GapMind for catabolism of small carbon sources

 

Alignments for a candidate for AO353_21725 in Moritella dasanensis ArB 0140

Align ABC transporter for D-glucosamine, ATPase component (characterized)
to candidate WP_017221498.1 A923_RS0109795 amino acid ABC transporter ATP-binding protein

Query= reanno::pseudo3_N2E3:AO353_21725
         (265 letters)



>NCBI__GCF_000276805.1:WP_017221498.1
          Length = 251

 Score =  225 bits (573), Expect = 8e-64
 Identities = 126/244 (51%), Positives = 157/244 (64%), Gaps = 11/244 (4%)

Query: 20  DLHKQY-GPLEVLKGVDLTMQRGNVVTLIGSSGSGKTTLLRCVNMLEEFQGGQILLDGES 78
           D+ K Y      LK V +T++RG VV +IG SGSGK+T LR +N LE    G I +DG +
Sbjct: 16  DVDKIYPNKCHALKKVSVTVKRGEVVVIIGPSGSGKSTFLRTLNQLETVTEGDITIDGIN 75

Query: 79  IGYHEVNGKRVRHSEKVIAQHRAMTGMAFQQFNLFPHLTALQNVTLGLLKVKKLHKDEAV 138
           +     N   +R +           GM FQ FNLFPHL+  +NV L  LKV  L K++  
Sbjct: 76  MYDSSTNINTLREN----------VGMVFQSFNLFPHLSVKENVKLAPLKVSNLGKEQVE 125

Query: 139 VLAEKWLERVGLLERRDHYPGQLSGGQQQRVAIARAIAMNPSLMLFDEVTSALDPELVGE 198
             A   L RVGL E+ D YP QLSGGQQQRVAIARA+AM P LMLFDE TSALDPE+VGE
Sbjct: 126 KDAISLLTRVGLAEKVDVYPSQLSGGQQQRVAIARALAMKPDLMLFDEPTSALDPEMVGE 185

Query: 199 VLSVIKGLAEDGMTMLLVTHEMRFAFEVSDKIVFMNQGRIEEQGPPKELFERPQSPRLAE 258
           VL V+K LAE+GMTM++VTHEM FA EV+D+++FM  G++     P   FE P  PRL +
Sbjct: 186 VLEVMKSLAEEGMTMVVVTHEMGFANEVADRVLFMEDGQLLVDDVPANFFENPSHPRLKK 245

Query: 259 FLKN 262
           FL +
Sbjct: 246 FLSS 249


Lambda     K      H
   0.319    0.135    0.379 

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: 174
Number of extensions: 7
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: 265
Length of database: 251
Length adjustment: 24
Effective length of query: 241
Effective length of database: 227
Effective search space:    54707
Effective search space used:    54707
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 Sep 24 2021. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

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