GapMind for catabolism of small carbon sources

 

Alignments for a candidate for AZOBR_RS08245 in Paucidesulfovibrio gracilis DSM 16080

Align Leucine/isoleucine/valine ABC transporter,ATPase component; EC 3.6.3.- (characterized, see rationale)
to candidate WP_078715624.1 B5D49_RS00115 ABC transporter ATP-binding protein

Query= uniprot:G8ALJ0
         (294 letters)



>NCBI__GCF_900167125.1:WP_078715624.1
          Length = 219

 Score = 80.1 bits (196), Expect = 4e-20
 Identities = 66/216 (30%), Positives = 102/216 (47%), Gaps = 44/216 (20%)

Query: 6   MTTTPLLTVEHLTMRFGGLVAVNDVSFSANNGEITAIIGPNGAGKTTLFNCITGFYTPTV 65
           M+T+PLL +E     +G  +   DV+ +   G++  + GPNGAGKTTL   + G   P+ 
Sbjct: 1   MSTSPLLRLEKAAKFYGAKLVFRDVTCAVEPGQVMLVAGPNGAGKTTLLKVMAGLSRPSA 60

Query: 66  GRLTLRHADGKEFLLERMPGYRISQKASVARTFQNIRLFGGMSVLENLIVAQHNKLIRAS 125
           G + L            +P  R +       TF    L+ G++ L+NL            
Sbjct: 61  GTVRL-----------DVPPERTAYLGHA--TF----LYPGLTALQNL------------ 91

Query: 126 GFSIAGLLGLPSYTRTEREAVDLAKYWLDRVRLLEFADWEAGNLPYGAQRRLEIARAMCT 185
           GF  A + GL    R+ ++ +++    L+RV L+  A+  AG+   G  +RL +AR    
Sbjct: 92  GF-WARMYGL---RRSRKQLMEM----LERVGLVRVAEERAGSFSRGMSQRLNLARVFLV 143

Query: 186 EPVMLCLDEPAAGLN-------PRESGELADLLTYI 214
           +P +L LDEP  GL+        RE G LA+  T I
Sbjct: 144 DPALLFLDEPGTGLDVTSLALLRREIGRLAEAGTSI 179


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: 142
Number of extensions: 6
Number of successful extensions: 2
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: 219
Length adjustment: 24
Effective length of query: 270
Effective length of database: 195
Effective search space:    52650
Effective search space used:    52650
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 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