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= 027011
(229 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 = 39.3 bits (90), 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 = 30.4 bits (67), Expect = 0.96, 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 = 29.6 bits (65), Expect = 1.5, 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 = 29.6 bits (65), Expect = 1.5, 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|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 = 29.6 bits (65), Expect = 1.5, 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|3E9S|A Chain A, A New Class Of Papain-Like ProteaseDEUBIQUITINASE
Inhibitors Blocks Sars Virus Replication
Length = 318
Score = 29.3 bits (64), Expect = 2.0, 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: 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 = 28.9 bits (63), Expect = 2.2, 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 = 28.9 bits (63), Expect = 2.2, 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|2DAG|A Chain A, Solution Structure Of The First Uba Domain In The Human
Ubiquitin Specific Protease 5 (Isopeptidase 5)
Length = 74
Score = 28.1 bits (61), Expect = 3.7, Method: Compositional matrix adjust.
Identities = 12/47 (25%), Positives = 22/47 (46%)
Query: 113 VDKELLKELEAMGFPVARATRALHYSGXXXXXXXXXXXXXXXXDPDI 159
+D+ ++ +L MGFP+ +A++Y+G DPD
Sbjct: 8 LDESVIIQLVEMGFPMDACRKAVYYTGNSGAEAAMNWVMSHMDDPDF 54
>pdb|3AI7|A Chain A, Crystal Structure Of Bifidobacterium Longum
Phosphoketolase
pdb|3AI7|B Chain B, Crystal Structure Of Bifidobacterium Longum
Phosphoketolase
pdb|3AI7|C Chain C, Crystal Structure Of Bifidobacterium Longum
Phosphoketolase
pdb|3AI7|D Chain D, Crystal Structure Of Bifidobacterium Longum
Phosphoketolase
pdb|3AI7|E Chain E, Crystal Structure Of Bifidobacterium Longum
Phosphoketolase
pdb|3AI7|F Chain F, Crystal Structure Of Bifidobacterium Longum
Phosphoketolase
pdb|3AI7|G Chain G, Crystal Structure Of Bifidobacterium Longum
Phosphoketolase
pdb|3AI7|H Chain H, Crystal Structure Of Bifidobacterium Longum
Phosphoketolase
Length = 831
Score = 27.3 bits (59), Expect = 6.7, Method: Compositional matrix adjust.
Identities = 16/51 (31%), Positives = 22/51 (43%)
Query: 82 SLEVPKATADSEEAIDVDMSGSQPEEMVEPEVDKELLKELEAMGFPVARAT 132
SL VP D E +G Q ++V P D +L L G+ +A T
Sbjct: 173 SLFVPAIVGDGEAETGPLATGWQSNKLVNPRTDGIVLPILHLNGYKIANPT 223
>pdb|2DAI|A Chain A, Solution Structure Of The First Uba Domain In The Human
Ubiquitin Associated Domain Containing 1 (Ubadc1)
Length = 83
Score = 27.3 bits (59), Expect = 7.0, Method: Compositional matrix adjust.
Identities = 11/21 (52%), Positives = 15/21 (71%)
Query: 118 LKELEAMGFPVARATRALHYS 138
L++L MGFP RAT+AL +
Sbjct: 33 LRQLTEMGFPENRATKALQLN 53
>pdb|2BEI|A Chain A, X-Ray Structure Of Thialysine N-Acetyltransferase
(Ssat2) From Homo Sapiens
pdb|2BEI|B Chain B, X-Ray Structure Of Thialysine N-Acetyltransferase
(Ssat2) From Homo Sapiens
pdb|2Q4V|A Chain A, Ensemble Refinement Of The Protein Crystal Structure Of
Thialysine N- Acetyltransferase (Ssat2) From Homo
Sapiens
pdb|2Q4V|B Chain B, Ensemble Refinement Of The Protein Crystal Structure Of
Thialysine N- Acetyltransferase (Ssat2) From Homo
Sapiens
Length = 170
Score = 27.3 bits (59), Expect = 7.4, Method: Compositional matrix adjust.
Identities = 12/29 (41%), Positives = 17/29 (58%)
Query: 7 KCGDCGALLRSVQEAQEHAELTSHSNFSE 35
K GDCG +LR ++E E +L+ SE
Sbjct: 10 KEGDCGDILRLIRELAEFEKLSDQVKISE 38
>pdb|1O8N|A Chain A, The Active Site Of The Molybdenum Cofactor Biosynthetic
Protein Domain Cnx1g
pdb|1O8N|B Chain B, The Active Site Of The Molybdenum Cofactor Biosynthetic
Protein Domain Cnx1g
pdb|1O8N|C Chain C, The Active Site Of The Molybdenum Cofactor Biosynthetic
Protein Domain Cnx1g
Length = 167
Score = 27.3 bits (59), Expect = 7.6, Method: Compositional matrix adjust.
Identities = 16/55 (29%), Positives = 25/55 (45%)
Query: 158 DIDEMPMVPVSGGGGASKSSLTPEEIKLKAQELRYGIFYAVYFFSDGYCNCYMLS 212
D+DEM ++ GG G + +TPE K + G+ + + S MLS
Sbjct: 68 DVDEMDLILTLGGAGFTPRDVTPEATKKVIERETPGLLFVMMQESLKITPFAMLS 122
>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 = 26.9 bits (58), Expect = 8.5, 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
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
0.315 0.131 0.382
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 6,102,112
Number of Sequences: 62578
Number of extensions: 221355
Number of successful extensions: 697
Number of sequences better than 100.0: 23
Number of HSP's better than 100.0 without gapping: 11
Number of HSP's successfully gapped in prelim test: 12
Number of HSP's that attempted gapping in prelim test: 686
Number of HSP's gapped (non-prelim): 24
length of query: 229
length of database: 14,973,337
effective HSP length: 95
effective length of query: 134
effective length of database: 9,028,427
effective search space: 1209809218
effective search space used: 1209809218
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 50 (23.9 bits)