Align Threonine/serine transporter TdcC; H(+)/threonine-serine symporter (characterized)
to candidate 5208227 Shew_0739 aromatic amino acid permease (RefSeq)
Query= SwissProt::P0AAD8 (443 letters) >FitnessBrowser__PV4:5208227 Length = 423 Score = 344 bits (882), Expect = 4e-99 Identities = 189/428 (44%), Positives = 259/428 (60%), Gaps = 22/428 (5%) Query: 13 KQSSWRKSDTTWTLGLFGTAIGAGVLFFPIRAGFGGLIPILLMLVLAYPIAFYCHRALAR 72 ++ W +SDTTW L LFGTA+GAG+LF PI AG GG P++LM V+ P+ + HR L+R Sbjct: 14 QRQGWTRSDTTWMLSLFGTAVGAGILFLPINAGMGGFWPLVLMAVIIGPMTYLAHRGLSR 73 Query: 73 LCLSGSNPSGNITETVEEHFGKTGGVVITFLYFFAICPLLWIYGVTITNTFMTFWENQLG 132 S +IT VEE+FG G IT LYFFAI P++ IYGV ITNT +F NQLG Sbjct: 74 FVCSSQRQGSDITHVVEEYFGVGAGKAITLLYFFAIYPIVLIYGVGITNTVDSFIVNQLG 133 Query: 133 FAPLNRGFVALFLLLLMAFVIWFGKDLMVKVMSYLVWPFIASLVLISLSLIPYWNSAVID 192 A R ++ L+L M V+ G+ M+KV LV+P + L +SL LIP W + Sbjct: 134 MASPPRFLLSGILVLGMMSVMVSGEKFMLKVTQLLVYPLVGILAFMSLYLIPSWKMDALM 193 Query: 193 QVDLGSLSLTGHDGILITVWLGISIMVFSFNFSPIVSSFVVSKREEYEKDFGRDFTERKC 252 +V L TVWL I ++VF+FN SP +S F VS +++Y + +K Sbjct: 194 EVPAAG-------EFLGTVWLTIPVLVFAFNHSPAISQFSVSLKKQYGSN-----AAKKA 241 Query: 253 SQIISRASMLMVAVVMFFAFSCLFTLSPANMAEAKAQNIPVLSYLANHFASMTGTKTTFA 312 I+ SM++V VM F FSC+ +LSPA +AEAKAQN+P+LSYLAN AS Sbjct: 242 DVILRNTSMMLVGFVMLFVFSCVLSLSPAQLAEAKAQNLPILSYLANVHASG-------- 293 Query: 313 ITLEYAASIIALVAIFKSFFGHYLGTLEGLNGLVLKFGYKGDKTKVSLGKLNTISMIFIM 372 + Y IIA++AI SFFGHYLG EGL G++ K + +VS K++ + F+ Sbjct: 294 -FVSYFGPIIAVIAIVSSFFGHYLGATEGLKGIITK-QLRSSNKEVSDAKIDKFILGFMF 351 Query: 373 GSTWVVAYANPNILDLIEAMGAPIIASLLCLLPMYAIRKAPSLAKYRGRLDNVFVTVIGL 432 + W VA NP+IL +IEA+G PIIA++L L+PMYA+ K P+L YRGR+ N+ V + GL Sbjct: 352 LTIWGVAVINPSILGMIEALGGPIIAAILYLMPMYAVYKVPALKAYRGRISNILVILAGL 411 Query: 433 LTILNIVY 440 L + I++ Sbjct: 412 LAMTAILF 419 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: 541 Number of extensions: 25 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: 423 Length adjustment: 32 Effective length of query: 411 Effective length of database: 391 Effective search space: 160701 Effective search space used: 160701 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