Align The 11 TMS Na+-dependent tyrosine transporter, Tyt1 (characterized)
to candidate AO353_05685 AO353_05685 symporter
Query= TCDB::Q8RHM5 (438 letters) >FitnessBrowser__pseudo3_N2E3:AO353_05685 Length = 467 Score = 166 bits (421), Expect = 1e-45 Identities = 109/348 (31%), Positives = 173/348 (49%), Gaps = 8/348 (2%) Query: 14 FILTCVGSAVGMANIWAFPYRVGKYGGAVFLLIYFMFIALFSYVGLSAEYLIGRRAETGT 73 FIL GSAVG+ +IW FPY VG YGG F+L++ IAL + AE LIGRRA Sbjct: 18 FILAATGSAVGLGSIWKFPYMVGVYGGGAFVLVFLACIALIGVPVMLAETLIGRRARQSP 77 Query: 74 LGSYEYAWKDVG-KGKLGYGLAYIPLLGSMSIAIGYAVIAAWVLRTFGAAVTGKILEVDT 132 + + + G K +G A+ ++ ++ I Y+V+ W L G V Sbjct: 78 ANALKVLALEAGHSAKWSWG-AFAGMITALLILSFYSVVGGWSLDYIIDMGRGDFQGVTA 136 Query: 133 AQ---FFGEAVTGNFVIMPWHIAVIVLTLLTLFAGAKS-IEKTNKIMMPAFFVLFFILAV 188 Q +FG + + + WH ++L+ + G + +E++ +IMMP FV+ IL Sbjct: 137 DQVGAYFGGVIADPWRLTLWHTLFMLLSAFVIARGVVAGLERSLRIMMPLLFVMLVILLG 196 Query: 189 RVAFLPGAIEGYKYLFVPDWSYLSNVETWINAMGQAFFSLSITGSGMIVCGAYLDKKEDI 248 +EG ++F D++ ++ + AMG AFFSLS+ +++ GAY+ K I Sbjct: 197 YSLTTGHFMEGVHFMF--DFNPDKLLDGLLPAMGHAFFSLSVGVGSIMIYGAYMPKHSSI 254 Query: 249 INGALQTGVFDTIAAMIAAFVVIPASFAFGYPASAGPSLMFMTIPEVFKQMPFGQLLAIL 308 + + DT +++A + P FA G S GP LMF+++P F + FGQL+ ++ Sbjct: 255 SGTIVGVALLDTFVSLLAGLALFPIVFAAGLNPSEGPGLMFVSLPFAFGNVAFGQLMGVV 314 Query: 309 FFVSVVFAAISSLQNMFEVVGESIQTRFKMTRKSVIVLLGIIALVIGI 356 FFV V AA SS ++ E + + R + R V L +G+ Sbjct: 315 FFVLVAIAAWSSAISLLEPMVAYLVERTNIRRGWVTFWLAFSCWFVGL 362 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: 607 Number of extensions: 29 Number of successful extensions: 4 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 438 Length of database: 467 Length adjustment: 33 Effective length of query: 405 Effective length of database: 434 Effective search space: 175770 Effective search space used: 175770 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 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