Alignments for a candidate for mglC in Tistlia consotensis USBA 355

GapMind for catabolism of small carbon sources

Alignments for a candidate for mglC in Tistlia consotensis USBA 355

Align GguB aka ATU2346 aka AGR_C_4262, component of Multiple sugar (arabinose, xylose, galactose, glucose, fucose) putative porter (characterized)
to candidate WP_085126166.1 B9O00_RS28460 multiple monosaccharide ABC transporter permease

Query= TCDB::O05177
         (398 letters)



>NCBI__GCF_900177295.1:WP_085126166.1
          Length = 413

 Score =  514 bits (1325), Expect = e-150
 Identities = 252/379 (66%), Positives = 318/379 (83%)

Query: 19  YIRSNIREYGMLIALVAIMVFFQFYTGGILFRPVNLTNLILQNSFIVIMALGMLLVIVAG 78
           +IR+++REYG+L+AL+AIM FFQ  T GIL +PVNLTNLILQNS+IVIMA+GMLLVIV+G
Sbjct: 34  FIRTHLREYGILVALIAIMAFFQIATDGILLKPVNLTNLILQNSYIVIMAVGMLLVIVSG 93

Query: 79  HIDLSVGSIVAFVGAIAAILTVQWGMNPFLAALICLVIGGIIGAAQGYWIAYHRIPSFIV 138
           +IDLSVGS++ FVGA+AA++ VQW +N  +  + CL +G +IGAAQGYWIAY +IPSFIV
Sbjct: 94  NIDLSVGSVLGFVGALAAVMIVQWDVNYVVTGIACLAVGALIGAAQGYWIAYWKIPSFIV 153

Query: 139 TLAGMLVFRGLTLFVLGGKNIGPFPTDFQVISTGFLPDIGGIEGLNTTSMILTVLITVAL 198
           TLAGMLVFRGLTL+VL G+++GPFP  FQ++S+GF+PD+  ++GLN  S++L +  +  L
Sbjct: 154 TLAGMLVFRGLTLWVLAGQSVGPFPHSFQLLSSGFIPDLFAVKGLNVFSLLLGIAASAGL 213

Query: 199 FYLAWRRRVVNVKHGIDVEPFGFFIVQNLLISGAILFLGYQLSTYRGLPNVLIVMLVLIA 258
             LA R R+   K G+  EP  FF+ +N L++ AIL++ + L+ +RGLPNVLI+M +LIA
Sbjct: 214 AALALRSRLRAQKGGVVDEPLAFFLAKNGLVAVAILYMTWLLAAFRGLPNVLIIMALLIA 273

Query: 259 LYSFVTRRTTIGRRVYAMGGNEKATKLSGINTERLSFLTFVNMGVLAGLAGMIIATRLNS 318
           LYSFVT RTT GRR+YA+GGNEKA +LSGINTERL+FLTF NMG+LA LAG++ A RLN+
Sbjct: 274 LYSFVTTRTTTGRRIYALGGNEKAARLSGINTERLTFLTFANMGMLAALAGLVFAARLNT 333

Query: 319 ATPKAGVGFELDVIAACFIGGASASGGVGKITGAVIGAFIMGVMNNGMSIVGLGIDFQQM 378
           ATPKAG+ FELDVIAA FIGGAS SGGVG + GAV GAFIMGVMNNGMSI+G+GID+QQ+
Sbjct: 334 ATPKAGITFELDVIAAVFIGGASMSGGVGTVVGAVAGAFIMGVMNNGMSILGIGIDYQQV 393

Query: 379 VKGLVLLAAVFFDVYNKNK 397
           +KGLVLLAAV FDVYNKNK
Sbjct: 394 IKGLVLLAAVIFDVYNKNK 412


Lambda     K      H
   0.329    0.145    0.422 

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: 670
Number of extensions: 29
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: 398
Length of database: 413
Length adjustment: 31
Effective length of query: 367
Effective length of database: 382
Effective search space:   140194
Effective search space used:   140194
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: 50 (23.9 bits)

This GapMind analysis is from Apr 09 2024. The underlying query database was built on Sep 17 2021.

Downloads

Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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:

the paper from 2019 on GapMind for amino acid biosynthesis
the 2024 update on GapMind for amino acid biosynthesis
the paper from 2022 on GapMind for carbon sources
the source code
instructions for running GapMind on your computer

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

GapMind for catabolism of small carbon sources