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); methylmalonate-semialdehyde dehydrogenase (CoA-acylating) (EC 1.2.1.27) (characterized)
to candidate WP_085121241.1 B9O00_RS04475 aldehyde dehydrogenase family protein

Query= BRENDA::Q02252
         (535 letters)



>NCBI__GCF_900177295.1:WP_085121241.1
          Length = 484

 Score =  212 bits (540), Expect = 2e-59
 Identities = 142/472 (30%), Positives = 230/472 (48%), Gaps = 11/472 (2%)

Query: 44  IGGKFVESKSDKWIDIHNPATNEVIGRVPQATKAEMDAAIASCKRAFPAWADTSVLSRQQ 103
           IGG+   ++S +     NP     I +V ++  A++ AA+A+ + A P WA T  + R  
Sbjct: 12  IGGEERPAESGRSFANVNPHDGSEICQVARSEAADVSAAVAAARAAQPGWAATPAVQRGH 71

Query: 104 VLLRYQQLIKENLKEIAKLITLEQGKTLADAEGDVFRGLQVVEHACSVTSLMMGETMPSI 163
           +L +    ++    EIA  +  E GK L D++G+V   +            + G TMPS 
Sbjct: 72  ILHQVMNALEARADEIAAAVAAEAGKRLKDSKGEVGGAILCGRFFAGEGQRLFGRTMPSG 131

Query: 164 TKDMDLYSYRLPLGVCAGIAPFNFPAMIPLWMFPMAMVCGNTFLMKPSERVPGATMLLAK 223
           T +    + R P GV   I   N PA    W    A++CGN  ++K +E  P +  L+A+
Sbjct: 132 TPNKYNMTVRTPCGVAGLIIAANTPAPNFAWKVFPALICGNAVVLKSAEDTPVSAWLMAR 191

Query: 224 LLQDSGAPDGTLNIIHG-QHEAVNFICDHPDIKAISFVGSNKAGEYIFERGSRHGKRVQA 282
           + +++G P G LN++HG   EA   + DHP +  +SF GS   G  I E   R  K++  
Sbjct: 192 ICEEAGLPKGVLNVVHGLGAEAGQPLVDHPGVDVLSFTGSTAVGRRIAESCGRQLKKLSL 251

Query: 283 NMGAKNHGVVMPDANKENTLNQLVGAAFGAAGQRCMALSTAVLVGEA--KKWLPELVEHA 340
            +G KN  VV  DA+ +N +     +A+  AGQRC A  +  LV E+  + +  +LVE  
Sbjct: 252 ELGGKNPFVVCDDADLDNAVKWACLSAYSNAGQRC-AAGSRFLVFESVYEAFRDKLVEAT 310

Query: 341 KNLRVNAGDQPGADLGPLITPQAKERVCNLIDSGTKEGASILLDGRKIKVKGYENGNFVG 400
           +  ++  G +   DLGP+I  +    +   I+  T +GA +L+ GR+   KG     ++ 
Sbjct: 311 RAQKL--GVEEDCDLGPVINERQLNNMLGAIERATGKGAKVLIGGRRAGDKGC----YLE 364

Query: 401 PTIISNVKPNMTCYKEEIFGPVLVVLETETLDEAIQIVNNNPYGNGTAIFTTNGATARKY 460
           PT++    P+    + E+FGPV  +       +A+ + N++PYG    I T +   A  +
Sbjct: 365 PTVVEGAAPDDEISQTELFGPVASLYRVRDFAQALAMANDHPYGLTACIHTRSLDRALAF 424

Query: 461 AHLVDVGQVGVNVPIPVPLPMFSFTGSRSSFRGDTNFYGKQGIQFYTQLKTI 512
           +H V  G   VN       P   F G + S  G T   G + +  Y++LK I
Sbjct: 425 SHGVQAGATVVNAGTYGSEPHMPFGGPKQSGNG-TREPGTEALDVYSELKDI 475


Lambda     K      H
   0.318    0.133    0.391 

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: 560
Number of extensions: 28
Number of successful extensions: 5
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: 535
Length of database: 484
Length adjustment: 34
Effective length of query: 501
Effective length of database: 450
Effective search space:   225450
Effective search space used:   225450
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 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