GapMind for catabolism of small carbon sources

 

Alignments for a candidate for SMc02869 in Rhizorhabdus wittichii RW1

Align N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized)
to candidate WP_041378948.1 SWIT_RS04010 ABC transporter ATP-binding protein

Query= reanno::Phaeo:GFF2754
         (331 letters)



>NCBI__GCF_000016765.1:WP_041378948.1
          Length = 252

 Score =  164 bits (416), Expect = 2e-45
 Identities = 90/212 (42%), Positives = 127/212 (59%), Gaps = 3/212 (1%)

Query: 4   LQLTNVCKSFGPVEVLKDINLTVEDGEFVVFVGPSGCGKSTLLRVISGLEDATAGEISIG 63
           +   +V K +    VL D++LT+E G FV  VG SG GK+TLL+ I+ L +   G I+I 
Sbjct: 2   ISFDHVGKHYAGRHVLDDVSLTIERGSFVALVGASGAGKTTLLKAINRLVEIDTGTIAIE 61

Query: 64  GQTVTTTPPA--KRGIAMVFQSYALYPHLSVRENMALALKQERQPKEEIAARVAEASRML 121
           G+ V   P A  +R I  VFQ   L+PH+SV EN+AL  + +  P+EE AARVAE   ++
Sbjct: 62  GRDVAAQPVAELRRRIGYVFQGIGLFPHMSVAENVALVPRLQGVPREERAARVAELLDLV 121

Query: 122 SLE-DYLDRRPSELSGGQRQRVAIGRAVVREPKLFLFDEPLSNLDAALRMNTRLEIARLH 180
           +L  D+ +RRP++LSGGQ QRV   RA+   P + L DEP   LD   R         LH
Sbjct: 122 ALPADFAERRPAQLSGGQAQRVGFARALAARPAIMLMDEPFGALDPVTRDELGAAYRALH 181

Query: 181 RQLSASMIYVTHDQIEAMTLADKIVVLRDGRI 212
             +  + + VTHD  EA+ LAD+++V+ +GRI
Sbjct: 182 EAMGLTSLIVTHDMAEALLLADRVIVIGEGRI 213


Lambda     K      H
   0.320    0.137    0.391 

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: 206
Number of extensions: 13
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: 331
Length of database: 252
Length adjustment: 26
Effective length of query: 305
Effective length of database: 226
Effective search space:    68930
Effective search space used:    68930
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 48 (23.1 bits)

This GapMind analysis is from Apr 09 2024. 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