GapMind for catabolism of small carbon sources

 

Alignments for a candidate for SMc02869 in Flavobacterium beibuense F44-8

Align N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized)
to candidate WP_035130044.1 Q763_RS00890 ABC transporter ATP-binding protein

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



>NCBI__GCF_000769915.1:WP_035130044.1
          Length = 319

 Score =  136 bits (343), Expect = 6e-37
 Identities = 81/265 (30%), Positives = 138/265 (52%), Gaps = 8/265 (3%)

Query: 12  SFGPVE--VLKDINLTVEDGEFVVFVGPSGCGKSTLLRVISGLEDATAGEISIGGQTVTT 69
           SFG  E  +L +++ TV+ G+ +  +G SGCGKSTLL++I GL D   GEI+  G+ V  
Sbjct: 8   SFGYTEKTILHNLSFTVKTGQNIAVIGESGCGKSTLLKLIYGLYDIEEGEITYKGEPVLG 67

Query: 70  TP----PAKRGIAMVFQSYALYPHLSVRENMALALKQERQPKEEIAARVAEASRMLSLED 125
                 P    +  + Q + L P+++  EN+   L       EE   R+ E   ++ + +
Sbjct: 68  PKFNLIPGMSYMKYLAQDFDLMPYITAAENVGAFLSNFYP--EEKQRRIMELLDIVEMRE 125

Query: 126 YLDRRPSELSGGQRQRVAIGRAVVREPKLFLFDEPLSNLDAALRMNTRLEIARLHRQLSA 185
           + D +   LSGGQ+QR+A+ + +  EP++ L DEP S++D   +   R  +    +Q   
Sbjct: 126 FADVKAQFLSGGQQQRIALAKVLALEPEVLLLDEPFSHIDNFRKNALRRNLFAYLKQKGV 185

Query: 186 SMIYVTHDQIEAMTLADKIVVLRDGRIEQVGTPMELYNNPANRFVAEFIGAPAMNFVPAQ 245
           + I  THD  +A++ AD+ +V++ GR+       ++Y NPA+++ A   G      +   
Sbjct: 186 TCIVATHDSTDALSFADETIVIKGGRMLSKAKSKDIYYNPADKYTASLFGEVNEIKLELL 245

Query: 246 RLGGNPGQFIGIRPEYARISPVGPL 270
            L  NP + + I P   ++   GPL
Sbjct: 246 TLTQNPEETVLIYPHQLKVVEEGPL 270


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: 233
Number of extensions: 13
Number of successful extensions: 2
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 1
Length of query: 331
Length of database: 319
Length adjustment: 28
Effective length of query: 303
Effective length of database: 291
Effective search space:    88173
Effective search space used:    88173
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 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