Align Tyrosine permease (characterized)
to candidate WP_011188199.1 DP_RS04805 amino acid permease
Query= TCDB::P0AAD4 (403 letters) >NCBI__GCF_000025945.1:WP_011188199.1 Length = 398 Score = 377 bits (969), Expect = e-109 Identities = 201/405 (49%), Positives = 271/405 (66%), Gaps = 9/405 (2%) Query: 1 MKN-RTLGSVFIVAGTTIGAGMLAMPLAAAGVGFSVTLILLIGLWALMCYTALLLLEVYQ 59 MKN + LGS I+AGT+IGAGMLA+PLA+AG+G + I+L+ +W LM YTALL+LEV+Q Sbjct: 1 MKNSKVLGSTLIIAGTSIGAGMLALPLASAGLGCFTSFIILLVMWLLMSYTALLMLEVHQ 60 Query: 60 HVPADTGLGTLAKRYLGRYGQWLTGFSMMFLMYALTAAYISGAGELLASSISDWTGISMS 119 H D L TLA ++LGR G + SM+FL YAL AAYI+G G ++DW +++ Sbjct: 61 HAAKDATLHTLASQFLGRRGDMVATVSMLFLFYALCAAYIAGGGAQFNVKLTDWFHLAVP 120 Query: 120 ATAGVLLFTFVAGGVVCVGTSLVDLFNRFLFSAKIIFLVVMLVLLLPHIHKVNLLTLPLQ 179 G +LFT + VV GT VD+ NR LFSAKI+ L +ML L P I+ NL+T+P+ Sbjct: 121 QEVGTILFTVIVATVVTFGTGSVDMVNRLLFSAKIVVLAIMLFFLTPSINPANLVTMPIH 180 Query: 180 QGLALSAIPVIFTSFGFHGSVPSIVSYMDGNIRKLRWVFIIGSAIPLVAYIFWQVATLGS 239 QGL LSA+PVIFTSFGFHGS+P++V Y+D +++ LR V IIGSA+PL+ YI W + TLG Sbjct: 181 QGLILSALPVIFTSFGFHGSIPAVVRYLDLDMKALRRVLIIGSALPLLIYILWLLTTLGV 240 Query: 240 IDSTTFMGLLANHAGLNGLLQALREMVASPHVELAVHLFADLALATSFLGVALGLFDYLA 299 + G+L + L ++ L + S + AV +FADLAL TSFLGV+LGLF++L Sbjct: 241 LS----QGVLLQNQNLAAFVKTLSGSIESSQIGRAVSIFADLALVTSFLGVSLGLFEFLG 296 Query: 300 DLFQRSNTVGGRLQTGAITFLPPLAFALFYPRGFVMALGYAGVALAVLALIIPSLLTWQS 359 D + G L ITFLPPL FALFYP+GF+ ALGYA +ALAVLA+++P + + Sbjct: 297 DSLGKGR---GGLFIALITFLPPLGFALFYPQGFITALGYAAIALAVLAVLLPVAMVKVA 353 Query: 360 RKHNPQAG-YRVKGGRPALVVVFLCGIAVIGVQFLIAAGLLPEVG 403 RK +G YR GG ALV+ L G+ +I Q LI+ G++P +G Sbjct: 354 RKRYTGSGFYRAPGGGGALVLTGLLGLVIIVSQVLISFGIVPAIG 398 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: 21 Number of successful extensions: 4 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: 398 Length adjustment: 31 Effective length of query: 372 Effective length of database: 367 Effective search space: 136524 Effective search space used: 136524 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 24 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