Align Threonine/serine transporter TdcC; H(+)/threonine-serine symporter (characterized)
to candidate GFF1000 PS417_05070 serine/threonine protein kinase
Query= SwissProt::P0AAD8 (443 letters) >FitnessBrowser__WCS417:GFF1000 Length = 428 Score = 387 bits (995), Expect = e-112 Identities = 210/444 (47%), Positives = 287/444 (64%), Gaps = 31/444 (6%) Query: 4 SDSIVSSQTKQSSWRKSDTTWTLGLFGTAIGAGVLFFPIRAGFGGLIPILLMLVLAYPIA 63 +++ ++ T + W + DTTW LGL+GTAIGAG LF PI AG GG P++++ +LA+P+ Sbjct: 9 AENPAATTTVTTGWTQYDTTWMLGLYGTAIGAGTLFLPINAGVGGFWPLIVLALLAFPMT 68 Query: 64 FYCHRALARLCLSGSNPSGNITETVEEHFGKTGGVVITFLYFFAICPLLWIYGVTITNTF 123 F+ HR L R LSG SG+ITE VEEHFG G +IT LYFFAI P+L +Y V +TNT Sbjct: 69 FFAHRGLTRFVLSGK--SGDITEVVEEHFGVGAGKLITLLYFFAIFPILLVYSVALTNTL 126 Query: 124 MTFWENQLGFAPLNRGFVALFLLLLMAFVIWFGKDLMVKVMSYLVWPFIASLVLISLSLI 183 +F E+QL P R ++L L+L + ++ G+ ++VK MS LV+PF+ASL+L++ SLI Sbjct: 127 GSFMEHQLHMTPPPRAILSLVLILGLMAIVRCGQGVIVKAMSVLVYPFVASLLLLAFSLI 186 Query: 184 PYWNSAVIDQVDLGSLSLTGHDGILI-----TVWLGISIMVFSFNFSPIVSSFVVSKREE 238 P WN G+ + DG+ + T+WL I +MVFSFN SPI+S+F V ++ Sbjct: 187 PNWN---------GAFFASAGDGMPMPLFFKTLWLAIPVMVFSFNHSPIISAFAVDQKRV 237 Query: 239 YEKDFGRDFTERKCSQIISRASMLMVAVVMFFAFSCLFTLSPANMAEAKAQNIPVLSYLA 298 Y ERK S I++ A +MV VMFF FSC+ LSPA++A AKAQNI +LSYLA Sbjct: 238 YGAQ-----AERKSSGILATAHGMMVLTVMFFCFSCVLALSPADLAAAKAQNISILSYLA 292 Query: 299 NHFASMTGTKTTFAITLEYAASIIALVAIFKSFFGHYLGTLEGLNGLVLKFGYKGDKTKV 358 NHF + + YAA +IALVAI KSF GHY+G EG GL++K +G + Sbjct: 293 NHFQTP---------VIAYAAPLIALVAITKSFLGHYIGASEGFQGLIVK-SLRGRNRSM 342 Query: 359 SLGKLNTISMIFIMGSTWVVAYANPNILDLIEAMGAPIIASLLCLLPMYAIRKAPSLAKY 418 S L + +F++ + W VA NP+IL +IE MG PIIA LL L+PMYAIR+ PSL KY Sbjct: 343 SAKWLERCTALFMVLTCWAVATFNPSILRMIETMGGPIIACLLFLMPMYAIRRVPSLRKY 402 Query: 419 RGRLDNVFVTVIGLLTILNIVYKL 442 G++ NVFV VIGL+ + IV+ + Sbjct: 403 SGQVSNVFVVVIGLIALSAIVFSV 426 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: 551 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: 428 Length adjustment: 32 Effective length of query: 411 Effective length of database: 396 Effective search space: 162756 Effective search space used: 162756 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