Align BgtA aka SLR1735, component of Arginine/lysine/histidine/glutamine porter (characterized)
to candidate 8500594 DvMF_1342 ABC transporter related (RefSeq)
Query= TCDB::P73721 (252 letters) >FitnessBrowser__Miya:8500594 Length = 243 Score = 251 bits (641), Expect = 1e-71 Identities = 133/229 (58%), Positives = 164/229 (71%), Gaps = 3/229 (1%) Query: 21 LQVLRGVTGEIYPKDVISIIGPSGCGKSTFLRCLNRLEPISGGRLEVAGVDLSGAKIDQK 80 L LRGV+ + P +V+ IIGPSG GKSTFLRCLNRLE G + + G D+ + Sbjct: 17 LHALRGVSLSVAPGEVVVIIGPSGSGKSTFLRCLNRLEYADEGAIRIEGRDILDPDCE-- 74 Query: 81 HLRQLRVRVGMVFQHFNLFPHLTVLQNLLLAPRKVLRIPMAEAKDRALTYLDKVGLGTKA 140 + ++R VGMVFQ FNLFPHLTVL+NL LA V + AEA+ + + L KVG+ K Sbjct: 75 -INEVRAEVGMVFQSFNLFPHLTVLENLTLAQTTVRKRGKAEAEKKGMELLRKVGIAEKH 133 Query: 141 DNYPDQLSGGQKQRVAIARGLCMKPEILLFDEPTSALDPELVGEVLNVMKQLAEEGMTMA 200 + YPDQLSGGQ+QRVAIAR L M P+ +LFDEPTSALDPE+VGEVL+VMK LA EGMTM Sbjct: 134 NVYPDQLSGGQQQRVAIARALAMDPKAMLFDEPTSALDPEMVGEVLDVMKNLAREGMTMV 193 Query: 201 VVTHEMQFAREVSNRVFFFNQGIIEEEGDPNEVFRNPKSDRLRAFLSRI 249 VVTHEM FAREV++RV F +QG I E G P++ F P+ DR + FLS+I Sbjct: 194 VVTHEMGFAREVADRVVFMDQGSILEVGSPDKFFTAPEHDRTKLFLSQI 242 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: 202 Number of extensions: 5 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