Query psy5036
Match_columns 176
No_of_seqs 182 out of 1008
Neff 5.0
Searched_HMMs 46136
Date Sat Aug 17 00:09:01 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy5036.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/5036hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG3248|consensus 100.0 1.1E-40 2.3E-45 293.9 5.9 138 6-148 134-276 (421)
2 KOG0527|consensus 99.9 3.7E-26 8E-31 202.2 8.2 79 58-136 57-138 (331)
3 cd01389 MATA_HMG-box MATA_HMG- 99.9 7E-24 1.5E-28 150.1 5.0 72 63-134 1-75 (77)
4 cd01388 SOX-TCF_HMG-box SOX-TC 99.9 5.4E-23 1.2E-27 144.1 4.5 69 63-131 1-72 (72)
5 PF00505 HMG_box: HMG (high mo 99.7 4.4E-19 9.5E-24 121.2 0.0 66 64-129 1-69 (69)
6 PTZ00199 high mobility group p 99.7 2.2E-18 4.7E-23 127.4 3.4 73 57-129 16-93 (94)
7 smart00398 HMG high mobility g 99.7 4.5E-18 9.7E-23 115.4 3.5 67 63-129 1-70 (70)
8 cd01390 HMGB-UBF_HMG-box HMGB- 99.7 2.3E-17 4.9E-22 111.6 3.4 62 64-125 1-65 (66)
9 KOG0528|consensus 99.7 1.4E-17 3.1E-22 152.6 3.0 79 58-136 320-401 (511)
10 cd00084 HMG-box High Mobility 99.7 6.4E-17 1.4E-21 108.5 3.5 63 64-126 1-66 (66)
11 PF09011 HMG_box_2: HMG-box do 99.5 9.2E-16 2E-20 107.6 0.4 67 62-128 2-72 (73)
12 KOG0381|consensus 99.5 2.1E-14 4.5E-19 104.4 3.0 70 61-130 20-93 (96)
13 COG5648 NHP6B Chromatin-associ 99.4 5.3E-14 1.1E-18 117.9 2.8 76 57-132 64-142 (211)
14 KOG0526|consensus 99.1 8.3E-11 1.8E-15 109.8 3.4 72 57-131 529-602 (615)
15 KOG2746|consensus 98.8 2.4E-09 5.2E-14 102.0 2.9 66 59-124 177-247 (683)
16 KOG4715|consensus 98.6 6.3E-08 1.4E-12 86.3 6.4 72 63-134 64-138 (410)
17 COG5648 NHP6B Chromatin-associ 96.1 0.0077 1.7E-07 51.1 4.3 69 59-127 139-210 (211)
18 PF06382 DUF1074: Protein of u 94.7 0.013 2.7E-07 48.8 0.8 48 68-118 83-132 (183)
19 PF04769 MAT_Alpha1: Mating-ty 94.3 0.023 4.9E-07 47.9 1.6 51 59-115 39-92 (201)
20 PF14887 HMG_box_5: HMG (high 93.6 0.043 9.2E-07 40.3 1.7 67 67-134 7-76 (85)
21 PF04690 YABBY: YABBY protein; 68.0 2.8 6.1E-05 34.6 1.3 39 65-103 123-164 (170)
22 TIGR03481 HpnM hopanoid biosyn 61.8 4.6 0.0001 33.5 1.5 45 86-130 62-110 (198)
23 PF05494 Tol_Tol_Ttg2: Toluene 51.9 8.3 0.00018 30.5 1.4 52 79-130 27-84 (170)
24 PF08073 CHDNT: CHDNT (NUC034) 50.6 2.8 6.1E-05 28.7 -1.3 36 68-103 13-51 (55)
25 PRK15117 ABC transporter perip 45.6 15 0.00033 30.7 2.0 52 79-130 57-114 (211)
26 PF12881 NUT_N: NUT protein N 39.2 76 0.0016 28.9 5.5 58 60-117 195-281 (328)
27 PF12650 DUF3784: Domain of un 38.1 26 0.00056 25.4 2.1 15 98-112 25-39 (97)
28 PF01352 KRAB: KRAB box; Inte 30.8 42 0.00091 21.2 1.9 27 89-115 2-31 (41)
29 KOG0528|consensus 28.7 43 0.00093 32.1 2.3 70 58-132 11-84 (511)
30 PF06945 DUF1289: Protein of u 26.5 68 0.0015 21.0 2.4 19 98-116 29-47 (51)
31 PF06244 DUF1014: Protein of u 25.6 19 0.00042 28.2 -0.4 39 65-103 74-115 (122)
32 PRK09706 transcriptional repre 24.9 36 0.00078 25.9 1.0 36 95-130 91-127 (135)
33 KOG1827|consensus 23.2 1.1E+02 0.0024 30.3 4.0 41 67-107 552-595 (629)
34 PF02026 RyR: RyR domain; Int 22.7 80 0.0017 23.3 2.4 21 98-118 60-80 (94)
No 1
>KOG3248|consensus
Probab=100.00 E-value=1.1e-40 Score=293.90 Aligned_cols=138 Identities=47% Similarity=0.663 Sum_probs=125.1
Q ss_pred CCCCCCCCCCCCCC--CCCCCCCCcccCCCCCCCCCCCCCCCCCcCCCCCCCCCCCCCCCCCCCCchhhhhhhhhccchh
Q psy5036 6 DYRFSPTSLMAAHP--GLSPHSHPAIVTPGPKQELLSDHNHSGMRWGGMSKPSIMSWHVGSVNFICNFILIGPQGQTKPE 83 (176)
Q Consensus 6 ~~rfs~~~~~~~~~--~~s~~~hpaiv~p~~~qe~~~~~~~~~~~~~~~~~~~~~~k~~~~KRPlNAFmLF~ke~R~kv~ 83 (176)
++||+||++.++|+ |++||||||||+|.++||.+.... .++.+...+.+.+.|++|||+||||||||++|+|++|+
T Consensus 134 msrf~ph~~~p~~p~~~tagiPhpaiv~P~~kqes~~~~~--nvk~~~~~k~e~e~KkphiKKPLNAFmlyMKEmRa~vv 211 (421)
T KOG3248|consen 134 MSRFSPHHVEPGHPGLHTAGIPHPAIVTPPVKQESDSAPQ--NVKRQAESKKEEEAKKPHIKKPLNAFMLYMKEMRAKVV 211 (421)
T ss_pred hhhcchhccCCCCCCccccCCCCccccCCcccCccccccc--ccchhhhccccccccCccccccHHHHHHHHHHHHHHHH
Confidence 46999999999887 999999999999999999765433 33444446667778999999999999999999999999
Q ss_pred hc-cCCCccccccce--eccCCCHHHHHHHHHHHHHHHHHHHHHCCCCccCCCCCCcccccccccccC
Q psy5036 84 AR-SGNEITNKNQMI--QWHSLTREEQAKYYEKARQERQLHMELYPGWSARDNYGYGAKKKKRKKERA 148 (176)
Q Consensus 84 ~e-P~~~~~eISKil--~Wk~Ls~eEK~~Y~~~A~k~ke~h~~~~P~Yk~~~n~~~~~kkkkrk~~~~ 148 (176)
+| ..++.++|++|| +|++||.||+++|+++|+++||.|+++||+|.+|+||+ |||||++|++
T Consensus 212 aEctlKeSAaiNqiLGrRWH~LSrEEQAKYyElArKerqlH~qlYP~WSARdNYg---KKkKrkReKq 276 (421)
T KOG3248|consen 212 AECTLKESAAINQILGRRWHALSREEQAKYYELARKERQLHMQLYPGWSARDNYG---KKKKRKREKQ 276 (421)
T ss_pred HHhhhhhHHHHHHHHhHHHhhhhHHHHHHHHHHHHHHHHHHHHhcCCcchhhhhh---hhhhhhhhcc
Confidence 99 999999999999 99999999999999999999999999999999999999 8899999984
No 2
>KOG0527|consensus
Probab=99.93 E-value=3.7e-26 Score=202.25 Aligned_cols=79 Identities=16% Similarity=0.259 Sum_probs=75.6
Q ss_pred CCCCCCCCCCCchhhhhhhhhccchhhc-cCCCccccccce--eccCCCHHHHHHHHHHHHHHHHHHHHHCCCCccCCCC
Q psy5036 58 MSWHVGSVNFICNFILIGPQGQTKPEAR-SGNEITNKNQMI--QWHSLTREEQAKYYEKARQERQLHMELYPGWSARDNY 134 (176)
Q Consensus 58 ~~k~~~~KRPlNAFmLF~ke~R~kv~~e-P~~~~~eISKil--~Wk~Ls~eEK~~Y~~~A~k~ke~h~~~~P~Yk~~~n~ 134 (176)
....+||||||||||||++.+|++|..+ |+++|+||||+| +|+.|+++||.+|+++|+++|++|+++||||||||++
T Consensus 57 k~~~~hIKRPMNAFMVWSq~~RRkma~qnP~mHNSEISK~LG~~WK~Lse~EKrPFi~EAeRLR~~HmkehPdYKYRPRR 136 (331)
T KOG0527|consen 57 KTSTDRIKRPMNAFMVWSQGQRRKLAKQNPKMHNSEISKRLGAEWKLLSEEEKRPFVDEAERLRAQHMKEYPDYKYRPRR 136 (331)
T ss_pred CCCccccCCCcchhhhhhHHHHHHHHHhCcchhhHHHHHHHHHHHhhcCHhhhccHHHHHHHHHHHHHHhCCCccccccc
Confidence 4567899999999999999999999999 999999999999 9999999999999999999999999999999999988
Q ss_pred CC
Q psy5036 135 GY 136 (176)
Q Consensus 135 ~~ 136 (176)
++
T Consensus 137 Kk 138 (331)
T KOG0527|consen 137 KK 138 (331)
T ss_pred cc
Confidence 73
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=99.89 E-value=7e-24 Score=150.11 Aligned_cols=72 Identities=22% Similarity=0.303 Sum_probs=69.8
Q ss_pred CCCCCCchhhhhhhhhccchhhc-cCCCccccccce--eccCCCHHHHHHHHHHHHHHHHHHHHHCCCCccCCCC
Q psy5036 63 GSVNFICNFILIGPQGQTKPEAR-SGNEITNKNQMI--QWHSLTREEQAKYYEKARQERQLHMELYPGWSARDNY 134 (176)
Q Consensus 63 ~~KRPlNAFmLF~ke~R~kv~~e-P~~~~~eISKil--~Wk~Ls~eEK~~Y~~~A~k~ke~h~~~~P~Yk~~~n~ 134 (176)
|||||+||||||+++.|..|.++ |+++++||+++| +|+.|+++||++|.++|++++++|+++||+|+|+|..
T Consensus 1 ~~kRP~naf~lf~~~~r~~~~~~~p~~~~~eisk~~g~~Wk~ls~eeK~~y~~~A~~~k~~~~~~~p~Yky~p~~ 75 (77)
T cd01389 1 KIPRPRNAFILYRQDKHAQLKTENPGLTNNEISRIIGRMWRSESPEVKAYYKELAEEEKERHAREYPDYKYTPRK 75 (77)
T ss_pred CCCCCCcHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHhhCCHHHHHHHHHHHHHHHHHHHHHCCCCcccCCC
Confidence 68999999999999999999999 999999999999 9999999999999999999999999999999999854
No 4
>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=99.87 E-value=5.4e-23 Score=144.09 Aligned_cols=69 Identities=28% Similarity=0.528 Sum_probs=67.5
Q ss_pred CCCCCCchhhhhhhhhccchhhc-cCCCccccccce--eccCCCHHHHHHHHHHHHHHHHHHHHHCCCCccC
Q psy5036 63 GSVNFICNFILIGPQGQTKPEAR-SGNEITNKNQMI--QWHSLTREEQAKYYEKARQERQLHMELYPGWSAR 131 (176)
Q Consensus 63 ~~KRPlNAFmLF~ke~R~kv~~e-P~~~~~eISKil--~Wk~Ls~eEK~~Y~~~A~k~ke~h~~~~P~Yk~~ 131 (176)
|||||+||||||++++|.+|..+ |++++.||+++| +|+.|+++||++|.++|++++++|.++||+|+|+
T Consensus 1 ~iKrP~naf~~F~~~~r~~~~~~~p~~~~~eisk~l~~~Wk~ls~~eK~~y~~~a~~~k~~y~~~~p~y~y~ 72 (72)
T cd01388 1 HIKRPMNAFMLFSKRHRRKVLQEYPLKENRAISKILGDRWKALSNEEKQPYYEEAKKLKELHMKLYPDYKWR 72 (72)
T ss_pred CCCCCCcHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHCcCCCCC
Confidence 69999999999999999999999 999999999999 9999999999999999999999999999999985
No 5
>PF00505 HMG_box: HMG (high mobility group) box; InterPro: IPR000910 High mobility group (HMG or HMGB) proteins are a family of relatively low molecular weight non-histone components in chromatin. HMG1 (also called HMG-T in fish) and HMG2 are two highly related proteins that bind single-stranded DNA preferentially and unwind double-stranded DNA. Although they have no sequence specificity, they have a high affinity for bent or distorted DNA, and bend linear DNA. HMG1 and HMG2 contain two DNA-binding HMG-box domains (A and B) that show structural and functional differences, and have a long acidic C-terminal domain rich in aspartic and glutamic acid residues. The acidic tail modulates the affinity of the tandem HMG boxes in HMG1 and 2 for a variety of DNA targets. HMG1 and 2 appear to play important architectural roles in the assembly of nucleoprotein complexes in a variety of biological processes, for example V(D)J recombination, the initiation of transcription, and DNA repair []. The profile in this entry describing the HMG-domains is much more general than the signature. In addition to the HMG1 and HMG2 proteins, HMG-domains occur in single or multiple copies in the following protein classes; the SOX family of transcription factors; SRY sex determining region Y protein and related proteins []; LEF1 lymphoid enhancer binding factor 1 []; SSRP recombination signal recognition protein; MTF1 mitochondrial transcription factor 1; UBF1/2 nucleolar transcription factors; Abf2 yeast ARS-binding factor []; and Saccharomyces cerevisiae transcription factors Ixr1, Rox1, Nhp6a, Nhp6b and Spp41.; GO: 0003677 DNA binding; PDB: 1I11_A 1J3C_A 1J3D_A 1WZ6_A 1WGF_A 2D7L_A 1GT0_D 3U2B_C 2CRJ_A 2CS1_A ....
Probab=99.73 E-value=4.4e-19 Score=121.20 Aligned_cols=66 Identities=20% Similarity=0.335 Sum_probs=62.1
Q ss_pred CCCCCchhhhhhhhhccchhhc-cCCCccccccce--eccCCCHHHHHHHHHHHHHHHHHHHHHCCCCc
Q psy5036 64 SVNFICNFILIGPQGQTKPEAR-SGNEITNKNQMI--QWHSLTREEQAKYYEKARQERQLHMELYPGWS 129 (176)
Q Consensus 64 ~KRPlNAFmLF~ke~R~kv~~e-P~~~~~eISKil--~Wk~Ls~eEK~~Y~~~A~k~ke~h~~~~P~Yk 129 (176)
||||+||||||++++|..+..+ |+++.++|+++| +|++|+++||++|.++|+++++.|.+++++|+
T Consensus 1 PkrP~~af~lf~~~~~~~~k~~~p~~~~~~i~~~~~~~W~~l~~~eK~~y~~~a~~~~~~y~~~~~~y~ 69 (69)
T PF00505_consen 1 PKRPPNAFMLFCKEKRAKLKEENPDLSNKEISKILAQMWKNLSEEEKAPYKEEAEEEKERYEKEMPEYK 69 (69)
T ss_dssp SSSS--HHHHHHHHHHHHHHHHSTTSTHHHHHHHHHHHHHCSHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred CcCCCCHHHHHHHHHHHHHHHHhcccccccchhhHHHHHhcCCHHHHHHHHHHHHHHHHHHHHHHHhcC
Confidence 7999999999999999999999 999999999999 99999999999999999999999999999884
No 6
>PTZ00199 high mobility group protein; Provisional
Probab=99.72 E-value=2.2e-18 Score=127.42 Aligned_cols=73 Identities=14% Similarity=0.242 Sum_probs=67.8
Q ss_pred CCCCCCCCCCCCchhhhhhhhhccchhhc-cCCC--ccccccce--eccCCCHHHHHHHHHHHHHHHHHHHHHCCCCc
Q psy5036 57 IMSWHVGSVNFICNFILIGPQGQTKPEAR-SGNE--ITNKNQMI--QWHSLTREEQAKYYEKARQERQLHMELYPGWS 129 (176)
Q Consensus 57 ~~~k~~~~KRPlNAFmLF~ke~R~kv~~e-P~~~--~~eISKil--~Wk~Ls~eEK~~Y~~~A~k~ke~h~~~~P~Yk 129 (176)
...+++.||||+||||||++++|..|..+ |++. +++|+++| +|++|+++||++|+++|+.++++|..++..|.
T Consensus 16 ~~kdp~~PKrP~sAY~~F~~~~R~~i~~~~P~~~~~~~evsk~ige~Wk~ls~eeK~~y~~~A~~dk~rY~~e~~~Y~ 93 (94)
T PTZ00199 16 KKKDPNAPKRALSAYMFFAKEKRAEIIAENPELAKDVAAVGKMVGEAWNKLSEEEKAPYEKKAQEDKVRYEKEKAEYA 93 (94)
T ss_pred CCCCCCCCCCCCcHHHHHHHHHHHHHHHHCcCCcccHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 34667899999999999999999999999 9976 79999999 99999999999999999999999999998884
No 7
>smart00398 HMG high mobility group.
Probab=99.71 E-value=4.5e-18 Score=115.37 Aligned_cols=67 Identities=22% Similarity=0.396 Sum_probs=64.7
Q ss_pred CCCCCCchhhhhhhhhccchhhc-cCCCccccccce--eccCCCHHHHHHHHHHHHHHHHHHHHHCCCCc
Q psy5036 63 GSVNFICNFILIGPQGQTKPEAR-SGNEITNKNQMI--QWHSLTREEQAKYYEKARQERQLHMELYPGWS 129 (176)
Q Consensus 63 ~~KRPlNAFmLF~ke~R~kv~~e-P~~~~~eISKil--~Wk~Ls~eEK~~Y~~~A~k~ke~h~~~~P~Yk 129 (176)
.||||+||||||+++.|..+..+ |+++.++|+++| +|+.|++++|++|.++|+.++++|..++++|+
T Consensus 1 ~pkrp~~~y~~f~~~~r~~~~~~~~~~~~~~i~~~~~~~W~~l~~~ek~~y~~~a~~~~~~y~~~~~~y~ 70 (70)
T smart00398 1 KPKRPMSAFMLFSQENRAKIKAENPDLSNAEISKKLGERWKLLSEEEKAPYEEKAKKDKERYEEEMPEYK 70 (70)
T ss_pred CcCCCCcHHHHHHHHHHHHHHHHCcCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHHhcC
Confidence 47999999999999999999999 999999999999 99999999999999999999999999999985
No 8
>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=99.68 E-value=2.3e-17 Score=111.58 Aligned_cols=62 Identities=19% Similarity=0.404 Sum_probs=60.0
Q ss_pred CCCCCchhhhhhhhhccchhhc-cCCCccccccce--eccCCCHHHHHHHHHHHHHHHHHHHHHC
Q psy5036 64 SVNFICNFILIGPQGQTKPEAR-SGNEITNKNQMI--QWHSLTREEQAKYYEKARQERQLHMELY 125 (176)
Q Consensus 64 ~KRPlNAFmLF~ke~R~kv~~e-P~~~~~eISKil--~Wk~Ls~eEK~~Y~~~A~k~ke~h~~~~ 125 (176)
||||+||||+|++++|..+..+ |++++++|+++| +|++|+++||++|.++|++++++|..++
T Consensus 1 Pkrp~saf~~f~~~~r~~~~~~~p~~~~~~i~~~~~~~W~~ls~~eK~~y~~~a~~~~~~y~~e~ 65 (66)
T cd01390 1 PKRPLSAYFLFSQEQRPKLKKENPDASVTEVTKILGEKWKELSEEEKKKYEEKAEKDKERYEKEM 65 (66)
T ss_pred CCCCCcHHHHHHHHHHHHHHHHCcCCCHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHhh
Confidence 6899999999999999999999 999999999999 9999999999999999999999999875
No 9
>KOG0528|consensus
Probab=99.68 E-value=1.4e-17 Score=152.62 Aligned_cols=79 Identities=18% Similarity=0.326 Sum_probs=73.6
Q ss_pred CCCCCCCCCCCchhhhhhhhhccchhhc-cCCCccccccce--eccCCCHHHHHHHHHHHHHHHHHHHHHCCCCccCCCC
Q psy5036 58 MSWHVGSVNFICNFILIGPQGQTKPEAR-SGNEITNKNQMI--QWHSLTREEQAKYYEKARQERQLHMELYPGWSARDNY 134 (176)
Q Consensus 58 ~~k~~~~KRPlNAFmLF~ke~R~kv~~e-P~~~~~eISKil--~Wk~Ls~eEK~~Y~~~A~k~ke~h~~~~P~Yk~~~n~ 134 (176)
...++||||||||||+|.++.|.+|... |++.+.+||||| +|++||-.||++||++-+.+=..|++.||+|+|+++.
T Consensus 320 ~ss~PHIKRPMNAFMVWAkDERRKILqA~PDMHNSnISKILGSRWKaMSN~eKQPYYEEQaRLSk~HlEk~PdYrYkPRP 399 (511)
T KOG0528|consen 320 ASSEPHIKRPMNAFMVWAKDERRKILQAFPDMHNSNISKILGSRWKAMSNTEKQPYYEEQARLSKLHLEKYPDYRYKPRP 399 (511)
T ss_pred CCCCccccCCcchhhcccchhhhhhhhcCccccccchhHHhcccccccccccccchHHHHHHHHHhhhccCcccccCCCC
Confidence 3567899999999999999999999999 999999999999 9999999999999999999989999999999998876
Q ss_pred CC
Q psy5036 135 GY 136 (176)
Q Consensus 135 ~~ 136 (176)
++
T Consensus 400 KR 401 (511)
T KOG0528|consen 400 KR 401 (511)
T ss_pred Cc
Confidence 43
No 10
>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=99.65 E-value=6.4e-17 Score=108.53 Aligned_cols=63 Identities=22% Similarity=0.444 Sum_probs=60.8
Q ss_pred CCCCCchhhhhhhhhccchhhc-cCCCccccccce--eccCCCHHHHHHHHHHHHHHHHHHHHHCC
Q psy5036 64 SVNFICNFILIGPQGQTKPEAR-SGNEITNKNQMI--QWHSLTREEQAKYYEKARQERQLHMELYP 126 (176)
Q Consensus 64 ~KRPlNAFmLF~ke~R~kv~~e-P~~~~~eISKil--~Wk~Ls~eEK~~Y~~~A~k~ke~h~~~~P 126 (176)
||||+||||||+++.|..+..+ |+++..+|+++| +|+.|++++|++|.++|++++++|.++++
T Consensus 1 pkrp~~af~~f~~~~~~~~~~~~~~~~~~~i~~~~~~~W~~l~~~~k~~y~~~a~~~~~~y~~~~~ 66 (66)
T cd00084 1 PKRPLSAYFLFSQEHRAEVKAENPGLSVGEISKILGEMWKSLSEEEKKKYEEKAEKDKERYEKEMP 66 (66)
T ss_pred CCCCCcHHHHHHHHHHHHHHHHCcCCCHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHhhC
Confidence 6899999999999999999999 999999999999 99999999999999999999999999875
No 11
>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=99.54 E-value=9.2e-16 Score=107.61 Aligned_cols=67 Identities=16% Similarity=0.283 Sum_probs=58.3
Q ss_pred CCCCCCCchhhhhhhhhccchhhc--cCCCccccccce--eccCCCHHHHHHHHHHHHHHHHHHHHHCCCC
Q psy5036 62 VGSVNFICNFILIGPQGQTKPEAR--SGNEITNKNQMI--QWHSLTREEQAKYYEKARQERQLHMELYPGW 128 (176)
Q Consensus 62 ~~~KRPlNAFmLF~ke~R~kv~~e--P~~~~~eISKil--~Wk~Ls~eEK~~Y~~~A~k~ke~h~~~~P~Y 128 (176)
++||||+|||+||+.+++..+..+ +.....||++.| .|++||++||.+|.++|+.++++|..++..|
T Consensus 2 ~kpK~~~say~lF~~~~~~~~k~~G~~~~~~~e~~k~~~~~Wk~Ls~~EK~~Y~~~A~~~k~~y~~e~~~~ 72 (73)
T PF09011_consen 2 KKPKRPPSAYNLFMKEMRKEVKEEGGQKQSFREVMKEISERWKSLSEEEKEPYEERAKEDKERYEREMKEW 72 (73)
T ss_dssp SS--SSSSHHHHHHHHHHHHHHHHT-T-SSHHHHHHHHHHHHHHS-HHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred cCCCCCCCHHHHHHHHHHHHHHHhcccCCCHHHHHHHHHHHHHhcCHHHHHHHHHHHHHHHHHHHHHHHhc
Confidence 568999999999999999999877 667899999999 9999999999999999999999999987655
No 12
>KOG0381|consensus
Probab=99.47 E-value=2.1e-14 Score=104.43 Aligned_cols=70 Identities=20% Similarity=0.334 Sum_probs=66.1
Q ss_pred CCCCCCCCchhhhhhhhhccchhhc-cCCCccccccce--eccCCCHHHHHHHHHHHHHHHHHHHHHCC-CCcc
Q psy5036 61 HVGSVNFICNFILIGPQGQTKPEAR-SGNEITNKNQMI--QWHSLTREEQAKYYEKARQERQLHMELYP-GWSA 130 (176)
Q Consensus 61 ~~~~KRPlNAFmLF~ke~R~kv~~e-P~~~~~eISKil--~Wk~Ls~eEK~~Y~~~A~k~ke~h~~~~P-~Yk~ 130 (176)
...+|||++|||+|+.+.|..+.++ |++++.||+++| +|++|++++|.+|...|..++++|..++. .|+.
T Consensus 20 ~~~pkrp~sa~~~f~~~~~~~~k~~~p~~~~~~v~k~~g~~W~~l~~~~k~~y~~ka~~~k~~Y~~~~~~~~~~ 93 (96)
T KOG0381|consen 20 AQAPKRPLSAFFLFSSEQRSKIKAENPGLSVGEVAKALGEMWKNLAEEEKQPYEEKASKLKEKYEKELAGEYKA 93 (96)
T ss_pred CCCCCCCCcHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Confidence 4689999999999999999999999 999999999999 99999999999999999999999999998 6653
No 13
>COG5648 NHP6B Chromatin-associated proteins containing the HMG domain [Chromatin structure and dynamics]
Probab=99.43 E-value=5.3e-14 Score=117.94 Aligned_cols=76 Identities=14% Similarity=0.269 Sum_probs=71.9
Q ss_pred CCCCCCCCCCCCchhhhhhhhhccchhhc-cCCCccccccce--eccCCCHHHHHHHHHHHHHHHHHHHHHCCCCccCC
Q psy5036 57 IMSWHVGSVNFICNFILIGPQGQTKPEAR-SGNEITNKNQMI--QWHSLTREEQAKYYEKARQERQLHMELYPGWSARD 132 (176)
Q Consensus 57 ~~~k~~~~KRPlNAFmLF~ke~R~kv~~e-P~~~~~eISKil--~Wk~Ls~eEK~~Y~~~A~k~ke~h~~~~P~Yk~~~ 132 (176)
...+++.||||++|||+|+.+.|.+|..+ |.+.++||+++| +|++|+++||++|+.+|..++++|+.+.-.|....
T Consensus 64 ~k~dpN~PKRp~sayf~y~~~~R~ei~~~~p~l~~~e~~k~~~e~WK~Ltd~eke~y~k~~~~~~erYq~ek~~y~~k~ 142 (211)
T COG5648 64 KKKDPNGPKRPLSAYFLYSAENRDEIRKENPKLTFGEVGKLLSEKWKELTDEEKEPYYKEANSDRERYQREKEEYNKKL 142 (211)
T ss_pred HhcCCCCCCCchhHHHHHHHHHHHHHHHhCCCCChHHHHHHHHHHHHhccHhhhhhHHHHHhhHHHHHHHHHHhhhccc
Confidence 46788999999999999999999999999 999999999999 99999999999999999999999999999997653
No 14
>KOG0526|consensus
Probab=99.06 E-value=8.3e-11 Score=109.78 Aligned_cols=72 Identities=8% Similarity=0.131 Sum_probs=67.5
Q ss_pred CCCCCCCCCCCCchhhhhhhhhccchhhccCCCccccccce--eccCCCHHHHHHHHHHHHHHHHHHHHHCCCCccC
Q psy5036 57 IMSWHVGSVNFICNFILIGPQGQTKPEARSGNEITNKNQMI--QWHSLTREEQAKYYEKARQERQLHMELYPGWSAR 131 (176)
Q Consensus 57 ~~~k~~~~KRPlNAFmLF~ke~R~kv~~eP~~~~~eISKil--~Wk~Ls~eEK~~Y~~~A~k~ke~h~~~~P~Yk~~ 131 (176)
+.+.+++|||+++|||||.+..|..|+.+ +.+++||+|.+ .|+.|+. |.+|++.|+..|++|+.+|-+|+..
T Consensus 529 k~kdpnapkra~sa~m~w~~~~r~~ik~d-gi~~~dv~kk~g~~wk~ms~--k~~we~ka~~dk~ry~~em~~yk~g 602 (615)
T KOG0526|consen 529 KKKDPNAPKRATSAYMLWLNASRESIKED-GISVGDVAKKAGEKWKQMSA--KEEWEDKAAVDKQRYEDEMKEYKNG 602 (615)
T ss_pred cCCCCCCCccchhHHHHHHHhhhhhHhhc-CchHHHHHHHHhHHHhhhcc--cchhhHHHHHHHHHHHHHHHhhcCC
Confidence 45667899999999999999999999998 89999999999 9999999 9999999999999999999999943
No 15
>KOG2746|consensus
Probab=98.80 E-value=2.4e-09 Score=101.98 Aligned_cols=66 Identities=15% Similarity=0.228 Sum_probs=62.4
Q ss_pred CCCCCCCCCCchhhhhhhhhc--cchhhc-cCCCccccccce--eccCCCHHHHHHHHHHHHHHHHHHHHH
Q psy5036 59 SWHVGSVNFICNFILIGPQGQ--TKPEAR-SGNEITNKNQMI--QWHSLTREEQAKYYEKARQERQLHMEL 124 (176)
Q Consensus 59 ~k~~~~KRPlNAFmLF~ke~R--~kv~~e-P~~~~~eISKil--~Wk~Ls~eEK~~Y~~~A~k~ke~h~~~ 124 (176)
..+.||.|||||||+|++.+| ..+.+. |+..+..|++|| .|-.|.+.||++|.++|.+.++.|-++
T Consensus 177 r~k~HirrPMnaf~ifskrhr~~g~vhq~~pn~DNrtIskiLgewWytL~~~Ekq~yhdLa~Qvk~Ahfka 247 (683)
T KOG2746|consen 177 RDKDHIRRPMNAFHIFSKRHRGEGRVHQRHPNQDNRTISKILGEWWYTLGPNEKQKYHDLAFQVKEAHFKA 247 (683)
T ss_pred CcchhhhhhhHHHHHHHhhcCCccchhccCccccchhHHHHHhhhHhhhCchhhhhHHHHHHHHHHHHhhh
Confidence 456899999999999999999 888888 999999999999 899999999999999999999999987
No 16
>KOG4715|consensus
Probab=98.63 E-value=6.3e-08 Score=86.31 Aligned_cols=72 Identities=14% Similarity=0.205 Sum_probs=68.4
Q ss_pred CCCCCCchhhhhhhhhccchhhc-cCCCccccccce--eccCCCHHHHHHHHHHHHHHHHHHHHHCCCCccCCCC
Q psy5036 63 GSVNFICNFILIGPQGQTKPEAR-SGNEITNKNQMI--QWHSLTREEQAKYYEKARQERQLHMELYPGWSARDNY 134 (176)
Q Consensus 63 ~~KRPlNAFmLF~ke~R~kv~~e-P~~~~~eISKil--~Wk~Ls~eEK~~Y~~~A~k~ke~h~~~~P~Yk~~~n~ 134 (176)
-|-+||-.||.|++...++|++. |.+..-||.|+| +|..|+++||+.|.++++.+|.+|++.|-.|...+-|
T Consensus 64 ppekpl~pymrySrkvWd~VkA~nPe~kLWeiGK~Ig~mW~dLpd~EK~ey~~EYeaEKieY~~smkayh~sp~y 138 (410)
T KOG4715|consen 64 PPEKPLMPYMRYSRKVWDQVKASNPELKLWEIGKIIGGMWLDLPDEEKQEYLNEYEAEKIEYNESMKAYHNSPAY 138 (410)
T ss_pred CCCcccchhhHHhhhhhhhhhccCcchHHHHHHHHHHHHHhhCcchHHHHHHHHHHHHHHHHHHHHHHhhCCchH
Confidence 35689999999999999999999 999999999999 9999999999999999999999999999999888866
No 17
>COG5648 NHP6B Chromatin-associated proteins containing the HMG domain [Chromatin structure and dynamics]
Probab=96.11 E-value=0.0077 Score=51.12 Aligned_cols=69 Identities=20% Similarity=0.359 Sum_probs=62.4
Q ss_pred CCCCCCCCCCchhhhhhhhhccchhhc-cCCCccccccce--eccCCCHHHHHHHHHHHHHHHHHHHHHCCC
Q psy5036 59 SWHVGSVNFICNFILIGPQGQTKPEAR-SGNEITNKNQMI--QWHSLTREEQAKYYEKARQERQLHMELYPG 127 (176)
Q Consensus 59 ~k~~~~KRPlNAFmLF~ke~R~kv~~e-P~~~~~eISKil--~Wk~Ls~eEK~~Y~~~A~k~ke~h~~~~P~ 127 (176)
.++-..++|.-.|+-+..+.|.++... +.....++.+++ .|..|++.-|.+|.+.+.+.+++|...||+
T Consensus 139 ~~k~~~~~~~~~~~e~~~~~r~~~~~~~~~~~~~e~~k~~~~~w~el~~skK~~~~~~~Kk~k~~~~~~~~~ 210 (211)
T COG5648 139 NKKLPNKAPIGPFIENEPKIRPKVEGPSPDKALVEETKIISKAWSELDESKKKKYIDKYKKLKEEYDSFYPE 210 (211)
T ss_pred hcccCCCCCCchhhhccHHhccccCCCCcchhhhHHhhhhhhhhhhhChhhhhHHHHHHHHHHHHHhhhccc
Confidence 444556788899999999999999999 999999999999 999999999999999999999999998874
No 18
>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=94.66 E-value=0.013 Score=48.83 Aligned_cols=48 Identities=19% Similarity=0.209 Sum_probs=40.6
Q ss_pred CchhhhhhhhhccchhhccCCCccccccce--eccCCCHHHHHHHHHHHHHHH
Q psy5036 68 ICNFILIGPQGQTKPEARSGNEITNKNQMI--QWHSLTREEQAKYYEKARQER 118 (176)
Q Consensus 68 lNAFmLF~ke~R~kv~~eP~~~~~eISKil--~Wk~Ls~eEK~~Y~~~A~k~k 118 (176)
-||||=|++++|.+. .++...|+-... .|..|++++|..|..++....
T Consensus 83 nnaYLNFLReFRrkh---~~L~p~dlI~~AAraW~rLSe~eK~rYrr~~~~~~ 132 (183)
T PF06382_consen 83 NNAYLNFLREFRRKH---CGLSPQDLIQRAARAWCRLSEAEKNRYRRMAPSVR 132 (183)
T ss_pred chHHHHHHHHHHHHc---cCCCHHHHHHHHHHHHHhCCHHHHHHHHhhcchhh
Confidence 589999999999876 468888876655 999999999999999877554
No 19
>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=94.28 E-value=0.023 Score=47.88 Aligned_cols=51 Identities=8% Similarity=0.010 Sum_probs=37.3
Q ss_pred CCCCCCCCCCchhhhhhhhhccchhhc-cCCCccccccce--eccCCCHHHHHHHHHHHH
Q psy5036 59 SWHVGSVNFICNFILIGPQGQTKPEAR-SGNEITNKNQMI--QWHSLTREEQAKYYEKAR 115 (176)
Q Consensus 59 ~k~~~~KRPlNAFmLF~ke~R~kv~~e-P~~~~~eISKil--~Wk~Ls~eEK~~Y~~~A~ 115 (176)
....+.+||+|+||+|+.-+- .. ++....++|.+| .|..-. -|..|.-+|.
T Consensus 39 ~~~~~~kr~lN~Fm~FRsyy~----~~~~~~~Qk~~S~~l~~lW~~dp--~k~~W~l~ak 92 (201)
T PF04769_consen 39 RSPEKAKRPLNGFMAFRSYYS----PIFPPLPQKELSGILTKLWEKDP--FKNKWSLMAK 92 (201)
T ss_pred ccccccccchhHHHHHHHHHH----hhcCCcCHHHHHHHHHHHHhCCc--cHhHHHHHhh
Confidence 344567899999999977665 33 778899999999 899733 3555655554
No 20
>PF14887 HMG_box_5: HMG (high mobility group) box 5; PDB: 1L8Y_A 1L8Z_A 2HDZ_A.
Probab=93.57 E-value=0.043 Score=40.33 Aligned_cols=67 Identities=10% Similarity=0.077 Sum_probs=45.3
Q ss_pred CCchhhhhhhhhccchhhc-cCCCccccccce--eccCCCHHHHHHHHHHHHHHHHHHHHHCCCCccCCCC
Q psy5036 67 FICNFILIGPQGQTKPEAR-SGNEITNKNQMI--QWHSLTREEQAKYYEKARQERQLHMELYPGWSARDNY 134 (176)
Q Consensus 67 PlNAFmLF~ke~R~kv~~e-P~~~~~eISKil--~Wk~Ls~eEK~~Y~~~A~k~ke~h~~~~P~Yk~~~n~ 134 (176)
|-+|==||-+.......+. +.-...+.. .+ .|++|++.+|-+|...|.++..+|+..+-+|..-.-.
T Consensus 7 PKt~qe~Wqq~vi~dYla~~~~dr~K~~k-am~~~W~~me~Kekl~WIkKA~EdqKrYE~el~e~r~~~~~ 76 (85)
T PF14887_consen 7 PKTAQEIWQQSVIGDYLAKFRNDRKKALK-AMEAQWSQMEKKEKLKWIKKAAEDQKRYERELREMRSAPAD 76 (85)
T ss_dssp --THHHHHHHHHHHHHHHHTTSTHHHHHH-HHHHHHHTTGGGHHHHHHHHHHHHHHHHHHHHHCCS-CCCT
T ss_pred CCCHHHHHHHHHHHHHHHHhhHhHHHHHH-HHHHHHHHhhhhhhhHHHHHHHHHHHHHHHHHHHHhcCCCC
Confidence 4455556655554444433 333333332 33 8999999999999999999999999999998765433
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=68.01 E-value=2.8 Score=34.64 Aligned_cols=39 Identities=5% Similarity=0.038 Sum_probs=33.7
Q ss_pred CCCCchhhhhhhhhccchhhc-cCCCccccccce--eccCCC
Q psy5036 65 VNFICNFILIGPQGQTKPEAR-SGNEITNKNQMI--QWHSLT 103 (176)
Q Consensus 65 KRPlNAFmLF~ke~R~kv~~e-P~~~~~eISKil--~Wk~Ls 103 (176)
.|-++||=.|+++.-.+|+++ |+++..|+=..+ .|...+
T Consensus 123 qR~psaYn~f~k~ei~rik~~~p~ishkeaFs~aAknW~h~p 164 (170)
T PF04690_consen 123 QRVPSAYNRFMKEEIQRIKAENPDISHKEAFSAAAKNWAHFP 164 (170)
T ss_pred CCCchhHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHhhhhCc
Confidence 466999999999999999999 999999986666 897654
No 22
>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=61.76 E-value=4.6 Score=33.47 Aligned_cols=45 Identities=11% Similarity=0.332 Sum_probs=38.5
Q ss_pred cCCCccccccce---eccCCCHHHHHHHHHHHHH-HHHHHHHHCCCCcc
Q psy5036 86 SGNEITNKNQMI---QWHSLTREEQAKYYEKARQ-ERQLHMELYPGWSA 130 (176)
Q Consensus 86 P~~~~~eISKil---~Wk~Ls~eEK~~Y~~~A~k-~ke~h~~~~P~Yk~ 130 (176)
+-..+..|++.+ -|+.+|+++|+.|.+.... ....|-..+-.|..
T Consensus 62 ~~~Df~~mar~vLG~~W~~~s~~Qr~~F~~~F~~~l~~tY~~~l~~y~~ 110 (198)
T TIGR03481 62 EAFDLPAMARLTLGSSWTSLSPEQRRRFIGAFRELSIATYASQFKSYAG 110 (198)
T ss_pred HhCCHHHHHHHHhhhhhhhCCHHHHHHHHHHHHHHHHHHHHHHHHhhcC
Confidence 667889999977 8999999999999998887 77888888877754
No 23
>PF05494 Tol_Tol_Ttg2: Toluene tolerance, Ttg2 ; InterPro: IPR008869 Toluene tolerance is mediated by increased cell membrane rigidity resulting from changes in fatty acid and phospholipid compositions, exclusion of toluene from the cell membrane, and removal of intracellular toluene by degradation []. Many proteins are involved in these processes. This family is a transporter which shows similarity to ABC transporters [].; PDB: 2QGU_A.
Probab=51.92 E-value=8.3 Score=30.49 Aligned_cols=52 Identities=12% Similarity=0.178 Sum_probs=37.0
Q ss_pred ccchhhc--cCCCccccccce---eccCCCHHHHHHHHHHHHH-HHHHHHHHCCCCcc
Q psy5036 79 QTKPEAR--SGNEITNKNQMI---QWHSLTREEQAKYYEKARQ-ERQLHMELYPGWSA 130 (176)
Q Consensus 79 R~kv~~e--P~~~~~eISKil---~Wk~Ls~eEK~~Y~~~A~k-~ke~h~~~~P~Yk~ 130 (176)
+..|... |-..+..|++.+ -|+.+|+++|+.|.+...+ ....|...+..|..
T Consensus 27 ~~~i~~~v~~~~D~~~~ar~~LG~~w~~~s~~q~~~F~~~f~~~l~~~Y~~~l~~y~~ 84 (170)
T PF05494_consen 27 RAKIEDIVDPYFDFERMARRVLGRYWRKASPAQRQRFVEAFKQLLVRTYAKRLDEYSG 84 (170)
T ss_dssp HHHHHHHTGGGB-HHHHHHHHHGGGTTTS-HHHHHHHHHHHHHHHHHHHHHHHHT-SS
T ss_pred HHHHHHHHHHhCCHHHHHHHHHHHhHhhCCHHHHHHHHHHHHHHHHHHHHHHHHhhCC
Confidence 3444444 777888899877 8999999999999876654 45678888877764
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=50.61 E-value=2.8 Score=28.70 Aligned_cols=36 Identities=6% Similarity=0.236 Sum_probs=30.3
Q ss_pred Cchhhhhhhhhccchhhc-cCCCccccccce--eccCCC
Q psy5036 68 ICNFILIGPQGQTKPEAR-SGNEITNKNQMI--QWHSLT 103 (176)
Q Consensus 68 lNAFmLF~ke~R~kv~~e-P~~~~~eISKil--~Wk~Ls 103 (176)
++.|=+|.+..|+.|... |+...+.|-.+| .|+.-+
T Consensus 13 lt~yK~Fsq~vRP~l~~~NPk~~~sKl~~l~~AKwrEF~ 51 (55)
T PF08073_consen 13 LTNYKAFSQHVRPLLAKANPKAPMSKLMMLLQAKWREFQ 51 (55)
T ss_pred HHHHHHHHHHHHHHHHHHCCCCcHHHHHHHHHHHHHHHH
Confidence 345678999999999999 999999998888 898543
No 25
>PRK15117 ABC transporter periplasmic binding protein MlaC; Provisional
Probab=45.57 E-value=15 Score=30.70 Aligned_cols=52 Identities=10% Similarity=0.176 Sum_probs=40.7
Q ss_pred ccchhhc--cCCCccccccce---eccCCCHHHHHHHHHHHHHH-HHHHHHHCCCCcc
Q psy5036 79 QTKPEAR--SGNEITNKNQMI---QWHSLTREEQAKYYEKARQE-RQLHMELYPGWSA 130 (176)
Q Consensus 79 R~kv~~e--P~~~~~eISKil---~Wk~Ls~eEK~~Y~~~A~k~-ke~h~~~~P~Yk~ 130 (176)
+..|..+ |-..+..+++.+ -|+.+|+|+|+.|.+..+.. ..-|...+-+|..
T Consensus 57 ~~~v~~~l~p~~Df~~~s~~vLG~~wr~as~eQr~~F~~~F~~~Lv~tYa~~l~~y~~ 114 (211)
T PRK15117 57 RTIVDQELLPYVQVKYAGALVLGRYYKDATPAQREAYFAAFREYLKQAYGQALAMYHG 114 (211)
T ss_pred HHHHHHHccccCCHHHHHHHHhhhhhhhCCHHHHHHHHHHHHHHHHHHHHHHHHHhCC
Confidence 3444554 778899999977 89999999999999876654 4578888887754
No 26
>PF12881 NUT_N: NUT protein N terminus; InterPro: IPR024309 This domain is found in the N-terminal region of Nuclear Testis (NUT) proteins. It is also found in FAM22, which are a family of uncharacterised mammalian proteins.
Probab=39.20 E-value=76 Score=28.91 Aligned_cols=58 Identities=16% Similarity=0.114 Sum_probs=37.5
Q ss_pred CCCCCCCCCchhhhhhhhhccchhhc------cC---------------------CCccccccc-e-eccCCCHHHHHHH
Q psy5036 60 WHVGSVNFICNFILIGPQGQTKPEAR------SG---------------------NEITNKNQM-I-QWHSLTREEQAKY 110 (176)
Q Consensus 60 k~~~~KRPlNAFmLF~ke~R~kv~~e------P~---------------------~~~~eISKi-l-~Wk~Ls~eEK~~Y 110 (176)
..+..-.|-+-|--|++.+|=|..+. |+ ++..|--.+ + +|...|.=+|--|
T Consensus 195 ~~d~sc~~ksVYeNfRrWQ~~K~LarrHlpQsPD~EAlSCFLIpvLrsLar~kPtMtlEeGl~ra~qEW~~~SnfdRmif 274 (328)
T PF12881_consen 195 SPDDSCNPKSVYENFRRWQHYKALARRHLPQSPDAEALSCFLIPVLRSLARLKPTMTLEEGLWRAVQEWQHTSNFDRMIF 274 (328)
T ss_pred CcccccccHhHHHHHHHHHHhHHHHHHhCCCCCchhhhhhhHHHHHHHHHhcCCCccHHHHHHHHHHHhhccccccHHHH
Confidence 33444566788888888776543322 22 333332222 2 8999999999999
Q ss_pred HHHHHHH
Q psy5036 111 YEKARQE 117 (176)
Q Consensus 111 ~~~A~k~ 117 (176)
|+||++=
T Consensus 275 yemaekF 281 (328)
T PF12881_consen 275 YEMAEKF 281 (328)
T ss_pred HHHHHHH
Confidence 9999863
No 27
>PF12650 DUF3784: Domain of unknown function (DUF3784); InterPro: IPR017259 This group represents an uncharacterised conserved protein.
Probab=38.06 E-value=26 Score=25.36 Aligned_cols=15 Identities=27% Similarity=0.687 Sum_probs=13.5
Q ss_pred eccCCCHHHHHHHHH
Q psy5036 98 QWHSLTREEQAKYYE 112 (176)
Q Consensus 98 ~Wk~Ls~eEK~~Y~~ 112 (176)
-|+.+|+|||++|.+
T Consensus 25 Gyntms~eEk~~~D~ 39 (97)
T PF12650_consen 25 GYNTMSKEEKEKYDK 39 (97)
T ss_pred hcccCCHHHHHHhhH
Confidence 799999999999964
No 28
>PF01352 KRAB: KRAB box; InterPro: IPR001909 The Krueppel-associated box (KRAB) is a domain of around 75 amino acids that is found in the N-terminal part of about one third of eukaryotic Krueppel-type C2H2 zinc finger proteins (ZFPs) []. It is enriched in charged amino acids and can be divided into subregions A and B, which are predicted to fold into two amphipathic alpha-helices. The KRAB A and B boxes can be separated by variable spacer segments and many KRAB proteins contain only the A box []. The functions currently known for members of the KRAB-containing protein family include transcriptional repression of RNA polymerase I, II, and III promoters, binding and splicing of RNA, and control of nucleolus function. The KRAB domain functions as a transcriptional repressor when tethered to the template DNA by a DNA-binding domain. A sequence of 45 amino acids in the KRAB A subdomain has been shown to be necessary and sufficient for transcriptional repression. The B box does not repress by itself but does potentiate the repression exerted by the KRAB A subdomain [, ]. Gene silencing requires the binding of the KRAB domain to the RING-B box-coiled coil (RBCC) domain of the KAP-1/TIF1-beta corepressor. As KAP-1 binds to the heterochromatin proteins HP1, it has been proposed that the KRAB-ZFP-bound target gene could be silenced following recruitment to heterochromatin [, ]. KRAB-ZFPs probably constitute the single largest class of transcription factors within the human genome []. Although the function of KRAB-ZFPs is largely unknown, they appear to play important roles during cell differentiation and development. The KRAB domain is generally encoded by two exons. The regions coded by the two exons are known as KRAB-A and KRAB-B.; GO: 0003676 nucleic acid binding, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 1V65_A.
Probab=30.82 E-value=42 Score=21.22 Aligned_cols=27 Identities=11% Similarity=0.279 Sum_probs=16.1
Q ss_pred Cccccccce---eccCCCHHHHHHHHHHHH
Q psy5036 89 EITNKNQMI---QWHSLTREEQAKYYEKAR 115 (176)
Q Consensus 89 ~~~eISKil---~Wk~Ls~eEK~~Y~~~A~ 115 (176)
.+.||+--+ +|..|.+.+|.-|.+...
T Consensus 2 tf~Dvav~fs~eEW~~L~~~Qk~ly~dvm~ 31 (41)
T PF01352_consen 2 TFEDVAVYFSQEEWELLDPAQKNLYRDVML 31 (41)
T ss_dssp -----TT---HHHHHTS-HHHHHHHHHHHH
T ss_pred eEEEEEEEcChhhcccccceecccchhHHH
Confidence 355676666 799999999999987653
No 29
>KOG0528|consensus
Probab=28.66 E-value=43 Score=32.11 Aligned_cols=70 Identities=7% Similarity=-0.107 Sum_probs=54.8
Q ss_pred CCCCCCCCCC-Cchhhhhhhhhccchhhc-cCCCccccccce--eccCCCHHHHHHHHHHHHHHHHHHHHHCCCCccCC
Q psy5036 58 MSWHVGSVNF-ICNFILIGPQGQTKPEAR-SGNEITNKNQMI--QWHSLTREEQAKYYEKARQERQLHMELYPGWSARD 132 (176)
Q Consensus 58 ~~k~~~~KRP-lNAFmLF~ke~R~kv~~e-P~~~~~eISKil--~Wk~Ls~eEK~~Y~~~A~k~ke~h~~~~P~Yk~~~ 132 (176)
..-++..++| +|+|+++.. ....| +......|+ +. .|.+.+..-+..|...-..+.+.|...-+.|.+.+
T Consensus 11 ~~~~~s~~~~e~~~~qe~~~----~~~~e~~~s~~q~i~-~~~ql~~~~s~q~~~a~~~~s~~~~q~h~~~q~~~~i~~ 84 (511)
T KOG0528|consen 11 KLQKNSVKLPEVNGTQESLA----EKELELPTSIHQLIS-LRGQLLANHSEQKKLAASDSSAQEQQMHLAEQQQEQIAP 84 (511)
T ss_pred cccccchhcccccccHHhhh----hhhhccCCCcceeee-cchhhcccccccchhhhhhhhHHHHHHHHHHhHHHhhhH
Confidence 4455677888 999998844 33444 666667777 44 89999999999999999999999999998887754
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=26.54 E-value=68 Score=21.01 Aligned_cols=19 Identities=21% Similarity=0.597 Sum_probs=14.6
Q ss_pred eccCCCHHHHHHHHHHHHH
Q psy5036 98 QWHSLTREEQAKYYEKARQ 116 (176)
Q Consensus 98 ~Wk~Ls~eEK~~Y~~~A~k 116 (176)
.|+.|++++|.........
T Consensus 29 ~W~~~s~~er~~i~~~l~~ 47 (51)
T PF06945_consen 29 DWKSMSDDERRAILARLRA 47 (51)
T ss_pred HHhhCCHHHHHHHHHHHHH
Confidence 8999999998776654443
No 31
>PF06244 DUF1014: Protein of unknown function (DUF1014); InterPro: IPR010422 This family consists of several hypothetical eukaryotic proteins of unknown function.
Probab=25.62 E-value=19 Score=28.21 Aligned_cols=39 Identities=10% Similarity=0.276 Sum_probs=33.2
Q ss_pred CCCCchhhhhhhhhccchhhc-cCCCccccccce--eccCCC
Q psy5036 65 VNFICNFILIGPQGQTKPEAR-SGNEITNKNQMI--QWHSLT 103 (176)
Q Consensus 65 KRPlNAFmLF~ke~R~kv~~e-P~~~~~eISKil--~Wk~Ls 103 (176)
+|=--||--|.-.+-+.|++| |++..+.+-.+| +|..-+
T Consensus 74 rR~KAAy~afeE~~Lp~lK~E~PgLrlsQ~kq~l~K~w~KSP 115 (122)
T PF06244_consen 74 RRMKAAYKAFEERRLPELKEENPGLRLSQYKQMLWKEWQKSP 115 (122)
T ss_pred hhHHHHHHHHHHHHhHHHHhhCCCchHHHHHHHHHHHHhcCC
Confidence 344479999999999999999 999999999988 897644
No 32
>PRK09706 transcriptional repressor DicA; Reviewed
Probab=24.94 E-value=36 Score=25.89 Aligned_cols=36 Identities=14% Similarity=0.235 Sum_probs=31.2
Q ss_pred cce-eccCCCHHHHHHHHHHHHHHHHHHHHHCCCCcc
Q psy5036 95 QMI-QWHSLTREEQAKYYEKARQERQLHMELYPGWSA 130 (176)
Q Consensus 95 Kil-~Wk~Ls~eEK~~Y~~~A~k~ke~h~~~~P~Yk~ 130 (176)
.++ .|+.|++++++...++++...+.+.+.|..|-.
T Consensus 91 ~ll~~~~~L~~~~~~~~l~~l~~~~~~~~~~~~~~~~ 127 (135)
T PRK09706 91 ELLELFDALPESEQDAQLSEMRARVENFNKLFEELLK 127 (135)
T ss_pred HHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 344 999999999999999999999999998877743
No 33
>KOG1827|consensus
Probab=23.16 E-value=1.1e+02 Score=30.29 Aligned_cols=41 Identities=12% Similarity=0.106 Sum_probs=36.6
Q ss_pred CCchhhhhhhhhccchhhc-cCCCccccccce--eccCCCHHHH
Q psy5036 67 FICNFILIGPQGQTKPEAR-SGNEITNKNQMI--QWHSLTREEQ 107 (176)
Q Consensus 67 PlNAFmLF~ke~R~kv~~e-P~~~~~eISKil--~Wk~Ls~eEK 107 (176)
=+.++++|..+.|..+..+ |+..+++++.+. .|..|+..-|
T Consensus 552 ~~~~~~~~s~~~~~~~~~~np~v~~~~~~~~vg~~~~~lp~~~k 595 (629)
T KOG1827|consen 552 SPEPYILDSIENRTIIWFENPTVGFGEVSIIVGNDWDKLPNINK 595 (629)
T ss_pred CCccccccccccCceeeeeCCCcccceeEEeecCCcccCccccc
Confidence 4578999999999999999 999999999999 9999994444
No 34
>PF02026 RyR: RyR domain; InterPro: IPR003032 This domain is called RyR for Ryanodine receptor []. The domain is found in four copies in the ryanodine receptor. The function of this domain is unknown.; PDB: 4ETV_A 3RQR_A 4ETT_A 4ERT_A 4ESU_A 4ETU_A 4ERV_A 3NRT_E.
Probab=22.67 E-value=80 Score=23.27 Aligned_cols=21 Identities=24% Similarity=0.370 Sum_probs=17.1
Q ss_pred eccCCCHHHHHHHHHHHHHHH
Q psy5036 98 QWHSLTREEQAKYYEKARQER 118 (176)
Q Consensus 98 ~Wk~Ls~eEK~~Y~~~A~k~k 118 (176)
-|..|+++||+.|.+.+...-
T Consensus 60 py~~L~e~eK~~dr~~~~e~l 80 (94)
T PF02026_consen 60 PYDELSEEEKEKDRDMVRETL 80 (94)
T ss_dssp -GGGS-HHHHHHHHHHHHHHH
T ss_pred ChhhCCHHHHHHhHHHHHHHH
Confidence 899999999999999887753
Done!