GapMind for catabolism of small carbon sources

 

Aligments for a candidate for braC 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_RS01885 BPHYT_RS01885 branched-chain amino acid ABC transporter substrate-binding protein

Query= SwissProt::P21175
         (373 letters)



>lcl|FitnessBrowser__BFirm:BPHYT_RS01885 BPHYT_RS01885
           branched-chain amino acid ABC transporter
           substrate-binding protein
          Length = 381

 Score =  211 bits (538), Expect = 2e-59
 Identities = 121/363 (33%), Positives = 196/363 (53%), Gaps = 5/363 (1%)

Query: 6   QRLSRLFAAMAIAGFASYSMAADTI-KIALAGPVTGPVAQYGDMQRAGALMAIEQINKAG 64
           Q+L  + AA  +    + S AADT+ KI    P+TG +A  G     GA +A+E+IN  G
Sbjct: 6   QKLLPISAAAMLFATLATSAAADTVVKIGHVAPLTGGIAHLGKDNENGARLAVEEINAKG 65

Query: 65  GVNGAQ---LEGVIYDDACDPKQAVAVANKVVNDGVKFVVGHVCSSSTQPATDIYEDEGV 121
              G Q   L+    DDA DP+ A  VA K+V+D V  VVGH+ S ++ PA+ IY D G+
Sbjct: 66  LTIGGQKITLQLDAQDDAADPRTATQVAQKLVDDKVVAVVGHLNSGTSIPASKIYSDAGI 125

Query: 122 LMITPSATAPEITSRGYKLIFRTIGLDNMQGPVAGKFIAERYKDKTIAVLHDKQQYGEGI 181
           + I+PSAT P  T +G+K  +R +  D  QGP    + A+  K K++A++ D   YG+G+
Sbjct: 126 VQISPSATNPAYTQQGFKTTYRVVATDAQQGPALANYAAKGLKVKSVAIVDDSTAYGQGL 185

Query: 182 ATEVKKTVEDAGIKVAVFEGLNAGDKDFNALISKLKKAGVQFVYFGGYHPEMGLLLRQAK 241
           A E +KT +  G+ V   +  N    DF A+++K+K      + +GG     G   +QAK
Sbjct: 186 ANEFEKTAKSLGLNVMSHDATNDKAVDFRAILTKIKGENPDAIMYGGMDATGGPFAKQAK 245

Query: 242 QAGLDARFMGPEGVGNSEITAIAGDASEGMLAT-LPRAFEQDPKNKALIDAFKAKNQDPS 300
           Q GL A+ +  +GV   ++  +AGDA++ ++ +    A E+     A +  ++ +   P 
Sbjct: 246 QLGLRAKVLAGDGVCTDKLADLAGDATDNIVCSEAGMALEKMAGGSAFLAKYQKRFGQPI 305

Query: 301 GIFVLPAYSAVTVIAKGIEKAGEADPEKVAEALRANTFETPTGNLGFDEKGDLKNFDFTV 360
            I+    Y AV +I   +++A   DP K+  A+ +  ++   G   FD KGDL++   ++
Sbjct: 306 QIYAPFTYDAVYIIVDAMKRANSTDPAKILAAMPSTDYKGVIGETTFDSKGDLQHGVISL 365

Query: 361 YEW 363
           Y +
Sbjct: 366 YNY 368


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: 393
Number of extensions: 17
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: 373
Length of database: 381
Length adjustment: 30
Effective length of query: 343
Effective length of database: 351
Effective search space:   120393
Effective search space used:   120393
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 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