GapMind for catabolism of small carbon sources

 

Alignments for a candidate for ybhL in Weissella oryzae SG25

Align The YbhL (AceP) protein. Possibly a pmf-dependent acetate uptake transporter. [14C]Acetate uptake was inhibited by CCCP as well as cold acetate, serine, α-ketoglutarate, lactate, and succinate (M. Inouye, personal communication) (characterized)
to candidate WP_027699118.1 TT13_RS05825 Bax inhibitor-1/YccA family protein

Query= TCDB::P0AAC4
         (234 letters)



>NCBI__GCF_000691805.2:WP_027699118.1
          Length = 240

 Score =  133 bits (335), Expect = 3e-36
 Identities = 76/233 (32%), Positives = 137/233 (58%), Gaps = 4/233 (1%)

Query: 1   MDRFPRSDSIVQP-RAGLQTYMAQVYGWMTVGLLLTAFVAWYAANS-AAVMELLFTNRVF 58
           MD F     +V P  AGL ++  +VY +MT+ LL+TA  A+  A    A +  +F++ + 
Sbjct: 1   MDNFKPKMRVVNPDSAGLNSFFKRVYSYMTMALLVTAGTAYLGATIFRAQIIAIFSSGIS 60

Query: 59  LIGLIIAQLALVIVLSAMIQKLSAGVTTMLFMLYSALTGLTLSSIFIVYTAASIASTFVV 118
            + LI     +V + S  + +  A    ML M Y+ + G+  S+I +++  ++IA+  + 
Sbjct: 61  QLALIAVMFGIVWMFSRRVLQNPAQAFGML-MGYAVINGVFFSTIGLMFNLSTIAAALLT 119

Query: 119 TAGMFGAMSLYGYTTKRDLSGFGNMLFMALIGIVLASLVNFWLKSEALMWAVTYIGVIVF 178
           TA +F  M++YG+TTKR ++  G +LF  +I +++  ++N +  +  +   ++ +GVIVF
Sbjct: 120 TALLFAGMAVYGFTTKRSMASMGAILFGGVIALIIGGIINIFFFNSIVFLFLSVVGVIVF 179

Query: 179 VGLTAYDTQKLKNMGEQIDTRDTSNLRK-YSILGALTLYLDFINLFLMLLRIF 230
             LTAYD  +LK M  +   +  + + +  ++ GAL+LY+DFINLF+ +LR+F
Sbjct: 180 ALLTAYDMNRLKTMYNEYGGQGQATVEQGLAVSGALSLYMDFINLFIYILRLF 232


Lambda     K      H
   0.330    0.140    0.403 

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: 192
Number of extensions: 12
Number of successful extensions: 3
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: 234
Length of database: 240
Length adjustment: 23
Effective length of query: 211
Effective length of database: 217
Effective search space:    45787
Effective search space used:    45787
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 (21.9 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