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)