Align The 11 TMS Na+-dependent tyrosine transporter, Tyt1 (characterized)
to candidate WP_043531208.1 JH15_RS13510 sodium-dependent transporter
Query= TCDB::Q8RHM5 (438 letters) >NCBI__GCF_000759345.1:WP_043531208.1 Length = 447 Score = 204 bits (518), Expect = 6e-57 Identities = 145/447 (32%), Positives = 221/447 (49%), Gaps = 21/447 (4%) Query: 4 SERKFQSKIGFILTCVGSAVGMANIWAFPYRVGKYGGAVFLLIYFMFIALFSYVGLSAEY 63 S ++ SK+ FIL GSAVG+ NIW F Y VG GGA F+L+Y +AL L +E+ Sbjct: 5 SHAQWSSKMTFILAAAGSAVGLGNIWRFSYMVGDSGGAAFVLVYLACVALVGLPILVSEW 64 Query: 64 LIGRRAETGTLGSYEYAWKDVGKGKLGYGLAYIPLLGSMSIAIGYAVIAAWVLRTFGAAV 123 LIGRR + + + GK K + +L + I Y+VI W L +V Sbjct: 65 LIGRRGQKNPINTMAELATQHGKSKAWAAIGISGVLAAFLILSFYSVIGGWSLSYTLGSV 124 Query: 124 TGKILEVDT---AQFFGEAVTGNFVIMPWHIAVIVLTLLTLFAGA-KSIEKTNKIMMPAF 179 TG D + F ++ ++ WH ++L ++ + G K +E + MMPA Sbjct: 125 TGAFSGQDADGISALFTGMLSSPGTLLLWHSIFMLLVIVIVARGVTKGLEAAVRTMMPAL 184 Query: 180 FVLFFILAVRVAFLPGAI-EGYKYLFVPDWSYLSNVETWINAMGQAFFSLSITGSGMIVC 238 +L +L V G E ++F PDWS LS + AMGQAFF+LS+ M+ Sbjct: 185 LILMLVL-VGYGMTTGHFGEAMSFMFNPDWSALSGGVV-LAAMGQAFFTLSLGMGIMMAY 242 Query: 239 GAYLDKKEDIINGALQTGVFDTIAAMIAAFVVIPASFAFGYPASAGPSLMFMTIPEVFKQ 298 G+YL ++ D+I A + DT+ A++A + P FA G GP L+F+T+P F Sbjct: 243 GSYLGQEVDLIGTARTVIILDTVVALLAGMAIFPIVFANGLSPGEGPGLIFVTLPLAFGS 302 Query: 299 MPFGQLLAILFFVSVVFAAISSLQNMFEVVGESIQTRFKMTRKSVIVLLGIIALVIGIFI 358 M G +L ++FF+ + FAA++S ++ E V E ++ R +TR ++ I+ ++GI Sbjct: 303 MTGGTILGLMFFLLLTFAALTSAISLLEPVVEFLEERTSLTRVPATLISAILVWLLGIAA 362 Query: 359 EPENKV--GP---------WMDVVTIYIIPFGAVLGAISWY-WILKKESYMEELNQGSKV 406 V GP +D T I+ LGAI + W L + S EL GS Sbjct: 363 LLSFNVWDGPVAFGFNTFDLLDNFTSKILLPLTGLGAIVFVAWCLDRASVQRELGLGS-- 420 Query: 407 TRSEIYHNVGKYVYVPLVLVVFVLGVI 433 T ++H +Y+ V+ VFV G+I Sbjct: 421 TGGTLWHITSRYIAPIGVICVFVGGLI 447 Lambda K H 0.328 0.143 0.434 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: 545 Number of extensions: 26 Number of successful extensions: 3 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: 438 Length of database: 447 Length adjustment: 32 Effective length of query: 406 Effective length of database: 415 Effective search space: 168490 Effective search space used: 168490 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 (21.7 bits) S2: 51 (24.3 bits)
This GapMind analysis is from Sep 24 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