Query 016887
Match_columns 381
No_of_seqs 144 out of 235
Neff 3.3
Searched_HMMs 46136
Date Fri Mar 29 03:42:16 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/016887.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/016887hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG0842 Transcription factor t 99.7 2.2E-18 4.7E-23 168.0 6.5 69 4-84 150-218 (307)
2 KOG0489 Transcription factor z 99.7 1.3E-18 2.8E-23 164.5 4.5 64 6-81 158-221 (261)
3 KOG0488 Transcription factor B 99.7 3.1E-18 6.7E-23 166.4 5.8 67 2-80 167-233 (309)
4 KOG0487 Transcription factor A 99.6 6.2E-17 1.3E-21 157.9 3.8 63 4-78 232-294 (308)
5 KOG0843 Transcription factor E 99.6 9.1E-16 2E-20 141.1 5.3 63 6-80 101-163 (197)
6 KOG0850 Transcription factor D 99.6 2.5E-15 5.3E-20 142.3 6.2 68 2-81 117-184 (245)
7 PF00046 Homeobox: Homeobox do 99.6 5.1E-15 1.1E-19 108.3 5.7 57 8-76 1-57 (57)
8 KOG0492 Transcription factor M 99.5 3.6E-15 7.8E-20 140.0 4.5 70 7-88 144-213 (246)
9 KOG0484 Transcription factor P 99.5 5E-15 1.1E-19 127.2 3.9 61 7-79 17-77 (125)
10 KOG0485 Transcription factor N 99.5 1.3E-14 2.7E-19 137.3 4.0 63 7-81 104-166 (268)
11 KOG0493 Transcription factor E 99.4 6.5E-14 1.4E-18 135.4 5.5 63 8-82 247-309 (342)
12 smart00389 HOX Homeodomain. DN 99.4 1.5E-13 3.2E-18 99.3 5.6 56 8-75 1-56 (56)
13 KOG2251 Homeobox transcription 99.4 1.4E-13 3.1E-18 129.5 5.3 62 6-79 36-97 (228)
14 cd00086 homeodomain Homeodomai 99.4 4.7E-13 1E-17 96.9 6.2 57 9-77 2-58 (59)
15 KOG0491 Transcription factor B 99.4 1.1E-13 2.4E-18 126.5 2.1 63 7-81 100-162 (194)
16 KOG0494 Transcription factor C 99.4 3.9E-13 8.3E-18 129.9 5.3 61 8-80 142-202 (332)
17 KOG0844 Transcription factor E 99.4 2E-13 4.3E-18 134.2 2.3 60 7-78 181-240 (408)
18 KOG0848 Transcription factor C 99.3 2.7E-13 5.8E-18 131.2 2.0 61 9-81 201-261 (317)
19 TIGR01565 homeo_ZF_HD homeobox 99.3 1.9E-12 4.1E-17 99.7 4.6 52 8-71 2-57 (58)
20 KOG0483 Transcription factor H 99.3 2.9E-12 6.2E-17 118.9 4.1 60 8-79 51-110 (198)
21 KOG0847 Transcription factor, 99.1 8.4E-11 1.8E-15 112.0 4.7 63 8-82 168-230 (288)
22 KOG0486 Transcription factor P 99.1 7.7E-11 1.7E-15 116.2 3.5 61 7-79 112-172 (351)
23 COG5576 Homeodomain-containing 99.0 2.3E-10 5E-15 102.6 5.6 61 8-80 52-112 (156)
24 KOG0490 Transcription factor, 99.0 1.4E-10 3.1E-15 103.4 3.8 62 6-79 59-120 (235)
25 KOG4577 Transcription factor L 98.8 5.6E-09 1.2E-13 102.8 4.5 61 6-78 166-226 (383)
26 KOG0849 Transcription factor P 98.6 3.3E-08 7.2E-13 98.1 4.2 61 6-78 175-235 (354)
27 KOG3802 Transcription factor O 98.3 4.3E-07 9.2E-12 92.0 3.8 64 3-79 290-354 (398)
28 KOG0775 Transcription factor S 98.0 1.8E-05 4E-10 77.7 8.9 53 14-78 183-235 (304)
29 PF05920 Homeobox_KN: Homeobox 98.0 4.9E-06 1.1E-10 59.8 3.2 38 26-73 3-40 (40)
30 KOG0490 Transcription factor, 97.7 2.8E-05 6.1E-10 69.6 3.8 62 6-79 152-213 (235)
31 KOG2252 CCAAT displacement pro 97.7 8.3E-05 1.8E-09 78.3 7.1 57 6-74 419-475 (558)
32 KOG0774 Transcription factor P 97.2 0.00027 5.8E-09 69.6 3.0 66 6-81 187-253 (334)
33 KOG1168 Transcription factor A 96.4 0.0012 2.6E-08 66.0 1.0 61 7-79 309-369 (385)
34 PF11717 Tudor-knot: RNA bindi 95.2 0.014 3.1E-07 43.8 2.3 40 151-192 12-51 (55)
35 KOG1146 Homeobox protein [Gene 95.1 0.018 3.8E-07 66.4 3.7 59 8-78 904-962 (1406)
36 PF15057 DUF4537: Domain of un 93.9 0.39 8.5E-06 41.8 8.5 108 147-272 6-113 (124)
37 KOG0773 Transcription factor M 93.6 0.056 1.2E-06 52.8 3.2 60 7-76 239-299 (342)
38 PF11569 Homez: Homeodomain le 91.4 0.17 3.6E-06 39.6 2.6 42 19-72 10-51 (56)
39 cd00024 CHROMO Chromatin organ 90.1 0.21 4.5E-06 35.8 1.9 37 156-192 3-40 (55)
40 PF04218 CENP-B_N: CENP-B N-te 90.0 0.64 1.4E-05 34.9 4.6 46 8-70 1-46 (53)
41 smart00333 TUDOR Tudor domain. 88.9 1.3 2.8E-05 32.1 5.3 54 209-273 2-55 (57)
42 PLN00104 MYST -like histone ac 86.2 2.3 5E-05 44.9 7.3 54 145-200 60-116 (450)
43 PF12824 MRP-L20: Mitochondria 85.8 1.6 3.4E-05 40.2 5.2 55 10-68 82-136 (164)
44 smart00298 CHROMO Chromatin or 84.7 0.73 1.6E-05 32.7 2.1 37 156-192 2-38 (55)
45 PF00385 Chromo: Chromo (CHRro 83.2 0.42 9.1E-06 34.9 0.3 37 156-192 1-39 (55)
46 cd04508 TUDOR Tudor domains ar 82.4 1.2 2.6E-05 31.3 2.4 36 146-186 5-40 (48)
47 smart00743 Agenet Tudor-like d 81.9 4 8.8E-05 30.3 5.2 50 209-268 2-53 (61)
48 smart00561 MBT Present in Dros 81.0 1.8 3.9E-05 36.3 3.4 45 143-192 32-76 (96)
49 PF06003 SMN: Survival motor n 80.7 3.5 7.5E-05 40.2 5.6 55 208-271 67-121 (264)
50 PF12148 DUF3590: Protein of u 76.6 3.8 8.3E-05 34.5 4.0 48 225-273 9-56 (85)
51 PF11717 Tudor-knot: RNA bindi 75.8 5 0.00011 30.1 4.1 38 210-255 1-38 (55)
52 PF02820 MBT: mbt repeat; Int 75.2 2.9 6.3E-05 32.8 2.8 45 143-192 1-45 (73)
53 PF12148 DUF3590: Protein of u 74.4 3.5 7.7E-05 34.7 3.2 70 146-218 3-74 (85)
54 KOG3623 Homeobox transcription 73.6 12 0.00026 42.3 7.9 52 14-78 564-615 (1007)
55 PF05641 Agenet: Agenet domain 70.7 12 0.00026 29.0 5.3 43 210-260 1-44 (68)
56 PF02796 HTH_7: Helix-turn-hel 69.3 4.8 0.0001 28.9 2.6 35 2-50 1-35 (45)
57 smart00333 TUDOR Tudor domain. 68.1 5.2 0.00011 29.0 2.6 43 146-197 10-52 (57)
58 PF13565 HTH_32: Homeodomain-l 66.8 21 0.00046 27.2 5.8 53 5-66 24-76 (77)
59 PF05641 Agenet: Agenet domain 64.5 4.3 9.3E-05 31.5 1.6 41 152-198 17-63 (68)
60 cd04508 TUDOR Tudor domains ar 58.5 25 0.00053 24.6 4.5 46 213-268 1-46 (48)
61 cd00569 HTH_Hin_like Helix-tur 57.3 27 0.0006 20.6 4.1 32 12-50 4-35 (42)
62 PF06003 SMN: Survival motor n 56.4 9.2 0.0002 37.3 2.7 43 144-190 74-116 (264)
63 PF04967 HTH_10: HTH DNA bindi 54.1 16 0.00034 28.0 3.1 34 14-50 1-37 (53)
64 smart00743 Agenet Tudor-like d 54.0 13 0.00027 27.7 2.6 34 146-184 10-45 (61)
65 PF13873 Myb_DNA-bind_5: Myb/S 48.0 33 0.00071 26.6 4.1 63 12-78 3-76 (78)
66 PF00249 Myb_DNA-binding: Myb- 41.6 72 0.0016 22.7 4.8 45 12-69 2-46 (48)
67 PF13551 HTH_29: Winged helix- 41.4 85 0.0019 24.8 5.7 53 8-68 52-109 (112)
68 smart00717 SANT SANT SWI3, AD 39.5 57 0.0012 21.6 3.8 44 12-69 2-45 (49)
69 PF10668 Phage_terminase: Phag 39.4 16 0.00036 28.9 1.2 30 24-67 14-43 (60)
70 smart00027 EH Eps15 homology d 37.6 77 0.0017 25.4 4.9 37 14-50 4-43 (96)
71 PF01527 HTH_Tnp_1: Transposas 36.4 47 0.001 25.1 3.3 46 9-70 2-47 (76)
72 cd06171 Sigma70_r4 Sigma70, re 35.1 30 0.00064 23.1 1.8 43 14-73 11-53 (55)
73 PF11523 DUF3223: Protein of u 34.0 44 0.00095 27.1 2.9 33 233-267 41-74 (76)
74 PF00567 TUDOR: Tudor domain; 31.9 35 0.00077 26.7 2.1 52 149-208 62-118 (121)
75 PRK03975 tfx putative transcri 31.7 63 0.0014 29.3 3.8 50 12-79 5-54 (141)
76 PF04545 Sigma70_r4: Sigma-70, 29.8 96 0.0021 22.1 3.9 46 13-75 4-49 (50)
77 cd00167 SANT 'SWI3, ADA2, N-Co 29.4 1E+02 0.0023 20.1 3.8 42 13-68 1-42 (45)
78 PF13518 HTH_28: Helix-turn-he 29.0 46 0.00099 23.3 2.0 23 38-70 14-36 (52)
79 PF13936 HTH_38: Helix-turn-he 29.0 48 0.001 23.8 2.1 32 12-50 3-34 (44)
80 PTZ00184 calmodulin; Provision 27.2 1.8E+02 0.0039 23.5 5.5 37 13-49 4-43 (149)
81 PLN00104 MYST -like histone ac 26.9 1.4E+02 0.0031 31.9 6.0 58 208-268 52-111 (450)
82 PF03672 UPF0154: Uncharacteri 26.2 1.1E+02 0.0024 24.7 3.9 36 20-65 20-55 (64)
83 PRK10072 putative transcriptio 25.6 49 0.0011 28.0 1.9 24 39-72 49-72 (96)
84 PRK07539 NADH dehydrogenase su 25.0 1.4E+02 0.0031 26.6 4.9 20 31-50 35-54 (154)
85 PF08281 Sigma70_r4_2: Sigma-7 24.8 76 0.0017 22.7 2.6 31 32-72 22-52 (54)
86 PF01343 Peptidase_S49: Peptid 24.1 1.3E+02 0.0028 26.4 4.4 54 2-70 68-121 (154)
87 COG3458 Acetyl esterase (deace 23.8 92 0.002 32.0 3.8 93 140-239 56-163 (321)
88 PTZ00183 centrin; Provisional 23.6 2.7E+02 0.0059 23.0 6.0 41 9-49 6-49 (158)
89 PRK07571 bidirectional hydroge 23.5 1.6E+02 0.0034 27.4 4.9 38 13-50 15-68 (169)
90 PTZ00064 histone acetyltransfe 23.4 61 0.0013 35.4 2.6 27 170-197 147-173 (552)
91 COG3413 Predicted DNA binding 22.4 92 0.002 28.8 3.3 35 13-50 155-192 (215)
92 TIGR02607 antidote_HigA addict 22.4 2E+02 0.0042 21.8 4.6 19 31-49 42-60 (78)
93 PF09894 DUF2121: Uncharacteri 21.9 1E+02 0.0022 29.7 3.5 51 8-66 20-70 (194)
94 PRK04980 hypothetical protein; 21.8 1.6E+02 0.0034 25.6 4.3 33 209-242 31-63 (102)
95 PF13921 Myb_DNA-bind_6: Myb-l 21.8 2.1E+02 0.0046 20.9 4.5 40 14-69 1-41 (60)
96 PF05506 DUF756: Domain of unk 21.7 93 0.002 25.0 2.8 23 150-180 66-88 (89)
97 TIGR01321 TrpR trp operon repr 21.7 63 0.0014 27.7 1.9 56 13-69 32-92 (94)
98 COG2944 Predicted transcriptio 21.6 1.2E+02 0.0025 26.6 3.5 39 14-71 44-82 (104)
99 KOG1911 Heterochromatin-associ 21.2 64 0.0014 31.1 2.1 45 146-191 39-83 (270)
100 PF00196 GerE: Bacterial regul 21.0 1.4E+02 0.003 21.9 3.4 44 13-74 3-46 (58)
No 1
>KOG0842 consensus Transcription factor tinman/NKX2-3, contains HOX domain [Transcription]
Probab=99.74 E-value=2.2e-18 Score=167.98 Aligned_cols=69 Identities=26% Similarity=0.329 Sum_probs=62.5
Q ss_pred CCCCCCCccccCHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHhCCCccccCCcccccchhHhhhhcchhhHhhhccCCCC
Q 016887 4 PPSNGGPAFRFNPAEVTEMEGILQEHHNAMPSREILVALAEKFSESPERKGKIMVQMKQVWNWFQNRRYAIRAKSIKSPG 83 (381)
Q Consensus 4 Pps~~~pRtrFT~~QI~eLEk~F~e~~n~Yp~r~~rq~LA~kfnlS~~RaGk~~Vq~kQVk~WFQNRR~K~Kkk~~~~p~ 83 (381)
+...|++|.-||+.||-|||+.|++ ++||+..+|+.||..|+|++ +||||||||||||.||+-.-...
T Consensus 150 ~~~kRKrRVLFSqAQV~ELERRFrq--QRYLSAPERE~LA~~LrLT~----------TQVKIWFQNrRYK~KR~~~dk~~ 217 (307)
T KOG0842|consen 150 KRKKRKRRVLFSQAQVYELERRFRQ--QRYLSAPEREHLASSLRLTP----------TQVKIWFQNRRYKTKRQQKDKAL 217 (307)
T ss_pred cccccccccccchhHHHHHHHHHHh--hhccccHhHHHHHHhcCCCc----------hheeeeeecchhhhhhhhhhhhh
Confidence 4467999999999999999999999 69999999999999999975 99999999999999998865544
Q ss_pred C
Q 016887 84 K 84 (381)
Q Consensus 84 k 84 (381)
.
T Consensus 218 ~ 218 (307)
T KOG0842|consen 218 E 218 (307)
T ss_pred h
Confidence 3
No 2
>KOG0489 consensus Transcription factor zerknullt and related HOX domain proteins [General function prediction only]
Probab=99.73 E-value=1.3e-18 Score=164.54 Aligned_cols=64 Identities=20% Similarity=0.294 Sum_probs=59.7
Q ss_pred CCCCCccccCHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHhCCCccccCCcccccchhHhhhhcchhhHhhhccCC
Q 016887 6 SNGGPAFRFNPAEVTEMEGILQEHHNAMPSREILVALAEKFSESPERKGKIMVQMKQVWNWFQNRRYAIRAKSIKS 81 (381)
Q Consensus 6 s~~~pRtrFT~~QI~eLEk~F~e~~n~Yp~r~~rq~LA~kfnlS~~RaGk~~Vq~kQVk~WFQNRR~K~Kkk~~~~ 81 (381)
..+|.||.||..|+.||||+|.. |+||+|..|.+||..|+|+ |+|||||||||||||||.....
T Consensus 158 ~~kR~RtayT~~QllELEkEFhf--N~YLtR~RRiEiA~~L~Lt----------ErQIKIWFQNRRMK~Kk~~k~~ 221 (261)
T KOG0489|consen 158 KSKRRRTAFTRYQLLELEKEFHF--NKYLTRSRRIEIAHALNLT----------ERQIKIWFQNRRMKWKKENKAK 221 (261)
T ss_pred CCCCCCcccchhhhhhhhhhhcc--ccccchHHHHHHHhhcchh----------HHHHHHHHHHHHHHHHHhhccc
Confidence 46899999999999999999999 7999999999999999997 5999999999999999987543
No 3
>KOG0488 consensus Transcription factor BarH and related HOX domain proteins [General function prediction only]
Probab=99.72 E-value=3.1e-18 Score=166.42 Aligned_cols=67 Identities=22% Similarity=0.324 Sum_probs=62.5
Q ss_pred CCCCCCCCCccccCHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHhCCCccccCCcccccchhHhhhhcchhhHhhhccC
Q 016887 2 GRPPSNGGPAFRFNPAEVTEMEGILQEHHNAMPSREILVALAEKFSESPERKGKIMVQMKQVWNWFQNRRYAIRAKSIK 80 (381)
Q Consensus 2 GrPps~~~pRtrFT~~QI~eLEk~F~e~~n~Yp~r~~rq~LA~kfnlS~~RaGk~~Vq~kQVk~WFQNRR~K~Kkk~~~ 80 (381)
+.|+..|+.||.||..||.+|||.|+. .+||+..+|.+||.+|||+. .|||+||||||+|||+....
T Consensus 167 ~~pkK~RksRTaFT~~Ql~~LEkrF~~--QKYLS~~DR~~LA~~LgLTd----------aQVKtWfQNRRtKWKrq~a~ 233 (309)
T KOG0488|consen 167 STPKKRRKSRTAFSDHQLFELEKRFEK--QKYLSVADRIELAASLGLTD----------AQVKTWFQNRRTKWKRQTAE 233 (309)
T ss_pred CCCcccccchhhhhHHHHHHHHHHHHH--hhcccHHHHHHHHHHcCCch----------hhHHHHHhhhhHHHHHHHHh
Confidence 467788999999999999999999999 69999999999999999974 99999999999999998764
No 4
>KOG0487 consensus Transcription factor Abd-B, contains HOX domain [Transcription]
Probab=99.65 E-value=6.2e-17 Score=157.92 Aligned_cols=63 Identities=21% Similarity=0.277 Sum_probs=59.1
Q ss_pred CCCCCCCccccCHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHhCCCccccCCcccccchhHhhhhcchhhHhhhc
Q 016887 4 PPSNGGPAFRFNPAEVTEMEGILQEHHNAMPSREILVALAEKFSESPERKGKIMVQMKQVWNWFQNRRYAIRAKS 78 (381)
Q Consensus 4 Pps~~~pRtrFT~~QI~eLEk~F~e~~n~Yp~r~~rq~LA~kfnlS~~RaGk~~Vq~kQVk~WFQNRR~K~Kkk~ 78 (381)
+.+.|+.|.-+|+.||.||||+|-- |.||+++.|.+|++.||||+ +||||||||||||.||..
T Consensus 232 ~~~~RKKRcPYTK~QtlELEkEFlf--N~YitkeKR~ElSr~lNLTe----------RQVKIWFQNRRMK~KK~~ 294 (308)
T KOG0487|consen 232 ARRGRKKRCPYTKHQTLELEKEFLF--NMYITKEKRLELSRTLNLTE----------RQVKIWFQNRRMKEKKVN 294 (308)
T ss_pred ccccccccCCchHHHHHHHHHHHHH--HHHHhHHHHHHHHHhcccch----------hheeeeehhhhhHHhhhh
Confidence 4467999999999999999999999 79999999999999999975 999999999999999876
No 5
>KOG0843 consensus Transcription factor EMX1 and related HOX domain proteins [Transcription]
Probab=99.59 E-value=9.1e-16 Score=141.13 Aligned_cols=63 Identities=25% Similarity=0.286 Sum_probs=58.4
Q ss_pred CCCCCccccCHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHhCCCccccCCcccccchhHhhhhcchhhHhhhccC
Q 016887 6 SNGGPAFRFNPAEVTEMEGILQEHHNAMPSREILVALAEKFSESPERKGKIMVQMKQVWNWFQNRRYAIRAKSIK 80 (381)
Q Consensus 6 s~~~pRtrFT~~QI~eLEk~F~e~~n~Yp~r~~rq~LA~kfnlS~~RaGk~~Vq~kQVk~WFQNRR~K~Kkk~~~ 80 (381)
..++.||.||.+|+..||..|+. ++|+...+|++||++||||+ +|||+||||||.|.||...+
T Consensus 101 ~~kr~RT~ft~~Ql~~LE~~F~~--~~Yvvg~eR~~LA~~L~Lse----------tQVkvWFQNRRtk~kr~~~e 163 (197)
T KOG0843|consen 101 RPKRIRTAFTPEQLLKLEHAFEG--NQYVVGAERKQLAQSLSLSE----------TQVKVWFQNRRTKHKRMQQE 163 (197)
T ss_pred CCCccccccCHHHHHHHHHHHhc--CCeeechHHHHHHHHcCCCh----------hHhhhhhhhhhHHHHHHHHH
Confidence 34789999999999999999999 79999999999999999985 99999999999999997754
No 6
>KOG0850 consensus Transcription factor DLX and related proteins with LIM Zn-binding and HOX domains [Transcription]
Probab=99.57 E-value=2.5e-15 Score=142.25 Aligned_cols=68 Identities=19% Similarity=0.273 Sum_probs=63.2
Q ss_pred CCCCCCCCCccccCHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHhCCCccccCCcccccchhHhhhhcchhhHhhhccCC
Q 016887 2 GRPPSNGGPAFRFNPAEVTEMEGILQEHHNAMPSREILVALAEKFSESPERKGKIMVQMKQVWNWFQNRRYAIRAKSIKS 81 (381)
Q Consensus 2 GrPps~~~pRtrFT~~QI~eLEk~F~e~~n~Yp~r~~rq~LA~kfnlS~~RaGk~~Vq~kQVk~WFQNRR~K~Kkk~~~~ 81 (381)
|++..-|+|||.|+..||+.|-+.|++ .+||...+|.+||..|||+. +||||||||||.|.||.+.-.
T Consensus 117 gk~KK~RKPRTIYSS~QLqaL~rRFQk--TQYLALPERAeLAAsLGLTQ----------TQVKIWFQNrRSK~KKl~k~g 184 (245)
T KOG0850|consen 117 GKGKKVRKPRTIYSSLQLQALNRRFQQ--TQYLALPERAELAASLGLTQ----------TQVKIWFQNRRSKFKKLKKQG 184 (245)
T ss_pred CCcccccCCcccccHHHHHHHHHHHhh--cchhcCcHHHHHHHHhCCch----------hHhhhhhhhhHHHHHHHHhcC
Confidence 677788999999999999999999999 79999999999999999975 999999999999999988633
No 7
>PF00046 Homeobox: Homeobox domain not present here.; InterPro: IPR001356 The homeobox domain was first identified in a number of drosophila homeotic and segmentation proteins, but is now known to be well-conserved in many other animals, including vertebrates [, , ]. Hox genes encode homeodomain-containing transcriptional regulators that operate differential genetic programs along the anterior-posterior axis of animal bodies []. The domain binds DNA through a helix-turn-helix (HTH) structure. The HTH motif is characterised by two alpha-helices, which make intimate contacts with the DNA and are joined by a short turn. The second helix binds to DNA via a number of hydrogen bonds and hydrophobic interactions, which occur between specific side chains and the exposed bases and thymine methyl groups within the major groove of the DNA []. The first helix helps to stabilise the structure. The motif is very similar in sequence and structure in a wide range of DNA-binding proteins (e.g., cro and repressor proteins, homeotic proteins, etc.). One of the principal differences between HTH motifs in these different proteins arises from the stereo-chemical requirement for glycine in the turn which is needed to avoid steric interference of the beta-carbon with the main chain: for cro and repressor proteins the glycine appears to be mandatory, while for many of the homeotic and other DNA-binding proteins the requirement is relaxed.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0043565 sequence-specific DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 2DA3_A 1LFB_A 2LFB_A 2ECB_A 2DA5_A 3D1N_O 3A03_A 2XSD_C 3CMY_A 1AHD_P ....
Probab=99.56 E-value=5.1e-15 Score=108.30 Aligned_cols=57 Identities=35% Similarity=0.511 Sum_probs=54.0
Q ss_pred CCCccccCHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHhCCCccccCCcccccchhHhhhhcchhhHhh
Q 016887 8 GGPAFRFNPAEVTEMEGILQEHHNAMPSREILVALAEKFSESPERKGKIMVQMKQVWNWFQNRRYAIRA 76 (381)
Q Consensus 8 ~~pRtrFT~~QI~eLEk~F~e~~n~Yp~r~~rq~LA~kfnlS~~RaGk~~Vq~kQVk~WFQNRR~K~Kk 76 (381)
+++|+.||.+|+..||..|.. +.||+.+.++.||..+|++. .||++||||||.+.|+
T Consensus 1 kr~r~~~t~~q~~~L~~~f~~--~~~p~~~~~~~la~~l~l~~----------~~V~~WF~nrR~k~kk 57 (57)
T PF00046_consen 1 KRKRTRFTKEQLKVLEEYFQE--NPYPSKEEREELAKELGLTE----------RQVKNWFQNRRRKEKK 57 (57)
T ss_dssp SSSSSSSSHHHHHHHHHHHHH--SSSCHHHHHHHHHHHHTSSH----------HHHHHHHHHHHHHHHH
T ss_pred CcCCCCCCHHHHHHHHHHHHH--hccccccccccccccccccc----------cccccCHHHhHHHhCc
Confidence 478999999999999999999 79999999999999999985 9999999999999885
No 8
>KOG0492 consensus Transcription factor MSH, contains HOX domain [General function prediction only]
Probab=99.54 E-value=3.6e-15 Score=140.01 Aligned_cols=70 Identities=23% Similarity=0.283 Sum_probs=61.2
Q ss_pred CCCCccccCHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHhCCCccccCCcccccchhHhhhhcchhhHhhhccCCCCCcc
Q 016887 7 NGGPAFRFNPAEVTEMEGILQEHHNAMPSREILVALAEKFSESPERKGKIMVQMKQVWNWFQNRRYAIRAKSIKSPGKLN 86 (381)
Q Consensus 7 ~~~pRtrFT~~QI~eLEk~F~e~~n~Yp~r~~rq~LA~kfnlS~~RaGk~~Vq~kQVk~WFQNRR~K~Kkk~~~~p~kl~ 86 (381)
+|+|||.||..||..||+.|++ .+||+..+|.+++.+|+|+ ++|||+||||||+|-||..--.-+|++
T Consensus 144 nRkPRtPFTtqQLlaLErkfre--kqYLSiaEraefSsSL~LT----------eTqVKIWFQNRRAKaKRlQeae~Ek~k 211 (246)
T KOG0492|consen 144 NRKPRTPFTTQQLLALERKFRE--KQYLSIAERAEFSSSLELT----------ETQVKIWFQNRRAKAKRLQEAELEKLK 211 (246)
T ss_pred CCCCCCCCCHHHHHHHHHHHhH--hhhhhHHHHHhhhhhhhhh----------hhheehhhhhhhHHHHHHHHHHHHHhh
Confidence 6999999999999999999999 5999999999999999996 599999999999999987654444444
Q ss_pred cc
Q 016887 87 VT 88 (381)
Q Consensus 87 ~~ 88 (381)
..
T Consensus 212 ma 213 (246)
T KOG0492|consen 212 MA 213 (246)
T ss_pred hh
Confidence 33
No 9
>KOG0484 consensus Transcription factor PHOX2/ARIX, contains HOX domain [Transcription]
Probab=99.53 E-value=5e-15 Score=127.15 Aligned_cols=61 Identities=26% Similarity=0.355 Sum_probs=56.5
Q ss_pred CCCCccccCHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHhCCCccccCCcccccchhHhhhhcchhhHhhhcc
Q 016887 7 NGGPAFRFNPAEVTEMEGILQEHHNAMPSREILVALAEKFSESPERKGKIMVQMKQVWNWFQNRRYAIRAKSI 79 (381)
Q Consensus 7 ~~~pRtrFT~~QI~eLEk~F~e~~n~Yp~r~~rq~LA~kfnlS~~RaGk~~Vq~kQVk~WFQNRR~K~Kkk~~ 79 (381)
.|+.||.||..||.|||++|.+ .+|||.-.|++||-++.|+ +.+||+||||||+|.||+..
T Consensus 17 QRRIRTTFTS~QLkELErvF~E--THYPDIYTREEiA~kidLT----------EARVQVWFQNRRAKfRKQEr 77 (125)
T KOG0484|consen 17 QRRIRTTFTSAQLKELERVFAE--THYPDIYTREEIALKIDLT----------EARVQVWFQNRRAKFRKQER 77 (125)
T ss_pred hhhhhhhhhHHHHHHHHHHHHh--hcCCcchhHHHHHHhhhhh----------HHHHHHHHHhhHHHHHHHHH
Confidence 3788999999999999999999 6999999999999999996 59999999999999988764
No 10
>KOG0485 consensus Transcription factor NKX-5.1/HMX1, contains HOX domain [Transcription]
Probab=99.49 E-value=1.3e-14 Score=137.30 Aligned_cols=63 Identities=24% Similarity=0.267 Sum_probs=58.4
Q ss_pred CCCCccccCHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHhCCCccccCCcccccchhHhhhhcchhhHhhhccCC
Q 016887 7 NGGPAFRFNPAEVTEMEGILQEHHNAMPSREILVALAEKFSESPERKGKIMVQMKQVWNWFQNRRYAIRAKSIKS 81 (381)
Q Consensus 7 ~~~pRtrFT~~QI~eLEk~F~e~~n~Yp~r~~rq~LA~kfnlS~~RaGk~~Vq~kQVk~WFQNRR~K~Kkk~~~~ 81 (381)
..++||.|+..||.+||-.|+. .+||+..+|..||.+|.|+ |+|||+||||||.|||++...-
T Consensus 104 KKktRTvFSraQV~qLEs~Fe~--krYLSsaeRa~LA~sLqLT----------ETQVKIWFQNRRnKwKRq~aad 166 (268)
T KOG0485|consen 104 KKKTRTVFSRAQVFQLESTFEL--KRYLSSAERAGLAASLQLT----------ETQVKIWFQNRRNKWKRQYAAD 166 (268)
T ss_pred cccchhhhhHHHHHHHHHHHHH--HhhhhHHHHhHHHHhhhhh----------hhhhhhhhhhhhHHHHHHHhhh
Confidence 4689999999999999999999 5999999999999999996 5999999999999999997653
No 11
>KOG0493 consensus Transcription factor Engrailed, contains HOX domain [General function prediction only]
Probab=99.45 E-value=6.5e-14 Score=135.38 Aligned_cols=63 Identities=22% Similarity=0.352 Sum_probs=58.3
Q ss_pred CCCccccCHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHhCCCccccCCcccccchhHhhhhcchhhHhhhccCCC
Q 016887 8 GGPAFRFNPAEVTEMEGILQEHHNAMPSREILVALAEKFSESPERKGKIMVQMKQVWNWFQNRRYAIRAKSIKSP 82 (381)
Q Consensus 8 ~~pRtrFT~~QI~eLEk~F~e~~n~Yp~r~~rq~LA~kfnlS~~RaGk~~Vq~kQVk~WFQNRR~K~Kkk~~~~p 82 (381)
.+|||.||.+||++|...|++ |+||+...||+||.+|+|.+ .|||+||||+|+|.||-....+
T Consensus 247 KRPRTAFtaeQL~RLK~EF~e--nRYlTEqRRQ~La~ELgLNE----------sQIKIWFQNKRAKiKKsTgskn 309 (342)
T KOG0493|consen 247 KRPRTAFTAEQLQRLKAEFQE--NRYLTEQRRQELAQELGLNE----------SQIKIWFQNKRAKIKKSTGSKN 309 (342)
T ss_pred cCccccccHHHHHHHHHHHhh--hhhHHHHHHHHHHHHhCcCH----------HHhhHHhhhhhhhhhhccCCCC
Confidence 789999999999999999999 79999999999999999985 9999999999999998765443
No 12
>smart00389 HOX Homeodomain. DNA-binding factors that are involved in the transcriptional regulation of key developmental processes
Probab=99.44 E-value=1.5e-13 Score=99.32 Aligned_cols=56 Identities=39% Similarity=0.534 Sum_probs=51.4
Q ss_pred CCCccccCHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHhCCCccccCCcccccchhHhhhhcchhhHh
Q 016887 8 GGPAFRFNPAEVTEMEGILQEHHNAMPSREILVALAEKFSESPERKGKIMVQMKQVWNWFQNRRYAIR 75 (381)
Q Consensus 8 ~~pRtrFT~~QI~eLEk~F~e~~n~Yp~r~~rq~LA~kfnlS~~RaGk~~Vq~kQVk~WFQNRR~K~K 75 (381)
+++|+.||++|+..||+.|.. +.||+...+++||..+|++. +||++||+|||++.+
T Consensus 1 ~k~r~~~~~~~~~~L~~~f~~--~~~P~~~~~~~la~~~~l~~----------~qV~~WF~nrR~~~~ 56 (56)
T smart00389 1 RRKRTSFTPEQLEELEKEFQK--NPYPSREEREELAAKLGLSE----------RQVKVWFQNRRAKWK 56 (56)
T ss_pred CCCCCcCCHHHHHHHHHHHHh--CCCCCHHHHHHHHHHHCcCH----------HHHHHhHHHHhhccC
Confidence 357889999999999999999 68999999999999999985 999999999998753
No 13
>KOG2251 consensus Homeobox transcription factor [Transcription]
Probab=99.42 E-value=1.4e-13 Score=129.55 Aligned_cols=62 Identities=21% Similarity=0.321 Sum_probs=57.6
Q ss_pred CCCCCccccCHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHhCCCccccCCcccccchhHhhhhcchhhHhhhcc
Q 016887 6 SNGGPAFRFNPAEVTEMEGILQEHHNAMPSREILVALAEKFSESPERKGKIMVQMKQVWNWFQNRRYAIRAKSI 79 (381)
Q Consensus 6 s~~~pRtrFT~~QI~eLEk~F~e~~n~Yp~r~~rq~LA~kfnlS~~RaGk~~Vq~kQVk~WFQNRR~K~Kkk~~ 79 (381)
..|+.||.||..|+++||++|.+ ++|||...|++||.+|||.+ .+||+||.|||+|+|++..
T Consensus 36 kqRRERTtFtr~QlevLe~LF~k--TqYPDv~~rEelAlklnLpe----------SrVqVWFKNRRAK~r~qq~ 97 (228)
T KOG2251|consen 36 KQRRERTTFTRKQLEVLEALFAK--TQYPDVFMREELALKLNLPE----------SRVQVWFKNRRAKCRRQQQ 97 (228)
T ss_pred hcccccceecHHHHHHHHHHHHh--hcCccHHHHHHHHHHhCCch----------hhhhhhhccccchhhHhhh
Confidence 45899999999999999999999 79999999999999999985 8899999999999887664
No 14
>cd00086 homeodomain Homeodomain; DNA binding domains involved in the transcriptional regulation of key eukaryotic developmental processes; may bind to DNA as monomers or as homo- and/or heterodimers, in a sequence-specific manner.
Probab=99.41 E-value=4.7e-13 Score=96.87 Aligned_cols=57 Identities=35% Similarity=0.565 Sum_probs=53.0
Q ss_pred CCccccCHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHhCCCccccCCcccccchhHhhhhcchhhHhhh
Q 016887 9 GPAFRFNPAEVTEMEGILQEHHNAMPSREILVALAEKFSESPERKGKIMVQMKQVWNWFQNRRYAIRAK 77 (381)
Q Consensus 9 ~pRtrFT~~QI~eLEk~F~e~~n~Yp~r~~rq~LA~kfnlS~~RaGk~~Vq~kQVk~WFQNRR~K~Kkk 77 (381)
+.+..|+.+|+..||+.|.. +.||+...+++||..+|++. +||++||+|||.+.++.
T Consensus 2 ~~r~~~~~~~~~~Le~~f~~--~~~P~~~~~~~la~~~~l~~----------~qV~~WF~nrR~~~~~~ 58 (59)
T cd00086 2 RKRTRFTPEQLEELEKEFEK--NPYPSREEREELAKELGLTE----------RQVKIWFQNRRAKLKRS 58 (59)
T ss_pred CCCCcCCHHHHHHHHHHHHh--CCCCCHHHHHHHHHHHCcCH----------HHHHHHHHHHHHHHhcc
Confidence 57889999999999999999 79999999999999999975 99999999999998763
No 15
>KOG0491 consensus Transcription factor BSH, contains HOX domain [General function prediction only]
Probab=99.38 E-value=1.1e-13 Score=126.45 Aligned_cols=63 Identities=24% Similarity=0.297 Sum_probs=58.6
Q ss_pred CCCCccccCHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHhCCCccccCCcccccchhHhhhhcchhhHhhhccCC
Q 016887 7 NGGPAFRFNPAEVTEMEGILQEHHNAMPSREILVALAEKFSESPERKGKIMVQMKQVWNWFQNRRYAIRAKSIKS 81 (381)
Q Consensus 7 ~~~pRtrFT~~QI~eLEk~F~e~~n~Yp~r~~rq~LA~kfnlS~~RaGk~~Vq~kQVk~WFQNRR~K~Kkk~~~~ 81 (381)
.++.|+.|+..|+.-||+.|+. .+||+..+|++||..||||+ +|||.||||||||.||...+.
T Consensus 100 r~K~Rtvfs~~ql~~l~~rFe~--QrYLS~~e~~ELan~L~LS~----------~QVKTWFQNrRMK~Kk~~r~~ 162 (194)
T KOG0491|consen 100 RRKARTVFSDPQLSGLEKRFER--QRYLSTPERQELANALSLSE----------TQVKTWFQNRRMKHKKQQRNN 162 (194)
T ss_pred hhhhcccccCccccccHHHHhh--hhhcccHHHHHHHHHhhhhH----------HHHHHHHHHHHHHHHHHHhcc
Confidence 4788999999999999999999 69999999999999999985 999999999999999987644
No 16
>KOG0494 consensus Transcription factor CHX10 and related HOX domain proteins [General function prediction only]
Probab=99.37 E-value=3.9e-13 Score=129.95 Aligned_cols=61 Identities=25% Similarity=0.302 Sum_probs=55.6
Q ss_pred CCCccccCHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHhCCCccccCCcccccchhHhhhhcchhhHhhhccC
Q 016887 8 GGPAFRFNPAEVTEMEGILQEHHNAMPSREILVALAEKFSESPERKGKIMVQMKQVWNWFQNRRYAIRAKSIK 80 (381)
Q Consensus 8 ~~pRtrFT~~QI~eLEk~F~e~~n~Yp~r~~rq~LA~kfnlS~~RaGk~~Vq~kQVk~WFQNRR~K~Kkk~~~ 80 (381)
|+-||.||..|+++||+.|++ -+|||...|+-||.++.|.+ .+|++||||||+||||+..+
T Consensus 142 Rh~RTiFT~~Qle~LEkaFke--aHYPDv~Are~la~ktelpE----------DRIqVWfQNRRAKWRk~Ek~ 202 (332)
T KOG0494|consen 142 RHFRTIFTSYQLEELEKAFKE--AHYPDVYAREMLADKTELPE----------DRIQVWFQNRRAKWRKTEKR 202 (332)
T ss_pred ccccchhhHHHHHHHHHHHhh--ccCccHHHHHHHhhhccCch----------hhhhHHhhhhhHHhhhhhhh
Confidence 344899999999999999999 59999999999999999975 89999999999999998753
No 17
>KOG0844 consensus Transcription factor EVX1, contains HOX domain [Transcription]
Probab=99.36 E-value=2e-13 Score=134.24 Aligned_cols=60 Identities=20% Similarity=0.252 Sum_probs=56.3
Q ss_pred CCCCccccCHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHhCCCccccCCcccccchhHhhhhcchhhHhhhc
Q 016887 7 NGGPAFRFNPAEVTEMEGILQEHHNAMPSREILVALAEKFSESPERKGKIMVQMKQVWNWFQNRRYAIRAKS 78 (381)
Q Consensus 7 ~~~pRtrFT~~QI~eLEk~F~e~~n~Yp~r~~rq~LA~kfnlS~~RaGk~~Vq~kQVk~WFQNRR~K~Kkk~ 78 (381)
-|+.||.||.+||.+|||.|-. +.|.++..|-+||..|||.+ +-||+||||||||.|++-
T Consensus 181 mRRYRTAFTReQIaRLEKEFyr--ENYVSRprRcELAAaLNLPE----------tTIKVWFQNRRMKDKRQR 240 (408)
T KOG0844|consen 181 MRRYRTAFTREQIARLEKEFYR--ENYVSRPRRCELAAALNLPE----------TTIKVWFQNRRMKDKRQR 240 (408)
T ss_pred HHHHHhhhhHHHHHHHHHHHHH--hccccCchhhhHHHhhCCCc----------ceeehhhhhchhhhhhhh
Confidence 3889999999999999999998 67999999999999999985 899999999999999876
No 18
>KOG0848 consensus Transcription factor Caudal, contains HOX domain [Transcription]
Probab=99.34 E-value=2.7e-13 Score=131.21 Aligned_cols=61 Identities=25% Similarity=0.251 Sum_probs=55.8
Q ss_pred CCccccCHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHhCCCccccCCcccccchhHhhhhcchhhHhhhccCC
Q 016887 9 GPAFRFNPAEVTEMEGILQEHHNAMPSREILVALAEKFSESPERKGKIMVQMKQVWNWFQNRRYAIRAKSIKS 81 (381)
Q Consensus 9 ~pRtrFT~~QI~eLEk~F~e~~n~Yp~r~~rq~LA~kfnlS~~RaGk~~Vq~kQVk~WFQNRR~K~Kkk~~~~ 81 (381)
+.|..+|..|-.||||+|.- .+|++.....+||..|+||+ +||||||||||+|.||...|.
T Consensus 201 KYRvVYTDhQRLELEKEfh~--SryITirRKSELA~~LgLsE----------RQVKIWFQNRRAKERK~nKKk 261 (317)
T KOG0848|consen 201 KYRVVYTDHQRLELEKEFHT--SRYITIRRKSELAATLGLSE----------RQVKIWFQNRRAKERKDNKKK 261 (317)
T ss_pred ceeEEecchhhhhhhhhhcc--ccceeeehhHHHHHhhCccH----------hhhhHhhhhhhHHHHHHHHHH
Confidence 56778999999999999999 69999999999999999985 999999999999988877654
No 19
>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=99.31 E-value=1.9e-12 Score=99.65 Aligned_cols=52 Identities=15% Similarity=0.269 Sum_probs=49.2
Q ss_pred CCCccccCHHHHHHHHHHHHHhcCCC----CCHHHHHHHHHHhCCCccccCCcccccchhHhhhhcch
Q 016887 8 GGPAFRFNPAEVTEMEGILQEHHNAM----PSREILVALAEKFSESPERKGKIMVQMKQVWNWFQNRR 71 (381)
Q Consensus 8 ~~pRtrFT~~QI~eLEk~F~e~~n~Y----p~r~~rq~LA~kfnlS~~RaGk~~Vq~kQVk~WFQNRR 71 (381)
++.||.||.+|+++||+.|+. +.| |+...|++||..+||++ .+||+||||-+
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 689999999999999999999 699 99999999999999985 99999999974
No 20
>KOG0483 consensus Transcription factor HEX, contains HOX and HALZ domains [Transcription]
Probab=99.26 E-value=2.9e-12 Score=118.86 Aligned_cols=60 Identities=28% Similarity=0.401 Sum_probs=55.1
Q ss_pred CCCccccCHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHhCCCccccCCcccccchhHhhhhcchhhHhhhcc
Q 016887 8 GGPAFRFNPAEVTEMEGILQEHHNAMPSREILVALAEKFSESPERKGKIMVQMKQVWNWFQNRRYAIRAKSI 79 (381)
Q Consensus 8 ~~pRtrFT~~QI~eLEk~F~e~~n~Yp~r~~rq~LA~kfnlS~~RaGk~~Vq~kQVk~WFQNRR~K~Kkk~~ 79 (381)
.+...+||.+|+..||+.|+. +.||....+.+||..|||.+ .||.+||||||++||.+..
T Consensus 51 ~~kk~Rlt~eQ~~~LE~~F~~--~~~L~p~~K~~LAk~LgL~p----------RQVavWFQNRRARwK~kql 110 (198)
T KOG0483|consen 51 KGKKRRLTSEQVKFLEKSFES--EKKLEPERKKKLAKELGLQP----------RQVAVWFQNRRARWKTKQL 110 (198)
T ss_pred ccccccccHHHHHHhHHhhcc--ccccChHHHHHHHHhhCCCh----------hHHHHHHhhccccccchhh
Confidence 356679999999999999999 68999999999999999975 9999999999999998764
No 21
>KOG0847 consensus Transcription factor, contains HOX domain [Transcription]
Probab=99.08 E-value=8.4e-11 Score=111.96 Aligned_cols=63 Identities=22% Similarity=0.270 Sum_probs=56.5
Q ss_pred CCCccccCHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHhCCCccccCCcccccchhHhhhhcchhhHhhhccCCC
Q 016887 8 GGPAFRFNPAEVTEMEGILQEHHNAMPSREILVALAEKFSESPERKGKIMVQMKQVWNWFQNRRYAIRAKSIKSP 82 (381)
Q Consensus 8 ~~pRtrFT~~QI~eLEk~F~e~~n~Yp~r~~rq~LA~kfnlS~~RaGk~~Vq~kQVk~WFQNRR~K~Kkk~~~~p 82 (381)
...|..|+-.||..||+-|++ .+||-...|-+||..+|+. +.||++||||||.|||||..-.+
T Consensus 168 k~srPTf~g~qi~~le~~feq--tkylaG~~ra~lA~~lgmt----------eSqvkVWFQNRRTKWRKkhAaEm 230 (288)
T KOG0847|consen 168 KQSRPTFTGHQIYQLERKFEQ--TKYLAGADRAQLAQELNMT----------ESQVKVWFQNRRTKWRKKHAAEM 230 (288)
T ss_pred cccCCCccchhhhhhhhhhhh--hhcccchhHHHhhcccccc----------HHHHHHHHhcchhhhhhhhccch
Confidence 345678999999999999999 6999999999999999996 59999999999999999986433
No 22
>KOG0486 consensus Transcription factor PTX1, contains HOX domain [Transcription]
Probab=99.06 E-value=7.7e-11 Score=116.16 Aligned_cols=61 Identities=23% Similarity=0.327 Sum_probs=57.5
Q ss_pred CCCCccccCHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHhCCCccccCCcccccchhHhhhhcchhhHhhhcc
Q 016887 7 NGGPAFRFNPAEVTEMEGILQEHHNAMPSREILVALAEKFSESPERKGKIMVQMKQVWNWFQNRRYAIRAKSI 79 (381)
Q Consensus 7 ~~~pRtrFT~~QI~eLEk~F~e~~n~Yp~r~~rq~LA~kfnlS~~RaGk~~Vq~kQVk~WFQNRR~K~Kkk~~ 79 (381)
.|+.|+-||..|++|||..|+. |+||+-+.|++||-..||+ |+.|.+||.|||+||||+..
T Consensus 112 qrrQrthFtSqqlqele~tF~r--NrypdMstrEEIavwtNlT----------E~rvrvwfknrrakwrkrEr 172 (351)
T KOG0486|consen 112 QRRQRTHFTSQQLQELEATFQR--NRYPDMSTREEIAVWTNLT----------EARVRVWFKNRRAKWRKRER 172 (351)
T ss_pred hhhhhhhhHHHHHHHHHHHHhh--ccCCccchhhHHHhhcccc----------chhhhhhcccchhhhhhhhh
Confidence 4789999999999999999999 8999999999999999997 49999999999999999864
No 23
>COG5576 Homeodomain-containing transcription factor [Transcription]
Probab=99.04 E-value=2.3e-10 Score=102.64 Aligned_cols=61 Identities=25% Similarity=0.303 Sum_probs=56.8
Q ss_pred CCCccccCHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHhCCCccccCCcccccchhHhhhhcchhhHhhhccC
Q 016887 8 GGPAFRFNPAEVTEMEGILQEHHNAMPSREILVALAEKFSESPERKGKIMVQMKQVWNWFQNRRYAIRAKSIK 80 (381)
Q Consensus 8 ~~pRtrFT~~QI~eLEk~F~e~~n~Yp~r~~rq~LA~kfnlS~~RaGk~~Vq~kQVk~WFQNRR~K~Kkk~~~ 80 (381)
.+.|.+-|..|+.-||+.|+. +.||+...|++|+..+|+++ +-||+||||||++.|++...
T Consensus 52 ~~~r~R~t~~Q~~vL~~~F~i--~p~Ps~~~r~~L~~~lnm~~----------ksVqIWFQNkR~~~k~~~~~ 112 (156)
T COG5576 52 KSKRRRTTDEQLMVLEREFEI--NPYPSSITRIKLSLLLNMPP----------KSVQIWFQNKRAKEKKKRSG 112 (156)
T ss_pred cccceechHHHHHHHHHHhcc--CCCCCHHHHHHHHHhcCCCh----------hhhhhhhchHHHHHHHhccc
Confidence 567889999999999999999 79999999999999999985 99999999999999988764
No 24
>KOG0490 consensus Transcription factor, contains HOX domain [General function prediction only]
Probab=99.03 E-value=1.4e-10 Score=103.36 Aligned_cols=62 Identities=24% Similarity=0.317 Sum_probs=57.7
Q ss_pred CCCCCccccCHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHhCCCccccCCcccccchhHhhhhcchhhHhhhcc
Q 016887 6 SNGGPAFRFNPAEVTEMEGILQEHHNAMPSREILVALAEKFSESPERKGKIMVQMKQVWNWFQNRRYAIRAKSI 79 (381)
Q Consensus 6 s~~~pRtrFT~~QI~eLEk~F~e~~n~Yp~r~~rq~LA~kfnlS~~RaGk~~Vq~kQVk~WFQNRR~K~Kkk~~ 79 (381)
..++.|+.|+..|+.+||++|+. .+||+...|+.||..+++++ ..|++||||||+||+++..
T Consensus 59 ~~rr~rt~~~~~ql~~ler~f~~--~h~Pd~~~r~~la~~~~~~e----------~rVqvwFqnrrak~r~~~~ 120 (235)
T KOG0490|consen 59 SKRCARCKFTISQLDELERAFEK--VHLPCFACRECLALLLTGDE----------FRVQVWFQNRRAKDRKEER 120 (235)
T ss_pred cccccCCCCCcCHHHHHHHhhcC--CCcCccchHHHHhhcCCCCe----------eeeehhhhhhcHhhhhhhc
Confidence 45889999999999999999999 59999999999999999975 9999999999999998874
No 25
>KOG4577 consensus Transcription factor LIM3, contains LIM and HOX domains [Transcription]
Probab=98.77 E-value=5.6e-09 Score=102.76 Aligned_cols=61 Identities=21% Similarity=0.329 Sum_probs=55.8
Q ss_pred CCCCCccccCHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHhCCCccccCCcccccchhHhhhhcchhhHhhhc
Q 016887 6 SNGGPAFRFNPAEVTEMEGILQEHHNAMPSREILVALAEKFSESPERKGKIMVQMKQVWNWFQNRRYAIRAKS 78 (381)
Q Consensus 6 s~~~pRtrFT~~QI~eLEk~F~e~~n~Yp~r~~rq~LA~kfnlS~~RaGk~~Vq~kQVk~WFQNRR~K~Kkk~ 78 (381)
++.+|||..|..||+-|..+|.. ..-|.+.+|++|+...||.. ..||+||||||+|.|+..
T Consensus 166 ~nKRPRTTItAKqLETLK~AYn~--SpKPARHVREQLsseTGLDM----------RVVQVWFQNRRAKEKRLK 226 (383)
T KOG4577|consen 166 SNKRPRTTITAKQLETLKQAYNT--SPKPARHVREQLSSETGLDM----------RVVQVWFQNRRAKEKRLK 226 (383)
T ss_pred ccCCCcceeeHHHHHHHHHHhcC--CCchhHHHHHHhhhccCcce----------eehhhhhhhhhHHHHhhh
Confidence 46899999999999999999998 48899999999999999974 889999999999987754
No 26
>KOG0849 consensus Transcription factor PRD and related proteins, contain PAX and HOX domains [Transcription]
Probab=98.59 E-value=3.3e-08 Score=98.10 Aligned_cols=61 Identities=25% Similarity=0.343 Sum_probs=56.7
Q ss_pred CCCCCccccCHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHhCCCccccCCcccccchhHhhhhcchhhHhhhc
Q 016887 6 SNGGPAFRFNPAEVTEMEGILQEHHNAMPSREILVALAEKFSESPERKGKIMVQMKQVWNWFQNRRYAIRAKS 78 (381)
Q Consensus 6 s~~~pRtrFT~~QI~eLEk~F~e~~n~Yp~r~~rq~LA~kfnlS~~RaGk~~Vq~kQVk~WFQNRR~K~Kkk~ 78 (381)
+.++.|+.|+++|+..||+.|+. ++||+...|++||.+.++++ .+|++||||||.+|+|..
T Consensus 175 ~~rr~rtsft~~Q~~~le~~f~r--t~yP~i~~Re~La~~i~l~e----------~riqvwf~nrra~~rr~~ 235 (354)
T KOG0849|consen 175 GGRRNRTSFSPSQLEALEECFQR--TPYPDIVGRETLAKETGLPE----------PRVQVWFQNRRAKWRRQH 235 (354)
T ss_pred cccccccccccchHHHHHHHhcC--CCCCchhhHHHHhhhccCCc----------hHHHHHHhhhhhhhhhcc
Confidence 34677899999999999999999 57999999999999999975 999999999999999988
No 27
>KOG3802 consensus Transcription factor OCT-1, contains POU and HOX domains [Transcription]
Probab=98.30 E-value=4.3e-07 Score=92.05 Aligned_cols=64 Identities=19% Similarity=0.240 Sum_probs=57.4
Q ss_pred CCCCCCCCccccCHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHhCCCccccCCcccccch-hHhhhhcchhhHhhhcc
Q 016887 3 RPPSNGGPAFRFNPAEVTEMEGILQEHHNAMPSREILVALAEKFSESPERKGKIMVQMKQ-VWNWFQNRRYAIRAKSI 79 (381)
Q Consensus 3 rPps~~~pRtrFT~~QI~eLEk~F~e~~n~Yp~r~~rq~LA~kfnlS~~RaGk~~Vq~kQ-Vk~WFQNRR~K~Kkk~~ 79 (381)
...-.|+.||.|.......||+.|.. |.-|+.+++-.||++|+|- |+ |++||=|||.|.||...
T Consensus 290 a~~RkRKKRTSie~~vr~aLE~~F~~--npKPt~qEIt~iA~~L~le-----------KEVVRVWFCNRRQkeKR~~~ 354 (398)
T KOG3802|consen 290 AQSRKRKKRTSIEVNVRGALEKHFLK--NPKPTSQEITHIAESLQLE-----------KEVVRVWFCNRRQKEKRITP 354 (398)
T ss_pred ccccccccccceeHHHHHHHHHHHHh--CCCCCHHHHHHHHHHhccc-----------cceEEEEeeccccccccCCC
Confidence 34456999999999999999999999 7999999999999999994 66 88999999999988664
No 28
>KOG0775 consensus Transcription factor SIX and related HOX domain proteins [Transcription]
Probab=98.05 E-value=1.8e-05 Score=77.66 Aligned_cols=53 Identities=32% Similarity=0.373 Sum_probs=44.9
Q ss_pred cCHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHhCCCccccCCcccccchhHhhhhcchhhHhhhc
Q 016887 14 FNPAEVTEMEGILQEHHNAMPSREILVALAEKFSESPERKGKIMVQMKQVWNWFQNRRYAIRAKS 78 (381)
Q Consensus 14 FT~~QI~eLEk~F~e~~n~Yp~r~~rq~LA~kfnlS~~RaGk~~Vq~kQVk~WFQNRR~K~Kkk~ 78 (381)
|-..--.-|-..|.+ +.||+.....+||+..+|+. +||-|||.|||++-|...
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 444444678888887 89999999999999999975 999999999999988544
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=98.01 E-value=4.9e-06 Score=59.75 Aligned_cols=38 Identities=42% Similarity=0.558 Sum_probs=30.9
Q ss_pred HHHhcCCCCCHHHHHHHHHHhCCCccccCCcccccchhHhhhhcchhh
Q 016887 26 LQEHHNAMPSREILVALAEKFSESPERKGKIMVQMKQVWNWFQNRRYA 73 (381)
Q Consensus 26 F~e~~n~Yp~r~~rq~LA~kfnlS~~RaGk~~Vq~kQVk~WFQNRR~K 73 (381)
+++..+.||+.+++++||...|+|. +||.+||-|.|.+
T Consensus 3 ~~h~~nPYPs~~ek~~L~~~tgls~----------~Qi~~WF~NaRrR 40 (40)
T PF05920_consen 3 LEHLHNPYPSKEEKEELAKQTGLSR----------KQISNWFINARRR 40 (40)
T ss_dssp HHTTTSGS--HHHHHHHHHHHTS-H----------HHHHHHHHHHHHH
T ss_pred HHHCCCCCCCHHHHHHHHHHcCCCH----------HHHHHHHHHhHcc
Confidence 4556689999999999999999985 9999999999864
No 30
>KOG0490 consensus Transcription factor, contains HOX domain [General function prediction only]
Probab=97.72 E-value=2.8e-05 Score=69.60 Aligned_cols=62 Identities=24% Similarity=0.383 Sum_probs=56.6
Q ss_pred CCCCCccccCHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHhCCCccccCCcccccchhHhhhhcchhhHhhhcc
Q 016887 6 SNGGPAFRFNPAEVTEMEGILQEHHNAMPSREILVALAEKFSESPERKGKIMVQMKQVWNWFQNRRYAIRAKSI 79 (381)
Q Consensus 6 s~~~pRtrFT~~QI~eLEk~F~e~~n~Yp~r~~rq~LA~kfnlS~~RaGk~~Vq~kQVk~WFQNRR~K~Kkk~~ 79 (381)
..+++++.|+..|+..|+..|.. +.+|+...+++|+..+++++ ..|++||||+|.+.++...
T Consensus 152 ~~~~~~~~~~~~~~~~~~~~~~~--~~~P~~~~~~~l~~~~~~~~----------~~~q~~~~~~~~~~~~~~~ 213 (235)
T KOG0490|consen 152 KPRRPRTTFTENQLEVLETVFRA--TPKPDADDREQLAEETGLSE----------RVIQVWFQNRRAKLRKHKR 213 (235)
T ss_pred ccCCCccccccchhHhhhhcccC--CCCCchhhHHHHHHhcCCCh----------hhhhhhcccHHHHHHhhcc
Confidence 35788999999999999999999 68999999999999999985 7799999999999988764
No 31
>KOG2252 consensus CCAAT displacement protein and related homeoproteins [Transcription]
Probab=97.68 E-value=8.3e-05 Score=78.31 Aligned_cols=57 Identities=25% Similarity=0.414 Sum_probs=52.5
Q ss_pred CCCCCccccCHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHhCCCccccCCcccccchhHhhhhcchhhH
Q 016887 6 SNGGPAFRFNPAEVTEMEGILQEHHNAMPSREILVALAEKFSESPERKGKIMVQMKQVWNWFQNRRYAI 74 (381)
Q Consensus 6 s~~~pRtrFT~~QI~eLEk~F~e~~n~Yp~r~~rq~LA~kfnlS~~RaGk~~Vq~kQVk~WFQNRR~K~ 74 (381)
...+||+.||..|...|-.+|++ +++|+++.++.|+..|||.. .-|.|||-|-|.+.
T Consensus 419 ~~KKPRlVfTd~QkrTL~aiFke--~~RPS~Emq~tIS~qL~L~~----------sTV~NfFmNaRRRs 475 (558)
T KOG2252|consen 419 QTKKPRLVFTDIQKRTLQAIFKE--NKRPSREMQETISQQLNLEL----------STVINFFMNARRRS 475 (558)
T ss_pred cCCCceeeecHHHHHHHHHHHhc--CCCCCHHHHHHHHHHhCCcH----------HHHHHHHHhhhhhc
Confidence 35789999999999999999999 79999999999999999975 78999999987764
No 32
>KOG0774 consensus Transcription factor PBX and related HOX domain proteins [Transcription]
Probab=97.15 E-value=0.00027 Score=69.60 Aligned_cols=66 Identities=23% Similarity=0.283 Sum_probs=57.2
Q ss_pred CCCCCccccCHHHHHHHHHHHH-HhcCCCCCHHHHHHHHHHhCCCccccCCcccccchhHhhhhcchhhHhhhccCC
Q 016887 6 SNGGPAFRFNPAEVTEMEGILQ-EHHNAMPSREILVALAEKFSESPERKGKIMVQMKQVWNWFQNRRYAIRAKSIKS 81 (381)
Q Consensus 6 s~~~pRtrFT~~QI~eLEk~F~-e~~n~Yp~r~~rq~LA~kfnlS~~RaGk~~Vq~kQVk~WFQNRR~K~Kkk~~~~ 81 (381)
+.||.|-.|++.-.+.|-+-|- +.+|.||+.+..++||++.|++- .||-+||-|+|.+.||-+-+-
T Consensus 187 darRKRRNFsK~aTeiLneyF~~h~~nPYPSee~K~eLAkqCnItv----------sQvsnwfgnkrIrykK~~~k~ 253 (334)
T KOG0774|consen 187 DARRKRRNFSKQATEILNEYFYSHLSNPYPSEEAKEELAKQCNITV----------SQVSNWFGNKRIRYKKNMGKN 253 (334)
T ss_pred HHHHhhcccchhHHHHHHHHHHHhcCCCCCcHHHHHHHHHHcCcee----------hhhccccccceeehhhhhhhh
Confidence 3578888999999999987765 55789999999999999999974 999999999999999877653
No 33
>KOG1168 consensus Transcription factor ACJ6/BRN-3, contains POU and HOX domains [Transcription]
Probab=96.39 E-value=0.0012 Score=66.02 Aligned_cols=61 Identities=23% Similarity=0.289 Sum_probs=54.9
Q ss_pred CCCCccccCHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHhCCCccccCCcccccchhHhhhhcchhhHhhhcc
Q 016887 7 NGGPAFRFNPAEVTEMEGILQEHHNAMPSREILVALAEKFSESPERKGKIMVQMKQVWNWFQNRRYAIRAKSI 79 (381)
Q Consensus 7 ~~~pRtrFT~~QI~eLEk~F~e~~n~Yp~r~~rq~LA~kfnlS~~RaGk~~Vq~kQVk~WFQNRR~K~Kkk~~ 79 (381)
..|.||..-.-|-..||..|.. ..-|+.+.+..||++|.|-- ..|++||=|.|+|+||...
T Consensus 309 kKRKRTSIAAPEKRsLEayFav--QPRPS~EkIAaIAekLDLKK----------NVVRVWFCNQRQKQKRm~~ 369 (385)
T KOG1168|consen 309 KKRKRTSIAAPEKRSLEAYFAV--QPRPSGEKIAAIAEKLDLKK----------NVVRVWFCNQRQKQKRMKR 369 (385)
T ss_pred cccccccccCcccccHHHHhcc--CCCCchhHHHHHHHhhhhhh----------ceEEEEeeccHHHHHHhhh
Confidence 5788999999999999999999 68999999999999999953 6699999999999998654
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=95.16 E-value=0.014 Score=43.79 Aligned_cols=40 Identities=33% Similarity=0.770 Sum_probs=32.3
Q ss_pred CCCceeehhhhhhccccCCCCCeEEEEecCCCCCcccccccc
Q 016887 151 RDGAWYDVSAFLAQRNFDTADPEVQVRFAGFGAEEDEWVNIK 192 (381)
Q Consensus 151 ~DgAWYDV~~fL~~r~l~tge~elrVrf~gFg~eeDEwvnvk 192 (381)
.+|.||...+.-. |. ..|+.+..|||.||..-.||||+..
T Consensus 12 ~~~~~y~A~I~~~-r~-~~~~~~YyVHY~g~nkR~DeWV~~~ 51 (55)
T PF11717_consen 12 KDGQWYEAKILDI-RE-KNGEPEYYVHYQGWNKRLDEWVPES 51 (55)
T ss_dssp TTTEEEEEEEEEE-EE-CTTCEEEEEEETTSTGCC-EEEETT
T ss_pred CCCcEEEEEEEEE-Ee-cCCCEEEEEEcCCCCCCceeeecHH
Confidence 4899999887633 32 6777999999999999999999865
No 35
>KOG1146 consensus Homeobox protein [General function prediction only]
Probab=95.09 E-value=0.018 Score=66.36 Aligned_cols=59 Identities=14% Similarity=0.187 Sum_probs=54.0
Q ss_pred CCCccccCHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHhCCCccccCCcccccchhHhhhhcchhhHhhhc
Q 016887 8 GGPAFRFNPAEVTEMEGILQEHHNAMPSREILVALAEKFSESPERKGKIMVQMKQVWNWFQNRRYAIRAKS 78 (381)
Q Consensus 8 ~~pRtrFT~~QI~eLEk~F~e~~n~Yp~r~~rq~LA~kfnlS~~RaGk~~Vq~kQVk~WFQNRR~K~Kkk~ 78 (381)
+..|+.|+..||..|-.+|+. ..|+..+.++.|-+.+.++. ..|+.||||-|.|.|+..
T Consensus 904 ~a~~~~~~d~qlk~i~~~~~~--q~~~~~~~~E~l~~~~~~~~----------~~i~vw~qna~~~s~k~~ 962 (1406)
T KOG1146|consen 904 RAYRTQESDLQLKIIKACYEA--QRTPTMQECEVLEEPIGLPK----------RVIQVWFQNARAKSKKAK 962 (1406)
T ss_pred hhhccchhHHHHHHHHHHHhh--ccCChHHHHHhhcccccCCc----------chhHHhhhhhhhhhhhhh
Confidence 778999999999999999999 69999999999999999985 668999999999987754
No 36
>PF15057 DUF4537: Domain of unknown function (DUF4537)
Probab=93.87 E-value=0.39 Score=41.75 Aligned_cols=108 Identities=19% Similarity=0.233 Sum_probs=68.5
Q ss_pred eeccCCCceeehhhhhhccccCCCCCeEEEEecCCCCCccccccccccccccCCcccccccccccCCceEEEeeecCCcc
Q 016887 147 AKSARDGAWYDVSAFLAQRNFDTADPEVQVRFAGFGAEEDEWVNIKRHVRQRSLPCEASECVAVLPGDLILCFQEGKDQA 226 (381)
Q Consensus 147 A~S~~DgAWYDV~~fL~~r~l~tge~elrVrf~gFg~eeDEwvnvk~rvR~rS~plE~sEC~~v~~Gd~VcCfqeg~d~a 226 (381)
|++.+||-+|--.+- +. + ....+.|.| .+.+-+.+... -=+++.+..|+.|++||.||+-.+.. +.
T Consensus 6 AR~~~DG~YY~GtV~-~~--~--~~~~~lV~f---~~~~~~~v~~~-----~iI~~~~~~~~~L~~GD~VLA~~~~~-~~ 71 (124)
T PF15057_consen 6 ARREEDGFYYPGTVK-KC--V--SSGQFLVEF---DDGDTQEVPIS-----DIIALSDAMRHSLQVGDKVLAPWEPD-DC 71 (124)
T ss_pred EeeCCCCcEEeEEEE-Ec--c--CCCEEEEEE---CCCCEEEeChH-----HeEEccCcccCcCCCCCEEEEecCcC-CC
Confidence 678889988876433 21 2 346799999 33333333332 23577888899999999999886655 55
Q ss_pred eEeeEEEeeeeecccCCCCcceEEEEEeecCCccccccCcceeecc
Q 016887 227 LYFDAHVLDAQRRRHDVRGCRCRFLVRYDHDQSEEIVPLRKVCRRP 272 (381)
Q Consensus 227 lyyDA~V~~Vqrr~Hd~~gCrC~FlVrw~hdp~ee~v~l~kvC~rp 272 (381)
.|+-|.|+..-.++ ....=.++|.+-.+. ...|+...+.-.|
T Consensus 72 ~Y~Pg~V~~~~~~~---~~~~~~~~V~f~ng~-~~~vp~~~~~~I~ 113 (124)
T PF15057_consen 72 RYGPGTVIAGPERR---ASEDKEYTVRFYNGK-TAKVPRGEVIWIS 113 (124)
T ss_pred EEeCEEEEECcccc---ccCCceEEEEEECCC-CCccchhhEEECC
Confidence 69999999876666 223334566665554 3344444443333
No 37
>KOG0773 consensus Transcription factor MEIS1 and related HOX domain proteins [Transcription]
Probab=93.65 E-value=0.056 Score=52.78 Aligned_cols=60 Identities=27% Similarity=0.294 Sum_probs=49.0
Q ss_pred CCCCccccCHHHHHHHHHHHHH-hcCCCCCHHHHHHHHHHhCCCccccCCcccccchhHhhhhcchhhHhh
Q 016887 7 NGGPAFRFNPAEVTEMEGILQE-HHNAMPSREILVALAEKFSESPERKGKIMVQMKQVWNWFQNRRYAIRA 76 (381)
Q Consensus 7 ~~~pRtrFT~~QI~eLEk~F~e-~~n~Yp~r~~rq~LA~kfnlS~~RaGk~~Vq~kQVk~WFQNRR~K~Kk 76 (381)
..++.-.|-..-+..|+.-+.+ ....||+......||.+.||+. .||.+||-|.|.+..+
T Consensus 239 ~~r~~~~lP~~a~~ilr~Wl~~h~~~PYPse~~K~~La~~TGLs~----------~Qv~NWFINaR~R~w~ 299 (342)
T KOG0773|consen 239 KWRPQRGLPKEAVSILRAWLFEHLLHPYPSDDEKLMLAKQTGLSR----------PQVSNWFINARVRLWK 299 (342)
T ss_pred CCCCCCCCCHHHHHHHHHHHHHhccCCCCcchhccccchhcCCCc----------ccCCchhhhcccccCC
Confidence 4556668888888888876555 4447999999999999999986 9999999999887644
No 38
>PF11569 Homez: Homeodomain leucine-zipper encoding, Homez; PDB: 2YS9_A.
Probab=91.45 E-value=0.17 Score=39.63 Aligned_cols=42 Identities=29% Similarity=0.380 Sum_probs=30.4
Q ss_pred HHHHHHHHHHhcCCCCCHHHHHHHHHHhCCCccccCCcccccchhHhhhhcchh
Q 016887 19 VTEMEGILQEHHNAMPSREILVALAEKFSESPERKGKIMVQMKQVWNWFQNRRY 72 (381)
Q Consensus 19 I~eLEk~F~e~~n~Yp~r~~rq~LA~kfnlS~~RaGk~~Vq~kQVk~WFQNRR~ 72 (381)
+.=||+-|..+ ++|.....+.|.++-++|. .||+.||--|+.
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 46699999985 8999999999999999985 999999987743
No 39
>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=90.06 E-value=0.21 Score=35.76 Aligned_cols=37 Identities=27% Similarity=0.548 Sum_probs=28.8
Q ss_pred eehhhhhhccccCC-CCCeEEEEecCCCCCcccccccc
Q 016887 156 YDVSAFLAQRNFDT-ADPEVQVRFAGFGAEEDEWVNIK 192 (381)
Q Consensus 156 YDV~~fL~~r~l~t-ge~elrVrf~gFg~eeDEwvnvk 192 (381)
|.|.-.|.+|.... |..++.|++.|++..+++|.+..
T Consensus 3 ~~ve~Il~~r~~~~~~~~~y~VkW~g~~~~~~tWe~~~ 40 (55)
T cd00024 3 YEVEKILDHRKKKDGGEYEYLVKWKGYSYSEDTWEPEE 40 (55)
T ss_pred ceEeeeeeeeecCCCCcEEEEEEECCCCCccCccccHH
Confidence 34555667775544 77899999999999999998754
No 40
>PF04218 CENP-B_N: CENP-B N-terminal DNA-binding domain; InterPro: IPR006695 Centromere Protein B (CENP-B) is a DNA-binding protein localized to the centromere. Within the N-terminal 125 residues, there is a DNA-binding region, which binds to a corresponding 17bp CENP-B box sequence. CENP-B dimers either bind two separate DNA molecules or alternatively, they may bind two CENP-B boxes on one DNA molecule, with the intervening stretch of DNA forming a loop structure. The CENP-B DNA-binding domain consists of two repeating domains, RP1 and RP2. This family corresponds to RP1 has been shown to consist of four helices in a helix-turn-helix structure [].; GO: 0003677 DNA binding, 0000775 chromosome, centromeric region; PDB: 1BW6_A 1HLV_A 2ELH_A.
Probab=90.01 E-value=0.64 Score=34.89 Aligned_cols=46 Identities=20% Similarity=0.146 Sum_probs=35.3
Q ss_pred CCCccccCHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHhCCCccccCCcccccchhHhhhhcc
Q 016887 8 GGPAFRFNPAEVTEMEGILQEHHNAMPSREILVALAEKFSESPERKGKIMVQMKQVWNWFQNR 70 (381)
Q Consensus 8 ~~pRtrFT~~QI~eLEk~F~e~~n~Yp~r~~rq~LA~kfnlS~~RaGk~~Vq~kQVk~WFQNR 70 (381)
+++|..+|.+|-.++=+.++. +. ...+||++||++. .+|..|..||
T Consensus 1 krkR~~LTl~eK~~iI~~~e~--g~-----s~~~ia~~fgv~~----------sTv~~I~K~k 46 (53)
T PF04218_consen 1 KRKRKSLTLEEKLEIIKRLEE--GE-----SKRDIAREFGVSR----------STVSTILKNK 46 (53)
T ss_dssp SSSSSS--HHHHHHHHHHHHC--TT------HHHHHHHHT--C----------CHHHHHHHCH
T ss_pred CCCCccCCHHHHHHHHHHHHc--CC-----CHHHHHHHhCCCH----------HHHHHHHHhH
Confidence 467889999999988888887 33 5889999999985 9999999997
No 41
>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=88.88 E-value=1.3 Score=32.15 Aligned_cols=54 Identities=19% Similarity=0.287 Sum_probs=39.8
Q ss_pred cccCCceEEEeeecCCcceEeeEEEeeeeecccCCCCcceEEEEEeecCCccccccCcceeeccc
Q 016887 209 AVLPGDLILCFQEGKDQALYFDAHVLDAQRRRHDVRGCRCRFLVRYDHDQSEEIVPLRKVCRRPE 273 (381)
Q Consensus 209 ~v~~Gd~VcCfqeg~d~alyyDA~V~~Vqrr~Hd~~gCrC~FlVrw~hdp~ee~v~l~kvC~rp~ 273 (381)
..++|+.+++.. ++..||.|+|+++... -.+.|.|....+.+.|+...|...|.
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 357898777654 3788999999999743 34678888867777888777766543
No 42
>PLN00104 MYST -like histone acetyltransferase; Provisional
Probab=86.24 E-value=2.3 Score=44.88 Aligned_cols=54 Identities=22% Similarity=0.399 Sum_probs=38.8
Q ss_pred EEeeccCCCceeehhhhhhcccc---CCCCCeEEEEecCCCCCccccccccccccccCC
Q 016887 145 FEAKSARDGAWYDVSAFLAQRNF---DTADPEVQVRFAGFGAEEDEWVNIKRHVRQRSL 200 (381)
Q Consensus 145 FEA~S~~DgAWYDV~~fL~~r~l---~tge~elrVrf~gFg~eeDEwvnvk~rvR~rS~ 200 (381)
.-++-..||.||... .++-|.. ..|+.+.+|||.||..--||||+.. |++..++
T Consensus 60 Vla~~~~Dg~~~~A~-VI~~R~~~~~~~~~~~YYVHY~g~nrRlDEWV~~~-rLdls~~ 116 (450)
T PLN00104 60 VMCRWRFDGKYHPVK-VIERRRGGSGGPNDYEYYVHYTEFNRRLDEWVKLE-QLDLDTV 116 (450)
T ss_pred EEEEECCCCCEEEEE-EEEEeccCCCCCCCceEEEEEecCCccHhhccCHh-hcccccc
Confidence 345555699999844 4455542 2355789999999999999999975 5655443
No 43
>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=85.79 E-value=1.6 Score=40.20 Aligned_cols=55 Identities=20% Similarity=0.261 Sum_probs=41.2
Q ss_pred CccccCHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHhCCCccccCCcccccchhHhhhh
Q 016887 10 PAFRFNPAEVTEMEGILQEHHNAMPSREILVALAEKFSESPERKGKIMVQMKQVWNWFQ 68 (381)
Q Consensus 10 pRtrFT~~QI~eLEk~F~e~~n~Yp~r~~rq~LA~kfnlS~~RaGk~~Vq~kQVk~WFQ 68 (381)
....+|+++|+||-++=.+ =|..-.+.+||++||+|+-..+-+.=...|-+.+-+
T Consensus 82 k~y~Lt~e~i~Eir~LR~~----DP~~wTr~~LAkkF~~S~~fV~~v~~~~~e~~~~~~ 136 (164)
T PF12824_consen 82 KKYHLTPEDIQEIRRLRAE----DPEKWTRKKLAKKFNCSPLFVSMVAPAPKEKKKEME 136 (164)
T ss_pred ccccCCHHHHHHHHHHHHc----CchHhhHHHHHHHhCCCHHHHHHhcCCCHHHHHHHH
Confidence 4578999999999998777 577889999999999997665555444444443333
No 44
>smart00298 CHROMO Chromatin organization modifier domain.
Probab=84.73 E-value=0.73 Score=32.72 Aligned_cols=37 Identities=27% Similarity=0.517 Sum_probs=28.6
Q ss_pred eehhhhhhccccCCCCCeEEEEecCCCCCcccccccc
Q 016887 156 YDVSAFLAQRNFDTADPEVQVRFAGFGAEEDEWVNIK 192 (381)
Q Consensus 156 YDV~~fL~~r~l~tge~elrVrf~gFg~eeDEwvnvk 192 (381)
|.|.-.|.+|....|..++.|+|.|++..++.|+...
T Consensus 2 ~~v~~Il~~r~~~~~~~~ylVkW~g~~~~~~tW~~~~ 38 (55)
T smart00298 2 YEVEKILDHRWKKKGELEYLVKWKGYSYSEDTWEPEE 38 (55)
T ss_pred cchheeeeeeecCCCcEEEEEEECCCCCccCceeeHH
Confidence 3355556666446677899999999999999998763
No 45
>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=83.16 E-value=0.42 Score=34.85 Aligned_cols=37 Identities=24% Similarity=0.495 Sum_probs=29.9
Q ss_pred eehhhhhhccccCCCC--CeEEEEecCCCCCcccccccc
Q 016887 156 YDVSAFLAQRNFDTAD--PEVQVRFAGFGAEEDEWVNIK 192 (381)
Q Consensus 156 YDV~~fL~~r~l~tge--~elrVrf~gFg~eeDEwvnvk 192 (381)
|-|.-.|.+|....+. .++.|++.|++.+++.|.+..
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 4566778888666665 499999999999999998864
No 46
>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=82.44 E-value=1.2 Score=31.33 Aligned_cols=36 Identities=33% Similarity=0.528 Sum_probs=26.4
Q ss_pred EeeccCCCceeehhhhhhccccCCCCCeEEEEecCCCCCcc
Q 016887 146 EAKSARDGAWYDVSAFLAQRNFDTADPEVQVRFAGFGAEED 186 (381)
Q Consensus 146 EA~S~~DgAWYDV~~fL~~r~l~tge~elrVrf~gFg~eeD 186 (381)
-|+...||.||-..+.--. ++..+.|.|..||+.+.
T Consensus 5 ~a~~~~d~~wyra~V~~~~-----~~~~~~V~f~DyG~~~~ 40 (48)
T cd04508 5 LAKYSDDGKWYRAKITSIL-----SDGKVEVFFVDYGNTEV 40 (48)
T ss_pred EEEECCCCeEEEEEEEEEC-----CCCcEEEEEEcCCCcEE
Confidence 3556668999998765221 25779999999999853
No 47
>smart00743 Agenet Tudor-like domain present in plant sequences. Domain in plant sequences with possible chromatin-associated functions.
Probab=81.92 E-value=4 Score=30.34 Aligned_cols=50 Identities=24% Similarity=0.419 Sum_probs=37.7
Q ss_pred cccCCceEEEeeecCCcceEeeEEEeeeeecccCCCCcceEEEEEeec--CCccccccCcce
Q 016887 209 AVLPGDLILCFQEGKDQALYFDAHVLDAQRRRHDVRGCRCRFLVRYDH--DQSEEIVPLRKV 268 (381)
Q Consensus 209 ~v~~Gd~VcCfqeg~d~alyyDA~V~~Vqrr~Hd~~gCrC~FlVrw~h--dp~ee~v~l~kv 268 (381)
.++.||.|-++... +.-||-|.|+.+.. .+ +|.|+|+. .+.++.+...+|
T Consensus 2 ~~~~G~~Ve~~~~~--~~~W~~a~V~~~~~-----~~---~~~V~~~~~~~~~~e~v~~~~L 53 (61)
T smart00743 2 DFKKGDRVEVFSKE--EDSWWEAVVTKVLG-----DG---KYLVRYLTESEPLKETVDWSDL 53 (61)
T ss_pred CcCCCCEEEEEECC--CCEEEEEEEEEECC-----CC---EEEEEECCCCcccEEEEeHHHc
Confidence 56899999987642 67899999998865 22 37999998 666676665554
No 48
>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=80.99 E-value=1.8 Score=36.25 Aligned_cols=45 Identities=20% Similarity=0.409 Sum_probs=36.7
Q ss_pred eeEEeeccCCCceeehhhhhhccccCCCCCeEEEEecCCCCCcccccccc
Q 016887 143 MEFEAKSARDGAWYDVSAFLAQRNFDTADPEVQVRFAGFGAEEDEWVNIK 192 (381)
Q Consensus 143 lEFEA~S~~DgAWYDV~~fL~~r~l~tge~elrVrf~gFg~eeDEwvnvk 192 (381)
|-+||...++-..|=|++..+-. | ..|+|+|.|+.+..|.|+++.
T Consensus 32 mkLEavD~~~~~~i~vAtV~~v~----g-~~l~v~~dg~~~~~D~W~~~~ 76 (96)
T smart00561 32 MKLEAVDPRNPSLICVATVVEVK----G-YRLLLHFDGWDDKYDFWCDAD 76 (96)
T ss_pred CEEEEECCCCCceEEEEEEEEEE----C-CEEEEEEccCCCcCCEEEECC
Confidence 77899988887888777765532 2 479999999999999999986
No 49
>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=80.71 E-value=3.5 Score=40.21 Aligned_cols=55 Identities=18% Similarity=0.220 Sum_probs=38.7
Q ss_pred ccccCCceEEEeeecCCcceEeeEEEeeeeecccCCCCcceEEEEEeecCCccccccCcceeec
Q 016887 208 VAVLPGDLILCFQEGKDQALYFDAHVLDAQRRRHDVRGCRCRFLVRYDHDQSEEIVPLRKVCRR 271 (381)
Q Consensus 208 ~~v~~Gd~VcCfqeg~d~alyyDA~V~~Vqrr~Hd~~gCrC~FlVrw~hdp~ee~v~l~kvC~r 271 (381)
+..++||..++.- .+|-.||.|+|.+|.. .+| +++|+|..-.++|+|.|.+|=-.
T Consensus 67 ~~WkvGd~C~A~~--s~Dg~~Y~A~I~~i~~----~~~---~~~V~f~gYgn~e~v~l~dL~~~ 121 (264)
T PF06003_consen 67 KKWKVGDKCMAVY--SEDGQYYPATIESIDE----EDG---TCVVVFTGYGNEEEVNLSDLKPS 121 (264)
T ss_dssp T---TT-EEEEE---TTTSSEEEEEEEEEET----TTT---EEEEEETTTTEEEEEEGGGEEET
T ss_pred cCCCCCCEEEEEE--CCCCCEEEEEEEEEcC----CCC---EEEEEEcccCCeEeeehhhhccc
Confidence 5788999988763 4466799999999952 222 33499999999999999998555
No 50
>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=76.57 E-value=3.8 Score=34.49 Aligned_cols=48 Identities=17% Similarity=0.358 Sum_probs=35.5
Q ss_pred cceEeeEEEeeeeecccCCCCcceEEEEEeecCCccccccCcceeeccc
Q 016887 225 QALYFDAHVLDAQRRRHDVRGCRCRFLVRYDHDQSEEIVPLRKVCRRPE 273 (381)
Q Consensus 225 ~alyyDA~V~~Vqrr~Hd~~gCrC~FlVrw~hdp~ee~v~l~kvC~rp~ 273 (381)
...||+|.|+.|.++. ....+.+.+-|.|+..|..+.+.+.....||-
T Consensus 9 ~gAWfEa~i~~i~~~~-~~~~e~viYhIkyddype~gvv~~~~~~iRpR 56 (85)
T PF12148_consen 9 MGAWFEAQIVTITKKC-MSDDEDVIYHIKYDDYPENGVVEMRSKDIRPR 56 (85)
T ss_dssp T-EEEEEEEEEEEES--SSSSTTEEEEEEETT-GGG-EEEEEGGGEEE-
T ss_pred CcceEEEEEEEeeccC-CCCCCCEEEEEEeccCCCcCceecccccccce
Confidence 4679999999999665 44459999999999999888777776677753
No 51
>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=75.79 E-value=5 Score=30.12 Aligned_cols=38 Identities=21% Similarity=0.560 Sum_probs=27.7
Q ss_pred ccCCceEEEeeecCCcceEeeEEEeeeeecccCCCCcceEEEEEee
Q 016887 210 VLPGDLILCFQEGKDQALYFDAHVLDAQRRRHDVRGCRCRFLVRYD 255 (381)
Q Consensus 210 v~~Gd~VcCfqeg~d~alyyDA~V~~Vqrr~Hd~~gCrC~FlVrw~ 255 (381)
+..|+.|.|+. .+-.+|.|+|+++...... =.|.|-|.
T Consensus 1 ~~vG~~v~~~~---~~~~~y~A~I~~~r~~~~~-----~~YyVHY~ 38 (55)
T PF11717_consen 1 FEVGEKVLCKY---KDGQWYEAKILDIREKNGE-----PEYYVHYQ 38 (55)
T ss_dssp --TTEEEEEEE---TTTEEEEEEEEEEEECTTC-----EEEEEEET
T ss_pred CCcCCEEEEEE---CCCcEEEEEEEEEEecCCC-----EEEEEEcC
Confidence 46899999999 4668999999999985433 34556555
No 52
>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=75.18 E-value=2.9 Score=32.81 Aligned_cols=45 Identities=24% Similarity=0.459 Sum_probs=33.8
Q ss_pred eeEEeeccCCCceeehhhhhhccccCCCCCeEEEEecCCCCCcccccccc
Q 016887 143 MEFEAKSARDGAWYDVSAFLAQRNFDTADPEVQVRFAGFGAEEDEWVNIK 192 (381)
Q Consensus 143 lEFEA~S~~DgAWYDV~~fL~~r~l~tge~elrVrf~gFg~eeDEwvnvk 192 (381)
|-+||....+...|=|++..+- . | ..|+|+|.|+.+++|.|+.+.
T Consensus 1 MkLEa~d~~~~~~~~vAtV~~v--~--g-~~l~v~~dg~~~~~d~w~~~~ 45 (73)
T PF02820_consen 1 MKLEAVDPRNPSLICVATVVKV--C--G-GRLLVRYDGWDDDYDFWCHID 45 (73)
T ss_dssp EEEEEEETTECCEEEEEEEEEE--E--T-TEEEEEETTSTGGGEEEEETT
T ss_pred CeEEEECCCCCCeEEEEEEEEE--e--C-CEEEEEEcCCCCCccEEEECC
Confidence 4578887778777767665442 1 2 339999999999999999874
No 53
>PF12148 DUF3590: Protein of unknown function (DUF3590); InterPro: IPR021991 This domain is found in eukaryotes, and is typically between 83 and 97 amino acids in length. It is found in association with PF00097 from PFAM, PF02182 from PFAM, PF00628 from PFAM, PF00240 from PFAM. There are two conserved sequence motifs: RAR and NYN. The domain is part of the protein NIRF which has zinc finger and ubiquitinating domains. The function of this domain is likely to be mainly structural, however this has not been confirmed. ; PDB: 3DB4_A 3ASK_A 3DB3_A 2L3R_A.
Probab=74.44 E-value=3.5 Score=34.71 Aligned_cols=70 Identities=13% Similarity=0.288 Sum_probs=38.5
Q ss_pred EeeccCCCceeehhhhhhccccC--CCCCeEEEEecCCCCCccccccccccccccCCcccccccccccCCceEEE
Q 016887 146 EAKSARDGAWYDVSAFLAQRNFD--TADPEVQVRFAGFGAEEDEWVNIKRHVRQRSLPCEASECVAVLPGDLILC 218 (381)
Q Consensus 146 EA~S~~DgAWYDV~~fL~~r~l~--tge~elrVrf~gFg~eeDEwvnvk~rvR~rS~plE~sEC~~v~~Gd~VcC 218 (381)
-|+....|||++..+.--.+.-. +.+.-..|.|.+|.+..-.-+.++ .+|+|..-+= .=..|.+|+.|..
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 36677799999976654444322 345667899988875554444444 8888877543 3467889999984
No 54
>KOG3623 consensus Homeobox transcription factor SIP1 [Transcription]
Probab=73.55 E-value=12 Score=42.28 Aligned_cols=52 Identities=21% Similarity=0.319 Sum_probs=40.1
Q ss_pred cCHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHhCCCccccCCcccccchhHhhhhcchhhHhhhc
Q 016887 14 FNPAEVTEMEGILQEHHNAMPSREILVALAEKFSESPERKGKIMVQMKQVWNWFQNRRYAIRAKS 78 (381)
Q Consensus 14 FT~~QI~eLEk~F~e~~n~Yp~r~~rq~LA~kfnlS~~RaGk~~Vq~kQVk~WFQNRR~K~Kkk~ 78 (381)
|++. +.-|...|.- |..|+.++..++|...|++- .-|+.||+|++.+.....
T Consensus 564 ~~~p-~sllkayyal--n~~ps~eelskia~qvglp~----------~vvk~wfE~~~a~e~sv~ 615 (1007)
T KOG3623|consen 564 FNHP-TSLLKAYYAL--NGLPSEEELSKIAQQVGLPF----------AVVKAWFEDEEAEEMSVE 615 (1007)
T ss_pred cCCc-HHHHHHHHHh--cCCCCHHHHHHHHHHhcccH----------HHHHHHHHhhhhhhhhhc
Confidence 4444 4444555555 78999999999999999973 669999999999876544
No 55
>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=70.73 E-value=12 Score=28.99 Aligned_cols=43 Identities=28% Similarity=0.397 Sum_probs=28.0
Q ss_pred ccCCceEEE-eeecCCcceEeeEEEeeeeecccCCCCcceEEEEEeecCCcc
Q 016887 210 VLPGDLILC-FQEGKDQALYFDAHVLDAQRRRHDVRGCRCRFLVRYDHDQSE 260 (381)
Q Consensus 210 v~~Gd~VcC-fqeg~d~alyyDA~V~~Vqrr~Hd~~gCrC~FlVrw~hdp~e 260 (381)
+++|+.|-. .++.....-||-|.|+++.... +|+|+|++-..+
T Consensus 1 F~~G~~VEV~s~e~g~~gaWf~a~V~~~~~~~--------~~~V~Y~~~~~~ 44 (68)
T PF05641_consen 1 FKKGDEVEVSSDEDGFRGAWFPATVLKENGDD--------KYLVEYDDLPDE 44 (68)
T ss_dssp --TT-EEEEEE-SBTT--EEEEEEEEEEETT---------EEEEEETT-SS-
T ss_pred CCCCCEEEEEEcCCCCCcEEEEEEEEEeCCCc--------EEEEEECCcccc
Confidence 468999984 4566669999999999987665 999999765544
No 56
>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=69.29 E-value=4.8 Score=28.90 Aligned_cols=35 Identities=26% Similarity=0.577 Sum_probs=25.3
Q ss_pred CCCCCCCCCccccCHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHhCCCc
Q 016887 2 GRPPSNGGPAFRFNPAEVTEMEGILQEHHNAMPSREILVALAEKFSESP 50 (381)
Q Consensus 2 GrPps~~~pRtrFT~~QI~eLEk~F~e~~n~Yp~r~~rq~LA~kfnlS~ 50 (381)
|||+. +++++++++-+++.+ + ....+||+.||+|.
T Consensus 1 GRp~~-------~~~~~~~~i~~l~~~--G-----~si~~IA~~~gvsr 35 (45)
T PF02796_consen 1 GRPPK-------LSKEQIEEIKELYAE--G-----MSIAEIAKQFGVSR 35 (45)
T ss_dssp SSSSS-------SSHCCHHHHHHHHHT--T-------HHHHHHHTTS-H
T ss_pred CcCCC-------CCHHHHHHHHHHHHC--C-----CCHHHHHHHHCcCH
Confidence 66665 567778888888888 2 34789999999984
No 57
>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=68.07 E-value=5.2 Score=28.96 Aligned_cols=43 Identities=28% Similarity=0.492 Sum_probs=29.6
Q ss_pred EeeccCCCceeehhhhhhccccCCCCCeEEEEecCCCCCccccccccccccc
Q 016887 146 EAKSARDGAWYDVSAFLAQRNFDTADPEVQVRFAGFGAEEDEWVNIKRHVRQ 197 (381)
Q Consensus 146 EA~S~~DgAWYDV~~fL~~r~l~tge~elrVrf~gFg~eeDEwvnvk~rvR~ 197 (381)
.|+- .||.||.+.+. +. +++..+.|.|..||.. ||++.. .+|+
T Consensus 10 ~a~~-~d~~wyra~I~-~~----~~~~~~~V~f~D~G~~--~~v~~~-~l~~ 52 (57)
T smart00333 10 AARW-EDGEWYRARII-KV----DGEQLYEVFFIDYGNE--EVVPPS-DLRP 52 (57)
T ss_pred EEEe-CCCCEEEEEEE-EE----CCCCEEEEEEECCCcc--EEEeHH-Heec
Confidence 3444 59999998754 22 1236799999999998 477744 4443
No 58
>PF13565 HTH_32: Homeodomain-like domain
Probab=66.77 E-value=21 Score=27.15 Aligned_cols=53 Identities=28% Similarity=0.429 Sum_probs=37.2
Q ss_pred CCCCCCccccCHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHhCCCccccCCcccccchhHhh
Q 016887 5 PSNGGPAFRFNPAEVTEMEGILQEHHNAMPSREILVALAEKFSESPERKGKIMVQMKQVWNW 66 (381)
Q Consensus 5 ps~~~pRtrFT~~QI~eLEk~F~e~~n~Yp~r~~rq~LA~kfnlS~~RaGk~~Vq~kQVk~W 66 (381)
|..|+|+. +.++.++|.+++.++ ...-.....+.|++.|+.+. .|+...|..|
T Consensus 24 ~~~Grp~~--~~e~~~~i~~~~~~~-p~wt~~~i~~~L~~~~g~~~------~~S~~tv~R~ 76 (77)
T PF13565_consen 24 PRPGRPRK--DPEQRERIIALIEEH-PRWTPREIAEYLEEEFGISV------RVSRSTVYRI 76 (77)
T ss_pred CCCCCCCC--cHHHHHHHHHHHHhC-CCCCHHHHHHHHHHHhCCCC------CccHhHHHHh
Confidence 55677766 777779999999984 23455578888999998741 3455666654
No 59
>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=64.51 E-value=4.3 Score=31.51 Aligned_cols=41 Identities=20% Similarity=0.447 Sum_probs=21.9
Q ss_pred CCceeehhhhhhccccCCCCCeEEEEecCCCCCccccc------ccccccccc
Q 016887 152 DGAWYDVSAFLAQRNFDTADPEVQVRFAGFGAEEDEWV------NIKRHVRQR 198 (381)
Q Consensus 152 DgAWYDV~~fL~~r~l~tge~elrVrf~gFg~eeDEwv------nvk~rvR~r 198 (381)
.||||...+.-... +..+.|+|..+..+++++. +.+ ++|+.
T Consensus 17 ~gaWf~a~V~~~~~-----~~~~~V~Y~~~~~~~~~~~~l~e~V~~~-~iRP~ 63 (68)
T PF05641_consen 17 RGAWFPATVLKENG-----DDKYLVEYDDLPDEDGESPPLKEWVDAR-RIRPC 63 (68)
T ss_dssp --EEEEEEEEEEET-----T-EEEEEETT-SS--------EEEEEGG-GEEE-
T ss_pred CcEEEEEEEEEeCC-----CcEEEEEECCcccccccccccEEEechh-eEECc
Confidence 68999988764432 2289999999999976653 333 56664
No 60
>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=58.46 E-value=25 Score=24.58 Aligned_cols=46 Identities=24% Similarity=0.369 Sum_probs=28.2
Q ss_pred CceEEEeeecCCcceEeeEEEeeeeecccCCCCcceEEEEEeecCCccccccCcce
Q 016887 213 GDLILCFQEGKDQALYFDAHVLDAQRRRHDVRGCRCRFLVRYDHDQSEEIVPLRKV 268 (381)
Q Consensus 213 Gd~VcCfqeg~d~alyyDA~V~~Vqrr~Hd~~gCrC~FlVrw~hdp~ee~v~l~kv 268 (381)
|+++++.- .++..||-|.|+++.. .-.+.|.|..-.+.+.|+..+|
T Consensus 1 G~~c~a~~--~~d~~wyra~V~~~~~--------~~~~~V~f~DyG~~~~v~~~~l 46 (48)
T cd04508 1 GDLCLAKY--SDDGKWYRAKITSILS--------DGKVEVFFVDYGNTEVVPLSDL 46 (48)
T ss_pred CCEEEEEE--CCCCeEEEEEEEEECC--------CCcEEEEEEcCCCcEEEeHHHc
Confidence 44444432 2378999999999974 2346677777444455655443
No 61
>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=57.26 E-value=27 Score=20.57 Aligned_cols=32 Identities=16% Similarity=0.328 Sum_probs=22.7
Q ss_pred cccCHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHhCCCc
Q 016887 12 FRFNPAEVTEMEGILQEHHNAMPSREILVALAEKFSESP 50 (381)
Q Consensus 12 trFT~~QI~eLEk~F~e~~n~Yp~r~~rq~LA~kfnlS~ 50 (381)
..|+.++...+...+.. .+ ...++|+.|+++.
T Consensus 4 ~~~~~~~~~~i~~~~~~---~~----s~~~ia~~~~is~ 35 (42)
T cd00569 4 PKLTPEQIEEARRLLAA---GE----SVAEIARRLGVSR 35 (42)
T ss_pred CcCCHHHHHHHHHHHHc---CC----CHHHHHHHHCCCH
Confidence 34677777777777654 22 5678999999974
No 62
>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=56.36 E-value=9.2 Score=37.32 Aligned_cols=43 Identities=26% Similarity=0.400 Sum_probs=30.3
Q ss_pred eEEeeccCCCceeehhhhhhccccCCCCCeEEEEecCCCCCcccccc
Q 016887 144 EFEAKSARDGAWYDVSAFLAQRNFDTADPEVQVRFAGFGAEEDEWVN 190 (381)
Q Consensus 144 EFEA~S~~DgAWYDV~~fL~~r~l~tge~elrVrf~gFg~eeDEwvn 190 (381)
.=.|+-+.||-||...+.--+ .......|+|.|||++|..++.
T Consensus 74 ~C~A~~s~Dg~~Y~A~I~~i~----~~~~~~~V~f~gYgn~e~v~l~ 116 (264)
T PF06003_consen 74 KCMAVYSEDGQYYPATIESID----EEDGTCVVVFTGYGNEEEVNLS 116 (264)
T ss_dssp EEEEE-TTTSSEEEEEEEEEE----TTTTEEEEEETTTTEEEEEEGG
T ss_pred EEEEEECCCCCEEEEEEEEEc----CCCCEEEEEEcccCCeEeeehh
Confidence 456777899999998765322 2234688999999998765543
No 63
>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=54.07 E-value=16 Score=28.05 Aligned_cols=34 Identities=18% Similarity=0.136 Sum_probs=29.1
Q ss_pred cCHHHHHHHHHHHHHhcCCCCC---HHHHHHHHHHhCCCc
Q 016887 14 FNPAEVTEMEGILQEHHNAMPS---REILVALAEKFSESP 50 (381)
Q Consensus 14 FT~~QI~eLEk~F~e~~n~Yp~---r~~rq~LA~kfnlS~ 50 (381)
+|+.|.+.|..+|+. .|.+ .....+||+.||+|.
T Consensus 1 LT~~Q~e~L~~A~~~---GYfd~PR~~tl~elA~~lgis~ 37 (53)
T PF04967_consen 1 LTDRQREILKAAYEL---GYFDVPRRITLEELAEELGISK 37 (53)
T ss_pred CCHHHHHHHHHHHHc---CCCCCCCcCCHHHHHHHhCCCH
Confidence 589999999999998 5655 567899999999984
No 64
>smart00743 Agenet Tudor-like domain present in plant sequences. Domain in plant sequences with possible chromatin-associated functions.
Probab=53.99 E-value=13 Score=27.67 Aligned_cols=34 Identities=18% Similarity=0.315 Sum_probs=23.2
Q ss_pred EeeccCCCceeehhhhhhccccCCCCCeEEEEecC--CCCC
Q 016887 146 EAKSARDGAWYDVSAFLAQRNFDTADPEVQVRFAG--FGAE 184 (381)
Q Consensus 146 EA~S~~DgAWYDV~~fL~~r~l~tge~elrVrf~g--Fg~e 184 (381)
||++..||+||...+.-- + ++..+.|+|.+ ++.+
T Consensus 10 e~~~~~~~~W~~a~V~~~---~--~~~~~~V~~~~~~~~~~ 45 (61)
T smart00743 10 EVFSKEEDSWWEAVVTKV---L--GDGKYLVRYLTESEPLK 45 (61)
T ss_pred EEEECCCCEEEEEEEEEE---C--CCCEEEEEECCCCcccE
Confidence 455555999998776622 2 24579999998 5443
No 65
>PF13873 Myb_DNA-bind_5: Myb/SANT-like DNA-binding domain
Probab=48.03 E-value=33 Score=26.55 Aligned_cols=63 Identities=16% Similarity=0.184 Sum_probs=43.9
Q ss_pred cccCHHHHHHHHHHHHHhcCCCCC-----------HHHHHHHHHHhCCCccccCCcccccchhHhhhhcchhhHhhhc
Q 016887 12 FRFNPAEVTEMEGILQEHHNAMPS-----------REILVALAEKFSESPERKGKIMVQMKQVWNWFQNRRYAIRAKS 78 (381)
Q Consensus 12 trFT~~QI~eLEk~F~e~~n~Yp~-----------r~~rq~LA~kfnlS~~RaGk~~Vq~kQVk~WFQNRR~K~Kkk~ 78 (381)
-.||.+|...|-.+++.+....-+ ...=++||..||.-. | ..=++.|++..++|=+...|++.
T Consensus 3 ~~fs~~E~~~Lv~~v~~~~~il~~k~~~~~~~~~k~~~W~~I~~~lN~~~---~-~~Rs~~~lkkkW~nlk~~~Kk~~ 76 (78)
T PF13873_consen 3 PNFSEEEKEILVELVEKHKDILENKFSDSVSNKEKRKAWEEIAEELNALG---P-GKRSWKQLKKKWKNLKSKAKKKL 76 (78)
T ss_pred CCCCHHHHHHHHHHHHHhHHHHhcccccHHHHHHHHHHHHHHHHHHHhcC---C-CCCCHHHHHHHHHHHHHHHHHHh
Confidence 479999998888887774211111 233468999998743 2 26688999998999888777754
No 66
>PF00249 Myb_DNA-binding: Myb-like DNA-binding domain; InterPro: IPR014778 The retroviral oncogene v-myb, and its cellular counterpart c-myb, encode nuclear DNA-binding proteins. These belong to the SANT domain family that specifically recognise the sequence YAAC(G/T)G [, ]. In myb, one of the most conserved regions consisting of three tandem repeats has been shown to be involved in DNA-binding [].; PDB: 1X41_A 2XAF_B 2XAG_B 2XAH_B 2UXN_B 2Y48_B 2XAQ_B 2X0L_B 2IW5_B 2XAJ_B ....
Probab=41.59 E-value=72 Score=22.73 Aligned_cols=45 Identities=13% Similarity=0.134 Sum_probs=32.2
Q ss_pred cccCHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHhCCCccccCCcccccchhHhhhhc
Q 016887 12 FRFNPAEVTEMEGILQEHHNAMPSREILVALAEKFSESPERKGKIMVQMKQVWNWFQN 69 (381)
Q Consensus 12 trFT~~QI~eLEk~F~e~~n~Yp~r~~rq~LA~kfnlS~~RaGk~~Vq~kQVk~WFQN 69 (381)
-.||.+|...|.+++..++.. .=..||+.|+.+- |..|++.=|+|
T Consensus 2 ~~Wt~eE~~~l~~~v~~~g~~-----~W~~Ia~~~~~~R--------t~~qc~~~~~~ 46 (48)
T PF00249_consen 2 GPWTEEEDEKLLEAVKKYGKD-----NWKKIAKRMPGGR--------TAKQCRSRYQN 46 (48)
T ss_dssp -SS-HHHHHHHHHHHHHSTTT-----HHHHHHHHHSSSS--------THHHHHHHHHH
T ss_pred CCCCHHHHHHHHHHHHHhCCc-----HHHHHHHHcCCCC--------CHHHHHHHHHh
Confidence 469999999999999996433 6788999998211 45888765554
No 67
>PF13551 HTH_29: Winged helix-turn helix
Probab=41.37 E-value=85 Score=24.82 Aligned_cols=53 Identities=19% Similarity=0.238 Sum_probs=32.9
Q ss_pred CCCccccCHHHHHHHHHHHHHhcC---CCCCH-HHHHHH-HHHhCCCccccCCcccccchhHhhhh
Q 016887 8 GGPAFRFNPAEVTEMEGILQEHHN---AMPSR-EILVAL-AEKFSESPERKGKIMVQMKQVWNWFQ 68 (381)
Q Consensus 8 ~~pRtrFT~~QI~eLEk~F~e~~n---~Yp~r-~~rq~L-A~kfnlS~~RaGk~~Vq~kQVk~WFQ 68 (381)
++++..+++++.+.|.+.+.+... ...+. ...+.| .+.+++ .|+...|+.|++
T Consensus 52 g~~~~~l~~~~~~~l~~~~~~~p~~g~~~~t~~~l~~~l~~~~~~~--------~~s~~ti~r~L~ 109 (112)
T PF13551_consen 52 GRPRKRLSEEQRAQLIELLRENPPEGRSRWTLEELAEWLIEEEFGI--------DVSPSTIRRILK 109 (112)
T ss_pred CCCCCCCCHHHHHHHHHHHHHCCCCCCCcccHHHHHHHHHHhccCc--------cCCHHHHHHHHH
Confidence 455555999999999999998411 01222 333334 334444 456788888875
No 68
>smart00717 SANT SANT SWI3, ADA2, N-CoR and TFIIIB'' DNA-binding domains.
Probab=39.54 E-value=57 Score=21.62 Aligned_cols=44 Identities=9% Similarity=0.105 Sum_probs=31.7
Q ss_pred cccCHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHhCCCccccCCcccccchhHhhhhc
Q 016887 12 FRFNPAEVTEMEGILQEHHNAMPSREILVALAEKFSESPERKGKIMVQMKQVWNWFQN 69 (381)
Q Consensus 12 trFT~~QI~eLEk~F~e~~n~Yp~r~~rq~LA~kfnlS~~RaGk~~Vq~kQVk~WFQN 69 (381)
..||.+|...|.+++...+. ..-..+|+.|.-- +..||+..|.+
T Consensus 2 ~~Wt~~E~~~l~~~~~~~g~-----~~w~~Ia~~~~~r---------t~~~~~~~~~~ 45 (49)
T smart00717 2 GEWTEEEDELLIELVKKYGK-----NNWEKIAKELPGR---------TAEQCRERWNN 45 (49)
T ss_pred CCCCHHHHHHHHHHHHHHCc-----CCHHHHHHHcCCC---------CHHHHHHHHHH
Confidence 46999999999999999642 2346788888721 45788765554
No 69
>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=39.42 E-value=16 Score=28.87 Aligned_cols=30 Identities=27% Similarity=0.437 Sum_probs=21.4
Q ss_pred HHHHHhcCCCCCHHHHHHHHHHhCCCccccCCcccccchhHhhh
Q 016887 24 GILQEHHNAMPSREILVALAEKFSESPERKGKIMVQMKQVWNWF 67 (381)
Q Consensus 24 k~F~e~~n~Yp~r~~rq~LA~kfnlS~~RaGk~~Vq~kQVk~WF 67 (381)
++|.++++.. ...+||++||.|+ .||..|=
T Consensus 14 e~y~~~~g~i----~lkdIA~~Lgvs~----------~tIr~WK 43 (60)
T PF10668_consen 14 EIYKESNGKI----KLKDIAEKLGVSE----------STIRKWK 43 (60)
T ss_pred HHHHHhCCCc----cHHHHHHHHCCCH----------HHHHHHh
Confidence 4556554333 4568999999985 9999983
No 70
>smart00027 EH Eps15 homology domain. Pair of EF hand motifs that recognise proteins containing Asn-Pro-Phe (NPF) sequences.
Probab=37.59 E-value=77 Score=25.44 Aligned_cols=37 Identities=11% Similarity=0.137 Sum_probs=27.7
Q ss_pred cCHHHHHHHHHHHHHh---cCCCCCHHHHHHHHHHhCCCc
Q 016887 14 FNPAEVTEMEGILQEH---HNAMPSREILVALAEKFSESP 50 (381)
Q Consensus 14 FT~~QI~eLEk~F~e~---~n~Yp~r~~rq~LA~kfnlS~ 50 (381)
+|++|+.++.++|... ++.+++.....++=..++++.
T Consensus 4 ls~~~~~~l~~~F~~~D~d~~G~Is~~el~~~l~~~~~~~ 43 (96)
T smart00027 4 ISPEDKAKYEQIFRSLDKNQDGTVTGAQAKPILLKSGLPQ 43 (96)
T ss_pred CCHHHHHHHHHHHHHhCCCCCCeEeHHHHHHHHHHcCCCH
Confidence 6889999999998873 456788877777666666653
No 71
>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=36.40 E-value=47 Score=25.07 Aligned_cols=46 Identities=22% Similarity=0.341 Sum_probs=29.8
Q ss_pred CCccccCHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHhCCCccccCCcccccchhHhhhhcc
Q 016887 9 GPAFRFNPAEVTEMEGILQEHHNAMPSREILVALAEKFSESPERKGKIMVQMKQVWNWFQNR 70 (381)
Q Consensus 9 ~pRtrFT~~QI~eLEk~F~e~~n~Yp~r~~rq~LA~kfnlS~~RaGk~~Vq~kQVk~WFQNR 70 (381)
+.+..||+++-.++=+.+.. ......+||..+|+++ .++.+|-+-=
T Consensus 2 ~~r~~ys~e~K~~~v~~~~~------~g~sv~~va~~~gi~~----------~~l~~W~~~~ 47 (76)
T PF01527_consen 2 RKRRRYSPEFKLQAVREYLE------SGESVSEVAREYGISP----------STLYNWRKQY 47 (76)
T ss_dssp -SS----HHHHHHHHHHHHH------HHCHHHHHHHHHTS-H----------HHHHHHHHHH
T ss_pred CCCCCCCHHHHHHHHHHHHH------CCCceEeeeccccccc----------ccccHHHHHH
Confidence 35678999998777666533 2467889999999985 8899996544
No 72
>cd06171 Sigma70_r4 Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in Escherichia coli (Ec) sigma70, the main housekeeping sigma, and related sigma-factors (SFs). A SF is a dissociable subunit of RNA polymerase, it directs bacterial or plastid core RNA polymerase to specific promoter elements located upstream of transcription initiation points. The SR4 of Ec sigma70 and other essential primary SFs contact promoter sequences located 35 base-pairs upstream of the initiation point, recognizing a 6-base-pair -35 consensus TTGACA. Sigma70 related SFs also include SFs which are dispensable for bacterial cell growth for example Ec sigmaS, SFs which activate regulons in response to a specific signal for example heat-shock Ec sigmaH, and a group of SFs which includes the extracytoplasmic function (ECF) SFs and is typified by Ec sigmaE which contains SR2 and -4 only. ECF SFs direct the transcription of genes that regulate various responses including periplas
Probab=35.12 E-value=30 Score=23.06 Aligned_cols=43 Identities=12% Similarity=-0.051 Sum_probs=29.0
Q ss_pred cCHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHhCCCccccCCcccccchhHhhhhcchhh
Q 016887 14 FNPAEVTEMEGILQEHHNAMPSREILVALAEKFSESPERKGKIMVQMKQVWNWFQNRRYA 73 (381)
Q Consensus 14 FT~~QI~eLEk~F~e~~n~Yp~r~~rq~LA~kfnlS~~RaGk~~Vq~kQVk~WFQNRR~K 73 (381)
+++.+...++..|. ......++|+.+|++. ..|..|.+.-+.+
T Consensus 11 l~~~~~~~~~~~~~-------~~~~~~~ia~~~~~s~----------~~i~~~~~~~~~~ 53 (55)
T cd06171 11 LPEREREVILLRFG-------EGLSYEEIAEILGISR----------STVRQRLHRALKK 53 (55)
T ss_pred CCHHHHHHHHHHHh-------cCCCHHHHHHHHCcCH----------HHHHHHHHHHHHH
Confidence 45666655555543 3345788899999985 8898888765544
No 73
>PF11523 DUF3223: Protein of unknown function (DUF3223); InterPro: IPR021602 This family of proteins has no known function. ; PDB: 2K0M_A.
Probab=34.01 E-value=44 Score=27.07 Aligned_cols=33 Identities=39% Similarity=0.486 Sum_probs=21.8
Q ss_pred EeeeeecccCCCC-cceEEEEEeecCCccccccCcc
Q 016887 233 VLDAQRRRHDVRG-CRCRFLVRYDHDQSEEIVPLRK 267 (381)
Q Consensus 233 V~~Vqrr~Hd~~g-CrC~FlVrw~hdp~ee~v~l~k 267 (381)
|..|+-+.|...+ .||.|+||= |.+++.++.+|
T Consensus 41 i~~i~V~~hp~~~~srCF~vvR~--DGs~~DFSy~K 74 (76)
T PF11523_consen 41 IDHIMVRKHPEFKDSRCFFVVRT--DGSEEDFSYRK 74 (76)
T ss_dssp EEEEEEEESSSS---EEEEEEET--TS-EEE--GGG
T ss_pred eeeEEEeecCCCCcceEEEEEEe--CCCeeeeEhhh
Confidence 6788999999765 999999985 66666555443
No 74
>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=31.94 E-value=35 Score=26.68 Aligned_cols=52 Identities=29% Similarity=0.546 Sum_probs=34.3
Q ss_pred ccCCCceeehhhhhhccccCCCCCeEEEEecCCCCCcccccccccccc-----ccCCcccccccc
Q 016887 149 SARDGAWYDVSAFLAQRNFDTADPEVQVRFAGFGAEEDEWVNIKRHVR-----QRSLPCEASECV 208 (381)
Q Consensus 149 S~~DgAWYDV~~fL~~r~l~tge~elrVrf~gFg~eeDEwvnvk~rvR-----~rS~plE~sEC~ 208 (381)
...||.||-+.+. ...++..+.|.|..||..+- ++.. .+| ...+|.+...|.
T Consensus 62 ~~~~~~w~Ra~I~-----~~~~~~~~~V~~iD~G~~~~--v~~~-~l~~l~~~~~~~P~~a~~~~ 118 (121)
T PF00567_consen 62 VSEDGRWYRAVIT-----VDIDENQYKVFLIDYGNTEK--VSAS-DLRPLPPEFASLPPQAIKCK 118 (121)
T ss_dssp ETTTSEEEEEEEE-----EEECTTEEEEEETTTTEEEE--EEGG-GEEE--HHHCSSSSSCEEEE
T ss_pred EecCCceeeEEEE-----EecccceeEEEEEecCceEE--EcHH-HhhhhCHHHhhCChhhEEEE
Confidence 3459999999981 33456889999999998753 4443 222 233566666653
No 75
>PRK03975 tfx putative transcriptional regulator; Provisional
Probab=31.72 E-value=63 Score=29.28 Aligned_cols=50 Identities=10% Similarity=-0.033 Sum_probs=38.3
Q ss_pred cccCHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHhCCCccccCCcccccchhHhhhhcchhhHhhhcc
Q 016887 12 FRFNPAEVTEMEGILQEHHNAMPSREILVALAEKFSESPERKGKIMVQMKQVWNWFQNRRYAIRAKSI 79 (381)
Q Consensus 12 trFT~~QI~eLEk~F~e~~n~Yp~r~~rq~LA~kfnlS~~RaGk~~Vq~kQVk~WFQNRR~K~Kkk~~ 79 (381)
..+|+.|.+-|+-.++. -..++||+.||+|. ..|+.|-++.+.+.++...
T Consensus 5 ~~Lt~rqreVL~lr~~G--------lTq~EIAe~LGiS~----------~tVs~ie~ra~kkLr~~~~ 54 (141)
T PRK03975 5 SFLTERQIEVLRLRERG--------LTQQEIADILGTSR----------ANVSSIEKRARENIEKARE 54 (141)
T ss_pred cCCCHHHHHHHHHHHcC--------CCHHHHHHHHCCCH----------HHHHHHHHHHHHHHHHHHH
Confidence 46788888888763322 24679999999985 7899999998888777654
No 76
>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=29.85 E-value=96 Score=22.08 Aligned_cols=46 Identities=20% Similarity=0.168 Sum_probs=30.1
Q ss_pred ccCHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHhCCCccccCCcccccchhHhhhhcchhhHh
Q 016887 13 RFNPAEVTEMEGILQEHHNAMPSREILVALAEKFSESPERKGKIMVQMKQVWNWFQNRRYAIR 75 (381)
Q Consensus 13 rFT~~QI~eLEk~F~e~~n~Yp~r~~rq~LA~kfnlS~~RaGk~~Vq~kQVk~WFQNRR~K~K 75 (381)
.+++.|-+-+.-.|-+ ....+++|+.+|+|. ..|+.+...=..|.|
T Consensus 4 ~L~~~er~vi~~~y~~-------~~t~~eIa~~lg~s~----------~~V~~~~~~al~kLR 49 (50)
T PF04545_consen 4 QLPPREREVIRLRYFE-------GLTLEEIAERLGISR----------STVRRILKRALKKLR 49 (50)
T ss_dssp TS-HHHHHHHHHHHTS-------T-SHHHHHHHHTSCH----------HHHHHHHHHHHHHHH
T ss_pred hCCHHHHHHHHHHhcC-------CCCHHHHHHHHCCcH----------HHHHHHHHHHHHHhc
Confidence 3567777777777733 345789999999985 667776654444443
No 77
>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=29.39 E-value=1e+02 Score=20.08 Aligned_cols=42 Identities=10% Similarity=0.090 Sum_probs=29.9
Q ss_pred ccCHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHhCCCccccCCcccccchhHhhhh
Q 016887 13 RFNPAEVTEMEGILQEHHNAMPSREILVALAEKFSESPERKGKIMVQMKQVWNWFQ 68 (381)
Q Consensus 13 rFT~~QI~eLEk~F~e~~n~Yp~r~~rq~LA~kfnlS~~RaGk~~Vq~kQVk~WFQ 68 (381)
.||.+|...|.+.+...+. ..-..||+.++.- +..||+.-|+
T Consensus 1 ~Wt~eE~~~l~~~~~~~g~-----~~w~~Ia~~~~~r---------s~~~~~~~~~ 42 (45)
T cd00167 1 PWTEEEDELLLEAVKKYGK-----NNWEKIAKELPGR---------TPKQCRERWR 42 (45)
T ss_pred CCCHHHHHHHHHHHHHHCc-----CCHHHHHhHcCCC---------CHHHHHHHHH
Confidence 3899999999999999642 2346788888632 3577775444
No 78
>PF13518 HTH_28: Helix-turn-helix domain
Probab=28.99 E-value=46 Score=23.29 Aligned_cols=23 Identities=22% Similarity=0.492 Sum_probs=19.1
Q ss_pred HHHHHHHHhCCCccccCCcccccchhHhhhhcc
Q 016887 38 ILVALAEKFSESPERKGKIMVQMKQVWNWFQNR 70 (381)
Q Consensus 38 ~rq~LA~kfnlS~~RaGk~~Vq~kQVk~WFQNR 70 (381)
...++|+.|++|. .+|..|.+.=
T Consensus 14 s~~~~a~~~gis~----------~tv~~w~~~y 36 (52)
T PF13518_consen 14 SVREIAREFGISR----------STVYRWIKRY 36 (52)
T ss_pred CHHHHHHHHCCCH----------hHHHHHHHHH
Confidence 5677999999985 8999998754
No 79
>PF13936 HTH_38: Helix-turn-helix domain; PDB: 2W48_A.
Probab=28.96 E-value=48 Score=23.83 Aligned_cols=32 Identities=19% Similarity=0.389 Sum_probs=15.3
Q ss_pred cccCHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHhCCCc
Q 016887 12 FRFNPAEVTEMEGILQEHHNAMPSREILVALAEKFSESP 50 (381)
Q Consensus 12 trFT~~QI~eLEk~F~e~~n~Yp~r~~rq~LA~kfnlS~ 50 (381)
..||.+|..+++.++++ ..-..+||+.||.|.
T Consensus 3 ~~Lt~~eR~~I~~l~~~-------G~s~~~IA~~lg~s~ 34 (44)
T PF13936_consen 3 KHLTPEERNQIEALLEQ-------GMSIREIAKRLGRSR 34 (44)
T ss_dssp ---------HHHHHHCS----------HHHHHHHTT--H
T ss_pred cchhhhHHHHHHHHHHc-------CCCHHHHHHHHCcCc
Confidence 46899999999988765 245677999999985
No 80
>PTZ00184 calmodulin; Provisional
Probab=27.20 E-value=1.8e+02 Score=23.55 Aligned_cols=37 Identities=5% Similarity=0.171 Sum_probs=28.7
Q ss_pred ccCHHHHHHHHHHHHHh---cCCCCCHHHHHHHHHHhCCC
Q 016887 13 RFNPAEVTEMEGILQEH---HNAMPSREILVALAEKFSES 49 (381)
Q Consensus 13 rFT~~QI~eLEk~F~e~---~n~Yp~r~~rq~LA~kfnlS 49 (381)
-++.+++.++++.|... +..+++......+...++.+
T Consensus 4 ~~~~~~~~~~~~~F~~~D~~~~G~i~~~e~~~~l~~~~~~ 43 (149)
T PTZ00184 4 QLTEEQIAEFKEAFSLFDKDGDGTITTKELGTVMRSLGQN 43 (149)
T ss_pred ccCHHHHHHHHHHHHHHcCCCCCcCCHHHHHHHHHHhCCC
Confidence 47889999999998763 45678888877777777765
No 81
>PLN00104 MYST -like histone acetyltransferase; Provisional
Probab=26.88 E-value=1.4e+02 Score=31.94 Aligned_cols=58 Identities=17% Similarity=0.281 Sum_probs=38.7
Q ss_pred ccccCCceEEEeeecCCcceEeeEEEeeeeecccCCCCcceEEEEEeecCCcc--ccccCcce
Q 016887 208 VAVLPGDLILCFQEGKDQALYFDAHVLDAQRRRHDVRGCRCRFLVRYDHDQSE--EIVPLRKV 268 (381)
Q Consensus 208 ~~v~~Gd~VcCfqeg~d~alyyDA~V~~Vqrr~Hd~~gCrC~FlVrw~hdp~e--e~v~l~kv 268 (381)
..+..|+.|+|+... +-.||.|+|+++.+..-...+. -.|-|.|..-+.- |=|+..+|
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 456799999999742 4568899999998643001121 2588998876655 55666555
No 82
>PF03672 UPF0154: Uncharacterised protein family (UPF0154); InterPro: IPR005359 The proteins in this entry are functionally uncharacterised.
Probab=26.19 E-value=1.1e+02 Score=24.73 Aligned_cols=36 Identities=25% Similarity=0.324 Sum_probs=31.8
Q ss_pred HHHHHHHHHhcCCCCCHHHHHHHHHHhCCCccccCCcccccchhHh
Q 016887 20 TEMEGILQEHHNAMPSREILVALAEKFSESPERKGKIMVQMKQVWN 65 (381)
Q Consensus 20 ~eLEk~F~e~~n~Yp~r~~rq~LA~kfnlS~~RaGk~~Vq~kQVk~ 65 (381)
..||+-|++ |..++.+....+....|-.+ +++||+.
T Consensus 20 ~~~~k~l~~--NPpine~mir~M~~QMG~kp--------Sekqi~Q 55 (64)
T PF03672_consen 20 KYMEKQLKE--NPPINEKMIRAMMMQMGRKP--------SEKQIKQ 55 (64)
T ss_pred HHHHHHHHH--CCCCCHHHHHHHHHHhCCCc--------cHHHHHH
Confidence 468999999 79999999999999999987 7888874
No 83
>PRK10072 putative transcriptional regulator; Provisional
Probab=25.56 E-value=49 Score=28.03 Aligned_cols=24 Identities=21% Similarity=0.249 Sum_probs=18.4
Q ss_pred HHHHHHHhCCCccccCCcccccchhHhhhhcchh
Q 016887 39 LVALAEKFSESPERKGKIMVQMKQVWNWFQNRRY 72 (381)
Q Consensus 39 rq~LA~kfnlS~~RaGk~~Vq~kQVk~WFQNRR~ 72 (381)
..+||+.+|+| ..-|..|.+.||.
T Consensus 49 Q~elA~~lGvS----------~~TVs~WE~G~r~ 72 (96)
T PRK10072 49 IDDFARVLGVS----------VAMVKEWESRRVK 72 (96)
T ss_pred HHHHHHHhCCC----------HHHHHHHHcCCCC
Confidence 56677777776 4779999999864
No 84
>PRK07539 NADH dehydrogenase subunit E; Validated
Probab=25.04 E-value=1.4e+02 Score=26.61 Aligned_cols=20 Identities=15% Similarity=0.170 Sum_probs=18.4
Q ss_pred CCCCCHHHHHHHHHHhCCCc
Q 016887 31 NAMPSREILVALAEKFSESP 50 (381)
Q Consensus 31 n~Yp~r~~rq~LA~kfnlS~ 50 (381)
..|++.+..+.+|+.+++++
T Consensus 35 ~g~ip~~~~~~iA~~l~v~~ 54 (154)
T PRK07539 35 RGWVPDEAIEAVADYLGMPA 54 (154)
T ss_pred hCCCCHHHHHHHHHHhCcCH
Confidence 47999999999999999986
No 85
>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=24.80 E-value=76 Score=22.68 Aligned_cols=31 Identities=16% Similarity=0.040 Sum_probs=21.8
Q ss_pred CCCCHHHHHHHHHHhCCCccccCCcccccchhHhhhhcchh
Q 016887 32 AMPSREILVALAEKFSESPERKGKIMVQMKQVWNWFQNRRY 72 (381)
Q Consensus 32 ~Yp~r~~rq~LA~kfnlS~~RaGk~~Vq~kQVk~WFQNRR~ 72 (381)
.|...-...++|+.+|+|+ ..|+.|.+.=|.
T Consensus 22 ~~~~g~s~~eIa~~l~~s~----------~~v~~~l~ra~~ 52 (54)
T PF08281_consen 22 RYFQGMSYAEIAEILGISE----------STVKRRLRRARK 52 (54)
T ss_dssp HHTS---HHHHHHHCTS-H----------HHHHHHHHHHHH
T ss_pred HHHHCcCHHHHHHHHCcCH----------HHHHHHHHHHHh
Confidence 4777888999999999985 789988875543
No 86
>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=24.11 E-value=1.3e+02 Score=26.38 Aligned_cols=54 Identities=22% Similarity=0.212 Sum_probs=40.8
Q ss_pred CCCCCCCCCccccCHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHhCCCccccCCcccccchhHhhhhcc
Q 016887 2 GRPPSNGGPAFRFNPAEVTEMEGILQEHHNAMPSREILVALAEKFSESPERKGKIMVQMKQVWNWFQNR 70 (381)
Q Consensus 2 GrPps~~~pRtrFT~~QI~eLEk~F~e~~n~Yp~r~~rq~LA~kfnlS~~RaGk~~Vq~kQVk~WFQNR 70 (381)
|.-.+..-++..+|+++.+.|++.+.+. -..+...+|+.=+++. .+|..||+++
T Consensus 68 g~~K~~~~~~~~~s~~~r~~~~~~l~~~-----~~~f~~~Va~~R~~~~----------~~v~~~~~~~ 121 (154)
T PF01343_consen 68 GEYKSAGFPRDPMSEEERENLQELLDEL-----YDQFVNDVAEGRGLSP----------DDVEEIADGG 121 (154)
T ss_dssp STTCCCCCTTSS--HHHHHHHHHHHHHH-----HHHHHHHHHHHHTS-H----------HHHHCHHCCH
T ss_pred CccccccCcCCCCCHHHHHHHHHHHHHH-----HHHHHHHHHHccCCCH----------HHHHHHHhhc
Confidence 3334455678889999999999999884 2788999999888875 7899999885
No 87
>COG3458 Acetyl esterase (deacetylase) [Secondary metabolites biosynthesis, transport, and catabolism]
Probab=23.81 E-value=92 Score=32.02 Aligned_cols=93 Identities=22% Similarity=0.348 Sum_probs=67.6
Q ss_pred CCceeEEeec-cCCCceeehhhhhhccccCCCCCeEEEEecCCCCCcccccc-----------ccccccccCCccccccc
Q 016887 140 STFMEFEAKS-ARDGAWYDVSAFLAQRNFDTADPEVQVRFAGFGAEEDEWVN-----------IKRHVRQRSLPCEASEC 207 (381)
Q Consensus 140 ~~~lEFEA~S-~~DgAWYDV~~fL~~r~l~tge~elrVrf~gFg~eeDEwvn-----------vk~rvR~rS~plE~sEC 207 (381)
-++|.|..+- .+=.+||-+..- +.|..-+.|+|.||+.--++|.+ +.-.+|=.|.--+|+-|
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 5667777543 344689988843 22557789999999999988855 34678888887778888
Q ss_pred cccc---CCceEEEeeecCCcceEeeEEEeeeeec
Q 016887 208 VAVL---PGDLILCFQEGKDQALYFDAHVLDAQRR 239 (381)
Q Consensus 208 ~~v~---~Gd~VcCfqeg~d~alyyDA~V~~Vqrr 239 (381)
...- +|-.+....+++ +..||=.+++|+-|.
T Consensus 130 ~p~~~s~pG~mtrGilD~k-d~yyyr~v~~D~~~a 163 (321)
T COG3458 130 PPGGPSDPGFMTRGILDRK-DTYYYRGVFLDAVRA 163 (321)
T ss_pred CCCCCcCCceeEeecccCC-CceEEeeehHHHHHH
Confidence 7766 676777777777 567887777776544
No 88
>PTZ00183 centrin; Provisional
Probab=23.56 E-value=2.7e+02 Score=23.00 Aligned_cols=41 Identities=5% Similarity=-0.031 Sum_probs=31.6
Q ss_pred CCccccCHHHHHHHHHHHHHh---cCCCCCHHHHHHHHHHhCCC
Q 016887 9 GPAFRFNPAEVTEMEGILQEH---HNAMPSREILVALAEKFSES 49 (381)
Q Consensus 9 ~pRtrFT~~QI~eLEk~F~e~---~n~Yp~r~~rq~LA~kfnlS 49 (381)
--+..|++.|+.+++++|... ++.+++......+-..+++.
T Consensus 6 ~~~~~~~~~~~~~~~~~F~~~D~~~~G~i~~~e~~~~l~~~g~~ 49 (158)
T PTZ00183 6 SERPGLTEDQKKEIREAFDLFDTDGSGTIDPKELKVAMRSLGFE 49 (158)
T ss_pred cccCCCCHHHHHHHHHHHHHhCCCCCCcccHHHHHHHHHHhCCC
Confidence 345679999999999999863 45788887777777776653
No 89
>PRK07571 bidirectional hydrogenase complex protein HoxE; Reviewed
Probab=23.48 E-value=1.6e+02 Score=27.39 Aligned_cols=38 Identities=11% Similarity=0.178 Sum_probs=29.2
Q ss_pred ccCHHHHHHHHHHHHHhc----------------CCCCCHHHHHHHHHHhCCCc
Q 016887 13 RFNPAEVTEMEGILQEHH----------------NAMPSREILVALAEKFSESP 50 (381)
Q Consensus 13 rFT~~QI~eLEk~F~e~~----------------n~Yp~r~~rq~LA~kfnlS~ 50 (381)
.|+.+++++++++..... ..|++.+..+.+|+.||+++
T Consensus 15 ~~~~~~~~~i~~ii~~~~~~~~~li~~L~~iQ~~~GyIp~e~~~~iA~~l~v~~ 68 (169)
T PRK07571 15 PSGDKRFKVLEATMKRNQYRQDALIEVLHKAQELFGYLERDLLLYVARQLKLPL 68 (169)
T ss_pred cCcHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHcCCCCHHHHHHHHHHhCcCH
Confidence 466777777766555432 46999999999999999986
No 90
>PTZ00064 histone acetyltransferase; Provisional
Probab=23.38 E-value=61 Score=35.38 Aligned_cols=27 Identities=33% Similarity=0.578 Sum_probs=22.6
Q ss_pred CCCeEEEEecCCCCCccccccccccccc
Q 016887 170 ADPEVQVRFAGFGAEEDEWVNIKRHVRQ 197 (381)
Q Consensus 170 ge~elrVrf~gFg~eeDEwvnvk~rvR~ 197 (381)
++-|.+|||.||.-.-||||.-. |++.
T Consensus 147 ~~~eyYVHy~g~nrRlD~WV~~~-ri~~ 173 (552)
T PTZ00064 147 EDYEFYVHFRGLNRRLDRWVKGK-DIKL 173 (552)
T ss_pred CCeEEEEEecCcCchHhhhcChh-hccc
Confidence 45689999999999999999954 5654
No 91
>COG3413 Predicted DNA binding protein [General function prediction only]
Probab=22.43 E-value=92 Score=28.76 Aligned_cols=35 Identities=11% Similarity=0.036 Sum_probs=30.1
Q ss_pred ccCHHHHHHHHHHHHHhcCCCCCH---HHHHHHHHHhCCCc
Q 016887 13 RFNPAEVTEMEGILQEHHNAMPSR---EILVALAEKFSESP 50 (381)
Q Consensus 13 rFT~~QI~eLEk~F~e~~n~Yp~r---~~rq~LA~kfnlS~ 50 (381)
.+|..|++-|..+|+. .|.+. -..++||+.||+|.
T Consensus 155 ~LTdrQ~~vL~~A~~~---GYFd~PR~~~l~dLA~~lGISk 192 (215)
T COG3413 155 DLTDRQLEVLRLAYKM---GYFDYPRRVSLKDLAKELGISK 192 (215)
T ss_pred cCCHHHHHHHHHHHHc---CCCCCCccCCHHHHHHHhCCCH
Confidence 6999999999999998 57554 56689999999994
No 92
>TIGR02607 antidote_HigA addiction module antidote protein, HigA family. Members of this family form a distinct clade within the larger family HTH_3 of helix-turn-helix proteins, described by Pfam model pfam01381. Members of this clade are strictly bacterial and nearly always shorter than 110 amino acids. This family includes the characterized member HigA, without which the killer protein HigB cannot be cloned. The hig (host inhibition of growth) system is noted to be unusual in that killer protein is uncoded by the upstream member of the gene pair.
Probab=22.36 E-value=2e+02 Score=21.78 Aligned_cols=19 Identities=16% Similarity=0.202 Sum_probs=14.8
Q ss_pred CCCCCHHHHHHHHHHhCCC
Q 016887 31 NAMPSREILVALAEKFSES 49 (381)
Q Consensus 31 n~Yp~r~~rq~LA~kfnlS 49 (381)
...++.+...+||+.|+.+
T Consensus 42 ~~~~~~~~~~~l~~~l~v~ 60 (78)
T TIGR02607 42 RRGITADMALRLAKALGTS 60 (78)
T ss_pred CCCCCHHHHHHHHHHcCCC
Confidence 4567888888888888886
No 93
>PF09894 DUF2121: Uncharacterized protein conserved in archaea (DUF2121); InterPro: IPR016754 There is currently no experimental data for members of this group or their homologues, nor do they exhibit features indicative of any function. They do show distant similarity to NTPases and to nucleic acid binding enzymes.
Probab=21.89 E-value=1e+02 Score=29.72 Aligned_cols=51 Identities=20% Similarity=0.157 Sum_probs=40.4
Q ss_pred CCCccccCHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHhCCCccccCCcccccchhHhh
Q 016887 8 GGPAFRFNPAEVTEMEGILQEHHNAMPSREILVALAEKFSESPERKGKIMVQMKQVWNW 66 (381)
Q Consensus 8 ~~pRtrFT~~QI~eLEk~F~e~~n~Yp~r~~rq~LA~kfnlS~~RaGk~~Vq~kQVk~W 66 (381)
|.-.|+=..++..+||+.+=. +..-+.++..+.|++|+.. +.|+..+=|+|
T Consensus 20 R~I~F~G~~~~re~LEeeLYs--G~IktdeEL~kkA~Elgv~------i~I~D~r~KV~ 70 (194)
T PF09894_consen 20 RNIAFRGDEEKREKLEEELYS--GKIKTDEELLKKAEELGVK------IKITDDREKVR 70 (194)
T ss_pred eeeeecCCHHHHHHHHHHHhC--CccCCHHHHHHHHHHcCCE------EEEecCchheE
Confidence 444555567889999999887 7899999999999999983 56666666665
No 94
>PRK04980 hypothetical protein; Provisional
Probab=21.81 E-value=1.6e+02 Score=25.64 Aligned_cols=33 Identities=18% Similarity=0.234 Sum_probs=26.2
Q ss_pred cccCCceEEEeeecCCcceEeeEEEeeeeecccC
Q 016887 209 AVLPGDLILCFQEGKDQALYFDAHVLDAQRRRHD 242 (381)
Q Consensus 209 ~v~~Gd~VcCfqeg~d~alyyDA~V~~Vqrr~Hd 242 (381)
..+|||.|..+-.+. +..|+++.|++|...+-+
T Consensus 31 ~~~~G~~~~V~~~e~-g~~~c~ieI~sV~~i~f~ 63 (102)
T PRK04980 31 HFKPGDVLRVGTFED-DRYFCTIEVLSVSPVTFD 63 (102)
T ss_pred CCCCCCEEEEEECCC-CcEEEEEEEEEEEEEehh
Confidence 467999999875554 789999999999876543
No 95
>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=21.81 E-value=2.1e+02 Score=20.88 Aligned_cols=40 Identities=20% Similarity=0.236 Sum_probs=29.4
Q ss_pred cCHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHhC-CCccccCCcccccchhHhhhhc
Q 016887 14 FNPAEVTEMEGILQEHHNAMPSREILVALAEKFS-ESPERKGKIMVQMKQVWNWFQN 69 (381)
Q Consensus 14 FT~~QI~eLEk~F~e~~n~Yp~r~~rq~LA~kfn-lS~~RaGk~~Vq~kQVk~WFQN 69 (381)
||++|...|-+++...++ .-..+|+.|+ .| +.||+.=|.+
T Consensus 1 WT~eEd~~L~~~~~~~g~------~W~~Ia~~l~~Rt----------~~~~~~r~~~ 41 (60)
T PF13921_consen 1 WTKEEDELLLELVKKYGN------DWKKIAEHLGNRT----------PKQCRNRWRN 41 (60)
T ss_dssp S-HHHHHHHHHHHHHHTS-------HHHHHHHSTTS-----------HHHHHHHHHH
T ss_pred CCHHHHHHHHHHHHHHCc------CHHHHHHHHCcCC----------HHHHHHHHHH
Confidence 689999999999998643 4678999998 65 4888864444
No 96
>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=21.74 E-value=93 Score=24.95 Aligned_cols=23 Identities=39% Similarity=0.726 Sum_probs=16.5
Q ss_pred cCCCceeehhhhhhccccCCCCCeEEEEecC
Q 016887 150 ARDGAWYDVSAFLAQRNFDTADPEVQVRFAG 180 (381)
Q Consensus 150 ~~DgAWYDV~~fL~~r~l~tge~elrVrf~g 180 (381)
+..+-|||+.+...+. ..=||.|
T Consensus 66 ~~s~gwYDl~v~~~~~--------F~rr~aG 88 (89)
T PF05506_consen 66 AASGGWYDLTVTGPNG--------FLRRFAG 88 (89)
T ss_pred cCCCCcEEEEEEcCCC--------EEEEecC
Confidence 4589999999886653 5556665
No 97
>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=21.71 E-value=63 Score=27.71 Aligned_cols=56 Identities=9% Similarity=0.077 Sum_probs=36.6
Q ss_pred ccCHHHHHHHHHHHHHhcCCCC-CHHHHHHHHHHhCCCcccc--CCcccc--cchhHhhhhc
Q 016887 13 RFNPAEVTEMEGILQEHHNAMP-SREILVALAEKFSESPERK--GKIMVQ--MKQVWNWFQN 69 (381)
Q Consensus 13 rFT~~QI~eLEk~F~e~~n~Yp-~r~~rq~LA~kfnlS~~Ra--Gk~~Vq--~kQVk~WFQN 69 (381)
-+|++|+..|...|.-.+ .-+ ..-...+||+++|.|..-- |.-.++ +-+++.|.+.
T Consensus 32 lLTp~E~~~l~~R~~i~~-~Ll~~~~tQrEIa~~lGiS~atIsR~sn~lk~~~~~~~~~l~~ 92 (94)
T TIGR01321 32 ILTRSEREDLGDRIRIVN-ELLNGNMSQREIASKLGVSIATITRGSNNLKTMDPNFKQFLRK 92 (94)
T ss_pred hCCHHHHHHHHHHHHHHH-HHHhCCCCHHHHHHHhCCChhhhhHHHhhcccCCHHHHHHHHh
Confidence 489999999999888752 111 2345678999999875222 444455 5566677653
No 98
>COG2944 Predicted transcriptional regulator [Transcription]
Probab=21.57 E-value=1.2e+02 Score=26.63 Aligned_cols=39 Identities=23% Similarity=0.358 Sum_probs=29.5
Q ss_pred cCHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHhCCCccccCCcccccchhHhhhhcch
Q 016887 14 FNPAEVTEMEGILQEHHNAMPSREILVALAEKFSESPERKGKIMVQMKQVWNWFQNRR 71 (381)
Q Consensus 14 FT~~QI~eLEk~F~e~~n~Yp~r~~rq~LA~kfnlS~~RaGk~~Vq~kQVk~WFQNRR 71 (381)
+++.||.+|-+.+.-+ ...+|..||.|. .-|+.|=|+|+
T Consensus 44 ls~~eIk~iRe~~~lS---------Q~vFA~~L~vs~----------~Tv~~WEqGr~ 82 (104)
T COG2944 44 LSPTEIKAIREKLGLS---------QPVFARYLGVSV----------STVRKWEQGRK 82 (104)
T ss_pred CCHHHHHHHHHHhCCC---------HHHHHHHHCCCH----------HHHHHHHcCCc
Confidence 7777887777766653 467788888873 55999999993
No 99
>KOG1911 consensus Heterochromatin-associated protein HP1 and related CHROMO domain proteins [Chromatin structure and dynamics]
Probab=21.22 E-value=64 Score=31.13 Aligned_cols=45 Identities=22% Similarity=0.419 Sum_probs=35.7
Q ss_pred EeeccCCCceeehhhhhhccccCCCCCeEEEEecCCCCCccccccc
Q 016887 146 EAKSARDGAWYDVSAFLAQRNFDTADPEVQVRFAGFGAEEDEWVNI 191 (381)
Q Consensus 146 EA~S~~DgAWYDV~~fL~~r~l~tge~elrVrf~gFg~eeDEwvnv 191 (381)
++-.-.+..=|-|...|.+|+ .-|..++.|+..||.++++-|=+.
T Consensus 39 ~~~~~~~~~~~vvEki~~~r~-~~g~~eYlvkW~Gy~~~~ntWEPe 83 (270)
T KOG1911|consen 39 EASEEEEEEEYVVEKILKRRK-KNGKIEYLVKWKGYPDPDNTWEPE 83 (270)
T ss_pred ccccccccchhhhhhhhhccc-cCCCceeeeecCCCCCccccCCch
Confidence 333334556688999999995 555689999999999999999775
No 100
>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=20.97 E-value=1.4e+02 Score=21.93 Aligned_cols=44 Identities=16% Similarity=0.067 Sum_probs=33.7
Q ss_pred ccCHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHhCCCccccCCcccccchhHhhhhcchhhH
Q 016887 13 RFNPAEVTEMEGILQEHHNAMPSREILVALAEKFSESPERKGKIMVQMKQVWNWFQNRRYAI 74 (381)
Q Consensus 13 rFT~~QI~eLEk~F~e~~n~Yp~r~~rq~LA~kfnlS~~RaGk~~Vq~kQVk~WFQNRR~K~ 74 (381)
.||+.|+.-|+-+..-. ..+++|+.+++|+ +-|..+..+=+.|.
T Consensus 3 ~LT~~E~~vl~~l~~G~--------~~~eIA~~l~is~----------~tV~~~~~~i~~Kl 46 (58)
T PF00196_consen 3 SLTERELEVLRLLAQGM--------SNKEIAEELGISE----------KTVKSHRRRIMKKL 46 (58)
T ss_dssp SS-HHHHHHHHHHHTTS---------HHHHHHHHTSHH----------HHHHHHHHHHHHHH
T ss_pred ccCHHHHHHHHHHHhcC--------CcchhHHhcCcch----------hhHHHHHHHHHHHh
Confidence 68999999888877763 4689999999985 88988877766654
Done!