Query 020330
Match_columns 327
No_of_seqs 296 out of 1606
Neff 6.4
Searched_HMMs 46136
Date Fri Mar 29 08:53:34 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/020330.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/020330hhsearch_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 2.8E-29 6.1E-34 253.4 12.1 185 23-207 153-339 (512)
2 smart00501 BRIGHT BRIGHT, ARID 99.9 1.3E-26 2.8E-31 185.1 9.6 91 32-122 1-92 (93)
3 PF01388 ARID: ARID/BRIGHT DNA 99.9 4E-25 8.6E-30 175.8 8.6 89 30-118 3-92 (92)
4 PTZ00199 high mobility group p 99.9 5.4E-22 1.2E-26 159.0 11.1 83 232-314 8-93 (94)
5 cd01389 MATA_HMG-box MATA_HMG- 99.8 1.2E-18 2.7E-23 134.2 7.7 73 246-318 1-74 (77)
6 cd01388 SOX-TCF_HMG-box SOX-TC 99.7 5.2E-18 1.1E-22 129.2 7.7 68 247-314 2-70 (72)
7 PF00505 HMG_box: HMG (high mo 99.7 1.5E-17 3.4E-22 124.4 9.1 68 247-314 1-69 (69)
8 PF09011 HMG_box_2: HMG-box do 99.7 2.5E-17 5.3E-22 125.7 9.2 71 244-314 1-73 (73)
9 COG5648 NHP6B Chromatin-associ 99.7 1.4E-17 3.1E-22 148.8 7.8 90 235-324 59-149 (211)
10 cd01390 HMGB-UBF_HMG-box HMGB- 99.7 5.1E-17 1.1E-21 120.4 9.0 65 247-311 1-66 (66)
11 smart00398 HMG high mobility g 99.7 1E-16 2.2E-21 119.6 8.9 69 246-314 1-70 (70)
12 KOG0381 HMG box-containing pro 99.7 2.3E-16 4.9E-21 126.0 10.7 75 243-317 17-95 (96)
13 cd00084 HMG-box High Mobility 99.6 3.9E-15 8.4E-20 109.8 9.0 64 247-310 1-65 (66)
14 KOG0526 Nucleosome-binding fac 99.6 1.2E-15 2.5E-20 151.6 7.2 78 234-315 523-601 (615)
15 KOG0527 HMG-box transcription 99.6 3.4E-15 7.4E-20 143.8 6.8 82 240-321 56-138 (331)
16 KOG3248 Transcription factor T 99.2 3.8E-11 8.1E-16 114.0 10.6 73 245-317 190-263 (421)
17 KOG2510 SWI-SNF chromatin-remo 99.2 3.4E-11 7.3E-16 119.3 7.1 91 32-129 292-383 (532)
18 KOG0528 HMG-box transcription 99.0 2.1E-10 4.6E-15 113.5 3.9 119 184-320 280-400 (511)
19 KOG4715 SWI/SNF-related matrix 98.9 1.6E-09 3.4E-14 102.3 6.6 76 241-316 59-135 (410)
20 KOG2746 HMG-box transcription 98.3 5.1E-07 1.1E-11 92.8 4.9 74 236-309 171-247 (683)
21 PF14887 HMG_box_5: HMG (high 97.9 8.2E-05 1.8E-09 57.1 7.6 73 246-319 3-76 (85)
22 PF04690 YABBY: YABBY protein; 96.8 0.0022 4.8E-08 56.7 5.5 46 243-288 118-164 (170)
23 COG5648 NHP6B Chromatin-associ 96.5 0.0023 4.9E-08 58.1 3.5 67 245-311 142-209 (211)
24 PF06382 DUF1074: Protein of u 95.8 0.046 9.9E-07 48.6 7.9 48 251-302 83-131 (183)
25 PF08073 CHDNT: CHDNT (NUC034) 89.8 0.56 1.2E-05 34.0 3.9 38 251-288 13-51 (55)
26 PF04769 MAT_Alpha1: Mating-ty 87.5 1.5 3.3E-05 40.0 6.1 55 240-300 37-92 (201)
27 PF06244 DUF1014: Protein of u 84.9 1.1 2.4E-05 37.7 3.6 45 246-290 72-117 (122)
28 TIGR01624 LRP1_Cterm LRP1 C-te 82.9 0.75 1.6E-05 32.4 1.5 34 170-203 14-48 (50)
29 PF00249 Myb_DNA-binding: Myb- 81.9 2.9 6.3E-05 28.7 4.2 38 66-114 11-48 (48)
30 PF05142 DUF702: Domain of unk 79.9 1.1 2.3E-05 39.2 1.7 34 170-203 116-149 (154)
31 TIGR03481 HpnM hopanoid biosyn 77.4 5.3 0.00012 36.1 5.6 45 272-316 65-111 (198)
32 PRK15117 ABC transporter perip 71.0 15 0.00032 33.6 6.9 47 270-316 66-115 (211)
33 PF09441 Abp2: ARS binding pro 63.5 12 0.00027 32.9 4.4 42 53-98 44-85 (175)
34 KOG3223 Uncharacterized conser 61.7 5.2 0.00011 36.2 1.8 52 245-299 162-215 (221)
35 PF13921 Myb_DNA-bind_6: Myb-l 57.6 19 0.00042 25.5 4.0 37 66-115 8-44 (60)
36 cd00167 SANT 'SWI3, ADA2, N-Co 52.9 27 0.00058 22.3 3.8 37 66-114 9-45 (45)
37 PF05494 Tol_Tol_Ttg2: Toluene 51.9 16 0.00035 31.8 3.3 44 272-315 39-84 (170)
38 PF11304 DUF3106: Protein of u 47.6 69 0.0015 26.1 6.2 42 274-315 10-58 (107)
39 COG2854 Ttg2D ABC-type transpo 44.4 34 0.00074 31.3 4.3 43 276-318 76-119 (202)
40 PF13873 Myb_DNA-bind_5: Myb/S 44.4 32 0.00069 25.7 3.5 54 62-115 14-70 (78)
41 smart00717 SANT SANT SWI3, AD 35.6 73 0.0016 20.4 3.9 26 84-114 22-47 (49)
42 PF12776 Myb_DNA-bind_3: Myb/S 32.0 52 0.0011 25.3 3.1 60 64-123 10-71 (96)
43 PRK10236 hypothetical protein; 28.7 1E+02 0.0022 29.0 4.8 46 253-298 88-140 (237)
44 PF10545 MADF_DNA_bdg: Alcohol 26.8 55 0.0012 24.2 2.3 38 81-118 24-64 (85)
45 PF12881 NUT_N: NUT protein N 26.6 1.7E+02 0.0037 28.6 6.0 64 253-316 231-296 (328)
46 PRK12750 cpxP periplasmic repr 26.4 2.1E+02 0.0046 25.3 6.3 35 276-310 126-160 (170)
47 PF12650 DUF3784: Domain of un 25.7 46 0.001 26.2 1.8 17 282-298 24-40 (97)
48 PF13875 DUF4202: Domain of un 24.5 1.4E+02 0.0031 26.9 4.8 40 252-293 130-169 (185)
49 PRK09706 transcriptional repre 24.2 2.1E+02 0.0046 23.7 5.7 43 276-318 88-130 (135)
50 PLN03212 Transcription repress 23.3 1.1E+02 0.0023 29.0 3.9 39 67-116 36-74 (249)
51 KOG1610 Corticosteroid 11-beta 23.0 1.7E+02 0.0038 28.6 5.4 58 254-314 185-256 (322)
52 PRK12751 cpxP periplasmic stre 22.5 1.8E+02 0.0039 25.6 5.0 27 277-303 120-146 (162)
53 PF00226 DnaJ: DnaJ domain; I 22.0 1.4E+02 0.003 21.0 3.6 34 259-292 19-59 (64)
54 TIGR00787 dctP tripartite ATP- 21.6 1.8E+02 0.0039 26.7 5.2 27 282-308 214-240 (257)
55 PF04967 HTH_10: HTH DNA bindi 21.4 76 0.0016 22.7 2.0 40 73-114 13-52 (53)
56 PF05066 HARE-HTH: HB1, ASXL, 21.4 69 0.0015 23.6 1.9 22 59-80 15-36 (72)
57 TIGR01557 myb_SHAQKYF myb-like 20.5 1.4E+02 0.0029 21.6 3.2 43 63-116 9-56 (57)
58 PF08914 Myb_DNA-bind_2: Rap1 20.5 1.3E+02 0.0028 22.4 3.1 52 66-121 12-64 (65)
No 1
>KOG2744 consensus DNA-binding proteins Bright/BRCAA1/RBP1 and related proteins containing BRIGHT domain [Transcription]
Probab=99.96 E-value=2.8e-29 Score=253.36 Aligned_cols=185 Identities=40% Similarity=0.495 Sum_probs=152.7
Q ss_pred CCCCCCcccCChHHHHHHHHHHHhhcCCCCC-CCeeCCeecchhhhHHHHHhcCchhhhhcccchHHhHhhhcCCC-CCC
Q 020330 23 PLSSHEDVSKDPIVFWDTLRRFHFIMGTKFM-IPVIGGKELDLHVLYVEATTRGGYEKVVAEKKWREVGAVFKFSP-TTT 100 (327)
Q Consensus 23 ~~~~~e~~~~~~~~F~~~L~~F~~~~G~~~~-~P~i~gk~lDL~~Ly~~V~~~GG~~~V~~~~~W~eV~~~l~~p~-~~~ 100 (327)
++...|.+..+++.||++|+.||+.+|++|+ +|+|+|++||||.||.+|+++||+++|+..++|++|+..|+||. ++|
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 6667777778999999999999999999996 99999999999999999999999999999999999999999999 999
Q ss_pred cHHHHHHHHHHHhhhhhhhhhhhcccCCCCCCCCcccCCCCCCCCCcccccCCcccccCCCCCCcCCCCCceeeeeeccc
Q 020330 101 SASFVLRKHYLTLLYHYEQVHFFKMQGPPCVPSASFSVHSPSCRPGLALVEYSPKRINDHPDSHIEGQSCFTAVGRIDGK 180 (327)
Q Consensus 101 ~~s~~Lk~~Y~k~L~~yE~~~~~~~~~~~~~p~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~g~Idgk 180 (327)
+++|.|+++|+++|++|||.+++.+..+...|.......+++-..+....+.+++.......+....++...+.++|+|+
T Consensus 233 saaf~lr~~y~K~L~~ye~~~~~~~~~pln~p~~~~~~a~~~~~rE~~~~~~~~~~~~~~~~~~~~~~~~~~aa~~~~g~ 312 (512)
T KOG2744|consen 233 SAAFTLRKQYLKLLFEYECEFEKNRHVPLNSPAELSEEASSSNRREGRRHELSPSKEFQANGPSEEEPAEAEAAPEILGN 312 (512)
T ss_pred hHHHHHHHHHHHHHHHHHHHHHHhccCCCCCcccccccccccccccccccccCcchhhccCCcccccccccccchhhhcc
Confidence 99999999999999999999999877666666543321233333333444444543333322333334466789999999
Q ss_pred cCCCceeEEeeccccccccccCCCCCC
Q 020330 181 FDCGYLVSVKLGSETLSGVLYHPDHPG 207 (327)
Q Consensus 181 fd~gylvtv~~gse~~~g~ly~~~~~~ 207 (327)
|++||+|++.+|++.++|++|+.++..
T Consensus 313 f~~~~~~~~~~~s~~ln~~~~~~~~~~ 339 (512)
T KOG2744|consen 313 FLQGLLVFMKDGSEPLNGVLYLGPPDL 339 (512)
T ss_pred ccccCceeccCcchhccCccccccCcc
Confidence 999999999999999999999997765
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=1.3e-26 Score=185.13 Aligned_cols=91 Identities=41% Similarity=0.679 Sum_probs=87.0
Q ss_pred CChHHHHHHHHHHHhhcCCCC-CCCeeCCeecchhhhHHHHHhcCchhhhhcccchHHhHhhhcCCCCCCcHHHHHHHHH
Q 020330 32 KDPIVFWDTLRRFHFIMGTKF-MIPVIGGKELDLHVLYVEATTRGGYEKVVAEKKWREVGAVFKFSPTTTSASFVLRKHY 110 (327)
Q Consensus 32 ~~~~~F~~~L~~F~~~~G~~~-~~P~i~gk~lDL~~Ly~~V~~~GG~~~V~~~~~W~eV~~~l~~p~~~~~~s~~Lk~~Y 110 (327)
++++.|++.|.+||+.+|+++ .+|+|+|++||||+||.+|+++|||++||.+++|.+|++.||++++++++++.|+++|
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 478999999999999999998 7999999999999999999999999999999999999999999988899999999999
Q ss_pred HHhhhhhhhhhh
Q 020330 111 LTLLYHYEQVHF 122 (327)
Q Consensus 111 ~k~L~~yE~~~~ 122 (327)
.+||++||+++.
T Consensus 81 ~k~L~~yE~~~~ 92 (93)
T smart00501 81 ERYLLPFERFLR 92 (93)
T ss_pred HHHhHHHHHHhh
Confidence 999999999753
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=4e-25 Score=175.76 Aligned_cols=89 Identities=44% Similarity=0.730 Sum_probs=82.1
Q ss_pred ccCChHHHHHHHHHHHhhcCCCC-CCCeeCCeecchhhhHHHHHhcCchhhhhcccchHHhHhhhcCCCCCCcHHHHHHH
Q 020330 30 VSKDPIVFWDTLRRFHFIMGTKF-MIPVIGGKELDLHVLYVEATTRGGYEKVVAEKKWREVGAVFKFSPTTTSASFVLRK 108 (327)
Q Consensus 30 ~~~~~~~F~~~L~~F~~~~G~~~-~~P~i~gk~lDL~~Ly~~V~~~GG~~~V~~~~~W~eV~~~l~~p~~~~~~s~~Lk~ 108 (327)
...+++.|++.|.+||+.+|+++ .+|+|+|++||||+||.+|+.+|||++|+.+++|.+||+.||+++.+++.+..|++
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 45678999999999999999997 79999999999999999999999999999999999999999999988888899999
Q ss_pred HHHHhhhhhh
Q 020330 109 HYLTLLYHYE 118 (327)
Q Consensus 109 ~Y~k~L~~yE 118 (327)
+|++||++||
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=5.4e-22 Score=159.03 Aligned_cols=83 Identities=35% Similarity=0.591 Sum_probs=77.4
Q ss_pred ccccccCCCCCCCCCCCCCCChHHHHHHHHHHHHHhhCCC-C--hHHHHHHHHHHhhcCChHHHHHHHHHHHHHHHHHHH
Q 020330 232 YGRRRRSKRRGDPSYPKPNRSGYNFFFAEKHYKLKSLYPN-R--EREFTKMIGESWTNLSPEERKVYQNIGLKDKERYNR 308 (327)
Q Consensus 232 ~~kkk~~k~~kdp~~PKrP~say~lF~~e~r~~vk~e~p~-~--~~eisk~lge~Wk~Ls~eeK~~Y~e~a~~dkery~~ 308 (327)
+.+|+++++++||++||||+|||+||+.++|..|+.+||+ . +.+|+++||++|+.|++++|++|+++|+.|+++|..
T Consensus 8 ~~~k~~~k~~kdp~~PKrP~sAY~~F~~~~R~~i~~~~P~~~~~~~evsk~ige~Wk~ls~eeK~~y~~~A~~dk~rY~~ 87 (94)
T PTZ00199 8 VLVRKNKRKKKDPNAPKRALSAYMFFAKEKRAEIIAENPELAKDVAAVGKMVGEAWNKLSEEEKAPYEKKAQEDKVRYEK 87 (94)
T ss_pred ccccccCCCCCCCCCCCCCCcHHHHHHHHHHHHHHHHCcCCcccHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHH
Confidence 3455666778999999999999999999999999999999 4 799999999999999999999999999999999999
Q ss_pred HHHHHH
Q 020330 309 ELKEYK 314 (327)
Q Consensus 309 e~~~yk 314 (327)
+|.+|+
T Consensus 88 e~~~Y~ 93 (94)
T PTZ00199 88 EKAEYA 93 (94)
T ss_pred HHHHHh
Confidence 999996
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=1.2e-18 Score=134.19 Aligned_cols=73 Identities=29% Similarity=0.539 Sum_probs=69.7
Q ss_pred CCCCCCChHHHHHHHHHHHHHhhCCC-ChHHHHHHHHHHhhcCChHHHHHHHHHHHHHHHHHHHHHHHHHHhcc
Q 020330 246 YPKPNRSGYNFFFAEKHYKLKSLYPN-REREFTKMIGESWTNLSPEERKVYQNIGLKDKERYNRELKEYKERLK 318 (327)
Q Consensus 246 ~PKrP~say~lF~~e~r~~vk~e~p~-~~~eisk~lge~Wk~Ls~eeK~~Y~e~a~~dkery~~e~~~yk~~~k 318 (327)
+||||+|||+||+++.|..|+.+||+ ++.+|+++||++|+.|++++|++|+++|++++++|.+++++|+-.-+
T Consensus 1 ~~kRP~naf~lf~~~~r~~~~~~~p~~~~~eisk~~g~~Wk~ls~eeK~~y~~~A~~~k~~~~~~~p~Yky~p~ 74 (77)
T cd01389 1 KIPRPRNAFILYRQDKHAQLKTENPGLTNNEISRIIGRMWRSESPEVKAYYKELAEEEKERHAREYPDYKYTPR 74 (77)
T ss_pred CCCCCCcHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHhhCCHHHHHHHHHHHHHHHHHHHHHCCCCcccCC
Confidence 58999999999999999999999999 99999999999999999999999999999999999999999986543
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=5.2e-18 Score=129.17 Aligned_cols=68 Identities=28% Similarity=0.441 Sum_probs=66.4
Q ss_pred CCCCCChHHHHHHHHHHHHHhhCCC-ChHHHHHHHHHHhhcCChHHHHHHHHHHHHHHHHHHHHHHHHH
Q 020330 247 PKPNRSGYNFFFAEKHYKLKSLYPN-REREFTKMIGESWTNLSPEERKVYQNIGLKDKERYNRELKEYK 314 (327)
Q Consensus 247 PKrP~say~lF~~e~r~~vk~e~p~-~~~eisk~lge~Wk~Ls~eeK~~Y~e~a~~dkery~~e~~~yk 314 (327)
.|||+|||++|++++|.+++.+||+ ++.||+++||++|+.|++++|++|.++|++++++|.+++++|+
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=99.73 E-value=1.5e-17 Score=124.44 Aligned_cols=68 Identities=38% Similarity=0.708 Sum_probs=65.0
Q ss_pred CCCCCChHHHHHHHHHHHHHhhCCC-ChHHHHHHHHHHhhcCChHHHHHHHHHHHHHHHHHHHHHHHHH
Q 020330 247 PKPNRSGYNFFFAEKHYKLKSLYPN-REREFTKMIGESWTNLSPEERKVYQNIGLKDKERYNRELKEYK 314 (327)
Q Consensus 247 PKrP~say~lF~~e~r~~vk~e~p~-~~~eisk~lge~Wk~Ls~eeK~~Y~e~a~~dkery~~e~~~yk 314 (327)
||||+|||++|+.+++..++.+||+ +..+|+++||++|++|++++|++|.++|++++++|.++|++|+
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=99.72 E-value=2.5e-17 Score=125.75 Aligned_cols=71 Identities=41% Similarity=0.645 Sum_probs=63.0
Q ss_pred CCCCCCCCChHHHHHHHHHHHHHhh-CCC-ChHHHHHHHHHHhhcCChHHHHHHHHHHHHHHHHHHHHHHHHH
Q 020330 244 PSYPKPNRSGYNFFFAEKHYKLKSL-YPN-REREFTKMIGESWTNLSPEERKVYQNIGLKDKERYNRELKEYK 314 (327)
Q Consensus 244 p~~PKrP~say~lF~~e~r~~vk~e-~p~-~~~eisk~lge~Wk~Ls~eeK~~Y~e~a~~dkery~~e~~~yk 314 (327)
|++||+|+|||+||+.+++..++.. .+. ...|+++.|+++|++||++||.+|+++|+.++++|+.+|..|+
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 566 8999999999999999999999999999999999999999995
No 9
>COG5648 NHP6B Chromatin-associated proteins containing the HMG domain [Chromatin structure and dynamics]
Probab=99.71 E-value=1.4e-17 Score=148.76 Aligned_cols=90 Identities=31% Similarity=0.552 Sum_probs=84.2
Q ss_pred cccCCCCCCCCCCCCCCChHHHHHHHHHHHHHhhCCC-ChHHHHHHHHHHhhcCChHHHHHHHHHHHHHHHHHHHHHHHH
Q 020330 235 RRRSKRRGDPSYPKPNRSGYNFFFAEKHYKLKSLYPN-REREFTKMIGESWTNLSPEERKVYQNIGLKDKERYNRELKEY 313 (327)
Q Consensus 235 kk~~k~~kdp~~PKrP~say~lF~~e~r~~vk~e~p~-~~~eisk~lge~Wk~Ls~eeK~~Y~e~a~~dkery~~e~~~y 313 (327)
+..+++++||+.||||+||||+|++++|.+++.++|. ++.++.+.+|++|++|+++||++|.+.|..++++|..++..|
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 020330 314 KERLKLRQGEG 324 (327)
Q Consensus 314 k~~~k~~~~~~ 324 (327)
..........+
T Consensus 139 ~~k~~~~~~~~ 149 (211)
T COG5648 139 NKKLPNKAPIG 149 (211)
T ss_pred hcccCCCCCCc
Confidence 99887766544
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=99.71 E-value=5.1e-17 Score=120.45 Aligned_cols=65 Identities=46% Similarity=0.720 Sum_probs=63.3
Q ss_pred CCCCCChHHHHHHHHHHHHHhhCCC-ChHHHHHHHHHHhhcCChHHHHHHHHHHHHHHHHHHHHHH
Q 020330 247 PKPNRSGYNFFFAEKHYKLKSLYPN-REREFTKMIGESWTNLSPEERKVYQNIGLKDKERYNRELK 311 (327)
Q Consensus 247 PKrP~say~lF~~e~r~~vk~e~p~-~~~eisk~lge~Wk~Ls~eeK~~Y~e~a~~dkery~~e~~ 311 (327)
||||+|||++|++++|..++.+||+ +..+|++.||++|++|++++|++|.++|++++++|..+|.
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=1e-16 Score=119.65 Aligned_cols=69 Identities=41% Similarity=0.660 Sum_probs=67.1
Q ss_pred CCCCCCChHHHHHHHHHHHHHhhCCC-ChHHHHHHHHHHhhcCChHHHHHHHHHHHHHHHHHHHHHHHHH
Q 020330 246 YPKPNRSGYNFFFAEKHYKLKSLYPN-REREFTKMIGESWTNLSPEERKVYQNIGLKDKERYNRELKEYK 314 (327)
Q Consensus 246 ~PKrP~say~lF~~e~r~~vk~e~p~-~~~eisk~lge~Wk~Ls~eeK~~Y~e~a~~dkery~~e~~~yk 314 (327)
+||+|+|||++|++++|..++.+||+ +..+|+++||++|+.|++++|++|.++|+.++++|..++..|+
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=99.68 E-value=2.3e-16 Score=126.01 Aligned_cols=75 Identities=40% Similarity=0.654 Sum_probs=71.8
Q ss_pred CC--CCCCCCCChHHHHHHHHHHHHHhhCCC-ChHHHHHHHHHHhhcCChHHHHHHHHHHHHHHHHHHHHHH-HHHHhc
Q 020330 243 DP--SYPKPNRSGYNFFFAEKHYKLKSLYPN-REREFTKMIGESWTNLSPEERKVYQNIGLKDKERYNRELK-EYKERL 317 (327)
Q Consensus 243 dp--~~PKrP~say~lF~~e~r~~vk~e~p~-~~~eisk~lge~Wk~Ls~eeK~~Y~e~a~~dkery~~e~~-~yk~~~ 317 (327)
|| +.||||+|||++|+.+.|.+++.+||+ ++.+|++++|++|++|++++|++|+.+|.+++++|..+|. +|+...
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=3.9e-15 Score=109.77 Aligned_cols=64 Identities=41% Similarity=0.676 Sum_probs=62.3
Q ss_pred CCCCCChHHHHHHHHHHHHHhhCCC-ChHHHHHHHHHHhhcCChHHHHHHHHHHHHHHHHHHHHH
Q 020330 247 PKPNRSGYNFFFAEKHYKLKSLYPN-REREFTKMIGESWTNLSPEERKVYQNIGLKDKERYNREL 310 (327)
Q Consensus 247 PKrP~say~lF~~e~r~~vk~e~p~-~~~eisk~lge~Wk~Ls~eeK~~Y~e~a~~dkery~~e~ 310 (327)
||||+|||++|+++.+..++.++|+ +..+|+++||++|+.|++++|++|.++|+.++++|..++
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
>KOG0526 consensus Nucleosome-binding factor SPN, POB3 subunit [Transcription; Replication, recombination and repair; Chromatin structure and dynamics]
Probab=99.60 E-value=1.2e-15 Score=151.55 Aligned_cols=78 Identities=28% Similarity=0.601 Sum_probs=73.6
Q ss_pred ccccCCCCCCCCCCCCCCChHHHHHHHHHHHHHhhCCC-ChHHHHHHHHHHhhcCChHHHHHHHHHHHHHHHHHHHHHHH
Q 020330 234 RRRRSKRRGDPSYPKPNRSGYNFFFAEKHYKLKSLYPN-REREFTKMIGESWTNLSPEERKVYQNIGLKDKERYNRELKE 312 (327)
Q Consensus 234 kkk~~k~~kdp~~PKrP~say~lF~~e~r~~vk~e~p~-~~~eisk~lge~Wk~Ls~eeK~~Y~e~a~~dkery~~e~~~ 312 (327)
++++.|+++||++|||++||||+|++..|..||.+ + +++||+|++|++|+.|+. |.+|+++|+.||+||+.||.+
T Consensus 523 ~~k~~kk~kdpnapkra~sa~m~w~~~~r~~ik~d--gi~~~dv~kk~g~~wk~ms~--k~~we~ka~~dk~ry~~em~~ 598 (615)
T KOG0526|consen 523 KKKKGKKKKDPNAPKRATSAYMLWLNASRESIKED--GISVGDVAKKAGEKWKQMSA--KEEWEDKAAVDKQRYEDEMKE 598 (615)
T ss_pred cccCcccCCCCCCCccchhHHHHHHHhhhhhHhhc--CchHHHHHHHHhHHHhhhcc--cchhhHHHHHHHHHHHHHHHh
Confidence 44566788999999999999999999999999999 7 999999999999999999 999999999999999999999
Q ss_pred HHH
Q 020330 313 YKE 315 (327)
Q Consensus 313 yk~ 315 (327)
|+.
T Consensus 599 yk~ 601 (615)
T KOG0526|consen 599 YKN 601 (615)
T ss_pred hcC
Confidence 993
No 15
>KOG0527 consensus HMG-box transcription factor [Transcription]
Probab=99.56 E-value=3.4e-15 Score=143.78 Aligned_cols=82 Identities=20% Similarity=0.342 Sum_probs=76.1
Q ss_pred CCCCCCCCCCCCChHHHHHHHHHHHHHhhCCC-ChHHHHHHHHHHhhcCChHHHHHHHHHHHHHHHHHHHHHHHHHHhcc
Q 020330 240 RRGDPSYPKPNRSGYNFFFAEKHYKLKSLYPN-REREFTKMIGESWTNLSPEERKVYQNIGLKDKERYNRELKEYKERLK 318 (327)
Q Consensus 240 ~~kdp~~PKrP~say~lF~~e~r~~vk~e~p~-~~~eisk~lge~Wk~Ls~eeK~~Y~e~a~~dkery~~e~~~yk~~~k 318 (327)
.++...+.||||||||+|.+..|.+|.+++|. .+.||+|+||.+||.|+++||.+|.+.|++.|+.|++|..+|+-+-+
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 99999999999999999999999999999999999999999998765
Q ss_pred ccc
Q 020330 319 LRQ 321 (327)
Q Consensus 319 ~~~ 321 (327)
...
T Consensus 136 RKk 138 (331)
T KOG0527|consen 136 RKK 138 (331)
T ss_pred ccc
Confidence 543
No 16
>KOG3248 consensus Transcription factor TCF-4 [Transcription]
Probab=99.25 E-value=3.8e-11 Score=113.95 Aligned_cols=73 Identities=16% Similarity=0.281 Sum_probs=67.7
Q ss_pred CCCCCCCChHHHHHHHHHHHHHhhCCC-ChHHHHHHHHHHhhcCChHHHHHHHHHHHHHHHHHHHHHHHHHHhc
Q 020330 245 SYPKPNRSGYNFFFAEKHYKLKSLYPN-REREFTKMIGESWTNLSPEERKVYQNIGLKDKERYNRELKEYKERL 317 (327)
Q Consensus 245 ~~PKrP~say~lF~~e~r~~vk~e~p~-~~~eisk~lge~Wk~Ls~eeK~~Y~e~a~~dkery~~e~~~yk~~~ 317 (327)
.+-|+|+|||+||++|+|++|.+|... .-.+|+++||++|++||.||.++|.|+|+++|+.+++-..+|-++.
T Consensus 190 phiKKPLNAFmlyMKEmRa~vvaEctlKeSAaiNqiLGrRWH~LSrEEQAKYyElArKerqlH~qlYP~WSARd 263 (421)
T KOG3248|consen 190 PHIKKPLNAFMLYMKEMRAKVVAECTLKESAAINQILGRRWHALSREEQAKYYELARKERQLHMQLYPGWSARD 263 (421)
T ss_pred ccccccHHHHHHHHHHHHHHHHHHhhhhhHHHHHHHHhHHHhhhhHHHHHHHHHHHHHHHHHHHHhcCCcchhh
Confidence 367999999999999999999999988 7789999999999999999999999999999999999988887643
No 17
>KOG2510 consensus SWI-SNF chromatin-remodeling complex protein [Chromatin structure and dynamics]
Probab=99.18 E-value=3.4e-11 Score=119.26 Aligned_cols=91 Identities=30% Similarity=0.464 Sum_probs=83.1
Q ss_pred CChHHHHHHHHHHHhhcCCCC-CCCeeCCeecchhhhHHHHHhcCchhhhhcccchHHhHhhhcCCCCCCcHHHHHHHHH
Q 020330 32 KDPIVFWDTLRRFHFIMGTKF-MIPVIGGKELDLHVLYVEATTRGGYEKVVAEKKWREVGAVFKFSPTTTSASFVLRKHY 110 (327)
Q Consensus 32 ~~~~~F~~~L~~F~~~~G~~~-~~P~i~gk~lDL~~Ly~~V~~~GG~~~V~~~~~W~eV~~~l~~p~~~~~~s~~Lk~~Y 110 (327)
.+++..+++|+.|++.+.+++ ..|.++.++||||+||..|..+||+..|+.++ ++++.-|| .+++..||++|
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 688899999999999999999 48999999999999999999999999999998 99999988 46888999999
Q ss_pred HHhhhhhhhhhhhcccCCC
Q 020330 111 LTLLYHYEQVHFFKMQGPP 129 (327)
Q Consensus 111 ~k~L~~yE~~~~~~~~~~~ 129 (327)
.+||+.|||.+..+.+.++
T Consensus 365 ~~~lf~fec~f~Rg~e~p~ 383 (532)
T KOG2510|consen 365 IQYLFAFECKFERGEEPPP 383 (532)
T ss_pred HHHHHhhceeeeccCCCCH
Confidence 9999999998776665544
No 18
>KOG0528 consensus HMG-box transcription factor SOX5 [Transcription]
Probab=99.00 E-value=2.1e-10 Score=113.46 Aligned_cols=119 Identities=15% Similarity=0.268 Sum_probs=90.2
Q ss_pred CceeEEeeccccccccccCCCCCCC-CCccCCCCCcccccCCCCCCcccccccccCCCCCCCCCCCCCCChHHHHHHHHH
Q 020330 184 GYLVSVKLGSETLSGVLYHPDHPGP-STSFCQSNDVGAIIPYTPNSKRRYGRRRRSKRRGDPSYPKPNRSGYNFFFAEKH 262 (327)
Q Consensus 184 gylvtv~~gse~~~g~ly~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~r~~kkk~~k~~kdp~~PKrP~say~lF~~e~r 262 (327)
+|-..++.++ +|.|.|....+. +...+|+.+..+. | +-+...+.+.||||||||+|.++.|
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 4545555554 488888877665 3333444333222 0 1223445678999999999999999
Q ss_pred HHHHhhCCC-ChHHHHHHHHHHhhcCChHHHHHHHHHHHHHHHHHHHHHHHHHHhcccc
Q 020330 263 YKLKSLYPN-REREFTKMIGESWTNLSPEERKVYQNIGLKDKERYNRELKEYKERLKLR 320 (327)
Q Consensus 263 ~~vk~e~p~-~~~eisk~lge~Wk~Ls~eeK~~Y~e~a~~dkery~~e~~~yk~~~k~~ 320 (327)
.+|.+..|+ ....|+|+||.+|+.|+..||++|.|.-.+.-..|.+..++|+-+-+..
T Consensus 342 RKILqA~PDMHNSnISKILGSRWKaMSN~eKQPYYEEQaRLSk~HlEk~PdYrYkPRPK 400 (511)
T KOG0528|consen 342 RKILQAFPDMHNSNISKILGSRWKAMSNTEKQPYYEEQARLSKLHLEKYPDYRYKPRPK 400 (511)
T ss_pred hhhhhcCccccccchhHHhcccccccccccccchHHHHHHHHHhhhccCcccccCCCCC
Confidence 999999999 8899999999999999999999998877777779999999988765543
No 19
>KOG4715 consensus SWI/SNF-related matrix-associated actin-dependent regulator of chromatin [Chromatin structure and dynamics]
Probab=98.93 E-value=1.6e-09 Score=102.29 Aligned_cols=76 Identities=26% Similarity=0.404 Sum_probs=71.7
Q ss_pred CCCCCCCCCCCChHHHHHHHHHHHHHhhCCC-ChHHHHHHHHHHhhcCChHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 020330 241 RGDPSYPKPNRSGYNFFFAEKHYKLKSLYPN-REREFTKMIGESWTNLSPEERKVYQNIGLKDKERYNRELKEYKER 316 (327)
Q Consensus 241 ~kdp~~PKrP~say~lF~~e~r~~vk~e~p~-~~~eisk~lge~Wk~Ls~eeK~~Y~e~a~~dkery~~e~~~yk~~ 316 (327)
.+-|.+|-+|+-.||.|+...+++|++.||+ ...||.|+||.||..|+++||+.|...++.+|..|.+.|..|...
T Consensus 59 pkpPkppekpl~pymrySrkvWd~VkA~nPe~kLWeiGK~Ig~mW~dLpd~EK~ey~~EYeaEKieY~~smkayh~s 135 (410)
T KOG4715|consen 59 PKPPKPPEKPLMPYMRYSRKVWDQVKASNPELKLWEIGKIIGGMWLDLPDEEKQEYLNEYEAEKIEYNESMKAYHNS 135 (410)
T ss_pred CCCCCCCCcccchhhHHhhhhhhhhhccCcchHHHHHHHHHHHHHhhCcchHHHHHHHHHHHHHHHHHHHHHHhhCC
Confidence 3467788999999999999999999999999 999999999999999999999999999999999999999998763
No 20
>KOG2746 consensus HMG-box transcription factor Capicua and related proteins [Transcription]
Probab=98.32 E-value=5.1e-07 Score=92.84 Aligned_cols=74 Identities=23% Similarity=0.462 Sum_probs=68.6
Q ss_pred ccCCCCCCCCCCCCCCChHHHHHHHHH--HHHHhhCCC-ChHHHHHHHHHHhhcCChHHHHHHHHHHHHHHHHHHHH
Q 020330 236 RRSKRRGDPSYPKPNRSGYNFFFAEKH--YKLKSLYPN-REREFTKMIGESWTNLSPEERKVYQNIGLKDKERYNRE 309 (327)
Q Consensus 236 k~~k~~kdp~~PKrP~say~lF~~e~r--~~vk~e~p~-~~~eisk~lge~Wk~Ls~eeK~~Y~e~a~~dkery~~e 309 (327)
.+..-++|..+.++|||||++|++.+| ..+.+.||+ .++-|+++||+.|-.|.+.||+.|.+.|.+.|+.|.++
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 345566778899999999999999999 999999999 99999999999999999999999999999999999886
No 21
>PF14887 HMG_box_5: HMG (high mobility group) box 5; PDB: 1L8Y_A 1L8Z_A 2HDZ_A.
Probab=97.86 E-value=8.2e-05 Score=57.09 Aligned_cols=73 Identities=18% Similarity=0.375 Sum_probs=59.3
Q ss_pred CCCCCCChHHHHHHHHHHHHHhhCCC-ChHHHHHHHHHHhhcCChHHHHHHHHHHHHHHHHHHHHHHHHHHhccc
Q 020330 246 YPKPNRSGYNFFFAEKHYKLKSLYPN-REREFTKMIGESWTNLSPEERKVYQNIGLKDKERYNRELKEYKERLKL 319 (327)
Q Consensus 246 ~PKrP~say~lF~~e~r~~vk~e~p~-~~~eisk~lge~Wk~Ls~eeK~~Y~e~a~~dkery~~e~~~yk~~~k~ 319 (327)
-|..|.+|--+|.+.......+.++. ...+ -+.+...|++|++.+|-+|..+|.+|..+|+.+|.+|++-...
T Consensus 3 lPE~PKt~qe~Wqq~vi~dYla~~~~dr~K~-~kam~~~W~~me~Kekl~WIkKA~EdqKrYE~el~e~r~~~~~ 76 (85)
T PF14887_consen 3 LPETPKTAQEIWQQSVIGDYLAKFRNDRKKA-LKAMEAQWSQMEKKEKLKWIKKAAEDQKRYERELREMRSAPAD 76 (85)
T ss_dssp -S----THHHHHHHHHHHHHHHHTTSTHHHH-HHHHHHHHHTTGGGHHHHHHHHHHHHHHHHHHHHHCCS-CCCT
T ss_pred CCCCCCCHHHHHHHHHHHHHHHHhhHhHHHH-HHHHHHHHHHhhhhhhhHHHHHHHHHHHHHHHHHHHHhcCCCC
Confidence 36678889999999999988888888 4444 5689999999999999999999999999999999999876544
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=96.81 E-value=0.0022 Score=56.72 Aligned_cols=46 Identities=22% Similarity=0.427 Sum_probs=40.5
Q ss_pred CCCCCCCCCChHHHHHHHHHHHHHhhCCC-ChHHHHHHHHHHhhcCC
Q 020330 243 DPSYPKPNRSGYNFFFAEKHYKLKSLYPN-REREFTKMIGESWTNLS 288 (327)
Q Consensus 243 dp~~PKrP~say~lF~~e~r~~vk~e~p~-~~~eisk~lge~Wk~Ls 288 (327)
.|.+-.|-+|||+.|+++.-++||+++|+ +.+|+-+..++.|...+
T Consensus 118 PPEKRqR~psaYn~f~k~ei~rik~~~p~ishkeaFs~aAknW~h~p 164 (170)
T PF04690_consen 118 PPEKRQRVPSAYNRFMKEEIQRIKAENPDISHKEAFSAAAKNWAHFP 164 (170)
T ss_pred CccccCCCchhHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHhhhhCc
Confidence 34444577899999999999999999999 99999999999998764
No 23
>COG5648 NHP6B Chromatin-associated proteins containing the HMG domain [Chromatin structure and dynamics]
Probab=96.52 E-value=0.0023 Score=58.12 Aligned_cols=67 Identities=22% Similarity=0.203 Sum_probs=60.0
Q ss_pred CCCCCCCChHHHHHHHHHHHHHhhCCC-ChHHHHHHHHHHhhcCChHHHHHHHHHHHHHHHHHHHHHH
Q 020330 245 SYPKPNRSGYNFFFAEKHYKLKSLYPN-REREFTKMIGESWTNLSPEERKVYQNIGLKDKERYNRELK 311 (327)
Q Consensus 245 ~~PKrP~say~lF~~e~r~~vk~e~p~-~~~eisk~lge~Wk~Ls~eeK~~Y~e~a~~dkery~~e~~ 311 (327)
.+++.+.-.|.=+-.+.|+++...+|+ ...++++++++.|++|+++-|.+|.+.++++++.|...++
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 356677778888888899999999999 9999999999999999999999999999999999987765
No 24
>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=95.80 E-value=0.046 Score=48.56 Aligned_cols=48 Identities=19% Similarity=0.331 Sum_probs=41.2
Q ss_pred CChHHHHHHHHHHHHHhhCCC-ChHHHHHHHHHHhhcCChHHHHHHHHHHHHH
Q 020330 251 RSGYNFFFAEKHYKLKSLYPN-REREFTKMIGESWTNLSPEERKVYQNIGLKD 302 (327)
Q Consensus 251 ~say~lF~~e~r~~vk~e~p~-~~~eisk~lge~Wk~Ls~eeK~~Y~e~a~~d 302 (327)
.+||+=|+.+.+.+ |.+ ...|+....+.+|..|++++|..|..++...
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 57999999998765 456 7789999999999999999999999876544
No 25
>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=89.84 E-value=0.56 Score=34.00 Aligned_cols=38 Identities=13% Similarity=0.295 Sum_probs=34.3
Q ss_pred CChHHHHHHHHHHHHHhhCCC-ChHHHHHHHHHHhhcCC
Q 020330 251 RSGYNFFFAEKHYKLKSLYPN-REREFTKMIGESWTNLS 288 (327)
Q Consensus 251 ~say~lF~~e~r~~vk~e~p~-~~~eisk~lge~Wk~Ls 288 (327)
.+.|-+|.+-.|+.|...||+ ....+...++.+|+.-+
T Consensus 13 lt~yK~Fsq~vRP~l~~~NPk~~~sKl~~l~~AKwrEF~ 51 (55)
T PF08073_consen 13 LTNYKAFSQHVRPLLAKANPKAPMSKLMMLLQAKWREFQ 51 (55)
T ss_pred HHHHHHHHHHHHHHHHHHCCCCcHHHHHHHHHHHHHHHH
Confidence 456889999999999999999 99999999999998644
No 26
>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=87.48 E-value=1.5 Score=39.97 Aligned_cols=55 Identities=15% Similarity=0.361 Sum_probs=39.3
Q ss_pred CCCCCCCCCCCCChHHHHHHHHHHHHHhhCCC-ChHHHHHHHHHHhhcCChHHHHHHHHHHH
Q 020330 240 RRGDPSYPKPNRSGYNFFFAEKHYKLKSLYPN-REREFTKMIGESWTNLSPEERKVYQNIGL 300 (327)
Q Consensus 240 ~~kdp~~PKrP~say~lF~~e~r~~vk~e~p~-~~~eisk~lge~Wk~Ls~eeK~~Y~e~a~ 300 (327)
++.....+|||.|+||.|..=.- ...|+ ...+++..|+.+|..=+- |..|.-.|+
T Consensus 37 ~~~~~~~~kr~lN~Fm~FRsyy~----~~~~~~~Qk~~S~~l~~lW~~dp~--k~~W~l~ak 92 (201)
T PF04769_consen 37 RKRSPEKAKRPLNGFMAFRSYYS----PIFPPLPQKELSGILTKLWEKDPF--KNKWSLMAK 92 (201)
T ss_pred ccccccccccchhHHHHHHHHHH----hhcCCcCHHHHHHHHHHHHhCCcc--HhHHHHHhh
Confidence 34455678999999999987664 34455 679999999999987433 455554443
No 27
>PF06244 DUF1014: Protein of unknown function (DUF1014); InterPro: IPR010422 This family consists of several hypothetical eukaryotic proteins of unknown function.
Probab=84.89 E-value=1.1 Score=37.72 Aligned_cols=45 Identities=18% Similarity=0.361 Sum_probs=39.2
Q ss_pred CCCCCCChHHHHHHHHHHHHHhhCCC-ChHHHHHHHHHHhhcCChH
Q 020330 246 YPKPNRSGYNFFFAEKHYKLKSLYPN-REREFTKMIGESWTNLSPE 290 (327)
Q Consensus 246 ~PKrP~say~lF~~e~r~~vk~e~p~-~~~eisk~lge~Wk~Ls~e 290 (327)
+-||-.-||.-|...+-++|+.++|+ ..+.+..+|-+.|...++.
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 33555679999999999999999999 9999999999999887653
No 28
>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=82.94 E-value=0.75 Score=32.36 Aligned_cols=34 Identities=24% Similarity=0.498 Sum_probs=28.6
Q ss_pred Cceeeeeecccc-CCCceeEEeeccccccccccCC
Q 020330 170 CFTAVGRIDGKF-DCGYLVSVKLGSETLSGVLYHP 203 (327)
Q Consensus 170 ~~~v~g~Idgkf-d~gylvtv~~gse~~~g~ly~~ 203 (327)
+.-|+++=||.- +..|--+|+||.-.+||+||..
T Consensus 14 cvRvs~idd~~~~e~aYQt~V~IgGHvFkGiLyDq 48 (50)
T TIGR01624 14 CVRVTAIDDGEQAEYAYQATVTIGGHVFKGFLHDQ 48 (50)
T ss_pred EEEEeccCCCCCceEEEEEEEEECceEEeeEEecc
Confidence 345777777777 7899999999999999999974
No 29
>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=81.86 E-value=2.9 Score=28.68 Aligned_cols=38 Identities=18% Similarity=0.280 Sum_probs=27.6
Q ss_pred hhHHHHHhcCchhhhhcccchHHhHhhhcCCCCCCcHHHHHHHHHHHhh
Q 020330 66 VLYVEATTRGGYEKVVAEKKWREVGAVFKFSPTTTSASFVLRKHYLTLL 114 (327)
Q Consensus 66 ~Ly~~V~~~GG~~~V~~~~~W~eV~~~l~~p~~~~~~s~~Lk~~Y~k~L 114 (327)
.|...|...|.- .|..|+..|+. +-...+++.+|.+||
T Consensus 11 ~l~~~v~~~g~~-------~W~~Ia~~~~~----~Rt~~qc~~~~~~~~ 48 (48)
T PF00249_consen 11 KLLEAVKKYGKD-------NWKKIAKRMPG----GRTAKQCRSRYQNLL 48 (48)
T ss_dssp HHHHHHHHSTTT-------HHHHHHHHHSS----SSTHHHHHHHHHHHT
T ss_pred HHHHHHHHhCCc-------HHHHHHHHcCC----CCCHHHHHHHHHhhC
Confidence 456666666643 79999999992 223448999999886
No 30
>PF05142 DUF702: Domain of unknown function (DUF702) ; InterPro: IPR007818 This is a family of plant proteins of unknown function.
Probab=79.94 E-value=1.1 Score=39.17 Aligned_cols=34 Identities=26% Similarity=0.598 Sum_probs=30.7
Q ss_pred CceeeeeeccccCCCceeEEeeccccccccccCC
Q 020330 170 CFTAVGRIDGKFDCGYLVSVKLGSETLSGVLYHP 203 (327)
Q Consensus 170 ~~~v~g~Idgkfd~gylvtv~~gse~~~g~ly~~ 203 (327)
..-|+++=||.-|..|.-+|.||.-.+||+||..
T Consensus 116 CVRVssiDdgedE~AYQTaV~IGGHVFKGiLYDq 149 (154)
T PF05142_consen 116 CVRVSSIDDGEDEYAYQTAVNIGGHVFKGILYDQ 149 (154)
T ss_pred EEEEecccCcccceeeEEeEEECCEEeeeeeecc
Confidence 4458888899999999999999999999999986
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=77.37 E-value=5.3 Score=36.14 Aligned_cols=45 Identities=27% Similarity=0.522 Sum_probs=39.1
Q ss_pred ChHHHHH-HHHHHhhcCChHHHHHHHHHHHH-HHHHHHHHHHHHHHh
Q 020330 272 REREFTK-MIGESWTNLSPEERKVYQNIGLK-DKERYNRELKEYKER 316 (327)
Q Consensus 272 ~~~eisk-~lge~Wk~Ls~eeK~~Y~e~a~~-dkery~~e~~~yk~~ 316 (327)
.+..|++ .||..|+.+|+++|+.|.+.... ....|-..+..|...
T Consensus 65 Df~~mar~vLG~~W~~~s~~Qr~~F~~~F~~~l~~tY~~~l~~y~~~ 111 (198)
T TIGR03481 65 DLPAMARLTLGSSWTSLSPEQRRRFIGAFRELSIATYASQFKSYAGE 111 (198)
T ss_pred CHHHHHHHHhhhhhhhCCHHHHHHHHHHHHHHHHHHHHHHHHhhcCc
Confidence 6777766 78999999999999999998888 778999999999763
No 32
>PRK15117 ABC transporter periplasmic binding protein MlaC; Provisional
Probab=71.05 E-value=15 Score=33.61 Aligned_cols=47 Identities=19% Similarity=0.371 Sum_probs=39.8
Q ss_pred CC-ChHHHHH-HHHHHhhcCChHHHHHHHHHHHH-HHHHHHHHHHHHHHh
Q 020330 270 PN-REREFTK-MIGESWTNLSPEERKVYQNIGLK-DKERYNRELKEYKER 316 (327)
Q Consensus 270 p~-~~~eisk-~lge~Wk~Ls~eeK~~Y~e~a~~-dkery~~e~~~yk~~ 316 (327)
|. .+..+++ .||.-|+.+|+++|+.|.+.... ...-|-..+.+|...
T Consensus 66 p~~Df~~~s~~vLG~~wr~as~eQr~~F~~~F~~~Lv~tYa~~l~~y~~q 115 (211)
T PRK15117 66 PYVQVKYAGALVLGRYYKDATPAQREAYFAAFREYLKQAYGQALAMYHGQ 115 (211)
T ss_pred ccCCHHHHHHHHhhhhhhhCCHHHHHHHHHHHHHHHHHHHHHHHHHhCCc
Confidence 55 7777865 78999999999999999988777 667899999999764
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=63.46 E-value=12 Score=32.89 Aligned_cols=42 Identities=17% Similarity=0.272 Sum_probs=35.0
Q ss_pred CCCeeCCeecchhhhHHHHHhcCchhhhhcccchHHhHhhhcCCCC
Q 020330 53 MIPVIGGKELDLHVLYVEATTRGGYEKVVAEKKWREVGAVFKFSPT 98 (327)
Q Consensus 53 ~~P~i~gk~lDL~~Ly~~V~~~GG~~~V~~~~~W~eV~~~l~~p~~ 98 (327)
.+|.-+|+..+.|.||..|.++-.- .-+.|.++|-.||..+.
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 3799999999999999999976432 34689999999999544
No 34
>KOG3223 consensus Uncharacterized conserved protein [Function unknown]
Probab=61.66 E-value=5.2 Score=36.21 Aligned_cols=52 Identities=17% Similarity=0.409 Sum_probs=43.5
Q ss_pred CCC-CCCCChHHHHHHHHHHHHHhhCCC-ChHHHHHHHHHHhhcCChHHHHHHHHHH
Q 020330 245 SYP-KPNRSGYNFFFAEKHYKLKSLYPN-REREFTKMIGESWTNLSPEERKVYQNIG 299 (327)
Q Consensus 245 ~~P-KrP~say~lF~~e~r~~vk~e~p~-~~~eisk~lge~Wk~Ls~eeK~~Y~e~a 299 (327)
.+| ||=+-||.-|-...-++|+.++|+ ..++.-.+|-.+|..-++. ||.+.+
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 344 566788999999999999999999 9999999999999988875 555543
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=57.62 E-value=19 Score=25.46 Aligned_cols=37 Identities=14% Similarity=0.285 Sum_probs=23.6
Q ss_pred hhHHHHHhcCchhhhhcccchHHhHhhhcCCCCCCcHHHHHHHHHHHhhh
Q 020330 66 VLYVEATTRGGYEKVVAEKKWREVGAVFKFSPTTTSASFVLRKHYLTLLY 115 (327)
Q Consensus 66 ~Ly~~V~~~GG~~~V~~~~~W~eV~~~l~~p~~~~~~s~~Lk~~Y~k~L~ 115 (327)
.|...|...|. .|..|+..|| . -...+++..|.++|.
T Consensus 8 ~L~~~~~~~g~--------~W~~Ia~~l~---~--Rt~~~~~~r~~~~l~ 44 (60)
T PF13921_consen 8 LLLELVKKYGN--------DWKKIAEHLG---N--RTPKQCRNRWRNHLR 44 (60)
T ss_dssp HHHHHHHHHTS---------HHHHHHHST---T--S-HHHHHHHHHHTTS
T ss_pred HHHHHHHHHCc--------CHHHHHHHHC---c--CCHHHHHHHHHHHCc
Confidence 34555555553 6999999996 1 123478888888663
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=52.92 E-value=27 Score=22.28 Aligned_cols=37 Identities=16% Similarity=0.310 Sum_probs=24.6
Q ss_pred hhHHHHHhcCchhhhhcccchHHhHhhhcCCCCCCcHHHHHHHHHHHhh
Q 020330 66 VLYVEATTRGGYEKVVAEKKWREVGAVFKFSPTTTSASFVLRKHYLTLL 114 (327)
Q Consensus 66 ~Ly~~V~~~GG~~~V~~~~~W~eV~~~l~~p~~~~~~s~~Lk~~Y~k~L 114 (327)
.|...|...|- ..|..|+..|+-- .+..++.+|.+++
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 35555566653 5799999998652 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=51.89 E-value=16 Score=31.76 Aligned_cols=44 Identities=20% Similarity=0.444 Sum_probs=33.5
Q ss_pred ChHHHHH-HHHHHhhcCChHHHHHHHHHHHH-HHHHHHHHHHHHHH
Q 020330 272 REREFTK-MIGESWTNLSPEERKVYQNIGLK-DKERYNRELKEYKE 315 (327)
Q Consensus 272 ~~~eisk-~lge~Wk~Ls~eeK~~Y~e~a~~-dkery~~e~~~yk~ 315 (327)
.+..+++ .||.-|+.+++++|+.|.+...+ ....|-..+..|..
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 5666654 57889999999999999987776 66788888988875
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=47.62 E-value=69 Score=26.09 Aligned_cols=42 Identities=19% Similarity=0.550 Sum_probs=25.5
Q ss_pred HHHHHHHHHHhhcCChHHHHHHHHHHHH-------HHHHHHHHHHHHHH
Q 020330 274 REFTKMIGESWTNLSPEERKVYQNIGLK-------DKERYNRELKEYKE 315 (327)
Q Consensus 274 ~eisk~lge~Wk~Ls~eeK~~Y~e~a~~-------dkery~~e~~~yk~ 315 (327)
.++..-+.+.|+.|+++.|..+.+.|.. +++++...|..|..
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 3455666666777766666666655533 55566666666654
No 39
>COG2854 Ttg2D ABC-type transport system involved in resistance to organic solvents, auxiliary component [Secondary metabolites biosynthesis, transport, and catabolism]
Probab=44.42 E-value=34 Score=31.29 Aligned_cols=43 Identities=21% Similarity=0.369 Sum_probs=36.7
Q ss_pred HHHHHHHHhhcCChHHHHHHHHHHHH-HHHHHHHHHHHHHHhcc
Q 020330 276 FTKMIGESWTNLSPEERKVYQNIGLK-DKERYNRELKEYKERLK 318 (327)
Q Consensus 276 isk~lge~Wk~Ls~eeK~~Y~e~a~~-dkery~~e~~~yk~~~k 318 (327)
-...||.-|+.+|+++++.|.+.... ....|-..|.+|+.+.-
T Consensus 76 a~~vLGk~~k~aspeQ~~~F~~aF~~yl~q~Y~~aL~~Y~~q~~ 119 (202)
T COG2854 76 AKLVLGKYYKTASPEQRQAFFKAFRTYLEQTYGQALLDYKGQTL 119 (202)
T ss_pred HHHHhccccccCCHHHHHHHHHHHHHHHHHHHHHHHHHccCCCc
Confidence 35678999999999999999988777 56789999999998643
No 40
>PF13873 Myb_DNA-bind_5: Myb/SANT-like DNA-binding domain
Probab=44.41 E-value=32 Score=25.73 Aligned_cols=54 Identities=13% Similarity=0.129 Sum_probs=34.2
Q ss_pred cchhhhHHHHHhc---CchhhhhcccchHHhHhhhcCCCCCCcHHHHHHHHHHHhhh
Q 020330 62 LDLHVLYVEATTR---GGYEKVVAEKKWREVGAVFKFSPTTTSASFVLRKHYLTLLY 115 (327)
Q Consensus 62 lDL~~Ly~~V~~~---GG~~~V~~~~~W~eV~~~l~~p~~~~~~s~~Lk~~Y~k~L~ 115 (327)
|+|..-|..|..- ++.........|.+|+..|+--....-...+|++.|.++..
T Consensus 14 v~~v~~~~~il~~k~~~~~~~~~k~~~W~~I~~~lN~~~~~~Rs~~~lkkkW~nlk~ 70 (78)
T PF13873_consen 14 VELVEKHKDILENKFSDSVSNKEKRKAWEEIAEELNALGPGKRSWKQLKKKWKNLKS 70 (78)
T ss_pred HHHHHHhHHHHhcccccHHHHHHHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHH
Confidence 4555556555543 33334445679999999997422223345589999988764
No 41
>smart00717 SANT SANT SWI3, ADA2, N-CoR and TFIIIB'' DNA-binding domains.
Probab=35.57 E-value=73 Score=20.40 Aligned_cols=26 Identities=15% Similarity=0.330 Sum_probs=18.7
Q ss_pred cchHHhHhhhcCCCCCCcHHHHHHHHHHHhh
Q 020330 84 KKWREVGAVFKFSPTTTSASFVLRKHYLTLL 114 (327)
Q Consensus 84 ~~W~eV~~~l~~p~~~~~~s~~Lk~~Y~k~L 114 (327)
..|..|+..|+-- .+..++..|..++
T Consensus 22 ~~w~~Ia~~~~~r-----t~~~~~~~~~~~~ 47 (49)
T smart00717 22 NNWEKIAKELPGR-----TAEQCRERWNNLL 47 (49)
T ss_pred CCHHHHHHHcCCC-----CHHHHHHHHHHHc
Confidence 5799999998721 2337888887765
No 42
>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=31.97 E-value=52 Score=25.28 Aligned_cols=60 Identities=17% Similarity=0.243 Sum_probs=41.2
Q ss_pred hhhhHHHHHhcCch--hhhhcccchHHhHhhhcCCCCCCcHHHHHHHHHHHhhhhhhhhhhh
Q 020330 64 LHVLYVEATTRGGY--EKVVAEKKWREVGAVFKFSPTTTSASFVLRKHYLTLLYHYEQVHFF 123 (327)
Q Consensus 64 L~~Ly~~V~~~GG~--~~V~~~~~W~eV~~~l~~p~~~~~~s~~Lk~~Y~k~L~~yE~~~~~ 123 (327)
|..|+.+....|.+ ...-....|..|+..|.-.....-...+|++.|..+=..|..+...
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 44566666677777 3344455899999999864443333458999999888888876543
No 43
>PRK10236 hypothetical protein; Provisional
Probab=28.71 E-value=1e+02 Score=28.96 Aligned_cols=46 Identities=13% Similarity=0.312 Sum_probs=33.1
Q ss_pred hHHHHHHHHHHHHHhhCCC--ChHH-----HHHHHHHHhhcCChHHHHHHHHH
Q 020330 253 GYNFFFAEKHYKLKSLYPN--RERE-----FTKMIGESWTNLSPEERKVYQNI 298 (327)
Q Consensus 253 ay~lF~~e~r~~vk~e~p~--~~~e-----isk~lge~Wk~Ls~eeK~~Y~e~ 298 (327)
.|-==..+.+..+|-.+.. +..+ +.+.+.+.|+.|+++|++.+.+.
T Consensus 88 ~YreIL~DVc~~LKV~y~~~~st~~iE~~il~kll~~a~~kms~eE~~~L~~~ 140 (237)
T PRK10236 88 LYRAILLDVSKRLKLKADKEMSTFEIEQQLLEQFLRNTWKKMDEEHKQEFLHA 140 (237)
T ss_pred cHHHHHHHHHHHcCCCCCCCCCHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHH
Confidence 3555556677777766544 3333 48899999999999999888654
No 44
>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=26.82 E-value=55 Score=24.16 Aligned_cols=38 Identities=18% Similarity=0.240 Sum_probs=23.6
Q ss_pred hcccchHHhHhhhcCCCC---CCcHHHHHHHHHHHhhhhhh
Q 020330 81 VAEKKWREVGAVFKFSPT---TTSASFVLRKHYLTLLYHYE 118 (327)
Q Consensus 81 ~~~~~W~eV~~~l~~p~~---~~~~s~~Lk~~Y~k~L~~yE 118 (327)
...+.|.+|+..||...+ +...-..|+..|.+.+...+
T Consensus 24 ~r~~aw~~Ia~~l~~~~~~~~~~~~w~~Lr~~y~~~~~~~~ 64 (85)
T PF10545_consen 24 LREEAWQEIARELGKEFSVDDCKKRWKNLRDRYRRELKKIK 64 (85)
T ss_pred HHHHHHHHHHHHHccchhHHHHHHHHHHHHHHHHHHHHHHh
Confidence 466799999999984322 22233356666666655555
No 45
>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=26.57 E-value=1.7e+02 Score=28.63 Aligned_cols=64 Identities=19% Similarity=0.162 Sum_probs=41.0
Q ss_pred hHHHHHHHHHHHHHhhCCC-ChHHHHHHHHHHhhcCChHHHHHHHHHHHHHHHH-HHHHHHHHHHh
Q 020330 253 GYNFFFAEKHYKLKSLYPN-REREFTKMIGESWTNLSPEERKVYQNIGLKDKER-YNRELKEYKER 316 (327)
Q Consensus 253 ay~lF~~e~r~~vk~e~p~-~~~eisk~lge~Wk~Ls~eeK~~Y~e~a~~dker-y~~e~~~yk~~ 316 (327)
|+-.|.--.-..+....|. +..|-....-..|...|.-+|..|+|+|++=.|- -++||+.-+-+
T Consensus 231 AlSCFLIpvLrsLar~kPtMtlEeGl~ra~qEW~~~SnfdRmifyemaekFmEFEaeEEmq~q~lq 296 (328)
T PF12881_consen 231 ALSCFLIPVLRSLARLKPTMTLEEGLWRAVQEWQHTSNFDRMIFYEMAEKFMEFEAEEEMQIQKLQ 296 (328)
T ss_pred hhhhhHHHHHHHHHhcCCCccHHHHHHHHHHHhhccccccHHHHHHHHHHHccCCcHHHHHHHHHH
Confidence 3444444443344455566 6667777777889999999999999999885431 12455544433
No 46
>PRK12750 cpxP periplasmic repressor CpxP; Reviewed
Probab=26.43 E-value=2.1e+02 Score=25.25 Aligned_cols=35 Identities=11% Similarity=0.268 Sum_probs=27.2
Q ss_pred HHHHHHHHhhcCChHHHHHHHHHHHHHHHHHHHHH
Q 020330 276 FTKMIGESWTNLSPEERKVYQNIGLKDKERYNREL 310 (327)
Q Consensus 276 isk~lge~Wk~Ls~eeK~~Y~e~a~~dkery~~e~ 310 (327)
..+...+++..|++++|+.|.+.-++-.+.|...+
T Consensus 126 ~~~~~~~~~~vLTpEQRak~~e~~~~r~~~~~~~~ 160 (170)
T PRK12750 126 MLEKRHQMLSILTPEQKAKFQELQQERMQECQDKM 160 (170)
T ss_pred HHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHHH
Confidence 34456678999999999999988777766666655
No 47
>PF12650 DUF3784: Domain of unknown function (DUF3784); InterPro: IPR017259 This group represents an uncharacterised conserved protein.
Probab=25.67 E-value=46 Score=26.19 Aligned_cols=17 Identities=24% Similarity=0.524 Sum_probs=14.0
Q ss_pred HHhhcCChHHHHHHHHH
Q 020330 282 ESWTNLSPEERKVYQNI 298 (327)
Q Consensus 282 e~Wk~Ls~eeK~~Y~e~ 298 (327)
.-|+.||+|||+.|.++
T Consensus 24 aGyntms~eEk~~~D~~ 40 (97)
T PF12650_consen 24 AGYNTMSKEEKEKYDKK 40 (97)
T ss_pred hhcccCCHHHHHHhhHH
Confidence 34899999999999764
No 48
>PF13875 DUF4202: Domain of unknown function (DUF4202)
Probab=24.54 E-value=1.4e+02 Score=26.92 Aligned_cols=40 Identities=10% Similarity=0.256 Sum_probs=33.7
Q ss_pred ChHHHHHHHHHHHHHhhCCCChHHHHHHHHHHhhcCChHHHH
Q 020330 252 SGYNFFFAEKHYKLKSLYPNREREFTKMIGESWTNLSPEERK 293 (327)
Q Consensus 252 say~lF~~e~r~~vk~e~p~~~~eisk~lge~Wk~Ls~eeK~ 293 (327)
-+-++|...+.+.+...| ....+..+|..-|+.||+.-++
T Consensus 130 vacLVFL~~~f~~F~~~~--deeK~v~Il~KTw~KMS~~g~~ 169 (185)
T PF13875_consen 130 VACLVFLEYYFEDFAAKH--DEEKIVDILRKTWRKMSERGHE 169 (185)
T ss_pred hHHHHhHHHHHHHHHhcC--CHHHHHHHHHHHHHHCCHHHHH
Confidence 467889999999999988 3467788889999999998764
No 49
>PRK09706 transcriptional repressor DicA; Reviewed
Probab=24.21 E-value=2.1e+02 Score=23.65 Aligned_cols=43 Identities=19% Similarity=0.122 Sum_probs=36.6
Q ss_pred HHHHHHHHhhcCChHHHHHHHHHHHHHHHHHHHHHHHHHHhcc
Q 020330 276 FTKMIGESWTNLSPEERKVYQNIGLKDKERYNRELKEYKERLK 318 (327)
Q Consensus 276 isk~lge~Wk~Ls~eeK~~Y~e~a~~dkery~~e~~~yk~~~k 318 (327)
-.+.|-+.|+.|+++++.......+...+.|.+-+++|-..-+
T Consensus 88 ~~~~ll~~~~~L~~~~~~~~l~~l~~~~~~~~~~~~~~~~~~~ 130 (135)
T PRK09706 88 DQKELLELFDALPESEQDAQLSEMRARVENFNKLFEELLKARK 130 (135)
T ss_pred HHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 3477889999999999999999999988889888888876543
No 50
>PLN03212 Transcription repressor MYB5; Provisional
Probab=23.30 E-value=1.1e+02 Score=29.04 Aligned_cols=39 Identities=15% Similarity=0.203 Sum_probs=26.9
Q ss_pred hHHHHHhcCchhhhhcccchHHhHhhhcCCCCCCcHHHHHHHHHHHhhhh
Q 020330 67 LYVEATTRGGYEKVVAEKKWREVGAVFKFSPTTTSASFVLRKHYLTLLYH 116 (327)
Q Consensus 67 Ly~~V~~~GG~~~V~~~~~W~eV~~~l~~p~~~~~~s~~Lk~~Y~k~L~~ 116 (327)
|...|...|. ..|..|+..++...+ +.+.|.-|.+||.+
T Consensus 36 L~~lV~kyG~-------~nW~~IAk~~g~gRT----~KQCReRW~N~L~P 74 (249)
T PLN03212 36 LVSFIKKEGE-------GRWRSLPKRAGLLRC----GKSCRLRWMNYLRP 74 (249)
T ss_pred HHHHHHHhCc-------ccHHHHHHhhhcCCC----cchHHHHHHHhhch
Confidence 5566776663 369999998874332 22678889988855
No 51
>KOG1610 consensus Corticosteroid 11-beta-dehydrogenase and related short chain-type dehydrogenases [Secondary metabolites biosynthesis, transport and catabolism; General function prediction only]
Probab=23.04 E-value=1.7e+02 Score=28.65 Aligned_cols=58 Identities=21% Similarity=0.385 Sum_probs=40.3
Q ss_pred HHHHHHHHHHHHHhh-------CCC-------ChHHHHHHHHHHhhcCChHHHHHHHHHHHHHHHHHHHHHHHHH
Q 020330 254 YNFFFAEKHYKLKSL-------YPN-------REREFTKMIGESWTNLSPEERKVYQNIGLKDKERYNRELKEYK 314 (327)
Q Consensus 254 y~lF~~e~r~~vk~e-------~p~-------~~~eisk~lge~Wk~Ls~eeK~~Y~e~a~~dkery~~e~~~yk 314 (327)
--.|+...|.++..- -|+ ....+.+.+.++|..|+++.|+.|-+.+..+. ++.+..|.
T Consensus 185 Veaf~D~lR~EL~~fGV~VsiiePG~f~T~l~~~~~~~~~~~~~w~~l~~e~k~~YGedy~~~~---~~~~~~~~ 256 (322)
T KOG1610|consen 185 VEAFSDSLRRELRPFGVKVSIIEPGFFKTNLANPEKLEKRMKEIWERLPQETKDEYGEDYFEDY---KKSLEKYL 256 (322)
T ss_pred HHHHHHHHHHHHHhcCcEEEEeccCccccccCChHHHHHHHHHHHhcCCHHHHHHHHHHHHHHH---HHHHHhhh
Confidence 345777777776642 243 34678899999999999999999987766553 34444444
No 52
>PRK12751 cpxP periplasmic stress adaptor protein CpxP; Reviewed
Probab=22.53 E-value=1.8e+02 Score=25.63 Aligned_cols=27 Identities=15% Similarity=0.284 Sum_probs=20.3
Q ss_pred HHHHHHHhhcCChHHHHHHHHHHHHHH
Q 020330 277 TKMIGESWTNLSPEERKVYQNIGLKDK 303 (327)
Q Consensus 277 sk~lge~Wk~Ls~eeK~~Y~e~a~~dk 303 (327)
.+...++++.|++|+|+.|.+..++-.
T Consensus 120 ~~~~~qmy~lLTPEQra~l~~~~e~r~ 146 (162)
T PRK12751 120 AKVRNQMYNLLTPEQKEALNKKHQERI 146 (162)
T ss_pred HHHHHHHHHcCCHHHHHHHHHHHHHHH
Confidence 455567889999999999987655543
No 53
>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=22.03 E-value=1.4e+02 Score=21.03 Aligned_cols=34 Identities=26% Similarity=0.245 Sum_probs=24.9
Q ss_pred HHHHHHHHhhCCC---ChH----HHHHHHHHHhhcCChHHH
Q 020330 259 AEKHYKLKSLYPN---RER----EFTKMIGESWTNLSPEER 292 (327)
Q Consensus 259 ~e~r~~vk~e~p~---~~~----eisk~lge~Wk~Ls~eeK 292 (327)
+..+..++.-||+ ... +....|.+.|..|++.++
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 4455567778888 334 788899999999886665
No 54
>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=21.60 E-value=1.8e+02 Score=26.70 Aligned_cols=27 Identities=19% Similarity=0.379 Sum_probs=20.9
Q ss_pred HHhhcCChHHHHHHHHHHHHHHHHHHH
Q 020330 282 ESWTNLSPEERKVYQNIGLKDKERYNR 308 (327)
Q Consensus 282 e~Wk~Ls~eeK~~Y~e~a~~dkery~~ 308 (327)
+.|..|+++.|+...+.+.+.-+....
T Consensus 214 ~~~~~L~~e~q~~i~~a~~~~~~~~~~ 240 (257)
T TIGR00787 214 AFWKSLPPDLQAVVKEAAKEAGEYQRK 240 (257)
T ss_pred HHHhcCCHHHHHHHHHHHHHHHHHHHH
Confidence 679999999999998877765444433
No 55
>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=21.41 E-value=76 Score=22.69 Aligned_cols=40 Identities=23% Similarity=0.199 Sum_probs=32.6
Q ss_pred hcCchhhhhcccchHHhHhhhcCCCCCCcHHHHHHHHHHHhh
Q 020330 73 TRGGYEKVVAEKKWREVGAVFKFSPTTTSASFVLRKHYLTLL 114 (327)
Q Consensus 73 ~~GG~~~V~~~~~W~eV~~~l~~p~~~~~~s~~Lk~~Y~k~L 114 (327)
-..||-.+-++-.-.+||..||+..+ .++..||+.-.+++
T Consensus 13 ~~~GYfd~PR~~tl~elA~~lgis~s--t~~~~LRrae~kli 52 (53)
T PF04967_consen 13 YELGYFDVPRRITLEELAEELGISKS--TVSEHLRRAERKLI 52 (53)
T ss_pred HHcCCCCCCCcCCHHHHHHHhCCCHH--HHHHHHHHHHHHHh
Confidence 34688888888889999999999864 37889999887765
No 56
>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=21.40 E-value=69 Score=23.64 Aligned_cols=22 Identities=27% Similarity=0.578 Sum_probs=15.1
Q ss_pred CeecchhhhHHHHHhcCchhhh
Q 020330 59 GKELDLHVLYVEATTRGGYEKV 80 (327)
Q Consensus 59 gk~lDL~~Ly~~V~~~GG~~~V 80 (327)
|+++....|+.+|..+|++...
T Consensus 15 ~~pm~~~eI~~~i~~~~~~~~~ 36 (72)
T PF05066_consen 15 GRPMTFKEIWEEIQERGLYKKS 36 (72)
T ss_dssp -S-EEHHHHHHHHHHHHTS---
T ss_pred CCCcCHHHHHHHHHHhCCCCcc
Confidence 3557888999999999999877
No 57
>TIGR01557 myb_SHAQKYF myb-like DNA-binding domain, SHAQKYF class. This model describes a DNA-binding domain restricted to (but common in) plant proteins, many of which also contain a response regulator domain. The domain appears related to the Myb-like DNA-binding domain described by Pfam model pfam00249. It is distinguished in part by a well-conserved motif SH[AL]QKY[RF] at the C-terminal end of the motif.
Probab=20.52 E-value=1.4e+02 Score=21.61 Aligned_cols=43 Identities=21% Similarity=0.379 Sum_probs=26.5
Q ss_pred chhhhHHHHHh-cCchhhhhcccch---HHhHhhhcCCC-CCCcHHHHHHHHHHHhhhh
Q 020330 63 DLHVLYVEATT-RGGYEKVVAEKKW---REVGAVFKFSP-TTTSASFVLRKHYLTLLYH 116 (327)
Q Consensus 63 DL~~Ly~~V~~-~GG~~~V~~~~~W---~eV~~~l~~p~-~~~~~s~~Lk~~Y~k~L~~ 116 (327)
+++.+|.+... .|+ ..| ..|++.++.+. +. .++++|+.+|.+.
T Consensus 9 eeh~~Fl~ai~~~G~-------g~~a~pk~I~~~~~~~~lT~----~qV~SH~QKy~~k 56 (57)
T TIGR01557 9 DLHDRFLQAVQKLGG-------PDWATPKRILELMVVDGLTR----DQVASHLQKYRLK 56 (57)
T ss_pred HHHHHHHHHHHHhCC-------CcccchHHHHHHcCCCCCCH----HHHHHHHHHHHcc
Confidence 45666665432 232 248 88888888754 33 3788888877543
No 58
>PF08914 Myb_DNA-bind_2: Rap1 Myb domain; InterPro: IPR015010 Rap1 Myb adopts a canonical three-helix bundle tertiary structure, with the second and third helices forming a helix-turn-helix variant motif. The function is unclear but it may either interact with DNA via an adaptor protein or it may be only involved in protein-protein interactions []. ; PDB: 1FEX_A.
Probab=20.51 E-value=1.3e+02 Score=22.37 Aligned_cols=52 Identities=17% Similarity=0.131 Sum_probs=28.5
Q ss_pred hhHHHHHhcCch-hhhhcccchHHhHhhhcCCCCCCcHHHHHHHHHHHhhhhhhhhh
Q 020330 66 VLYVEATTRGGY-EKVVAEKKWREVGAVFKFSPTTTSASFVLRKHYLTLLYHYEQVH 121 (327)
Q Consensus 66 ~Ly~~V~~~GG~-~~V~~~~~W~eV~~~l~~p~~~~~~s~~Lk~~Y~k~L~~yE~~~ 121 (327)
.|+.-|...... ..|+-++.|.+++..---.. .-..+|..|.+.|...+..|
T Consensus 12 ~l~~~v~~~~~~~~~~~Gn~iwk~le~~~~t~H----twQSwR~Ry~K~L~~~~~~~ 64 (65)
T PF08914_consen 12 ALLDYVKENERQGGSVSGNKIWKELEEKHPTRH----TWQSWRDRYLKHLRGRPRKY 64 (65)
T ss_dssp HHHHHHHHT--STTTTTSSHHHHHHHHS-SSS------SHHHHHHHHHHT-------
T ss_pred HHHHHHHHhccCCCCCchHHHHHHHHHHcCCCC----CHHHHHHHHHHHHhccccCC
Confidence 466667543222 45778889999988752122 23479999999998876543
Done!