GapMind for catabolism of small carbon sources

 

Aligments for a candidate for liuA in Marinobacter adhaerens HP15

Align Isovaleryl-CoA dehydrogenase (EC 1.3.8.4) (characterized)
to candidate GFF2 HP15_2 acyl-CoA dehydrogenase domain protein

Query= reanno::SB2B:6937192
         (389 letters)



>lcl|FitnessBrowser__Marino:GFF2 HP15_2 acyl-CoA dehydrogenase
           domain protein
          Length = 389

 Score =  616 bits (1589), Expect = 0.0
 Identities = 302/386 (78%), Positives = 341/386 (88%), Gaps = 1/386 (0%)

Query: 1   MSHLYSTLNFGLGEDVDMLRDAVYEFAKGEIAPLAEKVDRDNAFPNELWAKFGDMGLLGV 60
           M   YS LNFGLGE +DMLR+ +  FA  EIAP AE++DR+N FP +LW K GDMGLLG+
Sbjct: 1   MKSQYSELNFGLGETLDMLREQINGFAASEIAPRAEEIDRNNEFPMDLWRKMGDMGLLGI 60

Query: 61  TVAEEYGGVNMGYLAHVVAMEEISRASASIGLSYGAHSNLCVNQIYRNGNEAQRAKYLPK 120
           TV+EEYGG +MGYLAHV+AMEEISRASAS+GLSYGAHSNLCVNQI+RNG E Q+ KYLPK
Sbjct: 61  TVSEEYGGSDMGYLAHVIAMEEISRASASVGLSYGAHSNLCVNQIHRNGTEEQKQKYLPK 120

Query: 121 LISGEHIGALAMSEPNAGSDVVSMKLHARKEGDRYILNGNKMWITNGPDAHTYVIYAKTD 180
           L+SGEHIGALAMSEPNAGSDV+SMKL A+ EGD Y+LNGNKMWITNGPDA+TYVIYAKTD
Sbjct: 121 LVSGEHIGALAMSEPNAGSDVISMKLTAKDEGDHYLLNGNKMWITNGPDANTYVIYAKTD 180

Query: 181 LDKGPHGITAFIVERGFKGFSQAQKLDKLGMRGSNTCELVFEDCEVPEENILGGLNNGVK 240
              G  G+TAFIVER   GFS+ QKLDKLGMRGSNTCELVF+DC+VP+EN+LGG+ NG K
Sbjct: 181 TSAGSRGVTAFIVERDAPGFSRHQKLDKLGMRGSNTCELVFQDCKVPKENVLGGVGNGAK 240

Query: 241 VLMSGLDYERVVLSGGPLGIMTACMDIVVPYVHERVQFGKSIGEFQLVQGKLADMYTGMN 300
           VLMSGLDYER+VLSGGPLGIM A MD+VVPY+ ER QFG++IGEF+LVQGK+ADMYT MN
Sbjct: 241 VLMSGLDYERLVLSGGPLGIMQAAMDVVVPYIRERKQFGQAIGEFELVQGKVADMYTWMN 300

Query: 301 AAKSYVYNVARACDRG-ETTRKDAAGVILYAAELATKMALDAIQLLGGNGYVNEYATGRL 359
            AKSYVY VA + DRG ETTRKDAAG ILY+AE+ATK+ALDAIQLLGGNGY+NEY TGRL
Sbjct: 301 TAKSYVYMVAMSADRGAETTRKDAAGAILYSAEMATKIALDAIQLLGGNGYINEYPTGRL 360

Query: 360 LRDAKLYEIGAGTSEIRRMLIGRELF 385
           LRDAKLYEIGAGTSEIRRMLIGREL+
Sbjct: 361 LRDAKLYEIGAGTSEIRRMLIGRELY 386


Lambda     K      H
   0.318    0.137    0.396 

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: 575
Number of extensions: 14
Number of successful extensions: 2
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: 389
Length of database: 389
Length adjustment: 30
Effective length of query: 359
Effective length of database: 359
Effective search space:   128881
Effective search space used:   128881
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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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 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