Align Threonine/serine transporter TdcC; H(+)/threonine-serine symporter (characterized)
to candidate PP_3589 PP_3589 serine:H+ symport permease, threonine-insensitive
Query= SwissProt::P0AAD8 (443 letters) >FitnessBrowser__Putida:PP_3589 Length = 426 Score = 382 bits (982), Expect = e-111 Identities = 203/434 (46%), Positives = 277/434 (63%), Gaps = 24/434 (5%) Query: 9 SSQTKQSSWRKSDTTWTLGLFGTAIGAGVLFFPIRAGFGGLIPILLMLVLAYPIAFYCHR 68 S+ +W + DTTW LGLFGTAIGAG LF PI AG GG P+L++ VLA+P+ ++ HR Sbjct: 15 STPAALGTWARHDTTWMLGLFGTAIGAGTLFLPINAGLGGFWPLLILAVLAFPMTYFAHR 74 Query: 69 ALARLCLSGSNPSGNITETVEEHFGKTGGVVITFLYFFAICPLLWIYGVTITNTFMTFWE 128 L R LSG + S +ITE V+EHFG T G IT LYFFAI P+L IY V +TNT +F E Sbjct: 75 GLTRFVLSGRDGS-DITEVVKEHFGITAGASITVLYFFAIFPILLIYSVALTNTVSSFME 133 Query: 129 NQLGFAPLNRGFVALFLLLLMAFVIWFGKDLMVKVMSYLVWPFIASLVLISLSLIPYWNS 188 +QL P R ++ L+L + ++ G+ VKVMS LV+PFI +L L+ L L+P+W Sbjct: 134 HQLHMQPPPRAILSFVLILGLLAIVRCGEQATVKVMSLLVYPFIVALALLGLYLVPHWTG 193 Query: 189 AVIDQVDLGSLSLTGHDGILITVWLGISIMVFSFNFSPIVSSFVVSKREEYEKDFGRDFT 248 ++D + + L T+WL I +MVFSFN SPI+S+F V ++ Y G Sbjct: 194 GILD----SATEVPPASAFLHTLWLAIPVMVFSFNHSPIISAFAVDQKRRY----GAHAD 245 Query: 249 ERKCSQIISRASMLMVAVVMFFAFSCLFTLSPANMAEAKAQNIPVLSYLANHFASMTGTK 308 ER QI+ RA +LMV +V+FF FSC+ TLS A +AEAKAQN+ +LSYLANHF++ Sbjct: 246 ERS-GQILRRAHLLMVVMVLFFVFSCVLTLSSAQLAEAKAQNLSILSYLANHFSNP---- 300 Query: 309 TTFAITLEYAASIIALVAIFKSFFGHYLGTLEGLNGLVLKFGYKGDKTKVSLGKLNTISM 368 T+ +AA +IA VAI KSF GHY+G EGL G++ K G + L+ + Sbjct: 301 -----TIAFAAPLIAFVAIAKSFLGHYIGASEGLKGIIAKTG-----ARPGAKALDRVVA 350 Query: 369 IFIMGSTWVVAYANPNILDLIEAMGAPIIASLLCLLPMYAIRKAPSLAKYRGRLDNVFVT 428 ++ W+VA NP+IL +IE++G PI+A LL L+PMYAIR+ PS+ KY G NVFV Sbjct: 351 ALMLVVCWIVATLNPSILGMIESLGGPILAVLLFLMPMYAIRRVPSMRKYSGAASNVFVV 410 Query: 429 VIGLLTILNIVYKL 442 V+GL+ + ++VY L Sbjct: 411 VVGLVALTSVVYGL 424 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: 534 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: 426 Length adjustment: 32 Effective length of query: 411 Effective length of database: 394 Effective search space: 161934 Effective search space used: 161934 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