GapMind for catabolism of small carbon sources

 

Alignments for a candidate for srlA in Sporolactobacillus vineae SL153

Align PTS system glucitol/sorbitol-specific EIIC component; EIIC-Gut; Glucitol/sorbitol permease IIC component (characterized)
to candidate WP_010631560.1 RH97_RS06585 PTS sorbitol transporter subunit IIC

Query= SwissProt::O32332
         (182 letters)



>NCBI__GCF_000246965.1:WP_010631560.1
          Length = 183

 Score =  246 bits (627), Expect = 2e-70
 Identities = 114/180 (63%), Positives = 146/180 (81%)

Query: 1   MDAIVYFAKGFMYLFEVGGNTFVSWVTGIIPKVLLLLVFMNSIIAFIGQDKVDRFAKFAS 60
           MD +V+ AKGF+ LF+ G  TF+SW++GI+P VL+LLV MNS+I  IGQD++++ A  +S
Sbjct: 1   MDILVFLAKGFIGLFQYGAKTFISWMSGIVPVVLMLLVAMNSLIRLIGQDRINKLAAKSS 60

Query: 61  RNVILAYGVLPFLSAFMLGNPMALSMGKFLPERMKPSYYASASYHCHTNSGIFPHINVGE 120
           +N +L Y VLPFL AFML NPMALS+G+FLPER KPSYYASA+Y CHT++GIFPHIN GE
Sbjct: 61  KNPLLRYMVLPFLGAFMLANPMALSLGRFLPERYKPSYYASAAYFCHTSNGIFPHINAGE 120

Query: 121 IFIYLGIANGITTLGLDPTALGLRYLLVGLVMNFFAGWVTDFTTKIVMRQQGIELSNQLK 180
           +FI+LGIA G+  LGLD T L LRYLLVGLV NFF GW+TDFTT  V +QQ ++LS +++
Sbjct: 121 LFIWLGIAQGVQKLGLDTTPLALRYLLVGLVANFFCGWITDFTTPWVEKQQNVKLSKEIE 180


Lambda     K      H
   0.329    0.144    0.437 

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: 169
Number of extensions: 3
Number of successful extensions: 1
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: 182
Length of database: 183
Length adjustment: 19
Effective length of query: 163
Effective length of database: 164
Effective search space:    26732
Effective search space used:    26732
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: 44 (21.6 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