Aligments for a candidate for mmsA in Pseudomonas fluorescens FW300-N2C3

GapMind for catabolism of small carbon sources

Aligments for a candidate for mmsA in Pseudomonas fluorescens FW300-N2C3

Align malonate-semialdehyde dehydrogenase (acetylating) (EC 1.2.1.18); methylmalonate-semialdehyde dehydrogenase (CoA-acylating) (EC 1.2.1.27) (characterized)
to candidate AO356_07870 AO356_07870 methylmalonate-semialdehyde dehydrogenase

Query= BRENDA::Q02252
         (535 letters)



>lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_07870 AO356_07870
           methylmalonate-semialdehyde dehydrogenase
          Length = 508

 Score =  609 bits (1571), Expect = e-179
 Identities = 289/493 (58%), Positives = 378/493 (76%)

Query: 29  SASSFSSSVPTVKLFIGGKFVESKSDKWIDIHNPATNEVIGRVPQATKAEMDAAIASCKR 88
           S +   +++ TV+L I G++VES+S +W DI NPAT +V+ +VP AT +E+DAAIA+ +R
Sbjct: 4   SLTPSDTALQTVRLLIDGEWVESQSSEWHDIVNPATQQVLAKVPFATASEVDAAIAAAQR 63

Query: 89  AFPAWADTSVLSRQQVLLRYQQLIKENLKEIAKLITLEQGKTLADAEGDVFRGLQVVEHA 148
           AF  W  T + +R +++L+ Q LI+E+ K IA +++ EQGKT+ADAEGD+FRGL+VVEHA
Sbjct: 64  AFQTWKLTPIGARMRIMLKLQALIREHSKRIAAVLSAEQGKTIADAEGDIFRGLEVVEHA 123

Query: 149 CSVTSLMMGETMPSITKDMDLYSYRLPLGVCAGIAPFNFPAMIPLWMFPMAMVCGNTFLM 208
           CS+ +L MGE   ++   +D Y+ R P+GVCAGI PFNFPAMIPLWMFPMA+ CGNTF++
Sbjct: 124 CSIGTLQMGEFAENVAGGVDTYTLRQPIGVCAGITPFNFPAMIPLWMFPMAIACGNTFVL 183

Query: 209 KPSERVPGATMLLAKLLQDSGAPDGTLNIIHGQHEAVNFICDHPDIKAISFVGSNKAGEY 268
           KPSE+ P +TMLL +L  ++G P G LN++HG  + V+ +C H DIKA+SFVGS   G +
Sbjct: 184 KPSEQDPLSTMLLVELAIEAGVPAGVLNVVHGGKDVVDALCTHKDIKAVSFVGSTAVGTH 243

Query: 269 IFERGSRHGKRVQANMGAKNHGVVMPDANKENTLNQLVGAAFGAAGQRCMALSTAVLVGE 328
           +++   RHGKRVQ+ MGAKNH VV+PDAN+E TLN LVGA FGAAGQRCMA S  VLVG 
Sbjct: 244 VYDLAGRHGKRVQSMMGAKNHAVVLPDANREQTLNALVGAGFGAAGQRCMATSVVVLVGA 303

Query: 329 AKKWLPELVEHAKNLRVNAGDQPGADLGPLITPQAKERVCNLIDSGTKEGASILLDGRKI 388
           AK+WLPEL   A+ L+VNAG +PG D+GP+I+ +AK R+  LI+SG KEGA + LDGR I
Sbjct: 304 AKQWLPELKALAQKLKVNAGSEPGTDVGPVISKRAKARILELIESGVKEGAKLELDGRGI 363

Query: 389 KVKGYENGNFVGPTIISNVKPNMTCYKEEIFGPVLVVLETETLDEAIQIVNNNPYGNGTA 448
            V G+E GNFVGPT+ S V   M  Y EEIFGPVLVVLE +TLD+AI +VN NP+GNGT 
Sbjct: 364 SVPGFEQGNFVGPTLFSGVTTEMRIYTEEIFGPVLVVLEVDTLDQAIALVNANPFGNGTG 423

Query: 449 IFTTNGATARKYAHLVDVGQVGVNVPIPVPLPMFSFTGSRSSFRGDTNFYGKQGIQFYTQ 508
           +FT +GA ARK+   +DVGQVG+N+PIPVP+P FSFTGSR S  GD   YGKQ +QFYTQ
Sbjct: 424 LFTQSGAAARKFQSEIDVGQVGINIPIPVPVPFFSFTGSRGSKLGDLGPYGKQVVQFYTQ 483

Query: 509 LKTITSQWKEEDA 521
            KT+T++W ++D+
Sbjct: 484 TKTVTARWFDDDS 496


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: 654
Number of extensions: 28
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: 535
Length of database: 508
Length adjustment: 35
Effective length of query: 500
Effective length of database: 473
Effective search space:   236500
Effective search space used:   236500
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 Sep 17 2021. The underlying query database was built on Sep 17 2021.

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

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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:

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 paper from 2022 on GapMind for carbon sources, or view the source code.

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