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= 002207
(953 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>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 = 108 bits (269), Expect = 2e-23, Method: Compositional matrix adjust.
Identities = 111/396 (28%), Positives = 175/396 (44%), Gaps = 68/396 (17%)
Query: 82 LICGGPSAERGISLNSARSVLDHIQGDDLLVRCYYIDRNLNAYAISSAQVYSNTPADFDF 141
L+ GG SAER +S+ SA SV+ I D+ LV+ Y+I + A Q + + P++ D
Sbjct: 42 LLYGGRSAERDVSVLSAESVMRAINYDNFLVKTYFITQ---AGDFIKTQEFDSQPSETD- 97
Query: 142 KLESLAQGFGSLSEFAEHLAANVDIVFPTIHGRFGEDGGIQEVLEKYNVPFVGTGSRACR 201
KL + S + +VFP +HG GEDG IQ LE +P+VGT +
Sbjct: 98 KLMTNDTIIASQKIKPSDIYEEEAVVFPVLHGPMGEDGSIQGFLEVLKMPYVGTNILSSS 157
Query: 202 QAFDKYDASLEMSKQGFITVPSF----LLQGSEVNESELSNWFVTNKLDPNSGKVVVKPT 257
A DK + + + T+P L++G + ES+L+ V KL V VKP
Sbjct: 158 VAMDKITTNQVL--ESATTIPQVAYVALIEGEPL-ESKLAE--VEEKL---IYPVFVKPA 209
Query: 258 RAGSSIGVTVAYGVIDSLKKAKGIILEGIDDRVVVELFLEGGSEFTAIVLDVGSGFDCHP 317
GSS+G++ A D LK+A + L+ D RV++E G D
Sbjct: 210 NMGSSVGISKAENRTD-LKQAIALALK-YDSRVLIE-----------------QGVDAR- 249
Query: 318 VVLLPTEVELQFQGSVDVRE-------KD-AIFNYRRKYLPTQQVAYHTPPRFPIVVINS 369
E+E+ G+ DV+ KD A ++Y KY+ ++ P V++
Sbjct: 250 ------EIEVGILGNTDVKTTLPGEIVKDVAFYDYEAKYI-DNKITMAIPAEIDPVIVEK 302
Query: 370 IREGASLLFQRLGLCDFARIDGWFLPSSTHVFSSSETKYGSTEWGTILFTDINLISGMEQ 429
+R+ A+ F+ LG C +R D +FL TE G + ++N + G Q
Sbjct: 303 MRDYAATAFRTLGCCGLSRCD-FFL----------------TEDGKVYLNELNTMPGFTQ 345
Query: 430 TSFLFQQASKVGFSHSNILRTIIGHACSRFPNLASY 465
S +G S+S ++ ++ A F S+
Sbjct: 346 WSMYPLLWENMGLSYSVLIEELVSLAKEMFDKRESH 381
Score = 55.5 bits (132), Expect = 1e-07, Method: Compositional matrix adjust.
Identities = 35/116 (30%), Positives = 56/116 (48%), Gaps = 7/116 (6%)
Query: 633 ENQATVFIAVHGGIGEDGTLQSLLEAEGVPYTGPGVMASKTCMDKVATSLALNHLADLGV 692
E +A VF +HG +GEDG++Q LE +PY G +++S MDK+ T+ L +
Sbjct: 118 EEEAVVFPVLHGPMGEDGSIQGFLEVLKMPYVGTNILSSSVAMDKITTNQVLESATTIPQ 177
Query: 693 LTINKDVRRKEDLLKTPIVDIWHELTSKLQCKTLCVKPARDGCSTGVARLCCAEDL 748
+ + + P+ E+ KL + VKPA G S G+++ DL
Sbjct: 178 VAYVALIEGE------PLESKLAEVEEKL-IYPVFVKPANMGSSVGISKAENRTDL 226
>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 = 93.2 bits (230), Expect = 7e-19, Method: Compositional matrix adjust.
Identities = 101/386 (26%), Positives = 164/386 (42%), Gaps = 56/386 (14%)
Query: 79 RVGLICGGPSAERGISLNSARSVLDHIQGDDLLVRCYYIDRNLNAYAIS--SAQVYSNTP 136
++ +I GG S E +SL SA +V ++I + + I R+ Y + ++ +NT
Sbjct: 5 KIAVIFGGNSTEYEVSLQSASAVFENINTNKFDIIPIGITRSGEWYHYTGEKEKILNNTW 64
Query: 137 ADFDFKL-------ESLAQGFGSLSEFAEHLAANVDIVFPTIHGRFGEDGGIQEVLEKYN 189
+ L +GF ++ ++ VD+VFP +HG+ GEDG +Q + E
Sbjct: 65 FEDSKNLCPVVVSQNRSVKGFLEIAS-DKYRIIKVDLVFPVLHGKNGEDGTLQGIFELAG 123
Query: 190 VPFVGTGSRACRQAFDKYDASLEMSKQGFITVPSFLLQGSEVNESELSNWFVTNKLDPNS 249
+P VG + + DK A +S G I+VP + NE N P
Sbjct: 124 IPVVGCDTLSSALCMDKDRAHKLVSLAG-ISVPK-SVTFKRFNEEAAMKEIEANLTYP-- 179
Query: 250 GKVVVKPTRAGSSIGVTVAYGVIDSLKKAKGIILEGIDDRVVVELFLEGGSEFTAIVLDV 309
+ +KP RAGSS G+T ++E + +EL E +E IV +
Sbjct: 180 --LFIKPVRAGSSFGITK--------------VIEKQELDAAIELAFEHDTE--VIVEET 221
Query: 310 GSGFDCHPVVLLPTEVELQFQGSVD-VREKDAIFNYRRKY-LPTQQVAYHTPPRFPIVVI 367
+GF+ VL E+ G VD + F+Y KY L + ++ + P R
Sbjct: 222 INGFEVGCAVLGIDEL---IVGRVDEIELSSGFFDYTEKYTLKSSKI--YMPARIDAEAE 276
Query: 368 NSIREGASLLFQRLGLCDFARIDGWFLPSSTHVFSSSETKYGSTEWGTILFTDINLISGM 427
I+E A +++ LG F+R+D ++ PS G I+F ++N I G
Sbjct: 277 KRIQEAAVTIYKALGCSGFSRVDMFYTPS-----------------GEIVFNEVNTIPGF 319
Query: 428 EQTSFLFQQASKVGFSHSNILRTIIG 453
S +G S S +L +IG
Sbjct: 320 TSHSRYPNMMKGIGLSFSQMLDKLIG 345
Score = 55.8 bits (133), Expect = 1e-07, Method: Compositional matrix adjust.
Identities = 61/266 (22%), Positives = 108/266 (40%), Gaps = 76/266 (28%)
Query: 492 REVFVIFGGDTSERQVSLMSGTNVWLNLQAFNDIEVTPCLLASSIDCSSGMDANITDPDS 551
+++ VIFGG+++E +VSL S + V+ N+ N ++ P + S +
Sbjct: 4 KKIAVIFGGNSTEYEVSLQSASAVFENINT-NKFDIIPIGITRSGE-------------- 48
Query: 552 SSRVVWSLPYSLVLRHTTEEVLAACIEAIEPDRAAFTSHLRNQVVNDLVEGLKKHSWFTG 611
W H T E + +++N+ +WF
Sbjct: 49 -----W--------YHYTGE--------------------KEKILNN--------TWFE- 66
Query: 612 FDIADELPM----RHSINEWIKLAKENQATV-----FIAVHGGIGEDGTLQSLLEAEGVP 662
D + P+ S+ ++++A + + F +HG GEDGTLQ + E G+P
Sbjct: 67 -DSKNLCPVVVSQNRSVKGFLEIASDKYRIIKVDLVFPVLHGKNGEDGTLQGIFELAGIP 125
Query: 663 YTGPGVMASKTCMDKVATSLALNHLADLGVLTINKDVRRKEDLLKTPIVDIWHELTSKLQ 722
G ++S CMDK + L L +++ K V K + + +I LT
Sbjct: 126 VVGCDTLSSALCMDKDRA----HKLVSLAGISVPKSVTFKRFNEEAAMKEIEANLTY--- 178
Query: 723 CKTLCVKPARDGCSTGVARLCCAEDL 748
L +KP R G S G+ ++ ++L
Sbjct: 179 --PLFIKPVRAGSSFGITKVIEKQEL 202
Score = 38.1 bits (87), Expect = 0.020, Method: Compositional matrix adjust.
Identities = 23/55 (41%), Positives = 31/55 (56%), Gaps = 2/55 (3%)
Query: 865 PASIMSTEALDKCKQRIELIANALQLEGFSRIDAFVNVDNGEVLIIEVNTVPGMT 919
PA I EA + ++ I AL GFSR+D F +GE++ EVNT+PG T
Sbjct: 268 PARI-DAEAEKRIQEAAVTIYKALGCSGFSRVDMFYT-PSGEIVFNEVNTIPGFT 320
>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 = 92.4 bits (228), Expect = 1e-18, Method: Compositional matrix adjust.
Identities = 106/398 (26%), Positives = 164/398 (41%), Gaps = 65/398 (16%)
Query: 78 LRVGLICGGPSAERGISLNSARSVLDHIQGDDLLVRCYYIDRNLNAYAISSAQVY---SN 134
LRVG++ GG SAE +SL SA++++D I V ID+ + ++ A+ Y ++
Sbjct: 4 LRVGIVFGGKSAEHEVSLQSAKNIVDAIDKTRFDVVLLGIDK-AGQWHVNDAENYLQNAD 62
Query: 135 TPADFDFKLE--SLAQGFGSLSEFAEHLAAN---------VDIVFPTIHGRFGEDGGIQE 183
PA + SLAQ G +H N VD++FP +HG GEDG +Q
Sbjct: 63 DPAHIALRPSAISLAQVPGK----HQHQLINAQNGQPLPTVDVIFPIVHGTLGEDGSLQG 118
Query: 184 VLEKYNVPFVGTGSRACRQAFDKYDASLEMSKQGFITVPSFLLQGSEVNESELSNWFVTN 243
+L N+PFVG+ + DK A + G P L + N S V +
Sbjct: 119 MLRVANLPFVGSDVLSSAACMDKDVAKRLLRDAGLNIAPFITL--TRTNRHAFSFAEVES 176
Query: 244 KLDPNSGKVVVKPTRAGSSIGVTVAYGVIDSLKKAKGIILE-GIDDRVVVELFLEGGSEF 302
+L + VKP GSS+GV+ V + + + + L D +VVVE ++ G E
Sbjct: 177 RL---GLPLFVKPANQGSSVGVS---KVANEAQYQQAVALAFEFDHKVVVEQGIK-GREI 229
Query: 303 TAIVL--DVGSGFDCHPVVLLPTEVELQFQGSVDVREKDAIFNYRRKYLPTQQVAYHTPP 360
VL D C +VL + Y KY+ P
Sbjct: 230 ECAVLGNDNPQASTCGEIVL-----------------NSEFYAYDTKYIDDNGAQVVVPA 272
Query: 361 RFPIVVINSIREGASLLFQRLGLCDFARIDGWFLPSSTHVFSSSETKYGSTEWGTILFTD 420
+ P V + IR A +Q LG AR+D + + V + T G FT+
Sbjct: 273 QIPSEVNDKIRAIAIQAYQTLGCAGMARVDVFLTADNEVVINEINTLPG--------FTN 324
Query: 421 INLISGMEQTSFLFQQASKVGFSHSNILRTIIGHACSR 458
I++ + Q S G +++++ +I A R
Sbjct: 325 ISMYPKLWQAS---------GLGYTDLISRLIELALER 353
Score = 54.7 bits (130), Expect = 3e-07, Method: Compositional matrix adjust.
Identities = 37/111 (33%), Positives = 56/111 (50%), Gaps = 18/111 (16%)
Query: 638 VFIAVHGGIGEDGTLQSLLEAEGVPYTGPGVMASKTCMDKVATSLALNHLADLGV----- 692
+F VHG +GEDG+LQ +L +P+ G V++S CMDK +A L D G+
Sbjct: 102 IFPIVHGTLGEDGSLQGMLRVANLPFVGSDVLSSAACMDK---DVAKRLLRDAGLNIAPF 158
Query: 693 LTINKDVRRKEDLLKTPIVDIWHELTSKLQCKTLCVKPARDGCSTGVARLC 743
+T+ + R + E+ S+L L VKPA G S GV+++
Sbjct: 159 ITLTRTNRHAFS---------FAEVESRLGLP-LFVKPANQGSSVGVSKVA 199
Score = 36.2 bits (82), Expect = 0.10, Method: Compositional matrix adjust.
Identities = 23/55 (41%), Positives = 30/55 (54%), Gaps = 2/55 (3%)
Query: 865 PASIMSTEALDKCKQRIELIANALQLEGFSRIDAFVNVDNGEVLIIEVNTVPGMT 919
PA I S E DK + L G +R+D F+ DN EV+I E+NT+PG T
Sbjct: 271 PAQIPS-EVNDKIRAIAIQAYQTLGCAGMARVDVFLTADN-EVVINEINTLPGFT 323
>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 = 89.4 bits (220), Expect = 1e-17, Method: Compositional matrix adjust.
Identities = 104/398 (26%), Positives = 163/398 (40%), Gaps = 65/398 (16%)
Query: 78 LRVGLICGGPSAERGISLNSARSVLDHIQGDDLLVRCYYIDRNLNAYAISSAQVY---SN 134
LRVG++ GG SAE +SL SA++++D I V ID+ + ++ A+ Y ++
Sbjct: 7 LRVGIVFGGKSAEHEVSLQSAKNIVDAIDKTRFDVVLLGIDK-AGQWHVNDAENYLQNAD 65
Query: 135 TPADFDFKLE--SLAQGFGSLSEFAEHLAAN---------VDIVFPTIHGRFGEDGGIQE 183
PA + SLAQ G +H N VD++FP +HG GEDG +Q
Sbjct: 66 DPAHIALRPSAISLAQVPGK----HQHQLINAQNGQPLPTVDVIFPIVHGTLGEDGSLQG 121
Query: 184 VLEKYNVPFVGTGSRACRQAFDKYDASLEMSKQGFITVPSFLLQGSEVNESELSNWFVTN 243
L N+PFVG+ + DK A + G P L + N S V +
Sbjct: 122 XLRVANLPFVGSDVLSSAACXDKDVAKRLLRDAGLNIAPFITL--TRTNRHAFSFAEVES 179
Query: 244 KLDPNSGKVVVKPTRAGSSIGVTVAYGVIDSLKKAKGIILE-GIDDRVVVELFLEGGSEF 302
+L + VKP GSS+GV+ V + + + + L D +VVVE ++ G E
Sbjct: 180 RL---GLPLFVKPANQGSSVGVS---KVANEAQYQQAVALAFEFDHKVVVEQGIK-GREI 232
Query: 303 TAIVL--DVGSGFDCHPVVLLPTEVELQFQGSVDVREKDAIFNYRRKYLPTQQVAYHTPP 360
VL D C +VL + Y KY+ P
Sbjct: 233 ECAVLGNDNPQASTCGEIVL-----------------NSEFYAYDTKYIDDNGAQVVVPA 275
Query: 361 RFPIVVINSIREGASLLFQRLGLCDFARIDGWFLPSSTHVFSSSETKYGSTEWGTILFTD 420
+ P V + IR A +Q LG AR+D VF +++ + ++ +
Sbjct: 276 QIPSEVNDKIRAIAIQAYQTLGCAGXARVD---------VFLTADNE--------VVINE 318
Query: 421 INLISGMEQTSFLFQQASKVGFSHSNILRTIIGHACSR 458
IN + G S + G +++++ +I A R
Sbjct: 319 INTLPGFTNISXYPKLWQASGLGYTDLISRLIELALER 356
Score = 50.4 bits (119), Expect = 4e-06, Method: Compositional matrix adjust.
Identities = 36/111 (32%), Positives = 54/111 (48%), Gaps = 18/111 (16%)
Query: 638 VFIAVHGGIGEDGTLQSLLEAEGVPYTGPGVMASKTCMDKVATSLALNHLADLGV----- 692
+F VHG +GEDG+LQ L +P+ G V++S C DK +A L D G+
Sbjct: 105 IFPIVHGTLGEDGSLQGXLRVANLPFVGSDVLSSAACXDK---DVAKRLLRDAGLNIAPF 161
Query: 693 LTINKDVRRKEDLLKTPIVDIWHELTSKLQCKTLCVKPARDGCSTGVARLC 743
+T+ + R + E+ S+L L VKPA G S GV+++
Sbjct: 162 ITLTRTNRHAFS---------FAEVESRLGLP-LFVKPANQGSSVGVSKVA 202
Score = 35.4 bits (80), Expect = 0.15, Method: Compositional matrix adjust.
Identities = 23/55 (41%), Positives = 30/55 (54%), Gaps = 2/55 (3%)
Query: 865 PASIMSTEALDKCKQRIELIANALQLEGFSRIDAFVNVDNGEVLIIEVNTVPGMT 919
PA I S E DK + L G +R+D F+ DN EV+I E+NT+PG T
Sbjct: 274 PAQIPS-EVNDKIRAIAIQAYQTLGCAGXARVDVFLTADN-EVVINEINTLPGFT 326
>pdb|3E5N|A Chain A, Crystal Strucutre Of D-Alanine-D-Alanine Ligase From
Xanthomonas Oryzae Pv. Oryzae Kacc10331
Length = 386
Score = 81.3 bits (199), Expect = 2e-15, Method: Compositional matrix adjust.
Identities = 99/402 (24%), Positives = 145/402 (36%), Gaps = 69/402 (17%)
Query: 76 RVLRVGLICGGPSAERGISLNSARSVLDHIQGDDLLVRCYYIDRNLNAYAISSAQVYSNT 135
R +RVGLI GG SAE +SL SAR++LD + ID+ Q + N
Sbjct: 21 RKIRVGLIFGGKSAEHEVSLQSARNILDALDPQRFEPVLIGIDKQ--------GQWHVND 72
Query: 136 PADF--------DFKLESLAQGFGSLSEFA---------EHLAANVDIVFPTIHGRFGED 178
P F L +G L E A +D+VFP +HG GED
Sbjct: 73 PDSFLLHADDPARIALHRSGRGVALLPGAQQQQLRPIQPEQALAQIDVVFPIVHGTLGED 132
Query: 179 GGIQEVLEKYNVPFVGTGSRACRQAFDKYDASLEMSKQGFITVPSFLLQGSEVNESELSN 238
G +Q +L N+PFVG+G A DK A + P +++
Sbjct: 133 GSLQGLLRMANLPFVGSGVLGSAVAMDKDMAKRVLRDARLAVAPFVCFDRHTAAHADVDT 192
Query: 239 WFVTNKLDPNSGKVVVKPTRAGSSIGVTVAYGVIDSLKKAKGIILEGIDDRVVVELFLEG 298
L + VKP GSS+GV+ A + D +V+VE +
Sbjct: 193 LIAQLGL-----PLFVKPANQGSSVGVSQVR--TADAFAAALALALAYDHKVLVEAAV-A 244
Query: 299 GSEFTAIVLD--VGSGFDCHPVVLLPTEVELQFQGSVDVREKDAIFNYRRKYLPTQQVAY 356
G E VL V C VV+ DA ++Y KY+
Sbjct: 245 GREIECAVLGNAVPHASVCGEVVV-----------------HDAFYSYATKYISEHGAEI 287
Query: 357 HTPPRFPIVVINSIREGASLLFQRLGLCDFARIDGWFLPSSTHVFSSSETKYGSTEWGTI 416
P I++ A +Q LG AR+D VF ++ G I
Sbjct: 288 VIPADIDAQTQQRIQQIAVQAYQALGCAGMARVD---------VFLCAD--------GRI 330
Query: 417 LFTDINLISGMEQTSFLFQQASKVGFSHSNILRTIIGHACSR 458
+ ++N + G + S + G + ++ +I A R
Sbjct: 331 VINEVNTLPGFTRISVYPKLWQASGLDYRGLITRLIELALER 372
Score = 55.5 bits (132), Expect = 1e-07, Method: Compositional matrix adjust.
Identities = 69/258 (26%), Positives = 93/258 (36%), Gaps = 72/258 (27%)
Query: 493 EVFVIFGGDTSERQVSLMSGTNVWLNLQAFNDIEVTPCLLASSIDCSSGMDANITDPDSS 552
V +IFGG ++E +VSL S N+ L A + P L+ ID N DPDS
Sbjct: 24 RVGLIFGGKSAEHEVSLQSARNI---LDALDPQRFEPVLIG--IDKQGQWHVN--DPDSF 76
Query: 553 SRVVWSLPYSLVLRHTTEEVLAACIEAIEPDRAAFTSHLRNQVVNDLVEGLKKHSWFTGF 612
+ A +P R A R L+ G ++
Sbjct: 77 -----------------------LLHADDPARIALHRSGRGVA---LLPGAQQQQL---- 106
Query: 613 DIADELPMRHSINEWIKLAKENQATVFIAVHGGIGEDGTLQSLLEAEGVPYTGPGVMASK 672
I LA+ + VF VHG +GEDG+LQ LL +P+ G GV+ S
Sbjct: 107 ---------RPIQPEQALAQID--VVFPIVHGTLGEDGSLQGLLRMANLPFVGSGVLGSA 155
Query: 673 TCMDKVATSLALNHLADLGVLTINKDVRRKEDLLKTPIVDIWHELTSKLQCKTLC----- 727
MDK + K V R L P V + TL
Sbjct: 156 VAMDK----------------DMAKRVLRDARLAVAPFVCFDRHTAAHADVDTLIAQLGL 199
Query: 728 ---VKPARDGCSTGVARL 742
VKPA G S GV+++
Sbjct: 200 PLFVKPANQGSSVGVSQV 217
Score = 38.1 bits (87), Expect = 0.021, Method: Compositional matrix adjust.
Identities = 35/109 (32%), Positives = 52/109 (47%), Gaps = 13/109 (11%)
Query: 819 EITVGVIGKCGSMHSLMPSVTVKESGDILSLEEKFQGGTGINLTPPPASIMSTEALDKCK 878
EI V+G S+ V V ++ S K+ G + P A I + + +
Sbjct: 247 EIECAVLGNAVPHASVCGEVVVHDA--FYSYATKYISEHGAEIVIP-ADIDA-----QTQ 298
Query: 879 QRIELIA----NALQLEGFSRIDAFVNVDNGEVLIIEVNTVPGMTPSTV 923
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 = 81.3 bits (199), Expect = 3e-15, Method: Compositional matrix adjust.
Identities = 99/402 (24%), Positives = 145/402 (36%), Gaps = 69/402 (17%)
Query: 76 RVLRVGLICGGPSAERGISLNSARSVLDHIQGDDLLVRCYYIDRNLNAYAISSAQVYSNT 135
R +RVGLI GG SAE +SL SAR++LD + ID+ Q + N
Sbjct: 19 RKIRVGLIFGGKSAEHEVSLQSARNILDALDPQRFEPVLIGIDKQ--------GQWHVND 70
Query: 136 PADF--------DFKLESLAQGFGSLSEFA---------EHLAANVDIVFPTIHGRFGED 178
P F L +G L E A +D+VFP +HG GED
Sbjct: 71 PDSFLLHADDPARIALHRSGRGVALLPGAQQQQLRPIQPEQALAQIDVVFPIVHGTLGED 130
Query: 179 GGIQEVLEKYNVPFVGTGSRACRQAFDKYDASLEMSKQGFITVPSFLLQGSEVNESELSN 238
G +Q +L N+PFVG+G A DK A + P +++
Sbjct: 131 GSLQGLLRMANLPFVGSGVLGSAVAMDKDMAKRVLRDARLAVAPFVCFDRHTAAHADVDT 190
Query: 239 WFVTNKLDPNSGKVVVKPTRAGSSIGVTVAYGVIDSLKKAKGIILEGIDDRVVVELFLEG 298
L + VKP GSS+GV+ A + D +V+VE +
Sbjct: 191 LIAQLGL-----PLFVKPANQGSSVGVSQVR--TADAFAAALALALAYDHKVLVEAAV-A 242
Query: 299 GSEFTAIVLD--VGSGFDCHPVVLLPTEVELQFQGSVDVREKDAIFNYRRKYLPTQQVAY 356
G E VL V C VV+ DA ++Y KY+
Sbjct: 243 GREIECAVLGNAVPHASVCGEVVV-----------------HDAFYSYATKYISEHGAEI 285
Query: 357 HTPPRFPIVVINSIREGASLLFQRLGLCDFARIDGWFLPSSTHVFSSSETKYGSTEWGTI 416
P I++ A +Q LG AR+D VF ++ G I
Sbjct: 286 VIPADIDAQTQQRIQQIAVQAYQALGCAGMARVD---------VFLCAD--------GRI 328
Query: 417 LFTDINLISGMEQTSFLFQQASKVGFSHSNILRTIIGHACSR 458
+ ++N + G + S + G + ++ +I A R
Sbjct: 329 VINEVNTLPGFTRISVYPKLWQASGLDYRGLITRLIELALER 370
Score = 55.5 bits (132), Expect = 1e-07, Method: Compositional matrix adjust.
Identities = 69/258 (26%), Positives = 93/258 (36%), Gaps = 72/258 (27%)
Query: 493 EVFVIFGGDTSERQVSLMSGTNVWLNLQAFNDIEVTPCLLASSIDCSSGMDANITDPDSS 552
V +IFGG ++E +VSL S N+ L A + P L+ ID N DPDS
Sbjct: 22 RVGLIFGGKSAEHEVSLQSARNI---LDALDPQRFEPVLIG--IDKQGQWHVN--DPDSF 74
Query: 553 SRVVWSLPYSLVLRHTTEEVLAACIEAIEPDRAAFTSHLRNQVVNDLVEGLKKHSWFTGF 612
+ A +P R A R L+ G ++
Sbjct: 75 -----------------------LLHADDPARIALHRSGRGVA---LLPGAQQQQL---- 104
Query: 613 DIADELPMRHSINEWIKLAKENQATVFIAVHGGIGEDGTLQSLLEAEGVPYTGPGVMASK 672
I LA+ + VF VHG +GEDG+LQ LL +P+ G GV+ S
Sbjct: 105 ---------RPIQPEQALAQID--VVFPIVHGTLGEDGSLQGLLRMANLPFVGSGVLGSA 153
Query: 673 TCMDKVATSLALNHLADLGVLTINKDVRRKEDLLKTPIVDIWHELTSKLQCKTLC----- 727
MDK + K V R L P V + TL
Sbjct: 154 VAMDK----------------DMAKRVLRDARLAVAPFVCFDRHTAAHADVDTLIAQLGL 197
Query: 728 ---VKPARDGCSTGVARL 742
VKPA G S GV+++
Sbjct: 198 PLFVKPANQGSSVGVSQV 215
Score = 38.5 bits (88), Expect = 0.020, Method: Compositional matrix adjust.
Identities = 35/109 (32%), Positives = 52/109 (47%), Gaps = 13/109 (11%)
Query: 819 EITVGVIGKCGSMHSLMPSVTVKESGDILSLEEKFQGGTGINLTPPPASIMSTEALDKCK 878
EI V+G S+ V V ++ S K+ G + P A I + + +
Sbjct: 245 EIECAVLGNAVPHASVCGEVVVHDA--FYSYATKYISEHGAEIVIP-ADIDA-----QTQ 296
Query: 879 QRIELIA----NALQLEGFSRIDAFVNVDNGEVLIIEVNTVPGMTPSTV 923
QRI+ IA AL G +R+D F+ D G ++I EVNT+PG T +V
Sbjct: 297 QRIQQIAVQAYQALGCAGMARVDVFLCAD-GRIVINEVNTLPGFTRISV 344
>pdb|1IOW|A Chain A, Complex Of Y216f D-Ala:d-Ala Ligase With Adp And A
Phosphoryl Phosphinate
Length = 306
Score = 77.8 bits (190), Expect = 3e-14, Method: Compositional matrix adjust.
Identities = 89/314 (28%), Positives = 138/314 (43%), Gaps = 71/314 (22%)
Query: 638 VFIAVHGGIGEDGTLQSLLEAEGVPYTGPGVMASKTCMDKVATSLALNHLADLGVLTINK 697
VFIA+HG GEDGTLQ +LE G+PYTG GVMAS MDK+ + L L A L V
Sbjct: 58 VFIALHGRGGEDGTLQGMLELMGLPYTGSGVMASALSMDKLRSKL-LWQGAGLPVAPWVA 116
Query: 698 DVRRKEDLLKTPIVDIWHELTSKLQCKTLCVKPARDGCSTGVARLCCAEDLTVYVKALEE 757
R + + + D S L + VKP+R+G S G++++ V AL++
Sbjct: 117 LTRAE---FEKGLSDKQLAEISALGLPVI-VKPSREGSSVGMSKV-------VAENALQD 165
Query: 758 CLLRIPPNSFSRAHGMIEMPNPPPEILIFEPFVETDEILFSSQSTNKNADRLMWKGNSRW 817
LR+ F +E+L +W
Sbjct: 166 A-LRL-------------------------AFQHDEEVLI-----------------EKW 182
Query: 818 V---EITVGVIGKCGSMHSLMPSVTVKESGDILSLEEKFQGGTGINLTPPPASIMSTEAL 874
+ E TV ++G+ ++PS+ ++ SG E KF PA + +++
Sbjct: 183 LSGPEFTVAILGE-----EILPSIRIQPSGTFYDYEAKFLSDETQYFC--PAGLEASQ-- 233
Query: 875 DKCKQRIELIA-NALQLEGFSRIDAFVNVDNGEVLIIEVNTVPGMTPSTVLIHQALSEQP 933
+ Q + L A L +G+ RID ++ D G+ ++E NT PGMT +++ A Q
Sbjct: 234 EANLQALVLKAWTTLGCKGWGRIDVMLDSD-GQFYLLEANTSPGMTSHSLVPMAA--RQA 290
Query: 934 PMYPHQFFRKVLDL 947
M Q ++L+L
Sbjct: 291 GMSFSQLVVRILEL 304
Score = 71.2 bits (173), Expect = 2e-12, Method: Compositional matrix adjust.
Identities = 91/375 (24%), Positives = 156/375 (41%), Gaps = 77/375 (20%)
Query: 79 RVGLICGGPSAERGISLNSARSVLDHIQGDDLLVRCYYIDRNLNAYAISSAQVYSNTPAD 138
++ ++ GG SAER +SLNS +VL ++ + ++AY + P +
Sbjct: 4 KIAVLLGGTSAEREVSLNSGAAVLAGLR-----------EGGIDAYPVD--------PKE 44
Query: 139 FDF-KLESLAQGFGSLSEFAEHLAANVDIVFPTIHGRFGEDGGIQEVLEKYNVPFVGTGS 197
D +L+S+ GF VF +HGR GEDG +Q +LE +P+ G+G
Sbjct: 45 VDVTQLKSM--GFQK--------------VFIALHGRGGEDGTLQGMLELMGLPYTGSGV 88
Query: 198 RACRQAFDKYDASLEMSKQGFITVPSFLLQGSEVNESELSNWFVTNKLDPNSGKVVVKPT 257
A + DK + L G P L +E E LS+ + ++ V+VKP+
Sbjct: 89 MASALSMDKLRSKLLWQGAGLPVAPWVALTRAEF-EKGLSDKQLA-EISALGLPVIVKPS 146
Query: 258 RAGSSIGVTVAYGVIDSLKKAKGIILEGIDDRVVVELFLEGGSEFTAIVLDVGSGFDCHP 317
R GSS+G++ ++L+ A + + D+ V++E +L G EFT +L G + P
Sbjct: 147 REGSSVGMSKVVAE-NALQDALRLAFQH-DEEVLIEKWLS-GPEFTVAIL----GEEILP 199
Query: 318 VVLLPTEVELQFQGSVDVREKDAIFNYRRKYLPTQQVAYHTPPRFPIVVINSIREGASLL 377
S+ ++ ++Y K+L + + Y P +++
Sbjct: 200 --------------SIRIQPSGTFYDYEAKFL-SDETQYFCPAGLEASQEANLQALVLKA 244
Query: 378 FQRLGLCDFARIDGWFLPSSTHVFSSSETKYGSTEWGTILFTDINLISGMEQTSFLFQQA 437
+ LG + RID V S+ G + N GM S + A
Sbjct: 245 WTTLGCKGWGRID---------VMLDSD--------GQFYLLEANTSPGMTSHSLVPMAA 287
Query: 438 SKVGFSHSNILRTII 452
+ G S S ++ I+
Sbjct: 288 RQAGMSFSQLVVRIL 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 = 6e-14, Method: Compositional matrix adjust.
Identities = 88/314 (28%), Positives = 138/314 (43%), Gaps = 71/314 (22%)
Query: 638 VFIAVHGGIGEDGTLQSLLEAEGVPYTGPGVMASKTCMDKVATSLALNHLADLGVLTINK 697
VFIA+HG GEDGTLQ +LE G+PYTG GVMAS MDK+ + L L A L V
Sbjct: 58 VFIALHGRGGEDGTLQGMLELMGLPYTGSGVMASALSMDKLRSKL-LWQGAGLPVAPWVA 116
Query: 698 DVRRKEDLLKTPIVDIWHELTSKLQCKTLCVKPARDGCSTGVARLCCAEDLTVYVKALEE 757
R + + + D S L + VKP+R+G S G++++ V AL++
Sbjct: 117 LTRAE---FEKGLSDKQLAEISALGLPVI-VKPSREGSSVGMSKV-------VAENALQD 165
Query: 758 CLLRIPPNSFSRAHGMIEMPNPPPEILIFEPFVETDEILFSSQSTNKNADRLMWKGNSRW 817
LR+ F +E+L +W
Sbjct: 166 A-LRL-------------------------AFQHDEEVLI-----------------EKW 182
Query: 818 V---EITVGVIGKCGSMHSLMPSVTVKESGDILSLEEKFQGGTGINLTPPPASIMSTEAL 874
+ E TV ++G+ ++PS+ ++ SG E K+ PA + +++
Sbjct: 183 LSGPEFTVAILGE-----EILPSIRIQPSGTFYDYEAKYLSDETQYFC--PAGLEASQ-- 233
Query: 875 DKCKQRIELIA-NALQLEGFSRIDAFVNVDNGEVLIIEVNTVPGMTPSTVLIHQALSEQP 933
+ Q + L A L +G+ RID ++ D G+ ++E NT PGMT +++ A Q
Sbjct: 234 EANLQALVLKAWTTLGCKGWGRIDVMLDSD-GQFYLLEANTSPGMTSHSLVPMAA--RQA 290
Query: 934 PMYPHQFFRKVLDL 947
M Q ++L+L
Sbjct: 291 GMSFSQLVVRILEL 304
Score = 73.2 bits (178), Expect = 6e-13, Method: Compositional matrix adjust.
Identities = 92/375 (24%), Positives = 156/375 (41%), Gaps = 77/375 (20%)
Query: 79 RVGLICGGPSAERGISLNSARSVLDHIQGDDLLVRCYYIDRNLNAYAISSAQVYSNTPAD 138
++ ++ GG SAER +SLNS +VL ++ + ++AY + P +
Sbjct: 4 KIAVLLGGTSAEREVSLNSGAAVLAGLR-----------EGGIDAYPVD--------PKE 44
Query: 139 FDF-KLESLAQGFGSLSEFAEHLAANVDIVFPTIHGRFGEDGGIQEVLEKYNVPFVGTGS 197
D +L+S+ GF VF +HGR GEDG +Q +LE +P+ G+G
Sbjct: 45 VDVTQLKSM--GFQK--------------VFIALHGRGGEDGTLQGMLELMGLPYTGSGV 88
Query: 198 RACRQAFDKYDASLEMSKQGFITVPSFLLQGSEVNESELSNWFVTNKLDPNSGKVVVKPT 257
A + DK + L G P L +E E LS+ + ++ V+VKP+
Sbjct: 89 MASALSMDKLRSKLLWQGAGLPVAPWVALTRAEF-EKGLSDKQLA-EISALGLPVIVKPS 146
Query: 258 RAGSSIGVTVAYGVIDSLKKAKGIILEGIDDRVVVELFLEGGSEFTAIVLDVGSGFDCHP 317
R GSS+G++ ++L+ A + + D+ V++E +L G EFT +L G + P
Sbjct: 147 REGSSVGMSKVVAE-NALQDALRLAFQH-DEEVLIEKWLS-GPEFTVAIL----GEEILP 199
Query: 318 VVLLPTEVELQFQGSVDVREKDAIFNYRRKYLPTQQVAYHTPPRFPIVVINSIREGASLL 377
S+ ++ ++Y KYL + + Y P +++
Sbjct: 200 --------------SIRIQPSGTFYDYEAKYL-SDETQYFCPAGLEASQEANLQALVLKA 244
Query: 378 FQRLGLCDFARIDGWFLPSSTHVFSSSETKYGSTEWGTILFTDINLISGMEQTSFLFQQA 437
+ LG + RID V S+ G + N GM S + A
Sbjct: 245 WTTLGCKGWGRID---------VMLDSD--------GQFYLLEANTSPGMTSHSLVPMAA 287
Query: 438 SKVGFSHSNILRTII 452
+ G S S ++ I+
Sbjct: 288 RQAGMSFSQLVVRIL 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 = 76.6 bits (187), Expect = 7e-14, Method: Compositional matrix adjust.
Identities = 80/299 (26%), Positives = 124/299 (41%), Gaps = 67/299 (22%)
Query: 629 KLAKENQATVFIAVHGGIGEDGTLQSLLEAEGVPYTGPGVMASKTCMDKVATSLALNHLA 688
+L ++ VFIA+HG GEDGTLQ +LE +PYTG GVMAS MDK+ T L L
Sbjct: 52 QLKEQGFDKVFIALHGRGGEDGTLQGVLEFLQLPYTGSGVMASALTMDKLRTKLVWQALG 111
Query: 689 DLGVLTINKDVRRKEDLLKTPIVDIWHELTSKLQCKTLCVKPARDGCSTGVARLCCAEDL 748
L I+ V +T + +KL L VKP+ +G S G++++ A +L
Sbjct: 112 ----LPISPYVALNRQQFETLSPEELVACVAKLGLP-LIVKPSHEGSSVGMSKVDHASEL 166
Query: 749 TVYVKALEECLLRIPPNSFSRAHGMIEMPNPPPEILIFEPFVETDEILFSSQSTNKNADR 808
KAL E ++D
Sbjct: 167 Q---KALVEAF-------------------------------------------QHDSDV 180
Query: 809 LMWKGNSRWV---EITVGVIGKCGSMHSLMPSVTVKESGDILSLEEKFQGGTGINLTPPP 865
L+ +W+ E TV ++G ++PS+ ++ G + K+ P
Sbjct: 181 LI----EKWLSGPEFTVAILGD-----EVLPSIRIQPPGVFYDYDAKYLSDKTQYFCP-- 229
Query: 866 ASIMSTEALDKCKQRIELIANALQLEGFSRIDAFVNVDNGEVLIIEVNTVPGMTPSTVL 924
S +S E+ + +AL G+ R+D + D G ++EVNT PGMT +++
Sbjct: 230 -SGLSDESEQQLAALALQAYHALDCSGWGRVDVMQDRD-GHFYLLEVNTSPGMTSHSLV 286
Score = 66.6 bits (161), Expect = 5e-11, Method: Compositional matrix adjust.
Identities = 75/287 (26%), Positives = 119/287 (41%), Gaps = 70/287 (24%)
Query: 79 RVGLICGGPSAERGISLNSARSVLDHIQGDDLLVRCYYIDRNLNAYAISSAQVYSNTPAD 138
+V ++ GG SAER +SL S ++VL ++ + ++AY + +
Sbjct: 7 KVAVLLGGTSAEREVSLLSGQAVLAGLK-----------EAGIDAYGVDTK--------- 46
Query: 139 FDFKLESLA-QGFGSLSEFAEHLAANVDIVFPTIHGRFGEDGGIQEVLEKYNVPFVGTGS 197
DF + L QGF D VF +HGR GEDG +Q VLE +P+ G+G
Sbjct: 47 -DFPVTQLKEQGF--------------DKVFIALHGRGGEDGTLQGVLEFLQLPYTGSGV 91
Query: 198 RACRQAFDKYDASLEMSKQGFITVPSFLL---QGSEVNESELSNWFVTNKLDPNSGKVVV 254
A DK L G P L Q ++ EL L ++V
Sbjct: 92 MASALTMDKLRTKLVWQALGLPISPYVALNRQQFETLSPEELVACVAKLGL-----PLIV 146
Query: 255 KPTRAGSSIGVTVAYGVIDSLKKAKGIILEGI--DDRVVVELFLEGGSEFTAIVLDVGSG 312
KP+ GSS+G++ +D + + ++E D V++E +L G EFT +L G
Sbjct: 147 KPSHEGSSVGMS----KVDHASELQKALVEAFQHDSDVLIEKWLS-GPEFTVAIL----G 197
Query: 313 FDCHPVVLLPTEVELQFQGSVDVREKDAIFNYRRKYLPTQQVAYHTP 359
+ P S+ ++ ++Y KYL + + Y P
Sbjct: 198 DEVLP--------------SIRIQPPGVFYDYDAKYL-SDKTQYFCP 229
>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 = 73.6 bits (179), Expect = 5e-13, Method: Compositional matrix adjust.
Identities = 97/382 (25%), Positives = 149/382 (39%), Gaps = 65/382 (17%)
Query: 78 LRVGLICGGPSAERGISLNSARSVLDHIQ-GDDLLVRCYYIDRNLNAYAISSAQVYSNTP 136
+RV LI GG S E +SL SA VL HI DL V L A+++ + +
Sbjct: 1 MRVLLIAGGVSPEHEVSLLSAEGVLRHIPFPTDLAVIAQDGRWLLGEKALTALEAKAAPE 60
Query: 137 ADFDFKLESLAQGFGSLSEFAEHLAANVDIVFPTIHGRFGEDGGIQEVLEKYNVPFVGTG 196
+ F + + D+VFP +HGRFGEDG +Q LE P+VG G
Sbjct: 61 GEHPFPPPLSWERY--------------DVVFPLLHGRFGEDGTVQGFLELLGKPYVGAG 106
Query: 197 SRACRQAFDKYDASLEMSKQGFITVPSFLLQGSEVNESELSNWFVTNKLDPNSGKVVVKP 256
A DK + +++ G VP ++ E VKP
Sbjct: 107 VAASALCMDKDLSKRVLAQAGVPVVPWVAVRKGEPPVVPFDP------------PFFVKP 154
Query: 257 TRAGSSIGVTVAYGVIDSLKKAKGIILEGIDDRVVVELFLEGGSEFTAIVLDVGSGF-DC 315
GSS+G++ D L+ A + D++ VVE L E VL G+ F +
Sbjct: 155 ANTGSSVGISRVERFQD-LEAALALAFR-YDEKAVVEKALSPVRELEVGVL--GNVFGEA 210
Query: 316 HPVVLLPTEVELQFQGSVDVREKDAIFNYRRKYLPTQQVAYHTPPRFPIVVINSIREGAS 375
PV +VR + ++Y KY P + P P +++E A
Sbjct: 211 SPV--------------GEVRYEAPFYDYETKYTPGRAELLIPAPLDP-GTQETVQELAL 255
Query: 376 LLFQRLGLCDFARIDGWFLPSSTHVFSSSETKYGSTEWGTILFTDINLISGMEQTSFLFQ 435
++ LG+ AR+D +FL G + ++N I G TS +
Sbjct: 256 KAYKVLGVRGMARVD-FFLAE-----------------GELYLNELNTIPGFTPTSMYPR 297
Query: 436 QASKVGFSHSNILRTIIGHACS 457
G ++ +LR ++ A +
Sbjct: 298 LFEAGGVAYPELLRRLVELALT 319
Score = 72.0 bits (175), Expect = 2e-12, Method: Compositional matrix adjust.
Identities = 84/312 (26%), Positives = 115/312 (36%), Gaps = 82/312 (26%)
Query: 630 LAKENQATVFIAVHGGIGEDGTLQSLLEAEGVPYTGPGVMASKTCMDKVATSLALNHLAD 689
L+ E VF +HG GEDGT+Q LE G PY G GV AS CMDK L+ LA
Sbjct: 69 LSWERYDVVFPLLHGRFGEDGTVQGFLELLGKPYVGAGVAASALCMDK---DLSKRVLAQ 125
Query: 690 LGVLTINKDVRRKEDLLKTPIVDIWHELTSKLQCKTLCVKPARDGCSTGVARLCCAEDLT 749
GV + RK E VKPA G S G++R+ +DL
Sbjct: 126 AGVPVVPWVAVRK------------GEPPVVPFDPPFFVKPANTGSSVGISRVERFQDL- 172
Query: 750 VYVKALEECLLRIPPNSFSRAHGMIEMPNPPPEILIFEPFVETDEILFSSQSTNKNADRL 809
E L + + + +
Sbjct: 173 -------EAALAL--------------------------------------AFRYDEKAV 187
Query: 810 MWKGNSRWVEITVGVIGKCGSMHSLMPSVTVKESGDILSLEEKFQGGTGINLTPPPASIM 869
+ K S E+ VGV+G S P V+ E K+ G L P P
Sbjct: 188 VEKALSPVRELEVGVLGNVFGEAS--PVGEVRYEAPFYDYETKYTPGRAELLIPAPLDPG 245
Query: 870 STEALDKCKQRIELIA-NALQLEGFSRIDAFVNVDNGEVLIIEVNTVPGMTPSTVLIHQA 928
+ E + Q + L A L + G +R+D F+ GE+ + E+NT+PG TP++
Sbjct: 246 TQETV----QELALKAYKVLGVRGMARVDFFLA--EGELYLNELNTIPGFTPTS------ 293
Query: 929 LSEQPPMYPHQF 940
MYP F
Sbjct: 294 ------MYPRLF 299
>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 = 73.6 bits (179), Expect = 5e-13, Method: Compositional matrix adjust.
Identities = 97/382 (25%), Positives = 149/382 (39%), Gaps = 65/382 (17%)
Query: 78 LRVGLICGGPSAERGISLNSARSVLDHIQ-GDDLLVRCYYIDRNLNAYAISSAQVYSNTP 136
+RV LI GG S E +SL SA VL HI DL V L A+++ + +
Sbjct: 4 MRVLLIAGGVSPEHEVSLLSAEGVLRHIPFPTDLAVIAQDGRWLLGEKALTALEAKAAPE 63
Query: 137 ADFDFKLESLAQGFGSLSEFAEHLAANVDIVFPTIHGRFGEDGGIQEVLEKYNVPFVGTG 196
+ F + + D+VFP +HGRFGEDG +Q LE P+VG G
Sbjct: 64 GEHPFPPPLSWERY--------------DVVFPLLHGRFGEDGTVQGFLELLGKPYVGAG 109
Query: 197 SRACRQAFDKYDASLEMSKQGFITVPSFLLQGSEVNESELSNWFVTNKLDPNSGKVVVKP 256
A DK + +++ G VP ++ E VKP
Sbjct: 110 VAASALCMDKDLSKRVLAQAGVPVVPWVAVRKGEPPVVPFDP------------PFFVKP 157
Query: 257 TRAGSSIGVTVAYGVIDSLKKAKGIILEGIDDRVVVELFLEGGSEFTAIVLDVGSGF-DC 315
GSS+G++ D L+ A + D++ VVE L E VL G+ F +
Sbjct: 158 ANTGSSVGISRVERFQD-LEAALALAFR-YDEKAVVEKALSPVRELEVGVL--GNVFGEA 213
Query: 316 HPVVLLPTEVELQFQGSVDVREKDAIFNYRRKYLPTQQVAYHTPPRFPIVVINSIREGAS 375
PV +VR + ++Y KY P + P P +++E A
Sbjct: 214 SPV--------------GEVRYEAPFYDYETKYTPGRAELLIPAPLDP-GTQETVQELAL 258
Query: 376 LLFQRLGLCDFARIDGWFLPSSTHVFSSSETKYGSTEWGTILFTDINLISGMEQTSFLFQ 435
++ LG+ AR+D +FL G + ++N I G TS +
Sbjct: 259 KAYKVLGVRGMARVD-FFLAE-----------------GELYLNELNTIPGFTPTSMYPR 300
Query: 436 QASKVGFSHSNILRTIIGHACS 457
G ++ +LR ++ A +
Sbjct: 301 LFEAGGVAYPELLRRLVELALT 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: 630 LAKENQATVFIAVHGGIGEDGTLQSLLEAEGVPYTGPGVMASKTCMDKVATSLALNHLAD 689
L+ E VF +HG GEDGT+Q LE G PY G GV AS CMDK L+ LA
Sbjct: 72 LSWERYDVVFPLLHGRFGEDGTVQGFLELLGKPYVGAGVAASALCMDK---DLSKRVLAQ 128
Query: 690 LGVLTINKDVRRKEDLLKTPIVDIWHELTSKLQCKTLCVKPARDGCSTGVARLCCAEDLT 749
GV + RK E VKPA G S G++R+ +DL
Sbjct: 129 AGVPVVPWVAVRK------------GEPPVVPFDPPFFVKPANTGSSVGISRVERFQDL- 175
Query: 750 VYVKALEECLLRIPPNSFSRAHGMIEMPNPPPEILIFEPFVETDEILFSSQSTNKNADRL 809
E L + + + +
Sbjct: 176 -------EAALAL--------------------------------------AFRYDEKAV 190
Query: 810 MWKGNSRWVEITVGVIGKCGSMHSLMPSVTVKESGDILSLEEKFQGGTGINLTPPPASIM 869
+ K S E+ VGV+G S P V+ E K+ G L P P
Sbjct: 191 VEKALSPVRELEVGVLGNVFGEAS--PVGEVRYEAPFYDYETKYTPGRAELLIPAPLDPG 248
Query: 870 STEALDKCKQRIELIA-NALQLEGFSRIDAFVNVDNGEVLIIEVNTVPGMTPSTVLIHQA 928
+ E + Q + L A L + G +R+D F+ GE+ + E+NT+PG TP++
Sbjct: 249 TQETV----QELALKAYKVLGVRGMARVDFFLA--EGELYLNELNTIPGFTPTS------ 296
Query: 929 LSEQPPMYPHQF 940
MYP F
Sbjct: 297 ------MYPRLF 302
>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: 638 VFIAVHGGIGEDGTLQSLLEAEGVPYTGPGVMASKTCMDKVATSLALNH--LADLGVLTI 695
V +HG +GEDG +Q LLE G+PY G + +S CMDK T L +A T+
Sbjct: 94 VLPVLHGKLGEDGAIQGLLELSGIPYVGCDIQSSALCMDKSLTYLVARSAGIATPNFWTV 153
Query: 696 NKDVRRKEDLLKTPIVDIWHELTSKLQCKTLCVKPARDGCSTGVARLCCAEDLTVYVKAL 755
D + D L P+ VKPAR G S GV+++ EDL
Sbjct: 154 TADEKIPTDQLTYPVF----------------VKPARSGSSFGVSKVAREEDL------- 190
Query: 756 EECLLRIPPNSFSRAHGMIEMPNPPPEILIFEPFVETDEILFSSQSTNKNADRLMWKGNS 815
G +E ++ E V EI + +M G
Sbjct: 191 ---------------QGAVEAAREYDSKVLIEEAVIGTEIGCA----------VMGNGP- 224
Query: 816 RWVEITVGVIGKCGSMHSLMPSVTVKESGDILSLEEKFQGGTGINLTPPPASIMSTEALD 875
E+ G + + H + E + G+ + PA I ST +
Sbjct: 225 ---ELITGEVDQITLSHGFFK----------IHQESTPESGSDNSAVTVPADI-STTSRS 270
Query: 876 KCKQRIELIANALQLEGFSRIDAFVNVDNGEVLIIEVNTVPGMT 919
+ + + AL G SR+D F+ D G+V++ EVNT PGMT
Sbjct: 271 LVQDTAKAVYRALGCRGLSRVDLFLTED-GKVVLNEVNTFPGMT 313
Score = 66.6 bits (161), Expect = 6e-11, Method: Compositional matrix adjust.
Identities = 92/395 (23%), Positives = 157/395 (39%), Gaps = 69/395 (17%)
Query: 75 GRVLRVGLICGGPSAERGISLNSARSVLDHIQGDDLLVRCYYIDRNLNAYAISSAQVYSN 134
G +++G+I GG S E IS+ SAR V H+ G + Y A+ + +
Sbjct: 1 GSHMKIGIIFGGVSEEHDISVKSAREVATHL-GTGVFEPFYLGITKSGAWQLCDGPGENW 59
Query: 135 TPADFDFKLESLAQGFGSLS--EFAEHLAANVDIVFPTIHGRFGEDGGIQEVLEKYNVPF 192
+ + S + L E ++ +D+V P +HG+ GEDG IQ +LE +P+
Sbjct: 60 EDGNCRPAVLSPDRSVHGLLVLEQGKYETIRLDLVLPVLHGKLGEDGAIQGLLELSGIPY 119
Query: 193 VGTGSRACRQAFDKYDASLEMSKQGFITVPSFLLQGSEVNESELSNWFVTNK----LDPN 248
VG ++ DK L +++ I P+F W VT D
Sbjct: 120 VGCDIQSSALCMDKSLTYL-VARSAGIATPNF--------------WTVTADEKIPTDQL 164
Query: 249 SGKVVVKPTRAGSSIGVTVAYGVIDSLKKAKGIILEGIDDRVVVELFLEGGSEFTAIVLD 308
+ V VKP R+GSS GV+ K A+ L+G +E E+ + VL
Sbjct: 165 TYPVFVKPARSGSSFGVS---------KVAREEDLQGA---------VEAAREYDSKVLI 206
Query: 309 ----VGSGFDCHPVVLLPTEVELQFQGSVD-VREKDAIFNYRRKYLP---TQQVAYHTPP 360
+G+ C ++ EL G VD + F ++ P + A P
Sbjct: 207 EEAVIGTEIGC---AVMGNGPEL-ITGEVDQITLSHGFFKIHQESTPESGSDNSAVTVPA 262
Query: 361 RFPIVVINSIREGASLLFQRLGLCDFARIDGWFLPSSTHVFSSSETKYGSTEWGTILFTD 420
+ +++ A +++ LG +R+D FL TE G ++ +
Sbjct: 263 DISTTSRSLVQDTAKAVYRALGCRGLSRVD-LFL----------------TEDGKVVLNE 305
Query: 421 INLISGMEQTSFLFQQASKVGFSHSNILRTIIGHA 455
+N GM S + + G S ++++ ++ A
Sbjct: 306 VNTFPGMTSYSRYPRMMTAAGLSRADVIDRLVSLA 340
>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 = 70.9 bits (172), Expect = 4e-12, Method: Compositional matrix adjust.
Identities = 105/389 (26%), Positives = 158/389 (40%), Gaps = 53/389 (13%)
Query: 85 GGPSAERGISLNSARSVLDHIQGDDLLVRCYYI---------DRNLNAYAISS---AQVY 132
GG S E IS SA S+L ++ V I D N +A I++ QV
Sbjct: 18 GGRSNEHAISCVSAGSILRNLDSRRFDVIAVGITPAGSWVLTDANPDALTITNRELPQVK 77
Query: 133 SNTPADFDFKLESLAQG-FGSLSEFAEHLAANVDIVFPTIHGRFGEDGGIQEVLEKYNVP 191
S + + + G SL A + +VD+VFP +HG +GEDG IQ +LE VP
Sbjct: 78 SGSGTELALPADPRRGGQLVSLPPGAGEVLESVDVVFPVLHGPYGEDGTIQGLLELAGVP 137
Query: 192 FVGTGSRACRQAFDKYDASLEMSKQGFITVPSFLLQG--SEVNESELSNWFVTNKLDPNS 249
+VG G A DK ++ G +L+ S ++ E +
Sbjct: 138 YVGAGVLASAVGMDKEFTKKLLAADGLPVGAYAVLRPPRSTLHRQECERLGL-------- 189
Query: 250 GKVVVKPTRAGSSIGVTVAYGVIDSLKKAKGIILEGIDDRVVVELFLEGGSEFTAIVLDV 309
V VKP R GSSIGV+ D L A D +V+VE + G E VL++
Sbjct: 190 -PVFVKPARGGSSIGVS-RVSSWDQLPAAVARARRH-DPKVIVEAAIS-GRELECGVLEM 245
Query: 310 GSGFDCHPVVLLPTEVELQFQGSVDVREKDAIFNYRRKYLPTQQVAYHTPPRFPIVVINS 369
G + T E++ G V RE D+ +++ KYL P + V +
Sbjct: 246 PDG-----TLEASTLGEIRVAG-VRGRE-DSFYDFATKYL-DDAAELDVPAKVDDQVAEA 297
Query: 370 IREGASLLFQRLGLCDFARIDGWFLPSSTHVFSSSETKYGSTEWGTILFTDINLISGMEQ 429
IR+ A F + AR+D +FL T+ G ++ +IN + G
Sbjct: 298 IRQLAIRAFAAIDCRGLARVD-FFL----------------TDDGPVI-NEINTMPGFTT 339
Query: 430 TSFLFQQASKVGFSHSNILRTIIGHACSR 458
S + + G + +L T+I +R
Sbjct: 340 ISMYPRMWAASGVDYPTLLATMIETTLAR 368
Score = 62.4 bits (150), Expect = 1e-09, Method: Compositional matrix adjust.
Identities = 46/122 (37%), Positives = 60/122 (49%), Gaps = 14/122 (11%)
Query: 633 ENQATVFIAVHGGIGEDGTLQSLLEAEGVPYTGPGVMASKTCMDKVATS--LALNHLADL 690
E+ VF +HG GEDGT+Q LLE GVPY G GV+AS MDK T LA + L +
Sbjct: 108 ESVDVVFPVLHGPYGEDGTIQGLLELAGVPYVGAGVLASAVGMDKEFTKKLLAADGLP-V 166
Query: 691 GVLTINKDVRRKEDLLKTPIVDIWHELTSKLQCKTLCVKPARDGCSTGVARLCCAEDLTV 750
G + L+ P + + +L VKPAR G S GV+R+ + L
Sbjct: 167 GAYAV----------LRPPRSTLHRQECERLGLPVF-VKPARGGSSIGVSRVSSWDQLPA 215
Query: 751 YV 752
V
Sbjct: 216 AV 217
>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 = 70.9 bits (172), Expect = 4e-12, Method: Compositional matrix adjust.
Identities = 97/381 (25%), Positives = 148/381 (38%), Gaps = 65/381 (17%)
Query: 79 RVGLICGGPSAERGISLNSARSVLDHIQ-GDDLLVRCYYIDRNLNAYAISSAQVYSNTPA 137
RV LI GG S E +SL SA VL HI DL V L A+++ + +
Sbjct: 2 RVLLIAGGVSPEHEVSLLSAEGVLRHIPFPTDLAVIAQDGRWLLGEKALTALEAKAAPEG 61
Query: 138 DFDFKLESLAQGFGSLSEFAEHLAANVDIVFPTIHGRFGEDGGIQEVLEKYNVPFVGTGS 197
+ F + + D+VFP +HGRFGEDG +Q LE P+VG G
Sbjct: 62 EHPFPPPLSWERY--------------DVVFPLLHGRFGEDGTVQGFLELLGKPYVGAGV 107
Query: 198 RACRQAFDKYDASLEMSKQGFITVPSFLLQGSEVNESELSNWFVTNKLDPNSGKVVVKPT 257
A DK + +++ G VP ++ E VKP
Sbjct: 108 AASALCXDKDLSKRVLAQAGVPVVPWVAVRKGEPPVVPFDP------------PFFVKPA 155
Query: 258 RAGSSIGVTVAYGVIDSLKKAKGIILEGIDDRVVVELFLEGGSEFTAIVLDVGSGF-DCH 316
GSS+G++ D L+ A + D++ VVE L E VL G+ F +
Sbjct: 156 NTGSSVGISRVERFQD-LEAALALAFR-YDEKAVVEKALSPVRELEVGVL--GNVFGEAS 211
Query: 317 PVVLLPTEVELQFQGSVDVREKDAIFNYRRKYLPTQQVAYHTPPRFPIVVINSIREGASL 376
PV +VR + ++Y KY P + P P +++E A
Sbjct: 212 PV--------------GEVRYEAPFYDYETKYTPGRAELLIPAPLDP-GTQETVQELALK 256
Query: 377 LFQRLGLCDFARIDGWFLPSSTHVFSSSETKYGSTEWGTILFTDINLISGMEQTSFLFQQ 436
++ LG+ AR+D +FL G + ++N I G TS +
Sbjct: 257 AYKVLGVRGXARVD-FFLAE-----------------GELYLNELNTIPGFTPTSXYPRL 298
Query: 437 ASKVGFSHSNILRTIIGHACS 457
G ++ +LR ++ A +
Sbjct: 299 FEAGGVAYPELLRRLVELALT 319
Score = 67.8 bits (164), Expect = 3e-11, Method: Compositional matrix adjust.
Identities = 79/294 (26%), Positives = 110/294 (37%), Gaps = 70/294 (23%)
Query: 630 LAKENQATVFIAVHGGIGEDGTLQSLLEAEGVPYTGPGVMASKTCMDKVATSLALNHLAD 689
L+ E VF +HG GEDGT+Q LE G PY G GV AS C DK L+ LA
Sbjct: 69 LSWERYDVVFPLLHGRFGEDGTVQGFLELLGKPYVGAGVAASALCXDK---DLSKRVLAQ 125
Query: 690 LGVLTINKDVRRKEDLLKTPIVDIWHELTSKLQCKTLCVKPARDGCSTGVARLCCAEDLT 749
GV + RK E VKPA G S G++R+ +DL
Sbjct: 126 AGVPVVPWVAVRK------------GEPPVVPFDPPFFVKPANTGSSVGISRVERFQDL- 172
Query: 750 VYVKALEECLLRIPPNSFSRAHGMIEMPNPPPEILIFEPFVETDEILFSSQSTNKNADRL 809
E L + + + +
Sbjct: 173 -------EAALAL--------------------------------------AFRYDEKAV 187
Query: 810 MWKGNSRWVEITVGVIGKCGSMHSLMPSVTVKESGDILSLEEKFQGGTGINLTPPPASIM 869
+ K S E+ VGV+G S P V+ E K+ G L P P
Sbjct: 188 VEKALSPVRELEVGVLGNVFGEAS--PVGEVRYEAPFYDYETKYTPGRAELLIPAPLDPG 245
Query: 870 STEALDKCKQRIELIA-NALQLEGFSRIDAFVNVDNGEVLIIEVNTVPGMTPST 922
+ E + Q + L A L + G +R+D F+ GE+ + E+NT+PG TP++
Sbjct: 246 TQETV----QELALKAYKVLGVRGXARVDFFLA--EGELYLNELNTIPGFTPTS 293
>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 = 68.9 bits (167), Expect = 1e-11, Method: Compositional matrix adjust.
Identities = 95/396 (23%), Positives = 155/396 (39%), Gaps = 61/396 (15%)
Query: 78 LRVGLICGGPSAERGISLNSARSVLDHIQGDDLLVRCYYIDRNLNAYAISSAQVYSNTPA 137
L + ++CGG S E IS+ SA+++++ + L+ +ID Y I +++
Sbjct: 5 LHISVLCGGQSTEHEISIQSAKNIVNTLDAAKYLISVIFIDHVGRWYLIDQPEMFLAHSP 64
Query: 138 DFDFKLES---LAQGFGSLSEFAEHLAAN-----VDIVFPTIHGRFGEDGGIQEVLEKYN 189
D K S + FG ++ + L + D VFP +HG GEDG +Q +LE N
Sbjct: 65 DHLVKEGSARPITIAFGDAAKPWQSLNGDGRRYSADCVFPMVHGTQGEDGALQGLLELLN 124
Query: 190 VPFVGTGSRACRQAFDKYDASLEMSKQGFITV-------PSFLLQGSEVNESELSNWFVT 242
+P+VG ++ +K D + + + G I V P +G V + L W
Sbjct: 125 LPYVGANVQSSAVCMEK-DLTKTVLRAGGIPVVDWHTLSPRDATEG--VYQRLLDRW--- 178
Query: 243 NKLDPNSGKVVVKPTRAGSSIGVTVAYGVIDSLKKAKGIILEGIDDRVVVELFLEGGSEF 302
+ ++ VK GSS+ + K K + DDR++VE + G E
Sbjct: 179 -----GTSELFVKAVSLGSSVATLPVKTETEFTKAVKEVFR--YDDRLMVEPRIR-GREI 230
Query: 303 TAIVLDVGSGFDCHPVVLLPTEVELQFQGSVDVREKDAIFNYRRKYLPTQQVAYHTPPRF 362
VL G+ P LP E+ + D ++Y KYL T
Sbjct: 231 ECAVLGNGA-----PKASLPGEI---------IPHHD-YYSYDAKYLDPNGATTTTSVDL 275
Query: 363 PIVVINSIREGASLLFQRLGLCDFARIDGWFLPSSTHVFSSSETKYGSTEWGTILFTDIN 422
V I++ A F+ + AR+D + P++ +L +IN
Sbjct: 276 SESVTKQIQQIAIDAFKMVHCSGMARVDFFVTPNN-----------------KVLVNEIN 318
Query: 423 LISGMEQTSFLFQQASKVGFSHSNILRTIIGHACSR 458
I G S + G N+L +I A R
Sbjct: 319 TIPGFTNISMYPKMWEASGLPCPNLLDQLIELAIDR 354
Score = 56.2 bits (134), Expect = 8e-08, Method: Compositional matrix adjust.
Identities = 77/284 (27%), Positives = 117/284 (41%), Gaps = 63/284 (22%)
Query: 638 VFIAVHGGIGEDGTLQSLLEAEGVPYTGPGVMASKTCMDKVATSLALNHLADLGVLTINK 697
VF VHG GEDG LQ LLE +PY G V +S CM+K + K
Sbjct: 102 VFPMVHGTQGEDGALQGLLELLNLPYVGANVQSSAVCMEK----------------DLTK 145
Query: 698 DVRRKEDLLKTPIVDIWHELTSKLQCKTLCVKPARDGCSTGVARLCCAEDLTVYVKALEE 757
V R + P+VD WH TL + A +G + +L V +L
Sbjct: 146 TVLRAGGI---PVVD-WH---------TLSPRDATEGVYQRLLDRWGTSELFVKAVSLGS 192
Query: 758 CLLRIPPNSFSRAHGMIEMPNPPPEILIFEPFVETD-EILFSSQSTNKNADRLMWKGNSR 816
+ +P V+T+ E + + + DRLM + R
Sbjct: 193 SVATLP--------------------------VKTETEFTKAVKEVFRYDDRLMVEPRIR 226
Query: 817 WVEITVGVIGKCGSMHSLMPSVTVKESGDILSLEEKFQGGTGINLTPPPASIMSTEALDK 876
EI V+G G+ + +P + D S + K+ G T S+ +E++ K
Sbjct: 227 GREIECAVLGN-GAPKASLPGEIIPHH-DYYSYDAKYLDPNGATTT---TSVDLSESVTK 281
Query: 877 CKQRIELIA-NALQLEGFSRIDAFVNVDNGEVLIIEVNTVPGMT 919
Q+I + A + G +R+D FV +N +VL+ E+NT+PG T
Sbjct: 282 QIQQIAIDAFKMVHCSGMARVDFFVTPNN-KVLVNEINTIPGFT 324
>pdb|1E4E|A Chain A, D-Alanyl-D-Lacate Ligase
Length = 343
Score = 68.6 bits (166), Expect = 2e-11, Method: Compositional matrix adjust.
Identities = 66/287 (22%), Positives = 115/287 (40%), Gaps = 74/287 (25%)
Query: 639 FIAVHGGIGEDGTLQSLLEAEGVPYTGPGVMASKTCMDKVATSLALNH--LADLGVLTIN 696
F A+HG GEDG++Q L E G+P+ G + +S CMDK T + + +A IN
Sbjct: 95 FSALHGKSGEDGSIQGLFELSGIPFVGCDIQSSAICMDKSLTYIVAKNAGIATPAFWVIN 154
Query: 697 KDVRRKEDLLKTPIVDIWHELTSKLQCKTLCVKPARDGCSTGVARLCCAEDLTVYVKALE 756
KD R P+ VKPAR G S GV ++ A
Sbjct: 155 KDDRPVAATFTYPVF----------------VKPARSGSSFGVKKVNSA----------- 187
Query: 757 ECLLRIPPNSFSRAHGMIEMPNPPPEILIFEPFVETDEILFSSQSTNKNADRLMWKGNSR 816
DE+ ++ +S + +++ +
Sbjct: 188 ------------------------------------DELDYAIESARQYDSKILIEQAVS 211
Query: 817 WVEITVGVIGKCGSMHSLMPSV-TVKESGDILSLEEKFQ---GGTGINLTPPPASIMSTE 872
E+ V+G ++ ++ V ++ I + ++ + G +T P + +S E
Sbjct: 212 GCEVGCAVLGNSAAL--VVGEVDQIRLQYGIFRIHQEVEPEKGSENAVITVP--ADLSAE 267
Query: 873 ALDKCKQRIELIANALQLEGFSRIDAFVNVDNGEVLIIEVNTVPGMT 919
+ ++ ++ I L G +R+D F+ DNG +++ EVNT+PG T
Sbjct: 268 ERGRIQETVKKIYKTLGCRGLARVDMFLQ-DNGRIVLNEVNTLPGFT 313
Score = 55.8 bits (133), Expect = 1e-07, Method: Compositional matrix adjust.
Identities = 62/263 (23%), Positives = 103/263 (39%), Gaps = 39/263 (14%)
Query: 158 EHLAANVDIVFPTIHGRFGEDGGIQEVLEKYNVPFVGTGSRACRQAFDKYDASLEMSKQG 217
E+ +VD+ F +HG+ GEDG IQ + E +PFVG ++ DK + ++K
Sbjct: 85 EYEINHVDVAFSALHGKSGEDGSIQGLFELSGIPFVGCDIQSSAICMDK-SLTYIVAKNA 143
Query: 218 FITVPSFLLQGSEVNESELSNWFVTNKLDPNSGK----VVVKPTRAGSSIGVTVAYGVID 273
I P+F W + P + V VKP R+GSS GV D
Sbjct: 144 GIATPAF--------------WVINKDDRPVAATFTYPVFVKPARSGSSFGVKKVNSA-D 188
Query: 274 SLKKAKGIILEGIDDRVVVELFLEGGSEFTAIVLDVGSGFDCHPVVLLPTEVELQFQGSV 333
L A + D ++++E + G +VG + L+ EV+
Sbjct: 189 ELDYAIESARQ-YDSKILIEQAVSG--------CEVGCAVLGNSAALVVGEVD------- 232
Query: 334 DVREKDAIFNYRRKYLP---TQQVAYHTPPRFPIVVINSIREGASLLFQRLGLCDFARID 390
+R + IF ++ P ++ P I+E +++ LG AR+D
Sbjct: 233 QIRLQYGIFRIHQEVEPEKGSENAVITVPADLSAEERGRIQETVKKIYKTLGCRGLARVD 292
Query: 391 GWFLPSSTHVFSSSETKYGSTEW 413
+ + V + T G T +
Sbjct: 293 MFLQDNGRIVLNEVNTLPGFTSY 315
>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 = 66.6 bits (161), Expect = 7e-11, Method: Composition-based stats.
Identities = 81/374 (21%), Positives = 144/374 (38%), Gaps = 83/374 (22%)
Query: 79 RVGLICGGPSAERGISLNSARSVLDHIQGDDLLVRCYYIDRNLNAYAISSAQVYSNTPAD 138
R+G+I GG S+E+ +S+ + + ++ D+N Y P
Sbjct: 5 RIGVIXGGVSSEKQVSIXTGNEXIANL------------DKN----------KYEIVPIT 42
Query: 139 FDFKLESLAQGFGSLSEFAEHLAANVDIVFPTIHGRFGEDGGIQEVLEKYNVPFVGTGSR 198
+ K + + + A ++D +HG++GEDG +Q LE +P+ G+
Sbjct: 43 LNEKXDLIEK------------AKDIDFALLALHGKYGEDGTVQGTLESLGIPYSGSNXL 90
Query: 199 ACRQAFDKYDASLEMSKQGFITVPSFLLQGSEVNESELSNWFVTNKLDPNSGKVVVKPTR 258
+ DK + + +G I P ++ E+ + E N+ ++LD +VVKP
Sbjct: 91 SSGICXDKNISKKILRYEG-IETPDWI----ELTKXEDLNF---DELDKLGFPLVVKPNS 142
Query: 259 AGSSIGVTVAYGVIDSLKKAKGIILEGIDDRVVVELFLEGGSEFTAIVLDVGSGFDCHPV 318
GSS+GV + Y D L + E D VV+E +++ G E T + D
Sbjct: 143 GGSSVGVKIVYDK-DELISXLETVFEW-DSEVVIEKYIK-GEEITCSIFDGKQ------- 192
Query: 319 VLLPTEVELQFQGSVDVREKDAIFNYRRKYLPTQQVAYHTPPRFPIVVINSIREGASLLF 378
LP + +R F+Y KY + P + + + + +
Sbjct: 193 --LPI---------ISIRHAAEFFDYNAKYDDASTI--EEVIELPAELKERVNKASLACY 239
Query: 379 QRLGLCDFARIDGWFLPSSTHVFSSSETKYGSTEWGTILFTDINLISGMEQTSFLFQQAS 438
+ L +AR+D + G ++N + G Q S L + A
Sbjct: 240 KALKCSVYARVD------------------XXVKDGIPYVXEVNTLPGXTQASLLPKSAD 281
Query: 439 KVGFSHSNILRTII 452
G +S +L II
Sbjct: 282 AAGIHYSKLLDXII 295
Score = 50.4 bits (119), Expect = 4e-06, Method: Composition-based stats.
Identities = 41/128 (32%), Positives = 58/128 (45%), Gaps = 31/128 (24%)
Query: 623 SINEWIKLAKENQATVF--IAVHGGIGEDGTLQSLLEAEGVPYTGPGVMASKTCMDKVAT 680
++NE L ++ + F +A+HG GEDGT+Q LE+ G+PY+G ++S C DK
Sbjct: 42 TLNEKXDLIEKAKDIDFALLALHGKYGEDGTVQGTLESLGIPYSGSNXLSSGICXDK--- 98
Query: 681 SLALNHLADLGVLTINKDVRRKEDLLKTPIVDIWHELTSKLQCK---------TLCVKPA 731
I+K + R E ++TP W ELT L VKP
Sbjct: 99 -------------NISKKILRYEG-IETP---DWIELTKXEDLNFDELDKLGFPLVVKPN 141
Query: 732 RDGCSTGV 739
G S GV
Sbjct: 142 SGGSSVGV 149
Score = 30.0 bits (66), Expect = 6.1, Method: Composition-based stats.
Identities = 17/42 (40%), Positives = 22/42 (52%), Gaps = 1/42 (2%)
Query: 496 VIFGGDTSERQVSLMSGTNVWLNLQAFNDIEVTPCLLASSID 537
VI GG +SE+QVS+ +G NL N E+ P L D
Sbjct: 8 VIXGGVSSEKQVSIXTGNEXIANLDK-NKYEIVPITLNEKXD 48
>pdb|1E4E|B Chain B, D-Alanyl-D-Lacate Ligase
Length = 343
Score = 66.2 bits (160), Expect = 9e-11, Method: Compositional matrix adjust.
Identities = 65/287 (22%), Positives = 114/287 (39%), Gaps = 74/287 (25%)
Query: 639 FIAVHGGIGEDGTLQSLLEAEGVPYTGPGVMASKTCMDKVATSLALNH--LADLGVLTIN 696
F A+HG GEDG++Q L E G+P+ G + +S CMDK T + + +A IN
Sbjct: 95 FSALHGKSGEDGSIQGLFELSGIPFVGCDIQSSAICMDKSLTYIVAKNAGIATPAFWVIN 154
Query: 697 KDVRRKEDLLKTPIVDIWHELTSKLQCKTLCVKPARDGCSTGVARLCCAEDLTVYVKALE 756
KD R P+ VKPAR G S GV ++ A
Sbjct: 155 KDDRPVAATFTYPVF----------------VKPARSGSSFGVKKVNSA----------- 187
Query: 757 ECLLRIPPNSFSRAHGMIEMPNPPPEILIFEPFVETDEILFSSQSTNKNADRLMWKGNSR 816
DE+ ++ +S + +++ +
Sbjct: 188 ------------------------------------DELDYAIESARQYDSKILIEQAVS 211
Query: 817 WVEITVGVIGKCGSMHSLMPSV-TVKESGDILSLEEKFQ---GGTGINLTPPPASIMSTE 872
E+ V+G ++ ++ V ++ I + ++ + G +T P + +S E
Sbjct: 212 GCEVGCAVLGNSAAL--VVGEVDQIRLQYGIFRIHQEVEPEKGSENAVITVP--ADLSAE 267
Query: 873 ALDKCKQRIELIANALQLEGFSRIDAFVNVDNGEVLIIEVNTVPGMT 919
+ ++ ++ I L G +R+D F+ D G +++ EVNT+PG T
Sbjct: 268 ERGRIQETVKKIYKTLGCRGLARVDMFLQ-DRGRIVLNEVNTLPGFT 313
Score = 55.5 bits (132), Expect = 2e-07, Method: Compositional matrix adjust.
Identities = 66/302 (21%), Positives = 114/302 (37%), Gaps = 56/302 (18%)
Query: 158 EHLAANVDIVFPTIHGRFGEDGGIQEVLEKYNVPFVGTGSRACRQAFDKYDASLEMSKQG 217
E+ +VD+ F +HG+ GEDG IQ + E +PFVG ++ DK + ++K
Sbjct: 85 EYEINHVDVAFSALHGKSGEDGSIQGLFELSGIPFVGCDIQSSAICMDK-SLTYIVAKNA 143
Query: 218 FITVPSFLLQGSEVNESELSNWFVTNKLDPNSGK----VVVKPTRAGSSIGVTVAYGVID 273
I P+F W + P + V VKP R+GSS GV D
Sbjct: 144 GIATPAF--------------WVINKDDRPVAATFTYPVFVKPARSGSSFGVKKVNSA-D 188
Query: 274 SLKKAKGIILEGIDDRVVVELFLEGGSEFTAIVLDVGSGFDCHPVVLLPTEVELQFQGSV 333
L A + D ++++E + G +VG + L+ EV+
Sbjct: 189 ELDYAIESARQ-YDSKILIEQAVSG--------CEVGCAVLGNSAALVVGEVD------- 232
Query: 334 DVREKDAIFNYRRKYLP---TQQVAYHTPPRFPIVVINSIREGASLLFQRLGLCDFARID 390
+R + IF ++ P ++ P I+E +++ LG AR+D
Sbjct: 233 QIRLQYGIFRIHQEVEPEKGSENAVITVPADLSAEERGRIQETVKKIYKTLGCRGLARVD 292
Query: 391 GWFLPSSTHVFSSSETKYGSTEWGTILFTDINLISGMEQTSFLFQQASKVGFSHSNILRT 450
+ + G I+ ++N + G S + + G S ++
Sbjct: 293 MFL-----------------QDRGRIVLNEVNTLPGFTSYSRYPRMMAAAGISLPELIDR 335
Query: 451 II 452
+I
Sbjct: 336 LI 337
>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 = 65.9 bits (159), Expect = 1e-10, Method: Compositional matrix adjust.
Identities = 57/194 (29%), Positives = 90/194 (46%), Gaps = 18/194 (9%)
Query: 80 VGLICGGPSAERGISLNSARSVLDHIQGDDLLVRCYYI--DRNLNAYAISSAQVYSNTPA 137
+ ++ GG SAE +S+ +A++VL+ I D V YI D + +A++ S
Sbjct: 6 ICIVFGGKSAEHEVSILTAQNVLNAIDKDKYHVDIIYITNDGDWRKQNNITAEIKSTD-- 63
Query: 138 DFDFKLESLAQGFGSLSEFAEHLAAN-----VDIVFPTIHGRFGEDGGIQEVLEKYNVPF 192
+ LE+ G E ++ L + D VFP +HG GEDG IQ + E +VP+
Sbjct: 64 --ELHLEN-----GEALEISQLLKESSSGQPYDAVFPLLHGPNGEDGTIQGLFEVLDVPY 116
Query: 193 VGTGSRACRQAFDKYDASLEMSKQGFITVPSFLLQGSEVNESELSNWFVTNKLDPNSGKV 252
VG G + + DK +G +P SE + E + + N D + V
Sbjct: 117 VGNGVLSAASSMDKLVMKQLFEHRGLPQLPYISFLRSEYEKYEHNILKLVN--DKLNYPV 174
Query: 253 VVKPTRAGSSIGVT 266
VKP GSS+G++
Sbjct: 175 FVKPANLGSSVGIS 188
Score = 52.4 bits (124), Expect = 1e-06, Method: Compositional matrix adjust.
Identities = 37/112 (33%), Positives = 56/112 (50%), Gaps = 10/112 (8%)
Query: 637 TVFIAVHGGIGEDGTLQSLLEAEGVPYTGPGVMASKTCMDKVATSLALNH--LADLGVLT 694
VF +HG GEDGT+Q L E VPY G GV+++ + MDK+ H L L ++
Sbjct: 90 AVFPLLHGPNGEDGTIQGLFEVLDVPYVGNGVLSAASSMDKLVMKQLFEHRGLPQLPYIS 149
Query: 695 INKDVRRKEDLLKTPIVDIWHELTSKLQCKTLCVKPARDGCSTGVARLCCAE 746
+R + + + I+ + + KL VKPA G S G+++ C E
Sbjct: 150 F---LRSEYEKYEHNILKL---VNDKLNYPVF-VKPANLGSSVGISK-CNNE 193
>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 = 65.9 bits (159), Expect = 1e-10, Method: Compositional matrix adjust.
Identities = 57/194 (29%), Positives = 90/194 (46%), Gaps = 18/194 (9%)
Query: 80 VGLICGGPSAERGISLNSARSVLDHIQGDDLLVRCYYI--DRNLNAYAISSAQVYSNTPA 137
+ ++ GG SAE +S+ +A++VL+ I D V YI D + +A++ S
Sbjct: 6 ICIVFGGKSAEHEVSILTAQNVLNAIDKDKYHVDIIYITNDGDWRKQNNITAEIKSTD-- 63
Query: 138 DFDFKLESLAQGFGSLSEFAEHLAAN-----VDIVFPTIHGRFGEDGGIQEVLEKYNVPF 192
+ LE+ G E ++ L + D VFP +HG GEDG IQ + E +VP+
Sbjct: 64 --ELHLEN-----GEALEISQLLKESSSGQPYDAVFPLLHGPNGEDGTIQGLFEVLDVPY 116
Query: 193 VGTGSRACRQAFDKYDASLEMSKQGFITVPSFLLQGSEVNESELSNWFVTNKLDPNSGKV 252
VG G + + DK +G +P SE + E + + N D + V
Sbjct: 117 VGNGVLSAASSMDKLVMKQLFEHRGLPQLPYISFLRSEYEKYEHNILKLVN--DKLNYPV 174
Query: 253 VVKPTRAGSSIGVT 266
VKP GSS+G++
Sbjct: 175 FVKPANLGSSVGIS 188
Score = 52.4 bits (124), Expect = 1e-06, Method: Compositional matrix adjust.
Identities = 37/112 (33%), Positives = 56/112 (50%), Gaps = 10/112 (8%)
Query: 637 TVFIAVHGGIGEDGTLQSLLEAEGVPYTGPGVMASKTCMDKVATSLALNH--LADLGVLT 694
VF +HG GEDGT+Q L E VPY G GV+++ + MDK+ H L L ++
Sbjct: 90 AVFPLLHGPNGEDGTIQGLFEVLDVPYVGNGVLSAASSMDKLVMKQLFEHRGLPQLPYIS 149
Query: 695 INKDVRRKEDLLKTPIVDIWHELTSKLQCKTLCVKPARDGCSTGVARLCCAE 746
+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 = 65.5 bits (158), Expect = 1e-10, Method: Compositional matrix adjust.
Identities = 60/196 (30%), Positives = 92/196 (46%), Gaps = 22/196 (11%)
Query: 80 VGLICGGPSAERGISLNSARSVLDHIQGDDLLVRCYYI--DRNLNAYAISSAQVYSNTPA 137
+ ++ GG SAE +S+ +A++VL+ I D V YI D + +A++ S
Sbjct: 6 ICIVFGGKSAEHEVSILTAQNVLNAIDKDKYHVDIIYITNDGDWRKQNNITAEIKSTD-- 63
Query: 138 DFDFKLESLAQGFGSLSEFAEHLAAN-----VDIVFPTIHGRFGEDGGIQEVLEKYNVPF 192
+ LE+ G E ++ L + D VFP +HG GEDG IQ + E +VP+
Sbjct: 64 --ELHLEN-----GEALEISQLLKESSSGQPYDAVFPLLHGPNGEDGTIQGLFEVLDVPY 116
Query: 193 VGTGSRACRQAFDKYDASLEMSKQGFITVP--SFLLQGSEVNESELSNWFVTNKLDPNSG 250
VG G + + DK +G +P SFL E E + V +KL+
Sbjct: 117 VGNGVLSAASSMDKLVMKQLFEHRGLPQLPYISFLRSEYEKYEHNILK-LVNDKLN---Y 172
Query: 251 KVVVKPTRAGSSIGVT 266
V VKP GSS+G++
Sbjct: 173 PVFVKPANLGSSVGIS 188
Score = 52.4 bits (124), Expect = 1e-06, Method: Compositional matrix adjust.
Identities = 37/112 (33%), Positives = 56/112 (50%), Gaps = 10/112 (8%)
Query: 637 TVFIAVHGGIGEDGTLQSLLEAEGVPYTGPGVMASKTCMDKVATSLALNH--LADLGVLT 694
VF +HG GEDGT+Q L E VPY G GV+++ + MDK+ H L L ++
Sbjct: 90 AVFPLLHGPNGEDGTIQGLFEVLDVPYVGNGVLSAASSMDKLVMKQLFEHRGLPQLPYIS 149
Query: 695 INKDVRRKEDLLKTPIVDIWHELTSKLQCKTLCVKPARDGCSTGVARLCCAE 746
+R + + + I+ + + KL VKPA G S G+++ C E
Sbjct: 150 F---LRSEYEKYEHNILKL---VNDKLNYPVF-VKPANLGSSVGISK-CNNE 193
>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 = 65.5 bits (158), Expect = 2e-10, Method: Compositional matrix adjust.
Identities = 90/377 (23%), Positives = 144/377 (38%), Gaps = 83/377 (22%)
Query: 79 RVGLICGGPSAERGISLNSARSVLDHIQGDDLLVRCYYIDRNLNAYAISSAQVYSNTPAD 138
+V ++ GG SAER +SLNS R VL ++ D ++A+ A+
Sbjct: 32 KVAVLLGGNSAEREVSLNSGRLVLQGLR-----------DAGIDAHPFDPAERPLAA--- 77
Query: 139 FDFKLESLAQGFGSLSEFAEHLAANVDIVFPTIHGRFGEDGGIQEVLEKYNVPFVGTGSR 198
K E + F +L HG +GE+G IQ L+ Y + + G+G
Sbjct: 78 --LKEEGFVRAFNAL------------------HGGYGENGQIQGALDFYGIRYTGSGVL 117
Query: 199 ACRQAFDKYDASLEMSKQGFITVP-SFLLQGSEVNESELSNWFVTNKLDPNSGKVVVKPT 257
DK+ L + G T P +L+G ++ E + KL + VKP
Sbjct: 118 GSALGLDKFRTKLVWQQLGIPTPPFEAVLRG---DDYEARAKEIVAKL---GLPLFVKPA 171
Query: 258 RAGSSIGVTVAYGVIDSLKKAKGIILEGI--DDRVVVELFLEGGSEFTAIVLDVGSGFDC 315
GSS+ V + D+L A ++E + D VVVE +EGG E+TA + D
Sbjct: 172 SEGSSVAV-IKVKSADALPAA---LIEAVKFDRIVVVEKSIEGGGEYTAC---IAGNLDL 224
Query: 316 HPVVLLPTEVELQFQGSVDVREKDAIFNYRRKYLPTQQVAYHTPPRFPIVVINSIREGAS 375
+ ++P ++Y KY+ Y P ++ A
Sbjct: 225 PVIRIVPA---------------GEFYDYHAKYI-ANDTQYLIPCGLTADEEARLKVLAR 268
Query: 376 LLFQRLGLCDFARIDGWFLPSSTHVFSSSETKYGSTEWGTILFTDINLISGMEQTSFLFQ 435
F LG D+ R D F+ + G F ++N GM S +
Sbjct: 269 RAFDVLGCTDWGRAD--FMLDAD---------------GNPYFLEVNTAPGMTDHSLPPK 311
Query: 436 QASKVGFSHSNILRTII 452
A VG S+ ++ ++
Sbjct: 312 AARAVGISYQELVVAVL 328
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: 616 DELPMRHSINEWIKLAKENQATVFIAVHGGIGEDGTLQSLLEAEGVPYTGPGVMASKTCM 675
D P + L +E F A+HGG GE+G +Q L+ G+ YTG GV+ S +
Sbjct: 64 DAHPFDPAERPLAALKEEGFVRAFNALHGGYGENGQIQGALDFYGIRYTGSGVLGSALGL 123
Query: 676 DKVATSLALNHLADLGVLTIN-KDVRRKEDLLKTPIVDIWHELTSKLQCKTLCVKPARDG 734
DK T L LG+ T + V R +D E+ +KL L VKPA +G
Sbjct: 124 DKFRTKLVWQQ---LGIPTPPFEAVLRGDDYEARA-----KEIVAKLGL-PLFVKPASEG 174
Query: 735 CSTGVARLCCAEDL 748
S V ++ A+ L
Sbjct: 175 SSVAVIKVKSADAL 188
>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 = 64.7 bits (156), Expect = 2e-10, Method: Compositional matrix adjust.
Identities = 85/379 (22%), Positives = 141/379 (37%), Gaps = 81/379 (21%)
Query: 76 RVLRVGLICGGPSAERGISLNSARSVLDHIQGDDLLVRCYYIDRNLNAYAISSAQVYSNT 135
R +V ++ GG SAER +SL S R VL ++ D ++A+ A+ +
Sbjct: 12 RFGKVAVLFGGESAEREVSLTSGRLVLQGLR-----------DAGIDAHPFDPAERPLSA 60
Query: 136 PADFDFKLESLAQGFGSLSEFAEHLAANVDIVFPTIHGRFGEDGGIQEVLEKYNVPFVGT 195
K E + F +L HG +GE+G IQ L+ Y + + G+
Sbjct: 61 -----LKDEGFVRAFNAL------------------HGGYGENGQIQGALDFYGIRYTGS 97
Query: 196 GSRACRQAFDKYDASLEMSKQGFITVPSFLLQGSEVNESELSNWFVTNKLDPNSGKVVVK 255
G DK+ L + G T P + + + ++ L + VK
Sbjct: 98 GVLGSALGLDKFRTKLVWQQTGVPTPPFETVMRGDDYAARATDIVAKLGL-----PLFVK 152
Query: 256 PTRAGSSIGVTVAYGVIDSLKKAKGIILEGI--DDRVVVELFLEGGSEFTAIVLDVGSGF 313
P GSS+ V + D+L A + E D V+VE +EGG E+TA +
Sbjct: 153 PASEGSSVAV-LKVKTADALPAA---LSEAATHDKIVIVEKSIEGGGEYTAC---IAGDL 205
Query: 314 DCHPVVLLPTEVELQFQGSVDVREKDAIFNYRRKYLPTQQVAYHTPPRFPIVVINSIREG 373
D + ++P ++Y KY+ Y P P ++
Sbjct: 206 DLPLIKIVPA---------------GEFYDYHAKYV-ANDTQYLIPCGLPAEQETELKRI 249
Query: 374 ASLLFQRLGLCDFARIDGWFLPSSTHVFSSSETKYGSTEWGTILFTDINLISGMEQTSFL 433
A F LG D+ R D + L ++ G F ++N GM S
Sbjct: 250 ARRAFDVLGCTDWGRAD-FMLDAA----------------GNAYFLEVNTAPGMTDHSLP 292
Query: 434 FQQASKVGFSHSNILRTII 452
+ A +G +S ++ ++
Sbjct: 293 PKAARSIGIGYSELVVKVL 311
Score = 52.4 bits (124), Expect = 1e-06, Method: Compositional matrix adjust.
Identities = 40/119 (33%), Positives = 54/119 (45%), Gaps = 8/119 (6%)
Query: 630 LAKENQATVFIAVHGGIGEDGTLQSLLEAEGVPYTGPGVMASKTCMDKVATSLALNHLAD 689
L E F A+HGG GE+G +Q L+ G+ YTG GV+ S +DK T L
Sbjct: 61 LKDEGFVRAFNALHGGYGENGQIQGALDFYGIRYTGSGVLGSALGLDKFRTKLVWQQ--- 117
Query: 690 LGVLTINKDVRRKEDLLKTPIVDIWHELTSKLQCKTLCVKPARDGCSTGVARLCCAEDL 748
GV T + + D DI +L L VKPA +G S V ++ A+ L
Sbjct: 118 TGVPTPPFETVMRGDDYAARATDIVAKLG-----LPLFVKPASEGSSVAVLKVKTADAL 171
Score = 34.3 bits (77), Expect = 0.33, Method: Compositional matrix adjust.
Identities = 29/77 (37%), Positives = 38/77 (49%), Gaps = 25/77 (32%)
Query: 473 PGRSSGSKPTEALNKREGIREVFVIFGGDTSERQVSLMSGTNVWLNLQAFNDIEVTPCLL 532
PG SG P KR G +V V+FGG+++ER+VSL SG L LQ D
Sbjct: 2 PGSMSGIDP-----KRFG--KVAVLFGGESAEREVSLTSGR---LVLQGLRD-------- 43
Query: 533 ASSIDCSSGMDANITDP 549
+G+DA+ DP
Sbjct: 44 -------AGIDAHPFDP 53
>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 = 62.0 bits (149), Expect = 1e-09, Method: Compositional matrix adjust.
Identities = 87/383 (22%), Positives = 140/383 (36%), Gaps = 89/383 (23%)
Query: 76 RVLRVGLICGGPSAERGISLNSARSVLDHIQGDDLLVRCYYIDRNLNAYAISSAQVYSNT 135
R +V ++ GG SAER +SLNS R VL ++ D ++A+ AQ
Sbjct: 12 RFGKVAVLLGGDSAEREVSLNSGRLVLQGLR-----------DAGIDAHPFDPAQRPLAA 60
Query: 136 PADFDFKLESLAQGFGSLSEFAEHLAANVDIVFPTIHGRFGEDGGIQEVLEKYNVPFVGT 195
K E + F +L HG +GE+G IQ L+ Y + + G+
Sbjct: 61 -----LKDEGFVRAFNAL------------------HGGYGENGQIQGALDFYGIRYTGS 97
Query: 196 GSRACRQAFDKYDASLEMSKQGFITVP-SFLLQGSEVNESELSNWFVTNKLDPNSGKVVV 254
G DK+ L + G T P +++G + + KL + V
Sbjct: 98 GVLGSALGLDKFRTKLVWQQTGIPTPPFETVMRGDDYAARAQD---IVAKL---GVPLFV 151
Query: 255 KPTRAGSSIGVTVAYGVIDSLKKAKGIILEGI-----DDRVVVELFLEGGSEFTAIVLDV 309
KP GSS+ V + +K A + D V+VE +EGG E+TA +
Sbjct: 152 KPASEGSSVAV-------EKVKSADALPAALEEAAKHDKIVIVEKSIEGGGEYTAC---I 201
Query: 310 GSGFDCHPVVLLPTEVELQFQGSVDVREKDAIFNYRRKYLPTQQVAYHTPPRFPIVVINS 369
+ D + ++P ++Y KY+ Y P
Sbjct: 202 AADLDLPLIRIVPA---------------GEFYDYHAKYI-ANDTQYLIPCGLDAAKEAE 245
Query: 370 IREGASLLFQRLGLCDFARIDGWFLPSSTHVFSSSETKYGSTEWGTILFTDINLISGMEQ 429
+ A F LG D+ R D + L ++ G F ++N GM
Sbjct: 246 FKRIARRAFDVLGCTDWGRAD-FMLDAA----------------GNPYFLEVNTAPGMTD 288
Query: 430 TSFLFQQASKVGFSHSNILRTII 452
S + A VG +S ++ ++
Sbjct: 289 HSLPPKAARAVGIGYSELVVKVL 311
Score = 52.0 bits (123), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 41/132 (31%), Positives = 59/132 (44%), Gaps = 10/132 (7%)
Query: 616 DELPMRHSINEWIKLAKENQATVFIAVHGGIGEDGTLQSLLEAEGVPYTGPGVMASKTCM 675
D P + L E F A+HGG GE+G +Q L+ G+ YTG GV+ S +
Sbjct: 47 DAHPFDPAQRPLAALKDEGFVRAFNALHGGYGENGQIQGALDFYGIRYTGSGVLGSALGL 106
Query: 676 DKVATSLALNHLADLGVLTIN-KDVRRKEDLLKTPIVDIWHELTSKLQCKTLCVKPARDG 734
DK T L G+ T + V R +D ++ +KL L VKPA +G
Sbjct: 107 DKFRTKLVWQQ---TGIPTPPFETVMRGDDYAARA-----QDIVAKLGV-PLFVKPASEG 157
Query: 735 CSTGVARLCCAE 746
S V ++ A+
Sbjct: 158 SSVAVEKVKSAD 169
Score = 33.1 bits (74), Expect = 0.72, Method: Compositional matrix adjust.
Identities = 29/77 (37%), Positives = 37/77 (48%), Gaps = 25/77 (32%)
Query: 473 PGRSSGSKPTEALNKREGIREVFVIFGGDTSERQVSLMSGTNVWLNLQAFNDIEVTPCLL 532
PG SG P KR G +V V+ GGD++ER+VSL SG L LQ D
Sbjct: 2 PGSMSGIDP-----KRFG--KVAVLLGGDSAEREVSLNSGR---LVLQGLRD-------- 43
Query: 533 ASSIDCSSGMDANITDP 549
+G+DA+ DP
Sbjct: 44 -------AGIDAHPFDP 53
>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 = 61.2 bits (147), Expect = 2e-09, Method: Compositional matrix adjust.
Identities = 84/328 (25%), Positives = 141/328 (42%), Gaps = 45/328 (13%)
Query: 79 RVGLICGGPSAERGISLNSARSVLDHIQGDDLLVRCYYIDRNLNAYAISSAQVYSNTPAD 138
RV LI GG S+E +S SA++ + I+ Y I +AI+ + +T +
Sbjct: 5 RVALIFGGNSSEHDVSKRSAQNFYNAIEA----TGKYEII----VFAIAQNGFFLDTESS 56
Query: 139 FD-FKLES---LAQGFGSLSEFAEHLA--------ANVDIVFPTIHGRFGEDGGIQEVLE 186
LE + F + ++ LA + DI FP +HG GEDG +Q + +
Sbjct: 57 KKILALEDEQPIVDAFMKTVDASDPLARIHALKSAGDFDIFFPVVHGNLGEDGTLQGLFK 116
Query: 187 KYNVPFVGTGSRACRQAFDKYDASLEMSKQGFITVPSFLLQGSEVNESELSNWFVTNKLD 246
+ P+VG R +FDK ++K+ +TV V + E +N + +K+
Sbjct: 117 LLDKPYVGAPLRGHAVSFDK-----ALTKE-LLTVNGIRNTKYIVVDPESANNWSWDKIV 170
Query: 247 PNSGKVV-VKPTRAGSSIG---VTVAYGVIDSLKKAKGIILEGIDDRVVVELFLEGGSEF 302
G +V VK GSS+G VT A ++L + D +V++E + G E
Sbjct: 171 AELGNIVFVKAANQGSSVGISRVTNAEEYTEALSDSF-----QYDYKVLIEEAVNGARE- 224
Query: 303 TAIVLDVGSGFDCHPVVLLPTEVELQFQGSVDVREKDAIFNYRRKYLPTQQVAYHTPPRF 362
L+VG + P+V + QGS D ++Y K++ V + P +
Sbjct: 225 ----LEVGVIGNDQPLVSEIGAHTVPNQGS-----GDGWYDYNNKFVDNSAVHFQIPAQL 275
Query: 363 PIVVINSIREGASLLFQRLGLCDFARID 390
V +++ A ++ L L AR+D
Sbjct: 276 SPEVTKEVKQMALDAYKVLNLRGEARMD 303
Score = 57.8 bits (138), Expect = 3e-08, Method: Compositional matrix adjust.
Identities = 103/466 (22%), Positives = 173/466 (37%), Gaps = 119/466 (25%)
Query: 492 REVFVIFGGDTSERQVSLMSGTNVWLNLQAFNDIEVTPCLLASSIDCSSGMDANITDPDS 551
+ V +IFGG++SE VS S N + ++A E+ +A + D +S
Sbjct: 4 KRVALIFGGNSSEHDVSKRSAQNFYNAIEATGKYEIIVFAIAQ--------NGFFLDTES 55
Query: 552 SSRVVWSLPYSLVLRHTTEEVLAACIEAIEPDRAAFTSHLRNQVVNDLVEGLKKHSWFTG 611
S +++ +E +P AF +
Sbjct: 56 SKKIL-------------------ALEDEQPIVDAFMKTV-------------------- 76
Query: 612 FDIADELPMRHSINEWIKLAKENQATVFIAVHGGIGEDGTLQSLLEAEGVPYTGPGVMAS 671
D +D L H++ + + F VHG +GEDGTLQ L + PY G +
Sbjct: 77 -DASDPLARIHALK-----SAGDFDIFFPVVHGNLGEDGTLQGLFKLLDKPYVGAPLRGH 130
Query: 672 KTCMDKVATS--LALNHLADLGVLTINKDVRRKEDLLKTPIVDIWHELTSKLQCKTLCVK 729
DK T L +N + + + ++ + W ++ ++L + VK
Sbjct: 131 AVSFDKALTKELLTVNGIRNTKYIVVDPESANNWS---------WDKIVAEL-GNIVFVK 180
Query: 730 PARDGCSTGVARLCCAEDLTVYVKALEECLLRIPPNSFSRAHGMIEMPNPPPEILIFEPF 789
A G S G++R+ AE+ Y +AL + SF + ++LI E
Sbjct: 181 AANQGSSVGISRVTNAEE---YTEALSD--------SFQYDY----------KVLIEEAV 219
Query: 790 VETDEILFSSQSTNKNADRLMWKGNSRWVEITVGVIGKCGSMHSLMPSVTV--KESGD-I 846
N R E+ VGVIG + S + + TV + SGD
Sbjct: 220 ---------------NGAR----------ELEVGVIGNDQPLVSEIGAHTVPNQGSGDGW 254
Query: 847 LSLEEKFQGGTGINLTPPPASIMSTEALDKCKQRIELIANALQLEGFSRIDAFVNVDNGE 906
KF + ++ P +S E + KQ L L G +R+D ++ +N
Sbjct: 255 YDYNNKFVDNSAVHFQIPAQ--LSPEVTKEVKQMALDAYKVLNLRGEARMDFLLDENNVP 312
Query: 907 VLIIEVNTVPGMTPSTVLIHQALSEQPPMYPHQFFRKVLDLGSERF 952
L E NT+PG T ++ + L + + + ++D G E F
Sbjct: 313 YL-GEPNTLPGFTNMSLF--KRLWDYSDINNAKLVDMLIDYGFEDF 355
>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 = 58.5 bits (140), Expect = 2e-08, Method: Compositional matrix adjust.
Identities = 69/274 (25%), Positives = 120/274 (43%), Gaps = 35/274 (12%)
Query: 75 GRVLRVGLICGGPSAERGISLNSARSVLDHIQGDDLLVRCYYIDRNLNAYAISSAQVYSN 134
G + ++ GG S E IS+ SA ++ ++ D + ++D N + Y I + ++S
Sbjct: 18 GSHMEFCVLFGGASFEHEISIVSAIALKGVLK--DRIKYFIFLDENHHFYLIEESNMHSK 75
Query: 135 TPADF-DFKLESLAQGFGSL--SEFAEHLAANVDIVFPTIHGRFGEDGGIQEVLEKYNVP 191
A + KL L L + F + +V +HG GEDG + +LE Y +
Sbjct: 76 YFAQIKEKKLPPLILTHNGLLKNSFLGAKIIELPLVINLVHGGDGEDGKLASLLEFYRIA 135
Query: 192 FVGTGSRACRQAFDKYDASLEMSKQGFITVPSFLL-QGSEVNESELSNWFVTNKLDPNSG 250
F+G A +++KY L G T+ LL + + N +L N+ +
Sbjct: 136 FIGPRIEASVLSYNKYLTKLYAKDLGIKTLDYVLLNEKNRANALDLMNF---------NF 186
Query: 251 KVVVKPTRAGSSIGVTVAYGVIDSLKKAKGIILEGID------DRVVVELFLEGGSEFTA 304
+VKP+ AGSS+GV V +K+ K +I +D V++E F++G E+
Sbjct: 187 PFIVKPSNAGSSLGVNV-------VKEEKELIY-ALDSAFEYSKEVLIEPFIQGVKEYNL 238
Query: 305 IVLDVGSGFDCHPVVLLPTEVELQFQGSVDVREK 338
+ F C + P + E +D ++K
Sbjct: 239 AGCKIKKDF-CFSYIEEPNKQEF-----LDFKQK 266
Score = 45.4 bits (106), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 32/98 (32%), Positives = 49/98 (50%), Gaps = 11/98 (11%)
Query: 642 VHGGIGEDGTLQSLLEAEGVPYTGPGVMASKTCMDKVATSLALNHLADLGVLTINKDVRR 701
VHGG GEDG L SLLE + + GP + AS +K T L + DLG+ T++ +
Sbjct: 115 VHGGDGEDGKLASLLEFYRIAFIGPRIEASVLSYNKYLTKL---YAKDLGIKTLDYVLLN 171
Query: 702 KEDLLKTPIVDIWHELTSKLQCKTLCVKPARDGCSTGV 739
+++ + +D+ + VKP+ G S GV
Sbjct: 172 EKN--RANALDLMN------FNFPFIVKPSNAGSSLGV 201
>pdb|2VGY|A Chain A, Crystal Structure Of The Yersinia Enterocolitica Type Iii
Secretion Translocator Chaperone Sycd (Alternative
Dimer)
Length = 148
Score = 32.7 bits (73), Expect = 0.88, Method: Composition-based stats.
Identities = 29/90 (32%), Positives = 42/90 (46%), Gaps = 12/90 (13%)
Query: 184 VLEKYNVPFVGTGSRACRQAFDKYDASLEMSKQGF---ITVPSF-------LLQGSEVNE 233
VL+ Y+ F G ACRQA +YD ++ ++G I P F LLQ E+ E
Sbjct: 49 VLDHYDSRFF-LGLGACRQAMGQYDLAIHSYEEGAVMDIXEPRFPFHAAECLLQXGELAE 107
Query: 234 SELSNWFVTNKLDPNSGKVVVKPTRAGSSI 263
+E S F+ +L N + TR S +
Sbjct: 108 AE-SGLFLAQELIANXPEFXELSTRVSSML 136
>pdb|3ROF|A Chain A, Crystal Structure Of The S. Aureus Protein Tyrosine
Phosphatase Ptpa
Length = 158
Score = 32.0 bits (71), Expect = 1.8, Method: Compositional matrix adjust.
Identities = 21/77 (27%), Positives = 37/77 (48%), Gaps = 11/77 (14%)
Query: 180 GIQEVLEKYNVPFVGTGSRACRQAFDKYDASLEMSKQGFITVPSF----------LLQGS 229
G Q++L K+N+PF G S +A D +D + M + + S LL+ S
Sbjct: 58 GTQKILNKHNIPFDGMISELF-EATDDFDYIVAMDQSNVDNIKSINPNLKGQLFKLLEFS 116
Query: 230 EVNESELSNWFVTNKLD 246
+ ES++ + + TN +
Sbjct: 117 NMEESDVPDPYYTNNFE 133
>pdb|2VGX|A Chain A, Structure Of The Yersinia Enterocolitica Type Iii
Secretion Translocator Chaperone Sycd
Length = 148
Score = 31.2 bits (69), Expect = 2.6, Method: Composition-based stats.
Identities = 29/90 (32%), Positives = 40/90 (44%), Gaps = 12/90 (13%)
Query: 184 VLEKYNVPFVGTGSRACRQAFDKYDASLEMSKQGF---ITVPSF-------LLQGSEVNE 233
VL+ Y+ F G ACRQA +YD ++ G I P F LLQ E+ E
Sbjct: 49 VLDHYDSRFF-LGLGACRQAMGQYDLAIHSYSYGAVMDIXEPRFPFHAAECLLQXGELAE 107
Query: 234 SELSNWFVTNKLDPNSGKVVVKPTRAGSSI 263
+E S F+ +L N + TR S +
Sbjct: 108 AE-SGLFLAQELIANXPEFXELSTRVSSML 136
>pdb|2VGX|B Chain B, Structure Of The Yersinia Enterocolitica Type Iii
Secretion Translocator Chaperone Sycd
Length = 148
Score = 31.2 bits (69), Expect = 2.7, Method: Composition-based stats.
Identities = 29/90 (32%), Positives = 40/90 (44%), Gaps = 12/90 (13%)
Query: 184 VLEKYNVPFVGTGSRACRQAFDKYDASLEMSKQGF---ITVPSF-------LLQGSEVNE 233
VL+ Y+ F G ACRQA +YD ++ G I P F LLQ E+ E
Sbjct: 49 VLDHYDSRFF-LGLGACRQAMGQYDLAIHSYSYGAVMDIXEPRFPFHAAECLLQXGELAE 107
Query: 234 SELSNWFVTNKLDPNSGKVVVKPTRAGSSI 263
+E S F+ +L N + TR S +
Sbjct: 108 AE-SGLFLAQELIANXPEFXELSTRVSSML 136
>pdb|4AM9|A Chain A, Crystal Structure Of The Yersinia Enterocolitica Type Iii
Secretion Chaperone Sycd In Complex With A Peptide Of
The Translocator Yopd
Length = 148
Score = 31.2 bits (69), Expect = 3.1, Method: Composition-based stats.
Identities = 30/91 (32%), Positives = 42/91 (46%), Gaps = 14/91 (15%)
Query: 184 VLEKYNVPF-VGTGSRACRQAFDKYDASLEMSKQGF---ITVPSF-------LLQGSEVN 232
VL+ Y+ F +G G ACRQA +YD ++ G I P F LLQ E+
Sbjct: 49 VLDHYDSRFFLGLG--ACRQAMGQYDLAIHSYSYGAVMDIKEPRFPFHAAECLLQKGELA 106
Query: 233 ESELSNWFVTNKLDPNSGKVVVKPTRAGSSI 263
E+E S F+ +L N + TR S +
Sbjct: 107 EAE-SGLFLAQELIANKPEFKELSTRVSSML 136
>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 = 5.3, Method: Compositional matrix adjust.
Identities = 36/136 (26%), Positives = 57/136 (41%), Gaps = 17/136 (12%)
Query: 797 FSSQSTNKNADRLMWKGNSRW-VEITVGVIGKCGSMHSLMPSVTVKESGDILSLEEKFQG 855
++ Q A R++ +G ++ EIT+ + +H P +E GD E +Q
Sbjct: 179 YAQQGGRAGAGRVIVEGVVKFDFEITLLTVSAVDGVHFCAPVGHRQEDGD---YRESWQ- 234
Query: 856 GTGINLTPPPASIMSTEALDKCKQRIELIANALQLEGFSRIDAFVNVDNGEVLIIEVNTV 915
MS AL++ ++ + AL G ++ FV D EV+ EV+
Sbjct: 235 ----------PQQMSPLALERAQEIARKVVLALGGYGLFGVELFVCGD--EVIFSEVSPR 282
Query: 916 PGMTPSTVLIHQALSE 931
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 = 5.7, Method: Compositional matrix adjust.
Identities = 36/136 (26%), Positives = 57/136 (41%), Gaps = 17/136 (12%)
Query: 797 FSSQSTNKNADRLMWKGNSRW-VEITVGVIGKCGSMHSLMPSVTVKESGDILSLEEKFQG 855
++ Q A R++ +G ++ EIT+ + +H P +E GD E +Q
Sbjct: 180 YAQQGGRAGAGRVIVEGVVKFDFEITLLTVSAVDGVHFCAPVGHRQEDGD---YRESWQ- 235
Query: 856 GTGINLTPPPASIMSTEALDKCKQRIELIANALQLEGFSRIDAFVNVDNGEVLIIEVNTV 915
MS AL++ ++ + AL G ++ FV D EV+ EV+
Sbjct: 236 ----------PQQMSPLALERAQEIARKVVLALGGYGLFGVELFVCGD--EVIFSEVSPR 283
Query: 916 PGMTPSTVLIHQALSE 931
P T LI Q LSE
Sbjct: 284 PHDTGMVTLISQDLSE 299
>pdb|3K8Z|A Chain A, Crystal Structure Of Gudb1 A Decryptified Secondary
Glutamate Dehydrogenase From B. Subtilis
pdb|3K8Z|B Chain B, Crystal Structure Of Gudb1 A Decryptified Secondary
Glutamate Dehydrogenase From B. Subtilis
pdb|3K8Z|C Chain C, Crystal Structure Of Gudb1 A Decryptified Secondary
Glutamate Dehydrogenase From B. Subtilis
pdb|3K8Z|D Chain D, Crystal Structure Of Gudb1 A Decryptified Secondary
Glutamate Dehydrogenase From B. Subtilis
pdb|3K8Z|E Chain E, Crystal Structure Of Gudb1 A Decryptified Secondary
Glutamate Dehydrogenase From B. Subtilis
pdb|3K8Z|F Chain F, Crystal Structure Of Gudb1 A Decryptified Secondary
Glutamate Dehydrogenase From B. Subtilis
Length = 423
Score = 29.6 bits (65), Expect = 8.5, Method: Compositional matrix adjust.
Identities = 33/121 (27%), Positives = 46/121 (38%), Gaps = 30/121 (24%)
Query: 191 PFVGTGSRACRQAFDKYDASLEMSKQGFITVPSFLLQGSEVNESELSNWFVTNKLDPNSG 250
P V T S+ D+Y E + GFIT +L GS ES
Sbjct: 154 PDVFTNSQIMAWMMDEYSRIDEFNSPGFITGKPLVLGGSHGRES---------------- 197
Query: 251 KVVVKPTRAGSSIGVTVAYGVIDSLKKAKGIILEGIDDRVVVELFLEGGSEFTAIVLDVG 310
++ GVT+ I K +GI ++G RVVV+ F GS + D G
Sbjct: 198 ---------ATAKGVTIC---IKEAAKKRGIDIKGA--RVVVQGFGNAGSYLAKFMHDAG 243
Query: 311 S 311
+
Sbjct: 244 A 244
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 0.397
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 27,625,566
Number of Sequences: 62578
Number of extensions: 1154447
Number of successful extensions: 3062
Number of sequences better than 100.0: 47
Number of HSP's better than 100.0 without gapping: 30
Number of HSP's successfully gapped in prelim test: 17
Number of HSP's that attempted gapping in prelim test: 2900
Number of HSP's gapped (non-prelim): 125
length of query: 953
length of database: 14,973,337
effective HSP length: 108
effective length of query: 845
effective length of database: 8,214,913
effective search space: 6941601485
effective search space used: 6941601485
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: 56 (26.2 bits)