GapMind for catabolism of small carbon sources

 

Aligments for a candidate for mmsA in Paraburkholderia bryophila 376MFSha3.1

Align Methylmalonate-semialdehyde dehydrogenase [inositol] (EC 1.2.1.27) (characterized)
to candidate H281DRAFT_02464 H281DRAFT_02464 betaine aldehyde dehydrogenase

Query= reanno::Caulo:CCNA_01360
         (500 letters)



>lcl|FitnessBrowser__Burk376:H281DRAFT_02464 H281DRAFT_02464 betaine
           aldehyde dehydrogenase
          Length = 489

 Score =  265 bits (677), Expect = 3e-75
 Identities = 170/478 (35%), Positives = 251/478 (52%), Gaps = 15/478 (3%)

Query: 8   FIGGQKVDGASGRFGEVFDPNTGKVQARVALASAGELNTAIANAKVAQAAWAATNPQRRA 67
           +IGG  VD   G   +  DP  G+  A V  AS+ +++ A+ +A+  Q  WAA    +R+
Sbjct: 10  YIGGTYVDATGGETFDTVDPANGETLATVQQASSADVDRAVQSAREGQREWAALTGMQRS 69

Query: 68  RVMFEFKRLLEVHMDELAALLSSEHGKVIADSKG-DIQRGLEVIEFACGVPHLLKGEYTQ 126
           R++     +L    DELAAL + + GK IA+++  DI  G +VIE+  G+   ++G+   
Sbjct: 70  RILRRAVDILRERNDELAALETRDTGKPIAETQAVDIVTGADVIEYYAGLATAIEGQQIP 129

Query: 127 GAGPGIDVYSMRQPLGVVAGITPFNFPAMIPMWMFGPAIATGNAFILKPSERDPSVPVRL 186
              P   VY+ R+PLGV AGI  +N+P  I  W   PA+A GNA I KPSE  P   ++L
Sbjct: 130 -LRPTSFVYTRREPLGVCAGIGAWNYPIQIACWKSAPALAAGNAMIFKPSEVTPLSALKL 188

Query: 187 AELMIEAGLPPGVLNVVHGDKDCVEAILDHPDIKAVSFVGSSDIAQSVFQRAGAAG-KRV 245
           AE+  EAG+PPGV NVV GD      +  HPDI+ +SF G  +  + V   AGA+  K V
Sbjct: 189 AEIYTEAGVPPGVFNVVQGDGRVGAMLAAHPDIEKISFTGGVETGKKVMSMAGASSLKEV 248

Query: 246 QAMGGAKNHGLVMPDADLDQAVADIIGAAYGSAGERCMALPVVVPVGEKTATALREKLVA 305
               G K+  LV  DA+L++A    + A + S+G+ C      V V           ++ 
Sbjct: 249 TMELGGKSPLLVFDDANLERAADIAMSANFFSSGQVC-TNGTRVFVQRSVLERFEALVLE 307

Query: 306 AIGGLRVGVSTDPDAHYGPVVSAAHKARIESYIQMGVDEGAELVVDGRGFSLQGHEEGFF 365
            +  +RVG   D   ++GP+VSAA   ++  YI  GV EGA L+  G+  S     +G +
Sbjct: 308 RVKRIRVGAPGDASTNFGPLVSAAQLQKVLGYIDSGVQEGARLIAGGKRLSEGHFGQGQY 367

Query: 366 VGPTLFDHVKPTSRSYHDEIFGPVLQMVRAESLEEGIALASRHQYGNGVAIFTRNGDAAR 425
           V PT+F       R   +EIFGPV+ ++  ++ +E I  A+R  YG    + T N   A 
Sbjct: 368 VEPTVFTGCHDDMRIVREEIFGPVMSILIFDNEDEAIERANRTAYGLAAGVVTENLARAH 427

Query: 426 EFADQVEVGMVGINV----PIPVPVAYHSFGGWKRSGFGDLNQYGMDGVRFYTRTKTV 479
               ++E G+  IN     P  +PV     GG+K+SG G  N  G+  +  YTR K+V
Sbjct: 428 RVIHRLEAGICWINTWGESPAEMPV-----GGYKQSGVGREN--GITTLEHYTRIKSV 478


Lambda     K      H
   0.320    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: 589
Number of extensions: 23
Number of successful extensions: 4
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: 500
Length of database: 489
Length adjustment: 34
Effective length of query: 466
Effective length of database: 455
Effective search space:   212030
Effective search space used:   212030
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 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 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