GapMind for catabolism of small carbon sources

 

Aligments for a candidate for gabD in Acidovorax sp. GW101-3H11

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 Ac3H11_255 2-ketoglutaric semialdehyde dehydrogenase (EC 1.2.1.26)

Query= SwissProt::Q1JUP4
         (481 letters)



>lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_255 2-ketoglutaric
           semialdehyde dehydrogenase (EC 1.2.1.26)
          Length = 478

 Score =  718 bits (1854), Expect = 0.0
 Identities = 353/478 (73%), Positives = 404/478 (84%)

Query: 4   VTYTDTQLLIDGEWVDAASGKTIDVVNPATGKPIGRVAHAGIADLDRALAAAQSGFEAWR 63
           +TY +TQL I G+W DA  GKT+ V NPATGK IGRVAHA   DLDRAL AAQ GFEAWR
Sbjct: 1   MTYPNTQLFIAGQWQDAVEGKTLAVFNPATGKEIGRVAHATKVDLDRALDAAQKGFEAWR 60

Query: 64  KVPAHERAATMRKAAALVRERADAIAQLMTQEQGKPLTEARVEVLSAADIIEWFADEGRR 123
            +PA ERA TMR+AAAL+RERA+AIA +M QEQGKPL EA+VE +++ADIIEWFADE  R
Sbjct: 61  DIPAAERAKTMRRAAALMRERAEAIAAIMVQEQGKPLAEAKVETMASADIIEWFADESLR 120

Query: 124 VYGRIVPPRNLGAQQTVVKEPVGPVAAFTPWNFPVNQVVRKLSAALATGCSFLVKAPEET 183
           VYGRIVP RNL AQQ V+K+PVGPVAAFTPWNFP+NQVVRKL+AALA GCS LVKAPEET
Sbjct: 121 VYGRIVPSRNLKAQQMVLKDPVGPVAAFTPWNFPINQVVRKLAAALAAGCSILVKAPEET 180

Query: 184 PASPAALLRAFVDAGVPAGVIGLVYGDPAEISSYLIPHPVIRKVTFTGSTPVGKQLASLA 243
           PASPA L+RAF DAGVP G +GLVYGDPAEISSYLIPHP+IRKVTFTGSTPVGKQLA+LA
Sbjct: 181 PASPAELIRAFADAGVPVGTVGLVYGDPAEISSYLIPHPIIRKVTFTGSTPVGKQLAALA 240

Query: 244 GLHMKRATMELGGHAPVIVAEDADVALAVKAAGGAKFRNAGQVCISPTRFLVHNSIRDEF 303
           G HMKR TMELGGHAPVIVAEDAD+ LA+K + GAKFRNAGQVCISPTR+LVH +IR +F
Sbjct: 241 GKHMKRVTMELGGHAPVIVAEDADLELAIKISSGAKFRNAGQVCISPTRYLVHENIRADF 300

Query: 304 TRALVKHAEGLKVGNGLEEGTTLGALANPRRLTAMASVIDNARKVGASIETGGERIGSEG 363
                K+A+GLKVG+GL  GT +G LANPRR+TAMA ++ +A + GA +  GGERIGSEG
Sbjct: 301 VAGFAKYAQGLKVGDGLTAGTQMGPLANPRRITAMADLLADAVQQGAKVLAGGERIGSEG 360

Query: 364 NFFAPTVIANVPLDADVFNNEPFGPVAAIRGFDKLEEAIAEANRLPFGLAGYAFTRSFAN 423
           NFFAPTV+ +VPL A + N EPFGPVAA+RGF K+E+AIAEANRLPFGLAGYAFT S  N
Sbjct: 361 NFFAPTVLNDVPLSARIVNEEPFGPVAAVRGFTKIEDAIAEANRLPFGLAGYAFTTSLKN 420

Query: 424 VHLLTQRLEVGMLWINQPATPWPEMPFGGVKDSGYGSEGGPEALEPYLVTKSVTVMAV 481
            HLL QRLEVGMLWINQ A P  E+PFGG+KDSGYGSEGGPEA+E ++ T+ V++M V
Sbjct: 421 AHLLAQRLEVGMLWINQAAAPAAELPFGGLKDSGYGSEGGPEAIEAHMNTRLVSIMNV 478


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: 830
Number of extensions: 31
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: 478
Length adjustment: 34
Effective length of query: 447
Effective length of database: 444
Effective search space:   198468
Effective search space used:   198468
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 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