Alignments for a candidate for mglC in Azospirillum brasilense Sp245

GapMind for catabolism of small carbon sources

Alignments for a candidate for mglC in Azospirillum brasilense Sp245

Align GguB aka ATU2346 aka AGR_C_4262, component of Multiple sugar (arabinose, xylose, galactose, glucose, fucose) putative porter (characterized)
to candidate AZOBR_RS31250 AZOBR_RS31250 ABC transporter permease

Query= TCDB::O05177
         (398 letters)



>FitnessBrowser__azobra:AZOBR_RS31250
          Length = 403

 Score =  498 bits (1283), Expect = e-146
 Identities = 246/389 (63%), Positives = 316/389 (81%), Gaps = 5/389 (1%)

Query: 14  ISVGSYIRSNIREYGMLIALVAIMVFFQFYTGGILFRPVNLTNLILQNSFIVIMALGMLL 73
           +S+G ++++++REYGML++LVAI++FFQ+ T G L +P+NLTNL+LQNS+IVIMALGMLL
Sbjct: 14  VSMGRFVKAHMREYGMLLSLVAIVLFFQYMTDGTLLQPLNLTNLVLQNSYIVIMALGMLL 73

Query: 74  VIVAGHIDLSVGSIVAFVGAIAAILTVQWGMNPFLAALICLVIGGIIGAAQGYWIAYHRI 133
           VIVAGHIDLSVGS+VA +GA+AA L V+  ++     L+CL+ G  IGA QG+W+AY RI
Sbjct: 74  VIVAGHIDLSVGSVVALIGALAATLMVRLHLDFVTTTLLCLLAGAAIGAVQGFWVAYLRI 133

Query: 134 PSFIVTLAGMLVFRGLTLFVLGGKNIGPFPTDFQVISTGFLPDIGGIEGLNT-----TSM 188
           PSFIVTLAGMLVFRGL L +L G+++GPFP +FQ +S+GF+PD   ++ LN      TS+
Sbjct: 134 PSFIVTLAGMLVFRGLCLILLAGQSVGPFPVEFQRLSSGFIPDFLALDALNLGKFHLTSL 193

Query: 189 ILTVLITVALFYLAWRRRVVNVKHGIDVEPFGFFIVQNLLISGAILFLGYQLSTYRGLPN 248
           +L   +  A+  +  R R+      I+ EP   F+ +N+ ++  ++++G  +++YRGLPN
Sbjct: 194 LLCAAVAAAMVAMNTRARLRRQSVAIEQEPLPLFVAKNVALAAVLIYVGQLMASYRGLPN 253

Query: 249 VLIVMLVLIALYSFVTRRTTIGRRVYAMGGNEKATKLSGINTERLSFLTFVNMGVLAGLA 308
           VLI+M VLIALYSFVTR TT+GRRVYA+GGNEKA KLSGI+T RLSF TFVNMGVLA LA
Sbjct: 254 VLIIMSVLIALYSFVTRNTTVGRRVYALGGNEKAAKLSGIDTRRLSFYTFVNMGVLAALA 313

Query: 309 GMIIATRLNSATPKAGVGFELDVIAACFIGGASASGGVGKITGAVIGAFIMGVMNNGMSI 368
           G+I A RLN+ATPKAG  FELDVIAACFIGGASASGGVG++TGAVIGAFIMGVMNNGMSI
Sbjct: 314 GLIFAARLNTATPKAGASFELDVIAACFIGGASASGGVGRVTGAVIGAFIMGVMNNGMSI 373

Query: 369 VGLGIDFQQMVKGLVLLAAVFFDVYNKNK 397
           +G+GID+QQ++KG+VLLAAV  DVYNKNK
Sbjct: 374 LGIGIDWQQVIKGMVLLAAVTIDVYNKNK 402


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: 604
Number of extensions: 24
Number of successful extensions: 2
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: 403
Length adjustment: 31
Effective length of query: 367
Effective length of database: 372
Effective search space:   136524
Effective search space used:   136524
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 Sep 17 2021. The underlying query database was built on Sep 17 2021.

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

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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:

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 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