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= 024447
(267 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 = 32.7 bits (73), Expect = 0.24, Method: Compositional matrix adjust.
Identities = 13/38 (34%), Positives = 26/38 (68%)
Query: 142 QVPDESLSLVMSMGFKEQDAKRALRICSQDVGSAIDFL 179
Q P+E ++++ SMGF+ A +ALR + ++ A+D++
Sbjct: 76 QPPEEIVAIITSMGFQRNQAIQALRATNNNLERALDWI 113
Score = 27.7 bits (60), Expect = 7.3, Method: Compositional matrix adjust.
Identities = 15/51 (29%), Positives = 29/51 (56%), Gaps = 1/51 (1%)
Query: 206 YGLTPLKKAVDIEKIKELVSIGFEKELVAEALRRNENDSQKALDDL-TNPE 255
+G + L E + + S+GF++ +ALR N+ ++ALD + ++PE
Sbjct: 68 FGASGLDNQPPEEIVAIITSMGFQRNQAIQALRATNNNLERALDWIFSHPE 118
>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 = 30.8 bits (68), Expect = 0.89, Method: Compositional matrix adjust.
Identities = 25/75 (33%), Positives = 37/75 (49%), Gaps = 7/75 (9%)
Query: 108 LRMELLEGVAAYHSGQFDKARNA---LTSAQAKFFQLQVPDESL----SLVMSMGFKEQD 160
L+ ELL +A S +FD + L SA K + PD +L ++ + G
Sbjct: 232 LKPELLTEIAGERSARFDNKGDRFYDLISALHKSVRGSAPDAALYWYARIITAGGDPLYV 291
Query: 161 AKRALRICSQDVGSA 175
A+R L I S+DVG+A
Sbjct: 292 ARRCLAIASEDVGNA 306
>pdb|2DAK|A Chain A, Solution Structure Of The Second Uba Domain In The Human
Ubiquitin Specific Protease 5 (Isopeptidase 5)
Length = 63
Score = 30.0 bits (66), Expect = 1.5, Method: Composition-based stats.
Identities = 11/36 (30%), Positives = 23/36 (63%)
Query: 144 PDESLSLVMSMGFKEQDAKRALRICSQDVGSAIDFL 179
P++ ++ ++SMGF A +ALR + + A+D++
Sbjct: 9 PEDCVTTIVSMGFSRDQALKALRATNNSLERAVDWI 44
>pdb|1IFY|A Chain A, Solution Structure Of The Internal Uba Domain Of Hhr23a
Length = 49
Score = 29.6 bits (65), Expect = 2.0, Method: Composition-based stats.
Identities = 12/32 (37%), Positives = 23/32 (71%)
Query: 220 IKELVSIGFEKELVAEALRRNENDSQKALDDL 251
+ E++S+G+E+E V ALR + N+ +A++ L
Sbjct: 12 LTEIMSMGYERERVVAALRASYNNPHRAVEYL 43
>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 = 2.1, Method: Compositional matrix adjust.
Identities = 11/36 (30%), Positives = 23/36 (63%)
Query: 144 PDESLSLVMSMGFKEQDAKRALRICSQDVGSAIDFL 179
P++ ++ ++SMGF A +ALR + + A+D++
Sbjct: 720 PEDCVTTIVSMGFSRDQALKALRATNNSLERAVDWI 755
>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 = 28.5 bits (62), Expect = 3.8, Method: Compositional matrix adjust.
Identities = 12/32 (37%), Positives = 23/32 (71%)
Query: 220 IKELVSIGFEKELVAEALRRNENDSQKALDDL 251
+ E++S+G+E+E V ALR + N+ +A++ L
Sbjct: 172 LTEIMSMGYERERVVAALRASYNNPHRAVEYL 203
>pdb|3GVY|A Chain A, Crystal Structure Of Bacterioferritin From R.Sphaeroides
pdb|3GVY|B Chain B, Crystal Structure Of Bacterioferritin From R.Sphaeroides
pdb|3GVY|C Chain C, Crystal Structure Of Bacterioferritin From R.Sphaeroides
Length = 161
Score = 28.5 bits (62), Expect = 4.2, Method: Compositional matrix adjust.
Identities = 19/70 (27%), Positives = 32/70 (45%), Gaps = 5/70 (7%)
Query: 38 DPKVLEFVD---NGPLLQIDMVWCYFMLRDISWLSEAGIRLRKAREGIERAHGKDSSRVR 94
D KV+E+++ L + W ++ L++ W I + +E IE H D R
Sbjct: 4 DAKVIEYLNAALRSELTAVSQYWLHYRLQE-DW-GFGSIAHKSRKESIEEMHHADKLIQR 61
Query: 95 LLQAGRHPEL 104
++ G HP L
Sbjct: 62 IIFLGGHPNL 71
>pdb|2G3Q|A Chain A, Solution Structure Of Ede1 Uba-Ubiquitin Complex
Length = 43
Score = 28.1 bits (61), Expect = 5.1, Method: Composition-based stats.
Identities = 12/26 (46%), Positives = 18/26 (69%)
Query: 154 MGFKEQDAKRALRICSQDVGSAIDFL 179
MGF E++A AL C+ D+ +A +FL
Sbjct: 14 MGFTEEEAHNALEKCNWDLEAATNFL 39
>pdb|1Q02|A Chain A, Nmr Structure Of The Uba Domain Of P62 (Sqstm1)
pdb|2JY7|A Chain A, Nmr Structure Of The Ubiquitin Associated (Uba) Domain Of
P62 (Sqstm1). Rdc Refined
pdb|2JY8|A Chain A, Nmr Structure Of The Ubiquitin Associated (Uba) Domain Of
P62 (Sqstm1) In Complex With Ubiquitin. Rdc Refined
pdb|2K0B|X Chain X, Nmr Structure Of The Uba Domain Of P62 (Sqstm1)
pdb|2KNV|A Chain A, Nmr Dimer Structure Of The Uba Domain Of P62 (Sqstm1)
pdb|2KNV|B Chain B, Nmr Dimer Structure Of The Uba Domain Of P62 (Sqstm1)
Length = 52
Score = 28.1 bits (61), Expect = 5.8, Method: Composition-based stats.
Identities = 14/34 (41%), Positives = 23/34 (67%), Gaps = 2/34 (5%)
Query: 146 ESLSLVMSMGFKEQDA--KRALRICSQDVGSAID 177
ESLS ++SMGF ++ R L+ + D+G+A+D
Sbjct: 12 ESLSQMLSMGFSDEGGWLTRLLQTKNYDIGAALD 45
>pdb|2RRU|A Chain A, Solution Structure Of The Uba Omain Of P62 And Its
Interaction With Ubiquitin
pdb|3B0F|A Chain A, Crystal Structure Of The Uba Domain Of P62 And Its
Interaction With Ubiquitin
pdb|3B0F|B Chain B, Crystal Structure Of The Uba Domain Of P62 And Its
Interaction With Ubiquitin
Length = 53
Score = 27.7 bits (60), Expect = 6.1, Method: Composition-based stats.
Identities = 14/34 (41%), Positives = 23/34 (67%), Gaps = 2/34 (5%)
Query: 146 ESLSLVMSMGFKEQDA--KRALRICSQDVGSAID 177
ESLS ++SMGF ++ R L+ + D+G+A+D
Sbjct: 13 ESLSQMLSMGFSDEGGWLTRLLQTKNYDIGAALD 46
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
0.320 0.134 0.376
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 6,575,097
Number of Sequences: 62578
Number of extensions: 234331
Number of successful extensions: 662
Number of sequences better than 100.0: 12
Number of HSP's better than 100.0 without gapping: 7
Number of HSP's successfully gapped in prelim test: 5
Number of HSP's that attempted gapping in prelim test: 650
Number of HSP's gapped (non-prelim): 17
length of query: 267
length of database: 14,973,337
effective HSP length: 97
effective length of query: 170
effective length of database: 8,903,271
effective search space: 1513556070
effective search space used: 1513556070
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 50 (23.9 bits)