GapMind for catabolism of small carbon sources

 

Alignments for a candidate for AO353_21720 in Lactobacillus silagei IWT126

Align ABC transporter for D-glucosamine, permease component 2 (characterized)
to candidate WP_089136613.1 CES79_RS06000 amino acid ABC transporter permease

Query= reanno::pseudo3_N2E3:AO353_21720
         (220 letters)



>NCBI__GCF_002217945.1:WP_089136613.1
          Length = 229

 Score =  112 bits (279), Expect = 7e-30
 Identities = 62/205 (30%), Positives = 118/205 (57%), Gaps = 6/205 (2%)

Query: 18  LWSGFLTSVQCSVLAIMLGTLIGIVAGLVLTYGTLWMRAPFRFYVDLIRGTPVFVLVLAC 77
           L+ G  T+V+ + +A++LG ++G++ G++ T+    +R   R Y++  R  P  VL+   
Sbjct: 18  LFGGLWTTVEIAAVALVLGLILGVILGVLRTFPNRLLRLVLRLYLEFFRIVPTVVLLFLF 77

Query: 78  FYMAPA-LGWQIDAFQAGVLGLTLFCGSHVAEIVRGALQALPRGQMEASKAIGLTFYQAL 136
           +Y+ P  LG  + A Q   L   L+  + +++IVRGAL ++P+ Q E+  AIGL   Q  
Sbjct: 78  YYILPKQLGVNLPANQVATLVFALWTAAEMSDIVRGALISVPKHQRESGMAIGLNRLQLY 137

Query: 137 AYVLLPQALRQILPTWVNSSTEIVKASTLLSVIGVAELLLSTQQIIA---RTFMTLEFYL 193
            YVL+PQA+   LP  +N  T ++K ++LL +I V +++   QQ++    + + T  F++
Sbjct: 138 RYVLIPQAVSLELPATINLVTRVIKTTSLLMLISVMDVINVGQQVVEANNQKYPTGVFWV 197

Query: 194 FA--GFLFFIINYAIELLGRHIEKR 216
           +     ++F I+Y +    + ++K+
Sbjct: 198 YGIIFVMYFAIDYPLSWWAKRMDKK 222


Lambda     K      H
   0.330    0.142    0.440 

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: 151
Number of extensions: 12
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: 220
Length of database: 229
Length adjustment: 22
Effective length of query: 198
Effective length of database: 207
Effective search space:    40986
Effective search space used:    40986
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 (21.9 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