Align TreT, component of Trehalose porter (characterized)
to candidate GFF1647 PGA1_c16700 binding protein-dependent transport system, inner membrane component
Query= TCDB::Q97ZC2 (275 letters) >FitnessBrowser__Phaeo:GFF1647 Length = 316 Score = 100 bits (250), Expect = 3e-26 Identities = 83/277 (29%), Positives = 132/277 (47%), Gaps = 19/277 (6%) Query: 9 FLLVLPALAYVISFAFFPTIEAVYLSFQDPH-------GGFSLYNYKEL-SYFNLSSAII 60 FL + P + + S P I + SFQ G NY++L S A+ Sbjct: 34 FLYLSPMILLIGSVMLIPLIVGISYSFQSIELLNPFATGWVGFENYEKLWSDRKFWIALE 93 Query: 61 NTIVVTIGALAIQLALGFLVASVLSREFFGKRALSTITIIPMGIATVVAAVTFSFVFQTS 120 NT T ++ Q LG +A +L+ +FFGK+ + +P + T ++A+T++++F Sbjct: 94 NTFFWTFWSIFFQFFLGLGLAMLLNTQFFGKKLFQALVFLPWAVPTFLSALTWAWLFNPV 153 Query: 121 GGYANTILHSLFGLNV-----NWYQSSISSLLVVMIADSWKNTPIVALILLAGMSSIPKE 175 G I H L L V N ++ + A+ W P A+ LLA + SIP E Sbjct: 154 IG---PIPHWLAALGVLSEPYNILGDPDLAIWGPITANIWFGVPFFAITLLAALQSIPGE 210 Query: 176 LYYASAIDGAGPIRRFFYITLPNLRSFIGISLILRGVQEFNIFALPLILIGEHPPLLTTL 235 LY A+ IDGA P + F ITLP L I I+++LR + N L ++ G P T + Sbjct: 211 LYEAAEIDGATPWQSFTKITLPFLAPMIAITVMLRTIWIANFADLIFVMTGGGPANSTQI 270 Query: 236 IYD-LYTTTFPEVGLALAS--ATILLGFILVFSGIVI 269 + ++TT F ++ AS A LL +L ++ I++ Sbjct: 271 LSTYIFTTAFRKLDFGYASTIAVALLIILLAYAVILL 307 Lambda K H 0.328 0.143 0.414 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: 215 Number of extensions: 15 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: 275 Length of database: 316 Length adjustment: 26 Effective length of query: 249 Effective length of database: 290 Effective search space: 72210 Effective search space used: 72210 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 (21.7 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