GapMind for catabolism of small carbon sources

 

Alignments for a candidate for glpT in Thiothrix lacustris DSM 21227

Align ABC transporter for Glycerol, ATPase component 2 (characterized)
to candidate WP_028489030.1 Q394_RS0109195 ABC transporter ATP-binding protein

Query= reanno::acidovorax_3H11:Ac3H11_792
         (358 letters)



>NCBI__GCF_000621325.1:WP_028489030.1
          Length = 348

 Score =  204 bits (519), Expect = 3e-57
 Identities = 111/287 (38%), Positives = 171/287 (59%), Gaps = 18/287 (6%)

Query: 22  YALLPLKMEFEDGGAYALLGPSGCGKTTMLNIMSGLLVPSHGKVLFDGRDVTRASPQERN 81
           +A+  + +E + G     +GPSGCGK+T+L +++GL V + G+++ DGRD+T   P +R+
Sbjct: 17  HAIKQVSLEIQSGEFIVFVGPSGCGKSTLLRMIAGLEVINGGQLILDGRDITEVPPSQRD 76

Query: 82  IAQVFQFPVIYDTMTVAENLAFPLRNRKVPEGQIKQRVGVIAEMLEMSGQLNQRAAGLAA 141
           +A VFQ   +Y  MTV EN++F LR  KV    I+++V + A+ L ++  L +    L+ 
Sbjct: 77  LAMVFQSYALYPHMTVEENMSFALRLAKVDPAIIQEKVKMAADKLNLTAYLQRTPKALSG 136

Query: 142 DAKQKISLGRGLVRADVAAVLFDEPLTVIDPHLKWQLRRKLKQIHHELKLTLIYVTHDQV 201
             +Q++++GR +VR+     LFDEPL+ +D  L+   R ++  +H EL  T +YVTHDQV
Sbjct: 137 GQRQRVAIGRSIVRSP-KVFLFDEPLSNLDAALRGNTRVEIASLHRELGATTVYVTHDQV 195

Query: 202 EALTFADQVVVMTRGKAVQVGSADALFERPAHTFVGHFIGSPGMNFLPAHRDGENLSVAG 261
           EA+T AD+VVV+  G   QVG+   L+++P + FV  FIG P MN  PA   G+      
Sbjct: 196 EAMTLADRVVVLRDGIIEQVGTPLELYDQPINRFVARFIGMPQMNVAPASLFGQ------ 249

Query: 262 HRLASPVGRALPAGALQVGIRPEYLALAQPQQAGALPGTVVQVQDIG 308
                      PA   +VGIRPE+L +  P+  G L G VV V+ +G
Sbjct: 250 ----------FPAQVAEVGIRPEHLQMVSPED-GLLAGKVVLVEALG 285


Lambda     K      H
   0.320    0.136    0.395 

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: 304
Number of extensions: 16
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: 358
Length of database: 348
Length adjustment: 29
Effective length of query: 329
Effective length of database: 319
Effective search space:   104951
Effective search space used:   104951
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 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