GapMind for catabolism of small carbon sources

 

Alignments for a candidate for aatM in Desulfoscipio geothermicus DSM 3669

Align Glutamate/aspartate import permease protein GltK (characterized)
to candidate WP_092487756.1 BM299_RS18040 amino acid ABC transporter permease

Query= SwissProt::P0AER5
         (224 letters)



>NCBI__GCF_900115975.1:WP_092487756.1
          Length = 234

 Score =  145 bits (366), Expect = 6e-40
 Identities = 85/226 (37%), Positives = 133/226 (58%), Gaps = 12/226 (5%)

Query: 9   IVPSLPYLL-DGLVITLKITVTAVVIGILWGTMLAVMRLSSFAPVAWFAKAYVNVFRSIP 67
           ++ +LP L+  G  ITL+IT+ +V IG L G +  + RLS    + + A AYV+ FR  P
Sbjct: 4   VIENLPVLIFQGAKITLQITIISVAIGCLLGLIGGLSRLSRRKVLRFLATAYVDFFRGTP 63

Query: 68  LVMVLLWFYLIVP-------GFLQNVLGLSPKNDI----RLISAMVAFSMFEAAYYSEII 116
           L++ +   Y  +P        F+ +  G++P  D     R ++A++A S+   AY +EI 
Sbjct: 64  LLVQIFIVYFGIPKLLMDLQSFMVDSYGMTPVADSFALPRFLAAVIACSLNSGAYVAEIF 123

Query: 117 RAGIQSISRGQSSAALALGMTHWQSMKLIILPQAFRAMVPLLLTQGIVLFQDTSLVYVLS 176
           RAG+QSI RGQ  AA +LGMTH Q+M+ +ILPQAF+ ++P L  + I + +DTSL+ V+ 
Sbjct: 124 RAGVQSIERGQMEAARSLGMTHGQAMRYVILPQAFKRVIPPLGNEFIAMLKDTSLLSVIG 183

Query: 177 LADFFRTASTIGERDGTQVEMILFAGFVYFVISLSASLLVSYLKRR 222
            A+  R    I  R      + L  GF+Y +++ + S +V YL+RR
Sbjct: 184 FAELTRNGQLIIARTYESFAIWLTVGFIYLIMTFTLSRIVDYLERR 229


Lambda     K      H
   0.330    0.140    0.412 

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: 139
Number of extensions: 7
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: 224
Length of database: 234
Length adjustment: 23
Effective length of query: 201
Effective length of database: 211
Effective search space:    42411
Effective search space used:    42411
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 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 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