GapMind for catabolism of small carbon sources

 

Aligments for a candidate for fadB in Paraburkholderia bryophila 376MFSha3.1

Align (S)-3-hydroxybutanoyl-CoA dehydrogeanse (EC 1.1.1.35) (characterized)
to candidate H281DRAFT_05521 H281DRAFT_05521 3-hydroxyacyl-CoA dehydrogenase

Query= metacyc::MONOMER-19851
         (285 letters)



>lcl|FitnessBrowser__Burk376:H281DRAFT_05521 H281DRAFT_05521
           3-hydroxyacyl-CoA dehydrogenase
          Length = 283

 Score =  324 bits (830), Expect = 2e-93
 Identities = 164/278 (58%), Positives = 211/278 (75%)

Query: 8   IGVIGAGTMGNGIAQVCAVAGLNVTMLDVDDAALKRGMDTIIRNLDRMVAKEKLTASARD 67
           +G+IGAGTMGNGIAQ  A+AG++V ++DV  AAL  G  T++ +L R+ +K  L  +  +
Sbjct: 6   VGIIGAGTMGNGIAQTVALAGIDVVLIDVSQAALASGFATMVTSLQRLTSKGILEPALSE 65

Query: 68  AALAKISTGLDYGALQSADMVIEAATENLGLKLKILRQVANCVGKDAIIATNTSSISITQ 127
           AALA+I   +DY +L+ A++VIEAATEN+ LK  IL++V   V   AIIA+NTSSISIT+
Sbjct: 66  AALARIERSMDYASLRDAELVIEAATENVALKRDILKKVEAVVSSGAIIASNTSSISITE 125

Query: 128 LGAVLDAPECFIGIHFFNPVPLMSLLEVIRGVQTSDATHAATMAFAQKVGKAPITVRNSP 187
           + A LD P  F+G+HFFNPVPL+ L+EVIRG+QT++    +   FA+ + K PI+V NSP
Sbjct: 126 MAATLDDPSRFVGMHFFNPVPLLPLVEVIRGLQTAEDVANSVEQFARDLNKTPISVNNSP 185

Query: 188 GFVVNRILCPMINEAIFVLQEGLASAEGIDVGMRLGCNHPIGPLALADMIGLDTLLSIMG 247
           GFVVNRIL PMINEA FVL EG+ASA  ID G++LG NHPIGPL LAD+IGLD  LS+M 
Sbjct: 186 GFVVNRILVPMINEAFFVLAEGVASAAEIDAGLKLGANHPIGPLGLADLIGLDVCLSVMD 245

Query: 248 VLYDEFNDPKYRPALLLKEMVAAGRLGRKTKQGFYSYS 285
           VL ++  D KYR + LL+EMVAAGRLGRK+KQG YSYS
Sbjct: 246 VLTNDLGDQKYRASPLLREMVAAGRLGRKSKQGVYSYS 283


Lambda     K      H
   0.321    0.137    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: 265
Number of extensions: 10
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: 285
Length of database: 283
Length adjustment: 26
Effective length of query: 259
Effective length of database: 257
Effective search space:    66563
Effective search space used:    66563
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 (21.9 bits)
S2: 47 (22.7 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