Align NatA aka BRAF aka SLR0467, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE (characterized)
to candidate Dsui_0842 Dsui_0842 ABC-type branched-chain amino acid transport systems, ATPase component
Query= TCDB::Q55164 (267 letters) >FitnessBrowser__PS:Dsui_0842 Length = 593 Score = 175 bits (444), Expect = 2e-48 Identities = 101/259 (38%), Positives = 150/259 (57%), Gaps = 2/259 (0%) Query: 7 PAENLGSPESSLLLAQGLSKSFGGLRAVDHADIVVKEGSITGLIGPNGAGKTTLFNLLSN 66 P + + + LL A+G++K FGGL A + V+ G + LIGPNGAGK+T+FN +S Sbjct: 334 PRRQMPAAGTVLLQAEGVTKRFGGLVANKDMALTVQAGEVMALIGPNGAGKSTMFNCISG 393 Query: 67 FIRPDQGEVLFNGDSIGQLAPHQIALRGSVRTFQVAKVLSRLTVLENMLLADQHQTGEKF 126 P +G + F G + L IA G RTFQ ++LS +TVLEN+ + + + Sbjct: 394 VNPPSEGRISFLGQPVAGLEARDIARLGLSRTFQHVRLLSGMTVLENVAIGAHLRGRHNY 453 Query: 127 LPRLINFRRVQKEERANREKAMAMLESVGLGAKAQDYAGALSGGQRKLLEMARALMSNPK 186 L + R EE +A +E VGL D AG+L+ G+++++E+ARAL ++P Sbjct: 454 LAAGLRLERA--EEARLLAEAARQIERVGLAEHMFDAAGSLALGKQRIIEIARALAADPC 511 Query: 187 LILLDEPAAGVNPTLIGQICEHIVNWNRQGITFLVIEHNMDVIMTLCHHVWVLAEGRNLA 246 L+LLDEPAAG+ + E + +G+ L++EH+MD +M L V V+ G LA Sbjct: 512 LLLLDEPAAGLRYLEKQALAELLRKLRGEGMGILLVEHDMDFVMGLADRVVVMEFGEKLA 571 Query: 247 DGTPEQIQSDPRVLEAYLG 265 +G PE+IQ +P VLEAYLG Sbjct: 572 EGLPEEIQKNPAVLEAYLG 590 Lambda K H 0.319 0.136 0.389 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: 382 Number of extensions: 17 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: 267 Length of database: 593 Length adjustment: 31 Effective length of query: 236 Effective length of database: 562 Effective search space: 132632 Effective search space used: 132632 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 (21.7 bits) S2: 50 (23.9 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