GapMind for catabolism of small carbon sources

 

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

Align BgtA aka SLR1735, component of Arginine/lysine/histidine/glutamine porter (characterized)
to candidate 5210736 Shew_3164 ABC transporter-related protein (RefSeq)

Query= TCDB::P73721
         (252 letters)



>FitnessBrowser__PV4:5210736
          Length = 241

 Score =  250 bits (638), Expect = 2e-71
 Identities = 134/244 (54%), Positives = 171/244 (70%), Gaps = 7/244 (2%)

Query: 8   LISFDQLQKNFGALQVLRGVTGEIYPKDVISIIGPSGCGKSTFLRCLNRLEPISGGRLEV 67
           +I    L K FG  QVL+G+   I   +V+S+IGPSG GKSTFLRC+N LE  + G + +
Sbjct: 1   MIKISNLHKYFGDNQVLKGIDESIARGEVVSVIGPSGSGKSTFLRCINLLEQPTQGEIVI 60

Query: 68  AGVDLSG--AKIDQKHLRQLRVRVGMVFQHFNLFPHLTVLQNLLLAPRKVLRIPMAEAKD 125
            G  ++   A ID+     LR +VGMVFQ+FNLFPH TV QN+ LAP K+  +  AEA  
Sbjct: 61  DGQSITAPDACIDK-----LRQKVGMVFQNFNLFPHKTVQQNITLAPVKLGLMTQAEADS 115

Query: 126 RALTYLDKVGLGTKADNYPDQLSGGQKQRVAIARGLCMKPEILLFDEPTSALDPELVGEV 185
            A+  LD+VGL  KA  YP  LSGGQKQRVAIAR L MKPE++LFDEPTSALDPE+VG+V
Sbjct: 116 EAMRLLDQVGLSDKASAYPASLSGGQKQRVAIARALAMKPELMLFDEPTSALDPEMVGDV 175

Query: 186 LNVMKQLAEEGMTMAVVTHEMQFAREVSNRVFFFNQGIIEEEGDPNEVFRNPKSDRLRAF 245
           L+VMKQLA+ GMTM +VTHEM FA++VS+RV F + G + E   P  +F  P+  R +AF
Sbjct: 176 LDVMKQLAQAGMTMVIVTHEMGFAKDVSDRVIFMDGGYVVESNVPALLFGQPQEPRTQAF 235

Query: 246 LSRI 249
           LS++
Sbjct: 236 LSKV 239


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: 212
Number of extensions: 8
Number of successful extensions: 2
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: 241
Length adjustment: 24
Effective length of query: 228
Effective length of database: 217
Effective search space:    49476
Effective search space used:    49476
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: 46 (22.3 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