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= 038017
(610 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 = 85.1 bits (209), Expect = 9e-17, Method: Compositional matrix adjust.
Identities = 61/173 (35%), Positives = 83/173 (47%), Gaps = 4/173 (2%)
Query: 262 ASLIFCTASSSYKLHSVAMEQLKFLVIDEAAQLKESESAIPLQLPCIQHAILVGDECQLP 321
A +I CT + M Q + ++IDE+ Q E E +P+ L Q ILVGD CQL
Sbjct: 496 ADVICCTCVGAGDPRLAKM-QFRSILIDESTQATEPECMVPVVLGAKQ-LILVGDHCQLG 553
Query: 322 AMVESSVSGEAYFGRSLFERLSYLGHSKHLLSMQYRMHPSISFFPNSYFYENKILDAPTV 381
+V + +A +SLFERL LG L +QYRMHP++S FP++ FYE + + T
Sbjct: 554 PVVMCKKAAKAGLSQSLFERLVVLGIRPIRLQVQYRMHPALSAFPSNIFYEGSLQNGVTA 613
Query: 382 RKRSYEKQFLPGPMYGPYAFINVFGGREEFIEH--SCRNMVEVSVVMKILLNL 432
R + P F V G+EE S N E + V KI L
Sbjct: 614 ADRVKKGFDFQWPQPDKPMFFYVTQGQEEIASSGTSYLNRTEAANVEKITTKL 666
>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 = 84.7 bits (208), Expect = 1e-16, Method: Compositional matrix adjust.
Identities = 61/173 (35%), Positives = 83/173 (47%), Gaps = 4/173 (2%)
Query: 262 ASLIFCTASSSYKLHSVAMEQLKFLVIDEAAQLKESESAIPLQLPCIQHAILVGDECQLP 321
A +I CT + M Q + ++IDE+ Q E E +P+ L Q ILVGD CQL
Sbjct: 320 ADVICCTCVGAGDPRLAKM-QFRSILIDESTQATEPECMVPVVLGAKQ-LILVGDHCQLG 377
Query: 322 AMVESSVSGEAYFGRSLFERLSYLGHSKHLLSMQYRMHPSISFFPNSYFYENKILDAPTV 381
+V + +A +SLFERL LG L +QYRMHP++S FP++ FYE + + T
Sbjct: 378 PVVMCKKAAKAGLSQSLFERLVVLGIRPIRLQVQYRMHPALSAFPSNIFYEGSLQNGVTA 437
Query: 382 RKRSYEKQFLPGPMYGPYAFINVFGGREEFIEH--SCRNMVEVSVVMKILLNL 432
R + P F V G+EE S N E + V KI L
Sbjct: 438 ADRVKKGFDFQWPQPDKPMFFYVTQGQEEIASSGTSYLNRTEAANVEKITTKL 490
>pdb|2XZO|A Chain A, Upf1 Helicase - Rna Complex
pdb|2XZP|A Chain A, Upf1 Helicase
Length = 623
Score = 84.7 bits (208), Expect = 1e-16, Method: Compositional matrix adjust.
Identities = 61/173 (35%), Positives = 83/173 (47%), Gaps = 4/173 (2%)
Query: 262 ASLIFCTASSSYKLHSVAMEQLKFLVIDEAAQLKESESAIPLQLPCIQHAILVGDECQLP 321
A +I CT + M Q + ++IDE+ Q E E +P+ L Q ILVGD CQL
Sbjct: 319 ADVICCTCVGAGDPRLAKM-QFRSILIDESTQATEPECMVPVVLGAKQ-LILVGDHCQLG 376
Query: 322 AMVESSVSGEAYFGRSLFERLSYLGHSKHLLSMQYRMHPSISFFPNSYFYENKILDAPTV 381
+V + +A +SLFERL LG L +QYRMHP++S FP++ FYE + + T
Sbjct: 377 PVVMCKKAAKAGLSQSLFERLVVLGIRPIRLQVQYRMHPALSAFPSNIFYEGSLQNGVTA 436
Query: 382 RKRSYEKQFLPGPMYGPYAFINVFGGREEFIEH--SCRNMVEVSVVMKILLNL 432
R + P F V G+EE S N E + V KI L
Sbjct: 437 ADRVKKGFDFQWPQPDKPMFFYVTQGQEEIASSGTSYLNRTEAANVEKITTKL 489
>pdb|2XZL|A Chain A, Upf1-Rna Complex
Length = 802
Score = 84.7 bits (208), Expect = 1e-16, Method: Compositional matrix adjust.
Identities = 53/156 (33%), Positives = 83/156 (53%), Gaps = 9/156 (5%)
Query: 259 FTKASLIFCT--ASSSYKLHSVAMEQLKFLVIDEAAQLKESESAIPLQLPCIQHAILVGD 316
KA ++ CT + +L + + + ++IDE+ Q E E IP+ + + ILVGD
Sbjct: 496 LNKADVVCCTCVGAGDKRLDT----KFRTVLIDESTQASEPECLIPI-VKGAKQVILVGD 550
Query: 317 ECQLPAMVESSVSGEAYFGRSLFERLSYLGHSKHLLSMQYRMHPSISFFPNSYFYENKIL 376
QL ++ + +A +SLFERL LGH L +QYRM+P +S FP++ FYE +
Sbjct: 551 HQQLGPVILERKAADAGLKQSLFERLISLGHVPIRLEVQYRMNPYLSEFPSNMFYEGSLQ 610
Query: 377 DAPTVRKRSYEKQFLPGPMYG-PYAFINVFGGREEF 411
+ T+ +R+ P P+ G P F + GREE
Sbjct: 611 NGVTIEQRTVPNSKFPWPIRGIPMMFWANY-GREEI 645
>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 = 50.4 bits (119), Expect = 3e-06, Method: Compositional matrix adjust.
Identities = 55/190 (28%), Positives = 82/190 (43%), Gaps = 21/190 (11%)
Query: 199 LEELFSHSVD-----EDFSQSIVDIKYTLHES--RSKCHSVLRELWNSFKELNL-----P 246
LE + HS+D D +Q + DI+ + + ++K RE N E+ L
Sbjct: 270 LESIQQHSLDAVLARSDSAQIVADIRKDIDQVFVKNKKTQDKREKSNFRNEIKLLRKELK 329
Query: 247 SAMNMGLLKDFCFTKASLIFCT---ASSSYKLHSVAMEQLKFLVIDEAAQLKESESAIPL 303
+L+ T A+++ T AS+ L + +VIDE AQ E+ IPL
Sbjct: 330 EREEAAMLESL--TSANVVLATNTGASADGPLKLLPESYFDVVVIDECAQALEASCWIPL 387
Query: 304 QLPCIQHAILVGDECQLPAMVESSVSGEAYFGRSLFERLS--YLGHSKHLLSMQYRMHPS 361
+ IL GD QLP S + A SL ERL+ Y L++QYRMH +
Sbjct: 388 LKA--RKCILAGDHKQLPPTTVSHKAALAGLSLSLMERLAEEYGARVVRTLTVQYRMHQA 445
Query: 362 ISFFPNSYFY 371
I + + Y
Sbjct: 446 IMRWASDTMY 455
>pdb|4B3F|X Chain X, Crystal Structure Of 1ghmbp2 Helicase
Length = 646
Score = 50.4 bits (119), Expect = 3e-06, Method: Compositional matrix adjust.
Identities = 55/190 (28%), Positives = 82/190 (43%), Gaps = 21/190 (11%)
Query: 199 LEELFSHSVD-----EDFSQSIVDIKYTLHES--RSKCHSVLRELWNSFKELNL-----P 246
LE + HS+D D +Q + DI+ + + ++K RE N E+ L
Sbjct: 270 LESIQQHSLDAVLARSDSAQIVADIRKDIDQVFVKNKKTQDKREKSNFRNEIKLLRKELK 329
Query: 247 SAMNMGLLKDFCFTKASLIFCT---ASSSYKLHSVAMEQLKFLVIDEAAQLKESESAIPL 303
+L+ T A+++ T AS+ L + +VIDE AQ E+ IPL
Sbjct: 330 EREEAAMLESL--TSANVVLATNTGASADGPLKLLPESYFDVVVIDECAQALEASCWIPL 387
Query: 304 QLPCIQHAILVGDECQLPAMVESSVSGEAYFGRSLFERLS--YLGHSKHLLSMQYRMHPS 361
+ IL GD QLP S + A SL ERL+ Y L++QYRMH +
Sbjct: 388 LKA--RKCILAGDHKQLPPTTVSHKAALAGLSLSLMERLAEEYGARVVRTLTVQYRMHQA 445
Query: 362 ISFFPNSYFY 371
I + + Y
Sbjct: 446 IMRWASDTMY 455
>pdb|3SQN|A Chain A, Putative Mga Family Transcriptional Regulator From
Enterococcus Faecalis
pdb|3SQN|B Chain B, Putative Mga Family Transcriptional Regulator From
Enterococcus Faecalis
Length = 485
Score = 30.0 bits (66), Expect = 3.9, Method: Compositional matrix adjust.
Identities = 27/95 (28%), Positives = 45/95 (47%), Gaps = 11/95 (11%)
Query: 226 RSKCHSVLRELWNSFKELNLPSAMNMGLLKDFCFTKASLIFCTASSSYKLHSVAMEQLKF 285
R++ ++ ELW+ F LP ++++ LLK+ FTK + S+S V+ E LK
Sbjct: 76 RNQGNAQTNELWSLF----LPQSISIQLLKELLFTKELVTTSFLSTS----GVSYETLKR 127
Query: 286 LVIDEAAQLKESESAIPLQLPCIQHAILVGDECQL 320
+ L++ I L IQ L+G E +
Sbjct: 128 HIKKXNQALRDFHLTIQLTTXTIQ---LIGAESNI 159
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 0.395
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 17,814,382
Number of Sequences: 62578
Number of extensions: 746948
Number of successful extensions: 2094
Number of sequences better than 100.0: 7
Number of HSP's better than 100.0 without gapping: 4
Number of HSP's successfully gapped in prelim test: 3
Number of HSP's that attempted gapping in prelim test: 2082
Number of HSP's gapped (non-prelim): 7
length of query: 610
length of database: 14,973,337
effective HSP length: 105
effective length of query: 505
effective length of database: 8,402,647
effective search space: 4243336735
effective search space used: 4243336735
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: 54 (25.4 bits)