Align BgtA aka SLR1735, component of Arginine/lysine/histidine/glutamine porter (characterized)
to candidate WP_011911265.1 PST_RS00075 ectoine/hydroxyectoine ABC transporter ATP-binding protein EhuA
Query= TCDB::P73721 (252 letters) >NCBI__GCF_000013785.1:WP_011911265.1 Length = 279 Score = 240 bits (613), Expect = 2e-68 Identities = 127/259 (49%), Positives = 176/259 (67%), Gaps = 9/259 (3%) Query: 3 SPTAPLISFDQLQKNFGALQVLRGVTGEIYPKDVISIIGPSGCGKSTFLRCLNRLEPISG 62 +P P++ F + K +G L VL G+ ++ + ++IIGPSG GKST LR L LE I Sbjct: 20 APAQPMVRFASVTKRYGELTVLEGLDLDVQEGEKVAIIGPSGSGKSTLLRVLMTLEGIDD 79 Query: 63 GRLEVAGVDLSG--------AKIDQKHLRQLRVRVGMVFQHFNLFPHLTVLQNLLLAPRK 114 G +EV G L+ + +HLR++R +VGMVFQ FNLFPH+ LQN++ AP + Sbjct: 80 GLIEVDGEPLTHMPDGHGRLVPANARHLRRVRGKVGMVFQSFNLFPHMNALQNVMEAPVQ 139 Query: 115 VLRIPMAEAKDRALTYLDKVGLGTKADNYPDQLSGGQKQRVAIARGLCMKPEILLFDEPT 174 VL + EA++RA L VGL K +++P QLSGGQ+QRVAIAR L M+P+++LFDE T Sbjct: 140 VLGLSKREARERAEELLAMVGLEDKLEHFPAQLSGGQQQRVAIARALAMRPKVMLFDEVT 199 Query: 175 SALDPELVGEVLNVMKQLAE-EGMTMAVVTHEMQFAREVSNRVFFFNQGIIEEEGDPNEV 233 SALDPEL GEVL+V+++L E +TM +VTH+M FARE ++RV FF+QG I E+G P+ + Sbjct: 200 SALDPELCGEVLSVIRRLGEAHNLTMLMVTHQMGFAREFADRVCFFHQGRIHEQGSPDAL 259 Query: 234 FRNPKSDRLRAFLSRIQSS 252 F NP+ DR R FLS + + Sbjct: 260 FNNPQEDRTREFLSAVNEA 278 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: 199 Number of extensions: 7 Number of successful extensions: 3 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: 279 Length adjustment: 25 Effective length of query: 227 Effective length of database: 254 Effective search space: 57658 Effective search space used: 57658 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