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= psy10965
(400 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 = 259 bits (661), Expect = 2e-69, Method: Compositional matrix adjust.
Identities = 118/231 (51%), Positives = 158/231 (68%), Gaps = 1/231 (0%)
Query: 1 FVYVETSFFWRWWEEQNEQVRASVKELVDQGRLEFLLGGWCMSDEATPHYSSLIDQMTLG 60
F+YVE +FF RWW +Q + V+ELV QGRLEF GGW M+DEAT HY ++IDQMTLG
Sbjct: 67 FIYVEIAFFSRWWRQQTNATQKIVRELVRQGRLEFANGGWVMNDEATTHYGAIIDQMTLG 126
Query: 61 LKYLNDTFGECGQPRVAWQIDPFGHSAEVALEFADMGFDGVFFGRIDHEDIALRKKNKTM 120
L++L +TFG G+PRVAW IDPFGHS E A FA MGFDG FFGR+D++D +RKK M
Sbjct: 127 LRFLEETFGSDGRPRVAWHIDPFGHSREQASLFAQMGFDGFFFGRLDYQDKKVRKKTLQM 186
Query: 121 EMVWRPDDTLG-PEGDFFTGVMYNIYDPPPGFCFDTYCEDEPIMDNPKLHGVNVNARVDE 179
E VWR +L P D FT V+ N+Y+PP G C+D C D+P++++ + N V
Sbjct: 187 EQVWRASTSLKPPTADLFTSVLPNMYNPPEGLCWDMLCADKPVVEDTRSPEYNAKELVRY 246
Query: 180 FIEVVKKYAQAYRTNNVIITMGGDFHYVVASAWFKNIDKLIKYVNAKLNSD 230
F+++ + YRT + ++TMG DF Y A+ WFKN+DKLI+ VNA+ ++
Sbjct: 247 FLKLATDQGKLYRTKHTVMTMGSDFQYENANTWFKNLDKLIQLVNAQQRAN 297
>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 = 154 bits (389), Expect = 8e-38, Method: Compositional matrix adjust.
Identities = 108/386 (27%), Positives = 183/386 (47%), Gaps = 26/386 (6%)
Query: 1 FVYVETSFFWRWWEEQNEQVRASVKELVDQGRLEFLLGGWCMSDEATPHYSSLIDQMTLG 60
F++ E S+F R++ + E + +K +V G+LEF+ GGW M DEA H+ +++ Q+T G
Sbjct: 96 FIWAEISYFARFYHDLGENKKLQMKSIVKNGQLEFVTGGWVMPDEANSHWRNVLLQLTEG 155
Query: 61 LKYLNDTFGECGQPRVAWQIDPFGHSAEVALEFADMGFDGVFFGRIDHEDIALRKKNKTM 120
+L P +W IDPFGHS + GF + R + + + +
Sbjct: 156 QTWLKQFMNVT--PTASWAIDPFGHSPTMPYILQKSGFKNMLIQRTHYSVKKELAQQRQL 213
Query: 121 EMVWRPD-DTLGPEGDFFTGVMYNIYD------PPPGFC--FD-----TYCEDEPIMDNP 166
E +WR D G F + + YD P P C FD ++ P P
Sbjct: 214 EFLWRQIWDNKGDTALFTHMMPFYSYDIPHTCGPDPKVCCQFDFKRMGSFGLSCPWKVPP 273
Query: 167 K-LHGVNVNARVDEFIEVVKKYAQAYRTNNVIITMGGDFHYVVASAW---FKNIDKLIKY 222
+ + NV AR D ++ KK A+ YRTN ++I +G DF + + W N ++L ++
Sbjct: 274 RTISDQNVAARSDLLVDQWKKKAELYRTNVLLIPLGDDFRFKQNTEWDVQRVNYERLFEH 333
Query: 223 VNAKLNSDVHVLYSTPACYLQALNKENITWPSK---MDDDFFPFGSDEHSYWTGYFTSRP 279
+N++ + +V + T Y A+++ ++ + DFF + +YW+GY+TSRP
Sbjct: 334 INSQAHFNVQAQFGTLQEYFDAVHQAERAGQAEFPTLSGDFFTYADRSDNYWSGYYTSRP 393
Query: 280 SFKYFVYQTNVALQMTKQLKTSLPNDTLAE-EQFLIQ--RAMGIAQHHDAVSGTERQHVT 336
K ++ + L D +A E+ L Q R + + QHHD ++GT + HV
Sbjct: 394 YHKRMDRVLMHYVRAAEMLSAWHSWDGMARIEERLEQARRELSLFQHHDGITGTAKTHVV 453
Query: 337 NDYSLYLYEGIQAAMKIINVAYRHLL 362
DY + E ++A ++ + LL
Sbjct: 454 VDYEQRMQEALKACQMVMQQSVYRLL 479
>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 = 154 bits (389), Expect = 9e-38, Method: Compositional matrix adjust.
Identities = 108/386 (27%), Positives = 183/386 (47%), Gaps = 26/386 (6%)
Query: 1 FVYVETSFFWRWWEEQNEQVRASVKELVDQGRLEFLLGGWCMSDEATPHYSSLIDQMTLG 60
F++ E S+F R++ + E + +K +V G+LEF+ GGW M DEA H+ +++ Q+T G
Sbjct: 126 FIWAEISYFARFYHDLGENKKLQMKSIVKNGQLEFVTGGWVMPDEANSHWRNVLLQLTEG 185
Query: 61 LKYLNDTFGECGQPRVAWQIDPFGHSAEVALEFADMGFDGVFFGRIDHEDIALRKKNKTM 120
+L P +W IDPFGHS + GF + R + + + +
Sbjct: 186 QTWLKQFMNVT--PTASWAIDPFGHSPTMPYILQKSGFKNMLIQRTHYSVKKELAQQRQL 243
Query: 121 EMVWRPD-DTLGPEGDFFTGVMYNIYD------PPPGFC--FD-----TYCEDEPIMDNP 166
E +WR D G F + + YD P P C FD ++ P P
Sbjct: 244 EFLWRQIWDNKGDTALFTHMMPFYSYDIPHTCGPDPKVCCQFDFKRMGSFGLSCPWKVPP 303
Query: 167 K-LHGVNVNARVDEFIEVVKKYAQAYRTNNVIITMGGDFHYVVASAW---FKNIDKLIKY 222
+ + NV AR D ++ KK A+ YRTN ++I +G DF + + W N ++L ++
Sbjct: 304 RTISDQNVAARSDLLVDQWKKKAELYRTNVLLIPLGDDFRFKQNTEWDVQRVNYERLFEH 363
Query: 223 VNAKLNSDVHVLYSTPACYLQALNKENITWPSK---MDDDFFPFGSDEHSYWTGYFTSRP 279
+N++ + +V + T Y A+++ ++ + DFF + +YW+GY+TSRP
Sbjct: 364 INSQAHFNVQAQFGTLQEYFDAVHQAERAGQAEFPTLSGDFFTYADRSDNYWSGYYTSRP 423
Query: 280 SFKYFVYQTNVALQMTKQLKTSLPNDTLAE-EQFLIQ--RAMGIAQHHDAVSGTERQHVT 336
K ++ + L D +A E+ L Q R + + QHHD ++GT + HV
Sbjct: 424 YHKRMDRVLMHYVRAAEMLSAWHSWDGMARIEERLEQARRELSLFQHHDGITGTAKTHVV 483
Query: 337 NDYSLYLYEGIQAAMKIINVAYRHLL 362
DY + E ++A ++ + LL
Sbjct: 484 VDYEQRMQEALKACQMVMQQSVYRLL 509
>pdb|1PS3|A Chain A, Golgi Alpha-mannosidase Ii In Complex With Kifunensine
Length = 1045
Score = 154 bits (389), Expect = 9e-38, Method: Compositional matrix adjust.
Identities = 108/386 (27%), Positives = 183/386 (47%), Gaps = 26/386 (6%)
Query: 1 FVYVETSFFWRWWEEQNEQVRASVKELVDQGRLEFLLGGWCMSDEATPHYSSLIDQMTLG 60
F++ E S+F R++ + E + +K +V G+LEF+ GGW M DEA H+ +++ Q+T G
Sbjct: 126 FIWAEISYFARFYHDLGENKKLQMKSIVKNGQLEFVTGGWVMPDEANSHWRNVLLQLTEG 185
Query: 61 LKYLNDTFGECGQPRVAWQIDPFGHSAEVALEFADMGFDGVFFGRIDHEDIALRKKNKTM 120
+L P +W IDPFGHS + GF + R + + + +
Sbjct: 186 QTWLKQFMNVT--PTASWAIDPFGHSPTMPYILQKSGFKNMLIQRTHYSVKKELAQQRQL 243
Query: 121 EMVWRPD-DTLGPEGDFFTGVMYNIYD------PPPGFC--FD-----TYCEDEPIMDNP 166
E +WR D G F + + YD P P C FD ++ P P
Sbjct: 244 EFLWRQIWDNKGDTALFTHMMPFYSYDIPHTCGPDPKVCCQFDFKRMGSFGLSCPWKVPP 303
Query: 167 K-LHGVNVNARVDEFIEVVKKYAQAYRTNNVIITMGGDFHYVVASAW---FKNIDKLIKY 222
+ + NV AR D ++ KK A+ YRTN ++I +G DF + + W N ++L ++
Sbjct: 304 RTISDQNVAARSDLLVDQWKKKAELYRTNVLLIPLGDDFRFKQNTEWDVQRVNYERLFEH 363
Query: 223 VNAKLNSDVHVLYSTPACYLQALNKENITWPSK---MDDDFFPFGSDEHSYWTGYFTSRP 279
+N++ + +V + T Y A+++ ++ + DFF + +YW+GY+TSRP
Sbjct: 364 INSQAHFNVQAQFGTLQEYFDAVHQAERAGQAEFPTLSGDFFTYADRSDNYWSGYYTSRP 423
Query: 280 SFKYFVYQTNVALQMTKQLKTSLPNDTLAE-EQFLIQ--RAMGIAQHHDAVSGTERQHVT 336
K ++ + L D +A E+ L Q R + + QHHD ++GT + HV
Sbjct: 424 YHKRMDRVLMHYVRAAEMLSAWHSWDGMARIEERLEQARRELSLFQHHDGITGTAKTHVV 483
Query: 337 NDYSLYLYEGIQAAMKIINVAYRHLL 362
DY + E ++A ++ + LL
Sbjct: 484 VDYEQRMQEALKACQMVMQQSVYRLL 509
>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 = 154 bits (389), Expect = 9e-38, Method: Compositional matrix adjust.
Identities = 108/386 (27%), Positives = 183/386 (47%), Gaps = 26/386 (6%)
Query: 1 FVYVETSFFWRWWEEQNEQVRASVKELVDQGRLEFLLGGWCMSDEATPHYSSLIDQMTLG 60
F++ E S+F R++ + E + +K +V G+LEF+ GGW M DEA H+ +++ Q+T G
Sbjct: 126 FIWAEISYFARFYHDLGENKKLQMKSIVKNGQLEFVTGGWVMPDEANSHWRNVLLQLTEG 185
Query: 61 LKYLNDTFGECGQPRVAWQIDPFGHSAEVALEFADMGFDGVFFGRIDHEDIALRKKNKTM 120
+L P +W IDPFGHS + GF + R + + + +
Sbjct: 186 QTWLKQFMNVT--PTASWAIDPFGHSPTMPYILQKSGFKNMLIQRTHYSVKKELAQQRQL 243
Query: 121 EMVWRPD-DTLGPEGDFFTGVMYNIYD------PPPGFC--FD-----TYCEDEPIMDNP 166
E +WR D G F + + YD P P C FD ++ P P
Sbjct: 244 EFLWRQIWDNKGDTALFTHMMPFYSYDIPHTCGPDPKVCCQFDFKRMGSFGLSCPWKVPP 303
Query: 167 K-LHGVNVNARVDEFIEVVKKYAQAYRTNNVIITMGGDFHYVVASAW---FKNIDKLIKY 222
+ + NV AR D ++ KK A+ YRTN ++I +G DF + + W N ++L ++
Sbjct: 304 RTISDQNVAARSDLLVDQWKKKAELYRTNVLLIPLGDDFRFKQNTEWDVQRVNYERLFEH 363
Query: 223 VNAKLNSDVHVLYSTPACYLQALNKENITWPSK---MDDDFFPFGSDEHSYWTGYFTSRP 279
+N++ + +V + T Y A+++ ++ + DFF + +YW+GY+TSRP
Sbjct: 364 INSQAHFNVQAQFGTLQEYFDAVHQAERAGQAEFPTLSGDFFTYADRSDNYWSGYYTSRP 423
Query: 280 SFKYFVYQTNVALQMTKQLKTSLPNDTLAE-EQFLIQ--RAMGIAQHHDAVSGTERQHVT 336
K ++ + L D +A E+ L Q R + + QHHD ++GT + HV
Sbjct: 424 YHKRMDRVLMHYVRAAEMLSAWHSWDGMARIEERLEQARRELSLFQHHDGITGTAKTHVV 483
Query: 337 NDYSLYLYEGIQAAMKIINVAYRHLL 362
DY + E ++A ++ + LL
Sbjct: 484 VDYEQRMQEALKACQMVMQQSVYRLL 509
>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 = 152 bits (384), Expect = 3e-37, Method: Compositional matrix adjust.
Identities = 107/386 (27%), Positives = 183/386 (47%), Gaps = 26/386 (6%)
Query: 1 FVYVETSFFWRWWEEQNEQVRASVKELVDQGRLEFLLGGWCMSDEATPHYSSLIDQMTLG 60
F++ E S+F R++ + E + +K +V G+LEF+ GGW M DEA H+ +++ Q+T G
Sbjct: 126 FIWAEISYFARFYHDLGENKKLQMKSIVKNGQLEFVTGGWVMPDEANSHWRNVLLQLTEG 185
Query: 61 LKYLNDTFGECGQPRVAWQIDPFGHSAEVALEFADMGFDGVFFGRIDHEDIALRKKNKTM 120
+L P +W IDPFGHS + GF + R + + + +
Sbjct: 186 QTWLKQFMNVT--PTASWAIDPFGHSPTMPYILQKSGFKNMLIQRTHYSVKKELAQQRQL 243
Query: 121 EMVWRPD-DTLGPEGDFFTGVMYNIYD------PPPGFC--FD-----TYCEDEPIMDNP 166
E +WR D G F + + YD P P C FD ++ P P
Sbjct: 244 EFLWRQIWDNKGDTALFTHMMPFYSYDIPHTCGPDPKVCCQFDFKRMGSFGLSCPWKVPP 303
Query: 167 K-LHGVNVNARVDEFIEVVKKYAQAYRTNNVIITMGGDFHYVVASAW---FKNIDKLIKY 222
+ + NV AR D ++ KK A+ YRTN ++I +G +F + + W N ++L ++
Sbjct: 304 RTISDQNVAARSDLLVDQWKKKAELYRTNVLLIPLGDNFRFKQNTEWDVQRVNYERLFEH 363
Query: 223 VNAKLNSDVHVLYSTPACYLQALNKENITWPSK---MDDDFFPFGSDEHSYWTGYFTSRP 279
+N++ + +V + T Y A+++ ++ + DFF + +YW+GY+TSRP
Sbjct: 364 INSQAHFNVQAQFGTLQEYFDAVHQAERAGQAEFPTLSGDFFTYADRSDNYWSGYYTSRP 423
Query: 280 SFKYFVYQTNVALQMTKQLKTSLPNDTLAE-EQFLIQ--RAMGIAQHHDAVSGTERQHVT 336
K ++ + L D +A E+ L Q R + + QHHD ++GT + HV
Sbjct: 424 YHKRMDRVLMHYVRAAEMLSAWHSWDGMARIEERLEQARRELSLFQHHDGITGTAKTHVV 483
Query: 337 NDYSLYLYEGIQAAMKIINVAYRHLL 362
DY + E ++A ++ + LL
Sbjct: 484 VDYEQRMQEALKACQMVMQQSVYRLL 509
>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 = 151 bits (382), Expect = 6e-37, Method: Compositional matrix adjust.
Identities = 107/386 (27%), Positives = 182/386 (47%), Gaps = 26/386 (6%)
Query: 1 FVYVETSFFWRWWEEQNEQVRASVKELVDQGRLEFLLGGWCMSDEATPHYSSLIDQMTLG 60
F++ E S+F R++ + E + +K +V G+LEF+ GGW M DEA H+ +++ Q+T G
Sbjct: 126 FIWAEISYFARFYHDLGENKKLQMKSIVKNGQLEFVTGGWVMPDEANSHWRNVLLQLTEG 185
Query: 61 LKYLNDTFGECGQPRVAWQIDPFGHSAEVALEFADMGFDGVFFGRIDHEDIALRKKNKTM 120
+L P +W I PFGHS + GF + R + + + +
Sbjct: 186 QTWLKQFMNVT--PTASWAIAPFGHSPTMPYILQKSGFKNMLIQRTHYSVKKELAQQRQL 243
Query: 121 EMVWRPD-DTLGPEGDFFTGVMYNIYD------PPPGFC--FD-----TYCEDEPIMDNP 166
E +WR D G F + + YD P P C FD ++ P P
Sbjct: 244 EFLWRQIWDNKGDTALFTHMMPFYSYDIPHTCGPDPKVCCQFDFKRMGSFGLSCPWKVPP 303
Query: 167 K-LHGVNVNARVDEFIEVVKKYAQAYRTNNVIITMGGDFHYVVASAW---FKNIDKLIKY 222
+ + NV AR D ++ KK A+ YRTN ++I +G DF + + W N ++L ++
Sbjct: 304 RTISDQNVAARSDLLVDQWKKKAELYRTNVLLIPLGDDFRFKQNTEWDVQRVNYERLFEH 363
Query: 223 VNAKLNSDVHVLYSTPACYLQALNKENITWPSK---MDDDFFPFGSDEHSYWTGYFTSRP 279
+N++ + +V + T Y A+++ ++ + DFF + +YW+GY+TSRP
Sbjct: 364 INSQAHFNVQAQFGTLQEYFDAVHQAERAGQAEFPTLSGDFFTYADRSDNYWSGYYTSRP 423
Query: 280 SFKYFVYQTNVALQMTKQLKTSLPNDTLAE-EQFLIQ--RAMGIAQHHDAVSGTERQHVT 336
K ++ + L D +A E+ L Q R + + QHHD ++GT + HV
Sbjct: 424 YHKRMDRVLMHYVRAAEMLSAWHSWDGMARIEERLEQARRELSLFQHHDGITGTAKTHVV 483
Query: 337 NDYSLYLYEGIQAAMKIINVAYRHLL 362
DY + E ++A ++ + LL
Sbjct: 484 VDYEQRMQEALKACQMVMQQSVYRLL 509
>pdb|1HTY|A Chain A, Golgi Alpha-Mannosidase Ii
Length = 1015
Score = 147 bits (372), Expect = 8e-36, Method: Compositional matrix adjust.
Identities = 107/386 (27%), Positives = 177/386 (45%), Gaps = 26/386 (6%)
Query: 1 FVYVETSFFWRWWEEQNEQVRASVKELVDQGRLEFLLGGWCMSDEATPHYSSLIDQMTLG 60
F++ E S+F R++ + E + K +V G+LEF+ GGW DEA H+ +++ Q+T G
Sbjct: 96 FIWAEISYFARFYHDLGENKKLQXKSIVKNGQLEFVTGGWVXPDEANSHWRNVLLQLTEG 155
Query: 61 LKYLNDTFGECGQPRVAWQIDPFGHSAEVALEFADMGFDGVFFGRIDHEDIALRKKNKTM 120
+L P +W IDPFGHS GF + R + + + +
Sbjct: 156 QTWLKQFXNVT--PTASWAIDPFGHSPTXPYILQKSGFKNMLIQRTHYSVKKELAQQRQL 213
Query: 121 EMVWRPD-DTLGPEGDFFTGVMYNIYD------PPPGFC--FD-----TYCEDEPIMDNP 166
E +WR D G F + YD P P C FD ++ P P
Sbjct: 214 EFLWRQIWDNKGDTALFTHXXPFYSYDIPHTCGPDPKVCCQFDFKRXGSFGLSCPWKVPP 273
Query: 167 K-LHGVNVNARVDEFIEVVKKYAQAYRTNNVIITMGGDFHYVVASAW---FKNIDKLIKY 222
+ + NV AR D ++ KK A+ YRTN ++I +G DF + + W N ++L ++
Sbjct: 274 RTISDQNVAARSDLLVDQWKKKAELYRTNVLLIPLGDDFRFKQNTEWDVQRVNYERLFEH 333
Query: 223 VNAKLNSDVHVLYSTPACYLQALNKENITWPSK---MDDDFFPFGSDEHSYWTGYFTSRP 279
+N++ + +V + T Y A+++ ++ + DFF + +YW+GY+TSRP
Sbjct: 334 INSQAHFNVQAQFGTLQEYFDAVHQAERAGQAEFPTLSGDFFTYADRSDNYWSGYYTSRP 393
Query: 280 SFKYFVYQTNVALQMTKQLKTSLPNDTLAE-EQFLIQ--RAMGIAQHHDAVSGTERQHVT 336
K ++ + L D +A E+ L Q R + + QHHD ++GT + HV
Sbjct: 394 YHKRXDRVLXHYVRAAEXLSAWHSWDGMARIEERLEQARRELSLFQHHDGITGTAKTHVV 453
Query: 337 NDYSLYLYEGIQAAMKIINVAYRHLL 362
DY E ++A + + LL
Sbjct: 454 VDYEQRXQEALKACQXVXQQSVYRLL 479
>pdb|1O7D|B Chain B, The Structure Of The Bovine Lysosomal A-Mannosidase
Suggests A Novel Mechanism For Low Ph Activation
Length = 84
Score = 73.2 bits (178), Expect = 2e-13, Method: Compositional matrix adjust.
Identities = 35/70 (50%), Positives = 47/70 (67%), Gaps = 1/70 (1%)
Query: 231 VHVLYSTPACYLQALNKENITWPSKMDDDFFPFGSDEHSYWTGYFTSRPSFKYFVYQTNV 290
V+VLYSTPACYL LNK N++W K DDFFP+ + +WTGYF+SRP+ K + +
Sbjct: 3 VNVLYSTPACYLWELNKANLSWSVK-KDDFFPYADGPYMFWTGYFSSRPALKRYERLSYN 61
Query: 291 ALQMTKQLKT 300
LQ+ QL+
Sbjct: 62 FLQVCNQLEA 71
>pdb|1O7D|C Chain C, The Structure Of The Bovine Lysosomal A-Mannosidase
Suggests A Novel Mechanism For Low Ph Activation
Length = 159
Score = 56.6 bits (135), Expect = 2e-08, Method: Compositional matrix adjust.
Identities = 32/70 (45%), Positives = 41/70 (58%), Gaps = 3/70 (4%)
Query: 314 IQRAMGIAQHHDAVSGTERQHVTNDYSLYLYEGIQAAMKIINVAYRHLLGDYLPEQQP-C 372
+ AM + QHHDAVSGT RQHV NDY+ L EG + +++ A HL G L E C
Sbjct: 6 LNEAMAVLQHHDAVSGTSRQHVANDYARQLSEGWRPCEVLMSNALAHLSG--LKEDFAFC 63
Query: 373 LLMNVSQCEL 382
+N+S C L
Sbjct: 64 RKLNISICPL 73
>pdb|1YB4|A Chain A, Crystal Structure Of The Tartronic Semialdehyde Reductase
From Salmonella Typhimurium Lt2
pdb|1YB4|B Chain B, Crystal Structure Of The Tartronic Semialdehyde Reductase
From Salmonella Typhimurium Lt2
Length = 295
Score = 30.8 bits (68), Expect = 1.5, Method: Compositional matrix adjust.
Identities = 19/49 (38%), Positives = 25/49 (51%), Gaps = 2/49 (4%)
Query: 276 TSRPSFKYFVYQT--NVALQMTKQLKTSLPNDTLAEEQFLIQRAMGIAQ 322
T P FK ++Q N+ALQ K L +LPN +E F A G +Q
Sbjct: 228 TFEPGFKIALHQKDLNLALQSAKALALNLPNTATCQELFNTCAANGGSQ 276
>pdb|1WS6|A Chain A, The Structure Of Thermus Thermphillus Hb8 Hypothetical
Protein Ttha0928
Length = 171
Score = 29.3 bits (64), Expect = 3.9, Method: Compositional matrix adjust.
Identities = 17/44 (38%), Positives = 23/44 (52%), Gaps = 1/44 (2%)
Query: 74 PRVAWQIDPFGHSAEVALEFADMGFDGVFFGRIDHEDIALRKKN 117
PR +DPF S V LE A G++ V + D E + L K+N
Sbjct: 40 PRRGRFLDPFAGSGAVGLEAASEGWEAVLVEK-DPEAVRLLKEN 82
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
0.322 0.138 0.436
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 13,053,195
Number of Sequences: 62578
Number of extensions: 583738
Number of successful extensions: 1339
Number of sequences better than 100.0: 23
Number of HSP's better than 100.0 without gapping: 21
Number of HSP's successfully gapped in prelim test: 2
Number of HSP's that attempted gapping in prelim test: 1288
Number of HSP's gapped (non-prelim): 23
length of query: 400
length of database: 14,973,337
effective HSP length: 101
effective length of query: 299
effective length of database: 8,652,959
effective search space: 2587234741
effective search space used: 2587234741
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 52 (24.6 bits)