GapMind for catabolism of small carbon sources

 

Alignments for a candidate for HSERO_RS17020 in Dechlorosoma suillum PS

Align ABC-type sugar transport system, ATPase component protein (characterized, see rationale)
to candidate Dsui_3464 Dsui_3464 ABC-type nitrate/sulfonate/bicarbonate transport system, ATPase component

Query= uniprot:D8IPI1
         (406 letters)



>FitnessBrowser__PS:Dsui_3464
          Length = 263

 Score =  152 bits (384), Expect = 1e-41
 Identities = 86/202 (42%), Positives = 123/202 (60%), Gaps = 3/202 (1%)

Query: 7   QALAKHYAGGPPVLHPLDLHIGDGEFVVLLGPSGCGKSTMLRMIAGLEDISGGTLRIGGT 66
           Q + K   G    L  ++L +  GEFV LLGPSGCGKST+L  +AG +  S G + I G 
Sbjct: 10  QKVFKTPGGDVTALKDINLTVKQGEFVCLLGPSGCGKSTLLNAVAGFQPPSAGEIVIEGK 69

Query: 67  VVNDLPARERNVAMVFQNYALYPHMSVYDNIAFGLRRLKRPAAEIDRRVREVAALLNLEA 126
            +   P  +R   MVFQ YAL+P M+V  NIAFGL+  K+  AEID  V ++  LL+L+ 
Sbjct: 70  KILT-PGPDRG--MVFQEYALFPWMTVAQNIAFGLQIQKKEKAEIDLTVNQLLDLLHLKD 126

Query: 127 LLERKPRAMSGGQQQRAAIARAIIKTPSVFLFDEPLSNLDAKLRAQLRGDIKRLHQRLRT 186
             +R P+ +SGG +QR AIAR +     + L DEP   LDA  R  L+ ++ R+ ++L  
Sbjct: 127 FRDRFPKDLSGGMRQRVAIARVLALDSPIMLMDEPFGALDALTRRNLQDELLRIWEKLNK 186

Query: 187 TTVYVTHDQLEAMTLADRVILM 208
           T ++VTH   E++ LADR+++M
Sbjct: 187 TILFVTHSIEESIYLADRIVVM 208


Lambda     K      H
   0.321    0.137    0.403 

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: 247
Number of extensions: 6
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: 406
Length of database: 263
Length adjustment: 28
Effective length of query: 378
Effective length of database: 235
Effective search space:    88830
Effective search space used:    88830
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 (21.8 bits)
S2: 48 (23.1 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