GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__Phaeo:GFF3742
          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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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:

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:

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:

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:

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