Align Tyrosine permease (characterized)
to candidate 200256 SO1074 tyrosine-specific transport protein, putative (NCBI ptt file)
Query= TCDB::P0AAD4 (403 letters) >FitnessBrowser__MR1:200256 Length = 395 Score = 305 bits (782), Expect = 1e-87 Identities = 165/398 (41%), Positives = 240/398 (60%), Gaps = 7/398 (1%) Query: 1 MKNRTLGSVFIVAGTTIGAGMLAMPLAAAGVGFSVTLILLIGLWALMCYTALLLLEVYQH 60 M ++ LGS+ IVAGT IGAGMLA+PLA A +G ++L++ +W L YT+LL+LE+ Sbjct: 1 MNSKMLGSIAIVAGTAIGAGMLALPLATAALGMVPAILLMVVIWGLSAYTSLLMLEINLR 60 Query: 61 VPADTGLGTLAKRYLGRYGQWLTGFSMMFLMYALTAAYISGAGELLASSISDWTGISMSA 120 + + + LG+ GQ + G S + L+ ALTAAY++G LL + I + Sbjct: 61 SGVGDNVHAITGKLLGKKGQIVQGASFLSLLVALTAAYLTGGSSLLVLKAQNMFDIVLDN 120 Query: 121 TAGVLLFTFVAGGVVCVGTSLVDLFNRFLFSAKIIFLVVMLVLLLPHIHKVNLLTLPLQQ 180 V+LFT V GG +G + VD +RFLFS I+ L+V+++ LLP + + T + Q Sbjct: 121 QLAVVLFTIVLGGFAALGVAWVDKVSRFLFSLMILLLIVVVLFLLPEVSISTIATSAVAQ 180 Query: 181 GLA---LSAIPVIFTSFGFHGSVPSIVSYMDGNIRKLRWVFIIGSAIPLVAYIFWQVATL 237 L ++AIPV+FTSFGFH + ++V Y+DG+ LR V +IGS IPL YIFW + TL Sbjct: 181 SLTSSWMAAIPVVFTSFGFHVCIATLVRYLDGDTVSLRKVLLIGSTIPLACYIFWLLVTL 240 Query: 238 GSIDSTTFMGLLANHAGLNGLLQALREMVASPHVELAVHLFADLALATSFLGVALGLFDY 297 G++ G + L L+ AL+E+ +P + + LFADLAL TSFLGV L L+D+ Sbjct: 241 GTVGGNEINGF---NGSLPALISALQEIAHTPLISKCISLFADLALITSFLGVTLSLYDF 297 Query: 298 LADLFQRSNTVGGRLQTGAITFLPPLAFALFYPRGFVMALGYAGVALAVLALIIPSLLTW 357 +A+L + T GR QT +TF+PPL AL+ P GFV LG+A V L V+ + +P + Sbjct: 298 VAELTRAKKTFVGRAQTWLLTFVPPLLCALYVPEGFVAVLGFAAVPLVVMIIFLPIAMAL 357 Query: 358 QSRKHNPQAGYRVKGGRPALVVVFLCGIAVIGVQFLIA 395 + R+ PQ GY+V GG AL + + G +IG Q +A Sbjct: 358 RQRQIQPQ-GYQVVGGTFALGLAGILGAIIIGAQLFVA 394 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: 451 Number of extensions: 22 Number of successful extensions: 5 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: 395 Length adjustment: 31 Effective length of query: 372 Effective length of database: 364 Effective search space: 135408 Effective search space used: 135408 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