Align Serine/threonine transporter SstT; Na(+)/serine-threonine symporter (characterized)
to candidate 7024234 Shewana3_1426 serine/threonine transporter SstT (RefSeq)
Query= SwissProt::P0AGE4 (414 letters) >FitnessBrowser__ANA3:7024234 Length = 408 Score = 520 bits (1338), Expect = e-152 Identities = 265/403 (65%), Positives = 328/403 (81%) Query: 4 QRSPGLFRRLAHGSLVKQILVGLVLGILLAWISKPAAEAVGLLGTLFVGALKAVAPILVL 63 ++ L +LA+GSLV QILVG++ G+ LA S AA+ V LG+LFVGALKA+APILV Sbjct: 2 KQESSLLAKLANGSLVLQILVGIIAGVSLASFSHEAAKQVAFLGSLFVGALKAIAPILVF 61 Query: 64 MLVMASIANHQHGQKTNIRPILFLYLLGTFSAALAAVVFSFAFPSTLHLSSSAGDISPPS 123 +LV +SIAN + +TN+RPI+ LYL GTF+AAL AVV S FP+ L L + SPP Sbjct: 62 ILVASSIANQKKNTQTNMRPIVVLYLFGTFAAALTAVVLSMMFPTNLVLVAGVEGTSPPQ 121 Query: 124 GIVEVMRGLVMSMVSNPIDALLKGNYIGILVWAIGLGFALRHGNETTKNLVNDMSNAVTF 183 GI EV+ L+ +V NP++AL+ GNYIGIL W +GLG AL H +++TK + D+S+ ++ Sbjct: 122 GIGEVINTLLFKLVDNPVNALMTGNYIGILAWGVGLGLALHHASDSTKQVFADVSHGISQ 181 Query: 184 MVKLVIRFAPIGIFGLVSSTLATTGFSTLWGYAQLLVVLVGCMLLVALVVNPLLVWWKIR 243 MV+ +IR APIGIFGLV++T A TGF+ + GYA+LL VL+G M ++AL+VNPL+V+ KI+ Sbjct: 182 MVRFIIRLAPIGIFGLVAATFAETGFAAIAGYAKLLAVLLGAMAIIALIVNPLIVYVKIK 241 Query: 244 RNPFPLVLLCLRESGVYAFFTRSSAANIPVNMALCEKLNLDRDTYSVSIPLGATINMAGA 303 RNP+PLV+ CLRESGV AFFTRSSAANIPVNMALCEKL L DTYSVSIPLGATINM GA Sbjct: 242 RNPYPLVIRCLRESGVTAFFTRSSAANIPVNMALCEKLKLHEDTYSVSIPLGATINMGGA 301 Query: 304 AITITVLTLAAVNTLGIPVDLPTALLLSVVASLCACGASGVAGGSLLLIPLACNMFGISN 363 AITITVLTLAA +TLGI VDL TALLLSVVA++ ACGASGVAGGSLLLIPLAC++FGISN Sbjct: 302 AITITVLTLAAAHTLGIQVDLLTALLLSVVAAISACGASGVAGGSLLLIPLACSLFGISN 361 Query: 364 DIAMQVVAVGFIIGVLQDSCETALNSSTDVLFTAAACQAEDDR 406 D+AMQVVAVGFIIGV+QD+ ETALNSSTDV+FTAAAC+A +++ Sbjct: 362 DVAMQVVAVGFIIGVIQDAAETALNSSTDVIFTAAACEAAENK 404 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: 435 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: 408 Length adjustment: 31 Effective length of query: 383 Effective length of database: 377 Effective search space: 144391 Effective search space used: 144391 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