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.
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:
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