Align Threonine/serine transporter TdcC; H(+)/threonine-serine symporter (characterized)
to candidate AO353_21595 AO353_21595 serine/threonine protein kinase
Query= SwissProt::P0AAD8 (443 letters) >FitnessBrowser__pseudo3_N2E3:AO353_21595 Length = 426 Score = 401 bits (1030), Expect = e-116 Identities = 208/429 (48%), Positives = 287/429 (66%), Gaps = 26/429 (6%) Query: 15 SSWRKSDTTWTLGLFGTAIGAGVLFFPIRAGFGGLIPILLMLVLAYPIAFYCHRALARLC 74 SSW + DTTW LGLFGTAIGAG LF PI AG GG P+L++ +LA+P+ FY HR L R Sbjct: 21 SSWNRHDTTWMLGLFGTAIGAGTLFLPINAGLGGFWPLLILALLAFPMTFYAHRGLTRFV 80 Query: 75 LSGSNPSGNITETVEEHFGKTGGVVITFLYFFAICPLLWIYGVTITNTFMTFWENQLGFA 134 LSG +ITE VEEHFG G +IT LYFFAI P+L IY V +TNT +F E+QL Sbjct: 81 LSG-RAGADITEVVEEHFGIKAGALITLLYFFAIFPILLIYSVALTNTVGSFLEHQLHIM 139 Query: 135 PLNRGFVALFLLLLMAFVIWFGKDLMVKVMSYLVWPFIASLVLISLSLIPYWNSAVIDQV 194 P R ++ L+L + V+ G+ ++VK MS +V+PFI +L+ +++ LIP+WN +++ Sbjct: 140 PPPRAILSFVLILGLLAVVRCGEQMIVKAMSLMVYPFIVALLFLAVFLIPHWNGGILETA 199 Query: 195 DLGSLSLTGHDGILITVWLGISIMVFSFNFSPIVSSFVVSKREEYEKDFGRDFTERKCSQ 254 +L +L T+WL I +MVFSFN SPI+S+F V ++ Y E + SQ Sbjct: 200 S----TLPEPSALLHTLWLAIPVMVFSFNHSPIISAFAVDQKRRYGA-----HAEERSSQ 250 Query: 255 IISRASMLMVAVVMFFAFSCLFTLSPANMAEAKAQNIPVLSYLANHFASMTGTKTTFAIT 314 I+SRA LMV +V+FF FSC+ TLSPA +AEAKAQN+ +LSYLANHF++ T Sbjct: 251 ILSRAHTLMVVMVLFFVFSCVLTLSPAQLAEAKAQNLSILSYLANHFSNP---------T 301 Query: 315 LEYAASIIALVAIFKSFFGHYLGTLEGLNGLVLKFGYK-GDKTKVSLGKLNTISMIFIMG 373 + +AA +IA VAI KSF GHY+G EGL GL++K G + KT L+ ++ F++ Sbjct: 302 IAFAAPLIAFVAISKSFLGHYIGASEGLKGLIVKSGRRPAPKT------LDRMTAAFMLV 355 Query: 374 STWVVAYANPNILDLIEAMGAPIIASLLCLLPMYAIRKAPSLAKYRGRLDNVFVTVIGLL 433 W+VA NP+IL +IE +G P+IA++L L+PMYAIRK P++A+YRG+ NVFVT++GL+ Sbjct: 356 VCWIVATLNPSILGMIETLGGPVIAAILFLMPMYAIRKVPAMARYRGQASNVFVTLVGLV 415 Query: 434 TILNIVYKL 442 I ++Y L Sbjct: 416 AISALIYSL 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: 517 Number of extensions: 28 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