GapMind for catabolism of small carbon sources

 

Alignments for a candidate for aatM in Collimonas arenae Ter10

Align ABC transporter for L-Asparagine and possibly other L-amino acids, permease component 2 (characterized)
to candidate WP_061534651.1 CAter10_RS19010 amino acid ABC transporter permease

Query= reanno::pseudo13_GW456_L13:PfGW456L13_4772
         (223 letters)



>NCBI__GCF_001584165.1:WP_061534651.1
          Length = 231

 Score =  234 bits (596), Expect = 1e-66
 Identities = 121/225 (53%), Positives = 161/225 (71%), Gaps = 4/225 (1%)

Query: 3   FDFSGIIPSLPGLWN-GMIMTLKLMAMGVIGGIILGTILALMRLSHNKVLSNIAGAYVNY 61
           FDF  I  S   L+  GM  TL L  + +IGGI+ GT+LA+MRLSHNKV+S +A +YVN 
Sbjct: 5   FDFDVIQRSWFYLFTTGMKFTLTLTVVAMIGGILFGTVLAMMRLSHNKVISFVATSYVNL 64

Query: 62  FRSIPLLLVITWFYLAVPFVLRWITGEDTPI--GAFASCIVAFMMFEAAYFCEIVRAGVQ 119
            RS+PL+LVI WFY  VPF+  WITG   P+  GAF+S ++ F++FEAAY+CEI+R+G+Q
Sbjct: 65  IRSVPLVLVIFWFYFLVPFIGAWITGASQPVQVGAFSSALITFILFEAAYYCEIMRSGIQ 124

Query: 120 SIPKGQMGAAQALGMSYGQMMRLIILPQAFRKMTPLLLQQSIILFQDTSLVYAVGLV-DF 178
           SIP+GQ+ A  ALGM+Y QMM  ++LPQAFR M P+LL Q+I+LFQD SLVY +G V DF
Sbjct: 125 SIPRGQISAGYALGMNYWQMMGNVVLPQAFRNMIPILLTQTIVLFQDVSLVYVLGSVPDF 184

Query: 179 LNASRASGDIIGRSNEFLIFAGLVYFIISFAASQLVKRLQKRFAV 223
           +  +       GR  E  +F  +VYF++SF  S LVK+LQ+R A+
Sbjct: 185 VTVASKIAQRDGRLVEMYMFVAVVYFVMSFGLSTLVKKLQQRVAI 229


Lambda     K      H
   0.332    0.144    0.428 

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: 174
Number of extensions: 4
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: 223
Length of database: 231
Length adjustment: 22
Effective length of query: 201
Effective length of database: 209
Effective search space:    42009
Effective search space used:    42009
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (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