Align Asparagine permease (AnsP) of 497 aas and 12 TMSs (characterized)
to candidate PfGW456L13_318 Histidine transport protein (permease)
Query= TCDB::P40812 (497 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_318 Length = 468 Score = 333 bits (854), Expect = 8e-96 Identities = 166/442 (37%), Positives = 268/442 (60%), Gaps = 3/442 (0%) Query: 23 EEGYHKAMGNRQVQMIAIGGAIGTGLFLGAGARLQMAGPALALVYLICGIFSFFILRALG 82 E+G + + R ++ +A+G AIGTGLF G+ + +QMAGPA+ L YLI G F ++RALG Sbjct: 5 EKGLKRGLSARHIRFMALGSAIGTGLFYGSASAIQMAGPAVLLAYLIGGAAVFMVMRALG 64 Query: 83 ELVLHRPSSGSFVSYAREFLGEKAAYVAGWMYFINWAMTGIVDITAVALYMHYWGAFGDV 142 E+ +H P +GSF YA +LG A ++ GW Y + G+ D+TA +YM +W F +V Sbjct: 65 EMAVHNPVAGSFGQYASTYLGPMAGFILGWTYAFEMVIVGMADVTAFGIYMGFW--FPEV 122 Query: 143 PQWVFALGALTIVGTMNMIGVKWFAEMEFWFALIKVLAIVIFLVVGTIFLGTG-QPLEGN 201 +W++ LG ++IVG +N+ VK F EMEFW +L+KV AIV ++ G + G G Sbjct: 123 SRWIWVLGVVSIVGGLNLCNVKVFGEMEFWLSLLKVAAIVAMILGGFGIMWFGISSAPGQ 182 Query: 202 ATGFHLITDNGGFFPHGLLPALVLIQGVVFAFASIELVGTAAGECKDPQKMVPKAINSVI 261 AT + +GGF P+G+ + V+FAF IE++G AGE KDPQ ++P+AIN+V Sbjct: 183 ATDISNLWSHGGFMPNGMGGLIASFAVVMFAFGGIEIIGVTAGEAKDPQHVLPRAINAVP 242 Query: 262 WRIGLFYVGSVVLLVLLLPWNAYQAGQSPFVTFFSKLGVPYIGSIMNIVVLTAALSSLNS 321 RI LFYV ++++L+ + PW + SPFV F KLG+ +I+NIVV+TAA+S++NS Sbjct: 243 LRILLFYVLTMLVLMSIFPWQQIGSQGSPFVQIFDKLGISSAATILNIVVITAAISAINS 302 Query: 322 GLYCTGRILRSMSMGGSAPKFMAKMSRQHVPYAGILATLVVYVVGVFLNYLVPSRVFEIV 381 ++ GR++ ++ G APK A++SR VP+ ++ ++GV LNYL+P VF ++ Sbjct: 303 DIFGAGRMMFGLAQQGHAPKGFARLSRNGVPWMTVVVMSAALLLGVLLNYLIPENVFLLI 362 Query: 382 LNFASLGIIASWAFIMVCQMRLRQAIKEGKAADVSFKLPGAPFTSWLTLLFLLSVLVLMA 441 + A+ + W I+V Q+ +R+++ + A + F +P P+ + F+L + ++ Sbjct: 363 ASVATFATVWVWLMILVTQVAMRRSMSAEQVAQLKFPVPLWPYAPAAAIAFMLFIFGVLG 422 Query: 442 FDYPNGTYTIASLPLIAILLVA 463 + I + I +L++A Sbjct: 423 YFPDTQAALIVGVVWIVLLVLA 444 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: 655 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: 468 Length adjustment: 34 Effective length of query: 463 Effective length of database: 434 Effective search space: 200942 Effective search space used: 200942 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: 52 (24.6 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