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= 018267
(358 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|3TMP|A Chain A, The Catalytic Domain Of Human Deubiquitinase Duba In
Complex With Ubiquitin Aldehyde
pdb|3TMP|C Chain C, The Catalytic Domain Of Human Deubiquitinase Duba In
Complex With Ubiquitin Aldehyde
pdb|3TMP|E Chain E, The Catalytic Domain Of Human Deubiquitinase Duba In
Complex With Ubiquitin Aldehyde
pdb|3TMP|G Chain G, The Catalytic Domain Of Human Deubiquitinase Duba In
Complex With Ubiquitin Aldehyde
Length = 184
Score = 55.8 bits (133), Expect = 4e-08, Method: Compositional matrix adjust.
Identities = 32/126 (25%), Positives = 62/126 (49%), Gaps = 4/126 (3%)
Query: 217 LVENKVQGDGNCQFRSLSDQLYRSPEHHMFVRQQVVNQLKAHPEIYEGYVPMAYSDYLKK 276
+ +++ DG C FR+++DQ+Y + H VR+ ++ L + + + YV ++ Y+ +
Sbjct: 46 FIIKQMKEDGACLFRAVADQVYGDQDMHEVVRKHCMDYLMKNADYFSNYVTEDFTTYINR 105
Query: 277 MNKSGEWGDHVTLQAAADSYGVKVFVLTSFKDTCYIEILPHV----PKSKRVIFLSFWAE 332
K+ G+H+ +QA A+ Y V V T +E + I +S+
Sbjct: 106 KRKNNCHGNHIEMQAMAEMYNRPVEVYQYSTGTSAVEPINTFHGIHQNEDEPIRVSYHRN 165
Query: 333 VHYNSI 338
+HYNS+
Sbjct: 166 IHYNSV 171
>pdb|3TMO|A Chain A, The Catalytic Domain Of Human Deubiquitinase Duba
Length = 184
Score = 54.7 bits (130), Expect = 8e-08, Method: Compositional matrix adjust.
Identities = 32/118 (27%), Positives = 56/118 (47%), Gaps = 4/118 (3%)
Query: 225 DGNCQFRSLSDQLYRSPEHHMFVRQQVVNQLKAHPEIYEGYVPMAYSDYLKKMNKSGEWG 284
DG C FR+++DQ+Y + H VR+ + L + + + YV ++ Y+ + K+ G
Sbjct: 54 DGACLFRAVADQVYGDQDXHEVVRKHCXDYLXKNADYFSNYVTEDFTTYINRKRKNNCHG 113
Query: 285 DHVTLQAAADSYGVKVFVLTSFKDTCYIEILPHV----PKSKRVIFLSFWAEVHYNSI 338
+H+ QA A+ Y V V T +E + I +S+ +HYNS+
Sbjct: 114 NHIEXQAXAEXYNRPVEVYQYSTGTSAVEPINTFHGIHQNEDEPIRVSYHRNIHYNSV 171
>pdb|3PFY|A Chain A, The Catalytic Domain Of Human Otud5
Length = 185
Score = 53.5 bits (127), Expect = 2e-07, Method: Compositional matrix adjust.
Identities = 32/116 (27%), Positives = 60/116 (51%), Gaps = 5/116 (4%)
Query: 225 DGNCQFRSLSDQLYRSPEHHMFVRQQVVNQLKAHPEIYEGYVPMAYSDYLKKMNKSGEWG 284
DG C FR+++DQ+Y + H VR+ + L + + + YV ++ Y+ + K+ G
Sbjct: 67 DGACLFRAVADQVYGDQDXHEVVRKHCXDYLXKNADYFSNYVTEDFTTYINRKRKNNCHG 126
Query: 285 DHVTLQAAADSYG--VKVFVLTSFKDTCYIEILPHVPKSKRVIFLSFWAEVHYNSI 338
+H+ QA A+ Y V+V+ ++ + I + + RV S+ +HYNS+
Sbjct: 127 NHIEXQAXAEXYNRPVEVYQYSTEPINTFHGIHQNEDEPIRV---SYHRNIHYNSV 179
>pdb|3ZNH|A Chain A, Crimean Congo Hemorrhagic Fever Virus Otu Domain In
Complex With Ubiquitin-propargyl
Length = 183
Score = 35.8 bits (81), Expect = 0.040, Method: Compositional matrix adjust.
Identities = 25/99 (25%), Positives = 42/99 (42%), Gaps = 5/99 (5%)
Query: 211 RLQLYDLVENKVQ-GDGNCQFRSLSDQLYRSPEHHMFVRQQVVNQLKAHPEIYE----GY 265
R + D E Q GDGNC + S+++ + H + + + + A E
Sbjct: 22 RFNISDYFEIVRQPGDGNCFYHSIAELTMPNKTDHSYHYIKRLTESAARKYYQEEPEARL 81
Query: 266 VPMAYSDYLKKMNKSGEWGDHVTLQAAADSYGVKVFVLT 304
V ++ DYLK+M EWG + A G+ + + T
Sbjct: 82 VGLSLEDYLKRMLSDNEWGSTLEASMLAKEMGITIIIWT 120
>pdb|3PHW|A Chain A, Otu Domain Of Crimean Congo Hemorrhagic Fever Virus In
Complex With Ubiquitin
pdb|3PHW|C Chain C, Otu Domain Of Crimean Congo Hemorrhagic Fever Virus In
Complex With Ubiquitin
pdb|3PHW|E Chain E, Otu Domain Of Crimean Congo Hemorrhagic Fever Virus In
Complex With Ubiquitin
pdb|3PHW|G Chain G, Otu Domain Of Crimean Congo Hemorrhagic Fever Virus In
Complex With Ubiquitin
pdb|3PHX|A Chain A, Otu Domain Of Crimean Congo Hemorrhagic Fever Virus In
Complex With Isg15
Length = 185
Score = 35.8 bits (81), Expect = 0.043, Method: Compositional matrix adjust.
Identities = 25/99 (25%), Positives = 42/99 (42%), Gaps = 5/99 (5%)
Query: 211 RLQLYDLVENKVQ-GDGNCQFRSLSDQLYRSPEHHMFVRQQVVNQLKAHPEIYE----GY 265
R + D E Q GDGNC + S+++ + H + + + + A E
Sbjct: 24 RFNISDYFEIVRQPGDGNCFYHSIAELTMPNKTDHSYHYIKRLTESAARKYYQEEPEARL 83
Query: 266 VPMAYSDYLKKMNKSGEWGDHVTLQAAADSYGVKVFVLT 304
V ++ DYLK+M EWG + A G+ + + T
Sbjct: 84 VGLSLEDYLKRMLSDNEWGSTLEASMLAKEMGITIIIWT 122
>pdb|3PRP|A Chain A, Structural Analysis Of A Viral Otu Domain Protease From
The Crimean- Congo Hemorrhagic Fever Virus In Complex
With Human Ubiquitin
pdb|3PRP|C Chain C, Structural Analysis Of A Viral Otu Domain Protease From
The Crimean- Congo Hemorrhagic Fever Virus In Complex
With Human Ubiquitin
Length = 178
Score = 35.4 bits (80), Expect = 0.044, Method: Compositional matrix adjust.
Identities = 25/99 (25%), Positives = 42/99 (42%), Gaps = 5/99 (5%)
Query: 211 RLQLYDLVENKVQ-GDGNCQFRSLSDQLYRSPEHHMFVRQQVVNQLKAHPEIYE----GY 265
R + D E Q GDGNC + S+++ + H + + + + A E
Sbjct: 22 RFNISDYFEIVRQPGDGNCFYHSIAELTMPNKTDHSYHYIKRLTESAARKYYQEEPEARL 81
Query: 266 VPMAYSDYLKKMNKSGEWGDHVTLQAAADSYGVKVFVLT 304
V ++ DYLK+M EWG + A G+ + + T
Sbjct: 82 VGLSLEDYLKRMLSDNEWGSTLEASMLAKEMGITIIIWT 120
>pdb|3PSE|A Chain A, Structure Of A Viral Otu Domain Protease Bound To
Interferon- Stimulated Gene 15 (Isg15)
Length = 171
Score = 35.4 bits (80), Expect = 0.044, Method: Compositional matrix adjust.
Identities = 25/99 (25%), Positives = 42/99 (42%), Gaps = 5/99 (5%)
Query: 211 RLQLYDLVENKVQ-GDGNCQFRSLSDQLYRSPEHHMFVRQQVVNQLKAHPEIYE----GY 265
R + D E Q GDGNC + S+++ + H + + + + A E
Sbjct: 24 RFNISDYFEIVRQPGDGNCFYHSIAELTMPNKTDHSYHYIKRLTESAARKYYQEEPEARL 83
Query: 266 VPMAYSDYLKKMNKSGEWGDHVTLQAAADSYGVKVFVLT 304
V ++ DYLK+M EWG + A G+ + + T
Sbjct: 84 VGLSLEDYLKRMLSDNEWGSTLEASMLAKEMGITIIIWT 122
>pdb|3PT2|A Chain A, Structure Of A Viral Otu Domain Protease Bound To
Ubiquitin
Length = 187
Score = 33.1 bits (74), Expect = 0.24, Method: Compositional matrix adjust.
Identities = 24/99 (24%), Positives = 41/99 (41%), Gaps = 5/99 (5%)
Query: 211 RLQLYDLVENKVQ-GDGNCQFRSLSDQLYRSPEHHMFVRQQVVNQLKAHPEIYE----GY 265
R + D E Q GDGNC + S+++ + H + + + + A E
Sbjct: 25 RFNISDYFEIVRQPGDGNCFYHSIAELTXPNKTDHSYHYIKRLTESAARKYYQEEPEARL 84
Query: 266 VPMAYSDYLKKMNKSGEWGDHVTLQAAADSYGVKVFVLT 304
V ++ DYLK+ EWG + A G+ + + T
Sbjct: 85 VGLSLEDYLKRXLSDNEWGSTLEASXLAKEXGITIIIWT 123
>pdb|3PRM|A Chain A, Structural Analysis Of A Viral Otu Domain Protease From
The Crimean- Congo Hemorrhagic Fever Virus In Complex
With Human Ubiquitin
pdb|3PRM|C Chain C, Structural Analysis Of A Viral Otu Domain Protease From
The Crimean- Congo Hemorrhagic Fever Virus In Complex
With Human Ubiquitin
Length = 178
Score = 33.1 bits (74), Expect = 0.24, Method: Compositional matrix adjust.
Identities = 24/99 (24%), Positives = 41/99 (41%), Gaps = 5/99 (5%)
Query: 211 RLQLYDLVENKVQ-GDGNCQFRSLSDQLYRSPEHHMFVRQQVVNQLKAHPEIYE----GY 265
R + D E Q GDGNC + S+++ + H + + + + A E
Sbjct: 22 RFNISDYFEIVRQPGDGNCFYHSIAELTXPNKTDHSYHYIKRLTESAARKYYQEEPEARL 81
Query: 266 VPMAYSDYLKKMNKSGEWGDHVTLQAAADSYGVKVFVLT 304
V ++ DYLK+ EWG + A G+ + + T
Sbjct: 82 VGLSLEDYLKRXLSDNEWGSTLEASXLAKEXGITIIIWT 120
>pdb|3F2B|A Chain A, Dna Polymerase Polc From Geobacillus Kaustophilus Complex
With Dna, Dgtp, Mg And Zn
pdb|3F2C|A Chain A, Dna Polymerase Polc From Geobacillus Kaustophilus Complex
With Dna, Dgtp And Mn
pdb|3F2D|A Chain A, Dna Polymerase Polc From Geobacillus Kaustophilus Complex
With Dna, Dgtp, Mn And Zn
Length = 1041
Score = 32.3 bits (72), Expect = 0.44, Method: Compositional matrix adjust.
Identities = 22/72 (30%), Positives = 39/72 (54%), Gaps = 3/72 (4%)
Query: 250 QVVNQLKAHPEIYEGYVPMAYSDYLKKMNKSGEWGDHVTLQAAADSYGVKVFVLTSFKDT 309
+V+ L+A+ I + VP+AY++ +++ SG HVTL A ++ +F L S
Sbjct: 173 KVIYGLEAN--IVDDGVPIAYNETHRRLG-SGSGPFHVTLLAQNETGLKNLFKLVSLSHI 229
Query: 310 CYIEILPHVPKS 321
Y +P +P+S
Sbjct: 230 QYFHRVPRIPRS 241
>pdb|3PHU|A Chain A, Otu Domain Of Crimean Congo Hemorrhagic Fever Virus
pdb|3PHU|B Chain B, Otu Domain Of Crimean Congo Hemorrhagic Fever Virus
Length = 219
Score = 31.6 bits (70), Expect = 0.74, Method: Compositional matrix adjust.
Identities = 20/85 (23%), Positives = 36/85 (42%), Gaps = 4/85 (4%)
Query: 224 GDGNCQFRSLSDQLYRSPEHHMFVRQQVVNQLKAHPEIYE----GYVPMAYSDYLKKMNK 279
GDGN + S+++ + H + + + + A E V ++ DYLK+M
Sbjct: 38 GDGNXFYHSIAELTMPNKTDHSYHYIKRLTESAARKYYQEEPEARLVGLSLEDYLKRMLS 97
Query: 280 SGEWGDHVTLQAAADSYGVKVFVLT 304
EWG + A G+ + + T
Sbjct: 98 DNEWGSTLEASMLAKEMGITIIIWT 122
>pdb|4HXD|B Chain B, Diversity Of Ubiquitin And Isg15 Specificity Amongst
Nairoviruses Viral Ovarian Tumor Domain Proteases
pdb|4HXD|D Chain D, Diversity Of Ubiquitin And Isg15 Specificity Amongst
Nairoviruses Viral Ovarian Tumor Domain Proteases
Length = 174
Score = 29.6 bits (65), Expect = 2.6, Method: Compositional matrix adjust.
Identities = 19/67 (28%), Positives = 30/67 (44%), Gaps = 8/67 (11%)
Query: 224 GDGNCQFRSLSDQLYRSPEHHMFVRQQVVNQLKAHPEIYEGYVPMAYS------DYLKKM 277
GDGNC + S+++ + F ++V L+ E+Y P A +Y+K
Sbjct: 35 GDGNCFYHSIAELFFDVKTPSSF--RKVKEHLQLAAEVYYDTEPEAVGTGISKDEYIKVA 92
Query: 278 NKSGEWG 284
K EWG
Sbjct: 93 MKDNEWG 99
>pdb|2BIB|A Chain A, Crystal Structure Of The Complete Modular Teichioic Acid
Phosphorylcholine Esterase Pce (Cbpe) From Streptococcus
Pneumoniae
Length = 547
Score = 29.6 bits (65), Expect = 3.0, Method: Compositional matrix adjust.
Identities = 16/52 (30%), Positives = 25/52 (48%), Gaps = 12/52 (23%)
Query: 199 DEEISDHQRMLDRLQLYD------------LVENKVQGDGNCQFRSLSDQLY 238
D I++ +R+ D L YD +++N QGD + QF + QLY
Sbjct: 113 DSRITNSERLWDNLYGYDKVLQTATETGVSVIQNITQGDAHFQFGDMDIQLY 164
>pdb|1WRA|A Chain A, Crystal Structure Of Phosphorylcholine Esterase Domain Of
The Virulence Factor Choline Binding Protein E From
Streptococcus Pneumoniae
pdb|1WRA|B Chain B, Crystal Structure Of Phosphorylcholine Esterase Domain Of
The Virulence Factor Choline Binding Protein E From
Streptococcus Pneumoniae
Length = 308
Score = 28.9 bits (63), Expect = 5.2, Method: Compositional matrix adjust.
Identities = 16/52 (30%), Positives = 25/52 (48%), Gaps = 12/52 (23%)
Query: 199 DEEISDHQRMLDRLQLYD------------LVENKVQGDGNCQFRSLSDQLY 238
D I++ +R+ D L YD +++N QGD + QF + QLY
Sbjct: 112 DSRITNSERLWDNLYGYDKVLQTATETGVSVIQNITQGDAHFQFGDMDIQLY 163
>pdb|1Z59|A Chain A, Topoisomerase Vi-B, Adp-Bound Monomer Form
pdb|1Z5C|A Chain A, Topoisomerase Vi-B, Adp Pi Bound Dimer Form
pdb|1Z5C|B Chain B, Topoisomerase Vi-B, Adp Pi Bound Dimer Form
Length = 469
Score = 27.7 bits (60), Expect = 9.0, Method: Compositional matrix adjust.
Identities = 11/36 (30%), Positives = 20/36 (55%)
Query: 185 VPHIPKINGDIPSPDEEISDHQRMLDRLQLYDLVEN 220
V + P++ IP P +E+ H +DR ++ L+ N
Sbjct: 211 VTYYPRLTNKIPKPPQEVKPHPYGVDREEIKILINN 246
>pdb|2ZBK|B Chain B, Crystal Structure Of An Intact Type Ii Dna Topoisomerase:
Insights Into Dna Transfer Mechanisms
pdb|2ZBK|D Chain D, Crystal Structure Of An Intact Type Ii Dna Topoisomerase:
Insights Into Dna Transfer Mechanisms
pdb|2ZBK|F Chain F, Crystal Structure Of An Intact Type Ii Dna Topoisomerase:
Insights Into Dna Transfer Mechanisms
pdb|2ZBK|H Chain H, Crystal Structure Of An Intact Type Ii Dna Topoisomerase:
Insights Into Dna Transfer Mechanisms
Length = 530
Score = 27.7 bits (60), Expect = 9.0, Method: Compositional matrix adjust.
Identities = 11/36 (30%), Positives = 20/36 (55%)
Query: 185 VPHIPKINGDIPSPDEEISDHQRMLDRLQLYDLVEN 220
V + P++ IP P +E+ H +DR ++ L+ N
Sbjct: 212 VTYYPRLTNKIPKPPQEVKPHPYGVDREEIKILINN 247
>pdb|1MX0|A Chain A, Structure Of Topoisomerase Subunit
pdb|1MX0|B Chain B, Structure Of Topoisomerase Subunit
pdb|1MX0|C Chain C, Structure Of Topoisomerase Subunit
pdb|1MX0|D Chain D, Structure Of Topoisomerase Subunit
pdb|1MX0|E Chain E, Structure Of Topoisomerase Subunit
pdb|1MX0|F Chain F, Structure Of Topoisomerase Subunit
Length = 472
Score = 27.7 bits (60), Expect = 9.0, Method: Compositional matrix adjust.
Identities = 11/36 (30%), Positives = 20/36 (55%)
Query: 185 VPHIPKINGDIPSPDEEISDHQRMLDRLQLYDLVEN 220
V + P++ IP P +E+ H +DR ++ L+ N
Sbjct: 214 VTYYPRLTNKIPKPPQEVKPHPYGVDREEIKILINN 249
>pdb|1MU5|A Chain A, Structure Of Topoisomerase Subunit
Length = 471
Score = 27.7 bits (60), Expect = 9.0, Method: Compositional matrix adjust.
Identities = 11/36 (30%), Positives = 20/36 (55%)
Query: 185 VPHIPKINGDIPSPDEEISDHQRMLDRLQLYDLVEN 220
V + P++ IP P +E+ H +DR ++ L+ N
Sbjct: 213 VTYYPRLTNKIPKPPQEVKPHPYGVDREEIKILINN 248
>pdb|1Z5A|A Chain A, Topoisomerase Vi-B, Adp-Bound Dimer Form
pdb|1Z5A|B Chain B, Topoisomerase Vi-B, Adp-Bound Dimer Form
pdb|1Z5B|A Chain A, Topoisomerase Vi-B, Adp Alf4- Bound Dimer Form
pdb|1Z5B|B Chain B, Topoisomerase Vi-B, Adp Alf4- Bound Dimer Form
pdb|2HKJ|A Chain A, Topoisomerase Vi-B Bound To Radicicol
Length = 469
Score = 27.7 bits (60), Expect = 9.3, Method: Compositional matrix adjust.
Identities = 11/36 (30%), Positives = 20/36 (55%)
Query: 185 VPHIPKINGDIPSPDEEISDHQRMLDRLQLYDLVEN 220
V + P++ IP P +E+ H +DR ++ L+ N
Sbjct: 211 VTYYPRLTNKIPKPPQEVKPHPYGVDREEIKILINN 246
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
0.314 0.133 0.385
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 10,956,703
Number of Sequences: 62578
Number of extensions: 467702
Number of successful extensions: 936
Number of sequences better than 100.0: 30
Number of HSP's better than 100.0 without gapping: 14
Number of HSP's successfully gapped in prelim test: 16
Number of HSP's that attempted gapping in prelim test: 914
Number of HSP's gapped (non-prelim): 32
length of query: 358
length of database: 14,973,337
effective HSP length: 100
effective length of query: 258
effective length of database: 8,715,537
effective search space: 2248608546
effective search space used: 2248608546
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: 52 (24.6 bits)