GapMind for catabolism of small carbon sources

 

Alignments for a candidate for livG in Pedobacter sp. GW460-11-11-14-LB5

Align ABC transporter ATP-binding protein (characterized, see rationale)
to candidate CA265_RS01140 CA265_RS01140 ABC transporter

Query= uniprot:A0A165KC86
         (260 letters)



>FitnessBrowser__Pedo557:CA265_RS01140
          Length = 229

 Score = 96.3 bits (238), Expect = 5e-25
 Identities = 66/221 (29%), Positives = 105/221 (47%), Gaps = 25/221 (11%)

Query: 7   EVVLKVAGISKRFGG----LQALSDVGITIKRGQVYGLIGPNGAGKTTFFNVITGLYTPD 62
           E +L +  +SK +      L  L ++  +I  G    + GP+G+GKTT   +  GL    
Sbjct: 2   ESILNIRNVSKIYQSAGRELTVLDNINFSITAGSTVAITGPSGSGKTTLLGLCAGLDRAS 61

Query: 63  AGTFELAGKPYEPTAVHE---VAKAGIARTFQNIRLFAEMTALENVMVGRHIRTGSGLFG 119
           +GT EL G   E     E   V    +   FQN +L   +TALENVMV   +R       
Sbjct: 62  SGTVELNGIALEKLNEDERAAVRNQYVGFIFQNFQLLPTLTALENVMVPLELRGAKN--- 118

Query: 120 AVFRTKGFKAEEAAIAKRAQELLDYVGIGKFADYKARTLSYGDQRRLEIARALATDPQLI 179
                         I   A ELLD VG+   + +    LS G+Q+R+ +ARA +  P ++
Sbjct: 119 --------------IRAHALELLDKVGLADRSHHYPVQLSGGEQQRVSLARAFSNQPAIL 164

Query: 180 ALDEPAAGMNA-TEKVQLRELIDRIRNDNRTILLIEHDVKL 219
             DEP   ++A T +  ++ L D  ++   T++++ HD++L
Sbjct: 165 FADEPTGNLDAETSEKVIKLLFDLNKDAGTTLIIVTHDLEL 205


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: 154
Number of extensions: 16
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: 229
Length adjustment: 24
Effective length of query: 236
Effective length of database: 205
Effective search space:    48380
Effective search space used:    48380
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: 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