Query 022713
Match_columns 293
No_of_seqs 365 out of 1720
Neff 5.9
Searched_HMMs 46136
Date Fri Mar 29 05:36:41 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/022713.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/022713hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG0483 Transcription factor H 99.9 7.3E-25 1.6E-29 194.9 7.7 119 146-264 50-169 (198)
2 KOG0489 Transcription factor z 99.7 7.3E-19 1.6E-23 163.0 2.6 64 143-206 156-219 (261)
3 KOG0842 Transcription factor t 99.7 1.3E-17 2.8E-22 156.7 8.6 67 145-211 152-218 (307)
4 KOG0485 Transcription factor N 99.7 3E-17 6.5E-22 146.4 10.2 64 142-205 100-163 (268)
5 KOG0488 Transcription factor B 99.7 1E-17 2.2E-22 158.7 5.0 63 144-206 170-232 (309)
6 KOG0487 Transcription factor A 99.7 1.4E-17 3.1E-22 156.5 4.4 63 144-206 233-295 (308)
7 KOG0850 Transcription factor D 99.7 4.2E-17 9.1E-22 146.5 5.9 66 141-206 116-182 (245)
8 KOG0843 Transcription factor E 99.7 3.1E-17 6.8E-22 142.6 4.7 64 145-208 101-164 (197)
9 KOG0484 Transcription factor P 99.7 2.2E-17 4.8E-22 132.0 1.3 64 143-206 14-77 (125)
10 KOG2251 Homeobox transcription 99.6 2E-16 4.4E-21 141.5 4.7 66 142-207 33-98 (228)
11 KOG0494 Transcription factor C 99.6 4.9E-16 1.1E-20 141.7 6.9 64 146-209 140-204 (332)
12 PF00046 Homeobox: Homeobox do 99.6 4.1E-16 8.8E-21 111.7 3.5 57 147-203 1-57 (57)
13 KOG0492 Transcription factor M 99.6 8.3E-16 1.8E-20 136.4 6.1 63 144-206 142-204 (246)
14 KOG0493 Transcription factor E 99.6 3.2E-15 7E-20 136.5 6.2 63 146-208 246-308 (342)
15 KOG4577 Transcription factor L 99.5 2.3E-14 5E-19 132.5 8.3 73 141-213 162-234 (383)
16 KOG0848 Transcription factor C 99.5 2.1E-15 4.6E-20 138.1 1.4 59 148-206 201-259 (317)
17 KOG0486 Transcription factor P 99.5 1.9E-14 4E-19 134.5 4.9 67 145-211 111-177 (351)
18 TIGR01565 homeo_ZF_HD homeobox 99.5 4.1E-14 8.8E-19 102.9 5.6 53 146-198 1-57 (58)
19 KOG0844 Transcription factor E 99.5 9.7E-15 2.1E-19 135.9 2.9 65 143-207 178-242 (408)
20 cd00086 homeodomain Homeodomai 99.5 2.9E-14 6.3E-19 101.8 3.8 57 148-204 2-58 (59)
21 smart00389 HOX Homeodomain. DN 99.5 2.5E-14 5.4E-19 101.5 3.4 56 147-202 1-56 (56)
22 KOG0491 Transcription factor B 99.4 1.4E-14 3.1E-19 124.4 -0.3 62 146-207 100-161 (194)
23 COG5576 Homeodomain-containing 99.4 1.8E-13 3.9E-18 118.1 5.9 66 142-207 47-112 (156)
24 KOG3802 Transcription factor O 99.4 3.1E-13 6.6E-18 130.1 5.4 63 143-205 291-353 (398)
25 KOG0847 Transcription factor, 99.4 1.9E-13 4E-18 122.4 1.6 65 141-205 162-226 (288)
26 KOG0490 Transcription factor, 99.2 1.4E-11 3E-16 110.3 3.6 63 143-205 57-119 (235)
27 smart00340 HALZ homeobox assoc 99.0 5.5E-10 1.2E-14 75.3 4.7 44 204-247 1-44 (44)
28 KOG1168 Transcription factor A 99.0 6.5E-10 1.4E-14 103.4 4.9 63 143-205 306-368 (385)
29 KOG0849 Transcription factor P 98.9 5.4E-10 1.2E-14 108.1 3.5 64 143-206 173-236 (354)
30 KOG0775 Transcription factor S 98.8 5.1E-09 1.1E-13 96.8 3.9 51 153-203 183-233 (304)
31 KOG0774 Transcription factor P 98.7 7.2E-08 1.6E-12 88.8 8.3 58 146-203 188-248 (334)
32 KOG2252 CCAAT displacement pro 98.3 5.3E-07 1.1E-11 90.4 3.4 62 141-202 415-476 (558)
33 PF05920 Homeobox_KN: Homeobox 98.2 3.2E-07 6.9E-12 62.0 0.2 34 167-200 7-40 (40)
34 KOG0490 Transcription factor, 98.0 4.8E-06 1E-10 74.5 3.8 63 143-205 150-212 (235)
35 KOG1146 Homeobox protein [Gene 97.5 7.7E-05 1.7E-09 81.3 3.3 61 146-206 903-963 (1406)
36 KOG0773 Transcription factor M 96.8 0.00075 1.6E-08 64.7 2.5 58 146-203 239-299 (342)
37 PF11569 Homez: Homeodomain le 96.3 0.00089 1.9E-08 48.4 -0.3 42 157-198 9-50 (56)
38 PF02183 HALZ: Homeobox associ 95.2 0.04 8.7E-07 38.1 4.4 35 204-238 1-35 (45)
39 KOG3623 Homeobox transcription 94.2 0.027 5.8E-07 59.0 2.3 48 158-205 568-615 (1007)
40 PF04218 CENP-B_N: CENP-B N-te 92.0 0.19 4.2E-06 35.6 3.3 47 147-198 1-47 (53)
41 PRK09413 IS2 repressor TnpA; R 90.8 1.5 3.2E-05 36.0 7.9 79 149-231 9-101 (121)
42 PF04618 HD-ZIP_N: HD-ZIP prot 83.1 5.8 0.00013 32.6 7.0 34 73-111 70-103 (111)
43 KOG4196 bZIP transcription fac 79.2 7.6 0.00017 32.8 6.5 74 151-236 22-109 (135)
44 PF02183 HALZ: Homeobox associ 78.3 5.4 0.00012 27.5 4.5 31 206-236 10-40 (45)
45 PRK00888 ftsB cell division pr 68.1 7.9 0.00017 31.3 3.9 46 189-235 16-61 (105)
46 PF04545 Sigma70_r4: Sigma-70, 65.0 4.2 9.2E-05 27.7 1.5 39 152-195 4-42 (50)
47 PF01527 HTH_Tnp_1: Transposas 64.9 1 2.2E-05 33.1 -1.7 44 148-195 2-45 (76)
48 cd06171 Sigma70_r4 Sigma70, re 59.5 3.7 8.1E-05 26.8 0.5 43 152-199 10-52 (55)
49 KOG3623 Homeobox transcription 55.8 8.7 0.00019 41.1 2.6 61 146-206 626-686 (1007)
50 KOG1146 Homeobox protein [Gene 54.8 5.9 0.00013 44.6 1.2 57 147-203 445-501 (1406)
51 cd00569 HTH_Hin_like Helix-tur 53.5 14 0.00031 21.3 2.4 38 152-194 5-42 (42)
52 KOG3119 Basic region leucine z 51.9 46 0.001 31.2 6.6 32 208-239 222-253 (269)
53 PF04967 HTH_10: HTH DNA bindi 49.5 20 0.00044 25.5 2.9 38 153-190 1-40 (53)
54 PF00170 bZIP_1: bZIP transcri 47.9 74 0.0016 22.8 5.8 26 209-234 34-59 (64)
55 PRK03975 tfx putative transcri 47.6 17 0.00037 31.1 2.7 48 150-203 4-51 (141)
56 KOG4571 Activating transcripti 46.0 41 0.00089 32.2 5.2 28 209-236 256-283 (294)
57 PF08281 Sigma70_r4_2: Sigma-7 45.1 13 0.00028 25.4 1.4 41 153-198 11-51 (54)
58 cd04787 HTH_HMRTR_unk Helix-Tu 43.4 61 0.0013 26.8 5.4 69 151-234 37-105 (133)
59 PF13443 HTH_26: Cro/C1-type H 43.1 9.7 0.00021 26.8 0.5 29 175-203 12-40 (63)
60 COG3413 Predicted DNA binding 42.8 21 0.00045 31.9 2.6 49 152-202 155-205 (215)
61 KOG4571 Activating transcripti 42.4 56 0.0012 31.3 5.5 35 200-235 241-275 (294)
62 PF10668 Phage_terminase: Phag 41.9 7 0.00015 28.7 -0.4 19 175-193 24-42 (60)
63 KOG3755 SATB1 matrix attachmen 41.9 6 0.00013 41.3 -1.1 46 162-207 708-760 (769)
64 PF00196 GerE: Bacterial regul 41.4 16 0.00034 25.6 1.4 46 152-203 3-48 (58)
65 PF00170 bZIP_1: bZIP transcri 40.7 1.1E+02 0.0023 22.0 5.7 33 204-236 22-54 (64)
66 PF00424 REV: REV protein (ant 39.0 39 0.00084 26.9 3.3 35 158-206 14-48 (91)
67 PF07716 bZIP_2: Basic region 38.7 1.2E+02 0.0026 21.1 5.5 29 207-235 24-52 (54)
68 PHA03308 transcriptional regul 38.6 18 0.0004 38.8 1.8 17 144-160 1292-1308(1463)
69 cd01106 HTH_TipAL-Mta Helix-Tu 38.4 1E+02 0.0022 24.1 5.8 64 150-234 36-99 (103)
70 PF09607 BrkDBD: Brinker DNA-b 37.2 19 0.00041 26.4 1.1 43 150-194 3-46 (58)
71 PRK09646 RNA polymerase sigma 36.0 33 0.00072 29.6 2.8 46 152-202 142-187 (194)
72 smart00338 BRLZ basic region l 34.8 1.5E+02 0.0032 21.3 5.7 25 210-234 28-52 (65)
73 COG3416 Uncharacterized protei 32.8 4E+02 0.0086 24.6 9.6 18 153-170 1-18 (233)
74 PF04977 DivIC: Septum formati 32.5 1.2E+02 0.0025 22.1 4.9 30 205-234 21-50 (80)
75 smart00421 HTH_LUXR helix_turn 32.3 32 0.00069 22.7 1.7 39 152-196 3-41 (58)
76 PRK12526 RNA polymerase sigma 31.9 37 0.00081 29.8 2.5 46 152-202 153-198 (206)
77 PHA02955 hypothetical protein; 31.9 54 0.0012 30.0 3.4 44 155-198 60-104 (213)
78 PF12824 MRP-L20: Mitochondria 31.6 2.2E+02 0.0048 24.9 7.2 48 149-198 82-129 (164)
79 PRK09652 RNA polymerase sigma 31.4 36 0.00079 28.3 2.2 40 152-196 128-167 (182)
80 KOG3335 Predicted coiled-coil 31.3 1.3E+02 0.0029 26.8 5.7 49 187-235 85-133 (181)
81 TIGR02209 ftsL_broad cell divi 30.9 1.4E+02 0.003 22.3 5.2 31 205-235 28-58 (85)
82 PF10883 DUF2681: Protein of u 30.9 1.6E+02 0.0036 23.1 5.6 38 192-236 21-58 (87)
83 PRK06759 RNA polymerase factor 30.7 36 0.00079 27.8 2.1 45 152-201 106-150 (154)
84 PF15058 Speriolin_N: Sperioli 30.2 4.2E+02 0.0091 24.0 8.9 24 208-232 19-42 (200)
85 PRK00118 putative DNA-binding 30.1 1.7E+02 0.0037 23.7 5.8 46 152-202 17-62 (104)
86 KOG0709 CREB/ATF family transc 29.4 79 0.0017 32.2 4.5 78 150-234 218-298 (472)
87 PRK09642 RNA polymerase sigma 29.1 50 0.0011 27.3 2.7 46 152-202 106-151 (160)
88 PRK12512 RNA polymerase sigma 29.0 47 0.001 28.2 2.6 46 152-202 131-176 (184)
89 KOG2675 Adenylate cyclase-asso 28.7 2E+02 0.0042 29.3 7.0 27 192-218 168-194 (480)
90 PRK11924 RNA polymerase sigma 28.4 45 0.00098 27.6 2.3 46 152-202 125-170 (179)
91 TIGR02937 sigma70-ECF RNA poly 28.0 47 0.001 26.1 2.2 45 152-201 110-154 (158)
92 PF06156 DUF972: Protein of un 27.6 1.4E+02 0.003 24.3 4.9 33 204-236 18-50 (107)
93 PRK10072 putative transcriptio 27.2 35 0.00076 27.2 1.3 41 152-199 32-72 (96)
94 KOG4403 Cell surface glycoprot 27.1 1E+02 0.0022 31.3 4.7 31 191-221 229-262 (575)
95 smart00338 BRLZ basic region l 27.0 2.1E+02 0.0046 20.4 5.4 34 204-237 29-62 (65)
96 TIGR03879 near_KaiC_dom probab 26.9 9.3 0.0002 29.1 -1.9 32 165-196 24-55 (73)
97 PRK04217 hypothetical protein; 26.4 54 0.0012 26.8 2.3 40 152-196 42-81 (110)
98 PRK12519 RNA polymerase sigma 26.4 42 0.00092 28.8 1.8 45 153-202 142-186 (194)
99 PF01166 TSC22: TSC-22/dip/bun 26.3 1.5E+02 0.0032 21.8 4.2 32 207-238 13-44 (59)
100 cd01109 HTH_YyaN Helix-Turn-He 26.2 1.5E+02 0.0032 23.6 4.9 69 151-234 37-105 (113)
101 cd04779 HTH_MerR-like_sg4 Heli 26.2 2.1E+02 0.0046 24.0 5.9 16 149-164 34-49 (134)
102 PRK12514 RNA polymerase sigma 25.9 66 0.0014 27.1 2.9 45 153-202 130-174 (179)
103 cd04770 HTH_HMRTR Helix-Turn-H 25.6 2.2E+02 0.0048 22.8 5.8 72 150-236 36-107 (123)
104 PF13518 HTH_28: Helix-turn-he 25.6 21 0.00046 23.9 -0.2 20 176-195 15-34 (52)
105 PF07716 bZIP_2: Basic region 25.4 2E+02 0.0043 20.0 4.8 26 205-230 29-54 (54)
106 TIGR02989 Sig-70_gvs1 RNA poly 25.3 55 0.0012 26.8 2.3 39 152-195 111-149 (159)
107 TIGR02959 SigZ RNA polymerase 24.6 58 0.0013 27.5 2.3 39 152-195 100-138 (170)
108 COG4367 Uncharacterized protei 24.5 50 0.0011 26.3 1.6 38 153-190 3-40 (97)
109 PF07795 DUF1635: Protein of u 24.4 5.4E+02 0.012 23.6 8.6 39 198-236 23-61 (214)
110 TIGR02449 conserved hypothetic 24.1 2E+02 0.0044 21.4 4.8 26 209-234 8-33 (65)
111 PF08280 HTH_Mga: M protein tr 24.1 40 0.00087 23.9 1.0 33 155-191 5-37 (59)
112 PRK12515 RNA polymerase sigma 24.0 70 0.0015 27.4 2.7 46 152-202 131-176 (189)
113 PRK09644 RNA polymerase sigma 23.8 57 0.0012 27.2 2.1 46 152-202 108-153 (165)
114 cd04761 HTH_MerR-SF Helix-Turn 23.7 20 0.00044 23.6 -0.6 23 176-198 3-25 (49)
115 cd04781 HTH_MerR-like_sg6 Heli 23.4 2.6E+02 0.0056 22.5 5.8 68 149-235 34-101 (120)
116 PRK09648 RNA polymerase sigma 23.1 66 0.0014 27.5 2.4 39 152-195 139-177 (189)
117 PF11167 DUF2953: Protein of u 22.9 9.2 0.0002 26.7 -2.5 19 1-19 3-21 (53)
118 PRK00888 ftsB cell division pr 22.6 1.4E+02 0.003 24.1 4.0 39 192-230 25-63 (105)
119 TIGR02948 SigW_bacill RNA poly 22.5 62 0.0013 27.3 2.1 46 152-202 136-181 (187)
120 PRK12537 RNA polymerase sigma 22.5 83 0.0018 26.8 2.9 44 152-200 133-176 (182)
121 TIGR02985 Sig70_bacteroi1 RNA 22.1 70 0.0015 25.9 2.3 43 152-199 113-155 (161)
122 PRK05602 RNA polymerase sigma 22.1 65 0.0014 27.4 2.2 45 153-202 129-173 (186)
123 PF13936 HTH_38: Helix-turn-he 22.0 29 0.00063 23.3 -0.1 39 151-194 3-41 (44)
124 PF11365 DUF3166: Protein of u 21.7 1.9E+02 0.004 23.3 4.5 32 206-237 13-44 (96)
125 TIGR02999 Sig-70_X6 RNA polyme 21.5 75 0.0016 26.8 2.4 44 153-201 135-178 (183)
126 PRK13169 DNA replication intia 21.4 2.1E+02 0.0046 23.4 4.9 32 205-236 19-50 (110)
127 PRK15369 two component system 21.4 1E+02 0.0022 25.2 3.2 45 152-202 149-193 (211)
128 TIGR02939 RpoE_Sigma70 RNA pol 21.3 58 0.0012 27.6 1.6 41 153-198 139-179 (190)
129 PF10883 DUF2681: Protein of u 20.9 2E+02 0.0044 22.6 4.5 18 213-230 28-45 (87)
130 PRK09639 RNA polymerase sigma 20.8 74 0.0016 26.3 2.2 43 152-200 112-154 (166)
131 COG2963 Transposase and inacti 20.8 3.6E+02 0.0077 21.2 6.1 42 150-195 5-47 (116)
132 cd02413 40S_S3_KH K homology R 20.6 96 0.0021 23.8 2.6 21 175-195 55-75 (81)
133 PRK09047 RNA polymerase factor 20.5 82 0.0018 25.8 2.4 39 152-195 106-144 (161)
134 PF06056 Terminase_5: Putative 20.2 31 0.00066 24.9 -0.2 25 176-202 16-40 (58)
135 PRK14127 cell division protein 20.2 2.3E+02 0.0049 23.2 4.8 32 205-236 34-65 (109)
136 cd06170 LuxR_C_like C-terminal 20.2 71 0.0015 21.1 1.6 36 154-195 2-37 (57)
137 PRK12541 RNA polymerase sigma 20.1 70 0.0015 26.5 1.9 46 152-202 112-157 (161)
No 1
>KOG0483 consensus Transcription factor HEX, contains HOX and HALZ domains [Transcription]
Probab=99.91 E-value=7.3e-25 Score=194.88 Aligned_cols=119 Identities=50% Similarity=0.665 Sum_probs=111.5
Q ss_pred CCCCCCcCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCCCeeeeechhhhHHHHhhhhhhhhHHHHHHhhHhhHHHH
Q 022713 146 NARKKLRLTKEQSALLEESFKQHSTLNPKQKQALARQLNLRPRQVEVWFQNRRARTKLKQTEVDCEFLKKCCETLTDENR 225 (293)
Q Consensus 146 ~rR~Rt~ft~~Ql~~Le~~F~~~~~ps~~~r~~LA~~LgLs~rqVqvWFQNRRaK~Krkq~~~~~e~Lk~~~~~l~~en~ 225 (293)
..+++.||+.+|+..||..|+.+.++.+.++..||++|||.+|||.|||||||||||.+|++.+++.||.+++.|..+++
T Consensus 50 ~~~kk~Rlt~eQ~~~LE~~F~~~~~L~p~~K~~LAk~LgL~pRQVavWFQNRRARwK~kqlE~d~~~Lk~~~~~l~~~~~ 129 (198)
T KOG0483|consen 50 GKGKKRRLTSEQVKFLEKSFESEKKLEPERKKKLAKELGLQPRQVAVWFQNRRARWKTKQLEKDYESLKRQLESLRSEND 129 (198)
T ss_pred cccccccccHHHHHHhHHhhccccccChHHHHHHHHhhCCChhHHHHHHhhccccccchhhhhhHHHHHHHHHHHhhhhh
Confidence 45566789999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHHhhhcCCccccC-CcccccCCCCCccCCCC
Q 022713 226 RLHKELQELKALKLAQPLYMHM-PAATLTMCPSCERIGGG 264 (293)
Q Consensus 226 ~l~~e~~~l~al~~~~~~~~~~-p~a~~~~c~sc~~~~~~ 264 (293)
+|+.++.+|.++......+++. +..++.+|++|+.+...
T Consensus 130 ~Lq~e~~eL~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 169 (198)
T KOG0483|consen 130 RLQSEVQELVAELSSLKREMQKSPENTLTMCPNSESSSSV 169 (198)
T ss_pred HHHHHHHHHHHHHhhhhhhhccCcccccccCccccccCCc
Confidence 9999999999988888888888 88899999999976643
No 2
>KOG0489 consensus Transcription factor zerknullt and related HOX domain proteins [General function prediction only]
Probab=99.73 E-value=7.3e-19 Score=162.99 Aligned_cols=64 Identities=33% Similarity=0.545 Sum_probs=60.3
Q ss_pred cCCCCCCCCcCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCCCeeeeechhhhHHHHhhhh
Q 022713 143 DGVNARKKLRLTKEQSALLEESFKQHSTLNPKQKQALARQLNLRPRQVEVWFQNRRARTKLKQT 206 (293)
Q Consensus 143 ~~~~rR~Rt~ft~~Ql~~Le~~F~~~~~ps~~~r~~LA~~LgLs~rqVqvWFQNRRaK~Krkq~ 206 (293)
.++.||.|+.||..|+.+||+.|..++|+++..|.+||..|.|+++||||||||||+||||..+
T Consensus 156 ~~~~kR~RtayT~~QllELEkEFhfN~YLtR~RRiEiA~~L~LtErQIKIWFQNRRMK~Kk~~k 219 (261)
T KOG0489|consen 156 GGKSKRRRTAFTRYQLLELEKEFHFNKYLTRSRRIEIAHALNLTERQIKIWFQNRRMKWKKENK 219 (261)
T ss_pred cCCCCCCCcccchhhhhhhhhhhccccccchHHHHHHHhhcchhHHHHHHHHHHHHHHHHHhhc
Confidence 4567899999999999999999999999999999999999999999999999999999998554
No 3
>KOG0842 consensus Transcription factor tinman/NKX2-3, contains HOX domain [Transcription]
Probab=99.72 E-value=1.3e-17 Score=156.70 Aligned_cols=67 Identities=34% Similarity=0.586 Sum_probs=60.7
Q ss_pred CCCCCCCcCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCCCeeeeechhhhHHHHhhhhhhhhH
Q 022713 145 VNARKKLRLTKEQSALLEESFKQHSTLNPKQKQALARQLNLRPRQVEVWFQNRRARTKLKQTEVDCE 211 (293)
Q Consensus 145 ~~rR~Rt~ft~~Ql~~Le~~F~~~~~ps~~~r~~LA~~LgLs~rqVqvWFQNRRaK~Krkq~~~~~e 211 (293)
++||.|.-|+..|+.+||+.|++++|++..+|+.||..|+|+++||||||||||-|+||++++...+
T Consensus 152 ~kRKrRVLFSqAQV~ELERRFrqQRYLSAPERE~LA~~LrLT~TQVKIWFQNrRYK~KR~~~dk~~~ 218 (307)
T KOG0842|consen 152 KKRKRRVLFSQAQVYELERRFRQQRYLSAPEREHLASSLRLTPTQVKIWFQNRRYKTKRQQKDKALE 218 (307)
T ss_pred cccccccccchhHHHHHHHHHHhhhccccHhHHHHHHhcCCCchheeeeeecchhhhhhhhhhhhhh
Confidence 4455566699999999999999999999999999999999999999999999999999988766554
No 4
>KOG0485 consensus Transcription factor NKX-5.1/HMX1, contains HOX domain [Transcription]
Probab=99.72 E-value=3e-17 Score=146.37 Aligned_cols=64 Identities=30% Similarity=0.488 Sum_probs=60.1
Q ss_pred ccCCCCCCCCcCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCCCeeeeechhhhHHHHhhh
Q 022713 142 EDGVNARKKLRLTKEQSALLEESFKQHSTLNPKQKQALARQLNLRPRQVEVWFQNRRARTKLKQ 205 (293)
Q Consensus 142 ~~~~~rR~Rt~ft~~Ql~~Le~~F~~~~~ps~~~r~~LA~~LgLs~rqVqvWFQNRRaK~Krkq 205 (293)
.++++||.||+|+..|+..||..|+..+|++..+|..||++|.|++.||||||||||.||||+-
T Consensus 100 g~~RKKktRTvFSraQV~qLEs~Fe~krYLSsaeRa~LA~sLqLTETQVKIWFQNRRnKwKRq~ 163 (268)
T KOG0485|consen 100 GDDRKKKTRTVFSRAQVFQLESTFELKRYLSSAERAGLAASLQLTETQVKIWFQNRRNKWKRQY 163 (268)
T ss_pred cccccccchhhhhHHHHHHHHHHHHHHhhhhHHHHhHHHHhhhhhhhhhhhhhhhhhHHHHHHH
Confidence 4556788899999999999999999999999999999999999999999999999999999753
No 5
>KOG0488 consensus Transcription factor BarH and related HOX domain proteins [General function prediction only]
Probab=99.70 E-value=1e-17 Score=158.70 Aligned_cols=63 Identities=29% Similarity=0.439 Sum_probs=58.6
Q ss_pred CCCCCCCCcCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCCCeeeeechhhhHHHHhhhh
Q 022713 144 GVNARKKLRLTKEQSALLEESFKQHSTLNPKQKQALARQLNLRPRQVEVWFQNRRARTKLKQT 206 (293)
Q Consensus 144 ~~~rR~Rt~ft~~Ql~~Le~~F~~~~~ps~~~r~~LA~~LgLs~rqVqvWFQNRRaK~Krkq~ 206 (293)
.|+|+.|+.||..|+..||+.|++.+|++..+|.+||+.|||+..||++||||||+||||+..
T Consensus 170 kK~RksRTaFT~~Ql~~LEkrF~~QKYLS~~DR~~LA~~LgLTdaQVKtWfQNRRtKWKrq~a 232 (309)
T KOG0488|consen 170 KKRRKSRTAFSDHQLFELEKRFEKQKYLSVADRIELAASLGLTDAQVKTWFQNRRTKWKRQTA 232 (309)
T ss_pred cccccchhhhhHHHHHHHHHHHHHhhcccHHHHHHHHHHcCCchhhHHHHHhhhhHHHHHHHH
Confidence 455666999999999999999999999999999999999999999999999999999997554
No 6
>KOG0487 consensus Transcription factor Abd-B, contains HOX domain [Transcription]
Probab=99.68 E-value=1.4e-17 Score=156.48 Aligned_cols=63 Identities=35% Similarity=0.529 Sum_probs=59.1
Q ss_pred CCCCCCCCcCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCCCeeeeechhhhHHHHhhhh
Q 022713 144 GVNARKKLRLTKEQSALLEESFKQHSTLNPKQKQALARQLNLRPRQVEVWFQNRRARTKLKQT 206 (293)
Q Consensus 144 ~~~rR~Rt~ft~~Ql~~Le~~F~~~~~ps~~~r~~LA~~LgLs~rqVqvWFQNRRaK~Krkq~ 206 (293)
...||||..+|+.|+.+||+.|..|.|++.+.|.+|++.|+|++|||+|||||||+|+||..+
T Consensus 233 ~~~RKKRcPYTK~QtlELEkEFlfN~YitkeKR~ElSr~lNLTeRQVKIWFQNRRMK~KK~~r 295 (308)
T KOG0487|consen 233 RRGRKKRCPYTKHQTLELEKEFLFNMYITKEKRLELSRTLNLTERQVKIWFQNRRMKEKKVNR 295 (308)
T ss_pred cccccccCCchHHHHHHHHHHHHHHHHHhHHHHHHHHHhcccchhheeeeehhhhhHHhhhhh
Confidence 456788889999999999999999999999999999999999999999999999999998654
No 7
>KOG0850 consensus Transcription factor DLX and related proteins with LIM Zn-binding and HOX domains [Transcription]
Probab=99.67 E-value=4.2e-17 Score=146.50 Aligned_cols=66 Identities=29% Similarity=0.454 Sum_probs=59.2
Q ss_pred CccCCCC-CCCCcCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCCCeeeeechhhhHHHHhhhh
Q 022713 141 DEDGVNA-RKKLRLTKEQSALLEESFKQHSTLNPKQKQALARQLNLRPRQVEVWFQNRRARTKLKQT 206 (293)
Q Consensus 141 ~~~~~~r-R~Rt~ft~~Ql~~Le~~F~~~~~ps~~~r~~LA~~LgLs~rqVqvWFQNRRaK~Krkq~ 206 (293)
+..+||. +.||.++.-||..|.+.|++++|+...+|.+||..|||+..||||||||||.|.||..+
T Consensus 116 Ngk~KK~RKPRTIYSS~QLqaL~rRFQkTQYLALPERAeLAAsLGLTQTQVKIWFQNrRSK~KKl~k 182 (245)
T KOG0850|consen 116 NGKGKKVRKPRTIYSSLQLQALNRRFQQTQYLALPERAELAASLGLTQTQVKIWFQNRRSKFKKLKK 182 (245)
T ss_pred CCCcccccCCcccccHHHHHHHHHHHhhcchhcCcHHHHHHHHhCCchhHhhhhhhhhHHHHHHHHh
Confidence 4445554 45999999999999999999999999999999999999999999999999999997544
No 8
>KOG0843 consensus Transcription factor EMX1 and related HOX domain proteins [Transcription]
Probab=99.67 E-value=3.1e-17 Score=142.58 Aligned_cols=64 Identities=36% Similarity=0.490 Sum_probs=60.7
Q ss_pred CCCCCCCcCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCCCeeeeechhhhHHHHhhhhhh
Q 022713 145 VNARKKLRLTKEQSALLEESFKQHSTLNPKQKQALARQLNLRPRQVEVWFQNRRARTKLKQTEV 208 (293)
Q Consensus 145 ~~rR~Rt~ft~~Ql~~Le~~F~~~~~ps~~~r~~LA~~LgLs~rqVqvWFQNRRaK~Krkq~~~ 208 (293)
+.||.||.|+.+|+..||..|+.++|....+|++||..|+|++.||+|||||||.|.||++.+.
T Consensus 101 ~~kr~RT~ft~~Ql~~LE~~F~~~~Yvvg~eR~~LA~~L~LsetQVkvWFQNRRtk~kr~~~e~ 164 (197)
T KOG0843|consen 101 RPKRIRTAFTPEQLLKLEHAFEGNQYVVGAERKQLAQSLSLSETQVKVWFQNRRTKHKRMQQED 164 (197)
T ss_pred CCCccccccCHHHHHHHHHHHhcCCeeechHHHHHHHHcCCChhHhhhhhhhhhHHHHHHHHHh
Confidence 5788899999999999999999999999999999999999999999999999999999987653
No 9
>KOG0484 consensus Transcription factor PHOX2/ARIX, contains HOX domain [Transcription]
Probab=99.65 E-value=2.2e-17 Score=132.02 Aligned_cols=64 Identities=27% Similarity=0.428 Sum_probs=59.7
Q ss_pred cCCCCCCCCcCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCCCeeeeechhhhHHHHhhhh
Q 022713 143 DGVNARKKLRLTKEQSALLEESFKQHSTLNPKQKQALARQLNLRPRQVEVWFQNRRARTKLKQT 206 (293)
Q Consensus 143 ~~~~rR~Rt~ft~~Ql~~Le~~F~~~~~ps~~~r~~LA~~LgLs~rqVqvWFQNRRaK~Krkq~ 206 (293)
..++||-|+.||..|+..||+.|...+||+...|++||.++.|++.+|||||||||+|.|++.+
T Consensus 14 krKQRRIRTTFTS~QLkELErvF~ETHYPDIYTREEiA~kidLTEARVQVWFQNRRAKfRKQEr 77 (125)
T KOG0484|consen 14 KRKQRRIRTTFTSAQLKELERVFAETHYPDIYTREEIALKIDLTEARVQVWFQNRRAKFRKQER 77 (125)
T ss_pred HHHhhhhhhhhhHHHHHHHHHHHHhhcCCcchhHHHHHHhhhhhHHHHHHHHHhhHHHHHHHHH
Confidence 4567888999999999999999999999999999999999999999999999999999997543
No 10
>KOG2251 consensus Homeobox transcription factor [Transcription]
Probab=99.63 E-value=2e-16 Score=141.47 Aligned_cols=66 Identities=30% Similarity=0.488 Sum_probs=61.8
Q ss_pred ccCCCCCCCCcCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCCCeeeeechhhhHHHHhhhhh
Q 022713 142 EDGVNARKKLRLTKEQSALLEESFKQHSTLNPKQKQALARQLNLRPRQVEVWFQNRRARTKLKQTE 207 (293)
Q Consensus 142 ~~~~~rR~Rt~ft~~Ql~~Le~~F~~~~~ps~~~r~~LA~~LgLs~rqVqvWFQNRRaK~Krkq~~ 207 (293)
...+.||.||+|+..|+.+||..|.+.+||+...|++||.+|+|.+.+|+|||+|||+|+|++++.
T Consensus 33 ~pRkqRRERTtFtr~QlevLe~LF~kTqYPDv~~rEelAlklnLpeSrVqVWFKNRRAK~r~qq~q 98 (228)
T KOG2251|consen 33 GPRKQRRERTTFTRKQLEVLEALFAKTQYPDVFMREELALKLNLPESRVQVWFKNRRAKCRRQQQQ 98 (228)
T ss_pred cchhcccccceecHHHHHHHHHHHHhhcCccHHHHHHHHHHhCCchhhhhhhhccccchhhHhhhh
Confidence 345678999999999999999999999999999999999999999999999999999999987764
No 11
>KOG0494 consensus Transcription factor CHX10 and related HOX domain proteins [General function prediction only]
Probab=99.62 E-value=4.9e-16 Score=141.74 Aligned_cols=64 Identities=28% Similarity=0.423 Sum_probs=58.4
Q ss_pred CCCC-CCcCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCCCeeeeechhhhHHHHhhhhhhh
Q 022713 146 NARK-KLRLTKEQSALLEESFKQHSTLNPKQKQALARQLNLRPRQVEVWFQNRRARTKLKQTEVD 209 (293)
Q Consensus 146 ~rR~-Rt~ft~~Ql~~Le~~F~~~~~ps~~~r~~LA~~LgLs~rqVqvWFQNRRaK~Krkq~~~~ 209 (293)
+||. ||.||..|+..||+.|+..+||+...|+-||.++.|.+.+|+|||||||+||||+.++..
T Consensus 140 kRRh~RTiFT~~Qle~LEkaFkeaHYPDv~Are~la~ktelpEDRIqVWfQNRRAKWRk~Ek~wg 204 (332)
T KOG0494|consen 140 KRRHFRTIFTSYQLEELEKAFKEAHYPDVYAREMLADKTELPEDRIQVWFQNRRAKWRKTEKRWG 204 (332)
T ss_pred ccccccchhhHHHHHHHHHHHhhccCccHHHHHHHhhhccCchhhhhHHhhhhhHHhhhhhhhcC
Confidence 3444 899999999999999999999999999999999999999999999999999998765443
No 12
>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=99.60 E-value=4.1e-16 Score=111.66 Aligned_cols=57 Identities=44% Similarity=0.701 Sum_probs=55.1
Q ss_pred CCCCCcCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCCCeeeeechhhhHHHHh
Q 022713 147 ARKKLRLTKEQSALLEESFKQHSTLNPKQKQALARQLNLRPRQVEVWFQNRRARTKL 203 (293)
Q Consensus 147 rR~Rt~ft~~Ql~~Le~~F~~~~~ps~~~r~~LA~~LgLs~rqVqvWFQNRRaK~Kr 203 (293)
||+|+.|+.+|+.+|+.+|..++||+..+++.||.+|||+..+|++||+|||+++|+
T Consensus 1 kr~r~~~t~~q~~~L~~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrR~k~kk 57 (57)
T PF00046_consen 1 KRKRTRFTKEQLKVLEEYFQENPYPSKEEREELAKELGLTERQVKNWFQNRRRKEKK 57 (57)
T ss_dssp SSSSSSSSHHHHHHHHHHHHHSSSCHHHHHHHHHHHHTSSHHHHHHHHHHHHHHHHH
T ss_pred CcCCCCCCHHHHHHHHHHHHHhccccccccccccccccccccccccCHHHhHHHhCc
Confidence 578999999999999999999999999999999999999999999999999999985
No 13
>KOG0492 consensus Transcription factor MSH, contains HOX domain [General function prediction only]
Probab=99.60 E-value=8.3e-16 Score=136.36 Aligned_cols=63 Identities=32% Similarity=0.518 Sum_probs=58.6
Q ss_pred CCCCCCCCcCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCCCeeeeechhhhHHHHhhhh
Q 022713 144 GVNARKKLRLTKEQSALLEESFKQHSTLNPKQKQALARQLNLRPRQVEVWFQNRRARTKLKQT 206 (293)
Q Consensus 144 ~~~rR~Rt~ft~~Ql~~Le~~F~~~~~ps~~~r~~LA~~LgLs~rqVqvWFQNRRaK~Krkq~ 206 (293)
..+|+.|+.||..|+..||+-|+..+|+++.+|.+++..|.|++.||+|||||||+|.||.|.
T Consensus 142 k~nRkPRtPFTtqQLlaLErkfrekqYLSiaEraefSsSL~LTeTqVKIWFQNRRAKaKRlQe 204 (246)
T KOG0492|consen 142 KPNRKPRTPFTTQQLLALERKFREKQYLSIAERAEFSSSLELTETQVKIWFQNRRAKAKRLQE 204 (246)
T ss_pred CCCCCCCCCCCHHHHHHHHHHHhHhhhhhHHHHHhhhhhhhhhhhheehhhhhhhHHHHHHHH
Confidence 335677999999999999999999999999999999999999999999999999999998654
No 14
>KOG0493 consensus Transcription factor Engrailed, contains HOX domain [General function prediction only]
Probab=99.56 E-value=3.2e-15 Score=136.55 Aligned_cols=63 Identities=32% Similarity=0.553 Sum_probs=58.3
Q ss_pred CCCCCCcCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCCCeeeeechhhhHHHHhhhhhh
Q 022713 146 NARKKLRLTKEQSALLEESFKQHSTLNPKQKQALARQLNLRPRQVEVWFQNRRARTKLKQTEV 208 (293)
Q Consensus 146 ~rR~Rt~ft~~Ql~~Le~~F~~~~~ps~~~r~~LA~~LgLs~rqVqvWFQNRRaK~Krkq~~~ 208 (293)
-||.||.||.+|++.|+..|+.++|++...|++||.+|+|.+.||+|||||+|+|.||-....
T Consensus 246 eKRPRTAFtaeQL~RLK~EF~enRYlTEqRRQ~La~ELgLNEsQIKIWFQNKRAKiKKsTgsk 308 (342)
T KOG0493|consen 246 EKRPRTAFTAEQLQRLKAEFQENRYLTEQRRQELAQELGLNESQIKIWFQNKRAKIKKSTGSK 308 (342)
T ss_pred hcCccccccHHHHHHHHHHHhhhhhHHHHHHHHHHHHhCcCHHHhhHHhhhhhhhhhhccCCC
Confidence 368899999999999999999999999999999999999999999999999999999755433
No 15
>KOG4577 consensus Transcription factor LIM3, contains LIM and HOX domains [Transcription]
Probab=99.52 E-value=2.3e-14 Score=132.53 Aligned_cols=73 Identities=26% Similarity=0.422 Sum_probs=66.4
Q ss_pred CccCCCCCCCCcCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCCCeeeeechhhhHHHHhhhhhhhhHHH
Q 022713 141 DEDGVNARKKLRLTKEQSALLEESFKQHSTLNPKQKQALARQLNLRPRQVEVWFQNRRARTKLKQTEVDCEFL 213 (293)
Q Consensus 141 ~~~~~~rR~Rt~ft~~Ql~~Le~~F~~~~~ps~~~r~~LA~~LgLs~rqVqvWFQNRRaK~Krkq~~~~~e~L 213 (293)
+.++..||.||.+|..|++.|+..|...+.|.+..|++|+.++||..|.|||||||||||+||-++.......
T Consensus 162 ~gd~~nKRPRTTItAKqLETLK~AYn~SpKPARHVREQLsseTGLDMRVVQVWFQNRRAKEKRLKKDAGR~RW 234 (383)
T KOG4577|consen 162 EGDASNKRPRTTITAKQLETLKQAYNTSPKPARHVREQLSSETGLDMRVVQVWFQNRRAKEKRLKKDAGRTRW 234 (383)
T ss_pred ccccccCCCcceeeHHHHHHHHHHhcCCCchhHHHHHHhhhccCcceeehhhhhhhhhHHHHhhhhhcchhHH
Confidence 4556689999999999999999999999999999999999999999999999999999999997776666444
No 16
>KOG0848 consensus Transcription factor Caudal, contains HOX domain [Transcription]
Probab=99.52 E-value=2.1e-15 Score=138.08 Aligned_cols=59 Identities=34% Similarity=0.567 Sum_probs=55.0
Q ss_pred CCCCcCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCCCeeeeechhhhHHHHhhhh
Q 022713 148 RKKLRLTKEQSALLEESFKQHSTLNPKQKQALARQLNLRPRQVEVWFQNRRARTKLKQT 206 (293)
Q Consensus 148 R~Rt~ft~~Ql~~Le~~F~~~~~ps~~~r~~LA~~LgLs~rqVqvWFQNRRaK~Krkq~ 206 (293)
|.|.++|..|..+||+.|...+|.++..+.+||.-|+|+||||||||||||+|+||..+
T Consensus 201 KYRvVYTDhQRLELEKEfh~SryITirRKSELA~~LgLsERQVKIWFQNRRAKERK~nK 259 (317)
T KOG0848|consen 201 KYRVVYTDHQRLELEKEFHTSRYITIRRKSELAATLGLSERQVKIWFQNRRAKERKDNK 259 (317)
T ss_pred ceeEEecchhhhhhhhhhccccceeeehhHHHHHhhCccHhhhhHhhhhhhHHHHHHHH
Confidence 34677999999999999999999999999999999999999999999999999998654
No 17
>KOG0486 consensus Transcription factor PTX1, contains HOX domain [Transcription]
Probab=99.49 E-value=1.9e-14 Score=134.48 Aligned_cols=67 Identities=27% Similarity=0.458 Sum_probs=61.6
Q ss_pred CCCCCCCcCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCCCeeeeechhhhHHHHhhhhhhhhH
Q 022713 145 VNARKKLRLTKEQSALLEESFKQHSTLNPKQKQALARQLNLRPRQVEVWFQNRRARTKLKQTEVDCE 211 (293)
Q Consensus 145 ~~rR~Rt~ft~~Ql~~Le~~F~~~~~ps~~~r~~LA~~LgLs~rqVqvWFQNRRaK~Krkq~~~~~e 211 (293)
|+||.|+.|+..|+..||..|++++||+...|++||...+|++.+|+|||.|||+|||+++.....+
T Consensus 111 KqrrQrthFtSqqlqele~tF~rNrypdMstrEEIavwtNlTE~rvrvwfknrrakwrkrErN~~ae 177 (351)
T KOG0486|consen 111 KQRRQRTHFTSQQLQELEATFQRNRYPDMSTREEIAVWTNLTEARVRVWFKNRRAKWRKRERNQQAE 177 (351)
T ss_pred hhhhhhhhhHHHHHHHHHHHHhhccCCccchhhHHHhhccccchhhhhhcccchhhhhhhhhhHHHH
Confidence 4677899999999999999999999999999999999999999999999999999999877655544
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=99.49 E-value=4.1e-14 Score=102.94 Aligned_cols=53 Identities=13% Similarity=0.360 Sum_probs=50.9
Q ss_pred CCCCCCcCCHHHHHHHHHHHhhCCC----CCHHHHHHHHHHhCCCCCeeeeechhhh
Q 022713 146 NARKKLRLTKEQSALLEESFKQHST----LNPKQKQALARQLNLRPRQVEVWFQNRR 198 (293)
Q Consensus 146 ~rR~Rt~ft~~Ql~~Le~~F~~~~~----ps~~~r~~LA~~LgLs~rqVqvWFQNRR 198 (293)
+||.||.||.+|+..|+..|..++| |+..+|++||..|||++++|+|||||.+
T Consensus 1 ~kR~RT~Ft~~Q~~~Le~~fe~~~y~~~~~~~~~r~~la~~lgl~~~vvKVWfqN~k 57 (58)
T TIGR01565 1 KKRRRTKFTAEQKEKMRDFAEKLGWKLKDKRREEVREFCEEIGVTRKVFKVWMHNNK 57 (58)
T ss_pred CCCCCCCCCHHHHHHHHHHHHHcCCCCCCCCHHHHHHHHHHhCCCHHHeeeecccCC
Confidence 3788999999999999999999999 9999999999999999999999999975
No 19
>KOG0844 consensus Transcription factor EVX1, contains HOX domain [Transcription]
Probab=99.49 E-value=9.7e-15 Score=135.88 Aligned_cols=65 Identities=34% Similarity=0.508 Sum_probs=60.9
Q ss_pred cCCCCCCCCcCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCCCeeeeechhhhHHHHhhhhh
Q 022713 143 DGVNARKKLRLTKEQSALLEESFKQHSTLNPKQKQALARQLNLRPRQVEVWFQNRRARTKLKQTE 207 (293)
Q Consensus 143 ~~~~rR~Rt~ft~~Ql~~Le~~F~~~~~ps~~~r~~LA~~LgLs~rqVqvWFQNRRaK~Krkq~~ 207 (293)
+.+.||.||.||.+||..||+.|-+..|.++..|.+||..|+|.+..|||||||||+|+||++..
T Consensus 178 ~dqmRRYRTAFTReQIaRLEKEFyrENYVSRprRcELAAaLNLPEtTIKVWFQNRRMKDKRQRla 242 (408)
T KOG0844|consen 178 DDQMRRYRTAFTREQIARLEKEFYRENYVSRPRRCELAAALNLPETTIKVWFQNRRMKDKRQRLA 242 (408)
T ss_pred cHHHHHHHhhhhHHHHHHHHHHHHHhccccCchhhhHHHhhCCCcceeehhhhhchhhhhhhhhh
Confidence 34578999999999999999999999999999999999999999999999999999999987754
No 20
>cd00086 homeodomain Homeodomain; DNA binding domains involved in the transcriptional regulation of key eukaryotic developmental processes; may bind to DNA as monomers or as homo- and/or heterodimers, in a sequence-specific manner.
Probab=99.47 E-value=2.9e-14 Score=101.78 Aligned_cols=57 Identities=42% Similarity=0.692 Sum_probs=54.0
Q ss_pred CCCCcCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCCCeeeeechhhhHHHHhh
Q 022713 148 RKKLRLTKEQSALLEESFKQHSTLNPKQKQALARQLNLRPRQVEVWFQNRRARTKLK 204 (293)
Q Consensus 148 R~Rt~ft~~Ql~~Le~~F~~~~~ps~~~r~~LA~~LgLs~rqVqvWFQNRRaK~Krk 204 (293)
+.|..|+..|+.+|+.+|..++||+..++..||.++||+..||++||+|||++.++.
T Consensus 2 ~~r~~~~~~~~~~Le~~f~~~~~P~~~~~~~la~~~~l~~~qV~~WF~nrR~~~~~~ 58 (59)
T cd00086 2 RKRTRFTPEQLEELEKEFEKNPYPSREEREELAKELGLTERQVKIWFQNRRAKLKRS 58 (59)
T ss_pred CCCCcCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHHCcCHHHHHHHHHHHHHHHhcc
Confidence 567789999999999999999999999999999999999999999999999998863
No 21
>smart00389 HOX Homeodomain. DNA-binding factors that are involved in the transcriptional regulation of key developmental processes
Probab=99.47 E-value=2.5e-14 Score=101.50 Aligned_cols=56 Identities=43% Similarity=0.654 Sum_probs=52.5
Q ss_pred CCCCCcCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCCCeeeeechhhhHHHH
Q 022713 147 ARKKLRLTKEQSALLEESFKQHSTLNPKQKQALARQLNLRPRQVEVWFQNRRARTK 202 (293)
Q Consensus 147 rR~Rt~ft~~Ql~~Le~~F~~~~~ps~~~r~~LA~~LgLs~rqVqvWFQNRRaK~K 202 (293)
++.|++|+.+|+.+|+..|..++||+..++..||..+||+..||++||+|||++.|
T Consensus 1 ~k~r~~~~~~~~~~L~~~f~~~~~P~~~~~~~la~~~~l~~~qV~~WF~nrR~~~~ 56 (56)
T smart00389 1 RRKRTSFTPEQLEELEKEFQKNPYPSREEREELAAKLGLSERQVKVWFQNRRAKWK 56 (56)
T ss_pred CCCCCcCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHHCcCHHHHHHhHHHHhhccC
Confidence 35677899999999999999999999999999999999999999999999998764
No 22
>KOG0491 consensus Transcription factor BSH, contains HOX domain [General function prediction only]
Probab=99.43 E-value=1.4e-14 Score=124.43 Aligned_cols=62 Identities=32% Similarity=0.526 Sum_probs=58.0
Q ss_pred CCCCCCcCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCCCeeeeechhhhHHHHhhhhh
Q 022713 146 NARKKLRLTKEQSALLEESFKQHSTLNPKQKQALARQLNLRPRQVEVWFQNRRARTKLKQTE 207 (293)
Q Consensus 146 ~rR~Rt~ft~~Ql~~Le~~F~~~~~ps~~~r~~LA~~LgLs~rqVqvWFQNRRaK~Krkq~~ 207 (293)
+++.|++|+..|+..|++.|+..+|++..+|.+||..|+|++.||+.||||||+|.||.++.
T Consensus 100 r~K~Rtvfs~~ql~~l~~rFe~QrYLS~~e~~ELan~L~LS~~QVKTWFQNrRMK~Kk~~r~ 161 (194)
T KOG0491|consen 100 RRKARTVFSDPQLSGLEKRFERQRYLSTPERQELANALSLSETQVKTWFQNRRMKHKKQQRN 161 (194)
T ss_pred hhhhcccccCccccccHHHHhhhhhcccHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHHHhc
Confidence 45569999999999999999999999999999999999999999999999999999986653
No 23
>COG5576 Homeodomain-containing transcription factor [Transcription]
Probab=99.42 E-value=1.8e-13 Score=118.06 Aligned_cols=66 Identities=32% Similarity=0.506 Sum_probs=60.3
Q ss_pred ccCCCCCCCCcCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCCCeeeeechhhhHHHHhhhhh
Q 022713 142 EDGVNARKKLRLTKEQSALLEESFKQHSTLNPKQKQALARQLNLRPRQVEVWFQNRRARTKLKQTE 207 (293)
Q Consensus 142 ~~~~~rR~Rt~ft~~Ql~~Le~~F~~~~~ps~~~r~~LA~~LgLs~rqVqvWFQNRRaK~Krkq~~ 207 (293)
.....+++|++.+..|+.+|+..|..++||+...|..|+..|+|+++-||+||||||++.|++...
T Consensus 47 ~s~~~~~~r~R~t~~Q~~vL~~~F~i~p~Ps~~~r~~L~~~lnm~~ksVqIWFQNkR~~~k~~~~~ 112 (156)
T COG5576 47 GSSPPKSKRRRTTDEQLMVLEREFEINPYPSSITRIKLSLLLNMPPKSVQIWFQNKRAKEKKKRSG 112 (156)
T ss_pred CCCcCcccceechHHHHHHHHHHhccCCCCCHHHHHHHHHhcCCChhhhhhhhchHHHHHHHhccc
Confidence 334567888899999999999999999999999999999999999999999999999999986543
No 24
>KOG3802 consensus Transcription factor OCT-1, contains POU and HOX domains [Transcription]
Probab=99.39 E-value=3.1e-13 Score=130.09 Aligned_cols=63 Identities=24% Similarity=0.400 Sum_probs=59.0
Q ss_pred cCCCCCCCCcCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCCCeeeeechhhhHHHHhhh
Q 022713 143 DGVNARKKLRLTKEQSALLEESFKQHSTLNPKQKQALARQLNLRPRQVEVWFQNRRARTKLKQ 205 (293)
Q Consensus 143 ~~~~rR~Rt~ft~~Ql~~Le~~F~~~~~ps~~~r~~LA~~LgLs~rqVqvWFQNRRaK~Krkq 205 (293)
.+++|||||.|....+..||++|..|+.|+..++..||.+|+|.+.+|+|||+|||.|.||..
T Consensus 291 ~~RkRKKRTSie~~vr~aLE~~F~~npKPt~qEIt~iA~~L~leKEVVRVWFCNRRQkeKR~~ 353 (398)
T KOG3802|consen 291 QSRKRKKRTSIEVNVRGALEKHFLKNPKPTSQEITHIAESLQLEKEVVRVWFCNRRQKEKRIT 353 (398)
T ss_pred cccccccccceeHHHHHHHHHHHHhCCCCCHHHHHHHHHHhccccceEEEEeeccccccccCC
Confidence 346788899999999999999999999999999999999999999999999999999999743
No 25
>KOG0847 consensus Transcription factor, contains HOX domain [Transcription]
Probab=99.35 E-value=1.9e-13 Score=122.43 Aligned_cols=65 Identities=34% Similarity=0.529 Sum_probs=60.4
Q ss_pred CccCCCCCCCCcCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCCCeeeeechhhhHHHHhhh
Q 022713 141 DEDGVNARKKLRLTKEQSALLEESFKQHSTLNPKQKQALARQLNLRPRQVEVWFQNRRARTKLKQ 205 (293)
Q Consensus 141 ~~~~~~rR~Rt~ft~~Ql~~Le~~F~~~~~ps~~~r~~LA~~LgLs~rqVqvWFQNRRaK~Krkq 205 (293)
+.+|+++..|.+|+-.|+..||..|++.+|+-..+|.+||..+|+++.||+|||||||.||||+.
T Consensus 162 ~kdG~rk~srPTf~g~qi~~le~~feqtkylaG~~ra~lA~~lgmteSqvkVWFQNRRTKWRKkh 226 (288)
T KOG0847|consen 162 NLNGQRKQSRPTFTGHQIYQLERKFEQTKYLAGADRAQLAQELNMTESQVKVWFQNRRTKWRKKH 226 (288)
T ss_pred CcCccccccCCCccchhhhhhhhhhhhhhcccchhHHHhhccccccHHHHHHHHhcchhhhhhhh
Confidence 35677777788999999999999999999999999999999999999999999999999999864
No 26
>KOG0490 consensus Transcription factor, contains HOX domain [General function prediction only]
Probab=99.17 E-value=1.4e-11 Score=110.27 Aligned_cols=63 Identities=27% Similarity=0.318 Sum_probs=59.2
Q ss_pred cCCCCCCCCcCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCCCeeeeechhhhHHHHhhh
Q 022713 143 DGVNARKKLRLTKEQSALLEESFKQHSTLNPKQKQALARQLNLRPRQVEVWFQNRRARTKLKQ 205 (293)
Q Consensus 143 ~~~~rR~Rt~ft~~Ql~~Le~~F~~~~~ps~~~r~~LA~~LgLs~rqVqvWFQNRRaK~Krkq 205 (293)
..++||.|+.|+..|+.+||+.|...+||+...|+.||..+++++..|+|||||||+||+++.
T Consensus 57 ~~~~rr~rt~~~~~ql~~ler~f~~~h~Pd~~~r~~la~~~~~~e~rVqvwFqnrrak~r~~~ 119 (235)
T KOG0490|consen 57 KFSKRCARCKFTISQLDELERAFEKVHLPCFACRECLALLLTGDEFRVQVWFQNRRAKDRKEE 119 (235)
T ss_pred hccccccCCCCCcCHHHHHHHhhcCCCcCccchHHHHhhcCCCCeeeeehhhhhhcHhhhhhh
Confidence 345788899999999999999999999999999999999999999999999999999999765
No 27
>smart00340 HALZ homeobox associated leucin zipper.
Probab=99.00 E-value=5.5e-10 Score=75.27 Aligned_cols=44 Identities=75% Similarity=1.257 Sum_probs=41.5
Q ss_pred hhhhhhhHHHHHHhhHhhHHHHHHHHHHHHHHHhhhcCCccccC
Q 022713 204 KQTEVDCEFLKKCCETLTDENRRLHKELQELKALKLAQPLYMHM 247 (293)
Q Consensus 204 kq~~~~~e~Lk~~~~~l~~en~~l~~e~~~l~al~~~~~~~~~~ 247 (293)
+|+++||++||+||+.|.+||++|++|+++|++++.+.|+||++
T Consensus 1 KQTEvdCe~LKrcce~LteeNrRL~ke~~eLralk~~~~~~m~~ 44 (44)
T smart00340 1 KQTEVDCELLKRCCESLTEENRRLQKEVQELRALKLSPPLYMQH 44 (44)
T ss_pred CchHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcccCCcccccC
Confidence 58899999999999999999999999999999999999999863
No 28
>KOG1168 consensus Transcription factor ACJ6/BRN-3, contains POU and HOX domains [Transcription]
Probab=98.95 E-value=6.5e-10 Score=103.37 Aligned_cols=63 Identities=27% Similarity=0.454 Sum_probs=59.0
Q ss_pred cCCCCCCCCcCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCCCeeeeechhhhHHHHhhh
Q 022713 143 DGVNARKKLRLTKEQSALLEESFKQHSTLNPKQKQALARQLNLRPRQVEVWFQNRRARTKLKQ 205 (293)
Q Consensus 143 ~~~~rR~Rt~ft~~Ql~~Le~~F~~~~~ps~~~r~~LA~~LgLs~rqVqvWFQNRRaK~Krkq 205 (293)
.+.+|||||.+-....+.||++|...+.|+.+.+..||++|.|.+..|+|||+|.|.|.||.+
T Consensus 306 ~~ekKRKRTSIAAPEKRsLEayFavQPRPS~EkIAaIAekLDLKKNVVRVWFCNQRQKQKRm~ 368 (385)
T KOG1168|consen 306 GGEKKRKRTSIAAPEKRSLEAYFAVQPRPSGEKIAAIAEKLDLKKNVVRVWFCNQRQKQKRMK 368 (385)
T ss_pred ccccccccccccCcccccHHHHhccCCCCchhHHHHHHHhhhhhhceEEEEeeccHHHHHHhh
Confidence 456889999999999999999999999999999999999999999999999999999988744
No 29
>KOG0849 consensus Transcription factor PRD and related proteins, contain PAX and HOX domains [Transcription]
Probab=98.92 E-value=5.4e-10 Score=108.06 Aligned_cols=64 Identities=28% Similarity=0.459 Sum_probs=59.1
Q ss_pred cCCCCCCCCcCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCCCeeeeechhhhHHHHhhhh
Q 022713 143 DGVNARKKLRLTKEQSALLEESFKQHSTLNPKQKQALARQLNLRPRQVEVWFQNRRARTKLKQT 206 (293)
Q Consensus 143 ~~~~rR~Rt~ft~~Ql~~Le~~F~~~~~ps~~~r~~LA~~LgLs~rqVqvWFQNRRaK~Krkq~ 206 (293)
+.+.+|.|++|+..|+..|++.|+.++||+...|++||.++++++..|+|||+|||+|++|...
T Consensus 173 ~~~~rr~rtsft~~Q~~~le~~f~rt~yP~i~~Re~La~~i~l~e~riqvwf~nrra~~rr~~~ 236 (354)
T KOG0849|consen 173 QRGGRRNRTSFSPSQLEALEECFQRTPYPDIVGRETLAKETGLPEPRVQVWFQNRRAKWRRQHR 236 (354)
T ss_pred cccccccccccccchHHHHHHHhcCCCCCchhhHHHHhhhccCCchHHHHHHhhhhhhhhhccc
Confidence 3446777899999999999999999999999999999999999999999999999999998653
No 30
>KOG0775 consensus Transcription factor SIX and related HOX domain proteins [Transcription]
Probab=98.76 E-value=5.1e-09 Score=96.80 Aligned_cols=51 Identities=33% Similarity=0.574 Sum_probs=47.9
Q ss_pred CCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCCCeeeeechhhhHHHHh
Q 022713 153 LTKEQSALLEESFKQHSTLNPKQKQALARQLNLRPRQVEVWFQNRRARTKL 203 (293)
Q Consensus 153 ft~~Ql~~Le~~F~~~~~ps~~~r~~LA~~LgLs~rqVqvWFQNRRaK~Kr 203 (293)
|...-..+|+.+|.+++||++.++.+||+.+||+..||-.||+|||.|+|-
T Consensus 183 FKekSR~~LrewY~~~~YPsp~eKReLA~aTgLt~tQVsNWFKNRRQRDRa 233 (304)
T KOG0775|consen 183 FKEKSRSLLREWYLQNPYPSPREKRELAEATGLTITQVSNWFKNRRQRDRA 233 (304)
T ss_pred hhHhhHHHHHHHHhcCCCCChHHHHHHHHHhCCchhhhhhhhhhhhhhhhh
Confidence 566668899999999999999999999999999999999999999999983
No 31
>KOG0774 consensus Transcription factor PBX and related HOX domain proteins [Transcription]
Probab=98.67 E-value=7.2e-08 Score=88.76 Aligned_cols=58 Identities=33% Similarity=0.512 Sum_probs=54.5
Q ss_pred CCCCCCcCCHHHHHHHHHHHhh---CCCCCHHHHHHHHHHhCCCCCeeeeechhhhHHHHh
Q 022713 146 NARKKLRLTKEQSALLEESFKQ---HSTLNPKQKQALARQLNLRPRQVEVWFQNRRARTKL 203 (293)
Q Consensus 146 ~rR~Rt~ft~~Ql~~Le~~F~~---~~~ps~~~r~~LA~~LgLs~rqVqvWFQNRRaK~Kr 203 (293)
.+|||+.|++.-..+|..+|.. ++||+.+.+++||+++|++..||-.||.|+|.+.||
T Consensus 188 arRKRRNFsK~aTeiLneyF~~h~~nPYPSee~K~eLAkqCnItvsQvsnwfgnkrIrykK 248 (334)
T KOG0774|consen 188 ARRKRRNFSKQATEILNEYFYSHLSNPYPSEEAKEELAKQCNITVSQVSNWFGNKRIRYKK 248 (334)
T ss_pred HHHhhcccchhHHHHHHHHHHHhcCCCCCcHHHHHHHHHHcCceehhhccccccceeehhh
Confidence 4788889999999999999964 889999999999999999999999999999999986
No 32
>KOG2252 consensus CCAAT displacement protein and related homeoproteins [Transcription]
Probab=98.26 E-value=5.3e-07 Score=90.36 Aligned_cols=62 Identities=26% Similarity=0.340 Sum_probs=56.7
Q ss_pred CccCCCCCCCCcCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCCCeeeeechhhhHHHH
Q 022713 141 DEDGVNARKKLRLTKEQSALLEESFKQHSTLNPKQKQALARQLNLRPRQVEVWFQNRRARTK 202 (293)
Q Consensus 141 ~~~~~~rR~Rt~ft~~Ql~~Le~~F~~~~~ps~~~r~~LA~~LgLs~rqVqvWFQNRRaK~K 202 (293)
+...+.||.|.+||..|.+.|..+|+.+++|+.++.+.|+.+|+|..+.|.+||-|-|.|.+
T Consensus 415 d~~~~~KKPRlVfTd~QkrTL~aiFke~~RPS~Emq~tIS~qL~L~~sTV~NfFmNaRRRsl 476 (558)
T KOG2252|consen 415 DKMLQTKKPRLVFTDIQKRTLQAIFKENKRPSREMQETISQQLNLELSTVINFFMNARRRSL 476 (558)
T ss_pred cccccCCCceeeecHHHHHHHHHHHhcCCCCCHHHHHHHHHHhCCcHHHHHHHHHhhhhhcc
Confidence 34445678899999999999999999999999999999999999999999999999998864
No 33
>PF05920 Homeobox_KN: Homeobox KN domain; InterPro: IPR008422 This entry represents a homeobox transcription factor KN domain conserved from fungi to human and plants [].; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent, 0005634 nucleus; PDB: 3K2A_B 2LK2_A 1X2N_A 2DMN_A.
Probab=98.20 E-value=3.2e-07 Score=61.97 Aligned_cols=34 Identities=32% Similarity=0.572 Sum_probs=29.1
Q ss_pred hCCCCCHHHHHHHHHHhCCCCCeeeeechhhhHH
Q 022713 167 QHSTLNPKQKQALARQLNLRPRQVEVWFQNRRAR 200 (293)
Q Consensus 167 ~~~~ps~~~r~~LA~~LgLs~rqVqvWFQNRRaK 200 (293)
.++||+..+++.||.++||+..||..||-|.|.|
T Consensus 7 ~nPYPs~~ek~~L~~~tgls~~Qi~~WF~NaRrR 40 (40)
T PF05920_consen 7 HNPYPSKEEKEELAKQTGLSRKQISNWFINARRR 40 (40)
T ss_dssp TSGS--HHHHHHHHHHHTS-HHHHHHHHHHHHHH
T ss_pred CCCCCCHHHHHHHHHHcCCCHHHHHHHHHHhHcc
Confidence 4789999999999999999999999999999975
No 34
>KOG0490 consensus Transcription factor, contains HOX domain [General function prediction only]
Probab=98.00 E-value=4.8e-06 Score=74.48 Aligned_cols=63 Identities=29% Similarity=0.530 Sum_probs=58.2
Q ss_pred cCCCCCCCCcCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCCCeeeeechhhhHHHHhhh
Q 022713 143 DGVNARKKLRLTKEQSALLEESFKQHSTLNPKQKQALARQLNLRPRQVEVWFQNRRARTKLKQ 205 (293)
Q Consensus 143 ~~~~rR~Rt~ft~~Ql~~Le~~F~~~~~ps~~~r~~LA~~LgLs~rqVqvWFQNRRaK~Krkq 205 (293)
..+.++.|+.+...|+..|...|....+|+...+..|+..+|+.++.|++||||+|++.++..
T Consensus 150 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~P~~~~~~~l~~~~~~~~~~~q~~~~~~~~~~~~~~ 212 (235)
T KOG0490|consen 150 NKKPRRPRTTFTENQLEVLETVFRATPKPDADDREQLAEETGLSERVIQVWFQNRRAKLRKHK 212 (235)
T ss_pred ccccCCCccccccchhHhhhhcccCCCCCchhhHHHHHHhcCCChhhhhhhcccHHHHHHhhc
Confidence 345677889999999999999999999999999999999999999999999999999998754
No 35
>KOG1146 consensus Homeobox protein [General function prediction only]
Probab=97.45 E-value=7.7e-05 Score=81.31 Aligned_cols=61 Identities=21% Similarity=0.392 Sum_probs=57.0
Q ss_pred CCCCCCcCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCCCeeeeechhhhHHHHhhhh
Q 022713 146 NARKKLRLTKEQSALLEESFKQHSTLNPKQKQALARQLNLRPRQVEVWFQNRRARTKLKQT 206 (293)
Q Consensus 146 ~rR~Rt~ft~~Ql~~Le~~F~~~~~ps~~~r~~LA~~LgLs~rqVqvWFQNRRaK~Krkq~ 206 (293)
+|++|++++..|+..|..+|....||...+.+.|...+++..+.|+|||||-|+|.|+...
T Consensus 903 r~a~~~~~~d~qlk~i~~~~~~q~~~~~~~~E~l~~~~~~~~~~i~vw~qna~~~s~k~~~ 963 (1406)
T KOG1146|consen 903 RRAYRTQESDLQLKIIKACYEAQRTPTMQECEVLEEPIGLPKRVIQVWFQNARAKSKKAKL 963 (1406)
T ss_pred hhhhccchhHHHHHHHHHHHhhccCChHHHHHhhcccccCCcchhHHhhhhhhhhhhhhhh
Confidence 5678999999999999999999999999999999999999999999999999999987543
No 36
>KOG0773 consensus Transcription factor MEIS1 and related HOX domain proteins [Transcription]
Probab=96.78 E-value=0.00075 Score=64.72 Aligned_cols=58 Identities=31% Similarity=0.359 Sum_probs=49.3
Q ss_pred CCCCCCcCCHHHHHHHHHHHhh---CCCCCHHHHHHHHHHhCCCCCeeeeechhhhHHHHh
Q 022713 146 NARKKLRLTKEQSALLEESFKQ---HSTLNPKQKQALARQLNLRPRQVEVWFQNRRARTKL 203 (293)
Q Consensus 146 ~rR~Rt~ft~~Ql~~Le~~F~~---~~~ps~~~r~~LA~~LgLs~rqVqvWFQNRRaK~Kr 203 (293)
+.|.+..|....+.+|+.+... ++||+..++..||.++||+..||.+||-|.|.|..+
T Consensus 239 ~~r~~~~lP~~a~~ilr~Wl~~h~~~PYPse~~K~~La~~TGLs~~Qv~NWFINaR~R~w~ 299 (342)
T KOG0773|consen 239 KWRPQRGLPKEAVSILRAWLFEHLLHPYPSDDEKLMLAKQTGLSRPQVSNWFINARVRLWK 299 (342)
T ss_pred CCCCCCCCCHHHHHHHHHHHHHhccCCCCcchhccccchhcCCCcccCCchhhhcccccCC
Confidence 3445557999999999988433 579999999999999999999999999999987654
No 37
>PF11569 Homez: Homeodomain leucine-zipper encoding, Homez; PDB: 2YS9_A.
Probab=96.30 E-value=0.00089 Score=48.41 Aligned_cols=42 Identities=24% Similarity=0.430 Sum_probs=31.4
Q ss_pred HHHHHHHHHhhCCCCCHHHHHHHHHHhCCCCCeeeeechhhh
Q 022713 157 QSALLEESFKQHSTLNPKQKQALARQLNLRPRQVEVWFQNRR 198 (293)
Q Consensus 157 Ql~~Le~~F~~~~~ps~~~r~~LA~~LgLs~rqVqvWFQNRR 198 (293)
-+..|+++|..++++.......|..+.+|+..||+.||--|+
T Consensus 9 d~~pL~~Yy~~h~~L~E~DL~~L~~kS~ms~qqVr~WFa~~~ 50 (56)
T PF11569_consen 9 DIQPLEDYYLKHKQLQEEDLDELCDKSRMSYQQVRDWFAERM 50 (56)
T ss_dssp --HHHHHHHHHT----TTHHHHHHHHTT--HHHHHHHHHHHS
T ss_pred chHHHHHHHHHcCCccHhhHHHHHHHHCCCHHHHHHHHHHhc
Confidence 356799999999999999999999999999999999997554
No 38
>PF02183 HALZ: Homeobox associated leucine zipper; InterPro: IPR003106 This region is a plant specific leucine zipper that is always found associated with a homeobox []. ; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent, 0005634 nucleus
Probab=95.19 E-value=0.04 Score=38.13 Aligned_cols=35 Identities=37% Similarity=0.409 Sum_probs=30.7
Q ss_pred hhhhhhhHHHHHHhhHhhHHHHHHHHHHHHHHHhh
Q 022713 204 KQTEVDCEFLKKCCETLTDENRRLHKELQELKALK 238 (293)
Q Consensus 204 kq~~~~~e~Lk~~~~~l~~en~~l~~e~~~l~al~ 238 (293)
+|.+.|++.|+.+++.|..++++|.+|.+.|.+..
T Consensus 1 KQlE~Dy~~LK~~yd~Lk~~~~~L~~E~~~L~aev 35 (45)
T PF02183_consen 1 KQLERDYDALKASYDSLKAEYDSLKKENEKLRAEV 35 (45)
T ss_pred CchHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 47889999999999999999999999999887643
No 39
>KOG3623 consensus Homeobox transcription factor SIP1 [Transcription]
Probab=94.24 E-value=0.027 Score=59.04 Aligned_cols=48 Identities=19% Similarity=0.353 Sum_probs=44.9
Q ss_pred HHHHHHHHhhCCCCCHHHHHHHHHHhCCCCCeeeeechhhhHHHHhhh
Q 022713 158 SALLEESFKQHSTLNPKQKQALARQLNLRPRQVEVWFQNRRARTKLKQ 205 (293)
Q Consensus 158 l~~Le~~F~~~~~ps~~~r~~LA~~LgLs~rqVqvWFQNRRaK~Krkq 205 (293)
+.+|..+|..|..|+..+...||.+.||..+.|++||+++++....-+
T Consensus 568 ~sllkayyaln~~ps~eelskia~qvglp~~vvk~wfE~~~a~e~sv~ 615 (1007)
T KOG3623|consen 568 TSLLKAYYALNGLPSEEELSKIAQQVGLPFAVVKAWFEDEEAEEMSVE 615 (1007)
T ss_pred HHHHHHHHHhcCCCCHHHHHHHHHHhcccHHHHHHHHHhhhhhhhhhc
Confidence 788999999999999999999999999999999999999999887644
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=92.00 E-value=0.19 Score=35.59 Aligned_cols=47 Identities=21% Similarity=0.350 Sum_probs=35.1
Q ss_pred CCCCCcCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCCCeeeeechhhh
Q 022713 147 ARKKLRLTKEQSALLEESFKQHSTLNPKQKQALARQLNLRPRQVEVWFQNRR 198 (293)
Q Consensus 147 rR~Rt~ft~~Ql~~Le~~F~~~~~ps~~~r~~LA~~LgLs~rqVqvWFQNRR 198 (293)
||+|..+|-++...+-..++... ....||.++|+...+|..|..|+.
T Consensus 1 krkR~~LTl~eK~~iI~~~e~g~-----s~~~ia~~fgv~~sTv~~I~K~k~ 47 (53)
T PF04218_consen 1 KRKRKSLTLEEKLEIIKRLEEGE-----SKRDIAREFGVSRSTVSTILKNKD 47 (53)
T ss_dssp SSSSSS--HHHHHHHHHHHHCTT------HHHHHHHHT--CCHHHHHHHCHH
T ss_pred CCCCccCCHHHHHHHHHHHHcCC-----CHHHHHHHhCCCHHHHHHHHHhHH
Confidence 57888999999888877787665 477899999999999999998753
No 41
>PRK09413 IS2 repressor TnpA; Reviewed
Probab=90.78 E-value=1.5 Score=35.95 Aligned_cols=79 Identities=18% Similarity=0.194 Sum_probs=44.7
Q ss_pred CCCcCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCCCeeeeechhhhHH--------------HHhhhhhhhhHHHH
Q 022713 149 KKLRLTKEQSALLEESFKQHSTLNPKQKQALARQLNLRPRQVEVWFQNRRAR--------------TKLKQTEVDCEFLK 214 (293)
Q Consensus 149 ~Rt~ft~~Ql~~Le~~F~~~~~ps~~~r~~LA~~LgLs~rqVqvWFQNRRaK--------------~Krkq~~~~~e~Lk 214 (293)
+|.+|+.++....-.....+.+ ...++|.++|++..+|..|.+--+.. ....+.+.++..|+
T Consensus 9 ~rr~ys~EfK~~aV~~~~~~g~----sv~evA~e~gIs~~tl~~W~r~y~~~~~~~~~~~~~~~~~~~~~~~~~ei~~L~ 84 (121)
T PRK09413 9 KRRRRTTQEKIAIVQQSFEPGM----TVSLVARQHGVAASQLFLWRKQYQEGSLTAVAAGEQVVPASELAAAMKQIKELQ 84 (121)
T ss_pred CCCCCCHHHHHHHHHHHHcCCC----CHHHHHHHHCcCHHHHHHHHHHHhhcccccccccccCCchhHHHHHHHHHHHHH
Confidence 4556888775443333333332 34578999999999999996532211 01112334445555
Q ss_pred HHhhHhhHHHHHHHHHH
Q 022713 215 KCCETLTDENRRLHKEL 231 (293)
Q Consensus 215 ~~~~~l~~en~~l~~e~ 231 (293)
+....|..|++-|++.+
T Consensus 85 ~el~~L~~E~diLKKa~ 101 (121)
T PRK09413 85 RLLGKKTMENELLKEAV 101 (121)
T ss_pred HHHHHHHHHHHHHHHHH
Confidence 66666666665555543
No 42
>PF04618 HD-ZIP_N: HD-ZIP protein N terminus; InterPro: IPR006712 Homeodomain leucine zipper (HDZip) genes encode putative transcription factors that are unique to plants. This observation suggests that homeobox-leucine zipper genes evolved after the divergence of plants and animals, perhaps to mediate specific regulatory events []. This domain is the N-terminal of plant homeobox-leucine zipper proteins. Its function is unknown.; GO: 0006351 transcription, DNA-dependent, 0005634 nucleus
Probab=83.05 E-value=5.8 Score=32.63 Aligned_cols=34 Identities=32% Similarity=0.310 Sum_probs=18.5
Q ss_pred CCcccccCCCccccccchhhhhccCCCCCCCCCCCCCCC
Q 022713 73 SNSIDVNKGYEESAAAGVAEYQILNRQASPHSAVSNSFS 111 (293)
Q Consensus 73 ~~~i~~~~~~~~s~~~~~~~s~~l~~~~Sp~S~~s~s~S 111 (293)
.-.|||+-.+....+ +-.+....+||+|.+| |+|
T Consensus 70 lRgiDVNr~p~~~~~----d~eEe~gvSSPNStiS-S~s 103 (111)
T PF04618_consen 70 LRGIDVNRLPSTVEA----DCEEEAGVSSPNSTIS-SVS 103 (111)
T ss_pred ccceeccCCCccccc----cccccccccCCCccce-ecc
Confidence 347777764442211 1123355778888887 444
No 43
>KOG4196 consensus bZIP transcription factor MafK [Transcription]
Probab=79.16 E-value=7.6 Score=32.84 Aligned_cols=74 Identities=28% Similarity=0.313 Sum_probs=49.1
Q ss_pred CcCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCCCeeeeechhhhH----------HHHhhh----hhhhhHHHHHH
Q 022713 151 LRLTKEQSALLEESFKQHSTLNPKQKQALARQLNLRPRQVEVWFQNRRA----------RTKLKQ----TEVDCEFLKKC 216 (293)
Q Consensus 151 t~ft~~Ql~~Le~~F~~~~~ps~~~r~~LA~~LgLs~rqVqvWFQNRRa----------K~Krkq----~~~~~e~Lk~~ 216 (293)
.+|+.+++..+- .|+.-=+--|++...|-.|=|-||+ |.|+-+ .+.+...|.++
T Consensus 22 d~lsDd~LvsmS------------VReLNr~LrG~~reEVvrlKQrRRTLKNRGYA~sCR~KRv~Qk~eLE~~k~~L~qq 89 (135)
T KOG4196|consen 22 DRLSDDELVSMS------------VRELNRHLRGLSREEVVRLKQRRRTLKNRGYAQSCRVKRVQQKHELEKEKAELQQQ 89 (135)
T ss_pred CCcCHHHHHHhh------------HHHHHHHhcCCCHHHHHHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 478888876652 2222223347788888888888874 334433 33444567778
Q ss_pred hhHhhHHHHHHHHHHHHHHH
Q 022713 217 CETLTDENRRLHKELQELKA 236 (293)
Q Consensus 217 ~~~l~~en~~l~~e~~~l~a 236 (293)
.+.|.+||.+++.|++.++.
T Consensus 90 v~~L~~e~s~~~~E~da~k~ 109 (135)
T KOG4196|consen 90 VEKLKEENSRLRRELDAYKS 109 (135)
T ss_pred HHHHHHHHHHHHHHHHHHHH
Confidence 88999999999999887743
No 44
>PF02183 HALZ: Homeobox associated leucine zipper; InterPro: IPR003106 This region is a plant specific leucine zipper that is always found associated with a homeobox []. ; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent, 0005634 nucleus
Probab=78.28 E-value=5.4 Score=27.51 Aligned_cols=31 Identities=35% Similarity=0.491 Sum_probs=27.4
Q ss_pred hhhhhHHHHHHhhHhhHHHHHHHHHHHHHHH
Q 022713 206 TEVDCEFLKKCCETLTDENRRLHKELQELKA 236 (293)
Q Consensus 206 ~~~~~e~Lk~~~~~l~~en~~l~~e~~~l~a 236 (293)
....++.|+..++.|..||..|+.++..++.
T Consensus 10 LK~~yd~Lk~~~~~L~~E~~~L~aev~~L~~ 40 (45)
T PF02183_consen 10 LKASYDSLKAEYDSLKKENEKLRAEVQELKE 40 (45)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 4567889999999999999999999998865
No 45
>PRK00888 ftsB cell division protein FtsB; Reviewed
Probab=68.13 E-value=7.9 Score=31.28 Aligned_cols=46 Identities=20% Similarity=0.335 Sum_probs=26.1
Q ss_pred eeeeechhhhHHHHhhhhhhhhHHHHHHhhHhhHHHHHHHHHHHHHH
Q 022713 189 QVEVWFQNRRARTKLKQTEVDCEFLKKCCETLTDENRRLHKELQELK 235 (293)
Q Consensus 189 qVqvWFQNRRaK~Krkq~~~~~e~Lk~~~~~l~~en~~l~~e~~~l~ 235 (293)
++..||++.-- .+-.+.+.+.+.+++..+.+..+|++|+.++..|+
T Consensus 16 ~y~l~~g~~G~-~~~~~l~~q~~~~~~e~~~l~~~n~~L~~eI~~L~ 61 (105)
T PRK00888 16 QYSLWFGKNGI-LDYWRVNDQVAAQQQTNAKLKARNDQLFAEIDDLK 61 (105)
T ss_pred HHHHhccCCcH-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Confidence 34578755411 11123334555666666777777777777776663
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=64.98 E-value=4.2 Score=27.70 Aligned_cols=39 Identities=10% Similarity=0.215 Sum_probs=29.1
Q ss_pred cCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCCCeeeeech
Q 022713 152 RLTKEQSALLEESFKQHSTLNPKQKQALARQLNLRPRQVEVWFQ 195 (293)
Q Consensus 152 ~ft~~Ql~~Le~~F~~~~~ps~~~r~~LA~~LgLs~rqVqvWFQ 195 (293)
.+++.+..+|...|... ..-.++|..+|++...|+.|..
T Consensus 4 ~L~~~er~vi~~~y~~~-----~t~~eIa~~lg~s~~~V~~~~~ 42 (50)
T PF04545_consen 4 QLPPREREVIRLRYFEG-----LTLEEIAERLGISRSTVRRILK 42 (50)
T ss_dssp TS-HHHHHHHHHHHTST------SHHHHHHHHTSCHHHHHHHHH
T ss_pred hCCHHHHHHHHHHhcCC-----CCHHHHHHHHCCcHHHHHHHHH
Confidence 47888999999999332 2357899999999988876654
No 47
>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=64.92 E-value=1 Score=33.10 Aligned_cols=44 Identities=18% Similarity=0.335 Sum_probs=28.0
Q ss_pred CCCCcCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCCCeeeeech
Q 022713 148 RKKLRLTKEQSALLEESFKQHSTLNPKQKQALARQLNLRPRQVEVWFQ 195 (293)
Q Consensus 148 R~Rt~ft~~Ql~~Le~~F~~~~~ps~~~r~~LA~~LgLs~rqVqvWFQ 195 (293)
++|.+|+.++...+-..+.. ......++|.++||++.+|..|-.
T Consensus 2 ~~r~~ys~e~K~~~v~~~~~----~g~sv~~va~~~gi~~~~l~~W~~ 45 (76)
T PF01527_consen 2 RKRRRYSPEFKLQAVREYLE----SGESVSEVAREYGISPSTLYNWRK 45 (76)
T ss_dssp -SS----HHHHHHHHHHHHH----HHCHHHHHHHHHTS-HHHHHHHHH
T ss_pred CCCCCCCHHHHHHHHHHHHH----CCCceEeeecccccccccccHHHH
Confidence 45678999887776666522 124577899999999999998864
No 48
>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=59.53 E-value=3.7 Score=26.85 Aligned_cols=43 Identities=12% Similarity=0.182 Sum_probs=31.4
Q ss_pred cCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCCCeeeeechhhhH
Q 022713 152 RLTKEQSALLEESFKQHSTLNPKQKQALARQLNLRPRQVEVWFQNRRA 199 (293)
Q Consensus 152 ~ft~~Ql~~Le~~F~~~~~ps~~~r~~LA~~LgLs~rqVqvWFQNRRa 199 (293)
.++..+..++...|... ....++|..+|++...|..|....+.
T Consensus 10 ~l~~~~~~~~~~~~~~~-----~~~~~ia~~~~~s~~~i~~~~~~~~~ 52 (55)
T cd06171 10 KLPEREREVILLRFGEG-----LSYEEIAEILGISRSTVRQRLHRALK 52 (55)
T ss_pred hCCHHHHHHHHHHHhcC-----CCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 46777888888777432 23567899999999999888765443
No 49
>KOG3623 consensus Homeobox transcription factor SIP1 [Transcription]
Probab=55.83 E-value=8.7 Score=41.06 Aligned_cols=61 Identities=16% Similarity=0.298 Sum_probs=47.4
Q ss_pred CCCCCCcCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCCCeeeeechhhhHHHHhhhh
Q 022713 146 NARKKLRLTKEQSALLEESFKQHSTLNPKQKQALARQLNLRPRQVEVWFQNRRARTKLKQT 206 (293)
Q Consensus 146 ~rR~Rt~ft~~Ql~~Le~~F~~~~~ps~~~r~~LA~~LgLs~rqVqvWFQNRRaK~Krkq~ 206 (293)
.-|.|+....++-..|..+|..+-.++..+-..++.+|...+..|+|||++|+..-+....
T Consensus 626 p~kv~sp~k~~dq~ql~~a~elq~s~~n~~~pl~~t~~~n~~pv~ev~dhsrsstpsp~pl 686 (1007)
T KOG3623|consen 626 PVKVRSPIKEEDQQQLKQAYELQASPSNDEFPLIATRLQNDPPVVEVWDHSRSSTPSPMPL 686 (1007)
T ss_pred CccccCCCCccchhhhHhhhhcccCccCcccchhhhhccCCCcchhhcccCCCCCCCCCcc
Confidence 3345666777778888888888777777766667777888899999999999988776443
No 50
>KOG1146 consensus Homeobox protein [General function prediction only]
Probab=54.80 E-value=5.9 Score=44.63 Aligned_cols=57 Identities=18% Similarity=0.088 Sum_probs=50.7
Q ss_pred CCCCCcCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCCCeeeeechhhhHHHHh
Q 022713 147 ARKKLRLTKEQSALLEESFKQHSTLNPKQKQALARQLNLRPRQVEVWFQNRRARTKL 203 (293)
Q Consensus 147 rR~Rt~ft~~Ql~~Le~~F~~~~~ps~~~r~~LA~~LgLs~rqVqvWFQNRRaK~Kr 203 (293)
+-.|++++.-|..+|..+|+...+|.-.++..++.-|++..|.+-.||++++.++.+
T Consensus 445 ~~~s~r~~~~~t~~L~S~~kt~~cpkc~~~yk~a~~L~vhmRskhp~~~~~~c~~gq 501 (1406)
T KOG1146|consen 445 LLESKRSLEGQTVVLHSFFKTLKCPKCNWHYKLAQTLGVHMRSKHPESQSAYCKAGQ 501 (1406)
T ss_pred hhhhhcccccceeeeecccccccCCccchhhhhHHHhhhcccccccccchhHhHhcc
Confidence 334778999999999999999999999999999999999999988888888777764
No 51
>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=53.49 E-value=14 Score=21.31 Aligned_cols=38 Identities=18% Similarity=0.225 Sum_probs=25.7
Q ss_pred cCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCCCeeeeec
Q 022713 152 RLTKEQSALLEESFKQHSTLNPKQKQALARQLNLRPRQVEVWF 194 (293)
Q Consensus 152 ~ft~~Ql~~Le~~F~~~~~ps~~~r~~LA~~LgLs~rqVqvWF 194 (293)
.++..+...+...|... + ...++|..++++...|..|.
T Consensus 5 ~~~~~~~~~i~~~~~~~-~----s~~~ia~~~~is~~tv~~~~ 42 (42)
T cd00569 5 KLTPEQIEEARRLLAAG-E----SVAEIARRLGVSRSTLYRYL 42 (42)
T ss_pred cCCHHHHHHHHHHHHcC-C----CHHHHHHHHCCCHHHHHHhC
Confidence 46666666666666532 2 45678899999887776663
No 52
>KOG3119 consensus Basic region leucine zipper transcription factor [Transcription]
Probab=51.90 E-value=46 Score=31.21 Aligned_cols=32 Identities=34% Similarity=0.342 Sum_probs=21.9
Q ss_pred hhhHHHHHHhhHhhHHHHHHHHHHHHHHHhhh
Q 022713 208 VDCEFLKKCCETLTDENRRLHKELQELKALKL 239 (293)
Q Consensus 208 ~~~e~Lk~~~~~l~~en~~l~~e~~~l~al~~ 239 (293)
.....|.++++.|..+...|++++..++.+..
T Consensus 222 ~r~~~leken~~lr~~v~~l~~el~~~~~~~~ 253 (269)
T KOG3119|consen 222 HRVAELEKENEALRTQVEQLKKELATLRRLFL 253 (269)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 33456667777777777777777777766653
No 53
>PF04967 HTH_10: HTH DNA binding domain; InterPro: IPR007050 Numerous bacterial transcription regulatory proteins bind DNA via a helix-turn-helix (HTH) motif. This entry represents the HTH DNA binding domain found in Halobacterium salinarium (Halobacterium halobium) and described as a putative bacterio-opsin activator.
Probab=49.45 E-value=20 Score=25.49 Aligned_cols=38 Identities=21% Similarity=0.273 Sum_probs=30.2
Q ss_pred CCHHHHHHHHHHHhhCCC--CCHHHHHHHHHHhCCCCCee
Q 022713 153 LTKEQSALLEESFKQHST--LNPKQKQALARQLNLRPRQV 190 (293)
Q Consensus 153 ft~~Ql~~Le~~F~~~~~--ps~~~r~~LA~~LgLs~rqV 190 (293)
+|..|..+|...|..--| |-.....+||.+||++..-|
T Consensus 1 LT~~Q~e~L~~A~~~GYfd~PR~~tl~elA~~lgis~st~ 40 (53)
T PF04967_consen 1 LTDRQREILKAAYELGYFDVPRRITLEELAEELGISKSTV 40 (53)
T ss_pred CCHHHHHHHHHHHHcCCCCCCCcCCHHHHHHHhCCCHHHH
Confidence 578999999999987544 55556689999999987653
No 54
>PF00170 bZIP_1: bZIP transcription factor cAMP response element binding (CREB) protein signature fos transforming protein signature jun transcription factor signature; InterPro: IPR011616 The basic-leucine zipper (bZIP) transcription factors [, ] of eukaryotic are proteins that contain a basic region mediating sequence-specific DNA-binding followed by a leucine zipper region (see IPR002158 from INTERPRO) required for dimerization.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0043565 sequence-specific DNA binding, 0046983 protein dimerization activity, 0006355 regulation of transcription, DNA-dependent; PDB: 2H7H_B 2OQQ_B 1S9K_E 1JNM_A 1JUN_A 1FOS_H 1A02_J 1T2K_C 1CI6_A 1DH3_C ....
Probab=47.93 E-value=74 Score=22.85 Aligned_cols=26 Identities=38% Similarity=0.417 Sum_probs=12.2
Q ss_pred hhHHHHHHhhHhhHHHHHHHHHHHHH
Q 022713 209 DCEFLKKCCETLTDENRRLHKELQEL 234 (293)
Q Consensus 209 ~~e~Lk~~~~~l~~en~~l~~e~~~l 234 (293)
.+..|...+..|..++..|+.++..|
T Consensus 34 ~~~~L~~en~~L~~~~~~L~~~~~~L 59 (64)
T PF00170_consen 34 KVEELESENEELKKELEQLKKEIQSL 59 (64)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 33444444444444444444444444
No 55
>PRK03975 tfx putative transcriptional regulator; Provisional
Probab=47.64 E-value=17 Score=31.08 Aligned_cols=48 Identities=19% Similarity=0.102 Sum_probs=35.9
Q ss_pred CCcCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCCCeeeeechhhhHHHHh
Q 022713 150 KLRLTKEQSALLEESFKQHSTLNPKQKQALARQLNLRPRQVEVWFQNRRARTKL 203 (293)
Q Consensus 150 Rt~ft~~Ql~~Le~~F~~~~~ps~~~r~~LA~~LgLs~rqVqvWFQNRRaK~Kr 203 (293)
...+++.|..+|...++ . ....+||..||++...|..|-++.+.+.|+
T Consensus 4 ~~~Lt~rqreVL~lr~~-G-----lTq~EIAe~LGiS~~tVs~ie~ra~kkLr~ 51 (141)
T PRK03975 4 ESFLTERQIEVLRLRER-G-----LTQQEIADILGTSRANVSSIEKRARENIEK 51 (141)
T ss_pred ccCCCHHHHHHHHHHHc-C-----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 34689999999988432 1 134689999999999999998866655554
No 56
>KOG4571 consensus Activating transcription factor 4 [Transcription]
Probab=45.98 E-value=41 Score=32.18 Aligned_cols=28 Identities=36% Similarity=0.444 Sum_probs=14.1
Q ss_pred hhHHHHHHhhHhhHHHHHHHHHHHHHHH
Q 022713 209 DCEFLKKCCETLTDENRRLHKELQELKA 236 (293)
Q Consensus 209 ~~e~Lk~~~~~l~~en~~l~~e~~~l~a 236 (293)
+++.|.+.++.|++...+|++|++.|+-
T Consensus 256 e~~~Le~rN~~LK~qa~~lerEI~ylKq 283 (294)
T KOG4571|consen 256 ELEGLEKRNEELKDQASELEREIRYLKQ 283 (294)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3444445555555555555555555543
No 57
>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=45.09 E-value=13 Score=25.43 Aligned_cols=41 Identities=17% Similarity=0.211 Sum_probs=27.5
Q ss_pred CCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCCCeeeeechhhh
Q 022713 153 LTKEQSALLEESFKQHSTLNPKQKQALARQLNLRPRQVEVWFQNRR 198 (293)
Q Consensus 153 ft~~Ql~~Le~~F~~~~~ps~~~r~~LA~~LgLs~rqVqvWFQNRR 198 (293)
+++.+..++...|-.. ..-.++|..+|+++..|+.|.+.-|
T Consensus 11 L~~~~r~i~~l~~~~g-----~s~~eIa~~l~~s~~~v~~~l~ra~ 51 (54)
T PF08281_consen 11 LPERQREIFLLRYFQG-----MSYAEIAEILGISESTVKRRLRRAR 51 (54)
T ss_dssp S-HHHHHHHHHHHTS--------HHHHHHHCTS-HHHHHHHHHHHH
T ss_pred CCHHHHHHHHHHHHHC-----cCHHHHHHHHCcCHHHHHHHHHHHH
Confidence 5666777776665433 3567899999999999999986433
No 58
>cd04787 HTH_HMRTR_unk Helix-Turn-Helix DNA binding domain of putative Heavy Metal Resistance transcription regulators. Putative helix-turn-helix (HTH) heavy metal resistance transcription regulators (HMRTR), unknown subgroup. Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to heavy metal stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules, such as, metal ions, drugs, and organic substrates. This subgroup lacks one of the c
Probab=43.43 E-value=61 Score=26.78 Aligned_cols=69 Identities=10% Similarity=0.072 Sum_probs=37.7
Q ss_pred CcCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCCCeeeeechhhhHHHHhhhhhhhhHHHHHHhhHhhHHHHHHHHH
Q 022713 151 LRLTKEQSALLEESFKQHSTLNPKQKQALARQLNLRPRQVEVWFQNRRARTKLKQTEVDCEFLKKCCETLTDENRRLHKE 230 (293)
Q Consensus 151 t~ft~~Ql~~Le~~F~~~~~ps~~~r~~LA~~LgLs~rqVqvWFQNRRaK~Krkq~~~~~e~Lk~~~~~l~~en~~l~~e 230 (293)
+.|+..++..|.. ....+.+|++-.+|+.+|........ ....-.+.|+...+.+.++..+++..
T Consensus 37 R~Y~~~~~~~l~~-------------I~~lr~~G~sL~eI~~~l~~~~~~~~--~~~~~~~~l~~~~~~l~~~i~~l~~~ 101 (133)
T cd04787 37 RLYSEKDLSRLRF-------------ILSARQLGFSLKDIKEILSHADQGES--PCPMVRRLIEQRLAETERRIKELLKL 101 (133)
T ss_pred eeCCHHHHHHHHH-------------HHHHHHcCCCHHHHHHHHhhhccCCC--cHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 4799999998843 33456777777777777764322100 00111234444455555555555554
Q ss_pred HHHH
Q 022713 231 LQEL 234 (293)
Q Consensus 231 ~~~l 234 (293)
...+
T Consensus 102 ~~~l 105 (133)
T cd04787 102 RDRM 105 (133)
T ss_pred HHHH
Confidence 4444
No 59
>PF13443 HTH_26: Cro/C1-type HTH DNA-binding domain; PDB: 3TYR_A 3TYS_A 3B7H_A.
Probab=43.12 E-value=9.7 Score=26.81 Aligned_cols=29 Identities=14% Similarity=0.284 Sum_probs=18.1
Q ss_pred HHHHHHHHhCCCCCeeeeechhhhHHHHh
Q 022713 175 QKQALARQLNLRPRQVEVWFQNRRARTKL 203 (293)
Q Consensus 175 ~r~~LA~~LgLs~rqVqvWFQNRRaK~Kr 203 (293)
...+||+.+|++..+|..|+.++..+...
T Consensus 12 t~~~La~~~gis~~tl~~~~~~~~~~~~~ 40 (63)
T PF13443_consen 12 TQKDLARKTGISRSTLSRILNGKPSNPSL 40 (63)
T ss_dssp -HHHHHHHHT--HHHHHHHHTTT-----H
T ss_pred CHHHHHHHHCcCHHHHHHHHhcccccccH
Confidence 35679999999999999999877544443
No 60
>COG3413 Predicted DNA binding protein [General function prediction only]
Probab=42.83 E-value=21 Score=31.94 Aligned_cols=49 Identities=24% Similarity=0.233 Sum_probs=36.5
Q ss_pred cCCHHHHHHHHHHHhhCC--CCCHHHHHHHHHHhCCCCCeeeeechhhhHHHH
Q 022713 152 RLTKEQSALLEESFKQHS--TLNPKQKQALARQLNLRPRQVEVWFQNRRARTK 202 (293)
Q Consensus 152 ~ft~~Ql~~Le~~F~~~~--~ps~~~r~~LA~~LgLs~rqVqvWFQNRRaK~K 202 (293)
.+|..|+.+|...|..-- ||=.....+||++||+++.- +|..=|||..|
T Consensus 155 ~LTdrQ~~vL~~A~~~GYFd~PR~~~l~dLA~~lGISkst--~~ehLRrAe~K 205 (215)
T COG3413 155 DLTDRQLEVLRLAYKMGYFDYPRRVSLKDLAKELGISKST--LSEHLRRAERK 205 (215)
T ss_pred cCCHHHHHHHHHHHHcCCCCCCccCCHHHHHHHhCCCHHH--HHHHHHHHHHH
Confidence 699999999999998754 45556668999999998864 34444455444
No 61
>KOG4571 consensus Activating transcription factor 4 [Transcription]
Probab=42.43 E-value=56 Score=31.27 Aligned_cols=35 Identities=26% Similarity=0.317 Sum_probs=28.5
Q ss_pred HHHhhhhhhhhHHHHHHhhHhhHHHHHHHHHHHHHH
Q 022713 200 RTKLKQTEVDCEFLKKCCETLTDENRRLHKELQELK 235 (293)
Q Consensus 200 K~Krkq~~~~~e~Lk~~~~~l~~en~~l~~e~~~l~ 235 (293)
|+| ++++.+.+.|--+++.|...|++|+.++.++.
T Consensus 241 RYR-qKkRae~E~l~ge~~~Le~rN~~LK~qa~~le 275 (294)
T KOG4571|consen 241 RYR-QKKRAEKEALLGELEGLEKRNEELKDQASELE 275 (294)
T ss_pred HHH-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 444 44566778899999999999999999999883
No 62
>PF10668 Phage_terminase: Phage terminase small subunit; InterPro: IPR018925 This entry describes the terminase small subunit from Enterococcus phage phiFL1A, related proteins in other bacteriophage, and prophage regions of bacterial genomes. Packaging of double-stranded viral DNA concatemers requires interaction of the prohead with virus DNA. This process is mediated by a phage-encoded DNA recognition and terminase protein. The terminase enzymes described so far, which are hetero-oligomers composed of a small and a large subunit, do not have a significant level of sequence homology. The small terminase subunit is thought to form a nucleoprotein structure that helps to position the terminase large subunit at the packaging initiation site [].
Probab=41.90 E-value=7 Score=28.70 Aligned_cols=19 Identities=16% Similarity=0.510 Sum_probs=16.7
Q ss_pred HHHHHHHHhCCCCCeeeee
Q 022713 175 QKQALARQLNLRPRQVEVW 193 (293)
Q Consensus 175 ~r~~LA~~LgLs~rqVqvW 193 (293)
.-.+||.+||+++.+|+.|
T Consensus 24 ~lkdIA~~Lgvs~~tIr~W 42 (60)
T PF10668_consen 24 KLKDIAEKLGVSESTIRKW 42 (60)
T ss_pred cHHHHHHHHCCCHHHHHHH
Confidence 3567999999999999988
No 63
>KOG3755 consensus SATB1 matrix attachment region binding protein [Transcription]
Probab=41.89 E-value=6 Score=41.25 Aligned_cols=46 Identities=13% Similarity=0.153 Sum_probs=30.5
Q ss_pred HHHHhhCCCCCHHHHHHHHHHhC-------CCCCeeeeechhhhHHHHhhhhh
Q 022713 162 EESFKQHSTLNPKQKQALARQLN-------LRPRQVEVWFQNRRARTKLKQTE 207 (293)
Q Consensus 162 e~~F~~~~~ps~~~r~~LA~~Lg-------Ls~rqVqvWFQNRRaK~Krkq~~ 207 (293)
+.+|..++.+......+--.++. ...+.|+.||.|||+++|+.+..
T Consensus 708 ~~w~~k~~s~s~~~v~eYkee~~~~~~~e~~~~kn~~~~fk~~~ee~~~~k~~ 760 (769)
T KOG3755|consen 708 HHWKLKTRSGSWVDVAEYKEEELLMPYEEKFESKNVQFWFKVRREEEKRLKMS 760 (769)
T ss_pred hhheecccCchhHHHHHhhHHhhcchhhhhhhhcchHHHHHHHHHHHhhhhcc
Confidence 44455666666555544444333 35678999999999999976543
No 64
>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=41.42 E-value=16 Score=25.59 Aligned_cols=46 Identities=13% Similarity=0.174 Sum_probs=34.5
Q ss_pred cCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCCCeeeeechhhhHHHHh
Q 022713 152 RLTKEQSALLEESFKQHSTLNPKQKQALARQLNLRPRQVEVWFQNRRARTKL 203 (293)
Q Consensus 152 ~ft~~Ql~~Le~~F~~~~~ps~~~r~~LA~~LgLs~rqVqvWFQNRRaK~Kr 203 (293)
.||..++.+|.....-. ...++|..++++++.|..+..+=+.|..-
T Consensus 3 ~LT~~E~~vl~~l~~G~------~~~eIA~~l~is~~tV~~~~~~i~~Kl~~ 48 (58)
T PF00196_consen 3 SLTERELEVLRLLAQGM------SNKEIAEELGISEKTVKSHRRRIMKKLGV 48 (58)
T ss_dssp SS-HHHHHHHHHHHTTS-------HHHHHHHHTSHHHHHHHHHHHHHHHHT-
T ss_pred ccCHHHHHHHHHHHhcC------CcchhHHhcCcchhhHHHHHHHHHHHhCC
Confidence 58888999888876543 46789999999999999887766666543
No 65
>PF00170 bZIP_1: bZIP transcription factor cAMP response element binding (CREB) protein signature fos transforming protein signature jun transcription factor signature; InterPro: IPR011616 The basic-leucine zipper (bZIP) transcription factors [, ] of eukaryotic are proteins that contain a basic region mediating sequence-specific DNA-binding followed by a leucine zipper region (see IPR002158 from INTERPRO) required for dimerization.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0043565 sequence-specific DNA binding, 0046983 protein dimerization activity, 0006355 regulation of transcription, DNA-dependent; PDB: 2H7H_B 2OQQ_B 1S9K_E 1JNM_A 1JUN_A 1FOS_H 1A02_J 1T2K_C 1CI6_A 1DH3_C ....
Probab=40.68 E-value=1.1e+02 Score=21.97 Aligned_cols=33 Identities=36% Similarity=0.445 Sum_probs=25.9
Q ss_pred hhhhhhhHHHHHHhhHhhHHHHHHHHHHHHHHH
Q 022713 204 KQTEVDCEFLKKCCETLTDENRRLHKELQELKA 236 (293)
Q Consensus 204 kq~~~~~e~Lk~~~~~l~~en~~l~~e~~~l~a 236 (293)
..+....+.|......|..+|..|..++..|..
T Consensus 22 ~RKk~~~~~Le~~~~~L~~en~~L~~~~~~L~~ 54 (64)
T PF00170_consen 22 QRKKQYIEELEEKVEELESENEELKKELEQLKK 54 (64)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHhhHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 334455677888899999999999999888754
No 66
>PF00424 REV: REV protein (anti-repression trans-activator protein); InterPro: IPR000625 REV is a viral anti-repression trans-activator protein, which appears to act post-transcriptionally [] to relieve negative repression of GAG and ENV production. It is a phosphoprotein [, ] whose state of phosphorylation is mediated by a specific serine kinase activity present in the nucleus []. REV accumulates in the nucleoli [].; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0042025 host cell nucleus; PDB: 1ETF_B 1ETG_B 1ULL_B 3LPH_B 2X7L_R.
Probab=38.97 E-value=39 Score=26.92 Aligned_cols=35 Identities=20% Similarity=0.343 Sum_probs=19.3
Q ss_pred HHHHHHHHhhCCCCCHHHHHHHHHHhCCCCCeeeeechhhhHHHHhhhh
Q 022713 158 SALLEESFKQHSTLNPKQKQALARQLNLRPRQVEVWFQNRRARTKLKQT 206 (293)
Q Consensus 158 l~~Le~~F~~~~~ps~~~r~~LA~~LgLs~rqVqvWFQNRRaK~Krkq~ 206 (293)
+.+..-.|+.++||...--.. | =.|||.|||++|.
T Consensus 14 vRiIk~LyqsnPyP~~~GTr~-a-------------RRnRRRRWR~rq~ 48 (91)
T PF00424_consen 14 VRIIKILYQSNPYPSPEGTRQ-A-------------RRNRRRRWRARQR 48 (91)
T ss_dssp HHHHHHHHHTS-S--S-S-HH-H-------------HHHHHHHHHHHHH
T ss_pred HHHHHHHHccccCCCCCCccc-c-------------ccchhhhHHHHHH
Confidence 445556688899997441111 0 1589999998765
No 67
>PF07716 bZIP_2: Basic region leucine zipper; InterPro: IPR011700 The basic-leucine zipper (bZIP) transcription factors [, ] of eukaryotes are proteins that contain a basic region mediating sequence-specific DNA-binding, followed by a leucine zipper region (see IPR002158 from INTERPRO), which is required for dimerization.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0043565 sequence-specific DNA binding, 0046983 protein dimerization activity, 0006355 regulation of transcription, DNA-dependent; PDB: 1NWQ_A 1H89_B 1H88_A 1GTW_B 2E43_A 1IO4_A 1GU4_B 2E42_A 1H8A_B 1GU5_B ....
Probab=38.70 E-value=1.2e+02 Score=21.11 Aligned_cols=29 Identities=28% Similarity=0.421 Sum_probs=20.8
Q ss_pred hhhhHHHHHHhhHhhHHHHHHHHHHHHHH
Q 022713 207 EVDCEFLKKCCETLTDENRRLHKELQELK 235 (293)
Q Consensus 207 ~~~~e~Lk~~~~~l~~en~~l~~e~~~l~ 235 (293)
......|......|..+|..|+.++..|.
T Consensus 24 k~~~~~le~~~~~L~~en~~L~~~i~~L~ 52 (54)
T PF07716_consen 24 KQREEELEQEVQELEEENEQLRQEIAQLE 52 (54)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 34445566777788888888888877664
No 68
>PHA03308 transcriptional regulator ICP4; Provisional
Probab=38.55 E-value=18 Score=38.79 Aligned_cols=17 Identities=24% Similarity=0.317 Sum_probs=12.9
Q ss_pred CCCCCCCCcCCHHHHHH
Q 022713 144 GVNARKKLRLTKEQSAL 160 (293)
Q Consensus 144 ~~~rR~Rt~ft~~Ql~~ 160 (293)
+.+||-|.++..+|...
T Consensus 1292 ~~KKRGRK~LPpe~Ka~ 1308 (1463)
T PHA03308 1292 GGKRRGRQRLPIRDRVY 1308 (1463)
T ss_pred CccccCCCCCChHHhhh
Confidence 44677788899988776
No 69
>cd01106 HTH_TipAL-Mta Helix-Turn-Helix DNA binding domain of the transcription regulators TipAL, Mta, and SkgA. Helix-turn-helix (HTH) TipAL, Mta, and SkgA transcription regulators, and related proteins, N-terminal domain. TipAL regulates resistance to and activation by numerous cyclic thiopeptide antibiotics, such as thiostrepton. Mta is a global transcriptional regulator; the N-terminal DNA-binding domain of Mta interacts directly with the promoters of mta, bmr, blt, and ydfK, and induces transcription of these multidrug-efflux transport genes. SkgA has been shown to control stationary-phase expression of catalase-peroxidase in Caulobacter crescentus. These proteins are comprised of distinct domains that harbor an N-terminal active (DNA-binding) site and a regulatory (effector-binding) site. The conserved N-terminal domain of these transcription regulators contains winged HTH motifs that mediate DNA binding. These proteins share the N-terminal DNA binding domain with other transcrip
Probab=38.36 E-value=1e+02 Score=24.12 Aligned_cols=64 Identities=19% Similarity=0.244 Sum_probs=36.4
Q ss_pred CCcCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCCCeeeeechhhhHHHHhhhhhhhhHHHHHHhhHhhHHHHHHHH
Q 022713 150 KLRLTKEQSALLEESFKQHSTLNPKQKQALARQLNLRPRQVEVWFQNRRARTKLKQTEVDCEFLKKCCETLTDENRRLHK 229 (293)
Q Consensus 150 Rt~ft~~Ql~~Le~~F~~~~~ps~~~r~~LA~~LgLs~rqVqvWFQNRRaK~Krkq~~~~~e~Lk~~~~~l~~en~~l~~ 229 (293)
+..|+..++..|..... .+.+|++..+|+-++.... ..-.+.|+.....|.++..+++.
T Consensus 36 ~R~y~~~di~~l~~i~~-------------lr~~g~~l~~i~~~~~~~~--------~~~~~~l~~~~~~l~~~i~~l~~ 94 (103)
T cd01106 36 YRLYTEEDLERLQQILF-------------LKELGFSLKEIKELLKDPS--------EDLLEALREQKELLEEKKERLDK 94 (103)
T ss_pred ceeeCHHHHHHHHHHHH-------------HHHcCCCHHHHHHHHHcCc--------HHHHHHHHHHHHHHHHHHHHHHH
Confidence 44699999999866532 2345666666666665433 11223444555555555555555
Q ss_pred HHHHH
Q 022713 230 ELQEL 234 (293)
Q Consensus 230 e~~~l 234 (293)
.++.+
T Consensus 95 ~~~~l 99 (103)
T cd01106 95 LIKTI 99 (103)
T ss_pred HHHHH
Confidence 54443
No 70
>PF09607 BrkDBD: Brinker DNA-binding domain; InterPro: IPR018586 This DNA-binding domain is the first approx. 100 residues of the N-terminal end of Brinker. The structure of this domain in complex with DNA consists of four alpha-helices that contain a helix-turn-helix DNA recognition motif specific for GC-rich DNA. The Brinker nuclear repressor is a major element of the Drosophila Decapentaplegic morphogen signalling pathway []. ; PDB: 2GLO_A.
Probab=37.16 E-value=19 Score=26.36 Aligned_cols=43 Identities=30% Similarity=0.385 Sum_probs=21.0
Q ss_pred CCcCCHHH-HHHHHHHHhhCCCCCHHHHHHHHHHhCCCCCeeeeec
Q 022713 150 KLRLTKEQ-SALLEESFKQHSTLNPKQKQALARQLNLRPRQVEVWF 194 (293)
Q Consensus 150 Rt~ft~~Q-l~~Le~~F~~~~~ps~~~r~~LA~~LgLs~rqVqvWF 194 (293)
|..|+... +.+++..+..+. --..+| .-|.++|+.+++|+-|-
T Consensus 3 rrsy~~~FKL~Vv~~a~~~~n-c~~~~R-Aaarkf~V~r~~Vr~W~ 46 (58)
T PF09607_consen 3 RRSYTAEFKLKVVEYAEKDNN-CKGNQR-AAARKFNVSRRQVRKWR 46 (58)
T ss_dssp -----HHHHHHHHHHHHH-TT-TTT-HH-HHHHHTTS-HHHHHHHH
T ss_pred ccccChHHHHHHHHHHHHccc-hhhhHH-HHHHHhCccHHHHHHHH
Confidence 44566654 444444443322 222233 34999999999999884
No 71
>PRK09646 RNA polymerase sigma factor SigK; Reviewed
Probab=36.02 E-value=33 Score=29.63 Aligned_cols=46 Identities=15% Similarity=0.164 Sum_probs=32.9
Q ss_pred cCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCCCeeeeechhhhHHHH
Q 022713 152 RLTKEQSALLEESFKQHSTLNPKQKQALARQLNLRPRQVEVWFQNRRARTK 202 (293)
Q Consensus 152 ~ft~~Ql~~Le~~F~~~~~ps~~~r~~LA~~LgLs~rqVqvWFQNRRaK~K 202 (293)
.++..+..+|...|-.. ..-.+||..||++...|++|...-|.+.|
T Consensus 142 ~L~~~~r~vl~l~~~~~-----~s~~EIA~~Lgis~~tVk~~l~ra~~~Lr 187 (194)
T PRK09646 142 ALTDTQRESVTLAYYGG-----LTYREVAERLAVPLGTVKTRMRDGLIRLR 187 (194)
T ss_pred hCCHHHHHHHHHHHHcC-----CCHHHHHHHhCCChHhHHHHHHHHHHHHH
Confidence 47888888887765433 24568999999999999888754444433
No 72
>smart00338 BRLZ basic region leucin zipper.
Probab=34.77 E-value=1.5e+02 Score=21.26 Aligned_cols=25 Identities=44% Similarity=0.583 Sum_probs=13.3
Q ss_pred hHHHHHHhhHhhHHHHHHHHHHHHH
Q 022713 210 CEFLKKCCETLTDENRRLHKELQEL 234 (293)
Q Consensus 210 ~e~Lk~~~~~l~~en~~l~~e~~~l 234 (293)
...|......|..+|..|..++..|
T Consensus 28 ~~~Le~~~~~L~~en~~L~~~~~~l 52 (65)
T smart00338 28 IEELERKVEQLEAENERLKKEIERL 52 (65)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3344455555555555555555554
No 73
>COG3416 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=32.81 E-value=4e+02 Score=24.58 Aligned_cols=18 Identities=33% Similarity=0.514 Sum_probs=14.5
Q ss_pred CCHHHHHHHHHHHhhCCC
Q 022713 153 LTKEQSALLEESFKQHST 170 (293)
Q Consensus 153 ft~~Ql~~Le~~F~~~~~ 170 (293)
+|++..+.||..|.+-+.
T Consensus 1 MtpeE~qlle~lf~rlk~ 18 (233)
T COG3416 1 MTPEEKQLLENLFHRLKK 18 (233)
T ss_pred CCHHHHHHHHHHHHHHhh
Confidence 478889999999987554
No 74
>PF04977 DivIC: Septum formation initiator; InterPro: IPR007060 DivIC, from the spore-forming, Gram-positive bacterium Bacillus subtilis, is necessary for both vegetative and sporulation septum formation []. These proteins are mainly composed of an N-terminal coiled-coil. DivIB, DivIC and FtsL inter-depend on each other for stabilisation and localisation. The latter two form a heterodimer. DivIC is always centre cell but the other two associate with it during septation [].; GO: 0007049 cell cycle
Probab=32.47 E-value=1.2e+02 Score=22.12 Aligned_cols=30 Identities=33% Similarity=0.420 Sum_probs=23.8
Q ss_pred hhhhhhHHHHHHhhHhhHHHHHHHHHHHHH
Q 022713 205 QTEVDCEFLKKCCETLTDENRRLHKELQEL 234 (293)
Q Consensus 205 q~~~~~e~Lk~~~~~l~~en~~l~~e~~~l 234 (293)
+...+...|+...+.+..+|+.|+.++..+
T Consensus 21 ~~~~ei~~l~~~i~~l~~e~~~L~~ei~~l 50 (80)
T PF04977_consen 21 QLNQEIAELQKEIEELKKENEELKEEIERL 50 (80)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 444567778888888888888888888877
No 75
>smart00421 HTH_LUXR helix_turn_helix, Lux Regulon. lux regulon (activates the bioluminescence operon
Probab=32.31 E-value=32 Score=22.72 Aligned_cols=39 Identities=18% Similarity=0.291 Sum_probs=28.1
Q ss_pred cCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCCCeeeeechh
Q 022713 152 RLTKEQSALLEESFKQHSTLNPKQKQALARQLNLRPRQVEVWFQN 196 (293)
Q Consensus 152 ~ft~~Ql~~Le~~F~~~~~ps~~~r~~LA~~LgLs~rqVqvWFQN 196 (293)
.++..+..++...+.. + ...++|..+|++...|..|.+.
T Consensus 3 ~l~~~e~~i~~~~~~g--~----s~~eia~~l~is~~tv~~~~~~ 41 (58)
T smart00421 3 SLTPREREVLRLLAEG--L----TNKEIAERLGISEKTVKTHLSN 41 (58)
T ss_pred CCCHHHHHHHHHHHcC--C----CHHHHHHHHCCCHHHHHHHHHH
Confidence 4677788877664322 1 4578999999999999887653
No 76
>PRK12526 RNA polymerase sigma factor; Provisional
Probab=31.87 E-value=37 Score=29.77 Aligned_cols=46 Identities=24% Similarity=0.315 Sum_probs=31.2
Q ss_pred cCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCCCeeeeechhhhHHHH
Q 022713 152 RLTKEQSALLEESFKQHSTLNPKQKQALARQLNLRPRQVEVWFQNRRARTK 202 (293)
Q Consensus 152 ~ft~~Ql~~Le~~F~~~~~ps~~~r~~LA~~LgLs~rqVqvWFQNRRaK~K 202 (293)
.++..+..+|...|-.. ....+||..+|+++..|+++...-|.+.|
T Consensus 153 ~L~~~~r~vl~l~~~~g-----~s~~EIA~~lgis~~tV~~~l~Ra~~~Lr 198 (206)
T PRK12526 153 KLPEAQQTVVKGVYFQE-----LSQEQLAQQLNVPLGTVKSRLRLALAKLK 198 (206)
T ss_pred hCCHHHHHHHHHHHHcC-----CCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Confidence 36677777776554322 24578999999999999887754444433
No 77
>PHA02955 hypothetical protein; Provisional
Probab=31.87 E-value=54 Score=30.03 Aligned_cols=44 Identities=11% Similarity=0.175 Sum_probs=35.3
Q ss_pred HHHHHHHHHHHhhC-CCCCHHHHHHHHHHhCCCCCeeeeechhhh
Q 022713 155 KEQSALLEESFKQH-STLNPKQKQALARQLNLRPRQVEVWFQNRR 198 (293)
Q Consensus 155 ~~Ql~~Le~~F~~~-~~ps~~~r~~LA~~LgLs~rqVqvWFQNRR 198 (293)
..|+..|-+.|... ..++.++|.+++++||+....|..||.+.-
T Consensus 60 ~~sf~lli~a~~Et~~~Lp~~qk~~ia~~lgI~~~~~~~d~~t~~ 104 (213)
T PHA02955 60 EKNFQLLIEALIETIENFPEKEQKEIAADIGINIDDYKAGKKTDL 104 (213)
T ss_pred HHHHHHHHHHHHHHHHhCCHHHHHHHHHHhCCChhhccCcccchh
Confidence 46677777777664 678899999999999999887889987643
No 78
>PF12824 MRP-L20: Mitochondrial ribosomal protein subunit L20; InterPro: IPR024388 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. This entry represents the essential mitochondrial ribosomal protein L20 family from fungi [].
Probab=31.56 E-value=2.2e+02 Score=24.87 Aligned_cols=48 Identities=21% Similarity=0.210 Sum_probs=36.6
Q ss_pred CCCcCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCCCeeeeechhhh
Q 022713 149 KKLRLTKEQSALLEESFKQHSTLNPKQKQALARQLNLRPRQVEVWFQNRR 198 (293)
Q Consensus 149 ~Rt~ft~~Ql~~Le~~F~~~~~ps~~~r~~LA~~LgLs~rqVqvWFQNRR 198 (293)
++..++.+++..+...-..+ |..-.+..||+++|++..=|.+-..--+
T Consensus 82 k~y~Lt~e~i~Eir~LR~~D--P~~wTr~~LAkkF~~S~~fV~~v~~~~~ 129 (164)
T PF12824_consen 82 KKYHLTPEDIQEIRRLRAED--PEKWTRKKLAKKFNCSPLFVSMVAPAPK 129 (164)
T ss_pred ccccCCHHHHHHHHHHHHcC--chHhhHHHHHHHhCCCHHHHHHhcCCCH
Confidence 44689999999998876554 6667889999999998877766554333
No 79
>PRK09652 RNA polymerase sigma factor RpoE; Provisional
Probab=31.39 E-value=36 Score=28.27 Aligned_cols=40 Identities=10% Similarity=-0.007 Sum_probs=30.3
Q ss_pred cCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCCCeeeeechh
Q 022713 152 RLTKEQSALLEESFKQHSTLNPKQKQALARQLNLRPRQVEVWFQN 196 (293)
Q Consensus 152 ~ft~~Ql~~Le~~F~~~~~ps~~~r~~LA~~LgLs~rqVqvWFQN 196 (293)
.+++.+..+|...|-.. ....+||..+|++...|+.|...
T Consensus 128 ~L~~~~r~vl~l~~~~~-----~s~~eIA~~lgis~~tV~~~l~r 167 (182)
T PRK09652 128 SLPEELRTAITLREIEG-----LSYEEIAEIMGCPIGTVRSRIFR 167 (182)
T ss_pred hCCHHHHHHHHHHHHcC-----CCHHHHHHHHCCCHHHHHHHHHH
Confidence 47888888887765422 13458999999999999988763
No 80
>KOG3335 consensus Predicted coiled-coil protein [General function prediction only]
Probab=31.30 E-value=1.3e+02 Score=26.81 Aligned_cols=49 Identities=24% Similarity=0.281 Sum_probs=38.7
Q ss_pred CCeeeeechhhhHHHHhhhhhhhhHHHHHHhhHhhHHHHHHHHHHHHHH
Q 022713 187 PRQVEVWFQNRRARTKLKQTEVDCEFLKKCCETLTDENRRLHKELQELK 235 (293)
Q Consensus 187 ~rqVqvWFQNRRaK~Krkq~~~~~e~Lk~~~~~l~~en~~l~~e~~~l~ 235 (293)
.-...+|-+-|..+.|..+.+.+.+.|+...+.|..+.+++++.+.+|.
T Consensus 85 ~lv~Ey~R~~~~e~~kee~~~~e~~elr~~~~~l~~~i~~~~~~~~~L~ 133 (181)
T KOG3335|consen 85 VLVFEYWRQARKERKKEEKRKQEIMELRLKVEKLENAIAELTKFFSQLH 133 (181)
T ss_pred eeeehhHHhhhcchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3345677777777777777788888899899999889999999998884
No 81
>TIGR02209 ftsL_broad cell division protein FtsL. This model represents FtsL, both forms similar to that in E. coli and similar to that in B. subtilis. FtsL is one of the later proteins active in cell division septum formation. FtsL is small, low in complexity, and highly divergent. The scope of this model is broader than that of the Pfam model pfam04999.3 for FtsL, as this one includes FtsL from Bacillus subtilis and related species.
Probab=30.94 E-value=1.4e+02 Score=22.32 Aligned_cols=31 Identities=29% Similarity=0.289 Sum_probs=22.6
Q ss_pred hhhhhhHHHHHHhhHhhHHHHHHHHHHHHHH
Q 022713 205 QTEVDCEFLKKCCETLTDENRRLHKELQELK 235 (293)
Q Consensus 205 q~~~~~e~Lk~~~~~l~~en~~l~~e~~~l~ 235 (293)
+...+...+++..+.+..+|.+|+.|+..+.
T Consensus 28 ~~~~~~~~~~~~~~~l~~en~~L~~ei~~l~ 58 (85)
T TIGR02209 28 QLNNELQKLQLEIDKLQKEWRDLQLEVAELS 58 (85)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHc
Confidence 4455666677777788888888888887763
No 82
>PF10883 DUF2681: Protein of unknown function (DUF2681); InterPro: IPR020274 This entry contains membrane proteins with no known function.
Probab=30.87 E-value=1.6e+02 Score=23.14 Aligned_cols=38 Identities=21% Similarity=0.410 Sum_probs=24.5
Q ss_pred eechhhhHHHHhhhhhhhhHHHHHHhhHhhHHHHHHHHHHHHHHH
Q 022713 192 VWFQNRRARTKLKQTEVDCEFLKKCCETLTDENRRLHKELQELKA 236 (293)
Q Consensus 192 vWFQNRRaK~Krkq~~~~~e~Lk~~~~~l~~en~~l~~e~~~l~a 236 (293)
+|||=++++.+ ++.|..+++.|..|....++++...+.
T Consensus 21 ~~~k~~ka~~~-------~~kL~~en~qlk~Ek~~~~~qvkn~~v 58 (87)
T PF10883_consen 21 LWWKVKKAKKQ-------NAKLQKENEQLKTEKAVAETQVKNAKV 58 (87)
T ss_pred HHHHHHHHHHH-------HHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 46655555433 666777777777777777777766543
No 83
>PRK06759 RNA polymerase factor sigma-70; Validated
Probab=30.69 E-value=36 Score=27.81 Aligned_cols=45 Identities=16% Similarity=0.160 Sum_probs=32.4
Q ss_pred cCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCCCeeeeechhhhHHH
Q 022713 152 RLTKEQSALLEESFKQHSTLNPKQKQALARQLNLRPRQVEVWFQNRRART 201 (293)
Q Consensus 152 ~ft~~Ql~~Le~~F~~~~~ps~~~r~~LA~~LgLs~rqVqvWFQNRRaK~ 201 (293)
.+++.+..++...|-.. ....+||..+|++...|+.|...-|.+.
T Consensus 106 ~L~~~~r~ii~l~~~~~-----~s~~EIA~~l~is~~tV~~~~~ra~~~L 150 (154)
T PRK06759 106 VLDEKEKYIIFERFFVG-----KTMGEIALETEMTYYQVRWIYRQALEKM 150 (154)
T ss_pred hCCHHHHHHHHHHHhcC-----CCHHHHHHHHCCCHHHHHHHHHHHHHHH
Confidence 57777888777665433 2367899999999999999876444433
No 84
>PF15058 Speriolin_N: Speriolin N terminus
Probab=30.19 E-value=4.2e+02 Score=24.04 Aligned_cols=24 Identities=38% Similarity=0.378 Sum_probs=10.4
Q ss_pred hhhHHHHHHhhHhhHHHHHHHHHHH
Q 022713 208 VDCEFLKKCCETLTDENRRLHKELQ 232 (293)
Q Consensus 208 ~~~e~Lk~~~~~l~~en~~l~~e~~ 232 (293)
.+++.||+.-. |..||++|+.-+-
T Consensus 19 ~ENeeLKKlVr-LirEN~eLksaL~ 42 (200)
T PF15058_consen 19 RENEELKKLVR-LIRENHELKSALG 42 (200)
T ss_pred hhhHHHHHHHH-HHHHHHHHHHHHH
Confidence 34444555433 2344444444433
No 85
>PRK00118 putative DNA-binding protein; Validated
Probab=30.14 E-value=1.7e+02 Score=23.66 Aligned_cols=46 Identities=15% Similarity=0.145 Sum_probs=32.2
Q ss_pred cCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCCCeeeeechhhhHHHH
Q 022713 152 RLTKEQSALLEESFKQHSTLNPKQKQALARQLNLRPRQVEVWFQNRRARTK 202 (293)
Q Consensus 152 ~ft~~Ql~~Le~~F~~~~~ps~~~r~~LA~~LgLs~rqVqvWFQNRRaK~K 202 (293)
.++..|..++...|.... ...+||..+|++...|..|....|.+.|
T Consensus 17 ~L~ekqRevl~L~y~eg~-----S~~EIAe~lGIS~~TV~r~L~RArkkLr 62 (104)
T PRK00118 17 LLTEKQRNYMELYYLDDY-----SLGEIAEEFNVSRQAVYDNIKRTEKLLE 62 (104)
T ss_pred cCCHHHHHHHHHHHHcCC-----CHHHHHHHHCcCHHHHHHHHHHHHHHHH
Confidence 456777777766655432 3567999999999999998864444433
No 86
>KOG0709 consensus CREB/ATF family transcription factor [Transcription]
Probab=29.40 E-value=79 Score=32.17 Aligned_cols=78 Identities=22% Similarity=0.332 Sum_probs=38.9
Q ss_pred CCcCCHHHHHHHHHH-Hhh-CCCCCHHHHHHHHHHhCCCCCeeeeechhhhH-HHHhhhhhhhhHHHHHHhhHhhHHHHH
Q 022713 150 KLRLTKEQSALLEES-FKQ-HSTLNPKQKQALARQLNLRPRQVEVWFQNRRA-RTKLKQTEVDCEFLKKCCETLTDENRR 226 (293)
Q Consensus 150 Rt~ft~~Ql~~Le~~-F~~-~~~ps~~~r~~LA~~LgLs~rqVqvWFQNRRa-K~Krkq~~~~~e~Lk~~~~~l~~en~~ 226 (293)
-.+++.+....|.+. +.. ..+|-.+.-+++.++. +.=.+|+|. .++|+++..=.+.|......-..||+.
T Consensus 218 ~L~LteeEkrLL~kEG~slPs~lPLTKaEEriLKrv-------RRKIrNK~SAQESRrkKkeYid~LE~rv~~~taeNqe 290 (472)
T KOG0709|consen 218 PLVLTEEEKRLLTKEGYSLPSKLPLTKAEERILKRV-------RRKIRNKRSAQESRRKKKEYIDGLESRVSAFTAENQE 290 (472)
T ss_pred ceeccHHHHHHHHhccCcCcccCCchHHHHHHHHHH-------HHHHHhhhhhHHHHHhHhhHHHHHhhhhhhcccCcHH
Confidence 446788888888776 333 3345544445555444 222334442 233333333333444444444555555
Q ss_pred HHHHHHHH
Q 022713 227 LHKELQEL 234 (293)
Q Consensus 227 l~~e~~~l 234 (293)
|++++.+|
T Consensus 291 L~kkV~~L 298 (472)
T KOG0709|consen 291 LQKKVEEL 298 (472)
T ss_pred HHHHHHHH
Confidence 55555554
No 87
>PRK09642 RNA polymerase sigma factor SigW; Reviewed
Probab=29.05 E-value=50 Score=27.28 Aligned_cols=46 Identities=17% Similarity=0.213 Sum_probs=31.8
Q ss_pred cCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCCCeeeeechhhhHHHH
Q 022713 152 RLTKEQSALLEESFKQHSTLNPKQKQALARQLNLRPRQVEVWFQNRRARTK 202 (293)
Q Consensus 152 ~ft~~Ql~~Le~~F~~~~~ps~~~r~~LA~~LgLs~rqVqvWFQNRRaK~K 202 (293)
.++..+..++...|-... .-.+||..+|+++..|+++...-|.+.|
T Consensus 106 ~Lp~~~r~v~~l~~~~g~-----s~~EIA~~lgis~~tV~~~l~Rar~~Lr 151 (160)
T PRK09642 106 ELPENYRDVVLAHYLEEK-----SYQEIALQEKIEVKTVEMKLYRARKWIK 151 (160)
T ss_pred hCCHHHHHHHHHHHHhCC-----CHHHHHHHHCCCHHHHHHHHHHHHHHHH
Confidence 367777777766553332 3458999999999999988764444444
No 88
>PRK12512 RNA polymerase sigma factor; Provisional
Probab=29.02 E-value=47 Score=28.20 Aligned_cols=46 Identities=15% Similarity=0.121 Sum_probs=33.8
Q ss_pred cCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCCCeeeeechhhhHHHH
Q 022713 152 RLTKEQSALLEESFKQHSTLNPKQKQALARQLNLRPRQVEVWFQNRRARTK 202 (293)
Q Consensus 152 ~ft~~Ql~~Le~~F~~~~~ps~~~r~~LA~~LgLs~rqVqvWFQNRRaK~K 202 (293)
.++..+..+|...|-.. ..-.+||..||++...|+.++..-|.+.|
T Consensus 131 ~L~~~~r~v~~l~~~~g-----~s~~eIA~~l~is~~tV~~~l~ra~~~Lr 176 (184)
T PRK12512 131 TLPPRQRDVVQSISVEG-----ASIKETAAKLSMSEGAVRVALHRGLAALA 176 (184)
T ss_pred hCCHHHHHHHHHHHHcC-----CCHHHHHHHhCCCHHHHHHHHHHHHHHHH
Confidence 47777788887765443 23568999999999999998865555544
No 89
>KOG2675 consensus Adenylate cyclase-associated protein (CAP/Srv2p) [Cytoskeleton; Signal transduction mechanisms]
Probab=28.69 E-value=2e+02 Score=29.34 Aligned_cols=27 Identities=15% Similarity=0.265 Sum_probs=17.7
Q ss_pred eechhhhHHHHhhhhhhhhHHHHHHhh
Q 022713 192 VWFQNRRARTKLKQTEVDCEFLKKCCE 218 (293)
Q Consensus 192 vWFQNRRaK~Krkq~~~~~e~Lk~~~~ 218 (293)
.++-||-.|+-|..-....|..|...+
T Consensus 168 ~FY~NrvLkEyk~~D~~hveWvKa~l~ 194 (480)
T KOG2675|consen 168 QFYTNRVLKEYKEKDPRHVEWVKAYLA 194 (480)
T ss_pred HHHHHHHHHHhccCChhHHHHHHHHHH
Confidence 346788888877666666666665544
No 90
>PRK11924 RNA polymerase sigma factor; Provisional
Probab=28.40 E-value=45 Score=27.60 Aligned_cols=46 Identities=13% Similarity=0.146 Sum_probs=31.7
Q ss_pred cCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCCCeeeeechhhhHHHH
Q 022713 152 RLTKEQSALLEESFKQHSTLNPKQKQALARQLNLRPRQVEVWFQNRRARTK 202 (293)
Q Consensus 152 ~ft~~Ql~~Le~~F~~~~~ps~~~r~~LA~~LgLs~rqVqvWFQNRRaK~K 202 (293)
.+++.+..++...|... ..-.+||..+|++...|..|...-|.+.|
T Consensus 125 ~L~~~~r~i~~l~~~~~-----~~~~eIA~~lgis~~tv~~~~~ra~~~lr 170 (179)
T PRK11924 125 ALPVKQREVFLLRYVEG-----LSYREIAEILGVPVGTVKSRLRRARQLLR 170 (179)
T ss_pred hCCHHHHHHhhHHHHcC-----CCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Confidence 36666777776665332 23478999999999999998864444443
No 91
>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=28.04 E-value=47 Score=26.12 Aligned_cols=45 Identities=13% Similarity=0.220 Sum_probs=30.8
Q ss_pred cCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCCCeeeeechhhhHHH
Q 022713 152 RLTKEQSALLEESFKQHSTLNPKQKQALARQLNLRPRQVEVWFQNRRART 201 (293)
Q Consensus 152 ~ft~~Ql~~Le~~F~~~~~ps~~~r~~LA~~LgLs~rqVqvWFQNRRaK~ 201 (293)
.++..|..++...|-.. ....+||..+|+++..|..|...-+.|.
T Consensus 110 ~L~~~~~~ii~~~~~~g-----~s~~eIA~~l~~s~~~v~~~~~~~~~kl 154 (158)
T TIGR02937 110 KLPEREREVLVLRYLEG-----LSYKEIAEILGISVGTVKRRLKRARKKL 154 (158)
T ss_pred hCCHHHHHHHhhHHhcC-----CCHHHHHHHHCCCHHHHHHHHHHHHHHH
Confidence 46677777776654322 2456899999999999988776444443
No 92
>PF06156 DUF972: Protein of unknown function (DUF972); InterPro: IPR010377 FUNCTION: Involved in initiation control of chromosome replication. SUBUNIT: Interacts with both DnaA and DnaN, acting as a bridge between these two proteins. SIMILARITY: Belongs to the YabA family.
Probab=27.65 E-value=1.4e+02 Score=24.32 Aligned_cols=33 Identities=36% Similarity=0.339 Sum_probs=24.7
Q ss_pred hhhhhhhHHHHHHhhHhhHHHHHHHHHHHHHHH
Q 022713 204 KQTEVDCEFLKKCCETLTDENRRLHKELQELKA 236 (293)
Q Consensus 204 kq~~~~~e~Lk~~~~~l~~en~~l~~e~~~l~a 236 (293)
.+.-.+...||.....|.+||.+|+-|...|+.
T Consensus 18 ~~l~~~~~~LK~~~~~l~EEN~~L~~EN~~Lr~ 50 (107)
T PF06156_consen 18 GQLLEELEELKKQLQELLEENARLRIENEHLRE 50 (107)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 445566777888888888888888888877754
No 93
>PRK10072 putative transcriptional regulator; Provisional
Probab=27.19 E-value=35 Score=27.17 Aligned_cols=41 Identities=17% Similarity=0.165 Sum_probs=30.8
Q ss_pred cCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCCCeeeeechhhhH
Q 022713 152 RLTKEQSALLEESFKQHSTLNPKQKQALARQLNLRPRQVEVWFQNRRA 199 (293)
Q Consensus 152 ~ft~~Ql~~Le~~F~~~~~ps~~~r~~LA~~LgLs~rqVqvWFQNRRa 199 (293)
+.+...+..|......+ ..+||..+|++...|..|.+.+|.
T Consensus 32 ~~~~~eik~LR~~~glT-------Q~elA~~lGvS~~TVs~WE~G~r~ 72 (96)
T PRK10072 32 TTSFTEFEQLRKGTGLK-------IDDFARVLGVSVAMVKEWESRRVK 72 (96)
T ss_pred cCChHHHHHHHHHcCCC-------HHHHHHHhCCCHHHHHHHHcCCCC
Confidence 45677777775543322 578999999999999999987764
No 94
>KOG4403 consensus Cell surface glycoprotein STIM, contains SAM domain [General function prediction only]
Probab=27.05 E-value=1e+02 Score=31.31 Aligned_cols=31 Identities=29% Similarity=0.561 Sum_probs=21.9
Q ss_pred eeec---hhhhHHHHhhhhhhhhHHHHHHhhHhh
Q 022713 191 EVWF---QNRRARTKLKQTEVDCEFLKKCCETLT 221 (293)
Q Consensus 191 qvWF---QNRRaK~Krkq~~~~~e~Lk~~~~~l~ 221 (293)
-+|| ||+.+|.+-++...+.+.|+.....|.
T Consensus 229 gcw~ay~Qnk~akehv~km~kdle~Lq~aEqsl~ 262 (575)
T KOG4403|consen 229 GCWFAYRQNKKAKEHVNKMMKDLEGLQRAEQSLE 262 (575)
T ss_pred hhhhhhhhhhHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3588 899888887777777777766544443
No 95
>smart00338 BRLZ basic region leucin zipper.
Probab=27.03 E-value=2.1e+02 Score=20.44 Aligned_cols=34 Identities=35% Similarity=0.412 Sum_probs=27.8
Q ss_pred hhhhhhhHHHHHHhhHhhHHHHHHHHHHHHHHHh
Q 022713 204 KQTEVDCEFLKKCCETLTDENRRLHKELQELKAL 237 (293)
Q Consensus 204 kq~~~~~e~Lk~~~~~l~~en~~l~~e~~~l~al 237 (293)
...+.....|...+..|..+...|+.++..|+..
T Consensus 29 ~~Le~~~~~L~~en~~L~~~~~~l~~e~~~lk~~ 62 (65)
T smart00338 29 EELERKVEQLEAENERLKKEIERLRRELEKLKSE 62 (65)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 4466677788889999999999999998887654
No 96
>TIGR03879 near_KaiC_dom probable regulatory domain. This model describes a common domain shared by two different families of proteins, each of which occurs regularly next to its corresponding partner family, a probable regulatory with homology to KaiC. By implication, this protein family likely is also involved in sensory transduction and/or regulation.
Probab=26.89 E-value=9.3 Score=29.13 Aligned_cols=32 Identities=13% Similarity=0.085 Sum_probs=23.1
Q ss_pred HhhCCCCCHHHHHHHHHHhCCCCCeeeeechh
Q 022713 165 FKQHSTLNPKQKQALARQLNLRPRQVEVWFQN 196 (293)
Q Consensus 165 F~~~~~ps~~~r~~LA~~LgLs~rqVqvWFQN 196 (293)
|...+|.......+||..+|+++..|+.|+.+
T Consensus 24 f~L~R~~eGlS~kEIAe~LGIS~~TVk~~l~~ 55 (73)
T TIGR03879 24 AALAREEAGKTASEIAEELGRTEQTVRNHLKG 55 (73)
T ss_pred HHHHHHHcCCCHHHHHHHHCcCHHHHHHHHhc
Confidence 43333333345678999999999999999864
No 97
>PRK04217 hypothetical protein; Provisional
Probab=26.39 E-value=54 Score=26.82 Aligned_cols=40 Identities=10% Similarity=-0.002 Sum_probs=30.0
Q ss_pred cCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCCCeeeeechh
Q 022713 152 RLTKEQSALLEESFKQHSTLNPKQKQALARQLNLRPRQVEVWFQN 196 (293)
Q Consensus 152 ~ft~~Ql~~Le~~F~~~~~ps~~~r~~LA~~LgLs~rqVqvWFQN 196 (293)
.++.+|..++...|...- ...+||+.+|++...|...+..
T Consensus 42 ~Lt~eereai~l~~~eGl-----S~~EIAk~LGIS~sTV~r~L~R 81 (110)
T PRK04217 42 FMTYEEFEALRLVDYEGL-----TQEEAGKRMGVSRGTVWRALTS 81 (110)
T ss_pred cCCHHHHHHHHHHHHcCC-----CHHHHHHHHCcCHHHHHHHHHH
Confidence 578888888877764432 4568999999999988776643
No 98
>PRK12519 RNA polymerase sigma factor; Provisional
Probab=26.35 E-value=42 Score=28.75 Aligned_cols=45 Identities=16% Similarity=0.250 Sum_probs=30.4
Q ss_pred CCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCCCeeeeechhhhHHHH
Q 022713 153 LTKEQSALLEESFKQHSTLNPKQKQALARQLNLRPRQVEVWFQNRRARTK 202 (293)
Q Consensus 153 ft~~Ql~~Le~~F~~~~~ps~~~r~~LA~~LgLs~rqVqvWFQNRRaK~K 202 (293)
++..+..++...|-. .....+||..+|++...|++|+..-|.+.|
T Consensus 142 L~~~~~~v~~l~~~~-----g~s~~EIA~~lgis~~tV~~~l~Ra~~~Lr 186 (194)
T PRK12519 142 LPESQRQVLELAYYE-----GLSQSEIAKRLGIPLGTVKARARQGLLKLR 186 (194)
T ss_pred CCHHHhhhhhhhhhc-----CCCHHHHHHHhCCCHHHHHHHHHHHHHHHH
Confidence 566666666555422 234568999999999999999854444333
No 99
>PF01166 TSC22: TSC-22/dip/bun family; InterPro: IPR000580 Several eukaryotic proteins are evolutionary related and are thought to be involved in transcriptional regulation. These proteins are highly similar in a region of about 50 residues that include a conserved leucine-zipper domain most probably involved in homo- or hetero-dimerisation. Proteins containing this signature include: Vertebrate protein TSC-22 [], a transcriptional regulator which seems to act on C-type natriuretic peptide (CNP) promoter. Mammalian protein DIP (DSIP-immunoreactive peptide) [], a protein whose function is not yet known. Drosophila protein bunched [] (gene bun) (also known as shortsighted), a probable transcription factor required for peripheral nervous system morphogenesis, eye development and oogenesis. Caenorhabditis elegans hypothetical protein T18D3.7. ; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent; PDB: 1DIP_B.
Probab=26.25 E-value=1.5e+02 Score=21.80 Aligned_cols=32 Identities=28% Similarity=0.309 Sum_probs=27.3
Q ss_pred hhhhHHHHHHhhHhhHHHHHHHHHHHHHHHhh
Q 022713 207 EVDCEFLKKCCETLTDENRRLHKELQELKALK 238 (293)
Q Consensus 207 ~~~~e~Lk~~~~~l~~en~~l~~e~~~l~al~ 238 (293)
+.+.+.||.....|.+.|..|+.|..-|+..-
T Consensus 13 rEEVevLK~~I~eL~~~n~~Le~EN~~Lk~~~ 44 (59)
T PF01166_consen 13 REEVEVLKEQIAELEERNSQLEEENNLLKQNA 44 (59)
T ss_dssp TTSHHHHHHHHHHHHHHHHHHHHHHHHHHHHC
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcC
Confidence 45788899999999999999999988887763
No 100
>cd01109 HTH_YyaN Helix-Turn-Helix DNA binding domain of the MerR-like transcription regulators YyaN and YraB. Putative helix-turn-helix (HTH) MerR-like transcription regulators of Bacillus subtilis, YyaN and YraB, and related proteins; N-terminal domain. Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.
Probab=26.24 E-value=1.5e+02 Score=23.61 Aligned_cols=69 Identities=20% Similarity=0.229 Sum_probs=37.8
Q ss_pred CcCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCCCeeeeechhhhHHHHhhhhhhhhHHHHHHhhHhhHHHHHHHHH
Q 022713 151 LRLTKEQSALLEESFKQHSTLNPKQKQALARQLNLRPRQVEVWFQNRRARTKLKQTEVDCEFLKKCCETLTDENRRLHKE 230 (293)
Q Consensus 151 t~ft~~Ql~~Le~~F~~~~~ps~~~r~~LA~~LgLs~rqVqvWFQNRRaK~Krkq~~~~~e~Lk~~~~~l~~en~~l~~e 230 (293)
..|+..++..|... ...+.+|++-.+|+.++........ ......+.|......+..+...|+..
T Consensus 37 R~Y~~~~l~~l~~I-------------~~lr~~G~sL~eI~~~l~~~~~~~~--~~~~~~~~l~~~~~~l~~~i~~l~~~ 101 (113)
T cd01109 37 RDFTEEDLEWLEFI-------------KCLRNTGMSIKDIKEYAELRREGDS--TIPERLELLEEHREELEEQIAELQET 101 (113)
T ss_pred ccCCHHHHHHHHHH-------------HHHHHcCCCHHHHHHHHHHHccCCc--cHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 36999999888543 3345667777777766654322110 01112344555555555555555555
Q ss_pred HHHH
Q 022713 231 LQEL 234 (293)
Q Consensus 231 ~~~l 234 (293)
+..+
T Consensus 102 ~~~l 105 (113)
T cd01109 102 LAYL 105 (113)
T ss_pred HHHH
Confidence 5444
No 101
>cd04779 HTH_MerR-like_sg4 Helix-Turn-Helix DNA binding domain of putative transcription regulators from the MerR superfamily. Putative helix-turn-helix (HTH) MerR-like transcription regulators (subgroup 4). Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.
Probab=26.20 E-value=2.1e+02 Score=23.96 Aligned_cols=16 Identities=6% Similarity=-0.161 Sum_probs=12.1
Q ss_pred CCCcCCHHHHHHHHHH
Q 022713 149 KKLRLTKEQSALLEES 164 (293)
Q Consensus 149 ~Rt~ft~~Ql~~Le~~ 164 (293)
.+..|+..++..|...
T Consensus 34 g~R~Y~~~~l~~l~~I 49 (134)
T cd04779 34 NYRYYDETALDRLQLI 49 (134)
T ss_pred CCeeECHHHHHHHHHH
Confidence 3457999999888665
No 102
>PRK12514 RNA polymerase sigma factor; Provisional
Probab=25.92 E-value=66 Score=27.13 Aligned_cols=45 Identities=13% Similarity=0.343 Sum_probs=30.7
Q ss_pred CCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCCCeeeeechhhhHHHH
Q 022713 153 LTKEQSALLEESFKQHSTLNPKQKQALARQLNLRPRQVEVWFQNRRARTK 202 (293)
Q Consensus 153 ft~~Ql~~Le~~F~~~~~ps~~~r~~LA~~LgLs~rqVqvWFQNRRaK~K 202 (293)
++..+..++...|-.. ...++||..+|+++..|+++...-|.+.|
T Consensus 130 L~~~~r~i~~l~~~~g-----~s~~eIA~~lgis~~tV~~~l~Rar~~Lr 174 (179)
T PRK12514 130 LEKDRAAAVRRAYLEG-----LSYKELAERHDVPLNTMRTWLRRSLLKLR 174 (179)
T ss_pred CCHHHHHHHHHHHHcC-----CCHHHHHHHHCCChHHHHHHHHHHHHHHH
Confidence 6666766666665322 23578999999999999988764444443
No 103
>cd04770 HTH_HMRTR Helix-Turn-Helix DNA binding domain of Heavy Metal Resistance transcription regulators. Helix-turn-helix (HTH) heavy metal resistance transcription regulators (HMRTR): MerR1 (mercury), CueR (copper), CadR (cadmium), PbrR (lead), ZntR (zinc), and other related proteins. These transcription regulators mediate responses to heavy metal stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.
Probab=25.61 E-value=2.2e+02 Score=22.84 Aligned_cols=72 Identities=13% Similarity=0.020 Sum_probs=38.0
Q ss_pred CCcCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCCCeeeeechhhhHHHHhhhhhhhhHHHHHHhhHhhHHHHHHHH
Q 022713 150 KLRLTKEQSALLEESFKQHSTLNPKQKQALARQLNLRPRQVEVWFQNRRARTKLKQTEVDCEFLKKCCETLTDENRRLHK 229 (293)
Q Consensus 150 Rt~ft~~Ql~~Le~~F~~~~~ps~~~r~~LA~~LgLs~rqVqvWFQNRRaK~Krkq~~~~~e~Lk~~~~~l~~en~~l~~ 229 (293)
...|+..++..|+.. ...+.+|++-..|+..|.+..... .....-...|....+.+.++.++|+.
T Consensus 36 yR~Y~~~~i~~l~~I-------------~~lr~~G~sl~eI~~~l~~~~~~~--~~~~~~~~~l~~~~~~l~~~i~~l~~ 100 (123)
T cd04770 36 YRLYGEADLARLRFI-------------RRAQALGFSLAEIRELLSLRDDGA--APCAEVRALLEEKLAEVEAKIAELQA 100 (123)
T ss_pred CccCCHHHHHHHHHH-------------HHHHHCCCCHHHHHHHHHhhhcCC--CCHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 447999999999543 334666777666666665433210 00011123344445555555555555
Q ss_pred HHHHHHH
Q 022713 230 ELQELKA 236 (293)
Q Consensus 230 e~~~l~a 236 (293)
....+..
T Consensus 101 ~~~~l~~ 107 (123)
T cd04770 101 LRAELAG 107 (123)
T ss_pred HHHHHHH
Confidence 5444433
No 104
>PF13518 HTH_28: Helix-turn-helix domain
Probab=25.59 E-value=21 Score=23.86 Aligned_cols=20 Identities=20% Similarity=0.513 Sum_probs=17.5
Q ss_pred HHHHHHHhCCCCCeeeeech
Q 022713 176 KQALARQLNLRPRQVEVWFQ 195 (293)
Q Consensus 176 r~~LA~~LgLs~rqVqvWFQ 195 (293)
..++|.++|++..+|..|.+
T Consensus 15 ~~~~a~~~gis~~tv~~w~~ 34 (52)
T PF13518_consen 15 VREIAREFGISRSTVYRWIK 34 (52)
T ss_pred HHHHHHHHCCCHhHHHHHHH
Confidence 45699999999999999975
No 105
>PF07716 bZIP_2: Basic region leucine zipper; InterPro: IPR011700 The basic-leucine zipper (bZIP) transcription factors [, ] of eukaryotes are proteins that contain a basic region mediating sequence-specific DNA-binding, followed by a leucine zipper region (see IPR002158 from INTERPRO), which is required for dimerization.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0043565 sequence-specific DNA binding, 0046983 protein dimerization activity, 0006355 regulation of transcription, DNA-dependent; PDB: 1NWQ_A 1H89_B 1H88_A 1GTW_B 2E43_A 1IO4_A 1GU4_B 2E42_A 1H8A_B 1GU5_B ....
Probab=25.44 E-value=2e+02 Score=19.98 Aligned_cols=26 Identities=27% Similarity=0.326 Sum_probs=17.7
Q ss_pred hhhhhhHHHHHHhhHhhHHHHHHHHH
Q 022713 205 QTEVDCEFLKKCCETLTDENRRLHKE 230 (293)
Q Consensus 205 q~~~~~e~Lk~~~~~l~~en~~l~~e 230 (293)
..+.....|...+..|..++..|+.|
T Consensus 29 ~le~~~~~L~~en~~L~~~i~~L~~E 54 (54)
T PF07716_consen 29 ELEQEVQELEEENEQLRQEIAQLERE 54 (54)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHhcc
Confidence 34555567777777777777777654
No 106
>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=25.25 E-value=55 Score=26.80 Aligned_cols=39 Identities=26% Similarity=0.262 Sum_probs=28.9
Q ss_pred cCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCCCeeeeech
Q 022713 152 RLTKEQSALLEESFKQHSTLNPKQKQALARQLNLRPRQVEVWFQ 195 (293)
Q Consensus 152 ~ft~~Ql~~Le~~F~~~~~ps~~~r~~LA~~LgLs~rqVqvWFQ 195 (293)
.++..+..++...|-.. ....+||..+|++...|+++..
T Consensus 111 ~L~~~~r~v~~l~~~~g-----~~~~eIA~~l~is~~tv~~~l~ 149 (159)
T TIGR02989 111 KLPERQRELLQLRYQRG-----VSLTALAEQLGRTVNAVYKALS 149 (159)
T ss_pred HCCHHHHHHHHHHHhcC-----CCHHHHHHHhCCCHHHHHHHHH
Confidence 47777777777755322 2457899999999999997754
No 107
>TIGR02959 SigZ RNA polymerase sigma factor, SigZ family. This family of RNA polymerase sigma factors is a member of the Sigma-70 subfamily (TIGR02937). One of these is designated as SigZ in B. subtilis (Swiss_Prot: SIGZ_BACSU). Interestingly, this group has a very sporatic distribution, B. subtilis, for instance, being the only sequenced strain of Bacilli with a member. Dechloromonas aromatica RCB appears to have two of these sigma factors. A member appears on a plasmid found in Photobacterium profundum SS9 and Vibrio fischeri ES114 (where a second one is chromosomally encoded).
Probab=24.64 E-value=58 Score=27.52 Aligned_cols=39 Identities=18% Similarity=0.150 Sum_probs=29.3
Q ss_pred cCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCCCeeeeech
Q 022713 152 RLTKEQSALLEESFKQHSTLNPKQKQALARQLNLRPRQVEVWFQ 195 (293)
Q Consensus 152 ~ft~~Ql~~Le~~F~~~~~ps~~~r~~LA~~LgLs~rqVqvWFQ 195 (293)
.+++.+..+|...|-... ...+||..+|+++..|+++..
T Consensus 100 ~L~~~~r~v~~l~~~~g~-----s~~eIA~~lgis~~tV~~~l~ 138 (170)
T TIGR02959 100 ELPDEYREAIRLTELEGL-----SQQEIAEKLGLSLSGAKSRVQ 138 (170)
T ss_pred hCCHHHHHHHHHHHHcCC-----CHHHHHHHHCCCHHHHHHHHH
Confidence 577888888877664332 457899999999999887664
No 108
>COG4367 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=24.46 E-value=50 Score=26.31 Aligned_cols=38 Identities=21% Similarity=0.299 Sum_probs=29.9
Q ss_pred CCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCCCee
Q 022713 153 LTKEQSALLEESFKQHSTLNPKQKQALARQLNLRPRQV 190 (293)
Q Consensus 153 ft~~Ql~~Le~~F~~~~~ps~~~r~~LA~~LgLs~rqV 190 (293)
+.++|+..-...|+.+--.+.-..+++|.+|++++-.|
T Consensus 3 Ln~eq~~~Tk~elqan~el~~LS~~~iA~~Ln~t~~~l 40 (97)
T COG4367 3 LNPEQKQRTKQELQANFELCPLSDEEIATALNWTEVKL 40 (97)
T ss_pred CCHHHHHHHHHHHHHhhhhccccHHHHHHHhCCCHHHH
Confidence 56788887777777777777778889999999887543
No 109
>PF07795 DUF1635: Protein of unknown function (DUF1635); InterPro: IPR012862 The members of this family include sequences that are parts of hypothetical proteins expressed by plant species. The region in question is about 170 amino acids long.
Probab=24.42 E-value=5.4e+02 Score=23.60 Aligned_cols=39 Identities=23% Similarity=0.278 Sum_probs=29.8
Q ss_pred hHHHHhhhhhhhhHHHHHHhhHhhHHHHHHHHHHHHHHH
Q 022713 198 RARTKLKQTEVDCEFLKKCCETLTDENRRLHKELQELKA 236 (293)
Q Consensus 198 RaK~Krkq~~~~~e~Lk~~~~~l~~en~~l~~e~~~l~a 236 (293)
+|+...++.+.+...|+........|.++.+.+++.|-.
T Consensus 23 ~A~EElRk~eeqi~~L~~Ll~~a~~ERDEAr~qlq~Ll~ 61 (214)
T PF07795_consen 23 EANEELRKREEQIAHLKDLLKKAYQERDEAREQLQKLLL 61 (214)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 455556666777777888888888899999999988753
No 110
>TIGR02449 conserved hypothetical protein TIGR02449. Members of this family are small proteins, typically 73 amino acids in length, with single copies in each of several Proteobacteria, including Xylella fastidiosa, Pseudomonas aeruginosa, and Xanthomonas campestris. The function is unknown.
Probab=24.14 E-value=2e+02 Score=21.40 Aligned_cols=26 Identities=31% Similarity=0.350 Sum_probs=13.2
Q ss_pred hhHHHHHHhhHhhHHHHHHHHHHHHH
Q 022713 209 DCEFLKKCCETLTDENRRLHKELQEL 234 (293)
Q Consensus 209 ~~e~Lk~~~~~l~~en~~l~~e~~~l 234 (293)
..+.|-..|+.|..||..|+.++..+
T Consensus 8 kle~Li~~~~~L~~EN~~Lr~q~~~~ 33 (65)
T TIGR02449 8 QVEHLLEYLERLKSENRLLRAQEKTW 33 (65)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 34444555555555555555554444
No 111
>PF08280 HTH_Mga: M protein trans-acting positive regulator (MGA) HTH domain; InterPro: IPR013199 Mga is a DNA-binding protein that activates the expression of several important virulence genes in group A streptococcus in response to changing environmental conditions [].; PDB: 2WTE_A 3SQN_A.
Probab=24.07 E-value=40 Score=23.95 Aligned_cols=33 Identities=36% Similarity=0.478 Sum_probs=24.5
Q ss_pred HHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCCCeee
Q 022713 155 KEQSALLEESFKQHSTLNPKQKQALARQLNLRPRQVE 191 (293)
Q Consensus 155 ~~Ql~~Le~~F~~~~~ps~~~r~~LA~~LgLs~rqVq 191 (293)
..|+..|+-.|. +...+.. +||..+|++++.|+
T Consensus 5 ~rq~~Ll~~L~~-~~~~~~~---ela~~l~~S~rti~ 37 (59)
T PF08280_consen 5 KRQLKLLELLLK-NKWITLK---ELAKKLNISERTIK 37 (59)
T ss_dssp HHHHHHHHHHHH-HTSBBHH---HHHHHCTS-HHHHH
T ss_pred HHHHHHHHHHHc-CCCCcHH---HHHHHHCCCHHHHH
Confidence 357888888888 6666654 89999999987654
No 112
>PRK12515 RNA polymerase sigma factor; Provisional
Probab=23.98 E-value=70 Score=27.36 Aligned_cols=46 Identities=9% Similarity=0.224 Sum_probs=32.2
Q ss_pred cCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCCCeeeeechhhhHHHH
Q 022713 152 RLTKEQSALLEESFKQHSTLNPKQKQALARQLNLRPRQVEVWFQNRRARTK 202 (293)
Q Consensus 152 ~ft~~Ql~~Le~~F~~~~~ps~~~r~~LA~~LgLs~rqVqvWFQNRRaK~K 202 (293)
.++..+..+|...|-.. ....+||..+|+++..|++....-|.+.|
T Consensus 131 ~L~~~~r~vl~l~~~~~-----~s~~eIA~~lgis~~tV~~~l~Rar~~Lr 176 (189)
T PRK12515 131 KLSPAHREIIDLVYYHE-----KSVEEVGEIVGIPESTVKTRMFYARKKLA 176 (189)
T ss_pred hCCHHHHHHHHHHHHcC-----CCHHHHHHHHCcCHHHHHHHHHHHHHHHH
Confidence 47788888887765432 23568999999999999887654444444
No 113
>PRK09644 RNA polymerase sigma factor SigM; Provisional
Probab=23.81 E-value=57 Score=27.20 Aligned_cols=46 Identities=15% Similarity=0.070 Sum_probs=31.2
Q ss_pred cCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCCCeeeeechhhhHHHH
Q 022713 152 RLTKEQSALLEESFKQHSTLNPKQKQALARQLNLRPRQVEVWFQNRRARTK 202 (293)
Q Consensus 152 ~ft~~Ql~~Le~~F~~~~~ps~~~r~~LA~~LgLs~rqVqvWFQNRRaK~K 202 (293)
.++..+..++...|-.. ...++||..+|+++..|++|.+.-|.+.|
T Consensus 108 ~L~~~~r~v~~l~~~~g-----~s~~eIA~~lgis~~tv~~~l~Rar~~Lr 153 (165)
T PRK09644 108 TLPVIEAQAILLCDVHE-----LTYEEAASVLDLKLNTYKSHLFRGRKRLK 153 (165)
T ss_pred hCCHHHHHHHHhHHHhc-----CCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Confidence 46777777776543222 24578999999999999988764444433
No 114
>cd04761 HTH_MerR-SF Helix-Turn-Helix DNA binding domain of transcription regulators from the MerR superfamily. Helix-turn-helix (HTH) transcription regulator MerR superfamily, N-terminal domain. The MerR family transcription regulators have been shown to mediate responses to stress including exposure to heavy metals, drugs, or oxygen radicals in eubacterial and some archaeal species. They regulate transcription of multidrug/metal ion transporter genes and oxidative stress regulons by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.
Probab=23.65 E-value=20 Score=23.60 Aligned_cols=23 Identities=13% Similarity=0.137 Sum_probs=19.1
Q ss_pred HHHHHHHhCCCCCeeeeechhhh
Q 022713 176 KQALARQLNLRPRQVEVWFQNRR 198 (293)
Q Consensus 176 r~~LA~~LgLs~rqVqvWFQNRR 198 (293)
..++|+.+|++.+.|+.|.++-.
T Consensus 3 ~~e~a~~~gv~~~tlr~~~~~g~ 25 (49)
T cd04761 3 IGELAKLTGVSPSTLRYYERIGL 25 (49)
T ss_pred HHHHHHHHCcCHHHHHHHHHCCC
Confidence 45789999999999999976554
No 115
>cd04781 HTH_MerR-like_sg6 Helix-Turn-Helix DNA binding domain of putative transcription regulators from the MerR superfamily. Putative helix-turn-helix (HTH) MerR-like transcription regulators (subgroup 6) with at least two conserved cysteines present in the C-terminal portion of the protein. Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, an
Probab=23.38 E-value=2.6e+02 Score=22.53 Aligned_cols=68 Identities=16% Similarity=0.197 Sum_probs=37.8
Q ss_pred CCCcCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCCCeeeeechhhhHHHHhhhhhhhhHHHHHHhhHhhHHHHHHH
Q 022713 149 KKLRLTKEQSALLEESFKQHSTLNPKQKQALARQLNLRPRQVEVWFQNRRARTKLKQTEVDCEFLKKCCETLTDENRRLH 228 (293)
Q Consensus 149 ~Rt~ft~~Ql~~Le~~F~~~~~ps~~~r~~LA~~LgLs~rqVqvWFQNRRaK~Krkq~~~~~e~Lk~~~~~l~~en~~l~ 228 (293)
.+..|+..++..|.. ....+.+|++-.+|+.++.+.... ....+.+....+.+.++.++++
T Consensus 34 gyR~Y~~~~l~~l~~-------------I~~lr~~G~~L~eI~~~l~~~~~~------~~~~~~l~~~~~~l~~~i~~l~ 94 (120)
T cd04781 34 LRRQYDPQVLDRLAL-------------IALGRAAGFSLDEIQAMLSHDGKP------PIDRQLLKAKAAELDQQIQRLQ 94 (120)
T ss_pred CceecCHHHHHHHHH-------------HHHHHHcCCCHHHHHHHHhccCCc------HHHHHHHHHHHHHHHHHHHHHH
Confidence 345799999998854 344666677777777666554210 0112334444445555555555
Q ss_pred HHHHHHH
Q 022713 229 KELQELK 235 (293)
Q Consensus 229 ~e~~~l~ 235 (293)
.....+.
T Consensus 95 ~~~~~L~ 101 (120)
T cd04781 95 AMRELLR 101 (120)
T ss_pred HHHHHHH
Confidence 5544443
No 116
>PRK09648 RNA polymerase sigma factor SigD; Reviewed
Probab=23.11 E-value=66 Score=27.48 Aligned_cols=39 Identities=18% Similarity=0.127 Sum_probs=29.9
Q ss_pred cCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCCCeeeeech
Q 022713 152 RLTKEQSALLEESFKQHSTLNPKQKQALARQLNLRPRQVEVWFQ 195 (293)
Q Consensus 152 ~ft~~Ql~~Le~~F~~~~~ps~~~r~~LA~~LgLs~rqVqvWFQ 195 (293)
.++..|..++...|-.. ...++||..+|++...|+.+..
T Consensus 139 ~L~~~~r~i~~l~~~~g-----~s~~EIA~~lgis~~tV~~~l~ 177 (189)
T PRK09648 139 TLPEKQREILILRVVVG-----LSAEETAEAVGSTPGAVRVAQH 177 (189)
T ss_pred hCCHHHHHHHHHHHHcC-----CCHHHHHHHHCCCHHHHHHHHH
Confidence 57788888887765443 2467899999999999988764
No 117
>PF11167 DUF2953: Protein of unknown function (DUF2953); InterPro: IPR021338 This family of proteins has no known function.
Probab=22.92 E-value=9.2 Score=26.69 Aligned_cols=19 Identities=37% Similarity=0.758 Sum_probs=15.3
Q ss_pred CCCCCCCCCcceeeccccc
Q 022713 1 MGFDDGCNTGLVLGLGFAS 19 (293)
Q Consensus 1 ~~~~~~~~~~~~~~~~~~~ 19 (293)
+|++|.+.||++.|+--+.
T Consensus 3 ~G~~Daa~Tgi~~G~l~~~ 21 (53)
T PF11167_consen 3 IGLGDAADTGILYGLLWAI 21 (53)
T ss_pred eeccCHHHHHHHHHHHHHH
Confidence 5899999999988876544
No 118
>PRK00888 ftsB cell division protein FtsB; Reviewed
Probab=22.63 E-value=1.4e+02 Score=24.08 Aligned_cols=39 Identities=15% Similarity=0.067 Sum_probs=30.8
Q ss_pred eechhhhHHHHhhhhhhhhHHHHHHhhHhhHHHHHHHHH
Q 022713 192 VWFQNRRARTKLKQTEVDCEFLKKCCETLTDENRRLHKE 230 (293)
Q Consensus 192 vWFQNRRaK~Krkq~~~~~e~Lk~~~~~l~~en~~l~~e 230 (293)
-|+..+..+.+....+.+++.++..+..|..+..+|+..
T Consensus 25 G~~~~~~l~~q~~~~~~e~~~l~~~n~~L~~eI~~L~~~ 63 (105)
T PRK00888 25 GILDYWRVNDQVAAQQQTNAKLKARNDQLFAEIDDLKGG 63 (105)
T ss_pred cHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhCc
Confidence 456666777777778888888999999999998888763
No 119
>TIGR02948 SigW_bacill RNA polymerase sigma-W factor. This sigma factor is restricted to certain lineages of the order Bacillales.
Probab=22.51 E-value=62 Score=27.28 Aligned_cols=46 Identities=11% Similarity=0.166 Sum_probs=31.8
Q ss_pred cCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCCCeeeeechhhhHHHH
Q 022713 152 RLTKEQSALLEESFKQHSTLNPKQKQALARQLNLRPRQVEVWFQNRRARTK 202 (293)
Q Consensus 152 ~ft~~Ql~~Le~~F~~~~~ps~~~r~~LA~~LgLs~rqVqvWFQNRRaK~K 202 (293)
.+++.+..++...|-. ...-.++|..+|++...|+++++.-|.+.|
T Consensus 136 ~L~~~~r~v~~l~~~~-----g~s~~eIA~~lgis~~~v~~~l~Rar~~Lr 181 (187)
T TIGR02948 136 ALPPKYRMVIVLKYME-----DLSLKEISEILDLPVGTVKTRIHRGREALR 181 (187)
T ss_pred hCCHHHhHHhhhHHhc-----CCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Confidence 4777777777665432 224568999999999999988864444433
No 120
>PRK12537 RNA polymerase sigma factor; Provisional
Probab=22.46 E-value=83 Score=26.78 Aligned_cols=44 Identities=11% Similarity=0.244 Sum_probs=30.3
Q ss_pred cCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCCCeeeeechhhhHH
Q 022713 152 RLTKEQSALLEESFKQHSTLNPKQKQALARQLNLRPRQVEVWFQNRRAR 200 (293)
Q Consensus 152 ~ft~~Ql~~Le~~F~~~~~ps~~~r~~LA~~LgLs~rqVqvWFQNRRaK 200 (293)
.++..+..++...|-.. ....+||..+|++...|++|...-|.+
T Consensus 133 ~L~~~~r~i~~l~~~~~-----~s~~eIA~~lgis~~tV~~~l~ra~~~ 176 (182)
T PRK12537 133 QLEPARRNCILHAYVDG-----CSHAEIAQRLGAPLGTVKAWIKRSLKA 176 (182)
T ss_pred hCCHHHHHHHHHHHHcC-----CCHHHHHHHHCCChhhHHHHHHHHHHH
Confidence 46677777666655332 235689999999999999887544433
No 121
>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=22.12 E-value=70 Score=25.87 Aligned_cols=43 Identities=16% Similarity=0.187 Sum_probs=28.8
Q ss_pred cCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCCCeeeeechhhhH
Q 022713 152 RLTKEQSALLEESFKQHSTLNPKQKQALARQLNLRPRQVEVWFQNRRA 199 (293)
Q Consensus 152 ~ft~~Ql~~Le~~F~~~~~ps~~~r~~LA~~LgLs~rqVqvWFQNRRa 199 (293)
.++..+..+|...|-.. ....+||..+|+++..|+.+...-|.
T Consensus 113 ~L~~~~r~il~l~~~~~-----~~~~eIA~~lgis~~tv~~~~~ra~~ 155 (161)
T TIGR02985 113 KLPEQCRKIFILSRFEG-----KSYKEIAEELGISVKTVEYHISKALK 155 (161)
T ss_pred HCCHHHHHHHHHHHHcC-----CCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 35667777776655322 23457999999999999887653333
No 122
>PRK05602 RNA polymerase sigma factor; Reviewed
Probab=22.10 E-value=65 Score=27.41 Aligned_cols=45 Identities=13% Similarity=0.155 Sum_probs=30.2
Q ss_pred CCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCCCeeeeechhhhHHHH
Q 022713 153 LTKEQSALLEESFKQHSTLNPKQKQALARQLNLRPRQVEVWFQNRRARTK 202 (293)
Q Consensus 153 ft~~Ql~~Le~~F~~~~~ps~~~r~~LA~~LgLs~rqVqvWFQNRRaK~K 202 (293)
+++.+..++...|-.. ..-.+||..+|++...|+.+...-|.+.|
T Consensus 129 L~~~~r~i~~l~~~~g-----~s~~EIA~~lgis~~tV~~~l~Rar~~Lr 173 (186)
T PRK05602 129 LPERQREAIVLQYYQG-----LSNIEAAAVMDISVDALESLLARGRRALR 173 (186)
T ss_pred CCHHHHHHhhHHHhcC-----CCHHHHHHHhCcCHHHHHHHHHHHHHHHH
Confidence 5677777776654322 23568999999999999988754443333
No 123
>PF13936 HTH_38: Helix-turn-helix domain; PDB: 2W48_A.
Probab=21.99 E-value=29 Score=23.30 Aligned_cols=39 Identities=21% Similarity=0.209 Sum_probs=18.7
Q ss_pred CcCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCCCeeeeec
Q 022713 151 LRLTKEQSALLEESFKQHSTLNPKQKQALARQLNLRPRQVEVWF 194 (293)
Q Consensus 151 t~ft~~Ql~~Le~~F~~~~~ps~~~r~~LA~~LgLs~rqVqvWF 194 (293)
..+|.+|...++..+... .-..+||+.||.+...|..|.
T Consensus 3 ~~Lt~~eR~~I~~l~~~G-----~s~~~IA~~lg~s~sTV~rel 41 (44)
T PF13936_consen 3 KHLTPEERNQIEALLEQG-----MSIREIAKRLGRSRSTVSREL 41 (44)
T ss_dssp ---------HHHHHHCS--------HHHHHHHTT--HHHHHHHH
T ss_pred cchhhhHHHHHHHHHHcC-----CCHHHHHHHHCcCcHHHHHHH
Confidence 468888888888887533 345579999998887766554
No 124
>PF11365 DUF3166: Protein of unknown function (DUF3166); InterPro: IPR021507 This eukaryotic family of proteins has no known function.
Probab=21.68 E-value=1.9e+02 Score=23.28 Aligned_cols=32 Identities=34% Similarity=0.548 Sum_probs=26.9
Q ss_pred hhhhhHHHHHHhhHhhHHHHHHHHHHHHHHHh
Q 022713 206 TEVDCEFLKKCCETLTDENRRLHKELQELKAL 237 (293)
Q Consensus 206 ~~~~~e~Lk~~~~~l~~en~~l~~e~~~l~al 237 (293)
-+.+.+.|.+....+.++|+.|..|+.+++..
T Consensus 13 vEEEa~LlRRkl~ele~eN~~l~~EL~kyk~~ 44 (96)
T PF11365_consen 13 VEEEAELLRRKLSELEDENKQLTEELNKYKSK 44 (96)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 35567788888889999999999999998764
No 125
>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=21.52 E-value=75 Score=26.79 Aligned_cols=44 Identities=23% Similarity=0.213 Sum_probs=30.7
Q ss_pred CCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCCCeeeeechhhhHHH
Q 022713 153 LTKEQSALLEESFKQHSTLNPKQKQALARQLNLRPRQVEVWFQNRRART 201 (293)
Q Consensus 153 ft~~Ql~~Le~~F~~~~~ps~~~r~~LA~~LgLs~rqVqvWFQNRRaK~ 201 (293)
+++.|..++...|-.. ..-.++|..||+++..|++....-|.+.
T Consensus 135 Lp~~~r~v~~l~~~~g-----~s~~EIA~~lgis~~tVk~~l~Rar~~L 178 (183)
T TIGR02999 135 VDPRQAEVVELRFFAG-----LTVEEIAELLGVSVRTVERDWRFARAWL 178 (183)
T ss_pred CCHHHHHHHHHHHHcC-----CCHHHHHHHhCCCHHHHHHHHHHHHHHH
Confidence 6677777776665433 2356899999999999998876444433
No 126
>PRK13169 DNA replication intiation control protein YabA; Reviewed
Probab=21.43 E-value=2.1e+02 Score=23.41 Aligned_cols=32 Identities=28% Similarity=0.222 Sum_probs=23.0
Q ss_pred hhhhhhHHHHHHhhHhhHHHHHHHHHHHHHHH
Q 022713 205 QTEVDCEFLKKCCETLTDENRRLHKELQELKA 236 (293)
Q Consensus 205 q~~~~~e~Lk~~~~~l~~en~~l~~e~~~l~a 236 (293)
+.-.+...||.....+.+||.+|+-|.+.|+.
T Consensus 19 ~l~~el~~LK~~~~el~EEN~~L~iEN~~Lr~ 50 (110)
T PRK13169 19 VLLKELGALKKQLAELLEENTALRLENDKLRE 50 (110)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 44456667777777788888888888777754
No 127
>PRK15369 two component system sensor kinase SsrB; Provisional
Probab=21.39 E-value=1e+02 Score=25.15 Aligned_cols=45 Identities=20% Similarity=0.212 Sum_probs=34.1
Q ss_pred cCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCCCeeeeechhhhHHHH
Q 022713 152 RLTKEQSALLEESFKQHSTLNPKQKQALARQLNLRPRQVEVWFQNRRARTK 202 (293)
Q Consensus 152 ~ft~~Ql~~Le~~F~~~~~ps~~~r~~LA~~LgLs~rqVqvWFQNRRaK~K 202 (293)
.+|..+..+|... ... + ...++|..++++++.|+.|.+|=|.|..
T Consensus 149 ~lt~~e~~vl~l~-~~g-~----~~~~Ia~~l~~s~~tv~~~~~~~~~kl~ 193 (211)
T PRK15369 149 LLTPRERQILKLI-TEG-Y----TNRDIAEQLSISIKTVETHRLNMMRKLD 193 (211)
T ss_pred CCCHHHHHHHHHH-HCC-C----CHHHHHHHhCCCHHHHHHHHHHHHHHhC
Confidence 4888888888773 322 2 2578999999999999999877665554
No 128
>TIGR02939 RpoE_Sigma70 RNA polymerase sigma factor RpoE. A sigma factor is a DNA-binding protein protein that binds to the DNA-directed RNA polymerase core to produce the holoenzyme capable of initiating transcription at specific sites. Different sigma factors act in vegetative growth, heat shock, extracytoplasmic functions (ECF), etc. This model represents the clade of sigma factors called RpoE. This protein may be called sigma-24, sigma-E factor, sigma-H factor, fecI-like sigma factor or alternative sigma factor AlgU.
Probab=21.27 E-value=58 Score=27.57 Aligned_cols=41 Identities=12% Similarity=0.072 Sum_probs=27.1
Q ss_pred CCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCCCeeeeechhhh
Q 022713 153 LTKEQSALLEESFKQHSTLNPKQKQALARQLNLRPRQVEVWFQNRR 198 (293)
Q Consensus 153 ft~~Ql~~Le~~F~~~~~ps~~~r~~LA~~LgLs~rqVqvWFQNRR 198 (293)
++..+..++...|-. ...-.+||..+|+++..|++|...-|
T Consensus 139 L~~~~r~v~~l~~~~-----~~s~~EIA~~lgis~~tv~~~l~rar 179 (190)
T TIGR02939 139 LPEDLRTAITLRELE-----GLSYEDIARIMDCPVGTVRSRIFRAR 179 (190)
T ss_pred CCHHHhhhhhhhhhc-----CCCHHHHHHHHCcCHHHHHHHHHHHH
Confidence 555555666544322 22456899999999999988874333
No 129
>PF10883 DUF2681: Protein of unknown function (DUF2681); InterPro: IPR020274 This entry contains membrane proteins with no known function.
Probab=20.91 E-value=2e+02 Score=22.64 Aligned_cols=18 Identities=39% Similarity=0.431 Sum_probs=8.1
Q ss_pred HHHHhhHhhHHHHHHHHH
Q 022713 213 LKKCCETLTDENRRLHKE 230 (293)
Q Consensus 213 Lk~~~~~l~~en~~l~~e 230 (293)
++++++.|.+||+.++.|
T Consensus 28 a~~~~~kL~~en~qlk~E 45 (87)
T PF10883_consen 28 AKKQNAKLQKENEQLKTE 45 (87)
T ss_pred HHHHHHHHHHHHHHHHHH
Confidence 334444444444444444
No 130
>PRK09639 RNA polymerase sigma factor SigX; Provisional
Probab=20.82 E-value=74 Score=26.29 Aligned_cols=43 Identities=14% Similarity=0.271 Sum_probs=31.1
Q ss_pred cCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCCCeeeeechhhhHH
Q 022713 152 RLTKEQSALLEESFKQHSTLNPKQKQALARQLNLRPRQVEVWFQNRRAR 200 (293)
Q Consensus 152 ~ft~~Ql~~Le~~F~~~~~ps~~~r~~LA~~LgLs~rqVqvWFQNRRaK 200 (293)
.++..+..+|...| .. + .-.+||..+|++...|+.+...-|.+
T Consensus 112 ~L~~~~r~il~l~~-~g-~----s~~eIA~~lgis~~tV~~~i~ra~~~ 154 (166)
T PRK09639 112 KMTERDRTVLLLRF-SG-Y----SYKEIAEALGIKESSVGTTLARAKKK 154 (166)
T ss_pred cCCHHHHHHHHHHH-cC-C----CHHHHHHHHCCCHHHHHHHHHHHHHH
Confidence 47777888887777 32 2 35689999999999999887433333
No 131
>COG2963 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=20.80 E-value=3.6e+02 Score=21.24 Aligned_cols=42 Identities=12% Similarity=0.184 Sum_probs=32.2
Q ss_pred CCcCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCC-CCCeeeeech
Q 022713 150 KLRLTKEQSALLEESFKQHSTLNPKQKQALARQLNL-RPRQVEVWFQ 195 (293)
Q Consensus 150 Rt~ft~~Ql~~Le~~F~~~~~ps~~~r~~LA~~LgL-s~rqVqvWFQ 195 (293)
|.+|+.+....+-+.+....+ -..++|+++|+ ...++..|-+
T Consensus 5 ~r~~s~EfK~~iv~~~~~~g~----sv~~vAr~~gv~~~~~l~~W~~ 47 (116)
T COG2963 5 RKKYSPEFKLEAVALYLRGGD----TVSEVAREFGIVSATQLYKWRI 47 (116)
T ss_pred cccCCHHHHHHHHHHHHhcCc----cHHHHHHHhCCCChHHHHHHHH
Confidence 678999887777666655544 46789999996 9999888864
No 132
>cd02413 40S_S3_KH K homology RNA-binding (KH) domain of the eukaryotic 40S small ribosomal subunit protein S3. S3 is part of the head region of the 40S ribosomal subunit and is believed to interact with mRNA as it threads its way from the latch into the channel. The KH motif is a beta-alpha-alpha-beta-beta unit that folds into an alpha-beta structure with a three stranded beta-sheet interupted by two contiguous helices. In general, KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.
Probab=20.60 E-value=96 Score=23.76 Aligned_cols=21 Identities=14% Similarity=0.338 Sum_probs=17.9
Q ss_pred HHHHHHHHhCCCCCeeeeech
Q 022713 175 QKQALARQLNLRPRQVEVWFQ 195 (293)
Q Consensus 175 ~r~~LA~~LgLs~rqVqvWFQ 195 (293)
-+..|...++|..-||++|+.
T Consensus 55 L~~~L~k~~~~~~~~i~v~~~ 75 (81)
T cd02413 55 LTSLVQKRFNFPEGSVELYAE 75 (81)
T ss_pred HHHHHHHHhCCCCCeEEEEEE
Confidence 356788889999999999985
No 133
>PRK09047 RNA polymerase factor sigma-70; Validated
Probab=20.53 E-value=82 Score=25.83 Aligned_cols=39 Identities=10% Similarity=0.082 Sum_probs=28.5
Q ss_pred cCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCCCeeeeech
Q 022713 152 RLTKEQSALLEESFKQHSTLNPKQKQALARQLNLRPRQVEVWFQ 195 (293)
Q Consensus 152 ~ft~~Ql~~Le~~F~~~~~ps~~~r~~LA~~LgLs~rqVqvWFQ 195 (293)
.++..|..++...|-... .-.+||..||++...|+++..
T Consensus 106 ~Lp~~~r~v~~l~~~~g~-----s~~EIA~~lgis~~tV~~~l~ 144 (161)
T PRK09047 106 KLPARQREAFLLRYWEDM-----DVAETAAAMGCSEGSVKTHCS 144 (161)
T ss_pred hCCHHHHHHHHHHHHhcC-----CHHHHHHHHCCCHHHHHHHHH
Confidence 477777777777653321 256899999999999887654
No 134
>PF06056 Terminase_5: Putative ATPase subunit of terminase (gpP-like); InterPro: IPR010332 This family of proteins are annotated as ATPase subunits of phage terminase after []. Terminases are viral proteins that are involved in packaging viral DNA into the capsid.; GO: 0005524 ATP binding, 0019069 viral capsid assembly
Probab=20.25 E-value=31 Score=24.89 Aligned_cols=25 Identities=20% Similarity=0.330 Sum_probs=19.9
Q ss_pred HHHHHHHhCCCCCeeeeechhhhHHHH
Q 022713 176 KQALARQLNLRPRQVEVWFQNRRARTK 202 (293)
Q Consensus 176 r~~LA~~LgLs~rqVqvWFQNRRaK~K 202 (293)
..+||..||++.+.|..|-+ |-+|.
T Consensus 16 ~~eIA~~Lg~~~~TV~~W~~--r~~W~ 40 (58)
T PF06056_consen 16 IKEIAEELGVPRSTVYSWKD--RYKWD 40 (58)
T ss_pred HHHHHHHHCCChHHHHHHHH--hhCcc
Confidence 46899999999999999963 45544
No 135
>PRK14127 cell division protein GpsB; Provisional
Probab=20.21 E-value=2.3e+02 Score=23.23 Aligned_cols=32 Identities=34% Similarity=0.422 Sum_probs=24.3
Q ss_pred hhhhhhHHHHHHhhHhhHHHHHHHHHHHHHHH
Q 022713 205 QTEVDCEFLKKCCETLTDENRRLHKELQELKA 236 (293)
Q Consensus 205 q~~~~~e~Lk~~~~~l~~en~~l~~e~~~l~a 236 (293)
+-..+++.|......|.+++.+|+.++.++..
T Consensus 34 ~V~~dye~l~~e~~~Lk~e~~~l~~~l~e~~~ 65 (109)
T PRK14127 34 DVIKDYEAFQKEIEELQQENARLKAQVDELTK 65 (109)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 44557777778888888888888888887755
No 136
>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=20.20 E-value=71 Score=21.09 Aligned_cols=36 Identities=17% Similarity=0.274 Sum_probs=24.8
Q ss_pred CHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCCCeeeeech
Q 022713 154 TKEQSALLEESFKQHSTLNPKQKQALARQLNLRPRQVEVWFQ 195 (293)
Q Consensus 154 t~~Ql~~Le~~F~~~~~ps~~~r~~LA~~LgLs~rqVqvWFQ 195 (293)
+..|..++...+. . ....++|..++++...|+.|..
T Consensus 2 ~~~e~~i~~~~~~--~----~s~~eia~~l~~s~~tv~~~~~ 37 (57)
T cd06170 2 TPREREVLRLLAE--G----KTNKEIADILGISEKTVKTHLR 37 (57)
T ss_pred CHHHHHHHHHHHc--C----CCHHHHHHHHCCCHHHHHHHHH
Confidence 4556666655432 1 2457889999999999888875
No 137
>PRK12541 RNA polymerase sigma factor; Provisional
Probab=20.06 E-value=70 Score=26.46 Aligned_cols=46 Identities=20% Similarity=0.114 Sum_probs=31.3
Q ss_pred cCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCCCeeeeechhhhHHHH
Q 022713 152 RLTKEQSALLEESFKQHSTLNPKQKQALARQLNLRPRQVEVWFQNRRARTK 202 (293)
Q Consensus 152 ~ft~~Ql~~Le~~F~~~~~ps~~~r~~LA~~LgLs~rqVqvWFQNRRaK~K 202 (293)
.++..|..+|...|-.. ....++|..+|++...|+.+...-|.+.|
T Consensus 112 ~L~~~~r~v~~l~~~~~-----~s~~eIA~~lgis~~tv~~~l~Rar~~L~ 157 (161)
T PRK12541 112 SLPLERRNVLLLRDYYG-----FSYKEIAEMTGLSLAKVKIELHRGRKETK 157 (161)
T ss_pred HCCHHHHHHhhhHHhcC-----CCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Confidence 47777777776655332 23568999999999998887754444433
Done!