Align Asparagine permease (AnsP) of 497 aas and 12 TMSs (characterized)
to candidate AO353_12275 AO353_12275 proline-specific permease
Query= TCDB::P40812 (497 letters) >FitnessBrowser__pseudo3_N2E3:AO353_12275 Length = 468 Score = 328 bits (841), Expect = 2e-94 Identities = 166/440 (37%), Positives = 263/440 (59%), Gaps = 3/440 (0%) Query: 25 GYHKAMGNRQVQMIAIGGAIGTGLFLGAGARLQMAGPALALVYLICGIFSFFILRALGEL 84 G + + R ++ +A+G AIGTGLF G+ + +QMAGPA+ L YLI G F ++RALGE+ Sbjct: 7 GLKRGLSARHIRFMALGSAIGTGLFYGSASAIQMAGPAVLLAYLIGGAAVFMVMRALGEM 66 Query: 85 VLHRPSSGSFVSYAREFLGEKAAYVAGWMYFINWAMTGIVDITAVALYMHYWGAFGDVPQ 144 +H P +GSF YA +LG A ++ GW Y + G+ D+TA +YM +W F +V + Sbjct: 67 AVHNPVAGSFGQYASTYLGPMAGFILGWTYAFEMVIVGMADVTAFGIYMGFW--FPEVSR 124 Query: 145 WVFALGALTIVGTMNMIGVKWFAEMEFWFALIKVLAIVIFLVVGT-IFLGTGQPLEGNAT 203 W++ LG ++IVG +N+ VK F EMEFW +L+KV AIV ++ G I L G T Sbjct: 125 WIWVLGVVSIVGGLNLCNVKVFGEMEFWLSLLKVAAIVAMILGGFGIMLFGISTAPGQVT 184 Query: 204 GFHLITDNGGFFPHGLLPALVLIQGVVFAFASIELVGTAAGECKDPQKMVPKAINSVIWR 263 + GGF P+G+ + V+FAF IE++G AGE KDPQ ++P+AIN+V R Sbjct: 185 DISNLWTQGGFMPNGMGGLIASFAVVMFAFGGIEIIGVTAGEAKDPQHVLPRAINAVPLR 244 Query: 264 IGLFYVGSVVLLVLLLPWNAYQAGQSPFVTFFSKLGVPYIGSIMNIVVLTAALSSLNSGL 323 I LFYV ++++L+ + PW + SPFV F KLG+ +I+NIVV+TAA+S++NS + Sbjct: 245 ILLFYVLTMLVLMSIFPWQQIGSQGSPFVQIFDKLGISSAATILNIVVITAAISAINSDI 304 Query: 324 YCTGRILRSMSMGGSAPKFMAKMSRQHVPYAGILATLVVYVVGVFLNYLVPSRVFEIVLN 383 + GR++ ++ G APK A +SR VP+ ++ V ++GV LNYL+P VF ++ + Sbjct: 305 FGAGRMMFGLAQQGHAPKGFAHLSRNGVPWMTVVVMSVALLLGVLLNYLIPENVFLLIAS 364 Query: 384 FASLGIIASWAFIMVCQMRLRQAIKEGKAADVSFKLPGAPFTSWLTLLFLLSVLVLMAFD 443 A+ + W I+ Q+ +R+++ + A + F +P P+ + F+L V ++ + Sbjct: 365 IATFATVWVWLMILFTQVAMRRSMTAEQVAQLKFPVPFWPYAPMAAIAFMLFVFGVLGYF 424 Query: 444 YPNGTYTIASLPLIAILLVA 463 I + I +L++A Sbjct: 425 PDTQAALIVGVVWIVLLVLA 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: 646 Number of extensions: 36 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