GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__acidovorax_3H11:Ac3H11_3991
          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:

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