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= 017008
(379 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|4DQI|A Chain A, Ternary Complex Of Bacillus Dna Polymerase I Large
Fragment, Dna Duplex, And Dctp (Paired With Dg Of
Template)
pdb|4DQI|D Chain D, Ternary Complex Of Bacillus Dna Polymerase I Large
Fragment, Dna Duplex, And Dctp (Paired With Dg Of
Template)
pdb|4DQP|A Chain A, Ternary Complex Of Bacillus Dna Polymerase I Large
Fragment, Dna Duplex, And Ddctp (Paired With Dg Of
Template)
pdb|4DQP|D Chain D, Ternary Complex Of Bacillus Dna Polymerase I Large
Fragment, Dna Duplex, And Ddctp (Paired With Dg Of
Template)
pdb|4DS4|A Chain A, Ternary Complex Of Bacillus Dna Polymerase I Large
Fragment, Dna Duplex, And Rctp In Presence Of Mn2+
pdb|4DS4|D Chain D, Ternary Complex Of Bacillus Dna Polymerase I Large
Fragment, Dna Duplex, And Rctp In Presence Of Mn2+
pdb|4DS5|A Chain A, Ternary Complex Of Bacillus Dna Polymerase I Large
Fragment, Dna Duplex, And Rctp In Presence Of Mg2+
pdb|4DS5|D Chain D, Ternary Complex Of Bacillus Dna Polymerase I Large
Fragment, Dna Duplex, And Rctp In Presence Of Mg2+
Length = 592
Score = 33.9 bits (76), Expect = 0.17, Method: Compositional matrix adjust.
Identities = 26/105 (24%), Positives = 40/105 (38%), Gaps = 8/105 (7%)
Query: 241 VSGSGAANWFPASPTIGSKISRAS-------RASLATIRGDENDVXXXXXXXXXXXYIDD 293
V G GA P P + + R + R L +R +E D + +
Sbjct: 144 VYGKGAKRAVPDEPVLAEHLVRKAAAIWELERPFLDELRRNEQDRLLVELEQPLSSILAE 203
Query: 294 TEDYINIQLDNHRNQLIQLELFLSSGTVSLSIYSLVAGIFGMNIP 338
E + +++D R + + EL GTV IY L F +N P
Sbjct: 204 ME-FAGVKVDTKRLEQMGKELAEQLGTVEQRIYELAGQEFNINSP 247
>pdb|3PV8|A Chain A, Crystal Structure Of Bacillus Dna Polymerase I Large
Fragment Bound To Dna And Ddttp-Da In Closed
Conformation
pdb|3PV8|D Chain D, Crystal Structure Of Bacillus Dna Polymerase I Large
Fragment Bound To Dna And Ddttp-Da In Closed
Conformation
pdb|3PX0|A Chain A, Crystal Structure Of Bacillus Dna Polymerase I Large
Fragment Bound To Dna And Dctp-Da Mismatch (Tautomer) In
Closed Conformation
pdb|3PX0|D Chain D, Crystal Structure Of Bacillus Dna Polymerase I Large
Fragment Bound To Dna And Dctp-Da Mismatch (Tautomer) In
Closed Conformation
pdb|3PX4|A Chain A, Crystal Structure Of Bacillus Dna Polymerase I Large
Fragment Bound To Dna And Ddctp-Da Mismatch (Wobble) In
Ajar Conformation
pdb|3PX4|D Chain D, Crystal Structure Of Bacillus Dna Polymerase I Large
Fragment Bound To Dna And Ddctp-Da Mismatch (Wobble) In
Ajar Conformation
pdb|3PX6|A Chain A, Crystal Structure Of Bacillus Dna Polymerase I Large
Fragment Bound To Dna And Ddctp-Da Mismatch (Tautomer)
In Closed Conformation
pdb|3PX6|D Chain D, Crystal Structure Of Bacillus Dna Polymerase I Large
Fragment Bound To Dna And Ddctp-Da Mismatch (Tautomer)
In Closed Conformation
pdb|3THV|A Chain A, Crystal Structure Of Bacillus Dna Polymerase I Large
Fragment Bound To Dna And Ddatp-Dt In Closed
Conformation
pdb|3THV|D Chain D, Crystal Structure Of Bacillus Dna Polymerase I Large
Fragment Bound To Dna And Ddatp-Dt In Closed
Conformation
pdb|3TI0|A Chain A, Crystal Structure Of Bacillus Dna Polymerase I Large
Fragment Bound To Dna And Ddgtp-Dc In Closed
Conformation
pdb|3TI0|D Chain D, Crystal Structure Of Bacillus Dna Polymerase I Large
Fragment Bound To Dna And Ddgtp-Dc In Closed
Conformation
pdb|4DSE|A Chain A, Ternary Complex Of Bacillus Dna Polymerase I Large
Fragment F710y, Dna Duplex, And Rctp (Paired With Dg Of
Template) In Presence Of Mg2+
pdb|4DSE|D Chain D, Ternary Complex Of Bacillus Dna Polymerase I Large
Fragment F710y, Dna Duplex, And Rctp (Paired With Dg Of
Template) In Presence Of Mg2+
pdb|4DSF|A Chain A, Ternary Complex Of Bacillus Dna Polymerase I Large
Fragment F710y, Dna Duplex, And Rctp (Paired With Dg Of
Template) In Presence Of Mn2+
pdb|4DSF|D Chain D, Ternary Complex Of Bacillus Dna Polymerase I Large
Fragment F710y, Dna Duplex, And Rctp (Paired With Dg Of
Template) In Presence Of Mn2+
Length = 592
Score = 33.9 bits (76), Expect = 0.17, Method: Compositional matrix adjust.
Identities = 26/105 (24%), Positives = 40/105 (38%), Gaps = 8/105 (7%)
Query: 241 VSGSGAANWFPASPTIGSKISRAS-------RASLATIRGDENDVXXXXXXXXXXXYIDD 293
V G GA P P + + R + R L +R +E D + +
Sbjct: 144 VYGKGAKRAVPDEPVLAEHLVRKAAAIWELERPFLDELRRNEQDRLLVELEQPLSSILAE 203
Query: 294 TEDYINIQLDNHRNQLIQLELFLSSGTVSLSIYSLVAGIFGMNIP 338
E + +++D R + + EL GTV IY L F +N P
Sbjct: 204 ME-FAGVKVDTKRLEQMGKELAEQLGTVEQRIYELAGQEFNINSP 247
>pdb|3TAN|A Chain A, Crystal Structure Of Bacillus Dna Polymerase I Large
Fragment Bound To Duplex Dna With Cytosine-Adenine
Mismatch At (N-1) Position
pdb|3TAP|A Chain A, Crystal Structure Of Bacillus Dna Polymerase I Large
Fragment Bound To Duplex Dna With Cytosine-Adenine
Mismatch At (N-3) Position
pdb|3TAQ|A Chain A, Crystal Structure Of Bacillus Dna Polymerase I Large
Fragment Bound To Duplex Dna With Cytosine-Adenine
Mismatch At (N-4) Position
pdb|3TAR|A Chain A, Crystal Structure Of Bacillus Dna Polymerase I Large
Fragment Bound To Duplex Dna With Cytosine-Adenine
Mismatch At (N-6) Position
pdb|4DQS|A Chain A, Binary Complex Of Bacillus Dna Polymerase I Large Fragment
And Duplex Dna With Rc In Primer Terminus Paired With Dg
Of Template
Length = 592
Score = 33.9 bits (76), Expect = 0.17, Method: Compositional matrix adjust.
Identities = 26/105 (24%), Positives = 40/105 (38%), Gaps = 8/105 (7%)
Query: 241 VSGSGAANWFPASPTIGSKISRAS-------RASLATIRGDENDVXXXXXXXXXXXYIDD 293
V G GA P P + + R + R L +R +E D + +
Sbjct: 144 VYGKGAKRAVPDEPVLAEHLVRKAAAIWELERPFLDELRRNEQDRLLVELEQPLSSILAE 203
Query: 294 TEDYINIQLDNHRNQLIQLELFLSSGTVSLSIYSLVAGIFGMNIP 338
E + +++D R + + EL GTV IY L F +N P
Sbjct: 204 ME-FAGVKVDTKRLEQMGKELAEQLGTVEQRIYELAGQEFNINSP 247
>pdb|3HT3|A Chain A, Crystal Structure Of Fragment Dna Polymerase I From
Bacillus Stearothermophilus V713p Mutant Bound To G:dctp
pdb|3HT3|D Chain D, Crystal Structure Of Fragment Dna Polymerase I From
Bacillus Stearothermophilus V713p Mutant Bound To G:dctp
Length = 579
Score = 33.9 bits (76), Expect = 0.17, Method: Compositional matrix adjust.
Identities = 26/105 (24%), Positives = 40/105 (38%), Gaps = 8/105 (7%)
Query: 241 VSGSGAANWFPASPTIGSKISRAS-------RASLATIRGDENDVXXXXXXXXXXXYIDD 293
V G GA P P + + R + R L +R +E D + +
Sbjct: 131 VYGKGAKRAVPDEPVLAEHLVRKAAAIWELERPFLDELRRNEQDRLLVELEQPLSSILAE 190
Query: 294 TEDYINIQLDNHRNQLIQLELFLSSGTVSLSIYSLVAGIFGMNIP 338
E + +++D R + + EL GTV IY L F +N P
Sbjct: 191 ME-FAGVKVDTKRLEQMGKELAEQLGTVEQRIYELAGQEFNINSP 234
>pdb|4DQQ|A Chain A, Ternary Complex Of Bacillus Dna Polymerase I Large
Fragment E658a, Dna Duplex, And Rctp (Paired With Dg Of
Template) In Presence Of Mg2+
pdb|4DQQ|D Chain D, Ternary Complex Of Bacillus Dna Polymerase I Large
Fragment E658a, Dna Duplex, And Rctp (Paired With Dg Of
Template) In Presence Of Mg2+
pdb|4DQR|A Chain A, Ternary Complex Of Bacillus Dna Polymerase I Large
Fragment E658a, Dna Duplex, And Rctp (Paired With Dg Of
Template) In Presence Of Mn2+
pdb|4DQR|D Chain D, Ternary Complex Of Bacillus Dna Polymerase I Large
Fragment E658a, Dna Duplex, And Rctp (Paired With Dg Of
Template) In Presence Of Mn2+
pdb|4E0D|A Chain A, Binary Complex Of Bacillus Dna Polymerase I Large Fragment
E658a And Duplex Dna
Length = 592
Score = 33.9 bits (76), Expect = 0.18, Method: Compositional matrix adjust.
Identities = 26/105 (24%), Positives = 40/105 (38%), Gaps = 8/105 (7%)
Query: 241 VSGSGAANWFPASPTIGSKISRAS-------RASLATIRGDENDVXXXXXXXXXXXYIDD 293
V G GA P P + + R + R L +R +E D + +
Sbjct: 144 VYGKGAKRAVPDEPVLAEHLVRKAAAIWELERPFLDELRRNEQDRLLVELEQPLSSILAE 203
Query: 294 TEDYINIQLDNHRNQLIQLELFLSSGTVSLSIYSLVAGIFGMNIP 338
E + +++D R + + EL GTV IY L F +N P
Sbjct: 204 ME-FAGVKVDTKRLEQMGKELAEQLGTVEQRIYELAGQEFNINSP 247
>pdb|1LV5|A Chain A, Crystal Structure Of The Closed Conformation Of Bacillus
Dna Polymerase I Fragment Bound To Dna And Dctp
pdb|1LV5|B Chain B, Crystal Structure Of The Closed Conformation Of Bacillus
Dna Polymerase I Fragment Bound To Dna And Dctp
Length = 580
Score = 33.5 bits (75), Expect = 0.18, Method: Compositional matrix adjust.
Identities = 26/105 (24%), Positives = 40/105 (38%), Gaps = 8/105 (7%)
Query: 241 VSGSGAANWFPASPTIGSKISRAS-------RASLATIRGDENDVXXXXXXXXXXXYIDD 293
V G GA P P + + R + R L +R +E D + +
Sbjct: 132 VYGKGAKRAVPDEPVLAEHLVRKAAAIWELERPFLDELRRNEQDRLLVELEQPLSSILAE 191
Query: 294 TEDYINIQLDNHRNQLIQLELFLSSGTVSLSIYSLVAGIFGMNIP 338
E + +++D R + + EL GTV IY L F +N P
Sbjct: 192 ME-FAGVKVDTKRLEQMGKELAEQLGTVEQRIYELAGQEFNINSP 235
>pdb|1L3S|A Chain A, Crystal Structure Of Bacillus Dna Polymerase I Fragment
Complexed To 9 Base Pairs Of Duplex Dna.
pdb|1L3T|A Chain A, Crystal Structure Of Bacillus Dna Polymerase I Fragment
Product Complex With 10 Base Pairs Of Duplex Dna
Following Addition Of A Single Dttp Residue
pdb|1L3U|A Chain A, Crystal Structure Of Bacillus Dna Polymerase I Fragment
Product Complex With 11 Base Pairs Of Duplex Dna
Following Addition Of A Dttp And A Datp Residue.
pdb|1L3V|A Chain A, Crystal Structure Of Bacillus Dna Polymerase I Fragment
Product Complex With 15 Base Pairs Of Duplex Dna
Following Addition Of Dttp, Datp, Dctp, And Dgtp
Residues.
pdb|1L5U|A Chain A, Crystal Structure Of Bacillus Dna Polymerase I Fragment
Product Complex With 12 Base Pairs Of Duplex Dna
Following Addition Of A Dttp, A Datp, And A Dctp
Residue.
pdb|1NJW|A Chain A, Guanine-Thymine Mismatch At The Polymerase Active Site
pdb|1NJX|A Chain A, Thymine-Guanine Mismatch At The Polymerase Active Site
pdb|1NJY|A Chain A, Thymine-Thymine Mismatch At The Polymerase Active Site
pdb|1NJZ|A Chain A, Cytosine-thymine Mismatch At The Polymerase Active Site
pdb|1NK0|A Chain A, Adenine-Guanine Mismatch At The Polymerase Active Site
pdb|1NK4|A Chain A, Guanine-Guanine Mismatch At The Polymerase Active Site
pdb|1NK5|A Chain A, Adenine-Adenine Mismatch At The Polymerase Active Site
pdb|1NK6|A Chain A, Cytosine-Cytosine Mismatch At The Polymerase Active Site
pdb|1NK7|A Chain A, Guanine-Adenine Mismatch At The Polymerase Active Site
pdb|1NK8|A Chain A, A Bacillus Dna Polymerase I Product Complex Bound To A
Guanine-Thymine Mismatch After A Single Round Of Primer
Extension, Following Incorporation Of Dctp.
pdb|1NK9|A Chain A, A Bacillus Dna Polymerase I Product Complex Bound To A
Guanine-Thymine Mismatch After Two Rounds Of Primer
Extension, Following Incorporation Of Dctp And Dgtp.
pdb|1NKB|A Chain A, A Bacillus Dna Polymerase I Product Complex Bound To A
Guanine-Thymine Mismatch After Three Rounds Of Primer
Extension, Following Incorporation Of Dctp, Dgtp, And
Dttp.
pdb|1NKC|A Chain A, A Bacillus Dna Polymerase I Product Complex Bound To A
Guanine-Thymine Mismatch After Five Rounds Of Primer
Extension, Following Incorporation Of Dctp, Dgtp, Dttp,
And Datp.
pdb|1NKE|A Chain A, A Bacillus Dna Polymerase I Product Complex Bound To A
Cytosine-Thymine Mismatch After A Single Round Of Primer
Extension, Following Incorporation Of Dctp.
pdb|1XC9|A Chain A, Structure Of A High-Fidelity Polymerase Bound To A
Benzo[a]pyrene Adduct That Blocks Replication
pdb|1XWL|A Chain A, Bacillus Stearothermophilus (Newly Identified Strain As
Yet Unnamed) Dna Polymerase Fragment
Length = 580
Score = 33.5 bits (75), Expect = 0.18, Method: Compositional matrix adjust.
Identities = 26/105 (24%), Positives = 40/105 (38%), Gaps = 8/105 (7%)
Query: 241 VSGSGAANWFPASPTIGSKISRAS-------RASLATIRGDENDVXXXXXXXXXXXYIDD 293
V G GA P P + + R + R L +R +E D + +
Sbjct: 132 VYGKGAKRAVPDEPVLAEHLVRKAAAIWELERPFLDELRRNEQDRLLVELEQPLSSILAE 191
Query: 294 TEDYINIQLDNHRNQLIQLELFLSSGTVSLSIYSLVAGIFGMNIP 338
E + +++D R + + EL GTV IY L F +N P
Sbjct: 192 ME-FAGVKVDTKRLEQMGKELAEQLGTVEQRIYELAGQEFNINSP 235
>pdb|3BDP|A Chain A, Dna Polymerase IDNA COMPLEX
pdb|4BDP|A Chain A, Crystal Structure Of Bacillus Dna Polymerase I Fragment
Complexed To 11 Base Pairs Of Duplex Dna After Addition
Of Two Datp Residues
pdb|2BDP|A Chain A, Crystal Structure Of Bacillus Dna Polymerase I Fragment
Complexed To 9 Base Pairs Of Duplex Dna
Length = 580
Score = 33.5 bits (75), Expect = 0.18, Method: Compositional matrix adjust.
Identities = 26/105 (24%), Positives = 40/105 (38%), Gaps = 8/105 (7%)
Query: 241 VSGSGAANWFPASPTIGSKISRAS-------RASLATIRGDENDVXXXXXXXXXXXYIDD 293
V G GA P P + + R + R L +R +E D + +
Sbjct: 132 VYGKGAKRAVPDEPVLAEHLVRKAAAIWELERPFLDELRRNEQDRLLVELEQPLSSILAE 191
Query: 294 TEDYINIQLDNHRNQLIQLELFLSSGTVSLSIYSLVAGIFGMNIP 338
E + +++D R + + EL GTV IY L F +N P
Sbjct: 192 ME-FAGVKVDTKRLEQMGKELAEQLGTVEQRIYELAGQEFNINSP 235
>pdb|3EYZ|A Chain A, Cocrystal Structure Of Bacillus Fragment Dna Polymerase I
With Duplex Dna (Open Form)
Length = 580
Score = 33.5 bits (75), Expect = 0.18, Method: Compositional matrix adjust.
Identities = 26/105 (24%), Positives = 40/105 (38%), Gaps = 8/105 (7%)
Query: 241 VSGSGAANWFPASPTIGSKISRAS-------RASLATIRGDENDVXXXXXXXXXXXYIDD 293
V G GA P P + + R + R L +R +E D + +
Sbjct: 132 VYGKGAKRAVPDEPVLAEHLVRKAAAIWELERPFLDELRRNEQDRLLVELEQPLSSILAE 191
Query: 294 TEDYINIQLDNHRNQLIQLELFLSSGTVSLSIYSLVAGIFGMNIP 338
E + +++D R + + EL GTV IY L F +N P
Sbjct: 192 ME-FAGVKVDTKRLEQMGKELAEQLGTVEQRIYELAGQEFNINSP 235
>pdb|2HHW|A Chain A, Ddttp:o6-Methyl-Guanine Pair In The Polymerase Active
Site, In The Closed Conformation
pdb|2HHW|D Chain D, Ddttp:o6-Methyl-Guanine Pair In The Polymerase Active
Site, In The Closed Conformation
Length = 580
Score = 33.5 bits (75), Expect = 0.18, Method: Compositional matrix adjust.
Identities = 26/105 (24%), Positives = 40/105 (38%), Gaps = 8/105 (7%)
Query: 241 VSGSGAANWFPASPTIGSKISRAS-------RASLATIRGDENDVXXXXXXXXXXXYIDD 293
V G GA P P + + R + R L +R +E D + +
Sbjct: 132 VYGKGAKRAVPDEPVLAEHLVRKAAAIWELERPFLDELRRNEQDRLLVELEQPLSSILAE 191
Query: 294 TEDYINIQLDNHRNQLIQLELFLSSGTVSLSIYSLVAGIFGMNIP 338
E + +++D R + + EL GTV IY L F +N P
Sbjct: 192 ME-FAGVKVDTKRLEQMGKELAEQLGTVEQRIYELAGQEFNINSP 235
>pdb|2HHQ|A Chain A, O6-Methyl-Guanine:t Pair In The Polymerase-10 Basepair
Position
pdb|2HHS|A Chain A, O6-Methyl:c Pair In The Polymerase-10 Basepair Position
pdb|2HHT|A Chain A, C:o6-Methyl-Guanine Pair In The Polymerase-2 Basepair
Position
pdb|2HHU|A Chain A, C:o6-Methyl-Guanine In The Polymerase Postinsertion Site
(- 1 Basepair Position)
pdb|2HHV|A Chain A, T:o6-Methyl-Guanine In The Polymerase-2 Basepair Position
pdb|2HHX|A Chain A, O6-Methyl-Guanine In The Polymerase Template Preinsertion
Site
pdb|2HW3|A Chain A, T:o6-Methyl-Guanine Pair In The Polymerase Postinsertion
Site (-1 Basepair Position)
Length = 580
Score = 33.5 bits (75), Expect = 0.18, Method: Compositional matrix adjust.
Identities = 26/105 (24%), Positives = 40/105 (38%), Gaps = 8/105 (7%)
Query: 241 VSGSGAANWFPASPTIGSKISRAS-------RASLATIRGDENDVXXXXXXXXXXXYIDD 293
V G GA P P + + R + R L +R +E D + +
Sbjct: 132 VYGKGAKRAVPDEPVLAEHLVRKAAAIWELERPFLDELRRNEQDRLLVELEQPLSSILAE 191
Query: 294 TEDYINIQLDNHRNQLIQLELFLSSGTVSLSIYSLVAGIFGMNIP 338
E + +++D R + + EL GTV IY L F +N P
Sbjct: 192 ME-FAGVKVDTKRLEQMGKELAEQLGTVEQRIYELAGQEFNINSP 235
>pdb|2HVH|A Chain A, Ddctp:o6meg Pair In The Polymerase Active Site (0
Position)
pdb|2HVH|D Chain D, Ddctp:o6meg Pair In The Polymerase Active Site (0
Position)
pdb|2HVI|A Chain A, Ddctp:g Pair In The Polymerase Active Site (0 Position)
pdb|2HVI|D Chain D, Ddctp:g Pair In The Polymerase Active Site (0 Position)
pdb|3EZ5|A Chain A, Cocrystal Structure Of Bacillus Fragment Dna Polymerase I
With Duplex Dna , Dctp, And Zinc (Closed Form).
pdb|3EZ5|D Chain D, Cocrystal Structure Of Bacillus Fragment Dna Polymerase I
With Duplex Dna , Dctp, And Zinc (Closed Form)
Length = 580
Score = 33.5 bits (75), Expect = 0.18, Method: Compositional matrix adjust.
Identities = 26/105 (24%), Positives = 40/105 (38%), Gaps = 8/105 (7%)
Query: 241 VSGSGAANWFPASPTIGSKISRAS-------RASLATIRGDENDVXXXXXXXXXXXYIDD 293
V G GA P P + + R + R L +R +E D + +
Sbjct: 132 VYGKGAKRAVPDEPVLAEHLVRKAAAIWELERPFLDELRRNEQDRLLVELEQPLSSILAE 191
Query: 294 TEDYINIQLDNHRNQLIQLELFLSSGTVSLSIYSLVAGIFGMNIP 338
E + +++D R + + EL GTV IY L F +N P
Sbjct: 192 ME-FAGVKVDTKRLEQMGKELAEQLGTVEQRIYELAGQEFNINSP 235
>pdb|1U45|A Chain A, 8oxoguanine At The Pre-Insertion Site Of The Polymerase
Active Site
pdb|1U47|A Chain A, Cytosine-8-Oxoguanine Base Pair At The Polymerase Active
Site
pdb|1U48|A Chain A, Extension Of A Cytosine-8-Oxoguanine Base Pair
pdb|1U49|A Chain A, Adenine-8oxoguanine Mismatch At The Polymerase Active Site
pdb|1U4B|A Chain A, Extension Of An Adenine-8oxoguanine Mismatch
pdb|1UA0|A Chain A, Aminofluorene Dna Adduct At The Pre-Insertion Site Of A
Dna Polymerase
pdb|1UA1|A Chain A, Structure Of Aminofluorene Adduct Paired Opposite Cytosine
At The Polymerase Active Site
Length = 580
Score = 33.5 bits (75), Expect = 0.18, Method: Compositional matrix adjust.
Identities = 26/105 (24%), Positives = 40/105 (38%), Gaps = 8/105 (7%)
Query: 241 VSGSGAANWFPASPTIGSKISRAS-------RASLATIRGDENDVXXXXXXXXXXXYIDD 293
V G GA P P + + R + R L +R +E D + +
Sbjct: 132 VYGKGAKRAVPDEPVLAEHLVRKAAAIWELERPFLDELRRNEQDRLLVELEQPLSSILAE 191
Query: 294 TEDYINIQLDNHRNQLIQLELFLSSGTVSLSIYSLVAGIFGMNIP 338
E + +++D R + + EL GTV IY L F +N P
Sbjct: 192 ME-FAGVKVDTKRLEQMGKELAEQLGTVEQRIYELAGQEFNINSP 235
>pdb|3HP6|A Chain A, Crystal Structure Of Fragment Dna Polymerase I From
Bacillus Stearothermophilus F710y Mutant Bound To G:t
Mismatch
pdb|3HP6|D Chain D, Crystal Structure Of Fragment Dna Polymerase I From
Bacillus Stearothermophilus F710y Mutant Bound To G:t
Mismatch
Length = 580
Score = 33.5 bits (75), Expect = 0.19, Method: Compositional matrix adjust.
Identities = 26/105 (24%), Positives = 40/105 (38%), Gaps = 8/105 (7%)
Query: 241 VSGSGAANWFPASPTIGSKISRAS-------RASLATIRGDENDVXXXXXXXXXXXYIDD 293
V G GA P P + + R + R L +R +E D + +
Sbjct: 132 VYGKGAKRAVPDEPVLAEHLVRKAAAIWELERPFLDELRRNEQDRLLVELEQPLSSILAE 191
Query: 294 TEDYINIQLDNHRNQLIQLELFLSSGTVSLSIYSLVAGIFGMNIP 338
E + +++D R + + EL GTV IY L F +N P
Sbjct: 192 ME-FAGVKVDTKRLEQMGKELAEQLGTVEQRIYELAGQEFNINSP 235
>pdb|3HPO|A Chain A, Crystal Structure Of Fragment Dna Polymerase I From
Bacillus Stearothermophilus Y714s Mutant Bound To G:t
Mismatch
Length = 580
Score = 33.5 bits (75), Expect = 0.20, Method: Compositional matrix adjust.
Identities = 26/105 (24%), Positives = 40/105 (38%), Gaps = 8/105 (7%)
Query: 241 VSGSGAANWFPASPTIGSKISRAS-------RASLATIRGDENDVXXXXXXXXXXXYIDD 293
V G GA P P + + R + R L +R +E D + +
Sbjct: 132 VYGKGAKRAVPDEPVLAEHLVRKAAAIWELERPFLDELRRNEQDRLLVELEQPLSSILAE 191
Query: 294 TEDYINIQLDNHRNQLIQLELFLSSGTVSLSIYSLVAGIFGMNIP 338
E + +++D R + + EL GTV IY L F +N P
Sbjct: 192 ME-FAGVKVDTKRLEQMGKELAEQLGTVEQRIYELAGQEFNINSP 235
>pdb|3RKG|A Chain A, Structural And Functional Characterization Of The Yeast
Mg2+ Channel Mrs2
Length = 261
Score = 30.0 bits (66), Expect = 2.3, Method: Compositional matrix adjust.
Identities = 18/44 (40%), Positives = 27/44 (61%), Gaps = 1/44 (2%)
Query: 58 RDLRILD-PLLSYPSTILGREQAIVLNLEHIKAIITSEEVLLRD 100
RDLR +D + TI+ + IV+NL HIKA+I ++V + D
Sbjct: 49 RDLRKIDNSSIDIIPTIMCKPNCIVINLLHIKALIERDKVYVFD 92
>pdb|4EV6|A Chain A, The Complete Structure Of Cora Magnesium Transporter From
Methanocaldococcus Jannaschii
pdb|4EV6|B Chain B, The Complete Structure Of Cora Magnesium Transporter From
Methanocaldococcus Jannaschii
pdb|4EV6|C Chain C, The Complete Structure Of Cora Magnesium Transporter From
Methanocaldococcus Jannaschii
pdb|4EV6|D Chain D, The Complete Structure Of Cora Magnesium Transporter From
Methanocaldococcus Jannaschii
pdb|4EV6|E Chain E, The Complete Structure Of Cora Magnesium Transporter From
Methanocaldococcus Jannaschii
Length = 339
Score = 28.9 bits (63), Expect = 5.0, Method: Compositional matrix adjust.
Identities = 20/71 (28%), Positives = 38/71 (53%), Gaps = 5/71 (7%)
Query: 298 INIQLDNHR-NQLIQLELFLSSGTVSLSIYSLVAGIFGMNIPYTWNENHGYMFKWVVIFT 356
I + L+N + NQ++++ L+ T ++ + GI+GMN Y N+ F W+V+
Sbjct: 266 ITLSLENIKMNQIMKI---LTMVTTIFAVPMWITGIYGMNFSYLPLANNPQGF-WLVMAL 321
Query: 357 AIFCAVTFVFI 367
+ + FV+I
Sbjct: 322 MVVIIMIFVYI 332
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
0.320 0.136 0.395
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 8,998,322
Number of Sequences: 62578
Number of extensions: 314723
Number of successful extensions: 588
Number of sequences better than 100.0: 17
Number of HSP's better than 100.0 without gapping: 1
Number of HSP's successfully gapped in prelim test: 16
Number of HSP's that attempted gapping in prelim test: 586
Number of HSP's gapped (non-prelim): 18
length of query: 379
length of database: 14,973,337
effective HSP length: 100
effective length of query: 279
effective length of database: 8,715,537
effective search space: 2431634823
effective search space used: 2431634823
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 52 (24.6 bits)