Align GlpT, component of Glycerol uptake porter, GlpSTPQV (characterized)
to candidate HSERO_RS17020 HSERO_RS17020 sugar ABC transporter ATP-binding protein
Query= TCDB::G3LHY9 (356 letters) >FitnessBrowser__HerbieS:HSERO_RS17020 Length = 406 Score = 215 bits (548), Expect = 1e-60 Identities = 117/316 (37%), Positives = 184/316 (58%), Gaps = 14/316 (4%) Query: 25 LKEVDHEWNDGGAYALLGPSGCGKTTLLNIISGLLQPSHGRILFDGKDVTNLSTQSRNIA 84 L +D DG LLGPSGCGK+T+L +I+GL S G + G V +L + RN+A Sbjct: 20 LHPLDLHIGDGEFVVLLGPSGCGKSTMLRMIAGLEDISGGTLRIGGTVVNDLPARERNVA 79 Query: 85 QVFQFPVIYDTMTVYDNLAFPLRNRGVAEADVDRRVRDILEMIDLASWARRKAQGLTADQ 144 VFQ +Y M+VYDN+AF LR A++DRRVR++ +++L + RK + ++ Q Sbjct: 80 MVFQNYALYPHMSVYDNIAFGLRRLKRPAAEIDRRVREVAALLNLEALLERKPRAMSGGQ 139 Query: 145 KQKISLGRGLVRNDVNAILFDEPLTVIDPHMKWVLRSQLKRLHKQFGFTMVYVTHDQTEA 204 +Q+ ++ R +++ + LFDEPL+ +D ++ LR +KRLH++ T VYVTHDQ EA Sbjct: 140 QQRAAIARAIIKTP-SVFLFDEPLSNLDAKLRAQLRGDIKRLHQRLRTTTVYVTHDQLEA 198 Query: 205 LTFAEKVVVMYDGQIVQIGTPAELFERPSHTFVGYFIGSPGMNFMPARIEGSTVKVGDET 264 +T A++V++M DG+IVQ G+PAEL+ P + F FIG+P MNF+ ++ ++ ET Sbjct: 199 MTLADRVILMQDGRIVQAGSPAELYRYPRNLFAAGFIGTPAMNFLSGTVQRQDGQLFIET 258 Query: 265 ------LTLEYAPKTSGTAKTELGIRPEFIRLGRE-------GMPITISKVEDIGRQKIV 311 LT E + +L +RP+ +R+ E P+++ VE +G ++ Sbjct: 259 AHQRWALTGERFSRLRHAMAVKLAVRPDHVRIAGEREPAASLTCPVSVELVEILGADALL 318 Query: 312 RARFADQPIAIVVPED 327 R DQ + +VP D Sbjct: 319 TTRCGDQTLTALVPAD 334 Lambda K H 0.321 0.137 0.405 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: 345 Number of extensions: 14 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: 356 Length of database: 406 Length adjustment: 30 Effective length of query: 326 Effective length of database: 376 Effective search space: 122576 Effective search space used: 122576 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 (21.8 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