GapMind for catabolism of small carbon sources

 

Alignments for a candidate for glpS in Rhizorhabdus wittichii RW1

Align ABC transporter for Glycerol, ATPase component 1 (characterized)
to candidate WP_041378948.1 SWIT_RS04010 ABC transporter ATP-binding protein

Query= reanno::acidovorax_3H11:Ac3H11_791
         (363 letters)



>NCBI__GCF_000016765.1:WP_041378948.1
          Length = 252

 Score =  124 bits (311), Expect = 3e-33
 Identities = 86/253 (33%), Positives = 127/253 (50%), Gaps = 14/253 (5%)

Query: 3   LALDSISKKVGAQTWLYDMSLALQSGAVTVLLGATQAGKTSLMRIMAGLDAPTAGRVTVD 62
           ++ D + K    +  L D+SL ++ G+   L+GA+ AGKT+L++ +  L     G + ++
Sbjct: 2   ISFDHVGKHYAGRHVLDDVSLTIERGSFVALVGASGAGKTTLLKAINRLVEIDTGTIAIE 61

Query: 63  GKDVTGMPVRD--RNVAMVYQQFINYPSMKVAANIASPLKLRGEKNID--ARVREIASRL 118
           G+DV   PV +  R +  V+Q    +P M VA N+A   +L+G    +  ARV E+   +
Sbjct: 62  GRDVAAQPVAELRRRIGYVFQGIGLFPHMSVAENVALVPRLQGVPREERAARVAELLDLV 121

Query: 119 HIDM-FLDRYPAELSGGQQQRVALARALAKGAPLMLLDEPLVNLDYKLREELREELTQLF 177
            +   F +R PA+LSGGQ QRV  ARALA    +ML+DEP   LD   R+EL      L 
Sbjct: 122 ALPADFAERRPAQLSGGQAQRVGFARALAARPAIMLMDEPFGALDPVTRDELGAAYRALH 181

Query: 178 AAGQSTVVYATTEPGEALLLGGYTAVLDEGQLLQYGPTAEVFHAPNSLRVARAFSDPPMN 237
            A   T +  T +  EALLL     V+ EG++L   P   + H            DP + 
Sbjct: 182 EAMGLTSLIVTHDMAEALLLADRVIVIGEGRILADQPPRALIHGA---------GDPRIE 232

Query: 238 LMAASATAQGVRL 250
            M A A     RL
Sbjct: 233 AMIAVARRSAARL 245


Lambda     K      H
   0.318    0.133    0.375 

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: 185
Number of extensions: 6
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: 363
Length of database: 252
Length adjustment: 27
Effective length of query: 336
Effective length of database: 225
Effective search space:    75600
Effective search space used:    75600
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 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