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= psy2170
(78 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|1PS3|A Chain A, Golgi Alpha-mannosidase Ii In Complex With Kifunensine
Length = 1045
Score = 78.6 bits (192), Expect = 7e-16, Method: Compositional matrix adjust.
Identities = 35/71 (49%), Positives = 52/71 (73%), Gaps = 3/71 (4%)
Query: 10 VFLVPHSHNDPGWLKTFESYYHSQTRMILNNMVEKLVQHPNMTFIWSEISFFSQWWE--- 66
VF+VPHSHNDPGW++TFE YY T+ IL+N + L +P M FIW+EIS+F++++
Sbjct: 83 VFVVPHSHNDPGWIQTFEEYYQHDTKHILSNALRHLHDNPEMKFIWAEISYFARFYHDLG 142
Query: 67 RSRKLRIIPIV 77
++KL++ IV
Sbjct: 143 ENKKLQMKSIV 153
>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 = 78.6 bits (192), Expect = 8e-16, Method: Compositional matrix adjust.
Identities = 35/71 (49%), Positives = 52/71 (73%), Gaps = 3/71 (4%)
Query: 10 VFLVPHSHNDPGWLKTFESYYHSQTRMILNNMVEKLVQHPNMTFIWSEISFFSQWWE--- 66
VF+VPHSHNDPGW++TFE YY T+ IL+N + L +P M FIW+EIS+F++++
Sbjct: 83 VFVVPHSHNDPGWIQTFEEYYQHDTKHILSNALRHLHDNPEMKFIWAEISYFARFYHDLG 142
Query: 67 RSRKLRIIPIV 77
++KL++ IV
Sbjct: 143 ENKKLQMKSIV 153
>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 = 78.6 bits (192), Expect = 8e-16, Method: Compositional matrix adjust.
Identities = 35/71 (49%), Positives = 52/71 (73%), Gaps = 3/71 (4%)
Query: 10 VFLVPHSHNDPGWLKTFESYYHSQTRMILNNMVEKLVQHPNMTFIWSEISFFSQWWE--- 66
VF+VPHSHNDPGW++TFE YY T+ IL+N + L +P M FIW+EIS+F++++
Sbjct: 53 VFVVPHSHNDPGWIQTFEEYYQHDTKHILSNALRHLHDNPEMKFIWAEISYFARFYHDLG 112
Query: 67 RSRKLRIIPIV 77
++KL++ IV
Sbjct: 113 ENKKLQMKSIV 123
>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 = 78.6 bits (192), Expect = 8e-16, Method: Compositional matrix adjust.
Identities = 35/71 (49%), Positives = 52/71 (73%), Gaps = 3/71 (4%)
Query: 10 VFLVPHSHNDPGWLKTFESYYHSQTRMILNNMVEKLVQHPNMTFIWSEISFFSQWWE--- 66
VF+VPHSHNDPGW++TFE YY T+ IL+N + L +P M FIW+EIS+F++++
Sbjct: 83 VFVVPHSHNDPGWIQTFEEYYQHDTKHILSNALRHLHDNPEMKFIWAEISYFARFYHDLG 142
Query: 67 RSRKLRIIPIV 77
++KL++ IV
Sbjct: 143 ENKKLQMKSIV 153
>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 = 78.6 bits (192), Expect = 8e-16, Method: Compositional matrix adjust.
Identities = 35/71 (49%), Positives = 52/71 (73%), Gaps = 3/71 (4%)
Query: 10 VFLVPHSHNDPGWLKTFESYYHSQTRMILNNMVEKLVQHPNMTFIWSEISFFSQWWE--- 66
VF+VPHSHNDPGW++TFE YY T+ IL+N + L +P M FIW+EIS+F++++
Sbjct: 83 VFVVPHSHNDPGWIQTFEEYYQHDTKHILSNALRHLHDNPEMKFIWAEISYFARFYHDLG 142
Query: 67 RSRKLRIIPIV 77
++KL++ IV
Sbjct: 143 ENKKLQMKSIV 153
>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 = 78.6 bits (192), Expect = 8e-16, Method: Compositional matrix adjust.
Identities = 35/71 (49%), Positives = 52/71 (73%), Gaps = 3/71 (4%)
Query: 10 VFLVPHSHNDPGWLKTFESYYHSQTRMILNNMVEKLVQHPNMTFIWSEISFFSQWWE--- 66
VF+VPHSHNDPGW++TFE YY T+ IL+N + L +P M FIW+EIS+F++++
Sbjct: 83 VFVVPHSHNDPGWIQTFEEYYQHDTKHILSNALRHLHDNPEMKFIWAEISYFARFYHDLG 142
Query: 67 RSRKLRIIPIV 77
++KL++ IV
Sbjct: 143 ENKKLQMKSIV 153
>pdb|1HTY|A Chain A, Golgi Alpha-Mannosidase Ii
Length = 1015
Score = 76.6 bits (187), Expect = 3e-15, Method: Composition-based stats.
Identities = 34/71 (47%), Positives = 50/71 (70%), Gaps = 3/71 (4%)
Query: 10 VFLVPHSHNDPGWLKTFESYYHSQTRMILNNMVEKLVQHPNMTFIWSEISFFSQWWE--- 66
VF+VPHSHNDPGW++TFE YY T+ IL+N + L +P FIW+EIS+F++++
Sbjct: 53 VFVVPHSHNDPGWIQTFEEYYQHDTKHILSNALRHLHDNPEXKFIWAEISYFARFYHDLG 112
Query: 67 RSRKLRIIPIV 77
++KL+ IV
Sbjct: 113 ENKKLQXKSIV 123
>pdb|1O7D|A Chain A, The Structure Of The Bovine Lysosomal A-Mannosidase
Suggests A Novel Mechanism For Low Ph Activation
Length = 298
Score = 62.0 bits (149), Expect = 9e-11, Method: Composition-based stats.
Identities = 29/74 (39%), Positives = 48/74 (64%), Gaps = 9/74 (12%)
Query: 2 VKKELLTIVFLVPHSHNDPGWLKTFESYYH--------SQTRMILNNMVEKLVQHPNMTF 53
VK ++L V LVPH+H+D GWLKT + Y++ + + IL++++ L+ +P F
Sbjct: 9 VKPDMLN-VHLVPHTHDDVGWLKTVDQYFYGIYNNIQPAGVQYILDSVISSLLANPTRRF 67
Query: 54 IWSEISFFSQWWER 67
I+ EI+FFS+WW +
Sbjct: 68 IYVEIAFFSRWWRQ 81
>pdb|1Z7E|A Chain A, Crystal Structure Of Full Length Arna
pdb|1Z7E|B Chain B, Crystal Structure Of Full Length Arna
pdb|1Z7E|C Chain C, Crystal Structure Of Full Length Arna
pdb|1Z7E|D Chain D, Crystal Structure Of Full Length Arna
pdb|1Z7E|E Chain E, Crystal Structure Of Full Length Arna
pdb|1Z7E|F Chain F, Crystal Structure Of Full Length Arna
Length = 660
Score = 28.9 bits (63), Expect = 0.80, Method: Composition-based stats.
Identities = 15/54 (27%), Positives = 28/54 (51%), Gaps = 2/54 (3%)
Query: 27 ESYYHSQTRMILNNMVEKLVQHPNMTFIWSEISFFSQWWERSRKL--RIIPIVA 78
E +Y I ++ + + + HP+ F+ +IS S+W E K ++P+VA
Sbjct: 338 EDHYEVYGLDIGSDAISRFLNHPHFHFVEGDISIHSEWIEYHVKKCDVVLPLVA 391
>pdb|1Z75|A Chain A, Crystal Structure Of Arna Dehydrogenase (decarboxylase)
Domain, R619m Mutant
Length = 358
Score = 28.5 bits (62), Expect = 1.0, Method: Composition-based stats.
Identities = 15/54 (27%), Positives = 28/54 (51%), Gaps = 2/54 (3%)
Query: 27 ESYYHSQTRMILNNMVEKLVQHPNMTFIWSEISFFSQWWERSRKL--RIIPIVA 78
E +Y I ++ + + + HP+ F+ +IS S+W E K ++P+VA
Sbjct: 36 EDHYEVYGLDIGSDAISRFLNHPHFHFVEGDISIHSEWIEYHVKKCDVVLPLVA 89
>pdb|1Z73|A Chain A, Crystal Structure Of E. Coli Arna Dehydrogenase
(decarboxylase) Domain, S433a Mutant
Length = 358
Score = 28.5 bits (62), Expect = 1.0, Method: Composition-based stats.
Identities = 15/54 (27%), Positives = 28/54 (51%), Gaps = 2/54 (3%)
Query: 27 ESYYHSQTRMILNNMVEKLVQHPNMTFIWSEISFFSQWWERSRKL--RIIPIVA 78
E +Y I ++ + + + HP+ F+ +IS S+W E K ++P+VA
Sbjct: 36 EDHYEVYGLDIGSDAISRFLNHPHFHFVEGDISIHSEWIEYHVKKCDVVLPLVA 89
>pdb|1Z7B|A Chain A, Crystal Structure Of E.Coli Arna Dehydrogenase
(Decarboxylase) Domain, R619e Mutant
Length = 358
Score = 28.5 bits (62), Expect = 1.0, Method: Composition-based stats.
Identities = 15/54 (27%), Positives = 28/54 (51%), Gaps = 2/54 (3%)
Query: 27 ESYYHSQTRMILNNMVEKLVQHPNMTFIWSEISFFSQWWERSRKL--RIIPIVA 78
E +Y I ++ + + + HP+ F+ +IS S+W E K ++P+VA
Sbjct: 36 EDHYEVYGLDIGSDAISRFLNHPHFHFVEGDISIHSEWIEYHVKKCDVVLPLVA 89
>pdb|1Z74|A Chain A, Crystal Structure Of E.Coli Arna Dehydrogenase
(Decarboxylase) Domain, R619y Mutant
Length = 358
Score = 28.5 bits (62), Expect = 1.0, Method: Composition-based stats.
Identities = 15/54 (27%), Positives = 28/54 (51%), Gaps = 2/54 (3%)
Query: 27 ESYYHSQTRMILNNMVEKLVQHPNMTFIWSEISFFSQWWERSRKL--RIIPIVA 78
E +Y I ++ + + + HP+ F+ +IS S+W E K ++P+VA
Sbjct: 36 EDHYEVYGLDIGSDAISRFLNHPHFHFVEGDISIHSEWIEYHVKKCDVVLPLVA 89
>pdb|1U9J|A Chain A, Crystal Structure Of E. Coli Arna (Pmri) Decarboxylase
Domain
Length = 358
Score = 28.5 bits (62), Expect = 1.0, Method: Composition-based stats.
Identities = 15/54 (27%), Positives = 28/54 (51%), Gaps = 2/54 (3%)
Query: 27 ESYYHSQTRMILNNMVEKLVQHPNMTFIWSEISFFSQWWERSRKL--RIIPIVA 78
E +Y I ++ + + + HP+ F+ +IS S+W E K ++P+VA
Sbjct: 36 EDHYEVYGLDIGSDAISRFLNHPHFHFVEGDISIHSEWIEYHVKKCDVVLPLVA 89
>pdb|2BLL|A Chain A, Apo-Structure Of The C-Terminal Decarboxylase Domain Of
Arna
Length = 345
Score = 28.5 bits (62), Expect = 1.1, Method: Composition-based stats.
Identities = 15/54 (27%), Positives = 28/54 (51%), Gaps = 2/54 (3%)
Query: 27 ESYYHSQTRMILNNMVEKLVQHPNMTFIWSEISFFSQWWERSRKL--RIIPIVA 78
E +Y I ++ + + + HP+ F+ +IS S+W E K ++P+VA
Sbjct: 23 EDHYEVYGLDIGSDAISRFLNHPHFHFVEGDISIHSEWIEYHVKKCDVVLPLVA 76
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
0.326 0.136 0.446
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 2,453,766
Number of Sequences: 62578
Number of extensions: 73758
Number of successful extensions: 227
Number of sequences better than 100.0: 21
Number of HSP's better than 100.0 without gapping: 19
Number of HSP's successfully gapped in prelim test: 2
Number of HSP's that attempted gapping in prelim test: 207
Number of HSP's gapped (non-prelim): 21
length of query: 78
length of database: 14,973,337
effective HSP length: 47
effective length of query: 31
effective length of database: 12,032,171
effective search space: 372997301
effective search space used: 372997301
T: 11
A: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.7 bits)
S2: 45 (21.9 bits)