Align Serine/threonine transporter SstT; Na(+)/serine-threonine symporter (characterized)
to candidate PfGW456L13_2541 Sodium:dicarboxylate symporter
Query= SwissProt::P0AGE4 (414 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_2541 Length = 402 Score = 542 bits (1396), Expect = e-159 Identities = 278/401 (69%), Positives = 339/401 (84%), Gaps = 3/401 (0%) Query: 11 RRLAHGSLVKQILVGLVLGILLAWISKPAAEAVGLLGTLFVGALKAVAPILVLMLVMASI 70 +RL SLV QI++GL+ GI LA I+ A++ +G +FV ALKAVAPILV +LVMASI Sbjct: 2 QRLKRLSLVTQIVIGLIAGIALALIAPDMAKSTAFIGKVFVSALKAVAPILVFVLVMASI 61 Query: 71 ANHQHGQKTNIRPILFLYLLGTFSAALAAVVFSFAFPSTLHLSSSAGDISPPSGIVEVMR 130 ANH+HGQ+T+IRPILFLYLLGTF+AA+ AVV S FPS+L LS+ ++ P GI EV++ Sbjct: 62 ANHKHGQETHIRPILFLYLLGTFAAAVVAVVASMTFPSSLVLSTQDVAVTAPGGIGEVLQ 121 Query: 131 GLVMSMVSNPIDALLKGNYIGILVWAIGLGFALRHGNETTKNLVNDMSNAVTFMVKLVIR 190 L++S+V NP+ AL+ N+IGIL WAIG+G A+RH +TT+ ++ D+SN VT +V+LVI Sbjct: 122 SLLLSVVDNPVSALMNANFIGILAWAIGMGIAIRHAGDTTREVLGDLSNGVTVIVRLVIS 181 Query: 191 FAPIGIFGLVSSTLATTGFSTLWGYAQLLVVLVGCMLLVALVVNPLLVWWKIRRNPFPLV 250 FAP+GIFGLV+STLAT+GF L GYA LL VL+GCML VALV+NPL+V+WK+RRNP+PLV Sbjct: 182 FAPLGIFGLVASTLATSGFGALIGYAHLLAVLLGCMLFVALVMNPLIVFWKLRRNPYPLV 241 Query: 251 LLCLRESGVYAFFTRSSAANIPVNMALCEKLNLDRDTYSVSIPLGATINMAGAAITITVL 310 L CLRESG+ AFFTRSSAANIPVN+ L ++L L DTYSVSIPLGATINMAGAAITITVL Sbjct: 242 LTCLRESGITAFFTRSSAANIPVNLELSKRLGLHEDTYSVSIPLGATINMAGAAITITVL 301 Query: 311 TLAAVNTLGIPVDLPTALLLSVVASLCACGASGVAGGSLLLIPLACNMFGISNDIAMQVV 370 TLAAV+TLGI VD+PTA+LLSVVA++CACGASGVAGGSLLLIPLAC++FGI ++IAMQVV Sbjct: 302 TLAAVHTLGITVDVPTAILLSVVAAICACGASGVAGGSLLLIPLACSLFGIPSEIAMQVV 361 Query: 371 AVGFIIGVLQDSCETALNSSTDVLFTAAAC---QAEDDRLA 408 AVGFIIGVLQDS ETALNSSTDVLFTAAAC +A+ +RLA Sbjct: 362 AVGFIIGVLQDSAETALNSSTDVLFTAAACLGEEAKAERLA 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: 432 Number of extensions: 8 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: 402 Length adjustment: 31 Effective length of query: 383 Effective length of database: 371 Effective search space: 142093 Effective search space used: 142093 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