GapMind for catabolism of small carbon sources

 

Alignments for a candidate for AO353_03055 in Methanospirillum lacunae Ki8-1

Align ABC transporter for L-Arginine and L-Citrulline, periplasmic substrate-binding component (characterized)
to candidate WP_109969946.1 DK846_RS15725 basic amino acid ABC transporter substrate-binding protein

Query= reanno::pseudo3_N2E3:AO353_03055
         (258 letters)



>NCBI__GCF_003173355.1:WP_109969946.1
          Length = 270

 Score =  108 bits (269), Expect = 2e-28
 Identities = 70/228 (30%), Positives = 115/228 (50%), Gaps = 13/228 (5%)

Query: 27  KIGIEAAYPPFASKAPDGSIVGFDYDIGNALCEEMKVKCVWVEQEFDGLIPALKVRKIDA 86
           ++GI+  YPPF   +  G   GFD +    + ++   +  +    +DG+IPAL   KID 
Sbjct: 49  RVGIDPVYPPFTMMSEKGEPTGFDVESLKWIAKDQGFEAEFQGIAWDGIIPALNANKIDM 108

Query: 87  ILSSMSITDDRKKSVDFTNKYYNTPARLVMKAGTQVSDNLAELKGKKIGVQRGSIHNRFA 146
           + + M+ITD+RK+ VDF+  Y+     +V K G+ ++ +  +     IG QRG     + 
Sbjct: 109 VYAGMTITDERKEKVDFSKPYWTVNQTVVTKQGSPITMDQVKSGKATIGTQRGCTAAIWV 168

Query: 147 EE--VLKPL--GAEIKPYGSQNEIYLDVAAGRLDGTVADATLLDDGFLKTDSGKGFAFVG 202
           E+  V K L     +K Y +      D+ AGR D  + D+T+++D       GK    +G
Sbjct: 169 EDNLVNKSLMSADNLKQYDNTPLAVEDLVAGRTDAVIYDSTVIND----IIEGKPVQKIG 224

Query: 203 PAFTDEKYFGDGIGIAVRKGDKAELDKINAAIVAIRANGKYKQIQDKY 250
              T+E++     GIAVRK D   L K+N  +  + A+  +K +  KY
Sbjct: 225 SIETNEQF-----GIAVRKSDAELLKKLNTGLDHLMASPDWKALVQKY 267


Lambda     K      H
   0.318    0.138    0.395 

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: 168
Number of extensions: 11
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: 258
Length of database: 270
Length adjustment: 25
Effective length of query: 233
Effective length of database: 245
Effective search space:    57085
Effective search space used:    57085
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 47 (22.7 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