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= 040288
(413 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|3L4J|A Chain A, Topoisomerase Ii-Dna Cleavage Complex, Apo
pdb|3L4K|A Chain A, Topoisomerase Ii-Dna Cleavage Complex, Metal-Bound
Length = 722
Score = 32.3 bits (72), Expect = 0.49, Method: Compositional matrix adjust.
Identities = 22/63 (34%), Positives = 34/63 (53%), Gaps = 4/63 (6%)
Query: 255 YSLQNNCSDMIDISFAKELI---GKMVNDMHAKTEISPTLREIICQFDEDNQRSQIFSLG 311
+SLQ N D ID++F+K+ + + T + PTL+EI D N+ +FSL
Sbjct: 208 HSLQGNDKDYIDLAFSKKKADDRKEWLRQYEPGTVLDPTLKEIPIS-DFINKELILFSLA 266
Query: 312 ENI 314
+NI
Sbjct: 267 DNI 269
>pdb|1BGW|A Chain A, Topoisomerase Residues 410-1202
pdb|1BJT|A Chain A, Topoisomerase Ii Residues 409-1201
Length = 793
Score = 32.3 bits (72), Expect = 0.50, Method: Compositional matrix adjust.
Identities = 22/63 (34%), Positives = 34/63 (53%), Gaps = 4/63 (6%)
Query: 255 YSLQNNCSDMIDISFAKELI---GKMVNDMHAKTEISPTLREIICQFDEDNQRSQIFSLG 311
+SLQ N D ID++F+K+ + + T + PTL+EI D N+ +FSL
Sbjct: 220 HSLQGNDKDYIDLAFSKKKADDRKEWLRQYEPGTVLDPTLKEIPIS-DFINKELILFSLA 278
Query: 312 ENI 314
+NI
Sbjct: 279 DNI 281
>pdb|2RGR|A Chain A, Topoisomerase Iia Bound To G-segment Dna
Length = 759
Score = 32.3 bits (72), Expect = 0.54, Method: Compositional matrix adjust.
Identities = 22/63 (34%), Positives = 34/63 (53%), Gaps = 4/63 (6%)
Query: 255 YSLQNNCSDMIDISFAKELI---GKMVNDMHAKTEISPTLREIICQFDEDNQRSQIFSLG 311
+SLQ N D ID++F+K+ + + T + PTL+EI D N+ +FSL
Sbjct: 210 HSLQGNDKDYIDLAFSKKKADDRKEWLRQYEPGTVLDPTLKEIPIS-DFINKELILFSLA 268
Query: 312 ENI 314
+NI
Sbjct: 269 DNI 271
>pdb|4GFH|A Chain A, Topoisomerase Ii-Dna-Amppnp Complex
Length = 1103
Score = 31.6 bits (70), Expect = 0.80, Method: Compositional matrix adjust.
Identities = 22/63 (34%), Positives = 34/63 (53%), Gaps = 4/63 (6%)
Query: 255 YSLQNNCSDMIDISFAKELI---GKMVNDMHAKTEISPTLREIICQFDEDNQRSQIFSLG 311
+SLQ N D ID++F+K+ + + T + PTL+EI D N+ +FSL
Sbjct: 589 HSLQGNDKDYIDLAFSKKKADDRKEWLRQYEPGTVLDPTLKEIPIS-DFINKELILFSLA 647
Query: 312 ENI 314
+NI
Sbjct: 648 DNI 650
>pdb|4GFH|F Chain F, Topoisomerase Ii-Dna-Amppnp Complex
Length = 1099
Score = 31.6 bits (70), Expect = 0.82, Method: Compositional matrix adjust.
Identities = 22/63 (34%), Positives = 34/63 (53%), Gaps = 4/63 (6%)
Query: 255 YSLQNNCSDMIDISFAKELI---GKMVNDMHAKTEISPTLREIICQFDEDNQRSQIFSLG 311
+SLQ N D ID++F+K+ + + T + PTL+EI D N+ +FSL
Sbjct: 585 HSLQGNDKDYIDLAFSKKKADDRKEWLRQYEPGTVLDPTLKEIPIS-DFINKELILFSLA 643
Query: 312 ENI 314
+NI
Sbjct: 644 DNI 646
>pdb|1R6F|A Chain A, The Structure Of Yersinia Pestis V-Antigen, An Essential
Virulence Factor And Mediator Of Immunity Against Plague
Length = 310
Score = 30.0 bits (66), Expect = 2.5, Method: Compositional matrix adjust.
Identities = 31/91 (34%), Positives = 40/91 (43%), Gaps = 17/91 (18%)
Query: 61 LPEDPCLSEEQIVELLQNCIKLASENKINQNNT-WELKL---IDHLS--------EIIKV 108
LPED L LQN IK E + NT WEL+ + H S +I+KV
Sbjct: 57 LPEDAILKGGHYDNQLQNGIKRVKEFLESSPNTQWELRAFMAVMHFSLTADRIDDDILKV 116
Query: 109 ET-----VGDAETNFQKASCTLEAGVKIYSV 134
GDA + ++ L A +KIYSV
Sbjct: 117 IVDSMNHHGDARSKLREELAELTAELKIYSV 147
>pdb|1JVN|A Chain A, Crystal Structure Of Imidazole Glycerol Phosphate
Synthase: A Tunnel Through A (BetaALPHA)8 BARREL JOINS
TWO ACTIVE SITES
pdb|1JVN|B Chain B, Crystal Structure Of Imidazole Glycerol Phosphate
Synthase: A Tunnel Through A (BetaALPHA)8 BARREL JOINS
TWO ACTIVE SITES
pdb|1OX4|B Chain B, Towards Understanding The Mechanism Of The Complex
Cyclization Reaction Catalyzed By Imidazole
Glycerophosphate Synthase
pdb|1OX5|A Chain A, Towards Understanding The Mechanism Of The Complex
Cyclization Reaction Catalyzed By Imidazole
Glycerophosphate Synthase
pdb|1OX5|B Chain B, Towards Understanding The Mechanism Of The Complex
Cyclization Reaction Catalyzed By Imidazole
Glycerophosphate Synthase
Length = 555
Score = 28.5 bits (62), Expect = 8.2, Method: Compositional matrix adjust.
Identities = 12/41 (29%), Positives = 25/41 (60%), Gaps = 5/41 (12%)
Query: 74 ELLQNCIKLASENKINQNNTWELKLIDHLSEIIKVETVGDA 114
E+L NCI +K N+ ++L+LI+H+ + +K+ + +
Sbjct: 468 EILLNCI-----DKDGSNSGYDLELIEHVKDAVKIPVIASS 503
>pdb|1OX4|A Chain A, Towards Understanding The Mechanism Of The Complex
Cyclization Reaction Catalyzed By Imidazole
Glycerophosphate Synthase
pdb|1OX6|A Chain A, Towards Understanding The Mechanism Of The Complex
Cyclization Reaction Catalyzed By Imidazole
Glycerophosphate Synthase
pdb|1OX6|B Chain B, Towards Understanding The Mechanism Of The Complex
Cyclization Reaction Catalyzed By Imidazole
Glycerophosphate Synthase
Length = 555
Score = 28.1 bits (61), Expect = 8.4, Method: Compositional matrix adjust.
Identities = 12/41 (29%), Positives = 25/41 (60%), Gaps = 5/41 (12%)
Query: 74 ELLQNCIKLASENKINQNNTWELKLIDHLSEIIKVETVGDA 114
E+L NCI +K N+ ++L+LI+H+ + +K+ + +
Sbjct: 468 EILLNCI-----DKDGSNSGYDLELIEHVKDAVKIPVIASS 503
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
0.314 0.131 0.384
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 11,448,648
Number of Sequences: 62578
Number of extensions: 458179
Number of successful extensions: 684
Number of sequences better than 100.0: 11
Number of HSP's better than 100.0 without gapping: 1
Number of HSP's successfully gapped in prelim test: 10
Number of HSP's that attempted gapping in prelim test: 681
Number of HSP's gapped (non-prelim): 13
length of query: 413
length of database: 14,973,337
effective HSP length: 101
effective length of query: 312
effective length of database: 8,652,959
effective search space: 2699723208
effective search space used: 2699723208
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (22.0 bits)
S2: 53 (25.0 bits)