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= 000162
(1987 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|2XZL|A Chain A, Upf1-Rna Complex
Length = 802
Score = 158 bits (399), Expect = 4e-38, Method: Compositional matrix adjust.
Identities = 98/276 (35%), Positives = 156/276 (56%), Gaps = 11/276 (3%)
Query: 3 QLKFVVIDEAAQLKESESAIPLQLPCIQHAILVGDEVQLPAMVESSVSGEAYFGRSLFER 62
+ + V+IDE+ Q E E IP+ + + ILVGD QL ++ + +A +SLFER
Sbjct: 517 KFRTVLIDESTQASEPECLIPI-VKGAKQVILVGDHQQLGPVILERKAADAGLKQSLFER 575
Query: 63 LSYLGHPKHLLSMQYRMHPSISFFPNSYFYENKIRDAPTVRKRSYEKRFLPGPMYG-PYS 121
L LGH L +QYRM+P +S FP++ FYE +++ T+ +R+ P P+ G P
Sbjct: 576 LISLGHVPIRLEVQYRMNPYLSEFPSNMFYEGSLQNGVTIEQRTVPNSKFPWPIRGIPMM 635
Query: 122 FINVFGGREEFIEH--SCRNMVEVSVVMKILRNLYKAWVESKEKLSIGIVSPYSAQVIAI 179
F + GREE + S N +E +I+ L++ V+ ++ IG+++PY Q I
Sbjct: 636 FWANY-GREEISANGTSFLNRIEAMNCERIITKLFRDGVKPEQ---IGVITPYEGQRAYI 691
Query: 180 QE--KLGSKYEKIAGFAVKVKSIDGFQGGEEDIIIISTVRSNNTGSIGFASTPQRINVAL 237
+ ++ +K V+V S+D FQG E+D II+S VR+N +IGF P+R+NV L
Sbjct: 692 LQYMQMNGSLDKDLYIKVEVASVDAFQGREKDYIILSCVRANEQQAIGFLRDPRRLNVGL 751
Query: 238 TRARHCLWILGSERTLNHSESVWESLLDDAKARQCF 273
TRA++ L ILG+ R+L + ++W LL + + C
Sbjct: 752 TRAKYGLVILGNPRSLARN-TLWNHLLIHFREKGCL 786
>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 = 150 bits (380), Expect = 5e-36, Method: Compositional matrix adjust.
Identities = 99/268 (36%), Positives = 147/268 (54%), Gaps = 11/268 (4%)
Query: 3 QLKFVVIDEAAQLKESESAIPLQLPCIQHAILVGDEVQLPAMVESSVSGEAYFGRSLFER 62
Q + ++IDE+ Q E E +P+ L Q ILVGD QL +V + +A +SLFER
Sbjct: 515 QFRSILIDESTQATEPECMVPVVLGAKQ-LILVGDHCQLGPVVMCKKAAKAGLSQSLFER 573
Query: 63 LSYLGHPKHLLSMQYRMHPSISFFPNSYFYENKIRDAPTVRKRSYEKRFLPGPMYGPYSF 122
L LG L +QYRMHP++S FP++ FYE +++ T R + P F
Sbjct: 574 LVVLGIRPIRLQVQYRMHPALSAFPSNIFYEGSLQNGVTAADRVKKGFDFQWPQPDKPMF 633
Query: 123 INVFGGREEFIEH--SCRNMVEVSVVMKILRNLYKAWVESKEKLSIGIVSPYSAQ---VI 177
V G+EE S N E + V KI L KA + + IGI++PY Q ++
Sbjct: 634 FYVTQGQEEIASSGTSYLNRTEAANVEKITTKLLKAGAKPDQ---IGIITPYEGQRSYLV 690
Query: 178 AIQEKLGSKYEKIAGFAVKVKSIDGFQGGEEDIIIISTVRSNNTGSIGFASTPQRINVAL 237
+ GS + K+ V++ S+D FQG E+D II+S VR+N IGF + P+R+NVAL
Sbjct: 691 QYMQFSGSLHTKLYQ-EVEIASVDAFQGREKDFIILSCVRANEHQGIGFLNDPRRLNVAL 749
Query: 238 TRARHCLWILGSERTLNHSESVWESLLD 265
TRAR+ + I+G+ + L+ + +W LL+
Sbjct: 750 TRARYGVIIVGNPKALS-KQPLWNHLLN 776
>pdb|2XZO|A Chain A, Upf1 Helicase - Rna Complex
pdb|2XZP|A Chain A, Upf1 Helicase
Length = 623
Score = 150 bits (379), Expect = 6e-36, Method: Compositional matrix adjust.
Identities = 99/268 (36%), Positives = 147/268 (54%), Gaps = 11/268 (4%)
Query: 3 QLKFVVIDEAAQLKESESAIPLQLPCIQHAILVGDEVQLPAMVESSVSGEAYFGRSLFER 62
Q + ++IDE+ Q E E +P+ L Q ILVGD QL +V + +A +SLFER
Sbjct: 338 QFRSILIDESTQATEPECMVPVVLGAKQ-LILVGDHCQLGPVVMCKKAAKAGLSQSLFER 396
Query: 63 LSYLGHPKHLLSMQYRMHPSISFFPNSYFYENKIRDAPTVRKRSYEKRFLPGPMYGPYSF 122
L LG L +QYRMHP++S FP++ FYE +++ T R + P F
Sbjct: 397 LVVLGIRPIRLQVQYRMHPALSAFPSNIFYEGSLQNGVTAADRVKKGFDFQWPQPDKPMF 456
Query: 123 INVFGGREEFIEH--SCRNMVEVSVVMKILRNLYKAWVESKEKLSIGIVSPYSAQ---VI 177
V G+EE S N E + V KI L KA + + IGI++PY Q ++
Sbjct: 457 FYVTQGQEEIASSGTSYLNRTEAANVEKITTKLLKAGAKPDQ---IGIITPYEGQRSYLV 513
Query: 178 AIQEKLGSKYEKIAGFAVKVKSIDGFQGGEEDIIIISTVRSNNTGSIGFASTPQRINVAL 237
+ GS + K+ V++ S+D FQG E+D II+S VR+N IGF + P+R+NVAL
Sbjct: 514 QYMQFSGSLHTKLYQ-EVEIASVDAFQGREKDFIILSCVRANEHQGIGFLNDPRRLNVAL 572
Query: 238 TRARHCLWILGSERTLNHSESVWESLLD 265
TRAR+ + I+G+ + L+ + +W LL+
Sbjct: 573 TRARYGVIIVGNPKALS-KQPLWNHLLN 599
>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 = 150 bits (379), Expect = 7e-36, Method: Compositional matrix adjust.
Identities = 99/268 (36%), Positives = 147/268 (54%), Gaps = 11/268 (4%)
Query: 3 QLKFVVIDEAAQLKESESAIPLQLPCIQHAILVGDEVQLPAMVESSVSGEAYFGRSLFER 62
Q + ++IDE+ Q E E +P+ L Q ILVGD QL +V + +A +SLFER
Sbjct: 339 QFRSILIDESTQATEPECMVPVVLGAKQ-LILVGDHCQLGPVVMCKKAAKAGLSQSLFER 397
Query: 63 LSYLGHPKHLLSMQYRMHPSISFFPNSYFYENKIRDAPTVRKRSYEKRFLPGPMYGPYSF 122
L LG L +QYRMHP++S FP++ FYE +++ T R + P F
Sbjct: 398 LVVLGIRPIRLQVQYRMHPALSAFPSNIFYEGSLQNGVTAADRVKKGFDFQWPQPDKPMF 457
Query: 123 INVFGGREEFIEH--SCRNMVEVSVVMKILRNLYKAWVESKEKLSIGIVSPYSAQ---VI 177
V G+EE S N E + V KI L KA + + IGI++PY Q ++
Sbjct: 458 FYVTQGQEEIASSGTSYLNRTEAANVEKITTKLLKAGAKPDQ---IGIITPYEGQRSYLV 514
Query: 178 AIQEKLGSKYEKIAGFAVKVKSIDGFQGGEEDIIIISTVRSNNTGSIGFASTPQRINVAL 237
+ GS + K+ V++ S+D FQG E+D II+S VR+N IGF + P+R+NVAL
Sbjct: 515 QYMQFSGSLHTKLYQ-EVEIASVDAFQGREKDFIILSCVRANEHQGIGFLNDPRRLNVAL 573
Query: 238 TRARHCLWILGSERTLNHSESVWESLLD 265
TRAR+ + I+G+ + L+ + +W LL+
Sbjct: 574 TRARYGVIIVGNPKALS-KQPLWNHLLN 600
>pdb|4B3F|X Chain X, Crystal Structure Of 1ghmbp2 Helicase
Length = 646
Score = 118 bits (295), Expect = 4e-26, Method: Compositional matrix adjust.
Identities = 93/286 (32%), Positives = 146/286 (51%), Gaps = 26/286 (9%)
Query: 7 VVIDEAAQLKESESAIPLQLPCIQHAILVGDEVQLPAMVESSVSGEAYFGRSLFERLS-- 64
VVIDE AQ E+ IPL + IL GD QLP S + A SL ERL+
Sbjct: 370 VVIDECAQALEASCWIPLLKA--RKCILAGDHKQLPPTTVSHKAALAGLSLSLMERLAEE 427
Query: 65 YLGHPKHLLSMQYRMHPSISFFPNSYFYENKIRDAPTVRKRSYEKRFLPGPMYG-----P 119
Y L++QYRMH +I + + Y ++ +V + + R LPG P
Sbjct: 428 YGARVVRTLTVQYRMHQAIMRWASDTMYLGQLTAHSSVAR--HLLRDLPGVAATEETGVP 485
Query: 120 YSFINVFGG----REEFIEHSCRNMVEVSVVMKILRNLYKAWVESKEKLSIGIVSPYSAQ 175
++ G EE E S N EV +V ++ L A V +++ I +VSPY+ Q
Sbjct: 486 LLLVDTAGCGLFELEEEDEQSKGNPGEVRLVSLHIQALVDAGVPARD---IAVVSPYNLQ 542
Query: 176 VIAIQEKLGSKYEKIAGFAVKVKSIDGFQGGEEDIIIISTVRSNNTGSIGFASTPQRINV 235
V +++ L ++ ++ ++KS+DGFQG E++ +I+S VRSN G +GF + +RINV
Sbjct: 543 VDLLRQSLVHRHPEL-----EIKSVDGFQGREKEAVILSFVRSNRKGEVGFLAEDRRINV 597
Query: 236 ALTRARHCLWILGSERTLNHS---ESVWESLLDDAKARQCFFNIDE 278
A+TRAR + ++ RT+N+ +++ E + R F +D+
Sbjct: 598 AVTRARRHVAVICDSRTVNNHAFLKTLVEYFTQHGEVRTAFEYLDD 643
>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 = 118 bits (295), Expect = 4e-26, Method: Compositional matrix adjust.
Identities = 93/286 (32%), Positives = 146/286 (51%), Gaps = 26/286 (9%)
Query: 7 VVIDEAAQLKESESAIPLQLPCIQHAILVGDEVQLPAMVESSVSGEAYFGRSLFERLS-- 64
VVIDE AQ E+ IPL + IL GD QLP S + A SL ERL+
Sbjct: 370 VVIDECAQALEASCWIPLLKA--RKCILAGDHKQLPPTTVSHKAALAGLSLSLMERLAEE 427
Query: 65 YLGHPKHLLSMQYRMHPSISFFPNSYFYENKIRDAPTVRKRSYEKRFLPGPMYG-----P 119
Y L++QYRMH +I + + Y ++ +V + + R LPG P
Sbjct: 428 YGARVVRTLTVQYRMHQAIMRWASDTMYLGQLTAHSSVAR--HLLRDLPGVAATEETGVP 485
Query: 120 YSFINVFGG----REEFIEHSCRNMVEVSVVMKILRNLYKAWVESKEKLSIGIVSPYSAQ 175
++ G EE E S N EV +V ++ L A V +++ I +VSPY+ Q
Sbjct: 486 LLLVDTAGCGLFELEEEDEQSKGNPGEVRLVSLHIQALVDAGVPARD---IAVVSPYNLQ 542
Query: 176 VIAIQEKLGSKYEKIAGFAVKVKSIDGFQGGEEDIIIISTVRSNNTGSIGFASTPQRINV 235
V +++ L ++ ++ ++KS+DGFQG E++ +I+S VRSN G +GF + +RINV
Sbjct: 543 VDLLRQSLVHRHPEL-----EIKSVDGFQGREKEAVILSFVRSNRKGEVGFLAEDRRINV 597
Query: 236 ALTRARHCLWILGSERTLNHS---ESVWESLLDDAKARQCFFNIDE 278
A+TRAR + ++ RT+N+ +++ E + R F +D+
Sbjct: 598 AVTRARRHVAVICDSRTVNNHAFLKTLVEYFTQHGEVRTAFEYLDD 643
>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 = 32.7 bits (73), Expect = 1.9, Method: Compositional matrix adjust.
Identities = 25/91 (27%), Positives = 43/91 (47%), Gaps = 9/91 (9%)
Query: 721 VLTIVESKGLEFQDVLLYDF---FGSSPLKNQWRVVYEYMKEQALLDSTLPASFPSF--- 774
++TI SKGLEF V + F L + + E + L S+P+
Sbjct: 790 LMTIHSSKGLEFPVVFVAGLGRNFNMMDLNKSYLLDKELGFGTKYIHPQLRISYPTLPLI 849
Query: 775 ---NEAKHNVLCPELKQLYVAITRTRQRLWI 802
+ + +L EL+ LYVA+TR +++L++
Sbjct: 850 AMKKKMRRELLSEELRVLYVALTRAKEKLFL 880
>pdb|1ZQ1|C Chain C, Structure Of Gatde Trna-Dependent Amidotransferase From
Pyrococcus Abyssi
pdb|1ZQ1|D Chain D, Structure Of Gatde Trna-Dependent Amidotransferase From
Pyrococcus Abyssi
Length = 633
Score = 30.8 bits (68), Expect = 8.7, Method: Composition-based stats.
Identities = 26/72 (36%), Positives = 35/72 (48%), Gaps = 3/72 (4%)
Query: 1405 RESLEMNMITLRGTESYRNIIEEVIFKNIGL---KGIPSYGQIGTTVVMILGSGQLGNAV 1461
RE E +TL E IIEEVI +NI + KG+ + G I V+ + G V
Sbjct: 560 REVAEEKGLTLLSEEEVTRIIEEVIQQNIEVVKAKGMGAMGLIMGRVMAKVRGKADGKLV 619
Query: 1462 YQRVAKRLDENS 1473
Q V ++L E S
Sbjct: 620 SQIVRRKLQEIS 631
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
0.318 0.134 0.397
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 54,939,999
Number of Sequences: 62578
Number of extensions: 2223935
Number of successful extensions: 5507
Number of sequences better than 100.0: 14
Number of HSP's better than 100.0 without gapping: 6
Number of HSP's successfully gapped in prelim test: 8
Number of HSP's that attempted gapping in prelim test: 5478
Number of HSP's gapped (non-prelim): 19
length of query: 1987
length of database: 14,973,337
effective HSP length: 113
effective length of query: 1874
effective length of database: 7,902,023
effective search space: 14808391102
effective search space used: 14808391102
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: 59 (27.3 bits)