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)