Align Threonine/serine transporter TdcC; H(+)/threonine-serine symporter (characterized)
to candidate PfGW456L13_3379 Serine transporter
Query= SwissProt::P0AAD8 (443 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3379 Length = 396 Score = 386 bits (991), Expect = e-112 Identities = 201/417 (48%), Positives = 278/417 (66%), Gaps = 24/417 (5%) Query: 26 LGLFGTAIGAGVLFFPIRAGFGGLIPILLMLVLAYPIAFYCHRALARLCLSGSNPSGNIT 85 LGLFGTAIGAG LF PI AG GG P+L++ +LA+P+ FY HR L R LSG +IT Sbjct: 2 LGLFGTAIGAGTLFLPINAGLGGFWPLLILALLAFPMTFYAHRGLTRFVLSGRE-GADIT 60 Query: 86 ETVEEHFGKTGGVVITFLYFFAICPLLWIYGVTITNTFMTFWENQLGFAPLNRGFVALFL 145 E VEEHFG G +IT LYFFAI P+L IY V +TNT +F E+QL P R ++L L Sbjct: 61 EVVEEHFGIKAGALITLLYFFAIFPILLIYSVALTNTVGSFLEHQLHITPPPRAVLSLVL 120 Query: 146 LLLMAFVIWFGKDLMVKVMSYLVWPFIASLVLISLSLIPYWNSAVIDQVDLGSLSLTGHD 205 +L + V+ G+ ++VK MS +V+PFI +L+ +++ LIP+WN ++ + Sbjct: 121 ILGLLAVVRCGEQMIVKAMSLMVYPFIVALLFLAVYLIPHWNGGILATAS----QVPAPS 176 Query: 206 GILITVWLGISIMVFSFNFSPIVSSFVVSKREEYEKDFGRDFTERKCSQIISRASMLMVA 265 +L T+WL I +MVFSFN SPI+S+F V ++ Y + E + SQI+SRA +LMV Sbjct: 177 ALLHTLWLAIPVMVFSFNHSPIISAFAVDQKRRY-----GEHAEERSSQILSRAHLLMVV 231 Query: 266 VVMFFAFSCLFTLSPANMAEAKAQNIPVLSYLANHFASMTGTKTTFAITLEYAASIIALV 325 +V+FF FSC+ TLSPA +AEAKAQN+ +LSYLANHF++ T+ +AA +IA V Sbjct: 232 MVLFFVFSCVLTLSPAQLAEAKAQNLSILSYLANHFSNP---------TIAFAAPLIAFV 282 Query: 326 AIFKSFFGHYLGTLEGLNGLVLKFGYKGDKTKVSLGKLNTISMIFIMGSTWVVAYANPNI 385 AI KSF GHY+G EGL GL++K G + S L+ ++ F++ W+VA NP+I Sbjct: 283 AISKSFLGHYIGASEGLKGLIVKSG-----KRPSAKALDRMTAAFMLVVCWIVATLNPSI 337 Query: 386 LDLIEAMGAPIIASLLCLLPMYAIRKAPSLAKYRGRLDNVFVTVIGLLTILNIVYKL 442 L +IE +G P+IA++L L+PMYAIRK P++A+YRG+ NVFVT +GL+ I +VY L Sbjct: 338 LGMIETLGGPVIAAILFLMPMYAIRKVPAMARYRGQASNVFVTAVGLVAISALVYSL 394 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: 482 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: 396 Length adjustment: 32 Effective length of query: 411 Effective length of database: 364 Effective search space: 149604 Effective search space used: 149604 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: 50 (23.9 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