GapMind for catabolism of small carbon sources

 

Alignments for a candidate for bgtA in Rhizorhabdus wittichii RW1

Align ATPase (characterized, see rationale)
to candidate WP_041378948.1 SWIT_RS04010 ABC transporter ATP-binding protein

Query= uniprot:Q31RN8
         (261 letters)



>NCBI__GCF_000016765.1:WP_041378948.1
          Length = 252

 Score =  149 bits (377), Expect = 4e-41
 Identities = 92/240 (38%), Positives = 141/240 (58%), Gaps = 6/240 (2%)

Query: 21  MIYAEGVEKWYGNQFQALCGVSLTVQRGEVVVMMGPSGSGKSTFLRTLNALESHQRGEIW 80
           MI  + V K Y  +   L  VSLT++RG  V ++G SG+GK+T L+ +N L     G I 
Sbjct: 1   MISFDHVGKHYAGR-HVLDDVSLTIERGSFVALVGASGAGKTTLLKAINRLVEIDTGTIA 59

Query: 81  IEGHRLSHDRRDIATIRQEVGMVFQQFNLFPHLTVLQNLMLAPVQVRRWPVAQAEATARQ 140
           IEG  ++   + +A +R+ +G VFQ   LFPH++V +N+ L P +++  P  +  A   +
Sbjct: 60  IEGRDVA--AQPVAELRRRIGYVFQGIGLFPHMSVAENVALVP-RLQGVPREERAARVAE 116

Query: 141 LLERVRI-AEQADKYPGQLSGGQQQRVAIARALAMQPRILLFDEPTSALDPEMVREVLDV 199
           LL+ V + A+ A++ P QLSGGQ QRV  ARALA +P I+L DEP  ALDP    E+   
Sbjct: 117 LLDLVALPADFAERRPAQLSGGQAQRVGFARALAARPAIMLMDEPFGALDPVTRDELGAA 176

Query: 200 MRDL-ASEGMTMLVATHEVGFAREVADRVVLMADGQIVEEAPPDRFFTAPQSDRAKQFLA 258
            R L  + G+T L+ TH++  A  +ADRV+++ +G+I+ + PP          R +  +A
Sbjct: 177 YRALHEAMGLTSLIVTHDMAEALLLADRVIVIGEGRILADQPPRALIHGAGDPRIEAMIA 236


Lambda     K      H
   0.321    0.134    0.387 

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: 153
Number of extensions: 6
Number of successful extensions: 4
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: 261
Length of database: 252
Length adjustment: 24
Effective length of query: 237
Effective length of database: 228
Effective search space:    54036
Effective search space used:    54036
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 (21.9 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