GapMind for catabolism of small carbon sources

 

Alignments for a candidate for larD in Lactobacillus silagei IWT126

Align D/L-lactic acid transporter; Lactate racemization operon protein LarD; Lactic acid channel (characterized)
to candidate WP_089136227.1 CES79_RS02655 aquaporin family protein

Query= SwissProt::F9UST3
         (238 letters)



>NCBI__GCF_002217945.1:WP_089136227.1
          Length = 236

 Score =  141 bits (355), Expect = 1e-38
 Identities = 79/227 (34%), Positives = 121/227 (53%), Gaps = 7/227 (3%)

Query: 6   IAEFMGTALMIIFGVGVHCSSVLKGTKYRGSGHIFAITTWGFGISVALFIFGNVC----I 61
           I EF GT ++I  G G   S  L     +G+  ++   +WG  +++ ++  G +     +
Sbjct: 5   IGEFFGTMVLITLGAGTGASFNLNKAYAQGANWLYVSLSWGLAVTMGVYTAGVLGSDGHL 64

Query: 62  NPAMVLAQCLLGNIAWSLFIPYSVAEVLGGVVGSVIVWIMYADHFKASTDEISPITIRNL 121
           NPA+ +     G   WSL IPY + + LG  VG+ IV + +  HFKA+  E     +  +
Sbjct: 65  NPAVTIGFACAGLFKWSLVIPYLLGQFLGAFVGAAIVIVHFYPHFKATKTEEEGNQV-GI 123

Query: 122 FCTAPAVRNLPRNFFVELFDTFIFISGILAISEIKTPGIVPIGVGLLVWAIGMGLGGPTG 181
           F T PA+     NF  E+  TF F+  +L +    T G+ P+ VGL++  +G  LG  TG
Sbjct: 124 FATVPAINAPIWNFLSEVIATFFFVFILLNLGNF-TQGLKPLIVGLVITVVGTALGSTTG 182

Query: 182 FAMNLARDMGPRIAHAILPIANKADSDWQYGIIVPGIAPFVGAAIAA 228
           FA+N ARD GPR A+ +LP+ N+  + W+Y   VP   P VG  IA+
Sbjct: 183 FALNPARDWGPRFAYTVLPVPNRGRTHWEYA-WVPMCGPLVGGIIAS 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: 242
Number of extensions: 17
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: 236
Length adjustment: 23
Effective length of query: 215
Effective length of database: 213
Effective search space:    45795
Effective search space used:    45795
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 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