Align L-asparagine permease; L-asparagine transport protein (characterized)
to candidate Pf6N2E2_5633 Aromatic amino acid transport protein AroP
Query= SwissProt::P77610 (499 letters) >FitnessBrowser__pseudo6_N2E2:Pf6N2E2_5633 Length = 472 Score = 324 bits (830), Expect = 5e-93 Identities = 171/463 (36%), Positives = 273/463 (58%), Gaps = 15/463 (3%) Query: 20 NAHEEGYHKAMGNRQVQMIAIGGAIGTGLFLGAGARLQMAGPALALVYLICGLFSFFILR 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 GGVPQWVFALAALTIVGTMNMIGVKWFAEMEFWFALIKVLAIVTFLVVGTVFLGSGQPLD 199 +P WV A A ++ +N+ VK F E EFWFA+IKV+AIV + +G+ L SG Sbjct: 124 -DIPTWVSAAAFFILINVINLANVKVFGEAEFWFAIIKVVAIVGMIALGSYLLVSGH--G 180 Query: 200 GNTTGFHLITDNGGFFPHGLLPALVLIQGVVFAFASIEMVGTAAGECKDPQTMVPKAINS 259 G + +GGFFP+G+ ++ + ++F+F +EM+G A E P+T++PKAIN Sbjct: 181 GPQASVTNLWSHGGFFPNGVSGLVMAMAIIMFSFGGLEMLGFTAAEADKPKTVIPKAINQ 240 Query: 260 VIWRIGLFYVGSVVLLVMLLPWSAYQA---------GQSPFVTFFSKLGVPYIGSIMNIV 310 VI+RI +FY+G++V+L+ L PW + + SPFV FS LG I+N V Sbjct: 241 VIYRILIFYIGALVVLLSLTPWDSLLSTLNASGDAYSGSPFVQVFSMLGSNTAAHILNFV 300 Query: 311 VLTAALSSLNSGLYCTGRILRSMAMGGSAPSFMAKMSRQHVPYAGILATLVVYVVGVFLN 370 VLTAALS NSG YC R+L MA G AP ++K+ ++ VP ILA+ V +V V LN Sbjct: 301 VLTAALSVYNSGTYCNSRMLLGMAEQGDAPKVLSKIDKRGVPVRSILASAAVTLVAVLLN 360 Query: 371 YLVPSRVFEIVLNFASLGIIASWAFIIVCQMRLRKAIKEGKAADVSFKLPGAPFTSWLTL 430 YL+P E++++ ++ +WA I + R+ + + + FK P+ +++ L Sbjct: 361 YLIPQHALELLMSLVVATLVINWAMISYSHFKFRQHMNQTHQTPL-FKALWYPYGNYICL 419 Query: 431 LFLLSVLVLMAFDYPNGTYTIAALPIIGILLVIGWFGVRKRVA 473 F++ +L +M P ++ A+P+ + + + ++ KR A Sbjct: 420 AFVVFILGVMLL-IPGIQVSVYAIPVWVVFMAVCYWIKNKRSA 461 Lambda K H 0.327 0.141 0.435 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: 664 Number of extensions: 38 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: 499 Length of database: 472 Length adjustment: 34 Effective length of query: 465 Effective length of database: 438 Effective search space: 203670 Effective search space used: 203670 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