GapMind for catabolism of small carbon sources

 

Aligments for a candidate for deoD in Phaeobacter inhibens BS107

Align 5'-fluoro-5'-deoxy-adenosine phosphorylase (EC 2.4.2.1) (characterized)
to candidate GFF624 PGA1_c06380 putative methylthioadenosine phosphorylase

Query= metacyc::MONOMER-15923
         (299 letters)



>lcl|FitnessBrowser__Phaeo:GFF624 PGA1_c06380 putative
           methylthioadenosine phosphorylase
          Length = 337

 Score =  265 bits (678), Expect = 8e-76
 Identities = 143/279 (51%), Positives = 175/279 (62%), Gaps = 4/279 (1%)

Query: 15  LGIIGGSGLYEFPGLTDPEEFPVETPYGPPSAPPVVGTVGGRWVAFLARHGTGHRIPPSR 74
           + IIGGSGLY+  GL + E   VETP+G PS   + GT+ G  +AFL RHG GH   P+ 
Sbjct: 53  IAIIGGSGLYDIDGLQNAEWVTVETPWGAPSDQILTGTLDGVKMAFLPRHGRGHVHSPTE 112

Query: 75  IPVRANLYALKALGVTEVVSVSAVGSLREEYAPGHLVVPDQIIDRTRGGRPATFFSSGVV 134
           +P RAN+ ALK LGVT+V S+SA GS REE APG  V+ DQ IDRT   R  +FF +G V
Sbjct: 113 VPYRANIDALKRLGVTDVFSISACGSFREEMAPGDFVIVDQFIDRTFA-REKSFFGTGCV 171

Query: 135 VHVSLADPYCPRLRAALTDAARAAHPTVHPAGTYLCMEGPQFSTRAESQLYRAWGMDVIG 194
            HVS+A P C RL  A   AAR A   VH  GTYLCMEGPQFS+ AES++YR+WG DVIG
Sbjct: 172 AHVSVAHPTCERLSDAAETAARDAGINVHRGGTYLCMEGPQFSSMAESKMYRSWGCDVIG 231

Query: 195 MTAQPEAKLAREAELCYAGLSLVTDYDCWHTGHDSVDARTVAEVMAANVIAARAVLSGLA 254
           MT  PEAKLAREAELCYA +++VTD+D WH  H +V+   +   +  N    RA++  L 
Sbjct: 232 MTNMPEAKLAREAELCYASIAMVTDFDSWHPDHGAVEITDIIATLTGNSQNGRALVQRLP 291

Query: 255 HATAPADCACHHALDGAVLTDPLAAAQVPEEEVPALLRK 293
                   AC H  D A+     A    PE+   ALL K
Sbjct: 292 ALLGQTRAACPHGCDRAL---EHAIMTAPEKRSAALLAK 327


Lambda     K      H
   0.319    0.135    0.415 

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: 333
Number of extensions: 11
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: 299
Length of database: 337
Length adjustment: 27
Effective length of query: 272
Effective length of database: 310
Effective search space:    84320
Effective search space used:    84320
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 (21.8 bits)
S2: 48 (23.1 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, 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