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)