Alignments for a candidate for metA in Marinobacter adhaerens HP15

GapMind for Amino acid biosynthesis

Alignments for a candidate for metA in Marinobacter adhaerens HP15

Align Homoserine O-succinyltransferase; HST; Homoserine transsuccinylase; HTS; EC 2.3.1.46 (characterized)
to candidate GFF285 HP15_284 homoserine O-acetyltransferase

Query= SwissProt::S2L5R8
         (390 letters)



>FitnessBrowser__Marino:GFF285
          Length = 382

 Score =  569 bits (1467), Expect = e-167
 Identities = 272/381 (71%), Positives = 323/381 (84%), Gaps = 1/381 (0%)

Query: 7   MPE-LPSDSVGLVAPQTAHFDVPLALACGKTLQSYDLVYETYGKLNASRSNAVLICHALS 65
           MP+ LP+DSVG+V+PQT HFD P+ LACG++L++YDLV ETYG LNA  SNAVLICHALS
Sbjct: 1   MPDTLPADSVGIVSPQTYHFDAPIDLACGQSLENYDLVVETYGTLNADASNAVLICHALS 60

Query: 66  GHHHAAGYHSREDRKPGWWDAHIGPGKSIDTDRFFVISLNNLGGCHGSTGPCAINPDTGR 125
           GHHHAAGYHS EDRKPGWWD+ IGPGK IDTDRFFV+SLNNLGGCHGSTGP +INP+TG+
Sbjct: 61  GHHHAAGYHSAEDRKPGWWDSCIGPGKPIDTDRFFVVSLNNLGGCHGSTGPNSINPETGK 120

Query: 126 QWGPDFPMMTVGDWVHSQARLADRLGIERFAAVIGGSLGGMQVLQWSLAYPERIANAVVI 185
            +GP+FP++TVGDWV SQA LADRLGI+ +AAV+GGSLGGMQ LQWSL YP+R+ +AVVI
Sbjct: 121 PFGPEFPVITVGDWVKSQALLADRLGIQCWAAVVGGSLGGMQALQWSLDYPDRLRHAVVI 180

Query: 186 AATPKLSAQNIAFNEVARQAIRSDPDFYDGWYAEHDTLPRRGLKLARMVGHITYLSEDAM 245
           A+TP+L+AQNIAFNEVARQAI SD +F+DG Y + DT+PRRGL LARMVGHITYLS+ +M
Sbjct: 181 ASTPRLTAQNIAFNEVARQAITSDREFHDGRYYDFDTVPRRGLMLARMVGHITYLSDASM 240

Query: 246 GSKFGRDLRSDDLNFGYDVEFQVESYLRYQGDTFSTSFDANTYLLMTKALDYFDPAAAHD 305
           G KFGR+LR     FGYD EFQVESYLRYQG+ FS SFDANTYLLMT+ALDYFDPA    
Sbjct: 241 GEKFGRELRDQAYKFGYDAEFQVESYLRYQGERFSESFDANTYLLMTRALDYFDPAYEFG 300

Query: 306 GDLAAAVAPASCPFLVVSFSTDWRFPPSRSRELVDALIRAGKPVSYVCIDSPHGHDAFLL 365
           GDL+ A+A ASC +LV+SFSTDWRF P+RS E+V+A+I A + VSY  +D+P GHDAFL+
Sbjct: 301 GDLSKALAAASCEYLVLSFSTDWRFTPARSEEMVNAMIGARRKVSYAEVDAPWGHDAFLI 360

Query: 366 PETRYQAIFASFMGRVAHDSG 386
           P  RY  IF ++M RVA + G
Sbjct: 361 PTPRYTDIFNAYMDRVAREVG 381


Lambda     K      H
   0.321    0.136    0.428 

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: 587
Number of extensions: 24
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: 390
Length of database: 382
Length adjustment: 30
Effective length of query: 360
Effective length of database: 352
Effective search space:   126720
Effective search space used:   126720
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 (21.8 bits)
S2: 50 (23.9 bits)

This GapMind analysis is from Apr 09 2024. The underlying query database was built on Apr 09 2024.

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