Alignments for a candidate for gabD in Paraburkholderia bryophila 376MFSha3.1

GapMind for catabolism of small carbon sources

Alignments for a candidate for gabD in Paraburkholderia bryophila 376MFSha3.1

Align Alpha-ketoglutaric semialdehyde dehydrogenase 1; alphaKGSA dehydrogenase 1; 2,5-dioxovalerate dehydrogenase 1; 2-oxoglutarate semialdehyde dehydrogenase 1; KGSADH-I; Succinate-semialdehyde dehydrogenase [NAD(+)]; SSDH; EC 1.2.1.26; EC 1.2.1.24 (characterized)
to candidate H281DRAFT_01155 H281DRAFT_01155 2,5-dioxopentanoate dehydrogenase (NAD+)

Query= SwissProt::Q1JUP4
         (481 letters)



>FitnessBrowser__Burk376:H281DRAFT_01155
          Length = 481

 Score =  838 bits (2165), Expect = 0.0
 Identities = 415/480 (86%), Positives = 450/480 (93%)

Query: 1   MANVTYTDTQLLIDGEWVDAASGKTIDVVNPATGKPIGRVAHAGIADLDRALAAAQSGFE 60
           MA  +YTDT+LLI+GEW DAASGKTIDVVNPATG+ IG+VAHAGIADLDRAL AAQ GFE
Sbjct: 1   MAISSYTDTRLLINGEWCDAASGKTIDVVNPATGQVIGKVAHAGIADLDRALEAAQRGFE 60

Query: 61  AWRKVPAHERAATMRKAAALVRERADAIAQLMTQEQGKPLTEARVEVLSAADIIEWFADE 120
           AWRKVPAHERAA MRKAAALVRERA  I +LMTQEQGKP  EA++EVL+AADIIEWFADE
Sbjct: 61  AWRKVPAHERAAVMRKAAALVRERASDIGRLMTQEQGKPFAEAKIEVLAAADIIEWFADE 120

Query: 121 GRRVYGRIVPPRNLGAQQTVVKEPVGPVAAFTPWNFPVNQVVRKLSAALATGCSFLVKAP 180
           GRR+YGR+VP RNL AQQ V+KEP+GPVAAFTPWNFPVNQ+VRKLSAALA+GCSFLVKAP
Sbjct: 121 GRRLYGRVVPSRNLAAQQLVLKEPIGPVAAFTPWNFPVNQIVRKLSAALASGCSFLVKAP 180

Query: 181 EETPASPAALLRAFVDAGVPAGVIGLVYGDPAEISSYLIPHPVIRKVTFTGSTPVGKQLA 240
           EETPASPA LL+AFV+AGVPAG +GLV+GDPAEISSYLIPHPVIRKVTFTGSTPVGKQLA
Sbjct: 181 EETPASPAGLLQAFVEAGVPAGTVGLVFGDPAEISSYLIPHPVIRKVTFTGSTPVGKQLA 240

Query: 241 SLAGLHMKRATMELGGHAPVIVAEDADVALAVKAAGGAKFRNAGQVCISPTRFLVHNSIR 300
           SLAG HMKRATMELGGHAPVIVAEDADVALAVKAAGGAKFRNAGQVCISPTRFLVHNSIR
Sbjct: 241 SLAGAHMKRATMELGGHAPVIVAEDADVALAVKAAGGAKFRNAGQVCISPTRFLVHNSIR 300

Query: 301 DEFTRALVKHAEGLKVGNGLEEGTTLGALANPRRLTAMASVIDNARKVGASIETGGERIG 360
           +EF  ALVKHAEGLK+G+GL EGTTLG LAN RRLTAM+ V+D+ARK GA IETGGER+G
Sbjct: 301 EEFAAALVKHAEGLKLGDGLAEGTTLGPLANARRLTAMSKVLDDARKTGAKIETGGERVG 360

Query: 361 SEGNFFAPTVIANVPLDADVFNNEPFGPVAAIRGFDKLEEAIAEANRLPFGLAGYAFTRS 420
           SEGNFFAPTV+ NV L+ADVFNNEPFGP+AAIRGFDKLEEAIAEANRLPFGLAGYAFT+S
Sbjct: 361 SEGNFFAPTVLTNVSLEADVFNNEPFGPIAAIRGFDKLEEAIAEANRLPFGLAGYAFTKS 420

Query: 421 FANVHLLTQRLEVGMLWINQPATPWPEMPFGGVKDSGYGSEGGPEALEPYLVTKSVTVMA 480
           F+NVHLL+Q+LEVGMLWINQPATP PEMPFGGVKDSGYGSEGGPEA+E YLVTKSVTVM+
Sbjct: 421 FSNVHLLSQQLEVGMLWINQPATPTPEMPFGGVKDSGYGSEGGPEAMEAYLVTKSVTVMS 480


Lambda     K      H
   0.318    0.134    0.393 

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: 928
Number of extensions: 38
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: 481
Length of database: 481
Length adjustment: 34
Effective length of query: 447
Effective length of database: 447
Effective search space:   199809
Effective search space used:   199809
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 Sep 17 2021. The underlying query database was built on Sep 17 2021.

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Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

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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, or view the source code.

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 catabolism of small carbon sources