GapMind for catabolism of small carbon sources

 

Alignments for a candidate for AZOBR_RS08245 in Desulfovibrio vulgaris Miyazaki F

Align Leucine/isoleucine/valine ABC transporter,ATPase component; EC 3.6.3.- (characterized, see rationale)
to candidate 8500738 DvMF_1481 ABC transporter related (RefSeq)

Query= uniprot:G8ALJ0
         (294 letters)



>FitnessBrowser__Miya:8500738
          Length = 259

 Score =  212 bits (540), Expect = 6e-60
 Identities = 122/262 (46%), Positives = 162/262 (61%), Gaps = 10/262 (3%)

Query: 11  LLTVEHLTMRFGGLVAVNDVSFSANNGEITAIIGPNGAGKTTLFNCITGFYTPTVGRLTL 70
           LL V  L++ FGG+ A++  SF+A  G ITA+IGPNGAGKTTL NC+TG   P  G +  
Sbjct: 3   LLAVRDLSVAFGGIRALDAASFTAQAGAITALIGPNGAGKTTLVNCVTGMVRPDSGNVAF 62

Query: 71  RHADGKEFLLERMPGYRISQKASVARTFQNIRLFGGMSVLENLIVAQHNKLIRASGFSIA 130
              D       R+P      +  +ARTFQ++R+FG MS+LEN++V  H  +       ++
Sbjct: 63  DGRDITGMAAHRLP------RLGLARTFQHLRVFGSMSLLENVMVGLHGHVRTGM---LS 113

Query: 131 GLLGLPSYTRTEREAVDLAKYWLDRVRLLEFADWEAGNLPYGAQRRLEIARAMCTEPVML 190
            +L LP   RTER   D A   LD   L + AD  AG LPYG Q+RL +ARA+  +P M+
Sbjct: 114 SMLRLPGVRRTERAMRDAAMRALDFTGLADRADGAAGLLPYGDQKRLVLARALVGDPRMI 173

Query: 191 CLDEPAAGLNPRESGELADLLTYIRDEHKIGVLLIEHDMSVVMTISDHVVVLDYGRKISD 250
            LDEP AGLNP E+ E+  L+  +R    + VLLIEHDMS+VM +SD VVVL  G KI++
Sbjct: 174 LLDEPVAGLNPAETHEMGGLILALR-ARGVAVLLIEHDMSLVMRVSDAVVVLCSGAKIAE 232

Query: 251 GDPAFVKNDPAVIRAYLGEEED 272
           G P  VK +P V+ AYLG  E+
Sbjct: 233 GAPGEVKRNPEVVNAYLGGGEE 254


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: 9
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: 259
Length adjustment: 25
Effective length of query: 269
Effective length of database: 234
Effective search space:    62946
Effective search space used:    62946
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