Query psy14872
Match_columns 414
No_of_seqs 332 out of 2540
Neff 6.6
Searched_HMMs 46136
Date Fri Aug 16 22:57:53 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy14872.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/14872hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG0775|consensus 100.0 1.3E-44 2.7E-49 340.2 15.5 200 210-409 52-251 (304)
2 KOG0775|consensus 100.0 8.5E-38 1.8E-42 294.1 7.1 146 51-200 71-232 (304)
3 cd00086 homeodomain Homeodomai 99.3 4.3E-13 9.3E-18 100.3 2.9 54 148-201 4-57 (59)
4 smart00389 HOX Homeodomain. DN 99.3 7.7E-13 1.7E-17 98.1 3.7 51 150-200 6-56 (56)
5 PF00046 Homeobox: Homeobox do 99.3 7.3E-13 1.6E-17 98.9 3.6 55 337-391 3-57 (57)
6 KOG0843|consensus 99.3 1.4E-12 3.1E-17 117.2 5.5 61 336-396 104-164 (197)
7 PF00046 Homeobox: Homeobox do 99.3 2E-13 4.4E-18 101.9 -0.1 53 148-200 4-56 (57)
8 KOG0488|consensus 99.3 1.2E-12 2.6E-17 129.8 4.8 67 334-400 172-238 (309)
9 KOG2251|consensus 99.3 3E-12 6.6E-17 118.7 6.9 67 329-395 32-98 (228)
10 KOG0489|consensus 99.3 1.7E-12 3.7E-17 126.3 3.8 66 334-399 159-224 (261)
11 KOG0493|consensus 99.3 2.1E-12 4.5E-17 121.9 4.1 95 108-206 212-308 (342)
12 KOG0850|consensus 99.3 3.6E-12 7.8E-17 118.7 5.4 71 337-407 125-195 (245)
13 KOG0490|consensus 99.3 1.8E-11 3.8E-16 116.1 10.2 147 150-394 66-213 (235)
14 KOG3802|consensus 99.3 6.1E-12 1.3E-16 125.8 7.0 117 258-394 213-354 (398)
15 KOG0487|consensus 99.2 2.8E-12 6E-17 125.8 2.3 61 144-204 235-295 (308)
16 KOG0484|consensus 99.2 4.7E-12 1E-16 104.1 2.5 58 336-393 19-76 (125)
17 KOG0850|consensus 99.2 2.8E-12 6E-17 119.5 1.0 71 126-205 112-183 (245)
18 KOG0842|consensus 99.2 1.3E-11 2.7E-16 121.1 5.6 62 338-399 157-218 (307)
19 cd00086 homeodomain Homeodomai 99.2 1.1E-11 2.4E-16 92.5 3.9 55 338-392 4-58 (59)
20 KOG0487|consensus 99.2 8.6E-12 1.9E-16 122.4 4.0 62 334-395 235-296 (308)
21 KOG0492|consensus 99.2 9.9E-12 2.1E-16 114.0 4.0 64 334-397 144-207 (246)
22 PF05920 Homeobox_KN: Homeobox 99.2 2.2E-12 4.7E-17 89.9 -0.4 34 165-198 7-40 (40)
23 smart00389 HOX Homeodomain. DN 99.2 1.3E-11 2.7E-16 91.5 3.5 53 338-390 4-56 (56)
24 KOG0842|consensus 99.2 9.8E-12 2.1E-16 121.9 3.6 59 150-208 159-217 (307)
25 KOG0485|consensus 99.1 1.7E-11 3.7E-16 113.1 3.0 66 335-400 105-170 (268)
26 KOG0493|consensus 99.1 5.3E-11 1.1E-15 112.5 4.9 62 332-393 244-305 (342)
27 KOG0848|consensus 99.1 2.9E-11 6.3E-16 114.7 2.2 60 337-396 202-261 (317)
28 KOG0494|consensus 99.1 7.2E-11 1.6E-15 111.5 4.8 58 338-395 145-202 (332)
29 TIGR01565 homeo_ZF_HD homeobox 99.1 1.6E-10 3.5E-15 86.7 5.1 51 336-386 3-57 (58)
30 KOG4577|consensus 99.1 5.5E-11 1.2E-15 113.7 2.6 58 337-394 170-227 (383)
31 KOG0492|consensus 99.1 6.9E-11 1.5E-15 108.5 3.0 66 128-202 137-202 (246)
32 KOG0489|consensus 99.1 2.9E-11 6.4E-16 117.7 0.3 66 144-209 159-224 (261)
33 KOG0843|consensus 99.1 7.6E-11 1.7E-15 106.2 2.8 57 149-205 107-163 (197)
34 KOG0491|consensus 99.1 5.1E-11 1.1E-15 105.7 1.6 71 333-403 99-169 (194)
35 KOG0488|consensus 99.0 1.5E-10 3.2E-15 115.1 2.0 56 150-205 178-233 (309)
36 KOG0774|consensus 99.0 3.5E-10 7.7E-15 107.0 3.4 62 143-204 187-251 (334)
37 KOG0483|consensus 99.0 3.1E-10 6.8E-15 105.5 2.9 57 338-394 54-110 (198)
38 KOG0483|consensus 98.9 5E-10 1.1E-14 104.1 3.3 60 145-204 51-110 (198)
39 TIGR01565 homeo_ZF_HD homeobox 98.9 1.6E-09 3.5E-14 81.4 5.3 47 150-196 7-57 (58)
40 KOG0848|consensus 98.9 2.5E-10 5.3E-15 108.5 0.5 60 145-204 200-259 (317)
41 COG5576 Homeodomain-containing 98.9 1.7E-09 3.7E-14 97.2 5.7 62 338-399 55-116 (156)
42 KOG0485|consensus 98.9 3.4E-10 7.3E-15 104.6 0.9 57 149-205 109-165 (268)
43 KOG0844|consensus 98.9 9E-10 2E-14 106.2 2.7 62 334-395 181-242 (408)
44 KOG2251|consensus 98.9 1.8E-09 4E-14 100.4 4.3 69 136-204 29-97 (228)
45 KOG0486|consensus 98.8 1.7E-09 3.6E-14 105.0 3.4 62 333-394 111-172 (351)
46 KOG0491|consensus 98.8 5.6E-10 1.2E-14 99.1 -1.5 58 150-207 106-163 (194)
47 COG5576 Homeodomain-containing 98.7 4.8E-09 1E-13 94.3 2.6 56 148-203 55-110 (156)
48 KOG3802|consensus 98.7 1.3E-08 2.8E-13 102.2 5.2 55 150-204 300-354 (398)
49 KOG0847|consensus 98.7 7.3E-09 1.6E-13 95.9 2.5 59 336-394 169-227 (288)
50 KOG0773|consensus 98.6 1.7E-08 3.7E-13 101.9 1.5 52 340-391 245-299 (342)
51 KOG0484|consensus 98.5 1.2E-08 2.6E-13 84.2 -0.3 69 123-204 9-77 (125)
52 KOG0773|consensus 98.5 5E-08 1.1E-12 98.5 3.3 57 148-204 243-302 (342)
53 KOG0774|consensus 98.5 5.2E-08 1.1E-12 92.5 3.1 60 333-392 187-249 (334)
54 PF05920 Homeobox_KN: Homeobox 98.5 2.3E-08 5.1E-13 69.6 0.6 34 355-388 7-40 (40)
55 KOG0844|consensus 98.4 1E-07 2.2E-12 92.3 2.5 58 148-205 185-242 (408)
56 KOG0494|consensus 98.4 1.9E-07 4.2E-12 88.6 3.2 55 150-204 147-201 (332)
57 KOG0490|consensus 98.4 3.3E-07 7.2E-12 86.7 4.8 60 334-393 60-119 (235)
58 KOG0486|consensus 98.3 2.5E-07 5.4E-12 90.1 2.2 60 148-207 116-175 (351)
59 KOG0847|consensus 98.2 3.2E-07 7E-12 85.2 1.2 57 149-205 172-228 (288)
60 KOG2252|consensus 98.2 2.3E-06 5E-11 89.2 7.5 59 147-205 423-481 (558)
61 KOG0849|consensus 98.2 1.3E-06 2.8E-11 88.8 4.3 60 334-393 176-235 (354)
62 KOG1168|consensus 98.2 3.7E-06 8E-11 81.1 6.7 57 338-394 313-369 (385)
63 KOG4577|consensus 98.0 3.9E-06 8.5E-11 80.9 2.5 56 150-205 173-228 (383)
64 KOG0849|consensus 97.7 1.9E-05 4.1E-10 80.3 3.1 57 149-205 181-237 (354)
65 KOG2252|consensus 97.6 0.00012 2.5E-09 76.7 7.1 56 336-391 422-477 (558)
66 KOG1168|consensus 97.5 5.2E-05 1.1E-09 73.4 2.5 50 156-205 321-370 (385)
67 PF11569 Homez: Homeodomain le 97.3 7.2E-05 1.6E-09 55.6 0.7 41 156-196 10-50 (56)
68 KOG1146|consensus 97.3 0.00082 1.8E-08 76.6 8.7 61 334-394 903-963 (1406)
69 PF11569 Homez: Homeodomain le 96.6 0.00067 1.5E-08 50.5 0.5 42 346-387 10-51 (56)
70 KOG1146|consensus 94.1 0.04 8.7E-07 63.4 3.5 59 148-206 907-965 (1406)
71 KOG3623|consensus 90.3 0.27 5.8E-06 53.7 3.8 48 346-393 568-615 (1007)
72 KOG3623|consensus 89.7 0.38 8.1E-06 52.6 4.3 46 156-201 568-613 (1007)
73 PF04218 CENP-B_N: CENP-B N-te 63.1 8.8 0.00019 28.1 3.0 43 338-385 4-46 (53)
74 PF04218 CENP-B_N: CENP-B N-te 62.1 8.7 0.00019 28.1 2.8 42 150-196 6-47 (53)
75 COG4802 FtrB Ferredoxin-thiore 56.7 7.7 0.00017 32.5 1.9 36 16-56 68-106 (110)
76 cd06171 Sigma70_r4 Sigma70, re 54.9 5.1 0.00011 27.6 0.6 44 150-198 10-53 (55)
77 PF04967 HTH_10: HTH DNA bindi 46.9 21 0.00046 26.3 2.8 40 151-190 1-42 (53)
78 cd00569 HTH_Hin_like Helix-tur 42.7 34 0.00074 20.7 3.1 38 150-192 5-42 (42)
79 PF01527 HTH_Tnp_1: Transposas 41.5 11 0.00024 28.8 0.6 44 149-196 5-48 (76)
80 PF04967 HTH_10: HTH DNA bindi 38.4 31 0.00068 25.4 2.5 39 341-379 1-41 (53)
81 PF10668 Phage_terminase: Phag 36.6 15 0.00033 27.9 0.6 35 157-194 11-45 (60)
82 PF04545 Sigma70_r4: Sigma-70, 35.5 29 0.00062 24.5 1.9 46 340-390 4-49 (50)
83 PF13443 HTH_26: Cro/C1-type H 32.2 18 0.00039 26.6 0.4 23 173-195 12-34 (63)
84 PRK10072 putative transcriptio 32.0 22 0.00048 29.5 1.0 38 153-197 35-72 (96)
85 PF07526 POX: Associated with 29.9 33 0.00071 30.5 1.7 24 48-71 88-111 (140)
86 COG3413 Predicted DNA binding 29.4 48 0.001 31.1 2.9 41 150-190 155-197 (215)
87 PRK09413 IS2 repressor TnpA; R 28.4 77 0.0017 27.0 3.8 44 149-196 11-54 (121)
88 PF01381 HTH_3: Helix-turn-hel 26.8 28 0.00061 24.7 0.7 23 174-196 12-34 (55)
89 PF08281 Sigma70_r4_2: Sigma-7 25.1 52 0.0011 23.4 1.8 43 341-388 11-53 (54)
90 TIGR03070 couple_hipB transcri 24.3 34 0.00074 24.1 0.7 23 174-196 18-40 (58)
91 TIGR03650 violacein_E violacei 23.7 65 0.0014 28.9 2.4 31 12-44 136-166 (184)
92 PRK05988 formate dehydrogenase 23.7 90 0.0019 28.1 3.4 36 155-190 25-60 (156)
93 cd01392 HTH_LacI Helix-turn-he 23.3 28 0.0006 24.5 0.1 21 176-196 2-22 (52)
94 PRK12535 RNA polymerase sigma 22.8 89 0.0019 28.7 3.4 58 341-403 134-191 (196)
95 smart00421 HTH_LUXR helix_turn 22.6 40 0.00086 23.4 0.8 44 150-199 3-46 (58)
96 PF13518 HTH_28: Helix-turn-he 22.5 40 0.00087 23.5 0.8 25 173-197 14-38 (52)
97 TIGR01958 nuoE_fam NADH-quinon 21.4 1.2E+02 0.0026 26.9 3.7 37 154-190 17-53 (148)
98 PF13384 HTH_23: Homeodomain-l 21.2 37 0.00081 23.7 0.4 26 171-196 17-42 (50)
99 COG3413 Predicted DNA binding 20.9 86 0.0019 29.4 2.9 40 340-379 155-196 (215)
100 smart00574 POX domain associat 20.9 62 0.0013 28.8 1.7 25 47-71 87-111 (140)
101 PTZ00183 centrin; Provisional 20.9 2.3E+02 0.0049 24.1 5.4 42 132-183 2-48 (158)
102 PHA02955 hypothetical protein; 20.7 1.1E+02 0.0024 29.1 3.4 42 155-196 62-104 (213)
103 PF00196 GerE: Bacterial regul 20.6 23 0.00051 25.8 -0.8 45 150-200 3-47 (58)
104 PF13443 HTH_26: Cro/C1-type H 20.0 1.3E+02 0.0028 21.9 3.1 36 156-191 24-60 (63)
No 1
>KOG0775|consensus
Probab=100.00 E-value=1.3e-44 Score=340.15 Aligned_cols=200 Identities=79% Similarity=1.301 Sum_probs=188.7
Q ss_pred CCCCCCCCCCCccchhhhhhhhccCCchhhhhhhccCCCcccccccchhHHhHHHHHHhcccChHHHHHHHhcCCCCCCC
Q psy14872 210 ISPILPSFGFTQEQVACVCEVLQQSGNIERLGRFLWSLPACEKLHKNESVLKAKAMVAFHRGNFKDLYRILESHQFSPHN 289 (414)
Q Consensus 210 ~~~~~~~~~fSpeQ~a~i~eal~q~gd~e~l~~~l~slp~s~~l~~~e~v~ra~a~~~~~~~~~~~~~~ll~~~~f~~~~ 289 (414)
.+...|+..|+++|++|+|++|++.||+|+|.+|+|++|+++.+..+|+|++|+++++||.++|.++++||+++.|++.+
T Consensus 52 s~~~~pt~~fS~eQvacvCe~L~q~Gd~erL~rFlwsLp~~~~~~~nEsvLkArA~vafH~gnf~eLY~iLE~h~Fs~~~ 131 (304)
T KOG0775|consen 52 SMSALPTFGFSEEQVACVCESLQQGGDIERLGRFLWSLPVCEELLKNESVLKARAVVAFHSGNFRELYHILENHKFSPHN 131 (304)
T ss_pred ccccCCCcCCCHHHHHHHHHHHHhccCHHHHHHHHHcCchHHHHhhhHHHHHHHHHHHHhcccHHHHHHHHHhccCChhh
Confidence 35777888999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred chHHHHHHHHhhHHHHHhhcCCCCCCCCcCcccCCCCCCCcccCCCccccccCHHHHHHHHHHHhhCCCCCHHHHHHHHH
Q psy14872 290 HPKLQALWLKAHYVEAEKLRGRPLGAVGKYRVRRKFPLPRTIWDGEETSYCFKEKSRSVLRDWYTHNPYPSPREKRELAE 369 (414)
Q Consensus 290 ~~~lq~~w~~~~~~~~e~~~g~~l~~~~~~r~R~~~p~P~~~~~~~~~~~~ft~~q~~~L~~~F~~n~yPs~~~r~~LA~ 369 (414)
|+.||++|+.+||.++++.+|++||+|++||+|++.|.|+|||||+++.++|....+..|++||..++||++.++.+||+
T Consensus 132 h~~LQ~lWl~AhY~EAek~RGR~LgaV~KYRvRrKfPlPrTIWDGEet~yCFKekSR~~LrewY~~~~YPsp~eKReLA~ 211 (304)
T KOG0775|consen 132 HPKLQALWLKAHYKEAEKLRGRPLGAVDKYRVRRKFPLPRTIWDGEETVYCFKEKSRSLLREWYLQNPYPSPREKRELAE 211 (304)
T ss_pred hHHHHHHHHHHHHHHHHHhcCCcCCccccceeeccCCCCCccccCceeeeehhHhhHHHHHHHHhcCCCCChHHHHHHHH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HhCCCccccccccccchhHhHHHHhccCCCCcccccCCCC
Q psy14872 370 ATGLTTTQVSNWFKNRRQRDRAAEQKDGSVHSFRVNIGGD 409 (414)
Q Consensus 370 ~~gL~~~qV~vWFqNrR~R~Kr~~~~~~~~~~~~~s~gg~ 409 (414)
.|||+..||.+||+|||+|+|-..++.......+.+.|.+
T Consensus 212 aTgLt~tQVsNWFKNRRQRDRa~~ak~~~~~~~~~s~~~~ 251 (304)
T KOG0775|consen 212 ATGLTITQVSNWFKNRRQRDRAAAAKNSSNLSDSSSNGEE 251 (304)
T ss_pred HhCCchhhhhhhhhhhhhhhhhccccccCCCccccccccc
Confidence 9999999999999999999997666666555544444433
No 2
>KOG0775|consensus
Probab=100.00 E-value=8.5e-38 Score=294.10 Aligned_cols=146 Identities=47% Similarity=0.747 Sum_probs=122.5
Q ss_pred hhhhhhhhhHhhhhhccccCcCCCCCccCCchhHHHHHHHHHHhccccchhh-------------hhhHHHHhhcccccc
Q psy14872 51 RTCQQCSTITHRTTKSLALPTSRLVPIQAHPQLALVLSYQALASHKSIFDKV-------------VTSYKEVWKSPVKTY 117 (414)
Q Consensus 51 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~f~~~-------------~~~~~~lw~~~~~~~ 117 (414)
+++++=+||++++.|+|+||....+. -.|+..-+...++.|.+.|.++ |.+||+||+++||.=
T Consensus 71 e~L~q~Gd~erL~rFlwsLp~~~~~~----~nEsvLkArA~vafH~gnf~eLY~iLE~h~Fs~~~h~~LQ~lWl~AhY~E 146 (304)
T KOG0775|consen 71 ESLQQGGDIERLGRFLWSLPVCEELL----KNESVLKARAVVAFHSGNFRELYHILENHKFSPHNHPKLQALWLKAHYKE 146 (304)
T ss_pred HHHHhccCHHHHHHHHHcCchHHHHh----hhHHHHHHHHHHHHhcccHHHHHHHHHhccCChhhhHHHHHHHHHHHHHH
Confidence 46778899999999999999744432 2233332333344555444444 789999999986554
Q ss_pred cc---cccccccccccccCCCCCCCcccCCCcccccCCHhHHHHHHHHhhcCCCCCHHHHHHHHHHhCCCcccccccccc
Q psy14872 118 QS---SSIIINIIKYRVRRKFPLPRTIWDGEETSYCFKEKSRSVLRDWYTHNPYPSPREKRELAEATGLTTTQVSNWFSS 194 (414)
Q Consensus 118 ~~---~~~l~~v~k~r~rk~~p~P~t~~~g~~t~~~f~~~~~~~L~~~f~~~~yPs~~ek~~La~~tgLt~~QV~~WF~N 194 (414)
++ .+.||||+|||+|||+|+|+|||||++|.|||++..+.+|++||.+|+||++++|.+||+.||||..||.|||+|
T Consensus 147 Aek~RGR~LgaV~KYRvRrKfPlPrTIWDGEet~yCFKekSR~~LrewY~~~~YPsp~eKReLA~aTgLt~tQVsNWFKN 226 (304)
T KOG0775|consen 147 AEKLRGRPLGAVDKYRVRRKFPLPRTIWDGEETVYCFKEKSRSLLREWYLQNPYPSPREKRELAEATGLTITQVSNWFKN 226 (304)
T ss_pred HHHhcCCcCCccccceeeccCCCCCccccCceeeeehhHhhHHHHHHHHhcCCCCChHHHHHHHHHhCCchhhhhhhhhh
Confidence 43 366999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred cccCCC
Q psy14872 195 ANITSS 200 (414)
Q Consensus 195 rR~r~~ 200 (414)
||.|.+
T Consensus 227 RRQRDR 232 (304)
T KOG0775|consen 227 RRQRDR 232 (304)
T ss_pred hhhhhh
Confidence 999887
No 3
>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=99.35 E-value=4.3e-13 Score=100.27 Aligned_cols=54 Identities=33% Similarity=0.530 Sum_probs=50.7
Q ss_pred cccCCHhHHHHHHHHhhcCCCCCHHHHHHHHHHhCCCcccccccccccccCCCC
Q psy14872 148 SYCFKEKSRSVLRDWYTHNPYPSPREKRELAEATGLTTTQVSNWFSSANITSSP 201 (414)
Q Consensus 148 ~~~f~~~~~~~L~~~f~~~~yPs~~ek~~La~~tgLt~~QV~~WF~NrR~r~~~ 201 (414)
...|+.+++.+|+++|..|+||+.+++..||..|||+..||.+||+|+|.+.++
T Consensus 4 r~~~~~~~~~~Le~~f~~~~~P~~~~~~~la~~~~l~~~qV~~WF~nrR~~~~~ 57 (59)
T cd00086 4 RTRFTPEQLEELEKEFEKNPYPSREEREELAKELGLTERQVKIWFQNRRAKLKR 57 (59)
T ss_pred CCcCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHHCcCHHHHHHHHHHHHHHHhc
Confidence 347899999999999999999999999999999999999999999999988764
No 4
>smart00389 HOX Homeodomain. DNA-binding factors that are involved in the transcriptional regulation of key developmental processes
Probab=99.34 E-value=7.7e-13 Score=98.13 Aligned_cols=51 Identities=33% Similarity=0.575 Sum_probs=48.6
Q ss_pred cCCHhHHHHHHHHhhcCCCCCHHHHHHHHHHhCCCcccccccccccccCCC
Q psy14872 150 CFKEKSRSVLRDWYTHNPYPSPREKRELAEATGLTTTQVSNWFSSANITSS 200 (414)
Q Consensus 150 ~f~~~~~~~L~~~f~~~~yPs~~ek~~La~~tgLt~~QV~~WF~NrR~r~~ 200 (414)
.|+.+++.+|+++|..|+||+.+++..||+.+||+..||.+||+|+|++.+
T Consensus 6 ~~~~~~~~~L~~~f~~~~~P~~~~~~~la~~~~l~~~qV~~WF~nrR~~~~ 56 (56)
T smart00389 6 SFTPEQLEELEKEFQKNPYPSREEREELAAKLGLSERQVKVWFQNRRAKWK 56 (56)
T ss_pred cCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHHCcCHHHHHHhHHHHhhccC
Confidence 589999999999999999999999999999999999999999999998753
No 5
>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=99.33 E-value=7.3e-13 Score=98.91 Aligned_cols=55 Identities=42% Similarity=0.829 Sum_probs=52.6
Q ss_pred cccccCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCccccccccccchhHhHH
Q psy14872 337 TSYCFKEKSRSVLRDWYTHNPYPSPREKRELAEATGLTTTQVSNWFKNRRQRDRA 391 (414)
Q Consensus 337 ~~~~ft~~q~~~L~~~F~~n~yPs~~~r~~LA~~~gL~~~qV~vWFqNrR~R~Kr 391 (414)
.++.|+..|+.+|+.+|..++||+..+++.||..+||+..+|.+||+|+|.++|+
T Consensus 3 ~r~~~t~~q~~~L~~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrR~k~kk 57 (57)
T PF00046_consen 3 KRTRFTKEQLKVLEEYFQENPYPSKEEREELAKELGLTERQVKNWFQNRRRKEKK 57 (57)
T ss_dssp SSSSSSHHHHHHHHHHHHHSSSCHHHHHHHHHHHHTSSHHHHHHHHHHHHHHHHH
T ss_pred CCCCCCHHHHHHHHHHHHHhccccccccccccccccccccccccCHHHhHHHhCc
Confidence 4568999999999999999999999999999999999999999999999999986
No 6
>KOG0843|consensus
Probab=99.33 E-value=1.4e-12 Score=117.21 Aligned_cols=61 Identities=30% Similarity=0.509 Sum_probs=57.5
Q ss_pred ccccccCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCccccccccccchhHhHHHHhcc
Q psy14872 336 ETSYCFKEKSRSVLRDWYTHNPYPSPREKRELAEATGLTTTQVSNWFKNRRQRDRAAEQKD 396 (414)
Q Consensus 336 ~~~~~ft~~q~~~L~~~F~~n~yPs~~~r~~LA~~~gL~~~qV~vWFqNrR~R~Kr~~~~~ 396 (414)
+.|+.|+.+|+..|+..|+.++|....+|+.||..++|++.||+|||||||.|.||...+.
T Consensus 104 r~RT~ft~~Ql~~LE~~F~~~~Yvvg~eR~~LA~~L~LsetQVkvWFQNRRtk~kr~~~e~ 164 (197)
T KOG0843|consen 104 RIRTAFTPEQLLKLEHAFEGNQYVVGAERKQLAQSLSLSETQVKVWFQNRRTKHKRMQQED 164 (197)
T ss_pred ccccccCHHHHHHHHHHHhcCCeeechHHHHHHHHcCCChhHhhhhhhhhhHHHHHHHHHh
Confidence 4567999999999999999999999999999999999999999999999999999987663
No 7
>PF00046 Homeobox: Homeobox domain not present here.; InterPro: IPR001356 The homeobox domain was first identified in a number of drosophila homeotic and segmentation proteins, but is now known to be well-conserved in many other animals, including vertebrates [, , ]. Hox genes encode homeodomain-containing transcriptional regulators that operate differential genetic programs along the anterior-posterior axis of animal bodies []. The domain binds DNA through a helix-turn-helix (HTH) structure. The HTH motif is characterised by two alpha-helices, which make intimate contacts with the DNA and are joined by a short turn. The second helix binds to DNA via a number of hydrogen bonds and hydrophobic interactions, which occur between specific side chains and the exposed bases and thymine methyl groups within the major groove of the DNA []. The first helix helps to stabilise the structure. The motif is very similar in sequence and structure in a wide range of DNA-binding proteins (e.g., cro and repressor proteins, homeotic proteins, etc.). One of the principal differences between HTH motifs in these different proteins arises from the stereo-chemical requirement for glycine in the turn which is needed to avoid steric interference of the beta-carbon with the main chain: for cro and repressor proteins the glycine appears to be mandatory, while for many of the homeotic and other DNA-binding proteins the requirement is relaxed.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0043565 sequence-specific DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 2DA3_A 1LFB_A 2LFB_A 2ECB_A 2DA5_A 3D1N_O 3A03_A 2XSD_C 3CMY_A 1AHD_P ....
Probab=99.32 E-value=2e-13 Score=101.93 Aligned_cols=53 Identities=38% Similarity=0.702 Sum_probs=49.9
Q ss_pred cccCCHhHHHHHHHHhhcCCCCCHHHHHHHHHHhCCCcccccccccccccCCC
Q psy14872 148 SYCFKEKSRSVLRDWYTHNPYPSPREKRELAEATGLTTTQVSNWFSSANITSS 200 (414)
Q Consensus 148 ~~~f~~~~~~~L~~~f~~~~yPs~~ek~~La~~tgLt~~QV~~WF~NrR~r~~ 200 (414)
...|+.+|+.+|+++|..++||+.+++..||..+||+..||.+||+|+|.+.+
T Consensus 4 r~~~t~~q~~~L~~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrR~k~k 56 (57)
T PF00046_consen 4 RTRFTKEQLKVLEEYFQENPYPSKEEREELAKELGLTERQVKNWFQNRRRKEK 56 (57)
T ss_dssp SSSSSHHHHHHHHHHHHHSSSCHHHHHHHHHHHHTSSHHHHHHHHHHHHHHHH
T ss_pred CCCCCHHHHHHHHHHHHHhccccccccccccccccccccccccCHHHhHHHhC
Confidence 45899999999999999999999999999999999999999999999998654
No 8
>KOG0488|consensus
Probab=99.31 E-value=1.2e-12 Score=129.81 Aligned_cols=67 Identities=27% Similarity=0.472 Sum_probs=60.5
Q ss_pred CCccccccCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCccccccccccchhHhHHHHhccCCCC
Q psy14872 334 GEETSYCFKEKSRSVLRDWYTHNPYPSPREKRELAEATGLTTTQVSNWFKNRRQRDRAAEQKDGSVH 400 (414)
Q Consensus 334 ~~~~~~~ft~~q~~~L~~~F~~n~yPs~~~r~~LA~~~gL~~~qV~vWFqNrR~R~Kr~~~~~~~~~ 400 (414)
++..|+.||..|+..||..|++.+|.+..+|..||..+||+..||++||||||+|||+......+..
T Consensus 172 ~RksRTaFT~~Ql~~LEkrF~~QKYLS~~DR~~LA~~LgLTdaQVKtWfQNRRtKWKrq~a~g~~~~ 238 (309)
T KOG0488|consen 172 RRKSRTAFSDHQLFELEKRFEKQKYLSVADRIELAASLGLTDAQVKTWFQNRRTKWKRQTAEGGELL 238 (309)
T ss_pred cccchhhhhHHHHHHHHHHHHHhhcccHHHHHHHHHHcCCchhhHHHHHhhhhHHHHHHHHhhhccc
Confidence 3456789999999999999999999999999999999999999999999999999999877644433
No 9
>KOG2251|consensus
Probab=99.31 E-value=3e-12 Score=118.72 Aligned_cols=67 Identities=28% Similarity=0.436 Sum_probs=61.3
Q ss_pred CcccCCCccccccCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCccccccccccchhHhHHHHhc
Q psy14872 329 RTIWDGEETSYCFKEKSRSVLRDWYTHNPYPSPREKRELAEATGLTTTQVSNWFKNRRQRDRAAEQK 395 (414)
Q Consensus 329 ~~~~~~~~~~~~ft~~q~~~L~~~F~~n~yPs~~~r~~LA~~~gL~~~qV~vWFqNrR~R~Kr~~~~ 395 (414)
...+..++.|+.|+..|+++|+..|.+++||+...+++||.+++|.+.+|+|||+|||+|+|++++.
T Consensus 32 ~~pRkqRRERTtFtr~QlevLe~LF~kTqYPDv~~rEelAlklnLpeSrVqVWFKNRRAK~r~qq~q 98 (228)
T KOG2251|consen 32 SGPRKQRRERTTFTRKQLEVLEALFAKTQYPDVFMREELALKLNLPESRVQVWFKNRRAKCRRQQQQ 98 (228)
T ss_pred ccchhcccccceecHHHHHHHHHHHHhhcCccHHHHHHHHHHhCCchhhhhhhhccccchhhHhhhh
Confidence 3445566788999999999999999999999999999999999999999999999999999998664
No 10
>KOG0489|consensus
Probab=99.28 E-value=1.7e-12 Score=126.30 Aligned_cols=66 Identities=24% Similarity=0.370 Sum_probs=60.8
Q ss_pred CCccccccCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCccccccccccchhHhHHHHhccCCC
Q psy14872 334 GEETSYCFKEKSRSVLRDWYTHNPYPSPREKRELAEATGLTTTQVSNWFKNRRQRDRAAEQKDGSV 399 (414)
Q Consensus 334 ~~~~~~~ft~~q~~~L~~~F~~n~yPs~~~r~~LA~~~gL~~~qV~vWFqNrR~R~Kr~~~~~~~~ 399 (414)
.++.|+.||..|+..||..|..|.|.+...|.+||..+.|+++||+|||||||+||||.++.....
T Consensus 159 ~kR~RtayT~~QllELEkEFhfN~YLtR~RRiEiA~~L~LtErQIKIWFQNRRMK~Kk~~k~~~~~ 224 (261)
T KOG0489|consen 159 SKRRRTAFTRYQLLELEKEFHFNKYLTRSRRIEIAHALNLTERQIKIWFQNRRMKWKKENKAKSSQ 224 (261)
T ss_pred CCCCCcccchhhhhhhhhhhccccccchHHHHHHHhhcchhHHHHHHHHHHHHHHHHHhhcccccc
Confidence 456678999999999999999999999999999999999999999999999999999987765555
No 11
>KOG0493|consensus
Probab=99.28 E-value=2.1e-12 Score=121.87 Aligned_cols=95 Identities=18% Similarity=0.314 Sum_probs=74.7
Q ss_pred HHhhccc--ccccccccccccccccccCCCCCCCcccCCCcccccCCHhHHHHHHHHhhcCCCCCHHHHHHHHHHhCCCc
Q psy14872 108 EVWKSPV--KTYQSSSIIINIIKYRVRRKFPLPRTIWDGEETSYCFKEKSRSVLRDWYTHNPYPSPREKRELAEATGLTT 185 (414)
Q Consensus 108 ~lw~~~~--~~~~~~~~l~~v~k~r~rk~~p~P~t~~~g~~t~~~f~~~~~~~L~~~f~~~~yPs~~ek~~La~~tgLt~ 185 (414)
.||---+ .+|.++++.||..+..++|+.+ -=+..+-+..|+.+|++.|+..|.+|.|.++..|+.||.++||.+
T Consensus 212 ~mwPAWVycTRYSDRPSsGPR~Rk~kkkk~~----~~eeKRPRTAFtaeQL~RLK~EF~enRYlTEqRRQ~La~ELgLNE 287 (342)
T KOG0493|consen 212 SMWPAWVYCTRYSDRPSSGPRHRKPKKKKSS----SKEEKRPRTAFTAEQLQRLKAEFQENRYLTEQRRQELAQELGLNE 287 (342)
T ss_pred cccceeeeeecccCCCCCCcccccccccCCc----cchhcCccccccHHHHHHHHHHHhhhhhHHHHHHHHHHHHhCcCH
Confidence 5776644 5899999999855444444422 011222334789999999999999999999999999999999999
Q ss_pred ccccccccccccCCCCCCCCC
Q psy14872 186 TQVSNWFSSANITSSPNTSTS 206 (414)
Q Consensus 186 ~QV~~WF~NrR~r~~~~~~~~ 206 (414)
.||++||||+|.|.|+.+..+
T Consensus 288 sQIKIWFQNKRAKiKKsTgsk 308 (342)
T KOG0493|consen 288 SQIKIWFQNKRAKIKKSTGSK 308 (342)
T ss_pred HHhhHHhhhhhhhhhhccCCC
Confidence 999999999999999866554
No 12
>KOG0850|consensus
Probab=99.28 E-value=3.6e-12 Score=118.74 Aligned_cols=71 Identities=24% Similarity=0.356 Sum_probs=62.1
Q ss_pred cccccCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCccccccccccchhHhHHHHhccCCCCcccccCC
Q psy14872 337 TSYCFKEKSRSVLRDWYTHNPYPSPREKRELAEATGLTTTQVSNWFKNRRQRDRAAEQKDGSVHSFRVNIG 407 (414)
Q Consensus 337 ~~~~ft~~q~~~L~~~F~~n~yPs~~~r~~LA~~~gL~~~qV~vWFqNrR~R~Kr~~~~~~~~~~~~~s~g 407 (414)
.|+.|+.-|+..|...|++++|+-..||.+||..+||+.+||++||||||.|.||..+......+.+.+.+
T Consensus 125 PRTIYSS~QLqaL~rRFQkTQYLALPERAeLAAsLGLTQTQVKIWFQNrRSK~KKl~k~g~~~~e~~p~~~ 195 (245)
T KOG0850|consen 125 PRTIYSSLQLQALNRRFQQTQYLALPERAELAASLGLTQTQVKIWFQNRRSKFKKLKKQGSGPVEGDPSAS 195 (245)
T ss_pred CcccccHHHHHHHHHHHhhcchhcCcHHHHHHHHhCCchhHhhhhhhhhHHHHHHHHhcCCCccccCcccC
Confidence 35678999999999999999999999999999999999999999999999999999885555555554443
No 13
>KOG0490|consensus
Probab=99.27 E-value=1.8e-11 Score=116.07 Aligned_cols=147 Identities=22% Similarity=0.307 Sum_probs=106.6
Q ss_pred cCCHhHHHHHHHHhhcCCCCCHHHHHHHHHHhCCCcccccccccccccCCCCCCC-CCCCCCCCCCCCCCCCccchhhhh
Q psy14872 150 CFKEKSRSVLRDWYTHNPYPSPREKRELAEATGLTTTQVSNWFSSANITSSPNTS-TSTASISPILPSFGFTQEQVACVC 228 (414)
Q Consensus 150 ~f~~~~~~~L~~~f~~~~yPs~~ek~~La~~tgLt~~QV~~WF~NrR~r~~~~~~-~~~~~~~~~~~~~~fSpeQ~a~i~ 228 (414)
.|+..|+..|+..|..+.||+-..++.||..++|++..|.+||+|+|.+.++... .......+..+. +
T Consensus 66 ~~~~~ql~~ler~f~~~h~Pd~~~r~~la~~~~~~e~rVqvwFqnrrak~r~~~~~~~~~~~~~~~~~---~-------- 134 (235)
T KOG0490|consen 66 KFTISQLDELERAFEKVHLPCFACRECLALLLTGDEFRVQVWFQNRRAKDRKEERPLPEGENLPDLSG---T-------- 134 (235)
T ss_pred CCCcCHHHHHHHhhcCCCcCccchHHHHhhcCCCCeeeeehhhhhhcHhhhhhhccccccccCCCCCC---C--------
Confidence 6777899999999999999999999999999999999999999999998886553 110000000000 0
Q ss_pred hhhccCCchhhhhhhccCCCcccccccchhHHhHHHHHHhcccChHHHHHHHhcCCCCCCCchHHHHHHHHhhHHHHHhh
Q psy14872 229 EVLQQSGNIERLGRFLWSLPACEKLHKNESVLKAKAMVAFHRGNFKDLYRILESHQFSPHNHPKLQALWLKAHYVEAEKL 308 (414)
Q Consensus 229 eal~q~gd~e~l~~~l~slp~s~~l~~~e~v~ra~a~~~~~~~~~~~~~~ll~~~~f~~~~~~~lq~~w~~~~~~~~e~~ 308 (414)
.+.. . .. ..
T Consensus 135 ------------------~~~~----------------~------------------------------------~~-~~ 143 (235)
T KOG0490|consen 135 ------------------APPS----------------A------------------------------------SR-DK 143 (235)
T ss_pred ------------------CCcc----------------c------------------------------------cc-cc
Confidence 0000 0 00 00
Q ss_pred cCCCCCCCCcCcccCCCCCCCcccCCCccccccCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCccccccccccchhH
Q psy14872 309 RGRPLGAVGKYRVRRKFPLPRTIWDGEETSYCFKEKSRSVLRDWYTHNPYPSPREKRELAEATGLTTTQVSNWFKNRRQR 388 (414)
Q Consensus 309 ~g~~l~~~~~~r~R~~~p~P~~~~~~~~~~~~ft~~q~~~L~~~F~~n~yPs~~~r~~LA~~~gL~~~qV~vWFqNrR~R 388 (414)
... ..+ ....++.++.+...++..+...|..+++|+...+..|+..+|++...|++||+|+|.+
T Consensus 144 ~~~--~~~--------------~~~~~~~~~~~~~~~~~~~~~~~~~~~~P~~~~~~~l~~~~~~~~~~~q~~~~~~~~~ 207 (235)
T KOG0490|consen 144 LDK--GPS--------------NKKPRRPRTTFTENQLEVLETVFRATPKPDADDREQLAEETGLSERVIQVWFQNRRAK 207 (235)
T ss_pred ccc--CCC--------------ccccCCCccccccchhHhhhhcccCCCCCchhhHHHHHHhcCCChhhhhhhcccHHHH
Confidence 000 000 0011223446788899999999999999999999999999999999999999999999
Q ss_pred hHHHHh
Q psy14872 389 DRAAEQ 394 (414)
Q Consensus 389 ~Kr~~~ 394 (414)
.++...
T Consensus 208 ~~~~~~ 213 (235)
T KOG0490|consen 208 LRKHKR 213 (235)
T ss_pred HHhhcc
Confidence 998755
No 14
>KOG3802|consensus
Probab=99.27 E-value=6.1e-12 Score=125.80 Aligned_cols=117 Identities=28% Similarity=0.475 Sum_probs=85.8
Q ss_pred hHHhHH-HHHHhcccChHHHHHHHhcCCCCCCCc-----------------hHHHHHHHHhhHHHHHh--hcCCC-----
Q psy14872 258 SVLKAK-AMVAFHRGNFKDLYRILESHQFSPHNH-----------------PKLQALWLKAHYVEAEK--LRGRP----- 312 (414)
Q Consensus 258 ~v~ra~-a~~~~~~~~~~~~~~ll~~~~f~~~~~-----------------~~lq~~w~~~~~~~~e~--~~g~~----- 312 (414)
..++.+ ...-|.+++...+...|.+..|+...- +.|++ |+ .+++. ..+..
T Consensus 213 K~FKqRRIkLGfTQaDVGlALG~lyGn~FSQTTIcRFEALqLSFKNMCKLKPLL~K-WL----eEAes~~~~~~~~~~e~ 287 (398)
T KOG3802|consen 213 KTFKQRRIKLGFTQADVGLALGALYGNVFSQTTICRFEALQLSFKNMCKLKPLLEK-WL----EEAESRESTGSPNSIEK 287 (398)
T ss_pred HHHHhheeccccchhHHHHHHHhhhCcccchhhhhHhHhhccCHHHHhhhHHHHHH-HH----HHHhcccccCCCCCHHH
Confidence 334434 334499999999999999999988642 22222 33 22332 11211
Q ss_pred CCCCCcCcccCCCCCCCcccCCCccccccCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCccccccccccchhHhHHH
Q psy14872 313 LGAVGKYRVRRKFPLPRTIWDGEETSYCFKEKSRSVLRDWYTHNPYPSPREKRELAEATGLTTTQVSNWFKNRRQRDRAA 392 (414)
Q Consensus 313 l~~~~~~r~R~~~p~P~~~~~~~~~~~~ft~~q~~~L~~~F~~n~yPs~~~r~~LA~~~gL~~~qV~vWFqNrR~R~Kr~ 392 (414)
+++. .|+ +++|++|+...+..|+.+|.+|+.|+.+|...||.+++|.+.+|+|||+|||+|+||.
T Consensus 288 i~a~--~Rk-------------RKKRTSie~~vr~aLE~~F~~npKPt~qEIt~iA~~L~leKEVVRVWFCNRRQkeKR~ 352 (398)
T KOG3802|consen 288 IGAQ--SRK-------------RKKRTSIEVNVRGALEKHFLKNPKPTSQEITHIAESLQLEKEVVRVWFCNRRQKEKRI 352 (398)
T ss_pred hhcc--ccc-------------cccccceeHHHHHHHHHHHHhCCCCCHHHHHHHHHHhccccceEEEEeeccccccccC
Confidence 1111 122 3445689999999999999999999999999999999999999999999999999998
Q ss_pred Hh
Q psy14872 393 EQ 394 (414)
Q Consensus 393 ~~ 394 (414)
..
T Consensus 353 ~~ 354 (398)
T KOG3802|consen 353 TP 354 (398)
T ss_pred CC
Confidence 66
No 15
>KOG0487|consensus
Probab=99.23 E-value=2.8e-12 Score=125.79 Aligned_cols=61 Identities=20% Similarity=0.341 Sum_probs=56.1
Q ss_pred CCcccccCCHhHHHHHHHHhhcCCCCCHHHHHHHHHHhCCCcccccccccccccCCCCCCC
Q psy14872 144 GEETSYCFKEKSRSVLRDWYTHNPYPSPREKRELAEATGLTTTQVSNWFSSANITSSPNTS 204 (414)
Q Consensus 144 g~~t~~~f~~~~~~~L~~~f~~~~yPs~~ek~~La~~tgLt~~QV~~WF~NrR~r~~~~~~ 204 (414)
+.+|+-.||+.|+..||+.|.-|.|+|.+.|.+|+..|+||++||+|||||||.|.||-.+
T Consensus 235 ~RKKRcPYTK~QtlELEkEFlfN~YitkeKR~ElSr~lNLTeRQVKIWFQNRRMK~KK~~r 295 (308)
T KOG0487|consen 235 GRKKRCPYTKHQTLELEKEFLFNMYITKEKRLELSRTLNLTERQVKIWFQNRRMKEKKVNR 295 (308)
T ss_pred cccccCCchHHHHHHHHHHHHHHHHHhHHHHHHHHHhcccchhheeeeehhhhhHHhhhhh
Confidence 4555568999999999999999999999999999999999999999999999999987654
No 16
>KOG0484|consensus
Probab=99.22 E-value=4.7e-12 Score=104.14 Aligned_cols=58 Identities=28% Similarity=0.452 Sum_probs=54.8
Q ss_pred ccccccCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCccccccccccchhHhHHHH
Q psy14872 336 ETSYCFKEKSRSVLRDWYTHNPYPSPREKRELAEATGLTTTQVSNWFKNRRQRDRAAE 393 (414)
Q Consensus 336 ~~~~~ft~~q~~~L~~~F~~n~yPs~~~r~~LA~~~gL~~~qV~vWFqNrR~R~Kr~~ 393 (414)
+-++.|+..|+..|+..|..+.||++-.|++||..+.|++..|+|||||||+|.+|+.
T Consensus 19 RIRTTFTS~QLkELErvF~ETHYPDIYTREEiA~kidLTEARVQVWFQNRRAKfRKQE 76 (125)
T KOG0484|consen 19 RIRTTFTSAQLKELERVFAETHYPDIYTREEIALKIDLTEARVQVWFQNRRAKFRKQE 76 (125)
T ss_pred hhhhhhhHHHHHHHHHHHHhhcCCcchhHHHHHHhhhhhHHHHHHHHHhhHHHHHHHH
Confidence 4467899999999999999999999999999999999999999999999999999864
No 17
>KOG0850|consensus
Probab=99.21 E-value=2.8e-12 Score=119.48 Aligned_cols=71 Identities=27% Similarity=0.373 Sum_probs=60.3
Q ss_pred ccccccc-CCCCCCCcccCCCcccccCCHhHHHHHHHHhhcCCCCCHHHHHHHHHHhCCCcccccccccccccCCCCCCC
Q psy14872 126 IIKYRVR-RKFPLPRTIWDGEETSYCFKEKSRSVLRDWYTHNPYPSPREKRELAEATGLTTTQVSNWFSSANITSSPNTS 204 (414)
Q Consensus 126 v~k~r~r-k~~p~P~t~~~g~~t~~~f~~~~~~~L~~~f~~~~yPs~~ek~~La~~tgLt~~QV~~WF~NrR~r~~~~~~ 204 (414)
+.+++.+ ||..-||||+...+ +++|...|++..|.-..||.+||..+|||.+||++||||||.|.||...
T Consensus 112 e~~~Ngk~KK~RKPRTIYSS~Q---------LqaL~rRFQkTQYLALPERAeLAAsLGLTQTQVKIWFQNrRSK~KKl~k 182 (245)
T KOG0850|consen 112 ERRPNGKGKKVRKPRTIYSSLQ---------LQALNRRFQQTQYLALPERAELAASLGLTQTQVKIWFQNRRSKFKKLKK 182 (245)
T ss_pred eeccCCCcccccCCcccccHHH---------HHHHHHHHhhcchhcCcHHHHHHHHhCCchhHhhhhhhhhHHHHHHHHh
Confidence 4555554 55556899866555 9999999999999999999999999999999999999999999887555
Q ss_pred C
Q psy14872 205 T 205 (414)
Q Consensus 205 ~ 205 (414)
.
T Consensus 183 ~ 183 (245)
T KOG0850|consen 183 Q 183 (245)
T ss_pred c
Confidence 3
No 18
>KOG0842|consensus
Probab=99.21 E-value=1.3e-11 Score=121.14 Aligned_cols=62 Identities=27% Similarity=0.431 Sum_probs=56.4
Q ss_pred ccccCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCccccccccccchhHhHHHHhccCCC
Q psy14872 338 SYCFKEKSRSVLRDWYTHNPYPSPREKRELAEATGLTTTQVSNWFKNRRQRDRAAEQKDGSV 399 (414)
Q Consensus 338 ~~~ft~~q~~~L~~~F~~n~yPs~~~r~~LA~~~gL~~~qV~vWFqNrR~R~Kr~~~~~~~~ 399 (414)
|--|+..|+..||..|....|.+..||+.||..++|+.+||+|||||+|.|.||+.+.....
T Consensus 157 RVLFSqAQV~ELERRFrqQRYLSAPERE~LA~~LrLT~TQVKIWFQNrRYK~KR~~~dk~~~ 218 (307)
T KOG0842|consen 157 RVLFSQAQVYELERRFRQQRYLSAPEREHLASSLRLTPTQVKIWFQNRRYKTKRQQKDKALE 218 (307)
T ss_pred ccccchhHHHHHHHHHHhhhccccHhHHHHHHhcCCCchheeeeeecchhhhhhhhhhhhhh
Confidence 45799999999999999999999999999999999999999999999999999986544333
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=99.20 E-value=1.1e-11 Score=92.52 Aligned_cols=55 Identities=38% Similarity=0.636 Sum_probs=51.6
Q ss_pred ccccCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCccccccccccchhHhHHH
Q psy14872 338 SYCFKEKSRSVLRDWYTHNPYPSPREKRELAEATGLTTTQVSNWFKNRRQRDRAA 392 (414)
Q Consensus 338 ~~~ft~~q~~~L~~~F~~n~yPs~~~r~~LA~~~gL~~~qV~vWFqNrR~R~Kr~ 392 (414)
+..|+..++.+|+.+|..++||+..++..||..+||+..+|.+||+|+|.+.++.
T Consensus 4 r~~~~~~~~~~Le~~f~~~~~P~~~~~~~la~~~~l~~~qV~~WF~nrR~~~~~~ 58 (59)
T cd00086 4 RTRFTPEQLEELEKEFEKNPYPSREEREELAKELGLTERQVKIWFQNRRAKLKRS 58 (59)
T ss_pred CCcCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHHCcCHHHHHHHHHHHHHHHhcc
Confidence 3478999999999999999999999999999999999999999999999998753
No 20
>KOG0487|consensus
Probab=99.20 E-value=8.6e-12 Score=122.36 Aligned_cols=62 Identities=24% Similarity=0.464 Sum_probs=57.4
Q ss_pred CCccccccCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCccccccccccchhHhHHHHhc
Q psy14872 334 GEETSYCFKEKSRSVLRDWYTHNPYPSPREKRELAEATGLTTTQVSNWFKNRRQRDRAAEQK 395 (414)
Q Consensus 334 ~~~~~~~ft~~q~~~L~~~F~~n~yPs~~~r~~LA~~~gL~~~qV~vWFqNrR~R~Kr~~~~ 395 (414)
++++|-.+|..|+..||..|.-|.|++.+.|.+|++.++|+++||+|||||||+|.||..++
T Consensus 235 ~RKKRcPYTK~QtlELEkEFlfN~YitkeKR~ElSr~lNLTeRQVKIWFQNRRMK~KK~~re 296 (308)
T KOG0487|consen 235 GRKKRCPYTKHQTLELEKEFLFNMYITKEKRLELSRTLNLTERQVKIWFQNRRMKEKKVNRE 296 (308)
T ss_pred cccccCCchHHHHHHHHHHHHHHHHHhHHHHHHHHHhcccchhheeeeehhhhhHHhhhhhh
Confidence 45556679999999999999999999999999999999999999999999999999998753
No 21
>KOG0492|consensus
Probab=99.20 E-value=9.9e-12 Score=113.97 Aligned_cols=64 Identities=25% Similarity=0.400 Sum_probs=58.2
Q ss_pred CCccccccCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCccccccccccchhHhHHHHhccC
Q psy14872 334 GEETSYCFKEKSRSVLRDWYTHNPYPSPREKRELAEATGLTTTQVSNWFKNRRQRDRAAEQKDG 397 (414)
Q Consensus 334 ~~~~~~~ft~~q~~~L~~~F~~n~yPs~~~r~~LA~~~gL~~~qV~vWFqNrR~R~Kr~~~~~~ 397 (414)
.+..|+.||..|+..|+.-|.+.+|.++++|.+++..+.|++.||++||||||+|.||.+..+.
T Consensus 144 nRkPRtPFTtqQLlaLErkfrekqYLSiaEraefSsSL~LTeTqVKIWFQNRRAKaKRlQeae~ 207 (246)
T KOG0492|consen 144 NRKPRTPFTTQQLLALERKFREKQYLSIAERAEFSSSLELTETQVKIWFQNRRAKAKRLQEAEL 207 (246)
T ss_pred CCCCCCCCCHHHHHHHHHHHhHhhhhhHHHHHhhhhhhhhhhhheehhhhhhhHHHHHHHHHHH
Confidence 4455679999999999999999999999999999999999999999999999999999765443
No 22
>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=99.19 E-value=2.2e-12 Score=89.86 Aligned_cols=34 Identities=59% Similarity=0.977 Sum_probs=29.6
Q ss_pred cCCCCCHHHHHHHHHHhCCCcccccccccccccC
Q psy14872 165 HNPYPSPREKRELAEATGLTTTQVSNWFSSANIT 198 (414)
Q Consensus 165 ~~~yPs~~ek~~La~~tgLt~~QV~~WF~NrR~r 198 (414)
.|||||.+||..||..|||+.+||.+||.|+|+|
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 5899999999999999999999999999999975
No 23
>smart00389 HOX Homeodomain. DNA-binding factors that are involved in the transcriptional regulation of key developmental processes
Probab=99.19 E-value=1.3e-11 Score=91.54 Aligned_cols=53 Identities=38% Similarity=0.652 Sum_probs=49.7
Q ss_pred ccccCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCccccccccccchhHhH
Q psy14872 338 SYCFKEKSRSVLRDWYTHNPYPSPREKRELAEATGLTTTQVSNWFKNRRQRDR 390 (414)
Q Consensus 338 ~~~ft~~q~~~L~~~F~~n~yPs~~~r~~LA~~~gL~~~qV~vWFqNrR~R~K 390 (414)
++.|+..++.+|+.+|..++||+..++..||..+||+..+|++||+|+|.+.+
T Consensus 4 r~~~~~~~~~~L~~~f~~~~~P~~~~~~~la~~~~l~~~qV~~WF~nrR~~~~ 56 (56)
T smart00389 4 RTSFTPEQLEELEKEFQKNPYPSREEREELAAKLGLSERQVKVWFQNRRAKWK 56 (56)
T ss_pred CCcCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHHCcCHHHHHHhHHHHhhccC
Confidence 34689999999999999999999999999999999999999999999998864
No 24
>KOG0842|consensus
Probab=99.19 E-value=9.8e-12 Score=121.92 Aligned_cols=59 Identities=24% Similarity=0.364 Sum_probs=55.2
Q ss_pred cCCHhHHHHHHHHhhcCCCCCHHHHHHHHHHhCCCcccccccccccccCCCCCCCCCCC
Q psy14872 150 CFKEKSRSVLRDWYTHNPYPSPREKRELAEATGLTTTQVSNWFSSANITSSPNTSTSTA 208 (414)
Q Consensus 150 ~f~~~~~~~L~~~f~~~~yPs~~ek~~La~~tgLt~~QV~~WF~NrR~r~~~~~~~~~~ 208 (414)
-|+..|+-.||..|....|.|..||+.||..++||++||+|||||+|.|.|+...++..
T Consensus 159 LFSqAQV~ELERRFrqQRYLSAPERE~LA~~LrLT~TQVKIWFQNrRYK~KR~~~dk~~ 217 (307)
T KOG0842|consen 159 LFSQAQVYELERRFRQQRYLSAPEREHLASSLRLTPTQVKIWFQNRRYKTKRQQKDKAL 217 (307)
T ss_pred ccchhHHHHHHHHHHhhhccccHhHHHHHHhcCCCchheeeeeecchhhhhhhhhhhhh
Confidence 79999999999999999999999999999999999999999999999999987666543
No 25
>KOG0485|consensus
Probab=99.15 E-value=1.7e-11 Score=113.06 Aligned_cols=66 Identities=29% Similarity=0.358 Sum_probs=60.0
Q ss_pred CccccccCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCccccccccccchhHhHHHHhccCCCC
Q psy14872 335 EETSYCFKEKSRSVLRDWYTHNPYPSPREKRELAEATGLTTTQVSNWFKNRRQRDRAAEQKDGSVH 400 (414)
Q Consensus 335 ~~~~~~ft~~q~~~L~~~F~~n~yPs~~~r~~LA~~~gL~~~qV~vWFqNrR~R~Kr~~~~~~~~~ 400 (414)
+++|+.|+..|+..|+..|+...|.+..+|..||..+.|++.||++||||||.||||+.+.+.+..
T Consensus 105 KktRTvFSraQV~qLEs~Fe~krYLSsaeRa~LA~sLqLTETQVKIWFQNRRnKwKRq~aad~ea~ 170 (268)
T KOG0485|consen 105 KKTRTVFSRAQVFQLESTFELKRYLSSAERAGLAASLQLTETQVKIWFQNRRNKWKRQYAADLEAA 170 (268)
T ss_pred ccchhhhhHHHHHHHHHHHHHHhhhhHHHHhHHHHhhhhhhhhhhhhhhhhhHHHHHHHhhhhhhh
Confidence 456789999999999999999999999999999999999999999999999999999877654443
No 26
>KOG0493|consensus
Probab=99.12 E-value=5.3e-11 Score=112.47 Aligned_cols=62 Identities=23% Similarity=0.474 Sum_probs=58.1
Q ss_pred cCCCccccccCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCccccccccccchhHhHHHH
Q psy14872 332 WDGEETSYCFKEKSRSVLRDWYTHNPYPSPREKRELAEATGLTTTQVSNWFKNRRQRDRAAE 393 (414)
Q Consensus 332 ~~~~~~~~~ft~~q~~~L~~~F~~n~yPs~~~r~~LA~~~gL~~~qV~vWFqNrR~R~Kr~~ 393 (414)
...++.|+.|+.+|+..|+..|+.|.|.+...|.+||.++||.+.||++||||.|+|.||..
T Consensus 244 ~eeKRPRTAFtaeQL~RLK~EF~enRYlTEqRRQ~La~ELgLNEsQIKIWFQNKRAKiKKsT 305 (342)
T KOG0493|consen 244 KEEKRPRTAFTAEQLQRLKAEFQENRYLTEQRRQELAQELGLNESQIKIWFQNKRAKIKKST 305 (342)
T ss_pred chhcCccccccHHHHHHHHHHHhhhhhHHHHHHHHHHHHhCcCHHHhhHHhhhhhhhhhhcc
Confidence 34667789999999999999999999999999999999999999999999999999999864
No 27
>KOG0848|consensus
Probab=99.10 E-value=2.9e-11 Score=114.68 Aligned_cols=60 Identities=32% Similarity=0.552 Sum_probs=56.4
Q ss_pred cccccCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCccccccccccchhHhHHHHhcc
Q psy14872 337 TSYCFKEKSRSVLRDWYTHNPYPSPREKRELAEATGLTTTQVSNWFKNRRQRDRAAEQKD 396 (414)
Q Consensus 337 ~~~~ft~~q~~~L~~~F~~n~yPs~~~r~~LA~~~gL~~~qV~vWFqNrR~R~Kr~~~~~ 396 (414)
-|-++|.-|+-.||+.|..++|.++..+.+||..+||+++||++||||||+|+||.+++.
T Consensus 202 YRvVYTDhQRLELEKEfh~SryITirRKSELA~~LgLsERQVKIWFQNRRAKERK~nKKk 261 (317)
T KOG0848|consen 202 YRVVYTDHQRLELEKEFHTSRYITIRRKSELAATLGLSERQVKIWFQNRRAKERKDNKKK 261 (317)
T ss_pred eeEEecchhhhhhhhhhccccceeeehhHHHHHhhCccHhhhhHhhhhhhHHHHHHHHHH
Confidence 355799999999999999999999999999999999999999999999999999987765
No 28
>KOG0494|consensus
Probab=99.09 E-value=7.2e-11 Score=111.50 Aligned_cols=58 Identities=26% Similarity=0.461 Sum_probs=55.9
Q ss_pred ccccCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCccccccccccchhHhHHHHhc
Q psy14872 338 SYCFKEKSRSVLRDWYTHNPYPSPREKRELAEATGLTTTQVSNWFKNRRQRDRAAEQK 395 (414)
Q Consensus 338 ~~~ft~~q~~~L~~~F~~n~yPs~~~r~~LA~~~gL~~~qV~vWFqNrR~R~Kr~~~~ 395 (414)
|+.||.-|+..|++.|....||+...|+.||..|+|.+..|+|||||||+||||..++
T Consensus 145 RTiFT~~Qle~LEkaFkeaHYPDv~Are~la~ktelpEDRIqVWfQNRRAKWRk~Ek~ 202 (332)
T KOG0494|consen 145 RTIFTSYQLEELEKAFKEAHYPDVYAREMLADKTELPEDRIQVWFQNRRAKWRKTEKR 202 (332)
T ss_pred cchhhHHHHHHHHHHHhhccCccHHHHHHHhhhccCchhhhhHHhhhhhHHhhhhhhh
Confidence 7899999999999999999999999999999999999999999999999999998764
No 29
>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=99.08 E-value=1.6e-10 Score=86.75 Aligned_cols=51 Identities=22% Similarity=0.416 Sum_probs=48.4
Q ss_pred ccccccCHHHHHHHHHHHhhCCC----CCHHHHHHHHHHhCCCccccccccccch
Q psy14872 336 ETSYCFKEKSRSVLRDWYTHNPY----PSPREKRELAEATGLTTTQVSNWFKNRR 386 (414)
Q Consensus 336 ~~~~~ft~~q~~~L~~~F~~n~y----Ps~~~r~~LA~~~gL~~~qV~vWFqNrR 386 (414)
+.|+.||.+|+..|+..|+.++| |+..++++||..+||+..+|+|||+|.+
T Consensus 3 R~RT~Ft~~Q~~~Le~~fe~~~y~~~~~~~~~r~~la~~lgl~~~vvKVWfqN~k 57 (58)
T TIGR01565 3 RRRTKFTAEQKEKMRDFAEKLGWKLKDKRREEVREFCEEIGVTRKVFKVWMHNNK 57 (58)
T ss_pred CCCCCCCHHHHHHHHHHHHHcCCCCCCCCHHHHHHHHHHhCCCHHHeeeecccCC
Confidence 45679999999999999999999 9999999999999999999999999965
No 30
>KOG4577|consensus
Probab=99.06 E-value=5.5e-11 Score=113.74 Aligned_cols=58 Identities=26% Similarity=0.529 Sum_probs=55.0
Q ss_pred cccccCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCccccccccccchhHhHHHHh
Q psy14872 337 TSYCFKEKSRSVLRDWYTHNPYPSPREKRELAEATGLTTTQVSNWFKNRRQRDRAAEQ 394 (414)
Q Consensus 337 ~~~~ft~~q~~~L~~~F~~n~yPs~~~r~~LA~~~gL~~~qV~vWFqNrR~R~Kr~~~ 394 (414)
.|+.+|..|++.|+..|+..+.|....|++|+.+|||..+.|+|||||||+|+||.++
T Consensus 170 PRTTItAKqLETLK~AYn~SpKPARHVREQLsseTGLDMRVVQVWFQNRRAKEKRLKK 227 (383)
T KOG4577|consen 170 PRTTITAKQLETLKQAYNTSPKPARHVREQLSSETGLDMRVVQVWFQNRRAKEKRLKK 227 (383)
T ss_pred CcceeeHHHHHHHHHHhcCCCchhHHHHHHhhhccCcceeehhhhhhhhhHHHHhhhh
Confidence 3457899999999999999999999999999999999999999999999999999877
No 31
>KOG0492|consensus
Probab=99.06 E-value=6.9e-11 Score=108.46 Aligned_cols=66 Identities=26% Similarity=0.352 Sum_probs=58.2
Q ss_pred cccccCCCCCCCcccCCCcccccCCHhHHHHHHHHhhcCCCCCHHHHHHHHHHhCCCcccccccccccccCCCCC
Q psy14872 128 KYRVRRKFPLPRTIWDGEETSYCFKEKSRSVLRDWYTHNPYPSPREKRELAEATGLTTTQVSNWFSSANITSSPN 202 (414)
Q Consensus 128 k~r~rk~~p~P~t~~~g~~t~~~f~~~~~~~L~~~f~~~~yPs~~ek~~La~~tgLt~~QV~~WF~NrR~r~~~~ 202 (414)
..|++|-+..||| .|+..|+..|+.-|.+.+|.|.+|+.+++..+.||++||++||||||.|.|+.
T Consensus 137 ~LrKhk~nRkPRt---------PFTtqQLlaLErkfrekqYLSiaEraefSsSL~LTeTqVKIWFQNRRAKaKRl 202 (246)
T KOG0492|consen 137 TLRKHKPNRKPRT---------PFTTQQLLALERKFREKQYLSIAERAEFSSSLELTETQVKIWFQNRRAKAKRL 202 (246)
T ss_pred hhcccCCCCCCCC---------CCCHHHHHHHHHHHhHhhhhhHHHHHhhhhhhhhhhhheehhhhhhhHHHHHH
Confidence 3455555556776 79999999999999999999999999999999999999999999999988853
No 32
>KOG0489|consensus
Probab=99.05 E-value=2.9e-11 Score=117.68 Aligned_cols=66 Identities=18% Similarity=0.307 Sum_probs=58.6
Q ss_pred CCcccccCCHhHHHHHHHHhhcCCCCCHHHHHHHHHHhCCCcccccccccccccCCCCCCCCCCCC
Q psy14872 144 GEETSYCFKEKSRSVLRDWYTHNPYPSPREKRELAEATGLTTTQVSNWFSSANITSSPNTSTSTAS 209 (414)
Q Consensus 144 g~~t~~~f~~~~~~~L~~~f~~~~yPs~~ek~~La~~tgLt~~QV~~WF~NrR~r~~~~~~~~~~~ 209 (414)
..+.+..||..|+-.||+.|.-|.|.+...|.+||..+.||++||+|||||||+|.|+........
T Consensus 159 ~kR~RtayT~~QllELEkEFhfN~YLtR~RRiEiA~~L~LtErQIKIWFQNRRMK~Kk~~k~~~~~ 224 (261)
T KOG0489|consen 159 SKRRRTAFTRYQLLELEKEFHFNKYLTRSRRIEIAHALNLTERQIKIWFQNRRMKWKKENKAKSSQ 224 (261)
T ss_pred CCCCCcccchhhhhhhhhhhccccccchHHHHHHHhhcchhHHHHHHHHHHHHHHHHHhhcccccc
Confidence 345556899999999999999999999999999999999999999999999999999766655433
No 33
>KOG0843|consensus
Probab=99.05 E-value=7.6e-11 Score=106.17 Aligned_cols=57 Identities=23% Similarity=0.359 Sum_probs=52.6
Q ss_pred ccCCHhHHHHHHHHhhcCCCCCHHHHHHHHHHhCCCcccccccccccccCCCCCCCC
Q psy14872 149 YCFKEKSRSVLRDWYTHNPYPSPREKRELAEATGLTTTQVSNWFSSANITSSPNTST 205 (414)
Q Consensus 149 ~~f~~~~~~~L~~~f~~~~yPs~~ek~~La~~tgLt~~QV~~WF~NrR~r~~~~~~~ 205 (414)
..|+.+|+..|+..|+.+.|-..+||+.||..+||++.||++||||||.|.|+....
T Consensus 107 T~ft~~Ql~~LE~~F~~~~Yvvg~eR~~LA~~L~LsetQVkvWFQNRRtk~kr~~~e 163 (197)
T KOG0843|consen 107 TAFTPEQLLKLEHAFEGNQYVVGAERKQLAQSLSLSETQVKVWFQNRRTKHKRMQQE 163 (197)
T ss_pred cccCHHHHHHHHHHHhcCCeeechHHHHHHHHcCCChhHhhhhhhhhhHHHHHHHHH
Confidence 378999999999999999999999999999999999999999999999998865444
No 34
>KOG0491|consensus
Probab=99.05 E-value=5.1e-11 Score=105.70 Aligned_cols=71 Identities=28% Similarity=0.464 Sum_probs=61.7
Q ss_pred CCCccccccCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCccccccccccchhHhHHHHhccCCCCccc
Q psy14872 333 DGEETSYCFKEKSRSVLRDWYTHNPYPSPREKRELAEATGLTTTQVSNWFKNRRQRDRAAEQKDGSVHSFR 403 (414)
Q Consensus 333 ~~~~~~~~ft~~q~~~L~~~F~~n~yPs~~~r~~LA~~~gL~~~qV~vWFqNrR~R~Kr~~~~~~~~~~~~ 403 (414)
..+..|+.|+..|+..|++.|+...|.+..++.+||..++|++.||+.||||+|+|.||...+.....+.+
T Consensus 99 ~r~K~Rtvfs~~ql~~l~~rFe~QrYLS~~e~~ELan~L~LS~~QVKTWFQNrRMK~Kk~~r~~~p~nS~~ 169 (194)
T KOG0491|consen 99 RRRKARTVFSDPQLSGLEKRFERQRYLSTPERQELANALSLSETQVKTWFQNRRMKHKKQQRNNQPKNSNG 169 (194)
T ss_pred HhhhhcccccCccccccHHHHhhhhhcccHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHHHhccCCCCCCc
Confidence 34456789999999999999999999999999999999999999999999999999999877655333333
No 35
>KOG0488|consensus
Probab=98.98 E-value=1.5e-10 Score=115.07 Aligned_cols=56 Identities=27% Similarity=0.437 Sum_probs=52.5
Q ss_pred cCCHhHHHHHHHHhhcCCCCCHHHHHHHHHHhCCCcccccccccccccCCCCCCCC
Q psy14872 150 CFKEKSRSVLRDWYTHNPYPSPREKRELAEATGLTTTQVSNWFSSANITSSPNTST 205 (414)
Q Consensus 150 ~f~~~~~~~L~~~f~~~~yPs~~ek~~La~~tgLt~~QV~~WF~NrR~r~~~~~~~ 205 (414)
.||+.|+..||..|++-.|.|..||..||..+|||-.||++||||||.|+|+....
T Consensus 178 aFT~~Ql~~LEkrF~~QKYLS~~DR~~LA~~LgLTdaQVKtWfQNRRtKWKrq~a~ 233 (309)
T KOG0488|consen 178 AFSDHQLFELEKRFEKQKYLSVADRIELAASLGLTDAQVKTWFQNRRTKWKRQTAE 233 (309)
T ss_pred hhhHHHHHHHHHHHHHhhcccHHHHHHHHHHcCCchhhHHHHHhhhhHHHHHHHHh
Confidence 68999999999999999999999999999999999999999999999999975443
No 36
>KOG0774|consensus
Probab=98.96 E-value=3.5e-10 Score=106.96 Aligned_cols=62 Identities=34% Similarity=0.646 Sum_probs=55.8
Q ss_pred CCCcccccCCHhHHHHHHHHhh---cCCCCCHHHHHHHHHHhCCCcccccccccccccCCCCCCC
Q psy14872 143 DGEETSYCFKEKSRSVLRDWYT---HNPYPSPREKRELAEATGLTTTQVSNWFSSANITSSPNTS 204 (414)
Q Consensus 143 ~g~~t~~~f~~~~~~~L~~~f~---~~~yPs~~ek~~La~~tgLt~~QV~~WF~NrR~r~~~~~~ 204 (414)
+..+++++|++.++.+|.+||. .|||||+++|++||+++|++..||+|||.|.|-|.++...
T Consensus 187 darRKRRNFsK~aTeiLneyF~~h~~nPYPSee~K~eLAkqCnItvsQvsnwfgnkrIrykK~~~ 251 (334)
T KOG0774|consen 187 DARRKRRNFSKQATEILNEYFYSHLSNPYPSEEAKEELAKQCNITVSQVSNWFGNKRIRYKKNMG 251 (334)
T ss_pred HHHHhhcccchhHHHHHHHHHHHhcCCCCCcHHHHHHHHHHcCceehhhccccccceeehhhhhh
Confidence 3455666999999999999998 6899999999999999999999999999999999887544
No 37
>KOG0483|consensus
Probab=98.95 E-value=3.1e-10 Score=105.47 Aligned_cols=57 Identities=26% Similarity=0.445 Sum_probs=53.3
Q ss_pred ccccCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCccccccccccchhHhHHHHh
Q psy14872 338 SYCFKEKSRSVLRDWYTHNPYPSPREKRELAEATGLTTTQVSNWFKNRRQRDRAAEQ 394 (414)
Q Consensus 338 ~~~ft~~q~~~L~~~F~~n~yPs~~~r~~LA~~~gL~~~qV~vWFqNrR~R~Kr~~~ 394 (414)
..+|+.+|+..|+..|+.+.+..+..+..||.++||.++||.|||||||+|||.++.
T Consensus 54 k~Rlt~eQ~~~LE~~F~~~~~L~p~~K~~LAk~LgL~pRQVavWFQNRRARwK~kql 110 (198)
T KOG0483|consen 54 KRRLTSEQVKFLEKSFESEKKLEPERKKKLAKELGLQPRQVAVWFQNRRARWKTKQL 110 (198)
T ss_pred cccccHHHHHHhHHhhccccccChHHHHHHHHhhCCChhHHHHHHhhccccccchhh
Confidence 347899999999999999999999999999999999999999999999999997543
No 38
>KOG0483|consensus
Probab=98.93 E-value=5e-10 Score=104.13 Aligned_cols=60 Identities=18% Similarity=0.306 Sum_probs=54.7
Q ss_pred CcccccCCHhHHHHHHHHhhcCCCCCHHHHHHHHHHhCCCcccccccccccccCCCCCCC
Q psy14872 145 EETSYCFKEKSRSVLRDWYTHNPYPSPREKRELAEATGLTTTQVSNWFSSANITSSPNTS 204 (414)
Q Consensus 145 ~~t~~~f~~~~~~~L~~~f~~~~yPs~~ek~~La~~tgLt~~QV~~WF~NrR~r~~~~~~ 204 (414)
..+..+|+.+|+..|+..|..+.|..+++|..||+.+||.++||.+||||||.|.|....
T Consensus 51 ~~kk~Rlt~eQ~~~LE~~F~~~~~L~p~~K~~LAk~LgL~pRQVavWFQNRRARwK~kql 110 (198)
T KOG0483|consen 51 KGKKRRLTSEQVKFLEKSFESEKKLEPERKKKLAKELGLQPRQVAVWFQNRRARWKTKQL 110 (198)
T ss_pred ccccccccHHHHHHhHHhhccccccChHHHHHHHHhhCCChhHHHHHHhhccccccchhh
Confidence 345569999999999999999999999999999999999999999999999999885433
No 39
>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=98.93 E-value=1.6e-09 Score=81.41 Aligned_cols=47 Identities=21% Similarity=0.421 Sum_probs=45.5
Q ss_pred cCCHhHHHHHHHHhhcCCC----CCHHHHHHHHHHhCCCcccccccccccc
Q psy14872 150 CFKEKSRSVLRDWYTHNPY----PSPREKRELAEATGLTTTQVSNWFSSAN 196 (414)
Q Consensus 150 ~f~~~~~~~L~~~f~~~~y----Ps~~ek~~La~~tgLt~~QV~~WF~NrR 196 (414)
.|+.+|+..|+.+|..++| |+..++.+||..+||+..+|++||+|-+
T Consensus 7 ~Ft~~Q~~~Le~~fe~~~y~~~~~~~~~r~~la~~lgl~~~vvKVWfqN~k 57 (58)
T TIGR01565 7 KFTAEQKEKMRDFAEKLGWKLKDKRREEVREFCEEIGVTRKVFKVWMHNNK 57 (58)
T ss_pred CCCHHHHHHHHHHHHHcCCCCCCCCHHHHHHHHHHhCCCHHHeeeecccCC
Confidence 8999999999999999999 9999999999999999999999999954
No 40
>KOG0848|consensus
Probab=98.91 E-value=2.5e-10 Score=108.46 Aligned_cols=60 Identities=23% Similarity=0.420 Sum_probs=54.3
Q ss_pred CcccccCCHhHHHHHHHHhhcCCCCCHHHHHHHHHHhCCCcccccccccccccCCCCCCC
Q psy14872 145 EETSYCFKEKSRSVLRDWYTHNPYPSPREKRELAEATGLTTTQVSNWFSSANITSSPNTS 204 (414)
Q Consensus 145 ~~t~~~f~~~~~~~L~~~f~~~~yPs~~ek~~La~~tgLt~~QV~~WF~NrR~r~~~~~~ 204 (414)
+..+..|++.|+-.||+.|..++|+|...|.+||..+||+++||++||||||.|.++...
T Consensus 200 DKYRvVYTDhQRLELEKEfh~SryITirRKSELA~~LgLsERQVKIWFQNRRAKERK~nK 259 (317)
T KOG0848|consen 200 DKYRVVYTDHQRLELEKEFHTSRYITIRRKSELAATLGLSERQVKIWFQNRRAKERKDNK 259 (317)
T ss_pred cceeEEecchhhhhhhhhhccccceeeehhHHHHHhhCccHhhhhHhhhhhhHHHHHHHH
Confidence 344578999999999999999999999999999999999999999999999998776444
No 41
>COG5576 Homeodomain-containing transcription factor [Transcription]
Probab=98.90 E-value=1.7e-09 Score=97.23 Aligned_cols=62 Identities=21% Similarity=0.374 Sum_probs=55.4
Q ss_pred ccccCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCccccccccccchhHhHHHHhccCCC
Q psy14872 338 SYCFKEKSRSVLRDWYTHNPYPSPREKRELAEATGLTTTQVSNWFKNRRQRDRAAEQKDGSV 399 (414)
Q Consensus 338 ~~~ft~~q~~~L~~~F~~n~yPs~~~r~~LA~~~gL~~~qV~vWFqNrR~R~Kr~~~~~~~~ 399 (414)
+.+.+..|+.+|+..|..++||+..++..|+..++|++.-|++||||+|++.|+........
T Consensus 55 r~R~t~~Q~~vL~~~F~i~p~Ps~~~r~~L~~~lnm~~ksVqIWFQNkR~~~k~~~~~~~~~ 116 (156)
T COG5576 55 RRRTTDEQLMVLEREFEINPYPSSITRIKLSLLLNMPPKSVQIWFQNKRAKEKKKRSGKVEQ 116 (156)
T ss_pred ceechHHHHHHHHHHhccCCCCCHHHHHHHHHhcCCChhhhhhhhchHHHHHHHhcccchhc
Confidence 34568899999999999999999999999999999999999999999999999976543333
No 42
>KOG0485|consensus
Probab=98.90 E-value=3.4e-10 Score=104.62 Aligned_cols=57 Identities=25% Similarity=0.289 Sum_probs=52.9
Q ss_pred ccCCHhHHHHHHHHhhcCCCCCHHHHHHHHHHhCCCcccccccccccccCCCCCCCC
Q psy14872 149 YCFKEKSRSVLRDWYTHNPYPSPREKRELAEATGLTTTQVSNWFSSANITSSPNTST 205 (414)
Q Consensus 149 ~~f~~~~~~~L~~~f~~~~yPs~~ek~~La~~tgLt~~QV~~WF~NrR~r~~~~~~~ 205 (414)
..|+..|+..|+..|+-..|.|-.||..||..+.||++||++||||||.|.|+....
T Consensus 109 TvFSraQV~qLEs~Fe~krYLSsaeRa~LA~sLqLTETQVKIWFQNRRnKwKRq~aa 165 (268)
T KOG0485|consen 109 TVFSRAQVFQLESTFELKRYLSSAERAGLAASLQLTETQVKIWFQNRRNKWKRQYAA 165 (268)
T ss_pred hhhhHHHHHHHHHHHHHHhhhhHHHHhHHHHhhhhhhhhhhhhhhhhhHHHHHHHhh
Confidence 379999999999999999999999999999999999999999999999998875443
No 43
>KOG0844|consensus
Probab=98.87 E-value=9e-10 Score=106.23 Aligned_cols=62 Identities=26% Similarity=0.392 Sum_probs=57.6
Q ss_pred CCccccccCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCccccccccccchhHhHHHHhc
Q psy14872 334 GEETSYCFKEKSRSVLRDWYTHNPYPSPREKRELAEATGLTTTQVSNWFKNRRQRDRAAEQK 395 (414)
Q Consensus 334 ~~~~~~~ft~~q~~~L~~~F~~n~yPs~~~r~~LA~~~gL~~~qV~vWFqNrR~R~Kr~~~~ 395 (414)
-++-|+.||.+|+..|++.|.+..|.+...|.+||..++|++..|+|||||||+|+||+.-.
T Consensus 181 mRRYRTAFTReQIaRLEKEFyrENYVSRprRcELAAaLNLPEtTIKVWFQNRRMKDKRQRla 242 (408)
T KOG0844|consen 181 MRRYRTAFTREQIARLEKEFYRENYVSRPRRCELAAALNLPETTIKVWFQNRRMKDKRQRLA 242 (408)
T ss_pred HHHHHhhhhHHHHHHHHHHHHHhccccCchhhhHHHhhCCCcceeehhhhhchhhhhhhhhh
Confidence 34567899999999999999999999999999999999999999999999999999998654
No 44
>KOG2251|consensus
Probab=98.86 E-value=1.8e-09 Score=100.39 Aligned_cols=69 Identities=20% Similarity=0.339 Sum_probs=59.4
Q ss_pred CCCCcccCCCcccccCCHhHHHHHHHHhhcCCCCCHHHHHHHHHHhCCCcccccccccccccCCCCCCC
Q psy14872 136 PLPRTIWDGEETSYCFKEKSRSVLRDWYTHNPYPSPREKRELAEATGLTTTQVSNWFSSANITSSPNTS 204 (414)
Q Consensus 136 p~P~t~~~g~~t~~~f~~~~~~~L~~~f~~~~yPs~~ek~~La~~tgLt~~QV~~WF~NrR~r~~~~~~ 204 (414)
|.+.++|...+.+-.|+..|+.+|++.|.+..||+-..+++||.+++|.+.+|.+||+|||.|.+....
T Consensus 29 P~~~~pRkqRRERTtFtr~QlevLe~LF~kTqYPDv~~rEelAlklnLpeSrVqVWFKNRRAK~r~qq~ 97 (228)
T KOG2251|consen 29 PYSSGPRKQRRERTTFTRKQLEVLEALFAKTQYPDVFMREELALKLNLPESRVQVWFKNRRAKCRRQQQ 97 (228)
T ss_pred CcCccchhcccccceecHHHHHHHHHHHHhhcCccHHHHHHHHHHhCCchhhhhhhhccccchhhHhhh
Confidence 344555555555668999999999999999999999999999999999999999999999998775444
No 45
>KOG0486|consensus
Probab=98.84 E-value=1.7e-09 Score=105.02 Aligned_cols=62 Identities=31% Similarity=0.468 Sum_probs=57.8
Q ss_pred CCCccccccCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCccccccccccchhHhHHHHh
Q psy14872 333 DGEETSYCFKEKSRSVLRDWYTHNPYPSPREKRELAEATGLTTTQVSNWFKNRRQRDRAAEQ 394 (414)
Q Consensus 333 ~~~~~~~~ft~~q~~~L~~~F~~n~yPs~~~r~~LA~~~gL~~~qV~vWFqNrR~R~Kr~~~ 394 (414)
..++.++.|+..|+..||.+|.+|.||+.+.|++||.-++|++..|+|||+|||+||+|.+.
T Consensus 111 KqrrQrthFtSqqlqele~tF~rNrypdMstrEEIavwtNlTE~rvrvwfknrrakwrkrEr 172 (351)
T KOG0486|consen 111 KQRRQRTHFTSQQLQELEATFQRNRYPDMSTREEIAVWTNLTEARVRVWFKNRRAKWRKRER 172 (351)
T ss_pred hhhhhhhhhHHHHHHHHHHHHhhccCCccchhhHHHhhccccchhhhhhcccchhhhhhhhh
Confidence 45566789999999999999999999999999999999999999999999999999998654
No 46
>KOG0491|consensus
Probab=98.79 E-value=5.6e-10 Score=99.12 Aligned_cols=58 Identities=28% Similarity=0.474 Sum_probs=52.6
Q ss_pred cCCHhHHHHHHHHhhcCCCCCHHHHHHHHHHhCCCcccccccccccccCCCCCCCCCC
Q psy14872 150 CFKEKSRSVLRDWYTHNPYPSPREKRELAEATGLTTTQVSNWFSSANITSSPNTSTST 207 (414)
Q Consensus 150 ~f~~~~~~~L~~~f~~~~yPs~~ek~~La~~tgLt~~QV~~WF~NrR~r~~~~~~~~~ 207 (414)
.|+..|+..|++.|+...|.+..|+.+||..++|+++||+.||||+|.|.|+..+...
T Consensus 106 vfs~~ql~~l~~rFe~QrYLS~~e~~ELan~L~LS~~QVKTWFQNrRMK~Kk~~r~~~ 163 (194)
T KOG0491|consen 106 VFSDPQLSGLEKRFERQRYLSTPERQELANALSLSETQVKTWFQNRRMKHKKQQRNNQ 163 (194)
T ss_pred cccCccccccHHHHhhhhhcccHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHHHhccC
Confidence 5667779999999999999999999999999999999999999999999887665543
No 47
>COG5576 Homeodomain-containing transcription factor [Transcription]
Probab=98.73 E-value=4.8e-09 Score=94.34 Aligned_cols=56 Identities=20% Similarity=0.327 Sum_probs=51.3
Q ss_pred cccCCHhHHHHHHHHhhcCCCCCHHHHHHHHHHhCCCcccccccccccccCCCCCC
Q psy14872 148 SYCFKEKSRSVLRDWYTHNPYPSPREKRELAEATGLTTTQVSNWFSSANITSSPNT 203 (414)
Q Consensus 148 ~~~f~~~~~~~L~~~f~~~~yPs~~ek~~La~~tgLt~~QV~~WF~NrR~r~~~~~ 203 (414)
..+-+..|+.+|+..|..+|||+..+|..|+..+||+++-|.+||||+|.+.++..
T Consensus 55 r~R~t~~Q~~vL~~~F~i~p~Ps~~~r~~L~~~lnm~~ksVqIWFQNkR~~~k~~~ 110 (156)
T COG5576 55 RRRTTDEQLMVLEREFEINPYPSSITRIKLSLLLNMPPKSVQIWFQNKRAKEKKKR 110 (156)
T ss_pred ceechHHHHHHHHHHhccCCCCCHHHHHHHHHhcCCChhhhhhhhchHHHHHHHhc
Confidence 34778999999999999999999999999999999999999999999998877533
No 48
>KOG3802|consensus
Probab=98.71 E-value=1.3e-08 Score=102.23 Aligned_cols=55 Identities=24% Similarity=0.404 Sum_probs=51.7
Q ss_pred cCCHhHHHHHHHHhhcCCCCCHHHHHHHHHHhCCCcccccccccccccCCCCCCC
Q psy14872 150 CFKEKSRSVLRDWYTHNPYPSPREKRELAEATGLTTTQVSNWFSSANITSSPNTS 204 (414)
Q Consensus 150 ~f~~~~~~~L~~~f~~~~yPs~~ek~~La~~tgLt~~QV~~WF~NrR~r~~~~~~ 204 (414)
.+...++.+|+.+|.+||-||.+|...||+.++|....|.+||+|||.|.|+-..
T Consensus 300 Sie~~vr~aLE~~F~~npKPt~qEIt~iA~~L~leKEVVRVWFCNRRQkeKR~~~ 354 (398)
T KOG3802|consen 300 SIEVNVRGALEKHFLKNPKPTSQEITHIAESLQLEKEVVRVWFCNRRQKEKRITP 354 (398)
T ss_pred ceeHHHHHHHHHHHHhCCCCCHHHHHHHHHHhccccceEEEEeeccccccccCCC
Confidence 7888999999999999999999999999999999999999999999999886544
No 49
>KOG0847|consensus
Probab=98.69 E-value=7.3e-09 Score=95.94 Aligned_cols=59 Identities=24% Similarity=0.418 Sum_probs=54.6
Q ss_pred ccccccCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCccccccccccchhHhHHHHh
Q psy14872 336 ETSYCFKEKSRSVLRDWYTHNPYPSPREKRELAEATGLTTTQVSNWFKNRRQRDRAAEQ 394 (414)
Q Consensus 336 ~~~~~ft~~q~~~L~~~F~~n~yPs~~~r~~LA~~~gL~~~qV~vWFqNrR~R~Kr~~~ 394 (414)
.++..|+..|+..|+..|+..+|+-.+++.+||..+||++.||+|||||||.||||+-+
T Consensus 169 ~srPTf~g~qi~~le~~feqtkylaG~~ra~lA~~lgmteSqvkVWFQNRRTKWRKkhA 227 (288)
T KOG0847|consen 169 QSRPTFTGHQIYQLERKFEQTKYLAGADRAQLAQELNMTESQVKVWFQNRRTKWRKKHA 227 (288)
T ss_pred ccCCCccchhhhhhhhhhhhhhcccchhHHHhhccccccHHHHHHHHhcchhhhhhhhc
Confidence 33556999999999999999999999999999999999999999999999999999654
No 50
>KOG0773|consensus
Probab=98.57 E-value=1.7e-08 Score=101.91 Aligned_cols=52 Identities=46% Similarity=0.726 Sum_probs=47.4
Q ss_pred ccCHHHHHHHHHHHhh---CCCCCHHHHHHHHHHhCCCccccccccccchhHhHH
Q psy14872 340 CFKEKSRSVLRDWYTH---NPYPSPREKRELAEATGLTTTQVSNWFKNRRQRDRA 391 (414)
Q Consensus 340 ~ft~~q~~~L~~~F~~---n~yPs~~~r~~LA~~~gL~~~qV~vWFqNrR~R~Kr 391 (414)
.++.....+|+.|... ++||+..++..||.+|||+..||.+||.|.|.|..+
T Consensus 245 ~lP~~a~~ilr~Wl~~h~~~PYPse~~K~~La~~TGLs~~Qv~NWFINaR~R~w~ 299 (342)
T KOG0773|consen 245 GLPKEAVSILRAWLFEHLLHPYPSDDEKLMLAKQTGLSRPQVSNWFINARVRLWK 299 (342)
T ss_pred CCCHHHHHHHHHHHHHhccCCCCcchhccccchhcCCCcccCCchhhhcccccCC
Confidence 5778889999999755 699999999999999999999999999999999876
No 51
>KOG0484|consensus
Probab=98.55 E-value=1.2e-08 Score=84.22 Aligned_cols=69 Identities=20% Similarity=0.272 Sum_probs=59.0
Q ss_pred ccccccccccCCCCCCCcccCCCcccccCCHhHHHHHHHHhhcCCCCCHHHHHHHHHHhCCCcccccccccccccCCCCC
Q psy14872 123 IINIIKYRVRRKFPLPRTIWDGEETSYCFKEKSRSVLRDWYTHNPYPSPREKRELAEATGLTTTQVSNWFSSANITSSPN 202 (414)
Q Consensus 123 l~~v~k~r~rk~~p~P~t~~~g~~t~~~f~~~~~~~L~~~f~~~~yPs~~ek~~La~~tgLt~~QV~~WF~NrR~r~~~~ 202 (414)
||..+|...|+=+. .|+..|+..|+..|.+..||+.-.|++||-.+.||+..|.+||||||.|.++.
T Consensus 9 ~~l~ekrKQRRIRT-------------TFTS~QLkELErvF~ETHYPDIYTREEiA~kidLTEARVQVWFQNRRAKfRKQ 75 (125)
T KOG0484|consen 9 LGLTEKRKQRRIRT-------------TFTSAQLKELERVFAETHYPDIYTREEIALKIDLTEARVQVWFQNRRAKFRKQ 75 (125)
T ss_pred CChhHHHHhhhhhh-------------hhhHHHHHHHHHHHHhhcCCcchhHHHHHHhhhhhHHHHHHHHHhhHHHHHHH
Confidence 56656655554432 79999999999999999999999999999999999999999999999988764
Q ss_pred CC
Q psy14872 203 TS 204 (414)
Q Consensus 203 ~~ 204 (414)
.+
T Consensus 76 Er 77 (125)
T KOG0484|consen 76 ER 77 (125)
T ss_pred HH
Confidence 43
No 52
>KOG0773|consensus
Probab=98.52 E-value=5e-08 Score=98.51 Aligned_cols=57 Identities=39% Similarity=0.609 Sum_probs=51.3
Q ss_pred cccCCHhHHHHHHHHhhc---CCCCCHHHHHHHHHHhCCCcccccccccccccCCCCCCC
Q psy14872 148 SYCFKEKSRSVLRDWYTH---NPYPSPREKRELAEATGLTTTQVSNWFSSANITSSPNTS 204 (414)
Q Consensus 148 ~~~f~~~~~~~L~~~f~~---~~yPs~~ek~~La~~tgLt~~QV~~WF~NrR~r~~~~~~ 204 (414)
...|++.++.+|+.|+.+ +|||++.+|..||..|||+..||+|||+|+|+|.++...
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 348999999999999764 699999999999999999999999999999999886433
No 53
>KOG0774|consensus
Probab=98.52 E-value=5.2e-08 Score=92.46 Aligned_cols=60 Identities=37% Similarity=0.700 Sum_probs=54.7
Q ss_pred CCCccccccCHHHHHHHHHHHhh---CCCCCHHHHHHHHHHhCCCccccccccccchhHhHHH
Q psy14872 333 DGEETSYCFKEKSRSVLRDWYTH---NPYPSPREKRELAEATGLTTTQVSNWFKNRRQRDRAA 392 (414)
Q Consensus 333 ~~~~~~~~ft~~q~~~L~~~F~~---n~yPs~~~r~~LA~~~gL~~~qV~vWFqNrR~R~Kr~ 392 (414)
+.+++|.+|+...+++|.+||.. |+||+.+++++||++++++.+||.+||.|.|-|.||-
T Consensus 187 darRKRRNFsK~aTeiLneyF~~h~~nPYPSee~K~eLAkqCnItvsQvsnwfgnkrIrykK~ 249 (334)
T KOG0774|consen 187 DARRKRRNFSKQATEILNEYFYSHLSNPYPSEEAKEELAKQCNITVSQVSNWFGNKRIRYKKN 249 (334)
T ss_pred HHHHhhcccchhHHHHHHHHHHHhcCCCCCcHHHHHHHHHHcCceehhhccccccceeehhhh
Confidence 44556678999999999999974 8999999999999999999999999999999999984
No 54
>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=98.52 E-value=2.3e-08 Score=69.61 Aligned_cols=34 Identities=65% Similarity=1.102 Sum_probs=29.4
Q ss_pred hCCCCCHHHHHHHHHHhCCCccccccccccchhH
Q psy14872 355 HNPYPSPREKRELAEATGLTTTQVSNWFKNRRQR 388 (414)
Q Consensus 355 ~n~yPs~~~r~~LA~~~gL~~~qV~vWFqNrR~R 388 (414)
.+|||+.++++.||..+||+..||.+||.|.|.|
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 4799999999999999999999999999999976
No 55
>KOG0844|consensus
Probab=98.42 E-value=1e-07 Score=92.26 Aligned_cols=58 Identities=21% Similarity=0.335 Sum_probs=53.6
Q ss_pred cccCCHhHHHHHHHHhhcCCCCCHHHHHHHHHHhCCCcccccccccccccCCCCCCCC
Q psy14872 148 SYCFKEKSRSVLRDWYTHNPYPSPREKRELAEATGLTTTQVSNWFSSANITSSPNTST 205 (414)
Q Consensus 148 ~~~f~~~~~~~L~~~f~~~~yPs~~ek~~La~~tgLt~~QV~~WF~NrR~r~~~~~~~ 205 (414)
+..|+++|+..|++.|.+..|-+...|=+||..++|.+..|++||||||.|.|++...
T Consensus 185 RTAFTReQIaRLEKEFyrENYVSRprRcELAAaLNLPEtTIKVWFQNRRMKDKRQRla 242 (408)
T KOG0844|consen 185 RTAFTREQIARLEKEFYRENYVSRPRRCELAAALNLPETTIKVWFQNRRMKDKRQRLA 242 (408)
T ss_pred HhhhhHHHHHHHHHHHHHhccccCchhhhHHHhhCCCcceeehhhhhchhhhhhhhhh
Confidence 3579999999999999999999999999999999999999999999999998876554
No 56
>KOG0494|consensus
Probab=98.38 E-value=1.9e-07 Score=88.60 Aligned_cols=55 Identities=18% Similarity=0.329 Sum_probs=51.4
Q ss_pred cCCHhHHHHHHHHhhcCCCCCHHHHHHHHHHhCCCcccccccccccccCCCCCCC
Q psy14872 150 CFKEKSRSVLRDWYTHNPYPSPREKRELAEATGLTTTQVSNWFSSANITSSPNTS 204 (414)
Q Consensus 150 ~f~~~~~~~L~~~f~~~~yPs~~ek~~La~~tgLt~~QV~~WF~NrR~r~~~~~~ 204 (414)
.||.-|+..|++.|++.-||+-.-|+.||..|+|.+..|.+||||||.|+++...
T Consensus 147 iFT~~Qle~LEkaFkeaHYPDv~Are~la~ktelpEDRIqVWfQNRRAKWRk~Ek 201 (332)
T KOG0494|consen 147 IFTSYQLEELEKAFKEAHYPDVYAREMLADKTELPEDRIQVWFQNRRAKWRKTEK 201 (332)
T ss_pred hhhHHHHHHHHHHHhhccCccHHHHHHHhhhccCchhhhhHHhhhhhHHhhhhhh
Confidence 6889999999999999999999999999999999999999999999999886443
No 57
>KOG0490|consensus
Probab=98.38 E-value=3.3e-07 Score=86.74 Aligned_cols=60 Identities=23% Similarity=0.251 Sum_probs=56.5
Q ss_pred CCccccccCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCccccccccccchhHhHHHH
Q psy14872 334 GEETSYCFKEKSRSVLRDWYTHNPYPSPREKRELAEATGLTTTQVSNWFKNRRQRDRAAE 393 (414)
Q Consensus 334 ~~~~~~~ft~~q~~~L~~~F~~n~yPs~~~r~~LA~~~gL~~~qV~vWFqNrR~R~Kr~~ 393 (414)
.++.++.|+..|+..|+..|+.++||+...++.||..+++++..|++||||+|+++++..
T Consensus 60 ~rr~rt~~~~~ql~~ler~f~~~h~Pd~~~r~~la~~~~~~e~rVqvwFqnrrak~r~~~ 119 (235)
T KOG0490|consen 60 KRCARCKFTISQLDELERAFEKVHLPCFACRECLALLLTGDEFRVQVWFQNRRAKDRKEE 119 (235)
T ss_pred ccccCCCCCcCHHHHHHHhhcCCCcCccchHHHHhhcCCCCeeeeehhhhhhcHhhhhhh
Confidence 456678899999999999999999999999999999999999999999999999999876
No 58
>KOG0486|consensus
Probab=98.31 E-value=2.5e-07 Score=90.13 Aligned_cols=60 Identities=22% Similarity=0.339 Sum_probs=55.5
Q ss_pred cccCCHhHHHHHHHHhhcCCCCCHHHHHHHHHHhCCCcccccccccccccCCCCCCCCCC
Q psy14872 148 SYCFKEKSRSVLRDWYTHNPYPSPREKRELAEATGLTTTQVSNWFSSANITSSPNTSTST 207 (414)
Q Consensus 148 ~~~f~~~~~~~L~~~f~~~~yPs~~ek~~La~~tgLt~~QV~~WF~NrR~r~~~~~~~~~ 207 (414)
+.-|+..|++.|+.||..|.||+.+.|++||--|+||+..|.+||+|||.|.++..++..
T Consensus 116 rthFtSqqlqele~tF~rNrypdMstrEEIavwtNlTE~rvrvwfknrrakwrkrErN~~ 175 (351)
T KOG0486|consen 116 RTHFTSQQLQELEATFQRNRYPDMSTREEIAVWTNLTEARVRVWFKNRRAKWRKRERNQQ 175 (351)
T ss_pred hhhhHHHHHHHHHHHHhhccCCccchhhHHHhhccccchhhhhhcccchhhhhhhhhhHH
Confidence 347999999999999999999999999999999999999999999999999988766643
No 59
>KOG0847|consensus
Probab=98.24 E-value=3.2e-07 Score=85.17 Aligned_cols=57 Identities=18% Similarity=0.310 Sum_probs=52.3
Q ss_pred ccCCHhHHHHHHHHhhcCCCCCHHHHHHHHHHhCCCcccccccccccccCCCCCCCC
Q psy14872 149 YCFKEKSRSVLRDWYTHNPYPSPREKRELAEATGLTTTQVSNWFSSANITSSPNTST 205 (414)
Q Consensus 149 ~~f~~~~~~~L~~~f~~~~yPs~~ek~~La~~tgLt~~QV~~WF~NrR~r~~~~~~~ 205 (414)
..|+-.|+..|+..|+...||-.+++.+||..+|+++.||++||||||.|.+++...
T Consensus 172 PTf~g~qi~~le~~feqtkylaG~~ra~lA~~lgmteSqvkVWFQNRRTKWRKkhAa 228 (288)
T KOG0847|consen 172 PTFTGHQIYQLERKFEQTKYLAGADRAQLAQELNMTESQVKVWFQNRRTKWRKKHAA 228 (288)
T ss_pred CCccchhhhhhhhhhhhhhcccchhHHHhhccccccHHHHHHHHhcchhhhhhhhcc
Confidence 458899999999999999999999999999999999999999999999998865443
No 60
>KOG2252|consensus
Probab=98.23 E-value=2.3e-06 Score=89.16 Aligned_cols=59 Identities=19% Similarity=0.303 Sum_probs=53.6
Q ss_pred ccccCCHhHHHHHHHHhhcCCCCCHHHHHHHHHHhCCCcccccccccccccCCCCCCCC
Q psy14872 147 TSYCFKEKSRSVLRDWYTHNPYPSPREKRELAEATGLTTTQVSNWFSSANITSSPNTST 205 (414)
Q Consensus 147 t~~~f~~~~~~~L~~~f~~~~yPs~~ek~~La~~tgLt~~QV~~WF~NrR~r~~~~~~~ 205 (414)
.+..|++.|++.|+..|+.+++|+.++.+.|+..+||....|.|||-|+|+|.+.....
T Consensus 423 PRlVfTd~QkrTL~aiFke~~RPS~Emq~tIS~qL~L~~sTV~NfFmNaRRRsl~~~~~ 481 (558)
T KOG2252|consen 423 PRLVFTDIQKRTLQAIFKENKRPSREMQETISQQLNLELSTVINFFMNARRRSLDKKVD 481 (558)
T ss_pred ceeeecHHHHHHHHHHHhcCCCCCHHHHHHHHHHhCCcHHHHHHHHHhhhhhccccccc
Confidence 35689999999999999999999999999999999999999999999999997644443
No 61
>KOG0849|consensus
Probab=98.18 E-value=1.3e-06 Score=88.77 Aligned_cols=60 Identities=30% Similarity=0.587 Sum_probs=56.0
Q ss_pred CCccccccCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCccccccccccchhHhHHHH
Q psy14872 334 GEETSYCFKEKSRSVLRDWYTHNPYPSPREKRELAEATGLTTTQVSNWFKNRRQRDRAAE 393 (414)
Q Consensus 334 ~~~~~~~ft~~q~~~L~~~F~~n~yPs~~~r~~LA~~~gL~~~qV~vWFqNrR~R~Kr~~ 393 (414)
+++.++.|+..|...|++.|+.++||....|+.||.+++++...|.+||+|+|++++|..
T Consensus 176 ~rr~rtsft~~Q~~~le~~f~rt~yP~i~~Re~La~~i~l~e~riqvwf~nrra~~rr~~ 235 (354)
T KOG0849|consen 176 GRRNRTSFSPSQLEALEECFQRTPYPDIVGRETLAKETGLPEPRVQVWFQNRRAKWRRQH 235 (354)
T ss_pred ccccccccccchHHHHHHHhcCCCCCchhhHHHHhhhccCCchHHHHHHhhhhhhhhhcc
Confidence 344567899999999999999999999999999999999999999999999999999875
No 62
>KOG1168|consensus
Probab=98.17 E-value=3.7e-06 Score=81.13 Aligned_cols=57 Identities=23% Similarity=0.442 Sum_probs=50.1
Q ss_pred ccccCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCccccccccccchhHhHHHHh
Q psy14872 338 SYCFKEKSRSVLRDWYTHNPYPSPREKRELAEATGLTTTQVSNWFKNRRQRDRAAEQ 394 (414)
Q Consensus 338 ~~~ft~~q~~~L~~~F~~n~yPs~~~r~~LA~~~gL~~~qV~vWFqNrR~R~Kr~~~ 394 (414)
|+.+-.-..+.|+.+|...+.|+.+....||+++.|.+..|+|||+|.|+|.||.+.
T Consensus 313 RTSIAAPEKRsLEayFavQPRPS~EkIAaIAekLDLKKNVVRVWFCNQRQKQKRm~~ 369 (385)
T KOG1168|consen 313 RTSIAAPEKRSLEAYFAVQPRPSGEKIAAIAEKLDLKKNVVRVWFCNQRQKQKRMKR 369 (385)
T ss_pred cccccCcccccHHHHhccCCCCchhHHHHHHHhhhhhhceEEEEeeccHHHHHHhhh
Confidence 344444457789999999999999999999999999999999999999999998654
No 63
>KOG4577|consensus
Probab=97.96 E-value=3.9e-06 Score=80.92 Aligned_cols=56 Identities=21% Similarity=0.401 Sum_probs=50.7
Q ss_pred cCCHhHHHHHHHHhhcCCCCCHHHHHHHHHHhCCCcccccccccccccCCCCCCCC
Q psy14872 150 CFKEKSRSVLRDWYTHNPYPSPREKRELAEATGLTTTQVSNWFSSANITSSPNTST 205 (414)
Q Consensus 150 ~f~~~~~~~L~~~f~~~~yPs~~ek~~La~~tgLt~~QV~~WF~NrR~r~~~~~~~ 205 (414)
..+.+|+..|+..|...|-|..--|+.|+.+|||..+.|.+||||||.|.|+-..+
T Consensus 173 TItAKqLETLK~AYn~SpKPARHVREQLsseTGLDMRVVQVWFQNRRAKEKRLKKD 228 (383)
T KOG4577|consen 173 TITAKQLETLKQAYNTSPKPARHVREQLSSETGLDMRVVQVWFQNRRAKEKRLKKD 228 (383)
T ss_pred eeeHHHHHHHHHHhcCCCchhHHHHHHhhhccCcceeehhhhhhhhhHHHHhhhhh
Confidence 56888899999999999999999999999999999999999999999887754433
No 64
>KOG0849|consensus
Probab=97.72 E-value=1.9e-05 Score=80.27 Aligned_cols=57 Identities=23% Similarity=0.454 Sum_probs=53.0
Q ss_pred ccCCHhHHHHHHHHhhcCCCCCHHHHHHHHHHhCCCcccccccccccccCCCCCCCC
Q psy14872 149 YCFKEKSRSVLRDWYTHNPYPSPREKRELAEATGLTTTQVSNWFSSANITSSPNTST 205 (414)
Q Consensus 149 ~~f~~~~~~~L~~~f~~~~yPs~~ek~~La~~tgLt~~QV~~WF~NrR~r~~~~~~~ 205 (414)
..|+..|...|++.|..++||.-..++.||.++||++..|.+||+|+|.+.++....
T Consensus 181 tsft~~Q~~~le~~f~rt~yP~i~~Re~La~~i~l~e~riqvwf~nrra~~rr~~~~ 237 (354)
T KOG0849|consen 181 TSFSPSQLEALEECFQRTPYPDIVGRETLAKETGLPEPRVQVWFQNRRAKWRRQHRD 237 (354)
T ss_pred cccccchHHHHHHHhcCCCCCchhhHHHHhhhccCCchHHHHHHhhhhhhhhhcccc
Confidence 479999999999999999999999999999999999999999999999988876643
No 65
>KOG2252|consensus
Probab=97.62 E-value=0.00012 Score=76.73 Aligned_cols=56 Identities=21% Similarity=0.396 Sum_probs=52.3
Q ss_pred ccccccCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCccccccccccchhHhHH
Q psy14872 336 ETSYCFKEKSRSVLRDWYTHNPYPSPREKRELAEATGLTTTQVSNWFKNRRQRDRA 391 (414)
Q Consensus 336 ~~~~~ft~~q~~~L~~~F~~n~yPs~~~r~~LA~~~gL~~~qV~vWFqNrR~R~Kr 391 (414)
+.|..|+..|+..|...|+.+++|+.++.+.|+.+++|....|.|||-|.|+|.+-
T Consensus 422 KPRlVfTd~QkrTL~aiFke~~RPS~Emq~tIS~qL~L~~sTV~NfFmNaRRRsl~ 477 (558)
T KOG2252|consen 422 KPRLVFTDIQKRTLQAIFKENKRPSREMQETISQQLNLELSTVINFFMNARRRSLD 477 (558)
T ss_pred CceeeecHHHHHHHHHHHhcCCCCCHHHHHHHHHHhCCcHHHHHHHHHhhhhhccc
Confidence 34679999999999999999999999999999999999999999999999999643
No 66
>KOG1168|consensus
Probab=97.50 E-value=5.2e-05 Score=73.37 Aligned_cols=50 Identities=20% Similarity=0.385 Sum_probs=46.1
Q ss_pred HHHHHHHhhcCCCCCHHHHHHHHHHhCCCcccccccccccccCCCCCCCC
Q psy14872 156 RSVLRDWYTHNPYPSPREKRELAEATGLTTTQVSNWFSSANITSSPNTST 205 (414)
Q Consensus 156 ~~~L~~~f~~~~yPs~~ek~~La~~tgLt~~QV~~WF~NrR~r~~~~~~~ 205 (414)
.+-|+++|...|-|+.|....+|+++.|....|.+||+|.|.|+|+....
T Consensus 321 KRsLEayFavQPRPS~EkIAaIAekLDLKKNVVRVWFCNQRQKQKRm~~S 370 (385)
T KOG1168|consen 321 KRSLEAYFAVQPRPSGEKIAAIAEKLDLKKNVVRVWFCNQRQKQKRMKRS 370 (385)
T ss_pred cccHHHHhccCCCCchhHHHHHHHhhhhhhceEEEEeeccHHHHHHhhhh
Confidence 67899999999999999999999999999999999999999998874443
No 67
>PF11569 Homez: Homeodomain leucine-zipper encoding, Homez; PDB: 2YS9_A.
Probab=97.31 E-value=7.2e-05 Score=55.61 Aligned_cols=41 Identities=22% Similarity=0.443 Sum_probs=32.1
Q ss_pred HHHHHHHhhcCCCCCHHHHHHHHHHhCCCcccccccccccc
Q psy14872 156 RSVLRDWYTHNPYPSPREKRELAEATGLTTTQVSNWFSSAN 196 (414)
Q Consensus 156 ~~~L~~~f~~~~yPs~~ek~~La~~tgLt~~QV~~WF~NrR 196 (414)
++.|+++|..++++...+-..|..++||+..||..||.-++
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 67799999999999999999999999999999999998765
No 68
>KOG1146|consensus
Probab=97.27 E-value=0.00082 Score=76.56 Aligned_cols=61 Identities=20% Similarity=0.345 Sum_probs=56.4
Q ss_pred CCccccccCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCccccccccccchhHhHHHHh
Q psy14872 334 GEETSYCFKEKSRSVLRDWYTHNPYPSPREKRELAEATGLTTTQVSNWFKNRRQRDRAAEQ 394 (414)
Q Consensus 334 ~~~~~~~ft~~q~~~L~~~F~~n~yPs~~~r~~LA~~~gL~~~qV~vWFqNrR~R~Kr~~~ 394 (414)
.+..++.++..|+.+++..|....||...+.+.|...+++..+.|.+||||.|.+.++...
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 3455778999999999999999999999999999999999999999999999999998755
No 69
>PF11569 Homez: Homeodomain leucine-zipper encoding, Homez; PDB: 2YS9_A.
Probab=96.59 E-value=0.00067 Score=50.49 Aligned_cols=42 Identities=26% Similarity=0.494 Sum_probs=31.8
Q ss_pred HHHHHHHHhhCCCCCHHHHHHHHHHhCCCccccccccccchh
Q psy14872 346 RSVLRDWYTHNPYPSPREKRELAEATGLTTTQVSNWFKNRRQ 387 (414)
Q Consensus 346 ~~~L~~~F~~n~yPs~~~r~~LA~~~gL~~~qV~vWFqNrR~ 387 (414)
+..|+++|..++++...+...|+.++||+..||+.||..++.
T Consensus 10 ~~pL~~Yy~~h~~L~E~DL~~L~~kS~ms~qqVr~WFa~~~~ 51 (56)
T PF11569_consen 10 IQPLEDYYLKHKQLQEEDLDELCDKSRMSYQQVRDWFAERMQ 51 (56)
T ss_dssp -HHHHHHHHHT----TTHHHHHHHHTT--HHHHHHHHHHHS-
T ss_pred hHHHHHHHHHcCCccHhhHHHHHHHHCCCHHHHHHHHHHhcc
Confidence 567999999999999999999999999999999999986544
No 70
>KOG1146|consensus
Probab=94.09 E-value=0.04 Score=63.39 Aligned_cols=59 Identities=19% Similarity=0.296 Sum_probs=53.2
Q ss_pred cccCCHhHHHHHHHHhhcCCCCCHHHHHHHHHHhCCCcccccccccccccCCCCCCCCC
Q psy14872 148 SYCFKEKSRSVLRDWYTHNPYPSPREKRELAEATGLTTTQVSNWFSSANITSSPNTSTS 206 (414)
Q Consensus 148 ~~~f~~~~~~~L~~~f~~~~yPs~~ek~~La~~tgLt~~QV~~WF~NrR~r~~~~~~~~ 206 (414)
+..++..++.+++.+|....||..++.+.|.+..+|..+.|..||+|.|.+.++...+.
T Consensus 907 ~~~~~d~qlk~i~~~~~~q~~~~~~~~E~l~~~~~~~~~~i~vw~qna~~~s~k~~~n~ 965 (1406)
T KOG1146|consen 907 RTQESDLQLKIIKACYEAQRTPTMQECEVLEEPIGLPKRVIQVWFQNARAKSKKAKLNG 965 (1406)
T ss_pred ccchhHHHHHHHHHHHhhccCChHHHHHhhcccccCCcchhHHhhhhhhhhhhhhhhcc
Confidence 34788999999999999999999999999999999999999999999999988655443
No 71
>KOG3623|consensus
Probab=90.32 E-value=0.27 Score=53.72 Aligned_cols=48 Identities=29% Similarity=0.585 Sum_probs=45.2
Q ss_pred HHHHHHHHhhCCCCCHHHHHHHHHHhCCCccccccccccchhHhHHHH
Q psy14872 346 RSVLRDWYTHNPYPSPREKRELAEATGLTTTQVSNWFKNRRQRDRAAE 393 (414)
Q Consensus 346 ~~~L~~~F~~n~yPs~~~r~~LA~~~gL~~~qV~vWFqNrR~R~Kr~~ 393 (414)
+..|+.+|..|..|+.++...+|...||+...|+.||++.++.+....
T Consensus 568 ~sllkayyaln~~ps~eelskia~qvglp~~vvk~wfE~~~a~e~sv~ 615 (1007)
T KOG3623|consen 568 TSLLKAYYALNGLPSEEELSKIAQQVGLPFAVVKAWFEDEEAEEMSVE 615 (1007)
T ss_pred HHHHHHHHHhcCCCCHHHHHHHHHHhcccHHHHHHHHHhhhhhhhhhc
Confidence 789999999999999999999999999999999999999999888654
No 72
>KOG3623|consensus
Probab=89.73 E-value=0.38 Score=52.61 Aligned_cols=46 Identities=28% Similarity=0.536 Sum_probs=42.9
Q ss_pred HHHHHHHhhcCCCCCHHHHHHHHHHhCCCcccccccccccccCCCC
Q psy14872 156 RSVLRDWYTHNPYPSPREKRELAEATGLTTTQVSNWFSSANITSSP 201 (414)
Q Consensus 156 ~~~L~~~f~~~~yPs~~ek~~La~~tgLt~~QV~~WF~NrR~r~~~ 201 (414)
+.+|+++|.-|++|+.+|-..+|...||....|+.||.+.+.....
T Consensus 568 ~sllkayyaln~~ps~eelskia~qvglp~~vvk~wfE~~~a~e~s 613 (1007)
T KOG3623|consen 568 TSLLKAYYALNGLPSEEELSKIAQQVGLPFAVVKAWFEDEEAEEMS 613 (1007)
T ss_pred HHHHHHHHHhcCCCCHHHHHHHHHHhcccHHHHHHHHHhhhhhhhh
Confidence 8899999999999999999999999999999999999999876553
No 73
>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=63.05 E-value=8.8 Score=28.10 Aligned_cols=43 Identities=19% Similarity=0.297 Sum_probs=30.0
Q ss_pred ccccCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCccccccccccc
Q psy14872 338 SYCFKEKSRSVLRDWYTHNPYPSPREKRELAEATGLTTTQVSNWFKNR 385 (414)
Q Consensus 338 ~~~ft~~q~~~L~~~F~~n~yPs~~~r~~LA~~~gL~~~qV~vWFqNr 385 (414)
+..+|-++...+-..++... ....||..+|++.++|..|..|+
T Consensus 4 R~~LTl~eK~~iI~~~e~g~-----s~~~ia~~fgv~~sTv~~I~K~k 46 (53)
T PF04218_consen 4 RKSLTLEEKLEIIKRLEEGE-----SKRDIAREFGVSRSTVSTILKNK 46 (53)
T ss_dssp SSS--HHHHHHHHHHHHCTT------HHHHHHHHT--CCHHHHHHHCH
T ss_pred CccCCHHHHHHHHHHHHcCC-----CHHHHHHHhCCCHHHHHHHHHhH
Confidence 34667777666666677665 46789999999999999999984
No 74
>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=62.10 E-value=8.7 Score=28.12 Aligned_cols=42 Identities=14% Similarity=0.268 Sum_probs=28.1
Q ss_pred cCCHhHHHHHHHHhhcCCCCCHHHHHHHHHHhCCCcccccccccccc
Q psy14872 150 CFKEKSRSVLRDWYTHNPYPSPREKRELAEATGLTTTQVSNWFSSAN 196 (414)
Q Consensus 150 ~f~~~~~~~L~~~f~~~~yPs~~ek~~La~~tgLt~~QV~~WF~NrR 196 (414)
.+|-++.-.+-..++..+ -...||..+|++..+|..|..|+.
T Consensus 6 ~LTl~eK~~iI~~~e~g~-----s~~~ia~~fgv~~sTv~~I~K~k~ 47 (53)
T PF04218_consen 6 SLTLEEKLEIIKRLEEGE-----SKRDIAREFGVSRSTVSTILKNKD 47 (53)
T ss_dssp S--HHHHHHHHHHHHCTT------HHHHHHHHT--CCHHHHHHHCHH
T ss_pred cCCHHHHHHHHHHHHcCC-----CHHHHHHHhCCCHHHHHHHHHhHH
Confidence 556666555555556554 588899999999999999999853
No 75
>COG4802 FtrB Ferredoxin-thioredoxin reductase, catalytic subunit [Energy production and conversion]
Probab=56.67 E-value=7.7 Score=32.51 Aligned_cols=36 Identities=33% Similarity=0.736 Sum_probs=28.6
Q ss_pred Ccee---eeecCCcceeeeeecCCCCchhhhhhhccchhhhhhh
Q psy14872 16 PSVY---NVVDKGNCHCRMYRVPHDDRCCASELKSNQDRTCQQC 56 (414)
Q Consensus 16 ~~~~---~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 56 (414)
|-|| .+-+-|+|||-+|--|.++ |..|-.+++.+..
T Consensus 68 PCvy~~ddi~e~g~C~C~Lyl~~e~~-----e~~sIp~r~~e~r 106 (110)
T COG4802 68 PCVYRDDDIREYGECYCGLYLSPEKD-----EAQSIPERRAEVR 106 (110)
T ss_pred cCcCCccchhhhCceeEEEEeccccc-----chhhcchhhHhhh
Confidence 5666 5677899999999999988 7777777777543
No 76
>cd06171 Sigma70_r4 Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in Escherichia coli (Ec) sigma70, the main housekeeping sigma, and related sigma-factors (SFs). A SF is a dissociable subunit of RNA polymerase, it directs bacterial or plastid core RNA polymerase to specific promoter elements located upstream of transcription initiation points. The SR4 of Ec sigma70 and other essential primary SFs contact promoter sequences located 35 base-pairs upstream of the initiation point, recognizing a 6-base-pair -35 consensus TTGACA. Sigma70 related SFs also include SFs which are dispensable for bacterial cell growth for example Ec sigmaS, SFs which activate regulons in response to a specific signal for example heat-shock Ec sigmaH, and a group of SFs which includes the extracytoplasmic function (ECF) SFs and is typified by Ec sigmaE which contains SR2 and -4 only. ECF SFs direct the transcription of genes that regulate various responses including periplas
Probab=54.95 E-value=5.1 Score=27.56 Aligned_cols=44 Identities=20% Similarity=0.254 Sum_probs=33.2
Q ss_pred cCCHhHHHHHHHHhhcCCCCCHHHHHHHHHHhCCCcccccccccccccC
Q psy14872 150 CFKEKSRSVLRDWYTHNPYPSPREKRELAEATGLTTTQVSNWFSSANIT 198 (414)
Q Consensus 150 ~f~~~~~~~L~~~f~~~~yPs~~ek~~La~~tgLt~~QV~~WF~NrR~r 198 (414)
.+++.++.++...|... -.-..+|+.+|++..+|..|....+.+
T Consensus 10 ~l~~~~~~~~~~~~~~~-----~~~~~ia~~~~~s~~~i~~~~~~~~~~ 53 (55)
T cd06171 10 KLPEREREVILLRFGEG-----LSYEEIAEILGISRSTVRQRLHRALKK 53 (55)
T ss_pred hCCHHHHHHHHHHHhcC-----CCHHHHHHHHCcCHHHHHHHHHHHHHH
Confidence 45677788888876422 345678999999999999998776554
No 77
>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=46.86 E-value=21 Score=26.32 Aligned_cols=40 Identities=28% Similarity=0.443 Sum_probs=34.0
Q ss_pred CCHhHHHHHHHHhhc--CCCCCHHHHHHHHHHhCCCcccccc
Q psy14872 151 FKEKSRSVLRDWYTH--NPYPSPREKRELAEATGLTTTQVSN 190 (414)
Q Consensus 151 f~~~~~~~L~~~f~~--~~yPs~~ek~~La~~tgLt~~QV~~ 190 (414)
+|+.|+.+|...|.. -.+|-...-..||+.+|++...|..
T Consensus 1 LT~~Q~e~L~~A~~~GYfd~PR~~tl~elA~~lgis~st~~~ 42 (53)
T PF04967_consen 1 LTDRQREILKAAYELGYFDVPRRITLEELAEELGISKSTVSE 42 (53)
T ss_pred CCHHHHHHHHHHHHcCCCCCCCcCCHHHHHHHhCCCHHHHHH
Confidence 578899999999884 5778888999999999999887654
No 78
>cd00569 HTH_Hin_like Helix-turn-helix domain of Hin and related proteins, a family of DNA-binding domains unique to bacteria and represented by the Hin protein of Salmonella. The basic HTH domain is a simple fold comprised of three core helices that form a right-handed helical bundle. The principal DNA-protein interface is formed by the third helix, the recognition helix, inserting itself into the major groove of the DNA. A diverse array of HTH domains participate in a variety of functions that depend on their DNA-binding properties. HTH_Hin represents one of the simplest versions of the HTH domains; the characterization of homologous relationships between various sequence-diverse HTH domain families remains difficult. The Hin recombinase induces the site-specific inversion of a chromosomal DNA segment containing a promoter, which controls the alternate expression of two genes by reversibly switching orientation. The Hin recombinase consists of a single polypeptide chain containing a D
Probab=42.65 E-value=34 Score=20.67 Aligned_cols=38 Identities=11% Similarity=0.154 Sum_probs=26.6
Q ss_pred cCCHhHHHHHHHHhhcCCCCCHHHHHHHHHHhCCCcccccccc
Q psy14872 150 CFKEKSRSVLRDWYTHNPYPSPREKRELAEATGLTTTQVSNWF 192 (414)
Q Consensus 150 ~f~~~~~~~L~~~f~~~~yPs~~ek~~La~~tgLt~~QV~~WF 192 (414)
.++.+.+..+...+. +.+ ....+|+.+|++...|.+|.
T Consensus 5 ~~~~~~~~~i~~~~~-~~~----s~~~ia~~~~is~~tv~~~~ 42 (42)
T cd00569 5 KLTPEQIEEARRLLA-AGE----SVAEIARRLGVSRSTLYRYL 42 (42)
T ss_pred cCCHHHHHHHHHHHH-cCC----CHHHHHHHHCCCHHHHHHhC
Confidence 355566666666654 333 45678899999999999884
No 79
>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=41.54 E-value=11 Score=28.83 Aligned_cols=44 Identities=16% Similarity=0.211 Sum_probs=29.4
Q ss_pred ccCCHhHHHHHHHHhhcCCCCCHHHHHHHHHHhCCCcccccccccccc
Q psy14872 149 YCFKEKSRSVLRDWYTHNPYPSPREKRELAEATGLTTTQVSNWFSSAN 196 (414)
Q Consensus 149 ~~f~~~~~~~L~~~f~~~~yPs~~ek~~La~~tgLt~~QV~~WF~NrR 196 (414)
..|+.+....+-..+. -+......+|...|+++.+|.+|-.-.+
T Consensus 5 ~~ys~e~K~~~v~~~~----~~g~sv~~va~~~gi~~~~l~~W~~~~~ 48 (76)
T PF01527_consen 5 RRYSPEFKLQAVREYL----ESGESVSEVAREYGISPSTLYNWRKQYR 48 (76)
T ss_dssp ----HHHHHHHHHHHH----HHHCHHHHHHHHHTS-HHHHHHHHHHHH
T ss_pred CCCCHHHHHHHHHHHH----HCCCceEeeecccccccccccHHHHHHh
Confidence 4677887665544432 2357788999999999999999987765
No 80
>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=38.40 E-value=31 Score=25.43 Aligned_cols=39 Identities=28% Similarity=0.476 Sum_probs=32.0
Q ss_pred cCHHHHHHHHHHHhhC--CCCCHHHHHHHHHHhCCCccccc
Q psy14872 341 FKEKSRSVLRDWYTHN--PYPSPREKRELAEATGLTTTQVS 379 (414)
Q Consensus 341 ft~~q~~~L~~~F~~n--~yPs~~~r~~LA~~~gL~~~qV~ 379 (414)
+|+.|..+|...+... .+|-......||..+|++..-+.
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 4778999999999875 45777888999999999987654
No 81
>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=36.61 E-value=15 Score=27.90 Aligned_cols=35 Identities=17% Similarity=0.346 Sum_probs=24.7
Q ss_pred HHHHHHhhcCCCCCHHHHHHHHHHhCCCcccccccccc
Q psy14872 157 SVLRDWYTHNPYPSPREKRELAEATGLTTTQVSNWFSS 194 (414)
Q Consensus 157 ~~L~~~f~~~~yPs~~ek~~La~~tgLt~~QV~~WF~N 194 (414)
.+.+-|...+.-.+. ..||+++|.++.+|..|=..
T Consensus 11 kA~e~y~~~~g~i~l---kdIA~~Lgvs~~tIr~WK~~ 45 (60)
T PF10668_consen 11 KAFEIYKESNGKIKL---KDIAEKLGVSESTIRKWKSR 45 (60)
T ss_pred HHHHHHHHhCCCccH---HHHHHHHCCCHHHHHHHhhh
Confidence 445555555555554 45899999999999999544
No 82
>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=35.51 E-value=29 Score=24.50 Aligned_cols=46 Identities=24% Similarity=0.335 Sum_probs=33.6
Q ss_pred ccCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCccccccccccchhHhH
Q psy14872 340 CFKEKSRSVLRDWYTHNPYPSPREKRELAEATGLTTTQVSNWFKNRRQRDR 390 (414)
Q Consensus 340 ~ft~~q~~~L~~~F~~n~yPs~~~r~~LA~~~gL~~~qV~vWFqNrR~R~K 390 (414)
.+++.+..++...|... ..-.++|..+|++...|+.+......|.|
T Consensus 4 ~L~~~er~vi~~~y~~~-----~t~~eIa~~lg~s~~~V~~~~~~al~kLR 49 (50)
T PF04545_consen 4 QLPPREREVIRLRYFEG-----LTLEEIAERLGISRSTVRRILKRALKKLR 49 (50)
T ss_dssp TS-HHHHHHHHHHHTST------SHHHHHHHHTSCHHHHHHHHHHHHHHHH
T ss_pred hCCHHHHHHHHHHhcCC-----CCHHHHHHHHCCcHHHHHHHHHHHHHHhc
Confidence 46778889998888433 24678899999999998887766555544
No 83
>PF13443 HTH_26: Cro/C1-type HTH DNA-binding domain; PDB: 3TYR_A 3TYS_A 3B7H_A.
Probab=32.19 E-value=18 Score=26.59 Aligned_cols=23 Identities=22% Similarity=0.484 Sum_probs=18.0
Q ss_pred HHHHHHHHhCCCccccccccccc
Q psy14872 173 EKRELAEATGLTTTQVSNWFSSA 195 (414)
Q Consensus 173 ek~~La~~tgLt~~QV~~WF~Nr 195 (414)
-...||+.+|++..+|+.|+.+.
T Consensus 12 t~~~La~~~gis~~tl~~~~~~~ 34 (63)
T PF13443_consen 12 TQKDLARKTGISRSTLSRILNGK 34 (63)
T ss_dssp -HHHHHHHHT--HHHHHHHHTTT
T ss_pred CHHHHHHHHCcCHHHHHHHHhcc
Confidence 45679999999999999999975
No 84
>PRK10072 putative transcriptional regulator; Provisional
Probab=32.02 E-value=22 Score=29.48 Aligned_cols=38 Identities=18% Similarity=0.152 Sum_probs=27.8
Q ss_pred HhHHHHHHHHhhcCCCCCHHHHHHHHHHhCCCccccccccccccc
Q psy14872 153 EKSRSVLRDWYTHNPYPSPREKRELAEATGLTTTQVSNWFSSANI 197 (414)
Q Consensus 153 ~~~~~~L~~~f~~~~yPs~~ek~~La~~tgLt~~QV~~WF~NrR~ 197 (414)
...+..|+.... .+ ..+||+.+|++...|++|...+|.
T Consensus 35 ~~eik~LR~~~g----lT---Q~elA~~lGvS~~TVs~WE~G~r~ 72 (96)
T PRK10072 35 FTEFEQLRKGTG----LK---IDDFARVLGVSVAMVKEWESRRVK 72 (96)
T ss_pred hHHHHHHHHHcC----CC---HHHHHHHhCCCHHHHHHHHcCCCC
Confidence 334666665522 22 678999999999999999998763
No 85
>PF07526 POX: Associated with HOX; InterPro: IPR006563 This domain in found exclusively in plant proteins, associated with HOX domains which may suggest these proteins are homeodomain transcription factors.
Probab=29.95 E-value=33 Score=30.49 Aligned_cols=24 Identities=17% Similarity=0.140 Sum_probs=21.7
Q ss_pred cchhhhhhhhhhHhhhhhccccCc
Q psy14872 48 NQDRTCQQCSTITHRTTKSLALPT 71 (414)
Q Consensus 48 ~~~~~~~~~~~~~~~~~~~~~~~~ 71 (414)
.-|++|+||.++.+.++++|....
T Consensus 88 eVd~RY~qY~~Qmq~VvssFe~va 111 (140)
T PF07526_consen 88 EVDRRYRQYYDQMQAVVSSFEAVA 111 (140)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHh
Confidence 458999999999999999998876
No 86
>COG3413 Predicted DNA binding protein [General function prediction only]
Probab=29.36 E-value=48 Score=31.09 Aligned_cols=41 Identities=24% Similarity=0.395 Sum_probs=36.5
Q ss_pred cCCHhHHHHHHHHhh--cCCCCCHHHHHHHHHHhCCCcccccc
Q psy14872 150 CFKEKSRSVLRDWYT--HNPYPSPREKRELAEATGLTTTQVSN 190 (414)
Q Consensus 150 ~f~~~~~~~L~~~f~--~~~yPs~~ek~~La~~tgLt~~QV~~ 190 (414)
.+|+.|+++|+..|. ---||-...-..||+.+|+++..+..
T Consensus 155 ~LTdrQ~~vL~~A~~~GYFd~PR~~~l~dLA~~lGISkst~~e 197 (215)
T COG3413 155 DLTDRQLEVLRLAYKMGYFDYPRRVSLKDLAKELGISKSTLSE 197 (215)
T ss_pred cCCHHHHHHHHHHHHcCCCCCCccCCHHHHHHHhCCCHHHHHH
Confidence 699999999999999 46899999999999999999876643
No 87
>PRK09413 IS2 repressor TnpA; Reviewed
Probab=28.41 E-value=77 Score=26.96 Aligned_cols=44 Identities=9% Similarity=0.055 Sum_probs=29.6
Q ss_pred ccCCHhHHHHHHHHhhcCCCCCHHHHHHHHHHhCCCcccccccccccc
Q psy14872 149 YCFKEKSRSVLRDWYTHNPYPSPREKRELAEATGLTTTQVSNWFSSAN 196 (414)
Q Consensus 149 ~~f~~~~~~~L~~~f~~~~yPs~~ek~~La~~tgLt~~QV~~WF~NrR 196 (414)
.+|+.+.....-.....+.. -...+|..+|+++.+|.+|....+
T Consensus 11 r~ys~EfK~~aV~~~~~~g~----sv~evA~e~gIs~~tl~~W~r~y~ 54 (121)
T PRK09413 11 RRRTTQEKIAIVQQSFEPGM----TVSLVARQHGVAASQLFLWRKQYQ 54 (121)
T ss_pred CCCCHHHHHHHHHHHHcCCC----CHHHHHHHHCcCHHHHHHHHHHHh
Confidence 46667765433333333333 356789999999999999976654
No 88
>PF01381 HTH_3: Helix-turn-helix; InterPro: IPR001387 This is large family of DNA binding helix-turn helix proteins that include a bacterial plasmid copy control protein, bacterial methylases, various bacteriophage transcription control proteins and a vegetative specific protein from Dictyostelium discoideum (Slime mould).; GO: 0043565 sequence-specific DNA binding; PDB: 2AXU_A 2AWI_D 2AXV_D 2AXZ_C 2AW6_A 3KXA_C 3BS3_A 2CRO_A 1ZUG_A 3CRO_R ....
Probab=26.81 E-value=28 Score=24.70 Aligned_cols=23 Identities=26% Similarity=0.427 Sum_probs=19.4
Q ss_pred HHHHHHHhCCCcccccccccccc
Q psy14872 174 KRELAEATGLTTTQVSNWFSSAN 196 (414)
Q Consensus 174 k~~La~~tgLt~~QV~~WF~NrR 196 (414)
...||+.+|+++..|..|..+.+
T Consensus 12 ~~~la~~~gis~~~i~~~~~g~~ 34 (55)
T PF01381_consen 12 QKELAEKLGISRSTISRIENGKR 34 (55)
T ss_dssp HHHHHHHHTS-HHHHHHHHTTSS
T ss_pred HHHHHHHhCCCcchhHHHhcCCC
Confidence 37899999999999999999844
No 89
>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=25.11 E-value=52 Score=23.36 Aligned_cols=43 Identities=21% Similarity=0.398 Sum_probs=28.7
Q ss_pred cCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCccccccccccchhH
Q psy14872 341 FKEKSRSVLRDWYTHNPYPSPREKRELAEATGLTTTQVSNWFKNRRQR 388 (414)
Q Consensus 341 ft~~q~~~L~~~F~~n~yPs~~~r~~LA~~~gL~~~qV~vWFqNrR~R 388 (414)
+++.+..++.-.|..+ -...++|..+|++...|++|....|.+
T Consensus 11 L~~~~r~i~~l~~~~g-----~s~~eIa~~l~~s~~~v~~~l~ra~~~ 53 (54)
T PF08281_consen 11 LPERQREIFLLRYFQG-----MSYAEIAEILGISESTVKRRLRRARKK 53 (54)
T ss_dssp S-HHHHHHHHHHHTS--------HHHHHHHCTS-HHHHHHHHHHHHHH
T ss_pred CCHHHHHHHHHHHHHC-----cCHHHHHHHHCcCHHHHHHHHHHHHhh
Confidence 4566667776655544 357789999999999999998765543
No 90
>TIGR03070 couple_hipB transcriptional regulator, y4mF family. Members of this family belong to a clade of helix-turn-helix DNA-binding proteins, among the larger family pfam01381 (HTH_3; Helix-turn-helix). Members are similar in sequence to the HipB protein of E. coli. Genes for members of the seed alignment for this protein family were found to be closely linked to genes encoding proteins related to HipA. The HibBA operon appears to have some features in common with toxin-antitoxin post-segregational killing systems.
Probab=24.30 E-value=34 Score=24.12 Aligned_cols=23 Identities=13% Similarity=0.203 Sum_probs=20.0
Q ss_pred HHHHHHHhCCCcccccccccccc
Q psy14872 174 KRELAEATGLTTTQVSNWFSSAN 196 (414)
Q Consensus 174 k~~La~~tgLt~~QV~~WF~NrR 196 (414)
...||+.+|++...|+.|..+++
T Consensus 18 q~~lA~~~gvs~~~vs~~e~g~~ 40 (58)
T TIGR03070 18 QADLADLAGVGLRFIRDVENGKP 40 (58)
T ss_pred HHHHHHHhCCCHHHHHHHHCCCC
Confidence 46799999999999999997754
No 91
>TIGR03650 violacein_E violacein biosynthesis enzyme VioE. This enzyme catalyzes the third step in violacein biosynthesis from a pair of Trp residues, as in Chromobacterium violaceum, but the first step that distinguishes that pathway from staurosporine (an indolocarbazole antibiotic) biosynthesis.
Probab=23.72 E-value=65 Score=28.85 Aligned_cols=31 Identities=35% Similarity=0.343 Sum_probs=25.6
Q ss_pred ccCCCceeeeecCCcceeeeeecCCCCchhhhh
Q psy14872 12 CNKGPSVYNVVDKGNCHCRMYRVPHDDRCCASE 44 (414)
Q Consensus 12 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 44 (414)
-+||||||-+...||---|| |.-||--|+|-
T Consensus 136 pgK~ps~~Yl~aG~N~LlRM--vTG~~~~~~SV 166 (184)
T TIGR03650 136 PGKGPSTLYLDAGSNTLLRM--VTGDEASRASV 166 (184)
T ss_pred CCCCCeEEEEecCCceEEEE--ecCCchhhchh
Confidence 48999999999999988888 45677777763
No 92
>PRK05988 formate dehydrogenase subunit gamma; Validated
Probab=23.69 E-value=90 Score=28.12 Aligned_cols=36 Identities=19% Similarity=0.171 Sum_probs=31.6
Q ss_pred HHHHHHHHhhcCCCCCHHHHHHHHHHhCCCcccccc
Q psy14872 155 SRSVLRDWYTHNPYPSPREKRELAEATGLTTTQVSN 190 (414)
Q Consensus 155 ~~~~L~~~f~~~~yPs~~ek~~La~~tgLt~~QV~~ 190 (414)
.+.+|...=....|.+++-...+|+.+|+++.+|..
T Consensus 25 li~~L~~vQ~~~G~Ip~e~~~~iA~~l~v~~~~V~~ 60 (156)
T PRK05988 25 LLPILHAIQDEFGYVPEDAVPVIAEALNLSRAEVHG 60 (156)
T ss_pred HHHHHHHHHHHcCCCCHHHHHHHHHHhCCCHHHHHH
Confidence 477787777788999999999999999999998865
No 93
>cd01392 HTH_LacI Helix-turn-helix (HTH) DNA binding domain of the LacI family of transcriptional regulators. HTH-DNA binding domain of the LacI (lactose operon repressor) family of bacterial transcriptional regulators and their putative homologs found in plants. The LacI family has more than 500 members distributed among almost all bacterial species. The monomeric proteins of the LacI family contain common structural features that include a small DNA-binding domain with a helix-turn-helix motif in the N-terminus, a regulatory ligand-binding domain which exhibits the type I periplasmic binding protein fold in the C-terminus for oligomerization and for effector binding, and an approximately 18-amino acid linker connecting these two functional domains. In LacI-like transcriptional regulators, the ligands are monosaccharides including lactose, ribose, fructose, xylose, arabinose, galactose/glucose, and other sugars, with a few exceptions. When the C-terminal domain of the LacI family repre
Probab=23.27 E-value=28 Score=24.46 Aligned_cols=21 Identities=24% Similarity=0.431 Sum_probs=18.8
Q ss_pred HHHHHhCCCcccccccccccc
Q psy14872 176 ELAEATGLTTTQVSNWFSSAN 196 (414)
Q Consensus 176 ~La~~tgLt~~QV~~WF~NrR 196 (414)
+||+.+|++...|+.|+.+..
T Consensus 2 ~lA~~~gvs~~tvs~~l~g~~ 22 (52)
T cd01392 2 DIARAAGVSVATVSRVLNGKP 22 (52)
T ss_pred cHHHHHCcCHHHHHHHHcCCC
Confidence 589999999999999998853
No 94
>PRK12535 RNA polymerase sigma factor; Provisional
Probab=22.79 E-value=89 Score=28.69 Aligned_cols=58 Identities=12% Similarity=-0.003 Sum_probs=39.0
Q ss_pred cCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCccccccccccchhHhHHHHhccCCCCccc
Q psy14872 341 FKEKSRSVLRDWYTHNPYPSPREKRELAEATGLTTTQVSNWFKNRRQRDRAAEQKDGSVHSFR 403 (414)
Q Consensus 341 ft~~q~~~L~~~F~~n~yPs~~~r~~LA~~~gL~~~qV~vWFqNrR~R~Kr~~~~~~~~~~~~ 403 (414)
+++.+..++.-.|..+ ....++|..+|++...|+++....|.+.|+...........+
T Consensus 134 Lp~~~r~v~~l~~~~g-----~s~~EIAe~lgis~~tV~~~l~Rar~~Lr~~l~~~~~~~~~~ 191 (196)
T PRK12535 134 LPPERREALILTQVLG-----YTYEEAAKIADVRVGTIRSRVARARADLIAATATGQASAERG 191 (196)
T ss_pred CCHHHHHHhhhHHHhC-----CCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhccccchhhcc
Confidence 3455566665554333 246789999999999999999888888887655443333333
No 95
>smart00421 HTH_LUXR helix_turn_helix, Lux Regulon. lux regulon (activates the bioluminescence operon
Probab=22.58 E-value=40 Score=23.41 Aligned_cols=44 Identities=23% Similarity=0.295 Sum_probs=31.9
Q ss_pred cCCHhHHHHHHHHhhcCCCCCHHHHHHHHHHhCCCcccccccccccccCC
Q psy14872 150 CFKEKSRSVLRDWYTHNPYPSPREKRELAEATGLTTTQVSNWFSSANITS 199 (414)
Q Consensus 150 ~f~~~~~~~L~~~f~~~~yPs~~ek~~La~~tgLt~~QV~~WF~NrR~r~ 199 (414)
.+++.+..++..++. .+ ...++|+.+|++...|..|....+.+.
T Consensus 3 ~l~~~e~~i~~~~~~--g~----s~~eia~~l~is~~tv~~~~~~~~~kl 46 (58)
T smart00421 3 SLTPREREVLRLLAE--GL----TNKEIAERLGISEKTVKTHLSNIMRKL 46 (58)
T ss_pred CCCHHHHHHHHHHHc--CC----CHHHHHHHHCCCHHHHHHHHHHHHHHH
Confidence 467777887766432 22 457899999999999999987665543
No 96
>PF13518 HTH_28: Helix-turn-helix domain
Probab=22.52 E-value=40 Score=23.51 Aligned_cols=25 Identities=24% Similarity=0.464 Sum_probs=20.4
Q ss_pred HHHHHHHHhCCCccccccccccccc
Q psy14872 173 EKRELAEATGLTTTQVSNWFSSANI 197 (414)
Q Consensus 173 ek~~La~~tgLt~~QV~~WF~NrR~ 197 (414)
-...+|..+|++..+|..|.+..+.
T Consensus 14 s~~~~a~~~gis~~tv~~w~~~y~~ 38 (52)
T PF13518_consen 14 SVREIAREFGISRSTVYRWIKRYRE 38 (52)
T ss_pred CHHHHHHHHCCCHhHHHHHHHHHHh
Confidence 3455999999999999999876553
No 97
>TIGR01958 nuoE_fam NADH-quinone oxidoreductase, E subunit. This model describes the E chain of complexes that resemble NADH-quinone oxidoreductases. The electron acceptor is a quinone, ubiquinone, in mitochondria and most bacteria, including Escherichia coli, where the recommended gene symbol is nuoB. This model does not identify proteins from chloroplast and cyanobacteria.
Probab=21.39 E-value=1.2e+02 Score=26.88 Aligned_cols=37 Identities=16% Similarity=0.131 Sum_probs=31.1
Q ss_pred hHHHHHHHHhhcCCCCCHHHHHHHHHHhCCCcccccc
Q psy14872 154 KSRSVLRDWYTHNPYPSPREKRELAEATGLTTTQVSN 190 (414)
Q Consensus 154 ~~~~~L~~~f~~~~yPs~~ek~~La~~tgLt~~QV~~ 190 (414)
..+.+|+..=....|.+++....+|+.+|+++.+|..
T Consensus 17 ~li~~L~~vQ~~~G~i~~~~~~~iA~~l~~~~~~v~~ 53 (148)
T TIGR01958 17 AIMPALMIAQEQKGWVTPEAIAAVAEMLGIPPVWVYE 53 (148)
T ss_pred HHHHHHHHHHHHhCCCCHHHHHHHHHHhCcCHHHHHH
Confidence 3466777776678999999999999999999988764
No 98
>PF13384 HTH_23: Homeodomain-like domain; PDB: 2X48_C.
Probab=21.20 E-value=37 Score=23.71 Aligned_cols=26 Identities=23% Similarity=0.436 Sum_probs=17.9
Q ss_pred HHHHHHHHHHhCCCcccccccccccc
Q psy14872 171 PREKRELAEATGLTTTQVSNWFSSAN 196 (414)
Q Consensus 171 ~~ek~~La~~tgLt~~QV~~WF~NrR 196 (414)
..-..++|+.+|++...|.+|.+..+
T Consensus 17 G~s~~~ia~~lgvs~~Tv~~w~kr~~ 42 (50)
T PF13384_consen 17 GWSIREIAKRLGVSRSTVYRWIKRYR 42 (50)
T ss_dssp T--HHHHHHHHTS-HHHHHHHHT---
T ss_pred CCCHHHHHHHHCcCHHHHHHHHHHcc
Confidence 34567899999999999999986644
No 99
>COG3413 Predicted DNA binding protein [General function prediction only]
Probab=20.89 E-value=86 Score=29.36 Aligned_cols=40 Identities=25% Similarity=0.434 Sum_probs=34.5
Q ss_pred ccCHHHHHHHHHHHhhC--CCCCHHHHHHHHHHhCCCccccc
Q psy14872 340 CFKEKSRSVLRDWYTHN--PYPSPREKRELAEATGLTTTQVS 379 (414)
Q Consensus 340 ~ft~~q~~~L~~~F~~n--~yPs~~~r~~LA~~~gL~~~qV~ 379 (414)
.+|+.|+.+|+..|... -||-......||+++|+++.-+.
T Consensus 155 ~LTdrQ~~vL~~A~~~GYFd~PR~~~l~dLA~~lGISkst~~ 196 (215)
T COG3413 155 DLTDRQLEVLRLAYKMGYFDYPRRVSLKDLAKELGISKSTLS 196 (215)
T ss_pred cCCHHHHHHHHHHHHcCCCCCCccCCHHHHHHHhCCCHHHHH
Confidence 58999999999999875 66888899999999999987543
No 100
>smart00574 POX domain associated with HOX domains.
Probab=20.89 E-value=62 Score=28.79 Aligned_cols=25 Identities=12% Similarity=0.139 Sum_probs=22.0
Q ss_pred ccchhhhhhhhhhHhhhhhccccCc
Q psy14872 47 SNQDRTCQQCSTITHRTTKSLALPT 71 (414)
Q Consensus 47 ~~~~~~~~~~~~~~~~~~~~~~~~~ 71 (414)
..-|++|++|.++.+.++++|....
T Consensus 87 ~eVd~RY~qY~~qmq~v~ssFe~va 111 (140)
T smart00574 87 EEVDRRYKHYYEQMQTVVSSFDQAA 111 (140)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 3458999999999999999998776
No 101
>PTZ00183 centrin; Provisional
Probab=20.87 E-value=2.3e+02 Score=24.10 Aligned_cols=42 Identities=14% Similarity=0.264 Sum_probs=33.1
Q ss_pred cCCCCCCCcccCCCcccccCCHhHHHHHHHHhh-----cCCCCCHHHHHHHHHHhCC
Q psy14872 132 RRKFPLPRTIWDGEETSYCFKEKSRSVLRDWYT-----HNPYPSPREKRELAEATGL 183 (414)
Q Consensus 132 rk~~p~P~t~~~g~~t~~~f~~~~~~~L~~~f~-----~~~yPs~~ek~~La~~tgL 183 (414)
||+.|.|. .|++.+...|+.+|. .+++.+..+-..+...+|+
T Consensus 2 ~~~~~~~~----------~~~~~~~~~~~~~F~~~D~~~~G~i~~~e~~~~l~~~g~ 48 (158)
T PTZ00183 2 RKRRSERP----------GLTEDQKKEIREAFDLFDTDGSGTIDPKELKVAMRSLGF 48 (158)
T ss_pred CccccccC----------CCCHHHHHHHHHHHHHhCCCCCCcccHHHHHHHHHHhCC
Confidence 56666554 688999999999987 4788999998888877775
No 102
>PHA02955 hypothetical protein; Provisional
Probab=20.69 E-value=1.1e+02 Score=29.13 Aligned_cols=42 Identities=12% Similarity=0.107 Sum_probs=33.2
Q ss_pred HHHHHHHHhhcC-CCCCHHHHHHHHHHhCCCcccccccccccc
Q psy14872 155 SRSVLRDWYTHN-PYPSPREKRELAEATGLTTTQVSNWFSSAN 196 (414)
Q Consensus 155 ~~~~L~~~f~~~-~yPs~~ek~~La~~tgLt~~QV~~WF~NrR 196 (414)
+..+|-+.|.+. .-.+++||..+++++|.....|..||.+.-
T Consensus 62 sf~lli~a~~Et~~~Lp~~qk~~ia~~lgI~~~~~~~d~~t~~ 104 (213)
T PHA02955 62 NFQLLIEALIETIENFPEKEQKEIAADIGINIDDYKAGKKTDL 104 (213)
T ss_pred HHHHHHHHHHHHHHhCCHHHHHHHHHHhCCChhhccCcccchh
Confidence 455666665543 667899999999999999988999999854
No 103
>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=20.65 E-value=23 Score=25.82 Aligned_cols=45 Identities=20% Similarity=0.206 Sum_probs=34.7
Q ss_pred cCCHhHHHHHHHHhhcCCCCCHHHHHHHHHHhCCCcccccccccccccCCC
Q psy14872 150 CFKEKSRSVLRDWYTHNPYPSPREKRELAEATGLTTTQVSNWFSSANITSS 200 (414)
Q Consensus 150 ~f~~~~~~~L~~~f~~~~yPs~~ek~~La~~tgLt~~QV~~WF~NrR~r~~ 200 (414)
.||+.+..+|.-... .-...++|+.+|++++.|..+..+.+.|..
T Consensus 3 ~LT~~E~~vl~~l~~------G~~~~eIA~~l~is~~tV~~~~~~i~~Kl~ 47 (58)
T PF00196_consen 3 SLTERELEVLRLLAQ------GMSNKEIAEELGISEKTVKSHRRRIMKKLG 47 (58)
T ss_dssp SS-HHHHHHHHHHHT------TS-HHHHHHHHTSHHHHHHHHHHHHHHHHT
T ss_pred ccCHHHHHHHHHHHh------cCCcchhHHhcCcchhhHHHHHHHHHHHhC
Confidence 678888888888844 345678999999999999999988776543
No 104
>PF13443 HTH_26: Cro/C1-type HTH DNA-binding domain; PDB: 3TYR_A 3TYS_A 3B7H_A.
Probab=20.01 E-value=1.3e+02 Score=21.89 Aligned_cols=36 Identities=19% Similarity=0.258 Sum_probs=24.9
Q ss_pred HHHHHHHhhcC-CCCCHHHHHHHHHHhCCCccccccc
Q psy14872 156 RSVLRDWYTHN-PYPSPREKRELAEATGLTTTQVSNW 191 (414)
Q Consensus 156 ~~~L~~~f~~~-~yPs~~ek~~La~~tgLt~~QV~~W 191 (414)
...|..++... ..|+.+.-..||..+|+++.++-.|
T Consensus 24 ~~tl~~~~~~~~~~~~~~~l~~ia~~l~~~~~el~~~ 60 (63)
T PF13443_consen 24 RSTLSRILNGKPSNPSLDTLEKIAKALNCSPEELFEY 60 (63)
T ss_dssp HHHHHHHHTTT-----HHHHHHHHHHHT--HHHCTEC
T ss_pred HHHHHHHHhcccccccHHHHHHHHHHcCCCHHHHhhc
Confidence 45677788765 6899999999999999999988655
Done!