Align BgtA aka SLR1735, component of Arginine/lysine/histidine/glutamine porter (characterized)
to candidate GFF3087 HP15_3030 histidine/lysine/arginine/ornithine transporter subunit
Query= TCDB::P73721 (252 letters) >FitnessBrowser__Marino:GFF3087 Length = 256 Score = 256 bits (653), Expect = 4e-73 Identities = 135/250 (54%), Positives = 181/250 (72%), Gaps = 9/250 (3%) Query: 6 APLISFDQLQKNFGALQVLRGVTGEIYPKDVISIIGPSGCGKSTFLRCLNRLEPISGGRL 65 +PLI D + K F L+VL+G++ E DV+S+IG SG GKSTFLRC+N LE + G + Sbjct: 5 SPLICRD-IYKTFDQLEVLKGISLETRKGDVVSLIGSSGSGKSTFLRCINLLETPTSGDI 63 Query: 66 EVAG------VDLSGAKI--DQKHLRQLRVRVGMVFQHFNLFPHLTVLQNLLLAPRKVLR 117 V G + G +I D K + +R ++ MVFQ FNL+ H+TVL+N++ AP VL+ Sbjct: 64 IVHGDPIRFTTNRKGERIPADNKQVELIRAKLSMVFQSFNLWSHMTVLENIIEAPVHVLK 123 Query: 118 IPMAEAKDRALTYLDKVGLGTKADNYPDQLSGGQKQRVAIARGLCMKPEILLFDEPTSAL 177 +P EA +RA YL+KVG+ + D YP Q+SGGQ+QR AIAR L M+PE++LFDEPTSAL Sbjct: 124 VPKKEAIERAEAYLNKVGIYERKDYYPAQMSGGQQQRAAIARALAMEPEVMLFDEPTSAL 183 Query: 178 DPELVGEVLNVMKQLAEEGMTMAVVTHEMQFAREVSNRVFFFNQGIIEEEGDPNEVFRNP 237 DPELVGEVL VM+ LAEEG TM VVTHEM FAR+VS++V F +QG+IEE+G P +VF +P Sbjct: 184 DPELVGEVLKVMQGLAEEGRTMIVVTHEMAFARDVSSQVLFLHQGVIEEQGTPEKVFDHP 243 Query: 238 KSDRLRAFLS 247 S+R++ FL+ Sbjct: 244 DSERMKQFLT 253 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: 216 Number of extensions: 6 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: 256 Length adjustment: 24 Effective length of query: 228 Effective length of database: 232 Effective search space: 52896 Effective search space used: 52896 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: 47 (22.7 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