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= 033607
(115 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|2XM6|A Chain A, Crystal Structure Of The Protein Corresponding To Locus
C5321 From Cft073 E.Coli Strain
Length = 490
Score = 32.0 bits (71), Expect = 0.097, Method: Compositional matrix adjust.
Identities = 21/57 (36%), Positives = 29/57 (50%), Gaps = 4/57 (7%)
Query: 40 RWFRDTLKEAKGGDINMQVLVGQMYFSGYGVARDAQKGRIWISRASRTRSSVWKVGE 96
+WFR L +G D Q + G YF G GV RD R W S+A+ + +VW +
Sbjct: 136 KWFR--LAAEQGRDSGQQSM-GDAYFEGDGVTRDYVMAREWYSKAAE-QGNVWSCNQ 188
Score = 31.2 bits (69), Expect = 0.13, Method: Compositional matrix adjust.
Identities = 16/52 (30%), Positives = 29/52 (55%), Gaps = 3/52 (5%)
Query: 40 RWFRDTLKEAKGGDINMQVLVGQMYFSGYGVARDAQKGRIWISRASRTRSSV 91
+W+R K A GD Q+ + MY+ G GV +D + R+ S+++ +S+
Sbjct: 208 QWYR---KSATSGDELGQLHLADMYYFGIGVTQDYTQSRVLFSQSAEQGNSI 256
Score = 28.5 bits (62), Expect = 1.0, Method: Compositional matrix adjust.
Identities = 17/45 (37%), Positives = 23/45 (51%), Gaps = 3/45 (6%)
Query: 41 WFRDTLKEAKGGDINMQVLVGQMYFSGYGVARDAQKGRIWISRAS 85
W R K A+ G QV +G++Y+ G GV RD + W AS
Sbjct: 389 WMR---KAAEQGLSAAQVQLGEIYYYGLGVERDYVQAWAWFDTAS 430
>pdb|1OUV|A Chain A, Helicobacter Cysteine Rich Protein C (Hcpc)
Length = 273
Score = 28.9 bits (63), Expect = 0.79, Method: Compositional matrix adjust.
Identities = 14/43 (32%), Positives = 24/43 (55%), Gaps = 3/43 (6%)
Query: 49 AKGGDINMQV---LVGQMYFSGYGVARDAQKGRIWISRASRTR 88
AK D+N L+G +Y+SG GV+++ K + S+A +
Sbjct: 66 AKACDLNYSNGCHLLGNLYYSGQGVSQNTNKALQYYSKACDLK 108
>pdb|2OFZ|A Chain A, Ultrahigh Resolution Crystal Structure Of Rna Binding
Domain Of Sars Nucleopcapsid (n Protein) At 1.1 Angstrom
Resolution In Monoclinic Form.
pdb|2OG3|A Chain A, Structure Of The Rna Binding Domain Of N Protein From Sars
Coronavirus In Cubic Crystal Form
Length = 138
Score = 27.3 bits (59), Expect = 2.1, Method: Compositional matrix adjust.
Identities = 16/70 (22%), Positives = 32/70 (45%), Gaps = 7/70 (10%)
Query: 41 WFRDTLKEAKGGDINMQVLVGQMYFSGYGVARDA-------QKGRIWISRASRTRSSVWK 93
++R + +GGD M+ L + YF G +A ++G +W++ +
Sbjct: 51 YYRRATRRVRGGDGKMKELSPRWYFYYLGTGPEASLPYGANKEGIVWVATEGALNTPKDH 110
Query: 94 VGEKHPGYNA 103
+G ++P NA
Sbjct: 111 IGTRNPNNNA 120
>pdb|3GVC|A Chain A, Crystal Structure Of Probable Short-Chain Dehydrogenase-
Reductase From Mycobacterium Tuberculosis
pdb|3GVC|B Chain B, Crystal Structure Of Probable Short-Chain Dehydrogenase-
Reductase From Mycobacterium Tuberculosis
pdb|3GVC|C Chain C, Crystal Structure Of Probable Short-Chain Dehydrogenase-
Reductase From Mycobacterium Tuberculosis
pdb|3GVC|D Chain D, Crystal Structure Of Probable Short-Chain Dehydrogenase-
Reductase From Mycobacterium Tuberculosis
Length = 277
Score = 26.9 bits (58), Expect = 2.5, Method: Compositional matrix adjust.
Identities = 18/67 (26%), Positives = 29/67 (43%), Gaps = 2/67 (2%)
Query: 37 CVKRWFRDTLKEAKGGDINMQVLVGQMYFSGYGVARDAQKGRIWISR--ASRTRSSVWKV 94
C K ++ G +N+ L GQ+ G G ++ G I +SR A+ RSS +
Sbjct: 141 CTKHAAPRMIERGGGAIVNLSSLAGQVAVGGTGAYGMSKAGIIQLSRITAAELRSSGIRS 200
Query: 95 GEKHPGY 101
P +
Sbjct: 201 NTLLPAF 207
>pdb|1SSK|A Chain A, Structure Of The N-Terminal Rna-Binding Domain Of The Sars
Cov Nucleocapsid Protein
Length = 158
Score = 26.9 bits (58), Expect = 2.6, Method: Compositional matrix adjust.
Identities = 16/70 (22%), Positives = 32/70 (45%), Gaps = 7/70 (10%)
Query: 41 WFRDTLKEAKGGDINMQVLVGQMYFSGYGVARDA-------QKGRIWISRASRTRSSVWK 93
++R + +GGD M+ L + YF G +A ++G +W++ +
Sbjct: 64 YYRRATRRVRGGDGKMKELSPRWYFYYLGTGPEASLPYGANKEGIVWVATEGALNTPKDH 123
Query: 94 VGEKHPGYNA 103
+G ++P NA
Sbjct: 124 IGTRNPNNNA 133
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
0.315 0.130 0.392
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 2,662,000
Number of Sequences: 62578
Number of extensions: 82247
Number of successful extensions: 147
Number of sequences better than 100.0: 5
Number of HSP's better than 100.0 without gapping: 2
Number of HSP's successfully gapped in prelim test: 3
Number of HSP's that attempted gapping in prelim test: 141
Number of HSP's gapped (non-prelim): 9
length of query: 115
length of database: 14,973,337
effective HSP length: 78
effective length of query: 37
effective length of database: 10,092,253
effective search space: 373413361
effective search space used: 373413361
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)