GapMind for catabolism of small carbon sources

 

Alignments for a candidate for AO353_21720 in Paraburkholderia phymatum STM815

Align ABC transporter for D-Glucosamine, permease component 1 (characterized)
to candidate WP_012404721.1 BPHY_RS27410 amino acid ABC transporter permease

Query= reanno::pseudo5_N2C3_1:AO356_00470
         (220 letters)



>NCBI__GCF_000020045.1:WP_012404721.1
          Length = 219

 Score =  139 bits (349), Expect = 5e-38
 Identities = 71/201 (35%), Positives = 124/201 (61%)

Query: 18  LWAGFLTSVQCSLLAIVLGTLIGLVAGLVLTYGRTWMRAPFRFYVDLIRGTPVFVLVLAC 77
           L  G + +++ +L + VLG L+G +  ++   G+  +    R YV L+RGTP+ V +   
Sbjct: 14  LLLGAMVTLKFALASAVLGLLVGFIVAIMGISGQPIIAGIARAYVSLMRGTPLLVQIFVV 73

Query: 78  FYMAPALGWQIGAFQAGVLGLTLFCGSHVAEIVRGALQALPRGQMEASQAIGLTFYQSLG 137
           +Y  P LG  +    AG+L LT   G++++E +RGA+  + +GQ  A+ ++GLT  Q+L 
Sbjct: 74  YYGLPDLGISLDPTSAGILALTANAGAYLSESMRGAILGISQGQWGAAHSLGLTHMQTLR 133

Query: 138 YVLLPQALRQILPTWVNSSTEIVKASTLLSVIGVAELLLSTQQIIARTFMTLEFYLFAGF 197
           YV+ PQALR  +P+  N+   ++K ++L+SVI V E+L + Q++IA TF  L  YL A  
Sbjct: 134 YVICPQALRMAVPSLGNTLISLIKDTSLVSVITVTEMLRAAQEVIASTFQPLPLYLAAAA 193

Query: 198 LFFIINYAIELLGRHIEKRVA 218
           ++++++  +  + RH+E R+A
Sbjct: 194 IYWLLSTGMSWVQRHVEVRLA 214


Lambda     K      H
   0.330    0.142    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: 158
Number of extensions: 8
Number of successful extensions: 1
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: 220
Length of database: 219
Length adjustment: 22
Effective length of query: 198
Effective length of database: 197
Effective search space:    39006
Effective search space used:    39006
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: 45 (21.9 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