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= 010224
(514 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 = 67.8 bits (164), Expect = 1e-11, Method: Composition-based stats.
Identities = 33/90 (36%), Positives = 54/90 (60%), Gaps = 2/90 (2%)
Query: 8 TKVVVRNLPPAITQPAFTEQIDGAFGGRYNWVSFRQGKTSQKHQSCARAYLDFKKPEDVL 67
+KVV+R LPP +T+ E + +++ F TS ARAY++FK ED++
Sbjct: 2 SKVVIRRLPPTLTKEQLQEHLQPM--PEHDYFEFFSNDTSLYPHMYARAYINFKNQEDII 59
Query: 68 EFAEFFNGHVFVNEKGVQFKTIVEYAPSQR 97
F + F+G+VF++ KG ++ IVE+AP Q+
Sbjct: 60 LFRDRFDGYVFLDNKGQEYPAIVEFAPFQK 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 = 65.5 bits (158), Expect = 6e-11, Method: Composition-based stats.
Identities = 29/88 (32%), Positives = 54/88 (61%), Gaps = 2/88 (2%)
Query: 10 VVVRNLPPAITQPAFTEQIDGAFGGRYNWVSFRQGKTSQKHQSCARAYLDFKKPEDVLEF 69
VV+R LPP +T+ EQ+ +++ F S +RAY++F+ P+D+L F
Sbjct: 12 VVIRRLPPGLTKEQLEEQLRPLPA--HDYFEFFAADLSLYPHLYSRAYINFRNPDDILLF 69
Query: 70 AEFFNGHVFVNEKGVQFKTIVEYAPSQR 97
+ F+G++F++ KG+++ +VE+AP Q+
Sbjct: 70 RDRFDGYIFLDSKGLEYPAVVEFAPFQK 97
>pdb|2YFR|A Chain A, Crystal Structure Of Inulosucrase From Lactobacillus
Johnsonii Ncc533
pdb|2YFT|A Chain A, Crystal Structure Of Inulosucrase From Lactobacillus
Johnsonii Ncc533 In Complex With 1-Kestose
Length = 571
Score = 30.8 bits (68), Expect = 1.8, Method: Compositional matrix adjust.
Identities = 18/83 (21%), Positives = 36/83 (43%), Gaps = 2/83 (2%)
Query: 17 PAITQPAFTEQI--DGAFGGRYNWVSFRQGKTSQKHQSCARAYLDFKKPEDVLEFAEFFN 74
P I Q + + + DG+ Y V T+ + + A YL+ +K +D + A N
Sbjct: 191 PVIQQWSGSATLNKDGSIQLYYTKVDTSDNNTNHQKLASATVYLNLEKDQDKISIAHVDN 250
Query: 75 GHVFVNEKGVQFKTIVEYAPSQR 97
H+ G ++T ++ + +
Sbjct: 251 DHIVFEGDGYHYQTYDQWKETNK 273
>pdb|2YFS|A Chain A, Crystal Structure Of Inulosucrase From Lactobacillus
Johnsonii Ncc533 In Complex With Sucrose
Length = 571
Score = 30.8 bits (68), Expect = 1.9, Method: Compositional matrix adjust.
Identities = 18/83 (21%), Positives = 36/83 (43%), Gaps = 2/83 (2%)
Query: 17 PAITQPAFTEQI--DGAFGGRYNWVSFRQGKTSQKHQSCARAYLDFKKPEDVLEFAEFFN 74
P I Q + + + DG+ Y V T+ + + A YL+ +K +D + A N
Sbjct: 191 PVIQQWSGSATLNKDGSIQLYYTKVDTSDNNTNHQKLASATVYLNLEKDQDKISIAHVDN 250
Query: 75 GHVFVNEKGVQFKTIVEYAPSQR 97
H+ G ++T ++ + +
Sbjct: 251 DHIVFEGDGYHYQTYDQWKETNK 273
>pdb|4GZ8|A Chain A, Mouse Semaphorin 3a, Domains Sema-Psi-Ig
pdb|4GZ8|B Chain B, Mouse Semaphorin 3a, Domains Sema-Psi-Ig
Length = 667
Score = 29.3 bits (64), Expect = 5.2, Method: Compositional matrix adjust.
Identities = 26/113 (23%), Positives = 47/113 (41%), Gaps = 9/113 (7%)
Query: 33 GGRYNWVSFRQGKTSQKHQSC-ARAYLDFKK----PEDVLEFA----EFFNGHVFVNEKG 83
G Y WV ++ + +C ++ + F P+DV+ FA +N +N +
Sbjct: 344 GPNYQWVPYQGRVPYPRPGTCPSKTFGGFDSTKDLPDDVITFARSHPAMYNPVFPINNRP 403
Query: 84 VQFKTIVEYAPSQRVPKQWSKKDGREGTLLKDPEYLEFLEFISKPVENLPSAE 136
+ KT V Y +Q V + +DG+ + + L+ +S P E E
Sbjct: 404 IMIKTDVNYQFTQIVVDRVDAEDGQYDVMFIGTDVGTVLKVVSVPKETWHDLE 456
>pdb|1Q47|A Chain A, Structure Of The Semaphorin 3a Receptor-Binding Module
pdb|1Q47|B Chain B, Structure Of The Semaphorin 3a Receptor-Binding Module
Length = 495
Score = 29.3 bits (64), Expect = 5.9, Method: Compositional matrix adjust.
Identities = 26/113 (23%), Positives = 47/113 (41%), Gaps = 9/113 (7%)
Query: 33 GGRYNWVSFRQGKTSQKHQSC-ARAYLDFKK----PEDVLEFA----EFFNGHVFVNEKG 83
G Y WV ++ + +C ++ + F P+DV+ FA +N +N +
Sbjct: 336 GPNYQWVPYQGRVPYPRPGTCPSKTFGGFDSTKDLPDDVITFARSHPAMYNPVFPINNRP 395
Query: 84 VQFKTIVEYAPSQRVPKQWSKKDGREGTLLKDPEYLEFLEFISKPVENLPSAE 136
+ KT V Y +Q V + +DG+ + + L+ +S P E E
Sbjct: 396 IMIKTDVNYQFTQIVVDRVDAEDGQYDVMFIGTDVGTVLKVVSVPKETWHDLE 448
>pdb|4GZA|G Chain G, Complex Of Mouse Plexin A2 - Semaphorin 3a - Neuropilin-1
Length = 538
Score = 29.3 bits (64), Expect = 6.2, Method: Compositional matrix adjust.
Identities = 26/113 (23%), Positives = 47/113 (41%), Gaps = 9/113 (7%)
Query: 33 GGRYNWVSFRQGKTSQKHQSC-ARAYLDFKK----PEDVLEFA----EFFNGHVFVNEKG 83
G Y WV ++ + +C ++ + F P+DV+ FA +N +N +
Sbjct: 344 GPNYQWVPYQGRVPYPRPGTCPSKTFGGFDSTKDLPDDVITFARSHPAMYNPVFPINNRP 403
Query: 84 VQFKTIVEYAPSQRVPKQWSKKDGREGTLLKDPEYLEFLEFISKPVENLPSAE 136
+ KT V Y +Q V + +DG+ + + L+ +S P E E
Sbjct: 404 IMIKTDVNYQFTQIVVDRVDAEDGQYDVMFIGTDVGTVLKVVSVPKETWHDLE 456
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
0.313 0.131 0.376
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 13,090,166
Number of Sequences: 62578
Number of extensions: 490481
Number of successful extensions: 689
Number of sequences better than 100.0: 9
Number of HSP's better than 100.0 without gapping: 5
Number of HSP's successfully gapped in prelim test: 4
Number of HSP's that attempted gapping in prelim test: 682
Number of HSP's gapped (non-prelim): 9
length of query: 514
length of database: 14,973,337
effective HSP length: 103
effective length of query: 411
effective length of database: 8,527,803
effective search space: 3504927033
effective search space used: 3504927033
T: 11
A: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.9 bits)
S2: 54 (25.4 bits)