Align Tyrosine permease (characterized)
to candidate 17234 b3161 tryptophan transporter of high affinity (NCBI)
Query= TCDB::P0AAD4 (403 letters) >FitnessBrowser__Keio:17234 Length = 414 Score = 239 bits (611), Expect = 8e-68 Identities = 134/399 (33%), Positives = 218/399 (54%), Gaps = 5/399 (1%) Query: 6 LGSVFIVAGTTIGAGMLAMPLAAAGVGFSVTLILLIGLWALMCYTALLLLEVYQHVPADT 65 LG V I+ GT IGAGM ++P+ +G F ++ LI W M ++ L++LE + + Sbjct: 14 LGGVVIIGGTIIGAGMFSLPVVMSGAWFFWSMAALIFTWFCMLHSGLMILEANLNYRIGS 73 Query: 66 GLGTLAKRYLGRYGQWLTGFSMMFLMYALTAAYISGAGELLASSISDWTGISMSATAGVL 125 T+ K LG+ + G S+ F++Y LT AYIS +G +L + ++ + +++ A A Sbjct: 74 SFDTITKDLLGKGWNVVNGISIAFVLYILTYAYISASGSILHHTFAEMS-LNVPARAAGF 132 Query: 126 LFTFVAGGVVCVGTSLVDLFNRFLFSAKIIFLVVMLVLLLPHIHKVNLLTLPLQQG---- 181 F + VV + T V + AK+I + LL H+ L + Sbjct: 133 GFALLVAFVVWLSTKAVSRMTAIVLGAKVITFFLTFGSLLGHVQPATLFNVAESNASYAP 192 Query: 182 LALSAIPVIFTSFGFHGSVPSIVSYMDGNIRKLRWVFIIGSAIPLVAYIFWQVATLGSID 241 L +P SFG+HG+VPS++ Y + + + + G+ + L Y W +AT+G+I Sbjct: 193 YLLMTLPFCLASFGYHGNVPSLMKYYGKDPKTIVKCLVYGTLMALALYTIWLLATMGNIP 252 Query: 242 STTFMGLLANHAGLNGLLQALREMVASPHVELAVHLFADLALATSFLGVALGLFDYLADL 301 F+G+ ++ L+QAL ++ S ++L + +F++ A+A+SFLGV LGLFDYLADL Sbjct: 253 RPEFIGIAEKGGNIDVLVQALSGVLNSRSLDLLLVVFSNFAVASSFLGVTLGLFDYLADL 312 Query: 302 FQRSNTVGGRLQTGAITFLPPLAFALFYPRGFVMALGYAGVALAVLALIIPSLLTWQSRK 361 F ++ GRL+T +TF PP+ L +P GF+ A+GYAG+A + A I+P+LL SRK Sbjct: 313 FGFDDSAVGRLKTALLTFAPPVVGGLLFPNGFLYAIGYAGLAATIWAAIVPALLARASRK 372 Query: 362 HNPQAGYRVKGGRPALVVVFLCGIAVIGVQFLIAAGLLP 400 +RV GG+P + ++ + G+ V L + LLP Sbjct: 373 RFGSPKFRVWGGKPMIALILVFGVGNALVHILSSFNLLP 411 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: 390 Number of extensions: 13 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: 403 Length of database: 414 Length adjustment: 31 Effective length of query: 372 Effective length of database: 383 Effective search space: 142476 Effective search space used: 142476 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