GapMind for catabolism of small carbon sources

 

Alignments for a candidate for livJ 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)



>FitnessBrowser__BFirm:BPHYT_RS28270
          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:

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