GapMind for catabolism of small carbon sources

 

Alignments for a candidate for mmsA in Tistlia consotensis USBA 355

Align malonate-semialdehyde dehydrogenase (acetylating) (EC 1.2.1.18) (characterized)
to candidate WP_085123792.1 B9O00_RS16490 CoA-acylating methylmalonate-semialdehyde dehydrogenase

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



>NCBI__GCF_900177295.1:WP_085123792.1
          Length = 498

 Score =  672 bits (1733), Expect = 0.0
 Identities = 317/495 (64%), Positives = 396/495 (80%), Gaps = 1/495 (0%)

Query: 4   LGHFIDGKRVAGTSGRVSNIFNPATGEVQGTVALASDADLAAAVESAKAAQPKWAATNPQ 63
           L HFI G+ VAGTSGR S +FNPATGEV+  V LAS A+L +AV++AKAA P WAAT P 
Sbjct: 5   LHHFIGGRIVAGTSGRTSEVFNPATGEVKAKVDLASAAELDSAVQTAKAAFPGWAATAPL 64

Query: 64  RRARVFMKFVQLLNDNMNELAEMLSREHGKTIDDAKGDIVRGLEVCEFVIGIPHLQKSEF 123
           +RAR+  +F +LL  N  +LAE++  EHGK + DA G++ RG+EV EF  GIP L K EF
Sbjct: 65  QRARIMFRFKELLEANKAKLAELIGSEHGKVLGDAAGEVTRGIEVVEFACGIPQLLKGEF 124

Query: 124 TEGAGPGIDMYSIRQPVGIGAGITPFNFPGMIPMWMFAPAIACGNAFILKPSERDPSVPI 183
            E  G G+D YS+RQP+G+ AGITPFNFP M+PMWMF  A+ACGNAFILKPSERDPS P+
Sbjct: 125 NENVGTGVDAYSVRQPLGVVAGITPFNFPAMVPMWMFPVALACGNAFILKPSERDPSAPL 184

Query: 184 RLAELMIEAGLPAGILNVVNGDKGAVDAILTHPDIAAVSFVGSTPIARYVYGTAAMNGKR 243
            LAEL+ +AGLP G+ NVVNGDK AVDAIL HPDI AVSFVGSTPIA YVY T     KR
Sbjct: 185 YLAELLKQAGLPDGVFNVVNGDKEAVDAILAHPDIEAVSFVGSTPIAEYVYRTGTSTNKR 244

Query: 244 AQCFGGAKNHMIIMPDADLDQAANALIGAGYGSAGERCMAISVAVPVGEETANRLIDKLV 303
            Q  GGAKNHMI+MPDAD+DQA +AL+GA YGSAGERCMAISVAV VG +  ++L+++L 
Sbjct: 245 VQALGGAKNHMIVMPDADMDQATDALMGAAYGSAGERCMAISVAVAVG-DAGDKLMERLE 303

Query: 304 PMVESLRIGPYTDEKADMGPVVTKEAEQRIRSLIDSGIEQGAKLVVDGRDFKLQGYENGH 363
           P V  L+IG YTD +A+MGP+VT++  ++++  +D G+++GAKLVVDGRDF++QGYENG+
Sbjct: 304 PRVRGLKIGAYTDAEAEMGPLVTRQHYEKVKGYVDLGVQEGAKLVVDGRDFRMQGYENGY 363

Query: 364 FIGGCLFDDVTPDMDIYKTEIFGPVLSVVRARNYEEALSLPMKHEYGNGVAIYTRDGDAA 423
           FIGGCLFD+V P+M IYK EIFGPVL+V+R+ +YE+AL L   HE+GNG AI+TRDGDAA
Sbjct: 364 FIGGCLFDEVKPEMRIYKEEIFGPVLAVMRSGSYEDALDLVNAHEFGNGTAIFTRDGDAA 423

Query: 424 RDFASRINIGMVGVNVPIPVPLAYHSFGGWKSSSFGDLNQHGTDSIKFWTRTKTITSRWP 483
           R+FA R  IGMVG+NVPIPVP+A+HSFGGWK S FGD + HG + ++F+TR K +T+RWP
Sbjct: 424 RNFAQRARIGMVGINVPIPVPMAFHSFGGWKRSLFGDHHMHGPEGVRFYTRLKAVTTRWP 483

Query: 484 SGIKDGAEFSIPTMR 498
           +GI+ GAEF +PTM+
Sbjct: 484 TGIRSGAEFVMPTMK 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: 782
Number of extensions: 31
Number of successful extensions: 2
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.

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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