GapMind for catabolism of small carbon sources

 

Alignments for a candidate for mglA in Shewanella loihica PV-4

Align glucose transporter, ATPase component (characterized)
to candidate 5208462 Shew_0974 spermidine/putrescine ABC transporter ATPase subunit (RefSeq)

Query= reanno::Phaeo:GFF3641
         (260 letters)



>FitnessBrowser__PV4:5208462
          Length = 378

 Score =  109 bits (273), Expect = 7e-29
 Identities = 74/239 (30%), Positives = 126/239 (52%), Gaps = 15/239 (6%)

Query: 15  LVEMKDISISFGGIKAVDHVSVDLYPGEVVGLLGHNGAGKSTLIKVLSGAYQMDAGEIRV 74
           L++++ +S  F  ++AVD VS+++  GE+  LLG +G+GKSTL+++L+G  +   G I +
Sbjct: 20  LLKIERVSKLFDDVRAVDDVSLNINRGEIFALLGGSGSGKSTLLRMLAGFEKPTEGRIYL 79

Query: 75  NGDKVEITNPRDARSHNIETIYQTLALADNLDAASNLFLGRELVTPFGLVDDSAMEAECR 134
           +G  +    P +     I  ++Q+ AL  ++  A N+         FGL  D   +AE  
Sbjct: 80  DGQDITDMPPYE---RPINMMFQSYALFPHMTVAQNI--------AFGLKQDKMPKAEIE 128

Query: 135 ---KIMNRLNPNFQKFSEPVSALSGGQRQSVAIARAVYFNAKILIMDEPTAALGPH-ETQ 190
              K M +L           + LSGGQRQ VA+AR++    K+L++DEP  AL     TQ
Sbjct: 129 QRVKEMLKLVHMEPYAKRKPNQLSGGQRQRVALARSLAKRPKLLLLDEPMGALDKKLRTQ 188

Query: 191 MVAELIQQLKAQGIGIFLIDHDVNAVMELCDRASVMKNGQLVGTVDIDDVTDDDLLSMI 249
           M  E++  L+A G+   ++ HD    M + +R ++M +G +  T    D+ +     M+
Sbjct: 189 MQLEVVDILEAVGVTCVMVTHDQEEAMTMAERIAIMNDGWIAQTGSPMDIYESPANRMV 247


Lambda     K      H
   0.317    0.135    0.373 

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: 169
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: 260
Length of database: 378
Length adjustment: 27
Effective length of query: 233
Effective length of database: 351
Effective search space:    81783
Effective search space used:    81783
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