GapMind for catabolism of small carbon sources

 

Aligments for a candidate for bztD in Phaeobacter inhibens BS107

Align BztD, component of Glutamate/glutamine/aspartate/asparagine porter (characterized)
to candidate GFF197 PGA1_c02010 glutamate/glutamine/aspartate/asparagine transport ATP-binding protein BztD

Query= TCDB::Q52666
         (263 letters)



>lcl|FitnessBrowser__Phaeo:GFF197 PGA1_c02010
           glutamate/glutamine/aspartate/asparagine transport
           ATP-binding protein BztD
          Length = 263

 Score =  445 bits (1144), Expect = e-130
 Identities = 218/263 (82%), Positives = 239/263 (90%)

Query: 1   MSEPSYDHQVDRSHMQVSDEIAIQISQMNKWYGQFHVLRDINLTVHRGERIVIAGPSGSG 60
           MSE   D  +DRS MQVSDE+AI+I+ MNKWYG FHVLRDINLTV++GERIVIAGPSGSG
Sbjct: 1   MSELMSDRAIDRSKMQVSDEVAIEINNMNKWYGSFHVLRDINLTVNQGERIVIAGPSGSG 60

Query: 61  KSTMIRCINRLEEHQSGKIIVDGIELTSDLKNIDKVRSEVGMVFQHFNLFPHLTILENLT 120
           KST+IRC+N LEEHQ G I+VDG EL++DLKNIDK+RSEVGMVFQHFNLFPHLTILEN T
Sbjct: 61  KSTLIRCLNALEEHQQGNIMVDGTELSNDLKNIDKIRSEVGMVFQHFNLFPHLTILENCT 120

Query: 121 LAPIWVRKVPKREAEETAMYYLEKVKIPEQAQKYPGQLSGGQQQRVAIARSLCMKPKIML 180
           LAPIWVRK PK+EAEE AM++LEKVKIP+QA KYPG LSGGQQQRVAIARSLCM P+IML
Sbjct: 121 LAPIWVRKTPKKEAEERAMHFLEKVKIPDQAHKYPGMLSGGQQQRVAIARSLCMMPRIML 180

Query: 181 FDEPTSALDPEMIKEVLDTMIQLAEEGMTMLCVTHEMGFAQAVANRVIFMADGQIVEQNN 240
           FDEPTSALDPEMIKEVLDTMI+LAEEGMTMLCVTHEMGFA+ VANRVIFM  GQIVEQN 
Sbjct: 181 FDEPTSALDPEMIKEVLDTMIELAEEGMTMLCVTHEMGFARQVANRVIFMDAGQIVEQNE 240

Query: 241 PHDFFHNPQSERTKQFLSQILGH 263
           P +FF+NPQSERTK FLSQILGH
Sbjct: 241 PEEFFNNPQSERTKLFLSQILGH 263


Lambda     K      H
   0.320    0.134    0.391 

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: 301
Number of extensions: 5
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: 263
Length of database: 263
Length adjustment: 25
Effective length of query: 238
Effective length of database: 238
Effective search space:    56644
Effective search space used:    56644
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: 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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 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