Align Threonine/serine transporter TdcC; H(+)/threonine-serine symporter (characterized)
to candidate Pf1N1B4_1014 Serine transporter
Query= SwissProt::P0AAD8 (443 letters) >FitnessBrowser__pseudo1_N1B4:Pf1N1B4_1014 Length = 433 Score = 388 bits (997), Expect = e-112 Identities = 209/429 (48%), Positives = 281/429 (65%), Gaps = 31/429 (7%) Query: 17 WRKSDTTWTLGLFGTAIGAGVLFFPIRAGFGGLIPILLMLVLAYPIAFYCHRALARLCLS 76 W K DTTW LGL+GTAIGAG LF PI AG GG P+LL+ VLA+P+ F+ HR L R LS Sbjct: 27 WSKHDTTWMLGLYGTAIGAGTLFLPINAGVGGFWPLLLLAVLAFPMTFFAHRGLTRFVLS 86 Query: 77 GSNPSGNITETVEEHFGKTGGVVITFLYFFAICPLLWIYGVTITNTFMTFWENQLGFAPL 136 G SG+ITE VEEHFG G +IT LYFFAI P+L +Y V +TNT + E+QL P Sbjct: 87 GR--SGDITEVVEEHFGIGAGKLITLLYFFAIFPILLVYSVALTNTLSSLMEHQLHMTPP 144 Query: 137 NRGFVALFLLLLMAFVIWFGKDLMVKVMSYLVWPFIASLVLISLSLIPYWNSAVIDQVDL 196 R ++L L+L + ++ G+ ++VK MS LV+PF+A+L+L+ +SLIP WN Sbjct: 145 PRAILSLGLILGLMAIVRCGQGVIVKCMSVLVYPFVAALLLLGVSLIPNWN--------- 195 Query: 197 GSLSLTGHDGILI-----TVWLGISIMVFSFNFSPIVSSFVVSKREEYEKDFGRDFTERK 251 G+ T +G+ + T+WL I +MVFSFN SPI+S+F V +++ Y + ERK Sbjct: 196 GAFFATASEGMPLPLFFKTLWLAIPVMVFSFNHSPIISAFAVDQKQRYGEQ-----AERK 250 Query: 252 CSQIISRASMLMVAVVMFFAFSCLFTLSPANMAEAKAQNIPVLSYLANHFASMTGTKTTF 311 S I++ A ++MV VMFF FSC+ LSPA++A AKAQNI +LSYLANHF + Sbjct: 251 SSGILAIAHLMMVVTVMFFCFSCVLALSPADLAAAKAQNISILSYLANHFQTP------- 303 Query: 312 AITLEYAASIIALVAIFKSFFGHYLGTLEGLNGLVLKFGYKGDKTKVSLGKLNTISMIFI 371 + YAA +IALVAI KSF GHY+G EG GL++K +G +S LN I+ +F+ Sbjct: 304 --VIAYAAPLIALVAITKSFLGHYIGASEGFQGLIVK-SLRGRGRVMSASWLNRITALFM 360 Query: 372 MGSTWVVAYANPNILDLIEAMGAPIIASLLCLLPMYAIRKAPSLAKYRGRLDNVFVTVIG 431 + S W VA NP+IL +IE +G PIIA LL L+PMYAIR+ P+L +Y + NVFV +IG Sbjct: 361 ILSCWAVATFNPSILGMIETLGGPIIACLLFLMPMYAIRRVPALRQYSNQASNVFVVLIG 420 Query: 432 LLTILNIVY 440 L+ + I+Y Sbjct: 421 LIALSAIIY 429 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: 568 Number of extensions: 30 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