Align arginine permease (characterized)
to candidate GFF4342 PS417_22235 aromatic amino acid transporter
Query= CharProtDB::CH_091699 (590 letters) >FitnessBrowser__WCS417:GFF4342 Length = 473 Score = 246 bits (627), Expect = 2e-69 Identities = 153/471 (32%), Positives = 241/471 (51%), Gaps = 31/471 (6%) Query: 81 NAEVKRELKQRHIGMIALGGTIGTGLFIGLSTPLTNAGPVGALISYLFMGSLAYSVTQSL 140 + E+KR LK RHI +IALGG IGTGLF+G + L +AGP ++ Y G +A+ + + L Sbjct: 8 SGELKRGLKNRHIQLIALGGAIGTGLFLGSAGVLKSAGP-SMILGYAICGFIAFMIMRQL 66 Query: 141 GEMATFIPVTSSFTVFSQRFLSPAFGAANGYMYWFSWAITFALELSVVGQVIQFWTYKVP 200 GEM PV SF+ F+ ++ G +G+ W + + EL+ VG+ + +W ++P Sbjct: 67 GEMIVEEPVAGSFSHFAHKYWGGFAGFLSGWNCWILYILVGMSELTAVGKYVHYWWPEIP 126 Query: 201 LAAWISIFWVIITIMNLFPVKYYGEFEFWVASIKVLAIIGFL-IYCFCMVCGAGVTGPVG 259 + F+V+I ++NL VK +GE EFW A IKV+AI+G + + + +V G G Sbjct: 127 TWVSAAAFFVLINLINLANVKVFGEAEFWFAIIKVVAIVGMIALGSYLLVSGTGGPQASV 186 Query: 260 FRYWRNPGAWGPGIISKDKNEGRFLGWVSSLINAAFTFQGTELVGITAGEAANPRKSVPR 319 W + G + G+ G V ++ F+F G E++G TA EA PR +P+ Sbjct: 187 TNLWEHGGFFPHGV----------GGLVMAMAIIMFSFGGLEMLGFTAAEADKPRTVIPK 236 Query: 320 AIKKVVFRILTFYIGSLLFIGLLVPYND--PKLTQSTSYVSTSPFIIAIENSGTKVLPHI 377 AI +V++RIL FYIG+L+ + L P++ L S S SPF+ G+ HI Sbjct: 237 AINQVIYRILIFYIGALVVLLSLTPWDSLLATLNASGDAYSGSPFVQVFSMLGSDTAAHI 296 Query: 378 FNAVILTTIISAANSNIYVGSRILFGLSKNKLAPKFLSRTTKGGVPYIAVFVTAAFGALA 437 N V+LT +S NS Y SR+L G+++ APK L++ K GVP ++ +AA +A Sbjct: 297 LNFVVLTAALSVYNSGTYCNSRMLLGMAEQGDAPKALAKIDKRGVPVRSILASAAITLVA 356 Query: 438 YMETSTGGDKVFEWLLNITGVAGFFAWLFISISHIRFMQALKYRGISRDELP-FKAKLMP 496 + E L+++ W IS SH +F Q + G ++P FKA P Sbjct: 357 VLMNYLIPQHALELLMSLVVATLVINWAMISFSHFKFRQHMNRTG----QVPLFKALWYP 412 Query: 497 GLAYYAATFMTIIIIIQGFTAFAPKFNGVSFAAAYISIFLFLAVWILFQCI 547 Y F+ I++I + +S+F + VW++F + Sbjct: 413 YGNYVCLAFVVFILVIM-----------LMIPGIQVSVFA-IPVWVMFMAV 451 Lambda K H 0.325 0.140 0.438 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: 702 Number of extensions: 39 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: 590 Length of database: 473 Length adjustment: 35 Effective length of query: 555 Effective length of database: 438 Effective search space: 243090 Effective search space used: 243090 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.0 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.6 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