Align BgtA aka SLR1735, component of Arginine/lysine/histidine/glutamine porter (characterized)
to candidate 6937298 Sama_1468 putative macrolide efflux ABC transporter, ATP-binding protein (RefSeq)
Query= TCDB::P73721 (252 letters) >FitnessBrowser__SB2B:6937298 Length = 230 Score = 140 bits (354), Expect = 2e-38 Identities = 89/232 (38%), Positives = 134/232 (57%), Gaps = 11/232 (4%) Query: 8 LISFDQLQKNF----GALQVLRGVTGEIYPKDVISIIGPSGCGKSTFLRCLNRLEPISGG 63 +IS L K+F +Q LRGV I + ++I+GPSG GKST + + L+ + G Sbjct: 1 MISLQALTKSFRMGDAEVQALRGVDIHIRQNEFVAIMGPSGSGKSTLMNIIGCLDRPTSG 60 Query: 64 RLEVAGVDLSGAKIDQKHLRQLRVR-VGMVFQHFNLFPHLTVLQNLLLAPRKVLRIPMAE 122 + G + G D L +R R +G VFQ F+L P L+ L N+LL P + P + Sbjct: 61 NYLLNGSAVGGLSDDA--LSAVRNREIGFVFQSFHLLPRLSALDNVLL-PLRFSETPRGD 117 Query: 123 AKDRALTYLDKVGLGTKADNYPDQLSGGQKQRVAIARGLCMKPEILLFDEPTSALDPELV 182 + A+ L++VGLG + D+ P+QLSGGQ+QRVAIAR L +P +LL DEPT ALD + Sbjct: 118 -RQHAIELLERVGLGQRLDHRPNQLSGGQRQRVAIARALVNRPTLLLADEPTGALDSKTS 176 Query: 183 GEVLNVMKQLAEEGMTMAVVTHEMQFAREVSNRVFFFNQGIIEEEGD-PNEV 233 E++ + +L G T+ +VTHE + A E + R+ G+++++ P EV Sbjct: 177 VEIMALFDELHLSGQTIVLVTHEEEVA-ECAGRIIRMRDGVVQQDKQKPREV 227 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: 151 Number of extensions: 8 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: 252 Length of database: 230 Length adjustment: 23 Effective length of query: 229 Effective length of database: 207 Effective search space: 47403 Effective search space used: 47403 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