GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__pseudo5_N2C3_1:AO356_07870
          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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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