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= 020229
(329 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|1U1H|A Chain A, A. Thaliana Cobalamine Independent Methionine Synthase
pdb|1U1J|A Chain A, A. Thaliana Cobalamine Independent Methionine Synthase
pdb|1U1U|A Chain A, A. Thaliana Cobalamine Independent Methionine Synthase
pdb|1U22|A Chain A, A. Thaliana Cobalamine Independent Methionine Synthase
Length = 765
Score = 359 bits (922), Expect = e-100, Method: Compositional matrix adjust.
Identities = 172/225 (76%), Positives = 188/225 (83%)
Query: 2 ASHIVGYPRMGPKRELKFALESFWDGKSSAEDLQKVSADLRSSIWKQMSEAGIKYIPSNT 61
ASHIVGYPR GPKRELKFALESFWDGKS+AEDLQKVSADLRSSIWKQ S AG K+IPSNT
Sbjct: 2 ASHIVGYPRXGPKRELKFALESFWDGKSTAEDLQKVSADLRSSIWKQXSAAGTKFIPSNT 61
Query: 62 FSYYDQVLDTTAMLGAVPPRYNWNGGEIGFDVYFSMARGNASVPAMEMTKWFDTNYHFIV 121
F++YDQVLDTTA LGAVPPRY + GGEIG DVYFS ARGNASVPA E TKWFDTNYH+IV
Sbjct: 62 FAHYDQVLDTTAXLGAVPPRYGYTGGEIGLDVYFSXARGNASVPAXEXTKWFDTNYHYIV 121
Query: 122 PELGPDVKFSYASHKAVTEYKEAKGLGVETVPVLIGPVSYLLLSKPAKGVAKTFXXXXXX 181
PELGP+V FSYASHKAV EYKEAK LGV+TVPVL+GPVSYLLLSK AKGV K+F
Sbjct: 122 PELGPEVNFSYASHKAVNEYKEAKALGVDTVPVLVGPVSYLLLSKAAKGVDKSFELLSLL 181
Query: 182 XXXXXXXXEVISELKAAGASWIQFDEPLLVMDLDSHKLHAFIHSF 226
EVI+ELKAAGA+WIQ DEP+LV DL+ KL AF ++
Sbjct: 182 PKILPIYKEVITELKAAGATWIQLDEPVLVXDLEGQKLQAFTGAY 226
Score = 198 bits (503), Expect = 4e-51, Method: Compositional matrix adjust.
Identities = 108/142 (76%), Positives = 116/142 (81%), Gaps = 6/142 (4%)
Query: 192 ISELKAAGASWIQFDEPLLVMDLDSHKL-HAF-----IHSFRITNCGVQDTTQIHTHMCY 245
+ +L+ G IQ DE L L K HAF +HSFRITNCGVQD+TQIHTH CY
Sbjct: 591 VEDLEKGGIGVIQIDEAALREGLPLRKSEHAFYLDWAVHSFRITNCGVQDSTQIHTHXCY 650
Query: 246 SNFNDIIHSIIDMDADVITIENSRSDEKLLSVFREGVKYGAGIGPGVYDIHSPRIPSTEE 305
S+FNDIIHSIID DADVITIENSRSDEKLLSVFREGVKYGAGIGPGVYDIHSPRIPS+EE
Sbjct: 651 SHFNDIIHSIIDXDADVITIENSRSDEKLLSVFREGVKYGAGIGPGVYDIHSPRIPSSEE 710
Query: 306 IADRINKMLAVLETNILWVNPD 327
IADR+NK LAVLE NILWVNPD
Sbjct: 711 IADRVNKXLAVLEQNILWVNPD 732
>pdb|3PPH|A Chain A, Crystal Structure Of The Candida Albicans Methionine
Synthase By Surface Entropy Reduction, Threonine Variant
pdb|3PPH|B Chain B, Crystal Structure Of The Candida Albicans Methionine
Synthase By Surface Entropy Reduction, Threonine Variant
Length = 789
Score = 169 bits (429), Expect = 2e-42, Method: Compositional matrix adjust.
Identities = 94/228 (41%), Positives = 131/228 (57%), Gaps = 17/228 (7%)
Query: 1 MASHIVGYPRMGPKRELKFALESFWDGKSSAEDLQKVSADLRSSIWKQMSEAGIKYIPSN 60
+ S ++G+PR+G +RELK E++W GK++ E+L +LR WK +AG+ IPSN
Sbjct: 24 VQSSVLGFPRIGGQRELKKITEAYWSGKATVEELLAKGKELREHNWKLQQKAGVDIIPSN 83
Query: 61 TFSYYDQVLDTTAMLGAVPPRY-NWNGGEIGFDVYFSMARG----------NASVPAMEM 109
FSYYDQVLD + + A+P RY ++ I DV F+M RG V A+EM
Sbjct: 84 DFSYYDQVLDLSLLFNAIPERYTKFDLAPI--DVLFAMGRGLQTTATTTQAAVDVTALEM 141
Query: 110 TKWFDTNYHFIVPELGPDVKF---SYASHKAVTEYKEAKGLGVETVPVLIGPVSYLLLSK 166
KWFD+NYH++ P +F + A K V E+ EAK LGV+T PV++GPVSYL L K
Sbjct: 142 VKWFDSNYHYVRPTFSHSTEFKLNTAAGIKPVDEFNEAKALGVQTRPVILGPVSYLYLGK 201
Query: 167 PAKGVAKTFXXXXXXXXXXXXXXEVISELKAAGASWIQFDEPLLVMDL 214
K + E++ +LK AGA +Q DEP+LV+DL
Sbjct: 202 ADKD-SLDLEPISLLPKILPVYKELLQKLKEAGAEQVQIDEPVLVLDL 248
Score = 105 bits (262), Expect = 4e-23, Method: Compositional matrix adjust.
Identities = 65/181 (35%), Positives = 98/181 (54%), Gaps = 15/181 (8%)
Query: 154 VLIGPVSYLLLSKPAKGVAKTFXXXXXXXXXXXXXXEVISELKAAGASWIQFDEPLLVMD 213
+L GPV+ L S P V+ + +++L+ AG + IQ DEP +
Sbjct: 588 MLTGPVTILRWSFPRDDVSGKIQALQLGLALR----DEVNDLEGAGITVIQVDEPAIREG 643
Query: 214 L-------DSHKLHAFIHSFRITNCGVQDTTQIHTHMCYSNFNDIIHSIIDMDADVITIE 266
L S L+ SFR+ GV+++TQIH+H CYS+ + + I +DADV++IE
Sbjct: 644 LPLRAGKERSDYLNWAAQSFRVATSGVENSTQIHSHFCYSDLDP--NHIKALDADVVSIE 701
Query: 267 NSRSDEKLLSVFREGVKYGAGIGPGVYDIHSPRIPSTEEIADRINKMLAVLETNILWVNP 326
S+ D+ + +E +Y IG G++DIHSPRIPS +E RI ++L V + WVNP
Sbjct: 702 FSKKDDP--NYIQEFSEYPNHIGLGLFDIHSPRIPSKQEFVSRIEEILKVYPASKFWVNP 759
Query: 327 D 327
D
Sbjct: 760 D 760
>pdb|3PPF|A Chain A, Crystal Structure Of The Candida Albicans Methionine
Synthase By Surface Entropy Reduction, Alanine Variant
Without Zinc
pdb|3PPG|A Chain A, Crystal Structure Of The Candida Albicans Methionine
Synthase By Surface Entropy Reduction, Alanine Variant
With Zinc
Length = 789
Score = 169 bits (429), Expect = 2e-42, Method: Compositional matrix adjust.
Identities = 94/228 (41%), Positives = 131/228 (57%), Gaps = 17/228 (7%)
Query: 1 MASHIVGYPRMGPKRELKFALESFWDGKSSAEDLQKVSADLRSSIWKQMSEAGIKYIPSN 60
+ S ++G+PR+G +RELK E++W GK++ E+L +LR WK +AG+ IPSN
Sbjct: 24 VQSSVLGFPRIGGQRELKKITEAYWSGKATVEELLAKGKELREHNWKLQQKAGVDIIPSN 83
Query: 61 TFSYYDQVLDTTAMLGAVPPRY-NWNGGEIGFDVYFSMARG----------NASVPAMEM 109
FSYYDQVLD + + A+P RY ++ I DV F+M RG V A+EM
Sbjct: 84 DFSYYDQVLDLSLLFNAIPERYTKFDLAPI--DVLFAMGRGLQAAATATQAAVDVTALEM 141
Query: 110 TKWFDTNYHFIVPELGPDVKF---SYASHKAVTEYKEAKGLGVETVPVLIGPVSYLLLSK 166
KWFD+NYH++ P +F + A K V E+ EAK LGV+T PV++GPVSYL L K
Sbjct: 142 VKWFDSNYHYVRPTFSHSTEFKLNTAAGIKPVDEFNEAKALGVQTRPVILGPVSYLYLGK 201
Query: 167 PAKGVAKTFXXXXXXXXXXXXXXEVISELKAAGASWIQFDEPLLVMDL 214
K + E++ +LK AGA +Q DEP+LV+DL
Sbjct: 202 ADKD-SLDLEPISLLPKILPVYKELLQKLKEAGAEQVQIDEPVLVLDL 248
Score = 105 bits (262), Expect = 4e-23, Method: Compositional matrix adjust.
Identities = 65/181 (35%), Positives = 98/181 (54%), Gaps = 15/181 (8%)
Query: 154 VLIGPVSYLLLSKPAKGVAKTFXXXXXXXXXXXXXXEVISELKAAGASWIQFDEPLLVMD 213
+L GPV+ L S P V+ + +++L+ AG + IQ DEP +
Sbjct: 588 MLTGPVTILRWSFPRDDVSGKIQALQLGLALR----DEVNDLEGAGITVIQVDEPAIREG 643
Query: 214 L-------DSHKLHAFIHSFRITNCGVQDTTQIHTHMCYSNFNDIIHSIIDMDADVITIE 266
L S L+ SFR+ GV+++TQIH+H CYS+ + + I +DADV++IE
Sbjct: 644 LPLRAGKERSDYLNWAAQSFRVATSGVENSTQIHSHFCYSDLDP--NHIKALDADVVSIE 701
Query: 267 NSRSDEKLLSVFREGVKYGAGIGPGVYDIHSPRIPSTEEIADRINKMLAVLETNILWVNP 326
S+ D+ + +E +Y IG G++DIHSPRIPS +E RI ++L V + WVNP
Sbjct: 702 FSKKDDP--NYIQEFSEYPNHIGLGLFDIHSPRIPSKQEFVSRIEEILKVYPASKFWVNP 759
Query: 327 D 327
D
Sbjct: 760 D 760
>pdb|3PPC|A Chain A, Crystal Structure Of The Candida Albicans Methionine
Synthase By Surface Entropy Reduction, Tyrosine Variant
With Zinc
pdb|3PPC|B Chain B, Crystal Structure Of The Candida Albicans Methionine
Synthase By Surface Entropy Reduction, Tyrosine Variant
With Zinc
Length = 789
Score = 169 bits (428), Expect = 2e-42, Method: Compositional matrix adjust.
Identities = 94/228 (41%), Positives = 131/228 (57%), Gaps = 17/228 (7%)
Query: 1 MASHIVGYPRMGPKRELKFALESFWDGKSSAEDLQKVSADLRSSIWKQMSEAGIKYIPSN 60
+ S ++G+PR+G +RELK E++W GK++ E+L +LR WK +AG+ IPSN
Sbjct: 24 VQSSVLGFPRIGGQRELKKITEAYWSGKATVEELLAKGKELREHNWKLQQKAGVDIIPSN 83
Query: 61 TFSYYDQVLDTTAMLGAVPPRY-NWNGGEIGFDVYFSMARG----------NASVPAMEM 109
FSYYDQVLD + + A+P RY ++ I DV F+M RG V A+EM
Sbjct: 84 DFSYYDQVLDLSLLFNAIPERYTKFDLAPI--DVLFAMGRGLQYYATYTQAAVDVTALEM 141
Query: 110 TKWFDTNYHFIVPELGPDVKF---SYASHKAVTEYKEAKGLGVETVPVLIGPVSYLLLSK 166
KWFD+NYH++ P +F + A K V E+ EAK LGV+T PV++GPVSYL L K
Sbjct: 142 VKWFDSNYHYVRPTFSHSTEFKLNTAAGIKPVDEFNEAKALGVQTRPVILGPVSYLYLGK 201
Query: 167 PAKGVAKTFXXXXXXXXXXXXXXEVISELKAAGASWIQFDEPLLVMDL 214
K + E++ +LK AGA +Q DEP+LV+DL
Sbjct: 202 ADKD-SLDLEPISLLPKILPVYKELLQKLKEAGAEQVQIDEPVLVLDL 248
Score = 105 bits (262), Expect = 3e-23, Method: Compositional matrix adjust.
Identities = 65/181 (35%), Positives = 98/181 (54%), Gaps = 15/181 (8%)
Query: 154 VLIGPVSYLLLSKPAKGVAKTFXXXXXXXXXXXXXXEVISELKAAGASWIQFDEPLLVMD 213
+L GPV+ L S P V+ + +++L+ AG + IQ DEP +
Sbjct: 588 MLTGPVTILRWSFPRDDVSGKIQALQLGLALR----DEVNDLEGAGITVIQVDEPAIREG 643
Query: 214 L-------DSHKLHAFIHSFRITNCGVQDTTQIHTHMCYSNFNDIIHSIIDMDADVITIE 266
L S L+ SFR+ GV+++TQIH+H CYS+ + + I +DADV++IE
Sbjct: 644 LPLRAGKERSDYLNWAAQSFRVATSGVENSTQIHSHFCYSDLDP--NHIKALDADVVSIE 701
Query: 267 NSRSDEKLLSVFREGVKYGAGIGPGVYDIHSPRIPSTEEIADRINKMLAVLETNILWVNP 326
S+ D+ + +E +Y IG G++DIHSPRIPS +E RI ++L V + WVNP
Sbjct: 702 FSKKDDP--NYIQEFSEYPNHIGLGLFDIHSPRIPSKQEFVSRIEEILKVYPASKFWVNP 759
Query: 327 D 327
D
Sbjct: 760 D 760
>pdb|1T7L|A Chain A, Crystal Structure Of Cobalamin-Independent Methionine
Synthase From T. Maritima
pdb|1T7L|B Chain B, Crystal Structure Of Cobalamin-Independent Methionine
Synthase From T. Maritima
pdb|3BQ5|A Chain A, Crystal Structure Of T. Maritima Cobalamin-Independent
Methionine Synthase Complexed With Zn2+ And Homocysteine
(Monoclinic)
pdb|3BQ5|B Chain B, Crystal Structure Of T. Maritima Cobalamin-Independent
Methionine Synthase Complexed With Zn2+ And Homocysteine
(Monoclinic)
pdb|3BQ6|A Chain A, Crystal Structure Of T. Maritima Cobalamin-Independent
Methionine Synthase Complexed With Zn2+ (Monoclinic)
pdb|3BQ6|B Chain B, Crystal Structure Of T. Maritima Cobalamin-Independent
Methionine Synthase Complexed With Zn2+ (Monoclinic)
Length = 766
Score = 137 bits (344), Expect = 1e-32, Method: Compositional matrix adjust.
Identities = 82/226 (36%), Positives = 120/226 (53%), Gaps = 9/226 (3%)
Query: 3 SHIVGYPRMGPKRELKFALESFWDGKSSAEDLQKVSADLRSSIWKQMSEAGIKYIPSNTF 62
++ G+P++G KRE K ALE FW GK + E ++ LR + + + + IPSN
Sbjct: 35 AYAFGFPKIGEKREFKKALEDFWKGKITEEQFEEEMNKLRMYMVENYRK-NVDVIPSNEL 93
Query: 63 SYYDQVLDTTAMLGAVPPRYNWNGGEIGFDVYFSMARGNASVPAMEMTKWFDTNYHFIVP 122
SYYD VLDT M+GAVP R+ G G YF MARG A+EMTK+F+TNYH++VP
Sbjct: 94 SYYDFVLDTAVMVGAVPERF---GEYRGLSTYFDMARGGK---ALEMTKFFNTNYHYLVP 147
Query: 123 ELGPDVKFSYASHKAVTEYKEAKGLGVETVPVLIGPVSYLLLSKP-AKGVAKTFXXXXXX 181
E+ + +F +K + +Y K G+ET P +IGP ++L LSK + + +
Sbjct: 148 EIETE-EFYLLENKPLEDYLFFKSKGIETAPWVIGPFTFLYLSKRNGEWIRRPNQMEKLL 206
Query: 182 XXXXXXXXEVISELKAAGASWIQFDEPLLVMDLDSHKLHAFIHSFR 227
EV +L G I +EP V DL+ ++ +R
Sbjct: 207 ESLVSVYKEVFEKLVENGCKEILVNEPAFVCDLEKAHWDLILNVYR 252
Score = 102 bits (253), Expect = 4e-22, Method: Compositional matrix adjust.
Identities = 63/186 (33%), Positives = 93/186 (50%), Gaps = 16/186 (8%)
Query: 148 GVETVPVLIGPVSYLLLSKPAKGVAKTFXXXXXXXXXXXXXXEVISELKAAGASWIQFDE 207
G+ T PV I SY P + +A E + +L+ AG +Q DE
Sbjct: 560 GMLTGPVTIMSWSYYREDIPEREIA---------YQIALAINEEVKDLEEAGIKIVQIDE 610
Query: 208 PLLVMDLDSHK------LHAFIHSFRITNCGVQDTTQIHTHMCYSNFNDIIHSIIDMDAD 261
P K I++F + + TQIH HMCYS+FN+II I ++ D
Sbjct: 611 PAFREKAPIKKSKWPEYFEWAINAFNLA-ANARPETQIHAHMCYSDFNEIIEYIHQLEFD 669
Query: 262 VITIENSRSDEKLLSVFREGVKYGAGIGPGVYDIHSPRIPSTEEIADRINKMLAVLETNI 321
VI+IE SRS +++S F + IG GV+DIHSP +PS E+ + + ++L VL +
Sbjct: 670 VISIEASRSKGEIISAFENFKGWIKQIGVGVWDIHSPAVPSINEMREIVERVLRVLPKEL 729
Query: 322 LWVNPD 327
+W+NPD
Sbjct: 730 IWINPD 735
Score = 29.3 bits (64), Expect = 3.3, Method: Compositional matrix adjust.
Identities = 15/44 (34%), Positives = 24/44 (54%), Gaps = 5/44 (11%)
Query: 33 DLQKVSADLRSSIWKQMSEAGIKYIPSNTFSYYDQVLDTTAMLG 76
DL+K DL ++++++SE P F+YYD V D A +
Sbjct: 238 DLEKAHWDLILNVYRELSE-----FPLTVFTYYDSVSDYEACVS 276
>pdb|1XR2|A Chain A, Crystal Structure Of Oxidized T. Maritima Cobalamin-
Independent Methionine Synthase Complexed With
Methyltetrahydrofolate
pdb|1XR2|B Chain B, Crystal Structure Of Oxidized T. Maritima Cobalamin-
Independent Methionine Synthase Complexed With
Methyltetrahydrofolate
Length = 766
Score = 136 bits (343), Expect = 1e-32, Method: Compositional matrix adjust.
Identities = 82/226 (36%), Positives = 120/226 (53%), Gaps = 9/226 (3%)
Query: 3 SHIVGYPRMGPKRELKFALESFWDGKSSAEDLQKVSADLRSSIWKQMSEAGIKYIPSNTF 62
++ G+P++G KRE K ALE FW GK + E ++ LR + + + + IPSN
Sbjct: 35 AYAFGFPKIGEKREFKKALEDFWKGKITEEQFEEEMNKLRMYMVENYRK-NVDVIPSNEL 93
Query: 63 SYYDQVLDTTAMLGAVPPRYNWNGGEIGFDVYFSMARGNASVPAMEMTKWFDTNYHFIVP 122
SYYD VLDT M+GAVP R+ G G YF MARG A+EMTK+F+TNYH++VP
Sbjct: 94 SYYDFVLDTAVMVGAVPERF---GEYRGLSTYFDMARGGK---ALEMTKFFNTNYHYLVP 147
Query: 123 ELGPDVKFSYASHKAVTEYKEAKGLGVETVPVLIGPVSYLLLSKP-AKGVAKTFXXXXXX 181
E+ + +F +K + +Y K G+ET P +IGP ++L LSK + + +
Sbjct: 148 EIETE-EFYLLENKPLEDYLFFKSKGIETAPWVIGPFTFLYLSKRNGEWIRRPNQMEKLL 206
Query: 182 XXXXXXXXEVISELKAAGASWIQFDEPLLVMDLDSHKLHAFIHSFR 227
EV +L G I +EP V DL+ ++ +R
Sbjct: 207 ESLVSVYKEVFEKLVENGCKEILVNEPAFVCDLEKAHWDLILNVYR 252
Score = 102 bits (253), Expect = 4e-22, Method: Compositional matrix adjust.
Identities = 63/186 (33%), Positives = 93/186 (50%), Gaps = 16/186 (8%)
Query: 148 GVETVPVLIGPVSYLLLSKPAKGVAKTFXXXXXXXXXXXXXXEVISELKAAGASWIQFDE 207
G+ T PV I SY P + +A E + +L+ AG +Q DE
Sbjct: 560 GMLTGPVTIMSWSYYREDIPEREIA---------YQIALAINEEVKDLEEAGIKIVQIDE 610
Query: 208 PLLVMDLDSHK------LHAFIHSFRITNCGVQDTTQIHTHMCYSNFNDIIHSIIDMDAD 261
P K I++F + + TQIH HMCYS+FN+II I ++ D
Sbjct: 611 PAFREKAPIKKSKWPEYFEWAINAFNLA-ANARPETQIHAHMCYSDFNEIIEYIHQLEFD 669
Query: 262 VITIENSRSDEKLLSVFREGVKYGAGIGPGVYDIHSPRIPSTEEIADRINKMLAVLETNI 321
VI+IE SRS +++S F + IG GV+DIHSP +PS E+ + + ++L VL +
Sbjct: 670 VISIEASRSKGEIISAFENFKGWIKQIGVGVWDIHSPAVPSINEMREIVERVLRVLPKEL 729
Query: 322 LWVNPD 327
+W+NPD
Sbjct: 730 IWINPD 735
Score = 29.3 bits (64), Expect = 3.3, Method: Compositional matrix adjust.
Identities = 15/44 (34%), Positives = 24/44 (54%), Gaps = 5/44 (11%)
Query: 33 DLQKVSADLRSSIWKQMSEAGIKYIPSNTFSYYDQVLDTTAMLG 76
DL+K DL ++++++SE P F+YYD V D A +
Sbjct: 238 DLEKAHWDLILNVYRELSE-----FPLTVFTYYDSVSDYEACVS 276
>pdb|2NQ5|A Chain A, Crystal Structure Of Methyltransferase From Streptococcus
Mutans
Length = 755
Score = 132 bits (333), Expect = 2e-31, Method: Compositional matrix adjust.
Identities = 78/217 (35%), Positives = 113/217 (52%), Gaps = 10/217 (4%)
Query: 6 VGYPRMGPKRELKFALESFWDGKSSAEDLQKVSADLRSSIWKQMSEAGIKYIPSNTFSYY 65
+GYPR+G RE K +E++W GK S DL + +LR K+ AG+ IP FS Y
Sbjct: 9 LGYPRLGENREWKKLIEAYWAGKVSKNDLFAGAKELRLDFLKKQLNAGLDLIPVGDFSLY 68
Query: 66 DQVLDTTAMLGAVPPRYNWNGGEIGFDVYFSMARGNASVPAMEMTKWFDTNYHFIVPELG 125
D +LD + +P R+ I D+YF++ARGN A M KWF+TNYH+IVPE
Sbjct: 69 DHILDLSVQFNIIPKRFAKE--PIDIDLYFAIARGNKENVASSMKKWFNTNYHYIVPEWS 126
Query: 126 PDVKFSYASHKAVTEYKEAKG-LGVETVPVLIGPVSYLLLSKPAKGVAKTFXXXXXXXXX 184
+ +++ + Y EA+ +G + PV+ GP++Y+ LS +
Sbjct: 127 KQ-RPKLNNNRLLDLYLEAREVVGDKAKPVITGPITYVALSTGVEDFTAAV------KSL 179
Query: 185 XXXXXEVISELKAAGASWIQFDEPLLVMDLDSHKLHA 221
+V +EL AGAS+IQ DEP+ V D L A
Sbjct: 180 LPLYKQVFTELVKAGASYIQVDEPIFVTDEGKDYLQA 216
Score = 121 bits (304), Expect = 5e-28, Method: Compositional matrix adjust.
Identities = 67/142 (47%), Positives = 85/142 (59%), Gaps = 7/142 (4%)
Query: 192 ISELKAAGASWIQFDEPLLV--MDLDSHKLHAF----IHSFRITNCGVQDTTQIHTHMCY 245
I L+ AG + IQ DE L + L K A+ +H+F I V+D TQIHTHMCY
Sbjct: 576 IKLLENAGIAIIQVDEAALREGLPLRKSKQKAYLDDAVHAFHIATSSVKDETQIHTHMCY 635
Query: 246 SNFNDIIHSIIDMDADVITIENSRSDEKLLSVFREGVKYGAGIGPGVYDIHSPRIPSTEE 305
S F++II +I +DADVI+IE SRS ++ F V Y GIG GVYDIHSPR+P+ EE
Sbjct: 636 SKFDEIIDAIRALDADVISIETSRSHGDIIESFETAV-YPLGIGLGVYDIHSPRVPTKEE 694
Query: 306 IADRINKMLAVLETNILWVNPD 327
+ I + L L WVNPD
Sbjct: 695 VVANIERPLRQLSPTQFWVNPD 716
>pdb|3L7R|A Chain A, Crystal Structure Of Mete From Streptococcus Mutans
pdb|3T0C|A Chain A, Crystal Structure Of Streptococcus Mutans Mete Complexed
With Zinc
Length = 779
Score = 132 bits (332), Expect = 3e-31, Method: Compositional matrix adjust.
Identities = 78/217 (35%), Positives = 113/217 (52%), Gaps = 10/217 (4%)
Query: 6 VGYPRMGPKRELKFALESFWDGKSSAEDLQKVSADLRSSIWKQMSEAGIKYIPSNTFSYY 65
+GYPR+G RE K +E++W GK S DL + +LR K+ AG+ IP FS Y
Sbjct: 41 LGYPRLGENREWKKLIEAYWAGKVSKNDLFAGAKELRLDFLKKQLNAGLDLIPVGDFSLY 100
Query: 66 DQVLDTTAMLGAVPPRYNWNGGEIGFDVYFSMARGNASVPAMEMTKWFDTNYHFIVPELG 125
D +LD + +P R+ I D+YF++ARGN A M KWF+TNYH+IVPE
Sbjct: 101 DHILDLSVQFNIIPKRFAKE--PIDIDLYFAIARGNKENVASSMKKWFNTNYHYIVPEWS 158
Query: 126 PDVKFSYASHKAVTEYKEAKG-LGVETVPVLIGPVSYLLLSKPAKGVAKTFXXXXXXXXX 184
+ +++ + Y EA+ +G + PV+ GP++Y+ LS +
Sbjct: 159 KQ-RPKLNNNRLLDLYLEAREVVGDKAKPVITGPITYVALSTGVEDFTAAV------KSL 211
Query: 185 XXXXXEVISELKAAGASWIQFDEPLLVMDLDSHKLHA 221
+V +EL AGAS+IQ DEP+ V D L A
Sbjct: 212 LPLYKQVFTELVKAGASYIQVDEPIFVTDEGKDYLQA 248
Score = 121 bits (303), Expect = 6e-28, Method: Compositional matrix adjust.
Identities = 67/142 (47%), Positives = 85/142 (59%), Gaps = 7/142 (4%)
Query: 192 ISELKAAGASWIQFDEPLLV--MDLDSHKLHAF----IHSFRITNCGVQDTTQIHTHMCY 245
I L+ AG + IQ DE L + L K A+ +H+F I V+D TQIHTHMCY
Sbjct: 608 IKLLENAGIAIIQVDEAALREGLPLRKSKQKAYLDDAVHAFHIATSSVKDETQIHTHMCY 667
Query: 246 SNFNDIIHSIIDMDADVITIENSRSDEKLLSVFREGVKYGAGIGPGVYDIHSPRIPSTEE 305
S F++II +I +DADVI+IE SRS ++ F V Y GIG GVYDIHSPR+P+ EE
Sbjct: 668 SKFDEIIDAIRALDADVISIETSRSHGDIIESFETAV-YPLGIGLGVYDIHSPRVPTKEE 726
Query: 306 IADRINKMLAVLETNILWVNPD 327
+ I + L L WVNPD
Sbjct: 727 VVANIERPLRQLSPTQFWVNPD 748
>pdb|1XPG|A Chain A, Crystal Structure Of T. Maritima Cobalamin-Independent
Methionine Synthase Complexed With Zn2+ And
Methyltetrahydrofolate
pdb|1XPG|B Chain B, Crystal Structure Of T. Maritima Cobalamin-Independent
Methionine Synthase Complexed With Zn2+ And
Methyltetrahydrofolate
Length = 765
Score = 129 bits (323), Expect = 3e-30, Method: Compositional matrix adjust.
Identities = 80/226 (35%), Positives = 117/226 (51%), Gaps = 9/226 (3%)
Query: 3 SHIVGYPRMGPKRELKFALESFWDGKSSAEDLQKVSADLRSSIWKQMSEAGIKYIPSNTF 62
++ G+P++G KRE K ALE FW GK + E ++ LR + + + IPSN
Sbjct: 35 AYAFGFPKIGEKREFKKALEDFWKGKITEEQFEEEXNKLRXYXVENYRK-NVDVIPSNEL 93
Query: 63 SYYDQVLDTTAMLGAVPPRYNWNGGEIGFDVYFSMARGNASVPAMEMTKWFDTNYHFIVP 122
SYYD VLDT +GAVP R+ G G YF ARG A+E TK+F+TNYH++VP
Sbjct: 94 SYYDFVLDTAVXVGAVPERF---GEYRGLSTYFDXARGGK---ALEXTKFFNTNYHYLVP 147
Query: 123 ELGPDVKFSYASHKAVTEYKEAKGLGVETVPVLIGPVSYLLLSKP-AKGVAKTFXXXXXX 181
E+ + +F +K + +Y K G+ET P +IGP ++L LSK + + +
Sbjct: 148 EIETE-EFYLLENKPLEDYLFFKSKGIETAPWVIGPFTFLYLSKRNGEWIRRPNQXEKLL 206
Query: 182 XXXXXXXXEVISELKAAGASWIQFDEPLLVMDLDSHKLHAFIHSFR 227
EV +L G I +EP V DL+ ++ +R
Sbjct: 207 ESLVSVYKEVFEKLVENGCKEILVNEPAFVCDLEKAHWDLILNVYR 252
Score = 98.2 bits (243), Expect = 6e-21, Method: Compositional matrix adjust.
Identities = 62/186 (33%), Positives = 90/186 (48%), Gaps = 16/186 (8%)
Query: 148 GVETVPVLIGPVSYLLLSKPAKGVAKTFXXXXXXXXXXXXXXEVISELKAAGASWIQFDE 207
G T PV I SY P + +A E + +L+ AG +Q DE
Sbjct: 560 GXLTGPVTIXSWSYYREDIPEREIA---------YQIALAINEEVKDLEEAGIKIVQIDE 610
Query: 208 PLLVMDLDSHK------LHAFIHSFRITNCGVQDTTQIHTHMCYSNFNDIIHSIIDMDAD 261
P K I++F + + TQIH H CYS+FN+II I ++ D
Sbjct: 611 PAFREKAPIKKSKWPEYFEWAINAFNLA-ANARPETQIHAHXCYSDFNEIIEYIHQLEFD 669
Query: 262 VITIENSRSDEKLLSVFREGVKYGAGIGPGVYDIHSPRIPSTEEIADRINKMLAVLETNI 321
VI+IE SRS +++S F + IG GV+DIHSP +PS E + + ++L VL +
Sbjct: 670 VISIEASRSKGEIISAFENFKGWIKQIGVGVWDIHSPAVPSINEXREIVERVLRVLPKEL 729
Query: 322 LWVNPD 327
+W+NPD
Sbjct: 730 IWINPD 735
Score = 29.3 bits (64), Expect = 3.0, Method: Compositional matrix adjust.
Identities = 15/43 (34%), Positives = 24/43 (55%), Gaps = 5/43 (11%)
Query: 33 DLQKVSADLRSSIWKQMSEAGIKYIPSNTFSYYDQVLDTTAML 75
DL+K DL ++++++SE P F+YYD V D A +
Sbjct: 238 DLEKAHWDLILNVYRELSE-----FPLTVFTYYDSVSDYEACV 275
>pdb|1XDJ|A Chain A, Crystal Structure Of T. Maritima Cobalamin-Independent
Methionine Synthase Complexed With Zn2+ And Homocysteine
pdb|1XDJ|B Chain B, Crystal Structure Of T. Maritima Cobalamin-Independent
Methionine Synthase Complexed With Zn2+ And Homocysteine
Length = 766
Score = 128 bits (322), Expect = 3e-30, Method: Compositional matrix adjust.
Identities = 80/226 (35%), Positives = 117/226 (51%), Gaps = 9/226 (3%)
Query: 3 SHIVGYPRMGPKRELKFALESFWDGKSSAEDLQKVSADLRSSIWKQMSEAGIKYIPSNTF 62
++ G+P++G KRE K ALE FW GK + E ++ LR + + + IPSN
Sbjct: 35 AYAFGFPKIGEKREFKKALEDFWKGKITEEQFEEEXNKLRXYXVENYRK-NVDVIPSNEL 93
Query: 63 SYYDQVLDTTAMLGAVPPRYNWNGGEIGFDVYFSMARGNASVPAMEMTKWFDTNYHFIVP 122
SYYD VLDT +GAVP R+ G G YF ARG A+E TK+F+TNYH++VP
Sbjct: 94 SYYDFVLDTAVXVGAVPERF---GEYRGLSTYFDXARGGK---ALEXTKFFNTNYHYLVP 147
Query: 123 ELGPDVKFSYASHKAVTEYKEAKGLGVETVPVLIGPVSYLLLSKP-AKGVAKTFXXXXXX 181
E+ + +F +K + +Y K G+ET P +IGP ++L LSK + + +
Sbjct: 148 EIETE-EFYLLENKPLEDYLFFKSKGIETAPWVIGPFTFLYLSKRNGEWIRRPNQXEKLL 206
Query: 182 XXXXXXXXEVISELKAAGASWIQFDEPLLVMDLDSHKLHAFIHSFR 227
EV +L G I +EP V DL+ ++ +R
Sbjct: 207 ESLVSVYKEVFEKLVENGCKEILVNEPAFVCDLEKAHWDLILNVYR 252
Score = 98.2 bits (243), Expect = 5e-21, Method: Compositional matrix adjust.
Identities = 62/186 (33%), Positives = 90/186 (48%), Gaps = 16/186 (8%)
Query: 148 GVETVPVLIGPVSYLLLSKPAKGVAKTFXXXXXXXXXXXXXXEVISELKAAGASWIQFDE 207
G T PV I SY P + +A E + +L+ AG +Q DE
Sbjct: 560 GXLTGPVTIXSWSYYREDIPEREIA---------YQIALAINEEVKDLEEAGIKIVQIDE 610
Query: 208 PLLVMDLDSHK------LHAFIHSFRITNCGVQDTTQIHTHMCYSNFNDIIHSIIDMDAD 261
P K I++F + + TQIH H CYS+FN+II I ++ D
Sbjct: 611 PAFREKAPIKKSKWPEYFEWAINAFNLA-ANARPETQIHAHXCYSDFNEIIEYIHQLEFD 669
Query: 262 VITIENSRSDEKLLSVFREGVKYGAGIGPGVYDIHSPRIPSTEEIADRINKMLAVLETNI 321
VI+IE SRS +++S F + IG GV+DIHSP +PS E + + ++L VL +
Sbjct: 670 VISIEASRSKGEIISAFENFKGWIKQIGVGVWDIHSPAVPSINEXREIVERVLRVLPKEL 729
Query: 322 LWVNPD 327
+W+NPD
Sbjct: 730 IWINPD 735
Score = 29.3 bits (64), Expect = 3.0, Method: Compositional matrix adjust.
Identities = 15/44 (34%), Positives = 24/44 (54%), Gaps = 5/44 (11%)
Query: 33 DLQKVSADLRSSIWKQMSEAGIKYIPSNTFSYYDQVLDTTAMLG 76
DL+K DL ++++++SE P F+YYD V D A +
Sbjct: 238 DLEKAHWDLILNVYRELSE-----FPLTVFTYYDSVSDYEACVS 276
>pdb|3RPD|A Chain A, The Structure Of A B12-Independent Methionine Synthase
From Shewanella Sp. W3-18-1 In Complex With
Selenomethionine.
pdb|3RPD|B Chain B, The Structure Of A B12-Independent Methionine Synthase
From Shewanella Sp. W3-18-1 In Complex With
Selenomethionine
Length = 357
Score = 40.8 bits (94), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 38/154 (24%), Positives = 64/154 (41%), Gaps = 28/154 (18%)
Query: 190 EVISELKAAGASWIQFDEPLLVMDLDSHKLHAFIHSFRITNCGVQDTTQIHTHMCY---- 245
E EL+AAG IQFDEP + D R G++ T + H+CY
Sbjct: 175 EEAKELEAAGVDIIQFDEPAFNVFFDEVNDWGIACLERAIE-GLKCETAV--HICYGYGI 231
Query: 246 --------------SNFNDIIHSIIDMDADVITIE--NSRSDEKLLSVFREGVKYGAGIG 289
+ ++ + + D+I++E NS +LL + R G +
Sbjct: 232 KANTDWKKTLGSEWRQYEEVFPKLQKSNIDIISLECHNSHVPXELLELIR-----GKKVX 286
Query: 290 PGVYDIHSPRIPSTEEIADRINKMLAVLETNILW 323
G D+ + I + EE+AD + K L ++ + L+
Sbjct: 287 VGAIDVATDTIETAEEVADTLRKALKFVDADKLY 320
>pdb|3HI7|A Chain A, Crystal Structure Of Human Diamine Oxidase
pdb|3HI7|B Chain B, Crystal Structure Of Human Diamine Oxidase
pdb|3HIG|A Chain A, Crystal Structure Of Human Diamine Oxidase In Complex With
The Inhibitor Berenil
pdb|3HIG|B Chain B, Crystal Structure Of Human Diamine Oxidase In Complex With
The Inhibitor Berenil
pdb|3HII|A Chain A, Crystal Structure Of Human Diamine Oxidase In Complex With
The Inhibitor Pentamidine
pdb|3HII|B Chain B, Crystal Structure Of Human Diamine Oxidase In Complex With
The Inhibitor Pentamidine
pdb|3K5T|A Chain A, Crystal Structure Of Human Diamine Oxidase In Space Group
C2221
pdb|3MPH|A Chain A, The Structure Of Human Diamine Oxidase Complexed With An
Inhibitor Aminoguanidine
pdb|3MPH|B Chain B, The Structure Of Human Diamine Oxidase Complexed With An
Inhibitor Aminoguanidine
Length = 731
Score = 30.0 bits (66), Expect = 1.7, Method: Compositional matrix adjust.
Identities = 13/44 (29%), Positives = 27/44 (61%), Gaps = 2/44 (4%)
Query: 218 KLHA--FIHSFRITNCGVQDTTQIHTHMCYSNFNDIIHSIIDMD 259
K+HA ++H+ T G++ T++HTH+ + ++H +D+D
Sbjct: 458 KMHATGYVHATFYTPEGLRHGTRLHTHLIGNIHTHLVHYRVDLD 501
>pdb|2J1N|A Chain A, Osmoporin Ompc
pdb|2J1N|B Chain B, Osmoporin Ompc
pdb|2J1N|C Chain C, Osmoporin Ompc
pdb|2J4U|P Chain P, E.Coli Ompc - Camel Lactoferrin Complex
pdb|2J4U|Q Chain Q, E.Coli Ompc - Camel Lactoferrin Complex
pdb|2J4U|R Chain R, E.Coli Ompc - Camel Lactoferrin Complex
pdb|2J4U|U Chain U, E.Coli Ompc - Camel Lactoferrin Complex
pdb|2J4U|V Chain V, E.Coli Ompc - Camel Lactoferrin Complex
pdb|2J4U|W Chain W, E.Coli Ompc - Camel Lactoferrin Complex
pdb|2ZLE|D Chain D, Cryo-Em Structure Of Degp12OMP
pdb|3NB3|D Chain D, The Host Outer Membrane Proteins Ompa And Ompc Are Packed
At Specific Sites In The Shigella Phage Sf6 Virion As
Structural Components
pdb|4A8D|M Chain M, Degp Dodecamer With Bound Omp
Length = 346
Score = 28.9 bits (63), Expect = 4.6, Method: Compositional matrix adjust.
Identities = 28/102 (27%), Positives = 45/102 (44%), Gaps = 16/102 (15%)
Query: 8 YPRMGPKRELKFALESFWDGKSSAEDLQKVSADLRSSIWKQMSEAGIKYIPSNTFSY--- 64
Y R+G K E + + G+ + +Q SA+ ++ W +++ AG+K+ +F Y
Sbjct: 35 YMRLGFKGETQVTDQLTGYGQWEYQ-IQGNSAENENNSWTRVAFAGLKFQDVGSFDYGRN 93
Query: 65 YDQVLDTTAMLGAVPPRYNWNGGEIGFDVY----FSMARGNA 102
Y V D T+ +P E G D Y F RGN
Sbjct: 94 YGVVYDVTSWTDVLP--------EFGGDTYGSDNFMQQRGNG 127
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
0.319 0.135 0.408
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 9,965,982
Number of Sequences: 62578
Number of extensions: 409062
Number of successful extensions: 1119
Number of sequences better than 100.0: 17
Number of HSP's better than 100.0 without gapping: 11
Number of HSP's successfully gapped in prelim test: 6
Number of HSP's that attempted gapping in prelim test: 1051
Number of HSP's gapped (non-prelim): 31
length of query: 329
length of database: 14,973,337
effective HSP length: 99
effective length of query: 230
effective length of database: 8,778,115
effective search space: 2018966450
effective search space used: 2018966450
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 52 (24.6 bits)