GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__Pedo557:CA265_RS21385
          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:

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