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= psy874
(191 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 = 66.6 bits (161), Expect = 8e-12, Method: Compositional matrix adjust.
Identities = 39/115 (33%), Positives = 58/115 (50%), Gaps = 9/115 (7%)
Query: 7 VVVFTDGACPRNGKVGASAGYGVYFGENNPLNVAGKVTGRVTNNNAEIQGAIHALKQAKS 66
VVV+TDG C NG+ AG GVY+G +PLNV ++ GR TN AEI A A++QAK+
Sbjct: 8 VVVYTDGCCSSNGRRRPRAGIGVYWGPGHPLNVGIRLPGRQTNQRAEIHAACKAIEQAKT 67
Query: 67 ---------ANEKVKLKRSYNDTHAQKKVRNVSSVAMRIAQKVDYISHDVISVGI 112
N + N KK +S + K D+++ + ++ G+
Sbjct: 68 QNINKLVLYTNSMFTINGITNWVQGWKKNGWKTSAGKEVINKEDFVALERLTQGM 122
>pdb|2QKB|A Chain A, Human Rnase H Catalytic Domain Mutant D210n In Complex
With 20-Mer RnaDNA HYBRID
pdb|2QKB|B Chain B, Human Rnase H Catalytic Domain Mutant D210n In Complex
With 20-Mer RnaDNA HYBRID
Length = 154
Score = 65.9 bits (159), Expect = 1e-11, Method: Compositional matrix adjust.
Identities = 32/62 (51%), Positives = 41/62 (66%)
Query: 7 VVVFTDGACPRNGKVGASAGYGVYFGENNPLNVAGKVTGRVTNNNAEIQGAIHALKQAKS 66
VVV+TDG C NG+ AG GVY+G +PLNV ++ GR TN AEI A A++QAK+
Sbjct: 8 VVVYTDGCCSSNGRRRPRAGIGVYWGPGHPLNVGIRLPGRQTNQRAEIHAACKAIEQAKT 67
Query: 67 AN 68
N
Sbjct: 68 QN 69
>pdb|1RIL|A Chain A, Crystal Structure Of Ribonuclease H From Thermus
Thermophilus Hb8 Refined At 2.8 Angstroms Resolution
Length = 166
Score = 39.7 bits (91), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 31/84 (36%), Positives = 38/84 (45%), Gaps = 7/84 (8%)
Query: 3 PDNHVVVFTDGACPRNGKVGASAGYGVYFGENNPLNVAGKVTGRVTNNNAEIQGAIHALK 62
P V +FTDGAC N G A + F + L G+ TNN E++ AI LK
Sbjct: 5 PRKRVALFTDGACLGNPGPGGWAAL-LRFHAHEKLLSGGEAC--TTNNRMELKAAIEGLK 61
Query: 63 QAKSANEKVKLKRSYNDTHAQKKV 86
K E V L Y D+H KK
Sbjct: 62 ALKEPCE-VDL---YTDSHYLKKA 81
>pdb|2YV0|X Chain X, Structural And Thermodynamic Analyses Of E. Coli
Ribonuclease Hi Variant With Quintuple
Thermostabilizing Mutations
Length = 155
Score = 33.5 bits (75), Expect = 0.083, Method: Compositional matrix adjust.
Identities = 24/66 (36%), Positives = 30/66 (45%), Gaps = 3/66 (4%)
Query: 6 HVVVFTDGACPRNGKVGASAGYGVYFGENNPLNVAGKVTGRVTNNNAEIQGAIHALKQAK 65
V +FTDG+C N G A Y G + AG R TNN E+ AI AL+ K
Sbjct: 4 QVEIFTDGSCLGNPGPGGYAAILRYRGREKTFS-AGYT--RTTNNRMELMAAIVALEALK 60
Query: 66 SANEKV 71
E +
Sbjct: 61 EPCEVI 66
>pdb|3TTB|A Chain A, Structure Of The Thioalkalivibrio Paradoxus Cytochrome C
Nitrite Reductase In Complex With Sulfite
pdb|3TTB|B Chain B, Structure Of The Thioalkalivibrio Paradoxus Cytochrome C
Nitrite Reductase In Complex With Sulfite
pdb|3SXQ|A Chain A, Structure Of A Hexameric Multiheme C Nitrite Reductase
From The Extremophile Bacterium Thiolkalivibrio
Paradoxus
pdb|3SXQ|B Chain B, Structure Of A Hexameric Multiheme C Nitrite Reductase
From The Extremophile Bacterium Thiolkalivibrio
Paradoxus
Length = 525
Score = 28.1 bits (61), Expect = 3.0, Method: Compositional matrix adjust.
Identities = 13/55 (23%), Positives = 29/55 (52%), Gaps = 3/55 (5%)
Query: 97 AQKVDYISHDVISVGIPFPSIQDENVKLKRSYNDTHAQKKGIPFPSIQDEKVKLK 151
A+++D+ ++ G P P +Q + +L+ + TH ++ G+ +VKL+
Sbjct: 339 AKEIDFFDFTHVTTGAPLPKLQ--HPELETFWGSTH-ERNGVTCADCHMPRVKLE 390
>pdb|2Y4S|A Chain A, Barley Limit Dextrinase In Complex With Beta-Cyclodextrin
pdb|2Y5E|A Chain A, Barley Limit Dextrinase In Complex With Alpha-Cyclodextrin
pdb|4AIO|A Chain A, Crystal Structure Of The Starch Debranching Enzyme Barley
Limit Dextrinase
Length = 884
Score = 28.1 bits (61), Expect = 3.5, Method: Composition-based stats.
Identities = 17/53 (32%), Positives = 25/53 (47%)
Query: 106 DVISVGIPFPSIQDENVKLKRSYNDTHAQKKGIPFPSIQDEKVKLKRSYNDTH 158
DVISV P DE ++ + A +GIPF DE ++ K D++
Sbjct: 647 DVISVKTPMILSVDERCRINHLASSMMALSQGIPFFHAGDEILRSKSIDRDSY 699
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
0.314 0.130 0.366
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 5,816,923
Number of Sequences: 62578
Number of extensions: 224696
Number of successful extensions: 410
Number of sequences better than 100.0: 10
Number of HSP's better than 100.0 without gapping: 3
Number of HSP's successfully gapped in prelim test: 7
Number of HSP's that attempted gapping in prelim test: 407
Number of HSP's gapped (non-prelim): 10
length of query: 191
length of database: 14,973,337
effective HSP length: 93
effective length of query: 98
effective length of database: 9,153,583
effective search space: 897051134
effective search space used: 897051134
T: 11
A: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (22.0 bits)
S2: 48 (23.1 bits)