GapMind for catabolism of small carbon sources

 

Alignments for a candidate for AO353_21715 in Pseudomonas simiae WCS417

Align ABC transporter for D-glucosamine, permease component 1 (characterized)
to candidate GFF5509 PS417_28195 amino acid ABC transporter permease

Query= reanno::pseudo3_N2E3:AO353_21715
         (220 letters)



>FitnessBrowser__WCS417:GFF5509
          Length = 276

 Score =  132 bits (332), Expect = 6e-36
 Identities = 75/199 (37%), Positives = 119/199 (59%), Gaps = 4/199 (2%)

Query: 18  LAGLGLGLELALVSIAIGCVIGLLMAFALLSKHRALRVLASVYVTVIRNTPILVLILLIY 77
           L G  L + L L +I    ++G + A   LSK      +AS Y +  R TP+L+ ILLIY
Sbjct: 70  LQGAALTVFLCLCAIVASSILGFVTALGRLSKSAVAFGIASFYASFFRGTPLLIQILLIY 129

Query: 78  FALPSLGIRLDKLPSFIITLSLYAGAYLTEVFRGGLLSIPKGLREAGLAIGLGEWQVKAY 137
             LP LG+    + + II LSL  GAYL+E+FR G+L +P G REA LA+G+ +  +  +
Sbjct: 130 LGLPQLGLVPGAIVAGIIALSLNYGAYLSEIFRAGILGVPHGQREAALALGMRDSVIFWH 189

Query: 138 VTVPVMLRNVLPALSNNFISLFKDTSLAAAIAVPELTYYARKINVESYRVIETWLVTTAL 197
           VT+P  +R ++P  +N FIS+ KD+SL + + V E+ + A+     SYR IE  ++TTA 
Sbjct: 190 VTLPQAMRTIIPPATNQFISMLKDSSLISVMGVWEVMFLAQSYGRSSYRYIE--MLTTAA 247

Query: 198 YVAACYLIAMLLRYLEQRL 216
            +   +++++ L  ++ R+
Sbjct: 248 II--YWVMSLGLELIQARM 264


Lambda     K      H
   0.329    0.143    0.416 

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: 154
Number of extensions: 9
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: 276
Length adjustment: 24
Effective length of query: 196
Effective length of database: 252
Effective search space:    49392
Effective search space used:    49392
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 17 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