LA~~lgLsesQVkvWFQNRR~K~KK~~k~ 68 (341)
....++.|.+.+..|+..|+..|+.++||+...|..|+..++|+++-|++||||+|++.|+....
T Consensus 48 s~~~~~~r~R~t~~Q~~vL~~~F~i~p~Ps~~~r~~L~~~lnm~~ksVqIWFQNkR~~~k~~~~~ 112 (156)
T COG5576 48 SSPPKSKRRRTTDEQLMVLEREFEINPYPSSITRIKLSLLLNMPPKSVQIWFQNKRAKEKKKRSG 112 (156)
T ss_pred CCcCcccceechHHHHHHHHHHhccCCCCCHHHHHHHHHhcCCChhhhhhhhchHHHHHHHhccc
Confidence 34567788999999999999999999999999999999999999999999999999999998654
No 24
>KOG0486|consensus
Probab=99.20 E-value=6.9e-12 Score=121.37 Aligned_cols=64 Identities=25% Similarity=0.460 Sum_probs=60.0
Q ss_pred CCCCCCCCCcccHHHHHHHHHHHhcCCCCCHHHHHHHHHHhCCCccccccchhhhHHHHhhhhc
Q psy5913 4 NGARRKNATRETTSTLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKKENK 67 (341)
Q Consensus 4 ~~krRR~Rt~fS~~QL~~Le~~F~~npYPs~~eR~~LA~~lgLsesQVkvWFQNRR~K~KK~~k 67 (341)
.+|+||.|+.|+.+||.+||..|++|.||+...|+++|.-++|++.+|+|||.|||+||||..+
T Consensus 109 i~KqrrQrthFtSqqlqele~tF~rNrypdMstrEEIavwtNlTE~rvrvwfknrrakwrkrEr 172 (351)
T KOG0486|consen 109 ISKQRRQRTHFTSQQLQELEATFQRNRYPDMSTREEIAVWTNLTEARVRVWFKNRRAKWRKRER 172 (351)
T ss_pred hhhhhhhhhhhHHHHHHHHHHHHhhccCCccchhhHHHhhccccchhhhhhcccchhhhhhhhh
Confidence 3467889999999999999999999999999999999999999999999999999999998744
No 25
>KOG3802|consensus
Probab=99.13 E-value=3.1e-11 Score=120.03 Aligned_cols=65 Identities=26% Similarity=0.330 Sum_probs=61.0
Q ss_pred CCCCCCCCCCcccHHHHHHHHHHHhcCCCCCHHHHHHHHHHhCCCccccccchhhhHHHHhhhhc
Q psy5913 3 INGARRKNATRETTSTLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKKENK 67 (341)
Q Consensus 3 ~~~krRR~Rt~fS~~QL~~Le~~F~~npYPs~~eR~~LA~~lgLsesQVkvWFQNRR~K~KK~~k 67 (341)
..+||||+||.+...+...||+.|.+|+.|+..+..+||.+|+|....|+|||+|||.|.||...
T Consensus 290 a~~RkRKKRTSie~~vr~aLE~~F~~npKPt~qEIt~iA~~L~leKEVVRVWFCNRRQkeKR~~~ 354 (398)
T KOG3802|consen 290 AQSRKRKKRTSIEVNVRGALEKHFLKNPKPTSQEITHIAESLQLEKEVVRVWFCNRRQKEKRITP 354 (398)
T ss_pred ccccccccccceeHHHHHHHHHHHHhCCCCCHHHHHHHHHHhccccceEEEEeeccccccccCCC
Confidence 45688999999999999999999999999999999999999999999999999999999998644
No 26
>KOG0490|consensus
Probab=99.08 E-value=5.1e-11 Score=108.45 Aligned_cols=64 Identities=23% Similarity=0.278 Sum_probs=60.2
Q ss_pred CCCCCCCCCcccHHHHHHHHHHHhcCCCCCHHHHHHHHHHhCCCccccccchhhhHHHHhhhhc
Q psy5913 4 NGARRKNATRETTSTLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKKENK 67 (341)
Q Consensus 4 ~~krRR~Rt~fS~~QL~~Le~~F~~npYPs~~eR~~LA~~lgLsesQVkvWFQNRR~K~KK~~k 67 (341)
..++||.|+.|+..|+++|+..|++.+||+...|+.||..+.|++..|+|||||||+||+++.+
T Consensus 57 ~~~~rr~rt~~~~~ql~~ler~f~~~h~Pd~~~r~~la~~~~~~e~rVqvwFqnrrak~r~~~~ 120 (235)
T KOG0490|consen 57 KFSKRCARCKFTISQLDELERAFEKVHLPCFACRECLALLLTGDEFRVQVWFQNRRAKDRKEER 120 (235)
T ss_pred hccccccCCCCCcCHHHHHHHhhcCCCcCccchHHHHhhcCCCCeeeeehhhhhhcHhhhhhhc
Confidence 3467889999999999999999999999999999999999999999999999999999998754
No 27
>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=98.90 E-value=6.5e-10 Score=77.96 Aligned_cols=40 Identities=58% Similarity=0.927 Sum_probs=34.8
Q ss_pred HHHHHhcCCCCCHHHHHHHHHHhCCCccccccchhhhHHH
Q psy5913 22 WLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRR 61 (341)
Q Consensus 22 Le~~F~~npYPs~~eR~~LA~~lgLsesQVkvWFQNRR~K 61 (341)
|+..+..+|||+..+|..||..+||+..||.+||.|.|+|
T Consensus 1 Wl~~h~~nPYPs~~ek~~L~~~tgls~~Qi~~WF~NaRrR 40 (40)
T PF05920_consen 1 WLLEHLHNPYPSKEEKEELAKQTGLSRKQISNWFINARRR 40 (40)
T ss_dssp HHHHTTTSGS--HHHHHHHHHHHTS-HHHHHHHHHHHHHH
T ss_pred CHHHHCCCCCCCHHHHHHHHHHcCCCHHHHHHHHHHhHcc
Confidence 5678899999999999999999999999999999999986
No 28
>KOG0849|consensus
Probab=98.87 E-value=1.6e-09 Score=107.49 Aligned_cols=65 Identities=26% Similarity=0.419 Sum_probs=60.9
Q ss_pred CCCCCCCCCcccHHHHHHHHHHHhcCCCCCHHHHHHHHHHhCCCccccccchhhhHHHHhhhhcc
Q psy5913 4 NGARRKNATRETTSTLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKKENKM 68 (341)
Q Consensus 4 ~~krRR~Rt~fS~~QL~~Le~~F~~npYPs~~eR~~LA~~lgLsesQVkvWFQNRR~K~KK~~k~ 68 (341)
.++.||+|+.|+..|++.|+..|++++||....|+.||.+++|++.+|++||+|||.||+|...+
T Consensus 173 ~~~~rr~rtsft~~Q~~~le~~f~rt~yP~i~~Re~La~~i~l~e~riqvwf~nrra~~rr~~~~ 237 (354)
T KOG0849|consen 173 QRGGRRNRTSFSPSQLEALEECFQRTPYPDIVGRETLAKETGLPEPRVQVWFQNRRAKWRRQHRD 237 (354)
T ss_pred cccccccccccccchHHHHHHHhcCCCCCchhhHHHHhhhccCCchHHHHHHhhhhhhhhhcccc
Confidence 45677889999999999999999999999999999999999999999999999999999998643
No 29
>KOG0775|consensus
Probab=98.84 E-value=2.1e-09 Score=102.75 Aligned_cols=49 Identities=45% Similarity=0.749 Sum_probs=44.1
Q ss_pred cccHHHHHHHHHHHhcCCCCCHHHHHHHHHHhCCCccccccchhhhHHHHhh
Q psy5913 13 RETTSTLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKK 64 (341)
Q Consensus 13 ~fS~~QL~~Le~~F~~npYPs~~eR~~LA~~lgLsesQVkvWFQNRR~K~KK 64 (341)
..++..|++|+ ..++||++.+|++||++|||+.+||.|||+|||.|.|.
T Consensus 185 ekSR~~LrewY---~~~~YPsp~eKReLA~aTgLt~tQVsNWFKNRRQRDRa 233 (304)
T KOG0775|consen 185 EKSRSLLREWY---LQNPYPSPREKRELAEATGLTITQVSNWFKNRRQRDRA 233 (304)
T ss_pred HhhHHHHHHHH---hcCCCCChHHHHHHHHHhCCchhhhhhhhhhhhhhhhh
Confidence 34677777775 79999999999999999999999999999999999883
No 30
>KOG0774|consensus
Probab=98.76 E-value=3.2e-09 Score=101.05 Aligned_cols=65 Identities=35% Similarity=0.584 Sum_probs=60.5
Q ss_pred CCCCCCCCCcccHHHHHHHHHHHhcCCCCCHHHHHHHHHHhCCCccccccchhhhHHHHhhhhcc
Q psy5913 4 NGARRKNATRETTSTLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKKENKM 68 (341)
Q Consensus 4 ~~krRR~Rt~fS~~QL~~Le~~F~~npYPs~~eR~~LA~~lgLsesQVkvWFQNRR~K~KK~~k~ 68 (341)
.++|||++.+-+..+|.+|+..|..||||+..+|++||++++++..||.+||.|+|-|+||...+
T Consensus 188 arRKRRNFsK~aTeiLneyF~~h~~nPYPSee~K~eLAkqCnItvsQvsnwfgnkrIrykK~~~k 252 (334)
T KOG0774|consen 188 ARRKRRNFSKQATEILNEYFYSHLSNPYPSEEAKEELAKQCNITVSQVSNWFGNKRIRYKKNMGK 252 (334)
T ss_pred HHHhhcccchhHHHHHHHHHHHhcCCCCCcHHHHHHHHHHcCceehhhccccccceeehhhhhhh
Confidence 45678899999999999999999999999999999999999999999999999999999987543
No 31
>smart00548 IRO Motif in Iroquois-class homeodomain proteins (only). Unknown function.
Probab=98.68 E-value=5.7e-09 Score=65.98 Aligned_cols=18 Identities=50% Similarity=0.900 Sum_probs=15.3
Q ss_pred CCCCccccchhhcccCCC
Q psy5913 192 VNKPRIWSLADMASKEND 209 (341)
Q Consensus 192 ~~kPkiWsla~~at~d~~ 209 (341)
..||||||||||||+|..
T Consensus 3 ~~KPKIWSLAetAts~~~ 20 (26)
T smart00548 3 AAKPKIWSLADTATSSXX 20 (26)
T ss_pred CCCCceeeHHHhhhcccc
Confidence 469999999999998543
No 32
>KOG0773|consensus
Probab=98.32 E-value=2.4e-07 Score=90.72 Aligned_cols=60 Identities=47% Similarity=0.720 Sum_probs=55.2
Q ss_pred CCCCCcccHHHHHHHHHHHhcCCCCCHHHHHHHHHHhCCCccccccchhhhHHHHhhhhc
Q psy5913 8 RKNATRETTSTLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKKENK 67 (341)
Q Consensus 8 RR~Rt~fS~~QL~~Le~~F~~npYPs~~eR~~LA~~lgLsesQVkvWFQNRR~K~KK~~k 67 (341)
++..+..+..+|+.|+..|..++||+..+|..|+.++||+..||.+||.|.|.|.++...
T Consensus 243 ~~~lP~~a~~ilr~Wl~~h~~~PYPse~~K~~La~~TGLs~~Qv~NWFINaR~R~w~p~~ 302 (342)
T KOG0773|consen 243 QRGLPKEAVSILRAWLFEHLLHPYPSDDEKLMLAKQTGLSRPQVSNWFINARVRLWKPMI 302 (342)
T ss_pred CCCCCHHHHHHHHHHHHHhccCCCCcchhccccchhcCCCcccCCchhhhcccccCCchH
Confidence 446778899999999999999999999999999999999999999999999999887644
No 33
>KOG1168|consensus
Probab=98.14 E-value=1.2e-06 Score=84.77 Aligned_cols=63 Identities=17% Similarity=0.322 Sum_probs=56.5
Q ss_pred CCCCCCCCCcccHHHHHHHHHHHhcCCCCCHHHHHHHHHHhCCCccccccchhhhHHHHhhhh
Q psy5913 4 NGARRKNATRETTSTLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKKEN 66 (341)
Q Consensus 4 ~~krRR~Rt~fS~~QL~~Le~~F~~npYPs~~eR~~LA~~lgLsesQVkvWFQNRR~K~KK~~ 66 (341)
.+.|||+||.+..-.-+.||..|..+|-|+......+|.+|.|-...|+|||+|+|.|.||.+
T Consensus 306 ~~ekKRKRTSIAAPEKRsLEayFavQPRPS~EkIAaIAekLDLKKNVVRVWFCNQRQKQKRm~ 368 (385)
T KOG1168|consen 306 GGEKKRKRTSIAAPEKRSLEAYFAVQPRPSGEKIAAIAEKLDLKKNVVRVWFCNQRQKQKRMK 368 (385)
T ss_pred ccccccccccccCcccccHHHHhccCCCCchhHHHHHHHhhhhhhceEEEEeeccHHHHHHhh
Confidence 346788899888888899999999999999887778999999999999999999999999854
No 34
>KOG2252|consensus
Probab=97.76 E-value=2.7e-05 Score=80.80 Aligned_cols=57 Identities=23% Similarity=0.261 Sum_probs=54.0
Q ss_pred CCCCCCCcccHHHHHHHHHHHhcCCCCCHHHHHHHHHHhCCCccccccchhhhHHHH
Q psy5913 6 ARRKNATRETTSTLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRL 62 (341)
Q Consensus 6 krRR~Rt~fS~~QL~~Le~~F~~npYPs~~eR~~LA~~lgLsesQVkvWFQNRR~K~ 62 (341)
+-||.|..|+..|.+.|...|+.+++|+..+.+.|+.+|+|..+.|.|||-|.|+|.
T Consensus 419 ~~KKPRlVfTd~QkrTL~aiFke~~RPS~Emq~tIS~qL~L~~sTV~NfFmNaRRRs 475 (558)
T KOG2252|consen 419 QTKKPRLVFTDIQKRTLQAIFKENKRPSREMQETISQQLNLELSTVINFFMNARRRS 475 (558)
T ss_pred cCCCceeeecHHHHHHHHHHHhcCCCCCHHHHHHHHHHhCCcHHHHHHHHHhhhhhc
Confidence 446689999999999999999999999999999999999999999999999999986
No 35
>KOG0490|consensus
Probab=97.68 E-value=3.8e-05 Score=69.92 Aligned_cols=64 Identities=25% Similarity=0.402 Sum_probs=58.9
Q ss_pred CCCCCCCCCcccHHHHHHHHHHHhcCCCCCHHHHHHHHHHhCCCccccccchhhhHHHHhhhhc
Q psy5913 4 NGARRKNATRETTSTLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKKENK 67 (341)
Q Consensus 4 ~~krRR~Rt~fS~~QL~~Le~~F~~npYPs~~eR~~LA~~lgLsesQVkvWFQNRR~K~KK~~k 67 (341)
..+.++.++.+...|+..+...|...+||....+..|+..+++....|++||||+|.+.++...
T Consensus 150 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~P~~~~~~~l~~~~~~~~~~~q~~~~~~~~~~~~~~~ 213 (235)
T KOG0490|consen 150 NKKPRRPRTTFTENQLEVLETVFRATPKPDADDREQLAEETGLSERVIQVWFQNRRAKLRKHKR 213 (235)
T ss_pred ccccCCCccccccchhHhhhhcccCCCCCchhhHHHHHHhcCCChhhhhhhcccHHHHHHhhcc
Confidence 3566778899999999999999999999999999999999999999999999999999998644
No 36
>KOG1146|consensus
Probab=96.89 E-value=0.00061 Score=76.81 Aligned_cols=61 Identities=28% Similarity=0.294 Sum_probs=56.9
Q ss_pred CCCCCCcccHHHHHHHHHHHhcCCCCCHHHHHHHHHHhCCCccccccchhhhHHHHhhhhc
Q psy5913 7 RRKNATRETTSTLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKKENK 67 (341)
Q Consensus 7 rRR~Rt~fS~~QL~~Le~~F~~npYPs~~eR~~LA~~lgLsesQVkvWFQNRR~K~KK~~k 67 (341)
+|+.|++++..||+.+...|....|+...+-+.|.+.++|..+.|++||||.|.|.||...
T Consensus 903 r~a~~~~~~d~qlk~i~~~~~~q~~~~~~~~E~l~~~~~~~~~~i~vw~qna~~~s~k~~~ 963 (1406)
T KOG1146|consen 903 RRAYRTQESDLQLKIIKACYEAQRTPTMQECEVLEEPIGLPKRVIQVWFQNARAKSKKAKL 963 (1406)
T ss_pred hhhhccchhHHHHHHHHHHHhhccCChHHHHHhhcccccCCcchhHHhhhhhhhhhhhhhh
Confidence 5668999999999999999999999999999999999999999999999999999998744
No 37
>KOG0773|consensus
Probab=96.86 E-value=0.001 Score=65.31 Aligned_cols=76 Identities=72% Similarity=1.059 Sum_probs=66.3
Q ss_pred CCCCCCCCCcccHHHHHHHHHHHhcCCCCCHHHHHHHHHHhCCCccccccchhhhHHHHhhhhcccCCCCCcccccc
Q psy5913 4 NGARRKNATRETTSTLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKKENKMTWEPRNRVEDED 80 (341)
Q Consensus 4 ~~krRR~Rt~fS~~QL~~Le~~F~~npYPs~~eR~~LA~~lgLsesQVkvWFQNRR~K~KK~~k~~~~~~~~~ee~~ 80 (341)
.++++++.++.+ ..++.|..++..++|++..++..|+..+.|+..||.+||.|.|++.++..++.+..........
T Consensus 95 ~~~~~~n~~~~s-~~~~~~~~~~~~~~~~~k~~~~ll~~~~~~~~~~~~~~~~~a~r~~~~~~~~~~~~~~~~~~~~ 170 (342)
T KOG0773|consen 95 KGARRGNATRES-ATLKAWLEEHRLNPYPSKLEKILLAVITKLTLTQVSTWFANARRRLKKELKMTWGPTPLALDGI 170 (342)
T ss_pred cccccccccccc-cccccchhhhhhccCchHHHHHHHHHHHHhhhhhHHHHHHHHHHHHHhccCCCCCCccccccch
Confidence 345666778888 8999999999999999999999999999999999999999999999999998888765555443
No 38
>PF11569 Homez: Homeodomain leucine-zipper encoding, Homez; PDB: 2YS9_A.
Probab=94.61 E-value=0.011 Score=44.69 Aligned_cols=39 Identities=21% Similarity=0.215 Sum_probs=27.9
Q ss_pred HHHHHhcCCCCCHHHHHHHHHHhCCCccccccchhhhHH
Q psy5913 22 WLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARR 60 (341)
Q Consensus 22 Le~~F~~npYPs~~eR~~LA~~lgLsesQVkvWFQNRR~ 60 (341)
|+.-|...+++...+-..|+.+++|+..||+.||..++.
T Consensus 13 L~~Yy~~h~~L~E~DL~~L~~kS~ms~qqVr~WFa~~~~ 51 (56)
T PF11569_consen 13 LEDYYLKHKQLQEEDLDELCDKSRMSYQQVRDWFAERMQ 51 (56)
T ss_dssp HHHHHHHT----TTHHHHHHHHTT--HHHHHHHHHHHS-
T ss_pred HHHHHHHcCCccHhhHHHHHHHHCCCHHHHHHHHHHhcc
Confidence 566678888999899999999999999999999987543
No 39
>PF04218 CENP-B_N: CENP-B N-terminal DNA-binding domain; InterPro: IPR006695 Centromere Protein B (CENP-B) is a DNA-binding protein localized to the centromere. Within the N-terminal 125 residues, there is a DNA-binding region, which binds to a corresponding 17bp CENP-B box sequence. CENP-B dimers either bind two separate DNA molecules or alternatively, they may bind two CENP-B boxes on one DNA molecule, with the intervening stretch of DNA forming a loop structure. The CENP-B DNA-binding domain consists of two repeating domains, RP1 and RP2. This family corresponds to RP1 has been shown to consist of four helices in a helix-turn-helix structure [].; GO: 0003677 DNA binding, 0000775 chromosome, centromeric region; PDB: 1BW6_A 1HLV_A 2ELH_A.
Probab=87.17 E-value=1.1 Score=32.98 Aligned_cols=47 Identities=15% Similarity=0.077 Sum_probs=33.7
Q ss_pred CCCCCcccHHHHHHHHHHHhcCCCCCHHHHHHHHHHhCCCccccccchhhhH
Q psy5913 8 RKNATRETTSTLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANAR 59 (341)
Q Consensus 8 RR~Rt~fS~~QL~~Le~~F~~npYPs~~eR~~LA~~lgLsesQVkvWFQNRR 59 (341)
||.|...|-.+-..+...++... ....||+.+|+..++|..|..|+.
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 45667777777777777778776 467899999999999999999953
No 40
>KOG3623|consensus
Probab=84.09 E-value=1.3 Score=48.62 Aligned_cols=52 Identities=13% Similarity=0.144 Sum_probs=44.0
Q ss_pred HHHHHHHHhcCCCCCHHHHHHHHHHhCCCccccccchhhhHHHHhhhhcccC
Q psy5913 19 LKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKKENKMTW 70 (341)
Q Consensus 19 L~~Le~~F~~npYPs~~eR~~LA~~lgLsesQVkvWFQNRR~K~KK~~k~~~ 70 (341)
+..|...|..|.+|+..+-..+|.+.||...-|+.||++++.+...-.+...
T Consensus 568 ~sllkayyaln~~ps~eelskia~qvglp~~vvk~wfE~~~a~e~sv~rsps 619 (1007)
T KOG3623|consen 568 TSLLKAYYALNGLPSEEELSKIAQQVGLPFAVVKAWFEDEEAEEMSVERSPS 619 (1007)
T ss_pred HHHHHHHHHhcCCCCHHHHHHHHHHhcccHHHHHHHHHhhhhhhhhhccCcc
Confidence 3445556899999999999999999999999999999999998877654444
No 41
>PF12522 UL73_N: Cytomegalovirus glycoprotein N terminal; InterPro: IPR021003 This domain family is found in viruses, and is approximately 30 amino acids in length. The signature is found in association with PF03554 from PFAM. This family is an envelope glycoprotein of (Human herpesvirus 5) [].
Probab=58.00 E-value=6.9 Score=25.37 Aligned_cols=22 Identities=36% Similarity=0.450 Sum_probs=16.2
Q ss_pred ccceeecccccccCCCCCCcCC
Q psy5913 307 FGLAVTAGASSASSSGSSVSES 328 (341)
Q Consensus 307 ~~~~~~~~~~~~~~~~~~~~~~ 328 (341)
|-++|++|.++.++|++++...
T Consensus 4 lvlSv~~gSs~n~sSTsts~tt 25 (27)
T PF12522_consen 4 LVLSVAAGSSGNNSSTSTSATT 25 (27)
T ss_pred EEEEEEeccccCCccccccccC
Confidence 4578899988888877766543
No 42
>KOG0943|consensus
Probab=57.73 E-value=95 Score=37.02 Aligned_cols=7 Identities=29% Similarity=0.638 Sum_probs=3.9
Q ss_pred chhhhhh
Q psy5913 259 STEFLEQ 265 (341)
Q Consensus 259 ~~~~l~~ 265 (341)
--+||..
T Consensus 1930 rssflSN 1936 (3015)
T KOG0943|consen 1930 RSSFLSN 1936 (3015)
T ss_pred hhhhhhh
Confidence 3466664
No 43
>PF06284 Cytomega_UL84: Cytomegalovirus UL84 protein; InterPro: IPR010436 This family consists of several Cytomegalovirus UL84 proteins. The open reading frame UL84 of human cytomegalovirus encodes a multifunctional regulatory protein which is required for viral DNA replication and binds with high affinity to the immediate-early transactivator IE2-p86 [].
Probab=50.85 E-value=5.2 Score=41.55 Aligned_cols=11 Identities=55% Similarity=1.280 Sum_probs=10.0
Q ss_pred cccc-ccCCCCC
Q psy5913 244 DLYR-LYGSHLG 254 (341)
Q Consensus 244 ~~~r-~~~~~~~ 254 (341)
-+|| |||||||
T Consensus 393 RiYRrfYGp~LG 404 (530)
T PF06284_consen 393 RIYRRFYGPFLG 404 (530)
T ss_pred ehhhhhccccee
Confidence 4699 9999999
No 44
>KOG1924|consensus
Probab=42.73 E-value=85 Score=35.47 Aligned_cols=10 Identities=20% Similarity=0.301 Sum_probs=5.3
Q ss_pred CCcccc--ccCC
Q psy5913 242 RHDLYR--LYGS 251 (341)
Q Consensus 242 ~~~~~r--~~~~ 251 (341)
+|+|-- +|-|
T Consensus 611 P~gLkpKK~~k~ 622 (1102)
T KOG1924|consen 611 PFGLKPKKVYKP 622 (1102)
T ss_pred CCCCCccccCCC
Confidence 555544 6655
No 45
>cd06171 Sigma70_r4 Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in Escherichia coli (Ec) sigma70, the main housekeeping sigma, and related sigma-factors (SFs). A SF is a dissociable subunit of RNA polymerase, it directs bacterial or plastid core RNA polymerase to specific promoter elements located upstream of transcription initiation points. The SR4 of Ec sigma70 and other essential primary SFs contact promoter sequences located 35 base-pairs upstream of the initiation point, recognizing a 6-base-pair -35 consensus TTGACA. Sigma70 related SFs also include SFs which are dispensable for bacterial cell growth for example Ec sigmaS, SFs which activate regulons in response to a specific signal for example heat-shock Ec sigmaH, and a group of SFs which includes the extracytoplasmic function (ECF) SFs and is typified by Ec sigmaE which contains SR2 and -4 only. ECF SFs direct the transcription of genes that regulate various responses including periplas
Probab=38.51 E-value=36 Score=22.56 Aligned_cols=27 Identities=19% Similarity=0.199 Sum_probs=22.0
Q ss_pred HHHHHHHhCCCccccccchhhhHHHHh
Q psy5913 37 KIMLAIITKMTLTQVSTWFANARRRLK 63 (341)
Q Consensus 37 R~~LA~~lgLsesQVkvWFQNRR~K~K 63 (341)
-..+|..+|++...|..|....+.+.|
T Consensus 29 ~~~ia~~~~~s~~~i~~~~~~~~~~l~ 55 (55)
T cd06171 29 YEEIAEILGISRSTVRQRLHRALKKLR 55 (55)
T ss_pred HHHHHHHHCcCHHHHHHHHHHHHHHcC
Confidence 456799999999999999887766643
No 46
>PF04545 Sigma70_r4: Sigma-70, region 4; InterPro: IPR007630 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognised by the major sigma factors [, ]. Region 4 of sigma-70 like sigma-factors is involved in binding to the -35 promoter element via a helix-turn-helix motif []. Due to the way Pfam works, the threshold has been set artificially high to prevent overlaps with other helix-turn-helix families. Therefore there are many false negatives.; GO: 0003677 DNA binding, 0003700 sequence-specific DNA binding transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, DNA-dependent, 0006355 regulation of transcription, DNA-dependent; PDB: 2P7V_B 3IYD_F 1TLH_B 1KU7_A 1RIO_H 3N97_A 1KU3_A 1RP3_C 1SC5_A 1NR3_A ....
Probab=34.74 E-value=55 Score=22.89 Aligned_cols=45 Identities=11% Similarity=-0.006 Sum_probs=31.4
Q ss_pred cHHHHHHHHHHHhcCCCCCHHHHHHHHHHhCCCccccccchhhhHHHHhh
Q psy5913 15 TTSTLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKK 64 (341)
Q Consensus 15 S~~QL~~Le~~F~~npYPs~~eR~~LA~~lgLsesQVkvWFQNRR~K~KK 64 (341)
+..+.+.+...|.... .-.++|..+|++...|+.+......|.|+
T Consensus 6 ~~~er~vi~~~y~~~~-----t~~eIa~~lg~s~~~V~~~~~~al~kLR~ 50 (50)
T PF04545_consen 6 PPREREVIRLRYFEGL-----TLEEIAERLGISRSTVRRILKRALKKLRK 50 (50)
T ss_dssp -HHHHHHHHHHHTST------SHHHHHHHHTSCHHHHHHHHHHHHHHHHH
T ss_pred CHHHHHHHHHHhcCCC-----CHHHHHHHHCCcHHHHHHHHHHHHHHhcC
Confidence 3445555555563332 34578999999999999999888888774
No 47
>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=33.89 E-value=52 Score=23.19 Aligned_cols=28 Identities=21% Similarity=0.222 Sum_probs=21.5
Q ss_pred HHHHHHHHHhCCCccccccchhhhHHHH
Q psy5913 35 GEKIMLAIITKMTLTQVSTWFANARRRL 62 (341)
Q Consensus 35 ~eR~~LA~~lgLsesQVkvWFQNRR~K~ 62 (341)
-.-.++|..+|++...|++|....|.+.
T Consensus 27 ~s~~eIa~~l~~s~~~v~~~l~ra~~~L 54 (54)
T PF08281_consen 27 MSYAEIAEILGISESTVKRRLRRARKKL 54 (54)
T ss_dssp --HHHHHHHCTS-HHHHHHHHHHHHHHH
T ss_pred cCHHHHHHHHCcCHHHHHHHHHHHHhhC
Confidence 3566789999999999999999877653
No 48
>KOG1146|consensus
Probab=33.30 E-value=13 Score=43.35 Aligned_cols=56 Identities=11% Similarity=-0.029 Sum_probs=49.1
Q ss_pred CCCcccHHHHHHHHHHHhcCCCCCHHHHHHHHHHhCCCccccccchhhhHHHHhhh
Q psy5913 10 NATRETTSTLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKKE 65 (341)
Q Consensus 10 ~Rt~fS~~QL~~Le~~F~~npYPs~~eR~~LA~~lgLsesQVkvWFQNRR~K~KK~ 65 (341)
.++++...|+..|-.+|+...||.-.++..++..+++..+.+-.||++++-+|.+.
T Consensus 447 ~s~r~~~~~t~~L~S~~kt~~cpkc~~~yk~a~~L~vhmRskhp~~~~~~c~~gq~ 502 (1406)
T KOG1146|consen 447 ESKRSLEGQTVVLHSFFKTLKCPKCNWHYKLAQTLGVHMRSKHPESQSAYCKAGQN 502 (1406)
T ss_pred hhhcccccceeeeecccccccCCccchhhhhHHHhhhcccccccccchhHhHhccc
Confidence 56777788888888889999999999999999999999999899999977777765
No 49
>PRK03975 tfx putative transcriptional regulator; Provisional
Probab=33.26 E-value=62 Score=28.72 Aligned_cols=48 Identities=17% Similarity=0.099 Sum_probs=35.6
Q ss_pred cccHHHHHHHHHHHhcCCCCCHHHHHHHHHHhCCCccccccchhhhHHHHhhhh
Q psy5913 13 RETTSTLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKKEN 66 (341)
Q Consensus 13 ~fS~~QL~~Le~~F~~npYPs~~eR~~LA~~lgLsesQVkvWFQNRR~K~KK~~ 66 (341)
..+..|.+.|... .... ...++|..+|++...|+.|.++.+.|+|+..
T Consensus 6 ~Lt~rqreVL~lr-~~Gl-----Tq~EIAe~LGiS~~tVs~ie~ra~kkLr~~~ 53 (141)
T PRK03975 6 FLTERQIEVLRLR-ERGL-----TQQEIADILGTSRANVSSIEKRARENIEKAR 53 (141)
T ss_pred CCCHHHHHHHHHH-HcCC-----CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 4456666666553 2222 3457899999999999999999999988763
No 50
>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=31.58 E-value=22 Score=26.69 Aligned_cols=46 Identities=11% Similarity=0.027 Sum_probs=26.7
Q ss_pred CCCcccHHHHHHHHHHHhcCCCCCHHHHHHHHHHhCCCccccccchhhhH
Q psy5913 10 NATRETTSTLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANAR 59 (341)
Q Consensus 10 ~Rt~fS~~QL~~Le~~F~~npYPs~~eR~~LA~~lgLsesQVkvWFQNRR 59 (341)
.+..++..+-..+...+... ......+|..+|++..+|..|-.-.+
T Consensus 3 ~r~~ys~e~K~~~v~~~~~~----g~sv~~va~~~gi~~~~l~~W~~~~~ 48 (76)
T PF01527_consen 3 KRRRYSPEFKLQAVREYLES----GESVSEVAREYGISPSTLYNWRKQYR 48 (76)
T ss_dssp SS----HHHHHHHHHHHHHH----HCHHHHHHHHHTS-HHHHHHHHHHHH
T ss_pred CCCCCCHHHHHHHHHHHHHC----CCceEeeecccccccccccHHHHHHh
Confidence 44556665555555444222 23456789999999999998876544
No 51
>PRK09646 RNA polymerase sigma factor SigK; Reviewed
Probab=29.73 E-value=75 Score=28.20 Aligned_cols=32 Identities=19% Similarity=0.041 Sum_probs=27.1
Q ss_pred HHHHHHHHhCCCccccccchhhhHHHHhhhhc
Q psy5913 36 EKIMLAIITKMTLTQVSTWFANARRRLKKENK 67 (341)
Q Consensus 36 eR~~LA~~lgLsesQVkvWFQNRR~K~KK~~k 67 (341)
.-.++|..+|++...|+++....|.++|+..+
T Consensus 160 s~~EIA~~Lgis~~tVk~~l~ra~~~Lr~~l~ 191 (194)
T PRK09646 160 TYREVAERLAVPLGTVKTRMRDGLIRLRDCLG 191 (194)
T ss_pred CHHHHHHHhCCChHhHHHHHHHHHHHHHHHhc
Confidence 34567899999999999999999999988654
No 52
>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=28.96 E-value=56 Score=27.14 Aligned_cols=32 Identities=28% Similarity=0.364 Sum_probs=17.2
Q ss_pred HHHHHhcCCCCCHHHHHHHHHHhCCCccccccchhhhHHHHhhhhc
Q psy5913 22 WLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKKENK 67 (341)
Q Consensus 22 Le~~F~~npYPs~~eR~~LA~~lgLsesQVkvWFQNRR~K~KK~~k 67 (341)
....|+.||||...-... |+ .|||.|||+...
T Consensus 17 Ik~LyqsnPyP~~~GTr~-aR-------------RnRRRRWR~rq~ 48 (91)
T PF00424_consen 17 IKILYQSNPYPSPEGTRQ-AR-------------RNRRRRWRARQR 48 (91)
T ss_dssp HHHHHHTS-S--S-S-HH-HH-------------HHHHHHHHHHHH
T ss_pred HHHHHccccCCCCCCccc-cc-------------cchhhhHHHHHH
Confidence 334468899998553222 11 589999998743
No 53
>PF13443 HTH_26: Cro/C1-type HTH DNA-binding domain; PDB: 3TYR_A 3TYS_A 3B7H_A.
Probab=28.90 E-value=22 Score=25.76 Aligned_cols=26 Identities=15% Similarity=0.048 Sum_probs=18.3
Q ss_pred HHHHHHHhCCCccccccchhhhHHHH
Q psy5913 37 KIMLAIITKMTLTQVSTWFANARRRL 62 (341)
Q Consensus 37 R~~LA~~lgLsesQVkvWFQNRR~K~ 62 (341)
...||+.+|++..+|..|+.++..++
T Consensus 13 ~~~La~~~gis~~tl~~~~~~~~~~~ 38 (63)
T PF13443_consen 13 QKDLARKTGISRSTLSRILNGKPSNP 38 (63)
T ss_dssp HHHHHHHHT--HHHHHHHHTTT----
T ss_pred HHHHHHHHCcCHHHHHHHHhcccccc
Confidence 56799999999999999999884443
No 54
>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=27.66 E-value=98 Score=17.99 Aligned_cols=19 Identities=5% Similarity=0.032 Sum_probs=15.2
Q ss_pred HHHHHHHhCCCccccccch
Q psy5913 37 KIMLAIITKMTLTQVSTWF 55 (341)
Q Consensus 37 R~~LA~~lgLsesQVkvWF 55 (341)
...++..++++...|..|.
T Consensus 24 ~~~ia~~~~is~~tv~~~~ 42 (42)
T cd00569 24 VAEIARRLGVSRSTLYRYL 42 (42)
T ss_pred HHHHHHHHCCCHHHHHHhC
Confidence 4577889999988888774
No 55
>PRK06759 RNA polymerase factor sigma-70; Validated
Probab=27.30 E-value=73 Score=26.70 Aligned_cols=30 Identities=23% Similarity=0.241 Sum_probs=25.6
Q ss_pred HHHHHHHHhCCCccccccchhhhHHHHhhh
Q psy5913 36 EKIMLAIITKMTLTQVSTWFANARRRLKKE 65 (341)
Q Consensus 36 eR~~LA~~lgLsesQVkvWFQNRR~K~KK~ 65 (341)
.-.++|..+|++...|++|....|.|+|+.
T Consensus 124 s~~EIA~~l~is~~tV~~~~~ra~~~Lr~~ 153 (154)
T PRK06759 124 TMGEIALETEMTYYQVRWIYRQALEKMRNS 153 (154)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHhhc
Confidence 356789999999999999999888888763
No 56
>PRK13908 putative recombination protein RecO; Provisional
Probab=25.71 E-value=22 Score=33.42 Aligned_cols=9 Identities=56% Similarity=1.280 Sum_probs=7.8
Q ss_pred CccccccCC
Q psy5913 243 HDLYRLYGS 251 (341)
Q Consensus 243 ~~~~r~~~~ 251 (341)
+-+|||||.
T Consensus 27 ~tlYRFYGA 35 (204)
T PRK13908 27 KTLYRFYGA 35 (204)
T ss_pred HHHHHhccc
Confidence 468999999
No 57
>PRK11924 RNA polymerase sigma factor; Provisional
Probab=25.17 E-value=83 Score=26.68 Aligned_cols=32 Identities=19% Similarity=0.147 Sum_probs=27.6
Q ss_pred HHHHHHHhCCCccccccchhhhHHHHhhhhcc
Q psy5913 37 KIMLAIITKMTLTQVSTWFANARRRLKKENKM 68 (341)
Q Consensus 37 R~~LA~~lgLsesQVkvWFQNRR~K~KK~~k~ 68 (341)
-.++|..+|++...|.+|..-.|.|+|+..+.
T Consensus 144 ~~eIA~~lgis~~tv~~~~~ra~~~lr~~l~~ 175 (179)
T PRK11924 144 YREIAEILGVPVGTVKSRLRRARQLLRECLEA 175 (179)
T ss_pred HHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHH
Confidence 45789999999999999999999999886543
No 58
>PRK09480 slmA division inhibitor protein; Provisional
Probab=24.86 E-value=65 Score=27.86 Aligned_cols=47 Identities=15% Similarity=0.118 Sum_probs=37.0
Q ss_pred cccHHHHHHHHHHHhcCCCCCHHHHHHHHHHhCCCccccccchhhhHH
Q psy5913 13 RETTSTLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARR 60 (341)
Q Consensus 13 ~fS~~QL~~Le~~F~~npYPs~~eR~~LA~~lgLsesQVkvWFQNRR~ 60 (341)
.....+++.....|..+++ ....-..+|+..|++...+-.+|.|+-.
T Consensus 10 ~~r~~Il~aa~~l~~~~~G-~~~ti~~Ia~~agvs~gt~Y~~F~~K~~ 56 (194)
T PRK09480 10 ERREQILQALAQMLESPPG-ERITTAKLAARVGVSEAALYRHFPSKAR 56 (194)
T ss_pred hHHHHHHHHHHHHHHhcCC-CccCHHHHHHHhCCCHhHHHHHCCCHHH
Confidence 3345666776777777666 6677778999999999999999999764
No 59
>PRK12512 RNA polymerase sigma factor; Provisional
Probab=24.63 E-value=1.1e+02 Score=26.74 Aligned_cols=32 Identities=13% Similarity=-0.050 Sum_probs=27.6
Q ss_pred HHHHHHHHhCCCccccccchhhhHHHHhhhhc
Q psy5913 36 EKIMLAIITKMTLTQVSTWFANARRRLKKENK 67 (341)
Q Consensus 36 eR~~LA~~lgLsesQVkvWFQNRR~K~KK~~k 67 (341)
.-.++|..+|++...|++++...|.++|+...
T Consensus 149 s~~eIA~~l~is~~tV~~~l~ra~~~Lr~~l~ 180 (184)
T PRK12512 149 SIKETAAKLSMSEGAVRVALHRGLAALAAKFR 180 (184)
T ss_pred CHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhh
Confidence 35578999999999999999999999998754
No 60
>PRK12515 RNA polymerase sigma factor; Provisional
Probab=24.01 E-value=1e+02 Score=27.14 Aligned_cols=33 Identities=21% Similarity=0.143 Sum_probs=27.6
Q ss_pred HHHHHHHHhCCCccccccchhhhHHHHhhhhcc
Q psy5913 36 EKIMLAIITKMTLTQVSTWFANARRRLKKENKM 68 (341)
Q Consensus 36 eR~~LA~~lgLsesQVkvWFQNRR~K~KK~~k~ 68 (341)
.-.++|..+|++...|++.+...|.++|+..+.
T Consensus 149 s~~eIA~~lgis~~tV~~~l~Rar~~Lr~~l~~ 181 (189)
T PRK12515 149 SVEEVGEIVGIPESTVKTRMFYARKKLAELLKA 181 (189)
T ss_pred CHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHH
Confidence 345678899999999999999999999987554
No 61
>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=23.78 E-value=87 Score=22.58 Aligned_cols=47 Identities=11% Similarity=-0.035 Sum_probs=31.5
Q ss_pred cccHHHHHHHHHHHhcCCCCCHHHHHHHHHHhCCCccccccchhhhHHHHhhh
Q psy5913 13 RETTSTLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKKE 65 (341)
Q Consensus 13 ~fS~~QL~~Le~~F~~npYPs~~eR~~LA~~lgLsesQVkvWFQNRR~K~KK~ 65 (341)
.+|..+++.+.....-. ...++|..+++++..|..+..+-+.|+.-.
T Consensus 3 ~LT~~E~~vl~~l~~G~------~~~eIA~~l~is~~tV~~~~~~i~~Kl~~~ 49 (58)
T PF00196_consen 3 SLTERELEVLRLLAQGM------SNKEIAEELGISEKTVKSHRRRIMKKLGVK 49 (58)
T ss_dssp SS-HHHHHHHHHHHTTS-------HHHHHHHHTSHHHHHHHHHHHHHHHHT-S
T ss_pred ccCHHHHHHHHHHHhcC------CcchhHHhcCcchhhHHHHHHHHHHHhCCC
Confidence 45555555554333322 356789999999999999999988887644
No 62
>PRK12526 RNA polymerase sigma factor; Provisional
Probab=23.75 E-value=96 Score=27.95 Aligned_cols=32 Identities=22% Similarity=0.134 Sum_probs=26.9
Q ss_pred HHHHHHHHhCCCccccccchhhhHHHHhhhhc
Q psy5913 36 EKIMLAIITKMTLTQVSTWFANARRRLKKENK 67 (341)
Q Consensus 36 eR~~LA~~lgLsesQVkvWFQNRR~K~KK~~k 67 (341)
.-.++|..+|+++..|++++...|.++|+..+
T Consensus 171 s~~EIA~~lgis~~tV~~~l~Ra~~~Lr~~l~ 202 (206)
T PRK12526 171 SQEQLAQQLNVPLGTVKSRLRLALAKLKVQMG 202 (206)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHh
Confidence 34567999999999999999999999887643
No 63
>PRK09642 RNA polymerase sigma factor SigW; Reviewed
Probab=23.74 E-value=1e+02 Score=26.16 Aligned_cols=31 Identities=26% Similarity=0.265 Sum_probs=26.5
Q ss_pred HHHHHHHhCCCccccccchhhhHHHHhhhhc
Q psy5913 37 KIMLAIITKMTLTQVSTWFANARRRLKKENK 67 (341)
Q Consensus 37 R~~LA~~lgLsesQVkvWFQNRR~K~KK~~k 67 (341)
-.++|..+|+++..|++++...|.++|+..+
T Consensus 125 ~~EIA~~lgis~~tV~~~l~Rar~~Lr~~l~ 155 (160)
T PRK09642 125 YQEIALQEKIEVKTVEMKLYRARKWIKKHWK 155 (160)
T ss_pred HHHHHHHHCCCHHHHHHHHHHHHHHHHHHHh
Confidence 3467899999999999999999999888754
No 64
>PRK12519 RNA polymerase sigma factor; Provisional
Probab=23.44 E-value=78 Score=27.83 Aligned_cols=32 Identities=13% Similarity=-0.013 Sum_probs=27.1
Q ss_pred HHHHHHHHHhCCCccccccchhhhHHHHhhhh
Q psy5913 35 GEKIMLAIITKMTLTQVSTWFANARRRLKKEN 66 (341)
Q Consensus 35 ~eR~~LA~~lgLsesQVkvWFQNRR~K~KK~~ 66 (341)
..-.++|..+|++...|++|+...|.++|+..
T Consensus 158 ~s~~EIA~~lgis~~tV~~~l~Ra~~~Lr~~l 189 (194)
T PRK12519 158 LSQSEIAKRLGIPLGTVKARARQGLLKLRELL 189 (194)
T ss_pred CCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHH
Confidence 34567899999999999999999999988764
No 65
>PF01690 PLRV_ORF5: Potato leaf roll virus readthrough protein; InterPro: IPR002929 This family consists mainly of the Potato leafroll virus (PLrV) read through protein otherwise known as the minor capsid protein. This is generated via a readthrough of open reading frame 3, the coat protein, allowing transcription of open reading frame 5 to give an extended coat protein with a large C-terminal addition or read through domain []. The read through protein is essential for the circulative aphid transmission of PLrV [] and Beet western yellows virus []. The N-terminal region of the luteovirus readthrough domain determines virus binding to Buchnera GroEL and is essential for virus persistence in the aphid [].; GO: 0019028 viral capsid
Probab=22.37 E-value=80 Score=33.30 Aligned_cols=12 Identities=8% Similarity=0.202 Sum_probs=6.8
Q ss_pred CCCccccchhhc
Q psy5913 193 NKPRIWSLADMA 204 (341)
Q Consensus 193 ~kPkiWsla~~a 204 (341)
.+-|+|-..=+.
T Consensus 29 ~~~RF~~Y~G~p 40 (465)
T PF01690_consen 29 KHERFIGYEGVP 40 (465)
T ss_pred CccceEEEeccc
Confidence 355888654433
No 66
>PF13518 HTH_28: Helix-turn-helix domain
Probab=21.95 E-value=48 Score=22.87 Aligned_cols=24 Identities=17% Similarity=0.187 Sum_probs=19.8
Q ss_pred HHHHHHHhCCCccccccchhhhHH
Q psy5913 37 KIMLAIITKMTLTQVSTWFANARR 60 (341)
Q Consensus 37 R~~LA~~lgLsesQVkvWFQNRR~ 60 (341)
...+|..+|++..+|..|.+..+.
T Consensus 15 ~~~~a~~~gis~~tv~~w~~~y~~ 38 (52)
T PF13518_consen 15 VREIAREFGISRSTVYRWIKRYRE 38 (52)
T ss_pred HHHHHHHHCCCHhHHHHHHHHHHh
Confidence 446899999999999999886554
No 67
>PRK09652 RNA polymerase sigma factor RpoE; Provisional
Probab=21.70 E-value=1.1e+02 Score=25.95 Aligned_cols=31 Identities=19% Similarity=0.151 Sum_probs=26.1
Q ss_pred HHHHHHHhCCCccccccchhhhHHHHhhhhc
Q psy5913 37 KIMLAIITKMTLTQVSTWFANARRRLKKENK 67 (341)
Q Consensus 37 R~~LA~~lgLsesQVkvWFQNRR~K~KK~~k 67 (341)
-..+|..+|++...|++|....|.|+|+...
T Consensus 147 ~~eIA~~lgis~~tV~~~l~ra~~~Lr~~l~ 177 (182)
T PRK09652 147 YEEIAEIMGCPIGTVRSRIFRAREALRAKLQ 177 (182)
T ss_pred HHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Confidence 4467999999999999999988888887643
No 68
>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=20.54 E-value=42 Score=25.74 Aligned_cols=20 Identities=10% Similarity=0.129 Sum_probs=16.4
Q ss_pred HHHHHHHhCCCccccccchh
Q psy5913 37 KIMLAIITKMTLTQVSTWFA 56 (341)
Q Consensus 37 R~~LA~~lgLsesQVkvWFQ 56 (341)
-..+|.+||+++.+|..|=.
T Consensus 25 lkdIA~~Lgvs~~tIr~WK~ 44 (60)
T PF10668_consen 25 LKDIAEKLGVSESTIRKWKS 44 (60)
T ss_pred HHHHHHHHCCCHHHHHHHhh
Confidence 35689999999999988743
No 69
>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=20.50 E-value=1.5e+02 Score=25.71 Aligned_cols=31 Identities=16% Similarity=0.207 Sum_probs=26.8
Q ss_pred HHHHHHHhCCCccccccchhhhHHHHhhhhc
Q psy5913 37 KIMLAIITKMTLTQVSTWFANARRRLKKENK 67 (341)
Q Consensus 37 R~~LA~~lgLsesQVkvWFQNRR~K~KK~~k 67 (341)
-.++|..+|+++..|+++....|.++|+..+
T Consensus 119 ~~eIA~~lgis~~tV~~~l~Rar~~Lr~~l~ 149 (170)
T TIGR02959 119 QQEIAEKLGLSLSGAKSRVQRGRKKLKELLE 149 (170)
T ss_pred HHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Confidence 4567899999999999999999999988755
No 70
>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=20.44 E-value=41 Score=27.02 Aligned_cols=30 Identities=20% Similarity=0.268 Sum_probs=25.3
Q ss_pred HHHHHHHHhCCCccccccchhhhHHHHhhh
Q psy5913 36 EKIMLAIITKMTLTQVSTWFANARRRLKKE 65 (341)
Q Consensus 36 eR~~LA~~lgLsesQVkvWFQNRR~K~KK~ 65 (341)
.-..+|..+|++...|..|...-+.|.|+.
T Consensus 128 s~~eIA~~l~~s~~~v~~~~~~~~~kl~~~ 157 (158)
T TIGR02937 128 SYKEIAEILGISVGTVKRRLKRARKKLREL 157 (158)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHhh
Confidence 345789999999999999999888888763
No 71
>PRK09644 RNA polymerase sigma factor SigM; Provisional
Probab=20.14 E-value=1.2e+02 Score=25.85 Aligned_cols=32 Identities=22% Similarity=0.197 Sum_probs=27.3
Q ss_pred HHHHHHHHhCCCccccccchhhhHHHHhhhhc
Q psy5913 36 EKIMLAIITKMTLTQVSTWFANARRRLKKENK 67 (341)
Q Consensus 36 eR~~LA~~lgLsesQVkvWFQNRR~K~KK~~k 67 (341)
...++|..+|+++..|++|..-.|.|.|+..+
T Consensus 126 s~~eIA~~lgis~~tv~~~l~Rar~~Lr~~l~ 157 (165)
T PRK09644 126 TYEEAASVLDLKLNTYKSHLFRGRKRLKALLK 157 (165)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Confidence 35578899999999999999999999988754
Done!