Align Tyrosine permease (characterized)
to candidate BWI76_RS03530 BWI76_RS03530 tryptophan permease
Query= TCDB::P0AAD4 (403 letters) >FitnessBrowser__Koxy:BWI76_RS03530 Length = 418 Score = 234 bits (597), Expect = 4e-66 Identities = 132/399 (33%), Positives = 214/399 (53%), Gaps = 5/399 (1%) Query: 6 LGSVFIVAGTTIGAGMLAMPLAAAGVGFSVTLILLIGLWALMCYTALLLLEVYQHVPADT 65 +G I+ GT IGAGM ++P+ +G F +L+ LI W M ++ L++LE + Sbjct: 18 IGGAMIIGGTIIGAGMFSLPVVMSGAWFFWSLLALIFTWFCMLHSGLMILEANLNYHIGA 77 Query: 66 GLGTLAKRYLGRYGQWLTGFSMMFLMYALTAAYISGAGELLASSISDWTGISMSATAGVL 125 T+ K LG + G ++ F++Y LT AYIS +G ++ + + +++ A G L Sbjct: 78 SFDTITKDLLGNGWNIINGLTVAFVLYILTYAYISASGSVIQHTFAQMD-LAVPARLGGL 136 Query: 126 LFTFVAGGVVCVGTSLVDLFNRFLFSAKIIFLVVMLVLLLPHIHKVNLLTLPLQQG---- 181 F V +V + T V + AKI+ + L+ H+ L Sbjct: 137 AFALVVAFIVWLSTKAVSRMTTIVLGAKILTFFMTFGGLMWHVEPAILFNRAEGNASYLP 196 Query: 182 LALSAIPVIFTSFGFHGSVPSIVSYMDGNIRKLRWVFIIGSAIPLVAYIFWQVATLGSID 241 L +P SFG+HG+VPS++ Y + +R ++G+ + LV YI W V T+G+I Sbjct: 197 YVLMTLPFCLASFGYHGNVPSLMKYYGKDPLTIRRCLLLGTLMALVLYIIWLVGTMGNIP 256 Query: 242 STTFMGLLANHAGLNGLLQALREMVASPHVELAVHLFADLALATSFLGVALGLFDYLADL 301 F+ + ++ L+Q L ++ S ++L + +F++ A+A+SFLGV LGLFDYLADL Sbjct: 257 RPAFIAIAEKGGNIDVLVQTLSGLLNSSTLDLLLTVFSNFAVASSFLGVTLGLFDYLADL 316 Query: 302 FQRSNTVGGRLQTGAITFLPPLAFALFYPRGFVMALGYAGVALAVLALIIPSLLTWQSRK 361 F+ ++ GR +T +TFLPP+A L +P GF+ A+G+AG+A V A I+P+LL SR+ Sbjct: 317 FKFDDSRLGRFKTALVTFLPPIAGGLLWPNGFIYAIGFAGLAATVWAAIVPALLARASRR 376 Query: 362 HNPQAGYRVKGGRPALVVVFLCGIAVIGVQFLIAAGLLP 400 YRV GG ++++ G A + L + LLP Sbjct: 377 RFGSPNYRVWGGNAMIILILCFGGANAIIHILSSFNLLP 415 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: 420 Number of extensions: 13 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: 418 Length adjustment: 31 Effective length of query: 372 Effective length of database: 387 Effective search space: 143964 Effective search space used: 143964 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