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= 004630
(741 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|1IOW|A Chain A, Complex Of Y216f D-Ala:d-Ala Ligase With Adp And A
Phosphoryl Phosphinate
Length = 306
Score = 77.4 bits (189), Expect = 2e-14, Method: Compositional matrix adjust.
Identities = 89/314 (28%), Positives = 138/314 (43%), Gaps = 71/314 (22%)
Query: 426 VFIAVHGGIGEDGTLQSLLEAEGVPYTGPGVMASKTCMDKVATSLALNHLADLGVLTINK 485
VFIA+HG GEDGTLQ +LE G+PYTG GVMAS MDK+ + L L A L V
Sbjct: 58 VFIALHGRGGEDGTLQGMLELMGLPYTGSGVMASALSMDKLRSKL-LWQGAGLPVAPWVA 116
Query: 486 DVRRKEDLLKTPIVDIWHELTSKLQCKTLCVKPARDGCSTGVARLCCAEDLTVYVKALEE 545
R + + + D S L + VKP+R+G S G++++ V AL++
Sbjct: 117 LTRAE---FEKGLSDKQLAEISALGLPVI-VKPSREGSSVGMSKV-------VAENALQD 165
Query: 546 CLLRIPPNSFSRAHGMIEMPNPPPEILIFEPFVETDEILFSSQSTNKNADRLMWKGNSRW 605
LR+ F +E+L +W
Sbjct: 166 A-LRL-------------------------AFQHDEEVLI-----------------EKW 182
Query: 606 V---EITVGVIGKCGSMHSLMPSVTVKESGDILSLEEKFQGGTGINLTPPPASIMSTEAL 662
+ E TV ++G+ ++PS+ ++ SG E KF PA + +++
Sbjct: 183 LSGPEFTVAILGE-----EILPSIRIQPSGTFYDYEAKFLSDETQYFC--PAGLEASQ-- 233
Query: 663 DKCKQRIELIA-NALQLEGFSRIDAFVNVDNGEVLIIEVNTVPGMTPSTVLIHQALSEQP 721
+ Q + L A L +G+ RID ++ D G+ ++E NT PGMT +++ A Q
Sbjct: 234 EANLQALVLKAWTTLGCKGWGRIDVMLDSD-GQFYLLEANTSPGMTSHSLVPMAA--RQA 290
Query: 722 PMYPHQFFRKVLDL 735
M Q ++L+L
Sbjct: 291 GMSFSQLVVRILEL 304
Score = 32.3 bits (72), Expect = 0.86, Method: Compositional matrix adjust.
Identities = 45/201 (22%), Positives = 81/201 (40%), Gaps = 39/201 (19%)
Query: 40 VVVKPTRAGSSIGVTVAYGVIDSLKKAKGIILEGIDDRVVVELFLEGGSEFTAIVLDVGS 99
V+VKP+R GSS+G++ ++L+ A + + D+ V++E +L G EFT +L
Sbjct: 141 VIVKPSREGSSVGMSKVVAE-NALQDALRLAFQH-DEEVLIEKWLS-GPEFTVAIL---- 193
Query: 100 GFDCHPVVLLPTEVELQFQGSVDVREKDAIFNYRRKYLPTQQVAYHTPPRFPIVVINSIR 159
G + P S+ ++ ++Y K+L + + Y P +++
Sbjct: 194 GEEILP--------------SIRIQPSGTFYDYEAKFL-SDETQYFCPAGLEASQEANLQ 238
Query: 160 EGASLLFQRLGLCDFARIDGWFLPSSTHVFSSSETKYGSTEWGTILFTDINLISGMEQTS 219
+ LG + RID V S+ G + N GM S
Sbjct: 239 ALVLKAWTTLGCKGWGRID---------VMLDSD--------GQFYLLEANTSPGMTSHS 281
Query: 220 FLFQQASKVGFSHSNILRTII 240
+ A + G S S ++ I+
Sbjct: 282 LVPMAARQAGMSFSQLVVRIL 302
>pdb|1IOV|A Chain A, Complex Of D-Ala:d-Ala Ligase With Adp And A Phosphoryl
Phosphonate
pdb|2DLN|A Chain A, Vancomycin Resistance: Structure Of D-Alanine:d-Alanine
Ligase At 2.3 Angstroms Resolution
Length = 306
Score = 76.6 bits (187), Expect = 5e-14, Method: Compositional matrix adjust.
Identities = 88/314 (28%), Positives = 138/314 (43%), Gaps = 71/314 (22%)
Query: 426 VFIAVHGGIGEDGTLQSLLEAEGVPYTGPGVMASKTCMDKVATSLALNHLADLGVLTINK 485
VFIA+HG GEDGTLQ +LE G+PYTG GVMAS MDK+ + L L A L V
Sbjct: 58 VFIALHGRGGEDGTLQGMLELMGLPYTGSGVMASALSMDKLRSKL-LWQGAGLPVAPWVA 116
Query: 486 DVRRKEDLLKTPIVDIWHELTSKLQCKTLCVKPARDGCSTGVARLCCAEDLTVYVKALEE 545
R + + + D S L + VKP+R+G S G++++ V AL++
Sbjct: 117 LTRAE---FEKGLSDKQLAEISALGLPVI-VKPSREGSSVGMSKV-------VAENALQD 165
Query: 546 CLLRIPPNSFSRAHGMIEMPNPPPEILIFEPFVETDEILFSSQSTNKNADRLMWKGNSRW 605
LR+ F +E+L +W
Sbjct: 166 A-LRL-------------------------AFQHDEEVLI-----------------EKW 182
Query: 606 V---EITVGVIGKCGSMHSLMPSVTVKESGDILSLEEKFQGGTGINLTPPPASIMSTEAL 662
+ E TV ++G+ ++PS+ ++ SG E K+ PA + +++
Sbjct: 183 LSGPEFTVAILGE-----EILPSIRIQPSGTFYDYEAKYLSDETQYFC--PAGLEASQ-- 233
Query: 663 DKCKQRIELIA-NALQLEGFSRIDAFVNVDNGEVLIIEVNTVPGMTPSTVLIHQALSEQP 721
+ Q + L A L +G+ RID ++ D G+ ++E NT PGMT +++ A Q
Sbjct: 234 EANLQALVLKAWTTLGCKGWGRIDVMLDSD-GQFYLLEANTSPGMTSHSLVPMAA--RQA 290
Query: 722 PMYPHQFFRKVLDL 735
M Q ++L+L
Sbjct: 291 GMSFSQLVVRILEL 304
Score = 34.3 bits (77), Expect = 0.24, Method: Compositional matrix adjust.
Identities = 46/201 (22%), Positives = 81/201 (40%), Gaps = 39/201 (19%)
Query: 40 VVVKPTRAGSSIGVTVAYGVIDSLKKAKGIILEGIDDRVVVELFLEGGSEFTAIVLDVGS 99
V+VKP+R GSS+G++ ++L+ A + + D+ V++E +L G EFT +L
Sbjct: 141 VIVKPSREGSSVGMSKVVAE-NALQDALRLAFQH-DEEVLIEKWLS-GPEFTVAIL---- 193
Query: 100 GFDCHPVVLLPTEVELQFQGSVDVREKDAIFNYRRKYLPTQQVAYHTPPRFPIVVINSIR 159
G + P S+ ++ ++Y KYL + + Y P +++
Sbjct: 194 GEEILP--------------SIRIQPSGTFYDYEAKYL-SDETQYFCPAGLEASQEANLQ 238
Query: 160 EGASLLFQRLGLCDFARIDGWFLPSSTHVFSSSETKYGSTEWGTILFTDINLISGMEQTS 219
+ LG + RID V S+ G + N GM S
Sbjct: 239 ALVLKAWTTLGCKGWGRID---------VMLDSD--------GQFYLLEANTSPGMTSHS 281
Query: 220 FLFQQASKVGFSHSNILRTII 240
+ A + G S S ++ I+
Sbjct: 282 LVPMAARQAGMSFSQLVVRIL 302
>pdb|3V4Z|A Chain A, D-Alanine--D-Alanine Ligase From Yersinia Pestis
pdb|3V4Z|B Chain B, D-Alanine--D-Alanine Ligase From Yersinia Pestis
Length = 309
Score = 75.9 bits (185), Expect = 7e-14, Method: Compositional matrix adjust.
Identities = 80/299 (26%), Positives = 124/299 (41%), Gaps = 67/299 (22%)
Query: 417 KLAKENQATVFIAVHGGIGEDGTLQSLLEAEGVPYTGPGVMASKTCMDKVATSLALNHLA 476
+L ++ VFIA+HG GEDGTLQ +LE +PYTG GVMAS MDK+ T L L
Sbjct: 52 QLKEQGFDKVFIALHGRGGEDGTLQGVLEFLQLPYTGSGVMASALTMDKLRTKLVWQALG 111
Query: 477 DLGVLTINKDVRRKEDLLKTPIVDIWHELTSKLQCKTLCVKPARDGCSTGVARLCCAEDL 536
L I+ V +T + +KL L VKP+ +G S G++++ A +L
Sbjct: 112 ----LPISPYVALNRQQFETLSPEELVACVAKLGLP-LIVKPSHEGSSVGMSKVDHASEL 166
Query: 537 TVYVKALEECLLRIPPNSFSRAHGMIEMPNPPPEILIFEPFVETDEILFSSQSTNKNADR 596
KAL E ++D
Sbjct: 167 Q---KALVEAF-------------------------------------------QHDSDV 180
Query: 597 LMWKGNSRWV---EITVGVIGKCGSMHSLMPSVTVKESGDILSLEEKFQGGTGINLTPPP 653
L+ +W+ E TV ++G ++PS+ ++ G + K+ P
Sbjct: 181 LI----EKWLSGPEFTVAILGD-----EVLPSIRIQPPGVFYDYDAKYLSDKTQYFCP-- 229
Query: 654 ASIMSTEALDKCKQRIELIANALQLEGFSRIDAFVNVDNGEVLIIEVNTVPGMTPSTVL 712
S +S E+ + +AL G+ R+D + D G ++EVNT PGMT +++
Sbjct: 230 -SGLSDESEQQLAALALQAYHALDCSGWGRVDVMQDRD-GHFYLLEVNTSPGMTSHSLV 286
>pdb|2YZM|A Chain A, Structure Of D-Alanine:d-Alanine Ligase With Substrate
From Thermus Thermophilus Hb8
pdb|2YZM|B Chain B, Structure Of D-Alanine:d-Alanine Ligase With Substrate
From Thermus Thermophilus Hb8
pdb|2YZM|C Chain C, Structure Of D-Alanine:d-Alanine Ligase With Substrate
From Thermus Thermophilus Hb8
pdb|2YZN|A Chain A, Crystal Structure Of D-Alanine:d-Alanine Ligase With
Amppnp From Thermus Thermophilus Hb8.
pdb|2YZN|B Chain B, Crystal Structure Of D-Alanine:d-Alanine Ligase With
Amppnp From Thermus Thermophilus Hb8.
pdb|2YZN|C Chain C, Crystal Structure Of D-Alanine:d-Alanine Ligase With
Amppnp From Thermus Thermophilus Hb8.
pdb|2ZDG|A Chain A, Crystal Structure Of D-Alanine:d-Alanine Ligase With Adp
From Thermus Thermophius Hb8
pdb|2ZDG|B Chain B, Crystal Structure Of D-Alanine:d-Alanine Ligase With Adp
From Thermus Thermophius Hb8
pdb|2ZDG|C Chain C, Crystal Structure Of D-Alanine:d-Alanine Ligase With Adp
From Thermus Thermophius Hb8
pdb|2ZDG|D Chain D, Crystal Structure Of D-Alanine:d-Alanine Ligase With Adp
From Thermus Thermophius Hb8
pdb|2ZDH|A Chain A, Crystal Structure Of D-Alanine:d-Alanine Ligase With Adp
And D-Alanine From Thermus Thermophius Hb8
pdb|2ZDH|B Chain B, Crystal Structure Of D-Alanine:d-Alanine Ligase With Adp
And D-Alanine From Thermus Thermophius Hb8
pdb|2ZDH|C Chain C, Crystal Structure Of D-Alanine:d-Alanine Ligase With Adp
And D-Alanine From Thermus Thermophius Hb8
pdb|2ZDH|D Chain D, Crystal Structure Of D-Alanine:d-Alanine Ligase With Adp
And D-Alanine From Thermus Thermophius Hb8
pdb|2ZDQ|A Chain A, Crystal Structure Of D-Alanine:d-Alanine Ligase With Atp
And D-Alanine:d-Alanine From Thermus Thermophius Hb8
pdb|2ZDQ|B Chain B, Crystal Structure Of D-Alanine:d-Alanine Ligase With Atp
And D-Alanine:d-Alanine From Thermus Thermophius Hb8
Length = 319
Score = 72.0 bits (175), Expect = 1e-12, Method: Compositional matrix adjust.
Identities = 84/312 (26%), Positives = 115/312 (36%), Gaps = 82/312 (26%)
Query: 418 LAKENQATVFIAVHGGIGEDGTLQSLLEAEGVPYTGPGVMASKTCMDKVATSLALNHLAD 477
L+ E VF +HG GEDGT+Q LE G PY G GV AS CMDK L+ LA
Sbjct: 69 LSWERYDVVFPLLHGRFGEDGTVQGFLELLGKPYVGAGVAASALCMDK---DLSKRVLAQ 125
Query: 478 LGVLTINKDVRRKEDLLKTPIVDIWHELTSKLQCKTLCVKPARDGCSTGVARLCCAEDLT 537
GV + RK E VKPA G S G++R+ +DL
Sbjct: 126 AGVPVVPWVAVRK------------GEPPVVPFDPPFFVKPANTGSSVGISRVERFQDL- 172
Query: 538 VYVKALEECLLRIPPNSFSRAHGMIEMPNPPPEILIFEPFVETDEILFSSQSTNKNADRL 597
E L + + + +
Sbjct: 173 -------EAALAL--------------------------------------AFRYDEKAV 187
Query: 598 MWKGNSRWVEITVGVIGKCGSMHSLMPSVTVKESGDILSLEEKFQGGTGINLTPPPASIM 657
+ K S E+ VGV+G S P V+ E K+ G L P P
Sbjct: 188 VEKALSPVRELEVGVLGNVFGEAS--PVGEVRYEAPFYDYETKYTPGRAELLIPAPLDPG 245
Query: 658 STEALDKCKQRIELIA-NALQLEGFSRIDAFVNVDNGEVLIIEVNTVPGMTPSTVLIHQA 716
+ E + Q + L A L + G +R+D F+ GE+ + E+NT+PG TP++
Sbjct: 246 TQETV----QELALKAYKVLGVRGMARVDFFLA--EGELYLNELNTIPGFTPTS------ 293
Query: 717 LSEQPPMYPHQF 728
MYP F
Sbjct: 294 ------MYPRLF 299
Score = 31.2 bits (69), Expect = 2.2, Method: Compositional matrix adjust.
Identities = 48/204 (23%), Positives = 80/204 (39%), Gaps = 38/204 (18%)
Query: 43 KPTRAGSSIGVTVAYGVIDSLKKAKGIILEGIDDRVVVELFLEGGSEFTAIVLDVGSGF- 101
KP GSS+G++ D L+ A + D++ VVE L E VL G+ F
Sbjct: 153 KPANTGSSVGISRVERFQD-LEAALALAFR-YDEKAVVEKALSPVRELEVGVL--GNVFG 208
Query: 102 DCHPVVLLPTEVELQFQGSVDVREKDAIFNYRRKYLPTQQVAYHTPPRFPIVVINSIREG 161
+ PV +VR + ++Y KY P + P P +++E
Sbjct: 209 EASPV--------------GEVRYEAPFYDYETKYTPGRAELLIPAPLDP-GTQETVQEL 253
Query: 162 ASLLFQRLGLCDFARIDGWFLPSSTHVFSSSETKYGSTEWGTILFTDINLISGMEQTSFL 221
A ++ LG+ AR+D +FL G + ++N I G TS
Sbjct: 254 ALKAYKVLGVRGMARVD-FFLAE-----------------GELYLNELNTIPGFTPTSMY 295
Query: 222 FQQASKVGFSHSNILRTIIGHACS 245
+ G ++ +LR ++ A +
Sbjct: 296 PRLFEAGGVAYPELLRRLVELALT 319
>pdb|2FB9|A Chain A, Crystal Structure Of The Apo Form Of D-alanine: D-alanine
Ligase (ddl) From Thermus Caldophilus: A Basis For The
Substrate-induced Conformational Changes
Length = 322
Score = 72.0 bits (175), Expect = 1e-12, Method: Compositional matrix adjust.
Identities = 84/312 (26%), Positives = 115/312 (36%), Gaps = 82/312 (26%)
Query: 418 LAKENQATVFIAVHGGIGEDGTLQSLLEAEGVPYTGPGVMASKTCMDKVATSLALNHLAD 477
L+ E VF +HG GEDGT+Q LE G PY G GV AS CMDK L+ LA
Sbjct: 72 LSWERYDVVFPLLHGRFGEDGTVQGFLELLGKPYVGAGVAASALCMDK---DLSKRVLAQ 128
Query: 478 LGVLTINKDVRRKEDLLKTPIVDIWHELTSKLQCKTLCVKPARDGCSTGVARLCCAEDLT 537
GV + RK E VKPA G S G++R+ +DL
Sbjct: 129 AGVPVVPWVAVRK------------GEPPVVPFDPPFFVKPANTGSSVGISRVERFQDL- 175
Query: 538 VYVKALEECLLRIPPNSFSRAHGMIEMPNPPPEILIFEPFVETDEILFSSQSTNKNADRL 597
E L + + + +
Sbjct: 176 -------EAALAL--------------------------------------AFRYDEKAV 190
Query: 598 MWKGNSRWVEITVGVIGKCGSMHSLMPSVTVKESGDILSLEEKFQGGTGINLTPPPASIM 657
+ K S E+ VGV+G S P V+ E K+ G L P P
Sbjct: 191 VEKALSPVRELEVGVLGNVFGEAS--PVGEVRYEAPFYDYETKYTPGRAELLIPAPLDPG 248
Query: 658 STEALDKCKQRIELIA-NALQLEGFSRIDAFVNVDNGEVLIIEVNTVPGMTPSTVLIHQA 716
+ E + Q + L A L + G +R+D F+ GE+ + E+NT+PG TP++
Sbjct: 249 TQETV----QELALKAYKVLGVRGMARVDFFLA--EGELYLNELNTIPGFTPTS------ 296
Query: 717 LSEQPPMYPHQF 728
MYP F
Sbjct: 297 ------MYPRLF 302
Score = 31.2 bits (69), Expect = 2.4, Method: Compositional matrix adjust.
Identities = 48/204 (23%), Positives = 80/204 (39%), Gaps = 38/204 (18%)
Query: 43 KPTRAGSSIGVTVAYGVIDSLKKAKGIILEGIDDRVVVELFLEGGSEFTAIVLDVGSGF- 101
KP GSS+G++ D L+ A + D++ VVE L E VL G+ F
Sbjct: 156 KPANTGSSVGISRVERFQD-LEAALALAFR-YDEKAVVEKALSPVRELEVGVL--GNVFG 211
Query: 102 DCHPVVLLPTEVELQFQGSVDVREKDAIFNYRRKYLPTQQVAYHTPPRFPIVVINSIREG 161
+ PV +VR + ++Y KY P + P P +++E
Sbjct: 212 EASPV--------------GEVRYEAPFYDYETKYTPGRAELLIPAPLDPGTQ-ETVQEL 256
Query: 162 ASLLFQRLGLCDFARIDGWFLPSSTHVFSSSETKYGSTEWGTILFTDINLISGMEQTSFL 221
A ++ LG+ AR+D +FL G + ++N I G TS
Sbjct: 257 ALKAYKVLGVRGMARVD-FFLAE-----------------GELYLNELNTIPGFTPTSMY 298
Query: 222 FQQASKVGFSHSNILRTIIGHACS 245
+ G ++ +LR ++ A +
Sbjct: 299 PRLFEAGGVAYPELLRRLVELALT 322
>pdb|3SE7|A Chain A, Ancient Vana
pdb|3SE7|B Chain B, Ancient Vana
pdb|3SE7|C Chain C, Ancient Vana
pdb|3SE7|D Chain D, Ancient Vana
pdb|3SE7|E Chain E, Ancient Vana
pdb|3SE7|F Chain F, Ancient Vana
Length = 346
Score = 71.2 bits (173), Expect = 2e-12, Method: Compositional matrix adjust.
Identities = 76/284 (26%), Positives = 110/284 (38%), Gaps = 66/284 (23%)
Query: 426 VFIAVHGGIGEDGTLQSLLEAEGVPYTGPGVMASKTCMDKVATSLALNH--LADLGVLTI 483
V +HG +GEDG +Q LLE G+PY G + +S CMDK T L +A T+
Sbjct: 94 VLPVLHGKLGEDGAIQGLLELSGIPYVGCDIQSSALCMDKSLTYLVARSAGIATPNFWTV 153
Query: 484 NKDVRRKEDLLKTPIVDIWHELTSKLQCKTLCVKPARDGCSTGVARLCCAEDLTVYVKAL 543
D + D L P+ VKPAR G S GV+++ EDL
Sbjct: 154 TADEKIPTDQLTYPVF----------------VKPARSGSSFGVSKVAREEDL------- 190
Query: 544 EECLLRIPPNSFSRAHGMIEMPNPPPEILIFEPFVETDEILFSSQSTNKNADRLMWKGNS 603
G +E ++ E V EI + +M G
Sbjct: 191 ---------------QGAVEAAREYDSKVLIEEAVIGTEIGCA----------VMGNGP- 224
Query: 604 RWVEITVGVIGKCGSMHSLMPSVTVKESGDILSLEEKFQGGTGINLTPPPASIMSTEALD 663
E+ G + + H + E + G+ + PA I ST +
Sbjct: 225 ---ELITGEVDQITLSHGFFK----------IHQESTPESGSDNSAVTVPADI-STTSRS 270
Query: 664 KCKQRIELIANALQLEGFSRIDAFVNVDNGEVLIIEVNTVPGMT 707
+ + + AL G SR+D F+ D G+V++ EVNT PGMT
Sbjct: 271 LVQDTAKAVYRALGCRGLSRVDLFLTED-GKVVLNEVNTFPGMT 313
>pdb|1E4E|A Chain A, D-Alanyl-D-Lacate Ligase
Length = 343
Score = 68.9 bits (167), Expect = 1e-11, Method: Compositional matrix adjust.
Identities = 66/287 (22%), Positives = 115/287 (40%), Gaps = 74/287 (25%)
Query: 427 FIAVHGGIGEDGTLQSLLEAEGVPYTGPGVMASKTCMDKVATSLALNH--LADLGVLTIN 484
F A+HG GEDG++Q L E G+P+ G + +S CMDK T + + +A IN
Sbjct: 95 FSALHGKSGEDGSIQGLFELSGIPFVGCDIQSSAICMDKSLTYIVAKNAGIATPAFWVIN 154
Query: 485 KDVRRKEDLLKTPIVDIWHELTSKLQCKTLCVKPARDGCSTGVARLCCAEDLTVYVKALE 544
KD R P+ VKPAR G S GV ++ A
Sbjct: 155 KDDRPVAATFTYPVF----------------VKPARSGSSFGVKKVNSA----------- 187
Query: 545 ECLLRIPPNSFSRAHGMIEMPNPPPEILIFEPFVETDEILFSSQSTNKNADRLMWKGNSR 604
DE+ ++ +S + +++ +
Sbjct: 188 ------------------------------------DELDYAIESARQYDSKILIEQAVS 211
Query: 605 WVEITVGVIGKCGSMHSLMPSV-TVKESGDILSLEEKFQ---GGTGINLTPPPASIMSTE 660
E+ V+G ++ ++ V ++ I + ++ + G +T P + +S E
Sbjct: 212 GCEVGCAVLGNSAAL--VVGEVDQIRLQYGIFRIHQEVEPEKGSENAVITVP--ADLSAE 267
Query: 661 ALDKCKQRIELIANALQLEGFSRIDAFVNVDNGEVLIIEVNTVPGMT 707
+ ++ ++ I L G +R+D F+ DNG +++ EVNT+PG T
Sbjct: 268 ERGRIQETVKKIYKTLGCRGLARVDMFLQ-DNGRIVLNEVNTLPGFT 313
>pdb|2YZG|A Chain A, Crystal Structure Of D-Ala:d-Ala Ligase From Thermus
Thermophilus Hb8
pdb|2YZG|B Chain B, Crystal Structure Of D-Ala:d-Ala Ligase From Thermus
Thermophilus Hb8
pdb|2YZG|C Chain C, Crystal Structure Of D-Ala:d-Ala Ligase From Thermus
Thermophilus Hb8
Length = 319
Score = 68.2 bits (165), Expect = 2e-11, Method: Compositional matrix adjust.
Identities = 79/294 (26%), Positives = 110/294 (37%), Gaps = 70/294 (23%)
Query: 418 LAKENQATVFIAVHGGIGEDGTLQSLLEAEGVPYTGPGVMASKTCMDKVATSLALNHLAD 477
L+ E VF +HG GEDGT+Q LE G PY G GV AS C DK L+ LA
Sbjct: 69 LSWERYDVVFPLLHGRFGEDGTVQGFLELLGKPYVGAGVAASALCXDK---DLSKRVLAQ 125
Query: 478 LGVLTINKDVRRKEDLLKTPIVDIWHELTSKLQCKTLCVKPARDGCSTGVARLCCAEDLT 537
GV + RK E VKPA G S G++R+ +DL
Sbjct: 126 AGVPVVPWVAVRK------------GEPPVVPFDPPFFVKPANTGSSVGISRVERFQDL- 172
Query: 538 VYVKALEECLLRIPPNSFSRAHGMIEMPNPPPEILIFEPFVETDEILFSSQSTNKNADRL 597
E L + + + +
Sbjct: 173 -------EAALAL--------------------------------------AFRYDEKAV 187
Query: 598 MWKGNSRWVEITVGVIGKCGSMHSLMPSVTVKESGDILSLEEKFQGGTGINLTPPPASIM 657
+ K S E+ VGV+G S P V+ E K+ G L P P
Sbjct: 188 VEKALSPVRELEVGVLGNVFGEAS--PVGEVRYEAPFYDYETKYTPGRAELLIPAPLDPG 245
Query: 658 STEALDKCKQRIELIA-NALQLEGFSRIDAFVNVDNGEVLIIEVNTVPGMTPST 710
+ E + Q + L A L + G +R+D F+ GE+ + E+NT+PG TP++
Sbjct: 246 TQETV----QELALKAYKVLGVRGXARVDFFLA--EGELYLNELNTIPGFTPTS 293
Score = 29.6 bits (65), Expect = 6.3, Method: Compositional matrix adjust.
Identities = 48/204 (23%), Positives = 80/204 (39%), Gaps = 38/204 (18%)
Query: 43 KPTRAGSSIGVTVAYGVIDSLKKAKGIILEGIDDRVVVELFLEGGSEFTAIVLDVGSGF- 101
KP GSS+G++ D L+ A + D++ VVE L E VL G+ F
Sbjct: 153 KPANTGSSVGISRVERFQD-LEAALALAFR-YDEKAVVEKALSPVRELEVGVL--GNVFG 208
Query: 102 DCHPVVLLPTEVELQFQGSVDVREKDAIFNYRRKYLPTQQVAYHTPPRFPIVVINSIREG 161
+ PV +VR + ++Y KY P + P P +++E
Sbjct: 209 EASPV--------------GEVRYEAPFYDYETKYTPGRAELLIPAPLDP-GTQETVQEL 253
Query: 162 ASLLFQRLGLCDFARIDGWFLPSSTHVFSSSETKYGSTEWGTILFTDINLISGMEQTSFL 221
A ++ LG+ AR+D +FL G + ++N I G TS
Sbjct: 254 ALKAYKVLGVRGXARVD-FFLAE-----------------GELYLNELNTIPGFTPTSXY 295
Query: 222 FQQASKVGFSHSNILRTIIGHACS 245
+ G ++ +LR ++ A +
Sbjct: 296 PRLFEAGGVAYPELLRRLVELALT 319
>pdb|1E4E|B Chain B, D-Alanyl-D-Lacate Ligase
Length = 343
Score = 66.2 bits (160), Expect = 5e-11, Method: Compositional matrix adjust.
Identities = 65/287 (22%), Positives = 114/287 (39%), Gaps = 74/287 (25%)
Query: 427 FIAVHGGIGEDGTLQSLLEAEGVPYTGPGVMASKTCMDKVATSLALNH--LADLGVLTIN 484
F A+HG GEDG++Q L E G+P+ G + +S CMDK T + + +A IN
Sbjct: 95 FSALHGKSGEDGSIQGLFELSGIPFVGCDIQSSAICMDKSLTYIVAKNAGIATPAFWVIN 154
Query: 485 KDVRRKEDLLKTPIVDIWHELTSKLQCKTLCVKPARDGCSTGVARLCCAEDLTVYVKALE 544
KD R P+ VKPAR G S GV ++ A
Sbjct: 155 KDDRPVAATFTYPVF----------------VKPARSGSSFGVKKVNSA----------- 187
Query: 545 ECLLRIPPNSFSRAHGMIEMPNPPPEILIFEPFVETDEILFSSQSTNKNADRLMWKGNSR 604
DE+ ++ +S + +++ +
Sbjct: 188 ------------------------------------DELDYAIESARQYDSKILIEQAVS 211
Query: 605 WVEITVGVIGKCGSMHSLMPSV-TVKESGDILSLEEKFQ---GGTGINLTPPPASIMSTE 660
E+ V+G ++ ++ V ++ I + ++ + G +T P + +S E
Sbjct: 212 GCEVGCAVLGNSAAL--VVGEVDQIRLQYGIFRIHQEVEPEKGSENAVITVP--ADLSAE 267
Query: 661 ALDKCKQRIELIANALQLEGFSRIDAFVNVDNGEVLIIEVNTVPGMT 707
+ ++ ++ I L G +R+D F+ D G +++ EVNT+PG T
Sbjct: 268 ERGRIQETVKKIYKTLGCRGLARVDMFLQ-DRGRIVLNEVNTLPGFT 313
>pdb|3LWB|A Chain A, Crystal Structure Of Apo D-Alanine:d-Alanine Ligase (Ddl)
From Mycobacterium Tuberculosis
pdb|3LWB|B Chain B, Crystal Structure Of Apo D-Alanine:d-Alanine Ligase (Ddl)
From Mycobacterium Tuberculosis
Length = 373
Score = 62.4 bits (150), Expect = 9e-10, Method: Compositional matrix adjust.
Identities = 46/122 (37%), Positives = 60/122 (49%), Gaps = 14/122 (11%)
Query: 421 ENQATVFIAVHGGIGEDGTLQSLLEAEGVPYTGPGVMASKTCMDKVATS--LALNHLADL 478
E+ VF +HG GEDGT+Q LLE GVPY G GV+AS MDK T LA + L +
Sbjct: 108 ESVDVVFPVLHGPYGEDGTIQGLLELAGVPYVGAGVLASAVGMDKEFTKKLLAADGLP-V 166
Query: 479 GVLTINKDVRRKEDLLKTPIVDIWHELTSKLQCKTLCVKPARDGCSTGVARLCCAEDLTV 538
G + L+ P + + +L VKPAR G S GV+R+ + L
Sbjct: 167 GAYAV----------LRPPRSTLHRQECERLGLPVF-VKPARGGSSIGVSRVSSWDQLPA 215
Query: 539 YV 540
V
Sbjct: 216 AV 217
Score = 33.5 bits (75), Expect = 0.44, Method: Compositional matrix adjust.
Identities = 53/209 (25%), Positives = 86/209 (41%), Gaps = 33/209 (15%)
Query: 40 VVVKPTRAGSSIGVTVAYGVIDSLKKAKGIILEGI--DDRVVVELFLEGGSEFTAIVLDV 97
V VKP R GSSIGV+ + S + + D +V+VE + G E VL++
Sbjct: 191 VFVKPARGGSSIGVS----RVSSWDQLPAAVARARRHDPKVIVEAAIS-GRELECGVLEM 245
Query: 98 GSGFDCHPVVLLPTEVELQFQGSVDVREKDAIFNYRRKYLPTQQVAYHTPPRFPIVVINS 157
G + T E++ G V RE D+ +++ KYL P + V +
Sbjct: 246 PDG-----TLEASTLGEIRVAG-VRGRE-DSFYDFATKYL-DDAAELDVPAKVDDQVAEA 297
Query: 158 IREGASLLFQRLGLCDFARIDGWFLPSSTHVFSSSETKYGSTEWGTILFTDINLISGMEQ 217
IR+ A F + AR+D +FL T+ G ++ +IN + G
Sbjct: 298 IRQLAIRAFAAIDCRGLARVD-FFL----------------TDDGPVI-NEINTMPGFTT 339
Query: 218 TSFLFQQASKVGFSHSNILRTIIGHACSR 246
S + + G + +L T+I +R
Sbjct: 340 ISMYPRMWAASGVDYPTLLATMIETTLAR 368
>pdb|1EHI|A Chain A, D-Alanine:d-Lactate Ligase (Lmddl2) Of
Vancomycin-Resistant Leuconostoc Mesenteroides
pdb|1EHI|B Chain B, D-Alanine:d-Lactate Ligase (Lmddl2) Of
Vancomycin-Resistant Leuconostoc Mesenteroides
Length = 377
Score = 57.4 bits (137), Expect = 3e-08, Method: Compositional matrix adjust.
Identities = 106/467 (22%), Positives = 175/467 (37%), Gaps = 121/467 (25%)
Query: 280 REVFVIFGGDTSERQVSLMSGTNVWLNLQAFNDIEVTPCLLASSIDCSSGMDANITDPDS 339
+ V +IFGG++SE VS S N + ++A E+ +A + D +S
Sbjct: 4 KRVALIFGGNSSEHDVSKRSAQNFYNAIEATGKYEIIVFAIAQ--------NGFFLDTES 55
Query: 340 SSRVVWSLPYSLVLRHTTEEVLAACIEAIEPDRAAFTSHLRNQVVNDLVEGLKKHSWFTG 399
S +++ +E +P AF +
Sbjct: 56 SKKIL-------------------ALEDEQPIVDAFMKTV-------------------- 76
Query: 400 FDIADELPMRHSINEWIKLAKENQATVFIAVHGGIGEDGTLQSLLEAEGVPYTGPGVMAS 459
D +D L H++ + + F VHG +GEDGTLQ L + PY G +
Sbjct: 77 -DASDPLARIHALK-----SAGDFDIFFPVVHGNLGEDGTLQGLFKLLDKPYVGAPLRGH 130
Query: 460 KTCMDKVATSLALNHLADLGVLTINKDVRRKEDLLKTPIVD---IWHELTSKLQCKTLCV 516
DK T +LT+N +R + ++ P W ++ ++L + V
Sbjct: 131 AVSFDKALTK---------ELLTVNG-IRNTKYIVVDPESANNWSWDKIVAEL-GNIVFV 179
Query: 517 KPARDGCSTGVARLCCAEDLTVYVKALEECLLRIPPNSFSRAHGMIEMPNPPPEILIFEP 576
K A G S G++R+ AE+ Y +AL + SF + ++LI E
Sbjct: 180 KAANQGSSVGISRVTNAEE---YTEALSD--------SFQYDY----------KVLIEEA 218
Query: 577 FVETDEILFSSQSTNKNADRLMWKGNSRWVEITVGVIGKCGSMHSLMPSVTV--KESGD- 633
N R E+ VGVIG + S + + TV + SGD
Sbjct: 219 V---------------NGAR----------ELEVGVIGNDQPLVSEIGAHTVPNQGSGDG 253
Query: 634 ILSLEEKFQGGTGINLTPPPASIMSTEALDKCKQRIELIANALQLEGFSRIDAFVNVDNG 693
KF + ++ P +S E + KQ L L G +R+D ++ +N
Sbjct: 254 WYDYNNKFVDNSAVHFQIPAQ--LSPEVTKEVKQMALDAYKVLNLRGEARMDFLLDENNV 311
Query: 694 EVLIIEVNTVPGMTPSTVLIHQALSEQPPMYPHQFFRKVLDLGSERF 740
L E NT+PG T ++ + L + + + ++D G E F
Sbjct: 312 PYL-GEPNTLPGFTNMSLF--KRLWDYSDINNAKLVDMLIDYGFEDF 355
>pdb|4FU0|A Chain A, Crystal Structure Of Vang D-Ala:d-Ser Ligase From
Enterococcus Faecalis
pdb|4FU0|B Chain B, Crystal Structure Of Vang D-Ala:d-Ser Ligase From
Enterococcus Faecalis
Length = 357
Score = 57.0 bits (136), Expect = 3e-08, Method: Compositional matrix adjust.
Identities = 54/202 (26%), Positives = 85/202 (42%), Gaps = 40/202 (19%)
Query: 42 VKPTRAGSSIGVTVAYGVIDSLKKAKGIILEGIDDRVVVELFLEGGSEFTAIVLDVGSGF 101
+KP RAGSS G+T ++E + +EL E +E IV + +GF
Sbjct: 182 IKPVRAGSSFGITK--------------VIEKQELDAAIELAFEHDTE--VIVEETINGF 225
Query: 102 DCHPVVLLPTEVELQFQGSVD-VREKDAIFNYRRKY-LPTQQVAYHTPPRFPIVVINSIR 159
+ VL E+ G VD + F+Y KY L + ++ + P R I+
Sbjct: 226 EVGCAVLGIDEL---IVGRVDEIELSSGFFDYTEKYTLKSSKI--YMPARIDAEAEKRIQ 280
Query: 160 EGASLLFQRLGLCDFARIDGWFLPSSTHVFSSSETKYGSTEWGTILFTDINLISGMEQTS 219
E A +++ LG F+R+D ++ PS G I+F ++N I G S
Sbjct: 281 EAAVTIYKALGCSGFSRVDMFYTPS-----------------GEIVFNEVNTIPGFTSHS 323
Query: 220 FLFQQASKVGFSHSNILRTIIG 241
+G S S +L +IG
Sbjct: 324 RYPNMMKGIGLSFSQMLDKLIG 345
Score = 55.5 bits (132), Expect = 1e-07, Method: Compositional matrix adjust.
Identities = 61/266 (22%), Positives = 108/266 (40%), Gaps = 76/266 (28%)
Query: 280 REVFVIFGGDTSERQVSLMSGTNVWLNLQAFNDIEVTPCLLASSIDCSSGMDANITDPDS 339
+++ VIFGG+++E +VSL S + V+ N+ N ++ P + S +
Sbjct: 4 KKIAVIFGGNSTEYEVSLQSASAVFENINT-NKFDIIPIGITRSGE-------------- 48
Query: 340 SSRVVWSLPYSLVLRHTTEEVLAACIEAIEPDRAAFTSHLRNQVVNDLVEGLKKHSWFTG 399
W H T E + +++N+ +WF
Sbjct: 49 -----W--------YHYTGE--------------------KEKILNN--------TWFE- 66
Query: 400 FDIADELPM----RHSINEWIKLAKENQATV-----FIAVHGGIGEDGTLQSLLEAEGVP 450
D + P+ S+ ++++A + + F +HG GEDGTLQ + E G+P
Sbjct: 67 -DSKNLCPVVVSQNRSVKGFLEIASDKYRIIKVDLVFPVLHGKNGEDGTLQGIFELAGIP 125
Query: 451 YTGPGVMASKTCMDKVATSLALNHLADLGVLTINKDVRRKEDLLKTPIVDIWHELTSKLQ 510
G ++S CMDK + L L +++ K V K + + +I LT
Sbjct: 126 VVGCDTLSSALCMDKDRA----HKLVSLAGISVPKSVTFKRFNEEAAMKEIEANLTY--- 178
Query: 511 CKTLCVKPARDGCSTGVARLCCAEDL 536
L +KP R G S G+ ++ ++L
Sbjct: 179 --PLFIKPVRAGSSFGITKVIEKQEL 202
Score = 38.5 bits (88), Expect = 0.013, Method: Compositional matrix adjust.
Identities = 23/55 (41%), Positives = 31/55 (56%), Gaps = 2/55 (3%)
Query: 653 PASIMSTEALDKCKQRIELIANALQLEGFSRIDAFVNVDNGEVLIIEVNTVPGMT 707
PA I EA + ++ I AL GFSR+D F +GE++ EVNT+PG T
Sbjct: 268 PARI-DAEAEKRIQEAAVTIYKALGCSGFSRVDMFYT-PSGEIVFNEVNTIPGFT 320
>pdb|3TQT|A Chain A, Structure Of The D-Alanine-D-Alanine Ligase From Coxiella
Burnetii
pdb|3TQT|B Chain B, Structure Of The D-Alanine-D-Alanine Ligase From Coxiella
Burnetii
Length = 372
Score = 56.6 bits (135), Expect = 4e-08, Method: Compositional matrix adjust.
Identities = 76/283 (26%), Positives = 116/283 (40%), Gaps = 61/283 (21%)
Query: 426 VFIAVHGGIGEDGTLQSLLEAEGVPYTGPGVMASKTCMDKVATSLALNHLADLGVLTINK 485
VF VHG GEDG LQ LLE +PY G V +S CM+K + K
Sbjct: 102 VFPMVHGTQGEDGALQGLLELLNLPYVGANVQSSAVCMEK----------------DLTK 145
Query: 486 DVRRKEDLLKTPIVDIWHELTSKLQCKTLCVKPARDGCSTGVARLCCAEDLTVYVKALEE 545
V R + P+VD WH TL + A +G + +L V +L
Sbjct: 146 TVLRAGGI---PVVD-WH---------TLSPRDATEGVYQRLLDRWGTSELFVKAVSLGS 192
Query: 546 CLLRIPPNSFSRAHGMIEMPNPPPEILIFEPFVETDEILFSSQSTNKNADRLMWKGNSRW 605
+ +P + + E E+ ++ DRLM + R
Sbjct: 193 SVATLPVKTET------EFTKAVKEVFRYD-------------------DRLMVEPRIRG 227
Query: 606 VEITVGVIGKCGSMHSLMPSVTVKESGDILSLEEKFQGGTGINLTPPPASIMSTEALDKC 665
EI V+G G+ + +P + D S + K+ G T S+ +E++ K
Sbjct: 228 REIECAVLGN-GAPKASLPGEIIPHH-DYYSYDAKYLDPNGATTT---TSVDLSESVTKQ 282
Query: 666 KQRIELIA-NALQLEGFSRIDAFVNVDNGEVLIIEVNTVPGMT 707
Q+I + A + G +R+D FV +N +VL+ E+NT+PG T
Sbjct: 283 IQQIAIDAFKMVHCSGMARVDFFVTPNN-KVLVNEINTIPGFT 324
>pdb|3K3P|A Chain A, Crystal Structure Of The Apo Form Of D-Alanine:d-Alanine
Ligase (Ddl) From Streptococcus Mutans
pdb|3K3P|B Chain B, Crystal Structure Of The Apo Form Of D-Alanine:d-Alanine
Ligase (Ddl) From Streptococcus Mutans
Length = 383
Score = 55.5 bits (132), Expect = 1e-07, Method: Compositional matrix adjust.
Identities = 68/287 (23%), Positives = 112/287 (39%), Gaps = 60/287 (20%)
Query: 421 ENQATVFIAVHGGIGEDGTLQSLLEAEGVPYTGPGVMASKTCMDKVATSLALNHLADLGV 480
E +A VF +HG +GEDG++Q LE +PY G +++S MDK+ T+ L +
Sbjct: 118 EEEAVVFPVLHGPMGEDGSIQGFLEVLKMPYVGTNILSSSVAMDKITTNQVLESATTIPQ 177
Query: 481 LTINKDVRRKEDLLKTPIVDIWHELTSKLQCKTLCVKPARDGCSTGVARLCCAEDLTVYV 540
+ + + P+ E+ KL + VKPA G S G+++ AE+ T
Sbjct: 178 VAYVALIEGE------PLESKLAEVEEKL-IYPVFVKPANMGSSVGISK---AENRTDLK 227
Query: 541 KALEECLLRIPPNSFSRAHGMIEMPNPPPEILIFEPFVETDEILFSSQSTNKNADRLMWK 600
+A+ L K R++ +
Sbjct: 228 QAIALAL--------------------------------------------KYDSRVLIE 243
Query: 601 GNSRWVEITVGVIGKCGSMHSLMPSVTVKESGDILSLEEKFQGGTGINLTPPPASIMSTE 660
EI VG++G + + +P VK+ E K+ I + P +
Sbjct: 244 QGVDAREIEVGILGNT-DVKTTLPGEIVKDVA-FYDYEAKYIDNK-ITMAIPAE--IDPV 298
Query: 661 ALDKCKQRIELIANALQLEGFSRIDAFVNVDNGEVLIIEVNTVPGMT 707
++K + L G SR D F+ D G+V + E+NT+PG T
Sbjct: 299 IVEKMRDYAATAFRTLGCCGLSRCDFFLTED-GKVYLNELNTMPGFT 344
Score = 55.5 bits (132), Expect = 1e-07, Method: Compositional matrix adjust.
Identities = 56/222 (25%), Positives = 92/222 (41%), Gaps = 52/222 (23%)
Query: 40 VVVKPTRAGSSIGVTVAYGVIDSLKKAKGIILEGIDDRVVVELFLEGGSEFTAIVLDVGS 99
V VKP GSS+G++ A D LK+A + L+ D RV++E
Sbjct: 204 VFVKPANMGSSVGISKAENRTD-LKQAIALALK-YDSRVLIE-----------------Q 244
Query: 100 GFDCHPVVLLPTEVELQFQGSVDVRE-------KD-AIFNYRRKYLPTQQVAYHTPPRFP 151
G D E+E+ G+ DV+ KD A ++Y KY+ ++ P
Sbjct: 245 GVDAR-------EIEVGILGNTDVKTTLPGEIVKDVAFYDYEAKYI-DNKITMAIPAEID 296
Query: 152 IVVINSIREGASLLFQRLGLCDFARIDGWFLPSSTHVFSSSETKYGSTEWGTILFTDINL 211
V++ +R+ A+ F+ LG C +R D +FL TE G + ++N
Sbjct: 297 PVIVEKMRDYAATAFRTLGCCGLSRCD-FFL----------------TEDGKVYLNELNT 339
Query: 212 ISGMEQTSFLFQQASKVGFSHSNILRTIIGHACSRFPNLASY 253
+ G Q S +G S+S ++ ++ A F S+
Sbjct: 340 MPGFTQWSMYPLLWENMGLSYSVLIEELVSLAKEMFDKRESH 381
>pdb|3E5N|A Chain A, Crystal Strucutre Of D-Alanine-D-Alanine Ligase From
Xanthomonas Oryzae Pv. Oryzae Kacc10331
Length = 386
Score = 55.5 bits (132), Expect = 1e-07, Method: Compositional matrix adjust.
Identities = 68/262 (25%), Positives = 95/262 (36%), Gaps = 80/262 (30%)
Query: 281 EVFVIFGGDTSERQVSLMSGTNVWLNLQAFNDIEVTPCLLASSIDCSSGMDA----NITD 336
V +IFGG ++E +VSL S N+ L A + P L+ G+D ++ D
Sbjct: 24 RVGLIFGGKSAEHEVSLQSARNI---LDALDPQRFEPVLI--------GIDKQGQWHVND 72
Query: 337 PDSSSRVVWSLPYSLVLRHTTEEVLAACIEAIEPDRAAFTSHLRNQVVNDLVEGLKKHSW 396
PDS + A +P R A R L+ G ++
Sbjct: 73 PDSF-----------------------LLHADDPARIALHRSGRGVA---LLPGAQQQQL 106
Query: 397 FTGFDIADELPMRHSINEWIKLAKENQATVFIAVHGGIGEDGTLQSLLEAEGVPYTGPGV 456
I LA+ + VF VHG +GEDG+LQ LL +P+ G GV
Sbjct: 107 -------------RPIQPEQALAQID--VVFPIVHGTLGEDGSLQGLLRMANLPFVGSGV 151
Query: 457 MASKTCMDKVATSLALNHLADLGVLTINKDVRRKEDLLKTPIVDIWHELTSKLQCKTLC- 515
+ S MDK + K V R L P V + TL
Sbjct: 152 LGSAVAMDK----------------DMAKRVLRDARLAVAPFVCFDRHTAAHADVDTLIA 195
Query: 516 -------VKPARDGCSTGVARL 530
VKPA G S GV+++
Sbjct: 196 QLGLPLFVKPANQGSSVGVSQV 217
Score = 38.5 bits (88), Expect = 0.014, Method: Compositional matrix adjust.
Identities = 35/109 (32%), Positives = 52/109 (47%), Gaps = 13/109 (11%)
Query: 607 EITVGVIGKCGSMHSLMPSVTVKESGDILSLEEKFQGGTGINLTPPPASIMSTEALDKCK 666
EI V+G S+ V V ++ S K+ G + P A I + + +
Sbjct: 247 EIECAVLGNAVPHASVCGEVVVHDA--FYSYATKYISEHGAEIVIP-ADIDA-----QTQ 298
Query: 667 QRIELIA----NALQLEGFSRIDAFVNVDNGEVLIIEVNTVPGMTPSTV 711
QRI+ IA AL G +R+D F+ D G ++I EVNT+PG T +V
Sbjct: 299 QRIQQIAVQAYQALGCAGMARVDVFLCAD-GRIVINEVNTLPGFTRISV 346
>pdb|3RFC|A Chain A, Crystal Structure Of D-Alanine-D-Alanine Ligase A From
Xanthomonas Oryzae Pathovar Oryzae With Adp
pdb|3R5F|A Chain A, Crystal Structure Of D-Alanine-D-Alnine Ligase From
Xanthomonas Oryzae Pv. Oryzae With Atp
Length = 384
Score = 55.1 bits (131), Expect = 1e-07, Method: Compositional matrix adjust.
Identities = 68/262 (25%), Positives = 95/262 (36%), Gaps = 80/262 (30%)
Query: 281 EVFVIFGGDTSERQVSLMSGTNVWLNLQAFNDIEVTPCLLASSIDCSSGMDA----NITD 336
V +IFGG ++E +VSL S N+ L A + P L+ G+D ++ D
Sbjct: 22 RVGLIFGGKSAEHEVSLQSARNI---LDALDPQRFEPVLI--------GIDKQGQWHVND 70
Query: 337 PDSSSRVVWSLPYSLVLRHTTEEVLAACIEAIEPDRAAFTSHLRNQVVNDLVEGLKKHSW 396
PDS + A +P R A R L+ G ++
Sbjct: 71 PDSF-----------------------LLHADDPARIALHRSGRGVA---LLPGAQQQQL 104
Query: 397 FTGFDIADELPMRHSINEWIKLAKENQATVFIAVHGGIGEDGTLQSLLEAEGVPYTGPGV 456
I LA+ + VF VHG +GEDG+LQ LL +P+ G GV
Sbjct: 105 -------------RPIQPEQALAQID--VVFPIVHGTLGEDGSLQGLLRMANLPFVGSGV 149
Query: 457 MASKTCMDKVATSLALNHLADLGVLTINKDVRRKEDLLKTPIVDIWHELTSKLQCKTLC- 515
+ S MDK + K V R L P V + TL
Sbjct: 150 LGSAVAMDK----------------DMAKRVLRDARLAVAPFVCFDRHTAAHADVDTLIA 193
Query: 516 -------VKPARDGCSTGVARL 530
VKPA G S GV+++
Sbjct: 194 QLGLPLFVKPANQGSSVGVSQV 215
Score = 38.5 bits (88), Expect = 0.014, Method: Compositional matrix adjust.
Identities = 35/109 (32%), Positives = 52/109 (47%), Gaps = 13/109 (11%)
Query: 607 EITVGVIGKCGSMHSLMPSVTVKESGDILSLEEKFQGGTGINLTPPPASIMSTEALDKCK 666
EI V+G S+ V V ++ S K+ G + P A I + + +
Sbjct: 245 EIECAVLGNAVPHASVCGEVVVHDA--FYSYATKYISEHGAEIVIP-ADIDA-----QTQ 296
Query: 667 QRIELIA----NALQLEGFSRIDAFVNVDNGEVLIIEVNTVPGMTPSTV 711
QRI+ IA AL G +R+D F+ D G ++I EVNT+PG T +V
Sbjct: 297 QRIQQIAVQAYQALGCAGMARVDVFLCAD-GRIVINEVNTLPGFTRISV 344
>pdb|3I12|A Chain A, The Crystal Structure Of The D-alanyl-alanine Synthetase A
From Salmonella Enterica Subsp. Enterica Serovar
Typhimurium Str. Lt2
pdb|3I12|B Chain B, The Crystal Structure Of The D-alanyl-alanine Synthetase A
From Salmonella Enterica Subsp. Enterica Serovar
Typhimurium Str. Lt2
pdb|3I12|C Chain C, The Crystal Structure Of The D-alanyl-alanine Synthetase A
From Salmonella Enterica Subsp. Enterica Serovar
Typhimurium Str. Lt2
pdb|3I12|D Chain D, The Crystal Structure Of The D-alanyl-alanine Synthetase A
From Salmonella Enterica Subsp. Enterica Serovar
Typhimurium Str. Lt2
Length = 364
Score = 54.7 bits (130), Expect = 2e-07, Method: Compositional matrix adjust.
Identities = 37/111 (33%), Positives = 56/111 (50%), Gaps = 18/111 (16%)
Query: 426 VFIAVHGGIGEDGTLQSLLEAEGVPYTGPGVMASKTCMDKVATSLALNHLADLGV----- 480
+F VHG +GEDG+LQ +L +P+ G V++S CMDK +A L D G+
Sbjct: 102 IFPIVHGTLGEDGSLQGMLRVANLPFVGSDVLSSAACMDK---DVAKRLLRDAGLNIAPF 158
Query: 481 LTINKDVRRKEDLLKTPIVDIWHELTSKLQCKTLCVKPARDGCSTGVARLC 531
+T+ + R + E+ S+L L VKPA G S GV+++
Sbjct: 159 ITLTRTNRHAFS---------FAEVESRLGLP-LFVKPANQGSSVGVSKVA 199
Score = 37.7 bits (86), Expect = 0.022, Method: Compositional matrix adjust.
Identities = 50/208 (24%), Positives = 79/208 (37%), Gaps = 41/208 (19%)
Query: 42 VKPTRAGSSIGVTVAYGVIDSLKKAKGIILE-GIDDRVVVELFLEGGSEFTAIVL--DVG 98
VKP GSS+GV+ V + + + + L D +VVVE ++ G E VL D
Sbjct: 184 VKPANQGSSVGVS---KVANEAQYQQAVALAFEFDHKVVVEQGIK-GREIECAVLGNDNP 239
Query: 99 SGFDCHPVVLLPTEVELQFQGSVDVREKDAIFNYRRKYLPTQQVAYHTPPRFPIVVINSI 158
C +VL + Y KY+ P + P V + I
Sbjct: 240 QASTCGEIVL-----------------NSEFYAYDTKYIDDNGAQVVVPAQIPSEVNDKI 282
Query: 159 REGASLLFQRLGLCDFARIDGWFLPSSTHVFSSSETKYGSTEWGTILFTDINLISGMEQT 218
R A +Q LG AR+D + + V + T G FT+I++ + Q
Sbjct: 283 RAIAIQAYQTLGCAGMARVDVFLTADNEVVINEINTLPG--------FTNISMYPKLWQA 334
Query: 219 SFLFQQASKVGFSHSNILRTIIGHACSR 246
S G +++++ +I A R
Sbjct: 335 S---------GLGYTDLISRLIELALER 353
Score = 35.8 bits (81), Expect = 0.078, Method: Compositional matrix adjust.
Identities = 23/55 (41%), Positives = 30/55 (54%), Gaps = 2/55 (3%)
Query: 653 PASIMSTEALDKCKQRIELIANALQLEGFSRIDAFVNVDNGEVLIIEVNTVPGMT 707
PA I S E DK + L G +R+D F+ DN EV+I E+NT+PG T
Sbjct: 271 PAQIPS-EVNDKIRAIAIQAYQTLGCAGMARVDVFLTADN-EVVINEINTLPGFT 323
>pdb|4EGJ|A Chain A, Crystal Structure Of D-Alanine-D-Alanine Ligase From
Burkholderia Xenovorans
pdb|4EGJ|B Chain B, Crystal Structure Of D-Alanine-D-Alanine Ligase From
Burkholderia Xenovorans
pdb|4EGJ|C Chain C, Crystal Structure Of D-Alanine-D-Alanine Ligase From
Burkholderia Xenovorans
pdb|4EGJ|D Chain D, Crystal Structure Of D-Alanine-D-Alanine Ligase From
Burkholderia Xenovorans
Length = 334
Score = 54.3 bits (129), Expect = 3e-07, Method: Compositional matrix adjust.
Identities = 44/134 (32%), Positives = 62/134 (46%), Gaps = 10/134 (7%)
Query: 404 DELPMRHSINEWIKLAKENQATVFIAVHGGIGEDGTLQSLLEAEGVPYTGPGVMASKTCM 463
D P + L +E F A+HGG GE+G +Q L+ G+ YTG GV+ S +
Sbjct: 64 DAHPFDPAERPLAALKEEGFVRAFNALHGGYGENGQIQGALDFYGIRYTGSGVLGSALGL 123
Query: 464 DKVATSLALNHLADLGVLTIN-KDVRRKEDLLKTPIVDIWHELTSKLQCKTLCVKPARDG 522
DK T L LG+ T + V R +D E+ +KL L VKPA +G
Sbjct: 124 DKFRTKLVWQQ---LGIPTPPFEAVLRGDDYEARA-----KEIVAKLGL-PLFVKPASEG 174
Query: 523 CSTGVARLCCAEDL 536
S V ++ A+ L
Sbjct: 175 SSVAVIKVKSADAL 188
Score = 33.5 bits (75), Expect = 0.41, Method: Compositional matrix adjust.
Identities = 47/203 (23%), Positives = 76/203 (37%), Gaps = 42/203 (20%)
Query: 40 VVVKPTRAGSSIGVTVAYGVIDSLKKAKGIILEGI--DDRVVVELFLEGGSEFTAIVLDV 97
+ VKP GSS+ V + D+L A ++E + D VVVE +EGG E+TA +
Sbjct: 166 LFVKPASEGSSVAV-IKVKSADALPAA---LIEAVKFDRIVVVEKSIEGGGEYTAC---I 218
Query: 98 GSGFDCHPVVLLPTEVELQFQGSVDVREKDAIFNYRRKYLPTQQVAYHTPPRFPIVVINS 157
D + ++P ++Y KY+ Y P
Sbjct: 219 AGNLDLPVIRIVPA---------------GEFYDYHAKYI-ANDTQYLIPCGLTADEEAR 262
Query: 158 IREGASLLFQRLGLCDFARIDGWFLPSSTHVFSSSETKYGSTEWGTILFTDINLISGMEQ 217
++ A F LG D+ R D F+ + G F ++N GM
Sbjct: 263 LKVLARRAFDVLGCTDWGRAD--FMLDAD---------------GNPYFLEVNTAPGMTD 305
Query: 218 TSFLFQQASKVGFSHSNILRTII 240
S + A VG S+ ++ ++
Sbjct: 306 HSLPPKAARAVGISYQELVVAVL 328
>pdb|4EG0|A Chain A, Crystal Structure Of D-Alanine--D-Alanine Ligase From
Burkholderia Ambifaria
pdb|4EG0|B Chain B, Crystal Structure Of D-Alanine--D-Alanine Ligase From
Burkholderia Ambifaria
Length = 317
Score = 52.8 bits (125), Expect = 8e-07, Method: Compositional matrix adjust.
Identities = 40/119 (33%), Positives = 54/119 (45%), Gaps = 8/119 (6%)
Query: 418 LAKENQATVFIAVHGGIGEDGTLQSLLEAEGVPYTGPGVMASKTCMDKVATSLALNHLAD 477
L E F A+HGG GE+G +Q L+ G+ YTG GV+ S +DK T L
Sbjct: 61 LKDEGFVRAFNALHGGYGENGQIQGALDFYGIRYTGSGVLGSALGLDKFRTKLVWQQ--- 117
Query: 478 LGVLTINKDVRRKEDLLKTPIVDIWHELTSKLQCKTLCVKPARDGCSTGVARLCCAEDL 536
GV T + + D DI +L L VKPA +G S V ++ A+ L
Sbjct: 118 TGVPTPPFETVMRGDDYAARATDIVAKLG-----LPLFVKPASEGSSVAVLKVKTADAL 171
Score = 35.8 bits (81), Expect = 0.091, Method: Compositional matrix adjust.
Identities = 46/203 (22%), Positives = 76/203 (37%), Gaps = 42/203 (20%)
Query: 40 VVVKPTRAGSSIGVTVAYGVIDSLKKAKGIILEGI--DDRVVVELFLEGGSEFTAIVLDV 97
+ VKP GSS+ V + D+L A + E D V+VE +EGG E+TA +
Sbjct: 149 LFVKPASEGSSVAV-LKVKTADALPAA---LSEAATHDKIVIVEKSIEGGGEYTAC---I 201
Query: 98 GSGFDCHPVVLLPTEVELQFQGSVDVREKDAIFNYRRKYLPTQQVAYHTPPRFPIVVINS 157
D + ++P ++Y KY+ Y P P
Sbjct: 202 AGDLDLPLIKIVPA---------------GEFYDYHAKYV-ANDTQYLIPCGLPAEQETE 245
Query: 158 IREGASLLFQRLGLCDFARIDGWFLPSSTHVFSSSETKYGSTEWGTILFTDINLISGMEQ 217
++ A F LG D+ R D + L ++ G F ++N GM
Sbjct: 246 LKRIARRAFDVLGCTDWGRAD-FMLDAA----------------GNAYFLEVNTAPGMTD 288
Query: 218 TSFLFQQASKVGFSHSNILRTII 240
S + A +G +S ++ ++
Sbjct: 289 HSLPPKAARSIGIGYSELVVKVL 311
Score = 34.3 bits (77), Expect = 0.24, Method: Compositional matrix adjust.
Identities = 29/77 (37%), Positives = 38/77 (49%), Gaps = 25/77 (32%)
Query: 261 PGRSSGSKPTEALNKREGIREVFVIFGGDTSERQVSLMSGTNVWLNLQAFNDIEVTPCLL 320
PG SG P KR G +V V+FGG+++ER+VSL SG L LQ D
Sbjct: 2 PGSMSGIDP-----KRFG--KVAVLFGGESAEREVSLTSGR---LVLQGLRD-------- 43
Query: 321 ASSIDCSSGMDANITDP 337
+G+DA+ DP
Sbjct: 44 -------AGIDAHPFDP 53
>pdb|3N8D|A Chain A, Crystal Structure Of Staphylococcus Aureus Vrsa-9
D-Ala:d-Ala Ligase
pdb|3N8D|B Chain B, Crystal Structure Of Staphylococcus Aureus Vrsa-9
D-Ala:d-Ala Ligase
Length = 364
Score = 52.0 bits (123), Expect = 1e-06, Method: Compositional matrix adjust.
Identities = 37/112 (33%), Positives = 56/112 (50%), Gaps = 10/112 (8%)
Query: 425 TVFIAVHGGIGEDGTLQSLLEAEGVPYTGPGVMASKTCMDKVATSLALNH--LADLGVLT 482
VF +HG GEDGT+Q L E VPY G GV+++ + MDK+ H L L ++
Sbjct: 90 AVFPLLHGPNGEDGTIQGLFEVLDVPYVGNGVLSAASSMDKLVMKQLFEHRGLPQLPYIS 149
Query: 483 INKDVRRKEDLLKTPIVDIWHELTSKLQCKTLCVKPARDGCSTGVARLCCAE 534
+R + + + I+ + + KL VKPA G S G+++ C E
Sbjct: 150 F---LRSEYEKYEHNILKL---VNDKLNYPVF-VKPANLGSSVGISK-CNNE 193
>pdb|4EGQ|A Chain A, Crystal Structure Of D-Alanine-D-Alanine Ligase B From
Burkholderia Pseudomallei
pdb|4EGQ|B Chain B, Crystal Structure Of D-Alanine-D-Alanine Ligase B From
Burkholderia Pseudomallei
pdb|4EGQ|C Chain C, Crystal Structure Of D-Alanine-D-Alanine Ligase B From
Burkholderia Pseudomallei
pdb|4EGQ|D Chain D, Crystal Structure Of D-Alanine-D-Alanine Ligase B From
Burkholderia Pseudomallei
Length = 316
Score = 51.6 bits (122), Expect = 1e-06, Method: Compositional matrix adjust.
Identities = 41/132 (31%), Positives = 59/132 (44%), Gaps = 10/132 (7%)
Query: 404 DELPMRHSINEWIKLAKENQATVFIAVHGGIGEDGTLQSLLEAEGVPYTGPGVMASKTCM 463
D P + L E F A+HGG GE+G +Q L+ G+ YTG GV+ S +
Sbjct: 47 DAHPFDPAQRPLAALKDEGFVRAFNALHGGYGENGQIQGALDFYGIRYTGSGVLGSALGL 106
Query: 464 DKVATSLALNHLADLGVLTIN-KDVRRKEDLLKTPIVDIWHELTSKLQCKTLCVKPARDG 522
DK T L G+ T + V R +D ++ +KL L VKPA +G
Sbjct: 107 DKFRTKLVWQQ---TGIPTPPFETVMRGDDYAARA-----QDIVAKLGV-PLFVKPASEG 157
Query: 523 CSTGVARLCCAE 534
S V ++ A+
Sbjct: 158 SSVAVEKVKSAD 169
Score = 33.1 bits (74), Expect = 0.59, Method: Compositional matrix adjust.
Identities = 29/77 (37%), Positives = 37/77 (48%), Gaps = 25/77 (32%)
Query: 261 PGRSSGSKPTEALNKREGIREVFVIFGGDTSERQVSLMSGTNVWLNLQAFNDIEVTPCLL 320
PG SG P KR G +V V+ GGD++ER+VSL SG L LQ D
Sbjct: 2 PGSMSGIDP-----KRFG--KVAVLLGGDSAEREVSLNSGR---LVLQGLRD-------- 43
Query: 321 ASSIDCSSGMDANITDP 337
+G+DA+ DP
Sbjct: 44 -------AGIDAHPFDP 53
Score = 30.0 bits (66), Expect = 4.4, Method: Compositional matrix adjust.
Identities = 35/166 (21%), Positives = 59/166 (35%), Gaps = 36/166 (21%)
Query: 75 DDRVVVELFLEGGSEFTAIVLDVGSGFDCHPVVLLPTEVELQFQGSVDVREKDAIFNYRR 134
D V+VE +EGG E+TA + + D + ++P ++Y
Sbjct: 182 DKIVIVEKSIEGGGEYTAC---IAADLDLPLIRIVPA---------------GEFYDYHA 223
Query: 135 KYLPTQQVAYHTPPRFPIVVINSIREGASLLFQRLGLCDFARIDGWFLPSSTHVFSSSET 194
KY+ Y P + A F LG D+ R D + L ++
Sbjct: 224 KYI-ANDTQYLIPCGLDAAKEAEFKRIARRAFDVLGCTDWGRAD-FMLDAA--------- 272
Query: 195 KYGSTEWGTILFTDINLISGMEQTSFLFQQASKVGFSHSNILRTII 240
G F ++N GM S + A VG +S ++ ++
Sbjct: 273 -------GNPYFLEVNTAPGMTDHSLPPKAARAVGIGYSELVVKVL 311
>pdb|2I80|A Chain A, Allosteric Inhibition Of Staphylococcus Aureus
D-Alanine:d-Alanine Ligase Revealed By Crystallographic
Studies
pdb|2I80|B Chain B, Allosteric Inhibition Of Staphylococcus Aureus
D-Alanine:d-Alanine Ligase Revealed By Crystallographic
Studies
Length = 360
Score = 51.6 bits (122), Expect = 1e-06, Method: Compositional matrix adjust.
Identities = 37/112 (33%), Positives = 56/112 (50%), Gaps = 10/112 (8%)
Query: 425 TVFIAVHGGIGEDGTLQSLLEAEGVPYTGPGVMASKTCMDKVATSLALNH--LADLGVLT 482
VF +HG GEDGT+Q L E VPY G GV+++ + MDK+ H L L ++
Sbjct: 90 AVFPLLHGPNGEDGTIQGLFEVLDVPYVGNGVLSAASSMDKLVMKQLFEHRGLPQLPYIS 149
Query: 483 INKDVRRKEDLLKTPIVDIWHELTSKLQCKTLCVKPARDGCSTGVARLCCAE 534
+R + + + I+ + + KL VKPA G S G+++ C E
Sbjct: 150 F---LRSEYEKYEHNILKL---VNDKLNYPVF-VKPANLGSSVGISK-CNNE 193
>pdb|2I87|A Chain A, Allosteric Inhibition Of Staphylococcus Aureus
D-Alanine:d-Alanine Ligase Revealed By Crystallographic
Studies
pdb|2I87|B Chain B, Allosteric Inhibition Of Staphylococcus Aureus
D-Alanine:d-Alanine Ligase Revealed By Crystallographic
Studies
pdb|2I8C|A Chain A, Allosteric Inhibition Of Staphylococcus Aureus
D-Alanine:d-Alanine Ligase Revealed By Crystallographic
Studies
pdb|2I8C|B Chain B, Allosteric Inhibition Of Staphylococcus Aureus
D-Alanine:d-Alanine Ligase Revealed By Crystallographic
Studies
Length = 364
Score = 51.6 bits (122), Expect = 1e-06, Method: Compositional matrix adjust.
Identities = 37/112 (33%), Positives = 56/112 (50%), Gaps = 10/112 (8%)
Query: 425 TVFIAVHGGIGEDGTLQSLLEAEGVPYTGPGVMASKTCMDKVATSLALNH--LADLGVLT 482
VF +HG GEDGT+Q L E VPY G GV+++ + MDK+ H L L ++
Sbjct: 90 AVFPLLHGPNGEDGTIQGLFEVLDVPYVGNGVLSAASSMDKLVMKQLFEHRGLPQLPYIS 149
Query: 483 INKDVRRKEDLLKTPIVDIWHELTSKLQCKTLCVKPARDGCSTGVARLCCAE 534
+R + + + I+ + + KL VKPA G S G+++ C E
Sbjct: 150 F---LRSEYEKYEHNILKL---VNDKLNYPVF-VKPANLGSSVGISK-CNNE 193
>pdb|3Q1K|A Chain A, The Crystal Structure Of The D-Alanyl-Alanine Synthetase A
From Salmonella Enterica Typhimurium Complexed With Adp
pdb|3Q1K|B Chain B, The Crystal Structure Of The D-Alanyl-Alanine Synthetase A
From Salmonella Enterica Typhimurium Complexed With Adp
pdb|3Q1K|C Chain C, The Crystal Structure Of The D-Alanyl-Alanine Synthetase A
From Salmonella Enterica Typhimurium Complexed With Adp
pdb|3Q1K|D Chain D, The Crystal Structure Of The D-Alanyl-Alanine Synthetase A
From Salmonella Enterica Typhimurium Complexed With Adp
Length = 367
Score = 50.4 bits (119), Expect = 3e-06, Method: Compositional matrix adjust.
Identities = 36/111 (32%), Positives = 54/111 (48%), Gaps = 18/111 (16%)
Query: 426 VFIAVHGGIGEDGTLQSLLEAEGVPYTGPGVMASKTCMDKVATSLALNHLADLGV----- 480
+F VHG +GEDG+LQ L +P+ G V++S C DK +A L D G+
Sbjct: 105 IFPIVHGTLGEDGSLQGXLRVANLPFVGSDVLSSAACXDK---DVAKRLLRDAGLNIAPF 161
Query: 481 LTINKDVRRKEDLLKTPIVDIWHELTSKLQCKTLCVKPARDGCSTGVARLC 531
+T+ + R + E+ S+L L VKPA G S GV+++
Sbjct: 162 ITLTRTNRHAFS---------FAEVESRLGLP-LFVKPANQGSSVGVSKVA 202
Score = 36.2 bits (82), Expect = 0.068, Method: Compositional matrix adjust.
Identities = 48/208 (23%), Positives = 79/208 (37%), Gaps = 41/208 (19%)
Query: 42 VKPTRAGSSIGVTVAYGVIDSLKKAKGIILE-GIDDRVVVELFLEGGSEFTAIVL--DVG 98
VKP GSS+GV+ V + + + + L D +VVVE ++ G E VL D
Sbjct: 187 VKPANQGSSVGVS---KVANEAQYQQAVALAFEFDHKVVVEQGIK-GREIECAVLGNDNP 242
Query: 99 SGFDCHPVVLLPTEVELQFQGSVDVREKDAIFNYRRKYLPTQQVAYHTPPRFPIVVINSI 158
C +VL + Y KY+ P + P V + I
Sbjct: 243 QASTCGEIVL-----------------NSEFYAYDTKYIDDNGAQVVVPAQIPSEVNDKI 285
Query: 159 REGASLLFQRLGLCDFARIDGWFLPSSTHVFSSSETKYGSTEWGTILFTDINLISGMEQT 218
R A +Q LG AR+D VF +++ + ++ +IN + G
Sbjct: 286 RAIAIQAYQTLGCAGXARVD---------VFLTADNE--------VVINEINTLPGFTNI 328
Query: 219 SFLFQQASKVGFSHSNILRTIIGHACSR 246
S + G +++++ +I A R
Sbjct: 329 SXYPKLWQASGLGYTDLISRLIELALER 356
Score = 35.4 bits (80), Expect = 0.12, Method: Compositional matrix adjust.
Identities = 23/55 (41%), Positives = 30/55 (54%), Gaps = 2/55 (3%)
Query: 653 PASIMSTEALDKCKQRIELIANALQLEGFSRIDAFVNVDNGEVLIIEVNTVPGMT 707
PA I S E DK + L G +R+D F+ DN EV+I E+NT+PG T
Sbjct: 274 PAQIPS-EVNDKIRAIAIQAYQTLGCAGXARVDVFLTADN-EVVINEINTLPGFT 326
>pdb|3R23|A Chain A, Crystal Structure Of D-Alanine--D-Alanine Ligase From
Bacillus Anthracis
pdb|3R23|B Chain B, Crystal Structure Of D-Alanine--D-Alanine Ligase From
Bacillus Anthracis
pdb|3R5X|A Chain A, Crystal Structure Of D-Alanine--D-Alanine Ligase From
Bacillus Anthracis Complexed With Atp
pdb|3R5X|B Chain B, Crystal Structure Of D-Alanine--D-Alanine Ligase From
Bacillus Anthracis Complexed With Atp
pdb|3R5X|C Chain C, Crystal Structure Of D-Alanine--D-Alanine Ligase From
Bacillus Anthracis Complexed With Atp
pdb|3R5X|D Chain D, Crystal Structure Of D-Alanine--D-Alanine Ligase From
Bacillus Anthracis Complexed With Atp
Length = 307
Score = 50.4 bits (119), Expect = 4e-06, Method: Compositional matrix adjust.
Identities = 41/128 (32%), Positives = 58/128 (45%), Gaps = 31/128 (24%)
Query: 411 SINEWIKLAKENQATVF--IAVHGGIGEDGTLQSLLEAEGVPYTGPGVMASKTCMDKVAT 468
++NE L ++ + F +A+HG GEDGT+Q LE+ G+PY+G ++S C DK
Sbjct: 42 TLNEKXDLIEKAKDIDFALLALHGKYGEDGTVQGTLESLGIPYSGSNXLSSGICXDK--- 98
Query: 469 SLALNHLADLGVLTINKDVRRKEDLLKTPIVDIWHELTSKLQCK---------TLCVKPA 519
I+K + R E ++TP W ELT L VKP
Sbjct: 99 -------------NISKKILRYEG-IETP---DWIELTKXEDLNFDELDKLGFPLVVKPN 141
Query: 520 RDGCSTGV 527
G S GV
Sbjct: 142 SGGSSVGV 149
Score = 38.1 bits (87), Expect = 0.016, Method: Compositional matrix adjust.
Identities = 47/210 (22%), Positives = 77/210 (36%), Gaps = 41/210 (19%)
Query: 31 NKLDPNSGKVVVKPTRAGSSIGVTVAYGVIDSLKKAKGIILEGIDDRVVVELFLEGGSEF 90
++LD +VVKP GSS+GV + Y D L + E D VV+E +++ G E
Sbjct: 127 DELDKLGFPLVVKPNSGGSSVGVKIVYDK-DELISXLETVFEW-DSEVVIEKYIK-GEEI 183
Query: 91 TAIVLDVGSGFDCHPVVLLPTEVELQFQGSVDVREKDAIFNYRRKYLPTQQVAYHTPPRF 150
T + D LP + +R F+Y KY +
Sbjct: 184 TCSIFDGKQ---------LPI---------ISIRHAAEFFDYNAKYDDASTI--EEVIEL 223
Query: 151 PIVVINSIREGASLLFQRLGLCDFARIDGWFLPSSTHVFSSSETKYGSTEWGTILFTDIN 210
P + + + + ++ L +AR+D + G ++N
Sbjct: 224 PAELKERVNKASLACYKALKCSVYARVD------------------XXVKDGIPYVXEVN 265
Query: 211 LISGMEQTSFLFQQASKVGFSHSNILRTII 240
+ G Q S L + A G +S +L II
Sbjct: 266 TLPGXTQASLLPKSADAAGIHYSKLLDXII 295
Score = 30.4 bits (67), Expect = 3.6, Method: Compositional matrix adjust.
Identities = 17/42 (40%), Positives = 22/42 (52%), Gaps = 1/42 (2%)
Query: 284 VIFGGDTSERQVSLMSGTNVWLNLQAFNDIEVTPCLLASSID 325
VI GG +SE+QVS+ +G NL N E+ P L D
Sbjct: 8 VIXGGVSSEKQVSIXTGNEXIANLDK-NKYEIVPITLNEKXD 48
>pdb|2PVP|A Chain A, Crystal Structure Of D-Alanine-D-Alanine Ligase From
Helicobacter Pylori
pdb|2PVP|B Chain B, Crystal Structure Of D-Alanine-D-Alanine Ligase From
Helicobacter Pylori
Length = 367
Score = 45.8 bits (107), Expect = 8e-05, Method: Compositional matrix adjust.
Identities = 32/98 (32%), Positives = 49/98 (50%), Gaps = 11/98 (11%)
Query: 430 VHGGIGEDGTLQSLLEAEGVPYTGPGVMASKTCMDKVATSLALNHLADLGVLTINKDVRR 489
VHGG GEDG L SLLE + + GP + AS +K T L + DLG+ T++ +
Sbjct: 115 VHGGDGEDGKLASLLEFYRIAFIGPRIEASVLSYNKYLTKL---YAKDLGIKTLDYVLLN 171
Query: 490 KEDLLKTPIVDIWHELTSKLQCKTLCVKPARDGCSTGV 527
+++ + +D+ + VKP+ G S GV
Sbjct: 172 EKN--RANALDLMN------FNFPFIVKPSNAGSSLGV 201
>pdb|1KJ8|A Chain A, Crystal Structure Of Purt-Encoded Glycinamide
Ribonucleotide Transformylase In Complex With Mg-Atp And
Gar
pdb|1KJ8|B Chain B, Crystal Structure Of Purt-Encoded Glycinamide
Ribonucleotide Transformylase In Complex With Mg-Atp And
Gar
pdb|1KJ9|A Chain A, Crystal Structure Of Purt-Encoded Glycinamide
Ribonucleotide Transformylase Complexed With Mg-Atp
pdb|1KJ9|B Chain B, Crystal Structure Of Purt-Encoded Glycinamide
Ribonucleotide Transformylase Complexed With Mg-Atp
pdb|1KJI|A Chain A, Crystal Structure Of Glycinamide Ribonucleotide
Transformylase In Complex With Mg-Amppcp
pdb|1KJI|B Chain B, Crystal Structure Of Glycinamide Ribonucleotide
Transformylase In Complex With Mg-Amppcp
pdb|1KJJ|A Chain A, Crystal Structure Of Glycniamide Ribonucleotide
Transformylase In Complex With Mg-Atp-Gamma-S
pdb|1KJJ|B Chain B, Crystal Structure Of Glycniamide Ribonucleotide
Transformylase In Complex With Mg-Atp-Gamma-S
pdb|1KJQ|A Chain A, Crystal Structure Of Glycinamide Ribonucleotide
Transformylase In Complex With Mg-Adp
pdb|1KJQ|B Chain B, Crystal Structure Of Glycinamide Ribonucleotide
Transformylase In Complex With Mg-Adp
Length = 391
Score = 30.4 bits (67), Expect = 4.1, Method: Compositional matrix adjust.
Identities = 36/136 (26%), Positives = 57/136 (41%), Gaps = 17/136 (12%)
Query: 585 FSSQSTNKNADRLMWKGNSRW-VEITVGVIGKCGSMHSLMPSVTVKESGDILSLEEKFQG 643
++ Q A R++ +G ++ EIT+ + +H P +E GD E +Q
Sbjct: 179 YAQQGGRAGAGRVIVEGVVKFDFEITLLTVSAVDGVHFCAPVGHRQEDGD---YRESWQ- 234
Query: 644 GTGINLTPPPASIMSTEALDKCKQRIELIANALQLEGFSRIDAFVNVDNGEVLIIEVNTV 703
MS AL++ ++ + AL G ++ FV D EV+ EV+
Sbjct: 235 ----------PQQMSPLALERAQEIARKVVLALGGYGLFGVELFVCGD--EVIFSEVSPR 282
Query: 704 PGMTPSTVLIHQALSE 719
P T LI Q LSE
Sbjct: 283 PHDTGMVTLISQDLSE 298
>pdb|1EYZ|A Chain A, Structure Of Escherichia Coli Purt-Encoded Glycinamide
Ribonucleotide Transformylase Complexed With Mg And
Amppnp
pdb|1EYZ|B Chain B, Structure Of Escherichia Coli Purt-Encoded Glycinamide
Ribonucleotide Transformylase Complexed With Mg And
Amppnp
pdb|1EZ1|A Chain A, Structure Of Escherichia Coli Purt-Encoded Glycinamide
Ribonucleotide Transformylase Complexed With Mg, Amppnp,
And Gar
pdb|1EZ1|B Chain B, Structure Of Escherichia Coli Purt-Encoded Glycinamide
Ribonucleotide Transformylase Complexed With Mg, Amppnp,
And Gar
Length = 392
Score = 30.0 bits (66), Expect = 4.4, Method: Compositional matrix adjust.
Identities = 36/136 (26%), Positives = 57/136 (41%), Gaps = 17/136 (12%)
Query: 585 FSSQSTNKNADRLMWKGNSRW-VEITVGVIGKCGSMHSLMPSVTVKESGDILSLEEKFQG 643
++ Q A R++ +G ++ EIT+ + +H P +E GD E +Q
Sbjct: 180 YAQQGGRAGAGRVIVEGVVKFDFEITLLTVSAVDGVHFCAPVGHRQEDGD---YRESWQ- 235
Query: 644 GTGINLTPPPASIMSTEALDKCKQRIELIANALQLEGFSRIDAFVNVDNGEVLIIEVNTV 703
MS AL++ ++ + AL G ++ FV D EV+ EV+
Sbjct: 236 ----------PQQMSPLALERAQEIARKVVLALGGYGLFGVELFVCGD--EVIFSEVSPR 283
Query: 704 PGMTPSTVLIHQALSE 719
P T LI Q LSE
Sbjct: 284 PHDTGMVTLISQDLSE 299
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 0.400
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 22,024,612
Number of Sequences: 62578
Number of extensions: 914159
Number of successful extensions: 2430
Number of sequences better than 100.0: 39
Number of HSP's better than 100.0 without gapping: 30
Number of HSP's successfully gapped in prelim test: 9
Number of HSP's that attempted gapping in prelim test: 2316
Number of HSP's gapped (non-prelim): 103
length of query: 741
length of database: 14,973,337
effective HSP length: 106
effective length of query: 635
effective length of database: 8,340,069
effective search space: 5295943815
effective search space used: 5295943815
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: 55 (25.8 bits)