Align Threonine/serine transporter TdcC; H(+)/threonine-serine symporter (characterized)
to candidate GFF2931 PS417_14995 serine/threonine protein kinase
Query= SwissProt::P0AAD8 (443 letters) >FitnessBrowser__WCS417:GFF2931 Length = 425 Score = 406 bits (1044), Expect = e-118 Identities = 214/442 (48%), Positives = 293/442 (66%), Gaps = 24/442 (5%) Query: 2 STSDSIVSSQTKQSSWRKSDTTWTLGLFGTAIGAGVLFFPIRAGFGGLIPILLMLVLAYP 61 S + ++ +SW + DTTW LGLFGTAIGAG LF PI AG GG P++++ +LA+P Sbjct: 7 SVDERYATTPATLTSWSRQDTTWMLGLFGTAIGAGTLFLPINAGLGGFWPLVILALLAFP 66 Query: 62 IAFYCHRALARLCLSGSNPSGNITETVEEHFGKTGGVVITFLYFFAICPLLWIYGVTITN 121 + F+ HR L R LSG S +IT+ VEEHFG G +IT LYFFAI P+L IY V +TN Sbjct: 67 MTFFAHRGLTRFVLSGREGS-DITDVVEEHFGIKAGALITLLYFFAIFPILLIYSVALTN 125 Query: 122 TFMTFWENQLGFAPLNRGFVALFLLLLMAFVIWFGKDLMVKVMSYLVWPFIASLVLISLS 181 T +F E+QL P R ++ L+L + V+ G+ ++VK MS +V+PFI +L+ +++ Sbjct: 126 TVGSFMEHQLHIMPPPRAILSFVLILGLLAVVRCGEQVIVKAMSLMVYPFIVALLFLAVY 185 Query: 182 LIPYWNSAVIDQVDLGSLSLTGHDGILITVWLGISIMVFSFNFSPIVSSFVVSKREEYEK 241 LIP+WN ++ + +L T+WL I +MVFSFN SPI+S+F V ++ +Y Sbjct: 186 LIPHWNGGILSTAS----QVPTPSALLNTLWLAIPVMVFSFNHSPIISAFAVDQKRQY-- 239 Query: 242 DFGRDFTERKCSQIISRASMLMVAVVMFFAFSCLFTLSPANMAEAKAQNIPVLSYLANHF 301 G ER SQI+SRA +LMV +V+FF FSC+ TLSPA +AEAKAQN+ +LSYLANHF Sbjct: 240 --GIHADERS-SQILSRAHLLMVVMVLFFVFSCVLTLSPAQLAEAKAQNLSILSYLANHF 296 Query: 302 ASMTGTKTTFAITLEYAASIIALVAIFKSFFGHYLGTLEGLNGLVLKFGYKGDKTKVSLG 361 + T+E+AA +IA VAI KSF GHY+G EGL GLVLK G + Sbjct: 297 NNP---------TIEFAAPLIAFVAITKSFLGHYIGASEGLKGLVLKTG-----RRPGAK 342 Query: 362 KLNTISMIFIMGSTWVVAYANPNILDLIEAMGAPIIASLLCLLPMYAIRKAPSLAKYRGR 421 +L+ ++ F++ W+VA NP+IL +IEA+G PIIAS+L L+PMYAIRK P++AKYRG+ Sbjct: 343 RLDRMTAAFMLVVCWIVATLNPSILGMIEALGGPIIASILFLMPMYAIRKVPAMAKYRGQ 402 Query: 422 LDNVFVTVIGLLTILNIVYKLF 443 NVFVT +GL+ I +VY LF Sbjct: 403 ASNVFVTAVGLVAITAVVYSLF 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: 541 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: 425 Length adjustment: 32 Effective length of query: 411 Effective length of database: 393 Effective search space: 161523 Effective search space used: 161523 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