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= psy5156
(389 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|2QK9|A Chain A, Human Rnase H Catalytic Domain Mutant D210n In Complex
With 18-Mer RnaDNA HYBRID
pdb|2QKK|A Chain A, Human Rnase H Catalytic Domain Mutant D210n In Complex
With 14-Mer RnaDNA HYBRID
pdb|2QKK|B Chain B, Human Rnase H Catalytic Domain Mutant D210n In Complex
With 14-Mer RnaDNA HYBRID
pdb|2QKK|E Chain E, Human Rnase H Catalytic Domain Mutant D210n In Complex
With 14-Mer RnaDNA HYBRID
pdb|2QKK|F Chain F, Human Rnase H Catalytic Domain Mutant D210n In Complex
With 14-Mer RnaDNA HYBRID
pdb|2QKK|I Chain I, Human Rnase H Catalytic Domain Mutant D210n In Complex
With 14-Mer RnaDNA HYBRID
pdb|2QKK|J Chain J, Human Rnase H Catalytic Domain Mutant D210n In Complex
With 14-Mer RnaDNA HYBRID
pdb|2QKK|M Chain M, Human Rnase H Catalytic Domain Mutant D210n In Complex
With 14-Mer RnaDNA HYBRID
pdb|2QKK|N Chain N, Human Rnase H Catalytic Domain Mutant D210n In Complex
With 14-Mer RnaDNA HYBRID
pdb|2QKK|R Chain R, Human Rnase H Catalytic Domain Mutant D210n In Complex
With 14-Mer RnaDNA HYBRID
pdb|2QKK|S Chain S, Human Rnase H Catalytic Domain Mutant D210n In Complex
With 14-Mer RnaDNA HYBRID
pdb|2QKK|W Chain W, Human Rnase H Catalytic Domain Mutant D210n In Complex
With 14-Mer RnaDNA HYBRID
Length = 154
Score = 32.3 bits (72), Expect = 0.44, Method: Compositional matrix adjust.
Identities = 28/115 (24%), Positives = 51/115 (44%), Gaps = 17/115 (14%)
Query: 16 DFLKIYTDG-------SKDETGVGCALIIPQ-LNVTKRFTLNKYSSIFHAELFSILQSLK 67
DF+ +YTDG + G+G LNV R + + AE+ + ++++
Sbjct: 6 DFVVVYTDGCCSSNGRRRPRAGIGVYWGPGHPLNVGIRLPGRQTNQ--RAEIHAACKAIE 63
Query: 68 NAKLLNIKKVLIISDSLSSFQAISNLYHP-------NPLVKEIPHAELFSILQSL 115
AK NI K+++ ++S+ + I+N KE+ + E F L+ L
Sbjct: 64 QAKTQNINKLVLYTNSMFTINGITNWVQGWKKNGWKTSAGKEVINKEDFVALERL 118
>pdb|2YKN|A Chain A, Crystal Structure Of Hiv-1 Reverse Transcriptase (Rt) In
Complex With A Difluoromethylbenzoxazole (Dfmb)
Pyrimidine Thioether Derivative, A Non-Nucleoside Rt
Inhibitor (Nnrti)
Length = 562
Score = 28.9 bits (63), Expect = 4.8, Method: Compositional matrix adjust.
Identities = 9/19 (47%), Positives = 12/19 (63%)
Query: 186 IKFLWCPSHVGISGNDQAD 204
+ W P+H GI GN+Q D
Sbjct: 531 VYLAWVPAHKGIGGNEQVD 549
>pdb|2YKM|A Chain A, Crystal Structure Of Hiv-1 Reverse Transcriptase (Rt) In
Complex With A Difluoromethylbenzoxazole (Dfmb)
Pyrimidine Thioether Derivative, A Non-Nucleoside Rt
Inhibitor (Nnrti)
Length = 562
Score = 28.9 bits (63), Expect = 5.0, Method: Compositional matrix adjust.
Identities = 9/19 (47%), Positives = 12/19 (63%)
Query: 186 IKFLWCPSHVGISGNDQAD 204
+ W P+H GI GN+Q D
Sbjct: 531 VYLAWVPAHKGIGGNEQVD 549
>pdb|1HDS|B Chain B, Macromolecular Structure Refinement By Restrained Least-
Squares And Interactive Graphics As Applied To Sickling
Deer Type Iii Hemoglobin
pdb|1HDS|D Chain D, Macromolecular Structure Refinement By Restrained Least-
Squares And Interactive Graphics As Applied To Sickling
Deer Type Iii Hemoglobin
Length = 145
Score = 28.9 bits (63), Expect = 5.7, Method: Compositional matrix adjust.
Identities = 14/27 (51%), Positives = 18/27 (66%), Gaps = 2/27 (7%)
Query: 313 LHCNKLRFRPPSF--LGNSLANILSDN 337
LHCNKL P +F LGN LA +++ N
Sbjct: 90 LHCNKLHVNPQNFRLLGNVLALVVARN 116
>pdb|2A2P|A Chain A, Solution Structure Of Selm From Mus Musculus
Length = 129
Score = 28.5 bits (62), Expect = 7.4, Method: Composition-based stats.
Identities = 23/83 (27%), Positives = 39/83 (46%), Gaps = 16/83 (19%)
Query: 93 LYHPNPLVKEIPHAELFSILQSLKNAELLNIKKVLIISDSLSSFQAISNLYHPNPLVKEI 152
LYH N ++K +P A+ +L S EL I + D + N LV+E+
Sbjct: 43 LYH-NLVMKHLPGADPELVLLSRNYQELERIPLSQMTRDEI------------NALVQEL 89
Query: 153 ---QETYSSAQISIKFLWCPSHP 172
+++ AQ+ ++LW P+ P
Sbjct: 90 GFYRKSAPEAQVPPEYLWAPAKP 112
>pdb|4IB2|A Chain A, Crystal Structure Of A Putative Lipoprotein (rumgna_00858)
From Ruminococcus Gnavus Atcc 29149 At 1.76 A Resolution
pdb|4IB2|B Chain B, Crystal Structure Of A Putative Lipoprotein (rumgna_00858)
From Ruminococcus Gnavus Atcc 29149 At 1.76 A Resolution
Length = 252
Score = 28.1 bits (61), Expect = 8.7, Method: Compositional matrix adjust.
Identities = 15/34 (44%), Positives = 21/34 (61%), Gaps = 1/34 (2%)
Query: 216 TNHSLLLEEMKSLAKKHFYQKWNTTWSN-VNPNE 248
T H+ +LE+ KS+ KK YQ T + + V PNE
Sbjct: 20 TPHAEILEQAKSILKKEGYQLEVTVFDDYVQPNE 53
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
0.320 0.133 0.408
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 10,814,957
Number of Sequences: 62578
Number of extensions: 402995
Number of successful extensions: 1060
Number of sequences better than 100.0: 6
Number of HSP's better than 100.0 without gapping: 0
Number of HSP's successfully gapped in prelim test: 6
Number of HSP's that attempted gapping in prelim test: 1059
Number of HSP's gapped (non-prelim): 8
length of query: 389
length of database: 14,973,337
effective HSP length: 101
effective length of query: 288
effective length of database: 8,652,959
effective search space: 2492052192
effective search space used: 2492052192
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: 52 (24.6 bits)