Alignments for a candidate for iolA in Sinorhizobium medicae WSM419

GapMind for catabolism of small carbon sources

Alignments for a candidate for iolA in Sinorhizobium medicae WSM419

Align malonate-semialdehyde dehydrogenase (acetylating) (EC 1.2.1.18) (characterized)
to candidate WP_011974531.1 SMED_RS01625 CoA-acylating methylmalonate-semialdehyde dehydrogenase

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



>NCBI__GCF_000017145.1:WP_011974531.1
          Length = 498

 Score =  981 bits (2537), Expect = 0.0
 Identities = 486/498 (97%), Positives = 492/498 (98%)

Query: 1   MYELGHFIDGKRVAGTSGRVSNIFNPATGEVQGTVALASDADLAAAVESAKAAQPKWAAT 60
           MYELGHFIDGKRVAG SGRVS IFNPATGEVQGTVALASDADLAAAVESAKAAQPKWAAT
Sbjct: 1   MYELGHFIDGKRVAGKSGRVSKIFNPATGEVQGTVALASDADLAAAVESAKAAQPKWAAT 60

Query: 61  NPQRRARVFMKFVQLLNDNMNELAEMLSREHGKTIDDAKGDIVRGLEVCEFVIGIPHLQK 120
           NPQRRARVFMKFVQLLNDNM+ELAEMLSREHGKTIDDAKGDIVRGLEVCEFVIGIPHLQK
Sbjct: 61  NPQRRARVFMKFVQLLNDNMDELAEMLSREHGKTIDDAKGDIVRGLEVCEFVIGIPHLQK 120

Query: 121 SEFTEGAGPGIDMYSIRQPVGIGAGITPFNFPGMIPMWMFAPAIACGNAFILKPSERDPS 180
           SEFTEGAGPGIDMYS+RQPVG+GAGITPFNFPGMIPMWMFAPAIACGNAFILKPSERDPS
Sbjct: 121 SEFTEGAGPGIDMYSMRQPVGVGAGITPFNFPGMIPMWMFAPAIACGNAFILKPSERDPS 180

Query: 181 VPIRLAELMIEAGLPAGILNVVNGDKGAVDAILTHPDIAAVSFVGSTPIARYVYGTAAMN 240
           VPIRLAELMIEAGLPAGILNVVNGDKGAVDAILTHPDIAAVSFVGSTPIARYVYGTAAMN
Sbjct: 181 VPIRLAELMIEAGLPAGILNVVNGDKGAVDAILTHPDIAAVSFVGSTPIARYVYGTAAMN 240

Query: 241 GKRAQCFGGAKNHMIIMPDADLDQAANALIGAGYGSAGERCMAISVAVPVGEETANRLID 300
           GKRAQCFGGAKNHMIIMPDADLDQAANALIGAGYGSAGERCMAISVAVPVGEETANRLID
Sbjct: 241 GKRAQCFGGAKNHMIIMPDADLDQAANALIGAGYGSAGERCMAISVAVPVGEETANRLID 300

Query: 301 KLVPMVESLRIGPYTDEKADMGPVVTKEAEQRIRSLIDSGIEQGAKLVVDGRDFKLQGYE 360
           KLVPMVESLRIGPYTD+KADMGPVVTKEAEQRIR LI+SGIEQGAKLVVDGRDFKLQGYE
Sbjct: 301 KLVPMVESLRIGPYTDDKADMGPVVTKEAEQRIRGLIESGIEQGAKLVVDGRDFKLQGYE 360

Query: 361 NGHFIGGCLFDDVTPDMDIYKTEIFGPVLSVVRARNYEEALSLPMKHEYGNGVAIYTRDG 420
           NGHF+GGCLFD VTPDMDIYKTEIFGPVLSVVRA NYEEALSLPMKHEYGNGVAIYTRDG
Sbjct: 361 NGHFVGGCLFDHVTPDMDIYKTEIFGPVLSVVRATNYEEALSLPMKHEYGNGVAIYTRDG 420

Query: 421 DAARDFASRINIGMVGVNVPIPVPLAYHSFGGWKSSSFGDLNQHGTDSIKFWTRTKTITS 480
           DAARDFASRINIGMVGVNVPIPVPLAYHSFGGWKSSSFGDLNQHG DSIKFWTRTKTITS
Sbjct: 421 DAARDFASRINIGMVGVNVPIPVPLAYHSFGGWKSSSFGDLNQHGPDSIKFWTRTKTITS 480

Query: 481 RWPSGIKDGAEFSIPTMR 498
           RWPSGIKDGAEFSIPTMR
Sbjct: 481 RWPSGIKDGAEFSIPTMR 498


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: 989
Number of extensions: 22
Number of successful extensions: 1
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: 498
Length adjustment: 34
Effective length of query: 464
Effective length of database: 464
Effective search space:   215296
Effective search space used:   215296
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.

Downloads

Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

Related tools

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 2024 update 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

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