Alignments for a candidate for mmsA in Rhodomicrobium vannielii ATCC 17100

GapMind for catabolism of small carbon sources

Alignments for a candidate for mmsA in Rhodomicrobium vannielii ATCC 17100

Align malonate-semialdehyde dehydrogenase (acetylating) (EC 1.2.1.18) (characterized)
to candidate WP_013420951.1 RVAN_RS17095 CoA-acylating methylmalonate-semialdehyde dehydrogenase

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



>NCBI__GCF_000166055.1:WP_013420951.1
          Length = 496

 Score =  749 bits (1933), Expect = 0.0
 Identities = 357/495 (72%), Positives = 419/495 (84%)

Query: 3   ELGHFIDGKRVAGTSGRVSNIFNPATGEVQGTVALASDADLAAAVESAKAAQPKWAATNP 62
           ELGHF+ GK +AG SGR +++FNPATG+V+ TVALA+ A++ AAVE+AKAAQP WAA NP
Sbjct: 2   ELGHFVGGKMIAGQSGRFADVFNPATGKVEKTVALATKAEVRAAVENAKAAQPGWAAVNP 61

Query: 63  QRRARVFMKFVQLLNDNMNELAEMLSREHGKTIDDAKGDIVRGLEVCEFVIGIPHLQKSE 122
           QRRARV M+FV+LL+ +M++LAE LSREHGKT  DAKGDI+RGLEV EF IG PHL K E
Sbjct: 62  QRRARVIMEFVRLLHRDMDKLAEALSREHGKTFPDAKGDIIRGLEVAEFCIGAPHLLKGE 121

Query: 123 FTEGAGPGIDMYSIRQPVGIGAGITPFNFPGMIPMWMFAPAIACGNAFILKPSERDPSVP 182
           F+EG GPGID+YS+RQP+G+ AGITPFNFP MIPMW F PAIA GNAFILKPSER PSVP
Sbjct: 122 FSEGVGPGIDIYSVRQPLGVVAGITPFNFPAMIPMWKFCPAIAAGNAFILKPSERAPSVP 181

Query: 183 IRLAELMIEAGLPAGILNVVNGDKGAVDAILTHPDIAAVSFVGSTPIARYVYGTAAMNGK 242
           + LA LM EAGLP GILNVVNGDK AVDAIL   DI AV FVGST IA Y+Y      GK
Sbjct: 182 LMLAALMQEAGLPDGILNVVNGDKEAVDAILDDTDICAVGFVGSTAIAEYIYTRGCAAGK 241

Query: 243 RAQCFGGAKNHMIIMPDADLDQAANALIGAGYGSAGERCMAISVAVPVGEETANRLIDKL 302
           R QCFGGAKNHM+I PDADLDQ A+ALIGAGYG+AGERCMAISVAVP+G++TA+RL+++L
Sbjct: 242 RVQCFGGAKNHMVIAPDADLDQVADALIGAGYGAAGERCMAISVAVPIGKDTADRLLERL 301

Query: 303 VPMVESLRIGPYTDEKADMGPVVTKEAEQRIRSLIDSGIEQGAKLVVDGRDFKLQGYENG 362
           +P VE L++GPYT E  D GP+VT +A++R+  L+D GI +GA LVVDGR F LQGYE+G
Sbjct: 302 IPRVEKLKVGPYTSETVDFGPLVTADAKRRVLGLVDKGIAEGASLVVDGRGFSLQGYEDG 361

Query: 363 HFIGGCLFDDVTPDMDIYKTEIFGPVLSVVRARNYEEALSLPMKHEYGNGVAIYTRDGDA 422
            F+G CLFD+V PDM+IYK EIFGPVLS+VRA  YEEAL LPMKHEYGNGVAI+TRDGD 
Sbjct: 362 FFVGPCLFDNVKPDMEIYKAEIFGPVLSIVRADTYEEALDLPMKHEYGNGVAIFTRDGDT 421

Query: 423 ARDFASRINIGMVGVNVPIPVPLAYHSFGGWKSSSFGDLNQHGTDSIKFWTRTKTITSRW 482
           ARDFASR+N+GMVG+NVPIPVPLA+++FGGWK S FGDLNQ G DS +F+T+TKTITSRW
Sbjct: 422 ARDFASRVNVGMVGINVPIPVPLAHYTFGGWKRSGFGDLNQFGADSFRFYTKTKTITSRW 481

Query: 483 PSGIKDGAEFSIPTM 497
           PSG+K+GA F IPTM
Sbjct: 482 PSGVKEGASFVIPTM 496


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: 830
Number of extensions: 23
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: 496
Length adjustment: 34
Effective length of query: 464
Effective length of database: 462
Effective search space:   214368
Effective search space used:   214368
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