Query psy8980
Match_columns 355
No_of_seqs 362 out of 1901
Neff 6.5
Searched_HMMs 46136
Date Sat Aug 17 00:36:27 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy8980.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/8980hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG0774|consensus 100.0 1.6E-79 3.5E-84 561.7 27.4 266 33-312 8-273 (334)
2 PF03792 PBC: PBC domain; Int 100.0 4.5E-58 9.8E-63 406.5 18.7 190 29-226 2-191 (191)
3 KOG3802|consensus 99.7 1E-17 2.3E-22 163.6 7.3 127 159-290 205-354 (398)
4 KOG0775|consensus 99.7 4.2E-16 9.2E-21 145.3 10.4 122 143-288 113-234 (304)
5 KOG0484|consensus 99.6 7.4E-16 1.6E-20 124.5 4.9 66 225-293 15-80 (125)
6 KOG0488|consensus 99.5 8.6E-15 1.9E-19 142.1 6.8 66 225-293 170-235 (309)
7 KOG0485|consensus 99.5 9.5E-15 2.1E-19 132.2 5.3 70 226-298 103-172 (268)
8 PF00046 Homeobox: Homeobox do 99.5 7.8E-15 1.7E-19 107.4 2.7 57 228-287 1-57 (57)
9 KOG0850|consensus 99.5 7.5E-14 1.6E-18 127.6 8.2 65 224-291 119-183 (245)
10 KOG0489|consensus 99.5 1.2E-14 2.7E-19 138.2 2.6 64 226-292 158-221 (261)
11 KOG0842|consensus 99.5 2.9E-14 6.2E-19 136.9 5.1 70 226-298 152-221 (307)
12 KOG0843|consensus 99.5 3.1E-14 6.7E-19 125.7 4.6 62 226-290 101-162 (197)
13 KOG0487|consensus 99.4 4.2E-14 9.1E-19 135.8 2.8 63 225-290 233-295 (308)
14 KOG0492|consensus 99.4 1.9E-13 4.1E-18 123.1 6.1 69 226-297 143-211 (246)
15 cd00086 homeodomain Homeodomai 99.4 1.5E-13 3.2E-18 100.6 3.7 57 229-288 2-58 (59)
16 KOG1168|consensus 99.4 1.5E-13 3.3E-18 129.0 4.0 123 157-289 217-368 (385)
17 smart00389 HOX Homeodomain. DN 99.4 1.8E-13 3.9E-18 99.5 3.5 55 229-286 2-56 (56)
18 KOG2251|consensus 99.4 3.9E-13 8.5E-18 122.4 5.5 67 222-291 32-98 (228)
19 KOG0848|consensus 99.4 2.9E-13 6.3E-18 126.0 4.7 63 228-293 200-262 (317)
20 PF05920 Homeobox_KN: Homeobox 99.3 4.9E-13 1.1E-17 91.6 1.3 40 245-284 1-40 (40)
21 KOG0494|consensus 99.3 2.4E-12 5.1E-17 119.5 3.7 64 227-293 140-204 (332)
22 KOG0493|consensus 99.2 3.4E-12 7.5E-17 118.5 3.1 61 227-290 246-306 (342)
23 TIGR01565 homeo_ZF_HD homeobox 99.2 7.5E-12 1.6E-16 92.4 4.3 52 228-282 2-57 (58)
24 KOG0491|consensus 99.2 3.1E-12 6.6E-17 111.6 1.3 64 227-293 100-163 (194)
25 KOG0486|consensus 99.2 1.5E-11 3.2E-16 117.0 3.3 70 221-293 106-175 (351)
26 KOG0773|consensus 99.2 1.4E-10 3.1E-15 114.2 10.1 64 227-290 239-302 (342)
27 COG5576 Homeodomain-containing 99.1 5.3E-11 1.2E-15 104.9 5.2 63 226-291 50-112 (156)
28 KOG0483|consensus 99.1 2.5E-11 5.4E-16 110.6 3.0 60 228-290 51-110 (198)
29 KOG4577|consensus 99.0 1.3E-10 2.9E-15 109.3 4.3 64 227-293 167-230 (383)
30 KOG0844|consensus 99.0 5.9E-11 1.3E-15 112.4 1.6 61 228-291 182-242 (408)
31 KOG0847|consensus 98.9 2.2E-10 4.8E-15 104.2 1.6 61 227-290 167-227 (288)
32 KOG0490|consensus 98.7 6.4E-09 1.4E-13 96.1 3.6 63 225-290 58-120 (235)
33 KOG0849|consensus 98.5 1.6E-07 3.4E-12 93.3 7.4 63 226-291 175-237 (354)
34 PF03790 KNOX1: KNOX1 domain ; 98.4 3.3E-07 7.1E-12 63.9 3.3 41 55-106 2-42 (45)
35 KOG2252|consensus 98.1 3.5E-06 7.6E-11 86.2 5.9 58 225-285 418-475 (558)
36 KOG0490|consensus 97.3 0.00021 4.5E-09 65.9 3.8 62 225-289 151-212 (235)
37 PF03791 KNOX2: KNOX2 domain ; 97.1 0.00069 1.5E-08 48.9 4.3 35 145-179 8-42 (52)
38 KOG1146|consensus 96.6 0.002 4.4E-08 72.1 4.7 60 227-289 903-962 (1406)
39 PF11569 Homez: Homeodomain le 96.5 0.00046 9.9E-09 50.5 -0.7 42 239-283 10-51 (56)
40 KOG0773|consensus 95.7 0.0018 4E-08 63.9 -1.5 114 149-291 45-158 (342)
41 KOG3623|consensus 90.3 0.17 3.7E-06 54.1 2.4 48 239-289 568-615 (1007)
42 PF04218 CENP-B_N: CENP-B N-te 88.4 0.52 1.1E-05 34.0 3.0 46 228-281 1-46 (53)
43 PF08281 Sigma70_r4_2: Sigma-7 55.0 11 0.00025 26.3 2.4 44 233-284 10-53 (54)
44 PF04545 Sigma70_r4: Sigma-70, 52.8 10 0.00022 26.3 1.8 46 233-286 4-49 (50)
45 PF03791 KNOX2: KNOX2 domain ; 48.9 95 0.0021 22.5 6.3 39 140-178 10-48 (52)
46 PF01527 HTH_Tnp_1: Transposas 46.0 7.3 0.00016 29.2 0.2 42 229-278 2-44 (76)
47 cd06171 Sigma70_r4 Sigma70, re 45.3 9.6 0.00021 25.5 0.7 44 233-284 10-53 (55)
48 PF00157 Pou: Pou domain - N-t 41.1 6.9 0.00015 30.5 -0.6 52 159-210 6-58 (75)
49 PRK03975 tfx putative transcri 39.0 35 0.00077 29.7 3.4 50 231-289 4-53 (141)
50 cd00569 HTH_Hin_like Helix-tur 35.0 44 0.00095 19.6 2.6 38 233-278 5-42 (42)
51 PRK09652 RNA polymerase sigma 33.1 20 0.00044 30.8 1.0 49 233-289 128-176 (182)
52 PRK06759 RNA polymerase factor 32.4 23 0.0005 29.9 1.2 47 233-287 106-152 (154)
53 PRK11924 RNA polymerase sigma 31.9 25 0.00055 30.1 1.4 49 234-290 126-174 (179)
54 PF00424 REV: REV protein (ant 30.6 56 0.0012 26.4 3.0 30 250-293 22-51 (91)
55 PF13551 HTH_29: Winged helix- 30.6 1.6E+02 0.0034 23.1 5.8 49 230-278 54-108 (112)
56 KOG1146|consensus 30.1 42 0.0009 39.1 2.9 60 227-289 705-764 (1406)
57 PRK09646 RNA polymerase sigma 29.6 30 0.00065 30.8 1.5 49 233-289 142-190 (194)
58 PF10668 Phage_terminase: Phag 29.3 20 0.00043 26.7 0.2 18 260-277 25-42 (60)
59 PF00196 GerE: Bacterial regul 27.9 49 0.0011 23.6 2.1 48 233-289 3-50 (58)
60 TIGR02937 sigma70-ECF RNA poly 27.2 33 0.00072 27.9 1.3 47 233-287 110-156 (158)
61 PRK09642 RNA polymerase sigma 26.7 45 0.00098 28.4 2.1 49 233-289 106-154 (160)
62 PF13443 HTH_26: Cro/C1-type H 25.6 22 0.00048 25.5 -0.1 26 259-284 12-37 (63)
63 PRK12526 RNA polymerase sigma 25.1 38 0.00081 30.6 1.3 49 233-289 153-201 (206)
64 PRK09413 IS2 repressor TnpA; R 25.1 85 0.0018 26.1 3.4 43 229-279 8-51 (121)
65 PF06738 DUF1212: Protein of u 24.7 1.1E+02 0.0023 27.3 4.2 44 30-74 65-109 (193)
66 PRK00118 putative DNA-binding 24.0 46 0.00099 27.5 1.5 52 233-292 17-68 (104)
67 PRK09639 RNA polymerase sigma 23.8 51 0.0011 28.1 1.9 51 233-292 112-162 (166)
68 PRK12514 RNA polymerase sigma 22.9 47 0.001 28.9 1.4 49 233-289 129-177 (179)
69 PRK09644 RNA polymerase sigma 22.0 51 0.0011 28.3 1.5 50 232-289 107-156 (165)
70 PRK10072 putative transcriptio 21.9 33 0.00071 27.9 0.2 41 233-283 32-72 (96)
71 PRK12543 RNA polymerase sigma 21.6 86 0.0019 27.4 2.9 55 233-295 117-171 (179)
72 PRK12512 RNA polymerase sigma 21.6 47 0.001 29.1 1.2 49 233-289 131-179 (184)
73 PRK06811 RNA polymerase factor 21.4 48 0.001 29.3 1.2 49 233-289 131-179 (189)
74 PRK12519 RNA polymerase sigma 21.0 44 0.00095 29.5 0.9 49 233-289 141-189 (194)
75 TIGR02939 RpoE_Sigma70 RNA pol 20.8 45 0.00097 29.1 0.9 48 234-289 139-186 (190)
76 TIGR02985 Sig70_bacteroi1 RNA 20.7 50 0.0011 27.6 1.1 47 233-287 113-159 (161)
77 smart00421 HTH_LUXR helix_turn 20.6 92 0.002 20.9 2.3 45 233-286 3-47 (58)
78 PRK12538 RNA polymerase sigma 20.1 63 0.0014 30.0 1.7 51 233-291 171-221 (233)
No 1
>KOG0774|consensus
Probab=100.00 E-value=1.6e-79 Score=561.72 Aligned_cols=266 Identities=88% Similarity=1.292 Sum_probs=253.1
Q ss_pred CcHHHHHHHHHhhcccCchHHHHHHhhhhcCCChhHHHHHHHHhhhcccccccCCCCCCCCCchhhhhhhHHhhhcccCC
Q psy8980 33 QDIGEILQQIMNITDQCLDEAQARKHTLNCHRMKPSLFSVLCEIKEKTVLSLRNTQEEEPPDPQLMRLDNMLIAEGVAGP 112 (355)
Q Consensus 33 ~~~~~~~~~~~~~~~~~ld~~~~~k~~i~~Hpl~p~L~~~~~e~~e~~~~s~~~~~~e~~~d~q~~rldn~l~~~~v~~~ 112 (355)
+||+|||||||+|||||||||+++||+|+||||||+||+||||+||||++|+|+.++|+|+|||++||||||.||||+||
T Consensus 8 ~di~diL~qim~ItdqslDeaqa~K~~lnch~mk~AlfsVLcE~KeKt~lsir~~qdeep~dpqlmRLDnML~AEGVagP 87 (334)
T KOG0774|consen 8 KDIGDILQQIMKITDQSLDEAQARKHALNCHRMKPALFSVLCEIKEKTVLSIRGMQDEEPPDPQLMRLDNMLLAEGVAGP 87 (334)
T ss_pred hhHHHHHHHHHHhhhhccchHHhhhhccccccchHHHHHHHHHhhhhheeeeccccccCCCChHHHHHHHHHHHhcccCc
Confidence 89999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CCCCCchhHhhHhhhhCCCCCCCCCcccchhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhcCCCCCCHHHHH
Q psy8980 113 EKGGGANAAASASAAASGGPGQPDNAIEHSDYRAKLAQIRQIYHQELEKYEQACNEFTTHVMNLLREQSRTRPITPKEIE 192 (355)
Q Consensus 113 ~~~~~~~~~a~a~~~~~~~~~~~dn~~e~~~~~~kL~qvl~~y~~eLeky~~~~~~f~~~~i~ll~~qs~~~pls~~~~~ 192 (355)
+++|... ++| +++ | |.||+.||.||+++|+.||+||++.|++||++++++|++|+++||+.+++++
T Consensus 88 ekgga~~-----~~A-sgg----~----hsdYR~kL~qiR~iy~~ElekyeqaCneftthV~nlL~eQsr~RPi~~ke~e 153 (334)
T KOG0774|consen 88 EKGGARA-----AAA-SGG----D----HSDYRAKLLQIRQIYHNELEKYEQACNEFTTHVMNLLREQSRTRPIMPKEIE 153 (334)
T ss_pred cccchhh-----hhc-cCC----C----hHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcccCCCCHHHHH
Confidence 9998332 111 222 1 7899999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHhhhhHHHHHhhhhhHHHHHhhhhhhcccCCCCcCCCHHHHHHHHHHhhhcCCCCCCCHHHHHHHHHHcCCCcc
Q psy8980 193 RMVQIIHKKFSSIQMQLKQSTCEAVMILRSRFLDARRKRRNFSKQASEILNEYFYSHLSNPYPSEEAKEELARKCNITVS 272 (355)
Q Consensus 193 ~~~~~~~~~f~~~~~~lk~~~~~~~~~l~~~~~~~rr~R~~fs~~q~~~L~~~F~~H~~~pyPs~~er~~LA~~~gLt~~ 272 (355)
+++++|+++|+.++.+||+++|++++.|++++.+.||||++|++..+.+|..||+.|..||||++++|++||++|+++..
T Consensus 154 ~m~~~i~~kF~~iq~~lkqstce~vmiLr~r~ldarRKRRNFsK~aTeiLneyF~~h~~nPYPSee~K~eLAkqCnItvs 233 (334)
T KOG0774|consen 154 RMVQIISKKFSHIQMQLKQSTCEAVMILRSRFLDARRKRRNFSKQATEILNEYFYSHLSNPYPSEEAKEELAKQCNITVS 233 (334)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhcccchhHHHHHHHHHHHhcCCCCCcHHHHHHHHHHcCceeh
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred cccccccchhhhhhhhhhhhhHHHhHHHHhhhcCCCCCCC
Q psy8980 273 QVSNWFGNKRIRYKKNIGKAQEEANLYAAKKAAGASPYSM 312 (355)
Q Consensus 273 qV~~WFqNrR~R~Kk~~~~~~~e~~~~~~~~~~~~~~~s~ 312 (355)
||.|||.|+|.|+||...+.+++++.++.+.++..++.+.
T Consensus 234 QvsnwfgnkrIrykK~~~k~~ee~~l~~~kk~~~~~~~g~ 273 (334)
T KOG0774|consen 234 QVSNWFGNKRIRYKKNMGKNQEEANLYAAKKAVDATPPGA 273 (334)
T ss_pred hhccccccceeehhhhhhhhhhhhhhHhhcccccCCCCCC
Confidence 9999999999999999999999999999999887666333
No 2
>PF03792 PBC: PBC domain; InterPro: IPR005542 Pbx proteins are members of the TALE (three-amino-acid loop extension) family of atypical homeodomain proteins, whose members are characterised by a three-residue insertion in the first helix of the homeodomain involved in their interaction with Hox proteins. Examination of Pbx1 has shown that, in addition to the homeodomain, a short 16-residue C-terminal tail is essential for maximal cooperative interactions with Hox partners as well as for maximal monomeric binding of Pbx1 to DNA. The PBX domain is a bipartite acidic domain [].; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0005634 nucleus
Probab=100.00 E-value=4.5e-58 Score=406.51 Aligned_cols=190 Identities=84% Similarity=1.246 Sum_probs=179.8
Q ss_pred CcCcCcHHHHHHHHHhhcccCchHHHHHHhhhhcCCChhHHHHHHHHhhhcccccccCCCCCCCCCchhhhhhhHHhhhc
Q psy8980 29 EPRKQDIGEILQQIMNITDQCLDEAQARKHTLNCHRMKPSLFSVLCEIKEKTVLSLRNTQEEEPPDPQLMRLDNMLIAEG 108 (355)
Q Consensus 29 ~~~~~~~~~~~~~~~~~~~~~ld~~~~~k~~i~~Hpl~p~L~~~~~e~~e~~~~s~~~~~~e~~~d~q~~rldn~l~~~~ 108 (355)
+.+++||+|||||||+|||||||||+++|++|+||||||+||+||||+||+|++|+|++++|+|+|||++||||||.|||
T Consensus 2 ~~~~~~i~dlLqqim~ItdqsLDeaqa~K~~l~~hr~k~ALfsVLcE~KEkt~LSir~~qee~p~dpQl~RLDNML~AEG 81 (191)
T PF03792_consen 2 GERKQDIGDLLQQIMKITDQSLDEAQARKHALNCHRMKPALFSVLCEIKEKTVLSIRNIQEEDPPDPQLMRLDNMLLAEG 81 (191)
T ss_pred CcCcCCHHHHHHHHHHHhcCCHhHHHHhchhhcCCCCchhhHHHHHHHHhhcCccccccCCcCCCchhhhhhhcchhhhc
Confidence 47899999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred ccCCCCCCCchhHhhHhhhhCCCCCCCCCcccchhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhcCCCCCCH
Q psy8980 109 VAGPEKGGGANAAASASAAASGGPGQPDNAIEHSDYRAKLAQIRQIYHQELEKYEQACNEFTTHVMNLLREQSRTRPITP 188 (355)
Q Consensus 109 v~~~~~~~~~~~~a~a~~~~~~~~~~~dn~~e~~~~~~kL~qvl~~y~~eLeky~~~~~~f~~~~i~ll~~qs~~~pls~ 188 (355)
|+||++++..++++.+. . .||+++|+||+.+|.+|+.+|+.||++|++.|++|+.+++++|++|+++||+++
T Consensus 82 V~gPe~~~~~~~~~~~~------~--~~~~~d~~dYr~kL~~ir~~y~~el~kye~ac~eF~~hV~~lLreQs~~RPIs~ 153 (191)
T PF03792_consen 82 VAGPEKGGRAAAAAAGT------A--ADNSIDHSDYRAKLSQIRQIYHSELEKYEQACNEFTEHVMNLLREQSEFRPISP 153 (191)
T ss_pred CcCCCCcccchhhhhcc------C--cccccchHHHHHHHHHHHHHHHHHHHHHHHHhhhhHHHHHHHHHHhcccCCCCH
Confidence 99999998876443221 1 378999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHHhhhhHHHHHhhhhhHHHHHhhhhhhcc
Q psy8980 189 KEIERMVQIIHKKFSSIQMQLKQSTCEAVMILRSRFLD 226 (355)
Q Consensus 189 ~~~~~~~~~~~~~f~~~~~~lk~~~~~~~~~l~~~~~~ 226 (355)
.++++|+..|+++|+.++.+|||++|++++.|++++.+
T Consensus 154 keiE~m~~~i~~Kf~~iq~qLKQstCEaVm~LRsRflD 191 (191)
T PF03792_consen 154 KEIERMVNIIHRKFSKIQMQLKQSTCEAVMILRSRFLD 191 (191)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcC
Confidence 99999999999999999999999999999999998764
No 3
>KOG3802|consensus
Probab=99.71 E-value=1e-17 Score=163.64 Aligned_cols=127 Identities=24% Similarity=0.371 Sum_probs=102.8
Q ss_pred HHHHHHHHHHHHHHHHHHHHhhcCCC-CCCHHHHHHHHHHHHhhhhHHHHHhhhhhHHHHHhhhhhhc------------
Q psy8980 159 LEKYEQACNEFTTHVMNLLREQSRTR-PITPKEIERMVQIIHKKFSSIQMQLKQSTCEAVMILRSRFL------------ 225 (355)
Q Consensus 159 Leky~~~~~~f~~~~i~ll~~qs~~~-pls~~~~~~~~~~~~~~f~~~~~~lk~~~~~~~~~l~~~~~------------ 225 (355)
++.++++++.|+.++|.|..+|..++ .++......++++.+++|+.++..+|. .|. +.+|..+|+
T Consensus 205 leELEqFAK~FKqRRIkLGfTQaDVGlALG~lyGn~FSQTTIcRFEALqLSFKN-MCK-LKPLL~KWLeEAes~~~~~~~ 282 (398)
T KOG3802|consen 205 LEELEQFAKTFKQRRIKLGFTQADVGLALGALYGNVFSQTTICRFEALQLSFKN-MCK-LKPLLEKWLEEAESRESTGSP 282 (398)
T ss_pred HHHHHHHHHHHHhheeccccchhHHHHHHHhhhCcccchhhhhHhHhhccCHHH-Hhh-hHHHHHHHHHHHhcccccCCC
Confidence 34444559999999999999998764 344445567788899999988776662 232 333333332
Q ss_pred ----------ccCCCCcCCCHHHHHHHHHHhhhcCCCCCCCHHHHHHHHHHcCCCcccccccccchhhhhhhhhh
Q psy8980 226 ----------DARRKRRNFSKQASEILNEYFYSHLSNPYPSEEAKEELARKCNITVSQVSNWFGNKRIRYKKNIG 290 (355)
Q Consensus 226 ----------~~rr~R~~fs~~q~~~L~~~F~~H~~~pyPs~~er~~LA~~~gLt~~qV~~WFqNrR~R~Kk~~~ 290 (355)
++|||||.|....+..|+.+| ..|+.|+..|+..||.+++|.+.+|+|||||||+|.||...
T Consensus 283 ~~~e~i~a~~RkRKKRTSie~~vr~aLE~~F---~~npKPt~qEIt~iA~~L~leKEVVRVWFCNRRQkeKR~~~ 354 (398)
T KOG3802|consen 283 NSIEKIGAQSRKRKKRTSIEVNVRGALEKHF---LKNPKPTSQEITHIAESLQLEKEVVRVWFCNRRQKEKRITP 354 (398)
T ss_pred CCHHHhhccccccccccceeHHHHHHHHHHH---HhCCCCCHHHHHHHHHHhccccceEEEEeeccccccccCCC
Confidence 478899999999999999999 99999999999999999999999999999999999999873
No 4
>KOG0775|consensus
Probab=99.66 E-value=4.2e-16 Score=145.26 Aligned_cols=122 Identities=28% Similarity=0.415 Sum_probs=107.0
Q ss_pred hHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHHHhhhhHHHHHhhhhhHHHHHhhhh
Q psy8980 143 DYRAKLAQIRQIYHQELEKYEQACNEFTTHVMNLLREQSRTRPITPKEIERMVQIIHKKFSSIQMQLKQSTCEAVMILRS 222 (355)
Q Consensus 143 ~~~~kL~qvl~~y~~eLeky~~~~~~f~~~~i~ll~~qs~~~pls~~~~~~~~~~~~~~f~~~~~~lk~~~~~~~~~l~~ 222 (355)
+-..+|..|++.|++.-..| -.+++.+-++.....+.-+.+||.+++.+|+ +++| ++++
T Consensus 113 gnf~eLY~iLE~h~Fs~~~h-~~LQ~lWl~AhY~EAek~RGR~LgaV~KYRv----RrKf----------------PlPr 171 (304)
T KOG0775|consen 113 GNFRELYHILENHKFSPHNH-PKLQALWLKAHYKEAEKLRGRPLGAVDKYRV----RRKF----------------PLPR 171 (304)
T ss_pred ccHHHHHHHHHhccCChhhh-HHHHHHHHHHHHHHHHHhcCCcCCcccccee----eccC----------------CCCC
Confidence 34789999999998887766 4566777777677778888999999999986 6677 6889
Q ss_pred hhcccCCCCcCCCHHHHHHHHHHhhhcCCCCCCCHHHHHHHHHHcCCCcccccccccchhhhhhhh
Q psy8980 223 RFLDARRKRRNFSKQASEILNEYFYSHLSNPYPSEEAKEELARKCNITVSQVSNWFGNKRIRYKKN 288 (355)
Q Consensus 223 ~~~~~rr~R~~fs~~q~~~L~~~F~~H~~~pyPs~~er~~LA~~~gLt~~qV~~WFqNrR~R~Kk~ 288 (355)
++|++..+-..|....+.+|++|| ..++||+..+|.+||+.|||+..||.|||.|||+|+|-.
T Consensus 172 TIWDGEet~yCFKekSR~~LrewY---~~~~YPsp~eKReLA~aTgLt~tQVsNWFKNRRQRDRa~ 234 (304)
T KOG0775|consen 172 TIWDGEETVYCFKEKSRSLLREWY---LQNPYPSPREKRELAEATGLTITQVSNWFKNRRQRDRAA 234 (304)
T ss_pred ccccCceeeeehhHhhHHHHHHHH---hcCCCCChHHHHHHHHHhCCchhhhhhhhhhhhhhhhhc
Confidence 999999888899999999999999 999999999999999999999999999999999999843
No 5
>KOG0484|consensus
Probab=99.60 E-value=7.4e-16 Score=124.49 Aligned_cols=66 Identities=30% Similarity=0.514 Sum_probs=61.0
Q ss_pred cccCCCCcCCCHHHHHHHHHHhhhcCCCCCCCHHHHHHHHHHcCCCcccccccccchhhhhhhhhhhhh
Q psy8980 225 LDARRKRRNFSKQASEILNEYFYSHLSNPYPSEEAKEELARKCNITVSQVSNWFGNKRIRYKKNIGKAQ 293 (355)
Q Consensus 225 ~~~rr~R~~fs~~q~~~L~~~F~~H~~~pyPs~~er~~LA~~~gLt~~qV~~WFqNrR~R~Kk~~~~~~ 293 (355)
.+.||-|++|+..|+..|++.| ....||++-.|++||.++.||+..|+|||||||+|+||+.+...
T Consensus 15 rKQRRIRTTFTS~QLkELErvF---~ETHYPDIYTREEiA~kidLTEARVQVWFQNRRAKfRKQEr~a~ 80 (125)
T KOG0484|consen 15 RKQRRIRTTFTSAQLKELERVF---AETHYPDIYTREEIALKIDLTEARVQVWFQNRRAKFRKQERAAI 80 (125)
T ss_pred HHhhhhhhhhhHHHHHHHHHHH---HhhcCCcchhHHHHHHhhhhhHHHHHHHHHhhHHHHHHHHHHHH
Confidence 3567889999999999999999 99999999999999999999999999999999999999875544
No 6
>KOG0488|consensus
Probab=99.53 E-value=8.6e-15 Score=142.08 Aligned_cols=66 Identities=29% Similarity=0.451 Sum_probs=61.8
Q ss_pred cccCCCCcCCCHHHHHHHHHHhhhcCCCCCCCHHHHHHHHHHcCCCcccccccccchhhhhhhhhhhhh
Q psy8980 225 LDARRKRRNFSKQASEILNEYFYSHLSNPYPSEEAKEELARKCNITVSQVSNWFGNKRIRYKKNIGKAQ 293 (355)
Q Consensus 225 ~~~rr~R~~fs~~q~~~L~~~F~~H~~~pyPs~~er~~LA~~~gLt~~qV~~WFqNrR~R~Kk~~~~~~ 293 (355)
.|+||.|+.||..|+..||..| .+..|.+..+|.+||..+|||..||++||||||+||||......
T Consensus 170 kK~RksRTaFT~~Ql~~LEkrF---~~QKYLS~~DR~~LA~~LgLTdaQVKtWfQNRRtKWKrq~a~g~ 235 (309)
T KOG0488|consen 170 KKRRKSRTAFSDHQLFELEKRF---EKQKYLSVADRIELAASLGLTDAQVKTWFQNRRTKWKRQTAEGG 235 (309)
T ss_pred cccccchhhhhHHHHHHHHHHH---HHhhcccHHHHHHHHHHcCCchhhHHHHHhhhhHHHHHHHHhhh
Confidence 5667889999999999999999 99999999999999999999999999999999999999986633
No 7
>KOG0485|consensus
Probab=99.52 E-value=9.5e-15 Score=132.21 Aligned_cols=70 Identities=29% Similarity=0.432 Sum_probs=64.0
Q ss_pred ccCCCCcCCCHHHHHHHHHHhhhcCCCCCCCHHHHHHHHHHcCCCcccccccccchhhhhhhhhhhhhHHHhH
Q psy8980 226 DARRKRRNFSKQASEILNEYFYSHLSNPYPSEEAKEELARKCNITVSQVSNWFGNKRIRYKKNIGKAQEEANL 298 (355)
Q Consensus 226 ~~rr~R~~fs~~q~~~L~~~F~~H~~~pyPs~~er~~LA~~~gLt~~qV~~WFqNrR~R~Kk~~~~~~~e~~~ 298 (355)
++||.|++|+..|+..||..| ....|.+..+|..||.++.||+.||++||||||.||||+.....+.+..
T Consensus 103 RKKktRTvFSraQV~qLEs~F---e~krYLSsaeRa~LA~sLqLTETQVKIWFQNRRnKwKRq~aad~ea~sl 172 (268)
T KOG0485|consen 103 RKKKTRTVFSRAQVFQLESTF---ELKRYLSSAERAGLAASLQLTETQVKIWFQNRRNKWKRQYAADLEAASL 172 (268)
T ss_pred ccccchhhhhHHHHHHHHHHH---HHHhhhhHHHHhHHHHhhhhhhhhhhhhhhhhhHHHHHHHhhhhhhhhc
Confidence 457789999999999999999 9999999999999999999999999999999999999998776665544
No 8
>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=99.50 E-value=7.8e-15 Score=107.41 Aligned_cols=57 Identities=51% Similarity=0.901 Sum_probs=54.6
Q ss_pred CCCCcCCCHHHHHHHHHHhhhcCCCCCCCHHHHHHHHHHcCCCcccccccccchhhhhhh
Q psy8980 228 RRKRRNFSKQASEILNEYFYSHLSNPYPSEEAKEELARKCNITVSQVSNWFGNKRIRYKK 287 (355)
Q Consensus 228 rr~R~~fs~~q~~~L~~~F~~H~~~pyPs~~er~~LA~~~gLt~~qV~~WFqNrR~R~Kk 287 (355)
||+|+.|+.+++.+|+.+| ..++||+..++..||..+||+..+|.+||+|+|.++||
T Consensus 1 kr~r~~~t~~q~~~L~~~f---~~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrR~k~kk 57 (57)
T PF00046_consen 1 KRKRTRFTKEQLKVLEEYF---QENPYPSKEEREELAKELGLTERQVKNWFQNRRRKEKK 57 (57)
T ss_dssp SSSSSSSSHHHHHHHHHHH---HHSSSCHHHHHHHHHHHHTSSHHHHHHHHHHHHHHHHH
T ss_pred CcCCCCCCHHHHHHHHHHH---HHhccccccccccccccccccccccccCHHHhHHHhCc
Confidence 5789999999999999999 78999999999999999999999999999999999986
No 9
>KOG0850|consensus
Probab=99.48 E-value=7.5e-14 Score=127.61 Aligned_cols=65 Identities=29% Similarity=0.415 Sum_probs=61.1
Q ss_pred hcccCCCCcCCCHHHHHHHHHHhhhcCCCCCCCHHHHHHHHHHcCCCcccccccccchhhhhhhhhhh
Q psy8980 224 FLDARRKRRNFSKQASEILNEYFYSHLSNPYPSEEAKEELARKCNITVSQVSNWFGNKRIRYKKNIGK 291 (355)
Q Consensus 224 ~~~~rr~R~~fs~~q~~~L~~~F~~H~~~pyPs~~er~~LA~~~gLt~~qV~~WFqNrR~R~Kk~~~~ 291 (355)
..|-||.||.++.-|+..|.+.| +++.|.--.||.+||..+|||.+||+|||||||.|.||.++.
T Consensus 119 ~KK~RKPRTIYSS~QLqaL~rRF---QkTQYLALPERAeLAAsLGLTQTQVKIWFQNrRSK~KKl~k~ 183 (245)
T KOG0850|consen 119 GKKVRKPRTIYSSLQLQALNRRF---QQTQYLALPERAELAASLGLTQTQVKIWFQNRRSKFKKLKKQ 183 (245)
T ss_pred cccccCCcccccHHHHHHHHHHH---hhcchhcCcHHHHHHHHhCCchhHhhhhhhhhHHHHHHHHhc
Confidence 44667889999999999999999 999999999999999999999999999999999999998863
No 10
>KOG0489|consensus
Probab=99.47 E-value=1.2e-14 Score=138.18 Aligned_cols=64 Identities=28% Similarity=0.493 Sum_probs=60.3
Q ss_pred ccCCCCcCCCHHHHHHHHHHhhhcCCCCCCCHHHHHHHHHHcCCCcccccccccchhhhhhhhhhhh
Q psy8980 226 DARRKRRNFSKQASEILNEYFYSHLSNPYPSEEAKEELARKCNITVSQVSNWFGNKRIRYKKNIGKA 292 (355)
Q Consensus 226 ~~rr~R~~fs~~q~~~L~~~F~~H~~~pyPs~~er~~LA~~~gLt~~qV~~WFqNrR~R~Kk~~~~~ 292 (355)
+.||.|+.|+..|+..||.-| ..|.|.+...|.+||..+.|+++||+|||||||+||||..+..
T Consensus 158 ~~kR~RtayT~~QllELEkEF---hfN~YLtR~RRiEiA~~L~LtErQIKIWFQNRRMK~Kk~~k~~ 221 (261)
T KOG0489|consen 158 KSKRRRTAFTRYQLLELEKEF---HFNKYLTRSRRIEIAHALNLTERQIKIWFQNRRMKWKKENKAK 221 (261)
T ss_pred CCCCCCcccchhhhhhhhhhh---ccccccchHHHHHHHhhcchhHHHHHHHHHHHHHHHHHhhccc
Confidence 468899999999999999999 9999999999999999999999999999999999999987543
No 11
>KOG0842|consensus
Probab=99.47 E-value=2.9e-14 Score=136.94 Aligned_cols=70 Identities=31% Similarity=0.423 Sum_probs=62.3
Q ss_pred ccCCCCcCCCHHHHHHHHHHhhhcCCCCCCCHHHHHHHHHHcCCCcccccccccchhhhhhhhhhhhhHHHhH
Q psy8980 226 DARRKRRNFSKQASEILNEYFYSHLSNPYPSEEAKEELARKCNITVSQVSNWFGNKRIRYKKNIGKAQEEANL 298 (355)
Q Consensus 226 ~~rr~R~~fs~~q~~~L~~~F~~H~~~pyPs~~er~~LA~~~gLt~~qV~~WFqNrR~R~Kk~~~~~~~e~~~ 298 (355)
++||+|.-|+..|+..||+.| ....|.|..||+.||..++||.+||+|||||||-|.||..+....++..
T Consensus 152 ~kRKrRVLFSqAQV~ELERRF---rqQRYLSAPERE~LA~~LrLT~TQVKIWFQNrRYK~KR~~~dk~~~~~~ 221 (307)
T KOG0842|consen 152 KKRKRRVLFSQAQVYELERRF---RQQRYLSAPEREHLASSLRLTPTQVKIWFQNRRYKTKRQQKDKALEALL 221 (307)
T ss_pred cccccccccchhHHHHHHHHH---HhhhccccHhHHHHHHhcCCCchheeeeeecchhhhhhhhhhhhhhccc
Confidence 456677789999999999999 9999999999999999999999999999999999999988665544443
No 12
>KOG0843|consensus
Probab=99.47 E-value=3.1e-14 Score=125.72 Aligned_cols=62 Identities=26% Similarity=0.433 Sum_probs=59.4
Q ss_pred ccCCCCcCCCHHHHHHHHHHhhhcCCCCCCCHHHHHHHHHHcCCCcccccccccchhhhhhhhhh
Q psy8980 226 DARRKRRNFSKQASEILNEYFYSHLSNPYPSEEAKEELARKCNITVSQVSNWFGNKRIRYKKNIG 290 (355)
Q Consensus 226 ~~rr~R~~fs~~q~~~L~~~F~~H~~~pyPs~~er~~LA~~~gLt~~qV~~WFqNrR~R~Kk~~~ 290 (355)
+.||.||.|+.+|+..|+..| ..+.|....+|+.||+.++|++.||+|||||||.|.||...
T Consensus 101 ~~kr~RT~ft~~Ql~~LE~~F---~~~~Yvvg~eR~~LA~~L~LsetQVkvWFQNRRtk~kr~~~ 162 (197)
T KOG0843|consen 101 RPKRIRTAFTPEQLLKLEHAF---EGNQYVVGAERKQLAQSLSLSETQVKVWFQNRRTKHKRMQQ 162 (197)
T ss_pred CCCccccccCHHHHHHHHHHH---hcCCeeechHHHHHHHHcCCChhHhhhhhhhhhHHHHHHHH
Confidence 678899999999999999999 99999999999999999999999999999999999999773
No 13
>KOG0487|consensus
Probab=99.43 E-value=4.2e-14 Score=135.84 Aligned_cols=63 Identities=37% Similarity=0.518 Sum_probs=59.7
Q ss_pred cccCCCCcCCCHHHHHHHHHHhhhcCCCCCCCHHHHHHHHHHcCCCcccccccccchhhhhhhhhh
Q psy8980 225 LDARRKRRNFSKQASEILNEYFYSHLSNPYPSEEAKEELARKCNITVSQVSNWFGNKRIRYKKNIG 290 (355)
Q Consensus 225 ~~~rr~R~~fs~~q~~~L~~~F~~H~~~pyPs~~er~~LA~~~gLt~~qV~~WFqNrR~R~Kk~~~ 290 (355)
.+.||||-.+|+.|+..||+-| ..|.|.+.+.|.+|++.|+||++||+|||||||.|.||..+
T Consensus 233 ~~~RKKRcPYTK~QtlELEkEF---lfN~YitkeKR~ElSr~lNLTeRQVKIWFQNRRMK~KK~~r 295 (308)
T KOG0487|consen 233 RRGRKKRCPYTKHQTLELEKEF---LFNMYITKEKRLELSRTLNLTERQVKIWFQNRRMKEKKVNR 295 (308)
T ss_pred cccccccCCchHHHHHHHHHHH---HHHHHHhHHHHHHHHHhcccchhheeeeehhhhhHHhhhhh
Confidence 3568899999999999999999 89999999999999999999999999999999999999884
No 14
>KOG0492|consensus
Probab=99.42 E-value=1.9e-13 Score=123.12 Aligned_cols=69 Identities=26% Similarity=0.384 Sum_probs=62.5
Q ss_pred ccCCCCcCCCHHHHHHHHHHhhhcCCCCCCCHHHHHHHHHHcCCCcccccccccchhhhhhhhhhhhhHHHh
Q psy8980 226 DARRKRRNFSKQASEILNEYFYSHLSNPYPSEEAKEELARKCNITVSQVSNWFGNKRIRYKKNIGKAQEEAN 297 (355)
Q Consensus 226 ~~rr~R~~fs~~q~~~L~~~F~~H~~~pyPs~~er~~LA~~~gLt~~qV~~WFqNrR~R~Kk~~~~~~~e~~ 297 (355)
..|+.|+.|+.+|+..|++-| ...+|.++++|.+++..+.||++||++||||||+|.||.+....|...
T Consensus 143 ~nRkPRtPFTtqQLlaLErkf---rekqYLSiaEraefSsSL~LTeTqVKIWFQNRRAKaKRlQeae~Ek~k 211 (246)
T KOG0492|consen 143 PNRKPRTPFTTQQLLALERKF---REKQYLSIAERAEFSSSLELTETQVKIWFQNRRAKAKRLQEAELEKLK 211 (246)
T ss_pred CCCCCCCCCCHHHHHHHHHHH---hHhhhhhHHHHHhhhhhhhhhhhheehhhhhhhHHHHHHHHHHHHHhh
Confidence 357899999999999999999 999999999999999999999999999999999999998755554443
No 15
>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=100.60 Aligned_cols=57 Identities=44% Similarity=0.745 Sum_probs=53.8
Q ss_pred CCCcCCCHHHHHHHHHHhhhcCCCCCCCHHHHHHHHHHcCCCcccccccccchhhhhhhh
Q psy8980 229 RKRRNFSKQASEILNEYFYSHLSNPYPSEEAKEELARKCNITVSQVSNWFGNKRIRYKKN 288 (355)
Q Consensus 229 r~R~~fs~~q~~~L~~~F~~H~~~pyPs~~er~~LA~~~gLt~~qV~~WFqNrR~R~Kk~ 288 (355)
++++.|+..++.+|+.+| ..++||+..++..||..+||+..||++||+|+|.+.++.
T Consensus 2 ~~r~~~~~~~~~~Le~~f---~~~~~P~~~~~~~la~~~~l~~~qV~~WF~nrR~~~~~~ 58 (59)
T cd00086 2 RKRTRFTPEQLEELEKEF---EKNPYPSREEREELAKELGLTERQVKIWFQNRRAKLKRS 58 (59)
T ss_pred CCCCcCCHHHHHHHHHHH---HhCCCCCHHHHHHHHHHHCcCHHHHHHHHHHHHHHHhcc
Confidence 567899999999999999 789999999999999999999999999999999998864
No 16
>KOG1168|consensus
Probab=99.40 E-value=1.5e-13 Score=128.97 Aligned_cols=123 Identities=24% Similarity=0.378 Sum_probs=88.2
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHhhcCCC----CCCHHHHHHHHHHHHhhhhHH--------------HHHhhhhhHHHHH
Q psy8980 157 QELEKYEQACNEFTTHVMNLLREQSRTR----PITPKEIERMVQIIHKKFSSI--------------QMQLKQSTCEAVM 218 (355)
Q Consensus 157 ~eLeky~~~~~~f~~~~i~ll~~qs~~~----pls~~~~~~~~~~~~~~f~~~--------------~~~lk~~~~~~~~ 218 (355)
.|||.| +.+|..+.|.+..+|..++ .|.-.++..+.++++++|+++ +.||.... .
T Consensus 217 ReLEaF---AErFKQRRIKLGVTQADVG~ALAnLKiPGVGsLSQSTICRFESLTLSHNNMiALKPILqaWLEeAE----~ 289 (385)
T KOG1168|consen 217 RELEAF---AERFKQRRIKLGVTQADVGKALANLKIPGVGSLSQSTICRFESLTLSHNNMIALKPILQAWLEEAE----A 289 (385)
T ss_pred HHHHHH---HHHHHhhhhhhcccHHHHHHHHHhCcCCCcccccccceeeeeeeccccCcchhhhHHHHHHHHHHH----H
Confidence 556666 8899999999998886442 111112223344445555443 33443221 1
Q ss_pred hhhhhh-----------cccCCCCcCCCHHHHHHHHHHhhhcCCCCCCCHHHHHHHHHHcCCCcccccccccchhhhhhh
Q psy8980 219 ILRSRF-----------LDARRKRRNFSKQASEILNEYFYSHLSNPYPSEEAKEELARKCNITVSQVSNWFGNKRIRYKK 287 (355)
Q Consensus 219 ~l~~~~-----------~~~rr~R~~fs~~q~~~L~~~F~~H~~~pyPs~~er~~LA~~~gLt~~qV~~WFqNrR~R~Kk 287 (355)
..+.+. ..+|||||.+.....+.||.|| ...|.|+.+....||+++.|.+..|+|||||+|+|.||
T Consensus 290 a~keK~~~pd~~~l~~~~ekKRKRTSIAAPEKRsLEayF---avQPRPS~EkIAaIAekLDLKKNVVRVWFCNQRQKQKR 366 (385)
T KOG1168|consen 290 AMKEKDTKPDINELLPGGEKKRKRTSIAAPEKRSLEAYF---AVQPRPSGEKIAAIAEKLDLKKNVVRVWFCNQRQKQKR 366 (385)
T ss_pred HHHhhccCCchhhccCccccccccccccCcccccHHHHh---ccCCCCchhHHHHHHHhhhhhhceEEEEeeccHHHHHH
Confidence 111111 2367899999999999999999 99999999999999999999999999999999999998
Q ss_pred hh
Q psy8980 288 NI 289 (355)
Q Consensus 288 ~~ 289 (355)
..
T Consensus 367 m~ 368 (385)
T KOG1168|consen 367 MK 368 (385)
T ss_pred hh
Confidence 54
No 17
>smart00389 HOX Homeodomain. DNA-binding factors that are involved in the transcriptional regulation of key developmental processes
Probab=99.40 E-value=1.8e-13 Score=99.45 Aligned_cols=55 Identities=45% Similarity=0.776 Sum_probs=51.8
Q ss_pred CCCcCCCHHHHHHHHHHhhhcCCCCCCCHHHHHHHHHHcCCCcccccccccchhhhhh
Q psy8980 229 RKRRNFSKQASEILNEYFYSHLSNPYPSEEAKEELARKCNITVSQVSNWFGNKRIRYK 286 (355)
Q Consensus 229 r~R~~fs~~q~~~L~~~F~~H~~~pyPs~~er~~LA~~~gLt~~qV~~WFqNrR~R~K 286 (355)
+.|+.|+.+++.+|+.+| ..++||+..++..||..+||+..||++||+|+|.+.|
T Consensus 2 k~r~~~~~~~~~~L~~~f---~~~~~P~~~~~~~la~~~~l~~~qV~~WF~nrR~~~~ 56 (56)
T smart00389 2 RKRTSFTPEQLEELEKEF---QKNPYPSREEREELAAKLGLSERQVKVWFQNRRAKWK 56 (56)
T ss_pred CCCCcCCHHHHHHHHHHH---HhCCCCCHHHHHHHHHHHCcCHHHHHHhHHHHhhccC
Confidence 567789999999999999 8999999999999999999999999999999999864
No 18
>KOG2251|consensus
Probab=99.38 E-value=3.9e-13 Score=122.41 Aligned_cols=67 Identities=33% Similarity=0.557 Sum_probs=62.3
Q ss_pred hhhcccCCCCcCCCHHHHHHHHHHhhhcCCCCCCCHHHHHHHHHHcCCCcccccccccchhhhhhhhhhh
Q psy8980 222 SRFLDARRKRRNFSKQASEILNEYFYSHLSNPYPSEEAKEELARKCNITVSQVSNWFGNKRIRYKKNIGK 291 (355)
Q Consensus 222 ~~~~~~rr~R~~fs~~q~~~L~~~F~~H~~~pyPs~~er~~LA~~~gLt~~qV~~WFqNrR~R~Kk~~~~ 291 (355)
...++.||.||+|+..|+.+|+..| .+..||+...|++||.+++|.+.+|+|||.|||+|+|++.+.
T Consensus 32 ~~pRkqRRERTtFtr~QlevLe~LF---~kTqYPDv~~rEelAlklnLpeSrVqVWFKNRRAK~r~qq~q 98 (228)
T KOG2251|consen 32 SGPRKQRRERTTFTRKQLEVLEALF---AKTQYPDVFMREELALKLNLPESRVQVWFKNRRAKCRRQQQQ 98 (228)
T ss_pred ccchhcccccceecHHHHHHHHHHH---HhhcCccHHHHHHHHHHhCCchhhhhhhhccccchhhHhhhh
Confidence 3445678999999999999999999 999999999999999999999999999999999999998754
No 19
>KOG0848|consensus
Probab=99.38 E-value=2.9e-13 Score=125.99 Aligned_cols=63 Identities=25% Similarity=0.390 Sum_probs=59.1
Q ss_pred CCCCcCCCHHHHHHHHHHhhhcCCCCCCCHHHHHHHHHHcCCCcccccccccchhhhhhhhhhhhh
Q psy8980 228 RRKRRNFSKQASEILNEYFYSHLSNPYPSEEAKEELARKCNITVSQVSNWFGNKRIRYKKNIGKAQ 293 (355)
Q Consensus 228 rr~R~~fs~~q~~~L~~~F~~H~~~pyPs~~er~~LA~~~gLt~~qV~~WFqNrR~R~Kk~~~~~~ 293 (355)
-|-|.+++..|+-.||+.| ..++|.++..|.+||..+||+++||+|||||||+|+||.++|..
T Consensus 200 DKYRvVYTDhQRLELEKEf---h~SryITirRKSELA~~LgLsERQVKIWFQNRRAKERK~nKKk~ 262 (317)
T KOG0848|consen 200 DKYRVVYTDHQRLELEKEF---HTSRYITIRRKSELAATLGLSERQVKIWFQNRRAKERKDNKKKR 262 (317)
T ss_pred cceeEEecchhhhhhhhhh---ccccceeeehhHHHHHhhCccHhhhhHhhhhhhHHHHHHHHHHH
Confidence 4578899999999999999 99999999999999999999999999999999999999987763
No 20
>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=99.31 E-value=4.9e-13 Score=91.55 Aligned_cols=40 Identities=53% Similarity=0.934 Sum_probs=35.6
Q ss_pred HhhhcCCCCCCCHHHHHHHHHHcCCCcccccccccchhhh
Q psy8980 245 YFYSHLSNPYPSEEAKEELARKCNITVSQVSNWFGNKRIR 284 (355)
Q Consensus 245 ~F~~H~~~pyPs~~er~~LA~~~gLt~~qV~~WFqNrR~R 284 (355)
||.+|..+|||+.++|..||..+||+..||.+||.|.|+|
T Consensus 1 Wl~~h~~nPYPs~~ek~~L~~~tgls~~Qi~~WF~NaRrR 40 (40)
T PF05920_consen 1 WLLEHLHNPYPSKEEKEELAKQTGLSRKQISNWFINARRR 40 (40)
T ss_dssp HHHHTTTSGS--HHHHHHHHHHHTS-HHHHHHHHHHHHHH
T ss_pred CHHHHCCCCCCCHHHHHHHHHHcCCCHHHHHHHHHHhHcc
Confidence 7789999999999999999999999999999999999987
No 21
>KOG0494|consensus
Probab=99.27 E-value=2.4e-12 Score=119.46 Aligned_cols=64 Identities=30% Similarity=0.492 Sum_probs=58.7
Q ss_pred cCCC-CcCCCHHHHHHHHHHhhhcCCCCCCCHHHHHHHHHHcCCCcccccccccchhhhhhhhhhhhh
Q psy8980 227 ARRK-RRNFSKQASEILNEYFYSHLSNPYPSEEAKEELARKCNITVSQVSNWFGNKRIRYKKNIGKAQ 293 (355)
Q Consensus 227 ~rr~-R~~fs~~q~~~L~~~F~~H~~~pyPs~~er~~LA~~~gLt~~qV~~WFqNrR~R~Kk~~~~~~ 293 (355)
+||. ||.|+..|+..||+.| ....||+...|+.||.+|.|.+..|+|||||||+||||..+...
T Consensus 140 kRRh~RTiFT~~Qle~LEkaF---keaHYPDv~Are~la~ktelpEDRIqVWfQNRRAKWRk~Ek~wg 204 (332)
T KOG0494|consen 140 KRRHFRTIFTSYQLEELEKAF---KEAHYPDVYAREMLADKTELPEDRIQVWFQNRRAKWRKTEKRWG 204 (332)
T ss_pred ccccccchhhHHHHHHHHHHH---hhccCccHHHHHHHhhhccCchhhhhHHhhhhhHHhhhhhhhcC
Confidence 3444 8999999999999999 99999999999999999999999999999999999999876643
No 22
>KOG0493|consensus
Probab=99.24 E-value=3.4e-12 Score=118.46 Aligned_cols=61 Identities=34% Similarity=0.597 Sum_probs=57.6
Q ss_pred cCCCCcCCCHHHHHHHHHHhhhcCCCCCCCHHHHHHHHHHcCCCcccccccccchhhhhhhhhh
Q psy8980 227 ARRKRRNFSKQASEILNEYFYSHLSNPYPSEEAKEELARKCNITVSQVSNWFGNKRIRYKKNIG 290 (355)
Q Consensus 227 ~rr~R~~fs~~q~~~L~~~F~~H~~~pyPs~~er~~LA~~~gLt~~qV~~WFqNrR~R~Kk~~~ 290 (355)
-||.|+.|+.+|+..|+..| ..|.|.++..|.+||.+++|.+.||++||||+|+|.||...
T Consensus 246 eKRPRTAFtaeQL~RLK~EF---~enRYlTEqRRQ~La~ELgLNEsQIKIWFQNKRAKiKKsTg 306 (342)
T KOG0493|consen 246 EKRPRTAFTAEQLQRLKAEF---QENRYLTEQRRQELAQELGLNESQIKIWFQNKRAKIKKSTG 306 (342)
T ss_pred hcCccccccHHHHHHHHHHH---hhhhhHHHHHHHHHHHHhCcCHHHhhHHhhhhhhhhhhccC
Confidence 35689999999999999999 99999999999999999999999999999999999999763
No 23
>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=99.24 E-value=7.5e-12 Score=92.37 Aligned_cols=52 Identities=17% Similarity=0.404 Sum_probs=50.2
Q ss_pred CCCCcCCCHHHHHHHHHHhhhcCCCCC----CCHHHHHHHHHHcCCCcccccccccchh
Q psy8980 228 RRKRRNFSKQASEILNEYFYSHLSNPY----PSEEAKEELARKCNITVSQVSNWFGNKR 282 (355)
Q Consensus 228 rr~R~~fs~~q~~~L~~~F~~H~~~py----Ps~~er~~LA~~~gLt~~qV~~WFqNrR 282 (355)
||.||.|+.+|+..|+.+| ..++| |+..++.+||..+||+..+|++||+|.+
T Consensus 2 kR~RT~Ft~~Q~~~Le~~f---e~~~y~~~~~~~~~r~~la~~lgl~~~vvKVWfqN~k 57 (58)
T TIGR01565 2 KRRRTKFTAEQKEKMRDFA---EKLGWKLKDKRREEVREFCEEIGVTRKVFKVWMHNNK 57 (58)
T ss_pred CCCCCCCCHHHHHHHHHHH---HHcCCCCCCCCHHHHHHHHHHhCCCHHHeeeecccCC
Confidence 6899999999999999999 99999 9999999999999999999999999975
No 24
>KOG0491|consensus
Probab=99.21 E-value=3.1e-12 Score=111.58 Aligned_cols=64 Identities=31% Similarity=0.485 Sum_probs=59.7
Q ss_pred cCCCCcCCCHHHHHHHHHHhhhcCCCCCCCHHHHHHHHHHcCCCcccccccccchhhhhhhhhhhhh
Q psy8980 227 ARRKRRNFSKQASEILNEYFYSHLSNPYPSEEAKEELARKCNITVSQVSNWFGNKRIRYKKNIGKAQ 293 (355)
Q Consensus 227 ~rr~R~~fs~~q~~~L~~~F~~H~~~pyPs~~er~~LA~~~gLt~~qV~~WFqNrR~R~Kk~~~~~~ 293 (355)
++|.|++|+..|+..|++.| +...|.+..++.+||..++|+++||+.||||||.|.||..++..
T Consensus 100 r~K~Rtvfs~~ql~~l~~rF---e~QrYLS~~e~~ELan~L~LS~~QVKTWFQNrRMK~Kk~~r~~~ 163 (194)
T KOG0491|consen 100 RRKARTVFSDPQLSGLEKRF---ERQRYLSTPERQELANALSLSETQVKTWFQNRRMKHKKQQRNNQ 163 (194)
T ss_pred hhhhcccccCccccccHHHH---hhhhhcccHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHHHhccC
Confidence 46789999999999999999 99999999999999999999999999999999999999886544
No 25
>KOG0486|consensus
Probab=99.16 E-value=1.5e-11 Score=117.04 Aligned_cols=70 Identities=31% Similarity=0.563 Sum_probs=63.8
Q ss_pred hhhhcccCCCCcCCCHHHHHHHHHHhhhcCCCCCCCHHHHHHHHHHcCCCcccccccccchhhhhhhhhhhhh
Q psy8980 221 RSRFLDARRKRRNFSKQASEILNEYFYSHLSNPYPSEEAKEELARKCNITVSQVSNWFGNKRIRYKKNIGKAQ 293 (355)
Q Consensus 221 ~~~~~~~rr~R~~fs~~q~~~L~~~F~~H~~~pyPs~~er~~LA~~~gLt~~qV~~WFqNrR~R~Kk~~~~~~ 293 (355)
..++.|+||.|+.|+.+|+..||.|| .+|.||+...|++||.-++||+..|+|||.|||+||||+..-.+
T Consensus 106 ~kki~KqrrQrthFtSqqlqele~tF---~rNrypdMstrEEIavwtNlTE~rvrvwfknrrakwrkrErN~~ 175 (351)
T KOG0486|consen 106 KKKISKQRRQRTHFTSQQLQELEATF---QRNRYPDMSTREEIAVWTNLTEARVRVWFKNRRAKWRKRERNQQ 175 (351)
T ss_pred cchhhhhhhhhhhhHHHHHHHHHHHH---hhccCCccchhhHHHhhccccchhhhhhcccchhhhhhhhhhHH
Confidence 34455778899999999999999999 99999999999999999999999999999999999999875544
No 26
>KOG0773|consensus
Probab=99.15 E-value=1.4e-10 Score=114.22 Aligned_cols=64 Identities=39% Similarity=0.678 Sum_probs=60.2
Q ss_pred cCCCCcCCCHHHHHHHHHHhhhcCCCCCCCHHHHHHHHHHcCCCcccccccccchhhhhhhhhh
Q psy8980 227 ARRKRRNFSKQASEILNEYFYSHLSNPYPSEEAKEELARKCNITVSQVSNWFGNKRIRYKKNIG 290 (355)
Q Consensus 227 ~rr~R~~fs~~q~~~L~~~F~~H~~~pyPs~~er~~LA~~~gLt~~qV~~WFqNrR~R~Kk~~~ 290 (355)
.+|+++.|++..+.+|+.|+++|..+|||+..+|..||.+|||+..||.|||+|+|.|.++.+.
T Consensus 239 ~~r~~~~lP~~a~~ilr~Wl~~h~~~PYPse~~K~~La~~TGLs~~Qv~NWFINaR~R~w~p~~ 302 (342)
T KOG0773|consen 239 KWRPQRGLPKEAVSILRAWLFEHLLHPYPSDDEKLMLAKQTGLSRPQVSNWFINARVRLWKPMI 302 (342)
T ss_pred CCCCCCCCCHHHHHHHHHHHHHhccCCCCcchhccccchhcCCCcccCCchhhhcccccCCchH
Confidence 4556779999999999999999999999999999999999999999999999999999999883
No 27
>COG5576 Homeodomain-containing transcription factor [Transcription]
Probab=99.13 E-value=5.3e-11 Score=104.87 Aligned_cols=63 Identities=32% Similarity=0.471 Sum_probs=58.8
Q ss_pred ccCCCCcCCCHHHHHHHHHHhhhcCCCCCCCHHHHHHHHHHcCCCcccccccccchhhhhhhhhhh
Q psy8980 226 DARRKRRNFSKQASEILNEYFYSHLSNPYPSEEAKEELARKCNITVSQVSNWFGNKRIRYKKNIGK 291 (355)
Q Consensus 226 ~~rr~R~~fs~~q~~~L~~~F~~H~~~pyPs~~er~~LA~~~gLt~~qV~~WFqNrR~R~Kk~~~~ 291 (355)
..+++|++.+..|+.+|++.| ..+|||+...|..|+..++|+++-|++||||+|++.|+....
T Consensus 50 ~~~~~r~R~t~~Q~~vL~~~F---~i~p~Ps~~~r~~L~~~lnm~~ksVqIWFQNkR~~~k~~~~~ 112 (156)
T COG5576 50 PPKSKRRRTTDEQLMVLEREF---EINPYPSSITRIKLSLLLNMPPKSVQIWFQNKRAKEKKKRSG 112 (156)
T ss_pred cCcccceechHHHHHHHHHHh---ccCCCCCHHHHHHHHHhcCCChhhhhhhhchHHHHHHHhccc
Confidence 356788899999999999999 999999999999999999999999999999999999997644
No 28
>KOG0483|consensus
Probab=99.13 E-value=2.5e-11 Score=110.60 Aligned_cols=60 Identities=28% Similarity=0.478 Sum_probs=55.5
Q ss_pred CCCCcCCCHHHHHHHHHHhhhcCCCCCCCHHHHHHHHHHcCCCcccccccccchhhhhhhhhh
Q psy8980 228 RRKRRNFSKQASEILNEYFYSHLSNPYPSEEAKEELARKCNITVSQVSNWFGNKRIRYKKNIG 290 (355)
Q Consensus 228 rr~R~~fs~~q~~~L~~~F~~H~~~pyPs~~er~~LA~~~gLt~~qV~~WFqNrR~R~Kk~~~ 290 (355)
.+++.+|+.+|+..|+.-| ..+.|.....|..||+++||.++||.+||||||+|||....
T Consensus 51 ~~kk~Rlt~eQ~~~LE~~F---~~~~~L~p~~K~~LAk~LgL~pRQVavWFQNRRARwK~kql 110 (198)
T KOG0483|consen 51 KGKKRRLTSEQVKFLEKSF---ESEKKLEPERKKKLAKELGLQPRQVAVWFQNRRARWKTKQL 110 (198)
T ss_pred ccccccccHHHHHHhHHhh---ccccccChHHHHHHHHhhCCChhHHHHHHhhccccccchhh
Confidence 4566789999999999999 88999999999999999999999999999999999998653
No 29
>KOG4577|consensus
Probab=99.05 E-value=1.3e-10 Score=109.34 Aligned_cols=64 Identities=23% Similarity=0.470 Sum_probs=60.0
Q ss_pred cCCCCcCCCHHHHHHHHHHhhhcCCCCCCCHHHHHHHHHHcCCCcccccccccchhhhhhhhhhhhh
Q psy8980 227 ARRKRRNFSKQASEILNEYFYSHLSNPYPSEEAKEELARKCNITVSQVSNWFGNKRIRYKKNIGKAQ 293 (355)
Q Consensus 227 ~rr~R~~fs~~q~~~L~~~F~~H~~~pyPs~~er~~LA~~~gLt~~qV~~WFqNrR~R~Kk~~~~~~ 293 (355)
.||.||+++..|++.|+..| ...|.|....|++|+.+|||..+.|+|||||||+|.||.++.+.
T Consensus 167 nKRPRTTItAKqLETLK~AY---n~SpKPARHVREQLsseTGLDMRVVQVWFQNRRAKEKRLKKDAG 230 (383)
T KOG4577|consen 167 NKRPRTTITAKQLETLKQAY---NTSPKPARHVREQLSSETGLDMRVVQVWFQNRRAKEKRLKKDAG 230 (383)
T ss_pred cCCCcceeeHHHHHHHHHHh---cCCCchhHHHHHHhhhccCcceeehhhhhhhhhHHHHhhhhhcc
Confidence 57899999999999999999 99999999999999999999999999999999999999876643
No 30
>KOG0844|consensus
Probab=99.04 E-value=5.9e-11 Score=112.45 Aligned_cols=61 Identities=28% Similarity=0.468 Sum_probs=57.0
Q ss_pred CCCCcCCCHHHHHHHHHHhhhcCCCCCCCHHHHHHHHHHcCCCcccccccccchhhhhhhhhhh
Q psy8980 228 RRKRRNFSKQASEILNEYFYSHLSNPYPSEEAKEELARKCNITVSQVSNWFGNKRIRYKKNIGK 291 (355)
Q Consensus 228 rr~R~~fs~~q~~~L~~~F~~H~~~pyPs~~er~~LA~~~gLt~~qV~~WFqNrR~R~Kk~~~~ 291 (355)
||-||.|+.+|+..||+.| .+.-|.+...|.+||..++|.+..|+|||||||.|+||+.-.
T Consensus 182 RRYRTAFTReQIaRLEKEF---yrENYVSRprRcELAAaLNLPEtTIKVWFQNRRMKDKRQRla 242 (408)
T KOG0844|consen 182 RRYRTAFTREQIARLEKEF---YRENYVSRPRRCELAAALNLPETTIKVWFQNRRMKDKRQRLA 242 (408)
T ss_pred HHHHhhhhHHHHHHHHHHH---HHhccccCchhhhHHHhhCCCcceeehhhhhchhhhhhhhhh
Confidence 6789999999999999999 677799999999999999999999999999999999998754
No 31
>KOG0847|consensus
Probab=98.95 E-value=2.2e-10 Score=104.18 Aligned_cols=61 Identities=28% Similarity=0.496 Sum_probs=56.6
Q ss_pred cCCCCcCCCHHHHHHHHHHhhhcCCCCCCCHHHHHHHHHHcCCCcccccccccchhhhhhhhhh
Q psy8980 227 ARRKRRNFSKQASEILNEYFYSHLSNPYPSEEAKEELARKCNITVSQVSNWFGNKRIRYKKNIG 290 (355)
Q Consensus 227 ~rr~R~~fs~~q~~~L~~~F~~H~~~pyPs~~er~~LA~~~gLt~~qV~~WFqNrR~R~Kk~~~ 290 (355)
++..|.+|+..|+..|+.-| ....|+-..+|.+||..+|+++.||+|||||||.||||...
T Consensus 167 rk~srPTf~g~qi~~le~~f---eqtkylaG~~ra~lA~~lgmteSqvkVWFQNRRTKWRKkhA 227 (288)
T KOG0847|consen 167 RKQSRPTFTGHQIYQLERKF---EQTKYLAGADRAQLAQELNMTESQVKVWFQNRRTKWRKKHA 227 (288)
T ss_pred ccccCCCccchhhhhhhhhh---hhhhcccchhHHHhhccccccHHHHHHHHhcchhhhhhhhc
Confidence 34567789999999999999 99999999999999999999999999999999999999763
No 32
>KOG0490|consensus
Probab=98.73 E-value=6.4e-09 Score=96.09 Aligned_cols=63 Identities=24% Similarity=0.276 Sum_probs=59.1
Q ss_pred cccCCCCcCCCHHHHHHHHHHhhhcCCCCCCCHHHHHHHHHHcCCCcccccccccchhhhhhhhhh
Q psy8980 225 LDARRKRRNFSKQASEILNEYFYSHLSNPYPSEEAKEELARKCNITVSQVSNWFGNKRIRYKKNIG 290 (355)
Q Consensus 225 ~~~rr~R~~fs~~q~~~L~~~F~~H~~~pyPs~~er~~LA~~~gLt~~qV~~WFqNrR~R~Kk~~~ 290 (355)
.++|+.|+.|+..++..|++.| ..++||+...++.||..+++++..|++||||+|+||++...
T Consensus 58 ~~~rr~rt~~~~~ql~~ler~f---~~~h~Pd~~~r~~la~~~~~~e~rVqvwFqnrrak~r~~~~ 120 (235)
T KOG0490|consen 58 FSKRCARCKFTISQLDELERAF---EKVHLPCFACRECLALLLTGDEFRVQVWFQNRRAKDRKEER 120 (235)
T ss_pred ccccccCCCCCcCHHHHHHHhh---cCCCcCccchHHHHhhcCCCCeeeeehhhhhhcHhhhhhhc
Confidence 4567899999999999999999 88899999999999999999999999999999999998764
No 33
>KOG0849|consensus
Probab=98.54 E-value=1.6e-07 Score=93.27 Aligned_cols=63 Identities=32% Similarity=0.636 Sum_probs=58.7
Q ss_pred ccCCCCcCCCHHHHHHHHHHhhhcCCCCCCCHHHHHHHHHHcCCCcccccccccchhhhhhhhhhh
Q psy8980 226 DARRKRRNFSKQASEILNEYFYSHLSNPYPSEEAKEELARKCNITVSQVSNWFGNKRIRYKKNIGK 291 (355)
Q Consensus 226 ~~rr~R~~fs~~q~~~L~~~F~~H~~~pyPs~~er~~LA~~~gLt~~qV~~WFqNrR~R~Kk~~~~ 291 (355)
+.+|.|+.|+..|...|+++| ..++||....|+.||.++++++..|++||+|||.|++|....
T Consensus 175 ~~rr~rtsft~~Q~~~le~~f---~rt~yP~i~~Re~La~~i~l~e~riqvwf~nrra~~rr~~~~ 237 (354)
T KOG0849|consen 175 GGRRNRTSFSPSQLEALEECF---QRTPYPDIVGRETLAKETGLPEPRVQVWFQNRRAKWRRQHRD 237 (354)
T ss_pred cccccccccccchHHHHHHHh---cCCCCCchhhHHHHhhhccCCchHHHHHHhhhhhhhhhcccc
Confidence 356678999999999999999 999999999999999999999999999999999999998744
No 34
>PF03790 KNOX1: KNOX1 domain ; InterPro: IPR005540 The MEINOX region is comprised of two domains, KNOX1 and KNOX2. KNOX1 plays a role in suppressing target gene expression. KNOX2, essential for function, is thought to be necessary for homo-dimerization [].; GO: 0003677 DNA binding, 0005634 nucleus
Probab=98.37 E-value=3.3e-07 Score=63.87 Aligned_cols=41 Identities=27% Similarity=0.517 Sum_probs=35.1
Q ss_pred HHHhhhhcCCChhHHHHHHHHhhhcccccccCCCCCCCCCchhhhhhhHHhh
Q psy8980 55 ARKHTLNCHRMKPSLFSVLCEIKEKTVLSLRNTQEEEPPDPQLMRLDNMLIA 106 (355)
Q Consensus 55 ~~k~~i~~Hpl~p~L~~~~~e~~e~~~~s~~~~~~e~~~d~q~~rldn~l~~ 106 (355)
..|++|.+||+||.|++++++|.+ .++|+| ++.+||.++.+
T Consensus 2 ~iKA~I~~HP~Y~~Ll~Ayi~C~K----------VGAP~e-~~~~L~e~~~~ 42 (45)
T PF03790_consen 2 AIKAKIASHPLYPRLLAAYIDCQK----------VGAPPE-VVARLDEILAE 42 (45)
T ss_pred hHHHHHHcCCCcHHHHHHHHHHHh----------cCCCHH-HHHHHHHHHHH
Confidence 469999999999999999999874 567888 78999998654
No 35
>KOG2252|consensus
Probab=98.12 E-value=3.5e-06 Score=86.20 Aligned_cols=58 Identities=31% Similarity=0.477 Sum_probs=54.8
Q ss_pred cccCCCCcCCCHHHHHHHHHHhhhcCCCCCCCHHHHHHHHHHcCCCcccccccccchhhhh
Q psy8980 225 LDARRKRRNFSKQASEILNEYFYSHLSNPYPSEEAKEELARKCNITVSQVSNWFGNKRIRY 285 (355)
Q Consensus 225 ~~~rr~R~~fs~~q~~~L~~~F~~H~~~pyPs~~er~~LA~~~gLt~~qV~~WFqNrR~R~ 285 (355)
...||.|.+|+..|++.|...| ..+++|+.+..+.|+.+++|..+.|.|||-|.|+|.
T Consensus 418 ~~~KKPRlVfTd~QkrTL~aiF---ke~~RPS~Emq~tIS~qL~L~~sTV~NfFmNaRRRs 475 (558)
T KOG2252|consen 418 LQTKKPRLVFTDIQKRTLQAIF---KENKRPSREMQETISQQLNLELSTVINFFMNARRRS 475 (558)
T ss_pred ccCCCceeeecHHHHHHHHHHH---hcCCCCCHHHHHHHHHHhCCcHHHHHHHHHhhhhhc
Confidence 3467789999999999999999 999999999999999999999999999999999995
No 36
>KOG0490|consensus
Probab=97.30 E-value=0.00021 Score=65.94 Aligned_cols=62 Identities=27% Similarity=0.589 Sum_probs=57.6
Q ss_pred cccCCCCcCCCHHHHHHHHHHhhhcCCCCCCCHHHHHHHHHHcCCCcccccccccchhhhhhhhh
Q psy8980 225 LDARRKRRNFSKQASEILNEYFYSHLSNPYPSEEAKEELARKCNITVSQVSNWFGNKRIRYKKNI 289 (355)
Q Consensus 225 ~~~rr~R~~fs~~q~~~L~~~F~~H~~~pyPs~~er~~LA~~~gLt~~qV~~WFqNrR~R~Kk~~ 289 (355)
.+.++.|+.+...++..+...| ..++||....+..|+..+|++...|++||+|+|.+.++..
T Consensus 151 ~~~~~~~~~~~~~~~~~~~~~~---~~~~~P~~~~~~~l~~~~~~~~~~~q~~~~~~~~~~~~~~ 212 (235)
T KOG0490|consen 151 KKPRRPRTTFTENQLEVLETVF---RATPKPDADDREQLAEETGLSERVIQVWFQNRRAKLRKHK 212 (235)
T ss_pred cccCCCccccccchhHhhhhcc---cCCCCCchhhHHHHHHhcCCChhhhhhhcccHHHHHHhhc
Confidence 3456778899999999999999 9999999999999999999999999999999999999876
No 37
>PF03791 KNOX2: KNOX2 domain ; InterPro: IPR005541 The MEINOX region is comprised of two domains, KNOX1 and KNOX2. KNOX1 plays a role in suppressing target gene expression. KNOX2, essential for function, is thought to be necessary for homo-dimerization [].; GO: 0003677 DNA binding, 0005634 nucleus
Probab=97.15 E-value=0.00069 Score=48.90 Aligned_cols=35 Identities=26% Similarity=0.357 Sum_probs=32.2
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q psy8980 145 RAKLAQIRQIYHQELEKYEQACNEFTTHVMNLLRE 179 (355)
Q Consensus 145 ~~kL~qvl~~y~~eLeky~~~~~~f~~~~i~ll~~ 179 (355)
+++|||||+.|+..|.+|++.+++.+.+++.+++.
T Consensus 8 dpELDqFMeaYc~~L~kykeeL~~p~~EA~~f~~~ 42 (52)
T PF03791_consen 8 DPELDQFMEAYCDMLVKYKEELQRPFQEAMEFCRE 42 (52)
T ss_pred CccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 67899999999999999999999999999888873
No 38
>KOG1146|consensus
Probab=96.62 E-value=0.002 Score=72.08 Aligned_cols=60 Identities=22% Similarity=0.306 Sum_probs=56.9
Q ss_pred cCCCCcCCCHHHHHHHHHHhhhcCCCCCCCHHHHHHHHHHcCCCcccccccccchhhhhhhhh
Q psy8980 227 ARRKRRNFSKQASEILNEYFYSHLSNPYPSEEAKEELARKCNITVSQVSNWFGNKRIRYKKNI 289 (355)
Q Consensus 227 ~rr~R~~fs~~q~~~L~~~F~~H~~~pyPs~~er~~LA~~~gLt~~qV~~WFqNrR~R~Kk~~ 289 (355)
.|+.|+.++..++..++.+| ....||..++.+.|-..+++..+.|.+||||.|.|.|+..
T Consensus 903 r~a~~~~~~d~qlk~i~~~~---~~q~~~~~~~~E~l~~~~~~~~~~i~vw~qna~~~s~k~~ 962 (1406)
T KOG1146|consen 903 RRAYRTQESDLQLKIIKACY---EAQRTPTMQECEVLEEPIGLPKRVIQVWFQNARAKSKKAK 962 (1406)
T ss_pred hhhhccchhHHHHHHHHHHH---hhccCChHHHHHhhcccccCCcchhHHhhhhhhhhhhhhh
Confidence 56789999999999999999 9999999999999999999999999999999999998876
No 39
>PF11569 Homez: Homeodomain leucine-zipper encoding, Homez; PDB: 2YS9_A.
Probab=96.52 E-value=0.00046 Score=50.51 Aligned_cols=42 Identities=29% Similarity=0.560 Sum_probs=30.4
Q ss_pred HHHHHHHhhhcCCCCCCCHHHHHHHHHHcCCCcccccccccchhh
Q psy8980 239 SEILNEYFYSHLSNPYPSEEAKEELARKCNITVSQVSNWFGNKRI 283 (355)
Q Consensus 239 ~~~L~~~F~~H~~~pyPs~~er~~LA~~~gLt~~qV~~WFqNrR~ 283 (355)
+..|++|| ..+.++.+.+-..|+.+++|+..||+.||--++.
T Consensus 10 ~~pL~~Yy---~~h~~L~E~DL~~L~~kS~ms~qqVr~WFa~~~~ 51 (56)
T PF11569_consen 10 IQPLEDYY---LKHKQLQEEDLDELCDKSRMSYQQVRDWFAERMQ 51 (56)
T ss_dssp -HHHHHHH---HHT----TTHHHHHHHHTT--HHHHHHHHHHHS-
T ss_pred hHHHHHHH---HHcCCccHhhHHHHHHHHCCCHHHHHHHHHHhcc
Confidence 45699999 7778999999999999999999999999975543
No 40
>KOG0773|consensus
Probab=95.66 E-value=0.0018 Score=63.88 Aligned_cols=114 Identities=26% Similarity=0.361 Sum_probs=84.4
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHHHhhhhHHHHHhhhhhHHHHHhhhhhhcccC
Q psy8980 149 AQIRQIYHQELEKYEQACNEFTTHVMNLLREQSRTRPITPKEIERMVQIIHKKFSSIQMQLKQSTCEAVMILRSRFLDAR 228 (355)
Q Consensus 149 ~qvl~~y~~eLeky~~~~~~f~~~~i~ll~~qs~~~pls~~~~~~~~~~~~~~f~~~~~~lk~~~~~~~~~l~~~~~~~r 228 (355)
..+...+...+...+.+|.+||.....+........++... . + .........
T Consensus 45 ~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~--~---------~-----------------~~~~~~~~~ 96 (342)
T KOG0773|consen 45 IMVSLASSKYLTAAQELLDEFCSAGLDCLKGKMPYDPVPRS--P---------A-----------------SLSPPEDKG 96 (342)
T ss_pred cccccccccccccchhHHhHHhhccccccccccCcCccccc--c---------c-----------------cccCccccc
Confidence 44555666778889999999999999998766544433220 0 0 000011123
Q ss_pred CCCcCCCHHHHHHHHHHhhhcCCCCCCCHHHHHHHHHHcCCCcccccccccchhhhhhhhhhh
Q psy8980 229 RKRRNFSKQASEILNEYFYSHLSNPYPSEEAKEELARKCNITVSQVSNWFGNKRIRYKKNIGK 291 (355)
Q Consensus 229 r~R~~fs~~q~~~L~~~F~~H~~~pyPs~~er~~LA~~~gLt~~qV~~WFqNrR~R~Kk~~~~ 291 (355)
+++...+.+. ..|..|...|..++||+..++..++..+.++..+|.+||.|.|++.++..+.
T Consensus 97 ~~~~n~~~~s-~~~~~~~~~~~~~~~~~k~~~~ll~~~~~~~~~~~~~~~~~a~r~~~~~~~~ 158 (342)
T KOG0773|consen 97 ARRGNATRES-ATLKAWLEEHRLNPYPSKLEKILLAVITKLTLTQVSTWFANARRRLKKELKM 158 (342)
T ss_pred cccccccccc-cccccchhhhhhccCchHHHHHHHHHHHHhhhhhHHHHHHHHHHHHHhccCC
Confidence 3555666666 7888999999999999999999999999999999999999999998886543
No 41
>KOG3623|consensus
Probab=90.34 E-value=0.17 Score=54.13 Aligned_cols=48 Identities=23% Similarity=0.464 Sum_probs=44.4
Q ss_pred HHHHHHHhhhcCCCCCCCHHHHHHHHHHcCCCcccccccccchhhhhhhhh
Q psy8980 239 SEILNEYFYSHLSNPYPSEEAKEELARKCNITVSQVSNWFGNKRIRYKKNI 289 (355)
Q Consensus 239 ~~~L~~~F~~H~~~pyPs~~er~~LA~~~gLt~~qV~~WFqNrR~R~Kk~~ 289 (355)
+.+|+.+| ..|+.|+.++-..+|.+.||....|+.||.+++.......
T Consensus 568 ~sllkayy---aln~~ps~eelskia~qvglp~~vvk~wfE~~~a~e~sv~ 615 (1007)
T KOG3623|consen 568 TSLLKAYY---ALNGLPSEEELSKIAQQVGLPFAVVKAWFEDEEAEEMSVE 615 (1007)
T ss_pred HHHHHHHH---HhcCCCCHHHHHHHHHHhcccHHHHHHHHHhhhhhhhhhc
Confidence 78899999 9999999999999999999999999999999998876654
No 42
>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=88.45 E-value=0.52 Score=33.99 Aligned_cols=46 Identities=24% Similarity=0.367 Sum_probs=31.8
Q ss_pred CCCCcCCCHHHHHHHHHHhhhcCCCCCCCHHHHHHHHHHcCCCcccccccccch
Q psy8980 228 RRKRRNFSKQASEILNEYFYSHLSNPYPSEEAKEELARKCNITVSQVSNWFGNK 281 (355)
Q Consensus 228 rr~R~~fs~~q~~~L~~~F~~H~~~pyPs~~er~~LA~~~gLt~~qV~~WFqNr 281 (355)
||+|..+|-++...+-..+ ...+ ....||..+|++.++|..|..|+
T Consensus 1 krkR~~LTl~eK~~iI~~~---e~g~-----s~~~ia~~fgv~~sTv~~I~K~k 46 (53)
T PF04218_consen 1 KRKRKSLTLEEKLEIIKRL---EEGE-----SKRDIAREFGVSRSTVSTILKNK 46 (53)
T ss_dssp SSSSSS--HHHHHHHHHHH---HCTT------HHHHHHHHT--CCHHHHHHHCH
T ss_pred CCCCccCCHHHHHHHHHHH---HcCC-----CHHHHHHHhCCCHHHHHHHHHhH
Confidence 4678889988866665556 4443 47789999999999999999874
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=55.04 E-value=11 Score=26.34 Aligned_cols=44 Identities=18% Similarity=0.261 Sum_probs=29.1
Q ss_pred CCCHHHHHHHHHHhhhcCCCCCCCHHHHHHHHHHcCCCcccccccccchhhh
Q psy8980 233 NFSKQASEILNEYFYSHLSNPYPSEEAKEELARKCNITVSQVSNWFGNKRIR 284 (355)
Q Consensus 233 ~fs~~q~~~L~~~F~~H~~~pyPs~~er~~LA~~~gLt~~qV~~WFqNrR~R 284 (355)
.++..+..++.-.|. ..-.-.++|..+|++...|++|....|.+
T Consensus 10 ~L~~~~r~i~~l~~~--------~g~s~~eIa~~l~~s~~~v~~~l~ra~~~ 53 (54)
T PF08281_consen 10 QLPERQREIFLLRYF--------QGMSYAEIAEILGISESTVKRRLRRARKK 53 (54)
T ss_dssp CS-HHHHHHHHHHHT--------S---HHHHHHHCTS-HHHHHHHHHHHHHH
T ss_pred CCCHHHHHHHHHHHH--------HCcCHHHHHHHHCcCHHHHHHHHHHHHhh
Confidence 456667777766552 22345789999999999999998766654
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=52.78 E-value=10 Score=26.33 Aligned_cols=46 Identities=15% Similarity=0.273 Sum_probs=32.9
Q ss_pred CCCHHHHHHHHHHhhhcCCCCCCCHHHHHHHHHHcCCCcccccccccchhhhhh
Q psy8980 233 NFSKQASEILNEYFYSHLSNPYPSEEAKEELARKCNITVSQVSNWFGNKRIRYK 286 (355)
Q Consensus 233 ~fs~~q~~~L~~~F~~H~~~pyPs~~er~~LA~~~gLt~~qV~~WFqNrR~R~K 286 (355)
.+++.+..+|...|+.. ..-.++|..+|++...|+.+......|.|
T Consensus 4 ~L~~~er~vi~~~y~~~--------~t~~eIa~~lg~s~~~V~~~~~~al~kLR 49 (50)
T PF04545_consen 4 QLPPREREVIRLRYFEG--------LTLEEIAERLGISRSTVRRILKRALKKLR 49 (50)
T ss_dssp TS-HHHHHHHHHHHTST---------SHHHHHHHHTSCHHHHHHHHHHHHHHHH
T ss_pred hCCHHHHHHHHHHhcCC--------CCHHHHHHHHCCcHHHHHHHHHHHHHHhc
Confidence 57788888888887211 22468899999999999888766666554
No 45
>PF03791 KNOX2: KNOX2 domain ; InterPro: IPR005541 The MEINOX region is comprised of two domains, KNOX1 and KNOX2. KNOX1 plays a role in suppressing target gene expression. KNOX2, essential for function, is thought to be necessary for homo-dimerization [].; GO: 0003677 DNA binding, 0005634 nucleus
Probab=48.86 E-value=95 Score=22.50 Aligned_cols=39 Identities=21% Similarity=0.297 Sum_probs=34.9
Q ss_pred cchhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q psy8980 140 EHSDYRAKLAQIRQIYHQELEKYEQACNEFTTHVMNLLR 178 (355)
Q Consensus 140 e~~~~~~kL~qvl~~y~~eLeky~~~~~~f~~~~i~ll~ 178 (355)
|.|..|..=-.++.-|.++|.+--+.+-.||.+..+-|.
T Consensus 10 ELDqFMeaYc~~L~kykeeL~~p~~EA~~f~~~ie~qL~ 48 (52)
T PF03791_consen 10 ELDQFMEAYCDMLVKYKEELQRPFQEAMEFCREIEQQLS 48 (52)
T ss_pred cHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 678899999999999999999998999999998877665
No 46
>PF01527 HTH_Tnp_1: Transposase; InterPro: IPR002514 Transposase proteins are necessary for efficient DNA transposition. This family consists of various Escherichia coli insertion elements and other bacterial transposases some of which are members of the IS3 family. This region includes a helix-turn-helix motif (HTH) at the N terminus followed by a leucine zipper (LZ) motif. The LZ motif has been shown to mediate oligomerisation of the transposase components in IS911 []. More information about these proteins can be found at Protein of the Month: Transposase [].; GO: 0003677 DNA binding, 0004803 transposase activity, 0006313 transposition, DNA-mediated; PDB: 2JN6_A 2RN7_A.
Probab=45.99 E-value=7.3 Score=29.20 Aligned_cols=42 Identities=38% Similarity=0.555 Sum_probs=26.2
Q ss_pred CCCcCCCHHHHHHH-HHHhhhcCCCCCCCHHHHHHHHHHcCCCcccccccc
Q psy8980 229 RKRRNFSKQASEIL-NEYFYSHLSNPYPSEEAKEELARKCNITVSQVSNWF 278 (355)
Q Consensus 229 r~R~~fs~~q~~~L-~~~F~~H~~~pyPs~~er~~LA~~~gLt~~qV~~WF 278 (355)
++|+.||.++...+ ..++ -.......+|..+|++..++.+|-
T Consensus 2 ~~r~~ys~e~K~~~v~~~~--------~~g~sv~~va~~~gi~~~~l~~W~ 44 (76)
T PF01527_consen 2 RKRRRYSPEFKLQAVREYL--------ESGESVSEVAREYGISPSTLYNWR 44 (76)
T ss_dssp -SS----HHHHHHHHHHHH--------HHHCHHHHHHHHHTS-HHHHHHHH
T ss_pred CCCCCCCHHHHHHHHHHHH--------HCCCceEeeecccccccccccHHH
Confidence 46678888886544 4443 223567789999999999999995
No 47
>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=45.26 E-value=9.6 Score=25.47 Aligned_cols=44 Identities=18% Similarity=0.180 Sum_probs=30.3
Q ss_pred CCCHHHHHHHHHHhhhcCCCCCCCHHHHHHHHHHcCCCcccccccccchhhh
Q psy8980 233 NFSKQASEILNEYFYSHLSNPYPSEEAKEELARKCNITVSQVSNWFGNKRIR 284 (355)
Q Consensus 233 ~fs~~q~~~L~~~F~~H~~~pyPs~~er~~LA~~~gLt~~qV~~WFqNrR~R 284 (355)
.++..+..++..+| ... ..-..+|..+|++...|..|....+.+
T Consensus 10 ~l~~~~~~~~~~~~---~~~-----~~~~~ia~~~~~s~~~i~~~~~~~~~~ 53 (55)
T cd06171 10 KLPEREREVILLRF---GEG-----LSYEEIAEILGISRSTVRQRLHRALKK 53 (55)
T ss_pred hCCHHHHHHHHHHH---hcC-----CCHHHHHHHHCcCHHHHHHHHHHHHHH
Confidence 35666667776665 211 235678999999999999998665544
No 48
>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=41.12 E-value=6.9 Score=30.51 Aligned_cols=52 Identities=21% Similarity=0.256 Sum_probs=30.2
Q ss_pred HHHHHHHHHHHHHHHHHHHHhhcCCCC-CCHHHHHHHHHHHHhhhhHHHHHhh
Q psy8980 159 LEKYEQACNEFTTHVMNLLREQSRTRP-ITPKEIERMVQIIHKKFSSIQMQLK 210 (355)
Q Consensus 159 Leky~~~~~~f~~~~i~ll~~qs~~~p-ls~~~~~~~~~~~~~~f~~~~~~lk 210 (355)
++..+++.+.|..+.|.+..+|..++. +.......++++.+++|+.++..++
T Consensus 6 ~~ele~Fa~~fk~rRi~LG~TQ~dVg~al~~~~G~~~SQttI~RFE~L~LS~k 58 (75)
T PF00157_consen 6 LKELEQFAKEFKQRRIKLGYTQADVGAALGRLYGKEFSQTTICRFEALQLSFK 58 (75)
T ss_dssp HHHHHHHHHHHHHHHHHTT--HHHHHHHHHHHHSSGGSHHHHHHHHTTTSCHH
T ss_pred HHHHHHHHHHHHHhhhhcccCHHHHhHHHHHhcCccccchhhhhhHhcccCHH
Confidence 445556688999999999887754321 1111112345667778877755544
No 49
>PRK03975 tfx putative transcriptional regulator; Provisional
Probab=38.96 E-value=35 Score=29.72 Aligned_cols=50 Identities=16% Similarity=0.080 Sum_probs=39.1
Q ss_pred CcCCCHHHHHHHHHHhhhcCCCCCCCHHHHHHHHHHcCCCcccccccccchhhhhhhhh
Q psy8980 231 RRNFSKQASEILNEYFYSHLSNPYPSEEAKEELARKCNITVSQVSNWFGNKRIRYKKNI 289 (355)
Q Consensus 231 R~~fs~~q~~~L~~~F~~H~~~pyPs~~er~~LA~~~gLt~~qV~~WFqNrR~R~Kk~~ 289 (355)
...+++.+..+|...+ ... ...++|..+|++...|+.|-.+.+.+.++..
T Consensus 4 ~~~Lt~rqreVL~lr~---~Gl------Tq~EIAe~LGiS~~tVs~ie~ra~kkLr~~~ 53 (141)
T PRK03975 4 ESFLTERQIEVLRLRE---RGL------TQQEIADILGTSRANVSSIEKRARENIEKAR 53 (141)
T ss_pred ccCCCHHHHHHHHHHH---cCC------CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 3578889999997744 211 2468999999999999999998888877765
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=35.00 E-value=44 Score=19.63 Aligned_cols=38 Identities=13% Similarity=0.226 Sum_probs=24.7
Q ss_pred CCCHHHHHHHHHHhhhcCCCCCCCHHHHHHHHHHcCCCcccccccc
Q psy8980 233 NFSKQASEILNEYFYSHLSNPYPSEEAKEELARKCNITVSQVSNWF 278 (355)
Q Consensus 233 ~fs~~q~~~L~~~F~~H~~~pyPs~~er~~LA~~~gLt~~qV~~WF 278 (355)
.++......+...| . +.+ ....+|..++++...|.+|.
T Consensus 5 ~~~~~~~~~i~~~~---~-~~~----s~~~ia~~~~is~~tv~~~~ 42 (42)
T cd00569 5 KLTPEQIEEARRLL---A-AGE----SVAEIARRLGVSRSTLYRYL 42 (42)
T ss_pred cCCHHHHHHHHHHH---H-cCC----CHHHHHHHHCCCHHHHHHhC
Confidence 45555555555555 2 222 34578889999998888874
No 51
>PRK09652 RNA polymerase sigma factor RpoE; Provisional
Probab=33.09 E-value=20 Score=30.81 Aligned_cols=49 Identities=10% Similarity=0.076 Sum_probs=36.2
Q ss_pred CCCHHHHHHHHHHhhhcCCCCCCCHHHHHHHHHHcCCCcccccccccchhhhhhhhh
Q psy8980 233 NFSKQASEILNEYFYSHLSNPYPSEEAKEELARKCNITVSQVSNWFGNKRIRYKKNI 289 (355)
Q Consensus 233 ~fs~~q~~~L~~~F~~H~~~pyPs~~er~~LA~~~gLt~~qV~~WFqNrR~R~Kk~~ 289 (355)
.+++.+..++...|. . .+ .-.++|..+|++...|++|....+.+.|+..
T Consensus 128 ~L~~~~r~vl~l~~~--~--~~----s~~eIA~~lgis~~tV~~~l~ra~~~Lr~~l 176 (182)
T PRK09652 128 SLPEELRTAITLREI--E--GL----SYEEIAEIMGCPIGTVRSRIFRAREALRAKL 176 (182)
T ss_pred hCCHHHHHHHHHHHH--c--CC----CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 467777778866542 1 11 2457899999999999999988888777755
No 52
>PRK06759 RNA polymerase factor sigma-70; Validated
Probab=32.45 E-value=23 Score=29.90 Aligned_cols=47 Identities=17% Similarity=0.257 Sum_probs=34.3
Q ss_pred CCCHHHHHHHHHHhhhcCCCCCCCHHHHHHHHHHcCCCcccccccccchhhhhhh
Q psy8980 233 NFSKQASEILNEYFYSHLSNPYPSEEAKEELARKCNITVSQVSNWFGNKRIRYKK 287 (355)
Q Consensus 233 ~fs~~q~~~L~~~F~~H~~~pyPs~~er~~LA~~~gLt~~qV~~WFqNrR~R~Kk 287 (355)
.+++.+..++...|+ .. ..-.++|..+|++...|++|....|.+.|+
T Consensus 106 ~L~~~~r~ii~l~~~--~~------~s~~EIA~~l~is~~tV~~~~~ra~~~Lr~ 152 (154)
T PRK06759 106 VLDEKEKYIIFERFF--VG------KTMGEIALETEMTYYQVRWIYRQALEKMRN 152 (154)
T ss_pred hCCHHHHHHHHHHHh--cC------CCHHHHHHHHCCCHHHHHHHHHHHHHHHhh
Confidence 566777777765542 22 125689999999999999998777777665
No 53
>PRK11924 RNA polymerase sigma factor; Provisional
Probab=31.93 E-value=25 Score=30.09 Aligned_cols=49 Identities=12% Similarity=0.147 Sum_probs=35.1
Q ss_pred CCHHHHHHHHHHhhhcCCCCCCCHHHHHHHHHHcCCCcccccccccchhhhhhhhhh
Q psy8980 234 FSKQASEILNEYFYSHLSNPYPSEEAKEELARKCNITVSQVSNWFGNKRIRYKKNIG 290 (355)
Q Consensus 234 fs~~q~~~L~~~F~~H~~~pyPs~~er~~LA~~~gLt~~qV~~WFqNrR~R~Kk~~~ 290 (355)
+++.+..++...|. . ...-.++|..+|++...|++|..-.|.|.|+...
T Consensus 126 L~~~~r~i~~l~~~--~------~~~~~eIA~~lgis~~tv~~~~~ra~~~lr~~l~ 174 (179)
T PRK11924 126 LPVKQREVFLLRYV--E------GLSYREIAEILGVPVGTVKSRLRRARQLLRECLE 174 (179)
T ss_pred CCHHHHHHhhHHHH--c------CCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Confidence 55566666655541 1 1234689999999999999999888888777553
No 54
>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=30.63 E-value=56 Score=26.42 Aligned_cols=30 Identities=40% Similarity=0.678 Sum_probs=15.9
Q ss_pred CCCCCCCHHHHHHHHHHcCCCcccccccccchhhhhhhhhhhhh
Q psy8980 250 LSNPYPSEEAKEELARKCNITVSQVSNWFGNKRIRYKKNIGKAQ 293 (355)
Q Consensus 250 ~~~pyPs~~er~~LA~~~gLt~~qV~~WFqNrR~R~Kk~~~~~~ 293 (355)
..||||+..-... |+ .|||+||++......
T Consensus 22 qsnPyP~~~GTr~-aR-------------RnRRRRWR~rq~QI~ 51 (91)
T PF00424_consen 22 QSNPYPSPEGTRQ-AR-------------RNRRRRWRARQRQIR 51 (91)
T ss_dssp HTS-S--S-S-HH-HH-------------HHHHHHHHHHHHHHH
T ss_pred ccccCCCCCCccc-cc-------------cchhhhHHHHHHHHH
Confidence 7899998542221 11 389999988775444
No 55
>PF13551 HTH_29: Winged helix-turn helix
Probab=30.62 E-value=1.6e+02 Score=23.12 Aligned_cols=49 Identities=16% Similarity=0.181 Sum_probs=26.7
Q ss_pred CCcCCCHHHHHHHHHHhhhcCCCC--CCCHHHHHH-H-HHHcC--CCcccccccc
Q psy8980 230 KRRNFSKQASEILNEYFYSHLSNP--YPSEEAKEE-L-ARKCN--ITVSQVSNWF 278 (355)
Q Consensus 230 ~R~~fs~~q~~~L~~~F~~H~~~p--yPs~~er~~-L-A~~~g--Lt~~qV~~WF 278 (355)
.+..++.++...|.+++.++.... ..+...-.. | ....+ ++...|..|+
T Consensus 54 ~~~~l~~~~~~~l~~~~~~~p~~g~~~~t~~~l~~~l~~~~~~~~~s~~ti~r~L 108 (112)
T PF13551_consen 54 PRKRLSEEQRAQLIELLRENPPEGRSRWTLEELAEWLIEEEFGIDVSPSTIRRIL 108 (112)
T ss_pred CCCCCCHHHHHHHHHHHHHCCCCCCCcccHHHHHHHHHHhccCccCCHHHHHHHH
Confidence 333389999999999994332211 233333333 4 33333 5555566554
No 56
>KOG1146|consensus
Probab=30.10 E-value=42 Score=39.05 Aligned_cols=60 Identities=22% Similarity=0.242 Sum_probs=52.2
Q ss_pred cCCCCcCCCHHHHHHHHHHhhhcCCCCCCCHHHHHHHHHHcCCCcccccccccchhhhhhhhh
Q psy8980 227 ARRKRRNFSKQASEILNEYFYSHLSNPYPSEEAKEELARKCNITVSQVSNWFGNKRIRYKKNI 289 (355)
Q Consensus 227 ~rr~R~~fs~~q~~~L~~~F~~H~~~pyPs~~er~~LA~~~gLt~~qV~~WFqNrR~R~Kk~~ 289 (355)
.+.-+.+.-.++...|-.|| ..+--|+...+..|......+.+++.+||.|-|.|.++..
T Consensus 705 ~~~~~~~~~~~aa~~l~~a~---~~~~sps~k~~~civcd~~st~~l~~l~~h~~~~rs~ke~ 764 (1406)
T KOG1146|consen 705 DKLLRLTILPEAAMILGRAY---MQDNSPSLKVFDCIVCDVFSTDRLDQLWFHNTRERSRKEQ 764 (1406)
T ss_pred cccCcccccHHHHhhhhhcc---cCCCCHHHHHHHHhhhhhhhhhhHHHHhhcchhhhhhhhc
Confidence 34456667778999999999 8888999999999999999999999999999999988865
No 57
>PRK09646 RNA polymerase sigma factor SigK; Reviewed
Probab=29.57 E-value=30 Score=30.78 Aligned_cols=49 Identities=14% Similarity=0.251 Sum_probs=36.5
Q ss_pred CCCHHHHHHHHHHhhhcCCCCCCCHHHHHHHHHHcCCCcccccccccchhhhhhhhh
Q psy8980 233 NFSKQASEILNEYFYSHLSNPYPSEEAKEELARKCNITVSQVSNWFGNKRIRYKKNI 289 (355)
Q Consensus 233 ~fs~~q~~~L~~~F~~H~~~pyPs~~er~~LA~~~gLt~~qV~~WFqNrR~R~Kk~~ 289 (355)
.++..+..+|.-.|+ .. ..-.++|..+|++...|++|....|++.|+..
T Consensus 142 ~L~~~~r~vl~l~~~--~~------~s~~EIA~~Lgis~~tVk~~l~ra~~~Lr~~l 190 (194)
T PRK09646 142 ALTDTQRESVTLAYY--GG------LTYREVAERLAVPLGTVKTRMRDGLIRLRDCL 190 (194)
T ss_pred hCCHHHHHHHHHHHH--cC------CCHHHHHHHhCCChHhHHHHHHHHHHHHHHHh
Confidence 477777788866542 11 23468999999999999999988888877655
No 58
>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=29.28 E-value=20 Score=26.73 Aligned_cols=18 Identities=22% Similarity=0.599 Sum_probs=16.2
Q ss_pred HHHHHHHcCCCccccccc
Q psy8980 260 KEELARKCNITVSQVSNW 277 (355)
Q Consensus 260 r~~LA~~~gLt~~qV~~W 277 (355)
-..||.++|++..+|+.|
T Consensus 25 lkdIA~~Lgvs~~tIr~W 42 (60)
T PF10668_consen 25 LKDIAEKLGVSESTIRKW 42 (60)
T ss_pred HHHHHHHHCCCHHHHHHH
Confidence 457899999999999998
No 59
>PF00196 GerE: Bacterial regulatory proteins, luxR family; InterPro: IPR000792 This domain is a DNA-binding, helix-turn-helix (HTH) domain of about 65 amino acids, present in transcription regulators of the LuxR/FixJ family of response regulators. The domain is named after Vibrio fischeri luxR, a transcriptional activator for quorum-sensing control of luminescence. LuxR-type HTH domain proteins occur in a variety of organisms. The DNA-binding HTH domain is usually located in the C-terminal region; the N-terminal region often containing an autoinducer-binding domain or a response regulatory domain. Most luxR-type regulators act as transcription activators, but some can be repressors or have a dual role for different sites. LuxR-type HTH regulators control a wide variety of activities in various biological processes. The luxR-type, DNA-binding HTH domain forms a four-helical bundle structure. The HTH motif comprises the second and third helices, known as the scaffold and recognition helix, respectively. The HTH binds DNA in the major groove, where the N-terminal part of the recognition helix makes most of the DNA contacts. The fourth helix is involved in dimerisation of gerE and traR. Signalling events by one of the four activation mechanisms described below lead to multimerisation of the regulator. The regulators bind DNA as multimers [, , ]. LuxR-type HTH proteins can be activated by one of four different mechanisms: 1) Regulators which belong to a two-component sensory transduction system where the protein is activated by its phosphorylation, generally on an aspartate residue, by a transmembrane kinase [, ]. Some proteins that belong to this category are: Rhizobiaceae fixJ (global regulator inducing expression of nitrogen-fixation genes in microaerobiosis) Escherichia coli and Salmonella typhimurium uhpA (activates hexose phosphate transport gene uhpT) E. coli narL and narP (activate nitrate reductase operon) Enterobacteria rcsB (regulation of exopolysaccharide biosynthesis in enteric and plant pathogenesis) Bordetella pertussis bvgA (virulence factor) Bacillus subtilis coma (involved in expression of late-expressing competence genes) 2) Regulators which are activated, or in very rare cases repressed, when bound to N-acyl homoserine lactones, which are used as quorum sensing molecules in a variety of Gram-negative bacteria []: V. fischeri luxR (activates bioluminescence operon) Agrobacterium tumefaciens traR (regulation of Ti plasmid transfer) Erwinia carotovora carR (control of carbapenem antibiotics biosynthesis) E. carotovora expR (virulence factor for soft rot disease; activates plant tissue macerating enzyme genes) Pseudomonas aeruginosa lasR (activates elastase gene lasB) Erwinia chrysanthemi echR and Erwinia stewartii esaR Pseudomonas chlororaphis phzR (positive regulator of phenazine antibiotic production) Pseudomonas aeruginosa rhlR (activates rhlAB operon and lasB gene) 3) Autonomous effector domain regulators, without a regulatory domain, represented by gerE []. B. subtilis gerE (transcription activator and repressor for the regulation of spore formation) 4) Multiple ligand-binding regulators, exemplified by malT []. E. coli malT (activates maltose operon; MalT binds ATP and maltotriose); GO: 0003700 sequence-specific DNA binding transcription factor activity, 0043565 sequence-specific DNA binding, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 3SZT_A 3CLO_A 1H0M_A 1L3L_A 3C57_B 1ZLK_B 1ZLJ_H 3C3W_B 1RNL_A 1ZG1_A ....
Probab=27.94 E-value=49 Score=23.56 Aligned_cols=48 Identities=13% Similarity=0.108 Sum_probs=35.6
Q ss_pred CCCHHHHHHHHHHhhhcCCCCCCCHHHHHHHHHHcCCCcccccccccchhhhhhhhh
Q psy8980 233 NFSKQASEILNEYFYSHLSNPYPSEEAKEELARKCNITVSQVSNWFGNKRIRYKKNI 289 (355)
Q Consensus 233 ~fs~~q~~~L~~~F~~H~~~pyPs~~er~~LA~~~gLt~~qV~~WFqNrR~R~Kk~~ 289 (355)
.||..+..+|.-+. ... ...++|..+++++..|..+..+-+.|..-..
T Consensus 3 ~LT~~E~~vl~~l~---~G~------~~~eIA~~l~is~~tV~~~~~~i~~Kl~~~~ 50 (58)
T PF00196_consen 3 SLTERELEVLRLLA---QGM------SNKEIAEELGISEKTVKSHRRRIMKKLGVKN 50 (58)
T ss_dssp SS-HHHHHHHHHHH---TTS-------HHHHHHHHTSHHHHHHHHHHHHHHHHT-SS
T ss_pred ccCHHHHHHHHHHH---hcC------CcchhHHhcCcchhhHHHHHHHHHHHhCCCC
Confidence 57888888888776 222 3568899999999999999888888765544
No 60
>TIGR02937 sigma70-ECF RNA polymerase sigma factor, sigma-70 family. Several PFAM models hit segments of these sequences including Sigma-70 region 2 (pfam04542) and Sigma-70, region 4 (pfam04545), but not always above their respective trusted cutoffs.
Probab=27.22 E-value=33 Score=27.90 Aligned_cols=47 Identities=17% Similarity=0.297 Sum_probs=33.2
Q ss_pred CCCHHHHHHHHHHhhhcCCCCCCCHHHHHHHHHHcCCCcccccccccchhhhhhh
Q psy8980 233 NFSKQASEILNEYFYSHLSNPYPSEEAKEELARKCNITVSQVSNWFGNKRIRYKK 287 (355)
Q Consensus 233 ~fs~~q~~~L~~~F~~H~~~pyPs~~er~~LA~~~gLt~~qV~~WFqNrR~R~Kk 287 (355)
.+++.+..++...|. ..+ ...++|..+|++...|.+|....+.|.|+
T Consensus 110 ~L~~~~~~ii~~~~~----~g~----s~~eIA~~l~~s~~~v~~~~~~~~~kl~~ 156 (158)
T TIGR02937 110 KLPEREREVLVLRYL----EGL----SYKEIAEILGISVGTVKRRLKRARKKLRE 156 (158)
T ss_pred hCCHHHHHHHhhHHh----cCC----CHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Confidence 456667777765542 222 34589999999999999998777766654
No 61
>PRK09642 RNA polymerase sigma factor SigW; Reviewed
Probab=26.70 E-value=45 Score=28.36 Aligned_cols=49 Identities=16% Similarity=0.168 Sum_probs=35.9
Q ss_pred CCCHHHHHHHHHHhhhcCCCCCCCHHHHHHHHHHcCCCcccccccccchhhhhhhhh
Q psy8980 233 NFSKQASEILNEYFYSHLSNPYPSEEAKEELARKCNITVSQVSNWFGNKRIRYKKNI 289 (355)
Q Consensus 233 ~fs~~q~~~L~~~F~~H~~~pyPs~~er~~LA~~~gLt~~qV~~WFqNrR~R~Kk~~ 289 (355)
.++..+..++.-.|+ ..- .-.++|..+|++...|++++...|.+.|+..
T Consensus 106 ~Lp~~~r~v~~l~~~--~g~------s~~EIA~~lgis~~tV~~~l~Rar~~Lr~~l 154 (160)
T PRK09642 106 ELPENYRDVVLAHYL--EEK------SYQEIALQEKIEVKTVEMKLYRARKWIKKHW 154 (160)
T ss_pred hCCHHHHHHHHHHHH--hCC------CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 467777777765542 222 2358999999999999999988888877765
No 62
>PF13443 HTH_26: Cro/C1-type HTH DNA-binding domain; PDB: 3TYR_A 3TYS_A 3B7H_A.
Probab=25.57 E-value=22 Score=25.54 Aligned_cols=26 Identities=31% Similarity=0.411 Sum_probs=18.0
Q ss_pred HHHHHHHHcCCCcccccccccchhhh
Q psy8980 259 AKEELARKCNITVSQVSNWFGNKRIR 284 (355)
Q Consensus 259 er~~LA~~~gLt~~qV~~WFqNrR~R 284 (355)
....||+.+|++..+|..|+.++..+
T Consensus 12 t~~~La~~~gis~~tl~~~~~~~~~~ 37 (63)
T PF13443_consen 12 TQKDLARKTGISRSTLSRILNGKPSN 37 (63)
T ss_dssp -HHHHHHHHT--HHHHHHHHTTT---
T ss_pred CHHHHHHHHCcCHHHHHHHHhccccc
Confidence 35689999999999999999877433
No 63
>PRK12526 RNA polymerase sigma factor; Provisional
Probab=25.13 E-value=38 Score=30.60 Aligned_cols=49 Identities=12% Similarity=0.297 Sum_probs=35.9
Q ss_pred CCCHHHHHHHHHHhhhcCCCCCCCHHHHHHHHHHcCCCcccccccccchhhhhhhhh
Q psy8980 233 NFSKQASEILNEYFYSHLSNPYPSEEAKEELARKCNITVSQVSNWFGNKRIRYKKNI 289 (355)
Q Consensus 233 ~fs~~q~~~L~~~F~~H~~~pyPs~~er~~LA~~~gLt~~qV~~WFqNrR~R~Kk~~ 289 (355)
.++..+..++...|+ ... .-.++|..+|++...|+++....|.+.++..
T Consensus 153 ~L~~~~r~vl~l~~~--~g~------s~~EIA~~lgis~~tV~~~l~Ra~~~Lr~~l 201 (206)
T PRK12526 153 KLPEAQQTVVKGVYF--QEL------SQEQLAQQLNVPLGTVKSRLRLALAKLKVQM 201 (206)
T ss_pred hCCHHHHHHHHHHHH--cCC------CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 466777777765442 211 3568999999999999999888887777655
No 64
>PRK09413 IS2 repressor TnpA; Reviewed
Probab=25.12 E-value=85 Score=26.11 Aligned_cols=43 Identities=23% Similarity=0.298 Sum_probs=28.9
Q ss_pred CCCcCCCHHHHHH-HHHHhhhcCCCCCCCHHHHHHHHHHcCCCccccccccc
Q psy8980 229 RKRRNFSKQASEI-LNEYFYSHLSNPYPSEEAKEELARKCNITVSQVSNWFG 279 (355)
Q Consensus 229 r~R~~fs~~q~~~-L~~~F~~H~~~pyPs~~er~~LA~~~gLt~~qV~~WFq 279 (355)
++|++|+.+.... +...+ .+.+ ...++|..+|++..+|.+|..
T Consensus 8 ~~rr~ys~EfK~~aV~~~~----~~g~----sv~evA~e~gIs~~tl~~W~r 51 (121)
T PRK09413 8 EKRRRRTTQEKIAIVQQSF----EPGM----TVSLVARQHGVAASQLFLWRK 51 (121)
T ss_pred CCCCCCCHHHHHHHHHHHH----cCCC----CHHHHHHHHCcCHHHHHHHHH
Confidence 3456788887543 44443 2222 245789999999999999954
No 65
>PF06738 DUF1212: Protein of unknown function (DUF1212); InterPro: IPR010619 This entry represents a predicted domain found within a number of hypothetical proteins of unknown function found in eukaryotes, bacteria and archaea. Some of these sequences are predicted to be membrane proteins.
Probab=24.71 E-value=1.1e+02 Score=27.32 Aligned_cols=44 Identities=16% Similarity=0.295 Sum_probs=32.9
Q ss_pred cCcCcHHHHHHHHHhhcccCchHHHHHHhhhhcCC-ChhHHHHHHH
Q psy8980 30 PRKQDIGEILQQIMNITDQCLDEAQARKHTLNCHR-MKPSLFSVLC 74 (355)
Q Consensus 30 ~~~~~~~~~~~~~~~~~~~~ld~~~~~k~~i~~Hp-l~p~L~~~~~ 74 (355)
.+-..+.++..++.. .+.++||+.++..+|..-| -||..+.++.
T Consensus 65 ~~l~~v~~l~~~~~~-~~~~~~ea~~~L~~I~~~~~~y~~~~~~l~ 109 (193)
T PF06738_consen 65 DKLAAVNRLSRRIVA-GQLSLEEAIERLDEIDREPPRYPPWLVILA 109 (193)
T ss_pred HHHHHHHHHHHHHhc-CCCCHHHHHHHHHHHhhCCCCCCHHHHHHH
Confidence 444566777777776 8899999999877777655 8888866664
No 66
>PRK00118 putative DNA-binding protein; Validated
Probab=23.99 E-value=46 Score=27.49 Aligned_cols=52 Identities=12% Similarity=0.174 Sum_probs=38.1
Q ss_pred CCCHHHHHHHHHHhhhcCCCCCCCHHHHHHHHHHcCCCcccccccccchhhhhhhhhhhh
Q psy8980 233 NFSKQASEILNEYFYSHLSNPYPSEEAKEELARKCNITVSQVSNWFGNKRIRYKKNIGKA 292 (355)
Q Consensus 233 ~fs~~q~~~L~~~F~~H~~~pyPs~~er~~LA~~~gLt~~qV~~WFqNrR~R~Kk~~~~~ 292 (355)
.++..+..++..+|+. ...-.++|..+|++...|..|....|.+.|+...+.
T Consensus 17 ~L~ekqRevl~L~y~e--------g~S~~EIAe~lGIS~~TV~r~L~RArkkLr~~~~~~ 68 (104)
T PRK00118 17 LLTEKQRNYMELYYLD--------DYSLGEIAEEFNVSRQAVYDNIKRTEKLLEDYEEKL 68 (104)
T ss_pred cCCHHHHHHHHHHHHc--------CCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHHH
Confidence 4566677777666521 123457999999999999999988888888766553
No 67
>PRK09639 RNA polymerase sigma factor SigX; Provisional
Probab=23.81 E-value=51 Score=28.10 Aligned_cols=51 Identities=20% Similarity=0.311 Sum_probs=36.9
Q ss_pred CCCHHHHHHHHHHhhhcCCCCCCCHHHHHHHHHHcCCCcccccccccchhhhhhhhhhhh
Q psy8980 233 NFSKQASEILNEYFYSHLSNPYPSEEAKEELARKCNITVSQVSNWFGNKRIRYKKNIGKA 292 (355)
Q Consensus 233 ~fs~~q~~~L~~~F~~H~~~pyPs~~er~~LA~~~gLt~~qV~~WFqNrR~R~Kk~~~~~ 292 (355)
.++..+..+|.-.| . .+ .-.+||..+|++...|+++....|.+.|+...+.
T Consensus 112 ~L~~~~r~il~l~~-~----g~----s~~eIA~~lgis~~tV~~~i~ra~~~Lr~~l~~~ 162 (166)
T PRK09639 112 KMTERDRTVLLLRF-S----GY----SYKEIAEALGIKESSVGTTLARAKKKFRKIYEQM 162 (166)
T ss_pred cCCHHHHHHHHHHH-c----CC----CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHh
Confidence 35666666665544 1 22 3568999999999999999988888888766443
No 68
>PRK12514 RNA polymerase sigma factor; Provisional
Probab=22.86 E-value=47 Score=28.91 Aligned_cols=49 Identities=10% Similarity=0.380 Sum_probs=34.4
Q ss_pred CCCHHHHHHHHHHhhhcCCCCCCCHHHHHHHHHHcCCCcccccccccchhhhhhhhh
Q psy8980 233 NFSKQASEILNEYFYSHLSNPYPSEEAKEELARKCNITVSQVSNWFGNKRIRYKKNI 289 (355)
Q Consensus 233 ~fs~~q~~~L~~~F~~H~~~pyPs~~er~~LA~~~gLt~~qV~~WFqNrR~R~Kk~~ 289 (355)
.++..+..++...|+ .. + .-.++|..+|++...|+++....|.+.|+..
T Consensus 129 ~L~~~~r~i~~l~~~--~g--~----s~~eIA~~lgis~~tV~~~l~Rar~~Lr~~l 177 (179)
T PRK12514 129 ELEKDRAAAVRRAYL--EG--L----SYKELAERHDVPLNTMRTWLRRSLLKLRECL 177 (179)
T ss_pred hCCHHHHHHHHHHHH--cC--C----CHHHHHHHHCCChHHHHHHHHHHHHHHHHHh
Confidence 355566666655542 11 1 2568999999999999999888888777643
No 69
>PRK09644 RNA polymerase sigma factor SigM; Provisional
Probab=22.04 E-value=51 Score=28.31 Aligned_cols=50 Identities=12% Similarity=0.046 Sum_probs=36.4
Q ss_pred cCCCHHHHHHHHHHhhhcCCCCCCCHHHHHHHHHHcCCCcccccccccchhhhhhhhh
Q psy8980 232 RNFSKQASEILNEYFYSHLSNPYPSEEAKEELARKCNITVSQVSNWFGNKRIRYKKNI 289 (355)
Q Consensus 232 ~~fs~~q~~~L~~~F~~H~~~pyPs~~er~~LA~~~gLt~~qV~~WFqNrR~R~Kk~~ 289 (355)
..++..+..++.-+|..+ ...+++|..+|++...|++|..-.|.+.|+..
T Consensus 107 ~~L~~~~r~v~~l~~~~g--------~s~~eIA~~lgis~~tv~~~l~Rar~~Lr~~l 156 (165)
T PRK09644 107 HTLPVIEAQAILLCDVHE--------LTYEEAASVLDLKLNTYKSHLFRGRKRLKALL 156 (165)
T ss_pred HhCCHHHHHHHHhHHHhc--------CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 356677777776554211 23568999999999999999887777777755
No 70
>PRK10072 putative transcriptional regulator; Provisional
Probab=21.86 E-value=33 Score=27.88 Aligned_cols=41 Identities=20% Similarity=0.166 Sum_probs=29.9
Q ss_pred CCCHHHHHHHHHHhhhcCCCCCCCHHHHHHHHHHcCCCcccccccccchhh
Q psy8980 233 NFSKQASEILNEYFYSHLSNPYPSEEAKEELARKCNITVSQVSNWFGNKRI 283 (355)
Q Consensus 233 ~fs~~q~~~L~~~F~~H~~~pyPs~~er~~LA~~~gLt~~qV~~WFqNrR~ 283 (355)
..+...+..|.... .. ...+||+.+|++...|..|...+|.
T Consensus 32 ~~~~~eik~LR~~~---gl-------TQ~elA~~lGvS~~TVs~WE~G~r~ 72 (96)
T PRK10072 32 TTSFTEFEQLRKGT---GL-------KIDDFARVLGVSVAMVKEWESRRVK 72 (96)
T ss_pred cCChHHHHHHHHHc---CC-------CHHHHHHHhCCCHHHHHHHHcCCCC
Confidence 33566666776554 22 2578999999999999999987754
No 71
>PRK12543 RNA polymerase sigma factor; Provisional
Probab=21.62 E-value=86 Score=27.37 Aligned_cols=55 Identities=9% Similarity=0.121 Sum_probs=39.2
Q ss_pred CCCHHHHHHHHHHhhhcCCCCCCCHHHHHHHHHHcCCCcccccccccchhhhhhhhhhhhhHH
Q psy8980 233 NFSKQASEILNEYFYSHLSNPYPSEEAKEELARKCNITVSQVSNWFGNKRIRYKKNIGKAQEE 295 (355)
Q Consensus 233 ~fs~~q~~~L~~~F~~H~~~pyPs~~er~~LA~~~gLt~~qV~~WFqNrR~R~Kk~~~~~~~e 295 (355)
.++..+..++.-.|..+ ..-.++|..+|++...|++.....|.+.|+.......+
T Consensus 117 ~Lp~~~r~i~~l~~~e~--------~s~~EIA~~lgis~~tV~~~l~ra~~~Lr~~l~~~~~~ 171 (179)
T PRK12543 117 KLPYKLRQVIILRYLHD--------YSQEEIAQLLQIPIGTVKSRIHAALKKLRQKEQIEEIF 171 (179)
T ss_pred hCCHHHHHHHHHHHHcc--------CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 45666666666544211 12468899999999999999998898888877554433
No 72
>PRK12512 RNA polymerase sigma factor; Provisional
Probab=21.61 E-value=47 Score=29.05 Aligned_cols=49 Identities=8% Similarity=0.061 Sum_probs=37.3
Q ss_pred CCCHHHHHHHHHHhhhcCCCCCCCHHHHHHHHHHcCCCcccccccccchhhhhhhhh
Q psy8980 233 NFSKQASEILNEYFYSHLSNPYPSEEAKEELARKCNITVSQVSNWFGNKRIRYKKNI 289 (355)
Q Consensus 233 ~fs~~q~~~L~~~F~~H~~~pyPs~~er~~LA~~~gLt~~qV~~WFqNrR~R~Kk~~ 289 (355)
.++..+..++...|. .. ..-.+||..+|++...|++++...|.+.|+..
T Consensus 131 ~L~~~~r~v~~l~~~--~g------~s~~eIA~~l~is~~tV~~~l~ra~~~Lr~~l 179 (184)
T PRK12512 131 TLPPRQRDVVQSISV--EG------ASIKETAAKLSMSEGAVRVALHRGLAALAAKF 179 (184)
T ss_pred hCCHHHHHHHHHHHH--cC------CCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHh
Confidence 566777788877652 11 23568999999999999999988888887765
No 73
>PRK06811 RNA polymerase factor sigma-70; Validated
Probab=21.41 E-value=48 Score=29.32 Aligned_cols=49 Identities=31% Similarity=0.430 Sum_probs=36.1
Q ss_pred CCCHHHHHHHHHHhhhcCCCCCCCHHHHHHHHHHcCCCcccccccccchhhhhhhhh
Q psy8980 233 NFSKQASEILNEYFYSHLSNPYPSEEAKEELARKCNITVSQVSNWFGNKRIRYKKNI 289 (355)
Q Consensus 233 ~fs~~q~~~L~~~F~~H~~~pyPs~~er~~LA~~~gLt~~qV~~WFqNrR~R~Kk~~ 289 (355)
.+++.+..++.-.|+ .. -...++|+.+|++...|++...-.|.+.|++.
T Consensus 131 ~L~~~~r~i~~l~~~--~g------~s~~EIAe~lgis~~~V~~~l~Ra~~~Lr~~~ 179 (189)
T PRK06811 131 DLEKLDREIFIRRYL--LG------EKIEEIAKKLGLTRSAIDNRLSRGRKKLQKNK 179 (189)
T ss_pred hCCHHHHHHHHHHHH--cc------CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHcc
Confidence 577778888875542 22 23568999999999999988877777777665
No 74
>PRK12519 RNA polymerase sigma factor; Provisional
Probab=20.97 E-value=44 Score=29.52 Aligned_cols=49 Identities=12% Similarity=0.290 Sum_probs=34.5
Q ss_pred CCCHHHHHHHHHHhhhcCCCCCCCHHHHHHHHHHcCCCcccccccccchhhhhhhhh
Q psy8980 233 NFSKQASEILNEYFYSHLSNPYPSEEAKEELARKCNITVSQVSNWFGNKRIRYKKNI 289 (355)
Q Consensus 233 ~fs~~q~~~L~~~F~~H~~~pyPs~~er~~LA~~~gLt~~qV~~WFqNrR~R~Kk~~ 289 (355)
.++..+..++.-.|+ . ...-.++|..+|++...|++|+...|.+.|+..
T Consensus 141 ~L~~~~~~v~~l~~~--~------g~s~~EIA~~lgis~~tV~~~l~Ra~~~Lr~~l 189 (194)
T PRK12519 141 QLPESQRQVLELAYY--E------GLSQSEIAKRLGIPLGTVKARARQGLLKLRELL 189 (194)
T ss_pred hCCHHHhhhhhhhhh--c------CCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHH
Confidence 455566666655431 1 123568999999999999999988777777654
No 75
>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=20.77 E-value=45 Score=29.12 Aligned_cols=48 Identities=13% Similarity=0.074 Sum_probs=33.2
Q ss_pred CCHHHHHHHHHHhhhcCCCCCCCHHHHHHHHHHcCCCcccccccccchhhhhhhhh
Q psy8980 234 FSKQASEILNEYFYSHLSNPYPSEEAKEELARKCNITVSQVSNWFGNKRIRYKKNI 289 (355)
Q Consensus 234 fs~~q~~~L~~~F~~H~~~pyPs~~er~~LA~~~gLt~~qV~~WFqNrR~R~Kk~~ 289 (355)
++..+..++.-.|. ....-.++|..+|++...|+++....|.+.|+..
T Consensus 139 L~~~~r~v~~l~~~--------~~~s~~EIA~~lgis~~tv~~~l~rar~~Lr~~l 186 (190)
T TIGR02939 139 LPEDLRTAITLREL--------EGLSYEDIARIMDCPVGTVRSRIFRAREAIAIRL 186 (190)
T ss_pred CCHHHhhhhhhhhh--------cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHh
Confidence 44555666654442 1123468999999999999999887777777654
No 76
>TIGR02985 Sig70_bacteroi1 RNA polymerase sigma-70 factor, Bacteroides expansion family 1. This group of sigma factors are members of the sigma-70 family (TIGR02937) and are found primarily in the genus Bacteroides. This family appears to have resulted from a lineage-specific expansion as B. thetaiotaomicron VPI-5482, Bacteroides forsythus ATCC 43037, Bacteroides fragilis YCH46 and Bacteroides fragilis NCTC 9343 contain 25, 12, 24 and 23 members, respectively. There are currentlyonly two known members of this family outside of the Bacteroides, in Rhodopseudomonas and Bradyrhizobium.
Probab=20.67 E-value=50 Score=27.60 Aligned_cols=47 Identities=17% Similarity=0.214 Sum_probs=32.5
Q ss_pred CCCHHHHHHHHHHhhhcCCCCCCCHHHHHHHHHHcCCCcccccccccchhhhhhh
Q psy8980 233 NFSKQASEILNEYFYSHLSNPYPSEEAKEELARKCNITVSQVSNWFGNKRIRYKK 287 (355)
Q Consensus 233 ~fs~~q~~~L~~~F~~H~~~pyPs~~er~~LA~~~gLt~~qV~~WFqNrR~R~Kk 287 (355)
.++..+..++.-.|. ..+ ...++|..+|++...|+++....|.|.|+
T Consensus 113 ~L~~~~r~il~l~~~----~~~----~~~eIA~~lgis~~tv~~~~~ra~~~Lr~ 159 (161)
T TIGR02985 113 KLPEQCRKIFILSRF----EGK----SYKEIAEELGISVKTVEYHISKALKELRK 159 (161)
T ss_pred HCCHHHHHHHHHHHH----cCC----CHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Confidence 456667777766441 222 24578999999999999988766666654
No 77
>smart00421 HTH_LUXR helix_turn_helix, Lux Regulon. lux regulon (activates the bioluminescence operon
Probab=20.61 E-value=92 Score=20.90 Aligned_cols=45 Identities=16% Similarity=0.228 Sum_probs=30.9
Q ss_pred CCCHHHHHHHHHHhhhcCCCCCCCHHHHHHHHHHcCCCcccccccccchhhhhh
Q psy8980 233 NFSKQASEILNEYFYSHLSNPYPSEEAKEELARKCNITVSQVSNWFGNKRIRYK 286 (355)
Q Consensus 233 ~fs~~q~~~L~~~F~~H~~~pyPs~~er~~LA~~~gLt~~qV~~WFqNrR~R~K 286 (355)
.++..+..++..++ .. + ...++|..++++...|..|...-+.|..
T Consensus 3 ~l~~~e~~i~~~~~---~g--~----s~~eia~~l~is~~tv~~~~~~~~~kl~ 47 (58)
T smart00421 3 SLTPREREVLRLLA---EG--L----TNKEIAERLGISEKTVKTHLSNIMRKLG 47 (58)
T ss_pred CCCHHHHHHHHHHH---cC--C----CHHHHHHHHCCCHHHHHHHHHHHHHHHC
Confidence 46677777775544 22 1 3468899999999999988765555443
No 78
>PRK12538 RNA polymerase sigma factor; Provisional
Probab=20.07 E-value=63 Score=30.04 Aligned_cols=51 Identities=14% Similarity=0.164 Sum_probs=35.8
Q ss_pred CCCHHHHHHHHHHhhhcCCCCCCCHHHHHHHHHHcCCCcccccccccchhhhhhhhhhh
Q psy8980 233 NFSKQASEILNEYFYSHLSNPYPSEEAKEELARKCNITVSQVSNWFGNKRIRYKKNIGK 291 (355)
Q Consensus 233 ~fs~~q~~~L~~~F~~H~~~pyPs~~er~~LA~~~gLt~~qV~~WFqNrR~R~Kk~~~~ 291 (355)
.++..+..++.-.|+ ... .-.++|..+|++...|+++....|.+.|+....
T Consensus 171 ~Lp~~~R~v~~L~~~--eg~------s~~EIA~~Lgis~~tVk~~l~RAr~kLr~~l~~ 221 (233)
T PRK12538 171 RLPEQQRIAVILSYH--ENM------SNGEIAEVMDTTVAAVESLLKRGRQQLRDLLRR 221 (233)
T ss_pred hCCHHHHHHhhhHHh--cCC------CHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHH
Confidence 345556666544431 222 246899999999999999998888888876643
Done!