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= psy2388
(159 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|1NMP|A Chain A, Structural Genomics, Ybgi Protein, Unknown Function
pdb|1NMP|B Chain B, Structural Genomics, Ybgi Protein, Unknown Function
pdb|1NMP|C Chain C, Structural Genomics, Ybgi Protein, Unknown Function
pdb|1NMP|D Chain D, Structural Genomics, Ybgi Protein, Unknown Function
pdb|1NMP|E Chain E, Structural Genomics, Ybgi Protein, Unknown Function
pdb|1NMP|F Chain F, Structural Genomics, Ybgi Protein, Unknown Function
Length = 247
Score = 130 bits (327), Expect = 3e-31, Method: Compositional matrix adjust.
Identities = 62/155 (40%), Positives = 90/155 (58%), Gaps = 11/155 (7%)
Query: 1 MNADAILVHHGYFWKGENSNIVGIKKKRLEQLIINKINLYAYHLPLDMHPKLGNNAQLAK 60
+ ADA++VHHGYFWKGE+ I G+K+ RL+ L+ N INLY +HLPLD HP+LGNNAQLA
Sbjct: 55 LGADAVIVHHGYFWKGESPVIRGMKRNRLKTLLANDINLYGWHLPLDAHPELGNNAQLAA 114
Query: 61 ILNFSCTRRFSXXXXXXXXXXXXLKRYNFKKIITIKDLFHHITRKIGKKPIVIGDLNKKI 120
+L + + + +L I ++G+KP+ GD ++
Sbjct: 115 LLGITVMGEIE----------PLVPWGELTMPVPGLELASWIEARLGRKPLWCGDTGPEV 164
Query: 121 YE-IGWCTGAAQNLLTDAINEGVTAYISGEISEST 154
+ + WCTG Q+ + A GV A+I+GE+SE T
Sbjct: 165 VQRVAWCTGGGQSFIDSAARFGVDAFITGEVSEQT 199
>pdb|1NMO|A Chain A, Structural Genomics, Protein Ybgi, Unknown Function
pdb|1NMO|B Chain B, Structural Genomics, Protein Ybgi, Unknown Function
pdb|1NMO|C Chain C, Structural Genomics, Protein Ybgi, Unknown Function
pdb|1NMO|D Chain D, Structural Genomics, Protein Ybgi, Unknown Function
pdb|1NMO|E Chain E, Structural Genomics, Protein Ybgi, Unknown Function
pdb|1NMO|F Chain F, Structural Genomics, Protein Ybgi, Unknown Function
Length = 247
Score = 129 bits (325), Expect = 6e-31, Method: Compositional matrix adjust.
Identities = 62/155 (40%), Positives = 89/155 (57%), Gaps = 11/155 (7%)
Query: 1 MNADAILVHHGYFWKGENSNIVGIKKKRLEQLIINKINLYAYHLPLDMHPKLGNNAQLAK 60
+ ADA++VHHGYFWKGE+ I G K+ RL+ L+ N INLY +HLPLD HP+LGNNAQLA
Sbjct: 55 LGADAVIVHHGYFWKGESPVIRGXKRNRLKTLLANDINLYGWHLPLDAHPELGNNAQLAA 114
Query: 61 ILNFSCTRRFSXXXXXXXXXXXXLKRYNFKKIITIKDLFHHITRKIGKKPIVIGDLNKKI 120
+L + + + +L I ++G+KP+ GD ++
Sbjct: 115 LLGITVXGEIE----------PLVPWGELTXPVPGLELASWIEARLGRKPLWCGDTGPEV 164
Query: 121 YE-IGWCTGAAQNLLTDAINEGVTAYISGEISEST 154
+ + WCTG Q+ + A GV A+I+GE+SE T
Sbjct: 165 VQRVAWCTGGGQSFIDSAARFGVDAFITGEVSEQT 199
>pdb|2YYB|A Chain A, Crystal Structure Of Ttha1606 From Thermus Thermophilus
Hb8
pdb|2YYB|B Chain B, Crystal Structure Of Ttha1606 From Thermus Thermophilus
Hb8
Length = 242
Score = 63.9 bits (154), Expect = 3e-11, Method: Compositional matrix adjust.
Identities = 33/63 (52%), Positives = 40/63 (63%), Gaps = 1/63 (1%)
Query: 2 NADAILVHHGYFWKGENSNIVGIKKKRLEQLIINKINLYAYHLPLDMHPKLGNNAQLAKI 61
D ++VHHG FW G+ IVG K+RLE L INLYA HLPLD H ++GNN LA+
Sbjct: 57 EVDFLIVHHGLFW-GKPFPIVGHHKRRLETLFQGGINLYAAHLPLDAHEEVGNNFVLARE 115
Query: 62 LNF 64
L
Sbjct: 116 LGL 118
>pdb|2FYW|A Chain A, Crystal Structure Of A Conserved Protein Of Unknown
Function From Streptococcus Pneumoniae
pdb|2FYW|B Chain B, Crystal Structure Of A Conserved Protein Of Unknown
Function From Streptococcus Pneumoniae
pdb|2FYW|C Chain C, Crystal Structure Of A Conserved Protein Of Unknown
Function From Streptococcus Pneumoniae
Length = 267
Score = 35.0 bits (79), Expect = 0.017, Method: Compositional matrix adjust.
Identities = 15/43 (34%), Positives = 24/43 (55%)
Query: 115 DLNKKIYEIGWCTGAAQNLLTDAINEGVTAYISGEISESTKKN 157
DL K I + C G+ Q+ DA+ +G YI+G+I T ++
Sbjct: 172 DLQKPISRVAICGGSGQSFYKDALAKGADVYITGDIYYHTAQD 214
>pdb|3LNL|A Chain A, Crystal Structure Of Staphylococcus Aureus Protein Sa1388
pdb|3LNL|B Chain B, Crystal Structure Of Staphylococcus Aureus Protein Sa1388
Length = 370
Score = 29.6 bits (65), Expect = 0.84, Method: Compositional matrix adjust.
Identities = 21/59 (35%), Positives = 31/59 (52%), Gaps = 1/59 (1%)
Query: 4 DAILVHHGYFWKGENSNIVGIKKKRLEQLIINKINLYAYHLPLDMHPKLGNNAQLAKIL 62
+ I+ HH +KG S + +LI + INL A H LD++P G N LAK++
Sbjct: 63 NTIISHHPLIFKGVTSLKANGYGLIIRKLIQHDINLIAMHTNLDVNPH-GVNMMLAKVM 120
>pdb|2NYD|A Chain A, Crystal Structure Of Staphylococcus Aureus Hypothetical
Protein Sa1388
pdb|2NYD|B Chain B, Crystal Structure Of Staphylococcus Aureus Hypothetical
Protein Sa1388
Length = 370
Score = 29.6 bits (65), Expect = 0.84, Method: Compositional matrix adjust.
Identities = 21/59 (35%), Positives = 31/59 (52%), Gaps = 1/59 (1%)
Query: 4 DAILVHHGYFWKGENSNIVGIKKKRLEQLIINKINLYAYHLPLDMHPKLGNNAQLAKIL 62
+ I+ HH +KG S + +LI + INL A H LD++P G N LAK++
Sbjct: 63 NTIISHHPLIFKGVTSLKANGYGLIIRKLIQHDINLIAMHTNLDVNP-YGVNMMLAKVM 120
>pdb|3QC7|A Chain A, The Structure Of Bacteriophage Phi29 Head Fibers Has A
Supercoiled Triple Repeating Helix-Turn-Helix Motif
Length = 179
Score = 28.1 bits (61), Expect = 2.1, Method: Compositional matrix adjust.
Identities = 17/46 (36%), Positives = 29/46 (63%), Gaps = 3/46 (6%)
Query: 114 GDLNKKIYEIGWCTGAAQNLLTDAINEGVTAYISGEISESTKKNLK 159
GD K++ +I +GA +N++ + NE A I+GE + + KKNL+
Sbjct: 20 GDTGKRLLKINTPSGA-RNIIIE--NEDAKALINGETTNTNKKNLQ 62
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 0.138 0.412
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 4,335,726
Number of Sequences: 62578
Number of extensions: 149182
Number of successful extensions: 409
Number of sequences better than 100.0: 8
Number of HSP's better than 100.0 without gapping: 4
Number of HSP's successfully gapped in prelim test: 4
Number of HSP's that attempted gapping in prelim test: 400
Number of HSP's gapped (non-prelim): 12
length of query: 159
length of database: 14,973,337
effective HSP length: 91
effective length of query: 68
effective length of database: 9,278,739
effective search space: 630954252
effective search space used: 630954252
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 47 (22.7 bits)