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= psy5765
(205 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|3HQV|B Chain B, Low Resolution, Molecular Envelope Structure Of Type I
Collagen In Situ Determined By Fiber Diffraction. Single
Type I Collagen Molecule, Rigid Body Refinement
pdb|3HR2|B Chain B, Low Resolution, Molecular Envelope Structure Of Type I
Collagen In Situ Determined By Fiber Diffraction. Single
Type I Collagen Molecule, Post Rigid Body Refinement,
'relaxed'
Length = 1028
Score = 34.3 bits (77), Expect = 0.051, Method: Compositional matrix adjust.
Identities = 33/104 (31%), Positives = 38/104 (36%), Gaps = 6/104 (5%)
Query: 42 PSGRLRYLGPSGSLRYLGPSGRLRYLGPSGRLRYLGPSGSLRYLGPSGR------LRYLG 95
P G GP G G G GP G GPSG+ +G G G
Sbjct: 445 PDGNNGAQGPXGPQGVQGGKGEQGPAGPXGFQGLXGPSGTAGEVGKXGERGLPGEFGLXG 504
Query: 96 PSGRLRYLGPSGRLRYLGPSGRLRYLGPSGRLNSDGPSGRLRYL 139
P+G GP G GPSG + GPSG DG G +
Sbjct: 505 PAGPRGERGPXGESGAAGPSGPIGIRGPSGAXGPDGNKGEAGAV 548
Score = 32.3 bits (72), Expect = 0.18, Method: Compositional matrix adjust.
Identities = 54/174 (31%), Positives = 68/174 (39%), Gaps = 6/174 (3%)
Query: 12 NLGPSGRLRYLGPSGSLRYLGPSGSLRYLGPSGRLRYLGPSGSLRYLGPSGRLRYLGPSG 71
N+GP+G+ +G G GP G G +G + + GP G G G + G +G
Sbjct: 379 NVGPAGKEGPVGLXGIDGRXGPIGPAGPRGEAGNIGFXGPKGPSGDXGKXGEKGHPGLAG 438
Query: 72 RLRYLGPSGSLRYLGPSGRLRYLGPSGRLRYLGPSGRLRYLGPSGRLRYLGPSGRLNSDG 131
GP G+ GP G G G GP G GPSG + G+ G
Sbjct: 439 ARGAXGPDGNNGAQGPXGPQGVQGGKGEQGPAGPXGFQGLXGPSGTAGEV---GKXGERG 495
Query: 132 PSGRLRYLGPSGRLRYLGPSGRLRYLGPSGRLRYLGPSGRLRYLGPSGRLRYLG 185
G GP+G GP G GPSG + GPSG GP G G
Sbjct: 496 LPGEFGLXGPAGPRGERGPXGESGAAGPSGPIGIRGPSG---AXGPDGNKGEAG 546
Score = 32.0 bits (71), Expect = 0.26, Method: Compositional matrix adjust.
Identities = 61/219 (27%), Positives = 76/219 (34%), Gaps = 42/219 (19%)
Query: 16 SGRLRYLGPSGSLRYLGPSGSLRYLGPSGRLRY---LGP---SGSLRYLGPSGRLRYLGP 69
GR +GP G+ GP+G G +GR +GP GS +GP+G+ +G
Sbjct: 332 DGRAGVMGPPGNRGSTGPAGVRGPNGDAGRXGEXGLMGPRGLXGSXGNVGPAGKEGPVGL 391
Query: 70 SGRLRYLGPSGSLRYLGPSGRLRYLGPSG------------------RLRYLGPSGRLRY 111
G GP G G +G + + GP G GP G
Sbjct: 392 XGIDGRXGPIGPAGPRGEAGNIGFXGPKGPSGDXGKXGEKGHPGLAGARGAXGPDGNNGA 451
Query: 112 LGPSGRLRYLGPSGRLNSDGPSGRLRYLGPSGRLRYLG---------------PSGRLRY 156
GP G G G GP G GPSG +G P+G
Sbjct: 452 QGPXGPQGVQGGKGEQGPAGPXGFQGLXGPSGTAGEVGKXGERGLPGEFGLXGPAGPRGE 511
Query: 157 LGPSGRLRYLGPSGRLRYLGPSGRLRYLGPSGRLRYLGL 195
GP G GPSG + GPSG GP G G
Sbjct: 512 RGPXGESGAAGPSGPIGIRGPSG---AXGPDGNKGEAGA 547
Score = 30.0 bits (66), Expect = 0.91, Method: Compositional matrix adjust.
Identities = 54/175 (30%), Positives = 71/175 (40%), Gaps = 6/175 (3%)
Query: 14 GPSGRLRYLGPSGSLRYLGPSGSLRYLGPSGRLRYLGPSGSLRYLGPSGRLRYLGPSGRL 73
GP G GP G + GP+GS G +G G +G+ GPSG G G
Sbjct: 252 GPVGAAGATGPRGLVGEXGPAGS---XGETGNKGEXGSAGAQGPXGPSGEEGKRGSPGEP 308
Query: 74 RYLGPSGSLRYLGPSGRLRYLGPSGRLRYLGPSGRLRYLGPSGRLRYLGPSGRLNSDGPS 133
GP+G G G G GR +GP G GP+G GP+G G
Sbjct: 309 GSAGPAGPXGLRGSXGSRGLXGADGRAGVMGPPGNRGSTGPAG---VRGPNGDAGRXGEX 365
Query: 134 GRLRYLGPSGRLRYLGPSGRLRYLGPSGRLRYLGPSGRLRYLGPSGRLRYLGPSG 188
G + G G +GP+G+ +G G GP G G +G + + GP G
Sbjct: 366 GLMGPRGLXGSXGNVGPAGKEGPVGLXGIDGRXGPIGPAGPRGEAGNIGFXGPKG 420
Score = 28.5 bits (62), Expect = 2.8, Method: Compositional matrix adjust.
Identities = 47/154 (30%), Positives = 61/154 (39%), Gaps = 33/154 (21%)
Query: 14 GPSGRLRYLGPSGSLRYLGPSGSLRYLGPSGRLRYLGPSGSLRYLGPSGRLRYLGPSGRL 73
GP GR G G Y G +GP+G GP GS +GP+G+ G G
Sbjct: 855 GPXGRDGQXGHKGERGYXG------NIGPTGAAGAPGPHGS---VGPAGKHGNRGEPGPA 905
Query: 74 RYLGPSGSLRYLGPSGRLRYLGPSGR-----------------LRYL-------GPSGRL 109
+GP G++ GPSG G G L+ L G G
Sbjct: 906 GSVGPVGAVGPRGPSGPQGIRGDKGEPGDXGARGLPGLKGHNGLQGLPGLAGLHGDQGAP 965
Query: 110 RYLGPSGRLRYLGPSGRLNSDGPSGRLRYLGPSG 143
+GP+G GPSG + DG SG +GP+G
Sbjct: 966 GPVGPAGPRGPAGPSGPIGKDGRSGHPGPVGPAG 999
Score = 27.3 bits (59), Expect = 6.3, Method: Compositional matrix adjust.
Identities = 23/72 (31%), Positives = 29/72 (40%), Gaps = 6/72 (8%)
Query: 124 SGRLNSDGPSGRLRYLGPSGRLRYLGPSGRLRYLGPSGRLRYLGPSGRLRYLGPSGRLRY 183
G SDGP GR G G Y G +GP+G GP G + G G
Sbjct: 848 DGNXGSDGPXGRDGQXGHKGERGYXG------NIGPTGAAGAPGPHGSVGPAGKHGNRGE 901
Query: 184 LGPSGRLRYLGL 195
GP+G + +G
Sbjct: 902 PGPAGSVGPVGA 913
Score = 26.9 bits (58), Expect = 7.7, Method: Compositional matrix adjust.
Identities = 45/146 (30%), Positives = 60/146 (41%), Gaps = 6/146 (4%)
Query: 50 GPSGSLRYLGPSGRLRYLGPSGRLRYLGPSGSLRYLGPSGRLRYLGPSGRLRYLGPSGRL 109
GP G+ GP G + GP+G G +G+ G +G GPSG G G
Sbjct: 252 GPVGAAGATGPRGLVGEXGPAG---SXGETGNKGEXGSAGAQGPXGPSGEEGKRGSPGEP 308
Query: 110 RYLGPSGRLRYLGPSGRLNSDGPSGRLRYLGPSGRLRYLGPSGRLRYLGPSGRLRYLGPS 169
GP+G G G G GR +GP G GP+G GP+G G
Sbjct: 309 GSAGPAGPXGLRGSXGSRGLXGADGRAGVMGPPGNRGSTGPAG---VRGPNGDAGRXGEX 365
Query: 170 GRLRYLGPSGRLRYLGPSGRLRYLGL 195
G + G G +GP+G+ +GL
Sbjct: 366 GLMGPRGLXGSXGNVGPAGKEGPVGL 391
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 0.150 0.466
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 7,774,792
Number of Sequences: 62578
Number of extensions: 381963
Number of successful extensions: 1488
Number of sequences better than 100.0: 4
Number of HSP's better than 100.0 without gapping: 3
Number of HSP's successfully gapped in prelim test: 1
Number of HSP's that attempted gapping in prelim test: 703
Number of HSP's gapped (non-prelim): 360
length of query: 205
length of database: 14,973,337
effective HSP length: 94
effective length of query: 111
effective length of database: 9,091,005
effective search space: 1009101555
effective search space used: 1009101555
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 49 (23.5 bits)