GapMind for catabolism of small carbon sources

 

Alignments for a candidate for AZOBR_RS08245 in Paraburkholderia phymatum STM815

Align Leucine/isoleucine/valine ABC transporter,ATPase component; EC 3.6.3.- (characterized, see rationale)
to candidate WP_012402388.1 BPHY_RS15490 branched-chain amino acid ABC transporter ATP-binding protein/permease

Query= uniprot:G8ALJ0
         (294 letters)



>NCBI__GCF_000020045.1:WP_012402388.1
          Length = 594

 Score =  194 bits (494), Expect = 3e-54
 Identities = 118/267 (44%), Positives = 160/267 (59%), Gaps = 16/267 (5%)

Query: 7   TTTPLLTVEHLTMRFGGLVAVNDVSFSANNGEITAIIGPNGAGKTTLFNCITGFYTPTVG 66
           T  PLL V+    +FGGLVAVNDVSF    G+I  +IGPNGAGK+T FN +TG    T G
Sbjct: 342 TGEPLLVVDKARKQFGGLVAVNDVSFEVKAGQIIGLIGPNGAGKSTTFNLVTGVLQATSG 401

Query: 67  RLTLRHADGKEFLLERMPGYRISQ--KASVARTFQNIRLFGGMSVLENLIVAQHNKLIRA 124
            +T R         ER+      +  K  + RTFQ+++L  GM+VLEN+ +  H +    
Sbjct: 402 AITFRG--------ERIDALNSREIVKRGIGRTFQHVKLLPGMTVLENVAIGGHLRGRAG 453

Query: 125 SGFSIAGLLGLPSYTRTEREAVDLAKYWLDRVRLLEFADWEAGNLPYGAQRRLEIARAMC 184
              S+A L G       E   +  A   + RV L E    EAG+L  G QR LEIARA+C
Sbjct: 454 VWRSVARLNG-----AEEGRLMAEAARQIRRVGLEEHMYDEAGSLALGKQRILEIARALC 508

Query: 185 TEPVMLCLDEPAAGLNPRESGELADLLTYIRDEHKIGVLLIEHDMSVVMTISDHVVVLDY 244
            +P +L LDEPAAGL  +E  +LA LL  +R+E  + +LL+EHDM  VM ++D +VV+++
Sbjct: 509 CDPTLLLLDEPAAGLRYQEKQQLATLLRKLREE-GMSLLLVEHDMDFVMNLTDRLVVMEF 567

Query: 245 GRKISDGDPAFVKNDPAVIRAYLGEEE 271
           G +I++G P  V+NDPAV+ AYLG  E
Sbjct: 568 GTRIAEGLPQDVQNDPAVLEAYLGGVE 594


Lambda     K      H
   0.319    0.137    0.397 

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: 397
Number of extensions: 21
Number of successful extensions: 4
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: 294
Length of database: 594
Length adjustment: 31
Effective length of query: 263
Effective length of database: 563
Effective search space:   148069
Effective search space used:   148069
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 50 (23.9 bits)

This GapMind analysis is from Apr 09 2024. 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