Align BgtA aka SLR1735, component of Arginine/lysine/histidine/glutamine porter (characterized)
to candidate Echvi_4044 Echvi_4044 ABC-type transport system involved in resistance to organic solvents, ATPase component
Query= TCDB::P73721 (252 letters) >FitnessBrowser__Cola:Echvi_4044 Length = 249 Score = 141 bits (355), Expect = 1e-38 Identities = 81/234 (34%), Positives = 132/234 (56%), Gaps = 4/234 (1%) Query: 14 LQKNFGALQVLRGVTGEIYPKDVISIIGPSGCGKSTFLRCLNRLEPISGGRLEVAGVDLS 73 L+K+FG L VL GV ++Y + + ++G SG GKS ++ + L G + V G ++S Sbjct: 11 LKKSFGELDVLMGVDLDLYKGENVVVLGKSGTGKSVLIKIMVGLLTQDEGTMNVLGKEVS 70 Query: 74 GAKIDQKHLRQLRVRVGMVFQHFNLFPHLTVLQNLLLA-PRKVLRIPMAEAKDRALTYLD 132 + K L +LR+++G FQ L+ +TV +NL R V + E L+ Sbjct: 71 N--LGAKDLNELRLKIGFSFQASALYDSMTVRENLEFPLVRNVKGLSRTEKDKMVEEVLE 128 Query: 133 KVGLGTKADNYPDQLSGGQKQRVAIARGLCMKPEILLFDEPTSALDPELVGEVLNVMKQL 192 VGL + P +LSGGQ++R+ IAR L +KPEI+L+DEPT+ LDP ++ N++ ++ Sbjct: 129 AVGLSQTINQMPSELSGGQRKRIGIARTLILKPEIMLYDEPTAGLDPITCSDINNLINEV 188 Query: 193 AEEGMTMA-VVTHEMQFAREVSNRVFFFNQGIIEEEGDPNEVFRNPKSDRLRAF 245 E T + ++TH++ AR+ +RV G EG EVF+ P+ R+++F Sbjct: 189 RENYNTSSIIITHDLTCARDTGDRVAVLLDGQFGAEGKFEEVFKTPEDQRVKSF 242 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: 140 Number of extensions: 7 Number of successful extensions: 4 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: 249 Length adjustment: 24 Effective length of query: 228 Effective length of database: 225 Effective search space: 51300 Effective search space used: 51300 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 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