GapMind for catabolism of small carbon sources

 

Aligments for a candidate for mmsA in Klebsiella michiganensis M5al

Align Methylmalonate-semialdehyde dehydrogenase [inositol] (EC 1.2.1.27) (characterized)
to candidate BWI76_RS07615 BWI76_RS07615 betaine-aldehyde dehydrogenase

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



>lcl|FitnessBrowser__Koxy:BWI76_RS07615 BWI76_RS07615
           betaine-aldehyde dehydrogenase
          Length = 490

 Score =  242 bits (617), Expect = 2e-68
 Identities = 159/480 (33%), Positives = 246/480 (51%), Gaps = 18/480 (3%)

Query: 8   FIGGQKVDGASGRFGEVFDPNTGKVQARVALASAGELNTAIANAKVAQAAWAATNPQRRA 67
           +I G  V   SG+  E  +P  G+V A V  A   +++ A+ +A+  Q  WAA +   R+
Sbjct: 10  YIDGGYVSATSGKTFETINPANGEVLATVQAAGREDVDRAVKSAQKGQKIWAAMSAMERS 69

Query: 68  RVMFEFKRLLEVHMDELAALLSSEHGKVIADSKG-DIQRGLEVIEFACGVPHLLKGEYTQ 126
           R++ +   +L    DELA L + + GK ++++   DI  G +V+E+  G+   L+G    
Sbjct: 70  RILRKAVDILRARNDELARLETLDTGKPLSETAAVDIVTGADVLEYYAGLIPALEGSQIP 129

Query: 127 GAGPGIDVYSMRQPLGVVAGITPFNFPAMIPMWMFGPAIATGNAFILKPSERDPSVPVRL 186
                  VY+ R+PLGVVAGI  +N+P  I +W   PA+A GNA I KPSE  P   ++L
Sbjct: 130 LRDSSF-VYTRREPLGVVAGIGAWNYPIQIALWKSAPALAAGNAMIFKPSEVTPLTALKL 188

Query: 187 AELMIEAGLPPGVLNVVHG-DKDCVEAILDHPDIKAVSFVGSSDIAQSVFQRAGAAG-KR 244
           AE+  EAGLP GV NV+ G   +  + + +HPDI  +SF G     + V   A A+  K 
Sbjct: 189 AEIYREAGLPAGVFNVLPGTGAETGQYLTEHPDIAKISFTGGVASGKKVMANAAASSLKE 248

Query: 245 VQAMGGAKNHGLVMPDADLDQAVADIIGAAYGSAGERCM-ALPVVVPVGEKTATALREKL 303
           V    G K+  +V  DA LD A    + A + S+G+ C     V VP   +   A  EK+
Sbjct: 249 VTMELGGKSPLIVCEDASLDLAADIAMMANFYSSGQVCTNGTRVFVPT--RLKAAFEEKI 306

Query: 304 VAAIGGLRVGVSTDPDAHYGPVVSAAHKARIESYIQMGVDEGAELVVDGRGFSLQGHEEG 363
           +A +  +R G       ++GP+VS  H+  +  YI+ G  EGA L+  G     +G + G
Sbjct: 307 LARVARIRPGDLFAESTNFGPLVSFPHRDNVLRYIETGKQEGARLLCGGEALKGEGFDRG 366

Query: 364 FFVGPTLFDHVKPTSRSYHDEIFGPVLQMVRAESLEEGIALASRHQYGNGVAIFTRNGDA 423
            +V PT+F           +EIFGPV+ ++  +  EE +  A+  +YG    + T + + 
Sbjct: 367 AWVAPTVFTDCDDQMTIVREEIFGPVMSILSYDDEEEALRRANATEYGLAAGVVTPDLNR 426

Query: 424 AREFADQVEVGMVGINV----PIPVPVAYHSFGGWKRSGFGDLNQYGMDGVRFYTRTKTV 479
           A     ++E G+  IN     P  +PV     GG+K SG G  N  G+  +  YT+ K++
Sbjct: 427 AHRLIHRLEAGICWINTWGESPAEMPV-----GGYKHSGIGREN--GVQTLHSYTQIKSI 479


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: 590
Number of extensions: 32
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: 500
Length of database: 490
Length adjustment: 34
Effective length of query: 466
Effective length of database: 456
Effective search space:   212496
Effective search space used:   212496
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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 preprint 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