Query 039418
Match_columns 297
No_of_seqs 168 out of 337
Neff 6.7
Searched_HMMs 46136
Date Fri Mar 29 09:29:09 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/039418.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/039418hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF10536 PMD: Plant mobile dom 100.0 2E-29 4.3E-34 241.6 8.2 171 127-297 1-184 (363)
2 PTZ00199 high mobility group p 99.5 3.3E-14 7.1E-19 111.6 5.9 61 30-90 21-82 (94)
3 cd01389 MATA_HMG-box MATA_HMG- 99.5 3.8E-14 8.2E-19 107.0 5.7 59 31-90 1-59 (77)
4 cd01390 HMGB-UBF_HMG-box HMGB- 99.4 1.1E-13 2.5E-18 100.5 5.5 57 32-89 1-57 (66)
5 cd01388 SOX-TCF_HMG-box SOX-TC 99.4 2.5E-13 5.4E-18 101.2 5.6 58 32-90 2-59 (72)
6 PF00505 HMG_box: HMG (high mo 99.4 2.7E-13 5.8E-18 99.4 4.8 58 32-90 1-58 (69)
7 smart00398 HMG high mobility g 99.4 9E-13 1.9E-17 96.4 5.7 59 31-90 1-59 (70)
8 PF09011 HMG_box_2: HMG-box do 99.4 6.3E-13 1.4E-17 99.3 4.9 59 30-89 2-61 (73)
9 cd00084 HMG-box High Mobility 99.4 1.2E-12 2.7E-17 94.5 5.5 59 32-91 1-59 (66)
10 KOG0381 HMG box-containing pro 99.2 2.4E-11 5.2E-16 95.0 5.7 60 30-90 21-80 (96)
11 PF09331 DUF1985: Domain of un 99.0 4.7E-10 1E-14 94.5 6.7 123 156-279 14-142 (142)
12 KOG0527 HMG-box transcription 99.0 3.4E-10 7.5E-15 107.1 4.4 60 30-90 61-120 (331)
13 COG5648 NHP6B Chromatin-associ 99.0 6.6E-10 1.4E-14 97.7 5.3 61 29-90 68-128 (211)
14 KOG0526 Nucleosome-binding fac 98.2 8E-07 1.7E-11 87.5 3.4 56 30-90 534-589 (615)
15 KOG3248 Transcription factor T 97.5 7.5E-05 1.6E-09 70.1 3.4 57 33-90 193-249 (421)
16 KOG0528 HMG-box transcription 97.4 4.6E-05 9.9E-10 74.6 1.2 63 31-94 325-387 (511)
17 KOG2746 HMG-box transcription 95.5 0.0041 8.8E-08 63.4 0.2 62 32-94 182-245 (683)
18 KOG4715 SWI/SNF-related matrix 95.4 0.017 3.6E-07 54.3 3.9 61 27-88 59-120 (410)
19 PF06382 DUF1074: Protein of u 95.0 0.026 5.7E-07 48.9 3.6 48 35-87 82-129 (183)
20 PF14887 HMG_box_5: HMG (high 93.1 0.15 3.3E-06 38.4 4.0 55 32-88 4-58 (85)
21 PF04690 YABBY: YABBY protein; 91.7 0.26 5.7E-06 42.8 4.4 44 32-76 122-165 (170)
22 COG5648 NHP6B Chromatin-associ 90.1 0.16 3.5E-06 45.3 1.6 56 32-88 144-199 (211)
23 PF03078 ATHILA: ATHILA ORF-1 76.2 51 0.0011 33.1 12.4 168 101-278 63-262 (458)
24 PF11304 DUF3106: Protein of u 65.1 8 0.00017 30.9 3.4 21 67-87 34-54 (107)
25 PF04769 MAT_Alpha1: Mating-ty 61.8 17 0.00038 32.4 5.2 44 29-77 41-84 (201)
26 PF08073 CHDNT: CHDNT (NUC034) 44.5 25 0.00054 24.9 2.7 39 37-76 14-52 (55)
27 PF11943 DUF3460: Protein of u 41.2 57 0.0012 23.5 4.1 38 44-84 8-47 (60)
28 PF10234 Cluap1: Clusterin-ass 39.3 15 0.00033 34.2 1.2 32 124-155 1-37 (267)
29 COG5202 Predicted membrane pro 39.2 19 0.0004 35.1 1.8 27 12-38 189-217 (512)
30 PF06945 DUF1289: Protein of u 33.6 21 0.00046 24.5 0.9 20 69-88 28-47 (51)
31 PF01418 HTH_6: Helix-turn-hel 31.2 33 0.00071 25.3 1.7 60 65-135 5-67 (77)
32 PF13875 DUF4202: Domain of un 28.8 79 0.0017 27.9 3.9 64 11-80 99-169 (185)
33 PF14513 DAG_kinase_N: Diacylg 28.5 11 0.00023 31.8 -1.5 72 69-155 3-82 (138)
34 cd09071 FAR_C C-terminal domai 28.4 55 0.0012 24.5 2.6 21 261-282 70-90 (92)
35 PF05494 Tol_Tol_Ttg2: Toluene 27.0 48 0.001 28.1 2.3 30 59-88 39-69 (170)
36 PF03457 HA: Helicase associat 26.4 42 0.0009 23.9 1.5 16 113-128 52-67 (68)
37 PF07970 COPIIcoated_ERV: Endo 25.8 71 0.0015 28.6 3.2 35 16-51 13-47 (222)
38 TIGR03481 HpnM hopanoid biosyn 25.6 47 0.001 29.3 2.0 30 59-88 65-95 (198)
39 cd07321 Extradiol_Dioxygenase_ 25.2 69 0.0015 23.9 2.5 32 114-148 34-65 (77)
40 PRK15117 ABC transporter perip 24.9 47 0.001 29.6 1.9 25 64-88 75-99 (211)
41 cd02988 Phd_like_VIAF Phosduci 23.8 48 0.001 29.1 1.7 17 22-38 4-20 (192)
42 PF00701 DHDPS: Dihydrodipicol 23.2 66 0.0014 29.6 2.6 102 70-179 47-155 (289)
43 PF12650 DUF3784: Domain of un 23.2 45 0.00098 25.6 1.3 17 70-86 25-41 (97)
44 PF03015 Sterile: Male sterili 22.3 85 0.0018 23.8 2.6 54 227-283 33-91 (94)
45 smart00271 DnaJ DnaJ molecular 22.1 99 0.0022 20.9 2.7 36 42-77 18-58 (60)
46 PF06628 Catalase-rel: Catalas 21.8 50 0.0011 23.9 1.1 23 66-88 12-34 (68)
47 PF00226 DnaJ: DnaJ domain; I 20.1 1.1E+02 0.0023 21.1 2.6 39 42-80 17-60 (64)
No 1
>PF10536 PMD: Plant mobile domain; InterPro: IPR019557 This entry represents a domain found in a variety of transposases [].
Probab=99.96 E-value=2e-29 Score=241.61 Aligned_cols=171 Identities=19% Similarity=0.322 Sum_probs=146.2
Q ss_pred Ccccccccc--cccccHHHHHHHHhccccCcceEEECCeEeecCccchhheeccccCCccccccCChh---HHHHHHhhh
Q 039418 127 GLGSIIDLK--CGRLKRKLCAWLVERIDTARCVLQLNGHELELSPNSFGYIMGVTDGGMPMELQGDSA---EVAAYLDKF 201 (297)
Q Consensus 127 GFg~LL~i~--~~~l~~~L~~wL~~~~d~~t~~~~i~g~~i~iT~~dV~~VLGLP~gG~~v~~~~~~~---~~~~l~~~~ 201 (297)
|||+|+.|. ..++++.|+.+|+++|+++|++|++++++++||++||..|+|||+.|.+|....+.+ .++++....
T Consensus 1 ~~g~~~~i~~s~~~~~~~li~al~erW~~et~tF~~~~gEmtiTL~DV~~llGLpi~G~pv~~~~~~~~~~~~~~ll~~~ 80 (363)
T PF10536_consen 1 GFGILDAIMASRITIDRSLISALVERWDPETNTFHFPWGEMTITLEDVAMLLGLPIDGRPVTGPLPPDWRDLCEELLGVS 80 (363)
T ss_pred CchhHhhhhhhcCCCCHHHHHHHHHHhCcccCeeecccccccchhhhhhhccccccccccccCccccchhhHHHHHhccc
Confidence 899999999 899999999999999999999999999999999999999999999999998754332 333333222
Q ss_pred cc----CCCccchHHHHHHHhcCCCC-CchhhhHHHhhhhcceeCCCCCC-ccCcchhhhhhccccCcccchhHHHHHHH
Q 039418 202 NA----TSRGINIKTMEDILLTSKDA-DNDFKVAFMLFTLCTLLCPPGGV-HISYSFLFTLKDVHSIRNRNWATFCFERL 275 (297)
Q Consensus 202 ~~----~~~~isl~~L~~~ll~~~~~-~d~f~r~Fll~~i~~~L~Ptt~~-~vs~~yl~~l~D~~~I~~ynW~~~Vld~L 275 (297)
.. .+..+.+++|++.+...+++ ++.+.||||++.+|++|||+++. +|+..|++++.|++.+++||||++||++|
T Consensus 81 ~~~~~~~~~~~~~~wl~~~~~~~~~~d~~~~~rAFll~~lg~~lfp~~~~~~v~~~~l~~~~~l~~~~~~~wg~a~La~l 160 (363)
T PF10536_consen 81 PQIKSKKGSSIRLSWLEEFFSNRPEDDEEQYHRAFLLYWLGSFLFPDKSGDYVSPRYLPLAVDLARIKRYAWGSAVLAYL 160 (363)
T ss_pred ccccccccccchhhheeccccccccchHHHHHHHHHHHhhhceeccCCCcceeeeeEEeeeeccccccccccHHHHHHHH
Confidence 11 23456778888886333333 24799999999999999999998 89999999999999999999999999999
Q ss_pred HHHHHhhhccC--CceeecceecC
Q 039418 276 MRGITRYKDEK--LAHVGGCLLYL 297 (297)
Q Consensus 276 ~~~l~k~~~~k--~~~i~GCllfL 297 (297)
+++|++...+. ..+++||+.||
T Consensus 161 y~~L~~~~~~~~~~~~~~g~~~ll 184 (363)
T PF10536_consen 161 YRDLCKASRKSASQSNIGGPLWLL 184 (363)
T ss_pred HHHHHHHhhhcccccccccceeee
Confidence 99999988876 78999999986
No 2
>PTZ00199 high mobility group protein; Provisional
Probab=99.49 E-value=3.3e-14 Score=111.64 Aligned_cols=61 Identities=18% Similarity=0.269 Sum_probs=56.9
Q ss_pred CCCCCCCcchhhhHHHHHHHHHHhCCCCc-chhHHHHHHHhhhcCCChHhhhhhhhhhhcCC
Q 039418 30 SKDRENNHGFISFFAESVRQLKAKDGRAC-ITNEVRKEIRNAFKNLPVEEKCQYKFQSRRGG 90 (297)
Q Consensus 30 ~~~~r~~~~f~~~~~~~~~~~~~~~~~~~-~~~~v~k~~g~~wk~ls~~ek~~~~~~~~~~~ 90 (297)
|+||||+||||+|++++|.+++++||+.. .+.+|++++|+.|++||++||++|.++|.+..
T Consensus 21 ~~PKrP~sAY~~F~~~~R~~i~~~~P~~~~~~~evsk~ige~Wk~ls~eeK~~y~~~A~~dk 82 (94)
T PTZ00199 21 NAPKRALSAYMFFAKEKRAEIIAENPELAKDVAAVGKMVGEAWNKLSEEEKAPYEKKAQEDK 82 (94)
T ss_pred CCCCCCCcHHHHHHHHHHHHHHHHCcCCcccHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHH
Confidence 78999999999999999999999999875 58999999999999999999999999998743
No 3
>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=99.49 E-value=3.8e-14 Score=106.96 Aligned_cols=59 Identities=22% Similarity=0.259 Sum_probs=55.7
Q ss_pred CCCCCCcchhhhHHHHHHHHHHhCCCCcchhHHHHHHHhhhcCCChHhhhhhhhhhhcCC
Q 039418 31 KDRENNHGFISFFAESVRQLKAKDGRACITNEVRKEIRNAFKNLPVEEKCQYKFQSRRGG 90 (297)
Q Consensus 31 ~~~r~~~~f~~~~~~~~~~~~~~~~~~~~~~~v~k~~g~~wk~ls~~ek~~~~~~~~~~~ 90 (297)
+||||+||||+|++++|++++++||+ .++.+|++.+|..|+.||++||++|.+.|.+..
T Consensus 1 ~~kRP~naf~lf~~~~r~~~~~~~p~-~~~~eisk~~g~~Wk~ls~eeK~~y~~~A~~~k 59 (77)
T cd01389 1 KIPRPRNAFILYRQDKHAQLKTENPG-LTNNEISRIIGRMWRSESPEVKAYYKELAEEEK 59 (77)
T ss_pred CCCCCCcHHHHHHHHHHHHHHHHCCC-CCHHHHHHHHHHHHhhCCHHHHHHHHHHHHHHH
Confidence 58999999999999999999999994 689999999999999999999999999998754
No 4
>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=99.45 E-value=1.1e-13 Score=100.46 Aligned_cols=57 Identities=23% Similarity=0.332 Sum_probs=54.4
Q ss_pred CCCCCcchhhhHHHHHHHHHHhCCCCcchhHHHHHHHhhhcCCChHhhhhhhhhhhcC
Q 039418 32 DRENNHGFISFFAESVRQLKAKDGRACITNEVRKEIRNAFKNLPVEEKCQYKFQSRRG 89 (297)
Q Consensus 32 ~~r~~~~f~~~~~~~~~~~~~~~~~~~~~~~v~k~~g~~wk~ls~~ek~~~~~~~~~~ 89 (297)
||||+|||++|+.|+|.++++.||+ .++.+|++.+|..|++||++||++|.++|++.
T Consensus 1 Pkrp~saf~~f~~~~r~~~~~~~p~-~~~~~i~~~~~~~W~~ls~~eK~~y~~~a~~~ 57 (66)
T cd01390 1 PKRPLSAYFLFSQEQRPKLKKENPD-ASVTEVTKILGEKWKELSEEEKKKYEEKAEKD 57 (66)
T ss_pred CCCCCcHHHHHHHHHHHHHHHHCcC-CCHHHHHHHHHHHHHhCCHHHHHHHHHHHHHH
Confidence 8999999999999999999999995 68999999999999999999999999999874
No 5
>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=99.42 E-value=2.5e-13 Score=101.25 Aligned_cols=58 Identities=17% Similarity=0.178 Sum_probs=54.7
Q ss_pred CCCCCcchhhhHHHHHHHHHHhCCCCcchhHHHHHHHhhhcCCChHhhhhhhhhhhcCC
Q 039418 32 DRENNHGFISFFAESVRQLKAKDGRACITNEVRKEIRNAFKNLPVEEKCQYKFQSRRGG 90 (297)
Q Consensus 32 ~~r~~~~f~~~~~~~~~~~~~~~~~~~~~~~v~k~~g~~wk~ls~~ek~~~~~~~~~~~ 90 (297)
+|||+||||+|+++.|+.++++||+ .++.+|+|.+|+.|+.||++||++|.+.|++..
T Consensus 2 iKrP~naf~~F~~~~r~~~~~~~p~-~~~~eisk~l~~~Wk~ls~~eK~~y~~~a~~~k 59 (72)
T cd01388 2 IKRPMNAFMLFSKRHRRKVLQEYPL-KENRAISKILGDRWKALSNEEKQPYYEEAKKLK 59 (72)
T ss_pred CCCCCcHHHHHHHHHHHHHHHHCCC-CCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHH
Confidence 6999999999999999999999995 699999999999999999999999999998744
No 6
>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=99.40 E-value=2.7e-13 Score=99.44 Aligned_cols=58 Identities=26% Similarity=0.386 Sum_probs=52.5
Q ss_pred CCCCCcchhhhHHHHHHHHHHhCCCCcchhHHHHHHHhhhcCCChHhhhhhhhhhhcCC
Q 039418 32 DRENNHGFISFFAESVRQLKAKDGRACITNEVRKEIRNAFKNLPVEEKCQYKFQSRRGG 90 (297)
Q Consensus 32 ~~r~~~~f~~~~~~~~~~~~~~~~~~~~~~~v~k~~g~~wk~ls~~ek~~~~~~~~~~~ 90 (297)
||||+|||++|+++++.++++.||+. ...+|++.+|..|++||++||++|.+.|.+..
T Consensus 1 PkrP~~af~lf~~~~~~~~k~~~p~~-~~~~i~~~~~~~W~~l~~~eK~~y~~~a~~~~ 58 (69)
T PF00505_consen 1 PKRPPNAFMLFCKEKRAKLKEENPDL-SNKEISKILAQMWKNLSEEEKAPYKEEAEEEK 58 (69)
T ss_dssp SSSS--HHHHHHHHHHHHHHHHSTTS-THHHHHHHHHHHHHCSHHHHHHHHHHHHHHHH
T ss_pred CcCCCCHHHHHHHHHHHHHHHHhccc-ccccchhhHHHHHhcCCHHHHHHHHHHHHHHH
Confidence 89999999999999999999999955 59999999999999999999999999998744
No 7
>smart00398 HMG high mobility group.
Probab=99.37 E-value=9e-13 Score=96.36 Aligned_cols=59 Identities=24% Similarity=0.377 Sum_probs=55.0
Q ss_pred CCCCCCcchhhhHHHHHHHHHHhCCCCcchhHHHHHHHhhhcCCChHhhhhhhhhhhcCC
Q 039418 31 KDRENNHGFISFFAESVRQLKAKDGRACITNEVRKEIRNAFKNLPVEEKCQYKFQSRRGG 90 (297)
Q Consensus 31 ~~~r~~~~f~~~~~~~~~~~~~~~~~~~~~~~v~k~~g~~wk~ls~~ek~~~~~~~~~~~ 90 (297)
+||||+|||++|++++|+.++++||+ ....++++.+|..|+.||++||++|.++|++..
T Consensus 1 ~pkrp~~~y~~f~~~~r~~~~~~~~~-~~~~~i~~~~~~~W~~l~~~ek~~y~~~a~~~~ 59 (70)
T smart00398 1 KPKRPMSAFMLFSQENRAKIKAENPD-LSNAEISKKLGERWKLLSEEEKAPYEEKAKKDK 59 (70)
T ss_pred CcCCCCcHHHHHHHHHHHHHHHHCcC-CCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHH
Confidence 58999999999999999999999995 578999999999999999999999999988743
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=99.37 E-value=6.3e-13 Score=99.32 Aligned_cols=59 Identities=25% Similarity=0.343 Sum_probs=51.0
Q ss_pred CCCCCCCcchhhhHHHHHHHHHHh-CCCCcchhHHHHHHHhhhcCCChHhhhhhhhhhhcC
Q 039418 30 SKDRENNHGFISFFAESVRQLKAK-DGRACITNEVRKEIRNAFKNLPVEEKCQYKFQSRRG 89 (297)
Q Consensus 30 ~~~~r~~~~f~~~~~~~~~~~~~~-~~~~~~~~~v~k~~g~~wk~ls~~ek~~~~~~~~~~ 89 (297)
+|||||+|||++|+.|++..+++. .+ .....+|.+.+|..|++||++||++|.++|++.
T Consensus 2 ~kpK~~~say~lF~~~~~~~~k~~G~~-~~~~~e~~k~~~~~Wk~Ls~~EK~~Y~~~A~~~ 61 (73)
T PF09011_consen 2 KKPKRPPSAYNLFMKEMRKEVKEEGGQ-KQSFREVMKEISERWKSLSEEEKEPYEERAKED 61 (73)
T ss_dssp SS--SSSSHHHHHHHHHHHHHHHHT-T--SSHHHHHHHHHHHHHHS-HHHHHHHHHHHHHH
T ss_pred cCCCCCCCHHHHHHHHHHHHHHHhccc-CCCHHHHHHHHHHHHHhcCHHHHHHHHHHHHHH
Confidence 689999999999999999999999 55 778899999999999999999999999999874
No 9
>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=99.35 E-value=1.2e-12 Score=94.54 Aligned_cols=59 Identities=20% Similarity=0.306 Sum_probs=55.1
Q ss_pred CCCCCcchhhhHHHHHHHHHHhCCCCcchhHHHHHHHhhhcCCChHhhhhhhhhhhcCCC
Q 039418 32 DRENNHGFISFFAESVRQLKAKDGRACITNEVRKEIRNAFKNLPVEEKCQYKFQSRRGGK 91 (297)
Q Consensus 32 ~~r~~~~f~~~~~~~~~~~~~~~~~~~~~~~v~k~~g~~wk~ls~~ek~~~~~~~~~~~k 91 (297)
||||+|||++|+.|+++.+++.+|+ ....+|.+.+|..|+.||++||++|.++|++...
T Consensus 1 pkrp~~af~~f~~~~~~~~~~~~~~-~~~~~i~~~~~~~W~~l~~~~k~~y~~~a~~~~~ 59 (66)
T cd00084 1 PKRPLSAYFLFSQEHRAEVKAENPG-LSVGEISKILGEMWKSLSEEEKKKYEEKAEKDKE 59 (66)
T ss_pred CCCCCcHHHHHHHHHHHHHHHHCcC-CCHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHH
Confidence 7999999999999999999999995 6799999999999999999999999999987543
No 10
>KOG0381 consensus HMG box-containing protein [General function prediction only]
Probab=99.20 E-value=2.4e-11 Score=95.03 Aligned_cols=60 Identities=25% Similarity=0.314 Sum_probs=55.9
Q ss_pred CCCCCCCcchhhhHHHHHHHHHHhCCCCcchhHHHHHHHhhhcCCChHhhhhhhhhhhcCC
Q 039418 30 SKDRENNHGFISFFAESVRQLKAKDGRACITNEVRKEIRNAFKNLPVEEKCQYKFQSRRGG 90 (297)
Q Consensus 30 ~~~~r~~~~f~~~~~~~~~~~~~~~~~~~~~~~v~k~~g~~wk~ls~~ek~~~~~~~~~~~ 90 (297)
+.||||++|||+|+.+++..++..||+ ..+.+|+|++|..|++|+++||.+|..++.+-.
T Consensus 21 ~~pkrp~sa~~~f~~~~~~~~k~~~p~-~~~~~v~k~~g~~W~~l~~~~k~~y~~ka~~~k 80 (96)
T KOG0381|consen 21 QAPKRPLSAFFLFSSEQRSKIKAENPG-LSVGEVAKALGEMWKNLAEEEKQPYEEKASKLK 80 (96)
T ss_pred CCCCCCCcHHHHHHHHHHHHHHHhCCC-CCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHH
Confidence 479999999999999999999999996 899999999999999999999999988887643
No 11
>PF09331 DUF1985: Domain of unknown function (DUF1985); InterPro: IPR015410 This domain is functionally uncharacterised; it is found in a set of Arabidopsis thaliana (Mouse-ear cress) hypothetical proteins.
Probab=99.03 E-value=4.7e-10 Score=94.48 Aligned_cols=123 Identities=20% Similarity=0.390 Sum_probs=91.2
Q ss_pred ceEEECCeEeecCccchhheeccccCCccccccCChhHHH---HHH-hhhccCCCccchHHHHHHHhcC--CCCCchhhh
Q 039418 156 CVLQLNGHELELSPNSFGYIMGVTDGGMPMELQGDSAEVA---AYL-DKFNATSRGINIKTMEDILLTS--KDADNDFKV 229 (297)
Q Consensus 156 ~~~~i~g~~i~iT~~dV~~VLGLP~gG~~v~~~~~~~~~~---~l~-~~~~~~~~~isl~~L~~~ll~~--~~~~d~f~r 229 (297)
..+.++|..|.++..+.+.|+|||++..|-.......... .+- ..++ .+..+++..+.++|... .+.++.+.-
T Consensus 14 ~W~~~~g~piRfsl~Ef~lvTGL~C~~~p~~~~~~~~~~~~~~~fw~~Lf~-~~~~vtv~dv~~~L~~~~~~~~~~Rlrl 92 (142)
T PF09331_consen 14 IWFVFNGVPIRFSLREFALVTGLNCGPYPKEKKVDKKGKKEKGSFWNKLFG-REEDVTVEDVIAKLKKMKKWDSEDRLRL 92 (142)
T ss_pred EEEEECCEeeEecHHHHHhhcCCcCCCCCcccchhhccccchhhhhhhhcc-ccccCcHHHHHHHHhhcccCChhhHHHH
Confidence 7889999999999999999999999887766543221111 232 2333 34569999999998654 234444555
Q ss_pred HHHhhhhcceeCCCCCCccCcchhhhhhccccCcccchhHHHHHHHHHHH
Q 039418 230 AFMLFTLCTLLCPPGGVHISYSFLFTLKDVHSIRNRNWATFCFERLMRGI 279 (297)
Q Consensus 230 ~Fll~~i~~~L~Ptt~~~vs~~yl~~l~D~~~I~~ynW~~~Vld~L~~~l 279 (297)
++++++.|.+++++....|+..++..++|++.+.+|-||.+.++.++++|
T Consensus 93 a~L~~v~gvl~~~~~~~~i~~~~~~~v~Dl~~f~~yPWGr~sF~~~~~sI 142 (142)
T PF09331_consen 93 ALLLFVDGVLIATSKTTKIPKEHLKMVDDLEKFLNYPWGRYSFDMLMKSI 142 (142)
T ss_pred HHHHhhheeeeccCCCCCCCHHHHHHHhhHHHHhcCCcHHHHHHHHHhcC
Confidence 55555555555555556899999999999999999999999999999874
No 12
>KOG0527 consensus HMG-box transcription factor [Transcription]
Probab=98.98 E-value=3.4e-10 Score=107.09 Aligned_cols=60 Identities=18% Similarity=0.248 Sum_probs=56.2
Q ss_pred CCCCCCCcchhhhHHHHHHHHHHhCCCCcchhHHHHHHHhhhcCCChHhhhhhhhhhhcCC
Q 039418 30 SKDRENNHGFISFFAESVRQLKAKDGRACITNEVRKEIRNAFKNLPVEEKCQYKFQSRRGG 90 (297)
Q Consensus 30 ~~~~r~~~~f~~~~~~~~~~~~~~~~~~~~~~~v~k~~g~~wk~ls~~ek~~~~~~~~~~~ 90 (297)
.++|||-|||||+.++.||.+.+.|| .-.+++|+|.+|..||.|+|+||.||++-|++-.
T Consensus 61 ~hIKRPMNAFMVWSq~~RRkma~qnP-~mHNSEISK~LG~~WK~Lse~EKrPFi~EAeRLR 120 (331)
T KOG0527|consen 61 DRIKRPMNAFMVWSQGQRRKLAKQNP-KMHNSEISKRLGAEWKLLSEEEKRPFVDEAERLR 120 (331)
T ss_pred cccCCCcchhhhhhHHHHHHHHHhCc-chhhHHHHHHHHHHHhhcCHhhhccHHHHHHHHH
Confidence 45799999999999999999999999 5599999999999999999999999999998755
No 13
>COG5648 NHP6B Chromatin-associated proteins containing the HMG domain [Chromatin structure and dynamics]
Probab=98.97 E-value=6.6e-10 Score=97.67 Aligned_cols=61 Identities=18% Similarity=0.251 Sum_probs=57.4
Q ss_pred CCCCCCCCcchhhhHHHHHHHHHHhCCCCcchhHHHHHHHhhhcCCChHhhhhhhhhhhcCC
Q 039418 29 GSKDRENNHGFISFFAESVRQLKAKDGRACITNEVRKEIRNAFKNLPVEEKCQYKFQSRRGG 90 (297)
Q Consensus 29 ~~~~~r~~~~f~~~~~~~~~~~~~~~~~~~~~~~v~k~~g~~wk~ls~~ek~~~~~~~~~~~ 90 (297)
+|.||||-||||.|.++-|.++.+.+|.. .+++|+|.+|++||+|++.||+||...+..-+
T Consensus 68 pN~PKRp~sayf~y~~~~R~ei~~~~p~l-~~~e~~k~~~e~WK~Ltd~eke~y~k~~~~~~ 128 (211)
T COG5648 68 PNGPKRPLSAYFLYSAENRDEIRKENPKL-TFGEVGKLLSEKWKELTDEEKEPYYKEANSDR 128 (211)
T ss_pred CCCCCCchhHHHHHHHHHHHHHHHhCCCC-ChHHHHHHHHHHHHhccHhhhhhHHHHHhhHH
Confidence 48899999999999999999999999965 99999999999999999999999999988744
No 14
>KOG0526 consensus Nucleosome-binding factor SPN, POB3 subunit [Transcription; Replication, recombination and repair; Chromatin structure and dynamics]
Probab=98.21 E-value=8e-07 Score=87.50 Aligned_cols=56 Identities=11% Similarity=0.243 Sum_probs=51.1
Q ss_pred CCCCCCCcchhhhHHHHHHHHHHhCCCCcchhHHHHHHHhhhcCCChHhhhhhhhhhhcCC
Q 039418 30 SKDRENNHGFISFFAESVRQLKAKDGRACITNEVRKEIRNAFKNLPVEEKCQYKFQSRRGG 90 (297)
Q Consensus 30 ~~~~r~~~~f~~~~~~~~~~~~~~~~~~~~~~~v~k~~g~~wk~ls~~ek~~~~~~~~~~~ 90 (297)
|.||||-||||+|++.-|..+|++ .-.+.+|+|.+|++||.||. |++|.++|.+-+
T Consensus 534 napkra~sa~m~w~~~~r~~ik~d---gi~~~dv~kk~g~~wk~ms~--k~~we~ka~~dk 589 (615)
T KOG0526|consen 534 NAPKRATSAYMLWLNASRESIKED---GISVGDVAKKAGEKWKQMSA--KEEWEDKAAVDK 589 (615)
T ss_pred CCCccchhHHHHHHHhhhhhHhhc---CchHHHHHHHHhHHHhhhcc--cchhhHHHHHHH
Confidence 788999999999999999999998 45899999999999999999 788988887643
No 15
>KOG3248 consensus Transcription factor TCF-4 [Transcription]
Probab=97.49 E-value=7.5e-05 Score=70.13 Aligned_cols=57 Identities=14% Similarity=0.224 Sum_probs=53.1
Q ss_pred CCCCcchhhhHHHHHHHHHHhCCCCcchhHHHHHHHhhhcCCChHhhhhhhhhhhcCC
Q 039418 33 RENNHGFISFFAESVRQLKAKDGRACITNEVRKEIRNAFKNLPVEEKCQYKFQSRRGG 90 (297)
Q Consensus 33 ~r~~~~f~~~~~~~~~~~~~~~~~~~~~~~v~k~~g~~wk~ls~~ek~~~~~~~~~~~ 90 (297)
|.|.+||++||.|.|+-+-++-- .|..+++-+++|.+|-.||-+|.|.|..-|++..
T Consensus 193 KKPLNAFmlyMKEmRa~vvaEct-lKeSAaiNqiLGrRWH~LSrEEQAKYyElArKer 249 (421)
T KOG3248|consen 193 KKPLNAFMLYMKEMRAKVVAECT-LKESAAINQILGRRWHALSREEQAKYYELARKER 249 (421)
T ss_pred cccHHHHHHHHHHHHHHHHHHhh-hhhHHHHHHHHhHHHhhhhHHHHHHHHHHHHHHH
Confidence 89999999999999999999988 8999999999999999999999998888887643
No 16
>KOG0528 consensus HMG-box transcription factor SOX5 [Transcription]
Probab=97.44 E-value=4.6e-05 Score=74.59 Aligned_cols=63 Identities=14% Similarity=0.181 Sum_probs=53.9
Q ss_pred CCCCCCcchhhhHHHHHHHHHHhCCCCcchhHHHHHHHhhhcCCChHhhhhhhhhhhcCCCccc
Q 039418 31 KDRENNHGFISFFAESVRQLKAKDGRACITNEVRKEIRNAFKNLPVEEKCQYKFQSRRGGKANV 94 (297)
Q Consensus 31 ~~~r~~~~f~~~~~~~~~~~~~~~~~~~~~~~v~k~~g~~wk~ls~~ek~~~~~~~~~~~k~~v 94 (297)
-+|||-+||||+-.|=|+-.-...| .=.+..++|.+|..||.||..||.||..--.+-+|.+.
T Consensus 325 HIKRPMNAFMVWAkDERRKILqA~P-DMHNSnISKILGSRWKaMSN~eKQPYYEEQaRLSk~Hl 387 (511)
T KOG0528|consen 325 HIKRPMNAFMVWAKDERRKILQAFP-DMHNSNISKILGSRWKAMSNTEKQPYYEEQARLSKLHL 387 (511)
T ss_pred cccCCcchhhcccchhhhhhhhcCc-cccccchhHHhcccccccccccccchHHHHHHHHHhhh
Confidence 3599999999999999999999999 45889999999999999999999977665555455554
No 17
>KOG2746 consensus HMG-box transcription factor Capicua and related proteins [Transcription]
Probab=95.48 E-value=0.0041 Score=63.40 Aligned_cols=62 Identities=15% Similarity=0.096 Sum_probs=56.8
Q ss_pred CCCCCcchhhhHHHHH--HHHHHhCCCCcchhHHHHHHHhhhcCCChHhhhhhhhhhhcCCCccc
Q 039418 32 DRENNHGFISFFAESV--RQLKAKDGRACITNEVRKEIRNAFKNLPVEEKCQYKFQSRRGGKANV 94 (297)
Q Consensus 32 ~~r~~~~f~~~~~~~~--~~~~~~~~~~~~~~~v~k~~g~~wk~ls~~ek~~~~~~~~~~~k~~v 94 (297)
+.||-+||+.|.+-+| ...++.|| |..+..|+|.+|+.|=+|.+.||.-|++-|.+++-++-
T Consensus 182 irrPMnaf~ifskrhr~~g~vhq~~p-n~DNrtIskiLgewWytL~~~Ekq~yhdLa~Qvk~Ahf 245 (683)
T KOG2746|consen 182 IRRPMNAFHIFSKRHRGEGRVHQRHP-NQDNRTISKILGEWWYTLGPNEKQKYHDLAFQVKEAHF 245 (683)
T ss_pred hhhhhHHHHHHHhhcCCccchhccCc-cccchhHHHHHhhhHhhhCchhhhhHHHHHHHHHHHHh
Confidence 3899999999999999 99999999 88999999999999999999999999988888774443
No 18
>KOG4715 consensus SWI/SNF-related matrix-associated actin-dependent regulator of chromatin [Chromatin structure and dynamics]
Probab=95.38 E-value=0.017 Score=54.26 Aligned_cols=61 Identities=21% Similarity=0.230 Sum_probs=49.5
Q ss_pred hcCCCC-CCCCcchhhhHHHHHHHHHHhCCCCcchhHHHHHHHhhhcCCChHhhhhhhhhhhc
Q 039418 27 SRGSKD-RENNHGFISFFAESVRQLKAKDGRACITNEVRKEIRNAFKNLPVEEKCQYKFQSRR 88 (297)
Q Consensus 27 ~~~~~~-~r~~~~f~~~~~~~~~~~~~~~~~~~~~~~v~k~~g~~wk~ls~~ek~~~~~~~~~ 88 (297)
-+|-|| -||.-.||-|+.-.-.+.|++||+. -.=++||.||..|+-|+++||.-|..-=+.
T Consensus 59 pkpPkppekpl~pymrySrkvWd~VkA~nPe~-kLWeiGK~Ig~mW~dLpd~EK~ey~~EYea 120 (410)
T KOG4715|consen 59 PKPPKPPEKPLMPYMRYSRKVWDQVKASNPEL-KLWEIGKIIGGMWLDLPDEEKQEYLNEYEA 120 (410)
T ss_pred CCCCCCCCcccchhhHHhhhhhhhhhccCcch-HHHHHHHHHHHHHhhCcchHHHHHHHHHHH
Confidence 335444 5778889999999999999999955 678999999999999999999977654433
No 19
>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=94.97 E-value=0.026 Score=48.92 Aligned_cols=48 Identities=19% Similarity=0.324 Sum_probs=38.2
Q ss_pred CCcchhhhHHHHHHHHHHhCCCCcchhHHHHHHHhhhcCCChHhhhhhhhhhh
Q 039418 35 NNHGFISFFAESVRQLKAKDGRACITNEVRKEIRNAFKNLPVEEKCQYKFQSR 87 (297)
Q Consensus 35 ~~~~f~~~~~~~~~~~~~~~~~~~~~~~v~k~~g~~wk~ls~~ek~~~~~~~~ 87 (297)
-.+||+-|+.||++. |. .-+..++-..+...|..||++||.+|...+.
T Consensus 82 TnnaYLNFLReFRrk----h~-~L~p~dlI~~AAraW~rLSe~eK~rYrr~~~ 129 (183)
T PF06382_consen 82 TNNAYLNFLREFRRK----HC-GLSPQDLIQRAARAWCRLSEAEKNRYRRMAP 129 (183)
T ss_pred cchHHHHHHHHHHHH----cc-CCCHHHHHHHHHHHHHhCCHHHHHHHHhhcc
Confidence 357999999888874 44 3455677777889999999999999998654
No 20
>PF14887 HMG_box_5: HMG (high mobility group) box 5; PDB: 1L8Y_A 1L8Z_A 2HDZ_A.
Probab=93.06 E-value=0.15 Score=38.43 Aligned_cols=55 Identities=9% Similarity=0.048 Sum_probs=43.0
Q ss_pred CCCCCcchhhhHHHHHHHHHHhCCCCcchhHHHHHHHhhhcCCChHhhhhhhhhhhc
Q 039418 32 DRENNHGFISFFAESVRQLKAKDGRACITNEVRKEIRNAFKNLPVEEKCQYKFQSRR 88 (297)
Q Consensus 32 ~~r~~~~f~~~~~~~~~~~~~~~~~~~~~~~v~k~~g~~wk~ls~~ek~~~~~~~~~ 88 (297)
|--|-+|==.+.+.-+..|-+.+++... ++ .|+....|++|++.||=+|..+|.+
T Consensus 4 PE~PKt~qe~Wqq~vi~dYla~~~~dr~-K~-~kam~~~W~~me~Kekl~WIkKA~E 58 (85)
T PF14887_consen 4 PETPKTAQEIWQQSVIGDYLAKFRNDRK-KA-LKAMEAQWSQMEKKEKLKWIKKAAE 58 (85)
T ss_dssp S----THHHHHHHHHHHHHHHHTTSTHH-HH-HHHHHHHHHTTGGGHHHHHHHHHHH
T ss_pred CCCCCCHHHHHHHHHHHHHHHHhhHhHH-HH-HHHHHHHHHHhhhhhhhHHHHHHHH
Confidence 3445566667888899999999996643 33 6699999999999999999999987
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=91.71 E-value=0.26 Score=42.76 Aligned_cols=44 Identities=14% Similarity=0.291 Sum_probs=38.4
Q ss_pred CCCCCcchhhhHHHHHHHHHHhCCCCcchhHHHHHHHhhhcCCCh
Q 039418 32 DRENNHGFISFFAESVRQLKAKDGRACITNEVRKEIRNAFKNLPV 76 (297)
Q Consensus 32 ~~r~~~~f~~~~~~~~~~~~~~~~~~~~~~~v~k~~g~~wk~ls~ 76 (297)
..|-||||-.|+.|=++.+|++|| .-.++++=+++.+-|+..+.
T Consensus 122 RqR~psaYn~f~k~ei~rik~~~p-~ishkeaFs~aAknW~h~ph 165 (170)
T PF04690_consen 122 RQRVPSAYNRFMKEEIQRIKAENP-DISHKEAFSAAAKNWAHFPH 165 (170)
T ss_pred cCCCchhHHHHHHHHHHHHHhcCC-CCCHHHHHHHHHHhhhhCcc
Confidence 368999999999999999999999 55788888888899987653
No 22
>COG5648 NHP6B Chromatin-associated proteins containing the HMG domain [Chromatin structure and dynamics]
Probab=90.09 E-value=0.16 Score=45.27 Aligned_cols=56 Identities=16% Similarity=0.119 Sum_probs=47.8
Q ss_pred CCCCCcchhhhHHHHHHHHHHhCCCCcchhHHHHHHHhhhcCCChHhhhhhhhhhhc
Q 039418 32 DRENNHGFISFFAESVRQLKAKDGRACITNEVRKEIRNAFKNLPVEEKCQYKFQSRR 88 (297)
Q Consensus 32 ~~r~~~~f~~~~~~~~~~~~~~~~~~~~~~~v~k~~g~~wk~ls~~ek~~~~~~~~~ 88 (297)
+++|+..|+-+-++-|......+| .++....+|++|+.|++|++.-|++|.+.++.
T Consensus 144 ~~~~~~~~~e~~~~~r~~~~~~~~-~~~~~e~~k~~~~~w~el~~skK~~~~~~~Kk 199 (211)
T COG5648 144 NKAPIGPFIENEPKIRPKVEGPSP-DKALVEETKIISKAWSELDESKKKKYIDKYKK 199 (211)
T ss_pred CCCCCchhhhccHHhccccCCCCc-chhhhHHhhhhhhhhhhhChhhhhHHHHHHHH
Confidence 467777777777778888888888 66888899999999999999999999998875
No 23
>PF03078 ATHILA: ATHILA ORF-1 family; InterPro: IPR004312 ATHILA is a group of Arabidopsis thaliana retrotransposons [] belonging to the Ty3/gypsy family of the long terminal repeat (LTR) class of eukaryotic retrotransposons[, ]. The central region of ATHILA retrotransposons contains two or three open reading frames (ORFs). This family represents the ORF1 product. The function of ORF1 is unknown.
Probab=76.17 E-value=51 Score=33.12 Aligned_cols=168 Identities=17% Similarity=0.185 Sum_probs=94.5
Q ss_pred eec-CHHHHHHHHhhcCHHHHHHHHhcCcccccccccccccHHHHHHHHhccc-------c--------CcceEEECCeE
Q 039418 101 TRC-APDRLAALVSHLIEKQRKAVCDIGLGSIIDLKCGRLKRKLCAWLVERID-------T--------ARCVLQLNGHE 164 (297)
Q Consensus 101 trc-S~~~~~~~i~~Ls~~qk~~I~~~GFg~LL~i~~~~l~~~L~~wL~~~~d-------~--------~t~~~~i~g~~ 164 (297)
||. ++.-+..+ .|.++-..+++.+|.+.|..++...-+...+..|+..-= + ..-+|.|.|..
T Consensus 63 TRyp~~etl~~L--Gl~~dV~~lf~~~gL~~f~~~~~~~Y~eet~qFLaTl~v~~~~~~~~~~~e~~glG~l~F~V~~~~ 140 (458)
T PF03078_consen 63 TRYPDPETLQKL--GLLEDVEYLFKKCGLGTFMSYPYPTYPEETRQFLATLKVTFYNPSEPRAKELDGLGYLTFFVYGVE 140 (458)
T ss_pred cccCCHHHHHHh--ccHHHHHHHHHhcCchhhccCCCCCcHHHHHHhhheeeeeecccccchhhcccCcceEEEEEccee
Confidence 443 33444444 667888889999999999988886655544444443211 1 23567778999
Q ss_pred eecCccchhheeccccCCccccccCChhHHHHHHhhhccCCCccchHHHHHHHhcCCCCCchhhhHHHhhhhcceeCCCC
Q 039418 165 LELSPNSFGYIMGVTDGGMPMELQGDSAEVAAYLDKFNATSRGINIKTMEDILLTSKDADNDFKVAFMLFTLCTLLCPPG 244 (297)
Q Consensus 165 i~iT~~dV~~VLGLP~gG~~v~~~~~~~~~~~l~~~~~~~~~~isl~~L~~~ll~~~~~~d~f~r~Fll~~i~~~L~Ptt 244 (297)
..+|-.+...++|+|.|+. +...-..++...|-...|... .++...-... ..-.=+.+|+--+++..|+|..
T Consensus 141 y~lsi~~L~~i~GF~~~~~-i~~~~~~~el~~~W~~ig~~~-p~~~~~~ks~------~Ir~PviRy~hr~iA~tlf~R~ 212 (458)
T PF03078_consen 141 YSLSIKHLERIFGFPSGDE-IKPDFDPEELNDFWATIGGGK-PFNSARSKSN------QIRSPVIRYFHRLIANTLFARE 212 (458)
T ss_pred eeeeHHHHHHHhCCCCccc-cCCCCCchHHHHHHHHhcCCC-cccccccccc------cccChHHHHHHHHHHhhhcccc
Confidence 9999999999999999854 332223344444444444220 0111000010 1112234445555666666665
Q ss_pred CC-ccCcchhhhh-----------hcc----ccCcccchhHHHHHHHHHH
Q 039418 245 GV-HISYSFLFTL-----------KDV----HSIRNRNWATFCFERLMRG 278 (297)
Q Consensus 245 ~~-~vs~~yl~~l-----------~D~----~~I~~ynW~~~Vld~L~~~ 278 (297)
.. .|..+-|.++ .|. .+..+.+-+-..++||...
T Consensus 213 ~~~~v~~~El~~l~~~L~~~Lr~~~~g~~l~~d~~dt~~~~vl~~hL~~y 262 (458)
T PF03078_consen 213 ETGTVRNDELEMLDQALKHLLRRTKDGKLLRGDLNDTNVSMVLLDHLCSY 262 (458)
T ss_pred ccCceechhHHHHHHHHHHHHHhcCCCccccCcccccchhHHHHHHHHhh
Confidence 44 6776665542 111 1135556666666666654
No 24
>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=65.07 E-value=8 Score=30.91 Aligned_cols=21 Identities=14% Similarity=0.295 Sum_probs=11.1
Q ss_pred HHhhhcCCChHhhhhhhhhhh
Q 039418 67 IRNAFKNLPVEEKCQYKFQSR 87 (297)
Q Consensus 67 ~g~~wk~ls~~ek~~~~~~~~ 87 (297)
+.+.|.+||++|++.+..+..
T Consensus 34 ~a~r~~~mspeqq~r~~~rm~ 54 (107)
T PF11304_consen 34 IAERWPSMSPEQQQRLRERMR 54 (107)
T ss_pred HHHHHhcCCHHHHHHHHHHHH
Confidence 555556666665554444433
No 25
>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=61.82 E-value=17 Score=32.38 Aligned_cols=44 Identities=14% Similarity=0.187 Sum_probs=33.6
Q ss_pred CCCCCCCCcchhhhHHHHHHHHHHhCCCCcchhHHHHHHHhhhcCCChH
Q 039418 29 GSKDRENNHGFISFFAESVRQLKAKDGRACITNEVRKEIRNAFKNLPVE 77 (297)
Q Consensus 29 ~~~~~r~~~~f~~~~~~~~~~~~~~~~~~~~~~~v~k~~g~~wk~ls~~ 77 (297)
..+++||.++||.|+. -|+...|. --.+.++..++..|..=+..
T Consensus 41 ~~~~kr~lN~Fm~FRs----yy~~~~~~-~~Qk~~S~~l~~lW~~dp~k 84 (201)
T PF04769_consen 41 PEKAKRPLNGFMAFRS----YYSPIFPP-LPQKELSGILTKLWEKDPFK 84 (201)
T ss_pred ccccccchhHHHHHHH----HHHhhcCC-cCHHHHHHHHHHHHhCCccH
Confidence 3567999999998765 45556663 45899999999999984443
No 26
>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=44.48 E-value=25 Score=24.87 Aligned_cols=39 Identities=8% Similarity=0.148 Sum_probs=32.0
Q ss_pred cchhhhHHHHHHHHHHhCCCCcchhHHHHHHHhhhcCCCh
Q 039418 37 HGFISFFAESVRQLKAKDGRACITNEVRKEIRNAFKNLPV 76 (297)
Q Consensus 37 ~~f~~~~~~~~~~~~~~~~~~~~~~~v~k~~g~~wk~ls~ 76 (297)
+.+=.|.+--|++..++||.. .+..+-.-++.|||.-++
T Consensus 14 t~yK~Fsq~vRP~l~~~NPk~-~~sKl~~l~~AKwrEF~~ 52 (55)
T PF08073_consen 14 TNYKAFSQHVRPLLAKANPKA-PMSKLMMLLQAKWREFQE 52 (55)
T ss_pred HHHHHHHHHHHHHHHHHCCCC-cHHHHHHHHHHHHHHHHh
Confidence 446679999999999999954 677778889999997654
No 27
>PF11943 DUF3460: Protein of unknown function (DUF3460); InterPro: IPR021853 This family of proteins are functionally uncharacterised. This protein is found in bacteria. Proteins in this family are about 70 amino acids in length. This protein has a conserved WDK sequence motif.
Probab=41.25 E-value=57 Score=23.51 Aligned_cols=38 Identities=26% Similarity=0.357 Sum_probs=26.4
Q ss_pred HHHHHHHHHhCCCCcchhHHHHHHHhhh--cCCChHhhhhhhh
Q 039418 44 AESVRQLKAKDGRACITNEVRKEIRNAF--KNLPVEEKCQYKF 84 (297)
Q Consensus 44 ~~~~~~~~~~~~~~~~~~~v~k~~g~~w--k~ls~~ek~~~~~ 84 (297)
..|..+||++||+. .+=.+++...| |-++.+|.+.|.+
T Consensus 8 TqFl~~lk~~~Pel---e~~Q~~GRallWDk~~d~e~~~~~~~ 47 (60)
T PF11943_consen 8 TQFLNQLKAKHPEL---EEEQRAGRALLWDKPQDLEEQARFRA 47 (60)
T ss_pred HHHHHHHHHhCCch---HHHHHHhhHHhcCCCCCHHHHHHHHh
Confidence 46899999999954 44455555444 5788888776543
No 28
>PF10234 Cluap1: Clusterin-associated protein-1; InterPro: IPR019366 This protein of 413 amino acids contains a central coiled-coil domain, possibly the region that binds to clusterin. Cluap1 expression is highest in the nucleus and gradually increases during late S to G2/M phases of the cell cycle and returns to the basal level in the G0/G1 phases. In addition, it is upregulated in colon cancer tissues compared to corresponding non-cancerous mucosa. It thus plays a crucial role in the life of the cell [].
Probab=39.29 E-value=15 Score=34.22 Aligned_cols=32 Identities=25% Similarity=0.461 Sum_probs=25.4
Q ss_pred HhcCccccccccccccc-----HHHHHHHHhccccCc
Q 039418 124 CDIGLGSIIDLKCGRLK-----RKLCAWLVERIDTAR 155 (297)
Q Consensus 124 ~~~GFg~LL~i~~~~l~-----~~L~~wL~~~~d~~t 155 (297)
+.+||--++.|.+..-| -+++.||+.+|||+.
T Consensus 1 R~LGypr~iSmenFrtPNF~LVAeiL~WLv~rydP~~ 37 (267)
T PF10234_consen 1 RALGYPRLISMENFRTPNFELVAEILRWLVKRYDPDA 37 (267)
T ss_pred CCCCCCCCCcHHHcCCCChHHHHHHHHHHHHHcCCCC
Confidence 35799999999775444 478889999999985
No 29
>COG5202 Predicted membrane protein [Function unknown]
Probab=39.23 E-value=19 Score=35.15 Aligned_cols=27 Identities=26% Similarity=0.540 Sum_probs=23.8
Q ss_pred CCchh--hhHHHHHhHhhcCCCCCCCCcc
Q 039418 12 GDFES--SCEMLVDAHRSRGSKDRENNHG 38 (297)
Q Consensus 12 ~~~~~--~~~~~~~~~~~~~~~~~r~~~~ 38 (297)
.|||| .|||.-+--.+.+-+|+|||++
T Consensus 189 ~dfd~~lt~~mFr~l~e~pyEr~~~P~n~ 217 (512)
T COG5202 189 ADFDSWLTCEMFRSLMENPYERPKRPPNG 217 (512)
T ss_pred chhhhhhhHHHHhhhhcCcccccCCCCCc
Confidence 47787 7999999999999999999975
No 30
>PF06945 DUF1289: Protein of unknown function (DUF1289); InterPro: IPR010710 This family consists of a number of hypothetical bacterial proteins. The aligned region spans around 56 residues and contains 4 highly conserved cysteine residues towards the N terminus. The function of this family is unknown.
Probab=33.56 E-value=21 Score=24.53 Aligned_cols=20 Identities=15% Similarity=0.218 Sum_probs=15.0
Q ss_pred hhhcCCChHhhhhhhhhhhc
Q 039418 69 NAFKNLPVEEKCQYKFQSRR 88 (297)
Q Consensus 69 ~~wk~ls~~ek~~~~~~~~~ 88 (297)
..|+.||++||..-.++..+
T Consensus 28 ~~W~~~s~~er~~i~~~l~~ 47 (51)
T PF06945_consen 28 RDWKSMSDDERRAILARLRA 47 (51)
T ss_pred HHHhhCCHHHHHHHHHHHHH
Confidence 35999999998866655543
No 31
>PF01418 HTH_6: Helix-turn-helix domain, rpiR family; InterPro: IPR000281 This domain contains a helix-turn-helix motif []. Every member of this family is N-terminal to a SIS domain IPR001347 from INTERPRO. Members of this family are probably regulators of genes involved in phosphosugar metobolism.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent; PDB: 2O3F_B 3IWF_B.
Probab=31.20 E-value=33 Score=25.32 Aligned_cols=60 Identities=15% Similarity=0.325 Sum_probs=34.1
Q ss_pred HHHHhhhcCCChHhhh--hhhhh-hhcCCCccccccceeeecCHHHHHHHHhhcCHHHHHHHHhcCcccccccc
Q 039418 65 KEIRNAFKNLPVEEKC--QYKFQ-SRRGGKANVEKVKFLTRCAPDRLAALVSHLIEKQRKAVCDIGLGSIIDLK 135 (297)
Q Consensus 65 k~~g~~wk~ls~~ek~--~~~~~-~~~~~k~~v~k~~~~trcS~~~~~~~i~~Ls~~qk~~I~~~GFg~LL~i~ 135 (297)
..+...+.+||+.|+. .|.-+ -.+.....+....-.+-.|+..+..+ ++++||.|+-++.
T Consensus 5 ~~i~~~~~~ls~~e~~Ia~yil~~~~~~~~~si~elA~~~~vS~sti~Rf-----------~kkLG~~gf~efk 67 (77)
T PF01418_consen 5 EKIRSQYNSLSPTEKKIADYILENPDEIAFMSISELAEKAGVSPSTIVRF-----------CKKLGFSGFKEFK 67 (77)
T ss_dssp HHHHHHGGGS-HHHHHHHHHHHH-HHHHCT--HHHHHHHCTS-HHHHHHH-----------HHHCTTTCHHHHH
T ss_pred HHHHHHHhhCCHHHHHHHHHHHhCHHHHHHccHHHHHHHcCCCHHHHHHH-----------HHHhCCCCHHHHH
Confidence 4556677888988876 33333 22333333344444455566666655 7888999987764
No 32
>PF13875 DUF4202: Domain of unknown function (DUF4202)
Probab=28.82 E-value=79 Score=27.90 Aligned_cols=64 Identities=16% Similarity=0.226 Sum_probs=42.6
Q ss_pred cCCchhhhHHHHHhHhhcCCCCCCCC-------cchhhhHHHHHHHHHHhCCCCcchhHHHHHHHhhhcCCChHhhh
Q 039418 11 AGDFESSCEMLVDAHRSRGSKDRENN-------HGFISFFAESVRQLKAKDGRACITNEVRKEIRNAFKNLPVEEKC 80 (297)
Q Consensus 11 ~~~~~~~~~~~~~~~~~~~~~~~r~~-------~~f~~~~~~~~~~~~~~~~~~~~~~~v~k~~g~~wk~ls~~ek~ 80 (297)
+|-=+..|+-....-|.+| .|+-| -+=+||++.+-..|.++|...|.+ .++.+-|+-||+.-++
T Consensus 99 ~Gy~~~~i~rV~~lv~K~~--lk~d~e~Q~LEDvacLVFL~~~f~~F~~~~deeK~v----~Il~KTw~KMS~~g~~ 169 (185)
T PF13875_consen 99 AGYDEEEIDRVAALVRKEG--LKRDPETQALEDVACLVFLEYYFEDFAAKHDEEKIV----DILRKTWRKMSERGHE 169 (185)
T ss_pred CCCCHHHHHHHHHHHHhcc--CCCCchHHHHHhhHHHHhHHHHHHHHHhcCCHHHHH----HHHHHHHHHCCHHHHH
Confidence 4444555555555555544 34433 367899999999999999555544 4556679999998554
No 33
>PF14513 DAG_kinase_N: Diacylglycerol kinase N-terminus; PDB: 1TUZ_A.
Probab=28.52 E-value=11 Score=31.76 Aligned_cols=72 Identities=15% Similarity=0.191 Sum_probs=39.1
Q ss_pred hhhcCCChHhhhhhhhhhhcCCCccccccceeeecCHHHHHHHHhhcCHH-------HHHHHHhcCccccccccc-cccc
Q 039418 69 NAFKNLPVEEKCQYKFQSRRGGKANVEKVKFLTRCAPDRLAALVSHLIEK-------QRKAVCDIGLGSIIDLKC-GRLK 140 (297)
Q Consensus 69 ~~wk~ls~~ek~~~~~~~~~~~k~~v~k~~~~trcS~~~~~~~i~~Ls~~-------qk~~I~~~GFg~LL~i~~-~~l~ 140 (297)
++|.+||++|=+.-..-+ .-|.+++.+++..+.++ +.+-|.--||.-+|.+-. ..+|
T Consensus 3 ~~~~~lsp~eF~qLq~y~---------------eys~kklkdvl~eF~~~g~~~~~~~~~~Id~egF~~Fm~~yLe~d~P 67 (138)
T PF14513_consen 3 KEWVSLSPEEFAQLQKYS---------------EYSTKKLKDVLKEFHGDGSLAKYNPEEPIDYEGFKLFMKTYLEVDLP 67 (138)
T ss_dssp ---S-S-HHHHHHHHHHH---------------HH----HHHHHHHH-HTSGGGGGEETTEE-HHHHHHHHHHHTT-S--
T ss_pred cceeccCHHHHHHHHHHH---------------HHHHHHHHHHHHHHhcCCcccccCCCCCcCHHHHHHHHHHHHcCCCC
Confidence 579999999855433333 34677888888888644 234677778888888766 5599
Q ss_pred HHHHHHHHhccccCc
Q 039418 141 RKLCAWLVERIDTAR 155 (297)
Q Consensus 141 ~~L~~wL~~~~d~~t 155 (297)
.+||..|---|....
T Consensus 68 ~~lc~hLF~sF~~~~ 82 (138)
T PF14513_consen 68 EDLCQHLFLSFQKKP 82 (138)
T ss_dssp HHHHHHHHHHS----
T ss_pred HHHHHHHHHHHhCcc
Confidence 999999988877443
No 34
>cd09071 FAR_C C-terminal domain of fatty acyl CoA reductases. C-terminal domain of fatty acyl CoA reductases, a family of SDR-like proteins. SDRs or short-chain dehydrogenases/reductases are Rossmann-fold NAD(P)H-binding proteins. Many proteins in this FAR_C family may function as fatty acyl-CoA reductases (FARs), acting on medium and long chain fatty acids, and have been reported to be involved in diverse processes such as the biosynthesis of insect pheromones, plant cuticular wax production, and mammalian wax biosynthesis. In Arabidopsis thaliana, proteins with this particular architecture have also been identified as the MALE STERILITY 2 (MS2) gene product, which is implicated in male gametogenesis. Mutations in MS2 inhibit the synthesis of exine (sporopollenin), rendering plants unable to reduce pollen wall fatty acids to corresponding alcohols. The function of this C-terminal domain is unclear.
Probab=28.37 E-value=55 Score=24.52 Aligned_cols=21 Identities=24% Similarity=0.708 Sum_probs=18.4
Q ss_pred cCcccchhHHHHHHHHHHHHhh
Q 039418 261 SIRNRNWATFCFERLMRGITRY 282 (297)
Q Consensus 261 ~I~~ynW~~~Vld~L~~~l~k~ 282 (297)
++.++||..++.++ +.|+++|
T Consensus 70 D~~~idW~~Y~~~~-~~G~r~y 90 (92)
T cd09071 70 DIRSIDWDDYFENY-IPGLRKY 90 (92)
T ss_pred CCCCCCHHHHHHHH-HHHHHHH
Confidence 46899999999999 8888876
No 35
>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=26.97 E-value=48 Score=28.08 Aligned_cols=30 Identities=0% Similarity=0.066 Sum_probs=20.7
Q ss_pred chhHHHH-HHHhhhcCCChHhhhhhhhhhhc
Q 039418 59 ITNEVRK-EIRNAFKNLPVEEKCQYKFQSRR 88 (297)
Q Consensus 59 ~~~~v~k-~~g~~wk~ls~~ek~~~~~~~~~ 88 (297)
....+++ ++|.-|+.+|++|++.|...=++
T Consensus 39 D~~~~ar~~LG~~w~~~s~~q~~~F~~~f~~ 69 (170)
T PF05494_consen 39 DFERMARRVLGRYWRKASPAQRQRFVEAFKQ 69 (170)
T ss_dssp -HHHHHHHHHGGGTTTS-HHHHHHHHHHHHH
T ss_pred CHHHHHHHHHHHhHhhCCHHHHHHHHHHHHH
Confidence 4444444 78989999999999977665444
No 36
>PF03457 HA: Helicase associated domain; InterPro: IPR005114 This short domain is found in multiple copies in bacterial helicase proteins. The domain is predicted to contain 3 alpha helices. The function of this domain may be to bind nucleic acid.; PDB: 2KTA_A.
Probab=26.40 E-value=42 Score=23.90 Aligned_cols=16 Identities=13% Similarity=0.304 Sum_probs=11.2
Q ss_pred hhcCHHHHHHHHhcCc
Q 039418 113 SHLIEKQRKAVCDIGL 128 (297)
Q Consensus 113 ~~Ls~~qk~~I~~~GF 128 (297)
..|+++|.+.++++||
T Consensus 52 g~L~~er~~~L~~lg~ 67 (68)
T PF03457_consen 52 GKLTPERIERLDALGF 67 (68)
T ss_dssp T---HHHHHHHHHHT-
T ss_pred CCCCHHHHHHHHcCCC
Confidence 4599999999999998
No 37
>PF07970 COPIIcoated_ERV: Endoplasmic reticulum vesicle transporter ; InterPro: IPR012936 This domain occurs in many hypothetical proteins, and also two partially characterised proteins. One of these proteins, PTX1 Q96RQ1 from SWISSPROT, is a homeodomain-containing transcription factor involved in regulating all pituitary hormone genes []. This protein is down regulated in prostate carcinoma []. The other protein, ERGIC-32 Q969X5 from SWISSPROT, is involved in protein transport from the ER to the Golgi [].
Probab=25.82 E-value=71 Score=28.62 Aligned_cols=35 Identities=23% Similarity=0.310 Sum_probs=23.2
Q ss_pred hhhHHHHHhHhhcCCCCCCCCcchhhhHHHHHHHHH
Q 039418 16 SSCEMLVDAHRSRGSKDRENNHGFISFFAESVRQLK 51 (297)
Q Consensus 16 ~~~~~~~~~~~~~~~~~~r~~~~f~~~~~~~~~~~~ 51 (297)
.+||-+.+||+.+|.+++.+- .+=-..+|+.++.+
T Consensus 13 nTC~~V~~ay~~~~w~~~~~~-~~eQC~~~~~~~~~ 47 (222)
T PF07970_consen 13 NTCEDVREAYRKKGWAFPDLE-NIEQCRREYVKKIK 47 (222)
T ss_pred cCHHHHHHHHHHhCCCCCCcc-ccccccchhhhhhh
Confidence 589999999999999776654 33333334333333
No 38
>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=25.59 E-value=47 Score=29.33 Aligned_cols=30 Identities=10% Similarity=0.177 Sum_probs=22.9
Q ss_pred chhHHHH-HHHhhhcCCChHhhhhhhhhhhc
Q 039418 59 ITNEVRK-EIRNAFKNLPVEEKCQYKFQSRR 88 (297)
Q Consensus 59 ~~~~v~k-~~g~~wk~ls~~ek~~~~~~~~~ 88 (297)
....+++ ++|..|+.+|+++|+.|.+.=++
T Consensus 65 Df~~mar~vLG~~W~~~s~~Qr~~F~~~F~~ 95 (198)
T TIGR03481 65 DLPAMARLTLGSSWTSLSPEQRRRFIGAFRE 95 (198)
T ss_pred CHHHHHHHHhhhhhhhCCHHHHHHHHHHHHH
Confidence 4555554 88999999999999977765443
No 39
>cd07321 Extradiol_Dioxygenase_3A_like Subunit A of Class III extradiol dioxygenases. Extradiol dioxygenases catalyze the incorporation of both atoms of molecular oxygen into substrates using a variety of reaction mechanisms, resulting in the cleavage of aromatic rings. There are two major groups of dioxygenases according to the cleavage site of the aromatic ring. Intradiol enzymes cleave the aromatic ring between two hydroxyl groups, whereas extradiol enzymes cleave the aromatic ring between a hydroxylated carbon and an adjacent non-hydroxylated carbon. Extradiol dioxygenases can be divided into three classes. Class I and II enzymes are evolutionary related and show sequence similarity, with the two domain class II enzymes evolving from the class I enzyme through gene duplication. Class III enzymes are different in sequence and structure and usually have two subunits, designated A and B, which form a tetramer composed of two copies of each subunit. This model represents subunit A of c
Probab=25.19 E-value=69 Score=23.93 Aligned_cols=32 Identities=16% Similarity=0.210 Sum_probs=26.1
Q ss_pred hcCHHHHHHHHhcCcccccccccccccHHHHHHHH
Q 039418 114 HLIEKQRKAVCDIGLGSIIDLKCGRLKRKLCAWLV 148 (297)
Q Consensus 114 ~Ls~~qk~~I~~~GFg~LL~i~~~~l~~~L~~wL~ 148 (297)
.||++|+++|.+--+.+|+++.. |..++.++.
T Consensus 34 ~Lt~eE~~al~~rD~~~L~~lG~---~~~~l~k~~ 65 (77)
T cd07321 34 GLTPEEKAALLARDVGALYVLGV---NPMLLMHFA 65 (77)
T ss_pred CCCHHHHHHHHcCCHHHHHHcCC---CHHHHHHHH
Confidence 89999999999999999999874 555555554
No 40
>PRK15117 ABC transporter periplasmic binding protein MlaC; Provisional
Probab=24.93 E-value=47 Score=29.63 Aligned_cols=25 Identities=12% Similarity=0.114 Sum_probs=20.4
Q ss_pred HHHHHhhhcCCChHhhhhhhhhhhc
Q 039418 64 RKEIRNAFKNLPVEEKCQYKFQSRR 88 (297)
Q Consensus 64 ~k~~g~~wk~ls~~ek~~~~~~~~~ 88 (297)
..++|..|+..|+++|+.|.+.=++
T Consensus 75 ~~vLG~~wr~as~eQr~~F~~~F~~ 99 (211)
T PRK15117 75 ALVLGRYYKDATPAQREAYFAAFRE 99 (211)
T ss_pred HHHhhhhhhhCCHHHHHHHHHHHHH
Confidence 4489999999999999988765544
No 41
>cd02988 Phd_like_VIAF Phosducin (Phd)-like family, Viral inhibitor of apoptosis (IAP)-associated factor (VIAF) subfamily; VIAF is a Phd-like protein that functions in caspase activation during apoptosis. It was identified as an IAP binding protein through a screen of a human B-cell library using a prototype IAP. VIAF lacks a consensus IAP binding motif and while it does not function as an IAP antagonist, it still plays a regulatory role in the complete activation of caspases. VIAF itself is a substrate for IAP-mediated ubiquitination, suggesting that it may be a target of IAPs in the prevention of cell death. The similarity of VIAF to Phd points to a potential role distinct from apoptosis regulation. Phd functions as a cytosolic regulator of G protein by specifically binding to G protein betagamma (Gbg)-subunits. The C-terminal domain of Phd adopts a thioredoxin fold, but it does not contain a CXXC motif. Phd interacts with G protein beta mostly through the N-terminal helical domain.
Probab=23.80 E-value=48 Score=29.12 Aligned_cols=17 Identities=18% Similarity=0.120 Sum_probs=14.3
Q ss_pred HHhHhhcCCCCCCCCcc
Q 039418 22 VDAHRSRGSKDRENNHG 38 (297)
Q Consensus 22 ~~~~~~~~~~~~r~~~~ 38 (297)
=|++|.+|+-|+|||+.
T Consensus 4 ~di~r~~g~~p~~~~~~ 20 (192)
T cd02988 4 NDILRKKGILPPKPPSP 20 (192)
T ss_pred hHHHHHcCCCCCCCCCC
Confidence 38899999999999743
No 42
>PF00701 DHDPS: Dihydrodipicolinate synthetase family; InterPro: IPR002220 Dihydropicolinate synthase (DHDPS) is the key enzyme in lysine biosynthesis via the diaminopimelate pathway of prokaryotes, some phycomycetes and higher plants. The enzyme catalyses the condensation of L-aspartate-beta- semialdehyde and pyruvate to dihydropicolinic acid via a ping-pong mechanism in which pyruvate binds to the enzyme by forming a Schiff-base with a lysine residue []. Three other proteins are structurally related to DHDPS and probably also act via a similar catalytic mechanism. These are Escherichia coli N-acetylneuraminate lyase (4.1.3.3 from EC) (gene nanA), which catalyzes the condensation of N-acetyl-D-mannosamine and pyruvate to form N-acetylneuraminate; Rhizobium meliloti (Sinorhizobium meliloti) protein mosA [], which is involved in the biosynthesis of the rhizopine 3-o-methyl-scyllo-inosamine; and E. coli hypothetical protein yjhH. The sequences of DHDPS from different sources are well-conserved. The structure takes the form of a homotetramer, in which 2 monomers are related by an approximate 2-fold symmetry []. Each monomer comprises 2 domains: an 8-fold alpha-/beta-barrel, and a C-terminal alpha-helical domain. The fold resembles that of N-acetylneuraminate lyase. The active site lysine is located in the barrel domain, and has access via 2 channels on the C-terminal side of the barrel.; GO: 0016829 lyase activity, 0008152 metabolic process; PDB: 3B4U_B 3S8H_A 3QZE_B 1XXX_F 3L21_F 3IRD_A 3A5F_B 3G0S_B 3DAQ_C 3UQN_A ....
Probab=23.22 E-value=66 Score=29.64 Aligned_cols=102 Identities=13% Similarity=0.141 Sum_probs=63.9
Q ss_pred hhcCCChHhhhhhhhhhhcCCCccccccceeeecCHHHHHHHHhhcCHHHHHHHHhcCccccccccccc--c-cHHHHHH
Q 039418 70 AFKNLPVEEKCQYKFQSRRGGKANVEKVKFLTRCAPDRLAALVSHLIEKQRKAVCDIGLGSIIDLKCGR--L-KRKLCAW 146 (297)
Q Consensus 70 ~wk~ls~~ek~~~~~~~~~~~k~~v~k~~~~trcS~~~~~~~i~~Ls~~qk~~I~~~GFg~LL~i~~~~--l-~~~L~~w 146 (297)
.+-+||.+||....+-+.+..+.+++--.-....|.....+..+ ..+++|+.+++-++... . ...+..|
T Consensus 47 E~~~Lt~~Er~~l~~~~~~~~~~~~~vi~gv~~~st~~~i~~a~--------~a~~~Gad~v~v~~P~~~~~s~~~l~~y 118 (289)
T PF00701_consen 47 EFYSLTDEERKELLEIVVEAAAGRVPVIAGVGANSTEEAIELAR--------HAQDAGADAVLVIPPYYFKPSQEELIDY 118 (289)
T ss_dssp TGGGS-HHHHHHHHHHHHHHHTTSSEEEEEEESSSHHHHHHHHH--------HHHHTT-SEEEEEESTSSSCCHHHHHHH
T ss_pred ccccCCHHHHHHHHHHHHHHccCceEEEecCcchhHHHHHHHHH--------HHhhcCceEEEEeccccccchhhHHHHH
Confidence 46789999999999888887666655444455557766665543 46789999998886632 2 2456666
Q ss_pred HHhccccCcceEEECC----eEeecCccchhheeccc
Q 039418 147 LVERIDTARCVLQLNG----HELELSPNSFGYIMGVT 179 (297)
Q Consensus 147 L~~~~d~~t~~~~i~g----~~i~iT~~dV~~VLGLP 179 (297)
..+--+....-+.+.+ ....++++.+..+..+|
T Consensus 119 ~~~ia~~~~~pi~iYn~P~~tg~~ls~~~l~~L~~~~ 155 (289)
T PF00701_consen 119 FRAIADATDLPIIIYNNPARTGNDLSPETLARLAKIP 155 (289)
T ss_dssp HHHHHHHSSSEEEEEEBHHHHSSTSHHHHHHHHHTST
T ss_pred HHHHHhhcCCCEEEEECCCccccCCCHHHHHHHhcCC
Confidence 5555554445555532 23566666666666555
No 43
>PF12650 DUF3784: Domain of unknown function (DUF3784); InterPro: IPR017259 This group represents an uncharacterised conserved protein.
Probab=23.22 E-value=45 Score=25.65 Aligned_cols=17 Identities=24% Similarity=0.470 Sum_probs=13.1
Q ss_pred hhcCCChHhhhhhhhhh
Q 039418 70 AFKNLPVEEKCQYKFQS 86 (297)
Q Consensus 70 ~wk~ls~~ek~~~~~~~ 86 (297)
-+++||++||+.|-.+.
T Consensus 25 Gyntms~eEk~~~D~~~ 41 (97)
T PF12650_consen 25 GYNTMSKEEKEKYDKKK 41 (97)
T ss_pred hcccCCHHHHHHhhHHH
Confidence 37899999999775543
No 44
>PF03015 Sterile: Male sterility protein; InterPro: IPR004262 This family represents the C-terminal region of the male sterility protein in a number of organisms. The Arabidopsis thaliana male sterility 2 (MS2) protein is involved in male gametogenesis. The MS2 protein shows sequence similarity to a jojoba protein (also a member of this group) that converts wax fatty acids to fatty alcohols. It has been suggested that a possible function of the MS2 protein may be as a fatty acyl reductase in the formation of pollen wall substances [].; GO: 0016620 oxidoreductase activity, acting on the aldehyde or oxo group of donors, NAD or NADP as acceptor, 0055114 oxidation-reduction process
Probab=22.32 E-value=85 Score=23.83 Aligned_cols=54 Identities=17% Similarity=0.253 Sum_probs=31.9
Q ss_pred hhhHHHhhhhcceeCCCCCC-----ccCcchhhhhhccccCcccchhHHHHHHHHHHHHhhh
Q 039418 227 FKVAFMLFTLCTLLCPPGGV-----HISYSFLFTLKDVHSIRNRNWATFCFERLMRGITRYK 283 (297)
Q Consensus 227 f~r~Fll~~i~~~L~Ptt~~-----~vs~~yl~~l~D~~~I~~ynW~~~Vld~L~~~l~k~~ 283 (297)
...++-.|+.....+.+.+. ..++..-..+ +. +++++||-.++.++ +.|+++|-
T Consensus 33 ~~~~~~~F~~~eW~F~~~n~~~L~~~l~~~D~~~F-~f-D~~~idW~~Y~~~~-~~G~rkyl 91 (94)
T PF03015_consen 33 ALEVLEYFTTNEWIFDNDNTRRLWERLSPEDREIF-NF-DIRSIDWEEYFRNY-IPGIRKYL 91 (94)
T ss_pred HHHHHHHHHhCceeecchHHHHHHHhCchhcCcee-cC-CCCCCCHHHHHHHH-HHHHHHHH
Confidence 33444455555555544432 1233333222 12 57899999999999 88998874
No 45
>smart00271 DnaJ DnaJ molecular chaperone homology domain.
Probab=22.10 E-value=99 Score=20.86 Aligned_cols=36 Identities=17% Similarity=0.022 Sum_probs=25.0
Q ss_pred hHHHHHHHHHHhCCCCcc-----hhHHHHHHHhhhcCCChH
Q 039418 42 FFAESVRQLKAKDGRACI-----TNEVRKEIRNAFKNLPVE 77 (297)
Q Consensus 42 ~~~~~~~~~~~~~~~~~~-----~~~v~k~~g~~wk~ls~~ 77 (297)
-...|++..+.-||+... ....-..+.+.|..|++.
T Consensus 18 ik~ay~~l~~~~HPD~~~~~~~~~~~~~~~l~~Ay~~L~~~ 58 (60)
T smart00271 18 IKKAYRKLALKYHPDKNPGDKEEAEEKFKEINEAYEVLSDP 58 (60)
T ss_pred HHHHHHHHHHHHCcCCCCCchHHHHHHHHHHHHHHHHHcCC
Confidence 356788888899998876 334555667777777665
No 46
>PF06628 Catalase-rel: Catalase-related immune-responsive; InterPro: IPR010582 Catalases (1.11.1.6 from EC) are antioxidant enzymes that catalyse the conversion of hydrogen peroxide to water and molecular oxygen, serving to protect cells from its toxic effects []. Hydrogen peroxide is produced as a consequence of oxidative cellular metabolism and can be converted to the highly reactive hydroxyl radical via transition metals, this radical being able to damage a wide variety of molecules within a cell, leading to oxidative stress and cell death. Catalases act to neutralise hydrogen peroxide toxicity, and are produced by all aerobic organisms ranging from bacteria to man. Most catalases are mono-functional, haem-containing enzymes, although there are also bifunctional haem-containing peroxidase/catalases (IPR000763 from INTERPRO) that are closely related to plant peroxidases, and non-haem, manganese-containing catalases (IPR007760 from INTERPRO) that are found in bacteria []. This entry represents a small conserved region within catalase enzymes that carries the immune-responsive amphipathic octa-peptide that is recognised by T cells [].; PDB: 2CAH_A 1NM0_A 1H7K_A 1E93_A 1H6N_A 3HB6_A 2CAG_A 1M85_A 1MQF_A 1A4E_C ....
Probab=21.78 E-value=50 Score=23.93 Aligned_cols=23 Identities=17% Similarity=0.202 Sum_probs=18.1
Q ss_pred HHHhhhcCCChHhhhhhhhhhhc
Q 039418 66 EIRNAFKNLPVEEKCQYKFQSRR 88 (297)
Q Consensus 66 ~~g~~wk~ls~~ek~~~~~~~~~ 88 (297)
-.|..|++||++||+.....-..
T Consensus 12 Qa~~ly~~l~~~er~~lv~nia~ 34 (68)
T PF06628_consen 12 QARDLYRVLSDEERERLVENIAG 34 (68)
T ss_dssp HHHHHHHHSSHHHHHHHHHHHHH
T ss_pred hHHHHHHHCCHHHHHHHHHHHHH
Confidence 46789999999999977765444
No 47
>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=20.05 E-value=1.1e+02 Score=21.12 Aligned_cols=39 Identities=18% Similarity=0.052 Sum_probs=30.0
Q ss_pred hHHHHHHHHHHhCCCCcchh-----HHHHHHHhhhcCCChHhhh
Q 039418 42 FFAESVRQLKAKDGRACITN-----EVRKEIRNAFKNLPVEEKC 80 (297)
Q Consensus 42 ~~~~~~~~~~~~~~~~~~~~-----~v~k~~g~~wk~ls~~ek~ 80 (297)
-..-|++..+.-||+..... ..-..+.+.|+-|+++++.
T Consensus 17 ik~~y~~l~~~~HPD~~~~~~~~~~~~~~~i~~Ay~~L~~~~~R 60 (64)
T PF00226_consen 17 IKKAYRRLSKQYHPDKNSGDEAEAEEKFARINEAYEILSDPERR 60 (64)
T ss_dssp HHHHHHHHHHHTSTTTGTSTHHHHHHHHHHHHHHHHHHHSHHHH
T ss_pred HHHHHHhhhhccccccchhhhhhhhHHHHHHHHHHHHhCCHHHH
Confidence 35668888899999885544 4777899999999888754
Done!