Alignments for a candidate for ams in Pseudomonas fluorescens FW300-N1B4

GapMind for catabolism of small carbon sources

Alignments for a candidate for ams in Pseudomonas fluorescens FW300-N1B4

Align Sucrose alpha-glucosidase (EC 3.2.1.48) (characterized)
to candidate Pf1N1B4_5116 Sucrose-6-phosphate hydrolase (EC 3.2.1.B3)

Query= reanno::pseudo1_N1B4:Pf1N1B4_5116
         (489 letters)



>FitnessBrowser__pseudo1_N1B4:Pf1N1B4_5116
          Length = 489

 Score = 1043 bits (2697), Expect = 0.0
 Identities = 489/489 (100%), Positives = 489/489 (100%)

Query: 1   MSAALEIAQHALSDGLSRVTDDYRPGYHLAPPAGWMNDPNGVVYFRGEYHVFYQHHPFDA 60
           MSAALEIAQHALSDGLSRVTDDYRPGYHLAPPAGWMNDPNGVVYFRGEYHVFYQHHPFDA
Sbjct: 1   MSAALEIAQHALSDGLSRVTDDYRPGYHLAPPAGWMNDPNGVVYFRGEYHVFYQHHPFDA 60

Query: 61  KWGPMYWGHAKSADLVHWQHLPIALAPGDDFDRDGCFSGSAVVCGDTLALIYTGHTWLGE 120
           KWGPMYWGHAKSADLVHWQHLPIALAPGDDFDRDGCFSGSAVVCGDTLALIYTGHTWLGE
Sbjct: 61  KWGPMYWGHAKSADLVHWQHLPIALAPGDDFDRDGCFSGSAVVCGDTLALIYTGHTWLGE 120

Query: 121 VGDERYIRQVQCLATSTDGIQFVKHGAVIDTAPQDTIMHFRDPKVWQEDDGWYLIAGARL 180
           VGDERYIRQVQCLATSTDGIQFVKHGAVIDTAPQDTIMHFRDPKVWQEDDGWYLIAGARL
Sbjct: 121 VGDERYIRQVQCLATSTDGIQFVKHGAVIDTAPQDTIMHFRDPKVWQEDDGWYLIAGARL 180

Query: 181 GDVPLLPLYRSTDLHSWEFLDYVSSGSEGDGYMWECPDLFRLNGRDVLLYSPQGMQPEGY 240
           GDVPLLPLYRSTDLHSWEFLDYVSSGSEGDGYMWECPDLFRLNGRDVLLYSPQGMQPEGY
Sbjct: 181 GDVPLLPLYRSTDLHSWEFLDYVSSGSEGDGYMWECPDLFRLNGRDVLLYSPQGMQPEGY 240

Query: 241 ERLNKYQTGYRVGRLDSQWHFTGGPFIELDNGHDFYAAQTLLAADGRRLVWAWLDMWESP 300
           ERLNKYQTGYRVGRLDSQWHFTGGPFIELDNGHDFYAAQTLLAADGRRLVWAWLDMWESP
Sbjct: 241 ERLNKYQTGYRVGRLDSQWHFTGGPFIELDNGHDFYAAQTLLAADGRRLVWAWLDMWESP 300

Query: 301 MPSQAHHWCGMLGVPRELELHADRLCVYPARELTALRMAPLPGVSWWEGSGSRWVPEVNG 360
           MPSQAHHWCGMLGVPRELELHADRLCVYPARELTALRMAPLPGVSWWEGSGSRWVPEVNG
Sbjct: 301 MPSQAHHWCGMLGVPRELELHADRLCVYPARELTALRMAPLPGVSWWEGSGSRWVPEVNG 360

Query: 361 DMLEIHVHLDLRGCTSGHLGIALRCSDDGHEETLLYYDASLQRLVLDRSRAGAQVTGQRS 420
           DMLEIHVHLDLRGCTSGHLGIALRCSDDGHEETLLYYDASLQRLVLDRSRAGAQVTGQRS
Sbjct: 361 DMLEIHVHLDLRGCTSGHLGIALRCSDDGHEETLLYYDASLQRLVLDRSRAGAQVTGQRS 420

Query: 421 VSIDPTQERLELRVFLDRSSIEVFDENGRFSLSSRLYPRPDSLGVKLFANGSGGRVSIPK 480
           VSIDPTQERLELRVFLDRSSIEVFDENGRFSLSSRLYPRPDSLGVKLFANGSGGRVSIPK
Sbjct: 421 VSIDPTQERLELRVFLDRSSIEVFDENGRFSLSSRLYPRPDSLGVKLFANGSGGRVSIPK 480

Query: 481 AWPLASGWL 489
           AWPLASGWL
Sbjct: 481 AWPLASGWL 489


Lambda     K      H
   0.321    0.140    0.465 

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: 1313
Number of extensions: 59
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: 489
Length of database: 489
Length adjustment: 34
Effective length of query: 455
Effective length of database: 455
Effective search space:   207025
Effective search space used:   207025
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 52 (24.6 bits)

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

Downloads

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 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