RPS-BLAST 2.2.22 [Sep-27-2009] Database: mmdb70 33,805 sequences; 4,956,049 total letters Searching..................................................done Query= gi|254780496|ref|YP_003064909.1| integration host factor subunit alpha [Candidatus Liberibacter asiaticus str. psy62] (114 letters) >1mul_A NS2, HU-2, DNA binding protein HU-alpha; histone-like; HET: DNA; 2.30A {Escherichia coli} (A:) Length = 90 Score = 82.1 bits (203), Expect = 3e-17 Identities = 25/89 (28%), Positives = 46/89 (51%) Query: 5 ITRSDLVKSISKEFGLSRKDSTRFVTTLFNEICDSAVRGEAIKISSFATFHVKQKGSRVG 64 + ++ L+ I+++ LS+ + + + I +S G+A+++ F TF V + R G Sbjct: 1 MNKTQLIDVIAEKAELSKTQAKAALESTLAAITESLKEGDAVQLVGFGTFKVNHRAERTG 60 Query: 65 RNLQTNQEVKIDPRRVVVFKASSILKKRI 93 RN QT +E+KI V F + LK + Sbjct: 61 RNPQTGKEIKIAAANVPAFVSGKALKDAV 89 >2o97_B NS1, HU-1, DNA-binding protein HU-beta; heterodimer, DNA structure, DNA supercoiling, E. coli; 2.45A {Escherichia coli} (B:) Length = 90 Score = 81.8 bits (202), Expect = 3e-17 Identities = 25/88 (28%), Positives = 46/88 (52%) Query: 6 TRSDLVKSISKEFGLSRKDSTRFVTTLFNEICDSAVRGEAIKISSFATFHVKQKGSRVGR 65 +S L+ I+ +S+ + R + + + +S G+ + + F TF VK++ +R GR Sbjct: 2 NKSQLIDKIAAGADISKAAAGRALDAIIASVTESLKEGDDVALVGFGTFAVKERAARTGR 61 Query: 66 NLQTNQEVKIDPRRVVVFKASSILKKRI 93 N QT +E+ I +V F+A LK + Sbjct: 62 NPQTGKEITIAAAKVPSFRAGKALKDAV 89 >1p71_A DNA-binding protein HU; protein-DNA complex, DNA bending, DNA binding protein/DNA complex; 1.90A {Anabaena SP} (A:) Length = 94 Score = 81.8 bits (202), Expect = 3e-17 Identities = 19/89 (21%), Positives = 52/89 (58%) Query: 5 ITRSDLVKSISKEFGLSRKDSTRFVTTLFNEICDSAVRGEAIKISSFATFHVKQKGSRVG 64 + + +LV +++++ +++K + +T I ++ G+ + + F +F +++ +R G Sbjct: 1 MNKGELVDAVAEKASVTKKQADAVLTAALETIIEAVSSGDKVTLVGFGSFESRERKAREG 60 Query: 65 RNLQTNQEVKIDPRRVVVFKASSILKKRI 93 RN +TN++++I RV F A + ++++ Sbjct: 61 RNPKTNEKMEIPATRVPAFSAGKLFREKV 89 >1b8z_A Protein (histonelike protein HU); thermostable DNA binding protein; 1.60A {Thermotoga maritima} (A:) Length = 90 Score = 81.4 bits (201), Expect = 3e-17 Identities = 25/88 (28%), Positives = 49/88 (55%) Query: 6 TRSDLVKSISKEFGLSRKDSTRFVTTLFNEICDSAVRGEAIKISSFATFHVKQKGSRVGR 65 + +L+ ++K+ G +KD + T+ I ++ +GE ++I F +F V++ +R G Sbjct: 2 NKKELIDRVAKKAGAKKKDVKLILDTILETITEALAKGEKVQIVGFGSFEVRKAAARKGV 61 Query: 66 NLQTNQEVKIDPRRVVVFKASSILKKRI 93 N QT + + I R+V FK LK+++ Sbjct: 62 NPQTRKPITIPERKVPKFKPGKALKEKV 89 >1hue_A HU protein; DNA-binding; NMR {Geobacillus stearothermophilus} (A:) Length = 90 Score = 80.2 bits (198), Expect = 9e-17 Identities = 27/88 (30%), Positives = 56/88 (63%) Query: 6 TRSDLVKSISKEFGLSRKDSTRFVTTLFNEICDSAVRGEAIKISSFATFHVKQKGSRVGR 65 +++L+ ++++ GLS+KD+T+ V +F+ I ++ +G+ +++ F F V+++ +R GR Sbjct: 2 NKTELINAVAETSGLSKKDATKAVDAVFDSITEALRKGDKVQLIGFGNFEVRERAARKGR 61 Query: 66 NLQTNQEVKIDPRRVVVFKASSILKKRI 93 N QT +E++I +V FK LK + Sbjct: 62 NPQTGEEMEIPASKVPAFKPGKALKDAV 89 >3c4i_A DNA-binding protein HU homolog; dimerization by four helix bundle interaction, DNA condensation; 2.04A {Mycobacterium tuberculosis} (A:) Length = 99 Score = 79.5 bits (196), Expect = 1e-16 Identities = 21/88 (23%), Positives = 49/88 (55%) Query: 6 TRSDLVKSISKEFGLSRKDSTRFVTTLFNEICDSAVRGEAIKISSFATFHVKQKGSRVGR 65 +++L+ ++++ G R+ +T V + + I + +G+++ I+ F F +++ +RV R Sbjct: 2 NKAELIDVLTQKLGSDRRQATAAVENVVDTIVRAVHKGDSVTITGFGVFEQRRRAARVAR 61 Query: 66 NLQTNQEVKIDPRRVVVFKASSILKKRI 93 N +T + VK+ P V F+ + K + Sbjct: 62 NPRTGETVKVKPTSVPAFRPGAQFKAVV 89 >1owf_B IHF-beta, integration HOST factor beta-subunit; protein-DNA recognition, indirect readout, DNA bending, minor groove; 1.95A {Escherichia coli} (B:) Length = 94 Score = 78.7 bits (194), Expect = 2e-16 Identities = 22/90 (24%), Positives = 45/90 (50%), Gaps = 1/90 (1%) Query: 5 ITRSDLVKSISKEF-GLSRKDSTRFVTTLFNEICDSAVRGEAIKISSFATFHVKQKGSRV 63 +T+S+L++ ++ + + K V + + + +GE I I F +F + + R Sbjct: 1 MTKSELIERLATQQSHIPAKTVEDAVKEMLEHMASTLAQGERIAIRGFGSFSLHYRAPRT 60 Query: 64 GRNLQTNQEVKIDPRRVVVFKASSILKKRI 93 GRN +T +V+++ + V FK L+ R Sbjct: 61 GRNPKTGDKVELEGKYVPHFKPGKELRDRA 90 >1exe_A Transcription factor 1; beta ribbon ARMS, DNA-binding, DNA-bending protein; NMR {Bacillus phage SPO1} (A:) Length = 99 Score = 78.3 bits (193), Expect = 3e-16 Identities = 20/88 (22%), Positives = 47/88 (53%) Query: 6 TRSDLVKSISKEFGLSRKDSTRFVTTLFNEICDSAVRGEAIKISSFATFHVKQKGSRVGR 65 +++L+K+I+++ GL++ ++ + + I ++ +G+ ++++ F + +R G Sbjct: 2 NKTELIKAIAQDTGLTQVSVSKMLASFEKIITETVAKGDKVQLTGFLNIKPVARQARKGF 61 Query: 66 NLQTNQEVKIDPRRVVVFKASSILKKRI 93 N QT + ++I P V K LKK Sbjct: 62 NPQTQEALEIAPSVGVSVKPGESLKKAA 89 >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:) Length = 204 Score = 62.1 bits (150), Expect = 3e-11 Identities = 32/103 (31%), Positives = 56/103 (54%) Query: 1 MSKTITRSDLVKSISKEFGLSRKDSTRFVTTLFNEICDSAVRGEAIKISSFATFHVKQKG 60 S +T++++ + + + GLS++D+ V F EI + GE +K+S F F ++ K Sbjct: 43 GSGGLTKAEMSEYLFDKLGLSKRDAKELVELFFEEIRRALENGEQVKLSGFGNFDLRDKN 102 Query: 61 SRVGRNLQTNQEVKIDPRRVVVFKASSILKKRIMDDMRGRKCN 103 R GRN +T +++ I RRVV F+ LK R+ + G + Sbjct: 103 QRPGRNPKTGEDIPITARRVVTFRPGQKLKSRVENAGGGERIE 145 Score = 48.2 bits (114), Expect = 4e-07 Identities = 20/73 (27%), Positives = 35/73 (47%) Query: 21 SRKDSTRFVTTLFNEICDSAVRGEAIKISSFATFHVKQKGSRVGRNLQTNQEVKIDPRRV 80 +R+ T ++A GE I+I F +F + + R GRN +T +V+++ + V Sbjct: 119 ARRVVTFRPGQKLKSRVENAGGGERIEIRGFGSFSLHYRAPRTGRNPKTGDKVELEGKYV 178 Query: 81 VVFKASSILKKRI 93 FK L+ R Sbjct: 179 PHFKPGKELRDRA 191 >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) Length = 58 Score = 56.6 bits (137), Expect = 1e-09 Identities = 20/50 (40%), Positives = 30/50 (60%) Query: 44 EAIKISSFATFHVKQKGSRVGRNLQTNQEVKIDPRRVVVFKASSILKKRI 93 E +K+S F F ++ K R GRN +T +++ I RRVV F+ LK R+ Sbjct: 1 EQVKLSGFGNFDLRDKNQRPGRNPKTGEDIPITARRVVTFRPGQKLKSRV 50 >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) Length = 56 Score = 52.3 bits (126), Expect = 2e-08 Identities = 18/49 (36%), Positives = 27/49 (55%), Gaps = 1/49 (2%) Query: 46 IKISSFATFHVKQKGSR-VGRNLQTNQEVKIDPRRVVVFKASSILKKRI 93 I+ SF TF V+++ R RN QT + VK+ V F+ LK+R+ Sbjct: 3 IEFRSFGTFEVRKRKGRLNARNPQTGEYVKVLDHHVAYFRPGKDLKERV 51 >2odr_A Phosphoseryl-tRNA synthetase; phosphoserine tRNA synthetase class II, ligase; 3.23A {Methanococcus maripaludis S2} (A:550-614) Length = 65 Score = 29.3 bits (65), Expect = 0.16 Identities = 5/7 (71%), Positives = 6/7 (85%) Query: 70 NQEVKID 76 N EVKI+ Sbjct: 1 NVEVKIE 7 >2odr_B Phosphoseryl-tRNA synthetase; phosphoserine tRNA synthetase class II, ligase; 3.23A {Methanococcus maripaludis S2} (B:550-611) Length = 62 Score = 28.9 bits (64), Expect = 0.21 Identities = 5/7 (71%), Positives = 6/7 (85%) Query: 70 NQEVKID 76 N EVKI+ Sbjct: 1 NVEVKIE 7 >3a2b_A Serine palmitoyltransferase; vitamin B6-dependent enzyme fold type I, acyltransferase, pyridoxal phosphate; HET: PLP; 2.30A {Sphingobacterium multivorum} (A:29-54,A:294-398) Length = 131 Score = 24.5 bits (53), Expect = 5.4 Identities = 11/23 (47%), Positives = 17/23 (73%) Query: 70 NQEVKIDPRRVVVFKASSILKKR 92 + EVKID RRV++F ++S L + Sbjct: 7 DTEVKIDGRRVLMFGSNSYLPEH 29 >1zq9_A Probable dimethyladenosine transferase; SGC, structural genomics, structural genomics consortium; HET: SAM; 1.90A {Homo sapiens} (A:189-285) Length = 97 Score = 24.0 bits (52), Expect = 6.7 Identities = 12/58 (20%), Positives = 19/58 (32%), Gaps = 3/58 (5%) Query: 52 ATFHVKQKGSRVGRNLQTN---QEVKIDPRRVVVFKASSILKKRIMDDMRGRKCNKDD 106 A F + +N + + + I + K IL D R R + DD Sbjct: 24 AAFKSSAVQQLLEKNYRIHCSVHNIIIPEDFSIADKIQQILTSTGFSDKRARSMDIDD 81 >2h1r_A Dimethyladenosine transferase, putative; SGC toronto dimethyladenosine transferase, structural genomics, structural genomics consortium; 1.89A {Plasmodium falciparum} (A:202-299) Length = 98 Score = 23.6 bits (51), Expect = 9.4 Identities = 9/57 (15%), Positives = 19/57 (33%), Gaps = 2/57 (3%) Query: 52 ATFHVKQKGSRVGRNLQTNQEVKIDPRRVVVFKAS--SILKKRIMDDMRGRKCNKDD 106 A F + + N + + FK +L+ M + R +++D Sbjct: 24 AIFKRNAVLNMLEHNYKNWCTLNKQVPVNFPFKKYCLDVLEHLDMCEKRSINLDEND 80 Database: mmdb70 Posted date: Jun 20, 2010 3:12 AM Number of letters in database: 4,956,049 Number of sequences in database: 33,805 Lambda K H 0.318 0.131 0.355 Gapped Lambda K H 0.267 0.0751 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 33805 Number of Hits to DB: 751,982 Number of extensions: 27741 Number of successful extensions: 79 Number of sequences better than 10.0: 1 Number of HSP's gapped: 78 Number of HSP's successfully gapped: 19 Length of query: 114 Length of database: 4,956,049 Length adjustment: 68 Effective length of query: 46 Effective length of database: 2,657,309 Effective search space: 122236214 Effective search space used: 122236214 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 50 (23.0 bits)