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= 027304
(225 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|3M0C|C Chain C, The X-Ray Crystal Structure Of Pcsk9 In Complex With The
Ldl Receptor
Length = 791
Score = 36.2 bits (82), Expect = 0.016, Method: Compositional matrix adjust.
Identities = 34/106 (32%), Positives = 44/106 (41%), Gaps = 10/106 (9%)
Query: 10 IPLMSLCFLVVFVQCKSSLLGVHPLDEKYFSKEVIKCKDGSKSFTRDRLNDNFCDCIDGT 69
IP C V S G P K S++ +C DG K +R + D+ DC+DG+
Sbjct: 80 IPQFWRCDGQVDCDNGSDEQGCPP---KTCSQDEFRCHDG-KCISRQFVCDSDRDCLDGS 135
Query: 70 DEPGTS--ACPAGKFYCGNVGSTPQFIFSSRVNDRICDCCDGSDEY 113
DE C F C + PQ D DC DGSDE+
Sbjct: 136 DEASCPVLTCGPASFQCNSSTCIPQLWAC----DNDPDCEDGSDEW 177
>pdb|1N7D|A Chain A, Extracellular Domain Of The Ldl Receptor
Length = 699
Score = 35.8 bits (81), Expect = 0.018, Method: Compositional matrix adjust.
Identities = 34/106 (32%), Positives = 44/106 (41%), Gaps = 10/106 (9%)
Query: 10 IPLMSLCFLVVFVQCKSSLLGVHPLDEKYFSKEVIKCKDGSKSFTRDRLNDNFCDCIDGT 69
IP C V S G P K S++ +C DG K +R + D+ DC+DG+
Sbjct: 62 IPQFWRCDGQVDCDNGSDEQGCPP---KTCSQDEFRCHDG-KCISRQFVCDSDRDCLDGS 117
Query: 70 DEPGTS--ACPAGKFYCGNVGSTPQFIFSSRVNDRICDCCDGSDEY 113
DE C F C + PQ D DC DGSDE+
Sbjct: 118 DEASCPVLTCGPASFQCNSSTCIPQLW----ACDNDPDCEDGSDEW 159
>pdb|2FCW|B Chain B, Structure Of A Complex Between The Pair Of The Ldl
Receptor Ligand-Binding Modules 3-4 And The Receptor
Associated Protein (Rap)
Length = 80
Score = 32.3 bits (72), Expect = 0.21, Method: Compositional matrix adjust.
Identities = 27/79 (34%), Positives = 37/79 (46%), Gaps = 7/79 (8%)
Query: 37 KYFSKEVIKCKDGSKSFTRDRLNDNFCDCIDGTDEPGTS--ACPAGKFYCGNVGSTPQFI 94
K S+ +C DG K +R + D+ DC+DG+DE C F C + PQ
Sbjct: 1 KTCSQAEFRCHDG-KCISRQFVCDSDRDCLDGSDEASCPVLTCGPASFQCNSSTCIPQLW 59
Query: 95 FSSRVNDRICDCCDGSDEY 113
ND C+ DGSDE+
Sbjct: 60 ACD--NDPDCE--DGSDEW 74
>pdb|3H32|A Chain A, Crystal Structure Of D-Dimer From Human Fibrin Complexed
With Gly-His- Arg-Pro-Tyr-Amide
pdb|3H32|D Chain D, Crystal Structure Of D-Dimer From Human Fibrin Complexed
With Gly-His- Arg-Pro-Tyr-Amide
Length = 197
Score = 26.9 bits (58), Expect = 8.4, Method: Compositional matrix adjust.
Identities = 17/49 (34%), Positives = 24/49 (48%), Gaps = 5/49 (10%)
Query: 98 RVNDRICDCCDGSD-----EYDSSIKCPNTCVMGGNIEYKAQSYISTIN 141
RV +R C SD + D + KCP+ C M G I+ Q + + IN
Sbjct: 19 RVVERHQSACKDSDWPFCSDEDWNYKCPSGCRMKGLIDEVNQDFTNRIN 67
>pdb|1JY2|N Chain N, Crystal Structure Of The Central Region Of Bovine
Fibrinogen (E5 Fragment) At 1.4 Angstroms Resolution
pdb|1JY2|Q Chain Q, Crystal Structure Of The Central Region Of Bovine
Fibrinogen (E5 Fragment) At 1.4 Angstroms Resolution
pdb|1JY3|N Chain N, Crystal Structure Of The Central Region Of Bovine
Fibrinogen (E5 Fragment) At 1.4 Angstroms Resolution
pdb|1JY3|Q Chain Q, Crystal Structure Of The Central Region Of Bovine
Fibrinogen (E5 Fragment) At 1.4 Angstroms Resolution
Length = 53
Score = 26.9 bits (58), Expect = 9.3, Method: Compositional matrix adjust.
Identities = 15/32 (46%), Positives = 19/32 (59%), Gaps = 1/32 (3%)
Query: 110 SDEYDSSIKCPNTCVMGGNIEYKAQSYISTIN 141
SDE D + KCP+ C M G I+ Q + S IN
Sbjct: 12 SDE-DWNTKCPSGCRMKGLIDEVDQDFTSRIN 42
>pdb|3GHG|A Chain A, Crystal Structure Of Human Fibrinogen
pdb|3GHG|D Chain D, Crystal Structure Of Human Fibrinogen
pdb|3GHG|G Chain G, Crystal Structure Of Human Fibrinogen
pdb|3GHG|J Chain J, Crystal Structure Of Human Fibrinogen
Length = 562
Score = 26.9 bits (58), Expect = 9.8, Method: Compositional matrix adjust.
Identities = 17/53 (32%), Positives = 25/53 (47%), Gaps = 5/53 (9%)
Query: 94 IFSSRVNDRICDCCDGSD-----EYDSSIKCPNTCVMGGNIEYKAQSYISTIN 141
+ RV +R C SD + D + KCP+ C M G I+ Q + + IN
Sbjct: 15 VRGPRVVERHQSACKDSDWPFCSDEDWNYKCPSGCRMKGLIDEVNQDFTNRIN 67
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
0.326 0.141 0.437
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 6,212,511
Number of Sequences: 62578
Number of extensions: 258168
Number of successful extensions: 527
Number of sequences better than 100.0: 12
Number of HSP's better than 100.0 without gapping: 1
Number of HSP's successfully gapped in prelim test: 11
Number of HSP's that attempted gapping in prelim test: 513
Number of HSP's gapped (non-prelim): 14
length of query: 225
length of database: 14,973,337
effective HSP length: 95
effective length of query: 130
effective length of database: 9,028,427
effective search space: 1173695510
effective search space used: 1173695510
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)