Query 020305
Match_columns 328
No_of_seqs 307 out of 1604
Neff 6.3
Searched_HMMs 46136
Date Fri Mar 29 08:40:49 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/020305.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/020305hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG2744 DNA-binding proteins B 100.0 3.8E-29 8.2E-34 252.9 12.6 184 23-208 153-339 (512)
2 smart00501 BRIGHT BRIGHT, ARID 99.9 1.7E-26 3.7E-31 184.8 10.3 90 32-121 1-91 (93)
3 PF01388 ARID: ARID/BRIGHT DNA 99.9 4.7E-25 1E-29 175.6 8.9 89 30-118 3-92 (92)
4 PTZ00199 high mobility group p 99.9 1E-21 2.2E-26 157.8 10.8 82 234-315 9-93 (94)
5 cd01389 MATA_HMG-box MATA_HMG- 99.8 1.7E-18 3.7E-23 133.7 7.4 72 247-318 1-73 (77)
6 cd01388 SOX-TCF_HMG-box SOX-TC 99.7 5.7E-18 1.2E-22 129.2 7.4 68 248-315 2-70 (72)
7 PF00505 HMG_box: HMG (high mo 99.7 2.1E-17 4.5E-22 123.9 8.9 68 248-315 1-69 (69)
8 PF09011 HMG_box_2: HMG-box do 99.7 4.5E-17 9.7E-22 124.6 9.1 71 245-315 1-73 (73)
9 COG5648 NHP6B Chromatin-associ 99.7 1.8E-17 3.8E-22 148.6 7.8 90 236-325 59-149 (211)
10 cd01390 HMGB-UBF_HMG-box HMGB- 99.7 5.8E-17 1.3E-21 120.3 8.8 65 248-312 1-66 (66)
11 smart00398 HMG high mobility g 99.7 1.1E-16 2.5E-21 119.5 8.7 69 247-315 1-70 (70)
12 KOG0381 HMG box-containing pro 99.7 4.2E-16 9.1E-21 124.6 10.5 75 244-318 17-95 (96)
13 cd00084 HMG-box High Mobility 99.6 3.7E-15 8E-20 110.0 8.8 64 248-311 1-65 (66)
14 KOG0527 HMG-box transcription 99.6 1.7E-15 3.7E-20 146.2 6.4 83 241-323 56-139 (331)
15 KOG0526 Nucleosome-binding fac 99.6 5.9E-15 1.3E-19 147.0 7.6 76 236-315 524-600 (615)
16 KOG3248 Transcription factor T 99.2 6.7E-11 1.5E-15 112.6 10.9 74 246-319 190-264 (421)
17 KOG2510 SWI-SNF chromatin-remo 99.2 2.7E-11 5.9E-16 120.2 6.5 94 32-132 292-386 (532)
18 KOG0528 HMG-box transcription 99.0 1.9E-10 4.2E-15 114.0 3.7 119 185-321 280-400 (511)
19 KOG4715 SWI/SNF-related matrix 98.8 4.9E-09 1.1E-13 99.3 6.5 75 242-316 59-134 (410)
20 KOG2746 HMG-box transcription 98.4 3E-07 6.6E-12 94.7 4.6 74 237-310 171-247 (683)
21 PF14887 HMG_box_5: HMG (high 97.8 6.3E-05 1.4E-09 57.9 6.8 72 247-319 3-75 (85)
22 PF04690 YABBY: YABBY protein; 96.8 0.0025 5.3E-08 56.6 5.4 47 243-289 117-164 (170)
23 PF06382 DUF1074: Protein of u 96.4 0.011 2.4E-07 52.6 7.1 48 252-303 83-131 (183)
24 COG5648 NHP6B Chromatin-associ 96.3 0.0034 7.4E-08 57.1 3.5 67 246-312 142-209 (211)
25 TIGR01624 LRP1_Cterm LRP1 C-te 91.3 0.13 2.9E-06 36.2 1.8 34 171-204 14-48 (50)
26 PF05142 DUF702: Domain of unk 90.1 0.19 4.2E-06 43.8 2.1 35 171-205 116-150 (154)
27 PF08073 CHDNT: CHDNT (NUC034) 89.9 0.38 8.3E-06 35.0 3.2 39 252-290 13-52 (55)
28 PF04769 MAT_Alpha1: Mating-ty 89.0 1.1 2.3E-05 41.1 6.2 56 241-302 37-93 (201)
29 PF06244 DUF1014: Protein of u 84.7 1.1 2.4E-05 37.8 3.5 45 247-291 72-117 (122)
30 PF00249 Myb_DNA-binding: Myb- 81.5 3.2 6.9E-05 28.6 4.3 39 65-114 10-48 (48)
31 TIGR03481 HpnM hopanoid biosyn 72.6 8.8 0.00019 34.8 5.7 44 273-316 65-110 (198)
32 KOG3223 Uncharacterized conser 65.4 4.7 0.0001 36.6 2.3 52 246-300 162-215 (221)
33 PF09441 Abp2: ARS binding pro 62.9 16 0.00035 32.3 5.1 42 53-98 44-85 (175)
34 PRK15117 ABC transporter perip 62.8 19 0.00041 33.0 5.8 46 271-316 66-114 (211)
35 PF13921 Myb_DNA-bind_6: Myb-l 54.9 24 0.00052 25.0 4.2 36 66-114 8-43 (60)
36 cd00167 SANT 'SWI3, ADA2, N-Co 52.4 28 0.00061 22.2 3.9 37 66-114 9-45 (45)
37 PF05494 Tol_Tol_Ttg2: Toluene 46.7 21 0.00046 31.0 3.3 44 273-316 39-84 (170)
38 PF11304 DUF3106: Protein of u 44.1 81 0.0018 25.7 6.1 42 275-316 10-58 (107)
39 PF13873 Myb_DNA-bind_5: Myb/S 38.5 46 0.00099 24.9 3.6 54 62-116 14-71 (78)
40 smart00717 SANT SANT SWI3, AD 35.0 77 0.0017 20.4 3.9 26 84-114 22-47 (49)
41 PF12881 NUT_N: NUT protein N 32.7 1.1E+02 0.0023 30.0 5.8 52 265-316 242-295 (328)
42 PF13875 DUF4202: Domain of un 31.3 93 0.002 28.2 4.9 41 252-294 129-169 (185)
43 PF12776 Myb_DNA-bind_3: Myb/S 30.0 93 0.002 23.9 4.2 60 64-123 10-71 (96)
44 COG2854 Ttg2D ABC-type transpo 27.6 77 0.0017 29.1 3.7 41 277-317 76-117 (202)
45 PRK12750 cpxP periplasmic repr 25.6 2.2E+02 0.0048 25.2 6.2 34 278-311 127-160 (170)
46 KOG3838 Mannose lectin ERGIC-5 25.5 60 0.0013 32.9 2.8 37 288-324 269-305 (497)
47 PF05066 HARE-HTH: HB1, ASXL, 24.8 1.1E+02 0.0024 22.6 3.6 34 37-80 3-36 (72)
48 PF12650 DUF3784: Domain of un 23.9 52 0.0011 25.9 1.8 17 283-299 24-40 (97)
49 PF00226 DnaJ: DnaJ domain; I 23.8 1.1E+02 0.0025 21.6 3.4 34 260-293 19-59 (64)
50 PF10545 MADF_DNA_bdg: Alcohol 22.7 55 0.0012 24.2 1.6 38 81-118 24-64 (85)
51 PRK10236 hypothetical protein; 22.1 86 0.0019 29.5 3.0 24 277-300 118-141 (237)
52 KOG1610 Corticosteroid 11-beta 21.8 1.9E+02 0.004 28.5 5.4 52 254-305 184-249 (322)
53 PRK09706 transcriptional repre 21.8 2.4E+02 0.0052 23.4 5.6 43 277-319 88-130 (135)
54 PHA03102 Small T antigen; Revi 21.0 1.1E+02 0.0025 26.7 3.4 35 260-294 26-62 (153)
55 TIGR00787 dctP tripartite ATP- 20.6 1.9E+02 0.0042 26.6 5.1 28 282-309 213-240 (257)
56 cd07268 Glo_EDI_BRP_like_4 Thi 20.2 34 0.00073 29.9 -0.1 70 26-95 3-82 (149)
No 1
>KOG2744 consensus DNA-binding proteins Bright/BRCAA1/RBP1 and related proteins containing BRIGHT domain [Transcription]
Probab=99.96 E-value=3.8e-29 Score=252.89 Aligned_cols=184 Identities=41% Similarity=0.514 Sum_probs=148.6
Q ss_pred CCCCCCcccCChhHHHHHHHHHHhhcCCCCC-CCeeCCeecchhhHHHHHHhcCchhhhhcccchHHHHhhhcCCC-CCC
Q 020305 23 PLSSHEDVSKDPIVFWDTLRRFHFIMGTKFM-IPVIGGKELDLHVLYVEATTRGGYEKVVAEKKWREVGAVFKFSP-TTT 100 (328)
Q Consensus 23 ~~~~~e~~~~~~~~F~~~L~~F~~~~G~~~~-~P~i~gk~lDL~~Ly~~V~~~GG~~~V~~~~~W~~Va~~lg~p~-~~~ 100 (328)
+....|.+..+++.||+.|+.||+.+|++|+ +|+|+|++||||.||.+|+++||+++|+.+++|++|+..|+||. ++|
T Consensus 153 ~~~~~e~~~~~~eeF~~dl~~f~~~~~~~~~~iPii~~~~ldL~~Ly~lV~s~GG~~~V~~~k~Wrev~~~l~~pt~tiT 232 (512)
T KOG2744|consen 153 PLYETEGVPKSSEEFMEDLRRFMKKRGTKVKSIPIIGGQPLDLHWLYALVTSRGGLDEVTNKKLWREVIDGLNFPTPTIT 232 (512)
T ss_pred cccccccccccHHHHHHHHHHHHHHhCCcceeccccCCCcchHHHHHHHHhcCCchhHhhhhhhHHHHhccccCCCcccc
Confidence 5666777778999999999999999999996 99999999999999999999999999999999999999999999 999
Q ss_pred cHHHHHHHHHHHhhHHHHhhhhhhccCCCCCCCCCCCCC-CCCCCCCCcccccCCcccccCCCCCccCCCCCceeEEeec
Q 020305 101 SASFVLRKHYLTLLYHYEQVHFFKMQGPPCVPSAASFSV-HSPSCRPGLALVEYSPKRINDHPDSHIEGQSCFTAVGRID 179 (328)
Q Consensus 101 ~as~~Lk~~Y~k~L~~yE~~~~~~~~~~~~~~~~~~~~~-~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~id 179 (328)
+++|.|+++|+++|++|||.+++....++..+.+ ... .+++-+.....-+.++........+....+....+.|+|+
T Consensus 233 saaf~lr~~y~K~L~~ye~~~~~~~~~pln~p~~--~~~~a~~~~~rE~~~~~~~~~~~~~~~~~~~~~~~~~~aa~~~~ 310 (512)
T KOG2744|consen 233 SAAFTLRKQYLKLLFEYECEFEKNRHVPLNSPAE--LSEEASSSNRREGRRHELSPSKEFQANGPSEEEPAEAEAAPEIL 310 (512)
T ss_pred hHHHHHHHHHHHHHHHHHHHHHHhccCCCCCccc--ccccccccccccccccccCcchhhccCCcccccccccccchhhh
Confidence 9999999999999999999999998878777764 111 2222222222222222211111112211234578999999
Q ss_pred cccCCCceeEEeecceeecccccCCCCCC
Q 020305 180 GKFDCGYLVSVKLGSETLSGVLYHPDHPG 208 (328)
Q Consensus 180 gkf~~gylvtv~~gse~~~g~ly~~~~~~ 208 (328)
|+|++||+|++.+|++.++|++|+.++..
T Consensus 311 g~f~~~~~~~~~~~s~~ln~~~~~~~~~~ 339 (512)
T KOG2744|consen 311 GNFLQGLLVFMKDGSEPLNGVLYLGPPDL 339 (512)
T ss_pred ccccccCceeccCcchhccCccccccCcc
Confidence 99999999999999999999999997765
No 2
>smart00501 BRIGHT BRIGHT, ARID (A/T-rich interaction domain) domain. DNA-binding domain containing a helix-turn-helix structure
Probab=99.94 E-value=1.7e-26 Score=184.80 Aligned_cols=90 Identities=41% Similarity=0.699 Sum_probs=86.7
Q ss_pred CChhHHHHHHHHHHhhcCCCC-CCCeeCCeecchhhHHHHHHhcCchhhhhcccchHHHHhhhcCCCCCCcHHHHHHHHH
Q 020305 32 KDPIVFWDTLRRFHFIMGTKF-MIPVIGGKELDLHVLYVEATTRGGYEKVVAEKKWREVGAVFKFSPTTTSASFVLRKHY 110 (328)
Q Consensus 32 ~~~~~F~~~L~~F~~~~G~~~-~~P~i~gk~lDL~~Ly~~V~~~GG~~~V~~~~~W~~Va~~lg~p~~~~~as~~Lk~~Y 110 (328)
++++.|++.|.+||+.+|+++ .+|+|+|++||||+||.+|+++|||++||.+++|.+|++.||++++++++++.|+.+|
T Consensus 1 ~~~~~F~~~L~~F~~~~g~~~~~~P~i~g~~vdL~~Ly~~V~~~GG~~~v~~~~~W~~Va~~lg~~~~~~~~~~~lk~~Y 80 (93)
T smart00501 1 RERVLFLDRLYKFMEERGSPLKKIPVIGGKPLDLYRLYRLVQERGGYDQVTKDKKWKEIARELGIPDTSTSAASSLRKHY 80 (93)
T ss_pred CcHHHHHHHHHHHHHHcCCcCCcCCeECCEeCcHHHHHHHHHHccCHHHHcCCCCHHHHHHHhCCCcccchHHHHHHHHH
Confidence 468999999999999999998 7999999999999999999999999999999999999999999998899999999999
Q ss_pred HHhhHHHHhhh
Q 020305 111 LTLLYHYEQVH 121 (328)
Q Consensus 111 ~k~L~~yE~~~ 121 (328)
.+||++||+++
T Consensus 81 ~k~L~~yE~~~ 91 (93)
T smart00501 81 ERYLLPFERFL 91 (93)
T ss_pred HHHhHHHHHHh
Confidence 99999999975
No 3
>PF01388 ARID: ARID/BRIGHT DNA binding domain; InterPro: IPR001606 Members of the recently discovered ARID (AT-rich interaction domain; also known as BRIGHT domain)) family of DNA-binding proteins are found in fungi and invertebrate and vertebrate metazoans. ARID-encoding genes are involved in a variety of biological processes including embryonic development, cell lineage gene regulation and cell cycle control. Although the specific roles of this domain and of ARID-containing proteins in transcriptional regulation are yet to be elucidated, they include both positive and negative transcriptional regulation and a likely involvement in the modification of chromatin structure []. The basic structure of the ARID domain domain appears to be a series of six alpha-helices separated by beta-strands, loops, or turns, but the structured region may extend to an additional helix at either or both ends of the basic six. Based on primary sequence homology, they can be partitioned into three structural classes: Minimal ARID proteins that consist of a core domain formed by six alpha helices; ARID proteins that supplement the core domain with an N-terminal alpha-helix; and Extended-ARID proteins, which contain the core domain and additional alpha-helices at their N- and C-termini. The human SWI-SNF complex protein p270 is an ARID family member with non-sequence-specific DNA binding activity. The ARID consensus and other structural features are common to both p270 and yeast SWI1, suggesting that p270 is a human counterpart of SWI1 []. The approximately 100-residue ARID sequence is present in a series of proteins strongly implicated in the regulation of cell growth, development, and tissue-specific gene expression. Although about a dozen ARID proteins can be identified from database searches, to date, only Bright (a regulator of B-cell-specific gene expression), dead ringer (a Drosophila melanogaster gene product required for normal development), and MRF-2 (which represses expression from the Cytomegalovirus enhancer) have been analyzed directly in regard to their DNA binding properties. Each binds preferentially to AT-rich sites. In contrast, p270 shows no sequence preference in its DNA binding activity, thereby demonstrating that AT-rich binding is not an intrinsic property of ARID domains and that ARID family proteins may be involved in a wider range of DNA interactions [].; GO: 0003677 DNA binding, 0005622 intracellular; PDB: 1C20_A 1KQQ_A 2JRZ_A 2LM1_A 2YQE_A 2JXJ_A 2EH9_A 2CXY_A 2LI6_A 1KN5_A ....
Probab=99.92 E-value=4.7e-25 Score=175.61 Aligned_cols=89 Identities=44% Similarity=0.730 Sum_probs=82.1
Q ss_pred ccCChhHHHHHHHHHHhhcCCCC-CCCeeCCeecchhhHHHHHHhcCchhhhhcccchHHHHhhhcCCCCCCcHHHHHHH
Q 020305 30 VSKDPIVFWDTLRRFHFIMGTKF-MIPVIGGKELDLHVLYVEATTRGGYEKVVAEKKWREVGAVFKFSPTTTSASFVLRK 108 (328)
Q Consensus 30 ~~~~~~~F~~~L~~F~~~~G~~~-~~P~i~gk~lDL~~Ly~~V~~~GG~~~V~~~~~W~~Va~~lg~p~~~~~as~~Lk~ 108 (328)
...+++.|+..|.+||+.+|+++ .+|.|+|++||||+||.+|+++|||++|+.+++|.+||+.||+++.+++.+..|++
T Consensus 3 ~~~~~~~F~~~L~~f~~~~g~~~~~~P~i~g~~vDL~~Ly~~V~~~GG~~~V~~~~~W~~va~~lg~~~~~~~~~~~L~~ 82 (92)
T PF01388_consen 3 NTREREQFLEQLREFHESRGTPIDRPPVIGGKPVDLYKLYKAVMKRGGFDKVTKNKKWREVARKLGFPPSSTSAAQQLRQ 82 (92)
T ss_dssp SCHHHHHHHHHHHHHHHHTTSSSSS-SEETTSE-SHHHHHHHHHHHTSHHHHHHHTTHHHHHHHTTS-TTSCHHHHHHHH
T ss_pred cchHHHHHHHHHHHHHHHcCCCCCCCCcCCCEeCcHHHHHHHHHhCcCcccCcccchHHHHHHHhCCCCCCCcHHHHHHH
Confidence 35678999999999999999997 79999999999999999999999999999999999999999999988888899999
Q ss_pred HHHHhhHHHH
Q 020305 109 HYLTLLYHYE 118 (328)
Q Consensus 109 ~Y~k~L~~yE 118 (328)
+|++||++||
T Consensus 83 ~Y~~~L~~fE 92 (92)
T PF01388_consen 83 HYEKYLLPFE 92 (92)
T ss_dssp HHHHHTHHHH
T ss_pred HHHHHhHhhC
Confidence 9999999998
No 4
>PTZ00199 high mobility group protein; Provisional
Probab=99.87 E-value=1e-21 Score=157.84 Aligned_cols=82 Identities=35% Similarity=0.603 Sum_probs=76.9
Q ss_pred ccccccCCCCCCCCCCCCCChHHHHHHHHHHHHHhhCCC-C--hHHHHHHHHHHhccCChHHhHHHHHHHHHHHHHHHHH
Q 020305 234 GRRRRSKRRGDPSYPKPNRSGYNFFFAEKHYKLKSLYPN-R--EREFTKMIGESWTNLSPEERKVYQNIGLKDKERYNRE 310 (328)
Q Consensus 234 ~kkk~~k~~kdp~~PKrP~Say~lF~~e~r~~vk~~~P~-~--~~eisk~lge~Wk~Ls~~eK~~Y~e~A~~dkerY~~e 310 (328)
.+++++++.+||++||||+|||+||+.++|..|+.+||+ . +.+|+++||++|+.|+++||++|+++|+.|+++|..|
T Consensus 9 ~~k~~~k~~kdp~~PKrP~sAY~~F~~~~R~~i~~~~P~~~~~~~evsk~ige~Wk~ls~eeK~~y~~~A~~dk~rY~~e 88 (94)
T PTZ00199 9 LVRKNKRKKKDPNAPKRALSAYMFFAKEKRAEIIAENPELAKDVAAVGKMVGEAWNKLSEEEKAPYEKKAQEDKVRYEKE 88 (94)
T ss_pred cccccCCCCCCCCCCCCCCcHHHHHHHHHHHHHHHHCcCCcccHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHH
Confidence 445566678899999999999999999999999999999 4 7999999999999999999999999999999999999
Q ss_pred HHHHH
Q 020305 311 LKEYK 315 (328)
Q Consensus 311 ~~~yk 315 (328)
|.+|+
T Consensus 89 ~~~Y~ 93 (94)
T PTZ00199 89 KAEYA 93 (94)
T ss_pred HHHHh
Confidence 99996
No 5
>cd01389 MATA_HMG-box MATA_HMG-box, class I member of the HMG-box superfamily of DNA-binding proteins. These proteins contain a single HMG box, and bind the minor groove of DNA in a highly sequence-specific manner. Members include the fungal mating type gene products MC, MATA1 and Ste11.
Probab=99.76 E-value=1.7e-18 Score=133.67 Aligned_cols=72 Identities=29% Similarity=0.534 Sum_probs=69.2
Q ss_pred CCCCCCChHHHHHHHHHHHHHhhCCC-ChHHHHHHHHHHhccCChHHhHHHHHHHHHHHHHHHHHHHHHHHhc
Q 020305 247 YPKPNRSGYNFFFAEKHYKLKSLYPN-REREFTKMIGESWTNLSPEERKVYQNIGLKDKERYNRELKEYKERL 318 (328)
Q Consensus 247 ~PKrP~Say~lF~~e~r~~vk~~~P~-~~~eisk~lge~Wk~Ls~~eK~~Y~e~A~~dkerY~~e~~~yk~~~ 318 (328)
+||||+||||||+++.|.+|+.+||+ ++.+|+++||++|+.|++++|++|.++|++++++|.+++++|+-.-
T Consensus 1 ~~kRP~naf~lf~~~~r~~~~~~~p~~~~~eisk~~g~~Wk~ls~eeK~~y~~~A~~~k~~~~~~~p~Yky~p 73 (77)
T cd01389 1 KIPRPRNAFILYRQDKHAQLKTENPGLTNNEISRIIGRMWRSESPEVKAYYKELAEEEKERHAREYPDYKYTP 73 (77)
T ss_pred CCCCCCcHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHhhCCHHHHHHHHHHHHHHHHHHHHHCCCCcccC
Confidence 58999999999999999999999999 9999999999999999999999999999999999999999998643
No 6
>cd01388 SOX-TCF_HMG-box SOX-TCF_HMG-box, class I member of the HMG-box superfamily of DNA-binding proteins. These proteins contain a single HMG box, and bind the minor groove of DNA in a highly sequence-specific manner. Members include SRY and its homologs in insects and vertebrates, and transcription factor-like proteins, TCF-1, -3, -4, and LEF-1. They appear to bind the minor groove of the A/T C A A A G/C-motif.
Probab=99.74 E-value=5.7e-18 Score=129.20 Aligned_cols=68 Identities=28% Similarity=0.441 Sum_probs=66.4
Q ss_pred CCCCCChHHHHHHHHHHHHHhhCCC-ChHHHHHHHHHHhccCChHHhHHHHHHHHHHHHHHHHHHHHHH
Q 020305 248 PKPNRSGYNFFFAEKHYKLKSLYPN-REREFTKMIGESWTNLSPEERKVYQNIGLKDKERYNRELKEYK 315 (328)
Q Consensus 248 PKrP~Say~lF~~e~r~~vk~~~P~-~~~eisk~lge~Wk~Ls~~eK~~Y~e~A~~dkerY~~e~~~yk 315 (328)
.|||+|||++|++++|++++.+||+ ++.+|+++||++|+.|++++|++|.++|++++++|.+++++|+
T Consensus 2 iKrP~naf~~F~~~~r~~~~~~~p~~~~~eisk~l~~~Wk~ls~~eK~~y~~~a~~~k~~y~~~~p~y~ 70 (72)
T cd01388 2 IKRPMNAFMLFSKRHRRKVLQEYPLKENRAISKILGDRWKALSNEEKQPYYEEAKKLKELHMKLYPDYK 70 (72)
T ss_pred CCCCCcHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHCcCCC
Confidence 5899999999999999999999999 9999999999999999999999999999999999999999986
No 7
>PF00505 HMG_box: HMG (high mobility group) box; InterPro: IPR000910 High mobility group (HMG or HMGB) proteins are a family of relatively low molecular weight non-histone components in chromatin. HMG1 (also called HMG-T in fish) and HMG2 are two highly related proteins that bind single-stranded DNA preferentially and unwind double-stranded DNA. Although they have no sequence specificity, they have a high affinity for bent or distorted DNA, and bend linear DNA. HMG1 and HMG2 contain two DNA-binding HMG-box domains (A and B) that show structural and functional differences, and have a long acidic C-terminal domain rich in aspartic and glutamic acid residues. The acidic tail modulates the affinity of the tandem HMG boxes in HMG1 and 2 for a variety of DNA targets. HMG1 and 2 appear to play important architectural roles in the assembly of nucleoprotein complexes in a variety of biological processes, for example V(D)J recombination, the initiation of transcription, and DNA repair []. The profile in this entry describing the HMG-domains is much more general than the signature. In addition to the HMG1 and HMG2 proteins, HMG-domains occur in single or multiple copies in the following protein classes; the SOX family of transcription factors; SRY sex determining region Y protein and related proteins []; LEF1 lymphoid enhancer binding factor 1 []; SSRP recombination signal recognition protein; MTF1 mitochondrial transcription factor 1; UBF1/2 nucleolar transcription factors; Abf2 yeast ARS-binding factor []; and Saccharomyces cerevisiae transcription factors Ixr1, Rox1, Nhp6a, Nhp6b and Spp41.; GO: 0003677 DNA binding; PDB: 1I11_A 1J3C_A 1J3D_A 1WZ6_A 1WGF_A 2D7L_A 1GT0_D 3U2B_C 2CRJ_A 2CS1_A ....
Probab=99.72 E-value=2.1e-17 Score=123.91 Aligned_cols=68 Identities=38% Similarity=0.708 Sum_probs=65.0
Q ss_pred CCCCCChHHHHHHHHHHHHHhhCCC-ChHHHHHHHHHHhccCChHHhHHHHHHHHHHHHHHHHHHHHHH
Q 020305 248 PKPNRSGYNFFFAEKHYKLKSLYPN-REREFTKMIGESWTNLSPEERKVYQNIGLKDKERYNRELKEYK 315 (328)
Q Consensus 248 PKrP~Say~lF~~e~r~~vk~~~P~-~~~eisk~lge~Wk~Ls~~eK~~Y~e~A~~dkerY~~e~~~yk 315 (328)
||||+|||++|+.+++..++.+||+ +..+|+++||++|++|++++|++|.++|++++++|.++|.+|+
T Consensus 1 PkrP~~af~lf~~~~~~~~k~~~p~~~~~~i~~~~~~~W~~l~~~eK~~y~~~a~~~~~~y~~~~~~y~ 69 (69)
T PF00505_consen 1 PKRPPNAFMLFCKEKRAKLKEENPDLSNKEISKILAQMWKNLSEEEKAPYKEEAEEEKERYEKEMPEYK 69 (69)
T ss_dssp SSSS--HHHHHHHHHHHHHHHHSTTSTHHHHHHHHHHHHHCSHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred CcCCCCHHHHHHHHHHHHHHHHhcccccccchhhHHHHHhcCCHHHHHHHHHHHHHHHHHHHHHHHhcC
Confidence 8999999999999999999999999 9999999999999999999999999999999999999999996
No 8
>PF09011 HMG_box_2: HMG-box domain; InterPro: IPR015101 This domain is predominantly found in Maelstrom homologue proteins. It has no known function. ; GO: 0005634 nucleus; PDB: 2EQZ_A 1V64_A 2CTO_A 1H5P_A 3TQ6_A 3FGH_A 3TMM_A 1J3X_A 2YRQ_A 1AAB_A ....
Probab=99.71 E-value=4.5e-17 Score=124.55 Aligned_cols=71 Identities=41% Similarity=0.645 Sum_probs=63.0
Q ss_pred CCCCCCCCChHHHHHHHHHHHHHhh-CCC-ChHHHHHHHHHHhccCChHHhHHHHHHHHHHHHHHHHHHHHHH
Q 020305 245 PSYPKPNRSGYNFFFAEKHYKLKSL-YPN-REREFTKMIGESWTNLSPEERKVYQNIGLKDKERYNRELKEYK 315 (328)
Q Consensus 245 p~~PKrP~Say~lF~~e~r~~vk~~-~P~-~~~eisk~lge~Wk~Ls~~eK~~Y~e~A~~dkerY~~e~~~yk 315 (328)
|++||+|+|||+||+.+++..++.. .+. ...|+++.|++.|++||++||.+|+++|+.++++|..+|..|+
T Consensus 1 p~kpK~~~say~lF~~~~~~~~k~~G~~~~~~~e~~k~~~~~Wk~Ls~~EK~~Y~~~A~~~k~~y~~e~~~~~ 73 (73)
T PF09011_consen 1 PKKPKRPPSAYNLFMKEMRKEVKEEGGQKQSFREVMKEISERWKSLSEEEKEPYEERAKEDKERYEREMKEWN 73 (73)
T ss_dssp SSS--SSSSHHHHHHHHHHHHHHHHT-T-SSHHHHHHHHHHHHHHS-HHHHHHHHHHHHHHHHHHHHHHHHH-
T ss_pred CcCCCCCCCHHHHHHHHHHHHHHHhcccCCCHHHHHHHHHHHHHhcCHHHHHHHHHHHHHHHHHHHHHHHhcC
Confidence 6789999999999999999999988 666 8999999999999999999999999999999999999999995
No 9
>COG5648 NHP6B Chromatin-associated proteins containing the HMG domain [Chromatin structure and dynamics]
Probab=99.71 E-value=1.8e-17 Score=148.64 Aligned_cols=90 Identities=31% Similarity=0.552 Sum_probs=84.1
Q ss_pred ccccCCCCCCCCCCCCCChHHHHHHHHHHHHHhhCCC-ChHHHHHHHHHHhccCChHHhHHHHHHHHHHHHHHHHHHHHH
Q 020305 236 RRRSKRRGDPSYPKPNRSGYNFFFAEKHYKLKSLYPN-REREFTKMIGESWTNLSPEERKVYQNIGLKDKERYNRELKEY 314 (328)
Q Consensus 236 kk~~k~~kdp~~PKrP~Say~lF~~e~r~~vk~~~P~-~~~eisk~lge~Wk~Ls~~eK~~Y~e~A~~dkerY~~e~~~y 314 (328)
+...++++||+.||||+|||++|+.++|.+++.++|+ ++.++++.+|++|++|+++||++|...|..++++|..++..|
T Consensus 59 k~~~r~k~dpN~PKRp~sayf~y~~~~R~ei~~~~p~l~~~e~~k~~~e~WK~Ltd~eke~y~k~~~~~~erYq~ek~~y 138 (211)
T COG5648 59 KRLVRKKKDPNGPKRPLSAYFLYSAENRDEIRKENPKLTFGEVGKLLSEKWKELTDEEKEPYYKEANSDRERYQREKEEY 138 (211)
T ss_pred HHHHHHhcCCCCCCCchhHHHHHHHHHHHHHHHhCCCCChHHHHHHHHHHHHhccHhhhhhHHHHHhhHHHHHHHHHHhh
Confidence 4556788999999999999999999999999999999 999999999999999999999999999999999999999999
Q ss_pred HHhcccccccC
Q 020305 315 KERLKLRQGEG 325 (328)
Q Consensus 315 k~~~k~~~~~~ 325 (328)
.++.......+
T Consensus 139 ~~k~~~~~~~~ 149 (211)
T COG5648 139 NKKLPNKAPIG 149 (211)
T ss_pred hcccCCCCCCc
Confidence 99887765443
No 10
>cd01390 HMGB-UBF_HMG-box HMGB-UBF_HMG-box, class II and III members of the HMG-box superfamily of DNA-binding proteins. These proteins bind the minor groove of DNA in a non-sequence specific fashion and contain two or more tandem HMG boxes. Class II members include non-histone chromosomal proteins, HMG1 and HMG2, which bind to bent or distorted DNA such as four-way DNA junctions, synthetic DNA cruciforms, kinked cisplatin-modified DNA, DNA bulges, cross-overs in supercoiled DNA, and can cause looping of linear DNA. Class III members include nucleolar and mitochondrial transcription factors, UBF and mtTF1, which bind four-way DNA junctions.
Probab=99.70 E-value=5.8e-17 Score=120.33 Aligned_cols=65 Identities=46% Similarity=0.720 Sum_probs=63.4
Q ss_pred CCCCCChHHHHHHHHHHHHHhhCCC-ChHHHHHHHHHHhccCChHHhHHHHHHHHHHHHHHHHHHH
Q 020305 248 PKPNRSGYNFFFAEKHYKLKSLYPN-REREFTKMIGESWTNLSPEERKVYQNIGLKDKERYNRELK 312 (328)
Q Consensus 248 PKrP~Say~lF~~e~r~~vk~~~P~-~~~eisk~lge~Wk~Ls~~eK~~Y~e~A~~dkerY~~e~~ 312 (328)
||||+|||++|++++|.+++.+||+ ++.+|++.||++|++|++++|++|.+.|++++++|..+|.
T Consensus 1 Pkrp~saf~~f~~~~r~~~~~~~p~~~~~~i~~~~~~~W~~ls~~eK~~y~~~a~~~~~~y~~e~~ 66 (66)
T cd01390 1 PKRPLSAYFLFSQEQRPKLKKENPDASVTEVTKILGEKWKELSEEEKKKYEEKAEKDKERYEKEMK 66 (66)
T ss_pred CCCCCcHHHHHHHHHHHHHHHHCcCCCHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHhhC
Confidence 8999999999999999999999999 9999999999999999999999999999999999999873
No 11
>smart00398 HMG high mobility group.
Probab=99.69 E-value=1.1e-16 Score=119.50 Aligned_cols=69 Identities=41% Similarity=0.660 Sum_probs=67.1
Q ss_pred CCCCCCChHHHHHHHHHHHHHhhCCC-ChHHHHHHHHHHhccCChHHhHHHHHHHHHHHHHHHHHHHHHH
Q 020305 247 YPKPNRSGYNFFFAEKHYKLKSLYPN-REREFTKMIGESWTNLSPEERKVYQNIGLKDKERYNRELKEYK 315 (328)
Q Consensus 247 ~PKrP~Say~lF~~e~r~~vk~~~P~-~~~eisk~lge~Wk~Ls~~eK~~Y~e~A~~dkerY~~e~~~yk 315 (328)
+||+|+|||++|++++|..++.+||+ +..+|+++||++|+.|++++|++|.++|+.++++|.+++..|+
T Consensus 1 ~pkrp~~~y~~f~~~~r~~~~~~~~~~~~~~i~~~~~~~W~~l~~~ek~~y~~~a~~~~~~y~~~~~~y~ 70 (70)
T smart00398 1 KPKRPMSAFMLFSQENRAKIKAENPDLSNAEISKKLGERWKLLSEEEKAPYEEKAKKDKERYEEEMPEYK 70 (70)
T ss_pred CcCCCCcHHHHHHHHHHHHHHHHCcCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHHhcC
Confidence 58999999999999999999999999 9999999999999999999999999999999999999999984
No 12
>KOG0381 consensus HMG box-containing protein [General function prediction only]
Probab=99.67 E-value=4.2e-16 Score=124.63 Aligned_cols=75 Identities=40% Similarity=0.654 Sum_probs=71.9
Q ss_pred CC--CCCCCCCChHHHHHHHHHHHHHhhCCC-ChHHHHHHHHHHhccCChHHhHHHHHHHHHHHHHHHHHHH-HHHHhc
Q 020305 244 DP--SYPKPNRSGYNFFFAEKHYKLKSLYPN-REREFTKMIGESWTNLSPEERKVYQNIGLKDKERYNRELK-EYKERL 318 (328)
Q Consensus 244 dp--~~PKrP~Say~lF~~e~r~~vk~~~P~-~~~eisk~lge~Wk~Ls~~eK~~Y~e~A~~dkerY~~e~~-~yk~~~ 318 (328)
|| +.||||+|||++|+.+.|.+++.+||+ +..++++++|++|++|++++|++|+.+|.+++++|..+|. +|+..+
T Consensus 17 ~p~~~~pkrp~sa~~~f~~~~~~~~k~~~p~~~~~~v~k~~g~~W~~l~~~~k~~y~~ka~~~k~~Y~~~~~~~~~~~~ 95 (96)
T KOG0381|consen 17 DPNAQAPKRPLSAFFLFSSEQRSKIKAENPGLSVGEVAKALGEMWKNLAEEEKQPYEEKASKLKEKYEKELAGEYKASL 95 (96)
T ss_pred CCCCCCCCCCCcHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHHHHHHHHHHHHhhcc
Confidence 66 599999999999999999999999999 9999999999999999999999999999999999999999 998754
No 13
>cd00084 HMG-box High Mobility Group (HMG)-box is found in a variety of eukaryotic chromosomal proteins and transcription factors. HMGs bind to the minor groove of DNA and have been classified by DNA binding preferences. Two phylogenically distinct groups of Class I proteins bind DNA in a sequence specific fashion and contain a single HMG box. One group (SOX-TCF) includes transcription factors, TCF-1, -3, -4; and also SRY and LEF-1, which bind four-way DNA junctions and duplex DNA targets. The second group (MATA) includes fungal mating type gene products MC, MATA1 and Ste11. Class II and III proteins (HMGB-UBF) bind DNA in a non-sequence specific fashion and contain two or more tandem HMG boxes. Class II members include non-histone chromosomal proteins, HMG1 and HMG2, which bind to bent or distorted DNA such as four-way DNA junctions, synthetic DNA cruciforms, kinked cisplatin-modified DNA, DNA bulges, cross-overs in supercoiled DNA, and can cause looping of linear DNA. Class III member
Probab=99.61 E-value=3.7e-15 Score=110.04 Aligned_cols=64 Identities=41% Similarity=0.676 Sum_probs=62.4
Q ss_pred CCCCCChHHHHHHHHHHHHHhhCCC-ChHHHHHHHHHHhccCChHHhHHHHHHHHHHHHHHHHHH
Q 020305 248 PKPNRSGYNFFFAEKHYKLKSLYPN-REREFTKMIGESWTNLSPEERKVYQNIGLKDKERYNREL 311 (328)
Q Consensus 248 PKrP~Say~lF~~e~r~~vk~~~P~-~~~eisk~lge~Wk~Ls~~eK~~Y~e~A~~dkerY~~e~ 311 (328)
||||+|||++|+++.|..++.+||+ +..+|+++||++|+.|++++|++|.++|+.++++|.+++
T Consensus 1 pkrp~~af~~f~~~~~~~~~~~~~~~~~~~i~~~~~~~W~~l~~~~k~~y~~~a~~~~~~y~~~~ 65 (66)
T cd00084 1 PKRPLSAYFLFSQEHRAEVKAENPGLSVGEISKILGEMWKSLSEEEKKKYEEKAEKDKERYEKEM 65 (66)
T ss_pred CCCCCcHHHHHHHHHHHHHHHHCcCCCHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHhh
Confidence 7999999999999999999999999 999999999999999999999999999999999999875
No 14
>KOG0527 consensus HMG-box transcription factor [Transcription]
Probab=99.58 E-value=1.7e-15 Score=146.20 Aligned_cols=83 Identities=19% Similarity=0.334 Sum_probs=76.6
Q ss_pred CCCCCCCCCCCCChHHHHHHHHHHHHHhhCCC-ChHHHHHHHHHHhccCChHHhHHHHHHHHHHHHHHHHHHHHHHHhcc
Q 020305 241 RRGDPSYPKPNRSGYNFFFAEKHYKLKSLYPN-REREFTKMIGESWTNLSPEERKVYQNIGLKDKERYNRELKEYKERLK 319 (328)
Q Consensus 241 ~~kdp~~PKrP~Say~lF~~e~r~~vk~~~P~-~~~eisk~lge~Wk~Ls~~eK~~Y~e~A~~dkerY~~e~~~yk~~~k 319 (328)
.+....+.||||||||+|.+.+|.+|.+++|+ .+.||+|+||.+||.|+++||.+|.++|++.|+.|++|+.+|+-+-+
T Consensus 56 ~k~~~~hIKRPMNAFMVWSq~~RRkma~qnP~mHNSEISK~LG~~WK~Lse~EKrPFi~EAeRLR~~HmkehPdYKYRPR 135 (331)
T KOG0527|consen 56 DKTSTDRIKRPMNAFMVWSQGQRRKLAKQNPKMHNSEISKRLGAEWKLLSEEEKRPFVDEAERLRAQHMKEYPDYKYRPR 135 (331)
T ss_pred CCCCccccCCCcchhhhhhHHHHHHHHHhCcchhhHHHHHHHHHHHhhcCHhhhccHHHHHHHHHHHHHHhCCCcccccc
Confidence 44567789999999999999999999999999 99999999999999999999999999999999999999999998665
Q ss_pred cccc
Q 020305 320 LRQG 323 (328)
Q Consensus 320 ~~~~ 323 (328)
.+..
T Consensus 136 RKkk 139 (331)
T KOG0527|consen 136 RKKK 139 (331)
T ss_pred cccc
Confidence 5433
No 15
>KOG0526 consensus Nucleosome-binding factor SPN, POB3 subunit [Transcription; Replication, recombination and repair; Chromatin structure and dynamics]
Probab=99.55 E-value=5.9e-15 Score=147.00 Aligned_cols=76 Identities=29% Similarity=0.601 Sum_probs=72.2
Q ss_pred ccccCCCCCCCCCCCCCChHHHHHHHHHHHHHhhCCC-ChHHHHHHHHHHhccCChHHhHHHHHHHHHHHHHHHHHHHHH
Q 020305 236 RRRSKRRGDPSYPKPNRSGYNFFFAEKHYKLKSLYPN-REREFTKMIGESWTNLSPEERKVYQNIGLKDKERYNRELKEY 314 (328)
Q Consensus 236 kk~~k~~kdp~~PKrP~Say~lF~~e~r~~vk~~~P~-~~~eisk~lge~Wk~Ls~~eK~~Y~e~A~~dkerY~~e~~~y 314 (328)
+++.|+++||++|||++||||+|++..|..|+.+ + ++.+++|.+|++|+.|+. |.+|+++|++||+||+.||.+|
T Consensus 524 ~k~~kk~kdpnapkra~sa~m~w~~~~r~~ik~d--gi~~~dv~kk~g~~wk~ms~--k~~we~ka~~dk~ry~~em~~y 599 (615)
T KOG0526|consen 524 KKKGKKKKDPNAPKRATSAYMLWLNASRESIKED--GISVGDVAKKAGEKWKQMSA--KEEWEDKAAVDKQRYEDEMKEY 599 (615)
T ss_pred ccCcccCCCCCCCccchhHHHHHHHhhhhhHhhc--CchHHHHHHHHhHHHhhhcc--cchhhHHHHHHHHHHHHHHHhh
Confidence 3556778899999999999999999999999999 7 999999999999999999 8999999999999999999999
Q ss_pred H
Q 020305 315 K 315 (328)
Q Consensus 315 k 315 (328)
+
T Consensus 600 k 600 (615)
T KOG0526|consen 600 K 600 (615)
T ss_pred c
Confidence 9
No 16
>KOG3248 consensus Transcription factor TCF-4 [Transcription]
Probab=99.22 E-value=6.7e-11 Score=112.59 Aligned_cols=74 Identities=16% Similarity=0.280 Sum_probs=68.9
Q ss_pred CCCCCCCChHHHHHHHHHHHHHhhCCC-ChHHHHHHHHHHhccCChHHhHHHHHHHHHHHHHHHHHHHHHHHhcc
Q 020305 246 SYPKPNRSGYNFFFAEKHYKLKSLYPN-REREFTKMIGESWTNLSPEERKVYQNIGLKDKERYNRELKEYKERLK 319 (328)
Q Consensus 246 ~~PKrP~Say~lF~~e~r~~vk~~~P~-~~~eisk~lge~Wk~Ls~~eK~~Y~e~A~~dkerY~~e~~~yk~~~k 319 (328)
.+.|+|+||||+|++|+|++|.+|..- ...+|+++||.+|.+|+.||.++|.|+|+++|+.++.-..+|-++..
T Consensus 190 phiKKPLNAFmlyMKEmRa~vvaEctlKeSAaiNqiLGrRWH~LSrEEQAKYyElArKerqlH~qlYP~WSARdN 264 (421)
T KOG3248|consen 190 PHIKKPLNAFMLYMKEMRAKVVAECTLKESAAINQILGRRWHALSREEQAKYYELARKERQLHMQLYPGWSARDN 264 (421)
T ss_pred ccccccHHHHHHHHHHHHHHHHHHhhhhhHHHHHHHHhHHHhhhhHHHHHHHHHHHHHHHHHHHHhcCCcchhhh
Confidence 467999999999999999999999988 88999999999999999999999999999999999999999877543
No 17
>KOG2510 consensus SWI-SNF chromatin-remodeling complex protein [Chromatin structure and dynamics]
Probab=99.18 E-value=2.7e-11 Score=120.23 Aligned_cols=94 Identities=29% Similarity=0.436 Sum_probs=85.9
Q ss_pred CChhHHHHHHHHHHhhcCCCC-CCCeeCCeecchhhHHHHHHhcCchhhhhcccchHHHHhhhcCCCCCCcHHHHHHHHH
Q 020305 32 KDPIVFWDTLRRFHFIMGTKF-MIPVIGGKELDLHVLYVEATTRGGYEKVVAEKKWREVGAVFKFSPTTTSASFVLRKHY 110 (328)
Q Consensus 32 ~~~~~F~~~L~~F~~~~G~~~-~~P~i~gk~lDL~~Ly~~V~~~GG~~~V~~~~~W~~Va~~lg~p~~~~~as~~Lk~~Y 110 (328)
.+++.++++|+.|++.+.+++ .+|.++.++||||+||..|..+||+.+|+.++ +++|.-|| .++++.|+++|
T Consensus 292 p~r~~wvDR~raF~ee~~Sp~t~~p~~gakPldl~rlYvsvke~gg~~~v~knk--rd~a~~lg-----ssaa~~l~k~y 364 (532)
T KOG2510|consen 292 PERKEWVDRLRAFTEERASPMTNLPAVGAKPLDLYRLYVSVKEIGGLTQVNKNK--RDLATNLG-----SSAASSLKKQY 364 (532)
T ss_pred cchhhHHHHHHHHHHhhcCcccccccccccchhHHHHHHHHHHhccceeeccch--hhhhhccc-----hHHHHHHHHHH
Confidence 578899999999999999999 58999999999999999999999999999998 99999998 56889999999
Q ss_pred HHhhHHHHhhhhhhccCCCCCC
Q 020305 111 LTLLYHYEQVHFFKMQGPPCVP 132 (328)
Q Consensus 111 ~k~L~~yE~~~~~~~~~~~~~~ 132 (328)
.+||+.|||++..+++.++..-
T Consensus 365 ~~~lf~fec~f~Rg~e~p~~~~ 386 (532)
T KOG2510|consen 365 IQYLFAFECKFERGEEPPPDIF 386 (532)
T ss_pred HHHHHhhceeeeccCCCCHHHh
Confidence 9999999999887777665443
No 18
>KOG0528 consensus HMG-box transcription factor SOX5 [Transcription]
Probab=99.00 E-value=1.9e-10 Score=114.03 Aligned_cols=119 Identities=14% Similarity=0.254 Sum_probs=90.3
Q ss_pred CceeEEeecceeecccccCCCCCCC-CCccCCCCCcccccCCCCCcccccccccccCCCCCCCCCCCCCChHHHHHHHHH
Q 020305 185 GYLVSVKLGSETLSGVLYHPDHPGP-STSFCQSNDVGAIIPYTPNSKRRYGRRRRSKRRGDPSYPKPNRSGYNFFFAEKH 263 (328)
Q Consensus 185 gylvtv~~gse~~~g~ly~~~~~~~-~~~~~~~n~~~~~~~~~~~~~~r~~kkk~~k~~kdp~~PKrP~Say~lF~~e~r 263 (328)
+|-..++.++ .|.|.|....+. +...+++.+..+. + +-+...+.+.||||||||+|-++.|
T Consensus 280 ~~~l~~k~~~---dGql~~~~~~~s~~~~s~G~~~v~~s------r---------rg~~ss~PHIKRPMNAFMVWAkDER 341 (511)
T KOG0528|consen 280 TAQLAPKFNS---DGQLSHQSNSDSSPELSDGNAHVHES------R---------RGRASSEPHIKRPMNAFMVWAKDER 341 (511)
T ss_pred ccccccccCC---CCccccCcCCccccccCCCCcccccc------c---------cCcCCCCccccCCcchhhcccchhh
Confidence 4555555555 488888877664 3333333222221 0 1223445678999999999999999
Q ss_pred HHHHhhCCC-ChHHHHHHHHHHhccCChHHhHHHHHHHHHHHHHHHHHHHHHHHhcccc
Q 020305 264 YKLKSLYPN-REREFTKMIGESWTNLSPEERKVYQNIGLKDKERYNRELKEYKERLKLR 321 (328)
Q Consensus 264 ~~vk~~~P~-~~~eisk~lge~Wk~Ls~~eK~~Y~e~A~~dkerY~~e~~~yk~~~k~~ 321 (328)
.+|.+..|| .+..|+|+||.+|+.|+..||++|.+.-.+.-..|.+..++|+-+-+..
T Consensus 342 RKILqA~PDMHNSnISKILGSRWKaMSN~eKQPYYEEQaRLSk~HlEk~PdYrYkPRPK 400 (511)
T KOG0528|consen 342 RKILQAFPDMHNSNISKILGSRWKAMSNTEKQPYYEEQARLSKLHLEKYPDYRYKPRPK 400 (511)
T ss_pred hhhhhcCccccccchhHHhcccccccccccccchHHHHHHHHHhhhccCcccccCCCCC
Confidence 999999999 9999999999999999999999999888888789999999998765443
No 19
>KOG4715 consensus SWI/SNF-related matrix-associated actin-dependent regulator of chromatin [Chromatin structure and dynamics]
Probab=98.84 E-value=4.9e-09 Score=99.29 Aligned_cols=75 Identities=27% Similarity=0.410 Sum_probs=71.3
Q ss_pred CCCCCCCCCCCChHHHHHHHHHHHHHhhCCC-ChHHHHHHHHHHhccCChHHhHHHHHHHHHHHHHHHHHHHHHHH
Q 020305 242 RGDPSYPKPNRSGYNFFFAEKHYKLKSLYPN-REREFTKMIGESWTNLSPEERKVYQNIGLKDKERYNRELKEYKE 316 (328)
Q Consensus 242 ~kdp~~PKrP~Say~lF~~e~r~~vk~~~P~-~~~eisk~lge~Wk~Ls~~eK~~Y~e~A~~dkerY~~e~~~yk~ 316 (328)
-+-|.+|-+|+-.||.|++..+++|++.||+ ..-||-|+||.+|..|+++||+.|...++.+|..|.+.|..|..
T Consensus 59 pkpPkppekpl~pymrySrkvWd~VkA~nPe~kLWeiGK~Ig~mW~dLpd~EK~ey~~EYeaEKieY~~smkayh~ 134 (410)
T KOG4715|consen 59 PKPPKPPEKPLMPYMRYSRKVWDQVKASNPELKLWEIGKIIGGMWLDLPDEEKQEYLNEYEAEKIEYNESMKAYHN 134 (410)
T ss_pred CCCCCCCCcccchhhHHhhhhhhhhhccCcchHHHHHHHHHHHHHhhCcchHHHHHHHHHHHHHHHHHHHHHHhhC
Confidence 3467788999999999999999999999999 99999999999999999999999999999999999999999976
No 20
>KOG2746 consensus HMG-box transcription factor Capicua and related proteins [Transcription]
Probab=98.37 E-value=3e-07 Score=94.69 Aligned_cols=74 Identities=23% Similarity=0.462 Sum_probs=68.8
Q ss_pred cccCCCCCCCCCCCCCChHHHHHHHHH--HHHHhhCCC-ChHHHHHHHHHHhccCChHHhHHHHHHHHHHHHHHHHH
Q 020305 237 RRSKRRGDPSYPKPNRSGYNFFFAEKH--YKLKSLYPN-REREFTKMIGESWTNLSPEERKVYQNIGLKDKERYNRE 310 (328)
Q Consensus 237 k~~k~~kdp~~PKrP~Say~lF~~e~r--~~vk~~~P~-~~~eisk~lge~Wk~Ls~~eK~~Y~e~A~~dkerY~~e 310 (328)
.+...+++..+.++|||||++|++.+| ..+.+.||+ .++-|++|||+.|-.|.+.||+.|.++|.+.|+.|.++
T Consensus 171 grspnkr~k~HirrPMnaf~ifskrhr~~g~vhq~~pn~DNrtIskiLgewWytL~~~Ekq~yhdLa~Qvk~Ahfka 247 (683)
T KOG2746|consen 171 GRSPNKRDKDHIRRPMNAFHIFSKRHRGEGRVHQRHPNQDNRTISKILGEWWYTLGPNEKQKYHDLAFQVKEAHFKA 247 (683)
T ss_pred cCCCCcCcchhhhhhhHHHHHHHhhcCCccchhccCccccchhHHHHHhhhHhhhCchhhhhHHHHHHHHHHHHhhh
Confidence 445566788899999999999999999 999999999 99999999999999999999999999999999999986
No 21
>PF14887 HMG_box_5: HMG (high mobility group) box 5; PDB: 1L8Y_A 1L8Z_A 2HDZ_A.
Probab=97.84 E-value=6.3e-05 Score=57.94 Aligned_cols=72 Identities=18% Similarity=0.398 Sum_probs=58.9
Q ss_pred CCCCCCChHHHHHHHHHHHHHhhCCC-ChHHHHHHHHHHhccCChHHhHHHHHHHHHHHHHHHHHHHHHHHhcc
Q 020305 247 YPKPNRSGYNFFFAEKHYKLKSLYPN-REREFTKMIGESWTNLSPEERKVYQNIGLKDKERYNRELKEYKERLK 319 (328)
Q Consensus 247 ~PKrP~Say~lF~~e~r~~vk~~~P~-~~~eisk~lge~Wk~Ls~~eK~~Y~e~A~~dkerY~~e~~~yk~~~k 319 (328)
-|..|.++--+|.+.......+.++. ...+ .+.+...|++|++.+|.+|..+|.+|..+|+.+|.+|++...
T Consensus 3 lPE~PKt~qe~Wqq~vi~dYla~~~~dr~K~-~kam~~~W~~me~Kekl~WIkKA~EdqKrYE~el~e~r~~~~ 75 (85)
T PF14887_consen 3 LPETPKTAQEIWQQSVIGDYLAKFRNDRKKA-LKAMEAQWSQMEKKEKLKWIKKAAEDQKRYERELREMRSAPA 75 (85)
T ss_dssp -S----THHHHHHHHHHHHHHHHTTSTHHHH-HHHHHHHHHTTGGGHHHHHHHHHHHHHHHHHHHHHCCS-CCC
T ss_pred CCCCCCCHHHHHHHHHHHHHHHHhhHhHHHH-HHHHHHHHHHhhhhhhhHHHHHHHHHHHHHHHHHHHHhcCCC
Confidence 36678889999999999998888988 5454 558999999999999999999999999999999999987554
No 22
>PF04690 YABBY: YABBY protein; InterPro: IPR006780 YABBY proteins are a group of plant-specific transcription factors involved in the specification of abaxial polarity in lateral organs such as leaves and floral organs [, ].
Probab=96.77 E-value=0.0025 Score=56.60 Aligned_cols=47 Identities=21% Similarity=0.410 Sum_probs=41.6
Q ss_pred CCCCCCCCCCChHHHHHHHHHHHHHhhCCC-ChHHHHHHHHHHhccCC
Q 020305 243 GDPSYPKPNRSGYNFFFAEKHYKLKSLYPN-REREFTKMIGESWTNLS 289 (328)
Q Consensus 243 kdp~~PKrP~Say~lF~~e~r~~vk~~~P~-~~~eisk~lge~Wk~Ls 289 (328)
+.|.+-.|-+|||+.|+++.-.+||+.+|+ +.+|+-+..++.|...+
T Consensus 117 kPPEKRqR~psaYn~f~k~ei~rik~~~p~ishkeaFs~aAknW~h~p 164 (170)
T PF04690_consen 117 KPPEKRQRVPSAYNRFMKEEIQRIKAENPDISHKEAFSAAAKNWAHFP 164 (170)
T ss_pred CCccccCCCchhHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHhhhhCc
Confidence 344555677999999999999999999999 99999999999998765
No 23
>PF06382 DUF1074: Protein of unknown function (DUF1074); InterPro: IPR024460 This family consists of several proteins which appear to be specific to Insecta. The function of this family is unknown.
Probab=96.41 E-value=0.011 Score=52.57 Aligned_cols=48 Identities=19% Similarity=0.331 Sum_probs=41.7
Q ss_pred CChHHHHHHHHHHHHHhhCCC-ChHHHHHHHHHHhccCChHHhHHHHHHHHHH
Q 020305 252 RSGYNFFFAEKHYKLKSLYPN-REREFTKMIGESWTNLSPEERKVYQNIGLKD 303 (328)
Q Consensus 252 ~Say~lF~~e~r~~vk~~~P~-~~~eisk~lge~Wk~Ls~~eK~~Y~e~A~~d 303 (328)
.+||+=|+.++|.+ |.+ ...|+....+.+|..|++++|..|..++...
T Consensus 83 nnaYLNFLReFRrk----h~~L~p~dlI~~AAraW~rLSe~eK~rYrr~~~~~ 131 (183)
T PF06382_consen 83 NNAYLNFLREFRRK----HCGLSPQDLIQRAARAWCRLSEAEKNRYRRMAPSV 131 (183)
T ss_pred chHHHHHHHHHHHH----ccCCCHHHHHHHHHHHHHhCCHHHHHHHHhhcchh
Confidence 57999999998875 566 7799999999999999999999999876543
No 24
>COG5648 NHP6B Chromatin-associated proteins containing the HMG domain [Chromatin structure and dynamics]
Probab=96.32 E-value=0.0034 Score=57.14 Aligned_cols=67 Identities=22% Similarity=0.203 Sum_probs=60.2
Q ss_pred CCCCCCCChHHHHHHHHHHHHHhhCCC-ChHHHHHHHHHHhccCChHHhHHHHHHHHHHHHHHHHHHH
Q 020305 246 SYPKPNRSGYNFFFAEKHYKLKSLYPN-REREFTKMIGESWTNLSPEERKVYQNIGLKDKERYNRELK 312 (328)
Q Consensus 246 ~~PKrP~Say~lF~~e~r~~vk~~~P~-~~~eisk~lge~Wk~Ls~~eK~~Y~e~A~~dkerY~~e~~ 312 (328)
.+++.+.-.|.=+-.+.|+++...+|+ ...++++++++.|++|+++-|.+|.+.++++++.|...++
T Consensus 142 ~~~~~~~~~~~e~~~~~r~~~~~~~~~~~~~e~~k~~~~~w~el~~skK~~~~~~~Kk~k~~~~~~~~ 209 (211)
T COG5648 142 LPNKAPIGPFIENEPKIRPKVEGPSPDKALVEETKIISKAWSELDESKKKKYIDKYKKLKEEYDSFYP 209 (211)
T ss_pred cCCCCCCchhhhccHHhccccCCCCcchhhhHHhhhhhhhhhhhChhhhhHHHHHHHHHHHHHhhhcc
Confidence 456777777888888889999999999 9999999999999999999999999999999999988765
No 25
>TIGR01624 LRP1_Cterm LRP1 C-terminal domain. This model represents a tightly conserved small domain found in LRP1 and related plant proteins. This family also contains a well-conserved putative zinc finger domain (TIGR01623). The rest of the sequence of most members consists of highly divergent, low-complexity sequence.
Probab=91.33 E-value=0.13 Score=36.21 Aligned_cols=34 Identities=24% Similarity=0.498 Sum_probs=30.0
Q ss_pred CceeEEeecccc-CCCceeEEeecceeecccccCC
Q 020305 171 CFTAVGRIDGKF-DCGYLVSVKLGSETLSGVLYHP 204 (328)
Q Consensus 171 ~~~~~~~idgkf-~~gylvtv~~gse~~~g~ly~~ 204 (328)
+.-|+++=||.- +..|-.+|+||...+||+||..
T Consensus 14 cvRvs~idd~~~~e~aYQt~V~IgGHvFkGiLyDq 48 (50)
T TIGR01624 14 CVRVTAIDDGEQAEYAYQATVTIGGHVFKGFLHDQ 48 (50)
T ss_pred EEEEeccCCCCCceEEEEEEEEECceEEeeEEecc
Confidence 456888888887 8899999999999999999974
No 26
>PF05142 DUF702: Domain of unknown function (DUF702) ; InterPro: IPR007818 This is a family of plant proteins of unknown function.
Probab=90.07 E-value=0.19 Score=43.80 Aligned_cols=35 Identities=26% Similarity=0.582 Sum_probs=32.0
Q ss_pred CceeEEeeccccCCCceeEEeecceeecccccCCC
Q 020305 171 CFTAVGRIDGKFDCGYLVSVKLGSETLSGVLYHPD 205 (328)
Q Consensus 171 ~~~~~~~idgkf~~gylvtv~~gse~~~g~ly~~~ 205 (328)
+.-|+++=||.-+..|.-+|+||...|||+||..-
T Consensus 116 CVRVssiDdgedE~AYQTaV~IGGHVFKGiLYDqG 150 (154)
T PF05142_consen 116 CVRVSSIDDGEDEYAYQTAVNIGGHVFKGILYDQG 150 (154)
T ss_pred EEEEecccCcccceeeEEeEEECCEEeeeeeeccC
Confidence 55689999999999999999999999999999864
No 27
>PF08073 CHDNT: CHDNT (NUC034) domain; InterPro: IPR012958 The CHD N-terminal domain is found in PHD/RING fingers and chromo domain-associated helicases [].; GO: 0003677 DNA binding, 0005524 ATP binding, 0008270 zinc ion binding, 0016818 hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides, 0006355 regulation of transcription, DNA-dependent, 0005634 nucleus
Probab=89.93 E-value=0.38 Score=34.96 Aligned_cols=39 Identities=13% Similarity=0.284 Sum_probs=35.1
Q ss_pred CChHHHHHHHHHHHHHhhCCC-ChHHHHHHHHHHhccCCh
Q 020305 252 RSGYNFFFAEKHYKLKSLYPN-REREFTKMIGESWTNLSP 290 (328)
Q Consensus 252 ~Say~lF~~e~r~~vk~~~P~-~~~eisk~lge~Wk~Ls~ 290 (328)
.+.|-+|.+-.|+.|...||+ ....+...++.+|+..++
T Consensus 13 lt~yK~Fsq~vRP~l~~~NPk~~~sKl~~l~~AKwrEF~~ 52 (55)
T PF08073_consen 13 LTNYKAFSQHVRPLLAKANPKAPMSKLMMLLQAKWREFQE 52 (55)
T ss_pred HHHHHHHHHHHHHHHHHHCCCCcHHHHHHHHHHHHHHHHh
Confidence 467889999999999999999 999999999999987543
No 28
>PF04769 MAT_Alpha1: Mating-type protein MAT alpha 1; InterPro: IPR006856 This family includes Saccharomyces cerevisiae (Baker's yeast) mating type protein alpha 1 (P01365 from SWISSPROT). MAT alpha 1 is a transcription activator that activates mating-type alpha-specific genes with the help of the MADS-box containing MCM1 transcription factor, which together bind cooperatively to PQ elements upstream of alpha-specific genes. The MCM1-MATalpha1 complex is required for the proper DNA-bending that is needed for transcriptional activation []. Alpha 1 interacts in vivo with STE12, linking expression of alpha-specific genes to the alpha-pheromone (IPR006742 from INTERPRO) response pathway [].; GO: 0000772 mating pheromone activity, 0003677 DNA binding, 0045895 positive regulation of transcription, mating-type specific, 0005634 nucleus
Probab=88.99 E-value=1.1 Score=41.06 Aligned_cols=56 Identities=14% Similarity=0.353 Sum_probs=40.6
Q ss_pred CCCCCCCCCCCCChHHHHHHHHHHHHHhhCCC-ChHHHHHHHHHHhccCChHHhHHHHHHHHH
Q 020305 241 RRGDPSYPKPNRSGYNFFFAEKHYKLKSLYPN-REREFTKMIGESWTNLSPEERKVYQNIGLK 302 (328)
Q Consensus 241 ~~kdp~~PKrP~Say~lF~~e~r~~vk~~~P~-~~~eisk~lge~Wk~Ls~~eK~~Y~e~A~~ 302 (328)
++.....+|||.|+||.|..=+- ...|+ ...+++..|+..|..=+- |..|.-.|+.
T Consensus 37 ~~~~~~~~kr~lN~Fm~FRsyy~----~~~~~~~Qk~~S~~l~~lW~~dp~--k~~W~l~ak~ 93 (201)
T PF04769_consen 37 RKRSPEKAKRPLNGFMAFRSYYS----PIFPPLPQKELSGILTKLWEKDPF--KNKWSLMAKA 93 (201)
T ss_pred ccccccccccchhHHHHHHHHHH----hhcCCcCHHHHHHHHHHHHhCCcc--HhHHHHHhhh
Confidence 34456678999999999987654 44566 779999999999987433 4556554443
No 29
>PF06244 DUF1014: Protein of unknown function (DUF1014); InterPro: IPR010422 This family consists of several hypothetical eukaryotic proteins of unknown function.
Probab=84.71 E-value=1.1 Score=37.83 Aligned_cols=45 Identities=18% Similarity=0.361 Sum_probs=39.5
Q ss_pred CCCCCCChHHHHHHHHHHHHHhhCCC-ChHHHHHHHHHHhccCChH
Q 020305 247 YPKPNRSGYNFFFAEKHYKLKSLYPN-REREFTKMIGESWTNLSPE 291 (328)
Q Consensus 247 ~PKrP~Say~lF~~e~r~~vk~~~P~-~~~eisk~lge~Wk~Ls~~ 291 (328)
+-||-.-||.-|....-++|++++|+ ....+..+|-+.|..-++.
T Consensus 72 PErR~KAAy~afeE~~Lp~lK~E~PgLrlsQ~kq~l~K~w~KSPeN 117 (122)
T PF06244_consen 72 PERRMKAAYKAFEERRLPELKEENPGLRLSQYKQMLWKEWQKSPEN 117 (122)
T ss_pred cchhHHHHHHHHHHHHhHHHHhhCCCchHHHHHHHHHHHHhcCCCC
Confidence 33555689999999999999999999 9999999999999887764
No 30
>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=81.46 E-value=3.2 Score=28.56 Aligned_cols=39 Identities=18% Similarity=0.276 Sum_probs=28.0
Q ss_pred hhHHHHHHhcCchhhhhcccchHHHHhhhcCCCCCCcHHHHHHHHHHHhh
Q 020305 65 HVLYVEATTRGGYEKVVAEKKWREVGAVFKFSPTTTSASFVLRKHYLTLL 114 (328)
Q Consensus 65 ~~Ly~~V~~~GG~~~V~~~~~W~~Va~~lg~p~~~~~as~~Lk~~Y~k~L 114 (328)
..|...|...|.- .|..|+..|+. +-.+.+++.+|.+||
T Consensus 10 ~~l~~~v~~~g~~-------~W~~Ia~~~~~----~Rt~~qc~~~~~~~~ 48 (48)
T PF00249_consen 10 EKLLEAVKKYGKD-------NWKKIAKRMPG----GRTAKQCRSRYQNLL 48 (48)
T ss_dssp HHHHHHHHHSTTT-------HHHHHHHHHSS----SSTHHHHHHHHHHHT
T ss_pred HHHHHHHHHhCCc-------HHHHHHHHcCC----CCCHHHHHHHHHhhC
Confidence 3456666666643 69999999992 223448999999886
No 31
>TIGR03481 HpnM hopanoid biosynthesis associated membrane protein HpnM. The genomes containing members of this family share the machinery for the biosynthesis of hopanoid lipids. Furthermore, the genes of this family are usually located proximal to other components of this biological process. The proteins are members of the pfam05494 family of putative transporters known as "toluene tolerance protein Ttg2D", although it is unlikely that the members included here have anything to do with toluene per-se.
Probab=72.56 E-value=8.8 Score=34.81 Aligned_cols=44 Identities=27% Similarity=0.531 Sum_probs=38.3
Q ss_pred ChHHHHH-HHHHHhccCChHHhHHHHHHHHH-HHHHHHHHHHHHHH
Q 020305 273 REREFTK-MIGESWTNLSPEERKVYQNIGLK-DKERYNRELKEYKE 316 (328)
Q Consensus 273 ~~~eisk-~lge~Wk~Ls~~eK~~Y~e~A~~-dkerY~~e~~~yk~ 316 (328)
.+..+++ .+|..|+.+++++|+.|.+.... ....|-..+..|..
T Consensus 65 Df~~mar~vLG~~W~~~s~~Qr~~F~~~F~~~l~~tY~~~l~~y~~ 110 (198)
T TIGR03481 65 DLPAMARLTLGSSWTSLSPEQRRRFIGAFRELSIATYASQFKSYAG 110 (198)
T ss_pred CHHHHHHHHhhhhhhhCCHHHHHHHHHHHHHHHHHHHHHHHHhhcC
Confidence 5667765 78999999999999999998888 68899999999975
No 32
>KOG3223 consensus Uncharacterized conserved protein [Function unknown]
Probab=65.43 E-value=4.7 Score=36.58 Aligned_cols=52 Identities=17% Similarity=0.409 Sum_probs=44.0
Q ss_pred CCC-CCCCChHHHHHHHHHHHHHhhCCC-ChHHHHHHHHHHhccCChHHhHHHHHHH
Q 020305 246 SYP-KPNRSGYNFFFAEKHYKLKSLYPN-REREFTKMIGESWTNLSPEERKVYQNIG 300 (328)
Q Consensus 246 ~~P-KrP~Say~lF~~e~r~~vk~~~P~-~~~eisk~lge~Wk~Ls~~eK~~Y~e~A 300 (328)
.+| ||=+-||.-|-...-++|+.+||+ ...++-.+|-.+|..-++. ||.+.+
T Consensus 162 rHPEkRmrAA~~afEe~~LPrLK~e~P~lrlsQ~Kqll~Kew~KsPDN---P~Nq~~ 215 (221)
T KOG3223|consen 162 RHPEKRMRAAFKAFEEARLPRLKKENPGLRLSQYKQLLKKEWQKSPDN---PFNQAA 215 (221)
T ss_pred cChHHHHHHHHHHHHHhhchhhhhcCCCccHHHHHHHHHHHHhhCCCC---hhhHHh
Confidence 455 666788999999999999999999 9999999999999998876 565544
No 33
>PF09441 Abp2: ARS binding protein 2; InterPro: IPR018562 This DNA-binding protein binds to the autonomously replicating sequence (ARS) binding element. It may play a role in regulating the cell cycle response to stress signals [].
Probab=62.88 E-value=16 Score=32.27 Aligned_cols=42 Identities=17% Similarity=0.272 Sum_probs=34.6
Q ss_pred CCCeeCCeecchhhHHHHHHhcCchhhhhcccchHHHHhhhcCCCC
Q 020305 53 MIPVIGGKELDLHVLYVEATTRGGYEKVVAEKKWREVGAVFKFSPT 98 (328)
Q Consensus 53 ~~P~i~gk~lDL~~Ly~~V~~~GG~~~V~~~~~W~~Va~~lg~p~~ 98 (328)
.+|.-+|+..+.|.||..|.++-.- .-+.|.++|-.||+.+.
T Consensus 44 ~pPkS~Gk~Fs~~~Lf~LI~k~~~k----eikTW~~La~~LGVepp 85 (175)
T PF09441_consen 44 SPPKSDGKSFSTFTLFELIRKLESK----EIKTWAQLALELGVEPP 85 (175)
T ss_pred CCCCcCCccchHHHHHHHHHHHhhh----hHhHHHHHHHHhCCCCC
Confidence 4799999999999999999976433 23579999999999544
No 34
>PRK15117 ABC transporter periplasmic binding protein MlaC; Provisional
Probab=62.78 E-value=19 Score=32.98 Aligned_cols=46 Identities=20% Similarity=0.368 Sum_probs=39.3
Q ss_pred CC-ChHHHHH-HHHHHhccCChHHhHHHHHHHHH-HHHHHHHHHHHHHH
Q 020305 271 PN-REREFTK-MIGESWTNLSPEERKVYQNIGLK-DKERYNRELKEYKE 316 (328)
Q Consensus 271 P~-~~~eisk-~lge~Wk~Ls~~eK~~Y~e~A~~-dkerY~~e~~~yk~ 316 (328)
|. .+..+++ .+|.-|+.+++++|+.|.+.... ...-|-..+.+|..
T Consensus 66 p~~Df~~~s~~vLG~~wr~as~eQr~~F~~~F~~~Lv~tYa~~l~~y~~ 114 (211)
T PRK15117 66 PYVQVKYAGALVLGRYYKDATPAQREAYFAAFREYLKQAYGQALAMYHG 114 (211)
T ss_pred ccCCHHHHHHHHhhhhhhhCCHHHHHHHHHHHHHHHHHHHHHHHHHhCC
Confidence 55 7777765 78999999999999999988877 57789999999975
No 35
>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=54.91 E-value=24 Score=24.99 Aligned_cols=36 Identities=14% Similarity=0.310 Sum_probs=23.1
Q ss_pred hHHHHHHhcCchhhhhcccchHHHHhhhcCCCCCCcHHHHHHHHHHHhh
Q 020305 66 VLYVEATTRGGYEKVVAEKKWREVGAVFKFSPTTTSASFVLRKHYLTLL 114 (328)
Q Consensus 66 ~Ly~~V~~~GG~~~V~~~~~W~~Va~~lg~p~~~~~as~~Lk~~Y~k~L 114 (328)
.|...|...|. .|..||..|| . -....++..|.++|
T Consensus 8 ~L~~~~~~~g~--------~W~~Ia~~l~---~--Rt~~~~~~r~~~~l 43 (60)
T PF13921_consen 8 LLLELVKKYGN--------DWKKIAEHLG---N--RTPKQCRNRWRNHL 43 (60)
T ss_dssp HHHHHHHHHTS---------HHHHHHHST---T--S-HHHHHHHHHHTT
T ss_pred HHHHHHHHHCc--------CHHHHHHHHC---c--CCHHHHHHHHHHHC
Confidence 34455555553 6999999996 1 12347888888866
No 36
>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=52.36 E-value=28 Score=22.21 Aligned_cols=37 Identities=16% Similarity=0.310 Sum_probs=24.5
Q ss_pred hHHHHHHhcCchhhhhcccchHHHHhhhcCCCCCCcHHHHHHHHHHHhh
Q 020305 66 VLYVEATTRGGYEKVVAEKKWREVGAVFKFSPTTTSASFVLRKHYLTLL 114 (328)
Q Consensus 66 ~Ly~~V~~~GG~~~V~~~~~W~~Va~~lg~p~~~~~as~~Lk~~Y~k~L 114 (328)
.|...|...|- ..|..|+..++-- .+..++.+|..++
T Consensus 9 ~l~~~~~~~g~-------~~w~~Ia~~~~~r-----s~~~~~~~~~~~~ 45 (45)
T cd00167 9 LLLEAVKKYGK-------NNWEKIAKELPGR-----TPKQCRERWRNLL 45 (45)
T ss_pred HHHHHHHHHCc-------CCHHHHHhHcCCC-----CHHHHHHHHHHhC
Confidence 45555666653 5799999998651 2337888887653
No 37
>PF05494 Tol_Tol_Ttg2: Toluene tolerance, Ttg2 ; InterPro: IPR008869 Toluene tolerance is mediated by increased cell membrane rigidity resulting from changes in fatty acid and phospholipid compositions, exclusion of toluene from the cell membrane, and removal of intracellular toluene by degradation []. Many proteins are involved in these processes. This family is a transporter which shows similarity to ABC transporters [].; PDB: 2QGU_A.
Probab=46.65 E-value=21 Score=31.01 Aligned_cols=44 Identities=20% Similarity=0.444 Sum_probs=33.3
Q ss_pred ChHHHH-HHHHHHhccCChHHhHHHHHHHHH-HHHHHHHHHHHHHH
Q 020305 273 REREFT-KMIGESWTNLSPEERKVYQNIGLK-DKERYNRELKEYKE 316 (328)
Q Consensus 273 ~~~eis-k~lge~Wk~Ls~~eK~~Y~e~A~~-dkerY~~e~~~yk~ 316 (328)
.+..++ ..||.-|+.+++++|+.|.+...+ ....|-..+..|..
T Consensus 39 D~~~~ar~~LG~~w~~~s~~q~~~F~~~f~~~l~~~Y~~~l~~y~~ 84 (170)
T PF05494_consen 39 DFERMARRVLGRYWRKASPAQRQRFVEAFKQLLVRTYAKRLDEYSG 84 (170)
T ss_dssp -HHHHHHHHHGGGTTTS-HHHHHHHHHHHHHHHHHHHHHHHHT-SS
T ss_pred CHHHHHHHHHHHhHhhCCHHHHHHHHHHHHHHHHHHHHHHHHhhCC
Confidence 455554 457889999999999999988777 57788899988875
No 38
>PF11304 DUF3106: Protein of unknown function (DUF3106); InterPro: IPR021455 Some members in this family of proteins are annotated as transmembrane proteins however this cannot be confirmed. Currently no function is known.
Probab=44.08 E-value=81 Score=25.74 Aligned_cols=42 Identities=19% Similarity=0.550 Sum_probs=24.9
Q ss_pred HHHHHHHHHHhccCChHHhHHHHHHHHH-------HHHHHHHHHHHHHH
Q 020305 275 REFTKMIGESWTNLSPEERKVYQNIGLK-------DKERYNRELKEYKE 316 (328)
Q Consensus 275 ~eisk~lge~Wk~Ls~~eK~~Y~e~A~~-------dkerY~~e~~~yk~ 316 (328)
.++..-+.+.|+.|+++.|..+.+.+.. ++++....|..|..
T Consensus 10 q~~L~pl~~~W~~l~~~qr~k~l~~a~r~~~mspeqq~r~~~rm~~W~~ 58 (107)
T PF11304_consen 10 QQALAPLAERWNSLPPEQRRKWLQIAERWPSMSPEQQQRLRERMRRWAA 58 (107)
T ss_pred HHHHHHHHHHHhcCCHHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHh
Confidence 3445556666666666666666555543 45566666666653
No 39
>PF13873 Myb_DNA-bind_5: Myb/SANT-like DNA-binding domain
Probab=38.52 E-value=46 Score=24.90 Aligned_cols=54 Identities=15% Similarity=0.204 Sum_probs=34.3
Q ss_pred cchhhHHHHHHhc---CchhhhhcccchHHHHhhhcC-CCCCCcHHHHHHHHHHHhhHH
Q 020305 62 LDLHVLYVEATTR---GGYEKVVAEKKWREVGAVFKF-SPTTTSASFVLRKHYLTLLYH 116 (328)
Q Consensus 62 lDL~~Ly~~V~~~---GG~~~V~~~~~W~~Va~~lg~-p~~~~~as~~Lk~~Y~k~L~~ 116 (328)
|+|+.-|..|..- ++.........|.+|+..|+- .+. .-...+|++.|..+...
T Consensus 14 v~~v~~~~~il~~k~~~~~~~~~k~~~W~~I~~~lN~~~~~-~Rs~~~lkkkW~nlk~~ 71 (78)
T PF13873_consen 14 VELVEKHKDILENKFSDSVSNKEKRKAWEEIAEELNALGPG-KRSWKQLKKKWKNLKSK 71 (78)
T ss_pred HHHHHHhHHHHhcccccHHHHHHHHHHHHHHHHHHHhcCCC-CCCHHHHHHHHHHHHHH
Confidence 4555556555543 233344456799999999964 333 33445899999887653
No 40
>smart00717 SANT SANT SWI3, ADA2, N-CoR and TFIIIB'' DNA-binding domains.
Probab=34.97 E-value=77 Score=20.35 Aligned_cols=26 Identities=15% Similarity=0.330 Sum_probs=18.5
Q ss_pred cchHHHHhhhcCCCCCCcHHHHHHHHHHHhh
Q 020305 84 KKWREVGAVFKFSPTTTSASFVLRKHYLTLL 114 (328)
Q Consensus 84 ~~W~~Va~~lg~p~~~~~as~~Lk~~Y~k~L 114 (328)
..|..|+..|+- -.+..++..|..++
T Consensus 22 ~~w~~Ia~~~~~-----rt~~~~~~~~~~~~ 47 (49)
T smart00717 22 NNWEKIAKELPG-----RTAEQCRERWNNLL 47 (49)
T ss_pred CCHHHHHHHcCC-----CCHHHHHHHHHHHc
Confidence 579999999872 12336888887765
No 41
>PF12881 NUT_N: NUT protein N terminus; InterPro: IPR024309 This domain is found in the N-terminal region of Nuclear Testis (NUT) proteins. It is also found in FAM22, which are a family of uncharacterised mammalian proteins.
Probab=32.73 E-value=1.1e+02 Score=30.01 Aligned_cols=52 Identities=21% Similarity=0.168 Sum_probs=35.8
Q ss_pred HHHhhCCC-ChHHHHHHHHHHhccCChHHhHHHHHHHHHHHHHH-HHHHHHHHH
Q 020305 265 KLKSLYPN-REREFTKMIGESWTNLSPEERKVYQNIGLKDKERY-NRELKEYKE 316 (328)
Q Consensus 265 ~vk~~~P~-~~~eisk~lge~Wk~Ls~~eK~~Y~e~A~~dkerY-~~e~~~yk~ 316 (328)
.+....|. +..|-....-..|...|.-||..|+|+|++-.|== ++||+.-+-
T Consensus 242 sLar~kPtMtlEeGl~ra~qEW~~~SnfdRmifyemaekFmEFEaeEEmq~q~l 295 (328)
T PF12881_consen 242 SLARLKPTMTLEEGLWRAVQEWQHTSNFDRMIFYEMAEKFMEFEAEEEMQIQKL 295 (328)
T ss_pred HHHhcCCCccHHHHHHHHHHHhhccccccHHHHHHHHHHHccCCcHHHHHHHHH
Confidence 34444455 55566677778999999999999999999864322 245554443
No 42
>PF13875 DUF4202: Domain of unknown function (DUF4202)
Probab=31.29 E-value=93 Score=28.18 Aligned_cols=41 Identities=10% Similarity=0.244 Sum_probs=34.3
Q ss_pred CChHHHHHHHHHHHHHhhCCCChHHHHHHHHHHhccCChHHhH
Q 020305 252 RSGYNFFFAEKHYKLKSLYPNREREFTKMIGESWTNLSPEERK 294 (328)
Q Consensus 252 ~Say~lF~~e~r~~vk~~~P~~~~eisk~lge~Wk~Ls~~eK~ 294 (328)
--+-++|+..+.+.+...|. ...+..+|...|+.||+.-++
T Consensus 129 DvacLVFL~~~f~~F~~~~d--eeK~v~Il~KTw~KMS~~g~~ 169 (185)
T PF13875_consen 129 DVACLVFLEYYFEDFAAKHD--EEKIVDILRKTWRKMSERGHE 169 (185)
T ss_pred hhHHHHhHHHHHHHHHhcCC--HHHHHHHHHHHHHHCCHHHHH
Confidence 34689999999999998883 466888899999999998764
No 43
>PF12776 Myb_DNA-bind_3: Myb/SANT-like DNA-binding domain; InterPro: IPR024752 This domain, found in a range of uncharacterised proteins, may be related to Myb/SANT-like DNA binding domains.
Probab=30.02 E-value=93 Score=23.89 Aligned_cols=60 Identities=17% Similarity=0.243 Sum_probs=41.1
Q ss_pred hhhHHHHHHhcCch--hhhhcccchHHHHhhhcCCCCCCcHHHHHHHHHHHhhHHHHhhhhh
Q 020305 64 LHVLYVEATTRGGY--EKVVAEKKWREVGAVFKFSPTTTSASFVLRKHYLTLLYHYEQVHFF 123 (328)
Q Consensus 64 L~~Ly~~V~~~GG~--~~V~~~~~W~~Va~~lg~p~~~~~as~~Lk~~Y~k~L~~yE~~~~~ 123 (328)
|..|+.+....|.+ ...-....|..|+..|.-.....-...+|+..|..+=..|....-.
T Consensus 10 ll~~~~e~~~~g~~~~~~~fk~~~w~~i~~~~~~~~~~~~t~~qlknk~~~lk~~y~~~~~l 71 (96)
T PF12776_consen 10 LLDLLIEQINKGNRPTNGGFKKEGWNNIAEEFNEKTGLNYTKKQLKNKWKTLKKDYRIWKEL 71 (96)
T ss_pred HHHHHHHHHHhCCCCCCCCcCHHHHHHHHHHHHHHhCCcccHHHHHHHHHHHHHHHHHHHHH
Confidence 44556666667777 2444455899999999864343333458999999988888876533
No 44
>COG2854 Ttg2D ABC-type transport system involved in resistance to organic solvents, auxiliary component [Secondary metabolites biosynthesis, transport, and catabolism]
Probab=27.56 E-value=77 Score=29.09 Aligned_cols=41 Identities=22% Similarity=0.414 Sum_probs=35.4
Q ss_pred HHHHHHHHhccCChHHhHHHHHHHHH-HHHHHHHHHHHHHHh
Q 020305 277 FTKMIGESWTNLSPEERKVYQNIGLK-DKERYNRELKEYKER 317 (328)
Q Consensus 277 isk~lge~Wk~Ls~~eK~~Y~e~A~~-dkerY~~e~~~yk~~ 317 (328)
-..-||.-|+.+++++++.|....+. ....|-..+.+|+.+
T Consensus 76 a~~vLGk~~k~aspeQ~~~F~~aF~~yl~q~Y~~aL~~Y~~q 117 (202)
T COG2854 76 AKLVLGKYYKTASPEQRQAFFKAFRTYLEQTYGQALLDYKGQ 117 (202)
T ss_pred HHHHhccccccCCHHHHHHHHHHHHHHHHHHHHHHHHHccCC
Confidence 45678999999999999999988777 578899999999873
No 45
>PRK12750 cpxP periplasmic repressor CpxP; Reviewed
Probab=25.62 E-value=2.2e+02 Score=25.23 Aligned_cols=34 Identities=12% Similarity=0.261 Sum_probs=27.3
Q ss_pred HHHHHHHhccCChHHhHHHHHHHHHHHHHHHHHH
Q 020305 278 TKMIGESWTNLSPEERKVYQNIGLKDKERYNREL 311 (328)
Q Consensus 278 sk~lge~Wk~Ls~~eK~~Y~e~A~~dkerY~~e~ 311 (328)
.+..-+.+.-|++++|..|.+.-++-.+.+.+.+
T Consensus 127 ~~~~~~~~~vLTpEQRak~~e~~~~r~~~~~~~~ 160 (170)
T PRK12750 127 LEKRHQMLSILTPEQKAKFQELQQERMQECQDKM 160 (170)
T ss_pred HHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHHH
Confidence 4455668999999999999998877777777666
No 46
>KOG3838 consensus Mannose lectin ERGIC-53, involved in glycoprotein traffic [Intracellular trafficking, secretion, and vesicular transport]
Probab=25.50 E-value=60 Score=32.86 Aligned_cols=37 Identities=22% Similarity=0.191 Sum_probs=30.3
Q ss_pred CChHHhHHHHHHHHHHHHHHHHHHHHHHHhccccccc
Q 020305 288 LSPEERKVYQNIGLKDKERYNRELKEYKERLKLRQGE 324 (328)
Q Consensus 288 Ls~~eK~~Y~e~A~~dkerY~~e~~~yk~~~k~~~~~ 324 (328)
+.+.||++|++..+.....|+++..+|++...+.++.
T Consensus 269 ~qe~ek~kyqeEfe~~q~elek~k~efkk~hpd~~~e 305 (497)
T KOG3838|consen 269 MQELEKAKYQEEFEWAQLELEKRKDEFKKSHPDAQGE 305 (497)
T ss_pred hhHHHHHHHHHHHHHHHHHHhhhHhhhccCCchhhcc
Confidence 3456899999999999999999999999877766554
No 47
>PF05066 HARE-HTH: HB1, ASXL, restriction endonuclease HTH domain; InterPro: IPR007759 DNA-directed RNA polymerases 2.7.7.6 from EC (also known as DNA-dependent RNA polymerases) are responsible for the polymerisation of ribonucleotides into a sequence complementary to the template DNA. In eukaryotes, there are three different forms of DNA-directed RNA polymerases transcribing different sets of genes. Most RNA polymerases are multimeric enzymes and are composed of a variable number of subunits. The core RNA polymerase complex consists of five subunits (two alpha, one beta, one beta-prime and one omega) and 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 []. The core RNA polymerase complex forms a "crab claw"-like structure with an internal channel running along the full length []. The key functional sites of the enzyme, as defined by mutational and cross-linking analysis, are located on the inner wall of this channel. RNA synthesis follows after the attachment of RNA polymerase to a specific site, the promoter, on the template DNA strand. The RNA synthesis process continues until a termination sequence is reached. The RNA product, which is synthesised in the 5' to 3'direction, is known as the primary transcript. Eukaryotic nuclei contain three distinct types of RNA polymerases that differ in the RNA they synthesise: RNA polymerase I: located in the nucleoli, synthesises precursors of most ribosomal RNAs. RNA polymerase II: occurs in the nucleoplasm, synthesises mRNA precursors. RNA polymerase III: also occurs in the nucleoplasm, synthesises the precursors of 5S ribosomal RNA, the tRNAs, and a variety of other small nuclear and cytosolic RNAs. Eukaryotic cells are also known to contain separate mitochondrial and chloroplast RNA polymerases. Eukaryotic RNA polymerases, whose molecular masses vary in size from 500 to 700 kDa, contain two non-identical large (>100 kDa) subunits and an array of up to 12 different small (less than 50 kDa) subunits. The delta protein is a dispensable subunit of Bacillus subtilis RNA polymerase (RNAP) that has major effects on the biochemical properties of the purified enzyme. In the presence of delta, RNAP displays an increased specificity of transcription, a decreased affinity for nucleic acids, and an increased efficiency of RNA synthesis because of enhanced recycling []. The delta protein, contains two distinct regions, an N-terminal domain and a glutamate and aspartate residue-rich C-terminal region [].; GO: 0003677 DNA binding, 0006351 transcription, DNA-dependent; PDB: 2KRC_A.
Probab=24.83 E-value=1.1e+02 Score=22.57 Aligned_cols=34 Identities=21% Similarity=0.299 Sum_probs=21.7
Q ss_pred HHHHHHHHHhhcCCCCCCCeeCCeecchhhHHHHHHhcCchhhh
Q 020305 37 FWDTLRRFHFIMGTKFMIPVIGGKELDLHVLYVEATTRGGYEKV 80 (328)
Q Consensus 37 F~~~L~~F~~~~G~~~~~P~i~gk~lDL~~Ly~~V~~~GG~~~V 80 (328)
|.+.-..-++..|. ++....|+..|..+|++...
T Consensus 3 ~~eaa~~vL~~~~~----------pm~~~eI~~~i~~~~~~~~~ 36 (72)
T PF05066_consen 3 FKEAAYEVLEEAGR----------PMTFKEIWEEIQERGLYKKS 36 (72)
T ss_dssp HHHHHHHHHHHH-S-----------EEHHHHHHHHHHHHTS---
T ss_pred HHHHHHHHHHhcCC----------CcCHHHHHHHHHHhCCCCcc
Confidence 44555555555554 47889999999999999877
No 48
>PF12650 DUF3784: Domain of unknown function (DUF3784); InterPro: IPR017259 This group represents an uncharacterised conserved protein.
Probab=23.94 E-value=52 Score=25.94 Aligned_cols=17 Identities=24% Similarity=0.524 Sum_probs=13.9
Q ss_pred HHhccCChHHhHHHHHH
Q 020305 283 ESWTNLSPEERKVYQNI 299 (328)
Q Consensus 283 e~Wk~Ls~~eK~~Y~e~ 299 (328)
.-|+.||+|||+.|.++
T Consensus 24 aGyntms~eEk~~~D~~ 40 (97)
T PF12650_consen 24 AGYNTMSKEEKEKYDKK 40 (97)
T ss_pred hhcccCCHHHHHHhhHH
Confidence 34899999999999654
No 49
>PF00226 DnaJ: DnaJ domain; InterPro: IPR001623 The prokaryotic heat shock protein DnaJ interacts with the chaperone hsp70-like DnaK protein []. Structurally, the DnaJ protein consists of an N-terminal conserved domain (called 'J' domain) of about 70 amino acids, a glycine-rich region ('G' domain') of about 30 residues, a central domain containing four repeats of a CXXCXGXG motif ('CRR' domain) and a C-terminal region of 120 to 170 residues. Such a structure is shown in the following schematic representation: +------------+-+-------+-----+-----------+--------------------------------+ | N-terminal | | Gly-R | | CXXCXGXG | C-terminal | +------------+-+-------+-----+-----------+--------------------------------+ It is thought that the 'J' domain of DnaJ mediates the interaction with the dnaK protein and consists of four helices, the second of which has a charged surface that includes at least one pair of basic residues that are essential for interaction with the ATPase domain of Hsp70. The J- and CRR-domains are found in many prokaryotic and eukaryotic proteins [], either together or separately. In yeast, J-domains have been classified into 3 groups; the class III proteins are functionally distinct and do not appear to act as molecular chaperones []. ; GO: 0031072 heat shock protein binding; PDB: 2GUZ_C 2L6L_A 1HDJ_A 2EJ7_A 1FPO_C 2CUG_A 2QSA_A 2OCH_A 3BVO_B 3APQ_A ....
Probab=23.80 E-value=1.1e+02 Score=21.58 Aligned_cols=34 Identities=26% Similarity=0.245 Sum_probs=25.2
Q ss_pred HHHHHHHHhhCCC---ChH----HHHHHHHHHhccCChHHh
Q 020305 260 AEKHYKLKSLYPN---RER----EFTKMIGESWTNLSPEER 293 (328)
Q Consensus 260 ~e~r~~vk~~~P~---~~~----eisk~lge~Wk~Ls~~eK 293 (328)
+..+..++.-||+ ... +....|.+.|..|++.++
T Consensus 19 ~~y~~l~~~~HPD~~~~~~~~~~~~~~~i~~Ay~~L~~~~~ 59 (64)
T PF00226_consen 19 KAYRRLSKQYHPDKNSGDEAEAEEKFARINEAYEILSDPER 59 (64)
T ss_dssp HHHHHHHHHTSTTTGTSTHHHHHHHHHHHHHHHHHHHSHHH
T ss_pred HHHHhhhhccccccchhhhhhhhHHHHHHHHHHHHhCCHHH
Confidence 4456667788898 334 688889999999887665
No 50
>PF10545 MADF_DNA_bdg: Alcohol dehydrogenase transcription factor Myb/SANT-like; InterPro: IPR006578 The MADF (myb/SANT-like domain in Adf-1) domain is an approximately 80-amino-acid module that directs sequence specific DNA binding to a site consisting of multiple tri-nucleotide repeats. The MADF domain is found in one or more copies in eukaryotic and viral proteins and is often associated with the BESS domain []. MADF is related to the Myb DNA-binding domain (IPR001005 from INTERPRO). The retroviral oncogene v-myb, and its cellular counterpart c-myb, are nuclear DNA-binding proteins that specifically recognise the sequence YAAC(G/T)G. It is likely that the MADF domain is more closely related to the myb/SANT domain than it is to other HTH domains. Some proteins known to contain a MADF domain are listed below: Drosophila Adf-1, a transcription factor first identified on the basis of its interaction with the alcohol dehydrogenase promoter but that binds the promoters of a diverse group of genes []. Drosophila Dorsal-interacting protein 3 (Dip3), which functions both as an activator to bind DNA in a sequence specific manner and a coactivator to stimulate synergistic activation by Dorsal and Twist []. Drosophila Stonewall (Stwl), a putative transcription factor required for maintenance of female germline stem cells as well as oocyte differentiation.
Probab=22.69 E-value=55 Score=24.22 Aligned_cols=38 Identities=18% Similarity=0.240 Sum_probs=21.7
Q ss_pred hcccchHHHHhhhcCCCC---CCcHHHHHHHHHHHhhHHHH
Q 020305 81 VAEKKWREVGAVFKFSPT---TTSASFVLRKHYLTLLYHYE 118 (328)
Q Consensus 81 ~~~~~W~~Va~~lg~p~~---~~~as~~Lk~~Y~k~L~~yE 118 (328)
.....|.+|+..||...+ +...-..|+..|.+.+...+
T Consensus 24 ~r~~aw~~Ia~~l~~~~~~~~~~~~w~~Lr~~y~~~~~~~~ 64 (85)
T PF10545_consen 24 LREEAWQEIARELGKEFSVDDCKKRWKNLRDRYRRELKKIK 64 (85)
T ss_pred HHHHHHHHHHHHHccchhHHHHHHHHHHHHHHHHHHHHHHh
Confidence 456789999999984322 22222345555555544444
No 51
>PRK10236 hypothetical protein; Provisional
Probab=22.13 E-value=86 Score=29.50 Aligned_cols=24 Identities=8% Similarity=0.473 Sum_probs=20.5
Q ss_pred HHHHHHHHhccCChHHhHHHHHHH
Q 020305 277 FTKMIGESWTNLSPEERKVYQNIG 300 (328)
Q Consensus 277 isk~lge~Wk~Ls~~eK~~Y~e~A 300 (328)
+.+.+.+.|+.|+++|++.+.+.-
T Consensus 118 l~kll~~a~~kms~eE~~~L~~~l 141 (237)
T PRK10236 118 LEQFLRNTWKKMDEEHKQEFLHAV 141 (237)
T ss_pred HHHHHHHHHHHCCHHHHHHHHHHH
Confidence 588999999999999998886543
No 52
>KOG1610 consensus Corticosteroid 11-beta-dehydrogenase and related short chain-type dehydrogenases [Secondary metabolites biosynthesis, transport and catabolism; General function prediction only]
Probab=21.83 E-value=1.9e+02 Score=28.51 Aligned_cols=52 Identities=19% Similarity=0.339 Sum_probs=38.0
Q ss_pred hHHHHHHHHHHHHHhh-------CCC-------ChHHHHHHHHHHhccCChHHhHHHHHHHHHHHH
Q 020305 254 GYNFFFAEKHYKLKSL-------YPN-------REREFTKMIGESWTNLSPEERKVYQNIGLKDKE 305 (328)
Q Consensus 254 ay~lF~~e~r~~vk~~-------~P~-------~~~eisk~lge~Wk~Ls~~eK~~Y~e~A~~dke 305 (328)
|--.|+...|.++..- .|+ ....+.+.+.++|..|+++.|+.|-+.+..+..
T Consensus 184 aVeaf~D~lR~EL~~fGV~VsiiePG~f~T~l~~~~~~~~~~~~~w~~l~~e~k~~YGedy~~~~~ 249 (322)
T KOG1610|consen 184 AVEAFSDSLRRELRPFGVKVSIIEPGFFKTNLANPEKLEKRMKEIWERLPQETKDEYGEDYFEDYK 249 (322)
T ss_pred HHHHHHHHHHHHHHhcCcEEEEeccCccccccCChHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHH
Confidence 3455777777776642 243 346788999999999999999999877766533
No 53
>PRK09706 transcriptional repressor DicA; Reviewed
Probab=21.82 E-value=2.4e+02 Score=23.36 Aligned_cols=43 Identities=19% Similarity=0.122 Sum_probs=35.9
Q ss_pred HHHHHHHHhccCChHHhHHHHHHHHHHHHHHHHHHHHHHHhcc
Q 020305 277 FTKMIGESWTNLSPEERKVYQNIGLKDKERYNRELKEYKERLK 319 (328)
Q Consensus 277 isk~lge~Wk~Ls~~eK~~Y~e~A~~dkerY~~e~~~yk~~~k 319 (328)
-.+.|-+.|+.|+++++.......+...+.|.+-+++|-..-.
T Consensus 88 ~~~~ll~~~~~L~~~~~~~~l~~l~~~~~~~~~~~~~~~~~~~ 130 (135)
T PRK09706 88 DQKELLELFDALPESEQDAQLSEMRARVENFNKLFEELLKARK 130 (135)
T ss_pred HHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 3467888999999999999999999888888888888876433
No 54
>PHA03102 Small T antigen; Reviewed
Probab=20.99 E-value=1.1e+02 Score=26.71 Aligned_cols=35 Identities=11% Similarity=0.141 Sum_probs=27.2
Q ss_pred HHHHHHHHhhCCC--ChHHHHHHHHHHhccCChHHhH
Q 020305 260 AEKHYKLKSLYPN--REREFTKMIGESWTNLSPEERK 294 (328)
Q Consensus 260 ~e~r~~vk~~~P~--~~~eisk~lge~Wk~Ls~~eK~ 294 (328)
+.+|...+.-||| ...+..+.|.+.|..|++..+.
T Consensus 26 kAYr~la~~~HPDkgg~~e~~k~in~Ay~~L~d~~~r 62 (153)
T PHA03102 26 KAYLRKCLEFHPDKGGDEEKMKELNTLYKKFRESVKS 62 (153)
T ss_pred HHHHHHHHHHCcCCCchhHHHHHHHHHHHHHhhHHHh
Confidence 4566677888999 5677889999999999876553
No 55
>TIGR00787 dctP tripartite ATP-independent periplasmic transporter solute receptor, DctP family. TRAP-T (Tripartite ATP-independent Periplasmic Transporter) family proteins generally consist of three components, and these systems have so far been found in Gram-negative bacteria, Gram-postive bacteria and archaea. The best characterized example is the DctPQM system of Rhodobacter capsulatus, a C4 dicarboxylate (malate, fumarate, succinate) transporter. This model represents the DctP family, one of at least three major families of extracytoplasmic solute receptor for TRAP family transporters. Other are the SnoM family (see pfam03480) and TAXI (TRAP-associated extracytoplasmic immunogenic) family.
Probab=20.56 E-value=1.9e+02 Score=26.56 Aligned_cols=28 Identities=18% Similarity=0.353 Sum_probs=21.1
Q ss_pred HHHhccCChHHhHHHHHHHHHHHHHHHH
Q 020305 282 GESWTNLSPEERKVYQNIGLKDKERYNR 309 (328)
Q Consensus 282 ge~Wk~Ls~~eK~~Y~e~A~~dkerY~~ 309 (328)
.+.|..|+++.|+...+.+.+.-+....
T Consensus 213 ~~~~~~L~~e~q~~i~~a~~~~~~~~~~ 240 (257)
T TIGR00787 213 KAFWKSLPPDLQAVVKEAAKEAGEYQRK 240 (257)
T ss_pred HHHHhcCCHHHHHHHHHHHHHHHHHHHH
Confidence 3679999999999998877765444443
No 56
>cd07268 Glo_EDI_BRP_like_4 This conserved domain belongs to a superfamily including the bleomycin resistance protein, glyoxalase I, and type I ring-cleaving dioxygenases. This protein family belongs to a conserved domain superfamily that is found in a variety of structurally related metalloproteins, including the bleomycin resistance protein, glyoxalase I, and type I ring-cleaving dioxygenases. A bound metal ion is required for protein activities for the members of this superfamily. A variety of metal ions have been found in the catalytic centers of these proteins including Fe(II), Mn(II), Zn(II), Ni(II) and Mg(II). The protein superfamily contains members with or without domain swapping. The proteins of this family share three conserved metal binding amino acids with the type I extradiol dioxygenases, which shows no domain swapping.
Probab=20.18 E-value=34 Score=29.93 Aligned_cols=70 Identities=14% Similarity=0.099 Sum_probs=52.0
Q ss_pred CCCcccCChhHHHHHHHHHHhhcCCCCCCCeeCCeecchhhHHHHHHhcCchh----------hhhcccchHHHHhhhcC
Q 020305 26 SHEDVSKDPIVFWDTLRRFHFIMGTKFMIPVIGGKELDLHVLYVEATTRGGYE----------KVVAEKKWREVGAVFKF 95 (328)
Q Consensus 26 ~~e~~~~~~~~F~~~L~~F~~~~G~~~~~P~i~gk~lDL~~Ly~~V~~~GG~~----------~V~~~~~W~~Va~~lg~ 95 (328)
+|-++........++++.-+.+.|+-|.-=.|+||+|-||.|..-+.-.|..- +......|..|=-.+-.
T Consensus 3 DHialR~n~~~~A~~w~~~l~~~G~llSen~INGRPI~l~~L~qPl~~~~~~I~cvELP~P~~k~Yp~eGWEHIE~Vlp~ 82 (149)
T cd07268 3 DHIALRVNENQTAERWKEGLLQCGELLSENEINGRPIALIKLEKPLQFAGWSISIVELPFPKDKKYPQEGWEHIEIVIPS 82 (149)
T ss_pred ceEEEeeCCHHHHHHHHHHHHHhchhhhccccCCeeEEEEEcCCCceeCCcEEEEEEeCCCCCCCCCCCCceEEEEEecC
Confidence 44455566778889999999999999988999999999999988777555432 33335677776544443
Done!