GapMind for catabolism of small carbon sources

 

Alignments for a candidate for hisP in Lactobacillus oryzae SG293

Align BgtA aka SLR1735, component of Arginine/lysine/histidine/glutamine porter (characterized)
to candidate WP_034529147.1 LOSG293_RS08120 amino acid ABC transporter ATP-binding protein

Query= TCDB::P73721
         (252 letters)



>NCBI__GCF_000740055.1:WP_034529147.1
          Length = 247

 Score =  269 bits (688), Expect = 3e-77
 Identities = 135/243 (55%), Positives = 181/243 (74%), Gaps = 3/243 (1%)

Query: 9   ISFDQLQKNFGALQVLRGVTGEIYPKDVISIIGPSGCGKSTFLRCLNRLEPISGGRLEVA 68
           +S   L K++GA +VL G+  E++PK+V+ +IGPSG GKSTFLRCLN LE ++ G +E+ 
Sbjct: 7   VSVKDLHKSYGANEVLSGIDLEVFPKEVVCLIGPSGSGKSTFLRCLNGLEAVNSGVIEIN 66

Query: 69  GVDLSGAKIDQKHLRQLRVRVGMVFQHFNLFPHLTVLQNLLLAPRKVLRIPMAEAKDRAL 128
           GV+L     D   +RQ    +GMVFQHFNLFPHLTV++N++LAP ++ ++    A+++ +
Sbjct: 67  GVNLVAKHTDINKVRQ---NIGMVFQHFNLFPHLTVIENVMLAPVQLKKMDKQTAREKGM 123

Query: 129 TYLDKVGLGTKADNYPDQLSGGQKQRVAIARGLCMKPEILLFDEPTSALDPELVGEVLNV 188
             L +VGL  KAD  P  LSGGQ+QRVAIAR L M+PEI+LFDEPTSALDPE+VG+VL V
Sbjct: 124 KLLAQVGLAEKADVKPASLSGGQEQRVAIARALAMEPEIMLFDEPTSALDPEMVGDVLAV 183

Query: 189 MKQLAEEGMTMAVVTHEMQFAREVSNRVFFFNQGIIEEEGDPNEVFRNPKSDRLRAFLSR 248
           MK LA+ GMTM VVTHEM FA+E ++RV F + G I+E G P EVF +PK++R R FLS+
Sbjct: 184 MKDLAKAGMTMVVVTHEMGFAKEAADRVAFMDSGKIQEIGTPEEVFDHPKNERTRGFLSK 243

Query: 249 IQS 251
           I +
Sbjct: 244 IMN 246


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: 214
Number of extensions: 11
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: 247
Length adjustment: 24
Effective length of query: 228
Effective length of database: 223
Effective search space:    50844
Effective search space used:    50844
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: 46 (22.3 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