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= 019168
(345 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|4GMH|A Chain A, Crystal Structure Of Staphylococcus Aureus
5'-MethylthioadenosineS- Adenosylhomocysteine
Nucleosidase
Length = 230
Score = 59.7 bits (143), Expect = 3e-09, Method: Compositional matrix adjust.
Identities = 62/256 (24%), Positives = 111/256 (43%), Gaps = 55/256 (21%)
Query: 54 GPYIGLVMAYPPEESALITSRLFVHNSRIPFIDLAGRRFNVGKIKNVDVIYVMTGEQTVN 113
G IG++ A EE ++ ++L +++ I +A +F G +K+ +V+ +G VN
Sbjct: 1 GSMIGIIGAME-EEVTILKNKL----TQLSEISVAHVKFYTGILKDREVVITQSGIGKVN 55
Query: 114 SGITVQILLDAFDIRGVVHYGTAGSSNNSLSFGDVSVMKYVAFTGSWKWKAFKSETGQLP 173
+ I+ +L++ F +++ G+AG+ + SL+ GDV + V + + AF E GQ+P
Sbjct: 56 AAISTTLLINKFKPDVIINTGSAGALDESLNVGDVLISDDVKYHDA-DATAFGYEYGQIP 114
Query: 174 ELDFGAFNFPVRGKNLLAKVEFTPSQLYSAGKPMEELFWLPVDSEWFDIATQLQDLELRR 233
++ PV + + KP+ +E
Sbjct: 115 QM-------PVA---------------FQSSKPL---------------------IEKVS 131
Query: 234 CLNDTYCLPERPKVIVGLRGSTADIFLDNAAYREFLFKQF-NVSTVDEESAAIVMACLSN 292
+ L + +IV + D F+ + R+ + K F N V+ E+ AI C
Sbjct: 132 QVVQQQQLTAKVGLIV-----SGDSFIGSVEQRQKIKKAFPNAMAVEMEATAIAQTCYQF 186
Query: 293 AVPSIVFRGVSDLGGG 308
VP +V R VSDL G
Sbjct: 187 NVPFVVVRAVSDLANG 202
>pdb|3BL6|A Chain A, Crystal Structure Of Staphylococcus Aureus 5'-
MethylthioadenosineS-Adenosylhomocysteine Nucleosidase
In Complex With Formycin A
Length = 230
Score = 57.8 bits (138), Expect = 9e-09, Method: Compositional matrix adjust.
Identities = 61/253 (24%), Positives = 110/253 (43%), Gaps = 55/253 (21%)
Query: 57 IGLVMAYPPEESALITSRLFVHNSRIPFIDLAGRRFNVGKIKNVDVIYVMTGEQTVNSGI 116
IG++ A EE ++ ++L +++ I +A +F G +K+ +V+ +G VN+ I
Sbjct: 4 IGIIGAME-EEVTILKNKL----TQLSEISVAHVKFYTGILKDREVVITQSGIGKVNAAI 58
Query: 117 TVQILLDAFDIRGVVHYGTAGSSNNSLSFGDVSVMKYVAFTGSWKWKAFKSETGQLPELD 176
+ +L++ F +++ G+AG+ + SL+ GDV + V + + AF E GQ+P++
Sbjct: 59 STTLLINKFKPDVIINTGSAGALDESLNVGDVLISDDVKYHDA-DATAFGYEYGQIPQM- 116
Query: 177 FGAFNFPVRGKNLLAKVEFTPSQLYSAGKPMEELFWLPVDSEWFDIATQLQDLELRRCLN 236
PV + + KP+ +E +
Sbjct: 117 ------PVA---------------FQSSKPL---------------------IEKVSQVV 134
Query: 237 DTYCLPERPKVIVGLRGSTADIFLDNAAYREFLFKQF-NVSTVDEESAAIVMACLSNAVP 295
L + +IV + D F+ + R+ + K F N V+ E+ AI C VP
Sbjct: 135 QQQQLTAKVGLIV-----SGDSFIGSVEQRQKIKKAFPNAMAVEMEATAIAQTCYQFNVP 189
Query: 296 SIVFRGVSDLGGG 308
+V R VSDL G
Sbjct: 190 FVVVRAVSDLANG 202
>pdb|3DP9|A Chain A, Crystal Structure Of Vibrio Cholerae
5'-methylthioadenosine/s-adenosyl Homocysteine
Nucleosidase (mtan) Complexed With Butylthio-dadme-
Immucillin A
pdb|3DP9|C Chain C, Crystal Structure Of Vibrio Cholerae
5'-methylthioadenosine/s-adenosyl Homocysteine
Nucleosidase (mtan) Complexed With Butylthio-dadme-
Immucillin A
Length = 231
Score = 51.2 bits (121), Expect = 7e-07, Method: Compositional matrix adjust.
Identities = 53/224 (23%), Positives = 90/224 (40%), Gaps = 51/224 (22%)
Query: 85 IDLAGRRFNVGKIKNVDVIYVMTGEQTVNSGITVQILLDAFDIRGVVHYGTAGSSNNSLS 144
++ AG F G+I+ VDV+ + +G V++ + +L+ + V++ G+AG + SL+
Sbjct: 26 VNQAGCTFYSGQIQGVDVVLLQSGIGKVSAALGTALLISQYAPDVVINTGSAGGFDASLN 85
Query: 145 FGDVSVMKYVAFTGSWKWKAFKSETGQLPELDFGAFNFPVRGKNLLAKVEFTPSQLYSAG 204
GDV + V + AF E GQ+ AG
Sbjct: 86 VGDVVISSEVRHHDA-DVTAFGYEIGQM------------------------------AG 114
Query: 205 KPMEELFWLPVDSEWFDIATQ-LQDLELRRCLNDTYCLPERPKVIVGLRGSTADIFLDNA 263
+P D + +A Q L L + C T D F+ A
Sbjct: 115 QPA----AFKADEKLMTVAEQALAQLPNTHAVRGLIC--------------TGDAFVCTA 156
Query: 264 AYREFLFKQF-NVSTVDEESAAIVMACLSNAVPSIVFRGVSDLG 306
++F+ + F +V V+ E++AI C VP +V R +SD+
Sbjct: 157 ERQQFIRQHFPSVVAVEMEASAIAQTCHQFKVPFVVVRAISDVA 200
>pdb|4FFS|A Chain A, Crystal Structure Of
5'-MethylthioadenosineS-Adenosylhomocysteine
Nucleosidase From Helicobacter Pylori With
Butyl-Thio-Dadme- Immucillin-A
Length = 239
Score = 47.0 bits (110), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 48/220 (21%), Positives = 86/220 (39%), Gaps = 49/220 (22%)
Query: 85 IDLAGRRFNVGKIKNVDVIYVMTGEQTVNSGITVQILLDAFDIRGVVHYGTAGSSNNSLS 144
I L G F+ G N ++I + V+S +T ++ AF ++ V+ G AGS L
Sbjct: 37 IPLGGNVFHKGVYHNKEIIVAYSKIGKVHSTLTTTSMILAFGVQKVLFSGVAGSLVKDLK 96
Query: 145 FGDVSVMKYVAFTGSWKWKAFKSETGQLPELDFGAFNFPVRGKNLLAKVEFTPSQLYSAG 204
D+ V + ++D AF+ P
Sbjct: 97 INDLLVATQLV----------------QHDVDLSAFDHP--------------------- 119
Query: 205 KPMEELFWLPVDSEWFDIATQLQDLELRRCLNDTYCLPERPKVIVGLRGSTADIFLDNAA 264
L ++P + + + + L L ++ N+ + + + VI ++ D F+ +
Sbjct: 120 -----LGFIPESAIFIETSGSLNALA-KKIANEQH-IALKEGVI-----ASGDQFVHSKE 167
Query: 265 YREFLFKQFNVSTVDEESAAIVMACLSNAVPSIVFRGVSD 304
+EFL +F S V+ E A++ C VP V R +SD
Sbjct: 168 RKEFLVSEFKASAVEMEGASVAFVCQKFGVPCCVLRSISD 207
>pdb|3NM4|A Chain A, Helicobacter Pylori Mtan
pdb|3NM4|B Chain B, Helicobacter Pylori Mtan
pdb|3NM5|A Chain A, Helicobacter Pylori Mtan Complexed With Formycin A
pdb|3NM5|B Chain B, Helicobacter Pylori Mtan Complexed With Formycin A
pdb|3NM6|B Chain B, Helicobacter Pylori Mtan Complexed With Adenine And Tris
Length = 230
Score = 47.0 bits (110), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 48/220 (21%), Positives = 86/220 (39%), Gaps = 49/220 (22%)
Query: 85 IDLAGRRFNVGKIKNVDVIYVMTGEQTVNSGITVQILLDAFDIRGVVHYGTAGSSNNSLS 144
I L G F+ G N ++I + V+S +T ++ AF ++ V+ G AGS L
Sbjct: 28 IPLGGNVFHKGVYHNKEIIVAYSKIGKVHSTLTTTSMILAFGVQKVLFSGVAGSLVKDLK 87
Query: 145 FGDVSVMKYVAFTGSWKWKAFKSETGQLPELDFGAFNFPVRGKNLLAKVEFTPSQLYSAG 204
D+ V + ++D AF+ P
Sbjct: 88 INDLLVATQLV----------------QHDVDLSAFDHP--------------------- 110
Query: 205 KPMEELFWLPVDSEWFDIATQLQDLELRRCLNDTYCLPERPKVIVGLRGSTADIFLDNAA 264
L ++P + + + + L L ++ N+ + + + VI ++ D F+ +
Sbjct: 111 -----LGFIPESAIFIETSGSLNALA-KKIANEQH-IALKEGVI-----ASGDQFVHSKE 158
Query: 265 YREFLFKQFNVSTVDEESAAIVMACLSNAVPSIVFRGVSD 304
+EFL +F S V+ E A++ C VP V R +SD
Sbjct: 159 RKEFLVSEFKASAVEMEGASVAFVCQKFGVPCCVLRSISD 198
>pdb|1ZOS|A Chain A, Structure Of 5'-MethylthionadenosineS-Adenosylhomocysteine
Nucleosidase From S. Pneumoniae With A Transition-State
Inhibitor Mt-Imma
pdb|1ZOS|B Chain B, Structure Of 5'-MethylthionadenosineS-Adenosylhomocysteine
Nucleosidase From S. Pneumoniae With A Transition-State
Inhibitor Mt-Imma
pdb|1ZOS|C Chain C, Structure Of 5'-MethylthionadenosineS-Adenosylhomocysteine
Nucleosidase From S. Pneumoniae With A Transition-State
Inhibitor Mt-Imma
pdb|1ZOS|D Chain D, Structure Of 5'-MethylthionadenosineS-Adenosylhomocysteine
Nucleosidase From S. Pneumoniae With A Transition-State
Inhibitor Mt-Imma
pdb|1ZOS|E Chain E, Structure Of 5'-MethylthionadenosineS-Adenosylhomocysteine
Nucleosidase From S. Pneumoniae With A Transition-State
Inhibitor Mt-Imma
pdb|1ZOS|F Chain F, Structure Of 5'-MethylthionadenosineS-Adenosylhomocysteine
Nucleosidase From S. Pneumoniae With A Transition-State
Inhibitor Mt-Imma
Length = 230
Score = 46.2 bits (108), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 37/144 (25%), Positives = 69/144 (47%), Gaps = 10/144 (6%)
Query: 57 IGLVMAYPPEESALITSRLFVHNSRIPFIDLAGRRFNVGKIKNVDVIYVMTGEQTVNSGI 116
IG++ A P EE A + L ++ G ++ G I + +V+ V +G V S +
Sbjct: 3 IGIIAAMP-EELAYLVQHLDNTQEQVVL----GNTYHTGTIASHEVVLVESGIGKVMSAM 57
Query: 117 TVQILLDAFDIRGVVHYGTAGSSNNSLSFGDVSVMKYVAFTGSWKWKAFKSETGQLPELD 176
+V IL D F + +++ G+AG+ ++ GDV + +A+ AF GQ+ +
Sbjct: 58 SVAILADHFQVDALINTGSAGAVAEGIAVGDVVIADKLAYH-DVDVTAFGYAYGQMAQQP 116
Query: 177 FGAFNFPVRGKNLLAKVEFTPSQL 200
+ K +A+++ + SQL
Sbjct: 117 L----YFESDKTFVAQIQESLSQL 136
>pdb|3MMS|A Chain A, Crystal Structure Of Streptococcus Pneumoniae MtaSAH
NUCLEO Complex With 8-Aminoadenine
Length = 230
Score = 41.6 bits (96), Expect = 6e-04, Method: Compositional matrix adjust.
Identities = 36/144 (25%), Positives = 68/144 (47%), Gaps = 10/144 (6%)
Query: 57 IGLVMAYPPEESALITSRLFVHNSRIPFIDLAGRRFNVGKIKNVDVIYVMTGEQTVNSGI 116
IG++ A P EE A + L ++ G ++ G I + +V+ V +G V S +
Sbjct: 3 IGIIAAMP-EELAYLVQHLDNAQEQVVL----GNTYHTGTIVSHEVVLVESGIGKVMSAM 57
Query: 117 TVQILLDAFDIRGVVHYGTAGSSNNSLSFGDVSVMKYVAFTGSWKWKAFKSETGQLPELD 176
+V IL F + +++ G+AG+ ++ GDV + +A+ AF GQ+ +
Sbjct: 58 SVAILAVHFQVDALINTGSAGAVAEGIAVGDVVIADKLAYH-DVDVTAFGYAYGQMAQQP 116
Query: 177 FGAFNFPVRGKNLLAKVEFTPSQL 200
+ K +A+++ + SQL
Sbjct: 117 L----YFESDKTFVAQIQESLSQL 136
>pdb|4G41|A Chain A, Crystal Structure Of S-Adenosylhomocysteine Nucleosidase
From Streptococcus Pyogenes In Complex With
5-Methylthiotubericidin
pdb|4G41|B Chain B, Crystal Structure Of S-Adenosylhomocysteine Nucleosidase
From Streptococcus Pyogenes In Complex With
5-Methylthiotubericidin
Length = 236
Score = 38.1 bits (87), Expect = 0.006, Method: Compositional matrix adjust.
Identities = 19/61 (31%), Positives = 36/61 (59%)
Query: 90 RRFNVGKIKNVDVIYVMTGEQTVNSGITVQILLDAFDIRGVVHYGTAGSSNNSLSFGDVS 149
+ + G+ ++I V +G V S +TV IL++ F + +++ G+AG+ + L+ GDV
Sbjct: 36 KTYYTGRFGKHELILVQSGVGKVMSAMTVAILVEHFKAQAIINTGSAGAVASHLAIGDVV 95
Query: 150 V 150
V
Sbjct: 96 V 96
>pdb|4G89|A Chain A, Crystal Structure Of K. Pneumoniae MtaADOHCY NUCLEOSIDASE
IN COMPLEX With Fragmented S-Adenosyl-L-Homocysteine
pdb|4G89|B Chain B, Crystal Structure Of K. Pneumoniae MtaADOHCY NUCLEOSIDASE
IN COMPLEX With Fragmented S-Adenosyl-L-Homocysteine
Length = 237
Score = 36.2 bits (82), Expect = 0.027, Method: Compositional matrix adjust.
Identities = 31/117 (26%), Positives = 54/117 (46%), Gaps = 6/117 (5%)
Query: 57 IGLVMAYPPEESALITSRLFVHNSRIPFIDLAGRRFNVGKIKNVDVIYVMTGEQTVNSGI 116
IG++ A E + L R + N + I + G G++ VDV + +G V + +
Sbjct: 8 IGIIGAMEEEVTLL---RDKIENRQT--ITIGGSEIYTGQLHGVDVALLKSGIGKVAAAM 62
Query: 117 TVQILLDAFDIRGVVHYGTAGSSNNSLSFGDVSVMKYVAFTGSWKWKAFKSETGQLP 173
+LL+ +++ G+AG ++L GD+ V + + AF E GQLP
Sbjct: 63 GATLLLERCQPDVIINTGSAGGLASTLKVGDIVVSDEARYHDA-DVTAFGYEYGQLP 118
>pdb|3FAO|A Chain A, Crystal Structure Of S118a Mutant 3clsp Of Prrsv
Length = 213
Score = 29.3 bits (64), Expect = 3.3, Method: Compositional matrix adjust.
Identities = 15/35 (42%), Positives = 21/35 (60%), Gaps = 1/35 (2%)
Query: 95 GKIKNVDVIYVMTGEQTVNSGITVQILLDAFDIRG 129
GKIK V +V+TG SG+ +LD FD++G
Sbjct: 39 GKIKCVTAAHVLTGNSARVSGVGFNQMLD-FDVKG 72
>pdb|3FAN|A Chain A, Crystal Structure Of Chymotrypsin-Like ProteasePROTEINASE
(3clspNSP4) OF PORCINE REPRODUCTIVE AND RESPIRATORY
Syndrome Virus (Prrsv)
Length = 213
Score = 29.3 bits (64), Expect = 3.3, Method: Compositional matrix adjust.
Identities = 15/35 (42%), Positives = 21/35 (60%), Gaps = 1/35 (2%)
Query: 95 GKIKNVDVIYVMTGEQTVNSGITVQILLDAFDIRG 129
GKIK V +V+TG SG+ +LD FD++G
Sbjct: 39 GKIKCVTAAHVLTGNSARVSGVGFNQMLD-FDVKG 72
>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 = 28.9 bits (63), Expect = 4.2, Method: Compositional matrix adjust.
Identities = 33/157 (21%), Positives = 62/157 (39%), Gaps = 26/157 (16%)
Query: 86 DLAGRRFNVGKIKNVDVIY-------VMTGEQT--VNSGITVQILLDAFDI-RGVVHYGT 135
+LAG+ FN+ K + VI V+ +T S ++ L +I ++HY
Sbjct: 224 ELAGQEFNINSPKQLGVILFEKLQLPVLKKTKTGYSTSADVLEKLAPYHEIVENILHYRQ 283
Query: 136 AGSSNNSLSFGDVSVMKYVAFTGSWKWKAFKSETGQLPELDFGAFNFPVRGKNLLAKVEF 195
G ++ G + V++ + ++TG+L + N P+R
Sbjct: 284 LGKLQSTYIEGLLKVVRPATKKVHTIFNQALTQTGRLSSTEPNLQNIPIR---------- 333
Query: 196 TPSQLYSAGKPMEELFWLPVDSEWFDIATQLQDLELR 232
G+ + + F +P +S+W A +ELR
Sbjct: 334 -----LEEGRKIRQAF-VPSESDWLIFAADYSQIELR 364
>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 = 28.9 bits (63), Expect = 4.2, Method: Compositional matrix adjust.
Identities = 33/157 (21%), Positives = 62/157 (39%), Gaps = 26/157 (16%)
Query: 86 DLAGRRFNVGKIKNVDVIY-------VMTGEQT--VNSGITVQILLDAFDI-RGVVHYGT 135
+LAG+ FN+ K + VI V+ +T S ++ L +I ++HY
Sbjct: 223 ELAGQEFNINSPKQLGVILFEKLQLPVLKKTKTGYSTSADVLEKLAPYHEIVENILHYRQ 282
Query: 136 AGSSNNSLSFGDVSVMKYVAFTGSWKWKAFKSETGQLPELDFGAFNFPVRGKNLLAKVEF 195
G ++ G + V++ + ++TG+L + N P+R
Sbjct: 283 LGKLQSTYIEGLLKVVRPATKKVHTIFNQALTQTGRLSSTEPNLQNIPIR---------- 332
Query: 196 TPSQLYSAGKPMEELFWLPVDSEWFDIATQLQDLELR 232
G+ + + F +P +S+W A +ELR
Sbjct: 333 -----LEEGRKIRQAF-VPSESDWLIFAADYSQIELR 363
>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 = 28.9 bits (63), Expect = 4.3, Method: Compositional matrix adjust.
Identities = 33/157 (21%), Positives = 62/157 (39%), Gaps = 26/157 (16%)
Query: 86 DLAGRRFNVGKIKNVDVIY-------VMTGEQT--VNSGITVQILLDAFDI-RGVVHYGT 135
+LAG+ FN+ K + VI V+ +T S ++ L +I ++HY
Sbjct: 236 ELAGQEFNINSPKQLGVILFEKLQLPVLKKTKTGYSTSADVLEKLAPYHEIVENILHYRQ 295
Query: 136 AGSSNNSLSFGDVSVMKYVAFTGSWKWKAFKSETGQLPELDFGAFNFPVRGKNLLAKVEF 195
G ++ G + V++ + ++TG+L + N P+R
Sbjct: 296 LGKLQSTYIEGLLKVVRPATKKVHTIFNQALTQTGRLSSTEPNLQNIPIR---------- 345
Query: 196 TPSQLYSAGKPMEELFWLPVDSEWFDIATQLQDLELR 232
G+ + + F +P +S+W A +ELR
Sbjct: 346 -----LEEGRKIRQAF-VPSESDWLIFAADYSQIELR 376
>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 = 28.9 bits (63), Expect = 4.6, Method: Compositional matrix adjust.
Identities = 33/157 (21%), Positives = 62/157 (39%), Gaps = 26/157 (16%)
Query: 86 DLAGRRFNVGKIKNVDVIY-------VMTGEQT--VNSGITVQILLDAFDI-RGVVHYGT 135
+LAG+ FN+ K + VI V+ +T S ++ L +I ++HY
Sbjct: 236 ELAGQEFNINSPKQLGVILFEKLQLPVLKKTKTGYSTSADVLEKLAPYHEIVENILHYRQ 295
Query: 136 AGSSNNSLSFGDVSVMKYVAFTGSWKWKAFKSETGQLPELDFGAFNFPVRGKNLLAKVEF 195
G ++ G + V++ + ++TG+L + N P+R
Sbjct: 296 LGKLQSTYIEGLLKVVRPATKKVHTIFNQALTQTGRLSSTEPNLQNIPIR---------- 345
Query: 196 TPSQLYSAGKPMEELFWLPVDSEWFDIATQLQDLELR 232
G+ + + F +P +S+W A +ELR
Sbjct: 346 -----LEEGRKIRQAF-VPSESDWLIFAADYSQIELR 376
>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 = 28.9 bits (63), Expect = 4.7, Method: Compositional matrix adjust.
Identities = 33/157 (21%), Positives = 62/157 (39%), Gaps = 26/157 (16%)
Query: 86 DLAGRRFNVGKIKNVDVIY-------VMTGEQT--VNSGITVQILLDAFDI-RGVVHYGT 135
+LAG+ FN+ K + VI V+ +T S ++ L +I ++HY
Sbjct: 224 ELAGQEFNINSPKQLGVILFEKLQLPVLKKTKTGYSTSADVLEKLAPYHEIVENILHYRQ 283
Query: 136 AGSSNNSLSFGDVSVMKYVAFTGSWKWKAFKSETGQLPELDFGAFNFPVRGKNLLAKVEF 195
G ++ G + V++ + ++TG+L + N P+R
Sbjct: 284 LGKLQSTYIEGLLKVVRPATKKVHTIFNQALTQTGRLSSTEPNLQNIPIR---------- 333
Query: 196 TPSQLYSAGKPMEELFWLPVDSEWFDIATQLQDLELR 232
G+ + + F +P +S+W A +ELR
Sbjct: 334 -----LEEGRKIRQAF-VPSESDWLIFAADYSQIELR 364
>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 = 28.9 bits (63), Expect = 4.9, Method: Compositional matrix adjust.
Identities = 33/157 (21%), Positives = 62/157 (39%), Gaps = 26/157 (16%)
Query: 86 DLAGRRFNVGKIKNVDVIY-------VMTGEQT--VNSGITVQILLDAFDI-RGVVHYGT 135
+LAG+ FN+ K + VI V+ +T S ++ L +I ++HY
Sbjct: 224 ELAGQEFNINSPKQLGVILFEKLQLPVLKKTKTGYSTSADVLEKLAPYHEIVENILHYRQ 283
Query: 136 AGSSNNSLSFGDVSVMKYVAFTGSWKWKAFKSETGQLPELDFGAFNFPVRGKNLLAKVEF 195
G ++ G + V++ + ++TG+L + N P+R
Sbjct: 284 LGKLQSTYIEGLLKVVRPATKKVHTIFNQALTQTGRLSSTEPNLQNIPIR---------- 333
Query: 196 TPSQLYSAGKPMEELFWLPVDSEWFDIATQLQDLELR 232
G+ + + F +P +S+W A +ELR
Sbjct: 334 -----LEEGRKIRQAF-VPSESDWLIFAADYSQIELR 364
>pdb|1YF2|A Chain A, Three-dimensional Structure Of Dna Sequence Specificity
(s) Subunit Of A Type I Restriction-modification Enzyme
And Its Functional Implications
pdb|1YF2|B Chain B, Three-dimensional Structure Of Dna Sequence Specificity
(s) Subunit Of A Type I Restriction-modification Enzyme
And Its Functional Implications
Length = 425
Score = 28.1 bits (61), Expect = 6.9, Method: Compositional matrix adjust.
Identities = 13/59 (22%), Positives = 30/59 (50%)
Query: 4 GLNQRRRWVLDVKSVVMLGLGLLFAMAQHTVQLRSNHPMHGIVDRVNEIGGPYIGLVMA 62
GLN W++ SV+ G + A + +++ +N + GI+ + N + ++ ++A
Sbjct: 77 GLNNSNAWIVPKNSVLFAMYGSIGETAINKIEVATNQAILGIIPKDNILESEFLYYILA 135
>pdb|2XY7|A Chain A, Crystal Structure Of A Salicylic Aldehyde Base In The
Pre-Insertion Site Of Fragment Dna Polymerase I From
Bacillus Stearothermophilus
Length = 580
Score = 27.7 bits (60), Expect = 8.7, Method: Compositional matrix adjust.
Identities = 33/157 (21%), Positives = 62/157 (39%), Gaps = 26/157 (16%)
Query: 86 DLAGRRFNVGKIKNVDVIY-------VMTGEQT--VNSGITVQILLDAFDI-RGVVHYGT 135
+LAG+ FN+ K + VI V+ +T S ++ L +I ++HY
Sbjct: 224 ELAGQEFNINSPKQLGVILFEKLQLPVLKKSKTGYSTSADVLEKLAPYHEIVENILHYRQ 283
Query: 136 AGSSNNSLSFGDVSVMKYVAFTGSWKWKAFKSETGQLPELDFGAFNFPVRGKNLLAKVEF 195
G ++ G + V++ + ++TG+L + N P+R
Sbjct: 284 LGKLQSTYIEGLLKVVRPDTKKVHTIFNQALTQTGRLSSTEPNLQNIPIR---------- 333
Query: 196 TPSQLYSAGKPMEELFWLPVDSEWFDIATQLQDLELR 232
G+ + + F +P +S+W A +ELR
Sbjct: 334 -----LEEGRKIRQAF-VPSESDWLIFAADYSQIELR 364
>pdb|2XY5|A Chain A, Crystal Structure Of An Artificial Salen-Copper Basepair
In Complex With Fragment Dna Polymerase I From Bacillus
Stearothermophilus
Length = 581
Score = 27.7 bits (60), Expect = 8.7, Method: Compositional matrix adjust.
Identities = 33/157 (21%), Positives = 62/157 (39%), Gaps = 26/157 (16%)
Query: 86 DLAGRRFNVGKIKNVDVIY-------VMTGEQT--VNSGITVQILLDAFDI-RGVVHYGT 135
+LAG+ FN+ K + VI V+ +T S ++ L +I ++HY
Sbjct: 225 ELAGQEFNINSPKQLGVILFEKLQLPVLKKSKTGYSTSADVLEKLAPYHEIVENILHYRQ 284
Query: 136 AGSSNNSLSFGDVSVMKYVAFTGSWKWKAFKSETGQLPELDFGAFNFPVRGKNLLAKVEF 195
G ++ G + V++ + ++TG+L + N P+R
Sbjct: 285 LGKLQSTYIEGLLKVVRPDTKKVHTIFNQALTQTGRLSSTEPNLQNIPIR---------- 334
Query: 196 TPSQLYSAGKPMEELFWLPVDSEWFDIATQLQDLELR 232
G+ + + F +P +S+W A +ELR
Sbjct: 335 -----LEEGRKIRQAF-VPSESDWLIFAADYSQIELR 365
>pdb|2XO7|A Chain A, Crystal Structure Of A Da:o-Allylhydroxylamine-Dc Basepair
In Complex With Fragment Dna Polymerase I From Bacillus
Stearothermophilus
Length = 580
Score = 27.7 bits (60), Expect = 8.9, Method: Compositional matrix adjust.
Identities = 33/157 (21%), Positives = 62/157 (39%), Gaps = 26/157 (16%)
Query: 86 DLAGRRFNVGKIKNVDVIY-------VMTGEQT--VNSGITVQILLDAFDI-RGVVHYGT 135
+LAG+ FN+ K + VI V+ +T S ++ L +I ++HY
Sbjct: 224 ELAGQEFNINSPKQLGVILFEKLQLPVLKKSKTGYSTSADVLEKLAPYHEIVENILHYRQ 283
Query: 136 AGSSNNSLSFGDVSVMKYVAFTGSWKWKAFKSETGQLPELDFGAFNFPVRGKNLLAKVEF 195
G ++ G + V++ + ++TG+L + N P+R
Sbjct: 284 LGKLQSTYIEGLLKVVRPDTKKVHTIFNQALTQTGRLSSTEPNLQNIPIR---------- 333
Query: 196 TPSQLYSAGKPMEELFWLPVDSEWFDIATQLQDLELR 232
G+ + + F +P +S+W A +ELR
Sbjct: 334 -----LEEGRKIRQAF-VPSESDWLIFAADYSQIELR 364
>pdb|2XY6|A Chain A, Crystal Structure Of A Salicylic Aldehyde Basepair In
Complex With Fragment Dna Polymerase I From Bacillus
Stearothermophilus
Length = 581
Score = 27.7 bits (60), Expect = 9.0, Method: Compositional matrix adjust.
Identities = 33/157 (21%), Positives = 62/157 (39%), Gaps = 26/157 (16%)
Query: 86 DLAGRRFNVGKIKNVDVIY-------VMTGEQT--VNSGITVQILLDAFDI-RGVVHYGT 135
+LAG+ FN+ K + VI V+ +T S ++ L +I ++HY
Sbjct: 225 ELAGQEFNINSPKQLGVILFEKLQLPVLKKSKTGYSTSADVLEKLAPYHEIVENILHYRQ 284
Query: 136 AGSSNNSLSFGDVSVMKYVAFTGSWKWKAFKSETGQLPELDFGAFNFPVRGKNLLAKVEF 195
G ++ G + V++ + ++TG+L + N P+R
Sbjct: 285 LGKLQSTYIEGLLKVVRPDTKKVHTIFNQALTQTGRLSSTEPNLQNIPIR---------- 334
Query: 196 TPSQLYSAGKPMEELFWLPVDSEWFDIATQLQDLELR 232
G+ + + F +P +S+W A +ELR
Sbjct: 335 -----LEEGRKIRQAF-VPSESDWLIFAADYSQIELR 365
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
0.323 0.139 0.414
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 9,587,695
Number of Sequences: 62578
Number of extensions: 391579
Number of successful extensions: 791
Number of sequences better than 100.0: 38
Number of HSP's better than 100.0 without gapping: 16
Number of HSP's successfully gapped in prelim test: 22
Number of HSP's that attempted gapping in prelim test: 752
Number of HSP's gapped (non-prelim): 42
length of query: 345
length of database: 14,973,337
effective HSP length: 100
effective length of query: 245
effective length of database: 8,715,537
effective search space: 2135306565
effective search space used: 2135306565
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 52 (24.6 bits)