GapMind for catabolism of small carbon sources

 

Aligments for a candidate for puuC in Pseudomonas fluorescens FW300-N1B4

Align gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase (EC 1.2.1.54) (characterized)
to candidate Pf1N1B4_2132 Aldehyde dehydrogenase (EC 1.2.1.3)

Query= reanno::pseudo13_GW456_L13:PfGW456L13_805
         (497 letters)



>lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_2132 Aldehyde
           dehydrogenase (EC 1.2.1.3)
          Length = 497

 Score =  963 bits (2490), Expect = 0.0
 Identities = 484/497 (97%), Positives = 489/497 (98%)

Query: 1   MTTLTRADWEQRARDLKIEGRAYINGEYTDAVSGETFECISPVDGRLLGKIASCDAADAQ 60
           MTTLTRADWEQRARDLKIEGRAYINGEYTDAVSGETFECISPVDGRLLGKIASCDAADAQ
Sbjct: 1   MTTLTRADWEQRARDLKIEGRAYINGEYTDAVSGETFECISPVDGRLLGKIASCDAADAQ 60

Query: 61  RAVENARATFNSGVWSRLAPTKRKSTMIRFAGLLKQHAEELALLETLDMGKPISDSLYID 120
           RAV+NARATFNSG WSRLAPTKRK+TMIRFAGLLKQHAEELALLETLDMGKPISDSLYID
Sbjct: 61  RAVDNARATFNSGAWSRLAPTKRKATMIRFAGLLKQHAEELALLETLDMGKPISDSLYID 120

Query: 121 VPGAAQALSWSGEAIDKIYDEVAATPHDQLGLVTREPVGVVGAIVPWNFPLMMACWKLGP 180
           VPGAAQALSWSGEAIDKIYDEVAATPHDQLGLVTREPVGVVGAIVPWNFPLMMACWKLGP
Sbjct: 121 VPGAAQALSWSGEAIDKIYDEVAATPHDQLGLVTREPVGVVGAIVPWNFPLMMACWKLGP 180

Query: 181 ALSTGNSVILKPSEKSPLTAIRIAELAVEAGIPKGVLNVLPGYGHTVGKALALHNDVDTL 240
           ALSTGNSVILKPSEKSPLTAIRIA LAVEAGIPKGVLNVLPGYGHTVGKALALHNDVDTL
Sbjct: 181 ALSTGNSVILKPSEKSPLTAIRIAALAVEAGIPKGVLNVLPGYGHTVGKALALHNDVDTL 240

Query: 241 VFTGSTKIAKQLLIYSGESNMKRVWLEAGGKSPNIVFADAPNLQDAAEAAAGAIAFNQGE 300
           VFTGSTKIAKQLLIYSGESNMKRVWLEAGGKSPNIVFADAP+LQ AAEAAAGAIAFNQGE
Sbjct: 241 VFTGSTKIAKQLLIYSGESNMKRVWLEAGGKSPNIVFADAPDLQAAAEAAAGAIAFNQGE 300

Query: 301 VCTAGSRLLVERSIKDKFLPLVIEALKAWKPGNPLDPATNVGALVDTQQMNTVLSYIESG 360
           VCTAGSRLLVERSIKDKFLPLVIEALK WKPGNPLDPATNVGALVDTQQMNTVLSYIESG
Sbjct: 301 VCTAGSRLLVERSIKDKFLPLVIEALKTWKPGNPLDPATNVGALVDTQQMNTVLSYIESG 360

Query: 361 HADGARLVAGGKRTLQETGGTYVEPTIFDGVSNAMKIAQEEIFGPVLSVIEFDSAEEAIA 420
           H DGA+LVAGGKR LQETGGTYVEPTIFDGVSNAMKIAQEEIFGPVLSVI FDSAEEAI 
Sbjct: 361 HTDGAKLVAGGKRILQETGGTYVEPTIFDGVSNAMKIAQEEIFGPVLSVITFDSAEEAIQ 420

Query: 421 IANDTPYGLAAAVWTADISKAHLTARALRAGSVWVNQYDGGDMTAPFGGFKQSGNGRDKS 480
           IANDTPYGLAAAVWTADISKAHLTA+ALRAGSVWVNQYDGGDMTAPFGGFKQSGNGRDKS
Sbjct: 421 IANDTPYGLAAAVWTADISKAHLTAKALRAGSVWVNQYDGGDMTAPFGGFKQSGNGRDKS 480

Query: 481 LHAFDKYTELKATWIKL 497
           LHAFDKYTELKATWIKL
Sbjct: 481 LHAFDKYTELKATWIKL 497


Lambda     K      H
   0.316    0.132    0.390 

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: 1002
Number of extensions: 34
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 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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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, 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