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= 024882
(261 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|3IZ3|B Chain B, Cryoem Structure Of Cytoplasmic Polyhedrosis Virus
pdb|3IZ3|C Chain C, Cryoem Structure Of Cytoplasmic Polyhedrosis Virus
pdb|3J17|B Chain B, Structure Of A Transcribing Cypovirus By Cryo-Electron
Microscopy
pdb|3J17|C Chain C, Structure Of A Transcribing Cypovirus By Cryo-Electron
Microscopy
Length = 1333
Score = 30.4 bits (67), Expect = 0.96, Method: Composition-based stats.
Identities = 15/43 (34%), Positives = 27/43 (62%), Gaps = 2/43 (4%)
Query: 172 LNIPDYDAPTQLVKPRERNTRYVDA--VLTVPKGTLFPMCGMN 212
++I D + +++ P E T++VDA ++T PKG LF + M+
Sbjct: 1166 VDIHDIEYTAEVMTPSEGYTQHVDAESIMTAPKGKLFHLQFMD 1208
>pdb|1IJQ|A Chain A, Crystal Structure Of The Ldl Receptor Ywtd-Egf Domain Pair
pdb|1IJQ|B Chain B, Crystal Structure Of The Ldl Receptor Ywtd-Egf Domain Pair
Length = 316
Score = 29.6 bits (65), Expect = 1.6, Method: Compositional matrix adjust.
Identities = 22/86 (25%), Positives = 41/86 (47%), Gaps = 5/86 (5%)
Query: 60 DYELYNRNDINRILGPKASCISFKDSACRCFGYMVSKKKYIFT--IDDDCFVAKDPSGKE 117
D +L++ + I+ G + + + + F V + K +T I++ F A +G +
Sbjct: 182 DSKLHSISSIDVNGGNRKTILEDEKRLAHPFSLAVFEDKVFWTDIINEAIFSANRLTGSD 241
Query: 118 INALEQHIKNLLSPSTPLFFNTLYDP 143
+N L + NLLSP + F+ L P
Sbjct: 242 VNLLAE---NLLSPEDMVLFHNLTQP 264
>pdb|3O48|A Chain A, Crystal Structure Of Fission Protein Fis1 From
Saccharomyces Cerevisiae
Length = 134
Score = 29.6 bits (65), Expect = 1.8, Method: Compositional matrix adjust.
Identities = 21/110 (19%), Positives = 44/110 (40%), Gaps = 19/110 (17%)
Query: 43 IVQDGDPSKTIKVPDGFDYELYNRNDIN------RIL--------GPKASCISFKDSACR 88
+V +G P+ TI+ + + L D+N +IL + C+ + C
Sbjct: 30 VVSEGGPTATIQSRFNYAWGLIKSTDVNDERLGVKILTDIYKEAESRRRECLYYLTIGCY 89
Query: 89 CFGYMVSKKKYIFTIDDDCFVAKDPSGKEINALEQHIKNLLSPSTPLFFN 138
G K+Y+ D + + K++ AL+ +++ + L+F
Sbjct: 90 KLGEYSMAKRYV-----DTLFEHERNNKQVGALKSMVEDKIQKEENLYFQ 134
>pdb|2YWE|A Chain A, Crystal Structure Of Lepa From Aquifex Aeolicus
pdb|2YWF|A Chain A, Crystal Structure Of Gmppnp-Bound Lepa From Aquifex
Aeolicus
pdb|2YWH|A Chain A, Crystal Structure Of Gdp-Bound Lepa From Aquifex Aeolicus
Length = 600
Score = 28.1 bits (61), Expect = 5.7, Method: Compositional matrix adjust.
Identities = 12/32 (37%), Positives = 17/32 (53%)
Query: 130 SPSTPLFFNTLYDPYREGADFVRGYPFSLREG 161
P L F++ YDPYR FVR + ++ G
Sbjct: 191 KPLKALIFDSYYDPYRGAVAFVRIFDGEVKPG 222
>pdb|3P5B|L Chain L, The Structure Of The LdlrPCSK9 COMPLEX REVEALS THE
RECEPTOR IN AN Extended Conformation
Length = 400
Score = 28.1 bits (61), Expect = 5.7, Method: Compositional matrix adjust.
Identities = 22/86 (25%), Positives = 41/86 (47%), Gaps = 5/86 (5%)
Query: 60 DYELYNRNDINRILGPKASCISFKDSACRCFGYMVSKKKYIFT--IDDDCFVAKDPSGKE 117
D +L++ + I+ G + + + + F V + K +T I++ F A +G +
Sbjct: 264 DSKLHSISSIDVNGGNRKTILEDEKRLAHPFSLAVFEDKVFWTDIINEAIFSANRLTGSD 323
Query: 118 INALEQHIKNLLSPSTPLFFNTLYDP 143
+N L + NLLSP + F+ L P
Sbjct: 324 VNLLAE---NLLSPEDMVLFHNLTQP 346
>pdb|2YWG|A Chain A, Crystal Structure Of Gtp-Bound Lepa From Aquifex Aeolicus
Length = 600
Score = 27.7 bits (60), Expect = 6.7, Method: Compositional matrix adjust.
Identities = 12/32 (37%), Positives = 17/32 (53%)
Query: 130 SPSTPLFFNTLYDPYREGADFVRGYPFSLREG 161
P L F++ YDPYR FVR + ++ G
Sbjct: 191 KPLKALIFDSYYDPYRGAVAFVRIFDGEVKPG 222
>pdb|3M0C|C Chain C, The X-Ray Crystal Structure Of Pcsk9 In Complex With The
Ldl Receptor
Length = 791
Score = 27.7 bits (60), Expect = 7.3, Method: Composition-based stats.
Identities = 22/86 (25%), Positives = 41/86 (47%), Gaps = 5/86 (5%)
Query: 60 DYELYNRNDINRILGPKASCISFKDSACRCFGYMVSKKKYIFT--IDDDCFVAKDPSGKE 117
D +L++ + I+ G + + + + F V + K +T I++ F A +G +
Sbjct: 576 DSKLHSISSIDVNGGNRKTILEDEKRLAHPFSLAVFEDKVFWTDIINEAIFSANRLTGSD 635
Query: 118 INALEQHIKNLLSPSTPLFFNTLYDP 143
+N L + NLLSP + F+ L P
Sbjct: 636 VNLLAE---NLLSPEDMVLFHNLTQP 658
>pdb|3P5C|L Chain L, The Structure Of The LdlrPCSK9 COMPLEX REVEALS THE
RECEPTOR IN AN Extended Conformation
Length = 440
Score = 27.3 bits (59), Expect = 9.2, Method: Compositional matrix adjust.
Identities = 22/86 (25%), Positives = 41/86 (47%), Gaps = 5/86 (5%)
Query: 60 DYELYNRNDINRILGPKASCISFKDSACRCFGYMVSKKKYIFT--IDDDCFVAKDPSGKE 117
D +L++ + I+ G + + + + F V + K +T I++ F A +G +
Sbjct: 304 DSKLHSISSIDVNGGNRKTILEDEKRLAHPFSLAVFEDKVFWTDIINEAIFSANRLTGSD 363
Query: 118 INALEQHIKNLLSPSTPLFFNTLYDP 143
+N L + NLLSP + F+ L P
Sbjct: 364 VNLLAE---NLLSPEDMVLFHNLTQP 386
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
0.325 0.144 0.468
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 8,977,941
Number of Sequences: 62578
Number of extensions: 402024
Number of successful extensions: 933
Number of sequences better than 100.0: 9
Number of HSP's better than 100.0 without gapping: 3
Number of HSP's successfully gapped in prelim test: 6
Number of HSP's that attempted gapping in prelim test: 930
Number of HSP's gapped (non-prelim): 9
length of query: 261
length of database: 14,973,337
effective HSP length: 97
effective length of query: 164
effective length of database: 8,903,271
effective search space: 1460136444
effective search space used: 1460136444
T: 11
A: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 bits)
S2: 50 (23.9 bits)