GapMind for catabolism of small carbon sources

 

Alignments for a candidate for SMc02869 in Pseudovibrio axinellae Ad2

Align N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized)
to candidate WP_068010540.1 PsAD2_RS21550 ABC transporter ATP-binding protein

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



>NCBI__GCF_001623255.1:WP_068010540.1
          Length = 370

 Score =  286 bits (732), Expect = 6e-82
 Identities = 140/242 (57%), Positives = 179/242 (73%)

Query: 1   MTALQLTNVCKSFGPVEVLKDINLTVEDGEFVVFVGPSGCGKSTLLRVISGLEDATAGEI 60
           M  + + +  KSFG  +VLKDI+L V+DGEF+V +G SGCGKSTLL +I+GLE    G I
Sbjct: 1   MATISIEHASKSFGSTKVLKDISLDVKDGEFLVLLGASGCGKSTLLNIIAGLEPMADGTI 60

Query: 61  SIGGQTVTTTPPAKRGIAMVFQSYALYPHLSVRENMALALKQERQPKEEIAARVAEASRM 120
            + G+ V    P  R IAMVFQSYALYP+++V  N+A  L+  +  K E  A V E +  
Sbjct: 61  RLDGEVVNDVHPKNRDIAMVFQSYALYPNMTVERNIAFGLEMRKISKAERKATVREVAST 120

Query: 121 LSLEDYLDRRPSELSGGQRQRVAIGRAVVREPKLFLFDEPLSNLDAALRMNTRLEIARLH 180
           L +E  L R+PS+LSGGQRQRVA+GRA+VR PK+FLFDEPLSNLDA LR   R EI +LH
Sbjct: 121 LQIEHLLSRKPSQLSGGQRQRVAMGRALVRRPKIFLFDEPLSNLDAKLRGEMRTEIKKLH 180

Query: 181 RQLSASMIYVTHDQIEAMTLADKIVVLRDGRIEQVGTPMELYNNPANRFVAEFIGAPAMN 240
           + L A+M+YVTHDQIEAMTLAD+I +++DG I+Q+GTP E+Y+ PAN +VA F+GAP MN
Sbjct: 181 QTLKATMVYVTHDQIEAMTLADRIAIMKDGEIQQIGTPQEIYSKPANMYVAGFVGAPPMN 240

Query: 241 FV 242
           FV
Sbjct: 241 FV 242


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: 346
Number of extensions: 17
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: 331
Length of database: 370
Length adjustment: 29
Effective length of query: 302
Effective length of database: 341
Effective search space:   102982
Effective search space used:   102982
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: 49 (23.5 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