Align Serine/threonine transporter SstT; Na(+)/serine-threonine symporter (characterized)
to candidate GFF2046 PS417_10435 serine/threonine protein kinase
Query= SwissProt::P0AGE4 (414 letters) >FitnessBrowser__WCS417:GFF2046 Length = 406 Score = 563 bits (1450), Expect = e-165 Identities = 285/403 (70%), Positives = 347/403 (86%) Query: 6 SPGLFRRLAHGSLVKQILVGLVLGILLAWISKPAAEAVGLLGTLFVGALKAVAPILVLML 65 +P L +RLA SLV QI++GL+ GILLA + AA+A G +G +FV ALKAVAPILV +L Sbjct: 4 APSLLQRLARVSLVTQIVIGLIAGILLALLLPEAAKATGFIGKVFVTALKAVAPILVFVL 63 Query: 66 VMASIANHQHGQKTNIRPILFLYLLGTFSAALAAVVFSFAFPSTLHLSSSAGDISPPSGI 125 VMASIANH+HGQ+T+I+PILFLYLLGTF+AA+ AV+ S FPS+L L++ +S P GI Sbjct: 64 VMASIANHKHGQETHIKPILFLYLLGTFAAAVVAVIASMWFPSSLVLATHDATVSAPGGI 123 Query: 126 VEVMRGLVMSMVSNPIDALLKGNYIGILVWAIGLGFALRHGNETTKNLVNDMSNAVTFMV 185 EV++ L++S+V NP+ AL+ N+IGIL WAIG+G A+RH ETT+ L++D+SN VT +V Sbjct: 124 GEVLQSLLLSVVDNPVSALMNANFIGILAWAIGMGVAIRHAGETTRTLLDDLSNGVTLIV 183 Query: 186 KLVIRFAPIGIFGLVSSTLATTGFSTLWGYAQLLVVLVGCMLLVALVVNPLLVWWKIRRN 245 ++VIRFAP+GIFGLV+STLAT+GF L GYA LLVVL+GCML VALVVNP +V+WK+RRN Sbjct: 184 RVVIRFAPLGIFGLVASTLATSGFGALLGYAHLLVVLIGCMLFVALVVNPAIVFWKLRRN 243 Query: 246 PFPLVLLCLRESGVYAFFTRSSAANIPVNMALCEKLNLDRDTYSVSIPLGATINMAGAAI 305 P+PLVL+CLRESG+ AFFTRSSAANIPVN+AL ++L L DTYSVSIPLGATINMAGAAI Sbjct: 244 PYPLVLMCLRESGITAFFTRSSAANIPVNLALSKRLGLHEDTYSVSIPLGATINMAGAAI 303 Query: 306 TITVLTLAAVNTLGIPVDLPTALLLSVVASLCACGASGVAGGSLLLIPLACNMFGISNDI 365 TITVLTLAAV+TLGI VDLPTA+LLSVVA++CACGASGVAGGSLLLIPLAC++FGI +DI Sbjct: 304 TITVLTLAAVHTLGIAVDLPTAVLLSVVAAICACGASGVAGGSLLLIPLACSLFGIPSDI 363 Query: 366 AMQVVAVGFIIGVLQDSCETALNSSTDVLFTAAACQAEDDRLA 408 AMQVVAVGFIIGVLQDS ETALNSSTDVLFTAAAC ++++ A Sbjct: 364 AMQVVAVGFIIGVLQDSAETALNSSTDVLFTAAACLGKEEQPA 406 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: 7 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: 406 Length adjustment: 31 Effective length of query: 383 Effective length of database: 375 Effective search space: 143625 Effective search space used: 143625 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