Align Asparagine permease (AnsP) of 497 aas and 12 TMSs (characterized)
to candidate GFF344 PS417_01755 proline-specific permease
Query= TCDB::P40812 (497 letters) >FitnessBrowser__WCS417:GFF344 Length = 469 Score = 328 bits (841), Expect = 2e-94 Identities = 169/469 (36%), Positives = 279/469 (59%), Gaps = 7/469 (1%) Query: 19 LNAHEEGYHKAMGNRQVQMIAIGGAIGTGLFLGAGARLQMAGPALALVYLICGIFSFFIL 78 + E+G + + R ++ +A+G AIGTGLF G+ + +QMAGPA+ L YLI G F ++ Sbjct: 1 MQQQEKGLKRGLSARHIRFMALGSAIGTGLFYGSASAIQMAGPAVLLAYLIGGAAVFMVM 60 Query: 79 RALGELVLHRPSSGSFVSYAREFLGEKAAYVAGWMYFINWAMTGIVDITAVALYMHYWGA 138 RALGE+ +H P +GSF YA +LG A ++ GW Y + + D+TA +YM +W Sbjct: 61 RALGEMAVHNPVAGSFGQYASTYLGPMAGFILGWTYAFEMIIVCLADVTAFGIYMGFW-- 118 Query: 139 FGDVPQWVFALGALTIVGTMNMIGVKWFAEMEFWFALIKVLAIVIFLV--VGTIFLGTGQ 196 F DV +WV+ LG + ++G +N+ VK F EMEFW +L+KV AIV ++ G + G Sbjct: 119 FPDVARWVWVLGIVLLIGGLNLCNVKVFGEMEFWLSLLKVGAIVAMILGGFGIMLFGIHS 178 Query: 197 PLEGNATGFHLITDNGGFFPHGLLPALVLIQGVVFAFASIELVGTAAGECKDPQKMVPKA 256 E A+G + +GGF P+G+ + V+FAF IE++G AGE KDPQ+++PKA Sbjct: 179 AGETQASGLSNLWAHGGFMPNGIGGLIASFAVVMFAFGGIEIIGITAGEAKDPQRVIPKA 238 Query: 257 INSVIWRIGLFYVGSVVLLVLLLPWNAYQAGQSPFVTFFSKLGVPYIGSIMNIVVLTAAL 316 IN+V RI LFYV ++ +L+ + PW + SPFV FS LG+ +I+NIVV++AA+ Sbjct: 239 INAVPLRILLFYVLTLFVLMAIYPWPQIGSQGSPFVQIFSNLGIGSAATILNIVVISAAV 298 Query: 317 SSLNSGLYCTGRILRSMSMGGSAPKFMAKMSRQHVPYAGILATLVVYVVGVFLNYLVPSR 376 S++NS ++ GR++ ++ G APK A++S+Q VP+ ++ + GV LNYL+P Sbjct: 299 SAINSDIFGAGRMMYGLAQQGQAPKGFAQLSKQGVPWMTVVVMGAALLGGVVLNYLIPEN 358 Query: 377 VFEIVLNFASLGIIASWAFIMVCQMRLRQAIKEGKAADVSFKLPGAPFTSWLTLLFLLSV 436 VF ++ + A+ + W I+ Q+ +R+++ + + A++ F +P P+ ++F+L V Sbjct: 359 VFLVIASIATFATVWVWLMILFTQVAMRRSMTKEQVAELKFPVPFWPYAPAAAIVFMLFV 418 Query: 437 LVLMAFDYPNGTYTIASLPLIAILLVAGWFGVR---RRVAEIHRTAPVT 482 ++ + + I +L+VA V+ + A++H A ++ Sbjct: 419 FGVLGYFPDTQAALLVGAVWIVLLVVAYLLWVKPSAGQAAKVHYDAALS 467 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: 679 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: 469 Length adjustment: 34 Effective length of query: 463 Effective length of database: 435 Effective search space: 201405 Effective search space used: 201405 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