GapMind for catabolism of small carbon sources

 

Alignments for a candidate for larD in Paraburkholderia bryophila 376MFSha3.1

Align D/L-lactic acid transporter; Lactate racemization operon protein LarD; Lactic acid channel (characterized)
to candidate H281DRAFT_04230 H281DRAFT_04230 glycerol uptake facilitator protein

Query= SwissProt::F9UST3
         (238 letters)



>FitnessBrowser__Burk376:H281DRAFT_04230
          Length = 237

 Score =  176 bits (446), Expect = 4e-49
 Identities = 89/228 (39%), Positives = 138/228 (60%), Gaps = 9/228 (3%)

Query: 6   IAEFMGTALMIIFGVGVHCSSVLKGTKYRGSGHIFAITTWGFGISVALFI---FGNVCIN 62
           IAEF+GTAL+++ G G   + +L  TK +G+  I  +  W   + +A+++   +    +N
Sbjct: 5   IAEFIGTALVVLLGDGAVANVLLARTKGKGADLIVIVMGWAMAVFIAVYVTASYSGAHLN 64

Query: 63  PAMVLAQCLLGNIAWSLFIPYSVAEVLGGVVGSVIVWIMYADHFKASTDEISPITIRNLF 122
           P + ++  L G  AW+    Y  A++LGG+ G+++VW+ Y  HF    D    + +   F
Sbjct: 65  PVVTISLALAGKFAWAKVPGYIAAQMLGGMAGALLVWVAYRQHFAKEGDADVKLGV---F 121

Query: 123 CTAPAVRNLPRNFFVELFDTFIFISGILAIS--EIKTPGIVPIGVGLLVWAIGMGLGGPT 180
           CTAPA+R++P N   E+  TF+ I G+L ++  ++    +  + VGLLV  IG+ LGGPT
Sbjct: 122 CTAPAIRSVPHNLLTEMIATFVLILGVLYLASPQVGLGALDALPVGLLVLGIGISLGGPT 181

Query: 181 GFAMNLARDMGPRIAHAILPIANKADSDWQYGIIVPGIAPFVGAAIAA 228
           G+AM+ ARD+ PR+ HA+LPI  K DSDW+Y  I P   P VG A+AA
Sbjct: 182 GYAMSPARDLSPRLMHALLPIPGKRDSDWRYAWI-PVCGPLVGGAVAA 228


Lambda     K      H
   0.330    0.145    0.470 

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: 215
Number of extensions: 10
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: 238
Length of database: 237
Length adjustment: 23
Effective length of query: 215
Effective length of database: 214
Effective search space:    46010
Effective search space used:    46010
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.8 bits)
S2: 46 (22.3 bits)

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

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