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= 011304
(489 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|2KT6|A Chain A, Structural Homology Between The C-Terminal Domain Of The
Papc Usher And Its Plug
Length = 85
Score = 32.7 bits (73), Expect = 0.46, Method: Composition-based stats.
Identities = 20/72 (27%), Positives = 33/72 (45%), Gaps = 7/72 (9%)
Query: 300 FGKDDLSDKKRNVAIVTTASLPWMTGTAVNPLFRAAYLAKTEQQNVTLLVPWLCKSDQEL 359
FG S+K R + +V L W++G + K + Q + VP SDQ+L
Sbjct: 21 FGASVTSEKGRELGMVADEGLAWLSGVTPGETLSVNWDGKIQCQ---VNVPETAISDQQL 77
Query: 360 VYPNVTFCSPEE 371
+ P C+P++
Sbjct: 78 LLP----CTPQK 85
>pdb|3L48|A Chain A, Crystal Structure Of The C-Terminal Domain Of The Papc
Usher
pdb|3L48|B Chain B, Crystal Structure Of The C-Terminal Domain Of The Papc
Usher
pdb|3L48|C Chain C, Crystal Structure Of The C-Terminal Domain Of The Papc
Usher
pdb|3L48|D Chain D, Crystal Structure Of The C-Terminal Domain Of The Papc
Usher
pdb|3L48|E Chain E, Crystal Structure Of The C-Terminal Domain Of The Papc
Usher
Length = 94
Score = 32.7 bits (73), Expect = 0.48, Method: Composition-based stats.
Identities = 20/72 (27%), Positives = 33/72 (45%), Gaps = 7/72 (9%)
Query: 300 FGKDDLSDKKRNVAIVTTASLPWMTGTAVNPLFRAAYLAKTEQQNVTLLVPWLCKSDQEL 359
FG S+K R + +V L W++G + K + Q + VP SDQ+L
Sbjct: 24 FGASVTSEKGRELGMVADEGLAWLSGVTPGETLSVNWDGKIQCQ---VNVPETAISDQQL 80
Query: 360 VYPNVTFCSPEE 371
+ P C+P++
Sbjct: 81 LLP----CTPQK 88
>pdb|3BXJ|A Chain A, Crystal Structure Of The C2-Gap Fragment Of Syngap
pdb|3BXJ|B Chain B, Crystal Structure Of The C2-Gap Fragment Of Syngap
Length = 483
Score = 29.3 bits (64), Expect = 4.9, Method: Compositional matrix adjust.
Identities = 23/67 (34%), Positives = 32/67 (47%), Gaps = 3/67 (4%)
Query: 49 FDRELENFLNSANRSSAPAEIDFVKKLQPKISEFRRVYSAPEISKRVLEKWGPRARIRID 108
F E+ N N SS ID ++L + V P++SK L K GP R+ D
Sbjct: 412 FLYEISNLDTLTNSSSFEGYIDLGRELSTLHALLWEVL--PQLSKEALLKLGPLPRLLSD 469
Query: 109 LS-AIRN 114
+S A+RN
Sbjct: 470 ISTALRN 476
>pdb|3KO2|A Chain A, I-Msoi Re-Designed For Altered Dna Cleavage Specificity
(-7c)
pdb|3KO2|B Chain B, I-Msoi Re-Designed For Altered Dna Cleavage Specificity
(-7c)
pdb|3KO2|F Chain F, I-Msoi Re-Designed For Altered Dna Cleavage Specificity
(-7c)
pdb|3KO2|G Chain G, I-Msoi Re-Designed For Altered Dna Cleavage Specificity
(-7c)
Length = 170
Score = 28.9 bits (63), Expect = 7.3, Method: Compositional matrix adjust.
Identities = 14/36 (38%), Positives = 22/36 (61%), Gaps = 2/36 (5%)
Query: 31 DIQLMKNRANSFKNLATSFDRELENFLNSANRSSAP 66
D+Q + RA+ K +T++DR LE FL + S+P
Sbjct: 137 DVQNLNKRADELK--STNYDRLLEEFLKAGKIESSP 170
>pdb|2FLD|A Chain A, I-Msoi Re-Designed For Altered Dna Cleavage Specificity
pdb|2FLD|B Chain B, I-Msoi Re-Designed For Altered Dna Cleavage Specificity
Length = 165
Score = 28.9 bits (63), Expect = 7.6, Method: Compositional matrix adjust.
Identities = 14/36 (38%), Positives = 22/36 (61%), Gaps = 2/36 (5%)
Query: 31 DIQLMKNRANSFKNLATSFDRELENFLNSANRSSAP 66
D+Q + RA+ K +T++DR LE FL + S+P
Sbjct: 132 DVQNLNKRADELK--STNYDRLLEEFLKAGKIESSP 165
>pdb|3FD2|A Chain A, Crystal Structure Of MmsoiDNA COMPLEX WITH CALCIUM
Length = 373
Score = 28.5 bits (62), Expect = 8.0, Method: Compositional matrix adjust.
Identities = 14/36 (38%), Positives = 22/36 (61%), Gaps = 2/36 (5%)
Query: 31 DIQLMKNRANSFKNLATSFDRELENFLNSANRSSAP 66
D+Q + RA+ K +T++DR LE FL + S+P
Sbjct: 340 DVQNLNKRADELK--STNYDRLLEEFLKAGKIESSP 373
>pdb|1M5X|A Chain A, Crystal Structure Of The Homing Endonuclease I-Msoi Bound
To Its Dna Substrate
pdb|1M5X|B Chain B, Crystal Structure Of The Homing Endonuclease I-Msoi Bound
To Its Dna Substrate
Length = 170
Score = 28.5 bits (62), Expect = 8.2, Method: Compositional matrix adjust.
Identities = 14/36 (38%), Positives = 22/36 (61%), Gaps = 2/36 (5%)
Query: 31 DIQLMKNRANSFKNLATSFDRELENFLNSANRSSAP 66
D+Q + RA+ K +T++DR LE FL + S+P
Sbjct: 137 DVQNLNKRADELK--STNYDRLLEEFLKAGKIESSP 170
>pdb|1QGO|A Chain A, Anaerobic Cobalt Chelatase In Cobalamin Biosynthesis From
Salmonella Typhimurium
pdb|2XWP|A Chain A, Anaerobic Cobalt Chelatase (Cbik) From Salmonella
Typhimurium In Complex With Metalated Tetrapyrrole
Length = 264
Score = 28.5 bits (62), Expect = 8.9, Method: Compositional matrix adjust.
Identities = 13/44 (29%), Positives = 18/44 (40%)
Query: 299 DFGKDDLSDKKRNVAIVTTASLPWMTGTAVNPLFRAAYLAKTEQ 342
D DD K + PW++G NP RA ++A Q
Sbjct: 211 DMASDDGDSWKMRFNAAGIPATPWLSGLGENPAIRAMFVAHLHQ 254
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 0.135 0.411
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 15,144,011
Number of Sequences: 62578
Number of extensions: 656453
Number of successful extensions: 1523
Number of sequences better than 100.0: 11
Number of HSP's better than 100.0 without gapping: 1
Number of HSP's successfully gapped in prelim test: 10
Number of HSP's that attempted gapping in prelim test: 1521
Number of HSP's gapped (non-prelim): 12
length of query: 489
length of database: 14,973,337
effective HSP length: 103
effective length of query: 386
effective length of database: 8,527,803
effective search space: 3291731958
effective search space used: 3291731958
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 53 (25.0 bits)