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= 009879
(523 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 = 61.2 bits (147), Expect = 1e-09, Method: Composition-based stats.
Identities = 32/92 (34%), Positives = 54/92 (58%), Gaps = 6/92 (6%)
Query: 8 TKVVIRHLPPSLSQNDLLALFRDHFND--RYNWFCFRPGKSSYKHQRYSRAYVELKKPAG 65
+KVVIR LPP+L++ L ++H +++F F +S Y+RAY+ K
Sbjct: 2 SKVVIRRLPPTLTKEQL----QEHLQPMPEHDYFEFFSNDTSLYPHMYARAYINFKNQED 57
Query: 66 VFEFAELLNGHVFVNEKGAQFKAIVEYAPSQR 97
+ F + +G+VF++ KG ++ AIVE+AP Q+
Sbjct: 58 IILFRDRFDGYVFLDNKGQEYPAIVEFAPFQK 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 = 60.1 bits (144), Expect = 3e-09, Method: Composition-based stats.
Identities = 30/88 (34%), Positives = 49/88 (55%), Gaps = 2/88 (2%)
Query: 10 VVIRHLPPSLSQNDLLALFRDHFNDRYNWFCFRPGKSSYKHQRYSRAYVELKKPAGVFEF 69
VVIR LPP L++ L R +++F F S YSRAY+ + P + F
Sbjct: 12 VVIRRLPPGLTKEQLEEQLRPL--PAHDYFEFFAADLSLYPHLYSRAYINFRNPDDILLF 69
Query: 70 AELLNGHVFVNEKGAQFKAIVEYAPSQR 97
+ +G++F++ KG ++ A+VE+AP Q+
Sbjct: 70 RDRFDGYIFLDSKGLEYPAVVEFAPFQK 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 = 0.91, Method: Compositional matrix adjust.
Identities = 22/68 (32%), Positives = 35/68 (51%), Gaps = 10/68 (14%)
Query: 48 YKHQRYSRAYVELKKPAGVFEFAELLNG-HVFVNEKGAQFKAI--------VEYAPSQRV 98
+K Y R + ++ KPA +F+ +L+G H + G Q + I + YAPS +
Sbjct: 419 FKELDYERIHKKMLKPAFIFDGRRVLDGLHNELQTIGFQIETIGKKVSSKRIPYAPSGEI 478
Query: 99 PKPFSRKD 106
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 = 0.93, Method: Compositional matrix adjust.
Identities = 22/68 (32%), Positives = 35/68 (51%), Gaps = 10/68 (14%)
Query: 48 YKHQRYSRAYVELKKPAGVFEFAELLNG-HVFVNEKGAQFKAI--------VEYAPSQRV 98
+K Y R + ++ KPA +F+ +L+G H + G Q + I + YAPS +
Sbjct: 420 FKELDYERIHKKMLKPAFIFDGRRVLDGLHNELQTIGFQIETIGKKVSSKRIPYAPSGEI 479
Query: 99 PKPFSRKD 106
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: 48 YKHQRYSRAYVELKKPAGVFEFAELLNG-HVFVNEKGAQFKAI--------VEYAPSQRV 98
+K Y R + ++ KPA +F+ +L+G H + G Q + I + YAPS +
Sbjct: 420 FKELDYERIHKKMLKPAFIFDGRRVLDGLHNELQTIGFQIETIGKKVSSKRIPYAPSGEI 479
Query: 99 PKPFSRKD 106
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 = 31.6 bits (70), Expect = 1.00, Method: Compositional matrix adjust.
Identities = 22/68 (32%), Positives = 35/68 (51%), Gaps = 10/68 (14%)
Query: 48 YKHQRYSRAYVELKKPAGVFEFAELLNG-HVFVNEKGAQFKAI--------VEYAPSQRV 98
+K Y R + ++ KPA +F+ +L+G H + G Q + I + YAPS +
Sbjct: 420 FKELDYERIHKKMLKPAFIFDGRRVLDGLHNELQTIGFQIETIGKKVSSKRIPYAPSGEI 479
Query: 99 PKPFSRKD 106
PK FS +D
Sbjct: 480 PK-FSLQD 486
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
0.311 0.128 0.361
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 13,575,178
Number of Sequences: 62578
Number of extensions: 524108
Number of successful extensions: 775
Number of sequences better than 100.0: 8
Number of HSP's better than 100.0 without gapping: 2
Number of HSP's successfully gapped in prelim test: 6
Number of HSP's that attempted gapping in prelim test: 771
Number of HSP's gapped (non-prelim): 8
length of query: 523
length of database: 14,973,337
effective HSP length: 103
effective length of query: 420
effective length of database: 8,527,803
effective search space: 3581677260
effective search space used: 3581677260
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)