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= 009733
(527 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|1UW4|A Chain A, The Structural Basis Of The Interaction Between Nonsense
Mediated Decay Factors Upf2 And Upf3
pdb|1UW4|C Chain C, The Structural Basis Of The Interaction Between Nonsense
Mediated Decay Factors Upf2 And Upf3
Length = 91
Score = 58.5 bits (140), Expect = 9e-09, Method: Composition-based stats.
Identities = 34/96 (35%), Positives = 56/96 (58%), Gaps = 10/96 (10%)
Query: 8 TKVVIRHLPPSLSQNDLLALFRDHFND--RYNWFCFRPGKSSFFYSYKHQRYSRAYVELK 65
+KVVIR LPP+L++ L ++H +++F F +S Y H Y+RAY+ K
Sbjct: 2 SKVVIRRLPPTLTKEQL----QEHLQPMPEHDYFEFFSNDTSL---YPHM-YARAYINFK 53
Query: 66 KPAGVFEFAELLNGHVFVNEKGAQFKAIVEYAPSQR 101
+ F + +G+VF++ KG ++ AIVE+AP Q+
Sbjct: 54 NQEDIILFRDRFDGYVFLDNKGQEYPAIVEFAPFQK 89
>pdb|2L08|A Chain A, Solution Nmr Structure Of Nonsense Mrna Reducing Factor 3a
From H. Sapiens, Northeast Structural Genomics
Consortium Target Hr4714b
Length = 97
Score = 57.0 bits (136), Expect = 2e-08, Method: Composition-based stats.
Identities = 32/92 (34%), Positives = 51/92 (55%), Gaps = 6/92 (6%)
Query: 10 VVIRHLPPSLSQNDLLALFRDHFNDRYNWFCFRPGKSSFFYSYKHQRYSRAYVELKKPAG 69
VVIR LPP L++ L R +++F F S Y H YSRAY+ + P
Sbjct: 12 VVIRRLPPGLTKEQLEEQLRPL--PAHDYFEFFAADLSL---YPHL-YSRAYINFRNPDD 65
Query: 70 VFEFAELLNGHVFVNEKGAQFKAIVEYAPSQR 101
+ F + +G++F++ KG ++ A+VE+AP Q+
Sbjct: 66 ILLFRDRFDGYIFLDSKGLEYPAVVEFAPFQK 97
>pdb|3TF5|A Chain A, Structure Of Udp-Glucose Dehydrogenase V132 Deletion
pdb|3TF5|B Chain B, Structure Of Udp-Glucose Dehydrogenase V132 Deletion
pdb|3TF5|C Chain C, Structure Of Udp-Glucose Dehydrogenase V132 Deletion
Length = 493
Score = 32.0 bits (71), Expect = 0.93, Method: Compositional matrix adjust.
Identities = 22/68 (32%), Positives = 35/68 (51%), Gaps = 10/68 (14%)
Query: 52 YKHQRYSRAYVELKKPAGVFEFAELLNG-HVFVNEKGAQFKAI--------VEYAPSQRV 102
+K Y R + ++ KPA +F+ +L+G H + G Q + I + YAPS +
Sbjct: 419 FKELDYERIHKKMLKPAFIFDGRRVLDGLHNELQTIGFQIETIGKKVSSKRIPYAPSGEI 478
Query: 103 PKPFSRKD 110
PK FS +D
Sbjct: 479 PK-FSLQD 485
>pdb|4EDF|A Chain A, Dimeric Hugdh, K94e
pdb|4EDF|B Chain B, Dimeric Hugdh, K94e
pdb|4EDF|C Chain C, Dimeric Hugdh, K94e
pdb|4EDF|D Chain D, Dimeric Hugdh, K94e
Length = 494
Score = 32.0 bits (71), Expect = 0.95, Method: Compositional matrix adjust.
Identities = 22/68 (32%), Positives = 35/68 (51%), Gaps = 10/68 (14%)
Query: 52 YKHQRYSRAYVELKKPAGVFEFAELLNG-HVFVNEKGAQFKAI--------VEYAPSQRV 102
+K Y R + ++ KPA +F+ +L+G H + G Q + I + YAPS +
Sbjct: 420 FKELDYERIHKKMLKPAFIFDGRRVLDGLHNELQTIGFQIETIGKKVSSKRIPYAPSGEI 479
Query: 103 PKPFSRKD 110
PK FS +D
Sbjct: 480 PK-FSLQD 486
>pdb|3PRJ|A Chain A, Role Of Packing Defects In The Evolution Of Allostery And
Induced Fit In Human Udp-Glucose Dehydrogenase.
pdb|3PRJ|B Chain B, Role Of Packing Defects In The Evolution Of Allostery And
Induced Fit In Human Udp-Glucose Dehydrogenase.
pdb|3PRJ|C Chain C, Role Of Packing Defects In The Evolution Of Allostery And
Induced Fit In Human Udp-Glucose Dehydrogenase.
pdb|3PRJ|D Chain D, Role Of Packing Defects In The Evolution Of Allostery And
Induced Fit In Human Udp-Glucose Dehydrogenase.
pdb|3PRJ|E Chain E, Role Of Packing Defects In The Evolution Of Allostery And
Induced Fit In Human Udp-Glucose Dehydrogenase.
pdb|3PRJ|F Chain F, Role Of Packing Defects In The Evolution Of Allostery And
Induced Fit In Human Udp-Glucose Dehydrogenase.
pdb|3PTZ|A Chain A, Role Of Packing Defects In The Evolution Of Allostery And
Induced Fit In Human Udp-Glucose Dehydrogenase.
pdb|3PTZ|B Chain B, Role Of Packing Defects In The Evolution Of Allostery And
Induced Fit In Human Udp-Glucose Dehydrogenase.
pdb|3PTZ|C Chain C, Role Of Packing Defects In The Evolution Of Allostery And
Induced Fit In Human Udp-Glucose Dehydrogenase.
pdb|3PTZ|D Chain D, Role Of Packing Defects In The Evolution Of Allostery And
Induced Fit In Human Udp-Glucose Dehydrogenase.
pdb|3PTZ|E Chain E, Role Of Packing Defects In The Evolution Of Allostery And
Induced Fit In Human Udp-Glucose Dehydrogenase.
pdb|3PTZ|F Chain F, Role Of Packing Defects In The Evolution Of Allostery And
Induced Fit In Human Udp-Glucose Dehydrogenase
Length = 494
Score = 32.0 bits (71), Expect = 0.96, Method: Compositional matrix adjust.
Identities = 22/68 (32%), Positives = 35/68 (51%), Gaps = 10/68 (14%)
Query: 52 YKHQRYSRAYVELKKPAGVFEFAELLNG-HVFVNEKGAQFKAI--------VEYAPSQRV 102
+K Y R + ++ KPA +F+ +L+G H + G Q + I + YAPS +
Sbjct: 420 FKELDYERIHKKMLKPAFIFDGRRVLDGLHNELQTIGFQIETIGKKVSSKRIPYAPSGEI 479
Query: 103 PKPFSRKD 110
PK FS +D
Sbjct: 480 PK-FSLQD 486
>pdb|3TDK|A Chain A, Crystal Structure Of Human Udp-Glucose Dehydrogenase
pdb|3TDK|B Chain B, Crystal Structure Of Human Udp-Glucose Dehydrogenase
pdb|3TDK|G Chain G, Crystal Structure Of Human Udp-Glucose Dehydrogenase
pdb|3TDK|H Chain H, Crystal Structure Of Human Udp-Glucose Dehydrogenase
pdb|3TDK|L Chain L, Crystal Structure Of Human Udp-Glucose Dehydrogenase
pdb|3TDK|K Chain K, Crystal Structure Of Human Udp-Glucose Dehydrogenase
pdb|3TDK|F Chain F, Crystal Structure Of Human Udp-Glucose Dehydrogenase
pdb|3TDK|E Chain E, Crystal Structure Of Human Udp-Glucose Dehydrogenase
pdb|3TDK|D Chain D, Crystal Structure Of Human Udp-Glucose Dehydrogenase
pdb|3TDK|C Chain C, Crystal Structure Of Human Udp-Glucose Dehydrogenase
pdb|3TDK|J Chain J, Crystal Structure Of Human Udp-Glucose Dehydrogenase
pdb|3TDK|I Chain I, Crystal Structure Of Human Udp-Glucose Dehydrogenase
Length = 487
Score = 32.0 bits (71), Expect = 0.97, Method: Compositional matrix adjust.
Identities = 22/68 (32%), Positives = 35/68 (51%), Gaps = 10/68 (14%)
Query: 52 YKHQRYSRAYVELKKPAGVFEFAELLNG-HVFVNEKGAQFKAI--------VEYAPSQRV 102
+K Y R + ++ KPA +F+ +L+G H + G Q + I + YAPS +
Sbjct: 420 FKELDYERIHKKMLKPAFIFDGRRVLDGLHNELQTIGFQIETIGKKVSSKRIPYAPSGEI 479
Query: 103 PKPFSRKD 110
PK FS +D
Sbjct: 480 PK-FSLQD 486
>pdb|2C9K|A Chain A, Structure Of The Functional Form Of The
Mosquito-Larvicidal Cry4aa Toxin From Bacillus
Thuringiensis At 2.8 A Resolution
Length = 612
Score = 29.3 bits (64), Expect = 6.0, Method: Compositional matrix adjust.
Identities = 25/80 (31%), Positives = 37/80 (46%), Gaps = 11/80 (13%)
Query: 58 SRAYVELKKPAGVFEFAELLN----GHVFVNEKGAQFKAI-----VEYAPSQRVPKPFSR 108
+RA + L P GV E LN G + N K F+ + V++AP+Q + F+R
Sbjct: 533 TRAVINLSIP-GVAELGMALNPTFSGTDYTNLKYKDFQYLEFSNEVKFAPNQNISLVFNR 591
Query: 109 KDSREGTIFKDPDYLEFLKV 128
D T D +EFL +
Sbjct: 592 SDVYTNTTVL-IDKIEFLPI 610
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
0.312 0.128 0.363
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 13,675,274
Number of Sequences: 62578
Number of extensions: 527365
Number of successful extensions: 830
Number of sequences better than 100.0: 9
Number of HSP's better than 100.0 without gapping: 2
Number of HSP's successfully gapped in prelim test: 7
Number of HSP's that attempted gapping in prelim test: 826
Number of HSP's gapped (non-prelim): 9
length of query: 527
length of database: 14,973,337
effective HSP length: 103
effective length of query: 424
effective length of database: 8,527,803
effective search space: 3615788472
effective search space used: 3615788472
T: 11
A: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.8 bits)
S2: 54 (25.4 bits)