GapMind for catabolism of small carbon sources

 

Alignments for a candidate for PGA1_c12640 in Klebsiella michiganensis M5al

Align D-lactate transporter, ATP-binding component (characterized)
to candidate BWI76_RS26335 BWI76_RS26335 ABC transporter ATP-binding protein

Query= reanno::Phaeo:GFF1248
         (251 letters)



>FitnessBrowser__Koxy:BWI76_RS26335
          Length = 255

 Score =  185 bits (469), Expect = 9e-52
 Identities = 94/251 (37%), Positives = 156/251 (62%), Gaps = 3/251 (1%)

Query: 3   ILEVKNVGKRFGGLQALSDVNLSVRENTVHAIIGPNGAGKSTLLNCLVGKLIPDTGSVMF 62
           +L V  +  RFGGL A+++V+L +RE  + ++IGPNGAGK+T+ NCL G   P  G++M 
Sbjct: 5   LLSVNGLMMRFGGLLAVNNVSLELREREIVSLIGPNGAGKTTVFNCLTGFYKPTGGTIML 64

Query: 63  DGKSVLGRAPYEINQMGISRVFQTPEIFGDLSVLENMMIPCFAK-RDGAFE--MNAISAV 119
             + + G    +I +MG+ R FQ   +F +++V+EN+++    + + G F   +   S  
Sbjct: 65  RDQHLEGLPGQQIARMGVVRTFQHVRLFREMTVIENLLVAQHQQLKTGVFSGLLKTPSFR 124

Query: 120 SGQRDILEKAEHMLEEMNMADKRHMNAASMSRGDKRRLEIGMCLSQEPRLLLLDEPTAGM 179
             Q + L++A   LE + + +  +  A++++ GD+RRLEI  C+  +P +L+LDEP AG+
Sbjct: 125 RAQSEALDRAATWLERIGLLEHANRQASNLAYGDQRRLEIARCMVTQPEILMLDEPAAGL 184

Query: 180 ARADTNNTIDLLKQIKSERDITIAIIEHDMHVVFSLADRITVLAQGTPLVEDDPQNIKGN 239
              +T    +L+ +++S  + TI +IEHDM +V  ++DRI V+ QGTPL    P+ I+ N
Sbjct: 185 NPKETKELDELIAELRSHHNTTILLIEHDMKLVMGISDRIYVVNQGTPLANGTPEEIRNN 244

Query: 240 PKVREAYLGES 250
           P V  AYLGE+
Sbjct: 245 PDVIRAYLGEA 255


Lambda     K      H
   0.318    0.135    0.379 

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: 174
Number of extensions: 5
Number of successful extensions: 2
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: 251
Length of database: 255
Length adjustment: 24
Effective length of query: 227
Effective length of database: 231
Effective search space:    52437
Effective search space used:    52437
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: 46 (22.3 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