GapMind for catabolism of small carbon sources

 

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

Align ATP-binding component of a broad range amino acid ABC transporter (characterized, see rationale)
to candidate 5208462 Shew_0974 spermidine/putrescine ABC transporter ATPase subunit (RefSeq)

Query= uniprot:Q1MCU3
         (247 letters)



>FitnessBrowser__PV4:5208462
          Length = 378

 Score =  119 bits (297), Expect = 1e-31
 Identities = 73/236 (30%), Positives = 130/236 (55%), Gaps = 12/236 (5%)

Query: 8   GQPLLQVNGVETYYGNIRALAGVDVHVNKGEIVSLIGANGAGKSTLMMTICGSPQARTGS 67
           G+ LL++  V   + ++RA+  V +++N+GEI +L+G +G+GKSTL+  + G  +   G 
Sbjct: 17  GEVLLKIERVSKLFDDVRAVDDVSLNINRGEIFALLGGSGSGKSTLLRMLAGFEKPTEGR 76

Query: 68  VVFEGRDITRMPTHEIARLRIAQSPEGRRIFPRMTVLENLQMGAGLD-----NLKHFAED 122
           +  +G+DIT MP +E     + QS     +FP MTV +N+  G   D      ++   ++
Sbjct: 77  IYLDGQDITDMPPYERPINMMFQS---YALFPHMTVAQNIAFGLKQDKMPKAEIEQRVKE 133

Query: 123 VEKIFTLFPRLKERHAQRGGTLSGGEQQMLSIGRALMARPKLLLLDEPSLGLAPLIVKGI 182
           + K+  + P  K +  Q    LSGG++Q +++ R+L  RPKLLLLDEP   L   +   +
Sbjct: 134 MLKLVHMEPYAKRKPNQ----LSGGQRQRVALARSLAKRPKLLLLDEPMGALDKKLRTQM 189

Query: 183 FEAIRKLNEAEGLTVFLVEQNAFAALRLSHRAYVMVNGKVTMSGSGKELLANPEVR 238
              +  + EA G+T  +V  +   A+ ++ R  +M +G +  +GS  ++  +P  R
Sbjct: 190 QLEVVDILEAVGVTCVMVTHDQEEAMTMAERIAIMNDGWIAQTGSPMDIYESPANR 245


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: 219
Number of extensions: 12
Number of successful extensions: 4
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: 247
Length of database: 378
Length adjustment: 27
Effective length of query: 220
Effective length of database: 351
Effective search space:    77220
Effective search space used:    77220
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:

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