GapMind for catabolism of small carbon sources

 

Aligments for a candidate for glpC in Escherichia coli BW25113

Align anaerobic glycerol-3-phosphate dehydrogenase subunit C (EC 1.1.5.3) (characterized)
to candidate 16350 b2243 sn-glycerol-3-phosphate dehydrogenase (anaerobic), small subunit (NCBI)

Query= ecocyc::ANGLYC3PDEHYDROGSUBUNITC-MONOMER
         (396 letters)



>lcl|FitnessBrowser__Keio:16350 b2243 sn-glycerol-3-phosphate
           dehydrogenase (anaerobic), small subunit (NCBI)
          Length = 396

 Score =  818 bits (2114), Expect = 0.0
 Identities = 396/396 (100%), Positives = 396/396 (100%)

Query: 1   MNDTSFENCIKCTVCTTACPVSRVNPGYPGPKQAGPDGERLRLKDGALYDEALKYCINCK 60
           MNDTSFENCIKCTVCTTACPVSRVNPGYPGPKQAGPDGERLRLKDGALYDEALKYCINCK
Sbjct: 1   MNDTSFENCIKCTVCTTACPVSRVNPGYPGPKQAGPDGERLRLKDGALYDEALKYCINCK 60

Query: 61  RCEVACPSDVKIGDIIQRARAKYDTTRPSLRNFVLSHTDLMGSVSTPFAPIVNTATSLKP 120
           RCEVACPSDVKIGDIIQRARAKYDTTRPSLRNFVLSHTDLMGSVSTPFAPIVNTATSLKP
Sbjct: 61  RCEVACPSDVKIGDIIQRARAKYDTTRPSLRNFVLSHTDLMGSVSTPFAPIVNTATSLKP 120

Query: 121 VRQLLDAALKIDHRRTLPKYSFGTFRRWYRSVAAQQAQYKDQVAFFHGCFVNYNHPQLGK 180
           VRQLLDAALKIDHRRTLPKYSFGTFRRWYRSVAAQQAQYKDQVAFFHGCFVNYNHPQLGK
Sbjct: 121 VRQLLDAALKIDHRRTLPKYSFGTFRRWYRSVAAQQAQYKDQVAFFHGCFVNYNHPQLGK 180

Query: 181 DLIKVLNAMGTGVQLLSKEKCCGVPLIANGFTDKARKQAITNVESIREAVGVKGIPVIAT 240
           DLIKVLNAMGTGVQLLSKEKCCGVPLIANGFTDKARKQAITNVESIREAVGVKGIPVIAT
Sbjct: 181 DLIKVLNAMGTGVQLLSKEKCCGVPLIANGFTDKARKQAITNVESIREAVGVKGIPVIAT 240

Query: 241 SSTCTFALRDEYPEVLNVDNKGLRDHIELATRWLWRKLDEGKTLPLKPLPLKVVYHTPCH 300
           SSTCTFALRDEYPEVLNVDNKGLRDHIELATRWLWRKLDEGKTLPLKPLPLKVVYHTPCH
Sbjct: 241 SSTCTFALRDEYPEVLNVDNKGLRDHIELATRWLWRKLDEGKTLPLKPLPLKVVYHTPCH 300

Query: 301 MEKMGWTLYTLELLRNIPGLELTVLDSQCCGIAGTYGFKKENYPTSQAIGAPLFRQIEES 360
           MEKMGWTLYTLELLRNIPGLELTVLDSQCCGIAGTYGFKKENYPTSQAIGAPLFRQIEES
Sbjct: 301 MEKMGWTLYTLELLRNIPGLELTVLDSQCCGIAGTYGFKKENYPTSQAIGAPLFRQIEES 360

Query: 361 GADLVVTDCETCKWQIEMSTSLRCEHPITLLAQALA 396
           GADLVVTDCETCKWQIEMSTSLRCEHPITLLAQALA
Sbjct: 361 GADLVVTDCETCKWQIEMSTSLRCEHPITLLAQALA 396


Lambda     K      H
   0.321    0.136    0.426 

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: 753
Number of extensions: 27
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: 396
Length of database: 396
Length adjustment: 31
Effective length of query: 365
Effective length of database: 365
Effective search space:   133225
Effective search space used:   133225
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: 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 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