GapMind for catabolism of small carbon sources

 

Alignments for a candidate for mmsA in Methylocystis bryophila S285

Align malonate-semialdehyde dehydrogenase (acetylating) (EC 1.2.1.18) (characterized)
to candidate WP_085772038.1 B1812_RS13395 aldehyde dehydrogenase family protein

Query= reanno::Smeli:SMc00781
         (498 letters)



>NCBI__GCF_002117405.1:WP_085772038.1
          Length = 506

 Score =  183 bits (464), Expect = 1e-50
 Identities = 140/466 (30%), Positives = 224/466 (48%), Gaps = 15/466 (3%)

Query: 6   HFIDGKRVAGTSGRVSNIFNPATGEVQGTVALASDADLAAAVESAKAAQPKWAATNPQRR 65
           +FI G+ VA   G   +  +P TG     VA    AD+  A+++A  A+  W  T    R
Sbjct: 21  NFIGGQWVAPLGGEYFDNISPITGHPICQVARGRAADVELALDAAHKAKDAWGKTPAAER 80

Query: 66  ARVFMKFVQLLNDNMNELAEMLSREHGKTI-DDAKGDIVRGLEVCEFVIGIPHLQKSEFT 124
           A +  K  Q L+DN++ LA + + ++GK I +    DI   ++   +  G    Q+   +
Sbjct: 81  ANMLNKIAQRLDDNLSALALVETIDNGKPIRETTAADIPLAIDHFRYFAGCLRAQEGSLS 140

Query: 125 EGAGPGIDMYSIRQPVGIGAGITPFNFPGMIPMWMFAPAIACGNAFILKPSERDPSVPIR 184
           E     +  Y   +P+G+   I P+NFP ++  W  +PA+A GN  +LKP+E+ P   + 
Sbjct: 141 EIDHDTV-AYHFHEPLGVVGQIIPWNFPILMAAWKLSPALAAGNCVVLKPAEQTPMSILA 199

Query: 185 LAELMIEAGLPAGILNVVNG-DKGAVDAILTHPDIAAVSFVGSTPIARYVYGTAAMNGKR 243
           +AEL+ +  LP G+LN+VNG    A   + ++  IA ++F G T   R +   AA N   
Sbjct: 200 VAELIADL-LPPGVLNIVNGFGVEAGKPLASNKRIAKIAFTGETTTGRLIMQYAAENLIP 258

Query: 244 AQCFGGAKNHMIIM------PDADLDQAANALIGAGYGSAGERCMAISVAVPVGEETANR 297
                G K+  I         DA LD+A          + GE C   S A+ V     ++
Sbjct: 259 VTLELGGKSPNIFFADVMAEDDAFLDKALEGFASFAL-NQGEVCTCPSRAL-VQRSIYDK 316

Query: 298 LIDKLVPMVESLRIGPYTDEKADMGPVVTKEAEQRIRSLIDSGIEQGAKLVVDGRDFKLQ 357
            ++K +  V  +R G   D    +G   + +  ++I S +D G ++GAK+++ G    L+
Sbjct: 317 FMEKALARVAKIRQGHPLDPATMIGAQASNDQLEKILSYVDIGRKEGAKVLIGGERSVLE 376

Query: 358 G-YENGHFIGGCLFDDVTPDMDIYKTEIFGPVLSVVRARNYEEALSLPMKHEYGNGVAIY 416
           G  + G+++     +     M +++ EIFGPV+SV      EEAL +     YG G  ++
Sbjct: 377 GELKEGYYMQPTALEGHN-RMRVFQEEIFGPVVSVTTFETEEEALQIANDTLYGLGAGLW 435

Query: 417 TRDGDAARDFASRINIGMVGVNVPIPVPLAYHSFGGWKSSSFGDLN 462
           TRDG  A      I  G V  N     P A+ +FGG+K S  G  N
Sbjct: 436 TRDGSRAYRCGRAIRAGRVWTNCYHAYP-AHAAFGGYKQSGIGREN 480


Lambda     K      H
   0.319    0.137    0.409 

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: 544
Number of extensions: 30
Number of successful extensions: 6
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: 506
Length adjustment: 34
Effective length of query: 464
Effective length of database: 472
Effective search space:   219008
Effective search space used:   219008
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 Apr 09 2024. 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