Align Threonine/serine transporter TdcC; H(+)/threonine-serine symporter (characterized)
to candidate AO353_15495 AO353_15495 serine/threonine protein kinase
Query= SwissProt::P0AAD8 (443 letters) >FitnessBrowser__pseudo3_N2E3:AO353_15495 Length = 433 Score = 389 bits (998), Expect = e-112 Identities = 210/435 (48%), Positives = 281/435 (64%), Gaps = 23/435 (5%) Query: 9 SSQTKQSSWRKSDTTWTLGLFGTAIGAGVLFFPIRAGFGGLIPILLMLVLAYPIAFYCHR 68 S+ T W K DTTW LGL+GTAIGAG LF PI AG GG P+L++ +LA+P+ F+ HR Sbjct: 19 STATTSKGWSKHDTTWMLGLYGTAIGAGTLFLPINAGVGGFWPLLVLALLAFPMTFFAHR 78 Query: 69 ALARLCLSGSNPSGNITETVEEHFGKTGGVVITFLYFFAICPLLWIYGVTITNTFMTFWE 128 L R LSG SG+ITE VEEHFG G +IT LYFFAI P+L +Y V +TNT +F E Sbjct: 79 GLTRFVLSGR--SGDITEVVEEHFGIGAGKLITLLYFFAIFPILLVYSVALTNTLSSFME 136 Query: 129 NQLGFAPLNRGFVALFLLLLMAFVIWFGKDLMVKVMSYLVWPFIASLVLISLSLIPYWNS 188 +QL AP R ++L L+L + ++ G+ ++VK MS LV+PF+A+L+L+ +SLIP WN Sbjct: 137 HQLHIAPPPRSVLSLALILGLMAIVRCGQGVIVKCMSVLVYPFVAALLLLGVSLIPNWNG 196 Query: 189 AVIDQVDLG-SLSLTGHDGILITVWLGISIMVFSFNFSPIVSSFVVSKREEYEKDFGRDF 247 A G L L T+WL I +MVFSFN SPI+S+F V +++ Y Sbjct: 197 AFFASASEGMPLPL-----FFKTLWLAIPVMVFSFNHSPIISAFAVDQKQRYGTQ----- 246 Query: 248 TERKCSQIISRASMLMVAVVMFFAFSCLFTLSPANMAEAKAQNIPVLSYLANHFASMTGT 307 E K S I++ A +MV VMFF FSC+ LSPA++A AKAQNI +LSYLANHF + Sbjct: 247 AEPKSSGILAVAHSMMVLTVMFFCFSCVLALSPADLAAAKAQNISILSYLANHFQTP--- 303 Query: 308 KTTFAITLEYAASIIALVAIFKSFFGHYLGTLEGLNGLVLKFGYKGDKTKVSLGKLNTIS 367 + YAA +IALVAI KSF GHY+G EG GL++K +G + LN ++ Sbjct: 304 ------VIAYAAPLIALVAITKSFLGHYIGASEGFQGLIVK-SLRGRGRVMPTSWLNRVT 356 Query: 368 MIFIMGSTWVVAYANPNILDLIEAMGAPIIASLLCLLPMYAIRKAPSLAKYRGRLDNVFV 427 +F++ S W VA NP+IL +IE +G P+IA LL L+PMYAIR+ PSL +Y G+ NVFV Sbjct: 357 ALFMILSCWAVATFNPSILGMIETLGGPVIACLLFLMPMYAIRRVPSLRQYSGQASNVFV 416 Query: 428 TVIGLLTILNIVYKL 442 +IGL+ + I+Y + Sbjct: 417 VLIGLIALSAIIYSV 431 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: 553 Number of extensions: 28 Number of successful extensions: 6 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: 433 Length adjustment: 32 Effective length of query: 411 Effective length of database: 401 Effective search space: 164811 Effective search space used: 164811 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