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= 015122
(413 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 = 53.1 bits (126), Expect = 2e-07, Method: Compositional matrix adjust.
Identities = 27/64 (42%), Positives = 39/64 (60%), Gaps = 2/64 (3%)
Query: 324 AFQTLLTYIGNVAKNPNEEKFRKIRLSNQTFQDRVGALKGGLEFLELCGFEKIEGGEFLF 383
A + LLTY N+ +NPN+EK+R IR+ N F R+ ++G +E L GFE EG L
Sbjct: 21 ASKLLLTYADNILRNPNDEKYRSIRIGNTAFSTRLLPVRGAVECLFEMGFE--EGETHLI 78
Query: 384 LPRE 387
P++
Sbjct: 79 FPKK 82
>pdb|2HPL|A Chain A, Crystal Structure Of The Mouse P97PNGASE COMPLEX
Length = 100
Score = 51.6 bits (122), Expect = 7e-07, Method: Compositional matrix adjust.
Identities = 26/64 (40%), Positives = 39/64 (60%), Gaps = 2/64 (3%)
Query: 324 AFQTLLTYIGNVAKNPNEEKFRKIRLSNQTFQDRVGALKGGLEFLELCGFEKIEGGEFLF 383
A + LLTY N+ +NP++EK+R IR+ N F R+ ++G +E L GFE EG L
Sbjct: 20 ASKLLLTYADNILRNPSDEKYRSIRIGNTAFSTRLLPVRGAVECLFEMGFE--EGETHLI 77
Query: 384 LPRE 387
P++
Sbjct: 78 FPKK 81
>pdb|2HPJ|A Chain A, Crystal Structure Of The Pub Domain Of Mouse Pngase
Length = 99
Score = 51.6 bits (122), Expect = 8e-07, Method: Compositional matrix adjust.
Identities = 26/64 (40%), Positives = 39/64 (60%), Gaps = 2/64 (3%)
Query: 324 AFQTLLTYIGNVAKNPNEEKFRKIRLSNQTFQDRVGALKGGLEFLELCGFEKIEGGEFLF 383
A + LLTY N+ +NP++EK+R IR+ N F R+ ++G +E L GFE EG L
Sbjct: 20 ASKLLLTYADNILRNPSDEKYRSIRIGNTAFSTRLLPVRGAVECLFEMGFE--EGETHLI 77
Query: 384 LPRE 387
P++
Sbjct: 78 FPKK 81
>pdb|2D5U|A Chain A, Solution Structure Of The N-Terminal Portion Of The Pub
Domain Of Mouse Peptide:n-Glycanase
Length = 124
Score = 50.8 bits (120), Expect = 1e-06, Method: Compositional matrix adjust.
Identities = 26/64 (40%), Positives = 39/64 (60%), Gaps = 2/64 (3%)
Query: 324 AFQTLLTYIGNVAKNPNEEKFRKIRLSNQTFQDRVGALKGGLEFLELCGFEKIEGGEFLF 383
A + LLTY N+ +NP++EK+R IR+ N F R+ ++G +E L GFE EG L
Sbjct: 36 ASKLLLTYADNILRNPSDEKYRSIRIGNTAFSTRLLPVRGAVECLFEMGFE--EGETHLI 93
Query: 384 LPRE 387
P++
Sbjct: 94 FPKK 97
>pdb|2CM0|A Chain A, The Pub Domain Functions As A P97 Binding Module In Human
Peptide N-Glycanase
Length = 99
Score = 45.8 bits (107), Expect = 4e-05, Method: Compositional matrix adjust.
Identities = 25/64 (39%), Positives = 36/64 (56%), Gaps = 2/64 (3%)
Query: 324 AFQTLLTYIGNVAKNPNEEKFRKIRLSNQTFQDRVGALKGGLEFLELCGFEKIEGGEFLF 383
A + LLTY + +NPN+E R IR+ N F R+ ++G +E L GFE EG L
Sbjct: 21 ASKLLLTYADAILRNPNDEAARSIRIGNTAFSTRLLPVRGAVECLFEMGFE--EGETHLI 78
Query: 384 LPRE 387
P++
Sbjct: 79 FPKK 82
>pdb|3IHP|A Chain A, Covalent Ubiquitin-Usp5 Complex
pdb|3IHP|B Chain B, Covalent Ubiquitin-Usp5 Complex
Length = 854
Score = 40.4 bits (93), 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|2CRN|A Chain A, Solution Structure Of The Uba Domain Of Human Ubash3a
Protein
Length = 64
Score = 30.8 bits (68), Expect = 1.5, 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|2L3A|A Chain A, Solution Nmr Structure Of Homodimer Protein Sp_0782 (7-79)
From Streptococcus Pneumoniae Northeast Structural
Genomics Consortium Target Spr104 .
pdb|2L3A|B Chain B, Solution Nmr Structure Of Homodimer Protein Sp_0782 (7-79)
From Streptococcus Pneumoniae Northeast Structural
Genomics Consortium Target Spr104
Length = 82
Score = 29.3 bits (64), Expect = 4.0, Method: Compositional matrix adjust.
Identities = 23/67 (34%), Positives = 33/67 (49%), Gaps = 2/67 (2%)
Query: 302 QMRECLRSLKQNHKDDDAKVKR-AFQTLLTYIGNVAKNPNEEKFRK-IRLSNQTFQDRVG 359
++ E L +L +N K ++ R +F A +P+ K K I LSN+ FQ V
Sbjct: 10 EIEEHLLTLSENEKGWTKEINRVSFNGAPAKFDIRAWSPDHTKMGKGITLSNEEFQTMVD 69
Query: 360 ALKGGLE 366
A KG LE
Sbjct: 70 AFKGNLE 76
>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 = 29.3 bits (64), Expect = 4.6, 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|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 = 5.8, 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|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 = 5.9, 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|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 = 6.0, 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|3OBH|A Chain A, X-Ray Crystal Structure Of Protein Sp_0782 (7-79) From
Streptococcus Pneumoniae. Northeast Structural Genomics
Consortium Target Spr104
pdb|3OBH|B Chain B, X-Ray Crystal Structure Of Protein Sp_0782 (7-79) From
Streptococcus Pneumoniae. Northeast Structural Genomics
Consortium Target Spr104
Length = 82
Score = 28.9 bits (63), Expect = 6.0, Method: Compositional matrix adjust.
Identities = 23/67 (34%), Positives = 33/67 (49%), Gaps = 2/67 (2%)
Query: 302 QMRECLRSLKQNHKDDDAKVKR-AFQTLLTYIGNVAKNPNEEKFRK-IRLSNQTFQDRVG 359
++ E L +L +N K ++ R +F A +P+ K K I LSN+ FQ V
Sbjct: 10 EIEEHLLTLSENEKGWTKEINRVSFNGAPAKFDIRAWSPDHTKXGKGITLSNEEFQTXVD 69
Query: 360 ALKGGLE 366
A KG LE
Sbjct: 70 AFKGNLE 76
>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 = 7.3, 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|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 = 8.0, 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|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 = 28.5 bits (62), Expect = 8.0, 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|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 = 28.5 bits (62), Expect = 8.1, 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
0.312 0.130 0.363
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 9,344,121
Number of Sequences: 62578
Number of extensions: 328776
Number of successful extensions: 730
Number of sequences better than 100.0: 23
Number of HSP's better than 100.0 without gapping: 7
Number of HSP's successfully gapped in prelim test: 16
Number of HSP's that attempted gapping in prelim test: 720
Number of HSP's gapped (non-prelim): 27
length of query: 413
length of database: 14,973,337
effective HSP length: 101
effective length of query: 312
effective length of database: 8,652,959
effective search space: 2699723208
effective search space used: 2699723208
T: 11
A: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.9 bits)
S2: 53 (25.0 bits)