Alignments for a candidate for liuA in Magnetospirillum magneticum AMB-1

GapMind for catabolism of small carbon sources

Alignments for a candidate for liuA in Magnetospirillum magneticum AMB-1

Align Isovaleryl-CoA dehydrogenase (EC 1.3.8.4) (characterized)
to candidate WP_011383120.1 AMB_RS03480 isovaleryl-CoA dehydrogenase

Query= reanno::Smeli:SM_b21121
         (387 letters)



>NCBI__GCF_000009985.1:WP_011383120.1
          Length = 389

 Score =  617 bits (1591), Expect = 0.0
 Identities = 309/386 (80%), Positives = 331/386 (85%)

Query: 2   FEAGLNFALGEEIDALRASVRRFASERIAPLADDADRSNAFPMSLWREMGELGLLGITAD 61
           F + LNF LGE  D +R SV  FA+  IAP A + DRSN FP  LW  +G +GLLGIT D
Sbjct: 4   FNSALNFDLGETADMMRDSVAAFAATEIAPRAAEIDRSNEFPNELWPRLGAMGLLGITVD 63

Query: 62  EAHGGAGLGYLAHCVAMEEISRASASVGLSYGAHSNLCVNQINRNGKPAQKSRYLPKLIS 121
           E +GGAG+GYL H VAMEEISRASASVGLSYGAHSNLCVNQI RNG  AQK +YLPKLIS
Sbjct: 64  EKYGGAGMGYLEHVVAMEEISRASASVGLSYGAHSNLCVNQIKRNGTEAQKMKYLPKLIS 123

Query: 122 GEHVGALAMSEPGAGSDVVSMKLKADKRGDRYVLNGSKMWITNGPDADVLVVYAKTDPAA 181
           GE++GALAMSEP AGSDVVSMKLKA+K+GDRYVLNG+KMWITNGPDADV+VVYAKTD  A
Sbjct: 124 GEYIGALAMSEPNAGSDVVSMKLKAEKKGDRYVLNGTKMWITNGPDADVIVVYAKTDVTA 183

Query: 182 GPRGITAFLVEKAFPGFSAGQKLDKLGMRGSNTSELIFTDCEVPEENVLGGVGEGVKVLM 241
           GPRGITAFLVEK F GFS  QKLDKLGMRGSNT EL+F DCEVPEENVLG VG+GV VLM
Sbjct: 184 GPRGITAFLVEKTFKGFSVAQKLDKLGMRGSNTGELVFQDCEVPEENVLGAVGKGVNVLM 243

Query: 242 SGLDYERVVLSAGPLGIMAACLDVVVPYLHERKQFGQPIGEFQLMQGKLADMYVTMNAAR 301
           SGLDYERVVL+ GPLGIMAAC+DVVVPY+HER QFGQPIG FQLMQGKLADMY T NA R
Sbjct: 244 SGLDYERVVLTGGPLGIMAACMDVVVPYVHERTQFGQPIGTFQLMQGKLADMYTTFNACR 303

Query: 302 AYVYAVAAACDRGETARKDAAGCILYAAEKATAMALEAIQALGGNGYTNDYPAGRLLRDA 361
           AY YAVA ACDRGET+RKDAAG ILY AEKAT MALEAIQ LGGNGY N+Y  GRLLRDA
Sbjct: 304 AYTYAVAKACDRGETSRKDAAGVILYGAEKATWMALEAIQTLGGNGYINEYATGRLLRDA 363

Query: 362 KLYEIGAGTSEIRRMLIGRELFAETK 387
           KLYEIGAGTSEIRRMLIGRELF ETK
Sbjct: 364 KLYEIGAGTSEIRRMLIGRELFEETK 389


Lambda     K      H
   0.318    0.135    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: 475
Number of extensions: 11
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: 387
Length of database: 389
Length adjustment: 30
Effective length of query: 357
Effective length of database: 359
Effective search space:   128163
Effective search space used:   128163
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: 50 (23.9 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
the source code
instructions for running GapMind on your computer

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