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= 041671
(296 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|1FWK|A Chain A, Crystal Structure Of Homoserine Kinase Complexed With Adp
pdb|1FWK|B Chain B, Crystal Structure Of Homoserine Kinase Complexed With Adp
pdb|1FWK|C Chain C, Crystal Structure Of Homoserine Kinase Complexed With Adp
pdb|1FWK|D Chain D, Crystal Structure Of Homoserine Kinase Complexed With Adp
pdb|1FWL|A Chain A, Crystal Structure Of Homoserine Kinase
pdb|1FWL|B Chain B, Crystal Structure Of Homoserine Kinase
pdb|1FWL|C Chain C, Crystal Structure Of Homoserine Kinase
pdb|1FWL|D Chain D, Crystal Structure Of Homoserine Kinase
pdb|1H72|C Chain C, Crystal Structure Of Homoserine Kinase Complexed With Hse
pdb|1H74|A Chain A, Crystal Structure Of Homoserine Kinase Complexed With Ile
pdb|1H74|B Chain B, Crystal Structure Of Homoserine Kinase Complexed With Ile
pdb|1H74|C Chain C, Crystal Structure Of Homoserine Kinase Complexed With Ile
pdb|1H74|D Chain D, Crystal Structure Of Homoserine Kinase Complexed With Ile
pdb|1H73|A Chain A, Crystal Structure Of Homoserine Kinase Complexed With
Threonine
Length = 296
Score = 32.3 bits (72), Expect = 0.29, Method: Compositional matrix adjust.
Identities = 21/71 (29%), Positives = 33/71 (46%), Gaps = 5/71 (7%)
Query: 202 YALLADETFNIAEFRASEDKSSSNVTIEWVVEEKNCPDDPNSKVDGCGDNTNCYYSENGK 261
+ L E +++ E A +DK + IE V++KN P DP+ V G GK
Sbjct: 21 FGLCLKEPYDVIEVEAIDDKE---IIIE--VDDKNIPTDPDKNVAGIVAKKMIDDFNIGK 75
Query: 262 GYRCKCKQGFQ 272
G + K+G +
Sbjct: 76 GVKITIKKGVK 86
>pdb|4G1E|B Chain B, Crystal Structure Of Integrin Alpha V Beta 3 With
Coil-Coiled Tag
Length = 738
Score = 30.4 bits (67), Expect = 1.1, Method: Compositional matrix adjust.
Identities = 26/82 (31%), Positives = 37/82 (45%), Gaps = 13/82 (15%)
Query: 185 LRSVHNHEDMG-EFMQCDYALLADETFNIAEFRASEDKSSSNVTIEWVVEEKNCPDDPNS 243
+ SV +D G + + C Y +E + F+ ED SS +I +VVEE CP P S
Sbjct: 639 IESVKELKDTGKDAVNCTYK---NEDDCVVRFQYYED--SSGKSILYVVEEPECPKGPES 693
Query: 244 KVDGCGDNTNCYYSENGKGYRC 265
N Y+ GK +C
Sbjct: 694 M-------ENLYFQSGGKNAQC 708
>pdb|3P5B|L Chain L, The Structure Of The LdlrPCSK9 COMPLEX REVEALS THE
RECEPTOR IN AN Extended Conformation
Length = 400
Score = 30.4 bits (67), Expect = 1.3, Method: Compositional matrix adjust.
Identities = 14/28 (50%), Positives = 15/28 (53%)
Query: 262 GYRCKCKQGFQGNPYLGCVDIDECLDKE 289
GY C C GFQ C DIDEC D +
Sbjct: 20 GYECLCPDGFQLVAQRRCEDIDECQDPD 47
Score = 28.1 bits (61), Expect = 5.5, Method: Compositional matrix adjust.
Identities = 15/48 (31%), Positives = 25/48 (52%), Gaps = 7/48 (14%)
Query: 231 VVEEKNCPDDPNSKVDGCGDNTNCYY--SENGKGYRCKCKQGFQGNPY 276
+V ++ C D +D C D C GY+C+C++GFQ +P+
Sbjct: 31 LVAQRRCED-----IDECQDPDTCSQLCVNLEGGYKCQCEEGFQLDPH 73
>pdb|3P5C|L Chain L, The Structure Of The LdlrPCSK9 COMPLEX REVEALS THE
RECEPTOR IN AN Extended Conformation
Length = 440
Score = 30.0 bits (66), Expect = 1.4, Method: Compositional matrix adjust.
Identities = 21/64 (32%), Positives = 27/64 (42%), Gaps = 10/64 (15%)
Query: 235 KNCPDDPNSKVDGCGDNTNCYYSENG---------KGYRCKCKQGFQGNPYLGCVDIDEC 285
++C D + + CG N C + G GY C C GFQ C DIDEC
Sbjct: 25 RDCRDWSDEPIKECGTN-ECLDNNGGCSHVCNDLKIGYECLCPDGFQLVAQRRCEDIDEC 83
Query: 286 LDKE 289
D +
Sbjct: 84 QDPD 87
Score = 28.1 bits (61), Expect = 6.5, Method: Compositional matrix adjust.
Identities = 15/48 (31%), Positives = 25/48 (52%), Gaps = 7/48 (14%)
Query: 231 VVEEKNCPDDPNSKVDGCGDNTNCYY--SENGKGYRCKCKQGFQGNPY 276
+V ++ C D +D C D C GY+C+C++GFQ +P+
Sbjct: 71 LVAQRRCED-----IDECQDPDTCSQLCVNLEGGYKCQCEEGFQLDPH 113
>pdb|3M0C|C Chain C, The X-Ray Crystal Structure Of Pcsk9 In Complex With The
Ldl Receptor
Length = 791
Score = 29.6 bits (65), Expect = 1.8, Method: Compositional matrix adjust.
Identities = 14/28 (50%), Positives = 15/28 (53%)
Query: 262 GYRCKCKQGFQGNPYLGCVDIDECLDKE 289
GY C C GFQ C DIDEC D +
Sbjct: 332 GYECLCPDGFQLVAQRRCEDIDECQDPD 359
>pdb|1N7D|A Chain A, Extracellular Domain Of The Ldl Receptor
Length = 699
Score = 29.6 bits (65), Expect = 2.3, Method: Compositional matrix adjust.
Identities = 14/28 (50%), Positives = 15/28 (53%)
Query: 262 GYRCKCKQGFQGNPYLGCVDIDECLDKE 289
GY C C GFQ C DIDEC D +
Sbjct: 314 GYECLCPDGFQLVAQRRCEDIDECQDPD 341
>pdb|2W2M|E Chain E, Wt Pcsk9-Deltac Bound To Wt Egf-A Of Ldlr
pdb|2W2O|E Chain E, Pcsk9-deltac D374y Mutant Bound To Wt Egf-a Of Ldlr
pdb|2W2P|E Chain E, Pcsk9-Deltac D374a Mutant Bound To Wt Egf-A Of Ldlr
pdb|2W2Q|E Chain E, Pcsk9-Deltac D374h Mutant Bound To Wt Egf-A Of Ldlr
Length = 107
Score = 28.5 bits (62), Expect = 5.1, Method: Compositional matrix adjust.
Identities = 14/28 (50%), Positives = 15/28 (53%)
Query: 262 GYRCKCKQGFQGNPYLGCVDIDECLDKE 289
GY C C GFQ C DIDEC D +
Sbjct: 49 GYECLCPDGFQLVAQRRCEDIDECQDPD 76
>pdb|3UBH|A Chain A, Crystal Structure Of Drosophila N-Cadherin Ec1-4
Length = 419
Score = 28.5 bits (62), Expect = 5.3, Method: Compositional matrix adjust.
Identities = 25/86 (29%), Positives = 40/86 (46%), Gaps = 9/86 (10%)
Query: 180 SLELTLRSVHNHEDMGEFMQCDY-ALLADETF----NIAEFRASEDKSSSNVTIEWVVEE 234
S++LT+R +++ +F DY A DE +I +A + S SN IE++V +
Sbjct: 307 SVDLTIRVTDVNDNAPKFELPDYQAHNVDEDIPLGTSILRVKAMDSDSGSNAEIEYLVSD 366
Query: 235 KNCPDDPNSKVDGC----GDNTNCYY 256
+ D N + DN N YY
Sbjct: 367 DHFAVDSNGIIVNNKQLDADNNNAYY 392
>pdb|2W2N|E Chain E, Wt Pcsk9-Deltac Bound To Egf-A H306y Mutant Of Ldlr
Length = 107
Score = 28.5 bits (62), Expect = 5.3, Method: Compositional matrix adjust.
Identities = 14/28 (50%), Positives = 15/28 (53%)
Query: 262 GYRCKCKQGFQGNPYLGCVDIDECLDKE 289
GY C C GFQ C DIDEC D +
Sbjct: 49 GYECLCPDGFQLVAQRRCEDIDECQDPD 76
>pdb|1HZ8|A Chain A, Solution Structure And Backbone Dynamics Of A Concatemer
Of Egf-Homology Modules Of The Human Low Density
Lipoprotein Receptor
pdb|1I0U|A Chain A, Solution Structure And Backbone Dynamics Of A Concatemer
Of Egf-Homology Modules Of The Human Low Density
Lipoprotein Receptor
Length = 82
Score = 28.1 bits (61), Expect = 6.4, Method: Compositional matrix adjust.
Identities = 14/26 (53%), Positives = 14/26 (53%)
Query: 262 GYRCKCKQGFQGNPYLGCVDIDECLD 287
GY C C GFQ C DIDEC D
Sbjct: 22 GYECLCPDGFQLVAQRRCEDIDECQD 47
>pdb|1HJ7|A Chain A, Nmr Study Of A Pair Of Ldl Receptor Ca2+ Binding Epidermal
Growth Factor-Like Domains, 20 Structures
Length = 80
Score = 27.7 bits (60), Expect = 7.0, Method: Compositional matrix adjust.
Identities = 14/26 (53%), Positives = 14/26 (53%)
Query: 262 GYRCKCKQGFQGNPYLGCVDIDECLD 287
GY C C GFQ C DIDEC D
Sbjct: 22 GYECLCPDGFQLVAQRRCEDIDECQD 47
>pdb|3BPS|E Chain E, Pcsk9:egf-a Complex
pdb|3GCX|E Chain E, Pcsk9:egfa (Ph 7.4)
Length = 83
Score = 27.7 bits (60), Expect = 7.6, Method: Compositional matrix adjust.
Identities = 14/26 (53%), Positives = 14/26 (53%)
Query: 262 GYRCKCKQGFQGNPYLGCVDIDECLD 287
GY C C GFQ C DIDEC D
Sbjct: 25 GYECLCPDGFQLVAQRRCEDIDECQD 50
>pdb|3GCW|E Chain E, Pcsk9:egfa(H306y)
Length = 83
Score = 27.7 bits (60), Expect = 8.3, Method: Compositional matrix adjust.
Identities = 14/26 (53%), Positives = 14/26 (53%)
Query: 262 GYRCKCKQGFQGNPYLGCVDIDECLD 287
GY C C GFQ C DIDEC D
Sbjct: 25 GYECLCPDGFQLVAQRRCEDIDECQD 50
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 0.136 0.438
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 9,113,123
Number of Sequences: 62578
Number of extensions: 380900
Number of successful extensions: 775
Number of sequences better than 100.0: 20
Number of HSP's better than 100.0 without gapping: 10
Number of HSP's successfully gapped in prelim test: 10
Number of HSP's that attempted gapping in prelim test: 754
Number of HSP's gapped (non-prelim): 30
length of query: 296
length of database: 14,973,337
effective HSP length: 98
effective length of query: 198
effective length of database: 8,840,693
effective search space: 1750457214
effective search space used: 1750457214
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: 51 (24.3 bits)