Align Asparagine permease (AnsP) of 497 aas and 12 TMSs (characterized)
to candidate RR42_RS14635 RR42_RS14635 proline-specific permease
Query= TCDB::P40812 (497 letters) >FitnessBrowser__Cup4G11:RR42_RS14635 Length = 466 Score = 321 bits (823), Expect = 3e-92 Identities = 164/468 (35%), Positives = 271/468 (57%), Gaps = 4/468 (0%) Query: 19 LNAHEEGYHKAMGNRQVQMIAIGGAIGTGLFLGAGARLQMAGPALALVYLICGIFSFFIL 78 + +G + + R ++ +A+G AIGTGLF G+ + +Q AGPA+ L Y+I G + ++ Sbjct: 1 MQEQSQGLQRGLSARHIRFMALGSAIGTGLFYGSASAIQTAGPAVLLAYVIGGAAVYMVM 60 Query: 79 RALGELVLHRPSSGSFVSYAREFLGEKAAYVAGWMYFINWAMTGIVDITAVALYMHYWGA 138 RALGE+ + P +GSF YA LG A ++ GW Y + + D+TA +YM +W Sbjct: 61 RALGEMAVRNPVAGSFGQYASTGLGPLAGFLLGWTYAFEMIVVCLADVTAFGIYMGFW-- 118 Query: 139 FGDVPQWVFALGALTIVGTMNMIGVKWFAEMEFWFALIKVLAIVIFLVVGTIFL--GTGQ 196 F DVP+W++ LG + ++G +N++ VK F E+EFW +L+KV AIV + G + G G Sbjct: 119 FPDVPRWIWVLGIVFLIGGLNLLSVKVFGELEFWLSLLKVGAIVAMIGGGVAIMLFGFGM 178 Query: 197 PLEGNATGFHLITDNGGFFPHGLLPALVLIQGVVFAFASIELVGTAAGECKDPQKMVPKA 256 G ATG H + +GGF P+G+ + V+FAF IE++G AGE +DPQ+++P+A Sbjct: 179 ADGGVATGIHNLWTHGGFMPNGIAGVIASFAVVMFAFGGIEIIGITAGEARDPQRVIPRA 238 Query: 257 INSVIWRIGLFYVGSVVLLVLLLPWNAYQAGQSPFVTFFSKLGVPYIGSIMNIVVLTAAL 316 IN+V RI LFYV ++ +L+ L PW+ + SPFV FS+LG+ +++NIVV++AA+ Sbjct: 239 INAVPLRILLFYVLTLAVLMSLYPWHRIGSEGSPFVQIFSRLGIGSAAAVLNIVVISAAV 298 Query: 317 SSLNSGLYCTGRILRSMSMGGSAPKFMAKMSRQHVPYAGILATLVVYVVGVFLNYLVPSR 376 S++NS ++ GR+L M++ AP+ A +SR+ VP+ ++ + GV LNY++P Sbjct: 299 SAINSDIFGAGRMLYGMAVQRQAPRIFASVSRKGVPWMTVVVMAFALLAGVVLNYVMPED 358 Query: 377 VFEIVLNFASLGIIASWAFIMVCQMRLRQAIKEGKAADVSFKLPGAPFTSWLTLLFLLSV 436 VF ++ + A+ + W I++ Q+ LR+ + + A + F +P P F+L + Sbjct: 359 VFTLIASIATFATVWVWLMILLSQVALRRRMSRAEVAALKFPVPFWPVAPLAATAFMLFI 418 Query: 437 LVLMAFDYPNGTYTIASLPLIAILLVAGWFGVRRRVAEIHRTAPVTAD 484 ++ + + + +L+VA W R R E + AD Sbjct: 419 FGVLGWFPQTRAALLVGAVWLLLLVVAWWCWGRPRGQEGAPASSFAAD 466 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: 660 Number of extensions: 35 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: 466 Length adjustment: 34 Effective length of query: 463 Effective length of database: 432 Effective search space: 200016 Effective search space used: 200016 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