GapMind for catabolism of small carbon sources

 

Alignments for a candidate for braF in Pandoraea thiooxydans ATSB16

Align High-affinity branched-chain amino acid transport ATP-binding protein BraF, component of Branched chain amino acid uptake transporter. Transports alanine (characterized)
to candidate WP_052892752.1 PATSB16_RS19085 branched-chain amino acid ABC transporter ATP-binding protein/permease

Query= TCDB::P21629
         (255 letters)



>NCBI__GCF_001931675.1:WP_052892752.1
          Length = 598

 Score =  199 bits (507), Expect = 8e-56
 Identities = 112/255 (43%), Positives = 157/255 (61%), Gaps = 7/255 (2%)

Query: 5   ILEVSGLTMRFGGLLAVNGVNLKVEEKQVVSMIGPNGAGKTTVFNCLTGFYQPTGGLIRL 64
           IL+V      FGGL+AVN V+ +V+  ++V +IGPNGAGK+T FN +TG  Q T G I  
Sbjct: 342 ILDVRAARKEFGGLVAVNDVSFQVKAGEIVGLIGPNGAGKSTTFNLVTGVLQATSGEITF 401

Query: 65  DGEEIQGLPGHKIARKGVVRTFQNVRLFKEMTAVENLLVAQH----RHLNTNFLAGLFKT 120
            GE I  L   +I ++G+ RTFQ+VRL   M+ +EN+ +  H    + L      G++ +
Sbjct: 402 HGERIDKLASREIVKRGIGRTFQHVRLLPTMSVLENVAIGAHLRDRQGLRRRPQGGVWSS 461

Query: 121 --PAFRRSEREAMEYAAHWLEEVNLTEFANRSAGTLAYGQQRRLEIARCMMTRPRILMLD 178
                R  E   M  AA  +E V L E     AG+LA GQQR LEIAR +   P +L+LD
Sbjct: 462 VLRLDRAEEAMLMHEAARQIERVGLGEHMYEEAGSLALGQQRILEIARALACDPTLLLLD 521

Query: 179 EPAAGLNPKETDDLKALIAKLRSEHNVTVLLIEHDMKLVMSISDHIVVINQGAPLADGTP 238
           EPAAGL  KE   L  L+ KL S+  ++VLL+EHDM  VM+++DH+VV+  G  +A+G P
Sbjct: 522 EPAAGLRYKEKQALAELLRKL-SDEGMSVLLVEHDMDFVMNLTDHLVVMEFGTKIAEGLP 580

Query: 239 EQIRDNPDVIKAYLG 253
           E ++ +P V++AYLG
Sbjct: 581 EDVQKDPAVLEAYLG 595


Lambda     K      H
   0.320    0.137    0.391 

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: 331
Number of extensions: 14
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: 255
Length of database: 598
Length adjustment: 30
Effective length of query: 225
Effective length of database: 568
Effective search space:   127800
Effective search space used:   127800
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 Sep 24 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