GapMind for catabolism of small carbon sources

 

Alignments for a candidate for aapM in Desulfoscipio geothermicus DSM 3669

Align AapM, component of General L-amino acid porter; transports basic and acidic amino acids preferentially, but also transports aliphatic amino acids (catalyzes both uptake and efflux) (characterized)
to candidate WP_092487756.1 BM299_RS18040 amino acid ABC transporter permease

Query= TCDB::Q52814
         (384 letters)



>NCBI__GCF_900115975.1:WP_092487756.1
          Length = 234

 Score =  122 bits (307), Expect = 8e-33
 Identities = 75/239 (31%), Positives = 123/239 (51%), Gaps = 31/239 (12%)

Query: 164 LEVVETPLWGGLMVTLVLSFVGIAVSLPVGILLALGRRSRMPVIRMLCVTFIEVIRGVPL 223
           +E +   ++ G  +TL ++ + +A+   +G++  L R SR  V+R L   +++  RG PL
Sbjct: 5   IENLPVLIFQGAKITLQITIISVAIGCLLGLIGGLSRLSRRKVLRFLATAYVDFFRGTPL 64

Query: 224 ITVLFMASVMLPLFL----------------PTGWNVDKLLRALIGVSIFTSAYMAEVIR 267
           +  +F+    +P  L                   + + + L A+I  S+ + AY+AE+ R
Sbjct: 65  LVQIFIVYFGIPKLLMDLQSFMVDSYGMTPVADSFALPRFLAAVIACSLNSGAYVAEIFR 124

Query: 268 GGLQAIPKGQFEGADSLGLGYWQKTRLIIMPQAIKLVIPSIVNTFIGTFKDTSLVTIIGM 327
            G+Q+I +GQ E A SLG+ + Q  R +I+PQA K VIP + N FI   KDTSL+++IG 
Sbjct: 125 AGVQSIERGQMEAARSLGMTHGQAMRYVILPQAFKRVIPPLGNEFIAMLKDTSLLSVIGF 184

Query: 328 FDL-----LGIVKLNFSDANWASAVTPITGLIFAGFIFWLFCFGMSRYSGFMERHLDTG 381
            +L     L I +   S A W          +  GFI+ +  F +SR   ++ER   TG
Sbjct: 185 AELTRNGQLIIARTYESFAIW----------LTVGFIYLIMTFTLSRIVDYLERRYKTG 233


Lambda     K      H
   0.330    0.145    0.469 

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: 202
Number of extensions: 9
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: 384
Length of database: 234
Length adjustment: 27
Effective length of query: 357
Effective length of database: 207
Effective search space:    73899
Effective search space used:    73899
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 (21.8 bits)
S2: 48 (23.1 bits)

This GapMind analysis is from Apr 09 2024. 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