GapMind for catabolism of small carbon sources

 

Alignments for a candidate for aatQ in Lutibaculum baratangense AMV1

Align Glutamate/aspartate import permease protein GltJ (characterized)
to candidate WP_023432530.1 N177_RS11630 ectoine/hydroxyectoine ABC transporter permease subunit EhuC

Query= SwissProt::P0AER3
         (246 letters)



>NCBI__GCF_000496075.1:WP_023432530.1
          Length = 239

 Score = 93.6 bits (231), Expect = 3e-24
 Identities = 69/223 (30%), Positives = 114/223 (51%), Gaps = 19/223 (8%)

Query: 17  GNTTYLGWIWSGFQVTIALSI--CAWIIAF-LVGSFFGILRTVPNRFLSGLGTLYVELFR 73
           G   +L  + +G  VTI ++I  CA  +A  LV +   +    P R+L+     Y+ELFR
Sbjct: 23  GLRDFLPQLLAGAVVTIEITIGGCAVAVAAALVAAMAKMYGPAPLRWLA---VAYIELFR 79

Query: 74  NVPLIVQFFTWYLVIPELLPEKIGMWFKAELDPNIQFFLSSMLCLGLFTAARVCEQVRAA 133
               +VQ F  + V+P          F   L+P        ++ LGL   A   E VR A
Sbjct: 80  GTSALVQLFWLFYVLPH---------FGVLLEP----MTVGIVALGLNVGAYGAEVVRGA 126

Query: 134 IQSLPRGQKNAALAMGLTLPQAYRYVLLPNAYRVIVPPMTSEMMNLVKNSAIASTIGLVD 193
           + ++PRGQ  A +A+ +T  QA R V+LP A+  ++PP  +  + L+K +A+ S I + D
Sbjct: 127 VNAVPRGQWEATVALNMTRAQALRRVILPQAFVAMIPPWGNLFIELLKATALVSLITISD 186

Query: 194 MAAQAGKLLDYSAHAWESFTAITLAYVLINAFIMLVMTLVERK 236
           +A +A +L   +    + FT + L Y+ I++ I + M  +E +
Sbjct: 187 LAFRAQQLNQITFETVKIFTIVLLIYLAISSVITVGMRALEER 229


Lambda     K      H
   0.328    0.140    0.443 

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: 165
Number of extensions: 6
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: 246
Length of database: 239
Length adjustment: 23
Effective length of query: 223
Effective length of database: 216
Effective search space:    48168
Effective search space used:    48168
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: 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