GapMind for Amino acid biosynthesis

 

Alignments for a candidate for leuB in Xenophilus azovorans DSM 13620

Align D-malate dehydrogenase (decarboxylating) (EC 1.1.1.83) (characterized)
to candidate WP_038209403.1 Q392_RS15265 tartrate dehydrogenase

Query= BRENDA::P76251
         (361 letters)



>NCBI__GCF_000745855.1:WP_038209403.1
          Length = 362

 Score =  489 bits (1258), Expect = e-143
 Identities = 236/367 (64%), Positives = 291/367 (79%), Gaps = 13/367 (3%)

Query: 1   MMKTMRIAAIPGDGIGKEVLPEGIRVLQAAAERWGFALSFEQMEWASCEYYSHHGKMMPD 60
           M    RIA I GDGIGKE +PEG+RV+ AAA ++G  L+F+  +++S +Y   HGKM+PD
Sbjct: 1   MSSKKRIAVIAGDGIGKETMPEGLRVVDAAARKFGVDLAFDHFDFSSWDYCEKHGKMLPD 60

Query: 61  DWHEQLSRFDAIYFGAVGWPDTVPDHISLWGSLLKFRREFDQYVNLRPVRLFPGVPCPL- 119
           DW  Q+   DAI+FGAVGWP+ +PDH+SLWGSLL FRREFDQY+NLRP RL PG+  P+ 
Sbjct: 61  DWKAQIGGHDAIFFGAVGWPEKIPDHVSLWGSLLLFRREFDQYINLRPARLMPGITAPVV 120

Query: 120 ----AGKQPGDIDFYVVRENTEGEYSSLGGRVNEGTEHEVVIQESVFTRRGVDRILRYAF 175
               + ++PG+ID Y+VRENTEGEYSS+GGR+ EGT  E+V+QE+V +R GVDR+L++AF
Sbjct: 121 RRDGSPREPGEIDMYIVRENTEGEYSSIGGRMYEGTPREIVVQETVMSRHGVDRVLKFAF 180

Query: 176 ELAQSRPRKTLTSATKSNGLAISMPYWDERVEAMAENYPEIRWDKQHIDILCARFVMQPE 235
           +LAQSRP+K LTSATKSNG++I+MPYWDERV  MA+ YP++R DK HIDIL A FV +P+
Sbjct: 181 DLAQSRPKKHLTSATKSNGISITMPYWDERVAQMAKTYPDVRLDKFHIDILTAHFVQRPD 240

Query: 236 RFDVVVASNLFGDILSDLGPACTGTIGIAPSANLNPERTFPSLFEPVHGSAPDIYGKNIA 295
            FDVVVASNLFGDILSDLGPACTGTIGIAPSANLNPERT PSLFEPVHGSAPDI GK IA
Sbjct: 241 FFDVVVASNLFGDILSDLGPACTGTIGIAPSANLNPERTTPSLFEPVHGSAPDIAGKGIA 300

Query: 296 NPIATIWAGAMMLDFLGNGDERFQQAHNGILAAIEEVIAHG---PKTPDMKGNATTPQVA 352
           NPI  IW GAMML+FLG+ D     AH+ ILAAIE+V+  G   P+TPD+ G+A T  + 
Sbjct: 301 NPIGQIWCGAMMLEFLGHKD-----AHDAILAAIEKVLTPGSGAPRTPDIGGSARTQDLG 355

Query: 353 DAICKII 359
            AI + +
Sbjct: 356 RAIAEAL 362


Lambda     K      H
   0.321    0.138    0.432 

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: 497
Number of extensions: 17
Number of successful extensions: 4
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: 361
Length of database: 362
Length adjustment: 29
Effective length of query: 332
Effective length of database: 333
Effective search space:   110556
Effective search space used:   110556
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: 49 (23.5 bits)

This GapMind analysis is from Jul 25 2024. The underlying query database was built on Jul 25 2024.

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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:

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