BLASTP 2.2.26 [Sep-21-2011]
Reference: Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schaffer,
Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997),
"Gapped BLAST and PSI-BLAST: a new generation of protein database search
programs", Nucleic Acids Res. 25:3389-3402.
Reference for compositional score matrix adjustment: Altschul, Stephen F.,
John C. Wootton, E. Michael Gertz, Richa Agarwala, Aleksandr Morgulis,
Alejandro A. Schaffer, and Yi-Kuo Yu (2005) "Protein database searches
using compositionally adjusted substitution matrices", FEBS J. 272:5101-5109.
Query= 027819
(218 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|3ULP|A Chain A, Plasmodium Falciparum Ssb Complex With Ssdna
pdb|3ULP|B Chain B, Plasmodium Falciparum Ssb Complex With Ssdna
pdb|3ULP|C Chain C, Plasmodium Falciparum Ssb Complex With Ssdna
pdb|3ULP|D Chain D, Plasmodium Falciparum Ssb Complex With Ssdna
Length = 124
Score = 52.8 bits (125), Expect = 1e-07, Method: Compositional matrix adjust.
Identities = 36/118 (30%), Positives = 56/118 (47%), Gaps = 10/118 (8%)
Query: 83 KAILVGQVGQSPVQKKLKSGRTVTLFSLGTGGIXXXXXXXXXXXXTEYANRCAVQWHRVS 142
K +L+G+VG P K L G V FSL T T+ WHR+
Sbjct: 8 KIMLIGRVGCEPDIKILNGGDKVATFSLATNEFWRDRNTNELKSKTD--------WHRIV 59
Query: 143 VYPERLGGVVMKHLVPGSTIYVEGNLE-QKVFNDPITGLVRRIREIAIRRN-GRLVFL 198
VY + + ++ K+L G +YV+G+L +K + + ++I EI + N G L+FL
Sbjct: 60 VYDQNIVDLIDKYLRKGRRVYVQGSLHTRKWHTNDMNSQPKQITEIILSYNKGDLIFL 117
>pdb|1EQQ|A Chain A, Single Stranded Dna Binding Protein And Ssdna Complex
pdb|1EQQ|B Chain B, Single Stranded Dna Binding Protein And Ssdna Complex
pdb|1EQQ|C Chain C, Single Stranded Dna Binding Protein And Ssdna Complex
pdb|1EQQ|D Chain D, Single Stranded Dna Binding Protein And Ssdna Complex
Length = 178
Score = 51.2 bits (121), Expect = 5e-07, Method: Compositional matrix adjust.
Identities = 38/127 (29%), Positives = 58/127 (45%), Gaps = 12/127 (9%)
Query: 80 GIFKAILVGQVGQSPVQKKLKSGRTVTLFSLGTGGIXXXXXXXXXXXXTEYANRCAVQWH 139
G+ K ILVG +GQ P + + +G V +L T TE WH
Sbjct: 5 GVNKVILVGNLGQDPEVRYMPNGGAVANITLATSESWRDKATGEMKEQTE--------WH 56
Query: 140 RVSVYPERLGGVVMKHLVPGSTIYVEGNLEQKVFNDPITGLVRRIREIAIRRNGRLVFLG 199
RV ++ +L V ++L GS +Y+EG L + + D +G R E+ + G + LG
Sbjct: 57 RVVLFG-KLAEVASEYLRKGSQVYIEGQLRTRKWTDQ-SGQDRYTTEVVVNVGGTMQMLG 114
Query: 200 --KGGDA 204
+GG A
Sbjct: 115 GRQGGGA 121
>pdb|3PGZ|A Chain A, Crystal Structure Of A Single Strand Binding Protein (Ssb)
From Bartonella Henselae
pdb|3PGZ|B Chain B, Crystal Structure Of A Single Strand Binding Protein (Ssb)
From Bartonella Henselae
Length = 193
Score = 50.4 bits (119), Expect = 7e-07, Method: Compositional matrix adjust.
Identities = 32/109 (29%), Positives = 49/109 (44%), Gaps = 9/109 (8%)
Query: 83 KAILVGQVGQSPVQKKLKSGRTVTLFSLGTGGIXXXXXXXXXXXXTEYANRCAVQWHRVS 142
K IL+G +G P ++L SG V + T TE WH +
Sbjct: 28 KVILIGNLGADPEIRRLNSGDQVANLRIATSESWRDRNTNERKERTE--------WHNIV 79
Query: 143 VYPERLGGVVMKHLVPGSTIYVEGNLEQKVFNDPITGLVRRIREIAIRR 191
++ E L VV ++L GS IY+EG L+ + + D G R EI +++
Sbjct: 80 IFNENLVKVVEQYLKKGSKIYIEGQLQTRKWQDQ-NGNDRYTTEIVLQK 127
>pdb|3TQY|A Chain A, Structure Of A Single-Stranded Dna-Binding Protein (Ssb),
From Coxiella Burnetii
pdb|3TQY|B Chain B, Structure Of A Single-Stranded Dna-Binding Protein (Ssb),
From Coxiella Burnetii
pdb|3TQY|C Chain C, Structure Of A Single-Stranded Dna-Binding Protein (Ssb),
From Coxiella Burnetii
pdb|3TQY|D Chain D, Structure Of A Single-Stranded Dna-Binding Protein (Ssb),
From Coxiella Burnetii
Length = 158
Score = 50.4 bits (119), Expect = 7e-07, Method: Compositional matrix adjust.
Identities = 34/113 (30%), Positives = 51/113 (45%), Gaps = 10/113 (8%)
Query: 75 NGLDPGIFKAILVGQVGQSPVQKKLKSGRTVTLFSLGTGGIXXXXXXXXXXXXTEYANRC 134
N G+ K IL+G +GQ P + +G V +L T TE
Sbjct: 2 NAXARGVNKVILIGNLGQDPEVRYTPNGNAVANVTLATSTTWRDKQTGELQERTE----- 56
Query: 135 AVQWHRVSVYPERLGGVVMKHLVPGSTIYVEGNLEQKVFNDPITGLVRRIREI 187
WHR++ + RL +V ++L GS IY+EG+L + + D G+ R EI
Sbjct: 57 ---WHRIAFF-NRLAEIVGEYLRKGSKIYIEGSLRTRKWQDK-NGVDRYTTEI 104
>pdb|1QVC|A Chain A, Crystal Structure Analysis Of Single Stranded Dna Binding
Protein (Ssb) From E.Coli
pdb|1QVC|B Chain B, Crystal Structure Analysis Of Single Stranded Dna Binding
Protein (Ssb) From E.Coli
pdb|1QVC|C Chain C, Crystal Structure Analysis Of Single Stranded Dna Binding
Protein (Ssb) From E.Coli
pdb|1QVC|D Chain D, Crystal Structure Analysis Of Single Stranded Dna Binding
Protein (Ssb) From E.Coli
Length = 145
Score = 48.5 bits (114), Expect = 3e-06, Method: Compositional matrix adjust.
Identities = 38/127 (29%), Positives = 58/127 (45%), Gaps = 12/127 (9%)
Query: 80 GIFKAILVGQVGQSPVQKKLKSGRTVTLFSLGTGGIXXXXXXXXXXXXTEYANRCAVQWH 139
G+ K ILVG +GQ P + + +G V +L T TE WH
Sbjct: 4 GVNKVILVGNLGQDPEVRYMPNGGAVANITLATSESWRDKATGEMKEQTE--------WH 55
Query: 140 RVSVYPERLGGVVMKHLVPGSTIYVEGNLEQKVFNDPITGLVRRIREIAIRRNGRLVFLG 199
RV ++ +L V ++L GS +Y+EG L + + D +G R E+ + G + LG
Sbjct: 56 RVVLFG-KLAEVASEYLRKGSQVYIEGQLRTRKWTDQ-SGQDRYTTEVVVNVGGTMQMLG 113
Query: 200 --KGGDA 204
+GG A
Sbjct: 114 GRQGGGA 120
>pdb|1EYG|A Chain A, Crystal Structure Of Chymotryptic Fragment Of E. Coli Ssb
Bound To Two 35-Mer Single Strand Dnas
pdb|1EYG|B Chain B, Crystal Structure Of Chymotryptic Fragment Of E. Coli Ssb
Bound To Two 35-Mer Single Strand Dnas
pdb|1EYG|C Chain C, Crystal Structure Of Chymotryptic Fragment Of E. Coli Ssb
Bound To Two 35-Mer Single Strand Dnas
pdb|1EYG|D Chain D, Crystal Structure Of Chymotryptic Fragment Of E. Coli Ssb
Bound To Two 35-Mer Single Strand Dnas
Length = 116
Score = 47.8 bits (112), Expect = 5e-06, Method: Compositional matrix adjust.
Identities = 35/120 (29%), Positives = 54/120 (45%), Gaps = 10/120 (8%)
Query: 80 GIFKAILVGQVGQSPVQKKLKSGRTVTLFSLGTGGIXXXXXXXXXXXXTEYANRCAVQWH 139
G+ K ILVG +GQ P + + +G V +L T TE WH
Sbjct: 5 GVNKVILVGNLGQDPEVRYMPNGGAVANITLATSESWRDKATGEMKEQTE--------WH 56
Query: 140 RVSVYPERLGGVVMKHLVPGSTIYVEGNLEQKVFNDPITGLVRRIREIAIRRNGRLVFLG 199
RV ++ +L V ++L GS +Y+EG L + + D +G R E+ + G + LG
Sbjct: 57 RVVLFG-KLAEVASEYLRKGSQVYIEGQLRTRKWTDQ-SGQDRYTTEVVVNVGGTMQMLG 114
>pdb|1KAW|A Chain A, Structure Of Single Stranded Dna Binding Protein (Ssb)
pdb|1KAW|B Chain B, Structure Of Single Stranded Dna Binding Protein (Ssb)
pdb|1KAW|C Chain C, Structure Of Single Stranded Dna Binding Protein (Ssb)
pdb|1KAW|D Chain D, Structure Of Single Stranded Dna Binding Protein (Ssb)
Length = 135
Score = 47.0 bits (110), Expect = 7e-06, Method: Compositional matrix adjust.
Identities = 38/127 (29%), Positives = 58/127 (45%), Gaps = 12/127 (9%)
Query: 80 GIFKAILVGQVGQSPVQKKLKSGRTVTLFSLGTGGIXXXXXXXXXXXXTEYANRCAVQWH 139
G+ K ILVG +GQ P + + +G V +L T TE WH
Sbjct: 4 GVNKVILVGNLGQDPEVRYMPNGGAVANITLATSESWRDKATGEMKEQTE--------WH 55
Query: 140 RVSVYPERLGGVVMKHLVPGSTIYVEGNLEQKVFNDPITGLVRRIREIAIRRNGRLVFLG 199
RV ++ +L V ++L GS +Y+EG L + + D +G R E+ + G + LG
Sbjct: 56 RVVLFG-KLAEVASEYLRKGSQVYIEGQLRTRKWTDQ-SGQDRYTTEVVVNVGGTMQMLG 113
Query: 200 --KGGDA 204
+GG A
Sbjct: 114 GRQGGGA 120
>pdb|3LGJ|A Chain A, Crystal Structure Of Single-Stranded Binding Protein (Ssb)
From Bartonella Henselae
pdb|3LGJ|B Chain B, Crystal Structure Of Single-Stranded Binding Protein (Ssb)
From Bartonella Henselae
Length = 169
Score = 47.0 bits (110), Expect = 8e-06, Method: Compositional matrix adjust.
Identities = 32/117 (27%), Positives = 49/117 (41%), Gaps = 10/117 (8%)
Query: 83 KAILVGQVGQSPVQKKLKSGRTVTLFSLGTGGIXXXXXXXXXXXXTEYANRCAVQWHRVS 142
K +L+G +G P K + SG V F + T TE WH V
Sbjct: 25 KVMLIGYLGDDPESKTMTSGAEVVNFRMATFESYMNKNTHQKVEKTE--------WHSVV 76
Query: 143 VYPERLGGVVMKHLVPGSTIYVEGNLEQKVFNDPITGLVRRIREIAI-RRNGRLVFL 198
V+ + +++L GS +Y+EG L+ + + D G R EI + + G L L
Sbjct: 77 VFNPHFAKIALQYLHKGSKVYIEGKLQTRKWQDK-NGHDRYTTEIVLPQYKGELHLL 132
>pdb|1SRU|A Chain A, Crystal Structure Of Full Length E. Coli Ssb Protein
pdb|1SRU|B Chain B, Crystal Structure Of Full Length E. Coli Ssb Protein
pdb|1SRU|C Chain C, Crystal Structure Of Full Length E. Coli Ssb Protein
pdb|1SRU|D Chain D, Crystal Structure Of Full Length E. Coli Ssb Protein
Length = 113
Score = 45.8 bits (107), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 34/119 (28%), Positives = 53/119 (44%), Gaps = 10/119 (8%)
Query: 80 GIFKAILVGQVGQSPVQKKLKSGRTVTLFSLGTGGIXXXXXXXXXXXXTEYANRCAVQWH 139
G+ K ILVG +GQ P + + +G V +L T TE WH
Sbjct: 5 GVNKVILVGNLGQDPEVRYMPNGGAVANITLATSESWRDKATGEMKEQTE--------WH 56
Query: 140 RVSVYPERLGGVVMKHLVPGSTIYVEGNLEQKVFNDPITGLVRRIREIAIRRNGRLVFL 198
RV ++ +L V ++L GS +Y+EG L + + D +G R E+ + G + L
Sbjct: 57 RVVLFG-KLAEVASEYLRKGSQVYIEGQLRTRKWTDQ-SGQDRYTTEVVVNVGGTMQML 113
>pdb|3ULL|A Chain A, Human Mitochondrial Single-Stranded Dna Binding Protein
pdb|3ULL|B Chain B, Human Mitochondrial Single-Stranded Dna Binding Protein
pdb|1S3O|A Chain A, Human Mitochondrial Single Strand Dna Binding Protein
(Hmssb)
pdb|1S3O|B Chain B, Human Mitochondrial Single Strand Dna Binding Protein
(Hmssb)
Length = 132
Score = 45.4 bits (106), Expect = 3e-05, Method: Compositional matrix adjust.
Identities = 28/100 (28%), Positives = 51/100 (51%), Gaps = 3/100 (3%)
Query: 77 LDPGIFKAILVGQVGQSPVQKKLKSGRTVTLFSLGTGGIXXXXXXXXXXXXTEYANRCAV 136
L+ + + L+G+VGQ PV ++++ VT+FSL T + + + +
Sbjct: 10 LERSLNRVHLLGRVGQDPVLRQVEGKNPVTIFSLATNEMWRSGDSEVYQLG-DVSQKTT- 67
Query: 137 QWHRVSVYPERLGGVVMKHLVPGSTIYVEGNLEQKVFNDP 176
WHR+SV+ L V +++ GS IY+EG ++ + D
Sbjct: 68 -WHRISVFRPGLRDVAYQYVKKGSRIYLEGKIDYGEYMDK 106
>pdb|2DUD|A Chain A, Crystal Structure Of Human Mitochondrial Single-Stranded
Dna-Binding Protein(Hmtssb)
pdb|2DUD|B Chain B, Crystal Structure Of Human Mitochondrial Single-Stranded
Dna-Binding Protein(Hmtssb)
Length = 133
Score = 45.1 bits (105), Expect = 3e-05, Method: Compositional matrix adjust.
Identities = 35/122 (28%), Positives = 60/122 (49%), Gaps = 7/122 (5%)
Query: 77 LDPGIFKAILVGQVGQSPVQKKLKSGRTVTLFSLGTGGIXXXXXXXXXXXXTEYANRCAV 136
L+ + + L+G+VGQ PV ++++ VT+FSL T + + + +
Sbjct: 11 LERSLNRVHLLGRVGQDPVLRQVEGKNPVTIFSLATNEMWRSGDSEVYQLG-DVSQKTT- 68
Query: 137 QWHRVSVYPERLGGVVMKHLVPGSTIYVEGNLEQKVFNDPITGLVRRIREIAIRRNGRLV 196
WHR+SV+ L V +++ GS IY+EG ++ + D VRR I N ++
Sbjct: 69 -WHRISVFRPGLRDVAYQYVKKGSRIYLEGKIDYGEYMDK--NNVRRQATTIIADN--II 123
Query: 197 FL 198
FL
Sbjct: 124 FL 125
>pdb|3PB0|A Chain A, Characterisation Of The First Monomeric
Dihydrodipicolinate Synthase Variant Reveals
Evolutionary Insights
pdb|3PB0|B Chain B, Characterisation Of The First Monomeric
Dihydrodipicolinate Synthase Variant Reveals
Evolutionary Insights
pdb|3PB0|C Chain C, Characterisation Of The First Monomeric
Dihydrodipicolinate Synthase Variant Reveals
Evolutionary Insights
pdb|3PB0|D Chain D, Characterisation Of The First Monomeric
Dihydrodipicolinate Synthase Variant Reveals
Evolutionary Insights
Length = 300
Score = 26.9 bits (58), Expect = 8.5, Method: Compositional matrix adjust.
Identities = 12/38 (31%), Positives = 22/38 (57%)
Query: 57 SPTQNSGQQRESFDRPLENGLDPGIFKAILVGQVGQSP 94
+P +N ES++R + L+ G+ I++G G+SP
Sbjct: 17 TPFKNGELDLESYERLVRYQLENGVNALIVLGTTGESP 54
>pdb|1SNG|A Chain A, Structure Of A Thermophilic Serpin In The Native State
Length = 370
Score = 26.9 bits (58), Expect = 8.9, Method: Compositional matrix adjust.
Identities = 12/31 (38%), Positives = 17/31 (54%)
Query: 181 VRRIREIAIRRNGRLVFLGKGGDAQPPSPSE 211
V R I +RR G ++FLG D P P++
Sbjct: 340 VDRPFHIVVRRRGAILFLGSIADPHDPGPAQ 370
>pdb|1O5K|A Chain A, Crystal Structure Of Dihydrodipicolinate Synthase
(Tm1521) From Thermotoga Maritima At 1.80 A Resolution
pdb|1O5K|B Chain B, Crystal Structure Of Dihydrodipicolinate Synthase
(Tm1521) From Thermotoga Maritima At 1.80 A Resolution
Length = 306
Score = 26.9 bits (58), Expect = 8.9, Method: Compositional matrix adjust.
Identities = 12/38 (31%), Positives = 22/38 (57%)
Query: 57 SPTQNSGQQRESFDRPLENGLDPGIFKAILVGQVGQSP 94
+P +N ES++R + L+ G+ I++G G+SP
Sbjct: 23 TPFKNGELDLESYERLVRYQLENGVNALIVLGTTGESP 60
>pdb|3PB2|A Chain A, Characterisation Of The First Monomeric
Dihydrodipicolinate Synthase Variant Reveals
Evolutionary Insights
pdb|3PB2|B Chain B, Characterisation Of The First Monomeric
Dihydrodipicolinate Synthase Variant Reveals
Evolutionary Insights
pdb|3PB2|C Chain C, Characterisation Of The First Monomeric
Dihydrodipicolinate Synthase Variant Reveals
Evolutionary Insights
pdb|3PB2|D Chain D, Characterisation Of The First Monomeric
Dihydrodipicolinate Synthase Variant Reveals
Evolutionary Insights
pdb|3PB2|E Chain E, Characterisation Of The First Monomeric
Dihydrodipicolinate Synthase Variant Reveals
Evolutionary Insights
pdb|3PB2|F Chain F, Characterisation Of The First Monomeric
Dihydrodipicolinate Synthase Variant Reveals
Evolutionary Insights
Length = 300
Score = 26.9 bits (58), Expect = 9.1, Method: Compositional matrix adjust.
Identities = 12/38 (31%), Positives = 22/38 (57%)
Query: 57 SPTQNSGQQRESFDRPLENGLDPGIFKAILVGQVGQSP 94
+P +N ES++R + L+ G+ I++G G+SP
Sbjct: 17 TPFKNGELDLESYERLVRYQLENGVNALIVLGTTGESP 54
Database: pdbaa
Posted date: Mar 3, 2013 10:34 PM
Number of letters in database: 14,973,337
Number of sequences in database: 62,578
Lambda K H
0.317 0.136 0.399
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 6,476,577
Number of Sequences: 62578
Number of extensions: 257589
Number of successful extensions: 464
Number of sequences better than 100.0: 17
Number of HSP's better than 100.0 without gapping: 16
Number of HSP's successfully gapped in prelim test: 1
Number of HSP's that attempted gapping in prelim test: 439
Number of HSP's gapped (non-prelim): 17
length of query: 218
length of database: 14,973,337
effective HSP length: 95
effective length of query: 123
effective length of database: 9,028,427
effective search space: 1110496521
effective search space used: 1110496521
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 49 (23.5 bits)