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= 037641
(208 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 = 34.7 bits (78), Expect = 0.042, Method: Compositional matrix adjust.
Identities = 56/218 (25%), Positives = 82/218 (37%), Gaps = 35/218 (16%)
Query: 1 MQTIAQFELQMRNNSDNLSKTGLVVREAVLEIYKRSSKCRILVCAPINRTGDVLMRSLKK 60
++T+ Q L + KT V ++ R +LVCAP N D L + +
Sbjct: 365 VKTVLQRPLSLIQGPPGTGKT--VTSATIVYHLARQGNGPVLVCAPSNIAVDQLTEKIHQ 422
Query: 61 KIPKSDMFRANAAFREVDGVPVDILPLCLYEGGECFQLPSLQELM--------------- 105
K + R A RE PV L L + +P LQ+L
Sbjct: 423 TGLK--VVRLCAKSREAIDSPVSFLAL-HNQIRNMDSMPELQKLQQLKDETGELSSADEK 479
Query: 106 RFRVIFSTFTSSFRLHNEGI-----PAG-------HFSHIFLLDASSATEPETMIALTNL 153
R+R + T ++ + I AG F I + +++ ATEPE M+ +
Sbjct: 480 RYRALKRTAERELLMNADVICCTCVGAGDPRLAKMQFRSILIDESTQATEPECMVPVVLG 539
Query: 154 ANEHTTVILTGTPNNRTSWVRSDIARKNGLRVSHFERL 191
A + +IL G V A K GL S FERL
Sbjct: 540 AKQ---LILVGDHCQLGPVVMCKKAAKAGLSQSLFERL 574
>pdb|2XZO|A Chain A, Upf1 Helicase - Rna Complex
pdb|2XZP|A Chain A, Upf1 Helicase
Length = 623
Score = 34.3 bits (77), Expect = 0.053, Method: Compositional matrix adjust.
Identities = 56/218 (25%), Positives = 82/218 (37%), Gaps = 35/218 (16%)
Query: 1 MQTIAQFELQMRNNSDNLSKTGLVVREAVLEIYKRSSKCRILVCAPINRTGDVLMRSLKK 60
++T+ Q L + KT V ++ R +LVCAP N D L + +
Sbjct: 188 VKTVLQRPLSLIQGPPGTGKT--VTSATIVYHLARQGNGPVLVCAPSNIAVDQLTEKIHQ 245
Query: 61 KIPKSDMFRANAAFREVDGVPVDILPLCLYEGGECFQLPSLQELM--------------- 105
K + R A RE PV L L + +P LQ+L
Sbjct: 246 TGLK--VVRLCAKSREAIDSPVSFLALH-NQIRNMDSMPELQKLQQLKDETGELSSADEK 302
Query: 106 RFRVIFSTFTSSFRLHNEGI-----PAG-------HFSHIFLLDASSATEPETMIALTNL 153
R+R + T ++ + I AG F I + +++ ATEPE M+ +
Sbjct: 303 RYRALKRTAERELLMNADVICCTCVGAGDPRLAKMQFRSILIDESTQATEPECMVPVVLG 362
Query: 154 ANEHTTVILTGTPNNRTSWVRSDIARKNGLRVSHFERL 191
A + +IL G V A K GL S FERL
Sbjct: 363 AKQ---LILVGDHCQLGPVVMCKKAAKAGLSQSLFERL 397
>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 = 34.3 bits (77), Expect = 0.053, Method: Compositional matrix adjust.
Identities = 56/218 (25%), Positives = 82/218 (37%), Gaps = 35/218 (16%)
Query: 1 MQTIAQFELQMRNNSDNLSKTGLVVREAVLEIYKRSSKCRILVCAPINRTGDVLMRSLKK 60
++T+ Q L + KT V ++ R +LVCAP N D L + +
Sbjct: 189 VKTVLQRPLSLIQGPPGTGKT--VTSATIVYHLARQGNGPVLVCAPSNIAVDQLTEKIHQ 246
Query: 61 KIPKSDMFRANAAFREVDGVPVDILPLCLYEGGECFQLPSLQELM--------------- 105
K + R A RE PV L L + +P LQ+L
Sbjct: 247 TGLK--VVRLCAKSREAIDSPVSFLALH-NQIRNMDSMPELQKLQQLKDETGELSSADEK 303
Query: 106 RFRVIFSTFTSSFRLHNEGI-----PAG-------HFSHIFLLDASSATEPETMIALTNL 153
R+R + T ++ + I AG F I + +++ ATEPE M+ +
Sbjct: 304 RYRALKRTAERELLMNADVICCTCVGAGDPRLAKMQFRSILIDESTQATEPECMVPVVLG 363
Query: 154 ANEHTTVILTGTPNNRTSWVRSDIARKNGLRVSHFERL 191
A + +IL G V A K GL S FERL
Sbjct: 364 AKQ---LILVGDHCQLGPVVMCKKAAKAGLSQSLFERL 398
>pdb|2PNF|A Chain A, Structure Of Aquifex Aeolicus Fabg 3-oxoacyl-(acyl-carrier
Protein) Reductase
pdb|2PNF|B Chain B, Structure Of Aquifex Aeolicus Fabg 3-oxoacyl-(acyl-carrier
Protein) Reductase
pdb|2P68|A Chain A, Crystal Structure Of Aq_1716 From Aquifex Aeolicus Vf5
pdb|2P68|B Chain B, Crystal Structure Of Aq_1716 From Aquifex Aeolicus Vf5
Length = 248
Score = 30.8 bits (68), Expect = 0.56, Method: Compositional matrix adjust.
Identities = 15/37 (40%), Positives = 21/37 (56%)
Query: 153 LANEHTTVILTGTPNNRTSWVRSDIARKNGLRVSHFE 189
LA+ +TVI+TGT R V +IA K G++ E
Sbjct: 27 LASAGSTVIITGTSGERAKAVAEEIANKYGVKAHGVE 63
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
0.323 0.135 0.394
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 5,633,686
Number of Sequences: 62578
Number of extensions: 212789
Number of successful extensions: 599
Number of sequences better than 100.0: 5
Number of HSP's better than 100.0 without gapping: 1
Number of HSP's successfully gapped in prelim test: 4
Number of HSP's that attempted gapping in prelim test: 598
Number of HSP's gapped (non-prelim): 5
length of query: 208
length of database: 14,973,337
effective HSP length: 94
effective length of query: 114
effective length of database: 9,091,005
effective search space: 1036374570
effective search space used: 1036374570
T: 11
A: 40
X1: 16 ( 7.5 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.5 bits)
S2: 49 (23.5 bits)