Align Monosaccharide-transporting ATPase; EC 3.6.3.17; Flags: Precursor (characterized, see rationale)
to candidate HSERO_RS22215 HSERO_RS22215 branched-chain amino acid ABC transporter permease
Query= uniprot:B2T9V8 (351 letters) >FitnessBrowser__HerbieS:HSERO_RS22215 Length = 323 Score = 154 bits (389), Expect = 3e-42 Identities = 103/304 (33%), Positives = 160/304 (52%), Gaps = 12/304 (3%) Query: 41 LALLPALALLIVIGAFISPSFLTKANLISVLGASAALALVVLAESLIVLTGKFDLSLEST 100 LALL + +L+V +P FL+ ++ ++L SA ++ LA+ L++LT DLS+ S Sbjct: 2 LALLTVVLILLV--GVRAPVFLSAQSMDNLLTDSAITIMLALAQMLVILTRGIDLSVASN 59 Query: 101 VGIAPAVGAMLVMPAASAGFGMQWPAAAGLLAIVVVGAVIGFINGFLVVRLRLNAFIVTL 160 + ++ + A+L M + P +L V++G ++G +NG+L+ L L +VTL Sbjct: 60 LALSGMMSALLAMHFPAL------PVGVFILMAVLIGLMLGLLNGWLIGYLELPPIVVTL 113 Query: 161 AMLIVLRGMLVGATKGGTLF--DMPTSFFALATTIVLGLPLSVWLAAAAFAIAAFMLRYH 218 + V RGM+ + G + +MP F A + GL VWL A A F+ R+ Sbjct: 114 GSMSVYRGMVFVLSGGAWVSSRNMPADFIAFPLARLGGLTHLVWLGALAVVAIWFLARHT 173 Query: 219 RLGRALYAIGGNPEAARAAGIRVE-RITWGVFVLGSILASVGGLIVTGYVGAINANQGNG 277 R GR LYAIG +P AA GI R+ W + G++ G L V Y A G Sbjct: 174 RFGRDLYAIGNDPAAAAYVGIASRGRLLWTYGLSGAMAGLAGYLWVARYAVAY-TEIAYG 232 Query: 278 MIFTVFAAAVIGGISLDGGKGTMFGALTGVLLLGVVQNLLTLAQVPSFWIQAIYGAIILG 337 TV AA VIGG+S+ GG G + GA+ G L L V+ N L + ++ FW A+ G +IL Sbjct: 233 FELTVIAACVIGGVSIAGGVGQVSGAVLGALFLSVINNALPIMRISPFWQSALTGLVILC 292 Query: 338 SLMV 341 ++++ Sbjct: 293 AVVL 296 Lambda K H 0.326 0.140 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: 248 Number of extensions: 13 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: 351 Length of database: 323 Length adjustment: 28 Effective length of query: 323 Effective length of database: 295 Effective search space: 95285 Effective search space used: 95285 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.1 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.6 bits) S2: 49 (23.5 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