GapMind for Amino acid biosynthesis

 

Aligments for a candidate for hom in Shewanella loihica PV-4

Align fused aspartate kinase/homoserine dehydrogenase 2 (EC 2.7.2.4; EC 1.1.1.3) (characterized)
to candidate 5208005 Shew_0521 bifunctional aspartate kinase II/homoserine dehydrogenase II (RefSeq)

Query= ecocyc::ASPKINIIHOMOSERDEHYDROGII-MONOMER
         (810 letters)



>lcl|FitnessBrowser__PV4:5208005 Shew_0521 bifunctional aspartate
           kinase II/homoserine dehydrogenase II (RefSeq)
          Length = 797

 Score =  572 bits (1473), Expect = e-167
 Identities = 342/804 (42%), Positives = 479/804 (59%), Gaps = 26/804 (3%)

Query: 14  LHKFGGSSLADVKCYLRVAGIMAEYSQPDDMMVVSAAGSTTNQLINWLKLSQTDRLSAHQ 73
           LHKFGGSSLAD  CY RVA I+  +   DD++VVSAAG +TN L   L+L  TD+L   +
Sbjct: 6   LHKFGGSSLADADCYRRVAHILLTHGHSDDLIVVSAAGKSTNFLYRLLELCDTDQLWQEE 65

Query: 74  VQQTLRRYQCDLISGLLPAEEADSLISAFVSDLERLAALLD-SGINDAVYAEVVGHGEVW 132
           +Q  L  YQ +LI  LL  E+A SL     +D  +L +LL    +ND    +VV  GE W
Sbjct: 66  LQ-VLVSYQQNLIEQLLSNEQARSLRERLATDKSQLTSLLSLDELNDYQRNQVVSFGERW 124

Query: 133 SARLMSAVLNQQGLPAAWLDAREFLRAERAAQPQVDEGLSYPLLQQLLVQHPGKRLVVTG 192
           S+ L++A+L + G+ A  +DAR  L A+  A PQ+  G S   +Q LL  HP +RLV+TG
Sbjct: 125 SSCLLAALLRESGVAATDVDARTLLVADEGAVPQIRLGESRQKVQALLEAHPQERLVITG 184

Query: 193 FISRNNAGETVLLGRNGSDYSATQIGALAGVSRVTIWSDVAGVYSADPRKVKDACLLPLL 252
           FI  N  G+T+LLGRNGSD+SAT + +LA + RVTIW+DV GV++ADP ++ DA LL  +
Sbjct: 185 FICANEQGDTLLLGRNGSDFSATLLASLADIERVTIWTDVEGVFNADPNRINDAKLLKSM 244

Query: 253 RLDEASELARLAAPVLHARTLQPVSGSEIDLQLRCSYTPDQGSTRIERVLASGTGARIVT 312
            L EA+ LA L +PVLH RTLQP+  +E+ L +R SY P    T I    +S   A +VT
Sbjct: 245 SLTEANRLAHLGSPVLHNRTLQPLFDTEVSLAVRSSYAPHTDFTLIAPK-SSSASAPVVT 303

Query: 313 SHDDVCLIEFQVPASQDFKLAHKEIDQILK---RAQVRPLAV-GVHNDRQLLQFCYTSEV 368
           S   V L    +           E+ Q+L    +A + PLA   + + R  L F + ++ 
Sbjct: 304 SLSSVSLFSLTISV---------ELPQLLACFAQAGLTPLAYWSLAHGRAELAFTHENQK 354

Query: 369 ADSALKILDEAGLP-GELRLRQGLALVAMVGAGVTRNPLHCHRFWQQLKGQPVEFTWQSD 427
              A+     + L   EL+LR  L LVA+V A  +   L+   F + L  +        +
Sbjct: 355 QAQAIFEAKRSELGIDELQLRDDLGLVALVSADAS---LYRRGFSRLLSREAHPLC---N 408

Query: 428 DGISLVAVLRTGPTESLIQGLHQSVFRAEKRIGLVLFGKGNIGSRWLELFAREQSTLSAR 487
           DG+SLV ++       L Q +H+      KRIG++L G GNIG  W++LF R +  L+  
Sbjct: 409 DGLSLVTLVPKAQVNLLTQKVHRRCAGPRKRIGVLLLGIGNIGEAWIDLFKRARPVLNKE 468

Query: 488 TGFEFVLAGVVDSRRSLLSYDGLDASRALAFFNDEAVEQDEESLFLWMRAHPYDDLVVLD 547
                 L G++ S+++LLS   +D S     F +         LF  ++A   D+L+ LD
Sbjct: 469 LEVSVELVGLLSSKKALLSETDIDLSSWQQAFEERGTGWQYTHLFEQLQALNCDELIALD 528

Query: 548 VTASQQLADQYLDFASHGFHVISANKLAGASDSNKYRQIHDAFEKTGRHWLYNATVGAGL 607
           ++AS  L  QY +F + G H++SANKLAG+     Y+++          W YNA+ GAGL
Sbjct: 529 ISASADLTLQYPEFFARGIHIVSANKLAGSGPLAFYQELKQQLGNRRLFWRYNASCGAGL 588

Query: 608 PINHTVRDLIDSGDTILSISGIFSGTLSWLFLQFDGSVPFTELVDQAWQQGLTEPDPRDD 667
           P+ H + DL +SGD+I ++ GIFSGTL WLF  +D   PF+ELV +A   G+TEPDPRDD
Sbjct: 589 PVQHALNDLHNSGDSIEAVGGIFSGTLCWLFEHYDAKKPFSELVLEAKGLGITEPDPRDD 648

Query: 668 LSGKDVMRKLVILAREAGYNIEPDQVRVESLVPAHCEGGSIDHFFENGDELNEQMVQRLE 727
           LSG+D+ RKL+ILARE GY+IE D + +ESLVP       +D F +   EL+ +M+Q+ +
Sbjct: 649 LSGRDMQRKLLILAREIGYDIELDDIELESLVPTKLAEIPLDDFIKRMAELDGEMLQQYQ 708

Query: 728 AAREMGLVLRYVARFDANG---KARVGVEAVREDHPLASLLPCDNVFAIESRWYRDNPLV 784
           AA E   VLRYVA  D+     KA+VG++ V   HP A+L P DNVF I S +Y+DNPL+
Sbjct: 709 AAAEQNKVLRYVASLDSEQGQLKAKVGIQWVDRSHPYANLTPGDNVFVIRSDFYQDNPLI 768

Query: 785 IRGPGAGRDVTAGAIQSDINRLAQ 808
           IRGPGAGR+VTA A+QSD+ ++ +
Sbjct: 769 IRGPGAGREVTAAAVQSDLAQICR 792


Lambda     K      H
   0.320    0.135    0.397 

Gapped
Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 1
Number of Hits to DB: 1467
Number of extensions: 76
Number of successful extensions: 5
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 1
Number of HSP's successfully gapped: 1
Length of query: 810
Length of database: 797
Length adjustment: 41
Effective length of query: 769
Effective length of database: 756
Effective search space:   581364
Effective search space used:   581364
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: 55 (25.8 bits)

This GapMind analysis is from Aug 03 2021. The underlying query database was built on Aug 03 2021.

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About GapMind

Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.

A candidate for a step is "high confidence" if either:

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

Otherwise, a candidate is "medium confidence" if either:

Other blast hits with at least 50% coverage are "low confidence."

Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:

GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).

For more information, see the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code, or see changes to Amino acid biosynthesis since the publication.

If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know

by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory