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= psy5895
(152 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|1OW1|A Chain A, Crystal Structure Of The Spoc Domain Of The Human
Transcriptional Corepressor, Sharp
Length = 195
Score = 158 bits (399), Expect = 1e-39, Method: Compositional matrix adjust.
Identities = 74/146 (50%), Positives = 109/146 (74%), Gaps = 7/146 (4%)
Query: 1 MHYVFGNHLLARDALPLAAEGGLTPPTPTLRIAQRMRLEQTQIDGVVRKMQTDGEHCMLL 60
+H+V GN++LA +LPL+ EGG P LRIAQRMRLE TQ++GV R+M + ++C+LL
Sbjct: 55 LHFVSGNNVLAHRSLPLS-EGG-----PPLRIAQRMRLEATQLEGVARRMTVETDYCLLL 108
Query: 61 ALPCGRTEVDVVQQSAYLQSGFITYLQQKQAAGIVNIAAPGTQQAAYIVHVFPSCEFANN 120
ALPCGR + DVV Q+ L++ FITYLQ KQAAGI+N+ PG+ Q AY++ +FP CEF+ +
Sbjct: 109 ALPCGRDQEDVVSQTESLKAAFITYLQAKQAAGIINVPNPGSNQPAYVLQIFPPCEFSES 168
Query: 121 SLAQIDAQLLKKVSELT-YLVIIIAT 145
L+++ LL +S ++ +L+I+IA+
Sbjct: 169 HLSRLAPDLLASISNISPHLMIVIAS 194
>pdb|1XSN|A Chain A, Crystal Structure Of Human Dna Polymerase Lambda In
Complex With A One Nucleotide Dna Gap And Ddttp
pdb|1XSP|A Chain A, Crystal Structure Of Human Dna Polymerase Lambda In
Complex With Nicked Dna And Pyrophosphate
pdb|2PFN|A Chain A, Na In The Active Site Of Dna Polymerase Lambda
pdb|2PFO|A Chain A, Dna Polymerase Lambda In Complex With Dna And Dupnpp
pdb|2PFP|A Chain A, Dna Polymerase Lambda In Complex With Dna And Dctp
pdb|2PFQ|A Chain A, Manganese Promotes Catalysis In A Dna Polymerase
Lambda-Dna Crystal
pdb|3HW8|A Chain A, Ternary Complex Of Dna Polymerase Lambda Of A Two
Nucleotide Gapped Dna Substrate With A C In The Scrunch
Site
pdb|3HWT|A Chain A, Ternary Complex Of Dna Polymerase Lambda Bound To A Two
Nucleotide Gapped Dna Substrate With A Scrunched Da
Length = 335
Score = 28.1 bits (61), Expect = 1.9, Method: Compositional matrix adjust.
Identities = 20/81 (24%), Positives = 36/81 (44%), Gaps = 10/81 (12%)
Query: 48 RKMQTDGEHCMLLALPCGRTE-------VDVVQQSAYLQSGFITYL---QQKQAAGIVNI 97
R T G+ +L+ P GR+ +D ++Q +L ++ QQ++ G+ +
Sbjct: 180 RGKATCGDVDVLITHPDGRSHRGIFSRLLDSLRQEGFLTDDLVSQEENGQQQKYLGVCRL 239
Query: 98 AAPGTQQAAYIVHVFPSCEFA 118
PG + + V P EFA
Sbjct: 240 PGPGRRHRRLDIIVVPYSEFA 260
>pdb|3C5G|A Chain A, Structure Of A Ternary Complex Of The R517k Pol Lambda
Mutant
pdb|3C5G|B Chain B, Structure Of A Ternary Complex Of The R517k Pol Lambda
Mutant
Length = 335
Score = 28.1 bits (61), Expect = 2.0, Method: Compositional matrix adjust.
Identities = 20/81 (24%), Positives = 36/81 (44%), Gaps = 10/81 (12%)
Query: 48 RKMQTDGEHCMLLALPCGRTE-------VDVVQQSAYLQSGFITYL---QQKQAAGIVNI 97
R T G+ +L+ P GR+ +D ++Q +L ++ QQ++ G+ +
Sbjct: 180 RGKATCGDVDVLITHPDGRSHRGIFSRLLDSLRQEGFLTDDLVSQEENGQQQKYLGVCRL 239
Query: 98 AAPGTQQAAYIVHVFPSCEFA 118
PG + + V P EFA
Sbjct: 240 PGPGRRHRRLDIIVVPYSEFA 260
>pdb|3MDA|A Chain A, Dna Polymerase Lambda In Complex With Arac
pdb|3MDC|A Chain A, Dna Polymerase Lambda In Complex With Dfdctp
Length = 325
Score = 28.1 bits (61), Expect = 2.0, Method: Compositional matrix adjust.
Identities = 20/81 (24%), Positives = 36/81 (44%), Gaps = 10/81 (12%)
Query: 48 RKMQTDGEHCMLLALPCGRTE-------VDVVQQSAYLQSGFITYL---QQKQAAGIVNI 97
R T G+ +L+ P GR+ +D ++Q +L ++ QQ++ G+ +
Sbjct: 170 RGKATCGDVDVLITHPDGRSHRGIFSRLLDSLRQEGFLTDDLVSQEENGQQQKYLGVCRL 229
Query: 98 AAPGTQQAAYIVHVFPSCEFA 118
PG + + V P EFA
Sbjct: 230 PGPGRRHRRLDIIVVPYSEFA 250
>pdb|1XSL|A Chain A, Crystal Structure Of Human Dna Polymerase Lambda In
Complex With A One Nucleotide Dna Gap
pdb|1XSL|E Chain E, Crystal Structure Of Human Dna Polymerase Lambda In
Complex With A One Nucleotide Dna Gap
pdb|1XSL|I Chain I, Crystal Structure Of Human Dna Polymerase Lambda In
Complex With A One Nucleotide Dna Gap
pdb|1XSL|M Chain M, Crystal Structure Of Human Dna Polymerase Lambda In
Complex With A One Nucleotide Dna Gap
pdb|2BCQ|A Chain A, Dna Polymerase Lambda In Complex With A Dna Duplex
Containing An Unpaired Dtmp
pdb|2BCR|A Chain A, Dna Polymerase Lambda In Complex With A Dna Duplex
Containing An Unpaired Damp
pdb|2BCS|A Chain A, Dna Polymerase Lambda In Complex With A Dna Duplex
Containing An Unpaired Dcmp
pdb|2BCU|A Chain A, Dna Polymerase Lambda In Complex With A Dna Duplex
Containing An Unpaired Damp And A T:t Mismatch
pdb|2BCV|A Chain A, Dna Polymerase Lambda In Complex With Dttp And A Dna
Duplex Containing An Unpaired Dtmp
pdb|2GWS|A Chain A, Crystal Structure Of Human Dna Polymerase Lambda With A GG
MISMATCH In The Primer Terminus
pdb|2GWS|E Chain E, Crystal Structure Of Human Dna Polymerase Lambda With A GG
MISMATCH In The Primer Terminus
pdb|2GWS|I Chain I, Crystal Structure Of Human Dna Polymerase Lambda With A GG
MISMATCH In The Primer Terminus
pdb|2GWS|M Chain M, Crystal Structure Of Human Dna Polymerase Lambda With A GG
MISMATCH In The Primer Terminus
Length = 335
Score = 28.1 bits (61), Expect = 2.0, Method: Compositional matrix adjust.
Identities = 20/81 (24%), Positives = 36/81 (44%), Gaps = 10/81 (12%)
Query: 48 RKMQTDGEHCMLLALPCGRTE-------VDVVQQSAYLQSGFITYL---QQKQAAGIVNI 97
R T G+ +L+ P GR+ +D ++Q +L ++ QQ++ G+ +
Sbjct: 180 RGKATCGDVDVLITHPDGRSHRGIFSRLLDSLRQEGFLTDDLVSQEENGQQQKYLGVCRL 239
Query: 98 AAPGTQQAAYIVHVFPSCEFA 118
PG + + V P EFA
Sbjct: 240 PGPGRRHRRLDIIVVPYSEFA 260
>pdb|3HX0|A Chain A, Ternary Complex Of L277a, H511a, R514 Mutant Pol Lambda
Bound To A 2 Nucleotide Gapped Dna Substrate With A
Scrunched Da
pdb|3HX0|F Chain F, Ternary Complex Of L277a, H511a, R514 Mutant Pol Lambda
Bound To A 2 Nucleotide Gapped Dna Substrate With A
Scrunched Da
pdb|3HX0|K Chain K, Ternary Complex Of L277a, H511a, R514 Mutant Pol Lambda
Bound To A 2 Nucleotide Gapped Dna Substrate With A
Scrunched Da
pdb|3HX0|P Chain P, Ternary Complex Of L277a, H511a, R514 Mutant Pol Lambda
Bound To A 2 Nucleotide Gapped Dna Substrate With A
Scrunched Da
Length = 335
Score = 28.1 bits (61), Expect = 2.1, Method: Compositional matrix adjust.
Identities = 20/81 (24%), Positives = 36/81 (44%), Gaps = 10/81 (12%)
Query: 48 RKMQTDGEHCMLLALPCGRTE-------VDVVQQSAYLQSGFITYL---QQKQAAGIVNI 97
R T G+ +L+ P GR+ +D ++Q +L ++ QQ++ G+ +
Sbjct: 180 RGKATCGDVDVLITHPDGRSHRGIFSRLLDSLRQEGFLTDDLVSQEENGQQQKYLGVCRL 239
Query: 98 AAPGTQQAAYIVHVFPSCEFA 118
PG + + V P EFA
Sbjct: 240 PGPGRRHRRLDIIVVPYSEFA 260
>pdb|3C5F|A Chain A, Structure Of A Binary Complex Of The R517a Pol Lambda
Mutant
pdb|3C5F|B Chain B, Structure Of A Binary Complex Of The R517a Pol Lambda
Mutant
Length = 335
Score = 28.1 bits (61), Expect = 2.1, Method: Compositional matrix adjust.
Identities = 20/81 (24%), Positives = 36/81 (44%), Gaps = 10/81 (12%)
Query: 48 RKMQTDGEHCMLLALPCGRTE-------VDVVQQSAYLQSGFITYL---QQKQAAGIVNI 97
R T G+ +L+ P GR+ +D ++Q +L ++ QQ++ G+ +
Sbjct: 180 RGKATCGDVDVLITHPDGRSHRGIFSRLLDSLRQEGFLTDDLVSQEENGQQQKYLGVCRL 239
Query: 98 AAPGTQQAAYIVHVFPSCEFA 118
PG + + V P EFA
Sbjct: 240 PGPGRRHRRLDIIVVPYSEFA 260
>pdb|1RZT|A Chain A, Crystal Structure Of Dna Polymerase Lambda Complexed With
A Two Nucleotide Gap Dna Molecule
pdb|1RZT|E Chain E, Crystal Structure Of Dna Polymerase Lambda Complexed With
A Two Nucleotide Gap Dna Molecule
pdb|1RZT|I Chain I, Crystal Structure Of Dna Polymerase Lambda Complexed With
A Two Nucleotide Gap Dna Molecule
pdb|1RZT|M Chain M, Crystal Structure Of Dna Polymerase Lambda Complexed With
A Two Nucleotide Gap Dna Molecule
Length = 331
Score = 28.1 bits (61), Expect = 2.2, Method: Compositional matrix adjust.
Identities = 20/81 (24%), Positives = 36/81 (44%), Gaps = 10/81 (12%)
Query: 48 RKMQTDGEHCMLLALPCGRTE-------VDVVQQSAYLQSGFITYL---QQKQAAGIVNI 97
R T G+ +L+ P GR+ +D ++Q +L ++ QQ++ G+ +
Sbjct: 176 RGKATCGDVDVLITHPDGRSHRGIFSRLLDSLRQEGFLTDDLVSQEENGQQQKYLGVCRL 235
Query: 98 AAPGTQQAAYIVHVFPSCEFA 118
PG + + V P EFA
Sbjct: 236 PGPGRRHRRLDIIVVPYSEFA 256
>pdb|3LWB|A Chain A, Crystal Structure Of Apo D-Alanine:d-Alanine Ligase (Ddl)
From Mycobacterium Tuberculosis
pdb|3LWB|B Chain B, Crystal Structure Of Apo D-Alanine:d-Alanine Ligase (Ddl)
From Mycobacterium Tuberculosis
Length = 373
Score = 26.2 bits (56), Expect = 7.0, Method: Compositional matrix adjust.
Identities = 16/38 (42%), Positives = 18/38 (47%)
Query: 1 MHYVFGNHLLARDALPLAAEGGLTPPTPTLRIAQRMRL 38
M F LLA D LP+ A L PP TL + RL
Sbjct: 150 MDKEFTKKLLAADGLPVGAYAVLRPPRSTLHRQECERL 187
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 0.133 0.380
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 3,773,089
Number of Sequences: 62578
Number of extensions: 125573
Number of successful extensions: 284
Number of sequences better than 100.0: 12
Number of HSP's better than 100.0 without gapping: 4
Number of HSP's successfully gapped in prelim test: 8
Number of HSP's that attempted gapping in prelim test: 277
Number of HSP's gapped (non-prelim): 13
length of query: 152
length of database: 14,973,337
effective HSP length: 90
effective length of query: 62
effective length of database: 9,341,317
effective search space: 579161654
effective search space used: 579161654
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 47 (22.7 bits)