GapMind for catabolism of small carbon sources

 

Alignments for a candidate for braF in Burkholderia phytofirmans PsJN

Align ATP-binding component of a broad range amino acid ABC transporter (characterized, see rationale)
to candidate BPHYT_RS19450 BPHYT_RS19450 metal-dependent hydrolase

Query= uniprot:Q1MCU2
         (292 letters)



>FitnessBrowser__BFirm:BPHYT_RS19450
          Length = 594

 Score =  195 bits (496), Expect = 2e-54
 Identities = 114/260 (43%), Positives = 157/260 (60%), Gaps = 12/260 (4%)

Query: 12  DTLLKVEHLSMKFGGLMAINDFSFEAKRGDITALIGPNGAGKTTVFNCITGFYKPTMGMI 71
           + LL V     +FGGL+A+ND SFE K G I  LIGPNGAGK+T FN +TG  + T G I
Sbjct: 344 EDLLTVNKARKQFGGLVAVNDVSFEVKAGQIIGLIGPNGAGKSTTFNLVTGVLQATSGEI 403

Query: 72  TFNQKSGKQYLLERLPDFRITKEARVARTFQNIRLFSGLTVLENLLVAQHNKLMKASGYT 131
           TF    G++  ++ L    I K   + RTFQ+++L  G+TVLEN+ +  H +       +
Sbjct: 404 TF---CGER--IDSLSSREIVKRG-IGRTFQHVKLLPGMTVLENVAIGAHLRGQAGVWRS 457

Query: 132 ILGLIGVGPYKREAAEAIELARFWLEKADLIDRADDPAGDLPYGAQRRLEIARAMCTGPE 191
           ++ L      +  A  A ++ R  LE+        D AG L  G QR LEIARA+C  P 
Sbjct: 458 VVRLNSAEEARLMAEAARQIRRVGLEQ-----HMYDEAGSLALGQQRILEIARALCCDPT 512

Query: 192 LLCLDEPAAGLNPRESATLNALLKSIRAETGTSILLIEHDMSVVMEISDHVVVLEYGQKI 251
           LL LDEPAAGL  +E   L  LL+ ++AE G S+LL+EHDM  VM ++D +VV+E+G +I
Sbjct: 513 LLLLDEPAAGLRYQEKLQLADLLRRLKAE-GMSVLLVEHDMDFVMNLTDRLVVMEFGTRI 571

Query: 252 SDGTPDHVKNDPRVIAAYLG 271
           ++G P  V+ DP V+ AYLG
Sbjct: 572 AEGLPQEVQQDPAVLEAYLG 591


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: 412
Number of extensions: 24
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: 594
Length adjustment: 31
Effective length of query: 261
Effective length of database: 563
Effective search space:   146943
Effective search space used:   146943
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 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