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= 047960
(371 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 = 123 bits (309), Expect = 1e-28, Method: Compositional matrix adjust.
Identities = 76/196 (38%), Positives = 111/196 (56%), Gaps = 8/196 (4%)
Query: 3 LSVQYRMHPHIRDFPSRHFYQGRLTDSESVINLPDEVY-YKDPVLRPYVFFDVIHGRESH 61
L VQYRMHP + FPS FY+G L + + + + + ++ P +FF V G+E
Sbjct: 584 LQVQYRMHPALSAFPSNIFYEGSLQNGVTAADRVKKGFDFQWPQPDKPMFFYVTQGQEEI 643
Query: 62 RGGSVSYQNVDEAKFGVCLYEHLQKTLKSMGLGKVTVGIITPYKLQLKCLQH--EFRNVL 119
SY N EA E + L G +GIITPY+ Q L +F L
Sbjct: 644 ASSGTSYLNRTEAAN----VEKITTKLLKAGAKPDQIGIITPYEGQRSYLVQYMQFSGSL 699
Query: 120 NSEEGKDLYINTVDAFQGQERDVIIMSCVRASNH-GVGFVADIRRMNVALTRARRALWVM 178
+++ +++ I +VDAFQG+E+D II+SCVRA+ H G+GF+ D RR+NVALTRAR + ++
Sbjct: 700 HTKLYQEVEIASVDAFQGREKDFIILSCVRANEHQGIGFLNDPRRLNVALTRARYGVIIV 759
Query: 179 GNAGALTQSDDWAALI 194
GN AL++ W L+
Sbjct: 760 GNPKALSKQPLWNHLL 775
>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 = 123 bits (309), Expect = 2e-28, Method: Compositional matrix adjust.
Identities = 76/196 (38%), Positives = 111/196 (56%), Gaps = 8/196 (4%)
Query: 3 LSVQYRMHPHIRDFPSRHFYQGRLTDSESVINLPDEVY-YKDPVLRPYVFFDVIHGRESH 61
L VQYRMHP + FPS FY+G L + + + + + ++ P +FF V G+E
Sbjct: 408 LQVQYRMHPALSAFPSNIFYEGSLQNGVTAADRVKKGFDFQWPQPDKPMFFYVTQGQEEI 467
Query: 62 RGGSVSYQNVDEAKFGVCLYEHLQKTLKSMGLGKVTVGIITPYKLQLKCLQH--EFRNVL 119
SY N EA E + L G +GIITPY+ Q L +F L
Sbjct: 468 ASSGTSYLNRTEAAN----VEKITTKLLKAGAKPDQIGIITPYEGQRSYLVQYMQFSGSL 523
Query: 120 NSEEGKDLYINTVDAFQGQERDVIIMSCVRASNH-GVGFVADIRRMNVALTRARRALWVM 178
+++ +++ I +VDAFQG+E+D II+SCVRA+ H G+GF+ D RR+NVALTRAR + ++
Sbjct: 524 HTKLYQEVEIASVDAFQGREKDFIILSCVRANEHQGIGFLNDPRRLNVALTRARYGVIIV 583
Query: 179 GNAGALTQSDDWAALI 194
GN AL++ W L+
Sbjct: 584 GNPKALSKQPLWNHLL 599
>pdb|2XZO|A Chain A, Upf1 Helicase - Rna Complex
pdb|2XZP|A Chain A, Upf1 Helicase
Length = 623
Score = 123 bits (308), Expect = 2e-28, Method: Compositional matrix adjust.
Identities = 76/196 (38%), Positives = 111/196 (56%), Gaps = 8/196 (4%)
Query: 3 LSVQYRMHPHIRDFPSRHFYQGRLTDSESVINLPDEVY-YKDPVLRPYVFFDVIHGRESH 61
L VQYRMHP + FPS FY+G L + + + + + ++ P +FF V G+E
Sbjct: 407 LQVQYRMHPALSAFPSNIFYEGSLQNGVTAADRVKKGFDFQWPQPDKPMFFYVTQGQEEI 466
Query: 62 RGGSVSYQNVDEAKFGVCLYEHLQKTLKSMGLGKVTVGIITPYKLQLKCLQH--EFRNVL 119
SY N EA E + L G +GIITPY+ Q L +F L
Sbjct: 467 ASSGTSYLNRTEAAN----VEKITTKLLKAGAKPDQIGIITPYEGQRSYLVQYMQFSGSL 522
Query: 120 NSEEGKDLYINTVDAFQGQERDVIIMSCVRASNH-GVGFVADIRRMNVALTRARRALWVM 178
+++ +++ I +VDAFQG+E+D II+SCVRA+ H G+GF+ D RR+NVALTRAR + ++
Sbjct: 523 HTKLYQEVEIASVDAFQGREKDFIILSCVRANEHQGIGFLNDPRRLNVALTRARYGVIIV 582
Query: 179 GNAGALTQSDDWAALI 194
GN AL++ W L+
Sbjct: 583 GNPKALSKQPLWNHLL 598
>pdb|2XZL|A Chain A, Upf1-Rna Complex
Length = 802
Score = 112 bits (281), Expect = 3e-25, Method: Compositional matrix adjust.
Identities = 75/216 (34%), Positives = 119/216 (55%), Gaps = 16/216 (7%)
Query: 3 LSVQYRMHPHIRDFPSRHFYQGRLTDSESVI--NLPDEVYYKDPVLRPYVFFDVIHGRES 60
L VQYRM+P++ +FPS FY+G L + ++ +P+ + P+ + F +GRE
Sbjct: 586 LEVQYRMNPYLSEFPSNMFYEGSLQNGVTIEQRTVPNS-KFPWPIRGIPMMFWANYGREE 644
Query: 61 HRGGSVSYQNVDEAKFGVCLYEHLQKTLKSMGLGKVTVGIITPYKLQLKCLQHEFRNVLN 120
S+ N EA C E + L G+ +G+ITPY+ Q + + +N
Sbjct: 645 ISANGTSFLNRIEAMN--C--ERIITKLFRDGVKPEQIGVITPYEGQRAYILQYMQ--MN 698
Query: 121 SEEGKDLYIN----TVDAFQGQERDVIIMSCVRAS-NHGVGFVADIRRMNVALTRARRAL 175
KDLYI +VDAFQG+E+D II+SCVRA+ +GF+ D RR+NV LTRA+ L
Sbjct: 699 GSLDKDLYIKVEVASVDAFQGREKDYIILSCVRANEQQAIGFLRDPRRLNVGLTRAKYGL 758
Query: 176 WVMGNAGALTQSDDWAALIADSKARNCYMD--MDSL 209
++GN +L ++ W L+ + + C ++ +D+L
Sbjct: 759 VILGNPRSLARNTLWNHLLIHFREKGCLVEGTLDNL 794
>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 = 77.8 bits (190), Expect = 9e-15, Method: Compositional matrix adjust.
Identities = 61/189 (32%), Positives = 95/189 (50%), Gaps = 22/189 (11%)
Query: 3 LSVQYRMHPHIRDFPSRHFYQGRLTDSESVI-----NLPDEVYYKDPVLRPYVFFDVIHG 57
L+VQYRMH I + S Y G+LT SV +LP V + P + D
Sbjct: 436 LTVQYRMHQAIMRWASDTMYLGQLTAHSSVARHLLRDLPG-VAATEETGVPLLLVD---- 490
Query: 58 RESHRGGSVSYQNVDEAKFG----VCLYEHLQKTLKSMGLGKVTVGIITPYKLQLKCLQH 113
+ G + DE G V L + L G+ + +++PY LQ+ L+
Sbjct: 491 --TAGCGLFELEEEDEQSKGNPGEVRLVSLHIQALVDAGVPARDIAVVSPYNLQVDLLRQ 548
Query: 114 EFRNVLNSEEGKDLYINTVDAFQGQERDVIIMSCVRASNHG-VGFVADIRRMNVALTRAR 172
+ +L I +VD FQG+E++ +I+S VR++ G VGF+A+ RR+NVA+TRAR
Sbjct: 549 SLVH-----RHPELEIKSVDGFQGREKEAVILSFVRSNRKGEVGFLAEDRRINVAVTRAR 603
Query: 173 RALWVMGNA 181
R + V+ ++
Sbjct: 604 RHVAVICDS 612
>pdb|4B3F|X Chain X, Crystal Structure Of 1ghmbp2 Helicase
Length = 646
Score = 77.8 bits (190), Expect = 1e-14, Method: Compositional matrix adjust.
Identities = 61/189 (32%), Positives = 95/189 (50%), Gaps = 22/189 (11%)
Query: 3 LSVQYRMHPHIRDFPSRHFYQGRLTDSESVI-----NLPDEVYYKDPVLRPYVFFDVIHG 57
L+VQYRMH I + S Y G+LT SV +LP V + P + D
Sbjct: 436 LTVQYRMHQAIMRWASDTMYLGQLTAHSSVARHLLRDLPG-VAATEETGVPLLLVD---- 490
Query: 58 RESHRGGSVSYQNVDEAKFG----VCLYEHLQKTLKSMGLGKVTVGIITPYKLQLKCLQH 113
+ G + DE G V L + L G+ + +++PY LQ+ L+
Sbjct: 491 --TAGCGLFELEEEDEQSKGNPGEVRLVSLHIQALVDAGVPARDIAVVSPYNLQVDLLRQ 548
Query: 114 EFRNVLNSEEGKDLYINTVDAFQGQERDVIIMSCVRASNHG-VGFVADIRRMNVALTRAR 172
+ +L I +VD FQG+E++ +I+S VR++ G VGF+A+ RR+NVA+TRAR
Sbjct: 549 SLVH-----RHPELEIKSVDGFQGREKEAVILSFVRSNRKGEVGFLAEDRRINVAVTRAR 603
Query: 173 RALWVMGNA 181
R + V+ ++
Sbjct: 604 RHVAVICDS 612
>pdb|3OTR|A Chain A, 2.75 Angstrom Crystal Structure Of Enolase 1 From
Toxoplasma Gondii
pdb|3OTR|B Chain B, 2.75 Angstrom Crystal Structure Of Enolase 1 From
Toxoplasma Gondii
pdb|3OTR|C Chain C, 2.75 Angstrom Crystal Structure Of Enolase 1 From
Toxoplasma Gondii
pdb|3OTR|D Chain D, 2.75 Angstrom Crystal Structure Of Enolase 1 From
Toxoplasma Gondii
pdb|3OTR|E Chain E, 2.75 Angstrom Crystal Structure Of Enolase 1 From
Toxoplasma Gondii
pdb|3OTR|F Chain F, 2.75 Angstrom Crystal Structure Of Enolase 1 From
Toxoplasma Gondii
Length = 452
Score = 30.4 bits (67), Expect = 1.7, Method: Compositional matrix adjust.
Identities = 29/104 (27%), Positives = 46/104 (44%), Gaps = 23/104 (22%)
Query: 43 DPVLRPYVFFDVIHGRESHRGGSVSYQ----------NVDEA-KFGVCLYEHLQKTLKSM 91
D ++ P FF+VI+G E H G ++ Q N+ EA ++G Y HL+ +K+
Sbjct: 148 DKMVMPVPFFNVINGGE-HAGNGLALQEFLIAPVGAPNIREAIRYGSETYHHLKNVIKNK 206
Query: 92 -GLGKVTVGIITPYKLQLKCLQHEFRNVLNSEEGKDLYINTVDA 134
GL VG + NV +EE +L + + A
Sbjct: 207 YGLDATNVGDEGGFA----------PNVATAEEALNLLVEAIKA 240
>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 = 28.9 bits (63), Expect = 5.2, Method: Compositional matrix adjust.
Identities = 29/121 (23%), Positives = 47/121 (38%), Gaps = 15/121 (12%)
Query: 160 DIRRMNVALTRARRALWVMGNAG----------ALTQSDDWAALIADSKARNCYMDM--D 207
++R + VALTRA+ L+++G+ A DW D Y+D
Sbjct: 863 ELRVLYVALTRAKEKLFLIGSCKDHQKQLAKWQASASQTDWLLPEFDRYQARTYLDFIGP 922
Query: 208 SLPKEFSVALAAKAPGYGPLQGKIPHNARGLRSAGQRHRSFDMNMESRSGTPSEDDEKVS 267
+L + + A P + + G H AR + D ++E R SE E +
Sbjct: 923 ALARHRDLGDLAGVPAHADISG---HPARFAVQMIHSYDLLDDDLEERMEEKSERLEAIR 979
Query: 268 R 268
R
Sbjct: 980 R 980
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 0.136 0.419
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 11,504,333
Number of Sequences: 62578
Number of extensions: 475770
Number of successful extensions: 961
Number of sequences better than 100.0: 8
Number of HSP's better than 100.0 without gapping: 6
Number of HSP's successfully gapped in prelim test: 2
Number of HSP's that attempted gapping in prelim test: 940
Number of HSP's gapped (non-prelim): 10
length of query: 371
length of database: 14,973,337
effective HSP length: 100
effective length of query: 271
effective length of database: 8,715,537
effective search space: 2361910527
effective search space used: 2361910527
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: 52 (24.6 bits)