GapMind for catabolism of small carbon sources

 

Alignments for a candidate for aglK 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)



>NCBI__GCF_000009985.1:WP_011384270.1
          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.

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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