GapMind for catabolism of small carbon sources

 

Alignments for a candidate for braF in Pandoraea thiooxydans ATSB16

Align ATP-binding component of a broad range amino acid ABC transporter (characterized, see rationale)
to candidate WP_052892752.1 PATSB16_RS19085 branched-chain amino acid ABC transporter ATP-binding protein/permease

Query= uniprot:Q1MCU2
         (292 letters)



>NCBI__GCF_001931675.1:WP_052892752.1
          Length = 598

 Score =  190 bits (483), Expect = 6e-53
 Identities = 109/263 (41%), Positives = 158/263 (60%), Gaps = 10/263 (3%)

Query: 12  DTLLKVEHLSMKFGGLMAINDFSFEAKRGDITALIGPNGAGKTTVFNCITGFYKPTMGMI 71
           + +L V     +FGGL+A+ND SF+ K G+I  LIGPNGAGK+T FN +TG  + T G I
Sbjct: 340 EVILDVRAARKEFGGLVAVNDVSFQVKAGEIVGLIGPNGAGKSTTFNLVTGVLQATSGEI 399

Query: 72  TFNQKSGKQYLLERLPDFRITKEARVARTFQNIRLFSGLTVLENLLVAQHNKLMKASGYT 131
           TF+ +      +++L    I K   + RTFQ++RL   ++VLEN+ +  H +  +     
Sbjct: 400 TFHGER-----IDKLASREIVKRG-IGRTFQHVRLLPTMSVLENVAIGAHLRDRQGLRRR 453

Query: 132 ILGLIGVGPYKREAAEAIEL---ARFWLEKADLIDRADDPAGDLPYGAQRRLEIARAMCT 188
             G +     + + AE   L   A   +E+  L +   + AG L  G QR LEIARA+  
Sbjct: 454 PQGGVWSSVLRLDRAEEAMLMHEAARQIERVGLGEHMYEEAGSLALGQQRILEIARALAC 513

Query: 189 GPELLCLDEPAAGLNPRESATLNALLKSIRAETGTSILLIEHDMSVVMEISDHVVVLEYG 248
            P LL LDEPAAGL  +E   L  LL+ + ++ G S+LL+EHDM  VM ++DH+VV+E+G
Sbjct: 514 DPTLLLLDEPAAGLRYKEKQALAELLRKL-SDEGMSVLLVEHDMDFVMNLTDHLVVMEFG 572

Query: 249 QKISDGTPDHVKNDPRVIAAYLG 271
            KI++G P+ V+ DP V+ AYLG
Sbjct: 573 TKIAEGLPEDVQKDPAVLEAYLG 595


Lambda     K      H
   0.318    0.136    0.386 

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: 19
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: 292
Length of database: 598
Length adjustment: 31
Effective length of query: 261
Effective length of database: 567
Effective search space:   147987
Effective search space used:   147987
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: 41 (21.7 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