Query psy11043
Match_columns 217
No_of_seqs 274 out of 1445
Neff 6.8
Searched_HMMs 46136
Date Fri Aug 16 16:38:29 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy11043.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/11043hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG0775|consensus 100.0 6.6E-73 1.4E-77 481.6 16.2 191 16-210 49-239 (304)
2 KOG3802|consensus 99.8 2.4E-19 5.3E-24 160.9 8.4 138 41-207 200-354 (398)
3 KOG0850|consensus 99.5 2.5E-15 5.5E-20 126.4 3.5 69 135-212 119-187 (245)
4 KOG4577|consensus 99.5 8.3E-15 1.8E-19 126.8 5.6 147 43-208 78-228 (383)
5 KOG0843|consensus 99.5 8.7E-15 1.9E-19 119.1 3.6 64 137-209 101-164 (197)
6 KOG0488|consensus 99.5 7.9E-15 1.7E-19 130.4 3.3 69 136-213 170-238 (309)
7 PF00046 Homeobox: Homeobox do 99.5 7.4E-15 1.6E-19 98.9 1.9 53 152-204 5-57 (57)
8 KOG0848|consensus 99.5 2.9E-14 6.4E-19 122.3 2.9 65 142-215 203-267 (317)
9 KOG0842|consensus 99.4 7.2E-14 1.6E-18 123.2 4.0 64 138-210 153-216 (307)
10 KOG0492|consensus 99.4 1.1E-13 2.4E-18 115.0 3.8 69 132-209 138-206 (246)
11 cd00086 homeodomain Homeodomai 99.4 1.5E-13 3.3E-18 92.4 3.6 53 152-204 5-57 (59)
12 KOG0489|consensus 99.4 6.1E-14 1.3E-18 122.2 1.7 65 137-210 158-222 (261)
13 smart00389 HOX Homeodomain. DN 99.4 1.1E-13 2.3E-18 92.5 1.8 50 154-203 7-56 (56)
14 KOG0487|consensus 99.4 1.5E-13 3.3E-18 121.2 2.7 62 142-212 239-300 (308)
15 KOG2251|consensus 99.3 1.1E-12 2.3E-17 110.1 3.8 66 134-208 33-98 (228)
16 KOG0485|consensus 99.3 6.2E-13 1.4E-17 111.2 1.8 60 141-209 107-166 (268)
17 KOG0494|consensus 99.3 1.5E-12 3.2E-17 111.5 3.6 65 135-208 138-202 (332)
18 KOG0484|consensus 99.3 6.5E-13 1.4E-17 99.3 1.1 72 123-207 6-77 (125)
19 KOG0493|consensus 99.2 3.9E-12 8.4E-17 109.0 3.2 59 139-206 247-305 (342)
20 KOG1168|consensus 99.2 5.1E-11 1.1E-15 103.5 9.2 136 43-206 213-368 (385)
21 TIGR01565 homeo_ZF_HD homeobox 99.2 1.5E-11 3.3E-16 83.5 3.6 51 140-199 3-57 (58)
22 KOG0491|consensus 99.2 7.7E-12 1.7E-16 100.6 1.1 62 140-210 102-163 (194)
23 KOG0483|consensus 99.2 1.8E-11 3.8E-16 102.4 3.1 58 152-209 55-112 (198)
24 PF05920 Homeobox_KN: Homeobox 99.1 3.2E-11 7E-16 76.0 0.9 34 168-201 7-40 (40)
25 COG5576 Homeodomain-containing 99.0 1.6E-10 3.4E-15 93.5 3.9 53 158-210 62-114 (156)
26 KOG0774|consensus 98.9 3.6E-10 7.9E-15 97.0 2.7 67 145-211 186-255 (334)
27 KOG0486|consensus 98.9 3.2E-10 7E-15 99.5 2.2 63 137-208 111-173 (351)
28 KOG0847|consensus 98.9 5.4E-10 1.2E-14 93.9 1.6 59 140-207 169-227 (288)
29 KOG0844|consensus 98.8 1.7E-09 3.6E-14 94.8 3.5 54 154-207 188-241 (408)
30 KOG0490|consensus 98.5 5.2E-08 1.1E-12 82.2 3.2 62 136-206 58-119 (235)
31 KOG0849|consensus 98.4 1.5E-07 3.2E-12 85.6 3.1 65 134-207 172-236 (354)
32 KOG2252|consensus 98.4 1E-06 2.2E-11 82.8 7.9 53 141-202 423-475 (558)
33 KOG0773|consensus 98.3 2.9E-07 6.4E-12 82.9 1.7 56 152-207 244-302 (342)
34 KOG0490|consensus 97.7 3.2E-05 6.9E-10 65.2 4.1 63 136-207 151-213 (235)
35 PF11569 Homez: Homeodomain le 97.3 7.7E-05 1.7E-09 50.1 0.5 40 161-200 12-51 (56)
36 KOG1146|consensus 95.5 0.0069 1.5E-07 62.5 2.0 52 157-208 913-964 (1406)
37 KOG3623|consensus 93.2 0.07 1.5E-06 52.5 2.9 48 159-206 568-615 (1007)
38 PF04218 CENP-B_N: CENP-B N-te 77.4 1.5 3.2E-05 28.9 1.4 33 161-198 14-46 (53)
39 KOG0773|consensus 75.5 1.6 3.6E-05 39.2 1.7 46 161-206 108-156 (342)
40 PF14559 TPR_19: Tetratricopep 73.5 7.8 0.00017 25.4 4.3 42 69-110 24-65 (68)
41 PF00424 REV: REV protein (ant 67.7 5.7 0.00012 29.4 2.7 37 159-209 14-50 (91)
42 PF00157 Pou: Pou domain - N-t 53.6 7.1 0.00015 27.8 1.1 42 45-102 5-46 (75)
43 PF08281 Sigma70_r4_2: Sigma-7 51.1 11 0.00025 24.0 1.7 43 153-200 10-52 (54)
44 PF04545 Sigma70_r4: Sigma-70, 49.1 15 0.00032 23.2 2.0 45 153-202 4-48 (50)
45 PF10668 Phage_terminase: Phag 46.9 7.7 0.00017 26.4 0.4 19 178-196 26-44 (60)
46 cd06171 Sigma70_r4 Sigma70, re 40.7 18 0.0004 21.8 1.4 41 154-199 11-51 (55)
47 PF13371 TPR_9: Tetratricopept 37.1 86 0.0019 20.5 4.5 49 40-94 5-53 (73)
48 PRK09646 RNA polymerase sigma 34.3 44 0.00095 27.0 3.1 50 152-206 141-190 (194)
49 PF13432 TPR_16: Tetratricopep 34.1 1.1E+02 0.0023 19.6 4.5 49 39-93 6-54 (65)
50 cd00569 HTH_Hin_like Helix-tur 34.1 54 0.0012 17.4 2.7 32 159-195 11-42 (42)
51 cd04755 Commd7 COMM_Domain con 33.2 2.2E+02 0.0049 23.5 7.1 97 28-128 7-113 (180)
52 PF04967 HTH_10: HTH DNA bindi 31.6 48 0.001 21.9 2.4 39 154-192 1-41 (53)
53 PRK10072 putative transcriptio 31.5 19 0.00042 26.7 0.5 24 177-200 49-72 (96)
54 PF13384 HTH_23: Homeodomain-l 30.9 16 0.00035 22.8 -0.0 24 176-199 19-42 (50)
55 PRK06759 RNA polymerase factor 30.7 43 0.00094 25.6 2.4 47 152-203 105-151 (154)
56 PF13518 HTH_28: Helix-turn-he 29.6 20 0.00044 22.3 0.3 24 177-200 15-38 (52)
57 PRK09644 RNA polymerase sigma 28.2 64 0.0014 25.2 3.0 53 152-209 107-159 (165)
58 PF11791 Aconitase_B_N: Aconit 27.9 63 0.0014 26.2 2.9 39 21-59 12-53 (154)
59 PRK12526 RNA polymerase sigma 27.6 64 0.0014 26.4 3.0 50 152-206 152-201 (206)
60 cd01392 HTH_LacI Helix-turn-he 26.4 19 0.00041 22.6 -0.3 21 179-199 2-22 (52)
61 KOG3623|consensus 26.2 2E+02 0.0043 29.3 6.4 44 161-204 640-683 (1007)
62 PF01381 HTH_3: Helix-turn-hel 26.1 24 0.00053 22.3 0.2 23 177-199 12-34 (55)
63 PF06056 Terminase_5: Putative 25.9 29 0.00062 23.3 0.5 20 177-196 16-35 (58)
64 PRK09642 RNA polymerase sigma 25.5 80 0.0017 24.4 3.1 50 152-206 105-154 (160)
65 PRK00118 putative DNA-binding 25.1 94 0.002 23.4 3.2 49 153-206 17-65 (104)
66 cd04761 HTH_MerR-SF Helix-Turn 24.6 27 0.00059 21.4 0.2 21 178-198 4-24 (49)
67 PF13411 MerR_1: MerR HTH fami 24.5 30 0.00064 23.0 0.4 19 178-196 4-22 (69)
68 TIGR03070 couple_hipB transcri 24.4 29 0.00063 21.8 0.3 23 177-199 18-40 (58)
69 PF13443 HTH_26: Cro/C1-type H 23.4 1E+02 0.0023 19.8 2.9 20 171-190 37-56 (63)
70 PRK12512 RNA polymerase sigma 22.7 87 0.0019 24.8 2.9 49 152-205 130-178 (184)
71 PRK12514 RNA polymerase sigma 22.4 1E+02 0.0022 24.3 3.2 48 152-204 128-175 (179)
72 PRK12515 RNA polymerase sigma 22.4 1E+02 0.0022 24.7 3.2 51 152-207 130-180 (189)
73 PRK09652 RNA polymerase sigma 22.0 86 0.0019 24.3 2.7 47 153-204 128-174 (182)
74 TIGR02939 RpoE_Sigma70 RNA pol 21.8 68 0.0015 25.4 2.1 29 176-204 156-184 (190)
75 PRK05602 RNA polymerase sigma 21.7 98 0.0021 24.6 3.0 51 153-208 128-178 (186)
76 PRK03975 tfx putative transcri 21.5 1.2E+02 0.0026 24.1 3.4 49 153-207 6-54 (141)
77 KOG4330|consensus 20.9 1.3E+02 0.0028 25.1 3.5 20 26-45 144-163 (206)
78 TIGR02948 SigW_bacill RNA poly 20.8 84 0.0018 24.8 2.4 48 152-204 135-182 (187)
79 PF08452 DNAP_B_exo_N: DNA pol 20.6 33 0.00072 18.5 -0.0 8 192-199 6-13 (22)
80 TIGR02999 Sig-70_X6 RNA polyme 20.5 1E+02 0.0022 24.3 2.9 46 154-204 135-180 (183)
81 PRK11924 RNA polymerase sigma 20.5 1.2E+02 0.0026 23.5 3.2 47 154-205 126-172 (179)
82 KOG3755|consensus 20.5 57 0.0012 32.2 1.5 54 163-216 708-768 (769)
83 TIGR02937 sigma70-ECF RNA poly 20.4 96 0.0021 22.7 2.6 46 153-203 110-155 (158)
84 TIGR02989 Sig-70_gvs1 RNA poly 20.3 90 0.0019 23.9 2.4 45 152-201 110-154 (159)
No 1
>KOG0775|consensus
Probab=100.00 E-value=6.6e-73 Score=481.57 Aligned_cols=191 Identities=73% Similarity=1.219 Sum_probs=184.2
Q ss_pred CCCCCCCCCCCCCChhhhhhHhhHHhhcCCHHHHHHHHHhCCCCCCCcccCCCcHHHHHHHHHHhHhhhcHHHHHHhhcc
Q psy11043 16 IPCPMFALPTLNFTVSQVATVCETLEESGDIERLARFLWSLPVAHPNIGELNKNEAVLRARAIVSFHSGNYREMYSILEH 95 (217)
Q Consensus 16 ~~~~~~~~~~~~~~~~q~~~vc~~l~~~g~~~~l~~fl~slp~~~~~~~~~~~~e~vlrAr~~v~~h~~~~~~~~~lLe~ 95 (217)
.-.+++.+|++.||++||+||||+|++.||+|||.+|||+||+ ++.+..||+||||||+|+||.|+|+|||+|||+
T Consensus 49 ~~~s~~~~pt~~fS~eQvacvCe~L~q~Gd~erL~rFlwsLp~----~~~~~~nEsvLkArA~vafH~gnf~eLY~iLE~ 124 (304)
T KOG0775|consen 49 ASASMSALPTFGFSEEQVACVCESLQQGGDIERLGRFLWSLPV----CEELLKNESVLKARAVVAFHSGNFRELYHILEN 124 (304)
T ss_pred cccccccCCCcCCCHHHHHHHHHHHHhccCHHHHHHHHHcCch----HHHHhhhHHHHHHHHHHHHhcccHHHHHHHHHh
Confidence 3345889999999999999999999999999999999999998 588999999999999999999999999999999
Q ss_pred CCCCCcchhHHHHHHHHhhhHHHHHhcCCCCCCccccccccCCCCCCccCCCcccccccchHHHHHHHHHHhcCCCCCHH
Q psy11043 96 YKFTKDSHGKLQAMWLEAHYQEAEKLRGRPLGPVDKYRVRKKFPLPRTIWDGEQKTHCFKERTRSLLREWYLQDPYPNPT 175 (217)
Q Consensus 96 ~~f~~~~~~~lq~lw~~a~y~~~e~~~g~~l~~~~k~r~rkk~p~prt~~~~~~~~~~f~~~~r~~L~~~f~~~~yPs~~ 175 (217)
+.|++.+|.+||+||++|||.|+|+.|||+||+|+|||+|||+|.|||||||++++|||++++|.+|++||..|+||++.
T Consensus 125 h~Fs~~~h~~LQ~lWl~AhY~EAek~RGR~LgaV~KYRvRrKfPlPrTIWDGEet~yCFKekSR~~LrewY~~~~YPsp~ 204 (304)
T KOG0775|consen 125 HKFSPHNHPKLQALWLKAHYKEAEKLRGRPLGAVDKYRVRRKFPLPRTIWDGEETVYCFKEKSRSLLREWYLQNPYPSPR 204 (304)
T ss_pred ccCChhhhHHHHHHHHHHHHHHHHHhcCCcCCccccceeeccCCCCCccccCceeeeehhHhhHHHHHHHHhcCCCCChH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHhCCCccccccccccchhHHHHHHhhhh
Q psy11043 176 KKRELAQATGLTPTQVGNWFKNRRQRDRAAAAKNR 210 (217)
Q Consensus 176 ~k~~LA~~tgLt~~qV~~WFqNrR~R~kr~~~~~~ 210 (217)
+|.+||++|||+.+||.|||+|||+|||....+..
T Consensus 205 eKReLA~aTgLt~tQVsNWFKNRRQRDRa~~ak~~ 239 (304)
T KOG0775|consen 205 EKRELAEATGLTITQVSNWFKNRRQRDRAAAAKNS 239 (304)
T ss_pred HHHHHHHHhCCchhhhhhhhhhhhhhhhhcccccc
Confidence 99999999999999999999999999997666544
No 2
>KOG3802|consensus
Probab=99.79 E-value=2.4e-19 Score=160.91 Aligned_cols=138 Identities=24% Similarity=0.383 Sum_probs=105.4
Q ss_pred hhcCCHHHHHHHHHhCCCCCCCcccCCCcHHHHHHHHHHhHhhhcHHHHHHhhccCCCCCcc----------------hh
Q psy11043 41 EESGDIERLARFLWSLPVAHPNIGELNKNEAVLRARAIVSFHSGNYREMYSILEHYKFTKDS----------------HG 104 (217)
Q Consensus 41 ~~~g~~~~l~~fl~slp~~~~~~~~~~~~e~vlrAr~~v~~h~~~~~~~~~lLe~~~f~~~~----------------~~ 104 (217)
.++.|+|.|+.|...+.+. |+++.|.+++...++.-|++..|+... -.
T Consensus 200 ed~~~leELEqFAK~FKqR----------------RIkLGfTQaDVGlALG~lyGn~FSQTTIcRFEALqLSFKNMCKLK 263 (398)
T KOG3802|consen 200 EDTPDLEELEQFAKTFKQR----------------RIKLGFTQADVGLALGALYGNVFSQTTICRFEALQLSFKNMCKLK 263 (398)
T ss_pred ccccCHHHHHHHHHHHHhh----------------eeccccchhHHHHHHHhhhCcccchhhhhHhHhhccCHHHHhhhH
Confidence 5688999999999999986 999999999999999999999999987 12
Q ss_pred HHHHHHHHhhhHHHHHh-cCCCCCCccccccccCCCCCCccCCCcccccccchHHHHHHHHHHhcCCCCCHHHHHHHHHH
Q psy11043 105 KLQAMWLEAHYQEAEKL-RGRPLGPVDKYRVRKKFPLPRTIWDGEQKTHCFKERTRSLLREWYLQDPYPNPTKKRELAQA 183 (217)
Q Consensus 105 ~lq~lw~~a~y~~~e~~-~g~~l~~~~k~r~rkk~p~prt~~~~~~~~~~f~~~~r~~L~~~f~~~~yPs~~~k~~LA~~ 183 (217)
.|-+-|++ |+|.. ........++.-...|+++.||.++. .++..|+.+|..|+.|+..|+..||++
T Consensus 264 PLL~KWLe----EAes~~~~~~~~~~e~i~a~~RkRKKRTSie~---------~vr~aLE~~F~~npKPt~qEIt~iA~~ 330 (398)
T KOG3802|consen 264 PLLEKWLE----EAESRESTGSPNSIEKIGAQSRKRKKRTSIEV---------NVRGALEKHFLKNPKPTSQEITHIAES 330 (398)
T ss_pred HHHHHHHH----HHhcccccCCCCCHHHhhccccccccccceeH---------HHHHHHHHHHHhCCCCCHHHHHHHHHH
Confidence 23334654 44541 22222222332111122234555554 445599999999999999999999999
Q ss_pred hCCCccccccccccchhHHHHHHh
Q psy11043 184 TGLTPTQVGNWFKNRRQRDRAAAA 207 (217)
Q Consensus 184 tgLt~~qV~~WFqNrR~R~kr~~~ 207 (217)
++|.+++|+|||||||+|+||...
T Consensus 331 L~leKEVVRVWFCNRRQkeKR~~~ 354 (398)
T KOG3802|consen 331 LQLEKEVVRVWFCNRRQKEKRITP 354 (398)
T ss_pred hccccceEEEEeeccccccccCCC
Confidence 999999999999999999998766
No 3
>KOG0850|consensus
Probab=99.54 E-value=2.5e-15 Score=126.36 Aligned_cols=69 Identities=35% Similarity=0.469 Sum_probs=63.1
Q ss_pred ccCCCCCCccCCCcccccccchHHHHHHHHHHhcCCCCCHHHHHHHHHHhCCCccccccccccchhHHHHHHhhhhhh
Q psy11043 135 RKKFPLPRTIWDGEQKTHCFKERTRSLLREWYLQDPYPNPTKKRELAQATGLTPTQVGNWFKNRRQRDRAAAAKNRLE 212 (217)
Q Consensus 135 rkk~p~prt~~~~~~~~~~f~~~~r~~L~~~f~~~~yPs~~~k~~LA~~tgLt~~qV~~WFqNrR~R~kr~~~~~~~~ 212 (217)
.||.+.||||++.-|+. .|...|++++|.--.||.+||..+|||.+||+|||||||.|.||..+.+...
T Consensus 119 ~KK~RKPRTIYSS~QLq---------aL~rRFQkTQYLALPERAeLAAsLGLTQTQVKIWFQNrRSK~KKl~k~g~~~ 187 (245)
T KOG0850|consen 119 GKKVRKPRTIYSSLQLQ---------ALNRRFQQTQYLALPERAELAASLGLTQTQVKIWFQNRRSKFKKLKKQGSGP 187 (245)
T ss_pred cccccCCcccccHHHHH---------HHHHHHhhcchhcCcHHHHHHHHhCCchhHhhhhhhhhHHHHHHHHhcCCCc
Confidence 36677799999999988 9999999999999999999999999999999999999999999998855443
No 4
>KOG4577|consensus
Probab=99.53 E-value=8.3e-15 Score=126.81 Aligned_cols=147 Identities=20% Similarity=0.271 Sum_probs=109.2
Q ss_pred cCCHHHHHHHHHhCCCC-CCCcccCCCcHHHHHHHHHHhHhhhcHHHHH--Hhhc-cCCCCCcchhHHHHHHHHhhhHHH
Q psy11043 43 SGDIERLARFLWSLPVA-HPNIGELNKNEAVLRARAIVSFHSGNYREMY--SILE-HYKFTKDSHGKLQAMWLEAHYQEA 118 (217)
Q Consensus 43 ~g~~~~l~~fl~slp~~-~~~~~~~~~~e~vlrAr~~v~~h~~~~~~~~--~lLe-~~~f~~~~~~~lq~lw~~a~y~~~ 118 (217)
.|.+=.-+.|+..+-.. ..+...|.....|.||...|| |-.||.++. +.|+ +..|.--.. ..|.+++.|.++
T Consensus 78 ~~s~yCkedFfKrfGTKCsaC~~GIpPtqVVRkAqd~VY-Hl~CF~C~iC~R~L~TGdEFYLmeD---~rLvCK~DYE~A 153 (383)
T KOG4577|consen 78 EGSVYCKEDFFKRFGTKCSACQEGIPPTQVVRKAQDFVY-HLHCFACFICKRQLATGDEFYLMED---ARLVCKDDYETA 153 (383)
T ss_pred CCceeehHHHHHHhCCcchhhcCCCChHHHHHHhhccee-ehhhhhhHhhhcccccCCeeEEecc---ceeehhhhHHHH
Confidence 34444445677655432 333456777888999999996 999999886 4455 666655333 356778888776
Q ss_pred HHhcCCCCCCccccccccCCCCCCccCCCcccccccchHHHHHHHHHHhcCCCCCHHHHHHHHHHhCCCccccccccccc
Q psy11043 119 EKLRGRPLGPVDKYRVRKKFPLPRTIWDGEQKTHCFKERTRSLLREWYLQDPYPNPTKKRELAQATGLTPTQVGNWFKNR 198 (217)
Q Consensus 119 e~~~g~~l~~~~k~r~rkk~p~prt~~~~~~~~~~f~~~~r~~L~~~f~~~~yPs~~~k~~LA~~tgLt~~qV~~WFqNr 198 (217)
...-.-.|.. ....++|||.++.++.. .|+..|...+.|....|++|+..|||..++|+||||||
T Consensus 154 k~k~~~~l~g------d~~nKRPRTTItAKqLE---------TLK~AYn~SpKPARHVREQLsseTGLDMRVVQVWFQNR 218 (383)
T KOG4577|consen 154 KQKHCNELEG------DASNKRPRTTITAKQLE---------TLKQAYNTSPKPARHVREQLSSETGLDMRVVQVWFQNR 218 (383)
T ss_pred Hhcccccccc------ccccCCCcceeeHHHHH---------HHHHHhcCCCchhHHHHHHhhhccCcceeehhhhhhhh
Confidence 5432222211 12244589999999988 99999999999999999999999999999999999999
Q ss_pred hhHHHHHHhh
Q psy11043 199 RQRDRAAAAK 208 (217)
Q Consensus 199 R~R~kr~~~~ 208 (217)
|+|+|+.++-
T Consensus 219 RAKEKRLKKD 228 (383)
T KOG4577|consen 219 RAKEKRLKKD 228 (383)
T ss_pred hHHHHhhhhh
Confidence 9999998764
No 5
>KOG0843|consensus
Probab=99.51 E-value=8.7e-15 Score=119.08 Aligned_cols=64 Identities=28% Similarity=0.425 Sum_probs=59.8
Q ss_pred CCCCCCccCCCcccccccchHHHHHHHHHHhcCCCCCHHHHHHHHHHhCCCccccccccccchhHHHHHHhhh
Q psy11043 137 KFPLPRTIWDGEQKTHCFKERTRSLLREWYLQDPYPNPTKKRELAQATGLTPTQVGNWFKNRRQRDRAAAAKN 209 (217)
Q Consensus 137 k~p~prt~~~~~~~~~~f~~~~r~~L~~~f~~~~yPs~~~k~~LA~~tgLt~~qV~~WFqNrR~R~kr~~~~~ 209 (217)
|.++.||+|+.+|+. .|+..|+.+.|....+|+.||..++|+++||+|||||||.|.||...+.
T Consensus 101 ~~kr~RT~ft~~Ql~---------~LE~~F~~~~Yvvg~eR~~LA~~L~LsetQVkvWFQNRRtk~kr~~~e~ 164 (197)
T KOG0843|consen 101 RPKRIRTAFTPEQLL---------KLEHAFEGNQYVVGAERKQLAQSLSLSETQVKVWFQNRRTKHKRMQQED 164 (197)
T ss_pred CCCccccccCHHHHH---------HHHHHHhcCCeeechHHHHHHHHcCCChhHhhhhhhhhhHHHHHHHHHh
Confidence 456689999999988 9999999999999999999999999999999999999999999988874
No 6
>KOG0488|consensus
Probab=99.50 E-value=7.9e-15 Score=130.43 Aligned_cols=69 Identities=30% Similarity=0.409 Sum_probs=62.8
Q ss_pred cCCCCCCccCCCcccccccchHHHHHHHHHHhcCCCCCHHHHHHHHHHhCCCccccccccccchhHHHHHHhhhhhhh
Q psy11043 136 KKFPLPRTIWDGEQKTHCFKERTRSLLREWYLQDPYPNPTKKRELAQATGLTPTQVGNWFKNRRQRDRAAAAKNRLEV 213 (217)
Q Consensus 136 kk~p~prt~~~~~~~~~~f~~~~r~~L~~~f~~~~yPs~~~k~~LA~~tgLt~~qV~~WFqNrR~R~kr~~~~~~~~~ 213 (217)
||.+.+||+|+..|.. .||..|+...|.+..+|..||..+|||..||++||||||+|||+.........
T Consensus 170 kK~RksRTaFT~~Ql~---------~LEkrF~~QKYLS~~DR~~LA~~LgLTdaQVKtWfQNRRtKWKrq~a~g~~~~ 238 (309)
T KOG0488|consen 170 KKRRKSRTAFSDHQLF---------ELEKRFEKQKYLSVADRIELAASLGLTDAQVKTWFQNRRTKWKRQTAEGGELL 238 (309)
T ss_pred cccccchhhhhHHHHH---------HHHHHHHHhhcccHHHHHHHHHHcCCchhhHHHHHhhhhHHHHHHHHhhhccc
Confidence 6667799999988877 99999999999999999999999999999999999999999999988755443
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=99.49 E-value=7.4e-15 Score=98.86 Aligned_cols=53 Identities=38% Similarity=0.814 Sum_probs=48.0
Q ss_pred cccchHHHHHHHHHHhcCCCCCHHHHHHHHHHhCCCccccccccccchhHHHH
Q psy11043 152 HCFKERTRSLLREWYLQDPYPNPTKKRELAQATGLTPTQVGNWFKNRRQRDRA 204 (217)
Q Consensus 152 ~~f~~~~r~~L~~~f~~~~yPs~~~k~~LA~~tgLt~~qV~~WFqNrR~R~kr 204 (217)
..|+..+...|+.+|..++||+..+++.||..+||+..||.+||+|+|+++|+
T Consensus 5 ~~~t~~q~~~L~~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrR~k~kk 57 (57)
T PF00046_consen 5 TRFTKEQLKVLEEYFQENPYPSKEEREELAKELGLTERQVKNWFQNRRRKEKK 57 (57)
T ss_dssp SSSSHHHHHHHHHHHHHSSSCHHHHHHHHHHHHTSSHHHHHHHHHHHHHHHHH
T ss_pred CCCCHHHHHHHHHHHHHhccccccccccccccccccccccccCHHHhHHHhCc
Confidence 34555556699999999999999999999999999999999999999999986
No 8
>KOG0848|consensus
Probab=99.45 E-value=2.9e-14 Score=122.26 Aligned_cols=65 Identities=32% Similarity=0.554 Sum_probs=57.3
Q ss_pred CccCCCcccccccchHHHHHHHHHHhcCCCCCHHHHHHHHHHhCCCccccccccccchhHHHHHHhhhhhhhcc
Q psy11043 142 RTIWDGEQKTHCFKERTRSLLREWYLQDPYPNPTKKRELAQATGLTPTQVGNWFKNRRQRDRAAAAKNRLEVKT 215 (217)
Q Consensus 142 rt~~~~~~~~~~f~~~~r~~L~~~f~~~~yPs~~~k~~LA~~tgLt~~qV~~WFqNrR~R~kr~~~~~~~~~~~ 215 (217)
|.+++.-|.. .||+-|..++|.++..|.+||..+||+++||++||||||+|+||..++..+++.+
T Consensus 203 RvVYTDhQRL---------ELEKEfh~SryITirRKSELA~~LgLsERQVKIWFQNRRAKERK~nKKk~~~q~q 267 (317)
T KOG0848|consen 203 RVVYTDHQRL---------ELEKEFHTSRYITIRRKSELAATLGLSERQVKIWFQNRRAKERKDNKKKRLQQQQ 267 (317)
T ss_pred eEEecchhhh---------hhhhhhccccceeeehhHHHHHhhCccHhhhhHhhhhhhHHHHHHHHHHHHHHhh
Confidence 5566666655 9999999999999999999999999999999999999999999999988654443
No 9
>KOG0842|consensus
Probab=99.43 E-value=7.2e-14 Score=123.21 Aligned_cols=64 Identities=28% Similarity=0.434 Sum_probs=57.5
Q ss_pred CCCCCccCCCcccccccchHHHHHHHHHHhcCCCCCHHHHHHHHHHhCCCccccccccccchhHHHHHHhhhh
Q psy11043 138 FPLPRTIWDGEQKTHCFKERTRSLLREWYLQDPYPNPTKKRELAQATGLTPTQVGNWFKNRRQRDRAAAAKNR 210 (217)
Q Consensus 138 ~p~prt~~~~~~~~~~f~~~~r~~L~~~f~~~~yPs~~~k~~LA~~tgLt~~qV~~WFqNrR~R~kr~~~~~~ 210 (217)
++++|..|+..|+. .||..|.+..|.+..||+.||..+.||++||+|||||||-|.||..+...
T Consensus 153 kRKrRVLFSqAQV~---------ELERRFrqQRYLSAPERE~LA~~LrLT~TQVKIWFQNrRYK~KR~~~dk~ 216 (307)
T KOG0842|consen 153 KRKRRVLFSQAQVY---------ELERRFRQQRYLSAPEREHLASSLRLTPTQVKIWFQNRRYKTKRQQKDKA 216 (307)
T ss_pred ccccccccchhHHH---------HHHHHHHhhhccccHhHHHHHHhcCCCchheeeeeecchhhhhhhhhhhh
Confidence 34478888888877 99999999999999999999999999999999999999999999876543
No 10
>KOG0492|consensus
Probab=99.41 E-value=1.1e-13 Score=114.96 Aligned_cols=69 Identities=28% Similarity=0.409 Sum_probs=63.2
Q ss_pred cccccCCCCCCccCCCcccccccchHHHHHHHHHHhcCCCCCHHHHHHHHHHhCCCccccccccccchhHHHHHHhhh
Q psy11043 132 YRVRKKFPLPRTIWDGEQKTHCFKERTRSLLREWYLQDPYPNPTKKRELAQATGLTPTQVGNWFKNRRQRDRAAAAKN 209 (217)
Q Consensus 132 ~r~rkk~p~prt~~~~~~~~~~f~~~~r~~L~~~f~~~~yPs~~~k~~LA~~tgLt~~qV~~WFqNrR~R~kr~~~~~ 209 (217)
.|.+|-++.|||.|+..|.. .|+.-|.+.+|.++.++.+++..+.||.+||++||||||+|.||.+.-.
T Consensus 138 LrKhk~nRkPRtPFTtqQLl---------aLErkfrekqYLSiaEraefSsSL~LTeTqVKIWFQNRRAKaKRlQeae 206 (246)
T KOG0492|consen 138 LRKHKPNRKPRTPFTTQQLL---------ALERKFREKQYLSIAERAEFSSSLELTETQVKIWFQNRRAKAKRLQEAE 206 (246)
T ss_pred hcccCCCCCCCCCCCHHHHH---------HHHHHHhHhhhhhHHHHHhhhhhhhhhhhheehhhhhhhHHHHHHHHHH
Confidence 36677778899999999988 9999999999999999999999999999999999999999999976543
No 11
>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=99.41 E-value=1.5e-13 Score=92.38 Aligned_cols=53 Identities=34% Similarity=0.601 Sum_probs=49.0
Q ss_pred cccchHHHHHHHHHHhcCCCCCHHHHHHHHHHhCCCccccccccccchhHHHH
Q psy11043 152 HCFKERTRSLLREWYLQDPYPNPTKKRELAQATGLTPTQVGNWFKNRRQRDRA 204 (217)
Q Consensus 152 ~~f~~~~r~~L~~~f~~~~yPs~~~k~~LA~~tgLt~~qV~~WFqNrR~R~kr 204 (217)
..|+..+..+|+.+|..++||+..++..||..+||+..||.+||+|+|.+.++
T Consensus 5 ~~~~~~~~~~Le~~f~~~~~P~~~~~~~la~~~~l~~~qV~~WF~nrR~~~~~ 57 (59)
T cd00086 5 TRFTPEQLEELEKEFEKNPYPSREEREELAKELGLTERQVKIWFQNRRAKLKR 57 (59)
T ss_pred CcCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHHCcCHHHHHHHHHHHHHHHhc
Confidence 45667777799999999999999999999999999999999999999999876
No 12
>KOG0489|consensus
Probab=99.40 E-value=6.1e-14 Score=122.22 Aligned_cols=65 Identities=26% Similarity=0.340 Sum_probs=59.6
Q ss_pred CCCCCCccCCCcccccccchHHHHHHHHHHhcCCCCCHHHHHHHHHHhCCCccccccccccchhHHHHHHhhhh
Q psy11043 137 KFPLPRTIWDGEQKTHCFKERTRSLLREWYLQDPYPNPTKKRELAQATGLTPTQVGNWFKNRRQRDRAAAAKNR 210 (217)
Q Consensus 137 k~p~prt~~~~~~~~~~f~~~~r~~L~~~f~~~~yPs~~~k~~LA~~tgLt~~qV~~WFqNrR~R~kr~~~~~~ 210 (217)
+.++.||.|+..|+. .||.-|..|.|.+...|.+||..+.|+++||+|||||||+||||..+...
T Consensus 158 ~~kR~RtayT~~Qll---------ELEkEFhfN~YLtR~RRiEiA~~L~LtErQIKIWFQNRRMK~Kk~~k~~~ 222 (261)
T KOG0489|consen 158 KSKRRRTAFTRYQLL---------ELEKEFHFNKYLTRSRRIEIAHALNLTERQIKIWFQNRRMKWKKENKAKS 222 (261)
T ss_pred CCCCCCcccchhhhh---------hhhhhhccccccchHHHHHHHhhcchhHHHHHHHHHHHHHHHHHhhcccc
Confidence 355689999999988 99999999999999999999999999999999999999999998877544
No 13
>smart00389 HOX Homeodomain. DNA-binding factors that are involved in the transcriptional regulation of key developmental processes
Probab=99.39 E-value=1.1e-13 Score=92.46 Aligned_cols=50 Identities=34% Similarity=0.641 Sum_probs=46.0
Q ss_pred cchHHHHHHHHHHhcCCCCCHHHHHHHHHHhCCCccccccccccchhHHH
Q psy11043 154 FKERTRSLLREWYLQDPYPNPTKKRELAQATGLTPTQVGNWFKNRRQRDR 203 (217)
Q Consensus 154 f~~~~r~~L~~~f~~~~yPs~~~k~~LA~~tgLt~~qV~~WFqNrR~R~k 203 (217)
|+..++.+|+.+|..++||+..++..||..+||+..||.+||+|+|.+.+
T Consensus 7 ~~~~~~~~L~~~f~~~~~P~~~~~~~la~~~~l~~~qV~~WF~nrR~~~~ 56 (56)
T smart00389 7 FTPEQLEELEKEFQKNPYPSREEREELAAKLGLSERQVKVWFQNRRAKWK 56 (56)
T ss_pred CCHHHHHHHHHHHHhCCCCCHHHHHHHHHHHCcCHHHHHHhHHHHhhccC
Confidence 56666779999999999999999999999999999999999999998853
No 14
>KOG0487|consensus
Probab=99.38 E-value=1.5e-13 Score=121.24 Aligned_cols=62 Identities=32% Similarity=0.509 Sum_probs=53.9
Q ss_pred CccCCCcccccccchHHHHHHHHHHhcCCCCCHHHHHHHHHHhCCCccccccccccchhHHHHHHhhhhhh
Q psy11043 142 RTIWDGEQKTHCFKERTRSLLREWYLQDPYPNPTKKRELAQATGLTPTQVGNWFKNRRQRDRAAAAKNRLE 212 (217)
Q Consensus 142 rt~~~~~~~~~~f~~~~r~~L~~~f~~~~yPs~~~k~~LA~~tgLt~~qV~~WFqNrR~R~kr~~~~~~~~ 212 (217)
|..++..|+. .||.-|.-|.|.+.+.|.+|++.++||.+||+|||||||.|+||..++.+.+
T Consensus 239 RcPYTK~Qtl---------ELEkEFlfN~YitkeKR~ElSr~lNLTeRQVKIWFQNRRMK~KK~~re~r~~ 300 (308)
T KOG0487|consen 239 RCPYTKHQTL---------ELEKEFLFNMYITKEKRLELSRTLNLTERQVKIWFQNRRMKEKKVNRENRLK 300 (308)
T ss_pred cCCchHHHHH---------HHHHHHHHHHHHhHHHHHHHHHhcccchhheeeeehhhhhHHhhhhhhhhcc
Confidence 4445555555 9999999999999999999999999999999999999999999998655543
No 15
>KOG2251|consensus
Probab=99.31 E-value=1.1e-12 Score=110.05 Aligned_cols=66 Identities=29% Similarity=0.446 Sum_probs=59.6
Q ss_pred cccCCCCCCccCCCcccccccchHHHHHHHHHHhcCCCCCHHHHHHHHHHhCCCccccccccccchhHHHHHHhh
Q psy11043 134 VRKKFPLPRTIWDGEQKTHCFKERTRSLLREWYLQDPYPNPTKKRELAQATGLTPTQVGNWFKNRRQRDRAAAAK 208 (217)
Q Consensus 134 ~rkk~p~prt~~~~~~~~~~f~~~~r~~L~~~f~~~~yPs~~~k~~LA~~tgLt~~qV~~WFqNrR~R~kr~~~~ 208 (217)
..+|.++.||+|+-+|.. +|+..|.+..||+...+++||.+++|.+.+|+|||+|||+|+|+.+..
T Consensus 33 ~pRkqRRERTtFtr~Qle---------vLe~LF~kTqYPDv~~rEelAlklnLpeSrVqVWFKNRRAK~r~qq~q 98 (228)
T KOG2251|consen 33 GPRKQRRERTTFTRKQLE---------VLEALFAKTQYPDVFMREELALKLNLPESRVQVWFKNRRAKCRRQQQQ 98 (228)
T ss_pred cchhcccccceecHHHHH---------HHHHHHHhhcCccHHHHHHHHHHhCCchhhhhhhhccccchhhHhhhh
Confidence 345667788888888776 999999999999999999999999999999999999999999988775
No 16
>KOG0485|consensus
Probab=99.30 E-value=6.2e-13 Score=111.21 Aligned_cols=60 Identities=30% Similarity=0.422 Sum_probs=55.4
Q ss_pred CCccCCCcccccccchHHHHHHHHHHhcCCCCCHHHHHHHHHHhCCCccccccccccchhHHHHHHhhh
Q psy11043 141 PRTIWDGEQKTHCFKERTRSLLREWYLQDPYPNPTKKRELAQATGLTPTQVGNWFKNRRQRDRAAAAKN 209 (217)
Q Consensus 141 prt~~~~~~~~~~f~~~~r~~L~~~f~~~~yPs~~~k~~LA~~tgLt~~qV~~WFqNrR~R~kr~~~~~ 209 (217)
+||+|+..|.. .|+..|+...|.+..+|..||.++.||++||++||||||.|||++..-.
T Consensus 107 tRTvFSraQV~---------qLEs~Fe~krYLSsaeRa~LA~sLqLTETQVKIWFQNRRnKwKRq~aad 166 (268)
T KOG0485|consen 107 TRTVFSRAQVF---------QLESTFELKRYLSSAERAGLAASLQLTETQVKIWFQNRRNKWKRQYAAD 166 (268)
T ss_pred chhhhhHHHHH---------HHHHHHHHHhhhhHHHHhHHHHhhhhhhhhhhhhhhhhhHHHHHHHhhh
Confidence 78888887777 9999999999999999999999999999999999999999999987643
No 17
>KOG0494|consensus
Probab=99.29 E-value=1.5e-12 Score=111.47 Aligned_cols=65 Identities=29% Similarity=0.429 Sum_probs=58.9
Q ss_pred ccCCCCCCccCCCcccccccchHHHHHHHHHHhcCCCCCHHHHHHHHHHhCCCccccccccccchhHHHHHHhh
Q psy11043 135 RKKFPLPRTIWDGEQKTHCFKERTRSLLREWYLQDPYPNPTKKRELAQATGLTPTQVGNWFKNRRQRDRAAAAK 208 (217)
Q Consensus 135 rkk~p~prt~~~~~~~~~~f~~~~r~~L~~~f~~~~yPs~~~k~~LA~~tgLt~~qV~~WFqNrR~R~kr~~~~ 208 (217)
++|++.-||||+..|.. .|++.|.+..||+...|+.||.+|+|.+..|+|||||||+||||..++
T Consensus 138 k~kRRh~RTiFT~~Qle---------~LEkaFkeaHYPDv~Are~la~ktelpEDRIqVWfQNRRAKWRk~Ek~ 202 (332)
T KOG0494|consen 138 KKKRRHFRTIFTSYQLE---------ELEKAFKEAHYPDVYAREMLADKTELPEDRIQVWFQNRRAKWRKTEKR 202 (332)
T ss_pred ccccccccchhhHHHHH---------HHHHHHhhccCccHHHHHHHhhhccCchhhhhHHhhhhhHHhhhhhhh
Confidence 34455569999988887 999999999999999999999999999999999999999999998765
No 18
>KOG0484|consensus
Probab=99.29 E-value=6.5e-13 Score=99.33 Aligned_cols=72 Identities=31% Similarity=0.476 Sum_probs=60.8
Q ss_pred CCCCCCccccccccCCCCCCccCCCcccccccchHHHHHHHHHHhcCCCCCHHHHHHHHHHhCCCccccccccccchhHH
Q psy11043 123 GRPLGPVDKYRVRKKFPLPRTIWDGEQKTHCFKERTRSLLREWYLQDPYPNPTKKRELAQATGLTPTQVGNWFKNRRQRD 202 (217)
Q Consensus 123 g~~l~~~~k~r~rkk~p~prt~~~~~~~~~~f~~~~r~~L~~~f~~~~yPs~~~k~~LA~~tgLt~~qV~~WFqNrR~R~ 202 (217)
+.+++..++ +|.++-||.|+..|.. .|+..|.+..||++-.+++||.+..|++..|+|||||||+|.
T Consensus 6 ~~~~~l~ek----rKQRRIRTTFTS~QLk---------ELErvF~ETHYPDIYTREEiA~kidLTEARVQVWFQNRRAKf 72 (125)
T KOG0484|consen 6 DDPLGLTEK----RKQRRIRTTFTSAQLK---------ELERVFAETHYPDIYTREEIALKIDLTEARVQVWFQNRRAKF 72 (125)
T ss_pred CCCCChhHH----HHhhhhhhhhhHHHHH---------HHHHHHHhhcCCcchhHHHHHHhhhhhHHHHHHHHHhhHHHH
Confidence 345665554 3344578888877776 999999999999999999999999999999999999999999
Q ss_pred HHHHh
Q psy11043 203 RAAAA 207 (217)
Q Consensus 203 kr~~~ 207 (217)
||+..
T Consensus 73 RKQEr 77 (125)
T KOG0484|consen 73 RKQER 77 (125)
T ss_pred HHHHH
Confidence 98765
No 19
>KOG0493|consensus
Probab=99.24 E-value=3.9e-12 Score=109.03 Aligned_cols=59 Identities=31% Similarity=0.569 Sum_probs=53.1
Q ss_pred CCCCccCCCcccccccchHHHHHHHHHHhcCCCCCHHHHHHHHHHhCCCccccccccccchhHHHHHH
Q psy11043 139 PLPRTIWDGEQKTHCFKERTRSLLREWYLQDPYPNPTKKRELAQATGLTPTQVGNWFKNRRQRDRAAA 206 (217)
Q Consensus 139 p~prt~~~~~~~~~~f~~~~r~~L~~~f~~~~yPs~~~k~~LA~~tgLt~~qV~~WFqNrR~R~kr~~ 206 (217)
++|||.|+.+|+. .|+.-|..|.|.+...|++||.++||.+.||++||||+|+|-||..
T Consensus 247 KRPRTAFtaeQL~---------RLK~EF~enRYlTEqRRQ~La~ELgLNEsQIKIWFQNKRAKiKKsT 305 (342)
T KOG0493|consen 247 KRPRTAFTAEQLQ---------RLKAEFQENRYLTEQRRQELAQELGLNESQIKIWFQNKRAKIKKST 305 (342)
T ss_pred cCccccccHHHHH---------HHHHHHhhhhhHHHHHHHHHHHHhCcCHHHhhHHhhhhhhhhhhcc
Confidence 3577777777766 9999999999999999999999999999999999999999988754
No 20
>KOG1168|consensus
Probab=99.22 E-value=5.1e-11 Score=103.54 Aligned_cols=136 Identities=20% Similarity=0.289 Sum_probs=86.1
Q ss_pred cCCHHHHHHHHHhCCCCCCCcccCCCcHHHHHHHHHHhHhhhcHHHHHHhhc--------c---CCCCC-----cc---h
Q psy11043 43 SGDIERLARFLWSLPVAHPNIGELNKNEAVLRARAIVSFHSGNYREMYSILE--------H---YKFTK-----DS---H 103 (217)
Q Consensus 43 ~g~~~~l~~fl~slp~~~~~~~~~~~~e~vlrAr~~v~~h~~~~~~~~~lLe--------~---~~f~~-----~~---~ 103 (217)
..|--.|+.|...+.+. |+++...|.+......-|. . |.|.+ .+ -
T Consensus 213 dtDPReLEaFAErFKQR----------------RIKLGVTQADVG~ALAnLKiPGVGsLSQSTICRFESLTLSHNNMiAL 276 (385)
T KOG1168|consen 213 DTDPRELEAFAERFKQR----------------RIKLGVTQADVGKALANLKIPGVGSLSQSTICRFESLTLSHNNMIAL 276 (385)
T ss_pred CCCHHHHHHHHHHHHhh----------------hhhhcccHHHHHHHHHhCcCCCcccccccceeeeeeeccccCcchhh
Confidence 35677889999888775 7777777777776653332 1 11111 11 1
Q ss_pred hHHHHHHHHhhhHHHHHhcCCCCCCccccc-cccCCCCCCccCCCcccccccchHHHHHHHHHHhcCCCCCHHHHHHHHH
Q psy11043 104 GKLQAMWLEAHYQEAEKLRGRPLGPVDKYR-VRKKFPLPRTIWDGEQKTHCFKERTRSLLREWYLQDPYPNPTKKRELAQ 182 (217)
Q Consensus 104 ~~lq~lw~~a~y~~~e~~~g~~l~~~~k~r-~rkk~p~prt~~~~~~~~~~f~~~~r~~L~~~f~~~~yPs~~~k~~LA~ 182 (217)
...-+.|++............|-.+ +... ..|| +.||.+..-+++ .|+.||...|.|+.+.+..||+
T Consensus 277 KPILqaWLEeAE~a~keK~~~pd~~-~l~~~~ekK--RKRTSIAAPEKR---------sLEayFavQPRPS~EkIAaIAe 344 (385)
T KOG1168|consen 277 KPILQAWLEEAEAAMKEKDTKPDIN-ELLPGGEKK--RKRTSIAAPEKR---------SLEAYFAVQPRPSGEKIAAIAE 344 (385)
T ss_pred hHHHHHHHHHHHHHHHhhccCCchh-hccCccccc--cccccccCcccc---------cHHHHhccCCCCchhHHHHHHH
Confidence 2233456653322221112222100 0010 1121 246666655555 7999999999999999999999
Q ss_pred HhCCCccccccccccchhHHHHHH
Q psy11043 183 ATGLTPTQVGNWFKNRRQRDRAAA 206 (217)
Q Consensus 183 ~tgLt~~qV~~WFqNrR~R~kr~~ 206 (217)
++.|.+.+|+|||||.|+|.||.+
T Consensus 345 kLDLKKNVVRVWFCNQRQKQKRm~ 368 (385)
T KOG1168|consen 345 KLDLKKNVVRVWFCNQRQKQKRMK 368 (385)
T ss_pred hhhhhhceEEEEeeccHHHHHHhh
Confidence 999999999999999999999854
No 21
>TIGR01565 homeo_ZF_HD homeobox domain, ZF-HD class. This model represents a class of homoebox domain that differs substantially from the typical homoebox domain described in pfam model pfam00046. It is found in both C4 and C3 plants.
Probab=99.19 E-value=1.5e-11 Score=83.50 Aligned_cols=51 Identities=24% Similarity=0.399 Sum_probs=46.9
Q ss_pred CCCccCCCcccccccchHHHHHHHHHHhcCCC----CCHHHHHHHHHHhCCCccccccccccch
Q psy11043 140 LPRTIWDGEQKTHCFKERTRSLLREWYLQDPY----PNPTKKRELAQATGLTPTQVGNWFKNRR 199 (217)
Q Consensus 140 ~prt~~~~~~~~~~f~~~~r~~L~~~f~~~~y----Ps~~~k~~LA~~tgLt~~qV~~WFqNrR 199 (217)
++||.|+.+|+. .|+..|..++| |+..++.+||..+||+..+|++||+|.+
T Consensus 3 R~RT~Ft~~Q~~---------~Le~~fe~~~y~~~~~~~~~r~~la~~lgl~~~vvKVWfqN~k 57 (58)
T TIGR01565 3 RRRTKFTAEQKE---------KMRDFAEKLGWKLKDKRREEVREFCEEIGVTRKVFKVWMHNNK 57 (58)
T ss_pred CCCCCCCHHHHH---------HHHHHHHHcCCCCCCCCHHHHHHHHHHhCCCHHHeeeecccCC
Confidence 467777777777 99999999999 9999999999999999999999999975
No 22
>KOG0491|consensus
Probab=99.16 E-value=7.7e-12 Score=100.63 Aligned_cols=62 Identities=31% Similarity=0.540 Sum_probs=58.3
Q ss_pred CCCccCCCcccccccchHHHHHHHHHHhcCCCCCHHHHHHHHHHhCCCccccccccccchhHHHHHHhhhh
Q psy11043 140 LPRTIWDGEQKTHCFKERTRSLLREWYLQDPYPNPTKKRELAQATGLTPTQVGNWFKNRRQRDRAAAAKNR 210 (217)
Q Consensus 140 ~prt~~~~~~~~~~f~~~~r~~L~~~f~~~~yPs~~~k~~LA~~tgLt~~qV~~WFqNrR~R~kr~~~~~~ 210 (217)
.-||+|...+.. .|++.|+...|.+..++.+||..++|+++||+.||||||.|.||...++.
T Consensus 102 K~Rtvfs~~ql~---------~l~~rFe~QrYLS~~e~~ELan~L~LS~~QVKTWFQNrRMK~Kk~~r~~~ 163 (194)
T KOG0491|consen 102 KARTVFSDPQLS---------GLEKRFERQRYLSTPERQELANALSLSETQVKTWFQNRRMKHKKQQRNNQ 163 (194)
T ss_pred hhcccccCcccc---------ccHHHHhhhhhcccHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHHHhccC
Confidence 379999999998 99999999999999999999999999999999999999999999887654
No 23
>KOG0483|consensus
Probab=99.15 E-value=1.8e-11 Score=102.43 Aligned_cols=58 Identities=28% Similarity=0.516 Sum_probs=53.1
Q ss_pred cccchHHHHHHHHHHhcCCCCCHHHHHHHHHHhCCCccccccccccchhHHHHHHhhh
Q psy11043 152 HCFKERTRSLLREWYLQDPYPNPTKKRELAQATGLTPTQVGNWFKNRRQRDRAAAAKN 209 (217)
Q Consensus 152 ~~f~~~~r~~L~~~f~~~~yPs~~~k~~LA~~tgLt~~qV~~WFqNrR~R~kr~~~~~ 209 (217)
.+|+.++...|+..|..+.|..+..|..||..+||.++||.+||||||+|||.++...
T Consensus 55 ~Rlt~eQ~~~LE~~F~~~~~L~p~~K~~LAk~LgL~pRQVavWFQNRRARwK~kqlE~ 112 (198)
T KOG0483|consen 55 RRLTSEQVKFLEKSFESEKKLEPERKKKLAKELGLQPRQVAVWFQNRRARWKTKQLEK 112 (198)
T ss_pred ccccHHHHHHhHHhhccccccChHHHHHHHHhhCCChhHHHHHHhhccccccchhhhh
Confidence 5677777779999999999999999999999999999999999999999999876644
No 24
>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=99.07 E-value=3.2e-11 Score=76.04 Aligned_cols=34 Identities=50% Similarity=0.977 Sum_probs=29.5
Q ss_pred cCCCCCHHHHHHHHHHhCCCccccccccccchhH
Q psy11043 168 QDPYPNPTKKRELAQATGLTPTQVGNWFKNRRQR 201 (217)
Q Consensus 168 ~~~yPs~~~k~~LA~~tgLt~~qV~~WFqNrR~R 201 (217)
.+|||+.++|..||..|||+..||.+||.|.|.|
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 3899999999999999999999999999999986
No 25
>COG5576 Homeodomain-containing transcription factor [Transcription]
Probab=99.04 E-value=1.6e-10 Score=93.50 Aligned_cols=53 Identities=21% Similarity=0.489 Sum_probs=48.5
Q ss_pred HHHHHHHHHhcCCCCCHHHHHHHHHHhCCCccccccccccchhHHHHHHhhhh
Q psy11043 158 TRSLLREWYLQDPYPNPTKKRELAQATGLTPTQVGNWFKNRRQRDRAAAAKNR 210 (217)
Q Consensus 158 ~r~~L~~~f~~~~yPs~~~k~~LA~~tgLt~~qV~~WFqNrR~R~kr~~~~~~ 210 (217)
++.+|+..|..++||+...+..|+..++|+++-|++||||+|++.|+......
T Consensus 62 Q~~vL~~~F~i~p~Ps~~~r~~L~~~lnm~~ksVqIWFQNkR~~~k~~~~~~~ 114 (156)
T COG5576 62 QLMVLEREFEINPYPSSITRIKLSLLLNMPPKSVQIWFQNKRAKEKKKRSGKV 114 (156)
T ss_pred HHHHHHHHhccCCCCCHHHHHHHHHhcCCChhhhhhhhchHHHHHHHhcccch
Confidence 34499999999999999999999999999999999999999999998876543
No 26
>KOG0774|consensus
Probab=98.94 E-value=3.6e-10 Score=97.00 Aligned_cols=67 Identities=34% Similarity=0.661 Sum_probs=58.6
Q ss_pred CCCcccccccchHHHHHHHHHHhc---CCCCCHHHHHHHHHHhCCCccccccccccchhHHHHHHhhhhh
Q psy11043 145 WDGEQKTHCFKERTRSLLREWYLQ---DPYPNPTKKRELAQATGLTPTQVGNWFKNRRQRDRAAAAKNRL 211 (217)
Q Consensus 145 ~~~~~~~~~f~~~~r~~L~~~f~~---~~yPs~~~k~~LA~~tgLt~~qV~~WFqNrR~R~kr~~~~~~~ 211 (217)
.+...++++|...++.+|.+||.. |||||.++|++||++.+++..||+|||.|+|-|.||-..+..+
T Consensus 186 ldarRKRRNFsK~aTeiLneyF~~h~~nPYPSee~K~eLAkqCnItvsQvsnwfgnkrIrykK~~~k~~e 255 (334)
T KOG0774|consen 186 LDARRKRRNFSKQATEILNEYFYSHLSNPYPSEEAKEELAKQCNITVSQVSNWFGNKRIRYKKNMGKNQE 255 (334)
T ss_pred HHHHHhhcccchhHHHHHHHHHHHhcCCCCCcHHHHHHHHHHcCceehhhccccccceeehhhhhhhhhh
Confidence 344456689999999999999965 9999999999999999999999999999999999987665543
No 27
>KOG0486|consensus
Probab=98.94 E-value=3.2e-10 Score=99.50 Aligned_cols=63 Identities=32% Similarity=0.459 Sum_probs=56.0
Q ss_pred CCCCCCccCCCcccccccchHHHHHHHHHHhcCCCCCHHHHHHHHHHhCCCccccccccccchhHHHHHHhh
Q psy11043 137 KFPLPRTIWDGEQKTHCFKERTRSLLREWYLQDPYPNPTKKRELAQATGLTPTQVGNWFKNRRQRDRAAAAK 208 (217)
Q Consensus 137 k~p~prt~~~~~~~~~~f~~~~r~~L~~~f~~~~yPs~~~k~~LA~~tgLt~~qV~~WFqNrR~R~kr~~~~ 208 (217)
|.++-||.|+..|.. .|+.+|..|.||+...+++||.-++||+..|+|||+|||+||+|....
T Consensus 111 KqrrQrthFtSqqlq---------ele~tF~rNrypdMstrEEIavwtNlTE~rvrvwfknrrakwrkrErN 173 (351)
T KOG0486|consen 111 KQRRQRTHFTSQQLQ---------ELEATFQRNRYPDMSTREEIAVWTNLTEARVRVWFKNRRAKWRKRERN 173 (351)
T ss_pred hhhhhhhhhHHHHHH---------HHHHHHhhccCCccchhhHHHhhccccchhhhhhcccchhhhhhhhhh
Confidence 455577777777766 999999999999999999999999999999999999999999986553
No 28
>KOG0847|consensus
Probab=98.88 E-value=5.4e-10 Score=93.88 Aligned_cols=59 Identities=32% Similarity=0.459 Sum_probs=54.5
Q ss_pred CCCccCCCcccccccchHHHHHHHHHHhcCCCCCHHHHHHHHHHhCCCccccccccccchhHHHHHHh
Q psy11043 140 LPRTIWDGEQKTHCFKERTRSLLREWYLQDPYPNPTKKRELAQATGLTPTQVGNWFKNRRQRDRAAAA 207 (217)
Q Consensus 140 ~prt~~~~~~~~~~f~~~~r~~L~~~f~~~~yPs~~~k~~LA~~tgLt~~qV~~WFqNrR~R~kr~~~ 207 (217)
..|..|.+.+.. .|+..|+...|+-..++.+||..+|++..||+|||||||.||||+..
T Consensus 169 ~srPTf~g~qi~---------~le~~feqtkylaG~~ra~lA~~lgmteSqvkVWFQNRRTKWRKkhA 227 (288)
T KOG0847|consen 169 QSRPTFTGHQIY---------QLERKFEQTKYLAGADRAQLAQELNMTESQVKVWFQNRRTKWRKKHA 227 (288)
T ss_pred ccCCCccchhhh---------hhhhhhhhhhcccchhHHHhhccccccHHHHHHHHhcchhhhhhhhc
Confidence 367788888887 99999999999999999999999999999999999999999998764
No 29
>KOG0844|consensus
Probab=98.85 E-value=1.7e-09 Score=94.79 Aligned_cols=54 Identities=28% Similarity=0.513 Sum_probs=48.7
Q ss_pred cchHHHHHHHHHHhcCCCCCHHHHHHHHHHhCCCccccccccccchhHHHHHHh
Q psy11043 154 FKERTRSLLREWYLQDPYPNPTKKRELAQATGLTPTQVGNWFKNRRQRDRAAAA 207 (217)
Q Consensus 154 f~~~~r~~L~~~f~~~~yPs~~~k~~LA~~tgLt~~qV~~WFqNrR~R~kr~~~ 207 (217)
|+.++...|++-|-+..|.+...|.+||..++|.++.|+|||||||.||||++.
T Consensus 188 FTReQIaRLEKEFyrENYVSRprRcELAAaLNLPEtTIKVWFQNRRMKDKRQRl 241 (408)
T KOG0844|consen 188 FTREQIARLEKEFYRENYVSRPRRCELAAALNLPETTIKVWFQNRRMKDKRQRL 241 (408)
T ss_pred hhHHHHHHHHHHHHHhccccCchhhhHHHhhCCCcceeehhhhhchhhhhhhhh
Confidence 555555599999999999999999999999999999999999999999999764
No 30
>KOG0490|consensus
Probab=98.53 E-value=5.2e-08 Score=82.23 Aligned_cols=62 Identities=23% Similarity=0.188 Sum_probs=55.6
Q ss_pred cCCCCCCccCCCcccccccchHHHHHHHHHHhcCCCCCHHHHHHHHHHhCCCccccccccccchhHHHHHH
Q psy11043 136 KKFPLPRTIWDGEQKTHCFKERTRSLLREWYLQDPYPNPTKKRELAQATGLTPTQVGNWFKNRRQRDRAAA 206 (217)
Q Consensus 136 kk~p~prt~~~~~~~~~~f~~~~r~~L~~~f~~~~yPs~~~k~~LA~~tgLt~~qV~~WFqNrR~R~kr~~ 206 (217)
.+.++.|+.++..+.. .|+..|..++||+...++.||..+++++..|++||||+|+++++..
T Consensus 58 ~~~rr~rt~~~~~ql~---------~ler~f~~~h~Pd~~~r~~la~~~~~~e~rVqvwFqnrrak~r~~~ 119 (235)
T KOG0490|consen 58 FSKRCARCKFTISQLD---------ELERAFEKVHLPCFACRECLALLLTGDEFRVQVWFQNRRAKDRKEE 119 (235)
T ss_pred ccccccCCCCCcCHHH---------HHHHhhcCCCcCccchHHHHhhcCCCCeeeeehhhhhhcHhhhhhh
Confidence 3445578888877766 9999999999999999999999999999999999999999999876
No 31
>KOG0849|consensus
Probab=98.41 E-value=1.5e-07 Score=85.60 Aligned_cols=65 Identities=31% Similarity=0.502 Sum_probs=57.7
Q ss_pred cccCCCCCCccCCCcccccccchHHHHHHHHHHhcCCCCCHHHHHHHHHHhCCCccccccccccchhHHHHHHh
Q psy11043 134 VRKKFPLPRTIWDGEQKTHCFKERTRSLLREWYLQDPYPNPTKKRELAQATGLTPTQVGNWFKNRRQRDRAAAA 207 (217)
Q Consensus 134 ~rkk~p~prt~~~~~~~~~~f~~~~r~~L~~~f~~~~yPs~~~k~~LA~~tgLt~~qV~~WFqNrR~R~kr~~~ 207 (217)
..++.++.||.|+..+.. .|+++|..++||....++.||.+++++...|.+||+|+|.|+++..-
T Consensus 172 ~~~~~rr~rtsft~~Q~~---------~le~~f~rt~yP~i~~Re~La~~i~l~e~riqvwf~nrra~~rr~~~ 236 (354)
T KOG0849|consen 172 LQRGGRRNRTSFSPSQLE---------ALEECFQRTPYPDIVGRETLAKETGLPEPRVQVWFQNRRAKWRRQHR 236 (354)
T ss_pred ccccccccccccccchHH---------HHHHHhcCCCCCchhhHHHHhhhccCCchHHHHHHhhhhhhhhhccc
Confidence 344455568888888877 99999999999999999999999999999999999999999998763
No 32
>KOG2252|consensus
Probab=98.38 E-value=1e-06 Score=82.80 Aligned_cols=53 Identities=26% Similarity=0.446 Sum_probs=49.5
Q ss_pred CCccCCCcccccccchHHHHHHHHHHhcCCCCCHHHHHHHHHHhCCCccccccccccchhHH
Q psy11043 141 PRTIWDGEQKTHCFKERTRSLLREWYLQDPYPNPTKKRELAQATGLTPTQVGNWFKNRRQRD 202 (217)
Q Consensus 141 prt~~~~~~~~~~f~~~~r~~L~~~f~~~~yPs~~~k~~LA~~tgLt~~qV~~WFqNrR~R~ 202 (217)
||.+|+..|+. .|...|..+++|+.++.+.|+.+++|..+.|.|||-|.|+|.
T Consensus 423 PRlVfTd~Qkr---------TL~aiFke~~RPS~Emq~tIS~qL~L~~sTV~NfFmNaRRRs 475 (558)
T KOG2252|consen 423 PRLVFTDIQKR---------TLQAIFKENKRPSREMQETISQQLNLELSTVINFFMNARRRS 475 (558)
T ss_pred ceeeecHHHHH---------HHHHHHhcCCCCCHHHHHHHHHHhCCcHHHHHHHHHhhhhhc
Confidence 68777777776 999999999999999999999999999999999999999995
No 33
>KOG0773|consensus
Probab=98.27 E-value=2.9e-07 Score=82.87 Aligned_cols=56 Identities=38% Similarity=0.658 Sum_probs=51.3
Q ss_pred cccchHHHHHHHHHHhc---CCCCCHHHHHHHHHHhCCCccccccccccchhHHHHHHh
Q psy11043 152 HCFKERTRSLLREWYLQ---DPYPNPTKKRELAQATGLTPTQVGNWFKNRRQRDRAAAA 207 (217)
Q Consensus 152 ~~f~~~~r~~L~~~f~~---~~yPs~~~k~~LA~~tgLt~~qV~~WFqNrR~R~kr~~~ 207 (217)
..|++.++.+|+.|... +|||+..+|..||.+|||+..||.|||.|.|.|.++...
T Consensus 244 ~~lP~~a~~ilr~Wl~~h~~~PYPse~~K~~La~~TGLs~~Qv~NWFINaR~R~w~p~~ 302 (342)
T KOG0773|consen 244 RGLPKEAVSILRAWLFEHLLHPYPSDDEKLMLAKQTGLSRPQVSNWFINARVRLWKPMI 302 (342)
T ss_pred CCCCHHHHHHHHHHHHHhccCCCCcchhccccchhcCCCcccCCchhhhcccccCCchH
Confidence 68999999999999765 799999999999999999999999999999999886655
No 34
>KOG0490|consensus
Probab=97.73 E-value=3.2e-05 Score=65.16 Aligned_cols=63 Identities=32% Similarity=0.542 Sum_probs=54.0
Q ss_pred cCCCCCCccCCCcccccccchHHHHHHHHHHhcCCCCCHHHHHHHHHHhCCCccccccccccchhHHHHHHh
Q psy11043 136 KKFPLPRTIWDGEQKTHCFKERTRSLLREWYLQDPYPNPTKKRELAQATGLTPTQVGNWFKNRRQRDRAAAA 207 (217)
Q Consensus 136 kk~p~prt~~~~~~~~~~f~~~~r~~L~~~f~~~~yPs~~~k~~LA~~tgLt~~qV~~WFqNrR~R~kr~~~ 207 (217)
.+.+.+++.+...+.. .+...|..+++|+...+..|+..+|++...|.+||+|+|.+.++...
T Consensus 151 ~~~~~~~~~~~~~~~~---------~~~~~~~~~~~P~~~~~~~l~~~~~~~~~~~q~~~~~~~~~~~~~~~ 213 (235)
T KOG0490|consen 151 KKPRRPRTTFTENQLE---------VLETVFRATPKPDADDREQLAEETGLSERVIQVWFQNRRAKLRKHKR 213 (235)
T ss_pred cccCCCccccccchhH---------hhhhcccCCCCCchhhHHHHHHhcCCChhhhhhhcccHHHHHHhhcc
Confidence 3444566666666666 99999999999999999999999999999999999999999987643
No 35
>PF11569 Homez: Homeodomain leucine-zipper encoding, Homez; PDB: 2YS9_A.
Probab=97.27 E-value=7.7e-05 Score=50.15 Aligned_cols=40 Identities=28% Similarity=0.511 Sum_probs=30.6
Q ss_pred HHHHHHhcCCCCCHHHHHHHHHHhCCCccccccccccchh
Q psy11043 161 LLREWYLQDPYPNPTKKRELAQATGLTPTQVGNWFKNRRQ 200 (217)
Q Consensus 161 ~L~~~f~~~~yPs~~~k~~LA~~tgLt~~qV~~WFqNrR~ 200 (217)
.|+++|..+++....+...|+.+++|+..||+.||-.++.
T Consensus 12 pL~~Yy~~h~~L~E~DL~~L~~kS~ms~qqVr~WFa~~~~ 51 (56)
T PF11569_consen 12 PLEDYYLKHKQLQEEDLDELCDKSRMSYQQVRDWFAERMQ 51 (56)
T ss_dssp HHHHHHHHT----TTHHHHHHHHTT--HHHHHHHHHHHS-
T ss_pred HHHHHHHHcCCccHhhHHHHHHHHCCCHHHHHHHHHHhcc
Confidence 5999999999999999999999999999999999976543
No 36
>KOG1146|consensus
Probab=95.51 E-value=0.0069 Score=62.52 Aligned_cols=52 Identities=19% Similarity=0.384 Sum_probs=47.3
Q ss_pred HHHHHHHHHHhcCCCCCHHHHHHHHHHhCCCccccccccccchhHHHHHHhh
Q psy11043 157 RTRSLLREWYLQDPYPNPTKKRELAQATGLTPTQVGNWFKNRRQRDRAAAAK 208 (217)
Q Consensus 157 ~~r~~L~~~f~~~~yPs~~~k~~LA~~tgLt~~qV~~WFqNrR~R~kr~~~~ 208 (217)
...+.++.+|....||...+.+.|....++.++.|.+||||.|++.++....
T Consensus 913 ~qlk~i~~~~~~q~~~~~~~~E~l~~~~~~~~~~i~vw~qna~~~s~k~~~n 964 (1406)
T KOG1146|consen 913 LQLKIIKACYEAQRTPTMQECEVLEEPIGLPKRVIQVWFQNARAKSKKAKLN 964 (1406)
T ss_pred HHHHHHHHHHhhccCChHHHHHhhcccccCCcchhHHhhhhhhhhhhhhhhc
Confidence 3455999999999999999999999999999999999999999999987663
No 37
>KOG3623|consensus
Probab=93.17 E-value=0.07 Score=52.52 Aligned_cols=48 Identities=25% Similarity=0.514 Sum_probs=44.0
Q ss_pred HHHHHHHHhcCCCCCHHHHHHHHHHhCCCccccccccccchhHHHHHH
Q psy11043 159 RSLLREWYLQDPYPNPTKKRELAQATGLTPTQVGNWFKNRRQRDRAAA 206 (217)
Q Consensus 159 r~~L~~~f~~~~yPs~~~k~~LA~~tgLt~~qV~~WFqNrR~R~kr~~ 206 (217)
..+|+.+|..|..|+.++-..+|.+.||....|+.||.+.+.......
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 568999999999999999999999999999999999999988876543
No 38
>PF04218 CENP-B_N: CENP-B N-terminal DNA-binding domain; InterPro: IPR006695 Centromere Protein B (CENP-B) is a DNA-binding protein localized to the centromere. Within the N-terminal 125 residues, there is a DNA-binding region, which binds to a corresponding 17bp CENP-B box sequence. CENP-B dimers either bind two separate DNA molecules or alternatively, they may bind two CENP-B boxes on one DNA molecule, with the intervening stretch of DNA forming a loop structure. The CENP-B DNA-binding domain consists of two repeating domains, RP1 and RP2. This family corresponds to RP1 has been shown to consist of four helices in a helix-turn-helix structure [].; GO: 0003677 DNA binding, 0000775 chromosome, centromeric region; PDB: 1BW6_A 1HLV_A 2ELH_A.
Probab=77.35 E-value=1.5 Score=28.89 Aligned_cols=33 Identities=21% Similarity=0.361 Sum_probs=23.0
Q ss_pred HHHHHHhcCCCCCHHHHHHHHHHhCCCccccccccccc
Q psy11043 161 LLREWYLQDPYPNPTKKRELAQATGLTPTQVGNWFKNR 198 (217)
Q Consensus 161 ~L~~~f~~~~yPs~~~k~~LA~~tgLt~~qV~~WFqNr 198 (217)
.+-..+...+ ....||..+|++.++|+.|.+|+
T Consensus 14 ~iI~~~e~g~-----s~~~ia~~fgv~~sTv~~I~K~k 46 (53)
T PF04218_consen 14 EIIKRLEEGE-----SKRDIAREFGVSRSTVSTILKNK 46 (53)
T ss_dssp HHHHHHHCTT------HHHHHHHHT--CCHHHHHHHCH
T ss_pred HHHHHHHcCC-----CHHHHHHHhCCCHHHHHHHHHhH
Confidence 3344455554 46789999999999999999984
No 39
>KOG0773|consensus
Probab=75.50 E-value=1.6 Score=39.17 Aligned_cols=46 Identities=41% Similarity=0.651 Sum_probs=38.2
Q ss_pred HHHHHHh---cCCCCCHHHHHHHHHHhCCCccccccccccchhHHHHHH
Q psy11043 161 LLREWYL---QDPYPNPTKKRELAQATGLTPTQVGNWFKNRRQRDRAAA 206 (217)
Q Consensus 161 ~L~~~f~---~~~yPs~~~k~~LA~~tgLt~~qV~~WFqNrR~R~kr~~ 206 (217)
.|..|.. .++||+..++..++..+.|+..||.+||-|.|.+-+...
T Consensus 108 ~~~~~~~~~~~~~~~~k~~~~ll~~~~~~~~~~~~~~~~~a~r~~~~~~ 156 (342)
T KOG0773|consen 108 TLKAWLEEHRLNPYPSKLEKILLAVITKLTLTQVSTWFANARRRLKKEL 156 (342)
T ss_pred ccccchhhhhhccCchHHHHHHHHHHHHhhhhhHHHHHHHHHHHHHhcc
Confidence 4444433 399999999999999999999999999999998876543
No 40
>PF14559 TPR_19: Tetratricopeptide repeat; PDB: 2R5S_A 3QDN_B 3QOU_A 3ASG_A 3ASD_A 3AS5_A 3AS4_A 3ASH_B 3FP3_A 3LCA_A ....
Probab=73.53 E-value=7.8 Score=25.38 Aligned_cols=42 Identities=19% Similarity=0.188 Sum_probs=29.4
Q ss_pred cHHHHHHHHHHhHhhhcHHHHHHhhccCCCCCcchhHHHHHH
Q psy11043 69 NEAVLRARAIVSFHSGNYREMYSILEHYKFTKDSHGKLQAMW 110 (217)
Q Consensus 69 ~e~vlrAr~~v~~h~~~~~~~~~lLe~~~f~~~~~~~lq~lw 110 (217)
|..+.-.-+.+++..|+|.+...+|+...-...+++....++
T Consensus 24 ~~~~~~~la~~~~~~g~~~~A~~~l~~~~~~~~~~~~~~~l~ 65 (68)
T PF14559_consen 24 NPEARLLLAQCYLKQGQYDEAEELLERLLKQDPDNPEYQQLL 65 (68)
T ss_dssp SHHHHHHHHHHHHHTT-HHHHHHHHHCCHGGGTTHHHHHHHH
T ss_pred CHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHCcCHHHHHHHH
Confidence 567777788888899999999988886655554445444443
No 41
>PF00424 REV: REV protein (anti-repression trans-activator protein); InterPro: IPR000625 REV is a viral anti-repression trans-activator protein, which appears to act post-transcriptionally [] to relieve negative repression of GAG and ENV production. It is a phosphoprotein [, ] whose state of phosphorylation is mediated by a specific serine kinase activity present in the nucleus []. REV accumulates in the nucleoli [].; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0042025 host cell nucleus; PDB: 1ETF_B 1ETG_B 1ULL_B 3LPH_B 2X7L_R.
Probab=67.68 E-value=5.7 Score=29.37 Aligned_cols=37 Identities=35% Similarity=0.619 Sum_probs=21.0
Q ss_pred HHHHHHHHhcCCCCCHHHHHHHHHHhCCCccccccccccchhHHHHHHhhh
Q psy11043 159 RSLLREWYLQDPYPNPTKKRELAQATGLTPTQVGNWFKNRRQRDRAAAAKN 209 (217)
Q Consensus 159 r~~L~~~f~~~~yPs~~~k~~LA~~tgLt~~qV~~WFqNrR~R~kr~~~~~ 209 (217)
..+.+-.|+.||||++.-... | =.|||.||++.....
T Consensus 14 vRiIk~LyqsnPyP~~~GTr~-a-------------RRnRRRRWR~rq~QI 50 (91)
T PF00424_consen 14 VRIIKILYQSNPYPSPEGTRQ-A-------------RRNRRRRWRARQRQI 50 (91)
T ss_dssp HHHHHHHHHTS-S--S-S-HH-H-------------HHHHHHHHHHHHHHH
T ss_pred HHHHHHHHccccCCCCCCccc-c-------------ccchhhhHHHHHHHH
Confidence 446677788999998653322 1 148888988766543
No 42
>PF00157 Pou: Pou domain - N-terminal to homeobox domain; InterPro: IPR000327 POU proteins are eukaryotic transcription factors containing a bipartite DNA binding domain referred to as the POU domain. The acronym POU (pronounced 'pow') is derived from the names of three mammalian transcription factors, the pituitary-specific Pit-1, the octamer-binding proteins Oct-1 and Oct-2, and the neural Unc-86 from Caenorhabditis elegans. POU domain genes have been identified in diverse organisms including nematodes, flies, amphibians, fish and mammals but have not been yet identified in plants and fungi. The various members of the POU family have a wide variety of functions, all of which are related to the function of the neuroendocrine system [] and the development of an organism []. Some other genes are also regulated, including those for immunoglobulin light and heavy chains (Oct-2) [, ], and trophic hormone genes, such as those for prolactin and growth hormone (Pit-1). The POU domain is a bipartite domain composed of two subunits separated by a non-conserved region of 15-55 aa. The N-terminal subunit is known as the POU-specific (POUs) domain (IPR000327 from INTERPRO), while the C-terminal subunit is a homeobox domain (IPR007103 from INTERPRO). 3D structures of complexes including both POU subdomains bound to DNA are available. Both subdomains contain the structural motif 'helix-turn-helix', which directly associates with the two components of bipartite DNA binding sites, and both are required for high affinity sequence-specific DNA-binding. The domain may also be involved in protein-protein interactions []. The subdomains are connected by a flexible linker [, , ]. In proteins a POU-specific domain is always accompanied by a homeodomain. Despite of the lack of sequence homology, 3D structure of POUs is similar to 3D structure of bacteriophage lambda repressor and other members of HTH_3 family [, ]. This entry represents the POU-specific subunit of the POU domain.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent; PDB: 3D1N_O 1AU7_A 3L1P_A 2XSD_C 1O4X_A 1HF0_B 1GT0_C 1POU_A 1CQT_B 1E3O_C ....
Probab=53.56 E-value=7.1 Score=27.83 Aligned_cols=42 Identities=14% Similarity=0.270 Sum_probs=32.0
Q ss_pred CHHHHHHHHHhCCCCCCCcccCCCcHHHHHHHHHHhHhhhcHHHHHHhhccCCCCCcc
Q psy11043 45 DIERLARFLWSLPVAHPNIGELNKNEAVLRARAIVSFHSGNYREMYSILEHYKFTKDS 102 (217)
Q Consensus 45 ~~~~l~~fl~slp~~~~~~~~~~~~e~vlrAr~~v~~h~~~~~~~~~lLe~~~f~~~~ 102 (217)
+++.|..|...+.. -|..+.|.|.+++.....+.+..|+...
T Consensus 5 ~~~ele~Fa~~fk~----------------rRi~LG~TQ~dVg~al~~~~G~~~SQtt 46 (75)
T PF00157_consen 5 DLKELEQFAKEFKQ----------------RRIKLGYTQADVGAALGRLYGKEFSQTT 46 (75)
T ss_dssp HHHHHHHHHHHHHH----------------HHHHTT--HHHHHHHHHHHHSSGGSHHH
T ss_pred CHHHHHHHHHHHHH----------------hhhhcccCHHHHhHHHHHhcCccccchh
Confidence 46678888876654 3888999999999999999988887765
No 43
>PF08281 Sigma70_r4_2: Sigma-70, region 4; InterPro: IPR013249 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognised by the major sigma factors [, ]. Region 4 of sigma-70 like sigma-factors are involved in binding to the -35 promoter element via a helix-turn-helix motif [].; GO: 0003677 DNA binding, 0003700 sequence-specific DNA binding transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, DNA-dependent, 0006355 regulation of transcription, DNA-dependent; PDB: 2LFW_A 1OR7_B 2H27_D 2O8X_B.
Probab=51.15 E-value=11 Score=23.96 Aligned_cols=43 Identities=23% Similarity=0.402 Sum_probs=28.8
Q ss_pred ccchHHHHHHHHHHhcCCCCCHHHHHHHHHHhCCCccccccccccchh
Q psy11043 153 CFKERTRSLLREWYLQDPYPNPTKKRELAQATGLTPTQVGNWFKNRRQ 200 (217)
Q Consensus 153 ~f~~~~r~~L~~~f~~~~yPs~~~k~~LA~~tgLt~~qV~~WFqNrR~ 200 (217)
.+++..+.++.-.|..+ -.-.++|..+|++...|++|...-|.
T Consensus 10 ~L~~~~r~i~~l~~~~g-----~s~~eIa~~l~~s~~~v~~~l~ra~~ 52 (54)
T PF08281_consen 10 QLPERQREIFLLRYFQG-----MSYAEIAEILGISESTVKRRLRRARK 52 (54)
T ss_dssp CS-HHHHHHHHHHHTS--------HHHHHHHCTS-HHHHHHHHHHHHH
T ss_pred CCCHHHHHHHHHHHHHC-----cCHHHHHHHHCcCHHHHHHHHHHHHh
Confidence 45667777777766554 34678899999999999999865443
No 44
>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=49.10 E-value=15 Score=23.17 Aligned_cols=45 Identities=20% Similarity=0.338 Sum_probs=31.4
Q ss_pred ccchHHHHHHHHHHhcCCCCCHHHHHHHHHHhCCCccccccccccchhHH
Q psy11043 153 CFKERTRSLLREWYLQDPYPNPTKKRELAQATGLTPTQVGNWFKNRRQRD 202 (217)
Q Consensus 153 ~f~~~~r~~L~~~f~~~~yPs~~~k~~LA~~tgLt~~qV~~WFqNrR~R~ 202 (217)
.++++.+.++...|..+ ..-.++|..+|++...|+.+...-..|-
T Consensus 4 ~L~~~er~vi~~~y~~~-----~t~~eIa~~lg~s~~~V~~~~~~al~kL 48 (50)
T PF04545_consen 4 QLPPREREVIRLRYFEG-----LTLEEIAERLGISRSTVRRILKRALKKL 48 (50)
T ss_dssp TS-HHHHHHHHHHHTST------SHHHHHHHHTSCHHHHHHHHHHHHHHH
T ss_pred hCCHHHHHHHHHHhcCC-----CCHHHHHHHHCCcHHHHHHHHHHHHHHh
Confidence 46777788898888332 2356789999999999887765544443
No 45
>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=46.93 E-value=7.7 Score=26.43 Aligned_cols=19 Identities=16% Similarity=0.622 Sum_probs=16.5
Q ss_pred HHHHHHhCCCccccccccc
Q psy11043 178 RELAQATGLTPTQVGNWFK 196 (217)
Q Consensus 178 ~~LA~~tgLt~~qV~~WFq 196 (217)
..||.++|++..+|+.|=.
T Consensus 26 kdIA~~Lgvs~~tIr~WK~ 44 (60)
T PF10668_consen 26 KDIAEKLGVSESTIRKWKS 44 (60)
T ss_pred HHHHHHHCCCHHHHHHHhh
Confidence 4689999999999999953
No 46
>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=40.71 E-value=18 Score=21.83 Aligned_cols=41 Identities=17% Similarity=0.275 Sum_probs=28.9
Q ss_pred cchHHHHHHHHHHhcCCCCCHHHHHHHHHHhCCCccccccccccch
Q psy11043 154 FKERTRSLLREWYLQDPYPNPTKKRELAQATGLTPTQVGNWFKNRR 199 (217)
Q Consensus 154 f~~~~r~~L~~~f~~~~yPs~~~k~~LA~~tgLt~~qV~~WFqNrR 199 (217)
+++..+.++...|..+ .....+|..+|++...|..|....+
T Consensus 11 l~~~~~~~~~~~~~~~-----~~~~~ia~~~~~s~~~i~~~~~~~~ 51 (55)
T cd06171 11 LPEREREVILLRFGEG-----LSYEEIAEILGISRSTVRQRLHRAL 51 (55)
T ss_pred CCHHHHHHHHHHHhcC-----CCHHHHHHHHCcCHHHHHHHHHHHH
Confidence 4556666777776533 2345679999999999998886543
No 47
>PF13371 TPR_9: Tetratricopeptide repeat
Probab=37.10 E-value=86 Score=20.47 Aligned_cols=49 Identities=22% Similarity=0.165 Sum_probs=30.4
Q ss_pred HhhcCCHHHHHHHHHhCCCCCCCcccCCCcHHHHHHHHHHhHhhhcHHHHHHhhc
Q psy11043 40 LEESGDIERLARFLWSLPVAHPNIGELNKNEAVLRARAIVSFHSGNYREMYSILE 94 (217)
Q Consensus 40 l~~~g~~~~l~~fl~slp~~~~~~~~~~~~e~vlrAr~~v~~h~~~~~~~~~lLe 94 (217)
..+.+|++.-...+..+=.. ...+-.++..++.+++..|+|.+....++
T Consensus 5 ~~~~~~~~~A~~~~~~~l~~------~p~~~~~~~~~a~~~~~~g~~~~A~~~l~ 53 (73)
T PF13371_consen 5 YLQQEDYEEALEVLERALEL------DPDDPELWLQRARCLFQLGRYEEALEDLE 53 (73)
T ss_pred HHhCCCHHHHHHHHHHHHHh------CcccchhhHHHHHHHHHhccHHHHHHHHH
Confidence 45667776665555422110 11234566778888889999998876555
No 48
>PRK09646 RNA polymerase sigma factor SigK; Reviewed
Probab=34.35 E-value=44 Score=27.02 Aligned_cols=50 Identities=16% Similarity=0.171 Sum_probs=35.4
Q ss_pred cccchHHHHHHHHHHhcCCCCCHHHHHHHHHHhCCCccccccccccchhHHHHHH
Q psy11043 152 HCFKERTRSLLREWYLQDPYPNPTKKRELAQATGLTPTQVGNWFKNRRQRDRAAA 206 (217)
Q Consensus 152 ~~f~~~~r~~L~~~f~~~~yPs~~~k~~LA~~tgLt~~qV~~WFqNrR~R~kr~~ 206 (217)
..+++..+.+|.-.|..+ ..-.++|+.+|++...|+++...-|++-|+.-
T Consensus 141 ~~L~~~~r~vl~l~~~~~-----~s~~EIA~~Lgis~~tVk~~l~ra~~~Lr~~l 190 (194)
T PRK09646 141 DALTDTQRESVTLAYYGG-----LTYREVAERLAVPLGTVKTRMRDGLIRLRDCL 190 (194)
T ss_pred HhCCHHHHHHHHHHHHcC-----CCHHHHHHHhCCChHhHHHHHHHHHHHHHHHh
Confidence 456677777776655443 23567899999999999999876666655543
No 49
>PF13432 TPR_16: Tetratricopeptide repeat; PDB: 3CVP_A 3CVL_A 3CVQ_A 3CV0_A 2GW1_B 3CVN_A 3QKY_A 2PL2_B.
Probab=34.12 E-value=1.1e+02 Score=19.58 Aligned_cols=49 Identities=14% Similarity=0.161 Sum_probs=29.8
Q ss_pred HHhhcCCHHHHHHHHHhCCCCCCCcccCCCcHHHHHHHHHHhHhhhcHHHHHHhh
Q psy11043 39 TLEESGDIERLARFLWSLPVAHPNIGELNKNEAVLRARAIVSFHSGNYREMYSIL 93 (217)
Q Consensus 39 ~l~~~g~~~~l~~fl~slp~~~~~~~~~~~~e~vlrAr~~v~~h~~~~~~~~~lL 93 (217)
.+.+.|+++.=...+..+=. ....+..++...+.+++++|++.+....+
T Consensus 6 ~~~~~g~~~~A~~~~~~~l~------~~P~~~~a~~~lg~~~~~~g~~~~A~~~~ 54 (65)
T PF13432_consen 6 ALYQQGDYDEAIAAFEQALK------QDPDNPEAWYLLGRILYQQGRYDEALAYY 54 (65)
T ss_dssp HHHHCTHHHHHHHHHHHHHC------CSTTHHHHHHHHHHHHHHTT-HHHHHHHH
T ss_pred HHHHcCCHHHHHHHHHHHHH------HCCCCHHHHHHHHHHHHHcCCHHHHHHHH
Confidence 46677887766555543321 12335677777777788899998775443
No 50
>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=34.06 E-value=54 Score=17.38 Aligned_cols=32 Identities=13% Similarity=0.142 Sum_probs=20.9
Q ss_pred HHHHHHHHhcCCCCCHHHHHHHHHHhCCCcccccccc
Q psy11043 159 RSLLREWYLQDPYPNPTKKRELAQATGLTPTQVGNWF 195 (217)
Q Consensus 159 r~~L~~~f~~~~yPs~~~k~~LA~~tgLt~~qV~~WF 195 (217)
+..+...+.. .+ ....+|..+|++...|.+|.
T Consensus 11 ~~~i~~~~~~-~~----s~~~ia~~~~is~~tv~~~~ 42 (42)
T cd00569 11 IEEARRLLAA-GE----SVAEIARRLGVSRSTLYRYL 42 (42)
T ss_pred HHHHHHHHHc-CC----CHHHHHHHHCCCHHHHHHhC
Confidence 3345555543 22 34577889999998888874
No 51
>cd04755 Commd7 COMM_Domain containing protein 7. The COMM Domain is found at the C-terminus of a variety of proteins; presumably all COMM_Domain containing proteins are located in the nucleus and the COMM domain plays a role in protein-protein interactions. Several family members have been shown to bind and inhibit NF-kappaB.
Probab=33.17 E-value=2.2e+02 Score=23.53 Aligned_cols=97 Identities=13% Similarity=0.146 Sum_probs=65.0
Q ss_pred CChhhhhhHhhHHhh----cCCHHHHHHHHHhCCCCCCCcccCC--CcHHHHHHHHHH----hHhhhcHHHHHHhhccCC
Q psy11043 28 FTVSQVATVCETLEE----SGDIERLARFLWSLPVAHPNIGELN--KNEAVLRARAIV----SFHSGNYREMYSILEHYK 97 (217)
Q Consensus 28 ~~~~q~~~vc~~l~~----~g~~~~l~~fl~slp~~~~~~~~~~--~~e~vlrAr~~v----~~h~~~~~~~~~lLe~~~ 97 (217)
+++++++.+|+.+.+ ....+++...+..+ .. .-.+. +-..|+++-.++ ++|.=.-..+..-|++.-
T Consensus 7 l~~~~f~~l~~~i~~~L~~~k~~~~~~~~~~ef-~~---~~~~~~~dlk~vi~~l~fi~~~A~k~nv~~~~L~~eL~~lg 82 (180)
T cd04755 7 LSEQQFSRLTEILFEFLLEPKESERLLNQLDEF-AG---ENGISLGPLKNIVKSILLVPNGALKRNLTAEQLREDLIQLG 82 (180)
T ss_pred CCHHHHHHHHHHHHHHHhccchHhHHHHHHHHH-HH---hcCCCHHHHHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHcC
Confidence 789999999998854 45557777777766 21 12232 234667766654 334445557777777777
Q ss_pred CCCcchhHHHHHHHHhhhHHHHHhcCCCCCC
Q psy11043 98 FTKDSHGKLQAMWLEAHYQEAEKLRGRPLGP 128 (217)
Q Consensus 98 f~~~~~~~lq~lw~~a~y~~~e~~~g~~l~~ 128 (217)
-+......+.+.|.+..-...+..+++.+.+
T Consensus 83 L~~eka~~~~~~w~~~~~~L~~~~~~~tL~~ 113 (180)
T cd04755 83 LSEEKASYFSEQWKQHYSTLSRSAVGQTLMV 113 (180)
T ss_pred CCHHHHHHHHHHHHHhHHHHHHHHHHcccCc
Confidence 7777777899999876666667777776654
No 52
>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=31.63 E-value=48 Score=21.85 Aligned_cols=39 Identities=26% Similarity=0.485 Sum_probs=29.2
Q ss_pred cchHHHHHHHHHHhcCCC--CCHHHHHHHHHHhCCCccccc
Q psy11043 154 FKERTRSLLREWYLQDPY--PNPTKKRELAQATGLTPTQVG 192 (217)
Q Consensus 154 f~~~~r~~L~~~f~~~~y--Ps~~~k~~LA~~tgLt~~qV~ 192 (217)
+++.++.+|...|...-| |-...-.+||+.+|+++.-+.
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 356778899999887554 444556789999999987654
No 53
>PRK10072 putative transcriptional regulator; Provisional
Probab=31.51 E-value=19 Score=26.66 Aligned_cols=24 Identities=21% Similarity=0.429 Sum_probs=21.2
Q ss_pred HHHHHHHhCCCccccccccccchh
Q psy11043 177 KRELAQATGLTPTQVGNWFKNRRQ 200 (217)
Q Consensus 177 k~~LA~~tgLt~~qV~~WFqNrR~ 200 (217)
..+||+.+|++...|+.|...+|.
T Consensus 49 Q~elA~~lGvS~~TVs~WE~G~r~ 72 (96)
T PRK10072 49 IDDFARVLGVSVAMVKEWESRRVK 72 (96)
T ss_pred HHHHHHHhCCCHHHHHHHHcCCCC
Confidence 567899999999999999988764
No 54
>PF13384 HTH_23: Homeodomain-like domain; PDB: 2X48_C.
Probab=30.91 E-value=16 Score=22.82 Aligned_cols=24 Identities=33% Similarity=0.596 Sum_probs=17.1
Q ss_pred HHHHHHHHhCCCccccccccccch
Q psy11043 176 KKRELAQATGLTPTQVGNWFKNRR 199 (217)
Q Consensus 176 ~k~~LA~~tgLt~~qV~~WFqNrR 199 (217)
...++|+.+|++...|..|.+..+
T Consensus 19 s~~~ia~~lgvs~~Tv~~w~kr~~ 42 (50)
T PF13384_consen 19 SIREIAKRLGVSRSTVYRWIKRYR 42 (50)
T ss_dssp -HHHHHHHHTS-HHHHHHHHT---
T ss_pred CHHHHHHHHCcCHHHHHHHHHHcc
Confidence 456789999999999999986543
No 55
>PRK06759 RNA polymerase factor sigma-70; Validated
Probab=30.75 E-value=43 Score=25.63 Aligned_cols=47 Identities=19% Similarity=0.270 Sum_probs=33.4
Q ss_pred cccchHHHHHHHHHHhcCCCCCHHHHHHHHHHhCCCccccccccccchhHHH
Q psy11043 152 HCFKERTRSLLREWYLQDPYPNPTKKRELAQATGLTPTQVGNWFKNRRQRDR 203 (217)
Q Consensus 152 ~~f~~~~r~~L~~~f~~~~yPs~~~k~~LA~~tgLt~~qV~~WFqNrR~R~k 203 (217)
..+++..+.++.-.|..+ ..-.++|..+|++...|++|...-+.+-|
T Consensus 105 ~~L~~~~r~ii~l~~~~~-----~s~~EIA~~l~is~~tV~~~~~ra~~~Lr 151 (154)
T PRK06759 105 SVLDEKEKYIIFERFFVG-----KTMGEIALETEMTYYQVRWIYRQALEKMR 151 (154)
T ss_pred HhCCHHHHHHHHHHHhcC-----CCHHHHHHHHCCCHHHHHHHHHHHHHHHh
Confidence 456777777776655443 23568899999999999999865555443
No 56
>PF13518 HTH_28: Helix-turn-helix domain
Probab=29.61 E-value=20 Score=22.31 Aligned_cols=24 Identities=33% Similarity=0.634 Sum_probs=19.4
Q ss_pred HHHHHHHhCCCccccccccccchh
Q psy11043 177 KRELAQATGLTPTQVGNWFKNRRQ 200 (217)
Q Consensus 177 k~~LA~~tgLt~~qV~~WFqNrR~ 200 (217)
...+|..+|++..+|..|.+.-+.
T Consensus 15 ~~~~a~~~gis~~tv~~w~~~y~~ 38 (52)
T PF13518_consen 15 VREIAREFGISRSTVYRWIKRYRE 38 (52)
T ss_pred HHHHHHHHCCCHhHHHHHHHHHHh
Confidence 345899999999999999875443
No 57
>PRK09644 RNA polymerase sigma factor SigM; Provisional
Probab=28.22 E-value=64 Score=25.18 Aligned_cols=53 Identities=13% Similarity=0.072 Sum_probs=36.1
Q ss_pred cccchHHHHHHHHHHhcCCCCCHHHHHHHHHHhCCCccccccccccchhHHHHHHhhh
Q psy11043 152 HCFKERTRSLLREWYLQDPYPNPTKKRELAQATGLTPTQVGNWFKNRRQRDRAAAAKN 209 (217)
Q Consensus 152 ~~f~~~~r~~L~~~f~~~~yPs~~~k~~LA~~tgLt~~qV~~WFqNrR~R~kr~~~~~ 209 (217)
..+++..+.++.-.|..+ ...+++|..+|++...|++|..--|.+-++.-.+.
T Consensus 107 ~~L~~~~r~v~~l~~~~g-----~s~~eIA~~lgis~~tv~~~l~Rar~~Lr~~l~~~ 159 (165)
T PRK09644 107 HTLPVIEAQAILLCDVHE-----LTYEEAASVLDLKLNTYKSHLFRGRKRLKALLKEE 159 (165)
T ss_pred HhCCHHHHHHHHhHHHhc-----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHhh
Confidence 445566666665443332 23567899999999999999987777766655433
No 58
>PF11791 Aconitase_B_N: Aconitate B N-terminal domain; InterPro: IPR015933 Aconitase (aconitate hydratase; 4.2.1.3 from EC) is an iron-sulphur protein that contains a [4Fe-4S]-cluster and catalyses the interconversion of isocitrate and citrate via a cis-aconitate intermediate. Aconitase functions in both the TCA and glyoxylate cycles, however unlike the majority of iron-sulphur proteins that function as electron carriers, the [4Fe-4S]-cluster of aconitase reacts directly with an enzyme substrate. In eukaryotes there is a cytosolic form (cAcn) and a mitochondrial form (mAcn) of the enzyme. In bacteria there are also 2 forms, aconitase A (AcnA) and B (AcnB). Several aconitases are known to be multi-functional enzymes with a second non-catalytic, but essential function that arises when the cellular environment changes, such as when iron levels drop [, ]. Eukaryotic cAcn and mAcn, and bacterial AcnA have the same domain organisation, consisting of three N-terminal alpha/beta/alpha domains, a linker region, followed by a C-terminal 'swivel' domain with a beta/beta/alpha structure (1-2-3-linker-4), although mAcn is small than cAcn. However, bacterial AcnB has a different organisation: it contains an N-terminal HEAT-like domain, followed by the 'swivel' domain, then the three alpha/beta/alpha domains (HEAT-4-1-2-3) []. Below is a description of some of the multi-functional activities associated with different aconitases. Eukaryotic mAcn catalyses the second step of the mitochondrial TCA cycle, which is important for energy production, providing high energy electrons in the form of NADH and FADH2 to the mitochondrial oxidative phosphorylation pathway []. The TCA cycle also provides precursors for haem and amino acid production. This enzyme has a second, non-catalytic but essential role in mitochondrial DNA (mtDNA) maintenance: mAcn acts to stabilise mtDNA, forming part of mtDNA protein-DNA complexes known as nucleoids. mAcn is thought to reversibly model nucleoids to directly influence mitochondrial gene expression in response to changes in the cellular environment. Therefore, mAcn can influence the expression of components of the oxidative phosphorylation pathway encoded in mtDNA. Eukaryotic cAcn enzyme balances the amount of citrate and isocitrate in the cytoplasm, which in turn creates a balance between the amount of NADPH generated from isocitrate by isocitrate dehydrogenase with the amount of acetyl-CoA generated from citrate by citrate lyase. Fatty acid synthesis requires both NADPH and acetyl-CoA, as do other metabolic processes, including the need for NADPH to combat oxidative stress. The enzymatic form of cAcn predominates when iron levels are normal, but if they drop sufficiently to cause the disassembly of the [4Fe-4S]-cluster, then cAcn undergoes a conformational change from a compact enzyme to a more open L-shaped protein known as iron regulatory protein 1 (IRP1; or IRE-binding protein 1, IREBP1) [, ]. As IRP1, the catalytic site and the [4Fe-4S]-cluster are lost, and two new RNA-binding sites appear. IRP1 functions in the post-transcriptional regulation of genes involved in iron metabolism - it binds to mRNA iron-responsive elements (IRE), 30-nucleotide stem-loop structures at the 3' or 5' end of specific transcripts. Transcripts containing an IRE include ferritin L and H subunits (iron storage), transferrin (iron plasma chaperone), transferrin receptor (iron uptake into cells), ferroportin (iron exporter), mAcn, succinate dehydrogenase, erythroid aminolevulinic acid synthetase (tetrapyrrole biosynthesis), among others. If the IRE is in the 5'-UTR of the transcript (e.g. in ferritin mRNA), then IRP1-binding prevents its translation by blocking the transcript from binding to the ribosome. If the IRE is in the 3'-UTR of the transcript (e.g. transferrin receptor), then IRP1-binding protects it from endonuclease degradation, thereby prolonging the half-life of the transcript and enabling it to be translated []. IRP2 is another IRE-binding protein that binds to the same transcripts as IRP1. However, since IRP1 is predominantly in the enzymatic cAcn form, it is IRP2 that acts as the major metabolic regulator that maintains iron homeostasis []. Although IRP2 is homologous to IRP1, IRP2 lacks aconitase activity, and is known only to have a single function in the post-transcriptional regulation of iron metabolism genes []. In iron-replete cells, IRP2 activity is regulated primarily by iron-dependent degradation through the ubiquitin-proteasomal system. Bacterial AcnB is also known to be multi-functional. In addition to its role in the TCA cycle, AcnB was shown to be a post-transcriptional regulator of gene expression in Escherichia coli and Salmonella enterica [, ]. In S. enterica, AcnB initiates a regulatory cascade controlling flagella biosynthesis through an interaction with the ftsH transcript, an alternative RNA polymerase sigma factor. This binding lowers the intracellular concentration of FtsH protease, which in turn enhances the amount of RNA polymerase sigma32 factor (normally degraded by FtsH protease), and sigma32 then increases the synthesis of chaperone DnaK, which in turn promotes the synthesis of the flagellar protein FliC. AcnB regulates the synthesis of other proteins as well, such as superoxide dismutase (SodA) and other enzymes involved in oxidative stress. This entry represents the N-terminal HEAT-like domain, which is present in bacterial aconitase (AcnB), but not in AcnA or eukaryotic cAcn/IRP2 or mAcn. This domain is multi-helical, forming two curved layers in a right-handed alpha-alpha superhelix. HEAT-like domains are usually implicated in protein-protein interactions. The HEAT-like domain and the 'swivel' domain that follows it were shown to be sufficient for dimerisation and for AcnB binding to mRNA. An iron-mediated dimerisation mechanism may be responsible for switching AcnB between its catalytic and regulatory roles, as dimerisation requires iron while mRNA binding is inhibited by iron. More information about these proteins can be found at Protein of the Month: Aconitase [].; GO: 0003994 aconitate hydratase activity, 0006099 tricarboxylic acid cycle; PDB: 1L5J_B.
Probab=27.95 E-value=63 Score=26.19 Aligned_cols=39 Identities=26% Similarity=0.426 Sum_probs=20.5
Q ss_pred CCCCCCCCChhhhhhHhhHHhhc--CCHHHHHHHHH-hCCCC
Q psy11043 21 FALPTLNFTVSQVATVCETLEES--GDIERLARFLW-SLPVA 59 (217)
Q Consensus 21 ~~~~~~~~~~~q~~~vc~~l~~~--g~~~~l~~fl~-slp~~ 59 (217)
.++|.+.++.+|++.+|+-|... |+-+-|..+|. ..||-
T Consensus 12 ~GipPlPL~a~Qt~~lielLk~~~~~~~~~lldLL~~RV~PG 53 (154)
T PF11791_consen 12 LGIPPLPLNAEQTAELIELLKNPPAGEEAFLLDLLTNRVPPG 53 (154)
T ss_dssp TT-------HHHHHHHHHHHHS--TT-HHHHHHHHHHSS--T
T ss_pred CCCCCCCCCHHHHHHHHHHHhCCCCccHHHHHHHHHhcCCCC
Confidence 35788899999999999988864 45566655554 67763
No 59
>PRK12526 RNA polymerase sigma factor; Provisional
Probab=27.59 E-value=64 Score=26.44 Aligned_cols=50 Identities=14% Similarity=0.221 Sum_probs=34.0
Q ss_pred cccchHHHHHHHHHHhcCCCCCHHHHHHHHHHhCCCccccccccccchhHHHHHH
Q psy11043 152 HCFKERTRSLLREWYLQDPYPNPTKKRELAQATGLTPTQVGNWFKNRRQRDRAAA 206 (217)
Q Consensus 152 ~~f~~~~r~~L~~~f~~~~yPs~~~k~~LA~~tgLt~~qV~~WFqNrR~R~kr~~ 206 (217)
..+++..+.++.-.|..+ ..-+++|..+|++...|+++...-+.+-++.-
T Consensus 152 ~~L~~~~r~vl~l~~~~g-----~s~~EIA~~lgis~~tV~~~l~Ra~~~Lr~~l 201 (206)
T PRK12526 152 EKLPEAQQTVVKGVYFQE-----LSQEQLAQQLNVPLGTVKSRLRLALAKLKVQM 201 (206)
T ss_pred HhCCHHHHHHHHHHHHcC-----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 345666666666544332 23567899999999999998876666655543
No 60
>cd01392 HTH_LacI Helix-turn-helix (HTH) DNA binding domain of the LacI family of transcriptional regulators. HTH-DNA binding domain of the LacI (lactose operon repressor) family of bacterial transcriptional regulators and their putative homologs found in plants. The LacI family has more than 500 members distributed among almost all bacterial species. The monomeric proteins of the LacI family contain common structural features that include a small DNA-binding domain with a helix-turn-helix motif in the N-terminus, a regulatory ligand-binding domain which exhibits the type I periplasmic binding protein fold in the C-terminus for oligomerization and for effector binding, and an approximately 18-amino acid linker connecting these two functional domains. In LacI-like transcriptional regulators, the ligands are monosaccharides including lactose, ribose, fructose, xylose, arabinose, galactose/glucose, and other sugars, with a few exceptions. When the C-terminal domain of the LacI family repre
Probab=26.41 E-value=19 Score=22.57 Aligned_cols=21 Identities=19% Similarity=0.439 Sum_probs=19.0
Q ss_pred HHHHHhCCCccccccccccch
Q psy11043 179 ELAQATGLTPTQVGNWFKNRR 199 (217)
Q Consensus 179 ~LA~~tgLt~~qV~~WFqNrR 199 (217)
+||+.+|++...|+.|+.|..
T Consensus 2 ~lA~~~gvs~~tvs~~l~g~~ 22 (52)
T cd01392 2 DIARAAGVSVATVSRVLNGKP 22 (52)
T ss_pred cHHHHHCcCHHHHHHHHcCCC
Confidence 589999999999999999883
No 61
>KOG3623|consensus
Probab=26.21 E-value=2e+02 Score=29.33 Aligned_cols=44 Identities=18% Similarity=0.219 Sum_probs=33.1
Q ss_pred HHHHHHhcCCCCCHHHHHHHHHHhCCCccccccccccchhHHHH
Q psy11043 161 LLREWYLQDPYPNPTKKRELAQATGLTPTQVGNWFKNRRQRDRA 204 (217)
Q Consensus 161 ~L~~~f~~~~yPs~~~k~~LA~~tgLt~~qV~~WFqNrR~R~kr 204 (217)
.|...|..+--|+..+-..++..+...+..|.+||.+|+.+-+.
T Consensus 640 ql~~a~elq~s~~n~~~pl~~t~~~n~~pv~ev~dhsrsstpsp 683 (1007)
T KOG3623|consen 640 QLKQAYELQASPSNDEFPLIATRLQNDPPVVEVWDHSRSSTPSP 683 (1007)
T ss_pred hhHhhhhcccCccCcccchhhhhccCCCcchhhcccCCCCCCCC
Confidence 57777777666776666666666777888899999999877554
No 62
>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=26.13 E-value=24 Score=22.27 Aligned_cols=23 Identities=22% Similarity=0.471 Sum_probs=19.2
Q ss_pred HHHHHHHhCCCccccccccccch
Q psy11043 177 KRELAQATGLTPTQVGNWFKNRR 199 (217)
Q Consensus 177 k~~LA~~tgLt~~qV~~WFqNrR 199 (217)
..+||+.+|++...|..|..+.+
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 36789999999999999998855
No 63
>PF06056 Terminase_5: Putative ATPase subunit of terminase (gpP-like); InterPro: IPR010332 This family of proteins are annotated as ATPase subunits of phage terminase after []. Terminases are viral proteins that are involved in packaging viral DNA into the capsid.; GO: 0005524 ATP binding, 0019069 viral capsid assembly
Probab=25.87 E-value=29 Score=23.25 Aligned_cols=20 Identities=25% Similarity=0.511 Sum_probs=17.3
Q ss_pred HHHHHHHhCCCccccccccc
Q psy11043 177 KRELAQATGLTPTQVGNWFK 196 (217)
Q Consensus 177 k~~LA~~tgLt~~qV~~WFq 196 (217)
..+||+.+|++...|.+|-+
T Consensus 16 ~~eIA~~Lg~~~~TV~~W~~ 35 (58)
T PF06056_consen 16 IKEIAEELGVPRSTVYSWKD 35 (58)
T ss_pred HHHHHHHHCCChHHHHHHHH
Confidence 45789999999999999964
No 64
>PRK09642 RNA polymerase sigma factor SigW; Reviewed
Probab=25.45 E-value=80 Score=24.36 Aligned_cols=50 Identities=16% Similarity=0.161 Sum_probs=33.7
Q ss_pred cccchHHHHHHHHHHhcCCCCCHHHHHHHHHHhCCCccccccccccchhHHHHHH
Q psy11043 152 HCFKERTRSLLREWYLQDPYPNPTKKRELAQATGLTPTQVGNWFKNRRQRDRAAA 206 (217)
Q Consensus 152 ~~f~~~~r~~L~~~f~~~~yPs~~~k~~LA~~tgLt~~qV~~WFqNrR~R~kr~~ 206 (217)
..+++..+.++.-.|...- .-.++|..+|++...|++....-|.+-|+.-
T Consensus 105 ~~Lp~~~r~v~~l~~~~g~-----s~~EIA~~lgis~~tV~~~l~Rar~~Lr~~l 154 (160)
T PRK09642 105 RELPENYRDVVLAHYLEEK-----SYQEIALQEKIEVKTVEMKLYRARKWIKKHW 154 (160)
T ss_pred HhCCHHHHHHHHHHHHhCC-----CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 3455666666655544321 2457899999999999999876666655543
No 65
>PRK00118 putative DNA-binding protein; Validated
Probab=25.12 E-value=94 Score=23.39 Aligned_cols=49 Identities=18% Similarity=0.241 Sum_probs=34.5
Q ss_pred ccchHHHHHHHHHHhcCCCCCHHHHHHHHHHhCCCccccccccccchhHHHHHH
Q psy11043 153 CFKERTRSLLREWYLQDPYPNPTKKRELAQATGLTPTQVGNWFKNRRQRDRAAA 206 (217)
Q Consensus 153 ~f~~~~r~~L~~~f~~~~yPs~~~k~~LA~~tgLt~~qV~~WFqNrR~R~kr~~ 206 (217)
.+++..+.++.-+|...- ...++|+.+|++...|.+|....|.+-+..-
T Consensus 17 ~L~ekqRevl~L~y~eg~-----S~~EIAe~lGIS~~TV~r~L~RArkkLr~~~ 65 (104)
T PRK00118 17 LLTEKQRNYMELYYLDDY-----SLGEIAEEFNVSRQAVYDNIKRTEKLLEDYE 65 (104)
T ss_pred cCCHHHHHHHHHHHHcCC-----CHHHHHHHHCcCHHHHHHHHHHHHHHHHHHH
Confidence 345666667766665532 3456899999999999999987666665543
No 66
>cd04761 HTH_MerR-SF Helix-Turn-Helix DNA binding domain of transcription regulators from the MerR superfamily. Helix-turn-helix (HTH) transcription regulator MerR superfamily, N-terminal domain. The MerR family transcription regulators have been shown to mediate responses to stress including exposure to heavy metals, drugs, or oxygen radicals in eubacterial and some archaeal species. They regulate transcription of multidrug/metal ion transporter genes and oxidative stress regulons by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.
Probab=24.62 E-value=27 Score=21.38 Aligned_cols=21 Identities=29% Similarity=0.466 Sum_probs=17.6
Q ss_pred HHHHHHhCCCccccccccccc
Q psy11043 178 RELAQATGLTPTQVGNWFKNR 198 (217)
Q Consensus 178 ~~LA~~tgLt~~qV~~WFqNr 198 (217)
.++|+.+|++...|+.|-++-
T Consensus 4 ~e~a~~~gv~~~tlr~~~~~g 24 (49)
T cd04761 4 GELAKLTGVSPSTLRYYERIG 24 (49)
T ss_pred HHHHHHHCcCHHHHHHHHHCC
Confidence 468999999999999997544
No 67
>PF13411 MerR_1: MerR HTH family regulatory protein; PDB: 2JML_A 3GP4_A 3GPV_B.
Probab=24.55 E-value=30 Score=23.01 Aligned_cols=19 Identities=21% Similarity=0.541 Sum_probs=16.3
Q ss_pred HHHHHHhCCCccccccccc
Q psy11043 178 RELAQATGLTPTQVGNWFK 196 (217)
Q Consensus 178 ~~LA~~tgLt~~qV~~WFq 196 (217)
.++|+.+|++...|+.|=+
T Consensus 4 ~eva~~~gvs~~tlr~y~~ 22 (69)
T PF13411_consen 4 KEVAKLLGVSPSTLRYYER 22 (69)
T ss_dssp HHHHHHTTTTHHHHHHHHH
T ss_pred HHHHHHHCcCHHHHHHHHH
Confidence 4789999999999999943
No 68
>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=24.43 E-value=29 Score=21.75 Aligned_cols=23 Identities=13% Similarity=0.195 Sum_probs=20.1
Q ss_pred HHHHHHHhCCCccccccccccch
Q psy11043 177 KRELAQATGLTPTQVGNWFKNRR 199 (217)
Q Consensus 177 k~~LA~~tgLt~~qV~~WFqNrR 199 (217)
...||..+|++...|+.|..+++
T Consensus 18 q~~lA~~~gvs~~~vs~~e~g~~ 40 (58)
T TIGR03070 18 QADLADLAGVGLRFIRDVENGKP 40 (58)
T ss_pred HHHHHHHhCCCHHHHHHHHCCCC
Confidence 46789999999999999998764
No 69
>PF13443 HTH_26: Cro/C1-type HTH DNA-binding domain; PDB: 3TYR_A 3TYS_A 3B7H_A.
Probab=23.36 E-value=1e+02 Score=19.85 Aligned_cols=20 Identities=20% Similarity=0.365 Sum_probs=7.1
Q ss_pred CCCHHHHHHHHHHhCCCccc
Q psy11043 171 YPNPTKKRELAQATGLTPTQ 190 (217)
Q Consensus 171 yPs~~~k~~LA~~tgLt~~q 190 (217)
.|+...-..||..+|+++.+
T Consensus 37 ~~~~~~l~~ia~~l~~~~~e 56 (63)
T PF13443_consen 37 NPSLDTLEKIAKALNCSPEE 56 (63)
T ss_dssp ---HHHHHHHHHHHT--HHH
T ss_pred cccHHHHHHHHHHcCCCHHH
Confidence 44444444444444444443
No 70
>PRK12512 RNA polymerase sigma factor; Provisional
Probab=22.73 E-value=87 Score=24.82 Aligned_cols=49 Identities=12% Similarity=0.110 Sum_probs=35.5
Q ss_pred cccchHHHHHHHHHHhcCCCCCHHHHHHHHHHhCCCccccccccccchhHHHHH
Q psy11043 152 HCFKERTRSLLREWYLQDPYPNPTKKRELAQATGLTPTQVGNWFKNRRQRDRAA 205 (217)
Q Consensus 152 ~~f~~~~r~~L~~~f~~~~yPs~~~k~~LA~~tgLt~~qV~~WFqNrR~R~kr~ 205 (217)
..+++..+.++.-.|..+ ..-.++|..+|++...|.++...-|.+-|..
T Consensus 130 ~~L~~~~r~v~~l~~~~g-----~s~~eIA~~l~is~~tV~~~l~ra~~~Lr~~ 178 (184)
T PRK12512 130 ETLPPRQRDVVQSISVEG-----ASIKETAAKLSMSEGAVRVALHRGLAALAAK 178 (184)
T ss_pred HhCCHHHHHHHHHHHHcC-----CCHHHHHHHhCCCHHHHHHHHHHHHHHHHHH
Confidence 456667777776665443 2356789999999999999998777666654
No 71
>PRK12514 RNA polymerase sigma factor; Provisional
Probab=22.42 E-value=1e+02 Score=24.31 Aligned_cols=48 Identities=17% Similarity=0.332 Sum_probs=31.9
Q ss_pred cccchHHHHHHHHHHhcCCCCCHHHHHHHHHHhCCCccccccccccchhHHHH
Q psy11043 152 HCFKERTRSLLREWYLQDPYPNPTKKRELAQATGLTPTQVGNWFKNRRQRDRA 204 (217)
Q Consensus 152 ~~f~~~~r~~L~~~f~~~~yPs~~~k~~LA~~tgLt~~qV~~WFqNrR~R~kr 204 (217)
..+++..+.++.-.|..+ ...+++|..+|++...|+++...-|.+-|+
T Consensus 128 ~~L~~~~r~i~~l~~~~g-----~s~~eIA~~lgis~~tV~~~l~Rar~~Lr~ 175 (179)
T PRK12514 128 EELEKDRAAAVRRAYLEG-----LSYKELAERHDVPLNTMRTWLRRSLLKLRE 175 (179)
T ss_pred HhCCHHHHHHHHHHHHcC-----CCHHHHHHHHCCChHHHHHHHHHHHHHHHH
Confidence 345556666555555332 125678999999999999888765555554
No 72
>PRK12515 RNA polymerase sigma factor; Provisional
Probab=22.35 E-value=1e+02 Score=24.67 Aligned_cols=51 Identities=12% Similarity=0.190 Sum_probs=35.3
Q ss_pred cccchHHHHHHHHHHhcCCCCCHHHHHHHHHHhCCCccccccccccchhHHHHHHh
Q psy11043 152 HCFKERTRSLLREWYLQDPYPNPTKKRELAQATGLTPTQVGNWFKNRRQRDRAAAA 207 (217)
Q Consensus 152 ~~f~~~~r~~L~~~f~~~~yPs~~~k~~LA~~tgLt~~qV~~WFqNrR~R~kr~~~ 207 (217)
..+++..+.+|.-.|... ..-.++|..+|++...|++-...-|.+-++.-.
T Consensus 130 ~~L~~~~r~vl~l~~~~~-----~s~~eIA~~lgis~~tV~~~l~Rar~~Lr~~l~ 180 (189)
T PRK12515 130 AKLSPAHREIIDLVYYHE-----KSVEEVGEIVGIPESTVKTRMFYARKKLAELLK 180 (189)
T ss_pred HhCCHHHHHHHHHHHHcC-----CCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHH
Confidence 456666666666554433 234678999999999999988776766665443
No 73
>PRK09652 RNA polymerase sigma factor RpoE; Provisional
Probab=22.03 E-value=86 Score=24.34 Aligned_cols=47 Identities=19% Similarity=0.179 Sum_probs=32.5
Q ss_pred ccchHHHHHHHHHHhcCCCCCHHHHHHHHHHhCCCccccccccccchhHHHH
Q psy11043 153 CFKERTRSLLREWYLQDPYPNPTKKRELAQATGLTPTQVGNWFKNRRQRDRA 204 (217)
Q Consensus 153 ~f~~~~r~~L~~~f~~~~yPs~~~k~~LA~~tgLt~~qV~~WFqNrR~R~kr 204 (217)
.+++..+.++.-.|..+ ..-.++|..+|++...|++|...-+.+-++
T Consensus 128 ~L~~~~r~vl~l~~~~~-----~s~~eIA~~lgis~~tV~~~l~ra~~~Lr~ 174 (182)
T PRK09652 128 SLPEELRTAITLREIEG-----LSYEEIAEIMGCPIGTVRSRIFRAREALRA 174 (182)
T ss_pred hCCHHHHHHHHHHHHcC-----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 46666666666554432 124578999999999999999865555554
No 74
>TIGR02939 RpoE_Sigma70 RNA polymerase sigma factor RpoE. A sigma factor is a DNA-binding protein protein that binds to the DNA-directed RNA polymerase core to produce the holoenzyme capable of initiating transcription at specific sites. Different sigma factors act in vegetative growth, heat shock, extracytoplasmic functions (ECF), etc. This model represents the clade of sigma factors called RpoE. This protein may be called sigma-24, sigma-E factor, sigma-H factor, fecI-like sigma factor or alternative sigma factor AlgU.
Probab=21.83 E-value=68 Score=25.42 Aligned_cols=29 Identities=10% Similarity=0.024 Sum_probs=22.3
Q ss_pred HHHHHHHHhCCCccccccccccchhHHHH
Q psy11043 176 KKRELAQATGLTPTQVGNWFKNRRQRDRA 204 (217)
Q Consensus 176 ~k~~LA~~tgLt~~qV~~WFqNrR~R~kr 204 (217)
.-.++|..+|++...|+++...-|.+-|+
T Consensus 156 s~~EIA~~lgis~~tv~~~l~rar~~Lr~ 184 (190)
T TIGR02939 156 SYEDIARIMDCPVGTVRSRIFRAREAIAI 184 (190)
T ss_pred CHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 45688999999999999988655555444
No 75
>PRK05602 RNA polymerase sigma factor; Reviewed
Probab=21.72 E-value=98 Score=24.62 Aligned_cols=51 Identities=22% Similarity=0.236 Sum_probs=33.6
Q ss_pred ccchHHHHHHHHHHhcCCCCCHHHHHHHHHHhCCCccccccccccchhHHHHHHhh
Q psy11043 153 CFKERTRSLLREWYLQDPYPNPTKKRELAQATGLTPTQVGNWFKNRRQRDRAAAAK 208 (217)
Q Consensus 153 ~f~~~~r~~L~~~f~~~~yPs~~~k~~LA~~tgLt~~qV~~WFqNrR~R~kr~~~~ 208 (217)
.++++.+.++.-.|... ..-.++|..+|++...|+++...-|.+-|+.-..
T Consensus 128 ~L~~~~r~i~~l~~~~g-----~s~~EIA~~lgis~~tV~~~l~Rar~~Lr~~l~~ 178 (186)
T PRK05602 128 ALPERQREAIVLQYYQG-----LSNIEAAAVMDISVDALESLLARGRRALRAQLAD 178 (186)
T ss_pred hCCHHHHHHhhHHHhcC-----CCHHHHHHHhCcCHHHHHHHHHHHHHHHHHHHHh
Confidence 34555555555444322 2346789999999999999987666666654443
No 76
>PRK03975 tfx putative transcriptional regulator; Provisional
Probab=21.50 E-value=1.2e+02 Score=24.11 Aligned_cols=49 Identities=22% Similarity=0.243 Sum_probs=35.4
Q ss_pred ccchHHHHHHHHHHhcCCCCCHHHHHHHHHHhCCCccccccccccchhHHHHHHh
Q psy11043 153 CFKERTRSLLREWYLQDPYPNPTKKRELAQATGLTPTQVGNWFKNRRQRDRAAAA 207 (217)
Q Consensus 153 ~f~~~~r~~L~~~f~~~~yPs~~~k~~LA~~tgLt~~qV~~WFqNrR~R~kr~~~ 207 (217)
.+++..+.+|.-. ... ....++|..+|++...|+.|-.+.+.+-++...
T Consensus 6 ~Lt~rqreVL~lr-~~G-----lTq~EIAe~LGiS~~tVs~ie~ra~kkLr~~~~ 54 (141)
T PRK03975 6 FLTERQIEVLRLR-ERG-----LTQQEIADILGTSRANVSSIEKRARENIEKARE 54 (141)
T ss_pred CCCHHHHHHHHHH-HcC-----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Confidence 4566677788663 222 234578999999999999999987777666543
No 77
>KOG4330|consensus
Probab=20.90 E-value=1.3e+02 Score=25.09 Aligned_cols=20 Identities=35% Similarity=0.557 Sum_probs=16.4
Q ss_pred CCCChhhhhhHhhHHhhcCC
Q psy11043 26 LNFTVSQVATVCETLEESGD 45 (217)
Q Consensus 26 ~~~~~~q~~~vc~~l~~~g~ 45 (217)
-.|+..||--|||.|+....
T Consensus 144 ~~FTlrqVqmICErllKerE 163 (206)
T KOG4330|consen 144 PLFTLRQVQMICERLLKERE 163 (206)
T ss_pred chhhHHHHHHHHHHHHHHHH
Confidence 45999999999999986543
No 78
>TIGR02948 SigW_bacill RNA polymerase sigma-W factor. This sigma factor is restricted to certain lineages of the order Bacillales.
Probab=20.78 E-value=84 Score=24.78 Aligned_cols=48 Identities=15% Similarity=0.214 Sum_probs=32.0
Q ss_pred cccchHHHHHHHHHHhcCCCCCHHHHHHHHHHhCCCccccccccccchhHHHH
Q psy11043 152 HCFKERTRSLLREWYLQDPYPNPTKKRELAQATGLTPTQVGNWFKNRRQRDRA 204 (217)
Q Consensus 152 ~~f~~~~r~~L~~~f~~~~yPs~~~k~~LA~~tgLt~~qV~~WFqNrR~R~kr 204 (217)
..+++..+.++.-.|.. ...-.++|..+|++...|+++...-|.+-+.
T Consensus 135 ~~L~~~~r~v~~l~~~~-----g~s~~eIA~~lgis~~~v~~~l~Rar~~Lr~ 182 (187)
T TIGR02948 135 QALPPKYRMVIVLKYME-----DLSLKEISEILDLPVGTVKTRIHRGREALRK 182 (187)
T ss_pred HhCCHHHhHHhhhHHhc-----CCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 34555666665554332 2235678999999999999998766665554
No 79
>PF08452 DNAP_B_exo_N: DNA polymerase family B exonuclease domain, N-terminal; InterPro: IPR013660 This domain is found in viral DNA polymerases to the N terminus of DNA polymerase family B exonuclease domains (IPR006133 from INTERPRO). ; GO: 0003887 DNA-directed DNA polymerase activity
Probab=20.56 E-value=33 Score=18.50 Aligned_cols=8 Identities=50% Similarity=1.095 Sum_probs=6.3
Q ss_pred ccccccch
Q psy11043 192 GNWFKNRR 199 (217)
Q Consensus 192 ~~WFqNrR 199 (217)
-|||-|+.
T Consensus 6 iNWFE~~g 13 (22)
T PF08452_consen 6 INWFESRG 13 (22)
T ss_pred eehhhhCC
Confidence 48998875
No 80
>TIGR02999 Sig-70_X6 RNA polymerase sigma factor, TIGR02999 family. This group of sigma factors are members of the sigma-70 family (TIGR02937) and are found in a variety of species including Rhodopirellula baltica which encodes a paralogous group of five.
Probab=20.54 E-value=1e+02 Score=24.29 Aligned_cols=46 Identities=13% Similarity=0.159 Sum_probs=33.0
Q ss_pred cchHHHHHHHHHHhcCCCCCHHHHHHHHHHhCCCccccccccccchhHHHH
Q psy11043 154 FKERTRSLLREWYLQDPYPNPTKKRELAQATGLTPTQVGNWFKNRRQRDRA 204 (217)
Q Consensus 154 f~~~~r~~L~~~f~~~~yPs~~~k~~LA~~tgLt~~qV~~WFqNrR~R~kr 204 (217)
++++.+.++.-.|...- .-.++|..+|++...|++....-|.+-++
T Consensus 135 Lp~~~r~v~~l~~~~g~-----s~~EIA~~lgis~~tVk~~l~Rar~~Lr~ 180 (183)
T TIGR02999 135 VDPRQAEVVELRFFAGL-----TVEEIAELLGVSVRTVERDWRFARAWLAD 180 (183)
T ss_pred CCHHHHHHHHHHHHcCC-----CHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Confidence 77777777776655432 35678999999999999988755555443
No 81
>PRK11924 RNA polymerase sigma factor; Provisional
Probab=20.52 E-value=1.2e+02 Score=23.46 Aligned_cols=47 Identities=21% Similarity=0.310 Sum_probs=31.2
Q ss_pred cchHHHHHHHHHHhcCCCCCHHHHHHHHHHhCCCccccccccccchhHHHHH
Q psy11043 154 FKERTRSLLREWYLQDPYPNPTKKRELAQATGLTPTQVGNWFKNRRQRDRAA 205 (217)
Q Consensus 154 f~~~~r~~L~~~f~~~~yPs~~~k~~LA~~tgLt~~qV~~WFqNrR~R~kr~ 205 (217)
+++..+.++...|..+ ..-.++|..+|++...|++|..--|.+-|+.
T Consensus 126 L~~~~r~i~~l~~~~~-----~~~~eIA~~lgis~~tv~~~~~ra~~~lr~~ 172 (179)
T PRK11924 126 LPVKQREVFLLRYVEG-----LSYREIAEILGVPVGTVKSRLRRARQLLREC 172 (179)
T ss_pred CCHHHHHHhhHHHHcC-----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 4445555554444322 2346889999999999999997666665543
No 82
>KOG3755|consensus
Probab=20.52 E-value=57 Score=32.18 Aligned_cols=54 Identities=22% Similarity=0.344 Sum_probs=0.0
Q ss_pred HHHHhcCCCCCHHHHHHHHHHhCCCc-------cccccccccchhHHHHHHhhhhhhhccC
Q psy11043 163 REWYLQDPYPNPTKKRELAQATGLTP-------TQVGNWFKNRRQRDRAAAAKNRLEVKTQ 216 (217)
Q Consensus 163 ~~~f~~~~yPs~~~k~~LA~~tgLt~-------~qV~~WFqNrR~R~kr~~~~~~~~~~~~ 216 (217)
+.||..+..++-....+--+...+.+ .-|..||+|||.++++.+..-...++.+
T Consensus 708 ~~w~~k~~s~s~~~v~eYkee~~~~~~~e~~~~kn~~~~fk~~~ee~~~~k~~~d~n~~~~ 768 (769)
T KOG3755|consen 708 HHWKLKTRSGSWVDVAEYKEEELLMPYEEKFESKNVQFWFKVRREEEKRLKMSYDSNQDAQ 768 (769)
T ss_pred hhheecccCchhHHHHHhhHHhhcchhhhhhhhcchHHHHHHHHHHHhhhhccCCchhhhc
No 83
>TIGR02937 sigma70-ECF RNA polymerase sigma factor, sigma-70 family. Several PFAM models hit segments of these sequences including Sigma-70 region 2 (pfam04542) and Sigma-70, region 4 (pfam04545), but not always above their respective trusted cutoffs.
Probab=20.37 E-value=96 Score=22.75 Aligned_cols=46 Identities=28% Similarity=0.404 Sum_probs=30.0
Q ss_pred ccchHHHHHHHHHHhcCCCCCHHHHHHHHHHhCCCccccccccccchhHHH
Q psy11043 153 CFKERTRSLLREWYLQDPYPNPTKKRELAQATGLTPTQVGNWFKNRRQRDR 203 (217)
Q Consensus 153 ~f~~~~r~~L~~~f~~~~yPs~~~k~~LA~~tgLt~~qV~~WFqNrR~R~k 203 (217)
.+++..+.++...|.. .+ ...++|..+|++...|+++...-+.+-|
T Consensus 110 ~L~~~~~~ii~~~~~~-g~----s~~eIA~~l~~s~~~v~~~~~~~~~kl~ 155 (158)
T TIGR02937 110 KLPEREREVLVLRYLE-GL----SYKEIAEILGISVGTVKRRLKRARKKLR 155 (158)
T ss_pred hCCHHHHHHHhhHHhc-CC----CHHHHHHHHCCCHHHHHHHHHHHHHHHH
Confidence 3445555565544332 22 3457899999999999998876555544
No 84
>TIGR02989 Sig-70_gvs1 RNA polymerase sigma-70 factor, Rhodopirellula/Verrucomicrobium family. This group of sigma factors are members of the sigma-70 family (TIGR02937) and are abundantly found in the species Rhodopirellula baltica (11), and Verrucomicrobium spinosum (16) and to a lesser extent in Gemmata obscuriglobus (2).
Probab=20.28 E-value=90 Score=23.89 Aligned_cols=45 Identities=29% Similarity=0.295 Sum_probs=30.5
Q ss_pred cccchHHHHHHHHHHhcCCCCCHHHHHHHHHHhCCCccccccccccchhH
Q psy11043 152 HCFKERTRSLLREWYLQDPYPNPTKKRELAQATGLTPTQVGNWFKNRRQR 201 (217)
Q Consensus 152 ~~f~~~~r~~L~~~f~~~~yPs~~~k~~LA~~tgLt~~qV~~WFqNrR~R 201 (217)
..+++..+.++.-.|... ..-.++|..+|++...|.++...-|.+
T Consensus 110 ~~L~~~~r~v~~l~~~~g-----~~~~eIA~~l~is~~tv~~~l~Rar~~ 154 (159)
T TIGR02989 110 EKLPERQRELLQLRYQRG-----VSLTALAEQLGRTVNAVYKALSRLRVR 154 (159)
T ss_pred HHCCHHHHHHHHHHHhcC-----CCHHHHHHHhCCCHHHHHHHHHHHHHH
Confidence 456667777777655432 235678999999999999876544433
Done!