RPS-BLAST 2.2.22 [Sep-27-2009]
Database: mmdb70
33,805 sequences; 4,956,049 total letters
Searching..................................................done
Query= gi|254780748|ref|YP_003065161.1| integration host factor, beta
subunit [Candidatus Liberibacter asiaticus str. psy62]
(100 letters)
>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 = 89.1 bits (221), Expect = 2e-19
Identities = 39/92 (42%), Positives = 51/92 (55%)
Query: 1 MIKSSLIGTIAKKNPKLNYQDVEKIVNMLLEEMTQALANGGRVEIRGFGSFSVRKRAARL 60
M KS LI +A + + + VE V +LE M LA G R+ IRGFGSFS+ RA R
Sbjct: 1 MTKSELIERLATQQSHIPAKTVEDAVKEMLEHMASTLAQGERIAIRGFGSFSLHYRAPRT 60
Query: 61 ARAPLAQKVISVEEKMVPFFRAGKNLKERLNS 92
R P + +E K VP F+ GK L++R N
Sbjct: 61 GRNPKTGDKVELEGKYVPHFKPGKELRDRANI 92
>1p71_A DNA-binding protein HU; protein-DNA complex, DNA bending,
DNA binding protein/DNA complex; 1.90A {Anabaena SP}
(A:)
Length = 94
Score = 83.3 bits (206), Expect = 9e-18
Identities = 29/95 (30%), Positives = 52/95 (54%), Gaps = 1/95 (1%)
Query: 1 MIKSSLIGTIAKKNPKLNYQDVEKIVNMLLEEMTQALANGGRVEIRGFGSFSVRKRAARL 60
M K L+ +A+K + + + ++ LE + +A+++G +V + GFGSF R+R AR
Sbjct: 1 MNKGELVDAVAEK-ASVTKKQADAVLTAALETIIEAVSSGDKVTLVGFGSFESRERKARE 59
Query: 61 ARAPLAQKVISVEEKMVPFFRAGKNLKERLNSPDS 95
R P + + + VP F AGK +E++ P +
Sbjct: 60 GRNPKTNEKMEIPATRVPAFSAGKLFREKVAPPKA 94
>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 = 82.6 bits (204), Expect = 2e-17
Identities = 34/91 (37%), Positives = 53/91 (58%), Gaps = 1/91 (1%)
Query: 1 MIKSSLIGTIAKKNPKLNYQDVEKIVNMLLEEMTQALANGGRVEIRGFGSFSVRKRAARL 60
M KS LI IA ++ + ++ ++ +T++L G V + GFG+F+V++RAAR
Sbjct: 1 MNKSQLIDKIAAG-ADISKAAAGRALDAIIASVTESLKEGDDVALVGFGTFAVKERAART 59
Query: 61 ARAPLAQKVISVEEKMVPFFRAGKNLKERLN 91
R P K I++ VP FRAGK LK+ +N
Sbjct: 60 GRNPQTGKEITIAAAKVPSFRAGKALKDAVN 90
>1b8z_A Protein (histonelike protein HU); thermostable DNA binding
protein; 1.60A {Thermotoga maritima} (A:)
Length = 90
Score = 81.4 bits (201), Expect = 4e-17
Identities = 42/91 (46%), Positives = 59/91 (64%), Gaps = 1/91 (1%)
Query: 1 MIKSSLIGTIAKKNPKLNYQDVEKIVNMLLEEMTQALANGGRVEIRGFGSFSVRKRAARL 60
M K LI +AKK +DV+ I++ +LE +T+ALA G +V+I GFGSF VRK AAR
Sbjct: 1 MNKKELIDRVAKK-AGAKKKDVKLILDTILETITEALAKGEKVQIVGFGSFEVRKAAARK 59
Query: 61 ARAPLAQKVISVEEKMVPFFRAGKNLKERLN 91
P +K I++ E+ VP F+ GK LKE++
Sbjct: 60 GVNPQTRKPITIPERKVPKFKPGKALKEKVK 90
>3c4i_A DNA-binding protein HU homolog; dimerization by four helix
bundle interaction, DNA condensation; 2.04A
{Mycobacterium tuberculosis} (A:)
Length = 99
Score = 80.3 bits (198), Expect = 8e-17
Identities = 29/91 (31%), Positives = 47/91 (51%), Gaps = 1/91 (1%)
Query: 1 MIKSSLIGTIAKKNPKLNYQDVEKIVNMLLEEMTQALANGGRVEIRGFGSFSVRKRAARL 60
M K+ LI + +K + + V +++ + +A+ G V I GFG F R+RAAR+
Sbjct: 1 MNKAELIDVLTQKL-GSDRRQATAAVENVVDTIVRAVHKGDSVTITGFGVFEQRRRAARV 59
Query: 61 ARAPLAQKVISVEEKMVPFFRAGKNLKERLN 91
AR P + + V+ VP FR G K ++
Sbjct: 60 ARNPRTGETVKVKPTSVPAFRPGAQFKAVVS 90
>1exe_A Transcription factor 1; beta ribbon ARMS, DNA-binding,
DNA-bending protein; NMR {Bacillus phage SPO1} (A:)
Length = 99
Score = 79.5 bits (196), Expect = 1e-16
Identities = 23/92 (25%), Positives = 43/92 (46%), Gaps = 1/92 (1%)
Query: 1 MIKSSLIGTIAKKNPKLNYQDVEKIVNMLLEEMTQALANGGRVEIRGFGSFSVRKRAARL 60
M K+ LI IA+ L V K++ + +T+ +A G +V++ GF + R AR
Sbjct: 1 MNKTELIKAIAQDT-GLTQVSVSKMLASFEKIITETVAKGDKVQLTGFLNIKPVARQARK 59
Query: 61 ARAPLAQKVISVEEKMVPFFRAGKNLKERLNS 92
P Q+ + + + + G++LK+
Sbjct: 60 GFNPQTQEALEIAPSVGVSVKPGESLKKAAEG 91
>1hue_A HU protein; DNA-binding; NMR {Geobacillus
stearothermophilus} (A:)
Length = 90
Score = 79.5 bits (196), Expect = 2e-16
Identities = 33/90 (36%), Positives = 55/90 (61%), Gaps = 1/90 (1%)
Query: 1 MIKSSLIGTIAKKNPKLNYQDVEKIVNMLLEEMTQALANGGRVEIRGFGSFSVRKRAARL 60
M K+ LI +A+ + L+ +D K V+ + + +T+AL G +V++ GFG+F VR+RAAR
Sbjct: 1 MNKTELINAVAETS-GLSKKDATKAVDAVFDSITEALRKGDKVQLIGFGNFEVRERAARK 59
Query: 61 ARAPLAQKVISVEEKMVPFFRAGKNLKERL 90
R P + + + VP F+ GK LK+ +
Sbjct: 60 GRNPQTGEEMEIPASKVPAFKPGKALKDAV 89
>1mul_A NS2, HU-2, DNA binding protein HU-alpha; histone-like;
HET: DNA; 2.30A {Escherichia coli} (A:)
Length = 90
Score = 79.5 bits (196), Expect = 2e-16
Identities = 32/90 (35%), Positives = 48/90 (53%), Gaps = 1/90 (1%)
Query: 1 MIKSSLIGTIAKKNPKLNYQDVEKIVNMLLEEMTQALANGGRVEIRGFGSFSVRKRAARL 60
M K+ LI IA+K +L+ + + L +T++L G V++ GFG+F V RA R
Sbjct: 1 MNKTQLIDVIAEK-AELSKTQAKAALESTLAAITESLKEGDAVQLVGFGTFKVNHRAERT 59
Query: 61 ARAPLAQKVISVEEKMVPFFRAGKNLKERL 90
R P K I + VP F +GK LK+ +
Sbjct: 60 GRNPQTGKEIKIAAANVPAFVSGKALKDAV 89
>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 = 67.0 bits (164), Expect = 9e-13
Identities = 17/54 (31%), Positives = 29/54 (53%)
Query: 42 RVEIRGFGSFSVRKRAARLARAPLAQKVISVEEKMVPFFRAGKNLKERLNSPDS 95
+V++ GFG+F +R + R R P + I + + V FR G+ LK R+ +
Sbjct: 2 QVKLSGFGNFDLRDKNQRPGRNPKTGEDIPITARRVVTFRPGQKLKSRVENASP 55
>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 = 63.9 bits (156), Expect = 7e-12
Identities = 24/54 (44%), Positives = 32/54 (59%), Gaps = 1/54 (1%)
Query: 42 RVEIRGFGSFSVRKRAARL-ARAPLAQKVISVEEKMVPFFRAGKNLKERLNSPD 94
+E R FG+F VRKR RL AR P + + V + V +FR GK+LKER+
Sbjct: 2 VIEFRSFGTFEVRKRKGRLNARNPQTGEYVKVLDHHVAYFRPGKDLKERVWGIK 55
>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 = 57.4 bits (138), Expect = 7e-10
Identities = 24/81 (29%), Positives = 45/81 (55%), Gaps = 1/81 (1%)
Query: 1 MIKSSLIGTIAKKNPKLNYQDVEKIVNMLLEEMTQALANGGRVEIRGFGSFSVRKRAARL 60
+ K+ + + K L+ +D +++V + EE+ +AL NG +V++ GFG+F +R + R
Sbjct: 47 LTKAEMSEYLFDKL-GLSKRDAKELVELFFEEIRRALENGEQVKLSGFGNFDLRDKNQRP 105
Query: 61 ARAPLAQKVISVEEKMVPFFR 81
R P + I + + V FR
Sbjct: 106 GRNPKTGEDIPITARRVVTFR 126
Score = 49.3 bits (117), Expect = 2e-07
Identities = 29/81 (35%), Positives = 40/81 (49%)
Query: 12 KKNPKLNYQDVEKIVNMLLEEMTQALANGGRVEIRGFGSFSVRKRAARLARAPLAQKVIS 71
+ P + V L+ + G R+EIRGFGSFS+ RA R R P +
Sbjct: 113 EDIPITARRVVTFRPGQKLKSRVENAGGGERIEIRGFGSFSLHYRAPRTGRNPKTGDKVE 172
Query: 72 VEEKMVPFFRAGKNLKERLNS 92
+E K VP F+ GK L++R N
Sbjct: 173 LEGKYVPHFKPGKELRDRANI 193
>1q1l_A Chorismate synthase; beta alpha beta sandwich, structural
genomics, PSI, protein structure initiative, midwest
center for structural genomics; 2.05A {Aquifex aeolicus}
(A:)
Length = 401
Score = 25.9 bits (57), Expect = 1.9
Identities = 9/32 (28%), Positives = 14/32 (43%)
Query: 40 GGRVEIRGFGSFSVRKRAARLARAPLAQKVIS 71
R S R+ AAR+A + +K +S
Sbjct: 126 NQRDLRNILERASARETAARVAVGAVCKKFLS 157
>1sq1_A Chorismate synthase; structural genomics, bifunctional
alpha/beta tetrameric protein, PSI, protein structure
initiative; 2.80A {Campylobacter jejuni}
(A:1-144,A:310-349)
Length = 184
Score = 24.6 bits (54), Expect = 4.8
Identities = 10/37 (27%), Positives = 16/37 (43%)
Query: 41 GRVEIRGFGSFSVRKRAARLARAPLAQKVISVEEKMV 77
G + RG G S R+ AR+A +A ++
Sbjct: 113 GIRDHRGGGRSSARESVARVAGGAVAAXLLRENNLKF 149
>1kxp_D Human vitamin D-binding protein; DBP, actin scavenger
system, actin-binding protein, contractIle
protein/protein binding complex; HET: ATP; 2.10A {Homo
sapiens} (D:1-190)
Length = 190
Score = 24.6 bits (53), Expect = 5.0
Identities = 7/42 (16%), Positives = 17/42 (40%)
Query: 3 KSSLIGTIAKKNPKLNYQDVEKIVNMLLEEMTQALANGGRVE 44
S + ++K P ++ V ++V ++ A G +
Sbjct: 25 TSLSLVLYSRKFPSGTFEQVSQLVKEVVSLTEACCAEGADPD 66
>1um0_A Chorismate synthase; beta-alpha-beta sandwich fold, lyase;
HET: FMN; 1.95A {Helicobacter pylori}
(A:1-145,A:300-352)
Length = 198
Score = 24.6 bits (54), Expect = 5.0
Identities = 10/30 (33%), Positives = 16/30 (53%)
Query: 41 GRVEIRGFGSFSVRKRAARLARAPLAQKVI 70
G + RG G S R+ A R+A A+ ++
Sbjct: 114 GIRDFRGGGRSSARESAIRVAAGAFAKMLL 143
>2izo_A FEN1, flap structure-specific endonuclease; hydrolase, DNA
repair, DNA-binding, endonuclease, metal-binding,
excision repair, DNA replication, PCNA; HET: DNA; 2.9A
{Sulfolobus solfataricus} (A:1-208,A:301-346)
Length = 254
Score = 24.3 bits (52), Expect = 5.5
Identities = 14/70 (20%), Positives = 24/70 (34%), Gaps = 5/70 (7%)
Query: 11 AKKNPKLNYQDVEKIVNMLLEEMTQALANGGRVEIRGFGSFSVRKRAARLARAPLAQKVI 70
+K P + K + E++ L V F V+ RL +A K
Sbjct: 190 KRKLPNKDVYVEIKPELIEGEDIINIL-----VYEHNFSEERVKNGIERLTKAIKEAKGA 244
Query: 71 SVEEKMVPFF 80
S + + +F
Sbjct: 245 SRQTGLDRWF 254
>1kxp_D Human vitamin D-binding protein; DBP, actin scavenger
system, actin-binding protein, contractIle
protein/protein binding complex; HET: ATP; 2.10A {Homo
sapiens} (D:191-339)
Length = 149
Score = 24.1 bits (52), Expect = 6.1
Identities = 8/34 (23%), Positives = 17/34 (50%), Gaps = 4/34 (11%)
Query: 3 KSSLIGTIAKKNPKLNYQDVEKIVNMLLEEMTQA 36
+ S + +A+K P + +DV + E++T
Sbjct: 26 RLSNLIKLAQKVPTADLEDVLPLA----EDITNI 55
>3eh7_A 4-hydroxybutyrate COA-transferase; citrate lyase,
structural genomics, PSI-2, protein structure
initiative; HET: MSE; 2.05A {Porphyromonas gingivalis}
(A:1-190)
Length = 190
Score = 23.7 bits (51), Expect = 7.6
Identities = 6/19 (31%), Positives = 10/19 (52%)
Query: 56 RAARLARAPLAQKVISVEE 74
A + A A +++S EE
Sbjct: 2 NAXKDVLAEYASRIVSAEE 20
>1m3s_A Hypothetical protein YCKF; structural genomics, PSI,
protein structure initiative, midwest center for
structural genomics, MCSG; 1.95A {Bacillus subtilis}
(A:)
Length = 186
Score = 23.6 bits (50), Expect = 8.6
Identities = 6/70 (8%), Positives = 20/70 (28%), Gaps = 6/70 (8%)
Query: 8 GTIAKKNPKLNYQDVEKIVNML----LEEMTQALANGGRVEIRGFGS--FSVRKRAARLA 61
G + ++ + +++ + + ++ G G + A RL
Sbjct: 1 GMKTTEYVAEILNELHNSAAYISNEEADQLADHILSSHQIFTAGAGRSGLMAKSFAMRLM 60
Query: 62 RAPLAQKVIS 71
++
Sbjct: 61 HMGFNAHIVG 70
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
0.315 0.130 0.344
Gapped
Lambda K H
0.267 0.0664 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 33805
Number of Hits to DB: 701,389
Number of extensions: 28897
Number of successful extensions: 134
Number of sequences better than 10.0: 1
Number of HSP's gapped: 128
Number of HSP's successfully gapped: 24
Length of query: 100
Length of database: 4,956,049
Length adjustment: 59
Effective length of query: 41
Effective length of database: 2,961,554
Effective search space: 121423714
Effective search space used: 121423714
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 (21.6 bits)
S2: 50 (23.2 bits)