Align BgtA aka SLR1735, component of Arginine/lysine/histidine/glutamine porter (characterized)
to candidate 3608728 Dshi_2120 ABC transporter related (RefSeq)
Query= TCDB::P73721 (252 letters) >FitnessBrowser__Dino:3608728 Length = 376 Score = 147 bits (371), Expect = 3e-40 Identities = 93/247 (37%), Positives = 139/247 (56%), Gaps = 9/247 (3%) Query: 1 MTSPTAPLISFDQLQKNFGALQVLRGVTGEIYPKDVISIIGPSGCGKSTFLRCLNRLEPI 60 M + P++ FD + K FG+ ++ EI + ++I+G SGCGK+T LR L LE Sbjct: 7 MDQSSEPIVKFDNVVKRFGSFTAVKKADFEIGRGEFLAIMGSSGCGKTTTLRMLAGLEDP 66 Query: 61 SGGRLEVAGVDLSGAKIDQKHLRQLRVRVGMVFQHFNLFPHLTVLQNLLLAPRKVLRIPM 120 + G + + G ++G + MV+Q LFP LTV +N+ A K+ I Sbjct: 67 TEGAIYLDGEQVNGKATWDRD-------TPMVWQSLALFPFLTVQENVEFA-LKMRGIGK 118 Query: 121 AEAKDRALTYLDKVGLGTKADNYPDQLSGGQKQRVAIARGLCMKPEILLFDEPTSALDPE 180 E + RA +LDK+ + AD +QLSGGQKQRVA+AR L +P+ILL DEP SALD Sbjct: 119 EERRQRADKWLDKMQITEFADRNINQLSGGQKQRVALARALVTEPKILLLDEPLSALDAH 178 Query: 181 LVGEVLNVMKQLAEE-GMTMAVVTHEMQFAREVSNRVFFFNQGIIEEEGDPNEVFRNPKS 239 L + +V+ L ++ G+T VTH M A +++RV ++G IE+ G P E++R P + Sbjct: 179 LKVRMQSVLSNLQKDLGITFVYVTHSMSEAFSMADRVVIMSRGQIEQIGTPEEIYREPHN 238 Query: 240 DRLRAFL 246 + FL Sbjct: 239 RFVAEFL 245 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: 208 Number of extensions: 14 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: 376 Length adjustment: 27 Effective length of query: 225 Effective length of database: 349 Effective search space: 78525 Effective search space used: 78525 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: 48 (23.1 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