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= 020560
(324 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|3IHP|A Chain A, Covalent Ubiquitin-Usp5 Complex
pdb|3IHP|B Chain B, Covalent Ubiquitin-Usp5 Complex
Length = 854
Score = 38.9 bits (89), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 20/76 (26%), Positives = 37/76 (48%)
Query: 105 PEEMVEPEVDKELLKELEAMGFPVARATRALHYSGXXXXXXXXXXXXXXXXDPDIDEMPM 164
P+E P +D+ ++ +L MGFP+ +A++Y+G DPD +
Sbjct: 643 PDEPKAPMLDESVIIQLVEMGFPMDACRKAVYYTGNSGAEAAMNWVMSHMDDPDFANPLI 702
Query: 165 VPVSGGGGASKSSLTP 180
+P S G G++ ++ P
Sbjct: 703 LPGSSGPGSTSAAADP 718
>pdb|2CRN|A Chain A, Solution Structure Of The Uba Domain Of Human Ubash3a
Protein
Length = 64
Score = 30.4 bits (67), Expect = 1.3, Method: Compositional matrix adjust.
Identities = 19/53 (35%), Positives = 25/53 (47%), Gaps = 4/53 (7%)
Query: 117 LLKELEAMGFPVARATRALHYSGXXXXXXXXXXXXXXXXDPDIDEMPMVPVSG 169
LL+ L AMGFPV A +AL +G DP +D+ P+SG
Sbjct: 12 LLEPLLAMGFPVHTALKALAATGRKTAEEALAWLHDHCNDPSLDD----PISG 60
>pdb|1REQ|A Chain A, Methylmalonyl-Coa Mutase
pdb|1REQ|C Chain C, Methylmalonyl-Coa Mutase
pdb|2REQ|A Chain A, Methylmalonyl-Coa Mutase, Non-Productive Coa Complex, In
Open Conformation Representing Substrate-Free State
pdb|2REQ|C Chain C, Methylmalonyl-Coa Mutase, Non-Productive Coa Complex, In
Open Conformation Representing Substrate-Free State
pdb|3REQ|A Chain A, Methylmalonyl-Coa Mutase, Substrate-Free State (Poor
Quality Structure)
pdb|6REQ|A Chain A, Methylmalonyl-Coa Mutase, 3-Carboxypropyl-Coa Inhibitor
Complex
pdb|6REQ|C Chain C, Methylmalonyl-Coa Mutase, 3-Carboxypropyl-Coa Inhibitor
Complex
pdb|7REQ|A Chain A, Methylmalonyl-Coa Mutase, 2-Carboxypropyl-Coa Inhibitor
Complex
pdb|7REQ|C Chain C, Methylmalonyl-Coa Mutase, 2-Carboxypropyl-Coa Inhibitor
Complex
pdb|4REQ|A Chain A, Methylmalonyl-Coa Mutase Substrate Complex
pdb|4REQ|C Chain C, Methylmalonyl-Coa Mutase Substrate Complex
Length = 727
Score = 28.9 bits (63), Expect = 4.5, Method: Compositional matrix adjust.
Identities = 23/78 (29%), Positives = 31/78 (39%), Gaps = 8/78 (10%)
Query: 33 FSESTEAVLNLVCATCGKPCRSKTETDLHRKRTGHTDFVDKTSEAAKPISLEVPK----- 87
F + ++ G + DL RK GH V+K AK I +PK
Sbjct: 388 FLQQESGTTRVIDPWSGSAYVEELTWDLARKAWGHIQEVEKVGGMAKAIEKGIPKMRIEE 447
Query: 88 ATADSEEAIDVDMSGSQP 105
A A ++ ID SG QP
Sbjct: 448 AAARTQARID---SGRQP 462
>pdb|1E1C|A Chain A, Methylmalonyl-Coa Mutase H244a Mutant
pdb|1E1C|C Chain C, Methylmalonyl-Coa Mutase H244a Mutant
Length = 727
Score = 28.5 bits (62), Expect = 4.7, Method: Compositional matrix adjust.
Identities = 21/52 (40%), Positives = 25/52 (48%), Gaps = 8/52 (15%)
Query: 59 DLHRKRTGHTDFVDKTSEAAKPISLEVPK-----ATADSEEAIDVDMSGSQP 105
DL RK GH V+K AK I +PK A A ++ ID SG QP
Sbjct: 414 DLARKAWGHIQEVEKVGGMAKAIEKGIPKMRIEEAAARTQARID---SGRQP 462
>pdb|5REQ|A Chain A, Methylmalonyl-Coa Mutase, Y89f Mutant, Substrate Complex
pdb|5REQ|C Chain C, Methylmalonyl-Coa Mutase, Y89f Mutant, Substrate Complex
Length = 727
Score = 28.5 bits (62), Expect = 4.8, Method: Compositional matrix adjust.
Identities = 23/78 (29%), Positives = 31/78 (39%), Gaps = 8/78 (10%)
Query: 33 FSESTEAVLNLVCATCGKPCRSKTETDLHRKRTGHTDFVDKTSEAAKPISLEVPK----- 87
F + ++ G + DL RK GH V+K AK I +PK
Sbjct: 388 FLQQESGTTRVIDPWSGSAYVEELTWDLARKAWGHIQEVEKVGGMAKAIEKGIPKMRIEE 447
Query: 88 ATADSEEAIDVDMSGSQP 105
A A ++ ID SG QP
Sbjct: 448 AAARTQARID---SGRQP 462
>pdb|3H0G|A Chain A, Rna Polymerase Ii From Schizosaccharomyces Pombe
pdb|3H0G|M Chain M, Rna Polymerase Ii From Schizosaccharomyces Pombe
Length = 1752
Score = 28.5 bits (62), Expect = 5.0, Method: Compositional matrix adjust.
Identities = 15/48 (31%), Positives = 18/48 (37%), Gaps = 3/48 (6%)
Query: 6 LKCGDCGALLRSVQEAQEHAEL---TSHSNFSESTEAVLNLVCATCGK 50
KC CG + H EL H F + +L VC CGK
Sbjct: 67 FKCQTCGETMADCPGHFGHIELAKPVFHIGFLSKIKKILECVCWNCGK 114
>pdb|2DAG|A Chain A, Solution Structure Of The First Uba Domain In The Human
Ubiquitin Specific Protease 5 (Isopeptidase 5)
Length = 74
Score = 28.5 bits (62), Expect = 6.0, Method: Composition-based stats.
Identities = 12/46 (26%), Positives = 22/46 (47%)
Query: 113 VDKELLKELEAMGFPVARATRALHYSGXXXXXXXXXXXXXXXXDPD 158
+D+ ++ +L MGFP+ +A++Y+G DPD
Sbjct: 8 LDESVIIQLVEMGFPMDACRKAVYYTGNSGAEAAMNWVMSHMDDPD 53
>pdb|3E9S|A Chain A, A New Class Of Papain-Like ProteaseDEUBIQUITINASE
Inhibitors Blocks Sars Virus Replication
Length = 318
Score = 28.1 bits (61), Expect = 6.2, Method: Compositional matrix adjust.
Identities = 17/42 (40%), Positives = 23/42 (54%), Gaps = 3/42 (7%)
Query: 15 LRSVQEAQEHAELTSHSNFSESTEAVLNLVCATCGKPCRSKT 56
L V+E H L H+N ES + VLN+VC CG+ + T
Sbjct: 165 LGDVRETMTH--LLQHANL-ESAKRVLNVVCKHCGQKTTTLT 203
>pdb|3MJ5|A Chain A, Severe Acute Respiratory Syndrome-Coronavirus Papain-Like
Protease Inhibitors: Design, Synthesis, Protein-Ligand
X-Ray Structure And Biological Evaluation
pdb|3MJ5|B Chain B, Severe Acute Respiratory Syndrome-Coronavirus Papain-Like
Protease Inhibitors: Design, Synthesis, Protein-Ligand
X-Ray Structure And Biological Evaluation
Length = 316
Score = 28.1 bits (61), Expect = 7.0, Method: Compositional matrix adjust.
Identities = 17/42 (40%), Positives = 23/42 (54%), Gaps = 3/42 (7%)
Query: 15 LRSVQEAQEHAELTSHSNFSESTEAVLNLVCATCGKPCRSKT 56
L V+E H L H+N ES + VLN+VC CG+ + T
Sbjct: 163 LGDVRETMTH--LLQHANL-ESAKRVLNVVCKHCGQKTTTLT 201
>pdb|2FE8|A Chain A, Sars Coronavirus Papain-Like Protease: Structure Of A
Viral Deubiquitinating Enzyme
pdb|2FE8|B Chain B, Sars Coronavirus Papain-Like Protease: Structure Of A
Viral Deubiquitinating Enzyme
pdb|2FE8|C Chain C, Sars Coronavirus Papain-Like Protease: Structure Of A
Viral Deubiquitinating Enzyme
Length = 315
Score = 28.1 bits (61), Expect = 7.1, Method: Compositional matrix adjust.
Identities = 17/42 (40%), Positives = 23/42 (54%), Gaps = 3/42 (7%)
Query: 15 LRSVQEAQEHAELTSHSNFSESTEAVLNLVCATCGKPCRSKT 56
L V+E H L H+N ES + VLN+VC CG+ + T
Sbjct: 163 LGDVRETMTH--LLQHANL-ESAKRVLNVVCKHCGQKTTTLT 201
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
0.309 0.126 0.351
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 6,745,776
Number of Sequences: 62578
Number of extensions: 216635
Number of successful extensions: 531
Number of sequences better than 100.0: 17
Number of HSP's better than 100.0 without gapping: 5
Number of HSP's successfully gapped in prelim test: 12
Number of HSP's that attempted gapping in prelim test: 523
Number of HSP's gapped (non-prelim): 21
length of query: 324
length of database: 14,973,337
effective HSP length: 99
effective length of query: 225
effective length of database: 8,778,115
effective search space: 1975075875
effective search space used: 1975075875
T: 11
A: 40
X1: 16 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.7 bits)
S2: 51 (24.3 bits)