Align Asparagine permease (AnsP) of 497 aas and 12 TMSs (characterized)
to candidate WP_033101984.1 JG50_RS0115245 amino acid permease
Query= TCDB::P40812 (497 letters) >NCBI__GCF_000763315.1:WP_033101984.1 Length = 484 Score = 265 bits (677), Expect = 3e-75 Identities = 162/456 (35%), Positives = 251/456 (55%), Gaps = 27/456 (5%) Query: 33 RQVQMIAIGGAIGTGLFLGAGARLQMAGPALALV-YLICGIFSFFILRALGELVLHRPSS 91 R + MIAIGG+IGTG+FL +GA + AGP ALV YL GI +F++ +LGE+ P + Sbjct: 17 RHLSMIAIGGSIGTGVFLASGASISEAGPGGALVAYLAIGIMVYFLMTSLGEMATFMPVA 76 Query: 92 GSFVSYAREFLGEKAAYVAGWMYFINWAMTGIVDITAVALYMHYWGAFGDVPQWVFALGA 151 GSF +YA F+ + GW Y+ NWA+T V+++A +L M YW F P +++ Sbjct: 77 GSFSTYAGRFVDPALGFAMGWNYWYNWAITIAVELSAGSLIMDYW--FPHSPSILWSALF 134 Query: 152 LTIVGTMNMIGVKWFAEMEFWFALIKVLAIVIFLVVGTIFLGTGQPLEGNATGFHLITDN 211 L ++ +N + VK + E E+WF+ IKV ++IF+V+G + + + G A GF T N Sbjct: 135 LLLMFGLNALSVKGYGESEYWFSFIKVATVIIFIVIGLLMIFG--IMGGEAIGFKNFTIN 192 Query: 212 GGFFPHGLLPALVLIQGVVFAFASIELVGTAAGECKDPQKMVPKAINSVIWRIGLFYVGS 271 F HG L L + F+F ELVG AAGE ++P+K VPKAI V WRI LFY + Sbjct: 193 DAPFHHGWLGILSVFMIAGFSFQGTELVGVAAGESENPRKNVPKAIRQVFWRILLFYALA 252 Query: 272 VVLLVLLLPW--------NAYQAGQSPFVTFFSKLGVPYIGSIMNIVVLTAALSSLNSGL 323 ++++ L+LP+ + Q +SPF F K G+ + S+MN V+LT+ LS+ NSG+ Sbjct: 253 ILVMGLVLPYTNPNLVGGDVNQIAKSPFTIIFEKAGLAFAASVMNAVILTSVLSAGNSGM 312 Query: 324 YCTGRILRSMSMGGSAPKFMAKMSRQHVPYAGILATLVVYVVGVFLNYLVPSRVFEIVLN 383 Y + R+L M+ G APK AK++R+ VP +L T V V + + +++ +LN Sbjct: 313 YASTRMLWQMAKEGKAPKLFAKVNRRGVPVFALLLTTAVGAVAFLASLVGQGKIYIWLLN 372 Query: 384 FASLGIIASWAFIMVCQMRLRQA-IKEGKAAD-VSFKLPGAPFTSWLTLLFLLSVLV--- 438 + L +W I + R R+A + +G+ + + ++ PF L+ + V+V Sbjct: 373 ASGLSGFIAWLGIAISHYRFRRAYVAQGRDLNHLVYRAKWFPFGPLFALVLCVIVIVGQN 432 Query: 439 LMAF-----DYPNGTYTIASLPLIAILLVAGWFGVR 469 AF D+ + LPL +L W G + Sbjct: 433 YQAFTGNTIDWNGILVSYIGLPLFILL----WLGYK 464 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: 734 Number of extensions: 58 Number of successful extensions: 5 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: 484 Length adjustment: 34 Effective length of query: 463 Effective length of database: 450 Effective search space: 208350 Effective search space used: 208350 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 24 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