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= 042780
(122 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|3QDK|A Chain A, Structural Insight On Mechanism And Diverse Substrate
Selection Strategy Of Ribulokinase
pdb|3QDK|B Chain B, Structural Insight On Mechanism And Diverse Substrate
Selection Strategy Of Ribulokinase
pdb|3QDK|C Chain C, Structural Insight On Mechanism And Diverse Substrate
Selection Strategy Of Ribulokinase
pdb|3QDK|D Chain D, Structural Insight On Mechanism And Diverse Substrate
Selection Strategy Of Ribulokinase
Length = 572
Score = 26.9 bits (58), Expect = 3.0, Method: Composition-based stats.
Identities = 19/69 (27%), Positives = 33/69 (47%), Gaps = 4/69 (5%)
Query: 17 DLIDAWPLGSVVTQGCHASVSAIWSHKDDPHTLQYCSPQNINSMHKVTLEVKGETQIVNL 76
D I + G +V C A AIW ++ + ++ + H T +++G+ IV L
Sbjct: 188 DWIVSQMTGKIVKNSCTAGYKAIWHKREGYPSNEFFKALDPRLEHLTTTKLRGD--IVPL 245
Query: 77 SEKLNAGGI 85
E+ AGG+
Sbjct: 246 GER--AGGL 252
>pdb|3EJJ|X Chain X, Structure Of M-Csf Bound To The First Three Domains Of Fms
Length = 289
Score = 26.6 bits (57), Expect = 3.9, Method: Compositional matrix adjust.
Identities = 27/108 (25%), Positives = 42/108 (38%), Gaps = 19/108 (17%)
Query: 25 GSVVTQGCHASVSAIWSHKDDPH-TLQYCSPQNINSMHKVTLEVKGETQIVNLSEKLNAG 83
G VT C ++ S W P+ TL SP + + T + G + L + + AG
Sbjct: 19 GETVTLRCVSNGSVEWDGPISPYWTLDPESPGSTLTTRNATFKNTGTYRCTELEDPM-AG 77
Query: 84 GIAHKLWIEQP-----------------ENIPTCLATKPYPKSTVSLV 114
L+++ P E + CL T P K +VSL+
Sbjct: 78 STTIHLYVKDPAHSWNLLAQEVTVVEGQEAVLPCLITDPALKDSVSLM 125
>pdb|4EXP|X Chain X, Structure Of Mouse Interleukin-34 In Complex With Mouse
Fms
Length = 283
Score = 26.6 bits (57), Expect = 4.1, Method: Compositional matrix adjust.
Identities = 27/108 (25%), Positives = 42/108 (38%), Gaps = 19/108 (17%)
Query: 25 GSVVTQGCHASVSAIWSHKDDPH-TLQYCSPQNINSMHKVTLEVKGETQIVNLSEKLNAG 83
G VT C ++ S W P+ TL SP + + T + G + L + + AG
Sbjct: 19 GETVTLRCVSNGSVEWDGPISPYWTLDPESPGSTLTTRNATFKNTGTYRCTELEDPM-AG 77
Query: 84 GIAHKLWIEQP-----------------ENIPTCLATKPYPKSTVSLV 114
L+++ P E + CL T P K +VSL+
Sbjct: 78 STTIHLYVKDPAHSWNLLAQEVTVVEGQEAVLPCLITDPALKDSVSLM 125
>pdb|3O3U|N Chain N, Crystal Structure Of Human Receptor For Advanced Glycation
Endproducts (Rage)
Length = 581
Score = 26.2 bits (56), Expect = 5.2, Method: Composition-based stats.
Identities = 13/47 (27%), Positives = 24/47 (51%), Gaps = 9/47 (19%)
Query: 66 EVKGETQIVNLSEKLNAGGIAHKLWIEQPENIPTCLATKPYPKSTVS 112
++ G+ +IV+ + +L AG P + TC++ YP T+S
Sbjct: 469 QIPGKPEIVDSASELTAG---------VPNKVGTCVSEGSYPAGTLS 506
>pdb|2BQ4|A Chain A, Crystal Structure Of Type I Cytochrome C3 From
Desulfovibrio Africanus
pdb|2BQ4|B Chain B, Crystal Structure Of Type I Cytochrome C3 From
Desulfovibrio Africanus
Length = 116
Score = 25.8 bits (55), Expect = 6.0, Method: Compositional matrix adjust.
Identities = 15/52 (28%), Positives = 22/52 (42%), Gaps = 4/52 (7%)
Query: 24 LGSVVTQGCHASVSAIWSHKDDPHTLQYC----SPQNINSMHKVTLEVKGET 71
+G T+GCHA ++ + + DP L SP + HK K T
Sbjct: 53 IGGCATEGCHADTTSFKATEKDPKFLMTAFHSKSPMSCQGCHKEMKTAKKTT 104
>pdb|1YGA|A Chain A, Crystal Structure Of Saccharomyces Cerevisiae Yn9a
Protein, New York Structural Genomics Consortium
pdb|1YGA|B Chain B, Crystal Structure Of Saccharomyces Cerevisiae Yn9a
Protein, New York Structural Genomics Consortium
Length = 342
Score = 25.8 bits (55), Expect = 6.7, Method: Compositional matrix adjust.
Identities = 18/66 (27%), Positives = 32/66 (48%), Gaps = 3/66 (4%)
Query: 4 NGDVLVQ-YVVLRRDLIDAWPLGSVVTQGCHASVSAIWSHKDDPH--TLQYCSPQNINSM 60
NG +VQ Y ++ L D +G+ V + + ++S D PH T+ C N +S+
Sbjct: 38 NGQSVVQGYSNVQDYLTDGNMMGATVGRYANRIAKGVFSLDDGPHKLTVNNCGNTNHSSI 97
Query: 61 HKVTLE 66
+ L+
Sbjct: 98 SSLNLK 103
>pdb|3G66|A Chain A, The Crystal Structure Of Streptococcus Pneumoniae Sortase
C Provides Novel Insights Into Catalysis As Well As
Pilin Substrate Specificity
pdb|3G66|B Chain B, The Crystal Structure Of Streptococcus Pneumoniae Sortase
C Provides Novel Insights Into Catalysis As Well As
Pilin Substrate Specificity
pdb|3G69|A Chain A, The Crystal Structure Of Streptococcus Pneumoniae Sortase
C Provides Novel Insights Into Catalysis As Well As
Pilin Substrate Specificity
pdb|3G69|B Chain B, The Crystal Structure Of Streptococcus Pneumoniae Sortase
C Provides Novel Insights Into Catalysis As Well As
Pilin Substrate Specificity
Length = 212
Score = 25.4 bits (54), Expect = 7.9, Method: Compositional matrix adjust.
Identities = 16/55 (29%), Positives = 27/55 (49%), Gaps = 3/55 (5%)
Query: 5 GDVLVQYVVLRRDLIDAWPLGSVVTQGCHASVSAIWSHKDDPHTLQYCSPQNINS 59
GD+ +V+ D + A+ + +VT + + H +D TL C+P INS
Sbjct: 132 GDIFYLHVL---DQVLAYQVDQIVTVEPNDFEPVLIQHGEDYATLLTCTPYMINS 183
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
0.316 0.132 0.411
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 3,796,286
Number of Sequences: 62578
Number of extensions: 139203
Number of successful extensions: 224
Number of sequences better than 100.0: 13
Number of HSP's better than 100.0 without gapping: 3
Number of HSP's successfully gapped in prelim test: 10
Number of HSP's that attempted gapping in prelim test: 221
Number of HSP's gapped (non-prelim): 13
length of query: 122
length of database: 14,973,337
effective HSP length: 84
effective length of query: 38
effective length of database: 9,716,785
effective search space: 369237830
effective search space used: 369237830
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 45 (21.9 bits)