GapMind for catabolism of small carbon sources

 

Alignments for a candidate for levG in Weissella oryzae SG25

Align PTS system IID component, Man family, component of The hexose (glucose and fructose demonstrated) PTS uptake system (characterized)
to candidate WP_045477156.1 TT13_RS09605 PTS mannose/fructose/sorbose transporter family subunit IID

Query= TCDB::Q04GJ9
         (304 letters)



>NCBI__GCF_000691805.2:WP_045477156.1
          Length = 324

 Score =  380 bits (977), Expect = e-110
 Identities = 188/317 (59%), Positives = 244/317 (76%), Gaps = 17/317 (5%)

Query: 5   KITLTKGDRLHVAWRSTFIQGSWNYERMQNGGWVYALIPALNKLYKT-KEDRAAAYKRHL 63
           K+TL+KG R  V   S FIQGSWNYERMQN GW ++L+PAL +LYK   E+   A +RH+
Sbjct: 8   KVTLSKGTRFKVMMSSMFIQGSWNYERMQNVGWAFSLMPALKRLYKPGTEEAKLALQRHM 67

Query: 64  VFFNTHPYLASPIIGVTLALEEDRANGAPVDDVAIQGVKVGMMGPLAGVGDPVFWYTVRP 123
            FFNTHPYLASPI+GVTLALEE+RANGA +D+ AIQGVKVGMMGPLAG+GDPVFW+TVRP
Sbjct: 68  EFFNTHPYLASPILGVTLALEEERANGAKIDNAAIQGVKVGMMGPLAGIGDPVFWFTVRP 127

Query: 124 LLGALGATLALSGNVLGPILFWVLWNIIRWAFMWYTQEFGYRAGSRITDDLSGGLLKTVT 183
           ++GA+ A+LA+SG+++ PI+F+V WNIIR AF+WYTQEFGY+ G+ IT DL GG+L+ VT
Sbjct: 128 IIGAIAASLAVSGSIIAPIVFFVAWNIIRIAFLWYTQEFGYKQGTAITGDLGGGMLQKVT 187

Query: 184 RGASMMGMFVLAALIERWVSIKFT---PVVSKVTLSKGAYIDWGKLPSGTKGIREALTE- 239
           +GAS++GMFVL ALI+RWVSI +T    VVSK+ LSKGAY+DW  LPSG +GI+ A+T  
Sbjct: 188 KGASILGMFVLGALIQRWVSISWTGPNSVVSKLPLSKGAYLDWNSLPSGAQGIKTAITTL 247

Query: 240 ---------QANGLSLTKIQTTTLQQNLDSLIPGLMALLLTFACMWLLKK---KVSPIII 287
                      +G+ +T  + T LQ NL+ L+PGL ALLLTF  +WLL+K   + +P+ I
Sbjct: 248 FKQDASGNLTQSGVYMTPNKITYLQDNLNMLLPGLSALLLTFLVIWLLRKFKSRNTPLYI 307

Query: 288 ILGIFVIGVGGHLLGLL 304
           I+G+F+ G+  H  GL+
Sbjct: 308 IIGLFIFGILLHWAGLM 324


Lambda     K      H
   0.324    0.140    0.438 

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: 393
Number of extensions: 14
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: 304
Length of database: 324
Length adjustment: 27
Effective length of query: 277
Effective length of database: 297
Effective search space:    82269
Effective search space used:    82269
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (22.0 bits)
S2: 48 (23.1 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