Align Asparagine permease (AnsP) of 497 aas and 12 TMSs (characterized)
to candidate BPHYT_RS15500 BPHYT_RS15500 aromatic amino acid transporter
Query= TCDB::P40812 (497 letters) >FitnessBrowser__BFirm:BPHYT_RS15500 Length = 461 Score = 332 bits (850), Expect = 2e-95 Identities = 167/451 (37%), Positives = 274/451 (60%), Gaps = 6/451 (1%) Query: 23 EEGYHKAMGNRQVQMIAIGGAIGTGLFLGAGARLQMAGPALALVYLICGIFSFFILRALG 82 ++G + + NR +Q+IA+GGAIGTGLFLG+ + LQ AGP++ L Y I GI +F I+R LG Sbjct: 7 QDGLKRGLKNRHIQLIALGGAIGTGLFLGSASVLQAAGPSMILGYAIGGIIAFMIMRQLG 66 Query: 83 ELVLHRPSSGSFVSYAREFLGEKAAYVAGWMYFINWAMTGIVDITAVALYMHYWGAFGDV 142 E+V P +GSF +A ++ G+ +++GW Y++ + + + ++TAV Y+HYW + V Sbjct: 67 EMVAQEPVAGSFSHFAYKYWGDFPGFLSGWNYWVLYVLVSMAELTAVGTYIHYW--WPGV 124 Query: 143 PQWVFALGALTIVGTMNMIGVKWFAEMEFWFALIKVLAIVIFLVVGTIFLGTGQPLEGNA 202 P WV AL ++ +N+ VK + E EFWFA+IKV+A++ +V G L +G G Sbjct: 125 PTWVSALVCFALINAINLANVKAYGETEFWFAIIKVVAVIGMIVFGGYLLISGHG--GPQ 182 Query: 203 TGFHLITDNGGFFPHGLLPALVLIQGVVFAFASIELVGTAAGECKDPQKMVPKAINSVIW 262 + +GGFFPHG +++ ++F+F +EL+G A E PQK +PKA+N VI+ Sbjct: 183 ASITNLWSHGGFFPHGFHGLFMMLAVIMFSFGGLELIGITAAEADQPQKSIPKAVNQVIY 242 Query: 263 RIGLFYVGSVVLLVLLLPWNAYQAGQSPFVTFFSKLGVPYIGSIMNIVVLTAALSSLNSG 322 RI +FY+ S+ +L+ L PWN AG SPFV FS++G +++N+VVLTAALS NSG Sbjct: 243 RILIFYICSLTVLLSLYPWNEVAAGGSPFVMIFSQIGSTLTANVLNVVVLTAALSVYNSG 302 Query: 323 LYCTGRILRSMSMGGSAPKFMAKMSRQHVPYAGILATLVVYVVGVFLNYLVPSRVFEIVL 382 +Y R+L ++ G+AP+ + K+ R+ VPY I + + V +NYL+P+ +++ Sbjct: 303 VYANSRMLYGLAEQGNAPRALMKVDRRGVPYMAIGLSALATFTCVIVNYLIPAEALGLLM 362 Query: 383 NFASLGIIASWAFIMVCQMRLRQAIKEGKAADVSFKLPGAPFTSWLTLLFLLSVLVLMAF 442 ++ +WA I + ++ R+A+ + FK P ++W+ L F+ +LV++A Sbjct: 363 ALVVAALVLNWALISLTHLKSRKAM-VAAGETLVFKSFWFPVSNWICLAFMALILVILAM 421 Query: 443 DYPNGTYTIASLPLIAILLVAGWFGVRRRVA 473 P + ++ +P +++ AG+ RRR A Sbjct: 422 T-PGLSVSVWLVPAWLVVMWAGYVFKRRRAA 451 Lambda K H 0.328 0.140 0.434 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: 651 Number of extensions: 37 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: 497 Length of database: 461 Length adjustment: 34 Effective length of query: 463 Effective length of database: 427 Effective search space: 197701 Effective search space used: 197701 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: 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