GapMind for catabolism of small carbon sources

 

Alignments for a candidate for bgtA in Magnetovibrio blakemorei MV-1

Align BgtA aka SLR1735, component of Arginine/lysine/histidine/glutamine porter (characterized)
to candidate WP_069958139.1 BEN30_RS09690 ATP-binding cassette domain-containing protein

Query= TCDB::P73721
         (252 letters)



>NCBI__GCF_001746755.1:WP_069958139.1
          Length = 259

 Score =  250 bits (638), Expect = 2e-71
 Identities = 130/255 (50%), Positives = 176/255 (69%), Gaps = 8/255 (3%)

Query: 1   MTSPTAPLISFDQLQKNFGALQVLRGVTGEIYPKDVISIIGPSGCGKSTFLRCLNRLEPI 60
           M     PL+  + + K+FG   VL+G++      DVISI+G SG GKSTFLRC+N LE  
Sbjct: 1   MPDDNTPLLKVEDIHKSFGGQDVLKGISVNANRGDVISILGSSGSGKSTFLRCINYLEHP 60

Query: 61  SGGRLEVAGVDL------SGAKI--DQKHLRQLRVRVGMVFQHFNLFPHLTVLQNLLLAP 112
             GR+ +AG ++      SG+ +  D K L +LR R+G VFQ FNL+PHL VLQN++ AP
Sbjct: 61  DIGRVSIAGEEIRTKKDKSGSLVPADPKQLARLRARIGFVFQSFNLWPHLNVLQNVIEAP 120

Query: 113 RKVLRIPMAEAKDRALTYLDKVGLGTKADNYPDQLSGGQKQRVAIARGLCMKPEILLFDE 172
            +VL++   +A +RA   L +VGL  +  ++P  LSGGQ+QR AIAR L M+PE++LFDE
Sbjct: 121 MQVLKLSRKDATERAEVILARVGLADRMHHFPAHLSGGQQQRAAIARTLAMEPEVILFDE 180

Query: 173 PTSALDPELVGEVLNVMKQLAEEGMTMAVVTHEMQFAREVSNRVFFFNQGIIEEEGDPNE 232
           PTSALDPELV EVL V+  LAEEG TM +VTHEM FAREVS    F +QG +EE+G P++
Sbjct: 181 PTSALDPELVSEVLAVIGSLAEEGRTMLIVTHEMGFAREVSTWTMFLHQGKVEEQGPPDK 240

Query: 233 VFRNPKSDRLRAFLS 247
           +F+N  S+R+R F++
Sbjct: 241 IFKNADSERVRQFMA 255


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: 5
Number of successful extensions: 2
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: 259
Length adjustment: 24
Effective length of query: 228
Effective length of database: 235
Effective search space:    53580
Effective search space used:    53580
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: 47 (22.7 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