Align L-asparagine permease; L-asparagine transport protein (characterized)
to candidate AO353_18555 AO353_18555 aromatic amino acid transporter
Query= SwissProt::P77610 (499 letters) >FitnessBrowser__pseudo3_N2E3:AO353_18555 Length = 473 Score = 321 bits (822), Expect = 4e-92 Identities = 172/464 (37%), Positives = 270/464 (58%), Gaps = 15/464 (3%) Query: 20 NAHEEGYHKAMGNRQVQMIAIGGAIGTGLFLGAGARLQMAGPALALVYLICGLFSFFILR 79 N+H + + NR +Q+IA+GGAIGTGLFLG+ L+ AGP++ L Y ICG +F I+R Sbjct: 5 NSHSGTLQRGLKNRHIQLIALGGAIGTGLFLGSAGVLKSAGPSMILGYAICGFIAFMIMR 64 Query: 80 ALGELVLHRPSSGSFVSYAREFLGEKAAYVAGWMYFINWAMTGIVDITAVALYMHYWGAF 139 LGE+++ P +GSF +A ++ G A +++GW +I + + G+ ++TAV Y+HYW + Sbjct: 65 QLGEMIVEEPVAGSFSHFAHKYWGGFAGFLSGWNCWILYILVGMSELTAVGKYVHYW--W 122 Query: 140 GGVPQWVFALAALTIVGTMNMIGVKWFAEMEFWFALIKVLAIVTFLVVGTVFLGSGQPLD 199 VP W A ++ +N+ VK F E EFWFA+IKV+AIV + +G+ L SG Sbjct: 123 PDVPTWASAAVFFVMINAINLANVKVFGEAEFWFAIIKVVAIVGMIALGSYLLVSGH--G 180 Query: 200 GNTTGFHLITDNGGFFPHGLLPALVLIQGVVFAFASIEMVGTAAGECKDPQTMVPKAINS 259 G + ++GGFFP+G+ ++ + ++F+F +EM+G A E P+T++PKAIN Sbjct: 181 GPQASVSNLWEHGGFFPNGVSGLVMAMAIIMFSFGGLEMLGFTAAEADKPKTVIPKAINQ 240 Query: 260 VIWRIGLFYVGSVVLLVMLLPW---------SAYQAGQSPFVTFFSKLGVPYIGSIMNIV 310 VI+RI +FY+G++V+L+ L PW S SPFV FS LG I+N V Sbjct: 241 VIYRILIFYIGALVVLLSLTPWDSLLVSLNASGDAYSGSPFVQVFSMLGSKTAAHILNFV 300 Query: 311 VLTAALSSLNSGLYCTGRILRSMAMGGSAPSFMAKMSRQHVPYAGILATLVVYVVGVFLN 370 VLTAALS NSG YC R+L MA G AP +AK+ ++ VP ILA+ V V V +N Sbjct: 301 VLTAALSVYNSGTYCNSRMLLGMAEQGDAPKGLAKIDKRGVPVRSILASAAVTFVAVVMN 360 Query: 371 YLVPSRVFEIVLNFASLGIIASWAFIIVCQMRLRKAIKEGKAADVSFKLPGAPFTSWLTL 430 YL+P E++++ ++ +WA I + R+ + K + FK P+ +++ L Sbjct: 361 YLIPQHALELLMSLVVATLVINWAMISYSHFKFRQHMNRTKQTPL-FKALWYPYGNYICL 419 Query: 431 LFLLSVLVLMAFDYPNGTYTIAALPIIGILLVIGWFGVRKRVAE 474 F+ +L +M P ++ A+P+ + + + + KR A+ Sbjct: 420 AFVAFILCIMLM-IPGIQISVYAIPVWVLFMWVCYNIKNKRSAQ 462 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: 643 Number of extensions: 30 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: 473 Length adjustment: 34 Effective length of query: 465 Effective length of database: 439 Effective search space: 204135 Effective search space used: 204135 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