Align Serine/threonine transporter SstT; Na(+)/serine-threonine symporter (characterized)
to candidate BWI76_RS24715 BWI76_RS24715 serine/threonine transporter SstT
Query= SwissProt::P0AGE4 (414 letters) >FitnessBrowser__Koxy:BWI76_RS24715 Length = 415 Score = 701 bits (1809), Expect = 0.0 Identities = 358/406 (88%), Positives = 389/406 (95%) Query: 9 LFRRLAHGSLVKQILVGLVLGILLAWISKPAAEAVGLLGTLFVGALKAVAPILVLMLVMA 68 L RRLA GSLVKQIL+GLVLG+LLA +SKPAA AVGLLGTLFVGALKAVAP+LVLMLVMA Sbjct: 10 LLRRLAQGSLVKQILIGLVLGVLLATVSKPAAVAVGLLGTLFVGALKAVAPVLVLMLVMA 69 Query: 69 SIANHQHGQKTNIRPILFLYLLGTFSAALAAVVFSFAFPSTLHLSSSAGDISPPSGIVEV 128 SIANHQ GQKT+IRPILFLYLLGTF+AAL AVVFSF FPSTLHL+++A I+PPSGIVEV Sbjct: 70 SIANHQQGQKTSIRPILFLYLLGTFAAALTAVVFSFIFPSTLHLNAAAESITPPSGIVEV 129 Query: 129 MRGLVMSMVSNPIDALLKGNYIGILVWAIGLGFALRHGNETTKNLVNDMSNAVTFMVKLV 188 +RGL+MSMVSNPIDALL NYIGILVWA+GLGFALRHGNETTKNL+ND+S+AVTF+VK+V Sbjct: 130 LRGLLMSMVSNPIDALLNANYIGILVWAVGLGFALRHGNETTKNLINDVSHAVTFIVKVV 189 Query: 189 IRFAPIGIFGLVSSTLATTGFSTLWGYAQLLVVLVGCMLLVALVVNPLLVWWKIRRNPFP 248 IRFAP+GIFGLV+STLATTGF TLWGYAQLL+VLVGCMLLVALV+NPLLV+WKIRRNP+P Sbjct: 190 IRFAPLGIFGLVASTLATTGFETLWGYAQLLLVLVGCMLLVALVINPLLVFWKIRRNPYP 249 Query: 249 LVLLCLRESGVYAFFTRSSAANIPVNMALCEKLNLDRDTYSVSIPLGATINMAGAAITIT 308 LVLLCLRESGVYAFFTRSSAANIPVNMAL EKLNLDRDTYSVSIPLGATINMAGAAITIT Sbjct: 250 LVLLCLRESGVYAFFTRSSAANIPVNMALSEKLNLDRDTYSVSIPLGATINMAGAAITIT 309 Query: 309 VLTLAAVNTLGIPVDLPTALLLSVVASLCACGASGVAGGSLLLIPLACNMFGISNDIAMQ 368 VLTLAAV+TL +PVDLPTALLLSVVASLCACGASGVAGGSLLLIPLACNMFGI ND+AMQ Sbjct: 310 VLTLAAVHTLNVPVDLPTALLLSVVASLCACGASGVAGGSLLLIPLACNMFGIPNDVAMQ 369 Query: 369 VVAVGFIIGVLQDSCETALNSSTDVLFTAAACQAEDDRLANSALRN 414 VVAVGFIIGVLQDSCETALNSSTDVLFTAAAC AED+++A +ALRN Sbjct: 370 VVAVGFIIGVLQDSCETALNSSTDVLFTAAACIAEDEQIAKNALRN 415 Lambda K H 0.325 0.138 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: 545 Number of extensions: 16 Number of successful extensions: 1 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: 414 Length of database: 415 Length adjustment: 31 Effective length of query: 383 Effective length of database: 384 Effective search space: 147072 Effective search space used: 147072 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.0 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.6 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