GapMind for catabolism of small carbon sources

 

Alignments for a candidate for larD in Catellicoccus marimammalium M35/04/3

Align Glycerol uptake facilitator protein 4; D/L-lactic acid transporter; Lactic acid channel (characterized)
to candidate WP_009491900.1 C683_RS05610 aquaporin family protein

Query= SwissProt::F9UMX3
         (238 letters)



>NCBI__GCF_000313915.1:WP_009491900.1
          Length = 245

 Score =  119 bits (299), Expect = 4e-32
 Identities = 73/232 (31%), Positives = 116/232 (50%), Gaps = 13/232 (5%)

Query: 4   QLLAEFMGTALMIIFGVGVHCSEVLKGTKYRGSGHIFAITTWGFGITIALFIFGNVC--- 60
           ++++E + TALM++ G G   +  L GTK   +G +     +G  + +   IFG +    
Sbjct: 10  RVISEIIATALMVLIGNGSVANAELTGTKGHKTGWLLIAIGYGCAVMLPAMIFGGISGNH 69

Query: 61  INPAMVLAQCILGNLSWSLFIPYSVAEVLGGVVGAVIVWIMYADHFAASADEISPITIRN 120
           INPA  +   + G   W+  +PY  A+ LG  +G  +V++ +   F  +  E S +    
Sbjct: 70  INPAFTIGLAVSGLFPWNEVLPYVCAQFLGAFIGQFLVYVGFKPFFDKT--ENSELVFAP 127

Query: 121 LFSTAPAVRNLPRNFFVEFFDTFIFISGILAISEVK----TPGIVPIGVGLLVWAIGMGL 176
            F+T PA  +     F EF  +FI     L I++        G     +G LV A+ + L
Sbjct: 128 -FATTPAANSTWNGVFSEFVGSFILFFAALGITKAAFFQDNQGTAHFALGFLVLALVLSL 186

Query: 177 GGPTGFAMNLARDMGPRIAHAILPIKNKADSDWQYG---IIVPGIAPFVGAA 225
           GG TG A+N ARD+ PRI H +LP+K+K  S W Y    +++P +A  V  A
Sbjct: 187 GGLTGPALNPARDLAPRILHQVLPLKHKGSSHWDYAWVPVVMPILASIVAVA 238


Lambda     K      H
   0.330    0.146    0.468 

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: 194
Number of extensions: 15
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: 245
Length adjustment: 23
Effective length of query: 215
Effective length of database: 222
Effective search space:    47730
Effective search space used:    47730
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.

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