Query 022607
Match_columns 294
No_of_seqs 266 out of 1388
Neff 5.5
Searched_HMMs 46136
Date Fri Mar 29 04:50:06 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/022607.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/022607hhsearch_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 1.6E-30 3.4E-35 260.3 12.4 185 23-207 153-339 (512)
2 smart00501 BRIGHT BRIGHT, ARID 99.9 6.6E-27 1.4E-31 185.2 10.3 90 32-121 1-91 (93)
3 PF01388 ARID: ARID/BRIGHT DNA 99.9 2.1E-25 4.5E-30 175.5 8.8 89 30-118 3-92 (92)
4 PTZ00199 high mobility group p 99.7 1E-17 2.3E-22 133.5 5.5 63 232-294 8-73 (94)
5 cd01389 MATA_HMG-box MATA_HMG- 99.4 8.5E-14 1.8E-18 106.3 4.3 49 246-294 1-50 (77)
6 COG5648 NHP6B Chromatin-associ 99.4 6.7E-14 1.5E-18 125.5 3.7 60 235-294 59-119 (211)
7 cd01390 HMGB-UBF_HMG-box HMGB- 99.4 3.3E-13 7.1E-18 98.7 4.1 48 247-294 1-49 (66)
8 cd01388 SOX-TCF_HMG-box SOX-TC 99.4 3.4E-13 7.4E-18 101.8 4.3 48 247-294 2-50 (72)
9 KOG0381 HMG box-containing pro 99.4 7.6E-13 1.7E-17 104.3 5.1 52 243-294 17-71 (96)
10 PF00505 HMG_box: HMG (high mo 99.3 8.9E-13 1.9E-17 97.4 3.1 48 247-294 1-49 (69)
11 smart00398 HMG high mobility g 99.3 2.4E-12 5.3E-17 94.5 4.3 49 246-294 1-50 (70)
12 cd00084 HMG-box High Mobility 99.3 3.9E-12 8.5E-17 92.4 4.1 48 247-294 1-49 (66)
13 PF09011 HMG_box_2: HMG-box do 99.2 5E-12 1.1E-16 95.7 3.1 51 244-294 1-53 (73)
14 KOG2510 SWI-SNF chromatin-remo 99.2 3E-11 6.5E-16 119.5 6.3 92 31-129 291-383 (532)
15 KOG0527 HMG-box transcription 99.1 4.4E-11 9.6E-16 114.9 5.0 54 241-294 57-111 (331)
16 KOG0526 Nucleosome-binding fac 99.0 4.6E-10 1E-14 112.2 4.6 55 234-290 523-578 (615)
17 KOG3248 Transcription factor T 98.2 7.9E-07 1.7E-11 85.2 2.8 51 242-293 188-239 (421)
18 KOG0528 HMG-box transcription 98.0 2E-06 4.3E-11 85.7 2.3 56 239-294 318-374 (511)
19 KOG4715 SWI/SNF-related matrix 97.7 4.4E-05 9.5E-10 72.9 5.5 55 239-293 57-112 (410)
20 KOG2746 HMG-box transcription 97.2 0.00014 3.1E-09 75.1 2.1 59 235-293 170-231 (683)
21 PF04690 YABBY: YABBY protein; 96.6 0.0035 7.7E-08 55.5 5.2 44 245-288 120-164 (170)
22 TIGR01624 LRP1_Cterm LRP1 C-te 93.9 0.052 1.1E-06 38.6 2.6 34 170-203 14-48 (50)
23 PF06382 DUF1074: Protein of u 93.6 0.21 4.6E-06 44.5 6.5 39 251-293 83-122 (183)
24 PF08073 CHDNT: CHDNT (NUC034) 92.4 0.13 2.7E-06 37.7 2.7 40 250-289 12-52 (55)
25 PF05142 DUF702: Domain of unk 92.0 0.12 2.6E-06 45.1 2.6 36 170-205 116-151 (154)
26 PF06244 DUF1014: Protein of u 89.6 0.49 1.1E-05 39.9 4.0 49 242-290 68-117 (122)
27 PF04769 MAT_Alpha1: Mating-ty 88.3 0.79 1.7E-05 41.7 4.8 43 241-287 38-81 (201)
28 PF00249 Myb_DNA-binding: Myb- 84.1 2.3 5E-05 29.2 4.4 38 66-114 11-48 (48)
29 COG5648 NHP6B Chromatin-associ 77.3 0.99 2.1E-05 41.3 0.8 48 246-293 143-191 (211)
30 PF14887 HMG_box_5: HMG (high 72.6 8.2 0.00018 30.3 4.6 47 246-292 3-49 (85)
31 PF09441 Abp2: ARS binding pro 64.2 15 0.00032 32.6 5.1 41 54-98 45-85 (175)
32 PF13921 Myb_DNA-bind_6: Myb-l 56.9 22 0.00048 25.0 4.2 36 66-114 8-43 (60)
33 cd00167 SANT 'SWI3, ADA2, N-Co 56.1 23 0.0005 22.4 3.9 37 66-114 9-45 (45)
34 cd05694 S1_Rrp5_repeat_hs2_sc2 50.1 16 0.00034 27.5 2.6 30 170-201 5-34 (74)
35 KOG3223 Uncharacterized conser 48.0 11 0.00024 34.3 1.7 43 248-290 166-209 (221)
36 PF13873 Myb_DNA-bind_5: Myb/S 46.6 28 0.00061 25.9 3.5 54 62-116 14-71 (78)
37 smart00271 DnaJ DnaJ molecular 40.7 29 0.00064 24.0 2.7 34 259-292 20-60 (60)
38 PF12776 Myb_DNA-bind_3: Myb/S 37.8 70 0.0015 24.4 4.6 60 64-123 10-71 (96)
39 smart00717 SANT SANT SWI3, AD 37.8 67 0.0015 20.4 4.0 26 84-114 22-47 (49)
40 cd05699 S1_Rrp5_repeat_hs7 S1_ 35.1 44 0.00094 25.7 2.9 31 170-202 1-31 (72)
41 PF10545 MADF_DNA_bdg: Alcohol 33.6 42 0.00092 24.6 2.7 38 81-118 24-64 (85)
42 PHA03102 Small T antigen; Revi 29.9 42 0.00092 29.3 2.4 36 258-293 25-62 (153)
43 TIGR01557 myb_SHAQKYF myb-like 29.2 60 0.0013 23.6 2.7 42 63-115 9-55 (57)
44 KOG0493 Transcription factor E 27.2 58 0.0013 31.2 2.9 23 246-271 245-267 (342)
45 cd07268 Glo_EDI_BRP_like_4 Thi 26.3 26 0.00056 30.6 0.4 69 25-93 2-80 (149)
46 PF05066 HARE-HTH: HB1, ASXL, 26.3 1.1E+02 0.0023 22.5 3.8 34 37-80 3-36 (72)
47 PF13875 DUF4202: Domain of un 26.2 81 0.0018 28.5 3.6 50 241-292 119-168 (185)
48 PF00226 DnaJ: DnaJ domain; I 24.8 47 0.001 23.5 1.5 35 258-292 18-59 (64)
49 cd08306 Death_FADD Fas-associa 24.3 52 0.0011 25.6 1.8 15 84-98 14-28 (86)
50 smart00595 MADF subfamily of S 24.2 56 0.0012 24.7 1.9 41 79-119 23-64 (89)
51 PF12653 DUF3785: Protein of u 24.1 49 0.0011 28.3 1.7 15 178-192 109-123 (138)
52 cd04455 S1_NusA S1_NusA: N-uti 23.7 83 0.0018 22.7 2.7 29 169-201 3-31 (67)
53 TIGR03481 HpnM hopanoid biosyn 23.1 47 0.001 29.8 1.5 22 272-293 65-87 (198)
54 PLN03212 Transcription repress 22.9 1.1E+02 0.0024 28.9 4.0 40 66-116 35-74 (249)
55 PF13725 tRNA_bind_2: Possible 22.3 48 0.001 25.9 1.3 20 78-97 78-97 (101)
56 cd04465 S1_RPS1_repeat_ec2_hs2 21.2 1.1E+02 0.0023 21.8 2.8 27 170-200 1-27 (67)
57 cd06257 DnaJ DnaJ domain or J- 20.4 1.4E+02 0.0031 19.9 3.3 32 258-289 18-55 (55)
No 1
>KOG2744 consensus DNA-binding proteins Bright/BRCAA1/RBP1 and related proteins containing BRIGHT domain [Transcription]
Probab=99.97 E-value=1.6e-30 Score=260.31 Aligned_cols=185 Identities=40% Similarity=0.495 Sum_probs=152.9
Q ss_pred CCCCCCccccChhHHHHHHHHHHhhcCCCCC-CCeeCCeecchhhhHHHHHhcCcchhhhccccHHHHHhhhcCCC-CCC
Q 022607 23 PLSSHEDVSKDPIVFWDTLRRFHFIMGTKFM-IPVIGGKELDLHVLYVEATTRGGYEKVVAEKKWREVGAVFKFSP-TTT 100 (294)
Q Consensus 23 p~~~~e~~~~~~~~Fl~~L~~F~~~rG~~l~-~P~i~Gk~LDL~~Ly~~V~~rGG~~~V~~~k~W~eVa~~lg~p~-~~t 100 (294)
+....|.+..+++.||++|+.||+++|++|+ +|+|+|++||||.||.+|+++||+++|+.+++|++|+..|+||. ++|
T Consensus 153 ~~~~~e~~~~~~eeF~~dl~~f~~~~~~~~~~iPii~~~~ldL~~Ly~lV~s~GG~~~V~~~k~Wrev~~~l~~pt~tiT 232 (512)
T KOG2744|consen 153 PLYETEGVPKSSEEFMEDLRRFMKKRGTKVKSIPIIGGQPLDLHWLYALVTSRGGLDEVTNKKLWREVIDGLNFPTPTIT 232 (512)
T ss_pred cccccccccccHHHHHHHHHHHHHHhCCcceeccccCCCcchHHHHHHHHhcCCchhHhhhhhhHHHHhccccCCCcccc
Confidence 5666777778999999999999999999996 99999999999999999999999999999999999999999999 999
Q ss_pred cHHHHHHHHHHHhhHHHHHHHHhhccCCCCCCCCccccCCCCcCCCccccccCcccccCCCCCccCCCccceeeeeeccc
Q 022607 101 SASFVLRKHYLTLLYHYEQVHFFKMQGPPCVPSASFSVHSPSCRPGLALVEYSPKRINDHPDSHIEGQSCFTAVGRIDGK 180 (294)
Q Consensus 101 sas~~Lk~~Y~k~L~~YE~~~~~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~g~idgk 180 (294)
+++|.|+++|+++|++||+.+.+....+...|.+...-.+++-+++...-+.++........+....+....+.++|+|+
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 99999999999999999999999888777777643331333334444334444432222222222224467899999999
Q ss_pred ccCcceEEEeecceeeeeeeccCCCCC
Q 022607 181 FDCGYLVSVKLGSETLSGVLYHPDHPG 207 (294)
Q Consensus 181 fd~gylvtv~~gse~~~gvly~~~~~~ 207 (294)
|++||+|++++||+.|+|+|||.++..
T Consensus 313 f~~~~~~~~~~~s~~ln~~~~~~~~~~ 339 (512)
T KOG2744|consen 313 FLQGLLVFMKDGSEPLNGVLYLGPPDL 339 (512)
T ss_pred ccccCceeccCcchhccCccccccCcc
Confidence 999999999999999999999998866
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=6.6e-27 Score=185.20 Aligned_cols=90 Identities=41% Similarity=0.699 Sum_probs=86.7
Q ss_pred cChhHHHHHHHHHHhhcCCCC-CCCeeCCeecchhhhHHHHHhcCcchhhhccccHHHHHhhhcCCCCCCcHHHHHHHHH
Q 022607 32 KDPIVFWDTLRRFHFIMGTKF-MIPVIGGKELDLHVLYVEATTRGGYEKVVAEKKWREVGAVFKFSPTTTSASFVLRKHY 110 (294)
Q Consensus 32 ~~~~~Fl~~L~~F~~~rG~~l-~~P~i~Gk~LDL~~Ly~~V~~rGG~~~V~~~k~W~eVa~~lg~p~~~tsas~~Lk~~Y 110 (294)
++++.|+++|.+||+.+|+++ ++|+|+|++||||+||.+|+++|||++||++++|.+||+.||++++++++++.|+++|
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 7999999999999999999999999999999999999999999998899999999999
Q ss_pred HHhhHHHHHHH
Q 022607 111 LTLLYHYEQVH 121 (294)
Q Consensus 111 ~k~L~~YE~~~ 121 (294)
.+||++||+++
T Consensus 81 ~k~L~~yE~~~ 91 (93)
T smart00501 81 ERYLLPFERFL 91 (93)
T ss_pred HHHhHHHHHHh
Confidence 99999999975
No 3
>PF01388 ARID: ARID/BRIGHT DNA binding domain; InterPro: IPR001606 Members of the recently discovered ARID (AT-rich interaction domain; also known as BRIGHT domain)) family of DNA-binding proteins are found in fungi and invertebrate and vertebrate metazoans. ARID-encoding genes are involved in a variety of biological processes including embryonic development, cell lineage gene regulation and cell cycle control. Although the specific roles of this domain and of ARID-containing proteins in transcriptional regulation are yet to be elucidated, they include both positive and negative transcriptional regulation and a likely involvement in the modification of chromatin structure []. The basic structure of the ARID domain domain appears to be a series of six alpha-helices separated by beta-strands, loops, or turns, but the structured region may extend to an additional helix at either or both ends of the basic six. Based on primary sequence homology, they can be partitioned into three structural classes: Minimal ARID proteins that consist of a core domain formed by six alpha helices; ARID proteins that supplement the core domain with an N-terminal alpha-helix; and Extended-ARID proteins, which contain the core domain and additional alpha-helices at their N- and C-termini. The human SWI-SNF complex protein p270 is an ARID family member with non-sequence-specific DNA binding activity. The ARID consensus and other structural features are common to both p270 and yeast SWI1, suggesting that p270 is a human counterpart of SWI1 []. The approximately 100-residue ARID sequence is present in a series of proteins strongly implicated in the regulation of cell growth, development, and tissue-specific gene expression. Although about a dozen ARID proteins can be identified from database searches, to date, only Bright (a regulator of B-cell-specific gene expression), dead ringer (a Drosophila melanogaster gene product required for normal development), and MRF-2 (which represses expression from the Cytomegalovirus enhancer) have been analyzed directly in regard to their DNA binding properties. Each binds preferentially to AT-rich sites. In contrast, p270 shows no sequence preference in its DNA binding activity, thereby demonstrating that AT-rich binding is not an intrinsic property of ARID domains and that ARID family proteins may be involved in a wider range of DNA interactions [].; GO: 0003677 DNA binding, 0005622 intracellular; PDB: 1C20_A 1KQQ_A 2JRZ_A 2LM1_A 2YQE_A 2JXJ_A 2EH9_A 2CXY_A 2LI6_A 1KN5_A ....
Probab=99.92 E-value=2.1e-25 Score=175.46 Aligned_cols=89 Identities=44% Similarity=0.730 Sum_probs=82.3
Q ss_pred cccChhHHHHHHHHHHhhcCCCC-CCCeeCCeecchhhhHHHHHhcCcchhhhccccHHHHHhhhcCCCCCCcHHHHHHH
Q 022607 30 VSKDPIVFWDTLRRFHFIMGTKF-MIPVIGGKELDLHVLYVEATTRGGYEKVVAEKKWREVGAVFKFSPTTTSASFVLRK 108 (294)
Q Consensus 30 ~~~~~~~Fl~~L~~F~~~rG~~l-~~P~i~Gk~LDL~~Ly~~V~~rGG~~~V~~~k~W~eVa~~lg~p~~~tsas~~Lk~ 108 (294)
-..+++.|++.|.+||+.+|+++ .+|.|+|++||||+||.+|+++|||++|+++++|.+||+.||+++.+++.+..|++
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 45688999999999999999997 79999999999999999999999999999999999999999999988888899999
Q ss_pred HHHHhhHHHH
Q 022607 109 HYLTLLYHYE 118 (294)
Q Consensus 109 ~Y~k~L~~YE 118 (294)
+|++||++||
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=99.71 E-value=1e-17 Score=133.47 Aligned_cols=63 Identities=33% Similarity=0.554 Sum_probs=57.2
Q ss_pred ccccccccCCCCCCCCCCCCchhHhhhHHhHHHHHhhCCC-C--hHHHHHHHHHHhcCCCccccCC
Q 022607 232 YGRRRRSKRRGDPSYPKPNRSGYNFFFAEKHYKLKSLYPN-R--EREFTKMIGESWTNLSPEERKV 294 (294)
Q Consensus 232 ~~~kk~~k~~kDp~~PKrp~saY~lF~~e~r~~lk~~~P~-~--~~eisK~ige~Wk~Ls~eEK~p 294 (294)
+.+|+++++.+||++||||+|||+||++++|..|+.+||+ . +.||+++||++|++|+++||++
T Consensus 8 ~~~k~~~k~~kdp~~PKrP~sAY~~F~~~~R~~i~~~~P~~~~~~~evsk~ige~Wk~ls~eeK~~ 73 (94)
T PTZ00199 8 VLVRKNKRKKKDPNAPKRALSAYMFFAKEKRAEIIAENPELAKDVAAVGKMVGEAWNKLSEEEKAP 73 (94)
T ss_pred ccccccCCCCCCCCCCCCCCcHHHHHHHHHHHHHHHHCcCCcccHHHHHHHHHHHHHcCCHHHHHH
Confidence 3566666778999999999999999999999999999999 4 7999999999999999999864
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=99.44 E-value=8.5e-14 Score=106.33 Aligned_cols=49 Identities=27% Similarity=0.514 Sum_probs=46.8
Q ss_pred CCCCCCchhHhhhHHhHHHHHhhCCC-ChHHHHHHHHHHhcCCCccccCC
Q 022607 246 YPKPNRSGYNFFFAEKHYKLKSLYPN-REREFTKMIGESWTNLSPEERKV 294 (294)
Q Consensus 246 ~PKrp~saY~lF~~e~r~~lk~~~P~-~~~eisK~ige~Wk~Ls~eEK~p 294 (294)
+||||+||||||++++|..|+.+||+ ++.||+++||++|++|+++||++
T Consensus 1 ~~kRP~naf~lf~~~~r~~~~~~~p~~~~~eisk~~g~~Wk~ls~eeK~~ 50 (77)
T cd01389 1 KIPRPRNAFILYRQDKHAQLKTENPGLTNNEISRIIGRMWRSESPEVKAY 50 (77)
T ss_pred CCCCCCcHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHhhCCHHHHHH
Confidence 58999999999999999999999999 88999999999999999999863
No 6
>COG5648 NHP6B Chromatin-associated proteins containing the HMG domain [Chromatin structure and dynamics]
Probab=99.43 E-value=6.7e-14 Score=125.52 Aligned_cols=60 Identities=28% Similarity=0.524 Sum_probs=56.4
Q ss_pred cccccCCCCCCCCCCCCchhHhhhHHhHHHHHhhCCC-ChHHHHHHHHHHhcCCCccccCC
Q 022607 235 RRRSKRRGDPSYPKPNRSGYNFFFAEKHYKLKSLYPN-REREFTKMIGESWTNLSPEERKV 294 (294)
Q Consensus 235 kk~~k~~kDp~~PKrp~saY~lF~~e~r~~lk~~~P~-~~~eisK~ige~Wk~Ls~eEK~p 294 (294)
++.+++++|||.||||+||||||++++|.+|..++|+ ++.|++|+|||+|++|+|+||+|
T Consensus 59 k~~~r~k~dpN~PKRp~sayf~y~~~~R~ei~~~~p~l~~~e~~k~~~e~WK~Ltd~eke~ 119 (211)
T COG5648 59 KRLVRKKKDPNGPKRPLSAYFLYSAENRDEIRKENPKLTFGEVGKLLSEKWKELTDEEKEP 119 (211)
T ss_pred HHHHHHhcCCCCCCCchhHHHHHHHHHHHHHHHhCCCCChHHHHHHHHHHHHhccHhhhhh
Confidence 3456778999999999999999999999999999999 99999999999999999999975
No 7
>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=99.38 E-value=3.3e-13 Score=98.75 Aligned_cols=48 Identities=44% Similarity=0.652 Sum_probs=46.3
Q ss_pred CCCCCchhHhhhHHhHHHHHhhCCC-ChHHHHHHHHHHhcCCCccccCC
Q 022607 247 PKPNRSGYNFFFAEKHYKLKSLYPN-REREFTKMIGESWTNLSPEERKV 294 (294)
Q Consensus 247 PKrp~saY~lF~~e~r~~lk~~~P~-~~~eisK~ige~Wk~Ls~eEK~p 294 (294)
||+|+|||++|++++|..++.+||+ ++.+|+++||++|++|+++||++
T Consensus 1 Pkrp~saf~~f~~~~r~~~~~~~p~~~~~~i~~~~~~~W~~ls~~eK~~ 49 (66)
T cd01390 1 PKRPLSAYFLFSQEQRPKLKKENPDASVTEVTKILGEKWKELSEEEKKK 49 (66)
T ss_pred CCCCCcHHHHHHHHHHHHHHHHCcCCCHHHHHHHHHHHHHhCCHHHHHH
Confidence 8999999999999999999999999 99999999999999999999863
No 8
>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=99.38 E-value=3.4e-13 Score=101.83 Aligned_cols=48 Identities=27% Similarity=0.520 Sum_probs=45.9
Q ss_pred CCCCCchhHhhhHHhHHHHHhhCCC-ChHHHHHHHHHHhcCCCccccCC
Q 022607 247 PKPNRSGYNFFFAEKHYKLKSLYPN-REREFTKMIGESWTNLSPEERKV 294 (294)
Q Consensus 247 PKrp~saY~lF~~e~r~~lk~~~P~-~~~eisK~ige~Wk~Ls~eEK~p 294 (294)
.|||+|||++|++++|.+++++||+ ++.||+++||++|+.|+++||++
T Consensus 2 iKrP~naf~~F~~~~r~~~~~~~p~~~~~eisk~l~~~Wk~ls~~eK~~ 50 (72)
T cd01388 2 IKRPMNAFMLFSKRHRRKVLQEYPLKENRAISKILGDRWKALSNEEKQP 50 (72)
T ss_pred CCCCCcHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHcCCHHHHHH
Confidence 5899999999999999999999999 99999999999999999999864
No 9
>KOG0381 consensus HMG box-containing protein [General function prediction only]
Probab=99.36 E-value=7.6e-13 Score=104.34 Aligned_cols=52 Identities=37% Similarity=0.611 Sum_probs=49.5
Q ss_pred CCC--CCCCCCchhHhhhHHhHHHHHhhCCC-ChHHHHHHHHHHhcCCCccccCC
Q 022607 243 DPS--YPKPNRSGYNFFFAEKHYKLKSLYPN-REREFTKMIGESWTNLSPEERKV 294 (294)
Q Consensus 243 Dp~--~PKrp~saY~lF~~e~r~~lk~~~P~-~~~eisK~ige~Wk~Ls~eEK~p 294 (294)
||+ +||+|++||++|+.++|.+++.+||+ ...||+|+||++|++|+++||++
T Consensus 17 ~p~~~~pkrp~sa~~~f~~~~~~~~k~~~p~~~~~~v~k~~g~~W~~l~~~~k~~ 71 (96)
T KOG0381|consen 17 DPNAQAPKRPLSAFFLFSSEQRSKIKAENPGLSVGEVAKALGEMWKNLAEEEKQP 71 (96)
T ss_pred CCCCCCCCCCCcHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHhcCCHHHHHH
Confidence 884 99999999999999999999999999 89999999999999999999864
No 10
>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=99.32 E-value=8.9e-13 Score=97.39 Aligned_cols=48 Identities=35% Similarity=0.639 Sum_probs=44.1
Q ss_pred CCCCCchhHhhhHHhHHHHHhhCCC-ChHHHHHHHHHHhcCCCccccCC
Q 022607 247 PKPNRSGYNFFFAEKHYKLKSLYPN-REREFTKMIGESWTNLSPEERKV 294 (294)
Q Consensus 247 PKrp~saY~lF~~e~r~~lk~~~P~-~~~eisK~ige~Wk~Ls~eEK~p 294 (294)
||||+|+|++|+.+++..++.+||+ +..+|+++||++|++|+++||++
T Consensus 1 PkrP~~af~lf~~~~~~~~k~~~p~~~~~~i~~~~~~~W~~l~~~eK~~ 49 (69)
T PF00505_consen 1 PKRPPNAFMLFCKEKRAKLKEENPDLSNKEISKILAQMWKNLSEEEKAP 49 (69)
T ss_dssp SSSS--HHHHHHHHHHHHHHHHSTTSTHHHHHHHHHHHHHCSHHHHHHH
T ss_pred CcCCCCHHHHHHHHHHHHHHHHhcccccccchhhHHHHHhcCCHHHHHH
Confidence 8999999999999999999999999 89999999999999999999863
No 11
>smart00398 HMG high mobility group.
Probab=99.29 E-value=2.4e-12 Score=94.52 Aligned_cols=49 Identities=35% Similarity=0.552 Sum_probs=46.6
Q ss_pred CCCCCCchhHhhhHHhHHHHHhhCCC-ChHHHHHHHHHHhcCCCccccCC
Q 022607 246 YPKPNRSGYNFFFAEKHYKLKSLYPN-REREFTKMIGESWTNLSPEERKV 294 (294)
Q Consensus 246 ~PKrp~saY~lF~~e~r~~lk~~~P~-~~~eisK~ige~Wk~Ls~eEK~p 294 (294)
+||+|+|+|++|++++|..++.+||+ +..+|+++||++|+.|+++||++
T Consensus 1 ~pkrp~~~y~~f~~~~r~~~~~~~~~~~~~~i~~~~~~~W~~l~~~ek~~ 50 (70)
T smart00398 1 KPKRPMSAFMLFSQENRAKIKAENPDLSNAEISKKLGERWKLLSEEEKAP 50 (70)
T ss_pred CcCCCCcHHHHHHHHHHHHHHHHCcCCCHHHHHHHHHHHHHcCCHHHHHH
Confidence 58999999999999999999999999 88999999999999999999863
No 12
>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=99.27 E-value=3.9e-12 Score=92.39 Aligned_cols=48 Identities=38% Similarity=0.601 Sum_probs=46.0
Q ss_pred CCCCCchhHhhhHHhHHHHHhhCCC-ChHHHHHHHHHHhcCCCccccCC
Q 022607 247 PKPNRSGYNFFFAEKHYKLKSLYPN-REREFTKMIGESWTNLSPEERKV 294 (294)
Q Consensus 247 PKrp~saY~lF~~e~r~~lk~~~P~-~~~eisK~ige~Wk~Ls~eEK~p 294 (294)
||+|+|+|++|++++|..++.+||+ +..+|+++||++|+.|++++|++
T Consensus 1 pkrp~~af~~f~~~~~~~~~~~~~~~~~~~i~~~~~~~W~~l~~~~k~~ 49 (66)
T cd00084 1 PKRPLSAYFLFSQEHRAEVKAENPGLSVGEISKILGEMWKSLSEEEKKK 49 (66)
T ss_pred CCCCCcHHHHHHHHHHHHHHHHCcCCCHHHHHHHHHHHHHhCCHHHHHH
Confidence 8999999999999999999999999 89999999999999999999863
No 13
>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=99.23 E-value=5e-12 Score=95.70 Aligned_cols=51 Identities=37% Similarity=0.537 Sum_probs=43.1
Q ss_pred CCCCCCCCchhHhhhHHhHHHHHhh-CCC-ChHHHHHHHHHHhcCCCccccCC
Q 022607 244 PSYPKPNRSGYNFFFAEKHYKLKSL-YPN-REREFTKMIGESWTNLSPEERKV 294 (294)
Q Consensus 244 p~~PKrp~saY~lF~~e~r~~lk~~-~P~-~~~eisK~ige~Wk~Ls~eEK~p 294 (294)
|++||+|+|||+||+.+++.+++.+ ++. ...|+++.||++|++||++||++
T Consensus 1 p~kpK~~~say~lF~~~~~~~~k~~G~~~~~~~e~~k~~~~~Wk~Ls~~EK~~ 53 (73)
T PF09011_consen 1 PKKPKRPPSAYNLFMKEMRKEVKEEGGQKQSFREVMKEISERWKSLSEEEKEP 53 (73)
T ss_dssp SSS--SSSSHHHHHHHHHHHHHHHHT-T-SSHHHHHHHHHHHHHHS-HHHHHH
T ss_pred CcCCCCCCCHHHHHHHHHHHHHHHhcccCCCHHHHHHHHHHHHHhcCHHHHHH
Confidence 7899999999999999999999998 565 78999999999999999999863
No 14
>KOG2510 consensus SWI-SNF chromatin-remodeling complex protein [Chromatin structure and dynamics]
Probab=99.17 E-value=3e-11 Score=119.55 Aligned_cols=92 Identities=29% Similarity=0.460 Sum_probs=83.6
Q ss_pred ccChhHHHHHHHHHHhhcCCCC-CCCeeCCeecchhhhHHHHHhcCcchhhhccccHHHHHhhhcCCCCCCcHHHHHHHH
Q 022607 31 SKDPIVFWDTLRRFHFIMGTKF-MIPVIGGKELDLHVLYVEATTRGGYEKVVAEKKWREVGAVFKFSPTTTSASFVLRKH 109 (294)
Q Consensus 31 ~~~~~~Fl~~L~~F~~~rG~~l-~~P~i~Gk~LDL~~Ly~~V~~rGG~~~V~~~k~W~eVa~~lg~p~~~tsas~~Lk~~ 109 (294)
..+++..+++|+.|++.+.+++ ..|.++.++||||+||..|..+||+.+|++++ +|+|.-|| .++++.||++
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 4688999999999999999999 68999999999999999999999999999998 99999998 5688999999
Q ss_pred HHHhhHHHHHHHHhhccCCC
Q 022607 110 YLTLLYHYEQVHFFKMQGPP 129 (294)
Q Consensus 110 Y~k~L~~YE~~~~~~~~~~~ 129 (294)
|.+||+.||+.+..+++.++
T Consensus 364 y~~~lf~fec~f~Rg~e~p~ 383 (532)
T KOG2510|consen 364 YIQYLFAFECKFERGEEPPP 383 (532)
T ss_pred HHHHHHhhceeeeccCCCCH
Confidence 99999999998766665443
No 15
>KOG0527 consensus HMG-box transcription factor [Transcription]
Probab=99.13 E-value=4.4e-11 Score=114.88 Aligned_cols=54 Identities=22% Similarity=0.378 Sum_probs=50.5
Q ss_pred CCCCCCCCCCCchhHhhhHHhHHHHHhhCCC-ChHHHHHHHHHHhcCCCccccCC
Q 022607 241 RGDPSYPKPNRSGYNFFFAEKHYKLKSLYPN-REREFTKMIGESWTNLSPEERKV 294 (294)
Q Consensus 241 ~kDp~~PKrp~saY~lF~~e~r~~lk~~~P~-~~~eisK~ige~Wk~Ls~eEK~p 294 (294)
+....+.||||||||+|.+.+|.+|.++||+ .+.||||+||++||.|+|+||.|
T Consensus 57 k~~~~hIKRPMNAFMVWSq~~RRkma~qnP~mHNSEISK~LG~~WK~Lse~EKrP 111 (331)
T KOG0527|consen 57 KTSTDRIKRPMNAFMVWSQGQRRKLAKQNPKMHNSEISKRLGAEWKLLSEEEKRP 111 (331)
T ss_pred CCCccccCCCcchhhhhhHHHHHHHHHhCcchhhHHHHHHHHHHHhhcCHhhhcc
Confidence 4456688999999999999999999999999 99999999999999999999986
No 16
>KOG0526 consensus Nucleosome-binding factor SPN, POB3 subunit [Transcription; Replication, recombination and repair; Chromatin structure and dynamics]
Probab=98.96 E-value=4.6e-10 Score=112.17 Aligned_cols=55 Identities=24% Similarity=0.537 Sum_probs=50.6
Q ss_pred ccccccCCCCCCCCCCCCchhHhhhHHhHHHHHhhCCC-ChHHHHHHHHHHhcCCCcc
Q 022607 234 RRRRSKRRGDPSYPKPNRSGYNFFFAEKHYKLKSLYPN-REREFTKMIGESWTNLSPE 290 (294)
Q Consensus 234 ~kk~~k~~kDp~~PKrp~saY~lF~~e~r~~lk~~~P~-~~~eisK~ige~Wk~Ls~e 290 (294)
++++.|+.+|||+|||++||||||++..|..||.+ + ..+|++|..|++|+.|++.
T Consensus 523 ~~k~~kk~kdpnapkra~sa~m~w~~~~r~~ik~d--gi~~~dv~kk~g~~wk~ms~k 578 (615)
T KOG0526|consen 523 KKKKGKKKKDPNAPKRATSAYMLWLNASRESIKED--GISVGDVAKKAGEKWKQMSAK 578 (615)
T ss_pred cccCcccCCCCCCCccchhHHHHHHHhhhhhHhhc--CchHHHHHHHHhHHHhhhccc
Confidence 44566889999999999999999999999999998 6 8999999999999999983
No 17
>KOG3248 consensus Transcription factor TCF-4 [Transcription]
Probab=98.19 E-value=7.9e-07 Score=85.19 Aligned_cols=51 Identities=20% Similarity=0.363 Sum_probs=45.7
Q ss_pred CCCCCCCCCCchhHhhhHHhHHHHHhhCCC-ChHHHHHHHHHHhcCCCccccC
Q 022607 242 GDPSYPKPNRSGYNFFFAEKHYKLKSLYPN-REREFTKMIGESWTNLSPEERK 293 (294)
Q Consensus 242 kDp~~PKrp~saY~lF~~e~r~~lk~~~P~-~~~eisK~ige~Wk~Ls~eEK~ 293 (294)
+|| +-|+|+||||+|++|+|+++.++.-. ...+|.++||++|.+||-||.+
T Consensus 188 Kkp-hiKKPLNAFmlyMKEmRa~vvaEctlKeSAaiNqiLGrRWH~LSrEEQA 239 (421)
T KOG3248|consen 188 KKP-HIKKPLNAFMLYMKEMRAKVVAECTLKESAAINQILGRRWHALSREEQA 239 (421)
T ss_pred cCc-cccccHHHHHHHHHHHHHHHHHHhhhhhHHHHHHHHhHHHhhhhHHHHH
Confidence 444 57899999999999999999999877 6799999999999999999864
No 18
>KOG0528 consensus HMG-box transcription factor SOX5 [Transcription]
Probab=98.04 E-value=2e-06 Score=85.68 Aligned_cols=56 Identities=16% Similarity=0.408 Sum_probs=51.1
Q ss_pred cCCCCCCCCCCCCchhHhhhHHhHHHHHhhCCC-ChHHHHHHHHHHhcCCCccccCC
Q 022607 239 KRRGDPSYPKPNRSGYNFFFAEKHYKLKSLYPN-REREFTKMIGESWTNLSPEERKV 294 (294)
Q Consensus 239 k~~kDp~~PKrp~saY~lF~~e~r~~lk~~~P~-~~~eisK~ige~Wk~Ls~eEK~p 294 (294)
-+-..+.+.||||||||.|.++.|.+|-..+|| .+..|+|+||-+|+.|+-.||+|
T Consensus 318 g~~ss~PHIKRPMNAFMVWAkDERRKILqA~PDMHNSnISKILGSRWKaMSN~eKQP 374 (511)
T KOG0528|consen 318 GRASSEPHIKRPMNAFMVWAKDERRKILQAFPDMHNSNISKILGSRWKAMSNTEKQP 374 (511)
T ss_pred CcCCCCccccCCcchhhcccchhhhhhhhcCccccccchhHHhcccccccccccccc
Confidence 334566789999999999999999999999999 88999999999999999999986
No 19
>KOG4715 consensus SWI/SNF-related matrix-associated actin-dependent regulator of chromatin [Chromatin structure and dynamics]
Probab=97.73 E-value=4.4e-05 Score=72.91 Aligned_cols=55 Identities=25% Similarity=0.410 Sum_probs=50.8
Q ss_pred cCCCCCCCCCCCCchhHhhhHHhHHHHHhhCCC-ChHHHHHHHHHHhcCCCccccC
Q 022607 239 KRRGDPSYPKPNRSGYNFFFAEKHYKLKSLYPN-REREFTKMIGESWTNLSPEERK 293 (294)
Q Consensus 239 k~~kDp~~PKrp~saY~lF~~e~r~~lk~~~P~-~~~eisK~ige~Wk~Ls~eEK~ 293 (294)
.+.+-|..|-+|+-.||-|....+.++|++||+ ..=||.|+||.||..|+|+||+
T Consensus 57 t~pkpPkppekpl~pymrySrkvWd~VkA~nPe~kLWeiGK~Ig~mW~dLpd~EK~ 112 (410)
T KOG4715|consen 57 TRPKPPKPPEKPLMPYMRYSRKVWDQVKASNPELKLWEIGKIIGGMWLDLPDEEKQ 112 (410)
T ss_pred cCCCCCCCCCcccchhhHHhhhhhhhhhccCcchHHHHHHHHHHHHHhhCcchHHH
Confidence 345677889999999999999999999999999 8899999999999999999985
No 20
>KOG2746 consensus HMG-box transcription factor Capicua and related proteins [Transcription]
Probab=97.23 E-value=0.00014 Score=75.06 Aligned_cols=59 Identities=24% Similarity=0.481 Sum_probs=52.5
Q ss_pred cccccCCCCCCCCCCCCchhHhhhHHhH--HHHHhhCCC-ChHHHHHHHHHHhcCCCccccC
Q 022607 235 RRRSKRRGDPSYPKPNRSGYNFFFAEKH--YKLKSLYPN-REREFTKMIGESWTNLSPEERK 293 (294)
Q Consensus 235 kk~~k~~kDp~~PKrp~saY~lF~~e~r--~~lk~~~P~-~~~eisK~ige~Wk~Ls~eEK~ 293 (294)
..+..-++|-.+-++|||+|++|++.+| ..++..||+ .++-|+||+||.|-.|.+.||+
T Consensus 170 dgrspnkr~k~HirrPMnaf~ifskrhr~~g~vhq~~pn~DNrtIskiLgewWytL~~~Ekq 231 (683)
T KOG2746|consen 170 DGRSPNKRDKDHIRRPMNAFHIFSKRHRGEGRVHQRHPNQDNRTISKILGEWWYTLGPNEKQ 231 (683)
T ss_pred ccCCCCcCcchhhhhhhHHHHHHHhhcCCccchhccCccccchhHHHHHhhhHhhhCchhhh
Confidence 3344556777789999999999999999 999999999 7899999999999999999996
No 21
>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=96.60 E-value=0.0035 Score=55.45 Aligned_cols=44 Identities=20% Similarity=0.394 Sum_probs=39.3
Q ss_pred CCCCCCCchhHhhhHHhHHHHHhhCCC-ChHHHHHHHHHHhcCCC
Q 022607 245 SYPKPNRSGYNFFFAEKHYKLKSLYPN-REREFTKMIGESWTNLS 288 (294)
Q Consensus 245 ~~PKrp~saY~lF~~e~r~~lk~~~P~-~~~eisK~ige~Wk~Ls 288 (294)
.+-.|-+|||+.|++|.-++||++||+ +-+|..+..++.|...+
T Consensus 120 EKRqR~psaYn~f~k~ei~rik~~~p~ishkeaFs~aAknW~h~p 164 (170)
T PF04690_consen 120 EKRQRVPSAYNRFMKEEIQRIKAENPDISHKEAFSAAAKNWAHFP 164 (170)
T ss_pred cccCCCchhHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHhhhhCc
Confidence 344577899999999999999999999 88999999999998765
No 22
>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=93.95 E-value=0.052 Score=38.60 Aligned_cols=34 Identities=24% Similarity=0.498 Sum_probs=30.4
Q ss_pred cceeeeeecccc-cCcceEEEeecceeeeeeeccC
Q 022607 170 CFTAVGRIDGKF-DCGYLVSVKLGSETLSGVLYHP 203 (294)
Q Consensus 170 ~~~v~g~idgkf-d~gylvtv~~gse~~~gvly~~ 203 (294)
+.-|+++=||.- |..|--+|+||.-.+||+||.-
T Consensus 14 cvRvs~idd~~~~e~aYQt~V~IgGHvFkGiLyDq 48 (50)
T TIGR01624 14 CVRVTAIDDGEQAEYAYQATVTIGGHVFKGFLHDQ 48 (50)
T ss_pred EEEEeccCCCCCceEEEEEEEEECceEEeeEEecc
Confidence 556888888988 8999999999999999999963
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=93.64 E-value=0.21 Score=44.55 Aligned_cols=39 Identities=18% Similarity=0.314 Sum_probs=34.4
Q ss_pred CchhHhhhHHhHHHHHhhCCC-ChHHHHHHHHHHhcCCCccccC
Q 022607 251 RSGYNFFFAEKHYKLKSLYPN-REREFTKMIGESWTNLSPEERK 293 (294)
Q Consensus 251 ~saY~lF~~e~r~~lk~~~P~-~~~eisK~ige~Wk~Ls~eEK~ 293 (294)
.+||+=|..++|. .|.+ ...|+....+++|..|+++||.
T Consensus 83 nnaYLNFLReFRr----kh~~L~p~dlI~~AAraW~rLSe~eK~ 122 (183)
T PF06382_consen 83 NNAYLNFLREFRR----KHCGLSPQDLIQRAARAWCRLSEAEKN 122 (183)
T ss_pred chHHHHHHHHHHH----HccCCCHHHHHHHHHHHHHhCCHHHHH
Confidence 4799999999987 4567 8899999999999999999984
No 24
>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=92.36 E-value=0.13 Score=37.66 Aligned_cols=40 Identities=15% Similarity=0.308 Sum_probs=35.7
Q ss_pred CCchhHhhhHHhHHHHHhhCCC-ChHHHHHHHHHHhcCCCc
Q 022607 250 NRSGYNFFFAEKHYKLKSLYPN-REREFTKMIGESWTNLSP 289 (294)
Q Consensus 250 p~saY~lF~~e~r~~lk~~~P~-~~~eisK~ige~Wk~Ls~ 289 (294)
..+.|-.|.+..|+.|.+.||+ ....|..+++.+|++-++
T Consensus 12 ~lt~yK~Fsq~vRP~l~~~NPk~~~sKl~~l~~AKwrEF~~ 52 (55)
T PF08073_consen 12 NLTNYKAFSQHVRPLLAKANPKAPMSKLMMLLQAKWREFQE 52 (55)
T ss_pred HHHHHHHHHHHHHHHHHHHCCCCcHHHHHHHHHHHHHHHHh
Confidence 3578999999999999999999 779999999999997544
No 25
>PF05142 DUF702: Domain of unknown function (DUF702) ; InterPro: IPR007818 This is a family of plant proteins of unknown function.
Probab=91.96 E-value=0.12 Score=45.09 Aligned_cols=36 Identities=25% Similarity=0.555 Sum_probs=32.3
Q ss_pred cceeeeeecccccCcceEEEeecceeeeeeeccCCC
Q 022607 170 CFTAVGRIDGKFDCGYLVSVKLGSETLSGVLYHPDH 205 (294)
Q Consensus 170 ~~~v~g~idgkfd~gylvtv~~gse~~~gvly~~~~ 205 (294)
+.-|+++=||.-|..|.-+|.||.-.+||+||.-..
T Consensus 116 CVRVssiDdgedE~AYQTaV~IGGHVFKGiLYDqG~ 151 (154)
T PF05142_consen 116 CVRVSSIDDGEDEYAYQTAVNIGGHVFKGILYDQGP 151 (154)
T ss_pred EEEEecccCcccceeeEEeEEECCEEeeeeeeccCC
Confidence 566899999999999999999999999999997543
No 26
>PF06244 DUF1014: Protein of unknown function (DUF1014); InterPro: IPR010422 This family consists of several hypothetical eukaryotic proteins of unknown function.
Probab=89.56 E-value=0.49 Score=39.88 Aligned_cols=49 Identities=18% Similarity=0.325 Sum_probs=41.9
Q ss_pred CCCCCCCCCCchhHhhhHHhHHHHHhhCCC-ChHHHHHHHHHHhcCCCcc
Q 022607 242 GDPSYPKPNRSGYNFFFAEKHYKLKSLYPN-REREFTKMIGESWTNLSPE 290 (294)
Q Consensus 242 kDp~~PKrp~saY~lF~~e~r~~lk~~~P~-~~~eisK~ige~Wk~Ls~e 290 (294)
-|-.+-||-.-+|.-|...+-++||++||+ .-.++-.+|-++|..-+++
T Consensus 68 ~drHPErR~KAAy~afeE~~Lp~lK~E~PgLrlsQ~kq~l~K~w~KSPeN 117 (122)
T PF06244_consen 68 IDRHPERRMKAAYKAFEERRLPELKEENPGLRLSQYKQMLWKEWQKSPEN 117 (122)
T ss_pred CCCCcchhHHHHHHHHHHHHhHHHHhhCCCchHHHHHHHHHHHHhcCCCC
Confidence 344445666789999999999999999999 8899999999999988764
No 27
>PF04769 MAT_Alpha1: Mating-type protein MAT alpha 1; InterPro: IPR006856 This family includes Saccharomyces cerevisiae (Baker's yeast) mating type protein alpha 1 (P01365 from SWISSPROT). MAT alpha 1 is a transcription activator that activates mating-type alpha-specific genes with the help of the MADS-box containing MCM1 transcription factor, which together bind cooperatively to PQ elements upstream of alpha-specific genes. The MCM1-MATalpha1 complex is required for the proper DNA-bending that is needed for transcriptional activation []. Alpha 1 interacts in vivo with STE12, linking expression of alpha-specific genes to the alpha-pheromone (IPR006742 from INTERPRO) response pathway [].; GO: 0000772 mating pheromone activity, 0003677 DNA binding, 0045895 positive regulation of transcription, mating-type specific, 0005634 nucleus
Probab=88.26 E-value=0.79 Score=41.67 Aligned_cols=43 Identities=16% Similarity=0.420 Sum_probs=34.3
Q ss_pred CCCCCCCCCCCchhHhhhHHhHHHHHhhCCC-ChHHHHHHHHHHhcCC
Q 022607 241 RGDPSYPKPNRSGYNFFFAEKHYKLKSLYPN-REREFTKMIGESWTNL 287 (294)
Q Consensus 241 ~kDp~~PKrp~saY~lF~~e~r~~lk~~~P~-~~~eisK~ige~Wk~L 287 (294)
++.+..+||+.||||.|+.-.- ...|+ ...++|..|+.+|+.=
T Consensus 38 ~~~~~~~kr~lN~Fm~FRsyy~----~~~~~~~Qk~~S~~l~~lW~~d 81 (201)
T PF04769_consen 38 KRSPEKAKRPLNGFMAFRSYYS----PIFPPLPQKELSGILTKLWEKD 81 (201)
T ss_pred cccccccccchhHHHHHHHHHH----hhcCCcCHHHHHHHHHHHHhCC
Confidence 3445578999999999998876 33456 7899999999999863
No 28
>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=84.07 E-value=2.3 Score=29.16 Aligned_cols=38 Identities=18% Similarity=0.280 Sum_probs=27.5
Q ss_pred hhHHHHHhcCcchhhhccccHHHHHhhhcCCCCCCcHHHHHHHHHHHhh
Q 022607 66 VLYVEATTRGGYEKVVAEKKWREVGAVFKFSPTTTSASFVLRKHYLTLL 114 (294)
Q Consensus 66 ~Ly~~V~~rGG~~~V~~~k~W~eVa~~lg~p~~~tsas~~Lk~~Y~k~L 114 (294)
.|...|...|.- .|..||..|+. + -.+.+++.+|.+||
T Consensus 11 ~l~~~v~~~g~~-------~W~~Ia~~~~~--~--Rt~~qc~~~~~~~~ 48 (48)
T PF00249_consen 11 KLLEAVKKYGKD-------NWKKIAKRMPG--G--RTAKQCRSRYQNLL 48 (48)
T ss_dssp HHHHHHHHSTTT-------HHHHHHHHHSS--S--STHHHHHHHHHHHT
T ss_pred HHHHHHHHhCCc-------HHHHHHHHcCC--C--CCHHHHHHHHHhhC
Confidence 455666666643 69999999992 2 23459999999886
No 29
>COG5648 NHP6B Chromatin-associated proteins containing the HMG domain [Chromatin structure and dynamics]
Probab=77.27 E-value=0.99 Score=41.32 Aligned_cols=48 Identities=21% Similarity=0.228 Sum_probs=40.0
Q ss_pred CCCCCCchhHhhhHHhHHHHHhhCCC-ChHHHHHHHHHHhcCCCccccC
Q 022607 246 YPKPNRSGYNFFFAEKHYKLKSLYPN-REREFTKMIGESWTNLSPEERK 293 (294)
Q Consensus 246 ~PKrp~saY~lF~~e~r~~lk~~~P~-~~~eisK~ige~Wk~Ls~eEK~ 293 (294)
+++.+...|.-+-.+.|+.+...+|+ ...|+++++|+.|++|+++-|+
T Consensus 143 ~~~~~~~~~~e~~~~~r~~~~~~~~~~~~~e~~k~~~~~w~el~~skK~ 191 (211)
T COG5648 143 PNKAPIGPFIENEPKIRPKVEGPSPDKALVEETKIISKAWSELDESKKK 191 (211)
T ss_pred CCCCCCchhhhccHHhccccCCCCcchhhhHHhhhhhhhhhhhChhhhh
Confidence 45667777777788888888888888 6799999999999999987664
No 30
>PF14887 HMG_box_5: HMG (high mobility group) box 5; PDB: 1L8Y_A 1L8Z_A 2HDZ_A.
Probab=72.58 E-value=8.2 Score=30.34 Aligned_cols=47 Identities=11% Similarity=0.303 Sum_probs=33.9
Q ss_pred CCCCCCchhHhhhHHhHHHHHhhCCCChHHHHHHHHHHhcCCCcccc
Q 022607 246 YPKPNRSGYNFFFAEKHYKLKSLYPNREREFTKMIGESWTNLSPEER 292 (294)
Q Consensus 246 ~PKrp~saY~lF~~e~r~~lk~~~P~~~~eisK~ige~Wk~Ls~eEK 292 (294)
.|..|.++=-+|.+.......+.+++...---+.+...|++|++.+|
T Consensus 3 lPE~PKt~qe~Wqq~vi~dYla~~~~dr~K~~kam~~~W~~me~Kek 49 (85)
T PF14887_consen 3 LPETPKTAQEIWQQSVIGDYLAKFRNDRKKALKAMEAQWSQMEKKEK 49 (85)
T ss_dssp -S----THHHHHHHHHHHHHHHHTTSTHHHHHHHHHHHHHTTGGGHH
T ss_pred CCCCCCCHHHHHHHHHHHHHHHHhhHhHHHHHHHHHHHHHHhhhhhh
Confidence 36677888889999888888888888333235699999999999886
No 31
>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=64.17 E-value=15 Score=32.61 Aligned_cols=41 Identities=20% Similarity=0.319 Sum_probs=34.2
Q ss_pred CCeeCCeecchhhhHHHHHhcCcchhhhccccHHHHHhhhcCCCC
Q 022607 54 IPVIGGKELDLHVLYVEATTRGGYEKVVAEKKWREVGAVFKFSPT 98 (294)
Q Consensus 54 ~P~i~Gk~LDL~~Ly~~V~~rGG~~~V~~~k~W~eVa~~lg~p~~ 98 (294)
+|.-+||..+.|.||..|.++-.-+ =+.|.++|-.||..+.
T Consensus 45 pPkS~Gk~Fs~~~Lf~LI~k~~~ke----ikTW~~La~~LGVepp 85 (175)
T PF09441_consen 45 PPKSDGKSFSTFTLFELIRKLESKE----IKTWAQLALELGVEPP 85 (175)
T ss_pred CCCcCCccchHHHHHHHHHHHhhhh----HhHHHHHHHHhCCCCC
Confidence 7999999999999999999764332 2579999999999544
No 32
>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=56.87 E-value=22 Score=25.05 Aligned_cols=36 Identities=14% Similarity=0.310 Sum_probs=23.0
Q ss_pred hhHHHHHhcCcchhhhccccHHHHHhhhcCCCCCCcHHHHHHHHHHHhh
Q 022607 66 VLYVEATTRGGYEKVVAEKKWREVGAVFKFSPTTTSASFVLRKHYLTLL 114 (294)
Q Consensus 66 ~Ly~~V~~rGG~~~V~~~k~W~eVa~~lg~p~~~tsas~~Lk~~Y~k~L 114 (294)
.|...|...|. .|..||..|| . -...+++..|.++|
T Consensus 8 ~L~~~~~~~g~--------~W~~Ia~~l~---~--Rt~~~~~~r~~~~l 43 (60)
T PF13921_consen 8 LLLELVKKYGN--------DWKKIAEHLG---N--RTPKQCRNRWRNHL 43 (60)
T ss_dssp HHHHHHHHHTS---------HHHHHHHST---T--S-HHHHHHHHHHTT
T ss_pred HHHHHHHHHCc--------CHHHHHHHHC---c--CCHHHHHHHHHHHC
Confidence 34555555543 6999999996 1 12347888888766
No 33
>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=56.14 E-value=23 Score=22.43 Aligned_cols=37 Identities=16% Similarity=0.310 Sum_probs=24.3
Q ss_pred hhHHHHHhcCcchhhhccccHHHHHhhhcCCCCCCcHHHHHHHHHHHhh
Q 022607 66 VLYVEATTRGGYEKVVAEKKWREVGAVFKFSPTTTSASFVLRKHYLTLL 114 (294)
Q Consensus 66 ~Ly~~V~~rGG~~~V~~~k~W~eVa~~lg~p~~~tsas~~Lk~~Y~k~L 114 (294)
.|...|...|- ..|..|+..++-- .+..++.+|.+++
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 5799999998641 3347888887653
No 34
>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=50.07 E-value=16 Score=27.52 Aligned_cols=30 Identities=23% Similarity=0.414 Sum_probs=24.6
Q ss_pred cceeeeeecccccCcceEEEeecceeeeeeec
Q 022607 170 CFTAVGRIDGKFDCGYLVSVKLGSETLSGVLY 201 (294)
Q Consensus 170 ~~~v~g~idgkfd~gylvtv~~gse~~~gvly 201 (294)
|..|.|+|-..-|+||+|.+ |-+.+.|.|=
T Consensus 5 G~~v~g~V~si~d~G~~v~~--g~~gv~Gfl~ 34 (74)
T cd05694 5 GMVLSGCVSSVEDHGYILDI--GIPGTTGFLP 34 (74)
T ss_pred CCEEEEEEEEEeCCEEEEEe--CCCCcEEEEE
Confidence 56799999999999999987 5445888874
No 35
>KOG3223 consensus Uncharacterized conserved protein [Function unknown]
Probab=47.97 E-value=11 Score=34.30 Aligned_cols=43 Identities=19% Similarity=0.421 Sum_probs=38.6
Q ss_pred CCCCchhHhhhHHhHHHHHhhCCC-ChHHHHHHHHHHhcCCCcc
Q 022607 248 KPNRSGYNFFFAEKHYKLKSLYPN-REREFTKMIGESWTNLSPE 290 (294)
Q Consensus 248 Krp~saY~lF~~e~r~~lk~~~P~-~~~eisK~ige~Wk~Ls~e 290 (294)
||-+-+|.-|-..+.++|+.+||+ ...+.-.+|-++|+.-+|+
T Consensus 166 kRmrAA~~afEe~~LPrLK~e~P~lrlsQ~Kqll~Kew~KsPDN 209 (221)
T KOG3223|consen 166 KRMRAAFKAFEEARLPRLKKENPGLRLSQYKQLLKKEWQKSPDN 209 (221)
T ss_pred HHHHHHHHHHHHhhchhhhhcCCCccHHHHHHHHHHHHhhCCCC
Confidence 667789999999999999999999 7888989999999987764
No 36
>PF13873 Myb_DNA-bind_5: Myb/SANT-like DNA-binding domain
Probab=46.56 E-value=28 Score=25.88 Aligned_cols=54 Identities=15% Similarity=0.204 Sum_probs=33.7
Q ss_pred cchhhhHHHHHhc---CcchhhhccccHHHHHhhhcC-CCCCCcHHHHHHHHHHHhhHH
Q 022607 62 LDLHVLYVEATTR---GGYEKVVAEKKWREVGAVFKF-SPTTTSASFVLRKHYLTLLYH 116 (294)
Q Consensus 62 LDL~~Ly~~V~~r---GG~~~V~~~k~W~eVa~~lg~-p~~~tsas~~Lk~~Y~k~L~~ 116 (294)
|+|..-|..|..- ++.....++..|.+|+..|+- .+. .-....|++.|.++...
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 4455555555433 233334456799999999964 333 33455999999887653
No 37
>smart00271 DnaJ DnaJ molecular chaperone homology domain.
Probab=40.73 E-value=29 Score=24.04 Aligned_cols=34 Identities=24% Similarity=0.226 Sum_probs=25.2
Q ss_pred HHhHHHHHhhCCCC-------hHHHHHHHHHHhcCCCcccc
Q 022607 259 AEKHYKLKSLYPNR-------EREFTKMIGESWTNLSPEER 292 (294)
Q Consensus 259 ~e~r~~lk~~~P~~-------~~eisK~ige~Wk~Ls~eEK 292 (294)
+..|...+.-||+. ..+..+.|.+.|..|.+..|
T Consensus 20 ~ay~~l~~~~HPD~~~~~~~~~~~~~~~l~~Ay~~L~~~~~ 60 (60)
T smart00271 20 KAYRKLALKYHPDKNPGDKEEAEEKFKEINEAYEVLSDPEK 60 (60)
T ss_pred HHHHHHHHHHCcCCCCCchHHHHHHHHHHHHHHHHHcCCCC
Confidence 45566666778883 34788999999999988654
No 38
>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=37.82 E-value=70 Score=24.36 Aligned_cols=60 Identities=17% Similarity=0.243 Sum_probs=41.8
Q ss_pred hhhhHHHHHhcCcc--hhhhccccHHHHHhhhcCCCCCCcHHHHHHHHHHHhhHHHHHHHHh
Q 022607 64 LHVLYVEATTRGGY--EKVVAEKKWREVGAVFKFSPTTTSASFVLRKHYLTLLYHYEQVHFF 123 (294)
Q Consensus 64 L~~Ly~~V~~rGG~--~~V~~~k~W~eVa~~lg~p~~~tsas~~Lk~~Y~k~L~~YE~~~~~ 123 (294)
|..|+.+....|.+ ...-....|..|+.+|.-..+..-...+|+..|..+=..|..+...
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 34556666667777 3444455899999999864443333459999999998888886543
No 39
>smart00717 SANT SANT SWI3, ADA2, N-CoR and TFIIIB'' DNA-binding domains.
Probab=37.79 E-value=67 Score=20.44 Aligned_cols=26 Identities=15% Similarity=0.382 Sum_probs=18.7
Q ss_pred ccHHHHHhhhcCCCCCCcHHHHHHHHHHHhh
Q 022607 84 KKWREVGAVFKFSPTTTSASFVLRKHYLTLL 114 (294)
Q Consensus 84 k~W~eVa~~lg~p~~~tsas~~Lk~~Y~k~L 114 (294)
..|..|+..|+ +. .+..++..|..++
T Consensus 22 ~~w~~Ia~~~~---~r--t~~~~~~~~~~~~ 47 (49)
T smart00717 22 NNWEKIAKELP---GR--TAEQCRERWNNLL 47 (49)
T ss_pred CCHHHHHHHcC---CC--CHHHHHHHHHHHc
Confidence 57999999997 21 2347888887765
No 40
>cd05699 S1_Rrp5_repeat_hs7 S1_Rrp5_repeat_hs7: 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 7 (hs7). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=35.09 E-value=44 Score=25.72 Aligned_cols=31 Identities=19% Similarity=0.074 Sum_probs=26.5
Q ss_pred cceeeeeecccccCcceEEEeecceeeeeeecc
Q 022607 170 CFTAVGRIDGKFDCGYLVSVKLGSETLSGVLYH 202 (294)
Q Consensus 170 ~~~v~g~idgkfd~gylvtv~~gse~~~gvly~ 202 (294)
|..|+|+|=-|=+.+ |.|.++-..|+|+||-
T Consensus 1 G~lV~~~V~EKt~D~--l~v~l~~~~l~a~l~~ 31 (72)
T cd05699 1 GKLVDARVLKKTLNG--LEVAILPEEIRAFLPT 31 (72)
T ss_pred CceEEEEEEEEcCCc--EEEEecCCCcEEEEEc
Confidence 356889998888888 7888999999999995
No 41
>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=33.60 E-value=42 Score=24.55 Aligned_cols=38 Identities=18% Similarity=0.240 Sum_probs=21.3
Q ss_pred hccccHHHHHhhhcCCCC---CCcHHHHHHHHHHHhhHHHH
Q 022607 81 VAEKKWREVGAVFKFSPT---TTSASFVLRKHYLTLLYHYE 118 (294)
Q Consensus 81 ~~~k~W~eVa~~lg~p~~---~tsas~~Lk~~Y~k~L~~YE 118 (294)
.+.+.|.+||..|+..-+ +...-..|+..|.+.+...+
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 22222344444444444444
No 42
>PHA03102 Small T antigen; Reviewed
Probab=29.89 E-value=42 Score=29.28 Aligned_cols=36 Identities=11% Similarity=0.108 Sum_probs=28.3
Q ss_pred hHHhHHHHHhhCCC--ChHHHHHHHHHHhcCCCccccC
Q 022607 258 FAEKHYKLKSLYPN--REREFTKMIGESWTNLSPEERK 293 (294)
Q Consensus 258 ~~e~r~~lk~~~P~--~~~eisK~ige~Wk~Ls~eEK~ 293 (294)
.+..|...+.-||| ...|..+.|.+.|..|+++.+.
T Consensus 25 KkAYr~la~~~HPDkgg~~e~~k~in~Ay~~L~d~~~r 62 (153)
T PHA03102 25 RKAYLRKCLEFHPDKGGDEEKMKELNTLYKKFRESVKS 62 (153)
T ss_pred HHHHHHHHHHHCcCCCchhHHHHHHHHHHHHHhhHHHh
Confidence 34567777788998 4578889999999999887653
No 43
>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=29.23 E-value=60 Score=23.58 Aligned_cols=42 Identities=21% Similarity=0.383 Sum_probs=27.2
Q ss_pred chhhhHHHHHh-cCcchhhhccccH---HHHHhhhcCCC-CCCcHHHHHHHHHHHhhH
Q 022607 63 DLHVLYVEATT-RGGYEKVVAEKKW---REVGAVFKFSP-TTTSASFVLRKHYLTLLY 115 (294)
Q Consensus 63 DL~~Ly~~V~~-rGG~~~V~~~k~W---~eVa~~lg~p~-~~tsas~~Lk~~Y~k~L~ 115 (294)
++|.+|.+... +|+ ..| +.|++.|+.+. +. .+++.|+++|-.
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 56667766443 333 248 89999998764 32 377777777754
No 44
>KOG0493 consensus Transcription factor Engrailed, contains HOX domain [General function prediction only]
Probab=27.16 E-value=58 Score=31.23 Aligned_cols=23 Identities=30% Similarity=0.401 Sum_probs=17.9
Q ss_pred CCCCCCchhHhhhHHhHHHHHhhCCC
Q 022607 246 YPKPNRSGYNFFFAEKHYKLKSLYPN 271 (294)
Q Consensus 246 ~PKrp~saY~lF~~e~r~~lk~~~P~ 271 (294)
-=|||+++ |..|+.++||.+.-.
T Consensus 245 eeKRPRTA---FtaeQL~RLK~EF~e 267 (342)
T KOG0493|consen 245 EEKRPRTA---FTAEQLQRLKAEFQE 267 (342)
T ss_pred hhcCcccc---ccHHHHHHHHHHHhh
Confidence 35789998 568999999988644
No 45
>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=26.30 E-value=26 Score=30.64 Aligned_cols=69 Identities=14% Similarity=0.108 Sum_probs=52.0
Q ss_pred CCCCccccChhHHHHHHHHHHhhcCCCCCCCeeCCeecchhhhHHHHHhcCcch----------hhhccccHHHHHhhh
Q 022607 25 SSHEDVSKDPIVFWDTLRRFHFIMGTKFMIPVIGGKELDLHVLYVEATTRGGYE----------KVVAEKKWREVGAVF 93 (294)
Q Consensus 25 ~~~e~~~~~~~~Fl~~L~~F~~~rG~~l~~P~i~Gk~LDL~~Ly~~V~~rGG~~----------~V~~~k~W~eVa~~l 93 (294)
.+|-++.-......++++.-+.+.|.-|.-=+|+||+|-||+|..-+.-.|..- +.-....|..|=-.+
T Consensus 2 ~DHialR~n~~~~A~~w~~~l~~~G~llSen~INGRPI~l~~L~qPl~~~~~~I~cvELP~P~~k~Yp~eGWEHIE~Vl 80 (149)
T cd07268 2 IDHIALRVNENQTAERWKEGLLQCGELLSENEINGRPIALIKLEKPLQFAGWSISIVELPFPKDKKYPQEGWEHIEIVI 80 (149)
T ss_pred CceEEEeeCCHHHHHHHHHHHHHhchhhhccccCCeeEEEEEcCCCceeCCcEEEEEEeCCCCCCCCCCCCceEEEEEe
Confidence 355566667788889999999999999988899999999999988877655442 333356777654443
No 46
>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=26.28 E-value=1.1e+02 Score=22.54 Aligned_cols=34 Identities=21% Similarity=0.299 Sum_probs=21.7
Q ss_pred HHHHHHHHHhhcCCCCCCCeeCCeecchhhhHHHHHhcCcchhh
Q 022607 37 FWDTLRRFHFIMGTKFMIPVIGGKELDLHVLYVEATTRGGYEKV 80 (294)
Q Consensus 37 Fl~~L~~F~~~rG~~l~~P~i~Gk~LDL~~Ly~~V~~rGG~~~V 80 (294)
|.+.-.+-+++.|. ++....|+.++.++|++...
T Consensus 3 ~~eaa~~vL~~~~~----------pm~~~eI~~~i~~~~~~~~~ 36 (72)
T PF05066_consen 3 FKEAAYEVLEEAGR----------PMTFKEIWEEIQERGLYKKS 36 (72)
T ss_dssp HHHHHHHHHHHH-S-----------EEHHHHHHHHHHHHTS---
T ss_pred HHHHHHHHHHhcCC----------CcCHHHHHHHHHHhCCCCcc
Confidence 44555555555554 47888999999999999977
No 47
>PF13875 DUF4202: Domain of unknown function (DUF4202)
Probab=26.25 E-value=81 Score=28.51 Aligned_cols=50 Identities=12% Similarity=0.264 Sum_probs=36.9
Q ss_pred CCCCCCCCCCCchhHhhhHHhHHHHHhhCCCChHHHHHHHHHHhcCCCcccc
Q 022607 241 RGDPSYPKPNRSGYNFFFAEKHYKLKSLYPNREREFTKMIGESWTNLSPEER 292 (294)
Q Consensus 241 ~kDp~~PKrp~saY~lF~~e~r~~lk~~~P~~~~eisK~ige~Wk~Ls~eEK 292 (294)
++||..------+-+.|...+.+.+...| ....+-.+|.+-|+.||+.-+
T Consensus 119 k~d~e~Q~LEDvacLVFL~~~f~~F~~~~--deeK~v~Il~KTw~KMS~~g~ 168 (185)
T PF13875_consen 119 KRDPETQALEDVACLVFLEYYFEDFAAKH--DEEKIVDILRKTWRKMSERGH 168 (185)
T ss_pred CCCchHHHHHhhHHHHhHHHHHHHHHhcC--CHHHHHHHHHHHHHHCCHHHH
Confidence 34554333334567899999999999887 456677889999999998643
No 48
>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=24.76 E-value=47 Score=23.45 Aligned_cols=35 Identities=26% Similarity=0.242 Sum_probs=26.3
Q ss_pred hHHhHHHHHhhCCCC---hH----HHHHHHHHHhcCCCcccc
Q 022607 258 FAEKHYKLKSLYPNR---ER----EFTKMIGESWTNLSPEER 292 (294)
Q Consensus 258 ~~e~r~~lk~~~P~~---~~----eisK~ige~Wk~Ls~eEK 292 (294)
.+..+..++.-||+. .. +....|.+.|+.|+++++
T Consensus 18 k~~y~~l~~~~HPD~~~~~~~~~~~~~~~i~~Ay~~L~~~~~ 59 (64)
T PF00226_consen 18 KKAYRRLSKQYHPDKNSGDEAEAEEKFARINEAYEILSDPER 59 (64)
T ss_dssp HHHHHHHHHHTSTTTGTSTHHHHHHHHHHHHHHHHHHHSHHH
T ss_pred HHHHHhhhhccccccchhhhhhhhHHHHHHHHHHHHhCCHHH
Confidence 345666677778982 24 789999999999988765
No 49
>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=24.32 E-value=52 Score=25.59 Aligned_cols=15 Identities=27% Similarity=0.676 Sum_probs=13.2
Q ss_pred ccHHHHHhhhcCCCC
Q 022607 84 KKWREVGAVFKFSPT 98 (294)
Q Consensus 84 k~W~eVa~~lg~p~~ 98 (294)
..|+.+|+.|||+.+
T Consensus 14 ~~Wk~laR~LGlse~ 28 (86)
T cd08306 14 RDWRKLARKLGLSET 28 (86)
T ss_pred hhHHHHHHHcCCCHH
Confidence 479999999999865
No 50
>smart00595 MADF subfamily of SANT domain.
Probab=24.25 E-value=56 Score=24.65 Aligned_cols=41 Identities=22% Similarity=0.269 Sum_probs=27.0
Q ss_pred hhhccccHHHHHhhhcCCCC-CCcHHHHHHHHHHHhhHHHHH
Q 022607 79 KVVAEKKWREVGAVFKFSPT-TTSASFVLRKHYLTLLYHYEQ 119 (294)
Q Consensus 79 ~V~~~k~W~eVa~~lg~p~~-~tsas~~Lk~~Y~k~L~~YE~ 119 (294)
...+...|.+||..||.+.. |..-=..||..|.+.+...+.
T Consensus 23 ~~~r~~aW~~Ia~~l~~~~~~~~~kw~~LR~~y~~e~~r~~~ 64 (89)
T smart00595 23 KEEKRKAWEEIAEELGLSVEECKKRWKNLRDRYRRELKRLQN 64 (89)
T ss_pred hHHHHHHHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 44456699999999998422 322334677777776665554
No 51
>PF12653 DUF3785: Protein of unknown function (DUF3785); InterPro: IPR024210 This family of proteins is functionally uncharacterised. Proteins in this family are approximately 140 amino acids in length and share two CXXC motifs suggesting these are zinc binding proteins. In clostridia proteins are found in an operon with three signalling proteins, suggesting that they are involved in DNA-binding transcription regulator downstream of an as yet unknown signalling pathway.
Probab=24.09 E-value=49 Score=28.32 Aligned_cols=15 Identities=40% Similarity=0.634 Sum_probs=13.0
Q ss_pred cccccCcceEEEeec
Q 022607 178 DGKFDCGYLVSVKLG 192 (294)
Q Consensus 178 dgkfd~gylvtv~~g 192 (294)
+||-|..|||+|+|=
T Consensus 109 ~~kVD~SYiVsi~VC 123 (138)
T PF12653_consen 109 AGKVDDSYIVSIIVC 123 (138)
T ss_pred cCCcCcceEEEEEEC
Confidence 578899999999984
No 52
>cd04455 S1_NusA S1_NusA: N-utilizing substance A protein (NusA), S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. NusA is a transcription elongation factor containing an N-terminal catalytic domain and three RNA binding domains (RBD's). The RBD's include one S1 domain and two KH domains that form an RNA binding surface. DNA transcription by RNA polymerase (RNAP) includes three phases - initiation, elongation, and termination. During initiation, sigma factors bind RNAP and target RNAP to specific promoters. During elongation, N-utilization substances (NusA, B, E, and G) replace sigma factors and regulate pausing, termination, and antitermination. NusA is cold-shock-inducible.
Probab=23.66 E-value=83 Score=22.75 Aligned_cols=29 Identities=14% Similarity=0.153 Sum_probs=22.2
Q ss_pred ccceeeeeecccccCcceEEEeecceeeeeeec
Q 022607 169 SCFTAVGRIDGKFDCGYLVSVKLGSETLSGVLY 201 (294)
Q Consensus 169 ~~~~v~g~idgkfd~gylvtv~~gse~~~gvly 201 (294)
.|..|+|+|-+.-+.|++|.+ |. ..|+|=
T Consensus 3 ~g~iV~G~V~~~~~~~~~vdi--g~--~eg~lp 31 (67)
T cd04455 3 EGEIVTGIVKRVDRGNVIVDL--GK--VEAILP 31 (67)
T ss_pred CCCEEEEEEEEEcCCCEEEEc--CC--eEEEee
Confidence 356799999999998887655 64 678763
No 53
>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=23.07 E-value=47 Score=29.83 Aligned_cols=22 Identities=41% Similarity=0.851 Sum_probs=19.2
Q ss_pred ChHHHHH-HHHHHhcCCCccccC
Q 022607 272 REREFTK-MIGESWTNLSPEERK 293 (294)
Q Consensus 272 ~~~eisK-~ige~Wk~Ls~eEK~ 293 (294)
.+..|++ .+|..|+.+|++||+
T Consensus 65 Df~~mar~vLG~~W~~~s~~Qr~ 87 (198)
T TIGR03481 65 DLPAMARLTLGSSWTSLSPEQRR 87 (198)
T ss_pred CHHHHHHHHhhhhhhhCCHHHHH
Confidence 6788887 599999999999985
No 54
>PLN03212 Transcription repressor MYB5; Provisional
Probab=22.91 E-value=1.1e+02 Score=28.88 Aligned_cols=40 Identities=15% Similarity=0.223 Sum_probs=27.0
Q ss_pred hhHHHHHhcCcchhhhccccHHHHHhhhcCCCCCCcHHHHHHHHHHHhhHH
Q 022607 66 VLYVEATTRGGYEKVVAEKKWREVGAVFKFSPTTTSASFVLRKHYLTLLYH 116 (294)
Q Consensus 66 ~Ly~~V~~rGG~~~V~~~k~W~eVa~~lg~p~~~tsas~~Lk~~Y~k~L~~ 116 (294)
.|...|...|. ..|..||..++...+ +.+.|.-|.+||.+
T Consensus 35 ~L~~lV~kyG~-------~nW~~IAk~~g~gRT----~KQCReRW~N~L~P 74 (249)
T PLN03212 35 ILVSFIKKEGE-------GRWRSLPKRAGLLRC----GKSCRLRWMNYLRP 74 (249)
T ss_pred HHHHHHHHhCc-------ccHHHHHHhhhcCCC----cchHHHHHHHhhch
Confidence 34556766663 369999998874332 23778888888854
No 55
>PF13725 tRNA_bind_2: Possible tRNA binding domain; PDB: 2ZPA_B.
Probab=22.28 E-value=48 Score=25.86 Aligned_cols=20 Identities=25% Similarity=0.426 Sum_probs=13.6
Q ss_pred hhhhccccHHHHHhhhcCCC
Q 022607 78 EKVVAEKKWREVGAVFKFSP 97 (294)
Q Consensus 78 ~~V~~~k~W~eVa~~lg~p~ 97 (294)
.+|.+.+.|.+||++|+++.
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 46778899999999999984
No 56
>cd04465 S1_RPS1_repeat_ec2_hs2 S1_RPS1_repeat_ec2_hs2: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists of 4-6 tandem S1 domains. In some bacteria, the tandem S1 array is located C-terminal to a 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (HMBPP reductase) domain.While RPS1 is found primarily in bacteria, proteins with tandem RPS1-like domains have been identified in plants and humans, however these lack the N-terminal HMBPP reductase domain. This CD includes S1 repeat 2 of the Escherichia coli and Homo sapiens RPS1 (ec2 and hs2, respectively). Autoantibodies to double-stranded DNA from patients with systemic lupus erythematosus cross-react with the human RPS1 homolog.
Probab=21.17 E-value=1.1e+02 Score=21.85 Aligned_cols=27 Identities=19% Similarity=0.320 Sum_probs=21.9
Q ss_pred cceeeeeecccccCcceEEEeecceeeeeee
Q 022607 170 CFTAVGRIDGKFDCGYLVSVKLGSETLSGVL 200 (294)
Q Consensus 170 ~~~v~g~idgkfd~gylvtv~~gse~~~gvl 200 (294)
|..|.|.|...-+.|++|++ + .++|-|
T Consensus 1 G~iv~g~V~~v~~~G~~v~l--~--g~~gfi 27 (67)
T cd04465 1 GEIVEGKVTEKVKGGLIVDI--E--GVRAFL 27 (67)
T ss_pred CCEEEEEEEEEECCeEEEEE--C--CEEEEE
Confidence 34689999999999999987 3 378876
No 57
>cd06257 DnaJ DnaJ domain or J-domain. DnaJ/Hsp40 (heat shock protein 40) proteins are highly conserved and play crucial roles in protein translation, folding, unfolding, translocation, and degradation. They act primarily by stimulating the ATPase activity of Hsp70s, an important chaperonine family. Hsp40 proteins are characterized by the presence of a J domain, which mediates the interaction with Hsp70. They may contain other domains as well, and the architectures provide a means of classification.
Probab=20.45 E-value=1.4e+02 Score=19.95 Aligned_cols=32 Identities=22% Similarity=0.146 Sum_probs=23.0
Q ss_pred hHHhHHHHHhhCCCC------hHHHHHHHHHHhcCCCc
Q 022607 258 FAEKHYKLKSLYPNR------EREFTKMIGESWTNLSP 289 (294)
Q Consensus 258 ~~e~r~~lk~~~P~~------~~eisK~ige~Wk~Ls~ 289 (294)
.+..|..++.-||+. ..+....|.+.|..|++
T Consensus 18 k~~y~~l~~~~HPD~~~~~~~~~~~~~~l~~Ay~~L~d 55 (55)
T cd06257 18 KKAYRKLALKYHPDKNPDDPEAEEKFKEINEAYEVLSD 55 (55)
T ss_pred HHHHHHHHHHHCcCCCCCcHHHHHHHHHHHHHHHHhcC
Confidence 345666777778882 35677889999988864
Done!