GapMind for catabolism of small carbon sources

 

Aligments for a candidate for thuK in Magnetospirillum magneticum AMB-1

Align ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized)
to candidate WP_011384270.1 AMB_RS09430 ABC transporter ATP-binding protein

Query= reanno::Smeli:SMc03065
         (362 letters)



>lcl|NCBI__GCF_000009985.1:WP_011384270.1 AMB_RS09430 ABC
           transporter ATP-binding protein
          Length = 262

 Score =  139 bits (350), Expect = 8e-38
 Identities = 78/191 (40%), Positives = 113/191 (59%), Gaps = 5/191 (2%)

Query: 18  VIHGIDLDIKEGEFVVFVGPSGCGKSTLLRMIAGLEEITGGDMFIDGERVNDVPPSKRGI 77
           V+  +DL+++ G+F+  VG SG GKSTLLR+IAGL     G ++++  +     P  R I
Sbjct: 30  VLQDLDLEVRHGDFIALVGQSGAGKSTLLRVIAGLVPAVLGQVYVEPPK----EPDSRQI 85

Query: 78  AMVFQSYALYPHMTVYDNMAFGMRIARESKEEIDRRVRGAADMLQLTPYLDRLPKALSGG 137
            MVFQ   L P   V  N+ +G+    +S+ E  RR   A D++ LT + DR P  LSGG
Sbjct: 86  GMVFQDARLLPWRRVLANVEYGLEGLVKSRHERRRRALAALDLVGLTEFADRWPHHLSGG 145

Query: 138 QRQRVAIGRAICRNPKVFLFDEPLSNLDAALRVATRIEIAKLSERMSDTTMIYVTHDQVE 197
           QRQRV + RA+   P + L DEP   LD A R   + ++  + +  + T++I+VTHD  E
Sbjct: 146 QRQRVGLARALAVRPALLLMDEPFGALDPATRHGLQDQLLSIWQ-ATGTSIIFVTHDIDE 204

Query: 198 AMTLADRIVVL 208
           A  LADR++VL
Sbjct: 205 ATYLADRVIVL 215


Lambda     K      H
   0.320    0.137    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: 253
Number of extensions: 9
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: 362
Length of database: 262
Length adjustment: 27
Effective length of query: 335
Effective length of database: 235
Effective search space:    78725
Effective search space used:    78725
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 17 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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint 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