Align Asparagine permease (AnsP) of 497 aas and 12 TMSs (characterized)
to candidate Pf1N1B4_3559 Aromatic amino acid transport protein AroP
Query= TCDB::P40812 (497 letters) >FitnessBrowser__pseudo1_N1B4:Pf1N1B4_3559 Length = 473 Score = 322 bits (826), Expect = 1e-92 Identities = 171/462 (37%), Positives = 277/462 (59%), Gaps = 18/462 (3%) Query: 20 NAHEEGYHKAMGNRQVQMIAIGGAIGTGLFLGAGARLQMAGPALALVYLICGIFSFFILR 79 N+H + + NR +Q+IA+GGAIGTGLFLG+ L+ AGP++ L Y ICG +F I+R Sbjct: 5 NSHSGELKRGLKNRHIQLIALGGAIGTGLFLGSAGVLKSAGPSMILGYAICGFIAFMIMR 64 Query: 80 ALGELVLHRPSSGSFVSYAREFLGEKAAYVAGWMYFINWAMTGIVDITAVALYMHYWGAF 139 LGE+++ P +GSF +A ++ G A +++GW +I + + G+ ++TAV Y+HYW Sbjct: 65 QLGEMIVEEPVAGSFSHFAHKYWGGFAGFLSGWNCWILYILVGMSELTAVGKYIHYWAP- 123 Query: 140 GDVPQWVFALGALTIVGTMNMIGVKWFAEMEFWFALIKVLAIVIFLVVGTIFLGTGQPLE 199 D+P WV A G ++ +N+ VK F E EFWFA+IKV+AIV + +G+ L +G Sbjct: 124 -DIPTWVSAAGFFVLINLINLANVKVFGEAEFWFAIIKVVAIVGMIALGSYLLVSGD--G 180 Query: 200 GNATGFHLITDNGGFFPHGLLPALVLIQGVVFAFASIELVGTAAGECKDPQKMVPKAINS 259 G + ++GGFFP+G+ ++ + ++F+F +E++G A E P+ ++PKAIN Sbjct: 181 GPQASVTNLWEHGGFFPNGVSGLVMAMAIIMFSFGGLEMLGFTAAEADKPKTVIPKAINQ 240 Query: 260 VIWRIGLFYVGSVVLLVLLLPWNAYQA---------GQSPFVTFFSKLGVPYIGSIMNIV 310 VI+RI +FY+G++V+L+ L PW++ SPFV FS LG I+N V Sbjct: 241 VIYRILIFYIGALVVLLSLTPWDSLLTTLNASGDAYSGSPFVQVFSMLGSDTAAHILNFV 300 Query: 311 VLTAALSSLNSGLYCTGRILRSMSMGGSAPKFMAKMSRQHVPYAGILATLVVYVVGVFLN 370 VLTAALS NSG YC R+L M+ G APK ++K+ ++ VP ILA+ V +V V LN Sbjct: 301 VLTAALSVYNSGTYCNSRMLLGMAEQGDAPKALSKIDKRGVPVRSILASAAVTLVAVLLN 360 Query: 371 YLVPSRVFEIVLNFASLGIIASWAFIMVCQMRLRQAIKEGKAADVSFKLPGAPFTSWLTL 430 YLVP E++++ ++ +WA I + RQ + + K + FK P+ +++ L Sbjct: 361 YLVPQHALELLMSLVVATLVINWAMISFSHFKFRQHMNKTKQTPL-FKALWYPYGNYVCL 419 Query: 431 LFLLSVLVLMAFDYPNGTYTIASLPL-IAILLVAGWFGVRRR 471 F++ +L +M P ++ ++P+ +A + V +G++ + Sbjct: 420 AFVVFILGVMLL-IPGIQISVYAIPVWVAFMWVC--YGIKNK 458 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: 633 Number of extensions: 33 Number of successful extensions: 4 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: 473 Length adjustment: 34 Effective length of query: 463 Effective length of database: 439 Effective search space: 203257 Effective search space used: 203257 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