Align Tyrosine permease (characterized)
to candidate 208824 DVU3297 tryptophan-specific transport protein
Query= TCDB::P0AAD4 (403 letters) >MicrobesOnline__882:208824 Length = 419 Score = 219 bits (557), Expect = 2e-61 Identities = 131/397 (32%), Positives = 204/397 (51%), Gaps = 3/397 (0%) Query: 7 GSVFIVAGTTIGAGMLAMPLAAAGVGFSVTLILLIGLWALMCYTALLLLEVYQHVPADTG 66 G I+AGT+IGAGMLA+P +AG+ F +L +++ W +M ++ LLEV H Sbjct: 20 GGTMIIAGTSIGAGMLALPTISAGMWFGWSLAVMLLAWLVMLLSSQALLEVNLHFEPGAS 79 Query: 67 LGTLAKRYLGRYGQWLTGFSMMFLMYALTAAYISGAGELLASSISDWTGISMSATAGVLL 126 TL + LG + G ++ F++Y L AY+SG G ++ ++ +G S A L Sbjct: 80 FHTLVRETLGPGWSVINGAAVAFVLYILVYAYVSGGGSIMRHTLLAVSGYEPSKLAAGLS 139 Query: 127 FTFVAGGVVCVGTSLVDLFNRFLFSAKIIFLVVMLVLLLPHIHKVNLLTLPLQQGLAL-- 184 F + V T +VD + + ++ ++ + +L I L + G AL Sbjct: 140 FALLLAACVWWSTWIVDRLSVIMMGGMVVSFILSMSGMLSDIRADVLFDAGGEGGSALFV 199 Query: 185 -SAIPVIFTSFGFHGSVPSIVSYMDGNIRKLRWVFIIGSAIPLVAYIFWQVATLGSIDST 243 A+ TSF FH SVPS+V Y + + G+ I LV Y+ W VA G+I Sbjct: 200 WGALSTYLTSFCFHASVPSLVKYFGRRPADINRCLVGGTGIALVCYLLWIVACDGTIPRA 259 Query: 244 TFMGLLANHAGLNGLLQALREMVASPHVELAVHLFADLALATSFLGVALGLFDYLADLFQ 303 F ++A + L++A + S + + F+ LA+ATSFLG LGLFDY+ADL + Sbjct: 260 EFRDVIAAGGNVGDLVRAAGSNLNSGFILRMLEAFSALAVATSFLGAGLGLFDYIADLCR 319 Query: 304 RSNTVGGRLQTGAITFLPPLAFALFYPRGFVMALGYAGVALAVLALIIPSLLTWQSRKHN 363 +T GR +T +TF PP L +P GF++A+G+AG+A V ++++P+L+ SR Sbjct: 320 FDDTRAGRTKTTLVTFGPPTVGGLLWPDGFLLAIGWAGLAATVWSVVVPALMLRASRATR 379 Query: 364 PQAGYRVKGGRPALVVVFLCGIAVIGVQFLIAAGLLP 400 P GYRV GG + + G+ L G+LP Sbjct: 380 PAPGYRVGGGSLTVPALLAFGLVTAVCHTLFVFGVLP 416 Lambda K H 0.329 0.143 0.432 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: 436 Number of extensions: 20 Number of successful extensions: 2 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: 403 Length of database: 419 Length adjustment: 31 Effective length of query: 372 Effective length of database: 388 Effective search space: 144336 Effective search space used: 144336 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: 50 (23.9 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