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= 004024
(778 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|1J8M|F Chain F, Signal Recognition Particle Conserved Gtpase Domain From
A. Ambivalens
Length = 297
Score = 32.3 bits (72), Expect = 1.0, Method: Compositional matrix adjust.
Identities = 15/31 (48%), Positives = 23/31 (74%), Gaps = 3/31 (9%)
Query: 483 ARHGFGKDALMLFESMKTV--GIKPDDITMV 511
RHG+G++A +L E MK + IKPD++T+V
Sbjct: 190 GRHGYGEEAALL-EEMKNIYEAIKPDEVTLV 219
>pdb|1J8Y|F Chain F, Signal Recognition Particle Conserved Gtpase Domain From
A. Ambivalens T112a Mutant
Length = 297
Score = 32.3 bits (72), Expect = 1.0, Method: Compositional matrix adjust.
Identities = 15/31 (48%), Positives = 23/31 (74%), Gaps = 3/31 (9%)
Query: 483 ARHGFGKDALMLFESMKTV--GIKPDDITMV 511
RHG+G++A +L E MK + IKPD++T+V
Sbjct: 190 GRHGYGEEAALL-EEMKNIYEAIKPDEVTLV 219
>pdb|3Q1S|I Chain I, Hiv-1 Neutralizing Antibody Z13e1 In Complex With Epitope
Display Protein
Length = 151
Score = 30.8 bits (68), Expect = 3.0, Method: Compositional matrix adjust.
Identities = 18/57 (31%), Positives = 29/57 (50%), Gaps = 7/57 (12%)
Query: 625 WGDVSKVRLKMRDRGVKKVTGYSWLE---VQNKVHTFSVGDTLHPEKDRIYAYLEEL 678
W D++ VRL G K G S E + +V F++ + L P+ DR Y++E+
Sbjct: 38 WDDITDVRLI----GEKLFHGVSMSERCYLMKQVLNFTLEEVLFPQSDRFQPYMQEV 90
>pdb|1Z1B|A Chain A, Crystal Structure Of A Lambda Integrase Dimer Bound To A
Coc' Core Site
pdb|1Z1B|B Chain B, Crystal Structure Of A Lambda Integrase Dimer Bound To A
Coc' Core Site
Length = 356
Score = 30.4 bits (67), Expect = 3.9, Method: Compositional matrix adjust.
Identities = 19/74 (25%), Positives = 38/74 (51%), Gaps = 8/74 (10%)
Query: 261 NYLAEAQ---RLFEEAPVKDVFT--WTAMVSGYVQNGKVDEARMIFDAMPEKNTVSWNAM 315
NY+++ + R +AP++D+ T AM++GY+ GK A++I + + A+
Sbjct: 99 NYMSKIKAIRRGLPDAPLEDITTKEIAAMLNGYIDEGKAASAKLIRSTLSD---AFREAI 155
Query: 316 IAGYVQTKRMDMAR 329
G++ T + R
Sbjct: 156 AEGHITTNHVAATR 169
>pdb|2FM4|A Chain A, Nmr Structure Of The Phosphoryl Carrier Domain Of Pyruvate
Phosphate Dikinase
Length = 128
Score = 30.0 bits (66), Expect = 5.3, Method: Composition-based stats.
Identities = 27/107 (25%), Positives = 40/107 (37%), Gaps = 10/107 (9%)
Query: 569 MPFEPDAATWGALLGACRLYGKTELAEKAAEVIFEMEPENAGMYVLLSNLYAASG----R 624
+P P AA A E E+ V E PE+ + ++AA G R
Sbjct: 13 LPASPGAAAGKVYFTADEAKAAHEKGERVILVRLETSPED------IEGMHAAEGILTVR 66
Query: 625 WGDVSKVRLKMRDRGVKKVTGYSWLEVQNKVHTFSVGDTLHPEKDRI 671
G S + R G V+G +++ + TF +G E D I
Sbjct: 67 GGMTSHAAVVARGMGTCCVSGCGEIKINEEAKTFELGGHTFAEGDYI 113
>pdb|1P7D|A Chain A, Crystal Structure Of The Lambda Integrase (Residues
75-356) Bound To Dna
pdb|1P7D|B Chain B, Crystal Structure Of The Lambda Integrase (Residues
75-356) Bound To Dna
Length = 283
Score = 30.0 bits (66), Expect = 5.4, Method: Compositional matrix adjust.
Identities = 19/74 (25%), Positives = 38/74 (51%), Gaps = 8/74 (10%)
Query: 261 NYLAEAQ---RLFEEAPVKDVFT--WTAMVSGYVQNGKVDEARMIFDAMPEKNTVSWNAM 315
NY+++ + R +AP++D+ T AM++GY+ GK A++I + + A+
Sbjct: 26 NYMSKIKAIRRGLPDAPLEDITTKEIAAMLNGYIDEGKAASAKLIRSTLSD---AFREAI 82
Query: 316 IAGYVQTKRMDMAR 329
G++ T + R
Sbjct: 83 AEGHITTNHVAATR 96
>pdb|3SFX|A Chain A, Cryptococcus Neoformans Protein Farnesyltransferase In
Complex With Fpt-Ii And Tipifarnib
pdb|3SFY|A Chain A, Cryptococcus Neoformans Protein Farnesyltransferase In
Complex With Fpt-Ii And Ethylenediamine Inhibitor 2
Length = 349
Score = 30.0 bits (66), Expect = 5.6, Method: Compositional matrix adjust.
Identities = 16/62 (25%), Positives = 31/62 (50%), Gaps = 4/62 (6%)
Query: 269 LFEEAPVKDVFTWTAMVSGYVQNGKVDEARMIFDAMPEKNTVSWNAMIAGYVQTKRMDMA 328
L E+ P+ + +++ +VD+A +F EK + ++ M AGY + +R + A
Sbjct: 292 LPEDTPLPVPLALEYLADSFIEQNRVDDAAKVF----EKLSSEYDQMRAGYWEFRRRECA 347
Query: 329 RE 330
E
Sbjct: 348 EE 349
>pdb|1JDE|A Chain A, K22a Mutant Of Pyruvate, Phosphate Dikinase
Length = 873
Score = 29.6 bits (65), Expect = 6.5, Method: Compositional matrix adjust.
Identities = 27/107 (25%), Positives = 40/107 (37%), Gaps = 10/107 (9%)
Query: 569 MPFEPDAATWGALLGACRLYGKTELAEKAAEVIFEMEPENAGMYVLLSNLYAASG----R 624
+P P AA A E E+ V E PE+ + ++AA G R
Sbjct: 395 LPASPGAAAGKVYFTADEAKAAHEKGERVILVRLETSPED------IEGMHAAEGILTVR 448
Query: 625 WGDVSKVRLKMRDRGVKKVTGYSWLEVQNKVHTFSVGDTLHPEKDRI 671
G S + R G V+G +++ + TF +G E D I
Sbjct: 449 GGMTSHAAVVARGMGTCCVSGCGEIKINEEAKTFELGGHTFAEGDYI 495
>pdb|1KBL|A Chain A, Pyruvate Phosphate Dikinase
pdb|1KC7|A Chain A, Pyruvate Phosphate Dikinase With Bound
Mg-Phosphonopyruvate
Length = 873
Score = 29.6 bits (65), Expect = 6.6, Method: Compositional matrix adjust.
Identities = 27/107 (25%), Positives = 40/107 (37%), Gaps = 10/107 (9%)
Query: 569 MPFEPDAATWGALLGACRLYGKTELAEKAAEVIFEMEPENAGMYVLLSNLYAASG----R 624
+P P AA A E E+ V E PE+ + ++AA G R
Sbjct: 395 LPASPGAAAGKVYFTADEAKAAHEKGERVILVRLETSPED------IEGMHAAEGILTVR 448
Query: 625 WGDVSKVRLKMRDRGVKKVTGYSWLEVQNKVHTFSVGDTLHPEKDRI 671
G S + R G V+G +++ + TF +G E D I
Sbjct: 449 GGMTSHAAVVARGMGTCCVSGCGEIKINEEAKTFELGGHTFAEGDYI 495
>pdb|2R82|A Chain A, Pyruvate Phosphate Dikinase (Ppdk) Triple Mutant
R219eE271RS262D Adapts A Second Conformational State
Length = 874
Score = 29.6 bits (65), Expect = 6.7, Method: Compositional matrix adjust.
Identities = 27/107 (25%), Positives = 40/107 (37%), Gaps = 10/107 (9%)
Query: 569 MPFEPDAATWGALLGACRLYGKTELAEKAAEVIFEMEPENAGMYVLLSNLYAASG----R 624
+P P AA A E E+ V E PE+ + ++AA G R
Sbjct: 396 LPASPGAAAGKVYFTADEAKAAHEKGERVILVRLETSPED------IEGMHAAEGILTVR 449
Query: 625 WGDVSKVRLKMRDRGVKKVTGYSWLEVQNKVHTFSVGDTLHPEKDRI 671
G S + R G V+G +++ + TF +G E D I
Sbjct: 450 GGMTSHAAVVARGMGTCCVSGCGEIKINEEAKTFELGGHTFAEGDYI 496
>pdb|2DIK|A Chain A, R337a Mutant Of Pyruvate Phosphate Dikinase
Length = 873
Score = 29.6 bits (65), Expect = 6.8, Method: Compositional matrix adjust.
Identities = 27/107 (25%), Positives = 40/107 (37%), Gaps = 10/107 (9%)
Query: 569 MPFEPDAATWGALLGACRLYGKTELAEKAAEVIFEMEPENAGMYVLLSNLYAASG----R 624
+P P AA A E E+ V E PE+ + ++AA G R
Sbjct: 395 LPASPGAAAGKVYFTADEAKAAHEKGERVILVRLETSPED------IEGMHAAEGILTVR 448
Query: 625 WGDVSKVRLKMRDRGVKKVTGYSWLEVQNKVHTFSVGDTLHPEKDRI 671
G S + R G V+G +++ + TF +G E D I
Sbjct: 449 GGMTSHAAVVARGMGTCCVSGCGEIKINEEAKTFELGGHTFAEGDYI 495
>pdb|1DIK|A Chain A, Pyruvate Phosphate Dikinase
Length = 874
Score = 29.6 bits (65), Expect = 7.0, Method: Compositional matrix adjust.
Identities = 27/107 (25%), Positives = 40/107 (37%), Gaps = 10/107 (9%)
Query: 569 MPFEPDAATWGALLGACRLYGKTELAEKAAEVIFEMEPENAGMYVLLSNLYAASG----R 624
+P P AA A E E+ V E PE+ + ++AA G R
Sbjct: 396 LPASPGAAAGKVYFTADEAKAAHEKGERVILVRLETSPED------IEGMHAAEGILTVR 449
Query: 625 WGDVSKVRLKMRDRGVKKVTGYSWLEVQNKVHTFSVGDTLHPEKDRI 671
G S + R G V+G +++ + TF +G E D I
Sbjct: 450 GGMTSHAAVVARGMGTCCVSGCGEIKINEEAKTFELGGHTFAEGDYI 496
>pdb|1GGO|A Chain A, T453a Mutant Of Pyruvate, Phosphate Dikinase
Length = 873
Score = 29.6 bits (65), Expect = 7.1, Method: Compositional matrix adjust.
Identities = 27/107 (25%), Positives = 40/107 (37%), Gaps = 10/107 (9%)
Query: 569 MPFEPDAATWGALLGACRLYGKTELAEKAAEVIFEMEPENAGMYVLLSNLYAASG----R 624
+P P AA A E E+ V E PE+ + ++AA G R
Sbjct: 395 LPASPGAAAGKVYFTADEAKAAHEKGERVILVRLETSPED------IEGMHAAEGILTVR 448
Query: 625 WGDVSKVRLKMRDRGVKKVTGYSWLEVQNKVHTFSVGDTLHPEKDRI 671
G S + R G V+G +++ + TF +G E D I
Sbjct: 449 GGMASHAAVVARGMGTCCVSGCGEIKINEEAKTFELGGHTFAEGDYI 495
>pdb|2OXO|A Chain A, Crystallization And Structure Determination Of The Core-
Binding Domain Of Bacteriophage Lambda Integrase
Length = 103
Score = 29.3 bits (64), Expect = 8.1, Method: Composition-based stats.
Identities = 19/74 (25%), Positives = 38/74 (51%), Gaps = 8/74 (10%)
Query: 261 NYLAEAQ---RLFEEAPVKDVFT--WTAMVSGYVQNGKVDEARMIFDAMPEKNTVSWNAM 315
NY+++ + R +AP++D+ T AM++GY+ GK A++I + + A+
Sbjct: 26 NYMSKIKAIRRGLPDAPLEDITTKEIAAMLNGYIDEGKAASAKLIRSTLSDAFR---EAI 82
Query: 316 IAGYVQTKRMDMAR 329
G++ T + R
Sbjct: 83 AEGHITTNHVAATR 96
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
0.321 0.134 0.413
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 24,130,063
Number of Sequences: 62578
Number of extensions: 1003962
Number of successful extensions: 3011
Number of sequences better than 100.0: 17
Number of HSP's better than 100.0 without gapping: 0
Number of HSP's successfully gapped in prelim test: 17
Number of HSP's that attempted gapping in prelim test: 3011
Number of HSP's gapped (non-prelim): 18
length of query: 778
length of database: 14,973,337
effective HSP length: 106
effective length of query: 672
effective length of database: 8,340,069
effective search space: 5604526368
effective search space used: 5604526368
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 55 (25.8 bits)