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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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