GapMind for catabolism of small carbon sources

 

Alignments for a candidate for mtlK in Erythrobacter gangjinensis K7-2

Align ABC transporter for D-Mannitol, D-Mannose, and D-Sorbitol, ATPase component (characterized)
to candidate WP_047006727.1 AAW01_RS07155 ATP-binding cassette domain-containing protein

Query= reanno::WCS417:GFF2490
         (367 letters)



>NCBI__GCF_001010925.1:WP_047006727.1
          Length = 255

 Score =  154 bits (388), Expect = 3e-42
 Identities = 85/221 (38%), Positives = 129/221 (58%), Gaps = 5/221 (2%)

Query: 4   LKIKNLQKGFEGFSIIKGIDLEVNDKEFVVFVGPSGCGKSTLLRLIAGLEEVSEGTIELD 63
           L+I  L K ++G   +  + LE+   EFV  VG SG GKSTLL+ +  L E  EG++++D
Sbjct: 9   LRIAGLSKTYDGARAVDTVSLEIGAGEFVALVGASGSGKSTLLKCVNRLVEPDEGSVQID 68

Query: 64  GRDITEVTPA--KRDLAMVFQTYALYPHMSVRKNMSFALDLAGVDKKLVESKVSEAARIL 121
           G+D   + PA  +R +  VFQ   L+PH++V +N++    L      L   +++E   ++
Sbjct: 69  GQDTAGLPPAESRRRIGYVFQGIGLFPHLTVAQNIALPSRLES--NALSADRIAELLALV 126

Query: 122 ELGP-LLERKPKQLSGGQRQRVAIGRAIVRNPKIFLFDEPLSNLDAALRVQMRLELARLH 180
           EL P + +R P +LSGGQRQRV + RA+     + L DEP   LD   R ++   + RLH
Sbjct: 127 ELEPEMAQRMPSELSGGQRQRVGVARALSSESHLLLMDEPFGALDPLTRGELGKRVRRLH 186

Query: 181 KELQATMIYVTHDQVEAMTLADKVVVLNSGRIEQVGSPLEL 221
            +L  T + VTHD  EA+ LA +V+V++SGRI    +P  L
Sbjct: 187 DQLHLTTVLVTHDMAEALLLATRVLVMDSGRIVADETPAAL 227


Lambda     K      H
   0.319    0.136    0.384 

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: 11
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: 367
Length of database: 255
Length adjustment: 27
Effective length of query: 340
Effective length of database: 228
Effective search space:    77520
Effective search space used:    77520
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 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