GapMind for catabolism of small carbon sources

 

Alignments for a candidate for bgtA in Halomonas xinjiangensis TRM 0175

Align BgtA aka SLR1735, component of Arginine/lysine/histidine/glutamine porter (characterized)
to candidate WP_043532174.1 JH15_RS16045 ATP-binding cassette domain-containing protein

Query= TCDB::P73721
         (252 letters)



>NCBI__GCF_000759345.1:WP_043532174.1
          Length = 262

 Score =  233 bits (595), Expect = 2e-66
 Identities = 127/244 (52%), Positives = 162/244 (66%), Gaps = 8/244 (3%)

Query: 14  LQKNFGALQVLRGVTGEIYPKDVISIIGPSGCGKSTFLRCLNRLEPISGGRLEVAGVDL- 72
           LQK++G + VL  V+  +  + V+SIIG SG GKST LRC+N LE    G L +A   + 
Sbjct: 18  LQKHYGEVPVLHDVSLSVTDRHVVSIIGSSGSGKSTLLRCMNLLEIPDRGELTIANEAIR 77

Query: 73  -------SGAKIDQKHLRQLRVRVGMVFQHFNLFPHLTVLQNLLLAPRKVLRIPMAEAKD 125
                      ID++ + +LR +V MVFQ FNL+PHL+VL N++ AP +V  +   EA +
Sbjct: 78  FQRNAQGDNVGIDRRQVHKLRSQVSMVFQQFNLWPHLSVLGNVIEAPLRVHGLSRREAIE 137

Query: 126 RALTYLDKVGLGTKADNYPDQLSGGQKQRVAIARGLCMKPEILLFDEPTSALDPELVGEV 185
           R   YL KVGL  K + +P  LSGGQ+QRVAIAR L M+P +LLFDEPTSALDPELV EV
Sbjct: 138 RGEHYLAKVGLADKRNAFPSFLSGGQQQRVAIARALAMEPRVLLFDEPTSALDPELVNEV 197

Query: 186 LNVMKQLAEEGMTMAVVTHEMQFAREVSNRVFFFNQGIIEEEGDPNEVFRNPKSDRLRAF 245
           L V+  LA EG TM +VTHEM FAREVSN + F +QG +EE G P +VF   +SDR R F
Sbjct: 198 LGVIGGLAGEGRTMLLVTHEMSFAREVSNEIVFLHQGHVEEAGSPQQVFEQARSDRCRQF 257

Query: 246 LSRI 249
           LS +
Sbjct: 258 LSSV 261


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: 185
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: 262
Length adjustment: 24
Effective length of query: 228
Effective length of database: 238
Effective search space:    54264
Effective search space used:    54264
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