Align L-asparagine permease; L-asparagine transport protein (characterized)
to candidate GFF4632 PS417_23700 aromatic amino acid transporter
Query= SwissProt::P77610 (499 letters) >FitnessBrowser__WCS417:GFF4632 Length = 467 Score = 320 bits (819), Expect = 9e-92 Identities = 171/463 (36%), Positives = 276/463 (59%), Gaps = 16/463 (3%) Query: 25 GYHKAMGNRQVQMIAIGGAIGTGLFLGAGARLQMAGPALALVYLICGLFSFFILRALGEL 84 G + + NR +Q+IA+GGAIGTGLFLG+ L+ AGP++ L Y I G +F I+R LGE+ Sbjct: 10 GLKRGLKNRHIQLIALGGAIGTGLFLGSAGVLKSAGPSMILGYAIAGFIAFLIMRQLGEM 69 Query: 85 VLHRPSSGSFVSYAREFLGEKAAYVAGWMYFINWAMTGIVDITAVALYMHYWGAFGGVPQ 144 ++ P +GSF +A ++ G A ++AGW Y++ + + G+ ++TAV Y+ +W + +P Sbjct: 70 IVEEPVAGSFSHFAHKYWGGYAGFLAGWNYWVLYVLVGMAELTAVGKYIQFW--WPDIPT 127 Query: 145 WVFALAALTIVGTMNMIGVKWFAEMEFWFALIKVLAIVTFLVVGTVFLGSGQPLDGNTTG 204 WV AL V +N + VK+F E EFWFA+IKV+AIV +V+G L SG G Sbjct: 128 WVSALVFFVAVNLINTLNVKFFGETEFWFAIIKVVAIVGMIVLGCYLLFSG--TGGPQAS 185 Query: 205 FHLITDNGGFFPHGLLPALVLIQGVVFAFASIEMVGTAAGECKDPQTMVPKAINSVIWRI 264 + +GGFFP+G + L+ + ++F+F +E+VG A E +P+ ++PKAIN V++RI Sbjct: 186 VSNLWSHGGFFPNGGMGLLMSMAFIMFSFGGLELVGITAAEASEPRKVIPKAINQVVYRI 245 Query: 265 GLFYVGSVVLLVMLLPW---------SAYQAGQSPFVTFFSKLGVPYIGSIMNIVVLTAA 315 +FYVG++ +L+ L PW S SPFV FS +G I+N VVLTAA Sbjct: 246 LIFYVGALTVLLSLYPWDQLLQTLGASGDAYSGSPFVQIFSLIGNDTAAHILNFVVLTAA 305 Query: 316 LSSLNSGLYCTGRILRSMAMGGSAPSFMAKMSRQHVPYAGILATLVVYVVGVFLNYLVPS 375 LS NSG+YC R+L +A G AP + K+++Q VP + + +V ++ V +NY+ P Sbjct: 306 LSVYNSGVYCNSRMLFGLAEQGDAPKSLMKLNKQGVPIRALAISALVTMLCVVVNYVAPQ 365 Query: 376 RVFEIVLNFASLGIIASWAFIIVCQMRLRKAIKEGKAADVSFKLPGAPFTSWLTLLFLLS 435 E++ ++ +WA I + ++ RKA+ E + SFK PF+++L L F++ Sbjct: 366 SALELLFALVVASLMINWALISITHIKFRKAMGE-QGVTPSFKTFWFPFSNYLCLAFMVM 424 Query: 436 VLVLMAFDYPNGTYTIAALPI-IGILLVIGWFGVRKRVAEIHS 477 ++ +M P + ++ A+P+ +GI+ V VR+ A +++ Sbjct: 425 IISVM-LAIPGISESVYAMPVWVGIIYVAYRLRVRRSHAVVNA 466 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: 674 Number of extensions: 37 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: 467 Length adjustment: 34 Effective length of query: 465 Effective length of database: 433 Effective search space: 201345 Effective search space used: 201345 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