GapMind for catabolism of small carbon sources

 

Alignments for a candidate for liuA in Dyella japonica UNC79MFTsu3.2

Align Isovaleryl-CoA dehydrogenase (EC 1.3.8.4) (characterized)
to candidate N515DRAFT_0484 N515DRAFT_0484 glutaryl-CoA dehydrogenase

Query= reanno::ANA3:7024494
         (389 letters)



>FitnessBrowser__Dyella79:N515DRAFT_0484
          Length = 389

 Score =  211 bits (537), Expect = 3e-59
 Identities = 124/373 (33%), Positives = 195/373 (52%), Gaps = 6/373 (1%)

Query: 12  LGEEVDMLRDAVQDFAKHEIAPIAAKVDHDNAFPNEIWPVLGGMGLLGVTVPEEYGGANM 71
           L +E  M++D V  F    + PI         FP E+ P + G+GLLG T+PE+YG A M
Sbjct: 17  LTDEERMVQDTVGRFVDERVLPIIGDAFDQGRFPKELIPEIAGLGLLGATLPEQYGCAGM 76

Query: 72  GYLAHVVAMEEISRASASIGLSYGAHSNLCVNQINRNGNAEQKAKYLPKLVSGEHIGALA 131
             +++ +  +E+ R  + +       S+LC+  I   G  EQK  YLPK+ +GE IG   
Sbjct: 77  NGVSYGLICQELERGDSGLRSFASVQSSLCMYPIYAYGTEEQKLHYLPKMAAGEIIGCFG 136

Query: 132 MSEPNAGSDVVSMKLHARKEGDRYILNGNKMWITNGPDANTYVIYAKTDLTKGAHGITAF 191
           ++EP+ GSD  +MK +ARK+G  +I+NG KMWITNG  A+  +++A+T+      GI  F
Sbjct: 137 LTEPHGGSDPANMKTNARKDGGDWIINGAKMWITNGNLAHIAIVWAQTE-----DGIQGF 191

Query: 192 IVERGFKGFSQAQKLDKLGMRGSNTCELVFEDVEVPEENILGGLNNGVKVLMSGLDYERV 251
           IV    +GF+  +   K+ +R S T  L F+ V VPE N L  +  G+K  +  L   R 
Sbjct: 192 IVPTDSQGFTAQEVHKKMSLRASVTSALFFDSVRVPEANRLPNV-KGLKGPLGCLTQARY 250

Query: 252 VLSGGPLGIMNACMDIVVPYIHEREQFGKSIGEFQLVQGKLADMYTGMNAAKAYVYSVAK 311
            ++ GP+G   AC+  V+ Y  ER  FG+ +   Q +Q KLA+M   +  A+     + +
Sbjct: 251 GITWGPIGAAQACLKEVLDYTQERVLFGRPLASNQAIQLKLAEMARRITMAQLLSLQLGR 310

Query: 312 SCDRGETTRKDAAGAILYSAELATKMALDAIQLLGGNGYVNEYATGRLLRDAKLYEIGAG 371
             D G       + A   +  +A  +A +   +LGG G   E+   R   + +      G
Sbjct: 311 LKDAGNMQPTQVSLAKWNNCRIAIDIARECRDILGGAGITTEHVAIRHALNLESVITYEG 370

Query: 372 TSEIRRMLIGREL 384
           T  + ++++GREL
Sbjct: 371 TETVHQLVVGREL 383


Lambda     K      H
   0.316    0.135    0.388 

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: 337
Number of extensions: 14
Number of successful extensions: 3
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 (21.6 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