GapMind for catabolism of small carbon sources

 

Alignments for a candidate for SM_b21216 in Dechlorosoma suillum PS

Align ABC transporter for D-Glucosamine, ATPase component (characterized)
to candidate Dsui_3464 Dsui_3464 ABC-type nitrate/sulfonate/bicarbonate transport system, ATPase component

Query= reanno::Smeli:SM_b21216
         (360 letters)



>FitnessBrowser__PS:Dsui_3464
          Length = 263

 Score =  171 bits (433), Expect = 2e-47
 Identities = 97/220 (44%), Positives = 139/220 (63%), Gaps = 9/220 (4%)

Query: 1   MSALEIRNIRKRY----GEVETLKGIDIALESGEFLVLLGSSGCGKSTLLNIIAGLAEPS 56
           MS + I++++K +    G+V  LK I++ ++ GEF+ LLG SGCGKSTLLN +AG   PS
Sbjct: 1   MSDILIKDVQKVFKTPGGDVTALKDINLTVKQGEFVCLLGPSGCGKSTLLNAVAGFQPPS 60

Query: 57  GGDILIGERSVLGVHPKDRDIAMVFQSYALYPNLSVARNIGFGLEMRRVPQAEHDKAVRD 116
            G+I+I  + +L   P   D  MVFQ YAL+P ++VA+NI FGL++++  +AE D  V  
Sbjct: 61  AGEIVIEGKKILTPGP---DRGMVFQEYALFPWMTVAQNIAFGLQIQKKEKAEIDLTVNQ 117

Query: 117 TARLLQIENLLDRKPSQLSGGQRQRVAIGRALVRNPQVFLFDEPLSNLDAKLRMEMRTEL 176
              LL +++  DR P  LSGG RQRVAI R L  +  + L DEP   LDA  R  ++ EL
Sbjct: 118 LLDLLHLKDFRDRFPKDLSGGMRQRVAIARVLALDSPIMLMDEPFGALDALTRRNLQDEL 177

Query: 177 KRLHQMLRTTVVYVTHDQIEAMTLATRIAVM--RDGRIEQ 214
            R+ + L  T+++VTH   E++ LA RI VM  R G I++
Sbjct: 178 LRIWEKLNKTILFVTHSIEESIYLADRIVVMTYRPGTIKR 217


Lambda     K      H
   0.320    0.136    0.385 

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: 190
Number of extensions: 5
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: 360
Length of database: 263
Length adjustment: 27
Effective length of query: 333
Effective length of database: 236
Effective search space:    78588
Effective search space used:    78588
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