Alignments for a candidate for lysA in Methylomonas methanica MC09

GapMind for Amino acid biosynthesis

Alignments for a candidate for lysA in Methylomonas methanica MC09

Align Diaminopimelate decarboxylase; DAP decarboxylase; DAPDC; EC 4.1.1.20 (uncharacterized)
to candidate WP_013817912.1 METME_RS06135 pyridoxal-dependent decarboxylase, exosortase A system-associated

Query= curated2:O67262
         (420 letters)



>NCBI__GCF_000214665.1:WP_013817912.1
          Length = 411

 Score =  171 bits (434), Expect = 3e-47
 Identities = 128/399 (32%), Positives = 204/399 (51%), Gaps = 26/399 (6%)

Query: 17  ELFIEGVSLKELAQTFG-TPLYVYSSNFIKERFEAYRKAFPDAL-ICYAVKANFNPHLVK 74
           EL + G SL  LA+  G TP Y Y    +  R +  R+A P  L I YA+KAN  P +V+
Sbjct: 20  ELMVGGTSLSRLAERVGQTPFYAYDRQALTRRMQQLRQAMPPELKIHYAMKANPMPAVVQ 79

Query: 75  LLGELGAGADIVSGGELYLAKKAGIPPERIVYAGVGKTEKELTDAVDSEILMFNVESRQE 134
            +  L  G D+ S  E+ +A    +P E I +AG GK  +EL+ A+ + + + N+ES  E
Sbjct: 80  HMATLADGFDLASADEMKVALDTPMPAEHISFAGPGKRPQELSQAIAAGVTI-NIESAHE 138

Query: 135 LDVLNEIAGKLGKKARIAIRVNPDVDPKTHPYIATGMQ----KSKFGVDIREAQKEYEYA 190
           L+ + +    LG  A++A+R+NP  + K     A+GM+      +FG+D  +     +  
Sbjct: 139 LECIGKQCENLGVNAKVAVRINPAFELK-----ASGMKMGGGAKQFGIDEEQVPVILQRI 193

Query: 191 SKLENLEIVGIHCHIGSQILDISPYREAVEKVVSLYESLTQK-GFDIKYLDIGGGLGIKY 249
             L+ L+  G H + GSQ L      EA +K + L  +L+      I+ L+IGGG GI Y
Sbjct: 194 KTLD-LQFQGFHIYSGSQNLKADSIIEAQQKSLQLAANLSPLCPSPIRKLNIGGGFGIPY 252

Query: 250 KPEDKEPAPQDLADLLKDLL-----ENVKAKIILEPGRSIMGNAGILITQVQFLKDKGSK 304
            P D   A + + + L   L        +A+II+E GR ++G AGI +T++   K    +
Sbjct: 253 FPGDAPLAIEQVGNALASELVLTRQSLAEAEIIIELGRYLVGEAGIYVTRILDKKISRGQ 312

Query: 305 HFIIVDAGMNDLIRPS------IYNAYHHIIPVETKERKKVVADIVGPICETGDFLALDR 358
            F++VD G++  +  S      I   Y   I  +   ++    +IVGP+C   D LA   
Sbjct: 313 TFLVVDGGLHHHLAASGNFGQVIRKNYPVAIGNKMGVQELETVNIVGPLCTPLDILADKM 372

Query: 359 EIEEVQRGEYLAVLSAGAYGFAMS-SHYNMRPRAAEVLV 396
            + + + G+ + +  +GAYG+  S S +  +P A EVLV
Sbjct: 373 TLPKAEIGDLVVIFQSGAYGYTASPSKFLSQPDAREVLV 411


Lambda     K      H
   0.317    0.139    0.392 

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: 407
Number of extensions: 30
Number of successful extensions: 7
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: 420
Length of database: 411
Length adjustment: 31
Effective length of query: 389
Effective length of database: 380
Effective search space:   147820
Effective search space used:   147820
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: 41 (21.6 bits)
S2: 50 (23.9 bits)

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

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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