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= psy4375
(62 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|1O7D|A Chain A, The Structure Of The Bovine Lysosomal A-Mannosidase
Suggests A Novel Mechanism For Low Ph Activation
Length = 298
Score = 54.3 bits (129), Expect = 2e-08, Method: Composition-based stats.
Identities = 24/50 (48%), Positives = 35/50 (70%), Gaps = 6/50 (12%)
Query: 9 RNIVKKLIAEGRLEMVTGGWVMTDEATSHIFAMVDQL------IEETFST 52
+ IV++L+ +GRLE GGWVM DEAT+H A++DQ+ +EETF +
Sbjct: 87 QKIVRELVRQGRLEFANGGWVMNDEATTHYGAIIDQMTLGLRFLEETFGS 136
>pdb|1HXK|A Chain A, Golgi Alpha-Mannosidase Ii In Complex With
Deoxymannojirimicin
pdb|1HWW|A Chain A, Golgi Alpha-Mannosidase Ii In Complex With Swainsonine
Length = 1015
Score = 42.4 bits (98), Expect = 7e-05, Method: Composition-based stats.
Identities = 20/40 (50%), Positives = 27/40 (67%)
Query: 8 KRNIVKKLIAEGRLEMVTGGWVMTDEATSHIFAMVDQLIE 47
K+ +K ++ G+LE VTGGWVM DEA SH ++ QL E
Sbjct: 115 KKLQMKSIVKNGQLEFVTGGWVMPDEANSHWRNVLLQLTE 154
>pdb|1PS3|A Chain A, Golgi Alpha-mannosidase Ii In Complex With Kifunensine
Length = 1045
Score = 42.4 bits (98), Expect = 7e-05, Method: Composition-based stats.
Identities = 20/40 (50%), Positives = 27/40 (67%)
Query: 8 KRNIVKKLIAEGRLEMVTGGWVMTDEATSHIFAMVDQLIE 47
K+ +K ++ G+LE VTGGWVM DEA SH ++ QL E
Sbjct: 145 KKLQMKSIVKNGQLEFVTGGWVMPDEANSHWRNVLLQLTE 184
>pdb|1QWN|A Chain A, Golgi Alpha-Mannosidase Ii Covalent Intermediate Complex
With 5- Fluoro-Gulosyl-Fluoride
pdb|1R33|A Chain A, Golgi Alpha-Mannosidase Ii Complex With
5-Thio-D-Mannopyranosylamine
pdb|1R34|A Chain A, Golgi Alpha-Mannosidase Ii Complex With 5-Thio-D-
Mannopyranosylamidinium Salt
pdb|1TQS|A Chain A, Golgi Alpha-Mannosidase Ii In Complex With Salacinol
pdb|1TQT|A Chain A, Golgi Alpha-mannosidase Ii In Complex With A Diastereomer
Of Salacinol
pdb|1TQU|A Chain A, Golgi Alpha-mannosidase Ii In Complex With The Salacinol
Analog Ghavamiol
pdb|1TQV|A Chain A, Golgi Alpha-Mannosidase Ii In Complex With
Seleno-Salacinol (Blintol)
pdb|1TQW|A Chain A, Golgi Alpha-Mannosidase Ii In Complex With A Diastereomer
Of Seleno- Salacinol
pdb|2ALW|A Chain A, Golgi Alpha-Mannosidase Ii Complex With Noeuromycin
pdb|2F7O|A Chain A, Golgi Alpha-mannosidase Ii Complex With Mannostatin A
pdb|2F7P|A Chain A, Golgi Alpha-Mannosidase Ii Complex With Benzyl-Mannostatin
A
pdb|2F18|A Chain A, Golgi Alpha-Mannosidase Ii Complex With
(2r,3r,4s)-2-({[(1r)-2-
Hydroxy-1-Phenylethyl]amino}methyl)pyrrolidine-3,4-Diol
pdb|2F1A|A Chain A, Golgi Alpha-Mannosidase Ii Complex With
(2r,3r,4s)-2-({[(1s)-2-
Hydroxy-1-Phenylethyl]amino}methyl)pyrrolidine-3,4-Diol
pdb|2F1B|A Chain A, Golgi Alpha-Mannosidase Ii Complex With
(2r,3r,4s,5r)-2-({[(1r)-2-
Hydroxy-1-Phenylethyl]amino}methyl)-5-Methylpyrrolidine-
3,4-Diol
pdb|2F7Q|A Chain A, Golgi Alpha-Mannosidase Ii Complex With
Aminocyclopentitetrol
pdb|2F7R|A Chain A, Golgi Alpha-Mannosidase Ii Complex With
Benzyl-Aminocyclopentitetrol
pdb|2FYV|A Chain A, Golgi Alpha-Mannosidase Ii Complex With An Amino-Salacinol
Carboxylate Analog
pdb|2OW6|A Chain A, Golgi Alpha-Mannosidase Ii Complex With
(1r,5s,6s,7r,8s)-1-
Thioniabicyclo[4.3.0]nonan-5,7,8-Triol Chloride
pdb|2OW7|A Chain A, Golgi Alpha-Mannosidase Ii Complex With (1r,6s,7r,8s)-1-
Thioniabicyclo[4.3.0]nonan-7,8-Diol Chloride
pdb|3BLB|A Chain A, Crystal Structure Of Golgi Mannosidase Ii In Complex With
Swainsonine At 1.3 Angstrom Resolution
pdb|3BUB|A Chain A, Golgi Alpha-mannosidase Ii With An Empty Active Site
pdb|3DDF|A Chain A, Golgi Mannosidase Ii Complex With
(3r,4r,5r)-3,4-Dihydroxy-5-({[(1r)- 2-Hydroxy-1
Phenylethyl]amino}methyl) Pyrrolidin-2-One
pdb|3DDG|A Chain A, Golgi Mannosidase Ii Complex With
(3r,4r,5r)-3,4-Dihydroxy-5-({[(1r)- 2-Hydroxy-1
Phenylethyl]amino}methyl) Methylpyrrolidin-2-One
pdb|3D4Y|A Chain A, Golgi Mannosidase Ii Complex With Mannoimidazole
pdb|3D4Z|A Chain A, Golgi Mannosidase Ii Complex With Gluco-Imidazole
pdb|3D50|A Chain A, Golgi Mannosidase Ii Complex With
N-Octyl-6-Epi-Valienamine
pdb|3D51|A Chain A, Golgi Mannosidase Ii Complex With Gluco-Hydroxyiminolactam
pdb|3D52|A Chain A, Golgi Mannosidase Ii Complex With An N-Aryl Carbamate
Derivative Of Gluco-Hydroxyiminolactam
pdb|3DX0|A Chain A, Golgi Alpha-Mannosidase Ii In Complex With Mannostatin A
At Ph 5.75
pdb|3DX1|A Chain A, Golgi Alpha-Mannosidase Ii In Complex With Mannostatin
Analog (1s,2s, 3r,4r)-4-Aminocyclopentane-1,2,3-Triol
pdb|3DX2|A Chain A, Golgi Mannosidase Ii Complex With Mannostatin B
pdb|3DX4|A Chain A, Golgi Alpha-mannosidase Ii In Complex With Mannostatin
Analog (1r,2r,
3r,4s,5r)-4-amino-5-methoxycyclopentane-1,2,3-triol
pdb|3EJP|A Chain A, Golgi Alpha-Mannosidase Ii In Complex With 5-Substituted
Swainsonine Analog:
(5r)-5-[2'-Oxo-2'-(Phenyl)ethyl]-Swainsonine
pdb|3EJQ|A Chain A, Golgi Alpha-Mannosidase Ii In Complex With 5-Substitued
Swainsonine Analog:
(5r)-5-[2'-Oxo-2'-(4-Methylphenyl)ethyl]-Swainsonine
pdb|3EJR|A Chain A, Golgi Alpha-mannosidase Ii In Complex With 5-substitued
Swainsonine Analog:
(5r)-5-[2'-oxo-2'-(4-tert-butylphenyl)ethyl]-swainsonine
pdb|3EJS|A Chain A, Golgi Alpha-mannosidase Ii In Complex With 5-substituted
Swainsonine Analog:
(5s)-5-[2'-(4-tert-butylphenyl)ethyl]-swainsonine
pdb|3EJT|A Chain A, Golgi Alpha-Mannosidase Ii In Complex With 5-Substituted
Swainsonine
Analog:(5r)-5-[2'-(4-Tert-Butylphenyl)ethyl]-Swainsonine
pdb|3EJU|A Chain A, Golgi Alpha-Mannosidase Ii In Complex With 5-Substituted
Swainsonine
Analog:(5s)-5-[2'-Oxo-2'-(4-Tert-Butylphenyl)ethyl]-
Swainsonine
Length = 1045
Score = 42.4 bits (98), Expect = 8e-05, Method: Composition-based stats.
Identities = 20/40 (50%), Positives = 27/40 (67%)
Query: 8 KRNIVKKLIAEGRLEMVTGGWVMTDEATSHIFAMVDQLIE 47
K+ +K ++ G+LE VTGGWVM DEA SH ++ QL E
Sbjct: 145 KKLQMKSIVKNGQLEFVTGGWVMPDEANSHWRNVLLQLTE 184
>pdb|1QWU|A Chain A, Golgi Alpha-Mannosidase Ii D341n Mutant Complex With
5-F-Guloside
pdb|1QX1|A Chain A, Golgi Alpha-Mannosidase Ii D341n Mutant Complex With
2-F-Mannosyl-F
pdb|3BUP|A Chain A, Golgi Alpha-Mannosidase Ii D341n Acid-Base Catalyst Mutant
With Bound Mannose
Length = 1045
Score = 42.4 bits (98), Expect = 8e-05, Method: Composition-based stats.
Identities = 20/40 (50%), Positives = 27/40 (67%)
Query: 8 KRNIVKKLIAEGRLEMVTGGWVMTDEATSHIFAMVDQLIE 47
K+ +K ++ G+LE VTGGWVM DEA SH ++ QL E
Sbjct: 145 KKLQMKSIVKNGQLEFVTGGWVMPDEANSHWRNVLLQLTE 184
>pdb|3DX3|A Chain A, Golgi Alpha-Mannosidase Ii In Complex With Mannostatin
Analog (1r,2r,
3s,4r,5r)-5-Aminocyclopentane-1,2,3,4-Tetraol
Length = 1045
Score = 42.4 bits (98), Expect = 8e-05, Method: Composition-based stats.
Identities = 20/40 (50%), Positives = 27/40 (67%)
Query: 8 KRNIVKKLIAEGRLEMVTGGWVMTDEATSHIFAMVDQLIE 47
K+ +K ++ G+LE VTGGWVM DEA SH ++ QL E
Sbjct: 145 KKLQMKSIVKNGQLEFVTGGWVMPDEANSHWRNVLLQLTE 184
>pdb|3CV5|A Chain A, Golgi Mannosidase Ii D204a Catalytic Nucleophile Mutant
Complex With 3alpha,6alpha-Mannopentaose
pdb|3CZN|A Chain A, Golgi Alpha-Mannosidase Ii (D204a Nucleophile Mutant) In
Complex With Gnman5gn
pdb|3CZS|A Chain A, Golgi Alpha-Mannosidase Ii (D204a Nucleophile Mutant)
pdb|3BUD|A Chain A, Golgi Mannosidase Ii D204a Catalytic Nucleophile Mutant
With An Empty Active Site
pdb|3BUI|A Chain A, Golgi Mannosidase Ii D204a Catalytic Nucleophile Mutant
Complex With Tris
pdb|3BUQ|A Chain A, Golgi Alpha-Mannosidase Ii D204a Catalytic Nucleophile
Mutant With Bound Mannose.
pdb|3BVT|A Chain A, Golgi Mannosidase Ii D204a Catalytic Nucleophile Mutant
Complex With Methyl
(Alpha-D-Mannopyranosyl)-(1->3)-S-Alpha-D-
Mannopyranoside
pdb|3BVU|A Chain A, Golgi Mannosidase Ii D204a Catalytic Nucleophile Mutant
Complex With
Methyl(Alpha-D-Mannopyranosyl)-(1->3)-S-[(Alpha-D-
Mannopyranosyl)-(1- >6)]-Alpha-D-Mannopyranoside
pdb|3BVV|A Chain A, Golgi Mannosidase Ii D204a Catalytic Nucleophile Mutant
Complex With Methyl
Alpha-D-Mannopyranosyl-(1->3)-[6-Thio-
Alpha-D-Mannopyranosyl-(1->6)]-Beta-D-Mannopyranoside
pdb|3BVW|A Chain A, Golgi Mannosidase Ii D204a Catalytic Nucleophile Mutant
Complex With Methyl (2-Deoxy-2-Acetamido-Beta-D-
Glucopyranosyl)-(1->2)-Alpha-D-Mannopyranosyl- (1->3)-
[alpha-D-Mannopyranosyl-(1->6)-6-Thio-Alpha-D-
Mannopyranosyl- (1->6)]-Beta-D-Mannopyranoside
pdb|3BVX|A Chain A, Golgi Mannosidase Ii D204a Catalytic Nucleophile Mutant
Complex With Methyl (2-Deoxy-2-Acetamido-Beta-D-
Glucopyranosyl)-(1->2)-(Alpha-D-Mannopyranosyl)- (1->3)-
[(Alpha-D-Mannopyranosyl)-(1->6)-(Alpha-D-
Mannopyranosyl)- (1->6)]-Beta-D-Mannopyranoside
Length = 1045
Score = 42.4 bits (98), Expect = 8e-05, Method: Composition-based stats.
Identities = 20/40 (50%), Positives = 27/40 (67%)
Query: 8 KRNIVKKLIAEGRLEMVTGGWVMTDEATSHIFAMVDQLIE 47
K+ +K ++ G+LE VTGGWVM DEA SH ++ QL E
Sbjct: 145 KKLQMKSIVKNGQLEFVTGGWVMPDEANSHWRNVLLQLTE 184
>pdb|1HTY|A Chain A, Golgi Alpha-Mannosidase Ii
Length = 1015
Score = 39.7 bits (91), Expect = 5e-04, Method: Composition-based stats.
Identities = 18/35 (51%), Positives = 23/35 (65%)
Query: 13 KKLIAEGRLEMVTGGWVMTDEATSHIFAMVDQLIE 47
K ++ G+LE VTGGWV DEA SH ++ QL E
Sbjct: 120 KSIVKNGQLEFVTGGWVXPDEANSHWRNVLLQLTE 154
>pdb|2A7S|A Chain A, Crystal Structure Of The Acyl-Coa Carboxylase, Accd5,
From Mycobacterium Tuberculosis
pdb|2A7S|B Chain B, Crystal Structure Of The Acyl-Coa Carboxylase, Accd5,
From Mycobacterium Tuberculosis
pdb|2A7S|C Chain C, Crystal Structure Of The Acyl-Coa Carboxylase, Accd5,
From Mycobacterium Tuberculosis
pdb|2A7S|D Chain D, Crystal Structure Of The Acyl-Coa Carboxylase, Accd5,
From Mycobacterium Tuberculosis
pdb|2A7S|E Chain E, Crystal Structure Of The Acyl-Coa Carboxylase, Accd5,
From Mycobacterium Tuberculosis
pdb|2A7S|F Chain F, Crystal Structure Of The Acyl-Coa Carboxylase, Accd5,
From Mycobacterium Tuberculosis
Length = 548
Score = 26.2 bits (56), Expect = 5.1, Method: Composition-based stats.
Identities = 17/60 (28%), Positives = 31/60 (51%), Gaps = 4/60 (6%)
Query: 2 EIVHPTKRNIVKKLIAEGRLEMVTGGWVMTDEATSHIFAMVDQLIEETFSTFSVQSSKRP 61
E +HP + V+K+ A+G+L + + DE + F +D L + + F++ KRP
Sbjct: 38 ESLHPVGEDAVEKVHAKGKLTARERIYALLDEDS---FVELDALAKHRSTNFNL-GEKRP 93
>pdb|2BZR|A Chain A, Crystal Structure Of Accd5 (Rv3280), An Acyl-Coa
Carboxylase Beta-Subunit From Mycobacterium
Tuberculosis
pdb|2BZR|B Chain B, Crystal Structure Of Accd5 (Rv3280), An Acyl-Coa
Carboxylase Beta-Subunit From Mycobacterium
Tuberculosis
pdb|2BZR|C Chain C, Crystal Structure Of Accd5 (Rv3280), An Acyl-Coa
Carboxylase Beta-Subunit From Mycobacterium
Tuberculosis
pdb|2BZR|D Chain D, Crystal Structure Of Accd5 (Rv3280), An Acyl-Coa
Carboxylase Beta-Subunit From Mycobacterium
Tuberculosis
pdb|2BZR|E Chain E, Crystal Structure Of Accd5 (Rv3280), An Acyl-Coa
Carboxylase Beta-Subunit From Mycobacterium
Tuberculosis
pdb|2BZR|F Chain F, Crystal Structure Of Accd5 (Rv3280), An Acyl-Coa
Carboxylase Beta-Subunit From Mycobacterium
Tuberculosis
Length = 548
Score = 26.2 bits (56), Expect = 5.1, Method: Composition-based stats.
Identities = 17/60 (28%), Positives = 31/60 (51%), Gaps = 4/60 (6%)
Query: 2 EIVHPTKRNIVKKLIAEGRLEMVTGGWVMTDEATSHIFAMVDQLIEETFSTFSVQSSKRP 61
E +HP + V+K+ A+G+L + + DE + F +D L + + F++ KRP
Sbjct: 38 ESLHPVGEDAVEKVHAKGKLTARERIYALLDEDS---FVELDALAKHRSTNFNL-GEKRP 93
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 0.130 0.371
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 1,572,426
Number of Sequences: 62578
Number of extensions: 42587
Number of successful extensions: 127
Number of sequences better than 100.0: 10
Number of HSP's better than 100.0 without gapping: 8
Number of HSP's successfully gapped in prelim test: 2
Number of HSP's that attempted gapping in prelim test: 119
Number of HSP's gapped (non-prelim): 10
length of query: 62
length of database: 14,973,337
effective HSP length: 33
effective length of query: 29
effective length of database: 12,908,263
effective search space: 374339627
effective search space used: 374339627
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 45 (21.9 bits)