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= psy9623
(355 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|4DRF|A Chain A, Crystal Structure Of Bacterial Pnkp-CHEN1-N Heterodimer
pdb|4DRF|C Chain C, Crystal Structure Of Bacterial Pnkp-CHEN1-N Heterodimer
pdb|4E6N|A Chain A, Crystal Structure Of Bacterial Pnkp-CHEN1-N Heterodimer
pdb|4E6N|C Chain C, Crystal Structure Of Bacterial Pnkp-CHEN1-N Heterodimer
Length = 427
Score = 30.4 bits (67), Expect = 1.6, Method: Compositional matrix adjust.
Identities = 23/75 (30%), Positives = 32/75 (42%), Gaps = 18/75 (24%)
Query: 6 LPRVLQPRKTS-----LELERETFEKFQSASIGKAVNSQ-------------ETPVKEKH 47
LP + P +TS LE E FE F++ +GK V Q ++ V EK
Sbjct: 49 LPPTMSPCETSKKEGMLEHPIEAFEYFRTRGVGKVVCEQKHMGSRAVVIVCKDSQVAEKR 108
Query: 48 FHLKDGYGKLIYQYT 62
F + DG + Y T
Sbjct: 109 FGVLDGTAGICYTRT 123
>pdb|3TY5|A Chain A, Crystal Structure Of C. Thermocellum Pnkp Ligase Domain In
Complex With Atp
pdb|3TY5|B Chain B, Crystal Structure Of C. Thermocellum Pnkp Ligase Domain In
Complex With Atp
Length = 413
Score = 30.4 bits (67), Expect = 1.6, Method: Compositional matrix adjust.
Identities = 23/75 (30%), Positives = 32/75 (42%), Gaps = 18/75 (24%)
Query: 6 LPRVLQPRKTS-----LELERETFEKFQSASIGKAVNSQ-------------ETPVKEKH 47
LP + P +TS LE E FE F++ +GK V Q ++ V EK
Sbjct: 35 LPPTMSPCETSKKEGMLEHPIEAFEYFRTRGVGKVVCGQKHMGSRAVVIVCKDSQVAEKR 94
Query: 48 FHLKDGYGKLIYQYT 62
F + DG + Y T
Sbjct: 95 FGVLDGTAGICYTRT 109
>pdb|3TY9|A Chain A, Crystal Structure Of C. Thermocellum Pnkp Ligase Domain
Amp-Adenylate
pdb|3TY9|B Chain B, Crystal Structure Of C. Thermocellum Pnkp Ligase Domain
Amp-Adenylate
pdb|3TY9|C Chain C, Crystal Structure Of C. Thermocellum Pnkp Ligase Domain
Amp-Adenylate
pdb|3TY9|D Chain D, Crystal Structure Of C. Thermocellum Pnkp Ligase Domain
Amp-Adenylate
Length = 393
Score = 30.0 bits (66), Expect = 1.8, Method: Compositional matrix adjust.
Identities = 23/75 (30%), Positives = 32/75 (42%), Gaps = 18/75 (24%)
Query: 6 LPRVLQPRKTS-----LELERETFEKFQSASIGKAVNSQ-------------ETPVKEKH 47
LP + P +TS LE E FE F++ +GK V Q ++ V EK
Sbjct: 15 LPPTMSPCETSKKEGMLEHPIEAFEYFRTRGVGKVVCEQKHMGSRAVVIVCKDSQVAEKR 74
Query: 48 FHLKDGYGKLIYQYT 62
F + DG + Y T
Sbjct: 75 FGVLDGTAGICYTRT 89
>pdb|3TY8|A Chain A, Crystal Structure Of C. Thermocellum Pnkp Ligase Domain
Apo Form
pdb|3TY8|B Chain B, Crystal Structure Of C. Thermocellum Pnkp Ligase Domain
Apo Form
Length = 413
Score = 30.0 bits (66), Expect = 1.8, Method: Compositional matrix adjust.
Identities = 23/77 (29%), Positives = 33/77 (42%), Gaps = 18/77 (23%)
Query: 4 LSLPRVLQPRKTS-----LELERETFEKFQSASIGKAVNSQ-------------ETPVKE 45
+ LP + P +TS LE E FE F++ +GK V Q ++ V E
Sbjct: 33 IYLPPTMSPCETSKKEGMLEHPIEAFEYFRTRGVGKVVCEQKHMGSRAVVIVCKDSQVAE 92
Query: 46 KHFHLKDGYGKLIYQYT 62
K F + DG + Y T
Sbjct: 93 KRFGVLDGTAGICYTRT 109
>pdb|1RRI|A Chain A, Dhna Complex With 3-(5-Amino-7-Hydroxy-[1,2,3] Triazolo
[4,5- D]pyrimidin-2-Yl)-Benzoic Acid
pdb|1RRW|A Chain A, Dhna Complexed With 9-Methylguanine
pdb|1RRY|A Chain A, Dhna Complexed With
2-Amino-4-Hydroxy-5-Carboxyethylpyrimidine
pdb|1RS2|A Chain A, Dhna Complex With
8-Amino-1,3-Dimethyl-3,7-Dihydropurine-2,6-Dione
pdb|1RS4|A Chain A, Dhna, 7,8-Dihydroneopterin Aldolase Complexed With
3-(5-Amino-7-
Hydroxy-[1,2,3]triazolo[4,5-D]pyrimidin-2-Yl)-N-(3,
5-Dichlorobenzyl)- Benzamide
pdb|1RSD|A Chain A, Dhna Complex With
3-(5-Amino-7-Hydroxy-[1,2,3]triazolo[4,5-
D]pyrimidin-2-Yl)-N-[2-(2-Hydroxymethyl-Phenylsulfanyl)-
Benzyl]- Benzamide
pdb|1RSI|A Chain A, Dhna Complex With
2-amino-5-bromo-3-hydroxy-6-phenylpyrimidine
pdb|1U68|A Chain A, Dhna 7,8 Dihydroneopterin Complex
pdb|1DHN|A Chain A, 1.65 Angstrom Resolution Structure Of 7,8-dihydroneopterin
Aldolase From Staphylococcus Aureus
pdb|2DHN|A Chain A, Complex Of 7,8-Dihydroneopterin Aldolase From
Staphylococcus Aureus With
6-Hydroxymethyl-7,8-Dihydropterin At 2.2 A Resolution
pdb|2NM2|A Chain A, Crystal Structure Of Dihydroneopterin Aldolase From S.
Aureus In Complex With (1s,2r)-Neopterin At 1.50
Angstrom Resolution
pdb|2NM2|B Chain B, Crystal Structure Of Dihydroneopterin Aldolase From S.
Aureus In Complex With (1s,2r)-Neopterin At 1.50
Angstrom Resolution
pdb|2NM2|C Chain C, Crystal Structure Of Dihydroneopterin Aldolase From S.
Aureus In Complex With (1s,2r)-Neopterin At 1.50
Angstrom Resolution
pdb|2NM2|D Chain D, Crystal Structure Of Dihydroneopterin Aldolase From S.
Aureus In Complex With (1s,2r)-Neopterin At 1.50
Angstrom Resolution
pdb|2NM3|A Chain A, Crystal Structure Of Dihydroneopterin Aldolase From S.
Aureus In Complex With (1s,2s)-Monapterin At 1.68
Angstrom Resolution
Length = 121
Score = 28.9 bits (63), Expect = 4.5, Method: Compositional matrix adjust.
Identities = 21/60 (35%), Positives = 28/60 (46%), Gaps = 9/60 (15%)
Query: 22 ETFEKFQSASIGKAVNSQETPVKEKHFHLKDGYGKLIY-QYTRLLLGKLDFHRRNPGFPG 80
E FE+ +S GKAVN E HL + I QY R++ K+ + NP PG
Sbjct: 56 EVFEEVKSIMEGKAVNLLE--------HLAERIANRINSQYNRVMETKVRITKENPPIPG 107
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
0.322 0.135 0.397
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 9,425,467
Number of Sequences: 62578
Number of extensions: 354602
Number of successful extensions: 600
Number of sequences better than 100.0: 5
Number of HSP's better than 100.0 without gapping: 0
Number of HSP's successfully gapped in prelim test: 5
Number of HSP's that attempted gapping in prelim test: 599
Number of HSP's gapped (non-prelim): 5
length of query: 355
length of database: 14,973,337
effective HSP length: 100
effective length of query: 255
effective length of database: 8,715,537
effective search space: 2222461935
effective search space used: 2222461935
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (22.0 bits)
S2: 52 (24.6 bits)