Align Threonine/serine transporter TdcC; H(+)/threonine-serine symporter (characterized)
to candidate 16880 b2796 predicted serine transporter (NCBI)
Query= SwissProt::P0AAD8 (443 letters) >FitnessBrowser__Keio:16880 Length = 429 Score = 451 bits (1160), Expect = e-131 Identities = 225/442 (50%), Positives = 310/442 (70%), Gaps = 16/442 (3%) Query: 2 STSDSIVSSQTKQSSWRKSDTTWTLGLFGTAIGAGVLFFPIRAGFGGLIPILLMLVLAYP 61 +T S ++S+ +S+WRK+DT W LGL+GTAIGAGVLF PI AG GG+IP+++M +LA+P Sbjct: 3 TTQTSTIASKDSRSAWRKTDTMWMLGLYGTAIGAGVLFLPINAGVGGMIPLIIMAILAFP 62 Query: 62 IAFYCHRALARLCLSGSNPSGNITETVEEHFGKTGGVVITFLYFFAICPLLWIYGVTITN 121 + F+ HR L R LSG NP +ITE VEEHFG G +IT LYFFAI P+L +Y V ITN Sbjct: 63 MTFFAHRGLTRFVLSGKNPGEDITEVVEEHFGIGAGKLITLLYFFAIYPILLVYSVAITN 122 Query: 122 TFMTFWENQLGFAPLNRGFVALFLLLLMAFVIWFGKDLMVKVMSYLVWPFIASLVLISLS 181 T +F +QLG P R ++L L++ M ++ FG+ ++VK MS LV+PF+ L+L++L Sbjct: 123 TVESFMSHQLGMTPPPRAILSLILIVGMMTIVRFGEQMIVKAMSILVFPFVGVLMLLALY 182 Query: 182 LIPYWNSAVIDQVDLGSLSLTGHDGILITVWLGISIMVFSFNFSPIVSSFVVSKREEYEK 241 LIP WN A ++ + L + S TG +G+ +T+WL I +MVFSFN SPI+SSF V+KREEY Sbjct: 183 LIPQWNGAALETLSLDTASATG-NGLWMTLWLAIPVMVFSFNHSPIISSFAVAKREEY-- 239 Query: 242 DFGRDFTERKCSQIISRASMLMVAVVMFFAFSCLFTLSPANMAEAKAQNIPVLSYLANHF 301 D E+KCS+I++ A ++MV VMFF FSC+ +L+PA++A AK QNI +LSYLANHF Sbjct: 240 ---GDMAEQKCSKILAFAHIMMVLTVMFFVFSCVLSLTPADLAAAKEQNISILSYLANHF 296 Query: 302 ASMTGTKTTFAITLEYAASIIALVAIFKSFFGHYLGTLEGLNGLVLKFGYKGDKTKVSLG 361 A + + A IIA++AI KSF GHYLG EG NG+V+K +G + + Sbjct: 297 N---------APVIAWMAPIIAIIAITKSFLGHYLGAREGFNGMVIK-SLRGKGKSIEIN 346 Query: 362 KLNTISMIFIMGSTWVVAYANPNILDLIEAMGAPIIASLLCLLPMYAIRKAPSLAKYRGR 421 KLN I+ +F++ +TW+VA NP+IL +IE +G PIIA +L L+PMYAI+K P++ KY G Sbjct: 347 KLNRITALFMLVTTWIVATLNPSILGMIETLGGPIIAMILFLMPMYAIQKVPAMRKYSGH 406 Query: 422 LDNVFVTVIGLLTILNIVYKLF 443 + NVFV V+GL+ I I Y LF Sbjct: 407 ISNVFVVVMGLIAISAIFYSLF 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: 582 Number of extensions: 33 Number of successful extensions: 5 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: 429 Length adjustment: 32 Effective length of query: 411 Effective length of database: 397 Effective search space: 163167 Effective search space used: 163167 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