GapMind for catabolism of small carbon sources

 

Alignments for a candidate for hisM in Lactobacillus silagei IWT126

Align ABC transporter for L-Lysine, permease component 2 (characterized)
to candidate WP_054656298.1 CES79_RS03760 amino acid ABC transporter permease

Query= reanno::pseudo5_N2C3_1:AO356_09910
         (229 letters)



>NCBI__GCF_002217945.1:WP_054656298.1
          Length = 247

 Score =  110 bits (275), Expect = 2e-29
 Identities = 66/207 (31%), Positives = 109/207 (52%), Gaps = 10/207 (4%)

Query: 2   NWDVIIKWLPKLAQGATLTLELVAIAVIAGLLLAIPLGIARSSRLWQVRALPYAYIFFFR 61
           +W        KL     +TL +  +++I  + +   L   + S +  +R   + YI  FR
Sbjct: 4   DWHYFFSLFIKLPAYVPITLLMAILSMILAIFIGGFLTSLQLSTIAPLRGFAHFYISLFR 63

Query: 62  GTPLLVQLFLVYYGLAQFDAVRSSALWPYLR--DPFWCATVTMTLHTAAYIAEILRGAIQ 119
           G P LVQLF+++YGL Q        ++P LR    F    V +    A+Y+AEI R A+ 
Sbjct: 64  GMPTLVQLFIIFYGLPQ--------IFPALRGLSAFVAVVVGLGFKQASYLAEIFRAAVN 115

Query: 120 AIPKGEIEAARALGMSRPKALFYIMLPRAARIGLPAYSNEVILMLKASALASTVTLLELT 179
           ++ KG+IEA ++L +SR K    ++LP+A    LPA  N  + ++K ++LA T+ L EL 
Sbjct: 116 SVDKGQIEAGQSLNISRTKLFLNVVLPQATINALPATGNTFVSLVKETSLAFTLGLTELF 175

Query: 180 GMARTIIARTYLPVEIFFAAGMFYLLM 206
           G  + I  +++   E + A G+ Y L+
Sbjct: 176 GDGKLIAGQSFKYFETYLAVGIIYWLL 202


Lambda     K      H
   0.331    0.141    0.434 

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: 142
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: 229
Length of database: 247
Length adjustment: 23
Effective length of query: 206
Effective length of database: 224
Effective search space:    46144
Effective search space used:    46144
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.2 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 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