GapMind for catabolism of small carbon sources

 

Alignments for a candidate for bgtA in Shewanella oneidensis MR-1

Align BgtA aka SLR1735, component of Arginine/lysine/histidine/glutamine porter (characterized)
to candidate 202699 SO3602 sulfate ABC transporter, ATP-binding protein (NCBI ptt file)

Query= TCDB::P73721
         (252 letters)



>FitnessBrowser__MR1:202699
          Length = 376

 Score =  147 bits (370), Expect = 4e-40
 Identities = 94/246 (38%), Positives = 134/246 (54%), Gaps = 13/246 (5%)

Query: 9   ISFDQLQKNFGALQVLRGVTGEIYPKDVISIIGPSGCGKSTFLRCLNRLEPISGGRLEVA 68
           I    + K FG  Q L  +  +I   ++I ++GPSG GK+T LR +  LE    G +   
Sbjct: 3   IRLTNISKKFGQFQALSPLNLDIQEGEMIGLLGPSGSGKTTLLRIIAGLEGADSGHIHFG 62

Query: 69  GVDLSGAKIDQKHLRQLRVRVGMVFQHFNLFPHLTVLQN----LLLAPRKVLRIPMAEAK 124
             D++     Q H+R  RV  G VFQ++ LF H+TV  N    L + P+K  R   AE +
Sbjct: 63  NRDVT-----QVHVRDRRV--GFVFQNYALFRHMTVADNVAFGLEVIPKKQ-RPSAAEIQ 114

Query: 125 DRALTYLDKVGLGTKADNYPDQLSGGQKQRVAIARGLCMKPEILLFDEPTSALDPELVGE 184
            R    L+ V LG  A  YP+QLSGGQKQR+A+AR L  +PE+LL DEP  ALD ++  E
Sbjct: 115 KRVSHLLEMVQLGHLAQRYPEQLSGGQKQRIALARALATQPEVLLLDEPFGALDAKVRKE 174

Query: 185 VLNVMKQLAEE-GMTMAVVTHEMQFAREVSNRVFFFNQGIIEEEGDPNEVFRNPKSDRLR 243
           +   ++ L +E   T   VTH+   A E+S+RV   + G IE+   P E++  P S  + 
Sbjct: 175 LRRWLRSLHDELKFTSVFVTHDQDEALELSDRVVVMSNGNIEQVNTPIELYAQPNSRFVF 234

Query: 244 AFLSRI 249
            FL  +
Sbjct: 235 DFLGNV 240


Lambda     K      H
   0.321    0.139    0.397 

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: 9
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: 252
Length of database: 376
Length adjustment: 27
Effective length of query: 225
Effective length of database: 349
Effective search space:    78525
Effective search space used:    78525
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 (21.9 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