GapMind for catabolism of small carbon sources

 

Aligments for a candidate for Ac3H11_2396 in Burkholderia phytofirmans PsJN

Align Branched chain amino acid ABC transporter substrate-binding protein (characterized, see rationale)
to candidate BPHYT_RS28270 BPHYT_RS28270 ABC transporter substrate-binding protein

Query= uniprot:A0A165KTD4
         (375 letters)



>lcl|FitnessBrowser__BFirm:BPHYT_RS28270 BPHYT_RS28270 ABC
           transporter substrate-binding protein
          Length = 373

 Score =  343 bits (881), Expect = 3e-99
 Identities = 182/372 (48%), Positives = 245/372 (65%), Gaps = 5/372 (1%)

Query: 4   KLKLTVVAAIAAAAGVASAQEQVVKIGHVAPVSGAQAHYGKDNENGARMAIEELNAQGVT 63
           +L +T  A +AA   ++++ + VV IGH AP++G QA  GKDNENGAR+AI+ELN  GVT
Sbjct: 3   RLAMTAAALMAAGFTLSASAQVVVTIGHSAPLTGPQAPNGKDNENGARLAIDELNKSGVT 62

Query: 64  IGGKKIKFELVAEDDAADPKQGTAAAQKLCDAKVAGVVGHLNSGTTIPASKVYNDCGIPH 123
           + G+K+ F+L +EDD ADPK G   AQKL D+ V  VVG  NSG  IPAS+VYN   +P 
Sbjct: 63  VAGQKVTFKLDSEDDQADPKIGVQVAQKLVDSGVVAVVGPYNSGVAIPASRVYNTGNVPM 122

Query: 124 VTGAATNPNLTKPGYKTTFRIIANDNALGAGLAFYAVDTLKLKTVAIIDDRTAYGQGVAD 183
           +   A+NP LT+ G+K  FRI A+D  LG  +  +A  TLK KT A+IDDRTAYGQGVA+
Sbjct: 123 LP-VASNPALTRQGFKNIFRIGASDEQLGGTMGQFAAKTLKAKTAAVIDDRTAYGQGVAE 181

Query: 184 VFKKTATAKGMKVVDEQFTTDKATDFMAILTAIKAKNPDAIFYGGMDPQGGPMLRQMEQL 243
            F K A A G+++V+++FT   ATDF++ILT IKAKNPD IF+GG   QG PM +QM Q 
Sbjct: 182 QFVKVAKANGIQIVEQEFTNSSATDFLSILTTIKAKNPDVIFFGGYAAQGAPMAKQMRQR 241

Query: 244 GMGNVKYFGGDGICTSEIAKLAAGAKTLGNVICAEGGSSLAKMPGGTAWKAKYDAKYPNQ 303
           G+   K  GGDGIC++++ K+A  A ++  V CA+GG +L K   G  +  KY A Y   
Sbjct: 242 GL-RAKLLGGDGICSADMGKVAGEAASI--VYCAQGGIALEKTAAGREFLQKYKAAYNID 298

Query: 304 FQVYSPYTYDATFLIVDAMKRANSVDPKV-YTPELAKSSFKGVTSTIAFEPNGEMKNPAI 362
            QVY+   YD   L+ DAM +A +   K   T +LAK ++KGV  T +F+  G++K    
Sbjct: 299 TQVYAVSYYDGVKLLADAMVKAGTTTDKAKLTAQLAKENYKGVAGTYSFDEYGDLKGAPT 358

Query: 363 TLYVYKDGKKTP 374
           T+YV K+G  TP
Sbjct: 359 TVYVIKNGLPTP 370


Lambda     K      H
   0.315    0.131    0.375 

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: 452
Number of extensions: 26
Number of successful extensions: 5
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: 375
Length of database: 373
Length adjustment: 30
Effective length of query: 345
Effective length of database: 343
Effective search space:   118335
Effective search space used:   118335
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: 42 (22.0 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