Align BgtA aka SLR1735, component of Arginine/lysine/histidine/glutamine porter (characterized)
to candidate HSERO_RS23025 HSERO_RS23025 phosphate ABC transporter ATP-binding protein
Query= TCDB::P73721 (252 letters) >FitnessBrowser__HerbieS:HSERO_RS23025 Length = 239 Score = 239 bits (611), Expect = 3e-68 Identities = 127/240 (52%), Positives = 174/240 (72%), Gaps = 4/240 (1%) Query: 8 LISFDQLQKNFGALQVLRGVTGEIYPKDVISIIGPSGCGKSTFLRCLNRLEPISGGRLEV 67 ++ DQ+ K+FG QVL+GV+ E+ ++I+IIG SG GKST LRC++RLE I G +EV Sbjct: 1 IVKLDQVYKSFGDNQVLKGVSFEVARGEMIAIIGASGSGKSTALRCIDRLETIDSGSIEV 60 Query: 68 AGVDLSGAKIDQKHLRQLRVRVGMVFQHFNLFPHLTVLQNLLLAPRKVLRIPMAEAKDRA 127 AG+ + ++D L +LR VG+VFQ +NLFPHL VL+N++LA R V + AEA+ A Sbjct: 61 AGIRVDDPQVD---LHKLRREVGIVFQSYNLFPHLNVLENVMLALRHVKQQDKAEARRVA 117 Query: 128 LTYLDKVGLGTKADNYPDQLSGGQKQRVAIARGLCMKPEILLFDEPTSALDPELVGEVLN 187 L L +VGL KA+ YP+QLSGGQ+QRVAIAR L M P+++LFDE TSALDP+L GEVL Sbjct: 118 LAALAQVGLDEKANAYPEQLSGGQQQRVAIARSLAMAPKVMLFDEVTSALDPQLTGEVLR 177 Query: 188 VMKQLAEEGMTMAVVTHEMQFAREVSNRVFFFNQGIIEEEGDPNEVFRNPKSDRLRAFLS 247 VM+ LA GMTM +VTHEM FA+ V++R+ + +QG + E G P E+ +P + L+AFL+ Sbjct: 178 VMEDLAANGMTMLLVTHEMNFAKRVADRIIYMHQGRVWEVG-PGEMLDHPYTPELQAFLA 236 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: 197 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: 239 Length adjustment: 24 Effective length of query: 228 Effective length of database: 215 Effective search space: 49020 Effective search space used: 49020 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