Align Tryptophan-specific transport protein; Tryptophan permease (characterized)
to candidate 5210760 Shew_3188 aromatic amino acid permease (RefSeq)
Query= SwissProt::Q02DS7 (417 letters) >FitnessBrowser__PV4:5210760 Length = 395 Score = 203 bits (517), Expect = 6e-57 Identities = 129/405 (31%), Positives = 210/405 (51%), Gaps = 19/405 (4%) Query: 15 LLGGSMIIAGTAVGAGMFSLPIAMSGIWFGWSVAVFLLTWFCMLLSGMMILEANLNYPVG 74 +LG I+AGTA+G GM +LP+A + + ++ + + W + + +++LE NL VG Sbjct: 1 MLGSIAIVAGTAIGGGMLALPLATASLGTIPALLLLVAIWGVSIYTSLLMLEINLRAGVG 60 Query: 75 SSFSTITRDLLGQGWNVVNGLSIAFVLYILTYAYISGGGSIIGYTLSSGLGVTLPEKLAG 134 + IT LG+ ++ G S +L+ LT Y+ GG S++ LG+ + + A Sbjct: 61 LNVHAITGKTLGKVGQLIQGGSFLSLLFALTMVYLMGGSSLLESRFEP-LGIKVNHEAAV 119 Query: 135 LLFALA----VALVVWWSTRAVDRITTLMLGGMIITFGLSISGLLGRIQPAILFNSGEPD 190 L+F L +A+ V W +D+++ ++ M+ F + + LL + P+ + + Sbjct: 120 LIFTLVFGGFIAIGVSW----IDKVSRVLFSAMVALFVIVVLFLLPEVSPSYILRESATE 175 Query: 191 AVYWPYL----LATLPFCLTSFGYHGNVPSLMKYYGKDPQRISRSLWIGTLIALAIYLLW 246 V L LA +P TSFG+H + ++++Y D + + L IG+ I L Y+LW Sbjct: 176 LVSKGELGNLWLAAIPVVFTSFGFHVCIATIVRYLDGDAMSLRKVLMIGSTIPLVCYILW 235 Query: 247 QASTLGTIPREQFKGIIAGGSNVGTLVEYLHRITASDSLNALLTTFSNLAVASSFLGVTL 306 TLGT+ G ++ LV L I SD L + F+NLA+ +SFLGVT+ Sbjct: 236 LMVTLGTVGGATVYGF---EGSLPKLVSALQGIAHSDILRQCIDLFANLALITSFLGVTM 292 Query: 307 GLFDYLADLCRFDDSHFGRFKTALLTFVPPTIGGLLFPNGFIYAIGFAGLAAAFWAVIVP 366 LFDY+A+L R D+ GR +T L+TFVPP + L +P+GFI +GFA L + +P Sbjct: 293 SLFDYIAELTRARDNLLGRLQTWLITFVPPLLCALYYPDGFIKVLGFAALPLVVMIIFLP 352 Query: 367 ALMARASRKR-FGSPLFRAWGGTPAIVLVLLFGVANAVAHILASL 410 MA RK+ G ++ GG A+ L G+ A + +L Sbjct: 353 IAMALGQRKQNLGG--YQVSGGQFALAASALVGLVIIAAQLWVAL 395 Lambda K H 0.326 0.141 0.445 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: 503 Number of extensions: 24 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: 417 Length of database: 395 Length adjustment: 31 Effective length of query: 386 Effective length of database: 364 Effective search space: 140504 Effective search space used: 140504 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 (21.7 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