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= 008899
(549 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|2XZL|A Chain A, Upf1-Rna Complex
Length = 802
Score = 154 bits (389), Expect = 1e-37, Method: Compositional matrix adjust.
Identities = 95/277 (34%), Positives = 147/277 (53%), Gaps = 9/277 (3%)
Query: 201 LVIDEAAQLKESESTIPLQLAGINHAVLIGDECQLPAMVASKISDEAGFGRSLFERLTSL 260
++IDE+ Q E E IP+ + G +L+GD QL ++ + + +AG +SLFERL SL
Sbjct: 521 VLIDESTQASEPECLIPI-VKGAKQVILVGDHQQLGPVILERKAADAGLKQSLFERLISL 579
Query: 261 NHSKHLLNVQYRMHPSISLFPNLQFYRNQILDGANVKSKSYEKHYLPGTELGPYSFINII 320
H L VQYRM+P +S FP+ FY + +G ++ ++ P G
Sbjct: 580 GHVPIRLEVQYRMNPYLSEFPSNMFYEGSLQNGVTIEQRTVPNSKFPWPIRGIPMMFWAN 639
Query: 321 GGSEEFIYH--SCRNMVEVSVVIKILQKLYKAWVGSKQKVSIGVVSPYTAQAVAIRK--K 376
G EE + S N +E +I+ KL++ V +Q IGV++PY Q I + +
Sbjct: 640 YGREEISANGTSFLNRIEAMNCERIITKLFRDGVKPEQ---IGVITPYEGQRAYILQYMQ 696
Query: 377 IGSEYENKDGFTVKVKSIDGFQGGEEDIIIISTVRCNAGGSIGFISKPQRVNVALTRARH 436
+ + V+V S+D FQG E+D II+S VR N +IGF+ P+R+NV LTRA++
Sbjct: 697 MNGSLDKDLYIKVEVASVDAFQGREKDYIILSCVRANEQQAIGFLRDPRRLNVGLTRAKY 756
Query: 437 CLWILGNERTLISSESIWGALVCDAKARQCFFNADED 473
L ILGN R+L + ++W L+ + + C D
Sbjct: 757 GLVILGNPRSL-ARNTLWNHLLIHFREKGCLVEGTLD 792
>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 = 152 bits (383), Expect = 6e-37, Method: Compositional matrix adjust.
Identities = 95/262 (36%), Positives = 138/262 (52%), Gaps = 9/262 (3%)
Query: 201 LVIDEAAQLKESESTIPLQLAGINHAVLIGDECQLPAMVASKISDEAGFGRSLFERLTSL 260
++IDE+ Q E E +P+ L G +L+GD CQL +V K + +AG +SLFERL L
Sbjct: 519 ILIDESTQATEPECMVPVVL-GAKQLILVGDHCQLGPVVMCKKAAKAGLSQSLFERLVVL 577
Query: 261 NHSKHLLNVQYRMHPSISLFPNLQFYRNQILDGANVKSKSYEKHYLPGTELGPYSFINII 320
L VQYRMHP++S FP+ FY + +G + + + F +
Sbjct: 578 GIRPIRLQVQYRMHPALSAFPSNIFYEGSLQNGVTAADRVKKGFDFQWPQPDKPMFFYVT 637
Query: 321 GGSEEFIYH--SCRNMVEVSVVIKILQKLYKAWVGSKQKVSIGVVSPYTAQAVAIRK--K 376
G EE S N E + V KI KL KA Q IG+++PY Q + + +
Sbjct: 638 QGQEEIASSGTSYLNRTEAANVEKITTKLLKAGAKPDQ---IGIITPYEGQRSYLVQYMQ 694
Query: 377 IGSEYENKDGFTVKVKSIDGFQGGEEDIIIISTVRCNAGGSIGFISKPQRVNVALTRARH 436
K V++ S+D FQG E+D II+S VR N IGF++ P+R+NVALTRAR+
Sbjct: 695 FSGSLHTKLYQEVEIASVDAFQGREKDFIILSCVRANEHQGIGFLNDPRRLNVALTRARY 754
Query: 437 CLWILGNERTLISSESIWGALV 458
+ I+GN + L S + +W L+
Sbjct: 755 GVIIVGNPKAL-SKQPLWNHLL 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 = 151 bits (382), Expect = 7e-37, Method: Compositional matrix adjust.
Identities = 95/262 (36%), Positives = 138/262 (52%), Gaps = 9/262 (3%)
Query: 201 LVIDEAAQLKESESTIPLQLAGINHAVLIGDECQLPAMVASKISDEAGFGRSLFERLTSL 260
++IDE+ Q E E +P+ L G +L+GD CQL +V K + +AG +SLFERL L
Sbjct: 343 ILIDESTQATEPECMVPVVL-GAKQLILVGDHCQLGPVVMCKKAAKAGLSQSLFERLVVL 401
Query: 261 NHSKHLLNVQYRMHPSISLFPNLQFYRNQILDGANVKSKSYEKHYLPGTELGPYSFINII 320
L VQYRMHP++S FP+ FY + +G + + + F +
Sbjct: 402 GIRPIRLQVQYRMHPALSAFPSNIFYEGSLQNGVTAADRVKKGFDFQWPQPDKPMFFYVT 461
Query: 321 GGSEEFIYH--SCRNMVEVSVVIKILQKLYKAWVGSKQKVSIGVVSPYTAQAVAIRK--K 376
G EE S N E + V KI KL KA Q IG+++PY Q + + +
Sbjct: 462 QGQEEIASSGTSYLNRTEAANVEKITTKLLKAGAKPDQ---IGIITPYEGQRSYLVQYMQ 518
Query: 377 IGSEYENKDGFTVKVKSIDGFQGGEEDIIIISTVRCNAGGSIGFISKPQRVNVALTRARH 436
K V++ S+D FQG E+D II+S VR N IGF++ P+R+NVALTRAR+
Sbjct: 519 FSGSLHTKLYQEVEIASVDAFQGREKDFIILSCVRANEHQGIGFLNDPRRLNVALTRARY 578
Query: 437 CLWILGNERTLISSESIWGALV 458
+ I+GN + L S + +W L+
Sbjct: 579 GVIIVGNPKAL-SKQPLWNHLL 599
>pdb|2XZO|A Chain A, Upf1 Helicase - Rna Complex
pdb|2XZP|A Chain A, Upf1 Helicase
Length = 623
Score = 151 bits (382), Expect = 8e-37, Method: Compositional matrix adjust.
Identities = 95/262 (36%), Positives = 138/262 (52%), Gaps = 9/262 (3%)
Query: 201 LVIDEAAQLKESESTIPLQLAGINHAVLIGDECQLPAMVASKISDEAGFGRSLFERLTSL 260
++IDE+ Q E E +P+ L G +L+GD CQL +V K + +AG +SLFERL L
Sbjct: 342 ILIDESTQATEPECMVPVVL-GAKQLILVGDHCQLGPVVMCKKAAKAGLSQSLFERLVVL 400
Query: 261 NHSKHLLNVQYRMHPSISLFPNLQFYRNQILDGANVKSKSYEKHYLPGTELGPYSFINII 320
L VQYRMHP++S FP+ FY + +G + + + F +
Sbjct: 401 GIRPIRLQVQYRMHPALSAFPSNIFYEGSLQNGVTAADRVKKGFDFQWPQPDKPMFFYVT 460
Query: 321 GGSEEFIYH--SCRNMVEVSVVIKILQKLYKAWVGSKQKVSIGVVSPYTAQAVAIRK--K 376
G EE S N E + V KI KL KA Q IG+++PY Q + + +
Sbjct: 461 QGQEEIASSGTSYLNRTEAANVEKITTKLLKAGAKPDQ---IGIITPYEGQRSYLVQYMQ 517
Query: 377 IGSEYENKDGFTVKVKSIDGFQGGEEDIIIISTVRCNAGGSIGFISKPQRVNVALTRARH 436
K V++ S+D FQG E+D II+S VR N IGF++ P+R+NVALTRAR+
Sbjct: 518 FSGSLHTKLYQEVEIASVDAFQGREKDFIILSCVRANEHQGIGFLNDPRRLNVALTRARY 577
Query: 437 CLWILGNERTLISSESIWGALV 458
+ I+GN + L S + +W L+
Sbjct: 578 GVIIVGNPKAL-SKQPLWNHLL 598
>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 = 113 bits (283), Expect = 2e-25, Method: Compositional matrix adjust.
Identities = 88/260 (33%), Positives = 131/260 (50%), Gaps = 23/260 (8%)
Query: 199 NFLVIDEAAQLKESESTIPLQLAGINHAVLIGDECQLPAMVASKISDEAGFGRSLFERLT 258
+ +VIDE AQ E+ IPL A +L GD QLP S + AG SL ERL
Sbjct: 368 DVVVIDECAQALEASCWIPLLKA--RKCILAGDHKQLPPTTVSHKAALAGLSLSLMERLA 425
Query: 259 SLNHSK--HLLNVQYRMHPSISLFPNLQFYRNQILDGANVKSKSYEKHYLPGT----ELG 312
++ L VQYRMH +I + + Y Q+ ++V LPG E G
Sbjct: 426 EEYGARVVRTLTVQYRMHQAIMRWASDTMYLGQLTAHSSVARHLLRD--LPGVAATEETG 483
Query: 313 -PYSFINIIGGS----EEFIYHSCRNMVEVSVVIKILQKLYKAWVGSKQKVSIGVVSPYT 367
P ++ G EE S N EV +V +Q L A V ++ I VVSPY
Sbjct: 484 VPLLLVDTAGCGLFELEEEDEQSKGNPGEVRLVSLHIQALVDAGVPAR---DIAVVSPYN 540
Query: 368 AQAVAIRKKIGSEYENKDGFTVKVKSIDGFQGGEEDIIIISTVRCNAGGSIGFISKPQRV 427
Q +R+ + + +++KS+DGFQG E++ +I+S VR N G +GF+++ +R+
Sbjct: 541 LQVDLLRQSLVHRHPE-----LEIKSVDGFQGREKEAVILSFVRSNRKGEVGFLAEDRRI 595
Query: 428 NVALTRARHCLWILGNERTL 447
NVA+TRAR + ++ + RT+
Sbjct: 596 NVAVTRARRHVAVICDSRTV 615
>pdb|4B3F|X Chain X, Crystal Structure Of 1ghmbp2 Helicase
Length = 646
Score = 113 bits (283), Expect = 3e-25, Method: Compositional matrix adjust.
Identities = 88/260 (33%), Positives = 131/260 (50%), Gaps = 23/260 (8%)
Query: 199 NFLVIDEAAQLKESESTIPLQLAGINHAVLIGDECQLPAMVASKISDEAGFGRSLFERLT 258
+ +VIDE AQ E+ IPL A +L GD QLP S + AG SL ERL
Sbjct: 368 DVVVIDECAQALEASCWIPLLKA--RKCILAGDHKQLPPTTVSHKAALAGLSLSLMERLA 425
Query: 259 SLNHSK--HLLNVQYRMHPSISLFPNLQFYRNQILDGANVKSKSYEKHYLPGT----ELG 312
++ L VQYRMH +I + + Y Q+ ++V LPG E G
Sbjct: 426 EEYGARVVRTLTVQYRMHQAIMRWASDTMYLGQLTAHSSVARHLLRD--LPGVAATEETG 483
Query: 313 -PYSFINIIGGS----EEFIYHSCRNMVEVSVVIKILQKLYKAWVGSKQKVSIGVVSPYT 367
P ++ G EE S N EV +V +Q L A V ++ I VVSPY
Sbjct: 484 VPLLLVDTAGCGLFELEEEDEQSKGNPGEVRLVSLHIQALVDAGVPAR---DIAVVSPYN 540
Query: 368 AQAVAIRKKIGSEYENKDGFTVKVKSIDGFQGGEEDIIIISTVRCNAGGSIGFISKPQRV 427
Q +R+ + + +++KS+DGFQG E++ +I+S VR N G +GF+++ +R+
Sbjct: 541 LQVDLLRQSLVHRHPE-----LEIKSVDGFQGREKEAVILSFVRSNRKGEVGFLAEDRRI 595
Query: 428 NVALTRARHCLWILGNERTL 447
NVA+TRAR + ++ + RT+
Sbjct: 596 NVAVTRARRHVAVICDSRTV 615
>pdb|3TY3|A Chain A, Crystal Structure Of Homoisocitrate Dehydrogenase From
Schizosaccharomyces Pombe Bound To Glycyl-Glycyl-Glycine
pdb|3TY3|B Chain B, Crystal Structure Of Homoisocitrate Dehydrogenase From
Schizosaccharomyces Pombe Bound To Glycyl-Glycyl-Glycine
pdb|3TY4|A Chain A, Crystal Structure Of Homoisocitrate Dehydrogenase From
Schizosaccharomyces Pombe
pdb|3TY4|B Chain B, Crystal Structure Of Homoisocitrate Dehydrogenase From
Schizosaccharomyces Pombe
Length = 366
Score = 30.4 bits (67), Expect = 2.7, Method: Compositional matrix adjust.
Identities = 18/45 (40%), Positives = 28/45 (62%), Gaps = 5/45 (11%)
Query: 363 VSPYTAQAVAIRKKIGSEYENKDGFTVKVKSIDGFQGGEEDIIII 407
V+ Y++ VA+RKK+G Y N VKS+DG +G D++I+
Sbjct: 90 VAGYSSPIVALRKKMGL-YAN----VRPVKSLDGAKGKPVDLVIV 129
>pdb|1WZ8|A Chain A, Crystal Structure Of Probable Enoyl-Coa Dehydratase From
Thermus Thermophilus Hb8
pdb|1WZ8|B Chain B, Crystal Structure Of Probable Enoyl-Coa Dehydratase From
Thermus Thermophilus Hb8
pdb|1WZ8|C Chain C, Crystal Structure Of Probable Enoyl-Coa Dehydratase From
Thermus Thermophilus Hb8
pdb|1WZ8|D Chain D, Crystal Structure Of Probable Enoyl-Coa Dehydratase From
Thermus Thermophilus Hb8
pdb|1WZ8|E Chain E, Crystal Structure Of Probable Enoyl-Coa Dehydratase From
Thermus Thermophilus Hb8
pdb|1WZ8|F Chain F, Crystal Structure Of Probable Enoyl-Coa Dehydratase From
Thermus Thermophilus Hb8
Length = 264
Score = 29.6 bits (65), Expect = 4.1, Method: Compositional matrix adjust.
Identities = 21/65 (32%), Positives = 33/65 (50%), Gaps = 12/65 (18%)
Query: 228 LIGDECQLPAMVASKISDEAGFGRSL--FERLT-----SLNHSKHLLNVQYRMHPSISLF 280
L G+E + +VA + DE + ++L ERL +L+H+KH LN YR S
Sbjct: 175 LTGEEAERLGLVALAVEDEKVYEKALEVAERLAQGPKEALHHTKHALNHWYR-----SFL 229
Query: 281 PNLQF 285
P+ +
Sbjct: 230 PHFEL 234
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 0.134 0.389
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 15,163,233
Number of Sequences: 62578
Number of extensions: 603672
Number of successful extensions: 1420
Number of sequences better than 100.0: 12
Number of HSP's better than 100.0 without gapping: 7
Number of HSP's successfully gapped in prelim test: 5
Number of HSP's that attempted gapping in prelim test: 1397
Number of HSP's gapped (non-prelim): 13
length of query: 549
length of database: 14,973,337
effective HSP length: 104
effective length of query: 445
effective length of database: 8,465,225
effective search space: 3767025125
effective search space used: 3767025125
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)