GapMind for Amino acid biosynthesis

 

Alignments for a candidate for ilvE in Azospirillum brasilense Sp245

Align Probable branched-chain-amino-acid aminotransferase; BCAT; EC 2.6.1.42 (uncharacterized)
to candidate AZOBR_RS14455 AZOBR_RS14455 D-amino acid aminotransferase

Query= curated2:P74921
         (273 letters)



>FitnessBrowser__azobra:AZOBR_RS14455
          Length = 287

 Score = 77.0 bits (188), Expect = 4e-19
 Identities = 56/159 (35%), Positives = 86/159 (54%), Gaps = 9/159 (5%)

Query: 109 LETGVEVKISNVRRIPDLSTPPA-LKITGRTDIVLARREIVD--CYDVILLGLNGQVCEG 165
           LE GV V       +PD+      +K  G    VLA+++  +   Y+  L+  +G V EG
Sbjct: 128 LEKGVAVVT-----VPDIRWGRCDIKTVGLLAPVLAKQQAAESGAYEAWLIDPDGTVTEG 182

Query: 166 SFSNVFLV-KEGKLITPSLDSGILDGITRENVIKLAKSLEIPVEERVVWVWELFEADEMF 224
           S SN ++V ++G L+T +    IL+GITR ++++LA    IPVEER   V E   A E F
Sbjct: 183 SSSNAWIVTQDGVLVTRAPSQKILNGITRLSLLRLAGERGIPVEERSFTVEEALAAREAF 242

Query: 225 LTHTSAGVVPVRRLNEHSFFEEEPGPVTATLMENFEPFV 263
           ++      +PV R++     E +PGPVT TL + +  +V
Sbjct: 243 VSSAGTFALPVTRIDGKPVGEGKPGPVTRTLRQAYLDYV 281


Lambda     K      H
   0.322    0.140    0.415 

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: 155
Number of extensions: 10
Number of successful extensions: 1
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: 273
Length of database: 287
Length adjustment: 26
Effective length of query: 247
Effective length of database: 261
Effective search space:    64467
Effective search space used:    64467
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 (21.9 bits)
S2: 47 (22.7 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:

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