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= psy13778
(295 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|3HQV|A Chain A, Low Resolution, Molecular Envelope Structure Of Type I
Collagen In Situ Determined By Fiber Diffraction. Single
Type I Collagen Molecule, Rigid Body Refinement
pdb|3HQV|C Chain C, 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|A Chain A, 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'
pdb|3HR2|C Chain C, 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 = 1056
Score = 33.5 bits (75), Expect = 0.13, Method: Compositional matrix adjust.
Identities = 27/69 (39%), Positives = 32/69 (46%), Gaps = 3/69 (4%)
Query: 107 QGPTLPQGPTLPQGPTLPQGPTLPQGPTLLQGPTLLQGPTLLQGP---TLLQGPTLPQGP 163
+G T P GP P GP +GP PQGP G T QG + G + LQGP G
Sbjct: 904 RGETGPAGPAGPIGPAGARGPAGPQGPRGDXGETGEQGDRGIXGHRGFSGLQGPXGSXGS 963
Query: 164 TLLQGPTLL 172
QGP+
Sbjct: 964 XGEQGPSGA 972
>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 = 29.6 bits (65), Expect = 1.9, Method: Compositional matrix adjust.
Identities = 49/175 (28%), Positives = 57/175 (32%), Gaps = 28/175 (16%)
Query: 60 GPTLPQGPTLLQGPTLLQGPTLPQGPTLPQGPTLLQDPTLPQGPTLL------------- 106
GP +GP L G GP P GP G P P G
Sbjct: 381 GPAGKEGPVGLXGIDGRXGPIGPAGPRGEAGNIGFXGPKGPSGDXGKXGEKGHPGLAGAR 440
Query: 107 -----QGPTLPQGPTLPQGPTLPQGPTLPQGPTLLQGPTLLQGPTLLQGPTLLQGPTLPQ 161
G QGP PQG +G P GP QG L GP+ G
Sbjct: 441 GAXGPDGNNGAQGPXGPQGVQGGKGEQGPAGPXGFQG---------LXGPSGTAGEVGKX 491
Query: 162 GPTLLQGPTLLQGPRKGPTLPQGPTLPQGPTLPQDPTLLQDPTLLQGPRYKEKEL 216
G L G L GP GP +GP G P P ++ P+ GP + E
Sbjct: 492 GERGLPGEFGLXGP-AGPRGERGPXGESGAAGPSGPIGIRGPSGAXGPDGNKGEA 545
>pdb|3JVD|A Chain A, Crystal Structure Of Putative Transcription Regulation
Repressor (Laci Family) From Corynebacterium Glutamicum
pdb|3JVD|B Chain B, Crystal Structure Of Putative Transcription Regulation
Repressor (Laci Family) From Corynebacterium Glutamicum
Length = 333
Score = 28.5 bits (62), Expect = 4.8, Method: Compositional matrix adjust.
Identities = 11/28 (39%), Positives = 18/28 (64%)
Query: 57 LLQGPTLPQGPTLLQGPTLLQGPTLPQG 84
L++ P LP G +LQG +L+G + +G
Sbjct: 300 LIENPELPTGDVVLQGQVILRGSSTHEG 327
>pdb|2OLW|A Chain A, Crystal Structure Of E. Coli Pseudouridine Synthase Rlue
pdb|2OLW|B Chain B, Crystal Structure Of E. Coli Pseudouridine Synthase Rlue
Length = 217
Score = 28.1 bits (61), Expect = 5.7, Method: Compositional matrix adjust.
Identities = 14/29 (48%), Positives = 16/29 (55%)
Query: 172 LQGPRKGPTLPQGPTLPQGPTLPQDPTLL 200
L+ R G TL GPTLP G L +P L
Sbjct: 122 LEALRNGVTLNDGPTLPAGAELVDEPAWL 150
>pdb|1WIY|A Chain A, Crystal Structure Analysis Of A 6-Coordinated Cytochorome
P450 From Thermus Thermophilus Hb8
pdb|1WIY|B Chain B, Crystal Structure Analysis Of A 6-Coordinated Cytochorome
P450 From Thermus Thermophilus Hb8
Length = 389
Score = 28.1 bits (61), Expect = 6.3, Method: Compositional matrix adjust.
Identities = 30/99 (30%), Positives = 38/99 (38%), Gaps = 18/99 (18%)
Query: 49 WTL---LQGPTLLQGPTLPQGPTLLQGPTLLQGPTLPQGPTLPQGPTLLQDPTLPQGPTL 105
W L L+ P LL LPQG TL+ P + Q P+G Q
Sbjct: 269 WILTRRLERPLLLGEDRLPQGTTLVLSPYVTQRLYFPEGEAF-------------QPERF 315
Query: 106 LQGPTLPQGPTLPQGPTLPQGPTLPQGPTLLQGPTLLQG 144
L P G P G L Q L + LL+GP +L+
Sbjct: 316 LAERGTPSGRYFPFG--LGQRLCLGRDFALLEGPIVLRA 352
>pdb|2OML|A Chain A, Crystal Structure Of E. Coli Pseudouridine Synthase Rlue
Length = 189
Score = 28.1 bits (61), Expect = 6.5, Method: Compositional matrix adjust.
Identities = 14/29 (48%), Positives = 16/29 (55%)
Query: 172 LQGPRKGPTLPQGPTLPQGPTLPQDPTLL 200
L+ R G TL GPTLP G L +P L
Sbjct: 94 LEALRNGVTLNDGPTLPAGAELVDEPAWL 122
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 0.138 0.440
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 8,977,402
Number of Sequences: 62578
Number of extensions: 363447
Number of successful extensions: 1659
Number of sequences better than 100.0: 24
Number of HSP's better than 100.0 without gapping: 20
Number of HSP's successfully gapped in prelim test: 4
Number of HSP's that attempted gapping in prelim test: 732
Number of HSP's gapped (non-prelim): 420
length of query: 295
length of database: 14,973,337
effective HSP length: 98
effective length of query: 197
effective length of database: 8,840,693
effective search space: 1741616521
effective search space used: 1741616521
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.9 bits)
S2: 51 (24.3 bits)