Align BgtA aka SLR1735, component of Arginine/lysine/histidine/glutamine porter (characterized)
to candidate WP_011842387.1 RSPH17029_RS17510 amino acid ABC transporter ATP-binding protein
Query= TCDB::P73721 (252 letters) >NCBI__GCF_000015985.1:WP_011842387.1 Length = 266 Score = 248 bits (632), Expect = 1e-70 Identities = 131/254 (51%), Positives = 177/254 (69%), Gaps = 6/254 (2%) Query: 1 MTSPTAPLISFDQLQKNFGALQVLRGVTGEIYPKDVISIIGPSGCGKSTFLRCLNRLEPI 60 MT T PL+ +++K+FG +VL+GV+ ++ +V+SIIG SG GKSTFLR +N +E Sbjct: 1 MTDAT-PLLRLREIRKSFGTFEVLKGVSLDVAQGEVVSIIGASGSGKSTFLRSINVMEMP 59 Query: 61 SGGRLEVAGVDLSGAKIDQKH-----LRQLRVRVGMVFQHFNLFPHLTVLQNLLLAPRKV 115 G ++ K H L++LR +GMVFQ +NL+PH+TVLQN++ AP + Sbjct: 60 QAGTMDFGDFHFDFRKGAASHPTKVQLQKLRAEIGMVFQSYNLWPHMTVLQNVIHAPMTL 119 Query: 116 LRIPMAEAKDRALTYLDKVGLGTKADNYPDQLSGGQKQRVAIARGLCMKPEILLFDEPTS 175 R P A+A + A L ++GL K D+YP +LSGGQ+QRVAIAR L MKP ++LFDE TS Sbjct: 120 RRTPRAQAVEEAEALLARIGLYEKRDSYPARLSGGQQQRVAIARALAMKPRLMLFDEVTS 179 Query: 176 ALDPELVGEVLNVMKQLAEEGMTMAVVTHEMQFAREVSNRVFFFNQGIIEEEGDPNEVFR 235 ALDPELV EVL +M LA +GMTM +VTHE+ FAR+VS+RV FF+QG++ E+G P+ V R Sbjct: 180 ALDPELVHEVLVLMASLAADGMTMLLVTHEIAFARDVSSRVLFFDQGVMAEQGPPDRVLR 239 Query: 236 NPKSDRLRAFLSRI 249 NP+S RLR FL RI Sbjct: 240 NPESPRLRQFLHRI 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: 201 Number of extensions: 8 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: 266 Length adjustment: 24 Effective length of query: 228 Effective length of database: 242 Effective search space: 55176 Effective search space used: 55176 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 Apr 09 2024. 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