GapMind for Amino acid biosynthesis

 

Alignments for a candidate for leuB in Azoarcus olearius BH72

Align D-malate dehydrogenase (decarboxylating) (EC 1.1.1.83) (characterized)
to candidate WP_011767582.1 AZO_RS19370 tartrate dehydrogenase

Query= BRENDA::P76251
         (361 letters)



>NCBI__GCF_000061505.1:WP_011767582.1
          Length = 359

 Score =  569 bits (1466), Expect = e-167
 Identities = 266/354 (75%), Positives = 303/354 (85%)

Query: 6   RIAAIPGDGIGKEVLPEGIRVLQAAAERWGFALSFEQMEWASCEYYSHHGKMMPDDWHEQ 65
           RIA I GDGIG+EV+PEG+R +QAAA ++  AL F   +WA C+YY  HGKMMPDDW EQ
Sbjct: 6   RIAVIAGDGIGQEVMPEGLRAVQAAAAKFDIALEFTHFDWAHCDYYLQHGKMMPDDWFEQ 65

Query: 66  LSRFDAIYFGAVGWPDTVPDHISLWGSLLKFRREFDQYVNLRPVRLFPGVPCPLAGKQPG 125
           L  FDAI+FGAVGWPD VPDHISLWGSLLKFRR+FDQYVNLRPVRL PGVPCPLA K+ G
Sbjct: 66  LKGFDAIFFGAVGWPDKVPDHISLWGSLLKFRRDFDQYVNLRPVRLMPGVPCPLANKKVG 125

Query: 126 DIDFYVVRENTEGEYSSLGGRVNEGTEHEVVIQESVFTRRGVDRILRYAFELAQSRPRKT 185
           DIDFYVVRENTEGEYSS+GG++ EGTE E V+QES+FTR+GVDRIL+YAFELAQ RP+K 
Sbjct: 126 DIDFYVVRENTEGEYSSVGGKMYEGTERETVLQESIFTRKGVDRILKYAFELAQKRPKKH 185

Query: 186 LTSATKSNGLAISMPYWDERVEAMAENYPEIRWDKQHIDILCARFVMQPERFDVVVASNL 245
           LTSATKSNG+AISMPYWD RV+ M + YPE++WD+ HIDIL ARFV+ PERFDVVVASNL
Sbjct: 186 LTSATKSNGIAISMPYWDGRVKEMGKAYPEVKWDQYHIDILTARFVLSPERFDVVVASNL 245

Query: 246 FGDILSDLGPACTGTIGIAPSANLNPERTFPSLFEPVHGSAPDIYGKNIANPIATIWAGA 305
           FGDILSDLGPAC GTIGIAPSANLNP+RTFPSLFEPVHGSAPDIYG+NIANP+A IW+GA
Sbjct: 246 FGDILSDLGPACAGTIGIAPSANLNPDRTFPSLFEPVHGSAPDIYGRNIANPVAMIWSGA 305

Query: 306 MMLDFLGNGDERFQQAHNGILAAIEEVIAHGPKTPDMKGNATTPQVADAICKII 359
           MMLDFLGNGD R+  AH+ I+ AIE V+  GP+TPDM G A T +V  A+   I
Sbjct: 306 MMLDFLGNGDARYTAAHDAIVKAIETVLVEGPRTPDMGGTANTTEVGKAVAAAI 359


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: 541
Number of extensions: 18
Number of successful extensions: 2
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: 359
Length adjustment: 29
Effective length of query: 332
Effective length of database: 330
Effective search space:   109560
Effective search space used:   109560
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