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= 028005
(215 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|3UDG|A Chain A, Structure Of Deinococcus Radiodurans Ssb Bound To Ssdna
pdb|3UDG|B Chain B, Structure Of Deinococcus Radiodurans Ssb Bound To Ssdna
pdb|3UDG|C Chain C, Structure Of Deinococcus Radiodurans Ssb Bound To Ssdna
Length = 301
Score = 32.3 bits (72), Expect = 0.23, Method: Compositional matrix adjust.
Identities = 14/40 (35%), Positives = 25/40 (62%), Gaps = 1/40 (2%)
Query: 168 RPNQKQQGKIYFGQNLVWKDNLSNGKVLKLGDPVFVMRKV 207
R Q+Q+ K+++ +W+D N K L+ GDPV +M ++
Sbjct: 167 RQGQRQE-KVHYIDATLWRDLAENMKELRKGDPVMIMGRL 205
>pdb|3NNE|A Chain A, Crystal Structure Of Choline Oxidase S101a Mutant
pdb|3NNE|B Chain B, Crystal Structure Of Choline Oxidase S101a Mutant
pdb|3NNE|C Chain C, Crystal Structure Of Choline Oxidase S101a Mutant
pdb|3NNE|D Chain D, Crystal Structure Of Choline Oxidase S101a Mutant
pdb|3NNE|E Chain E, Crystal Structure Of Choline Oxidase S101a Mutant
pdb|3NNE|F Chain F, Crystal Structure Of Choline Oxidase S101a Mutant
pdb|3NNE|G Chain G, Crystal Structure Of Choline Oxidase S101a Mutant
pdb|3NNE|H Chain H, Crystal Structure Of Choline Oxidase S101a Mutant
Length = 546
Score = 30.4 bits (67), Expect = 0.69, Method: Compositional matrix adjust.
Identities = 23/73 (31%), Positives = 34/73 (46%), Gaps = 10/73 (13%)
Query: 1 MQALKISLSKPRDIADGVSVWEWCGSALAEGAEASN--WFTNYLGK-------PSRLVRY 51
M+ + + K R+IA ++ EW G L+ G EA +Y+ K P VR
Sbjct: 414 MRVMVAGIRKAREIAAQPAMAEWTGRELSPGVEAQTDEELQDYIRKTHNTVYHPVGTVRM 473
Query: 52 NA-ESETRPVDPK 63
A E E P+DP+
Sbjct: 474 GAVEDEMSPLDPE 486
>pdb|3LJP|A Chain A, Crystal Structure Of Choline Oxidase V464a Mutant
pdb|3LJP|B Chain B, Crystal Structure Of Choline Oxidase V464a Mutant
Length = 546
Score = 30.4 bits (67), Expect = 0.73, Method: Compositional matrix adjust.
Identities = 23/73 (31%), Positives = 34/73 (46%), Gaps = 10/73 (13%)
Query: 1 MQALKISLSKPRDIADGVSVWEWCGSALAEGAEASN--WFTNYLGK-------PSRLVRY 51
M+ + + K R+IA ++ EW G L+ G EA +Y+ K P VR
Sbjct: 414 MRVMVAGIRKAREIAAQPAMAEWTGRELSPGVEAQTDEELQDYIRKTHNTAYHPVGTVRM 473
Query: 52 NA-ESETRPVDPK 63
A E E P+DP+
Sbjct: 474 GAVEDEMSPLDPE 486
>pdb|2JBV|A Chain A, Crystal Structure Of Choline Oxidase Reveals Insights Into
The Catalytic Mechanism
pdb|2JBV|B Chain B, Crystal Structure Of Choline Oxidase Reveals Insights Into
The Catalytic Mechanism
Length = 546
Score = 30.4 bits (67), Expect = 0.73, Method: Compositional matrix adjust.
Identities = 23/73 (31%), Positives = 34/73 (46%), Gaps = 10/73 (13%)
Query: 1 MQALKISLSKPRDIADGVSVWEWCGSALAEGAEASN--WFTNYLGK-------PSRLVRY 51
M+ + + K R+IA ++ EW G L+ G EA +Y+ K P VR
Sbjct: 414 MRVMVAGIRKAREIAAQPAMAEWTGRELSPGVEAQTDEELQDYIRKTHNTVYHPVGTVRM 473
Query: 52 NA-ESETRPVDPK 63
A E E P+DP+
Sbjct: 474 GAVEDEMSPLDPE 486
>pdb|2XSZ|D Chain D, The Dodecameric Human Ruvbl1:ruvbl2 Complex With Truncated
Domains Ii
pdb|2XSZ|E Chain E, The Dodecameric Human Ruvbl1:ruvbl2 Complex With Truncated
Domains Ii
pdb|2XSZ|F Chain F, The Dodecameric Human Ruvbl1:ruvbl2 Complex With Truncated
Domains Ii
Length = 378
Score = 30.0 bits (66), Expect = 1.1, Method: Compositional matrix adjust.
Identities = 16/53 (30%), Positives = 21/53 (39%)
Query: 125 NNCTFQGVKLCDRCKVPTINQDTGVAGPEPSETLRQIRSDKVLRPNQKQQGKI 177
N FQG + KVP I T + +R + D L P Q QG +
Sbjct: 10 ENLYFQGATVTATTKVPEIRDVTRIERIGAHSHIRGLGLDDALEPRQASQGXV 62
>pdb|1SE8|A Chain A, Structure Of Single-Stranded Dna-Binding Protein (Ssb)
From D. Radiodurans
Length = 301
Score = 29.6 bits (65), Expect = 1.5, Method: Compositional matrix adjust.
Identities = 13/40 (32%), Positives = 24/40 (60%), Gaps = 1/40 (2%)
Query: 168 RPNQKQQGKIYFGQNLVWKDNLSNGKVLKLGDPVFVMRKV 207
R Q+Q+ K+++ +W+D N K L+ GDPV + ++
Sbjct: 167 RQGQRQE-KVHYIDATLWRDLAENXKELRKGDPVXIXGRL 205
>pdb|1WGZ|A Chain A, Crystal Structure Of Carboxypeptidase 1 From Thermus
Thermophilus
pdb|1WGZ|B Chain B, Crystal Structure Of Carboxypeptidase 1 From Thermus
Thermophilus
pdb|1WGZ|C Chain C, Crystal Structure Of Carboxypeptidase 1 From Thermus
Thermophilus
Length = 510
Score = 29.3 bits (64), Expect = 1.6, Method: Compositional matrix adjust.
Identities = 29/102 (28%), Positives = 42/102 (41%), Gaps = 25/102 (24%)
Query: 11 PRDIADGV-SVWEWCGSALAEGAEASNWFTNY-LGKPSRLVRYN-AESETRPVDPKYAAG 67
P+D DGV W G +F Y LG + AE+E P++P++A G
Sbjct: 406 PKDYKDGVMQDVHWAGGLF-------GYFPTYTLGNLYAAQFFQKAEAELGPLEPRFARG 458
Query: 68 EKIMFSDCYPFMLLSQGSLDALNKLLKEPIPINRFRPNILVD 109
E F D + ++GS RFRP +LV+
Sbjct: 459 EFQPFLDWTRARIHAEGS---------------RFRPRVLVE 485
>pdb|3HOA|A Chain A, Crystal Structure Of The Thermus Thermophilus M32
Carboxypeptidase
pdb|3HOA|B Chain B, Crystal Structure Of The Thermus Thermophilus M32
Carboxypeptidase
Length = 509
Score = 29.3 bits (64), Expect = 1.6, Method: Compositional matrix adjust.
Identities = 29/102 (28%), Positives = 42/102 (41%), Gaps = 25/102 (24%)
Query: 11 PRDIADGV-SVWEWCGSALAEGAEASNWFTNY-LGKPSRLVRYN-AESETRPVDPKYAAG 67
P+D DGV W G +F Y LG + AE+E P++P++A G
Sbjct: 406 PKDYKDGVMQDVHWAGGLF-------GYFPTYTLGNLYAAQFFQKAEAELGPLEPRFARG 458
Query: 68 EKIMFSDCYPFMLLSQGSLDALNKLLKEPIPINRFRPNILVD 109
E F D + ++GS RFRP +LV+
Sbjct: 459 EFQPFLDWTRARIHAEGS---------------RFRPRVLVE 485
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
0.318 0.135 0.416
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 6,564,512
Number of Sequences: 62578
Number of extensions: 268586
Number of successful extensions: 693
Number of sequences better than 100.0: 11
Number of HSP's better than 100.0 without gapping: 3
Number of HSP's successfully gapped in prelim test: 8
Number of HSP's that attempted gapping in prelim test: 690
Number of HSP's gapped (non-prelim): 11
length of query: 215
length of database: 14,973,337
effective HSP length: 95
effective length of query: 120
effective length of database: 9,028,427
effective search space: 1083411240
effective search space used: 1083411240
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 49 (23.5 bits)