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= 017845
(365 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|2LBC|A Chain A, Solution Structure Of Tandem Uba Of Usp13
Length = 126
Score = 32.3 bits (72), Expect = 0.44, Method: Compositional matrix adjust.
Identities = 13/38 (34%), Positives = 26/38 (68%)
Query: 88 QVPDESLSLVMSMGFKEQDAKRALRICSQDVGSAIDFL 125
Q P+E ++++ SMGF+ A +ALR + ++ A+D++
Sbjct: 76 QPPEEIVAIITSMGFQRNQAIQALRATNNNLERALDWI 113
>pdb|1OQY|A Chain A, Structure Of The Dna Repair Protein Hhr23a
pdb|1QZE|A Chain A, Hhr23a Protein Structure Based On Residual Dipolar
Coupling Data
Length = 368
Score = 31.2 bits (69), Expect = 1.0, Method: Compositional matrix adjust.
Identities = 15/38 (39%), Positives = 26/38 (68%), Gaps = 1/38 (2%)
Query: 226 IEQLVAMGFERPRVIEACRAGGDDIHQIMLQLL-GEPG 262
+ ++++MG+ER RV+ A RA ++ H+ + LL G PG
Sbjct: 172 LTEIMSMGYERERVVAALRASYNNPHRAVEYLLTGIPG 209
Score = 29.3 bits (64), Expect = 3.3, Method: Compositional matrix adjust.
Identities = 12/32 (37%), Positives = 23/32 (71%)
Query: 166 IKELVSIGFEKELVAEALRRNENDSQKALDDL 197
+ E++S+G+E+E V ALR + N+ +A++ L
Sbjct: 172 LTEIMSMGYERERVVAALRASYNNPHRAVEYL 203
>pdb|1IFY|A Chain A, Solution Structure Of The Internal Uba Domain Of Hhr23a
Length = 49
Score = 30.8 bits (68), Expect = 1.3, Method: Composition-based stats.
Identities = 15/41 (36%), Positives = 27/41 (65%), Gaps = 1/41 (2%)
Query: 223 DAKIEQLVAMGFERPRVIEACRAGGDDIHQIMLQLL-GEPG 262
+ + ++++MG+ER RV+ A RA ++ H+ + LL G PG
Sbjct: 9 ETMLTEIMSMGYERERVVAALRASYNNPHRAVEYLLTGIPG 49
Score = 29.3 bits (64), Expect = 3.9, Method: Composition-based stats.
Identities = 12/32 (37%), Positives = 23/32 (71%)
Query: 166 IKELVSIGFEKELVAEALRRNENDSQKALDDL 197
+ E++S+G+E+E V ALR + N+ +A++ L
Sbjct: 12 LTEIMSMGYERERVVAALRASYNNPHRAVEYL 43
>pdb|3PVS|A Chain A, Structure And Biochemical Activities Of Escherichia Coli
Mgsa
pdb|3PVS|B Chain B, Structure And Biochemical Activities Of Escherichia Coli
Mgsa
pdb|3PVS|C Chain C, Structure And Biochemical Activities Of Escherichia Coli
Mgsa
pdb|3PVS|D Chain D, Structure And Biochemical Activities Of Escherichia Coli
Mgsa
Length = 447
Score = 30.0 bits (66), Expect = 2.3, Method: Compositional matrix adjust.
Identities = 25/75 (33%), Positives = 37/75 (49%), Gaps = 7/75 (9%)
Query: 54 LRMELLEGVAAYHSGQFDKARNA---LTSAQAKFFQLQVPDESLS----LVMSMGFKEQD 106
L+ ELL +A S +FD + L SA K + PD +L ++ + G
Sbjct: 232 LKPELLTEIAGERSARFDNKGDRFYDLISALHKSVRGSAPDAALYWYARIITAGGDPLYV 291
Query: 107 AKRALRICSQDVGSA 121
A+R L I S+DVG+A
Sbjct: 292 ARRCLAIASEDVGNA 306
>pdb|1VG5|A Chain A, Solution Structure Of Rsgi Ruh-014, A Uba Domain From
Arabidopsis Cdna
Length = 73
Score = 29.3 bits (64), Expect = 3.2, Method: Compositional matrix adjust.
Identities = 16/42 (38%), Positives = 27/42 (64%)
Query: 221 AADAKIEQLVAMGFERPRVIEACRAGGDDIHQIMLQLLGEPG 262
A++ +I++LVAMGF+R +V A A DD+ + L+ + G
Sbjct: 28 ASEEQIQKLVAMGFDRTQVEVALAAADDDLTVAVEILMSQSG 69
>pdb|3IHP|A Chain A, Covalent Ubiquitin-Usp5 Complex
pdb|3IHP|B Chain B, Covalent Ubiquitin-Usp5 Complex
Length = 854
Score = 29.3 bits (64), Expect = 3.3, Method: Compositional matrix adjust.
Identities = 11/36 (30%), Positives = 23/36 (63%)
Query: 90 PDESLSLVMSMGFKEQDAKRALRICSQDVGSAIDFL 125
P++ ++ ++SMGF A +ALR + + A+D++
Sbjct: 720 PEDCVTTIVSMGFSRDQALKALRATNNSLERAVDWI 755
>pdb|1SVD|A Chain A, The Structure Of Halothiobacillus Neapolitanus Rubisco
Length = 473
Score = 28.9 bits (63), Expect = 4.8, Method: Compositional matrix adjust.
Identities = 14/46 (30%), Positives = 24/46 (52%)
Query: 313 GRDVEMEDELANDLTGDVFADYDIEVTKEGEAISEYLSLLDSVAGI 358
GR +ED +D F Y I++ +EG ++ + SL+ +V G
Sbjct: 75 GRAYRIEDVPGDDAAFYAFIAYPIDLFEEGSVVNVFTSLVGNVFGF 120
>pdb|2DAK|A Chain A, Solution Structure Of The Second Uba Domain In The Human
Ubiquitin Specific Protease 5 (Isopeptidase 5)
Length = 63
Score = 28.9 bits (63), Expect = 4.8, Method: Compositional matrix adjust.
Identities = 11/36 (30%), Positives = 23/36 (63%)
Query: 90 PDESLSLVMSMGFKEQDAKRALRICSQDVGSAIDFL 125
P++ ++ ++SMGF A +ALR + + A+D++
Sbjct: 9 PEDCVTTIVSMGFSRDQALKALRATNNSLERAVDWI 44
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 0.132 0.365
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 9,286,049
Number of Sequences: 62578
Number of extensions: 337144
Number of successful extensions: 746
Number of sequences better than 100.0: 14
Number of HSP's better than 100.0 without gapping: 9
Number of HSP's successfully gapped in prelim test: 5
Number of HSP's that attempted gapping in prelim test: 726
Number of HSP's gapped (non-prelim): 25
length of query: 365
length of database: 14,973,337
effective HSP length: 100
effective length of query: 265
effective length of database: 8,715,537
effective search space: 2309617305
effective search space used: 2309617305
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (22.0 bits)
S2: 52 (24.6 bits)