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= 002849
(874 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 = 194 bits (492), Expect = 2e-49, Method: Compositional matrix adjust.
Identities = 153/457 (33%), Positives = 218/457 (47%), Gaps = 76/457 (16%)
Query: 390 NLNEEQMCSIEKILGLKGAPPYLIYGPPGTGKTMTLVEAILQLYATREDARLLVCAPSNS 449
+LN Q+ +++ +L P LI GPPGTGKT+T + L A + + +LVCAPSN
Sbjct: 180 DLNHSQVYAVKTVLQ---RPLSLIQGPPGTGKTVTSATIVYHL-ARQGNGPVLVCAPSNI 235
Query: 450 AADHLLEKI--LGEKAVEVRENEIFRLNAPSRPYEDVNADHIRFCFFDEQIFKC---PPL 504
A D L EKI G K V RL A SR D + F QI P L
Sbjct: 236 AVDQLTEKIHQTGLKVV--------RLCAKSREAID---SPVSFLALHNQIRNMDSMPEL 284
Query: 505 AALVC---------------YRIIIST-----YMSASLIYAEGVDRG-------HFSHIF 537
L YR + T M+A +I V G F I
Sbjct: 285 QKLQQLKDETGELSSADEKRYRALKRTAERELLMNADVICCTCVGAGDPRLAKMQFRSIL 344
Query: 538 LDEAGQASEPESMVPISSYCKKDTVVVLAGDPMQLGPVIYSREAETYGMGKSYLERL--F 595
+DE+ QA+EPE MVP+ K+ ++L GD QLGPV+ ++A G+ +S ERL
Sbjct: 345 IDESTQATEPECMVPVVLGAKQ---LILVGDHCQLGPVVMCKKAAKAGLSQSLFERLVVL 401
Query: 596 ECEPYCHGNENYVTKLVRNYRSHPQILHLPSKLFYEEELIACKDESISCTAYLNF-LPNK 654
P +L YR HP + PS +FYE L + +F P
Sbjct: 402 GIRP---------IRLQVQYRMHPALSAFPSNIFYEGSLQNGVTAADRVKKGFDFQWPQP 452
Query: 655 EFPVLFFGIQGCDEREGSNPSWFNRIEVSKVVEIIQKLTSTGNLSEEDIGVITPYRQQ-- 712
+ P+ F+ QG +E S S+ NR E + V +I KL G ++ IG+ITPY Q
Sbjct: 453 DKPMFFYVTQGQEEIASSGTSYLNRTEAANVEKITTKLLKAGAKPDQ-IGIITPYEGQRS 511
Query: 713 ----VLKLNKALESLYMPDIKVGSVEQFQGQERQVIIVSTVRSTIKHNDFDRKHCLGFLS 768
++ + +L + ++++ SV+ FQG+E+ II+S VR+ + +GFL+
Sbjct: 512 YLVQYMQFSGSLHTKLYQEVEIASVDAFQGREKDFIILSCVRA-------NEHQGIGFLN 564
Query: 769 NPRRFNVAVTRAISLLIIIGNPHIVSKDPYWHQLLWY 805
+PRR NVA+TRA +II+GNP +SK P W+ LL Y
Sbjct: 565 DPRRLNVALTRARYGVIIVGNPKALSKQPLWNHLLNY 601
>pdb|2XZO|A Chain A, Upf1 Helicase - Rna Complex
pdb|2XZP|A Chain A, Upf1 Helicase
Length = 623
Score = 194 bits (492), Expect = 2e-49, Method: Compositional matrix adjust.
Identities = 153/457 (33%), Positives = 218/457 (47%), Gaps = 76/457 (16%)
Query: 390 NLNEEQMCSIEKILGLKGAPPYLIYGPPGTGKTMTLVEAILQLYATREDARLLVCAPSNS 449
+LN Q+ +++ +L P LI GPPGTGKT+T + L A + + +LVCAPSN
Sbjct: 179 DLNHSQVYAVKTVLQ---RPLSLIQGPPGTGKTVTSATIVYHL-ARQGNGPVLVCAPSNI 234
Query: 450 AADHLLEKI--LGEKAVEVRENEIFRLNAPSRPYEDVNADHIRFCFFDEQIFKC---PPL 504
A D L EKI G K V RL A SR D + F QI P L
Sbjct: 235 AVDQLTEKIHQTGLKVV--------RLCAKSREAID---SPVSFLALHNQIRNMDSMPEL 283
Query: 505 AALVC---------------YRIIIST-----YMSASLIYAEGVDRG-------HFSHIF 537
L YR + T M+A +I V G F I
Sbjct: 284 QKLQQLKDETGELSSADEKRYRALKRTAERELLMNADVICCTCVGAGDPRLAKMQFRSIL 343
Query: 538 LDEAGQASEPESMVPISSYCKKDTVVVLAGDPMQLGPVIYSREAETYGMGKSYLERL--F 595
+DE+ QA+EPE MVP+ K+ ++L GD QLGPV+ ++A G+ +S ERL
Sbjct: 344 IDESTQATEPECMVPVVLGAKQ---LILVGDHCQLGPVVMCKKAAKAGLSQSLFERLVVL 400
Query: 596 ECEPYCHGNENYVTKLVRNYRSHPQILHLPSKLFYEEELIACKDESISCTAYLNF-LPNK 654
P +L YR HP + PS +FYE L + +F P
Sbjct: 401 GIRP---------IRLQVQYRMHPALSAFPSNIFYEGSLQNGVTAADRVKKGFDFQWPQP 451
Query: 655 EFPVLFFGIQGCDEREGSNPSWFNRIEVSKVVEIIQKLTSTGNLSEEDIGVITPYRQQ-- 712
+ P+ F+ QG +E S S+ NR E + V +I KL G ++ IG+ITPY Q
Sbjct: 452 DKPMFFYVTQGQEEIASSGTSYLNRTEAANVEKITTKLLKAGAKPDQ-IGIITPYEGQRS 510
Query: 713 ----VLKLNKALESLYMPDIKVGSVEQFQGQERQVIIVSTVRSTIKHNDFDRKHCLGFLS 768
++ + +L + ++++ SV+ FQG+E+ II+S VR+ + +GFL+
Sbjct: 511 YLVQYMQFSGSLHTKLYQEVEIASVDAFQGREKDFIILSCVRA-------NEHQGIGFLN 563
Query: 769 NPRRFNVAVTRAISLLIIIGNPHIVSKDPYWHQLLWY 805
+PRR NVA+TRA +II+GNP +SK P W+ LL Y
Sbjct: 564 DPRRLNVALTRARYGVIIVGNPKALSKQPLWNHLLNY 600
>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 = 192 bits (489), Expect = 6e-49, Method: Compositional matrix adjust.
Identities = 153/457 (33%), Positives = 218/457 (47%), Gaps = 76/457 (16%)
Query: 390 NLNEEQMCSIEKILGLKGAPPYLIYGPPGTGKTMTLVEAILQLYATREDARLLVCAPSNS 449
+LN Q+ +++ +L P LI GPPGTGKT+T + L A + + +LVCAPSN
Sbjct: 356 DLNHSQVYAVKTVLQ---RPLSLIQGPPGTGKTVTSATIVYHL-ARQGNGPVLVCAPSNI 411
Query: 450 AADHLLEKI--LGEKAVEVRENEIFRLNAPSRPYEDVNADHIRFCFFDEQIFKC---PPL 504
A D L EKI G K V RL A SR D + F QI P L
Sbjct: 412 AVDQLTEKIHQTGLKVV--------RLCAKSREAID---SPVSFLALHNQIRNMDSMPEL 460
Query: 505 AALVC---------------YRIIIST-----YMSASLIYAEGVDRG-------HFSHIF 537
L YR + T M+A +I V G F I
Sbjct: 461 QKLQQLKDETGELSSADEKRYRALKRTAERELLMNADVICCTCVGAGDPRLAKMQFRSIL 520
Query: 538 LDEAGQASEPESMVPISSYCKKDTVVVLAGDPMQLGPVIYSREAETYGMGKSYLERL--F 595
+DE+ QA+EPE MVP+ K+ ++L GD QLGPV+ ++A G+ +S ERL
Sbjct: 521 IDESTQATEPECMVPVVLGAKQ---LILVGDHCQLGPVVMCKKAAKAGLSQSLFERLVVL 577
Query: 596 ECEPYCHGNENYVTKLVRNYRSHPQILHLPSKLFYEEELIACKDESISCTAYLNF-LPNK 654
P +L YR HP + PS +FYE L + +F P
Sbjct: 578 GIRP---------IRLQVQYRMHPALSAFPSNIFYEGSLQNGVTAADRVKKGFDFQWPQP 628
Query: 655 EFPVLFFGIQGCDEREGSNPSWFNRIEVSKVVEIIQKLTSTGNLSEEDIGVITPYRQQ-- 712
+ P+ F+ QG +E S S+ NR E + V +I KL G ++ IG+ITPY Q
Sbjct: 629 DKPMFFYVTQGQEEIASSGTSYLNRTEAANVEKITTKLLKAGAKPDQ-IGIITPYEGQRS 687
Query: 713 ----VLKLNKALESLYMPDIKVGSVEQFQGQERQVIIVSTVRSTIKHNDFDRKHCLGFLS 768
++ + +L + ++++ SV+ FQG+E+ II+S VR+ + +GFL+
Sbjct: 688 YLVQYMQFSGSLHTKLYQEVEIASVDAFQGREKDFIILSCVRA-------NEHQGIGFLN 740
Query: 769 NPRRFNVAVTRAISLLIIIGNPHIVSKDPYWHQLLWY 805
+PRR NVA+TRA +II+GNP +SK P W+ LL Y
Sbjct: 741 DPRRLNVALTRARYGVIIVGNPKALSKQPLWNHLLNY 777
>pdb|2XZL|A Chain A, Upf1-Rna Complex
Length = 802
Score = 187 bits (476), Expect = 2e-47, Method: Compositional matrix adjust.
Identities = 150/461 (32%), Positives = 215/461 (46%), Gaps = 80/461 (17%)
Query: 385 VPISCNLNEEQMCSIEKILGLKGAPPYLIYGPPGTGKTMTLVEAILQLYATREDARLLVC 444
+P LN Q ++ +L P LI GPPGTGKT+T + L +D R+LVC
Sbjct: 355 IPNFAQLNSSQSNAVSHVLQ---RPLSLIQGPPGTGKTVTSATIVYHLSKIHKD-RILVC 410
Query: 445 APSNSAADHLLEKI--LGEKAVEVRENEIFRLNAPSRPYEDVNADHIRFCFFD------- 495
APSN A DHL K+ LG K V RL A SR EDV + +
Sbjct: 411 APSNVAVDHLAAKLRDLGLKVV--------RLTAKSR--EDVESSVSNLALHNLVGRGAK 460
Query: 496 ---EQIFKCP----PLAALVCYRII-------ISTYMSASLIYAEGVDRG------HFSH 535
+ + K L+A R + A ++ V G F
Sbjct: 461 GELKNLLKLKDEVGELSASDTKRFVKLVRKTEAEILNKADVVCCTCVGAGDKRLDTKFRT 520
Query: 536 IFLDEAGQASEPESMVPISSYCKKDTVVVLAGDPMQLGPVIYSREAETYGMGKSYLERLF 595
+ +DE+ QASEPE ++PI K+ V+L GD QLGPVI R+A G+ +S ERL
Sbjct: 521 VLIDESTQASEPECLIPIVKGAKQ---VILVGDHQQLGPVILERKAADAGLKQSLFERLI 577
Query: 596 ECEPYCHGNENYVTKLVRNYRSHPQILHLPSKLFYEEELIACKDESISCTAYLNFLPNKE 655
+ +L YR +P + PS +FYE L T +PN +
Sbjct: 578 SLG-------HVPIRLEVQYRMNPYLSEFPSNMFYEGSL------QNGVTIEQRTVPNSK 624
Query: 656 FP-------VLFFGIQGCDEREGSNPSWFNRIEVSKVVEIIQKLTSTGNLSEEDIGVITP 708
FP ++F+ G +E + S+ NRIE II KL G + E IGVITP
Sbjct: 625 FPWPIRGIPMMFWANYGREEISANGTSFLNRIEAMNCERIITKLFRDG-VKPEQIGVITP 683
Query: 709 YRQQ------VLKLNKALESLYMPDIKVGSVEQFQGQERQVIIVSTVRSTIKHNDFDRKH 762
Y Q +++N +L+ ++V SV+ FQG+E+ II+S VR+ + +
Sbjct: 684 YEGQRAYILQYMQMNGSLDKDLYIKVEVASVDAFQGREKDYIILSCVRA-------NEQQ 736
Query: 763 CLGFLSNPRRFNVAVTRAISLLIIIGNPHIVSKDPYWHQLL 803
+GFL +PRR NV +TRA L+I+GNP ++++ W+ LL
Sbjct: 737 AIGFLRDPRRLNVGLTRAKYGLVILGNPRSLARNTLWNHLL 777
>pdb|4B3F|X Chain X, Crystal Structure Of 1ghmbp2 Helicase
Length = 646
Score = 166 bits (419), Expect = 7e-41, Method: Compositional matrix adjust.
Identities = 178/623 (28%), Positives = 263/623 (42%), Gaps = 127/623 (20%)
Query: 266 NVTLMRKGLYLSLVVP------GLAERRPS--LVNGDFIFAKHAYEDTSSAYQGFIHRVE 317
V+ R GLY L+V G A PS +GD + A + S G + RV
Sbjct: 49 QVSSQRTGLYGRLLVTFEPRRYGSAAALPSNSFTSGDIVGLYDAANEGSQLATGILTRVT 108
Query: 318 ADEVHLKF--ASDFQLNHRDENLYNVQFTYNRVNMRRLYQATDAAQELDT-------EFL 368
V + F + DFQL+ EN Y + N V RRL +A A ++ + E L
Sbjct: 109 QKSVTVAFDESHDFQLSLDRENSYRLLKLANDVTYRRLKKALIALKKYHSGPASSLIEVL 168
Query: 369 F----PSESSGIRLIESNTLVPISCNLNEEQMCSIEKILGLKGAPPYLIYGPPGTGKTMT 424
F PS +S I + L + L+ Q ++ + L +I+GPPGTGKT T
Sbjct: 169 FGRSAPSPASEI-----HPLTFFNTCLDTSQKEAV--LFALSQKELAIIHGPPGTGKTTT 221
Query: 425 LVEAILQLYATREDARLLVCAPSNSAADHLLEKILGEKAVEVRENEIFRLNAPSRPYEDV 484
+VE ILQ A ++ ++L CAPSN A D+L+E++ + + I RL P+R E +
Sbjct: 222 VVEIILQ--AVKQGLKVLCCAPSNIAVDNLVERL------ALCKQRILRLGHPARLLESI 273
Query: 485 NADHIRFCFFD--------------EQIF------------------------------K 500
+ +Q+F +
Sbjct: 274 QQHSLDAVLARSDSAQIVADIRKDIDQVFVKNKKTQDKREKSNFRNEIKLLRKELKEREE 333
Query: 501 CPPLAALVCYRIIISTYMSASLIYAEG----VDRGHFSHIFLDEAGQASEPESMVPISSY 556
L +L ++++T AS A+G + +F + +DE QA E +P+
Sbjct: 334 AAMLESLTSANVVLATNTGAS---ADGPLKLLPESYFDVVVIDECAQALEASCWIPLLKA 390
Query: 557 CKKDTVVVLAGDPMQLGPVIYSREAETYGMGKSYLERLFECEPYCHGNENYVTKLVRNYR 616
K +LAGD QL P S +A G+ S +ERL E Y V L YR
Sbjct: 391 RK----CILAGDHKQLPPTTVSHKAALAGLSLSLMERL--AEEY---GARVVRTLTVQYR 441
Query: 617 SHPQILHLPSKLFYEEELIACKDESISCTAYLNFLPN------KEFPVLFFGIQGC---- 666
H I+ S Y +L A S L LP P+L GC
Sbjct: 442 MHQAIMRWASDTMYLGQLTA---HSSVARHLLRDLPGVAATEETGVPLLLVDTAGCGLFE 498
Query: 667 ----DEREGSNPSWFNRIEVSKVVEIIQKLTSTGNLSEEDIGVITPYRQQVLKLNKALES 722
DE+ NP EV V IQ L G + DI V++PY QV L ++L
Sbjct: 499 LEEEDEQSKGNPG-----EVRLVSLHIQALVDAG-VPARDIAVVSPYNLQVDLLRQSLVH 552
Query: 723 LYMPDIKVGSVEQFQGQERQVIIVSTVRSTIKHNDFDRKHCLGFLSNPRRFNVAVTRAIS 782
+ P++++ SV+ FQG+E++ +I+S VRS +RK +GFL+ RR NVAVTRA
Sbjct: 553 RH-PELEIKSVDGFQGREKEAVILSFVRS-------NRKGEVGFLAEDRRINVAVTRARR 604
Query: 783 LLIIIGNPHIVSKDPYWHQLLWY 805
+ +I + V+ + L+ Y
Sbjct: 605 HVAVICDSRTVNNHAFLKTLVEY 627
>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 = 163 bits (412), Expect = 4e-40, Method: Compositional matrix adjust.
Identities = 177/623 (28%), Positives = 262/623 (42%), Gaps = 127/623 (20%)
Query: 266 NVTLMRKGLYLSLVVP------GLAERRPS--LVNGDFIFAKHAYEDTSSAYQGFIHRVE 317
V+ R GLY L+V G A PS +GD + A + S G + RV
Sbjct: 49 QVSSQRTGLYGRLLVTFEPRRYGSAAALPSNSFTSGDIVGLYDAANEGSQLATGILTRVT 108
Query: 318 ADEVHLKF--ASDFQLNHRDENLYNVQFTYNRVNMRRLYQATDAAQELDT-------EFL 368
V + F + DFQ + EN Y + N V RRL +A A ++ + E L
Sbjct: 109 QKSVTVAFDESHDFQQSLDRENSYRLLKLANDVTYRRLKKALIALKKYHSGPASSLIEVL 168
Query: 369 F----PSESSGIRLIESNTLVPISCNLNEEQMCSIEKILGLKGAPPYLIYGPPGTGKTMT 424
F PS +S I + L + L+ Q ++ + L +I+GPPGTGKT T
Sbjct: 169 FGRSAPSPASEI-----HPLTFFNTCLDTSQKEAV--LFALSQKELAIIHGPPGTGKTTT 221
Query: 425 LVEAILQLYATREDARLLVCAPSNSAADHLLEKILGEKAVEVRENEIFRLNAPSRPYEDV 484
+VE ILQ A ++ ++L CAPSN A D+L+E++ + + I RL P+R E +
Sbjct: 222 VVEIILQ--AVKQGLKVLCCAPSNIAVDNLVERL------ALCKQRILRLGHPARLLESI 273
Query: 485 NADHIRFCFFD--------------EQIF------------------------------K 500
+ +Q+F +
Sbjct: 274 QQHSLDAVLARSDSAQIVADIRKDIDQVFVKNKKTQDKREKSNFRNEIKLLRKELKEREE 333
Query: 501 CPPLAALVCYRIIISTYMSASLIYAEG----VDRGHFSHIFLDEAGQASEPESMVPISSY 556
L +L ++++T AS A+G + +F + +DE QA E +P+
Sbjct: 334 AAMLESLTSANVVLATNTGAS---ADGPLKLLPESYFDVVVIDECAQALEASCWIPLLKA 390
Query: 557 CKKDTVVVLAGDPMQLGPVIYSREAETYGMGKSYLERLFECEPYCHGNENYVTKLVRNYR 616
K +LAGD QL P S +A G+ S +ERL E Y V L YR
Sbjct: 391 RK----CILAGDHKQLPPTTVSHKAALAGLSLSLMERL--AEEY---GARVVRTLTVQYR 441
Query: 617 SHPQILHLPSKLFYEEELIACKDESISCTAYLNFLPN------KEFPVLFFGIQGC---- 666
H I+ S Y +L A S L LP P+L GC
Sbjct: 442 MHQAIMRWASDTMYLGQLTA---HSSVARHLLRDLPGVAATEETGVPLLLVDTAGCGLFE 498
Query: 667 ----DEREGSNPSWFNRIEVSKVVEIIQKLTSTGNLSEEDIGVITPYRQQVLKLNKALES 722
DE+ NP EV V IQ L G + DI V++PY QV L ++L
Sbjct: 499 LEEEDEQSKGNPG-----EVRLVSLHIQALVDAG-VPARDIAVVSPYNLQVDLLRQSLVH 552
Query: 723 LYMPDIKVGSVEQFQGQERQVIIVSTVRSTIKHNDFDRKHCLGFLSNPRRFNVAVTRAIS 782
+ P++++ SV+ FQG+E++ +I+S VRS +RK +GFL+ RR NVAVTRA
Sbjct: 553 RH-PELEIKSVDGFQGREKEAVILSFVRS-------NRKGEVGFLAEDRRINVAVTRARR 604
Query: 783 LLIIIGNPHIVSKDPYWHQLLWY 805
+ +I + V+ + L+ Y
Sbjct: 605 HVAVICDSRTVNNHAFLKTLVEY 627
>pdb|4B4T|K Chain K, Near-Atomic Resolution Structural Model Of The Yeast 26s
Proteasome
Length = 428
Score = 39.3 bits (90), Expect = 0.010, Method: Compositional matrix adjust.
Identities = 38/94 (40%), Positives = 46/94 (48%), Gaps = 18/94 (19%)
Query: 409 PP--YLIYGPPGTGKTMTLVEAILQLYATREDARLLVCAPSNSAADHLLEKILGEKAVEV 466
PP L+YGPPGTGKTM LV+A+ A A + S + K LGE V
Sbjct: 205 PPRGVLLYGPPGTGKTM-LVKAV----ANSTKAAFIRVNGS-----EFVHKYLGEGPRMV 254
Query: 467 RENEIFRL---NAPSRPYEDVNADHIRFCFFDEQ 497
R ++FRL NAPS + D D I FD Q
Sbjct: 255 R--DVFRLARENAPSIIFID-EVDSIATKRFDAQ 285
>pdb|1SXJ|D Chain D, Crystal Structure Of The Eukaryotic Clamp Loader
(Replication Factor C, Rfc) Bound To The Dna Sliding
Clamp (Proliferating Cell Nuclear Antigen, Pcna)
Length = 353
Score = 36.6 bits (83), Expect = 0.059, Method: Compositional matrix adjust.
Identities = 16/36 (44%), Positives = 21/36 (58%)
Query: 399 IEKILGLKGAPPYLIYGPPGTGKTMTLVEAILQLYA 434
++K L P L YGPPGTGKT T++ +LY
Sbjct: 49 LKKTLKSANLPHMLFYGPPGTGKTSTILALTKELYG 84
>pdb|1SXJ|C Chain C, Crystal Structure Of The Eukaryotic Clamp Loader
(Replication Factor C, Rfc) Bound To The Dna Sliding
Clamp (Proliferating Cell Nuclear Antigen, Pcna)
Length = 340
Score = 36.6 bits (83), Expect = 0.063, Method: Compositional matrix adjust.
Identities = 16/41 (39%), Positives = 23/41 (56%)
Query: 394 EQMCSIEKILGLKGAPPYLIYGPPGTGKTMTLVEAILQLYA 434
E + ++ K + P L YGPPGTGKT T+V ++Y
Sbjct: 32 EVITTVRKFVDEGKLPHLLFYGPPGTGKTSTIVALAREIYG 72
>pdb|4B4T|H Chain H, Near-Atomic Resolution Structural Model Of The Yeast 26s
Proteasome
Length = 467
Score = 36.6 bits (83), Expect = 0.068, Method: Compositional matrix adjust.
Identities = 25/66 (37%), Positives = 33/66 (50%), Gaps = 10/66 (15%)
Query: 403 LGLKGAPPYLIYGPPGTGKTMTLVEAILQLYATREDARLLVCAPSNSAADHLLEKILGEK 462
LG+ L+YGPPGTGKT+ + A R DA + S L++K +GE
Sbjct: 238 LGIDPPKGILLYGPPGTGKTLC-----ARAVANRTDATFIRVIGS-----ELVQKYVGEG 287
Query: 463 AVEVRE 468
A VRE
Sbjct: 288 ARMVRE 293
>pdb|4B4T|M Chain M, Near-Atomic Resolution Structural Model Of The Yeast 26s
Proteasome
Length = 434
Score = 36.2 bits (82), Expect = 0.084, Method: Compositional matrix adjust.
Identities = 24/68 (35%), Positives = 34/68 (50%), Gaps = 10/68 (14%)
Query: 401 KILGLKGAPPYLIYGPPGTGKTMTLVEAILQLYATREDARLLVCAPSNSAADHLLEKILG 460
K +G++ L+YGPPGTGKT+ Q AT L + AP L++ +G
Sbjct: 208 KDMGIRAPKGALMYGPPGTGKTLLARACAAQTNAT----FLKLAAP------QLVQMYIG 257
Query: 461 EKAVEVRE 468
E A VR+
Sbjct: 258 EGAKLVRD 265
>pdb|3H4M|A Chain A, Aaa Atpase Domain Of The Proteasome- Activating
Nucleotidase
pdb|3H4M|B Chain B, Aaa Atpase Domain Of The Proteasome- Activating
Nucleotidase
pdb|3H4M|C Chain C, Aaa Atpase Domain Of The Proteasome- Activating
Nucleotidase
Length = 285
Score = 36.2 bits (82), Expect = 0.091, Method: Composition-based stats.
Identities = 28/74 (37%), Positives = 40/74 (54%), Gaps = 14/74 (18%)
Query: 409 PP--YLIYGPPGTGKTMTLVEAILQLYATREDARLLVCAPSNSAADHLLEKILGEKAVEV 466
PP L+YGPPGTGKT+ L +A+ AT +A + S L++K +GE A V
Sbjct: 50 PPKGILLYGPPGTGKTL-LAKAV----ATETNATFIRVVGS-----ELVKKFIGEGASLV 99
Query: 467 RENEIFRLNAPSRP 480
+ +IF+L P
Sbjct: 100 K--DIFKLAKEKAP 111
>pdb|4B4T|L Chain L, Near-Atomic Resolution Structural Model Of The Yeast 26s
Proteasome
Length = 437
Score = 34.7 bits (78), Expect = 0.26, Method: Compositional matrix adjust.
Identities = 22/66 (33%), Positives = 34/66 (51%), Gaps = 10/66 (15%)
Query: 403 LGLKGAPPYLIYGPPGTGKTMTLVEAILQLYATREDARLLVCAPSNSAADHLLEKILGEK 462
+G+K L+YGPPGTGKT+ L +A+ + +P++ D K +GE
Sbjct: 210 VGIKPPKGVLLYGPPGTGKTL-LAKAVAATIGAN-----FIFSPASGIVD----KYIGES 259
Query: 463 AVEVRE 468
A +RE
Sbjct: 260 ARIIRE 265
>pdb|4B4T|J Chain J, Near-Atomic Resolution Structural Model Of The Yeast 26s
Proteasome
Length = 405
Score = 34.3 bits (77), Expect = 0.28, Method: Compositional matrix adjust.
Identities = 28/82 (34%), Positives = 41/82 (50%), Gaps = 11/82 (13%)
Query: 403 LGLKGAPPYLIYGPPGTGKTMTLVEAILQLYATREDARLLVCAPSNSAADHLLEKILGEK 462
LG+ ++YGPPGTGKT+ L A+ A D C + L++K +GE
Sbjct: 177 LGIAQPKGVILYGPPGTGKTL-LARAV----AHHTD-----CKFIRVSGAELVQKYIGEG 226
Query: 463 AVEVRENEIF-RLNAPSRPYED 483
+ VRE + R +APS + D
Sbjct: 227 SRMVRELFVMAREHAPSIIFMD 248
>pdb|2WBK|A Chain A, Structure Of The Michaelis Complex Of Beta-Mannosidase,
Man2a, Provides Insight Into The Conformational
Itinerary Of Mannoside Hydrolysis
pdb|2WBK|B Chain B, Structure Of The Michaelis Complex Of Beta-Mannosidase,
Man2a, Provides Insight Into The Conformational
Itinerary Of Mannoside Hydrolysis
Length = 847
Score = 32.7 bits (73), Expect = 0.92, Method: Compositional matrix adjust.
Identities = 26/94 (27%), Positives = 42/94 (44%), Gaps = 16/94 (17%)
Query: 229 DAITDGLTLKNYTSFFKTLLIMEEIQLKEDMRAYDMENVTLMRKGLYLSLVVPGLAERRP 288
DA+ +T + Y + F+ DM+ +M V + G Y + + LA+
Sbjct: 341 DALLPNVTTERYQTLFR------------DMKEANMNMVRIWGGGTYENNLFYDLADENG 388
Query: 289 SLVNGDFIFAKHAYEDTSSAYQGFIHRVEADEVH 322
LV DF+FA Y + F+ RVEA+ V+
Sbjct: 389 ILVWQDFMFACTPYPSDPT----FLKRVEAEAVY 418
>pdb|2VQU|A Chain A, Structural And Biochemical Evidence For A Boat-Like
Transition State In Beta-Mannosidases
pdb|2VQU|B Chain B, Structural And Biochemical Evidence For A Boat-Like
Transition State In Beta-Mannosidases
Length = 846
Score = 32.7 bits (73), Expect = 0.94, Method: Compositional matrix adjust.
Identities = 26/94 (27%), Positives = 42/94 (44%), Gaps = 16/94 (17%)
Query: 229 DAITDGLTLKNYTSFFKTLLIMEEIQLKEDMRAYDMENVTLMRKGLYLSLVVPGLAERRP 288
DA+ +T + Y + F+ DM+ +M V + G Y + + LA+
Sbjct: 341 DALLPNVTTERYQTLFR------------DMKEANMNMVRIWGGGTYENNLFYDLADENG 388
Query: 289 SLVNGDFIFAKHAYEDTSSAYQGFIHRVEADEVH 322
LV DF+FA Y + F+ RVEA+ V+
Sbjct: 389 ILVWQDFMFACTPYPSDPT----FLKRVEAEAVY 418
>pdb|2VJX|A Chain A, Structural And Biochemical Evidence For A Boat-Like
Transition State In Beta-Mannosidases
pdb|2VJX|B Chain B, Structural And Biochemical Evidence For A Boat-Like
Transition State In Beta-Mannosidases
pdb|2VL4|A Chain A, Structural And Biochemical Evidence For A Boat-Like
Transition State In Beta-Mannosidases
pdb|2VL4|B Chain B, Structural And Biochemical Evidence For A Boat-Like
Transition State In Beta-Mannosidases
pdb|2VMF|A Chain A, Structural And Biochemical Evidence For A Boat-Like
Transition State In Beta-Mannosidases
pdb|2VMF|B Chain B, Structural And Biochemical Evidence For A Boat-Like
Transition State In Beta-Mannosidases
pdb|2VO5|A Chain A, Structural And Biochemical Evidence For A Boat-Like
Transition State In Beta-Mannosidases
pdb|2VO5|B Chain B, Structural And Biochemical Evidence For A Boat-Like
Transition State In Beta-Mannosidases
pdb|2VOT|A Chain A, Structural And Biochemical Evidence For A Boat-like
Transition State In Beta-mannosidases
pdb|2VOT|B Chain B, Structural And Biochemical Evidence For A Boat-like
Transition State In Beta-mannosidases
pdb|2VQT|A Chain A, Structural And Biochemical Evidence For A Boat-Like
Transition State In Beta-Mannosidases
pdb|2VQT|B Chain B, Structural And Biochemical Evidence For A Boat-Like
Transition State In Beta-Mannosidases
pdb|2VR4|A Chain A, Transition-state Mimicry In Mannoside Hydrolysis:
Characterisation Of Twenty Six Inhibitors And Insight
Into Binding From Linear Free Energy Relationships And
3-d Structure
pdb|2VR4|B Chain B, Transition-state Mimicry In Mannoside Hydrolysis:
Characterisation Of Twenty Six Inhibitors And Insight
Into Binding From Linear Free Energy Relationships And
3-d Structure
Length = 846
Score = 32.7 bits (73), Expect = 0.95, Method: Compositional matrix adjust.
Identities = 26/94 (27%), Positives = 42/94 (44%), Gaps = 16/94 (17%)
Query: 229 DAITDGLTLKNYTSFFKTLLIMEEIQLKEDMRAYDMENVTLMRKGLYLSLVVPGLAERRP 288
DA+ +T + Y + F+ DM+ +M V + G Y + + LA+
Sbjct: 341 DALLPNVTTERYQTLFR------------DMKEANMNMVRIWGGGTYENNLFYDLADENG 388
Query: 289 SLVNGDFIFAKHAYEDTSSAYQGFIHRVEADEVH 322
LV DF+FA Y + F+ RVEA+ V+
Sbjct: 389 ILVWQDFMFACTPYPSDPT----FLKRVEAEAVY 418
>pdb|2JE8|A Chain A, Structure Of A Beta-Mannosidase From Bacteroides
Thetaiotaomicron
pdb|2JE8|B Chain B, Structure Of A Beta-Mannosidase From Bacteroides
Thetaiotaomicron
Length = 848
Score = 32.7 bits (73), Expect = 0.95, Method: Compositional matrix adjust.
Identities = 26/94 (27%), Positives = 42/94 (44%), Gaps = 16/94 (17%)
Query: 229 DAITDGLTLKNYTSFFKTLLIMEEIQLKEDMRAYDMENVTLMRKGLYLSLVVPGLAERRP 288
DA+ +T + Y + F+ DM+ +M V + G Y + + LA+
Sbjct: 343 DALLPNVTTERYQTLFR------------DMKEANMNMVRIWGGGTYENNLFYDLADENG 390
Query: 289 SLVNGDFIFAKHAYEDTSSAYQGFIHRVEADEVH 322
LV DF+FA Y + F+ RVEA+ V+
Sbjct: 391 ILVWQDFMFACTPYPSDPT----FLKRVEAEAVY 420
>pdb|1R7R|A Chain A, The Crystal Structure Of Murine P97VCP AT 3.6A
Length = 816
Score = 32.7 bits (73), Expect = 1.0, Method: Compositional matrix adjust.
Identities = 13/23 (56%), Positives = 17/23 (73%)
Query: 401 KILGLKGAPPYLIYGPPGTGKTM 423
K +G+K L+YGPPGTGKT+
Sbjct: 231 KAIGVKPPRGILLYGPPGTGKTL 253
>pdb|3CF1|A Chain A, Structure Of P97VCP IN COMPLEX WITH ADPADP.ALFX
pdb|3CF1|B Chain B, Structure Of P97VCP IN COMPLEX WITH ADPADP.ALFX
pdb|3CF1|C Chain C, Structure Of P97VCP IN COMPLEX WITH ADPADP.ALFX
pdb|3CF2|A Chain A, Structure Of P97VCP IN COMPLEX WITH ADPAMP-Pnp
pdb|3CF2|B Chain B, Structure Of P97VCP IN COMPLEX WITH ADPAMP-Pnp
pdb|3CF2|C Chain C, Structure Of P97VCP IN COMPLEX WITH ADPAMP-Pnp
pdb|3CF2|D Chain D, Structure Of P97VCP IN COMPLEX WITH ADPAMP-Pnp
pdb|3CF3|A Chain A, Structure Of P97VCP IN COMPLEX WITH ADP
pdb|3CF3|B Chain B, Structure Of P97VCP IN COMPLEX WITH ADP
pdb|3CF3|C Chain C, Structure Of P97VCP IN COMPLEX WITH ADP
Length = 806
Score = 32.7 bits (73), Expect = 1.0, Method: Compositional matrix adjust.
Identities = 13/23 (56%), Positives = 17/23 (73%)
Query: 401 KILGLKGAPPYLIYGPPGTGKTM 423
K +G+K L+YGPPGTGKT+
Sbjct: 231 KAIGVKPPRGILLYGPPGTGKTL 253
>pdb|3HU3|A Chain A, Structure Of P97 N-D1 R155h Mutant In Complex With Atpgs
pdb|3HU3|B Chain B, Structure Of P97 N-D1 R155h Mutant In Complex With Atpgs
Length = 489
Score = 32.7 bits (73), Expect = 1.0, Method: Compositional matrix adjust.
Identities = 13/23 (56%), Positives = 17/23 (73%)
Query: 401 KILGLKGAPPYLIYGPPGTGKTM 423
K +G+K L+YGPPGTGKT+
Sbjct: 231 KAIGVKPPRGILLYGPPGTGKTL 253
>pdb|3HU2|A Chain A, Structure Of P97 N-D1 R86a Mutant In Complex With Atpgs
pdb|3HU2|B Chain B, Structure Of P97 N-D1 R86a Mutant In Complex With Atpgs
pdb|3HU2|C Chain C, Structure Of P97 N-D1 R86a Mutant In Complex With Atpgs
pdb|3HU2|D Chain D, Structure Of P97 N-D1 R86a Mutant In Complex With Atpgs
pdb|3HU2|E Chain E, Structure Of P97 N-D1 R86a Mutant In Complex With Atpgs
pdb|3HU2|F Chain F, Structure Of P97 N-D1 R86a Mutant In Complex With Atpgs
Length = 489
Score = 32.7 bits (73), Expect = 1.0, Method: Compositional matrix adjust.
Identities = 13/23 (56%), Positives = 17/23 (73%)
Query: 401 KILGLKGAPPYLIYGPPGTGKTM 423
K +G+K L+YGPPGTGKT+
Sbjct: 231 KAIGVKPPRGILLYGPPGTGKTL 253
>pdb|1E32|A Chain A, Structure Of The N-Terminal Domain And The D1 Aaa Domain
Of Membrane Fusion Atpase P97
pdb|1S3S|A Chain A, Crystal Structure Of Aaa Atpase P97VCP ND1 IN COMPLEX WITH
P47 C
pdb|1S3S|B Chain B, Crystal Structure Of Aaa Atpase P97VCP ND1 IN COMPLEX WITH
P47 C
pdb|1S3S|C Chain C, Crystal Structure Of Aaa Atpase P97VCP ND1 IN COMPLEX WITH
P47 C
pdb|1S3S|D Chain D, Crystal Structure Of Aaa Atpase P97VCP ND1 IN COMPLEX WITH
P47 C
pdb|1S3S|E Chain E, Crystal Structure Of Aaa Atpase P97VCP ND1 IN COMPLEX WITH
P47 C
pdb|1S3S|F Chain F, Crystal Structure Of Aaa Atpase P97VCP ND1 IN COMPLEX WITH
P47 C
Length = 458
Score = 32.7 bits (73), Expect = 1.0, Method: Compositional matrix adjust.
Identities = 13/23 (56%), Positives = 17/23 (73%)
Query: 401 KILGLKGAPPYLIYGPPGTGKTM 423
K +G+K L+YGPPGTGKT+
Sbjct: 231 KAIGVKPPRGILLYGPPGTGKTL 253
>pdb|3HU1|A Chain A, Structure Of P97 N-D1 R95g Mutant In Complex With Atpgs
pdb|3HU1|B Chain B, Structure Of P97 N-D1 R95g Mutant In Complex With Atpgs
pdb|3HU1|C Chain C, Structure Of P97 N-D1 R95g Mutant In Complex With Atpgs
pdb|3HU1|D Chain D, Structure Of P97 N-D1 R95g Mutant In Complex With Atpgs
pdb|3HU1|E Chain E, Structure Of P97 N-D1 R95g Mutant In Complex With Atpgs
pdb|3HU1|F Chain F, Structure Of P97 N-D1 R95g Mutant In Complex With Atpgs
Length = 489
Score = 32.3 bits (72), Expect = 1.1, Method: Compositional matrix adjust.
Identities = 13/23 (56%), Positives = 17/23 (73%)
Query: 401 KILGLKGAPPYLIYGPPGTGKTM 423
K +G+K L+YGPPGTGKT+
Sbjct: 231 KAIGVKPPRGILLYGPPGTGKTL 253
>pdb|1OUW|A Chain A, Crystal Structure Of Calystegia Sepium Agglutinin
pdb|1OUW|B Chain B, Crystal Structure Of Calystegia Sepium Agglutinin
pdb|1OUW|C Chain C, Crystal Structure Of Calystegia Sepium Agglutinin
pdb|1OUW|D Chain D, Crystal Structure Of Calystegia Sepium Agglutinin
Length = 152
Score = 32.3 bits (72), Expect = 1.2, Method: Composition-based stats.
Identities = 21/70 (30%), Positives = 33/70 (47%), Gaps = 7/70 (10%)
Query: 2 MDTVGD---DNWGNEWEKRDIGFIDFEDYKSECSYNPSEEDPVQISFPFPFIDGKPQSVS 58
MDT+ +N GN W R + I+ + SY +P+ ++F DG +++
Sbjct: 4 MDTISGPWGNNGGNFWSFRPVNKIN----QIVISYGGGGNNPIALTFSSTKADGSKDTIT 59
Query: 59 VGETAVDSIT 68
VG DSIT
Sbjct: 60 VGGGGPDSIT 69
>pdb|3VKH|A Chain A, X-Ray Structure Of A Functional Full-Length Dynein Motor
Domain
pdb|3VKH|B Chain B, X-Ray Structure Of A Functional Full-Length Dynein Motor
Domain
Length = 3367
Score = 31.6 bits (70), Expect = 1.8, Method: Compositional matrix adjust.
Identities = 11/20 (55%), Positives = 15/20 (75%)
Query: 410 PYLIYGPPGTGKTMTLVEAI 429
P ++ GPPG+GKTMTL +
Sbjct: 1306 PLILCGPPGSGKTMTLTSTL 1325
>pdb|3VKG|A Chain A, X-Ray Structure Of An Mtbd Truncation Mutant Of Dynein Motor
Domain
pdb|3VKG|B Chain B, X-Ray Structure Of An Mtbd Truncation Mutant Of Dynein Motor
Domain
Length = 3245
Score = 31.6 bits (70), Expect = 1.8, Method: Compositional matrix adjust.
Identities = 11/20 (55%), Positives = 15/20 (75%)
Query: 410 PYLIYGPPGTGKTMTLVEAI 429
P ++ GPPG+GKTMTL +
Sbjct: 1306 PLILCGPPGSGKTMTLTSTL 1325
>pdb|3D8B|A Chain A, Crystal Structure Of Human Fidgetin-Like Protein 1 In
Complex With Adp
pdb|3D8B|B Chain B, Crystal Structure Of Human Fidgetin-Like Protein 1 In
Complex With Adp
Length = 357
Score = 31.6 bits (70), Expect = 1.9, Method: Compositional matrix adjust.
Identities = 23/65 (35%), Positives = 33/65 (50%), Gaps = 11/65 (16%)
Query: 404 GLKGAPP-YLIYGPPGTGKTMTLVEAILQLYATREDARLLVCAPSNSAADHLLEKILGEK 462
GL+G P L++GPPGTGKT+ I + A++ A + +A L K +GE
Sbjct: 112 GLRGPPKGILLFGPPGTGKTL-----IGKCIASQSGATFF-----SISASSLTSKWVGEG 161
Query: 463 AVEVR 467
VR
Sbjct: 162 EKMVR 166
>pdb|4B4T|I Chain I, Near-Atomic Resolution Structural Model Of The Yeast 26s
Proteasome
Length = 437
Score = 30.4 bits (67), Expect = 4.0, Method: Compositional matrix adjust.
Identities = 27/79 (34%), Positives = 41/79 (51%), Gaps = 15/79 (18%)
Query: 403 LGLKGAPPYLIYGPPGTGKTMTLVEAILQLYATREDARLLVCAPSNSAADHLLEKILGEK 462
+G+K ++YG PGTGKT+ L +A+ A + A L S L++K LG+
Sbjct: 211 MGIKPPKGVILYGAPGTGKTL-LAKAV----ANQTSATFLRIVGS-----ELIQKYLGDG 260
Query: 463 AVEVRENEIFRL---NAPS 478
R +IF++ NAPS
Sbjct: 261 PRLCR--QIFKVAGENAPS 277
>pdb|3MGG|A Chain A, Crystal Structure Of Methyl Transferase From
Methanosarcina Mazei
pdb|3MGG|B Chain B, Crystal Structure Of Methyl Transferase From
Methanosarcina Mazei
Length = 276
Score = 30.0 bits (66), Expect = 5.6, Method: Compositional matrix adjust.
Identities = 33/135 (24%), Positives = 59/135 (43%), Gaps = 17/135 (12%)
Query: 439 ARLLVCAPSNSAADHLLEKILGEKAVEVREN---------EIFRLNAPSRPYEDVNADHI 489
A+ ++ A +N A+ I E + REN + + N S P+ED + DHI
Sbjct: 50 AQTVILAKNNPDAEITSIDISPESLEKARENTEKNGIKNVKFLQANIFSLPFEDSSFDHI 109
Query: 490 RFCFFDEQIFKCPPLAALVCYRIIISTYMSASLIYAEGVDRGHFSHIFLDEAGQASEP-E 548
CF E + P AL + ++ + ++I + H S F E +A E
Sbjct: 110 FVCFVLEHL--QSPEEALKSLKKVLKPGGTITVIEGD-----HGSCYFHPEGKKAIEAWN 162
Query: 549 SMVPISSYCKKDTVV 563
++ + +Y K +++V
Sbjct: 163 CLIRVQAYXKGNSLV 177
>pdb|2CHG|A Chain A, Replication Factor C Domains 1 And 2
pdb|2CHG|B Chain B, Replication Factor C Domains 1 And 2
pdb|2CHG|C Chain C, Replication Factor C Domains 1 And 2
pdb|2CHG|D Chain D, Replication Factor C Domains 1 And 2
Length = 226
Score = 30.0 bits (66), Expect = 6.6, Method: Compositional matrix adjust.
Identities = 13/29 (44%), Positives = 15/29 (51%)
Query: 406 KGAPPYLIYGPPGTGKTMTLVEAILQLYA 434
K P L GPPGTGKT T + L+
Sbjct: 36 KNIPHLLFSGPPGTGKTATAIALARDLFG 64
>pdb|2CHQ|A Chain A, Replication Factor C Adpnp Complex
pdb|2CHQ|B Chain B, Replication Factor C Adpnp Complex
pdb|2CHQ|C Chain C, Replication Factor C Adpnp Complex
pdb|2CHV|A Chain A, Replication Factor C Adpnp Complex
pdb|2CHV|B Chain B, Replication Factor C Adpnp Complex
pdb|2CHV|C Chain C, Replication Factor C Adpnp Complex
pdb|2CHV|D Chain D, Replication Factor C Adpnp Complex
pdb|2CHV|E Chain E, Replication Factor C Adpnp Complex
pdb|2CHV|F Chain F, Replication Factor C Adpnp Complex
Length = 319
Score = 29.6 bits (65), Expect = 7.0, Method: Compositional matrix adjust.
Identities = 13/29 (44%), Positives = 15/29 (51%)
Query: 406 KGAPPYLIYGPPGTGKTMTLVEAILQLYA 434
K P L GPPGTGKT T + L+
Sbjct: 36 KNIPHLLFSGPPGTGKTATAIALARDLFG 64
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
0.319 0.136 0.410
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 27,270,728
Number of Sequences: 62578
Number of extensions: 1177146
Number of successful extensions: 2753
Number of sequences better than 100.0: 37
Number of HSP's better than 100.0 without gapping: 25
Number of HSP's successfully gapped in prelim test: 12
Number of HSP's that attempted gapping in prelim test: 2681
Number of HSP's gapped (non-prelim): 56
length of query: 874
length of database: 14,973,337
effective HSP length: 107
effective length of query: 767
effective length of database: 8,277,491
effective search space: 6348835597
effective search space used: 6348835597
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 56 (26.2 bits)