GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__acidovorax_3H11:Ac3H11_255
          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:

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