GapMind for catabolism of small carbon sources

 

Alignments for a candidate for AZOBR_RS08245 in Dethiosulfovibrio salsuginis USBA 82

Align Leucine/isoleucine/valine ABC transporter,ATPase component; EC 3.6.3.- (characterized, see rationale)
to candidate WP_085543795.1 B9Y55_RS02610 ABC transporter ATP-binding protein

Query= uniprot:G8ALJ0
         (294 letters)



>NCBI__GCF_900177735.1:WP_085543795.1
          Length = 256

 Score =  189 bits (481), Expect = 4e-53
 Identities = 117/266 (43%), Positives = 158/266 (59%), Gaps = 17/266 (6%)

Query: 9   TPLLTVEHLTMRFGGLVAVNDVSFSANNGEITAIIGPNGAGKTTLFNCITGFYTPTVGRL 68
           T +L ++ L   FGG+ AV DVSF+   GE+  +IGPNGAGKTT+FN ITG Y    G +
Sbjct: 2   TEVLVLDTLNKFFGGVHAVRDVSFTLQKGELAGLIGPNGAGKTTVFNLITGVYPLDSGHV 61

Query: 69  TLRHADGKEFLLERMPGYRISQKAS--VARTFQNIRLFGGMSVLENLIVAQHNKLIRASG 126
           ++   D        + G R        +ARTFQN+RLF G SVLEN++ A   +    S 
Sbjct: 62  SMEGQD--------VTGIRTCDAVGKGIARTFQNLRLFKGSSVLENVMTAGQ-RYHPYSF 112

Query: 127 FSIAGLLGLPSYTRT--EREAVDLAKYWLDRVRLLEFADWEAGNLPYGAQRRLEIARAMC 184
           F  A  +G    T     +E++DL    L+RV L + AD  A  LPYG QRRLEIARA+ 
Sbjct: 113 FEAATHMGRWRSTEKAIRKESMDL----LERVGLAKDADRVADTLPYGHQRRLEIARALA 168

Query: 185 TEPVMLCLDEPAAGLNPRESGELADLLTYIRDEHKIGVLLIEHDMSVVMTISDHVVVLDY 244
             P +L LDEPAAG+NP E  EL  L+  I  +  + +L+IEH M +VM I  HV+ L++
Sbjct: 169 LRPRLLLLDEPAAGMNPEEVQELNVLIKNIHRDFDLTILVIEHHMELVMEICPHVICLNF 228

Query: 245 GRKISDGDPAFVKNDPAVIRAYLGEE 270
           G  I+DG P  ++ +  V++AYLGEE
Sbjct: 229 GAVIADGTPEDIQGNKEVLKAYLGEE 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: 183
Number of extensions: 8
Number of successful extensions: 3
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: 256
Length adjustment: 25
Effective length of query: 269
Effective length of database: 231
Effective search space:    62139
Effective search space used:    62139
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 24 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