GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__Burk376:H281DRAFT_02464
          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:

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