GapMind for catabolism of small carbon sources

 

Alignments for a candidate for AO353_03050 in Lactobacillus silagei IWT126

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

Query= reanno::pseudo3_N2E3:AO353_03050
         (229 letters)



>NCBI__GCF_002217945.1:WP_054656298.1
          Length = 247

 Score =  101 bits (251), Expect = 1e-26
 Identities = 66/194 (34%), Positives = 106/194 (54%), Gaps = 9/194 (4%)

Query: 15  LTLQLALSSMALAIVLGLIGVALRLSPIRWLARLGDLYSTVIRGIPDLVLILLIFYGGQD 74
           +TL +A+ SM LAI +G    +L+LS I  L      Y ++ RG+P LV + +IFYG   
Sbjct: 21  ITLLMAILSMILAIFIGGFLTSLQLSTIAPLRGFAHFYISLFRGMPTLVQLFIIFYG--- 77

Query: 75  LLNRVAPLLGYDDYIDLNPLVAGIGTLGFIFGAYLSETFRGAFMAIPKGQAEAGAAYGMS 134
            L ++ P L       L+  VA +  LGF   +YL+E FR A  ++ KGQ EAG +  +S
Sbjct: 78  -LPQIFPALR-----GLSAFVAVVVGLGFKQASYLAEIFRAAVNSVDKGQIEAGQSLNIS 131

Query: 135 SFQVFFRVLVPQMIRLAIPGFTNNWLVLTKATALISVVGLQDMMFKAKQAADATREPFTF 194
             ++F  V++PQ    A+P   N ++ L K T+L   +GL ++    K  A  + + F  
Sbjct: 132 RTKLFLNVVLPQATINALPATGNTFVSLVKETSLAFTLGLTELFGDGKLIAGQSFKYFET 191

Query: 195 FLAVAAMYLVITSV 208
           +LAV  +Y ++ ++
Sbjct: 192 YLAVGIIYWLLITI 205


Lambda     K      H
   0.329    0.144    0.421 

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: 148
Number of extensions: 9
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 ( 7.1 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