GapMind for catabolism of small carbon sources

 

Alignments for a candidate for bgtA in Thiothrix lacustris DSM 21227

Align BgtA aka SLR1735, component of Arginine/lysine/histidine/glutamine porter (characterized)
to candidate WP_028489030.1 Q394_RS0109195 ABC transporter ATP-binding protein

Query= TCDB::P73721
         (252 letters)



>NCBI__GCF_000621325.1:WP_028489030.1
          Length = 348

 Score =  140 bits (353), Expect = 3e-38
 Identities = 87/243 (35%), Positives = 129/243 (53%), Gaps = 9/243 (3%)

Query: 9   ISFDQLQKNFGALQVLRGVTGEIYPKDVISIIGPSGCGKSTFLRCLNRLEPISGGRLEVA 68
           +    + K +G L  ++ V+ EI   + I  +GPSGCGKST LR +  LE I+GG+L + 
Sbjct: 4   LELKNVDKYYGKLHAIKQVSLEIQSGEFIVFVGPSGCGKSTLLRMIAGLEVINGGQLILD 63

Query: 69  GVDLSGAKIDQKHLRQLRVRVGMVFQHFNLFPHLTVLQNLLLAPRKVLRIPMAEAKDRAL 128
           G D++     Q+ L        MVFQ + L+PH+TV +N+  A R + ++  A  +++  
Sbjct: 64  GRDITEVPPSQRDL-------AMVFQSYALYPHMTVEENMSFALR-LAKVDPAIIQEKVK 115

Query: 129 TYLDKVGLGTKADNYPDQLSGGQKQRVAIARGLCMKPEILLFDEPTSALDPELVGEVLNV 188
              DK+ L       P  LSGGQ+QRVAI R +   P++ LFDEP S LD  L G     
Sbjct: 116 MAADKLNLTAYLQRTPKALSGGQRQRVAIGRSIVRSPKVFLFDEPLSNLDAALRGNTRVE 175

Query: 189 MKQLAEE-GMTMAVVTHEMQFAREVSNRVFFFNQGIIEEEGDPNEVFRNPKSDRLRAFLS 247
           +  L  E G T   VTH+   A  +++RV     GIIE+ G P E++  P +  +  F+ 
Sbjct: 176 IASLHRELGATTVYVTHDQVEAMTLADRVVVLRDGIIEQVGTPLELYDQPINRFVARFIG 235

Query: 248 RIQ 250
             Q
Sbjct: 236 MPQ 238


Lambda     K      H
   0.321    0.139    0.397 

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: 212
Number of extensions: 11
Number of successful extensions: 4
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: 252
Length of database: 348
Length adjustment: 26
Effective length of query: 226
Effective length of database: 322
Effective search space:    72772
Effective search space used:    72772
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 (21.9 bits)
S2: 48 (23.1 bits)

This GapMind analysis is from Apr 09 2024. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

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