Align Serine/threonine transporter SstT; Na(+)/serine-threonine symporter (characterized)
to candidate 5208972 Shew_1458 serine/threonine transporter SstT (RefSeq)
Query= SwissProt::P0AGE4 (414 letters) >FitnessBrowser__PV4:5208972 Length = 407 Score = 533 bits (1372), Expect = e-156 Identities = 272/396 (68%), Positives = 327/396 (82%) Query: 9 LFRRLAHGSLVKQILVGLVLGILLAWISKPAAEAVGLLGTLFVGALKAVAPILVLMLVMA 68 LF +LA GSLV QI++G++ G+ LA S +AE+V LG LFVGALKA+APILV +LV A Sbjct: 7 LFAKLADGSLVLQIILGIIAGVALASFSPSSAESVAFLGDLFVGALKAIAPILVFILVAA 66 Query: 69 SIANHQHGQKTNIRPILFLYLLGTFSAALAAVVFSFAFPSTLHLSSSAGDISPPSGIVEV 128 SIAN + KTN+RPI+ LYL GTF+AA+ AV SF FP++L L S A +PP GI EV Sbjct: 67 SIANQKKNTKTNMRPIIVLYLFGTFAAAITAVTMSFLFPTSLVLVSGAQGATPPEGIGEV 126 Query: 129 MRGLVMSMVSNPIDALLKGNYIGILVWAIGLGFALRHGNETTKNLVNDMSNAVTFMVKLV 188 + L+ +V NP++AL+ GNYIGIL W +GLG AL H +E TK + D+S+ V+ MV+ V Sbjct: 127 LNTLLFKVVDNPVNALMTGNYIGILAWGVGLGIALHHASENTKTVFADVSHGVSQMVRFV 186 Query: 189 IRFAPIGIFGLVSSTLATTGFSTLWGYAQLLVVLVGCMLLVALVVNPLLVWWKIRRNPFP 248 IR APIGIFGLV++T A TGF + GYAQLL VL+G ML++AL++NPL+VW+KIRRNP+P Sbjct: 187 IRLAPIGIFGLVANTFAATGFEAIAGYAQLLAVLLGSMLIIALIINPLIVWFKIRRNPYP 246 Query: 249 LVLLCLRESGVYAFFTRSSAANIPVNMALCEKLNLDRDTYSVSIPLGATINMAGAAITIT 308 LV CLRESGV AFFTRSSAANIPVNMALCEKL+L DT+SVSIPLGATINMAGAAITIT Sbjct: 247 LVFTCLRESGVTAFFTRSSAANIPVNMALCEKLDLHEDTFSVSIPLGATINMAGAAITIT 306 Query: 309 VLTLAAVNTLGIPVDLPTALLLSVVASLCACGASGVAGGSLLLIPLACNMFGISNDIAMQ 368 VLTLAAV+T GI VD+ TA+LLSVVA++ ACGASGVAGGSLLLIPLAC++FGISND+AMQ Sbjct: 307 VLTLAAVHTEGIQVDILTAILLSVVAAVSACGASGVAGGSLLLIPLACSLFGISNDVAMQ 366 Query: 369 VVAVGFIIGVLQDSCETALNSSTDVLFTAAACQAED 404 VVAVGFIIGV+QDS ETALNSSTDVLFTAAAC+A + Sbjct: 367 VVAVGFIIGVIQDSAETALNSSTDVLFTAAACEAAE 402 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: 438 Number of extensions: 14 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: 407 Length adjustment: 31 Effective length of query: 383 Effective length of database: 376 Effective search space: 144008 Effective search space used: 144008 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