Query 025634
Match_columns 250
No_of_seqs 156 out of 211
Neff 4.0
Searched_HMMs 46136
Date Fri Mar 29 07:52:57 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/025634.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/025634hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG0489 Transcription factor z 99.8 1E-18 2.2E-23 157.9 6.2 58 7-76 158-215 (261)
2 KOG0842 Transcription factor t 99.7 4E-18 8.7E-23 158.4 5.1 64 7-82 152-215 (307)
3 KOG0488 Transcription factor B 99.7 2.6E-17 5.6E-22 152.8 4.6 57 8-76 172-228 (309)
4 KOG0484 Transcription factor P 99.6 4E-16 8.7E-21 126.9 5.2 58 7-76 16-73 (125)
5 KOG0487 Transcription factor A 99.6 1.2E-16 2.7E-21 148.6 2.3 59 6-76 233-291 (308)
6 KOG0843 Transcription factor E 99.6 2.9E-16 6.4E-21 137.2 4.1 59 7-77 101-159 (197)
7 KOG0492 Transcription factor M 99.6 8.1E-16 1.7E-20 137.3 4.2 62 3-76 139-200 (246)
8 PF00046 Homeobox: Homeobox do 99.6 5E-15 1.1E-19 103.5 5.3 55 9-75 1-55 (57)
9 KOG0850 Transcription factor D 99.5 1.1E-14 2.3E-19 131.3 6.5 57 8-76 122-178 (245)
10 KOG2251 Homeobox transcription 99.5 4.6E-14 1E-18 126.4 6.9 60 5-76 34-93 (228)
11 smart00389 HOX Homeodomain. DN 99.5 7.8E-14 1.7E-18 96.3 6.4 54 10-75 2-55 (56)
12 KOG0485 Transcription factor N 99.5 1.5E-14 3.3E-19 130.1 2.1 61 7-79 103-163 (268)
13 KOG0493 Transcription factor E 99.4 6.2E-14 1.3E-18 129.0 4.8 69 9-89 247-316 (342)
14 TIGR01565 homeo_ZF_HD homeobox 99.4 1.7E-13 3.7E-18 100.0 4.6 52 9-72 2-57 (58)
15 cd00086 homeodomain Homeodomai 99.4 3.7E-13 8E-18 93.2 6.0 55 10-76 2-56 (59)
16 KOG0491 Transcription factor B 99.4 3E-13 6.5E-18 117.5 2.7 58 7-76 99-156 (194)
17 KOG0494 Transcription factor C 99.3 8.4E-13 1.8E-17 121.5 4.2 57 9-77 142-198 (332)
18 KOG0844 Transcription factor E 99.3 5E-13 1.1E-17 125.2 1.2 57 8-76 181-237 (408)
19 KOG0848 Transcription factor C 99.3 7.6E-13 1.6E-17 121.9 1.3 54 11-76 202-255 (317)
20 KOG0483 Transcription factor H 99.3 2.9E-12 6.3E-17 113.2 4.6 57 11-79 53-109 (198)
21 COG5576 Homeodomain-containing 99.1 1.6E-10 3.4E-15 98.8 4.6 61 6-78 49-109 (156)
22 KOG0486 Transcription factor P 99.0 7.2E-11 1.6E-15 110.7 2.6 58 7-76 111-168 (351)
23 KOG0490 Transcription factor, 99.0 7E-11 1.5E-15 101.0 1.5 61 6-78 58-118 (235)
24 KOG0847 Transcription factor, 99.0 4.5E-10 9.8E-15 101.8 4.5 57 11-79 170-226 (288)
25 KOG4577 Transcription factor L 98.7 1.1E-08 2.3E-13 95.9 3.7 58 6-75 165-222 (383)
26 KOG0849 Transcription factor P 98.7 1.9E-08 4E-13 95.3 4.8 64 3-78 171-234 (354)
27 KOG0775 Transcription factor S 98.1 7.8E-06 1.7E-10 76.2 7.1 53 15-79 183-235 (304)
28 KOG3802 Transcription factor O 98.1 1.9E-06 4.1E-11 83.2 3.1 58 7-76 293-350 (398)
29 PF05920 Homeobox_KN: Homeobox 98.0 3.7E-06 8E-11 57.1 2.9 37 27-73 3-39 (40)
30 KOG2252 CCAAT displacement pro 97.8 8.8E-05 1.9E-09 74.3 8.5 58 6-75 418-475 (558)
31 KOG0490 Transcription factor, 97.5 6.3E-05 1.4E-09 64.4 2.7 59 6-76 151-209 (235)
32 KOG0774 Transcription factor P 97.4 0.00047 1E-08 64.5 7.0 58 8-75 188-246 (334)
33 PF15057 DUF4537: Domain of un 96.3 0.042 9.2E-07 45.2 9.4 104 123-244 6-109 (124)
34 PF11717 Tudor-knot: RNA bindi 96.3 0.0084 1.8E-07 42.6 4.5 40 127-168 12-51 (55)
35 KOG1168 Transcription factor A 95.2 0.0032 7E-08 59.8 -1.5 59 8-78 309-367 (385)
36 KOG1146 Homeobox protein [Gene 95.0 0.031 6.8E-07 61.3 5.2 56 9-76 904-959 (1406)
37 cd00024 CHROMO Chromatin organ 94.2 0.063 1.4E-06 36.5 3.5 36 132-167 3-39 (55)
38 PF04218 CENP-B_N: CENP-B N-te 93.7 0.18 3.9E-06 35.7 5.0 47 9-72 1-47 (53)
39 PF00385 Chromo: Chromo (CHRro 93.3 0.097 2.1E-06 36.2 3.1 37 132-168 1-39 (55)
40 PF11569 Homez: Homeodomain le 93.2 0.11 2.4E-06 38.2 3.3 42 20-73 10-51 (56)
41 KOG0773 Transcription factor M 93.1 0.075 1.6E-06 49.4 3.0 56 10-75 241-297 (342)
42 smart00333 TUDOR Tudor domain. 92.2 0.48 1E-05 32.5 5.4 54 185-249 2-55 (57)
43 PLN00104 MYST -like histone ac 92.1 0.69 1.5E-05 46.1 8.3 52 123-176 62-116 (450)
44 cd04508 TUDOR Tudor domains ar 92.0 0.26 5.6E-06 32.8 3.8 36 122-162 5-40 (48)
45 smart00561 MBT Present in Dros 91.5 0.37 7.9E-06 38.2 4.7 45 119-168 32-76 (96)
46 smart00298 CHROMO Chromatin or 91.4 0.23 5E-06 33.5 3.0 37 132-168 2-38 (55)
47 PF02820 MBT: mbt repeat; Int 89.8 0.54 1.2E-05 34.9 4.0 45 119-168 1-45 (73)
48 smart00743 Agenet Tudor-like d 87.8 1.9 4.1E-05 30.4 5.5 51 185-245 2-54 (61)
49 PF12148 DUF3590: Protein of u 86.9 2 4.3E-05 34.1 5.6 70 122-194 3-74 (85)
50 PF10668 Phage_terminase: Phag 86.0 1.3 2.9E-05 32.9 4.0 32 23-68 12-43 (60)
51 smart00333 TUDOR Tudor domain. 85.7 1.4 3E-05 30.2 3.8 40 121-168 9-48 (57)
52 smart00743 Agenet Tudor-like d 84.5 1.9 4.2E-05 30.3 4.2 30 122-156 10-39 (61)
53 PF05641 Agenet: Agenet domain 83.8 1.6 3.5E-05 32.0 3.6 45 124-174 10-63 (68)
54 PF11717 Tudor-knot: RNA bindi 82.0 7.6 0.00017 27.4 6.4 41 186-234 1-41 (55)
55 PF12824 MRP-L20: Mitochondria 81.6 1.8 3.9E-05 37.6 3.7 48 12-63 83-130 (164)
56 PF06003 SMN: Survival motor n 81.5 3.1 6.8E-05 38.4 5.4 53 184-245 67-119 (264)
57 PF06003 SMN: Survival motor n 77.2 2.8 6.2E-05 38.6 3.7 41 122-166 76-116 (264)
58 PF05641 Agenet: Agenet domain 76.7 7.4 0.00016 28.5 5.1 51 186-244 1-60 (68)
59 cd04508 TUDOR Tudor domains ar 76.5 7.2 0.00016 25.7 4.6 46 189-244 1-46 (48)
60 KOG3623 Homeobox transcription 70.6 12 0.00025 40.3 6.6 49 14-75 563-611 (1007)
61 PF12148 DUF3590: Protein of u 68.2 9.6 0.00021 30.2 4.2 48 200-248 8-55 (85)
62 PF00249 Myb_DNA-binding: Myb- 68.2 21 0.00046 24.0 5.5 44 12-70 1-46 (48)
63 PTZ00183 centrin; Provisional 65.6 20 0.00043 28.3 5.7 39 11-49 7-48 (158)
64 smart00717 SANT SANT SWI3, AD 64.3 19 0.00042 22.6 4.5 44 12-70 1-45 (49)
65 PF13551 HTH_29: Winged helix- 58.9 33 0.00072 25.7 5.7 22 9-30 52-73 (112)
66 smart00027 EH Eps15 homology d 57.4 32 0.00069 26.1 5.4 45 15-69 4-51 (96)
67 COG3458 Acetyl esterase (deace 56.9 18 0.00039 34.8 4.6 92 116-214 56-162 (321)
68 PF01527 HTH_Tnp_1: Transposas 56.2 24 0.00053 25.2 4.3 47 10-72 2-48 (76)
69 cd00569 HTH_Hin_like Helix-tur 53.7 38 0.00082 18.8 4.4 37 14-67 5-41 (42)
70 PF13936 HTH_38: Helix-turn-he 53.5 15 0.00033 24.8 2.7 33 12-51 2-34 (44)
71 PF04967 HTH_10: HTH DNA bindi 53.2 20 0.00043 25.8 3.3 37 15-51 1-37 (53)
72 PF13565 HTH_32: Homeodomain-l 51.8 55 0.0012 23.4 5.6 40 8-50 26-65 (77)
73 PF00196 GerE: Bacterial regul 51.0 28 0.00061 24.1 3.8 47 12-76 1-47 (58)
74 PF13518 HTH_28: Helix-turn-he 48.2 19 0.00041 23.8 2.5 24 39-72 14-37 (52)
75 cd00167 SANT 'SWI3, ADA2, N-Co 46.9 56 0.0012 20.1 4.5 42 14-70 1-43 (45)
76 PF11516 DUF3220: Protein of u 43.6 18 0.00038 29.1 2.0 19 52-71 22-40 (106)
77 PRK07539 NADH dehydrogenase su 42.5 57 0.0012 27.5 5.1 20 32-51 35-54 (154)
78 cd06171 Sigma70_r4 Sigma70, re 41.3 57 0.0012 20.4 3.9 42 14-72 10-51 (55)
79 PRK07571 bidirectional hydroge 41.1 59 0.0013 28.4 5.1 40 12-51 13-68 (169)
80 PF02796 HTH_7: Helix-turn-hel 40.4 47 0.001 22.3 3.5 31 14-51 5-35 (45)
81 PRK10072 putative transcriptio 35.9 48 0.001 26.4 3.4 23 40-72 49-71 (96)
82 PF00567 TUDOR: Tudor domain; 35.5 49 0.0011 24.5 3.3 54 123-184 60-118 (121)
83 PF13720 Acetyltransf_11: Udp 35.4 60 0.0013 24.9 3.8 40 12-51 25-65 (83)
84 PLN00104 MYST -like histone ac 35.1 90 0.0019 31.6 5.9 58 184-244 52-111 (450)
85 PF11523 DUF3223: Protein of u 33.0 54 0.0012 25.0 3.1 32 209-242 41-73 (76)
86 PRK11511 DNA-binding transcrip 32.7 32 0.0007 27.7 2.0 38 21-71 12-49 (127)
87 KOG3026 Splicing factor SPF30 31.9 1.9E+02 0.0042 27.3 7.1 47 110-164 90-136 (262)
88 KOG1911 Heterochromatin-associ 31.2 27 0.00058 31.9 1.4 39 127-166 44-82 (270)
89 COG3413 Predicted DNA binding 30.9 56 0.0012 28.5 3.3 39 13-51 154-192 (215)
90 PF08880 QLQ: QLQ; InterPro: 30.5 42 0.00091 22.6 1.9 16 13-28 1-16 (37)
91 PF13921 Myb_DNA-bind_6: Myb-l 29.5 1.5E+02 0.0033 20.3 4.8 40 15-70 1-41 (60)
92 PF13873 Myb_DNA-bind_5: Myb/S 29.0 1.3E+02 0.0027 21.9 4.5 55 13-71 3-68 (78)
93 PF08281 Sigma70_r4_2: Sigma-7 28.2 72 0.0016 21.4 2.9 28 33-70 22-49 (54)
94 PF13384 HTH_23: Homeodomain-l 28.0 53 0.0011 21.8 2.1 23 38-70 18-40 (50)
95 PF01476 LysM: LysM domain; I 27.7 52 0.0011 21.0 2.0 21 37-67 6-26 (44)
96 TIGR03070 couple_hipB transcri 26.9 1.6E+02 0.0035 19.2 4.4 31 15-50 27-57 (58)
97 PF05506 DUF756: Domain of unk 26.9 73 0.0016 24.0 3.0 28 119-156 61-88 (89)
98 PRK09413 IS2 repressor TnpA; R 26.5 1.7E+02 0.0036 23.5 5.2 43 12-70 10-52 (121)
99 PTZ00184 calmodulin; Provision 26.3 2.9E+02 0.0064 21.1 6.4 37 14-50 4-43 (149)
100 PHA01976 helix-turn-helix prot 26.0 1.7E+02 0.0038 20.2 4.6 20 32-51 39-58 (67)
101 cd04761 HTH_MerR-SF Helix-Turn 25.8 62 0.0013 21.0 2.1 22 40-71 3-24 (49)
102 COG5126 FRQ1 Ca2+-binding prot 25.6 1.6E+02 0.0035 25.6 5.2 41 11-51 10-53 (160)
103 PF09607 BrkDBD: Brinker DNA-b 25.1 45 0.00097 24.8 1.4 44 14-71 5-49 (58)
104 PRK12461 UDP-N-acetylglucosami 24.8 1.1E+02 0.0024 27.9 4.2 41 11-51 196-237 (255)
105 PF01343 Peptidase_S49: Peptid 24.3 84 0.0018 26.0 3.1 46 11-71 76-121 (154)
106 cd00110 LamG Laminin G domain; 23.9 1.1E+02 0.0025 23.6 3.6 31 118-153 68-99 (151)
107 PF04545 Sigma70_r4: Sigma-70, 23.7 1.5E+02 0.0032 19.8 3.7 38 14-68 4-41 (50)
108 cd04762 HTH_MerR-trunc Helix-T 23.2 83 0.0018 19.7 2.3 23 40-72 3-25 (49)
109 PF04539 Sigma70_r3: Sigma-70 23.2 1.3E+02 0.0029 21.5 3.7 37 20-69 6-42 (78)
110 PF15057 DUF4537: Domain of un 22.7 1.8E+02 0.0038 23.9 4.7 36 189-234 1-36 (124)
111 PF10777 YlaC: Inner membrane 22.1 69 0.0015 28.1 2.2 24 139-168 85-108 (155)
112 COG5484 Uncharacterized conser 22.0 47 0.001 31.5 1.3 32 33-76 15-46 (279)
113 PF06191 DUF995: Protein of un 21.6 1.2E+02 0.0026 26.1 3.6 67 113-192 77-144 (145)
114 PF13730 HTH_36: Helix-turn-he 21.6 2.6E+02 0.0055 18.7 4.6 46 14-69 2-47 (55)
115 smart00421 HTH_LUXR helix_turn 21.3 1.7E+02 0.0037 18.6 3.6 44 14-75 3-46 (58)
116 TIGR01321 TrpR trp operon repr 21.2 68 0.0015 25.8 1.9 55 14-69 32-91 (94)
117 PRK03975 tfx putative transcri 21.1 1.2E+02 0.0026 25.9 3.4 45 13-75 5-49 (141)
118 PF06056 Terminase_5: Putative 21.1 81 0.0018 22.8 2.1 28 37-76 13-40 (58)
119 PF04936 DUF658: Protein of un 20.9 84 0.0018 28.2 2.5 32 38-79 15-46 (186)
120 PF13443 HTH_26: Cro/C1-type H 20.8 85 0.0018 21.6 2.1 34 23-72 2-35 (63)
121 PRK04980 hypothetical protein; 20.6 1.8E+02 0.0039 23.7 4.2 31 185-216 31-61 (102)
122 COG4367 Uncharacterized protei 20.5 1.1E+02 0.0024 24.9 3.0 36 14-51 2-37 (97)
123 COG2963 Transposase and inacti 20.5 2.5E+02 0.0055 21.8 5.0 45 12-72 5-50 (116)
124 COG2944 Predicted transcriptio 20.5 1.4E+02 0.003 24.6 3.5 39 15-72 44-82 (104)
125 PRK12373 NADH dehydrogenase su 20.4 2.6E+02 0.0057 27.9 6.1 48 3-51 4-69 (400)
126 PF02210 Laminin_G_2: Laminin 20.4 1.1E+02 0.0025 22.6 2.9 19 119-137 44-62 (128)
127 PRK09726 antitoxin HipB; Provi 20.4 1.6E+02 0.0034 22.2 3.7 32 15-51 37-68 (88)
128 PF03672 UPF0154: Uncharacteri 20.2 2.3E+02 0.0051 21.4 4.5 29 21-51 20-48 (64)
129 PRK10430 DNA-binding transcrip 20.2 1.6E+02 0.0034 25.3 4.1 46 13-71 157-202 (239)
No 1
>KOG0489 consensus Transcription factor zerknullt and related HOX domain proteins [General function prediction only]
Probab=99.75 E-value=1e-18 Score=157.87 Aligned_cols=58 Identities=22% Similarity=0.402 Sum_probs=55.5
Q ss_pred CCCCCCccCCHHHHHHHHHHHHhhCCCCCCHHHHHHHHHHhCCCCcCCCCCccchhHHHHHHhhhcccCC
Q 025634 7 RQRSVFTGFTKTELEKMEKLLMESKDDLLSKEFCQKIAKSFSCSAGRAGKPVVKWTEVQSWFQSRQQDRP 76 (250)
Q Consensus 7 ~~Rr~Rt~FT~~Ql~eLEk~f~~~~~~y~~~~~rq~LA~~f~lS~~RaGK~~Vq~~QVk~WFQNRR~k~~ 76 (250)
-.||.||.||..||.||||+|+. |+||++..|.+||..|+|+| +|||||||||||||+
T Consensus 158 ~~kR~RtayT~~QllELEkEFhf--N~YLtR~RRiEiA~~L~LtE----------rQIKIWFQNRRMK~K 215 (261)
T KOG0489|consen 158 KSKRRRTAFTRYQLLELEKEFHF--NKYLTRSRRIEIAHALNLTE----------RQIKIWFQNRRMKWK 215 (261)
T ss_pred CCCCCCcccchhhhhhhhhhhcc--ccccchHHHHHHHhhcchhH----------HHHHHHHHHHHHHHH
Confidence 35779999999999999999999 79999999999999999998 999999999999998
No 2
>KOG0842 consensus Transcription factor tinman/NKX2-3, contains HOX domain [Transcription]
Probab=99.72 E-value=4e-18 Score=158.41 Aligned_cols=64 Identities=20% Similarity=0.363 Sum_probs=57.9
Q ss_pred CCCCCCccCCHHHHHHHHHHHHhhCCCCCCHHHHHHHHHHhCCCCcCCCCCccchhHHHHHHhhhcccCCCCCCCC
Q 025634 7 RQRSVFTGFTKTELEKMEKLLMESKDDLLSKEFCQKIAKSFSCSAGRAGKPVVKWTEVQSWFQSRQQDRPTKVTSS 82 (250)
Q Consensus 7 ~~Rr~Rt~FT~~Ql~eLEk~f~~~~~~y~~~~~rq~LA~~f~lS~~RaGK~~Vq~~QVk~WFQNRR~k~~~~~~~~ 82 (250)
++||.|..||+.||.|||+.|++ ++||+..+|+.||..|+||+ |||||||||||||.+.+-..+
T Consensus 152 ~kRKrRVLFSqAQV~ELERRFrq--QRYLSAPERE~LA~~LrLT~----------TQVKIWFQNrRYK~KR~~~dk 215 (307)
T KOG0842|consen 152 KKRKRRVLFSQAQVYELERRFRQ--QRYLSAPEREHLASSLRLTP----------TQVKIWFQNRRYKTKRQQKDK 215 (307)
T ss_pred cccccccccchhHHHHHHHHHHh--hhccccHhHHHHHHhcCCCc----------hheeeeeecchhhhhhhhhhh
Confidence 45668999999999999999999 89999999999999999999 999999999999987554433
No 3
>KOG0488 consensus Transcription factor BarH and related HOX domain proteins [General function prediction only]
Probab=99.67 E-value=2.6e-17 Score=152.80 Aligned_cols=57 Identities=26% Similarity=0.416 Sum_probs=54.3
Q ss_pred CCCCCccCCHHHHHHHHHHHHhhCCCCCCHHHHHHHHHHhCCCCcCCCCCccchhHHHHHHhhhcccCC
Q 025634 8 QRSVFTGFTKTELEKMEKLLMESKDDLLSKEFCQKIAKSFSCSAGRAGKPVVKWTEVQSWFQSRQQDRP 76 (250)
Q Consensus 8 ~Rr~Rt~FT~~Ql~eLEk~f~~~~~~y~~~~~rq~LA~~f~lS~~RaGK~~Vq~~QVk~WFQNRR~k~~ 76 (250)
.|+.||.||..||.+|||.|+. .+||+..+|.+||.+||||. +|||+||||||+||+
T Consensus 172 ~RksRTaFT~~Ql~~LEkrF~~--QKYLS~~DR~~LA~~LgLTd----------aQVKtWfQNRRtKWK 228 (309)
T KOG0488|consen 172 RRKSRTAFSDHQLFELEKRFEK--QKYLSVADRIELAASLGLTD----------AQVKTWFQNRRTKWK 228 (309)
T ss_pred cccchhhhhHHHHHHHHHHHHH--hhcccHHHHHHHHHHcCCch----------hhHHHHHhhhhHHHH
Confidence 4557999999999999999999 78999999999999999998 999999999999996
No 4
>KOG0484 consensus Transcription factor PHOX2/ARIX, contains HOX domain [Transcription]
Probab=99.62 E-value=4e-16 Score=126.95 Aligned_cols=58 Identities=28% Similarity=0.442 Sum_probs=55.0
Q ss_pred CCCCCCccCCHHHHHHHHHHHHhhCCCCCCHHHHHHHHHHhCCCCcCCCCCccchhHHHHHHhhhcccCC
Q 025634 7 RQRSVFTGFTKTELEKMEKLLMESKDDLLSKEFCQKIAKSFSCSAGRAGKPVVKWTEVQSWFQSRQQDRP 76 (250)
Q Consensus 7 ~~Rr~Rt~FT~~Ql~eLEk~f~~~~~~y~~~~~rq~LA~~f~lS~~RaGK~~Vq~~QVk~WFQNRR~k~~ 76 (250)
.+||.||.||..||.|||++|.+ .+|||.-.|++||-++.|++ ..||+||||||+|.+
T Consensus 16 KQRRIRTTFTS~QLkELErvF~E--THYPDIYTREEiA~kidLTE----------ARVQVWFQNRRAKfR 73 (125)
T KOG0484|consen 16 KQRRIRTTFTSAQLKELERVFAE--THYPDIYTREEIALKIDLTE----------ARVQVWFQNRRAKFR 73 (125)
T ss_pred HhhhhhhhhhHHHHHHHHHHHHh--hcCCcchhHHHHHHhhhhhH----------HHHHHHHHhhHHHHH
Confidence 37889999999999999999999 89999999999999999998 999999999999964
No 5
>KOG0487 consensus Transcription factor Abd-B, contains HOX domain [Transcription]
Probab=99.62 E-value=1.2e-16 Score=148.59 Aligned_cols=59 Identities=22% Similarity=0.385 Sum_probs=56.1
Q ss_pred CCCCCCCccCCHHHHHHHHHHHHhhCCCCCCHHHHHHHHHHhCCCCcCCCCCccchhHHHHHHhhhcccCC
Q 025634 6 PRQRSVFTGFTKTELEKMEKLLMESKDDLLSKEFCQKIAKSFSCSAGRAGKPVVKWTEVQSWFQSRQQDRP 76 (250)
Q Consensus 6 ~~~Rr~Rt~FT~~Ql~eLEk~f~~~~~~y~~~~~rq~LA~~f~lS~~RaGK~~Vq~~QVk~WFQNRR~k~~ 76 (250)
.+.|++|-.+|+.||.||||+|-- |.||+++.|-+|+..||||+ +||||||||||||.+
T Consensus 233 ~~~RKKRcPYTK~QtlELEkEFlf--N~YitkeKR~ElSr~lNLTe----------RQVKIWFQNRRMK~K 291 (308)
T KOG0487|consen 233 RRGRKKRCPYTKHQTLELEKEFLF--NMYITKEKRLELSRTLNLTE----------RQVKIWFQNRRMKEK 291 (308)
T ss_pred cccccccCCchHHHHHHHHHHHHH--HHHHhHHHHHHHHHhcccch----------hheeeeehhhhhHHh
Confidence 357888999999999999999999 78999999999999999998 999999999999987
No 6
>KOG0843 consensus Transcription factor EMX1 and related HOX domain proteins [Transcription]
Probab=99.61 E-value=2.9e-16 Score=137.25 Aligned_cols=59 Identities=29% Similarity=0.468 Sum_probs=55.1
Q ss_pred CCCCCCccCCHHHHHHHHHHHHhhCCCCCCHHHHHHHHHHhCCCCcCCCCCccchhHHHHHHhhhcccCCC
Q 025634 7 RQRSVFTGFTKTELEKMEKLLMESKDDLLSKEFCQKIAKSFSCSAGRAGKPVVKWTEVQSWFQSRQQDRPT 77 (250)
Q Consensus 7 ~~Rr~Rt~FT~~Ql~eLEk~f~~~~~~y~~~~~rq~LA~~f~lS~~RaGK~~Vq~~QVk~WFQNRR~k~~~ 77 (250)
+.+|.||.||.+||..||..|+. ++|+...+|.+||..||||+ +|||+||||||.|.+.
T Consensus 101 ~~kr~RT~ft~~Ql~~LE~~F~~--~~Yvvg~eR~~LA~~L~Lse----------tQVkvWFQNRRtk~kr 159 (197)
T KOG0843|consen 101 RPKRIRTAFTPEQLLKLEHAFEG--NQYVVGAERKQLAQSLSLSE----------TQVKVWFQNRRTKHKR 159 (197)
T ss_pred CCCccccccCHHHHHHHHHHHhc--CCeeechHHHHHHHHcCCCh----------hHhhhhhhhhhHHHHH
Confidence 35568999999999999999999 89999999999999999998 9999999999999763
No 7
>KOG0492 consensus Transcription factor MSH, contains HOX domain [General function prediction only]
Probab=99.58 E-value=8.1e-16 Score=137.32 Aligned_cols=62 Identities=27% Similarity=0.380 Sum_probs=57.2
Q ss_pred CCCCCCCCCCccCCHHHHHHHHHHHHhhCCCCCCHHHHHHHHHHhCCCCcCCCCCccchhHHHHHHhhhcccCC
Q 025634 3 RLRPRQRSVFTGFTKTELEKMEKLLMESKDDLLSKEFCQKIAKSFSCSAGRAGKPVVKWTEVQSWFQSRQQDRP 76 (250)
Q Consensus 3 r~r~~~Rr~Rt~FT~~Ql~eLEk~f~~~~~~y~~~~~rq~LA~~f~lS~~RaGK~~Vq~~QVk~WFQNRR~k~~ 76 (250)
|-+-++|++||.||..||..||+.|++ .+||+..+|.+++.+|+|++ +||||||||||+|.+
T Consensus 139 rKhk~nRkPRtPFTtqQLlaLErkfre--kqYLSiaEraefSsSL~LTe----------TqVKIWFQNRRAKaK 200 (246)
T KOG0492|consen 139 RKHKPNRKPRTPFTTQQLLALERKFRE--KQYLSIAERAEFSSSLELTE----------TQVKIWFQNRRAKAK 200 (246)
T ss_pred cccCCCCCCCCCCCHHHHHHHHHHHhH--hhhhhHHHHHhhhhhhhhhh----------hheehhhhhhhHHHH
Confidence 344568999999999999999999999 68999999999999999998 999999999999864
No 8
>PF00046 Homeobox: Homeobox domain not present here.; InterPro: IPR001356 The homeobox domain was first identified in a number of drosophila homeotic and segmentation proteins, but is now known to be well-conserved in many other animals, including vertebrates [, , ]. Hox genes encode homeodomain-containing transcriptional regulators that operate differential genetic programs along the anterior-posterior axis of animal bodies []. The domain binds DNA through a helix-turn-helix (HTH) structure. The HTH motif is characterised by two alpha-helices, which make intimate contacts with the DNA and are joined by a short turn. The second helix binds to DNA via a number of hydrogen bonds and hydrophobic interactions, which occur between specific side chains and the exposed bases and thymine methyl groups within the major groove of the DNA []. The first helix helps to stabilise the structure. The motif is very similar in sequence and structure in a wide range of DNA-binding proteins (e.g., cro and repressor proteins, homeotic proteins, etc.). One of the principal differences between HTH motifs in these different proteins arises from the stereo-chemical requirement for glycine in the turn which is needed to avoid steric interference of the beta-carbon with the main chain: for cro and repressor proteins the glycine appears to be mandatory, while for many of the homeotic and other DNA-binding proteins the requirement is relaxed.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0043565 sequence-specific DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 2DA3_A 1LFB_A 2LFB_A 2ECB_A 2DA5_A 3D1N_O 3A03_A 2XSD_C 3CMY_A 1AHD_P ....
Probab=99.56 E-value=5e-15 Score=103.50 Aligned_cols=55 Identities=31% Similarity=0.521 Sum_probs=51.8
Q ss_pred CCCCccCCHHHHHHHHHHHHhhCCCCCCHHHHHHHHHHhCCCCcCCCCCccchhHHHHHHhhhcccC
Q 025634 9 RSVFTGFTKTELEKMEKLLMESKDDLLSKEFCQKIAKSFSCSAGRAGKPVVKWTEVQSWFQSRQQDR 75 (250)
Q Consensus 9 Rr~Rt~FT~~Ql~eLEk~f~~~~~~y~~~~~rq~LA~~f~lS~~RaGK~~Vq~~QVk~WFQNRR~k~ 75 (250)
|+.|+.||.+|+..||..|.. +.||+...++.||..+|++. .||++||||||.+.
T Consensus 1 kr~r~~~t~~q~~~L~~~f~~--~~~p~~~~~~~la~~l~l~~----------~~V~~WF~nrR~k~ 55 (57)
T PF00046_consen 1 KRKRTRFTKEQLKVLEEYFQE--NPYPSKEEREELAKELGLTE----------RQVKNWFQNRRRKE 55 (57)
T ss_dssp SSSSSSSSHHHHHHHHHHHHH--SSSCHHHHHHHHHHHHTSSH----------HHHHHHHHHHHHHH
T ss_pred CcCCCCCCHHHHHHHHHHHHH--hccccccccccccccccccc----------cccccCHHHhHHHh
Confidence 468999999999999999999 79999999999999999998 99999999999764
No 9
>KOG0850 consensus Transcription factor DLX and related proteins with LIM Zn-binding and HOX domains [Transcription]
Probab=99.53 E-value=1.1e-14 Score=131.31 Aligned_cols=57 Identities=21% Similarity=0.342 Sum_probs=54.0
Q ss_pred CCCCCccCCHHHHHHHHHHHHhhCCCCCCHHHHHHHHHHhCCCCcCCCCCccchhHHHHHHhhhcccCC
Q 025634 8 QRSVFTGFTKTELEKMEKLLMESKDDLLSKEFCQKIAKSFSCSAGRAGKPVVKWTEVQSWFQSRQQDRP 76 (250)
Q Consensus 8 ~Rr~Rt~FT~~Ql~eLEk~f~~~~~~y~~~~~rq~LA~~f~lS~~RaGK~~Vq~~QVk~WFQNRR~k~~ 76 (250)
-|++||.|+..||+.|-+.|++ .+||...+|.+||..||||. +||||||||||.|.+
T Consensus 122 ~RKPRTIYSS~QLqaL~rRFQk--TQYLALPERAeLAAsLGLTQ----------TQVKIWFQNrRSK~K 178 (245)
T KOG0850|consen 122 VRKPRTIYSSLQLQALNRRFQQ--TQYLALPERAELAASLGLTQ----------TQVKIWFQNRRSKFK 178 (245)
T ss_pred ccCCcccccHHHHHHHHHHHhh--cchhcCcHHHHHHHHhCCch----------hHhhhhhhhhHHHHH
Confidence 4668999999999999999999 89999999999999999998 999999999998865
No 10
>KOG2251 consensus Homeobox transcription factor [Transcription]
Probab=99.49 E-value=4.6e-14 Score=126.40 Aligned_cols=60 Identities=25% Similarity=0.399 Sum_probs=56.1
Q ss_pred CCCCCCCCccCCHHHHHHHHHHHHhhCCCCCCHHHHHHHHHHhCCCCcCCCCCccchhHHHHHHhhhcccCC
Q 025634 5 RPRQRSVFTGFTKTELEKMEKLLMESKDDLLSKEFCQKIAKSFSCSAGRAGKPVVKWTEVQSWFQSRQQDRP 76 (250)
Q Consensus 5 r~~~Rr~Rt~FT~~Ql~eLEk~f~~~~~~y~~~~~rq~LA~~f~lS~~RaGK~~Vq~~QVk~WFQNRR~k~~ 76 (250)
..++||-||.||-.|+.+||++|.+ ++|||...|++||.++||.+ .+||+||.|||+|++
T Consensus 34 pRkqRRERTtFtr~QlevLe~LF~k--TqYPDv~~rEelAlklnLpe----------SrVqVWFKNRRAK~r 93 (228)
T KOG2251|consen 34 PRKQRRERTTFTRKQLEVLEALFAK--TQYPDVFMREELALKLNLPE----------SRVQVWFKNRRAKCR 93 (228)
T ss_pred chhcccccceecHHHHHHHHHHHHh--hcCccHHHHHHHHHHhCCch----------hhhhhhhccccchhh
Confidence 3457889999999999999999999 89999999999999999998 889999999999974
No 11
>smart00389 HOX Homeodomain. DNA-binding factors that are involved in the transcriptional regulation of key developmental processes
Probab=99.48 E-value=7.8e-14 Score=96.32 Aligned_cols=54 Identities=30% Similarity=0.456 Sum_probs=50.4
Q ss_pred CCCccCCHHHHHHHHHHHHhhCCCCCCHHHHHHHHHHhCCCCcCCCCCccchhHHHHHHhhhcccC
Q 025634 10 SVFTGFTKTELEKMEKLLMESKDDLLSKEFCQKIAKSFSCSAGRAGKPVVKWTEVQSWFQSRQQDR 75 (250)
Q Consensus 10 r~Rt~FT~~Ql~eLEk~f~~~~~~y~~~~~rq~LA~~f~lS~~RaGK~~Vq~~QVk~WFQNRR~k~ 75 (250)
+.|+.||++|+..||..|.. +.||+...++.||..+|++. +||++||+|||++.
T Consensus 2 k~r~~~~~~~~~~L~~~f~~--~~~P~~~~~~~la~~~~l~~----------~qV~~WF~nrR~~~ 55 (56)
T smart00389 2 RKRTSFTPEQLEELEKEFQK--NPYPSREEREELAAKLGLSE----------RQVKVWFQNRRAKW 55 (56)
T ss_pred CCCCcCCHHHHHHHHHHHHh--CCCCCHHHHHHHHHHHCcCH----------HHHHHhHHHHhhcc
Confidence 46788999999999999999 67999999999999999997 99999999999764
No 12
>KOG0485 consensus Transcription factor NKX-5.1/HMX1, contains HOX domain [Transcription]
Probab=99.46 E-value=1.5e-14 Score=130.11 Aligned_cols=61 Identities=23% Similarity=0.363 Sum_probs=57.2
Q ss_pred CCCCCCccCCHHHHHHHHHHHHhhCCCCCCHHHHHHHHHHhCCCCcCCCCCccchhHHHHHHhhhcccCCCCC
Q 025634 7 RQRSVFTGFTKTELEKMEKLLMESKDDLLSKEFCQKIAKSFSCSAGRAGKPVVKWTEVQSWFQSRQQDRPTKV 79 (250)
Q Consensus 7 ~~Rr~Rt~FT~~Ql~eLEk~f~~~~~~y~~~~~rq~LA~~f~lS~~RaGK~~Vq~~QVk~WFQNRR~k~~~~~ 79 (250)
|.+++||.|+.+||..||-.|+- .+||+..+|-.||.+|.|++ +||||||||||.||+.+.
T Consensus 103 RKKktRTvFSraQV~qLEs~Fe~--krYLSsaeRa~LA~sLqLTE----------TQVKIWFQNRRnKwKRq~ 163 (268)
T KOG0485|consen 103 RKKKTRTVFSRAQVFQLESTFEL--KRYLSSAERAGLAASLQLTE----------TQVKIWFQNRRNKWKRQY 163 (268)
T ss_pred ccccchhhhhHHHHHHHHHHHHH--HhhhhHHHHhHHHHhhhhhh----------hhhhhhhhhhhHHHHHHH
Confidence 67788999999999999999999 68999999999999999998 999999999999997554
No 13
>KOG0493 consensus Transcription factor Engrailed, contains HOX domain [General function prediction only]
Probab=99.45 E-value=6.2e-14 Score=129.02 Aligned_cols=69 Identities=16% Similarity=0.326 Sum_probs=58.7
Q ss_pred CCCCccCCHHHHHHHHHHHHhhCCCCCCHHHHHHHHHHhCCCCcCCCCCccchhHHHHHHhhhcccCCCCC-CCCCCCCC
Q 025634 9 RSVFTGFTKTELEKMEKLLMESKDDLLSKEFCQKIAKSFSCSAGRAGKPVVKWTEVQSWFQSRQQDRPTKV-TSSTNESK 87 (250)
Q Consensus 9 Rr~Rt~FT~~Ql~eLEk~f~~~~~~y~~~~~rq~LA~~f~lS~~RaGK~~Vq~~QVk~WFQNRR~k~~~~~-~~~~~~~~ 87 (250)
+|+||.||.+||++|...|++ |+||+...||+||.+|+|.+ .||||||||+|+|.+.-. +..+++..
T Consensus 247 KRPRTAFtaeQL~RLK~EF~e--nRYlTEqRRQ~La~ELgLNE----------sQIKIWFQNKRAKiKKsTgskn~la~~ 314 (342)
T KOG0493|consen 247 KRPRTAFTAEQLQRLKAEFQE--NRYLTEQRRQELAQELGLNE----------SQIKIWFQNKRAKIKKSTGSKNRLALH 314 (342)
T ss_pred cCccccccHHHHHHHHHHHhh--hhhHHHHHHHHHHHHhCcCH----------HHhhHHhhhhhhhhhhccCCCCchhhh
Confidence 458999999999999999999 89999999999999999998 999999999999987322 23344444
Q ss_pred CC
Q 025634 88 KG 89 (250)
Q Consensus 88 ~~ 89 (250)
.+
T Consensus 315 lm 316 (342)
T KOG0493|consen 315 LM 316 (342)
T ss_pred hh
Confidence 43
No 14
>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=99.42 E-value=1.7e-13 Score=99.98 Aligned_cols=52 Identities=15% Similarity=0.266 Sum_probs=49.3
Q ss_pred CCCCccCCHHHHHHHHHHHHhhCCCC----CCHHHHHHHHHHhCCCCcCCCCCccchhHHHHHHhhhc
Q 025634 9 RSVFTGFTKTELEKMEKLLMESKDDL----LSKEFCQKIAKSFSCSAGRAGKPVVKWTEVQSWFQSRQ 72 (250)
Q Consensus 9 Rr~Rt~FT~~Ql~eLEk~f~~~~~~y----~~~~~rq~LA~~f~lS~~RaGK~~Vq~~QVk~WFQNRR 72 (250)
||.||.||++|+.+||+.|+. ++| |+...+++||..+|+++ .+||+||||-.
T Consensus 2 kR~RT~Ft~~Q~~~Le~~fe~--~~y~~~~~~~~~r~~la~~lgl~~----------~vvKVWfqN~k 57 (58)
T TIGR01565 2 KRRRTKFTAEQKEKMRDFAEK--LGWKLKDKRREEVREFCEEIGVTR----------KVFKVWMHNNK 57 (58)
T ss_pred CCCCCCCCHHHHHHHHHHHHH--cCCCCCCCCHHHHHHHHHHhCCCH----------HHeeeecccCC
Confidence 568999999999999999999 789 99999999999999998 99999999964
No 15
>cd00086 homeodomain Homeodomain; DNA binding domains involved in the transcriptional regulation of key eukaryotic developmental processes; may bind to DNA as monomers or as homo- and/or heterodimers, in a sequence-specific manner.
Probab=99.42 E-value=3.7e-13 Score=93.21 Aligned_cols=55 Identities=29% Similarity=0.439 Sum_probs=51.4
Q ss_pred CCCccCCHHHHHHHHHHHHhhCCCCCCHHHHHHHHHHhCCCCcCCCCCccchhHHHHHHhhhcccCC
Q 025634 10 SVFTGFTKTELEKMEKLLMESKDDLLSKEFCQKIAKSFSCSAGRAGKPVVKWTEVQSWFQSRQQDRP 76 (250)
Q Consensus 10 r~Rt~FT~~Ql~eLEk~f~~~~~~y~~~~~rq~LA~~f~lS~~RaGK~~Vq~~QVk~WFQNRR~k~~ 76 (250)
+.++.|+.+|+..||+.|.. +.||+...++.||..+|++. +||++||+|||.+..
T Consensus 2 ~~r~~~~~~~~~~Le~~f~~--~~~P~~~~~~~la~~~~l~~----------~qV~~WF~nrR~~~~ 56 (59)
T cd00086 2 RKRTRFTPEQLEELEKEFEK--NPYPSREEREELAKELGLTE----------RQVKIWFQNRRAKLK 56 (59)
T ss_pred CCCCcCCHHHHHHHHHHHHh--CCCCCHHHHHHHHHHHCcCH----------HHHHHHHHHHHHHHh
Confidence 46789999999999999999 78999999999999999998 999999999998765
No 16
>KOG0491 consensus Transcription factor BSH, contains HOX domain [General function prediction only]
Probab=99.35 E-value=3e-13 Score=117.47 Aligned_cols=58 Identities=33% Similarity=0.496 Sum_probs=54.3
Q ss_pred CCCCCCccCCHHHHHHHHHHHHhhCCCCCCHHHHHHHHHHhCCCCcCCCCCccchhHHHHHHhhhcccCC
Q 025634 7 RQRSVFTGFTKTELEKMEKLLMESKDDLLSKEFCQKIAKSFSCSAGRAGKPVVKWTEVQSWFQSRQQDRP 76 (250)
Q Consensus 7 ~~Rr~Rt~FT~~Ql~eLEk~f~~~~~~y~~~~~rq~LA~~f~lS~~RaGK~~Vq~~QVk~WFQNRR~k~~ 76 (250)
+.|+.||.|+..|+.-||+.|+. .+||+-.++++||..||||+ +|||+||||||||.+
T Consensus 99 ~r~K~Rtvfs~~ql~~l~~rFe~--QrYLS~~e~~ELan~L~LS~----------~QVKTWFQNrRMK~K 156 (194)
T KOG0491|consen 99 RRRKARTVFSDPQLSGLEKRFER--QRYLSTPERQELANALSLSE----------TQVKTWFQNRRMKHK 156 (194)
T ss_pred HhhhhcccccCccccccHHHHhh--hhhcccHHHHHHHHHhhhhH----------HHHHHHHHHHHHHHH
Confidence 35567999999999999999999 78999999999999999998 999999999999975
No 17
>KOG0494 consensus Transcription factor CHX10 and related HOX domain proteins [General function prediction only]
Probab=99.33 E-value=8.4e-13 Score=121.49 Aligned_cols=57 Identities=26% Similarity=0.333 Sum_probs=53.0
Q ss_pred CCCCccCCHHHHHHHHHHHHhhCCCCCCHHHHHHHHHHhCCCCcCCCCCccchhHHHHHHhhhcccCCC
Q 025634 9 RSVFTGFTKTELEKMEKLLMESKDDLLSKEFCQKIAKSFSCSAGRAGKPVVKWTEVQSWFQSRQQDRPT 77 (250)
Q Consensus 9 Rr~Rt~FT~~Ql~eLEk~f~~~~~~y~~~~~rq~LA~~f~lS~~RaGK~~Vq~~QVk~WFQNRR~k~~~ 77 (250)
|+.||.||..||++||+.|++ .+|||..-|+-||.++.|.+ ..|++||||||+||+.
T Consensus 142 Rh~RTiFT~~Qle~LEkaFke--aHYPDv~Are~la~ktelpE----------DRIqVWfQNRRAKWRk 198 (332)
T KOG0494|consen 142 RHFRTIFTSYQLEELEKAFKE--AHYPDVYAREMLADKTELPE----------DRIQVWFQNRRAKWRK 198 (332)
T ss_pred ccccchhhHHHHHHHHHHHhh--ccCccHHHHHHHhhhccCch----------hhhhHHhhhhhHHhhh
Confidence 335999999999999999999 79999999999999999998 8899999999999973
No 18
>KOG0844 consensus Transcription factor EVX1, contains HOX domain [Transcription]
Probab=99.30 E-value=5e-13 Score=125.20 Aligned_cols=57 Identities=23% Similarity=0.459 Sum_probs=53.2
Q ss_pred CCCCCccCCHHHHHHHHHHHHhhCCCCCCHHHHHHHHHHhCCCCcCCCCCccchhHHHHHHhhhcccCC
Q 025634 8 QRSVFTGFTKTELEKMEKLLMESKDDLLSKEFCQKIAKSFSCSAGRAGKPVVKWTEVQSWFQSRQQDRP 76 (250)
Q Consensus 8 ~Rr~Rt~FT~~Ql~eLEk~f~~~~~~y~~~~~rq~LA~~f~lS~~RaGK~~Vq~~QVk~WFQNRR~k~~ 76 (250)
-||.||.||.+||.+|||.|-. +.|.++..|-+||..|||.+ +-||+||||||||.+
T Consensus 181 mRRYRTAFTReQIaRLEKEFyr--ENYVSRprRcELAAaLNLPE----------tTIKVWFQNRRMKDK 237 (408)
T KOG0844|consen 181 MRRYRTAFTREQIARLEKEFYR--ENYVSRPRRCELAAALNLPE----------TTIKVWFQNRRMKDK 237 (408)
T ss_pred HHHHHhhhhHHHHHHHHHHHHH--hccccCchhhhHHHhhCCCc----------ceeehhhhhchhhhh
Confidence 3679999999999999999998 66999999999999999998 999999999999964
No 19
>KOG0848 consensus Transcription factor Caudal, contains HOX domain [Transcription]
Probab=99.28 E-value=7.6e-13 Score=121.94 Aligned_cols=54 Identities=19% Similarity=0.301 Sum_probs=51.3
Q ss_pred CCccCCHHHHHHHHHHHHhhCCCCCCHHHHHHHHHHhCCCCcCCCCCccchhHHHHHHhhhcccCC
Q 025634 11 VFTGFTKTELEKMEKLLMESKDDLLSKEFCQKIAKSFSCSAGRAGKPVVKWTEVQSWFQSRQQDRP 76 (250)
Q Consensus 11 ~Rt~FT~~Ql~eLEk~f~~~~~~y~~~~~rq~LA~~f~lS~~RaGK~~Vq~~QVk~WFQNRR~k~~ 76 (250)
.|..+|..|-+||||+|.- ++|++....-+||..|+||| +||||||||||+|.+
T Consensus 202 YRvVYTDhQRLELEKEfh~--SryITirRKSELA~~LgLsE----------RQVKIWFQNRRAKER 255 (317)
T KOG0848|consen 202 YRVVYTDHQRLELEKEFHT--SRYITIRRKSELAATLGLSE----------RQVKIWFQNRRAKER 255 (317)
T ss_pred eeEEecchhhhhhhhhhcc--ccceeeehhHHHHHhhCccH----------hhhhHhhhhhhHHHH
Confidence 4788999999999999999 79999999999999999998 999999999999975
No 20
>KOG0483 consensus Transcription factor HEX, contains HOX and HALZ domains [Transcription]
Probab=99.28 E-value=2.9e-12 Score=113.18 Aligned_cols=57 Identities=26% Similarity=0.356 Sum_probs=52.8
Q ss_pred CCccCCHHHHHHHHHHHHhhCCCCCCHHHHHHHHHHhCCCCcCCCCCccchhHHHHHHhhhcccCCCCC
Q 025634 11 VFTGFTKTELEKMEKLLMESKDDLLSKEFCQKIAKSFSCSAGRAGKPVVKWTEVQSWFQSRQQDRPTKV 79 (250)
Q Consensus 11 ~Rt~FT~~Ql~eLEk~f~~~~~~y~~~~~rq~LA~~f~lS~~RaGK~~Vq~~QVk~WFQNRR~k~~~~~ 79 (250)
...+||.+|+..||+.|+. +.||.+..+.+||..|||++ .||.+||||||++|+.|-
T Consensus 53 kk~Rlt~eQ~~~LE~~F~~--~~~L~p~~K~~LAk~LgL~p----------RQVavWFQNRRARwK~kq 109 (198)
T KOG0483|consen 53 KKRRLTSEQVKFLEKSFES--EKKLEPERKKKLAKELGLQP----------RQVAVWFQNRRARWKTKQ 109 (198)
T ss_pred ccccccHHHHHHhHHhhcc--ccccChHHHHHHHHhhCCCh----------hHHHHHHhhccccccchh
Confidence 4568999999999999999 67999999999999999998 999999999999998663
No 21
>COG5576 Homeodomain-containing transcription factor [Transcription]
Probab=99.05 E-value=1.6e-10 Score=98.76 Aligned_cols=61 Identities=20% Similarity=0.218 Sum_probs=55.9
Q ss_pred CCCCCCCccCCHHHHHHHHHHHHhhCCCCCCHHHHHHHHHHhCCCCcCCCCCccchhHHHHHHhhhcccCCCC
Q 025634 6 PRQRSVFTGFTKTELEKMEKLLMESKDDLLSKEFCQKIAKSFSCSAGRAGKPVVKWTEVQSWFQSRQQDRPTK 78 (250)
Q Consensus 6 ~~~Rr~Rt~FT~~Ql~eLEk~f~~~~~~y~~~~~rq~LA~~f~lS~~RaGK~~Vq~~QVk~WFQNRR~k~~~~ 78 (250)
+..++.|++-|..|+.-||+.|+. +.||+...|++||..+|+++ +-||+||||||++.+.+
T Consensus 49 ~~~~~~r~R~t~~Q~~vL~~~F~i--~p~Ps~~~r~~L~~~lnm~~----------ksVqIWFQNkR~~~k~~ 109 (156)
T COG5576 49 SPPKSKRRRTTDEQLMVLEREFEI--NPYPSSITRIKLSLLLNMPP----------KSVQIWFQNKRAKEKKK 109 (156)
T ss_pred CcCcccceechHHHHHHHHHHhcc--CCCCCHHHHHHHHHhcCCCh----------hhhhhhhchHHHHHHHh
Confidence 446668999999999999999999 89999999999999999998 99999999999997644
No 22
>KOG0486 consensus Transcription factor PTX1, contains HOX domain [Transcription]
Probab=99.05 E-value=7.2e-11 Score=110.74 Aligned_cols=58 Identities=22% Similarity=0.350 Sum_probs=55.9
Q ss_pred CCCCCCccCCHHHHHHHHHHHHhhCCCCCCHHHHHHHHHHhCCCCcCCCCCccchhHHHHHHhhhcccCC
Q 025634 7 RQRSVFTGFTKTELEKMEKLLMESKDDLLSKEFCQKIAKSFSCSAGRAGKPVVKWTEVQSWFQSRQQDRP 76 (250)
Q Consensus 7 ~~Rr~Rt~FT~~Ql~eLEk~f~~~~~~y~~~~~rq~LA~~f~lS~~RaGK~~Vq~~QVk~WFQNRR~k~~ 76 (250)
++||.||-||..|++|||..|+. |.|||-+.|++||-..||++ +.|.+||.|||+||+
T Consensus 111 KqrrQrthFtSqqlqele~tF~r--NrypdMstrEEIavwtNlTE----------~rvrvwfknrrakwr 168 (351)
T KOG0486|consen 111 KQRRQRTHFTSQQLQELEATFQR--NRYPDMSTREEIAVWTNLTE----------ARVRVWFKNRRAKWR 168 (351)
T ss_pred hhhhhhhhhHHHHHHHHHHHHhh--ccCCccchhhHHHhhccccc----------hhhhhhcccchhhhh
Confidence 57889999999999999999999 89999999999999999998 999999999999996
No 23
>KOG0490 consensus Transcription factor, contains HOX domain [General function prediction only]
Probab=99.03 E-value=7e-11 Score=100.99 Aligned_cols=61 Identities=21% Similarity=0.301 Sum_probs=56.4
Q ss_pred CCCCCCCccCCHHHHHHHHHHHHhhCCCCCCHHHHHHHHHHhCCCCcCCCCCccchhHHHHHHhhhcccCCCC
Q 025634 6 PRQRSVFTGFTKTELEKMEKLLMESKDDLLSKEFCQKIAKSFSCSAGRAGKPVVKWTEVQSWFQSRQQDRPTK 78 (250)
Q Consensus 6 ~~~Rr~Rt~FT~~Ql~eLEk~f~~~~~~y~~~~~rq~LA~~f~lS~~RaGK~~Vq~~QVk~WFQNRR~k~~~~ 78 (250)
..+|+.||.||..|+.+||++|.. .+||+...++.||..+++++ ..|++||||||+|+...
T Consensus 58 ~~~rr~rt~~~~~ql~~ler~f~~--~h~Pd~~~r~~la~~~~~~e----------~rVqvwFqnrrak~r~~ 118 (235)
T KOG0490|consen 58 FSKRCARCKFTISQLDELERAFEK--VHLPCFACRECLALLLTGDE----------FRVQVWFQNRRAKDRKE 118 (235)
T ss_pred ccccccCCCCCcCHHHHHHHhhcC--CCcCccchHHHHhhcCCCCe----------eeeehhhhhhcHhhhhh
Confidence 346778999999999999999999 69999999999999999998 99999999999999743
No 24
>KOG0847 consensus Transcription factor, contains HOX domain [Transcription]
Probab=98.97 E-value=4.5e-10 Score=101.76 Aligned_cols=57 Identities=19% Similarity=0.363 Sum_probs=53.7
Q ss_pred CCccCCHHHHHHHHHHHHhhCCCCCCHHHHHHHHHHhCCCCcCCCCCccchhHHHHHHhhhcccCCCCC
Q 025634 11 VFTGFTKTELEKMEKLLMESKDDLLSKEFCQKIAKSFSCSAGRAGKPVVKWTEVQSWFQSRQQDRPTKV 79 (250)
Q Consensus 11 ~Rt~FT~~Ql~eLEk~f~~~~~~y~~~~~rq~LA~~f~lS~~RaGK~~Vq~~QVk~WFQNRR~k~~~~~ 79 (250)
.|..|+-.||..||+-|++ .+||....|-+||..+|+++ .||++||||||.||+.|-
T Consensus 170 srPTf~g~qi~~le~~feq--tkylaG~~ra~lA~~lgmte----------SqvkVWFQNRRTKWRKkh 226 (288)
T KOG0847|consen 170 SRPTFTGHQIYQLERKFEQ--TKYLAGADRAQLAQELNMTE----------SQVKVWFQNRRTKWRKKH 226 (288)
T ss_pred cCCCccchhhhhhhhhhhh--hhcccchhHHHhhccccccH----------HHHHHHHhcchhhhhhhh
Confidence 5888999999999999999 78999999999999999998 999999999999998554
No 25
>KOG4577 consensus Transcription factor LIM3, contains LIM and HOX domains [Transcription]
Probab=98.69 E-value=1.1e-08 Score=95.93 Aligned_cols=58 Identities=17% Similarity=0.291 Sum_probs=53.6
Q ss_pred CCCCCCCccCCHHHHHHHHHHHHhhCCCCCCHHHHHHHHHHhCCCCcCCCCCccchhHHHHHHhhhcccC
Q 025634 6 PRQRSVFTGFTKTELEKMEKLLMESKDDLLSKEFCQKIAKSFSCSAGRAGKPVVKWTEVQSWFQSRQQDR 75 (250)
Q Consensus 6 ~~~Rr~Rt~FT~~Ql~eLEk~f~~~~~~y~~~~~rq~LA~~f~lS~~RaGK~~Vq~~QVk~WFQNRR~k~ 75 (250)
..++|+||..|..||+-|...|.. ..-|.+-+|++|+...||.. ..||+||||||+|.
T Consensus 165 ~~nKRPRTTItAKqLETLK~AYn~--SpKPARHVREQLsseTGLDM----------RVVQVWFQNRRAKE 222 (383)
T KOG4577|consen 165 ASNKRPRTTITAKQLETLKQAYNT--SPKPARHVREQLSSETGLDM----------RVVQVWFQNRRAKE 222 (383)
T ss_pred cccCCCcceeeHHHHHHHHHHhcC--CCchhHHHHHHhhhccCcce----------eehhhhhhhhhHHH
Confidence 457789999999999999999998 67899999999999999996 89999999999985
No 26
>KOG0849 consensus Transcription factor PRD and related proteins, contain PAX and HOX domains [Transcription]
Probab=98.67 E-value=1.9e-08 Score=95.26 Aligned_cols=64 Identities=23% Similarity=0.309 Sum_probs=57.3
Q ss_pred CCCCCCCCCCccCCHHHHHHHHHHHHhhCCCCCCHHHHHHHHHHhCCCCcCCCCCccchhHHHHHHhhhcccCCCC
Q 025634 3 RLRPRQRSVFTGFTKTELEKMEKLLMESKDDLLSKEFCQKIAKSFSCSAGRAGKPVVKWTEVQSWFQSRQQDRPTK 78 (250)
Q Consensus 3 r~r~~~Rr~Rt~FT~~Ql~eLEk~f~~~~~~y~~~~~rq~LA~~f~lS~~RaGK~~Vq~~QVk~WFQNRR~k~~~~ 78 (250)
.+-+..||.||.||+.|+..||+.|+. ++||+...|++||.+.++++ ..|++||||||++++..
T Consensus 171 ~~~~~~rr~rtsft~~Q~~~le~~f~r--t~yP~i~~Re~La~~i~l~e----------~riqvwf~nrra~~rr~ 234 (354)
T KOG0849|consen 171 ALQRGGRRNRTSFSPSQLEALEECFQR--TPYPDIVGRETLAKETGLPE----------PRVQVWFQNRRAKWRRQ 234 (354)
T ss_pred cccccccccccccccchHHHHHHHhcC--CCCCchhhHHHHhhhccCCc----------hHHHHHHhhhhhhhhhc
Confidence 344556778999999999999999999 67999999999999999998 99999999999988643
No 27
>KOG0775 consensus Transcription factor SIX and related HOX domain proteins [Transcription]
Probab=98.09 E-value=7.8e-06 Score=76.17 Aligned_cols=53 Identities=17% Similarity=0.346 Sum_probs=44.5
Q ss_pred CCHHHHHHHHHHHHhhCCCCCCHHHHHHHHHHhCCCCcCCCCCccchhHHHHHHhhhcccCCCCC
Q 025634 15 FTKTELEKMEKLLMESKDDLLSKEFCQKIAKSFSCSAGRAGKPVVKWTEVQSWFQSRQQDRPTKV 79 (250)
Q Consensus 15 FT~~Ql~eLEk~f~~~~~~y~~~~~rq~LA~~f~lS~~RaGK~~Vq~~QVk~WFQNRR~k~~~~~ 79 (250)
|-..--.-|-..|.+ +.||++.+..+||+..+|+. +||-|||.|||++.++..
T Consensus 183 FKekSR~~LrewY~~--~~YPsp~eKReLA~aTgLt~----------tQVsNWFKNRRQRDRa~~ 235 (304)
T KOG0775|consen 183 FKEKSRSLLREWYLQ--NPYPSPREKRELAEATGLTI----------TQVSNWFKNRRQRDRAAA 235 (304)
T ss_pred hhHhhHHHHHHHHhc--CCCCChHHHHHHHHHhCCch----------hhhhhhhhhhhhhhhhcc
Confidence 333334678888887 79999999999999999998 999999999998877443
No 28
>KOG3802 consensus Transcription factor OCT-1, contains POU and HOX domains [Transcription]
Probab=98.09 E-value=1.9e-06 Score=83.18 Aligned_cols=58 Identities=22% Similarity=0.313 Sum_probs=53.5
Q ss_pred CCCCCCccCCHHHHHHHHHHHHhhCCCCCCHHHHHHHHHHhCCCCcCCCCCccchhHHHHHHhhhcccCC
Q 025634 7 RQRSVFTGFTKTELEKMEKLLMESKDDLLSKEFCQKIAKSFSCSAGRAGKPVVKWTEVQSWFQSRQQDRP 76 (250)
Q Consensus 7 ~~Rr~Rt~FT~~Ql~eLEk~f~~~~~~y~~~~~rq~LA~~f~lS~~RaGK~~Vq~~QVk~WFQNRR~k~~ 76 (250)
|.|++||.|+......||+.|.. |.-|+..++-.||++|+|-- ..|.+||=|||.|.+
T Consensus 293 RkRKKRTSie~~vr~aLE~~F~~--npKPt~qEIt~iA~~L~leK----------EVVRVWFCNRRQkeK 350 (398)
T KOG3802|consen 293 RKRKKRTSIEVNVRGALEKHFLK--NPKPTSQEITHIAESLQLEK----------EVVRVWFCNRRQKEK 350 (398)
T ss_pred cccccccceeHHHHHHHHHHHHh--CCCCCHHHHHHHHHHhcccc----------ceEEEEeeccccccc
Confidence 57788999999999999999999 78999999999999999995 558899999999987
No 29
>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=3.7e-06 Score=57.14 Aligned_cols=37 Identities=24% Similarity=0.369 Sum_probs=30.1
Q ss_pred HHhhCCCCCCHHHHHHHHHHhCCCCcCCCCCccchhHHHHHHhhhcc
Q 025634 27 LMESKDDLLSKEFCQKIAKSFSCSAGRAGKPVVKWTEVQSWFQSRQQ 73 (250)
Q Consensus 27 f~~~~~~y~~~~~rq~LA~~f~lS~~RaGK~~Vq~~QVk~WFQNRR~ 73 (250)
++...+.||+.++.++||...|+|. +||.+||-|.|.
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 3445689999999999999999998 999999999884
No 30
>KOG2252 consensus CCAAT displacement protein and related homeoproteins [Transcription]
Probab=97.77 E-value=8.8e-05 Score=74.32 Aligned_cols=58 Identities=14% Similarity=0.255 Sum_probs=52.7
Q ss_pred CCCCCCCccCCHHHHHHHHHHHHhhCCCCCCHHHHHHHHHHhCCCCcCCCCCccchhHHHHHHhhhcccC
Q 025634 6 PRQRSVFTGFTKTELEKMEKLLMESKDDLLSKEFCQKIAKSFSCSAGRAGKPVVKWTEVQSWFQSRQQDR 75 (250)
Q Consensus 6 ~~~Rr~Rt~FT~~Ql~eLEk~f~~~~~~y~~~~~rq~LA~~f~lS~~RaGK~~Vq~~QVk~WFQNRR~k~ 75 (250)
+.++++|..||..|..-|-.+|++ +++|+++.++.|+..|||.. +-|.|||-|=|.+.
T Consensus 418 ~~~KKPRlVfTd~QkrTL~aiFke--~~RPS~Emq~tIS~qL~L~~----------sTV~NfFmNaRRRs 475 (558)
T KOG2252|consen 418 LQTKKPRLVFTDIQKRTLQAIFKE--NKRPSREMQETISQQLNLEL----------STVINFFMNARRRS 475 (558)
T ss_pred ccCCCceeeecHHHHHHHHHHHhc--CCCCCHHHHHHHHHHhCCcH----------HHHHHHHHhhhhhc
Confidence 346678999999999999999999 89999999999999999998 89999999976553
No 31
>KOG0490 consensus Transcription factor, contains HOX domain [General function prediction only]
Probab=97.50 E-value=6.3e-05 Score=64.40 Aligned_cols=59 Identities=24% Similarity=0.345 Sum_probs=53.9
Q ss_pred CCCCCCCccCCHHHHHHHHHHHHhhCCCCCCHHHHHHHHHHhCCCCcCCCCCccchhHHHHHHhhhcccCC
Q 025634 6 PRQRSVFTGFTKTELEKMEKLLMESKDDLLSKEFCQKIAKSFSCSAGRAGKPVVKWTEVQSWFQSRQQDRP 76 (250)
Q Consensus 6 ~~~Rr~Rt~FT~~Ql~eLEk~f~~~~~~y~~~~~rq~LA~~f~lS~~RaGK~~Vq~~QVk~WFQNRR~k~~ 76 (250)
+..++.++.|+..|+..|+..|.. +.+|+...++.||..+++++ ..|++||||+|.+..
T Consensus 151 ~~~~~~~~~~~~~~~~~~~~~~~~--~~~P~~~~~~~l~~~~~~~~----------~~~q~~~~~~~~~~~ 209 (235)
T KOG0490|consen 151 KKPRRPRTTFTENQLEVLETVFRA--TPKPDADDREQLAEETGLSE----------RVIQVWFQNRRAKLR 209 (235)
T ss_pred cccCCCccccccchhHhhhhcccC--CCCCchhhHHHHHHhcCCCh----------hhhhhhcccHHHHHH
Confidence 345668999999999999999999 78999999999999999997 889999999998876
No 32
>KOG0774 consensus Transcription factor PBX and related HOX domain proteins [Transcription]
Probab=97.38 E-value=0.00047 Score=64.49 Aligned_cols=58 Identities=19% Similarity=0.349 Sum_probs=51.7
Q ss_pred CCCCCccCCHHHHHHHHHHHHhh-CCCCCCHHHHHHHHHHhCCCCcCCCCCccchhHHHHHHhhhcccC
Q 025634 8 QRSVFTGFTKTELEKMEKLLMES-KDDLLSKEFCQKIAKSFSCSAGRAGKPVVKWTEVQSWFQSRQQDR 75 (250)
Q Consensus 8 ~Rr~Rt~FT~~Ql~eLEk~f~~~-~~~y~~~~~rq~LA~~f~lS~~RaGK~~Vq~~QVk~WFQNRR~k~ 75 (250)
.||.|..|+..--+.|-.-|..| +|.||+.+..++||.+-|++- .||-+||-|+|...
T Consensus 188 arRKRRNFsK~aTeiLneyF~~h~~nPYPSee~K~eLAkqCnItv----------sQvsnwfgnkrIry 246 (334)
T KOG0774|consen 188 ARRKRRNFSKQATEILNEYFYSHLSNPYPSEEAKEELAKQCNITV----------SQVSNWFGNKRIRY 246 (334)
T ss_pred HHHhhcccchhHHHHHHHHHHHhcCCCCCcHHHHHHHHHHcCcee----------hhhccccccceeeh
Confidence 56788899999999998888766 889999999999999999998 99999999997654
No 33
>PF15057 DUF4537: Domain of unknown function (DUF4537)
Probab=96.27 E-value=0.042 Score=45.22 Aligned_cols=104 Identities=21% Similarity=0.270 Sum_probs=67.9
Q ss_pred ecccCCCceeeeeeeheeeecccCcceEEEEecCCCCCcccceeccccccccCCCCCcccccccccCceEEEEeeeCCcc
Q 025634 123 ARSSKDGAWYDVDMFLAHRFLDCGEAEVRVRFVGFGADEDEWVNVKNAVRERSVPLEPSDCHKLKVGGHVLCFQERRDQG 202 (250)
Q Consensus 123 Ars~~D~AWYdV~~fl~hR~~~~ge~ev~Vrf~gFg~eeDEw~~v~~~~R~rS~p~e~~eC~~v~~G~~v~cf~~~~~~~ 202 (250)
||+.+||-+|--.+- ..+..| .+.|.| .+.+-+.+... -=|++.++.|+.|.+||-||+-.+..+ .
T Consensus 6 AR~~~DG~YY~GtV~---~~~~~~--~~lV~f---~~~~~~~v~~~-----~iI~~~~~~~~~L~~GD~VLA~~~~~~-~ 71 (124)
T PF15057_consen 6 ARREEDGFYYPGTVK---KCVSSG--QFLVEF---DDGDTQEVPIS-----DIIALSDAMRHSLQVGDKVLAPWEPDD-C 71 (124)
T ss_pred EeeCCCCcEEeEEEE---EccCCC--EEEEEE---CCCCEEEeChH-----HeEEccCcccCcCCCCCEEEEecCcCC-C
Confidence 799999999887663 223334 889997 33333333322 235788888999999999999976554 5
Q ss_pred eeEeeEEeeeeeccCCCCceeeEEEEEEecCCcccccccccc
Q 025634 203 IHYDAHIAEIHRRMHDIRGCRCLFLVRYNHDNTEERVRLRRL 244 (250)
Q Consensus 203 ~yyDA~V~~v~r~~Hd~~~C~C~F~Vr~~h~~~ee~v~~~~~ 244 (250)
.|+-|.|+..-.++ ....=.++|.+-.|. ...||...+
T Consensus 72 ~Y~Pg~V~~~~~~~---~~~~~~~~V~f~ng~-~~~vp~~~~ 109 (124)
T PF15057_consen 72 RYGPGTVIAGPERR---ASEDKEYTVRFYNGK-TAKVPRGEV 109 (124)
T ss_pred EEeCEEEEECcccc---ccCCceEEEEEECCC-CCccchhhE
Confidence 59999999875544 222334566555443 444554443
No 34
>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=96.26 E-value=0.0084 Score=42.64 Aligned_cols=40 Identities=38% Similarity=0.752 Sum_probs=33.0
Q ss_pred CCCceeeeeeeheeeecccCcceEEEEecCCCCCcccceecc
Q 025634 127 KDGAWYDVDMFLAHRFLDCGEAEVRVRFVGFGADEDEWVNVK 168 (250)
Q Consensus 127 ~D~AWYdV~~fl~hR~~~~ge~ev~Vrf~gFg~eeDEw~~v~ 168 (250)
.+|.||...+. .-|. +.|..+..|||.|+..-.||||+..
T Consensus 12 ~~~~~y~A~I~-~~r~-~~~~~~YyVHY~g~nkR~DeWV~~~ 51 (55)
T PF11717_consen 12 KDGQWYEAKIL-DIRE-KNGEPEYYVHYQGWNKRLDEWVPES 51 (55)
T ss_dssp TTTEEEEEEEE-EEEE-CTTCEEEEEEETTSTGCC-EEEETT
T ss_pred CCCcEEEEEEE-EEEe-cCCCEEEEEEcCCCCCCceeeecHH
Confidence 69999999885 4454 5677899999999999999999864
No 35
>KOG1168 consensus Transcription factor ACJ6/BRN-3, contains POU and HOX domains [Transcription]
Probab=95.15 E-value=0.0032 Score=59.77 Aligned_cols=59 Identities=19% Similarity=0.240 Sum_probs=53.0
Q ss_pred CCCCCccCCHHHHHHHHHHHHhhCCCCCCHHHHHHHHHHhCCCCcCCCCCccchhHHHHHHhhhcccCCCC
Q 025634 8 QRSVFTGFTKTELEKMEKLLMESKDDLLSKEFCQKIAKSFSCSAGRAGKPVVKWTEVQSWFQSRQQDRPTK 78 (250)
Q Consensus 8 ~Rr~Rt~FT~~Ql~eLEk~f~~~~~~y~~~~~rq~LA~~f~lS~~RaGK~~Vq~~QVk~WFQNRR~k~~~~ 78 (250)
.+|.||....-|-..||..|.. +.-|+.+.+..||++|.|-- ..|.+||=|-|+|++..
T Consensus 309 kKRKRTSIAAPEKRsLEayFav--QPRPS~EkIAaIAekLDLKK----------NVVRVWFCNQRQKQKRm 367 (385)
T KOG1168|consen 309 KKRKRTSIAAPEKRSLEAYFAV--QPRPSGEKIAAIAEKLDLKK----------NVVRVWFCNQRQKQKRM 367 (385)
T ss_pred cccccccccCcccccHHHHhcc--CCCCchhHHHHHHHhhhhhh----------ceEEEEeeccHHHHHHh
Confidence 4568999999999999999999 78899999999999999996 67889999999998743
No 36
>KOG1146 consensus Homeobox protein [General function prediction only]
Probab=95.02 E-value=0.031 Score=61.30 Aligned_cols=56 Identities=14% Similarity=0.258 Sum_probs=51.8
Q ss_pred CCCCccCCHHHHHHHHHHHHhhCCCCCCHHHHHHHHHHhCCCCcCCCCCccchhHHHHHHhhhcccCC
Q 025634 9 RSVFTGFTKTELEKMEKLLMESKDDLLSKEFCQKIAKSFSCSAGRAGKPVVKWTEVQSWFQSRQQDRP 76 (250)
Q Consensus 9 Rr~Rt~FT~~Ql~eLEk~f~~~~~~y~~~~~rq~LA~~f~lS~~RaGK~~Vq~~QVk~WFQNRR~k~~ 76 (250)
|+.||.|+..||..|-.+|.. ..|+....++.|-..+.++. ..|+.||||-|.|..
T Consensus 904 ~a~~~~~~d~qlk~i~~~~~~--q~~~~~~~~E~l~~~~~~~~----------~~i~vw~qna~~~s~ 959 (1406)
T KOG1146|consen 904 RAYRTQESDLQLKIIKACYEA--QRTPTMQECEVLEEPIGLPK----------RVIQVWFQNARAKSK 959 (1406)
T ss_pred hhhccchhHHHHHHHHHHHhh--ccCChHHHHHhhcccccCCc----------chhHHhhhhhhhhhh
Confidence 457999999999999999999 89999999999999999997 778999999998875
No 37
>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=94.24 E-value=0.063 Score=36.48 Aligned_cols=36 Identities=36% Similarity=0.620 Sum_probs=30.8
Q ss_pred eeeeeeheeeeccc-CcceEEEEecCCCCCcccceec
Q 025634 132 YDVDMFLAHRFLDC-GEAEVRVRFVGFGADEDEWVNV 167 (250)
Q Consensus 132 YdV~~fl~hR~~~~-ge~ev~Vrf~gFg~eeDEw~~v 167 (250)
|.|.-.|.||.... |..+..|++.|++..+++|...
T Consensus 3 ~~ve~Il~~r~~~~~~~~~y~VkW~g~~~~~~tWe~~ 39 (55)
T cd00024 3 YEVEKILDHRKKKDGGEYEYLVKWKGYSYSEDTWEPE 39 (55)
T ss_pred ceEeeeeeeeecCCCCcEEEEEEECCCCCccCccccH
Confidence 55677789998775 7789999999999999999874
No 38
>PF04218 CENP-B_N: CENP-B N-terminal DNA-binding domain; InterPro: IPR006695 Centromere Protein B (CENP-B) is a DNA-binding protein localized to the centromere. Within the N-terminal 125 residues, there is a DNA-binding region, which binds to a corresponding 17bp CENP-B box sequence. CENP-B dimers either bind two separate DNA molecules or alternatively, they may bind two CENP-B boxes on one DNA molecule, with the intervening stretch of DNA forming a loop structure. The CENP-B DNA-binding domain consists of two repeating domains, RP1 and RP2. This family corresponds to RP1 has been shown to consist of four helices in a helix-turn-helix structure [].; GO: 0003677 DNA binding, 0000775 chromosome, centromeric region; PDB: 1BW6_A 1HLV_A 2ELH_A.
Probab=93.65 E-value=0.18 Score=35.72 Aligned_cols=47 Identities=21% Similarity=0.263 Sum_probs=35.9
Q ss_pred CCCCccCCHHHHHHHHHHHHhhCCCCCCHHHHHHHHHHhCCCCcCCCCCccchhHHHHHHhhhc
Q 025634 9 RSVFTGFTKTELEKMEKLLMESKDDLLSKEFCQKIAKSFSCSAGRAGKPVVKWTEVQSWFQSRQ 72 (250)
Q Consensus 9 Rr~Rt~FT~~Ql~eLEk~f~~~~~~y~~~~~rq~LA~~f~lS~~RaGK~~Vq~~QVk~WFQNRR 72 (250)
+|.|..+|.+|-.++=+.++. +. ...+||..||++. .+|..|..||-
T Consensus 1 krkR~~LTl~eK~~iI~~~e~--g~-----s~~~ia~~fgv~~----------sTv~~I~K~k~ 47 (53)
T PF04218_consen 1 KRKRKSLTLEEKLEIIKRLEE--GE-----SKRDIAREFGVSR----------STVSTILKNKD 47 (53)
T ss_dssp SSSSSS--HHHHHHHHHHHHC--TT------HHHHHHHHT--C----------CHHHHHHHCHH
T ss_pred CCCCccCCHHHHHHHHHHHHc--CC-----CHHHHHHHhCCCH----------HHHHHHHHhHH
Confidence 357899999999888888877 33 5889999999998 99999999973
No 39
>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=93.32 E-value=0.097 Score=36.17 Aligned_cols=37 Identities=30% Similarity=0.623 Sum_probs=32.0
Q ss_pred eeeeeeheeeecccCc--ceEEEEecCCCCCcccceecc
Q 025634 132 YDVDMFLAHRFLDCGE--AEVRVRFVGFGADEDEWVNVK 168 (250)
Q Consensus 132 YdV~~fl~hR~~~~ge--~ev~Vrf~gFg~eeDEw~~v~ 168 (250)
|-|.-.|.||+...|. .++.|++.|++.+++.|.+..
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 5688889999888776 599999999999999998843
No 40
>PF11569 Homez: Homeodomain leucine-zipper encoding, Homez; PDB: 2YS9_A.
Probab=93.16 E-value=0.11 Score=38.17 Aligned_cols=42 Identities=21% Similarity=0.424 Sum_probs=30.8
Q ss_pred HHHHHHHHHhhCCCCCCHHHHHHHHHHhCCCCcCCCCCccchhHHHHHHhhhcc
Q 025634 20 LEKMEKLLMESKDDLLSKEFCQKIAKSFSCSAGRAGKPVVKWTEVQSWFQSRQQ 73 (250)
Q Consensus 20 l~eLEk~f~~~~~~y~~~~~rq~LA~~f~lS~~RaGK~~Vq~~QVk~WFQNRR~ 73 (250)
+.=|++-|..| +.|.....+.|.++-++|. .||+.||--|+.
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 46699999995 6899999999999999997 999999988753
No 41
>KOG0773 consensus Transcription factor MEIS1 and related HOX domain proteins [Transcription]
Probab=93.10 E-value=0.075 Score=49.41 Aligned_cols=56 Identities=20% Similarity=0.236 Sum_probs=47.8
Q ss_pred CCCccCCHHHHHHHHHHHHhh-CCCCCCHHHHHHHHHHhCCCCcCCCCCccchhHHHHHHhhhcccC
Q 025634 10 SVFTGFTKTELEKMEKLLMES-KDDLLSKEFCQKIAKSFSCSAGRAGKPVVKWTEVQSWFQSRQQDR 75 (250)
Q Consensus 10 r~Rt~FT~~Ql~eLEk~f~~~-~~~y~~~~~rq~LA~~f~lS~~RaGK~~Vq~~QVk~WFQNRR~k~ 75 (250)
|+...|...-+..|..-+.+| ...||+......||.+.||+. .||.|||-|.|.+.
T Consensus 241 r~~~~lP~~a~~ilr~Wl~~h~~~PYPse~~K~~La~~TGLs~----------~Qv~NWFINaR~R~ 297 (342)
T KOG0773|consen 241 RPQRGLPKEAVSILRAWLFEHLLHPYPSDDEKLMLAKQTGLSR----------PQVSNWFINARVRL 297 (342)
T ss_pred CCCCCCCHHHHHHHHHHHHHhccCCCCcchhccccchhcCCCc----------ccCCchhhhccccc
Confidence 355689999898888877765 447999999999999999998 99999999998664
No 42
>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=92.21 E-value=0.48 Score=32.55 Aligned_cols=54 Identities=28% Similarity=0.317 Sum_probs=41.2
Q ss_pred ccccCceEEEEeeeCCcceeEeeEEeeeeeccCCCCceeeEEEEEEecCCcccccccccccccCC
Q 025634 185 KLKVGGHVLCFQERRDQGIHYDAHIAEIHRRMHDIRGCRCLFLVRYNHDNTEERVRLRRLCCRPT 249 (250)
Q Consensus 185 ~v~~G~~v~cf~~~~~~~~yyDA~V~~v~r~~Hd~~~C~C~F~Vr~~h~~~ee~v~~~~~c~~p~ 249 (250)
..++|+.+++.- ++..||.|+|+++... -.+.|.|...++.+.|+...|..-|.
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 467898888765 3688999999999732 34678888877778999888876553
No 43
>PLN00104 MYST -like histone acetyltransferase; Provisional
Probab=92.10 E-value=0.69 Score=46.12 Aligned_cols=52 Identities=25% Similarity=0.385 Sum_probs=38.1
Q ss_pred ecccCCCceeeeeeeheeeec---ccCcceEEEEecCCCCCcccceeccccccccCC
Q 025634 123 ARSSKDGAWYDVDMFLAHRFL---DCGEAEVRVRFVGFGADEDEWVNVKNAVRERSV 176 (250)
Q Consensus 123 Ars~~D~AWYdV~~fl~hR~~---~~ge~ev~Vrf~gFg~eeDEw~~v~~~~R~rS~ 176 (250)
|+...||.||...+ +.-|.. +.|+.+..|||.||..--||||+.. ++...++
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 45567999998555 556652 2355689999999999999999965 5544443
No 44
>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=92.05 E-value=0.26 Score=32.84 Aligned_cols=36 Identities=36% Similarity=0.675 Sum_probs=27.3
Q ss_pred EecccCCCceeeeeeeheeeecccCcceEEEEecCCCCCcc
Q 025634 122 EARSSKDGAWYDVDMFLAHRFLDCGEAEVRVRFVGFGADED 162 (250)
Q Consensus 122 EArs~~D~AWYdV~~fl~hR~~~~ge~ev~Vrf~gFg~eeD 162 (250)
-|+...||.||-..+. .+.. +..+.|.|..||+.+.
T Consensus 5 ~a~~~~d~~wyra~V~---~~~~--~~~~~V~f~DyG~~~~ 40 (48)
T cd04508 5 LAKYSDDGKWYRAKIT---SILS--DGKVEVFFVDYGNTEV 40 (48)
T ss_pred EEEECCCCeEEEEEEE---EECC--CCcEEEEEEcCCCcEE
Confidence 3666789999999886 2322 4489999999999853
No 45
>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=91.50 E-value=0.37 Score=38.17 Aligned_cols=45 Identities=20% Similarity=0.374 Sum_probs=37.4
Q ss_pred eeEEecccCCCceeeeeeeheeeecccCcceEEEEecCCCCCcccceecc
Q 025634 119 MEFEARSSKDGAWYDVDMFLAHRFLDCGEAEVRVRFVGFGADEDEWVNVK 168 (250)
Q Consensus 119 ~efEArs~~D~AWYdV~~fl~hR~~~~ge~ev~Vrf~gFg~eeDEw~~v~ 168 (250)
|-+||....+-..+=|++.. .+ .|. .|+|+|.|+.+.+|.|+++.
T Consensus 32 mkLEavD~~~~~~i~vAtV~--~v--~g~-~l~v~~dg~~~~~D~W~~~~ 76 (96)
T smart00561 32 MKLEAVDPRNPSLICVATVV--EV--KGY-RLLLHFDGWDDKYDFWCDAD 76 (96)
T ss_pred CEEEEECCCCCceEEEEEEE--EE--ECC-EEEEEEccCCCcCCEEEECC
Confidence 88999999988888888763 12 254 89999999999999999965
No 46
>smart00298 CHROMO Chromatin organization modifier domain.
Probab=91.39 E-value=0.23 Score=33.48 Aligned_cols=37 Identities=35% Similarity=0.689 Sum_probs=30.4
Q ss_pred eeeeeeheeeecccCcceEEEEecCCCCCcccceecc
Q 025634 132 YDVDMFLAHRFLDCGEAEVRVRFVGFGADEDEWVNVK 168 (250)
Q Consensus 132 YdV~~fl~hR~~~~ge~ev~Vrf~gFg~eeDEw~~v~ 168 (250)
|.|.-.|.||+...|..++.|++.|++..++.|+...
T Consensus 2 ~~v~~Il~~r~~~~~~~~ylVkW~g~~~~~~tW~~~~ 38 (55)
T smart00298 2 YEVEKILDHRWKKKGELEYLVKWKGYSYSEDTWEPEE 38 (55)
T ss_pred cchheeeeeeecCCCcEEEEEEECCCCCccCceeeHH
Confidence 3456667888667788899999999999999999753
No 47
>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=89.78 E-value=0.54 Score=34.90 Aligned_cols=45 Identities=27% Similarity=0.584 Sum_probs=35.6
Q ss_pred eeEEecccCCCceeeeeeeheeeecccCcceEEEEecCCCCCcccceecc
Q 025634 119 MEFEARSSKDGAWYDVDMFLAHRFLDCGEAEVRVRFVGFGADEDEWVNVK 168 (250)
Q Consensus 119 ~efEArs~~D~AWYdV~~fl~hR~~~~ge~ev~Vrf~gFg~eeDEw~~v~ 168 (250)
|-+||....+...+=|++.. .+ .|. .|+|+|.|..+++|.|+.+.
T Consensus 1 MkLEa~d~~~~~~~~vAtV~--~v--~g~-~l~v~~dg~~~~~d~w~~~~ 45 (73)
T PF02820_consen 1 MKLEAVDPRNPSLICVATVV--KV--CGG-RLLVRYDGWDDDYDFWCHID 45 (73)
T ss_dssp EEEEEEETTECCEEEEEEEE--EE--ETT-EEEEEETTSTGGGEEEEETT
T ss_pred CeEEEECCCCCCeEEEEEEE--EE--eCC-EEEEEEcCCCCCccEEEECC
Confidence 56889999998888777763 22 354 59999999999999999854
No 48
>smart00743 Agenet Tudor-like domain present in plant sequences. Domain in plant sequences with possible chromatin-associated functions.
Probab=87.83 E-value=1.9 Score=30.35 Aligned_cols=51 Identities=25% Similarity=0.438 Sum_probs=41.0
Q ss_pred ccccCceEEEEeeeCCcceeEeeEEeeeeeccCCCCceeeEEEEEEec--CCccccccccccc
Q 025634 185 KLKVGGHVLCFQERRDQGIHYDAHIAEIHRRMHDIRGCRCLFLVRYNH--DNTEERVRLRRLC 245 (250)
Q Consensus 185 ~v~~G~~v~cf~~~~~~~~yyDA~V~~v~r~~Hd~~~C~C~F~Vr~~h--~~~ee~v~~~~~c 245 (250)
.++.||.|-++... +.-||-|.|+++.. .. .|.|+|.. .+.++.++..+|-
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 56899999998753 57899999999874 22 37999999 7788888888773
No 49
>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=86.88 E-value=2 Score=34.08 Aligned_cols=70 Identities=19% Similarity=0.339 Sum_probs=41.6
Q ss_pred EecccCCCceeeeeeeheeeecc--cCcceEEEEecCCCCCcccceeccccccccCCCCCcccccccccCceEEE
Q 025634 122 EARSSKDGAWYDVDMFLAHRFLD--CGEAEVRVRFVGFGADEDEWVNVKNAVRERSVPLEPSDCHKLKVGGHVLC 194 (250)
Q Consensus 122 EArs~~D~AWYdV~~fl~hR~~~--~ge~ev~Vrf~gFg~eeDEw~~v~~~~R~rS~p~e~~eC~~v~~G~~v~c 194 (250)
-||+...|||++..+.=.++--. ..+.-..|.|.+|.+..-.-+.++ .+|+|..-+= .=..|.+|+.|..
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 37889999999988775444322 235678899999987666556666 7888876543 3457889999985
No 50
>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=85.98 E-value=1.3 Score=32.86 Aligned_cols=32 Identities=19% Similarity=0.361 Sum_probs=23.6
Q ss_pred HHHHHHhhCCCCCCHHHHHHHHHHhCCCCcCCCCCccchhHHHHHH
Q 025634 23 MEKLLMESKDDLLSKEFCQKIAKSFSCSAGRAGKPVVKWTEVQSWF 68 (250)
Q Consensus 23 LEk~f~~~~~~y~~~~~rq~LA~~f~lS~~RaGK~~Vq~~QVk~WF 68 (250)
--.+|.++++.. ...+||++||.|+ .||..|=
T Consensus 12 A~e~y~~~~g~i----~lkdIA~~Lgvs~----------~tIr~WK 43 (60)
T PF10668_consen 12 AFEIYKESNGKI----KLKDIAEKLGVSE----------STIRKWK 43 (60)
T ss_pred HHHHHHHhCCCc----cHHHHHHHHCCCH----------HHHHHHh
Confidence 345667765443 4568999999998 9999983
No 51
>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=85.66 E-value=1.4 Score=30.24 Aligned_cols=40 Identities=33% Similarity=0.615 Sum_probs=29.6
Q ss_pred EEecccCCCceeeeeeeheeeecccCcceEEEEecCCCCCcccceecc
Q 025634 121 FEARSSKDGAWYDVDMFLAHRFLDCGEAEVRVRFVGFGADEDEWVNVK 168 (250)
Q Consensus 121 fEArs~~D~AWYdV~~fl~hR~~~~ge~ev~Vrf~gFg~eeDEw~~v~ 168 (250)
-.|+- .||.||.+.+. .+ .++..+.|.|..||+. +|++..
T Consensus 9 ~~a~~-~d~~wyra~I~---~~--~~~~~~~V~f~D~G~~--~~v~~~ 48 (57)
T smart00333 9 VAARW-EDGEWYRARII---KV--DGEQLYEVFFIDYGNE--EVVPPS 48 (57)
T ss_pred EEEEe-CCCCEEEEEEE---EE--CCCCEEEEEEECCCcc--EEEeHH
Confidence 34566 79999999885 22 2224899999999998 488744
No 52
>smart00743 Agenet Tudor-like domain present in plant sequences. Domain in plant sequences with possible chromatin-associated functions.
Probab=84.50 E-value=1.9 Score=30.30 Aligned_cols=30 Identities=20% Similarity=0.499 Sum_probs=22.7
Q ss_pred EecccCCCceeeeeeeheeeecccCcceEEEEecC
Q 025634 122 EARSSKDGAWYDVDMFLAHRFLDCGEAEVRVRFVG 156 (250)
Q Consensus 122 EArs~~D~AWYdV~~fl~hR~~~~ge~ev~Vrf~g 156 (250)
||.+..||+||...+. .++. + ....|.|.+
T Consensus 10 e~~~~~~~~W~~a~V~---~~~~-~-~~~~V~~~~ 39 (61)
T smart00743 10 EVFSKEEDSWWEAVVT---KVLG-D-GKYLVRYLT 39 (61)
T ss_pred EEEECCCCEEEEEEEE---EECC-C-CEEEEEECC
Confidence 5576779999998876 3443 3 379999999
No 53
>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=83.83 E-value=1.6 Score=31.99 Aligned_cols=45 Identities=22% Similarity=0.614 Sum_probs=24.3
Q ss_pred cccC---CCceeeeeeeheeeecccCcceEEEEecCCCCCccc------ceecccccccc
Q 025634 124 RSSK---DGAWYDVDMFLAHRFLDCGEAEVRVRFVGFGADEDE------WVNVKNAVRER 174 (250)
Q Consensus 124 rs~~---D~AWYdV~~fl~hR~~~~ge~ev~Vrf~gFg~eeDE------w~~v~~~~R~r 174 (250)
+|-. .||||...+. -..+...+.|.|..+.+++++ |++.+ ++|+.
T Consensus 10 ~s~e~g~~gaWf~a~V~-----~~~~~~~~~V~Y~~~~~~~~~~~~l~e~V~~~-~iRP~ 63 (68)
T PF05641_consen 10 SSDEDGFRGAWFPATVL-----KENGDDKYLVEYDDLPDEDGESPPLKEWVDAR-RIRPC 63 (68)
T ss_dssp EE-SBTT--EEEEEEEE-----EEETT-EEEEEETT-SS--------EEEEEGG-GEEE-
T ss_pred EEcCCCCCcEEEEEEEE-----EeCCCcEEEEEECCcccccccccccEEEechh-eEECc
Confidence 5544 6799999985 122222999999999988655 45554 46654
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=82.00 E-value=7.6 Score=27.42 Aligned_cols=41 Identities=32% Similarity=0.545 Sum_probs=29.2
Q ss_pred cccCceEEEEeeeCCcceeEeeEEeeeeeccCCCCceeeEEEEEEecCC
Q 025634 186 LKVGGHVLCFQERRDQGIHYDAHIAEIHRRMHDIRGCRCLFLVRYNHDN 234 (250)
Q Consensus 186 v~~G~~v~cf~~~~~~~~yyDA~V~~v~r~~Hd~~~C~C~F~Vr~~h~~ 234 (250)
+..|+.|.|.. .+..+|.|.|+++...... =.|.|-|..-+
T Consensus 1 ~~vG~~v~~~~---~~~~~y~A~I~~~r~~~~~-----~~YyVHY~g~n 41 (55)
T PF11717_consen 1 FEVGEKVLCKY---KDGQWYEAKILDIREKNGE-----PEYYVHYQGWN 41 (55)
T ss_dssp --TTEEEEEEE---TTTEEEEEEEEEEEECTTC-----EEEEEEETTST
T ss_pred CCcCCEEEEEE---CCCcEEEEEEEEEEecCCC-----EEEEEEcCCCC
Confidence 46899999999 4567899999999974433 34667666444
No 55
>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=81.55 E-value=1.8 Score=37.61 Aligned_cols=48 Identities=23% Similarity=0.180 Sum_probs=37.1
Q ss_pred CccCCHHHHHHHHHHHHhhCCCCCCHHHHHHHHHHhCCCCcCCCCCccchhH
Q 025634 12 FTGFTKTELEKMEKLLMESKDDLLSKEFCQKIAKSFSCSAGRAGKPVVKWTE 63 (250)
Q Consensus 12 Rt~FT~~Ql~eLEk~f~~~~~~y~~~~~rq~LA~~f~lS~~RaGK~~Vq~~Q 63 (250)
...+|+++|+||-++=.+ -|..-.+.+||++||+|+--.+-++=...|
T Consensus 83 ~y~Lt~e~i~Eir~LR~~----DP~~wTr~~LAkkF~~S~~fV~~v~~~~~e 130 (164)
T PF12824_consen 83 KYHLTPEDIQEIRRLRAE----DPEKWTRKKLAKKFNCSPLFVSMVAPAPKE 130 (164)
T ss_pred cccCCHHHHHHHHHHHHc----CchHhhHHHHHHHhCCCHHHHHHhcCCCHH
Confidence 467999999999998877 377789999999999998655444433333
No 56
>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=81.49 E-value=3.1 Score=38.37 Aligned_cols=53 Identities=30% Similarity=0.458 Sum_probs=37.3
Q ss_pred cccccCceEEEEeeeCCcceeEeeEEeeeeeccCCCCceeeEEEEEEecCCccccccccccc
Q 025634 184 HKLKVGGHVLCFQERRDQGIHYDAHIAEIHRRMHDIRGCRCLFLVRYNHDNTEERVRLRRLC 245 (250)
Q Consensus 184 ~~v~~G~~v~cf~~~~~~~~yyDA~V~~v~r~~Hd~~~C~C~F~Vr~~h~~~ee~v~~~~~c 245 (250)
...++||..+|.- .++..||.|.|.+|.. +...| +|+|..-+++|+|.|..|-
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 5788999999874 3456799999999962 22334 4999999999999998873
No 57
>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=77.18 E-value=2.8 Score=38.65 Aligned_cols=41 Identities=24% Similarity=0.385 Sum_probs=29.6
Q ss_pred EecccCCCceeeeeeeheeeecccCcceEEEEecCCCCCccccee
Q 025634 122 EARSSKDGAWYDVDMFLAHRFLDCGEAEVRVRFVGFGADEDEWVN 166 (250)
Q Consensus 122 EArs~~D~AWYdV~~fl~hR~~~~ge~ev~Vrf~gFg~eeDEw~~ 166 (250)
.|.-+.||-||...+. .+-..++ .+.|+|.|||++|..++.
T Consensus 76 ~A~~s~Dg~~Y~A~I~---~i~~~~~-~~~V~f~gYgn~e~v~l~ 116 (264)
T PF06003_consen 76 MAVYSEDGQYYPATIE---SIDEEDG-TCVVVFTGYGNEEEVNLS 116 (264)
T ss_dssp EEE-TTTSSEEEEEEE---EEETTTT-EEEEEETTTTEEEEEEGG
T ss_pred EEEECCCCCEEEEEEE---EEcCCCC-EEEEEEcccCCeEeeehh
Confidence 4566899999998886 2333333 788999999998765544
No 58
>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=76.70 E-value=7.4 Score=28.46 Aligned_cols=51 Identities=25% Similarity=0.322 Sum_probs=33.6
Q ss_pred cccCceEEEEe-eeCCcceeEeeEEeeeeeccCCCCceeeEEEEEEecCC--------cccccccccc
Q 025634 186 LKVGGHVLCFQ-ERRDQGIHYDAHIAEIHRRMHDIRGCRCLFLVRYNHDN--------TEERVRLRRL 244 (250)
Q Consensus 186 v~~G~~v~cf~-~~~~~~~yyDA~V~~v~r~~Hd~~~C~C~F~Vr~~h~~--------~ee~v~~~~~ 244 (250)
+++|+.|-.+. +.+-..-||-|.|+++.... +|+|+|++=. ..|.|+...|
T Consensus 1 F~~G~~VEV~s~e~g~~gaWf~a~V~~~~~~~--------~~~V~Y~~~~~~~~~~~~l~e~V~~~~i 60 (68)
T PF05641_consen 1 FKKGDEVEVSSDEDGFRGAWFPATVLKENGDD--------KYLVEYDDLPDEDGESPPLKEWVDARRI 60 (68)
T ss_dssp --TT-EEEEEE-SBTT--EEEEEEEEEEETT---------EEEEEETT-SS--------EEEEEGGGE
T ss_pred CCCCCEEEEEEcCCCCCcEEEEEEEEEeCCCc--------EEEEEECCcccccccccccEEEechheE
Confidence 36899998765 66668999999999988544 8999996432 3566777665
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=76.52 E-value=7.2 Score=25.75 Aligned_cols=46 Identities=28% Similarity=0.270 Sum_probs=31.1
Q ss_pred CceEEEEeeeCCcceeEeeEEeeeeeccCCCCceeeEEEEEEecCCcccccccccc
Q 025634 189 GGHVLCFQERRDQGIHYDAHIAEIHRRMHDIRGCRCLFLVRYNHDNTEERVRLRRL 244 (250)
Q Consensus 189 G~~v~cf~~~~~~~~yyDA~V~~v~r~~Hd~~~C~C~F~Vr~~h~~~ee~v~~~~~ 244 (250)
|+++++.-. ++..||-|.|+++.. .-.+.|.|..-++.+.|++..|
T Consensus 1 G~~c~a~~~--~d~~wyra~V~~~~~--------~~~~~V~f~DyG~~~~v~~~~l 46 (48)
T cd04508 1 GDLCLAKYS--DDGKWYRAKITSILS--------DGKVEVFFVDYGNTEVVPLSDL 46 (48)
T ss_pred CCEEEEEEC--CCCeEEEEEEEEECC--------CCcEEEEEEcCCCcEEEeHHHc
Confidence 444444322 368999999999973 2346788887566666887766
No 60
>KOG3623 consensus Homeobox transcription factor SIP1 [Transcription]
Probab=70.58 E-value=12 Score=40.28 Aligned_cols=49 Identities=20% Similarity=0.351 Sum_probs=38.6
Q ss_pred cCCHHHHHHHHHHHHhhCCCCCCHHHHHHHHHHhCCCCcCCCCCccchhHHHHHHhhhcccC
Q 025634 14 GFTKTELEKMEKLLMESKDDLLSKEFCQKIAKSFSCSAGRAGKPVVKWTEVQSWFQSRQQDR 75 (250)
Q Consensus 14 ~FT~~Ql~eLEk~f~~~~~~y~~~~~rq~LA~~f~lS~~RaGK~~Vq~~QVk~WFQNRR~k~ 75 (250)
.|++. +.-|...|.- |..|+.++..++|...|++- .-|+.||+|++++.
T Consensus 563 ~~~~p-~sllkayyal--n~~ps~eelskia~qvglp~----------~vvk~wfE~~~a~e 611 (1007)
T KOG3623|consen 563 QFNHP-TSLLKAYYAL--NGLPSEEELSKIAQQVGLPF----------AVVKAWFEDEEAEE 611 (1007)
T ss_pred ccCCc-HHHHHHHHHh--cCCCCHHHHHHHHHHhcccH----------HHHHHHHHhhhhhh
Confidence 35544 4445555555 67899999999999999996 77999999998875
No 61
>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=68.20 E-value=9.6 Score=30.24 Aligned_cols=48 Identities=19% Similarity=0.383 Sum_probs=32.6
Q ss_pred CcceeEeeEEeeeeeccCCCCceeeEEEEEEecCCcccccccccccccC
Q 025634 200 DQGIHYDAHIAEIHRRMHDIRGCRCLFLVRYNHDNTEERVRLRRLCCRP 248 (250)
Q Consensus 200 ~~~~yyDA~V~~v~r~~Hd~~~C~C~F~Vr~~h~~~ee~v~~~~~c~~p 248 (250)
....||+|.|..|.++. ....+.+.+-|.|+..|....|.+....=||
T Consensus 8 ~~gAWfEa~i~~i~~~~-~~~~e~viYhIkyddype~gvv~~~~~~iRp 55 (85)
T PF12148_consen 8 NMGAWFEAQIVTITKKC-MSDDEDVIYHIKYDDYPENGVVEMRSKDIRP 55 (85)
T ss_dssp TT-EEEEEEEEEEEES--SSSSTTEEEEEEETT-GGG-EEEEEGGGEEE
T ss_pred CCcceEEEEEEEeeccC-CCCCCCEEEEEEeccCCCcCceecccccccc
Confidence 34679999999999554 4455999999999999866555544444344
No 62
>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=68.18 E-value=21 Score=23.98 Aligned_cols=44 Identities=27% Similarity=0.288 Sum_probs=33.0
Q ss_pred CccCCHHHHHHHHHHHHhhCCCCCCHHHHHHHHHHhC--CCCcCCCCCccchhHHHHHHhh
Q 025634 12 FTGFTKTELEKMEKLLMESKDDLLSKEFCQKIAKSFS--CSAGRAGKPVVKWTEVQSWFQS 70 (250)
Q Consensus 12 Rt~FT~~Ql~eLEk~f~~~~~~y~~~~~rq~LA~~f~--lS~~RaGK~~Vq~~QVk~WFQN 70 (250)
|-.||++|...|.+++..++.. .=..||..++ -|. .|++.=|+|
T Consensus 1 r~~Wt~eE~~~l~~~v~~~g~~-----~W~~Ia~~~~~~Rt~----------~qc~~~~~~ 46 (48)
T PF00249_consen 1 RGPWTEEEDEKLLEAVKKYGKD-----NWKKIAKRMPGGRTA----------KQCRSRYQN 46 (48)
T ss_dssp S-SS-HHHHHHHHHHHHHSTTT-----HHHHHHHHHSSSSTH----------HHHHHHHHH
T ss_pred CCCCCHHHHHHHHHHHHHhCCc-----HHHHHHHHcCCCCCH----------HHHHHHHHh
Confidence 3579999999999999997643 6788999998 454 888765554
No 63
>PTZ00183 centrin; Provisional
Probab=65.65 E-value=20 Score=28.26 Aligned_cols=39 Identities=8% Similarity=0.063 Sum_probs=31.0
Q ss_pred CCccCCHHHHHHHHHHHHhh---CCCCCCHHHHHHHHHHhCC
Q 025634 11 VFTGFTKTELEKMEKLLMES---KDDLLSKEFCQKIAKSFSC 49 (250)
Q Consensus 11 ~Rt~FT~~Ql~eLEk~f~~~---~~~y~~~~~rq~LA~~f~l 49 (250)
.++.|++.|+.+++++|... ++.+++..+...+...+++
T Consensus 7 ~~~~~~~~~~~~~~~~F~~~D~~~~G~i~~~e~~~~l~~~g~ 48 (158)
T PTZ00183 7 ERPGLTEDQKKEIREAFDLFDTDGSGTIDPKELKVAMRSLGF 48 (158)
T ss_pred ccCCCCHHHHHHHHHHHHHhCCCCCCcccHHHHHHHHHHhCC
Confidence 48899999999999999873 4577888777776666654
No 64
>smart00717 SANT SANT SWI3, ADA2, N-CoR and TFIIIB'' DNA-binding domains.
Probab=64.34 E-value=19 Score=22.60 Aligned_cols=44 Identities=20% Similarity=0.229 Sum_probs=32.4
Q ss_pred CccCCHHHHHHHHHHHHhhCCCCCCHHHHHHHHHHhC-CCCcCCCCCccchhHHHHHHhh
Q 025634 12 FTGFTKTELEKMEKLLMESKDDLLSKEFCQKIAKSFS-CSAGRAGKPVVKWTEVQSWFQS 70 (250)
Q Consensus 12 Rt~FT~~Ql~eLEk~f~~~~~~y~~~~~rq~LA~~f~-lS~~RaGK~~Vq~~QVk~WFQN 70 (250)
+..||++|...|.+++..++. ..-..||..|+ -|+ .||+..|.+
T Consensus 1 ~~~Wt~~E~~~l~~~~~~~g~-----~~w~~Ia~~~~~rt~----------~~~~~~~~~ 45 (49)
T smart00717 1 KGEWTEEEDELLIELVKKYGK-----NNWEKIAKELPGRTA----------EQCRERWNN 45 (49)
T ss_pred CCCCCHHHHHHHHHHHHHHCc-----CCHHHHHHHcCCCCH----------HHHHHHHHH
Confidence 357999999999999999752 23467888887 443 788766554
No 65
>PF13551 HTH_29: Winged helix-turn helix
Probab=58.85 E-value=33 Score=25.70 Aligned_cols=22 Identities=14% Similarity=0.163 Sum_probs=17.9
Q ss_pred CCCCccCCHHHHHHHHHHHHhh
Q 025634 9 RSVFTGFTKTELEKMEKLLMES 30 (250)
Q Consensus 9 Rr~Rt~FT~~Ql~eLEk~f~~~ 30 (250)
.+++..+|+++.+.+.+++.++
T Consensus 52 g~~~~~l~~~~~~~l~~~~~~~ 73 (112)
T PF13551_consen 52 GRPRKRLSEEQRAQLIELLREN 73 (112)
T ss_pred CCCCCCCCHHHHHHHHHHHHHC
Confidence 3345559999999999999995
No 66
>smart00027 EH Eps15 homology domain. Pair of EF hand motifs that recognise proteins containing Asn-Pro-Phe (NPF) sequences.
Probab=57.43 E-value=32 Score=26.07 Aligned_cols=45 Identities=11% Similarity=0.141 Sum_probs=33.2
Q ss_pred CCHHHHHHHHHHHHhh---CCCCCCHHHHHHHHHHhCCCCcCCCCCccchhHHHHHHh
Q 025634 15 FTKTELEKMEKLLMES---KDDLLSKEFCQKIAKSFSCSAGRAGKPVVKWTEVQSWFQ 69 (250)
Q Consensus 15 FT~~Ql~eLEk~f~~~---~~~y~~~~~rq~LA~~f~lS~~RaGK~~Vq~~QVk~WFQ 69 (250)
+|++|+.++..+|... ++.+++.....++-..+++++ .+|...|.
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 6889999999998873 557888887777666677665 56665554
No 67
>COG3458 Acetyl esterase (deacetylase) [Secondary metabolites biosynthesis, transport, and catabolism]
Probab=56.87 E-value=18 Score=34.84 Aligned_cols=92 Identities=18% Similarity=0.296 Sum_probs=68.1
Q ss_pred CCceeEEe-cccCCCceeeeeeeheeeecccCcceEEEEecCCCCCccccee-----------ccccccccCCCCCcccc
Q 025634 116 VSEMEFEA-RSSKDGAWYDVDMFLAHRFLDCGEAEVRVRFVGFGADEDEWVN-----------VKNAVRERSVPLEPSDC 183 (250)
Q Consensus 116 ~~~~efEA-rs~~D~AWYdV~~fl~hR~~~~ge~ev~Vrf~gFg~eeDEw~~-----------v~~~~R~rS~p~e~~eC 183 (250)
-+++-|+. +-.+=.+||-+..- .+|-+-..|+|-||+.--++|.+ |.-.+|-.|.--+|+-|
T Consensus 56 ~ydvTf~g~~g~rI~gwlvlP~~------~~~~~P~vV~fhGY~g~~g~~~~~l~wa~~Gyavf~MdvRGQg~~~~dt~~ 129 (321)
T COG3458 56 VYDVTFTGYGGARIKGWLVLPRH------EKGKLPAVVQFHGYGGRGGEWHDMLHWAVAGYAVFVMDVRGQGSSSQDTAD 129 (321)
T ss_pred EEEEEEeccCCceEEEEEEeecc------cCCccceEEEEeeccCCCCCccccccccccceeEEEEecccCCCccccCCC
Confidence 35677732 22233589999884 44778899999999999888855 56678888888788888
Q ss_pred cccc---cCceEEEEeeeCCcceeEeeEEeeeee
Q 025634 184 HKLK---VGGHVLCFQERRDQGIHYDAHIAEIHR 214 (250)
Q Consensus 184 ~~v~---~G~~v~cf~~~~~~~~yyDA~V~~v~r 214 (250)
.... ||-.+.+..+++| ..||-.+++|+-|
T Consensus 130 ~p~~~s~pG~mtrGilD~kd-~yyyr~v~~D~~~ 162 (321)
T COG3458 130 PPGGPSDPGFMTRGILDRKD-TYYYRGVFLDAVR 162 (321)
T ss_pred CCCCCcCCceeEeecccCCC-ceEEeeehHHHHH
Confidence 7766 7777778778775 6778777777543
No 68
>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=56.21 E-value=24 Score=25.15 Aligned_cols=47 Identities=13% Similarity=0.210 Sum_probs=30.7
Q ss_pred CCCccCCHHHHHHHHHHHHhhCCCCCCHHHHHHHHHHhCCCCcCCCCCccchhHHHHHHhhhc
Q 025634 10 SVFTGFTKTELEKMEKLLMESKDDLLSKEFCQKIAKSFSCSAGRAGKPVVKWTEVQSWFQSRQ 72 (250)
Q Consensus 10 r~Rt~FT~~Ql~eLEk~f~~~~~~y~~~~~rq~LA~~f~lS~~RaGK~~Vq~~QVk~WFQNRR 72 (250)
+.|..||+++-..+=+.+... .....+||..+|+++ .++-+|-+-=+
T Consensus 2 ~~r~~ys~e~K~~~v~~~~~~------g~sv~~va~~~gi~~----------~~l~~W~~~~~ 48 (76)
T PF01527_consen 2 RKRRRYSPEFKLQAVREYLES------GESVSEVAREYGISP----------STLYNWRKQYR 48 (76)
T ss_dssp -SS----HHHHHHHHHHHHHH------HCHHHHHHHHHTS-H----------HHHHHHHHHHH
T ss_pred CCCCCCCHHHHHHHHHHHHHC------CCceEeeeccccccc----------ccccHHHHHHh
Confidence 356789999887775555332 247889999999998 99999976554
No 69
>cd00569 HTH_Hin_like Helix-turn-helix domain of Hin and related proteins, a family of DNA-binding domains unique to bacteria and represented by the Hin protein of Salmonella. The basic HTH domain is a simple fold comprised of three core helices that form a right-handed helical bundle. The principal DNA-protein interface is formed by the third helix, the recognition helix, inserting itself into the major groove of the DNA. A diverse array of HTH domains participate in a variety of functions that depend on their DNA-binding properties. HTH_Hin represents one of the simplest versions of the HTH domains; the characterization of homologous relationships between various sequence-diverse HTH domain families remains difficult. The Hin recombinase induces the site-specific inversion of a chromosomal DNA segment containing a promoter, which controls the alternate expression of two genes by reversibly switching orientation. The Hin recombinase consists of a single polypeptide chain containing a D
Probab=53.68 E-value=38 Score=18.81 Aligned_cols=37 Identities=19% Similarity=0.321 Sum_probs=26.6
Q ss_pred cCCHHHHHHHHHHHHhhCCCCCCHHHHHHHHHHhCCCCcCCCCCccchhHHHHH
Q 025634 14 GFTKTELEKMEKLLMESKDDLLSKEFCQKIAKSFSCSAGRAGKPVVKWTEVQSW 67 (250)
Q Consensus 14 ~FT~~Ql~eLEk~f~~~~~~y~~~~~rq~LA~~f~lS~~RaGK~~Vq~~QVk~W 67 (250)
.++.++...+...+.. + + ...++|+.|++|. ..|..|
T Consensus 5 ~~~~~~~~~i~~~~~~--~-~----s~~~ia~~~~is~----------~tv~~~ 41 (42)
T cd00569 5 KLTPEQIEEARRLLAA--G-E----SVAEIARRLGVSR----------STLYRY 41 (42)
T ss_pred cCCHHHHHHHHHHHHc--C-C----CHHHHHHHHCCCH----------HHHHHh
Confidence 4677877777777654 2 2 4678999999996 667766
No 70
>PF13936 HTH_38: Helix-turn-helix domain; PDB: 2W48_A.
Probab=53.50 E-value=15 Score=24.77 Aligned_cols=33 Identities=27% Similarity=0.334 Sum_probs=15.7
Q ss_pred CccCCHHHHHHHHHHHHhhCCCCCCHHHHHHHHHHhCCCC
Q 025634 12 FTGFTKTELEKMEKLLMESKDDLLSKEFCQKIAKSFSCSA 51 (250)
Q Consensus 12 Rt~FT~~Ql~eLEk~f~~~~~~y~~~~~rq~LA~~f~lS~ 51 (250)
...+|.+|..+++.++++ + .-..+||+.||.|+
T Consensus 2 ~~~Lt~~eR~~I~~l~~~--G-----~s~~~IA~~lg~s~ 34 (44)
T PF13936_consen 2 YKHLTPEERNQIEALLEQ--G-----MSIREIAKRLGRSR 34 (44)
T ss_dssp ----------HHHHHHCS----------HHHHHHHTT--H
T ss_pred ccchhhhHHHHHHHHHHc--C-----CCHHHHHHHHCcCc
Confidence 356899999999998876 2 25678999999997
No 71
>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=53.23 E-value=20 Score=25.83 Aligned_cols=37 Identities=14% Similarity=0.093 Sum_probs=29.3
Q ss_pred CCHHHHHHHHHHHHhhCCCCCCHHHHHHHHHHhCCCC
Q 025634 15 FTKTELEKMEKLLMESKDDLLSKEFCQKIAKSFSCSA 51 (250)
Q Consensus 15 FT~~Ql~eLEk~f~~~~~~y~~~~~rq~LA~~f~lS~ 51 (250)
+|+.|...|...++.-=-.+|-.....+||+.||+|.
T Consensus 1 LT~~Q~e~L~~A~~~GYfd~PR~~tl~elA~~lgis~ 37 (53)
T PF04967_consen 1 LTDRQREILKAAYELGYFDVPRRITLEELAEELGISK 37 (53)
T ss_pred CCHHHHHHHHHHHHcCCCCCCCcCCHHHHHHHhCCCH
Confidence 5889999999999982222344678899999999995
No 72
>PF13565 HTH_32: Homeodomain-like domain
Probab=51.82 E-value=55 Score=23.42 Aligned_cols=40 Identities=15% Similarity=0.202 Sum_probs=28.4
Q ss_pred CCCCCccCCHHHHHHHHHHHHhhCCCCCCHHHHHHHHHHhCCC
Q 025634 8 QRSVFTGFTKTELEKMEKLLMESKDDLLSKEFCQKIAKSFSCS 50 (250)
Q Consensus 8 ~Rr~Rt~FT~~Ql~eLEk~f~~~~~~y~~~~~rq~LA~~f~lS 50 (250)
.-++++ +.++.+.|.+++.++. ..-.....+.|++.|+.+
T Consensus 26 ~Grp~~--~~e~~~~i~~~~~~~p-~wt~~~i~~~L~~~~g~~ 65 (77)
T PF13565_consen 26 PGRPRK--DPEQRERIIALIEEHP-RWTPREIAEYLEEEFGIS 65 (77)
T ss_pred CCCCCC--cHHHHHHHHHHHHhCC-CCCHHHHHHHHHHHhCCC
Confidence 333445 7777799999999853 344556778888888854
No 73
>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=51.02 E-value=28 Score=24.12 Aligned_cols=47 Identities=23% Similarity=0.227 Sum_probs=36.1
Q ss_pred CccCCHHHHHHHHHHHHhhCCCCCCHHHHHHHHHHhCCCCcCCCCCccchhHHHHHHhhhcccCC
Q 025634 12 FTGFTKTELEKMEKLLMESKDDLLSKEFCQKIAKSFSCSAGRAGKPVVKWTEVQSWFQSRQQDRP 76 (250)
Q Consensus 12 Rt~FT~~Ql~eLEk~f~~~~~~y~~~~~rq~LA~~f~lS~~RaGK~~Vq~~QVk~WFQNRR~k~~ 76 (250)
+..||+.|+.-|.-+..-. ...++|+.+++|+ +-|..+.+|=+.|..
T Consensus 1 ~~~LT~~E~~vl~~l~~G~--------~~~eIA~~l~is~----------~tV~~~~~~i~~Kl~ 47 (58)
T PF00196_consen 1 FPSLTERELEVLRLLAQGM--------SNKEIAEELGISE----------KTVKSHRRRIMKKLG 47 (58)
T ss_dssp SGSS-HHHHHHHHHHHTTS---------HHHHHHHHTSHH----------HHHHHHHHHHHHHHT
T ss_pred CCccCHHHHHHHHHHHhcC--------CcchhHHhcCcch----------hhHHHHHHHHHHHhC
Confidence 3579999999998887763 4689999999998 889888777655544
No 74
>PF13518 HTH_28: Helix-turn-helix domain
Probab=48.24 E-value=19 Score=23.81 Aligned_cols=24 Identities=25% Similarity=0.504 Sum_probs=20.2
Q ss_pred HHHHHHHHhCCCCcCCCCCccchhHHHHHHhhhc
Q 025634 39 FCQKIAKSFSCSAGRAGKPVVKWTEVQSWFQSRQ 72 (250)
Q Consensus 39 ~rq~LA~~f~lS~~RaGK~~Vq~~QVk~WFQNRR 72 (250)
...++|..|++|. .+|..|.+.=+
T Consensus 14 s~~~~a~~~gis~----------~tv~~w~~~y~ 37 (52)
T PF13518_consen 14 SVREIAREFGISR----------STVYRWIKRYR 37 (52)
T ss_pred CHHHHHHHHCCCH----------hHHHHHHHHHH
Confidence 4567999999997 99999987654
No 75
>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=46.89 E-value=56 Score=20.12 Aligned_cols=42 Identities=17% Similarity=0.218 Sum_probs=30.3
Q ss_pred cCCHHHHHHHHHHHHhhCCCCCCHHHHHHHHHHhC-CCCcCCCCCccchhHHHHHHhh
Q 025634 14 GFTKTELEKMEKLLMESKDDLLSKEFCQKIAKSFS-CSAGRAGKPVVKWTEVQSWFQS 70 (250)
Q Consensus 14 ~FT~~Ql~eLEk~f~~~~~~y~~~~~rq~LA~~f~-lS~~RaGK~~Vq~~QVk~WFQN 70 (250)
.+|.+|...|.+.+..++. ..=..||+.++ -|+ .||+.-|+|
T Consensus 1 ~Wt~eE~~~l~~~~~~~g~-----~~w~~Ia~~~~~rs~----------~~~~~~~~~ 43 (45)
T cd00167 1 PWTEEEDELLLEAVKKYGK-----NNWEKIAKELPGRTP----------KQCRERWRN 43 (45)
T ss_pred CCCHHHHHHHHHHHHHHCc-----CCHHHHHhHcCCCCH----------HHHHHHHHH
Confidence 3799999999999999752 23467888886 343 788754443
No 76
>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=43.62 E-value=18 Score=29.08 Aligned_cols=19 Identities=32% Similarity=0.531 Sum_probs=14.7
Q ss_pred cCCCCCccchhHHHHHHhhh
Q 025634 52 GRAGKPVVKWTEVQSWFQSR 71 (250)
Q Consensus 52 ~RaGK~~Vq~~QVk~WFQNR 71 (250)
-|+|.+++|- .|+.|.||=
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 4899999985 589999993
No 77
>PRK07539 NADH dehydrogenase subunit E; Validated
Probab=42.54 E-value=57 Score=27.50 Aligned_cols=20 Identities=15% Similarity=0.197 Sum_probs=18.8
Q ss_pred CCCCCHHHHHHHHHHhCCCC
Q 025634 32 DDLLSKEFCQKIAKSFSCSA 51 (250)
Q Consensus 32 ~~y~~~~~rq~LA~~f~lS~ 51 (250)
..|++.+..+.+|+.+|+++
T Consensus 35 ~g~ip~~~~~~iA~~l~v~~ 54 (154)
T PRK07539 35 RGWVPDEAIEAVADYLGMPA 54 (154)
T ss_pred hCCCCHHHHHHHHHHhCcCH
Confidence 46999999999999999998
No 78
>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=41.32 E-value=57 Score=20.39 Aligned_cols=42 Identities=17% Similarity=0.105 Sum_probs=30.1
Q ss_pred cCCHHHHHHHHHHHHhhCCCCCCHHHHHHHHHHhCCCCcCCCCCccchhHHHHHHhhhc
Q 025634 14 GFTKTELEKMEKLLMESKDDLLSKEFCQKIAKSFSCSAGRAGKPVVKWTEVQSWFQSRQ 72 (250)
Q Consensus 14 ~FT~~Ql~eLEk~f~~~~~~y~~~~~rq~LA~~f~lS~~RaGK~~Vq~~QVk~WFQNRR 72 (250)
.+++.+...++..+.+ .....++|+.+|+|. ..|..|.+.-+
T Consensus 10 ~l~~~~~~~~~~~~~~-------~~~~~~ia~~~~~s~----------~~i~~~~~~~~ 51 (55)
T cd06171 10 KLPEREREVILLRFGE-------GLSYEEIAEILGISR----------STVRQRLHRAL 51 (55)
T ss_pred hCCHHHHHHHHHHHhc-------CCCHHHHHHHHCcCH----------HHHHHHHHHHH
Confidence 4566777766666643 224678999999997 88998877654
No 79
>PRK07571 bidirectional hydrogenase complex protein HoxE; Reviewed
Probab=41.11 E-value=59 Score=28.36 Aligned_cols=40 Identities=8% Similarity=0.115 Sum_probs=31.5
Q ss_pred CccCCHHHHHHHHHHHHhhC----------------CCCCCHHHHHHHHHHhCCCC
Q 025634 12 FTGFTKTELEKMEKLLMESK----------------DDLLSKEFCQKIAKSFSCSA 51 (250)
Q Consensus 12 Rt~FT~~Ql~eLEk~f~~~~----------------~~y~~~~~rq~LA~~f~lS~ 51 (250)
-..|+.+++++++++....+ ..|++.+..+.+|+.+|+++
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 34567777777777665543 46999999999999999998
No 80
>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=40.41 E-value=47 Score=22.31 Aligned_cols=31 Identities=29% Similarity=0.438 Sum_probs=23.9
Q ss_pred cCCHHHHHHHHHHHHhhCCCCCCHHHHHHHHHHhCCCC
Q 025634 14 GFTKTELEKMEKLLMESKDDLLSKEFCQKIAKSFSCSA 51 (250)
Q Consensus 14 ~FT~~Ql~eLEk~f~~~~~~y~~~~~rq~LA~~f~lS~ 51 (250)
.+++++++++-+++.+ + ....+||+.||+|.
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 5788888888888888 3 25789999999996
No 81
>PRK10072 putative transcriptional regulator; Provisional
Probab=35.89 E-value=48 Score=26.40 Aligned_cols=23 Identities=22% Similarity=0.397 Sum_probs=19.1
Q ss_pred HHHHHHHhCCCCcCCCCCccchhHHHHHHhhhc
Q 025634 40 CQKIAKSFSCSAGRAGKPVVKWTEVQSWFQSRQ 72 (250)
Q Consensus 40 rq~LA~~f~lS~~RaGK~~Vq~~QVk~WFQNRR 72 (250)
..+||+.+|+|. .-|..|.+.+|
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 567888888875 78999999986
No 82
>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=35.55 E-value=49 Score=24.48 Aligned_cols=54 Identities=26% Similarity=0.543 Sum_probs=36.3
Q ss_pred ecccCCCceeeeeeeheeeecccCcceEEEEecCCCCCcccceeccccc-----cccCCCCCccccc
Q 025634 123 ARSSKDGAWYDVDMFLAHRFLDCGEAEVRVRFVGFGADEDEWVNVKNAV-----RERSVPLEPSDCH 184 (250)
Q Consensus 123 Ars~~D~AWYdV~~fl~hR~~~~ge~ev~Vrf~gFg~eeDEw~~v~~~~-----R~rS~p~e~~eC~ 184 (250)
+....||.||=+.+. ...++..+.|.|.-||..+- ++.. .+ ...++|.+...|.
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 355889999999882 23455599999999998753 4433 22 2334677766664
No 83
>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=35.39 E-value=60 Score=24.90 Aligned_cols=40 Identities=18% Similarity=0.252 Sum_probs=27.7
Q ss_pred CccCCHHHHHHHHHHHHhhC-CCCCCHHHHHHHHHHhCCCC
Q 025634 12 FTGFTKTELEKMEKLLMESK-DDLLSKEFCQKIAKSFSCSA 51 (250)
Q Consensus 12 Rt~FT~~Ql~eLEk~f~~~~-~~y~~~~~rq~LA~~f~lS~ 51 (250)
|..||.++|..|.++|+..- ....-.+..++|.+.++.++
T Consensus 25 R~Gfs~~~i~~l~~ayr~l~~~~~~~~~a~~~l~~~~~~~~ 65 (83)
T PF13720_consen 25 RRGFSKEEISALRRAYRILFRSGLTLEEALEELEEEYPDSP 65 (83)
T ss_dssp HTTS-HHHHHHHHHHHHHHHTSSS-HHHHHHHHHHHTTSCH
T ss_pred HcCCCHHHHHHHHHHHHHHHhCCCCHHHHHHHHHHhccCCH
Confidence 67899999999999999863 22333456667766677664
No 84
>PLN00104 MYST -like histone acetyltransferase; Provisional
Probab=35.11 E-value=90 Score=31.58 Aligned_cols=58 Identities=26% Similarity=0.290 Sum_probs=36.5
Q ss_pred cccccCceEEEEeeeCCcceeEeeEEeeeeeccCCCCceeeEEEEEEecCCcc--cccccccc
Q 025634 184 HKLKVGGHVLCFQERRDQGIHYDAHIAEIHRRMHDIRGCRCLFLVRYNHDNTE--ERVRLRRL 244 (250)
Q Consensus 184 ~~v~~G~~v~cf~~~~~~~~yyDA~V~~v~r~~Hd~~~C~C~F~Vr~~h~~~e--e~v~~~~~ 244 (250)
..+..|+.|+|+... +-.||.|.|+++....-...+. =.|-|.|..-+.. |=|+.++|
T Consensus 52 ~~~~VGekVla~~~~--Dg~~~~A~VI~~R~~~~~~~~~-~~YYVHY~g~nrRlDEWV~~~rL 111 (450)
T PLN00104 52 LPLEVGTRVMCRWRF--DGKYHPVKVIERRRGGSGGPND-YEYYVHYTEFNRRLDEWVKLEQL 111 (450)
T ss_pred ceeccCCEEEEEECC--CCCEEEEEEEEEeccCCCCCCC-ceEEEEEecCCccHhhccCHhhc
Confidence 356799999999853 3567899999998633001111 1589999876622 33444443
No 85
>PF11523 DUF3223: Protein of unknown function (DUF3223); InterPro: IPR021602 This family of proteins has no known function. ; PDB: 2K0M_A.
Probab=32.99 E-value=54 Score=24.96 Aligned_cols=32 Identities=41% Similarity=0.602 Sum_probs=21.1
Q ss_pred EeeeeeccCCCCc-eeeEEEEEEecCCcccccccc
Q 025634 209 IAEIHRRMHDIRG-CRCLFLVRYNHDNTEERVRLR 242 (250)
Q Consensus 209 V~~v~r~~Hd~~~-C~C~F~Vr~~h~~~ee~v~~~ 242 (250)
|..|+-+.|...+ .+|.|+||= |++++.....
T Consensus 41 i~~i~V~~hp~~~~srCF~vvR~--DGs~~DFSy~ 73 (76)
T PF11523_consen 41 IDHIMVRKHPEFKDSRCFFVVRT--DGSEEDFSYR 73 (76)
T ss_dssp EEEEEEEESSSS---EEEEEEET--TS-EEE--GG
T ss_pred eeeEEEeecCCCCcceEEEEEEe--CCCeeeeEhh
Confidence 6778888998865 999999984 6666655543
No 86
>PRK11511 DNA-binding transcriptional activator MarA; Provisional
Probab=32.68 E-value=32 Score=27.67 Aligned_cols=38 Identities=16% Similarity=0.174 Sum_probs=24.9
Q ss_pred HHHHHHHHhhCCCCCCHHHHHHHHHHhCCCCcCCCCCccchhHHHHHHhhh
Q 025634 21 EKMEKLLMESKDDLLSKEFCQKIAKSFSCSAGRAGKPVVKWTEVQSWFQSR 71 (250)
Q Consensus 21 ~eLEk~f~~~~~~y~~~~~rq~LA~~f~lS~~RaGK~~Vq~~QVk~WFQNR 71 (250)
.++-....+ .+-..-..++||+.+|+|+ .++..+|+.-
T Consensus 12 ~~~~~~I~~---~~~~~~sl~~lA~~~g~S~----------~~l~r~Fk~~ 49 (127)
T PRK11511 12 HSILDWIED---NLESPLSLEKVSERSGYSK----------WHLQRMFKKE 49 (127)
T ss_pred HHHHHHHHH---hcCCCCCHHHHHHHHCcCH----------HHHHHHHHHH
Confidence 344444444 3444566799999999998 7776666654
No 87
>KOG3026 consensus Splicing factor SPF30 [RNA processing and modification]
Probab=31.88 E-value=1.9e+02 Score=27.28 Aligned_cols=47 Identities=30% Similarity=0.480 Sum_probs=32.8
Q ss_pred CCCCCCCCceeEEecccCCCceeeeeeeheeeecccCcceEEEEecCCCCCcccc
Q 025634 110 GEKVPDVSEMEFEARSSKDGAWYDVDMFLAHRFLDCGEAEVRVRFVGFGADEDEW 164 (250)
Q Consensus 110 g~~~~~~~~~efEArs~~D~AWYdV~~fl~hR~~~~ge~ev~Vrf~gFg~eeDEw 164 (250)
|..+-+-....| +.||-|||+.+=- +..-+.++-|-|+++|.-.---
T Consensus 90 ~w~vg~K~~A~~----~ddg~~y~AtIe~----ita~~~~~ai~f~s~~~a~~t~ 136 (262)
T KOG3026|consen 90 GWKVGDKVQAVF----SDDGQIYDATIEH----ITAMEGTVAIIFASYGTAPSTY 136 (262)
T ss_pred ccccCCEEEEee----cCCCceEEeehhh----ccCCCCceeEEEeecccccccc
Confidence 555555566677 9999999998741 3333458899999998765433
No 88
>KOG1911 consensus Heterochromatin-associated protein HP1 and related CHROMO domain proteins [Chromatin structure and dynamics]
Probab=31.22 E-value=27 Score=31.92 Aligned_cols=39 Identities=21% Similarity=0.384 Sum_probs=33.1
Q ss_pred CCCceeeeeeeheeeecccCcceEEEEecCCCCCccccee
Q 025634 127 KDGAWYDVDMFLAHRFLDCGEAEVRVRFVGFGADEDEWVN 166 (250)
Q Consensus 127 ~D~AWYdV~~fl~hR~~~~ge~ev~Vrf~gFg~eeDEw~~ 166 (250)
.+..=|-|...|.||+...+ .+..|+..||.++++-|=+
T Consensus 44 ~~~~~~vvEki~~~r~~~g~-~eYlvkW~Gy~~~~ntWEP 82 (270)
T KOG1911|consen 44 EEEEEYVVEKILKRRKKNGK-IEYLVKWKGYPDPDNTWEP 82 (270)
T ss_pred cccchhhhhhhhhccccCCC-ceeeeecCCCCCccccCCc
Confidence 34445889999999998855 7999999999999999976
No 89
>COG3413 Predicted DNA binding protein [General function prediction only]
Probab=30.90 E-value=56 Score=28.53 Aligned_cols=39 Identities=18% Similarity=0.136 Sum_probs=30.8
Q ss_pred ccCCHHHHHHHHHHHHhhCCCCCCHHHHHHHHHHhCCCC
Q 025634 13 TGFTKTELEKMEKLLMESKDDLLSKEFCQKIAKSFSCSA 51 (250)
Q Consensus 13 t~FT~~Ql~eLEk~f~~~~~~y~~~~~rq~LA~~f~lS~ 51 (250)
..+|+.|++-|-..|+.-=--||-+....+||+.||.|.
T Consensus 154 ~~LTdrQ~~vL~~A~~~GYFd~PR~~~l~dLA~~lGISk 192 (215)
T COG3413 154 NDLTDRQLEVLRLAYKMGYFDYPRRVSLKDLAKELGISK 192 (215)
T ss_pred ccCCHHHHHHHHHHHHcCCCCCCccCCHHHHHHHhCCCH
Confidence 369999999999999982223344566789999999995
No 90
>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=30.53 E-value=42 Score=22.58 Aligned_cols=16 Identities=19% Similarity=0.517 Sum_probs=12.8
Q ss_pred ccCCHHHHHHHHHHHH
Q 025634 13 TGFTKTELEKMEKLLM 28 (250)
Q Consensus 13 t~FT~~Ql~eLEk~f~ 28 (250)
+.||++|+.+||.-..
T Consensus 1 s~FT~~Ql~~L~~Qi~ 16 (37)
T PF08880_consen 1 SPFTPAQLQELRAQIL 16 (37)
T ss_pred CCCCHHHHHHHHHHHH
Confidence 3699999999997433
No 91
>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=29.51 E-value=1.5e+02 Score=20.31 Aligned_cols=40 Identities=20% Similarity=0.281 Sum_probs=30.3
Q ss_pred CCHHHHHHHHHHHHhhCCCCCCHHHHHHHHHHhC-CCCcCCCCCccchhHHHHHHhh
Q 025634 15 FTKTELEKMEKLLMESKDDLLSKEFCQKIAKSFS-CSAGRAGKPVVKWTEVQSWFQS 70 (250)
Q Consensus 15 FT~~Ql~eLEk~f~~~~~~y~~~~~rq~LA~~f~-lS~~RaGK~~Vq~~QVk~WFQN 70 (250)
+|++|...|-.+....++ .=..||+.|+ -|+ .||++=|.+
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 689999999999998653 4678999999 776 999865555
No 92
>PF13873 Myb_DNA-bind_5: Myb/SANT-like DNA-binding domain
Probab=28.99 E-value=1.3e+02 Score=21.88 Aligned_cols=55 Identities=18% Similarity=0.322 Sum_probs=35.9
Q ss_pred ccCCHHHHHHHHHHHHhhCCCCCC-----------HHHHHHHHHHhCCCCcCCCCCccchhHHHHHHhhh
Q 025634 13 TGFTKTELEKMEKLLMESKDDLLS-----------KEFCQKIAKSFSCSAGRAGKPVVKWTEVQSWFQSR 71 (250)
Q Consensus 13 t~FT~~Ql~eLEk~f~~~~~~y~~-----------~~~rq~LA~~f~lS~~RaGK~~Vq~~QVk~WFQNR 71 (250)
..||++|...|-.++.++....-+ ...=++||..||.-.+. .=++.|++..++|=
T Consensus 3 ~~fs~~E~~~Lv~~v~~~~~il~~k~~~~~~~~~k~~~W~~I~~~lN~~~~~----~Rs~~~lkkkW~nl 68 (78)
T PF13873_consen 3 PNFSEEEKEILVELVEKHKDILENKFSDSVSNKEKRKAWEEIAEELNALGPG----KRSWKQLKKKWKNL 68 (78)
T ss_pred CCCCHHHHHHHHHHHHHhHHHHhcccccHHHHHHHHHHHHHHHHHHHhcCCC----CCCHHHHHHHHHHH
Confidence 479999999988888775321111 12336799999885432 45667777666554
No 93
>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=28.24 E-value=72 Score=21.43 Aligned_cols=28 Identities=14% Similarity=0.164 Sum_probs=20.1
Q ss_pred CCCCHHHHHHHHHHhCCCCcCCCCCccchhHHHHHHhh
Q 025634 33 DLLSKEFCQKIAKSFSCSAGRAGKPVVKWTEVQSWFQS 70 (250)
Q Consensus 33 ~y~~~~~rq~LA~~f~lS~~RaGK~~Vq~~QVk~WFQN 70 (250)
.|...-...++|+.+|.|+ ..|+.|.+.
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 3566668899999999998 889988865
No 94
>PF13384 HTH_23: Homeodomain-like domain; PDB: 2X48_C.
Probab=28.02 E-value=53 Score=21.76 Aligned_cols=23 Identities=26% Similarity=0.397 Sum_probs=17.0
Q ss_pred HHHHHHHHHhCCCCcCCCCCccchhHHHHHHhh
Q 025634 38 EFCQKIAKSFSCSAGRAGKPVVKWTEVQSWFQS 70 (250)
Q Consensus 38 ~~rq~LA~~f~lS~~RaGK~~Vq~~QVk~WFQN 70 (250)
....++|+.||+|. ..|..|.+.
T Consensus 18 ~s~~~ia~~lgvs~----------~Tv~~w~kr 40 (50)
T PF13384_consen 18 WSIREIAKRLGVSR----------STVYRWIKR 40 (50)
T ss_dssp --HHHHHHHHTS-H----------HHHHHHHT-
T ss_pred CCHHHHHHHHCcCH----------HHHHHHHHH
Confidence 36789999999997 889999754
No 95
>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=27.72 E-value=52 Score=21.04 Aligned_cols=21 Identities=24% Similarity=0.245 Sum_probs=14.7
Q ss_pred HHHHHHHHHHhCCCCcCCCCCccchhHHHHH
Q 025634 37 KEFCQKIAKSFSCSAGRAGKPVVKWTEVQSW 67 (250)
Q Consensus 37 ~~~rq~LA~~f~lS~~RaGK~~Vq~~QVk~W 67 (250)
.+.+..||.+|+++. .+++.|
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 467899999999996 777655
No 96
>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=26.92 E-value=1.6e+02 Score=19.20 Aligned_cols=31 Identities=3% Similarity=0.051 Sum_probs=20.6
Q ss_pred CCHHHHHHHHHHHHhhCCCCCCHHHHHHHHHHhCCC
Q 025634 15 FTKTELEKMEKLLMESKDDLLSKEFCQKIAKSFSCS 50 (250)
Q Consensus 15 FT~~Ql~eLEk~f~~~~~~y~~~~~rq~LA~~f~lS 50 (250)
.++..|..+|+ +...|+.....+||+.||++
T Consensus 27 vs~~~vs~~e~-----g~~~~~~~~~~~i~~~lgv~ 57 (58)
T TIGR03070 27 VGLRFIRDVEN-----GKPTVRLDKVLRVLDALGLE 57 (58)
T ss_pred CCHHHHHHHHC-----CCCCCCHHHHHHHHHHcCCC
Confidence 44444444442 24468888899999988875
No 97
>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=26.91 E-value=73 Score=24.05 Aligned_cols=28 Identities=25% Similarity=0.547 Sum_probs=18.4
Q ss_pred eeEEecccCCCceeeeeeeheeeecccCcceEEEEecC
Q 025634 119 MEFEARSSKDGAWYDVDMFLAHRFLDCGEAEVRVRFVG 156 (250)
Q Consensus 119 ~efEArs~~D~AWYdV~~fl~hR~~~~ge~ev~Vrf~g 156 (250)
+.+ --...+-|||+.+.. .++ ..=||+|
T Consensus 61 ~~w--~l~~s~gwYDl~v~~------~~~--F~rr~aG 88 (89)
T PF05506_consen 61 LTW--PLAASGGWYDLTVTG------PNG--FLRRFAG 88 (89)
T ss_pred EEE--eecCCCCcEEEEEEc------CCC--EEEEecC
Confidence 445 337789999999973 232 5666665
No 98
>PRK09413 IS2 repressor TnpA; Reviewed
Probab=26.48 E-value=1.7e+02 Score=23.45 Aligned_cols=43 Identities=14% Similarity=0.131 Sum_probs=28.5
Q ss_pred CccCCHHHHHHHHHHHHhhCCCCCCHHHHHHHHHHhCCCCcCCCCCccchhHHHHHHhh
Q 025634 12 FTGFTKTELEKMEKLLMESKDDLLSKEFCQKIAKSFSCSAGRAGKPVVKWTEVQSWFQS 70 (250)
Q Consensus 12 Rt~FT~~Ql~eLEk~f~~~~~~y~~~~~rq~LA~~f~lS~~RaGK~~Vq~~QVk~WFQN 70 (250)
|..||.++-.++=....+. + ....+||.+|++|+ .+|-+|-+.
T Consensus 10 rr~ys~EfK~~aV~~~~~~-g-----~sv~evA~e~gIs~----------~tl~~W~r~ 52 (121)
T PRK09413 10 RRRRTTQEKIAIVQQSFEP-G-----MTVSLVARQHGVAA----------SQLFLWRKQ 52 (121)
T ss_pred CCCCCHHHHHHHHHHHHcC-C-----CCHHHHHHHHCcCH----------HHHHHHHHH
Confidence 4568888754433322331 1 14568899999998 999999654
No 99
>PTZ00184 calmodulin; Provisional
Probab=26.32 E-value=2.9e+02 Score=21.06 Aligned_cols=37 Identities=8% Similarity=0.164 Sum_probs=26.9
Q ss_pred cCCHHHHHHHHHHHHhh---CCCCCCHHHHHHHHHHhCCC
Q 025634 14 GFTKTELEKMEKLLMES---KDDLLSKEFCQKIAKSFSCS 50 (250)
Q Consensus 14 ~FT~~Ql~eLEk~f~~~---~~~y~~~~~rq~LA~~f~lS 50 (250)
.+|..++.++.+.|... +...++......+...++.+
T Consensus 4 ~~~~~~~~~~~~~F~~~D~~~~G~i~~~e~~~~l~~~~~~ 43 (149)
T PTZ00184 4 QLTEEQIAEFKEAFSLFDKDGDGTITTKELGTVMRSLGQN 43 (149)
T ss_pred ccCHHHHHHHHHHHHHHcCCCCCcCCHHHHHHHHHHhCCC
Confidence 47889999999998773 45667777776666666654
No 100
>PHA01976 helix-turn-helix protein
Probab=26.02 E-value=1.7e+02 Score=20.22 Aligned_cols=20 Identities=10% Similarity=0.149 Sum_probs=15.9
Q ss_pred CCCCCHHHHHHHHHHhCCCC
Q 025634 32 DDLLSKEFCQKIAKSFSCSA 51 (250)
Q Consensus 32 ~~y~~~~~rq~LA~~f~lS~ 51 (250)
...|+.+...+||+.||++.
T Consensus 39 ~~~p~~~~l~~ia~~l~v~~ 58 (67)
T PHA01976 39 KRLPNLKTLLRLADALGVTL 58 (67)
T ss_pred CCCCCHHHHHHHHHHHCcCH
Confidence 45688888888888888884
No 101
>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=25.81 E-value=62 Score=20.98 Aligned_cols=22 Identities=14% Similarity=0.120 Sum_probs=18.1
Q ss_pred HHHHHHHhCCCCcCCCCCccchhHHHHHHhhh
Q 025634 40 CQKIAKSFSCSAGRAGKPVVKWTEVQSWFQSR 71 (250)
Q Consensus 40 rq~LA~~f~lS~~RaGK~~Vq~~QVk~WFQNR 71 (250)
..++|+.+|+|+ ..|+.|-++-
T Consensus 3 ~~e~a~~~gv~~----------~tlr~~~~~g 24 (49)
T cd04761 3 IGELAKLTGVSP----------STLRYYERIG 24 (49)
T ss_pred HHHHHHHHCcCH----------HHHHHHHHCC
Confidence 357899999998 8899997654
No 102
>COG5126 FRQ1 Ca2+-binding protein (EF-Hand superfamily) [Signal transduction mechanisms / Cytoskeleton / Cell division and chromosome partitioning / General function prediction only]
Probab=25.64 E-value=1.6e+02 Score=25.64 Aligned_cols=41 Identities=20% Similarity=0.359 Sum_probs=32.1
Q ss_pred CCccCCHHHHHHHHHHHHhh---CCCCCCHHHHHHHHHHhCCCC
Q 025634 11 VFTGFTKTELEKMEKLLMES---KDDLLSKEFCQKIAKSFSCSA 51 (250)
Q Consensus 11 ~Rt~FT~~Ql~eLEk~f~~~---~~~y~~~~~rq~LA~~f~lS~ 51 (250)
.++.||.+||++|-+.|.-. +...+++.....+=+.|+..+
T Consensus 10 ~~~~~t~~qi~~lkeaF~l~D~d~~G~I~~~el~~ilr~lg~~~ 53 (160)
T COG5126 10 TFTQLTEEQIQELKEAFQLFDRDSDGLIDRNELGKILRSLGFNP 53 (160)
T ss_pred hcccCCHHHHHHHHHHHHHhCcCCCCCCcHHHHHHHHHHcCCCC
Confidence 58899999999999999864 356788888877766666554
No 103
>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=25.14 E-value=45 Score=24.80 Aligned_cols=44 Identities=20% Similarity=0.311 Sum_probs=24.4
Q ss_pred cCCHHH-HHHHHHHHHhhCCCCCCHHHHHHHHHHhCCCCcCCCCCccchhHHHHHHhhh
Q 025634 14 GFTKTE-LEKMEKLLMESKDDLLSKEFCQKIAKSFSCSAGRAGKPVVKWTEVQSWFQSR 71 (250)
Q Consensus 14 ~FT~~Q-l~eLEk~f~~~~~~y~~~~~rq~LA~~f~lS~~RaGK~~Vq~~QVk~WFQNR 71 (250)
.||..- |.-+|-..+..+ ...-...-|.+||.++ ++|+.|-+-+
T Consensus 5 sy~~~FKL~Vv~~a~~~~n----c~~~~RAaarkf~V~r----------~~Vr~W~kqe 49 (58)
T PF09607_consen 5 SYTAEFKLKVVEYAEKDNN----CKGNQRAAARKFNVSR----------RQVRKWRKQE 49 (58)
T ss_dssp ---HHHHHHHHHHHHH-TT----TTT-HHHHHHHTTS-H----------HHHHHHHTTH
T ss_pred ccChHHHHHHHHHHHHccc----hhhhHHHHHHHhCccH----------HHHHHHHHHH
Confidence 455443 344454444432 2223457899999998 9999998754
No 104
>PRK12461 UDP-N-acetylglucosamine acyltransferase; Provisional
Probab=24.85 E-value=1.1e+02 Score=27.91 Aligned_cols=41 Identities=7% Similarity=-0.002 Sum_probs=29.7
Q ss_pred CCccCCHHHHHHHHHHHHhhCCCC-CCHHHHHHHHHHhCCCC
Q 025634 11 VFTGFTKTELEKMEKLLMESKDDL-LSKEFCQKIAKSFSCSA 51 (250)
Q Consensus 11 ~Rt~FT~~Ql~eLEk~f~~~~~~y-~~~~~rq~LA~~f~lS~ 51 (250)
.|-.||++++..|++.|+..=..- +-.+..++|++.+..++
T Consensus 196 ~r~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 237 (255)
T PRK12461 196 RRRGFSSRAIRALKRAYKIIYRSGLSVQQAVAELELQQFESP 237 (255)
T ss_pred hhcCCCHHHHHHHHHHHHHHHhcCCCHHHHHHHHHHhccCCH
Confidence 367899999999999998752223 33455777777777665
No 105
>PF01343 Peptidase_S49: Peptidase family S49 peptidase classification.; InterPro: IPR002142 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. Proteolytic enzymes that exploit serine in their catalytic activity are ubiquitous, being found in viruses, bacteria and eukaryotes []. They include a wide range of peptidase activity, including exopeptidase, endopeptidase, oligopeptidase and omega-peptidase activity. Over 20 families (denoted S1 - S66) of serine protease have been identified, these being grouped into clans on the basis of structural similarity and other functional evidence []. Structures are known for members of the clans and the structures indicate that some appear to be totally unrelated, suggesting different evolutionary origins for the serine peptidases []. Not withstanding their different evolutionary origins, there are similarities in the reaction mechanisms of several peptidases. Chymotrypsin, subtilisin and carboxypeptidase C have a catalytic triad of serine, aspartate and histidine in common: serine acts as a nucleophile, aspartate as an electrophile, and histidine as a base []. The geometric orientations of the catalytic residues are similar between families, despite different protein folds []. The linear arrangements of the catalytic residues commonly reflect clan relationships. For example the catalytic triad in the chymotrypsin clan (PA) is ordered HDS, but is ordered DHS in the subtilisin clan (SB) and SDH in the carboxypeptidase clan (SC) [, ]. This group of serine peptidases belong to MEROPS peptidase family S49 (protease IV family, clan S-). The predicted active site serine for members of this family occurs in a transmembrane domain. The domain defines sequences in viruses, archaea, bacteria and plants. These sequences are variously annotated in the different taxonomic groups, examples are: Viruses: capsid protein Archaea: proteinase IV homolog Bacteria: proteinase IV, sohB, SppA, pfaP, putative protease Plants: SppA, protease IV This group also contains proteins classified as non-peptidase homologues that either have been found experimentally to be without peptidase activity, or lack amino acid residues that are believed to be essential for the catalytic activity of peptidases. Related proteins, non-peptidase homologs and unclassified S49 members are also to be found in IPR002810 from INTERPRO.; GO: 0008233 peptidase activity, 0006508 proteolysis; PDB: 3RST_B 3BEZ_D 3BF0_A.
Probab=24.32 E-value=84 Score=26.04 Aligned_cols=46 Identities=20% Similarity=0.245 Sum_probs=36.6
Q ss_pred CCccCCHHHHHHHHHHHHhhCCCCCCHHHHHHHHHHhCCCCcCCCCCccchhHHHHHHhhh
Q 025634 11 VFTGFTKTELEKMEKLLMESKDDLLSKEFCQKIAKSFSCSAGRAGKPVVKWTEVQSWFQSR 71 (250)
Q Consensus 11 ~Rt~FT~~Ql~eLEk~f~~~~~~y~~~~~rq~LA~~f~lS~~RaGK~~Vq~~QVk~WFQNR 71 (250)
++..+|+++.+.|++.+... -..+...+|+.=+++. .+|..|++++
T Consensus 76 ~~~~~s~~~r~~~~~~l~~~-----~~~f~~~Va~~R~~~~----------~~v~~~~~~~ 121 (154)
T PF01343_consen 76 PRDPMSEEERENLQELLDEL-----YDQFVNDVAEGRGLSP----------DDVEEIADGG 121 (154)
T ss_dssp TTSS--HHHHHHHHHHHHHH-----HHHHHHHHHHHHTS-H----------HHHHCHHCCH
T ss_pred cCCCCCHHHHHHHHHHHHHH-----HHHHHHHHHHccCCCH----------HHHHHHHhhc
Confidence 57889999999999999883 3679999999999887 8899999874
No 106
>cd00110 LamG Laminin G domain; Laminin G-like domains are usually Ca++ mediated receptors that can have binding sites for steroids, beta1 integrins, heparin, sulfatides, fibulin-1, and alpha-dystroglycans. Proteins that contain LamG domains serve a variety of purposes including signal transduction via cell-surface steroid receptors, adhesion, migration and differentiation through mediation of cell adhesion molecules.
Probab=23.87 E-value=1.1e+02 Score=23.62 Aligned_cols=31 Identities=16% Similarity=0.371 Sum_probs=20.4
Q ss_pred ceeEEecc-cCCCceeeeeeeheeeecccCcceEEEE
Q 025634 118 EMEFEARS-SKDGAWYDVDMFLAHRFLDCGEAEVRVR 153 (250)
Q Consensus 118 ~~efEArs-~~D~AWYdV~~fl~hR~~~~ge~ev~Vr 153 (250)
.+.+.... ..||.||.|.+.. ..+...|.|.
T Consensus 68 ~~~~~~~~~v~dg~Wh~v~i~~-----~~~~~~l~VD 99 (151)
T cd00110 68 SLVLSSKTPLNDGQWHSVSVER-----NGRSVTLSVD 99 (151)
T ss_pred cEEEEccCccCCCCEEEEEEEE-----CCCEEEEEEC
Confidence 35554443 8899999999973 4454555554
No 107
>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=23.74 E-value=1.5e+02 Score=19.77 Aligned_cols=38 Identities=18% Similarity=0.171 Sum_probs=27.3
Q ss_pred cCCHHHHHHHHHHHHhhCCCCCCHHHHHHHHHHhCCCCcCCCCCccchhHHHHHH
Q 025634 14 GFTKTELEKMEKLLMESKDDLLSKEFCQKIAKSFSCSAGRAGKPVVKWTEVQSWF 68 (250)
Q Consensus 14 ~FT~~Ql~eLEk~f~~~~~~y~~~~~rq~LA~~f~lS~~RaGK~~Vq~~QVk~WF 68 (250)
.+++.|-.-+.-.|-+ .-..+++|+.+|+|. ..|+.+.
T Consensus 4 ~L~~~er~vi~~~y~~-------~~t~~eIa~~lg~s~----------~~V~~~~ 41 (50)
T PF04545_consen 4 QLPPREREVIRLRYFE-------GLTLEEIAERLGISR----------STVRRIL 41 (50)
T ss_dssp TS-HHHHHHHHHHHTS-------T-SHHHHHHHHTSCH----------HHHHHHH
T ss_pred hCCHHHHHHHHHHhcC-------CCCHHHHHHHHCCcH----------HHHHHHH
Confidence 4677888888888844 225789999999997 6676554
No 108
>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=23.18 E-value=83 Score=19.69 Aligned_cols=23 Identities=13% Similarity=0.419 Sum_probs=19.0
Q ss_pred HHHHHHHhCCCCcCCCCCccchhHHHHHHhhhc
Q 025634 40 CQKIAKSFSCSAGRAGKPVVKWTEVQSWFQSRQ 72 (250)
Q Consensus 40 rq~LA~~f~lS~~RaGK~~Vq~~QVk~WFQNRR 72 (250)
..++|+.|++|+ .-|+.|-++-.
T Consensus 3 ~~e~a~~lgvs~----------~tl~~~~~~g~ 25 (49)
T cd04762 3 TKEAAELLGVSP----------STLRRWVKEGK 25 (49)
T ss_pred HHHHHHHHCcCH----------HHHHHHHHcCC
Confidence 468899999997 88999988754
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=23.18 E-value=1.3e+02 Score=21.52 Aligned_cols=37 Identities=22% Similarity=0.309 Sum_probs=22.4
Q ss_pred HHHHHHHHHhhCCCCCCHHHHHHHHHHhCCCCcCCCCCccchhHHHHHHh
Q 025634 20 LEKMEKLLMESKDDLLSKEFCQKIAKSFSCSAGRAGKPVVKWTEVQSWFQ 69 (250)
Q Consensus 20 l~eLEk~f~~~~~~y~~~~~rq~LA~~f~lS~~RaGK~~Vq~~QVk~WFQ 69 (250)
|.+-.+.|.+..++.|+. ++||+.+|+|. ++|...++
T Consensus 6 i~~a~~~L~~~lgr~Pt~---eEiA~~lgis~----------~~v~~~l~ 42 (78)
T PF04539_consen 6 IERARRELEQELGREPTD---EEIAEELGISV----------EEVRELLQ 42 (78)
T ss_dssp HHHHHHHHHHHHSS--BH---HHHHHHHTS-H----------HHHHHHHH
T ss_pred HHHHHHHHHHHhCCCCCH---HHHHHHHcccH----------HHHHHHHH
Confidence 334444444444565554 78999999998 88886655
No 110
>PF15057 DUF4537: Domain of unknown function (DUF4537)
Probab=22.74 E-value=1.8e+02 Score=23.94 Aligned_cols=36 Identities=25% Similarity=0.500 Sum_probs=26.9
Q ss_pred CceEEEEeeeCCcceeEeeEEeeeeeccCCCCceeeEEEEEEecCC
Q 025634 189 GGHVLCFQERRDQGIHYDAHIAEIHRRMHDIRGCRCLFLVRYNHDN 234 (250)
Q Consensus 189 G~~v~cf~~~~~~~~yyDA~V~~v~r~~Hd~~~C~C~F~Vr~~h~~ 234 (250)
|..|+|-.+ .+..||=+.|..... ...|+|.|+++.
T Consensus 1 g~~VlAR~~--~DG~YY~GtV~~~~~--------~~~~lV~f~~~~ 36 (124)
T PF15057_consen 1 GQKVLARRE--EDGFYYPGTVKKCVS--------SGQFLVEFDDGD 36 (124)
T ss_pred CCeEEEeeC--CCCcEEeEEEEEccC--------CCEEEEEECCCC
Confidence 678888765 346799999988772 346999995554
No 111
>PF10777 YlaC: Inner membrane protein YlaC; InterPro: IPR019713 The extracytoplasmic function (ECF) sigma factors are small regulatory proteins that are quite divergent in sequence relative to most other sigma factors. YlaC, regulated by YlaA, is important in oxidative stress resistance. It contributes to hydrogen peroxide resistance in Bacillus subtilis [].
Probab=22.11 E-value=69 Score=28.11 Aligned_cols=24 Identities=38% Similarity=0.692 Sum_probs=20.8
Q ss_pred eeeecccCcceEEEEecCCCCCcccceecc
Q 025634 139 AHRFLDCGEAEVRVRFVGFGADEDEWVNVK 168 (250)
Q Consensus 139 ~hR~~~~ge~ev~Vrf~gFg~eeDEw~~v~ 168 (250)
-||+-+.|-+.|||-|.| ||++.+
T Consensus 85 ~YrfEDIdvLDLRVCYNG------EWy~tr 108 (155)
T PF10777_consen 85 RYRFEDIDVLDLRVCYNG------EWYNTR 108 (155)
T ss_pred eeeecccCeeEEeEEEcc------eeeeec
Confidence 478889999999999998 999854
No 112
>COG5484 Uncharacterized conserved protein [Function unknown]
Probab=22.02 E-value=47 Score=31.52 Aligned_cols=32 Identities=25% Similarity=0.414 Sum_probs=26.2
Q ss_pred CCCCHHHHHHHHHHhCCCCcCCCCCccchhHHHHHHhhhcccCC
Q 025634 33 DLLSKEFCQKIAKSFSCSAGRAGKPVVKWTEVQSWFQSRQQDRP 76 (250)
Q Consensus 33 ~y~~~~~rq~LA~~f~lS~~RaGK~~Vq~~QVk~WFQNRR~k~~ 76 (250)
.|+..--..+||+++|+|+ .||+.|= ||..|.
T Consensus 15 ~yl~gmk~~dIAeklGvsp----------ntiksWK--rr~gWs 46 (279)
T COG5484 15 DYLKGMKLKDIAEKLGVSP----------NTIKSWK--RRDGWS 46 (279)
T ss_pred HHHhhccHHHHHHHhCCCh----------HHHHHHH--HhcCCC
Confidence 4666667789999999999 9999995 577884
No 113
>PF06191 DUF995: Protein of unknown function (DUF995); InterPro: IPR009337 This is a family of uncharacterised Proteobacteria proteins.
Probab=21.61 E-value=1.2e+02 Score=26.07 Aligned_cols=67 Identities=28% Similarity=0.362 Sum_probs=43.4
Q ss_pred CCCCCceeEEec-ccCCCceeeeeeeheeeecccCcceEEEEecCCCCCcccceeccccccccCCCCCcccccccccCce
Q 025634 113 VPDVSEMEFEAR-SSKDGAWYDVDMFLAHRFLDCGEAEVRVRFVGFGADEDEWVNVKNAVRERSVPLEPSDCHKLKVGGH 191 (250)
Q Consensus 113 ~~~~~~~efEAr-s~~D~AWYdV~~fl~hR~~~~ge~ev~Vrf~gFg~eeDEw~~v~~~~R~rS~p~e~~eC~~v~~G~~ 191 (250)
+++...|=|+|. .+.+|+.=+...| +||+.. | .|.=+. +.+.|||-|| .+-+-.+-|=.+|+.||.
T Consensus 77 Vt~~GklC~~a~W~~~~g~~~~~tCf-~H~~~g-g--~IyQr~----~pdg~WYvfk-----~~~~~~~DE~~kl~~gd~ 143 (145)
T PF06191_consen 77 VTDNGKLCFRATWHSKSGSGPASTCF-SHRIDG-G--VIYQRK----EPDGEWYVFK-----HNPVRKGDEFRKLVRGDY 143 (145)
T ss_pred ECCCCCEEEEeEEECCCCCcCCCcee-eEEEEC-C--EEEEee----CCCCCeEeec-----CCCCCCCchHHhhccCCc
Confidence 666667888762 2233333345566 699864 4 444442 2368999998 345556678999999998
Q ss_pred E
Q 025634 192 V 192 (250)
Q Consensus 192 v 192 (250)
|
T Consensus 144 v 144 (145)
T PF06191_consen 144 V 144 (145)
T ss_pred c
Confidence 7
No 114
>PF13730 HTH_36: Helix-turn-helix domain
Probab=21.60 E-value=2.6e+02 Score=18.74 Aligned_cols=46 Identities=15% Similarity=-0.005 Sum_probs=29.7
Q ss_pred cCCHHHHHHHHHHHHhhCCCCCCHHHHHHHHHHhCCCCcCCCCCccchhHHHHHHh
Q 025634 14 GFTKTELEKMEKLLMESKDDLLSKEFCQKIAKSFSCSAGRAGKPVVKWTEVQSWFQ 69 (250)
Q Consensus 14 ~FT~~Ql~eLEk~f~~~~~~y~~~~~rq~LA~~f~lS~~RaGK~~Vq~~QVk~WFQ 69 (250)
..++.+..-+=-+....++..-.-.-.+.||+.+|+|. +.|+.+.+
T Consensus 2 ~Ls~~~~~v~~~l~~~~~~~~~~~pS~~~la~~~g~s~----------~Tv~~~i~ 47 (55)
T PF13730_consen 2 NLSPTAKLVYLYLASYANKNGGCFPSQETLAKDLGVSR----------RTVQRAIK 47 (55)
T ss_pred CCCHHHHHHHHHHHHhcCCCCCCCcCHHHHHHHHCcCH----------HHHHHHHH
Confidence 45677776666666654211113335789999999997 77776654
No 115
>smart00421 HTH_LUXR helix_turn_helix, Lux Regulon. lux regulon (activates the bioluminescence operon
Probab=21.29 E-value=1.7e+02 Score=18.62 Aligned_cols=44 Identities=20% Similarity=0.200 Sum_probs=30.5
Q ss_pred cCCHHHHHHHHHHHHhhCCCCCCHHHHHHHHHHhCCCCcCCCCCccchhHHHHHHhhhcccC
Q 025634 14 GFTKTELEKMEKLLMESKDDLLSKEFCQKIAKSFSCSAGRAGKPVVKWTEVQSWFQSRQQDR 75 (250)
Q Consensus 14 ~FT~~Ql~eLEk~f~~~~~~y~~~~~rq~LA~~f~lS~~RaGK~~Vq~~QVk~WFQNRR~k~ 75 (250)
.+|+.|...++-. .. +. ...++|+.+++|. ..|..|.+.=+.+.
T Consensus 3 ~l~~~e~~i~~~~-~~--g~-----s~~eia~~l~is~----------~tv~~~~~~~~~kl 46 (58)
T smart00421 3 SLTPREREVLRLL-AE--GL-----TNKEIAERLGISE----------KTVKTHLSNIMRKL 46 (58)
T ss_pred CCCHHHHHHHHHH-Hc--CC-----CHHHHHHHHCCCH----------HHHHHHHHHHHHHH
Confidence 4788888877553 22 21 4589999999997 77888877544333
No 116
>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=21.20 E-value=68 Score=25.82 Aligned_cols=55 Identities=18% Similarity=0.237 Sum_probs=33.9
Q ss_pred cCCHHHHHHHHHHHHhhCCCCC-CHHHHHHHHHHhCCCCcCC--CCCccc--hhHHHHHHh
Q 025634 14 GFTKTELEKMEKLLMESKDDLL-SKEFCQKIAKSFSCSAGRA--GKPVVK--WTEVQSWFQ 69 (250)
Q Consensus 14 ~FT~~Ql~eLEk~f~~~~~~y~-~~~~rq~LA~~f~lS~~Ra--GK~~Vq--~~QVk~WFQ 69 (250)
.+|++|+..|...+.-.+ .-+ ..-...+||+++|.|..-. |.-.++ .-.++.|.+
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 378999999998877643 011 1235678899999885221 334444 445566654
No 117
>PRK03975 tfx putative transcriptional regulator; Provisional
Probab=21.09 E-value=1.2e+02 Score=25.89 Aligned_cols=45 Identities=18% Similarity=0.106 Sum_probs=34.5
Q ss_pred ccCCHHHHHHHHHHHHhhCCCCCCHHHHHHHHHHhCCCCcCCCCCccchhHHHHHHhhhcccC
Q 025634 13 TGFTKTELEKMEKLLMESKDDLLSKEFCQKIAKSFSCSAGRAGKPVVKWTEVQSWFQSRQQDR 75 (250)
Q Consensus 13 t~FT~~Ql~eLEk~f~~~~~~y~~~~~rq~LA~~f~lS~~RaGK~~Vq~~QVk~WFQNRR~k~ 75 (250)
+.+|+.|.+-|+-.+ + +. ..++||+.+|+|. ..|++|-++-+.+.
T Consensus 5 ~~Lt~rqreVL~lr~-~--Gl-----Tq~EIAe~LGiS~----------~tVs~ie~ra~kkL 49 (141)
T PRK03975 5 SFLTERQIEVLRLRE-R--GL-----TQQEIADILGTSR----------ANVSSIEKRARENI 49 (141)
T ss_pred cCCCHHHHHHHHHHH-c--CC-----CHHHHHHHHCCCH----------HHHHHHHHHHHHHH
Confidence 467888888887643 3 11 4689999999997 88999999877664
No 118
>PF06056 Terminase_5: Putative ATPase subunit of terminase (gpP-like); InterPro: IPR010332 This family of proteins are annotated as ATPase subunits of phage terminase after []. Terminases are viral proteins that are involved in packaging viral DNA into the capsid.; GO: 0005524 ATP binding, 0019069 viral capsid assembly
Probab=21.07 E-value=81 Score=22.80 Aligned_cols=28 Identities=18% Similarity=0.222 Sum_probs=21.8
Q ss_pred HHHHHHHHHHhCCCCcCCCCCccchhHHHHHHhhhcccCC
Q 025634 37 KEFCQKIAKSFSCSAGRAGKPVVKWTEVQSWFQSRQQDRP 76 (250)
Q Consensus 37 ~~~rq~LA~~f~lS~~RaGK~~Vq~~QVk~WFQNRR~k~~ 76 (250)
.-...+||+.||++. ..|.+|=+ |.+|.
T Consensus 13 G~~~~eIA~~Lg~~~----------~TV~~W~~--r~~W~ 40 (58)
T PF06056_consen 13 GWSIKEIAEELGVPR----------STVYSWKD--RYKWD 40 (58)
T ss_pred CCCHHHHHHHHCCCh----------HHHHHHHH--hhCcc
Confidence 335678999999998 99999965 55554
No 119
>PF04936 DUF658: Protein of unknown function (DUF658); InterPro: IPR007020 This entry is represented by Bacteriophage r1t, Orf18. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. These are proteins of unknown function found in Lactococcus lactis and in their associated bacteriophage.
Probab=20.95 E-value=84 Score=28.19 Aligned_cols=32 Identities=22% Similarity=0.400 Sum_probs=27.3
Q ss_pred HHHHHHHHHhCCCCcCCCCCccchhHHHHHHhhhcccCCCCC
Q 025634 38 EFCQKIAKSFSCSAGRAGKPVVKWTEVQSWFQSRQQDRPTKV 79 (250)
Q Consensus 38 ~~rq~LA~~f~lS~~RaGK~~Vq~~QVk~WFQNRR~k~~~~~ 79 (250)
-...+||.-|+.|. ++|+.|-.|=+...++++
T Consensus 15 gt~~e~~~~~~VS~----------~sv~~WiKNG~~~~~a~~ 46 (186)
T PF04936_consen 15 GTIDELADYFDVSR----------TSVSVWIKNGKDPKRAKP 46 (186)
T ss_pred ccHHHHHHHHccCH----------HHHHHHHHcCCCcccccc
Confidence 36789999999998 999999999987776554
No 120
>PF13443 HTH_26: Cro/C1-type HTH DNA-binding domain; PDB: 3TYR_A 3TYS_A 3B7H_A.
Probab=20.78 E-value=85 Score=21.57 Aligned_cols=34 Identities=12% Similarity=0.271 Sum_probs=22.9
Q ss_pred HHHHHHhhCCCCCCHHHHHHHHHHhCCCCcCCCCCccchhHHHHHHhhhc
Q 025634 23 MEKLLMESKDDLLSKEFCQKIAKSFSCSAGRAGKPVVKWTEVQSWFQSRQ 72 (250)
Q Consensus 23 LEk~f~~~~~~y~~~~~rq~LA~~f~lS~~RaGK~~Vq~~QVk~WFQNRR 72 (250)
|.++..+++ + ...+||+..|+|. .+|..|+.++.
T Consensus 2 L~~~m~~~~--i----t~~~La~~~gis~----------~tl~~~~~~~~ 35 (63)
T PF13443_consen 2 LKELMAERG--I----TQKDLARKTGISR----------STLSRILNGKP 35 (63)
T ss_dssp HHHHHHHTT--------HHHHHHHHT--H----------HHHHHHHTTT-
T ss_pred HHHHHHHcC--C----CHHHHHHHHCcCH----------HHHHHHHhccc
Confidence 455566643 1 5689999999997 88999999884
No 121
>PRK04980 hypothetical protein; Provisional
Probab=20.59 E-value=1.8e+02 Score=23.71 Aligned_cols=31 Identities=6% Similarity=-0.008 Sum_probs=25.1
Q ss_pred ccccCceEEEEeeeCCcceeEeeEEeeeeecc
Q 025634 185 KLKVGGHVLCFQERRDQGIHYDAHIAEIHRRM 216 (250)
Q Consensus 185 ~v~~G~~v~cf~~~~~~~~yyDA~V~~v~r~~ 216 (250)
..+|||.|..+..+. ...|+++.|++|...+
T Consensus 31 ~~~~G~~~~V~~~e~-g~~~c~ieI~sV~~i~ 61 (102)
T PRK04980 31 HFKPGDVLRVGTFED-DRYFCTIEVLSVSPVT 61 (102)
T ss_pred CCCCCCEEEEEECCC-CcEEEEEEEEEEEEEe
Confidence 467999999876555 4788999999998654
No 122
>COG4367 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=20.52 E-value=1.1e+02 Score=24.86 Aligned_cols=36 Identities=11% Similarity=0.113 Sum_probs=31.6
Q ss_pred cCCHHHHHHHHHHHHhhCCCCCCHHHHHHHHHHhCCCC
Q 025634 14 GFTKTELEKMEKLLMESKDDLLSKEFCQKIAKSFSCSA 51 (250)
Q Consensus 14 ~FT~~Ql~eLEk~f~~~~~~y~~~~~rq~LA~~f~lS~ 51 (250)
.+.++|+..-.+.|+. |.-++.-..+++|++||.|+
T Consensus 2 SLn~eq~~~Tk~elqa--n~el~~LS~~~iA~~Ln~t~ 37 (97)
T COG4367 2 SLNPEQKQRTKQELQA--NFELCPLSDEEIATALNWTE 37 (97)
T ss_pred CCCHHHHHHHHHHHHH--hhhhccccHHHHHHHhCCCH
Confidence 3678999988899998 57788888999999999998
No 123
>COG2963 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=20.51 E-value=2.5e+02 Score=21.79 Aligned_cols=45 Identities=18% Similarity=0.197 Sum_probs=34.3
Q ss_pred CccCCHHHHHHHHHHHHhhCCCCCCHHHHHHHHHHhCC-CCcCCCCCccchhHHHHHHhhhc
Q 025634 12 FTGFTKTELEKMEKLLMESKDDLLSKEFCQKIAKSFSC-SAGRAGKPVVKWTEVQSWFQSRQ 72 (250)
Q Consensus 12 Rt~FT~~Ql~eLEk~f~~~~~~y~~~~~rq~LA~~f~l-S~~RaGK~~Vq~~QVk~WFQNRR 72 (250)
+..||++.-.++=+.+.+.+ + ...+||.+|++ ++ .++..|-+.=+
T Consensus 5 ~r~~s~EfK~~iv~~~~~~g--~----sv~~vAr~~gv~~~----------~~l~~W~~~~~ 50 (116)
T COG2963 5 RKKYSPEFKLEAVALYLRGG--D----TVSEVAREFGIVSA----------TQLYKWRIQLQ 50 (116)
T ss_pred cccCCHHHHHHHHHHHHhcC--c----cHHHHHHHhCCCCh----------HHHHHHHHHHH
Confidence 67899998888777777732 2 67899999996 87 88887765443
No 124
>COG2944 Predicted transcriptional regulator [Transcription]
Probab=20.47 E-value=1.4e+02 Score=24.58 Aligned_cols=39 Identities=23% Similarity=0.344 Sum_probs=29.6
Q ss_pred CCHHHHHHHHHHHHhhCCCCCCHHHHHHHHHHhCCCCcCCCCCccchhHHHHHHhhhc
Q 025634 15 FTKTELEKMEKLLMESKDDLLSKEFCQKIAKSFSCSAGRAGKPVVKWTEVQSWFQSRQ 72 (250)
Q Consensus 15 FT~~Ql~eLEk~f~~~~~~y~~~~~rq~LA~~f~lS~~RaGK~~Vq~~QVk~WFQNRR 72 (250)
+++.||.+|-+.+.- -....|..||.|. .-|++|=|+|+
T Consensus 44 ls~~eIk~iRe~~~l---------SQ~vFA~~L~vs~----------~Tv~~WEqGr~ 82 (104)
T COG2944 44 LSPTEIKAIREKLGL---------SQPVFARYLGVSV----------STVRKWEQGRK 82 (104)
T ss_pred CCHHHHHHHHHHhCC---------CHHHHHHHHCCCH----------HHHHHHHcCCc
Confidence 777777777666655 2467788888885 66999999996
No 125
>PRK12373 NADH dehydrogenase subunit E; Provisional
Probab=20.45 E-value=2.6e+02 Score=27.89 Aligned_cols=48 Identities=19% Similarity=0.196 Sum_probs=36.4
Q ss_pred CCCCCCCCCCccCCHHHHHHHHHHHHhhC------------------CCCCCHHHHHHHHHHhCCCC
Q 025634 3 RLRPRQRSVFTGFTKTELEKMEKLLMESK------------------DDLLSKEFCQKIAKSFSCSA 51 (250)
Q Consensus 3 r~r~~~Rr~Rt~FT~~Ql~eLEk~f~~~~------------------~~y~~~~~rq~LA~~f~lS~ 51 (250)
||-+-+. ....||++.++.++.++.... ..|++.+..+.||+.|+++.
T Consensus 4 ~~~~~~p-~~f~f~~e~~~~i~~ii~~yp~~~~~salIplL~~~Qe~~GyIp~~ai~~VAe~Lgvp~ 69 (400)
T PRK12373 4 RLHEDQP-DSFAFTPENAAWAEKQITKYPEGRQASAVIPLLMRAQEQEGWVTRAAIEKVADMLDMAY 69 (400)
T ss_pred cccccCC-ccccCCHHHHHHHHHHHHHCCCccCHHHHHHHHHHHHHHcCCCCHHHHHHHHHHhCCCH
Confidence 4444444 455789988888887766542 45999999999999999997
No 126
>PF02210 Laminin_G_2: Laminin G domain; InterPro: IPR012680 Laminins are large heterotrimeric glycoproteins involved in basement membrane function []. The laminin globular (G) domain can be found in one to several copies in various laminin family members, including a large number of extracellular proteins. The C terminus of the laminin alpha chain contains a tandem repeat of five laminin G domains, which are critical for heparin-binding and cell attachment activity []. Laminin alpha4 is distributed in a variety of tissues including peripheral nerves, dorsal root ganglion, skeletal muscle and capillaries; in the neuromuscular junction, it is required for synaptic specialisation []. The structure of the laminin-G domain has been predicted to resemble that of pentraxin []. Laminin G domains can vary in their function, and a variety of binding functions have been ascribed to different LamG modules. For example, the laminin alpha1 and alpha2 chains each have five C-teminal laminin G domains, where only domains LG4 and LG5 contain binding sites for heparin, sulphatides and the cell surface receptor dystroglycan []. Laminin G-containing proteins appear to have a wide variety of roles in cell adhesion, signalling, migration, assembly and differentiation. This entry represents one subtype of laminin G domains, which is sometimes found in association with thrombospondin-type laminin G domains (IPR012679 from INTERPRO).; PDB: 3POY_A 3QCW_B 3R05_B 3ASI_A 3MW4_B 3MW3_A 1QU0_D 1DYK_A 1OKQ_A 3SH4_A ....
Probab=20.43 E-value=1.1e+02 Score=22.64 Aligned_cols=19 Identities=26% Similarity=0.576 Sum_probs=14.4
Q ss_pred eeEEecccCCCceeeeeee
Q 025634 119 MEFEARSSKDGAWYDVDMF 137 (250)
Q Consensus 119 ~efEArs~~D~AWYdV~~f 137 (250)
+.+......||.||.|.+.
T Consensus 44 ~~~~~~~~~dg~wh~v~i~ 62 (128)
T PF02210_consen 44 TTFSNSNLNDGQWHKVSIS 62 (128)
T ss_dssp EEECSSSSTSSSEEEEEEE
T ss_pred eeccCccccccceeEEEEE
Confidence 3444456789999999997
No 127
>PRK09726 antitoxin HipB; Provisional
Probab=20.37 E-value=1.6e+02 Score=22.22 Aligned_cols=32 Identities=19% Similarity=0.200 Sum_probs=21.2
Q ss_pred CCHHHHHHHHHHHHhhCCCCCCHHHHHHHHHHhCCCC
Q 025634 15 FTKTELEKMEKLLMESKDDLLSKEFCQKIAKSFSCSA 51 (250)
Q Consensus 15 FT~~Ql~eLEk~f~~~~~~y~~~~~rq~LA~~f~lS~ 51 (250)
.++..|..||+ +...|+.....+||+.||++.
T Consensus 37 vs~~tis~~e~-----g~~~ps~~~l~~ia~~lgv~~ 68 (88)
T PRK09726 37 IKQATISNFEN-----NPDNTTLTTFFKILQSLELSM 68 (88)
T ss_pred cCHHHHHHHHC-----CCCCCCHHHHHHHHHHcCCCc
Confidence 34444444444 245688888888888888885
No 128
>PF03672 UPF0154: Uncharacterised protein family (UPF0154); InterPro: IPR005359 The proteins in this entry are functionally uncharacterised.
Probab=20.20 E-value=2.3e+02 Score=21.40 Aligned_cols=29 Identities=17% Similarity=0.260 Sum_probs=25.7
Q ss_pred HHHHHHHHhhCCCCCCHHHHHHHHHHhCCCC
Q 025634 21 EKMEKLLMESKDDLLSKEFCQKIAKSFSCSA 51 (250)
Q Consensus 21 ~eLEk~f~~~~~~y~~~~~rq~LA~~f~lS~ 51 (250)
.-||+-|++ |..++.+....+....|-.|
T Consensus 20 ~~~~k~l~~--NPpine~mir~M~~QMG~kp 48 (64)
T PF03672_consen 20 KYMEKQLKE--NPPINEKMIRAMMMQMGRKP 48 (64)
T ss_pred HHHHHHHHH--CCCCCHHHHHHHHHHhCCCc
Confidence 458999999 78999999999999999876
No 129
>PRK10430 DNA-binding transcriptional activator DcuR; Provisional
Probab=20.16 E-value=1.6e+02 Score=25.30 Aligned_cols=46 Identities=11% Similarity=0.096 Sum_probs=33.4
Q ss_pred ccCCHHHHHHHHHHHHhhCCCCCCHHHHHHHHHHhCCCCcCCCCCccchhHHHHHHhhh
Q 025634 13 TGFTKTELEKMEKLLMESKDDLLSKEFCQKIAKSFSCSAGRAGKPVVKWTEVQSWFQSR 71 (250)
Q Consensus 13 t~FT~~Ql~eLEk~f~~~~~~y~~~~~rq~LA~~f~lS~~RaGK~~Vq~~QVk~WFQNR 71 (250)
..+|+.|+.+|..+..++ +=....-++||+++++|+ +.|++-+++=
T Consensus 157 ~~Lt~re~~~l~~~i~~~---~~~g~s~~eIA~~l~iS~----------~Tv~~~~~~~ 202 (239)
T PRK10430 157 KGLTPQTLRTLCQWIDAH---QDYEFSTDELANAVNISR----------VSCRKYLIWL 202 (239)
T ss_pred CCCCHHHHHHHHHHHHhC---CCCCcCHHHHHHHhCchH----------HHHHHHHHHH
Confidence 357888888877777653 222335688999999998 8899877653
Done!