Align L-asparagine permease; L-asparagine transport protein (characterized)
to candidate PfGW456L13_4400 Aromatic amino acid transport protein AroP
Query= SwissProt::P77610 (499 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_4400 Length = 473 Score = 322 bits (824), Expect = 2e-92 Identities = 173/461 (37%), Positives = 272/461 (59%), Gaps = 20/461 (4%) Query: 28 KAMGNRQVQMIAIGGAIGTGLFLGAGARLQMAGPALALVYLICGLFSFFILRALGELVLH 87 + + NR +Q+IA+GGAIGTGLFLG+ L+ AGP++ L Y ICG +F I+R LGE+++ Sbjct: 13 RGLKNRHIQLIALGGAIGTGLFLGSAGVLKSAGPSMILGYAICGFIAFMIMRQLGEMIVE 72 Query: 88 RPSSGSFVSYAREFLGEKAAYVAGWMYFINWAMTGIVDITAVALYMHYWGAFGGVPQWVF 147 P +GSF +A ++ G A +++GW +I + + G+ ++TAV Y+HYW +P W Sbjct: 73 DPVAGSFSHFAHKYWGGFAGFLSGWNCWILYILVGMSELTAVGKYIHYWAP--DIPTWAS 130 Query: 148 ALAALTIVGTMNMIGVKWFAEMEFWFALIKVLAIVTFLVVGTVFLGSGQPLDGNTTGFHL 207 A A ++ +N+ VK F E EFWFA+IKV+AIV + +G+ L SG G Sbjct: 131 AAAFFVLINAINLANVKVFGEAEFWFAIIKVVAIVGMIALGSYLLVSGN--GGPQAAVSN 188 Query: 208 ITDNGGFFPHGLLPALVLIQGVVFAFASIEMVGTAAGECKDPQTMVPKAINSVIWRIGLF 267 + +GGFFP+G+ ++ + ++F+F +EM+G A E P+T++PKAIN VI+RI +F Sbjct: 189 LWSHGGFFPNGVTGLVMAMAFIMFSFGGLEMLGFTAAEADKPKTVIPKAINQVIYRILIF 248 Query: 268 YVGSVVLLVMLLPW---------SAYQAGQSPFVTFFSKLGVPYIGSIMNIVVLTAALSS 318 Y+G++V+L+ L PW S SPFV FS LG I+N VVLTAALS Sbjct: 249 YIGALVILLSLTPWDSLLTTLNASGDSYSGSPFVQVFSMLGSNTAAHILNFVVLTAALSV 308 Query: 319 LNSGLYCTGRILRSMAMGGSAPSFMAKMSRQHVPYAGILATLVVYVVGVFLNYLVPSRVF 378 NSG YC R+L MA G AP +AK+ ++ VP ILA+ V ++ V LNYL+P Sbjct: 309 YNSGTYCNSRMLLGMAEQGDAPKALAKIDKRGVPVRSILASAAVTLIAVLLNYLIPHSAL 368 Query: 379 EIVLNFASLGIIASWAFIIVCQMRLRKAIKEGKAADVSFKLPGAPFTSWLTLLFLLSVLV 438 E++++ ++ +WA I + R+ + + K + FK P+ +++ L F+L +L Sbjct: 369 ELLMSLVVATLVINWAMISYSHFKFRQHMNKTKQTPL-FKALWYPYGNYICLAFVLFILG 427 Query: 439 LMAFDYPNGTYTIAALPIIGILLVIGW--FGVRKRVAEIHS 477 +M P ++ A+P + LV W +G++ + + H+ Sbjct: 428 VMLL-IPGIQTSVYAIP---VWLVFMWVCYGIKNKRSAQHA 464 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: 677 Number of extensions: 38 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: 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