GapMind for catabolism of small carbon sources

 

Alignments for a candidate for AZOBR_RS08245 in Mesorhizobium ciceri biovar biserrulae WSM1271

Align Leucine/isoleucine/valine ABC transporter,ATPase component; EC 3.6.3.- (characterized, see rationale)
to candidate WP_013529094.1 MESCI_RS06155 ATP-binding cassette domain-containing protein

Query= uniprot:G8ALJ0
         (294 letters)



>NCBI__GCF_000185905.1:WP_013529094.1
          Length = 518

 Score =  350 bits (899), Expect = e-101
 Identities = 173/276 (62%), Positives = 217/276 (78%), Gaps = 5/276 (1%)

Query: 11  LLTVEHLTMRFGGLVAVNDVSFSANNGEITAIIGPNGAGKTTLFNCITGFYTPTVGRLTL 70
           +L V+HL+M+FGGLVA+ D+SF+A  GEITA+IGPNGAGKTT+FNCITGFY P+ G +TL
Sbjct: 17  ILQVDHLSMKFGGLVAIGDLSFAAKRGEITALIGPNGAGKTTVFNCITGFYKPSEGMITL 76

Query: 71  RHADGKEFLLERMPGYRISQKASVARTFQNIRLFGGMSVLENLIVAQHNKLIRASGFSIA 130
              DG  FLLER+P + I  +A VARTFQNIRLF GM++LENL+VAQHNKL++ASG+++ 
Sbjct: 77  NRNDGSTFLLERLPNHEIPARAKVARTFQNIRLFSGMTLLENLLVAQHNKLMKASGYTVL 136

Query: 131 GLLGLPSYTRTEREAVDLAKYWLDRVRLLEFADWEAGNLPYGAQRRLEIARAMCTEPVML 190
           GL G   Y +   E+V+LAK+WL++  L++ AD  AG+LPYGAQRRLEIARAMCT P +L
Sbjct: 137 GLFGFSGYRKASAESVELAKHWLEKADLVDRADDPAGDLPYGAQRRLEIARAMCTGPELL 196

Query: 191 CLDEPAAGLNPRESGELADLLTYIRDEHKIGVLLIEHDMSVVMTISDHVVVLDYGRKISD 250
           CLDEPAAGLNP+ES  L +LL  I++     +LLIEHDMSVVM ISDHVVVL+YGRKISD
Sbjct: 197 CLDEPAAGLNPKESAALNELLIDIKNTSGASILLIEHDMSVVMQISDHVVVLEYGRKISD 256

Query: 251 GDPAFVKNDPAVIRAYLGEEEDEELPPEIKADLPEV 286
           G P  V+ DP VI AYLG +++     E++A L EV
Sbjct: 257 GSPQSVRTDPRVIAAYLGVDDE-----EVEAVLTEV 287


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: 390
Number of extensions: 14
Number of successful extensions: 1
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: 518
Length adjustment: 30
Effective length of query: 264
Effective length of database: 488
Effective search space:   128832
Effective search space used:   128832
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: 50 (23.9 bits)

This GapMind analysis is from Apr 09 2024. 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