GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gtsD in Magnetospirillum magneticum AMB-1

Align ABC transporter for D-Glucose-6-Phosphate, ATPase component (characterized)
to candidate WP_043745616.1 AMB_RS21885 ABC transporter

Query= reanno::WCS417:GFF4321
         (386 letters)



>NCBI__GCF_000009985.1:WP_043745616.1
          Length = 229

 Score =  124 bits (312), Expect = 2e-33
 Identities = 86/223 (38%), Positives = 120/223 (53%), Gaps = 13/223 (5%)

Query: 1   MATLELRNVNKTYGAGLPDTLKNIELSIKEGEFLILVGPSGCGKSTLMNCIAGLETITGG 60
           + +LE  ++N    AG  + L  I+L +  GE L +VGPSG GKSTL+  +AGLE  T G
Sbjct: 11  LVSLEAVHLNLASLAGEVNVLDGIDLQVASGETLGVVGPSGSGKSTLLMVMAGLERPTSG 70

Query: 61  AIMIGDQDVS-----GMSPKDRD-IAMVFQSYALYPTMSVRENIEFGLKI--RKMPQADI 112
            + +  QD       G++   RD I +VFQS+ L PTM+  EN+   L++     P    
Sbjct: 71  KVAVAGQDFGPMDEDGLARFRRDSIGIVFQSFHLIPTMTALENVAVPLELAGHADPFGAA 130

Query: 113 DAEVARVAKLLQIEHLLNRKPGQLSGGQQQRVAMGRALARRPKIYLFDEPLSNLDAKLRV 172
             E+ RV     + H L+  PGQLSGG+QQRVA+ RA   RPK+ L DEP  NLD     
Sbjct: 131 QEELGRVG----LAHRLSHYPGQLSGGEQQRVALARAFVPRPKLLLADEPTGNLDGATGR 186

Query: 173 EMRTEMKLMHQRLKTTTVYVTHDQIEAMTLGDKVAVMKDGIIQ 215
            +   +  ++ R  T  V VTHD   A     +V  ++DG I+
Sbjct: 187 AVMDLLFDLNARFGTALVLVTHDDSLAARC-TRVVRVEDGKIK 228


Lambda     K      H
   0.318    0.135    0.382 

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: 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: 386
Length of database: 229
Length adjustment: 26
Effective length of query: 360
Effective length of database: 203
Effective search space:    73080
Effective search space used:    73080
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: 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