GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__Phaeo:GFF197
          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:

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