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= psy16758
(186 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|2DOS|A Chain A, Structural Basis For The Recognition Of Lys48-Linked
Polyubiquitin Chain By The Josephin Domain Of Ataxin-3,
A Putative Deubiquitinating Enzyme
Length = 176
Score = 53.5 bits (127), Expect = 7e-08, Method: Compositional matrix adjust.
Identities = 55/187 (29%), Positives = 78/187 (41%), Gaps = 42/187 (22%)
Query: 7 AQEIIYHEKQMKELCALHALNNLFQNPKTFSKADLDEICINLSPQ--------------- 51
+ E I+HEKQ LCA H LNNL Q + FS +L I L +
Sbjct: 5 SMESIFHEKQEGSLCAQHCLNNLLQG-EYFSPVELSSIAHQLDEEERMRMAEGGVTSEDY 63
Query: 52 -TWL-NPHRSILGLGNYDINVIMTALQKKGFESNWFDRRKDPKC-IDQQKVEGYILNIPS 108
T+L P ++ G + I VI AL+ G E F+ + + ID +I N
Sbjct: 64 RTFLQQPSGNMDDSGFFSIQVISNALKVWGLELILFNSPEYQRLRIDPINERSFICNY-- 121
Query: 109 QFKIGKYVPTPIKRRHWLTVRNINGIYYNLDSKLDNPEHIGREEDLVEYLRDVLSDIDKE 168
+ HW TVR + ++NL+S L PE I YL L+ + +E
Sbjct: 122 -------------KEHWFTVRKLGKQWFNLNSLLTGPELISD-----TYLALFLAQLQQE 163
Query: 169 ---LFVV 172
+FVV
Sbjct: 164 GYSIFVV 170
>pdb|2AGA|A Chain A, De-Ubiquitinating Function Of Ataxin-3: Insights From The
Solution Structure Of The Josephin Domain
Length = 190
Score = 52.8 bits (125), Expect = 1e-07, Method: Compositional matrix adjust.
Identities = 55/187 (29%), Positives = 78/187 (41%), Gaps = 42/187 (22%)
Query: 7 AQEIIYHEKQMKELCALHALNNLFQNPKTFSKADLDEICINLSPQ--------------- 51
+ E I+HEKQ LCA H LNNL Q + FS +L I L +
Sbjct: 5 SMESIFHEKQEGSLCAQHCLNNLLQG-EYFSPVELSSIAHQLDEEERMRMAEGGVTSEDY 63
Query: 52 -TWL-NPHRSILGLGNYDINVIMTALQKKGFESNWFDRRKDPKC-IDQQKVEGYILNIPS 108
T+L P ++ G + I VI AL+ G E F+ + + ID +I N
Sbjct: 64 RTFLQQPSGNMDDSGFFSIQVISNALKVWGLELILFNSPEYQRLRIDPINERSFICNY-- 121
Query: 109 QFKIGKYVPTPIKRRHWLTVRNINGIYYNLDSKLDNPEHIGREEDLVEYLRDVLSDIDKE 168
+ HW TVR + ++NL+S L PE I YL L+ + +E
Sbjct: 122 -------------KEHWFTVRKLGKQWFNLNSLLTGPELISD-----TYLALFLAQLQQE 163
Query: 169 ---LFVV 172
+FVV
Sbjct: 164 GYSIFVV 170
>pdb|2JRI|A Chain A, Solution Structure Of The Josephin Domain Of Ataxin-3 In
Complex With Ubiquitin Molecule.
pdb|1YZB|A Chain A, Solution Structure Of The Josephin Domain Of Ataxin-3
Length = 182
Score = 52.8 bits (125), Expect = 1e-07, Method: Compositional matrix adjust.
Identities = 55/185 (29%), Positives = 77/185 (41%), Gaps = 42/185 (22%)
Query: 9 EIIYHEKQMKELCALHALNNLFQNPKTFSKADLDEICINLSPQ----------------T 52
E I+HEKQ LCA H LNNL Q + FS +L I L + T
Sbjct: 2 ESIFHEKQEGSLCAQHCLNNLLQG-EYFSPVELSSIAHQLDEEERMRMAEGGVTSEDYRT 60
Query: 53 WL-NPHRSILGLGNYDINVIMTALQKKGFESNWFDRRKDPKC-IDQQKVEGYILNIPSQF 110
+L P ++ G + I VI AL+ G E F+ + + ID +I N
Sbjct: 61 FLQQPSGNMDDSGFFSIQVISNALKVWGLELILFNSPEYQRLRIDPINERSFICNY---- 116
Query: 111 KIGKYVPTPIKRRHWLTVRNINGIYYNLDSKLDNPEHIGREEDLVEYLRDVLSDIDKE-- 168
+ HW TVR + ++NL+S L PE I YL L+ + +E
Sbjct: 117 -----------KEHWFTVRKLGKQWFNLNSLLTGPELISD-----TYLALFLAQLQQEGY 160
Query: 169 -LFVV 172
+FVV
Sbjct: 161 SIFVV 165
>pdb|3O65|A Chain A, Crystal Structure Of A Josephin-Ubiquitin Complex:
Evolutionary Restraints On Ataxin-3 Deubiquitinating
Activity
pdb|3O65|C Chain C, Crystal Structure Of A Josephin-Ubiquitin Complex:
Evolutionary Restraints On Ataxin-3 Deubiquitinating
Activity
pdb|3O65|E Chain E, Crystal Structure Of A Josephin-Ubiquitin Complex:
Evolutionary Restraints On Ataxin-3 Deubiquitinating
Activity
pdb|3O65|G Chain G, Crystal Structure Of A Josephin-Ubiquitin Complex:
Evolutionary Restraints On Ataxin-3 Deubiquitinating
Activity
Length = 191
Score = 47.8 bits (112), Expect = 4e-06, Method: Compositional matrix adjust.
Identities = 46/160 (28%), Positives = 65/160 (40%), Gaps = 34/160 (21%)
Query: 7 AQEIIYHEKQMKELCALHALNNLFQNPKTFSKADLDEICINL-------------SPQTW 53
+ I+HEKQ LCA H LNNL Q + FS +L I L + + +
Sbjct: 1 GXDFIFHEKQEGFLCAQHCLNNLLQG-EYFSPVELASIAHQLDEEERXRXAEGGVTSEEY 59
Query: 54 L----NPHRSILGLGNYDINVIMTALQKKGFESNWFDRRKDPKC-IDQQKVEGYILNIPS 108
L P + G + I VI AL+ G E F+ + K ID +I N
Sbjct: 60 LAFLQQPSENXDDTGFFSIQVISNALKFWGLEIIHFNNPEYQKLGIDPINERSFICNY-- 117
Query: 109 QFKIGKYVPTPIKRRHWLTVRNINGIYYNLDSKLDNPEHI 148
++HW T+R ++NL+S L PE I
Sbjct: 118 -------------KQHWFTIRKFGKHWFNLNSLLAGPELI 144
>pdb|2ETW|A Chain A, Principles Of Protein-Dna Recognition Revealed In The
Structural Analysis Of Ndt80-Mse Dna Complexes
pdb|2EUV|A Chain A, Principles Of Protein-Dna Recognition Revealed In The
Structural Analysis Of Ndt80-Mse Dna Complexes
pdb|2EUW|A Chain A, Structure Of A Ndt80-Dna Complex (Mse Mutant Ma4t)
pdb|2EUX|A Chain A, Structure Of A Ndt80-Dna Complex (Mse Variant Va4g)
pdb|2EUZ|A Chain A, Structure Of A Ndt80-Dna Complex (Mse Mutant Mc5t)
pdb|2EVF|A Chain A, Structure Of A Ndt80-Dna Complex (Mse Mutant Ma6t)
pdb|2EVG|A Chain A, Structure Of A Ndt80-Dna Complex (Mse Mutant Ma7t)
pdb|2EVH|A Chain A, Structure Of A Ndt80-Dna Complex (Mse Mutant Ma7g)
pdb|2EVI|A Chain A, Structure Of A Ndt80-Dna Complex (Mse Mutant Ma8t)
pdb|2EVJ|A Chain A, Structure Of An Ndt80-Dna Complex (Mse Mutant Ma9c)
Length = 345
Score = 28.9 bits (63), Expect = 1.9, Method: Compositional matrix adjust.
Identities = 12/23 (52%), Positives = 16/23 (69%)
Query: 67 DINVIMTALQKKGFESNWFDRRK 89
D VI+T L + G SN+FD+RK
Sbjct: 35 DTPVILTQLNEDGTTSNYFDKRK 57
>pdb|1MNN|A Chain A, Structure Of The Sporulation Specific Transcription
Factor Ndt80 Bound To Dna
Length = 340
Score = 28.9 bits (63), Expect = 1.9, Method: Compositional matrix adjust.
Identities = 12/23 (52%), Positives = 16/23 (69%)
Query: 67 DINVIMTALQKKGFESNWFDRRK 89
D VI+T L + G SN+FD+RK
Sbjct: 30 DTPVILTQLNEDGTTSNYFDKRK 52
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
0.318 0.137 0.412
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 6,041,455
Number of Sequences: 62578
Number of extensions: 260131
Number of successful extensions: 644
Number of sequences better than 100.0: 8
Number of HSP's better than 100.0 without gapping: 8
Number of HSP's successfully gapped in prelim test: 0
Number of HSP's that attempted gapping in prelim test: 632
Number of HSP's gapped (non-prelim): 8
length of query: 186
length of database: 14,973,337
effective HSP length: 93
effective length of query: 93
effective length of database: 9,153,583
effective search space: 851283219
effective search space used: 851283219
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 48 (23.1 bits)