Align GlpT, component of Glycerol uptake porter, GlpSTPQV (characterized)
to candidate GFF1380 HP15_1347 sulfate/thiosulfate transporter subunit
Query= TCDB::G3LHY9 (356 letters) >FitnessBrowser__Marino:GFF1380 Length = 362 Score = 187 bits (474), Expect = 5e-52 Identities = 116/304 (38%), Positives = 168/304 (55%), Gaps = 15/304 (4%) Query: 14 GANPKSDKDYSLKEVDHEWNDGGAYALLGPSGCGKTTLLNIISGLLQPSHGRILFDGKDV 73 G N DK +L +++ DG ALLGPSG GKTTLL II+GL P GRI F GKDV Sbjct: 7 GINKFFDKFQALHDINLTIPDGQLTALLGPSGSGKTTLLRIIAGLETPEEGRIRFSGKDV 66 Query: 74 TNLSTQSRNIAQVFQFPVIYDTMTVYDNLAFPL----RNRGVAEADVDRRVRDILEMIDL 129 T+L + R + VFQ ++ MTV +N+AF L R + ++ +RV+D+LEM+ L Sbjct: 67 TDLHVRDRRVGFVFQHYALFRHMTVAENVAFGLNVLPRKERPGKPEIRKRVKDLLEMVQL 126 Query: 130 ASWARRKAQGLTADQKQKISLGRGLVRNDVNAILFDEPLTVIDPHMKWVLRSQLKRLHKQ 189 A R L+ QKQ+I+L R + +L DEP +D ++ LR L+ LH + Sbjct: 127 EHLADRYPAQLSGGQKQRIALARAMAMRP-EILLLDEPFGALDAKVRKDLRRWLRSLHDE 185 Query: 190 FGFTMVYVTHDQTEALTFAEKVVVMYDGQIVQIGTPAELFERPSHTFVGYFIGSPGMNFM 249 FT V+VTHDQ EAL +++VVVM +G+I Q+ TP EL+ RP FV F+G +N + Sbjct: 186 LHFTSVFVTHDQEEALELSDQVVVMSNGRIEQVDTPLELYGRPDSRFVFEFLGQ--VNVL 243 Query: 250 PARIEGSTVKVGDETLTLEYAPKTSGTAKTELGIRPEFIRLGREG-----MPITISKVED 304 +I ++ GD + L P+ +L +RP +RL + +P I + Sbjct: 244 SGKIRDGVMRQGDAWIRL---PEGCENDDAQLYLRPHEVRLTQSASDDAHLPFRIEAINL 300 Query: 305 IGRQ 308 IG + Sbjct: 301 IGAE 304 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: 305 Number of extensions: 18 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: 362 Length adjustment: 29 Effective length of query: 327 Effective length of database: 333 Effective search space: 108891 Effective search space used: 108891 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: 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