Alignments for a candidate for agx1 in Pseudomonas fluorescens GW456-L13

GapMind for Amino acid biosynthesis

Alignments for a candidate for agx1 in Pseudomonas fluorescens GW456-L13

Align alanine-glyoxylate transaminase (EC 2.6.1.44) (characterized)
to candidate PfGW456L13_1928 Uncharacterized PLP-dependent aminotransferase YfdZ

Query= BRENDA::D2Z0I0
         (402 letters)



>FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1928
          Length = 405

 Score =  444 bits (1143), Expect = e-129
 Identities = 217/386 (56%), Positives = 282/386 (73%), Gaps = 5/386 (1%)

Query: 7   FPKVKKLPKYVFAMVNELKYQLRREGEDIVDLGMGNPDIPPSQHIIDKLCEVANRPNVHG 66
           F ++ +LP YVF +  ELK   RR GEDI+DL MGNPD     HI++KL  VA R + HG
Sbjct: 10  FARIDRLPPYVFNITAELKMAARRRGEDIIDLSMGNPDGATPPHIVEKLVTVAQREDTHG 69

Query: 67  YSASKGIPRLRKAICDFYKRRYGVELDPERNAIMTIGAKEGYSHLMLAMLEPGDTVIVPN 126
           YS SKGIPRLR+AI ++YK RY V++DPE  AI+TIG+KEG +HLMLA L+ GDTV+VPN
Sbjct: 70  YSTSKGIPRLRRAISNWYKDRYEVDIDPESEAIVTIGSKEGLAHLMLATLDQGDTVLVPN 129

Query: 127 PTYPIHYYAPIICGGDAISVPILPEEDFPEVFLRRLYDLIKTSFRKPKAVVLSFPHNPTT 186
           P+YPIH Y  +I G    SVP++P  DF       L   I+ S  KPK ++L FP NPT 
Sbjct: 130 PSYPIHIYGAVIAGAQVRSVPLVPGVDF----FAELERAIRGSIPKPKMMILGFPSNPTA 185

Query: 187 LCVDLEFFQEVVKLAKQEGIWIVHDFAYADLGFDGYTPPSILQVEGALDVAVELYSMSKG 246
            CV+L+FF+ V+ LAKQ  + +VHD AYAD+ +DG+  PSI+QV GA D+AVE +++SK 
Sbjct: 186 QCVELDFFERVIALAKQYDVLVVHDLAYADIVYDGWKAPSIMQVPGAKDIAVEFFTLSKS 245

Query: 247 FSMAGWRVAFVVGNEMLIKNLAHLKSYLDYGVFTPIQVASIIALESPYEVVEKNREIYRR 306
           ++MAGWR+ F+VGN  L+  LA +KSY DYG FTP+QVA+I ALE   + V    E YR+
Sbjct: 246 YNMAGWRIGFMVGNPELVNALARIKSYHDYGTFTPLQVAAIAALEGDQQCVRDIAEQYRQ 305

Query: 307 RRDVLVEGLNRVGWEVKKPKGSMFVWAKVPEEVG-MNSLDFSLFLLREAKVAVSPGIGFG 365
           RR+VLV+GL+ +GW V+ PK SM+VWAK+PE    + SL+F+  LL EAKV VSPG+GFG
Sbjct: 306 RRNVLVKGLHELGWMVENPKASMYVWAKIPEAYAHLGSLEFAKKLLAEAKVCVSPGVGFG 365

Query: 366 EYGEGYVRFALVENEHRIRQAVRGIK 391
           EYG+ +VRFAL+EN+ RIRQAVRGI+
Sbjct: 366 EYGDDHVRFALIENQDRIRQAVRGIR 391


Lambda     K      H
   0.322    0.141    0.425 

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: 555
Number of extensions: 27
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: 402
Length of database: 405
Length adjustment: 31
Effective length of query: 371
Effective length of database: 374
Effective search space:   138754
Effective search space used:   138754
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: 50 (23.9 bits)

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