Align Threonine/serine transporter TdcC; H(+)/threonine-serine symporter (characterized)
to candidate 6938669 Sama_2772 amino acid transporter, transmembrane (RefSeq)
Query= SwissProt::P0AAD8 (443 letters) >FitnessBrowser__SB2B:6938669 Length = 438 Score = 355 bits (911), Expect = e-102 Identities = 190/426 (44%), Positives = 263/426 (61%), Gaps = 22/426 (5%) Query: 17 WRKSDTTWTLGLFGTAIGAGVLFFPIRAGFGGLIPILLMLVLAYPIAFYCHRALARLCLS 76 W DTTW L LFGTA+GAG+LF PI AG GG P+++M +L P+ + HR L+R S Sbjct: 33 WTAQDTTWMLSLFGTAVGAGILFLPINAGMGGFWPLVVMALLIGPMTYLAHRGLSRFVCS 92 Query: 77 GSNPSGNITETVEEHFGKTGGVVITFLYFFAICPLLWIYGVTITNTFMTFWENQLGFAPL 136 S +IT+ VEEHFGK G IT LYFFAI P++ IYGV ITN +F NQLG L Sbjct: 93 SSIAGSDITQVVEEHFGKGAGKAITVLYFFAIYPIVLIYGVGITNVVDSFMVNQLGLESL 152 Query: 137 NRGFVALFLLLLMAFVIWFGKDLMVKVMSYLVWPFIASLVLISLSLIPYWNSAVIDQVDL 196 R ++ L+L M V+ G+ +M+KV +LV+P +A L +SL L+P WN A + +V Sbjct: 153 PRWLLSGVLILGMMSVMVAGEKIMLKVTQFLVYPLVAILAFMSLYLMPNWNLAAVKEV-- 210 Query: 197 GSLSLTGHDGILITVWLGISIMVFSFNFSPIVSSFVVSKREEYEKDFGRDFTERKCSQII 256 L T+WL I +++F+FN SP +S F VS + ++ + RK I+ Sbjct: 211 -----PAVGDFLGTIWLTIPVLIFAFNHSPAISQFAVSLKRDHGSN-----ASRKADIIL 260 Query: 257 SRASMLMVAVVMFFAFSCLFTLSPANMAEAKAQNIPVLSYLANHFASMTGTKTTFAITLE 316 +M++V VM F FSC+ +LSPA +AEAK+QN+P+LSYLAN F S + Sbjct: 261 RNTAMMLVGFVMLFVFSCVLSLSPAQLAEAKSQNLPILSYLANVFDSG---------FVS 311 Query: 317 YAASIIALVAIFKSFFGHYLGTLEGLNGLVLKFGYKGDKTKVSLGKLNTISMIFIMGSTW 376 Y IA VAI SFFGHY+G EG++G++ K +G V GKLN + F+ + W Sbjct: 312 YFGPFIAFVAIVSSFFGHYMGASEGMSGIIKK-QLEGKGKPVDEGKLNRFILGFMFLTIW 370 Query: 377 VVAYANPNILDLIEAMGAPIIASLLCLLPMYAIRKAPSLAKYRGRLDNVFVTVIGLLTIL 436 VA NP+IL +IEA+G PIIA++L L+PMYA+ + P+L YRGR+ N+FV + GLL++ Sbjct: 371 AVAVINPSILGMIEALGGPIIAAILYLMPMYAVYRVPALKAYRGRISNIFVIIAGLLSMT 430 Query: 437 NIVYKL 442 I+Y L Sbjct: 431 AILYGL 436 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: 564 Number of extensions: 29 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: 438 Length adjustment: 32 Effective length of query: 411 Effective length of database: 406 Effective search space: 166866 Effective search space used: 166866 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 Apr 09 2024. 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