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= 000161
(1988 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|2JGU|A Chain A, Crystal Structure Of Dna-directed Dna Polymerase
Length = 775
Score = 106 bits (264), Expect = 2e-22, Method: Compositional matrix adjust.
Identities = 106/387 (27%), Positives = 175/387 (45%), Gaps = 66/387 (17%)
Query: 189 CIVDLREYDVPYHIRFAIDNDVRCGQWYDVSISSTGPLLEKRVDLLQRAEVHVCAFDIET 248
+VD+ EYD+P+ R+ ID + + + E+ + AFDIET
Sbjct: 105 AVVDIFEYDIPFAKRYLIDKGL--------------------IPMEGEEELKILAFDIET 144
Query: 249 TKLPLKFPDADYDIIMMISYMLDGQGYLIINRECVGEDIEDLEYTPKPEFEGYFKVTNVN 308
L + + I+MISY + + +I + DL Y V +V+
Sbjct: 145 --LYHEGEEFGKGPIIMISYADENEARVITWKNI------DLPY-----------VESVS 185
Query: 309 NEIELLRLWFAHMQEVKPGIYVTYNGDYFDWPFLETRAAHHGFKMS-----EELGFQCDK 363
E E+++ + ++E P I VTYNGD FD+P+L RA G K++ E Q
Sbjct: 186 TEKEMIKRFLRIIREKDPDIIVTYNGDSFDFPYLAKRAEKLGIKLTIGRDGSEPKMQRIG 245
Query: 364 NQGECRAKFACHLDCFAWVKRDSYLPQGSQGLKAVTKAKLGYDPLEVNPEDMVRF--AKE 421
+ K H D + ++ LP + L+AV +A G +V +++ + + E
Sbjct: 246 DMTAVEVKGRIHFDLYHVIRTTINLP--TYTLEAVYEAIFGKPKEKVYADEIAKAWESGE 303
Query: 422 KPQMMASYSVSDAVATYYLYMTYVHPFIFSLATIIPMSPDEVLRKGSGTLCEMLLMVQAY 481
+ +A YS+ DA ATY L ++ P L+ ++ +V R +G L E L+ +AY
Sbjct: 304 NLERVAKYSMEDAKATYELGKEFL-PMEIQLSRLVGQPLWDVSRSSTGNLVEWFLLRKAY 362
Query: 482 KANVICPNKHQSDPEKFYRNHLLESETYIGGHVECLESGVFRSDLPTSFK-LDPSAYEQL 540
+ N + PNK E+ Y+ L ES Y GG V+ E G++ + + +K L PS +
Sbjct: 363 ERNEVAPNKPS---EEEYQRRLRES--YTGGFVKEPEKGLWENIVYLDYKSLYPSII--I 415
Query: 541 LNNLDRDLQYAIKVEGKMDLESVSNYD 567
+N+ D ++LE NYD
Sbjct: 416 THNVSPDT---------LNLEGCKNYD 433
Score = 67.8 bits (164), Expect = 7e-11, Method: Compositional matrix adjust.
Identities = 65/226 (28%), Positives = 91/226 (40%), Gaps = 46/226 (20%)
Query: 760 KIQEAQDMV--VLYDSLQLAHKCILNSFYGYVMRKGARWYSMEMAGVVTYTGAKIIQNA- 816
K++E QD + +L D Q A K + NSFYGY ARWY E A VT G K I+
Sbjct: 467 KMKETQDPIEKILLDYRQKAIKLLANSFYGYYGYAKARWYCKECAESVTAWGRKYIELVW 526
Query: 817 RLLIEKIG-KPLELDTDGIWCVLPGSFPENXXXXXXXXXXXXXISYPCVMLNVDVARNNT 875
+ L EK G K L +DTDG++ +PG E P ++
Sbjct: 527 KELEEKFGFKVLYIDTDGLYATIPGGESEEIKKKALEFVKYINSKLPGLL---------- 576
Query: 876 NDQYQTLVDPVSKTYETHSECSIEFEVDGPYKAMILPASKEEGILIKKRYAVFNDDGTLA 935
E E +G YK + KKRYAV +++G +
Sbjct: 577 -----------------------ELEYEGFYKRGFF--------VTKKRYAVIDEEGKVI 605
Query: 936 ELKGFEIKRRGELKLIKVFQAELFDKFLHGSTIEECYSAVAAVANR 981
+G EI RR ++ K QA + + L +EE V V +
Sbjct: 606 -TRGLEIVRRDWSEIAKETQARVLETILKHGDVEEAVRIVKEVIQK 650
>pdb|1QQC|A Chain A, Crystal Structure Of An Archaebacterial Dna Polymerase
D.Tok
Length = 773
Score = 101 bits (252), Expect = 4e-21, Method: Compositional matrix adjust.
Identities = 97/355 (27%), Positives = 161/355 (45%), Gaps = 56/355 (15%)
Query: 189 CIVDLREYDVPYHIRFAIDNDVRCGQWYDVSISSTGPLLEKRVDLLQRAEVHVCAFDIET 248
+VD+ EYD+P+ R+ ID + + + E+ + AFDIET
Sbjct: 105 AVVDIYEYDIPFAKRYLIDRGL--------------------IPMEGDEELRMLAFDIET 144
Query: 249 TKLPLKFPDADYDIIMMISYMLDGQGYLIINRECVGEDIEDLEYTPKPEFEGYFKVTNVN 308
L + + I+MISY D +G +I + + DL Y V +V+
Sbjct: 145 --LYHEGEEFGEGPILMISYA-DEEGARVITWKNI-----DLPY-----------VESVS 185
Query: 309 NEIELLRLWFAHMQEVKPGIYVTYNGDYFDWPFLETRAAHHGFKM-----SEELGFQCDK 363
E E+++ + +QE P + +TYNGD FD+ +L+ R+ G K E Q
Sbjct: 186 TEKEMIKRFLKVIQEKDPDVLITYNGDNFDFAYLKKRSEMLGVKFILGRDGSEPKIQRMG 245
Query: 364 NQGECRAKFACHLDCFAWVKRDSYLPQGSQGLKAVTKAKLGYDPLEVNPEDMVRF--AKE 421
++ K H D + ++R LP + L+ V + G +V E++ R + E
Sbjct: 246 DRFAVEVKGRIHFDLYPVIRRTINLP--TYTLETVYEPVFGQPKEKVYAEEIARAWESGE 303
Query: 422 KPQMMASYSVSDAVATYYLYMTYVHPFIFSLATIIPMSPDEVLRKGSGTLCEMLLMVQAY 481
+ +A YS+ DA ATY L + P L+ ++ S +V R +G L E L+ +AY
Sbjct: 304 GLERVARYSMEDAKATYELGKEFF-PMEAQLSRLVGQSLWDVSRSSTGNLVEWFLLRKAY 362
Query: 482 KANVICPNKHQSDPEKFYRNHLLESETYIGGHVECLESGVFRSDLPTSFK-LDPS 535
+ N + PNK R +E+Y GG+V+ E G++ + + +K L PS
Sbjct: 363 ERNDVAPNKPDE------RELARRTESYAGGYVKEPEKGLWENIVYLDYKSLYPS 411
Score = 43.1 bits (100), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 75/302 (24%), Positives = 116/302 (38%), Gaps = 60/302 (19%)
Query: 770 LYDSLQLAHKCILNSFYGYVMRKGARWYSMEMAGVVTYTGAKIIQNA-RLLIEKIG-KPL 827
L D Q A K + NS+YGY ARWY E A VT G + I+ R + EK G K L
Sbjct: 478 LLDYRQRAIKILANSYYGYYAYANARWYCRECAESVTAWGRQYIETTMREIEEKFGFKVL 537
Query: 828 ELDTDGIWCVLPGSFPENXXXXXXXXXXXXXISYPCVMLNVDVARNNTNDQYQTLVDPVS 887
DTDG + +PG+ E N ++ ++P
Sbjct: 538 YADTDGFFATIPGADAETV--------------------------KNKAKEFLNYINP-- 569
Query: 888 KTYETHSECSIEFEVDGPYKAMILPASKEEGILIKKRYAVFNDDGTLAELKGFEIKRRGE 947
+E E +G Y+ + KK+YAV +++ + +G EI RR
Sbjct: 570 -----RLPGLLELEYEGFYRRGFF--------VTKKKYAVIDEEDKIT-TRGLEIVRRDW 615
Query: 948 LKLIKVFQAELFDKFLHGSTIEECYSAVAAVANRWLDLLDNQGKDIADSELIDYISESST 1007
++ K QA + + L +EE V V + ++ +L+ Y
Sbjct: 616 SEIAKETQARVLEAILKHGDVEEAVRIVKEVTEKL------SRHEVPPEKLVIY----EQ 665
Query: 1008 MSKSLADYGEQKSCAVTTARRLSDFLGDTMVKDKGLRCQYIVACEPQGTPVSERAVPVAI 1067
+++ L Y V A+RL+ + G YIV P V +RA+P
Sbjct: 666 ITRDLRSY-RATGPHVAVAKRLA---ARGIKIRPGTVISYIVLKGPGR--VGDRAIPFDE 719
Query: 1068 FE 1069
F+
Sbjct: 720 FD 721
>pdb|3A2F|A Chain A, Crystal Structure Of Pyrococcus Furiosus Dna
PolymerasePCNA Monomer Mutant Complex
Length = 775
Score = 101 bits (251), Expect = 5e-21, Method: Compositional matrix adjust.
Identities = 108/387 (27%), Positives = 172/387 (44%), Gaps = 66/387 (17%)
Query: 189 CIVDLREYDVPYHIRFAIDNDVRCGQWYDVSISSTGPLLEKRVDLLQRAEVHVCAFDIET 248
+VD+ EYD+P+ R+ ID + I G E+ + AFDIET
Sbjct: 105 AVVDIFEYDIPFAKRYLIDKGL---------IPXEG-----------EEELKILAFDIET 144
Query: 249 TKLPLKFPDADYDIIMMISYMLDGQGYLIINRECVGEDIEDLEYTPKPEFEGYFKVTNVN 308
L + + I+ ISY + + +I + DL Y V V+
Sbjct: 145 --LYHEGEEFGKGPIIXISYADENEAKVITWKNI------DLPY-----------VEVVS 185
Query: 309 NEIELLRLWFAHMQEVKPGIYVTYNGDYFDWPFLETRAAHHGFKMS-----EELGFQCDK 363
+E E ++ + ++E P I VTYNGD FD+P+L RA G K++ E Q
Sbjct: 186 SEREXIKRFLRIIREKDPDIIVTYNGDSFDFPYLAKRAEKLGIKLTIGRDGSEPKXQRIG 245
Query: 364 NQGECRAKFACHLDCFAWVKRDSYLPQGSQGLKAVTKAKLGYDPLEVNPEDMVRF--AKE 421
+ K H D + + R LP + L+AV +A G +V +++ + + E
Sbjct: 246 DXTAVEVKGRIHFDLYHVITRTINLP--TYTLEAVYEAIFGKPKEKVYADEIAKAWESGE 303
Query: 422 KPQMMASYSVSDAVATYYLYMTYVHPFIFSLATIIPMSPDEVLRKGSGTLCEMLLMVQAY 481
+ +A YS DA ATY L ++ P L+ ++ +V R +G L E L+ +AY
Sbjct: 304 NLERVAKYSXEDAKATYELGKEFL-PXEIQLSRLVGQPLWDVSRSSTGNLVEWFLLRKAY 362
Query: 482 KANVICPNKHQSDPEKFYRNHLLESETYIGGHVECLESGVFRSDLPTSFK-LDPSAYEQL 540
+ N + PNK E+ Y+ L ES Y GG V+ E G++ + + F+ L PS +
Sbjct: 363 ERNEVAPNKPS---EEEYQRRLRES--YTGGFVKEPEKGLWENIVYLDFRALYPSII--I 415
Query: 541 LNNLDRDLQYAIKVEGKMDLESVSNYD 567
+N+ D ++LE NYD
Sbjct: 416 THNVSPDT---------LNLEGCKNYD 433
Score = 67.0 bits (162), Expect = 1e-10, Method: Compositional matrix adjust.
Identities = 65/226 (28%), Positives = 90/226 (39%), Gaps = 46/226 (20%)
Query: 760 KIQEAQDMV--VLYDSLQLAHKCILNSFYGYVMRKGARWYSMEMAGVVTYTGAKIIQNA- 816
K +E QD + +L D Q A K + NSFYGY ARWY E A VT G K I+
Sbjct: 467 KXKETQDPIEKILLDYRQKAIKLLANSFYGYYGYAKARWYCKECAESVTAWGRKYIELVW 526
Query: 817 RLLIEKIG-KPLELDTDGIWCVLPGSFPENXXXXXXXXXXXXXISYPCVMLNVDVARNNT 875
+ L EK G K L +DTDG++ +PG E P ++
Sbjct: 527 KELEEKFGFKVLYIDTDGLYATIPGGESEEIKKKALEFVKYINSKLPGLL---------- 576
Query: 876 NDQYQTLVDPVSKTYETHSECSIEFEVDGPYKAMILPASKEEGILIKKRYAVFNDDGTLA 935
E E +G YK + KKRYAV +++G +
Sbjct: 577 -----------------------ELEYEGFYKRGFF--------VTKKRYAVIDEEGKVI 605
Query: 936 ELKGFEIKRRGELKLIKVFQAELFDKFLHGSTIEECYSAVAAVANR 981
+G EI RR ++ K QA + + L +EE V V +
Sbjct: 606 -TRGLEIVRRDWSEIAKETQARVLETILKHGDVEEAVRIVKEVIQK 650
>pdb|4AHC|A Chain A, Crystal Structure Of An Evolved Replicating Dna Polymerase
pdb|4AHC|B Chain B, Crystal Structure Of An Evolved Replicating Dna Polymerase
pdb|4AIL|C Chain C, Crystal Structure Of An Evolved Replicating Dna Polymerase
Length = 775
Score = 100 bits (248), Expect = 1e-20, Method: Compositional matrix adjust.
Identities = 106/387 (27%), Positives = 171/387 (44%), Gaps = 66/387 (17%)
Query: 189 CIVDLREYDVPYHIRFAIDNDVRCGQWYDVSISSTGPLLEKRVDLLQRAEVHVCAFDIET 248
+VD+ EYD+P+ R+ ID + + + E+ + AF I T
Sbjct: 105 AVVDIFEYDIPFAKRYLIDKGL--------------------IPMEGEEELKILAFAIAT 144
Query: 249 TKLPLKFPDADYDIIMMISYMLDGQGYLIINRECVGEDIEDLEYTPKPEFEGYFKVTNVN 308
L + + I+MISY + + +I + DL Y V V+
Sbjct: 145 --LYHEGEEFGKGPIIMISYADENEAKVITWKNI------DLPY-----------VEVVS 185
Query: 309 NEIELLRLWFAHMQEVKPGIYVTYNGDYFDWPFLETRAAHHGFKMS-----EELGFQCDK 363
+E E+++ + ++E P I VTYNGD FD+P+L RA G K++ E Q
Sbjct: 186 SEREMIKRFLRIIREKDPDIIVTYNGDSFDFPYLAKRAEKLGIKLTIGRDGSEPKMQRIG 245
Query: 364 NQGECRAKFACHLDCFAWVKRDSYLPQGSQGLKAVTKAKLGYDPLEVNPEDMVRF--AKE 421
+ K H D + + R LP + L+AV +A G +V +++ + + E
Sbjct: 246 DMTAVEVKGRIHFDLYHVITRTINLP--TYTLEAVYEAIFGKPKEKVYADEIAKAWESGE 303
Query: 422 KPQMMASYSVSDAVATYYLYMTYVHPFIFSLATIIPMSPDEVLRKGSGTLCEMLLMVQAY 481
+ +A YS+ DA ATY L ++ P L+ +I +V R +G L E L+ +AY
Sbjct: 304 NLERVAKYSMEDAKATYELGKEFL-PMEIQLSRLIGQPLWDVSRSSTGNLVEWFLLRKAY 362
Query: 482 KANVICPNKHQSDPEKFYRNHLLESETYIGGHVECLESGVFRSDLPTSF-KLDPSAYEQL 540
+ N + PNK E+ Y+ L ES Y GG V+ E G++ + F L PS +
Sbjct: 363 ERNEVAPNKPS---EEEYQRRLRES--YTGGFVKEPEKGLWDDIVYLDFIALYPSII--I 415
Query: 541 LNNLDRDLQYAIKVEGKMDLESVSNYD 567
+N+ D ++LE NYD
Sbjct: 416 THNVSPDT---------LNLEGCKNYD 433
Score = 65.9 bits (159), Expect = 2e-10, Method: Compositional matrix adjust.
Identities = 65/226 (28%), Positives = 90/226 (39%), Gaps = 46/226 (20%)
Query: 760 KIQEAQDMV--VLYDSLQLAHKCILNSFYGYVMRKGARWYSMEMAGVVTYTGAKIIQNA- 816
K++E QD + +L D Q A K + NSFYGY ARWY E A VT G K I+
Sbjct: 467 KMKETQDPIEKILLDYRQKAIKLLANSFYGYYGYAKARWYCKECAESVTAWGRKYIELVW 526
Query: 817 RLLIEKIG-KPLELDTDGIWCVLPGSFPENXXXXXXXXXXXXXISYPCVMLNVDVARNNT 875
+ L EK G K L +DTDG+ +PG E P ++
Sbjct: 527 KELEEKFGFKVLYIDTDGLHATIPGGESEEIKKKALEFVKYINSKLPGLL---------- 576
Query: 876 NDQYQTLVDPVSKTYETHSECSIEFEVDGPYKAMILPASKEEGILIKKRYAVFNDDGTLA 935
E E +G YK + KKRYAV +++G +
Sbjct: 577 -----------------------ELEYEGFYKRGFF--------VTKKRYAVIDEEGKVI 605
Query: 936 ELKGFEIKRRGELKLIKVFQAELFDKFLHGSTIEECYSAVAAVANR 981
+G EI RR ++ K QA + + L +EE V V +
Sbjct: 606 -TRGLEIVRRDWSEIAKETQARVLETILKHGDVEEAVRIVKEVIQK 650
>pdb|1D5A|A Chain A, Crystal Structure Of An Archaebacterial Dna Polymerase
D.Tok. Deposition Of Second Native Structure At 2.4
Angstrom
Length = 733
Score = 99.8 bits (247), Expect = 2e-20, Method: Compositional matrix adjust.
Identities = 97/355 (27%), Positives = 159/355 (44%), Gaps = 56/355 (15%)
Query: 189 CIVDLREYDVPYHIRFAIDNDVRCGQWYDVSISSTGPLLEKRVDLLQRAEVHVCAFDIET 248
+VD+ EYD+P+ R+ ID + + + E+ + AFDIET
Sbjct: 105 AVVDIYEYDIPFAKRYLIDRGL--------------------IPMEGDEELRMLAFDIET 144
Query: 249 TKLPLKFPDADYDIIMMISYMLDGQGYLIINRECVGEDIEDLEYTPKPEFEGYFKVTNVN 308
L A I+MISY D +G +I + + DL Y V +V+
Sbjct: 145 --LAHAGAAAGAGPILMISYA-DEEGARVITWKNI-----DLPY-----------VESVS 185
Query: 309 NEIELLRLWFAHMQEVKPGIYVTYNGDYFDWPFLETRAAHHGFKM-----SEELGFQCDK 363
E E+++ + +QE P + +TYNGD FD+ +L+ R+ G K E Q
Sbjct: 186 TEKEMIKRFLKVIQEKDPDVLITYNGDNFDFAYLKKRSEMLGVKFILGRDGSEPKIQRMG 245
Query: 364 NQGECRAKFACHLDCFAWVKRDSYLPQGSQGLKAVTKAKLGYDPLEVNPEDMVR--FAKE 421
++ K H D + ++R LP + L+ V + G +V E++ + E
Sbjct: 246 DRFAVEVKGRIHFDLYPVIRRTINLP--TYTLETVYEPVFGQPAEKVYAEEIAEAWASGE 303
Query: 422 KPQMMASYSVSDAVATYYLYMTYVHPFIFSLATIIPMSPDEVLRKGSGTLCEMLLMVQAY 481
+ +A YS+ DA ATY L + P L+ ++ S +V R +G L E L+ +AY
Sbjct: 304 GLERVARYSMEDAKATYELGKEF-FPMEAQLSRLVGQSLWDVSRSSTGNLVEWFLLRKAY 362
Query: 482 KANVICPNKHQSDPEKFYRNHLLESETYIGGHVECLESGVFRSDLPTSFK-LDPS 535
+ N + PNK R +E+Y GG+V+ E G++ + + +K L PS
Sbjct: 363 ERNDVAPNKPDE------RELARRTESYAGGYVKEPEKGLWENIVYLDYKSLYPS 411
Score = 42.7 bits (99), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 57/214 (26%), Positives = 85/214 (39%), Gaps = 44/214 (20%)
Query: 770 LYDSLQLAHKCILNSFYGYVMRKGARWYSMEMAGVVTYTGAKIIQNA-RLLIEKIG-KPL 827
L D Q A K + NS+YGY ARWY E A VT G + I+ R + EK G K L
Sbjct: 478 LLDYRQRAIKILANSYYGYYAYANARWYCRECAESVTAWGRQYIETTMREIEEKFGFKVL 537
Query: 828 ELDTDGIWCVLPGSFPENXXXXXXXXXXXXXISYPCVMLNVDVARNNTNDQYQTLVDPVS 887
DTDG + +PG+ E N ++ ++P
Sbjct: 538 YADTDGFFATIPGADAETV--------------------------KNKAKEFLNYINP-- 569
Query: 888 KTYETHSECSIEFEVDGPYKAMILPASKEEGILIKKRYAVFNDDGTLAELKGFEIKRRGE 947
+E E +G Y+ + KK+YAV +++ + +G EI RR
Sbjct: 570 -----RLPGLLELEYEGFYRRGFF--------VTKKKYAVIDEEDKIT-TRGLEIVRRDW 615
Query: 948 LKLIKVFQAELFDKFLHGSTIEECYSAVAAVANR 981
++ K QA + + L +EE V V +
Sbjct: 616 SEIAKETQARVLEAILKHGDVEEAVRIVKEVTEK 649
>pdb|1TGO|A Chain A, Thermostable B Type Dna Polymerase From Thermococcus
Gorgonarius
Length = 773
Score = 96.3 bits (238), Expect = 2e-19, Method: Compositional matrix adjust.
Identities = 96/355 (27%), Positives = 159/355 (44%), Gaps = 56/355 (15%)
Query: 189 CIVDLREYDVPYHIRFAIDNDVRCGQWYDVSISSTGPLLEKRVDLLQRAEVHVCAFDIET 248
+VD+ EYD+P+ R+ ID + + + E+ + AFDIET
Sbjct: 105 AVVDIYEYDIPFAKRYLIDKGL--------------------IPMEGDEELKMLAFDIET 144
Query: 249 TKLPLKFPDADYDIIMMISYMLDGQGYLIINRECVGEDIEDLEYTPKPEFEGYFKVTNVN 308
L + + I+MISY D +G +I + + DL Y V V+
Sbjct: 145 --LYHEGEEFAEGPILMISYA-DEEGARVITWKNI-----DLPY-----------VDVVS 185
Query: 309 NEIELLRLWFAHMQEVKPGIYVTYNGDYFDWPFLETRAAHHGFKM-----SEELGFQCDK 363
E E+++ + ++E P + +TYNGD FD+ +L+ R+ G K E Q
Sbjct: 186 TEKEMIKRFLKVVKEKDPDVLITYNGDNFDFAYLKKRSEKLGVKFILGREGSEPKIQRMG 245
Query: 364 NQGECRAKFACHLDCFAWVKRDSYLPQGSQGLKAVTKAKLGYDPLEVNPEDMVRF--AKE 421
++ K H D + ++R LP + L+AV +A G +V E++ + E
Sbjct: 246 DRFAVEVKGRIHFDLYPVIRRTINLP--TYTLEAVYEAIFGQPKEKVYAEEIAQAWETGE 303
Query: 422 KPQMMASYSVSDAVATYYLYMTYVHPFIFSLATIIPMSPDEVLRKGSGTLCEMLLMVQAY 481
+ +A YS+ DA TY L + P L+ ++ S +V R +G L E L+ +AY
Sbjct: 304 GLERVARYSMEDAKVTYELGKEF-FPMEAQLSRLVGQSLWDVSRSSTGNLVEWFLLRKAY 362
Query: 482 KANVICPNKHQSDPEKFYRNHLLESETYIGGHVECLESGVFRSDLPTSFK-LDPS 535
+ N + PNK R E+Y GG+V+ E G++ + + F+ L PS
Sbjct: 363 ERNELAPNKPDE------RELARRRESYAGGYVKEPERGLWENIVYLDFRSLYPS 411
Score = 58.9 bits (141), Expect = 3e-08, Method: Compositional matrix adjust.
Identities = 67/263 (25%), Positives = 100/263 (38%), Gaps = 55/263 (20%)
Query: 770 LYDSLQLAHKCILNSFYGYVMRKGARWYSMEMAGVVTYTGAKIIQNA-RLLIEKIG-KPL 827
L D Q A K + NSFYGY ARWY E A VT G + I+ R + EK G K L
Sbjct: 478 LLDYRQRAIKILANSFYGYYGYAKARWYCKECAESVTAWGRQYIETTIREIEEKFGFKVL 537
Query: 828 ELDTDGIWCVLPGSFPENXXXXXXXXXXXXXISYPCVMLNVDVARNNTNDQYQTLVDPVS 887
DTDG + +PG+ E P ++
Sbjct: 538 YADTDGFFATIPGADAETVKKKAKEFLDYINAKLPGLL---------------------- 575
Query: 888 KTYETHSECSIEFEVDGPYKAMILPASKEEGILIKKRYAVFNDDGTLAELKGFEIKRRGE 947
E E +G YK + KK+YAV +++ + +G EI RR
Sbjct: 576 -----------ELEYEGFYKRGFF--------VTKKKYAVIDEEDKIT-TRGLEIVRRDW 615
Query: 948 LKLIKVFQAELFDKFLHGSTIEECYSAVAAVANRWLDLLDNQGKDIADSELIDYISESST 1007
++ K QA + + L +EE V V + ++ +L+ Y
Sbjct: 616 SEIAKETQARVLEAILKHGDVEEAVRIVKEVTEKL------SKYEVPPEKLVIY----EQ 665
Query: 1008 MSKSLADYGEQKSCAVTTARRLS 1030
+++ L DY + V A+RL+
Sbjct: 666 ITRDLKDY-KATGPHVAVAKRLA 687
Score = 33.1 bits (74), Expect = 1.6, Method: Compositional matrix adjust.
Identities = 34/143 (23%), Positives = 60/143 (41%), Gaps = 38/143 (26%)
Query: 582 EEPIREECPLIYHLDVAAMYPNIILTNRLQPPSIVTDEVCTACDFNRPGKTCLRKLEWVW 641
+EP R I +LD ++YP+II+T+ + P ++ NR G C
Sbjct: 390 KEPERGLWENIVYLDFRSLYPSIIITHNVSPDTL-----------NREG--C-------- 428
Query: 642 RGEIFMGKRSDYYHLKKQIESEFVDGTNGHLSKSFLDLPKMEQQSRLKDRLKKYCQKAYK 701
+ Y + Q+ +F G + DL +E++ ++K ++K K
Sbjct: 429 ----------EEYDVAPQVGHKFCKDFPGFIPSLLGDL--LEERQKVKKKMKATIDPIEK 476
Query: 702 RVLDKPVTELREAGICMRENSFY 724
++LD R+ I + NSFY
Sbjct: 477 KLLD-----YRQRAIKILANSFY 494
>pdb|2VWK|A Chain A, Uracil Recognition In Archaeal Dna Polymerases Captured By
X-Ray Crystallography. V93q Polymerase Variant
Length = 773
Score = 94.0 bits (232), Expect = 7e-19, Method: Compositional matrix adjust.
Identities = 96/356 (26%), Positives = 157/356 (44%), Gaps = 58/356 (16%)
Query: 189 CIVDLREYDVPYHIRFAIDNDVRCGQWYDVSISSTGPLLEKRVDLLQRAEVHVCAFDIET 248
+VD+ EYD+P+ R+ ID + + + E+ + AFDIET
Sbjct: 105 AVVDIYEYDIPFAKRYLIDKGL--------------------IPMEGDEELKMLAFDIET 144
Query: 249 T-KLPLKFPDADYDIIMMISYMLDGQGYLIINRECVGEDIEDLEYTPKPEFEGYFKVTNV 307
KF + I+MISY D +G +I + DL Y V V
Sbjct: 145 LYHEGEKFAEGP---ILMISYA-DEEGARVITWRNI-----DLPY-----------VDVV 184
Query: 308 NNEIELLRLWFAHMQEVKPGIYVTYNGDYFDWPFLETRAAHHGFKM-----SEELGFQCD 362
+ E E+++ + ++E P + +TYNGD F + +L+ R+ G K E Q
Sbjct: 185 STEKEMIKRFLKVVKEKDPDVLITYNGDNFAFAYLKKRSEKLGVKFILGREGSEPKIQRM 244
Query: 363 KNQGECRAKFACHLDCFAWVKRDSYLPQGSQGLKAVTKAKLGYDPLEVNPEDMVRF--AK 420
++ K H D + ++R LP + L+AV +A G +V E++ +
Sbjct: 245 GDRFAVEVKGRIHFDLYPVIRRTINLP--TYTLEAVYEAIFGQPKEKVYAEEIAQAWETG 302
Query: 421 EKPQMMASYSVSDAVATYYLYMTYVHPFIFSLATIIPMSPDEVLRKGSGTLCEMLLMVQA 480
E + +A YS+ DA TY L + P L+ ++ S +V R +G L E L+ +A
Sbjct: 303 EGLERVARYSMEDAKVTYELGKEFF-PMEAQLSRLVGQSLWDVSRSSTGNLVEWFLLRKA 361
Query: 481 YKANVICPNKHQSDPEKFYRNHLLESETYIGGHVECLESGVFRSDLPTSFK-LDPS 535
Y+ N + PNK R E+Y GG+V+ E G++ + + F+ L PS
Sbjct: 362 YERNELAPNKPDE------RELARRRESYAGGYVKEPERGLWENIVYLDFRSLYPS 411
Score = 58.9 bits (141), Expect = 3e-08, Method: Compositional matrix adjust.
Identities = 76/303 (25%), Positives = 116/303 (38%), Gaps = 62/303 (20%)
Query: 770 LYDSLQLAHKCILNSFYGYVMRKGARWYSMEMAGVVTYTGAKIIQNA-RLLIEKIG-KPL 827
L D Q A K + NSFYGY ARWY E A VT G + I+ R + EK G K L
Sbjct: 478 LLDYRQRAIKILANSFYGYYGYAKARWYCKECAESVTAWGRQYIETTIREIEEKFGFKVL 537
Query: 828 ELDTDGIWCVLPGSFPENXXXXXXXXXXXXXISYPCVMLNVDVARNNTNDQYQTLVDPVS 887
DTDG + +PG+ E P ++
Sbjct: 538 YADTDGFFATIPGADAETVKKKAKEFLDYINAKLPGLL---------------------- 575
Query: 888 KTYETHSECSIEFEVDGPYKAMILPASKEEGILIKKRYAVFNDDGTLAELKGFEIKRRGE 947
E E +G YK + KK+YAV +++ + +G EI RR
Sbjct: 576 -----------ELEYEGFYKRGFF--------VTKKKYAVIDEEDKIT-TRGLEIVRRDW 615
Query: 948 LKLIKVFQAELFDKFLHGSTIEECYSAVAAVANRWLDLLDNQGKDIADSELIDYISESST 1007
++ K QA + + L +EE V V + ++ +L+ Y
Sbjct: 616 SEIAKETQARVLEAILKHGDVEEAVRIVKEVTEKL------SKYEVPPEKLVIY----EQ 665
Query: 1008 MSKSLADYGEQKSCAVTTARRLSDFLGDTMVKDKGLRCQYIVACEPQGTP-VSERAVPVA 1066
+++ L DY + V A+RL+ + G YIV +G+ + +RA+P
Sbjct: 666 ITRDLKDY-KATGPHVAVAKRLA---ARGIKIRPGTVISYIVL---KGSGRIGDRAIPFD 718
Query: 1067 IFE 1069
F+
Sbjct: 719 EFD 721
Score = 33.1 bits (74), Expect = 1.6, Method: Compositional matrix adjust.
Identities = 34/143 (23%), Positives = 60/143 (41%), Gaps = 38/143 (26%)
Query: 582 EEPIREECPLIYHLDVAAMYPNIILTNRLQPPSIVTDEVCTACDFNRPGKTCLRKLEWVW 641
+EP R I +LD ++YP+II+T+ + P ++ NR G C
Sbjct: 390 KEPERGLWENIVYLDFRSLYPSIIITHNVSPDTL-----------NREG--C-------- 428
Query: 642 RGEIFMGKRSDYYHLKKQIESEFVDGTNGHLSKSFLDLPKMEQQSRLKDRLKKYCQKAYK 701
+ Y + Q+ +F G + DL +E++ ++K ++K K
Sbjct: 429 ----------EEYDVAPQVGHKFCKDFPGFIPSLLGDL--LEERQKVKKKMKATIDPIEK 476
Query: 702 RVLDKPVTELREAGICMRENSFY 724
++LD R+ I + NSFY
Sbjct: 477 KLLD-----YRQRAIKILANSFY 494
>pdb|2VWJ|A Chain A, Uracil Recognition In Archaeal Dna Polymerases Captured By
X-Ray Crystallography
Length = 773
Score = 94.0 bits (232), Expect = 8e-19, Method: Compositional matrix adjust.
Identities = 96/356 (26%), Positives = 157/356 (44%), Gaps = 58/356 (16%)
Query: 189 CIVDLREYDVPYHIRFAIDNDVRCGQWYDVSISSTGPLLEKRVDLLQRAEVHVCAFDIET 248
+VD+ EYD+P+ R+ ID + + + E+ + AFDIET
Sbjct: 105 AVVDIYEYDIPFAKRYLIDKGL--------------------IPMEGDEELKMLAFDIET 144
Query: 249 T-KLPLKFPDADYDIIMMISYMLDGQGYLIINRECVGEDIEDLEYTPKPEFEGYFKVTNV 307
KF + I+MISY D +G +I + DL Y V V
Sbjct: 145 LYHEGEKFAEGP---ILMISYA-DEEGARVITWRNI-----DLPY-----------VDVV 184
Query: 308 NNEIELLRLWFAHMQEVKPGIYVTYNGDYFDWPFLETRAAHHGFKM-----SEELGFQCD 362
+ E E+++ + ++E P + +TYNGD F + +L+ R+ G K E Q
Sbjct: 185 STEKEMIKRFLKVVKEKDPDVLITYNGDNFAFAYLKKRSEKLGVKFILGREGSEPKIQRM 244
Query: 363 KNQGECRAKFACHLDCFAWVKRDSYLPQGSQGLKAVTKAKLGYDPLEVNPEDMVRF--AK 420
++ K H D + ++R LP + L+AV +A G +V E++ +
Sbjct: 245 GDRFAVEVKGRIHFDLYPVIRRTINLP--TYTLEAVYEAIFGQPKEKVYAEEIAQAWETG 302
Query: 421 EKPQMMASYSVSDAVATYYLYMTYVHPFIFSLATIIPMSPDEVLRKGSGTLCEMLLMVQA 480
E + +A YS+ DA TY L + P L+ ++ S +V R +G L E L+ +A
Sbjct: 303 EGLERVARYSMEDAKVTYELGKEF-FPMEAQLSRLVGQSLWDVSRSSTGNLVEWFLLRKA 361
Query: 481 YKANVICPNKHQSDPEKFYRNHLLESETYIGGHVECLESGVFRSDLPTSFK-LDPS 535
Y+ N + PNK R E+Y GG+V+ E G++ + + F+ L PS
Sbjct: 362 YERNELAPNKPDE------RELARRRESYAGGYVKEPERGLWENIVYLDFRSLYPS 411
Score = 58.9 bits (141), Expect = 3e-08, Method: Compositional matrix adjust.
Identities = 67/263 (25%), Positives = 100/263 (38%), Gaps = 55/263 (20%)
Query: 770 LYDSLQLAHKCILNSFYGYVMRKGARWYSMEMAGVVTYTGAKIIQNA-RLLIEKIG-KPL 827
L D Q A K + NSFYGY ARWY E A VT G + I+ R + EK G K L
Sbjct: 478 LLDYRQRAIKILANSFYGYYGYAKARWYCKECAESVTAWGRQYIETTIREIEEKFGFKVL 537
Query: 828 ELDTDGIWCVLPGSFPENXXXXXXXXXXXXXISYPCVMLNVDVARNNTNDQYQTLVDPVS 887
DTDG + +PG+ E P ++
Sbjct: 538 YADTDGFFATIPGADAETVKKKAKEFLDYINAKLPGLL---------------------- 575
Query: 888 KTYETHSECSIEFEVDGPYKAMILPASKEEGILIKKRYAVFNDDGTLAELKGFEIKRRGE 947
E E +G YK + KK+YAV +++ + +G EI RR
Sbjct: 576 -----------ELEYEGFYKRGFF--------VTKKKYAVIDEEDKIT-TRGLEIVRRDW 615
Query: 948 LKLIKVFQAELFDKFLHGSTIEECYSAVAAVANRWLDLLDNQGKDIADSELIDYISESST 1007
++ K QA + + L +EE V V + ++ +L+ Y
Sbjct: 616 SEIAKETQARVLEAILKHGDVEEAVRIVKEVTEKL------SKYEVPPEKLVIY----EQ 665
Query: 1008 MSKSLADYGEQKSCAVTTARRLS 1030
+++ L DY + V A+RL+
Sbjct: 666 ITRDLKDY-KATGPHVAVAKRLA 687
Score = 33.1 bits (74), Expect = 1.5, Method: Compositional matrix adjust.
Identities = 34/143 (23%), Positives = 60/143 (41%), Gaps = 38/143 (26%)
Query: 582 EEPIREECPLIYHLDVAAMYPNIILTNRLQPPSIVTDEVCTACDFNRPGKTCLRKLEWVW 641
+EP R I +LD ++YP+II+T+ + P ++ NR G C
Sbjct: 390 KEPERGLWENIVYLDFRSLYPSIIITHNVSPDTL-----------NREG--C-------- 428
Query: 642 RGEIFMGKRSDYYHLKKQIESEFVDGTNGHLSKSFLDLPKMEQQSRLKDRLKKYCQKAYK 701
+ Y + Q+ +F G + DL +E++ ++K ++K K
Sbjct: 429 ----------EEYDVAPQVGHKFCKDFPGFIPSLLGDL--LEERQKVKKKMKATIDPIEK 476
Query: 702 RVLDKPVTELREAGICMRENSFY 724
++LD R+ I + NSFY
Sbjct: 477 KLLD-----YRQRAIKILANSFY 494
>pdb|1WN7|A Chain A, Crystal Structure Of Archaeal Family B Dna Polymerase
Mutant
Length = 774
Score = 94.0 bits (232), Expect = 8e-19, Method: Compositional matrix adjust.
Identities = 97/355 (27%), Positives = 161/355 (45%), Gaps = 56/355 (15%)
Query: 189 CIVDLREYDVPYHIRFAIDNDVRCGQWYDVSISSTGPLLEKRVDLLQRAEVHVCAFDIET 248
++D+ EYD+P+ R+ ID + V + E+ + AFDIET
Sbjct: 105 AVIDIYEYDIPFAKRYLIDKGL--------------------VPMEGDEELKMLAFDIET 144
Query: 249 TKLPLKFPDADYDIIMMISYMLDGQGYLIINRECVGEDIEDLEYTPKPEFEGYFKVTNVN 308
L + + I+MISY D +G +I + V DL Y V V+
Sbjct: 145 --LYEEGEEFAEGPILMISYA-DEEGARVITWKNV-----DLPY-----------VDVVS 185
Query: 309 NEIELLRLWFAHMQEVKPGIYVTYNGDYFDWPFLETRAAHHGFKMS-----EELGFQCDK 363
E E+++ + ++E P + +TYNGD FD+ +L+ R G + E Q
Sbjct: 186 TEREMIKRFLRVVKEKDPDVLITYNGDNFDFAYLKKRCEKLGINFALGRDGSEPKIQRMG 245
Query: 364 NQGECRAKFACHLDCFAWVKRDSYLPQGSQGLKAVTKAKLGYDPLEVNPEDMVRF--AKE 421
++ K H D + ++R LP + L+AV +A G +V E++ E
Sbjct: 246 DRFAVEVKGRIHFDLYPVIRRTINLP--TYTLEAVYEAVFGQPKEKVYAEEITTAWETGE 303
Query: 422 KPQMMASYSVSDAVATYYLYMTYVHPFIFSLATIIPMSPDEVLRKGSGTLCEMLLMVQAY 481
+ +A YS+ DA TY L ++ P L+ +I S +V R +G L E L+ +AY
Sbjct: 304 NLERVARYSMEDAKVTYELGKEFL-PMEAQLSRLIGQSLWDVSRSSTGNLVEWFLLRKAY 362
Query: 482 KANVICPNKHQSDPEKFYRNHLLESETYIGGHVECLESGVFRSDLPTSFK-LDPS 535
+ N + PNK D ++ R ++Y GG+V+ E G++ + + F+ L PS
Sbjct: 363 ERNELAPNK--PDEKELARRR----QSYEGGYVKEPERGLWENIVYLDFRSLYPS 411
Score = 40.4 bits (93), Expect = 0.011, Method: Compositional matrix adjust.
Identities = 56/215 (26%), Positives = 82/215 (38%), Gaps = 46/215 (21%)
Query: 770 LYDSLQLAHKCILNSFYGYVMRKGARWYSMEMAGVVTYTGAK-IIQNARLLIEKIG-KPL 827
L D Q A K + NS+YGY ARWY E A VT G + I + + EK G K +
Sbjct: 478 LLDYRQRAIKILANSYYGYYGYARARWYCKECAESVTAWGREYITMTIKEIEEKYGFKVI 537
Query: 828 ELDTDGIWCVLPGSFPENXXXXXXXXXXXXXISYPCVMLNVDVARNNTNDQYQTLVDPVS 887
DTDG + +PG+ E P
Sbjct: 538 YSDTDGFFATIPGADAETVKKKAMEFLKYINAKLP------------------------- 572
Query: 888 KTYETHSECSIEFEVDGPYKAMILPASKEEGILI-KKRYAVFNDDGTLAELKGFEIKRRG 946
++E E +G Y E G + KK+YAV +++G + +G EI RR
Sbjct: 573 --------GALELEYEGFY---------ERGFFVTKKKYAVIDEEGKIT-TRGLEIVRRD 614
Query: 947 ELKLIKVFQAELFDKFLHGSTIEECYSAVAAVANR 981
++ K QA + + L +E+ V V +
Sbjct: 615 WSEIAKETQARVLEALLKDGDVEKAVRIVKEVTEK 649
>pdb|1WNS|A Chain A, Crystal Structure Of Family B Dna Polymerase From
Hyperthermophilic Archaeon Pyrococcus Kodakaraensis Kod1
Length = 774
Score = 93.6 bits (231), Expect = 9e-19, Method: Compositional matrix adjust.
Identities = 97/355 (27%), Positives = 161/355 (45%), Gaps = 56/355 (15%)
Query: 189 CIVDLREYDVPYHIRFAIDNDVRCGQWYDVSISSTGPLLEKRVDLLQRAEVHVCAFDIET 248
++D+ EYD+P+ R+ ID + V + E+ + AFDIET
Sbjct: 105 AVIDIYEYDIPFAKRYLIDKGL--------------------VPMEGDEELKMLAFDIET 144
Query: 249 TKLPLKFPDADYDIIMMISYMLDGQGYLIINRECVGEDIEDLEYTPKPEFEGYFKVTNVN 308
L + + I+MISY D +G +I + V DL Y V V+
Sbjct: 145 --LYHEGEEFAEGPILMISYA-DEEGARVITWKNV-----DLPY-----------VDVVS 185
Query: 309 NEIELLRLWFAHMQEVKPGIYVTYNGDYFDWPFLETRAAHHGFKMS-----EELGFQCDK 363
E E+++ + ++E P + +TYNGD FD+ +L+ R G + E Q
Sbjct: 186 TEREMIKRFLRVVKEKDPDVLITYNGDNFDFAYLKKRCEKLGINFALGRDGSEPKIQRMG 245
Query: 364 NQGECRAKFACHLDCFAWVKRDSYLPQGSQGLKAVTKAKLGYDPLEVNPEDMVRF--AKE 421
++ K H D + ++R LP + L+AV +A G +V E++ E
Sbjct: 246 DRFAVEVKGRIHFDLYPVIRRTINLP--TYTLEAVYEAVFGQPKEKVYAEEITTAWETGE 303
Query: 422 KPQMMASYSVSDAVATYYLYMTYVHPFIFSLATIIPMSPDEVLRKGSGTLCEMLLMVQAY 481
+ +A YS+ DA TY L ++ P L+ +I S +V R +G L E L+ +AY
Sbjct: 304 NLERVARYSMEDAKVTYELGKEFL-PMEAQLSRLIGQSLWDVSRSSTGNLVEWFLLRKAY 362
Query: 482 KANVICPNKHQSDPEKFYRNHLLESETYIGGHVECLESGVFRSDLPTSFK-LDPS 535
+ N + PNK D ++ R ++Y GG+V+ E G++ + + F+ L PS
Sbjct: 363 ERNELAPNK--PDEKELARRR----QSYEGGYVKEPERGLWENIVYLDFRSLYPS 411
Score = 40.8 bits (94), Expect = 0.008, Method: Compositional matrix adjust.
Identities = 55/214 (25%), Positives = 81/214 (37%), Gaps = 44/214 (20%)
Query: 770 LYDSLQLAHKCILNSFYGYVMRKGARWYSMEMAGVVTYTGAK-IIQNARLLIEKIG-KPL 827
L D Q A K + NS+YGY ARWY E A VT G + I + + EK G K +
Sbjct: 478 LLDYRQRAIKILANSYYGYYGYARARWYCKECAESVTAWGREYITMTIKEIEEKYGFKVI 537
Query: 828 ELDTDGIWCVLPGSFPENXXXXXXXXXXXXXISYPCVMLNVDVARNNTNDQYQTLVDPVS 887
DTDG + +PG+ E P
Sbjct: 538 YSDTDGFFATIPGADAETVKKKAMEFLKYINAKLP------------------------- 572
Query: 888 KTYETHSECSIEFEVDGPYKAMILPASKEEGILIKKRYAVFNDDGTLAELKGFEIKRRGE 947
++E E +G YK + KK+YAV +++G + +G EI RR
Sbjct: 573 --------GALELEYEGFYKRGFF--------VTKKKYAVIDEEGKIT-TRGLEIVRRDW 615
Query: 948 LKLIKVFQAELFDKFLHGSTIEECYSAVAAVANR 981
++ K QA + + L +E+ V V +
Sbjct: 616 SEIAKETQARVLEALLKDGDVEKAVRIVKEVTEK 649
>pdb|2XHB|A Chain A, Crystal Structure Of Dna Polymerase From Thermococcus
Gorgonarius In Complex With Hypoxanthine-Containing Dna
Length = 773
Score = 93.2 bits (230), Expect = 1e-18, Method: Compositional matrix adjust.
Identities = 95/355 (26%), Positives = 158/355 (44%), Gaps = 56/355 (15%)
Query: 189 CIVDLREYDVPYHIRFAIDNDVRCGQWYDVSISSTGPLLEKRVDLLQRAEVHVCAFDIET 248
+VD+ EYD+P+ R+ ID + + + E+ + AFDIET
Sbjct: 105 AVVDIYEYDIPFAKRYLIDKGL--------------------IPMEGDEELKMLAFDIET 144
Query: 249 TKLPLKFPDADYDIIMMISYMLDGQGYLIINRECVGEDIEDLEYTPKPEFEGYFKVTNVN 308
L + + I+MISY D +G +I + + DL Y V V+
Sbjct: 145 --LYHEGEEFAEGPILMISYA-DEEGARVITWKNI-----DLPY-----------VDVVS 185
Query: 309 NEIELLRLWFAHMQEVKPGIYVTYNGDYFDWPFLETRAAHHGFKM-----SEELGFQCDK 363
E E+++ + ++E P + +TYNGD F + +L+ R+ G K E Q
Sbjct: 186 TEKEMIKRFLKVVKEKDPDVLITYNGDNFAFAYLKKRSEKLGVKFILGREGSEPKIQRMG 245
Query: 364 NQGECRAKFACHLDCFAWVKRDSYLPQGSQGLKAVTKAKLGYDPLEVNPEDMVRF--AKE 421
++ K H D + ++R LP + L+AV +A G +V E++ + E
Sbjct: 246 DRFAVEVKGRIHFDLYPVIRRTINLP--TYTLEAVYEAIFGQPKEKVYAEEIAQAWETGE 303
Query: 422 KPQMMASYSVSDAVATYYLYMTYVHPFIFSLATIIPMSPDEVLRKGSGTLCEMLLMVQAY 481
+ +A YS+ DA TY L + P L+ ++ S +V R +G L E L+ +AY
Sbjct: 304 GLERVARYSMEDAKVTYELGKEF-FPMEAQLSRLVGQSLWDVSRSSTGNLVEWFLLRKAY 362
Query: 482 KANVICPNKHQSDPEKFYRNHLLESETYIGGHVECLESGVFRSDLPTSFK-LDPS 535
+ N + PNK R E+Y GG+V+ E G++ + + F+ L PS
Sbjct: 363 ERNELAPNKPDE------RELARRRESYAGGYVKEPERGLWENIVYLDFRSLYPS 411
Score = 58.9 bits (141), Expect = 3e-08, Method: Compositional matrix adjust.
Identities = 67/263 (25%), Positives = 100/263 (38%), Gaps = 55/263 (20%)
Query: 770 LYDSLQLAHKCILNSFYGYVMRKGARWYSMEMAGVVTYTGAKIIQNA-RLLIEKIG-KPL 827
L D Q A K + NSFYGY ARWY E A VT G + I+ R + EK G K L
Sbjct: 478 LLDYRQRAIKILANSFYGYYGYAKARWYCKECAESVTAWGRQYIETTIREIEEKFGFKVL 537
Query: 828 ELDTDGIWCVLPGSFPENXXXXXXXXXXXXXISYPCVMLNVDVARNNTNDQYQTLVDPVS 887
DTDG + +PG+ E P ++
Sbjct: 538 YADTDGFFATIPGADAETVKKKAKEFLDYINAKLPGLL---------------------- 575
Query: 888 KTYETHSECSIEFEVDGPYKAMILPASKEEGILIKKRYAVFNDDGTLAELKGFEIKRRGE 947
E E +G YK + KK+YAV +++ + +G EI RR
Sbjct: 576 -----------ELEYEGFYKRGFF--------VTKKKYAVIDEEDKIT-TRGLEIVRRDW 615
Query: 948 LKLIKVFQAELFDKFLHGSTIEECYSAVAAVANRWLDLLDNQGKDIADSELIDYISESST 1007
++ K QA + + L +EE V V + ++ +L+ Y
Sbjct: 616 SEIAKETQARVLEAILKHGDVEEAVRIVKEVTEKL------SKYEVPPEKLVIY----EQ 665
Query: 1008 MSKSLADYGEQKSCAVTTARRLS 1030
+++ L DY + V A+RL+
Sbjct: 666 ITRDLKDY-KATGPHVAVAKRLA 687
Score = 33.1 bits (74), Expect = 1.5, Method: Compositional matrix adjust.
Identities = 34/143 (23%), Positives = 60/143 (41%), Gaps = 38/143 (26%)
Query: 582 EEPIREECPLIYHLDVAAMYPNIILTNRLQPPSIVTDEVCTACDFNRPGKTCLRKLEWVW 641
+EP R I +LD ++YP+II+T+ + P ++ NR G C
Sbjct: 390 KEPERGLWENIVYLDFRSLYPSIIITHNVSPDTL-----------NREG--C-------- 428
Query: 642 RGEIFMGKRSDYYHLKKQIESEFVDGTNGHLSKSFLDLPKMEQQSRLKDRLKKYCQKAYK 701
+ Y + Q+ +F G + DL +E++ ++K ++K K
Sbjct: 429 ----------EEYDVAPQVGHKFCKDFPGFIPSLLGDL--LEERQKVKKKMKATIDPIEK 476
Query: 702 RVLDKPVTELREAGICMRENSFY 724
++LD R+ I + NSFY
Sbjct: 477 KLLD-----YRQRAIKILANSFY 494
>pdb|1QHT|A Chain A, Dna Polymerase From Thermococcus Sp. 9on-7 Archaeon
Length = 775
Score = 89.0 bits (219), Expect = 3e-17, Method: Compositional matrix adjust.
Identities = 96/355 (27%), Positives = 158/355 (44%), Gaps = 56/355 (15%)
Query: 189 CIVDLREYDVPYHIRFAIDNDVRCGQWYDVSISSTGPLLEKRVDLLQRAEVHVCAFDIET 248
+VD+ EYD+P+ R+ ID + + + E+ + AF I T
Sbjct: 105 AVVDIYEYDIPFAKRYLIDKGL--------------------IPMEGDEELTMLAFAIAT 144
Query: 249 TKLPLKFPDADYDIIMMISYMLDGQGYLIINRECVGEDIEDLEYTPKPEFEGYFKVTNVN 308
L + + I+MISY DG +I + + DL Y V V+
Sbjct: 145 --LYHEGEEFGTGPILMISYA-DGSEARVITWKKI-----DLPY-----------VDVVS 185
Query: 309 NEIELLRLWFAHMQEVKPGIYVTYNGDYFDWPFLETRAAHHGFKMS-----EELGFQCDK 363
E E+++ + ++E P + +TYNGD FD+ +L+ R G K + E Q
Sbjct: 186 TEKEMIKRFLRVVREKDPDVLITYNGDNFDFAYLKKRCEELGIKFTLGRDGSEPKIQRMG 245
Query: 364 NQGECRAKFACHLDCFAWVKRDSYLPQGSQGLKAVTKAKLGYDPLEVNPEDMVRF--AKE 421
++ K H D + ++R LP + L+AV +A G +V E++ + + E
Sbjct: 246 DRFAVEVKGRIHFDLYPVIRRTINLP--TYTLEAVYEAVFGKPKEKVYAEEIAQAWESGE 303
Query: 422 KPQMMASYSVSDAVATYYLYMTYVHPFIFSLATIIPMSPDEVLRKGSGTLCEMLLMVQAY 481
+ +A YS+ DA TY L + P L+ +I S +V R +G L E L+ +AY
Sbjct: 304 GLERVARYSMEDAKVTYELGREFF-PMEAQLSRLIGQSLWDVSRSSTGNLVEWFLLRKAY 362
Query: 482 KANVICPNKHQSDPEKFYRNHLLESETYIGGHVECLESGVFRSDLPTSFK-LDPS 535
K N + PNK P++ R Y GG+V+ E G++ + + F+ L PS
Sbjct: 363 KRNELAPNK----PDE--RELARRRGGYAGGYVKEPERGLWDNIVYLDFRSLYPS 411
Score = 57.8 bits (138), Expect = 6e-08, Method: Compositional matrix adjust.
Identities = 59/214 (27%), Positives = 81/214 (37%), Gaps = 44/214 (20%)
Query: 770 LYDSLQLAHKCILNSFYGYVMRKGARWYSMEMAGVVTYTGAKIIQNA-RLLIEKIG-KPL 827
L D Q A K + NSFYGY ARWY E A VT G + I+ R L EK G K L
Sbjct: 478 LLDYRQRAIKILANSFYGYYGYAKARWYCKECAESVTAWGREYIEMVIRELEEKFGFKVL 537
Query: 828 ELDTDGIWCVLPGSFPENXXXXXXXXXXXXXISYPCVMLNVDVARNNTNDQYQTLVDPVS 887
DTDG+ +PG+ E P ++
Sbjct: 538 YADTDGLHATIPGADAETVKKKAKEFLKYINPKLPGLL---------------------- 575
Query: 888 KTYETHSECSIEFEVDGPYKAMILPASKEEGILIKKRYAVFNDDGTLAELKGFEIKRRGE 947
E E +G Y + KK+YAV +++G + +G EI RR
Sbjct: 576 -----------ELEYEGFYVRGFF--------VTKKKYAVIDEEGKIT-TRGLEIVRRDW 615
Query: 948 LKLIKVFQAELFDKFLHGSTIEECYSAVAAVANR 981
++ K QA + + L +EE V V +
Sbjct: 616 SEIAKETQARVLEAILKHGDVEEAVRIVKEVTEK 649
>pdb|4FLT|A Chain A, Pyrococcus Abyssi B Family Dna Polymerase Bound To A
Dsdna, In Edition Mode
pdb|4FLU|A Chain A, Pyrococcus Abyssi B Family Dna Polymerase Bound To A
Dsdna, In Edition Mode
pdb|4FLV|A Chain A, Pyrococcus Abyssi B Family Dna Polymerase Bound To A
Dsdna, In Edition Mode
pdb|4FLW|A Chain A, Pyrococcus Abyssi B Family Dna Polymerase Bound To A
Dsdna, In Edition Mode
pdb|4FLX|A Chain A, Pyrococcus Abyssi B Family Dna Polymerase Bound To A
Dsdna, In Edition Mode
pdb|4FLY|A Chain A, Pyrococcus Abyssi B Family Dna Polymerase Bound To A
Dsdna, In Edition Mode
pdb|4FLZ|A Chain A, Pyrococcus Abyssi B Family Dna Polymerase Bound To A
Dsdna, In Edition Mode
pdb|4FM0|A Chain A, Pyrococcus Abyssi B Family Dna Polymerase Bound To A
Dsdna, In Edition Mode
pdb|4FM1|A Chain A, Pyrococcus Abyssi B Family Dna Polymerase Bound To A
Dsdna, In Edition Mode
Length = 793
Score = 85.1 bits (209), Expect = 4e-16, Method: Compositional matrix adjust.
Identities = 117/492 (23%), Positives = 197/492 (40%), Gaps = 102/492 (20%)
Query: 65 CIDLYFVSQDG-----------STFKSKY--KFRPYFYAATKEKMEMDVEAYLRRRYESQ 111
ID ++++DG FK +Y FRPY YA K+ +D + +
Sbjct: 24 IIDADYITEDGKPIIRIFKKEKGEFKVEYDRTFRPYIYALLKDDSAIDEVKKITAERHGK 83
Query: 112 IADIEILEKEDLDLKNHLSGLHKSYLKISFDTVQQLMDVKKDLLHVVERNQAKFDAAEAY 171
I I +EK + K +L + + ++ +D+ + E+ +
Sbjct: 84 IVRITEVEK-----------VQKKFLGRPIEVWKLYLEHPQDVPAIREKIR--------- 123
Query: 172 ESILTGKREQRPQDFLDCIVDLREYDVPYHIRFAIDNDVRCGQWYDVSISSTGPLLEKRV 231
+ P +VD+ EYD+P+ R+ ID +
Sbjct: 124 ---------EHP-----AVVDIFEYDIPFAKRYLIDKGL--------------------T 149
Query: 232 DLLQRAEVHVCAFDIETTKLPLKFPDADYDIIMMISYMLDGQGYLIINRECVGEDIEDLE 291
+ E+ A DIET L + + I+MISY D +G +I + + DL
Sbjct: 150 PMEGNEELTFLAVDIET--LYHEGEEFGKGPIIMISYA-DEEGAKVITWKSI-----DLP 201
Query: 292 YTPKPEFEGYFKVTNVNNEIELLRLWFAHMQEVKPGIYVTYNGDYFDWPFLETRAAHHGF 351
Y V V++E E+++ ++E P + +TYNGD F +P+L RA G
Sbjct: 202 Y-----------VEVVSSEREMIKRLVKVIREKDPDVIITYNGDNFAFPYLLKRAEKLGI 250
Query: 352 KM-----SEELGFQCDKNQGECRAKFACHLDCFAWVKRDSYLPQGSQGLKAVTKAKLGYD 406
K+ + E Q + K H D F ++R LP + L+AV +A G
Sbjct: 251 KLPLGRDNSEPKMQRMGDSLAVEIKGRIHFDLFPVIRRTINLP--TYTLEAVYEAIFGKS 308
Query: 407 PLEVNPEDMVRF--AKEKPQMMASYSVSDAVATYYLYMTYVHPFIFSLATIIPMSPDEVL 464
+V ++ + + +A YS+ DA T+ L + P LA ++ +V
Sbjct: 309 KEKVYAHEIAEAWETGKGLERVAKYSMEDAKVTFELGKEFF-PMEAQLARLVGQPVWDVS 367
Query: 465 RKGSGTLCEMLLMVQAYKANVICPNKHQSDPEKFYRNHLLESETYIGGHVECLESGVFRS 524
R +G L E L+ +AY+ N + PNK E+Y GG+V+ E G++
Sbjct: 368 RSSTGNLVEWFLLRKAYERNELAPNKPDER-----EYERRLRESYEGGYVKEPEKGLWEG 422
Query: 525 DLPTSFK-LDPS 535
+ F+ L PS
Sbjct: 423 IVSLDFRSLYPS 434
Score = 51.6 bits (122), Expect = 5e-06, Method: Compositional matrix adjust.
Identities = 75/313 (23%), Positives = 126/313 (40%), Gaps = 61/313 (19%)
Query: 760 KIQEAQDMV--VLYDSLQLAHKCILNSFYGYVMRKGARWYSMEMAGVVTYTGAKIIQNAR 817
+++E++D V L D Q A K + NS+YGY ARWY E A VT G + I R
Sbjct: 489 RMKESKDPVEKKLLDYRQRAIKILANSYYGYYGYAKARWYCKECAESVTAWGRQYIDLVR 548
Query: 818 LLIEKIG-KPLELDTDGIWCVLPGSFPENXXXXXXXXXXXXXISYPCVMLNVDVARNNTN 876
+E G K L +DTDG++ +PG+ E P ++
Sbjct: 549 RELESRGFKVLYIDTDGLYATIPGAKHEEIKEKALKFVEYINSKLPGLL----------- 597
Query: 877 DQYQTLVDPVSKTYETHSECSIEFEVDGPYKAMILPASKEEGILIKKRYAVFNDDGTLAE 936
E E +G Y + KK+YA+ +++G +
Sbjct: 598 ----------------------ELEYEGFYARGFF--------VTKKKYALIDEEGKIV- 626
Query: 937 LKGFEIKRRGELKLIKVFQAELFDKFLHGSTIEECYSAVAAVANRWLDLLDNQGKDIADS 996
+G EI RR ++ K QA++ + L ++E V V + +I
Sbjct: 627 TRGLEIVRRDWSEIAKETQAKVLEAILKHGNVDEAVKIVKEVTEKLSKY------EIPPE 680
Query: 997 ELIDYISESSTMSKSLADYGEQKSCAVTTARRLSDFLGDTMVKDKGLRCQYIVACEPQGT 1056
+L+ Y +++ L++Y + V A+RL+ + G+ YIV
Sbjct: 681 KLVIY----EQITRPLSEY-KAIGPHVAVAKRLA---AKGVKVKPGMVIGYIVLR--GDG 730
Query: 1057 PVSERAVPVAIFE 1069
P+S+RA+ + F+
Sbjct: 731 PISKRAIAIEEFD 743
>pdb|4FM2|A Chain A, Pyrococcus Abyssi B Family Dna Polymerase (Triple Mutant)
Bound To A Dsdna, In Edition Mode
Length = 793
Score = 82.0 bits (201), Expect = 3e-15, Method: Compositional matrix adjust.
Identities = 93/355 (26%), Positives = 150/355 (42%), Gaps = 55/355 (15%)
Query: 189 CIVDLREYDVPYHIRFAIDNDVRCGQWYDVSISSTGPLLEKRVDLLQRAEVHVCAFDIET 248
+VD+ EYD+P+ R+ ID + + E+ A DIET
Sbjct: 127 AVVDIFEYDIPFAKRYLIDKGL--------------------TPMEGNEELTFLAVDIET 166
Query: 249 TKLPLKFPDADYDIIMMISYMLDGQGYLIINRECVGEDIEDLEYTPKPEFEGYFKVTNVN 308
L + + I+MISY D +G +I + + DL Y V V+
Sbjct: 167 --LYHEGEEFGKGPIIMISYA-DEEGAKVITWKSI-----DLPY-----------VEVVS 207
Query: 309 NEIELLRLWFAHMQEVKPGIYVTYNGDYFDWPFLETRAAHHGFKM-----SEELGFQCDK 363
+E E+++ ++E P + +TYNGD F +P+L RA G K+ + E Q
Sbjct: 208 SEREMIKRLVKVIREKDPDVIITYNGDNFAFPYLLKRAEKLGIKLPLGRDNSEPKMQRMG 267
Query: 364 NQGECRAKFACHLDCFAWVKRDSYLPQGSQGLKAVTKAKLGYDPLEVNPEDMVRF--AKE 421
+ K H D F ++R LP + L+AV +A G +V ++ +
Sbjct: 268 DSLAVAIKGRIHFDLFPVIRRTINLP--TYTLEAVYEAIFGKSKEKVYAHEIAEAWETGK 325
Query: 422 KPQMMASYSVSDAVATYYLYMTYVHPFIFSLATIIPMSPDEVLRKGSGTLCEMLLMVQAY 481
+ +A YS+ DA T+ L + P LA ++ V R +G L E L+ +AY
Sbjct: 326 GLERVAKYSMEDAKVTFELGKEF-FPMEAQLARLVGQPVWAVSRSSTGNLVEWFLLRKAY 384
Query: 482 KANVICPNKHQSDPEKFYRNHLLESETYIGGHVECLESGVFRSDLPTSFK-LDPS 535
+ N + PNK E+Y GG+V+ E G++ + F+ L PS
Sbjct: 385 ERNELAPNKPDER-----EYERRLRESYEGGYVKEPEKGLWEGIVSLDFRSLYPS 434
Score = 51.2 bits (121), Expect = 6e-06, Method: Compositional matrix adjust.
Identities = 75/313 (23%), Positives = 126/313 (40%), Gaps = 61/313 (19%)
Query: 760 KIQEAQDMV--VLYDSLQLAHKCILNSFYGYVMRKGARWYSMEMAGVVTYTGAKIIQNAR 817
+++E++D V L D Q A K + NS+YGY ARWY E A VT G + I R
Sbjct: 489 RMKESKDPVEKKLLDYRQRAIKILANSYYGYYGYAKARWYCKECAESVTAWGRQYIDLVR 548
Query: 818 LLIEKIG-KPLELDTDGIWCVLPGSFPENXXXXXXXXXXXXXISYPCVMLNVDVARNNTN 876
+E G K L +DTDG++ +PG+ E P ++
Sbjct: 549 RELESRGFKVLYIDTDGLYATIPGAKHEEIKEKALKFVEYINSKLPGLL----------- 597
Query: 877 DQYQTLVDPVSKTYETHSECSIEFEVDGPYKAMILPASKEEGILIKKRYAVFNDDGTLAE 936
E E +G Y + KK+YA+ +++G +
Sbjct: 598 ----------------------ELEYEGFYARGFF--------VTKKKYALIDEEGKIV- 626
Query: 937 LKGFEIKRRGELKLIKVFQAELFDKFLHGSTIEECYSAVAAVANRWLDLLDNQGKDIADS 996
+G EI RR ++ K QA++ + L ++E V V + +I
Sbjct: 627 TRGLEIVRRDWSEIAKETQAKVLEAILKHGNVDEAVKIVKEVTEKLSKY------EIPPE 680
Query: 997 ELIDYISESSTMSKSLADYGEQKSCAVTTARRLSDFLGDTMVKDKGLRCQYIVACEPQGT 1056
+L+ Y +++ L++Y + V A+RL+ + G+ YIV
Sbjct: 681 KLVIY----EQITRPLSEY-KAIGPHVAVAKRLA---AKGVKVKPGMVIGYIVLR--GDG 730
Query: 1057 PVSERAVPVAIFE 1069
P+S+RA+ + F+
Sbjct: 731 PISKRAIAIEEFD 743
>pdb|1Q8I|A Chain A, Crystal Structure Of Escherichia Coli Dna Polymerase Ii
Length = 783
Score = 50.1 bits (118), Expect = 1e-05, Method: Compositional matrix adjust.
Identities = 55/233 (23%), Positives = 85/233 (36%), Gaps = 41/233 (17%)
Query: 741 LNKVWKGKLSEAKASGNSIKIQEAQDMVVLYDSLQLAHKCILNSFYGYVMRKGARWYSME 800
+ +W G+ EAK GN L A K I+N+FYG + R++
Sbjct: 470 VTNIWHGR-DEAKRQGNK--------------PLSQALKIIMNAFYGVLGTTACRFFDPR 514
Query: 801 MAGVVTYTGAKIIQNARLLIEKIG-KPLELDTDGIWCVLPGSFPENXXXXXXXXXXXXXI 859
+A +T G +I++ + LIE G + DTD + L G+ E
Sbjct: 515 LASSITMRGHQIMRQTKALIEAQGYDVIYGDTDSTFVWLKGAHSEEEAAKIGRALVQHVN 574
Query: 860 SYPCVMLNVDVARNNTNDQYQTLVDPVSKTYETHSECSIEFEVDGPYKAMILPASKEEGI 919
++ L Q Q L + YETH + ++P +
Sbjct: 575 AWWAETL-----------QKQRLTSALELEYETH------------FCRFLMPTIRGADT 611
Query: 920 LIKKRYAVFNDDGTLAEL--KGFEIKRRGELKLIKVFQAELFDKFLHGSTIEE 970
KKRYA +G + KG E R L + FQ EL+ + +E
Sbjct: 612 GSKKRYAGLIQEGDKQRMVFKGLETVRTDWTPLAQQFQQELYLRIFRNEPYQE 664
Score = 41.2 bits (95), Expect = 0.005, Method: Compositional matrix adjust.
Identities = 55/241 (22%), Positives = 99/241 (41%), Gaps = 27/241 (11%)
Query: 311 IELLRLWFAHMQEVKPGIYVTYNGDYFDWPFLETRAAHHGFKMSEELGFQCDKNQGECRA 370
+E L WFA+ P + + +N FD L+ A +++ LG D ++ E R
Sbjct: 205 LEKLNAWFANYD---PDVIIGWNVVQFDLRMLQKHAER--YRLPLRLG--RDNSELEWRE 257
Query: 371 KFACHLDCFAWVK-----------RDSYLPQGSQGLKAVTKAKLGYDPLEVNPEDMV--- 416
+ FA K + ++ S L+ V + LG NP D +
Sbjct: 258 HGFKNGVFFAQAKGRLIIDGIEALKSAFWNFSSFSLETVAQELLGEGKSIDNPWDRMDEI 317
Query: 417 --RFAKEKPQMMASYSVSDA-VATYYLYMTYVHPFIFSLATIIPMSPDEVLRKGSGTLCE 473
RFA++KP +A+Y++ D + T + T + PF+ AT+ + D GS
Sbjct: 318 DRRFAEDKP-ALATYNLKDCELVTQIFHKTEIMPFLLERATVNGLPVDR--HGGSVAAFG 374
Query: 474 MLLMVQAYKANVICPNKHQSDPEKFYRNHLLESETYIGGHVECLESGVFRSDLPTSFKLD 533
L + ++A + PN + P ++++S + V L+ + +F +D
Sbjct: 375 HLYFPRMHRAGYVAPNLGEVPPHASPGGYVMDSRPGLYDSVLVLDYKSLYPSIVRTFLID 434
Query: 534 P 534
P
Sbjct: 435 P 435
>pdb|3K5L|A Chain A, Crystal Structure Of E.Coli Pol Ii-Abasic Dna-Datp Lt(0,
3) Ternary Complex
pdb|3K5M|A Chain A, Crystal Structure Of E.Coli Pol Ii-Abasic Dna-Ddgtp Lt(-2,
2) Ternary Complex
pdb|3K5N|A Chain A, Crystal Structure Of E.Coli Pol Ii-Abasic Dna Binary
Complex
pdb|3K5N|B Chain B, Crystal Structure Of E.Coli Pol Ii-Abasic Dna Binary
Complex
pdb|3K5O|A Chain A, Crystal Structure Of E.Coli Pol Ii
pdb|3K5O|B Chain B, Crystal Structure Of E.Coli Pol Ii
pdb|3K57|A Chain A, Crystal Structure Of E.Coli Pol Ii-Normal Dna-Datp Ternary
Complex
pdb|3K58|A Chain A, Crystal Structure Of E.Coli Pol Ii-Normal Dna-Dttp Ternary
Complex
pdb|3K59|A Chain A, Crystal Structure Of E.Coli Pol Ii-Normal Dna-Dctp Ternary
Complex
pdb|3MAQ|A Chain A, Crystal Structure Of E.coli Pol Ii-normal Dna-dgtp Ternary
Complex
Length = 786
Score = 50.1 bits (118), Expect = 1e-05, Method: Compositional matrix adjust.
Identities = 55/233 (23%), Positives = 85/233 (36%), Gaps = 41/233 (17%)
Query: 741 LNKVWKGKLSEAKASGNSIKIQEAQDMVVLYDSLQLAHKCILNSFYGYVMRKGARWYSME 800
+ +W G+ EAK GN L A K I+N+FYG + R++
Sbjct: 473 VTNIWHGR-DEAKRQGNK--------------PLSQALKIIMNAFYGVLGTTACRFFDPR 517
Query: 801 MAGVVTYTGAKIIQNARLLIEKIG-KPLELDTDGIWCVLPGSFPENXXXXXXXXXXXXXI 859
+A +T G +I++ + LIE G + DTD + L G+ E
Sbjct: 518 LASSITMRGHQIMRQTKALIEAQGYDVIYGDTDSTFVWLKGAHSEEEAAKIGRALVQHVN 577
Query: 860 SYPCVMLNVDVARNNTNDQYQTLVDPVSKTYETHSECSIEFEVDGPYKAMILPASKEEGI 919
++ L Q Q L + YETH + ++P +
Sbjct: 578 AWWAETL-----------QKQRLTSALELEYETH------------FCRFLMPTIRGADT 614
Query: 920 LIKKRYAVFNDDGTLAEL--KGFEIKRRGELKLIKVFQAELFDKFLHGSTIEE 970
KKRYA +G + KG E R L + FQ EL+ + +E
Sbjct: 615 GSKKRYAGLIQEGDKQRMVFKGLETVRTDWTPLAQQFQQELYLRIFRNEPYQE 667
Score = 39.3 bits (90), Expect = 0.020, Method: Compositional matrix adjust.
Identities = 54/241 (22%), Positives = 99/241 (41%), Gaps = 27/241 (11%)
Query: 311 IELLRLWFAHMQEVKPGIYVTYNGDYFDWPFLETRAAHHGFKMSEELGFQCDKNQGECRA 370
+E L WFA+ P + + +N FD L+ A +++ LG D ++ E R
Sbjct: 208 LEKLNAWFANYD---PDVIIGWNVVQFDLRMLQKHAER--YRLPLRLG--RDNSELEWRE 260
Query: 371 KFACHLDCFAWVK-----------RDSYLPQGSQGLKAVTKAKLGYDPLEVNPEDMV--- 416
+ FA K + ++ S L+ V + LG NP D +
Sbjct: 261 HGFKNGVFFAQAKGRLIIDGIEALKSAFWNFSSFSLETVAQELLGEGKSIDNPWDRMDEI 320
Query: 417 --RFAKEKPQMMASYSVSDA-VATYYLYMTYVHPFIFSLATIIPMSPDEVLRKGSGTLCE 473
RFA++KP +A+Y++ + + T + T + PF+ AT+ + D GS
Sbjct: 321 DRRFAEDKP-ALATYNLKNCELVTQIFHKTEIMPFLLERATVNGLPVDR--HGGSVAAFG 377
Query: 474 MLLMVQAYKANVICPNKHQSDPEKFYRNHLLESETYIGGHVECLESGVFRSDLPTSFKLD 533
L + ++A + PN + P ++++S + V L+ + +F +D
Sbjct: 378 HLYFPRMHRAGYVAPNLGEVPPHASPGGYVMDSRPGLYDSVLVLDYKSLYPSIIRTFLID 437
Query: 534 P 534
P
Sbjct: 438 P 438
>pdb|1S5J|A Chain A, Insight In Dna Replication: The Crystal Structure Of Dna
Polymerase B1 From The Archaeon Sulfolobus Solfataricus
Length = 847
Score = 48.5 bits (114), Expect = 4e-05, Method: Compositional matrix adjust.
Identities = 77/317 (24%), Positives = 129/317 (40%), Gaps = 44/317 (13%)
Query: 225 PLLEKRVDLLQRAEVHVCAFDIET-TKLPLKFPDADYDIIMMISYMLDG----QGYLIIN 279
P+ E + ++R A DIE T + + PD+ +IS L G + L++N
Sbjct: 181 PIFETEIPKIKR-----VAIDIEVYTPVKGRIPDSQKAEFPIISIALAGSDGLKKVLVLN 235
Query: 280 RECVGEDIEDLEYTPKPEFEGYFKVTNVNNEIELLRLWFAHMQEVKPGIYVTYNGDYFDW 339
R V E L+ V N E ELL +F + E I +T+NGD FD
Sbjct: 236 RNDVNEGSVKLDG---------ISVERFNTEYELLGRFFDILLEYP--IVLTFNGDDFDL 284
Query: 340 PFLETRAAHHGFKMSEELGFQCDKNQGECRAKF--ACHLDCFAWVKRDSYLPQGSQG--- 394
P++ RA G+ EE+ G+ AK+ H+D + + + +G
Sbjct: 285 PYIYFRALKLGY-FPEEIPIDV---AGKDEAKYLAGLHIDLYKFFFNKAVRNYAFEGKYN 340
Query: 395 ---LKAVTKAKLGYDPLEVNPEDMVRFAKEKPQMMASYSVSDAVATYYLYMTYVHPFIFS 451
L AV KA LG ++V + ++ F + + Y+ DA T L T+ +
Sbjct: 341 EYNLDAVAKALLGTSKVKV--DTLISFL--DVEKLIEYNFRDAEITLQL-TTFNNDLTMK 395
Query: 452 LATIIP----MSPDEVLRKGSGTLCEMLLMVQAYKANVICPNKHQ--SDPEKFYRNHLLE 505
L + + +E+ R T + L + K N + P K + + + L++
Sbjct: 396 LIVLFSRISRLGIEELTRTEISTWVKNLYYWEHRKRNWLIPLKEEILAKSSNIRTSALIK 455
Query: 506 SETYIGGHVECLESGVF 522
+ Y G V +G+F
Sbjct: 456 GKGYKGAVVIDPPAGIF 472
>pdb|3IAY|A Chain A, Ternary Complex Of Dna Polymerase Delta
Length = 919
Score = 35.8 bits (81), Expect = 0.27, Method: Compositional matrix adjust.
Identities = 30/115 (26%), Positives = 52/115 (45%), Gaps = 7/115 (6%)
Query: 232 DLLQRAEVHVCAFDIETTKLPLKFPDADYDIIMMISYMLDGQGYLIINRECVGEDIEDLE 291
D A + + +FDIE FP+ +YD ++ I+ ++ G ++ ++ L
Sbjct: 242 DWSHTAPLRIMSFDIECAGRIGVFPEPEYDPVIQIANVVSIAG----AKKPFIRNVFTLN 297
Query: 292 YTPKPEFEGYFKVTNVNNEIELLRLWFAHMQEVKPGIYVTYNGDYFDWPFLETRA 346
T P G ++ E E+L W + +V P + + YN FD P+L RA
Sbjct: 298 -TCSP-ITGSMIFSHATEE-EMLSNWRNFIIKVDPDVIIGYNTTNFDIPYLLNRA 349
>pdb|4FYD|A Chain A, Crystal Structure Of Yeast Dna Polymerase Alpha Bound To
Dna/rna And Dgtp
pdb|4FYD|B Chain B, Crystal Structure Of Yeast Dna Polymerase Alpha Bound To
Dna/rna And Dgtp
Length = 910
Score = 34.7 bits (78), Expect = 0.49, Method: Compositional matrix adjust.
Identities = 19/53 (35%), Positives = 28/53 (52%)
Query: 772 DSLQLAHKCILNSFYGYVMRKGARWYSMEMAGVVTYTGAKIIQNARLLIEKIG 824
D Q A K NS YG + +R+Y+ +A +VT G +I+ N R L E +
Sbjct: 589 DIRQQALKLTANSMYGCLGYVNSRFYAKPLAMLVTNKGREILMNTRQLAESMN 641
>pdb|4FVM|A Chain A, Crystal Structure Of Yeast Dna Polymerase Alpha
pdb|4FXD|A Chain A, Crystal Structure Of Yeast Dna Polymerase Alpha Bound To
Dna/rna
pdb|4FXD|B Chain B, Crystal Structure Of Yeast Dna Polymerase Alpha Bound To
Dna/rna
Length = 910
Score = 34.7 bits (78), Expect = 0.49, Method: Compositional matrix adjust.
Identities = 19/53 (35%), Positives = 28/53 (52%)
Query: 772 DSLQLAHKCILNSFYGYVMRKGARWYSMEMAGVVTYTGAKIIQNARLLIEKIG 824
D Q A K NS YG + +R+Y+ +A +VT G +I+ N R L E +
Sbjct: 589 DIRQQALKLTANSMYGCLGYVNSRFYAKPLAMLVTNKGREILMNTRQLAESMN 641
>pdb|4B08|A Chain A, Crystal Structure Of Yeast Dna Polymerase Alpha,
Selenomethionine Protein
Length = 910
Score = 34.7 bits (78), Expect = 0.60, Method: Compositional matrix adjust.
Identities = 19/50 (38%), Positives = 27/50 (54%)
Query: 772 DSLQLAHKCILNSFYGYVMRKGARWYSMEMAGVVTYTGAKIIQNARLLIE 821
D Q A K NS YG + +R+Y+ +A +VT G +I+ N R L E
Sbjct: 589 DIRQQALKLTANSXYGCLGYVNSRFYAKPLAXLVTNKGREILXNTRQLAE 638
>pdb|2NTF|L Chain L, Crystal Structure Of A Quorum-Quenching Antibody In Complex
With An N- Acyl-L-Homoserine Lactone Analog
pdb|2NTF|A Chain A, Crystal Structure Of A Quorum-Quenching Antibody In Complex
With An N- Acyl-L-Homoserine Lactone Analog
Length = 211
Score = 32.0 bits (71), Expect = 3.4, Method: Composition-based stats.
Identities = 16/47 (34%), Positives = 23/47 (48%)
Query: 1639 CDSLLKALQTRELFEWIELEPVHFWHSLLFMDQYNYGGIPARADESL 1685
C S A+ TR W++ +P HF+ L+ G+PAR SL
Sbjct: 22 CRSSTGAVTTRNYANWVQEKPDHFFTGLIGDTNNRAPGVPARFSGSL 68
>pdb|2OP4|L Chain L, Crystal Structure Of Quorum-Quenching Antibody 1g9
Length = 212
Score = 32.0 bits (71), Expect = 3.4, Method: Composition-based stats.
Identities = 16/47 (34%), Positives = 23/47 (48%)
Query: 1639 CDSLLKALQTRELFEWIELEPVHFWHSLLFMDQYNYGGIPARADESL 1685
C S A+ TR W++ +P HF+ L+ G+PAR SL
Sbjct: 22 CRSSTGAVTTRNYANWVQEKPDHFFTGLIGDTNNRAPGVPARFSGSL 68
>pdb|1QLG|A Chain A, Crystal Structure Of Phytase With Magnesium From Bacillus
Amyloliquefaciens
Length = 355
Score = 30.8 bits (68), Expect = 7.2, Method: Composition-based stats.
Identities = 31/119 (26%), Positives = 52/119 (43%), Gaps = 27/119 (22%)
Query: 264 MMISYMLDGQGYL-----------IINRECVGEDIEDLEYTPKPEFEGYFKVTNVNNEIE 312
+ I Y DG+GYL I R+ + + D + T PE +G T+ + I+
Sbjct: 234 LTIYYAADGKGYLLASSQGNSSYAIYERQGQNKYVADFQITDGPETDG----TSDTDGID 289
Query: 313 LLRLWFAHMQEVKPGIYVTYNGDYFDWPFLETRAAHHGFKM------SEELGFQCDKNQ 365
+L F E G++V NG+ D + A+ FKM ++++GF N+
Sbjct: 290 VLG--FGLGPEYPFGLFVAQNGENID----HGQKANQNFKMVPWERIADKIGFHPQVNK 342
>pdb|1CVM|A Chain A, Cadmium Inhibited Crystal Structure Of Phytase From
Bacillus Amyloliquefaciens
pdb|1H6L|A Chain A, Beta-Propeller Phytase In Complex With Phosphate And
Calcium Ions
Length = 353
Score = 30.8 bits (68), Expect = 7.3, Method: Composition-based stats.
Identities = 31/119 (26%), Positives = 52/119 (43%), Gaps = 27/119 (22%)
Query: 264 MMISYMLDGQGYL-----------IINRECVGEDIEDLEYTPKPEFEGYFKVTNVNNEIE 312
+ I Y DG+GYL I R+ + + D + T PE +G T+ + I+
Sbjct: 234 LTIYYAADGKGYLLASSQGNSSYAIYERQGQNKYVADFQITDGPETDG----TSDTDGID 289
Query: 313 LLRLWFAHMQEVKPGIYVTYNGDYFDWPFLETRAAHHGFKM------SEELGFQCDKNQ 365
+L F E G++V NG+ D + A+ FKM ++++GF N+
Sbjct: 290 VLG--FGLGPEYPFGLFVAQNGENID----HGQKANQNFKMVPWERIADKIGFHPQVNK 342
>pdb|2OH3|A Chain A, Crystal Structure Of Cog1633: Uncharacterized Conserved
Protein (Zp_00055496.1) From Magnetospirillum
Magnetotacticum Ms-1 At 2.00 A Resolution
Length = 167
Score = 30.8 bits (68), Expect = 8.9, Method: Composition-based stats.
Identities = 21/66 (31%), Positives = 33/66 (50%), Gaps = 5/66 (7%)
Query: 192 DLREYDVPYH-IRFAIDNDVRCGQWYDVSISSTGPLLEKRV--DLLQRAEVHVCAFD--I 246
D+ PYH +R+A DN++R ++Y + +++ KR+ D HV A D I
Sbjct: 87 DIHYLXTPYHALRYARDNEIRGXEYYKEAAANSADPEVKRLGADFAAEEAEHVVALDKWI 146
Query: 247 ETTKLP 252
E T P
Sbjct: 147 EKTPRP 152
>pdb|1AII|A Chain A, Annexin Iii
Length = 323
Score = 30.4 bits (67), Expect = 9.2, Method: Compositional matrix adjust.
Identities = 21/71 (29%), Positives = 34/71 (47%), Gaps = 11/71 (15%)
Query: 1758 IVQYVKGEISSYFTGKLLSIVR----------DAIHH-MKKMNNDQHNSPGVMQTAANIH 1806
IV +KGE+S +F LL+IV + +H +K + D+ +M + + I
Sbjct: 224 IVDSIKGELSGHFEDLLLAIVNCVRNTPAFLAERLHRALKGIGTDEFTLNRIMVSRSEID 283
Query: 1807 KVDAPLEFIKH 1817
+D EF KH
Sbjct: 284 LLDIRTEFKKH 294
>pdb|1AXN|A Chain A, The High Resolution Structure Of Annexin Iii Shows
Differences With Annexin V
Length = 323
Score = 30.4 bits (67), Expect = 9.3, Method: Compositional matrix adjust.
Identities = 21/71 (29%), Positives = 34/71 (47%), Gaps = 11/71 (15%)
Query: 1758 IVQYVKGEISSYFTGKLLSIVR----------DAIHH-MKKMNNDQHNSPGVMQTAANIH 1806
IV +KGE+S +F LL+IV + +H +K + D+ +M + + I
Sbjct: 224 IVDSIKGELSGHFEDLLLAIVNCVRNTPAFLAERLHRALKGIGTDEFTLNRIMVSRSEID 283
Query: 1807 KVDAPLEFIKH 1817
+D EF KH
Sbjct: 284 LLDIRTEFKKH 294
>pdb|2QM3|A Chain A, Crystal Structure Of A Predicted Methyltransferase From
Pyrococcus Furiosus
Length = 373
Score = 30.4 bits (67), Expect = 9.5, Method: Compositional matrix adjust.
Identities = 32/124 (25%), Positives = 52/124 (41%), Gaps = 9/124 (7%)
Query: 228 EKRVDLLQRAEVHVCAFDIETTKLPLKFPDADYDIIMMISYMLDGQGYLIINRECVGEDI 287
E+ +++A + DIE L+ P DY + +++ D L R VG I
Sbjct: 205 ERLTKFIEKAANEIGYEDIEIFTFDLRKPLPDYALHKFDTFITDPPETLEAIRAFVGRGI 264
Query: 288 EDLEYTPKPEFEGYFKVTNVNNEI----ELLRLWFAHMQEVKPGIYVTYNGDYFDWPFL- 342
L+ P GYF +T + + E+ +L V I +N +Y +W +
Sbjct: 265 ATLK---GPRCAGYFGITRRESSLDKWREIQKLLLNEFNVVITDIIRNFN-EYVNWGYAE 320
Query: 343 ETRA 346
ETRA
Sbjct: 321 ETRA 324
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 0.135 0.407
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 58,525,722
Number of Sequences: 62578
Number of extensions: 2480873
Number of successful extensions: 5585
Number of sequences better than 100.0: 36
Number of HSP's better than 100.0 without gapping: 21
Number of HSP's successfully gapped in prelim test: 15
Number of HSP's that attempted gapping in prelim test: 5435
Number of HSP's gapped (non-prelim): 112
length of query: 1988
length of database: 14,973,337
effective HSP length: 113
effective length of query: 1875
effective length of database: 7,902,023
effective search space: 14816293125
effective search space used: 14816293125
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: 59 (27.3 bits)