Align histidine permease (characterized)
to candidate BPHYT_RS15500 BPHYT_RS15500 aromatic amino acid transporter
Query= reanno::pseudo3_N2E3:AO353_12275 (468 letters) >FitnessBrowser__BFirm:BPHYT_RS15500 Length = 461 Score = 389 bits (1000), Expect = e-113 Identities = 195/458 (42%), Positives = 289/458 (63%), Gaps = 6/458 (1%) Query: 6 NGLKRGLSARHIRFMALGSAIGTGLFYGSASAIQMAGPAVLLAYLIGGAAVFMVMRALGE 65 +GLKRGL RHI+ +ALG AIGTGLF GSAS +Q AGP+++L Y IGG FM+MR LGE Sbjct: 8 DGLKRGLKNRHIQLIALGGAIGTGLFLGSASVLQAAGPSMILGYAIGGIIAFMIMRQLGE 67 Query: 66 MAVHNPVAGSFGQYASTYLGPMAGFILGWTYAFEMVIVGMADVTAFGIYMGFWFPEVSRW 125 M PVAGSF +A Y G GF+ GW Y V+V MA++TA G Y+ +W+P V W Sbjct: 68 MVAQEPVAGSFSHFAYKYWGDFPGFLSGWNYWVLYVLVSMAELTAVGTYIHYWWPGVPTW 127 Query: 126 IWVLGVVSIVGGLNLCNVKVFGEMEFWLSLLKVAAIVAMILGGFGIMLFGISTAPGQVTD 185 + L +++ +NL NVK +GE EFW +++KV A++ MI+ G G +L IS G Sbjct: 128 VSALVCFALINAINLANVKAYGETEFWFAIIKVVAVIGMIVFG-GYLL--ISGHGGPQAS 184 Query: 186 ISNLWTQGGFMPNGMGGLIASFAVVMFAFGGIEIIGVTAGEAKDPQHVLPRAINAVPLRI 245 I+NLW+ GGF P+G GL AV+MF+FGG+E+IG+TA EA PQ +P+A+N V RI Sbjct: 185 ITNLWSHGGFFPHGFHGLFMMLAVIMFSFGGLELIGITAAEADQPQKSIPKAVNQVIYRI 244 Query: 246 LLFYVLTMLVLMSIFPWQQIGSQGSPFVQIFDKLGISSAATILNIVVITAAISAINSDIF 305 L+FY+ ++ VL+S++PW ++ + GSPFV IF ++G + A +LN+VV+TAA+S NS ++ Sbjct: 245 LIFYICSLTVLLSLYPWNEVAAGGSPFVMIFSQIGSTLTANVLNVVVLTAALSVYNSGVY 304 Query: 306 GAGRMMFGLAQQGHAPKGFAHLSRNGVPWMTVVVMSVALLLGVLLNYLIPENVFLLIASI 365 RM++GLA+QG+AP+ + R GVP+M + + ++A V++NYLIP L+ ++ Sbjct: 305 ANSRMLYGLAEQGNAPRALMKVDRRGVPYMAIGLSALATFTCVIVNYLIPAEALGLLMAL 364 Query: 366 ATFATVWVWLMILFTQVAMRRSMTAEQVAQLKFPVPFWPYAPMAAIAFMLFVFGVLGYFP 425 A V W +I T + R++M A L F ++P + +AFM + +L P Sbjct: 365 VVAALVLNWALISLTHLKSRKAMVAAG-ETLVFKSFWFPVSNWICLAFMALILVILAMTP 423 Query: 426 DTQAALIVGVVWIVLLVLAYLMWVKPAA--GQAALVAR 461 ++ + W+V++ Y+ + AA G A +V R Sbjct: 424 GLSVSVWLVPAWLVVMWAGYVFKRRRAAVQGGARVVGR 461 Lambda K H 0.329 0.142 0.441 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: 684 Number of extensions: 34 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: 468 Length of database: 461 Length adjustment: 33 Effective length of query: 435 Effective length of database: 428 Effective search space: 186180 Effective search space used: 186180 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: 51 (24.3 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