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= 002586
(904 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|2J7N|A Chain A, Structure Of The Rnai Polymerase From Neurospora Crassa
pdb|2J7N|B Chain B, Structure Of The Rnai Polymerase From Neurospora Crassa
pdb|2J7O|A Chain A, Structure Of The Rnai Polymerase From Neurospora Crassa
Length = 1022
Score = 84.7 bits (208), Expect = 2e-16, Method: Compositional matrix adjust.
Identities = 96/383 (25%), Positives = 153/383 (39%), Gaps = 55/383 (14%)
Query: 309 TKYVFSDGIGKVSAEFARKVASKCGLKDNPPSAFQIRYGGYKG--VVAADPTSSKK-LSL 365
T V +DG+G++S A+++ GL D P SA Q R+G KG V+ D T + +
Sbjct: 323 TGEVMNDGVGRMSRSVAKRIRDVLGLGDVP-SAVQGRFGSAKGMWVIDVDDTGDEDWIET 381
Query: 366 RDSMRKYESELT-----KLDVLA-WSKYQPCFLNRQLISLLS---------TLGIWDEIF 410
S RK+E + L+V + S+ + LN QL+ +L I D +
Sbjct: 382 YPSQRKWECDFVDKHQRTLEVRSVASELKSAGLNLQLLPVLEDRARDKVKMRQAIGDRLI 441
Query: 411 EKKQREAVRQLDAILTDPLK-AQEALELMS-----------------PGENTNILKELLI 452
QR+ Q A L P++ Q E S P L L+
Sbjct: 442 NDLQRQFSEQKHA-LNRPVEFRQWVYESYSSRATRVSHGRVPFLAGLPDSQEETLNFLMN 500
Query: 453 CGYKPDAEPFLSMMLQTFRASKLLELRTKTRIFIPNGRSMMGCLDETRTLNYGQVFVQIS 512
G+ P + +L + + K L++K I + + D L +V V S
Sbjct: 501 SGFDPKKQKYLQDIAWDLQKRKCDTLKSKLNIRVGRSAYIYMIADFWGVLEENEVHVGFS 560
Query: 513 GAGYRQLHGEXXXXXXXXXXXXXIVQGLVVVAKNPCLHPGDVRVLKAVNVPALHHMVDCV 572
+ +R + V+VA++P P D++ ++AV P LH + D +
Sbjct: 561 -SKFRD----------EEESFTLLSDCDVLVARSPAHFPSDIQRVRAVFKPELHSLKDVI 609
Query: 573 VFPQKGMRPHPNECSGSDLDGDIYFVCWDDELIPPQQDPPMDYTPAQSMQLDHDVQIEDV 632
+F KG P + SG D DGD+ +VCWD E++ + M P S L D
Sbjct: 610 IFSTKGDVPLAKKLSGGDYDGDMAWVCWDPEIVDGFVNAEMPLEPDLSRYLKKD------ 663
Query: 633 EEYFTNYIVNDSLGIIANAHTVF 655
+ F + + G A T +
Sbjct: 664 KTTFKQLMASHGTGSAAKEQTTY 686
>pdb|1E5E|A Chain A, Methionine Gamma-Lyase (Mgl) From Trichomonas Vaginalis In
Complex With Propargylglycine
pdb|1E5E|B Chain B, Methionine Gamma-Lyase (Mgl) From Trichomonas Vaginalis In
Complex With Propargylglycine
pdb|1E5F|A Chain A, Methionine Gamma-Lyase (Mgl) From Trichomonas Vaginalis
pdb|1E5F|B Chain B, Methionine Gamma-Lyase (Mgl) From Trichomonas Vaginalis
Length = 404
Score = 33.1 bits (74), Expect = 0.63, Method: Compositional matrix adjust.
Identities = 24/77 (31%), Positives = 32/77 (41%), Gaps = 13/77 (16%)
Query: 674 KFSIAVDFPKTGVPAEIPPHLYVKEYPDFMEKPDKPTYESQNVIGKLFRAVKD------- 726
KF I VDF T +P E+ H+ + E P PT + I + R KD
Sbjct: 124 KFGIQVDFINTAIPGEVKKHMKPNTKIVYFETPANPTLK----IIDMERVCKDAHSQEGV 179
Query: 727 --IAPHTSCIRLFTKEV 741
IA +T C + T V
Sbjct: 180 LVIADNTFCSPMITNPV 196
>pdb|1OAX|H Chain H, Fv Structure Of The Ige Spe-7 In Complex With
Acenaphthenequinone
pdb|1OAX|J Chain J, Fv Structure Of The Ige Spe-7 In Complex With
Acenaphthenequinone
pdb|1OAY|H Chain H, Antibody Multispecificity Mediated By Conformational
Diversity
pdb|1OAY|I Chain I, Antibody Multispecificity Mediated By Conformational
Diversity
pdb|1OAY|J Chain J, Antibody Multispecificity Mediated By Conformational
Diversity
pdb|1OAY|K Chain K, Antibody Multispecificity Mediated By Conformational
Diversity
Length = 122
Score = 31.6 bits (70), Expect = 2.0, Method: Composition-based stats.
Identities = 16/44 (36%), Positives = 23/44 (52%), Gaps = 1/44 (2%)
Query: 812 AVRALRKEARAWFKEKSGSDTEDDA-YAKASAWYHVTYHPDYWG 854
A + K + + + S +ED A Y A WY+ TY+ DYWG
Sbjct: 68 ATLTVDKPSSTAYMQLSSLTSEDSAVYYCARMWYYGTYYFDYWG 111
>pdb|1OAR|H Chain H, Fv Ige Spe-7 In Complex With Alizarin Red
pdb|1OAR|I Chain I, Fv Ige Spe-7 In Complex With Alizarin Red
pdb|1OAR|J Chain J, Fv Ige Spe-7 In Complex With Alizarin Red
pdb|1OAR|K Chain K, Fv Ige Spe-7 In Complex With Alizarin Red
pdb|1OAU|I Chain I, Fv Structure Of The Ige Spe-7 In Complex With Dnp-Ser
(Immunising Hapten)
pdb|1OAU|K Chain K, Fv Structure Of The Ige Spe-7 In Complex With Dnp-Ser
(Immunising Hapten)
pdb|1OAZ|H Chain H, Ige Fv Spe7 Complexed With A Recombinant Thioredoxin
pdb|1OAZ|J Chain J, Ige Fv Spe7 Complexed With A Recombinant Thioredoxin
pdb|1OAU|H Chain H, Fv Structure Of The Ige Spe-7 In Complex With Dnp-Ser
(Immunising Hapten)
pdb|1OAU|J Chain J, Fv Structure Of The Ige Spe-7 In Complex With Dnp-Ser
(Immunising Hapten)
Length = 122
Score = 31.6 bits (70), Expect = 2.1, Method: Composition-based stats.
Identities = 16/44 (36%), Positives = 23/44 (52%), Gaps = 1/44 (2%)
Query: 812 AVRALRKEARAWFKEKSGSDTEDDA-YAKASAWYHVTYHPDYWG 854
A + K + + + S +ED A Y A WY+ TY+ DYWG
Sbjct: 68 ATLTVDKPSSTAYMQLSSLTSEDSAVYYCARMWYYGTYYFDYWG 111
>pdb|2BJM|H Chain H, Spe7:anthrone Complex
Length = 120
Score = 31.6 bits (70), Expect = 2.2, Method: Composition-based stats.
Identities = 16/44 (36%), Positives = 23/44 (52%), Gaps = 1/44 (2%)
Query: 812 AVRALRKEARAWFKEKSGSDTEDDA-YAKASAWYHVTYHPDYWG 854
A + K + + + S +ED A Y A WY+ TY+ DYWG
Sbjct: 68 ATLTVDKPSSTAYMQLSSLTSEDSAVYYCARMWYYGTYYFDYWG 111
>pdb|1OAQ|H Chain H, Free Conformation Ab1 Of The Ige Spe-7
pdb|1OCW|H Chain H, Free Conformation Ab2 Of The Ige Spe-7
Length = 121
Score = 31.6 bits (70), Expect = 2.2, Method: Composition-based stats.
Identities = 16/44 (36%), Positives = 23/44 (52%), Gaps = 1/44 (2%)
Query: 812 AVRALRKEARAWFKEKSGSDTEDDA-YAKASAWYHVTYHPDYWG 854
A + K + + + S +ED A Y A WY+ TY+ DYWG
Sbjct: 68 ATLTVDKPSSTAYMQLSSLTSEDSAVYYCARMWYYGTYYFDYWG 111
>pdb|1N1B|A Chain A, Crystal Structure Of (+)-bornyl Diphosphate Synthase From
Sage
pdb|1N1B|B Chain B, Crystal Structure Of (+)-bornyl Diphosphate Synthase From
Sage
pdb|1N1Z|A Chain A, (+)-Bornyl Diphosphate Synthase: Complex With Mg And
Pyrophosphate
pdb|1N1Z|B Chain B, (+)-Bornyl Diphosphate Synthase: Complex With Mg And
Pyrophosphate
pdb|1N20|A Chain A, (+)-bornyl Diphosphate Synthase: Complex With Mg And
3-aza- 2,3-dihydrogeranyl Diphosphate
pdb|1N20|B Chain B, (+)-bornyl Diphosphate Synthase: Complex With Mg And
3-aza- 2,3-dihydrogeranyl Diphosphate
pdb|1N21|A Chain A, (+)-Bornyl Diphosphate Synthase: Cocrystal With Mg And 3-
Aza-2,3-Dihydrogeranyl Diphosphate
pdb|1N22|A Chain A, (+)-Bornyl Diphosphate Synthase: Complex With Mg,
Pyrophosphate, And (4r)-7-Aza-7,8-Dihydrolimonene
pdb|1N22|B Chain B, (+)-Bornyl Diphosphate Synthase: Complex With Mg,
Pyrophosphate, And (4r)-7-Aza-7,8-Dihydrolimonene
pdb|1N23|A Chain A, (+)-Bornyl Diphosphate Synthase: Complex With Mg,
Pyrophosphate, And (1r,4s)-2-Azabornane
pdb|1N23|B Chain B, (+)-Bornyl Diphosphate Synthase: Complex With Mg,
Pyrophosphate, And (1r,4s)-2-Azabornane
pdb|1N24|A Chain A, (+)-Bornyl Diphosphate Synthase: Complex With Mg And
Product
pdb|1N24|B Chain B, (+)-Bornyl Diphosphate Synthase: Complex With Mg And
Product
Length = 549
Score = 31.6 bits (70), Expect = 2.2, Method: Compositional matrix adjust.
Identities = 15/46 (32%), Positives = 26/46 (56%), Gaps = 1/46 (2%)
Query: 617 PAQSMQLDHDVQIEDVEEYFTNYIVNDSLGIIANAHTVFADREPRK 662
P Q ++L HD++ + ++F + I + LG+I N H F + E K
Sbjct: 54 PVQQLELIHDLKYLGLSDFFQDEI-KEILGVIYNEHKCFHNNEVEK 98
>pdb|2Y06|H Chain H, Crystal Structure Analysis Of The Anti-(4-Hydroxy-3-
Nitrophenyl) -Acetyl Murine Germline Antibody Bbe6.12h3
Fab Fragment In Complex With A Phage Display Derived
Dodecapeptide Gdprpsyishll
pdb|2Y07|H Chain H, Crystal Structure Analysis Of The Anti-(4-Hydroxy-3-
Nitrophenyl) -Acetyl Murine Germline Monoclonal Antibody
Bbe6.12h3 Fab Fragment In Complex With A Phage Display
Derived Dodecapeptide Ppypawhapgni
Length = 220
Score = 29.3 bits (64), Expect = 9.8, Method: Composition-based stats.
Identities = 12/32 (37%), Positives = 18/32 (56%)
Query: 760 DDAIYHKGNYDYKLGNLMDYYGIKTEAEILTG 791
D A+Y+ YDY G+ DY+G T + +G
Sbjct: 90 DSAVYYCARYDYYGGSYFDYWGQGTTLTVSSG 121
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
0.320 0.137 0.414
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 27,180,060
Number of Sequences: 62578
Number of extensions: 1154581
Number of successful extensions: 2486
Number of sequences better than 100.0: 9
Number of HSP's better than 100.0 without gapping: 7
Number of HSP's successfully gapped in prelim test: 2
Number of HSP's that attempted gapping in prelim test: 2476
Number of HSP's gapped (non-prelim): 11
length of query: 904
length of database: 14,973,337
effective HSP length: 108
effective length of query: 796
effective length of database: 8,214,913
effective search space: 6539070748
effective search space used: 6539070748
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 56 (26.2 bits)