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= 001501
(1066 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>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 = 931 bits (2405), Expect = 0.0, Method: Compositional matrix adjust.
Identities = 430/597 (72%), Positives = 516/597 (86%), Gaps = 5/597 (0%)
Query: 241 MKESQSKDNVTIRWDIGLNKKRVAYFVFPKEDNELRLVPGDELRLRYSGDAAHPAWQSVG 300
+KESQ++DN+T+RWD+GLNKKR+AYF PK D+++RL+ GDE+ LRY GD A P W+ +G
Sbjct: 30 LKESQTQDNITVRWDLGLNKKRIAYFTLPKTDSDMRLMQGDEICLRYKGDLA-PLWKGIG 88
Query: 301 HVIKLTAQ--EEVALELRASQGVPVDINHGFSVDFVWKSTSFDRMQGAMKTFAVDETSVS 358
HVIK+ +E+A+ELR+S G PV++ H F VDFVWKSTSFDRMQ A+KTFAVDETSVS
Sbjct: 89 HVIKVPDNYGDEIAIELRSSVGAPVEVTHNFQVDFVWKSTSFDRMQSALKTFAVDETSVS 148
Query: 359 GYIYHHLLGHEVEVQMVRNTLPRRFGAPGLPELNASQVFAVKSVLQRPISLIQGPPGTGK 418
GYIYH LLGHEVE +++ LP+RF A GLP+LN SQV+AVK+VLQRP+SLIQGPPGTGK
Sbjct: 149 GYIYHKLLGHEVEDVIIKCQLPKRFTAQGLPDLNHSQVYAVKTVLQRPLSLIQGPPGTGK 208
Query: 419 TVTSAAIVYHMAKQGQGQVLVCAPSNVAVDQLAEKISATGLKVVRLCAKSREAVSSPVEH 478
TVTSA IVYH+A+QG G VLVCAPSN+AVDQL EKI TGLKVVRLCAKSREA+ SPV
Sbjct: 209 TVTSATIVYHLARQGNGPVLVCAPSNIAVDQLTEKIHQTGLKVVRLCAKSREAIDSPVSF 268
Query: 479 LTLHYQVRHLDTSEKSELHKLQQLKDEQGELSSSDEKKYKALKRATEREISQSADVICCT 538
L LH Q+R++D+ EL KLQQLKDE GELSS+DEK+Y+ALKR ERE+ +ADVICCT
Sbjct: 269 LALHNQIRNMDSM--PELQKLQQLKDETGELSSADEKRYRALKRTAERELLMNADVICCT 326
Query: 539 CVGAGDPRLANFRFRQVLIDESTQATEPECLIPLVLGAKQVVLVGDHCQLGPVIMCKKAA 598
CVGAGDPRLA +FR +LIDESTQATEPEC++P+VLGAKQ++LVGDHCQLGPV+MCKKAA
Sbjct: 327 CVGAGDPRLAKMQFRSILIDESTQATEPECMVPVVLGAKQLILVGDHCQLGPVVMCKKAA 386
Query: 599 RAGLAQSLFERLVLLGLKPIRLQVQYRMHPSLSEFPSNSFYEGTLQNGVTINERQSSGID 658
+AGL+QSLFERLV+LG++PIRLQVQYRMHP+LS FPSN FYEG+LQNGVT +R G D
Sbjct: 387 KAGLSQSLFERLVVLGIRPIRLQVQYRMHPALSAFPSNIFYEGSLQNGVTAADRVKKGFD 446
Query: 659 FPWPVPNRPMFFYVQMGQEEISASGTSYLNRTEAANVEKIVTTFLRSGVVPSQIGVITPY 718
F WP P++PMFFYV GQEEI++SGTSYLNRTEAANVEKI T L++G P QIG+ITPY
Sbjct: 447 FQWPQPDKPMFFYVTQGQEEIASSGTSYLNRTEAANVEKITTKLLKAGAKPDQIGIITPY 506
Query: 719 EGQRAYIVNYMSRNGALRQQLYKEIEVASVDSFQGREKDYIILSCVRSNEHQGIGFLNDP 778
EGQR+Y+V YM +G+L +LY+E+E+ASVD+FQGREKD+IILSCVR+NEHQGIGFLNDP
Sbjct: 507 EGQRSYLVQYMQFSGSLHTKLYQEVEIASVDAFQGREKDFIILSCVRANEHQGIGFLNDP 566
Query: 779 RRLNVALTRARYGIVILGNPKVLSKQPLWNGLLTHYKEHECLVEGPLNNLKQSMVQF 835
RRLNVALTRARYG++I+GNPK LSKQPLWN LL +YKE + LVEGPLNNL++S++QF
Sbjct: 567 RRLNVALTRARYGVIIVGNPKALSKQPLWNHLLNYYKEQKVLVEGPLNNLRESLMQF 623
>pdb|2XZO|A Chain A, Upf1 Helicase - Rna Complex
pdb|2XZP|A Chain A, Upf1 Helicase
Length = 623
Score = 931 bits (2405), Expect = 0.0, Method: Compositional matrix adjust.
Identities = 430/597 (72%), Positives = 516/597 (86%), Gaps = 5/597 (0%)
Query: 241 MKESQSKDNVTIRWDIGLNKKRVAYFVFPKEDNELRLVPGDELRLRYSGDAAHPAWQSVG 300
+KESQ++DN+T+RWD+GLNKKR+AYF PK D+++RL+ GDE+ LRY GD A P W+ +G
Sbjct: 29 LKESQTQDNITVRWDLGLNKKRIAYFTLPKTDSDMRLMQGDEICLRYKGDLA-PLWKGIG 87
Query: 301 HVIKLTAQ--EEVALELRASQGVPVDINHGFSVDFVWKSTSFDRMQGAMKTFAVDETSVS 358
HVIK+ +E+A+ELR+S G PV++ H F VDFVWKSTSFDRMQ A+KTFAVDETSVS
Sbjct: 88 HVIKVPDNYGDEIAIELRSSVGAPVEVTHNFQVDFVWKSTSFDRMQSALKTFAVDETSVS 147
Query: 359 GYIYHHLLGHEVEVQMVRNTLPRRFGAPGLPELNASQVFAVKSVLQRPISLIQGPPGTGK 418
GYIYH LLGHEVE +++ LP+RF A GLP+LN SQV+AVK+VLQRP+SLIQGPPGTGK
Sbjct: 148 GYIYHKLLGHEVEDVIIKCQLPKRFTAQGLPDLNHSQVYAVKTVLQRPLSLIQGPPGTGK 207
Query: 419 TVTSAAIVYHMAKQGQGQVLVCAPSNVAVDQLAEKISATGLKVVRLCAKSREAVSSPVEH 478
TVTSA IVYH+A+QG G VLVCAPSN+AVDQL EKI TGLKVVRLCAKSREA+ SPV
Sbjct: 208 TVTSATIVYHLARQGNGPVLVCAPSNIAVDQLTEKIHQTGLKVVRLCAKSREAIDSPVSF 267
Query: 479 LTLHYQVRHLDTSEKSELHKLQQLKDEQGELSSSDEKKYKALKRATEREISQSADVICCT 538
L LH Q+R++D+ EL KLQQLKDE GELSS+DEK+Y+ALKR ERE+ +ADVICCT
Sbjct: 268 LALHNQIRNMDSM--PELQKLQQLKDETGELSSADEKRYRALKRTAERELLMNADVICCT 325
Query: 539 CVGAGDPRLANFRFRQVLIDESTQATEPECLIPLVLGAKQVVLVGDHCQLGPVIMCKKAA 598
CVGAGDPRLA +FR +LIDESTQATEPEC++P+VLGAKQ++LVGDHCQLGPV+MCKKAA
Sbjct: 326 CVGAGDPRLAKMQFRSILIDESTQATEPECMVPVVLGAKQLILVGDHCQLGPVVMCKKAA 385
Query: 599 RAGLAQSLFERLVLLGLKPIRLQVQYRMHPSLSEFPSNSFYEGTLQNGVTINERQSSGID 658
+AGL+QSLFERLV+LG++PIRLQVQYRMHP+LS FPSN FYEG+LQNGVT +R G D
Sbjct: 386 KAGLSQSLFERLVVLGIRPIRLQVQYRMHPALSAFPSNIFYEGSLQNGVTAADRVKKGFD 445
Query: 659 FPWPVPNRPMFFYVQMGQEEISASGTSYLNRTEAANVEKIVTTFLRSGVVPSQIGVITPY 718
F WP P++PMFFYV GQEEI++SGTSYLNRTEAANVEKI T L++G P QIG+ITPY
Sbjct: 446 FQWPQPDKPMFFYVTQGQEEIASSGTSYLNRTEAANVEKITTKLLKAGAKPDQIGIITPY 505
Query: 719 EGQRAYIVNYMSRNGALRQQLYKEIEVASVDSFQGREKDYIILSCVRSNEHQGIGFLNDP 778
EGQR+Y+V YM +G+L +LY+E+E+ASVD+FQGREKD+IILSCVR+NEHQGIGFLNDP
Sbjct: 506 EGQRSYLVQYMQFSGSLHTKLYQEVEIASVDAFQGREKDFIILSCVRANEHQGIGFLNDP 565
Query: 779 RRLNVALTRARYGIVILGNPKVLSKQPLWNGLLTHYKEHECLVEGPLNNLKQSMVQF 835
RRLNVALTRARYG++I+GNPK LSKQPLWN LL +YKE + LVEGPLNNL++S++QF
Sbjct: 566 RRLNVALTRARYGVIIVGNPKALSKQPLWNHLLNYYKEQKVLVEGPLNNLRESLMQF 622
>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 = 926 bits (2394), Expect = 0.0, Method: Compositional matrix adjust.
Identities = 430/597 (72%), Positives = 516/597 (86%), Gaps = 5/597 (0%)
Query: 241 MKESQSKDNVTIRWDIGLNKKRVAYFVFPKEDNELRLVPGDELRLRYSGDAAHPAWQSVG 300
+KESQ++DN+T+RWD+GLNKKR+AYF PK D+++RL+ GDE+ LRY GD A P W+ +G
Sbjct: 206 LKESQTQDNITVRWDLGLNKKRIAYFTLPKTDSDMRLMQGDEICLRYKGDLA-PLWKGIG 264
Query: 301 HVIKLTAQ--EEVALELRASQGVPVDINHGFSVDFVWKSTSFDRMQGAMKTFAVDETSVS 358
HVIK+ +E+A+ELR+S G PV++ H F VDFVWKSTSFDRMQ A+KTFAVDETSVS
Sbjct: 265 HVIKVPDNYGDEIAIELRSSVGAPVEVTHNFQVDFVWKSTSFDRMQSALKTFAVDETSVS 324
Query: 359 GYIYHHLLGHEVEVQMVRNTLPRRFGAPGLPELNASQVFAVKSVLQRPISLIQGPPGTGK 418
GYIYH LLGHEVE +++ LP+RF A GLP+LN SQV+AVK+VLQRP+SLIQGPPGTGK
Sbjct: 325 GYIYHKLLGHEVEDVIIKCQLPKRFTAQGLPDLNHSQVYAVKTVLQRPLSLIQGPPGTGK 384
Query: 419 TVTSAAIVYHMAKQGQGQVLVCAPSNVAVDQLAEKISATGLKVVRLCAKSREAVSSPVEH 478
TVTSA IVYH+A+QG G VLVCAPSN+AVDQL EKI TGLKVVRLCAKSREA+ SPV
Sbjct: 385 TVTSATIVYHLARQGNGPVLVCAPSNIAVDQLTEKIHQTGLKVVRLCAKSREAIDSPVSF 444
Query: 479 LTLHYQVRHLDTSEKSELHKLQQLKDEQGELSSSDEKKYKALKRATEREISQSADVICCT 538
L LH Q+R++D+ EL KLQQLKDE GELSS+DEK+Y+ALKR ERE+ +ADVICCT
Sbjct: 445 LALHNQIRNMDSM--PELQKLQQLKDETGELSSADEKRYRALKRTAERELLMNADVICCT 502
Query: 539 CVGAGDPRLANFRFRQVLIDESTQATEPECLIPLVLGAKQVVLVGDHCQLGPVIMCKKAA 598
CVGAGDPRLA +FR +LIDESTQATEPEC++P+VLGAKQ++LVGDHCQLGPV+MCKKAA
Sbjct: 503 CVGAGDPRLAKMQFRSILIDESTQATEPECMVPVVLGAKQLILVGDHCQLGPVVMCKKAA 562
Query: 599 RAGLAQSLFERLVLLGLKPIRLQVQYRMHPSLSEFPSNSFYEGTLQNGVTINERQSSGID 658
+AGL+QSLFERLV+LG++PIRLQVQYRMHP+LS FPSN FYEG+LQNGVT +R G D
Sbjct: 563 KAGLSQSLFERLVVLGIRPIRLQVQYRMHPALSAFPSNIFYEGSLQNGVTAADRVKKGFD 622
Query: 659 FPWPVPNRPMFFYVQMGQEEISASGTSYLNRTEAANVEKIVTTFLRSGVVPSQIGVITPY 718
F WP P++PMFFYV GQEEI++SGTSYLNRTEAANVEKI T L++G P QIG+ITPY
Sbjct: 623 FQWPQPDKPMFFYVTQGQEEIASSGTSYLNRTEAANVEKITTKLLKAGAKPDQIGIITPY 682
Query: 719 EGQRAYIVNYMSRNGALRQQLYKEIEVASVDSFQGREKDYIILSCVRSNEHQGIGFLNDP 778
EGQR+Y+V YM +G+L +LY+E+E+ASVD+FQGREKD+IILSCVR+NEHQGIGFLNDP
Sbjct: 683 EGQRSYLVQYMQFSGSLHTKLYQEVEIASVDAFQGREKDFIILSCVRANEHQGIGFLNDP 742
Query: 779 RRLNVALTRARYGIVILGNPKVLSKQPLWNGLLTHYKEHECLVEGPLNNLKQSMVQF 835
RRLNVALTRARYG++I+GNPK LSKQPLWN LL +YKE + LVEGPLNNL++S++QF
Sbjct: 743 RRLNVALTRARYGVIIVGNPKALSKQPLWNHLLNYYKEQKVLVEGPLNNLRESLMQF 799
Score = 177 bits (448), Expect = 4e-44, Method: Compositional matrix adjust.
Identities = 83/117 (70%), Positives = 92/117 (78%), Gaps = 8/117 (6%)
Query: 139 DFTEHACRYCGVSNPACVVRCNVPSCRKWFCNSRGNTSGSHIVNHLVRAKHKEVCLHKDS 198
D HAC YCG+ +PACVV CN + +KWFCN RGNTSGSHIVNHLVRAK KEV LHKD
Sbjct: 3 DLPIHACSYCGIHDPACVVYCN--TSKKWFCNGRGNTSGSHIVNHLVRAKCKEVTLHKDG 60
Query: 199 PLGETILECYNCGCRNVFLLGFISAKTESVVVLLCREPCLNMMKESQSKDNVTIRWD 255
PLGET+LECYNCGCRNVFLLGFI AK +SVVVLLCR+PC + +S KD I WD
Sbjct: 61 PLGETVLECYNCGCRNVFLLGFIPAKADSVVVLLCRQPCAS---QSSLKD---INWD 111
>pdb|2XZL|A Chain A, Upf1-Rna Complex
Length = 802
Score = 712 bits (1839), Expect = 0.0, Method: Compositional matrix adjust.
Identities = 355/599 (59%), Positives = 441/599 (73%), Gaps = 9/599 (1%)
Query: 241 MKESQSKDNVTIRWDIGLNKKRVAYFVFPK-EDNELRLVPGDELRLRYSGDAAHPAWQSV 299
+KESQ+ +++++ W + LN + +A F E NEL++ GDE+ L YSG HP W+
Sbjct: 208 LKESQALEHISVSWSLALNNRHLASFTLSTFESNELKVAIGDEMILWYSG-MQHPDWEGR 266
Query: 300 GHVIKL--TAQEEVALELRASQGVP-VDINHGFSVDFVWKSTSFDRMQGAMKTFAVDETS 356
G++++L + Q+ LEL+ S+ P + GF+ +F+WK TS+DRMQ A+K FA+D+ S
Sbjct: 267 GYIVRLPNSFQDTFTLELKPSKTPPPTHLTTGFTAEFIWKGTSYDRMQDALKKFAIDKKS 326
Query: 357 VSGYIYHHLLGHEVEVQMVRNTLPRRFGAPGLPELNASQVFAVKSVLQRPISLIQGPPGT 416
+SGY+Y+ +LGH+V LP+ F P +LN+SQ AV VLQRP+SLIQGPPGT
Sbjct: 327 ISGYLYYKILGHQVVDISFDVPLPKEFSIPNFAQLNSSQSNAVSHVLQRPLSLIQGPPGT 386
Query: 417 GKTVTSAAIVYHMAKQGQGQVLVCAPSNVAVDQLAEKISATGLKVVRLCAKSREAVSSPV 476
GKTVTSA IVYH++K + ++LVCAPSNVAVD LA K+ GLKVVRL AKSRE V S V
Sbjct: 387 GKTVTSATIVYHLSKIHKDRILVCAPSNVAVDHLAAKLRDLGLKVVRLTAKSREDVESSV 446
Query: 477 EHLTLHYQVRHLDTSEKSELHKLQQLKDEQGELSSSDEKKYKALKRATEREISQSADVIC 536
+L LH V K EL L +LKDE GELS+SD K++ L R TE EI ADV+C
Sbjct: 447 SNLALHNLVGR---GAKGELKNLLKLKDEVGELSASDTKRFVKLVRKTEAEILNKADVVC 503
Query: 537 CTCVGAGDPRLANFRFRQVLIDESTQATEPECLIPLVLGAKQVVLVGDHCQLGPVIMCKK 596
CTCVGAGD RL + +FR VLIDESTQA+EPECLIP+V GAKQV+LVGDH QLGPVI+ +K
Sbjct: 504 CTCVGAGDKRL-DTKFRTVLIDESTQASEPECLIPIVKGAKQVILVGDHQQLGPVILERK 562
Query: 597 AARAGLAQSLFERLVLLGLKPIRLQVQYRMHPSLSEFPSNSFYEGTLQNGVTINERQSSG 656
AA AGL QSLFERL+ LG PIRL+VQYRM+P LSEFPSN FYEG+LQNGVTI +R
Sbjct: 563 AADAGLKQSLFERLISLGHVPIRLEVQYRMNPYLSEFPSNMFYEGSLQNGVTIEQRTVPN 622
Query: 657 IDFPWPVPNRPMFFYVQMGQEEISASGTSYLNRTEAANVEKIVTTFLRSGVVPSQIGVIT 716
FPWP+ PM F+ G+EEISA+GTS+LNR EA N E+I+T R GV P QIGVIT
Sbjct: 623 SKFPWPIRGIPMMFWANYGREEISANGTSFLNRIEAMNCERIITKLFRDGVKPEQIGVIT 682
Query: 717 PYEGQRAYIVNYMSRNGALRQQLYKEIEVASVDSFQGREKDYIILSCVRSNEHQGIGFLN 776
PYEGQRAYI+ YM NG+L + LY ++EVASVD+FQGREKDYIILSCVR+NE Q IGFL
Sbjct: 683 PYEGQRAYILQYMQMNGSLDKDLYIKVEVASVDAFQGREKDYIILSCVRANEQQAIGFLR 742
Query: 777 DPRRLNVALTRARYGIVILGNPKVLSKQPLWNGLLTHYKEHECLVEGPLNNLKQSMVQF 835
DPRRLNV LTRA+YG+VILGNP+ L++ LWN LL H++E CLVEG L+NL+ VQ
Sbjct: 743 DPRRLNVGLTRAKYGLVILGNPRSLARNTLWNHLLIHFREKGCLVEGTLDNLQLCTVQL 801
Score = 146 bits (369), Expect = 5e-35, Method: Compositional matrix adjust.
Identities = 67/138 (48%), Positives = 99/138 (71%), Gaps = 8/138 (5%)
Query: 141 TEHACRYCGVSNPACVVRCNVPSCRKWFCNSRGNTSGSHIVNHLVRAKHKEVCLHKDSPL 200
++++C YCG+ + CV++CN SC+KWFCN++ TS SHIVNHLV + H V LH DS L
Sbjct: 10 SDNSCAYCGIDSAKCVIKCN--SCKKWFCNTKNGTSSSHIVNHLVLSHHNVVSLHPDSDL 67
Query: 201 GETILECYNCGCRNVFLLGFISAKTESVVVLLCREPCLNMMKESQSKDNVTIRWDIGLNK 260
G+T+LECYNCG +NVFLLGF+SAK+E+VVVLLCR PC ++++ + T +W +
Sbjct: 68 GDTVLECYNCGRKNVFLLGFVSAKSEAVVVLLCRIPC----AQTKNANWDTDQWQPLIED 123
Query: 261 KRVAYFVF--PKEDNELR 276
+++ +V P E+ +L+
Sbjct: 124 RQLLSWVAEQPTEEEKLK 141
>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 = 189 bits (479), Expect = 9e-48, Method: Compositional matrix adjust.
Identities = 151/459 (32%), Positives = 228/459 (49%), Gaps = 49/459 (10%)
Query: 391 LNASQVFAVKSVL-QRPISLIQGPPGTGKTVTSAAIVYHMAKQGQGQVLVCAPSNVAVDQ 449
L+ SQ AV L Q+ +++I GPPGTGKT T I+ KQG +VL CAPSN+AVD
Sbjct: 190 LDTSQKEAVLFALSQKELAIIHGPPGTGKTTTVVEIILQAVKQGL-KVLCCAPSNIAVDN 248
Query: 450 LAEKISATGLKVVRLCAKSR----------EAVSSPVEHLTLHYQVRHLDTSEKSELHKL 499
L E+++ +++RL +R +AV + + + +R D + +K
Sbjct: 249 LVERLALCKQRILRLGHPARLLESIQQHSLDAVLARSDSAQIVADIRK-DIDQVFVKNKK 307
Query: 500 QQLKDEQGELSSSDEKKYKALKRATEREISQS---ADVICCTCVGAGD----PRLANFRF 552
Q K E+ + + K LK E + +S A+V+ T GA L F
Sbjct: 308 TQDKREKSNFRNEIKLLRKELKEREEAAMLESLTSANVVLATNTGASADGPLKLLPESYF 367
Query: 553 RQVLIDESTQATEPECLIPLVLGAKQVVLVGDHCQLGPVIMCKKAARAGLAQSLFERLVL 612
V+IDE QA E C IPL L A++ +L GDH QL P + KAA AGL+ SL ERL
Sbjct: 368 DVVVIDECAQALEASCWIPL-LKARKCILAGDHKQLPPTTVSHKAALAGLSLSLMERLAE 426
Query: 613 -LGLKPIR-LQVQYRMHPSLSEFPSNSFYEGTLQNGVTINE---RQSSGID------FPW 661
G + +R L VQYRMH ++ + S++ Y G L ++ R G+ P
Sbjct: 427 EYGARVVRTLTVQYRMHQAIMRWASDTMYLGQLTAHSSVARHLLRDLPGVAATEETGVPL 486
Query: 662 PVPNRPMFFYVQMGQEEISASGTSYLNRTEAANVEKIVTTFLRSGVVPSQIGVITPYEGQ 721
+ + ++ +E+ + G N E V + + +GV I V++PY Q
Sbjct: 487 LLVDTAGCGLFELEEEDEQSKG----NPGEVRLVSLHIQALVDAGVPARDIAVVSPYNLQ 542
Query: 722 RAYIVNYMSRNGALRQQL---YKEIEVASVDSFQGREKDYIILSCVRSNEHQGIGFLNDP 778
LRQ L + E+E+ SVD FQGREK+ +ILS VRSN +GFL +
Sbjct: 543 ----------VDLLRQSLVHRHPELEIKSVDGFQGREKEAVILSFVRSNRKGEVGFLAED 592
Query: 779 RRLNVALTRARYGIVILGNPKVLSKQPLWNGLLTHYKEH 817
RR+NVA+TRAR + ++ + + ++ L+ ++ +H
Sbjct: 593 RRINVAVTRARRHVAVICDSRTVNNHAFLKTLVEYFTQH 631
>pdb|4B3F|X Chain X, Crystal Structure Of 1ghmbp2 Helicase
Length = 646
Score = 189 bits (479), Expect = 9e-48, Method: Compositional matrix adjust.
Identities = 151/459 (32%), Positives = 228/459 (49%), Gaps = 49/459 (10%)
Query: 391 LNASQVFAVKSVL-QRPISLIQGPPGTGKTVTSAAIVYHMAKQGQGQVLVCAPSNVAVDQ 449
L+ SQ AV L Q+ +++I GPPGTGKT T I+ KQG +VL CAPSN+AVD
Sbjct: 190 LDTSQKEAVLFALSQKELAIIHGPPGTGKTTTVVEIILQAVKQGL-KVLCCAPSNIAVDN 248
Query: 450 LAEKISATGLKVVRLCAKSR----------EAVSSPVEHLTLHYQVRHLDTSEKSELHKL 499
L E+++ +++RL +R +AV + + + +R D + +K
Sbjct: 249 LVERLALCKQRILRLGHPARLLESIQQHSLDAVLARSDSAQIVADIRK-DIDQVFVKNKK 307
Query: 500 QQLKDEQGELSSSDEKKYKALKRATEREISQS---ADVICCTCVGAGD----PRLANFRF 552
Q K E+ + + K LK E + +S A+V+ T GA L F
Sbjct: 308 TQDKREKSNFRNEIKLLRKELKEREEAAMLESLTSANVVLATNTGASADGPLKLLPESYF 367
Query: 553 RQVLIDESTQATEPECLIPLVLGAKQVVLVGDHCQLGPVIMCKKAARAGLAQSLFERLVL 612
V+IDE QA E C IPL L A++ +L GDH QL P + KAA AGL+ SL ERL
Sbjct: 368 DVVVIDECAQALEASCWIPL-LKARKCILAGDHKQLPPTTVSHKAALAGLSLSLMERLAE 426
Query: 613 -LGLKPIR-LQVQYRMHPSLSEFPSNSFYEGTLQNGVTINE---RQSSGID------FPW 661
G + +R L VQYRMH ++ + S++ Y G L ++ R G+ P
Sbjct: 427 EYGARVVRTLTVQYRMHQAIMRWASDTMYLGQLTAHSSVARHLLRDLPGVAATEETGVPL 486
Query: 662 PVPNRPMFFYVQMGQEEISASGTSYLNRTEAANVEKIVTTFLRSGVVPSQIGVITPYEGQ 721
+ + ++ +E+ + G N E V + + +GV I V++PY Q
Sbjct: 487 LLVDTAGCGLFELEEEDEQSKG----NPGEVRLVSLHIQALVDAGVPARDIAVVSPYNLQ 542
Query: 722 RAYIVNYMSRNGALRQQL---YKEIEVASVDSFQGREKDYIILSCVRSNEHQGIGFLNDP 778
LRQ L + E+E+ SVD FQGREK+ +ILS VRSN +GFL +
Sbjct: 543 ----------VDLLRQSLVHRHPELEIKSVDGFQGREKEAVILSFVRSNRKGEVGFLAED 592
Query: 779 RRLNVALTRARYGIVILGNPKVLSKQPLWNGLLTHYKEH 817
RR+NVA+TRAR + ++ + + ++ L+ ++ +H
Sbjct: 593 RRINVAVTRARRHVAVICDSRTVNNHAFLKTLVEYFTQH 631
>pdb|2IYK|A Chain A, Crystal Structure Of The Upf2-Interacting Domain Of
Nonsense Mediated Mrna Decay Factor Upf1
pdb|2IYK|B Chain B, Crystal Structure Of The Upf2-Interacting Domain Of
Nonsense Mediated Mrna Decay Factor Upf1
Length = 162
Score = 172 bits (435), Expect = 1e-42, Method: Compositional matrix adjust.
Identities = 89/148 (60%), Positives = 103/148 (69%), Gaps = 15/148 (10%)
Query: 136 GKADFTEHACRYCGVSNPACVVRCNVPSCRKWFCNSRGNTSGSHIVNHLVRAKHKEVCLH 195
G D HAC YCG+ +PACVV CN +KWFCN RGNTSGSHIVNHLVRAK KEV LH
Sbjct: 4 GTKDLPIHACSYCGIHDPACVVYCNTS--KKWFCNGRGNTSGSHIVNHLVRAKCKEVTLH 61
Query: 196 KDSPLGETILECYNCGCRNVFLLGFISAKTESVVVLLCREPCLNMMKESQSKDNVTIRWD 255
KD PLGET+LECYNCGCRNVFLLGFI AK +SVVVLLCR+PC +S KD I WD
Sbjct: 62 KDGPLGETVLECYNCGCRNVFLLGFIPAKADSVVVLLCRQPC---ASQSSLKD---INWD 115
Query: 256 ------IGLNKKRVAYFV-FPKEDNELR 276
+ ++ +++ V P E +LR
Sbjct: 116 SSQWQPLIQDRCFLSWLVKIPSEQEQLR 143
>pdb|1D2M|A Chain A, Uvrb Protein Of Thermus Thermophilus Hb8; A Nucleotide
Excision Repair Enzyme
Length = 665
Score = 37.0 bits (84), Expect = 0.056, Method: Compositional matrix adjust.
Identities = 42/160 (26%), Positives = 68/160 (42%), Gaps = 34/160 (21%)
Query: 404 QRPISLIQGPPGTGKTVTSAAIVYHMAKQGQGQVLVCAPSNVAVDQLAEKISATGLKVVR 463
+R ++L+ G GTGKTVT A ++ + + LV AP+ + QLA
Sbjct: 29 ERFVTLL-GATGTGKTVTMAKVIEALGRPA----LVLAPNKILAAQLA------------ 71
Query: 464 LCAKSREAV-SSPVEHLTLHYQVRHLDTSEKSELHKLQQLKDEQGELSSSDEKKYKALKR 522
A+ RE + VE+ +Y + KD E +S + + L+
Sbjct: 72 --AEFRELFPENAVEYFISYYDYYQPEAYVPG--------KDLYIEKDASINPEIERLRH 121
Query: 523 ATEREISQSADVICCTCV----GAGDPRLANFRFRQVLID 558
+T R + DVI V G GDPR +R R ++++
Sbjct: 122 STTRSLLTRRDVIVVASVSAIYGLGDPR--EYRARNLVVE 159
>pdb|1C4O|A Chain A, Crystal Structure Of The Dna Nucleotide Excision Repair
Enzyme Uvrb From Thermus Thermophilus
Length = 664
Score = 37.0 bits (84), Expect = 0.059, Method: Compositional matrix adjust.
Identities = 42/160 (26%), Positives = 68/160 (42%), Gaps = 34/160 (21%)
Query: 404 QRPISLIQGPPGTGKTVTSAAIVYHMAKQGQGQVLVCAPSNVAVDQLAEKISATGLKVVR 463
+R ++L+ G GTGKTVT A ++ + + LV AP+ + QLA
Sbjct: 28 ERFVTLL-GATGTGKTVTMAKVIEALGRPA----LVLAPNKILAAQLA------------ 70
Query: 464 LCAKSREAV-SSPVEHLTLHYQVRHLDTSEKSELHKLQQLKDEQGELSSSDEKKYKALKR 522
A+ RE + VE+ +Y + KD E +S + + L+
Sbjct: 71 --AEFRELFPENAVEYFISYYDYYQPEAYVPG--------KDLYIEKDASINPEIERLRH 120
Query: 523 ATEREISQSADVICCTCV----GAGDPRLANFRFRQVLID 558
+T R + DVI V G GDPR +R R ++++
Sbjct: 121 STTRSLLTRRDVIVVASVSAIYGLGDPR--EYRARNLVVE 158
>pdb|1B57|A Chain A, Class Ii Fructose-1,6-Bisphosphate Aldolase In Complex
With Phosphoglycolohydroxamate
pdb|1B57|B Chain B, Class Ii Fructose-1,6-Bisphosphate Aldolase In Complex
With Phosphoglycolohydroxamate
pdb|1GYN|A Chain A, Class Ii Fructose 1,6-Bisphosphate Aldolase With Cadmium
(Not Zinc) In The Active Site
pdb|1ZEN|A Chain A, Class Ii Fructose-1,6-Bisphosphate Aldolase
Length = 358
Score = 36.6 bits (83), Expect = 0.073, Method: Compositional matrix adjust.
Identities = 21/63 (33%), Positives = 33/63 (52%), Gaps = 5/63 (7%)
Query: 790 YGIVILGNPKVLSKQPLWNGLLTHYKEHECLVEGPLNNLKQSMVQFQKPKKIYNDRRLFF 849
YG+V + N ++ W G+L +YK +E ++G L N K +P K Y D R++
Sbjct: 280 YGVVKM-NIDTDTQWATWEGVLNYYKANEAYLQGQLGNPKGE----DQPNKKYYDPRVWL 334
Query: 850 GAG 852
AG
Sbjct: 335 RAG 337
>pdb|1DOS|A Chain A, Structure Of Fructose-Bisphosphate Aldolase
pdb|1DOS|B Chain B, Structure Of Fructose-Bisphosphate Aldolase
Length = 358
Score = 36.6 bits (83), Expect = 0.073, Method: Compositional matrix adjust.
Identities = 21/63 (33%), Positives = 33/63 (52%), Gaps = 5/63 (7%)
Query: 790 YGIVILGNPKVLSKQPLWNGLLTHYKEHECLVEGPLNNLKQSMVQFQKPKKIYNDRRLFF 849
YG+V + N ++ W G+L +YK +E ++G L N K +P K Y D R++
Sbjct: 280 YGVVKM-NIDTDTQWATWEGVLNYYKANEAYLQGQLGNPKGE----DQPNKKYYDPRVWL 334
Query: 850 GAG 852
AG
Sbjct: 335 RAG 337
>pdb|3E1S|A Chain A, Structure Of An N-Terminal Truncation Of Deinococcus
Radiodurans Recd2
pdb|3GP8|A Chain A, Crystal Structure Of The Binary Complex Of Recd2 With Dna
pdb|3GPL|A Chain A, Crystal Structure Of The Ternary Complex Of Recd2 With Dna
And Adpnp
pdb|3GPL|B Chain B, Crystal Structure Of The Ternary Complex Of Recd2 With Dna
And Adpnp
Length = 574
Score = 33.1 bits (74), Expect = 0.75, Method: Compositional matrix adjust.
Identities = 22/75 (29%), Positives = 37/75 (49%), Gaps = 1/75 (1%)
Query: 391 LNASQVFAVKSVLQRPISLIQGPPGTGKTVTSAAIVYHMAKQGQGQVLVCAPSNVAVDQL 450
L+ Q + + + ++ G PGTGK+ T+ A+ +A+ +V +CAP+ A +L
Sbjct: 190 LSEEQASVLDQLAGHRLVVLTGGPGTGKSTTTKAVA-DLAESLGLEVGLCAPTGKAARRL 248
Query: 451 AEKISATGLKVVRLC 465
E T V RL
Sbjct: 249 GEVTGRTASTVHRLL 263
>pdb|4DDT|A Chain A, Thermotoga Maritima Reverse Gyrase, C2 Form 2
pdb|4DDU|A Chain A, Thermotoga Maritima Reverse Gyrase, C2 Form 1
pdb|4DDV|A Chain A, Thermotoga Maritima Reverse Gyrase, Triclinic Form
pdb|4DDV|B Chain B, Thermotoga Maritima Reverse Gyrase, Triclinic Form
pdb|4DDW|A Chain A, Thermotoga Maritima Reverse Gyrase, C-centered
Orthorhombic Form
pdb|4DDX|A Chain A, Thermotoga Maritima Reverse Gyrase, Primitive Monoclinic
Form
pdb|4DDX|B Chain B, Thermotoga Maritima Reverse Gyrase, Primitive Monoclinic
Form
Length = 1104
Score = 32.7 bits (73), Expect = 0.99, Method: Compositional matrix adjust.
Identities = 25/113 (22%), Positives = 49/113 (43%), Gaps = 7/113 (6%)
Query: 352 VDETSVSGYIYHHLLGHEVEVQMVRNTLPRRFGAPGLPELNASQVFAVKSVLQRPISLIQ 411
++ ++ Y ++H +E E R+ ++FG +L Q K ++Q +
Sbjct: 46 LERKTLKEYRFYHEFWNEYE--DFRSFFKKKFG----KDLTGYQRLWAKRIVQGKSFTMV 99
Query: 412 GPPGTGKTVTSAAIVYHMAKQGQGQVLVCAPSNVAVDQLAEKISATGLKVVRL 464
P G GKT +A++G+ LV P+ V Q E++ + V++
Sbjct: 100 APTGVGKTTFGMMTALWLARKGKKSALVF-PTVTLVKQTLERLQKLADEKVKI 151
>pdb|3ZXJ|A Chain A, Engineering The Active Site Of A Gh43 Glycoside Hydrolase
Generates A Biotechnologically Significant Enzyme That
Displays Both Endo-Xylanase And Exo-Arabinofuranosidase
Activity
pdb|3ZXJ|B Chain B, Engineering The Active Site Of A Gh43 Glycoside Hydrolase
Generates A Biotechnologically Significant Enzyme That
Displays Both Endo-Xylanase And Exo-Arabinofuranosidase
Activity
Length = 542
Score = 32.7 bits (73), Expect = 1.0, Method: Compositional matrix adjust.
Identities = 22/62 (35%), Positives = 32/62 (51%), Gaps = 2/62 (3%)
Query: 258 LNKKRVAYFVFPKEDNELRLVPGDELRLRYSG--DAAHPAWQSVGHVIKLTAQEEVALEL 315
L + R AY K+ NE R+V D+LRL G A+ + G VI AQ+++ L +
Sbjct: 402 LFRDRAAYIGVWKQGNEARIVXVDDLRLNEDGWRTASTGRVAANGPVIDTNAQQDIWLRI 461
Query: 316 RA 317
A
Sbjct: 462 DA 463
>pdb|4B4T|J Chain J, Near-Atomic Resolution Structural Model Of The Yeast 26s
Proteasome
Length = 405
Score = 32.7 bits (73), Expect = 1.2, Method: Compositional matrix adjust.
Identities = 47/220 (21%), Positives = 89/220 (40%), Gaps = 53/220 (24%)
Query: 272 DNELRLVPGDELRLRYSGDAAHPAWQSVGHVIKLTAQEEVALELRASQGVPVDINHGFSV 331
++++R + DELRL VG VIK+ + ++V ++++ VD+ +V
Sbjct: 52 NDKVRFIK-DELRL------LQEPGSYVGEVIKIVSDKKVLVKVQPEGKYIVDVAKDINV 104
Query: 332 DFVWKSTSFDRMQGAMKTFAVDETSVSGYIYHHLLGHE----VEVQMVRNTLPRRFGAPG 387
+ S +++ Y+ H +L ++ V + MV + G
Sbjct: 105 KDLKASQRV-----CLRS--------DSYMLHKVLENKADPLVSLMMVEKVPDSTYDMVG 151
Query: 388 LPELNASQVFAVKSVLQRPIS----------------LIQGPPGTGKTVTSAAIVYHMAK 431
Q+ +K V++ P+ ++ GPPGTGKT+ + A+ +H
Sbjct: 152 GL---TKQIKEIKEVIELPVKHPELFESLGIAQPKGVILYGPPGTGKTLLARAVAHHTD- 207
Query: 432 QGQGQVLVCAPSNVAVDQLAEKISATGLKVVR-LCAKSRE 470
C V+ +L +K G ++VR L +RE
Sbjct: 208 --------CKFIRVSGAELVQKYIGEGSRMVRELFVMARE 239
>pdb|3ZXL|A Chain A, Engineering The Active Site Of A Gh43 Glycoside Hydrolase
Generates A Biotechnologically Significant Enzyme That
Displays Both Endo-Xylanase And Exo-Arabinofuranosidase
Activity
pdb|3ZXL|B Chain B, Engineering The Active Site Of A Gh43 Glycoside Hydrolase
Generates A Biotechnologically Significant Enzyme That
Displays Both Endo-Xylanase And Exo-Arabinofuranosidase
Activity
Length = 542
Score = 32.7 bits (73), Expect = 1.2, Method: Compositional matrix adjust.
Identities = 22/62 (35%), Positives = 32/62 (51%), Gaps = 2/62 (3%)
Query: 258 LNKKRVAYFVFPKEDNELRLVPGDELRLRYSG--DAAHPAWQSVGHVIKLTAQEEVALEL 315
L + R AY K+ NE R+V D+LRL G A+ + G VI AQ+++ L +
Sbjct: 402 LFRDRAAYIGVWKQGNEARIVMVDDLRLNEDGWRTASTGRVAANGPVIDTNAQQDIWLRI 461
Query: 316 RA 317
A
Sbjct: 462 DA 463
>pdb|3ZXK|A Chain A, Engineering The Active Site Of A Gh43 Glycoside Hydrolase
Generates A Biotechnologically Significant Enzyme That
Displays Both Endo-Xylanase And Exo-Arabinofuranosidase
Activity
pdb|3ZXK|B Chain B, Engineering The Active Site Of A Gh43 Glycoside Hydrolase
Generates A Biotechnologically Significant Enzyme That
Displays Both Endo-Xylanase And Exo-Arabinofuranosidase
Activity
Length = 542
Score = 32.3 bits (72), Expect = 1.3, Method: Compositional matrix adjust.
Identities = 22/62 (35%), Positives = 32/62 (51%), Gaps = 2/62 (3%)
Query: 258 LNKKRVAYFVFPKEDNELRLVPGDELRLRYSG--DAAHPAWQSVGHVIKLTAQEEVALEL 315
L + R AY K+ NE R+V D+LRL G A+ + G VI AQ+++ L +
Sbjct: 402 LFRDRAAYIGVWKQGNEARIVMVDDLRLNEDGWRTASTGRVAANGPVIDTNAQQDIWLRI 461
Query: 316 RA 317
A
Sbjct: 462 DA 463
>pdb|3UPU|A Chain A, Crystal Structure Of The T4 Phage Sf1b Helicase Dda
pdb|3UPU|B Chain B, Crystal Structure Of The T4 Phage Sf1b Helicase Dda
pdb|3UPU|C Chain C, Crystal Structure Of The T4 Phage Sf1b Helicase Dda
Length = 459
Score = 32.0 bits (71), Expect = 1.9, Method: Compositional matrix adjust.
Identities = 34/138 (24%), Positives = 58/138 (42%), Gaps = 23/138 (16%)
Query: 410 IQGPPGTGKTVTSAAIVYHMAKQGQGQVLVCAPSNVAVDQLAEKISATGLKVVRLCAKSR 469
I GP GTG T + I+ + G+ +++ AP++ A L+ +L K
Sbjct: 50 INGPAGTGATTLTKFIIEALISTGETGIILAAPTHAAKKILS-----------KLSGKEA 98
Query: 470 EAVSSPVEHLTLHYQVRHL-DTSEKSELHKLQQLKDEQGELSSSDEKKYKALKRATEREI 528
+ S ++ + Y+ L + E +L K + L + E+S D K +K L
Sbjct: 99 STIHSILKINPVTYEENVLFEQKEVPDLAKCRVLICD--EVSXYDRKLFKIL-------- 148
Query: 529 SQSADVICCTCVGAGDPR 546
S CT +G GD +
Sbjct: 149 -LSTIPPWCTIIGIGDNK 165
>pdb|3JVV|A Chain A, Crystal Structure Of P. Aeruginosa Pilt With Bound Amp-Pcp
pdb|3JVV|B Chain B, Crystal Structure Of P. Aeruginosa Pilt With Bound Amp-Pcp
pdb|3JVV|C Chain C, Crystal Structure Of P. Aeruginosa Pilt With Bound Amp-Pcp
pdb|3JVU|A Chain A, Crystal Structure Of Unliganded P. Aeruginosa Pilt
pdb|3JVU|B Chain B, Crystal Structure Of Unliganded P. Aeruginosa Pilt
pdb|3JVU|C Chain C, Crystal Structure Of Unliganded P. Aeruginosa Pilt
Length = 356
Score = 32.0 bits (71), Expect = 2.1, Method: Compositional matrix adjust.
Identities = 15/42 (35%), Positives = 26/42 (61%)
Query: 388 LPELNASQVFAVKSVLQRPISLIQGPPGTGKTVTSAAIVYHM 429
+ EL +VF S + R + L+ GP G+GK+ T AA++ ++
Sbjct: 106 MEELGMGEVFKRVSDVPRGLVLVTGPTGSGKSTTLAAMLDYL 147
>pdb|3KL4|A Chain A, Recognition Of A Signal Peptide By The Signal Recognition
Particle
Length = 433
Score = 32.0 bits (71), Expect = 2.1, Method: Compositional matrix adjust.
Identities = 26/93 (27%), Positives = 44/93 (47%), Gaps = 12/93 (12%)
Query: 372 VQMVRNTLPRRFGAPGLPELNASQVFAVKSVLQRP-ISLIQGPPGTGKTVTSAAIVYHMA 430
+ +V + L + FG P +N +++ P I ++ G G+GKT T+ + Y
Sbjct: 72 ISIVYDELSKLFGGDKEPNVNPTKL---------PFIIMLVGVQGSGKTTTAGKLAYFYK 122
Query: 431 KQGQGQVLVCAPSN--VAVDQLAEKISATGLKV 461
K+G LV A A DQL + + G++V
Sbjct: 123 KRGYKVGLVAADVYRPAAYDQLLQLGNQIGVQV 155
>pdb|1QZW|A Chain A, Crystal Structure Of The Complete Core Of Archaeal Srp And
Implications For Inter-Domain Communication
pdb|1QZW|C Chain C, Crystal Structure Of The Complete Core Of Archaeal Srp And
Implications For Inter-Domain Communication
pdb|1QZW|E Chain E, Crystal Structure Of The Complete Core Of Archaeal Srp And
Implications For Inter-Domain Communication
pdb|1QZW|G Chain G, Crystal Structure Of The Complete Core Of Archaeal Srp And
Implications For Inter-Domain Communication
pdb|1QZX|A Chain A, Crystal Structure Of The Complete Core Of Archaeal Srp And
Implications For Inter-Domain Communication
pdb|1QZX|B Chain B, Crystal Structure Of The Complete Core Of Archaeal Srp And
Implications For Inter-Domain Communication
Length = 440
Score = 31.6 bits (70), Expect = 2.2, Method: Compositional matrix adjust.
Identities = 26/93 (27%), Positives = 44/93 (47%), Gaps = 12/93 (12%)
Query: 372 VQMVRNTLPRRFGAPGLPELNASQVFAVKSVLQRP-ISLIQGPPGTGKTVTSAAIVYHMA 430
+ +V + L + FG P +N +++ P I ++ G G+GKT T+ + Y
Sbjct: 79 ISIVYDELSKLFGGDKEPNVNPTKL---------PFIIMLVGVQGSGKTTTAGKLAYFYK 129
Query: 431 KQGQGQVLVCAPSN--VAVDQLAEKISATGLKV 461
K+G LV A A DQL + + G++V
Sbjct: 130 KRGYKVGLVAADVYRPAAYDQLLQLGNQIGVQV 162
>pdb|2HXY|A Chain A, Crystal Structure Of Human Apo-Eif4aiii
pdb|2HXY|B Chain B, Crystal Structure Of Human Apo-Eif4aiii
pdb|2HXY|C Chain C, Crystal Structure Of Human Apo-Eif4aiii
pdb|2HXY|D Chain D, Crystal Structure Of Human Apo-Eif4aiii
Length = 391
Score = 30.8 bits (68), Expect = 3.9, Method: Compositional matrix adjust.
Identities = 25/86 (29%), Positives = 43/86 (50%), Gaps = 2/86 (2%)
Query: 375 VRNTLPRRFGAPGLPELNASQVFAVKSVLQRPISLIQGPPGTGKTVT-SAAIVYHMAKQ- 432
+R L R A G + +A Q A+K +++ + Q GTGKT T S +++ + Q
Sbjct: 23 LREDLLRGIYAYGFEKPSAIQQRAIKQIIKGRDVIAQSQSGTGKTATFSISVLQCLDIQV 82
Query: 433 GQGQVLVCAPSNVAVDQLAEKISATG 458
+ Q L+ AP+ Q+ + + A G
Sbjct: 83 RETQALILAPTRELAVQIQKGLLALG 108
>pdb|2HYI|C Chain C, Structure Of The Human Exon Junction Complex With A
Trapped Dead-Box Helicase Bound To Rna
pdb|2HYI|I Chain I, Structure Of The Human Exon Junction Complex With A
Trapped Dead-Box Helicase Bound To Rna
pdb|3EX7|C Chain C, The Crystal Structure Of Ejc In Its Transition State
pdb|3EX7|H Chain H, The Crystal Structure Of Ejc In Its Transition State
Length = 413
Score = 30.8 bits (68), Expect = 4.1, Method: Compositional matrix adjust.
Identities = 25/86 (29%), Positives = 43/86 (50%), Gaps = 2/86 (2%)
Query: 375 VRNTLPRRFGAPGLPELNASQVFAVKSVLQRPISLIQGPPGTGKTVT-SAAIVYHMAKQ- 432
+R L R A G + +A Q A+K +++ + Q GTGKT T S +++ + Q
Sbjct: 45 LREDLLRGIYAYGFEKPSAIQQRAIKQIIKGRDVIAQSQSGTGKTATFSISVLQCLDIQV 104
Query: 433 GQGQVLVCAPSNVAVDQLAEKISATG 458
+ Q L+ AP+ Q+ + + A G
Sbjct: 105 RETQALILAPTRELAVQIQKGLLALG 130
>pdb|2XB2|A Chain A, Crystal Structure Of The Core Mago-Y14-Eif4aiii-Barentsz-
Upf3b Assembly Shows How The Ejc Is Bridged To The Nmd
Machinery
pdb|2XB2|X Chain X, Crystal Structure Of The Core Mago-Y14-Eif4aiii-Barentsz-
Upf3b Assembly Shows How The Ejc Is Bridged To The Nmd
Machinery
Length = 411
Score = 30.8 bits (68), Expect = 4.2, Method: Compositional matrix adjust.
Identities = 25/86 (29%), Positives = 43/86 (50%), Gaps = 2/86 (2%)
Query: 375 VRNTLPRRFGAPGLPELNASQVFAVKSVLQRPISLIQGPPGTGKTVT-SAAIVYHMAKQ- 432
+R L R A G + +A Q A+K +++ + Q GTGKT T S +++ + Q
Sbjct: 45 LREDLLRGIYAYGFEKPSAIQQRAIKQIIKGRDVIAQSQSGTGKTATFSISVLQCLDIQV 104
Query: 433 GQGQVLVCAPSNVAVDQLAEKISATG 458
+ Q L+ AP+ Q+ + + A G
Sbjct: 105 RETQALILAPTRELAVQIQKGLLALG 130
>pdb|2J0Q|A Chain A, The Crystal Structure Of The Exon Junction Complex At 3.2
A Resolution
pdb|2J0Q|B Chain B, The Crystal Structure Of The Exon Junction Complex At 3.2
A Resolution
pdb|2J0S|A Chain A, The Crystal Structure Of The Exon Junction Complex At 2.2
A Resolution
Length = 410
Score = 30.8 bits (68), Expect = 4.3, Method: Compositional matrix adjust.
Identities = 25/86 (29%), Positives = 43/86 (50%), Gaps = 2/86 (2%)
Query: 375 VRNTLPRRFGAPGLPELNASQVFAVKSVLQRPISLIQGPPGTGKTVT-SAAIVYHMAKQ- 432
+R L R A G + +A Q A+K +++ + Q GTGKT T S +++ + Q
Sbjct: 44 LREDLLRGIYAYGFEKPSAIQQRAIKQIIKGRDVIAQSQSGTGKTATFSISVLQCLDIQV 103
Query: 433 GQGQVLVCAPSNVAVDQLAEKISATG 458
+ Q L+ AP+ Q+ + + A G
Sbjct: 104 RETQALILAPTRELAVQIQKGLLALG 129
>pdb|2J0U|A Chain A, The Crystal Structure Of Eif4aiii-Barentsz Complex At 3.0
A Resolution
Length = 374
Score = 30.8 bits (68), Expect = 4.4, Method: Compositional matrix adjust.
Identities = 25/86 (29%), Positives = 43/86 (50%), Gaps = 2/86 (2%)
Query: 375 VRNTLPRRFGAPGLPELNASQVFAVKSVLQRPISLIQGPPGTGKTVT-SAAIVYHMAKQ- 432
+R L R A G + +A Q A+K +++ + Q GTGKT T S +++ + Q
Sbjct: 8 LREDLLRGIYAYGFEKPSAIQQRAIKQIIKGRDVIAQSQSGTGKTATFSVSVLQCLDIQV 67
Query: 433 GQGQVLVCAPSNVAVDQLAEKISATG 458
+ Q L+ AP+ Q+ + + A G
Sbjct: 68 RETQALILAPTRELAVQVQKGLLALG 93
>pdb|2J0U|B Chain B, The Crystal Structure Of Eif4aiii-Barentsz Complex At 3.0
A Resolution
Length = 374
Score = 30.8 bits (68), Expect = 4.6, Method: Compositional matrix adjust.
Identities = 25/86 (29%), Positives = 43/86 (50%), Gaps = 2/86 (2%)
Query: 375 VRNTLPRRFGAPGLPELNASQVFAVKSVLQRPISLIQGPPGTGKTVT-SAAIVYHMAKQ- 432
+R L R A G + +A Q A+K +++ + Q GTGKT T S +++ + Q
Sbjct: 8 LREDLLRGIYAYGFEKPSAIQQRAIKQIIKGRDVIAQSQSGTGKTATFSVSVLQCLDIQV 67
Query: 433 GQGQVLVCAPSNVAVDQLAEKISATG 458
+ Q L+ AP+ Q+ + + A G
Sbjct: 68 RETQALILAPTRELAVQVQKGLLALG 93
>pdb|2DR3|A Chain A, Crystal Structure Of Reca Superfamily Atpase Ph0284 From
Pyrococcus Horikoshii Ot3
pdb|2DR3|B Chain B, Crystal Structure Of Reca Superfamily Atpase Ph0284 From
Pyrococcus Horikoshii Ot3
pdb|2DR3|C Chain C, Crystal Structure Of Reca Superfamily Atpase Ph0284 From
Pyrococcus Horikoshii Ot3
pdb|2DR3|D Chain D, Crystal Structure Of Reca Superfamily Atpase Ph0284 From
Pyrococcus Horikoshii Ot3
pdb|2DR3|E Chain E, Crystal Structure Of Reca Superfamily Atpase Ph0284 From
Pyrococcus Horikoshii Ot3
pdb|2DR3|F Chain F, Crystal Structure Of Reca Superfamily Atpase Ph0284 From
Pyrococcus Horikoshii Ot3
Length = 247
Score = 30.4 bits (67), Expect = 5.6, Method: Compositional matrix adjust.
Identities = 17/57 (29%), Positives = 29/57 (50%), Gaps = 6/57 (10%)
Query: 384 GAPGLPELNASQVFAVKSVLQRPISLIQGPPGTGKTVTSAAIVYHMAKQGQGQVLVC 440
G PG+ E+ + +R + L+ G PGTGKT+ S +++ K G+ + V
Sbjct: 8 GIPGVDEILHG------GIPERNVVLLSGGPGTGKTIFSQQFLWNGLKMGEPGIYVA 58
>pdb|3NDB|B Chain B, Crystal Structure Of A Signal Sequence Bound To The Signal
Recognition Particle
Length = 454
Score = 29.6 bits (65), Expect = 9.9, Method: Compositional matrix adjust.
Identities = 18/53 (33%), Positives = 29/53 (54%), Gaps = 5/53 (9%)
Query: 407 ISLIQGPPGTGKTVTSAAIVYHMAKQGQGQVLVCA-----PSNVAVDQLAEKI 454
+ L+ G G+GKT T+A + ++ K+G L+ A + + QLAEKI
Sbjct: 101 VILLVGIQGSGKTTTAAKLARYIQKRGLKPALIAADTYRPAAYEQLKQLAEKI 153
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
0.318 0.134 0.404
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 30,645,531
Number of Sequences: 62578
Number of extensions: 1277712
Number of successful extensions: 3020
Number of sequences better than 100.0: 39
Number of HSP's better than 100.0 without gapping: 11
Number of HSP's successfully gapped in prelim test: 28
Number of HSP's that attempted gapping in prelim test: 2968
Number of HSP's gapped (non-prelim): 44
length of query: 1066
length of database: 14,973,337
effective HSP length: 109
effective length of query: 957
effective length of database: 8,152,335
effective search space: 7801784595
effective search space used: 7801784595
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 57 (26.6 bits)