Query 020460
Match_columns 326
No_of_seqs 301 out of 1562
Neff 6.1
Searched_HMMs 46136
Date Fri Mar 29 02:32:52 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/020460.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/020460hhsearch_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 99.9 7.1E-27 1.5E-31 236.6 15.7 179 38-220 153-339 (512)
2 smart00501 BRIGHT BRIGHT, ARID 99.9 7.5E-27 1.6E-31 187.0 10.6 91 47-137 1-92 (93)
3 PF01388 ARID: ARID/BRIGHT DNA 99.9 3.4E-25 7.3E-30 176.5 8.9 88 46-133 4-92 (92)
4 PTZ00199 high mobility group p 99.9 9.7E-22 2.1E-26 158.1 10.4 84 234-317 7-93 (94)
5 cd01389 MATA_HMG-box MATA_HMG- 99.8 7.8E-19 1.7E-23 135.7 7.3 71 249-319 1-72 (77)
6 cd01388 SOX-TCF_HMG-box SOX-TC 99.8 2.2E-18 4.8E-23 131.6 7.4 69 249-317 1-70 (72)
7 PF00505 HMG_box: HMG (high mo 99.7 1.4E-17 3.1E-22 124.8 8.5 68 250-317 1-69 (69)
8 PF09011 HMG_box_2: HMG-box do 99.7 3.6E-17 7.8E-22 125.2 8.6 71 247-317 1-73 (73)
9 cd01390 HMGB-UBF_HMG-box HMGB- 99.7 5.1E-17 1.1E-21 120.7 8.5 65 250-314 1-66 (66)
10 smart00398 HMG high mobility g 99.7 7.5E-17 1.6E-21 120.5 8.6 69 249-317 1-70 (70)
11 KOG0381 HMG box-containing pro 99.7 4.8E-16 1E-20 124.3 10.3 75 246-320 17-95 (96)
12 COG5648 NHP6B Chromatin-associ 99.7 1.5E-16 3.3E-21 143.0 7.8 85 238-322 59-144 (211)
13 cd00084 HMG-box High Mobility 99.6 2.9E-15 6.2E-20 110.6 8.5 64 250-313 1-65 (66)
14 KOG0527 HMG-box transcription 99.6 5.7E-16 1.2E-20 149.7 5.9 76 244-319 57-133 (331)
15 KOG3248 Transcription factor T 99.5 5.8E-14 1.3E-18 133.5 11.5 136 182-318 110-261 (421)
16 KOG0526 Nucleosome-binding fac 99.5 2E-14 4.4E-19 143.5 6.8 77 238-318 524-601 (615)
17 KOG2510 SWI-SNF chromatin-remo 99.2 1.7E-11 3.6E-16 122.0 7.1 95 46-147 291-386 (532)
18 KOG0528 HMG-box transcription 99.0 2.7E-10 5.8E-15 113.3 4.3 78 244-321 320-398 (511)
19 KOG4715 SWI/SNF-related matrix 98.9 3.4E-09 7.4E-14 100.6 9.5 76 243-318 58-134 (410)
20 KOG2746 HMG-box transcription 98.3 8.1E-07 1.8E-11 91.8 4.8 79 238-318 170-251 (683)
21 PF14887 HMG_box_5: HMG (high 97.9 4.8E-05 1E-09 58.8 6.4 73 249-321 3-75 (85)
22 PF04690 YABBY: YABBY protein; 96.9 0.0016 3.5E-08 57.9 5.1 45 247-291 119-164 (170)
23 PF06382 DUF1074: Protein of u 96.6 0.01 2.2E-07 52.9 8.3 48 254-305 83-131 (183)
24 COG5648 NHP6B Chromatin-associ 96.2 0.0055 1.2E-07 55.9 4.0 66 249-314 143-209 (211)
25 PF08073 CHDNT: CHDNT (NUC034) 88.2 0.51 1.1E-05 34.5 2.8 39 254-292 13-52 (55)
26 PF04769 MAT_Alpha1: Mating-ty 87.4 1.2 2.6E-05 40.8 5.4 53 244-302 38-91 (201)
27 PF00249 Myb_DNA-binding: Myb- 81.8 3.5 7.5E-05 28.4 4.6 38 81-129 11-48 (48)
28 PF06244 DUF1014: Protein of u 78.3 2.1 4.6E-05 36.2 3.0 45 249-293 71-117 (122)
29 TIGR01624 LRP1_Cterm LRP1 C-te 73.1 2.3 5E-05 30.2 1.5 31 185-215 16-47 (50)
30 TIGR03481 HpnM hopanoid biosyn 67.2 15 0.00034 33.2 6.1 42 277-318 67-110 (198)
31 PRK15117 ABC transporter perip 65.7 14 0.00031 33.8 5.6 46 273-318 66-114 (211)
32 PF05142 DUF702: Domain of unk 65.7 3.8 8.2E-05 36.0 1.7 32 185-216 118-149 (154)
33 PF09441 Abp2: ARS binding pro 61.3 16 0.00036 32.4 4.8 42 68-113 44-85 (175)
34 PF12881 NUT_N: NUT protein N 55.7 22 0.00048 34.7 5.1 51 270-320 245-297 (328)
35 cd00167 SANT 'SWI3, ADA2, N-Co 54.7 28 0.0006 22.3 4.1 37 81-129 9-45 (45)
36 PF05494 Tol_Tol_Ttg2: Toluene 52.0 34 0.00073 29.8 5.4 42 277-318 42-84 (170)
37 PF13921 Myb_DNA-bind_6: Myb-l 51.9 32 0.00069 24.4 4.4 36 81-129 8-43 (60)
38 PF11304 DUF3106: Protein of u 46.5 70 0.0015 26.2 6.1 23 279-301 12-34 (107)
39 COG2854 Ttg2D ABC-type transpo 43.0 34 0.00073 31.5 4.0 44 277-320 74-118 (202)
40 KOG0493 Transcription factor E 42.8 49 0.0011 31.8 5.1 23 249-274 245-267 (342)
41 PF06394 Pepsin-I3: Pepsin inh 39.6 27 0.00059 27.2 2.5 31 288-326 38-68 (76)
42 PF12776 Myb_DNA-bind_3: Myb/S 39.1 71 0.0015 24.6 4.9 61 79-139 10-72 (96)
43 PF13873 Myb_DNA-bind_5: Myb/S 38.2 41 0.00089 25.2 3.3 54 77-131 14-71 (78)
44 smart00717 SANT SANT SWI3, AD 38.0 75 0.0016 20.4 4.3 26 99-129 22-47 (49)
45 KOG3223 Uncharacterized conser 37.9 33 0.00072 31.4 3.1 46 248-293 162-209 (221)
46 PF10545 MADF_DNA_bdg: Alcohol 37.4 34 0.00073 25.4 2.7 38 96-133 24-64 (85)
47 cd05694 S1_Rrp5_repeat_hs2_sc2 32.5 27 0.00058 26.5 1.4 32 180-213 2-33 (74)
48 PF12650 DUF3784: Domain of un 32.4 31 0.00067 27.3 1.8 17 286-302 25-41 (97)
49 PF13875 DUF4202: Domain of un 31.0 79 0.0017 28.7 4.4 39 256-297 131-170 (185)
50 PRK10363 cpxP periplasmic repr 30.8 1.1E+02 0.0025 27.3 5.3 39 277-316 111-149 (166)
51 PRK09706 transcriptional repre 30.4 1.2E+02 0.0026 25.2 5.3 41 279-319 88-128 (135)
52 PRK12751 cpxP periplasmic stre 29.7 1.1E+02 0.0024 27.1 5.0 34 277-310 117-150 (162)
53 smart00595 MADF subfamily of S 29.2 39 0.00084 25.8 1.9 42 94-135 23-65 (89)
54 PF02337 Gag_p10: Retroviral G 26.8 2.2E+02 0.0047 22.8 5.8 54 50-110 8-64 (90)
55 PF05066 HARE-HTH: HB1, ASXL, 26.3 1.1E+02 0.0024 22.6 3.9 43 52-105 3-45 (72)
56 PRK12750 cpxP periplasmic repr 26.1 2E+02 0.0043 25.6 6.0 36 278-313 125-160 (170)
57 cd08306 Death_FADD Fas-associa 25.6 43 0.00093 26.2 1.6 15 99-113 14-28 (86)
58 TIGR01557 myb_SHAQKYF myb-like 25.6 97 0.0021 22.5 3.3 42 78-130 9-55 (57)
59 PRK10236 hypothetical protein; 25.3 71 0.0015 30.1 3.1 41 260-300 92-139 (237)
60 TIGR00787 dctP tripartite ATP- 25.1 1.3E+02 0.0027 27.8 4.8 28 284-311 213-240 (257)
61 PF15076 DUF4543: Domain of un 23.6 55 0.0012 24.9 1.7 25 242-266 24-50 (75)
62 COG1638 DctP TRAP-type C4-dica 22.9 1.3E+02 0.0027 29.6 4.6 43 277-319 237-279 (332)
63 PF13725 tRNA_bind_2: Possible 22.0 54 0.0012 25.9 1.5 20 93-112 78-97 (101)
64 PF04967 HTH_10: HTH DNA bindi 21.6 1.2E+02 0.0026 21.8 3.1 40 88-129 13-52 (53)
65 cd07268 Glo_EDI_BRP_like_4 Thi 21.5 46 0.00099 29.2 1.0 68 41-108 3-80 (149)
66 KOG3838 Mannose lectin ERGIC-5 21.4 1E+02 0.0022 31.4 3.5 35 289-323 268-302 (497)
67 cd08780 Death_TRADD Death Doma 20.2 87 0.0019 25.2 2.3 11 99-109 14-24 (90)
No 1
>KOG2744 consensus DNA-binding proteins Bright/BRCAA1/RBP1 and related proteins containing BRIGHT domain [Transcription]
Probab=99.94 E-value=7.1e-27 Score=236.62 Aligned_cols=179 Identities=39% Similarity=0.575 Sum_probs=145.2
Q ss_pred CCCCchhhhhcHHHHHHHHHHHHHhcCCCCC-CCeeCCeecchhHHHHHHHhcCcchhhcccccHHHHHHHhCCCC-CCC
Q 020460 38 PTAKYEDIAQSSDLFWATLEAFHKSFGDKFK-VPTVGGKALDLHRLFVEVTSRGGLGKVIRDRRWKEVVVVFNFPT-TIT 115 (326)
Q Consensus 38 p~~~~e~~~~~~~~F~~~L~~F~~~rG~~l~-~P~i~gk~lDL~~Ly~~V~~rGG~~~V~~~~~W~eVa~~l~~~~-~~t 115 (326)
+....|.+..+++.||+.|+.||+.+|++|+ +|+|+|++||||.||.+|+++||++.|+..++|++|+..|.||. ++|
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 5666677777999999999999999999997 99999999999999999999999999999999999999999999 999
Q ss_pred cHHHHHHHHHHHhhHHHHHHHhhhcCCCCCCCCCCCC-CCCCC-CCCCCCCCCcc-ccc---CCCCCCcccccCCceeec
Q 020460 116 SASFVLRKYYLSLLYHFEQVYYFRREAPSSSMPDAVS-GSSLD-NGSASPEEGST-INQ---LGSQGSSKLQIGCSVSGV 189 (326)
Q Consensus 116 ~as~~Lk~~Y~k~L~~fE~~~~~~~~~~~~~~~~~~~-~~~~~-~~~~~~~~~~~-~~~---~~~~~~~~~~~~~~v~~~ 189 (326)
++++.||++|.++|++||+.+++....+...+.+... ..++. .+...-+.++. ... .....++ ...+.++
T Consensus 233 saaf~lr~~y~K~L~~ye~~~~~~~~~pln~p~~~~~~a~~~~~rE~~~~~~~~~~~~~~~~~~~~~~~----~~~aa~~ 308 (512)
T KOG2744|consen 233 SAAFTLRKQYLKLLFEYECEFEKNRHVPLNSPAELSEEASSSNRREGRRHELSPSKEFQANGPSEEEPA----EAEAAPE 308 (512)
T ss_pred hHHHHHHHHHHHHHHHHHHHHHHhccCCCCCcccccccccccccccccccccCcchhhccCCccccccc----ccccchh
Confidence 9999999999999999999999998777776665433 22222 11112222221 111 1111111 2578999
Q ss_pred ccCccCCCceEEEeeccccccccccccCCCC
Q 020460 190 IDGKFDNGYLVTVNLGSEQLKGVLYHIPHAH 220 (326)
Q Consensus 190 idgkf~~gy~vtv~~gse~~~g~ly~~p~~~ 220 (326)
|+|+|+.||++++.++++.+++++|+.+...
T Consensus 309 ~~g~f~~~~~~~~~~~s~~ln~~~~~~~~~~ 339 (512)
T KOG2744|consen 309 ILGNFLQGLLVFMKDGSEPLNGVLYLGPPDL 339 (512)
T ss_pred hhccccccCceeccCcchhccCccccccCcc
Confidence 9999999999999999999999999986644
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=7.5e-27 Score=187.00 Aligned_cols=91 Identities=40% Similarity=0.652 Sum_probs=87.3
Q ss_pred hcHHHHHHHHHHHHHhcCCCC-CCCeeCCeecchhHHHHHHHhcCcchhhcccccHHHHHHHhCCCCCCCcHHHHHHHHH
Q 020460 47 QSSDLFWATLEAFHKSFGDKF-KVPTVGGKALDLHRLFVEVTSRGGLGKVIRDRRWKEVVVVFNFPTTITSASFVLRKYY 125 (326)
Q Consensus 47 ~~~~~F~~~L~~F~~~rG~~l-~~P~i~gk~lDL~~Ly~~V~~rGG~~~V~~~~~W~eVa~~l~~~~~~t~as~~Lk~~Y 125 (326)
++++.|++.|.+||+.+|+++ ++|+|+|++||||+||.+|+++|||++||++++|.+||+.||+++++++++..|+++|
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 7999999999999999999999999999999999999999999998999999999999
Q ss_pred HHhhHHHHHHHh
Q 020460 126 LSLLYHFEQVYY 137 (326)
Q Consensus 126 ~k~L~~fE~~~~ 137 (326)
.+||++||+++.
T Consensus 81 ~k~L~~yE~~~~ 92 (93)
T smart00501 81 ERYLLPFERFLR 92 (93)
T ss_pred HHHhHHHHHHhh
Confidence 999999999864
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=3.4e-25 Score=176.54 Aligned_cols=88 Identities=38% Similarity=0.711 Sum_probs=81.9
Q ss_pred hhcHHHHHHHHHHHHHhcCCCC-CCCeeCCeecchhHHHHHHHhcCcchhhcccccHHHHHHHhCCCCCCCcHHHHHHHH
Q 020460 46 AQSSDLFWATLEAFHKSFGDKF-KVPTVGGKALDLHRLFVEVTSRGGLGKVIRDRRWKEVVVVFNFPTTITSASFVLRKY 124 (326)
Q Consensus 46 ~~~~~~F~~~L~~F~~~rG~~l-~~P~i~gk~lDL~~Ly~~V~~rGG~~~V~~~~~W~eVa~~l~~~~~~t~as~~Lk~~ 124 (326)
..+++.|++.|.+||+.+|+++ .+|.|+|++||||+||.+|+++|||++|+++++|.+||+.||+++.+++.+..|+++
T Consensus 4 ~~~~~~F~~~L~~f~~~~g~~~~~~P~i~g~~vDL~~Ly~~V~~~GG~~~V~~~~~W~~va~~lg~~~~~~~~~~~L~~~ 83 (92)
T PF01388_consen 4 TREREQFLEQLREFHESRGTPIDRPPVIGGKPVDLYKLYKAVMKRGGFDKVTKNKKWREVARKLGFPPSSTSAAQQLRQH 83 (92)
T ss_dssp CHHHHHHHHHHHHHHHHTTSSSSS-SEETTSE-SHHHHHHHHHHHTSHHHHHHHTTHHHHHHHTTS-TTSCHHHHHHHHH
T ss_pred chHHHHHHHHHHHHHHHcCCCCCCCCcCCCEeCcHHHHHHHHHhCcCcccCcccchHHHHHHHhCCCCCCCcHHHHHHHH
Confidence 4678999999999999999997 799999999999999999999999999999999999999999999888888999999
Q ss_pred HHHhhHHHH
Q 020460 125 YLSLLYHFE 133 (326)
Q Consensus 125 Y~k~L~~fE 133 (326)
|++||++||
T Consensus 84 Y~~~L~~fE 92 (92)
T PF01388_consen 84 YEKYLLPFE 92 (92)
T ss_dssp HHHHTHHHH
T ss_pred HHHHhHhhC
Confidence 999999998
No 4
>PTZ00199 high mobility group protein; Provisional
Probab=99.86 E-value=9.7e-22 Score=158.12 Aligned_cols=84 Identities=32% Similarity=0.519 Sum_probs=78.0
Q ss_pred ccccccccccCCCCCCCCCCCChHHHHHHHHHHHhhccCCCCc---hHHHHHHHHHhhcCCHHHhHHHHHHHHHHHHHHH
Q 020460 234 HRRRKRSRLALRDPSRPKSNRSGYNFFFAEHYARLKPHYYGQE---KAISKKIGVLWSNLTEAEKQVYQEKGLKDKERYK 310 (326)
Q Consensus 234 r~kkkk~~kk~kdp~~PKrP~SaY~lF~~e~r~~lk~e~p~~~---~eisk~ige~Wk~LseeeK~~Y~e~A~~dkerY~ 310 (326)
++.+++++++.+||++||||+|||++|+.++|..|+.+||++. .+|+++||++|+.|+++||.+|+++|+.|+++|.
T Consensus 7 ~~~~k~~~k~~kdp~~PKrP~sAY~~F~~~~R~~i~~~~P~~~~~~~evsk~ige~Wk~ls~eeK~~y~~~A~~dk~rY~ 86 (94)
T PTZ00199 7 KVLVRKNKRKKKDPNAPKRALSAYMFFAKEKRAEIIAENPELAKDVAAVGKMVGEAWNKLSEEEKAPYEKKAQEDKVRYE 86 (94)
T ss_pred CccccccCCCCCCCCCCCCCCcHHHHHHHHHHHHHHHHCcCCcccHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHH
Confidence 4445666677899999999999999999999999999999974 8999999999999999999999999999999999
Q ss_pred HHHHHHH
Q 020460 311 SEMLEYR 317 (326)
Q Consensus 311 ~em~~Yk 317 (326)
.||.+|+
T Consensus 87 ~e~~~Y~ 93 (94)
T PTZ00199 87 KEKAEYA 93 (94)
T ss_pred HHHHHHh
Confidence 9999996
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=99.77 E-value=7.8e-19 Score=135.70 Aligned_cols=71 Identities=25% Similarity=0.427 Sum_probs=68.8
Q ss_pred CCCCCCChHHHHHHHHHHHhhccCCCCc-hHHHHHHHHHhhcCCHHHhHHHHHHHHHHHHHHHHHHHHHHhc
Q 020460 249 RPKSNRSGYNFFFAEHYARLKPHYYGQE-KAISKKIGVLWSNLTEAEKQVYQEKGLKDKERYKSEMLEYRSS 319 (326)
Q Consensus 249 ~PKrP~SaY~lF~~e~r~~lk~e~p~~~-~eisk~ige~Wk~LseeeK~~Y~e~A~~dkerY~~em~~Yk~~ 319 (326)
+||||+||||||+++.|..++.++|+++ .+|+++||++|+.|++++|++|.++|++++++|.+++++|+-.
T Consensus 1 ~~kRP~naf~lf~~~~r~~~~~~~p~~~~~eisk~~g~~Wk~ls~eeK~~y~~~A~~~k~~~~~~~p~Yky~ 72 (77)
T cd01389 1 KIPRPRNAFILYRQDKHAQLKTENPGLTNNEISRIIGRMWRSESPEVKAYYKELAEEEKERHAREYPDYKYT 72 (77)
T ss_pred CCCCCCcHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHhhCCHHHHHHHHHHHHHHHHHHHHHCCCCccc
Confidence 5899999999999999999999999999 9999999999999999999999999999999999999999854
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=99.75 E-value=2.2e-18 Score=131.59 Aligned_cols=69 Identities=30% Similarity=0.401 Sum_probs=67.1
Q ss_pred CCCCCCChHHHHHHHHHHHhhccCCCCc-hHHHHHHHHHhhcCCHHHhHHHHHHHHHHHHHHHHHHHHHH
Q 020460 249 RPKSNRSGYNFFFAEHYARLKPHYYGQE-KAISKKIGVLWSNLTEAEKQVYQEKGLKDKERYKSEMLEYR 317 (326)
Q Consensus 249 ~PKrP~SaY~lF~~e~r~~lk~e~p~~~-~eisk~ige~Wk~LseeeK~~Y~e~A~~dkerY~~em~~Yk 317 (326)
+.|||+|||++|++++|.+++.+||+++ .+|+++||+.|+.|++++|++|.++|++++++|++++++|+
T Consensus 1 ~iKrP~naf~~F~~~~r~~~~~~~p~~~~~eisk~l~~~Wk~ls~~eK~~y~~~a~~~k~~y~~~~p~y~ 70 (72)
T cd01388 1 HIKRPMNAFMLFSKRHRRKVLQEYPLKENRAISKILGDRWKALSNEEKQPYYEEAKKLKELHMKLYPDYK 70 (72)
T ss_pred CCCCCCcHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHCcCCC
Confidence 4689999999999999999999999999 99999999999999999999999999999999999999996
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=1.4e-17 Score=124.85 Aligned_cols=68 Identities=40% Similarity=0.651 Sum_probs=65.0
Q ss_pred CCCCCChHHHHHHHHHHHhhccCCCCc-hHHHHHHHHHhhcCCHHHhHHHHHHHHHHHHHHHHHHHHHH
Q 020460 250 PKSNRSGYNFFFAEHYARLKPHYYGQE-KAISKKIGVLWSNLTEAEKQVYQEKGLKDKERYKSEMLEYR 317 (326)
Q Consensus 250 PKrP~SaY~lF~~e~r~~lk~e~p~~~-~eisk~ige~Wk~LseeeK~~Y~e~A~~dkerY~~em~~Yk 317 (326)
||||+|||++|+.+++..++.++|++. .+|+++||++|++|+++||++|.+.|++++++|+.+|++|+
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 899999999999999999999999999 99999999999999999999999999999999999999996
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=3.6e-17 Score=125.21 Aligned_cols=71 Identities=38% Similarity=0.655 Sum_probs=62.3
Q ss_pred CCCCCCCCChHHHHHHHHHHHhhcc-CCCCc-hHHHHHHHHHhhcCCHHHhHHHHHHHHHHHHHHHHHHHHHH
Q 020460 247 PSRPKSNRSGYNFFFAEHYARLKPH-YYGQE-KAISKKIGVLWSNLTEAEKQVYQEKGLKDKERYKSEMLEYR 317 (326)
Q Consensus 247 p~~PKrP~SaY~lF~~e~r~~lk~e-~p~~~-~eisk~ige~Wk~LseeeK~~Y~e~A~~dkerY~~em~~Yk 317 (326)
|++||+|+|||+||+.+++.+++.. .+... .|+++.|++.|++||++||.+|+++|+.++++|..+|..|+
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 5789999999999999999999988 66666 99999999999999999999999999999999999999995
No 9
>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=5.1e-17 Score=120.66 Aligned_cols=65 Identities=40% Similarity=0.615 Sum_probs=63.2
Q ss_pred CCCCCChHHHHHHHHHHHhhccCCCCc-hHHHHHHHHHhhcCCHHHhHHHHHHHHHHHHHHHHHHH
Q 020460 250 PKSNRSGYNFFFAEHYARLKPHYYGQE-KAISKKIGVLWSNLTEAEKQVYQEKGLKDKERYKSEML 314 (326)
Q Consensus 250 PKrP~SaY~lF~~e~r~~lk~e~p~~~-~eisk~ige~Wk~LseeeK~~Y~e~A~~dkerY~~em~ 314 (326)
||+|+|||++|++++|..++.++|+++ .+|++.||++|++|+++||.+|.++|++++++|+.+|.
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 899999999999999999999999998 99999999999999999999999999999999999873
No 10
>smart00398 HMG high mobility group.
Probab=99.70 E-value=7.5e-17 Score=120.47 Aligned_cols=69 Identities=43% Similarity=0.662 Sum_probs=67.2
Q ss_pred CCCCCCChHHHHHHHHHHHhhccCCCCc-hHHHHHHHHHhhcCCHHHhHHHHHHHHHHHHHHHHHHHHHH
Q 020460 249 RPKSNRSGYNFFFAEHYARLKPHYYGQE-KAISKKIGVLWSNLTEAEKQVYQEKGLKDKERYKSEMLEYR 317 (326)
Q Consensus 249 ~PKrP~SaY~lF~~e~r~~lk~e~p~~~-~eisk~ige~Wk~LseeeK~~Y~e~A~~dkerY~~em~~Yk 317 (326)
+||+|+|||++|++++|..++.++|++. .+|+++||++|+.|++++|++|.++|++++++|..++++|+
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 5899999999999999999999999999 99999999999999999999999999999999999999985
No 11
>KOG0381 consensus HMG box-containing protein [General function prediction only]
Probab=99.66 E-value=4.8e-16 Score=124.31 Aligned_cols=75 Identities=39% Similarity=0.671 Sum_probs=71.8
Q ss_pred CC--CCCCCCCChHHHHHHHHHHHhhccCCCCc-hHHHHHHHHHhhcCCHHHhHHHHHHHHHHHHHHHHHHH-HHHhcC
Q 020460 246 DP--SRPKSNRSGYNFFFAEHYARLKPHYYGQE-KAISKKIGVLWSNLTEAEKQVYQEKGLKDKERYKSEML-EYRSSY 320 (326)
Q Consensus 246 dp--~~PKrP~SaY~lF~~e~r~~lk~e~p~~~-~eisk~ige~Wk~LseeeK~~Y~e~A~~dkerY~~em~-~Yk~~~ 320 (326)
|+ ..||+|++||++|+.+.|.+++.+||++. .++++++|++|++|++++|.+|+..|.+++++|..+|. +|+..+
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 59999999999999999999999999988 99999999999999999999999999999999999999 998765
No 12
>COG5648 NHP6B Chromatin-associated proteins containing the HMG domain [Chromatin structure and dynamics]
Probab=99.66 E-value=1.5e-16 Score=142.99 Aligned_cols=85 Identities=28% Similarity=0.444 Sum_probs=80.6
Q ss_pred ccccccCCCCCCCCCCCChHHHHHHHHHHHhhccCCCCc-hHHHHHHHHHhhcCCHHHhHHHHHHHHHHHHHHHHHHHHH
Q 020460 238 KRSRLALRDPSRPKSNRSGYNFFFAEHYARLKPHYYGQE-KAISKKIGVLWSNLTEAEKQVYQEKGLKDKERYKSEMLEY 316 (326)
Q Consensus 238 kk~~kk~kdp~~PKrP~SaY~lF~~e~r~~lk~e~p~~~-~eisk~ige~Wk~LseeeK~~Y~e~A~~dkerY~~em~~Y 316 (326)
+...++++||+.||||+|||++|++++|.++..++|++. .++++++|++|++|+++||++|.+.|..++++|..++..|
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 455677899999999999999999999999999999999 9999999999999999999999999999999999999999
Q ss_pred HhcCCc
Q 020460 317 RSSYDS 322 (326)
Q Consensus 317 k~~~~~ 322 (326)
.++...
T Consensus 139 ~~k~~~ 144 (211)
T COG5648 139 NKKLPN 144 (211)
T ss_pred hcccCC
Confidence 997754
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=2.9e-15 Score=110.62 Aligned_cols=64 Identities=47% Similarity=0.707 Sum_probs=62.3
Q ss_pred CCCCCChHHHHHHHHHHHhhccCCCCc-hHHHHHHHHHhhcCCHHHhHHHHHHHHHHHHHHHHHH
Q 020460 250 PKSNRSGYNFFFAEHYARLKPHYYGQE-KAISKKIGVLWSNLTEAEKQVYQEKGLKDKERYKSEM 313 (326)
Q Consensus 250 PKrP~SaY~lF~~e~r~~lk~e~p~~~-~eisk~ige~Wk~LseeeK~~Y~e~A~~dkerY~~em 313 (326)
||+|+|||++|+++.|..++.++|++. .+|++++|++|+.|++++|.+|.++|++++++|+.++
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 799999999999999999999999988 9999999999999999999999999999999999876
No 14
>KOG0527 consensus HMG-box transcription factor [Transcription]
Probab=99.61 E-value=5.7e-16 Score=149.65 Aligned_cols=76 Identities=18% Similarity=0.298 Sum_probs=72.4
Q ss_pred CCCCCCCCCCCChHHHHHHHHHHHhhccCCCCc-hHHHHHHHHHhhcCCHHHhHHHHHHHHHHHHHHHHHHHHHHhc
Q 020460 244 LRDPSRPKSNRSGYNFFFAEHYARLKPHYYGQE-KAISKKIGVLWSNLTEAEKQVYQEKGLKDKERYKSEMLEYRSS 319 (326)
Q Consensus 244 ~kdp~~PKrP~SaY~lF~~e~r~~lk~e~p~~~-~eisk~ige~Wk~LseeeK~~Y~e~A~~dkerY~~em~~Yk~~ 319 (326)
++...+.||||||||+|.+.+|.+|.+++|++. .||+|+||.+||.|+|+||++|.++|++.|..|++|+++||-+
T Consensus 57 k~~~~hIKRPMNAFMVWSq~~RRkma~qnP~mHNSEISK~LG~~WK~Lse~EKrPFi~EAeRLR~~HmkehPdYKYR 133 (331)
T KOG0527|consen 57 KTSTDRIKRPMNAFMVWSQGQRRKLAKQNPKMHNSEISKRLGAEWKLLSEEEKRPFVDEAERLRAQHMKEYPDYKYR 133 (331)
T ss_pred CCCccccCCCcchhhhhhHHHHHHHHHhCcchhhHHHHHHHHHHHhhcCHhhhccHHHHHHHHHHHHHHhCCCcccc
Confidence 445679999999999999999999999999999 9999999999999999999999999999999999999999874
No 15
>KOG3248 consensus Transcription factor TCF-4 [Transcription]
Probab=99.53 E-value=5.8e-14 Score=133.55 Aligned_cols=136 Identities=18% Similarity=0.238 Sum_probs=99.0
Q ss_pred cCCceeecccCccCCCceEEEeecccccccccc--ccCCCC----------CCCCCCC-CCCC--ccccccccccccCCC
Q 020460 182 IGCSVSGVIDGKFDNGYLVTVNLGSEQLKGVLY--HIPHAH----------NVSQSSN-NSAA--PTHRRRKRSRLALRD 246 (326)
Q Consensus 182 ~~~~v~~~idgkf~~gy~vtv~~gse~~~g~ly--~~p~~~----------~~~~~~~-~~a~--~~r~kkkk~~kk~kd 246 (326)
+|-+|+-+..|.|.+.|+-+|...-..|.-..+ ..|... .+++.+. .++. ..++...+++.+.|+
T Consensus 110 l~wp~y~~pt~~~~~p~p~~~~asmsrf~ph~~~p~~p~~~tagiPhpaiv~P~~kqes~~~~~nvk~~~~~k~e~e~Kk 189 (421)
T KOG3248|consen 110 LGWPVYPIPTFGFRHPYPGVVNASMSRFSPHHVEPGHPGLHTAGIPHPAIVTPPVKQESDSAPQNVKRQAESKKEEEAKK 189 (421)
T ss_pred cCCccccCCCCCCCCCCchhhhhhhhhcchhccCCCCCCccccCCCCccccCCcccCcccccccccchhhhccccccccC
Confidence 466889999999999999866655555542211 112211 1222222 1111 222222233333344
Q ss_pred CCCCCCCCChHHHHHHHHHHHhhccCCCCc-hHHHHHHHHHhhcCCHHHhHHHHHHHHHHHHHHHHHHHHHHh
Q 020460 247 PSRPKSNRSGYNFFFAEHYARLKPHYYGQE-KAISKKIGVLWSNLTEAEKQVYQEKGLKDKERYKSEMLEYRS 318 (326)
Q Consensus 247 p~~PKrP~SaY~lF~~e~r~~lk~e~p~~~-~eisk~ige~Wk~LseeeK~~Y~e~A~~dkerY~~em~~Yk~ 318 (326)
+ +.|+|+||||+||+|.|++|.+|+.-.. .+|++++|++|.+||.||.++|.|+|++||+.|+.-+++|-+
T Consensus 190 p-hiKKPLNAFmlyMKEmRa~vvaEctlKeSAaiNqiLGrRWH~LSrEEQAKYyElArKerqlH~qlYP~WSA 261 (421)
T KOG3248|consen 190 P-HIKKPLNAFMLYMKEMRAKVVAECTLKESAAINQILGRRWHALSREEQAKYYELARKERQLHMQLYPGWSA 261 (421)
T ss_pred c-cccccHHHHHHHHHHHHHHHHHHhhhhhHHHHHHHHhHHHhhhhHHHHHHHHHHHHHHHHHHHHhcCCcch
Confidence 4 8999999999999999999999999777 999999999999999999999999999999999998888865
No 16
>KOG0526 consensus Nucleosome-binding factor SPN, POB3 subunit [Transcription; Replication, recombination and repair; Chromatin structure and dynamics]
Probab=99.50 E-value=2e-14 Score=143.53 Aligned_cols=77 Identities=30% Similarity=0.595 Sum_probs=72.3
Q ss_pred ccccccCCCCCCCCCCCChHHHHHHHHHHHhhccCCCCc-hHHHHHHHHHhhcCCHHHhHHHHHHHHHHHHHHHHHHHHH
Q 020460 238 KRSRLALRDPSRPKSNRSGYNFFFAEHYARLKPHYYGQE-KAISKKIGVLWSNLTEAEKQVYQEKGLKDKERYKSEMLEY 316 (326)
Q Consensus 238 kk~~kk~kdp~~PKrP~SaY~lF~~e~r~~lk~e~p~~~-~eisk~ige~Wk~LseeeK~~Y~e~A~~dkerY~~em~~Y 316 (326)
+++.+++|||++|||++||||+|++..|..||.+ +.. .+++|..|++|+.|+. |.+|+++|+.||.||+.||.+|
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 3555678999999999999999999999999998 888 9999999999999999 9999999999999999999999
Q ss_pred Hh
Q 020460 317 RS 318 (326)
Q Consensus 317 k~ 318 (326)
+.
T Consensus 600 k~ 601 (615)
T KOG0526|consen 600 KN 601 (615)
T ss_pred cC
Confidence 93
No 17
>KOG2510 consensus SWI-SNF chromatin-remodeling complex protein [Chromatin structure and dynamics]
Probab=99.22 E-value=1.7e-11 Score=122.00 Aligned_cols=95 Identities=29% Similarity=0.513 Sum_probs=87.0
Q ss_pred hhcHHHHHHHHHHHHHhcCCCCC-CCeeCCeecchhHHHHHHHhcCcchhhcccccHHHHHHHhCCCCCCCcHHHHHHHH
Q 020460 46 AQSSDLFWATLEAFHKSFGDKFK-VPTVGGKALDLHRLFVEVTSRGGLGKVIRDRRWKEVVVVFNFPTTITSASFVLRKY 124 (326)
Q Consensus 46 ~~~~~~F~~~L~~F~~~rG~~l~-~P~i~gk~lDL~~Ly~~V~~rGG~~~V~~~~~W~eVa~~l~~~~~~t~as~~Lk~~ 124 (326)
..+++..+++|+.|++.+.+++. +|.++.|+||||+||..|..+||+..|++++ +++|..|| .++++.||++
T Consensus 291 qp~r~~wvDR~raF~ee~~Sp~t~~p~~gakPldl~rlYvsvke~gg~~~v~knk--rd~a~~lg-----ssaa~~l~k~ 363 (532)
T KOG2510|consen 291 QPERKEWVDRLRAFTEERASPMTNLPAVGAKPLDLYRLYVSVKEIGGLTQVNKNK--RDLATNLG-----SSAASSLKKQ 363 (532)
T ss_pred CcchhhHHHHHHHHHHhhcCcccccccccccchhHHHHHHHHHHhccceeeccch--hhhhhccc-----hHHHHHHHHH
Confidence 46789999999999999999995 8999999999999999999999999999999 99999998 5788899999
Q ss_pred HHHhhHHHHHHHhhhcCCCCCCC
Q 020460 125 YLSLLYHFEQVYYFRREAPSSSM 147 (326)
Q Consensus 125 Y~k~L~~fE~~~~~~~~~~~~~~ 147 (326)
|.+||+.||+.+-.|++++....
T Consensus 364 y~~~lf~fec~f~Rg~e~p~~~~ 386 (532)
T KOG2510|consen 364 YIQYLFAFECKFERGEEPPPDIF 386 (532)
T ss_pred HHHHHHhhceeeeccCCCCHHHh
Confidence 99999999999888887776443
No 18
>KOG0528 consensus HMG-box transcription factor SOX5 [Transcription]
Probab=98.99 E-value=2.7e-10 Score=113.26 Aligned_cols=78 Identities=17% Similarity=0.255 Sum_probs=70.4
Q ss_pred CCCCCCCCCCCChHHHHHHHHHHHhhccCCCCc-hHHHHHHHHHhhcCCHHHhHHHHHHHHHHHHHHHHHHHHHHhcCC
Q 020460 244 LRDPSRPKSNRSGYNFFFAEHYARLKPHYYGQE-KAISKKIGVLWSNLTEAEKQVYQEKGLKDKERYKSEMLEYRSSYD 321 (326)
Q Consensus 244 ~kdp~~PKrP~SaY~lF~~e~r~~lk~e~p~~~-~eisk~ige~Wk~LseeeK~~Y~e~A~~dkerY~~em~~Yk~~~~ 321 (326)
...+.+.||||||||+|.++.|.+|.+.+||+. ..|+|++|.+|+.||..||++|+|.-.+.-..|...+++||-+-+
T Consensus 320 ~ss~PHIKRPMNAFMVWAkDERRKILqA~PDMHNSnISKILGSRWKaMSN~eKQPYYEEQaRLSk~HlEk~PdYrYkPR 398 (511)
T KOG0528|consen 320 ASSEPHIKRPMNAFMVWAKDERRKILQAFPDMHNSNISKILGSRWKAMSNTEKQPYYEEQARLSKLHLEKYPDYRYKPR 398 (511)
T ss_pred CCCCccccCCcchhhcccchhhhhhhhcCccccccchhHHhcccccccccccccchHHHHHHHHHhhhccCcccccCCC
Confidence 344568999999999999999999999999999 999999999999999999999998777777799999999987644
No 19
>KOG4715 consensus SWI/SNF-related matrix-associated actin-dependent regulator of chromatin [Chromatin structure and dynamics]
Probab=98.94 E-value=3.4e-09 Score=100.61 Aligned_cols=76 Identities=24% Similarity=0.364 Sum_probs=71.9
Q ss_pred cCCCCCCCCCCCChHHHHHHHHHHHhhccCCCCc-hHHHHHHHHHhhcCCHHHhHHHHHHHHHHHHHHHHHHHHHHh
Q 020460 243 ALRDPSRPKSNRSGYNFFFAEHYARLKPHYYGQE-KAISKKIGVLWSNLTEAEKQVYQEKGLKDKERYKSEMLEYRS 318 (326)
Q Consensus 243 k~kdp~~PKrP~SaY~lF~~e~r~~lk~e~p~~~-~eisk~ige~Wk~LseeeK~~Y~e~A~~dkerY~~em~~Yk~ 318 (326)
..+.|..|-+|+-.||.|++..++++|+.||++. .||.|+||.+|..|+|+||+.|...++.+|..|.+.|..|..
T Consensus 58 ~pkpPkppekpl~pymrySrkvWd~VkA~nPe~kLWeiGK~Ig~mW~dLpd~EK~ey~~EYeaEKieY~~smkayh~ 134 (410)
T KOG4715|consen 58 RPKPPKPPEKPLMPYMRYSRKVWDQVKASNPELKLWEIGKIIGGMWLDLPDEEKQEYLNEYEAEKIEYNESMKAYHN 134 (410)
T ss_pred CCCCCCCCCcccchhhHHhhhhhhhhhccCcchHHHHHHHHHHHHHhhCcchHHHHHHHHHHHHHHHHHHHHHHhhC
Confidence 3456778899999999999999999999999999 999999999999999999999999999999999999999976
No 20
>KOG2746 consensus HMG-box transcription factor Capicua and related proteins [Transcription]
Probab=98.26 E-value=8.1e-07 Score=91.80 Aligned_cols=79 Identities=24% Similarity=0.378 Sum_probs=70.8
Q ss_pred ccccccCCCCCCCCCCCChHHHHHHHHH--HHhhccCCCCc-hHHHHHHHHHhhcCCHHHhHHHHHHHHHHHHHHHHHHH
Q 020460 238 KRSRLALRDPSRPKSNRSGYNFFFAEHY--ARLKPHYYGQE-KAISKKIGVLWSNLTEAEKQVYQEKGLKDKERYKSEML 314 (326)
Q Consensus 238 kk~~kk~kdp~~PKrP~SaY~lF~~e~r--~~lk~e~p~~~-~eisk~ige~Wk~LseeeK~~Y~e~A~~dkerY~~em~ 314 (326)
..+..-++|..+.++|||||++|++.+| ..+.+.||+.+ +.|++++|+.|-.|-+.||+.|-++|.+.|+.|.++
T Consensus 170 dgrspnkr~k~HirrPMnaf~ifskrhr~~g~vhq~~pn~DNrtIskiLgewWytL~~~Ekq~yhdLa~Qvk~Ahfka-- 247 (683)
T KOG2746|consen 170 DGRSPNKRDKDHIRRPMNAFHIFSKRHRGEGRVHQRHPNQDNRTISKILGEWWYTLGPNEKQKYHDLAFQVKEAHFKA-- 247 (683)
T ss_pred ccCCCCcCcchhhhhhhHHHHHHHhhcCCccchhccCccccchhHHHHHhhhHhhhCchhhhhHHHHHHHHHHHHhhh--
Confidence 4444556777799999999999999999 89999999999 999999999999999999999999999999999986
Q ss_pred HHHh
Q 020460 315 EYRS 318 (326)
Q Consensus 315 ~Yk~ 318 (326)
+|+.
T Consensus 248 e~~k 251 (683)
T KOG2746|consen 248 EWKK 251 (683)
T ss_pred hccc
Confidence 4443
No 21
>PF14887 HMG_box_5: HMG (high mobility group) box 5; PDB: 1L8Y_A 1L8Z_A 2HDZ_A.
Probab=97.85 E-value=4.8e-05 Score=58.83 Aligned_cols=73 Identities=21% Similarity=0.374 Sum_probs=58.0
Q ss_pred CCCCCCChHHHHHHHHHHHhhccCCCCchHHHHHHHHHhhcCCHHHhHHHHHHHHHHHHHHHHHHHHHHhcCC
Q 020460 249 RPKSNRSGYNFFFAEHYARLKPHYYGQEKAISKKIGVLWSNLTEAEKQVYQEKGLKDKERYKSEMLEYRSSYD 321 (326)
Q Consensus 249 ~PKrP~SaY~lF~~e~r~~lk~e~p~~~~eisk~ige~Wk~LseeeK~~Y~e~A~~dkerY~~em~~Yk~~~~ 321 (326)
-|..|.++--+|.+.......+.++.-..-..+.+...|++|++.+|.+|..+|.+|..+|+.+|.+|++-..
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 LPETPKTAQEIWQQSVIGDYLAKFRNDRKKALKAMEAQWSQMEKKEKLKWIKKAAEDQKRYERELREMRSAPA 75 (85)
T ss_dssp -S----THHHHHHHHHHHHHHHHTTSTHHHHHHHHHHHHHTTGGGHHHHHHHHHHHHHHHHHHHHHCCS-CCC
T ss_pred CCCCCCCHHHHHHHHHHHHHHHHhhHhHHHHHHHHHHHHHHhhhhhhhHHHHHHHHHHHHHHHHHHHHhcCCC
Confidence 4778889999999888887777777666333668999999999999999999999999999999999998554
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=96.88 E-value=0.0016 Score=57.93 Aligned_cols=45 Identities=22% Similarity=0.360 Sum_probs=40.4
Q ss_pred CCCCCCCCChHHHHHHHHHHHhhccCCCCc-hHHHHHHHHHhhcCC
Q 020460 247 PSRPKSNRSGYNFFFAEHYARLKPHYYGQE-KAISKKIGVLWSNLT 291 (326)
Q Consensus 247 p~~PKrP~SaY~lF~~e~r~~lk~e~p~~~-~eisk~ige~Wk~Ls 291 (326)
|.+-.|-+|||+.|++|.-++||+++|+++ +|.-+..++.|+..+
T Consensus 119 PEKRqR~psaYn~f~k~ei~rik~~~p~ishkeaFs~aAknW~h~p 164 (170)
T PF04690_consen 119 PEKRQRVPSAYNRFMKEEIQRIKAENPDISHKEAFSAAAKNWAHFP 164 (170)
T ss_pred ccccCCCchhHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHhhhhCc
Confidence 344557789999999999999999999999 999999999998765
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=96.63 E-value=0.01 Score=52.92 Aligned_cols=48 Identities=23% Similarity=0.392 Sum_probs=41.8
Q ss_pred CChHHHHHHHHHHHhhccCCCCc-hHHHHHHHHHhhcCCHHHhHHHHHHHHHH
Q 020460 254 RSGYNFFFAEHYARLKPHYYGQE-KAISKKIGVLWSNLTEAEKQVYQEKGLKD 305 (326)
Q Consensus 254 ~SaY~lF~~e~r~~lk~e~p~~~-~eisk~ige~Wk~LseeeK~~Y~e~A~~d 305 (326)
.+||+-|+.+++.+ |.++. .|+....+..|..|+++||..|..++...
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 57899999998875 56677 99999999999999999999999876544
No 24
>COG5648 NHP6B Chromatin-associated proteins containing the HMG domain [Chromatin structure and dynamics]
Probab=96.17 E-value=0.0055 Score=55.94 Aligned_cols=66 Identities=23% Similarity=0.168 Sum_probs=58.5
Q ss_pred CCCCCCChHHHHHHHHHHHhhccCCCCc-hHHHHHHHHHhhcCCHHHhHHHHHHHHHHHHHHHHHHH
Q 020460 249 RPKSNRSGYNFFFAEHYARLKPHYYGQE-KAISKKIGVLWSNLTEAEKQVYQEKGLKDKERYKSEML 314 (326)
Q Consensus 249 ~PKrP~SaY~lF~~e~r~~lk~e~p~~~-~eisk~ige~Wk~LseeeK~~Y~e~A~~dkerY~~em~ 314 (326)
+++.+.-.|+-+-.+.|+++...+|+.. .+..++++..|++|++.-|.+|.+.+.++++.|...|+
T Consensus 143 ~~~~~~~~~~e~~~~~r~~~~~~~~~~~~~e~~k~~~~~w~el~~skK~~~~~~~Kk~k~~~~~~~~ 209 (211)
T COG5648 143 PNKAPIGPFIENEPKIRPKVEGPSPDKALVEETKIISKAWSELDESKKKKYIDKYKKLKEEYDSFYP 209 (211)
T ss_pred CCCCCCchhhhccHHhccccCCCCcchhhhHHhhhhhhhhhhhChhhhhHHHHHHHHHHHHHhhhcc
Confidence 4566677777777888888888899988 99999999999999999999999999999999988765
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=88.16 E-value=0.51 Score=34.46 Aligned_cols=39 Identities=13% Similarity=0.160 Sum_probs=34.9
Q ss_pred CChHHHHHHHHHHHhhccCCCCc-hHHHHHHHHHhhcCCH
Q 020460 254 RSGYNFFFAEHYARLKPHYYGQE-KAISKKIGVLWSNLTE 292 (326)
Q Consensus 254 ~SaY~lF~~e~r~~lk~e~p~~~-~eisk~ige~Wk~Lse 292 (326)
.+.|-+|.+-.|+.|...||+.. ..+...++.+|+.-++
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 35688999999999999999999 9999999999987554
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=87.38 E-value=1.2 Score=40.82 Aligned_cols=53 Identities=21% Similarity=0.271 Sum_probs=38.1
Q ss_pred CCCCCCCCCCCChHHHHHHHHHHHhhccCCCCc-hHHHHHHHHHhhcCCHHHhHHHHHHH
Q 020460 244 LRDPSRPKSNRSGYNFFFAEHYARLKPHYYGQE-KAISKKIGVLWSNLTEAEKQVYQEKG 302 (326)
Q Consensus 244 ~kdp~~PKrP~SaY~lF~~e~r~~lk~e~p~~~-~eisk~ige~Wk~LseeeK~~Y~e~A 302 (326)
+....++|||.|+||.|..=+- ...++.. .+++..|+..|..=+- |..|.-.|
T Consensus 38 ~~~~~~~kr~lN~Fm~FRsyy~----~~~~~~~Qk~~S~~l~~lW~~dp~--k~~W~l~a 91 (201)
T PF04769_consen 38 KRSPEKAKRPLNGFMAFRSYYS----PIFPPLPQKELSGILTKLWEKDPF--KNKWSLMA 91 (201)
T ss_pred cccccccccchhHHHHHHHHHH----hhcCCcCHHHHHHHHHHHHhCCcc--HhHHHHHh
Confidence 3445578999999999986654 4456666 9999999999987433 44454443
No 27
>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=81.77 E-value=3.5 Score=28.42 Aligned_cols=38 Identities=24% Similarity=0.319 Sum_probs=27.1
Q ss_pred HHHHHHHhcCcchhhcccccHHHHHHHhCCCCCCCcHHHHHHHHHHHhh
Q 020460 81 RLFVEVTSRGGLGKVIRDRRWKEVVVVFNFPTTITSASFVLRKYYLSLL 129 (326)
Q Consensus 81 ~Ly~~V~~rGG~~~V~~~~~W~eVa~~l~~~~~~t~as~~Lk~~Y~k~L 129 (326)
.|...|...|.- .|..||..|+. +-...+++.+|.+||
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 455666666643 79999999992 223348899998886
No 28
>PF06244 DUF1014: Protein of unknown function (DUF1014); InterPro: IPR010422 This family consists of several hypothetical eukaryotic proteins of unknown function.
Probab=78.28 E-value=2.1 Score=36.21 Aligned_cols=45 Identities=18% Similarity=0.321 Sum_probs=39.0
Q ss_pred CCCCC-CChHHHHHHHHHHHhhccCCCCc-hHHHHHHHHHhhcCCHH
Q 020460 249 RPKSN-RSGYNFFFAEHYARLKPHYYGQE-KAISKKIGVLWSNLTEA 293 (326)
Q Consensus 249 ~PKrP-~SaY~lF~~e~r~~lk~e~p~~~-~eisk~ige~Wk~Lsee 293 (326)
+|-|. .-||.-|....-++|++++|++- ..+..+|-+.|..-+++
T Consensus 71 HPErR~KAAy~afeE~~Lp~lK~E~PgLrlsQ~kq~l~K~w~KSPeN 117 (122)
T PF06244_consen 71 HPERRMKAAYKAFEERRLPELKEENPGLRLSQYKQMLWKEWQKSPEN 117 (122)
T ss_pred CcchhHHHHHHHHHHHHhHHHHhhCCCchHHHHHHHHHHHHhcCCCC
Confidence 55444 47899999999999999999999 99999999999887754
No 29
>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=73.08 E-value=2.3 Score=30.25 Aligned_cols=31 Identities=32% Similarity=0.557 Sum_probs=27.2
Q ss_pred ceeecccCcc-CCCceEEEeeccccccccccc
Q 020460 185 SVSGVIDGKF-DNGYLVTVNLGSEQLKGVLYH 215 (326)
Q Consensus 185 ~v~~~idgkf-~~gy~vtv~~gse~~~g~ly~ 215 (326)
-|+++-||.- +..|--+|+||--.|+|+||-
T Consensus 16 Rvs~idd~~~~e~aYQt~V~IgGHvFkGiLyD 47 (50)
T TIGR01624 16 RVTAIDDGEQAEYAYQATVTIGGHVFKGFLHD 47 (50)
T ss_pred EEeccCCCCCceEEEEEEEEECceEEeeEEec
Confidence 4777778876 789999999999999999995
No 30
>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=67.18 E-value=15 Score=33.25 Aligned_cols=42 Identities=17% Similarity=0.419 Sum_probs=36.3
Q ss_pred hHHHH-HHHHHhhcCCHHHhHHHHHHHHH-HHHHHHHHHHHHHh
Q 020460 277 KAISK-KIGVLWSNLTEAEKQVYQEKGLK-DKERYKSEMLEYRS 318 (326)
Q Consensus 277 ~eisk-~ige~Wk~LseeeK~~Y~e~A~~-dkerY~~em~~Yk~ 318 (326)
..|++ .+|.-|+.+|++||+.|.+.-.. ....|-..+..|..
T Consensus 67 ~~mar~vLG~~W~~~s~~Qr~~F~~~F~~~l~~tY~~~l~~y~~ 110 (198)
T TIGR03481 67 PAMARLTLGSSWTSLSPEQRRRFIGAFRELSIATYASQFKSYAG 110 (198)
T ss_pred HHHHHHHhhhhhhhCCHHHHHHHHHHHHHHHHHHHHHHHHhhcC
Confidence 55554 78999999999999999987777 88899999999975
No 31
>PRK15117 ABC transporter periplasmic binding protein MlaC; Provisional
Probab=65.73 E-value=14 Score=33.82 Aligned_cols=46 Identities=17% Similarity=0.212 Sum_probs=37.5
Q ss_pred CCCc-hHHHH-HHHHHhhcCCHHHhHHHHHHHHH-HHHHHHHHHHHHHh
Q 020460 273 YGQE-KAISK-KIGVLWSNLTEAEKQVYQEKGLK-DKERYKSEMLEYRS 318 (326)
Q Consensus 273 p~~~-~eisk-~ige~Wk~LseeeK~~Y~e~A~~-dkerY~~em~~Yk~ 318 (326)
|..+ ..+++ .+|.-|+.+|+++|+.|.+.-+. ....|-..+.+|..
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 4455 55655 78999999999999999876665 67889999999975
No 32
>PF05142 DUF702: Domain of unknown function (DUF702) ; InterPro: IPR007818 This is a family of plant proteins of unknown function.
Probab=65.70 E-value=3.8 Score=35.99 Aligned_cols=32 Identities=38% Similarity=0.655 Sum_probs=29.1
Q ss_pred ceeecccCccCCCceEEEeecccccccccccc
Q 020460 185 SVSGVIDGKFDNGYLVTVNLGSEQLKGVLYHI 216 (326)
Q Consensus 185 ~v~~~idgkf~~gy~vtv~~gse~~~g~ly~~ 216 (326)
-|+++=||.-+..|--+|+||--.|+|+||--
T Consensus 118 RVssiDdgedE~AYQTaV~IGGHVFKGiLYDq 149 (154)
T PF05142_consen 118 RVSSIDDGEDEYAYQTAVNIGGHVFKGILYDQ 149 (154)
T ss_pred EEecccCcccceeeEEeEEECCEEeeeeeecc
Confidence 37888899999999999999999999999963
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=61.25 E-value=16 Score=32.36 Aligned_cols=42 Identities=14% Similarity=0.320 Sum_probs=35.6
Q ss_pred CCCeeCCeecchhHHHHHHHhcCcchhhcccccHHHHHHHhCCCCC
Q 020460 68 KVPTVGGKALDLHRLFVEVTSRGGLGKVIRDRRWKEVVVVFNFPTT 113 (326)
Q Consensus 68 ~~P~i~gk~lDL~~Ly~~V~~rGG~~~V~~~~~W~eVa~~l~~~~~ 113 (326)
.+|.-+||..+.|.||..|.++-.- .-+.|.++|-.||+.+.
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 3899999999999999999986543 34689999999999765
No 34
>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=55.74 E-value=22 Score=34.70 Aligned_cols=51 Identities=12% Similarity=-0.011 Sum_probs=37.1
Q ss_pred ccCCCCc-hHHHHHHHHHhhcCCHHHhHHHHHHHHHHHHHHH-HHHHHHHhcC
Q 020460 270 PHYYGQE-KAISKKIGVLWSNLTEAEKQVYQEKGLKDKERYK-SEMLEYRSSY 320 (326)
Q Consensus 270 ~e~p~~~-~eisk~ige~Wk~LseeeK~~Y~e~A~~dkerY~-~em~~Yk~~~ 320 (326)
...|.++ .|-....-+.|...|.-+|..|+|+|++=+|=-- +||..-+-++
T Consensus 245 r~kPtMtlEeGl~ra~qEW~~~SnfdRmifyemaekFmEFEaeEEmq~q~lq~ 297 (328)
T PF12881_consen 245 RLKPTMTLEEGLWRAVQEWQHTSNFDRMIFYEMAEKFMEFEAEEEMQIQKLQL 297 (328)
T ss_pred hcCCCccHHHHHHHHHHHhhccccccHHHHHHHHHHHccCCcHHHHHHHHHHH
Confidence 3456677 7777778899999999999999999998654222 5555555443
No 35
>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=54.71 E-value=28 Score=22.30 Aligned_cols=37 Identities=19% Similarity=0.277 Sum_probs=23.8
Q ss_pred HHHHHHHhcCcchhhcccccHHHHHHHhCCCCCCCcHHHHHHHHHHHhh
Q 020460 81 RLFVEVTSRGGLGKVIRDRRWKEVVVVFNFPTTITSASFVLRKYYLSLL 129 (326)
Q Consensus 81 ~Ly~~V~~rGG~~~V~~~~~W~eVa~~l~~~~~~t~as~~Lk~~Y~k~L 129 (326)
.|...|...|- ..|..|+..|+-- .+..++.+|..++
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 34555555552 5799999999641 2337777776653
No 36
>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=51.98 E-value=34 Score=29.79 Aligned_cols=42 Identities=19% Similarity=0.361 Sum_probs=31.9
Q ss_pred hHHHHHHHHHhhcCCHHHhHHHHHHHHH-HHHHHHHHHHHHHh
Q 020460 277 KAISKKIGVLWSNLTEAEKQVYQEKGLK-DKERYKSEMLEYRS 318 (326)
Q Consensus 277 ~eisk~ige~Wk~LseeeK~~Y~e~A~~-dkerY~~em~~Yk~ 318 (326)
.-....+|.-|+.+|++||+.|.+...+ ....|-..+.+|..
T Consensus 42 ~~ar~~LG~~w~~~s~~q~~~F~~~f~~~l~~~Y~~~l~~y~~ 84 (170)
T PF05494_consen 42 RMARRVLGRYWRKASPAQRQRFVEAFKQLLVRTYAKRLDEYSG 84 (170)
T ss_dssp HHHHHHHGGGTTTS-HHHHHHHHHHHHHHHHHHHHHHHHT-SS
T ss_pred HHHHHHHHHhHhhCCHHHHHHHHHHHHHHHHHHHHHHHHhhCC
Confidence 3344567889999999999999876655 67788888888875
No 37
>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=51.90 E-value=32 Score=24.40 Aligned_cols=36 Identities=19% Similarity=0.280 Sum_probs=22.5
Q ss_pred HHHHHHHhcCcchhhcccccHHHHHHHhCCCCCCCcHHHHHHHHHHHhh
Q 020460 81 RLFVEVTSRGGLGKVIRDRRWKEVVVVFNFPTTITSASFVLRKYYLSLL 129 (326)
Q Consensus 81 ~Ly~~V~~rGG~~~V~~~~~W~eVa~~l~~~~~~t~as~~Lk~~Y~k~L 129 (326)
.|...|...|. .|..||..|| .. ....++..|..+|
T Consensus 8 ~L~~~~~~~g~--------~W~~Ia~~l~-~R----t~~~~~~r~~~~l 43 (60)
T PF13921_consen 8 LLLELVKKYGN--------DWKKIAEHLG-NR----TPKQCRNRWRNHL 43 (60)
T ss_dssp HHHHHHHHHTS---------HHHHHHHST-TS-----HHHHHHHHHHTT
T ss_pred HHHHHHHHHCc--------CHHHHHHHHC-cC----CHHHHHHHHHHHC
Confidence 34555555553 6999999997 11 2236777777755
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=46.52 E-value=70 Score=26.18 Aligned_cols=23 Identities=9% Similarity=0.309 Sum_probs=10.2
Q ss_pred HHHHHHHHhhcCCHHHhHHHHHH
Q 020460 279 ISKKIGVLWSNLTEAEKQVYQEK 301 (326)
Q Consensus 279 isk~ige~Wk~LseeeK~~Y~e~ 301 (326)
+..-+.+.|+.|+++.|..+.+.
T Consensus 12 ~L~pl~~~W~~l~~~qr~k~l~~ 34 (107)
T PF11304_consen 12 ALAPLAERWNSLPPEQRRKWLQI 34 (107)
T ss_pred HHHHHHHHHhcCCHHHHHHHHHH
Confidence 33444444444444444444433
No 39
>COG2854 Ttg2D ABC-type transport system involved in resistance to organic solvents, auxiliary component [Secondary metabolites biosynthesis, transport, and catabolism]
Probab=42.98 E-value=34 Score=31.49 Aligned_cols=44 Identities=14% Similarity=0.271 Sum_probs=37.3
Q ss_pred hHHHHHHHHHhhcCCHHHhHHHHHHHHH-HHHHHHHHHHHHHhcC
Q 020460 277 KAISKKIGVLWSNLTEAEKQVYQEKGLK-DKERYKSEMLEYRSSY 320 (326)
Q Consensus 277 ~eisk~ige~Wk~LseeeK~~Y~e~A~~-dkerY~~em~~Yk~~~ 320 (326)
..-...+|.-|+.+|+++++.|.+..+. ....|-..+.+|+.+.
T Consensus 74 ~~a~~vLGk~~k~aspeQ~~~F~~aF~~yl~q~Y~~aL~~Y~~q~ 118 (202)
T COG2854 74 YAAKLVLGKYYKTASPEQRQAFFKAFRTYLEQTYGQALLDYKGQT 118 (202)
T ss_pred HHHHHHhccccccCCHHHHHHHHHHHHHHHHHHHHHHHHHccCCC
Confidence 5567788999999999999999876655 7789999999998753
No 40
>KOG0493 consensus Transcription factor Engrailed, contains HOX domain [General function prediction only]
Probab=42.77 E-value=49 Score=31.75 Aligned_cols=23 Identities=30% Similarity=0.491 Sum_probs=16.7
Q ss_pred CCCCCCChHHHHHHHHHHHhhccCCC
Q 020460 249 RPKSNRSGYNFFFAEHYARLKPHYYG 274 (326)
Q Consensus 249 ~PKrP~SaY~lF~~e~r~~lk~e~p~ 274 (326)
-=|||++|| ..|+-++||.|+-.
T Consensus 245 eeKRPRTAF---taeQL~RLK~EF~e 267 (342)
T KOG0493|consen 245 EEKRPRTAF---TAEQLQRLKAEFQE 267 (342)
T ss_pred hhcCccccc---cHHHHHHHHHHHhh
Confidence 347899985 56888888877643
No 41
>PF06394 Pepsin-I3: Pepsin inhibitor-3-like repeated domain; InterPro: IPR010480 Peptide proteinase inhibitors can be found as single domain proteins or as single or multiple domains within proteins; these are referred to as either simple or compound inhibitors, respectively. In many cases they are synthesised as part of a larger precursor protein, either as a prepropeptide or as an N-terminal domain associated with an inactive peptidase or zymogen. This domain prevents access of the substrate to the active site. Removal of the N-terminal inhibitor domain either by interaction with a second peptidase or by autocatalytic cleavage activates the zymogen. Other inhibitors interact direct with proteinases using a simple noncovalent lock and key mechanism; while yet others use a conformational change-based trapping mechanism that depends on their structural and thermodynamic properties. The members of this group of proteins belong to MEROPS inhibitor family I33, clan IR; the nematode aspartyl protease inhibitors or Aspins. They are restricted to parasitic nematode species. Structural features common to the nematode Aspins include the presence of a signal peptide sequence and the conservation of all four cysteine residues in the mature protein. The Y[V.A]RDLT sequence motif has been suggested as being of crucial functional importance in several filarial nematode inhibitors [], this sequence is not conserved in Tco-API-1 from Trichostrongylus colubriformis (Black scour worm) and it has been demonstrated that Tco-API-1, is not an Aspin as it does not inhibit porcine pepsin []. Related inhibitors from Onchocerca volvulus, Ov33 [] and Ascaris suum (Pig roundworm), PI-3 [] inhibit the in vitro activity of aspartyl proteases such as pepsin and cathepsin E (MEROPS peptidase family A1). Aspin may facilitate the safe passage of the eggs of Ascaris through the host stomach without digestion by pepsin [, ]. The other parasitic nematodes known to express homologous proteins do not pass through the stomach of their hosts []. Several proteins in the family are potent allergens in mammals. The three-dimensional structures of pepsin inhibitor-3 (PI-3) from A. suum and of the complex between PI-3 and porcine pepsin at 1. 75 A and 2.45 A resolution, respectively, have revealed the mechanism of aspartic protease inhibition. PI-3 has a new fold consisting of two identical domains, each comprising an antiparallel beta-sheet flanked by an alpha-helix. In the enzyme-inhibitor complex, the N-terminal beta-strand of PI-3 pairs with one strand of the 'active site flap' (residues 70-82) of pepsin, thus forming an eight-stranded beta-sheet that spans the two proteins. PI-3 has a novel mode of inhibition, using its N-terminal residues to occupy and therefore block the first three binding pockets in pepsin for substrate residues C-terminal to the scissile bond (S1'-S3') [].; PDB: 1F32_A 1F34_B.
Probab=39.58 E-value=27 Score=27.18 Aligned_cols=31 Identities=19% Similarity=0.500 Sum_probs=19.3
Q ss_pred hcCCHHHhHHHHHHHHHHHHHHHHHHHHHHhcCCcccCC
Q 020460 288 SNLTEAEKQVYQEKGLKDKERYKSEMLEYRSSYDSTVQQ 326 (326)
Q Consensus 288 k~LseeeK~~Y~e~A~~dkerY~~em~~Yk~~~~~~~q~ 326 (326)
+.|+++|+ ++-+.|.+++..|++.+....||
T Consensus 38 R~Lt~~E~--------~eL~~y~~~v~~y~~~l~~~iq~ 68 (76)
T PF06394_consen 38 RDLTPDEQ--------QELKTYQKKVAAYKEQLQQQIQE 68 (76)
T ss_dssp EE--HHHH--------HHHHHHHHHHHHHHHHHTT----
T ss_pred ccCCHHHH--------HHHHHHHHHHHHHHHHHHHHHHH
Confidence 56788875 44577889999999887776654
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=39.07 E-value=71 Score=24.59 Aligned_cols=61 Identities=18% Similarity=0.290 Sum_probs=42.8
Q ss_pred hhHHHHHHHhcCcc--hhhcccccHHHHHHHhCCCCCCCcHHHHHHHHHHHhhHHHHHHHhhh
Q 020460 79 LHRLFVEVTSRGGL--GKVIRDRRWKEVVVVFNFPTTITSASFVLRKYYLSLLYHFEQVYYFR 139 (326)
Q Consensus 79 L~~Ly~~V~~rGG~--~~V~~~~~W~eVa~~l~~~~~~t~as~~Lk~~Y~k~L~~fE~~~~~~ 139 (326)
|..|+......|.+ ...-....|..|+..|.-.....-...+|+..|..+=..|..+....
T Consensus 10 ll~~~~e~~~~g~~~~~~~fk~~~w~~i~~~~~~~~~~~~t~~qlknk~~~lk~~y~~~~~l~ 72 (96)
T PF12776_consen 10 LLDLLIEQINKGNRPTNGGFKKEGWNNIAEEFNEKTGLNYTKKQLKNKWKTLKKDYRIWKELR 72 (96)
T ss_pred HHHHHHHHHHhCCCCCCCCcCHHHHHHHHHHHHHHhCCcccHHHHHHHHHHHHHHHHHHHHHH
Confidence 44556666667777 35555668999999998544433334589999999999988876444
No 43
>PF13873 Myb_DNA-bind_5: Myb/SANT-like DNA-binding domain
Probab=38.24 E-value=41 Score=25.20 Aligned_cols=54 Identities=13% Similarity=0.245 Sum_probs=32.6
Q ss_pred cchhHHHHHHHhc---CcchhhcccccHHHHHHHhC-CCCCCCcHHHHHHHHHHHhhHH
Q 020460 77 LDLHRLFVEVTSR---GGLGKVIRDRRWKEVVVVFN-FPTTITSASFVLRKYYLSLLYH 131 (326)
Q Consensus 77 lDL~~Ly~~V~~r---GG~~~V~~~~~W~eVa~~l~-~~~~~t~as~~Lk~~Y~k~L~~ 131 (326)
|+|..-|..|..- ++.....+...|.+|+..|+ +.+. .--...|++.|..+...
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 3444444444432 22334445679999999996 3333 34445899999887653
No 44
>smart00717 SANT SANT SWI3, ADA2, N-CoR and TFIIIB'' DNA-binding domains.
Probab=38.01 E-value=75 Score=20.44 Aligned_cols=26 Identities=15% Similarity=0.276 Sum_probs=18.2
Q ss_pred ccHHHHHHHhCCCCCCCcHHHHHHHHHHHhh
Q 020460 99 RRWKEVVVVFNFPTTITSASFVLRKYYLSLL 129 (326)
Q Consensus 99 ~~W~eVa~~l~~~~~~t~as~~Lk~~Y~k~L 129 (326)
..|..|+..|+- -....++..|..++
T Consensus 22 ~~w~~Ia~~~~~-----rt~~~~~~~~~~~~ 47 (49)
T smart00717 22 NNWEKIAKELPG-----RTAEQCRERWNNLL 47 (49)
T ss_pred CCHHHHHHHcCC-----CCHHHHHHHHHHHc
Confidence 579999999971 12336777777665
No 45
>KOG3223 consensus Uncharacterized conserved protein [Function unknown]
Probab=37.90 E-value=33 Score=31.38 Aligned_cols=46 Identities=20% Similarity=0.341 Sum_probs=38.7
Q ss_pred CCC-CCCCChHHHHHHHHHHHhhccCCCCc-hHHHHHHHHHhhcCCHH
Q 020460 248 SRP-KSNRSGYNFFFAEHYARLKPHYYGQE-KAISKKIGVLWSNLTEA 293 (326)
Q Consensus 248 ~~P-KrP~SaY~lF~~e~r~~lk~e~p~~~-~eisk~ige~Wk~Lsee 293 (326)
.+| ||=+-||.-|-...-++|+.++|++. .+.-.+|-..|..-+|+
T Consensus 162 rHPEkRmrAA~~afEe~~LPrLK~e~P~lrlsQ~Kqll~Kew~KsPDN 209 (221)
T KOG3223|consen 162 RHPEKRMRAAFKAFEEARLPRLKKENPGLRLSQYKQLLKKEWQKSPDN 209 (221)
T ss_pred cChHHHHHHHHHHHHHhhchhhhhcCCCccHHHHHHHHHHHHhhCCCC
Confidence 455 34456788888888899999999999 99999999999988775
No 46
>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=37.41 E-value=34 Score=25.42 Aligned_cols=38 Identities=18% Similarity=0.273 Sum_probs=21.9
Q ss_pred cccccHHHHHHHhCCCCC---CCcHHHHHHHHHHHhhHHHH
Q 020460 96 IRDRRWKEVVVVFNFPTT---ITSASFVLRKYYLSLLYHFE 133 (326)
Q Consensus 96 ~~~~~W~eVa~~l~~~~~---~t~as~~Lk~~Y~k~L~~fE 133 (326)
.+.+.|.+|+..|+...+ +...-..||..|.+.+...+
T Consensus 24 ~r~~aw~~Ia~~l~~~~~~~~~~~~w~~Lr~~y~~~~~~~~ 64 (85)
T PF10545_consen 24 LREEAWQEIARELGKEFSVDDCKKRWKNLRDRYRRELKKIK 64 (85)
T ss_pred HHHHHHHHHHHHHccchhHHHHHHHHHHHHHHHHHHHHHHh
Confidence 456799999999984322 22222345555555554444
No 47
>cd05694 S1_Rrp5_repeat_hs2_sc2 S1_Rrp5_repeat_hs2_sc2: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 2 (hs2) and S. cerevisiae S1 repeat 2 (sc2). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=32.54 E-value=27 Score=26.46 Aligned_cols=32 Identities=28% Similarity=0.550 Sum_probs=25.1
Q ss_pred cccCCceeecccCccCCCceEEEeeccccccccc
Q 020460 180 LQIGCSVSGVIDGKFDNGYLVTVNLGSEQLKGVL 213 (326)
Q Consensus 180 ~~~~~~v~~~idgkf~~gy~vtv~~gse~~~g~l 213 (326)
|+.|..|.|.|-..-|+||+|.+.+ +.+.|.+
T Consensus 2 l~~G~~v~g~V~si~d~G~~v~~g~--~gv~Gfl 33 (74)
T cd05694 2 LVEGMVLSGCVSSVEDHGYILDIGI--PGTTGFL 33 (74)
T ss_pred CCCCCEEEEEEEEEeCCEEEEEeCC--CCcEEEE
Confidence 5678999999999999999888743 3466644
No 48
>PF12650 DUF3784: Domain of unknown function (DUF3784); InterPro: IPR017259 This group represents an uncharacterised conserved protein.
Probab=32.40 E-value=31 Score=27.33 Aligned_cols=17 Identities=24% Similarity=0.499 Sum_probs=13.8
Q ss_pred HhhcCCHHHhHHHHHHH
Q 020460 286 LWSNLTEAEKQVYQEKG 302 (326)
Q Consensus 286 ~Wk~LseeeK~~Y~e~A 302 (326)
-|+.||+|||+.|.++.
T Consensus 25 Gyntms~eEk~~~D~~~ 41 (97)
T PF12650_consen 25 GYNTMSKEEKEKYDKKK 41 (97)
T ss_pred hcccCCHHHHHHhhHHH
Confidence 38999999999996543
No 49
>PF13875 DUF4202: Domain of unknown function (DUF4202)
Probab=31.04 E-value=79 Score=28.73 Aligned_cols=39 Identities=10% Similarity=0.290 Sum_probs=33.1
Q ss_pred hHHHHHHHHHHHhhccCCCCc-hHHHHHHHHHhhcCCHHHhHH
Q 020460 256 GYNFFFAEHYARLKPHYYGQE-KAISKKIGVLWSNLTEAEKQV 297 (326)
Q Consensus 256 aY~lF~~e~r~~lk~e~p~~~-~eisk~ige~Wk~LseeeK~~ 297 (326)
+-++|...+.+.+...| + ..+..++.+.|+.||++-++-
T Consensus 131 acLVFL~~~f~~F~~~~---deeK~v~Il~KTw~KMS~~g~~~ 170 (185)
T PF13875_consen 131 ACLVFLEYYFEDFAAKH---DEEKIVDILRKTWRKMSERGHEA 170 (185)
T ss_pred HHHHhHHHHHHHHHhcC---CHHHHHHHHHHHHHHCCHHHHHH
Confidence 57789999999888888 4 778899999999999998753
No 50
>PRK10363 cpxP periplasmic repressor CpxP; Reviewed
Probab=30.84 E-value=1.1e+02 Score=27.25 Aligned_cols=39 Identities=18% Similarity=0.298 Sum_probs=31.1
Q ss_pred hHHHHHHHHHhhcCCHHHhHHHHHHHHHHHHHHHHHHHHH
Q 020460 277 KAISKKIGVLWSNLTEAEKQVYQEKGLKDKERYKSEMLEY 316 (326)
Q Consensus 277 ~eisk~ige~Wk~LseeeK~~Y~e~A~~dkerY~~em~~Y 316 (326)
.++.++-.++.+-|++|+|+.|++..++-.+++.. +..+
T Consensus 111 Vem~k~~nqmy~lLTPEQKaq~~~~~~~rm~~~~~-~~~~ 149 (166)
T PRK10363 111 VEMAKVRNQMYRLLTPEQQAVLNEKHQQRMEQLRD-VTQW 149 (166)
T ss_pred HHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHH-HHhc
Confidence 66788888999999999999998887777776644 4443
No 51
>PRK09706 transcriptional repressor DicA; Reviewed
Probab=30.36 E-value=1.2e+02 Score=25.23 Aligned_cols=41 Identities=17% Similarity=0.152 Sum_probs=35.9
Q ss_pred HHHHHHHHhhcCCHHHhHHHHHHHHHHHHHHHHHHHHHHhc
Q 020460 279 ISKKIGVLWSNLTEAEKQVYQEKGLKDKERYKSEMLEYRSS 319 (326)
Q Consensus 279 isk~ige~Wk~LseeeK~~Y~e~A~~dkerY~~em~~Yk~~ 319 (326)
-.+.+-+.|+.|+++++.......+...+.|.+-+++|-++
T Consensus 88 ~~~~ll~~~~~L~~~~~~~~l~~l~~~~~~~~~~~~~~~~~ 128 (135)
T PRK09706 88 DQKELLELFDALPESEQDAQLSEMRARVENFNKLFEELLKA 128 (135)
T ss_pred HHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 35778899999999999999999999999999888888654
No 52
>PRK12751 cpxP periplasmic stress adaptor protein CpxP; Reviewed
Probab=29.67 E-value=1.1e+02 Score=27.07 Aligned_cols=34 Identities=18% Similarity=0.258 Sum_probs=25.4
Q ss_pred hHHHHHHHHHhhcCCHHHhHHHHHHHHHHHHHHH
Q 020460 277 KAISKKIGVLWSNLTEAEKQVYQEKGLKDKERYK 310 (326)
Q Consensus 277 ~eisk~ige~Wk~LseeeK~~Y~e~A~~dkerY~ 310 (326)
.++.+..-++++.|++|+|+.|.+.-++-.++..
T Consensus 117 v~~~~~~~qmy~lLTPEQra~l~~~~e~r~~~~~ 150 (162)
T PRK12751 117 VEMAKVRNQMYNLLTPEQKEALNKKHQERIEKLQ 150 (162)
T ss_pred HHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHH
Confidence 3455666788999999999999877666555443
No 53
>smart00595 MADF subfamily of SANT domain.
Probab=29.23 E-value=39 Score=25.84 Aligned_cols=42 Identities=17% Similarity=0.236 Sum_probs=28.1
Q ss_pred hhcccccHHHHHHHhCCCCC-CCcHHHHHHHHHHHhhHHHHHH
Q 020460 94 KVIRDRRWKEVVVVFNFPTT-ITSASFVLRKYYLSLLYHFEQV 135 (326)
Q Consensus 94 ~V~~~~~W~eVa~~l~~~~~-~t~as~~Lk~~Y~k~L~~fE~~ 135 (326)
...+...|.+|+..||.+.. |..-=..||..|.+.+......
T Consensus 23 ~~~r~~aW~~Ia~~l~~~~~~~~~kw~~LR~~y~~e~~r~~~~ 65 (89)
T smart00595 23 KEEKRKAWEEIAEELGLSVEECKKRWKNLRDRYRRELKRLQNG 65 (89)
T ss_pred hHHHHHHHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 44456699999999999433 3333336777787777666543
No 54
>PF02337 Gag_p10: Retroviral GAG p10 protein; InterPro: IPR003322 Retroviral matrix proteins (or major core proteins) are components of envelope-associated capsids, which line the inner surface of virus envelopes and are associated with viral membranes []. Matrix proteins are produced as part of Gag precursor polyproteins. During viral maturation, the Gag polyprotein is cleaved into major structural proteins by the viral protease, yielding the matrix (MA), capsid (CA), nucleocapsid (NC), and some smaller peptides. Gag-derived proteins govern the entire assembly and release of the virus particles, with matrix proteins playing key roles in Gag stability, capsid assembly, transport and budding. Although matrix proteins from different retroviruses appear to perform similar functions and can have similar structural folds, their primary sequences can be very different. This entry represents matrix proteins from beta-retroviruses such as Mason-Pfizer monkey virus (MPMV) (Simian Mason-Pfizer virus) and Mouse mammary tumor virus (MMTV) [, ]. This entry also identifies matrix proteins from several eukaryotic endogenous retroviruses, which arise when one or more copies of the retroviral genome becomes integrated into the host genome [].; GO: 0005198 structural molecule activity, 0019028 viral capsid; PDB: 2F77_X 2F76_X.
Probab=26.81 E-value=2.2e+02 Score=22.84 Aligned_cols=54 Identities=19% Similarity=0.108 Sum_probs=35.8
Q ss_pred HHHHHHHHHHHHhcCCCCCCCeeCCeecchhHHHHHHHhcCcchhhc---ccccHHHHHHHhCC
Q 020460 50 DLFWATLEAFHKSFGDKFKVPTVGGKALDLHRLFVEVTSRGGLGKVI---RDRRWKEVVVVFNF 110 (326)
Q Consensus 50 ~~F~~~L~~F~~~rG~~l~~P~i~gk~lDL~~Ly~~V~~rGG~~~V~---~~~~W~eVa~~l~~ 110 (326)
+.|+..|..++..+|..+ +.=||-.+|..+.+..=.=.+. .-..|..|.+.|.-
T Consensus 8 ~~fv~~Lk~lLk~rGi~v-------~~~~L~~f~~~i~~~~PWF~~eG~l~~~~W~kvG~~l~~ 64 (90)
T PF02337_consen 8 QPFVSILKHLLKERGIRV-------KKKDLINFLSFIDKVCPWFPEEGTLDLDNWKKVGEELKR 64 (90)
T ss_dssp HHHHHHHHHHHHCCT-----------HHHHHHHHHHHHHHTT-SS--SS-HHHHHHHHHHHHHH
T ss_pred hHHHHHHHHHHHHcCeee-------cHHHHHHHHHHHHHhCCCCCCCCCcCHHHHHHHHHHHHH
Confidence 799999999999999988 4557778888776543322222 23589999998843
No 55
>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=26.31 E-value=1.1e+02 Score=22.58 Aligned_cols=43 Identities=14% Similarity=0.228 Sum_probs=25.2
Q ss_pred HHHHHHHHHHhcCCCCCCCeeCCeecchhHHHHHHHhcCcchhhcccccHHHHH
Q 020460 52 FWATLEAFHKSFGDKFKVPTVGGKALDLHRLFVEVTSRGGLGKVIRDRRWKEVV 105 (326)
Q Consensus 52 F~~~L~~F~~~rG~~l~~P~i~gk~lDL~~Ly~~V~~rGG~~~V~~~~~W~eVa 105 (326)
|++...+-+++.| +++....|+..|.++|++... ...-|..|+
T Consensus 3 ~~eaa~~vL~~~~----------~pm~~~eI~~~i~~~~~~~~~-~k~p~~~i~ 45 (72)
T PF05066_consen 3 FKEAAYEVLEEAG----------RPMTFKEIWEEIQERGLYKKS-GKTPEATIA 45 (72)
T ss_dssp HHHHHHHHHHHH-----------S-EEHHHHHHHHHHHHTS----GGGGGHHHH
T ss_pred HHHHHHHHHHhcC----------CCcCHHHHHHHHHHhCCCCcc-cCCHHHHHH
Confidence 4455555555544 558889999999999999887 222444444
No 56
>PRK12750 cpxP periplasmic repressor CpxP; Reviewed
Probab=26.10 E-value=2e+02 Score=25.58 Aligned_cols=36 Identities=22% Similarity=0.232 Sum_probs=28.8
Q ss_pred HHHHHHHHHhhcCCHHHhHHHHHHHHHHHHHHHHHH
Q 020460 278 AISKKIGVLWSNLTEAEKQVYQEKGLKDKERYKSEM 313 (326)
Q Consensus 278 eisk~ige~Wk~LseeeK~~Y~e~A~~dkerY~~em 313 (326)
++.+..-+++.-|++|+|+.|.+.-.+-.+.+...+
T Consensus 125 ~~~~~~~~~~~vLTpEQRak~~e~~~~r~~~~~~~~ 160 (170)
T PRK12750 125 KMLEKRHQMLSILTPEQKAKFQELQQERMQECQDKM 160 (170)
T ss_pred HHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHHH
Confidence 344556678999999999999998877777777766
No 57
>cd08306 Death_FADD Fas-associated Death Domain protein-protein interaction domain. Death domain (DD) found in FAS-associated via death domain (FADD). FADD is a component of the death-inducing signaling complex (DISC) and serves as an adaptor in the signaling pathway of death receptor proteins. It modulates apoptosis as well as non-apoptotic processes such as cell cycle progression, survival, innate immune signaling, and hematopoiesis. FADD contains an N-terminal DED and a C-terminal DD. Its DD interacts with the DD of the activated death receptor, FAS, and its DED recruits the initiator caspases, caspase-8 and -10, to the DISC complex via a homotypic interaction with the N-terminal DED of the caspase. DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily including CARD (Caspase activation and recruitment domain),
Probab=25.63 E-value=43 Score=26.21 Aligned_cols=15 Identities=20% Similarity=0.621 Sum_probs=13.2
Q ss_pred ccHHHHHHHhCCCCC
Q 020460 99 RRWKEVVVVFNFPTT 113 (326)
Q Consensus 99 ~~W~eVa~~l~~~~~ 113 (326)
+.|+++|+.|||+..
T Consensus 14 ~~Wk~laR~LGlse~ 28 (86)
T cd08306 14 RDWRKLARKLGLSET 28 (86)
T ss_pred hhHHHHHHHcCCCHH
Confidence 589999999999854
No 58
>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=25.59 E-value=97 Score=22.53 Aligned_cols=42 Identities=21% Similarity=0.339 Sum_probs=25.7
Q ss_pred chhHHHHHHH-hcCcchhhcccccH---HHHHHHhCCCC-CCCcHHHHHHHHHHHhhH
Q 020460 78 DLHRLFVEVT-SRGGLGKVIRDRRW---KEVVVVFNFPT-TITSASFVLRKYYLSLLY 130 (326)
Q Consensus 78 DL~~Ly~~V~-~rGG~~~V~~~~~W---~eVa~~l~~~~-~~t~as~~Lk~~Y~k~L~ 130 (326)
+++.+|.... .+|+ ..| ..|++.++.+. +. .++++|+.+|-+
T Consensus 9 eeh~~Fl~ai~~~G~-------g~~a~pk~I~~~~~~~~lT~----~qV~SH~QKy~~ 55 (57)
T TIGR01557 9 DLHDRFLQAVQKLGG-------PDWATPKRILELMVVDGLTR----DQVASHLQKYRL 55 (57)
T ss_pred HHHHHHHHHHHHhCC-------CcccchHHHHHHcCCCCCCH----HHHHHHHHHHHc
Confidence 4566665533 2222 258 89999998764 32 367777777654
No 59
>PRK10236 hypothetical protein; Provisional
Probab=25.30 E-value=71 Score=30.10 Aligned_cols=41 Identities=20% Similarity=0.320 Sum_probs=27.9
Q ss_pred HHHHHHHHhhccCCCC------c-hHHHHHHHHHhhcCCHHHhHHHHH
Q 020460 260 FFAEHYARLKPHYYGQ------E-KAISKKIGVLWSNLTEAEKQVYQE 300 (326)
Q Consensus 260 F~~e~r~~lk~e~p~~------~-~eisk~ige~Wk~LseeeK~~Y~e 300 (326)
-..+....+|-.+... + .-+.+.+.+.|+.|+++|++.+.+
T Consensus 92 IL~DVc~~LKV~y~~~~st~~iE~~il~kll~~a~~kms~eE~~~L~~ 139 (237)
T PRK10236 92 ILLDVSKRLKLKADKEMSTFEIEQQLLEQFLRNTWKKMDEEHKQEFLH 139 (237)
T ss_pred HHHHHHHHcCCCCCCCCCHHHHHHHHHHHHHHHHHHHCCHHHHHHHHH
Confidence 3344555555443331 2 447899999999999999988764
No 60
>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=25.05 E-value=1.3e+02 Score=27.81 Aligned_cols=28 Identities=18% Similarity=0.312 Sum_probs=21.0
Q ss_pred HHHhhcCCHHHhHHHHHHHHHHHHHHHH
Q 020460 284 GVLWSNLTEAEKQVYQEKGLKDKERYKS 311 (326)
Q Consensus 284 ge~Wk~LseeeK~~Y~e~A~~dkerY~~ 311 (326)
.+.|..|+++.|+...+.+.+.-+....
T Consensus 213 ~~~~~~L~~e~q~~i~~a~~~~~~~~~~ 240 (257)
T TIGR00787 213 KAFWKSLPPDLQAVVKEAAKEAGEYQRK 240 (257)
T ss_pred HHHHhcCCHHHHHHHHHHHHHHHHHHHH
Confidence 4679999999999998876665444433
No 61
>PF15076 DUF4543: Domain of unknown function (DUF4543)
Probab=23.56 E-value=55 Score=24.90 Aligned_cols=25 Identities=24% Similarity=0.301 Sum_probs=19.5
Q ss_pred ccCCCCCCCCCCCChHHHHHH--HHHH
Q 020460 242 LALRDPSRPKSNRSGYNFFFA--EHYA 266 (326)
Q Consensus 242 kk~kdp~~PKrP~SaY~lF~~--e~r~ 266 (326)
-+...++.|.-||.-||++++ |+|+
T Consensus 24 dr~~K~GfpdepmrE~ml~l~~Leqra 50 (75)
T PF15076_consen 24 DRPRKPGFPDEPMREYMLHLQALEQRA 50 (75)
T ss_pred cCCCCCCCCcchHHHHHHHHHHHHHHH
Confidence 345568899999999999986 5554
No 62
>COG1638 DctP TRAP-type C4-dicarboxylate transport system, periplasmic component [Carbohydrate transport and metabolism]
Probab=22.85 E-value=1.3e+02 Score=29.60 Aligned_cols=43 Identities=14% Similarity=0.224 Sum_probs=32.0
Q ss_pred hHHHHHHHHHhhcCCHHHhHHHHHHHHHHHHHHHHHHHHHHhc
Q 020460 277 KAISKKIGVLWSNLTEAEKQVYQEKGLKDKERYKSEMLEYRSS 319 (326)
Q Consensus 277 ~eisk~ige~Wk~LseeeK~~Y~e~A~~dkerY~~em~~Yk~~ 319 (326)
..+.-+-...|..|++++|+...+.+.+..++..+...+..+.
T Consensus 237 ~~~~~~s~~~w~~L~~e~q~il~~aa~e~~~~~~~~~~~~e~~ 279 (332)
T COG1638 237 PLAVLVSKAFWDSLPEEDQTILLEAAKEAAEEQRKLVEELEDE 279 (332)
T ss_pred ceeeEEcHHHHhcCCHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3344444577999999999999998888877777666666553
No 63
>PF13725 tRNA_bind_2: Possible tRNA binding domain; PDB: 2ZPA_B.
Probab=22.04 E-value=54 Score=25.86 Aligned_cols=20 Identities=25% Similarity=0.619 Sum_probs=13.8
Q ss_pred hhhcccccHHHHHHHhCCCC
Q 020460 93 GKVIRDRRWKEVVVVFNFPT 112 (326)
Q Consensus 93 ~~V~~~~~W~eVa~~l~~~~ 112 (326)
.+|..++-|.+||+.|+++.
T Consensus 78 ~k~LQ~ksw~~~a~~l~l~g 97 (101)
T PF13725_consen 78 AKGLQGKSWEEVAKELGLPG 97 (101)
T ss_dssp HHHCS---HHHHHHHCT-SS
T ss_pred HHHHCCCCHHHHHHHcCCCC
Confidence 36788999999999999985
No 64
>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=21.58 E-value=1.2e+02 Score=21.77 Aligned_cols=40 Identities=20% Similarity=0.130 Sum_probs=32.6
Q ss_pred hcCcchhhcccccHHHHHHHhCCCCCCCcHHHHHHHHHHHhh
Q 020460 88 SRGGLGKVIRDRRWKEVVVVFNFPTTITSASFVLRKYYLSLL 129 (326)
Q Consensus 88 ~rGG~~~V~~~~~W~eVa~~l~~~~~~t~as~~Lk~~Y~k~L 129 (326)
-..||-.+-++-.-.+||..||++. +..+..||+.-.+++
T Consensus 13 ~~~GYfd~PR~~tl~elA~~lgis~--st~~~~LRrae~kli 52 (53)
T PF04967_consen 13 YELGYFDVPRRITLEELAEELGISK--STVSEHLRRAERKLI 52 (53)
T ss_pred HHcCCCCCCCcCCHHHHHHHhCCCH--HHHHHHHHHHHHHHh
Confidence 3468888888889999999999985 467778888877765
No 65
>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=21.45 E-value=46 Score=29.19 Aligned_cols=68 Identities=12% Similarity=0.129 Sum_probs=49.2
Q ss_pred CchhhhhcHHHHHHHHHHHHHhcCCCCCCCeeCCeecchhHHHHHHHhcCcch----------hhcccccHHHHHHHh
Q 020460 41 KYEDIAQSSDLFWATLEAFHKSFGDKFKVPTVGGKALDLHRLFVEVTSRGGLG----------KVIRDRRWKEVVVVF 108 (326)
Q Consensus 41 ~~e~~~~~~~~F~~~L~~F~~~rG~~l~~P~i~gk~lDL~~Ly~~V~~rGG~~----------~V~~~~~W~eVa~~l 108 (326)
+|=.+........++++.-+.+.|+-+.-=+|+||+|-||+|..-+.-.|..= +.--...|..|=-.+
T Consensus 3 DHialR~n~~~~A~~w~~~l~~~G~llSen~INGRPI~l~~L~qPl~~~~~~I~cvELP~P~~k~Yp~eGWEHIE~Vl 80 (149)
T cd07268 3 DHIALRVNENQTAERWKEGLLQCGELLSENEINGRPIALIKLEKPLQFAGWSISIVELPFPKDKKYPQEGWEHIEIVI 80 (149)
T ss_pred ceEEEeeCCHHHHHHHHHHHHHhchhhhccccCCeeEEEEEcCCCceeCCcEEEEEEeCCCCCCCCCCCCceEEEEEe
Confidence 34444455677888999999999999998999999999999988877555432 223355776653333
No 66
>KOG3838 consensus Mannose lectin ERGIC-53, involved in glycoprotein traffic [Intracellular trafficking, secretion, and vesicular transport]
Probab=21.36 E-value=1e+02 Score=31.41 Aligned_cols=35 Identities=23% Similarity=0.210 Sum_probs=27.6
Q ss_pred cCCHHHhHHHHHHHHHHHHHHHHHHHHHHhcCCcc
Q 020460 289 NLTEAEKQVYQEKGLKDKERYKSEMLEYRSSYDST 323 (326)
Q Consensus 289 ~LseeeK~~Y~e~A~~dkerY~~em~~Yk~~~~~~ 323 (326)
.+.+.||++|++..+..+..|.++.++|++...+.
T Consensus 268 E~qe~ek~kyqeEfe~~q~elek~k~efkk~hpd~ 302 (497)
T KOG3838|consen 268 EMQELEKAKYQEEFEWAQLELEKRKDEFKKSHPDA 302 (497)
T ss_pred hhhHHHHHHHHHHHHHHHHHHhhhHhhhccCCchh
Confidence 34566888999999988888988888888866544
No 67
>cd08780 Death_TRADD Death Domain of Tumor Necrosis Factor Receptor 1-Associated Death Domain protein. Death domain (DD) of TRADD (TNF Receptor 1-Associated Death Domain or TNFRSF1A-associated via death domain) protein. TRADD is a central signaling adaptor for TNF-receptor 1 (TNFR1), mediating activation of Nuclear Factor -kappaB (NF-kB) and c-Jun N-terminal kinase (JNK), as well as caspase-dependent apoptosis. It also carries important immunological roles including germinal center formation, DR3-mediated T-cell stimulation, and TNFalpha-mediated inflammatory responses. In general, DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily including CARD (Caspase activation and recruitment domain), DED (Death Effector Domain), and PYRIN. They serve as adaptors in signaling pathways and can recruit other proteins into s
Probab=20.24 E-value=87 Score=25.20 Aligned_cols=11 Identities=27% Similarity=0.670 Sum_probs=10.6
Q ss_pred ccHHHHHHHhC
Q 020460 99 RRWKEVVVVFN 109 (326)
Q Consensus 99 ~~W~eVa~~l~ 109 (326)
++|+.+++.||
T Consensus 14 r~WK~laR~Lg 24 (90)
T cd08780 14 KKWKPVGRSLQ 24 (90)
T ss_pred HHHHHHHHHHc
Confidence 69999999999
Done!