GapMind for catabolism of small carbon sources

 

Alignments for a candidate for AZOBR_RS08245 in Dechlorosoma suillum PS

Align Leucine/isoleucine/valine ABC transporter,ATPase component; EC 3.6.3.- (characterized, see rationale)
to candidate Dsui_0627 Dsui_0627 ABC-type branched-chain amino acid transport systems, ATPase component

Query= uniprot:G8ALJ0
         (294 letters)



>FitnessBrowser__PS:Dsui_0627
          Length = 267

 Score =  202 bits (514), Expect = 7e-57
 Identities = 123/261 (47%), Positives = 160/261 (61%), Gaps = 12/261 (4%)

Query: 11  LLTVEHLTMRFGGLVAVNDVSFSANNGEITAIIGPNGAGKTTLFNCITGFYTPTVGRLTL 70
           LL    +   FGG+ A+  VS +   GEI  +IGPNGAGKTT FNC+TG Y P  GR+  
Sbjct: 7   LLEASDVAKHFGGVKALRGVSLTIREGEIYGLIGPNGAGKTTFFNCLTGLYVPNGGRIVF 66

Query: 71  RHADGKEFLLERMPGYRISQKASVARTFQNIRLFGGMSVLENLIVAQHNKLIRASGFSIA 130
             A+     L+    ++++ +  +ARTFQNIRLF  M+ LEN++V +H +  RA  F   
Sbjct: 67  AGAE-----LDTSAPHKVAAR-GIARTFQNIRLFAHMTALENVMVGRHQR-TRAGVF--- 116

Query: 131 GLLGLPSYTRTEREAVD-LAKYWLDRVRLLEFADWEAGNLPYGAQRRLEIARAMCTEPVM 189
           G +     TR E  A+   A+  L  V + + A   A +L YG QRRLEIARA+ TEP +
Sbjct: 117 GAIFRTPGTRAEEAAIQRRAEELLHYVGIADRAHDLAKHLSYGDQRRLEIARALATEPKL 176

Query: 190 LCLDEPAAGLNPRESGELADLLTYIRDEHKIGVLLIEHDMSVVMTISDHVVVLDYGRKIS 249
           L LDEPAAG+N  E+GEL  L+  IR +  I VLLIEHD+ +VM + D V VLDYG KI 
Sbjct: 177 LALDEPAAGMNASETGELRTLIEGIRKD-GITVLLIEHDVKLVMGLCDRVAVLDYGEKIC 235

Query: 250 DGDPAFVKNDPAVIRAYLGEE 270
           +  PA V+ DP VI AYLG E
Sbjct: 236 EDVPAVVQKDPRVITAYLGAE 256


Lambda     K      H
   0.319    0.137    0.397 

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: 220
Number of extensions: 10
Number of successful extensions: 4
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: 294
Length of database: 267
Length adjustment: 26
Effective length of query: 268
Effective length of database: 241
Effective search space:    64588
Effective search space used:    64588
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: 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