Aligments for a candidate for mmsA in Phaeobacter inhibens BS107

GapMind for catabolism of small carbon sources

Aligments for a candidate for mmsA in Phaeobacter inhibens BS107

Align malonate-semialdehyde dehydrogenase (EC 1.2.1.15); malonate-semialdehyde dehydrogenase (acetylating) (EC 1.2.1.18); methylmalonate-semialdehyde dehydrogenase (CoA-acylating) (EC 1.2.1.27) (characterized)
to candidate GFF3742 PGA1_262p01460 aldehyde dehydrogenase

Query= BRENDA::A0A081YAY7
         (498 letters)



>lcl|FitnessBrowser__Phaeo:GFF3742 PGA1_262p01460 aldehyde
           dehydrogenase
          Length = 497

 Score =  226 bits (576), Expect = 1e-63
 Identities = 147/472 (31%), Positives = 235/472 (49%), Gaps = 5/472 (1%)

Query: 5   KHLIGGELIADTGRTADVFNPSTGEAVRKVPLADRETMQQAIDAAKAAFPAWRNTPPAKR 64
           K+LI GE +A      +       + V     A  + ++  +D A+ A   W      ++
Sbjct: 21  KNLIAGEWLAGESEVENRNPSDLSDLVGIFAQASADQLEATLDQAQVAQREWAAYGLERK 80

Query: 65  AQVLFRFKQLLEANEERIVKLISEEHGKTIEDAAGELKRGIENVEYATAAPEILKGEYSR 124
             VL      + A  E +  L+S E GK + +  GE+ R  +   Y  A      GE + 
Sbjct: 81  QAVLNAIGNEMMARAEELGTLLSREEGKPLAEGKGEVYRAGQFFTYYAAECLRQIGENAD 140

Query: 125 NVGPNIDAWSDFQPIGVVAGITPFNFPAMVPLWMYPLAIACGNTFILKPSERDPSSTLLI 184
           +V P+I+     + +G VA I+P+NFP     W    A+  GN  + KP+   P+S + +
Sbjct: 141 SVRPDIEVDVRREAVGTVAIISPWNFPTATASWKIAPALCYGNAVVWKPANITPASAVAL 200

Query: 185 AELFHEAGLPKGVLNVVHGDKGAV-DALIEAPEVKALSFVGSTPIAEYIYSEGTKRGKRV 243
           AE+     +PKG+ ++V G   ++   L+E+P+V A+SF GS P+ + I S   +   +V
Sbjct: 201 AEIIERQDIPKGLFSLVMGSGRSIGQRLVESPKVNAISFTGSVPVGKGIASAAIQNLTKV 260

Query: 244 QALGGAKNHAVLMPDADLDNAVSALMGAAYGSCGERCMAISVAVCVGDQIADALVQKLVP 303
           Q   G+KN   +M DADLD AV+  +G A+G  G++C A S  V V   I DA V+KLV 
Sbjct: 261 QMEMGSKNALAVMDDADLDLAVTLALGGAFGGTGQKCTASSRLV-VHAGIHDAFVEKLVT 319

Query: 304 QIKGLKIGAGTSCGLDMGPLVTGAARDKVTGYIDTGVAQGAELVVDGRGYKVAGHENGFF 363
             K +K+G     G+ MGP+V+    ++   Y+D G  +GAEL   G+  ++     GF+
Sbjct: 320 GAKAMKVGHALEAGVQMGPVVSEQQLNENLAYVDLGKTEGAELACGGQRLEMP--HQGFY 377

Query: 364 LGGTLFDRVTPEMTIYKEEIFGPVLCIVRVNSLEEAMQLINDHEYGNGTCIFTRDGEAAR 423
           +   +F   T +M I +EE+F P+  +++V S +EA+ ++ND  +G  + I T+    A 
Sbjct: 378 MSPGVFLNTTNDMRINREEMFAPLTSVIKVGSYDEALSVVNDTNFGLTSGIVTQSLARAT 437

Query: 424 LFCDEIEVGMVGVNVPLPVPVAYHSFGGWKRSLFGDLHAYGPDGVRFYTKRK 475
            F      G+V VN+P      +  FGG   S +G     G     FYT  K
Sbjct: 438 HFRRNARTGVVTVNLPTAGTDYHVPFGGRGDSSYGP-REQGKAAAEFYTTVK 488


Lambda     K      H
   0.319    0.137    0.411 

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: 579
Number of extensions: 25
Number of successful extensions: 4
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: 498
Length of database: 497
Length adjustment: 34
Effective length of query: 464
Effective length of database: 463
Effective search space:   214832
Effective search space used:   214832
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 (21.7 bits)
S2: 52 (24.6 bits)

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

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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 preprint on GapMind for carbon sources, or view the source code.

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 catabolism of small carbon sources