Align Serine/threonine transporter SstT; Na(+)/serine-threonine symporter (characterized)
to candidate Pf1N1B4_3934 Sodium:dicarboxylate symporter
Query= SwissProt::P0AGE4 (414 letters) >FitnessBrowser__pseudo1_N1B4:Pf1N1B4_3934 Length = 410 Score = 553 bits (1424), Expect = e-162 Identities = 278/402 (69%), Positives = 338/402 (84%) Query: 3 TQRSPGLFRRLAHGSLVKQILVGLVLGILLAWISKPAAEAVGLLGTLFVGALKAVAPILV 62 T SP L +RL H SLV QI++GL+ GI LA + A++ +G +FV ALKAVAPILV Sbjct: 2 TASSPSLLQRLKHSSLVTQIIIGLIAGITLALFAPELAKSTAFIGKVFVSALKAVAPILV 61 Query: 63 LMLVMASIANHQHGQKTNIRPILFLYLLGTFSAALAAVVFSFAFPSTLHLSSSAGDISPP 122 +LVMASIANH+HGQ+T+IRPILFLYLLGTF+AA+ AV+ S FPS+L LS+ ++ P Sbjct: 62 FVLVMASIANHKHGQETHIRPILFLYLLGTFAAAVVAVIASTLFPSSLVLSTQDVAVTAP 121 Query: 123 SGIVEVMRGLVMSMVSNPIDALLKGNYIGILVWAIGLGFALRHGNETTKNLVNDMSNAVT 182 GI EV++ L++S+V NP+ AL+ N+IGIL WAIG+G A+RH ETT+ ++ D+SN VT Sbjct: 122 GGISEVLQSLLLSVVDNPVSALMNANFIGILAWAIGMGVAIRHAGETTREVLGDLSNGVT 181 Query: 183 FMVKLVIRFAPIGIFGLVSSTLATTGFSTLWGYAQLLVVLVGCMLLVALVVNPLLVWWKI 242 +V+LVIRFAP+GIFGLV+STLAT+GF L GY LL VL+GCML VALV+NP +V+WK+ Sbjct: 182 LIVRLVIRFAPLGIFGLVASTLATSGFGALIGYMHLLAVLLGCMLFVALVMNPAIVFWKL 241 Query: 243 RRNPFPLVLLCLRESGVYAFFTRSSAANIPVNMALCEKLNLDRDTYSVSIPLGATINMAG 302 RRNP+PLVL CLRESG+ AFFTRSSAANIPVN+ L ++L L DTYSVSIPLGATINMAG Sbjct: 242 RRNPYPLVLTCLRESGITAFFTRSSAANIPVNLELSKRLGLHEDTYSVSIPLGATINMAG 301 Query: 303 AAITITVLTLAAVNTLGIPVDLPTALLLSVVASLCACGASGVAGGSLLLIPLACNMFGIS 362 AAITITVLTLAAV+TLGI VD+PTA+LLS+VA++CACGASGVAGGSLLLIPLAC++FGI Sbjct: 302 AAITITVLTLAAVHTLGIAVDIPTAILLSIVAAICACGASGVAGGSLLLIPLACSLFGIP 361 Query: 363 NDIAMQVVAVGFIIGVLQDSCETALNSSTDVLFTAAACQAED 404 ++IAMQVVAVGFIIGVLQDS ETALNSSTDVLFTAAACQ E+ Sbjct: 362 SEIAMQVVAVGFIIGVLQDSAETALNSSTDVLFTAAACQREE 403 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: 437 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: 410 Length adjustment: 31 Effective length of query: 383 Effective length of database: 379 Effective search space: 145157 Effective search space used: 145157 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