GapMind for catabolism of small carbon sources


Aligments for a candidate for Ac3H11_2560 in Sphingomonas koreensis DSMZ 15582

Align ABC transporter for L-Histidine, ATPase component (characterized)
to candidate Ga0059261_1321 Ga0059261_1321 ABC-type antimicrobial peptide transport system, ATPase component

Query= reanno::acidovorax_3H11:Ac3H11_2560
         (259 letters)

>lcl|FitnessBrowser__Korea:Ga0059261_1321 Ga0059261_1321 ABC-type
           antimicrobial peptide transport system, ATPase component
          Length = 238

 Score =  124 bits (310), Expect = 2e-33
 Identities = 74/189 (39%), Positives = 100/189 (52%), Gaps = 9/189 (4%)

           QAL+ VD ++ + DFV ++GPSG GKST + I+  LD  TSG  L  G  +E    ++  

                  G VFQ + L       +N+   L  RG  +  + E     + KVGL  +  H 

           P +LSGG  QR AIARA+   P +LL DEP G LD+   V + ELL  + +    TVL V

Query: 193 THDIDEAIF 201
           TH+ D A F
Sbjct: 205 THEPDMAAF 213

Lambda     K      H
   0.322    0.136    0.394 

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: 119
Number of extensions: 5
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: 259
Length of database: 238
Length adjustment: 24
Effective length of query: 235
Effective length of database: 214
Effective search space:    50290
Effective search space used:    50290
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: 46 (22.3 bits)

This GapMind analysis is from Sep 17 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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code.

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