Query 026004
Match_columns 245
No_of_seqs 140 out of 196
Neff 4.1
Searched_HMMs 46136
Date Fri Mar 29 02:34:25 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/026004.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/026004hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG0489 Transcription factor z 99.6 9E-17 2E-21 144.9 2.3 56 7-74 163-218 (261)
2 KOG0842 Transcription factor t 99.6 9.4E-16 2E-20 142.3 4.6 56 9-76 159-214 (307)
3 KOG0488 Transcription factor B 99.6 2.4E-15 5.2E-20 139.3 4.3 54 8-73 177-230 (309)
4 KOG0487 Transcription factor A 99.5 3.8E-15 8.3E-20 138.3 2.2 51 10-72 242-292 (308)
5 KOG0843 Transcription factor E 99.5 3.2E-14 6.9E-19 124.2 3.9 57 5-73 104-160 (197)
6 KOG0484 Transcription factor P 99.4 9.6E-14 2.1E-18 112.8 5.3 53 7-71 21-73 (125)
7 PF00046 Homeobox: Homeobox do 99.4 1.1E-13 2.3E-18 96.5 4.3 53 7-71 4-56 (57)
8 KOG0492 Transcription factor M 99.4 2.9E-13 6.2E-18 120.8 3.5 55 5-71 146-200 (246)
9 smart00389 HOX Homeodomain. DN 99.4 1.1E-12 2.3E-17 90.4 5.2 52 7-70 4-55 (56)
10 cd00086 homeodomain Homeodomai 99.3 2.5E-12 5.4E-17 88.8 5.2 54 7-72 4-57 (59)
11 KOG0485 Transcription factor N 99.3 8.1E-13 1.8E-17 118.7 2.4 59 6-76 107-165 (268)
12 KOG0483 Transcription factor H 99.3 1.7E-12 3.6E-17 114.4 4.1 56 8-75 55-110 (198)
13 KOG0493 Transcription factor E 99.3 2E-12 4.3E-17 118.9 4.2 58 2-71 245-302 (342)
14 KOG0850 Transcription factor D 99.3 3.2E-12 6.9E-17 115.1 3.6 55 5-71 124-178 (245)
15 KOG2251 Homeobox transcription 99.2 5.4E-12 1.2E-16 112.9 4.5 52 8-71 42-93 (228)
16 KOG0494 Transcription factor C 99.2 9.5E-12 2E-16 114.3 3.9 57 6-74 144-200 (332)
17 TIGR01565 homeo_ZF_HD homeobox 99.2 2E-11 4.3E-16 88.9 4.6 49 7-67 5-57 (58)
18 KOG0491 Transcription factor B 99.2 7.8E-12 1.7E-16 108.4 1.1 52 8-71 105-156 (194)
19 KOG0848 Transcription factor C 99.1 7.9E-12 1.7E-16 115.0 0.9 51 9-71 205-255 (317)
20 KOG0844 Transcription factor E 99.1 2.3E-11 5E-16 113.8 2.6 53 7-71 185-237 (408)
21 KOG0847 Transcription factor, 99.0 3.3E-10 7.1E-15 102.4 4.1 62 6-79 170-231 (288)
22 COG5576 Homeodomain-containing 98.8 1.8E-09 3.9E-14 92.0 3.5 56 7-74 55-110 (156)
23 KOG0490 Transcription factor, 98.8 1.5E-09 3.2E-14 92.7 2.5 56 8-75 65-120 (235)
24 KOG0486 Transcription factor P 98.8 3E-09 6.5E-14 99.7 3.1 53 8-72 117-169 (351)
25 KOG4577 Transcription factor L 98.3 2.9E-07 6.2E-12 86.2 3.2 55 5-71 169-223 (383)
26 KOG0775 Transcription factor S 98.2 2.5E-06 5.5E-11 79.1 6.8 62 2-75 175-236 (304)
27 KOG0849 Transcription factor P 98.2 9.3E-07 2E-11 83.6 3.4 55 8-74 181-235 (354)
28 PF05920 Homeobox_KN: Homeobox 98.0 3.1E-06 6.7E-11 57.3 2.5 37 22-68 3-39 (40)
29 KOG3802 Transcription factor O 97.2 0.00026 5.6E-09 68.5 3.7 55 8-74 299-353 (398)
30 KOG0774 Transcription factor P 97.0 0.0019 4.1E-08 60.3 6.6 53 9-71 194-247 (334)
31 KOG0490 Transcription factor, 96.8 0.00061 1.3E-08 58.2 2.0 57 6-74 156-212 (235)
32 KOG2252 CCAAT displacement pro 96.6 0.0025 5.3E-08 64.1 4.8 54 6-71 423-476 (558)
33 PF11717 Tudor-knot: RNA bindi 95.7 0.02 4.3E-07 40.6 4.3 40 122-163 12-51 (55)
34 PF15057 DUF4537: Domain of un 95.6 0.11 2.4E-06 42.6 9.1 95 118-229 6-100 (124)
35 cd00024 CHROMO Chromatin organ 93.1 0.14 2.9E-06 34.7 3.5 36 127-162 3-39 (55)
36 KOG1168 Transcription factor A 92.8 0.031 6.6E-07 53.2 -0.0 51 11-73 317-367 (385)
37 PF11569 Homez: Homeodomain le 92.7 0.11 2.3E-06 38.2 2.6 42 15-68 10-51 (56)
38 PF00385 Chromo: Chromo (CHRro 92.0 0.19 4.1E-06 34.6 3.1 37 127-163 1-39 (55)
39 cd04508 TUDOR Tudor domains ar 91.7 0.27 5.9E-06 32.6 3.6 36 117-157 5-40 (48)
40 smart00333 TUDOR Tudor domain. 91.5 0.66 1.4E-05 31.8 5.5 54 180-244 2-55 (57)
41 KOG0773 Transcription factor M 91.3 0.17 3.6E-06 47.0 3.0 54 7-70 243-297 (342)
42 KOG1146 Homeobox protein [Gene 91.2 0.18 4E-06 55.4 3.5 52 8-71 908-959 (1406)
43 smart00561 MBT Present in Dros 88.8 0.83 1.8E-05 36.0 4.6 46 113-163 31-76 (96)
44 smart00298 CHROMO Chromatin or 87.7 0.62 1.3E-05 31.2 2.9 36 128-163 3-38 (55)
45 PF02820 MBT: mbt repeat; Int 87.0 1 2.2E-05 33.3 3.9 45 114-163 1-45 (73)
46 PLN00104 MYST -like histone ac 86.8 2.7 5.8E-05 42.0 7.8 52 118-171 62-116 (450)
47 smart00743 Agenet Tudor-like d 86.5 2.3 5.1E-05 29.8 5.4 51 180-240 2-54 (61)
48 PF12824 MRP-L20: Mitochondria 84.8 0.87 1.9E-05 39.5 3.0 54 8-65 84-137 (164)
49 PF05641 Agenet: Agenet domain 84.7 1.4 3E-05 32.2 3.6 44 119-169 10-63 (68)
50 smart00333 TUDOR Tudor domain. 84.5 1.5 3.3E-05 29.9 3.6 39 117-163 10-48 (57)
51 PF12148 DUF3590: Protein of u 83.2 3.2 7E-05 32.8 5.3 70 117-189 3-74 (85)
52 smart00743 Agenet Tudor-like d 82.5 2.5 5.5E-05 29.6 4.1 34 117-155 10-45 (61)
53 PF12148 DUF3590: Protein of u 81.8 2.2 4.9E-05 33.6 3.9 48 196-244 9-56 (85)
54 PF11717 Tudor-knot: RNA bindi 78.6 11 0.00025 26.4 6.4 42 181-230 1-42 (55)
55 PF06003 SMN: Survival motor n 77.5 4.9 0.00011 37.0 5.3 53 179-240 67-119 (264)
56 PF04218 CENP-B_N: CENP-B N-te 77.1 4.5 9.8E-05 28.5 3.9 42 9-67 6-47 (53)
57 PF05641 Agenet: Agenet domain 74.8 9 0.0002 27.9 5.2 53 181-243 1-62 (68)
58 PF06003 SMN: Survival motor n 67.5 6.6 0.00014 36.2 3.7 41 117-161 76-116 (264)
59 cd04508 TUDOR Tudor domains ar 67.3 13 0.00029 24.3 4.3 46 184-239 1-46 (48)
60 PF10668 Phage_terminase: Phag 64.1 6.8 0.00015 29.0 2.5 31 19-63 13-43 (60)
61 COG3458 Acetyl esterase (deace 63.4 11 0.00024 36.1 4.4 93 110-209 55-162 (321)
62 KOG3623 Homeobox transcription 60.7 11 0.00024 40.3 4.2 44 15-70 568-611 (1007)
63 PF00196 GerE: Bacterial regul 59.2 7.7 0.00017 26.9 2.0 48 7-72 1-48 (58)
64 PF13936 HTH_38: Helix-turn-he 55.3 9.3 0.0002 25.7 1.8 33 7-46 2-34 (44)
65 smart00027 EH Eps15 homology d 53.1 37 0.0008 25.6 5.1 45 10-64 4-51 (96)
66 PF00249 Myb_DNA-binding: Myb- 52.8 42 0.0009 22.4 4.8 42 9-65 3-46 (48)
67 PF04967 HTH_10: HTH DNA bindi 50.7 21 0.00045 25.6 3.1 34 10-46 1-37 (53)
68 smart00717 SANT SANT SWI3, AD 48.5 39 0.00085 21.0 4.0 43 8-65 2-45 (49)
69 cd00167 SANT 'SWI3, ADA2, N-Co 44.9 52 0.0011 20.2 4.1 41 9-64 1-42 (45)
70 PF13518 HTH_28: Helix-turn-he 42.5 20 0.00044 23.6 1.9 23 34-66 14-36 (52)
71 PTZ00184 calmodulin; Provision 41.4 1E+02 0.0022 23.6 6.0 40 7-46 2-44 (149)
72 cd06171 Sigma70_r4 Sigma70, re 41.4 30 0.00066 21.6 2.6 43 9-68 10-52 (55)
73 PF09465 LBR_tudor: Lamin-B re 39.7 63 0.0014 23.7 4.2 49 179-237 4-52 (55)
74 cd00569 HTH_Hin_like Helix-tur 38.7 69 0.0015 17.6 3.8 37 9-62 5-41 (42)
75 PRK07571 bidirectional hydroge 38.5 80 0.0017 27.5 5.5 40 7-46 13-68 (169)
76 PRK07539 NADH dehydrogenase su 38.1 69 0.0015 26.9 4.9 20 27-46 35-54 (154)
77 PF00567 TUDOR: Tudor domain; 37.8 42 0.00092 24.8 3.3 54 118-179 60-118 (121)
78 PF13921 Myb_DNA-bind_6: Myb-l 35.3 1.3E+02 0.0028 20.6 5.2 40 10-65 1-41 (60)
79 PF13873 Myb_DNA-bind_5: Myb/S 35.2 42 0.00091 24.3 2.8 59 8-70 3-72 (78)
80 PF03672 UPF0154: Uncharacteri 33.9 73 0.0016 24.0 3.9 36 16-61 20-55 (64)
81 PRK10072 putative transcriptio 33.7 32 0.00069 27.3 2.1 23 35-67 49-71 (96)
82 PF11523 DUF3223: Protein of u 33.6 50 0.0011 25.0 3.0 31 204-236 41-72 (76)
83 PF02796 HTH_7: Helix-turn-hel 33.3 50 0.0011 22.1 2.7 31 9-46 5-35 (45)
84 PF08880 QLQ: QLQ; InterPro: 33.1 37 0.00079 22.8 2.0 14 8-21 1-14 (37)
85 COG3413 Predicted DNA binding 32.3 56 0.0012 28.5 3.6 36 8-46 154-192 (215)
86 KOG3026 Splicing factor SPF30 31.5 1.2E+02 0.0026 28.5 5.7 47 105-159 90-136 (262)
87 PF13443 HTH_26: Cro/C1-type H 30.6 74 0.0016 21.8 3.3 23 34-66 12-34 (63)
88 PLN00104 MYST -like histone ac 29.5 1.3E+02 0.0028 30.4 5.9 49 179-230 52-100 (450)
89 PTZ00183 centrin; Provisional 29.1 1.7E+02 0.0037 22.8 5.5 39 6-44 7-48 (158)
90 PRK11511 DNA-binding transcrip 29.1 33 0.00071 27.5 1.5 38 18-65 11-48 (127)
91 PF11516 DUF3220: Protein of u 27.5 37 0.00079 27.2 1.4 19 47-66 22-40 (106)
92 PRK03975 tfx putative transcri 26.4 50 0.0011 28.0 2.2 46 8-71 5-50 (141)
93 PF01476 LysM: LysM domain; I 26.1 51 0.0011 21.0 1.7 21 32-62 6-26 (44)
94 smart00421 HTH_LUXR helix_turn 26.1 87 0.0019 20.0 2.9 44 9-70 3-46 (58)
95 COG5126 FRQ1 Ca2+-binding prot 25.6 1.7E+02 0.0037 25.4 5.3 42 5-46 9-53 (160)
96 PF08281 Sigma70_r4_2: Sigma-7 25.4 78 0.0017 21.2 2.6 28 28-65 22-49 (54)
97 KOG0031 Myosin regulatory ligh 25.3 87 0.0019 27.8 3.5 64 3-66 19-93 (171)
98 PF09225 Endonuc-PvuII: Restri 25.1 1.1E+02 0.0024 26.5 4.0 69 13-121 2-70 (155)
99 PF01381 HTH_3: Helix-turn-hel 25.0 86 0.0019 20.8 2.8 21 36-66 13-33 (55)
100 TIGR01321 TrpR trp operon repr 24.9 47 0.001 26.6 1.7 55 9-64 32-91 (94)
101 PRK10100 DNA-binding transcrip 24.6 68 0.0015 28.1 2.8 49 7-73 153-201 (216)
102 PF01527 HTH_Tnp_1: Transposas 24.5 89 0.0019 22.1 2.9 44 8-67 5-48 (76)
103 PRK15451 tRNA cmo(5)U34 methyl 24.4 1.7E+02 0.0038 25.7 5.3 46 8-66 188-233 (247)
104 PRK00523 hypothetical protein; 24.1 1.3E+02 0.0028 23.3 3.8 36 16-61 28-63 (72)
105 PF05506 DUF756: Domain of unk 23.6 89 0.0019 23.5 2.9 29 113-151 60-88 (89)
106 TIGR03070 couple_hipB transcri 23.4 2.1E+02 0.0046 18.5 4.4 19 27-45 39-57 (58)
107 PF13720 Acetyltransf_11: Udp 23.3 1.7E+02 0.0036 22.4 4.4 38 9-46 27-65 (83)
108 PF13384 HTH_23: Homeodomain-l 23.2 63 0.0014 21.3 1.8 22 33-64 18-39 (50)
109 PF04539 Sigma70_r3: Sigma-70 22.5 1.3E+02 0.0027 21.6 3.4 38 14-64 5-42 (78)
110 cd04761 HTH_MerR-SF Helix-Turn 22.4 65 0.0014 20.8 1.7 22 35-66 3-24 (49)
111 PF10844 DUF2577: Protein of u 22.1 94 0.002 24.4 2.8 21 179-200 75-95 (100)
112 PF09607 BrkDBD: Brinker DNA-b 21.9 69 0.0015 23.7 1.9 22 35-66 28-49 (58)
113 PHA01976 helix-turn-helix prot 21.3 1.2E+02 0.0026 21.0 3.0 20 27-46 39-58 (67)
114 TIGR02607 antidote_HigA addict 20.9 1E+02 0.0022 21.9 2.6 19 28-46 43-61 (78)
115 PF04545 Sigma70_r4: Sigma-70, 20.7 1.1E+02 0.0024 20.4 2.6 40 8-64 3-42 (50)
116 PRK10430 DNA-binding transcrip 20.4 1.4E+02 0.003 25.5 3.8 44 9-65 158-201 (239)
117 cd04762 HTH_MerR-trunc Helix-T 20.1 87 0.0019 19.5 1.9 23 35-67 3-25 (49)
118 PRK04217 hypothetical protein; 20.1 1.5E+02 0.0032 24.2 3.6 51 4-71 37-87 (110)
No 1
>KOG0489 consensus Transcription factor zerknullt and related HOX domain proteins [General function prediction only]
Probab=99.63 E-value=9e-17 Score=144.91 Aligned_cols=56 Identities=20% Similarity=0.375 Sum_probs=52.0
Q ss_pred cCCCCHHHHHHHHHHHHHhCCCCCCHHHHHHHHHHcCCCcccCCCCcCCcchhhhhhhcccccccccc
Q 026004 7 WPDFTLAEIKEMESMYKEIGEASLTQEYCKALATSFSFSASRAARPAITWLQVQSWFRDKQKKSQAKS 74 (245)
Q Consensus 7 ~~~FT~~Ql~eMEk~f~~~~~~y~~~~~rq~LA~~f~lS~~r~Gk~~v~~~QVk~WFQNRR~k~k~k~ 74 (245)
=+.||..|+.||||+|+. |+||++..|.+||..|+|+| +||||||||||||||...
T Consensus 163 RtayT~~QllELEkEFhf--N~YLtR~RRiEiA~~L~LtE----------rQIKIWFQNRRMK~Kk~~ 218 (261)
T KOG0489|consen 163 RTAFTRYQLLELEKEFHF--NKYLTRSRRIEIAHALNLTE----------RQIKIWFQNRRMKWKKEN 218 (261)
T ss_pred Ccccchhhhhhhhhhhcc--ccccchHHHHHHHhhcchhH----------HHHHHHHHHHHHHHHHhh
Confidence 367999999999999999 59999999999999999988 999999999999998443
No 2
>KOG0842 consensus Transcription factor tinman/NKX2-3, contains HOX domain [Transcription]
Probab=99.58 E-value=9.4e-16 Score=142.29 Aligned_cols=56 Identities=25% Similarity=0.497 Sum_probs=51.4
Q ss_pred CCCHHHHHHHHHHHHHhCCCCCCHHHHHHHHHHcCCCcccCCCCcCCcchhhhhhhcccccccccccC
Q 026004 9 DFTLAEIKEMESMYKEIGEASLTQEYCKALATSFSFSASRAARPAITWLQVQSWFRDKQKKSQAKSKS 76 (245)
Q Consensus 9 ~FT~~Ql~eMEk~f~~~~~~y~~~~~rq~LA~~f~lS~~r~Gk~~v~~~QVk~WFQNRR~k~k~k~~~ 76 (245)
-||+.||-|||+.|++ .+||+..+|+.||..|+||+ +||||||||||||.|.+-.-
T Consensus 159 LFSqAQV~ELERRFrq--QRYLSAPERE~LA~~LrLT~----------TQVKIWFQNrRYK~KR~~~d 214 (307)
T KOG0842|consen 159 LFSQAQVYELERRFRQ--QRYLSAPEREHLASSLRLTP----------TQVKIWFQNRRYKTKRQQKD 214 (307)
T ss_pred ccchhHHHHHHHHHHh--hhccccHhHHHHHHhcCCCc----------hheeeeeecchhhhhhhhhh
Confidence 4999999999999999 59999999999999999988 99999999999998755433
No 3
>KOG0488 consensus Transcription factor BarH and related HOX domain proteins [General function prediction only]
Probab=99.55 E-value=2.4e-15 Score=139.34 Aligned_cols=54 Identities=22% Similarity=0.418 Sum_probs=51.0
Q ss_pred CCCCHHHHHHHHHHHHHhCCCCCCHHHHHHHHHHcCCCcccCCCCcCCcchhhhhhhccccccccc
Q 026004 8 PDFTLAEIKEMESMYKEIGEASLTQEYCKALATSFSFSASRAARPAITWLQVQSWFRDKQKKSQAK 73 (245)
Q Consensus 8 ~~FT~~Ql~eMEk~f~~~~~~y~~~~~rq~LA~~f~lS~~r~Gk~~v~~~QVk~WFQNRR~k~k~k 73 (245)
+.||.-||.+|||.|+.. +||+...|.+||.+||||. .|||+||||||+|||.-
T Consensus 177 TaFT~~Ql~~LEkrF~~Q--KYLS~~DR~~LA~~LgLTd----------aQVKtWfQNRRtKWKrq 230 (309)
T KOG0488|consen 177 TAFSDHQLFELEKRFEKQ--KYLSVADRIELAASLGLTD----------AQVKTWFQNRRTKWKRQ 230 (309)
T ss_pred hhhhHHHHHHHHHHHHHh--hcccHHHHHHHHHHcCCch----------hhHHHHHhhhhHHHHHH
Confidence 679999999999999994 8999999999999999988 99999999999999843
No 4
>KOG0487 consensus Transcription factor Abd-B, contains HOX domain [Transcription]
Probab=99.51 E-value=3.8e-15 Score=138.32 Aligned_cols=51 Identities=22% Similarity=0.405 Sum_probs=48.7
Q ss_pred CCHHHHHHHHHHHHHhCCCCCCHHHHHHHHHHcCCCcccCCCCcCCcchhhhhhhcccccccc
Q 026004 10 FTLAEIKEMESMYKEIGEASLTQEYCKALATSFSFSASRAARPAITWLQVQSWFRDKQKKSQA 72 (245)
Q Consensus 10 FT~~Ql~eMEk~f~~~~~~y~~~~~rq~LA~~f~lS~~r~Gk~~v~~~QVk~WFQNRR~k~k~ 72 (245)
+|+.||.||||+|.- |.||+++.|-+|++.||||+ +||||||||||||.|.
T Consensus 242 YTK~QtlELEkEFlf--N~YitkeKR~ElSr~lNLTe----------RQVKIWFQNRRMK~KK 292 (308)
T KOG0487|consen 242 YTKHQTLELEKEFLF--NMYITKEKRLELSRTLNLTE----------RQVKIWFQNRRMKEKK 292 (308)
T ss_pred chHHHHHHHHHHHHH--HHHHhHHHHHHHHHhcccch----------hheeeeehhhhhHHhh
Confidence 899999999999999 59999999999999999999 9999999999999863
No 5
>KOG0843 consensus Transcription factor EMX1 and related HOX domain proteins [Transcription]
Probab=99.46 E-value=3.2e-14 Score=124.24 Aligned_cols=57 Identities=25% Similarity=0.408 Sum_probs=52.3
Q ss_pred CCcCCCCHHHHHHHHHHHHHhCCCCCCHHHHHHHHHHcCCCcccCCCCcCCcchhhhhhhccccccccc
Q 026004 5 DSWPDFTLAEIKEMESMYKEIGEASLTQEYCKALATSFSFSASRAARPAITWLQVQSWFRDKQKKSQAK 73 (245)
Q Consensus 5 ~~~~~FT~~Ql~eMEk~f~~~~~~y~~~~~rq~LA~~f~lS~~r~Gk~~v~~~QVk~WFQNRR~k~k~k 73 (245)
-+-+.||.+||..||..|+. ++|+...+|++||.+||||+ +|||+||||||.|.|..
T Consensus 104 r~RT~ft~~Ql~~LE~~F~~--~~Yvvg~eR~~LA~~L~Lse----------tQVkvWFQNRRtk~kr~ 160 (197)
T KOG0843|consen 104 RIRTAFTPEQLLKLEHAFEG--NQYVVGAERKQLAQSLSLSE----------TQVKVWFQNRRTKHKRM 160 (197)
T ss_pred ccccccCHHHHHHHHHHHhc--CCeeechHHHHHHHHcCCCh----------hHhhhhhhhhhHHHHHH
Confidence 34578999999999999999 69999999999999999999 99999999999997643
No 6
>KOG0484 consensus Transcription factor PHOX2/ARIX, contains HOX domain [Transcription]
Probab=99.44 E-value=9.6e-14 Score=112.81 Aligned_cols=53 Identities=25% Similarity=0.429 Sum_probs=49.6
Q ss_pred cCCCCHHHHHHHHHHHHHhCCCCCCHHHHHHHHHHcCCCcccCCCCcCCcchhhhhhhccccccc
Q 026004 7 WPDFTLAEIKEMESMYKEIGEASLTQEYCKALATSFSFSASRAARPAITWLQVQSWFRDKQKKSQ 71 (245)
Q Consensus 7 ~~~FT~~Ql~eMEk~f~~~~~~y~~~~~rq~LA~~f~lS~~r~Gk~~v~~~QVk~WFQNRR~k~k 71 (245)
-+.||..||.|||++|.+ .+|||...|++||-++.|++ ..||+||||||+|-+
T Consensus 21 RTTFTS~QLkELErvF~E--THYPDIYTREEiA~kidLTE----------ARVQVWFQNRRAKfR 73 (125)
T KOG0484|consen 21 RTTFTSAQLKELERVFAE--THYPDIYTREEIALKIDLTE----------ARVQVWFQNRRAKFR 73 (125)
T ss_pred hhhhhHHHHHHHHHHHHh--hcCCcchhHHHHHHhhhhhH----------HHHHHHHHhhHHHHH
Confidence 468999999999999999 59999999999999999988 999999999999854
No 7
>PF00046 Homeobox: Homeobox domain not present here.; InterPro: IPR001356 The homeobox domain was first identified in a number of drosophila homeotic and segmentation proteins, but is now known to be well-conserved in many other animals, including vertebrates [, , ]. Hox genes encode homeodomain-containing transcriptional regulators that operate differential genetic programs along the anterior-posterior axis of animal bodies []. The domain binds DNA through a helix-turn-helix (HTH) structure. The HTH motif is characterised by two alpha-helices, which make intimate contacts with the DNA and are joined by a short turn. The second helix binds to DNA via a number of hydrogen bonds and hydrophobic interactions, which occur between specific side chains and the exposed bases and thymine methyl groups within the major groove of the DNA []. The first helix helps to stabilise the structure. The motif is very similar in sequence and structure in a wide range of DNA-binding proteins (e.g., cro and repressor proteins, homeotic proteins, etc.). One of the principal differences between HTH motifs in these different proteins arises from the stereo-chemical requirement for glycine in the turn which is needed to avoid steric interference of the beta-carbon with the main chain: for cro and repressor proteins the glycine appears to be mandatory, while for many of the homeotic and other DNA-binding proteins the requirement is relaxed.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0043565 sequence-specific DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 2DA3_A 1LFB_A 2LFB_A 2ECB_A 2DA5_A 3D1N_O 3A03_A 2XSD_C 3CMY_A 1AHD_P ....
Probab=99.43 E-value=1.1e-13 Score=96.49 Aligned_cols=53 Identities=25% Similarity=0.526 Sum_probs=49.8
Q ss_pred cCCCCHHHHHHHHHHHHHhCCCCCCHHHHHHHHHHcCCCcccCCCCcCCcchhhhhhhccccccc
Q 026004 7 WPDFTLAEIKEMESMYKEIGEASLTQEYCKALATSFSFSASRAARPAITWLQVQSWFRDKQKKSQ 71 (245)
Q Consensus 7 ~~~FT~~Ql~eMEk~f~~~~~~y~~~~~rq~LA~~f~lS~~r~Gk~~v~~~QVk~WFQNRR~k~k 71 (245)
-+.||++|+..||..|.. ++||+.+.++.||..+|++. .||++||||||++.|
T Consensus 4 r~~~t~~q~~~L~~~f~~--~~~p~~~~~~~la~~l~l~~----------~~V~~WF~nrR~k~k 56 (57)
T PF00046_consen 4 RTRFTKEQLKVLEEYFQE--NPYPSKEEREELAKELGLTE----------RQVKNWFQNRRRKEK 56 (57)
T ss_dssp SSSSSHHHHHHHHHHHHH--SSSCHHHHHHHHHHHHTSSH----------HHHHHHHHHHHHHHH
T ss_pred CCCCCHHHHHHHHHHHHH--hccccccccccccccccccc----------cccccCHHHhHHHhC
Confidence 368999999999999999 69999999999999999998 999999999998865
No 8
>KOG0492 consensus Transcription factor MSH, contains HOX domain [General function prediction only]
Probab=99.37 E-value=2.9e-13 Score=120.80 Aligned_cols=55 Identities=20% Similarity=0.431 Sum_probs=51.3
Q ss_pred CCcCCCCHHHHHHHHHHHHHhCCCCCCHHHHHHHHHHcCCCcccCCCCcCCcchhhhhhhccccccc
Q 026004 5 DSWPDFTLAEIKEMESMYKEIGEASLTQEYCKALATSFSFSASRAARPAITWLQVQSWFRDKQKKSQ 71 (245)
Q Consensus 5 ~~~~~FT~~Ql~eMEk~f~~~~~~y~~~~~rq~LA~~f~lS~~r~Gk~~v~~~QVk~WFQNRR~k~k 71 (245)
-|-+.||..||..||+.|++. +||+..+|.+++.+|+|++ +|||+||||||+|.|
T Consensus 146 kPRtPFTtqQLlaLErkfrek--qYLSiaEraefSsSL~LTe----------TqVKIWFQNRRAKaK 200 (246)
T KOG0492|consen 146 KPRTPFTTQQLLALERKFREK--QYLSIAERAEFSSSLELTE----------TQVKIWFQNRRAKAK 200 (246)
T ss_pred CCCCCCCHHHHHHHHHHHhHh--hhhhHHHHHhhhhhhhhhh----------hheehhhhhhhHHHH
Confidence 366789999999999999995 8999999999999999988 999999999999865
No 9
>smart00389 HOX Homeodomain. DNA-binding factors that are involved in the transcriptional regulation of key developmental processes
Probab=99.36 E-value=1.1e-12 Score=90.35 Aligned_cols=52 Identities=25% Similarity=0.478 Sum_probs=48.4
Q ss_pred cCCCCHHHHHHHHHHHHHhCCCCCCHHHHHHHHHHcCCCcccCCCCcCCcchhhhhhhcccccc
Q 026004 7 WPDFTLAEIKEMESMYKEIGEASLTQEYCKALATSFSFSASRAARPAITWLQVQSWFRDKQKKS 70 (245)
Q Consensus 7 ~~~FT~~Ql~eMEk~f~~~~~~y~~~~~rq~LA~~f~lS~~r~Gk~~v~~~QVk~WFQNRR~k~ 70 (245)
-+.||++|+..||..|.. +.||+...++.||..+|++. +||++||+|||++.
T Consensus 4 r~~~~~~~~~~L~~~f~~--~~~P~~~~~~~la~~~~l~~----------~qV~~WF~nrR~~~ 55 (56)
T smart00389 4 RTSFTPEQLEELEKEFQK--NPYPSREEREELAAKLGLSE----------RQVKVWFQNRRAKW 55 (56)
T ss_pred CCcCCHHHHHHHHHHHHh--CCCCCHHHHHHHHHHHCcCH----------HHHHHhHHHHhhcc
Confidence 356999999999999999 57999999999999999988 99999999999875
No 10
>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=99.32 E-value=2.5e-12 Score=88.81 Aligned_cols=54 Identities=22% Similarity=0.455 Sum_probs=50.0
Q ss_pred cCCCCHHHHHHHHHHHHHhCCCCCCHHHHHHHHHHcCCCcccCCCCcCCcchhhhhhhcccccccc
Q 026004 7 WPDFTLAEIKEMESMYKEIGEASLTQEYCKALATSFSFSASRAARPAITWLQVQSWFRDKQKKSQA 72 (245)
Q Consensus 7 ~~~FT~~Ql~eMEk~f~~~~~~y~~~~~rq~LA~~f~lS~~r~Gk~~v~~~QVk~WFQNRR~k~k~ 72 (245)
-..|+.+++..||+.|.. +.||+...++.||..+|++. +||++||+|||.+.+.
T Consensus 4 r~~~~~~~~~~Le~~f~~--~~~P~~~~~~~la~~~~l~~----------~qV~~WF~nrR~~~~~ 57 (59)
T cd00086 4 RTRFTPEQLEELEKEFEK--NPYPSREEREELAKELGLTE----------RQVKIWFQNRRAKLKR 57 (59)
T ss_pred CCcCCHHHHHHHHHHHHh--CCCCCHHHHHHHHHHHCcCH----------HHHHHHHHHHHHHHhc
Confidence 457999999999999999 58999999999999999988 9999999999988753
No 11
>KOG0485 consensus Transcription factor NKX-5.1/HMX1, contains HOX domain [Transcription]
Probab=99.30 E-value=8.1e-13 Score=118.73 Aligned_cols=59 Identities=22% Similarity=0.399 Sum_probs=54.2
Q ss_pred CcCCCCHHHHHHHHHHHHHhCCCCCCHHHHHHHHHHcCCCcccCCCCcCCcchhhhhhhcccccccccccC
Q 026004 6 SWPDFTLAEIKEMESMYKEIGEASLTQEYCKALATSFSFSASRAARPAITWLQVQSWFRDKQKKSQAKSKS 76 (245)
Q Consensus 6 ~~~~FT~~Ql~eMEk~f~~~~~~y~~~~~rq~LA~~f~lS~~r~Gk~~v~~~QVk~WFQNRR~k~k~k~~~ 76 (245)
+-+.|+-+||.+||..|+- .+||+..+|-.||.+|.|++ +|||+||||||.|||.+.+.
T Consensus 107 tRTvFSraQV~qLEs~Fe~--krYLSsaeRa~LA~sLqLTE----------TQVKIWFQNRRnKwKRq~aa 165 (268)
T KOG0485|consen 107 TRTVFSRAQVFQLESTFEL--KRYLSSAERAGLAASLQLTE----------TQVKIWFQNRRNKWKRQYAA 165 (268)
T ss_pred chhhhhHHHHHHHHHHHHH--HhhhhHHHHhHHHHhhhhhh----------hhhhhhhhhhhHHHHHHHhh
Confidence 4577999999999999999 48999999999999999988 99999999999999976654
No 12
>KOG0483 consensus Transcription factor HEX, contains HOX and HALZ domains [Transcription]
Probab=99.30 E-value=1.7e-12 Score=114.40 Aligned_cols=56 Identities=25% Similarity=0.427 Sum_probs=52.1
Q ss_pred CCCCHHHHHHHHHHHHHhCCCCCCHHHHHHHHHHcCCCcccCCCCcCCcchhhhhhhccccccccccc
Q 026004 8 PDFTLAEIKEMESMYKEIGEASLTQEYCKALATSFSFSASRAARPAITWLQVQSWFRDKQKKSQAKSK 75 (245)
Q Consensus 8 ~~FT~~Ql~eMEk~f~~~~~~y~~~~~rq~LA~~f~lS~~r~Gk~~v~~~QVk~WFQNRR~k~k~k~~ 75 (245)
.+||.+|+..||+.|+. +.||.+..+.+||..|||++ .||.+||||||++||.|-.
T Consensus 55 ~Rlt~eQ~~~LE~~F~~--~~~L~p~~K~~LAk~LgL~p----------RQVavWFQNRRARwK~kql 110 (198)
T KOG0483|consen 55 RRLTSEQVKFLEKSFES--EKKLEPERKKKLAKELGLQP----------RQVAVWFQNRRARWKTKQL 110 (198)
T ss_pred ccccHHHHHHhHHhhcc--ccccChHHHHHHHHhhCCCh----------hHHHHHHhhccccccchhh
Confidence 47999999999999999 58999999999999999988 9999999999999996653
No 13
>KOG0493 consensus Transcription factor Engrailed, contains HOX domain [General function prediction only]
Probab=99.29 E-value=2e-12 Score=118.88 Aligned_cols=58 Identities=21% Similarity=0.496 Sum_probs=54.0
Q ss_pred CCCCCcCCCCHHHHHHHHHHHHHhCCCCCCHHHHHHHHHHcCCCcccCCCCcCCcchhhhhhhccccccc
Q 026004 2 DDEDSWPDFTLAEIKEMESMYKEIGEASLTQEYCKALATSFSFSASRAARPAITWLQVQSWFRDKQKKSQ 71 (245)
Q Consensus 2 ~~~~~~~~FT~~Ql~eMEk~f~~~~~~y~~~~~rq~LA~~f~lS~~r~Gk~~v~~~QVk~WFQNRR~k~k 71 (245)
+|--|-+.||.+||++|...|++ |+||+...||+||.+|+|.+ .|||+||||+|+|.|
T Consensus 245 eeKRPRTAFtaeQL~RLK~EF~e--nRYlTEqRRQ~La~ELgLNE----------sQIKIWFQNKRAKiK 302 (342)
T KOG0493|consen 245 EEKRPRTAFTAEQLQRLKAEFQE--NRYLTEQRRQELAQELGLNE----------SQIKIWFQNKRAKIK 302 (342)
T ss_pred hhcCccccccHHHHHHHHHHHhh--hhhHHHHHHHHHHHHhCcCH----------HHhhHHhhhhhhhhh
Confidence 34567899999999999999999 59999999999999999988 999999999999986
No 14
>KOG0850 consensus Transcription factor DLX and related proteins with LIM Zn-binding and HOX domains [Transcription]
Probab=99.25 E-value=3.2e-12 Score=115.12 Aligned_cols=55 Identities=16% Similarity=0.368 Sum_probs=51.2
Q ss_pred CCcCCCCHHHHHHHHHHHHHhCCCCCCHHHHHHHHHHcCCCcccCCCCcCCcchhhhhhhccccccc
Q 026004 5 DSWPDFTLAEIKEMESMYKEIGEASLTQEYCKALATSFSFSASRAARPAITWLQVQSWFRDKQKKSQ 71 (245)
Q Consensus 5 ~~~~~FT~~Ql~eMEk~f~~~~~~y~~~~~rq~LA~~f~lS~~r~Gk~~v~~~QVk~WFQNRR~k~k 71 (245)
.|=|.|+..||+.|-+.|++ .+||...+|.+||..||||. +||||||||||.|.|
T Consensus 124 KPRTIYSS~QLqaL~rRFQk--TQYLALPERAeLAAsLGLTQ----------TQVKIWFQNrRSK~K 178 (245)
T KOG0850|consen 124 KPRTIYSSLQLQALNRRFQQ--TQYLALPERAELAASLGLTQ----------TQVKIWFQNRRSKFK 178 (245)
T ss_pred CCcccccHHHHHHHHHHHhh--cchhcCcHHHHHHHHhCCch----------hHhhhhhhhhHHHHH
Confidence 35688999999999999999 59999999999999999988 999999999999865
No 15
>KOG2251 consensus Homeobox transcription factor [Transcription]
Probab=99.24 E-value=5.4e-12 Score=112.93 Aligned_cols=52 Identities=19% Similarity=0.422 Sum_probs=49.5
Q ss_pred CCCCHHHHHHHHHHHHHhCCCCCCHHHHHHHHHHcCCCcccCCCCcCCcchhhhhhhccccccc
Q 026004 8 PDFTLAEIKEMESMYKEIGEASLTQEYCKALATSFSFSASRAARPAITWLQVQSWFRDKQKKSQ 71 (245)
Q Consensus 8 ~~FT~~Ql~eMEk~f~~~~~~y~~~~~rq~LA~~f~lS~~r~Gk~~v~~~QVk~WFQNRR~k~k 71 (245)
+.||-.|+.+||++|.+ ++|||...|++||.++||.+ .+||+||.|||+|++
T Consensus 42 TtFtr~QlevLe~LF~k--TqYPDv~~rEelAlklnLpe----------SrVqVWFKNRRAK~r 93 (228)
T KOG2251|consen 42 TTFTRKQLEVLEALFAK--TQYPDVFMREELALKLNLPE----------SRVQVWFKNRRAKCR 93 (228)
T ss_pred ceecHHHHHHHHHHHHh--hcCccHHHHHHHHHHhCCch----------hhhhhhhccccchhh
Confidence 67999999999999999 59999999999999999988 889999999999966
No 16
>KOG0494 consensus Transcription factor CHX10 and related HOX domain proteins [General function prediction only]
Probab=99.20 E-value=9.5e-12 Score=114.31 Aligned_cols=57 Identities=21% Similarity=0.295 Sum_probs=52.3
Q ss_pred CcCCCCHHHHHHHHHHHHHhCCCCCCHHHHHHHHHHcCCCcccCCCCcCCcchhhhhhhcccccccccc
Q 026004 6 SWPDFTLAEIKEMESMYKEIGEASLTQEYCKALATSFSFSASRAARPAITWLQVQSWFRDKQKKSQAKS 74 (245)
Q Consensus 6 ~~~~FT~~Ql~eMEk~f~~~~~~y~~~~~rq~LA~~f~lS~~r~Gk~~v~~~QVk~WFQNRR~k~k~k~ 74 (245)
.-+.||..|+++||+.|++ .+|||..-|+-||.++.|.+ ..|++||||||+|||.+-
T Consensus 144 ~RTiFT~~Qle~LEkaFke--aHYPDv~Are~la~ktelpE----------DRIqVWfQNRRAKWRk~E 200 (332)
T KOG0494|consen 144 FRTIFTSYQLEELEKAFKE--AHYPDVYAREMLADKTELPE----------DRIQVWFQNRRAKWRKTE 200 (332)
T ss_pred ccchhhHHHHHHHHHHHhh--ccCccHHHHHHHhhhccCch----------hhhhHHhhhhhHHhhhhh
Confidence 3477999999999999999 59999999999999999988 889999999999998544
No 17
>TIGR01565 homeo_ZF_HD homeobox domain, ZF-HD class. This model represents a class of homoebox domain that differs substantially from the typical homoebox domain described in pfam model pfam00046. It is found in both C4 and C3 plants.
Probab=99.19 E-value=2e-11 Score=88.91 Aligned_cols=49 Identities=10% Similarity=0.249 Sum_probs=46.0
Q ss_pred cCCCCHHHHHHHHHHHHHhCCCC----CCHHHHHHHHHHcCCCcccCCCCcCCcchhhhhhhccc
Q 026004 7 WPDFTLAEIKEMESMYKEIGEAS----LTQEYCKALATSFSFSASRAARPAITWLQVQSWFRDKQ 67 (245)
Q Consensus 7 ~~~FT~~Ql~eMEk~f~~~~~~y----~~~~~rq~LA~~f~lS~~r~Gk~~v~~~QVk~WFQNRR 67 (245)
=+.||++|+++||+.|+. ++| |+...+++||..+|+++ .+||+||||.+
T Consensus 5 RT~Ft~~Q~~~Le~~fe~--~~y~~~~~~~~~r~~la~~lgl~~----------~vvKVWfqN~k 57 (58)
T TIGR01565 5 RTKFTAEQKEKMRDFAEK--LGWKLKDKRREEVREFCEEIGVTR----------KVFKVWMHNNK 57 (58)
T ss_pred CCCCCHHHHHHHHHHHHH--cCCCCCCCCHHHHHHHHHHhCCCH----------HHeeeecccCC
Confidence 378999999999999999 589 99999999999999998 99999999975
No 18
>KOG0491 consensus Transcription factor BSH, contains HOX domain [General function prediction only]
Probab=99.15 E-value=7.8e-12 Score=108.44 Aligned_cols=52 Identities=23% Similarity=0.478 Sum_probs=49.1
Q ss_pred CCCCHHHHHHHHHHHHHhCCCCCCHHHHHHHHHHcCCCcccCCCCcCCcchhhhhhhccccccc
Q 026004 8 PDFTLAEIKEMESMYKEIGEASLTQEYCKALATSFSFSASRAARPAITWLQVQSWFRDKQKKSQ 71 (245)
Q Consensus 8 ~~FT~~Ql~eMEk~f~~~~~~y~~~~~rq~LA~~f~lS~~r~Gk~~v~~~QVk~WFQNRR~k~k 71 (245)
+.|+..|+.-||+.|+. .+||+-.++++||..||||+ +|||.||||||||.|
T Consensus 105 tvfs~~ql~~l~~rFe~--QrYLS~~e~~ELan~L~LS~----------~QVKTWFQNrRMK~K 156 (194)
T KOG0491|consen 105 TVFSDPQLSGLEKRFER--QRYLSTPERQELANALSLSE----------TQVKTWFQNRRMKHK 156 (194)
T ss_pred ccccCccccccHHHHhh--hhhcccHHHHHHHHHhhhhH----------HHHHHHHHHHHHHHH
Confidence 56999999999999998 48999999999999999999 999999999999976
No 19
>KOG0848 consensus Transcription factor Caudal, contains HOX domain [Transcription]
Probab=99.15 E-value=7.9e-12 Score=114.97 Aligned_cols=51 Identities=24% Similarity=0.394 Sum_probs=47.7
Q ss_pred CCCHHHHHHHHHHHHHhCCCCCCHHHHHHHHHHcCCCcccCCCCcCCcchhhhhhhccccccc
Q 026004 9 DFTLAEIKEMESMYKEIGEASLTQEYCKALATSFSFSASRAARPAITWLQVQSWFRDKQKKSQ 71 (245)
Q Consensus 9 ~FT~~Ql~eMEk~f~~~~~~y~~~~~rq~LA~~f~lS~~r~Gk~~v~~~QVk~WFQNRR~k~k 71 (245)
.+|.-|-.||||+|.- ++|++....-+||..|+||| +|||+||||||+|-|
T Consensus 205 VYTDhQRLELEKEfh~--SryITirRKSELA~~LgLsE----------RQVKIWFQNRRAKER 255 (317)
T KOG0848|consen 205 VYTDHQRLELEKEFHT--SRYITIRRKSELAATLGLSE----------RQVKIWFQNRRAKER 255 (317)
T ss_pred Eecchhhhhhhhhhcc--ccceeeehhHHHHHhhCccH----------hhhhHhhhhhhHHHH
Confidence 3788999999999999 59999999999999999999 999999999999854
No 20
>KOG0844 consensus Transcription factor EVX1, contains HOX domain [Transcription]
Probab=99.12 E-value=2.3e-11 Score=113.84 Aligned_cols=53 Identities=19% Similarity=0.420 Sum_probs=49.2
Q ss_pred cCCCCHHHHHHHHHHHHHhCCCCCCHHHHHHHHHHcCCCcccCCCCcCCcchhhhhhhccccccc
Q 026004 7 WPDFTLAEIKEMESMYKEIGEASLTQEYCKALATSFSFSASRAARPAITWLQVQSWFRDKQKKSQ 71 (245)
Q Consensus 7 ~~~FT~~Ql~eMEk~f~~~~~~y~~~~~rq~LA~~f~lS~~r~Gk~~v~~~QVk~WFQNRR~k~k 71 (245)
-+.||-+||++|||.|-. +.|.++..|-+||..|||.+ +-||+||||||||.|
T Consensus 185 RTAFTReQIaRLEKEFyr--ENYVSRprRcELAAaLNLPE----------tTIKVWFQNRRMKDK 237 (408)
T KOG0844|consen 185 RTAFTREQIARLEKEFYR--ENYVSRPRRCELAAALNLPE----------TTIKVWFQNRRMKDK 237 (408)
T ss_pred HhhhhHHHHHHHHHHHHH--hccccCchhhhHHHhhCCCc----------ceeehhhhhchhhhh
Confidence 367999999999999988 46999999999999999998 999999999999966
No 21
>KOG0847 consensus Transcription factor, contains HOX domain [Transcription]
Probab=98.98 E-value=3.3e-10 Score=102.40 Aligned_cols=62 Identities=24% Similarity=0.408 Sum_probs=55.6
Q ss_pred CcCCCCHHHHHHHHHHHHHhCCCCCCHHHHHHHHHHcCCCcccCCCCcCCcchhhhhhhcccccccccccCCcc
Q 026004 6 SWPDFTLAEIKEMESMYKEIGEASLTQEYCKALATSFSFSASRAARPAITWLQVQSWFRDKQKKSQAKSKSSSK 79 (245)
Q Consensus 6 ~~~~FT~~Ql~eMEk~f~~~~~~y~~~~~rq~LA~~f~lS~~r~Gk~~v~~~QVk~WFQNRR~k~k~k~~~~p~ 79 (245)
.-+.|+-.||..||+-|++ .+||..+.|-+||..+|+++ .||++||||||.|||.|..--|.
T Consensus 170 srPTf~g~qi~~le~~feq--tkylaG~~ra~lA~~lgmte----------SqvkVWFQNRRTKWRKkhAaEma 231 (288)
T KOG0847|consen 170 SRPTFTGHQIYQLERKFEQ--TKYLAGADRAQLAQELNMTE----------SQVKVWFQNRRTKWRKKHAAEMA 231 (288)
T ss_pred cCCCccchhhhhhhhhhhh--hhcccchhHHHhhccccccH----------HHHHHHHhcchhhhhhhhccchh
Confidence 3457999999999999999 58999999999999999988 99999999999999988755444
No 22
>COG5576 Homeodomain-containing transcription factor [Transcription]
Probab=98.85 E-value=1.8e-09 Score=92.05 Aligned_cols=56 Identities=18% Similarity=0.227 Sum_probs=51.2
Q ss_pred cCCCCHHHHHHHHHHHHHhCCCCCCHHHHHHHHHHcCCCcccCCCCcCCcchhhhhhhcccccccccc
Q 026004 7 WPDFTLAEIKEMESMYKEIGEASLTQEYCKALATSFSFSASRAARPAITWLQVQSWFRDKQKKSQAKS 74 (245)
Q Consensus 7 ~~~FT~~Ql~eMEk~f~~~~~~y~~~~~rq~LA~~f~lS~~r~Gk~~v~~~QVk~WFQNRR~k~k~k~ 74 (245)
-.+-|..|+.-||+.|+. +.||+...|++||..+|+++ +-||+||||||++.+.+.
T Consensus 55 r~R~t~~Q~~vL~~~F~i--~p~Ps~~~r~~L~~~lnm~~----------ksVqIWFQNkR~~~k~~~ 110 (156)
T COG5576 55 RRRTTDEQLMVLEREFEI--NPYPSSITRIKLSLLLNMPP----------KSVQIWFQNKRAKEKKKR 110 (156)
T ss_pred ceechHHHHHHHHHHhcc--CCCCCHHHHHHHHHhcCCCh----------hhhhhhhchHHHHHHHhc
Confidence 356899999999999999 69999999999999999998 999999999999977554
No 23
>KOG0490 consensus Transcription factor, contains HOX domain [General function prediction only]
Probab=98.83 E-value=1.5e-09 Score=92.66 Aligned_cols=56 Identities=20% Similarity=0.443 Sum_probs=51.8
Q ss_pred CCCCHHHHHHHHHHHHHhCCCCCCHHHHHHHHHHcCCCcccCCCCcCCcchhhhhhhccccccccccc
Q 026004 8 PDFTLAEIKEMESMYKEIGEASLTQEYCKALATSFSFSASRAARPAITWLQVQSWFRDKQKKSQAKSK 75 (245)
Q Consensus 8 ~~FT~~Ql~eMEk~f~~~~~~y~~~~~rq~LA~~f~lS~~r~Gk~~v~~~QVk~WFQNRR~k~k~k~~ 75 (245)
+.||..|+.+||++|... +||+...++.||..+++++ ..|++||||||+||+....
T Consensus 65 t~~~~~ql~~ler~f~~~--h~Pd~~~r~~la~~~~~~e----------~rVqvwFqnrrak~r~~~~ 120 (235)
T KOG0490|consen 65 CKFTISQLDELERAFEKV--HLPCFACRECLALLLTGDE----------FRVQVWFQNRRAKDRKEER 120 (235)
T ss_pred CCCCcCHHHHHHHhhcCC--CcCccchHHHHhhcCCCCe----------eeeehhhhhhcHhhhhhhc
Confidence 569999999999999995 9999999999999999988 9999999999999986654
No 24
>KOG0486 consensus Transcription factor PTX1, contains HOX domain [Transcription]
Probab=98.78 E-value=3e-09 Score=99.74 Aligned_cols=53 Identities=17% Similarity=0.396 Sum_probs=50.3
Q ss_pred CCCCHHHHHHHHHHHHHhCCCCCCHHHHHHHHHHcCCCcccCCCCcCCcchhhhhhhcccccccc
Q 026004 8 PDFTLAEIKEMESMYKEIGEASLTQEYCKALATSFSFSASRAARPAITWLQVQSWFRDKQKKSQA 72 (245)
Q Consensus 8 ~~FT~~Ql~eMEk~f~~~~~~y~~~~~rq~LA~~f~lS~~r~Gk~~v~~~QVk~WFQNRR~k~k~ 72 (245)
+-||..|++|||..|+. |.|||-+.|++||-..||++ +.|.+||.|||+||+.
T Consensus 117 thFtSqqlqele~tF~r--NrypdMstrEEIavwtNlTE----------~rvrvwfknrrakwrk 169 (351)
T KOG0486|consen 117 THFTSQQLQELEATFQR--NRYPDMSTREEIAVWTNLTE----------ARVRVWFKNRRAKWRK 169 (351)
T ss_pred hhhHHHHHHHHHHHHhh--ccCCccchhhHHHhhccccc----------hhhhhhcccchhhhhh
Confidence 56999999999999999 69999999999999999988 9999999999999983
No 25
>KOG4577 consensus Transcription factor LIM3, contains LIM and HOX domains [Transcription]
Probab=98.34 E-value=2.9e-07 Score=86.24 Aligned_cols=55 Identities=15% Similarity=0.355 Sum_probs=49.8
Q ss_pred CCcCCCCHHHHHHHHHHHHHhCCCCCCHHHHHHHHHHcCCCcccCCCCcCCcchhhhhhhccccccc
Q 026004 5 DSWPDFTLAEIKEMESMYKEIGEASLTQEYCKALATSFSFSASRAARPAITWLQVQSWFRDKQKKSQ 71 (245)
Q Consensus 5 ~~~~~FT~~Ql~eMEk~f~~~~~~y~~~~~rq~LA~~f~lS~~r~Gk~~v~~~QVk~WFQNRR~k~k 71 (245)
-|-+..|..||+-|..+|.. ..-|.+-+|++|+...||.. +.||+||||||+|-|
T Consensus 169 RPRTTItAKqLETLK~AYn~--SpKPARHVREQLsseTGLDM----------RVVQVWFQNRRAKEK 223 (383)
T KOG4577|consen 169 RPRTTITAKQLETLKQAYNT--SPKPARHVREQLSSETGLDM----------RVVQVWFQNRRAKEK 223 (383)
T ss_pred CCcceeeHHHHHHHHHHhcC--CCchhHHHHHHhhhccCcce----------eehhhhhhhhhHHHH
Confidence 46688999999999999987 58999999999999999977 999999999999843
No 26
>KOG0775 consensus Transcription factor SIX and related HOX domain proteins [Transcription]
Probab=98.23 E-value=2.5e-06 Score=79.14 Aligned_cols=62 Identities=18% Similarity=0.334 Sum_probs=51.8
Q ss_pred CCCCCcCCCCHHHHHHHHHHHHHhCCCCCCHHHHHHHHHHcCCCcccCCCCcCCcchhhhhhhccccccccccc
Q 026004 2 DDEDSWPDFTLAEIKEMESMYKEIGEASLTQEYCKALATSFSFSASRAARPAITWLQVQSWFRDKQKKSQAKSK 75 (245)
Q Consensus 2 ~~~~~~~~FT~~Ql~eMEk~f~~~~~~y~~~~~rq~LA~~f~lS~~r~Gk~~v~~~QVk~WFQNRR~k~k~k~~ 75 (245)
|.|-.-..|-..--.-|-..|.. +.||++....+||+..+|+. +||-|||.|||++.|+...
T Consensus 175 DGEet~yCFKekSR~~LrewY~~--~~YPsp~eKReLA~aTgLt~----------tQVsNWFKNRRQRDRa~~a 236 (304)
T KOG0775|consen 175 DGEETVYCFKEKSRSLLREWYLQ--NPYPSPREKRELAEATGLTI----------TQVSNWFKNRRQRDRAAAA 236 (304)
T ss_pred cCceeeeehhHhhHHHHHHHHhc--CCCCChHHHHHHHHHhCCch----------hhhhhhhhhhhhhhhhccc
Confidence 44555566777777788888997 69999999999999999988 9999999999999875443
No 27
>KOG0849 consensus Transcription factor PRD and related proteins, contain PAX and HOX domains [Transcription]
Probab=98.20 E-value=9.3e-07 Score=83.59 Aligned_cols=55 Identities=16% Similarity=0.341 Sum_probs=50.7
Q ss_pred CCCCHHHHHHHHHHHHHhCCCCCCHHHHHHHHHHcCCCcccCCCCcCCcchhhhhhhcccccccccc
Q 026004 8 PDFTLAEIKEMESMYKEIGEASLTQEYCKALATSFSFSASRAARPAITWLQVQSWFRDKQKKSQAKS 74 (245)
Q Consensus 8 ~~FT~~Ql~eMEk~f~~~~~~y~~~~~rq~LA~~f~lS~~r~Gk~~v~~~QVk~WFQNRR~k~k~k~ 74 (245)
+.||+.|+..||+.|+.. +||+...|+.||.+.++++ ..|++||||||++++...
T Consensus 181 tsft~~Q~~~le~~f~rt--~yP~i~~Re~La~~i~l~e----------~riqvwf~nrra~~rr~~ 235 (354)
T KOG0849|consen 181 TSFSPSQLEALEECFQRT--PYPDIVGRETLAKETGLPE----------PRVQVWFQNRRAKWRRQH 235 (354)
T ss_pred cccccchHHHHHHHhcCC--CCCchhhHHHHhhhccCCc----------hHHHHHHhhhhhhhhhcc
Confidence 679999999999999994 6999999999999999988 999999999999887544
No 28
>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=98.04 E-value=3.1e-06 Score=57.35 Aligned_cols=37 Identities=19% Similarity=0.365 Sum_probs=30.3
Q ss_pred HHHhCCCCCCHHHHHHHHHHcCCCcccCCCCcCCcchhhhhhhcccc
Q 026004 22 YKEIGEASLTQEYCKALATSFSFSASRAARPAITWLQVQSWFRDKQK 68 (245)
Q Consensus 22 f~~~~~~y~~~~~rq~LA~~f~lS~~r~Gk~~v~~~QVk~WFQNRR~ 68 (245)
+++..+.||+.++++.||...|+|. +||.+||-|.|.
T Consensus 3 ~~h~~nPYPs~~ek~~L~~~tgls~----------~Qi~~WF~NaRr 39 (40)
T PF05920_consen 3 LEHLHNPYPSKEEKEELAKQTGLSR----------KQISNWFINARR 39 (40)
T ss_dssp HHTTTSGS--HHHHHHHHHHHTS-H----------HHHHHHHHHHHH
T ss_pred HHHCCCCCCCHHHHHHHHHHcCCCH----------HHHHHHHHHhHc
Confidence 3455679999999999999999998 999999999875
No 29
>KOG3802 consensus Transcription factor OCT-1, contains POU and HOX domains [Transcription]
Probab=97.23 E-value=0.00026 Score=68.51 Aligned_cols=55 Identities=15% Similarity=0.289 Sum_probs=47.8
Q ss_pred CCCCHHHHHHHHHHHHHhCCCCCCHHHHHHHHHHcCCCcccCCCCcCCcchhhhhhhcccccccccc
Q 026004 8 PDFTLAEIKEMESMYKEIGEASLTQEYCKALATSFSFSASRAARPAITWLQVQSWFRDKQKKSQAKS 74 (245)
Q Consensus 8 ~~FT~~Ql~eMEk~f~~~~~~y~~~~~rq~LA~~f~lS~~r~Gk~~v~~~QVk~WFQNRR~k~k~k~ 74 (245)
+.|+......||+.|.. +.-|+..++-.||++|+|-- ..|.+||=|||+|-|.-.
T Consensus 299 TSie~~vr~aLE~~F~~--npKPt~qEIt~iA~~L~leK----------EVVRVWFCNRRQkeKR~~ 353 (398)
T KOG3802|consen 299 TSIEVNVRGALEKHFLK--NPKPTSQEITHIAESLQLEK----------EVVRVWFCNRRQKEKRIT 353 (398)
T ss_pred cceeHHHHHHHHHHHHh--CCCCCHHHHHHHHHHhcccc----------ceEEEEeeccccccccCC
Confidence 45777888999999999 58999999999999999955 568999999999986444
No 30
>KOG0774 consensus Transcription factor PBX and related HOX domain proteins [Transcription]
Probab=96.97 E-value=0.0019 Score=60.33 Aligned_cols=53 Identities=17% Similarity=0.336 Sum_probs=45.6
Q ss_pred CCCHHHHHHHHHHHHHh-CCCCCCHHHHHHHHHHcCCCcccCCCCcCCcchhhhhhhccccccc
Q 026004 9 DFTLAEIKEMESMYKEI-GEASLTQEYCKALATSFSFSASRAARPAITWLQVQSWFRDKQKKSQ 71 (245)
Q Consensus 9 ~FT~~Ql~eMEk~f~~~-~~~y~~~~~rq~LA~~f~lS~~r~Gk~~v~~~QVk~WFQNRR~k~k 71 (245)
.|++.-.+.|-.-|-.+ +|.||+.+..++||.+-|++- .||-+||-|+|.+.+
T Consensus 194 NFsK~aTeiLneyF~~h~~nPYPSee~K~eLAkqCnItv----------sQvsnwfgnkrIryk 247 (334)
T KOG0774|consen 194 NFSKQATEILNEYFYSHLSNPYPSEEAKEELAKQCNITV----------SQVSNWFGNKRIRYK 247 (334)
T ss_pred ccchhHHHHHHHHHHHhcCCCCCcHHHHHHHHHHcCcee----------hhhccccccceeehh
Confidence 47777777787777655 899999999999999999988 999999999987765
No 31
>KOG0490 consensus Transcription factor, contains HOX domain [General function prediction only]
Probab=96.82 E-value=0.00061 Score=58.19 Aligned_cols=57 Identities=18% Similarity=0.379 Sum_probs=51.2
Q ss_pred CcCCCCHHHHHHHHHHHHHhCCCCCCHHHHHHHHHHcCCCcccCCCCcCCcchhhhhhhcccccccccc
Q 026004 6 SWPDFTLAEIKEMESMYKEIGEASLTQEYCKALATSFSFSASRAARPAITWLQVQSWFRDKQKKSQAKS 74 (245)
Q Consensus 6 ~~~~FT~~Ql~eMEk~f~~~~~~y~~~~~rq~LA~~f~lS~~r~Gk~~v~~~QVk~WFQNRR~k~k~k~ 74 (245)
+-+.|+..|+..|+..|.. +.+|+...++.||..+++++ ..|++||||+|.+.+...
T Consensus 156 ~~~~~~~~~~~~~~~~~~~--~~~P~~~~~~~l~~~~~~~~----------~~~q~~~~~~~~~~~~~~ 212 (235)
T KOG0490|consen 156 PRTTFTENQLEVLETVFRA--TPKPDADDREQLAEETGLSE----------RVIQVWFQNRRAKLRKHK 212 (235)
T ss_pred CccccccchhHhhhhcccC--CCCCchhhHHHHHHhcCCCh----------hhhhhhcccHHHHHHhhc
Confidence 3468999999999999999 58999999999999999988 889999999999986544
No 32
>KOG2252 consensus CCAAT displacement protein and related homeoproteins [Transcription]
Probab=96.62 E-value=0.0025 Score=64.05 Aligned_cols=54 Identities=15% Similarity=0.315 Sum_probs=48.6
Q ss_pred CcCCCCHHHHHHHHHHHHHhCCCCCCHHHHHHHHHHcCCCcccCCCCcCCcchhhhhhhccccccc
Q 026004 6 SWPDFTLAEIKEMESMYKEIGEASLTQEYCKALATSFSFSASRAARPAITWLQVQSWFRDKQKKSQ 71 (245)
Q Consensus 6 ~~~~FT~~Ql~eMEk~f~~~~~~y~~~~~rq~LA~~f~lS~~r~Gk~~v~~~QVk~WFQNRR~k~k 71 (245)
|=..||..|..-|-.+|++ +++|++++++.|+..|||.. .-|.|||-|=|.+..
T Consensus 423 PRlVfTd~QkrTL~aiFke--~~RPS~Emq~tIS~qL~L~~----------sTV~NfFmNaRRRsl 476 (558)
T KOG2252|consen 423 PRLVFTDIQKRTLQAIFKE--NKRPSREMQETISQQLNLEL----------STVINFFMNARRRSL 476 (558)
T ss_pred ceeeecHHHHHHHHHHHhc--CCCCCHHHHHHHHHHhCCcH----------HHHHHHHHhhhhhcc
Confidence 3456999999999999999 69999999999999999988 899999999776643
No 33
>PF11717 Tudor-knot: RNA binding activity-knot of a chromodomain ; PDB: 2EKO_A 2RO0_A 2RNZ_A 1WGS_A 3E9G_A 3E9F_A 2K3X_A 2K3Y_A 2EFI_A 2F5K_F ....
Probab=95.68 E-value=0.02 Score=40.58 Aligned_cols=40 Identities=40% Similarity=0.719 Sum_probs=32.1
Q ss_pred CCCceeeeeecceeeeeecCceeEEEEecCCCCCcccccccc
Q 026004 122 KDDAWYDVASFLTYRVTCAGELEVRVRFSGFNNTEDEWVNVK 163 (245)
Q Consensus 122 ~D~AWYdV~~fl~~R~~~~g~~el~Vrf~gF~~eeDEw~~~~ 163 (245)
.+|.||...+ |.-|. ..|..+..|||.|+..-.|||++..
T Consensus 12 ~~~~~y~A~I-~~~r~-~~~~~~YyVHY~g~nkR~DeWV~~~ 51 (55)
T PF11717_consen 12 KDGQWYEAKI-LDIRE-KNGEPEYYVHYQGWNKRLDEWVPES 51 (55)
T ss_dssp TTTEEEEEEE-EEEEE-CTTCEEEEEEETTSTGCC-EEEETT
T ss_pred CCCcEEEEEE-EEEEe-cCCCEEEEEEcCCCCCCceeeecHH
Confidence 6999999885 34444 5677899999999999999999854
No 34
>PF15057 DUF4537: Domain of unknown function (DUF4537)
Probab=95.63 E-value=0.11 Score=42.64 Aligned_cols=95 Identities=23% Similarity=0.295 Sum_probs=63.0
Q ss_pred ecccCCCceeeeeecceeeeeecCceeEEEEecCCCCCccccccccccccccCCCccccccccccCCceEEEeeecCCce
Q 026004 118 ARSSKDDAWYDVASFLTYRVTCAGELEVRVRFSGFNNTEDEWVNVKTAVRQRSIPLEQSECVKVNVGDLVLCYQEREDQA 197 (245)
Q Consensus 118 Ars~~D~AWYdV~~fl~~R~~~~g~~el~Vrf~gF~~eeDEw~~~~~~~R~rS~ple~~eC~~v~~G~~v~cf~~~~~~~ 197 (245)
||+.+||-+|--.+ ..+ +..| .+.|.|. +.+-+.+... -=|++.++.|+.|.+||-||+-.+..+ .
T Consensus 6 AR~~~DG~YY~GtV--~~~-~~~~--~~lV~f~---~~~~~~v~~~-----~iI~~~~~~~~~L~~GD~VLA~~~~~~-~ 71 (124)
T PF15057_consen 6 ARREEDGFYYPGTV--KKC-VSSG--QFLVEFD---DGDTQEVPIS-----DIIALSDAMRHSLQVGDKVLAPWEPDD-C 71 (124)
T ss_pred EeeCCCCcEEeEEE--EEc-cCCC--EEEEEEC---CCCEEEeChH-----HeEEccCcccCcCCCCCEEEEecCcCC-C
Confidence 89999999997763 222 2334 6999992 2222222222 235788888999999999998876654 4
Q ss_pred eEEeeEEeeeeecccCCCCceeEEEEEEccCC
Q 026004 198 VYCDAHVLDIQRRVHDTEGCQCIFVVRYDHDF 229 (245)
Q Consensus 198 ~yyDA~V~~v~r~~Hd~~~C~C~F~Vr~~h~~ 229 (245)
.|+=|.|+..-.++ ....=.++|.+-.|.
T Consensus 72 ~Y~Pg~V~~~~~~~---~~~~~~~~V~f~ng~ 100 (124)
T PF15057_consen 72 RYGPGTVIAGPERR---ASEDKEYTVRFYNGK 100 (124)
T ss_pred EEeCEEEEECcccc---ccCCceEEEEEECCC
Confidence 69999999876555 333335666666554
No 35
>cd00024 CHROMO Chromatin organization modifier (chromo) domain is a conserved region of around 50 amino acids found in a variety of chromosomal proteins, which appear to play a role in the functional organization of the eukaryotic nucleus. Experimental evidence implicates the chromo domain in the binding activity of these proteins to methylated histone tails and maybe RNA. May occur as single instance, in a tandem arrangement or followd by a related "chromo shadow" domain.
Probab=93.06 E-value=0.14 Score=34.70 Aligned_cols=36 Identities=33% Similarity=0.625 Sum_probs=30.2
Q ss_pred eeeeecceeeeeec-CceeEEEEecCCCCCccccccc
Q 026004 127 YDVASFLTYRVTCA-GELEVRVRFSGFNNTEDEWVNV 162 (245)
Q Consensus 127 YdV~~fl~~R~~~~-g~~el~Vrf~gF~~eeDEw~~~ 162 (245)
|.|.--|.||.... |..+..|++.|++..+++|...
T Consensus 3 ~~ve~Il~~r~~~~~~~~~y~VkW~g~~~~~~tWe~~ 39 (55)
T cd00024 3 YEVEKILDHRKKKDGGEYEYLVKWKGYSYSEDTWEPE 39 (55)
T ss_pred ceEeeeeeeeecCCCCcEEEEEEECCCCCccCccccH
Confidence 45667788887765 7789999999999999999873
No 36
>KOG1168 consensus Transcription factor ACJ6/BRN-3, contains POU and HOX domains [Transcription]
Probab=92.80 E-value=0.031 Score=53.19 Aligned_cols=51 Identities=18% Similarity=0.354 Sum_probs=43.8
Q ss_pred CHHHHHHHHHHHHHhCCCCCCHHHHHHHHHHcCCCcccCCCCcCCcchhhhhhhccccccccc
Q 026004 11 TLAEIKEMESMYKEIGEASLTQEYCKALATSFSFSASRAARPAITWLQVQSWFRDKQKKSQAK 73 (245)
Q Consensus 11 T~~Ql~eMEk~f~~~~~~y~~~~~rq~LA~~f~lS~~r~Gk~~v~~~QVk~WFQNRR~k~k~k 73 (245)
..-|-..||..|.. ..-|+.+.+..||++|.|-- ..|.+||=|.|+|.|..
T Consensus 317 AAPEKRsLEayFav--QPRPS~EkIAaIAekLDLKK----------NVVRVWFCNQRQKQKRm 367 (385)
T KOG1168|consen 317 AAPEKRSLEAYFAV--QPRPSGEKIAAIAEKLDLKK----------NVVRVWFCNQRQKQKRM 367 (385)
T ss_pred cCcccccHHHHhcc--CCCCchhHHHHHHHhhhhhh----------ceEEEEeeccHHHHHHh
Confidence 33466789999999 58999999999999999955 77999999999998753
No 37
>PF11569 Homez: Homeodomain leucine-zipper encoding, Homez; PDB: 2YS9_A.
Probab=92.70 E-value=0.11 Score=38.18 Aligned_cols=42 Identities=26% Similarity=0.460 Sum_probs=30.7
Q ss_pred HHHHHHHHHHhCCCCCCHHHHHHHHHHcCCCcccCCCCcCCcchhhhhhhcccc
Q 026004 15 IKEMESMYKEIGEASLTQEYCKALATSFSFSASRAARPAITWLQVQSWFRDKQK 68 (245)
Q Consensus 15 l~eMEk~f~~~~~~y~~~~~rq~LA~~f~lS~~r~Gk~~v~~~QVk~WFQNRR~ 68 (245)
+.=|++-|..+ +.|.....+.|..+-++|. .||+.||--|+.
T Consensus 10 ~~pL~~Yy~~h--~~L~E~DL~~L~~kS~ms~----------qqVr~WFa~~~~ 51 (56)
T PF11569_consen 10 IQPLEDYYLKH--KQLQEEDLDELCDKSRMSY----------QQVRDWFAERMQ 51 (56)
T ss_dssp -HHHHHHHHHT------TTHHHHHHHHTT--H----------HHHHHHHHHHS-
T ss_pred hHHHHHHHHHc--CCccHhhHHHHHHHHCCCH----------HHHHHHHHHhcc
Confidence 46699999996 7999999999999999988 999999987643
No 38
>PF00385 Chromo: Chromo (CHRromatin Organisation MOdifier) domain; InterPro: IPR023780 The CHROMO (CHRromatin Organization MOdifier) domain [, , , ] is a conserved region of around 60 amino acids, originally identified in Drosophila modifiers of variegation. These are proteins that alter the structure of chromatin to the condensed morphology of heterochromatin, a cytologically visible condition where gene expression is repressed. In one of these proteins, Polycomb, the chromo domain has been shown to be important for chromatin targeting. Proteins that contain a chromo domain appear to fall into 3 classes. The first class includes proteins having an N-terminal chromo domain followed by a region termed the chromo shadow domain, with weak but significant sequence similarity to the N-terminal chromo domain,[], eg. Drosophila and human heterochromatin protein Su(var)205 (HP1). The second class includes proteins with a single chromo domain, eg. Drosophila protein Polycomb (Pc); mammalian modifier 3; human Mi-2 autoantigen and several yeast and Caenorhabditis elegans hypothetical proteins. In the third class paired tandem chromo domains are found, eg. in mammalian DNA-binding/helicase proteins CHD-1 to CHD-4 and yeast protein CHD1. Functional dissections of chromo domain proteins suggests a mechanistic role for chromo domains in targeting chromo domain proteins to specific regions of the nucleus. The mechanism of targeting may involve protein-protein and/or protein/nucleic acid interactions. Hence, several line of evidence show that the HP1 chromo domain is a methyl-specific histone binding module, whereas the chromo domain of two protein components of the drosophila dosage compensation complex, MSL3 and MOF, contain chromo domains that bind to RNA in vitro []. The high resolution structures of HP1-family protein chromo and chromo shadow domain reveal a conserved chromo domain fold motif consisting of three beta strands packed against an alpha helix. The chromo domain fold belongs to the OB (oligonucleotide/oligosaccharide binding)-fold class found in a variety of prokaryotic and eukaryotic nucleic acid binding protein [].; PDB: 2H1E_B 3MWY_W 2DY8_A 1KNE_A 1KNA_A 1Q3L_A 2EE1_A 1AP0_A 1GUW_A 1X3P_A ....
Probab=92.00 E-value=0.19 Score=34.61 Aligned_cols=37 Identities=30% Similarity=0.606 Sum_probs=31.5
Q ss_pred eeeeecceeeeeecCc--eeEEEEecCCCCCcccccccc
Q 026004 127 YDVASFLTYRVTCAGE--LEVRVRFSGFNNTEDEWVNVK 163 (245)
Q Consensus 127 YdV~~fl~~R~~~~g~--~el~Vrf~gF~~eeDEw~~~~ 163 (245)
|-|..-|.||+...|. .++.|++.|++.+++.|.+..
T Consensus 1 ~~Ve~Il~~r~~~~~~~~~~ylVkW~g~~~~~~tWe~~~ 39 (55)
T PF00385_consen 1 YEVERILDHRVVKGGNKVYEYLVKWKGYPYSENTWEPEE 39 (55)
T ss_dssp EEEEEEEEEEEETTEESEEEEEEEETTSSGGGEEEEEGG
T ss_pred CEEEEEEEEEEeCCCcccEEEEEEECCCCCCCCeEeeHH
Confidence 5677889999877775 599999999999999998843
No 39
>cd04508 TUDOR Tudor domains are found in many eukaryotic organisms and have been implicated in protein-protein interactions in which methylated protein substrates bind to these domains. For example, the Tudor domain of Survival of Motor Neuron (SMN) binds to symmetrically dimethylated arginines of arginine-glycine (RG) rich sequences found in the C-terminal tails of Sm proteins. The SMN protein is linked to spinal muscular atrophy. Another example is the tandem tudor domains of 53BP1, which bind to histone H4 specifically dimethylated at Lys20 (H4-K20me2). 53BP1 is a key transducer of the DNA damage checkpoint signal.
Probab=91.72 E-value=0.27 Score=32.65 Aligned_cols=36 Identities=31% Similarity=0.438 Sum_probs=26.7
Q ss_pred eecccCCCceeeeeecceeeeeecCceeEEEEecCCCCCcc
Q 026004 117 EARSSKDDAWYDVASFLTYRVTCAGELEVRVRFSGFNNTED 157 (245)
Q Consensus 117 EArs~~D~AWYdV~~fl~~R~~~~g~~el~Vrf~gF~~eeD 157 (245)
-|+...||.||-..+-- + .+...+.|.|..||+.+.
T Consensus 5 ~a~~~~d~~wyra~V~~---~--~~~~~~~V~f~DyG~~~~ 40 (48)
T cd04508 5 LAKYSDDGKWYRAKITS---I--LSDGKVEVFFVDYGNTEV 40 (48)
T ss_pred EEEECCCCeEEEEEEEE---E--CCCCcEEEEEEcCCCcEE
Confidence 36777899999988521 2 224579999999999854
No 40
>smart00333 TUDOR Tudor domain. Domain of unknown function present in several RNA-binding proteins. 10 copies in the Drosophila Tudor protein. Initial proposal that the survival motor neuron gene product contain a Tudor domain are corroborated by more recent database search techniques such as PSI-BLAST (unpublished).
Probab=91.51 E-value=0.66 Score=31.77 Aligned_cols=54 Identities=20% Similarity=0.243 Sum_probs=40.7
Q ss_pred cccCCceEEEeeecCCceeEEeeEEeeeeecccCCCCceeEEEEEEccCCccccccccceeeccC
Q 026004 180 KVNVGDLVLCYQEREDQAVYCDAHVLDIQRRVHDTEGCQCIFVVRYDHDFSEEQVKVERLCCRPT 244 (245)
Q Consensus 180 ~v~~G~~v~cf~~~~~~~~yyDA~V~~v~r~~Hd~~~C~C~F~Vr~~h~~~ee~v~~~~ic~rp~ 244 (245)
..++|+.+++.. ++..||.|+|+++... -.+.|.|....+.+.|+..+|..-|.
T Consensus 2 ~~~~G~~~~a~~---~d~~wyra~I~~~~~~--------~~~~V~f~D~G~~~~v~~~~l~~l~~ 55 (57)
T smart00333 2 TFKVGDKVAARW---EDGEWYRARIIKVDGE--------QLYEVFFIDYGNEEVVPPSDLRPLPE 55 (57)
T ss_pred CCCCCCEEEEEe---CCCCEEEEEEEEECCC--------CEEEEEEECCCccEEEeHHHeecCCC
Confidence 467898888654 2568999999999732 34678898877778888888876554
No 41
>KOG0773 consensus Transcription factor MEIS1 and related HOX domain proteins [Transcription]
Probab=91.35 E-value=0.17 Score=47.02 Aligned_cols=54 Identities=15% Similarity=0.136 Sum_probs=44.3
Q ss_pred cCCCCHHHHHHHHHHHHHh-CCCCCCHHHHHHHHHHcCCCcccCCCCcCCcchhhhhhhcccccc
Q 026004 7 WPDFTLAEIKEMESMYKEI-GEASLTQEYCKALATSFSFSASRAARPAITWLQVQSWFRDKQKKS 70 (245)
Q Consensus 7 ~~~FT~~Ql~eMEk~f~~~-~~~y~~~~~rq~LA~~f~lS~~r~Gk~~v~~~QVk~WFQNRR~k~ 70 (245)
-..|...-+..|..-+.+| ...||+......||.+.||+. .||.|||-|.|.+.
T Consensus 243 ~~~lP~~a~~ilr~Wl~~h~~~PYPse~~K~~La~~TGLs~----------~Qv~NWFINaR~R~ 297 (342)
T KOG0773|consen 243 QRGLPKEAVSILRAWLFEHLLHPYPSDDEKLMLAKQTGLSR----------PQVSNWFINARVRL 297 (342)
T ss_pred CCCCCHHHHHHHHHHHHHhccCCCCcchhccccchhcCCCc----------ccCCchhhhccccc
Confidence 3467777777777766664 457999999999999999988 99999999998763
No 42
>KOG1146 consensus Homeobox protein [General function prediction only]
Probab=91.16 E-value=0.18 Score=55.43 Aligned_cols=52 Identities=19% Similarity=0.425 Sum_probs=48.0
Q ss_pred CCCCHHHHHHHHHHHHHhCCCCCCHHHHHHHHHHcCCCcccCCCCcCCcchhhhhhhccccccc
Q 026004 8 PDFTLAEIKEMESMYKEIGEASLTQEYCKALATSFSFSASRAARPAITWLQVQSWFRDKQKKSQ 71 (245)
Q Consensus 8 ~~FT~~Ql~eMEk~f~~~~~~y~~~~~rq~LA~~f~lS~~r~Gk~~v~~~QVk~WFQNRR~k~k 71 (245)
+.|+..||..|-.+|.. ..|+....++.|-..+.++. ..|+.||||-|.|.+
T Consensus 908 ~~~~d~qlk~i~~~~~~--q~~~~~~~~E~l~~~~~~~~----------~~i~vw~qna~~~s~ 959 (1406)
T KOG1146|consen 908 TQESDLQLKIIKACYEA--QRTPTMQECEVLEEPIGLPK----------RVIQVWFQNARAKSK 959 (1406)
T ss_pred cchhHHHHHHHHHHHhh--ccCChHHHHHhhcccccCCc----------chhHHhhhhhhhhhh
Confidence 57899999999999999 58999999999999999988 889999999999865
No 43
>smart00561 MBT Present in Drosophila Scm, l(3)mbt, and vertebrate SCML2. Present in Drosophila Scm, l(3)mbt, and vertebrate SCML2. These proteins are involved in transcriptional regulation.
Probab=88.75 E-value=0.83 Score=36.05 Aligned_cols=46 Identities=20% Similarity=0.447 Sum_probs=37.8
Q ss_pred ceeEeecccCCCceeeeeecceeeeeecCceeEEEEecCCCCCcccccccc
Q 026004 113 ELAFEARSSKDDAWYDVASFLTYRVTCAGELEVRVRFSGFNNTEDEWVNVK 163 (245)
Q Consensus 113 ~~efEArs~~D~AWYdV~~fl~~R~~~~g~~el~Vrf~gF~~eeDEw~~~~ 163 (245)
.|-+||....+-..+=|++-.. ..|. .|+|+|.|+.+.+|.|+++.
T Consensus 31 GmkLEavD~~~~~~i~vAtV~~----v~g~-~l~v~~dg~~~~~D~W~~~~ 76 (96)
T smart00561 31 GMKLEAVDPRNPSLICVATVVE----VKGY-RLLLHFDGWDDKYDFWCDAD 76 (96)
T ss_pred CCEEEEECCCCCceEEEEEEEE----EECC-EEEEEEccCCCcCCEEEECC
Confidence 4788999999988888886433 2364 89999999999999999965
No 44
>smart00298 CHROMO Chromatin organization modifier domain.
Probab=87.74 E-value=0.62 Score=31.24 Aligned_cols=36 Identities=33% Similarity=0.592 Sum_probs=28.9
Q ss_pred eeeecceeeeeecCceeEEEEecCCCCCcccccccc
Q 026004 128 DVASFLTYRVTCAGELEVRVRFSGFNNTEDEWVNVK 163 (245)
Q Consensus 128 dV~~fl~~R~~~~g~~el~Vrf~gF~~eeDEw~~~~ 163 (245)
.|.--|.||+...|..++.|++.|++..++.|+...
T Consensus 3 ~v~~Il~~r~~~~~~~~ylVkW~g~~~~~~tW~~~~ 38 (55)
T smart00298 3 EVEKILDHRWKKKGELEYLVKWKGYSYSEDTWEPEE 38 (55)
T ss_pred chheeeeeeecCCCcEEEEEEECCCCCccCceeeHH
Confidence 345557777666788899999999999999998743
No 45
>PF02820 MBT: mbt repeat; InterPro: IPR004092 The function of the malignant brain tumor (MBT) repeat is unknown, but is found in a number of nuclear proteins involved in transcriptional repression. The repeat contains a completely conserved glutamate at its amino terminus that may be important for function. The crystal structure of the two MBT repeats of human SCM-like 2 protein has been reported. Each repeat consists of an extended "arm" and a globular core. The arm of the first repeat packs against the core of the second repeat and vice versa. The structure of the core-interacting part of each arm consists of an N-terminal alpha-helix and a turn of 310 helix connected by a short beta-strand. The core consists of an Src homology 3-like five-stranded beta-barrel followed by a C-terminal alpha-helix and another short beta-strand. Each arm interacts with its partner core in a similar way, with the orientation of the N-terminal helix relative to the barrel varying slightly. There are also extensive interactions between the two barrels [].; GO: 0006355 regulation of transcription, DNA-dependent, 0005634 nucleus; PDB: 2P0K_A 3F70_B 3CEY_A 2VYT_A 2BIV_A 1OI1_A 3OQ5_A 2RJE_B 2RJD_A 2RI3_A ....
Probab=87.00 E-value=1 Score=33.34 Aligned_cols=45 Identities=22% Similarity=0.527 Sum_probs=35.2
Q ss_pred eeEeecccCCCceeeeeecceeeeeecCceeEEEEecCCCCCcccccccc
Q 026004 114 LAFEARSSKDDAWYDVASFLTYRVTCAGELEVRVRFSGFNNTEDEWVNVK 163 (245)
Q Consensus 114 ~efEArs~~D~AWYdV~~fl~~R~~~~g~~el~Vrf~gF~~eeDEw~~~~ 163 (245)
|-+||....+...+=|++-.. ..|. .|+|+|.|..+.+|.|+.+.
T Consensus 1 MkLEa~d~~~~~~~~vAtV~~----v~g~-~l~v~~dg~~~~~d~w~~~~ 45 (73)
T PF02820_consen 1 MKLEAVDPRNPSLICVATVVK----VCGG-RLLVRYDGWDDDYDFWCHID 45 (73)
T ss_dssp EEEEEEETTECCEEEEEEEEE----EETT-EEEEEETTSTGGGEEEEETT
T ss_pred CeEEEECCCCCCeEEEEEEEE----EeCC-EEEEEEcCCCCCccEEEECC
Confidence 568999999988887775432 2354 49999999999999999854
No 46
>PLN00104 MYST -like histone acetyltransferase; Provisional
Probab=86.79 E-value=2.7 Score=41.97 Aligned_cols=52 Identities=23% Similarity=0.400 Sum_probs=37.8
Q ss_pred ecccCCCceeeeeecceeeee---ecCceeEEEEecCCCCCccccccccccccccCC
Q 026004 118 ARSSKDDAWYDVASFLTYRVT---CAGELEVRVRFSGFNNTEDEWVNVKTAVRQRSI 171 (245)
Q Consensus 118 Ars~~D~AWYdV~~fl~~R~~---~~g~~el~Vrf~gF~~eeDEw~~~~~~~R~rS~ 171 (245)
|+...||.||...+ +.-|.. ..|+.+..|||.||..--||||+.. ++...++
T Consensus 62 a~~~~Dg~~~~A~V-I~~R~~~~~~~~~~~YYVHY~g~nrRlDEWV~~~-rLdls~~ 116 (450)
T PLN00104 62 CRWRFDGKYHPVKV-IERRRGGSGGPNDYEYYVHYTEFNRRLDEWVKLE-QLDLDTV 116 (450)
T ss_pred EEECCCCCEEEEEE-EEEeccCCCCCCCceEEEEEecCCccHhhccCHh-hcccccc
Confidence 46677999998654 554542 2345689999999999999999965 5555443
No 47
>smart00743 Agenet Tudor-like domain present in plant sequences. Domain in plant sequences with possible chromatin-associated functions.
Probab=86.48 E-value=2.3 Score=29.77 Aligned_cols=51 Identities=24% Similarity=0.369 Sum_probs=39.5
Q ss_pred cccCCceEEEeeecCCceeEEeeEEeeeeecccCCCCceeEEEEEEcc--CCcccccccccee
Q 026004 180 KVNVGDLVLCYQEREDQAVYCDAHVLDIQRRVHDTEGCQCIFVVRYDH--DFSEEQVKVERLC 240 (245)
Q Consensus 180 ~v~~G~~v~cf~~~~~~~~yyDA~V~~v~r~~Hd~~~C~C~F~Vr~~h--~~~ee~v~~~~ic 240 (245)
.++.||.|-++... +..||-|.|+.+.. .. +|.|+|.. .+.++.++..+|-
T Consensus 2 ~~~~G~~Ve~~~~~--~~~W~~a~V~~~~~-----~~---~~~V~~~~~~~~~~e~v~~~~LR 54 (61)
T smart00743 2 DFKKGDRVEVFSKE--EDSWWEAVVTKVLG-----DG---KYLVRYLTESEPLKETVDWSDLR 54 (61)
T ss_pred CcCCCCEEEEEECC--CCEEEEEEEEEECC-----CC---EEEEEECCCCcccEEEEeHHHcc
Confidence 56899999987653 55899999999874 22 38999999 7777888777663
No 48
>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=84.83 E-value=0.87 Score=39.45 Aligned_cols=54 Identities=19% Similarity=0.083 Sum_probs=40.9
Q ss_pred CCCCHHHHHHHHHHHHHhCCCCCCHHHHHHHHHHcCCCcccCCCCcCCcchhhhhhhc
Q 026004 8 PDFTLAEIKEMESMYKEIGEASLTQEYCKALATSFSFSASRAARPAITWLQVQSWFRD 65 (245)
Q Consensus 8 ~~FT~~Ql~eMEk~f~~~~~~y~~~~~rq~LA~~f~lS~~r~Gk~~v~~~QVk~WFQN 65 (245)
..+|+++|+||-++=.+ -|..-.+.+||++||+|+-..+-++=...|-+.+-+.
T Consensus 84 y~Lt~e~i~Eir~LR~~----DP~~wTr~~LAkkF~~S~~fV~~v~~~~~e~~~~~~~ 137 (164)
T PF12824_consen 84 YHLTPEDIQEIRRLRAE----DPEKWTRKKLAKKFNCSPLFVSMVAPAPKEKKKEMEA 137 (164)
T ss_pred ccCCHHHHHHHHHHHHc----CchHhhHHHHHHHhCCCHHHHHHhcCCCHHHHHHHHH
Confidence 56999999999998877 4777899999999999996666555444454444333
No 49
>PF05641 Agenet: Agenet domain; InterPro: IPR008395 This domain is related to the TUDOR domain IPR008191 from INTERPRO []. The function of the agenet domain is unknown. This signature matches one of the two Agenet domains in the FMR proteins [].; GO: 0003723 RNA binding; PDB: 2BKD_N 3O8V_A 3KUF_A 3H8Z_A.
Probab=84.68 E-value=1.4 Score=32.22 Aligned_cols=44 Identities=16% Similarity=0.324 Sum_probs=23.6
Q ss_pred cccC---CCceeeeeecceeeeeecCce-eEEEEecCCCCCcccc------cccccccccc
Q 026004 119 RSSK---DDAWYDVASFLTYRVTCAGEL-EVRVRFSGFNNTEDEW------VNVKTAVRQR 169 (245)
Q Consensus 119 rs~~---D~AWYdV~~fl~~R~~~~g~~-el~Vrf~gF~~eeDEw------~~~~~~~R~r 169 (245)
+|-. .||||...+ +..... .+.|+|..+.++++++ ++.+ ++|+.
T Consensus 10 ~s~e~g~~gaWf~a~V------~~~~~~~~~~V~Y~~~~~~~~~~~~l~e~V~~~-~iRP~ 63 (68)
T PF05641_consen 10 SSDEDGFRGAWFPATV------LKENGDDKYLVEYDDLPDEDGESPPLKEWVDAR-RIRPC 63 (68)
T ss_dssp EE-SBTT--EEEEEEE------EEEETT-EEEEEETT-SS--------EEEEEGG-GEEE-
T ss_pred EEcCCCCCcEEEEEEE------EEeCCCcEEEEEECCcccccccccccEEEechh-eEECc
Confidence 6655 679999985 333333 8999999999886654 4444 45554
No 50
>smart00333 TUDOR Tudor domain. Domain of unknown function present in several RNA-binding proteins. 10 copies in the Drosophila Tudor protein. Initial proposal that the survival motor neuron gene product contain a Tudor domain are corroborated by more recent database search techniques such as PSI-BLAST (unpublished).
Probab=84.53 E-value=1.5 Score=29.90 Aligned_cols=39 Identities=31% Similarity=0.457 Sum_probs=28.6
Q ss_pred eecccCCCceeeeeecceeeeeecCceeEEEEecCCCCCcccccccc
Q 026004 117 EARSSKDDAWYDVASFLTYRVTCAGELEVRVRFSGFNNTEDEWVNVK 163 (245)
Q Consensus 117 EArs~~D~AWYdV~~fl~~R~~~~g~~el~Vrf~gF~~eeDEw~~~~ 163 (245)
.|+- .||.||.+.+ ++ ..++..+.|.|..||.. +|++..
T Consensus 10 ~a~~-~d~~wyra~I-~~----~~~~~~~~V~f~D~G~~--~~v~~~ 48 (57)
T smart00333 10 AARW-EDGEWYRARI-IK----VDGEQLYEVFFIDYGNE--EVVPPS 48 (57)
T ss_pred EEEe-CCCCEEEEEE-EE----ECCCCEEEEEEECCCcc--EEEeHH
Confidence 4577 8999999984 22 23325799999999998 487744
No 51
>PF12148 DUF3590: Protein of unknown function (DUF3590); InterPro: IPR021991 This domain is found in eukaryotes, and is typically between 83 and 97 amino acids in length. It is found in association with PF00097 from PFAM, PF02182 from PFAM, PF00628 from PFAM, PF00240 from PFAM. There are two conserved sequence motifs: RAR and NYN. The domain is part of the protein NIRF which has zinc finger and ubiquitinating domains. The function of this domain is likely to be mainly structural, however this has not been confirmed. ; PDB: 3DB4_A 3ASK_A 3DB3_A 2L3R_A.
Probab=83.16 E-value=3.2 Score=32.77 Aligned_cols=70 Identities=14% Similarity=0.329 Sum_probs=39.9
Q ss_pred eecccCCCceeeeeecceeeeee--cCceeEEEEecCCCCCccccccccccccccCCCccccccccccCCceEEE
Q 026004 117 EARSSKDDAWYDVASFLTYRVTC--AGELEVRVRFSGFNNTEDEWVNVKTAVRQRSIPLEQSECVKVNVGDLVLC 189 (245)
Q Consensus 117 EArs~~D~AWYdV~~fl~~R~~~--~g~~el~Vrf~gF~~eeDEw~~~~~~~R~rS~ple~~eC~~v~~G~~v~c 189 (245)
-||....|||++...-=.++--. +.+.-..|.|.+|.+..-.-+.++ -+|+|..-+= .=..|.+|+.|..
T Consensus 3 D~~d~~~gAWfEa~i~~i~~~~~~~~e~viYhIkyddype~gvv~~~~~-~iRpRARt~l--~w~~L~VG~~VMv 74 (85)
T PF12148_consen 3 DARDRNMGAWFEAQIVTITKKCMSDDEDVIYHIKYDDYPENGVVEMRSK-DIRPRARTIL--KWDELKVGQVVMV 74 (85)
T ss_dssp EEE-TTT-EEEEEEEEEEEES-SSSSTTEEEEEEETT-GGG-EEEEEGG-GEEE---SBE---GGG--TT-EEEE
T ss_pred ccccCCCcceEEEEEEEeeccCCCCCCCEEEEEEeccCCCcCceecccc-cccceeeEec--cHHhCCcccEEEE
Confidence 37889999999987543332211 235678899999887666556666 7888876543 3457889999873
No 52
>smart00743 Agenet Tudor-like domain present in plant sequences. Domain in plant sequences with possible chromatin-associated functions.
Probab=82.49 E-value=2.5 Score=29.60 Aligned_cols=34 Identities=24% Similarity=0.350 Sum_probs=23.8
Q ss_pred eecccCCCceeeeeecceeeeeecCceeEEEEecC--CCCC
Q 026004 117 EARSSKDDAWYDVASFLTYRVTCAGELEVRVRFSG--FNNT 155 (245)
Q Consensus 117 EArs~~D~AWYdV~~fl~~R~~~~g~~el~Vrf~g--F~~e 155 (245)
||++..||+||...+.- +. ++....|+|.+ ++..
T Consensus 10 e~~~~~~~~W~~a~V~~---~~--~~~~~~V~~~~~~~~~~ 45 (61)
T smart00743 10 EVFSKEEDSWWEAVVTK---VL--GDGKYLVRYLTESEPLK 45 (61)
T ss_pred EEEECCCCEEEEEEEEE---EC--CCCEEEEEECCCCcccE
Confidence 56777799999887642 22 33469999999 5443
No 53
>PF12148 DUF3590: Protein of unknown function (DUF3590); InterPro: IPR021991 This domain is found in eukaryotes, and is typically between 83 and 97 amino acids in length. It is found in association with PF00097 from PFAM, PF02182 from PFAM, PF00628 from PFAM, PF00240 from PFAM. There are two conserved sequence motifs: RAR and NYN. The domain is part of the protein NIRF which has zinc finger and ubiquitinating domains. The function of this domain is likely to be mainly structural, however this has not been confirmed. ; PDB: 3DB4_A 3ASK_A 3DB3_A 2L3R_A.
Probab=81.75 E-value=2.2 Score=33.65 Aligned_cols=48 Identities=17% Similarity=0.368 Sum_probs=34.5
Q ss_pred ceeEEeeEEeeeeecccCCCCceeEEEEEEccCCccccccccceeeccC
Q 026004 196 QAVYCDAHVLDIQRRVHDTEGCQCIFVVRYDHDFSEEQVKVERLCCRPT 244 (245)
Q Consensus 196 ~~~yyDA~V~~v~r~~Hd~~~C~C~F~Vr~~h~~~ee~v~~~~ic~rp~ 244 (245)
...||+|.|..|.++. ....+.+.+-|.|+..|....+.+.-...||.
T Consensus 9 ~gAWfEa~i~~i~~~~-~~~~e~viYhIkyddype~gvv~~~~~~iRpR 56 (85)
T PF12148_consen 9 MGAWFEAQIVTITKKC-MSDDEDVIYHIKYDDYPENGVVEMRSKDIRPR 56 (85)
T ss_dssp T-EEEEEEEEEEEES--SSSSTTEEEEEEETT-GGG-EEEEEGGGEEE-
T ss_pred CcceEEEEEEEeeccC-CCCCCCEEEEEEeccCCCcCceecccccccce
Confidence 4579999999999554 54569999999999999776666666666663
No 54
>PF11717 Tudor-knot: RNA binding activity-knot of a chromodomain ; PDB: 2EKO_A 2RO0_A 2RNZ_A 1WGS_A 3E9G_A 3E9F_A 2K3X_A 2K3Y_A 2EFI_A 2F5K_F ....
Probab=78.60 E-value=11 Score=26.43 Aligned_cols=42 Identities=26% Similarity=0.455 Sum_probs=29.7
Q ss_pred ccCCceEEEeeecCCceeEEeeEEeeeeecccCCCCceeEEEEEEccCCc
Q 026004 181 VNVGDLVLCYQEREDQAVYCDAHVLDIQRRVHDTEGCQCIFVVRYDHDFS 230 (245)
Q Consensus 181 v~~G~~v~cf~~~~~~~~yyDA~V~~v~r~~Hd~~~C~C~F~Vr~~h~~~ 230 (245)
+..|+.|.|.. .+..+|.|.|+++...... =.|.|-|..-+.
T Consensus 1 ~~vG~~v~~~~---~~~~~y~A~I~~~r~~~~~-----~~YyVHY~g~nk 42 (55)
T PF11717_consen 1 FEVGEKVLCKY---KDGQWYEAKILDIREKNGE-----PEYYVHYQGWNK 42 (55)
T ss_dssp --TTEEEEEEE---TTTEEEEEEEEEEEECTTC-----EEEEEEETTSTG
T ss_pred CCcCCEEEEEE---CCCcEEEEEEEEEEecCCC-----EEEEEEcCCCCC
Confidence 46899999999 3447899999999874433 456777765443
No 55
>PF06003 SMN: Survival motor neuron protein (SMN); InterPro: IPR010304 This family consists of several eukaryotic survival motor neuron (SMN) proteins. The Survival of Motor Neurons (SMN) protein, the product of the spinal muscular atrophy-determining gene, is part of a large macromolecular complex (SMN complex) that functions in the assembly of spliceosomal small nuclear ribonucleoproteins (snRNPs). The SMN complex functions as a specificity factor essential for the efficient assembly of Sm proteins on U snRNAs and likely protects cells from illicit, and potentially deleterious, non-specific binding of Sm proteins to RNAs.; GO: 0003723 RNA binding, 0006397 mRNA processing, 0005634 nucleus, 0005737 cytoplasm; PDB: 1MHN_A 4A4G_A 3S6N_M 4A4E_A 1G5V_A 4A4H_A 4A4F_A 2D9T_A.
Probab=77.47 E-value=4.9 Score=37.02 Aligned_cols=53 Identities=26% Similarity=0.379 Sum_probs=36.7
Q ss_pred ccccCCceEEEeeecCCceeEEeeEEeeeeecccCCCCceeEEEEEEccCCcccccccccee
Q 026004 179 VKVNVGDLVLCYQEREDQAVYCDAHVLDIQRRVHDTEGCQCIFVVRYDHDFSEEQVKVERLC 240 (245)
Q Consensus 179 ~~v~~G~~v~cf~~~~~~~~yyDA~V~~v~r~~Hd~~~C~C~F~Vr~~h~~~ee~v~~~~ic 240 (245)
...++||..++.- .++-.||.|.|..|.. +...| +|+|..-.+.|+|.|.+|=
T Consensus 67 ~~WkvGd~C~A~~--s~Dg~~Y~A~I~~i~~---~~~~~----~V~f~gYgn~e~v~l~dL~ 119 (264)
T PF06003_consen 67 KKWKVGDKCMAVY--SEDGQYYPATIESIDE---EDGTC----VVVFTGYGNEEEVNLSDLK 119 (264)
T ss_dssp T---TT-EEEEE---TTTSSEEEEEEEEEET---TTTEE----EEEETTTTEEEEEEGGGEE
T ss_pred cCCCCCCEEEEEE--CCCCCEEEEEEEEEcC---CCCEE----EEEEcccCCeEeeehhhhc
Confidence 5788999988763 3345799999999962 12333 4999999999999998873
No 56
>PF04218 CENP-B_N: CENP-B N-terminal DNA-binding domain; InterPro: IPR006695 Centromere Protein B (CENP-B) is a DNA-binding protein localized to the centromere. Within the N-terminal 125 residues, there is a DNA-binding region, which binds to a corresponding 17bp CENP-B box sequence. CENP-B dimers either bind two separate DNA molecules or alternatively, they may bind two CENP-B boxes on one DNA molecule, with the intervening stretch of DNA forming a loop structure. The CENP-B DNA-binding domain consists of two repeating domains, RP1 and RP2. This family corresponds to RP1 has been shown to consist of four helices in a helix-turn-helix structure [].; GO: 0003677 DNA binding, 0000775 chromosome, centromeric region; PDB: 1BW6_A 1HLV_A 2ELH_A.
Probab=77.12 E-value=4.5 Score=28.46 Aligned_cols=42 Identities=24% Similarity=0.277 Sum_probs=29.7
Q ss_pred CCCHHHHHHHHHHHHHhCCCCCCHHHHHHHHHHcCCCcccCCCCcCCcchhhhhhhccc
Q 026004 9 DFTLAEIKEMESMYKEIGEASLTQEYCKALATSFSFSASRAARPAITWLQVQSWFRDKQ 67 (245)
Q Consensus 9 ~FT~~Ql~eMEk~f~~~~~~y~~~~~rq~LA~~f~lS~~r~Gk~~v~~~QVk~WFQNRR 67 (245)
.+|..|-.++=+.++.. . ...+||..||++. .+|..|..||.
T Consensus 6 ~LTl~eK~~iI~~~e~g--~-----s~~~ia~~fgv~~----------sTv~~I~K~k~ 47 (53)
T PF04218_consen 6 SLTLEEKLEIIKRLEEG--E-----SKRDIAREFGVSR----------STVSTILKNKD 47 (53)
T ss_dssp S--HHHHHHHHHHHHCT--T------HHHHHHHHT--C----------CHHHHHHHCHH
T ss_pred cCCHHHHHHHHHHHHcC--C-----CHHHHHHHhCCCH----------HHHHHHHHhHH
Confidence 46777777776777662 2 5789999999988 99999999973
No 57
>PF05641 Agenet: Agenet domain; InterPro: IPR008395 This domain is related to the TUDOR domain IPR008191 from INTERPRO []. The function of the agenet domain is unknown. This signature matches one of the two Agenet domains in the FMR proteins [].; GO: 0003723 RNA binding; PDB: 2BKD_N 3O8V_A 3KUF_A 3H8Z_A.
Probab=74.75 E-value=9 Score=27.91 Aligned_cols=53 Identities=28% Similarity=0.343 Sum_probs=32.9
Q ss_pred ccCCceEEE-eeecCCceeEEeeEEeeeeecccCCCCceeEEEEEEccCCc--------cccccccceeecc
Q 026004 181 VNVGDLVLC-YQEREDQAVYCDAHVLDIQRRVHDTEGCQCIFVVRYDHDFS--------EEQVKVERLCCRP 243 (245)
Q Consensus 181 v~~G~~v~c-f~~~~~~~~yyDA~V~~v~r~~Hd~~~C~C~F~Vr~~h~~~--------ee~v~~~~ic~rp 243 (245)
+++|+.|-. .++.+-..-||-|.|+++.... +++|+|++=.. .|.|....| ||
T Consensus 1 F~~G~~VEV~s~e~g~~gaWf~a~V~~~~~~~--------~~~V~Y~~~~~~~~~~~~l~e~V~~~~i--RP 62 (68)
T PF05641_consen 1 FKKGDEVEVSSDEDGFRGAWFPATVLKENGDD--------KYLVEYDDLPDEDGESPPLKEWVDARRI--RP 62 (68)
T ss_dssp --TT-EEEEEE-SBTT--EEEEEEEEEEETT---------EEEEEETT-SS--------EEEEEGGGE--EE
T ss_pred CCCCCEEEEEEcCCCCCcEEEEEEEEEeCCCc--------EEEEEECCcccccccccccEEEechheE--EC
Confidence 368999984 4455558899999999987544 89999965432 455666654 65
No 58
>PF06003 SMN: Survival motor neuron protein (SMN); InterPro: IPR010304 This family consists of several eukaryotic survival motor neuron (SMN) proteins. The Survival of Motor Neurons (SMN) protein, the product of the spinal muscular atrophy-determining gene, is part of a large macromolecular complex (SMN complex) that functions in the assembly of spliceosomal small nuclear ribonucleoproteins (snRNPs). The SMN complex functions as a specificity factor essential for the efficient assembly of Sm proteins on U snRNAs and likely protects cells from illicit, and potentially deleterious, non-specific binding of Sm proteins to RNAs.; GO: 0003723 RNA binding, 0006397 mRNA processing, 0005634 nucleus, 0005737 cytoplasm; PDB: 1MHN_A 4A4G_A 3S6N_M 4A4E_A 1G5V_A 4A4H_A 4A4F_A 2D9T_A.
Probab=67.50 E-value=6.6 Score=36.17 Aligned_cols=41 Identities=22% Similarity=0.258 Sum_probs=28.9
Q ss_pred eecccCCCceeeeeecceeeeeecCceeEEEEecCCCCCcccccc
Q 026004 117 EARSSKDDAWYDVASFLTYRVTCAGELEVRVRFSGFNNTEDEWVN 161 (245)
Q Consensus 117 EArs~~D~AWYdV~~fl~~R~~~~g~~el~Vrf~gF~~eeDEw~~ 161 (245)
-|.-+.||-||.....- |-..+ -...|+|.|||+.|...+.
T Consensus 76 ~A~~s~Dg~~Y~A~I~~---i~~~~-~~~~V~f~gYgn~e~v~l~ 116 (264)
T PF06003_consen 76 MAVYSEDGQYYPATIES---IDEED-GTCVVVFTGYGNEEEVNLS 116 (264)
T ss_dssp EEE-TTTSSEEEEEEEE---EETTT-TEEEEEETTTTEEEEEEGG
T ss_pred EEEECCCCCEEEEEEEE---EcCCC-CEEEEEEcccCCeEeeehh
Confidence 45678999999988431 22223 2789999999999876654
No 59
>cd04508 TUDOR Tudor domains are found in many eukaryotic organisms and have been implicated in protein-protein interactions in which methylated protein substrates bind to these domains. For example, the Tudor domain of Survival of Motor Neuron (SMN) binds to symmetrically dimethylated arginines of arginine-glycine (RG) rich sequences found in the C-terminal tails of Sm proteins. The SMN protein is linked to spinal muscular atrophy. Another example is the tandem tudor domains of 53BP1, which bind to histone H4 specifically dimethylated at Lys20 (H4-K20me2). 53BP1 is a key transducer of the DNA damage checkpoint signal.
Probab=67.31 E-value=13 Score=24.34 Aligned_cols=46 Identities=24% Similarity=0.238 Sum_probs=29.9
Q ss_pred CceEEEeeecCCceeEEeeEEeeeeecccCCCCceeEEEEEEccCCccccccccce
Q 026004 184 GDLVLCYQEREDQAVYCDAHVLDIQRRVHDTEGCQCIFVVRYDHDFSEEQVKVERL 239 (245)
Q Consensus 184 G~~v~cf~~~~~~~~yyDA~V~~v~r~~Hd~~~C~C~F~Vr~~h~~~ee~v~~~~i 239 (245)
|+++++.- .++..||-|.|+++.. .-.+.|.|..-.+.+.|++.+|
T Consensus 1 G~~c~a~~--~~d~~wyra~V~~~~~--------~~~~~V~f~DyG~~~~v~~~~l 46 (48)
T cd04508 1 GDLCLAKY--SDDGKWYRAKITSILS--------DGKVEVFFVDYGNTEVVPLSDL 46 (48)
T ss_pred CCEEEEEE--CCCCeEEEEEEEEECC--------CCcEEEEEEcCCCcEEEeHHHc
Confidence 44555432 2356999999999973 2346788887555566776655
No 60
>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=64.11 E-value=6.8 Score=29.01 Aligned_cols=31 Identities=23% Similarity=0.342 Sum_probs=22.9
Q ss_pred HHHHHHhCCCCCCHHHHHHHHHHcCCCcccCCCCcCCcchhhhhh
Q 026004 19 ESMYKEIGEASLTQEYCKALATSFSFSASRAARPAITWLQVQSWF 63 (245)
Q Consensus 19 Ek~f~~~~~~y~~~~~rq~LA~~f~lS~~r~Gk~~v~~~QVk~WF 63 (245)
-.+|.++++... ..+||++||.|+ .||..|=
T Consensus 13 ~e~y~~~~g~i~----lkdIA~~Lgvs~----------~tIr~WK 43 (60)
T PF10668_consen 13 FEIYKESNGKIK----LKDIAEKLGVSE----------STIRKWK 43 (60)
T ss_pred HHHHHHhCCCcc----HHHHHHHHCCCH----------HHHHHHh
Confidence 346666654433 468999999999 9999983
No 61
>COG3458 Acetyl esterase (deacetylase) [Secondary metabolites biosynthesis, transport, and catabolism]
Probab=63.39 E-value=11 Score=36.10 Aligned_cols=93 Identities=20% Similarity=0.362 Sum_probs=69.1
Q ss_pred cccceeEee-cccCCCceeeeeecceeeeeecCceeEEEEecCCCCCcccccc-----------ccccccccCCCccccc
Q 026004 110 ELKELAFEA-RSSKDDAWYDVASFLTYRVTCAGELEVRVRFSGFNNTEDEWVN-----------VKTAVRQRSIPLEQSE 177 (245)
Q Consensus 110 ~~~~~efEA-rs~~D~AWYdV~~fl~~R~~~~g~~el~Vrf~gF~~eeDEw~~-----------~~~~~R~rS~ple~~e 177 (245)
+-++|.|+. +-.+=.+||-+.. ..+|..-+.|+|-||+.--++|.+ |.-.+|-.|.--+|+-
T Consensus 55 e~ydvTf~g~~g~rI~gwlvlP~------~~~~~~P~vV~fhGY~g~~g~~~~~l~wa~~Gyavf~MdvRGQg~~~~dt~ 128 (321)
T COG3458 55 EVYDVTFTGYGGARIKGWLVLPR------HEKGKLPAVVQFHGYGGRGGEWHDMLHWAVAGYAVFVMDVRGQGSSSQDTA 128 (321)
T ss_pred EEEEEEEeccCCceEEEEEEeec------ccCCccceEEEEeeccCCCCCccccccccccceeEEEEecccCCCccccCC
Confidence 446677721 2334468999982 345888999999999999988855 6667888888878888
Q ss_pred ccccc---CCceEEEeeecCCceeEEeeEEeeeee
Q 026004 178 CVKVN---VGDLVLCYQEREDQAVYCDAHVLDIQR 209 (245)
Q Consensus 178 C~~v~---~G~~v~cf~~~~~~~~yyDA~V~~v~r 209 (245)
|.... ||-.+....+++|+ .||-.+++|+-|
T Consensus 129 ~~p~~~s~pG~mtrGilD~kd~-yyyr~v~~D~~~ 162 (321)
T COG3458 129 DPPGGPSDPGFMTRGILDRKDT-YYYRGVFLDAVR 162 (321)
T ss_pred CCCCCCcCCceeEeecccCCCc-eEEeeehHHHHH
Confidence 88776 77777788888855 788777776654
No 62
>KOG3623 consensus Homeobox transcription factor SIP1 [Transcription]
Probab=60.70 E-value=11 Score=40.31 Aligned_cols=44 Identities=16% Similarity=0.342 Sum_probs=35.7
Q ss_pred HHHHHHHHHHhCCCCCCHHHHHHHHHHcCCCcccCCCCcCCcchhhhhhhcccccc
Q 026004 15 IKEMESMYKEIGEASLTQEYCKALATSFSFSASRAARPAITWLQVQSWFRDKQKKS 70 (245)
Q Consensus 15 l~eMEk~f~~~~~~y~~~~~rq~LA~~f~lS~~r~Gk~~v~~~QVk~WFQNRR~k~ 70 (245)
+.-|...|.- |..|..++..++|...|++- .-|+.||+|++++.
T Consensus 568 ~sllkayyal--n~~ps~eelskia~qvglp~----------~vvk~wfE~~~a~e 611 (1007)
T KOG3623|consen 568 TSLLKAYYAL--NGLPSEEELSKIAQQVGLPF----------AVVKAWFEDEEAEE 611 (1007)
T ss_pred HHHHHHHHHh--cCCCCHHHHHHHHHHhcccH----------HHHHHHHHhhhhhh
Confidence 3344455555 58999999999999999977 77999999999863
No 63
>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=59.23 E-value=7.7 Score=26.89 Aligned_cols=48 Identities=23% Similarity=0.245 Sum_probs=36.7
Q ss_pred cCCCCHHHHHHHHHHHHHhCCCCCCHHHHHHHHHHcCCCcccCCCCcCCcchhhhhhhcccccccc
Q 026004 7 WPDFTLAEIKEMESMYKEIGEASLTQEYCKALATSFSFSASRAARPAITWLQVQSWFRDKQKKSQA 72 (245)
Q Consensus 7 ~~~FT~~Ql~eMEk~f~~~~~~y~~~~~rq~LA~~f~lS~~r~Gk~~v~~~QVk~WFQNRR~k~k~ 72 (245)
|..||+.|+.-|.-+..- ...+++|+.+++|+ +-|....+|=+.|...
T Consensus 1 ~~~LT~~E~~vl~~l~~G--------~~~~eIA~~l~is~----------~tV~~~~~~i~~Kl~~ 48 (58)
T PF00196_consen 1 FPSLTERELEVLRLLAQG--------MSNKEIAEELGISE----------KTVKSHRRRIMKKLGV 48 (58)
T ss_dssp SGSS-HHHHHHHHHHHTT--------S-HHHHHHHHTSHH----------HHHHHHHHHHHHHHT-
T ss_pred CCccCHHHHHHHHHHHhc--------CCcchhHHhcCcch----------hhHHHHHHHHHHHhCC
Confidence 578999999999887766 34689999999988 8899888776666543
No 64
>PF13936 HTH_38: Helix-turn-helix domain; PDB: 2W48_A.
Probab=55.26 E-value=9.3 Score=25.74 Aligned_cols=33 Identities=15% Similarity=0.222 Sum_probs=15.5
Q ss_pred cCCCCHHHHHHHHHHHHHhCCCCCCHHHHHHHHHHcCCCc
Q 026004 7 WPDFTLAEIKEMESMYKEIGEASLTQEYCKALATSFSFSA 46 (245)
Q Consensus 7 ~~~FT~~Ql~eMEk~f~~~~~~y~~~~~rq~LA~~f~lS~ 46 (245)
+..+|++|..+++.++.+. .-..+||+.||.|+
T Consensus 2 ~~~Lt~~eR~~I~~l~~~G-------~s~~~IA~~lg~s~ 34 (44)
T PF13936_consen 2 YKHLTPEERNQIEALLEQG-------MSIREIAKRLGRSR 34 (44)
T ss_dssp ----------HHHHHHCS----------HHHHHHHTT--H
T ss_pred ccchhhhHHHHHHHHHHcC-------CCHHHHHHHHCcCc
Confidence 3578999999999887652 44667999999988
No 65
>smart00027 EH Eps15 homology domain. Pair of EF hand motifs that recognise proteins containing Asn-Pro-Phe (NPF) sequences.
Probab=53.05 E-value=37 Score=25.64 Aligned_cols=45 Identities=7% Similarity=0.216 Sum_probs=33.8
Q ss_pred CCHHHHHHHHHHHHHh---CCCCCCHHHHHHHHHHcCCCcccCCCCcCCcchhhhhhh
Q 026004 10 FTLAEIKEMESMYKEI---GEASLTQEYCKALATSFSFSASRAARPAITWLQVQSWFR 64 (245)
Q Consensus 10 FT~~Ql~eMEk~f~~~---~~~y~~~~~rq~LA~~f~lS~~r~Gk~~v~~~QVk~WFQ 64 (245)
+|++|+.++..+|... +..+++......+-..+++++ .+|...|.
T Consensus 4 ls~~~~~~l~~~F~~~D~d~~G~Is~~el~~~l~~~~~~~----------~ev~~i~~ 51 (96)
T smart00027 4 ISPEDKAKYEQIFRSLDKNQDGTVTGAQAKPILLKSGLPQ----------TLLAKIWN 51 (96)
T ss_pred CCHHHHHHHHHHHHHhCCCCCCeEeHHHHHHHHHHcCCCH----------HHHHHHHH
Confidence 6889999999999873 567888877776666677665 66776664
No 66
>PF00249 Myb_DNA-binding: Myb-like DNA-binding domain; InterPro: IPR014778 The retroviral oncogene v-myb, and its cellular counterpart c-myb, encode nuclear DNA-binding proteins. These belong to the SANT domain family that specifically recognise the sequence YAAC(G/T)G [, ]. In myb, one of the most conserved regions consisting of three tandem repeats has been shown to be involved in DNA-binding [].; PDB: 1X41_A 2XAF_B 2XAG_B 2XAH_B 2UXN_B 2Y48_B 2XAQ_B 2X0L_B 2IW5_B 2XAJ_B ....
Probab=52.77 E-value=42 Score=22.43 Aligned_cols=42 Identities=21% Similarity=0.272 Sum_probs=31.7
Q ss_pred CCCHHHHHHHHHHHHHhCCCCCCHHHHHHHHHHcC--CCcccCCCCcCCcchhhhhhhc
Q 026004 9 DFTLAEIKEMESMYKEIGEASLTQEYCKALATSFS--FSASRAARPAITWLQVQSWFRD 65 (245)
Q Consensus 9 ~FT~~Ql~eMEk~f~~~~~~y~~~~~rq~LA~~f~--lS~~r~Gk~~v~~~QVk~WFQN 65 (245)
.||++|...|.+++..++.. .=..||..++ .|+ .|+++=|+|
T Consensus 3 ~Wt~eE~~~l~~~v~~~g~~-----~W~~Ia~~~~~~Rt~----------~qc~~~~~~ 46 (48)
T PF00249_consen 3 PWTEEEDEKLLEAVKKYGKD-----NWKKIAKRMPGGRTA----------KQCRSRYQN 46 (48)
T ss_dssp SS-HHHHHHHHHHHHHSTTT-----HHHHHHHHHSSSSTH----------HHHHHHHHH
T ss_pred CCCHHHHHHHHHHHHHhCCc-----HHHHHHHHcCCCCCH----------HHHHHHHHh
Confidence 58999999999999996533 6788999998 444 888765553
No 67
>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=50.68 E-value=21 Score=25.64 Aligned_cols=34 Identities=15% Similarity=0.171 Sum_probs=29.2
Q ss_pred CCHHHHHHHHHHHHHhCCCCCC---HHHHHHHHHHcCCCc
Q 026004 10 FTLAEIKEMESMYKEIGEASLT---QEYCKALATSFSFSA 46 (245)
Q Consensus 10 FT~~Ql~eMEk~f~~~~~~y~~---~~~rq~LA~~f~lS~ 46 (245)
+|+.|.+.|..+++. .|.+ .....+||+.||.|.
T Consensus 1 LT~~Q~e~L~~A~~~---GYfd~PR~~tl~elA~~lgis~ 37 (53)
T PF04967_consen 1 LTDRQREILKAAYEL---GYFDVPRRITLEELAEELGISK 37 (53)
T ss_pred CCHHHHHHHHHHHHc---CCCCCCCcCCHHHHHHHhCCCH
Confidence 589999999999998 4655 567899999999987
No 68
>smart00717 SANT SANT SWI3, ADA2, N-CoR and TFIIIB'' DNA-binding domains.
Probab=48.52 E-value=39 Score=21.04 Aligned_cols=43 Identities=16% Similarity=0.235 Sum_probs=31.3
Q ss_pred CCCCHHHHHHHHHHHHHhCCCCCCHHHHHHHHHHcC-CCcccCCCCcCCcchhhhhhhc
Q 026004 8 PDFTLAEIKEMESMYKEIGEASLTQEYCKALATSFS-FSASRAARPAITWLQVQSWFRD 65 (245)
Q Consensus 8 ~~FT~~Ql~eMEk~f~~~~~~y~~~~~rq~LA~~f~-lS~~r~Gk~~v~~~QVk~WFQN 65 (245)
..||++|...|.+++...+. ..-..||..|+ -|+ .||+..|.+
T Consensus 2 ~~Wt~~E~~~l~~~~~~~g~-----~~w~~Ia~~~~~rt~----------~~~~~~~~~ 45 (49)
T smart00717 2 GEWTEEEDELLIELVKKYGK-----NNWEKIAKELPGRTA----------EQCRERWNN 45 (49)
T ss_pred CCCCHHHHHHHHHHHHHHCc-----CCHHHHHHHcCCCCH----------HHHHHHHHH
Confidence 36899999999999999742 22467888887 433 788765554
No 69
>cd00167 SANT 'SWI3, ADA2, N-CoR and TFIIIB' DNA-binding domains. Tandem copies of the domain bind telomeric DNA tandem repeatsas part of the capping complex. Binding is sequence dependent for repeats which contain the G/C rich motif [C2-3 A (CA)1-6]. The domain is also found in regulatory transcriptional repressor complexes where it also binds DNA.
Probab=44.91 E-value=52 Score=20.22 Aligned_cols=41 Identities=17% Similarity=0.209 Sum_probs=29.6
Q ss_pred CCCHHHHHHHHHHHHHhCCCCCCHHHHHHHHHHcC-CCcccCCCCcCCcchhhhhhh
Q 026004 9 DFTLAEIKEMESMYKEIGEASLTQEYCKALATSFS-FSASRAARPAITWLQVQSWFR 64 (245)
Q Consensus 9 ~FT~~Ql~eMEk~f~~~~~~y~~~~~rq~LA~~f~-lS~~r~Gk~~v~~~QVk~WFQ 64 (245)
.+|.+|...|.+.+...+. ..-..||..++ -|+ .||+.-|+
T Consensus 1 ~Wt~eE~~~l~~~~~~~g~-----~~w~~Ia~~~~~rs~----------~~~~~~~~ 42 (45)
T cd00167 1 PWTEEEDELLLEAVKKYGK-----NNWEKIAKELPGRTP----------KQCRERWR 42 (45)
T ss_pred CCCHHHHHHHHHHHHHHCc-----CCHHHHHhHcCCCCH----------HHHHHHHH
Confidence 4799999999999999742 22467888886 333 77775444
No 70
>PF13518 HTH_28: Helix-turn-helix domain
Probab=42.51 E-value=20 Score=23.57 Aligned_cols=23 Identities=22% Similarity=0.449 Sum_probs=19.4
Q ss_pred HHHHHHHHcCCCcccCCCCcCCcchhhhhhhcc
Q 026004 34 YCKALATSFSFSASRAARPAITWLQVQSWFRDK 66 (245)
Q Consensus 34 ~rq~LA~~f~lS~~r~Gk~~v~~~QVk~WFQNR 66 (245)
-..++|..|++|. .+|..|.+.=
T Consensus 14 s~~~~a~~~gis~----------~tv~~w~~~y 36 (52)
T PF13518_consen 14 SVREIAREFGISR----------STVYRWIKRY 36 (52)
T ss_pred CHHHHHHHHCCCH----------hHHHHHHHHH
Confidence 4567999999988 9999998744
No 71
>PTZ00184 calmodulin; Provisional
Probab=41.44 E-value=1e+02 Score=23.59 Aligned_cols=40 Identities=15% Similarity=0.253 Sum_probs=30.8
Q ss_pred cCCCCHHHHHHHHHHHHHh---CCCCCCHHHHHHHHHHcCCCc
Q 026004 7 WPDFTLAEIKEMESMYKEI---GEASLTQEYCKALATSFSFSA 46 (245)
Q Consensus 7 ~~~FT~~Ql~eMEk~f~~~---~~~y~~~~~rq~LA~~f~lS~ 46 (245)
.+.+|..++.++.+.|... +...++......+...++.++
T Consensus 2 ~~~~~~~~~~~~~~~F~~~D~~~~G~i~~~e~~~~l~~~~~~~ 44 (149)
T PTZ00184 2 ADQLTEEQIAEFKEAFSLFDKDGDGTITTKELGTVMRSLGQNP 44 (149)
T ss_pred CCccCHHHHHHHHHHHHHHcCCCCCcCCHHHHHHHHHHhCCCC
Confidence 3558899999999999774 567888888877777777654
No 72
>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=41.42 E-value=30 Score=21.65 Aligned_cols=43 Identities=14% Similarity=0.091 Sum_probs=30.0
Q ss_pred CCCHHHHHHHHHHHHHhCCCCCCHHHHHHHHHHcCCCcccCCCCcCCcchhhhhhhcccc
Q 026004 9 DFTLAEIKEMESMYKEIGEASLTQEYCKALATSFSFSASRAARPAITWLQVQSWFRDKQK 68 (245)
Q Consensus 9 ~FT~~Ql~eMEk~f~~~~~~y~~~~~rq~LA~~f~lS~~r~Gk~~v~~~QVk~WFQNRR~ 68 (245)
.+++.+...++-.+.+ .....++|+.+|+|. ..|..|.+.-+.
T Consensus 10 ~l~~~~~~~~~~~~~~-------~~~~~~ia~~~~~s~----------~~i~~~~~~~~~ 52 (55)
T cd06171 10 KLPEREREVILLRFGE-------GLSYEEIAEILGISR----------STVRQRLHRALK 52 (55)
T ss_pred hCCHHHHHHHHHHHhc-------CCCHHHHHHHHCcCH----------HHHHHHHHHHHH
Confidence 4566666666665533 234678899999988 889988875443
No 73
>PF09465 LBR_tudor: Lamin-B receptor of TUDOR domain; InterPro: IPR019023 The Lamin-B receptor is a chromatin and lamin binding protein in the inner nuclear membrane. It is one of the integral inner nuclear envelope membrane proteins responsible for targeting nuclear membranes to chromatin, being a downstream effector of Ran, a small Ras-like nuclear GTPase which regulates NE assembly. Lamin-B receptor interacts with importin beta, a Ran-binding protein, thereby directly contributing to the fusion of membrane vesicles and the formation of the nuclear envelope []. ; PDB: 2L8D_A 2DIG_A.
Probab=39.68 E-value=63 Score=23.74 Aligned_cols=49 Identities=20% Similarity=0.409 Sum_probs=29.6
Q ss_pred ccccCCceEEEeeecCCceeEEeeEEeeeeecccCCCCceeEEEEEEccCCcccccccc
Q 026004 179 VKVNVGDLVLCYQEREDQAVYCDAHVLDIQRRVHDTEGCQCIFVVRYDHDFSEEQVKVE 237 (245)
Q Consensus 179 ~~v~~G~~v~cf~~~~~~~~yyDA~V~~v~r~~Hd~~~C~C~F~Vr~~h~~~ee~v~~~ 237 (245)
.+...|+.|..-= ++..+||.|.|++.-.+.| ...|.|..|- +..++-.
T Consensus 4 ~k~~~Ge~V~~rW--P~s~lYYe~kV~~~d~~~~-------~y~V~Y~DGt-el~lke~ 52 (55)
T PF09465_consen 4 RKFAIGEVVMVRW--PGSSLYYEGKVLSYDSKSD-------RYTVLYEDGT-ELELKEN 52 (55)
T ss_dssp SSS-SS-EEEEE---TTTS-EEEEEEEEEETTTT-------EEEEEETTS--EEEEECC
T ss_pred ccccCCCEEEEEC--CCCCcEEEEEEEEecccCc-------eEEEEEcCCC-EEEeccc
Confidence 4566788887533 4567999999999665555 4678887754 3444433
No 74
>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=38.74 E-value=69 Score=17.58 Aligned_cols=37 Identities=14% Similarity=0.221 Sum_probs=25.6
Q ss_pred CCCHHHHHHHHHHHHHhCCCCCCHHHHHHHHHHcCCCcccCCCCcCCcchhhhh
Q 026004 9 DFTLAEIKEMESMYKEIGEASLTQEYCKALATSFSFSASRAARPAITWLQVQSW 62 (245)
Q Consensus 9 ~FT~~Ql~eMEk~f~~~~~~y~~~~~rq~LA~~f~lS~~r~Gk~~v~~~QVk~W 62 (245)
.++.++...+...+.. .+ -..++|+.|++|. ..|..|
T Consensus 5 ~~~~~~~~~i~~~~~~---~~----s~~~ia~~~~is~----------~tv~~~ 41 (42)
T cd00569 5 KLTPEQIEEARRLLAA---GE----SVAEIARRLGVSR----------STLYRY 41 (42)
T ss_pred cCCHHHHHHHHHHHHc---CC----CHHHHHHHHCCCH----------HHHHHh
Confidence 4667777777666653 22 4668999999987 667666
No 75
>PRK07571 bidirectional hydrogenase complex protein HoxE; Reviewed
Probab=38.50 E-value=80 Score=27.45 Aligned_cols=40 Identities=13% Similarity=0.003 Sum_probs=32.5
Q ss_pred cCCCCHHHHHHHHHHHHHhC----------------CCCCCHHHHHHHHHHcCCCc
Q 026004 7 WPDFTLAEIKEMESMYKEIG----------------EASLTQEYCKALATSFSFSA 46 (245)
Q Consensus 7 ~~~FT~~Ql~eMEk~f~~~~----------------~~y~~~~~rq~LA~~f~lS~ 46 (245)
-..|+.+++++++++....+ -.|++.+..+.+|+.+|+++
T Consensus 13 ~~~~~~~~~~~i~~ii~~~~~~~~~li~~L~~iQ~~~GyIp~e~~~~iA~~l~v~~ 68 (169)
T PRK07571 13 THPSGDKRFKVLEATMKRNQYRQDALIEVLHKAQELFGYLERDLLLYVARQLKLPL 68 (169)
T ss_pred cCcCcHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHcCCCCHHHHHHHHHHhCcCH
Confidence 45688888888887666543 46999999999999999988
No 76
>PRK07539 NADH dehydrogenase subunit E; Validated
Probab=38.06 E-value=69 Score=26.90 Aligned_cols=20 Identities=20% Similarity=0.225 Sum_probs=18.6
Q ss_pred CCCCCHHHHHHHHHHcCCCc
Q 026004 27 EASLTQEYCKALATSFSFSA 46 (245)
Q Consensus 27 ~~y~~~~~rq~LA~~f~lS~ 46 (245)
..|++.+..+.+|+.+|+++
T Consensus 35 ~g~ip~~~~~~iA~~l~v~~ 54 (154)
T PRK07539 35 RGWVPDEAIEAVADYLGMPA 54 (154)
T ss_pred hCCCCHHHHHHHHHHhCcCH
Confidence 46999999999999999998
No 77
>PF00567 TUDOR: Tudor domain; InterPro: IPR008191 There are multiple copies of this domain in the Drosophila melanogaster tudor protein and it has been identified in several RNA-binding proteins []. Although the function of this domain is unknown, in Drosophila melanogaster the tudor protein is required during oogenesis for the formation of primordial germ cells and for normal abdominal segmentation [].; PDB: 3NTI_A 3NTK_B 3NTH_A 2DIQ_A 3FDR_A 3PNW_O 3S6W_A 3PMT_A 2WAC_A 2O4X_A ....
Probab=37.84 E-value=42 Score=24.76 Aligned_cols=54 Identities=24% Similarity=0.394 Sum_probs=36.4
Q ss_pred ecccCCCceeeeeecceeeeeecCceeEEEEecCCCCCccccccccccc-----cccCCCccccccc
Q 026004 118 ARSSKDDAWYDVASFLTYRVTCAGELEVRVRFSGFNNTEDEWVNVKTAV-----RQRSIPLEQSECV 179 (245)
Q Consensus 118 Ars~~D~AWYdV~~fl~~R~~~~g~~el~Vrf~gF~~eeDEw~~~~~~~-----R~rS~ple~~eC~ 179 (245)
+....||.||=+.+. ...++..+.|.|-.||..+- ++.. .+ +..++|.+...|.
T Consensus 60 ~~~~~~~~w~Ra~I~-----~~~~~~~~~V~~iD~G~~~~--v~~~-~l~~l~~~~~~~P~~a~~~~ 118 (121)
T PF00567_consen 60 CVVSEDGRWYRAVIT-----VDIDENQYKVFLIDYGNTEK--VSAS-DLRPLPPEFASLPPQAIKCK 118 (121)
T ss_dssp EEETTTSEEEEEEEE-----EEECTTEEEEEETTTTEEEE--EEGG-GEEE--HHHCSSSSSCEEEE
T ss_pred EEEecCCceeeEEEE-----EecccceeEEEEEecCceEE--EcHH-HhhhhCHHHhhCChhhEEEE
Confidence 467889999999861 23445589999999998754 4433 22 2334677766664
No 78
>PF13921 Myb_DNA-bind_6: Myb-like DNA-binding domain; PDB: 1A5J_A 1MBH_A 1GV5_A 1H89_C 1IDY_A 1MBK_A 1IDZ_A 1H88_C 1GVD_A 1MBG_A ....
Probab=35.26 E-value=1.3e+02 Score=20.63 Aligned_cols=40 Identities=20% Similarity=0.269 Sum_probs=30.3
Q ss_pred CCHHHHHHHHHHHHHhCCCCCCHHHHHHHHHHcC-CCcccCCCCcCCcchhhhhhhc
Q 026004 10 FTLAEIKEMESMYKEIGEASLTQEYCKALATSFS-FSASRAARPAITWLQVQSWFRD 65 (245)
Q Consensus 10 FT~~Ql~eMEk~f~~~~~~y~~~~~rq~LA~~f~-lS~~r~Gk~~v~~~QVk~WFQN 65 (245)
+|++|...|-.++...++ .=..||+.|+ -|+ .||+.=|.+
T Consensus 1 WT~eEd~~L~~~~~~~g~------~W~~Ia~~l~~Rt~----------~~~~~r~~~ 41 (60)
T PF13921_consen 1 WTKEEDELLLELVKKYGN------DWKKIAEHLGNRTP----------KQCRNRWRN 41 (60)
T ss_dssp S-HHHHHHHHHHHHHHTS-------HHHHHHHSTTS-H----------HHHHHHHHH
T ss_pred CCHHHHHHHHHHHHHHCc------CHHHHHHHHCcCCH----------HHHHHHHHH
Confidence 589999999999998643 3678999999 766 999865555
No 79
>PF13873 Myb_DNA-bind_5: Myb/SANT-like DNA-binding domain
Probab=35.17 E-value=42 Score=24.34 Aligned_cols=59 Identities=12% Similarity=0.253 Sum_probs=39.1
Q ss_pred CCCCHHHHHHHHHHHHHhCCCCCC-----------HHHHHHHHHHcCCCcccCCCCcCCcchhhhhhhcccccc
Q 026004 8 PDFTLAEIKEMESMYKEIGEASLT-----------QEYCKALATSFSFSASRAARPAITWLQVQSWFRDKQKKS 70 (245)
Q Consensus 8 ~~FT~~Ql~eMEk~f~~~~~~y~~-----------~~~rq~LA~~f~lS~~r~Gk~~v~~~QVk~WFQNRR~k~ 70 (245)
..||++|...|-.++..+....-+ ...=++||..||.-.+ ..=++.|++..++|=+...
T Consensus 3 ~~fs~~E~~~Lv~~v~~~~~il~~k~~~~~~~~~k~~~W~~I~~~lN~~~~----~~Rs~~~lkkkW~nlk~~~ 72 (78)
T PF13873_consen 3 PNFSEEEKEILVELVEKHKDILENKFSDSVSNKEKRKAWEEIAEELNALGP----GKRSWKQLKKKWKNLKSKA 72 (78)
T ss_pred CCCCHHHHHHHHHHHHHhHHHHhcccccHHHHHHHHHHHHHHHHHHHhcCC----CCCCHHHHHHHHHHHHHHH
Confidence 579999999888887774211111 2334679999988442 2567888887777765443
No 80
>PF03672 UPF0154: Uncharacterised protein family (UPF0154); InterPro: IPR005359 The proteins in this entry are functionally uncharacterised.
Probab=33.87 E-value=73 Score=24.04 Aligned_cols=36 Identities=19% Similarity=0.274 Sum_probs=31.2
Q ss_pred HHHHHHHHHhCCCCCCHHHHHHHHHHcCCCcccCCCCcCCcchhhh
Q 026004 16 KEMESMYKEIGEASLTQEYCKALATSFSFSASRAARPAITWLQVQS 61 (245)
Q Consensus 16 ~eMEk~f~~~~~~y~~~~~rq~LA~~f~lS~~r~Gk~~v~~~QVk~ 61 (245)
.-||+-|++ |..++.+....+....|-.| +++||+.
T Consensus 20 ~~~~k~l~~--NPpine~mir~M~~QMG~kp--------Sekqi~Q 55 (64)
T PF03672_consen 20 KYMEKQLKE--NPPINEKMIRAMMMQMGRKP--------SEKQIKQ 55 (64)
T ss_pred HHHHHHHHH--CCCCCHHHHHHHHHHhCCCc--------cHHHHHH
Confidence 468999999 58999999999999999988 7788774
No 81
>PRK10072 putative transcriptional regulator; Provisional
Probab=33.74 E-value=32 Score=27.30 Aligned_cols=23 Identities=17% Similarity=0.306 Sum_probs=17.1
Q ss_pred HHHHHHHcCCCcccCCCCcCCcchhhhhhhccc
Q 026004 35 CKALATSFSFSASRAARPAITWLQVQSWFRDKQ 67 (245)
Q Consensus 35 rq~LA~~f~lS~~r~Gk~~v~~~QVk~WFQNRR 67 (245)
..+||+.+|+|. .-|.+|.+.+|
T Consensus 49 Q~elA~~lGvS~----------~TVs~WE~G~r 71 (96)
T PRK10072 49 IDDFARVLGVSV----------AMVKEWESRRV 71 (96)
T ss_pred HHHHHHHhCCCH----------HHHHHHHcCCC
Confidence 455666666655 88999999875
No 82
>PF11523 DUF3223: Protein of unknown function (DUF3223); InterPro: IPR021602 This family of proteins has no known function. ; PDB: 2K0M_A.
Probab=33.63 E-value=50 Score=25.04 Aligned_cols=31 Identities=39% Similarity=0.467 Sum_probs=20.3
Q ss_pred EeeeeecccCCCC-ceeEEEEEEccCCccccccc
Q 026004 204 VLDIQRRVHDTEG-CQCIFVVRYDHDFSEEQVKV 236 (245)
Q Consensus 204 V~~v~r~~Hd~~~-C~C~F~Vr~~h~~~ee~v~~ 236 (245)
|..|+-+.|...+ .+|.|+||= |++.+..+.
T Consensus 41 i~~i~V~~hp~~~~srCF~vvR~--DGs~~DFSy 72 (76)
T PF11523_consen 41 IDHIMVRKHPEFKDSRCFFVVRT--DGSEEDFSY 72 (76)
T ss_dssp EEEEEEEESSSS---EEEEEEET--TS-EEE--G
T ss_pred eeeEEEeecCCCCcceEEEEEEe--CCCeeeeEh
Confidence 6778888998865 999999985 555554443
No 83
>PF02796 HTH_7: Helix-turn-helix domain of resolvase; InterPro: IPR006120 Site-specific recombination plays an important role in DNA rearrangement in prokaryotic organisms. Two types of site-specific recombination are known to occur: Recombination between inverted repeats resulting in the reversal of a DNA segment. Recombination between repeat sequences on two DNA molecules resulting in their cointegration, or between repeats on one DNA molecule resulting in the excision of a DNA fragment. Site-specific recombination is characterised by a strand exchange mechanism that requires no DNA synthesis or high energy cofactor; the phosphodiester bond energy is conserved in a phospho-protein linkage during strand cleavage and re-ligation. Two unrelated families of recombinases are currently known []. The first, called the 'phage integrase' family, groups a number of bacterial phage and yeast plasmid enzymes. The second [], called the 'resolvase' family, groups enzymes which share the following structural characteristics: an N-terminal catalytic and dimerization domain that contains a conserved serine residue involved in the transient covalent attachment to DNA IPR006119 from INTERPRO, and a C-terminal helix-turn-helix DNA-binding domain. ; GO: 0000150 recombinase activity, 0003677 DNA binding, 0006310 DNA recombination; PDB: 1ZR2_A 2GM4_B 1RES_A 1ZR4_A 1RET_A 1GDT_B 2R0Q_C 1JKP_C 1IJW_C 1JJ6_C ....
Probab=33.33 E-value=50 Score=22.08 Aligned_cols=31 Identities=23% Similarity=0.415 Sum_probs=23.2
Q ss_pred CCCHHHHHHHHHHHHHhCCCCCCHHHHHHHHHHcCCCc
Q 026004 9 DFTLAEIKEMESMYKEIGEASLTQEYCKALATSFSFSA 46 (245)
Q Consensus 9 ~FT~~Ql~eMEk~f~~~~~~y~~~~~rq~LA~~f~lS~ 46 (245)
.+++++++++-+++.+ + .-..+||+.||+|.
T Consensus 5 ~~~~~~~~~i~~l~~~--G-----~si~~IA~~~gvsr 35 (45)
T PF02796_consen 5 KLSKEQIEEIKELYAE--G-----MSIAEIAKQFGVSR 35 (45)
T ss_dssp SSSHCCHHHHHHHHHT--T-------HHHHHHHTTS-H
T ss_pred CCCHHHHHHHHHHHHC--C-----CCHHHHHHHHCcCH
Confidence 4677788888888887 2 34689999999988
No 84
>PF08880 QLQ: QLQ; InterPro: IPR014978 QLQ is named after the conserved Gln, Leu, Gln motif. QLQ is found at the N terminus of SWI2/SNF2 protein, which has been shown to be involved in protein-protein interactions. QLQ has been postulated to be involved in mediating protein interactions []. ; GO: 0005524 ATP binding, 0016818 hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides, 0006355 regulation of transcription, DNA-dependent, 0005634 nucleus
Probab=33.12 E-value=37 Score=22.79 Aligned_cols=14 Identities=29% Similarity=0.529 Sum_probs=11.9
Q ss_pred CCCCHHHHHHHHHH
Q 026004 8 PDFTLAEIKEMESM 21 (245)
Q Consensus 8 ~~FT~~Ql~eMEk~ 21 (245)
+.||++|+.+||.-
T Consensus 1 s~FT~~Ql~~L~~Q 14 (37)
T PF08880_consen 1 SPFTPAQLQELRAQ 14 (37)
T ss_pred CCCCHHHHHHHHHH
Confidence 46999999999963
No 85
>COG3413 Predicted DNA binding protein [General function prediction only]
Probab=32.32 E-value=56 Score=28.45 Aligned_cols=36 Identities=22% Similarity=0.236 Sum_probs=30.6
Q ss_pred CCCCHHHHHHHHHHHHHhCCCCCCH---HHHHHHHHHcCCCc
Q 026004 8 PDFTLAEIKEMESMYKEIGEASLTQ---EYCKALATSFSFSA 46 (245)
Q Consensus 8 ~~FT~~Ql~eMEk~f~~~~~~y~~~---~~rq~LA~~f~lS~ 46 (245)
..+|+.|++-|..+|+. .|.+. -..++||+.||.|.
T Consensus 154 ~~LTdrQ~~vL~~A~~~---GYFd~PR~~~l~dLA~~lGISk 192 (215)
T COG3413 154 NDLTDRQLEVLRLAYKM---GYFDYPRRVSLKDLAKELGISK 192 (215)
T ss_pred ccCCHHHHHHHHHHHHc---CCCCCCccCCHHHHHHHhCCCH
Confidence 35999999999999998 56655 55689999999988
No 86
>KOG3026 consensus Splicing factor SPF30 [RNA processing and modification]
Probab=31.48 E-value=1.2e+02 Score=28.51 Aligned_cols=47 Identities=19% Similarity=0.386 Sum_probs=31.2
Q ss_pred CCccCcccceeEeecccCCCceeeeeecceeeeeecCceeEEEEecCCCCCcccc
Q 026004 105 GSRISELKELAFEARSSKDDAWYDVASFLTYRVTCAGELEVRVRFSGFNNTEDEW 159 (245)
Q Consensus 105 g~~~~~~~~~efEArs~~D~AWYdV~~fl~~R~~~~g~~el~Vrf~gF~~eeDEw 159 (245)
|...-+-....| +.||-|||+. +-|=... +.++-|-|.+++.-.---
T Consensus 90 ~w~vg~K~~A~~----~ddg~~y~At--Ie~ita~--~~~~ai~f~s~~~a~~t~ 136 (262)
T KOG3026|consen 90 GWKVGDKVQAVF----SDDGQIYDAT--IEHITAM--EGTVAIIFASYGTAPSTY 136 (262)
T ss_pred ccccCCEEEEee----cCCCceEEee--hhhccCC--CCceeEEEeecccccccc
Confidence 444555556666 8899999998 3332222 346999999988765443
No 87
>PF13443 HTH_26: Cro/C1-type HTH DNA-binding domain; PDB: 3TYR_A 3TYS_A 3B7H_A.
Probab=30.60 E-value=74 Score=21.80 Aligned_cols=23 Identities=22% Similarity=0.135 Sum_probs=16.8
Q ss_pred HHHHHHHHcCCCcccCCCCcCCcchhhhhhhcc
Q 026004 34 YCKALATSFSFSASRAARPAITWLQVQSWFRDK 66 (245)
Q Consensus 34 ~rq~LA~~f~lS~~r~Gk~~v~~~QVk~WFQNR 66 (245)
...+||+..|+|. .+|..|+.++
T Consensus 12 t~~~La~~~gis~----------~tl~~~~~~~ 34 (63)
T PF13443_consen 12 TQKDLARKTGISR----------STLSRILNGK 34 (63)
T ss_dssp -HHHHHHHHT--H----------HHHHHHHTTT
T ss_pred CHHHHHHHHCcCH----------HHHHHHHhcc
Confidence 4678888999888 8888888876
No 88
>PLN00104 MYST -like histone acetyltransferase; Provisional
Probab=29.50 E-value=1.3e+02 Score=30.37 Aligned_cols=49 Identities=18% Similarity=0.268 Sum_probs=32.9
Q ss_pred ccccCCceEEEeeecCCceeEEeeEEeeeeecccCCCCceeEEEEEEccCCc
Q 026004 179 VKVNVGDLVLCYQEREDQAVYCDAHVLDIQRRVHDTEGCQCIFVVRYDHDFS 230 (245)
Q Consensus 179 ~~v~~G~~v~cf~~~~~~~~yyDA~V~~v~r~~Hd~~~C~C~F~Vr~~h~~~ 230 (245)
..+..|+.|+|+.... -.||.|.|+++.+..-...+. =.|-|.|..-+.
T Consensus 52 ~~~~VGekVla~~~~D--g~~~~A~VI~~R~~~~~~~~~-~~YYVHY~g~nr 100 (450)
T PLN00104 52 LPLEVGTRVMCRWRFD--GKYHPVKVIERRRGGSGGPND-YEYYVHYTEFNR 100 (450)
T ss_pred ceeccCCEEEEEECCC--CCEEEEEEEEEeccCCCCCCC-ceEEEEEecCCc
Confidence 4567999999997533 367899999998633001111 158999987664
No 89
>PTZ00183 centrin; Provisional
Probab=29.10 E-value=1.7e+02 Score=22.81 Aligned_cols=39 Identities=21% Similarity=0.356 Sum_probs=30.6
Q ss_pred CcCCCCHHHHHHHHHHHHHh---CCCCCCHHHHHHHHHHcCC
Q 026004 6 SWPDFTLAEIKEMESMYKEI---GEASLTQEYCKALATSFSF 44 (245)
Q Consensus 6 ~~~~FT~~Ql~eMEk~f~~~---~~~y~~~~~rq~LA~~f~l 44 (245)
..+.|++.|+++++++|... ++.+++......+-..+++
T Consensus 7 ~~~~~~~~~~~~~~~~F~~~D~~~~G~i~~~e~~~~l~~~g~ 48 (158)
T PTZ00183 7 ERPGLTEDQKKEIREAFDLFDTDGSGTIDPKELKVAMRSLGF 48 (158)
T ss_pred ccCCCCHHHHHHHHHHHHHhCCCCCCcccHHHHHHHHHHhCC
Confidence 45679999999999999873 4678888777777676665
No 90
>PRK11511 DNA-binding transcriptional activator MarA; Provisional
Probab=29.08 E-value=33 Score=27.54 Aligned_cols=38 Identities=13% Similarity=0.191 Sum_probs=24.7
Q ss_pred HHHHHHHhCCCCCCHHHHHHHHHHcCCCcccCCCCcCCcchhhhhhhc
Q 026004 18 MESMYKEIGEASLTQEYCKALATSFSFSASRAARPAITWLQVQSWFRD 65 (245)
Q Consensus 18 MEk~f~~~~~~y~~~~~rq~LA~~f~lS~~r~Gk~~v~~~QVk~WFQN 65 (245)
++++.....+.+-.....++||+.+|+|+ .++..+|+.
T Consensus 11 i~~~~~~I~~~~~~~~sl~~lA~~~g~S~----------~~l~r~Fk~ 48 (127)
T PRK11511 11 IHSILDWIEDNLESPLSLEKVSERSGYSK----------WHLQRMFKK 48 (127)
T ss_pred HHHHHHHHHHhcCCCCCHHHHHHHHCcCH----------HHHHHHHHH
Confidence 33333333334545566799999999998 777777763
No 91
>PF11516 DUF3220: Protein of unknown function (DUF3120); InterPro: IPR021597 This family of proteins with unknown function appears to be restricted to Bordetella. ; PDB: 2JPF_A.
Probab=27.49 E-value=37 Score=27.21 Aligned_cols=19 Identities=26% Similarity=0.462 Sum_probs=14.4
Q ss_pred ccCCCCcCCcchhhhhhhcc
Q 026004 47 SRAARPAITWLQVQSWFRDK 66 (245)
Q Consensus 47 ~r~Gk~~v~~~QVk~WFQNR 66 (245)
-|+|..++|- .|+.|.||=
T Consensus 22 lragsmalqg-dvkvwmqnl 40 (106)
T PF11516_consen 22 LRAGSMALQG-DVKVWMQNL 40 (106)
T ss_dssp -SSSSSSS-H-HHHHHHHHH
T ss_pred hhhhhhHhcc-cHHHHHHHH
Confidence 4889999874 599999983
No 92
>PRK03975 tfx putative transcriptional regulator; Provisional
Probab=26.41 E-value=50 Score=28.04 Aligned_cols=46 Identities=13% Similarity=0.060 Sum_probs=35.4
Q ss_pred CCCCHHHHHHHHHHHHHhCCCCCCHHHHHHHHHHcCCCcccCCCCcCCcchhhhhhhccccccc
Q 026004 8 PDFTLAEIKEMESMYKEIGEASLTQEYCKALATSFSFSASRAARPAITWLQVQSWFRDKQKKSQ 71 (245)
Q Consensus 8 ~~FT~~Ql~eMEk~f~~~~~~y~~~~~rq~LA~~f~lS~~r~Gk~~v~~~QVk~WFQNRR~k~k 71 (245)
+.+|+.|.+-|+-. .+ - -..++||+.+|+|. ..|++|-++-+.+.+
T Consensus 5 ~~Lt~rqreVL~lr-~~----G---lTq~EIAe~LGiS~----------~tVs~ie~ra~kkLr 50 (141)
T PRK03975 5 SFLTERQIEVLRLR-ER----G---LTQQEIADILGTSR----------ANVSSIEKRARENIE 50 (141)
T ss_pred cCCCHHHHHHHHHH-Hc----C---CCHHHHHHHHCCCH----------HHHHHHHHHHHHHHH
Confidence 46789999888763 22 1 34679999999988 889999998777644
No 93
>PF01476 LysM: LysM domain; InterPro: IPR018392 This domain is about 40 residues long and is found in a variety of enzymes involved in bacterial cell wall degradation []. This domain may have a general peptidoglycan binding function.; GO: 0016998 cell wall macromolecule catabolic process; PDB: 2DJP_A 3ZQD_A 1Y7M_B 4A52_A 2L9Y_A 1E0G_A.
Probab=26.10 E-value=51 Score=21.00 Aligned_cols=21 Identities=10% Similarity=0.126 Sum_probs=14.8
Q ss_pred HHHHHHHHHHcCCCcccCCCCcCCcchhhhh
Q 026004 32 QEYCKALATSFSFSASRAARPAITWLQVQSW 62 (245)
Q Consensus 32 ~~~rq~LA~~f~lS~~r~Gk~~v~~~QVk~W 62 (245)
.+.+..||.+|+++. .+++.|
T Consensus 6 gDtl~~IA~~~~~~~----------~~l~~~ 26 (44)
T PF01476_consen 6 GDTLWSIAKRYGISV----------DELMEL 26 (44)
T ss_dssp T--HHHHHHHTTS-H----------HHHHHH
T ss_pred CCcHHHHHhhhhhhH----------hHHHHh
Confidence 467899999999977 777765
No 94
>smart00421 HTH_LUXR helix_turn_helix, Lux Regulon. lux regulon (activates the bioluminescence operon
Probab=26.07 E-value=87 Score=20.00 Aligned_cols=44 Identities=18% Similarity=0.165 Sum_probs=30.6
Q ss_pred CCCHHHHHHHHHHHHHhCCCCCCHHHHHHHHHHcCCCcccCCCCcCCcchhhhhhhcccccc
Q 026004 9 DFTLAEIKEMESMYKEIGEASLTQEYCKALATSFSFSASRAARPAITWLQVQSWFRDKQKKS 70 (245)
Q Consensus 9 ~FT~~Ql~eMEk~f~~~~~~y~~~~~rq~LA~~f~lS~~r~Gk~~v~~~QVk~WFQNRR~k~ 70 (245)
.+|+.|...+.- +.. + ....++|+.+++|. ..|..|.+.=+.+.
T Consensus 3 ~l~~~e~~i~~~-~~~--g-----~s~~eia~~l~is~----------~tv~~~~~~~~~kl 46 (58)
T smart00421 3 SLTPREREVLRL-LAE--G-----LTNKEIAERLGISE----------KTVKTHLSNIMRKL 46 (58)
T ss_pred CCCHHHHHHHHH-HHc--C-----CCHHHHHHHHCCCH----------HHHHHHHHHHHHHH
Confidence 578888887755 322 1 24589999999988 88888877434443
No 95
>COG5126 FRQ1 Ca2+-binding protein (EF-Hand superfamily) [Signal transduction mechanisms / Cytoskeleton / Cell division and chromosome partitioning / General function prediction only]
Probab=25.63 E-value=1.7e+02 Score=25.45 Aligned_cols=42 Identities=12% Similarity=0.304 Sum_probs=31.6
Q ss_pred CCcCCCCHHHHHHHHHHHHHh---CCCCCCHHHHHHHHHHcCCCc
Q 026004 5 DSWPDFTLAEIKEMESMYKEI---GEASLTQEYCKALATSFSFSA 46 (245)
Q Consensus 5 ~~~~~FT~~Ql~eMEk~f~~~---~~~y~~~~~rq~LA~~f~lS~ 46 (245)
..++.||.+||++|-++|.-. +...+++.....+=+.|+..+
T Consensus 9 ~~~~~~t~~qi~~lkeaF~l~D~d~~G~I~~~el~~ilr~lg~~~ 53 (160)
T COG5126 9 LTFTQLTEEQIQELKEAFQLFDRDSDGLIDRNELGKILRSLGFNP 53 (160)
T ss_pred hhcccCCHHHHHHHHHHHHHhCcCCCCCCcHHHHHHHHHHcCCCC
Confidence 457899999999999999754 356777777777755666544
No 96
>PF08281 Sigma70_r4_2: Sigma-70, region 4; InterPro: IPR013249 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognised by the major sigma factors [, ]. Region 4 of sigma-70 like sigma-factors are involved in binding to the -35 promoter element via a helix-turn-helix motif [].; GO: 0003677 DNA binding, 0003700 sequence-specific DNA binding transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, DNA-dependent, 0006355 regulation of transcription, DNA-dependent; PDB: 2LFW_A 1OR7_B 2H27_D 2O8X_B.
Probab=25.35 E-value=78 Score=21.18 Aligned_cols=28 Identities=14% Similarity=0.121 Sum_probs=20.4
Q ss_pred CCCCHHHHHHHHHHcCCCcccCCCCcCCcchhhhhhhc
Q 026004 28 ASLTQEYCKALATSFSFSASRAARPAITWLQVQSWFRD 65 (245)
Q Consensus 28 ~y~~~~~rq~LA~~f~lS~~r~Gk~~v~~~QVk~WFQN 65 (245)
.|...-...++|+.+|.|+ ..|++|.+.
T Consensus 22 ~~~~g~s~~eIa~~l~~s~----------~~v~~~l~r 49 (54)
T PF08281_consen 22 RYFQGMSYAEIAEILGISE----------STVKRRLRR 49 (54)
T ss_dssp HHTS---HHHHHHHCTS-H----------HHHHHHHHH
T ss_pred HHHHCcCHHHHHHHHCcCH----------HHHHHHHHH
Confidence 3677788899999999998 889988874
No 97
>KOG0031 consensus Myosin regulatory light chain, EF-Hand protein superfamily [Cytoskeleton]
Probab=25.29 E-value=87 Score=27.80 Aligned_cols=64 Identities=17% Similarity=0.265 Sum_probs=43.2
Q ss_pred CCCCcCCCCHHHHHHHHHHHHH---hCCCCCCHHHHHHHHHHcCCCccc--------CCCCcCCcchhhhhhhcc
Q 026004 3 DEDSWPDFTLAEIKEMESMYKE---IGEASLTQEYCKALATSFSFSASR--------AARPAITWLQVQSWFRDK 66 (245)
Q Consensus 3 ~~~~~~~FT~~Ql~eMEk~f~~---~~~~y~~~~~rq~LA~~f~lS~~r--------~Gk~~v~~~QVk~WFQNR 66 (245)
.+..|+-|++.||+|+..+|.- +....++++.....=.++|-.+.- -+.-||+.++.-+-|=+|
T Consensus 19 sSnvFamf~q~QIqEfKEAF~~mDqnrDG~IdkeDL~d~~aSlGk~~~d~elDaM~~Ea~gPINft~FLTmfGek 93 (171)
T KOG0031|consen 19 SSNVFAMFDQSQIQEFKEAFNLMDQNRDGFIDKEDLRDMLASLGKIASDEELDAMMKEAPGPINFTVFLTMFGEK 93 (171)
T ss_pred cchHHHHhhHHHHHHHHHHHHHHhccCCCcccHHHHHHHHHHcCCCCCHHHHHHHHHhCCCCeeHHHHHHHHHHH
Confidence 3567899999999999999974 456788888877777777654311 133455555555555544
No 98
>PF09225 Endonuc-PvuII: Restriction endonuclease PvuII; InterPro: IPR015306 There are four classes of restriction endonucleases: types I, II,III and IV. All types of enzymes recognise specific short DNA sequences and carry out the endonucleolytic cleavage of DNA to give specific double-stranded fragments with terminal 5'-phosphates. They differ in their recognition sequence, subunit composition, cleavage position, and cofactor requirements [, ], as summarised below: Type I enzymes (3.1.21.3 from EC) cleave at sites remote from recognition site; require both ATP and S-adenosyl-L-methionine to function; multifunctional protein with both restriction and methylase (2.1.1.72 from EC) activities. Type II enzymes (3.1.21.4 from EC) cleave within or at short specific distances from recognition site; most require magnesium; single function (restriction) enzymes independent of methylase. Type III enzymes (3.1.21.5 from EC) cleave at sites a short distance from recognition site; require ATP (but doesn't hydrolyse it); S-adenosyl-L-methionine stimulates reaction but is not required; exists as part of a complex with a modification methylase methylase (2.1.1.72 from EC). Type IV enzymes target methylated DNA. Type II restriction endonucleases (3.1.21.4 from EC) are components of prokaryotic DNA restriction-modification mechanisms that protect the organism against invading foreign DNA. These site-specific deoxyribonucleases catalyse the endonucleolytic cleavage of DNA to give specific double-stranded fragments with terminal 5'-phosphates. Of the 3000 restriction endonucleases that have been characterised, most are homodimeric or tetrameric enzymes that cleave target DNA at sequence-specific sites close to the recognition site. For homodimeric enzymes, the recognition site is usually a palindromic sequence 4-8 bp in length. Most enzymes require magnesium ions as a cofactor for catalysis. Although they can vary in their mode of recognition, many restriction endonucleases share a similar structural core comprising four beta-strands and one alpha-helix, as well as a similar mechanism of cleavage, suggesting a common ancestral origin []. However, there is still considerable diversity amongst restriction endonucleases [, ]. The target site recognition process triggers large conformational changes of the enzyme and the target DNA, leading to the activation of the catalytic centres. Like other DNA binding proteins, restriction enzymes are capable of non-specific DNA binding as well, which is the prerequisite for efficient target site location by facilitated diffusion. Non-specific binding usually does not involve interactions with the bases but only with the DNA backbone []. This entry represents the type II restriction endonuclease PvuII, which recognise the double-stranded DNA sequence 5'-CAGCTG-3' and cleave after G-3 []. ; PDB: 1H56_B 1EYU_A 3KSK_B 1F0O_A 1PVI_B 1PVU_B 3PVI_A 1K0Z_B 1NI0_A 2PVI_A ....
Probab=25.09 E-value=1.1e+02 Score=26.52 Aligned_cols=69 Identities=19% Similarity=0.307 Sum_probs=43.6
Q ss_pred HHHHHHHHHHHHhCCCCCCHHHHHHHHHHcCCCcccCCCCcCCcchhhhhhhcccccccccccCCcccchhhhcccCCCC
Q 026004 13 AEIKEMESMYKEIGEASLTQEYCKALATSFSFSASRAARPAITWLQVQSWFRDKQKKSQAKSKSSSKDLKLFIDLCGESI 92 (245)
Q Consensus 13 ~Ql~eMEk~f~~~~~~y~~~~~rq~LA~~f~lS~~r~Gk~~v~~~QVk~WFQNRR~k~k~k~~~~p~~~~~~~d~~~~~~ 92 (245)
.+++.||.+|-.. .+.|.||.+.+.+. =||+.=.|.= .-+ +..
T Consensus 2 ~d~~~l~~L~p~i-------~eyq~lA~k~gInD---------------IFQDNGgKlL-------qvL-l~~------- 44 (155)
T PF09225_consen 2 TDIAKLEELWPQI-------REYQRLASKYGIND---------------IFQDNGGKLL-------QVL-LIT------- 44 (155)
T ss_dssp THHHHHHHHHHHH-------HHHHHHHHHTT-S----------------TTSTTHHHHH-------HHH-HHH-------
T ss_pred chHHHHHHHHHHH-------HHHHHHHHHcChhH---------------hHhhcchhHH-------HHH-HHh-------
Confidence 3678899998884 78999999999977 5997643320 000 011
Q ss_pred CCCCCCCCCCCcCCccCcccceeEeeccc
Q 026004 93 SSNEPEMSDKPIGSRISELKELAFEARSS 121 (245)
Q Consensus 93 ~~~~~~~~~~~~g~~~~~~~~~efEArs~ 121 (245)
...+.+..+|+.+.|....|||-||-
T Consensus 45 ---gl~i~pgREGNDavd~~G~E~ElKSv 70 (155)
T PF09225_consen 45 ---GLKILPGREGNDAVDSTGNEYELKSV 70 (155)
T ss_dssp ---T-EE-TTTSSSEEE-TTS-EEEEEEE
T ss_pred ---CCeecCCCcCccccccCCCEEEeeee
Confidence 11233445899999999999999984
No 99
>PF01381 HTH_3: Helix-turn-helix; InterPro: IPR001387 This is large family of DNA binding helix-turn helix proteins that include a bacterial plasmid copy control protein, bacterial methylases, various bacteriophage transcription control proteins and a vegetative specific protein from Dictyostelium discoideum (Slime mould).; GO: 0043565 sequence-specific DNA binding; PDB: 2AXU_A 2AWI_D 2AXV_D 2AXZ_C 2AW6_A 3KXA_C 3BS3_A 2CRO_A 1ZUG_A 3CRO_R ....
Probab=24.99 E-value=86 Score=20.79 Aligned_cols=21 Identities=24% Similarity=0.216 Sum_probs=15.3
Q ss_pred HHHHHHcCCCcccCCCCcCCcchhhhhhhcc
Q 026004 36 KALATSFSFSASRAARPAITWLQVQSWFRDK 66 (245)
Q Consensus 36 q~LA~~f~lS~~r~Gk~~v~~~QVk~WFQNR 66 (245)
.+||+.+|.|. ..|..|..++
T Consensus 13 ~~la~~~gis~----------~~i~~~~~g~ 33 (55)
T PF01381_consen 13 KELAEKLGISR----------STISRIENGK 33 (55)
T ss_dssp HHHHHHHTS-H----------HHHHHHHTTS
T ss_pred HHHHHHhCCCc----------chhHHHhcCC
Confidence 67888888877 7788887764
No 100
>TIGR01321 TrpR trp operon repressor, proteobacterial. This model represents TrpR, the repressor of the trp operon. It is found so far only in the gamma subdivision of the proteobacteria and in Chlamydia trachomatis. All members belong to species capable of tryptophan biosynthesis.
Probab=24.91 E-value=47 Score=26.62 Aligned_cols=55 Identities=11% Similarity=0.149 Sum_probs=34.5
Q ss_pred CCCHHHHHHHHHHHHHhCCCCC-CHHHHHHHHHHcCCCcccC--CCCcCC--cchhhhhhh
Q 026004 9 DFTLAEIKEMESMYKEIGEASL-TQEYCKALATSFSFSASRA--ARPAIT--WLQVQSWFR 64 (245)
Q Consensus 9 ~FT~~Ql~eMEk~f~~~~~~y~-~~~~rq~LA~~f~lS~~r~--Gk~~v~--~~QVk~WFQ 64 (245)
-+|+.|+..|...|.-.+ .-+ ..-...+||+++|.|..-. |.-.++ .-+++.|.+
T Consensus 32 lLTp~E~~~l~~R~~i~~-~Ll~~~~tQrEIa~~lGiS~atIsR~sn~lk~~~~~~~~~l~ 91 (94)
T TIGR01321 32 ILTRSEREDLGDRIRIVN-ELLNGNMSQREIASKLGVSIATITRGSNNLKTMDPNFKQFLR 91 (94)
T ss_pred hCCHHHHHHHHHHHHHHH-HHHhCCCCHHHHHHHhCCChhhhhHHHhhcccCCHHHHHHHH
Confidence 379999999998887753 011 1234678999999877332 333444 445666654
No 101
>PRK10100 DNA-binding transcriptional regulator CsgD; Provisional
Probab=24.56 E-value=68 Score=28.15 Aligned_cols=49 Identities=18% Similarity=0.081 Sum_probs=38.0
Q ss_pred cCCCCHHHHHHHHHHHHHhCCCCCCHHHHHHHHHHcCCCcccCCCCcCCcchhhhhhhccccccccc
Q 026004 7 WPDFTLAEIKEMESMYKEIGEASLTQEYCKALATSFSFSASRAARPAITWLQVQSWFRDKQKKSQAK 73 (245)
Q Consensus 7 ~~~FT~~Ql~eMEk~f~~~~~~y~~~~~rq~LA~~f~lS~~r~Gk~~v~~~QVk~WFQNRR~k~k~k 73 (245)
+..+|+.|.+-|+-+.+- ..-+++|+++++|+ ..|+++.+|=..|...+
T Consensus 153 ~~~Lt~rE~~Vl~l~~~G--------~s~~eIA~~L~iS~----------~TVk~~~~~i~~Kl~v~ 201 (216)
T PRK10100 153 SALLTHREKEILNKLRIG--------ASNNEIARSLFISE----------NTVKTHLYNLFKKIAVK 201 (216)
T ss_pred cCCCCHHHHHHHHHHHcC--------CCHHHHHHHhCCCH----------HHHHHHHHHHHHHhCCC
Confidence 456888888888777664 23578999999999 99999998877776543
No 102
>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=24.45 E-value=89 Score=22.10 Aligned_cols=44 Identities=14% Similarity=0.226 Sum_probs=28.2
Q ss_pred CCCCHHHHHHHHHHHHHhCCCCCCHHHHHHHHHHcCCCcccCCCCcCCcchhhhhhhccc
Q 026004 8 PDFTLAEIKEMESMYKEIGEASLTQEYCKALATSFSFSASRAARPAITWLQVQSWFRDKQ 67 (245)
Q Consensus 8 ~~FT~~Ql~eMEk~f~~~~~~y~~~~~rq~LA~~f~lS~~r~Gk~~v~~~QVk~WFQNRR 67 (245)
..||+++-..+=+.+.. ......+||..+|+++ .++-+|-+-=+
T Consensus 5 ~~ys~e~K~~~v~~~~~------~g~sv~~va~~~gi~~----------~~l~~W~~~~~ 48 (76)
T PF01527_consen 5 RRYSPEFKLQAVREYLE------SGESVSEVAREYGISP----------STLYNWRKQYR 48 (76)
T ss_dssp ----HHHHHHHHHHHHH------HHCHHHHHHHHHTS-H----------HHHHHHHHHHH
T ss_pred CCCCHHHHHHHHHHHHH------CCCceEeeeccccccc----------ccccHHHHHHh
Confidence 35788877666555533 1366789999999988 99999976443
No 103
>PRK15451 tRNA cmo(5)U34 methyltransferase; Provisional
Probab=24.39 E-value=1.7e+02 Score=25.69 Aligned_cols=46 Identities=22% Similarity=0.269 Sum_probs=35.9
Q ss_pred CCCCHHHHHHHHHHHHHhCCCCCCHHHHHHHHHHcCCCcccCCCCcCCcchhhhhhhcc
Q 026004 8 PDFTLAEIKEMESMYKEIGEASLTQEYCKALATSFSFSASRAARPAITWLQVQSWFRDK 66 (245)
Q Consensus 8 ~~FT~~Ql~eMEk~f~~~~~~y~~~~~rq~LA~~f~lS~~r~Gk~~v~~~QVk~WFQNR 66 (245)
..+|..|+.++.+.++.. -...+.+.-.+|.++-|. ++|..|||+-
T Consensus 188 ~g~s~~ei~~~~~~~~~~-~~~~~~~~~~~~L~~aGF------------~~v~~~~~~~ 233 (247)
T PRK15451 188 NGYSELEISQKRSMLENV-MLTDSVETHKARLHKAGF------------EHSELWFQCF 233 (247)
T ss_pred cCCCHHHHHHHHHHHHhh-cccCCHHHHHHHHHHcCc------------hhHHHHHHHH
Confidence 367888998887777653 344588888899999999 6799999975
No 104
>PRK00523 hypothetical protein; Provisional
Probab=24.13 E-value=1.3e+02 Score=23.26 Aligned_cols=36 Identities=14% Similarity=0.224 Sum_probs=31.0
Q ss_pred HHHHHHHHHhCCCCCCHHHHHHHHHHcCCCcccCCCCcCCcchhhh
Q 026004 16 KEMESMYKEIGEASLTQEYCKALATSFSFSASRAARPAITWLQVQS 61 (245)
Q Consensus 16 ~eMEk~f~~~~~~y~~~~~rq~LA~~f~lS~~r~Gk~~v~~~QVk~ 61 (245)
.-||+.|++ |..++.+....+....|-.| +++||+.
T Consensus 28 k~~~k~l~~--NPpine~mir~M~~QMGqKP--------Sekki~Q 63 (72)
T PRK00523 28 KMFKKQIRE--NPPITENMIRAMYMQMGRKP--------SESQIKQ 63 (72)
T ss_pred HHHHHHHHH--CcCCCHHHHHHHHHHhCCCc--------cHHHHHH
Confidence 458999999 59999999999999999888 6677764
No 105
>PF05506 DUF756: Domain of unknown function (DUF756); InterPro: IPR008475 This domain is found, normally as a tandem repeat, at the C terminus of bacterial phospholipase C proteins.; GO: 0004629 phospholipase C activity, 0016042 lipid catabolic process
Probab=23.64 E-value=89 Score=23.50 Aligned_cols=29 Identities=24% Similarity=0.533 Sum_probs=18.9
Q ss_pred ceeEeecccCCCceeeeeecceeeeeecCceeEEEEecC
Q 026004 113 ELAFEARSSKDDAWYDVASFLTYRVTCAGELEVRVRFSG 151 (245)
Q Consensus 113 ~~efEArs~~D~AWYdV~~fl~~R~~~~g~~el~Vrf~g 151 (245)
++.+ --...+-|||+.+. ..+. ..=||+|
T Consensus 60 ~~~w--~l~~s~gwYDl~v~------~~~~--F~rr~aG 88 (89)
T PF05506_consen 60 SLTW--PLAASGGWYDLTVT------GPNG--FLRRFAG 88 (89)
T ss_pred EEEE--eecCCCCcEEEEEE------cCCC--EEEEecC
Confidence 3445 44678899999953 3343 6667766
No 106
>TIGR03070 couple_hipB transcriptional regulator, y4mF family. Members of this family belong to a clade of helix-turn-helix DNA-binding proteins, among the larger family pfam01381 (HTH_3; Helix-turn-helix). Members are similar in sequence to the HipB protein of E. coli. Genes for members of the seed alignment for this protein family were found to be closely linked to genes encoding proteins related to HipA. The HibBA operon appears to have some features in common with toxin-antitoxin post-segregational killing systems.
Probab=23.36 E-value=2.1e+02 Score=18.52 Aligned_cols=19 Identities=0% Similarity=0.128 Sum_probs=13.9
Q ss_pred CCCCCHHHHHHHHHHcCCC
Q 026004 27 EASLTQEYCKALATSFSFS 45 (245)
Q Consensus 27 ~~y~~~~~rq~LA~~f~lS 45 (245)
...|+......||+.||++
T Consensus 39 ~~~~~~~~~~~i~~~lgv~ 57 (58)
T TIGR03070 39 KPTVRLDKVLRVLDALGLE 57 (58)
T ss_pred CCCCCHHHHHHHHHHcCCC
Confidence 3467778888888888764
No 107
>PF13720 Acetyltransf_11: Udp N-acetylglucosamine O-acyltransferase; Domain 2; PDB: 3I3A_A 3I3X_A 3HSQ_B 2JF2_A 1LXA_A 2AQ9_A 2QIV_X 2QIA_A 2JF3_A 4EQY_F ....
Probab=23.31 E-value=1.7e+02 Score=22.38 Aligned_cols=38 Identities=18% Similarity=0.250 Sum_probs=26.2
Q ss_pred CCCHHHHHHHHHHHHHhC-CCCCCHHHHHHHHHHcCCCc
Q 026004 9 DFTLAEIKEMESMYKEIG-EASLTQEYCKALATSFSFSA 46 (245)
Q Consensus 9 ~FT~~Ql~eMEk~f~~~~-~~y~~~~~rq~LA~~f~lS~ 46 (245)
.||.++|..|.++|+..= +...-.+..++|.+.++.++
T Consensus 27 Gfs~~~i~~l~~ayr~l~~~~~~~~~a~~~l~~~~~~~~ 65 (83)
T PF13720_consen 27 GFSKEEISALRRAYRILFRSGLTLEEALEELEEEYPDSP 65 (83)
T ss_dssp TS-HHHHHHHHHHHHHHHTSSS-HHHHHHHHHHHTTSCH
T ss_pred CCCHHHHHHHHHHHHHHHhCCCCHHHHHHHHHHhccCCH
Confidence 599999999999999862 22333466677777677655
No 108
>PF13384 HTH_23: Homeodomain-like domain; PDB: 2X48_C.
Probab=23.22 E-value=63 Score=21.30 Aligned_cols=22 Identities=18% Similarity=0.333 Sum_probs=17.2
Q ss_pred HHHHHHHHHcCCCcccCCCCcCCcchhhhhhh
Q 026004 33 EYCKALATSFSFSASRAARPAITWLQVQSWFR 64 (245)
Q Consensus 33 ~~rq~LA~~f~lS~~r~Gk~~v~~~QVk~WFQ 64 (245)
.-..++|+.||.|. ..|..|.+
T Consensus 18 ~s~~~ia~~lgvs~----------~Tv~~w~k 39 (50)
T PF13384_consen 18 WSIREIAKRLGVSR----------STVYRWIK 39 (50)
T ss_dssp --HHHHHHHHTS-H----------HHHHHHHT
T ss_pred CCHHHHHHHHCcCH----------HHHHHHHH
Confidence 56789999999999 88999976
No 109
>PF04539 Sigma70_r3: Sigma-70 region 3; InterPro: IPR007624 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 3 forms a discrete compact three helical domain within the sigma-factor. Region is not normally involved in the recognition of promoter DNA, but in some specific bacterial promoters containing an extended -10 promoter element, residues within region 3 play an important role. Region 3 primarily is involved in binding the core RNA polymerase in the holoenzyme [].; 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: 1L0O_C 1KU2_B 1RP3_C 1SC5_A 1TTY_A 2BE5_F 2A6E_F 2CW0_F 2A69_P 2A6H_P ....
Probab=22.52 E-value=1.3e+02 Score=21.60 Aligned_cols=38 Identities=13% Similarity=0.133 Sum_probs=23.8
Q ss_pred HHHHHHHHHHHhCCCCCCHHHHHHHHHHcCCCcccCCCCcCCcchhhhhhh
Q 026004 14 EIKEMESMYKEIGEASLTQEYCKALATSFSFSASRAARPAITWLQVQSWFR 64 (245)
Q Consensus 14 Ql~eMEk~f~~~~~~y~~~~~rq~LA~~f~lS~~r~Gk~~v~~~QVk~WFQ 64 (245)
+|.+-.+.|.+..++.|+ .++||+.+|+|. ++|...++
T Consensus 5 ~i~~a~~~L~~~lgr~Pt---~eEiA~~lgis~----------~~v~~~l~ 42 (78)
T PF04539_consen 5 KIERARRELEQELGREPT---DEEIAEELGISV----------EEVRELLQ 42 (78)
T ss_dssp HHHHHHHHHHHHHSS--B---HHHHHHHHTS-H----------HHHHHHHH
T ss_pred HHHHHHHHHHHHhCCCCC---HHHHHHHHcccH----------HHHHHHHH
Confidence 344444445544456666 578999999999 89886665
No 110
>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=22.39 E-value=65 Score=20.79 Aligned_cols=22 Identities=18% Similarity=0.037 Sum_probs=18.1
Q ss_pred HHHHHHHcCCCcccCCCCcCCcchhhhhhhcc
Q 026004 35 CKALATSFSFSASRAARPAITWLQVQSWFRDK 66 (245)
Q Consensus 35 rq~LA~~f~lS~~r~Gk~~v~~~QVk~WFQNR 66 (245)
..++|+.+|+|+ ..|+.|-++-
T Consensus 3 ~~e~a~~~gv~~----------~tlr~~~~~g 24 (49)
T cd04761 3 IGELAKLTGVSP----------STLRYYERIG 24 (49)
T ss_pred HHHHHHHHCcCH----------HHHHHHHHCC
Confidence 357899999988 8999997643
No 111
>PF10844 DUF2577: Protein of unknown function (DUF2577); InterPro: IPR022555 This family of proteins has no known function
Probab=22.12 E-value=94 Score=24.42 Aligned_cols=21 Identities=33% Similarity=0.401 Sum_probs=15.8
Q ss_pred ccccCCceEEEeeecCCceeEE
Q 026004 179 VKVNVGDLVLCYQEREDQAVYC 200 (245)
Q Consensus 179 ~~v~~G~~v~cf~~~~~~~~yy 200 (245)
..|++||.|+++...+.| +||
T Consensus 75 ~~Lk~GD~V~ll~~~~gQ-~yi 95 (100)
T PF10844_consen 75 DGLKVGDKVLLLRVQGGQ-KYI 95 (100)
T ss_pred cCCcCCCEEEEEEecCCC-EEE
Confidence 368999999999865545 554
No 112
>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=21.90 E-value=69 Score=23.73 Aligned_cols=22 Identities=32% Similarity=0.527 Sum_probs=17.7
Q ss_pred HHHHHHHcCCCcccCCCCcCCcchhhhhhhcc
Q 026004 35 CKALATSFSFSASRAARPAITWLQVQSWFRDK 66 (245)
Q Consensus 35 rq~LA~~f~lS~~r~Gk~~v~~~QVk~WFQNR 66 (245)
..+-|.+||.++ ++|+.|-+-+
T Consensus 28 ~RAaarkf~V~r----------~~Vr~W~kqe 49 (58)
T PF09607_consen 28 QRAAARKFNVSR----------RQVRKWRKQE 49 (58)
T ss_dssp HHHHHHHTTS-H----------HHHHHHHTTH
T ss_pred HHHHHHHhCccH----------HHHHHHHHHH
Confidence 457899999988 9999998844
No 113
>PHA01976 helix-turn-helix protein
Probab=21.28 E-value=1.2e+02 Score=21.01 Aligned_cols=20 Identities=10% Similarity=0.011 Sum_probs=12.1
Q ss_pred CCCCCHHHHHHHHHHcCCCc
Q 026004 27 EASLTQEYCKALATSFSFSA 46 (245)
Q Consensus 27 ~~y~~~~~rq~LA~~f~lS~ 46 (245)
...|+.+...+||+.||++.
T Consensus 39 ~~~p~~~~l~~ia~~l~v~~ 58 (67)
T PHA01976 39 KRLPNLKTLLRLADALGVTL 58 (67)
T ss_pred CCCCCHHHHHHHHHHHCcCH
Confidence 34566666666666666654
No 114
>TIGR02607 antidote_HigA addiction module antidote protein, HigA family. Members of this family form a distinct clade within the larger family HTH_3 of helix-turn-helix proteins, described by Pfam model pfam01381. Members of this clade are strictly bacterial and nearly always shorter than 110 amino acids. This family includes the characterized member HigA, without which the killer protein HigB cannot be cloned. The hig (host inhibition of growth) system is noted to be unusual in that killer protein is uncoded by the upstream member of the gene pair.
Probab=20.88 E-value=1e+02 Score=21.91 Aligned_cols=19 Identities=21% Similarity=0.274 Sum_probs=10.6
Q ss_pred CCCCHHHHHHHHHHcCCCc
Q 026004 28 ASLTQEYCKALATSFSFSA 46 (245)
Q Consensus 28 ~y~~~~~rq~LA~~f~lS~ 46 (245)
..|+.....+||+.|+.++
T Consensus 43 ~~~~~~~~~~l~~~l~v~~ 61 (78)
T TIGR02607 43 RGITADMALRLAKALGTSP 61 (78)
T ss_pred CCCCHHHHHHHHHHcCCCH
Confidence 4455555555555555544
No 115
>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=20.65 E-value=1.1e+02 Score=20.36 Aligned_cols=40 Identities=15% Similarity=0.140 Sum_probs=28.0
Q ss_pred CCCCHHHHHHHHHHHHHhCCCCCCHHHHHHHHHHcCCCcccCCCCcCCcchhhhhhh
Q 026004 8 PDFTLAEIKEMESMYKEIGEASLTQEYCKALATSFSFSASRAARPAITWLQVQSWFR 64 (245)
Q Consensus 8 ~~FT~~Ql~eMEk~f~~~~~~y~~~~~rq~LA~~f~lS~~r~Gk~~v~~~QVk~WFQ 64 (245)
..+++.|-.-+.-.|-+ .-..+++|+.+|+|. ..|+.+..
T Consensus 3 ~~L~~~er~vi~~~y~~-------~~t~~eIa~~lg~s~----------~~V~~~~~ 42 (50)
T PF04545_consen 3 DQLPPREREVIRLRYFE-------GLTLEEIAERLGISR----------STVRRILK 42 (50)
T ss_dssp CTS-HHHHHHHHHHHTS-------T-SHHHHHHHHTSCH----------HHHHHHHH
T ss_pred hhCCHHHHHHHHHHhcC-------CCCHHHHHHHHCCcH----------HHHHHHHH
Confidence 35678888888877743 244789999999988 66776543
No 116
>PRK10430 DNA-binding transcriptional activator DcuR; Provisional
Probab=20.45 E-value=1.4e+02 Score=25.52 Aligned_cols=44 Identities=9% Similarity=0.062 Sum_probs=32.4
Q ss_pred CCCHHHHHHHHHHHHHhCCCCCCHHHHHHHHHHcCCCcccCCCCcCCcchhhhhhhc
Q 026004 9 DFTLAEIKEMESMYKEIGEASLTQEYCKALATSFSFSASRAARPAITWLQVQSWFRD 65 (245)
Q Consensus 9 ~FT~~Ql~eMEk~f~~~~~~y~~~~~rq~LA~~f~lS~~r~Gk~~v~~~QVk~WFQN 65 (245)
.+|+.|+.+|..+..++ +=....-++||+++++|+ +.|++-+++
T Consensus 158 ~Lt~re~~~l~~~i~~~---~~~g~s~~eIA~~l~iS~----------~Tv~~~~~~ 201 (239)
T PRK10430 158 GLTPQTLRTLCQWIDAH---QDYEFSTDELANAVNISR----------VSCRKYLIW 201 (239)
T ss_pred CCCHHHHHHHHHHHHhC---CCCCcCHHHHHHHhCchH----------HHHHHHHHH
Confidence 47888888877777653 223345688999999999 899986663
No 117
>cd04762 HTH_MerR-trunc Helix-Turn-Helix DNA binding domain of truncated MerR-like proteins. Proteins in this family mostly have a truncated helix-turn-helix (HTH) MerR-like domain. They lack a portion of the C-terminal region, called Wing 2 and the long dimerization helix that is typically present in MerR-like proteins. These truncated domains are found in response regulator receiver (REC) domain proteins (i.e., CheY), cytosine-C5 specific DNA methylases, IS607 transposase-like proteins, and RacA, a bacterial protein that anchors chromosomes to cell poles.
Probab=20.12 E-value=87 Score=19.55 Aligned_cols=23 Identities=17% Similarity=0.404 Sum_probs=19.0
Q ss_pred HHHHHHHcCCCcccCCCCcCCcchhhhhhhccc
Q 026004 35 CKALATSFSFSASRAARPAITWLQVQSWFRDKQ 67 (245)
Q Consensus 35 rq~LA~~f~lS~~r~Gk~~v~~~QVk~WFQNRR 67 (245)
..++|+.|++|+ .-|+.|-++-.
T Consensus 3 ~~e~a~~lgvs~----------~tl~~~~~~g~ 25 (49)
T cd04762 3 TKEAAELLGVSP----------STLRRWVKEGK 25 (49)
T ss_pred HHHHHHHHCcCH----------HHHHHHHHcCC
Confidence 467899999988 88999988653
No 118
>PRK04217 hypothetical protein; Provisional
Probab=20.06 E-value=1.5e+02 Score=24.23 Aligned_cols=51 Identities=14% Similarity=-0.042 Sum_probs=37.2
Q ss_pred CCCcCCCCHHHHHHHHHHHHHhCCCCCCHHHHHHHHHHcCCCcccCCCCcCCcchhhhhhhccccccc
Q 026004 4 EDSWPDFTLAEIKEMESMYKEIGEASLTQEYCKALATSFSFSASRAARPAITWLQVQSWFRDKQKKSQ 71 (245)
Q Consensus 4 ~~~~~~FT~~Ql~eMEk~f~~~~~~y~~~~~rq~LA~~f~lS~~r~Gk~~v~~~QVk~WFQNRR~k~k 71 (245)
+.|...+|.+|.+.+...+.+. -..++||+.+++|. ..|.+.++.-+.+.+
T Consensus 37 ~~p~~~Lt~eereai~l~~~eG-------lS~~EIAk~LGIS~----------sTV~r~L~RArkkLr 87 (110)
T PRK04217 37 PKPPIFMTYEEFEALRLVDYEG-------LTQEEAGKRMGVSR----------GTVWRALTSARKKVA 87 (110)
T ss_pred CCCcccCCHHHHHHHHHHHHcC-------CCHHHHHHHHCcCH----------HHHHHHHHHHHHHHH
Confidence 3457789999987776666541 25678999999998 888877765555554
Done!