Align Tyrosine permease (characterized)
to candidate 207689 DVU2205 tryptophan-specific transport protein
Query= TCDB::P0AAD4 (403 letters) >MicrobesOnline__882:207689 Length = 425 Score = 256 bits (653), Expect = 1e-72 Identities = 142/402 (35%), Positives = 219/402 (54%), Gaps = 4/402 (0%) Query: 6 LGSVFIVAGTTIGAGMLAMPLAAAGVGFSVTLILLIGLWALMCYTALLLLEVYQHVPADT 65 LG I+AGTTIGAGM ++P +AG+ F +L +L G W MC++ L++LE + PA T Sbjct: 23 LGGAMIIAGTTIGAGMFSLPSVSAGMWFFYSLFVLFGTWLCMCHSGLMILEANLNYPAGT 82 Query: 66 GLGTLAKRYLGRYGQWLTGFSMMFLMYALTAAYISGAGELLASSISDWTGISMSATAGVL 125 +AK L R + L S+ F++Y LT AYISG G ++A ++ GI + G Sbjct: 83 SFDNIAKDCLARPVRLLNSLSVAFVLYILTYAYISGGGSIVAHTVKAAVGIDVPMKLGGF 142 Query: 126 LFTFVAGGVVCVGTSLVDLFNRFLFSAKIIFLVVMLVLLLPHIHKVNLL----TLPLQQG 181 LF V VV + T VD + + I+ + L+ ++ L T Sbjct: 143 LFALVLAFVVWLSTRAVDRISTIMLGGMILTFFSSVSGLMFNVQPAVLFDTGDTSAPYSP 202 Query: 182 LALSAIPVIFTSFGFHGSVPSIVSYMDGNIRKLRWVFIIGSAIPLVAYIFWQVATLGSID 241 L+ +P TSFG+HG+VP +V Y + + + + I GS + L+ Y+ WQ++ LG+I Sbjct: 203 FILATLPYFLTSFGYHGNVPGLVKYYNKDPKAVAKTIIYGSFLGLILYVCWQLSVLGNIP 262 Query: 242 STTFMGLLANHAGLNGLLQALREMVASPHVELAVHLFADLALATSFLGVALGLFDYLADL 301 F+ ++A + L+ AL ++ S +++ + +F+ LA+ATSFLGV LGLFD +AD Sbjct: 263 REEFLDIVAKGGNMGILVGALSKVTGSTNLDYLLQVFSHLAVATSFLGVTLGLFDCIADT 322 Query: 302 FQRSNTVGGRLQTGAITFLPPLAFALFYPRGFVMALGYAGVALAVLALIIPSLLTWQSRK 361 ++ GR +T +TF+PP LFYP GF+MA+G+AG+A V A+I+P+++ +R+ Sbjct: 323 LGFDDSRLGRTKTAIVTFVPPAIGGLFYPDGFIMAIGFAGLAATVFAVIVPAMMALATRR 382 Query: 362 HNPQAGYRVKGGRPALVVVFLCGIAVIGVQFLIAAGLLPEVG 403 YR GG L V GI V L +LP G Sbjct: 383 KFGNTTYRAPGGNVMLYVTIAYGITVAICHVLTMFDMLPVYG 424 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: 418 Number of extensions: 17 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: 425 Length adjustment: 31 Effective length of query: 372 Effective length of database: 394 Effective search space: 146568 Effective search space used: 146568 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