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= 030281
(180 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>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 = 52.4 bits (124), Expect = 1e-07, Method: Compositional matrix adjust.
Identities = 30/114 (26%), Positives = 59/114 (51%), Gaps = 4/114 (3%)
Query: 48 RGVHKAIICGKVKDTPVQKILRNGKTVTIFSVGTGGLFDQRIVGSKDLPKPVQWHRIAVH 107
RGV+K I+ G + P + + NG V ++ T + + G ++ + +WHR+ +
Sbjct: 4 RGVNKVILVGNLGQDPEVRYMPNGGAVANITLATSESWRDKATG--EMKEQTEWHRVVLF 61
Query: 108 NEILGSYAVKQLVKNSSVYVEGDIEIRVYNDSINGEVKNIPEICIRRDGTLRLV 161
+ L A + L K S VY+EG + R + D +G+ + E+ + GT++++
Sbjct: 62 GK-LAEVASEYLRKGSQVYIEGQLRTRKWTDQ-SGQDRYTTEVVVNVGGTMQML 113
>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 = 52.4 bits (124), Expect = 1e-07, Method: Compositional matrix adjust.
Identities = 30/114 (26%), Positives = 59/114 (51%), Gaps = 4/114 (3%)
Query: 48 RGVHKAIICGKVKDTPVQKILRNGKTVTIFSVGTGGLFDQRIVGSKDLPKPVQWHRIAVH 107
RGV+K I+ G + P + + NG V ++ T + + G ++ + +WHR+ +
Sbjct: 4 RGVNKVILVGNLGQDPEVRYMPNGGAVANITLATSESWRDKATG--EMKEQTEWHRVVLF 61
Query: 108 NEILGSYAVKQLVKNSSVYVEGDIEIRVYNDSINGEVKNIPEICIRRDGTLRLV 161
+ L A + L K S VY+EG + R + D +G+ + E+ + GT++++
Sbjct: 62 GK-LAEVASEYLRKGSQVYIEGQLRTRKWTDQ-SGQDRYTTEVVVNVGGTMQML 113
>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 = 52.4 bits (124), Expect = 1e-07, Method: Compositional matrix adjust.
Identities = 30/114 (26%), Positives = 59/114 (51%), Gaps = 4/114 (3%)
Query: 48 RGVHKAIICGKVKDTPVQKILRNGKTVTIFSVGTGGLFDQRIVGSKDLPKPVQWHRIAVH 107
RGV+K I+ G + P + + NG V ++ T + + G ++ + +WHR+ +
Sbjct: 3 RGVNKVILVGNLGQDPEVRYMPNGGAVANITLATSESWRDKATG--EMKEQTEWHRVVLF 60
Query: 108 NEILGSYAVKQLVKNSSVYVEGDIEIRVYNDSINGEVKNIPEICIRRDGTLRLV 161
+ L A + L K S VY+EG + R + D +G+ + E+ + GT++++
Sbjct: 61 GK-LAEVASEYLRKGSQVYIEGQLRTRKWTDQ-SGQDRYTTEVVVNVGGTMQML 112
>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 = 52.4 bits (124), Expect = 1e-07, Method: Compositional matrix adjust.
Identities = 30/114 (26%), Positives = 59/114 (51%), Gaps = 4/114 (3%)
Query: 48 RGVHKAIICGKVKDTPVQKILRNGKTVTIFSVGTGGLFDQRIVGSKDLPKPVQWHRIAVH 107
RGV+K I+ G + P + + NG V ++ T + + G ++ + +WHR+ +
Sbjct: 3 RGVNKVILVGNLGQDPEVRYMPNGGAVANITLATSESWRDKATG--EMKEQTEWHRVVLF 60
Query: 108 NEILGSYAVKQLVKNSSVYVEGDIEIRVYNDSINGEVKNIPEICIRRDGTLRLV 161
+ L A + L K S VY+EG + R + D +G+ + E+ + GT++++
Sbjct: 61 GK-LAEVASEYLRKGSQVYIEGQLRTRKWTDQ-SGQDRYTTEVVVNVGGTMQML 112
>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 = 52.4 bits (124), Expect = 1e-07, Method: Compositional matrix adjust.
Identities = 30/114 (26%), Positives = 59/114 (51%), Gaps = 4/114 (3%)
Query: 48 RGVHKAIICGKVKDTPVQKILRNGKTVTIFSVGTGGLFDQRIVGSKDLPKPVQWHRIAVH 107
RGV+K I+ G + P + + NG V ++ T + + G ++ + +WHR+ +
Sbjct: 4 RGVNKVILVGNLGQDPEVRYMPNGGAVANITLATSESWRDKATG--EMKEQTEWHRVVLF 61
Query: 108 NEILGSYAVKQLVKNSSVYVEGDIEIRVYNDSINGEVKNIPEICIRRDGTLRLV 161
+ L A + L K S VY+EG + R + D +G+ + E+ + GT++++
Sbjct: 62 GK-LAEVASEYLRKGSQVYIEGQLRTRKWTDQ-SGQDRYTTEVVVNVGGTMQML 113
>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 = 52.0 bits (123), Expect = 2e-07, Method: Compositional matrix adjust.
Identities = 32/106 (30%), Positives = 54/106 (50%), Gaps = 3/106 (2%)
Query: 48 RGVHKAIICGKVKDTPVQKILRNGKTVTIFSVGTGGLFDQRIVGSKDLPKPVQWHRIAVH 107
+ ++K ++ G+V P KIL G V FS+ T + R + +L WHRI V+
Sbjct: 4 KSLNKIMLIGRVGCEPDIKILNGGDKVATFSLATNEFWRDR--NTNELKSKTDWHRIVVY 61
Query: 108 NEILGSYAVKQLVKNSSVYVEGDIEIRVYN-DSINGEVKNIPEICI 152
++ + K L K VYV+G + R ++ + +N + K I EI +
Sbjct: 62 DQNIVDLIDKYLRKGRRVYVQGSLHTRKWHTNDMNSQPKQITEIIL 107
>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 = 6e-07, Method: Compositional matrix adjust.
Identities = 31/94 (32%), Positives = 47/94 (50%), Gaps = 9/94 (9%)
Query: 48 RGVHKAIICGKVKDTPVQKILRNGKTVTIFSVGTGGLFDQRIVGSKDLPKPVQWHRIAVH 107
RGV+K I+ G + P + NG V ++ T + + G +L + +WHRIA
Sbjct: 6 RGVNKVILIGNLGQDPEVRYTPNGNAVANVTLATSTTWRDKQTG--ELQERTEWHRIAFF 63
Query: 108 N---EILGSYAVKQLVKNSSVYVEGDIEIRVYND 138
N EI+G Y L K S +Y+EG + R + D
Sbjct: 64 NRLAEIVGEY----LRKGSKIYIEGSLRTRKWQD 93
>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 = 47.8 bits (112), Expect = 4e-06, Method: Compositional matrix adjust.
Identities = 29/97 (29%), Positives = 48/97 (49%), Gaps = 3/97 (3%)
Query: 48 RGVHKAIICGKVKDTPVQKILRNGKTVTIFSVGTGGLF---DQRIVGSKDLPKPVQWHRI 104
R +++ + G+V PV + + VTIFS+ T ++ D + D+ + WHRI
Sbjct: 12 RSLNRVHLLGRVGQDPVLRQVEGKNPVTIFSLATNEMWRSGDSEVYQLGDVSQKTTWHRI 71
Query: 105 AVHNEILGSYAVKQLVKNSSVYVEGDIEIRVYNDSIN 141
+V L A + + K S +Y+EG I+ Y D N
Sbjct: 72 SVFRPGLRDVAYQYVKKGSRIYLEGKIDYGEYMDKNN 108
>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 = 47.4 bits (111), Expect = 4e-06, Method: Compositional matrix adjust.
Identities = 31/115 (26%), Positives = 55/115 (47%), Gaps = 4/115 (3%)
Query: 50 VHKAIICGKVKDTPVQKILRNGKTVTIFSVGTGGLFDQRIVGSKDLPKPVQWHRIAVHNE 109
++K ++ G + D P K + +G V F + T + + K + +WH + V N
Sbjct: 23 LNKVMLIGYLGDDPESKTMTSGAEVVNFRMATFESYMNKNTHQK--VEKTEWHSVVVFNP 80
Query: 110 ILGSYAVKQLVKNSSVYVEGDIEIRVYNDSINGEVKNIPEICI-RRDGTLRLVKS 163
A++ L K S VY+EG ++ R + D NG + EI + + G L L+ +
Sbjct: 81 HFAKIALQYLHKGSKVYIEGKLQTRKWQDK-NGHDRYTTEIVLPQYKGELHLLDA 134
>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 = 47.4 bits (111), Expect = 4e-06, Method: Compositional matrix adjust.
Identities = 29/97 (29%), Positives = 48/97 (49%), Gaps = 3/97 (3%)
Query: 48 RGVHKAIICGKVKDTPVQKILRNGKTVTIFSVGTGGLF---DQRIVGSKDLPKPVQWHRI 104
R +++ + G+V PV + + VTIFS+ T ++ D + D+ + WHRI
Sbjct: 13 RSLNRVHLLGRVGQDPVLRQVEGKNPVTIFSLATNEMWRSGDSEVYQLGDVSQKTTWHRI 72
Query: 105 AVHNEILGSYAVKQLVKNSSVYVEGDIEIRVYNDSIN 141
+V L A + + K S +Y+EG I+ Y D N
Sbjct: 73 SVFRPGLRDVAYQYVKKGSRIYLEGKIDYGEYMDKNN 109
>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 = 44.3 bits (103), Expect = 4e-05, Method: Compositional matrix adjust.
Identities = 32/122 (26%), Positives = 55/122 (45%), Gaps = 7/122 (5%)
Query: 33 ELQPQGVDPRRGWGFRGVHKAIICGKVKDTPVQKILRNGKTVTIFSVGTGGLFDQRIVGS 92
E Q QG G ++K I+ G + P + L +G V + T + R +
Sbjct: 13 EAQTQGPGSMAG----SLNKVILIGNLGADPEIRRLNSGDQVANLRIATSESWRDR--NT 66
Query: 93 KDLPKPVQWHRIAVHNEILGSYAVKQLVKNSSVYVEGDIEIRVYNDSINGEVKNIPEICI 152
+ + +WH I + NE L + L K S +Y+EG ++ R + D NG + EI +
Sbjct: 67 NERKERTEWHNIVIFNENLVKVVEQYLKKGSKIYIEGQLQTRKWQDQ-NGNDRYTTEIVL 125
Query: 153 RR 154
++
Sbjct: 126 QK 127
>pdb|3UDG|A Chain A, Structure Of Deinococcus Radiodurans Ssb Bound To Ssdna
pdb|3UDG|B Chain B, Structure Of Deinococcus Radiodurans Ssb Bound To Ssdna
pdb|3UDG|C Chain C, Structure Of Deinococcus Radiodurans Ssb Bound To Ssdna
Length = 301
Score = 30.0 bits (66), Expect = 0.66, Method: Compositional matrix adjust.
Identities = 21/90 (23%), Positives = 42/90 (46%), Gaps = 5/90 (5%)
Query: 48 RGVHKAIICGKVKDTPVQKILRNGKTVTIFSVGTGGLFDQRIVGSKDLPKPVQW-HRIAV 106
RG++ + G + P + NG + +F G + R++G+ + + W HR+++
Sbjct: 3 RGMNHVYLIGALARDPELRYTGNG--MAVFEATVAG--EDRVIGNDGRERNLPWYHRVSI 58
Query: 107 HNEILGSYAVKQLVKNSSVYVEGDIEIRVY 136
+ A + L +V VEG +E R +
Sbjct: 59 LGKPAEWQAERNLKGGDAVVVEGTLEYRQW 88
>pdb|1CNT|1 Chain 1, Ciliary Neurotrophic Factor
pdb|1CNT|2 Chain 2, Ciliary Neurotrophic Factor
pdb|1CNT|3 Chain 3, Ciliary Neurotrophic Factor
pdb|1CNT|4 Chain 4, Ciliary Neurotrophic Factor
Length = 187
Score = 29.6 bits (65), Expect = 1.1, Method: Compositional matrix adjust.
Identities = 16/43 (37%), Positives = 25/43 (58%)
Query: 66 KILRNGKTVTIFSVGTGGLFDQRIVGSKDLPKPVQWHRIAVHN 108
KI RN +VG GGLF++++ G K L + QW ++H+
Sbjct: 133 KIPRNEADGMPINVGDGGLFEKKLWGLKVLQELSQWTVRSIHD 175
>pdb|1SE8|A Chain A, Structure Of Single-Stranded Dna-Binding Protein (Ssb)
From D. Radiodurans
Length = 301
Score = 28.9 bits (63), Expect = 1.7, Method: Compositional matrix adjust.
Identities = 22/90 (24%), Positives = 40/90 (44%), Gaps = 5/90 (5%)
Query: 48 RGVHKAIICGKVKDTPVQKILRNGKTVTIFSVGTGGLFDQRIVGSKDLPKPVQW-HRIAV 106
RG + + G + P + NG V F G + R++G+ + + W HR+++
Sbjct: 3 RGXNHVYLIGALARDPELRYTGNGXAV--FEATVAG--EDRVIGNDGRERNLPWYHRVSI 58
Query: 107 HNEILGSYAVKQLVKNSSVYVEGDIEIRVY 136
+ A + L +V VEG +E R +
Sbjct: 59 LGKPAEWQAERNLKGGDAVVVEGTLEYRQW 88
>pdb|1GV1|A Chain A, Structural Basis For Thermophilic Protein Stability:
Structures Of Thermophilic And Mesophilic Malate
Dehydrogenases
pdb|1GV1|B Chain B, Structural Basis For Thermophilic Protein Stability:
Structures Of Thermophilic And Mesophilic Malate
Dehydrogenases
pdb|1GV1|C Chain C, Structural Basis For Thermophilic Protein Stability:
Structures Of Thermophilic And Mesophilic Malate
Dehydrogenases
pdb|1GV1|D Chain D, Structural Basis For Thermophilic Protein Stability:
Structures Of Thermophilic And Mesophilic Malate
Dehydrogenases
Length = 310
Score = 26.2 bits (56), Expect = 9.6, Method: Compositional matrix adjust.
Identities = 11/25 (44%), Positives = 15/25 (60%)
Query: 70 NGKTVTIFSVGTGGLFDQRIVGSKD 94
GK + ++ G GLFD +I GS D
Sbjct: 39 QGKGLDMYETGPVGLFDTKITGSND 63
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
0.319 0.140 0.422
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 5,232,329
Number of Sequences: 62578
Number of extensions: 212999
Number of successful extensions: 410
Number of sequences better than 100.0: 17
Number of HSP's better than 100.0 without gapping: 9
Number of HSP's successfully gapped in prelim test: 8
Number of HSP's that attempted gapping in prelim test: 396
Number of HSP's gapped (non-prelim): 17
length of query: 180
length of database: 14,973,337
effective HSP length: 93
effective length of query: 87
effective length of database: 9,153,583
effective search space: 796361721
effective search space used: 796361721
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 48 (23.1 bits)