GapMind for catabolism of small carbon sources

 

Alignments for a candidate for glpS in Pseudomonas litoralis 2SM5

Align ABC transporter for Glycerol, ATPase component 1 (characterized)
to candidate WP_090274680.1 BLU11_RS14815 polyamine ABC transporter ATP-binding protein

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



>NCBI__GCF_900105005.1:WP_090274680.1
          Length = 378

 Score =  153 bits (387), Expect = 6e-42
 Identities = 82/226 (36%), Positives = 137/226 (60%), Gaps = 2/226 (0%)

Query: 5   LDSISKKVGAQTWLYDMSLALQSGAVTVLLGATQAGKTSLMRIMAGLDAPTAGRVTVDGK 64
           ++ +SK+      + D++L +  G +  LLG + +GK++L+RI+AG + P+ GRV +DG+
Sbjct: 23  IERVSKQFDDALAVDDVTLTINRGEIFALLGGSGSGKSTLLRILAGFETPSEGRVLLDGQ 82

Query: 65  DVTGMPVRDRNVAMVYQQFINYPSMKVAANIASPLKLRGEKN--IDARVREIASRLHIDM 122
           ++T +P   R + M++Q +  +P M V  NIA  LK     N  I  RV E+   +H+  
Sbjct: 83  NITALPPHKRPINMMFQSYALFPHMTVEQNIAFGLKQDKLSNTEISERVAEMLKLVHMAK 142

Query: 123 FLDRYPAELSGGQQQRVALARALAKGAPLMLLDEPLVNLDYKLREELREELTQLFAAGQS 182
           +  R P +LSGGQ+QRVALAR+LAK   L+LLDEP+  LD KLR +++ EL ++      
Sbjct: 143 YAKRKPHQLSGGQRQRVALARSLAKRPKLLLLDEPMGALDKKLRSQMQLELVEIIERVGV 202

Query: 183 TVVYATTEPGEALLLGGYTAVLDEGQLLQYGPTAEVFHAPNSLRVA 228
           T +  T +  EA+ +    A++D+G ++Q G   +++ +P +  VA
Sbjct: 203 TCIMVTHDQEEAMTMAQRIAIMDQGWIVQVGTPMDIYESPVNRHVA 248


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: 234
Number of extensions: 13
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: 363
Length of database: 378
Length adjustment: 30
Effective length of query: 333
Effective length of database: 348
Effective search space:   115884
Effective search space used:   115884
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: 49 (23.5 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