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= psy2719
(808 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|1UQU|A Chain A, Trehalose-6-Phosphate From E. Coli Bound With Udp-Glucose.
pdb|1UQU|B Chain B, Trehalose-6-Phosphate From E. Coli Bound With Udp-Glucose.
pdb|1UQT|A Chain A, Trehalose-6-Phosphate From E. Coli Bound With Udp-2-Fluoro
Glucose.
pdb|1UQT|B Chain B, Trehalose-6-Phosphate From E. Coli Bound With Udp-2-Fluoro
Glucose
Length = 482
Score = 221 bits (563), Expect = 1e-57, Method: Compositional matrix adjust.
Identities = 149/441 (33%), Positives = 212/441 (48%), Gaps = 69/441 (15%)
Query: 109 GIWIGWSGLYDLAPDEVIPEADPNDQAPTSGLTSSQVIPVHVDKDEFEAYYNGCCNGTFW 168
G+W GWSG E E P + +T + D DE YYN N W
Sbjct: 37 GLWFGWSG-------ETGNEDQPLKKVKKGNITWASFNLSEQDLDE---YYNQFSNAVLW 86
Query: 169 PLFHSMPDRAVFNAETWKTYCKVNEEFANCTLNALRNVIKDLDAAGKTNVVPVVWIHDYQ 228
P FH D F W Y +VN + L +++D D ++WIHDY
Sbjct: 87 PAFHYRLDLVQFQRPAWDGYLRVNA----LLADKLLPLLQDDD---------IIWIHDYH 133
Query: 229 LLVAATTIRQVA----------------------------------YDFVGFHIEDYCLN 254
LL A +R+ YD +GF E+ L
Sbjct: 134 LLPFAHELRKRGVNNRIGFFLHIPFPTPEIFNALPTYDTLLEQLCDYDLLGFQTENDRLA 193
Query: 255 FIDCCCR--RLGSRVDRNNMLVELAGRTVHVKALPIGI-PFERFVQLAENAPENLKD--- 308
F+DC R+ +R +++ G+ + PIGI P E Q A P L
Sbjct: 194 FLDCLSNLTRVTTRSAKSHTAW---GKAFRTEVYPIGIEPKEIAKQAAGPLPPKLAQLKA 250
Query: 309 --ENLKVILGVDRLDYTKGLVHRIKAFERLLEKHPEYVEKVTFLQISVPSRTDVLEYKAL 366
+N++ I V+RLDY+KGL R A+E LLEK+P++ K+ + QI+ SR DV Y+ +
Sbjct: 251 ELKNVQNIFSVERLDYSKGLPERFLAYEALLEKYPQHHGKIRYTQIAPTSRGDVQAYQDI 310
Query: 367 KDEMDQLVGRINGRFSKPNWSPIRYIFGCIGQEELAALYRDSAIALVTPLRDGMNLVAKE 426
+ +++ GRING++ + W+P+ Y+ ++ L ++R S + LVTPLRDGMNLVAKE
Sbjct: 311 RHQLENEAGRINGKYGQLGWTPLYYLNQHFDRKLLMKIFRYSDVGLVTPLRDGMNLVAKE 370
Query: 427 YVACQ-IREPGVLILSPFAGAGGMMHEALLVNPYEIDAAANVLHRALCMPRDERELRMSQ 485
YVA Q PGVL+LS FAGA + AL+VNPY+ D A L RAL M ER R ++
Sbjct: 371 YVAAQDPANPGVLVLSQFAGAANELTSALIVNPYDRDEVAAALDRALTMSLAERISRHAE 430
Query: 486 LRHREQQLDVNHWMNSFLSSM 506
+ + D+NHW F+S +
Sbjct: 431 MLDVIVKNDINHWQECFISDL 451
Score = 47.0 bits (110), Expect = 4e-05, Method: Compositional matrix adjust.
Identities = 30/102 (29%), Positives = 39/102 (38%), Gaps = 11/102 (10%)
Query: 1 AGGLVTAVAPVVIDCKGIWIGWSGLYDLAPDEVIPEADPNDQAPTSGLTSSQVIPVHVDK 60
AGGL + + G+W GWSG E E P + +T + D
Sbjct: 21 AGGLAVGILGALKAAGGLWFGWSG-------ETGNEDQPLKKVKKGNITWASFNLSEQDL 73
Query: 61 DEFEAYYNGCCNGTFWPLFHSMPDRAVFNAETWKVSHLKMNG 102
DE YYN N WP FH D F W +L++N
Sbjct: 74 DE---YYNQFSNAVLWPAFHYRLDLVQFQRPAWD-GYLRVNA 111
>pdb|2WTX|A Chain A, Insight Into The Mechanism Of Enzymatic Glycosyltransfer
With Retention Through The Synthesis And Analysis Of
Bisubstrate Glycomimetics Of Trehalose-6-Phosphate
Synthase
pdb|2WTX|B Chain B, Insight Into The Mechanism Of Enzymatic Glycosyltransfer
With Retention Through The Synthesis And Analysis Of
Bisubstrate Glycomimetics Of Trehalose-6-Phosphate
Synthase
pdb|2WTX|C Chain C, Insight Into The Mechanism Of Enzymatic Glycosyltransfer
With Retention Through The Synthesis And Analysis Of
Bisubstrate Glycomimetics Of Trehalose-6-Phosphate
Synthase
pdb|2WTX|D Chain D, Insight Into The Mechanism Of Enzymatic Glycosyltransfer
With Retention Through The Synthesis And Analysis Of
Bisubstrate Glycomimetics Of Trehalose-6-Phosphate
Synthase
Length = 474
Score = 221 bits (562), Expect = 2e-57, Method: Compositional matrix adjust.
Identities = 149/441 (33%), Positives = 212/441 (48%), Gaps = 69/441 (15%)
Query: 109 GIWIGWSGLYDLAPDEVIPEADPNDQAPTSGLTSSQVIPVHVDKDEFEAYYNGCCNGTFW 168
G+W GWSG E E P + +T + D DE YYN N W
Sbjct: 37 GLWFGWSG-------ETGNEDQPLKKVKKGNITWASFNLSEQDLDE---YYNQFSNAVLW 86
Query: 169 PLFHSMPDRAVFNAETWKTYCKVNEEFANCTLNALRNVIKDLDAAGKTNVVPVVWIHDYQ 228
P FH D F W Y +VN + L +++D D ++WIHDY
Sbjct: 87 PAFHYRLDLVQFQRPAWDGYLRVNA----LLADKLLPLLQDDD---------IIWIHDYH 133
Query: 229 LLVAATTIRQVA----------------------------------YDFVGFHIEDYCLN 254
LL A +R+ YD +GF E+ L
Sbjct: 134 LLPFAHELRKRGVNNRIGFFLHIPFPTPEIFNALPTYDTLLEQLCDYDLLGFQTENDRLA 193
Query: 255 FIDCCCR--RLGSRVDRNNMLVELAGRTVHVKALPIGI-PFERFVQLAENAPENLKD--- 308
F+DC R+ +R +++ G+ + PIGI P E Q A P L
Sbjct: 194 FLDCLSNLTRVTTRSAKSHTAW---GKAFRTEVYPIGIEPKEIAKQAAGPLPPKLAQLKA 250
Query: 309 --ENLKVILGVDRLDYTKGLVHRIKAFERLLEKHPEYVEKVTFLQISVPSRTDVLEYKAL 366
+N++ I V+RLDY+KGL R A+E LLEK+P++ K+ + QI+ SR DV Y+ +
Sbjct: 251 ELKNVQNIFSVERLDYSKGLPERFLAYEALLEKYPQHHGKIRYTQIAPTSRGDVQAYQDI 310
Query: 367 KDEMDQLVGRINGRFSKPNWSPIRYIFGCIGQEELAALYRDSAIALVTPLRDGMNLVAKE 426
+ +++ GRING++ + W+P+ Y+ ++ L ++R S + LVTPLRDGMNLVAKE
Sbjct: 311 RHQLENEAGRINGKYGQLGWTPLYYLNQHFDRKLLMKIFRYSDVGLVTPLRDGMNLVAKE 370
Query: 427 YVACQ-IREPGVLILSPFAGAGGMMHEALLVNPYEIDAAANVLHRALCMPRDERELRMSQ 485
YVA Q PGVL+LS FAGA + AL+VNPY+ D A L RAL M ER R ++
Sbjct: 371 YVAAQDPANPGVLVLSQFAGAANELTSALIVNPYDRDEVAAALDRALTMSLAERISRHAE 430
Query: 486 LRHREQQLDVNHWMNSFLSSM 506
+ + D+NHW F+S +
Sbjct: 431 MLDVIVKNDINHWQECFISDL 451
Score = 47.0 bits (110), Expect = 4e-05, Method: Compositional matrix adjust.
Identities = 30/102 (29%), Positives = 39/102 (38%), Gaps = 11/102 (10%)
Query: 1 AGGLVTAVAPVVIDCKGIWIGWSGLYDLAPDEVIPEADPNDQAPTSGLTSSQVIPVHVDK 60
AGGL + + G+W GWSG E E P + +T + D
Sbjct: 21 AGGLAVGILGALKAAGGLWFGWSG-------ETGNEDQPLKKVKKGNITWASFNLSEQDL 73
Query: 61 DEFEAYYNGCCNGTFWPLFHSMPDRAVFNAETWKVSHLKMNG 102
DE YYN N WP FH D F W +L++N
Sbjct: 74 DE---YYNQFSNAVLWPAFHYRLDLVQFQRPAWD-GYLRVNA 111
>pdb|1GZ5|A Chain A, Trehalose-6-Phosphate Synthase. Otsa
pdb|1GZ5|B Chain B, Trehalose-6-Phosphate Synthase. Otsa
pdb|1GZ5|C Chain C, Trehalose-6-Phosphate Synthase. Otsa
pdb|1GZ5|D Chain D, Trehalose-6-Phosphate Synthase. Otsa
Length = 456
Score = 215 bits (547), Expect = 9e-56, Method: Compositional matrix adjust.
Identities = 147/441 (33%), Positives = 209/441 (47%), Gaps = 69/441 (15%)
Query: 109 GIWIGWSGLYDLAPDEVIPEADPNDQAPTSGLTSSQVIPVHVDKDEFEAYYNGCCNGTFW 168
G+W GWSG E E P + +T + D DE YYN N W
Sbjct: 36 GLWFGWSG-------ETGNEDQPLKKVKKGNITWASFNLSEQDLDE---YYNQFSNAVLW 85
Query: 169 PLFHSMPDRAVFNAETWKTYCKVNEEFANCTLNALRNVIKDLDAAGKTNVVPVVWIHDYQ 228
P FH D F W Y +VN + L +++D D ++WIHDY
Sbjct: 86 PAFHYRLDLVQFQRPAWDGYLRVNA----LLADKLLPLLQDDD---------IIWIHDYH 132
Query: 229 LLVAATTIRQVA----------------------------------YDFVGFHIEDYCLN 254
LL A +R+ YD +GF E+ L
Sbjct: 133 LLPFAHELRKRGVNNRIGFFLHIPFPTPEIFNALPTYDTLLEQLCDYDLLGFQTENDRLA 192
Query: 255 FIDCCCR--RLGSRVDRNNMLVELAGRTVHVKALPIGI-PFERFVQLAENAPENLKD--- 308
F+DC R+ +R +++ G+ + PIGI P E Q A P L
Sbjct: 193 FLDCLSNLTRVTTRSAKSHTAW---GKAFRTEVYPIGIEPKEIAKQAAGPLPPKLAQLKA 249
Query: 309 --ENLKVILGVDRLDYTKGLVHRIKAFERLLEKHPEYVEKVTFLQISVPSRTDVLEYKAL 366
+N++ I V+RLDY+KGL R A+E LLEK+P++ K+ + QI+ SR DV Y+ +
Sbjct: 250 ELKNVQNIFSVERLDYSKGLPERFLAYEALLEKYPQHHGKIRYTQIAPTSRGDVQAYQDI 309
Query: 367 KDEMDQLVGRINGRFSKPNWSPIRYIFGCIGQEELAALYRDSAIALVTPLRDGMNLVAKE 426
+ +++ GRING++ + W+P+ Y+ ++ L ++R S + LVTPLRDG NLVAKE
Sbjct: 310 RHQLENEAGRINGKYGQLGWTPLYYLNQHFDRKLLXKIFRYSDVGLVTPLRDGXNLVAKE 369
Query: 427 YVACQ-IREPGVLILSPFAGAGGMMHEALLVNPYEIDAAANVLHRALCMPRDERELRMSQ 485
YVA Q PGVL+LS FAGA + AL+VNPY+ D A L RAL ER R ++
Sbjct: 370 YVAAQDPANPGVLVLSQFAGAANELTSALIVNPYDRDEVAAALDRALTXSLAERISRHAE 429
Query: 486 LRHREQQLDVNHWMNSFLSSM 506
+ D+NHW F+S +
Sbjct: 430 XLDVIVKNDINHWQECFISDL 450
Score = 47.0 bits (110), Expect = 4e-05, Method: Compositional matrix adjust.
Identities = 30/102 (29%), Positives = 39/102 (38%), Gaps = 11/102 (10%)
Query: 1 AGGLVTAVAPVVIDCKGIWIGWSGLYDLAPDEVIPEADPNDQAPTSGLTSSQVIPVHVDK 60
AGGL + + G+W GWSG E E P + +T + D
Sbjct: 20 AGGLAVGILGALKAAGGLWFGWSG-------ETGNEDQPLKKVKKGNITWASFNLSEQDL 72
Query: 61 DEFEAYYNGCCNGTFWPLFHSMPDRAVFNAETWKVSHLKMNG 102
DE YYN N WP FH D F W +L++N
Sbjct: 73 DE---YYNQFSNAVLWPAFHYRLDLVQFQRPAWD-GYLRVNA 110
>pdb|4F96|B Chain B, Crystal Structure Of Vlde, The Pseudo-Glycosyltransferase,
In Complex With Gdp
pdb|4F96|A Chain A, Crystal Structure Of Vlde, The Pseudo-Glycosyltransferase,
In Complex With Gdp
pdb|4F97|A Chain A, Crystal Structure Of Vlde, The Pseudo-Glycosyltransferase,
In Complex With Gdp And Validoxylamine A 7'-Phosphate
pdb|4F97|B Chain B, Crystal Structure Of Vlde, The Pseudo-Glycosyltransferase,
In Complex With Gdp And Validoxylamine A 7'-Phosphate
pdb|4F9F|A Chain A, Crystal Structure Of Vlde, The Pseudo-Glycosyltransferase,
In Complex With Gdp And Trehalose
pdb|4F9F|B Chain B, Crystal Structure Of Vlde, The Pseudo-Glycosyltransferase,
In Complex With Gdp And Trehalose
pdb|4F9F|C Chain C, Crystal Structure Of Vlde, The Pseudo-Glycosyltransferase,
In Complex With Gdp And Trehalose
pdb|4F9F|D Chain D, Crystal Structure Of Vlde, The Pseudo-Glycosyltransferase,
In Complex With Gdp And Trehalose
pdb|4F9F|E Chain E, Crystal Structure Of Vlde, The Pseudo-Glycosyltransferase,
In Complex With Gdp And Trehalose
pdb|4F9F|F Chain F, Crystal Structure Of Vlde, The Pseudo-Glycosyltransferase,
In Complex With Gdp And Trehalose
pdb|3VDM|A Chain A, Crystal Structure Of Vlde, The Pseudo-Glycosyltransferase
Which Catalyzes Non-Glycosidic C-N Coupling In
Validamycin A Biosynthesis
pdb|3VDM|B Chain B, Crystal Structure Of Vlde, The Pseudo-Glycosyltransferase
Which Catalyzes Non-Glycosidic C-N Coupling In
Validamycin A Biosynthesis
pdb|3VDN|B Chain B, Crystal Structure Of Vlde, The Pseudo-Glycosyltransferase,
In Complex With Gdp
Length = 497
Score = 46.6 bits (109), Expect = 6e-05, Method: Compositional matrix adjust.
Identities = 66/326 (20%), Positives = 117/326 (35%), Gaps = 72/326 (22%)
Query: 183 ETWKTYCKVNEEFANCTLNALRNVIKDLDAAGKTNVVPVVWIHDYQLLVAATTIRQVAYD 242
E W + + +FA+ L + + PV +HDYQL+ +R+ D
Sbjct: 126 EGWADFGRFTRDFADAILKS-----------SAQSADPVYLVHDYQLVGVPALLREQRPD 174
Query: 243 ------------------------------------FVGFHIEDYCLNFIDCCCRRL-GS 265
+GF + +C NF++ L +
Sbjct: 175 APILLFVHIPWPSADYWRILPKEIRTGILHGMLPATTIGFFADRWCRNFLESVADLLPDA 234
Query: 266 RVDRNNMLVELAGRTVHVKALPIGIPFERFVQLAENAPENLKD--ENLKVILGVDRLDYT 323
R+DR M VE G ++ +P+G PE +++ + ++++ R D
Sbjct: 235 RIDREAMTVEWRGHRTRLRTMPLGYSPLTLDGRNPQLPEGIEEWADGHRLVVHSGRTDPI 294
Query: 324 KGLVHRIKAFERLLEKHPEYVEKVTFL------QISVPSRTD-VLEYKALKDEMDQLVGR 376
K ++AF +L +EK L ++ VP+ D V + E + +G
Sbjct: 295 KNAERAVRAF--VLAARGGGLEKTRMLVRMNPNRLYVPANADYVHRVETAVAEANAELGS 352
Query: 377 INGRFSKPNWSPIRYIFGCIGQEELAALYRDSAIALVTPLRDGMNLVAKEYVACQIREPG 436
R N + + C +R + + + DG NL E R+
Sbjct: 353 DTVRIDNDN--DVNHTIAC---------FRRADLLIFNSTVDGQNLSTFEAPLVNERDAD 401
Query: 437 VLILSPFAGAGGMMHE-ALLVNPYEI 461
V ILS GA ++ E VNP+++
Sbjct: 402 V-ILSETCGAAEVLGEYCRSVNPFDL 426
>pdb|3T5T|A Chain A, Vall From Streptomyces Hygroscopicus In Apo Form
pdb|3T5T|B Chain B, Vall From Streptomyces Hygroscopicus In Apo Form
Length = 496
Score = 46.6 bits (109), Expect = 6e-05, Method: Compositional matrix adjust.
Identities = 66/326 (20%), Positives = 117/326 (35%), Gaps = 72/326 (22%)
Query: 183 ETWKTYCKVNEEFANCTLNALRNVIKDLDAAGKTNVVPVVWIHDYQLLVAATTIRQVAYD 242
E W + + +FA+ L + + PV +HDYQL+ +R+ D
Sbjct: 125 EGWADFGRFTRDFADAILKS-----------SAQSADPVYLVHDYQLVGVPALLREQRPD 173
Query: 243 ------------------------------------FVGFHIEDYCLNFIDCCCRRL-GS 265
+GF + +C NF++ L +
Sbjct: 174 APILLFVHIPWPSADYWRILPKEIRTGILHGMLPATTIGFFADRWCRNFLESVADLLPDA 233
Query: 266 RVDRNNMLVELAGRTVHVKALPIGIPFERFVQLAENAPENLKD--ENLKVILGVDRLDYT 323
R+DR M VE G ++ +P+G PE +++ + ++++ R D
Sbjct: 234 RIDREAMTVEWRGHRTRLRTMPLGYSPLTLDGRNPQLPEGIEEWADGHRLVVHSGRTDPI 293
Query: 324 KGLVHRIKAFERLLEKHPEYVEKVTFL------QISVPSRTD-VLEYKALKDEMDQLVGR 376
K ++AF +L +EK L ++ VP+ D V + E + +G
Sbjct: 294 KNAERAVRAF--VLAARGGGLEKTRMLVRMNPNRLYVPANADYVHRVETAVAEANAELGS 351
Query: 377 INGRFSKPNWSPIRYIFGCIGQEELAALYRDSAIALVTPLRDGMNLVAKEYVACQIREPG 436
R N + + C +R + + + DG NL E R+
Sbjct: 352 DTVRIDNDN--DVNHTIAC---------FRRADLLIFNSTVDGQNLSTFEAPLVNERDAD 400
Query: 437 VLILSPFAGAGGMMHE-ALLVNPYEI 461
V ILS GA ++ E VNP+++
Sbjct: 401 V-ILSETCGAAEVLGEYCRSVNPFDL 425
>pdb|3T7D|A Chain A, Vall From Streptomyces Hygroscopicus In Complex With
Trehalose
pdb|3T7D|B Chain B, Vall From Streptomyces Hygroscopicus In Complex With
Trehalose
Length = 497
Score = 42.4 bits (98), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 63/324 (19%), Positives = 111/324 (34%), Gaps = 68/324 (20%)
Query: 183 ETWKTYCKVNEEFANCTLNALRNVIKDLDAAGKTNVVPVVWIHDYQLLVAATTIRQVAYD 242
E W + + +FA+ L + + PV +HDYQL+ +R+ D
Sbjct: 126 EGWADFGRFTRDFADAILKS-----------SAQSADPVYLVHDYQLVGVPALLREQRPD 174
Query: 243 ------------------------------------FVGFHIEDYCLNFIDCCCRRL-GS 265
+GF + +C NF++ L +
Sbjct: 175 APILLFVHIPWPSADYWRILPKEIRTGILHGXLPATTIGFFADRWCRNFLESVADLLPDA 234
Query: 266 RVDRNNMLVELAGRTVHVKALPIGIPFERFVQLAENAPENLKD--ENLKVILGVDRLDYT 323
R+DR VE G ++ P+G PE +++ + ++++ R D
Sbjct: 235 RIDREAXTVEWRGHRTRLRTXPLGYSPLTLDGRNPQLPEGIEEWADGHRLVVHSGRTDPI 294
Query: 324 KGLVHRIKAFERLLEKHPEYVEKVTFLQISVPSRTDVLEYKALKDEMDQLVGRINGRFSK 383
K ++AF +L +EK L P+R V ++ V N
Sbjct: 295 KNAERAVRAF--VLAARGGGLEKTRXLVRXNPNRLYVPANADYVHRVETAVAEANAELGS 352
Query: 384 P-----NWSPIRYIFGCIGQEELAALYRDSAIALVTPLRDGMNLVAKEYVACQIREPGVL 438
N + + + C +R + + + DG NL E R+ V
Sbjct: 353 DTVRIDNDNDVNHTIAC---------FRRADLLIFNSTVDGQNLSTFEAPLVNERDADV- 402
Query: 439 ILSPFAGAGGMMHE-ALLVNPYEI 461
ILS GA ++ E VNP+++
Sbjct: 403 ILSETCGAAEVLGEYCRSVNPFDL 426
>pdb|4IKN|A Chain A, Crystal Structure Of Adaptor Protein Complex 3 (ap-3) Mu3a
Subunit C- Terminal Domain, In Complex With A Sorting
Peptide From Tgn38
Length = 261
Score = 35.0 bits (79), Expect = 0.19, Method: Compositional matrix adjust.
Identities = 20/64 (31%), Positives = 39/64 (60%), Gaps = 3/64 (4%)
Query: 576 RLANMPDVNIGIISGRTLENLRHHPDLAVMSEETKRVLERLANMPDVNIGIISGR-TLEN 634
+L+ MPD+++ ++ R L+++ HP + E++RVL + PD N +IS R + +N
Sbjct: 54 KLSGMPDLSLSFMNPRLLDDVSFHPCIRFKRWESERVLSFIP--PDGNFRLISYRVSSQN 111
Query: 635 LMKM 638
L+ +
Sbjct: 112 LVAI 115
>pdb|1YZ4|A Chain A, Crystal Structure Of Dusp15
pdb|1YZ4|B Chain B, Crystal Structure Of Dusp15
Length = 160
Score = 32.0 bits (71), Expect = 1.4, Method: Compositional matrix adjust.
Identities = 23/72 (31%), Positives = 34/72 (47%), Gaps = 11/72 (15%)
Query: 208 KDLDAAGKTNVVPVVWIHD--YQLLVAATTIRQVAYDFVGFHIEDY---CLNFIDCCCRR 262
KDLD G+ + ++ IH+ LL T +R D I+ + C+NFI CC
Sbjct: 24 KDLDQLGRNKITHIISIHESPQPLLQDITYLRIPVADTPEVPIKKHFKECINFIHCC--- 80
Query: 263 LGSRVDRNNMLV 274
R++ N LV
Sbjct: 81 ---RLNGGNCLV 89
>pdb|1TAQ|A Chain A, Structure Of Taq Dna Polymerase
Length = 832
Score = 32.0 bits (71), Expect = 1.5, Method: Compositional matrix adjust.
Identities = 41/152 (26%), Positives = 65/152 (42%), Gaps = 27/152 (17%)
Query: 552 GTLTPLTSH---PDLAVMSEETKRVLER-LANMPDVNIGIISGRTLE------------- 594
G L +++H +LA+ EE + +ER + P V I +TLE
Sbjct: 668 GVLYGMSAHRLSQELAIPYEEAQAFIERYFQSFPKVRAWI--EKTLEEGRRRGYVETLFG 725
Query: 595 NLRHHPDLAVMSEETKRVLERLA-NMPDVNIGIISGRTLENLMKMVNIEKVTYAGSHGLE 653
R+ PDL + + ER+A NMP + G T +LMK+ ++ G
Sbjct: 726 RRRYVPDLEARVKSVREAAERMAFNMP------VQG-TAADLMKLAMVKLFPRLEEMGAR 778
Query: 654 ILHPDGTKFVHPVPKEYAEKLRQLIKALQDEV 685
+L + V PKE AE + +L K + + V
Sbjct: 779 MLLQVHDELVLEAPKERAEAVARLAKEVMEGV 810
>pdb|1BGX|T Chain T, Taq Polymerase In Complex With Tp7, An Inhibitory Fab
pdb|1TAU|A Chain A, Taq Polymerase (E.C.2.7.7.7)DNAB-Octylglucoside Complex
Length = 832
Score = 31.6 bits (70), Expect = 1.6, Method: Compositional matrix adjust.
Identities = 41/152 (26%), Positives = 65/152 (42%), Gaps = 27/152 (17%)
Query: 552 GTLTPLTSH---PDLAVMSEETKRVLER-LANMPDVNIGIISGRTLE------------- 594
G L +++H +LA+ EE + +ER + P V I +TLE
Sbjct: 668 GVLYGMSAHRLSQELAIPYEEAQAFIERYFQSFPKVRAWI--EKTLEEGRRRGYVETLFG 725
Query: 595 NLRHHPDLAVMSEETKRVLERLA-NMPDVNIGIISGRTLENLMKMVNIEKVTYAGSHGLE 653
R+ PDL + + ER+A NMP + G T +LMK+ ++ G
Sbjct: 726 RRRYVPDLEARVKSVREAAERMAFNMP------VQG-TAADLMKLAMVKLFPRLEEMGAR 778
Query: 654 ILHPDGTKFVHPVPKEYAEKLRQLIKALQDEV 685
+L + V PKE AE + +L K + + V
Sbjct: 779 MLLQVHDELVLEAPKERAEAVARLAKEVMEGV 810
>pdb|1QTM|A Chain A, Ddttp-trapped Closed Ternary Complex Of The Large Fragment
Of Dna Polymerase I From Thermus Aquaticus
Length = 539
Score = 31.6 bits (70), Expect = 1.8, Method: Compositional matrix adjust.
Identities = 41/152 (26%), Positives = 65/152 (42%), Gaps = 27/152 (17%)
Query: 552 GTLTPLTSH---PDLAVMSEETKRVLER-LANMPDVNIGIISGRTLE------------- 594
G L +++H +LA+ EE + +ER + P V I +TLE
Sbjct: 376 GVLYGMSAHRLSQELAIPYEEAQAFIERYFQSFPKVRAWI--EKTLEEGRRRGYVETLFG 433
Query: 595 NLRHHPDLAVMSEETKRVLERLA-NMPDVNIGIISGRTLENLMKMVNIEKVTYAGSHGLE 653
R+ PDL + + ER+A NMP + G T +LMK+ ++ G
Sbjct: 434 RRRYVPDLEARVKSVREAAERMAFNMP------VQG-TAADLMKLAMVKLFPRLEEMGAR 486
Query: 654 ILHPDGTKFVHPVPKEYAEKLRQLIKALQDEV 685
+L + V PKE AE + +L K + + V
Sbjct: 487 MLLQVHDELVLEAPKERAEAVARLAKEVMEGV 518
>pdb|1QSS|A Chain A, Ddgtp-Trapped Closed Ternary Complex Of The Large Fragment
Of Dna Polymerase I From Thermus Aquaticus
pdb|1QSY|A Chain A, Ddatp-Trapped Closed Ternary Complex Of The Large Fragment
Of Dna Polymerase I From Thermus Aquaticus
Length = 539
Score = 31.6 bits (70), Expect = 1.8, Method: Compositional matrix adjust.
Identities = 41/152 (26%), Positives = 65/152 (42%), Gaps = 27/152 (17%)
Query: 552 GTLTPLTSH---PDLAVMSEETKRVLER-LANMPDVNIGIISGRTLE------------- 594
G L +++H +LA+ EE + +ER + P V I +TLE
Sbjct: 376 GVLYGMSAHRLSQELAIPYEEAQAFIERYFQSFPKVRAWI--EKTLEEGRRRGYVETLFG 433
Query: 595 NLRHHPDLAVMSEETKRVLERLA-NMPDVNIGIISGRTLENLMKMVNIEKVTYAGSHGLE 653
R+ PDL + + ER+A NMP + G T +LMK+ ++ G
Sbjct: 434 RRRYVPDLEARVKSVREAAERMAFNMP------VQG-TAADLMKLAMVKLFPRLEEMGAR 486
Query: 654 ILHPDGTKFVHPVPKEYAEKLRQLIKALQDEV 685
+L + V PKE AE + +L K + + V
Sbjct: 487 MLLQVHDELVLEAPKERAEAVARLAKEVMEGV 518
>pdb|4KTQ|A Chain A, Binary Complex Of The Large Fragment Of Dna Polymerase I
From T. Aquaticus Bound To A PrimerTEMPLATE DNA
Length = 539
Score = 31.6 bits (70), Expect = 1.8, Method: Compositional matrix adjust.
Identities = 41/152 (26%), Positives = 65/152 (42%), Gaps = 27/152 (17%)
Query: 552 GTLTPLTSH---PDLAVMSEETKRVLER-LANMPDVNIGIISGRTLE------------- 594
G L +++H +LA+ EE + +ER + P V I +TLE
Sbjct: 375 GVLYGMSAHRLSQELAIPYEEAQAFIERYFQSFPKVRAWI--EKTLEEGRRRGYVETLFG 432
Query: 595 NLRHHPDLAVMSEETKRVLERLA-NMPDVNIGIISGRTLENLMKMVNIEKVTYAGSHGLE 653
R+ PDL + + ER+A NMP + G T +LMK+ ++ G
Sbjct: 433 RRRYVPDLEARVKSVREAAERMAFNMP------VQG-TAADLMKLAMVKLFPRLEEMGAR 485
Query: 654 ILHPDGTKFVHPVPKEYAEKLRQLIKALQDEV 685
+L + V PKE AE + +L K + + V
Sbjct: 486 MLLQVHDELVLEAPKERAEAVARLAKEVMEGV 517
>pdb|3KTQ|A Chain A, Crystal Structure Of An Active Ternary Complex Of The
Large Fragment Of Dna Polymerase I From Thermus
Aquaticus
pdb|1JXE|A Chain A, Stoffel Fragment Of Taq Dna Polymerase I
pdb|3LWL|A Chain A, Structure Of Klenow Fragment Of Taq Polymerase In Complex
Wi Abasic Site
pdb|3LWM|A Chain A, Structure Of The Large Fragment Of Thermus Aquaticus Dna
Pol In Complex With A Blunt-Ended Dna And Ddatp
pdb|3M8R|A Chain A, Crystal Structure Of The Large Fragment Of Dna Polymerase
I From Thermus Aquaticus In A Closed Ternary Complex
With Trapped 4'- Ethylated Dttp
pdb|3M8S|A Chain A, Crystal Structure Of The Large Fragment Of Dna Polymerase
I From Thermus Aquaticus In A Closed Ternary Complex
With Trapped 4'- Methylated Dttp
pdb|3OJS|A Chain A, Snapshots Of The Large Fragment Of Dna Polymerase I From
Thermus Aquaticus Processing C5 Modified Thymidines
pdb|3OJU|A Chain A, Snapshot Of The Large Fragment Of Dna Polymerase I From
Thermus Aquaticus Processing C5 Modified Thymidies
pdb|3RR7|A Chain A, Binary Structure Of The Large Fragment Of Taq Dna
Polymerase Bound To An Abasic Site
pdb|3RR8|A Chain A, Ternary Structure Of The Large Fragment Of Taq Dna
Polymerase Bound To An Abasic Site And A Ddgtp
pdb|3RRG|A Chain A, Ternary Structure Of The Large Fragment Of Taq Dna
Polymerase Bound To An Abasic Site And A Ddgtp
pdb|3RRH|A Chain A, Ternary Structure Of The Large Fragment Of Taq Dna
Polymerase Bound To An Abasic Site And A Ddttp
pdb|3T3F|A Chain A, Ternary Structure Of The Large Fragment Of Taq Dna
Polymerase Bound To An Abasic Site And Dnitp
pdb|4DF4|A Chain A, Crystal Structure Of The Large Fragment Of Dna Polymerase
I From Thermus Aquaticus In A Closed Ternary Complex
With 7-(N-(10- Hydroxydecanoyl)-Aminopentinyl)-7-Deaza-2
-Datp
pdb|4DF8|A Chain A, Crystal Structure Of The Large Fragment Of Dna Polymerase
I From Thermus Aquaticus In A Closed Ternary Complex
With Aminopentinyl-7- Deaza-2-Datp
pdb|4DFJ|A Chain A, Crystal Structure Of The Large Fragment Of Dna Polymerase
I From Thermus Aquaticus In A Closed Ternary Complex
With 5-(Aminopentinyl)- Dttp
pdb|4DFK|A Chain A, Large Fragment Of Dna Polymerase I From Thermus Aquaticus
In A Closed Ternary Complex With
5-(N-(10-Hydroxydecanoyl)-Aminopentinyl)-2-Dutp
pdb|4DFM|A Chain A, Crystal Structure Of The Large Fragment Of Dna Polymerase
I From Thermus Aquaticus In Ternary Complex With
5-(Aminopentinyl)-2-Dctp
pdb|4DFP|A Chain A, Crystal Structure Of The Large Fragment Of Dna Polymerase
I From Thermus Aqauticus In A Ternary Complex With
7-(Aminopentinyl)-7- Deaza-Dgtp
pdb|3RTV|A Chain A, Crystal Structure Of The Large Fragment Of Dna Polymerase
I From Thermus Aquaticus In A Closed Ternary Complex
With Natural PrimerTEMPLATE DNA
pdb|3SV3|A Chain A, Crystal Structure Of The Large Fragment Of Dna Polymerase
I From Thermus Aquaticus In A Closed Ternary Complex
With The Artificial Base Pair Dnam-D5sicstp
pdb|3SV4|A Chain A, Crystal Structure Of The Large Fragment Of Dna Polymerase
I From Thermus Aquaticus In An Open Binary Complex With
Dt As Templating Nucleobase
pdb|3SYZ|A Chain A, Crystal Structure Of The Large Fragment Of Dna Polymerase
I From Thermus Aquaticus In An Open Binary Complex With
Dnam As Templating Nucleobase
pdb|3SZ2|A Chain A, Crystal Structure Of The Large Fragment Of Dna Polymerase
I From Thermus Aquaticus In An Open Binary Complex With
Dg As Templating Nucleobase
pdb|4DLG|A Chain A, Ternary Structure Of The Large Fragment Of Taq Dna
Polymerase
Length = 540
Score = 31.6 bits (70), Expect = 1.8, Method: Compositional matrix adjust.
Identities = 41/152 (26%), Positives = 65/152 (42%), Gaps = 27/152 (17%)
Query: 552 GTLTPLTSH---PDLAVMSEETKRVLER-LANMPDVNIGIISGRTLE------------- 594
G L +++H +LA+ EE + +ER + P V I +TLE
Sbjct: 376 GVLYGMSAHRLSQELAIPYEEAQAFIERYFQSFPKVRAWI--EKTLEEGRRRGYVETLFG 433
Query: 595 NLRHHPDLAVMSEETKRVLERLA-NMPDVNIGIISGRTLENLMKMVNIEKVTYAGSHGLE 653
R+ PDL + + ER+A NMP + G T +LMK+ ++ G
Sbjct: 434 RRRYVPDLEARVKSVREAAERMAFNMP------VQG-TAADLMKLAMVKLFPRLEEMGAR 486
Query: 654 ILHPDGTKFVHPVPKEYAEKLRQLIKALQDEV 685
+L + V PKE AE + +L K + + V
Sbjct: 487 MLLQVHDELVLEAPKERAEAVARLAKEVMEGV 518
>pdb|2KTQ|A Chain A, Open Ternary Complex Of The Large Fragment Of Dna
Polymerase I From Thermus Aquaticus
Length = 538
Score = 31.6 bits (70), Expect = 1.8, Method: Compositional matrix adjust.
Identities = 41/152 (26%), Positives = 65/152 (42%), Gaps = 27/152 (17%)
Query: 552 GTLTPLTSH---PDLAVMSEETKRVLER-LANMPDVNIGIISGRTLE------------- 594
G L +++H +LA+ EE + +ER + P V I +TLE
Sbjct: 374 GVLYGMSAHRLSQELAIPYEEAQAFIERYFQSFPKVRAWI--EKTLEEGRRRGYVETLFG 431
Query: 595 NLRHHPDLAVMSEETKRVLERLA-NMPDVNIGIISGRTLENLMKMVNIEKVTYAGSHGLE 653
R+ PDL + + ER+A NMP + G T +LMK+ ++ G
Sbjct: 432 RRRYVPDLEARVKSVREAAERMAFNMP------VQG-TAADLMKLAMVKLFPRLEEMGAR 484
Query: 654 ILHPDGTKFVHPVPKEYAEKLRQLIKALQDEV 685
+L + V PKE AE + +L K + + V
Sbjct: 485 MLLQVHDELVLEAPKERAEAVARLAKEVMEGV 516
>pdb|5KTQ|A Chain A, Large Fragment Of Taq Dna Polymerase Bound To Dctp
pdb|1KTQ|A Chain A, Dna Polymerase
Length = 543
Score = 31.2 bits (69), Expect = 2.1, Method: Compositional matrix adjust.
Identities = 41/152 (26%), Positives = 65/152 (42%), Gaps = 27/152 (17%)
Query: 552 GTLTPLTSH---PDLAVMSEETKRVLER-LANMPDVNIGIISGRTLE------------- 594
G L +++H +LA+ EE + +ER + P V I +TLE
Sbjct: 379 GVLYGMSAHRLSQELAIPYEEAQAFIERYFQSFPKVRAWI--EKTLEEGRRRGYVETLFG 436
Query: 595 NLRHHPDLAVMSEETKRVLERLA-NMPDVNIGIISGRTLENLMKMVNIEKVTYAGSHGLE 653
R+ PDL + + ER+A NMP + G T +LMK+ ++ G
Sbjct: 437 RRRYVPDLEARVKSVREAAERMAFNMP------VQG-TAADLMKLAMVKLFPRLEEMGAR 489
Query: 654 ILHPDGTKFVHPVPKEYAEKLRQLIKALQDEV 685
+L + V PKE AE + +L K + + V
Sbjct: 490 MLLQVHDELVLEAPKERAEAVARLAKEVMEGV 521
>pdb|3PO4|A Chain A, Structure Of A Mutant Of The Large Fragment Of Dna
Polymerase I From Thermus Aquaticus In Complex With A
Blunt-Ended Dna And Ddatp
pdb|3PO5|A Chain A, Structure Of A Mutant Of The Large Fragment Of Dna
Polymerase I From Thermus Auqaticus In Complex With An
Abasic Site And Ddatp
pdb|3PY8|A Chain A, Crystal Structure Of A Mutant Of The Large Fragment Of Dna
Polymerase I From Thermus Aquaticus In A Closed Ternary
Complex With Dna And Ddctp
Length = 540
Score = 29.6 bits (65), Expect = 6.8, Method: Compositional matrix adjust.
Identities = 41/152 (26%), Positives = 64/152 (42%), Gaps = 27/152 (17%)
Query: 552 GTLTPLTSH---PDLAVMSEETKRVLER-LANMPDVNIGIISGRTLE------------- 594
G L +++H +LA+ EE + +ER + P V I +TLE
Sbjct: 376 GVLYGMSAHRLSQELAIPYEEAQAFIERYFQSFPKVRAWI--EKTLEEGRRRGYVETLFG 433
Query: 595 NLRHHPDLAVMSEETKRVLERLA-NMPDVNIGIISGRTLENLMKMVNIEKVTYAGSHGLE 653
R+ PDL + + ER A NMP + G T +LMK+ ++ G
Sbjct: 434 RRRYVPDLEARVKSVREAAERKAFNMP------VQG-TAADLMKLAMVKLFPRLEEMGAR 486
Query: 654 ILHPDGTKFVHPVPKEYAEKLRQLIKALQDEV 685
+L + V PKE AE + +L K + + V
Sbjct: 487 MLLQVHDELVLEAPKERAEAVARLAKEVMEGV 518
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 0.137 0.423
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 25,840,637
Number of Sequences: 62578
Number of extensions: 1139696
Number of successful extensions: 2794
Number of sequences better than 100.0: 18
Number of HSP's better than 100.0 without gapping: 4
Number of HSP's successfully gapped in prelim test: 14
Number of HSP's that attempted gapping in prelim test: 2760
Number of HSP's gapped (non-prelim): 28
length of query: 808
length of database: 14,973,337
effective HSP length: 107
effective length of query: 701
effective length of database: 8,277,491
effective search space: 5802521191
effective search space used: 5802521191
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: 55 (25.8 bits)