Alignments for a candidate for glyXL in Desulfarculus baarsii DSM 2075

GapMind for Amino acid biosynthesis

Alignments for a candidate for glyXL in Desulfarculus baarsii DSM 2075

Align UPF0210 protein MMP1427 (characterized, see rationale)
to candidate WP_013258744.1 DEBA_RS09675 PFL family protein

Query= uniprot:Q6LXC5
         (458 letters)



>NCBI__GCF_000143965.1:WP_013258744.1
          Length = 452

 Score =  489 bits (1258), Expect = e-142
 Identities = 244/454 (53%), Positives = 326/454 (71%), Gaps = 7/454 (1%)

Query: 5   EEIIETIKMIEYQNLDIRTTTLGINLKDCADKDLDLLKENIYDKITSLGGNLVETANKVS 64
           +E +ET  MI + N DIR  TLG+NLKD  D+D++ +   +  ++  +G  LV+ A+++S
Sbjct: 6   QEALETAGMILFDNFDIRAVTLGVNLKDLIDRDIERMSAAVAGRLADMGRRLVDEASRIS 65

Query: 65  QKYGIPIVNKRISVTPIGLIMGSTVKGLSDEEAVDACVEVGITLDKIAKEVGVDFIGGYS 124
             +G+PIVNKR+S+TP   ++ +           +A V +   +D+ A   GVDF+GG+ 
Sbjct: 66  DSFGVPIVNKRLSITPAAWLLEACPHD-------EAPVVLAQAIDRGACRAGVDFVGGFG 118

Query: 125 ALVQKRATYEEKMLIRSIPKLMTKTDKVCASVNVATTKAGINMYAVKKMGEIVKETSEIT 184
           ALV+K AT  ++ L+ ++P+ +  T ++C  +N+A+T AG+NM A+ ++G I+K  +   
Sbjct: 119 ALVEKGATKADRRLMEALPQALGSTQRLCGFLNLASTSAGMNMDAIARLGHILKAMAAAA 178

Query: 185 KDAIGCAKIVVFCNAPEDNPFMAGAFHGPGEGDAVINAGVSGPGVVRAVVEQLKGKDIGT 244
              + CAK V F NAP DNPFMAGAFHG  EGD  +N G+SGPGVVRAVVE+    D+  
Sbjct: 179 PLGLACAKFVAFANAPSDNPFMAGAFHGAQEGDTALNVGISGPGVVRAVVEKHPDCDLTM 238

Query: 245 VSDEIKKTAFKITRMGELVGKEVANELGVNFGIVDLSLAPTPAIGDSIANILEAVGLERC 304
           +S+ I++T FKITR GELVG+E+A  LGVNFG+VD+SLAPT A+GDS+  ILE++GLE+ 
Sbjct: 239 LSEVIRRTVFKITRAGELVGRELAKRLGVNFGVVDISLAPTTAVGDSVGQILESMGLEKV 298

Query: 305 GTHGTTAALAMLNDAVKKGGAMASSNVGGLSGAFIPVSEDAGMIEAVEVGALRLEKLEAM 364
           G  GTTAALA+L DAVK+GGAMAS NVGGLSG FIPVSED  MI+AVE GAL LEKLEAM
Sbjct: 299 GAPGTTAALALLIDAVKRGGAMASGNVGGLSGTFIPVSEDLAMIDAVECGALGLEKLEAM 358

Query: 365 TCVCSVGLDMIAVPGKTPASTLSAIMADEMAIGMINKKTTAVRIIPVPGKDVGDYVEYGG 424
           T VCSVGLDM AVPG    +TLSAI+ADE++IG+ N KTT VR+IP PG   GD V++GG
Sbjct: 359 TAVCSVGLDMFAVPGDVEPATLSAIIADELSIGVANNKTTGVRMIPAPGTKPGDSVDFGG 418

Query: 425 LLGTAPIMPVSEFSSEELIERGGRIPAPIQSLTN 458
           LLG AP+M V+ FS  + I RGGR+PAPI +L N
Sbjct: 419 LLGRAPVMAVNRFSGAKFIGRGGRMPAPITALRN 452


Lambda     K      H
   0.315    0.135    0.374 

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: 656
Number of extensions: 28
Number of successful extensions: 2
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: 458
Length of database: 452
Length adjustment: 33
Effective length of query: 425
Effective length of database: 419
Effective search space:   178075
Effective search space used:   178075
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: 42 (22.0 bits)
S2: 51 (24.3 bits)

This GapMind analysis is from Apr 10 2024. The underlying query database was built on Apr 09 2024.

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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