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= 008587
(560 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|3P5C|L Chain L, The Structure Of The LdlrPCSK9 COMPLEX REVEALS THE
RECEPTOR IN AN Extended Conformation
Length = 440
Score = 38.1 bits (87), Expect = 0.014, Method: Compositional matrix adjust.
Identities = 37/96 (38%), Positives = 42/96 (43%), Gaps = 26/96 (27%)
Query: 420 TNECLDNNGGCWQDKTANVTACKDTFRGRVCECPLVDGVQFKGDGYSHCEVSGPGKCKIN 479
TNECLDNNGGC C D G C CP DG Q CE I+
Sbjct: 40 TNECLDNNGGCSH-------VCNDLKIGYECLCP--DGFQLVAQ--RRCE-------DID 81
Query: 480 NGGCWHESKDGHTYSA-CLDSENG-KCQCPPGFKGD 513
E +D T S C++ E G KCQC GF+ D
Sbjct: 82 ------ECQDPDTCSQLCVNLEGGYKCQCEEGFQLD 111
>pdb|3P5B|L Chain L, The Structure Of The LdlrPCSK9 COMPLEX REVEALS THE
RECEPTOR IN AN Extended Conformation
Length = 400
Score = 37.0 bits (84), Expect = 0.032, Method: Compositional matrix adjust.
Identities = 38/101 (37%), Positives = 44/101 (43%), Gaps = 27/101 (26%)
Query: 421 NECLDNNGGCWQDKTANVTACKDTFRGRVCECPLVDGVQFKGDGYSHCEVSGPGKCKINN 480
NECLDNNGGC C D G C CP DG Q CE I+
Sbjct: 1 NECLDNNGGCSH-------VCNDLKIGYECLCP--DGFQLVAQ--RRCE-------DID- 41
Query: 481 GGCWHESKDGHTYSA-CLDSENG-KCQCPPGFKGD-GVKSC 518
E +D T S C++ E G KCQC GF+ D K+C
Sbjct: 42 -----ECQDPDTCSQLCVNLEGGYKCQCEEGFQLDPHTKAC 77
>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 = 36.2 bits (82), Expect = 0.044, Method: Compositional matrix adjust.
Identities = 39/114 (34%), Positives = 47/114 (41%), Gaps = 26/114 (22%)
Query: 402 SGFEETTEPAVCLSGDVETNECLDNNGGCWQDKTANVTACKDTFRGRVCECPLVDGVQFK 461
S ++ T + G + TNECLDNNGGC C D G C CP DG Q
Sbjct: 11 SDYDIPTTENLYFQGAMGTNECLDNNGGCSH-------VCNDLKIGYECLCP--DGFQLV 61
Query: 462 GDGYSHCEVSGPGKCKINNGGCWHESKDGHTYSA-CLDSENG-KCQCPPGFKGD 513
CE E +D T S C++ E G KCQC GF+ D
Sbjct: 62 AQ--RRCED-------------IDECQDPDTCSQLCVNLEGGYKCQCEEGFQLD 100
>pdb|2W2N|E Chain E, Wt Pcsk9-Deltac Bound To Egf-A H306y Mutant Of Ldlr
Length = 107
Score = 36.2 bits (82), Expect = 0.055, Method: Compositional matrix adjust.
Identities = 39/114 (34%), Positives = 47/114 (41%), Gaps = 26/114 (22%)
Query: 402 SGFEETTEPAVCLSGDVETNECLDNNGGCWQDKTANVTACKDTFRGRVCECPLVDGVQFK 461
S ++ T + G + TNECLDNNGGC C D G C CP DG Q
Sbjct: 11 SDYDIPTTENLYFQGAMGTNECLDNNGGC-------SYVCNDLKIGYECLCP--DGFQLV 61
Query: 462 GDGYSHCEVSGPGKCKINNGGCWHESKDGHTYSA-CLDSENG-KCQCPPGFKGD 513
CE E +D T S C++ E G KCQC GF+ D
Sbjct: 62 AQ--RRCED-------------IDECQDPDTCSQLCVNLEGGYKCQCEEGFQLD 100
>pdb|3M0C|C Chain C, The X-Ray Crystal Structure Of Pcsk9 In Complex With The
Ldl Receptor
Length = 791
Score = 35.8 bits (81), Expect = 0.063, Method: Compositional matrix adjust.
Identities = 37/96 (38%), Positives = 42/96 (43%), Gaps = 26/96 (27%)
Query: 420 TNECLDNNGGCWQDKTANVTACKDTFRGRVCECPLVDGVQFKGDGYSHCEVSGPGKCKIN 479
TNECLDNNGGC C D G C CP DG Q CE I+
Sbjct: 312 TNECLDNNGGCSH-------VCNDLKIGYECLCP--DGFQLV--AQRRCE-------DID 353
Query: 480 NGGCWHESKDGHTYSA-CLDSENG-KCQCPPGFKGD 513
E +D T S C++ E G KCQC GF+ D
Sbjct: 354 ------ECQDPDTCSQLCVNLEGGYKCQCEEGFQLD 383
>pdb|1N7D|A Chain A, Extracellular Domain Of The Ldl Receptor
Length = 699
Score = 35.4 bits (80), Expect = 0.093, Method: Compositional matrix adjust.
Identities = 37/96 (38%), Positives = 42/96 (43%), Gaps = 26/96 (27%)
Query: 420 TNECLDNNGGCWQDKTANVTACKDTFRGRVCECPLVDGVQFKGDGYSHCEVSGPGKCKIN 479
TNECLDNNGGC C D G C CP DG Q CE I+
Sbjct: 294 TNECLDNNGGCSH-------VCNDLKIGYECLCP--DGFQLV--AQRRCE-------DID 335
Query: 480 NGGCWHESKDGHTYSA-CLDSENG-KCQCPPGFKGD 513
E +D T S C++ E G KCQC GF+ D
Sbjct: 336 ------ECQDPDTCSQLCVNLEGGYKCQCEEGFQLD 365
>pdb|3EIF|A Chain A, 1.9 Angstrom Crystal Structure Of The Active Form Of The
C5a Peptidase From Streptococcus Pyogenes (Scpa)
Length = 936
Score = 35.0 bits (79), Expect = 0.11, Method: Compositional matrix adjust.
Identities = 23/71 (32%), Positives = 36/71 (50%), Gaps = 11/71 (15%)
Query: 98 FVLVDRGDCFFALKVWNAQKAGASAVLVADDIEEALITMDTPEEDISSAKYIENITIPSA 157
L++RGD F K+ NA+KAGA VL+ D+ ++ ++ P D +P+A
Sbjct: 292 IALIERGDIDFKDKIANAKKAGAVGVLIYDNQDKGF-PIELPNVD----------QMPAA 340
Query: 158 LIDKSFGETLK 168
I + G LK
Sbjct: 341 FISRKDGLLLK 351
>pdb|3BPS|E Chain E, Pcsk9:egf-a Complex
pdb|3GCX|E Chain E, Pcsk9:egfa (Ph 7.4)
Length = 83
Score = 34.3 bits (77), Expect = 0.19, Method: Compositional matrix adjust.
Identities = 37/100 (37%), Positives = 42/100 (42%), Gaps = 26/100 (26%)
Query: 416 GDVETNECLDNNGGCWQDKTANVTACKDTFRGRVCECPLVDGVQFKGDGYSHCEVSGPGK 475
G + TNECLDNNGGC C D G C CP DG Q CE
Sbjct: 1 GAMGTNECLDNNGGCSH-------VCNDLKIGYECLCP--DGFQLV--AQRRCED----- 44
Query: 476 CKINNGGCWHESKDGHTYSA-CLDSENG-KCQCPPGFKGD 513
E +D T S C++ E G KCQC GF+ D
Sbjct: 45 --------IDECQDPDTCSQLCVNLEGGYKCQCEEGFQLD 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 = 34.3 bits (77), Expect = 0.21, Method: Compositional matrix adjust.
Identities = 36/96 (37%), Positives = 40/96 (41%), Gaps = 26/96 (27%)
Query: 420 TNECLDNNGGCWQDKTANVTACKDTFRGRVCECPLVDGVQFKGDGYSHCEVSGPGKCKIN 479
TNECLDNNGGC C D G C CP DG Q CE
Sbjct: 2 TNECLDNNGGCSH-------VCNDLKIGYECLCP--DGFQLVAQ--RRCED--------- 41
Query: 480 NGGCWHESKDGHTYSA-CLDSENG-KCQCPPGFKGD 513
E +D T S C++ E G KCQC GF+ D
Sbjct: 42 ----IDECQDPDTCSQLCVNLEGGYKCQCEEGFQLD 73
>pdb|3GCW|E Chain E, Pcsk9:egfa(H306y)
Length = 83
Score = 33.9 bits (76), Expect = 0.24, Method: Compositional matrix adjust.
Identities = 37/100 (37%), Positives = 42/100 (42%), Gaps = 26/100 (26%)
Query: 416 GDVETNECLDNNGGCWQDKTANVTACKDTFRGRVCECPLVDGVQFKGDGYSHCEVSGPGK 475
G + TNECLDNNGGC C D G C CP DG Q CE
Sbjct: 1 GAMGTNECLDNNGGC-------SYVCNDLKIGYECLCP--DGFQLVAQ--RRCED----- 44
Query: 476 CKINNGGCWHESKDGHTYSA-CLDSENG-KCQCPPGFKGD 513
E +D T S C++ E G KCQC GF+ D
Sbjct: 45 --------IDECQDPDTCSQLCVNLEGGYKCQCEEGFQLD 76
>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 = 33.5 bits (75), Expect = 0.29, Method: Compositional matrix adjust.
Identities = 36/96 (37%), Positives = 40/96 (41%), Gaps = 26/96 (27%)
Query: 420 TNECLDNNGGCWQDKTANVTACKDTFRGRVCECPLVDGVQFKGDGYSHCEVSGPGKCKIN 479
TNECLDNNGGC C D G C CP DG Q CE
Sbjct: 2 TNECLDNNGGCSH-------VCNDLKIGYECLCP--DGFQLV--AQRRCED--------- 41
Query: 480 NGGCWHESKDGHTYSA-CLDSENG-KCQCPPGFKGD 513
E +D T S C++ E G KCQC GF+ D
Sbjct: 42 ----IDECQDPDTCSQLCVNLEGGYKCQCEEGFQLD 73
>pdb|3V64|C Chain C, Crystal Structure Of Agrin And Lrp4
pdb|3V64|D Chain D, Crystal Structure Of Agrin And Lrp4
Length = 349
Score = 32.7 bits (73), Expect = 0.52, Method: Compositional matrix adjust.
Identities = 19/51 (37%), Positives = 24/51 (47%), Gaps = 10/51 (19%)
Query: 471 SGPGKCKINNGGCWHESKDGHTYSACLDS-ENGKCQCPPGFKGDGVKSCIL 520
+G +C NNGGC H CL S +N C CP GF+ +C L
Sbjct: 302 AGKNRCGDNNGGCTH---------LCLPSGQNYTCACPTGFRKINSHACAL 343
>pdb|2Q14|A Chain A, Crystal Structure Of Phosphohydrolase (Bt4208) From
Bacteroides Thetaiotaomicron Vpi-5482 At 2.20 A
Resolution
pdb|2Q14|B Chain B, Crystal Structure Of Phosphohydrolase (Bt4208) From
Bacteroides Thetaiotaomicron Vpi-5482 At 2.20 A
Resolution
pdb|2Q14|C Chain C, Crystal Structure Of Phosphohydrolase (Bt4208) From
Bacteroides Thetaiotaomicron Vpi-5482 At 2.20 A
Resolution
pdb|2Q14|D Chain D, Crystal Structure Of Phosphohydrolase (Bt4208) From
Bacteroides Thetaiotaomicron Vpi-5482 At 2.20 A
Resolution
pdb|2Q14|E Chain E, Crystal Structure Of Phosphohydrolase (Bt4208) From
Bacteroides Thetaiotaomicron Vpi-5482 At 2.20 A
Resolution
pdb|2Q14|F Chain F, Crystal Structure Of Phosphohydrolase (Bt4208) From
Bacteroides Thetaiotaomicron Vpi-5482 At 2.20 A
Resolution
pdb|2Q14|G Chain G, Crystal Structure Of Phosphohydrolase (Bt4208) From
Bacteroides Thetaiotaomicron Vpi-5482 At 2.20 A
Resolution
pdb|2Q14|H Chain H, Crystal Structure Of Phosphohydrolase (Bt4208) From
Bacteroides Thetaiotaomicron Vpi-5482 At 2.20 A
Resolution
Length = 410
Score = 32.0 bits (71), Expect = 0.82, Method: Compositional matrix adjust.
Identities = 23/83 (27%), Positives = 37/83 (44%), Gaps = 4/83 (4%)
Query: 88 FKAKPGALPNFVLVDRGDCFFALKVWNAQKAGASAVLVADDIEEALITMDTPEEDISSAK 147
F P L NF+ +D D + ALKVW+ + L I + ++ E I +
Sbjct: 271 FHNNPDCLENFIQLDDNDIWTALKVWSNHPDKVLSTLSLGXINRNIFKVENSAEPIGEDR 330
Query: 148 YIENITIPSALIDKSFGETLKKA 170
I+ +T+ I + G TL +A
Sbjct: 331 -IKELTLQ---ISQQLGITLSEA 349
>pdb|3V65|B Chain B, Crystal Structure Of Agrin And Lrp4 Complex
pdb|3V65|D Chain D, Crystal Structure Of Agrin And Lrp4 Complex
Length = 386
Score = 31.2 bits (69), Expect = 1.8, Method: Compositional matrix adjust.
Identities = 18/49 (36%), Positives = 23/49 (46%), Gaps = 10/49 (20%)
Query: 471 SGPGKCKINNGGCWHESKDGHTYSACLDS-ENGKCQCPPGFKGDGVKSC 518
+G +C NNGGC H CL S +N C CP GF+ +C
Sbjct: 345 AGKNRCGDNNGGCTH---------LCLPSGQNYTCACPTGFRKINSHAC 384
>pdb|1XFE|A Chain A, Solution Structure Of The La7-Egfa Pair From The Ldl
Receptor
Length = 83
Score = 30.8 bits (68), Expect = 2.1, Method: Compositional matrix adjust.
Identities = 20/41 (48%), Positives = 20/41 (48%), Gaps = 9/41 (21%)
Query: 420 TNECLDNNGGCWQDKTANVTACKDTFRGRVCECPLVDGVQF 460
TNECLDNNGGC C D G C CP DG Q
Sbjct: 45 TNECLDNNGGCSH-------VCNDLKIGYECLCP--DGFQL 76
>pdb|2DTG|E Chain E, Insulin Receptor (Ir) Ectodomain In Complex With Fab's
Length = 897
Score = 30.8 bits (68), Expect = 2.4, Method: Compositional matrix adjust.
Identities = 31/106 (29%), Positives = 40/106 (37%), Gaps = 4/106 (3%)
Query: 129 IEEALITMDTPEEDISSAKYIENITIPSALIDKSFGETLKKALSGGEMVNVNLDWREAVP 188
IE DTPEE S A Y+ T+P A D G + V+L W+E
Sbjct: 762 IELQACNQDTPEERCSVAAYVSARTMPEAKADDIVGPVTHEIFENNV---VHLMWQEPKE 818
Query: 189 HPDDRVEYEL-WTNSNDECGVKCDMLMAFVKEFRGPAQILEKGGYT 233
V YE+ + DE CD F E + L G Y+
Sbjct: 819 PNGLIVLYEVSYRRYGDEELHLCDTRKHFALERGCRLRGLSPGNYS 864
>pdb|3LOH|E Chain E, Structure Of The Insulin Receptor Ectodomain, Including Ct
P
Length = 917
Score = 30.4 bits (67), Expect = 2.4, Method: Compositional matrix adjust.
Identities = 31/106 (29%), Positives = 40/106 (37%), Gaps = 4/106 (3%)
Query: 129 IEEALITMDTPEEDISSAKYIENITIPSALIDKSFGETLKKALSGGEMVNVNLDWREAVP 188
IE DTPEE S A Y+ T+P A D G + V+L W+E
Sbjct: 781 IELQACNQDTPEERCSVAAYVSARTMPEAKADDIVGPVTHEIFENNV---VHLMWQEPKE 837
Query: 189 HPDDRVEYEL-WTNSNDECGVKCDMLMAFVKEFRGPAQILEKGGYT 233
V YE+ + DE CD F E + L G Y+
Sbjct: 838 PNGLIVLYEVSYRRYGDEELHLCDTRKHFALERGCRLRGLSPGNYS 883
>pdb|3KW3|A Chain A, Crystal Structure Of Alanine Racemase From Bartonella
Henselae With Covalently Bound Pyridoxal Phosphate
pdb|3KW3|B Chain B, Crystal Structure Of Alanine Racemase From Bartonella
Henselae With Covalently Bound Pyridoxal Phosphate
Length = 376
Score = 29.6 bits (65), Expect = 4.2, Method: Compositional matrix adjust.
Identities = 14/45 (31%), Positives = 24/45 (53%), Gaps = 1/45 (2%)
Query: 306 WDYVTDFQIRCPMKDKKYNKECAAAV-IKSLGLDAKKIEKCMGDP 349
W + D+Q C K+KK+ + LGLD K+++K + +P
Sbjct: 121 WSTIEDWQTLCQKKNKKFPAIIQVDTNMSRLGLDKKELQKLIKNP 165
>pdb|1MEJ|B Chain B, Human Glycinamide Ribonucleotide Transformylase Domain At
Ph 8.5
pdb|1MEJ|A Chain A, Human Glycinamide Ribonucleotide Transformylase Domain At
Ph 8.5
pdb|1MEJ|C Chain C, Human Glycinamide Ribonucleotide Transformylase Domain At
Ph 8.5
pdb|1MEN|A Chain A, Complex Structure Of Human Gar Tfase And Substrate
Beta-Gar
pdb|1MEN|B Chain B, Complex Structure Of Human Gar Tfase And Substrate
Beta-Gar
pdb|1MEN|C Chain C, Complex Structure Of Human Gar Tfase And Substrate
Beta-Gar
Length = 223
Score = 29.3 bits (64), Expect = 6.5, Method: Compositional matrix adjust.
Identities = 21/98 (21%), Positives = 46/98 (46%), Gaps = 8/98 (8%)
Query: 321 KKYNKECAAAVIKSLGLDAKKIEKCMGDPDADADNPVLKEEQDAQVG--KGSRGDVTILP 378
++ + A +I G + + + +P++ A ++ + A G K R + P
Sbjct: 7 QQMGRILVAVLISGTGSNLQALIDSTREPNSSAQIDIVISNKAAVAGLDKAERAGI---P 63
Query: 379 TLVVNNRQYRGKLEKGAVLKAICSGFEETTEPAVCLSG 416
T V+N++ Y+ ++E + + + EE + VCL+G
Sbjct: 64 TRVINHKLYKNRVEFDSAIDLV---LEEFSIDIVCLAG 98
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
0.317 0.135 0.423
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 18,157,564
Number of Sequences: 62578
Number of extensions: 824302
Number of successful extensions: 1645
Number of sequences better than 100.0: 57
Number of HSP's better than 100.0 without gapping: 15
Number of HSP's successfully gapped in prelim test: 42
Number of HSP's that attempted gapping in prelim test: 1590
Number of HSP's gapped (non-prelim): 83
length of query: 560
length of database: 14,973,337
effective HSP length: 104
effective length of query: 456
effective length of database: 8,465,225
effective search space: 3860142600
effective search space used: 3860142600
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: 54 (25.4 bits)