RPS-BLAST 2.2.22 [Sep-27-2009] Database: CddB 21,608 sequences; 5,994,473 total letters Searching..................................................done Query= gi|254781102|ref|YP_003065515.1| UDP-N-acetylmuramoylalanyl-D-glutamate--2,6-diaminopimelate ligase [Candidatus Liberibacter asiaticus str. psy62] (497 letters) >gnl|CDD|178894 PRK00139, murE, UDP-N-acetylmuramoylalanyl-D-glutamate--2, 6-diaminopimelate ligase; Provisional. Length = 460 Score = 498 bits (1286), Expect = e-141 Identities = 196/504 (38%), Positives = 267/504 (52%), Gaps = 59/504 (11%) Query: 1 MKLQDLIYKDFPELINQLSIFPMQWRERKINEVSSDSRHIQAGWIFVAIVGNKEDGHLFI 60 MKL+DL+ +I ++ DSR ++ G +FVA+ G+K DG FI Sbjct: 4 MKLRDLL------------------APVEITGLTYDSRKVKPGDLFVALPGHKVDGRDFI 45 Query: 61 PQAIAQGAEAIVVSSAYSLQDFSATIRSNTPILVVDNTRKFLSLFASRLYGKHPEN---I 117 QAIA GA A+V + P+++V + RK L+L A+ YG HP + + Sbjct: 46 AQAIANGAAAVVAEADGEAGT-------GVPVIIVPDLRKALALLAAAFYG-HPSDKLKL 97 Query: 118 LAVTGTSGKSSVASFVQQICQRSGLSSFQIGPTSTISSFAQDNR----LTTPSPIYLAKA 173 + VTGT+GK++ A + QI + G + IG T+ + LTTP + L + Sbjct: 98 IGVTGTNGKTTTAYLLAQILRLLGEKTALIG---TLGNGIGGELIPSGLTTPDALDLQRL 154 Query: 174 LSYLSSQGVTHVSVEASSHGLDQHRLDGIKLIAGSFTNLGRDHIDYHQTQQAYFNAKMRL 233 L+ L GVT+ ++E SSH LDQ R+DG+K FTNL RDH+DYH T + Y AK RL Sbjct: 155 LAELVDAGVTYAAMEVSSHALDQGRVDGLKFDVAVFTNLSRDHLDYHGTMEDYLAAKARL 214 Query: 234 FEELLPKESPAIIYADDAYSKEVMKRAHNAGCRVLSVGYQGKFIHLKKVCAIHNKQQVTI 293 F EL A+I ADD + ++ A +V G + V + Q T+ Sbjct: 215 FSELGLA---AVINADDEVGRRLL-----ALPDAYAVSMAGADLRATDVEYTDSGQTFTL 266 Query: 294 SVEGKDFDFLFPLPGEFQVYNALVAAGLCIAIGIDSALVLEHLEKLHVVPGRFEFVGTNS 353 + PL G F V N L A +A+G+ L L KL VPGR E V Sbjct: 267 -----VTEVESPLIGRFNVSNLLAALAALLALGVPLEDALAALAKLQGVPGRMERVDAGQ 321 Query: 354 RGGRIYVDYAHTSNSLEMILKNIRTITSGRIIVVFGCGGDRDQGKRPIMGKIALDLADIA 413 G + VDYAHT ++LE +L+ +R GR+I VFGCGGDRD+GKRP+MG IA LAD+ Sbjct: 322 -GPLVIVDYAHTPDALEKVLEALRPHAKGRLICVFGCGGDRDKGKRPLMGAIAERLADVV 380 Query: 414 IVTDDNPRSEDPEKIRAEIIHGIPGFIEKGNRIEAIRTAIEMLNKQDVLVVAGKGHETVH 473 IVT DNPRSEDP I A+I+ GI IE +R EAIR AI DV+++AGKGHE Sbjct: 381 IVTSDNPRSEDPAAIIADILAGIYDVIE--DRAEAIRYAIAQAKPGDVVLIAGKGHEDYQ 438 Query: 474 IVTNGEKKMSV---DCDIIREILG 494 I+ G K + D ++ RE L Sbjct: 439 II-GGVK---IPFDDREVAREALA 458 >gnl|CDD|183385 PRK11929, PRK11929, putative bifunctional UDP-N-acetylmuramoylalanyl-D-glutamate--2, 6-diaminopimelate ligase/UDP-N-acetylmuramoyl-tripeptide:D-alanyl-D- alanine ligase; Provisional. Length = 958 Score = 387 bits (995), Expect = e-108 Identities = 183/476 (38%), Positives = 256/476 (53%), Gaps = 24/476 (5%) Query: 23 MQWRERKINEVSSDSRHIQAGWIFVAIVGNKEDGHLFIPQAIAQGAEAIVVSSAYSLQDF 82 ++ ++ DSR +Q G +FVA G DG FI QA+A+GA A++V + Q Sbjct: 22 LRGCVAATADLRLDSREVQPGDLFVACRGAASDGRAFIDQALARGAAAVLVEAEGEDQVA 81 Query: 83 SATIRSNTPILVVDNTRKFLSLFASRLYGKHPE--NILAVTGTSGKSSVASFVQQICQRS 140 +A +L V + RK L A+R YG+ E +++AVTGT+GK+S A + Q+ R Sbjct: 82 AADAL----VLPVADLRKALGELAARWYGRPSEQLSLVAVTGTNGKTSCAQLLAQLLTRL 137 Query: 141 GLSSFQIGPTST-ISSFAQDNRLTTPSPIYLAKALSYLSSQGVTHVSVEASSHGLDQHRL 199 G IG + LTTP I L + L+ + + G V++EASSHGL+Q RL Sbjct: 138 GKPCGSIGTLGARLDGRLIPGSLTTPDAIILHRILARMRAAGADAVAMEASSHGLEQGRL 197 Query: 200 DGIKLIAGSFTNLGRDHIDYHQTQQAYFNAKMRLFEELLPKESPAIIYADDAYSKEVMKR 259 DG+++ FTNL RDH+DYH T Q Y AK LF +L P A+I ADD + R Sbjct: 198 DGLRIAVAGFTNLTRDHLDYHGTMQDYEEAKAALFSKL-PGLGAAVINADDPAAA----R 252 Query: 260 AHNAGCRVLSVGYQ----GKFIHLKKVCAIHNKQQVTISVEGKDFDFLFPLPGEFQVYNA 315 A R L VGY G + + + A + Q T++ + + L G F V N Sbjct: 253 LLAALPRGLKVGYSPQNAGADVQARDLRATAHGQVFTLATPDGSYQLVTRLLGRFNVSNL 312 Query: 316 LVAAGLCIAIGIDSALVLEHLEKLHVVPGRFEFVG--TNSRGGRIYVDYAHTSNSLEMIL 373 L+ A +G+ A + L + VPGR E VG ++G + VDYAHT ++L L Sbjct: 313 LLVAAALKKLGLPLAQIARALAAVSPVPGRMERVGPTAGAQGPLVVVDYAHTPDALAKAL 372 Query: 374 KNIRTIT---SGRIIVVFGCGGDRDQGKRPIMGKIALDLADIAIVTDDNPRSEDPEKIRA 430 +R + +GR++ VFGCGGDRD+GKRP MG+IA +LAD +VT DNPRSE PE I Sbjct: 373 TALRPVAQARNGRLVCVFGCGGDRDKGKRPEMGRIAAELADRVVVTSDNPRSEAPEAIID 432 Query: 431 EIIHGIPG---FIEKGNRIEAIRTAIEMLNKQDVLVVAGKGHETVHIVTNGEKKMS 483 +I+ GIP +R EAIR AI M DV+++AGKGHET + + Sbjct: 433 QILAGIPAGARVFVISDRAEAIRQAIWMAAPGDVILIAGKGHETYQEIGGRKLFFD 488 Score = 107 bits (270), Expect = 6e-24 Identities = 91/373 (24%), Positives = 154/373 (41%), Gaps = 37/373 (9%) Query: 28 RKINEVSSDSRHIQAGWIFVAIVGNKEDGHLFIPQAIAQGAEAIVVSSAYSLQDFSATIR 87 VS+DSR + G +FVA+ G DGH ++PQA A GA A VV + D Sbjct: 524 PHAGAVSTDSRSVGRGELFVALRGENFDGHDYLPQAFAAGACAAVVERQVADVDL----- 578 Query: 88 SNTPILVVDNTRKFLSLFASRLYGKHPENILAVTGTSGKSSVASFVQQICQRSGLSSFQI 147 P +VVD+TR L A+ + ++A+TG++GK++ + I L+++Q Sbjct: 579 ---PQIVVDDTRAALGRLATAWRARFSLPVVAITGSNGKTTTKEMIAAI-----LAAWQG 630 Query: 148 GPTSTISSFAQDNRLTTPSPIYLAKALSYLSSQGVTHVSV-EASSHGLDQ-HRLDGI-KL 204 + +N + P L+ L + +V E + + L I Sbjct: 631 EDRVLATEGNFNNEIGVP--------LTLLRLRAQHRAAVFELGMNHPGEIAYLAAIAAP 682 Query: 205 IAGSFTNLGRDHIDYHQTQQAYFNAKMRLFEELLPKESPAIIYADDAYSKEVMKRAHNAG 264 TN R+H ++ + +A AK + LP++ A++ DD Y+ K A Sbjct: 683 TVALVTNAQREHQEFMHSVEAVARAKGEIIAA-LPEDGVAVVNGDDPYTAIWAKLA--GA 739 Query: 265 CRVLSVGYQ-GKFIHLKKVCAIHNKQQVT-----ISVEGKDFDFLFPLPGEFQVYNALVA 318 RVL G Q G ++ +K+ + + + + PL GE + NAL A Sbjct: 740 RRVLRFGLQPGADVYAEKIAKDISVGEAGGTRCQVVTPAGSAEVYLPLIGEHNLRNALAA 799 Query: 319 AGLCIAIGIDSALVLEHLEKLHVVPGRFEFVGTNSRGGRIYVDYAHTSNSLEM--ILKNI 376 +A G + LE+ V GR + + G +D + +N M + + Sbjct: 800 IACALAAGASLKQIRAGLERFQPVAGRMQRRRLS--CGTRIIDDTYNANPDSMRAAIDVL 857 Query: 377 RTITSGRIIVVFG 389 + +G +V G Sbjct: 858 AELPNGPRALVLG 870 >gnl|CDD|162196 TIGR01085, murE, UDP-N-acetylmuramyl-tripeptide synthetase. A close homolog, scoring just below the trusted cutoff, is found (with introns) in Arabidopsis thaliana. Its role is unknown. Length = 464 Score = 382 bits (984), Expect = e-107 Identities = 175/459 (38%), Positives = 238/459 (51%), Gaps = 23/459 (5%) Query: 33 VSSDSRHIQAGWIFVAIVGNKEDGHLFIPQAIAQGAEAIVVSSAYSLQDFSATIRSNTPI 92 ++ DSR ++ G +FVAI G DGH FI AIA GA A+VV + P+ Sbjct: 7 LTLDSREVKPGDLFVAIKGTHVDGHDFIHDAIANGAVAVVVERDVDFY------VAPVPV 60 Query: 93 LVVDNTRKFLSLFASRLYG--KHPENILAVTGTSGKSSVASFVQQICQRSGLSSFQIGPT 150 ++V + R LS A+ YG ++ VTGT+GK++ S + Q+ + G + IG Sbjct: 61 IIVPDLRHALSSLAAAFYGHPSKKLKVIGVTGTNGKTTTTSLIAQLLRLLGKKTGLIGTI 120 Query: 151 STI----SSFAQDNRLTTPSPIYLAKALSYLSSQGVTHVSVEASSHGLDQHRLDGIKLIA 206 LTTP + L L+ + G + +E SSH L Q R+ G++ A Sbjct: 121 GYRLGGNDLIKNPAALTTPEALTLQSTLAEMVEAGAQYAVMEVSSHALAQGRVRGVRFDA 180 Query: 207 GSFTNLGRDHIDYHQTQQAYFNAKMRLFEELLPKESPAIIYADDAYSKEVMKRAHNAGCR 266 FTNL RDH+D+H T + YF AK LF EL K A+I DD Y + +KR Sbjct: 181 AVFTNLSRDHLDFHGTMENYFAAKASLFTELGLK-RFAVINLDDEYGAQFVKRLPKD-IT 238 Query: 267 VLSVGYQG----KFIHLKKVCAIHNKQQVTISVEGKDFDFLFPLPGEFQVYNALVA-AGL 321 V ++ + I + QQ T + PL G F VYN L A A L Sbjct: 239 VSAITQPADGRAQDIKITDSGYSFEGQQFTFETPAGEGHLHTPLIGRFNVYNLLAALATL 298 Query: 322 CIAIGIDSALVLEHLEKLHVVPGRFEFVGTNSRGGRIYVDYAHTSNSLEMILKNIRTITS 381 GID ++ LEK VPGR E V + + VDYAHT ++LE L+ +R Sbjct: 299 LHLGGIDLEDIVAALEKFRGVPGRMELV-DGGQKFLVIVDYAHTPDALEKALRTLRKHKD 357 Query: 382 GRIIVVFGCGGDRDQGKRPIMGKIALDLADIAIVTDDNPRSEDPEKIRAEIIHGIP---G 438 GR+IVVFGCGGDRD+GKRP+MG IA LAD+ I+T DNPR EDPE+I A+I+ GI Sbjct: 358 GRLIVVFGCGGDRDRGKRPLMGAIAEQLADLVILTSDNPRGEDPEQIIADILAGISEKEK 417 Query: 439 FIEKGNRIEAIRTAIEMLNKQDVLVVAGKGHETVHIVTN 477 + +R +AIR AI DV+++AGKGHE I+ Sbjct: 418 VVIIADRRQAIRYAISNAKAGDVVLIAGKGHEDYQIIGG 456 >gnl|CDD|184459 PRK14022, PRK14022, UDP-N-acetylmuramoylalanyl-D-glutamate--L-lysine ligase; Provisional. Length = 481 Score = 238 bits (608), Expect = 3e-63 Identities = 137/499 (27%), Positives = 229/499 (45%), Gaps = 57/499 (11%) Query: 2 KLQDLIYKD--FPELINQLSIFPMQWRERKINEVSSDSRHIQAGWIFVAIVGNKEDGHLF 59 L D++ KD F E+I+Q + + +++S DSR G +F A + H F Sbjct: 5 TLLDILKKDHNFREIIDQDHYH-YNYSGVQFDDISYDSRTADEGTLFFAKGAYFK--HKF 61 Query: 60 IPQAIAQGAEAIVVSSAYSLQDFSATIRSNTPILVVDNTRKFLSLFASRLYGKHPEN--- 116 + AI QG + V Y + P ++V + +K +SL A Y +P++ Sbjct: 62 LQNAITQGLKLYVSEKDYEV---------GIPQVIVPDIKKAMSLIAMEFYD-NPQHKLK 111 Query: 117 ILAVTGTSGKSSVASFVQQICQR-------SGLSSFQIGPTSTISSFAQDNRLTTPSPIY 169 +LA TGT GK++ A F I ++ S +++ G T S+ LTTP + Sbjct: 112 LLAFTGTKGKTTAAYFAYHILKQLHKPAMLSTMNTTLDGETFFKSA------LTTPESLD 165 Query: 170 LAKALSYLSSQGVTHVSVEASSHGLDQHRLDGIKLIAGSFTNLGRDHIDY--HQTQQAYF 227 L K ++ G+TH+ +E SS R+ G+ G F N+ DHI H T + YF Sbjct: 166 LFKMMAEAVDNGMTHLIMEVSSQAYLVGRVYGLTFDVGVFLNITPDHIGPIEHPTFEDYF 225 Query: 228 NAKMRLFEELLPKESPAIIYAD-DAYSKEVMKRAHNAGCRVLSVGYQGKFIHLKKVCA-I 285 K RL L+ ++ +D D +S+ + V Q + I Sbjct: 226 YHK-RL---LMENSKAVVVNSDMDHFSELLE-----------QVTPQEHDFYGIDSENQI 270 Query: 286 HNKQQVTISVEGKDF-DFLFPLPGEFQVYNALVAAGLCIAIGIDSALVLEHLEKLHVVPG 344 + GK + L G+F NA+ A C+ +G + + + + VPG Sbjct: 271 MASNAFSFEATGKLAGTYDIQLIGKFNQENAMAAGLACLRLGASLEDIQKGIAQ-TPVPG 329 Query: 345 RFEFVGTNSRGGRIYVDYAHTSNSLEMILKNIRTITSGRIIVVFGCGGDRDQGKRPIMGK 404 R E V T S G ++++DYAH +SL ++ + G++I++ G G++ + +RP G+ Sbjct: 330 RME-VLTQSNGAKVFIDYAHNGDSLNKLIDVVEEHQKGKLILLLGAAGNKGESRRPDFGR 388 Query: 405 IALDLADIA-IVTDDNPRSEDPEKIRAEIIHGIPGFIEK-GNRIEAIRTAIEMLN-KQDV 461 +A + I+T D+P +EDP+ I EI I +E +R EAI+ A+ + D Sbjct: 389 VANRHPYLQVILTADDPNNEDPKMITQEIASHITHPVEIIDDRAEAIKHAMSITEGPGDA 448 Query: 462 LVVAGKGHETVHIVTNGEK 480 +++AGKG + IV G + Sbjct: 449 VIIAGKGADAYQIV-PGHR 466 >gnl|CDD|149357 pfam08245, Mur_ligase_M, Mur ligase middle domain. Length = 188 Score = 143 bits (362), Expect = 1e-34 Identities = 62/206 (30%), Positives = 97/206 (47%), Gaps = 21/206 (10%) Query: 120 VTGTSGKSSVASFVQQICQRSGLSSFQIGPTSTISSFAQDNRLTTPSPIYLAKALSYLSS 179 +TGT+GK++ + + +G G T + I L L+ + Sbjct: 1 ITGTNGKTTTTELIAALLSAAGGVVGTGG--------------NTNNAIGLPLLLALMER 46 Query: 180 QGVTHVSVEASSHGLDQHRLDGI-KLIAGSFTNLGRDHIDYHQTQQAYFNAKMRLFEELL 238 +G + +E SS GL + RL+G+ K TN+ DH+DYH T + Y AK +F E L Sbjct: 47 KGADYAVLELSSFGLGEGRLEGLAKPDIAVITNISPDHLDYHGTMENYAAAKAEIF-EGL 105 Query: 239 PKESPAIIYADDAYSKEVMKRAHNAGCRVLSVGYQGKFIHLKKVCAIHNKQQ--VTISVE 296 P++ A+I ADD E+ KR NAG +V++ G + + + ++ V +V Sbjct: 106 PEDGIAVINADD---PELAKRLKNAGAKVITFGLENEADDRAANIYVSSEGGKIVLFTVP 162 Query: 297 GKDFDFLFPLPGEFQVYNALVAAGLC 322 G + + PLPG VYNAL A Sbjct: 163 GGELEISLPLPGRHNVYNALAALAAA 188 >gnl|CDD|162224 TIGR01143, murF, UDP-N-acetylmuramoyl-tripeptide--D-alanyl-D-alanine ligase. This family consists of the strictly bacterial MurF gene of peptidoglycan biosynthesis. This enzyme is almost always UDP-N-acetylmuramoylalanyl-D-glutamyl-2, 6-diaminopimelate--D-alanyl-D-alanyl ligase, but in a few species, MurE adds lysine rather than diaminopimelate. This enzyme acts on the product from MurE activity, and so is also subfamily rather than equivalog. Staphylococcus aureus is an example of species in this MurF protein would differ. Length = 417 Score = 124 bits (313), Expect = 5e-29 Identities = 98/359 (27%), Positives = 156/359 (43%), Gaps = 34/359 (9%) Query: 36 DSRHIQAGWIFVAIVGNKEDGHLFIPQAIAQGAEAIVVSSAYSLQDFSATIRSNTPILVV 95 DSR I+ G +F+A+ G + DGH F+ QA+A GA A++V D P ++V Sbjct: 2 DSRAIKPGDLFIALKGERFDGHDFVEQALAAGAVAVLVDREV-GPDNGL------PQILV 54 Query: 96 DNTRKFLSLFASRLYGKHPENILAVTGTSGKSSVASFVQQICQRSGLSSFQIGPTSTISS 155 D+T + L AS K ++ +TG+SGK++ + I +T + Sbjct: 55 DDTLEALQALASAKRAKFSGKVIGITGSSGKTTTKEMLAAILSHKY------KVFATPGN 108 Query: 156 FAQDNRLTTPSPIYLAKALSYLSSQGVTHVSV-E--ASSHGLDQHRLDGIKLIAGSFTNL 212 F +N + P L+ L + G +V E AS G + + K TN+ Sbjct: 109 F--NNEIGLP--------LTLLRAPGDHDYAVLEMGASHPGEIAYLAEIAKPDIAVITNI 158 Query: 213 GRDHIDYHQTQQAYFNAKMRLFEELLPKESPAIIYADDAYSKEVMKRAHNAGCRVLSVGY 272 G H++ + + AK + + L + A+I ADD + KR N +LS G+ Sbjct: 159 GPAHLEGFGSLEGIAEAKGEILQG-LKENGIAVINADDPAFAKFAKRLPN--KAILSFGF 215 Query: 273 QGKFIHLKKVC-AIHNKQQVTISVEGKDFDFLFPLPGEFQVYNALVAAGLCIAIGIDSAL 331 +G + + T+ G +F+ PL G V NAL AA L + +GI Sbjct: 216 EGGDFSAADISYSALGSTGFTLVAPGGEFEVSLPLLGRHNVMNALAAAALALELGIPLEE 275 Query: 332 VLEHLEKLHVVPGRFEFVGTNSRGGRIYVDYAHTSNSLEMI-LKNIRTITSGRIIVVFG 389 + E L +L +V GRFE N G +D + +N M + G+ I+V G Sbjct: 276 IAEGLAELKLVKGRFEIQTKN---GLTLIDDTYNANPDSMRAALDALARFPGKKILVLG 331 >gnl|CDD|162197 TIGR01087, murD, UDP-N-acetylmuramoylalanine--D-glutamate ligase. Length = 433 Score = 107 bits (269), Expect = 7e-24 Identities = 56/245 (22%), Positives = 101/245 (41%), Gaps = 35/245 (14%) Query: 117 ILAVTGTSGKSSVASFVQQICQRSGLSSFQIGPTSTISSFAQDNRLTTPSPIYLAKALSY 176 ++A+TGT+GK++ S + + + +GL +F G + TP AL Sbjct: 104 VVAITGTNGKTTTTSLLYHLLKAAGLKAFLGG------------NIGTP-------ALEV 144 Query: 177 LSSQGVTHVSVEASSHGLDQHRLDGIKLIAGSFTNLGRDHIDYHQTQQAYFNAKMRLFEE 236 L +G +E SS L + ++ N+ DH+D+H + + Y AK+++F Sbjct: 145 LDQEGAELYVLELSSFQL--ETTESLRPEIALILNISEDHLDWHGSFEDYVAAKLKIFA- 201 Query: 237 LLPKESPAIIYADDAYSKEVMKRAHNAGCRVLSVGYQGKFIHLKKVCAIHNKQQVTISVE 296 + A++ ADD + A + +V+ + + +C I + Sbjct: 202 RQTEGDVAVLNADD---PRFARLAQKSKAQVIWFSVEK--DAERGLC-IRDGGLYL---- 251 Query: 297 GKDFDFLFPLPGEFQVYNALVAAGLCIAIGIDSALVLEHLEKLHVVPGRFEFVGTNSRGG 356 K D L G N L A L ++G++ +LE L +P R E+VG G Sbjct: 252 -KPNDLEGSLLGLHNAENILAAIALAKSLGLNLEAILEALRSFKGLPHRLEYVGQK--NG 308 Query: 357 RIYVD 361 + + Sbjct: 309 VHFYN 313 >gnl|CDD|162195 TIGR01082, murC, UDP-N-acetylmuramate--alanine ligase. UDP-N-acetylmuramate:L-alanyl-gamma-D-glutamyl-meso- diaminopimelate ligase (murein tripeptide ligase) is described by TIGR01081. Length = 448 Score = 85.8 bits (213), Expect = 2e-17 Identities = 83/343 (24%), Positives = 138/343 (40%), Gaps = 52/343 (15%) Query: 59 FIPQAIAQ--GAEAIVVSSAY--SLQDFSATIRSNTPILVVDNTRKFLSLFASRLYGKHP 114 +I + A+ +VVS+A + P++ R + A + +H Sbjct: 48 YIGHSAENLDDADVVVVSAAIKDDNPEIVEAKERGIPVI----RRA--EMLAELMRFRHS 101 Query: 115 ENILAVTGTSGKSSVASFVQQICQRSGLS-SFQIGPTSTISSFAQDNRLTTPSPIYLAKA 173 +AV GT GK++ + + I + +GL + +G + + RL + +A+A Sbjct: 102 ---IAVAGTHGKTTTTAMIAVILKEAGLDPTVVVG--GLVKEAGTNARLGS-GEYLVAEA 155 Query: 174 ----LSYLSSQGVTHVSVEASSHGLDQHRLDGIKLIAGSFTNLGRDHIDYHQTQQAYFNA 229 S+L Q +V++ TN+ DH+D + + A Sbjct: 156 DESDASFLHLQ--PNVAI---------------------VTNIEPDHLDTYGSSFERLKA 192 Query: 230 KMRLFEELLPKESPAIIYADDAYSKEVMKRAHNAGCRVLSVGYQGKFIHLKKVCAIHNKQ 289 F LP A+I ADD +E++ +A +V++ G G+ + + Sbjct: 193 AFEKFIHNLPFYGLAVICADDPVLRELVPKATE---QVITYGGSGEDADYRAENIQQSGA 249 Query: 290 QVTISVEGKD---FDFLFPLPGEFQVYNALVAAGLCIAIGIDSALVLEHLEKLHVVPGRF 346 + SV GK +F LPG V NAL A + + +GID +L L V RF Sbjct: 250 EGKFSVRGKGKLYLEFTLNLPGRHNVLNALAAIAVALELGIDFEAILRALANFQGVKRRF 309 Query: 347 EFVGTNSRGGRIYVDYAHTSNSLEMILKNIRTI-TSGRIIVVF 388 E +G G + DYAH ++ LK R RI+VVF Sbjct: 310 EILGEF-GGVLLIDDYAHHPTEIKATLKAARQGYPDKRIVVVF 351 >gnl|CDD|179018 PRK00421, murC, UDP-N-acetylmuramate--L-alanine ligase; Provisional. Length = 461 Score = 75.9 bits (188), Expect = 2e-14 Identities = 71/287 (24%), Positives = 107/287 (37%), Gaps = 52/287 (18%) Query: 210 TNLGRDHIDYHQTQQAYFNAKMRLFEELLPKESPAIIYADDAYSKEVMKRAHNAGCRVLS 269 TN+ DH+DY+ + +A + F LP + DD +E++ R V++ Sbjct: 181 TNIDADHLDYYGDFEDLKDA-FQEFAHNLPFYGALVACGDDPELRELLPRV---SRPVIT 236 Query: 270 VGYQGK-FIHLKKVCAIHNKQQVTISVEGKDF-DFLFPLPGEFQVYNALVAAGLCIAIGI 327 G+ + + + G+ DF PLPG V NAL A + + +GI Sbjct: 237 YGFSEDADFRAENIRQDGGGTHFDVLRRGEVLGDFTLPLPGRHNVLNALAAIAVALELGI 296 Query: 328 DSALVLEHLEKLHVVPGRFEFVGTNSRGGRIYV-DYAH--TSNSLEMI--LKNIRTIT-S 381 D + E L V RFE G GG + + DYAH T E+ LK R Sbjct: 297 DDEAIREALATFKGVKRRFEEKGEV--GGVVLIDDYAHHPT----EIKATLKAARQGYPD 350 Query: 382 GRIIVVFGCGGDRDQ--------------GKRPIMGKIALDLADIAIVTDDNPRSEDP-- 425 RI+ VF Q + AL AD I+ D E+P Sbjct: 351 KRIVAVF-------QPHRYSRTRDLLDEFAE-------ALSDADEVILLDIYAAGEEPIG 396 Query: 426 ----EKIRAEIIHGIPGFIEKGNRIEAIRTAIEMLNKQDVLVVAGKG 468 E + +I G I + + E+L D+++ G G Sbjct: 397 GVDSEDLARKIKRGHRDPIFVPDLEDLAELLAEVLKPGDLVLTMGAG 443 >gnl|CDD|162681 TIGR02068, cya_phycin_syn, cyanophycin synthetase. Cyanophycin synthesis is analogous to polyhydroxyalkanoic acid (PHA) biosynthesis, except that PHA polymers lack nitrogen and may be made under nitrogen-limiting conditions. Length = 864 Score = 75.2 bits (185), Expect = 3e-14 Identities = 89/402 (22%), Positives = 146/402 (36%), Gaps = 66/402 (16%) Query: 104 LFASRLYGKHPENILAVTGTSGKSSVASFVQQICQRSGLSSFQIGPTSTISSFAQDNRLT 163 LF + G+ P I++VTGT+GK++ V I +++G +G T+T + + Sbjct: 470 LFPAEDDGRIP--IVSVTGTNGKTTTTRLVAHILKQTG---KVVGMTTTDGVYIGKYLVE 524 Query: 164 TPSPIYLAKALSYLSSQGVTHVSVEASSHGLDQHRLDGIKLIAGSFTNLGRDHI---DYH 220 A A L V +E + G+ + L + G TN+ DH+ D + Sbjct: 525 KGDNTGPASARRILMDPTVDAAVLETARGGILREGLAFDRCDVGVVTNIAGDHLGIGDIN 584 Query: 221 QTQQ-----------------AYFNAKMRLFEELLPKESPAIIYADDAYSKEVMKRAHNA 263 + A NA + + K I Y + + Sbjct: 585 TIEDLADVKRVVVEVVLPDGYAVLNADDPMVAAMAEKCKGKIAYFSMDPNNPTVAAHIAD 644 Query: 264 GCRVLSV--GY----QGKFIHLKKVCAIHNKQQVTISVEGKDFDFLFPLPGEFQVYNALV 317 G R + GY +G AI + +++ G+ FQ+ NAL Sbjct: 645 GGRAVYYENGYIVIARGGDEV-----AIARIAAIPLTMGGR---------VAFQIENALA 690 Query: 318 AAGLCIAIGIDSALVLEHLEKLHV----VPGRFEFVGTNSRGGRIYVDYAHTSNSLEMIL 373 A A+G+ L+ + PGRF N G + VDY H ++E + Sbjct: 691 AVAAAWALGVPIELIRAGIRTFDADAAQAPGRFNLF--NLGGAHVLVDYGHNPAAIEAVG 748 Query: 374 KNIRTITSGRIIVVFGCGGDRDQGKRPIMGKIALDLAD-IAIVTDDNPRSEDPEKIRAEI 432 IR + R I V G GDR G++ D I + DD+ R + A + Sbjct: 749 AAIRNWPARRRIGVIGGPGDRRDEDLVEQGELLGGAFDQIILKEDDDVRGRPRGEAAALL 808 Query: 433 IHGIPGFIEKGNR----------IEAIRTAIEMLNKQDVLVV 464 G + + R EAI A++ L D++V+ Sbjct: 809 RQG----LRQSARKAAIEDILDETEAIAAALDDLRAGDLVVI 846 >gnl|CDD|182718 PRK10773, murF, UDP-N-acetylmuramoyl-tripeptide--D-alanyl-D-alanine ligase; Reviewed. Length = 453 Score = 74.7 bits (184), Expect = 5e-14 Identities = 35/100 (35%), Positives = 56/100 (56%), Gaps = 9/100 (9%) Query: 30 INEVSSDSRHIQAGWIFVAIVGNKEDGHLFIPQAIAQGAEAIVVSSAYSLQDFSATIRSN 89 I+ V++D+R + G +FVA+ G + D H F A A GA A++VS + + Sbjct: 24 IDAVTTDTRKVTPGCLFVALKGERFDAHDFADDAKAAGAGALLVSRPLDI---------D 74 Query: 90 TPILVVDNTRKFLSLFASRLYGKHPENILAVTGTSGKSSV 129 P LVV +TR A+ + + P ++A+TG+SGK+SV Sbjct: 75 LPQLVVKDTRLAFGQLAAWVRQQVPARVVALTGSSGKTSV 114 Score = 44.3 bits (105), Expect = 7e-05 Identities = 20/47 (42%), Positives = 24/47 (51%) Query: 299 DFDFLFPLPGEFQVYNALVAAGLCIAIGIDSALVLEHLEKLHVVPGR 345 D L PLPG + NAL AA L +++G V L L VPGR Sbjct: 271 SVDVLLPLPGRHNIANALAAAALAMSVGATLDAVKAGLANLKAVPGR 317 >gnl|CDD|183386 PRK11930, PRK11930, putative bifunctional UDP-N-acetylmuramoyl-tripeptide:D-alanyl-D-alanine ligase/alanine racemase; Provisional. Length = 822 Score = 70.0 bits (172), Expect = 1e-12 Identities = 75/339 (22%), Positives = 129/339 (38%), Gaps = 60/339 (17%) Query: 30 INEVSSDSRHIQ--AGWIFVAIVGNKEDGHLFIPQAIAQGAEAIVVSSAYSLQDFSATIR 87 I+++ +DSR + +F A+ G + DGH +I + +G VVS Sbjct: 24 IDQILTDSRSLSFPENTLFFALKGERNDGHRYIQELYEKGVRNFVVSEEKH----PEESY 79 Query: 88 SNTPILVVDNTRKFLSLFASRLYGKHPENILAVTGTSGKSSVASFVQQICQRSGLSSFQI 147 + L V + K L A+ + ++ +TG++GK+ V ++ Q+ LS Sbjct: 80 PDANFLKVKDPLKALQELAAYHRSQFDIPVIGITGSNGKTIVKEWLYQL-----LS---- 130 Query: 148 GPTSTISSFAQDNRLTTPSPIYLAKALSYLSSQGVTHVSV------------EAS-SHGL 194 + SP SY S GV +SV EA S Sbjct: 131 -----------PDYNIVRSP------RSYNSQIGVP-LSVWQLNEEHELGIFEAGISQPG 172 Query: 195 DQHRL-DGIKLIAGSFTNLGRDHIDYHQTQQAYFNAKMRLFEELLPKESPAIIYADD--A 251 + L IK G TN+G H + ++ + K++LF K+ IIY D Sbjct: 173 EMEALQKIIKPTIGILTNIGGAHQENFRSIKQKIMEKLKLF-----KDCDVIIYNGDNEL 227 Query: 252 YSKEVMKRAHNAGCRVLSVGYQGKFIHLKKVCAIHNKQ-QVTISVEGKDFDFLFPLP--G 308 S + N +++S + L + + K+ IS K DF F +P Sbjct: 228 ISSCI--TKSNLTLKLISWSRKDPEAPL-YIPFVEKKEDHTVISYTYKGEDFHFEIPFID 284 Query: 309 EFQVYNALVAAGLCIAIGIDSALVLEHLEKLHVVPGRFE 347 + + N + + + +G + + E + +L V R E Sbjct: 285 DASIENLIHCIAVLLYLGYSADQIQERMARLEPVAMRLE 323 >gnl|CDD|179291 PRK01390, murD, UDP-N-acetylmuramoyl-L-alanyl-D-glutamate synthetase; Provisional. Length = 460 Score = 69.5 bits (171), Expect = 2e-12 Identities = 63/251 (25%), Positives = 97/251 (38%), Gaps = 36/251 (14%) Query: 117 ILAVTGTSGKSSVASFVQQICQRSGLSSFQIGPTSTISSFAQDNRLTTPSPIYLAKALSY 176 +A+TGT+GKS+ + + I + +G Q+G + T L Sbjct: 116 FIAITGTNGKSTTTALIAHILREAGRDV-QMG-----------GNIGTA-----VLTLEP 158 Query: 177 LSSQGVTHVSVEASSHGLDQHRLDGIKLIAGSFTNLGRDHIDYHQTQQAYFNAKMRLFEE 236 + V +V +E SS+ +D + G NL DH+D H T + Y AK RLF Sbjct: 159 PPAGRV-YV-LELSSYQID--LAPSLDPDVGVLLNLTPDHLDRHGTMEGYAAAKERLFAG 214 Query: 237 LLPKESPAIIYADDAYSKEVMKRAHNAGCRVLSVGYQGKFIHLKKVCAIHNKQQVTISVE 296 P A+I DDAY + + R AG RV+ + ++ + Sbjct: 215 QGP--DTAVIGVDDAYCRAIADRLEAAGRRVVRISAGKPL-----ADGVYADGGKLVDAR 267 Query: 297 GKDFDFLFP------LPGEFQVYNALVAAGLCIAIGIDSALVLEHLEKLHVVPGRFEFVG 350 G + LPG NA A A+G+ + L + R E VG Sbjct: 268 GGRQVEIADLRGIPSLPGAHNAQNAAAAYAAARALGLSPEEIAAGLASFPGLAHRMEQVG 327 Query: 351 TNSRGGRIYVD 361 RGG ++V+ Sbjct: 328 R--RGGVLFVN 336 >gnl|CDD|184511 PRK14106, murD, UDP-N-acetylmuramoyl-L-alanyl-D-glutamate synthetase; Provisional. Length = 450 Score = 68.8 bits (169), Expect = 3e-12 Identities = 72/307 (23%), Positives = 122/307 (39%), Gaps = 60/307 (19%) Query: 59 FIPQAIAQGAEAIVVSSAYSLQDFSATIRSNTPILVVDNTRKFLSL----FASRLYGKHP 114 P+ +G + +VVS L +P +V + + + A R Sbjct: 60 EYPEEFLEGVDLVVVSPGVPLD---------SPPVVQAHKKGIEVIGEVELAYRF---SK 107 Query: 115 ENILAVTGTSGKSSVASFVQQICQRSGLSSFQIGPTSTISSFAQDNRLTTPSPIYLAKAL 174 I+A+TGT+GK++ + + +I + +G + G N I Sbjct: 108 APIVAITGTNGKTTTTTLLGEIFKNAGRKTLVAG-----------N-------IGYPLID 149 Query: 175 SYLSSQGVTHVSVEASSHGLDQHRLDGIKLIAGSFTNLGRDHIDYHQTQQAYFNAKMRLF 234 + + E SS L+ + K G N+ DH+D H+T + Y AK R+F Sbjct: 150 AVEEYGEDDIIVAEVSSFQLET--IKEFKPKVGCILNITPDHLDRHKTMENYIKAKARIF 207 Query: 235 EELLPKESPAIIYADDAYSKEVMKRAHNAGCRVL-----SVGYQGKFIHLKKVCAIHNKQ 289 E P + ++ DD ++ + K+A RV+ S+ +G F+ Sbjct: 208 ENQRPSDY-TVLNYDDPRTRSLAKKAK---ARVIFFSRKSLLEEGVFV---------KNG 254 Query: 290 QVTISVEGK-----DFDFLFPLPGEFQVYNALVAAGLCIAIGIDSALVLEHLEKLHVVPG 344 ++ IS+ GK D D +F +PGE + NAL A +GI ++ L+ V Sbjct: 255 KIVISLGGKEEEVIDIDEIF-IPGEHNLENALAATAAAYLLGISPDVIANTLKTFKGVEH 313 Query: 345 RFEFVGT 351 R EFV Sbjct: 314 RIEFVAE 320 >gnl|CDD|179297 PRK01438, murD, UDP-N-acetylmuramoyl-L-alanyl-D-glutamate synthetase; Provisional. Length = 480 Score = 67.8 bits (166), Expect = 6e-12 Identities = 64/276 (23%), Positives = 103/276 (37%), Gaps = 58/276 (21%) Query: 106 ASRLYGK-HPENILAVTGTSGKSSVASFVQQICQRSGLSSFQIGPTSTISSFAQDNRLTT 164 A RL P LAVTGT+GK++ + + + +GL + +G T Sbjct: 112 AWRLRDPDRPAPWLAVTGTNGKTTTVQMLASMLRAAGLRAAAVGNIGT------------ 159 Query: 165 PSPIYLAKALSYLSSQGVTHVSVEASSHGLDQHRLDGIKLIAGSFTNLGRDHIDYHQTQQ 224 P+ A +G ++VE SS L H + + + NL DH+D+H + + Sbjct: 160 --PVLDA----VRDPEGYDVLAVELSSFQL--HWSPSVSPHSAAVLNLAPDHLDWHGSME 211 Query: 225 AYFNAKMRLFEELLPKESPAIIY-ADDAYSKEVMKRAHNA-GCRVLSVGYQGKFIHLKKV 282 AY AK R++E + A +Y D ++++++ A G R + Sbjct: 212 AYAAAKARIYE----GTTVACVYNVADPATEDLVEEADVVEGARAIGFTL---------- 257 Query: 283 CAIHNKQQVTISVEGKDFDFLF-----------------PLPGEFQVYNALVAAGLCIAI 325 Q+ + V+G D F + NAL AA L + Sbjct: 258 -GTPGPSQLGV-VDGILVDRAFVEDRQTSALELATLEDLRPAAPHNIANALAAAALARSF 315 Query: 326 GIDSALVLEHLEKLHVVPGRFEFVGTNSRGGRIYVD 361 G+ A V + L R E V G +VD Sbjct: 316 GVPPAAVRDGLRAFRPDAHRIEHVAD--ADGVTWVD 349 >gnl|CDD|179428 PRK02472, murD, UDP-N-acetylmuramoyl-L-alanyl-D-glutamate synthetase; Provisional. Length = 447 Score = 67.6 bits (166), Expect = 6e-12 Identities = 59/251 (23%), Positives = 101/251 (40%), Gaps = 41/251 (16%) Query: 117 ILAVTGTSGKSSVASFVQQICQRSGLSSFQIGPTST-ISSFAQDNRLTTPSPIYLAKALS 175 I+ +TG++GK++ + + ++ + G + G S AQ A A Sbjct: 110 IIGITGSNGKTTTTTLIGEMLKAGGQHALLAGNIGYPASEVAQK-----------ATADD 158 Query: 176 YLSSQGVTHVSVEASSH---GLDQHRLDGIKLIAGSFTNLGRDHIDYHQTQQAYFNAKMR 232 L V E SS G++ R I +I TN+ H+DYH T + Y AK Sbjct: 159 TL----VM----ELSSFQLMGIETFRPH-IAVI----TNIYPAHLDYHGTFENYVAAKWN 205 Query: 233 LFEELLPKESPAIIYADDAYSKEVMKRAHNAGCRVLSVGYQGKFIHLKKVC--AIHNKQQ 290 + + ++ +I D +EV + A V+ K + A++ K + Sbjct: 206 IQKNQT-EDDYLVINFDQ---EEVKELAKQTKATVVPFSTTEKVEDGAYIKDGALYFKGE 261 Query: 291 VTISVEGKDFDFLFPLPGEFQVYNALVAAGLCIAIGIDSALVLEHLEKLHVVPGRFEFVG 350 ++ + D + LPG + NAL A +G+ + + E L V R ++VG Sbjct: 262 KIMAAD----DIV--LPGSHNLENALAAIAAAKLLGVSNEAIREVLSTFSGVKHRLQYVG 315 Query: 351 TNSRGGRIYVD 361 T G + Y D Sbjct: 316 TI-DGRKFYND 325 >gnl|CDD|162392 TIGR01499, folC, folylpolyglutamate synthase/dihydrofolate synthase. A mutation study of the FolC gene of E. coli suggests that both activitities belong to the same active site. Because some examples are monofunctional (and these cannot be separated phylogenetically), the model is treated as subfamily, not equivalog. Length = 397 Score = 61.1 bits (149), Expect = 5e-10 Identities = 84/403 (20%), Positives = 151/403 (37%), Gaps = 84/403 (20%) Query: 113 HPEN---ILAVTGTSGKSSVASFVQQICQRSGLSSFQIGP-TST-ISSF----------A 157 +P++ ++ V GT+GK S +F++ I + +G +++G TS + SF Sbjct: 13 NPQDLYPVIHVAGTNGKGSTCAFLESILRAAG---YKVGLFTSPHLVSFNERIRINGEPI 69 Query: 158 QDNRLT-------------TPSPIY----LAKALSYLSSQGVTHVSVEASSHGLDQHRLD 200 D L + P Y A Y + V +E G RLD Sbjct: 70 SDEELAQAFEQVRPILEKLSQQPTYFELLTLLAFLYFAQAQVDVAVLEVGLGG----RLD 125 Query: 201 G---IKLIAGSFTNLGRDHID---YHQTQQAYFNAKMRLFEELLPKESPAIIYAD---DA 251 I+ + T++G DH + + A+ K + +E +P I+ +A Sbjct: 126 ATNVIEPLVSVITSIGLDHTEILGDTLEEIAW--EKAGIIKEGVP-----IVTGPQEPEA 178 Query: 252 YSKEVMKRAHNAGCRVLSVGYQGKFIHLKKVCAIHNKQQVTISVEGKDF---DFLFPLPG 308 + + K+A G + VG + +S G + L G Sbjct: 179 LN-VLKKKAQEKGAPLFVVGRD---------FNYSETDENYLSFSGANLFLEPLALSLLG 228 Query: 309 EFQVYNALVAAGLCIAIG-----IDSALVLEHLEKLHVVPGRFEFVGTNSRGGRIYVDYA 363 + Q NA +A +G + + + L PGR E + I +D A Sbjct: 229 DHQAENAALALAALEVLGKQRPKLSEEAIRKGLANTIW-PGRLEILSE--DNPNILLDGA 285 Query: 364 HTSNSLEMILKNIRTITSGR-IIVVFGCGGDRD--QGKRPIMGKIALDLADIAIVTDDNP 420 H +S E + + + +GR II++FG D+D P+ + ++ + D P Sbjct: 286 HNPHSAEALAEWFKKRFNGRPIILLFGALADKDAAAMLAPLKPVVD---KEVFVTPFDYP 342 Query: 421 RSEDPEKIRAEIIHGIPGFIEKGNRIEAIRTAIEMLNKQDVLV 463 R++D + A + G + EA+ A+ + D+LV Sbjct: 343 RADDAADLAA--LAETFGKETVEDWREALALALNASAEDDILV 383 >gnl|CDD|179571 PRK03369, murD, UDP-N-acetylmuramoyl-L-alanyl-D-glutamate synthetase; Provisional. Length = 488 Score = 59.4 bits (144), Expect = 2e-09 Identities = 83/336 (24%), Positives = 124/336 (36%), Gaps = 61/336 (18%) Query: 54 EDGHLFIPQAIAQGAEAIVVSSA------YSLQDFSATIRSNTPILVVDNTRKF------ 101 +D + +G + S A Y+L S R P+L Sbjct: 42 DDDPDALRPHAERGVATVSTSDAVQQIADYALVVTSPGFRPTAPVLAAAAAAGVPIWGDV 101 Query: 102 -LS--LFASRLYGKHPENILAVTGTSGKSSVASFVQQICQRSGLSSFQIGPTSTISSFAQ 158 L+ L A+ YG P L VTGT+GK++ S + + +G S G I S Sbjct: 102 ELAWRLDAAGCYGP-PRRWLVVTGTNGKTTTTSMLHAMLIAAGRRSVLCG---NIGSPVL 157 Query: 159 DNRLTTPSPIYLAKALSYLSSQGVTHVSVEASSHGLDQHRLDGIKLIAGSFTNLGRDHID 218 D + LA VE SS L H ++ AG+ N+ DH+D Sbjct: 158 D--VLDEPAELLA---------------VELSSFQL--HWAPSLRPEAGAVLNIAEDHLD 198 Query: 219 YHQTQQAYFNAKMRLFEELLPKESPAIIYADDAYSKEVMKRAHNAGCRV---LSVGYQGK 275 +H T AY AK R + A++ DD+ + ++ A A RV L G+ Sbjct: 199 WHGTMAAYAAAKARALTGRV-----AVVGLDDSRAAALLDTA-PAPVRVGFRLGEPAAGE 252 Query: 276 FIHLKKVCAIHNKQQVTISVEGKDFDFL----FPLPGEFQVYNALVAAGLCIAIGIDSAL 331 + + V + D P+PG V +AL AA L A+G+ + Sbjct: 253 L-------GVRDGHLVDRAF-ADDLRLAPVASIPVPGPVGVLDALAAAALARAVGVPAGA 304 Query: 332 VLEHLEKLHVVPGRFEFVGTNSRGGRIYVDYAHTSN 367 + + L V R E V G YVD + +N Sbjct: 305 IADALASFRVGRHRAEVVAV--ADGITYVDDSKATN 338 >gnl|CDD|179359 PRK02006, murD, UDP-N-acetylmuramoyl-L-alanyl-D-glutamate synthetase; Provisional. Length = 498 Score = 58.5 bits (142), Expect = 3e-09 Identities = 71/296 (23%), Positives = 107/296 (36%), Gaps = 84/296 (28%) Query: 102 LSLFASRLY-----GKHPENILAVTGTSGKSSVASFVQQICQRSGLSSFQIGPTSTISSF 156 + LFA L G P+ +LA+TGT+GK++ + +C+R+G + IS Sbjct: 104 IELFAQALAALGASGYAPK-VLAITGTNGKTTTTALTGLLCERAGKK---VAVAGNIS-- 157 Query: 157 AQDNRLTTPSPIYLAKALSYLSSQGVTHVSV-EASS------HGLDQHRLDGIKLIAGSF 209 P L K + + + + V V E SS H L A + Sbjct: 158 ----------PAALDKLMEAIDAGALPDVWVLELSSFQLETTHTLAPD--------AATV 199 Query: 210 TNLGRDHIDYHQTQQAYFNAKMRLFEELLPKESPAIIYADDAYSKEVMKRAH-NAGCRVL 268 N+ +DH+D+H + AY AK R+F + ++ DDA VM A + Sbjct: 200 LNITQDHLDWHGSMAAYAAAKARIF----GPRTVRVLNRDDA---RVMAMAPPGGAADAV 252 Query: 269 SVG-----YQGKFIHLKKVCAIHNKQQVTISVEGKDFDFLFPLP---------------- 307 + G G + + + VE +D D P P Sbjct: 253 TFGLDEPAADGDY-------GLLRDNGMAWLVEAEDRDAADPAPSRRRKKDAAPPPDIRL 305 Query: 308 ------------GEFQVYNALVAAGLCIAIGIDSALVLEHLEKLHVVPGRFEFVGT 351 G NAL A L AIG+ +A +L L + P R E V T Sbjct: 306 KRLMPADALRIRGLHNAANALAALALARAIGLPAAPLLHGLREYRGEPHRVELVAT 361 >gnl|CDD|184501 PRK14093, PRK14093, UDP-N-acetylmuramoylalanyl-D-glutamyl-2, 6-diaminopimelate--D-alanyl-D-alanine ligase; Provisional. Length = 479 Score = 56.3 bits (136), Expect = 2e-08 Identities = 31/101 (30%), Positives = 48/101 (47%), Gaps = 5/101 (4%) Query: 28 RKINEVSSDSRHIQAGWIFVAIVGNKEDGHLFIPQAIAQGAEAIVVSSAYSLQDFSATIR 87 R + +S DSR + G + AI G+ DGH F+ A+ GA VV + Sbjct: 26 RDVTGISIDSRTLAPGDAYFAIKGDVHDGHAFVAAALKAGAALAVVE-----RAQRDKFA 80 Query: 88 SNTPILVVDNTRKFLSLFASRLYGKHPENILAVTGTSGKSS 128 ++ P+LVVD+ L + ++AVTG+ GK+S Sbjct: 81 ADAPLLVVDDVLAALRDLGRAARARLEAKVIAVTGSVGKTS 121 >gnl|CDD|178896 PRK00141, murD, UDP-N-acetylmuramoyl-L-alanyl-D-glutamate synthetase; Provisional. Length = 473 Score = 55.9 bits (135), Expect = 3e-08 Identities = 96/439 (21%), Positives = 158/439 (35%), Gaps = 85/439 (19%) Query: 43 GWIFVAIVGNKEDGHLFIPQAIAQGAEAIVVSSAYS-LQDFSATI-----RSNTPILVVD 96 G V N+ H I G I + A L FS + R ++P+LV Sbjct: 38 GCDVVVADDNETARHKLIEVT---GVADISTAEASDQLDSFSLVVTSPGWRPDSPLLVDA 94 Query: 97 NTRKF-------LSLFASR--LYGKHPENILAVTGTSGKSSVASFVQQICQRSGLSSFQI 147 ++ L+ + ++G+ P LAVTGT+GK++ + + + Q G ++ + Sbjct: 95 QSQGLEVIGDVELAWRLDQAGVFGE-PRTWLAVTGTNGKTTTTAMLAAMMQEGGFAAQAV 153 Query: 148 GPTSTISSFAQDNRLTTPSPIYLAKALSYLSSQGVTHVSVEASSHGLDQHRLDGIKLIAG 207 G S A L I + A E SS L H + G Sbjct: 154 GNIGVPVSAA----LVAQPRIDVLVA--------------ELSSFQL--HWSPTLTPDVG 193 Query: 208 SFTNLGRDHIDYHQTQQAYFNAKMRLFEELLPKESPAIIYADDAYSKEVMKRAHNAGCRV 267 NL DHID+H + + Y K ++ + A+I ADD Y ++ A +G Sbjct: 194 VVLNLAEDHIDWHGSMRDYAADKAKVL-----RGPVAVIGADDEYVVQLTSAADLSGLIG 248 Query: 268 LSVGYQGKFIHLKKVCAIHNKQQVTI----SVEGKDFDFLFPLPGEFQVYNALVAAGLCI 323 ++G + + + V +V + + P G V +AL AA + Sbjct: 249 FTMGEPA-----AGQVGVRDGELVDNAFGQNVVLASAEGISP-AGPAGVLDALAAAAVAR 302 Query: 324 AIGIDSALVLEHLEKLHVVPGRFEFVGTNSRGGRIYVDYAHTSN---------SLEMI-- 372 + G+ + L V R + V + GG ++D + +N E + Sbjct: 303 SQGVAPEAIARALSSFEVAGHRGQVVAEH--GGVTWIDNSKATNPHAADAALAGHESVVW 360 Query: 373 -----LKN------IRTITSGRIIVVFGCGGDRDQGKRPIMGKIALDLADIAIVTDDN-- 419 LK IRT + RI G DR + I+ +A D + D+ Sbjct: 361 VAGGQLKGADIDDLIRTH-APRIKAAVVLGVDRAE----IVAALAEHAPDAPVTVTDSTD 415 Query: 420 PRSEDPEKIRAEIIHGIPG 438 P E + A + PG Sbjct: 416 PEEAMEEAVSAAVSLAEPG 434 >gnl|CDD|167786 PRK04308, murD, UDP-N-acetylmuramoyl-L-alanyl-D-glutamate synthetase; Provisional. Length = 445 Score = 54.5 bits (131), Expect = 6e-08 Identities = 83/413 (20%), Positives = 166/413 (40%), Gaps = 66/413 (15%) Query: 63 AIAQGAEAIVVSSAYSL-QDFSATIRSNTPILVVDNTRKFLSLFASRLYGKHPENILAVT 121 A+ G + + +S S Q + N ++ D + L A + + + ++A+T Sbjct: 63 ALDNGFDILALSPGISERQPDIEAFKQNGGRVLGD-----IELLA-DIVNRRGDKVIAIT 116 Query: 122 GTSGKSSVASFVQQICQRSGLSSFQIGPTSTISSFAQDNRLTTPSPIYLAKALSYLSSQG 181 G++GK++V S V +C + GL + G T A+ R + +++ Sbjct: 117 GSNGKTTVTSLVGYLCIKCGLDTVIAGNIGTPVLEAELQREGKKADVWV----------- 165 Query: 182 VTHVSVEASSHGLDQHRLDGIKLIAGSFTNLGRDHIDYHQTQQAYFNAKMRLFEELLPKE 241 +E SS L+ + ++ A + N+ DH+D + Y + K ++F + Sbjct: 166 -----LELSSFQLEN--TESLRPTAATVLNISEDHLDRYDDLLDYAHTKAKIFR----GD 214 Query: 242 SPAIIYADDAYSKEVMKRAHNAGCRVLSVGYQGKFIHLKKVCAIH-NKQQVTISVEGKD- 299 ++ ADDA+ + MKRA G + K+ L+ ++ + +D Sbjct: 215 GVQVLNADDAFCR-AMKRA----------GREVKWFSLEHEADFWLERETGRLKQGNEDL 263 Query: 300 FDFL-FPLPGEFQVYNALVAAGLCIAIGIDSALVLEHLEKLHVVPGRFEFVGTNSRGGRI 358 PL G N + A LC A+G+ +LEH++ +P R E +G + G + Sbjct: 264 IATQDIPLQGLHNAANVMAAVALCEAVGLPREALLEHVKTFQGLPHRVEKIGEKN--GVV 321 Query: 359 YVDYAHTSN--SLEMILKNIRTITSGRIIVVFGCGGDRDQGKRPIMGKIALDLADIA--- 413 ++D + +N + + ++ + V GG GK + LA A Sbjct: 322 FIDDSKGTNVGATAAAIAGLQ-----NPLFVI-LGGM---GKGQDFTPLRDALAGKAKGV 372 Query: 414 -IVTDDNPRSEDPEKIRAEIIHGIPGFIEKGNRIEAIRTAIEMLNKQDVLVVA 465 ++ D P+ IR ++ + EA++ A D+++++ Sbjct: 373 FLIGVDAPQ------IRRDLDGCGLNLTDCATLEEAVQRAYAQAEAGDIVLLS 419 >gnl|CDD|179086 PRK00683, murD, UDP-N-acetylmuramoyl-L-alanyl-D-glutamate synthetase; Provisional. Length = 418 Score = 53.7 bits (129), Expect = 1e-07 Identities = 32/116 (27%), Positives = 49/116 (42%), Gaps = 21/116 (18%) Query: 118 LAVTGTSGKSSVASFVQQICQRSGLSSFQIGPTSTISSFAQDNRLTTPSPIYLAKALSYL 177 L +TG++GK++ F++ + +R G+ +F +G PI L + Sbjct: 105 LGITGSTGKTTTILFLEHLLKRLGIPAFAMGNIGI--------------PI-----LDGM 145 Query: 178 SSQGVTHVSVEASSHGLDQHRLDGIKLIAGSFTNLGRDHIDYHQTQQAYFNAKMRL 233 GV VE SS L L G N+ +H+DYH AYF AK + Sbjct: 146 QQPGVR--VVEISSFQLADQEKSYPVLSGGMILNISDNHLDYHGNLSAYFQAKQNI 199 >gnl|CDD|179651 PRK03806, murD, UDP-N-acetylmuramoyl-L-alanyl-D-glutamate synthetase; Provisional. Length = 438 Score = 49.9 bits (120), Expect = 1e-06 Identities = 64/247 (25%), Positives = 104/247 (42%), Gaps = 54/247 (21%) Query: 117 ILAVTGTSGKSSVASFVQQICQRSGLSSFQIGPTSTISSFAQDNRLTTPSPIYLAKALSY 176 I+A+TG++GKS+V + V ++ + +G ++G I P ALS Sbjct: 107 IVAITGSNGKSTVTTLVGEMAKAAGW---KVGVGGNIG---------LP-------ALSL 147 Query: 177 LSSQGVTHVSVEASSHGLDQHRLDGIKLIAGSFTNLGRDHID-YHQTQQAYFNAKMRLFE 235 L + +V +E SS L+ +K A + N+ DH+D Y Q Y AK+R++E Sbjct: 148 LDQECELYV-LELSSFQLETTS--SLKAAAATILNVTEDHMDRYPFGLQQYRAAKLRIYE 204 Query: 236 ELLPKESPAIIYADDAYSKEVMKRAHNAGCRVLSVG----------YQGKFIHLKKVCAI 285 ++ ADDA + + A R +S G QG+ K + Sbjct: 205 ----NAKVCVVNADDALTMPI----RGADKRCVSFGVNMGDYHLNRQQGETWLRVKGEKV 256 Query: 286 HNKQQVTISVEGKDFDFLFPLPGEFQVYNALVAAGLCIAIGIDSALVLEHLEKLHVVPGR 345 N +++ +S G+ NAL A L A+GI A L+ L +P R Sbjct: 257 LNTKEMKLS-------------GQHNYTNALAALALADAVGIPRASSLKALTTFTGLPHR 303 Query: 346 FEFVGTN 352 F+ V + Sbjct: 304 FQLVLEH 310 >gnl|CDD|179872 PRK04690, murD, UDP-N-acetylmuramoyl-L-alanyl-D-glutamate synthetase; Provisional. Length = 468 Score = 48.7 bits (116), Expect = 3e-06 Identities = 77/362 (21%), Positives = 129/362 (35%), Gaps = 50/362 (13%) Query: 67 GAEAIVVSSA----YSLQDFSATIRSNTPILVVDNTRKFLSLFASRLYGKHPENILAVTG 122 A +VV S Y + +A R + T + + A+R + VTG Sbjct: 68 AAFDVVVKSPGISPYRPEALAAAARGTP---FIGGTALWFAEHAARDGVVPG--TVCVTG 122 Query: 123 TSGKSSVASFVQQICQRSGLSSFQIGPTSTISSFAQDNRLTTPSPIYLAKALSYLSSQGV 182 T GKS+ + + + + +G + +G I + P+P Y A Sbjct: 123 TKGKSTTTALLAHLLRAAGHRTALVG---NIGVPLLEVLAPQPAPEYWA----------- 168 Query: 183 THVSVEASSHGLDQHRLDGIKLIAGSFTNLGRDHIDYHQTQQAYFNAKMRLFEELLPKES 242 +E SS+ G + NL +H+D+H + Y+ K+ L E P+ Sbjct: 169 ----IELSSYQTGDVARSGARPELAVVLNLFPEHLDWHGGEARYYRDKLSLVTEGRPRI- 223 Query: 243 PAIIYADDAYSKEVMKRAHNAGCRVLSVGYQGKFIHLKKVCAIHNKQQVTISVEGKDFDF 302 A++ A D L + + + H + V E FD Sbjct: 224 -ALLNAADPRLAA------------LQLP-DSEVVWFNHPDGWHVRGDVVYRGEQALFDT 269 Query: 303 -LFPLPGEFQVYNALVAAGLCIAIGIDSALVLEHLEKLHVVPGRFEFVGTNSRGGRIYVD 361 L PLPG N A+G+D+ + +P R + +G+ R G YV+ Sbjct: 270 ALVPLPGRHNRGNLCAVLAALEALGLDAVALAPAAAGFRPLPNRLQELGS--RDGITYVN 327 Query: 362 YAHTSNSLEMILKNIRTITSGRIIVVFGCGGDRDQGKRPIMGKIALDLADIAIVT--DDN 419 + S + L + R+ ++ G G DR +A A + IVT + Sbjct: 328 DS-ISTTPHASLAALDCFAGRRVALLVG-GHDRGLDWTDFAAHMAQR-APLEIVTMGANG 384 Query: 420 PR 421 PR Sbjct: 385 PR 386 >gnl|CDD|179286 PRK01368, murD, UDP-N-acetylmuramoyl-L-alanyl-D-glutamate synthetase; Provisional. Length = 454 Score = 46.8 bits (111), Expect = 1e-05 Identities = 38/156 (24%), Positives = 64/156 (41%), Gaps = 39/156 (25%) Query: 109 LYGKHPE-NILAVTGTSGKSSVASFVQQICQRSGLSSFQIGPTSTISSFAQDNRLTTPSP 167 L+ K +A+TGT+GKS+ + + I +GL + + Sbjct: 97 LFEKSKNLKFIAITGTNGKSTTTALISHILNSNGLD-YPVA------------------- 136 Query: 168 IYLAKALSYLSSQGVTHVSVEASSHG----LDQHRLDGIKLIAGSFT---NLGRDHIDYH 220 + GV + +AS G L +LD +K N+ DH+D H Sbjct: 137 ----------GNIGVPALQAKASKDGYVLELSSFQLDLVKTFTAKIAVLLNITPDHLDRH 186 Query: 221 QTQQAYFNAKMRLFEELLPKESPAIIYADDAYSKEV 256 Q Y AK ++F + + K+S A+I D+ Y +E+ Sbjct: 187 QDMDGYIAAKSKIF-DRMDKDSYAVINIDNDYCREI 221 >gnl|CDD|179461 PRK02705, murD, UDP-N-acetylmuramoyl-L-alanyl-D-glutamate synthetase; Provisional. Length = 459 Score = 46.1 bits (110), Expect = 2e-05 Identities = 53/238 (22%), Positives = 88/238 (36%), Gaps = 27/238 (11%) Query: 118 LAVTGTSGKSSVASFVQQICQRSGLSSFQIGPTST-ISSFAQDNRLTTPSPIYLAKALSY 176 + +TGT+GK++V + + I Q +GL++ G A P ++ LS Sbjct: 112 VGITGTNGKTTVTALLAHILQAAGLNAPACGNIGYAACELALLRSGKAQKPDWIVAELS- 170 Query: 177 LSSQGVTHVSVEASSHGLDQHRLDGIKLIAGSFTNLGRDHIDYHQTQQAYFNAKMRLFEE 236 S Q +E+S + G +T DH++ H T + YF K Sbjct: 171 -SYQ------IESSPE---------LAPKIGIWTTFTPDHLERHGTLENYFAIKAS---- 210 Query: 237 LLPKESPAIIYADDAYSKEVMKRAHNAGCRVLSVGYQGKFIHLKKVCAIHNKQQVTISVE 296 LL + I+ DD Y ++ QGK L + ++ + Sbjct: 211 LLERSEIRILNGDDPYLRQHRSSWPKG----YWTSTQGKASLLGQADGWILEEGWVVERG 266 Query: 297 GKDFDF-LFPLPGEFQVYNALVAAGLCIAIGIDSALVLEHLEKLHVVPGRFEFVGTNS 353 F +PG + N L+A G+ + + E L VP R E +GT + Sbjct: 267 EPLFPLSALKMPGAHNLQNLLLAVAAARLAGLSAEAIAEALRSFPGVPHRLERIGTIN 324 >gnl|CDD|179871 PRK04663, murD, UDP-N-acetylmuramoyl-L-alanyl-D-glutamate synthetase; Provisional. Length = 438 Score = 45.5 bits (108), Expect = 3e-05 Identities = 61/240 (25%), Positives = 97/240 (40%), Gaps = 42/240 (17%) Query: 117 ILAVTGTSGKSSVASFVQQICQRSGLSSFQIGPTSTISSFAQDNRLTTPSPIYLAKALSY 176 ++A+TG++GKS+V + + +G+ ++ I A D Sbjct: 110 VIAITGSNGKSTVTDLTGVMAKAAGV---KVAVGGNIGVPALD----------------- 149 Query: 177 LSSQGVTHVSVEASSHGLDQHRLDGIKLIAGSFTNLGRDHIDYHQTQQAYFNAKMRLFEE 236 L Q +E SS L+ +KL A +F NL DH+D +Q + Y AK+R+F+ Sbjct: 150 LLEQDAELYVLELSSFQLET--TSSLKLKAAAFLNLSEDHMDRYQGMEDYRQAKLRIFDH 207 Query: 237 LLPKESPAIIYADDAYSKEVMKRAHNAGCRVLSVGYQ----GKFIHLKKVCAIHNKQQVT 292 A++ DD K+ A ++++ G+ G H + N Q V Sbjct: 208 ----AELAVVNRDD---KQTYPDH--AELQLVTFGFDQQDFGLAQHQGREWLADNGQPVL 258 Query: 293 ISVEGKDFDFLFPLPGEFQVYNALVAAGLCIAIGIDSALVLEHLEKLHVVPGRFEFVGTN 352 S E K L G V N LV L A G+D L+ L+ + R + V N Sbjct: 259 ASAELK-------LVGRHNVANVLVVLALLDAAGVDYRKALDALKSYTGLTHRCQVVADN 311 >gnl|CDD|179650 PRK03803, murD, UDP-N-acetylmuramoyl-L-alanyl-D-glutamate synthetase; Provisional. Length = 448 Score = 41.8 bits (99), Expect = 4e-04 Identities = 60/252 (23%), Positives = 98/252 (38%), Gaps = 42/252 (16%) Query: 104 LFASRLYGKHPENILAVTGTSGKSSVASFVQQICQRSGLSSFQIGPTSTISSFAQDNRLT 163 LFA K P ++A+TG++GKS+V + V ++ + +G A + Sbjct: 101 LFAR--EAKAP--VIAITGSNGKSTVTTLVGEMAKAAGKR------------VAVGGNIG 144 Query: 164 TPSPIYLAKALSYLSSQGVTHVSVEASSHGLDQ-HRLDGIKLIAGSFTNLGRDHIDYHQT 222 TP AL LS +V +E SS L+ H L+ + N+ DH+D + Sbjct: 145 TP-------ALDLLSDDPELYV-LELSSFQLETTHSLNAE---VATVLNISEDHMDRYSD 193 Query: 223 QQAYFNAKMRLFEELLPKESPAIIYADDAYSK--EVMKRAHNA-GCRVLSVGYQGKFIHL 279 +AY AK R++ + DDA ++ + + G G Sbjct: 194 LEAYHQAKHRIY----RGAKQVVFNRDDALTRPLVPDNQPCLSFGLNAPDFDEWGLREGD 249 Query: 280 KKVCAIHNKQQVTISVEGKDFDFLFPLPGEFQVYNALVAAGLCIAIGIDSALVLEHLEKL 339 + H +++ + V L G + NAL A L A G+ +LE L Sbjct: 250 GETYLAHGFERL-MPVRE------LKLRGSHNLANALAALALGEAAGLPKEAMLEVLRTF 302 Query: 340 HVVPGRFEFVGT 351 +P R E+V Sbjct: 303 TGLPHRCEWVRE 314 >gnl|CDD|184752 PRK14573, PRK14573, bifunctional D-alanyl-alanine synthetase A/UDP-N-acetylmuramate--L-alanine ligase; Provisional. Length = 809 Score = 41.7 bits (98), Expect = 4e-04 Identities = 34/138 (24%), Positives = 51/138 (36%), Gaps = 11/138 (7%) Query: 261 HNAGCRVLSVGYQGKFIHLKKVCAIH---NKQQ-----VTISVEGKDF-DFLFPLPGEFQ 311 +N C L QG C +H Q+ + G + D L G Sbjct: 213 YNGDCPRLKGCLQGHSYGFSSSCDLHILSYYQEGWRSYFSAKFLGVVYQDIELNLVGMHN 272 Query: 312 VYNALVAAGLCIAIGIDSALVLEHLEKLHVVPGRFEFVGTNSRGGRIYVDYAHTSNSLEM 371 V NA A G+ + +GID + L+ V R E + S DYAH + + Sbjct: 273 VANAAAAMGIALTLGIDEGAIRNALKGFSGVQRRLERKNS-SETFLFLEDYAHHPSEISC 331 Query: 372 ILKNIRT-ITSGRIIVVF 388 L+ +R + RII + Sbjct: 332 TLRAVRDAVGLRRIIAIC 349 >gnl|CDD|130153 TIGR01081, mpl, UDP-N-acetylmuramate:L-alanyl-gamma-D-glutamyl-meso- diaminopimelate ligase. Alternate name: murein tripeptide ligase. Length = 448 Score = 39.4 bits (92), Expect = 0.002 Identities = 70/288 (24%), Positives = 109/288 (37%), Gaps = 53/288 (18%) Query: 117 ILAVTGTSGKSSVASFVQQICQRSGLSS-FQIGPTSTISSFAQDNRLTTPSPIYLAKALS 175 +LAV GT GK++ AS + + ++ GL F IG +F RL SP ++ +A Sbjct: 104 VLAVAGTHGKTTTASMLAWVLEQCGLKPGFLIG--GVPGNFGVSARLGE-SPFFVIEADE 160 Query: 176 YLSSQGVTHVSVEASSHGLDQHRLDGIKLIAGSFTNLGRDHIDYHQTQQAYFNAKMRLFE 235 Y ++ + S + + NL DH D A R F Sbjct: 161 YDTA------FFDKRSKFVHYRPRTLV------LNNLEFDHADIF----DDLKAIQRQFH 204 Query: 236 ELL---PKESPAIIYADDAYSKEVMKRAHNAGC--RVLSVGYQGKFIHLKKVCAIHNKQQ 290 L+ P E + D K+ + + GC G QG++ Q Sbjct: 205 HLVRTVPGEGLILCPGRDQSLKDTLAK----GCWSEQEFFGEQGEW------------QA 248 Query: 291 VTISVEGKDFDFL----------FPLPGEFQVYNALVAAGLCIAIGIDSALVLEHLEKLH 340 I+ +G FD L + L G ++NAL+A +G+ E L Sbjct: 249 EKITADGSHFDVLLDGEKVGEVKWSLVGRHNMHNALMAIAAARHVGVAIEDACEALGSFV 308 Query: 341 VVPGRFEFVGTNSRGGRIYVDYAHTSNSLEMILKNIRTITSG-RIIVV 387 R E G + G +Y D+AH ++E L+ +R G RI+ V Sbjct: 309 NAKRRLELKGE-ANGITVYDDFAHHPTAIEATLQGLRQKVGGARILAV 355 >gnl|CDD|182774 PRK10846, PRK10846, bifunctional folylpolyglutamate synthase/ dihydrofolate synthase; Provisional. Length = 416 Score = 36.6 bits (85), Expect = 0.013 Identities = 43/184 (23%), Positives = 74/184 (40%), Gaps = 41/184 (22%) Query: 305 PLPGEFQVYNALVAAGL--CIAIGIDSALVLEHLEKLHVVPGRFEFVGTNSRGGRIYVDY 362 PLP NA A + + + + + ++PGRF+ V S R+ +D Sbjct: 254 PLP------NAATALAALRASGLEVSEQAIRDGIASA-ILPGRFQIV---SESPRVILDV 303 Query: 363 AHTSNSLEMILKNIRTI-TSGRIIVVFGCGGDRDQGKRPIMGKIALDLADIAIVTD---- 417 AH ++ E + ++ + +GR++ V G D+D IA LA + V D Sbjct: 304 AHNPHAAEYLTGRLKALPKNGRVLAVIGMLHDKD---------IAGTLACLKSVVDDWYC 354 Query: 418 ---DNPRSEDPEKIRAEIIHGIPGFIEKGNRIE----AIRTAIEMLNKQDVLVVAGKGHE 470 + PR E++ AE H + G + A A+ +D ++V G H Sbjct: 355 APLEGPRGATAEQL-AE--H-----LGNGKSFDSVAQAWDAAMADAKPEDTVLVCGSFHT 406 Query: 471 TVHI 474 H+ Sbjct: 407 VAHV 410 >gnl|CDD|184454 PRK14016, PRK14016, cyanophycin synthetase; Provisional. Length = 727 Score = 36.7 bits (86), Expect = 0.014 Identities = 61/276 (22%), Positives = 101/276 (36%), Gaps = 79/276 (28%) Query: 117 ILAVTGTSGKSSVASFVQQICQRSGLSSFQIGPTSTISSFAQDNRL----TTPSPIYLAK 172 I+AVTGT+GK++ + I + SG ++G T+T + + T Sbjct: 482 IVAVTGTNGKTTTTRLIAHILKLSGK---RVGMTTTDGVYIDGRLIDKGDCT-------- 530 Query: 173 ALSYLSSQGV-THVSVEAS----------SHGLDQHRLDGIKLIAGSFTNLGRDH--IDY 219 S++ V + VEA+ GL R D G TN+G DH + Sbjct: 531 --GPKSARRVLMNPDVEAAVLETARGGILREGLAYDRCD-----VGVVTNIGEDHLGLGG 583 Query: 220 HQTQQAYFNAKMRLFEELLPKESPAIIYADDAYSKEVMKR------------------AH 261 T + K R+ E + + A++ ADD + +R H Sbjct: 584 INTLEDLAKVK-RVVVEAVKPDGYAVLNADDPMVAAMAERCKGKVIFFSMDPDNPVIAEH 642 Query: 262 -NAGCRVLSVG------YQGKFIHLKKVCAIHNKQQVTISVEGKDFDFLFPLPGEFQVYN 314 G R + V +G + ++ ++ + + +++ GK F + N Sbjct: 643 RAQGGRAVYVEGDYIVLAEGGWEI--RIISLAD---IPLTLGGK---------AGFNIEN 688 Query: 315 ALVAAGLCIAIGIDSALVLEHLEKLHV----VPGRF 346 AL A A+GID L+ L PGRF Sbjct: 689 ALAAIAAAWALGIDIELIRAGLRTFVSDAAQAPGRF 724 >gnl|CDD|179223 PRK01109, PRK01109, ATP-dependent DNA ligase; Provisional. Length = 590 Score = 33.8 bits (78), Expect = 0.11 Identities = 20/76 (26%), Positives = 39/76 (51%), Gaps = 8/76 (10%) Query: 1 MKLQDLIYKDFPELINQLSIFPMQWRERKINEVSSDSRHIQ-AGWIFVAIVGNKEDGHLF 59 + L DL+Y D +L ++ P+ R +K+ E+ ++ ++ A I I + E+ F Sbjct: 342 VFLFDLLYVDGEDLTDK----PLPERRKKLEEIVKENDKVKLAERI---ITDDVEELEKF 394 Query: 60 IPQAIAQGAEAIVVSS 75 +AI +G E ++ S Sbjct: 395 FHRAIEEGCEGLMAKS 410 >gnl|CDD|178501 PLN02913, PLN02913, dihydrofolate synthetase. Length = 510 Score = 31.7 bits (72), Expect = 0.40 Identities = 32/125 (25%), Positives = 53/125 (42%), Gaps = 23/125 (18%) Query: 291 VTISVEGKDFDFLF------PLPGEFQVYNALVAAGLCIAIG-------IDSALVLEHLE 337 + I VE D F+ + G Q+ NA+ AA C A+ I A + LE Sbjct: 288 IVIRVEKDDPLFIELSDVNLRMLGSHQLQNAVTAA--CAALCLRDQGWRISDASIRAGLE 345 Query: 338 KLHVVPGRFEFVGTNS------RGGRIYVDYAHTSNSLEMILKNIRTI-TSGRIIVVFGC 390 ++ GR +F+ + G + +D AHT S + ++ I+T R+ +V Sbjct: 346 NTNL-LGRSQFLTSKEAEVLGLPGATVLLDGAHTKESAKALVDTIKTAFPEARLALVVAM 404 Query: 391 GGDRD 395 D+D Sbjct: 405 ASDKD 409 >gnl|CDD|162664 TIGR02023, BchP-ChlP, geranylgeranyl reductase. This model represents a group of geranylgeranyl reductases specific for the biosyntheses of bacteriochlorophyll and chlorophyll. It is unclear whether the processes of isoprenoid ligation to the chlorin ring and reduction of the geranylgeranyl chain to a phytyl chain are necessarily ordered the same way in all species (see introduction to ). Length = 388 Score = 30.5 bits (69), Expect = 1.1 Identities = 18/54 (33%), Positives = 21/54 (38%), Gaps = 3/54 (5%) Query: 201 GIKLIAGSFTNLGRDHIDYHQTQQAYFNAKMRLFEELLPKESPAIIYADDAYSK 254 G +LI G F L RD T Y K E E+ +I AD A S Sbjct: 106 GAELIHGLFLKLERDRDGVTLT---YRTPKKGAGGEKGSVEADVVIGADGANSP 156 >gnl|CDD|178517 PLN02929, PLN02929, NADH kinase. Length = 301 Score = 29.6 bits (67), Expect = 1.9 Identities = 9/20 (45%), Positives = 15/20 (75%) Query: 352 NSRGGRIYVDYAHTSNSLEM 371 NSR G IY+D +H +S+++ Sbjct: 259 NSRKGTIYIDGSHVMHSIKL 278 >gnl|CDD|180540 PRK06354, PRK06354, pyruvate kinase; Provisional. Length = 590 Score = 29.5 bits (67), Expect = 2.1 Identities = 21/57 (36%), Positives = 24/57 (42%), Gaps = 13/57 (22%) Query: 414 IVTDDNPRSEDPEKIRAEII-----------HGIPGFIEKGNRIEAIRTAIEMLNKQ 459 IV P SE PEK+R I HG E G RI+ IR A + L K Sbjct: 12 IVATIGPASESPEKLRQLIEAGATTARLNFSHG--DHEEHGARIKNIREASKKLGKT 66 >gnl|CDD|179323 PRK01710, murD, UDP-N-acetylmuramoyl-L-alanyl-D-glutamate synthetase; Provisional. Length = 458 Score = 29.3 bits (66), Expect = 2.3 Identities = 10/25 (40%), Positives = 16/25 (64%) Query: 210 TNLGRDHIDYHQTQQAYFNAKMRLF 234 TNL +H+D H+ + Y +AK +F Sbjct: 191 TNLSPNHLDVHKDMEEYIDAKKNIF 215 >gnl|CDD|180177 PRK05636, PRK05636, replicative DNA helicase; Provisional. Length = 505 Score = 28.7 bits (64), Expect = 3.3 Identities = 14/36 (38%), Positives = 22/36 (61%) Query: 239 PKESPAIIYADDAYSKEVMKRAHNAGCRVLSVGYQG 274 P + A YA+ K V++R +AG RV+ +GY+G Sbjct: 157 PTAANARYYAEIVSEKAVLRRLVDAGTRVVQLGYEG 192 >gnl|CDD|185350 PRK15453, PRK15453, phosphoribulokinase; Provisional. Length = 290 Score = 28.6 bits (65), Expect = 3.6 Identities = 13/38 (34%), Positives = 24/38 (63%), Gaps = 4/38 (10%) Query: 112 KHPENILAVTGTS--GKSSVASFVQQICQRSGLSSFQI 147 KHP I+AVTG+S G ++V ++I +R +++ + Sbjct: 4 KHP--IIAVTGSSGAGTTTVKRAFEKIFRRENINAAVV 39 >gnl|CDD|163480 TIGR03768, RPA4764, metallophosphoesterase, RPA4764 family. This model describes a small collection of probable metallophosphoresterases, related to pfam00149. Members of this protein family usually have a Sec-independent TAT (twin-arginine translocation) signal sequence, N-terminal to the region modeled by this alignment. This model and TIGR03767 divide a narrow clade of pfam00149-related enzymes. Length = 492 Score = 28.7 bits (64), Expect = 3.9 Identities = 11/27 (40%), Positives = 14/27 (51%) Query: 199 LDGIKLIAGSFTNLGRDHIDYHQTQQA 225 LDG + S + G D IDY + QA Sbjct: 125 LDGKPITPSSGAHAGADTIDYQKPFQA 151 >gnl|CDD|179400 PRK02261, PRK02261, methylaspartate mutase subunit S; Provisional. Length = 137 Score = 28.4 bits (64), Expect = 4.2 Identities = 11/19 (57%), Positives = 13/19 (68%) Query: 59 FIPQAIAQGAEAIVVSSAY 77 FI AI A+AI+VSS Y Sbjct: 46 FIDAAIETDADAILVSSLY 64 >gnl|CDD|132511 TIGR03471, HpnJ, hopanoid biosynthesis associated radical SAM protein HpnJ. One of the well-described hopanoid intermediates is bacteriohopanetetrol. In the conversion from hopene several reactions must occur in the side chain for which a radical mechanism might be reasonable. These include the four (presumably anaerobic) hydroxylations and a methyl shift. Length = 472 Score = 28.1 bits (63), Expect = 4.9 Identities = 20/68 (29%), Positives = 29/68 (42%), Gaps = 14/68 (20%) Query: 255 EVMKRAHNAGCRVLSVGY----QGKFIHLKKVCAIHNKQQVT-------ISVEGKDFDFL 303 E +K G R+L VGY Q ++KK + ++ T I V G F+ Sbjct: 288 ETLKVMKENGLRLLLVGYESGDQQILKNIKKGLTVEIARRFTRDCHKLGIKVHG---TFI 344 Query: 304 FPLPGEFQ 311 LPGE + Sbjct: 345 LGLPGETR 352 >gnl|CDD|163013 TIGR02776, NHEJ_ligase_prk, DNA ligase D. Members of this protein family are DNA ligases involved in the repair of DNA double-stranded breaks by non-homologous end joining (NHEJ). The system of the bacterial Ku protein (TIGR02772) plus this DNA ligase is seen in about 20 % of bacterial genomes to date and at least one archaeon (Archeoglobus fulgidus). This model describes a central and a C-terminal domain. These two domains may be permuted, as in genus Mycobacterium, or divided into tandem ORFs, and therefore not be identified by this model. An additional N-terminal 3'-phosphoesterase (PE) domain present in some but not all examples of this ligase is not included in the seed alignment for this model; This alignment models only the central ATP-dependent ligase domain and the C-terminal polymerase domain. Most examples of genes for this ligase are adjacent to the gene for Ku. Length = 552 Score = 28.4 bits (64), Expect = 4.9 Identities = 12/32 (37%), Positives = 18/32 (56%), Gaps = 3/32 (9%) Query: 332 VLEHLEKLHVVPGRFEFV-GTNSRGGRIYVDY 362 + E+L + P RF G +R GRI++DY Sbjct: 460 IAEYLARQ--FPERFTTEMGKKNRVGRIFIDY 489 >gnl|CDD|173541 PTZ00348, PTZ00348, tyrosyl-tRNA synthetase; Provisional. Length = 682 Score = 27.9 bits (62), Expect = 6.1 Identities = 16/54 (29%), Positives = 25/54 (46%), Gaps = 4/54 (7%) Query: 253 SKEVMKRAHNAGCRVLSVGYQGKFIHLKKVCAIHNKQQVTISVEGKDFDFLFPL 306 S+E+ A+ VL +G Q +KK C I K + T++ L+PL Sbjct: 116 SEEITNHANTYWRTVLDIGRQNTIARIKKCCTIMGKTEGTLTAA----QVLYPL 165 >gnl|CDD|117168 pfam08594, UPF0300, Uncharacterized protein family (UPF0300). This family of proteins appear to be specific to S. pombe. Length = 215 Score = 27.8 bits (62), Expect = 7.0 Identities = 13/18 (72%), Positives = 14/18 (77%) Query: 224 QAYFNAKMRLFEELLPKE 241 AY NAK RL+EE LPKE Sbjct: 159 HAYLNAKERLYEEFLPKE 176 >gnl|CDD|131383 TIGR02330, prpD, 2-methylcitrate dehydratase. Members of this family are bacterial proteins known or predicted to act as 2-methylcitrate dehydratase, an enzyme involved in the methylcitrate cycle of propionate catabolism. A related clade of archaeal proteins that may or may not be functionally equivalent is reserved for a future model and is excluded from this family. The PrpD enzyme of E. coli is responsible for the minor aconitase activity (AcnC) not accounted for by AcnA and AcnB. Length = 468 Score = 27.9 bits (62), Expect = 7.1 Identities = 21/72 (29%), Positives = 30/72 (41%), Gaps = 5/72 (6%) Query: 197 HRLDGIKLIAGSFTNLGRDHIDYHQTQQAYFNAKMR--LFEELLPKESPAIIYADDAYSK 254 H + G+ + SF +G DH+ + AKM EE+L S A + D S Sbjct: 140 HEIQGVIALENSFNRVGLDHVLLVKVASTAVVAKMLGGTREEILNALSHAWV---DGQSL 196 Query: 255 EVMKRAHNAGCR 266 + A N G R Sbjct: 197 RTYRHAPNTGSR 208 >gnl|CDD|182649 PRK10689, PRK10689, transcription-repair coupling factor; Provisional. Length = 1147 Score = 27.4 bits (61), Expect = 8.0 Identities = 11/31 (35%), Positives = 16/31 (51%), Gaps = 2/31 (6%) Query: 10 DFPELINQLSIFPMQWRERKINEVSSDSRHI 40 +FP + +F QWR+ EV D+ HI Sbjct: 216 EFPTDKAAIELFRSQWRDT--FEVKRDAEHI 244 >gnl|CDD|177786 PLN00192, PLN00192, aldehyde oxidase. Length = 1344 Score = 27.4 bits (61), Expect = 8.5 Identities = 26/83 (31%), Positives = 39/83 (46%), Gaps = 14/83 (16%) Query: 139 RSGLSSFQIGPTSTISSFAQDNRL-----TTPSPIYLAKALSYLSSQGVTHVSVEASSHG 193 +S L S +I P+ T SS + L P P L AL YL++ + VS +ASS G Sbjct: 397 KSLLLSVEI-PSWTSSSGSDTKLLFETYRAAPRP--LGNALPYLNAAFLAEVSQDASSGG 453 Query: 194 LDQHRLDGIKLIAGSFTNLGRDH 216 ++ +L G++ G H Sbjct: 454 ---IVVNDCRLAFGAY---GTKH 470 >gnl|CDD|184999 PRK15039, PRK15039, transcriptional repressor RcnR to maintain nickel and cobalt homeostasis; Provisional. Length = 90 Score = 27.3 bits (60), Expect = 9.2 Identities = 18/50 (36%), Positives = 29/50 (58%), Gaps = 6/50 (12%) Query: 445 RIEAIRTAIEMLNKQDVLVVAGKGHETVHIVTNGEK-KMSVDCDIIREIL 493 +I AIR A+ L ++ + KGH T HIV G++ K D D++ ++L Sbjct: 41 QIAAIRGAVNGLMREVI-----KGHLTEHIVHQGDELKREEDLDVVLKVL 85 >gnl|CDD|184314 PRK13767, PRK13767, ATP-dependent helicase; Provisional. Length = 876 Score = 27.2 bits (61), Expect = 9.5 Identities = 15/32 (46%), Positives = 21/32 (65%), Gaps = 5/32 (15%) Query: 333 LEHLEK--LHVVPGR-FEFVGTNSRGGRIYVD 361 LE LE + V+ GR +EF+ SRG ++YVD Sbjct: 539 LERLEPGDVFVLGGRTYEFLY--SRGSKVYVD 568 Database: CddB Posted date: Feb 4, 2011 9:54 PM Number of letters in database: 5,994,473 Number of sequences in database: 21,608 Lambda K H 0.321 0.137 0.394 Gapped Lambda K H 0.267 0.0603 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 21608 Number of Hits to DB: 8,105,370 Number of extensions: 536961 Number of successful extensions: 1364 Number of sequences better than 10.0: 1 Number of HSP's gapped: 1302 Number of HSP's successfully gapped: 91 Length of query: 497 Length of database: 5,994,473 Length adjustment: 97 Effective length of query: 400 Effective length of database: 3,898,497 Effective search space: 1559398800 Effective search space used: 1559398800 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 bits) S2: 59 (26.8 bits)