Align Threonine/serine transporter TdcC; H(+)/threonine-serine symporter (characterized)
to candidate 7026223 Shewana3_3365 serine transporter, putative (RefSeq)
Query= SwissProt::P0AAD8 (443 letters) >FitnessBrowser__ANA3:7026223 Length = 430 Score = 349 bits (896), Expect = e-101 Identities = 191/443 (43%), Positives = 263/443 (59%), Gaps = 24/443 (5%) Query: 1 MSTSDSIVSSQTKQSSWRKSDTTWTLGLFGTAIGAGVLFFPIRAGFGGLIPILLMLVLAY 60 + T S S T+ W + DTTW L LFGTA+GAG+LF PI AG GG P++LM ++ Sbjct: 9 LETPQSTQESTTRHLPWTRQDTTWMLSLFGTAVGAGILFLPINAGMGGFWPLVLMAIIIG 68 Query: 61 PIAFYCHRALARLCLSGSNPSGNITETVEEHFGKTGGVVITFLYFFAICPLLWIYGVTIT 120 P+ + HR L+R S S P +IT+ VEEHFG G IT LYF AI P++ IYGV IT Sbjct: 69 PMTYLAHRGLSRFVCSSSIPGSDITQVVEEHFGIGAGKAITLLYFLAIYPIVLIYGVGIT 128 Query: 121 NTFMTFWENQLGFAPLNRGFVALFLLLLMAFVIWFGKDLMVKVMSYLVWPFIASLVLISL 180 NT +F NQLG A R ++ L+ M V+ G+ M+KV LV+P + L +S+ Sbjct: 129 NTVDSFIVNQLGMASPPRFLLSGVLIFGMMAVMVAGEQFMLKVTQLLVYPLVGILAFMSI 188 Query: 181 SLIPYWNSAVIDQV-DLGSLSLTGHDGILITVWLGISIMVFSFNFSPIVSSFVVSKREEY 239 LIP W + V D G+ L TVWL I ++VF+FN SP +S F VS + ++ Sbjct: 189 YLIPEWKMDALQVVPDTGA--------FLGTVWLTIPVLVFAFNHSPAISQFSVSLKRDH 240 Query: 240 EKDFGRDFTERKCSQIISRASMLMVAVVMFFAFSCLFTLSPANMAEAKAQNIPVLSYLAN 299 + RK I+ SM++V VM F FSC+ +LSP +AEAKA+N+P+LSYLAN Sbjct: 241 GVN-----AARKADVILRNTSMMLVGFVMLFVFSCVLSLSPEQLAEAKAKNLPILSYLAN 295 Query: 300 HFASMTGTKTTFAITLEYAASIIALVAIFKSFFGHYLGTLEGLNGLVLKFGYKGDKTKVS 359 S + Y IA VAI SFFGHY+G EG+ G+++K + ++S Sbjct: 296 VHDSG---------FVSYFGPFIAFVAIVSSFFGHYMGATEGMKGIIVK-QLRSSNKQIS 345 Query: 360 LGKLNTISMIFIMGSTWVVAYANPNILDLIEAMGAPIIASLLCLLPMYAIRKAPSLAKYR 419 KLN ++F+ + W VA NP+IL +IEA+G PIIA++L L+PMYA+ K P+L YR Sbjct: 346 ENKLNKFILVFMFATIWAVAIKNPSILGMIEALGGPIIAAILYLMPMYAVYKVPALKAYR 405 Query: 420 GRLDNVFVTVIGLLTILNIVYKL 442 R+ NVFV + GLL + I++ L Sbjct: 406 NRISNVFVIIAGLLAMTAILFGL 428 Lambda K H 0.328 0.141 0.430 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: 527 Number of extensions: 22 Number of successful extensions: 6 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: 443 Length of database: 430 Length adjustment: 32 Effective length of query: 411 Effective length of database: 398 Effective search space: 163578 Effective search space used: 163578 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.1 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.8 bits) S2: 51 (24.3 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