Query gi|254780496|ref|YP_003064909.1| integration host factor subunit alpha [Candidatus Liberibacter asiaticus str. psy62] Match_columns 114 No_of_seqs 103 out of 2506 Neff 6.4 Searched_HMMs 33803 Date Wed Jun 1 18:33:03 2011 Command /home/congqian_1/programs/hhpred/hhsearch -i 254780496.hhm -d /home/congqian_1/database/mmdb/mmdb70.hhm No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM 1 >1p71_A DNA-binding protein HU 99.9 2E-25 5.8E-30 177.0 11.2 92 5-96 1-92 (94) 2 >3c4i_A DNA-binding protein HU 99.9 4.6E-25 1.3E-29 174.8 11.6 96 5-100 1-96 (99) 3 >1owf_B IHF-beta, integration 99.9 6.5E-25 1.9E-29 173.8 11.2 92 5-96 1-93 (94) 4 >1mul_A NS2, HU-2, DNA binding 99.9 7.6E-25 2.2E-29 173.4 10.1 90 5-94 1-90 (90) 5 >2o97_B NS1, HU-1, DNA-binding 99.9 8.4E-25 2.5E-29 173.1 9.3 90 5-94 1-90 (90) 6 >2iie_A Integration HOST facto 99.9 2E-24 5.9E-29 170.9 10.8 100 1-100 43-142 (204) 7 >1b8z_A Protein (histonelike p 99.9 7.4E-25 2.2E-29 173.5 8.5 90 5-94 1-90 (90) 8 >1exe_A Transcription factor 1 99.9 5.1E-25 1.5E-29 174.5 3.6 96 5-100 1-96 (99) 9 >1hue_A HU protein; DNA-bindin 99.9 7.9E-24 2.3E-28 167.2 8.3 90 5-94 1-90 (90) 10 >2iie_A Integration HOST facto 99.7 3E-17 8.9E-22 126.9 7.5 70 29-98 127-196 (204) 11 >1owf_A IHF-alpha, integration 99.6 1.4E-15 4.2E-20 116.6 5.5 55 44-98 1-55 (58) 12 >2np2_A HBB; protein-DNA compl 99.5 7E-15 2.1E-19 112.3 4.1 53 44-96 1-54 (56) 13 >1i27_A Transcription factor I 50.0 15 0.00044 18.4 2.9 36 1-36 20-56 (73) 14 >1aip_C EF-TS, elongation fact 44.6 24 0.00071 17.1 3.3 54 5-58 1-66 (137) 15 >1z67_A Hypothetical protein S 41.2 29 0.00085 16.6 5.3 40 8-47 57-96 (117) 16 >2ysk_A Hypothetical protein T 40.6 13 0.00037 18.8 1.4 43 4-46 13-56 (145) 17 >1nha_A TFIIF-alpha, transcrip 35.7 23 0.00068 17.2 2.1 36 1-36 29-65 (82) 18 >2hhv_A DNA polymerase I; DNA 32.7 39 0.0012 15.8 3.9 24 12-35 52-75 (76) 19 >2j37_W Signal recognition par 30.9 42 0.0012 15.6 4.6 32 3-34 67-113 (127) 20 >3g2b_A Coenzyme PQQ synthesis 30.3 43 0.0013 15.5 6.0 36 3-38 15-50 (56) 21 >1o17_A Anthranilate PRT, anth 28.3 47 0.0014 15.3 3.5 30 5-34 1-30 (95) 22 >1w6s_A Methanol dehydrogenase 27.8 26 0.00076 16.9 1.3 17 63-79 56-72 (73) 23 >1dul_A Signal recognition par 26.4 51 0.0015 15.1 4.2 32 3-34 20-61 (69) 24 >1brw_A PYNP, protein (pyrimid 26.3 51 0.0015 15.1 3.5 30 5-34 1-30 (191) 25 >2kfn_A Klenow fragment of DNA 26.3 37 0.0011 16.0 1.8 24 12-35 52-75 (76) 26 >1tk9_A Phosphoheptose isomera 25.8 40 0.0012 15.8 1.9 48 7-54 3-53 (188) 27 >2hye_C Cullin-4A, CUL-4A; bet 25.6 52 0.0015 15.0 3.3 33 2-34 34-68 (86) 28 >2heo_A Z-DNA binding protein 25.2 53 0.0016 15.0 4.1 38 11-56 28-65 (67) 29 >1qzx_A SRP54, signal recognit 24.0 56 0.0017 14.8 4.0 32 3-34 19-60 (69) 30 >2do7_A Cullin-4B, CUL-4B; hel 23.4 58 0.0017 14.8 4.4 33 2-34 43-77 (101) 31 >2ftc_E Mitochondrial ribosoma 22.1 42 0.0012 15.6 1.5 37 6-42 15-52 (72) 32 >1hq1_A Signal recognition par 22.0 61 0.0018 14.6 4.0 32 3-34 54-95 (105) 33 >2v3c_C SRP54, signal recognit 21.8 62 0.0018 14.6 4.6 32 3-34 68-109 (123) 34 >2wvr_C DNA replication factor 21.3 23 0.00068 17.2 0.0 38 3-40 471-510 (546) 35 >2cp9_A EF-TS, EF-TSMT, elonga 20.8 65 0.0019 14.4 3.2 31 8-38 10-40 (64) 36 >2e7j_A SEP-tRNA:Cys-tRNA synt 20.8 65 0.0019 14.4 3.4 21 18-38 98-118 (120) 37 >3dm5_A SRP54, signal recognit 20.5 66 0.002 14.4 4.4 33 3-35 68-110 (131) No 1 >>1p71_A DNA-binding protein HU; protein-DNA complex, DNA bending, DNA binding protein/DNA complex; 1.90A {Anabaena SP} (A:) Probab=99.93 E-value=2e-25 Score=177.03 Aligned_cols=92 Identities=21% Similarity=0.520 Sum_probs=90.6 Q ss_pred CCHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCEEEEEEECCCCCCCCCCCCCEEEECCCCEEEEC Q ss_conf 66999999999971999999999999999999999755996000041699985026764306889888995688537761 Q gi|254780496|r 5 ITRSDLVKSISKEFGLSRKDSTRFVTTLFNEICDSAVRGEAIKISSFATFHVKQKGSRVGRNLQTNQEVKIDPRRVVVFK 84 (114) Q Consensus 5 mtK~eli~~ia~~~g~s~~~~~~~v~~~~~~i~~~L~~g~~V~l~gfGtF~~~~~~~R~~rNP~Tge~i~ip~k~~v~Fk 84 (114) |||+|||+.||+++++++.+++.++++|+++|.++|.+|+.|+|+|||+|+++.+++|.++||+|||.+.||++++|+|+ T Consensus 1 MtK~eli~~ia~~~~ls~~~v~~~i~~~~~~i~~~L~~~~~V~l~~fG~F~v~~~~~r~~~Np~Tge~i~i~~~~~v~Fk 80 (94) T 1p71_A 1 MNKGELVDAVAEKASVTKKQADAVLTAALETIIEAVSSGDKVTLVGFGSFESRERKAREGRNPKTNEKMEIPATRVPAFS 80 (94) T ss_dssp CBHHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHHHHHTTCCEEETTTEEEEEEEECCEEEECTTTCCEEEECCEEEEEEE T ss_pred CCHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHCCCCCEECCEEEEEEEEECCCEEECCCCCCEEEECCCCCEEEE T ss_conf 98899999999845979999999999999999999864886050352699999836723289799978996487408995 Q ss_pred CCHHHHHHHHHH Q ss_conf 698999997311 Q gi|254780496|r 85 ASSILKKRIMDD 96 (114) Q Consensus 85 psk~Lk~~in~~ 96 (114) ||+.|+++||+. T Consensus 81 psk~lk~~in~~ 92 (94) T 1p71_A 81 AGKLFREKVAPP 92 (94) T ss_dssp ECHHHHHHHSCC T ss_pred CCHHHHHHHCCC T ss_conf 498999975778 No 2 >>3c4i_A DNA-binding protein HU homolog; dimerization by four helix bundle interaction, DNA condensation; 2.04A {Mycobacterium tuberculosis} (A:) Probab=99.92 E-value=4.6e-25 Score=174.78 Aligned_cols=96 Identities=23% Similarity=0.508 Sum_probs=93.0 Q ss_pred CCHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCEEEEEEECCCCCCCCCCCCCEEEECCCCEEEEC Q ss_conf 66999999999971999999999999999999999755996000041699985026764306889888995688537761 Q gi|254780496|r 5 ITRSDLVKSISKEFGLSRKDSTRFVTTLFNEICDSAVRGEAIKISSFATFHVKQKGSRVGRNLQTNQEVKIDPRRVVVFK 84 (114) Q Consensus 5 mtK~eli~~ia~~~g~s~~~~~~~v~~~~~~i~~~L~~g~~V~l~gfGtF~~~~~~~R~~rNP~Tge~i~ip~k~~v~Fk 84 (114) |||+|||..||+++|+++.++..+|++|+++|.++|.+|+.|+|+|||+|+++.+++|.++||+|||.+.||++++|+|+ T Consensus 1 Mtk~eli~~ia~~~~~s~~~v~~~i~~~~~~i~~~L~~g~~V~l~~fG~F~~~~~~~r~~~np~T~e~i~i~~k~~v~Fk 80 (99) T 3c4i_A 1 MNKAELIDVLTQKLGSDRRQATAAVENVVDTIVRAVHKGDSVTITGFGVFEQRRRAARVARNPRTGETVKVKPTSVPAFR 80 (99) T ss_dssp CBHHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHHHHHTTCCEEETTTEEEEEEEECSEEEECTTTCCEEEECCEEEEEEE T ss_pred CCHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHCCCCEECCCEEEEEEEEECCEEEECCCCCCEEEECCCCEEEEE T ss_conf 97899999999874989999999999999999999964996131556899998756811068599988986387228996 Q ss_pred CCHHHHHHHHHHHCCC Q ss_conf 6989999973111013 Q gi|254780496|r 85 ASSILKKRIMDDMRGR 100 (114) Q Consensus 85 psk~Lk~~in~~~~~~ 100 (114) ||+.|++.||...... T Consensus 81 psk~Lk~~in~~~~~~ 96 (99) T 3c4i_A 81 PGAQFKAVVSGAQRLP 96 (99) T ss_dssp ECHHHHHHHHTSSCCC T ss_pred CCHHHHHHHCCCCCCC T ss_conf 2989999866666899 No 3 >>1owf_B IHF-beta, integration HOST factor beta-subunit; protein-DNA recognition, indirect readout, DNA bending, minor groove; 1.95A {Escherichia coli} (B:) Probab=99.92 E-value=6.5e-25 Score=173.83 Aligned_cols=92 Identities=24% Similarity=0.437 Sum_probs=89.8 Q ss_pred CCHHHHHHHHHHH-CCCCHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCEEEEEEECCCCCCCCCCCCCEEEECCCCEEEE Q ss_conf 6699999999997-199999999999999999999975599600004169998502676430688988899568853776 Q gi|254780496|r 5 ITRSDLVKSISKE-FGLSRKDSTRFVTTLFNEICDSAVRGEAIKISSFATFHVKQKGSRVGRNLQTNQEVKIDPRRVVVF 83 (114) Q Consensus 5 mtK~eli~~ia~~-~g~s~~~~~~~v~~~~~~i~~~L~~g~~V~l~gfGtF~~~~~~~R~~rNP~Tge~i~ip~k~~v~F 83 (114) |||+|||+.|+++ +++++.+++.++++|+++|.++|.+|++|+|+|||+|+++.+++|.++||+|||.+.||++++|+| T Consensus 1 MtK~eli~~ia~~~~~~sk~~~~~~v~~~~~~i~~~L~~~~~V~l~gfG~F~~~~r~~r~~~nP~Tge~~~ip~k~~v~F 80 (94) T 1owf_B 1 MTKSELIERLATQQSHIPAKTVEDAVKEMLEHMASTLAQGERIAIRGFGSFSLHYRAPRTGRNPKTGDKVELEGKYVPHF 80 (94) T ss_dssp CBHHHHHHHHHHHCTTSCHHHHHHHHHHHHHHHHHHHHTTCCEEETTTEEEEEEEECCEEEECTTTCCEEEECCEEEEEE T ss_pred CCHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHCCCEEEECCCEEEEEEEECCCCCCCCCCCCEEEECCCCCEEE T ss_conf 97899999999876999999999999999999999997699599657379999860683333849999898648631898 Q ss_pred CCCHHHHHHHHHH Q ss_conf 1698999997311 Q gi|254780496|r 84 KASSILKKRIMDD 96 (114) Q Consensus 84 kpsk~Lk~~in~~ 96 (114) +||+.||+.||.. T Consensus 81 kpsk~lk~~vn~~ 93 (94) T 1owf_B 81 KPGKELRDRANIY 93 (94) T ss_dssp EECHHHHHHHCCC T ss_pred ECCHHHHHHHCCC T ss_conf 1698999987559 No 4 >>1mul_A NS2, HU-2, DNA binding protein HU-alpha; histone-like; HET: DNA; 2.30A {Escherichia coli} (A:) Probab=99.92 E-value=7.6e-25 Score=173.42 Aligned_cols=90 Identities=28% Similarity=0.506 Sum_probs=88.6 Q ss_pred CCHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCEEEEEEECCCCCCCCCCCCCEEEECCCCEEEEC Q ss_conf 66999999999971999999999999999999999755996000041699985026764306889888995688537761 Q gi|254780496|r 5 ITRSDLVKSISKEFGLSRKDSTRFVTTLFNEICDSAVRGEAIKISSFATFHVKQKGSRVGRNLQTNQEVKIDPRRVVVFK 84 (114) Q Consensus 5 mtK~eli~~ia~~~g~s~~~~~~~v~~~~~~i~~~L~~g~~V~l~gfGtF~~~~~~~R~~rNP~Tge~i~ip~k~~v~Fk 84 (114) |||+|||+.|++++|+++.+++.+|++|+++|.++|.+|+.|+|+|||+|+++.+++|.++||+|||.+.||+|++|+|+ T Consensus 1 Mtk~eli~~ia~~~~~s~~~v~~~v~~~~~~i~~~L~~~~~v~l~~fG~F~v~~r~~r~~~Np~Tge~i~ip~k~~v~Fr 80 (90) T 1mul_A 1 MNKTQLIDVIAEKAELSKTQAKAALESTLAAITESLKEGDAVQLVGFGTFKVNHRAERTGRNPQTGKEIKIAAANVPAFV 80 (90) T ss_dssp CCHHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHHHHHTTCCEEETTTEEEEEEEECC--------------CCEEEEEEE T ss_pred CCHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHCCCCCEEEEEEEEEEEECCCEEEECCCCCCEEEECCCCCEEEE T ss_conf 97899999999704969999999999999999999971998772036999998628843089399978997487408997 Q ss_pred CCHHHHHHHH Q ss_conf 6989999973 Q gi|254780496|r 85 ASSILKKRIM 94 (114) Q Consensus 85 psk~Lk~~in 94 (114) ||+.|++.|. T Consensus 81 p~k~lk~~i~ 90 (90) T 1mul_A 81 SGKALKDAVK 90 (90) T ss_dssp ECHHHHHHHC T ss_pred CCHHHHHHHC T ss_conf 2989998639 No 5 >>2o97_B NS1, HU-1, DNA-binding protein HU-beta; heterodimer, DNA structure, DNA supercoiling, E. coli; 2.45A {Escherichia coli} (B:) Probab=99.92 E-value=8.4e-25 Score=173.14 Aligned_cols=90 Identities=28% Similarity=0.517 Sum_probs=89.3 Q ss_pred CCHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCEEEEEEECCCCCCCCCCCCCEEEECCCCEEEEC Q ss_conf 66999999999971999999999999999999999755996000041699985026764306889888995688537761 Q gi|254780496|r 5 ITRSDLVKSISKEFGLSRKDSTRFVTTLFNEICDSAVRGEAIKISSFATFHVKQKGSRVGRNLQTNQEVKIDPRRVVVFK 84 (114) Q Consensus 5 mtK~eli~~ia~~~g~s~~~~~~~v~~~~~~i~~~L~~g~~V~l~gfGtF~~~~~~~R~~rNP~Tge~i~ip~k~~v~Fk 84 (114) |||+|||+.|++++++++++++.++++|++.|.++|.+|++|+|+|||+|+++.+++|.++||+|||.+.||+|++|+|+ T Consensus 1 Mtk~eli~~ia~~~~~t~~~v~~~v~~~~~~i~~~L~~~~~V~l~~fG~F~v~~~~~r~~~np~tge~~~i~~k~~v~Fk 80 (90) T 2o97_B 1 MNKSQLIDKIAAGADISKAAAGRALDAIIASVTESLKEGDDVALVGFGTFAVKERAARTGRNPQTGKEITIAAAKVPSFR 80 (90) T ss_dssp CBHHHHHHHHHHTTC-CHHHHHHHHHHHHHHHHHHHHTTCCEEETTTEEEEEECCC------------------CEEEEE T ss_pred CCHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHCCCCCCCCEEEEEEEEECCCEEECCCCCCEEEECCCCEEEEE T ss_conf 97899999999720999999999999999999999980764445505899998405640288999978995386228996 Q ss_pred CCHHHHHHHH Q ss_conf 6989999973 Q gi|254780496|r 85 ASSILKKRIM 94 (114) Q Consensus 85 psk~Lk~~in 94 (114) ||+.|++.|| T Consensus 81 p~k~lk~~iN 90 (90) T 2o97_B 81 AGKALKDAVN 90 (90) T ss_dssp ECHHHHHHCC T ss_pred CCHHHHHHHC T ss_conf 3989997629 No 6 >>2iie_A Integration HOST factor; DNA kinking, bending, U-turn, intercalation, divalent, metal, recombination/DNA complex; HET: DNA; 2.41A {Escherichia coli} PDB: 2iif_A* (A:) Probab=99.91 E-value=2e-24 Score=170.86 Aligned_cols=100 Identities=32% Similarity=0.583 Sum_probs=90.7 Q ss_pred CCCCCCHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCEEEEEEECCCCCCCCCCCCCEEEECCCCE Q ss_conf 98766699999999997199999999999999999999975599600004169998502676430688988899568853 Q gi|254780496|r 1 MSKTITRSDLVKSISKEFGLSRKDSTRFVTTLFNEICDSAVRGEAIKISSFATFHVKQKGSRVGRNLQTNQEVKIDPRRV 80 (114) Q Consensus 1 m~~~mtK~eli~~ia~~~g~s~~~~~~~v~~~~~~i~~~L~~g~~V~l~gfGtF~~~~~~~R~~rNP~Tge~i~ip~k~~ 80 (114) |.++|||+|||+.||+++|+++++++.+|++|+++|.++|.+|+.|+|+|||+|+++.+++|.++||+|||.+.+|++++ T Consensus 43 ~~~~MtK~eLi~~ia~~~glskk~a~~ii~~~~~~I~e~L~~g~~V~l~gfGtF~v~~r~~R~~rNP~Tge~i~i~~kk~ 122 (204) T 2iie_A 43 GSGGLTKAEMSEYLFDKLGLSKRDAKELVELFFEEIRRALENGEQVKLSGFGNFDLRDKNQRPGRNPKTGEDIPITARRV 122 (204) T ss_dssp CSSSBCHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHTTCEEEETTTEEEEEEEECCBCCBCTTTCCBCCBCCEEE T ss_pred CCCCCCHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHCCCCEEEEEEEEEEEEEECCCCCCCCCCCCEEEECCCCC T ss_conf 56883599999999998697999999999999999999996699256511589999876471123889998898648651 Q ss_pred EEECCCHHHHHHHHHHHCCC Q ss_conf 77616989999973111013 Q gi|254780496|r 81 VVFKASSILKKRIMDDMRGR 100 (114) Q Consensus 81 v~Fkpsk~Lk~~in~~~~~~ 100 (114) |+|+||+.|+..++....+. T Consensus 123 vkFk~~k~LK~iveaL~~ge 142 (204) T 2iie_A 123 VTFRPGQKLKSRVENAGGGE 142 (204) T ss_dssp EEEEECHHHHHHHHHHCCCC T ss_pred EEEEECHHHHHHHHCCCCCC T ss_conf 79995479998864134465 No 7 >>1b8z_A Protein (histonelike protein HU); thermostable DNA binding protein; 1.60A {Thermotoga maritima} (A:) Probab=99.91 E-value=7.4e-25 Score=173.50 Aligned_cols=90 Identities=28% Similarity=0.556 Sum_probs=89.3 Q ss_pred CCHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCEEEEEEECCCCCCCCCCCCCEEEECCCCEEEEC Q ss_conf 66999999999971999999999999999999999755996000041699985026764306889888995688537761 Q gi|254780496|r 5 ITRSDLVKSISKEFGLSRKDSTRFVTTLFNEICDSAVRGEAIKISSFATFHVKQKGSRVGRNLQTNQEVKIDPRRVVVFK 84 (114) Q Consensus 5 mtK~eli~~ia~~~g~s~~~~~~~v~~~~~~i~~~L~~g~~V~l~gfGtF~~~~~~~R~~rNP~Tge~i~ip~k~~v~Fk 84 (114) |||+|||..|++++++++++++.++++|++.|.++|.+|++|+|+|||+|+++.+++|.++||+|||.+.||++++|+|+ T Consensus 1 Mtk~eli~~ia~~~~~s~~~~~~~v~~~~~~i~~~L~~~~~V~l~~fG~F~v~~~~~r~~~np~tge~i~i~~k~~v~Fk 80 (90) T 1b8z_A 1 MNKKELIDRVAKKAGAKKKDVKLILDTILETITEALAKGEKVQIVGFGSFEVRKAAARKGVNPQTRKPITIPERKVPKFK 80 (90) T ss_dssp CCHHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHHHHHTTCCEEETTTEEEEC-----------------------CCEEE T ss_pred CCHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHCCCCEECCEEEEEEECCCCEEEECCCCCCEEEECCCCEEEEE T ss_conf 97899999999854989999999999999999999872886374665789886135444457999988986387218997 Q ss_pred CCHHHHHHHH Q ss_conf 6989999973 Q gi|254780496|r 85 ASSILKKRIM 94 (114) Q Consensus 85 psk~Lk~~in 94 (114) ||+.||+.|| T Consensus 81 ~sk~Lk~~in 90 (90) T 1b8z_A 81 PGKALKEKVK 90 (90) T ss_dssp ECHHHHHHHC T ss_pred ECHHHHHHHC T ss_conf 3899998639 No 8 >>1exe_A Transcription factor 1; beta ribbon ARMS, DNA-binding, DNA-bending protein; NMR {Bacillus phage SPO1} (A:) Probab=99.90 E-value=5.1e-25 Score=174.47 Aligned_cols=96 Identities=21% Similarity=0.381 Sum_probs=92.8 Q ss_pred CCHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCEEEEEEECCCCCCCCCCCCCEEEECCCCEEEEC Q ss_conf 66999999999971999999999999999999999755996000041699985026764306889888995688537761 Q gi|254780496|r 5 ITRSDLVKSISKEFGLSRKDSTRFVTTLFNEICDSAVRGEAIKISSFATFHVKQKGSRVGRNLQTNQEVKIDPRRVVVFK 84 (114) Q Consensus 5 mtK~eli~~ia~~~g~s~~~~~~~v~~~~~~i~~~L~~g~~V~l~gfGtF~~~~~~~R~~rNP~Tge~i~ip~k~~v~Fk 84 (114) |||+|||..|++++++++.+++.++++|+++|.++|.+|+.|+|+|||+|+++.+++|.++||+|||.+.||++++|+|+ T Consensus 1 Mtk~eli~~ia~~~~~s~~~v~~~i~~~~~~i~~~L~~g~~V~l~gfG~F~v~~~~~r~~~np~Tge~i~i~~k~~v~Fk 80 (99) T 1exe_A 1 MNKTELIKAIAQDTGLTQVSVSKMLASFEKIITETVAKGDKVQLTGFLNIKPVARQARKGFNPQTQEALEIAPSVGVSVK 80 (99) T ss_dssp CCTTHHHHHHHHHHCSCCTTHHHHHHHHHHHHHHHHHHTCCCCBTTTBCCCCCCCCCCCCCCSSSSSCCCCCCCCCCCCC T ss_pred CCHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHCCCEEEECCCEEEEEEEECCCCCCCCCCCCEEEECCCCCEEEE T ss_conf 98899999999986969999999999999999999968995997367899987555734478999988984285347993 Q ss_pred CCHHHHHHHHHHHCCC Q ss_conf 6989999973111013 Q gi|254780496|r 85 ASSILKKRIMDDMRGR 100 (114) Q Consensus 85 psk~Lk~~in~~~~~~ 100 (114) ||+.||+.||...... T Consensus 81 psk~LK~~in~~~~~~ 96 (99) T 1exe_A 81 PGESLKKAAEGLKYED 96 (99) T ss_dssp CCHHHHHHHHHHTHHH T ss_pred CCHHHHHHHCCCCHHH T ss_conf 4989999882898544 No 9 >>1hue_A HU protein; DNA-binding; NMR {Geobacillus stearothermophilus} (A:) Probab=99.90 E-value=7.9e-24 Score=167.19 Aligned_cols=90 Identities=30% Similarity=0.628 Sum_probs=88.5 Q ss_pred CCHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCEEEEEEECCCCCCCCCCCCCEEEECCCCEEEEC Q ss_conf 66999999999971999999999999999999999755996000041699985026764306889888995688537761 Q gi|254780496|r 5 ITRSDLVKSISKEFGLSRKDSTRFVTTLFNEICDSAVRGEAIKISSFATFHVKQKGSRVGRNLQTNQEVKIDPRRVVVFK 84 (114) Q Consensus 5 mtK~eli~~ia~~~g~s~~~~~~~v~~~~~~i~~~L~~g~~V~l~gfGtF~~~~~~~R~~rNP~Tge~i~ip~k~~v~Fk 84 (114) |||+|||..|++++++++.+++.++++|++.|.++|.+|+.|+|+|||+|+++.+++|.++||+|||.+.+|++++|+|+ T Consensus 1 Mtk~~li~~i~~~~~~s~~~v~~~i~~~~~~i~~~L~~~~~v~l~~fG~F~v~~~~~r~~~Np~Tge~~~i~~k~~vkFr 80 (90) T 1hue_A 1 MNKTELINAVAETSGLSKKDATKAVDAVFDSITEALRKGDKVQLIGFGNFEVRERAARKGRNPQTGEEMEIPASKVPAFK 80 (90) T ss_dssp CBSHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHTCCCCBTTTBEECCCCCCCCEEECSSSSSEEECCCCCCCCEE T ss_pred CCHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHCCCEEEEECCEEEEEEEECCCCCCCCCCCCEEEECCCCEEEEE T ss_conf 97899999999854989999999999999999999965982884024399998616844558399988995487418981 Q ss_pred CCHHHHHHHH Q ss_conf 6989999973 Q gi|254780496|r 85 ASSILKKRIM 94 (114) Q Consensus 85 psk~Lk~~in 94 (114) ||+.|++.|. T Consensus 81 ~sk~lk~~ik 90 (90) T 1hue_A 81 PGKALKDAVK 90 (90) T ss_dssp CTTHHHHHTC T ss_pred CCHHHHHHHC T ss_conf 3989998639 No 10 >>2iie_A Integration HOST factor; DNA kinking, bending, U-turn, intercalation, divalent, metal, recombination/DNA complex; HET: DNA; 2.41A {Escherichia coli} PDB: 2iif_A* (A:) Probab=99.70 E-value=3e-17 Score=126.85 Aligned_cols=70 Identities=26% Similarity=0.361 Sum_probs=65.5 Q ss_pred HHHHHHHHHHHHHCCCCCCCCCCEEEEEEECCCCCCCCCCCCCEEEECCCCEEEECCCHHHHHHHHHHHC Q ss_conf 9999999999975599600004169998502676430688988899568853776169899999731110 Q gi|254780496|r 29 VTTLFNEICDSAVRGEAIKISSFATFHVKQKGSRVGRNLQTNQEVKIDPRRVVVFKASSILKKRIMDDMR 98 (114) Q Consensus 29 v~~~~~~i~~~L~~g~~V~l~gfGtF~~~~~~~R~~rNP~Tge~i~ip~k~~v~Fkpsk~Lk~~in~~~~ 98 (114) ...+++.+.+++..++.|.|+|||+|+++.+++|.||||+|||.|.||++++|+|+||+.||++||.... T Consensus 127 ~~k~LK~iveaL~~ge~V~i~~fG~F~~~~r~~R~grNP~Tge~i~Ipa~~~~~Fk~~k~lk~~vn~~~~ 196 (204) T 2iie_A 127 PGQKLKSRVENAGGGERIEIRGFGSFSLHYRAPRTGRNPKTGDKVELEGKYVPHFKPGKELRDRANIYGG 196 (204) T ss_dssp ECHHHHHHHHHHCCCCCEEETTTEEEEEEEECCEEEECTTTCCEEEECCEEEEEEEECHHHHHHHCSSCC T ss_pred ECHHHHHHHHCCCCCCCCCCCCEEEEEEEECCCCCCCCCCCCCEEEECCCCCEEECCCHHHHHHHCCCCC T ss_conf 5479998864134465422265688998740673561929999888659753687878899998757999 No 11 >>1owf_A IHF-alpha, integration HOST factor alpha-subunit; protein-DNA recognition, indirect readout, DNA bending, minor groove; 1.95A {Escherichia coli} (A:42-99) Probab=99.59 E-value=1.4e-15 Score=116.60 Aligned_cols=55 Identities=36% Similarity=0.657 Sum_probs=52.1 Q ss_pred CCCCCCCCEEEEEEECCCCCCCCCCCCCEEEECCCCEEEECCCHHHHHHHHHHHC Q ss_conf 9600004169998502676430688988899568853776169899999731110 Q gi|254780496|r 44 EAIKISSFATFHVKQKGSRVGRNLQTNQEVKIDPRRVVVFKASSILKKRIMDDMR 98 (114) Q Consensus 44 ~~V~l~gfGtF~~~~~~~R~~rNP~Tge~i~ip~k~~v~Fkpsk~Lk~~in~~~~ 98 (114) ++|.|+|||+|+++.+++|.||||+|||.|.||++++|+|+||+.|+++||+... T Consensus 1 ekV~l~gfGtF~~~~r~~R~grNP~Tge~i~I~ak~~v~Fk~sk~Lk~~vn~~~~ 55 (58) T 1owf_A 1 EQVKLSGFGNFDLRDKNQRPGRNPKTGEDIPITARRVVTFRPGQKLKSRVENASP 55 (58) T ss_dssp CCEEETTTEEEEEEEECCEEEECSSSCCEEEECCEEEEEEEECHHHHHHHHTCCC T ss_pred CEEEECCEEEEEEEEECCCCCCCCCCCCEEEECCCCEEEEEECHHHHHHHHCCCC T ss_conf 9799511379999876682125889998899538722899749999999807896 No 12 >>2np2_A HBB; protein-DNA complex, DNA-binding protein, DNA-bending protein, dnabii family, HU/IHF family, DNA binding protein/DNA complex; 3.02A {Borrelia burgdorferi} (A:53-108) Probab=99.52 E-value=7e-15 Score=112.33 Aligned_cols=53 Identities=34% Similarity=0.484 Sum_probs=50.2 Q ss_pred CCCCCCCCEEEEEEECCCC-CCCCCCCCCEEEECCCCEEEECCCHHHHHHHHHH Q ss_conf 9600004169998502676-4306889888995688537761698999997311 Q gi|254780496|r 44 EAIKISSFATFHVKQKGSR-VGRNLQTNQEVKIDPRRVVVFKASSILKKRIMDD 96 (114) Q Consensus 44 ~~V~l~gfGtF~~~~~~~R-~~rNP~Tge~i~ip~k~~v~Fkpsk~Lk~~in~~ 96 (114) ++|.|+|||+|+++.+++| .||||+|||.|.||++++|+|+||+.||++||+. T Consensus 1 d~V~l~gFGtF~~~~r~~R~~grNP~Tge~i~I~a~~v~~Fk~~k~lk~~vn~~ 54 (56) T 2np2_A 1 NVIEFRSFGTFEVRKRKGRLNARNPQTGEYVKVLDHHVAYFRPGKDLKERVWGI 54 (56) T ss_dssp CEEEETTTEEEEEEEECCBSSCBCTTTCCBCCBCCEEEEEEEECHHHHHHHHSC T ss_pred CEEEEEEEEEEEEEEECCCCCCCCCCCCCEEEECCCCCEEECCCHHHHHHHHCC T ss_conf 969984468999973047655538899988985387567874898999997067 No 13 >>1i27_A Transcription factor IIF; general transcription factor, RAP74, RAP30, TFIIF, RNA polymerase II, winged-helix domain; 1.02A {Homo sapiens} (A:) Probab=50.05 E-value=15 Score=18.40 Aligned_cols=36 Identities=25% Similarity=0.486 Sum_probs=26.9 Q ss_pred CCCCCCHHHHHHHHH-HHCCCCHHHHHHHHHHHHHHH Q ss_conf 987666999999999-971999999999999999999 Q gi|254780496|r 1 MSKTITRSDLVKSIS-KEFGLSRKDSTRFVTTLFNEI 36 (114) Q Consensus 1 m~~~mtK~eli~~ia-~~~g~s~~~~~~~v~~~~~~i 36 (114) |.+-||-.||+.... .++|++..+...++..++.-| T Consensus 20 ~rKP~TT~eLl~KFk~k~t~l~~~e~v~~~a~ILkkI 56 (73) T 1i27_A 20 TRKPMTTKDLLKKFQTKKTGLSSEQTVNVLAQILKRL 56 (73) T ss_dssp HHSCBCHHHHHHTSCHHHHCCCHHHHHHHHHHHHHHH T ss_pred HCCCCCHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHH T ss_conf 3188728999999853244774488899999999972 No 14 >>1aip_C EF-TS, elongation factor TS; nucleotide exchange, GTP-binding, complex of two elongation factors; 3.00A {Thermus thermophilus} (C:1-104,C:164-196) Probab=44.57 E-value=24 Score=17.11 Aligned_cols=54 Identities=11% Similarity=0.131 Sum_probs=37.4 Q ss_pred CCHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHH------------HHHCCCCCCCCCCEEEEEEE Q ss_conf 6699999999997199999999999999999999------------97559960000416999850 Q gi|254780496|r 5 ITRSDLVKSISKEFGLSRKDSTRFVTTLFNEICD------------SAVRGEAIKISSFATFHVKQ 58 (114) Q Consensus 5 mtK~eli~~ia~~~g~s~~~~~~~v~~~~~~i~~------------~L~~g~~V~l~gfGtF~~~~ 58 (114) |...++|+.|-++||.+..++++.++..-.-+.. +-....++.-.|+....+.. T Consensus 1 mis~e~IK~LR~~Tgagi~dCKkAL~es~gDiekAi~~Lrk~G~~kA~Kk~~r~t~eG~v~~~v~~ 66 (137) T 1aip_C 1 MSQMELIKKLREATGAGMMDVKRALEDAGWDEEKAVQLLRERGAMKAAKKADREAREGIIGHYIHH 66 (137) T ss_dssp -CHHHHHHHHHHHHCCCHHHHHHHHHHTTTCHHHHHHHHHHHHHHHHHHHTTSCCCCCEEEEEECT T ss_pred CCCHHHHHHHHHHHCCCHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHCEEEEEEEC T ss_conf 984799999999869889999999998499899999999987776777877799874100047854 No 15 >>1z67_A Hypothetical protein S4005; structural genomics, PSI, protein structure initiative, midwest center for structural genomics, MCSG; 1.45A {Shigella flexneri 2a str} (A:19-135) Probab=41.18 E-value=29 Score=16.61 Aligned_cols=40 Identities=10% Similarity=0.315 Sum_probs=35.2 Q ss_pred HHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHCCCCCC Q ss_conf 9999999997199999999999999999999975599600 Q gi|254780496|r 8 SDLVKSISKEFGLSRKDSTRFVTTLFNEICDSAVRGEAIK 47 (114) Q Consensus 8 ~eli~~ia~~~g~s~~~~~~~v~~~~~~i~~~L~~g~~V~ 47 (114) .|-+..+|.++|++..++...+..++=.+.+.+.-+++|. T Consensus 57 ~d~i~~lA~k~Gl~~~~~~~~La~~LP~~VD~lTP~G~~p 96 (117) T 1z67_A 57 TNAVSDLGQKLGVDTSTASSLLAEQLPKIIDALSPQGEVS 96 (117) T ss_dssp HHHHHHHHHHHTCCHHHHHHHHHHHHHHHHHHTCTTSCC- T ss_pred HHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHCCCCCCCC T ss_conf 5999999999891999999999999779997119899899 No 16 >>2ysk_A Hypothetical protein TTHA1432; conserved hypothetical, NPPSFA, national project on protein structural and functional analyses; 1.90A {Thermus thermophilus HB8} (A:) Probab=40.57 E-value=13 Score=18.80 Aligned_cols=43 Identities=16% Similarity=0.220 Sum_probs=32.5 Q ss_pred CCCHHHHHHHHHHHCCC-CHHHHHHHHHHHHHHHHHHHHCCCCC Q ss_conf 66699999999997199-99999999999999999997559960 Q gi|254780496|r 4 TITRSDLVKSISKEFGL-SRKDSTRFVTTLFNEICDSAVRGEAI 46 (114) Q Consensus 4 ~mtK~eli~~ia~~~g~-s~~~~~~~v~~~~~~i~~~L~~g~~V 46 (114) .|...++++.+.++.|+ +..++..++.+.+.++.+.|..++.. T Consensus 13 ~~~~~~fl~~V~~~~~~~~~~~A~~a~raVL~~Lr~RL~~~ea~ 56 (145) T 2ysk_A 13 LHKTHAWLKAIMEELGTEDRHKAYLALRAVLHALRDRLTVEEVA 56 (145) T ss_dssp HHHHHHHHHHHHHHHTCCCHHHHHHHHHHHHHHHHTTSCHHHHH T ss_pred HHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHCCHHHHH T ss_conf 99999999999998389988999999999999999877867899 No 17 >>1nha_A TFIIF-alpha, transcription initiation factor IIF, alpha subunit; transcription factor, human general transcription factor TFIIF, RAP74; NMR {Homo sapiens} (A:) Probab=35.67 E-value=23 Score=17.20 Aligned_cols=36 Identities=22% Similarity=0.457 Sum_probs=26.7 Q ss_pred CCCCCCHHHHHHHHHHH-CCCCHHHHHHHHHHHHHHH Q ss_conf 98766699999999997-1999999999999999999 Q gi|254780496|r 1 MSKTITRSDLVKSISKE-FGLSRKDSTRFVTTLFNEI 36 (114) Q Consensus 1 m~~~mtK~eli~~ia~~-~g~s~~~~~~~v~~~~~~i 36 (114) |.+-||-.||+.....+ +|++..+...++..++.-| T Consensus 29 ~rkP~Tt~eLl~KFk~k~t~l~~~e~v~~~a~ILkkI 65 (82) T 1nha_A 29 TRKPMTTKDLLKKFQTKKTGLSSEQTVNVLAQILKRL 65 (82) T ss_dssp HHSCBCHHHHHHHTTSSCCSSCHHHHHHHHHHHHHHH T ss_pred HHCCCCHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHC T ss_conf 7189739999999986246788599999999999970 No 18 >>2hhv_A DNA polymerase I; DNA replication, klenow fragment, protein- DNA complex, O6-methyl-guanine, transferase/DNA complex; HET: DNA 6OG SUC; 1.55A {Geobacillus stearothermophilus} (A:372-447) Probab=32.72 E-value=39 Score=15.78 Aligned_cols=24 Identities=21% Similarity=0.592 Sum_probs=21.1 Q ss_pred HHHHHHCCCCHHHHHHHHHHHHHH Q ss_conf 999997199999999999999999 Q gi|254780496|r 12 KSISKEFGLSRKDSTRFVTTLFNE 35 (114) Q Consensus 12 ~~ia~~~g~s~~~~~~~v~~~~~~ 35 (114) ..|+++.|++..++..+++.|+.. T Consensus 52 ~~La~~lgis~~eA~~~i~~f~~~ 75 (76) T 2hhv_A 52 YGLAQNLNISRKEAAEFIERYFES 75 (76) T ss_dssp HHHHHHHTCCHHHHHHHHHHHHHH T ss_pred CCCCHHHCCCHHHHHHHHHHHHHH T ss_conf 444502023388888888778777 No 19 >>2j37_W Signal recognition particle 54 kDa protein (SRP54); ribosome, SRP, translation/RNA; 8.00A {Canis SP} PDB: 1wgw_A (W:314-440) Probab=30.94 E-value=42 Score=15.60 Aligned_cols=32 Identities=16% Similarity=0.432 Sum_probs=26.4 Q ss_pred CCCCHHHH---------------HHHHHHHCCCCHHHHHHHHHHHHH Q ss_conf 76669999---------------999999719999999999999999 Q gi|254780496|r 3 KTITRSDL---------------VKSISKEFGLSRKDSTRFVTTLFN 34 (114) Q Consensus 3 ~~mtK~el---------------i~~ia~~~g~s~~~~~~~v~~~~~ 34 (114) .+||..|+ +.+||.-+|.+..+|..++..|.. T Consensus 67 ~SMT~~Er~~P~~i~~~~~~~SR~~RIA~GSG~~~~eV~~Ll~~~~~ 113 (127) T 2j37_W 67 DSMNDQELDSTDGAKVFSKQPGRIQRVARGSGVSTRDVQELLTQYTK 113 (127) T ss_dssp TTSCHHHHHCTTHHHHHHHCTHHHHHHHHHTTCCHHHHHHHHHHHHH T ss_pred HCCCHHHHCCCCHHHHCCCCCHHHHHHHCCCCCCHHHHHHHHHHHHH T ss_conf 51698774396301111567018888556699999999999999999 No 20 >>3g2b_A Coenzyme PQQ synthesis protein D; helix-turn-helix, PQQ biosynthesis, biosynthetic protein; 1.66A {Xanthomonas campestris PV} (A:40-95) Probab=30.31 E-value=43 Score=15.53 Aligned_cols=36 Identities=14% Similarity=0.216 Sum_probs=31.5 Q ss_pred CCCCHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHH Q ss_conf 766699999999997199999999999999999999 Q gi|254780496|r 3 KTITRSDLVKSISKEFGLSRKDSTRFVTTLFNEICD 38 (114) Q Consensus 3 ~~mtK~eli~~ia~~~g~s~~~~~~~v~~~~~~i~~ 38 (114) ..-|-.+|+..++++.+....+++.-|..|+..+.+ T Consensus 15 g~~tv~~I~~~L~~~y~~~~~~~~~dv~~fl~~L~~ 50 (56) T 3g2b_A 15 GTQSLAQIAQTLAAEFDADASEIETDVIELTTTLHQ 50 (56) T ss_dssp SSSCHHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHH T ss_pred CCCCHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHH T ss_conf 986599999999999698888999999999999998 No 21 >>1o17_A Anthranilate PRT, anthranilate phosphoribosyltransferase, TRPD; nucleoside-phosphorylases; 2.05A {Sulfolobus solfataricus} (A:1-74,A:156-176) Probab=28.32 E-value=47 Score=15.32 Aligned_cols=30 Identities=7% Similarity=0.290 Sum_probs=25.0 Q ss_pred CCHHHHHHHHHHHCCCCHHHHHHHHHHHHH Q ss_conf 669999999999719999999999999999 Q gi|254780496|r 5 ITRSDLVKSISKEFGLSRKDSTRFVTTLFN 34 (114) Q Consensus 5 mtK~eli~~ia~~~g~s~~~~~~~v~~~~~ 34 (114) |+=++++..+...-.+|.+++..+++.+++ T Consensus 1 M~~k~iL~kl~~g~~LT~eE~~~~~~~il~ 30 (95) T 1o17_A 1 MNINEILKKLINKSDLEINEAEELAKAIIR 30 (95) T ss_dssp CCHHHHHHHHHTTCCCCHHHHHHHHHHHHT T ss_pred CCHHHHHHHHHCCCCCCHHHHHHHHHHHHC T ss_conf 988999999866999699999999999987 No 22 >>1w6s_A Methanol dehydrogenase subunit 1; anisotropic, electron transfer, oxidoreductase, calcium- binding, methanol utilization, PQQ; HET: PQQ; 1.2A {Methylobacterium extorquens} (A:304-376) Probab=27.81 E-value=26 Score=16.90 Aligned_cols=17 Identities=24% Similarity=0.155 Sum_probs=14.3 Q ss_pred CCCCCCCCCEEEECCCC Q ss_conf 43068898889956885 Q gi|254780496|r 63 VGRNLQTNQEVKIDPRR 79 (114) Q Consensus 63 ~~rNP~Tge~i~ip~k~ 79 (114) .+.+|+||.+|+.|++. T Consensus 56 ~gid~ktGrPi~~p~~~ 72 (73) T 1w6s_A 56 KSVDLKTGQPVRDPEYG 72 (73) T ss_dssp EEECTTTCCEEECGGGC T ss_pred CCCCCCCCCCCCCCCCC T ss_conf 54221244321173002 No 23 >>1dul_A Signal recognition particle protein (fifty-four homolog); protein-RNA complex, double helix, tetraloop, internal loop, SRP, ribonucleoprotein; HET: CCC; 1.80A {Escherichia coli} (A:) Probab=26.36 E-value=51 Score=15.11 Aligned_cols=32 Identities=16% Similarity=0.273 Sum_probs=26.6 Q ss_pred CCCCHHHH----------HHHHHHHCCCCHHHHHHHHHHHHH Q ss_conf 76669999----------999999719999999999999999 Q gi|254780496|r 3 KTITRSDL----------VKSISKEFGLSRKDSTRFVTTLFN 34 (114) Q Consensus 3 ~~mtK~el----------i~~ia~~~g~s~~~~~~~v~~~~~ 34 (114) .+||..|+ +..||.-+|.+..+|..++..|.. T Consensus 20 ~SMT~~Er~~p~~l~~sR~~RIArGSG~~~~eV~~Ll~q~~~ 61 (69) T 1dul_A 20 NSXTXKERAKPEIIKGSRKRRIAAGSGXQVQDVNRLLKQFDD 61 (69) T ss_dssp HTSCHHHHHCGGGCCHHHHHHHHHHTTCCHHHHHHHHHHHHH T ss_pred HCCCHHHHHCHHHHCHHHHHHHHCCCCCCHHHHHHHHHHHHH T ss_conf 818999984926302159999982589989999999999999 No 24 >>1brw_A PYNP, protein (pyrimidine nucleoside phosphorylase); domain movement; HET: MES; 2.10A {Bacillus stearothermophilus} (A:1-94,A:156-242,A:424-433) Probab=26.31 E-value=51 Score=15.10 Aligned_cols=30 Identities=17% Similarity=0.213 Sum_probs=24.8 Q ss_pred CCHHHHHHHHHHHCCCCHHHHHHHHHHHHH Q ss_conf 669999999999719999999999999999 Q gi|254780496|r 5 ITRSDLVKSISKEFGLSRKDSTRFVTTLFN 34 (114) Q Consensus 5 mtK~eli~~ia~~~g~s~~~~~~~v~~~~~ 34 (114) |+-+++++.+.....|+.+++..+++.+++ T Consensus 1 M~i~eli~kl~~G~~Ls~eEa~~~i~~il~ 30 (191) T 1brw_A 1 MRMVDLIAKKRDGKALTKEEIEWIVRGYTN 30 (191) T ss_dssp CCHHHHHHHHHTTCCCCHHHHHHHHHHHHT T ss_pred CCHHHHHHHHHCCCCCCHHHHHHHHHHHHC T ss_conf 987999999877999699999999999986 No 25 >>2kfn_A Klenow fragment of DNA polymerase I; complex (polymerase/DNA), exonuclease, transferase, transferase/DNA complex; HET: US1; 2.03A {Escherichia coli} (A:397-472) Probab=26.29 E-value=37 Score=15.97 Aligned_cols=24 Identities=13% Similarity=0.544 Sum_probs=20.5 Q ss_pred HHHHHHCCCCHHHHHHHHHHHHHH Q ss_conf 999997199999999999999999 Q gi|254780496|r 12 KSISKEFGLSRKDSTRFVTTLFNE 35 (114) Q Consensus 12 ~~ia~~~g~s~~~~~~~v~~~~~~ 35 (114) ..|+++.|++..+++.+++.|+.. T Consensus 52 ~~La~~lgis~~eA~~~i~~f~~~ 75 (76) T 2kfn_A 52 FGLARQLNIPRKEAQKYMDLYFER 75 (76) T ss_dssp THHHHHHTCCTTTHHHHHHHHHHH T ss_pred HHHHHHCCCCHHHHHHHHHHHHHH T ss_conf 789988397999999999999865 No 26 >>1tk9_A Phosphoheptose isomerase 1; lipopolysaccharide biosynthesis, structural genomics, NYSGXRC, LPC1_camje, PSI, protein structure initiative; 2.10A {Campylobacter jejuni} (A:) Probab=25.82 E-value=40 Score=15.77 Aligned_cols=48 Identities=17% Similarity=0.114 Sum_probs=32.6 Q ss_pred HHHHHHHHHHHCCCCHHHHHHHHH---HHHHHHHHHHHCCCCCCCCCCEEE Q ss_conf 999999999971999999999999---999999999755996000041699 Q gi|254780496|r 7 RSDLVKSISKEFGLSRKDSTRFVT---TLFNEICDSAVRGEAIKISSFATF 54 (114) Q Consensus 7 K~eli~~ia~~~g~s~~~~~~~v~---~~~~~i~~~L~~g~~V~l~gfGtF 54 (114) -.++++.+.+...-....++..++ ..++.+.+.|.++++|.+-|.|.= T Consensus 3 ~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~rI~~~G~G~S 53 (188) T 1tk9_A 3 LINLVEKEWQEHQKIVQASEILKGQIAKVGELLCECLKKGGKILICGNGGS 53 (188) T ss_dssp HHHHHHHHHHHHHHHHHHGGGGHHHHHHHHHHHHHHHHTTCCEEEEESTHH T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCEEEEEECCCC T ss_conf 699999999999999999887199999999999999985998999916887 No 27 >>2hye_C Cullin-4A, CUL-4A; beta propeller, ring finger, zinc finger, propeller cluster, helical repeats, cullin repeats, protein binding; HET: DNA; 3.10A {Homo sapiens} (C:674-759) Probab=25.60 E-value=52 Score=15.02 Aligned_cols=33 Identities=18% Similarity=0.310 Sum_probs=27.5 Q ss_pred CCCCCHHHHHHHHHHHCC--CCHHHHHHHHHHHHH Q ss_conf 876669999999999719--999999999999999 Q gi|254780496|r 2 SKTITRSDLVKSISKEFG--LSRKDSTRFVTTLFN 34 (114) Q Consensus 2 ~~~mtK~eli~~ia~~~g--~s~~~~~~~v~~~~~ 34 (114) .++|+-.||+..+..... .+..+++..++.|++ T Consensus 34 ~k~l~~~eL~~~v~~~l~f~p~~~~iK~~Ie~LIe 68 (86) T 2hye_C 34 RKTLGHNLLVSELYNQLKFPVKPGDLKKRIESLID 68 (86) T ss_dssp SSEEETHHHHHHHHHHSSSCCCHHHHHHHHHHHHH T ss_pred CCCCCHHHHHHHHHHHHCCCCCHHHHHHHHHHHHH T ss_conf 58888999999999982799999999999999970 No 28 >>2heo_A Z-DNA binding protein 1; protein DLM1/Z-DNA complex, immune system/DNA complex; 1.70A {Mus musculus} PDB: 1j75_A (A:) Probab=25.24 E-value=53 Score=14.98 Aligned_cols=38 Identities=8% Similarity=0.157 Sum_probs=28.7 Q ss_pred HHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCEEEEE Q ss_conf 9999997199999999999999999999975599600004169998 Q gi|254780496|r 11 VKSISKEFGLSRKDSTRFVTTLFNEICDSAVRGEAIKISSFATFHV 56 (114) Q Consensus 11 i~~ia~~~g~s~~~~~~~v~~~~~~i~~~L~~g~~V~l~gfGtF~~ 56 (114) ...|++.+|++++++.+++.. |...+.|..+.=+.|.+ T Consensus 28 a~~Iae~lgv~kkeV~k~L~~--------Lkkeg~I~~~~r~~w~l 65 (67) T 2heo_A 28 IFQLVKKCQVPKKTLNQVLYR--------LKKEDRVSSPSPKYWSI 65 (67) T ss_dssp HHHHHHHHCSCHHHHHHHHHH--------HHHTTSEEEEETTEEEE T ss_pred HHHHHHHHCCCHHHHHHHHHH--------HHHCCCCCCCCCCCCCC T ss_conf 999999978888999999999--------98774805899862047 No 29 >>1qzx_A SRP54, signal recognition 54 kDa protein; signal recognition particle, protein targeting, signaling protein; 4.00A {Sulfolobus solfataricus} (A:372-440) Probab=24.03 E-value=56 Score=14.84 Aligned_cols=32 Identities=19% Similarity=0.334 Sum_probs=26.5 Q ss_pred CCCCHHHH----------HHHHHHHCCCCHHHHHHHHHHHHH Q ss_conf 76669999----------999999719999999999999999 Q gi|254780496|r 3 KTITRSDL----------VKSISKEFGLSRKDSTRFVTTLFN 34 (114) Q Consensus 3 ~~mtK~el----------i~~ia~~~g~s~~~~~~~v~~~~~ 34 (114) .+||..|+ +..||.-+|.+..+|..++..|.. T Consensus 19 dSMT~~Er~~p~ll~~sR~~RIA~GSG~~~~eV~~Ll~q~~~ 60 (69) T 1qzx_A 19 NSMTYKELENPNIIDKSRMRRIAEGSGLEVEEVRELLEWYNN 60 (69) T ss_dssp HSCBHHHHHCGGGCCHHHHHHHHHHHTCCHHHHHHHHHHHHH T ss_pred HCCCHHHHHCCHHHCHHHHHHHHCCCCCCHHHHHHHHHHHHH T ss_conf 738999872934114479999775599999999999999999 No 30 >>2do7_A Cullin-4B, CUL-4B; helix-turn-helix motif, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} (A:) Probab=23.42 E-value=58 Score=14.77 Aligned_cols=33 Identities=18% Similarity=0.348 Sum_probs=27.4 Q ss_pred CCCCCHHHHHHHHHHHCCC--CHHHHHHHHHHHHH Q ss_conf 8766699999999997199--99999999999999 Q gi|254780496|r 2 SKTITRSDLVKSISKEFGL--SRKDSTRFVTTLFN 34 (114) Q Consensus 2 ~~~mtK~eli~~ia~~~g~--s~~~~~~~v~~~~~ 34 (114) .++|+-.||+..+.....+ +..+++..++.|++ T Consensus 43 ~K~l~~~eL~~~V~~~l~F~p~~~~iKk~Ie~LIe 77 (101) T 2do7_A 43 RKTLSHNLLVSEVYNQLKFPVKPADLKKRIESLID 77 (101) T ss_dssp SSEEEHHHHHHHHHHHCSSCCCHHHHHHHHHHHHH T ss_pred CCCCCHHHHHHHHHHHHCCCCCHHHHHHHHHHHHH T ss_conf 06475999999999985699999999999999981 No 31 >>2ftc_E Mitochondrial ribosomal protein L7/12, mitochondrial 39S ribosomal protein L3; mitochondrial ribosome, large ribosomal subunit, ribosomal RNA; 12.10A {Bos taurus} (E:66-137) Probab=22.06 E-value=42 Score=15.61 Aligned_cols=37 Identities=22% Similarity=0.364 Sum_probs=30.0 Q ss_pred CHHHHHHHHHH-HCCCCHHHHHHHHHHHHHHHHHHHHC Q ss_conf 69999999999-71999999999999999999999755 Q gi|254780496|r 6 TRSDLVKSISK-EFGLSRKDSTRFVTTLFNEICDSAVR 42 (114) Q Consensus 6 tK~eli~~ia~-~~g~s~~~~~~~v~~~~~~i~~~L~~ 42 (114) +|-.+|+.|-. -+|++-.++..+++.+=..|.+.+.. T Consensus 15 kKi~vIK~vr~~~tglgL~eAK~lVe~~P~~ike~v~k 52 (72) T 2ftc_E 15 DKVKLIKEIKNYVQGINLVQAKKLVESLPQEIKANVAK 52 (72) T ss_pred CHHHHHHHHHHHCCCCCHHHHHHHHHHCCHHHHCCCCH T ss_conf 14579999998717998799999987088888708999 No 32 >>1hq1_A Signal recognition particle protein; protein-RNA complex, double helix, tetraloop, internal loop, SRP, ribonucleoprotein; HET: CCC; 1.52A {Escherichia coli} (A:) Probab=22.00 E-value=61 Score=14.59 Aligned_cols=32 Identities=16% Similarity=0.311 Sum_probs=26.1 Q ss_pred CCCCHHHH----------HHHHHHHCCCCHHHHHHHHHHHHH Q ss_conf 76669999----------999999719999999999999999 Q gi|254780496|r 3 KTITRSDL----------VKSISKEFGLSRKDSTRFVTTLFN 34 (114) Q Consensus 3 ~~mtK~el----------i~~ia~~~g~s~~~~~~~v~~~~~ 34 (114) .+||+.|+ +.+||.-+|.+..+|..++..|-. T Consensus 54 ~SMT~~Er~~p~ll~~sR~~RIA~GSG~~~~eV~~Ll~q~~~ 95 (105) T 1hq1_A 54 NSMTMKERAKPEIIKGSRKRRIAAGSGMQVQDVNRLLKQFDD 95 (105) T ss_dssp HTSCHHHHHCGGGCCHHHHHHHHHHHTCCHHHHHHHHHHHHH T ss_pred HHCCHHHHCCCCCCCCCHHHHHHCCCCCCHHHHHHHHHHHHH T ss_conf 867999880952366344678764489899999999999999 No 33 >>2v3c_C SRP54, signal recognition 54 kDa protein; nucleotide-binding, signal recognition particle, GTP-binding, RNA-binding; 2.50A {Methanocaldococcus jannaschii} (C:310-432) Probab=21.77 E-value=62 Score=14.56 Aligned_cols=32 Identities=13% Similarity=0.294 Sum_probs=26.6 Q ss_pred CCCCHHHH----------HHHHHHHCCCCHHHHHHHHHHHHH Q ss_conf 76669999----------999999719999999999999999 Q gi|254780496|r 3 KTITRSDL----------VKSISKEFGLSRKDSTRFVTTLFN 34 (114) Q Consensus 3 ~~mtK~el----------i~~ia~~~g~s~~~~~~~v~~~~~ 34 (114) ++||..|+ +.+||.-+|.+..+|..++..|-. T Consensus 68 ~SMT~~Er~~P~ll~~SR~~RIA~GSG~~~~eVn~Llkq~~~ 109 (123) T 2v3c_C 68 SSMTKEERENPKIIKASRIRRIARGSGTTENDVREVLRYYET 109 (123) T ss_dssp TTSCHHHHSSCTTCCHHHHHHHHHHTTSCHHHHHHHHHHHHH T ss_pred HCCCHHHHHCCCCCCHHHHHHHHCCCCCCHHHHHHHHHHHHH T ss_conf 728999873940014689989774599999999999999999 No 34 >>2wvr_C DNA replication factor CDT1; DNA replication license, DNA replication inhibitor, phosphoprotein, UBL conjugation, DNA-binding, polymorphism; HET: DNA; 3.30A {Homo sapiens} PDB: 2klo_A* (C:) Probab=21.27 E-value=23 Score=17.20 Aligned_cols=38 Identities=8% Similarity=-0.010 Sum_probs=30.2 Q ss_pred CCCCHHHHHHHHHHHC--CCCHHHHHHHHHHHHHHHHHHH Q ss_conf 7666999999999971--9999999999999999999997 Q gi|254780496|r 3 KTITRSDLVKSISKEF--GLSRKDSTRFVTTLFNEICDSA 40 (114) Q Consensus 3 ~~mtK~eli~~ia~~~--g~s~~~~~~~v~~~~~~i~~~L 40 (114) ..|+..+|+..|.+.. .++..|+++.|+.|.+++-+-| T Consensus 471 ~~~~~~~~~~~i~~s~~~~~~~~e~~~~l~~l~~~~p~~~ 510 (546) T 2wvr_C 471 PALSMEVACARMVGSCCTIMSPGEMEKHLLLLSELLPDWL 510 (546) T ss_dssp ---------------------------------------- T ss_pred CCCCHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHCCCCE T ss_conf 7507999999999854576999999999999998687206 No 35 >>2cp9_A EF-TS, EF-TSMT, elongation factor TS, mitochondrial; UBA, structural genomics, human, NPPSFA; NMR {Homo sapiens} (A:) Probab=20.82 E-value=65 Score=14.44 Aligned_cols=31 Identities=13% Similarity=0.215 Sum_probs=24.8 Q ss_pred HHHHHHHHHHCCCCHHHHHHHHHHHHHHHHH Q ss_conf 9999999997199999999999999999999 Q gi|254780496|r 8 SDLVKSISKEFGLSRKDSTRFVTTLFNEICD 38 (114) Q Consensus 8 ~eli~~ia~~~g~s~~~~~~~v~~~~~~i~~ 38 (114) .++|+.|-++||.+..++.+.+...-.-|.. T Consensus 10 ~~~ik~LR~~Tga~~~dCKkAL~e~~gD~~~ 40 (64) T 2cp9_A 10 KELLMKLRRKTGYSFVNCKKALETCGGDLKQ 40 (64) T ss_dssp CHHHHHHHHHHCCCHHHHHHHHHHHTSCHHH T ss_pred HHHHHHHHHHHCCCHHHHHHHHHHCCCCHHH T ss_conf 9999999999698899999999993899999 No 36 >>2e7j_A SEP-tRNA:Cys-tRNA synthase; seven-stranded BETE-strand, lyase, structural genomics, NPPSFA; HET: PLP; 2.40A {Archaeoglobus fulgidus} (A:1-18,A:270-371) Probab=20.80 E-value=65 Score=14.44 Aligned_cols=21 Identities=19% Similarity=0.320 Sum_probs=17.7 Q ss_pred CCCCHHHHHHHHHHHHHHHHH Q ss_conf 199999999999999999999 Q gi|254780496|r 18 FGLSRKDSTRFVTTLFNEICD 38 (114) Q Consensus 18 ~g~s~~~~~~~v~~~~~~i~~ 38 (114) .|++.++++.++|+|.+++.+ T Consensus 98 YGl~~eqv~yv~daF~EIaek 118 (120) T 2e7j_A 98 YGLSDEEVDYVLNAFKEIIEK 118 (120) T ss_dssp TTCCHHHHHHHHHHHHHHHHH T ss_pred CCCCHHHHHHHHHHHHHHHHH T ss_conf 789999999999999999998 No 37 >>3dm5_A SRP54, signal recognition 54 kDa protein; protein-RNA, signal recognition particle, SRP-GTPase, protein targeting, cytoplasm, GTP-binding; HET: GDP; 2.51A {Pyrococcus furiosus} (A:313-443) Probab=20.54 E-value=66 Score=14.41 Aligned_cols=33 Identities=24% Similarity=0.391 Sum_probs=26.8 Q ss_pred CCCCHHHH----------HHHHHHHCCCCHHHHHHHHHHHHHH Q ss_conf 76669999----------9999997199999999999999999 Q gi|254780496|r 3 KTITRSDL----------VKSISKEFGLSRKDSTRFVTTLFNE 35 (114) Q Consensus 3 ~~mtK~el----------i~~ia~~~g~s~~~~~~~v~~~~~~ 35 (114) ++||..|+ +.+||.-+|.+..+|..++..|-.. T Consensus 68 ~SMT~~Er~~p~ll~~sR~~RIA~GSG~~~~dVn~Llk~~~~~ 110 (131) T 3dm5_A 68 DSMTEEELLNPEIINYSRIKRIARGSGTSTKDVKELLDQYRQM 110 (131) T ss_dssp TTSCHHHHHCGGGCCHHHHHHHHHHHTSCHHHHHHHHHHHHHH T ss_pred HCCCHHHHHCCCCCCHHHHHHHHCCCCCCHHHHHHHHHHHHHH T ss_conf 7399998739401366899998753898999999999999999 Done!