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= 000053
(2576 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|2XZL|A Chain A, Upf1-Rna Complex
Length = 802
Score = 157 bits (398), Expect = 6e-38, Method: Compositional matrix adjust.
Identities = 99/279 (35%), Positives = 152/279 (54%), Gaps = 13/279 (4%)
Query: 582 LVIDEAAQLKESESTIPLQLSGIKHAVLFGDECQL-PAMVESKVSDEACFGRSLFEXXXX 640
++IDE+ Q E E IP+ + G K +L GD QL P ++E K +D A +SLFE
Sbjct: 521 VLIDESTQASEPECLIPI-VKGAKQVILVGDHQQLGPVILERKAAD-AGLKQSLFERLIS 578
Query: 641 XXXXXXXXXIQYRMHPSISFFPNSYFYENKIHDSPTVEKRSYEKRFLPGPMYG-PYSFIN 699
+QYRM+P +S FP++ FYE + + T+E+R+ P P+ G P F
Sbjct: 579 LGHVPIRLEVQYRMNPYLSEFPSNMFYEGSLQNGVTIEQRTVPNSKFPWPIRGIPMMFWA 638
Query: 700 VFGGREEFIEHSCR--NMVEVSVVMKILLNLYKGWINSKEKLSIGIVSPYIAQVAAIQE- 756
+G REE + N +E +I+ L++ + ++ IG+++PY Q A I +
Sbjct: 639 NYG-REEISANGTSFLNRIEAMNCERIITKLFRDGVKPEQ---IGVITPYEGQRAYILQY 694
Query: 757 -KLGSKYVNSAGFAVKVMSVDGFQGGEEDIIIISTVRSNNGGSIGFISNPRRVNVALTRA 815
++ V+V SVD FQG E+D II+S VR+N +IGF+ +PRR+NV LTRA
Sbjct: 695 MQMNGSLDKDLYIKVEVASVDAFQGREKDYIILSCVRANEQQAIGFLRDPRRLNVGLTRA 754
Query: 816 RHCLWILGNERTLTRNRSVWKALVDDAKARQCFFNADDD 854
++ L ILGN R+L RN ++W L+ + + C D
Sbjct: 755 KYGLVILGNPRSLARN-TLWNHLLIHFREKGCLVEGTLD 792
Score = 44.3 bits (103), Expect = 8e-04, Method: Compositional matrix adjust.
Identities = 27/64 (42%), Positives = 39/64 (60%), Gaps = 8/64 (12%)
Query: 229 VQLIWGPPGTGKTKTVSMLLVILLQM-KFRTLVCTPTIVAIKELAS-------RVVKLVK 280
+ LI GPPGTGKT T + ++ L ++ K R LVC P+ VA+ LA+ +VV+L
Sbjct: 377 LSLIQGPPGTGKTVTSATIVYHLSKIHKDRILVCAPSNVAVDHLAAKLRDLGLKVVRLTA 436
Query: 281 ESVE 284
+S E
Sbjct: 437 KSRE 440
>pdb|2WJV|A Chain A, Crystal Structure Of The Complex Between Human Nonsense
Mediated Decay Factors Upf1 And Upf2
pdb|2WJV|B Chain B, Crystal Structure Of The Complex Between Human Nonsense
Mediated Decay Factors Upf1 And Upf2
pdb|2WJY|A Chain A, Crystal Structure Of The Complex Between Human Nonsense
Mediated Decay Factors Upf1 And Upf2 Orthorhombic Form
Length = 800
Score = 147 bits (370), Expect = 9e-35, Method: Compositional matrix adjust.
Identities = 93/263 (35%), Positives = 143/263 (54%), Gaps = 9/263 (3%)
Query: 582 LVIDEAAQLKESESTIPLQLSGIKHAVLFGDECQLPAMVESKVSDEACFGRSLFEXXXXX 641
++IDE+ Q E E +P+ L G K +L GD CQL +V K + +A +SLFE
Sbjct: 519 ILIDESTQATEPECMVPVVL-GAKQLILVGDHCQLGPVVMCKKAAKAGLSQSLFERLVVL 577
Query: 642 XXXXXXXXIQYRMHPSISFFPNSYFYENKIHDSPTVEKRSYEKRFLPGPMYGPYSFINVF 701
+QYRMHP++S FP++ FYE + + T R + P F V
Sbjct: 578 GIRPIRLQVQYRMHPALSAFPSNIFYEGSLQNGVTAADRVKKGFDFQWPQPDKPMFFYVT 637
Query: 702 GGREEFIEH--SCRNMVEVSVVMKILLNLYKGWINSKEKLSIGIVSPYIAQVAAIQEKLG 759
G+EE S N E + V KI L K + IGI++PY Q + + + +
Sbjct: 638 QGQEEIASSGTSYLNRTEAANVEKITTKLLKAGAKPDQ---IGIITPYEGQRSYLVQYMQ 694
Query: 760 -SKYVNSAGFA-VKVMSVDGFQGGEEDIIIISTVRSNNGGSIGFISNPRRVNVALTRARH 817
S +++ + V++ SVD FQG E+D II+S VR+N IGF+++PRR+NVALTRAR+
Sbjct: 695 FSGSLHTKLYQEVEIASVDAFQGREKDFIILSCVRANEHQGIGFLNDPRRLNVALTRARY 754
Query: 818 CLWILGNERTLTRNRSVWKALVD 840
+ I+GN + L++ + +W L++
Sbjct: 755 GVIIVGNPKALSK-QPLWNHLLN 776
Score = 38.9 bits (89), Expect = 0.036, Method: Compositional matrix adjust.
Identities = 19/48 (39%), Positives = 29/48 (60%), Gaps = 1/48 (2%)
Query: 229 VQLIWGPPGTGKTKTVSMLLVILL-QMKFRTLVCTPTIVAIKELASRV 275
+ LI GPPGTGKT T + ++ L Q LVC P+ +A+ +L ++
Sbjct: 373 LSLIQGPPGTGKTVTSATIVYHLARQGNGPVLVCAPSNIAVDQLTEKI 420
>pdb|2XZO|A Chain A, Upf1 Helicase - Rna Complex
pdb|2XZP|A Chain A, Upf1 Helicase
Length = 623
Score = 147 bits (370), Expect = 1e-34, Method: Compositional matrix adjust.
Identities = 93/263 (35%), Positives = 143/263 (54%), Gaps = 9/263 (3%)
Query: 582 LVIDEAAQLKESESTIPLQLSGIKHAVLFGDECQLPAMVESKVSDEACFGRSLFEXXXXX 641
++IDE+ Q E E +P+ L G K +L GD CQL +V K + +A +SLFE
Sbjct: 342 ILIDESTQATEPECMVPVVL-GAKQLILVGDHCQLGPVVMCKKAAKAGLSQSLFERLVVL 400
Query: 642 XXXXXXXXIQYRMHPSISFFPNSYFYENKIHDSPTVEKRSYEKRFLPGPMYGPYSFINVF 701
+QYRMHP++S FP++ FYE + + T R + P F V
Sbjct: 401 GIRPIRLQVQYRMHPALSAFPSNIFYEGSLQNGVTAADRVKKGFDFQWPQPDKPMFFYVT 460
Query: 702 GGREEFIEH--SCRNMVEVSVVMKILLNLYKGWINSKEKLSIGIVSPYIAQVAAIQEKLG 759
G+EE S N E + V KI L K + IGI++PY Q + + + +
Sbjct: 461 QGQEEIASSGTSYLNRTEAANVEKITTKLLKAGAKPDQ---IGIITPYEGQRSYLVQYMQ 517
Query: 760 -SKYVNSAGFA-VKVMSVDGFQGGEEDIIIISTVRSNNGGSIGFISNPRRVNVALTRARH 817
S +++ + V++ SVD FQG E+D II+S VR+N IGF+++PRR+NVALTRAR+
Sbjct: 518 FSGSLHTKLYQEVEIASVDAFQGREKDFIILSCVRANEHQGIGFLNDPRRLNVALTRARY 577
Query: 818 CLWILGNERTLTRNRSVWKALVD 840
+ I+GN + L++ + +W L++
Sbjct: 578 GVIIVGNPKALSK-QPLWNHLLN 599
Score = 39.3 bits (90), Expect = 0.032, Method: Compositional matrix adjust.
Identities = 19/48 (39%), Positives = 29/48 (60%), Gaps = 1/48 (2%)
Query: 229 VQLIWGPPGTGKTKTVSMLLVILL-QMKFRTLVCTPTIVAIKELASRV 275
+ LI GPPGTGKT T + ++ L Q LVC P+ +A+ +L ++
Sbjct: 196 LSLIQGPPGTGKTVTSATIVYHLARQGNGPVLVCAPSNIAVDQLTEKI 243
>pdb|2GJK|A Chain A, Structural And Functional Insights Into The Human Upf1
Helicase Core
pdb|2GK6|A Chain A, Structural And Functional Insights Into The Human Upf1
Helicase Core
pdb|2GK6|B Chain B, Structural And Functional Insights Into The Human Upf1
Helicase Core
pdb|2GK7|A Chain A, Structural And Functional Insights Into The Human Upf1
Helicase Core
Length = 624
Score = 147 bits (370), Expect = 1e-34, Method: Compositional matrix adjust.
Identities = 93/263 (35%), Positives = 143/263 (54%), Gaps = 9/263 (3%)
Query: 582 LVIDEAAQLKESESTIPLQLSGIKHAVLFGDECQLPAMVESKVSDEACFGRSLFEXXXXX 641
++IDE+ Q E E +P+ L G K +L GD CQL +V K + +A +SLFE
Sbjct: 343 ILIDESTQATEPECMVPVVL-GAKQLILVGDHCQLGPVVMCKKAAKAGLSQSLFERLVVL 401
Query: 642 XXXXXXXXIQYRMHPSISFFPNSYFYENKIHDSPTVEKRSYEKRFLPGPMYGPYSFINVF 701
+QYRMHP++S FP++ FYE + + T R + P F V
Sbjct: 402 GIRPIRLQVQYRMHPALSAFPSNIFYEGSLQNGVTAADRVKKGFDFQWPQPDKPMFFYVT 461
Query: 702 GGREEFIEH--SCRNMVEVSVVMKILLNLYKGWINSKEKLSIGIVSPYIAQVAAIQEKLG 759
G+EE S N E + V KI L K + IGI++PY Q + + + +
Sbjct: 462 QGQEEIASSGTSYLNRTEAANVEKITTKLLKAGAKPDQ---IGIITPYEGQRSYLVQYMQ 518
Query: 760 -SKYVNSAGFA-VKVMSVDGFQGGEEDIIIISTVRSNNGGSIGFISNPRRVNVALTRARH 817
S +++ + V++ SVD FQG E+D II+S VR+N IGF+++PRR+NVALTRAR+
Sbjct: 519 FSGSLHTKLYQEVEIASVDAFQGREKDFIILSCVRANEHQGIGFLNDPRRLNVALTRARY 578
Query: 818 CLWILGNERTLTRNRSVWKALVD 840
+ I+GN + L++ + +W L++
Sbjct: 579 GVIIVGNPKALSK-QPLWNHLLN 600
Score = 38.9 bits (89), Expect = 0.034, Method: Compositional matrix adjust.
Identities = 19/48 (39%), Positives = 29/48 (60%), Gaps = 1/48 (2%)
Query: 229 VQLIWGPPGTGKTKTVSMLLVILL-QMKFRTLVCTPTIVAIKELASRV 275
+ LI GPPGTGKT T + ++ L Q LVC P+ +A+ +L ++
Sbjct: 197 LSLIQGPPGTGKTVTSATIVYHLARQGNGPVLVCAPSNIAVDQLTEKI 244
>pdb|4B3F|X Chain X, Crystal Structure Of 1ghmbp2 Helicase
Length = 646
Score = 104 bits (260), Expect = 5e-22, Method: Compositional matrix adjust.
Identities = 88/289 (30%), Positives = 138/289 (47%), Gaps = 28/289 (9%)
Query: 580 NFLVIDEAAQLKESESTIPLQLSGIKHAVLFGDECQLPAMVESKVSDEACFGRSLFEXXX 639
+ +VIDE AQ E+ IPL + + +L GD QLP S + A SL E
Sbjct: 368 DVVVIDECAQALEASCWIPLLKA--RKCILAGDHKQLPPTTVSHKAALAGLSLSLMERLA 425
Query: 640 XX--XXXXXXXXIQYRMHPSISFFPNSYFYENKIHDSPTVEKRSYEKRFLPGPMYG---- 693
+QYRMH +I + + Y ++ +V + + R LPG
Sbjct: 426 EEYGARVVRTLTVQYRMHQAIMRWASDTMYLGQLTAHSSVAR--HLLRDLPGVAATEETG 483
Query: 694 -PYSFINVFG----GREEFIEHSCRNMVEVSVVMKILLNLYKGWINSKEKLSIGIVSPYI 748
P ++ G EE E S N EV +V + L + +++ I +VSPY
Sbjct: 484 VPLLLVDTAGCGLFELEEEDEQSKGNPGEVRLVSLHIQALVDAGVPARD---IAVVSPYN 540
Query: 749 AQVAAIQEKLGSKYVNSAGFAVKVMSVDGFQGGEEDIIIISTVRSNNGGSIGFISNPRRV 808
QV +++ L ++ +++ SVDGFQG E++ +I+S VRSN G +GF++ RR+
Sbjct: 541 LQVDLLRQSLVHRHPE-----LEIKSVDGFQGREKEAVILSFVRSNRKGEVGFLAEDRRI 595
Query: 809 NVALTRARHCLWILGNERTLTRNRSVWKALVD----DAKARQCFFNADD 853
NVA+TRAR + ++ + RT+ N + K LV+ + R F DD
Sbjct: 596 NVAVTRARRHVAVICDSRTVN-NHAFLKTLVEYFTQHGEVRTAFEYLDD 643
Score = 43.5 bits (101), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 20/55 (36%), Positives = 33/55 (60%), Gaps = 1/55 (1%)
Query: 231 LIWGPPGTGKTKTVSMLLVILLQMKFRTLVCTPTIVAIKELASRVVKLVKESVER 285
+I GPPGTGKT TV +++ ++ + L C P+ +A+ L R+ L K+ + R
Sbjct: 209 IIHGPPGTGKTTTVVEIILQAVKQGLKVLCCAPSNIAVDNLVERLA-LCKQRILR 262
>pdb|4B3G|A Chain A, Crystal Structure Of Ighmbp2 Helicase In Complex With Rna
pdb|4B3G|B Chain B, Crystal Structure Of Ighmbp2 Helicase In Complex With Rna
Length = 646
Score = 104 bits (260), Expect = 6e-22, Method: Compositional matrix adjust.
Identities = 88/289 (30%), Positives = 138/289 (47%), Gaps = 28/289 (9%)
Query: 580 NFLVIDEAAQLKESESTIPLQLSGIKHAVLFGDECQLPAMVESKVSDEACFGRSLFEXXX 639
+ +VIDE AQ E+ IPL + + +L GD QLP S + A SL E
Sbjct: 368 DVVVIDECAQALEASCWIPLLKA--RKCILAGDHKQLPPTTVSHKAALAGLSLSLMERLA 425
Query: 640 XX--XXXXXXXXIQYRMHPSISFFPNSYFYENKIHDSPTVEKRSYEKRFLPGPMYG---- 693
+QYRMH +I + + Y ++ +V + + R LPG
Sbjct: 426 EEYGARVVRTLTVQYRMHQAIMRWASDTMYLGQLTAHSSVAR--HLLRDLPGVAATEETG 483
Query: 694 -PYSFINVFG----GREEFIEHSCRNMVEVSVVMKILLNLYKGWINSKEKLSIGIVSPYI 748
P ++ G EE E S N EV +V + L + +++ I +VSPY
Sbjct: 484 VPLLLVDTAGCGLFELEEEDEQSKGNPGEVRLVSLHIQALVDAGVPARD---IAVVSPYN 540
Query: 749 AQVAAIQEKLGSKYVNSAGFAVKVMSVDGFQGGEEDIIIISTVRSNNGGSIGFISNPRRV 808
QV +++ L ++ +++ SVDGFQG E++ +I+S VRSN G +GF++ RR+
Sbjct: 541 LQVDLLRQSLVHRHPE-----LEIKSVDGFQGREKEAVILSFVRSNRKGEVGFLAEDRRI 595
Query: 809 NVALTRARHCLWILGNERTLTRNRSVWKALVD----DAKARQCFFNADD 853
NVA+TRAR + ++ + RT+ N + K LV+ + R F DD
Sbjct: 596 NVAVTRARRHVAVICDSRTVN-NHAFLKTLVEYFTQHGEVRTAFEYLDD 643
Score = 43.5 bits (101), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 20/55 (36%), Positives = 33/55 (60%), Gaps = 1/55 (1%)
Query: 231 LIWGPPGTGKTKTVSMLLVILLQMKFRTLVCTPTIVAIKELASRVVKLVKESVER 285
+I GPPGTGKT TV +++ ++ + L C P+ +A+ L R+ L K+ + R
Sbjct: 209 IIHGPPGTGKTTTVVEIILQAVKQGLKVLCCAPSNIAVDNLVERLA-LCKQRILR 262
>pdb|1QHH|B Chain B, Structure Of Dna Helicase With Adpnp
Length = 273
Score = 46.2 bits (108), Expect = 2e-04, Method: Composition-based stats.
Identities = 45/182 (24%), Positives = 80/182 (43%), Gaps = 27/182 (14%)
Query: 1328 IYDIFESYEQMKMRNGEFDLADLVN---DLHHRLKEE-SYKGDEFHFVYIDEVQDLTMSQ 1383
+ D+++ Y+Q +RN D DL+ L R+ + Y +F +++IDE QD +Q
Sbjct: 6 VSDVYQEYQQRLLRNHSLDFDDLIMTTIQLFDRVPDVLHYYQYKFQYIHIDEYQDTNRAQ 65
Query: 1384 VALFKYVCKNIEEGFVFSGDTAQTIARGIDFRFQDIRSLFYKKFVLESRNNGNDGRQEKR 1443
L K + + + GD Q+I R +R DI+++ F + N
Sbjct: 66 YTLVKKLAERFQN-ICAVGDADQSIYR---WRGADIQNIL--SFERDYPN---------- 109
Query: 1444 QLSDIFNLRQNFRTHVGVLNLAQSIIELLYRFFPHSVDILKPETSLIYGEPPILLESGDE 1503
+ + L QN+R+ +L A +IE P + PE G+P + E+ +E
Sbjct: 110 --AKVILLEQNYRSTKRILQAANEVIEHNVNRKPKRIWTENPE-----GKPILYYEAMNE 162
Query: 1504 EN 1505
+
Sbjct: 163 AD 164
>pdb|2PJR|A Chain A, Helicase Product Complex
pdb|2PJR|F Chain F, Helicase Product Complex
Length = 548
Score = 45.1 bits (105), Expect = 5e-04, Method: Compositional matrix adjust.
Identities = 60/258 (23%), Positives = 104/258 (40%), Gaps = 35/258 (13%)
Query: 1328 IYDIFESYEQMKMRNGEFDLADLVN---DLHHRLKEE-SYKGDEFHFVYIDEVQDLTMSQ 1383
+ D+++ Y+Q +RN D DL+ L R+ + Y +F +++IDE QD +Q
Sbjct: 173 VSDVYQEYQQRLLRNHSLDFDDLIMTTIQLFDRVPDVLHYYQYKFQYIHIDEYQDTNRAQ 232
Query: 1384 VALFKYVCKNIEEGFVFSGDTAQTIARGIDFRFQDIRSLFYKKFVLESRNNGNDGRQEKR 1443
L K + + + GD Q+I R Q+I S R+ N
Sbjct: 233 YTLVKKLAERF-QNICAVGDADQSIYRWRGADIQNILSF--------ERDYPN------- 276
Query: 1444 QLSDIFNLRQNFRTHVGVLNLAQSIIELLYRFFPHSVDILKPETSLIYGEPPILLESGDE 1503
+ + L QN+R+ +L A +IE P + PE G+P + E+ +E
Sbjct: 277 --AKVILLEQNYRSTKRILQAANEVIEHNVNRKPKRIWTENPE-----GKPILYYEAMNE 329
Query: 1504 ENAILKIFGNTGEVGGNMVGFGAEQVILVRDDCVRKEISNYVGKQALVLTIVESKGLEF- 1562
+ + G E + +L R + + + + K + IV GL+F
Sbjct: 330 ADEAQFVAGRIREAVERGERRYRDFAVLYRTNAQSRVMEEMLLKANIPYQIV--GGLKFY 387
Query: 1563 -----QDVLLYKFFSASP 1575
+D+L Y A+P
Sbjct: 388 DRKEIKDILAYLRVIANP 405
>pdb|3PJR|A Chain A, Helicase Substrate Complex
pdb|1QHG|A Chain A, Structure Of Dna Helicase Mutant With Adpnp
pdb|1PJR|A Chain A, Structure Of Dna Helicase
Length = 724
Score = 44.7 bits (104), Expect = 8e-04, Method: Compositional matrix adjust.
Identities = 47/194 (24%), Positives = 83/194 (42%), Gaps = 27/194 (13%)
Query: 1328 IYDIFESYEQMKMRNGEFDLADLVN---DLHHRLKEE-SYKGDEFHFVYIDEVQDLTMSQ 1383
+ D+++ Y+Q +RN D DL+ L R+ + Y +F +++IDE QD +Q
Sbjct: 173 VSDVYQEYQQRLLRNHSLDFDDLIMTTIQLFDRVPDVLHYYQYKFQYIHIDEYQDTNRAQ 232
Query: 1384 VALFKYVCKNIEEGFVFSGDTAQTIARGIDFRFQDIRSLFYKKFVLESRNNGNDGRQEKR 1443
L K + + + GD Q+I R +R DI+++ F + N
Sbjct: 233 YTLVKKLAERF-QNICAVGDADQSIYR---WRGADIQNIL--SFERDYPN---------- 276
Query: 1444 QLSDIFNLRQNFRTHVGVLNLAQSIIELLYRFFPHSVDILKPETSLIYGEPPILLESGDE 1503
+ + L QN+R+ +L A +IE P + PE G+P + E+ +E
Sbjct: 277 --AKVILLEQNYRSTKRILQAANEVIEHNVNRKPKRIWTENPE-----GKPILYYEAMNE 329
Query: 1504 ENAILKIFGNTGEV 1517
+ + G E
Sbjct: 330 ADEAQFVAGRIREA 343
>pdb|3U44|A Chain A, Crystal Structure Of Addab-Dna Complex
pdb|3U4Q|A Chain A, Structure Of Addab-Dna Complex At 2.8 Angstroms
Length = 1232
Score = 37.4 bits (85), Expect = 0.10, Method: Compositional matrix adjust.
Identities = 30/100 (30%), Positives = 49/100 (49%), Gaps = 14/100 (14%)
Query: 1366 DEFHFVYIDEVQDLTMSQVALFKYVCKNIEE-GFVFS-GDTAQTIARGIDFRFQDIRSLF 1423
++FH V +DE QD + Q ++ + V EE G +F GD Q+I R FR + LF
Sbjct: 399 EQFHEVLVDEYQDTNLVQESILQLVTSGPEETGNLFMVGDVKQSIYR---FRLAE-PLLF 454
Query: 1424 YKKFVLESRNNGNDGRQEKRQLSDIFNLRQNFRTHVGVLN 1463
K+ + + GR+ +L +NFR+ +L+
Sbjct: 455 LSKYKRFTESGEGTGRK--------IDLNKNFRSRADILD 486
Score = 31.2 bits (69), Expect = 7.4, Method: Compositional matrix adjust.
Identities = 25/91 (27%), Positives = 45/91 (49%), Gaps = 9/91 (9%)
Query: 1551 VLTIVESKGLEFQDVL---LYKFFSASPLKNQWRVVYEYMKEQDLLDSTSPGSFPSF--- 1604
++TI SKGLEF V L + F+ L + + E + S+P+
Sbjct: 790 LMTIHSSKGLEFPVVFVAGLGRNFNMMDLNKSYLLDKELGFGTKYIHPQLRISYPTLPLI 849
Query: 1605 ---NEVKHNILCSELKQLYVAITRTRQRLWI 1632
+++ +L EL+ LYVA+TR +++L++
Sbjct: 850 AMKKKMRRELLSEELRVLYVALTRAKEKLFL 880
>pdb|2ZWR|A Chain A, Crystal Structure Of Ttha1623 From Thermus Thermophilus Hb8
pdb|2ZWR|B Chain B, Crystal Structure Of Ttha1623 From Thermus Thermophilus Hb8
pdb|2ZZI|A Chain A, Crystal Structure Of Ttha1623 In A Di-Iron-Bound Form
pdb|2ZZI|B Chain B, Crystal Structure Of Ttha1623 In A Di-Iron-Bound Form
Length = 207
Score = 33.1 bits (74), Expect = 2.2, Method: Composition-based stats.
Identities = 16/43 (37%), Positives = 25/43 (58%), Gaps = 1/43 (2%)
Query: 1474 RFFPHSVDILKPETSLI-YGEPPILLESGDEENAILKIFGNTG 1515
R FP ++ L+ L+ GE P+L++ GDE +L +F TG
Sbjct: 2 RVFPVTLGPLQENAYLVETGEGPVLIDPGDEPEKLLALFQTTG 44
>pdb|3EVG|A Chain A, Crystal Structure Of Dengue-2 Virus Methyltransferase
Complexed With S-Adenosyl-L-Homocysteine
Length = 275
Score = 32.3 bits (72), Expect = 3.8, Method: Compositional matrix adjust.
Identities = 17/54 (31%), Positives = 28/54 (51%), Gaps = 1/54 (1%)
Query: 709 EHSCRNMVEVSVVMKILLNLYKGWINSKEKLSIGIVSPYIAQVAAIQEKLGSKY 762
E S VE +++L NL + W+N+ + I +++PY+ V E L KY
Sbjct: 149 ESSPNPTVEAGRTLRVL-NLVENWLNNNTQFCIKVLNPYMPSVIEKMEALQRKY 201
>pdb|3SYS|A Chain A, Improved Crystal Structure Of Pseudomonas Aeruginosa Occk1
(Opdk)
pdb|3SYS|B Chain B, Improved Crystal Structure Of Pseudomonas Aeruginosa Occk1
(Opdk)
Length = 398
Score = 31.2 bits (69), Expect = 8.9, Method: Composition-based stats.
Identities = 14/40 (35%), Positives = 24/40 (60%)
Query: 2126 GDAEWVRDLNNGHALRSGNLASINVHQLVSAGRNYWSSEL 2165
G EW RD+ G+ ++SG LA +NV ++ R ++S+
Sbjct: 338 GGKEWERDVELGYTVQSGPLARLNVRLNHASNRRSFNSDF 377
>pdb|2QTK|A Chain A, Crystal Structure Of The Outer Membrane Protein Opdk From
Pseudomonas Aeruginosa
pdb|2QTK|B Chain B, Crystal Structure Of The Outer Membrane Protein Opdk From
Pseudomonas Aeruginosa
pdb|2Y2X|A Chain A, Crystal Structure Of Pseudomonas Aeruginosa Opdk With
Vanillate
pdb|2Y2X|B Chain B, Crystal Structure Of Pseudomonas Aeruginosa Opdk With
Vanillate
Length = 390
Score = 31.2 bits (69), Expect = 8.9, Method: Composition-based stats.
Identities = 14/40 (35%), Positives = 24/40 (60%)
Query: 2126 GDAEWVRDLNNGHALRSGNLASINVHQLVSAGRNYWSSEL 2165
G EW RD+ G+ ++SG LA +NV ++ R ++S+
Sbjct: 338 GGKEWERDVELGYTVQSGPLARLNVRLNHASNRRSFNSDF 377
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
0.322 0.137 0.409
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 71,310,181
Number of Sequences: 62578
Number of extensions: 2869424
Number of successful extensions: 6590
Number of sequences better than 100.0: 15
Number of HSP's better than 100.0 without gapping: 10
Number of HSP's successfully gapped in prelim test: 5
Number of HSP's that attempted gapping in prelim test: 6538
Number of HSP's gapped (non-prelim): 46
length of query: 2576
length of database: 14,973,337
effective HSP length: 115
effective length of query: 2461
effective length of database: 7,776,867
effective search space: 19138869687
effective search space used: 19138869687
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 60 (27.7 bits)