Align BgtA aka SLR1735, component of Arginine/lysine/histidine/glutamine porter (characterized)
to candidate 8502075 DvMF_2788 ABC transporter related (RefSeq)
Query= TCDB::P73721 (252 letters) >FitnessBrowser__Miya:8502075 Length = 243 Score = 262 bits (669), Expect = 5e-75 Identities = 136/243 (55%), Positives = 173/243 (71%), Gaps = 4/243 (1%) Query: 8 LISFDQLQKNFGA-LQVLRGVTGEIYPKDVISIIGPSGCGKSTFLRCLNRLEPISGGRLE 66 +I FD + K + + L VL+ +T EI +V+ I GPSG GKST +RC+N+LEPI G + Sbjct: 1 MIKFDHVHKWYASGLHVLQDITLEIKQGEVVVICGPSGSGKSTLIRCINKLEPIQKGHIV 60 Query: 67 VAGVDLSGAKIDQKHLRQLRVRVGMVFQHFNLFPHLTVLQNLLLAPRKVLRIPMAEAKDR 126 V GVD++ + + L LR VG VFQ FNL+PH+TVL+N+ LAP V P AEA+ Sbjct: 61 VDGVDINDPRTN---LTMLRAEVGFVFQQFNLYPHMTVLENITLAPLLVRNTPRAEAEKT 117 Query: 127 ALTYLDKVGLGTKADNYPDQLSGGQKQRVAIARGLCMKPEILLFDEPTSALDPELVGEVL 186 A+ L+KV + KA YP QLSGGQ+QRVAIARGL MKP I+LFDEPTSALDPE++ EVL Sbjct: 118 AMELLEKVNIPDKAGAYPGQLSGGQQQRVAIARGLAMKPRIMLFDEPTSALDPEMINEVL 177 Query: 187 NVMKQLAEEGMTMAVVTHEMQFAREVSNRVFFFNQGIIEEEGDPNEVFRNPKSDRLRAFL 246 +VM+QLA EGMTM VTHEM FAREV++RV F +QG++ EE P F NP DR + FL Sbjct: 178 DVMRQLAREGMTMVCVTHEMGFAREVADRVIFMDQGVMVEENTPEAFFSNPVHDRTKEFL 237 Query: 247 SRI 249 S+I Sbjct: 238 SKI 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: 192 Number of extensions: 2 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: 243 Length adjustment: 24 Effective length of query: 228 Effective length of database: 219 Effective search space: 49932 Effective search space used: 49932 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