GapMind for catabolism of small carbon sources

 

Alignments for a candidate for AZOBR_RS08245 in Marinobacter adhaerens HP15

Align Leucine/isoleucine/valine ABC transporter,ATPase component; EC 3.6.3.- (characterized, see rationale)
to candidate GFF3713 HP15_3655 urea ABC transporter, ATP-binding protein UrtD

Query= uniprot:G8ALJ0
         (294 letters)



>FitnessBrowser__Marino:GFF3713
          Length = 253

 Score =  143 bits (361), Expect = 3e-39
 Identities = 98/258 (37%), Positives = 141/258 (54%), Gaps = 18/258 (6%)

Query: 11  LLTVEHLTMRFGGLVAVNDVSFSANNGEITAIIGPNGAGKTTLFNCITGFYTPTVGRLTL 70
           LL VE LT+ F G  AV+D+SF  +  EI  IIGPNGAGKTT+ + I G    T G +  
Sbjct: 13  LLAVEGLTVSFDGFKAVDDLSFYLDPKEIRVIIGPNGAGKTTVLDLICGKTKATSGSIKF 72

Query: 71  RHADGKEFLLERMPGYRISQKASVARTFQNIRLFGGMSVLENLIVAQHNKLIRASGFSIA 130
              DGKE  L ++  ++I   + V R FQ   +F  ++V ENL V+         G S+ 
Sbjct: 73  ---DGKE--LTKLKEHQIVH-SGVGRKFQTPSVFEDLTVFENLEVSY------PKGHSVM 120

Query: 131 GLLGLPSYTRTEREAVDLAKYWLDRVRLLEFADWEAGNLPYGAQRRLEIARAMCTEPVML 190
           G LG     + + E +   +   + + L E  +  A +L +G ++ LEI   +  +P +L
Sbjct: 121 GALGF----KRDAEVISAVEEVAETIFLTEALNEPAASLSHGQKQWLEIGMLLIQKPDLL 176

Query: 191 CLDEPAAGLNPRESGELADLLTYIRDEHKIGVLLIEHDMSVVMTISDHVVVLDYGRKISD 250
            LDEP AG++  E  + A+LL  I  +H   VL+IEHDM  V  I+D V V+  G+ +S+
Sbjct: 177 MLDEPVAGMSVTERKKTAELLRVITRDHT--VLVIEHDMQFVGDIADRVTVMHQGKVLSE 234

Query: 251 GDPAFVKNDPAVIRAYLG 268
           G    VK+DP VI  YLG
Sbjct: 235 GSIEHVKSDPKVIEVYLG 252


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: 162
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: 253
Length adjustment: 25
Effective length of query: 269
Effective length of database: 228
Effective search space:    61332
Effective search space used:    61332
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