Align Threonine/serine transporter TdcC; H(+)/threonine-serine symporter (characterized)
to candidate Pf1N1B4_4562 Serine transporter
Query= SwissProt::P0AAD8 (443 letters) >FitnessBrowser__pseudo1_N1B4:Pf1N1B4_4562 Length = 426 Score = 399 bits (1026), Expect = e-116 Identities = 206/437 (47%), Positives = 288/437 (65%), Gaps = 26/437 (5%) Query: 7 IVSSQTKQSSWRKSDTTWTLGLFGTAIGAGVLFFPIRAGFGGLIPILLMLVLAYPIAFYC 66 + ++ SW + DTTW LGLFGTAIGAG LF PI AG GG P+L++ VLA+P+ FY Sbjct: 13 VAATPASLESWNRHDTTWMLGLFGTAIGAGTLFLPINAGLGGFWPLLILAVLAFPMTFYA 72 Query: 67 HRALARLCLSGSNPSGNITETVEEHFGKTGGVVITFLYFFAICPLLWIYGVTITNTFMTF 126 HR L R LSG +ITE VEEHFG G +IT LYFFAI P+L IY V +TNT +F Sbjct: 73 HRGLTRFVLSGRE-GADITEVVEEHFGIKAGALITLLYFFAIFPILLIYSVALTNTVGSF 131 Query: 127 WENQLGFAPLNRGFVALFLLLLMAFVIWFGKDLMVKVMSYLVWPFIASLVLISLSLIPYW 186 E+QL P R ++ L+L + V+ G+ ++VK MS +V+PFI +L+ +++ L+P+W Sbjct: 132 LEHQLHIMPPPRAVLSFVLILGLLAVVRCGEQVIVKAMSLMVYPFIVALLFLAVFLVPHW 191 Query: 187 NSAVIDQVDLGSLSLTGHDGILITVWLGISIMVFSFNFSPIVSSFVVSKREEYEKDFGRD 246 N ++ +L +L T+WL I +MVFSFN SPI+S+F V ++ Y Sbjct: 192 NGGILSTAS----TLPESSALLHTLWLAIPVMVFSFNHSPIISAFAVDQKRRYGA----- 242 Query: 247 FTERKCSQIISRASMLMVAVVMFFAFSCLFTLSPANMAEAKAQNIPVLSYLANHFASMTG 306 E + SQI+SRA +LMV +V+FF FSC+ TLSPA +AEAKAQN+ +LSYLANHF++ Sbjct: 243 HAEERSSQILSRAHLLMVVMVLFFVFSCVLTLSPAQLAEAKAQNLSILSYLANHFSNP-- 300 Query: 307 TKTTFAITLEYAASIIALVAIFKSFFGHYLGTLEGLNGLVLKFGYK-GDKTKVSLGKLNT 365 T+ +AA +IA VAI KSF GHY+G EGL GL++K G + KT L+ Sbjct: 301 -------TIAFAAPLIAFVAISKSFLGHYIGASEGLKGLIIKSGKRPAPKT------LDR 347 Query: 366 ISMIFIMGSTWVVAYANPNILDLIEAMGAPIIASLLCLLPMYAIRKAPSLAKYRGRLDNV 425 ++ F++ W+VA NP+IL +IE +G PIIA++L L+PMYA+RK P++A++RG+ NV Sbjct: 348 MTAAFMLVVCWIVATLNPSILGMIETLGGPIIAAILFLMPMYAVRKVPAMARFRGQASNV 407 Query: 426 FVTVIGLLTILNIVYKL 442 FVT +GL+ I ++Y L Sbjct: 408 FVTAVGLVAISALIYSL 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: 522 Number of extensions: 27 Number of successful extensions: 7 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