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= 047050
(186 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|3RIZ|A Chain A, Crystal Structure Of The Plant Steroid Receptor Bri1
Ectodomain
pdb|3RJ0|A Chain A, Plant Steroid Receptor Bri1 Ectodomain In Complex With
Brassinolide
Length = 772
Score = 48.9 bits (115), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 47/186 (25%), Positives = 80/186 (43%), Gaps = 33/186 (17%)
Query: 5 WIQLQPLDCEFPDVLKTQHQLQLLIISRNQIHGRISNWMWDMG----VRTFTNNFHGRIP 60
++Q + P L +L L +S N + G I + + + ++ + N G IP
Sbjct: 397 YLQNNGFTGKIPPTLSNCSELVSLHLSFNYLSGTIPSSLGSLSKLRDLKLWLNMLEGEIP 456
Query: 61 QTYVQGCNLDFLRLNGNCLERPIPTSLIDYVNMNFLNVGNNKLSGPIPKCKNIQTERILT 120
Q + L+ L L+ N L IP+ L + N+N++++ NN+L+G IPK
Sbjct: 457 QELMYVKTLETLILDFNDLTGEIPSGLSNCTNLNWISLSNNRLTGEIPKW---------- 506
Query: 121 TSATIDLSSNRFQEKILEVVGKLNSLKNSNISHNNLIGGIPSSLRNLTEFESLDLSLNKF 180
+G+L +L +S+N+ G IP+ L + LDL+ N F
Sbjct: 507 -------------------IGRLENLAILKLSNNSFSGNIPAELGDCRSLIWLDLNTNLF 547
Query: 181 VEHIPT 186
IP
Sbjct: 548 NGTIPA 553
Score = 43.1 bits (100), Expect = 9e-05, Method: Compositional matrix adjust.
Identities = 51/184 (27%), Positives = 83/184 (45%), Gaps = 24/184 (13%)
Query: 24 QLQLLIISRNQIHGRI--SNWMWDMGVRTFTNNFHGRIPQTYVQGCN-LDFLRLNGNCLE 80
+L+ L IS N+I G + S + + +NNF IP ++ C+ L L ++GN L
Sbjct: 176 ELKHLAISGNKISGDVDVSRCVNLEFLDVSSNNFSTGIP--FLGDCSALQHLDISGNKLS 233
Query: 81 RPIPTSLIDYVNMNFLNVGNNKLSGPIP--KCKNIQ----TERILT------------TS 122
++ + LN+ +N+ GPIP K++Q E T T
Sbjct: 234 GDFSRAISTCTELKLLNISSNQFVGPIPPLPLKSLQYLSLAENKFTGEIPDFLSGACDTL 293
Query: 123 ATIDLSSNRFQEKILEVVGKLNSLKNSNISHNNLIGGIP-SSLRNLTEFESLDLSLNKFV 181
+DLS N F + G + L++ +S NN G +P +L + + LDLS N+F
Sbjct: 294 TGLDLSGNHFYGAVPPFFGSCSLLESLALSSNNFSGELPMDTLLKMRGLKVLDLSFNEFS 353
Query: 182 EHIP 185
+P
Sbjct: 354 GELP 357
Score = 41.2 bits (95), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 57/225 (25%), Positives = 90/225 (40%), Gaps = 45/225 (20%)
Query: 6 IQLQPLDCEFPDVLKTQHQLQLLIISRNQIHGRISNWMW---DMGVRTFTNN-FHGRIPQ 61
+ L E P L L + +S N++ G I W+ ++ + +NN F G IP
Sbjct: 470 LDFNDLTGEIPSGLSNCTNLNWISLSNNRLTGEIPKWIGRLENLAILKLSNNSFSGNIPA 529
Query: 62 TYVQGCNLDFLRLNGNCLERPIPTSLI---DYVNMNFL---------NVGNNKL---SGP 106
+L +L LN N IP ++ + NF+ N G K +G
Sbjct: 530 ELGDCRSLIWLDLNTNLFNGTIPAAMFKQSGKIAANFIAGKRYVYIKNDGMKKECHGAGN 589
Query: 107 IPKCKNIQTE---RILT--------------TSAT---------IDLSSNRFQEKILEVV 140
+ + + I++E R+ T TS T +D+S N I + +
Sbjct: 590 LLEFQGIRSEQLNRLSTRNPCNITSRVYGGHTSPTFDNNGSMMFLDMSYNMLSGYIPKEI 649
Query: 141 GKLNSLKNSNISHNNLIGGIPSSLRNLTEFESLDLSLNKFVEHIP 185
G + L N+ HN++ G IP + +L LDLS NK IP
Sbjct: 650 GSMPYLFILNLGHNDISGSIPDEVGDLRGLNILDLSSNKLDGRIP 694
Score = 38.1 bits (87), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 33/94 (35%), Positives = 45/94 (47%), Gaps = 5/94 (5%)
Query: 92 NMNFLNVGNNKLSGPIPKCKNIQTERILTTSATIDLSSNRFQEKILEVVGKLNSLKNSNI 151
+M FL++ N LSG IPK I + L ++L N I + VG L L ++
Sbjct: 630 SMMFLDMSYNMLSGYIPK--EIGSMPYL---FILNLGHNDISGSIPDEVGDLRGLNILDL 684
Query: 152 SHNNLIGGIPSSLRNLTEFESLDLSLNKFVEHIP 185
S N L G IP ++ LT +DLS N IP
Sbjct: 685 SSNKLDGRIPQAMSALTMLTEIDLSNNNLSGPIP 718
Score = 37.4 bits (85), Expect = 0.005, Method: Compositional matrix adjust.
Identities = 53/201 (26%), Positives = 83/201 (41%), Gaps = 28/201 (13%)
Query: 14 EFPDVLKTQ-HQLQLLIISRNQIHGRISNWMWDMGVRTFT----NNFHGRIP-QTYVQGC 67
E PD L L L +S N +G + + + NNF G +P T ++
Sbjct: 281 EIPDFLSGACDTLTGLDLSGNHFYGAVPPFFGSCSLLESLALSSNNFSGELPMDTLLKMR 340
Query: 68 NLDFLRLNGNCLERPIPTSLIDY-VNMNFLNVGNNKLSGPI-PK-CKNIQ---------- 114
L L L+ N +P SL + ++ L++ +N SGPI P C+N +
Sbjct: 341 GLKVLDLSFNEFSGELPESLTNLSASLLTLDLSSNNFSGPILPNLCQNPKNTLQELYLQN 400
Query: 115 ---TERILTTSA------TIDLSSNRFQEKILEVVGKLNSLKNSNISHNNLIGGIPSSLR 165
T +I T + ++ LS N I +G L+ L++ + N L G IP L
Sbjct: 401 NGFTGKIPPTLSNCSELVSLHLSFNYLSGTIPSSLGSLSKLRDLKLWLNMLEGEIPQELM 460
Query: 166 NLTEFESLDLSLNKFVEHIPT 186
+ E+L L N IP+
Sbjct: 461 YVKTLETLILDFNDLTGEIPS 481
Score = 36.2 bits (82), Expect = 0.012, Method: Compositional matrix adjust.
Identities = 33/109 (30%), Positives = 47/109 (43%), Gaps = 6/109 (5%)
Query: 53 NNFHGRIPQTYVQGCNLDFLRLNGNCLERPIPTSLIDYVNMNFLNVGNNKLSGPIPKCKN 112
N G IP+ L L L N + IP + D +N L++ +NKL G IP
Sbjct: 639 NMLSGYIPKEIGSMPYLFILNLGHNDISGSIPDEVGDLRGLNILDLSSNKLDGRIP---- 694
Query: 113 IQTERILTTSATIDLSSNRFQEKILEVVGKLNSLKNSNISHNNLIGGIP 161
Q LT IDLS+N I E +G+ + + +N + G P
Sbjct: 695 -QAMSALTMLTEIDLSNNNLSGPIPE-MGQFETFPPAKFLNNPGLCGYP 741
Score = 35.4 bits (80), Expect = 0.020, Method: Compositional matrix adjust.
Identities = 27/96 (28%), Positives = 42/96 (43%), Gaps = 4/96 (4%)
Query: 24 QLQLLIISRNQIHGRISNWMWDMGVRTFTNNFH----GRIPQTYVQGCNLDFLRLNGNCL 79
+ L +S N + G I + M N H G IP L+ L L+ N L
Sbjct: 630 SMMFLDMSYNMLSGYIPKEIGSMPYLFILNLGHNDISGSIPDEVGDLRGLNILDLSSNKL 689
Query: 80 ERPIPTSLIDYVNMNFLNVGNNKLSGPIPKCKNIQT 115
+ IP ++ + +++ NN LSGPIP+ +T
Sbjct: 690 DGRIPQAMSALTMLTEIDLSNNNLSGPIPEMGQFET 725
Score = 31.6 bits (70), Expect = 0.25, Method: Compositional matrix adjust.
Identities = 31/102 (30%), Positives = 45/102 (44%), Gaps = 9/102 (8%)
Query: 16 PDVLKTQHQLQLLIISRNQIHGRISNWMWDM-GVRTF---TNNFHGRIPQTYVQGCNLDF 71
P + + L +L + N I G I + + D+ G+ +N GRIPQ L
Sbjct: 646 PKEIGSMPYLFILNLGHNDISGSIPDEVGDLRGLNILDLSSNKLDGRIPQAMSALTMLTE 705
Query: 72 LRLNGNCLERPIPT--SLIDYVNMNFLNVGNNKLSG-PIPKC 110
+ L+ N L PIP + FLN N L G P+P+C
Sbjct: 706 IDLSNNNLSGPIPEMGQFETFPPAKFLN--NPGLCGYPLPRC 745
Score = 30.4 bits (67), Expect = 0.52, Method: Compositional matrix adjust.
Identities = 41/166 (24%), Positives = 64/166 (38%), Gaps = 48/166 (28%)
Query: 67 CNLDFLRLNGNCLERPIPT--SLIDYVNMNFLNVGNNKLS--GPIPKCKNIQTERILTTS 122
+L L L+ N L P+ T SL + FLNV +N L G + + + +L S
Sbjct: 97 ASLTSLDLSRNSLSGPVTTLTSLGSCSGLKFLNVSSNTLDFPGKVSGGLKLNSLEVLDLS 156
Query: 123 AT-------------------------------------------IDLSSNRFQEKILEV 139
A +D+SSN F I
Sbjct: 157 ANSISGANVVGWVLSDGCGELKHLAISGNKISGDVDVSRCVNLEFLDVSSNNFSTGI-PF 215
Query: 140 VGKLNSLKNSNISHNNLIGGIPSSLRNLTEFESLDLSLNKFVEHIP 185
+G ++L++ +IS N L G ++ TE + L++S N+FV IP
Sbjct: 216 LGDCSALQHLDISGNKLSGDFSRAISTCTELKLLNISSNQFVGPIP 261
>pdb|3RGX|A Chain A, Structural Insight Into Brassinosteroid Perception By Bri1
pdb|3RGZ|A Chain A, Structural Insight Into Brassinosteroid Perception By Bri1
Length = 768
Score = 48.9 bits (115), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 47/186 (25%), Positives = 80/186 (43%), Gaps = 33/186 (17%)
Query: 5 WIQLQPLDCEFPDVLKTQHQLQLLIISRNQIHGRISNWMWDMG----VRTFTNNFHGRIP 60
++Q + P L +L L +S N + G I + + + ++ + N G IP
Sbjct: 400 YLQNNGFTGKIPPTLSNCSELVSLHLSFNYLSGTIPSSLGSLSKLRDLKLWLNMLEGEIP 459
Query: 61 QTYVQGCNLDFLRLNGNCLERPIPTSLIDYVNMNFLNVGNNKLSGPIPKCKNIQTERILT 120
Q + L+ L L+ N L IP+ L + N+N++++ NN+L+G IPK
Sbjct: 460 QELMYVKTLETLILDFNDLTGEIPSGLSNCTNLNWISLSNNRLTGEIPKW---------- 509
Query: 121 TSATIDLSSNRFQEKILEVVGKLNSLKNSNISHNNLIGGIPSSLRNLTEFESLDLSLNKF 180
+G+L +L +S+N+ G IP+ L + LDL+ N F
Sbjct: 510 -------------------IGRLENLAILKLSNNSFSGNIPAELGDCRSLIWLDLNTNLF 550
Query: 181 VEHIPT 186
IP
Sbjct: 551 NGTIPA 556
Score = 43.1 bits (100), Expect = 9e-05, Method: Compositional matrix adjust.
Identities = 51/184 (27%), Positives = 83/184 (45%), Gaps = 24/184 (13%)
Query: 24 QLQLLIISRNQIHGRI--SNWMWDMGVRTFTNNFHGRIPQTYVQGCN-LDFLRLNGNCLE 80
+L+ L IS N+I G + S + + +NNF IP ++ C+ L L ++GN L
Sbjct: 179 ELKHLAISGNKISGDVDVSRCVNLEFLDVSSNNFSTGIP--FLGDCSALQHLDISGNKLS 236
Query: 81 RPIPTSLIDYVNMNFLNVGNNKLSGPIP--KCKNIQ----TERILT------------TS 122
++ + LN+ +N+ GPIP K++Q E T T
Sbjct: 237 GDFSRAISTCTELKLLNISSNQFVGPIPPLPLKSLQYLSLAENKFTGEIPDFLSGACDTL 296
Query: 123 ATIDLSSNRFQEKILEVVGKLNSLKNSNISHNNLIGGIP-SSLRNLTEFESLDLSLNKFV 181
+DLS N F + G + L++ +S NN G +P +L + + LDLS N+F
Sbjct: 297 TGLDLSGNHFYGAVPPFFGSCSLLESLALSSNNFSGELPMDTLLKMRGLKVLDLSFNEFS 356
Query: 182 EHIP 185
+P
Sbjct: 357 GELP 360
Score = 41.2 bits (95), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 57/225 (25%), Positives = 90/225 (40%), Gaps = 45/225 (20%)
Query: 6 IQLQPLDCEFPDVLKTQHQLQLLIISRNQIHGRISNWMW---DMGVRTFTNN-FHGRIPQ 61
+ L E P L L + +S N++ G I W+ ++ + +NN F G IP
Sbjct: 473 LDFNDLTGEIPSGLSNCTNLNWISLSNNRLTGEIPKWIGRLENLAILKLSNNSFSGNIPA 532
Query: 62 TYVQGCNLDFLRLNGNCLERPIPTSLI---DYVNMNFL---------NVGNNKL---SGP 106
+L +L LN N IP ++ + NF+ N G K +G
Sbjct: 533 ELGDCRSLIWLDLNTNLFNGTIPAAMFKQSGKIAANFIAGKRYVYIKNDGMKKECHGAGN 592
Query: 107 IPKCKNIQTE---RILT--------------TSAT---------IDLSSNRFQEKILEVV 140
+ + + I++E R+ T TS T +D+S N I + +
Sbjct: 593 LLEFQGIRSEQLNRLSTRNPCNITSRVYGGHTSPTFDNNGSMMFLDMSYNMLSGYIPKEI 652
Query: 141 GKLNSLKNSNISHNNLIGGIPSSLRNLTEFESLDLSLNKFVEHIP 185
G + L N+ HN++ G IP + +L LDLS NK IP
Sbjct: 653 GSMPYLFILNLGHNDISGSIPDEVGDLRGLNILDLSSNKLDGRIP 697
Score = 37.7 bits (86), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 33/94 (35%), Positives = 45/94 (47%), Gaps = 5/94 (5%)
Query: 92 NMNFLNVGNNKLSGPIPKCKNIQTERILTTSATIDLSSNRFQEKILEVVGKLNSLKNSNI 151
+M FL++ N LSG IPK I + L ++L N I + VG L L ++
Sbjct: 633 SMMFLDMSYNMLSGYIPK--EIGSMPYL---FILNLGHNDISGSIPDEVGDLRGLNILDL 687
Query: 152 SHNNLIGGIPSSLRNLTEFESLDLSLNKFVEHIP 185
S N L G IP ++ LT +DLS N IP
Sbjct: 688 SSNKLDGRIPQAMSALTMLTEIDLSNNNLSGPIP 721
Score = 37.4 bits (85), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 53/201 (26%), Positives = 83/201 (41%), Gaps = 28/201 (13%)
Query: 14 EFPDVLKTQ-HQLQLLIISRNQIHGRISNWMWDMGVRTFT----NNFHGRIP-QTYVQGC 67
E PD L L L +S N +G + + + NNF G +P T ++
Sbjct: 284 EIPDFLSGACDTLTGLDLSGNHFYGAVPPFFGSCSLLESLALSSNNFSGELPMDTLLKMR 343
Query: 68 NLDFLRLNGNCLERPIPTSLIDY-VNMNFLNVGNNKLSGPI-PK-CKNIQ---------- 114
L L L+ N +P SL + ++ L++ +N SGPI P C+N +
Sbjct: 344 GLKVLDLSFNEFSGELPESLTNLSASLLTLDLSSNNFSGPILPNLCQNPKNTLQELYLQN 403
Query: 115 ---TERILTTSA------TIDLSSNRFQEKILEVVGKLNSLKNSNISHNNLIGGIPSSLR 165
T +I T + ++ LS N I +G L+ L++ + N L G IP L
Sbjct: 404 NGFTGKIPPTLSNCSELVSLHLSFNYLSGTIPSSLGSLSKLRDLKLWLNMLEGEIPQELM 463
Query: 166 NLTEFESLDLSLNKFVEHIPT 186
+ E+L L N IP+
Sbjct: 464 YVKTLETLILDFNDLTGEIPS 484
Score = 36.2 bits (82), Expect = 0.012, Method: Compositional matrix adjust.
Identities = 33/109 (30%), Positives = 47/109 (43%), Gaps = 6/109 (5%)
Query: 53 NNFHGRIPQTYVQGCNLDFLRLNGNCLERPIPTSLIDYVNMNFLNVGNNKLSGPIPKCKN 112
N G IP+ L L L N + IP + D +N L++ +NKL G IP
Sbjct: 642 NMLSGYIPKEIGSMPYLFILNLGHNDISGSIPDEVGDLRGLNILDLSSNKLDGRIP---- 697
Query: 113 IQTERILTTSATIDLSSNRFQEKILEVVGKLNSLKNSNISHNNLIGGIP 161
Q LT IDLS+N I E +G+ + + +N + G P
Sbjct: 698 -QAMSALTMLTEIDLSNNNLSGPIPE-MGQFETFPPAKFLNNPGLCGYP 744
Score = 35.4 bits (80), Expect = 0.019, Method: Compositional matrix adjust.
Identities = 27/96 (28%), Positives = 42/96 (43%), Gaps = 4/96 (4%)
Query: 24 QLQLLIISRNQIHGRISNWMWDMGVRTFTNNFH----GRIPQTYVQGCNLDFLRLNGNCL 79
+ L +S N + G I + M N H G IP L+ L L+ N L
Sbjct: 633 SMMFLDMSYNMLSGYIPKEIGSMPYLFILNLGHNDISGSIPDEVGDLRGLNILDLSSNKL 692
Query: 80 ERPIPTSLIDYVNMNFLNVGNNKLSGPIPKCKNIQT 115
+ IP ++ + +++ NN LSGPIP+ +T
Sbjct: 693 DGRIPQAMSALTMLTEIDLSNNNLSGPIPEMGQFET 728
Score = 32.0 bits (71), Expect = 0.23, Method: Compositional matrix adjust.
Identities = 31/102 (30%), Positives = 45/102 (44%), Gaps = 9/102 (8%)
Query: 16 PDVLKTQHQLQLLIISRNQIHGRISNWMWDM-GVRTF---TNNFHGRIPQTYVQGCNLDF 71
P + + L +L + N I G I + + D+ G+ +N GRIPQ L
Sbjct: 649 PKEIGSMPYLFILNLGHNDISGSIPDEVGDLRGLNILDLSSNKLDGRIPQAMSALTMLTE 708
Query: 72 LRLNGNCLERPIPT--SLIDYVNMNFLNVGNNKLSG-PIPKC 110
+ L+ N L PIP + FLN N L G P+P+C
Sbjct: 709 IDLSNNNLSGPIPEMGQFETFPPAKFLN--NPGLCGYPLPRC 748
Score = 30.4 bits (67), Expect = 0.57, Method: Compositional matrix adjust.
Identities = 41/166 (24%), Positives = 64/166 (38%), Gaps = 48/166 (28%)
Query: 67 CNLDFLRLNGNCLERPIPT--SLIDYVNMNFLNVGNNKLS--GPIPKCKNIQTERILTTS 122
+L L L+ N L P+ T SL + FLNV +N L G + + + +L S
Sbjct: 100 ASLTSLDLSRNSLSGPVTTLTSLGSCSGLKFLNVSSNTLDFPGKVSGGLKLNSLEVLDLS 159
Query: 123 AT-------------------------------------------IDLSSNRFQEKILEV 139
A +D+SSN F I
Sbjct: 160 ANSISGANVVGWVLSDGCGELKHLAISGNKISGDVDVSRCVNLEFLDVSSNNFSTGI-PF 218
Query: 140 VGKLNSLKNSNISHNNLIGGIPSSLRNLTEFESLDLSLNKFVEHIP 185
+G ++L++ +IS N L G ++ TE + L++S N+FV IP
Sbjct: 219 LGDCSALQHLDISGNKLSGDFSRAISTCTELKLLNISSNQFVGPIP 264
>pdb|1OGQ|A Chain A, The Crystal Structure Of Pgip (Polygalacturonase
Inhibiting Protein), A Leucine Rich Repeat Protein
Involved In Plant Defense
Length = 313
Score = 41.6 bits (96), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 34/129 (26%), Positives = 57/129 (44%), Gaps = 7/129 (5%)
Query: 59 IPQTYVQGCNLDFLRLNG-NCLERPIPTSLIDYVNMNFLNVGNNKLSGPIPKCKNIQTER 117
IP + L+FL + G N L PIP ++ +++L + + +SG IP
Sbjct: 68 IPSSLANLPYLNFLYIGGINNLVGPIPPAIAKLTQLHYLYITHTNVSGAIP-----DFLS 122
Query: 118 ILTTSATIDLSSNRFQEKILEVVGKLNSLKNSNISHNNLIGGIPSSLRNLTE-FESLDLS 176
+ T T+D S N + + L +L N + G IP S + ++ F S+ +S
Sbjct: 123 QIKTLVTLDFSYNALSGTLPPSISSLPNLVGITFDGNRISGAIPDSYGSFSKLFTSMTIS 182
Query: 177 LNKFVEHIP 185
N+ IP
Sbjct: 183 RNRLTGKIP 191
Score = 34.3 bits (77), Expect = 0.042, Method: Compositional matrix adjust.
Identities = 41/153 (26%), Positives = 64/153 (41%), Gaps = 16/153 (10%)
Query: 36 HGRISNWMWDMGVRTFTNNFHGRIPQTYVQGCNLDFLRLNGNCLERPIPTSLIDYVNMNF 95
+G S M + N G+IP T+ NL F+ L+ N LE N
Sbjct: 169 YGSFSKLFTSMTISR--NRLTGKIPPTFAN-LNLAFVDLSRNMLEGDASVLFGSDKNTQK 225
Query: 96 LNVGNNKLS---GPIPKCKNIQTERILTTSATIDLSSNRFQEKILEVVGKLNSLKNSNIS 152
+++ N L+ G + KN+ +DL +NR + + + +L L + N+S
Sbjct: 226 IHLAKNSLAFDLGKVGLSKNLNG---------LDLRNNRIYGTLPQGLTQLKFLHSLNVS 276
Query: 153 HNNLIGGIPSSLRNLTEFESLDLSLNKFVEHIP 185
NNL G IP NL F+ + NK + P
Sbjct: 277 FNNLCGEIPQG-GNLQRFDVSAYANNKCLCGSP 308
>pdb|2Z62|A Chain A, Crystal Structure Of The Tv3 Hybrid Of Human Tlr4 And
Hagfish Vlrb.61
pdb|2Z65|A Chain A, Crystal Structure Of The Human Tlr4 Tv3
Hybrid-Md-2-Eritoran Complex
pdb|2Z65|B Chain B, Crystal Structure Of The Human Tlr4 Tv3
Hybrid-Md-2-Eritoran Complex
Length = 276
Score = 32.0 bits (71), Expect = 0.21, Method: Compositional matrix adjust.
Identities = 18/41 (43%), Positives = 24/41 (58%), Gaps = 1/41 (2%)
Query: 140 VGKLNSLKNSNISHNNLIG-GIPSSLRNLTEFESLDLSLNK 179
+G L +LK N++HN + +P NLT E LDLS NK
Sbjct: 120 IGHLKTLKELNVAHNLIQSFKLPEYFSNLTNLEHLDLSSNK 160
>pdb|3FXI|A Chain A, Crystal Structure Of The Human Tlr4-Human Md-2-E.Coli Lps
Ra Complex
pdb|3FXI|B Chain B, Crystal Structure Of The Human Tlr4-Human Md-2-E.Coli Lps
Ra Complex
Length = 605
Score = 32.0 bits (71), Expect = 0.21, Method: Compositional matrix adjust.
Identities = 20/42 (47%), Positives = 25/42 (59%), Gaps = 3/42 (7%)
Query: 140 VGKLNSLKNSNISHNNLIGG--IPSSLRNLTEFESLDLSLNK 179
+G L +LK N++HN LI +P NLT E LDLS NK
Sbjct: 120 IGHLKTLKELNVAHN-LIQSFKLPEYFSNLTNLEHLDLSSNK 160
>pdb|3UL7|A Chain A, Crystal Structure Of The Tv3 Mutant F63w
Length = 278
Score = 32.0 bits (71), Expect = 0.21, Method: Compositional matrix adjust.
Identities = 18/41 (43%), Positives = 24/41 (58%), Gaps = 1/41 (2%)
Query: 140 VGKLNSLKNSNISHNNLIG-GIPSSLRNLTEFESLDLSLNK 179
+G L +LK N++HN + +P NLT E LDLS NK
Sbjct: 121 IGHLKTLKELNVAHNLIQSFKLPEYFSNLTNLEHLDLSSNK 161
>pdb|4G8A|A Chain A, Crystal Structure Of Human Tlr4 Polymorphic Variant D299g
And T399i In Complex With Md-2 And Lps
pdb|4G8A|B Chain B, Crystal Structure Of Human Tlr4 Polymorphic Variant D299g
And T399i In Complex With Md-2 And Lps
Length = 635
Score = 32.0 bits (71), Expect = 0.22, Method: Compositional matrix adjust.
Identities = 20/42 (47%), Positives = 25/42 (59%), Gaps = 3/42 (7%)
Query: 140 VGKLNSLKNSNISHNNLIGG--IPSSLRNLTEFESLDLSLNK 179
+G L +LK N++HN LI +P NLT E LDLS NK
Sbjct: 144 IGHLKTLKELNVAHN-LIQSFKLPEYFSNLTNLEHLDLSSNK 184
>pdb|3ULA|A Chain A, Crystal Structure Of The Tv3 Mutant F63w-Md-2-Eritoran
Complex
pdb|3ULA|C Chain C, Crystal Structure Of The Tv3 Mutant F63w-Md-2-Eritoran
Complex
Length = 279
Score = 32.0 bits (71), Expect = 0.22, Method: Compositional matrix adjust.
Identities = 18/41 (43%), Positives = 24/41 (58%), Gaps = 1/41 (2%)
Query: 140 VGKLNSLKNSNISHNNLIG-GIPSSLRNLTEFESLDLSLNK 179
+G L +LK N++HN + +P NLT E LDLS NK
Sbjct: 122 IGHLKTLKELNVAHNLIQSFKLPEYFSNLTNLEHLDLSSNK 162
>pdb|3UL9|A Chain A, Structure Of The Tv3 Mutant M41e
Length = 278
Score = 32.0 bits (71), Expect = 0.22, Method: Compositional matrix adjust.
Identities = 18/41 (43%), Positives = 24/41 (58%), Gaps = 1/41 (2%)
Query: 140 VGKLNSLKNSNISHNNLIG-GIPSSLRNLTEFESLDLSLNK 179
+G L +LK N++HN + +P NLT E LDLS NK
Sbjct: 121 IGHLKTLKELNVAHNLIQSFKLPEYFSNLTNLEHLDLSSNK 161
>pdb|3UL8|A Chain A, Crystal Structure Of The Tv3 Mutant V134l
Length = 279
Score = 32.0 bits (71), Expect = 0.22, Method: Compositional matrix adjust.
Identities = 18/41 (43%), Positives = 24/41 (58%), Gaps = 1/41 (2%)
Query: 140 VGKLNSLKNSNISHNNLIG-GIPSSLRNLTEFESLDLSLNK 179
+G L +LK N++HN + +P NLT E LDLS NK
Sbjct: 122 IGHLKTLKELNVAHNLIQSFKLPEYFSNLTNLEHLDLSSNK 162
>pdb|2Z63|A Chain A, Crystal Structure Of The Tv8 Hybrid Of Human Tlr4 And
Hagfish Vlrb.61
Length = 570
Score = 31.6 bits (70), Expect = 0.26, Method: Compositional matrix adjust.
Identities = 18/41 (43%), Positives = 24/41 (58%), Gaps = 1/41 (2%)
Query: 140 VGKLNSLKNSNISHNNLIG-GIPSSLRNLTEFESLDLSLNK 179
+G L +LK N++HN + +P NLT E LDLS NK
Sbjct: 120 IGHLKTLKELNVAHNLIQSFKLPEYFSNLTNLEHLDLSSNK 160
Score = 27.7 bits (60), Expect = 3.8, Method: Compositional matrix adjust.
Identities = 18/58 (31%), Positives = 30/58 (51%), Gaps = 3/58 (5%)
Query: 46 MGVRTFTNNFHGRIPQTYVQGCNLDFLRLNGNCLERPIPTSLIDYVNMNFLNVGNNKL 103
M +F NF +P + + NL FL L+ LE+ PT+ ++ LN+ +N+L
Sbjct: 452 MAGNSFQENF---LPDIFTELRNLTFLDLSQCQLEQLSPTAFNSLSSLQVLNMASNQL 506
>pdb|3SPY|A Chain A, Rb69 Dna Polymerase(L415aL561AS565GY567A) TERNARY COMPLEX
WITH Dupcpp Opposite Da
Length = 901
Score = 28.9 bits (63), Expect = 1.6, Method: Composition-based stats.
Identities = 13/37 (35%), Positives = 21/37 (56%)
Query: 84 PTSLIDYVNMNFLNVGNNKLSGPIPKCKNIQTERILT 120
P+ +DY++ LNVG K GPI K + +R ++
Sbjct: 286 PSYSLDYISEFELNVGKLKYDGPISKLRESNHQRYIS 322
>pdb|3SCX|A Chain A, Rb69 Dna Polymerase Triple Mutant(L561aS565GY567A) TERNARY
COMPLEX With Dupnpp And A Deoxy-Terminated Primer In The
Presence Of Ca2+
pdb|3SI6|A Chain A, Rb69 Dna Polymerase Triple Mutant (L561aS565GY567A)
TERNARY COMPLEX With Dupnpp And A Deoxy-Terminated
Primer In The Presence Of Mg2+
pdb|3SJJ|A Chain A, Rb69 Dna Polymerase Triple Mutant (L561aS565GY567A)
TERNARY COMPLEX With Dupnpp And A Deoxy-Terminated
Primer In The Presence Of Mn2+
pdb|3SNN|A Chain A, Rb69 Dna Polymerase (L561aS565GY567A) TERNARY COMPLEX WITH
DCTP Opposite Dg In The Presence Of Mg2+
Length = 903
Score = 28.9 bits (63), Expect = 1.6, Method: Composition-based stats.
Identities = 13/37 (35%), Positives = 21/37 (56%)
Query: 84 PTSLIDYVNMNFLNVGNNKLSGPIPKCKNIQTERILT 120
P+ +DY++ LNVG K GPI K + +R ++
Sbjct: 286 PSYSLDYISEFELNVGKLKYDGPISKLRESNHQRYIS 322
>pdb|3SPZ|A Chain A, Dna Polymerase(L415aL561AS565GY567A) TERNARY COMPLEX WITH
DUPCPP Opposite Da (Ca2+)
pdb|4FJ5|A Chain A, Rb69 Dna Polymerase Ternary Complex With Datp/dt
pdb|4FJ7|A Chain A, Rb69 Dna Polymerase Ternary Complex With Dgtp/dt
pdb|4FJ8|A Chain A, Rb69 Dna Polymerase Ternary Complex With Dctp/dt
pdb|4FJ9|A Chain A, Rb69 Dna Polymerase Ternary Complex With Dttp/dt
pdb|4FJG|A Chain A, Rb69 Dna Polymerase Ternary Complex With Datp/dc
pdb|4FJH|A Chain A, Rb69 Dna Polymerase Ternary Complex With Dgtp/dc
pdb|4FJI|A Chain A, Rb69 Dna Polymerase Ternary Complex With Dctp/dc
pdb|4FJJ|A Chain A, Rb69 Dna Polymerase Ternary Complex With Dttp/dc
pdb|4FJK|A Chain A, Rb69 Dna Polymerase Ternary Complex With Datp/da
pdb|4FJL|A Chain A, Rb69 Dna Polymerase Ternary Complex With Dgtp/da
pdb|4FJN|A Chain A, Rb69 Dna Polymerase Ternary Complex With Dttp/da
pdb|4FJX|A Chain A, Rb69 Dna Polymerase Ternary Complex With Datp/dg
pdb|4FK0|A Chain A, Rb69 Dna Polymerase Ternary Complex With Dctp/dg
pdb|4FK2|A Chain A, Rb69 Dna Polymerase Ternary Complex With Dttp/dg
pdb|4FK4|A Chain A, Rb69 Dna Polymerase Ternary Complex With Dgtp/dg
Length = 903
Score = 28.9 bits (63), Expect = 1.6, Method: Composition-based stats.
Identities = 13/37 (35%), Positives = 21/37 (56%)
Query: 84 PTSLIDYVNMNFLNVGNNKLSGPIPKCKNIQTERILT 120
P+ +DY++ LNVG K GPI K + +R ++
Sbjct: 286 PSYSLDYISEFELNVGKLKYDGPISKLRESNHQRYIS 322
>pdb|3KD1|E Chain E, Closed Binary Complex Of An Rb69 Gp43 Fingers Domain
Mutant Complexed With An Acyclic Gmp Terminated Primer
Template Pair.
pdb|3KD5|E Chain E, Closed Ternary Complex Of An Rb69 Gp43 Fingers Domain
Mutant Complexed With An Acyclic Gmp Terminated Primer
Template Pair And Phosphonoformic Acid
Length = 913
Score = 28.9 bits (63), Expect = 1.6, Method: Composition-based stats.
Identities = 13/37 (35%), Positives = 21/37 (56%)
Query: 84 PTSLIDYVNMNFLNVGNNKLSGPIPKCKNIQTERILT 120
P+ +DY++ LNVG K GPI K + +R ++
Sbjct: 286 PSYSLDYISEFELNVGKLKYDGPISKLRESNHQRYIS 322
>pdb|2DY4|A Chain A, Crystal Structure Of Rb69 Gp43 In Complex With Dna
Containing Thymine Glycol
pdb|2DY4|B Chain B, Crystal Structure Of Rb69 Gp43 In Complex With Dna
Containing Thymine Glycol
pdb|2DY4|C Chain C, Crystal Structure Of Rb69 Gp43 In Complex With Dna
Containing Thymine Glycol
pdb|2DY4|D Chain D, Crystal Structure Of Rb69 Gp43 In Complex With Dna
Containing Thymine Glycol
pdb|2P5O|A Chain A, Crystal Structure Of Rb69 Gp43 In Complex With Dna
Containing An Abasic Site Analog
pdb|2P5O|B Chain B, Crystal Structure Of Rb69 Gp43 In Complex With Dna
Containing An Abasic Site Analog
pdb|2P5O|C Chain C, Crystal Structure Of Rb69 Gp43 In Complex With Dna
Containing An Abasic Site Analog
pdb|2P5O|D Chain D, Crystal Structure Of Rb69 Gp43 In Complex With Dna
Containing An Abasic Site Analog
pdb|2P5G|A Chain A, Crystal Structure Of Rb69 Gp43 In Complex With Dna With
Damp Opposite An Abasic Site Analog In A 21mer Template
pdb|2P5G|B Chain B, Crystal Structure Of Rb69 Gp43 In Complex With Dna With
Damp Opposite An Abasic Site Analog In A 21mer Template
pdb|2P5G|C Chain C, Crystal Structure Of Rb69 Gp43 In Complex With Dna With
Damp Opposite An Abasic Site Analog In A 21mer Template
pdb|2P5G|D Chain D, Crystal Structure Of Rb69 Gp43 In Complex With Dna With
Damp Opposite An Abasic Site Analog In A 21mer Template
Length = 903
Score = 28.9 bits (63), Expect = 1.6, Method: Composition-based stats.
Identities = 13/37 (35%), Positives = 21/37 (56%)
Query: 84 PTSLIDYVNMNFLNVGNNKLSGPIPKCKNIQTERILT 120
P+ +DY++ LNVG K GPI K + +R ++
Sbjct: 286 PSYSLDYISEFELNVGKLKYDGPISKLRESNHQRYIS 322
>pdb|4DTJ|A Chain A, Rb69 Dna Polymerase Ternary Complex With Dttp Opposite An
Abasic Site And DdtDA AS THE PENULTIMATE BASE-Pair
pdb|4DTM|A Chain A, Rb69 Dna Polymerase Ternary Complex With Dctp Opposite An
Abasic Site And DdgDC AS THE PENULTIMATE BASE-Pair
Length = 901
Score = 28.9 bits (63), Expect = 1.6, Method: Composition-based stats.
Identities = 13/37 (35%), Positives = 21/37 (56%)
Query: 84 PTSLIDYVNMNFLNVGNNKLSGPIPKCKNIQTERILT 120
P+ +DY++ LNVG K GPI K + +R ++
Sbjct: 286 PSYSLDYISEFELNVGKLKYDGPISKLRESNHQRYIS 322
>pdb|3SUO|A Chain A, Rb69 Dna Polymerase (Y567a) Ternary Complex With Dttp
Opposite 2ap (Gc Rich Sequence)
Length = 900
Score = 28.9 bits (63), Expect = 1.6, Method: Composition-based stats.
Identities = 13/37 (35%), Positives = 21/37 (56%)
Query: 84 PTSLIDYVNMNFLNVGNNKLSGPIPKCKNIQTERILT 120
P+ +DY++ LNVG K GPI K + +R ++
Sbjct: 286 PSYSLDYISEFELNVGKLKYDGPISKLRESNHQRYIS 322
>pdb|3QEP|A Chain A, Rb69 Dna Polymerase (L561aS565GY567A) TERNARY COMPLEX WITH
DTTP Opposite Difluorotoluene Nucleoside
pdb|3S9H|A Chain A, Rb69 Dna Polymerase Triple Mutant(L561aS565GY567A) TERNARY
COMPLEX With Dupnpp And A Dideoxy-Terminated Primer In
The Presence Of Ca2+
pdb|3SQ0|A Chain A, Dna Polymerase(L561aS565GY567A) TERNARY COMPLEX WITH
DUPNPP OPPOSITE Da (Mn2+)
pdb|3QEI|A Chain A, Rb69 Dna Polymerase (L561aS565GY567A) TERNARY COMPLEX WITH
DCTP Opposite Difluorotoluene Nucleoside
pdb|3QER|A Chain A, Rb69 Dna Polymerase (L561aS565GY567A) TERNARY COMPLEX WITH
DATP Opposite Difluorotoluene Nucleoside
pdb|3QES|A Chain A, Rb69 Dna Polymerase (L561aS565GY567A) TERNARY COMPLEX WITH
DGTP Opposite Difluorotoluene Nucleoside
pdb|3QET|A Chain A, Rb69 Dna Polymerase (L561aS565GY567A) TERNARY COMPLEX WITH
DTTP Opposite Dt
pdb|3QEV|A Chain A, Rb69 Dna Polymerase (L561aS565GY567A) TERNARY COMPLEX WITH
DCTP Opposite Dt
pdb|3QEW|A Chain A, Rb69 Dna Polymerase (L561aS565GY567A) TERNARY COMPLEX WITH
DDTP Opposite Dt
pdb|3QEX|A Chain A, Rb69 Dna Polymerase (L561aS565GY567A) TERNARY COMPLEX WITH
DGTP Opposite Dt
pdb|4E3S|A Chain A, Rb69 Dna Polymerase Ternary Complex With Dqtp Opposite Dt
pdb|4DTN|A Chain A, Rb69 Dna Polymerase Ternary Complex With Datp Opposite An
Abasic Site And DdaDT AS THE PENULTIMATE BASE-Pair
pdb|4DTO|A Chain A, Rb69 Dna Polymerase Ternary Complex With Dctp Opposite An
Abasic Site And DdaDT AS THE PENULTIMATE BASE-Pair
pdb|4DTP|A Chain A, Rb69 Dna Polymerase Ternary Complex With Dgtp Opposite An
Abasic Site And DdaDT AS THE PENULTIMATE BASE-Pair
pdb|4DTR|A Chain A, Rb69 Dna Polymerase Ternary Complex With Datp Opposite An
Abasic Site And DdcDG AS THE PENULTIMATE BASE-Pair
pdb|4DTS|A Chain A, Rb69 Dna Polymerase Ternary Complex With Dctp Opposite An
Abasic Site And DdcDG AS THE PENULTIMATE BASE-Pair
pdb|4DTU|A Chain A, Rb69 Dna Polymerase Ternary Complex With Dgtp Opposite An
Abasic Site And DdcDG AS THE PENULTIMATE BASE-Pair
pdb|4DTX|A Chain A, Rb69 Dna Polymerase Ternary Complex With Dttp Opposite An
Abasic Site And DdcDG AS THE PENULTIMATE BASE-Pair
pdb|4FJM|A Chain A, Rb69 Dna Polymerase Ternary Complex With Dctp/da
Length = 903
Score = 28.9 bits (63), Expect = 1.6, Method: Composition-based stats.
Identities = 13/37 (35%), Positives = 21/37 (56%)
Query: 84 PTSLIDYVNMNFLNVGNNKLSGPIPKCKNIQTERILT 120
P+ +DY++ LNVG K GPI K + +R ++
Sbjct: 286 PSYSLDYISEFELNVGKLKYDGPISKLRESNHQRYIS 322
>pdb|3NE6|A Chain A, Rb69 Dna Polymerase (S565gY567A) TERNARY COMPLEX WITH DCTP
OPPOSITE Dg
pdb|3NHG|A Chain A, Rb69 Dna Polymerase (S565gY567A) TERNARY COMPLEX WITH DTTP
OPPOSITE Dg
Length = 903
Score = 28.9 bits (63), Expect = 1.6, Method: Composition-based stats.
Identities = 13/37 (35%), Positives = 21/37 (56%)
Query: 84 PTSLIDYVNMNFLNVGNNKLSGPIPKCKNIQTERILT 120
P+ +DY++ LNVG K GPI K + +R ++
Sbjct: 286 PSYSLDYISEFELNVGKLKYDGPISKLRESNHQRYIS 322
>pdb|3LDS|A Chain A, Crystal Structure Of Rb69 Gp43 With Dna And Datp Opposite
8-
Length = 903
Score = 28.9 bits (63), Expect = 1.6, Method: Composition-based stats.
Identities = 13/37 (35%), Positives = 21/37 (56%)
Query: 84 PTSLIDYVNMNFLNVGNNKLSGPIPKCKNIQTERILT 120
P+ +DY++ LNVG K GPI K + +R ++
Sbjct: 286 PSYSLDYISEFELNVGKLKYDGPISKLRESNHQRYIS 322
>pdb|3CFO|A Chain A, Triple Mutant Apo Structure
pdb|3CFP|A Chain A, Structure Of The Replicating Complex Of A Pol Alpha Family
Dna Polymerase, Ternary Complex 1
pdb|3CFR|A Chain A, Structure Of The Replicating Complex Of A Pol Alpha Family
Dna Polymerase, Ternary Complex 2
Length = 909
Score = 28.9 bits (63), Expect = 1.6, Method: Composition-based stats.
Identities = 13/37 (35%), Positives = 21/37 (56%)
Query: 84 PTSLIDYVNMNFLNVGNNKLSGPIPKCKNIQTERILT 120
P+ +DY++ LNVG K GPI K + +R ++
Sbjct: 286 PSYSLDYISEFELNVGKLKYDGPISKLRESNHQRYIS 322
>pdb|3CQ8|A Chain A, Ternary Complex Of The L415f Mutant Rb69 Exo(-)polymerase
Length = 903
Score = 28.9 bits (63), Expect = 1.6, Method: Composition-based stats.
Identities = 13/37 (35%), Positives = 21/37 (56%)
Query: 84 PTSLIDYVNMNFLNVGNNKLSGPIPKCKNIQTERILT 120
P+ +DY++ LNVG K GPI K + +R ++
Sbjct: 286 PSYSLDYISEFELNVGKLKYDGPISKLRESNHQRYIS 322
>pdb|2DTU|A Chain A, Crystal Structure Of The Beta Hairpin Loop Deletion
Variant Of Rb69 Gp43 In Complex With Dna Containing An
Abasic Site Analog
pdb|2DTU|B Chain B, Crystal Structure Of The Beta Hairpin Loop Deletion
Variant Of Rb69 Gp43 In Complex With Dna Containing An
Abasic Site Analog
pdb|2DTU|C Chain C, Crystal Structure Of The Beta Hairpin Loop Deletion
Variant Of Rb69 Gp43 In Complex With Dna Containing An
Abasic Site Analog
pdb|2DTU|D Chain D, Crystal Structure Of The Beta Hairpin Loop Deletion
Variant Of Rb69 Gp43 In Complex With Dna Containing An
Abasic Site Analog
Length = 896
Score = 28.9 bits (63), Expect = 1.6, Method: Composition-based stats.
Identities = 13/37 (35%), Positives = 21/37 (56%)
Query: 84 PTSLIDYVNMNFLNVGNNKLSGPIPKCKNIQTERILT 120
P+ +DY++ LNVG K GPI K + +R ++
Sbjct: 279 PSYSLDYISEFELNVGKLKYDGPISKLRESNHQRYIS 315
>pdb|1Q9Y|A Chain A, Crystal Structure Of Enterobacteria Phage Rb69 Gp43 Dna
Polymerase Complexed With 8-Oxoguanosine Containing Dna
Length = 906
Score = 28.9 bits (63), Expect = 1.7, Method: Composition-based stats.
Identities = 13/37 (35%), Positives = 21/37 (56%)
Query: 84 PTSLIDYVNMNFLNVGNNKLSGPIPKCKNIQTERILT 120
P+ +DY++ LNVG K GPI K + +R ++
Sbjct: 289 PSYSLDYISEFELNVGKLKYDGPISKLRESNHQRYIS 325
>pdb|1IG9|A Chain A, Structure Of The Replicating Complex Of A Pol Alpha Family
Dna Polymerase
pdb|1Q9X|A Chain A, Crystal Structure Of Enterobacteria Phage Rb69 Gp43 Dna
Polymerase Complexed With Tetrahydrofuran Containing Dna
pdb|1Q9X|B Chain B, Crystal Structure Of Enterobacteria Phage Rb69 Gp43 Dna
Polymerase Complexed With Tetrahydrofuran Containing Dna
pdb|1Q9X|C Chain C, Crystal Structure Of Enterobacteria Phage Rb69 Gp43 Dna
Polymerase Complexed With Tetrahydrofuran Containing Dna
pdb|1Q9X|D Chain D, Crystal Structure Of Enterobacteria Phage Rb69 Gp43 Dna
Polymerase Complexed With Tetrahydrofuran Containing Dna
pdb|2ATQ|A Chain A, Rb69 Single-Stranded Dna Binding Protein-Dna Polymerase
Fusion
pdb|2OYQ|A Chain A, Crystal Structure Of Rb69 Gp43 In Complex With Dna With 5-
Nimp Opposite An Abasic Site Analog
pdb|2OYQ|B Chain B, Crystal Structure Of Rb69 Gp43 In Complex With Dna With 5-
Nimp Opposite An Abasic Site Analog
pdb|2OYQ|C Chain C, Crystal Structure Of Rb69 Gp43 In Complex With Dna With 5-
Nimp Opposite An Abasic Site Analog
pdb|2OYQ|D Chain D, Crystal Structure Of Rb69 Gp43 In Complex With Dna With 5-
Nimp Opposite An Abasic Site Analog
pdb|2OZM|A Chain A, Crystal Structure Of Rb69 Gp43 In Complex With Dna With 5-
Nitp Opposite An Abasic Site Analog
pdb|2OZS|A Chain A, Crystal Structure Of Rb69 Gp43 In Complex With Dna With
Datp Opposite Dtmp
pdb|3NCI|A Chain A, Rb69 Dna Polymerase Ternary Complex With Dctp Opposite Dg
At 1.8 Angstrom Resolution
pdb|4DU1|A Chain A, Rb69 Dna Polymerase Ternary Complex With Datp Opposite Dt
pdb|4DU3|A Chain A, Rb69 Dna Polymerase Ternary Complex With Ddtp Opposite Dt
With 3- Deaza-Adenine At The N-1 Position Of Template
Strand
pdb|4DU4|A Chain A, Rb69 Dna Polymerase Ternary Complex With Datp Opposite Dt
With 3- Deaza-Adenine At The N-3 Position Of Primer
Strand
Length = 903
Score = 28.9 bits (63), Expect = 1.7, Method: Composition-based stats.
Identities = 13/37 (35%), Positives = 21/37 (56%)
Query: 84 PTSLIDYVNMNFLNVGNNKLSGPIPKCKNIQTERILT 120
P+ +DY++ LNVG K GPI K + +R ++
Sbjct: 286 PSYSLDYISEFELNVGKLKYDGPISKLRESNHQRYIS 322
>pdb|3SUN|A Chain A, Rb69 Dna Polymerase (Y567a) Ternary Complex With Dttp
Opposite 2ap (At Rich Sequence)
Length = 895
Score = 28.9 bits (63), Expect = 1.7, Method: Composition-based stats.
Identities = 13/37 (35%), Positives = 21/37 (56%)
Query: 84 PTSLIDYVNMNFLNVGNNKLSGPIPKCKNIQTERILT 120
P+ +DY++ LNVG K GPI K + +R ++
Sbjct: 286 PSYSLDYISEFELNVGKLKYDGPISKLRESNHQRYIS 322
>pdb|3SQ2|A Chain A, Rb69 Dna Polymerase Ternary Complex With Dttp Opposite 2ap
(At Rich Sequence)
pdb|3SQ4|A Chain A, Rb69 Dna Polymerase Ternary Complex With Dttp Opposite 2ap
(Gc Rich Sequence)
Length = 902
Score = 28.9 bits (63), Expect = 1.7, Method: Composition-based stats.
Identities = 13/37 (35%), Positives = 21/37 (56%)
Query: 84 PTSLIDYVNMNFLNVGNNKLSGPIPKCKNIQTERILT 120
P+ +DY++ LNVG K GPI K + +R ++
Sbjct: 286 PSYSLDYISEFELNVGKLKYDGPISKLRESNHQRYIS 322
>pdb|3SQ1|A Chain A, Rb69 Dna Polymerase Ternary Complex With Dupcpp Opposite
Da
Length = 901
Score = 28.9 bits (63), Expect = 1.7, Method: Composition-based stats.
Identities = 13/37 (35%), Positives = 21/37 (56%)
Query: 84 PTSLIDYVNMNFLNVGNNKLSGPIPKCKNIQTERILT 120
P+ +DY++ LNVG K GPI K + +R ++
Sbjct: 286 PSYSLDYISEFELNVGKLKYDGPISKLRESNHQRYIS 322
>pdb|3RWU|A Chain A, Rb69 Dna Polymerase (Y567a) Ternary Complex With Datp
Opposite Difluorotoluene Nucleoside
pdb|3QNN|A Chain A, Rb69 Dna Polymerase (Y567a) Ternary Complex With Dgt
Opposite 3tco
pdb|3QNO|A Chain A, Rb69 Dna Polymerase (Y567a) Ternary Complex With Datp
Opposite 3tco
Length = 901
Score = 28.9 bits (63), Expect = 1.7, Method: Composition-based stats.
Identities = 13/37 (35%), Positives = 21/37 (56%)
Query: 84 PTSLIDYVNMNFLNVGNNKLSGPIPKCKNIQTERILT 120
P+ +DY++ LNVG K GPI K + +R ++
Sbjct: 286 PSYSLDYISEFELNVGKLKYDGPISKLRESNHQRYIS 322
>pdb|3LZI|A Chain A, Rb69 Dna Polymerase (Y567a) Ternary Complex With Datp
Opposite 7,8- Dihydro-8-Oxoguanine
pdb|3LZJ|A Chain A, Rb69 Dna Polymerase (Y567a) Ternary Complex With Dctp
Opposite 7,8- Dihydro-8-Oxoguanine
pdb|3NAE|A Chain A, Rb69 Dna Polymerase (Y567a) Ternary Complex With Datp
Opposite Guanidinohydantoin
pdb|3NDK|A Chain A, Rb69 Dna Polymerase (Y567a) Ternary Complex With Dctp
Opposite Dg
pdb|3NGI|A Chain A, Rb69 Dna Polymerase (Y567a) Ternary Complex With Dttp
Opposite Dg
pdb|3SUP|A Chain A, Rb69 Dna Polymerase (Y567a) Ternary Complex With Dctp
Opposite 2ap (Gc Rich Sequence)
Length = 903
Score = 28.9 bits (63), Expect = 1.7, Method: Composition-based stats.
Identities = 13/37 (35%), Positives = 21/37 (56%)
Query: 84 PTSLIDYVNMNFLNVGNNKLSGPIPKCKNIQTERILT 120
P+ +DY++ LNVG K GPI K + +R ++
Sbjct: 286 PSYSLDYISEFELNVGKLKYDGPISKLRESNHQRYIS 322
>pdb|3L8B|A Chain A, Crystal Structure Of A Replicative Dna Polymerase Bound To
The Oxidized Guanine Lesion Guanidinohydantoin
pdb|3L8B|B Chain B, Crystal Structure Of A Replicative Dna Polymerase Bound To
The Oxidized Guanine Lesion Guanidinohydantoin
pdb|3RMA|A Chain A, Crystal Structure Of A Replicative Dna Polymerase Bound To
Dna Containing Thymine Glycol
pdb|3RMA|B Chain B, Crystal Structure Of A Replicative Dna Polymerase Bound To
Dna Containing Thymine Glycol
pdb|3RMA|C Chain C, Crystal Structure Of A Replicative Dna Polymerase Bound To
Dna Containing Thymine Glycol
pdb|3RMA|D Chain D, Crystal Structure Of A Replicative Dna Polymerase Bound To
Dna Containing Thymine Glycol
pdb|3RMB|A Chain A, Crystal Structure Of A Replicative Dna Polymerase Bound To
Dna Containing Thymine Glycol
pdb|3RMB|B Chain B, Crystal Structure Of A Replicative Dna Polymerase Bound To
Dna Containing Thymine Glycol
pdb|3RMB|C Chain C, Crystal Structure Of A Replicative Dna Polymerase Bound To
Dna Containing Thymine Glycol
pdb|3RMB|D Chain D, Crystal Structure Of A Replicative Dna Polymerase Bound To
Dna Containing Thymine Glycol
pdb|3RMC|A Chain A, Crystal Structure Of A Replicative Dna Polymerase Bound To
Dna Containing Thymine Glycol
pdb|3RMC|B Chain B, Crystal Structure Of A Replicative Dna Polymerase Bound To
Dna Containing Thymine Glycol
pdb|3RMC|C Chain C, Crystal Structure Of A Replicative Dna Polymerase Bound To
Dna Containing Thymine Glycol
pdb|3RMC|D Chain D, Crystal Structure Of A Replicative Dna Polymerase Bound To
Dna Containing Thymine Glycol
pdb|3RMD|A Chain A, Crystal Structure Of A Replicative Dna Polymerase Bound To
Dna Containing Thymine Glycol
pdb|3RMD|B Chain B, Crystal Structure Of A Replicative Dna Polymerase Bound To
Dna Containing Thymine Glycol
pdb|3RMD|C Chain C, Crystal Structure Of A Replicative Dna Polymerase Bound To
Dna Containing Thymine Glycol
pdb|3RMD|D Chain D, Crystal Structure Of A Replicative Dna Polymerase Bound To
Dna Containing Thymine Glycol
pdb|3TAB|A Chain A, 5-Hydroxycytosine Paired With Dgmp In Rb69 Gp43
pdb|3TAB|B Chain B, 5-Hydroxycytosine Paired With Dgmp In Rb69 Gp43
pdb|3TAB|C Chain C, 5-Hydroxycytosine Paired With Dgmp In Rb69 Gp43
pdb|3TAB|D Chain D, 5-Hydroxycytosine Paired With Dgmp In Rb69 Gp43
pdb|3TAE|A Chain A, 5-Hydroxycytosine Paired With Damp In Rb69 Gp43
pdb|3TAE|B Chain B, 5-Hydroxycytosine Paired With Damp In Rb69 Gp43
pdb|3TAE|C Chain C, 5-Hydroxycytosine Paired With Damp In Rb69 Gp43
pdb|3TAE|D Chain D, 5-Hydroxycytosine Paired With Damp In Rb69 Gp43
pdb|3TAF|A Chain A, 5-Fluorocytosine Paired With Ddgmp In Rb69 Gp43
pdb|3TAF|B Chain B, 5-Fluorocytosine Paired With Ddgmp In Rb69 Gp43
pdb|3TAF|C Chain C, 5-Fluorocytosine Paired With Ddgmp In Rb69 Gp43
pdb|3TAF|D Chain D, 5-Fluorocytosine Paired With Ddgmp In Rb69 Gp43
pdb|3TAG|A Chain A, 5-Fluorocytosine Paired With Damp In Rb69 Gp43
pdb|3TAG|B Chain B, 5-Fluorocytosine Paired With Damp In Rb69 Gp43
pdb|3TAG|C Chain C, 5-Fluorocytosine Paired With Damp In Rb69 Gp43
pdb|3TAG|D Chain D, 5-Fluorocytosine Paired With Damp In Rb69 Gp43
Length = 906
Score = 28.9 bits (63), Expect = 1.7, Method: Composition-based stats.
Identities = 13/37 (35%), Positives = 21/37 (56%)
Query: 84 PTSLIDYVNMNFLNVGNNKLSGPIPKCKNIQTERILT 120
P+ +DY++ LNVG K GPI K + +R ++
Sbjct: 286 PSYSLDYISEFELNVGKLKYDGPISKLRESNHQRYIS 322
>pdb|1WAF|A Chain A, Dna Polymerase From Bacteriophage Rb69
pdb|1WAF|B Chain B, Dna Polymerase From Bacteriophage Rb69
pdb|1CLQ|A Chain A, Crystal Structure Of A Replication Fork Dna Polymerase
Editing Complex At 2.7 A Resolution
pdb|1IH7|A Chain A, High-Resolution Structure Of Apo Rb69 Dna Polymerase
pdb|1WAJ|A Chain A, Dna Polymerase From Bacteriophage Rb69
pdb|3UIQ|A Chain A, Rb69 Dna Polymerase Ternary Complex Containing Dupnpp
Length = 903
Score = 28.9 bits (63), Expect = 1.7, Method: Composition-based stats.
Identities = 13/37 (35%), Positives = 21/37 (56%)
Query: 84 PTSLIDYVNMNFLNVGNNKLSGPIPKCKNIQTERILT 120
P+ +DY++ LNVG K GPI K + +R ++
Sbjct: 286 PSYSLDYISEFELNVGKLKYDGPISKLRESNHQRYIS 322
>pdb|3SUQ|A Chain A, Rb69 Dna Polymerase (Y567a) Ternary Complex With Dctp
Opposite 2ap (At Rich Sequence)
Length = 897
Score = 28.9 bits (63), Expect = 1.7, Method: Composition-based stats.
Identities = 13/37 (35%), Positives = 21/37 (56%)
Query: 84 PTSLIDYVNMNFLNVGNNKLSGPIPKCKNIQTERILT 120
P+ +DY++ LNVG K GPI K + +R ++
Sbjct: 286 PSYSLDYISEFELNVGKLKYDGPISKLRESNHQRYIS 322
>pdb|3RFS|A Chain A, Design Of A Binding Scaffold Based On Variable Lymphocyte
Receptors Of Jawless Vertebrates By Module Engineering
pdb|3RFS|B Chain B, Design Of A Binding Scaffold Based On Variable Lymphocyte
Receptors Of Jawless Vertebrates By Module Engineering
Length = 272
Score = 28.5 bits (62), Expect = 2.3, Method: Compositional matrix adjust.
Identities = 39/128 (30%), Positives = 58/128 (45%), Gaps = 25/128 (19%)
Query: 64 VQGC----NLDFLRLNGNCLERPIPTSLIDYVNMNFLNVGNNKL----SGPIPKCKNIQT 115
VQG N+ +L L GN L ++L + N+ +L + N+L +G K N++
Sbjct: 56 VQGIQYLPNVRYLALGGNKLHDI--SALKELTNLTYLILTGNQLQSLPNGVFDKLTNLKE 113
Query: 116 ERILTTSATIDLSSNRFQEKILEVVGKLNSLKNSNISHNNLIG---GIPSSLRNLTEFES 172
+ L N+ Q V KL +L N++HN L G+ L NLTE
Sbjct: 114 ---------LVLVENQLQSLPDGVFDKLTNLTYLNLAHNQLQSLPKGVFDKLTNLTE--- 161
Query: 173 LDLSLNKF 180
LDLS N+
Sbjct: 162 LDLSYNQL 169
>pdb|2OMX|A Chain A, Crystal Structure Of Inla S192n G194s+sHEC1 COMPLEX
Length = 462
Score = 28.1 bits (61), Expect = 3.0, Method: Compositional matrix adjust.
Identities = 32/98 (32%), Positives = 47/98 (47%), Gaps = 11/98 (11%)
Query: 85 TSLIDYVNMNFLNVGNNKLSGPIPKCKNIQTERILTTSATIDLSSNRFQEKILEVVGKLN 144
T L + N+ L + NN+++ I KN LT ++LSSN + + + L
Sbjct: 101 TPLANLTNLTGLTLFNNQITD-IDPLKN------LTNLNRLELSSNTISD--ISALSGLT 151
Query: 145 SLKNSNISHNNLIGGIPSSLRNLTEFESLDLSLNKFVE 182
SL+ N S N + P L NLT E LD+S NK +
Sbjct: 152 SLQQLNFSSNQVTDLKP--LANLTTLERLDISSNKVSD 187
>pdb|3VQ1|A Chain A, Crystal Structure Of Mouse Tlr4MD-2LIPID IVA COMPLEX
pdb|3VQ1|B Chain B, Crystal Structure Of Mouse Tlr4MD-2LIPID IVA COMPLEX
pdb|3VQ2|A Chain A, Crystal Structure Of Mouse Tlr4MD-2LPS COMPLEX
pdb|3VQ2|B Chain B, Crystal Structure Of Mouse Tlr4MD-2LPS COMPLEX
Length = 606
Score = 27.7 bits (60), Expect = 3.6, Method: Compositional matrix adjust.
Identities = 20/67 (29%), Positives = 32/67 (47%), Gaps = 6/67 (8%)
Query: 125 IDLSSNRFQEKILEVVGKLNSLKNSNISHNNLIGGIPSSLRNLTEFESLDLSLNK----- 179
+DLS + ++ V L+ L+ N+SHNNL+ S L +LD S N+
Sbjct: 478 LDLSKCQLEQISWGVFDTLHRLQLLNMSHNNLLFLDSSHYNQLYSLSTLDCSFNRIETSK 537
Query: 180 -FVEHIP 185
++H P
Sbjct: 538 GILQHFP 544
Score = 26.9 bits (58), Expect = 6.4, Method: Compositional matrix adjust.
Identities = 15/40 (37%), Positives = 24/40 (60%), Gaps = 1/40 (2%)
Query: 140 VGKLNSLKNSNISHNNLIG-GIPSSLRNLTEFESLDLSLN 178
+G+L +LK N++HN + +P+ NLT +DLS N
Sbjct: 124 IGQLITLKKLNVAHNFIHSCKLPAYFSNLTNLVHVDLSYN 163
>pdb|2Z64|A Chain A, Crystal Structure Of Mouse Tlr4 And Mouse Md-2 Complex
Length = 599
Score = 27.7 bits (60), Expect = 3.7, Method: Compositional matrix adjust.
Identities = 20/67 (29%), Positives = 32/67 (47%), Gaps = 6/67 (8%)
Query: 125 IDLSSNRFQEKILEVVGKLNSLKNSNISHNNLIGGIPSSLRNLTEFESLDLSLNK----- 179
+DLS + ++ V L+ L+ N+SHNNL+ S L +LD S N+
Sbjct: 473 LDLSKCQLEQISWGVFDTLHRLQLLNMSHNNLLFLDSSHYNQLYSLSTLDCSFNRIETSK 532
Query: 180 -FVEHIP 185
++H P
Sbjct: 533 GILQHFP 539
Score = 26.9 bits (58), Expect = 6.3, Method: Compositional matrix adjust.
Identities = 15/40 (37%), Positives = 24/40 (60%), Gaps = 1/40 (2%)
Query: 140 VGKLNSLKNSNISHNNLIG-GIPSSLRNLTEFESLDLSLN 178
+G+L +LK N++HN + +P+ NLT +DLS N
Sbjct: 119 IGQLITLKKLNVAHNFIHSCKLPAYFSNLTNLVHVDLSYN 158
>pdb|4B8C|D Chain D, Nuclease Module Of The Yeast Ccr4-Not Complex
pdb|4B8C|J Chain J, Nuclease Module Of The Yeast Ccr4-Not Complex
pdb|4B8C|K Chain K, Nuclease Module Of The Yeast Ccr4-Not Complex
pdb|4B8C|L Chain L, Nuclease Module Of The Yeast Ccr4-Not Complex
Length = 727
Score = 27.7 bits (60), Expect = 4.4, Method: Compositional matrix adjust.
Identities = 21/74 (28%), Positives = 35/74 (47%), Gaps = 10/74 (13%)
Query: 14 EFPDVLKTQHQLQLLIISRNQIHGRISNWMWDMG------VRTFTNNFHGRIPQTYVQGC 67
E P +K L++L +S H R+++ ++G F +N +P + C
Sbjct: 261 ELPAEIKNLSNLRVLDLS----HNRLTSLPAELGSCFQLKYFYFFDNMVTTLPWEFGNLC 316
Query: 68 NLDFLRLNGNCLER 81
NL FL + GN LE+
Sbjct: 317 NLQFLGVEGNPLEK 330
>pdb|2PD2|A Chain A, Crystal Structure Of (St0148) Conserved Hypothetical From
Sulfolobus Tokodaii Strain7
pdb|2PD2|B Chain B, Crystal Structure Of (St0148) Conserved Hypothetical From
Sulfolobus Tokodaii Strain7
Length = 108
Score = 27.3 bits (59), Expect = 5.2, Method: Compositional matrix adjust.
Identities = 19/58 (32%), Positives = 30/58 (51%), Gaps = 8/58 (13%)
Query: 111 KNIQTERILTTSATIDLSSNRFQEKILE--------VVGKLNSLKNSNISHNNLIGGI 160
K+ + E +L SA L + I+E +VG NS+++ N+SH+ LI GI
Sbjct: 28 KDAEIEVVLHQSAIKALLKDSDTRSIIEDLIKKNILIVGCENSIRSQNLSHDQLIPGI 85
>pdb|2DI3|A Chain A, Crystal Structure Of The Transcriptional Factor Cgl2915
From Corynebacterium Glutamicum
pdb|2DI3|B Chain B, Crystal Structure Of The Transcriptional Factor Cgl2915
From Corynebacterium Glutamicum
Length = 239
Score = 26.9 bits (58), Expect = 7.0, Method: Compositional matrix adjust.
Identities = 20/83 (24%), Positives = 38/83 (45%), Gaps = 7/83 (8%)
Query: 86 SLIDYVNMNFLNVGNNKLSGPIPKCKNIQTERILTTSATIDLSSNRFQEKILEVVGKLNS 145
S++D+V L G K+ +P +ER L+ + + SS R ++LE +G +++
Sbjct: 8 SVMDWVTEE-LRSGRLKIGDHLP------SERALSETLGVSRSSLREALRVLEALGTIST 60
Query: 146 LKNSNISHNNLIGGIPSSLRNLT 168
S +I P +L+
Sbjct: 61 ATGSGPRSGTIITAAPGQALSLS 83
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
0.321 0.137 0.417
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 5,390,513
Number of Sequences: 62578
Number of extensions: 206515
Number of successful extensions: 610
Number of sequences better than 100.0: 67
Number of HSP's better than 100.0 without gapping: 42
Number of HSP's successfully gapped in prelim test: 25
Number of HSP's that attempted gapping in prelim test: 460
Number of HSP's gapped (non-prelim): 137
length of query: 186
length of database: 14,973,337
effective HSP length: 93
effective length of query: 93
effective length of database: 9,153,583
effective search space: 851283219
effective search space used: 851283219
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: 48 (23.1 bits)