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_089229754.1 B9O00_RS20310 betaine-aldehyde dehydrogenase

Query= metacyc::MONOMER-15203
         (503 letters)



>NCBI__GCF_900177295.1:WP_089229754.1
          Length = 477

 Score =  248 bits (633), Expect = 3e-70
 Identities = 152/465 (32%), Positives = 243/465 (52%), Gaps = 18/465 (3%)

Query: 24  EVTNPATGQVTGQVALASQADVDSAVAAAQAAFPAWSDTPPIRRARVMFKFLELLNAHKD 83
           E  +PATG+V  +V +A +A V++AVAAA+A F  WS      R RV+ +  E++ A  D
Sbjct: 15  ETRDPATGEVLAEVQVAGEAAVEAAVAAAEAGFRVWSRMTGTERGRVLRRAAEIVRARND 74

Query: 84  ELAEAITREHGKVFTDAQ-GEVARGIDIVEFACGIPQLLKGDYTEQVSTGIDNWTTRQPL 142
           EL+E  TR+ GK   +    + A G D +E+  G+   L G++ +        +T R+PL
Sbjct: 75  ELSEIETRDTGKPIQETLVADAASGADCLEYYGGLAGSLAGEHIDLGHAFA--YTRREPL 132

Query: 143 GVVAGITPFNFPVMVPMWMFPLAIAAGNSFVLKPSPLDPSASLMMADLLKQAGLPDGVFN 202
           G+ AGI  +N+P+ +  W    A+A GN+ + KP+ L P  ++ +A++ ++AGLPDGVFN
Sbjct: 133 GICAGIGAWNYPIQIACWKSAPALACGNAMIFKPAELTPLTAVKLAEIYREAGLPDGVFN 192

Query: 203 VVQGDKDSVEALIDHPDVKALSFVGSTPIANLIYERGARSGKRIQALGGAKNHMVVMPDA 262
           VVQG  ++   L  HP +  +S  G       +    A   K +    G K+ ++V  DA
Sbjct: 193 VVQGFAETGRLLTRHPKIAKVSLTGEVGTGRKVMADAAGGLKHVTLELGGKSPILVFEDA 252

Query: 263 NLDKAVDALIGAAYGSAGERCMAISVAVLVGDVADKIVPRLAERARDLKIKNGLELDAEM 322
           +LD+AV   +   + SAGE C   +   +   V    + +L  R   + + + L+   ++
Sbjct: 253 DLDRAVSGALLGNFFSAGEVCSNGTRVFVQESVRAAFLEKLVARTEAMTVGDPLDPATQV 312

Query: 323 GPIVTSQAHQRITGYIEKGVAEGAEMVVDGRDFDSSVTGEGCADGFWMGGTLFDHVTPEM 382
           G +++     ++ GYIE G AEGA  +  G      +T   CA G+++  T+FD    +M
Sbjct: 313 GALISEGHMAKVLGYIETGKAEGATALTGG----GRITEGACAKGWFVAPTVFDGCRDDM 368

Query: 383 TIYREEIFGPVLACVRVPDVATAIQLINDHEFGNGVSCFTESGSVAREFGRRIQVGMVGI 442
           T+ REEIFGPV+A +   D   AI+  N  +FG     FT   + A     R+Q G   I
Sbjct: 369 TVVREEIFGPVMAVLSFEDEEEAIRRANATDFGLSAGVFTRDLARAHRTIARLQAGTCWI 428

Query: 443 N----VPIPVPMAWHGFGGWKRSMFGDTHAYGEEGVRFYTKQKSI 483
           N     P+ +P     FGG K+S  G  +  G+  +  Y++ KS+
Sbjct: 429 NTYNVTPVEMP-----FGGVKQSGLGREN--GKAAIEHYSQLKSV 466


Lambda     K      H
   0.319    0.136    0.406 

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: 597
Number of extensions: 40
Number of successful extensions: 3
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: 503
Length of database: 477
Length adjustment: 34
Effective length of query: 469
Effective length of database: 443
Effective search space:   207767
Effective search space used:   207767
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 (21.8 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