GapMind for catabolism of small carbon sources

 

Aligments for a candidate for puuC in Pedobacter sp. GW460-11-11-14-LB5

Align gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase (EC 1.2.1.54) (characterized)
to candidate CA265_RS21385 CA265_RS21385 aldehyde dehydrogenase family protein

Query= reanno::WCS417:GFF5420
         (497 letters)



>lcl|FitnessBrowser__Pedo557:CA265_RS21385 CA265_RS21385 aldehyde
           dehydrogenase family protein
          Length = 465

 Score =  139 bits (349), Expect = 3e-37
 Identities = 105/339 (30%), Positives = 155/339 (45%), Gaps = 10/339 (2%)

Query: 156 EPVGVVGAIVPWNFPLMMACWKLGPALSTGNSVILKPSEKSPLTAIRIAALAVEAGIPKG 215
           EP GV   I PWN+PL +    L  A++ GN VILKPSE S  TA  I+ L       + 
Sbjct: 104 EPKGVCLIIAPWNYPLQLIMSPLVSAIAAGNCVILKPSELSAATADVISKLISNTFEAE- 162

Query: 216 VFNVLPGYGHTVGNALALHMDVDTLVFTGSTKIAKQLLIRSGESNMKRVWLEAGGKSPNI 275
              +    G    +   L +  D + FTGST I K +++ +   N+  V LE GGKSP I
Sbjct: 163 --EIACFEGDAEVSTALLKLPFDHIFFTGSTAIGK-VVMEAAAKNLTSVTLELGGKSPAI 219

Query: 276 VFADAPDLQAAAESAAGAIAFNQGEVCTAGSRLLVERSIKDKFLPLVIEALKGWKPGNPL 335
           V  +  DL+ AAE  A     N G+ C A   +L++ +I   F      A++        
Sbjct: 220 V-DETCDLKKAAEKIAWGKLVNAGQTCIAPDYVLIKENISADFEMYYQAAVQKMFFNEAA 278

Query: 336 DPATNVGALVDTQQMNTVLSYIEAGHADGAKLVAGGKRTLEETGGTYVEPTIFDGVTNAM 395
               +   +++ +Q   +   IE    DGA L  GGK    +     + PT+   V  + 
Sbjct: 279 INKNDYAKIINIKQFQRLNKLIEEAIRDGAVLAFGGK---SDEQNLTITPTLLTSVAESS 335

Query: 396 KIAKEEIFGPVLSVITFDSAEEAVAIANDTIYGLAAAVWTADISKAHLTAKALRAGSVWV 455
            I +EEIFGPVL VIT+ + +EA+ + N     LA  +++   +  +       AG   V
Sbjct: 336 AIMQEEIFGPVLPVITYQNLQEAIDVVNRKAKPLALYIFSDSTTNQNKIISETSAGGTCV 395

Query: 456 NQ--YDGGDMTAPFGGFKQSGNGRDKSLHAFDKYTELKA 492
           N      G+   PFGG   SG G    +  F  ++  +A
Sbjct: 396 NDVLVHIGNPDLPFGGVNNSGIGSCHGIFGFKTFSHERA 434


Lambda     K      H
   0.316    0.132    0.386 

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: 412
Number of extensions: 18
Number of successful extensions: 6
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: 497
Length of database: 465
Length adjustment: 34
Effective length of query: 463
Effective length of database: 431
Effective search space:   199553
Effective search space used:   199553
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 (21.6 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