GapMind for catabolism of small carbon sources

 

Alignments for a candidate for braD in Burkholderia phytofirmans PsJN

Align Transmembrane component of a broad range amino acid ABC transporter (characterized, see rationale)
to candidate BPHYT_RS19475 BPHYT_RS19475 ABC transporter permease

Query= uniprot:Q1MCU0
         (300 letters)



>FitnessBrowser__BFirm:BPHYT_RS19475
          Length = 294

 Score =  144 bits (362), Expect = 3e-39
 Identities = 91/292 (31%), Positives = 152/292 (52%), Gaps = 13/292 (4%)

Query: 5   VQQLLNGLTLGSIYGLVAIGYTMVYGIIGMINFAHGDIFMLGGFAALIVFLVLTSIFAGL 64
           + QLL GL  GS Y ++++G  +++G++ +INFAHG +FMLG   A + F      + GL
Sbjct: 12  LSQLLLGLVNGSFYAILSLGLAVIFGLLNVINFAHGALFMLGAMLAWMGF-----SYFGL 66

Query: 65  PVAVLLLVMLVVAMLMTSLWNWTIERVAYRPLRGSFRLAPLITAIGMSITLSNFIQVTQG 124
           P      VMLV+A L+  L+   IER   R L     L  L+   G+++ +    +   G
Sbjct: 67  P----YWVMLVLAPLVVGLFGIAIERSMLRWLYKLDHLYGLLLTFGLTLVVEGVFRSIYG 122

Query: 125 PRNKP--IPPMVSSVYQFGNISVSLKQIIIIVITAVLLTIFWYIVNRTALGRAQRATEQD 182
              +P  +P  +S     G + +   +  ++V +  +    W+++ +T LG   RA  ++
Sbjct: 123 SSGQPYDVPSALSGATNLGFMFLPNYRAWVVVASLAVCFATWFVIEKTRLGAYLRAGTEN 182

Query: 183 RKMAALLGVNVDQTISITFVMGAALAAVAGTMYLMYYGVASFNDGFTPGVKAFTAAVLGG 242
            K+    G+NV   I++T+  G ALAA AG +      V+    G    +  F   V+GG
Sbjct: 183 PKLVEAFGINVPLMITLTYGFGVALAAFAGVLAAPVIQVSPLM-GQPMIITVFAVVVIGG 241

Query: 243 IGSLPGAVFGGLLIGLIESLWSAYFTIAYKDVATFAILAFVLIFKPTGILGR 294
           +GS+ G++  GLL+G+IE L   ++  A   V  F I+A VL+ +P G+ G+
Sbjct: 242 MGSIMGSILTGLLLGVIEGLTRVFYPEASATV-VFVIMALVLLVRPAGLFGK 292


Lambda     K      H
   0.329    0.143    0.421 

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: 302
Number of extensions: 11
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: 300
Length of database: 294
Length adjustment: 26
Effective length of query: 274
Effective length of database: 268
Effective search space:    73432
Effective search space used:    73432
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