RPS-BLAST 2.2.22 [Sep-27-2009]
Database: pdb70
24,244 sequences; 5,693,230 total letters
Searching..................................................done
Query= gi|254780496|ref|YP_003064909.1| integration host factor
subunit alpha [Candidatus Liberibacter asiaticus str. psy62]
(114 letters)
>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*
Length = 204
Score = 92.3 bits (229), Expect = 2e-20
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
>1owf_A IHF-alpha, integration HOST factor alpha-subunit; protein-DNA
recognition, indirect readout, DNA bending, minor
groove; 1.95A {Escherichia coli} SCOP: a.55.1.1 PDB:
1ouz_A 1ihf_A 1owg_A 2ht0_A
Length = 99
Score = 92.1 bits (229), Expect = 3e-20
Identities = 30/90 (33%), Positives = 52/90 (57%)
Query: 4 TITRSDLVKSISKEFGLSRKDSTRFVTTLFNEICDSAVRGEAIKISSFATFHVKQKGSRV 63
+T++++ + + + GLS++D+ V F EI + GE +K+S F F ++ K R
Sbjct: 2 ALTKAEMSEYLFDKLGLSKRDAKELVELFFEEIRRALENGEQVKLSGFGNFDLRDKNQRP 61
Query: 64 GRNLQTNQEVKIDPRRVVVFKASSILKKRI 93
GRN +T +++ I RRVV F+ LK R+
Sbjct: 62 GRNPKTGEDIPITARRVVTFRPGQKLKSRV 91
>3c4i_A DNA-binding protein HU homolog; dimerization by four helix bundle
interaction, DNA condensation; 2.04A {Mycobacterium
tuberculosis}
Length = 99
Score = 88.3 bits (219), Expect = 4e-19
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
>1hue_A HU protein; DNA-binding; NMR {Geobacillus stearothermophilus}
SCOP: a.55.1.1 PDB: 1huu_A
Length = 90
Score = 87.8 bits (218), Expect = 6e-19
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
>1mul_A NS2, HU-2, DNA binding protein HU-alpha; histone-like; HET: DNA;
2.30A {Escherichia coli} SCOP: a.55.1.1 PDB: 2o97_A
Length = 90
Score = 87.5 bits (217), Expect = 6e-19
Identities = 25/88 (28%), Positives = 45/88 (51%)
Query: 6 TRSDLVKSISKEFGLSRKDSTRFVTTLFNEICDSAVRGEAIKISSFATFHVKQKGSRVGR 65
++ L+ I+++ LS+ + + + I +S G+A+++ F TF V + R GR
Sbjct: 2 NKTQLIDVIAEKAELSKTQAKAALESTLAAITESLKEGDAVQLVGFGTFKVNHRAERTGR 61
Query: 66 NLQTNQEVKIDPRRVVVFKASSILKKRI 93
N QT +E+KI V F + LK +
Sbjct: 62 NPQTGKEIKIAAANVPAFVSGKALKDAV 89
>1owf_B IHF-beta, integration HOST factor beta-subunit; protein-DNA
recognition, indirect readout, DNA bending, minor
groove; 1.95A {Escherichia coli} SCOP: a.55.1.1 PDB:
1ouz_B 2ht0_B 1ihf_B 1owg_B
Length = 94
Score = 86.3 bits (214), Expect = 1e-18
Identities = 22/89 (24%), Positives = 44/89 (49%), Gaps = 1/89 (1%)
Query: 6 TRSDLVKSISKEF-GLSRKDSTRFVTTLFNEICDSAVRGEAIKISSFATFHVKQKGSRVG 64
T+S+L++ ++ + + K V + + + +GE I I F +F + + R G
Sbjct: 2 TKSELIERLATQQSHIPAKTVEDAVKEMLEHMASTLAQGERIAIRGFGSFSLHYRAPRTG 61
Query: 65 RNLQTNQEVKIDPRRVVVFKASSILKKRI 93
RN +T +V+++ + V FK L+ R
Sbjct: 62 RNPKTGDKVELEGKYVPHFKPGKELRDRA 90
>1p71_A DNA-binding protein HU; protein-DNA complex, DNA bending, DNA
binding protein/DNA complex; 1.90A {Anabaena SP} SCOP:
a.55.1.1 PDB: 1p51_A 1p78_A
Length = 94
Score = 84.1 bits (208), Expect = 7e-18
Identities = 19/88 (21%), Positives = 51/88 (57%)
Query: 6 TRSDLVKSISKEFGLSRKDSTRFVTTLFNEICDSAVRGEAIKISSFATFHVKQKGSRVGR 65
+ +LV +++++ +++K + +T I ++ G+ + + F +F +++ +R GR
Sbjct: 2 NKGELVDAVAEKASVTKKQADAVLTAALETIIEAVSSGDKVTLVGFGSFESRERKAREGR 61
Query: 66 NLQTNQEVKIDPRRVVVFKASSILKKRI 93
N +TN++++I RV F A + ++++
Sbjct: 62 NPKTNEKMEIPATRVPAFSAGKLFREKV 89
>1exe_A Transcription factor 1; beta ribbon ARMS, DNA-binding,
DNA-bending protein; NMR {Bacillus phage SPO1} SCOP:
a.55.1.1 PDB: 1wtu_A
Length = 99
Score = 82.1 bits (203), Expect = 2e-17
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
>1b8z_A Protein (histonelike protein HU); thermostable DNA binding
protein; 1.60A {Thermotoga maritima} SCOP: a.55.1.1
PDB: 1riy_A
Length = 90
Score = 80.3 bits (198), Expect = 9e-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
>2o97_B NS1, HU-1, DNA-binding protein HU-beta; heterodimer, DNA
structure, DNA supercoiling, E. coli; 2.45A
{Escherichia coli} SCOP: a.55.1.1
Length = 90
Score = 78.0 bits (192), Expect = 5e-16
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
>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}
Length = 108
Score = 74.5 bits (183), Expect = 5e-15
Identities = 27/97 (27%), Positives = 45/97 (46%), Gaps = 6/97 (6%)
Query: 3 KTITRSDLVKSISKEF-----GLSRKDSTRFVTTLFNEICDSAVRGEAIKISSFATFHVK 57
+T+SD+V I+ L +K + F E+ + I+ SF TF V+
Sbjct: 7 PKVTKSDIVDQIALNIKNNNLKLEKKYIRLVIDAFFEELKSNLCSNNVIEFRSFGTFEVR 66
Query: 58 QKGSRV-GRNLQTNQEVKIDPRRVVVFKASSILKKRI 93
++ R+ RN QT + VK+ V F+ LK+R+
Sbjct: 67 KRKGRLNARNPQTGEYVKVLDHHVAYFRPGKDLKERV 103
>2pff_B Fatty acid synthase subunit beta; fatty acid synthase,
acyl-carrier-protein, beta-ketoacyl reductase,
beta-ketoacyl synthase, dehydratase; 4.00A
{Saccharomyces cerevisiae}
Length = 2006
Score = 42.2 bits (99), Expect = 3e-05
Identities = 16/98 (16%), Positives = 30/98 (30%), Gaps = 35/98 (35%)
Query: 21 SRKD--STRF--VTTLF--------NEICDSAVRGEAIKISS----FATFHVKQKGSRVG 64
RK S RF V + F +++ + + + ++ + + G
Sbjct: 411 ERKLKFSNRFLPVASPFHSHLLVPASDLINKDLVKNNVSFNAKDIQIPVYD-----TFDG 465
Query: 65 RNLQTNQEVKIDPR-------------RVVVFKASSIL 89
+L+ I R FKA+ IL
Sbjct: 466 SDLRVLSG-SISERIVDCIIRLPVKWETTTQFKATHIL 502
>3kwp_A Predicted methyltransferase; putative methyltransferase, MCSG,
structural genomics, PSI-2, protein structure
initiative; 2.29A {Lactobacillus brevis atcc 367}
Length = 296
Score = 25.4 bits (55), Expect = 3.0
Identities = 4/24 (16%), Positives = 13/24 (54%)
Query: 1 MSKTITRSDLVKSISKEFGLSRKD 24
++ +D +K ++K G +++
Sbjct: 262 IAAGEKPNDAIKEVAKLRGAKKQE 285
>1coy_A Cholesterol oxidase; oxidoreductase(oxygen receptor); HET: AND FAD;
1.80A {Brevibacterium sterolicum} SCOP: c.3.1.2 d.16.1.1
PDB: 3cox_A*
Length = 507
Score = 25.2 bits (54), Expect = 4.1
Identities = 11/48 (22%), Positives = 18/48 (37%)
Query: 26 TRFVTTLFNEICDSAVRGEAIKISSFATFHVKQKGSRVGRNLQTNQEV 73
T+ VT +V + +S A H+ S+VG N +
Sbjct: 277 TKVVTADRVFFAAGSVGTSKLLVSMKAQGHLPNLSSQVGEGWGNNGNI 324
Database: pdb70
Posted date: Jan 26, 2011 11:21 AM
Number of letters in database: 5,693,230
Number of sequences in database: 24,244
Lambda K H
0.318 0.131 0.355
Gapped
Lambda K H
0.267 0.0523 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 24244
Number of Hits to DB: 870,392
Number of extensions: 33467
Number of successful extensions: 102
Number of sequences better than 10.0: 1
Number of HSP's gapped: 99
Number of HSP's successfully gapped: 16
Length of query: 114
Length of database: 5,693,230
Length adjustment: 77
Effective length of query: 37
Effective length of database: 3,826,442
Effective search space: 141578354
Effective search space used: 141578354
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 (23.5 bits)