GapMind for catabolism of small carbon sources

 

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

Align 5-aminovalerate transaminase (EC 2.6.1.48) (characterized)
to candidate Ac3H11_3991 Glutamate-1-semialdehyde aminotransferase (EC 5.4.3.8)

Query= BRENDA::Q9I6M4
         (426 letters)



>lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_3991
           Glutamate-1-semialdehyde aminotransferase (EC 5.4.3.8)
          Length = 434

 Score =  156 bits (395), Expect = 1e-42
 Identities = 122/361 (33%), Positives = 171/361 (47%), Gaps = 35/361 (9%)

Query: 5   NESLLKRRQAAVPRGVGQI---------HPVVAERAENSTVWDVEGREYIDFAGGIAVLN 55
           N  L +R +A +P GV             P   +RA+ +  WD   + +ID+ G    + 
Sbjct: 8   NIPLFERAKALIPGGVNSPVRAFKAVGGTPRFVKRAQGAYFWDANDQRFIDYIGSWGPMI 67

Query: 56  TGHLHPKVIAAVQEQLGKLSHTCFQVLAYEPYIELAEEIAKRVPGDFPKKTLLVTSGSEA 115
            GH HP V+ AVQ     L    F     E  +ELAEEI   VP    +   LV+SG+EA
Sbjct: 68  LGHGHPAVLEAVQS--AALEGFSFGAPT-EREVELAEEILGLVPS--MEMIRLVSSGTEA 122

Query: 116 VENAVKIARAATGRAGVIAFTGAYHGRTMMTLGLTGKVVPYSAGMGLMP-GGIFRALAPC 174
             +A+++AR ATGR+  I F G YHG     L          AG GL   G    A  P 
Sbjct: 123 GMSAIRLARGATGRSKFIKFEGCYHGHADSLL--------VKAGSGLATFGNATSAGVPP 174

Query: 175 ELHG---VSEDDSIASIERIFKNDAQPQDIAAIIIEPVQGEGGFYVNSKSFMQRLRALCD 231
           E+     V E +++A +E  F      +++A ++IEP+ G       S  FM+R R LC 
Sbjct: 175 EVVQHTIVLEYNNVAQLEEAFA--LHGKELACVMIEPIAGNMNLVRASVPFMKRCRELCT 232

Query: 232 QHGILLIADEVQTG----AGRTGTFFATEQLGIVPDLTTFAKSVGGGFPISGVAGKAEIM 287
           +HG LL+ DEV TG     G   + +A    G  PDLT   K +GGG P++   G   IM
Sbjct: 233 EHGALLVLDEVMTGFRVALGSAQSVYAKSIPGFKPDLTVLGKVIGGGMPLAAFGGPRAIM 292

Query: 288 DAIAP-GGL--GGTYAGSPIACAAALAVLKVFEEEKLLERSQAVGERLKAGLREIQAKHK 344
           + +AP GG+   GT +G+P+A A  LA L+  ++    +   A    L  GL    A   
Sbjct: 293 EHLAPLGGVYQAGTLSGNPVATACGLATLREIKKPGFFDALSARTRSLVDGLAAAAAAEG 352

Query: 345 V 345
           V
Sbjct: 353 V 353


Lambda     K      H
   0.319    0.137    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: 472
Number of extensions: 32
Number of successful extensions: 5
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: 426
Length of database: 434
Length adjustment: 32
Effective length of query: 394
Effective length of database: 402
Effective search space:   158388
Effective search space used:   158388
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 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