Alignments for a candidate for hom in Mycolicibacterium vanbaalenii PYR-1

GapMind for Amino acid biosynthesis

Alignments for a candidate for hom in Mycolicibacterium vanbaalenii PYR-1

Align homoserine dehydrogenase (EC 1.1.1.3) (characterized)
to candidate WP_011781503.1 MVAN_RS21825 homoserine dehydrogenase

Query= BRENDA::P46806
         (441 letters)



>NCBI__GCF_000015305.1:WP_011781503.1
          Length = 438

 Score =  689 bits (1778), Expect = 0.0
 Identities = 366/438 (83%), Positives = 396/438 (90%), Gaps = 2/438 (0%)

Query: 3   SDERTVGVAVLGLGNVGSEVVRIIEGSADDLAARIGAPLMLRGIGVRRVAVDRGVPVDLL 62
           SDE  +GVAVLGLGNVGSEVVRIIE SA DL ARIGAPL++RGIGVRRV  DRGVPV+LL
Sbjct: 2   SDE--IGVAVLGLGNVGSEVVRIIEESAADLTARIGAPLVIRGIGVRRVDADRGVPVELL 59

Query: 63  TDNIEELVSRADVDIVVEVMGPVELSRKAILSALEHGKSVVTANKALLAASTGELAQAAE 122
           TD+IE LVSR DVDIVVE+MGPVE +RKAIL+ALE GKSVVTANKAL+A S G+LA+AAE
Sbjct: 60  TDDIEALVSRDDVDIVVELMGPVEPARKAILAALEQGKSVVTANKALMAVSAGKLAEAAE 119

Query: 123 SAHVDLYFEAAVAGAIPVIRPLTQSLAGDTVLRVAGIVNGTTNYILSAMDSTGADYDSAL 182
            AHVDLYFEAAVAGAIPVIRPLTQSLAGDTVLRVAGIVNGTTNYILS MDSTGADY SAL
Sbjct: 120 KAHVDLYFEAAVAGAIPVIRPLTQSLAGDTVLRVAGIVNGTTNYILSEMDSTGADYASAL 179

Query: 183 AGARALGYAEADPTADVEGHDAAAKAAILASIAFHTRVTADDVYREGITKITPADFVSAR 242
           A A ALGYAEADPTADVEG DAAAKAAILASIAFHTRVTADDVYREGITK++ ADF SAR
Sbjct: 180 ADASALGYAEADPTADVEGWDAAAKAAILASIAFHTRVTADDVYREGITKVSAADFASAR 239

Query: 243 ALGCTIKLLFICERITAADGQQRVSARVYPALVPMSHPLATVSGAFNAVVVEAEAAGRLM 302
           ALGCTIKLL ICER+T   G+Q+VSARVYPALVP+ HPLA+V+GAFNAVVVEAEAAGRLM
Sbjct: 240 ALGCTIKLLAICERLTTGKGKQQVSARVYPALVPLEHPLASVNGAFNAVVVEAEAAGRLM 299

Query: 303 FYGQGAGGAPTASAVTGDLVMAARNRVLGSRGPKESKYAQLPMETIGFISTRYYVSMNVA 362
           FYGQGAGGAPTASAV GDLVMAARNRV G RGP+ESKYA+LP+  IG I TRYYV+MNVA
Sbjct: 300 FYGQGAGGAPTASAVLGDLVMAARNRVQGGRGPRESKYAKLPVAPIGVIPTRYYVNMNVA 359

Query: 363 DKPGVLSGVAAEFAKREVSIAEVRQEGVVDDGGRRVGARIVVVTHGATDAALSETVDALA 422
           D+PGVLS V+AEF+KREVSIAEVRQEG+VDD G+R GARIVVVTH A DAALSETV ALA
Sbjct: 360 DRPGVLSAVSAEFSKREVSIAEVRQEGMVDDEGQRCGARIVVVTHQAKDAALSETVAALA 419

Query: 423 DLDVVQGVTSVLRLEGIS 440
           DLDVVQ + SVLR+EG S
Sbjct: 420 DLDVVQSINSVLRMEGTS 437


Lambda     K      H
   0.317    0.133    0.362 

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: 589
Number of extensions: 12
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: 441
Length of database: 438
Length adjustment: 32
Effective length of query: 409
Effective length of database: 406
Effective search space:   166054
Effective search space used:   166054
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 51 (24.3 bits)

This GapMind analysis is from Apr 10 2024. The underlying query database was built on Apr 09 2024.

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Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
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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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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
the source code
instructions for running GapMind on your computer
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

GapMind for Amino acid biosynthesis