Align BztD, component of Glutamate/glutamine/aspartate/asparagine porter (characterized)
to candidate GFF3087 HP15_3030 histidine/lysine/arginine/ornithine transporter subunit
Query= TCDB::Q52666 (263 letters) >FitnessBrowser__Marino:GFF3087 Length = 256 Score = 236 bits (603), Expect = 3e-67 Identities = 125/253 (49%), Positives = 169/253 (66%), Gaps = 11/253 (4%) Query: 17 VSDEIAIQISQMNKWYGQFHVLRDINLTVHRGERIVIAGPSGSGKSTMIRCINRLEEHQS 76 ++D+ + + K + Q VL+ I+L +G+ + + G SGSGKST +RCIN LE S Sbjct: 1 MADQSPLICRDIYKTFDQLEVLKGISLETRKGDVVSLIGSSGSGKSTFLRCINLLETPTS 60 Query: 77 GKIIVDGI-----------ELTSDLKNIDKVRSEVGMVFQHFNLFPHLTILENLTLAPIW 125 G IIV G + +D K ++ +R+++ MVFQ FNL+ H+T+LEN+ AP+ Sbjct: 61 GDIIVHGDPIRFTTNRKGERIPADNKQVELIRAKLSMVFQSFNLWSHMTVLENIIEAPVH 120 Query: 126 VRKVPKREAEETAMYYLEKVKIPEQAQKYPGQLSGGQQQRVAIARSLCMKPKIMLFDEPT 185 V KVPK+EA E A YL KV I E+ YP Q+SGGQQQR AIAR+L M+P++MLFDEPT Sbjct: 121 VLKVPKKEAIERAEAYLNKVGIYERKDYYPAQMSGGQQQRAAIARALAMEPEVMLFDEPT 180 Query: 186 SALDPEMIKEVLDTMIQLAEEGMTMLCVTHEMGFAQAVANRVIFMADGQIVEQNNPHDFF 245 SALDPE++ EVL M LAEEG TM+ VTHEM FA+ V+++V+F+ G I EQ P F Sbjct: 181 SALDPELVGEVLKVMQGLAEEGRTMIVVTHEMAFARDVSSQVLFLHQGVIEEQGTPEKVF 240 Query: 246 HNPQSERTKQFLS 258 +P SER KQFL+ Sbjct: 241 DHPDSERMKQFLT 253 Lambda K H 0.320 0.134 0.391 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: 180 Number of extensions: 4 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: 263 Length of database: 256 Length adjustment: 24 Effective length of query: 239 Effective length of database: 232 Effective search space: 55448 Effective search space used: 55448 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 (21.8 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