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= 017706
(367 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|2CCQ|A Chain A, The Pub Domain Functions As A P97 Binding Module In Human
Peptide N-Glycanase
Length = 99
Score = 40.0 bits (92), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 16/31 (51%), Positives = 22/31 (70%)
Query: 324 AFQTLLTYIGNVAKNPNEEKFRKIRLSNQTF 354
A + LLTY N+ +NPN+EK+R IR+ N F
Sbjct: 21 ASKLLLTYADNILRNPNDEKYRSIRIGNTAF 51
>pdb|3IHP|A Chain A, Covalent Ubiquitin-Usp5 Complex
pdb|3IHP|B Chain B, Covalent Ubiquitin-Usp5 Complex
Length = 854
Score = 39.7 bits (91), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 23/88 (26%), Positives = 41/88 (46%)
Query: 93 EEAIDVDMSGSQPEEMVEPEVDKELLKELEAMGFPVARATRALHYSGXXXXXXXXXXXXX 152
EE D+ P+E P +D+ ++ +L MGFP+ +A++Y+G
Sbjct: 631 EELPDIAPPLVTPDEPKAPMLDESVIIQLVEMGFPMDACRKAVYYTGNSGAEAAMNWVMS 690
Query: 153 XXXDPDIDEMPMVPVSGGGGASKSSLTP 180
DPD ++P S G G++ ++ P
Sbjct: 691 HMDDPDFANPLILPGSSGPGSTSAAADP 718
>pdb|2D5U|A Chain A, Solution Structure Of The N-Terminal Portion Of The Pub
Domain Of Mouse Peptide:n-Glycanase
Length = 124
Score = 38.1 bits (87), Expect = 0.007, Method: Compositional matrix adjust.
Identities = 15/31 (48%), Positives = 22/31 (70%)
Query: 324 AFQTLLTYIGNVAKNPNEEKFRKIRLSNQTF 354
A + LLTY N+ +NP++EK+R IR+ N F
Sbjct: 36 ASKLLLTYADNILRNPSDEKYRSIRIGNTAF 66
>pdb|2HPL|A Chain A, Crystal Structure Of The Mouse P97PNGASE COMPLEX
Length = 100
Score = 38.1 bits (87), Expect = 0.007, Method: Compositional matrix adjust.
Identities = 15/31 (48%), Positives = 22/31 (70%)
Query: 324 AFQTLLTYIGNVAKNPNEEKFRKIRLSNQTF 354
A + LLTY N+ +NP++EK+R IR+ N F
Sbjct: 20 ASKLLLTYADNILRNPSDEKYRSIRIGNTAF 50
>pdb|2HPJ|A Chain A, Crystal Structure Of The Pub Domain Of Mouse Pngase
Length = 99
Score = 38.1 bits (87), Expect = 0.008, Method: Compositional matrix adjust.
Identities = 15/31 (48%), Positives = 22/31 (70%)
Query: 324 AFQTLLTYIGNVAKNPNEEKFRKIRLSNQTF 354
A + LLTY N+ +NP++EK+R IR+ N F
Sbjct: 20 ASKLLLTYADNILRNPSDEKYRSIRIGNTAF 50
>pdb|2CM0|A Chain A, The Pub Domain Functions As A P97 Binding Module In Human
Peptide N-Glycanase
Length = 99
Score = 32.7 bits (73), Expect = 0.30, Method: Compositional matrix adjust.
Identities = 14/31 (45%), Positives = 19/31 (61%)
Query: 324 AFQTLLTYIGNVAKNPNEEKFRKIRLSNQTF 354
A + LLTY + +NPN+E R IR+ N F
Sbjct: 21 ASKLLLTYADAILRNPNDEAARSIRIGNTAF 51
>pdb|2CRN|A Chain A, Solution Structure Of The Uba Domain Of Human Ubash3a
Protein
Length = 64
Score = 30.8 bits (68), 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|1E1C|A Chain A, Methylmalonyl-Coa Mutase H244a Mutant
pdb|1E1C|C Chain C, Methylmalonyl-Coa Mutase H244a Mutant
Length = 727
Score = 28.9 bits (63), Expect = 4.8, 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|3H0G|A Chain A, Rna Polymerase Ii From Schizosaccharomyces Pombe
pdb|3H0G|M Chain M, Rna Polymerase Ii From Schizosaccharomyces Pombe
Length = 1752
Score = 28.9 bits (63), Expect = 4.9, Method: Compositional matrix adjust.
Identities = 15/48 (31%), Positives = 18/48 (37%), Gaps = 3/48 (6%)
Query: 6 LKCGDCGALLRSVQEAQEHAELTS---HSNFSESTEAVLNLVCATCGK 50
KC CG + H EL H F + +L VC CGK
Sbjct: 67 FKCQTCGETMADCPGHFGHIELAKPVFHIGFLSKIKKILECVCWNCGK 114
>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 = 4.9, 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 = 28.9 bits (63), Expect = 5.0, 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|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 = 5.9, 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 = 28.5 bits (62), Expect = 6.8, 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 = 7.2, 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: 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 = 7.4, 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
0.312 0.128 0.361
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 7,997,801
Number of Sequences: 62578
Number of extensions: 265297
Number of successful extensions: 646
Number of sequences better than 100.0: 19
Number of HSP's better than 100.0 without gapping: 7
Number of HSP's successfully gapped in prelim test: 12
Number of HSP's that attempted gapping in prelim test: 636
Number of HSP's gapped (non-prelim): 23
length of query: 367
length of database: 14,973,337
effective HSP length: 100
effective length of query: 267
effective length of database: 8,715,537
effective search space: 2327048379
effective search space used: 2327048379
T: 11
A: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.8 bits)
S2: 52 (24.6 bits)