GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__Marino:GFF2
          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:

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