GapMind for catabolism of small carbon sources

 

Alignments for a candidate for livJ in Burkholderia phytofirmans PsJN

Align Leucine-, isoleucine-, valine-, threonine-, and alanine-binding protein; LIVAT-BP; Leu/Ile/Val/Thr/Ala-binding protein (characterized)
to candidate BPHYT_RS26525 BPHYT_RS26525 amino acid ABC transporter substrate-binding protein

Query= SwissProt::P21175
         (373 letters)



>FitnessBrowser__BFirm:BPHYT_RS26525
          Length = 383

 Score =  201 bits (512), Expect = 2e-56
 Identities = 118/353 (33%), Positives = 193/353 (54%), Gaps = 6/353 (1%)

Query: 16  AIAGFASYSMAADT--IKIALAGPVTGPVAQYGDMQRAGALMAIEQIN-KAGGVNGAQLE 72
           A+A +  +S AAD   +KI   GP+TGPVA+ G   + GA +A+++ N K   + G  ++
Sbjct: 14  ALATYMPFSWAADPQIVKIGFVGPLTGPVARVGKDLQYGAQLALDEENAKNPMIGGKPVK 73

Query: 73  GV--IYDDACDPKQAVAVANKVVNDGVKFVVGHVCSSSTQPATDIYEDEGVLMITPSATA 130
            V  + DD  DP+ A+ VA K+V+DGV  V+GH  S  + PA+ +Y    V MITP +T 
Sbjct: 74  FVLDVQDDQADPRVAIQVAQKLVDDGVVGVIGHYNSGCSIPASTVYHQANVAMITPGSTN 133

Query: 131 PEITSRGYKLIFRTIGLDNMQGPVAGKFIAERYKDKTIAVLHDKQQYGEGIATEVKKTVE 190
           P++T +G+K +FRT+G D + G VAG F+ E+ K K IA++ D+  +G+G+A   +K V+
Sbjct: 134 PQLTKQGFKNVFRTMGHDGIGGVVAGHFVVEQMKAKRIAIIDDRTAFGQGLADAFEKGVK 193

Query: 191 DAGIKVAVFEGLNAGDKDFNALISKLKKAGVQFVYFGGYHPEMGLLLRQAKQAGLDARFM 250
           +A   +   E  N    DF A+++ LK   V  ++FGG   +  +L++Q +  G+  +  
Sbjct: 194 EANGNIVDREFTNDKAIDFRAILTTLKSKNVDLIFFGGLDEQGAMLVKQMRSLGMSTQLF 253

Query: 251 GPEGVGNSEITAIAGDASEGMLATLP-RAFEQDPKNKALIDAFKAKNQDPSGIFVLPAYS 309
           G   + ++    IAG A  G     P  A ++ P  +A    +KA+      ++   +Y 
Sbjct: 254 GAGALKSNAFLQIAGTAGNGTQDLEPGPALDKLPAAQAFGKRYKARFNQDVELYAPFSYD 313

Query: 310 AVTVIAKGIEKAGEADPEKVAEALRANTFETPTGNLGFDEKGDLKNFDFTVYE 362
           A   + K I  A   D  K+ ++L   T    TGN+ FD  GDL    +T+++
Sbjct: 314 AALAMLKAIHTADSLDRAKIVDSLAKVTVTGVTGNITFDPYGDLIKPPYTLFQ 366


Lambda     K      H
   0.316    0.133    0.377 

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: 345
Number of extensions: 10
Number of successful extensions: 3
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 1
Length of query: 373
Length of database: 383
Length adjustment: 30
Effective length of query: 343
Effective length of database: 353
Effective search space:   121079
Effective search space used:   121079
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 (21.6 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 (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