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= 035724
(1939 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>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 = 89.7 bits (221), Expect = 1e-17, Method: Compositional matrix adjust.
Identities = 61/175 (34%), Positives = 89/175 (50%), Gaps = 4/175 (2%)
Query: 258 ASLIFCTASSSYKLHRVAMEQLKFLVIDEAAQLKEVESAIPLKLPGIQHAILIGDECQLP 317
A +I CT + R+A Q + ++IDE+ Q E E +P+ L G + IL+GD CQL
Sbjct: 496 ADVICCTCVGAGD-PRLAKMQFRSILIDESTQATEPECMVPVVL-GAKQLILVGDHCQLG 553
Query: 318 AMVESSVSGEACLGRSLFERLSNLGQAKHLLSIQYRMHPSISSFPNSYFYDNKIFDSPNV 377
+V + +A L +SLFERL LG L +QYRMHP++S+FP++ FY+ + +
Sbjct: 554 PVVMCKKAAKAGLSQSLFERLVVLGIRPIRLQVQYRMHPALSAFPSNIFYEGSLQNGVTA 613
Query: 378 KEKNYEKRFLPGRMYGPYSFINVLDGREE--SIAHSYRNMVEVFVVMKILLNLYK 430
++ + F V G+EE S SY N E V KI L K
Sbjct: 614 ADRVKKGFDFQWPQPDKPMFFYVTQGQEEIASSGTSYLNRTEAANVEKITTKLLK 668
Score = 33.9 bits (76), Expect = 0.98, Method: Compositional matrix adjust.
Identities = 19/43 (44%), Positives = 25/43 (58%), Gaps = 7/43 (16%)
Query: 209 LNDSQAQAVLSCLRRTHCDHKATVELIWGPPGTGKTKTVSMLL 251
LN SQ AV + L+R + LI GPPGTGKT T + ++
Sbjct: 357 LNHSQVYAVKTVLQRP-------LSLIQGPPGTGKTVTSATIV 392
>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 = 88.6 bits (218), Expect = 3e-17, Method: Compositional matrix adjust.
Identities = 61/175 (34%), Positives = 89/175 (50%), Gaps = 4/175 (2%)
Query: 258 ASLIFCTASSSYKLHRVAMEQLKFLVIDEAAQLKEVESAIPLKLPGIQHAILIGDECQLP 317
A +I CT + R+A Q + ++IDE+ Q E E +P+ L G + IL+GD CQL
Sbjct: 320 ADVICCTCVGAGD-PRLAKMQFRSILIDESTQATEPECMVPVVL-GAKQLILVGDHCQLG 377
Query: 318 AMVESSVSGEACLGRSLFERLSNLGQAKHLLSIQYRMHPSISSFPNSYFYDNKIFDSPNV 377
+V + +A L +SLFERL LG L +QYRMHP++S+FP++ FY+ + +
Sbjct: 378 PVVMCKKAAKAGLSQSLFERLVVLGIRPIRLQVQYRMHPALSAFPSNIFYEGSLQNGVTA 437
Query: 378 KEKNYEKRFLPGRMYGPYSFINVLDGREE--SIAHSYRNMVEVFVVMKILLNLYK 430
++ + F V G+EE S SY N E V KI L K
Sbjct: 438 ADRVKKGFDFQWPQPDKPMFFYVTQGQEEIASSGTSYLNRTEAANVEKITTKLLK 492
Score = 34.3 bits (77), Expect = 0.69, Method: Compositional matrix adjust.
Identities = 23/81 (28%), Positives = 41/81 (50%), Gaps = 15/81 (18%)
Query: 209 LNDSQAQAVLSCLRRTHCDHKATVELIWGPPGTGKTKTVSMLLDFCFTKAS--LIFCTAS 266
LN SQ AV + L+R + LI GPPGTGKT T + ++ + + ++ C S
Sbjct: 181 LNHSQVYAVKTVLQRP-------LSLIQGPPGTGKTVTSATIVYHLARQGNGPVLVCAPS 233
Query: 267 S------SYKLHRVAMEQLKF 281
+ + K+H+ ++ ++
Sbjct: 234 NIAVDQLTEKIHQTGLKVVRL 254
>pdb|2XZO|A Chain A, Upf1 Helicase - Rna Complex
pdb|2XZP|A Chain A, Upf1 Helicase
Length = 623
Score = 88.6 bits (218), Expect = 3e-17, Method: Compositional matrix adjust.
Identities = 61/175 (34%), Positives = 89/175 (50%), Gaps = 4/175 (2%)
Query: 258 ASLIFCTASSSYKLHRVAMEQLKFLVIDEAAQLKEVESAIPLKLPGIQHAILIGDECQLP 317
A +I CT + R+A Q + ++IDE+ Q E E +P+ L G + IL+GD CQL
Sbjct: 319 ADVICCTCVGAGD-PRLAKMQFRSILIDESTQATEPECMVPVVL-GAKQLILVGDHCQLG 376
Query: 318 AMVESSVSGEACLGRSLFERLSNLGQAKHLLSIQYRMHPSISSFPNSYFYDNKIFDSPNV 377
+V + +A L +SLFERL LG L +QYRMHP++S+FP++ FY+ + +
Sbjct: 377 PVVMCKKAAKAGLSQSLFERLVVLGIRPIRLQVQYRMHPALSAFPSNIFYEGSLQNGVTA 436
Query: 378 KEKNYEKRFLPGRMYGPYSFINVLDGREE--SIAHSYRNMVEVFVVMKILLNLYK 430
++ + F V G+EE S SY N E V KI L K
Sbjct: 437 ADRVKKGFDFQWPQPDKPMFFYVTQGQEEIASSGTSYLNRTEAANVEKITTKLLK 491
Score = 34.3 bits (77), Expect = 0.70, Method: Compositional matrix adjust.
Identities = 23/81 (28%), Positives = 41/81 (50%), Gaps = 15/81 (18%)
Query: 209 LNDSQAQAVLSCLRRTHCDHKATVELIWGPPGTGKTKTVSMLLDFCFTKAS--LIFCTAS 266
LN SQ AV + L+R + LI GPPGTGKT T + ++ + + ++ C S
Sbjct: 180 LNHSQVYAVKTVLQRP-------LSLIQGPPGTGKTVTSATIVYHLARQGNGPVLVCAPS 232
Query: 267 S------SYKLHRVAMEQLKF 281
+ + K+H+ ++ ++
Sbjct: 233 NIAVDQLTEKIHQTGLKVVRL 253
>pdb|2XZL|A Chain A, Upf1-Rna Complex
Length = 802
Score = 82.4 bits (202), Expect = 2e-15, Method: Compositional matrix adjust.
Identities = 52/178 (29%), Positives = 91/178 (51%), Gaps = 5/178 (2%)
Query: 255 FTKASLIFCTASSSYKLHRVAMEQLKFLVIDEAAQLKEVESAIPLKLPGIQHAILIGDEC 314
KA ++ CT + + + + ++IDE+ Q E E IP+ + G + IL+GD
Sbjct: 496 LNKADVVCCTCVGAGD--KRLDTKFRTVLIDESTQASEPECLIPI-VKGAKQVILVGDHQ 552
Query: 315 QLPAMVESSVSGEACLGRSLFERLSNLGQAKHLLSIQYRMHPSISSFPNSYFYDNKIFDS 374
QL ++ + +A L +SLFERL +LG L +QYRM+P +S FP++ FY+ + +
Sbjct: 553 QLGPVILERKAADAGLKQSLFERLISLGHVPIRLEVQYRMNPYLSEFPSNMFYEGSLQNG 612
Query: 375 PNVKEKNYEKRFLPGRMYGPYSFINVLDGREESIAH--SYRNMVEVFVVMKILLNLYK 430
++++ P + G GREE A+ S+ N +E +I+ L++
Sbjct: 613 VTIEQRTVPNSKFPWPIRGIPMMFWANYGREEISANGTSFLNRIEAMNCERIITKLFR 670
Score = 37.0 bits (84), Expect = 0.11, Method: Compositional matrix adjust.
Identities = 31/95 (32%), Positives = 47/95 (49%), Gaps = 11/95 (11%)
Query: 207 STLNDSQAQAVLSCLRRTHCDHKATVELIWGPPGTGKTKTVSMLLDFC--FTKASLIFCT 264
+ LN SQ+ AV L+R + LI GPPGTGKT T + ++ K ++ C
Sbjct: 359 AQLNSSQSNAVSHVLQRP-------LSLIQGPPGTGKTVTSATIVYHLSKIHKDRILVCA 411
Query: 265 ASSSYKLHRVA-MEQLKFLVIDEAAQLKE-VESAI 297
S+ H A + L V+ A+ +E VES++
Sbjct: 412 PSNVAVDHLAAKLRDLGLKVVRLTAKSREDVESSV 446
>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 = 50.1 bits (118), Expect = 1e-05, Method: Compositional matrix adjust.
Identities = 45/140 (32%), Positives = 64/140 (45%), Gaps = 9/140 (6%)
Query: 255 FTKASLIFCT---ASSSYKLHRVAMEQLKFLVIDEAAQLKEVESAIPLKLPGIQHAILIG 311
T A+++ T AS+ L + +VIDE AQ E IPL + IL G
Sbjct: 340 LTSANVVLATNTGASADGPLKLLPESYFDVVVIDECAQALEASCWIPLL--KARKCILAG 397
Query: 312 DECQLPAMVESSVSGEACLGRSLFERLSNLGQAK--HLLSIQYRMHPSISSFPNSYFYDN 369
D QLP S + A L SL ERL+ A+ L++QYRMH +I + + Y
Sbjct: 398 DHKQLPPTTVSHKAALAGLSLSLMERLAEEYGARVVRTLTVQYRMHQAIMRWASDTMYLG 457
Query: 370 KIFDSPNVKEKNYEKRFLPG 389
++ +V + R LPG
Sbjct: 458 QLTAHSSV--ARHLLRDLPG 475
Score = 38.5 bits (88), Expect = 0.038, Method: Compositional matrix adjust.
Identities = 27/91 (29%), Positives = 46/91 (50%), Gaps = 10/91 (10%)
Query: 206 SSTLNDSQAQAVLSCLRRTHCDHKATVELIWGPPGTGKTKTVSMLLDFCFTKASLIFCTA 265
++ L+ SQ +AVL L + + +I GPPGTGKT TV ++ + + C A
Sbjct: 187 NTCLDTSQKEAVLFALSQKE------LAIIHGPPGTGKTTTVVEIILQAVKQGLKVLCCA 240
Query: 266 SSSYK----LHRVAMEQLKFLVIDEAAQLKE 292
S+ + R+A+ + + L + A+L E
Sbjct: 241 PSNIAVDNLVERLALCKQRILRLGHPARLLE 271
>pdb|4B3F|X Chain X, Crystal Structure Of 1ghmbp2 Helicase
Length = 646
Score = 50.1 bits (118), Expect = 1e-05, Method: Compositional matrix adjust.
Identities = 45/140 (32%), Positives = 64/140 (45%), Gaps = 9/140 (6%)
Query: 255 FTKASLIFCT---ASSSYKLHRVAMEQLKFLVIDEAAQLKEVESAIPLKLPGIQHAILIG 311
T A+++ T AS+ L + +VIDE AQ E IPL + IL G
Sbjct: 340 LTSANVVLATNTGASADGPLKLLPESYFDVVVIDECAQALEASCWIPLL--KARKCILAG 397
Query: 312 DECQLPAMVESSVSGEACLGRSLFERLSNLGQAK--HLLSIQYRMHPSISSFPNSYFYDN 369
D QLP S + A L SL ERL+ A+ L++QYRMH +I + + Y
Sbjct: 398 DHKQLPPTTVSHKAALAGLSLSLMERLAEEYGARVVRTLTVQYRMHQAIMRWASDTMYLG 457
Query: 370 KIFDSPNVKEKNYEKRFLPG 389
++ +V + R LPG
Sbjct: 458 QLTAHSSV--ARHLLRDLPG 475
Score = 38.5 bits (88), Expect = 0.041, Method: Compositional matrix adjust.
Identities = 27/91 (29%), Positives = 46/91 (50%), Gaps = 10/91 (10%)
Query: 206 SSTLNDSQAQAVLSCLRRTHCDHKATVELIWGPPGTGKTKTVSMLLDFCFTKASLIFCTA 265
++ L+ SQ +AVL L + + +I GPPGTGKT TV ++ + + C A
Sbjct: 187 NTCLDTSQKEAVLFALSQKE------LAIIHGPPGTGKTTTVVEIILQAVKQGLKVLCCA 240
Query: 266 SSSYK----LHRVAMEQLKFLVIDEAAQLKE 292
S+ + R+A+ + + L + A+L E
Sbjct: 241 PSNIAVDNLVERLALCKQRILRLGHPARLLE 271
>pdb|1D2Z|B Chain B, Three-Dimensional Structure Of A Complex Between The Death
Domains Of Pelle And Tube
pdb|1D2Z|D Chain D, Three-Dimensional Structure Of A Complex Between The Death
Domains Of Pelle And Tube
Length = 153
Score = 37.4 bits (85), Expect = 0.075, Method: Compositional matrix adjust.
Identities = 21/55 (38%), Positives = 31/55 (56%), Gaps = 6/55 (10%)
Query: 1686 NDVYERVAKWFDGNSLWKELFESLSWNMGSKSCQGSASCHNFDELKESHIQKFYK 1740
ND+Y R+AK D NS W++L + M ++C G A C NF + I+K +K
Sbjct: 17 NDIY-RLAKILDENSCWRKLMSIIPKGMDVQACSG-AGCLNF----PAEIKKGFK 65
>pdb|1DD5|A Chain A, Crystal Structure Of Thermotoga Maritima Ribosome
Recycling Factor, Rrf
pdb|1T1M|C Chain C, Binding Position Of Ribosome Recycling Factor (Rrf) On
The E. Coli 70s Ribosome
Length = 185
Score = 32.0 bits (71), Expect = 3.4, Method: Composition-based stats.
Identities = 14/48 (29%), Positives = 29/48 (60%), Gaps = 4/48 (8%)
Query: 19 VFPLLEETRAQLSSSMEKISEAPFAQVVDLEDSKPYGAMLSDVKVDYW 66
V P ++E + ++ ++EKI + ++ + KP A+L ++KVDY+
Sbjct: 2 VNPFIKEAKEKMKRTLEKIED----ELRKMRTGKPSPAILEEIKVDYY 45
>pdb|1XRS|B Chain B, Crystal Structure Of Lysine 5,6-Aminomutase In Complex
With Plp, Cobalamin, And 5'-Deoxyadenosine
Length = 262
Score = 31.2 bits (69), Expect = 6.3, Method: Compositional matrix adjust.
Identities = 14/34 (41%), Positives = 22/34 (64%)
Query: 30 LSSSMEKISEAPFAQVVDLEDSKPYGAMLSDVKV 63
+SS + + + F +V+DLE KPYG ++D KV
Sbjct: 1 MSSGLYSMEKKEFDKVLDLERVKPYGDTMNDGKV 34
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 0.135 0.405
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 55,373,748
Number of Sequences: 62578
Number of extensions: 2282371
Number of successful extensions: 5653
Number of sequences better than 100.0: 10
Number of HSP's better than 100.0 without gapping: 5
Number of HSP's successfully gapped in prelim test: 5
Number of HSP's that attempted gapping in prelim test: 5627
Number of HSP's gapped (non-prelim): 23
length of query: 1939
length of database: 14,973,337
effective HSP length: 113
effective length of query: 1826
effective length of database: 7,902,023
effective search space: 14429093998
effective search space used: 14429093998
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: 59 (27.3 bits)