Align Serine/threonine transporter SstT; Na(+)/serine-threonine symporter (characterized)
to candidate 6938067 Sama_2200 serine/threonine transporter SstT (RefSeq)
Query= SwissProt::P0AGE4 (414 letters) >FitnessBrowser__SB2B:6938067 Length = 405 Score = 520 bits (1339), Expect = e-152 Identities = 270/404 (66%), Positives = 328/404 (81%), Gaps = 2/404 (0%) Query: 1 MTTQRSPGLFRRLAHGSLVKQILVGLVLGILLAWISKPAAEAVGLLGTLFVGALKAVAPI 60 M+T++S L A GSLV QI VG++ G+ LA S AA V LG LFVGALKA+AP+ Sbjct: 1 MSTEKS--LLANAAGGSLVLQIFVGIIAGVALAGFSPEAANQVAFLGDLFVGALKAIAPV 58 Query: 61 LVLMLVMASIANHQHGQKTNIRPILFLYLLGTFSAALAAVVFSFAFPSTLHLSSSAGDIS 120 LV +LV +SIAN G +TN+RPI+ LYL+GTF+AAL AV+ SFAFP++L L +A + Sbjct: 59 LVFVLVASSIANQVSGAQTNMRPIILLYLVGTFAAALTAVLMSFAFPTSLVLIDAAAGAN 118 Query: 121 PPSGIVEVMRGLVMSMVSNPIDALLKGNYIGILVWAIGLGFALRHGNETTKNLVNDMSNA 180 PP GI +V+ L+ +V NP++AL+ NYIG+L W +GLG ALRH + +TKN+++D+S+ Sbjct: 119 PPEGIGQVLNTLLFKLVDNPVNALINANYIGLLAWGVGLGIALRHASTSTKNMLHDVSHG 178 Query: 181 VTFMVKLVIRFAPIGIFGLVSSTLATTGFSTLWGYAQLLVVLVGCMLLVALVVNPLLVWW 240 V+ +V+ VI APIGIFGLV++T+A TGF L YAQLL VL+G M ++A VVNPL+V+ Sbjct: 179 VSQLVRFVICLAPIGIFGLVAATIAQTGFEALAAYAQLLGVLLGAMAVIAFVVNPLIVFL 238 Query: 241 KIRRNPFPLVLLCLRESGVYAFFTRSSAANIPVNMALCEKLNLDRDTYSVSIPLGATINM 300 KIRRNP+PLV CLRESGV AFFTRSSAANIPVNMALCE+L L DTYSVSIPLGATINM Sbjct: 239 KIRRNPYPLVFKCLRESGVTAFFTRSSAANIPVNMALCERLKLHEDTYSVSIPLGATINM 298 Query: 301 AGAAITITVLTLAAVNTLGIPVDLPTALLLSVVASLCACGASGVAGGSLLLIPLACNMFG 360 AGAAITITVLTLAAV+TLGI VDL TALLLSV+A++ ACGASGVAGGSLLLIPLAC++FG Sbjct: 299 AGAAITITVLTLAAVHTLGIEVDLATALLLSVIAAVSACGASGVAGGSLLLIPLACSLFG 358 Query: 361 ISNDIAMQVVAVGFIIGVLQDSCETALNSSTDVLFTAAACQAED 404 ISNDIAMQVVAVGF IGV+QDS ETALNSSTDVLFTAAAC+A + Sbjct: 359 ISNDIAMQVVAVGFTIGVIQDSAETALNSSTDVLFTAAACEAAE 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: 451 Number of extensions: 17 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: 405 Length adjustment: 31 Effective length of query: 383 Effective length of database: 374 Effective search space: 143242 Effective search space used: 143242 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