Query 005500
Match_columns 693
No_of_seqs 316 out of 1039
Neff 3.9
Searched_HMMs 46136
Date Fri Mar 29 00:26:47 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/005500.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/005500hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF07526 POX: Associated with 100.0 1.2E-43 2.5E-48 334.4 13.6 139 172-314 1-140 (140)
2 smart00574 POX domain associat 100.0 1.6E-43 3.4E-48 331.6 13.0 139 168-313 1-139 (140)
3 KOG0773 Transcription factor M 100.0 5.7E-34 1.2E-38 298.0 9.7 259 170-434 45-312 (342)
4 KOG0774 Transcription factor P 99.8 8.3E-19 1.8E-23 179.0 11.2 154 243-427 99-254 (334)
5 PF05920 Homeobox_KN: Homeobox 99.6 2.2E-15 4.8E-20 115.5 3.3 40 379-418 1-40 (40)
6 KOG0775 Transcription factor S 99.4 6.6E-14 1.4E-18 144.3 2.8 81 331-420 148-232 (304)
7 cd00086 homeodomain Homeodomai 99.4 1E-12 2.2E-17 103.9 5.8 57 363-422 2-58 (59)
8 PF00046 Homeobox: Homeobox do 99.3 1.4E-12 3E-17 103.8 4.7 57 362-421 1-57 (57)
9 smart00389 HOX Homeodomain. DN 99.3 2.5E-12 5.3E-17 101.3 6.1 55 363-420 2-56 (56)
10 KOG0487 Transcription factor A 99.1 3.2E-11 7E-16 127.2 3.6 61 360-423 233-294 (308)
11 KOG0842 Transcription factor t 99.1 6.8E-11 1.5E-15 124.7 4.4 63 361-426 152-215 (307)
12 KOG0488 Transcription factor B 98.8 2.6E-09 5.7E-14 113.1 5.0 62 361-425 171-233 (309)
13 KOG0489 Transcription factor z 98.8 1.8E-09 3.9E-14 111.6 3.0 59 361-422 159-217 (261)
14 KOG0843 Transcription factor E 98.8 4.4E-09 9.6E-14 103.9 4.5 64 360-426 101-164 (197)
15 KOG0483 Transcription factor H 98.7 1.1E-08 2.5E-13 102.5 5.5 67 360-429 49-115 (198)
16 KOG0850 Transcription factor D 98.7 8.1E-09 1.8E-13 105.1 4.4 60 361-423 121-181 (245)
17 KOG0493 Transcription factor E 98.7 1.2E-08 2.7E-13 105.4 4.2 60 360-422 245-304 (342)
18 TIGR01565 homeo_ZF_HD homeobox 98.7 3.9E-08 8.5E-13 81.4 5.7 53 361-416 1-57 (58)
19 KOG0485 Transcription factor N 98.6 1.7E-08 3.7E-13 102.2 3.9 64 361-427 104-167 (268)
20 KOG0484 Transcription factor P 98.6 3.3E-08 7.1E-13 90.7 4.5 63 363-428 19-81 (125)
21 KOG3802 Transcription factor O 98.6 3.9E-08 8.5E-13 106.5 5.7 60 361-423 293-353 (398)
22 KOG0492 Transcription factor M 98.5 1.7E-07 3.7E-12 94.6 5.5 58 363-423 146-203 (246)
23 COG5576 Homeodomain-containing 98.5 1.3E-07 2.8E-12 91.9 4.3 61 360-423 50-110 (156)
24 KOG0848 Transcription factor C 98.4 6.4E-08 1.4E-12 100.5 2.0 57 364-423 201-258 (317)
25 KOG0486 Transcription factor P 98.4 1.4E-07 3.1E-12 99.6 3.9 60 362-424 112-172 (351)
26 KOG0491 Transcription factor B 98.4 1E-07 2.3E-12 93.3 0.9 59 361-422 99-158 (194)
27 KOG2251 Homeobox transcription 98.3 4.3E-07 9.2E-12 92.3 4.4 58 362-422 38-95 (228)
28 KOG0494 Transcription factor C 98.2 8.7E-07 1.9E-11 91.9 4.4 53 367-422 147-199 (332)
29 KOG0847 Transcription factor, 98.0 3.1E-06 6.7E-11 86.3 2.9 63 367-432 173-235 (288)
30 KOG4577 Transcription factor L 98.0 3.5E-06 7.6E-11 88.6 2.9 61 359-422 165-225 (383)
31 KOG2252 CCAAT displacement pro 97.9 1.2E-05 2.6E-10 90.5 5.1 56 361-419 420-475 (558)
32 KOG0844 Transcription factor E 97.8 9.4E-06 2E-10 86.0 1.7 58 365-425 185-242 (408)
33 KOG0490 Transcription factor, 97.5 4.1E-05 8.9E-10 75.4 2.5 60 361-423 60-119 (235)
34 KOG0849 Transcription factor P 97.5 6.7E-05 1.5E-09 81.3 3.7 59 362-423 177-235 (354)
35 KOG1168 Transcription factor A 97.3 0.00011 2.4E-09 77.7 1.7 59 360-421 308-366 (385)
36 KOG0773 Transcription factor M 97.0 0.00024 5.3E-09 75.6 1.5 61 362-423 96-156 (342)
37 PF11569 Homez: Homeodomain le 95.4 0.011 2.5E-07 49.2 2.6 43 373-418 10-52 (56)
38 KOG0490 Transcription factor, 94.4 0.028 6.1E-07 55.6 2.8 61 361-424 153-213 (235)
39 KOG1146 Homeobox protein [Gene 90.2 0.19 4.1E-06 62.5 2.9 60 361-423 903-962 (1406)
40 PF04218 CENP-B_N: CENP-B N-te 77.6 3.2 7E-05 33.8 3.7 47 362-416 1-47 (53)
41 PF11285 DUF3086: Protein of u 76.7 28 0.00061 37.5 11.2 60 247-322 7-66 (283)
42 KOG3623 Homeobox transcription 74.2 3.6 7.9E-05 49.3 4.4 45 373-420 568-612 (1007)
43 cd06171 Sigma70_r4 Sigma70, re 57.4 11 0.00024 27.9 2.7 45 368-420 11-55 (55)
44 PF03792 PBC: PBC domain; Int 57.1 2.1E+02 0.0046 29.8 12.4 41 240-280 100-140 (191)
45 PF01527 HTH_Tnp_1: Transposas 53.6 14 0.00031 30.7 3.1 46 363-416 2-48 (76)
46 PF04545 Sigma70_r4: Sigma-70, 49.5 13 0.00028 29.1 2.1 47 367-421 4-50 (50)
47 cd00569 HTH_Hin_like Helix-tur 48.7 34 0.00074 22.4 3.9 38 367-412 5-42 (42)
48 PF08281 Sigma70_r4_2: Sigma-7 43.6 24 0.00052 27.7 2.8 45 367-419 10-54 (54)
49 PRK09642 RNA polymerase sigma 42.1 24 0.00052 33.0 3.0 49 367-423 106-154 (160)
50 PF13443 HTH_26: Cro/C1-type H 41.0 24 0.00052 28.4 2.5 27 393-419 12-38 (63)
51 PRK00118 putative DNA-binding 40.8 32 0.0007 32.1 3.6 57 367-432 17-73 (104)
52 PRK06759 RNA polymerase factor 40.5 24 0.00051 32.7 2.7 47 367-421 106-152 (154)
53 PF03791 KNOX2: KNOX2 domain ; 39.2 50 0.0011 27.7 4.0 38 262-309 10-51 (52)
54 PF12998 ING: Inhibitor of gro 37.4 2.9E+02 0.0063 24.3 10.6 69 252-320 16-85 (105)
55 smart00421 HTH_LUXR helix_turn 37.3 55 0.0012 24.6 3.9 51 367-426 3-53 (58)
56 PRK09644 RNA polymerase sigma 37.1 32 0.00069 32.5 3.0 50 366-423 107-156 (165)
57 PRK03975 tfx putative transcri 34.8 31 0.00068 33.8 2.6 49 366-423 5-53 (141)
58 PF10168 Nup88: Nuclear pore c 34.7 4.7E+02 0.01 32.0 12.7 17 366-382 680-696 (717)
59 TIGR02937 sigma70-ECF RNA poly 34.4 39 0.00085 29.8 3.0 47 367-421 110-156 (158)
60 PRK12851 groEL chaperonin GroE 33.7 2.6E+02 0.0057 32.6 10.2 60 242-302 358-430 (541)
61 PRK11924 RNA polymerase sigma 33.1 47 0.001 31.0 3.4 49 367-423 125-173 (179)
62 TIGR02985 Sig70_bacteroi1 RNA 33.1 52 0.0011 30.1 3.7 48 367-422 113-160 (161)
63 PRK09652 RNA polymerase sigma 32.5 39 0.00086 31.6 2.8 49 367-423 128-176 (182)
64 CHL00093 groEL chaperonin GroE 32.5 3.2E+02 0.0068 31.8 10.5 60 242-302 357-429 (529)
65 PRK12849 groEL chaperonin GroE 32.5 1.8E+02 0.004 33.9 8.7 60 242-302 357-429 (542)
66 PF00196 GerE: Bacterial regul 32.2 46 0.001 26.8 2.8 53 367-428 3-55 (58)
67 PRK09646 RNA polymerase sigma 31.7 37 0.0008 33.2 2.6 49 367-423 142-190 (194)
68 PRK09415 RNA polymerase factor 31.7 2.3E+02 0.005 27.3 8.0 50 366-423 126-175 (179)
69 PRK12512 RNA polymerase sigma 31.6 33 0.00072 32.9 2.2 49 367-423 131-179 (184)
70 TIGR02348 GroEL chaperonin Gro 31.5 2.9E+02 0.0062 32.1 10.0 58 242-300 356-426 (524)
71 TIGR02939 RpoE_Sigma70 RNA pol 31.4 29 0.00063 33.1 1.8 50 366-423 137-186 (190)
72 PRK12541 RNA polymerase sigma 31.1 36 0.00079 31.9 2.4 48 366-421 111-158 (161)
73 COG1734 DksA DnaK suppressor p 30.8 3.4E+02 0.0073 26.2 8.7 93 247-340 4-97 (120)
74 PRK12514 RNA polymerase sigma 30.7 41 0.00088 32.2 2.7 49 366-422 128-176 (179)
75 PRK12519 RNA polymerase sigma 30.7 37 0.0008 32.9 2.4 50 366-423 140-189 (194)
76 PRK15369 two component system 29.4 1.1E+02 0.0024 28.1 5.2 54 366-428 148-201 (211)
77 TIGR02941 Sigma_B RNA polymera 29.4 43 0.00093 34.4 2.7 49 367-423 205-253 (255)
78 TIGR02999 Sig-70_X6 RNA polyme 28.8 45 0.00098 31.8 2.6 48 367-422 134-181 (183)
79 PRK08583 RNA polymerase sigma 28.8 51 0.0011 33.9 3.1 49 367-423 205-253 (257)
80 PRK12526 RNA polymerase sigma 28.7 44 0.00096 33.2 2.6 49 367-423 153-201 (206)
81 PRK09648 RNA polymerase sigma 28.5 47 0.001 32.1 2.7 50 366-423 138-187 (189)
82 PRK12547 RNA polymerase sigma 28.3 47 0.001 31.5 2.6 50 366-423 111-160 (164)
83 PRK12530 RNA polymerase sigma 28.1 57 0.0012 31.9 3.2 50 367-424 134-183 (189)
84 cd06170 LuxR_C_like C-terminal 26.7 82 0.0018 23.9 3.3 47 368-423 1-47 (57)
85 cd03344 GroEL GroEL_like type 26.7 2.9E+02 0.0063 32.1 9.0 61 242-303 355-428 (520)
86 PRK12531 RNA polymerase sigma 26.5 53 0.0011 32.1 2.7 50 366-423 140-189 (194)
87 TIGR02947 SigH_actino RNA poly 26.2 25 0.00055 34.2 0.4 49 367-423 131-179 (193)
88 TIGR02948 SigW_bacill RNA poly 26.2 55 0.0012 31.2 2.7 50 366-423 135-184 (187)
89 PRK06811 RNA polymerase factor 26.1 52 0.0011 32.0 2.5 49 366-422 130-178 (189)
90 PRK12520 RNA polymerase sigma 26.0 87 0.0019 30.4 4.0 49 367-423 131-179 (191)
91 TIGR03001 Sig-70_gmx1 RNA poly 26.0 64 0.0014 33.6 3.3 50 366-423 160-209 (244)
92 TIGR02983 SigE-fam_strep RNA p 25.9 54 0.0012 30.6 2.5 50 366-423 109-158 (162)
93 PRK12852 groEL chaperonin GroE 25.8 4.2E+02 0.0092 30.9 10.1 60 242-302 358-430 (545)
94 PRK00013 groEL chaperonin GroE 25.7 3.4E+02 0.0074 31.8 9.3 59 242-301 357-428 (542)
95 PRK05602 RNA polymerase sigma 25.7 51 0.0011 31.8 2.4 49 367-423 128-176 (186)
96 PF09712 PHA_synth_III_E: Poly 25.5 8.1E+02 0.017 26.7 11.5 120 247-403 158-283 (293)
97 PRK04217 hypothetical protein; 25.3 72 0.0016 30.1 3.2 50 366-423 41-90 (110)
98 PRK12542 RNA polymerase sigma 25.2 67 0.0014 31.0 3.1 58 366-432 121-178 (185)
99 PRK12546 RNA polymerase sigma 25.1 51 0.0011 32.5 2.3 49 367-423 113-161 (188)
100 TIGR02989 Sig-70_gvs1 RNA poly 24.9 56 0.0012 30.3 2.4 48 366-421 110-157 (159)
101 PRK10778 dksA RNA polymerase-b 24.8 2.5E+02 0.0054 27.9 6.9 30 247-276 35-64 (151)
102 PRK09639 RNA polymerase sigma 24.7 54 0.0012 30.7 2.3 48 367-423 112-159 (166)
103 PRK12516 RNA polymerase sigma 24.5 65 0.0014 31.6 2.9 49 367-423 116-164 (187)
104 KOG0809 SNARE protein TLG2/Syn 24.0 2.6E+02 0.0056 31.0 7.4 60 258-317 104-168 (305)
105 PRK12523 RNA polymerase sigma 23.8 65 0.0014 30.8 2.7 48 366-421 118-165 (172)
106 PRK12536 RNA polymerase sigma 23.8 64 0.0014 31.1 2.6 49 367-423 129-177 (181)
107 PRK09047 RNA polymerase factor 23.2 1E+02 0.0022 28.7 3.8 50 366-423 105-154 (161)
108 TIGR02954 Sig70_famx3 RNA poly 23.1 56 0.0012 30.9 2.1 49 367-423 119-167 (169)
109 PRK13919 putative RNA polymera 23.1 57 0.0012 31.3 2.2 49 367-423 135-183 (186)
110 cd00131 PAX Paired Box domain 22.9 3.2E+02 0.0069 26.0 7.0 47 366-415 74-127 (128)
111 PF07765 KIP1: KIP1-like prote 22.9 1.1E+02 0.0025 27.3 3.7 30 242-271 40-70 (74)
112 PTZ00114 Heat shock protein 60 22.6 4.4E+02 0.0096 30.9 9.5 60 242-302 370-442 (555)
113 PRK12524 RNA polymerase sigma 22.5 86 0.0019 30.7 3.3 49 367-423 136-184 (196)
114 PRK06986 fliA flagellar biosyn 22.4 56 0.0012 33.1 2.1 49 367-423 184-232 (236)
115 PRK09647 RNA polymerase sigma 22.2 98 0.0021 31.0 3.7 49 367-423 138-186 (203)
116 PRK12532 RNA polymerase sigma 21.9 81 0.0018 30.7 3.0 49 367-423 136-184 (195)
117 PRK06288 RNA polymerase sigma 21.8 78 0.0017 33.0 3.0 49 367-423 212-260 (268)
118 PRK12515 RNA polymerase sigma 21.6 86 0.0019 30.4 3.1 50 366-423 130-179 (189)
119 PF14643 DUF4455: Domain of un 21.6 3.1E+02 0.0066 31.5 7.8 34 247-280 407-440 (473)
120 PRK12544 RNA polymerase sigma 21.3 1.2E+02 0.0025 30.6 4.0 51 366-424 147-197 (206)
121 PRK09649 RNA polymerase sigma 21.2 71 0.0015 31.1 2.4 48 366-421 129-176 (185)
122 PRK12545 RNA polymerase sigma 21.2 83 0.0018 31.2 2.9 50 366-423 138-187 (201)
123 PRK12533 RNA polymerase sigma 21.1 68 0.0015 32.7 2.3 50 366-423 133-182 (216)
124 PRK12850 groEL chaperonin GroE 21.1 5.2E+02 0.011 30.3 9.6 59 242-301 358-429 (544)
125 PF13518 HTH_28: Helix-turn-he 21.0 67 0.0015 24.6 1.8 25 393-417 14-38 (52)
126 TIGR02479 FliA_WhiG RNA polyme 20.9 85 0.0018 31.5 3.0 48 367-422 175-222 (224)
127 PRK12539 RNA polymerase sigma 20.4 71 0.0015 30.9 2.2 50 366-423 130-179 (184)
128 cd01392 HTH_LacI Helix-turn-he 20.2 80 0.0017 24.3 2.1 21 396-416 2-22 (52)
129 TIGR02481 hemeryth_dom hemeryt 20.0 4.1E+02 0.0089 24.2 7.0 19 367-385 98-116 (126)
130 PF04740 LXG: LXG domain of WX 20.0 7E+02 0.015 24.7 9.1 66 255-320 7-81 (204)
No 1
>PF07526 POX: Associated with HOX; InterPro: IPR006563 This domain in found exclusively in plant proteins, associated with HOX domains which may suggest these proteins are homeodomain transcription factors.
Probab=100.00 E-value=1.2e-43 Score=334.40 Aligned_cols=139 Identities=49% Similarity=0.714 Sum_probs=103.8
Q ss_pred hhcccccchhHHHHHHHHHHhccCCcccccccccccCCCCCCCCcccccCCCCC-CCCCCCCCCCCcCcccChHHHHHHH
Q 005500 172 SVLLSSKYLKAAQELLDEVVNVNNSGISNKSEFSKKGSGNNNSNINKVIGESSA-AAGDDGQSAGKRAAELTTAERQEIQ 250 (693)
Q Consensus 172 ~vl~~SryLk~aQeLL~E~~~vg~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~ls~~er~ElQ 250 (693)
+||++|||||||||||||||+|++............. ... .......... ..+....+......+++++||+|+|
T Consensus 1 q~l~~SryLk~aQeLL~E~~~v~~~~~~~~~~~~~~~--~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~ls~~~~~e~q 76 (140)
T PF07526_consen 1 QVLLGSRYLKPAQELLDEFCSVGGANKKKSDDSSSGA--PGG--ANSSGSSSSSGGSSSSSSSSDSSSPELSPAERQELQ 76 (140)
T ss_pred CccccchhHHHHHHHHHHHHcccchhhhcchhhcccc--ccc--cccCCCCCCCCCCCCCccccCCCCCCCChhhHHHHH
Confidence 5899999999999999999999763221111100000 000 0000000011 0111122334456799999999999
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHhchhhhccCCchhhhHHHHHHHHHHhhhhHHHHHHH
Q 005500 251 MKKAKLINMLDEVEQRYRQYHHQMQIVISSFEQAAGIESAKTYTALALKTISKQFRCLKDAITG 314 (693)
Q Consensus 251 ~Kk~KLl~mLdeVd~RY~qY~~qmq~v~ssFe~~ag~gaa~~yt~laL~~iSr~Fr~LkdaI~~ 314 (693)
+||+|||+||||||+||+|||+|||+||++||+|||+|+|++||+||||+||||||||||+|++
T Consensus 77 ~kK~KLl~mL~eVd~RY~qY~~Qmq~VvssFe~vaG~gaA~~YtalAlqamSrhFR~LRdaI~~ 140 (140)
T PF07526_consen 77 RKKAKLLSMLDEVDRRYRQYYDQMQAVVSSFEAVAGLGAAAPYTALALQAMSRHFRCLRDAISD 140 (140)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCcchhhHHHHHHHHHHHHHHHHHHhcC
Confidence 9999999999999999999999999999999999999999999999999999999999999964
No 2
>smart00574 POX domain associated with HOX domains.
Probab=100.00 E-value=1.6e-43 Score=331.60 Aligned_cols=139 Identities=55% Similarity=0.787 Sum_probs=109.0
Q ss_pred ccchhhcccccchhHHHHHHHHHHhccCCcccccccccccCCCCCCCCcccccCCCCCCCCCCCCCCCCcCcccChHHHH
Q 005500 168 SGMQSVLLSSKYLKAAQELLDEVVNVNNSGISNKSEFSKKGSGNNNSNINKVIGESSAAAGDDGQSAGKRAAELTTAERQ 247 (693)
Q Consensus 168 tg~a~vl~~SryLk~aQeLL~E~~~vg~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ls~~er~ 247 (693)
+||+.+|++|||||||||||||||+| ++++..+. ..++ . +........+ ..+....+.++++..++++++||+
T Consensus 1 ~g~~~~l~~SkyLk~aQeLLdEf~sv-~~~~~~~~--~~~~--~-~~~~~~~~~~-~~~~~~~g~s~~~~~~~ls~~~r~ 73 (140)
T smart00574 1 TGGVFILRNSKYLKAAQELLDEFCNV-GRGSSKKK--KQSG--N-DSPVSTSSNE-GGGENLSGGSSSSEVPPLSTAERQ 73 (140)
T ss_pred CchhhhccCccccccHHHHHHHHhcc-cHHhhccc--cccc--c-cccccccccC-CCcCCCCCCCCCCCCCCCchhHHH
Confidence 58999999999999999999999999 55553221 1111 0 0000000000 001111223445567899999999
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhchhhhccCCchhhhHHHHHHHHHHhhhhHHHHHH
Q 005500 248 EIQMKKAKLINMLDEVEQRYRQYHHQMQIVISSFEQAAGIESAKTYTALALKTISKQFRCLKDAIT 313 (693)
Q Consensus 248 ElQ~Kk~KLl~mLdeVd~RY~qY~~qmq~v~ssFe~~ag~gaa~~yt~laL~~iSr~Fr~LkdaI~ 313 (693)
|+|+||+|||+||||||+||+|||+|||+|+++||+|||+|+|++||+||||+||||||||||+|+
T Consensus 74 e~q~kk~kLl~mL~eVd~RY~qY~~qmq~v~ssFe~vaG~g~a~~yt~lAl~a~SrhFr~LrdaI~ 139 (140)
T smart00574 74 ELQRKKAKLLSMLEEVDRRYKHYYEQMQTVVSSFDQAAGLGAAKPYTALALKTISRHFRCLKDAIA 139 (140)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCchHHHHHHHHHHHHHHHHHHHHHhc
Confidence 999999999999999999999999999999999999999999999999999999999999999996
No 3
>KOG0773 consensus Transcription factor MEIS1 and related HOX domain proteins [Transcription]
Probab=100.00 E-value=5.7e-34 Score=298.00 Aligned_cols=259 Identities=39% Similarity=0.584 Sum_probs=194.9
Q ss_pred chhhcccccchhHHHHHHHHHHhccCCcccccccccccCCCCCCCCcccccCCCCCCCCCCCCCCCCcCcccChHHHHHH
Q 005500 170 MQSVLLSSKYLKAAQELLDEVVNVNNSGISNKSEFSKKGSGNNNSNINKVIGESSAAAGDDGQSAGKRAAELTTAERQEI 249 (693)
Q Consensus 170 ~a~vl~~SryLk~aQeLL~E~~~vg~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ls~~er~El 249 (693)
+...+..+|||++||+||+++|++...... .+....... ..+......-..+...+......+...+..+++++
T Consensus 45 ~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~--~~~~~~~~~----~~~~~~~~~~~~~~~~~n~~~~s~~~~~~~~~~~~ 118 (342)
T KOG0773|consen 45 IMVSLASSKYLTAAQELLDEFCSAGLDCLK--GKMPYDPVP----RSPASLSPPEDKGARRGNATRESATLKAWLEEHRL 118 (342)
T ss_pred cccccccccccccchhHHhHHhhccccccc--cccCcCccc----cccccccCccccccccccccccccccccchhhhhh
Confidence 556788999999999999999999655432 111110000 00000000000000000111111345567899999
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHhchhhhccCCchhhhHHHHHHHHHHhhhhHHH--HHHHHHHHHHhhhCccc
Q 005500 250 QMKKAKLINMLDEVEQRYRQYHHQMQIVISSFEQAAGIESAKTYTALALKTISKQFRCLKD--AITGQIKAANKMLGEED 327 (693)
Q Consensus 250 Q~Kk~KLl~mLdeVd~RY~qY~~qmq~v~ssFe~~ag~gaa~~yt~laL~~iSr~Fr~Lkd--aI~~qi~~~~~slgeed 327 (693)
+.+++||+.||.+|+.||.+|+..|+.|.+.|+...+++.+..|+..++..++++|+++++ +|..|+......+++.+
T Consensus 119 ~~~~~k~~~~ll~~~~~~~~~~~~~~~~~a~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~q~~~~~~~~~~~~ 198 (342)
T KOG0773|consen 119 NPYPSKLEKILLAVITKLTLTQVSTWFANARRRLKKELKMTWGPTPLALDGISRHFSDLEKEKAIGGQLSSSEELLGESE 198 (342)
T ss_pred ccCchHHHHHHHHHHHHhhhhhHHHHHHHHHHHHHhccCCCCCCccccccchhhhhhhhhhccccccccccccccccccc
Confidence 9999999999999999999999999999999999999999999999999999999999998 77888777766554332
Q ss_pred --cCC----CcccCccccchhhHHHHHHH-HhhhcccccCCCCCCCCCChhHHHHHHHHHHHhhCCCCCCHHHHHHHHHH
Q 005500 328 --CVG----SKIEGSRLKFVDHHLRQQRA-LQQLGMIQHNAWRPQRGLPERSVSVLRAWLFEHFLHPYPKDSDKQMLAKQ 400 (693)
Q Consensus 328 --~~g----g~~e~~rl~~vD~~lrqqra-~qqlG~l~~~~kRkrR~Lpk~qv~iLr~Wf~eH~~nPYPS~~EK~~LAk~ 400 (693)
... .....++....++.+++++. ....+..+..+||++++||+.++.+|+.||++|+.||||++.+|..||++
T Consensus 199 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~r~~~~lP~~a~~ilr~Wl~~h~~~PYPse~~K~~La~~ 278 (342)
T KOG0773|consen 199 QDDSEDESGPSGSEPPLRLAKQSLRQQRSAYDGSGGKKQSKWRPQRGLPKEAVSILRAWLFEHLLHPYPSDDEKLMLAKQ 278 (342)
T ss_pred ccccccccCcccccCCcccccccccccccccccccccccCCCCCCCCCCHHHHHHHHHHHHHhccCCCCcchhccccchh
Confidence 111 11123445555666666553 22333345679999999999999999999999999999999999999999
Q ss_pred hCCChhhhhccchhhhhhcChhhHHHHhHHHhhh
Q 005500 401 TGLTRSQVSNWFINARVRLWKPMVEEMYLEEIKD 434 (693)
Q Consensus 401 TGLS~kQVsNWFiNaR~R~kKp~ieem~~~~~~~ 434 (693)
|||++.||+|||||+|+|+|+||+++++..+...
T Consensus 279 TGLs~~Qv~NWFINaR~R~w~p~~~~~~~~~~~~ 312 (342)
T KOG0773|consen 279 TGLSRPQVSNWFINARVRLWKPMIEEMYLLEDKD 312 (342)
T ss_pred cCCCcccCCchhhhcccccCCchHHHHHHHhhcc
Confidence 9999999999999999999999999999988776
No 4
>KOG0774 consensus Transcription factor PBX and related HOX domain proteins [Transcription]
Probab=99.78 E-value=8.3e-19 Score=178.95 Aligned_cols=154 Identities=25% Similarity=0.444 Sum_probs=109.6
Q ss_pred hHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhchhhhccCCch--hhhHHHHHHHHHHhhhhHHHHHHHHHHHHH
Q 005500 243 TAERQEIQMKKAKLINMLDEVEQRYRQYHHQMQIVISSFEQAAGIESA--KTYTALALKTISKQFRCLKDAITGQIKAAN 320 (693)
Q Consensus 243 ~~er~ElQ~Kk~KLl~mLdeVd~RY~qY~~qmq~v~ssFe~~ag~gaa--~~yt~laL~~iSr~Fr~LkdaI~~qi~~~~ 320 (693)
.-+..|++.|..++..++++--++|+|-|.+.-+.|...-.--+.--+ ---+.-+++.|++-|...+. +|+.
T Consensus 99 gg~hsdYR~kL~qiR~iy~~ElekyeqaCneftthV~nlL~eQsr~RPi~~ke~e~m~~~i~~kF~~iq~----~lkq-- 172 (334)
T KOG0774|consen 99 GGDHSDYRAKLLQIRQIYHNELEKYEQACNEFTTHVMNLLREQSRTRPIMPKEIERMVQIISKKFSHIQM----QLKQ-- 172 (334)
T ss_pred CCChHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcccCCCCHHHHHHHHHHHHHHHHHHHH----HHHH--
Confidence 334779999999999999999999999999998887763222111101 11123345555555543332 2221
Q ss_pred hhhCccccCCCcccCccccchhhHHHHHHHHhhhcccccCCCCCCCCCChhHHHHHHHHHHHhhCCCCCCHHHHHHHHHH
Q 005500 321 KMLGEEDCVGSKIEGSRLKFVDHHLRQQRALQQLGMIQHNAWRPQRGLPERSVSVLRAWLFEHFLHPYPKDSDKQMLAKQ 400 (693)
Q Consensus 321 ~slgeed~~gg~~e~~rl~~vD~~lrqqra~qqlG~l~~~~kRkrR~Lpk~qv~iLr~Wf~eH~~nPYPS~~EK~~LAk~ 400 (693)
+-| +.+-.-|.+++| .+||||+|+|.++.||..||..|+.||||++++|++||++
T Consensus 173 -----stc--e~vmiLr~r~ld------------------arRKRRNFsK~aTeiLneyF~~h~~nPYPSee~K~eLAkq 227 (334)
T KOG0774|consen 173 -----STC--EAVMILRSRFLD------------------ARRKRRNFSKQATEILNEYFYSHLSNPYPSEEAKEELAKQ 227 (334)
T ss_pred -----HHH--HHHHHHHHHHHH------------------HHHhhcccchhHHHHHHHHHHHhcCCCCCcHHHHHHHHHH
Confidence 111 111111112222 4688999999999999999999999999999999999999
Q ss_pred hCCChhhhhccchhhhhhcChhhHHHH
Q 005500 401 TGLTRSQVSNWFINARVRLWKPMVEEM 427 (693)
Q Consensus 401 TGLS~kQVsNWFiNaR~R~kKp~ieem 427 (693)
++++..||+|||-|.|-|.||.+....
T Consensus 228 CnItvsQvsnwfgnkrIrykK~~~k~~ 254 (334)
T KOG0774|consen 228 CNITVSQVSNWFGNKRIRYKKNMGKNQ 254 (334)
T ss_pred cCceehhhccccccceeehhhhhhhhh
Confidence 999999999999999999999875433
No 5
>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=99.55 E-value=2.2e-15 Score=115.47 Aligned_cols=40 Identities=65% Similarity=1.189 Sum_probs=36.5
Q ss_pred HHHHhhCCCCCCHHHHHHHHHHhCCChhhhhccchhhhhh
Q 005500 379 WLFEHFLHPYPKDSDKQMLAKQTGLTRSQVSNWFINARVR 418 (693)
Q Consensus 379 Wf~eH~~nPYPS~~EK~~LAk~TGLS~kQVsNWFiNaR~R 418 (693)
||.+|+.||||+++||..||++|||+.+||+|||+|+|+|
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 9999999999999999999999999999999999999998
No 6
>KOG0775 consensus Transcription factor SIX and related HOX domain proteins [Transcription]
Probab=99.41 E-value=6.6e-14 Score=144.27 Aligned_cols=81 Identities=41% Similarity=0.693 Sum_probs=69.7
Q ss_pred CcccCccccchhhH-HHHHHHHhhhcccccCCCCCCC---CCChhHHHHHHHHHHHhhCCCCCCHHHHHHHHHHhCCChh
Q 005500 331 SKIEGSRLKFVDHH-LRQQRALQQLGMIQHNAWRPQR---GLPERSVSVLRAWLFEHFLHPYPKDSDKQMLAKQTGLTRS 406 (693)
Q Consensus 331 g~~e~~rl~~vD~~-lrqqra~qqlG~l~~~~kRkrR---~Lpk~qv~iLr~Wf~eH~~nPYPS~~EK~~LAk~TGLS~k 406 (693)
++.++..|..||++ ||++.++. ...|...- +|.++.+.+||.||.. +|||++++|.+||+.|||+..
T Consensus 148 ek~RGR~LgaV~KYRvRrKfPlP------rTIWDGEet~yCFKekSR~~LrewY~~---~~YPsp~eKReLA~aTgLt~t 218 (304)
T KOG0775|consen 148 EKLRGRPLGAVDKYRVRRKFPLP------RTIWDGEETVYCFKEKSRSLLREWYLQ---NPYPSPREKRELAEATGLTIT 218 (304)
T ss_pred HHhcCCcCCccccceeeccCCCC------CccccCceeeeehhHhhHHHHHHHHhc---CCCCChHHHHHHHHHhCCchh
Confidence 35678889999998 76654433 36777443 4999999999999997 999999999999999999999
Q ss_pred hhhccchhhhhhcC
Q 005500 407 QVSNWFINARVRLW 420 (693)
Q Consensus 407 QVsNWFiNaR~R~k 420 (693)
||.|||+|+|.|.+
T Consensus 219 QVsNWFKNRRQRDR 232 (304)
T KOG0775|consen 219 QVSNWFKNRRQRDR 232 (304)
T ss_pred hhhhhhhhhhhhhh
Confidence 99999999999997
No 7
>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=99.36 E-value=1e-12 Score=103.90 Aligned_cols=57 Identities=32% Similarity=0.558 Sum_probs=53.4
Q ss_pred CCCCCCChhHHHHHHHHHHHhhCCCCCCHHHHHHHHHHhCCChhhhhccchhhhhhcChh
Q 005500 363 RPQRGLPERSVSVLRAWLFEHFLHPYPKDSDKQMLAKQTGLTRSQVSNWFINARVRLWKP 422 (693)
Q Consensus 363 RkrR~Lpk~qv~iLr~Wf~eH~~nPYPS~~EK~~LAk~TGLS~kQVsNWFiNaR~R~kKp 422 (693)
+++..|+++++.+|+.||.. +|||+.+++..||.+|||+..||.+||.|+|.|.++.
T Consensus 2 ~~r~~~~~~~~~~Le~~f~~---~~~P~~~~~~~la~~~~l~~~qV~~WF~nrR~~~~~~ 58 (59)
T cd00086 2 RKRTRFTPEQLEELEKEFEK---NPYPSREEREELAKELGLTERQVKIWFQNRRAKLKRS 58 (59)
T ss_pred CCCCcCCHHHHHHHHHHHHh---CCCCCHHHHHHHHHHHCcCHHHHHHHHHHHHHHHhcc
Confidence 45667999999999999999 9999999999999999999999999999999998764
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=99.32 E-value=1.4e-12 Score=103.82 Aligned_cols=57 Identities=37% Similarity=0.643 Sum_probs=53.9
Q ss_pred CCCCCCCChhHHHHHHHHHHHhhCCCCCCHHHHHHHHHHhCCChhhhhccchhhhhhcCh
Q 005500 362 WRPQRGLPERSVSVLRAWLFEHFLHPYPKDSDKQMLAKQTGLTRSQVSNWFINARVRLWK 421 (693)
Q Consensus 362 kRkrR~Lpk~qv~iLr~Wf~eH~~nPYPS~~EK~~LAk~TGLS~kQVsNWFiNaR~R~kK 421 (693)
+|+++.|+++++.+|+.+|.. +|||+.+++..||..+||+..||.+||+|+|.|.||
T Consensus 1 kr~r~~~t~~q~~~L~~~f~~---~~~p~~~~~~~la~~l~l~~~~V~~WF~nrR~k~kk 57 (57)
T PF00046_consen 1 KRKRTRFTKEQLKVLEEYFQE---NPYPSKEEREELAKELGLTERQVKNWFQNRRRKEKK 57 (57)
T ss_dssp SSSSSSSSHHHHHHHHHHHHH---SSSCHHHHHHHHHHHHTSSHHHHHHHHHHHHHHHHH
T ss_pred CcCCCCCCHHHHHHHHHHHHH---hccccccccccccccccccccccccCHHHhHHHhCc
Confidence 467788999999999999998 999999999999999999999999999999999875
No 9
>smart00389 HOX Homeodomain. DNA-binding factors that are involved in the transcriptional regulation of key developmental processes
Probab=99.32 E-value=2.5e-12 Score=101.30 Aligned_cols=55 Identities=27% Similarity=0.522 Sum_probs=50.8
Q ss_pred CCCCCCChhHHHHHHHHHHHhhCCCCCCHHHHHHHHHHhCCChhhhhccchhhhhhcC
Q 005500 363 RPQRGLPERSVSVLRAWLFEHFLHPYPKDSDKQMLAKQTGLTRSQVSNWFINARVRLW 420 (693)
Q Consensus 363 RkrR~Lpk~qv~iLr~Wf~eH~~nPYPS~~EK~~LAk~TGLS~kQVsNWFiNaR~R~k 420 (693)
+++..|+++++.+|++||.. +|||+.+++..||..+||+..||.+||+|+|+|.+
T Consensus 2 k~r~~~~~~~~~~L~~~f~~---~~~P~~~~~~~la~~~~l~~~qV~~WF~nrR~~~~ 56 (56)
T smart00389 2 RKRTSFTPEQLEELEKEFQK---NPYPSREEREELAAKLGLSERQVKVWFQNRRAKWK 56 (56)
T ss_pred CCCCcCCHHHHHHHHHHHHh---CCCCCHHHHHHHHHHHCcCHHHHHHhHHHHhhccC
Confidence 34455999999999999998 89999999999999999999999999999999864
No 10
>KOG0487 consensus Transcription factor Abd-B, contains HOX domain [Transcription]
Probab=99.11 E-value=3.2e-11 Score=127.16 Aligned_cols=61 Identities=23% Similarity=0.262 Sum_probs=55.7
Q ss_pred CCCCCCCC-CChhHHHHHHHHHHHhhCCCCCCHHHHHHHHHHhCCChhhhhccchhhhhhcChhh
Q 005500 360 NAWRPQRG-LPERSVSVLRAWLFEHFLHPYPKDSDKQMLAKQTGLTRSQVSNWFINARVRLWKPM 423 (693)
Q Consensus 360 ~~kRkrR~-Lpk~qv~iLr~Wf~eH~~nPYPS~~EK~~LAk~TGLS~kQVsNWFiNaR~R~kKp~ 423 (693)
.+-||||+ ++|.|+..|++.|+- |-|.+++-|.+|++.++||++||++||||||+|+||-.
T Consensus 233 ~~~RKKRcPYTK~QtlELEkEFlf---N~YitkeKR~ElSr~lNLTeRQVKIWFQNRRMK~KK~~ 294 (308)
T KOG0487|consen 233 RRGRKKRCPYTKHQTLELEKEFLF---NMYITKEKRLELSRTLNLTERQVKIWFQNRRMKEKKVN 294 (308)
T ss_pred cccccccCCchHHHHHHHHHHHHH---HHHHhHHHHHHHHHhcccchhheeeeehhhhhHHhhhh
Confidence 35567777 999999999999998 89999999999999999999999999999999998744
No 11
>KOG0842 consensus Transcription factor tinman/NKX2-3, contains HOX domain [Transcription]
Probab=99.08 E-value=6.8e-11 Score=124.68 Aligned_cols=63 Identities=24% Similarity=0.337 Sum_probs=57.8
Q ss_pred CCCCCCC-CChhHHHHHHHHHHHhhCCCCCCHHHHHHHHHHhCCChhhhhccchhhhhhcChhhHHH
Q 005500 361 AWRPQRG-LPERSVSVLRAWLFEHFLHPYPKDSDKQMLAKQTGLTRSQVSNWFINARVRLWKPMVEE 426 (693)
Q Consensus 361 ~kRkrR~-Lpk~qv~iLr~Wf~eH~~nPYPS~~EK~~LAk~TGLS~kQVsNWFiNaR~R~kKp~iee 426 (693)
+|||+|. |++.||-.|++-|.+ ..|.+..||+.||+.++||..||++||||+|.|.||..++.
T Consensus 152 ~kRKrRVLFSqAQV~ELERRFrq---QRYLSAPERE~LA~~LrLT~TQVKIWFQNrRYK~KR~~~dk 215 (307)
T KOG0842|consen 152 KKRKRRVLFSQAQVYELERRFRQ---QRYLSAPEREHLASSLRLTPTQVKIWFQNRRYKTKRQQKDK 215 (307)
T ss_pred cccccccccchhHHHHHHHHHHh---hhccccHhHHHHHHhcCCCchheeeeeecchhhhhhhhhhh
Confidence 5667777 999999999999999 99999999999999999999999999999999999866543
No 12
>KOG0488 consensus Transcription factor BarH and related HOX domain proteins [General function prediction only]
Probab=98.83 E-value=2.6e-09 Score=113.13 Aligned_cols=62 Identities=27% Similarity=0.406 Sum_probs=55.5
Q ss_pred CCCCCCC-CChhHHHHHHHHHHHhhCCCCCCHHHHHHHHHHhCCChhhhhccchhhhhhcChhhHH
Q 005500 361 AWRPQRG-LPERSVSVLRAWLFEHFLHPYPKDSDKQMLAKQTGLTRSQVSNWFINARVRLWKPMVE 425 (693)
Q Consensus 361 ~kRkrR~-Lpk~qv~iLr~Wf~eH~~nPYPS~~EK~~LAk~TGLS~kQVsNWFiNaR~R~kKp~ie 425 (693)
|+||.|. |+..|+..|+.-|.. -.|.+..||.+||+.+|||..||+.||+|||+|+||..-+
T Consensus 171 K~RksRTaFT~~Ql~~LEkrF~~---QKYLS~~DR~~LA~~LgLTdaQVKtWfQNRRtKWKrq~a~ 233 (309)
T KOG0488|consen 171 KRRKSRTAFSDHQLFELEKRFEK---QKYLSVADRIELAASLGLTDAQVKTWFQNRRTKWKRQTAE 233 (309)
T ss_pred ccccchhhhhHHHHHHHHHHHHH---hhcccHHHHHHHHHHcCCchhhHHHHHhhhhHHHHHHHHh
Confidence 4455555 999999999999998 8999999999999999999999999999999998886633
No 13
>KOG0489 consensus Transcription factor zerknullt and related HOX domain proteins [General function prediction only]
Probab=98.82 E-value=1.8e-09 Score=111.60 Aligned_cols=59 Identities=22% Similarity=0.288 Sum_probs=54.6
Q ss_pred CCCCCCCCChhHHHHHHHHHHHhhCCCCCCHHHHHHHHHHhCCChhhhhccchhhhhhcChh
Q 005500 361 AWRPQRGLPERSVSVLRAWLFEHFLHPYPKDSDKQMLAKQTGLTRSQVSNWFINARVRLWKP 422 (693)
Q Consensus 361 ~kRkrR~Lpk~qv~iLr~Wf~eH~~nPYPS~~EK~~LAk~TGLS~kQVsNWFiNaR~R~kKp 422 (693)
.||.|..|+..|+..|+.-|-. |.|.++..|.+||..+.|++.||++||+|||+|+||.
T Consensus 159 ~kR~RtayT~~QllELEkEFhf---N~YLtR~RRiEiA~~L~LtErQIKIWFQNRRMK~Kk~ 217 (261)
T KOG0489|consen 159 SKRRRTAFTRYQLLELEKEFHF---NKYLTRSRRIEIAHALNLTERQIKIWFQNRRMKWKKE 217 (261)
T ss_pred CCCCCcccchhhhhhhhhhhcc---ccccchHHHHHHHhhcchhHHHHHHHHHHHHHHHHHh
Confidence 4556666999999999999998 9999999999999999999999999999999999973
No 14
>KOG0843 consensus Transcription factor EMX1 and related HOX domain proteins [Transcription]
Probab=98.79 E-value=4.4e-09 Score=103.86 Aligned_cols=64 Identities=20% Similarity=0.304 Sum_probs=57.2
Q ss_pred CCCCCCCCCChhHHHHHHHHHHHhhCCCCCCHHHHHHHHHHhCCChhhhhccchhhhhhcChhhHHH
Q 005500 360 NAWRPQRGLPERSVSVLRAWLFEHFLHPYPKDSDKQMLAKQTGLTRSQVSNWFINARVRLWKPMVEE 426 (693)
Q Consensus 360 ~~kRkrR~Lpk~qv~iLr~Wf~eH~~nPYPS~~EK~~LAk~TGLS~kQVsNWFiNaR~R~kKp~iee 426 (693)
+.||.|+.|+.+++..|+..|.. +-|-.-.||++||+.++|++.||++||+|+|.|.||.-.++
T Consensus 101 ~~kr~RT~ft~~Ql~~LE~~F~~---~~Yvvg~eR~~LA~~L~LsetQVkvWFQNRRtk~kr~~~e~ 164 (197)
T KOG0843|consen 101 RPKRIRTAFTPEQLLKLEHAFEG---NQYVVGAERKQLAQSLSLSETQVKVWFQNRRTKHKRMQQED 164 (197)
T ss_pred CCCccccccCHHHHHHHHHHHhc---CCeeechHHHHHHHHcCCChhHhhhhhhhhhHHHHHHHHHh
Confidence 34556666999999999999998 99999999999999999999999999999999999865444
No 15
>KOG0483 consensus Transcription factor HEX, contains HOX and HALZ domains [Transcription]
Probab=98.73 E-value=1.1e-08 Score=102.52 Aligned_cols=67 Identities=28% Similarity=0.337 Sum_probs=60.5
Q ss_pred CCCCCCCCCChhHHHHHHHHHHHhhCCCCCCHHHHHHHHHHhCCChhhhhccchhhhhhcChhhHHHHhH
Q 005500 360 NAWRPQRGLPERSVSVLRAWLFEHFLHPYPKDSDKQMLAKQTGLTRSQVSNWFINARVRLWKPMVEEMYL 429 (693)
Q Consensus 360 ~~kRkrR~Lpk~qv~iLr~Wf~eH~~nPYPS~~EK~~LAk~TGLS~kQVsNWFiNaR~R~kKp~ieem~~ 429 (693)
+.++++++|+.+++..|+.-|.. +-|..+.+|..||+++||.+.||.+||+|||+|.|.+-.|.-|.
T Consensus 49 ~~~~kk~Rlt~eQ~~~LE~~F~~---~~~L~p~~K~~LAk~LgL~pRQVavWFQNRRARwK~kqlE~d~~ 115 (198)
T KOG0483|consen 49 KGKGKKRRLTSEQVKFLEKSFES---EKKLEPERKKKLAKELGLQPRQVAVWFQNRRARWKTKQLEKDYE 115 (198)
T ss_pred ccccccccccHHHHHHhHHhhcc---ccccChHHHHHHHHhhCCChhHHHHHHhhccccccchhhhhhHH
Confidence 36788999999999999999998 78888899999999999999999999999999999877665553
No 16
>KOG0850 consensus Transcription factor DLX and related proteins with LIM Zn-binding and HOX domains [Transcription]
Probab=98.73 E-value=8.1e-09 Score=105.13 Aligned_cols=60 Identities=27% Similarity=0.356 Sum_probs=54.5
Q ss_pred CCCCCCC-CChhHHHHHHHHHHHhhCCCCCCHHHHHHHHHHhCCChhhhhccchhhhhhcChhh
Q 005500 361 AWRPQRG-LPERSVSVLRAWLFEHFLHPYPKDSDKQMLAKQTGLTRSQVSNWFINARVRLWKPM 423 (693)
Q Consensus 361 ~kRkrR~-Lpk~qv~iLr~Wf~eH~~nPYPS~~EK~~LAk~TGLS~kQVsNWFiNaR~R~kKp~ 423 (693)
|.||-|+ ++.-+...|++.|.+ .-|.--.||.+||..+|||..||++||+|+|-|.||-+
T Consensus 121 K~RKPRTIYSS~QLqaL~rRFQk---TQYLALPERAeLAAsLGLTQTQVKIWFQNrRSK~KKl~ 181 (245)
T KOG0850|consen 121 KVRKPRTIYSSLQLQALNRRFQQ---TQYLALPERAELAASLGLTQTQVKIWFQNRRSKFKKLK 181 (245)
T ss_pred cccCCcccccHHHHHHHHHHHhh---cchhcCcHHHHHHHHhCCchhHhhhhhhhhHHHHHHHH
Confidence 4455555 999999999999999 99999999999999999999999999999999998844
No 17
>KOG0493 consensus Transcription factor Engrailed, contains HOX domain [General function prediction only]
Probab=98.68 E-value=1.2e-08 Score=105.37 Aligned_cols=60 Identities=30% Similarity=0.513 Sum_probs=56.7
Q ss_pred CCCCCCCCCChhHHHHHHHHHHHhhCCCCCCHHHHHHHHHHhCCChhhhhccchhhhhhcChh
Q 005500 360 NAWRPQRGLPERSVSVLRAWLFEHFLHPYPKDSDKQMLAKQTGLTRSQVSNWFINARVRLWKP 422 (693)
Q Consensus 360 ~~kRkrR~Lpk~qv~iLr~Wf~eH~~nPYPS~~EK~~LAk~TGLS~kQVsNWFiNaR~R~kKp 422 (693)
..||+|.-|+.++.+.|++.|.+ |.|.++..|..||.+++|.+.||++||+|+|.|+||.
T Consensus 245 eeKRPRTAFtaeQL~RLK~EF~e---nRYlTEqRRQ~La~ELgLNEsQIKIWFQNKRAKiKKs 304 (342)
T KOG0493|consen 245 EEKRPRTAFTAEQLQRLKAEFQE---NRYLTEQRRQELAQELGLNESQIKIWFQNKRAKIKKS 304 (342)
T ss_pred hhcCccccccHHHHHHHHHHHhh---hhhHHHHHHHHHHHHhCcCHHHhhHHhhhhhhhhhhc
Confidence 46788888999999999999999 9999999999999999999999999999999999974
No 18
>TIGR01565 homeo_ZF_HD homeobox domain, ZF-HD class. This model represents a class of homoebox domain that differs substantially from the typical homoebox domain described in pfam model pfam00046. It is found in both C4 and C3 plants.
Probab=98.66 E-value=3.9e-08 Score=81.45 Aligned_cols=53 Identities=13% Similarity=0.293 Sum_probs=49.4
Q ss_pred CCCCCCCCChhHHHHHHHHHHHhhCCCC----CCHHHHHHHHHHhCCChhhhhccchhhh
Q 005500 361 AWRPQRGLPERSVSVLRAWLFEHFLHPY----PKDSDKQMLAKQTGLTRSQVSNWFINAR 416 (693)
Q Consensus 361 ~kRkrR~Lpk~qv~iLr~Wf~eH~~nPY----PS~~EK~~LAk~TGLS~kQVsNWFiNaR 416 (693)
++|+|..|+.+|+..|+..|.. ++| |+..++..||..+||++.+|.+||+|.+
T Consensus 1 ~kR~RT~Ft~~Q~~~Le~~fe~---~~y~~~~~~~~~r~~la~~lgl~~~vvKVWfqN~k 57 (58)
T TIGR01565 1 KKRRRTKFTAEQKEKMRDFAEK---LGWKLKDKRREEVREFCEEIGVTRKVFKVWMHNNK 57 (58)
T ss_pred CCCCCCCCCHHHHHHHHHHHHH---cCCCCCCCCHHHHHHHHHHhCCCHHHeeeecccCC
Confidence 3667777999999999999999 999 9999999999999999999999999964
No 19
>KOG0485 consensus Transcription factor NKX-5.1/HMX1, contains HOX domain [Transcription]
Probab=98.65 E-value=1.7e-08 Score=102.24 Aligned_cols=64 Identities=20% Similarity=0.269 Sum_probs=57.5
Q ss_pred CCCCCCCCChhHHHHHHHHHHHhhCCCCCCHHHHHHHHHHhCCChhhhhccchhhhhhcChhhHHHH
Q 005500 361 AWRPQRGLPERSVSVLRAWLFEHFLHPYPKDSDKQMLAKQTGLTRSQVSNWFINARVRLWKPMVEEM 427 (693)
Q Consensus 361 ~kRkrR~Lpk~qv~iLr~Wf~eH~~nPYPS~~EK~~LAk~TGLS~kQVsNWFiNaR~R~kKp~ieem 427 (693)
|||.|..|+..|+..|+.-|.. ..|.+..||..||+++.||+.||++||||+|.|+|+....++
T Consensus 104 KKktRTvFSraQV~qLEs~Fe~---krYLSsaeRa~LA~sLqLTETQVKIWFQNRRnKwKRq~aad~ 167 (268)
T KOG0485|consen 104 KKKTRTVFSRAQVFQLESTFEL---KRYLSSAERAGLAASLQLTETQVKIWFQNRRNKWKRQYAADL 167 (268)
T ss_pred cccchhhhhHHHHHHHHHHHHH---HhhhhHHHHhHHHHhhhhhhhhhhhhhhhhhHHHHHHHhhhh
Confidence 5555666999999999999998 899999999999999999999999999999999998775554
No 20
>KOG0484 consensus Transcription factor PHOX2/ARIX, contains HOX domain [Transcription]
Probab=98.62 E-value=3.3e-08 Score=90.65 Aligned_cols=63 Identities=22% Similarity=0.343 Sum_probs=55.8
Q ss_pred CCCCCCChhHHHHHHHHHHHhhCCCCCCHHHHHHHHHHhCCChhhhhccchhhhhhcChhhHHHHh
Q 005500 363 RPQRGLPERSVSVLRAWLFEHFLHPYPKDSDKQMLAKQTGLTRSQVSNWFINARVRLWKPMVEEMY 428 (693)
Q Consensus 363 RkrR~Lpk~qv~iLr~Wf~eH~~nPYPS~~EK~~LAk~TGLS~kQVsNWFiNaR~R~kKp~ieem~ 428 (693)
|-|.+|+..+...|++.|.+ ..||+.-.|++||-++.|++..|..||+|+|.+.+|...-..+
T Consensus 19 RIRTTFTS~QLkELErvF~E---THYPDIYTREEiA~kidLTEARVQVWFQNRRAKfRKQEr~a~~ 81 (125)
T KOG0484|consen 19 RIRTTFTSAQLKELERVFAE---THYPDIYTREEIALKIDLTEARVQVWFQNRRAKFRKQERAAIA 81 (125)
T ss_pred hhhhhhhHHHHHHHHHHHHh---hcCCcchhHHHHHHhhhhhHHHHHHHHHhhHHHHHHHHHHHHH
Confidence 34455999999999999999 8999999999999999999999999999999999986544433
No 21
>KOG3802 consensus Transcription factor OCT-1, contains POU and HOX domains [Transcription]
Probab=98.61 E-value=3.9e-08 Score=106.51 Aligned_cols=60 Identities=20% Similarity=0.330 Sum_probs=55.8
Q ss_pred CCCCCCC-CChhHHHHHHHHHHHhhCCCCCCHHHHHHHHHHhCCChhhhhccchhhhhhcChhh
Q 005500 361 AWRPQRG-LPERSVSVLRAWLFEHFLHPYPKDSDKQMLAKQTGLTRSQVSNWFINARVRLWKPM 423 (693)
Q Consensus 361 ~kRkrR~-Lpk~qv~iLr~Wf~eH~~nPYPS~~EK~~LAk~TGLS~kQVsNWFiNaR~R~kKp~ 423 (693)
+|||||+ +.-.++..|++.|.+ ||.|+.+|.-.||.+++|.+..|++||+|||.|+|+..
T Consensus 293 RkRKKRTSie~~vr~aLE~~F~~---npKPt~qEIt~iA~~L~leKEVVRVWFCNRRQkeKR~~ 353 (398)
T KOG3802|consen 293 RKRKKRTSIEVNVRGALEKHFLK---NPKPTSQEITHIAESLQLEKEVVRVWFCNRRQKEKRIT 353 (398)
T ss_pred cccccccceeHHHHHHHHHHHHh---CCCCCHHHHHHHHHHhccccceEEEEeeccccccccCC
Confidence 5666666 999999999999999 99999999999999999999999999999999998754
No 22
>KOG0492 consensus Transcription factor MSH, contains HOX domain [General function prediction only]
Probab=98.47 E-value=1.7e-07 Score=94.61 Aligned_cols=58 Identities=21% Similarity=0.349 Sum_probs=52.9
Q ss_pred CCCCCCChhHHHHHHHHHHHhhCCCCCCHHHHHHHHHHhCCChhhhhccchhhhhhcChhh
Q 005500 363 RPQRGLPERSVSVLRAWLFEHFLHPYPKDSDKQMLAKQTGLTRSQVSNWFINARVRLWKPM 423 (693)
Q Consensus 363 RkrR~Lpk~qv~iLr~Wf~eH~~nPYPS~~EK~~LAk~TGLS~kQVsNWFiNaR~R~kKp~ 423 (693)
++|..|+..|...|++-|.+ ..|.+.+||.+++..+.||..||++||+|||.|.|+--
T Consensus 146 kPRtPFTtqQLlaLErkfre---kqYLSiaEraefSsSL~LTeTqVKIWFQNRRAKaKRlQ 203 (246)
T KOG0492|consen 146 KPRTPFTTQQLLALERKFRE---KQYLSIAERAEFSSSLELTETQVKIWFQNRRAKAKRLQ 203 (246)
T ss_pred CCCCCCCHHHHHHHHHHHhH---hhhhhHHHHHhhhhhhhhhhhheehhhhhhhHHHHHHH
Confidence 34455999999999999999 89999999999999999999999999999999998643
No 23
>COG5576 Homeodomain-containing transcription factor [Transcription]
Probab=98.46 E-value=1.3e-07 Score=91.86 Aligned_cols=61 Identities=21% Similarity=0.285 Sum_probs=56.8
Q ss_pred CCCCCCCCCChhHHHHHHHHHHHhhCCCCCCHHHHHHHHHHhCCChhhhhccchhhhhhcChhh
Q 005500 360 NAWRPQRGLPERSVSVLRAWLFEHFLHPYPKDSDKQMLAKQTGLTRSQVSNWFINARVRLWKPM 423 (693)
Q Consensus 360 ~~kRkrR~Lpk~qv~iLr~Wf~eH~~nPYPS~~EK~~LAk~TGLS~kQVsNWFiNaR~R~kKp~ 423 (693)
..+++|++.+..++.+|++-|.. +|||+..+|..|+..++++++-|..||+|+|.+.|+..
T Consensus 50 ~~~~~r~R~t~~Q~~vL~~~F~i---~p~Ps~~~r~~L~~~lnm~~ksVqIWFQNkR~~~k~~~ 110 (156)
T COG5576 50 PPKSKRRRTTDEQLMVLEREFEI---NPYPSSITRIKLSLLLNMPPKSVQIWFQNKRAKEKKKR 110 (156)
T ss_pred cCcccceechHHHHHHHHHHhcc---CCCCCHHHHHHHHHhcCCChhhhhhhhchHHHHHHHhc
Confidence 46677888999999999999998 99999999999999999999999999999999998754
No 24
>KOG0848 consensus Transcription factor Caudal, contains HOX domain [Transcription]
Probab=98.45 E-value=6.4e-08 Score=100.48 Aligned_cols=57 Identities=26% Similarity=0.270 Sum_probs=52.2
Q ss_pred CCCC-CChhHHHHHHHHHHHhhCCCCCCHHHHHHHHHHhCCChhhhhccchhhhhhcChhh
Q 005500 364 PQRG-LPERSVSVLRAWLFEHFLHPYPKDSDKQMLAKQTGLTRSQVSNWFINARVRLWKPM 423 (693)
Q Consensus 364 krR~-Lpk~qv~iLr~Wf~eH~~nPYPS~~EK~~LAk~TGLS~kQVsNWFiNaR~R~kKp~ 423 (693)
|-|. ++..++-.|++.|-- .+|.+...|.+||..+||+++||++||+|||+|++|..
T Consensus 201 KYRvVYTDhQRLELEKEfh~---SryITirRKSELA~~LgLsERQVKIWFQNRRAKERK~n 258 (317)
T KOG0848|consen 201 KYRVVYTDHQRLELEKEFHT---SRYITIRRKSELAATLGLSERQVKIWFQNRRAKERKDN 258 (317)
T ss_pred ceeEEecchhhhhhhhhhcc---ccceeeehhHHHHHhhCccHhhhhHhhhhhhHHHHHHH
Confidence 3344 899999999999987 99999999999999999999999999999999998744
No 25
>KOG0486 consensus Transcription factor PTX1, contains HOX domain [Transcription]
Probab=98.42 E-value=1.4e-07 Score=99.64 Aligned_cols=60 Identities=30% Similarity=0.403 Sum_probs=54.2
Q ss_pred CCCCCC-CChhHHHHHHHHHHHhhCCCCCCHHHHHHHHHHhCCChhhhhccchhhhhhcChhhH
Q 005500 362 WRPQRG-LPERSVSVLRAWLFEHFLHPYPKDSDKQMLAKQTGLTRSQVSNWFINARVRLWKPMV 424 (693)
Q Consensus 362 kRkrR~-Lpk~qv~iLr~Wf~eH~~nPYPS~~EK~~LAk~TGLS~kQVsNWFiNaR~R~kKp~i 424 (693)
+|++|+ |+-.+.+.|+.||.+ |.||+.+.|++||--|+||+..|++||.|+|.+.+|...
T Consensus 112 qrrQrthFtSqqlqele~tF~r---NrypdMstrEEIavwtNlTE~rvrvwfknrrakwrkrEr 172 (351)
T KOG0486|consen 112 QRRQRTHFTSQQLQELEATFQR---NRYPDMSTREEIAVWTNLTEARVRVWFKNRRAKWRKRER 172 (351)
T ss_pred hhhhhhhhHHHHHHHHHHHHhh---ccCCccchhhHHHhhccccchhhhhhcccchhhhhhhhh
Confidence 344444 999999999999999 999999999999999999999999999999999988653
No 26
>KOG0491 consensus Transcription factor BSH, contains HOX domain [General function prediction only]
Probab=98.36 E-value=1e-07 Score=93.28 Aligned_cols=59 Identities=27% Similarity=0.414 Sum_probs=53.2
Q ss_pred CCCCCCC-CChhHHHHHHHHHHHhhCCCCCCHHHHHHHHHHhCCChhhhhccchhhhhhcChh
Q 005500 361 AWRPQRG-LPERSVSVLRAWLFEHFLHPYPKDSDKQMLAKQTGLTRSQVSNWFINARVRLWKP 422 (693)
Q Consensus 361 ~kRkrR~-Lpk~qv~iLr~Wf~eH~~nPYPS~~EK~~LAk~TGLS~kQVsNWFiNaR~R~kKp 422 (693)
++||.|. |+..+...|++.|.. -.|.+-.|+.+||..++|+++||+.||+|+|+|.||-
T Consensus 99 ~r~K~Rtvfs~~ql~~l~~rFe~---QrYLS~~e~~ELan~L~LS~~QVKTWFQNrRMK~Kk~ 158 (194)
T KOG0491|consen 99 RRRKARTVFSDPQLSGLEKRFER---QRYLSTPERQELANALSLSETQVKTWFQNRRMKHKKQ 158 (194)
T ss_pred HhhhhcccccCccccccHHHHhh---hhhcccHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHH
Confidence 4455555 999999999999997 7899999999999999999999999999999999874
No 27
>KOG2251 consensus Homeobox transcription factor [Transcription]
Probab=98.33 E-value=4.3e-07 Score=92.34 Aligned_cols=58 Identities=26% Similarity=0.423 Sum_probs=53.2
Q ss_pred CCCCCCCChhHHHHHHHHHHHhhCCCCCCHHHHHHHHHHhCCChhhhhccchhhhhhcChh
Q 005500 362 WRPQRGLPERSVSVLRAWLFEHFLHPYPKDSDKQMLAKQTGLTRSQVSNWFINARVRLWKP 422 (693)
Q Consensus 362 kRkrR~Lpk~qv~iLr~Wf~eH~~nPYPS~~EK~~LAk~TGLS~kQVsNWFiNaR~R~kKp 422 (693)
+|.|..|+..+..+|++-|.+ .-||+...+++||.+++|.+.+|.+||.|+|+|.++.
T Consensus 38 RRERTtFtr~QlevLe~LF~k---TqYPDv~~rEelAlklnLpeSrVqVWFKNRRAK~r~q 95 (228)
T KOG2251|consen 38 RRERTTFTRKQLEVLEALFAK---TQYPDVFMREELALKLNLPESRVQVWFKNRRAKCRRQ 95 (228)
T ss_pred ccccceecHHHHHHHHHHHHh---hcCccHHHHHHHHHHhCCchhhhhhhhccccchhhHh
Confidence 344555999999999999999 9999999999999999999999999999999998873
No 28
>KOG0494 consensus Transcription factor CHX10 and related HOX domain proteins [General function prediction only]
Probab=98.24 E-value=8.7e-07 Score=91.93 Aligned_cols=53 Identities=26% Similarity=0.412 Sum_probs=50.6
Q ss_pred CCChhHHHHHHHHHHHhhCCCCCCHHHHHHHHHHhCCChhhhhccchhhhhhcChh
Q 005500 367 GLPERSVSVLRAWLFEHFLHPYPKDSDKQMLAKQTGLTRSQVSNWFINARVRLWKP 422 (693)
Q Consensus 367 ~Lpk~qv~iLr~Wf~eH~~nPYPS~~EK~~LAk~TGLS~kQVsNWFiNaR~R~kKp 422 (693)
.|+..+...|++-|.+ --||+-..|+.||.+|+|.+.+|.+||+|||.|++|.
T Consensus 147 iFT~~Qle~LEkaFke---aHYPDv~Are~la~ktelpEDRIqVWfQNRRAKWRk~ 199 (332)
T KOG0494|consen 147 IFTSYQLEELEKAFKE---AHYPDVYAREMLADKTELPEDRIQVWFQNRRAKWRKT 199 (332)
T ss_pred hhhHHHHHHHHHHHhh---ccCccHHHHHHHhhhccCchhhhhHHhhhhhHHhhhh
Confidence 3999999999999999 8999999999999999999999999999999998874
No 29
>KOG0847 consensus Transcription factor, contains HOX domain [Transcription]
Probab=98.01 E-value=3.1e-06 Score=86.27 Aligned_cols=63 Identities=25% Similarity=0.344 Sum_probs=57.4
Q ss_pred CCChhHHHHHHHHHHHhhCCCCCCHHHHHHHHHHhCCChhhhhccchhhhhhcChhhHHHHhHHHh
Q 005500 367 GLPERSVSVLRAWLFEHFLHPYPKDSDKQMLAKQTGLTRSQVSNWFINARVRLWKPMVEEMYLEEI 432 (693)
Q Consensus 367 ~Lpk~qv~iLr~Wf~eH~~nPYPS~~EK~~LAk~TGLS~kQVsNWFiNaR~R~kKp~ieem~~~~~ 432 (693)
+|.-.++..|+.-|.+ ..||--.++.+||...|+++.||.+||+|+|.|++|...-||-....
T Consensus 173 Tf~g~qi~~le~~feq---tkylaG~~ra~lA~~lgmteSqvkVWFQNRRTKWRKkhAaEmasakk 235 (288)
T KOG0847|consen 173 TFTGHQIYQLERKFEQ---TKYLAGADRAQLAQELNMTESQVKVWFQNRRTKWRKKHAAEMASAKK 235 (288)
T ss_pred Cccchhhhhhhhhhhh---hhcccchhHHHhhccccccHHHHHHHHhcchhhhhhhhccchhhccc
Confidence 3999999999999998 89999999999999999999999999999999999988777754443
No 30
>KOG4577 consensus Transcription factor LIM3, contains LIM and HOX domains [Transcription]
Probab=97.98 E-value=3.5e-06 Score=88.58 Aligned_cols=61 Identities=23% Similarity=0.389 Sum_probs=56.6
Q ss_pred cCCCCCCCCCChhHHHHHHHHHHHhhCCCCCCHHHHHHHHHHhCCChhhhhccchhhhhhcChh
Q 005500 359 HNAWRPQRGLPERSVSVLRAWLFEHFLHPYPKDSDKQMLAKQTGLTRSQVSNWFINARVRLWKP 422 (693)
Q Consensus 359 ~~~kRkrR~Lpk~qv~iLr~Wf~eH~~nPYPS~~EK~~LAk~TGLS~kQVsNWFiNaR~R~kKp 422 (693)
...||+|.+++.++...|+.-+.. .|.|-+--|++|+.+|||+.+.|..||+|+|+|+|+-
T Consensus 165 ~~nKRPRTTItAKqLETLK~AYn~---SpKPARHVREQLsseTGLDMRVVQVWFQNRRAKEKRL 225 (383)
T KOG4577|consen 165 ASNKRPRTTITAKQLETLKQAYNT---SPKPARHVREQLSSETGLDMRVVQVWFQNRRAKEKRL 225 (383)
T ss_pred cccCCCcceeeHHHHHHHHHHhcC---CCchhHHHHHHhhhccCcceeehhhhhhhhhHHHHhh
Confidence 357899999999999999999887 9999999999999999999999999999999988753
No 31
>KOG2252 consensus CCAAT displacement protein and related homeoproteins [Transcription]
Probab=97.89 E-value=1.2e-05 Score=90.46 Aligned_cols=56 Identities=27% Similarity=0.356 Sum_probs=52.7
Q ss_pred CCCCCCCCChhHHHHHHHHHHHhhCCCCCCHHHHHHHHHHhCCChhhhhccchhhhhhc
Q 005500 361 AWRPQRGLPERSVSVLRAWLFEHFLHPYPKDSDKQMLAKQTGLTRSQVSNWFINARVRL 419 (693)
Q Consensus 361 ~kRkrR~Lpk~qv~iLr~Wf~eH~~nPYPS~~EK~~LAk~TGLS~kQVsNWFiNaR~R~ 419 (693)
.||+|-.|+..+++.|++.|.+ ++||+.++-+.|+.+++|...-|.|||-|+|+|.
T Consensus 420 ~KKPRlVfTd~QkrTL~aiFke---~~RPS~Emq~tIS~qL~L~~sTV~NfFmNaRRRs 475 (558)
T KOG2252|consen 420 TKKPRLVFTDIQKRTLQAIFKE---NKRPSREMQETISQQLNLELSTVINFFMNARRRS 475 (558)
T ss_pred CCCceeeecHHHHHHHHHHHhc---CCCCCHHHHHHHHHHhCCcHHHHHHHHHhhhhhc
Confidence 5666666999999999999999 9999999999999999999999999999999996
No 32
>KOG0844 consensus Transcription factor EVX1, contains HOX domain [Transcription]
Probab=97.77 E-value=9.4e-06 Score=85.97 Aligned_cols=58 Identities=16% Similarity=0.326 Sum_probs=52.7
Q ss_pred CCCCChhHHHHHHHHHHHhhCCCCCCHHHHHHHHHHhCCChhhhhccchhhhhhcChhhHH
Q 005500 365 QRGLPERSVSVLRAWLFEHFLHPYPKDSDKQMLAKQTGLTRSQVSNWFINARVRLWKPMVE 425 (693)
Q Consensus 365 rR~Lpk~qv~iLr~Wf~eH~~nPYPS~~EK~~LAk~TGLS~kQVsNWFiNaR~R~kKp~ie 425 (693)
|.-|+.+|+..|++.|++ --|-++..|-+||..++|.+..|+.||||+|+|.|+..+-
T Consensus 185 RTAFTReQIaRLEKEFyr---ENYVSRprRcELAAaLNLPEtTIKVWFQNRRMKDKRQRla 242 (408)
T KOG0844|consen 185 RTAFTREQIARLEKEFYR---ENYVSRPRRCELAAALNLPETTIKVWFQNRRMKDKRQRLA 242 (408)
T ss_pred HhhhhHHHHHHHHHHHHH---hccccCchhhhHHHhhCCCcceeehhhhhchhhhhhhhhh
Confidence 345999999999998887 6799999999999999999999999999999999987754
No 33
>KOG0490 consensus Transcription factor, contains HOX domain [General function prediction only]
Probab=97.55 E-value=4.1e-05 Score=75.43 Aligned_cols=60 Identities=17% Similarity=0.078 Sum_probs=54.4
Q ss_pred CCCCCCCCChhHHHHHHHHHHHhhCCCCCCHHHHHHHHHHhCCChhhhhccchhhhhhcChhh
Q 005500 361 AWRPQRGLPERSVSVLRAWLFEHFLHPYPKDSDKQMLAKQTGLTRSQVSNWFINARVRLWKPM 423 (693)
Q Consensus 361 ~kRkrR~Lpk~qv~iLr~Wf~eH~~nPYPS~~EK~~LAk~TGLS~kQVsNWFiNaR~R~kKp~ 423 (693)
++|.|.+|+..+..+|++-|.. .+||+...++.||..+++++..|.+||+|+|++.++..
T Consensus 60 ~rr~rt~~~~~ql~~ler~f~~---~h~Pd~~~r~~la~~~~~~e~rVqvwFqnrrak~r~~~ 119 (235)
T KOG0490|consen 60 KRCARCKFTISQLDELERAFEK---VHLPCFACRECLALLLTGDEFRVQVWFQNRRAKDRKEE 119 (235)
T ss_pred ccccCCCCCcCHHHHHHHhhcC---CCcCccchHHHHhhcCCCCeeeeehhhhhhcHhhhhhh
Confidence 4556666999999999999998 69999999999999999999999999999999998754
No 34
>KOG0849 consensus Transcription factor PRD and related proteins, contain PAX and HOX domains [Transcription]
Probab=97.51 E-value=6.7e-05 Score=81.30 Aligned_cols=59 Identities=27% Similarity=0.512 Sum_probs=53.8
Q ss_pred CCCCCCCChhHHHHHHHHHHHhhCCCCCCHHHHHHHHHHhCCChhhhhccchhhhhhcChhh
Q 005500 362 WRPQRGLPERSVSVLRAWLFEHFLHPYPKDSDKQMLAKQTGLTRSQVSNWFINARVRLWKPM 423 (693)
Q Consensus 362 kRkrR~Lpk~qv~iLr~Wf~eH~~nPYPS~~EK~~LAk~TGLS~kQVsNWFiNaR~R~kKp~ 423 (693)
+|.|..|+..+...|+.||.. +|||.-..|+.||++++|+...|..||.|+|.|.+|..
T Consensus 177 rr~rtsft~~Q~~~le~~f~r---t~yP~i~~Re~La~~i~l~e~riqvwf~nrra~~rr~~ 235 (354)
T KOG0849|consen 177 RRNRTSFSPSQLEALEECFQR---TPYPDIVGRETLAKETGLPEPRVQVWFQNRRAKWRRQH 235 (354)
T ss_pred cccccccccchHHHHHHHhcC---CCCCchhhHHHHhhhccCCchHHHHHHhhhhhhhhhcc
Confidence 344456999999999999998 88999999999999999999999999999999998844
No 35
>KOG1168 consensus Transcription factor ACJ6/BRN-3, contains POU and HOX domains [Transcription]
Probab=97.26 E-value=0.00011 Score=77.70 Aligned_cols=59 Identities=20% Similarity=0.366 Sum_probs=53.3
Q ss_pred CCCCCCCCCChhHHHHHHHHHHHhhCCCCCCHHHHHHHHHHhCCChhhhhccchhhhhhcCh
Q 005500 360 NAWRPQRGLPERSVSVLRAWLFEHFLHPYPKDSDKQMLAKQTGLTRSQVSNWFINARVRLWK 421 (693)
Q Consensus 360 ~~kRkrR~Lpk~qv~iLr~Wf~eH~~nPYPS~~EK~~LAk~TGLS~kQVsNWFiNaR~R~kK 421 (693)
.|||||...-..-++.|+++|.. -|-|+.+....+|.++.|.+..|..||+|+|.|.|+
T Consensus 308 ekKRKRTSIAAPEKRsLEayFav---QPRPS~EkIAaIAekLDLKKNVVRVWFCNQRQKQKR 366 (385)
T KOG1168|consen 308 EKKRKRTSIAAPEKRSLEAYFAV---QPRPSGEKIAAIAEKLDLKKNVVRVWFCNQRQKQKR 366 (385)
T ss_pred ccccccccccCcccccHHHHhcc---CCCCchhHHHHHHHhhhhhhceEEEEeeccHHHHHH
Confidence 46777777777778899999998 999999999999999999999999999999999987
No 36
>KOG0773 consensus Transcription factor MEIS1 and related HOX domain proteins [Transcription]
Probab=97.03 E-value=0.00024 Score=75.55 Aligned_cols=61 Identities=46% Similarity=0.659 Sum_probs=55.3
Q ss_pred CCCCCCCChhHHHHHHHHHHHhhCCCCCCHHHHHHHHHHhCCChhhhhccchhhhhhcChhh
Q 005500 362 WRPQRGLPERSVSVLRAWLFEHFLHPYPKDSDKQMLAKQTGLTRSQVSNWFINARVRLWKPM 423 (693)
Q Consensus 362 kRkrR~Lpk~qv~iLr~Wf~eH~~nPYPS~~EK~~LAk~TGLS~kQVsNWFiNaR~R~kKp~ 423 (693)
.+++..++.+. .+|+.|+.+|..+|||++-++..|+..++++..||++||+|+|+|+++.+
T Consensus 96 ~~~~~n~~~~s-~~~~~~~~~~~~~~~~~k~~~~ll~~~~~~~~~~~~~~~~~a~r~~~~~~ 156 (342)
T KOG0773|consen 96 GARRGNATRES-ATLKAWLEEHRLNPYPSKLEKILLAVITKLTLTQVSTWFANARRRLKKEL 156 (342)
T ss_pred ccccccccccc-cccccchhhhhhccCchHHHHHHHHHHHHhhhhhHHHHHHHHHHHHHhcc
Confidence 34445689899 99999999999999999999999999999999999999999999998644
No 37
>PF11569 Homez: Homeodomain leucine-zipper encoding, Homez; PDB: 2YS9_A.
Probab=95.42 E-value=0.011 Score=49.24 Aligned_cols=43 Identities=19% Similarity=0.434 Sum_probs=31.3
Q ss_pred HHHHHHHHHHhhCCCCCCHHHHHHHHHHhCCChhhhhccchhhhhh
Q 005500 373 VSVLRAWLFEHFLHPYPKDSDKQMLAKQTGLTRSQVSNWFINARVR 418 (693)
Q Consensus 373 v~iLr~Wf~eH~~nPYPS~~EK~~LAk~TGLS~kQVsNWFiNaR~R 418 (693)
++.|++.|.. |.++.+.+-..|..+++|+..||.+||.-++.+
T Consensus 10 ~~pL~~Yy~~---h~~L~E~DL~~L~~kS~ms~qqVr~WFa~~~~e 52 (56)
T PF11569_consen 10 IQPLEDYYLK---HKQLQEEDLDELCDKSRMSYQQVRDWFAERMQE 52 (56)
T ss_dssp -HHHHHHHHH---T----TTHHHHHHHHTT--HHHHHHHHHHHS--
T ss_pred hHHHHHHHHH---cCCccHhhHHHHHHHHCCCHHHHHHHHHHhccc
Confidence 4559999998 899999999999999999999999999877544
No 38
>KOG0490 consensus Transcription factor, contains HOX domain [General function prediction only]
Probab=94.41 E-value=0.028 Score=55.57 Aligned_cols=61 Identities=31% Similarity=0.549 Sum_probs=53.4
Q ss_pred CCCCCCCCChhHHHHHHHHHHHhhCCCCCCHHHHHHHHHHhCCChhhhhccchhhhhhcChhhH
Q 005500 361 AWRPQRGLPERSVSVLRAWLFEHFLHPYPKDSDKQMLAKQTGLTRSQVSNWFINARVRLWKPMV 424 (693)
Q Consensus 361 ~kRkrR~Lpk~qv~iLr~Wf~eH~~nPYPS~~EK~~LAk~TGLS~kQVsNWFiNaR~R~kKp~i 424 (693)
.++.+..+...+..+|..-|.. .+||....+..|+..+|++...|.+||+|.|.+.++...
T Consensus 153 ~~~~~~~~~~~~~~~~~~~~~~---~~~P~~~~~~~l~~~~~~~~~~~q~~~~~~~~~~~~~~~ 213 (235)
T KOG0490|consen 153 PRRPRTTFTENQLEVLETVFRA---TPKPDADDREQLAEETGLSERVIQVWFQNRRAKLRKHKR 213 (235)
T ss_pred cCCCccccccchhHhhhhcccC---CCCCchhhHHHHHHhcCCChhhhhhhcccHHHHHHhhcc
Confidence 3445556889999999888887 999999999999999999999999999999999987654
No 39
>KOG1146 consensus Homeobox protein [General function prediction only]
Probab=90.24 E-value=0.19 Score=62.50 Aligned_cols=60 Identities=18% Similarity=0.301 Sum_probs=54.1
Q ss_pred CCCCCCCCChhHHHHHHHHHHHhhCCCCCCHHHHHHHHHHhCCChhhhhccchhhhhhcChhh
Q 005500 361 AWRPQRGLPERSVSVLRAWLFEHFLHPYPKDSDKQMLAKQTGLTRSQVSNWFINARVRLWKPM 423 (693)
Q Consensus 361 ~kRkrR~Lpk~qv~iLr~Wf~eH~~nPYPS~~EK~~LAk~TGLS~kQVsNWFiNaR~R~kKp~ 423 (693)
+++.|..+...++.+|+..|.. .-||..++-+.|.+..+|....|..||+|+|.+.+|+.
T Consensus 903 r~a~~~~~~d~qlk~i~~~~~~---q~~~~~~~~E~l~~~~~~~~~~i~vw~qna~~~s~k~~ 962 (1406)
T KOG1146|consen 903 RRAYRTQESDLQLKIIKACYEA---QRTPTMQECEVLEEPIGLPKRVIQVWFQNARAKSKKAK 962 (1406)
T ss_pred hhhhccchhHHHHHHHHHHHhh---ccCChHHHHHhhcccccCCcchhHHhhhhhhhhhhhhh
Confidence 3344555999999999999998 89999999999999999999999999999999999876
No 40
>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=77.61 E-value=3.2 Score=33.77 Aligned_cols=47 Identities=26% Similarity=0.252 Sum_probs=31.2
Q ss_pred CCCCCCCChhHHHHHHHHHHHhhCCCCCCHHHHHHHHHHhCCChhhhhccchhhh
Q 005500 362 WRPQRGLPERSVSVLRAWLFEHFLHPYPKDSDKQMLAKQTGLTRSQVSNWFINAR 416 (693)
Q Consensus 362 kRkrR~Lpk~qv~iLr~Wf~eH~~nPYPS~~EK~~LAk~TGLS~kQVsNWFiNaR 416 (693)
+|+|+.|+-+.+-.+-.-+.. .+ -+..||+..|++..+|++|..|+.
T Consensus 1 krkR~~LTl~eK~~iI~~~e~---g~-----s~~~ia~~fgv~~sTv~~I~K~k~ 47 (53)
T PF04218_consen 1 KRKRKSLTLEEKLEIIKRLEE---GE-----SKRDIAREFGVSRSTVSTILKNKD 47 (53)
T ss_dssp SSSSSS--HHHHHHHHHHHHC---TT------HHHHHHHHT--CCHHHHHHHCHH
T ss_pred CCCCccCCHHHHHHHHHHHHc---CC-----CHHHHHHHhCCCHHHHHHHHHhHH
Confidence 466777887775555444444 33 589999999999999999999853
No 41
>PF11285 DUF3086: Protein of unknown function (DUF3086); InterPro: IPR021437 This family of proteins with unknown function appears to be restricted to Cyanobacteria.
Probab=76.69 E-value=28 Score=37.50 Aligned_cols=60 Identities=18% Similarity=0.381 Sum_probs=49.0
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhchhhhccCCchhhhHHHHHHHHHHhhhhHHHHHHHHHHHHHhh
Q 005500 247 QEIQMKKAKLINMLDEVEQRYRQYHHQMQIVISSFEQAAGIESAKTYTALALKTISKQFRCLKDAITGQIKAANKM 322 (693)
Q Consensus 247 ~ElQ~Kk~KLl~mLdeVd~RY~qY~~qmq~v~ssFe~~ag~gaa~~yt~laL~~iSr~Fr~LkdaI~~qi~~~~~s 322 (693)
.||+.+|..|..-++++++|-++-..+|.+-. || .-+.|.+.-+-+||..++.|.....+
T Consensus 7 ~eL~qrk~~Lq~eIe~LerR~~ri~~EmrtsF------aG----------~Sq~lA~RVqGFkdYLvGsLQDLa~s 66 (283)
T PF11285_consen 7 KELEQRKQALQIEIEQLERRRERIEKEMRTSF------AG----------QSQDLAIRVQGFKDYLVGSLQDLAQS 66 (283)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHccc------cc----------chHHHHHHHhhhHHHHHHHHHHHHHH
Confidence 58999999999999999999999999987533 34 45667788888899999988876543
No 42
>KOG3623 consensus Homeobox transcription factor SIP1 [Transcription]
Probab=74.23 E-value=3.6 Score=49.25 Aligned_cols=45 Identities=24% Similarity=0.440 Sum_probs=41.1
Q ss_pred HHHHHHHHHHhhCCCCCCHHHHHHHHHHhCCChhhhhccchhhhhhcC
Q 005500 373 VSVLRAWLFEHFLHPYPKDSDKQMLAKQTGLTRSQVSNWFINARVRLW 420 (693)
Q Consensus 373 v~iLr~Wf~eH~~nPYPS~~EK~~LAk~TGLS~kQVsNWFiNaR~R~k 420 (693)
+.+|+++|.. |+.|+.+|-..+|.+.||...-|+.||.+.+....
T Consensus 568 ~sllkayyal---n~~ps~eelskia~qvglp~~vvk~wfE~~~a~e~ 612 (1007)
T KOG3623|consen 568 TSLLKAYYAL---NGLPSEEELSKIAQQVGLPFAVVKAWFEDEEAEEM 612 (1007)
T ss_pred HHHHHHHHHh---cCCCCHHHHHHHHHHhcccHHHHHHHHHhhhhhhh
Confidence 7888999888 99999999999999999999999999999876543
No 43
>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=57.38 E-value=11 Score=27.86 Aligned_cols=45 Identities=29% Similarity=0.309 Sum_probs=35.5
Q ss_pred CChhHHHHHHHHHHHhhCCCCCCHHHHHHHHHHhCCChhhhhccchhhhhhcC
Q 005500 368 LPERSVSVLRAWLFEHFLHPYPKDSDKQMLAKQTGLTRSQVSNWFINARVRLW 420 (693)
Q Consensus 368 Lpk~qv~iLr~Wf~eH~~nPYPS~~EK~~LAk~TGLS~kQVsNWFiNaR~R~k 420 (693)
|++....++..++.+. -.-.++|..+|++...|..|....+.+++
T Consensus 11 l~~~~~~~~~~~~~~~--------~~~~~ia~~~~~s~~~i~~~~~~~~~~l~ 55 (55)
T cd06171 11 LPEREREVILLRFGEG--------LSYEEIAEILGISRSTVRQRLHRALKKLR 55 (55)
T ss_pred CCHHHHHHHHHHHhcC--------CCHHHHHHHHCcCHHHHHHHHHHHHHHcC
Confidence 6777888887776542 24577899999999999999988887764
No 44
>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=57.05 E-value=2.1e+02 Score=29.76 Aligned_cols=41 Identities=7% Similarity=0.172 Sum_probs=35.7
Q ss_pred ccChHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhc
Q 005500 240 ELTTAERQEIQMKKAKLINMLDEVEQRYRQYHHQMQIVISS 280 (693)
Q Consensus 240 ~ls~~er~ElQ~Kk~KLl~mLdeVd~RY~qY~~qmq~v~ss 280 (693)
+..+.|..+|+.|.+++..++.+--++|++-|.+.-..|..
T Consensus 100 ~~~~~d~~dYr~kL~~ir~~y~~el~kye~ac~eF~~hV~~ 140 (191)
T PF03792_consen 100 ADNSIDHSDYRAKLSQIRQIYHSELEKYEQACNEFTEHVMN 140 (191)
T ss_pred cccccchHHHHHHHHHHHHHHHHHHHHHHHHhhhhHHHHHH
Confidence 34566888999999999999999999999999998777766
No 45
>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=53.64 E-value=14 Score=30.66 Aligned_cols=46 Identities=22% Similarity=0.302 Sum_probs=29.6
Q ss_pred CCCCCCChhHHHHH-HHHHHHhhCCCCCCHHHHHHHHHHhCCChhhhhccchhhh
Q 005500 363 RPQRGLPERSVSVL-RAWLFEHFLHPYPKDSDKQMLAKQTGLTRSQVSNWFINAR 416 (693)
Q Consensus 363 RkrR~Lpk~qv~iL-r~Wf~eH~~nPYPS~~EK~~LAk~TGLS~kQVsNWFiNaR 416 (693)
++++.|+++.+..+ ...+.. ......+|+..|++..+|.+|-.-.+
T Consensus 2 ~~r~~ys~e~K~~~v~~~~~~--------g~sv~~va~~~gi~~~~l~~W~~~~~ 48 (76)
T PF01527_consen 2 RKRRRYSPEFKLQAVREYLES--------GESVSEVAREYGISPSTLYNWRKQYR 48 (76)
T ss_dssp -SS----HHHHHHHHHHHHHH--------HCHHHHHHHHHTS-HHHHHHHHHHHH
T ss_pred CCCCCCCHHHHHHHHHHHHHC--------CCceEeeecccccccccccHHHHHHh
Confidence 34567888886555 444332 47788999999999999999976655
No 46
>PF04545 Sigma70_r4: Sigma-70, region 4; InterPro: IPR007630 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognised by the major sigma factors [, ]. Region 4 of sigma-70 like sigma-factors is involved in binding to the -35 promoter element via a helix-turn-helix motif []. Due to the way Pfam works, the threshold has been set artificially high to prevent overlaps with other helix-turn-helix families. Therefore there are many false negatives.; GO: 0003677 DNA binding, 0003700 sequence-specific DNA binding transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, DNA-dependent, 0006355 regulation of transcription, DNA-dependent; PDB: 2P7V_B 3IYD_F 1TLH_B 1KU7_A 1RIO_H 3N97_A 1KU3_A 1RP3_C 1SC5_A 1NR3_A ....
Probab=49.54 E-value=13 Score=29.08 Aligned_cols=47 Identities=32% Similarity=0.419 Sum_probs=37.1
Q ss_pred CCChhHHHHHHHHHHHhhCCCCCCHHHHHHHHHHhCCChhhhhccchhhhhhcCh
Q 005500 367 GLPERSVSVLRAWLFEHFLHPYPKDSDKQMLAKQTGLTRSQVSNWFINARVRLWK 421 (693)
Q Consensus 367 ~Lpk~qv~iLr~Wf~eH~~nPYPS~~EK~~LAk~TGLS~kQVsNWFiNaR~R~kK 421 (693)
.||++...+|...|++ . -.-.++|+..|+|...|+.|...+..|+++
T Consensus 4 ~L~~~er~vi~~~y~~----~----~t~~eIa~~lg~s~~~V~~~~~~al~kLR~ 50 (50)
T PF04545_consen 4 QLPPREREVIRLRYFE----G----LTLEEIAERLGISRSTVRRILKRALKKLRK 50 (50)
T ss_dssp TS-HHHHHHHHHHHTS----T-----SHHHHHHHHTSCHHHHHHHHHHHHHHHHH
T ss_pred hCCHHHHHHHHHHhcC----C----CCHHHHHHHHCCcHHHHHHHHHHHHHHhcC
Confidence 4788999999887754 2 335789999999999999999998888764
No 47
>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=48.73 E-value=34 Score=22.37 Aligned_cols=38 Identities=18% Similarity=0.274 Sum_probs=26.6
Q ss_pred CCChhHHHHHHHHHHHhhCCCCCCHHHHHHHHHHhCCChhhhhccc
Q 005500 367 GLPERSVSVLRAWLFEHFLHPYPKDSDKQMLAKQTGLTRSQVSNWF 412 (693)
Q Consensus 367 ~Lpk~qv~iLr~Wf~eH~~nPYPS~~EK~~LAk~TGLS~kQVsNWF 412 (693)
.++.+....+..++. +.+ ....+|+.+|++...|.+|.
T Consensus 5 ~~~~~~~~~i~~~~~----~~~----s~~~ia~~~~is~~tv~~~~ 42 (42)
T cd00569 5 KLTPEQIEEARRLLA----AGE----SVAEIARRLGVSRSTLYRYL 42 (42)
T ss_pred cCCHHHHHHHHHHHH----cCC----CHHHHHHHHCCCHHHHHHhC
Confidence 366666655555543 333 45688999999999999984
No 48
>PF08281 Sigma70_r4_2: Sigma-70, region 4; InterPro: IPR013249 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognised by the major sigma factors [, ]. Region 4 of sigma-70 like sigma-factors are involved in binding to the -35 promoter element via a helix-turn-helix motif [].; GO: 0003677 DNA binding, 0003700 sequence-specific DNA binding transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, DNA-dependent, 0006355 regulation of transcription, DNA-dependent; PDB: 2LFW_A 1OR7_B 2H27_D 2O8X_B.
Probab=43.62 E-value=24 Score=27.72 Aligned_cols=45 Identities=27% Similarity=0.386 Sum_probs=32.9
Q ss_pred CCChhHHHHHHHHHHHhhCCCCCCHHHHHHHHHHhCCChhhhhccchhhhhhc
Q 005500 367 GLPERSVSVLRAWLFEHFLHPYPKDSDKQMLAKQTGLTRSQVSNWFINARVRL 419 (693)
Q Consensus 367 ~Lpk~qv~iLr~Wf~eH~~nPYPS~~EK~~LAk~TGLS~kQVsNWFiNaR~R~ 419 (693)
.||+..+.++...+.+ .-.-.++|+.+|+|...|.+|...+|+++
T Consensus 10 ~L~~~~r~i~~l~~~~--------g~s~~eIa~~l~~s~~~v~~~l~ra~~~L 54 (54)
T PF08281_consen 10 QLPERQREIFLLRYFQ--------GMSYAEIAEILGISESTVKRRLRRARKKL 54 (54)
T ss_dssp CS-HHHHHHHHHHHTS-----------HHHHHHHCTS-HHHHHHHHHHHHHHH
T ss_pred CCCHHHHHHHHHHHHH--------CcCHHHHHHHHCcCHHHHHHHHHHHHhhC
Confidence 3788888888766554 24457899999999999999999998763
No 49
>PRK09642 RNA polymerase sigma factor SigW; Reviewed
Probab=42.10 E-value=24 Score=33.02 Aligned_cols=49 Identities=27% Similarity=0.210 Sum_probs=40.1
Q ss_pred CCChhHHHHHHHHHHHhhCCCCCCHHHHHHHHHHhCCChhhhhccchhhhhhcChhh
Q 005500 367 GLPERSVSVLRAWLFEHFLHPYPKDSDKQMLAKQTGLTRSQVSNWFINARVRLWKPM 423 (693)
Q Consensus 367 ~Lpk~qv~iLr~Wf~eH~~nPYPS~~EK~~LAk~TGLS~kQVsNWFiNaR~R~kKp~ 423 (693)
.||+..+.++...+++. .+ -.++|+.+|++...|.+++.-+|.++++.+
T Consensus 106 ~Lp~~~r~v~~l~~~~g--~s------~~EIA~~lgis~~tV~~~l~Rar~~Lr~~l 154 (160)
T PRK09642 106 ELPENYRDVVLAHYLEE--KS------YQEIALQEKIEVKTVEMKLYRARKWIKKHW 154 (160)
T ss_pred hCCHHHHHHHHHHHHhC--CC------HHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 48999999997766652 22 258999999999999999999999998755
No 50
>PF13443 HTH_26: Cro/C1-type HTH DNA-binding domain; PDB: 3TYR_A 3TYS_A 3B7H_A.
Probab=40.99 E-value=24 Score=28.40 Aligned_cols=27 Identities=26% Similarity=0.356 Sum_probs=18.0
Q ss_pred HHHHHHHHhCCChhhhhccchhhhhhc
Q 005500 393 DKQMLAKQTGLTRSQVSNWFINARVRL 419 (693)
Q Consensus 393 EK~~LAk~TGLS~kQVsNWFiNaR~R~ 419 (693)
....||+.+|++..+|+.|+.+...+.
T Consensus 12 t~~~La~~~gis~~tl~~~~~~~~~~~ 38 (63)
T PF13443_consen 12 TQKDLARKTGISRSTLSRILNGKPSNP 38 (63)
T ss_dssp -HHHHHHHHT--HHHHHHHHTTT----
T ss_pred CHHHHHHHHCcCHHHHHHHHhcccccc
Confidence 467899999999999999999774333
No 51
>PRK00118 putative DNA-binding protein; Validated
Probab=40.80 E-value=32 Score=32.10 Aligned_cols=57 Identities=16% Similarity=0.152 Sum_probs=44.6
Q ss_pred CCChhHHHHHHHHHHHhhCCCCCCHHHHHHHHHHhCCChhhhhccchhhhhhcChhhHHHHhHHHh
Q 005500 367 GLPERSVSVLRAWLFEHFLHPYPKDSDKQMLAKQTGLTRSQVSNWFINARVRLWKPMVEEMYLEEI 432 (693)
Q Consensus 367 ~Lpk~qv~iLr~Wf~eH~~nPYPS~~EK~~LAk~TGLS~kQVsNWFiNaR~R~kKp~ieem~~~~~ 432 (693)
.||+.++.++..++.+. -.-..+|+.+|+|+.-|.+|...+|.++++ .++.+.+-+.
T Consensus 17 ~L~ekqRevl~L~y~eg--------~S~~EIAe~lGIS~~TV~r~L~RArkkLr~-~~~~~~~~~~ 73 (104)
T PRK00118 17 LLTEKQRNYMELYYLDD--------YSLGEIAEEFNVSRQAVYDNIKRTEKLLED-YEEKLHLYEK 73 (104)
T ss_pred cCCHHHHHHHHHHHHcC--------CCHHHHHHHHCcCHHHHHHHHHHHHHHHHH-HHHHHChHHH
Confidence 47899999998877752 234569999999999999999999999976 4466665543
No 52
>PRK06759 RNA polymerase factor sigma-70; Validated
Probab=40.49 E-value=24 Score=32.69 Aligned_cols=47 Identities=19% Similarity=0.147 Sum_probs=38.5
Q ss_pred CCChhHHHHHHHHHHHhhCCCCCCHHHHHHHHHHhCCChhhhhccchhhhhhcCh
Q 005500 367 GLPERSVSVLRAWLFEHFLHPYPKDSDKQMLAKQTGLTRSQVSNWFINARVRLWK 421 (693)
Q Consensus 367 ~Lpk~qv~iLr~Wf~eH~~nPYPS~~EK~~LAk~TGLS~kQVsNWFiNaR~R~kK 421 (693)
.||+..+.++..-+++. -.-.++|..+|++...|.+|...+|.++++
T Consensus 106 ~L~~~~r~ii~l~~~~~--------~s~~EIA~~l~is~~tV~~~~~ra~~~Lr~ 152 (154)
T PRK06759 106 VLDEKEKYIIFERFFVG--------KTMGEIALETEMTYYQVRWIYRQALEKMRN 152 (154)
T ss_pred hCCHHHHHHHHHHHhcC--------CCHHHHHHHHCCCHHHHHHHHHHHHHHHhh
Confidence 58999999887665542 225789999999999999999999999875
No 53
>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=39.17 E-value=50 Score=27.65 Aligned_cols=38 Identities=21% Similarity=0.351 Sum_probs=24.1
Q ss_pred HHHHHHHHHHHHH----HHHHhchhhhccCCchhhhHHHHHHHHHHhhhhHH
Q 005500 262 EVEQRYRQYHHQM----QIVISSFEQAAGIESAKTYTALALKTISKQFRCLK 309 (693)
Q Consensus 262 eVd~RY~qY~~qm----q~v~ssFe~~ag~gaa~~yt~laL~~iSr~Fr~Lk 309 (693)
|+|+-.++||.-+ +.+..+|..|+- |++.|+.+++.|.
T Consensus 10 ELDqFMeaYc~~L~kykeeL~~p~~EA~~----------f~~~ie~qL~~Lt 51 (52)
T PF03791_consen 10 ELDQFMEAYCDMLVKYKEELQRPFQEAME----------FCREIEQQLSSLT 51 (52)
T ss_pred cHHHHHHHHHHHHHHHHHHHHHHHHHHHH----------HHHHHHHHHHHHh
Confidence 5666667777655 334455554443 8888888887664
No 54
>PF12998 ING: Inhibitor of growth proteins N-terminal histone-binding; InterPro: IPR024610 Histones undergo numerous post-translational modifications, including acetylation and methylation, at residues which are then probable docking sites for various chromatin remodelling complexes. Inhibitor of growth proteins (INGs) specifically bind to residues that have been thus modified. INGs carry a well-characterised C-terminal PHD-type zinc-finger domain, binding with lysine 4-tri-methylated histone H3 (H3K4me3), as well as this N-terminal domain that binds unmodified H3 tails. Although these two regions can bind histones independently, together they increase the apparent association of the ING for the H3 tail. This entry represents the N-terminal histone binding domain found in inhibitor proteins.; PDB: 4AFL_A.
Probab=37.38 E-value=2.9e+02 Score=24.35 Aligned_cols=69 Identities=13% Similarity=0.218 Sum_probs=47.1
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHhchhhhccCCch-hhhHHHHHHHHHHhhhhHHHHHHHHHHHHH
Q 005500 252 KKAKLINMLDEVEQRYRQYHHQMQIVISSFEQAAGIESA-KTYTALALKTISKQFRCLKDAITGQIKAAN 320 (693)
Q Consensus 252 Kk~KLl~mLdeVd~RY~qY~~qmq~v~ssFe~~ag~gaa-~~yt~laL~~iSr~Fr~LkdaI~~qi~~~~ 320 (693)
...+.+.++.|+|.++....+++...+..|-...+.++. ..=..-.++.|...+..++..-...+.-+.
T Consensus 16 el~r~l~~irelD~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~I~~~~~~~~~l~deKv~lA~ 85 (105)
T PF12998_consen 16 ELQRNLTLIRELDAKSQDLLEELDQQIQKFIKNHGSPSLSPEKRRELLKEIQEEYERALELSDEKVALAQ 85 (105)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTCTTS--S-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHhhhhHHHHHHHHHHHHHHHHhhcccccCChHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 467788999999999999999999999998887775211 113334566677777666654444444443
No 55
>smart00421 HTH_LUXR helix_turn_helix, Lux Regulon. lux regulon (activates the bioluminescence operon
Probab=37.27 E-value=55 Score=24.64 Aligned_cols=51 Identities=22% Similarity=0.239 Sum_probs=37.0
Q ss_pred CCChhHHHHHHHHHHHhhCCCCCCHHHHHHHHHHhCCChhhhhccchhhhhhcChhhHHH
Q 005500 367 GLPERSVSVLRAWLFEHFLHPYPKDSDKQMLAKQTGLTRSQVSNWFINARVRLWKPMVEE 426 (693)
Q Consensus 367 ~Lpk~qv~iLr~Wf~eH~~nPYPS~~EK~~LAk~TGLS~kQVsNWFiNaR~R~kKp~iee 426 (693)
.|++....++..+ .+ .+ ...++|+.+|++...|..|....+.++.-....+
T Consensus 3 ~l~~~e~~i~~~~-~~----g~----s~~eia~~l~is~~tv~~~~~~~~~kl~~~~~~~ 53 (58)
T smart00421 3 SLTPREREVLRLL-AE----GL----TNKEIAERLGISEKTVKTHLSNIMRKLGVRSRTQ 53 (58)
T ss_pred CCCHHHHHHHHHH-Hc----CC----CHHHHHHHHCCCHHHHHHHHHHHHHHHCCCCHHH
Confidence 4777778877543 32 22 4578999999999999999998888776544333
No 56
>PRK09644 RNA polymerase sigma factor SigM; Provisional
Probab=37.09 E-value=32 Score=32.55 Aligned_cols=50 Identities=14% Similarity=0.076 Sum_probs=41.4
Q ss_pred CCCChhHHHHHHHHHHHhhCCCCCCHHHHHHHHHHhCCChhhhhccchhhhhhcChhh
Q 005500 366 RGLPERSVSVLRAWLFEHFLHPYPKDSDKQMLAKQTGLTRSQVSNWFINARVRLWKPM 423 (693)
Q Consensus 366 R~Lpk~qv~iLr~Wf~eH~~nPYPS~~EK~~LAk~TGLS~kQVsNWFiNaR~R~kKp~ 423 (693)
..||++.+.++..++.++ . .-.++|..+|++...|.+|..-+|+++++-.
T Consensus 107 ~~L~~~~r~v~~l~~~~g--~------s~~eIA~~lgis~~tv~~~l~Rar~~Lr~~l 156 (165)
T PRK09644 107 HTLPVIEAQAILLCDVHE--L------TYEEAASVLDLKLNTYKSHLFRGRKRLKALL 156 (165)
T ss_pred HhCCHHHHHHHHhHHHhc--C------CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 458999999998887663 2 3468999999999999999999999997643
No 57
>PRK03975 tfx putative transcriptional regulator; Provisional
Probab=34.81 E-value=31 Score=33.81 Aligned_cols=49 Identities=31% Similarity=0.239 Sum_probs=39.9
Q ss_pred CCCChhHHHHHHHHHHHhhCCCCCCHHHHHHHHHHhCCChhhhhccchhhhhhcChhh
Q 005500 366 RGLPERSVSVLRAWLFEHFLHPYPKDSDKQMLAKQTGLTRSQVSNWFINARVRLWKPM 423 (693)
Q Consensus 366 R~Lpk~qv~iLr~Wf~eH~~nPYPS~~EK~~LAk~TGLS~kQVsNWFiNaR~R~kKp~ 423 (693)
..|++.++.+|+. +.+ . -.-.++|..+|++...|++|-..+|.++++-.
T Consensus 5 ~~Lt~rqreVL~l-r~~----G----lTq~EIAe~LGiS~~tVs~ie~ra~kkLr~~~ 53 (141)
T PRK03975 5 SFLTERQIEVLRL-RER----G----LTQQEIADILGTSRANVSSIEKRARENIEKAR 53 (141)
T ss_pred cCCCHHHHHHHHH-HHc----C----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 4589999999976 332 2 23468999999999999999999999988765
No 58
>PF10168 Nup88: Nuclear pore component; InterPro: IPR019321 Nup88 can be divided into two structural domains; the N-terminal two-thirds of the protein have no obvious structural motifs. It is, however, where it binds to Nup98; one of the components of the nuclear pore. The C-terminal end is a predicted coiled-coil domain []. Nup88 is over expressed in tumour cells [].
Probab=34.73 E-value=4.7e+02 Score=32.05 Aligned_cols=17 Identities=18% Similarity=0.130 Sum_probs=14.5
Q ss_pred CCCChhHHHHHHHHHHH
Q 005500 366 RGLPERSVSVLRAWLFE 382 (693)
Q Consensus 366 R~Lpk~qv~iLr~Wf~e 382 (693)
-.|++.|.+.++.-+.+
T Consensus 680 ~~L~~~Q~~~I~~iL~~ 696 (717)
T PF10168_consen 680 IVLSESQKRTIKEILKQ 696 (717)
T ss_pred ccCCHHHHHHHHHHHHH
Confidence 35999999999988887
No 59
>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=34.38 E-value=39 Score=29.84 Aligned_cols=47 Identities=28% Similarity=0.344 Sum_probs=36.5
Q ss_pred CCChhHHHHHHHHHHHhhCCCCCCHHHHHHHHHHhCCChhhhhccchhhhhhcCh
Q 005500 367 GLPERSVSVLRAWLFEHFLHPYPKDSDKQMLAKQTGLTRSQVSNWFINARVRLWK 421 (693)
Q Consensus 367 ~Lpk~qv~iLr~Wf~eH~~nPYPS~~EK~~LAk~TGLS~kQVsNWFiNaR~R~kK 421 (693)
.||+....++..-+.. .+ .-.++|+.+|+++..|.+|....+.++++
T Consensus 110 ~L~~~~~~ii~~~~~~----g~----s~~eIA~~l~~s~~~v~~~~~~~~~kl~~ 156 (158)
T TIGR02937 110 KLPEREREVLVLRYLE----GL----SYKEIAEILGISVGTVKRRLKRARKKLRE 156 (158)
T ss_pred hCCHHHHHHHhhHHhc----CC----CHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Confidence 4778888887544333 33 34589999999999999999999988875
No 60
>PRK12851 groEL chaperonin GroEL; Reviewed
Probab=33.71 E-value=2.6e+02 Score=32.65 Aligned_cols=60 Identities=20% Similarity=0.213 Sum_probs=49.4
Q ss_pred ChHHHHHHHHHHHHHH-------------HHHHHHHHHHHHHHHHHHHHHhchhhhccCCchhhhHHHHHHHHH
Q 005500 242 TTAERQEIQMKKAKLI-------------NMLDEVEQRYRQYHHQMQIVISSFEQAAGIESAKTYTALALKTIS 302 (693)
Q Consensus 242 s~~er~ElQ~Kk~KLl-------------~mLdeVd~RY~qY~~qmq~v~ssFe~~ag~gaa~~yt~laL~~iS 302 (693)
+..+|..|+.+.++|- .+|+|++|+++-...-++..+.. --|.|.|++..+++..|+..+
T Consensus 358 ~~~~~~~l~~ri~~l~g~~~tI~irG~t~~~l~E~er~i~DAl~a~~~al~~-g~VpGGGa~e~~~s~~L~~~~ 430 (541)
T PRK12851 358 SDYDREKLQERLAKLAGGVAVIRVGASTEVEVKEKKDRVDDALHATRAAVEE-GIVPGGGVALLRAVKALDKLE 430 (541)
T ss_pred CHHHHHHHHHHHHHhcCCeEEEEecCCCHHHHHHHHHHHHHHHHHHHHHHHc-CcccCchHHHHHHHHHHHHHh
Confidence 4567788888876663 47899999999999999998888 489999999999998887654
No 61
>PRK11924 RNA polymerase sigma factor; Provisional
Probab=33.08 E-value=47 Score=31.03 Aligned_cols=49 Identities=20% Similarity=0.200 Sum_probs=39.1
Q ss_pred CCChhHHHHHHHHHHHhhCCCCCCHHHHHHHHHHhCCChhhhhccchhhhhhcChhh
Q 005500 367 GLPERSVSVLRAWLFEHFLHPYPKDSDKQMLAKQTGLTRSQVSNWFINARVRLWKPM 423 (693)
Q Consensus 367 ~Lpk~qv~iLr~Wf~eH~~nPYPS~~EK~~LAk~TGLS~kQVsNWFiNaR~R~kKp~ 423 (693)
.||+..+.++..-+.+ - -.-.++|+.+|++...|.+|..-+|.++++.+
T Consensus 125 ~L~~~~r~i~~l~~~~----~----~~~~eIA~~lgis~~tv~~~~~ra~~~lr~~l 173 (179)
T PRK11924 125 ALPVKQREVFLLRYVE----G----LSYREIAEILGVPVGTVKSRLRRARQLLRECL 173 (179)
T ss_pred hCCHHHHHHhhHHHHc----C----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 3788888888765544 1 23478999999999999999999999998654
No 62
>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=33.05 E-value=52 Score=30.08 Aligned_cols=48 Identities=23% Similarity=0.250 Sum_probs=38.3
Q ss_pred CCChhHHHHHHHHHHHhhCCCCCCHHHHHHHHHHhCCChhhhhccchhhhhhcChh
Q 005500 367 GLPERSVSVLRAWLFEHFLHPYPKDSDKQMLAKQTGLTRSQVSNWFINARVRLWKP 422 (693)
Q Consensus 367 ~Lpk~qv~iLr~Wf~eH~~nPYPS~~EK~~LAk~TGLS~kQVsNWFiNaR~R~kKp 422 (693)
.||++...++...+.+ .+ .-.++|+.+|+++..|.++...+|+++++-
T Consensus 113 ~L~~~~r~il~l~~~~----~~----~~~eIA~~lgis~~tv~~~~~ra~~~Lr~~ 160 (161)
T TIGR02985 113 KLPEQCRKIFILSRFE----GK----SYKEIAEELGISVKTVEYHISKALKELRKE 160 (161)
T ss_pred HCCHHHHHHHHHHHHc----CC----CHHHHHHHHCCCHHHHHHHHHHHHHHHHhh
Confidence 5788888988875554 23 235699999999999999999999988763
No 63
>PRK09652 RNA polymerase sigma factor RpoE; Provisional
Probab=32.53 E-value=39 Score=31.60 Aligned_cols=49 Identities=20% Similarity=0.209 Sum_probs=39.2
Q ss_pred CCChhHHHHHHHHHHHhhCCCCCCHHHHHHHHHHhCCChhhhhccchhhhhhcChhh
Q 005500 367 GLPERSVSVLRAWLFEHFLHPYPKDSDKQMLAKQTGLTRSQVSNWFINARVRLWKPM 423 (693)
Q Consensus 367 ~Lpk~qv~iLr~Wf~eH~~nPYPS~~EK~~LAk~TGLS~kQVsNWFiNaR~R~kKp~ 423 (693)
.||+..+.++..-++.. .+ -.++|+.+|++...|.+|...+|+++++-+
T Consensus 128 ~L~~~~r~vl~l~~~~~--~s------~~eIA~~lgis~~tV~~~l~ra~~~Lr~~l 176 (182)
T PRK09652 128 SLPEELRTAITLREIEG--LS------YEEIAEIMGCPIGTVRSRIFRAREALRAKL 176 (182)
T ss_pred hCCHHHHHHHHHHHHcC--CC------HHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 48899999887654431 22 358999999999999999999999998755
No 64
>CHL00093 groEL chaperonin GroEL
Probab=32.46 E-value=3.2e+02 Score=31.84 Aligned_cols=60 Identities=17% Similarity=0.184 Sum_probs=50.1
Q ss_pred ChHHHHHHHHHHHHHH-------------HHHHHHHHHHHHHHHHHHHHHhchhhhccCCchhhhHHHHHHHHH
Q 005500 242 TTAERQEIQMKKAKLI-------------NMLDEVEQRYRQYHHQMQIVISSFEQAAGIESAKTYTALALKTIS 302 (693)
Q Consensus 242 s~~er~ElQ~Kk~KLl-------------~mLdeVd~RY~qY~~qmq~v~ssFe~~ag~gaa~~yt~laL~~iS 302 (693)
+..||..|+.+.++|- ..|+|.+|+++-...-++..+.. --+.|.|++..+++.+|+...
T Consensus 357 ~~~~~~~l~eR~~~l~g~~~~I~irg~t~~~l~E~er~i~DAl~a~r~a~~~-gvVpGGGa~e~~~s~~L~~~~ 429 (529)
T CHL00093 357 SSYEKEKLQERLAKLSGGVAVIKVGAATETEMKDKKLRLEDAINATKAAVEE-GIVPGGGATLVHLSENLKTWA 429 (529)
T ss_pred CHHHHHHHHHHHHHhcCCeEEEEeccCcHHHHHHHHHHHHHHHHHHHHHHHc-CcccCCcHHHHHHHHHHHHHh
Confidence 4567788888888773 57899999999999999998888 589999999999998887653
No 65
>PRK12849 groEL chaperonin GroEL; Reviewed
Probab=32.45 E-value=1.8e+02 Score=33.91 Aligned_cols=60 Identities=22% Similarity=0.193 Sum_probs=50.1
Q ss_pred ChHHHHHHHHHHHHHH-------------HHHHHHHHHHHHHHHHHHHHHhchhhhccCCchhhhHHHHHHHHH
Q 005500 242 TTAERQEIQMKKAKLI-------------NMLDEVEQRYRQYHHQMQIVISSFEQAAGIESAKTYTALALKTIS 302 (693)
Q Consensus 242 s~~er~ElQ~Kk~KLl-------------~mLdeVd~RY~qY~~qmq~v~ssFe~~ag~gaa~~yt~laL~~iS 302 (693)
+..+++.|+.+.++|. .+|+|++|+++-...-++..+... -|.|.|++..+++..|+...
T Consensus 357 ~~~~~~~l~eR~~~l~~~~~TI~irG~t~~~l~E~er~i~DAl~~~~~a~~~g-~VpGGGa~e~~ls~~L~~~~ 429 (542)
T PRK12849 357 SDYDREKLQERLAKLAGGVAVIKVGAATEVELKERKDRVEDALNATRAAVEEG-IVPGGGVALLRAAKALDELA 429 (542)
T ss_pred cHHHHHHHHHHHHHhcCCeEEEEeCCCCHHHHHHHHHHHHHHHHHHHHHHHcC-eecCCCHHHHHHHHHHHHhh
Confidence 4567788888888774 479999999999999999999985 89999999999888877543
No 66
>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=32.17 E-value=46 Score=26.78 Aligned_cols=53 Identities=21% Similarity=0.217 Sum_probs=39.8
Q ss_pred CCChhHHHHHHHHHHHhhCCCCCCHHHHHHHHHHhCCChhhhhccchhhhhhcChhhHHHHh
Q 005500 367 GLPERSVSVLRAWLFEHFLHPYPKDSDKQMLAKQTGLTRSQVSNWFINARVRLWKPMVEEMY 428 (693)
Q Consensus 367 ~Lpk~qv~iLr~Wf~eH~~nPYPS~~EK~~LAk~TGLS~kQVsNWFiNaR~R~kKp~ieem~ 428 (693)
.|++....+|+.+..- -...++|...+++++.|..+..+.+.|+.-+...++.
T Consensus 3 ~LT~~E~~vl~~l~~G---------~~~~eIA~~l~is~~tV~~~~~~i~~Kl~~~~~~~l~ 55 (58)
T PF00196_consen 3 SLTERELEVLRLLAQG---------MSNKEIAEELGISEKTVKSHRRRIMKKLGVKNRAELI 55 (58)
T ss_dssp SS-HHHHHHHHHHHTT---------S-HHHHHHHHTSHHHHHHHHHHHHHHHHT-SSHHHHH
T ss_pred ccCHHHHHHHHHHHhc---------CCcchhHHhcCcchhhHHHHHHHHHHHhCCCCHHHHH
Confidence 4778888888766543 3457899999999999999999999998866655543
No 67
>PRK09646 RNA polymerase sigma factor SigK; Reviewed
Probab=31.69 E-value=37 Score=33.19 Aligned_cols=49 Identities=10% Similarity=0.126 Sum_probs=40.0
Q ss_pred CCChhHHHHHHHHHHHhhCCCCCCHHHHHHHHHHhCCChhhhhccchhhhhhcChhh
Q 005500 367 GLPERSVSVLRAWLFEHFLHPYPKDSDKQMLAKQTGLTRSQVSNWFINARVRLWKPM 423 (693)
Q Consensus 367 ~Lpk~qv~iLr~Wf~eH~~nPYPS~~EK~~LAk~TGLS~kQVsNWFiNaR~R~kKp~ 423 (693)
.||+..+.+|..-+++. -.-.++|+.+|++...|.+|...+|+++++-+
T Consensus 142 ~L~~~~r~vl~l~~~~~--------~s~~EIA~~Lgis~~tVk~~l~ra~~~Lr~~l 190 (194)
T PRK09646 142 ALTDTQRESVTLAYYGG--------LTYREVAERLAVPLGTVKTRMRDGLIRLRDCL 190 (194)
T ss_pred hCCHHHHHHHHHHHHcC--------CCHHHHHHHhCCChHhHHHHHHHHHHHHHHHh
Confidence 48999999997766552 23468999999999999999999999987644
No 68
>PRK09415 RNA polymerase factor sigma C; Reviewed
Probab=31.69 E-value=2.3e+02 Score=27.29 Aligned_cols=50 Identities=22% Similarity=0.302 Sum_probs=40.1
Q ss_pred CCCChhHHHHHHHHHHHhhCCCCCCHHHHHHHHHHhCCChhhhhccchhhhhhcChhh
Q 005500 366 RGLPERSVSVLRAWLFEHFLHPYPKDSDKQMLAKQTGLTRSQVSNWFINARVRLWKPM 423 (693)
Q Consensus 366 R~Lpk~qv~iLr~Wf~eH~~nPYPS~~EK~~LAk~TGLS~kQVsNWFiNaR~R~kKp~ 423 (693)
..||+..+.++..-+++. .+ -.++|+.+|++...|.++..-+|.++++-+
T Consensus 126 ~~L~~~~r~v~~l~~~~g--~s------~~EIA~~l~is~~tv~~~l~Ra~~~Lr~~l 175 (179)
T PRK09415 126 MSLPIKYREVIYLFYYEE--LS------IKEIAEVTGVNENTVKTRLKKAKELLKKGL 175 (179)
T ss_pred HhCCHHHhhHhHhHHhcC--CC------HHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 358999999987766552 22 368999999999999999999999987643
No 69
>PRK12512 RNA polymerase sigma factor; Provisional
Probab=31.62 E-value=33 Score=32.92 Aligned_cols=49 Identities=16% Similarity=0.146 Sum_probs=40.9
Q ss_pred CCChhHHHHHHHHHHHhhCCCCCCHHHHHHHHHHhCCChhhhhccchhhhhhcChhh
Q 005500 367 GLPERSVSVLRAWLFEHFLHPYPKDSDKQMLAKQTGLTRSQVSNWFINARVRLWKPM 423 (693)
Q Consensus 367 ~Lpk~qv~iLr~Wf~eH~~nPYPS~~EK~~LAk~TGLS~kQVsNWFiNaR~R~kKp~ 423 (693)
.||+..+.++..-+++. -.-.++|..+|++...|.+++..+|+++++.+
T Consensus 131 ~L~~~~r~v~~l~~~~g--------~s~~eIA~~l~is~~tV~~~l~ra~~~Lr~~l 179 (184)
T PRK12512 131 TLPPRQRDVVQSISVEG--------ASIKETAAKLSMSEGAVRVALHRGLAALAAKF 179 (184)
T ss_pred hCCHHHHHHHHHHHHcC--------CCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHh
Confidence 58999999998876652 23478999999999999999999999998654
No 70
>TIGR02348 GroEL chaperonin GroL. This family consists of GroEL, the larger subunit of the GroEL/GroES cytosolic chaperonin. It is found in bacteria, organelles derived from bacteria, and occasionally in the Archaea. The bacterial GroEL/GroES group I chaperonin is replaced a group II chaperonin, usually called the thermosome in the Archaeota and CCT (chaperone-containing TCP) in the Eukaryota. GroEL, thermosome subunits, and CCT subunits all fall under the scope of Pfam model pfam00118.
Probab=31.48 E-value=2.9e+02 Score=32.14 Aligned_cols=58 Identities=21% Similarity=0.166 Sum_probs=49.5
Q ss_pred ChHHHHHHHHHHHHH-------------HHHHHHHHHHHHHHHHHHHHHHhchhhhccCCchhhhHHHHHHH
Q 005500 242 TTAERQEIQMKKAKL-------------INMLDEVEQRYRQYHHQMQIVISSFEQAAGIESAKTYTALALKT 300 (693)
Q Consensus 242 s~~er~ElQ~Kk~KL-------------l~mLdeVd~RY~qY~~qmq~v~ssFe~~ag~gaa~~yt~laL~~ 300 (693)
+..+|+.|+.+.++| -.+++|++|+++-...-++..+..- -+.|.|++..+++..|+.
T Consensus 356 ~~~~~~~l~eR~~~l~~~~~tI~irG~t~~~l~E~er~i~Dal~~~r~a~~~g-~VpGGGa~e~~~s~~L~~ 426 (524)
T TIGR02348 356 SDYDREKLQERLAKLAGGVAVIKVGAATETEMKEKKLRVEDALNATRAAVEEG-IVPGGGVALLRAAAALEG 426 (524)
T ss_pred CHHHHHHHHHHHHHhcCCeEEEEecCCCHHHHHHHHHHHHHHHHHHHHHHhcC-CccCCcHHHHHHHHHHHH
Confidence 567888888888885 3478999999999999999999885 999999999999888875
No 71
>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=31.43 E-value=29 Score=33.15 Aligned_cols=50 Identities=16% Similarity=0.138 Sum_probs=39.8
Q ss_pred CCCChhHHHHHHHHHHHhhCCCCCCHHHHHHHHHHhCCChhhhhccchhhhhhcChhh
Q 005500 366 RGLPERSVSVLRAWLFEHFLHPYPKDSDKQMLAKQTGLTRSQVSNWFINARVRLWKPM 423 (693)
Q Consensus 366 R~Lpk~qv~iLr~Wf~eH~~nPYPS~~EK~~LAk~TGLS~kQVsNWFiNaR~R~kKp~ 423 (693)
..||+..+.++..-++++ -.-.++|..+|++...|.+|...+|+++++-+
T Consensus 137 ~~L~~~~r~v~~l~~~~~--------~s~~EIA~~lgis~~tv~~~l~rar~~Lr~~l 186 (190)
T TIGR02939 137 EALPEDLRTAITLRELEG--------LSYEDIARIMDCPVGTVRSRIFRAREAIAIRL 186 (190)
T ss_pred HcCCHHHhhhhhhhhhcC--------CCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHh
Confidence 347888888887655442 23478999999999999999999999998754
No 72
>PRK12541 RNA polymerase sigma factor; Provisional
Probab=31.13 E-value=36 Score=31.93 Aligned_cols=48 Identities=21% Similarity=0.150 Sum_probs=39.4
Q ss_pred CCCChhHHHHHHHHHHHhhCCCCCCHHHHHHHHHHhCCChhhhhccchhhhhhcCh
Q 005500 366 RGLPERSVSVLRAWLFEHFLHPYPKDSDKQMLAKQTGLTRSQVSNWFINARVRLWK 421 (693)
Q Consensus 366 R~Lpk~qv~iLr~Wf~eH~~nPYPS~~EK~~LAk~TGLS~kQVsNWFiNaR~R~kK 421 (693)
..||+.++.++.-.+.+. .+ -.++|..+|++...|..+...+|.|+++
T Consensus 111 ~~L~~~~r~v~~l~~~~~--~s------~~eIA~~lgis~~tv~~~l~Rar~~L~~ 158 (161)
T PRK12541 111 SSLPLERRNVLLLRDYYG--FS------YKEIAEMTGLSLAKVKIELHRGRKETKS 158 (161)
T ss_pred HHCCHHHHHHhhhHHhcC--CC------HHHHHHHHCCCHHHHHHHHHHHHHHHHh
Confidence 458999999998766552 22 3689999999999999999999999875
No 73
>COG1734 DksA DnaK suppressor protein [Signal transduction mechanisms]
Probab=30.84 E-value=3.4e+02 Score=26.17 Aligned_cols=93 Identities=15% Similarity=0.130 Sum_probs=55.1
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhchhhhccCCchhhhHHHHHHHHHHhhhhHHHHHHHHHHHH-HhhhCc
Q 005500 247 QEIQMKKAKLINMLDEVEQRYRQYHHQMQIVISSFEQAAGIESAKTYTALALKTISKQFRCLKDAITGQIKAA-NKMLGE 325 (693)
Q Consensus 247 ~ElQ~Kk~KLl~mLdeVd~RY~qY~~qmq~v~ssFe~~ag~gaa~~yt~laL~~iSr~Fr~LkdaI~~qi~~~-~~slge 325 (693)
..++.-|.+|+.+-.+...+.++.-..++.....|.-.+-. +...|..-...+...+-+.+...|...+..+ ...+|.
T Consensus 4 ~~~~~fk~~L~~~k~~l~~~~~~~~~~~~~~~~~~~d~aD~-a~~~~~~~~~~~~~~r~r~~l~~i~~al~rIe~gtYG~ 82 (120)
T COG1734 4 EQLEHFKNKLLEWKKDLLEELEQTEEHLQDENEASPDPADR-ATQEEERELELRLRDRERKLLRKIESALDRIEEGTYGI 82 (120)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhcCCchhhh-hHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCccc
Confidence 35677889999999999999999999999755544332221 1222444444444444444555555555443 234455
Q ss_pred cccCCCcccCccccc
Q 005500 326 EDCVGSKIEGSRLKF 340 (693)
Q Consensus 326 ed~~gg~~e~~rl~~ 340 (693)
.+..|..|...||.+
T Consensus 83 Ce~cG~~Ip~~RL~A 97 (120)
T COG1734 83 CEECGEPIPEARLEA 97 (120)
T ss_pred hhccCCcCCHHHHhh
Confidence 555566665555543
No 74
>PRK12514 RNA polymerase sigma factor; Provisional
Probab=30.71 E-value=41 Score=32.17 Aligned_cols=49 Identities=14% Similarity=0.266 Sum_probs=40.5
Q ss_pred CCCChhHHHHHHHHHHHhhCCCCCCHHHHHHHHHHhCCChhhhhccchhhhhhcChh
Q 005500 366 RGLPERSVSVLRAWLFEHFLHPYPKDSDKQMLAKQTGLTRSQVSNWFINARVRLWKP 422 (693)
Q Consensus 366 R~Lpk~qv~iLr~Wf~eH~~nPYPS~~EK~~LAk~TGLS~kQVsNWFiNaR~R~kKp 422 (693)
..||++...++...+++. + .-.++|+.+|++...|.+++..+|+++++-
T Consensus 128 ~~L~~~~r~i~~l~~~~g----~----s~~eIA~~lgis~~tV~~~l~Rar~~Lr~~ 176 (179)
T PRK12514 128 EELEKDRAAAVRRAYLEG----L----SYKELAERHDVPLNTMRTWLRRSLLKLREC 176 (179)
T ss_pred HhCCHHHHHHHHHHHHcC----C----CHHHHHHHHCCChHHHHHHHHHHHHHHHHH
Confidence 348999999998887752 2 247899999999999999999999999764
No 75
>PRK12519 RNA polymerase sigma factor; Provisional
Probab=30.66 E-value=37 Score=32.89 Aligned_cols=50 Identities=22% Similarity=0.275 Sum_probs=40.2
Q ss_pred CCCChhHHHHHHHHHHHhhCCCCCCHHHHHHHHHHhCCChhhhhccchhhhhhcChhh
Q 005500 366 RGLPERSVSVLRAWLFEHFLHPYPKDSDKQMLAKQTGLTRSQVSNWFINARVRLWKPM 423 (693)
Q Consensus 366 R~Lpk~qv~iLr~Wf~eH~~nPYPS~~EK~~LAk~TGLS~kQVsNWFiNaR~R~kKp~ 423 (693)
..||++...++..-+++. -.-.++|..+|++...|.+|+..+|+++++-+
T Consensus 140 ~~L~~~~~~v~~l~~~~g--------~s~~EIA~~lgis~~tV~~~l~Ra~~~Lr~~l 189 (194)
T PRK12519 140 AQLPESQRQVLELAYYEG--------LSQSEIAKRLGIPLGTVKARARQGLLKLRELL 189 (194)
T ss_pred HhCCHHHhhhhhhhhhcC--------CCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHH
Confidence 358888888887665542 23468999999999999999999999998755
No 76
>PRK15369 two component system sensor kinase SsrB; Provisional
Probab=29.45 E-value=1.1e+02 Score=28.06 Aligned_cols=54 Identities=22% Similarity=0.218 Sum_probs=41.9
Q ss_pred CCCChhHHHHHHHHHHHhhCCCCCCHHHHHHHHHHhCCChhhhhccchhhhhhcChhhHHHHh
Q 005500 366 RGLPERSVSVLRAWLFEHFLHPYPKDSDKQMLAKQTGLTRSQVSNWFINARVRLWKPMVEEMY 428 (693)
Q Consensus 366 R~Lpk~qv~iLr~Wf~eH~~nPYPS~~EK~~LAk~TGLS~kQVsNWFiNaR~R~kKp~ieem~ 428 (693)
..|++...++|+-+ .++ |. ..++|+.++++.+.|.+|..+.|+|+.-.-..++.
T Consensus 148 ~~lt~~e~~vl~l~-~~g----~~----~~~Ia~~l~~s~~tv~~~~~~~~~kl~~~~~~~l~ 201 (211)
T PRK15369 148 PLLTPRERQILKLI-TEG----YT----NRDIAEQLSISIKTVETHRLNMMRKLDVHKVAELL 201 (211)
T ss_pred cCCCHHHHHHHHHH-HCC----CC----HHHHHHHhCCCHHHHHHHHHHHHHHhCCCCHHHHH
Confidence 34999999999875 332 32 57899999999999999999999998754444443
No 77
>TIGR02941 Sigma_B RNA polymerase sigma-B factor. This sigma factor is restricted to certain lineages of the order Bacillales including Staphylococcus, Listeria and Bacillus.
Probab=29.42 E-value=43 Score=34.40 Aligned_cols=49 Identities=20% Similarity=0.243 Sum_probs=40.9
Q ss_pred CCChhHHHHHHHHHHHhhCCCCCCHHHHHHHHHHhCCChhhhhccchhhhhhcChhh
Q 005500 367 GLPERSVSVLRAWLFEHFLHPYPKDSDKQMLAKQTGLTRSQVSNWFINARVRLWKPM 423 (693)
Q Consensus 367 ~Lpk~qv~iLr~Wf~eH~~nPYPS~~EK~~LAk~TGLS~kQVsNWFiNaR~R~kKp~ 423 (693)
.||+..+.++...|++.+ .-.++|+.+|++...|+.|...++.++++.+
T Consensus 205 ~L~~~~r~ii~l~~~~g~--------s~~eIA~~lgis~~~V~~~~~ra~~~Lr~~~ 253 (255)
T TIGR02941 205 ILSEREKSIIHCTFEENL--------SQKETGERLGISQMHVSRLQRQAISKLKEAA 253 (255)
T ss_pred cCCHHHHHHHHHHHcCCC--------CHHHHHHHHCcCHHHHHHHHHHHHHHHHHHh
Confidence 589999999988776532 2378999999999999999999999998754
No 78
>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=28.82 E-value=45 Score=31.83 Aligned_cols=48 Identities=19% Similarity=0.178 Sum_probs=40.1
Q ss_pred CCChhHHHHHHHHHHHhhCCCCCCHHHHHHHHHHhCCChhhhhccchhhhhhcChh
Q 005500 367 GLPERSVSVLRAWLFEHFLHPYPKDSDKQMLAKQTGLTRSQVSNWFINARVRLWKP 422 (693)
Q Consensus 367 ~Lpk~qv~iLr~Wf~eH~~nPYPS~~EK~~LAk~TGLS~kQVsNWFiNaR~R~kKp 422 (693)
.||++.+.++...+++. . .-.++|..+|++...|.+....+|.++++-
T Consensus 134 ~Lp~~~r~v~~l~~~~g--~------s~~EIA~~lgis~~tVk~~l~Rar~~Lr~~ 181 (183)
T TIGR02999 134 QVDPRQAEVVELRFFAG--L------TVEEIAELLGVSVRTVERDWRFARAWLADE 181 (183)
T ss_pred cCCHHHHHHHHHHHHcC--C------CHHHHHHHhCCCHHHHHHHHHHHHHHHHHH
Confidence 48999999998887652 2 236899999999999999999999998763
No 79
>PRK08583 RNA polymerase sigma factor SigB; Validated
Probab=28.81 E-value=51 Score=33.88 Aligned_cols=49 Identities=18% Similarity=0.293 Sum_probs=40.4
Q ss_pred CCChhHHHHHHHHHHHhhCCCCCCHHHHHHHHHHhCCChhhhhccchhhhhhcChhh
Q 005500 367 GLPERSVSVLRAWLFEHFLHPYPKDSDKQMLAKQTGLTRSQVSNWFINARVRLWKPM 423 (693)
Q Consensus 367 ~Lpk~qv~iLr~Wf~eH~~nPYPS~~EK~~LAk~TGLS~kQVsNWFiNaR~R~kKp~ 423 (693)
.||+..+.+|...|++.+ .-.++|+.+|++...|..|...+|+++++.+
T Consensus 205 ~L~~~~r~vl~l~~~~g~--------s~~eIA~~l~is~~tV~~~~~ra~~kLr~~l 253 (257)
T PRK08583 205 VLSDREKSIIQCTFIENL--------SQKETGERLGISQMHVSRLQRQAIKKLREAA 253 (257)
T ss_pred hCCHHHHHHHHHHHhCCC--------CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHh
Confidence 489999999988776522 2378999999999999999999999987643
No 80
>PRK12526 RNA polymerase sigma factor; Provisional
Probab=28.72 E-value=44 Score=33.17 Aligned_cols=49 Identities=24% Similarity=0.303 Sum_probs=39.9
Q ss_pred CCChhHHHHHHHHHHHhhCCCCCCHHHHHHHHHHhCCChhhhhccchhhhhhcChhh
Q 005500 367 GLPERSVSVLRAWLFEHFLHPYPKDSDKQMLAKQTGLTRSQVSNWFINARVRLWKPM 423 (693)
Q Consensus 367 ~Lpk~qv~iLr~Wf~eH~~nPYPS~~EK~~LAk~TGLS~kQVsNWFiNaR~R~kKp~ 423 (693)
.||++.+.+|..-+++. -.-.++|..+|++...|.+++..+|+++++-+
T Consensus 153 ~L~~~~r~vl~l~~~~g--------~s~~EIA~~lgis~~tV~~~l~Ra~~~Lr~~l 201 (206)
T PRK12526 153 KLPEAQQTVVKGVYFQE--------LSQEQLAQQLNVPLGTVKSRLRLALAKLKVQM 201 (206)
T ss_pred hCCHHHHHHHHHHHHcC--------CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 48999999998666542 23468999999999999999999999987654
No 81
>PRK09648 RNA polymerase sigma factor SigD; Reviewed
Probab=28.51 E-value=47 Score=32.14 Aligned_cols=50 Identities=22% Similarity=0.158 Sum_probs=40.8
Q ss_pred CCCChhHHHHHHHHHHHhhCCCCCCHHHHHHHHHHhCCChhhhhccchhhhhhcChhh
Q 005500 366 RGLPERSVSVLRAWLFEHFLHPYPKDSDKQMLAKQTGLTRSQVSNWFINARVRLWKPM 423 (693)
Q Consensus 366 R~Lpk~qv~iLr~Wf~eH~~nPYPS~~EK~~LAk~TGLS~kQVsNWFiNaR~R~kKp~ 423 (693)
..||+..+.++..-+++. -.-.++|..+|++...|..+...+|.++++.+
T Consensus 138 ~~L~~~~r~i~~l~~~~g--------~s~~EIA~~lgis~~tV~~~l~Ra~~~Lr~~l 187 (189)
T PRK09648 138 DTLPEKQREILILRVVVG--------LSAEETAEAVGSTPGAVRVAQHRALARLRAEI 187 (189)
T ss_pred HhCCHHHHHHHHHHHHcC--------CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHh
Confidence 358999999998766652 23578999999999999999999999988643
No 82
>PRK12547 RNA polymerase sigma factor; Provisional
Probab=28.32 E-value=47 Score=31.53 Aligned_cols=50 Identities=16% Similarity=0.058 Sum_probs=40.5
Q ss_pred CCCChhHHHHHHHHHHHhhCCCCCCHHHHHHHHHHhCCChhhhhccchhhhhhcChhh
Q 005500 366 RGLPERSVSVLRAWLFEHFLHPYPKDSDKQMLAKQTGLTRSQVSNWFINARVRLWKPM 423 (693)
Q Consensus 366 R~Lpk~qv~iLr~Wf~eH~~nPYPS~~EK~~LAk~TGLS~kQVsNWFiNaR~R~kKp~ 423 (693)
..||+..+.++.-.+.+.+ .-.++|+.+|++...|.++..-+|+++++-+
T Consensus 111 ~~L~~~~r~v~~l~~~~g~--------s~~eIA~~lgis~~tV~~~l~Rar~~Lr~~l 160 (164)
T PRK12547 111 NLLSADQREAIILIGASGF--------SYEDAAAICGCAVGTIKSRVSRARNRLQELL 160 (164)
T ss_pred HhCCHHHHHHHHHHHHcCC--------CHHHHHHHhCCCHHHHHHHHHHHHHHHHHHH
Confidence 3489999999888766532 2468999999999999999999999987543
No 83
>PRK12530 RNA polymerase sigma factor; Provisional
Probab=28.15 E-value=57 Score=31.87 Aligned_cols=50 Identities=14% Similarity=0.241 Sum_probs=41.1
Q ss_pred CCChhHHHHHHHHHHHhhCCCCCCHHHHHHHHHHhCCChhhhhccchhhhhhcChhhH
Q 005500 367 GLPERSVSVLRAWLFEHFLHPYPKDSDKQMLAKQTGLTRSQVSNWFINARVRLWKPMV 424 (693)
Q Consensus 367 ~Lpk~qv~iLr~Wf~eH~~nPYPS~~EK~~LAk~TGLS~kQVsNWFiNaR~R~kKp~i 424 (693)
.||+..+.++..-+++. - .-.++|..+|+++..|.++..-+|+++++-+.
T Consensus 134 ~Lp~~~R~v~~L~~~~g--~------s~~EIA~~lgis~~tVk~~l~RAr~~Lr~~l~ 183 (189)
T PRK12530 134 HLPAQQARVFMMREYLE--L------SSEQICQECDISTSNLHVLLYRARLQLQACLS 183 (189)
T ss_pred hCCHHHHHHHhHHHHcC--C------CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Confidence 48999999988776652 2 24789999999999999999999999987653
No 84
>cd06170 LuxR_C_like C-terminal DNA-binding domain of LuxR-like proteins. This domain contains a helix-turn-helix motif and binds DNA. Proteins belonging to this group are response regulators; some act as transcriptional activators, others as transcriptional repressors. Many are active as homodimers. Many are two domain proteins in which the DNA binding property of the C-terminal DNA binding domain is modulated by modifications of the N-terminal domain. For example in the case of Lux R which participates in the regulation of gene expression in response to fluctuations in cell-population density (quorum-sensing), a signaling molecule, the pheromone Acyl HSL (N-acyl derivatives of homoserine lactone), binds to the N-terminal domain and leads to LuxR dimerization. For others phophorylation of the N-terminal domain leads to multimerization, for example Escherichia coli NarL and Sinorhizobium melilot FixJ. NarL controls gene expression of many respiratory-related operons when environmental
Probab=26.73 E-value=82 Score=23.93 Aligned_cols=47 Identities=23% Similarity=0.229 Sum_probs=33.3
Q ss_pred CChhHHHHHHHHHHHhhCCCCCCHHHHHHHHHHhCCChhhhhccchhhhhhcChhh
Q 005500 368 LPERSVSVLRAWLFEHFLHPYPKDSDKQMLAKQTGLTRSQVSNWFINARVRLWKPM 423 (693)
Q Consensus 368 Lpk~qv~iLr~Wf~eH~~nPYPS~~EK~~LAk~TGLS~kQVsNWFiNaR~R~kKp~ 423 (693)
|++....++..+ .. . -...++|+.++++...|..|..-.+.++..+.
T Consensus 1 l~~~e~~i~~~~-~~----~----~s~~eia~~l~~s~~tv~~~~~~~~~~l~~~~ 47 (57)
T cd06170 1 LTPREREVLRLL-AE----G----KTNKEIADILGISEKTVKTHLRNIMRKLGVKS 47 (57)
T ss_pred CCHHHHHHHHHH-Hc----C----CCHHHHHHHHCCCHHHHHHHHHHHHHHhCCCC
Confidence 355666666443 22 2 25578999999999999999987777766544
No 85
>cd03344 GroEL GroEL_like type I chaperonin. Chaperonins are involved in productive folding of proteins. They share a common general morphology, a double toroid of 2 stacked rings, each composed of 7-9 subunits. The symmetry of type I is seven-fold and they are found in eubacteria (GroEL) and in organelles of eubacterial descent (hsp60 and RBP). With the aid of cochaperonin GroES, GroEL encapsulates non-native substrate proteins inside the cavity of the GroEL-ES complex and promotes folding by using energy derived from ATP hydrolysis.
Probab=26.66 E-value=2.9e+02 Score=32.10 Aligned_cols=61 Identities=18% Similarity=0.161 Sum_probs=50.4
Q ss_pred ChHHHHHHHHHHHHHH-------------HHHHHHHHHHHHHHHHHHHHHhchhhhccCCchhhhHHHHHHHHHH
Q 005500 242 TTAERQEIQMKKAKLI-------------NMLDEVEQRYRQYHHQMQIVISSFEQAAGIESAKTYTALALKTISK 303 (693)
Q Consensus 242 s~~er~ElQ~Kk~KLl-------------~mLdeVd~RY~qY~~qmq~v~ssFe~~ag~gaa~~yt~laL~~iSr 303 (693)
+..+|+.|..+.++|. .+++|++|+++-...-++..+... -+.|.|++..+++..|+..+.
T Consensus 355 ~~~~~~~l~eR~~~l~~~~~TI~irG~t~~~l~E~~r~i~Dal~~~k~a~~~g-~VpGGGa~e~~~s~~L~~~~~ 428 (520)
T cd03344 355 SDYDKEKLQERLAKLSGGVAVIKVGGATEVELKEKKDRVEDALNATRAAVEEG-IVPGGGVALLRASPALDKLKA 428 (520)
T ss_pred CHHHHHHHHHHHHHhcCCeEEEEEecCcHHHHHHHHHHHHHHHHHHHHHHhcC-CCcCCcHHHHHHHHHHHHhcc
Confidence 3467788888887774 478999999999999999999985 999999999999888876543
No 86
>PRK12531 RNA polymerase sigma factor; Provisional
Probab=26.51 E-value=53 Score=32.10 Aligned_cols=50 Identities=26% Similarity=0.295 Sum_probs=40.3
Q ss_pred CCCChhHHHHHHHHHHHhhCCCCCCHHHHHHHHHHhCCChhhhhccchhhhhhcChhh
Q 005500 366 RGLPERSVSVLRAWLFEHFLHPYPKDSDKQMLAKQTGLTRSQVSNWFINARVRLWKPM 423 (693)
Q Consensus 366 R~Lpk~qv~iLr~Wf~eH~~nPYPS~~EK~~LAk~TGLS~kQVsNWFiNaR~R~kKp~ 423 (693)
..||++.+.++..-+++. .+ -.++|..+|++...|.+.+..+|+++++-+
T Consensus 140 ~~Lp~~~r~v~~l~~~eg--~s------~~EIA~~lgis~~tVk~rl~ra~~~Lr~~l 189 (194)
T PRK12531 140 DRLPKAQRDVLQAVYLEE--LP------HQQVAEMFDIPLGTVKSRLRLAVEKLRHSM 189 (194)
T ss_pred HhCCHHHHHHHHHHHHcC--CC------HHHHHHHhCcCHHHHHHHHHHHHHHHHHHh
Confidence 458999999998765552 23 368999999999999999999999888755
No 87
>TIGR02947 SigH_actino RNA polymerase sigma-70 factor, TIGR02947 family. This group of sigma factors are members of the sigma-70 family (TIGR02937). They and appear by homology, tree building, bidirectional best hits and (with the exception of a paralog in Thermobifida fusca YX) one-to-a-genome distribution, to represent a conserved family. This family is restricted to the Actinobacteria and each gene examined is followed by an anti-sigma factor in an apparent operon.
Probab=26.23 E-value=25 Score=34.16 Aligned_cols=49 Identities=22% Similarity=0.188 Sum_probs=38.8
Q ss_pred CCChhHHHHHHHHHHHhhCCCCCCHHHHHHHHHHhCCChhhhhccchhhhhhcChhh
Q 005500 367 GLPERSVSVLRAWLFEHFLHPYPKDSDKQMLAKQTGLTRSQVSNWFINARVRLWKPM 423 (693)
Q Consensus 367 ~Lpk~qv~iLr~Wf~eH~~nPYPS~~EK~~LAk~TGLS~kQVsNWFiNaR~R~kKp~ 423 (693)
.||+..+.++.-.+++. -.-.++|+.+|++...|.++..-+|+++++-+
T Consensus 131 ~Lp~~~r~i~~L~~~~g--------~s~~EIA~~lgis~~tVk~~l~Rar~~Lr~~l 179 (193)
T TIGR02947 131 GLPEEFRQAVYLADVEG--------FAYKEIAEIMGTPIGTVMSRLHRGRKQLRKQL 179 (193)
T ss_pred hCCHHHhhheeehhhcC--------CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 47888888776554442 23468999999999999999999999998765
No 88
>TIGR02948 SigW_bacill RNA polymerase sigma-W factor. This sigma factor is restricted to certain lineages of the order Bacillales.
Probab=26.19 E-value=55 Score=31.21 Aligned_cols=50 Identities=18% Similarity=0.183 Sum_probs=39.2
Q ss_pred CCCChhHHHHHHHHHHHhhCCCCCCHHHHHHHHHHhCCChhhhhccchhhhhhcChhh
Q 005500 366 RGLPERSVSVLRAWLFEHFLHPYPKDSDKQMLAKQTGLTRSQVSNWFINARVRLWKPM 423 (693)
Q Consensus 366 R~Lpk~qv~iLr~Wf~eH~~nPYPS~~EK~~LAk~TGLS~kQVsNWFiNaR~R~kKp~ 423 (693)
..||+..+.++..-+++ . -.-.++|+.+|++...|.+++..+|+++++-+
T Consensus 135 ~~L~~~~r~v~~l~~~~----g----~s~~eIA~~lgis~~~v~~~l~Rar~~Lr~~l 184 (187)
T TIGR02948 135 QALPPKYRMVIVLKYME----D----LSLKEISEILDLPVGTVKTRIHRGREALRKQL 184 (187)
T ss_pred HhCCHHHhHHhhhHHhc----C----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHh
Confidence 35899999998764443 1 23478999999999999999999999987643
No 89
>PRK06811 RNA polymerase factor sigma-70; Validated
Probab=26.05 E-value=52 Score=32.01 Aligned_cols=49 Identities=24% Similarity=0.286 Sum_probs=40.0
Q ss_pred CCCChhHHHHHHHHHHHhhCCCCCCHHHHHHHHHHhCCChhhhhccchhhhhhcChh
Q 005500 366 RGLPERSVSVLRAWLFEHFLHPYPKDSDKQMLAKQTGLTRSQVSNWFINARVRLWKP 422 (693)
Q Consensus 366 R~Lpk~qv~iLr~Wf~eH~~nPYPS~~EK~~LAk~TGLS~kQVsNWFiNaR~R~kKp 422 (693)
..||++.+.++...|.+. .+ -.++|+.+|++...|.+...-+|.++++.
T Consensus 130 ~~L~~~~r~i~~l~~~~g--~s------~~EIAe~lgis~~~V~~~l~Ra~~~Lr~~ 178 (189)
T PRK06811 130 NDLEKLDREIFIRRYLLG--EK------IEEIAKKLGLTRSAIDNRLSRGRKKLQKN 178 (189)
T ss_pred HhCCHHHHHHHHHHHHcc--CC------HHHHHHHHCCCHHHHHHHHHHHHHHHHHc
Confidence 358999999998766552 22 36899999999999999999999998864
No 90
>PRK12520 RNA polymerase sigma factor; Provisional
Probab=26.01 E-value=87 Score=30.41 Aligned_cols=49 Identities=18% Similarity=0.228 Sum_probs=40.4
Q ss_pred CCChhHHHHHHHHHHHhhCCCCCCHHHHHHHHHHhCCChhhhhccchhhhhhcChhh
Q 005500 367 GLPERSVSVLRAWLFEHFLHPYPKDSDKQMLAKQTGLTRSQVSNWFINARVRLWKPM 423 (693)
Q Consensus 367 ~Lpk~qv~iLr~Wf~eH~~nPYPS~~EK~~LAk~TGLS~kQVsNWFiNaR~R~kKp~ 423 (693)
.||++++.++.-.+++. .+ -.++|..+|++..-|.+....+|+++++-+
T Consensus 131 ~Lp~~~r~v~~l~~~~g--~s------~~EIA~~lgis~~tV~~~l~Rar~~Lr~~l 179 (191)
T PRK12520 131 RLPPRTGRVFMMREWLE--LE------TEEICQELQITATNAWVLLYRARMRLRECL 179 (191)
T ss_pred hCCHHHHHHHHHHHHcC--CC------HHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 48999999998776652 23 368999999999999999999999997644
No 91
>TIGR03001 Sig-70_gmx1 RNA polymerase sigma-70 factor, Myxococcales family 1. This group of sigma factors are members of the sigma-70 family (TIGR02937) and are found in multiple copies in the order Myxococcales. This model supercedes TIGR02233, which has now been retired.
Probab=25.99 E-value=64 Score=33.57 Aligned_cols=50 Identities=28% Similarity=0.422 Sum_probs=41.5
Q ss_pred CCCChhHHHHHHHHHHHhhCCCCCCHHHHHHHHHHhCCChhhhhccchhhhhhcChhh
Q 005500 366 RGLPERSVSVLRAWLFEHFLHPYPKDSDKQMLAKQTGLTRSQVSNWFINARVRLWKPM 423 (693)
Q Consensus 366 R~Lpk~qv~iLr~Wf~eH~~nPYPS~~EK~~LAk~TGLS~kQVsNWFiNaR~R~kKp~ 423 (693)
..||+..+.++.-.+++.+ + -.++|..+|++...|.++...+|+++++.+
T Consensus 160 ~~Lp~~~R~v~~L~~~eg~--S------~~EIA~~Lgis~~TVk~rl~RAr~~Lr~~l 209 (244)
T TIGR03001 160 AALSERERHLLRLHFVDGL--S------MDRIGAMYQVHRSTVSRWVAQARERLLERT 209 (244)
T ss_pred HhCCHHHHHHHHHHHHcCC--C------HHHHHHHHCcCHHHHHHHHHHHHHHHHHHH
Confidence 3489999999988777632 2 368999999999999999999999998765
No 92
>TIGR02983 SigE-fam_strep RNA polymerase sigma-70 factor, sigma-E family. This group of similar sigma-70 factors includes the sigE factor from Streptomyces coelicolor. The family appears to include a paralagous expansion in the Streptomycetes lineage, while related Actinomycetales have at most two representatives.
Probab=25.92 E-value=54 Score=30.64 Aligned_cols=50 Identities=24% Similarity=0.367 Sum_probs=39.6
Q ss_pred CCCChhHHHHHHHHHHHhhCCCCCCHHHHHHHHHHhCCChhhhhccchhhhhhcChhh
Q 005500 366 RGLPERSVSVLRAWLFEHFLHPYPKDSDKQMLAKQTGLTRSQVSNWFINARVRLWKPM 423 (693)
Q Consensus 366 R~Lpk~qv~iLr~Wf~eH~~nPYPS~~EK~~LAk~TGLS~kQVsNWFiNaR~R~kKp~ 423 (693)
..||+..+.++..-+++. + .-.++|..+|++...|.++...+|.++++-+
T Consensus 109 ~~L~~~~r~i~~l~~~~g----~----s~~eIA~~lgis~~tV~~~l~ra~~~Lr~~l 158 (162)
T TIGR02983 109 RRLPARQRAVVVLRYYED----L----SEAQVAEALGISVGTVKSRLSRALARLRELL 158 (162)
T ss_pred HhCCHHHHHHhhhHHHhc----C----CHHHHHHHhCCCHHHHHHHHHHHHHHHHHHh
Confidence 348899988887766542 2 2367899999999999999999999988643
No 93
>PRK12852 groEL chaperonin GroEL; Reviewed
Probab=25.84 E-value=4.2e+02 Score=30.95 Aligned_cols=60 Identities=18% Similarity=0.151 Sum_probs=48.1
Q ss_pred ChHHHHHHHHHHHHHH-------------HHHHHHHHHHHHHHHHHHHHHhchhhhccCCchhhhHHHHHHHHH
Q 005500 242 TTAERQEIQMKKAKLI-------------NMLDEVEQRYRQYHHQMQIVISSFEQAAGIESAKTYTALALKTIS 302 (693)
Q Consensus 242 s~~er~ElQ~Kk~KLl-------------~mLdeVd~RY~qY~~qmq~v~ssFe~~ag~gaa~~yt~laL~~iS 302 (693)
+..++..++.++++|- .+|+|++|+++-...-++..+..- -|.|.|++..+++..|+.++
T Consensus 358 ~~~~~~~l~~R~~~l~~~~~tI~irG~t~~~l~E~er~i~DAl~a~~~a~~~g-~VpGGGa~e~~~s~~L~~~~ 430 (545)
T PRK12852 358 SDYDREKLQERLAKLAGGVAVIRVGGATEVEVKEKKDRVEDALNATRAAVQEG-IVPGGGVALLRAKKAVGRIN 430 (545)
T ss_pred cHHHHHHHHHHHHHhCCCeEEEEECCCCHHHHHHHHHHHHHHHHHHHHHHhcC-CCcCchHHHHHHHHHHHHhh
Confidence 3456777777776663 468999999999998888888884 89999999999988887654
No 94
>PRK00013 groEL chaperonin GroEL; Reviewed
Probab=25.72 E-value=3.4e+02 Score=31.79 Aligned_cols=59 Identities=22% Similarity=0.219 Sum_probs=48.9
Q ss_pred ChHHHHHHHHHHHHHH-------------HHHHHHHHHHHHHHHHHHHHHhchhhhccCCchhhhHHHHHHHH
Q 005500 242 TTAERQEIQMKKAKLI-------------NMLDEVEQRYRQYHHQMQIVISSFEQAAGIESAKTYTALALKTI 301 (693)
Q Consensus 242 s~~er~ElQ~Kk~KLl-------------~mLdeVd~RY~qY~~qmq~v~ssFe~~ag~gaa~~yt~laL~~i 301 (693)
+..+|+.|+.+.++|- .+++|++|+++-...-++..+... -|.|.|++..+++..|+..
T Consensus 357 ~~~~~~~l~eRi~~l~g~~~tI~irG~t~~~l~E~er~i~Dal~~vk~al~~g-~VpGGGa~e~~~s~~L~~~ 428 (542)
T PRK00013 357 SDYDREKLQERLAKLAGGVAVIKVGAATEVEMKEKKDRVEDALHATRAAVEEG-IVPGGGVALLRAAPALEAL 428 (542)
T ss_pred CHHHHHHHHHHHHHhcCCeEEEEecCCCHHHHHHHHHHHHHHHHHHHHHHHcC-cccCcHHHHHHHHHHHHHh
Confidence 4567888888887773 478999999999999999988885 8999999988888877654
No 95
>PRK05602 RNA polymerase sigma factor; Reviewed
Probab=25.66 E-value=51 Score=31.79 Aligned_cols=49 Identities=14% Similarity=0.199 Sum_probs=39.0
Q ss_pred CCChhHHHHHHHHHHHhhCCCCCCHHHHHHHHHHhCCChhhhhccchhhhhhcChhh
Q 005500 367 GLPERSVSVLRAWLFEHFLHPYPKDSDKQMLAKQTGLTRSQVSNWFINARVRLWKPM 423 (693)
Q Consensus 367 ~Lpk~qv~iLr~Wf~eH~~nPYPS~~EK~~LAk~TGLS~kQVsNWFiNaR~R~kKp~ 423 (693)
.||++.+.++..-+++. . .-.++|+.+|++...|.++...+|+++++.+
T Consensus 128 ~L~~~~r~i~~l~~~~g--~------s~~EIA~~lgis~~tV~~~l~Rar~~Lr~~l 176 (186)
T PRK05602 128 ALPERQREAIVLQYYQG--L------SNIEAAAVMDISVDALESLLARGRRALRAQL 176 (186)
T ss_pred hCCHHHHHHhhHHHhcC--C------CHHHHHHHhCcCHHHHHHHHHHHHHHHHHHH
Confidence 47888888886655542 2 2368999999999999999999999988744
No 96
>PF09712 PHA_synth_III_E: Poly(R)-hydroxyalkanoic acid synthase subunit (PHA_synth_III_E)
Probab=25.54 E-value=8.1e+02 Score=26.68 Aligned_cols=120 Identities=17% Similarity=0.187 Sum_probs=64.0
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-hchhhhccCCchhhhHHHHHHHHHH-----hhhhHHHHHHHHHHHHH
Q 005500 247 QEIQMKKAKLINMLDEVEQRYRQYHHQMQIVI-SSFEQAAGIESAKTYTALALKTISK-----QFRCLKDAITGQIKAAN 320 (693)
Q Consensus 247 ~ElQ~Kk~KLl~mLdeVd~RY~qY~~qmq~v~-ssFe~~ag~gaa~~yt~laL~~iSr-----~Fr~LkdaI~~qi~~~~ 320 (693)
+|.|.+..+|..-+.+..+.+.-|...+..|. .+|+.+.- -....+.. -+|.|.|.+.+.+..+-
T Consensus 158 Re~q~~~~~l~~a~~~~~~a~~ey~~~l~~~~~~a~~~~~~---------~l~~~~~~g~~~~s~re~~d~Wi~~ae~~~ 228 (293)
T PF09712_consen 158 REHQEQLQALFDAWMEYQRASQEYQAQLSEAWMKAFERMME---------KLQERAEEGEQIKSWREFYDIWIDAAEEAY 228 (293)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH---------HHHHhhccCCCCcCHHHHHHHHHHHHHHHH
Confidence 46788888888888888888888888776553 33332211 11001110 24555555555544433
Q ss_pred hhhCccccCCCcccCccccchhhHHHHHHHHhhhcccccCCCCCCCCCChhHHHHHHHHHHHhhCCCCCCHHHHHHHHHH
Q 005500 321 KMLGEEDCVGSKIEGSRLKFVDHHLRQQRALQQLGMIQHNAWRPQRGLPERSVSVLRAWLFEHFLHPYPKDSDKQMLAKQ 400 (693)
Q Consensus 321 ~slgeed~~gg~~e~~rl~~vD~~lrqqra~qqlG~l~~~~kRkrR~Lpk~qv~iLr~Wf~eH~~nPYPS~~EK~~LAk~ 400 (693)
..+-..+ +...-.-++|+..++ |.+..-.+++.+|.. -+.|++.|-..|.++
T Consensus 229 ~~~~~S~----ef~~~~g~~~~a~m~---------------------~r~~~~~~~e~~L~~---l~lPTr~evd~l~k~ 280 (293)
T PF09712_consen 229 EELFRSE----EFAQAYGQLVNALMD---------------------LRKQQQEVVEEYLRS---LNLPTRSEVDELYKR 280 (293)
T ss_pred HHHHCCH----HHHHHHHHHHHHHHH---------------------HHHHHHHHHHHHHHH---CCCCCHHHHHHHHHH
Confidence 2211000 000000011222111 234556677788777 899999999999887
Q ss_pred hCC
Q 005500 401 TGL 403 (693)
Q Consensus 401 TGL 403 (693)
+--
T Consensus 281 l~e 283 (293)
T PF09712_consen 281 LHE 283 (293)
T ss_pred HHH
Confidence 643
No 97
>PRK04217 hypothetical protein; Provisional
Probab=25.35 E-value=72 Score=30.11 Aligned_cols=50 Identities=18% Similarity=0.206 Sum_probs=40.3
Q ss_pred CCCChhHHHHHHHHHHHhhCCCCCCHHHHHHHHHHhCCChhhhhccchhhhhhcChhh
Q 005500 366 RGLPERSVSVLRAWLFEHFLHPYPKDSDKQMLAKQTGLTRSQVSNWFINARVRLWKPM 423 (693)
Q Consensus 366 R~Lpk~qv~iLr~Wf~eH~~nPYPS~~EK~~LAk~TGLS~kQVsNWFiNaR~R~kKp~ 423 (693)
..|+++.+.++..++++.+ .-.++|+.+|++...|.+.+..+|.+++.-+
T Consensus 41 ~~Lt~eereai~l~~~eGl--------S~~EIAk~LGIS~sTV~r~L~RArkkLre~L 90 (110)
T PRK04217 41 IFMTYEEFEALRLVDYEGL--------TQEEAGKRMGVSRGTVWRALTSARKKVAQML 90 (110)
T ss_pred ccCCHHHHHHHHHHHHcCC--------CHHHHHHHHCcCHHHHHHHHHHHHHHHHHHH
Confidence 3489999999888876532 4567999999999999999999888886543
No 98
>PRK12542 RNA polymerase sigma factor; Provisional
Probab=25.23 E-value=67 Score=31.03 Aligned_cols=58 Identities=22% Similarity=0.292 Sum_probs=43.5
Q ss_pred CCCChhHHHHHHHHHHHhhCCCCCCHHHHHHHHHHhCCChhhhhccchhhhhhcChhhHHHHhHHHh
Q 005500 366 RGLPERSVSVLRAWLFEHFLHPYPKDSDKQMLAKQTGLTRSQVSNWFINARVRLWKPMVEEMYLEEI 432 (693)
Q Consensus 366 R~Lpk~qv~iLr~Wf~eH~~nPYPS~~EK~~LAk~TGLS~kQVsNWFiNaR~R~kKp~ieem~~~~~ 432 (693)
..||+..+.++...+++. . .-.++|..+|++...|.+....+|+++++-+ ++....++
T Consensus 121 ~~L~~~~r~i~~l~~~~g--~------s~~EIA~~lgis~~tVk~~l~Rar~~Lr~~l-~~~~~~~~ 178 (185)
T PRK12542 121 KELNESNRQVFKYKVFYN--L------TYQEISSVMGITEANVRKQFERARKRVQNMI-GGIQHDEF 178 (185)
T ss_pred HhCCHHHHHHHHHHHHcC--C------CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH-cccchHHH
Confidence 458999999998765542 2 2368999999999999999999999997644 44444444
No 99
>PRK12546 RNA polymerase sigma factor; Provisional
Probab=25.10 E-value=51 Score=32.51 Aligned_cols=49 Identities=20% Similarity=0.176 Sum_probs=40.5
Q ss_pred CCChhHHHHHHHHHHHhhCCCCCCHHHHHHHHHHhCCChhhhhccchhhhhhcChhh
Q 005500 367 GLPERSVSVLRAWLFEHFLHPYPKDSDKQMLAKQTGLTRSQVSNWFINARVRLWKPM 423 (693)
Q Consensus 367 ~Lpk~qv~iLr~Wf~eH~~nPYPS~~EK~~LAk~TGLS~kQVsNWFiNaR~R~kKp~ 423 (693)
.||+..+.++.-++++. + .-.++|..+|+|...|.+++.-+|+++++-+
T Consensus 113 ~Lp~~~r~v~~L~~~~g----~----s~~EIA~~LgiS~~tVk~~l~Rar~~Lr~~l 161 (188)
T PRK12546 113 QLPDEQREALILVGASG----F----SYEEAAEMCGVAVGTVKSRANRARARLAELL 161 (188)
T ss_pred hCCHHHhHHhhhHHhcC----C----CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 58999999998886652 2 2367999999999999999999999998644
No 100
>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=24.95 E-value=56 Score=30.27 Aligned_cols=48 Identities=31% Similarity=0.302 Sum_probs=38.4
Q ss_pred CCCChhHHHHHHHHHHHhhCCCCCCHHHHHHHHHHhCCChhhhhccchhhhhhcCh
Q 005500 366 RGLPERSVSVLRAWLFEHFLHPYPKDSDKQMLAKQTGLTRSQVSNWFINARVRLWK 421 (693)
Q Consensus 366 R~Lpk~qv~iLr~Wf~eH~~nPYPS~~EK~~LAk~TGLS~kQVsNWFiNaR~R~kK 421 (693)
..||+..+.++..-+++ .+ .-.++|+.+|++...|.++..-+|+++++
T Consensus 110 ~~L~~~~r~v~~l~~~~----g~----~~~eIA~~l~is~~tv~~~l~Rar~~Lr~ 157 (159)
T TIGR02989 110 EKLPERQRELLQLRYQR----GV----SLTALAEQLGRTVNAVYKALSRLRVRLRD 157 (159)
T ss_pred HHCCHHHHHHHHHHHhc----CC----CHHHHHHHhCCCHHHHHHHHHHHHHHHHh
Confidence 45899999999875554 22 23689999999999999999999988865
No 101
>PRK10778 dksA RNA polymerase-binding transcription factor; Provisional
Probab=24.78 E-value=2.5e+02 Score=27.87 Aligned_cols=30 Identities=13% Similarity=0.063 Sum_probs=22.5
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 005500 247 QEIQMKKAKLINMLDEVEQRYRQYHHQMQI 276 (693)
Q Consensus 247 ~ElQ~Kk~KLl~mLdeVd~RY~qY~~qmq~ 276 (693)
.+++.-|.+|+.+.+++..+-.+-..+++.
T Consensus 35 ~ql~~fr~~L~~~r~eL~~~i~~~~~~~~~ 64 (151)
T PRK10778 35 AQLAHFKRILEAWRNQLRDEVDRTVTHMQD 64 (151)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHhc
Confidence 456667888888888888887766666654
No 102
>PRK09639 RNA polymerase sigma factor SigX; Provisional
Probab=24.68 E-value=54 Score=30.72 Aligned_cols=48 Identities=21% Similarity=0.250 Sum_probs=38.7
Q ss_pred CCChhHHHHHHHHHHHhhCCCCCCHHHHHHHHHHhCCChhhhhccchhhhhhcChhh
Q 005500 367 GLPERSVSVLRAWLFEHFLHPYPKDSDKQMLAKQTGLTRSQVSNWFINARVRLWKPM 423 (693)
Q Consensus 367 ~Lpk~qv~iLr~Wf~eH~~nPYPS~~EK~~LAk~TGLS~kQVsNWFiNaR~R~kKp~ 423 (693)
.||++...+|..-+ +. -.-.++|..+|++...|.++...+|.++++-+
T Consensus 112 ~L~~~~r~il~l~~-~g--------~s~~eIA~~lgis~~tV~~~i~ra~~~Lr~~l 159 (166)
T PRK09639 112 KMTERDRTVLLLRF-SG--------YSYKEIAEALGIKESSVGTTLARAKKKFRKIY 159 (166)
T ss_pred cCCHHHHHHHHHHH-cC--------CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 47888888887665 42 24578999999999999999999999987744
No 103
>PRK12516 RNA polymerase sigma factor; Provisional
Probab=24.47 E-value=65 Score=31.63 Aligned_cols=49 Identities=18% Similarity=0.173 Sum_probs=40.0
Q ss_pred CCChhHHHHHHHHHHHhhCCCCCCHHHHHHHHHHhCCChhhhhccchhhhhhcChhh
Q 005500 367 GLPERSVSVLRAWLFEHFLHPYPKDSDKQMLAKQTGLTRSQVSNWFINARVRLWKPM 423 (693)
Q Consensus 367 ~Lpk~qv~iLr~Wf~eH~~nPYPS~~EK~~LAk~TGLS~kQVsNWFiNaR~R~kKp~ 423 (693)
.||+..+.++.-.+++. .+| .++|+.+|++...|.++...+|+++++-+
T Consensus 116 ~Lp~~~r~i~~L~~~~g--~s~------~EIA~~Lgis~~tVk~~l~Rar~~Lr~~l 164 (187)
T PRK12516 116 QLPDDQREAIILVGASG--FAY------EEAAEICGCAVGTIKSRVNRARQRLQEIL 164 (187)
T ss_pred hCCHHHHHHHHHHHHcC--CCH------HHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 47999999998776652 232 58999999999999999999999998754
No 104
>KOG0809 consensus SNARE protein TLG2/Syntaxin 16 [Intracellular trafficking, secretion, and vesicular transport]
Probab=24.00 E-value=2.6e+02 Score=30.97 Aligned_cols=60 Identities=23% Similarity=0.387 Sum_probs=46.4
Q ss_pred HHHHHHHHHHHHHHHHHHHHHhchh-----hhccCCchhhhHHHHHHHHHHhhhhHHHHHHHHHH
Q 005500 258 NMLDEVEQRYRQYHHQMQIVISSFE-----QAAGIESAKTYTALALKTISKQFRCLKDAITGQIK 317 (693)
Q Consensus 258 ~mLdeVd~RY~qY~~qmq~v~ssFe-----~~ag~gaa~~yt~laL~~iSr~Fr~LkdaI~~qi~ 317 (693)
.+-++|-+=..+|+..||.+-++-. .+-..-++..|.++.|+++|+.||-+-..-...|+
T Consensus 104 ~ltq~Itqll~~cqk~iq~~~a~~n~~~~~e~~~~~n~~~~la~~LQ~~s~~fR~~Qs~YLK~l~ 168 (305)
T KOG0809|consen 104 ELTQEITQLLQKCQKLIQRLSASLNQLSPSERLLRKNAQGYLALQLQTLSREFRGLQSKYLKRLR 168 (305)
T ss_pred HHHHHHHHHHHHHHHHHHHHHhccCCCChHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Confidence 3446777777899999999998874 33445578889999999999999987766555554
No 105
>PRK12523 RNA polymerase sigma factor; Reviewed
Probab=23.85 E-value=65 Score=30.75 Aligned_cols=48 Identities=10% Similarity=0.158 Sum_probs=39.1
Q ss_pred CCCChhHHHHHHHHHHHhhCCCCCCHHHHHHHHHHhCCChhhhhccchhhhhhcCh
Q 005500 366 RGLPERSVSVLRAWLFEHFLHPYPKDSDKQMLAKQTGLTRSQVSNWFINARVRLWK 421 (693)
Q Consensus 366 R~Lpk~qv~iLr~Wf~eH~~nPYPS~~EK~~LAk~TGLS~kQVsNWFiNaR~R~kK 421 (693)
..||++.+.++.-.+++. .+ -.++|..+|++..-|.++...+|+|++.
T Consensus 118 ~~Lp~~~r~v~~L~~~~g--~s------~~EIA~~lgis~~tV~~~l~ra~~~~~~ 165 (172)
T PRK12523 118 GKLSSKARAAFLYNRLDG--MG------HAEIAERLGVSVSRVRQYLAQGLRQCYI 165 (172)
T ss_pred HhCCHHHHHHHHHHHHcC--CC------HHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 348999999998776652 33 3689999999999999999999999864
No 106
>PRK12536 RNA polymerase sigma factor; Provisional
Probab=23.76 E-value=64 Score=31.11 Aligned_cols=49 Identities=22% Similarity=0.129 Sum_probs=39.1
Q ss_pred CCChhHHHHHHHHHHHhhCCCCCCHHHHHHHHHHhCCChhhhhccchhhhhhcChhh
Q 005500 367 GLPERSVSVLRAWLFEHFLHPYPKDSDKQMLAKQTGLTRSQVSNWFINARVRLWKPM 423 (693)
Q Consensus 367 ~Lpk~qv~iLr~Wf~eH~~nPYPS~~EK~~LAk~TGLS~kQVsNWFiNaR~R~kKp~ 423 (693)
.||+..+.++...+.+. -.-.++|+.+|+++..|.+....+|+++++.+
T Consensus 129 ~L~~~~r~v~~l~~~~g--------~s~~EIA~~l~is~~tV~~~l~rar~~Lr~~l 177 (181)
T PRK12536 129 QLPDRQRLPIVHVKLEG--------LSVAETAQLTGLSESAVKVGIHRGLKALAAKI 177 (181)
T ss_pred HCCHHHHHHHHHHHHcC--------CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHh
Confidence 47888888876655542 23478999999999999999999999998744
No 107
>PRK09047 RNA polymerase factor sigma-70; Validated
Probab=23.19 E-value=1e+02 Score=28.66 Aligned_cols=50 Identities=20% Similarity=0.193 Sum_probs=40.7
Q ss_pred CCCChhHHHHHHHHHHHhhCCCCCCHHHHHHHHHHhCCChhhhhccchhhhhhcChhh
Q 005500 366 RGLPERSVSVLRAWLFEHFLHPYPKDSDKQMLAKQTGLTRSQVSNWFINARVRLWKPM 423 (693)
Q Consensus 366 R~Lpk~qv~iLr~Wf~eH~~nPYPS~~EK~~LAk~TGLS~kQVsNWFiNaR~R~kKp~ 423 (693)
..||+..+.++.--+++. .+ -.++|..+|++...|.++..-+|+++++.+
T Consensus 105 ~~Lp~~~r~v~~l~~~~g--~s------~~EIA~~lgis~~tV~~~l~ra~~~Lr~~l 154 (161)
T PRK09047 105 QKLPARQREAFLLRYWED--MD------VAETAAAMGCSEGSVKTHCSRATHALAKAL 154 (161)
T ss_pred HhCCHHHHHHHHHHHHhc--CC------HHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 458999999998766652 22 378999999999999999999999987654
No 108
>TIGR02954 Sig70_famx3 RNA polymerase sigma-70 factor, TIGR02954 family. This group of sigma factors are members of the sigma-70 family (TIGR02937). They and appear by homology, tree building, bidirectional best hits and one-to-a-genome distribution, to represent a conserved family. This family is found in certain Bacillus and Clostridium species.
Probab=23.07 E-value=56 Score=30.95 Aligned_cols=49 Identities=12% Similarity=0.158 Sum_probs=39.7
Q ss_pred CCChhHHHHHHHHHHHhhCCCCCCHHHHHHHHHHhCCChhhhhccchhhhhhcChhh
Q 005500 367 GLPERSVSVLRAWLFEHFLHPYPKDSDKQMLAKQTGLTRSQVSNWFINARVRLWKPM 423 (693)
Q Consensus 367 ~Lpk~qv~iLr~Wf~eH~~nPYPS~~EK~~LAk~TGLS~kQVsNWFiNaR~R~kKp~ 423 (693)
.||++.+.++..-+++. -.-.++|+.+|+|...|.++..-+|+++++-+
T Consensus 119 ~L~~~~r~i~~l~~~~g--------~s~~eiA~~lgis~~tv~~~l~Ra~~~Lr~~l 167 (169)
T TIGR02954 119 TLNDKYQTAIILRYYHD--------LTIKEIAEVMNKPEGTVKTYLHRALKKLKKRL 167 (169)
T ss_pred hCCHHHhHHHHHHHHcC--------CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHh
Confidence 47888888887776652 22367999999999999999999999987744
No 109
>PRK13919 putative RNA polymerase sigma E protein; Provisional
Probab=23.06 E-value=57 Score=31.28 Aligned_cols=49 Identities=16% Similarity=0.166 Sum_probs=39.8
Q ss_pred CCChhHHHHHHHHHHHhhCCCCCCHHHHHHHHHHhCCChhhhhccchhhhhhcChhh
Q 005500 367 GLPERSVSVLRAWLFEHFLHPYPKDSDKQMLAKQTGLTRSQVSNWFINARVRLWKPM 423 (693)
Q Consensus 367 ~Lpk~qv~iLr~Wf~eH~~nPYPS~~EK~~LAk~TGLS~kQVsNWFiNaR~R~kKp~ 423 (693)
.||+..+.+|.-.+.+. -.-.++|..+|++...|.++...+|.++++.+
T Consensus 135 ~L~~~~r~vl~l~~~~~--------~s~~eIA~~lgis~~~V~~~l~ra~~~Lr~~l 183 (186)
T PRK13919 135 ALSPEERRVIEVLYYQG--------YTHREAAQLLGLPLGTLKTRARRALSRLKEVL 183 (186)
T ss_pred hCCHHHHHHHHHHHHcC--------CCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHh
Confidence 48999999998765542 23478999999999999999999999987644
No 110
>cd00131 PAX Paired Box domain
Probab=22.92 E-value=3.2e+02 Score=25.99 Aligned_cols=47 Identities=17% Similarity=0.101 Sum_probs=32.9
Q ss_pred CCCChhHHHHHHHHHHHhhCCCCCCHHHHHHHHHHhCC-------Chhhhhccchhh
Q 005500 366 RGLPERSVSVLRAWLFEHFLHPYPKDSDKQMLAKQTGL-------TRSQVSNWFINA 415 (693)
Q Consensus 366 R~Lpk~qv~iLr~Wf~eH~~nPYPS~~EK~~LAk~TGL-------S~kQVsNWFiNa 415 (693)
+.+..+....+..+..+ ||..+..|-.++-...|+ +...|+.||.++
T Consensus 74 r~~~~~~~~~i~~~v~~---~p~~Tl~El~~~L~~~gv~~~~~~~s~stI~R~L~~~ 127 (128)
T cd00131 74 RVATPEVVKKIEIYKQE---NPGMFAWEIRDRLLQEGVCDKSNVPSVSSINRILRNK 127 (128)
T ss_pred CcCCHHHHHHHHHHHHH---CCCCCHHHHHHHHHHcCCcccCCCCCHHHHHHHHHhc
Confidence 34556666666667666 898888776665335566 899999997663
No 111
>PF07765 KIP1: KIP1-like protein; InterPro: IPR011684 This is a group of sequences found exclusively in plants. They are similar to kinase interacting protein 1 (KIP1), which has been found to interact with the kinase domain of PRK1, a receptor-like kinase []. This particular region contains two coiled-coils, which are described as motifs involved in protein-protein interactions []. It has also been suggested that the coiled-coils of the protein allow it to dimerise in vivo [].
Probab=22.91 E-value=1.1e+02 Score=27.33 Aligned_cols=30 Identities=30% Similarity=0.549 Sum_probs=21.8
Q ss_pred ChHHHHHHHH-HHHHHHHHHHHHHHHHHHHH
Q 005500 242 TTAERQEIQM-KKAKLINMLDEVEQRYRQYH 271 (693)
Q Consensus 242 s~~er~ElQ~-Kk~KLl~mLdeVd~RY~qY~ 271 (693)
|.++|.|.-- |+-.||+|++|+.+.|+--.
T Consensus 40 SfakrAEmyy~kRp~Li~~vee~yr~YrsLA 70 (74)
T PF07765_consen 40 SFAKRAEMYYKKRPELISLVEEFYRSYRSLA 70 (74)
T ss_pred hHHHhhHHHhcccHHHHHHHHHHHHHHHHHH
Confidence 4566666544 45599999999999887543
No 112
>PTZ00114 Heat shock protein 60; Provisional
Probab=22.60 E-value=4.4e+02 Score=30.91 Aligned_cols=60 Identities=13% Similarity=0.139 Sum_probs=48.9
Q ss_pred ChHHHHHHHHHHHHHH-------------HHHHHHHHHHHHHHHHHHHHHhchhhhccCCchhhhHHHHHHHHH
Q 005500 242 TTAERQEIQMKKAKLI-------------NMLDEVEQRYRQYHHQMQIVISSFEQAAGIESAKTYTALALKTIS 302 (693)
Q Consensus 242 s~~er~ElQ~Kk~KLl-------------~mLdeVd~RY~qY~~qmq~v~ssFe~~ag~gaa~~yt~laL~~iS 302 (693)
+..+|..|+.+.++|- .+|+|++|+++-...-++..+... -|.|.|++..+++..|+..+
T Consensus 370 ~~~~~~~l~eR~~~l~~~~~tI~i~G~t~~~l~E~~r~i~Dal~~~k~a~~~g-vVpGGGa~e~~~s~~L~~~~ 442 (555)
T PTZ00114 370 SEYDKEKLKERLAKLSGGVAVIKVGGASEVEVNEKKDRIEDALNATRAAVEEG-IVPGGGVALLRASKLLDKLE 442 (555)
T ss_pred CHHHHHHHHHHHHhcCCCeEEEEecCCCHHHHHHHHHHHHHHHHHHHHHHhcC-cccCCcHHHHHHHHHHHHHh
Confidence 3456777777777775 368999999999999999988887 89999999999888887653
No 113
>PRK12524 RNA polymerase sigma factor; Provisional
Probab=22.51 E-value=86 Score=30.69 Aligned_cols=49 Identities=16% Similarity=0.148 Sum_probs=39.5
Q ss_pred CCChhHHHHHHHHHHHhhCCCCCCHHHHHHHHHHhCCChhhhhccchhhhhhcChhh
Q 005500 367 GLPERSVSVLRAWLFEHFLHPYPKDSDKQMLAKQTGLTRSQVSNWFINARVRLWKPM 423 (693)
Q Consensus 367 ~Lpk~qv~iLr~Wf~eH~~nPYPS~~EK~~LAk~TGLS~kQVsNWFiNaR~R~kKp~ 423 (693)
.||+..+.++.--+++ -|+ -.++|+.+|++...|.+++.-+|+++++-+
T Consensus 136 ~L~~~~r~i~~L~~~~----g~s----~~eIA~~lgis~~tV~~~l~Ra~~~Lr~~l 184 (196)
T PRK12524 136 ALPERQRQAVVLRHIE----GLS----NPEIAEVMEIGVEAVESLTARGKRALAALL 184 (196)
T ss_pred hCCHHHHHHHHHHHHc----CCC----HHHHHHHHCcCHHHHHHHHHHHHHHHHHHH
Confidence 4899999888776554 222 468999999999999999999999998643
No 114
>PRK06986 fliA flagellar biosynthesis sigma factor; Validated
Probab=22.40 E-value=56 Score=33.13 Aligned_cols=49 Identities=29% Similarity=0.343 Sum_probs=40.5
Q ss_pred CCChhHHHHHHHHHHHhhCCCCCCHHHHHHHHHHhCCChhhhhccchhhhhhcChhh
Q 005500 367 GLPERSVSVLRAWLFEHFLHPYPKDSDKQMLAKQTGLTRSQVSNWFINARVRLWKPM 423 (693)
Q Consensus 367 ~Lpk~qv~iLr~Wf~eH~~nPYPS~~EK~~LAk~TGLS~kQVsNWFiNaR~R~kKp~ 423 (693)
.||+..+.++..-|++. -.-.++|+.+|++...|.+|...+|+++++.+
T Consensus 184 ~L~~~~r~vl~l~~~~g--------~s~~EIA~~lgis~~tV~~~~~ra~~~Lr~~l 232 (236)
T PRK06986 184 SLPEREQLVLSLYYQEE--------LNLKEIGAVLGVSESRVSQIHSQAIKRLRARL 232 (236)
T ss_pred hCCHHHHHHHHhHhccC--------CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 48999999987766542 23578999999999999999999999998754
No 115
>PRK09647 RNA polymerase sigma factor SigE; Reviewed
Probab=22.20 E-value=98 Score=30.98 Aligned_cols=49 Identities=18% Similarity=0.228 Sum_probs=39.2
Q ss_pred CCChhHHHHHHHHHHHhhCCCCCCHHHHHHHHHHhCCChhhhhccchhhhhhcChhh
Q 005500 367 GLPERSVSVLRAWLFEHFLHPYPKDSDKQMLAKQTGLTRSQVSNWFINARVRLWKPM 423 (693)
Q Consensus 367 ~Lpk~qv~iLr~Wf~eH~~nPYPS~~EK~~LAk~TGLS~kQVsNWFiNaR~R~kKp~ 423 (693)
.||+..+.++..-+++. .+| .++|+.+|++...|.++..-+|+++++-+
T Consensus 138 ~L~~~~r~v~~L~~~~g--~s~------~EIA~~Lgis~~tV~~~l~RArk~Lr~~l 186 (203)
T PRK09647 138 SLPPEFRAAVVLCDIEG--LSY------EEIAATLGVKLGTVRSRIHRGRQQLRAAL 186 (203)
T ss_pred hCCHHHHHHHHHHHHcC--CCH------HHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 47888888776665542 333 68999999999999999999999998655
No 116
>PRK12532 RNA polymerase sigma factor; Provisional
Probab=21.90 E-value=81 Score=30.70 Aligned_cols=49 Identities=18% Similarity=0.209 Sum_probs=39.9
Q ss_pred CCChhHHHHHHHHHHHhhCCCCCCHHHHHHHHHHhCCChhhhhccchhhhhhcChhh
Q 005500 367 GLPERSVSVLRAWLFEHFLHPYPKDSDKQMLAKQTGLTRSQVSNWFINARVRLWKPM 423 (693)
Q Consensus 367 ~Lpk~qv~iLr~Wf~eH~~nPYPS~~EK~~LAk~TGLS~kQVsNWFiNaR~R~kKp~ 423 (693)
.||+..+.++.-.+.+. -.-.++|..+|++...|.++...+|+++++-+
T Consensus 136 ~L~~~~r~i~~L~~~~g--------~s~~EIA~~lgis~~tVk~~l~Rar~~Lr~~l 184 (195)
T PRK12532 136 NLPENTARVFTLKEILG--------FSSDEIQQMCGISTSNYHTIMHRARESLRQCL 184 (195)
T ss_pred hCCHHHHHHhhhHHHhC--------CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 58999999887655542 22468999999999999999999999998755
No 117
>PRK06288 RNA polymerase sigma factor WhiG; Reviewed
Probab=21.81 E-value=78 Score=32.95 Aligned_cols=49 Identities=29% Similarity=0.421 Sum_probs=41.2
Q ss_pred CCChhHHHHHHHHHHHhhCCCCCCHHHHHHHHHHhCCChhhhhccchhhhhhcChhh
Q 005500 367 GLPERSVSVLRAWLFEHFLHPYPKDSDKQMLAKQTGLTRSQVSNWFINARVRLWKPM 423 (693)
Q Consensus 367 ~Lpk~qv~iLr~Wf~eH~~nPYPS~~EK~~LAk~TGLS~kQVsNWFiNaR~R~kKp~ 423 (693)
.||+..+.+|...|++. -.-.++|..+|++...|..+...+++++++.+
T Consensus 212 ~L~~~~r~vl~l~~~~~--------~s~~eIA~~lgis~~tV~~~~~ra~~~Lr~~l 260 (268)
T PRK06288 212 TLPEREKKVLILYYYED--------LTLKEIGKVLGVTESRISQLHTKAVLQLRAKL 260 (268)
T ss_pred hCCHHHHHHHHHHHHcC--------CCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHH
Confidence 58999999998877652 23578999999999999999999999998765
No 118
>PRK12515 RNA polymerase sigma factor; Provisional
Probab=21.60 E-value=86 Score=30.38 Aligned_cols=50 Identities=14% Similarity=0.225 Sum_probs=40.1
Q ss_pred CCCChhHHHHHHHHHHHhhCCCCCCHHHHHHHHHHhCCChhhhhccchhhhhhcChhh
Q 005500 366 RGLPERSVSVLRAWLFEHFLHPYPKDSDKQMLAKQTGLTRSQVSNWFINARVRLWKPM 423 (693)
Q Consensus 366 R~Lpk~qv~iLr~Wf~eH~~nPYPS~~EK~~LAk~TGLS~kQVsNWFiNaR~R~kKp~ 423 (693)
..||++.+.+|..-+++. -.-.++|..+|++...|.+.+..+|+++++-.
T Consensus 130 ~~L~~~~r~vl~l~~~~~--------~s~~eIA~~lgis~~tV~~~l~Rar~~Lr~~l 179 (189)
T PRK12515 130 AKLSPAHREIIDLVYYHE--------KSVEEVGEIVGIPESTVKTRMFYARKKLAELL 179 (189)
T ss_pred HhCCHHHHHHHHHHHHcC--------CCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHH
Confidence 358999999997765541 23478999999999999999999998887643
No 119
>PF14643 DUF4455: Domain of unknown function (DUF4455)
Probab=21.58 E-value=3.1e+02 Score=31.53 Aligned_cols=34 Identities=18% Similarity=0.571 Sum_probs=30.2
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhc
Q 005500 247 QEIQMKKAKLINMLDEVEQRYRQYHHQMQIVISS 280 (693)
Q Consensus 247 ~ElQ~Kk~KLl~mLdeVd~RY~qY~~qmq~v~ss 280 (693)
.+|..-..+-+.+|+.++.+|+.||.++..++..
T Consensus 407 e~L~~~l~~~~~~Ld~Ie~~Y~~fh~~~~~~~~~ 440 (473)
T PF14643_consen 407 EKLKEHLEKALDLLDQIEEEYEDFHKKQTAIVME 440 (473)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3677778899999999999999999999988877
No 120
>PRK12544 RNA polymerase sigma factor; Provisional
Probab=21.25 E-value=1.2e+02 Score=30.57 Aligned_cols=51 Identities=22% Similarity=0.295 Sum_probs=41.7
Q ss_pred CCCChhHHHHHHHHHHHhhCCCCCCHHHHHHHHHHhCCChhhhhccchhhhhhcChhhH
Q 005500 366 RGLPERSVSVLRAWLFEHFLHPYPKDSDKQMLAKQTGLTRSQVSNWFINARVRLWKPMV 424 (693)
Q Consensus 366 R~Lpk~qv~iLr~Wf~eH~~nPYPS~~EK~~LAk~TGLS~kQVsNWFiNaR~R~kKp~i 424 (693)
..||++.+.++..-+++. .+ -.++|..+|++...|.++..-+|+++++-+.
T Consensus 147 ~~L~~~~r~v~~L~~~~g--~s------~~EIAe~lgis~~tV~~~l~RAr~~Lr~~l~ 197 (206)
T PRK12544 147 DGLPAKYARVFMMREFIE--LE------TNEICHAVDLSVSNLNVLLYRARLRLRECLE 197 (206)
T ss_pred HhCCHHHHHHHHHHHHcC--CC------HHHHHHHHCcCHHHHHHHHHHHHHHHHHHHH
Confidence 458999988887776652 22 3789999999999999999999999988664
No 121
>PRK09649 RNA polymerase sigma factor SigC; Reviewed
Probab=21.24 E-value=71 Score=31.14 Aligned_cols=48 Identities=15% Similarity=0.009 Sum_probs=39.5
Q ss_pred CCCChhHHHHHHHHHHHhhCCCCCCHHHHHHHHHHhCCChhhhhccchhhhhhcCh
Q 005500 366 RGLPERSVSVLRAWLFEHFLHPYPKDSDKQMLAKQTGLTRSQVSNWFINARVRLWK 421 (693)
Q Consensus 366 R~Lpk~qv~iLr~Wf~eH~~nPYPS~~EK~~LAk~TGLS~kQVsNWFiNaR~R~kK 421 (693)
..||++++.++.-.+++. + .-.++|..+|++...|.++..-+|+++++
T Consensus 129 ~~Lp~~~r~v~~L~~~~g----~----s~~EIA~~lgis~~tVk~~l~Rar~~Lr~ 176 (185)
T PRK09649 129 ADLTTDQREALLLTQLLG----L----SYADAAAVCGCPVGTIRSRVARARDALLA 176 (185)
T ss_pred HhCCHHHhHHhhhHHHcC----C----CHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Confidence 458999999998776652 1 23689999999999999999999999886
No 122
>PRK12545 RNA polymerase sigma factor; Provisional
Probab=21.20 E-value=83 Score=31.15 Aligned_cols=50 Identities=24% Similarity=0.226 Sum_probs=40.7
Q ss_pred CCCChhHHHHHHHHHHHhhCCCCCCHHHHHHHHHHhCCChhhhhccchhhhhhcChhh
Q 005500 366 RGLPERSVSVLRAWLFEHFLHPYPKDSDKQMLAKQTGLTRSQVSNWFINARVRLWKPM 423 (693)
Q Consensus 366 R~Lpk~qv~iLr~Wf~eH~~nPYPS~~EK~~LAk~TGLS~kQVsNWFiNaR~R~kKp~ 423 (693)
..||+..+.++.--+++. .+ -.++|..+|++...|.+....+|+++++-+
T Consensus 138 ~~Lp~~~r~v~~L~~~eg--~s------~~EIA~~lgis~~tVk~~l~RAr~~Lr~~l 187 (201)
T PRK12545 138 DHLPEQIGRVFMMREFLD--FE------IDDICTELTLTANHCSVLLYRARTRLRTCL 187 (201)
T ss_pred HhCCHHHHHHHHHHHHcC--CC------HHHHHHHHCcCHHHHHHHHHHHHHHHHHHH
Confidence 348999999988766652 22 368999999999999999999999998755
No 123
>PRK12533 RNA polymerase sigma factor; Provisional
Probab=21.13 E-value=68 Score=32.68 Aligned_cols=50 Identities=22% Similarity=0.162 Sum_probs=41.2
Q ss_pred CCCChhHHHHHHHHHHHhhCCCCCCHHHHHHHHHHhCCChhhhhccchhhhhhcChhh
Q 005500 366 RGLPERSVSVLRAWLFEHFLHPYPKDSDKQMLAKQTGLTRSQVSNWFINARVRLWKPM 423 (693)
Q Consensus 366 R~Lpk~qv~iLr~Wf~eH~~nPYPS~~EK~~LAk~TGLS~kQVsNWFiNaR~R~kKp~ 423 (693)
..||+..+.++...++++ -+ -.++|..+|++...|.++...+|+++++-+
T Consensus 133 ~~Lp~~~R~v~~L~y~eg--~s------~~EIAe~LgiS~~tVk~~L~RAr~~Lr~~l 182 (216)
T PRK12533 133 AKLPVEYREVLVLRELED--MS------YREIAAIADVPVGTVMSRLARARRRLAALL 182 (216)
T ss_pred HcCCHHHHhHhhhHHhcC--CC------HHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 358999999998877763 23 367999999999999999999999988755
No 124
>PRK12850 groEL chaperonin GroEL; Reviewed
Probab=21.09 E-value=5.2e+02 Score=30.31 Aligned_cols=59 Identities=20% Similarity=0.206 Sum_probs=48.0
Q ss_pred ChHHHHHHHHHHHHH-------------HHHHHHHHHHHHHHHHHHHHHHhchhhhccCCchhhhHHHHHHHH
Q 005500 242 TTAERQEIQMKKAKL-------------INMLDEVEQRYRQYHHQMQIVISSFEQAAGIESAKTYTALALKTI 301 (693)
Q Consensus 242 s~~er~ElQ~Kk~KL-------------l~mLdeVd~RY~qY~~qmq~v~ssFe~~ag~gaa~~yt~laL~~i 301 (693)
+..+|..|+.++++| -.+++|++|+++-...-++..+.. --|.|.|++..+++..|+.+
T Consensus 358 ~~~~~~~l~eR~~~l~~~~~tI~irG~t~~~l~E~er~i~DAl~~~k~a~~~-g~VpGGGa~e~~~s~~L~~~ 429 (544)
T PRK12850 358 SDYDREKLQERLAKLAGGVAVIRVGGATEVEVKEKKDRVDDALHATRAAVEE-GIVPGGGVALLRARSALRGL 429 (544)
T ss_pred cHHHHHHHHHHHHHhcCCeEEEEECCCcHHHHHHHHHHHHHHHHHHHHHHhc-CCccCCcHHHHHHHHHHHhc
Confidence 344666677777666 357999999999999999999999 49999999999988888755
No 125
>PF13518 HTH_28: Helix-turn-helix domain
Probab=20.96 E-value=67 Score=24.61 Aligned_cols=25 Identities=28% Similarity=0.525 Sum_probs=20.8
Q ss_pred HHHHHHHHhCCChhhhhccchhhhh
Q 005500 393 DKQMLAKQTGLTRSQVSNWFINARV 417 (693)
Q Consensus 393 EK~~LAk~TGLS~kQVsNWFiNaR~ 417 (693)
...++|+..|++..+|..|....+.
T Consensus 14 s~~~~a~~~gis~~tv~~w~~~y~~ 38 (52)
T PF13518_consen 14 SVREIAREFGISRSTVYRWIKRYRE 38 (52)
T ss_pred CHHHHHHHHCCCHhHHHHHHHHHHh
Confidence 3466999999999999999876654
No 126
>TIGR02479 FliA_WhiG RNA polymerase sigma factor, FliA/WhiG family. Most members of this family are the flagellar operon sigma factor FliA, controlling transcription of bacterial flagellar genes by RNA polymerase. An exception is the sigma factor WhiG in the genus Streptomyces, involved in the production of sporulating aerial mycelium.
Probab=20.86 E-value=85 Score=31.53 Aligned_cols=48 Identities=29% Similarity=0.371 Sum_probs=40.3
Q ss_pred CCChhHHHHHHHHHHHhhCCCCCCHHHHHHHHHHhCCChhhhhccchhhhhhcChh
Q 005500 367 GLPERSVSVLRAWLFEHFLHPYPKDSDKQMLAKQTGLTRSQVSNWFINARVRLWKP 422 (693)
Q Consensus 367 ~Lpk~qv~iLr~Wf~eH~~nPYPS~~EK~~LAk~TGLS~kQVsNWFiNaR~R~kKp 422 (693)
.||+..+.+|...|++. + .-.++|+.+|++...|..|...++.++++.
T Consensus 175 ~L~~~~r~il~l~y~~~----~----s~~eIA~~lgis~~tV~~~~~ra~~~Lr~~ 222 (224)
T TIGR02479 175 SLSEREQLVLSLYYYEE----L----NLKEIGEVLGLTESRVSQIHSQALKKLRAK 222 (224)
T ss_pred hCCHHHHHHHHHHHhCC----C----CHHHHHHHhCCCHHHHHHHHHHHHHHHHHH
Confidence 48999999998887652 2 347899999999999999999999988763
No 127
>PRK12539 RNA polymerase sigma factor; Provisional
Probab=20.39 E-value=71 Score=30.90 Aligned_cols=50 Identities=20% Similarity=0.146 Sum_probs=40.6
Q ss_pred CCCChhHHHHHHHHHHHhhCCCCCCHHHHHHHHHHhCCChhhhhccchhhhhhcChhh
Q 005500 366 RGLPERSVSVLRAWLFEHFLHPYPKDSDKQMLAKQTGLTRSQVSNWFINARVRLWKPM 423 (693)
Q Consensus 366 R~Lpk~qv~iLr~Wf~eH~~nPYPS~~EK~~LAk~TGLS~kQVsNWFiNaR~R~kKp~ 423 (693)
..||+..+.++.--+++. -.-.++|+.+|++...|.++...+|+++++-+
T Consensus 130 ~~L~~~~r~v~~l~~~~g--------~s~~eIA~~lgis~~tV~~~l~ra~~~Lr~~l 179 (184)
T PRK12539 130 ARLPEKMRLAIQAVKLEG--------LSVAEAATRSGMSESAVKVSVHRGLKALAALI 179 (184)
T ss_pred HhCCHHHHHHHHHHHHcC--------CcHHHHHHHHCcCHHHHHHHHHHHHHHHHHHH
Confidence 348999999998766552 23468999999999999999999999988644
No 128
>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=20.20 E-value=80 Score=24.34 Aligned_cols=21 Identities=19% Similarity=0.254 Sum_probs=18.8
Q ss_pred HHHHHhCCChhhhhccchhhh
Q 005500 396 MLAKQTGLTRSQVSNWFINAR 416 (693)
Q Consensus 396 ~LAk~TGLS~kQVsNWFiNaR 416 (693)
+||+.+|++...|+.|+.+.+
T Consensus 2 ~lA~~~gvs~~tvs~~l~g~~ 22 (52)
T cd01392 2 DIARAAGVSVATVSRVLNGKP 22 (52)
T ss_pred cHHHHHCcCHHHHHHHHcCCC
Confidence 589999999999999998875
No 129
>TIGR02481 hemeryth_dom hemerythrin-like metal-binding domain. This model describes both members of the hemerythrin (TIGR00058) family of marine invertebrates and a broader collection of bacterial and archaeal homologs. Many of the latter group are multidomain proteins with signal-transducing domains such as the GGDEF diguanylate cyclase domain (TIGR00254, pfam00990) and methyl-accepting chemotaxis protein signaling domain (pfam00015). Most hemerythrins are oxygen-carriers with a bound non-heme iron, but at least one example is a cadmium-binding protein, apparently with a role in sequestering toxic metals rather than in binding oxygen. Patterns of conserved residues suggest that all prokaryotic instances of this domain bind iron or another heavy metal, but the exact function is unknown. Not surprisingly, the prokaryote with the most instances of this domain is Magnetococcus sp. MC-1, a magnetotactic bacterium.
Probab=20.05 E-value=4.1e+02 Score=24.19 Aligned_cols=19 Identities=37% Similarity=0.800 Sum_probs=15.1
Q ss_pred CCChhHHHHHHHHHHHhhC
Q 005500 367 GLPERSVSVLRAWLFEHFL 385 (693)
Q Consensus 367 ~Lpk~qv~iLr~Wf~eH~~ 385 (693)
.+.......|..||..|+.
T Consensus 98 ~~~~~~~~~l~~Wl~~HI~ 116 (126)
T TIGR02481 98 SLAEELLDFLKDWLVNHIL 116 (126)
T ss_pred hHHHHHHHHHHHHHHHHhH
Confidence 3566788899999999854
No 130
>PF04740 LXG: LXG domain of WXG superfamily; InterPro: IPR006829 This group of putative transposases is found in Gram-positive bacteria, mostly Bacillus members and is thought to be a Cytosolic protein. However, we have also found a Bacillus subtilis bacteriophage SPbetac2 homologue (O64023 from SWISSPROT), possibly arising as a result of horizontal transfer. More information about these proteins can be found at Protein of the Month: Transposase [].
Probab=20.02 E-value=7e+02 Score=24.67 Aligned_cols=66 Identities=12% Similarity=0.166 Sum_probs=37.1
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHhchhhhcc---------CCchhhhHHHHHHHHHHhhhhHHHHHHHHHHHHH
Q 005500 255 KLINMLDEVEQRYRQYHHQMQIVISSFEQAAG---------IESAKTYTALALKTISKQFRCLKDAITGQIKAAN 320 (693)
Q Consensus 255 KLl~mLdeVd~RY~qY~~qmq~v~ssFe~~ag---------~gaa~~yt~laL~~iSr~Fr~LkdaI~~qi~~~~ 320 (693)
.|+...+.+.+-++++-.++..+..++..... ..+++.|..-.+.-+-.-+..+.+.+...+..+.
T Consensus 7 el~~~~~~~~~~~~~~~~~l~~l~~ai~~~~~~~~~LkGka~dsiK~y~~~vh~pll~~~~~~~~~~~~~l~~~~ 81 (204)
T PF04740_consen 7 ELHSQAESTNSSLKELKEQLESLQKAINQFISSESSLKGKAYDSIKNYFSEVHIPLLQGLILLLEEYQEALKFIK 81 (204)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCcchhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHH
Confidence 34445555555555555555555555554433 3456677666666666666666666666664443
Done!