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= psy13396
(328 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|1ZT2|A Chain A, Heterodimeric Structure Of The Core Primase.
pdb|1ZT2|C Chain C, Heterodimeric Structure Of The Core Primase
Length = 330
Score = 42.4 bits (98), Expect = 4e-04, Method: Compositional matrix adjust.
Identities = 48/171 (28%), Positives = 74/171 (43%), Gaps = 29/171 (16%)
Query: 42 REFSFT-LNGDIYARYISYNSPNELKKDLIKR-CPQKIDL-GAIYDICPKDHLQHSVFTP 98
REF+ D Y R++S++S EL+ L+ R P + A Y + +++ +
Sbjct: 36 REFALQPFGSDTYVRHLSFSSSEELRDYLVNRNLPLHLFYSSARYQLPSARNMEEKAWMG 95
Query: 99 KMKELVFDID---MTDYDDVRNC--CSGADICEKCWR---------YMSIAC-------- 136
+L+FDID + +R C C A + EKC R M+ C
Sbjct: 96 --SDLLFDIDADHLCKLRSIRFCPVCGNAVVSEKCERDNVETLEYVEMTSECIKRGLEQT 153
Query: 137 KILDTALREDFDFQLLLWVFSGRRGIHCWV-CDEAALALDGRGRSCLAEYM 186
+ L L +DF + ++ FSG RG H V C LD R +AEY+
Sbjct: 154 RNLVEILEDDFGLKPKVY-FSGNRGFHVQVDCYGNCALLDSDERKEIAEYV 203
>pdb|2XSP|A Chain A, Structure Of Cellobiohydrolase 1 (Cel7a) From
Heterobasidion Annosum
pdb|2YG1|A Chain A, Apo Structure Of Cellobiohydrolase 1 (Cel7a) From
Heterobasidion Annosum
pdb|2YG1|B Chain B, Apo Structure Of Cellobiohydrolase 1 (Cel7a) From
Heterobasidion Annosum
Length = 440
Score = 32.0 bits (71), Expect = 0.54, Method: Compositional matrix adjust.
Identities = 15/61 (24%), Positives = 26/61 (42%)
Query: 51 DIYARYISYNSPNELKKDLIKRCPQKIDLGAIYDICPKDHLQHSVFTPKMKELVFDIDMT 110
D Y S N L + P ++G+ + D + +F K +E FD+DM+
Sbjct: 77 DYSGTYGISTSGNALTLKFVTNGPYSTNIGSRVYLMSADDTNYEIFKLKNQEFAFDVDMS 136
Query: 111 D 111
+
Sbjct: 137 N 137
>pdb|1X8D|A Chain A, Crystal Structure Of E. Coli Yiil Protein Containing L-
Rhamnose
pdb|1X8D|B Chain B, Crystal Structure Of E. Coli Yiil Protein Containing L-
Rhamnose
pdb|1X8D|C Chain C, Crystal Structure Of E. Coli Yiil Protein Containing L-
Rhamnose
pdb|1X8D|D Chain D, Crystal Structure Of E. Coli Yiil Protein Containing L-
Rhamnose
Length = 104
Score = 30.4 bits (67), Expect = 1.3, Method: Composition-based stats.
Identities = 12/48 (25%), Positives = 27/48 (56%), Gaps = 2/48 (4%)
Query: 88 KDHLQH--SVFTPKMKELVFDIDMTDYDDVRNCCSGADICEKCWRYMS 133
K H H +++ K + L+F + + ++ N + D+C++ W+YM+
Sbjct: 34 KSHGAHNYAIYLDKARNLLFAMVEIESEERWNAVASTDVCQRWWKYMT 81
>pdb|3MPR|A Chain A, Crystal Structure Of EndonucleaseEXONUCLEASEPHOSPHATASE
FAMILY Protein From Bacteroides Thetaiotaomicron,
Northeast Structural Genomics Consortium Target Btr318a
pdb|3MPR|B Chain B, Crystal Structure Of EndonucleaseEXONUCLEASEPHOSPHATASE
FAMILY Protein From Bacteroides Thetaiotaomicron,
Northeast Structural Genomics Consortium Target Btr318a
pdb|3MPR|C Chain C, Crystal Structure Of EndonucleaseEXONUCLEASEPHOSPHATASE
FAMILY Protein From Bacteroides Thetaiotaomicron,
Northeast Structural Genomics Consortium Target Btr318a
pdb|3MPR|D Chain D, Crystal Structure Of EndonucleaseEXONUCLEASEPHOSPHATASE
FAMILY Protein From Bacteroides Thetaiotaomicron,
Northeast Structural Genomics Consortium Target Btr318a
Length = 298
Score = 28.9 bits (63), Expect = 3.7, Method: Compositional matrix adjust.
Identities = 26/92 (28%), Positives = 40/92 (43%), Gaps = 18/92 (19%)
Query: 29 RWLFYGNLDNFRKREFSFTLNGDIYA-------RYI----SYNSPNE-LKKDLIKRCPQK 76
R+ G +NF F+ + I+ RY +Y S E KK+ ++ CP++
Sbjct: 207 RYALNGTFNNFDPNSFTESRIDHIFVSPSFHVKRYGVLTDTYRSVRENSKKEDVRDCPEE 266
Query: 77 IDLGAIYDICPKDHLQHSVFTPKMKELVFDID 108
I + A P DH P ELVFD++
Sbjct: 267 ITIKAYEARTPSDHF------PVKVELVFDLE 292
>pdb|1PX8|A Chain A, Crystal Structure Of Beta-D-Xylosidase From
Thermoanaerobacterium Saccharolyticum, A Family 39
Glycoside Hydrolase
pdb|1PX8|B Chain B, Crystal Structure Of Beta-D-Xylosidase From
Thermoanaerobacterium Saccharolyticum, A Family 39
Glycoside Hydrolase
pdb|1UHV|A Chain A, Crystal Structure Of Beta-D-Xylosidase From
Thermoanaerobacterium Saccharolyticum, A Family 39
Glycoside Hydrolase
pdb|1UHV|B Chain B, Crystal Structure Of Beta-D-Xylosidase From
Thermoanaerobacterium Saccharolyticum, A Family 39
Glycoside Hydrolase
pdb|1UHV|C Chain C, Crystal Structure Of Beta-D-Xylosidase From
Thermoanaerobacterium Saccharolyticum, A Family 39
Glycoside Hydrolase
pdb|1UHV|D Chain D, Crystal Structure Of Beta-D-Xylosidase From
Thermoanaerobacterium Saccharolyticum, A Family 39
Glycoside Hydrolase
Length = 500
Score = 28.1 bits (61), Expect = 7.1, Method: Compositional matrix adjust.
Identities = 14/37 (37%), Positives = 19/37 (51%), Gaps = 6/37 (16%)
Query: 258 IGPGQDVEKWDRLVAIIKHHQAKNSDRKLKYAIEEIL 294
+ P +D EKW LV + HH +Y IEE+L
Sbjct: 121 VTPPKDYEKWSDLVKAVLHHFIS------RYGIEEVL 151
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
0.324 0.141 0.452
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 10,468,583
Number of Sequences: 62578
Number of extensions: 432995
Number of successful extensions: 1088
Number of sequences better than 100.0: 6
Number of HSP's better than 100.0 without gapping: 3
Number of HSP's successfully gapped in prelim test: 3
Number of HSP's that attempted gapping in prelim test: 1085
Number of HSP's gapped (non-prelim): 6
length of query: 328
length of database: 14,973,337
effective HSP length: 99
effective length of query: 229
effective length of database: 8,778,115
effective search space: 2010188335
effective search space used: 2010188335
T: 11
A: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.5 bits)
S2: 52 (24.6 bits)