GapMind for catabolism of small carbon sources

 

Alignments for a candidate for Ac3H11_1693 in Pseudomonas simiae WCS417

Align ABC transporter ATP-binding protein (characterized, see rationale)
to candidate GFF524 PS417_02670 ABC transporter

Query= uniprot:A0A165KC86
         (260 letters)



>FitnessBrowser__WCS417:GFF524
          Length = 291

 Score =  216 bits (549), Expect = 6e-61
 Identities = 120/283 (42%), Positives = 166/283 (58%), Gaps = 31/283 (10%)

Query: 5   SNEVVLKVAGISKRFGGLQALSDVGITIKRGQVYGLIGPNGAGKTTFFNVITGLYTPDAG 64
           S EVVL V  +   FGG++ALSDV + ++R  ++ LIGPNGAGKTT FN +TG Y    G
Sbjct: 2   SKEVVLSVEHLMMHFGGIKALSDVSLKVERNSIFALIGPNGAGKTTVFNCLTGFYKASGG 61

Query: 65  TFEL------------AGKPYEPT------------------AVHEVAKAGIARTFQNIR 94
             EL             G+ ++PT                    H V +AG+ARTFQNIR
Sbjct: 62  KIELNIRGKRTNVIQLLGERFQPTDFVSPKRFFSRVFYKMFGGTHWVNRAGLARTFQNIR 121

Query: 95  LFAEMTALENVMVGRHIRTGSGLFGAVFRTKGFKAEEAAIAKRAQELLDYVGIGKFADYK 154
           LF EM+ +EN++V +H+     +   +  TKG++  E+     A   L+ V +   A+  
Sbjct: 122 LFKEMSVVENLLVAQHMWVNRNMLAGILNTKGYRKAESDALDHAFYWLEVVDLVDCANRL 181

Query: 155 ARTLSYGDQRRLEIARALATDPQLIALDEPAAGMNATEKVQLRELIDRIRND-NRTILLI 213
           A  LSYG QRRLEIARA+ T PQ+I LDEPAAG+N  E   L  +I  +R++ + T++LI
Sbjct: 182 AGELSYGQQRRLEIARAMCTRPQIICLDEPAAGLNPQETEALSAMIRLLRDEHDLTVVLI 241

Query: 214 EHDVKLVMGLCDRVTVLDYGKQIAEGNPAEVQKNEKVIEAYLG 256
           EHD+ +VM + D + VLD+G  IAEG P  ++ + KVI AYLG
Sbjct: 242 EHDMGMVMSISDHIVVLDHGNVIAEGGPDAIRNDPKVIAAYLG 284


Lambda     K      H
   0.319    0.137    0.384 

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: 215
Number of extensions: 11
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: 260
Length of database: 291
Length adjustment: 25
Effective length of query: 235
Effective length of database: 266
Effective search space:    62510
Effective search space used:    62510
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 47 (22.7 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