Alignments for a candidate for hom in Bacteroides thetaiotaomicron VPI-5482

GapMind for Amino acid biosynthesis

Alignments for a candidate for hom in Bacteroides thetaiotaomicron VPI-5482

Align aspartate kinase / homoserine dehydrogenase (EC 2.7.2.4; EC 1.1.1.3) (characterized)
to candidate 351931 BT2403 aspartokinase/homoserine dehydrogenase (NCBI ptt file)

Query= reanno::Btheta:351931
         (811 letters)



>FitnessBrowser__Btheta:351931
          Length = 811

 Score = 1577 bits (4083), Expect = 0.0
 Identities = 811/811 (100%), Positives = 811/811 (100%)

Query: 1   MKVMKFGGTSVGSVNSILSVKRIVESAGEPVIVVVSALGGITDKLINTSKMAAAGDSAYE 60
           MKVMKFGGTSVGSVNSILSVKRIVESAGEPVIVVVSALGGITDKLINTSKMAAAGDSAYE
Sbjct: 1   MKVMKFGGTSVGSVNSILSVKRIVESAGEPVIVVVSALGGITDKLINTSKMAAAGDSAYE 60

Query: 61  GEFREIVYRHVEMIKEVIPAGAGQVALQRQIGELLNELKDIFQGIYLIRDLSPKTSDTIV 120
           GEFREIVYRHVEMIKEVIPAGAGQVALQRQIGELLNELKDIFQGIYLIRDLSPKTSDTIV
Sbjct: 61  GEFREIVYRHVEMIKEVIPAGAGQVALQRQIGELLNELKDIFQGIYLIRDLSPKTSDTIV 120

Query: 121 SYGERLSSIIVAELIDEAKWFDSRTFIKTEKKHNKHTIDADLTNQLVKEAFHSIPKVSLV 180
           SYGERLSSIIVAELIDEAKWFDSRTFIKTEKKHNKHTIDADLTNQLVKEAFHSIPKVSLV
Sbjct: 121 SYGERLSSIIVAELIDEAKWFDSRTFIKTEKKHNKHTIDADLTNQLVKEAFHSIPKVSLV 180

Query: 181 PGFISSDKVSGDVTNLGRGGSDYTAAIIAAALDASSLEIWTDVDGFMTADPRVISTAYTI 240
           PGFISSDKVSGDVTNLGRGGSDYTAAIIAAALDASSLEIWTDVDGFMTADPRVISTAYTI
Sbjct: 181 PGFISSDKVSGDVTNLGRGGSDYTAAIIAAALDASSLEIWTDVDGFMTADPRVISTAYTI 240

Query: 241 SELSYVEATELCNFGAKVVYPPTIYPVCHKNIPIIIKNTFNPDGVGTVIKQETSNPQSKA 300
           SELSYVEATELCNFGAKVVYPPTIYPVCHKNIPIIIKNTFNPDGVGTVIKQETSNPQSKA
Sbjct: 241 SELSYVEATELCNFGAKVVYPPTIYPVCHKNIPIIIKNTFNPDGVGTVIKQETSNPQSKA 300

Query: 301 IKGISSINDTSLITVQGLGMVGVIGVNYRIFKALAKNGISVFLVSQASSENSTSIGVRNA 360
           IKGISSINDTSLITVQGLGMVGVIGVNYRIFKALAKNGISVFLVSQASSENSTSIGVRNA
Sbjct: 301 IKGISSINDTSLITVQGLGMVGVIGVNYRIFKALAKNGISVFLVSQASSENSTSIGVRNA 360

Query: 361 DADLACEVLNEEFAKEIEMGEISPILAERNLATVAIVGENMKHTPGIAGKLFGTLGRNGI 420
           DADLACEVLNEEFAKEIEMGEISPILAERNLATVAIVGENMKHTPGIAGKLFGTLGRNGI
Sbjct: 361 DADLACEVLNEEFAKEIEMGEISPILAERNLATVAIVGENMKHTPGIAGKLFGTLGRNGI 420

Query: 421 NVIACAQGASETNISFVVDSKSLRKSLNVIHDSFFLSEYQVLNLFICGIGTVGGSLVEQI 480
           NVIACAQGASETNISFVVDSKSLRKSLNVIHDSFFLSEYQVLNLFICGIGTVGGSLVEQI
Sbjct: 421 NVIACAQGASETNISFVVDSKSLRKSLNVIHDSFFLSEYQVLNLFICGIGTVGGSLVEQI 480

Query: 481 RCQQQKLMMENGLKLHVVGIIDAAKAMFSREGFDLANFREELQKKGKDSNLQTIRDEIVG 540
           RCQQQKLMMENGLKLHVVGIIDAAKAMFSREGFDLANFREELQKKGKDSNLQTIRDEIVG
Sbjct: 481 RCQQQKLMMENGLKLHVVGIIDAAKAMFSREGFDLANFREELQKKGKDSNLQTIRDEIVG 540

Query: 541 MNIFNSVFVDCTASPDIASLYKDLLQHNVSVVAANKIAASSAYENYRELKTIARQRGVKY 600
           MNIFNSVFVDCTASPDIASLYKDLLQHNVSVVAANKIAASSAYENYRELKTIARQRGVKY
Sbjct: 541 MNIFNSVFVDCTASPDIASLYKDLLQHNVSVVAANKIAASSAYENYRELKTIARQRGVKY 600

Query: 601 LFETNVGAGLPIINTINDLIHSGDKILKIEAVLSGTLNYIFNKISADIPFSRTIKMAQEE 660
           LFETNVGAGLPIINTINDLIHSGDKILKIEAVLSGTLNYIFNKISADIPFSRTIKMAQEE
Sbjct: 601 LFETNVGAGLPIINTINDLIHSGDKILKIEAVLSGTLNYIFNKISADIPFSRTIKMAQEE 660

Query: 661 RYSEPDPRIDLSGKDVIRKLVILAREAGYHIEQEDVEKNLFVPNDFFEGSLDDFWKRVPS 720
           RYSEPDPRIDLSGKDVIRKLVILAREAGYHIEQEDVEKNLFVPNDFFEGSLDDFWKRVPS
Sbjct: 661 RYSEPDPRIDLSGKDVIRKLVILAREAGYHIEQEDVEKNLFVPNDFFEGSLDDFWKRVPS 720

Query: 721 LDADFEARRQVLEKEHKHWRFVAKLEDGKASVGLQEVGANHPFYGLEGSNNIILLTTERY 780
           LDADFEARRQVLEKEHKHWRFVAKLEDGKASVGLQEVGANHPFYGLEGSNNIILLTTERY
Sbjct: 721 LDADFEARRQVLEKEHKHWRFVAKLEDGKASVGLQEVGANHPFYGLEGSNNIILLTTERY 780

Query: 781 KEYPMMIQGYGAGAGVTAAGVFADIMSIANV 811
           KEYPMMIQGYGAGAGVTAAGVFADIMSIANV
Sbjct: 781 KEYPMMIQGYGAGAGVTAAGVFADIMSIANV 811


Lambda     K      H
   0.317    0.135    0.377 

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: 1908
Number of extensions: 45
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: 811
Length of database: 811
Length adjustment: 41
Effective length of query: 770
Effective length of database: 770
Effective search space:   592900
Effective search space used:   592900
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: 56 (26.2 bits)

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

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Candidates (tab-delimited)
Steps (tab-delimited)
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