Align Tyrosine permease (characterized)
to candidate 7024668 Shewana3_1846 aromatic amino acid transporter (RefSeq)
Query= TCDB::P0AAD4 (403 letters) >FitnessBrowser__ANA3:7024668 Length = 395 Score = 397 bits (1021), Expect = e-115 Identities = 194/396 (48%), Positives = 276/396 (69%), Gaps = 8/396 (2%) Query: 2 KNRTLGSVFIVAGTTIGAGMLAMPLAAAGVGFSVTLILLIGLWALMCYTALLLLEVYQHV 61 +N+ GS+ ++AGTTIGAGMLA+P+A+AG+GF V+ ++++ LWALM YTALL++E++Q Sbjct: 3 QNKFFGSLLLIAGTTIGAGMLALPIASAGLGFGVSSLIMLLLWALMAYTALLMVEIHQFA 62 Query: 62 PADTGLGTLAKRYLGRYGQWLTGFSMMFLMYALTAAYISGAGELLASSISDWTGISMSAT 121 P+D L LA+ LG GQ + ++MFL+YAL AAYI+G GE + ++ W G+ + Sbjct: 63 PSDASLNQLARTLLGAKGQVIASIALMFLLYALCAAYIAGGGEQVNQKLNAWLGLELPTQ 122 Query: 122 AGVLLFTFVAGGVVCVGTSLVDLFNRFLFSAKIIFLVVMLVLLLPHIHKVNLLTLPLQQG 181 AG + FT + G +V +GT VDL NR LFS KII L++ML LLLP + +LL LPL+QG Sbjct: 123 AGAIFFTLLIGTIVGLGTHCVDLINRVLFSLKIIALILMLALLLPQVEGTHLLELPLEQG 182 Query: 182 LALSAIPVIFTSFGFHGSVPSIVSYMDGNIRKLRWVFIIGSAIPLVAYIFWQVATLGSID 241 L +SAIPVIFTSFGFHGS+PS+V Y+ ++ LR + ++GSA+PL+ Y+ WQ+ + G + Sbjct: 183 LIVSAIPVIFTSFGFHGSIPSVVRYLGVEVKSLRKIMLLGSALPLLIYLLWQLGSQGVLS 242 Query: 242 STTFMGLLANHAGLNGLLQALREMVASPHVELAVHLFADLALATSFLGVALGLFDYLADL 301 + M + L+G + L ++ S ++ A+ +FADLALATSFLGV+LGLFD++A Sbjct: 243 QSQLM----TNQSLSGFINQLASVLHSQYLSSAISVFADLALATSFLGVSLGLFDFMAAN 298 Query: 302 FQRSNTVGGRLQTGAITFLPPLAFALFYPRGFVMALGYAGVALAVLALIIPSLLTWQSR- 360 ++ + GR T AITF+PPL FALFYP+GF+ ALGYA +AL +LA+ +P + W R Sbjct: 299 LRQQDNAAGRSITAAITFVPPLGFALFYPQGFITALGYAAIALVILAIFLPVTMVWVQRQ 358 Query: 361 ---KHNPQAGYRVKGGRPALVVVFLCGIAVIGVQFL 393 K N GYRV GG+ L++ LCG+AVIG Q L Sbjct: 359 TRDKANLPQGYRVAGGKLGLLLAMLCGVAVIGAQLL 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: 443 Number of extensions: 16 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: 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