Alignments for a candidate for agx1 in Pseudomonas fluorescens FW300-N1B4

GapMind for Amino acid biosynthesis

Alignments for a candidate for agx1 in Pseudomonas fluorescens FW300-N1B4

Align (R)-3-amino-2-methylpropionate-pyruvate transaminase (EC 2.6.1.40); alanine-glyoxylate transaminase (EC 2.6.1.44) (characterized)
to candidate Pf1N1B4_1733 5-aminovalerate aminotransferase (EC 2.6.1.48) / Gamma-aminobutyrate:alpha-ketoglutarate aminotransferase (EC 2.6.1.19)

Query= BRENDA::Q64565
         (512 letters)



>FitnessBrowser__pseudo1_N1B4:Pf1N1B4_1733
          Length = 425

 Score =  189 bits (479), Expect = 2e-52
 Identities = 130/425 (30%), Positives = 199/425 (46%), Gaps = 27/425 (6%)

Query: 83  PLLLHQGHMEWLFDSEGNRYLDFFSGIVTVGVGHCHPKVTAVAKKQMDRLWHTS-SVFFH 141
           P+         + D EG  ++DF  GI  +  GH HPK+ A   +Q+++L HT   V  +
Sbjct: 25  PIFAESAKNATVTDVEGREFIDFAGGIAVLNTGHVHPKIIAAVTEQLNKLTHTCFQVLAY 84

Query: 142 SPMHEYAERLSALLPEPL-KVIFLVNSGSEANDLAMVMARAYSNHTDIISFRGAYHGCSP 200
            P  E  E+++A +P    K   LV +GSEA + ++ +ARA +    +I+F GAYHG + 
Sbjct: 85  EPYVEVCEKINAKVPGDFAKKTLLVTTGSEAVENSIKIARAATGRAGVIAFTGAYHGRTM 144

Query: 201 YTLGLTNVGIYKMKVPSTIACQSTMCPDVFRGPWGGSHCRDSPVQTVRKCSCAPDGCQAK 260
            TLGLT       KV    A    M   +FR  +       S            D   + 
Sbjct: 145 MTLGLTG------KVVPYSAGMGLMPGGIFRALYPNELHGVS----------IDDSIASI 188

Query: 261 ERYIEQFKDTLNTSVATSIAGFFAEPIQGVNGVVQYPKEFLKEAFALVRERGGVCIADEV 320
           ER  +      N +    IA    EP+QG  G    PKEF+K   AL  + G + IADEV
Sbjct: 189 ERIFK------NDAEPRDIAAIIIEPVQGEGGFYVAPKEFMKRLRALCDQHGILLIADEV 242

Query: 321 QTGFGRLGSHFWGFQTHDTMPDIVTMAKGIGNGFPMAAVVTTPEIASSLAKHLHHFSTFG 380
           QTG GR G+ F+  +      D+ T AK I  GFP+A V    E   ++A       T+ 
Sbjct: 243 QTGAGRTGT-FFAMEQMGVAADLTTFAKSIAGGFPLAGVCGKAEYMDAIAPG-GLGGTYA 300

Query: 381 GSPLACAIGSAVLEVIEEENLQRNSQEVGTYMLLKFAKLRDEFDIVGDVRGKGLMVGIEM 440
           GSP+ACA   AV+EV EEE+L    + VG  ++     ++ ++ ++G+VR  G M+ +E+
Sbjct: 301 GSPIACAAALAVMEVFEEEHLLDRCKAVGERLVTGLKAIQAKYPVIGEVRALGAMIAVEL 360

Query: 441 VQDKISRQPLPKTEVNQIHEDCKDMGLLVGRGGNFSQTFRIAPPMRVTKLEVDFAFEVFR 500
             D  S +P     V  +    +D GL++   G +    R+  P+     ++D    +  
Sbjct: 361 FVDGDSHKP-NAAAVASVVAKARDKGLILLSCGTYGNVLRVLVPLTSPDEQLDKGLAIIE 419

Query: 501 SALTQ 505
               +
Sbjct: 420 ECFAE 424


Lambda     K      H
   0.322    0.136    0.419 

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: 466
Number of extensions: 31
Number of successful extensions: 5
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 2
Length of query: 512
Length of database: 425
Length adjustment: 33
Effective length of query: 479
Effective length of database: 392
Effective search space:   187768
Effective search space used:   187768
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: 51 (24.3 bits)

This GapMind analysis is from Aug 03 2021. The underlying query database was built on Aug 03 2021.

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Protein sequences (fasta format)
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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, or view the source code, or see changes to Amino acid biosynthesis since the publication.

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 Amino acid biosynthesis