GapMind for catabolism of small carbon sources

 

Alignments for a candidate for bztC in Burkholderia phytofirmans PsJN

Align BztC, component of Glutamate/glutamine/aspartate/asparagine porter (characterized)
to candidate BPHYT_RS13290 BPHYT_RS13290 cysteine ABC transporter permease

Query= TCDB::Q52665
         (434 letters)



>FitnessBrowser__BFirm:BPHYT_RS13290
          Length = 225

 Score = 91.3 bits (225), Expect = 3e-23
 Identities = 68/216 (31%), Positives = 112/216 (51%), Gaps = 23/216 (10%)

Query: 224 FGGFLLALVIGVTAIVVSLPLGILLALGRQSDMLIVKSLSVGIIEFV----RGVPLITLL 279
           + G +  + + + +  + L L  L+AL R    L     +V I+ F     RG PL+  L
Sbjct: 17  YAGLVFTVPLTLISFAIGLALAFLVALVR----LFGPKWAVAIVRFYVWLFRGSPLLVQL 72

Query: 280 FTASLLLQYFLPP-GTNFDLILRVVILVTLFAAAYIAEVIRGGLAALPRGQYEAADALGL 338
           F    ++ Y LP  G   D +   +I  +L   AY +EVIRG + ++P+GQ+EAA ++G+
Sbjct: 73  F----VIFYGLPNVGIVLDPLTAAIIGFSLNVGAYNSEVIRGVIESIPKGQWEAAYSMGM 128

Query: 339 DYWQAQRLIIMPQALKISIPGIVSSFIGLFKDTTLVAFVGLFDPLKGISNVVRSDMAWKG 398
              QA R  I+PQA ++++P + +SFI L KDT+L A +        +  V ++      
Sbjct: 129 TREQALRRAILPQAARVALPPLSNSFIALVKDTSLAAVL-------TVPEVFQAAQRIAS 181

Query: 399 TYWEP---YIFVALIFFLFNFSMSRYSMYLERKLKR 431
             +EP   Y   AL++ +F+  +S   + LERK  R
Sbjct: 182 VTYEPLILYTEAALVYLVFSSVLSSAQVRLERKFGR 217


Lambda     K      H
   0.329    0.143    0.457 

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: 314
Number of extensions: 26
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: 434
Length of database: 225
Length adjustment: 27
Effective length of query: 407
Effective length of database: 198
Effective search space:    80586
Effective search space used:    80586
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (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 (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