GapMind for catabolism of small carbon sources

 

Alignments for a candidate for AZOBR_RS08245 in Methylocystis bryophila S285

Align Leucine/isoleucine/valine ABC transporter,ATPase component; EC 3.6.3.- (characterized, see rationale)
to candidate WP_085771912.1 B1812_RS12645 LPS export ABC transporter ATP-binding protein

Query= uniprot:G8ALJ0
         (294 letters)



>NCBI__GCF_002117405.1:WP_085771912.1
          Length = 288

 Score =  116 bits (290), Expect = 7e-31
 Identities = 82/264 (31%), Positives = 132/264 (50%), Gaps = 33/264 (12%)

Query: 11  LLTVEHLTMRFGGLVAVNDVSFSANNGEITAIIGPNGAGKTTLFNCITGFYTPTVGRLTL 70
           +L + +L   +     V DVS     GE   ++GPNGAGKTT+F  ITG   P  GR+TL
Sbjct: 51  VLAIHNLAKSYKTRRVVEDVSLHVRRGEAVGLLGPNGAGKTTVFYMITGLVKPDSGRITL 110

Query: 71  RHADGKEFLLERMPGYRISQKASVARTFQNIRLFGGMSVLENLI----VAQHNKLIRASG 126
              DG +  +  +P YR   +  +    Q + +F G++V EN++    + + +K  RA  
Sbjct: 111 ---DGYD--VTPLPMYR-RARLGIGYLPQEMSVFRGLTVEENILAVLEIVEPDKKKRAE- 163

Query: 127 FSIAGLLGLPSYTRTEREAVDLAKYWLDRVRLLEFADWEAGNLPYGAQRRLEIARAMCTE 186
             + GL                    L+  RL       A  +  G +RR EIARA+   
Sbjct: 164 -QLDGL--------------------LEEFRLAHLRKTPAIAVSGGERRRCEIARAIAGR 202

Query: 187 PVMLCLDEPAAGLNPRESGELADLLTYIRDEHKIGVLLIEHDMSVVMTISDHVVVLDYGR 246
           P  + LDEP AG++P   G + DL+ +++ +  IGVL+ +H +   + ++D   ++  G 
Sbjct: 203 PSFMLLDEPFAGIDPIAIGGIQDLVRHLK-QRGIGVLITDHSVRETLGLTDRAYIIYNGH 261

Query: 247 KISDGDPAFVKNDPAVIRAYLGEE 270
            +++G PA +  +P V R YLGE+
Sbjct: 262 VLTEGAPAEIVANPDVRRIYLGED 285


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: 203
Number of extensions: 9
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: 288
Length adjustment: 26
Effective length of query: 268
Effective length of database: 262
Effective search space:    70216
Effective search space used:    70216
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: 48 (23.1 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