GapMind for catabolism of small carbon sources

 

Aligments for a candidate for braG in Burkholderia phytofirmans PsJN

Align High-affinity branched-chain amino acid transport ATP-binding protein BraG, component of Branched chain amino acid uptake transporter. Transports alanine (characterized)
to candidate BPHYT_RS04430 BPHYT_RS04430 amino acid ABC transporter ATPase

Query= TCDB::P21630
         (233 letters)



>lcl|FitnessBrowser__BFirm:BPHYT_RS04430 BPHYT_RS04430 amino acid
           ABC transporter ATPase
          Length = 244

 Score =  215 bits (547), Expect = 7e-61
 Identities = 112/241 (46%), Positives = 158/241 (65%), Gaps = 9/241 (3%)

Query: 1   MLSFDKVSTYYGKIQALHDVSVEVKKGEIVTLIGANGAGKSTLLMTLCGSPQAASGSIRY 60
           MLS   +   YGK++ LH +S++V K  +VTLIG+NGAGK+T +  + G  + ++G I  
Sbjct: 1   MLSIRNLHAGYGKVKVLHGISIDVPKASVVTLIGSNGAGKTTTMRAISGMIRPSAGEITM 60

Query: 61  ----EGEELVGLPSSTIMRKSIAVVPEGRRVFSRLTVEENLAMGGF-----FTDKDDYQV 111
               + + +  L S  I R  +A  PEGRRVF+ ++V +NL +G F        + D + 
Sbjct: 61  GVGTDAKRIDALDSHRIARLGLAHSPEGRRVFATMSVTDNLILGAFPRLTSARPRGDVKA 120

Query: 112 QMDKVLELFPRLKERYEQRAGTMSGGEQQMLAIGRALMSKPKLLLLDEPSLGLAPIIIQQ 171
            +++ +E+FPRLKER  Q AGT+SGGEQQMLA+ RA+M  P L+LLDEPS+GLAPI++++
Sbjct: 121 DLERAIEMFPRLKERRHQLAGTLSGGEQQMLAMARAIMMNPDLVLLDEPSMGLAPILVEE 180

Query: 172 IFEIIEQLRREGVTVFLVEQNANQALKLADRAYVLENGRIVMHDTGAALLTNPKVRDAYL 231
           +F II  L+ +GVT+ LVEQ A  AL +AD  YVLENGRI  H     L  +P V+ AYL
Sbjct: 181 VFRIIGNLKSQGVTMLLVEQFAAAALNVADYGYVLENGRIAAHGPATELRNDPSVKAAYL 240

Query: 232 G 232
           G
Sbjct: 241 G 241


Lambda     K      H
   0.318    0.136    0.374 

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: 157
Number of extensions: 8
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: 233
Length of database: 244
Length adjustment: 23
Effective length of query: 210
Effective length of database: 221
Effective search space:    46410
Effective search space used:    46410
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 46 (22.3 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 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