GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__Burk376:H281DRAFT_05521
          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 (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