Alignments for a candidate for kauB in Pseudomonas fluorescens FW300-N2E3

GapMind for catabolism of small carbon sources

Alignments for a candidate for kauB in Pseudomonas fluorescens FW300-N2E3

Align gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase (EC 1.2.1.54) (characterized)
to candidate AO353_09195 AO353_09195 aldehyde dehydrogenase

Query= reanno::pseudo6_N2E2:Pf6N2E2_4383
         (497 letters)



>FitnessBrowser__pseudo3_N2E3:AO353_09195
          Length = 497

 Score =  947 bits (2449), Expect = 0.0
 Identities = 471/497 (94%), Positives = 487/497 (97%)

Query: 1   MTTLTRADWEQRARDLKIEGRAFINGEYTDAVSGETFDCLSPVDGRLLGKIASCDVADAQ 60
           MTTLTRADWEQRARDLKIEGRA+INGEYT AVSGETFDC+SPVDGRLLGKIASCD ADAQ
Sbjct: 1   MTTLTRADWEQRARDLKIEGRAYINGEYTAAVSGETFDCISPVDGRLLGKIASCDAADAQ 60

Query: 61  RAVENARATFSSGVWSRLAPSKRKATMIRFAGLLKQHAEELALLETLDMGKPISDSLNID 120
           RAVENAR+TF+SGVWSRLAP+KRKATMIRFAGLLKQHAEELALLETLDMGKPISDSL ID
Sbjct: 61  RAVENARSTFNSGVWSRLAPAKRKATMIRFAGLLKQHAEELALLETLDMGKPISDSLYID 120

Query: 121 VPGAAQALSWSGEAIDKLYDEVAATPHDQLGLVTREPVGVVGAIVPWNFPLMMACWKLGP 180
           VPGAAQALSWSGEAIDK+YDEVAATPHDQLGLVTREPVGVVGAIVPWNFPLMMACWKLGP
Sbjct: 121 VPGAAQALSWSGEAIDKIYDEVAATPHDQLGLVTREPVGVVGAIVPWNFPLMMACWKLGP 180

Query: 181 ALSTGNSVVLKPSEKSPLTALRIAALAIEAGIPKGVLNVLPGYGHTVGKALALHMDVDTL 240
           ALSTGNSV+LKPSEKSPLTA+R+AALA+EAGIPKGVLNVLPGYGHTVGKALALHMDVDTL
Sbjct: 181 ALSTGNSVILKPSEKSPLTAIRLAALAVEAGIPKGVLNVLPGYGHTVGKALALHMDVDTL 240

Query: 241 VFTGSTKIAKQLMIYSGESNMKRIWLEAGGKSPNIVFADAPDLQAAAESAASAIAFNQGE 300
           VFTGSTKIAKQLMIYSGESNMKR+WLEAGGKSPNIVFADAPDLQAAAESAASAIAFNQGE
Sbjct: 241 VFTGSTKIAKQLMIYSGESNMKRVWLEAGGKSPNIVFADAPDLQAAAESAASAIAFNQGE 300

Query: 301 VCTAGSRLLVERSIKDTFLPLVIEALKGWKPGNPLDPATNVGALVDTQQMNTVLSYIEAG 360
           VCTAGSRLLVERSIKD FLPLVIEALK WKPGNPLDPATNVGALVDTQQMNTVLSYIE+G
Sbjct: 301 VCTAGSRLLVERSIKDKFLPLVIEALKTWKPGNPLDPATNVGALVDTQQMNTVLSYIESG 360

Query: 361 HSDGAKLVAGGKRILEETGGTYVEPTIFDGVSNAMKIAQEEIFGPVLSVIAFDTAEQAIE 420
           HSDGAKLVAGGKRIL+ETGGTYVEPTIFDGVSNAMKIAQEEIFGPVLSVI FD+ E+AI 
Sbjct: 361 HSDGAKLVAGGKRILQETGGTYVEPTIFDGVSNAMKIAQEEIFGPVLSVITFDSVEEAIR 420

Query: 421 IANDTPYGLAAAVWTKDISKAHLTAKALRAGSVWVNQYDGGDMTAPFGGFKQSGNGRDKS 480
           IANDTPYGLAAAVWT DISK HLTAKALRAGSVWVNQYDGGDMTAPFGGFKQSGNGRDKS
Sbjct: 421 IANDTPYGLAAAVWTSDISKGHLTAKALRAGSVWVNQYDGGDMTAPFGGFKQSGNGRDKS 480

Query: 481 LHAFDKYTELKSTWIKL 497
           LHAFDKYTELK+TWIKL
Sbjct: 481 LHAFDKYTELKATWIKL 497


Lambda     K      H
   0.316    0.132    0.389 

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: 993
Number of extensions: 33
Number of successful extensions: 1
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 Apr 09 2024. The underlying query database was built on Sep 17 2021.

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Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

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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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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 2024 update on GapMind for amino acid biosynthesis
the paper from 2022 on GapMind for carbon sources
the source code
instructions for running GapMind on your computer

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

GapMind for catabolism of small carbon sources