Align Serine/threonine transporter SstT; Na(+)/serine-threonine symporter (characterized)
to candidate 202237 SO3122 sodium/dicarboxylate symporter (NCBI ptt file)
Query= SwissProt::P0AGE4 (414 letters) >FitnessBrowser__MR1:202237 Length = 408 Score = 517 bits (1331), Expect = e-151 Identities = 262/395 (66%), Positives = 325/395 (82%) Query: 12 RLAHGSLVKQILVGLVLGILLAWISKPAAEAVGLLGTLFVGALKAVAPILVLMLVMASIA 71 +LA+GSLV QILVG++ G+ LA S A+ V LG+LFVGALKA+APILV +LV +SIA Sbjct: 10 KLANGSLVLQILVGIIAGVALASFSHEWAKQVAFLGSLFVGALKAIAPILVFILVASSIA 69 Query: 72 NHQHGQKTNIRPILFLYLLGTFSAALAAVVFSFAFPSTLHLSSSAGDISPPSGIVEVMRG 131 N + +TN+RPI+ LYLLGTF+AAL AV+ S FP+TL L++ SPP GI EV+ Sbjct: 70 NQKKNTQTNMRPIVVLYLLGTFAAALTAVILSMMFPTTLVLAAGVEGTSPPQGISEVIST 129 Query: 132 LVMSMVSNPIDALLKGNYIGILVWAIGLGFALRHGNETTKNLVNDMSNAVTFMVKLVIRF 191 L+ +V NP++AL+ GNYIGIL W +GLG AL H +++TK + D+S+ ++ MV +IR Sbjct: 130 LLFKLVDNPVNALMTGNYIGILAWGVGLGLALHHSSDSTKQVFADVSHGISQMVHFIIRL 189 Query: 192 APIGIFGLVSSTLATTGFSTLWGYAQLLVVLVGCMLLVALVVNPLLVWWKIRRNPFPLVL 251 APIGIFGLV++T A TGF+ + GYAQLL VL+G M +AL++NPL+V+ KI+RNP+PLV+ Sbjct: 190 APIGIFGLVAATFAETGFAAIAGYAQLLAVLLGAMAFIALIINPLIVYVKIKRNPYPLVI 249 Query: 252 LCLRESGVYAFFTRSSAANIPVNMALCEKLNLDRDTYSVSIPLGATINMAGAAITITVLT 311 CLRESG+ AFFTRSSAANIPVNMALCEKL L DTY+VSIPLGATINM GAAITITVLT Sbjct: 250 RCLRESGMTAFFTRSSAANIPVNMALCEKLKLHEDTYAVSIPLGATINMGGAAITITVLT 309 Query: 312 LAAVNTLGIPVDLPTALLLSVVASLCACGASGVAGGSLLLIPLACNMFGISNDIAMQVVA 371 LAA +TLGI VDL TALLLSVVA++ ACGASGVAGGSLLLIPLAC++FGISND+AMQVVA Sbjct: 310 LAAAHTLGIQVDLLTALLLSVVAAISACGASGVAGGSLLLIPLACSLFGISNDVAMQVVA 369 Query: 372 VGFIIGVLQDSCETALNSSTDVLFTAAACQAEDDR 406 VGFIIGV+QD+ ETALNSSTDV+FTAAAC+A +++ Sbjct: 370 VGFIIGVIQDAAETALNSSTDVIFTAAACEAAENK 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: 428 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