GapMind for catabolism of small carbon sources

 

Alignments for a candidate for puuC in Pseudomonas simiae WCS417

Align gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase (EC 1.2.1.54) (characterized)
to candidate GFF5420 PS417_27745 aldehyde dehydrogenase

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



>FitnessBrowser__WCS417:GFF5420
          Length = 497

 Score =  981 bits (2537), Expect = 0.0
 Identities = 497/497 (100%), Positives = 497/497 (100%)

Query: 1   MTTLTRADWEQRAKDLKIEGRAYINGEYTAAVSGDTFECISPVDGRLLATVASCDAADAQ 60
           MTTLTRADWEQRAKDLKIEGRAYINGEYTAAVSGDTFECISPVDGRLLATVASCDAADAQ
Sbjct: 1   MTTLTRADWEQRAKDLKIEGRAYINGEYTAAVSGDTFECISPVDGRLLATVASCDAADAQ 60

Query: 61  RAVENARATFNSGVWSRLAPAKRKSAMLRFAALLKANAEELALLETLDMGKPISDSLNID 120
           RAVENARATFNSGVWSRLAPAKRKSAMLRFAALLKANAEELALLETLDMGKPISDSLNID
Sbjct: 61  RAVENARATFNSGVWSRLAPAKRKSAMLRFAALLKANAEELALLETLDMGKPISDSLNID 120

Query: 121 VPGAANALSWSGEAIDKIYDEVAATPHDQLGLVTREPVGVVGAIVPWNFPLMMACWKLGP 180
           VPGAANALSWSGEAIDKIYDEVAATPHDQLGLVTREPVGVVGAIVPWNFPLMMACWKLGP
Sbjct: 121 VPGAANALSWSGEAIDKIYDEVAATPHDQLGLVTREPVGVVGAIVPWNFPLMMACWKLGP 180

Query: 181 ALSTGNSVILKPSEKSPLTAIRIAALAVEAGIPKGVFNVLPGYGHTVGNALALHMDVDTL 240
           ALSTGNSVILKPSEKSPLTAIRIAALAVEAGIPKGVFNVLPGYGHTVGNALALHMDVDTL
Sbjct: 181 ALSTGNSVILKPSEKSPLTAIRIAALAVEAGIPKGVFNVLPGYGHTVGNALALHMDVDTL 240

Query: 241 VFTGSTKIAKQLLIRSGESNMKRVWLEAGGKSPNIVFADAPDLQAAAESAAGAIAFNQGE 300
           VFTGSTKIAKQLLIRSGESNMKRVWLEAGGKSPNIVFADAPDLQAAAESAAGAIAFNQGE
Sbjct: 241 VFTGSTKIAKQLLIRSGESNMKRVWLEAGGKSPNIVFADAPDLQAAAESAAGAIAFNQGE 300

Query: 301 VCTAGSRLLVERSIKDKFLPLVIEALKGWKPGNPLDPATNVGALVDTQQMNTVLSYIEAG 360
           VCTAGSRLLVERSIKDKFLPLVIEALKGWKPGNPLDPATNVGALVDTQQMNTVLSYIEAG
Sbjct: 301 VCTAGSRLLVERSIKDKFLPLVIEALKGWKPGNPLDPATNVGALVDTQQMNTVLSYIEAG 360

Query: 361 HADGAKLVAGGKRTLEETGGTYVEPTIFDGVTNAMKIAKEEIFGPVLSVITFDSAEEAVA 420
           HADGAKLVAGGKRTLEETGGTYVEPTIFDGVTNAMKIAKEEIFGPVLSVITFDSAEEAVA
Sbjct: 361 HADGAKLVAGGKRTLEETGGTYVEPTIFDGVTNAMKIAKEEIFGPVLSVITFDSAEEAVA 420

Query: 421 IANDTIYGLAAAVWTADISKAHLTAKALRAGSVWVNQYDGGDMTAPFGGFKQSGNGRDKS 480
           IANDTIYGLAAAVWTADISKAHLTAKALRAGSVWVNQYDGGDMTAPFGGFKQSGNGRDKS
Sbjct: 421 IANDTIYGLAAAVWTADISKAHLTAKALRAGSVWVNQYDGGDMTAPFGGFKQSGNGRDKS 480

Query: 481 LHAFDKYTELKATWIKL 497
           LHAFDKYTELKATWIKL
Sbjct: 481 LHAFDKYTELKATWIKL 497


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: 972
Number of extensions: 20
Number of successful extensions: 3
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: 497
Length adjustment: 34
Effective length of query: 463
Effective length of database: 463
Effective search space:   214369
Effective search space used:   214369
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: 52 (24.6 bits)

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

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