Align Asparagine permease (AnsP) of 497 aas and 12 TMSs (characterized)
to candidate PfGW456L13_4291 Aromatic amino acid transport protein AroP
Query= TCDB::P40812 (497 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_4291 Length = 467 Score = 317 bits (812), Expect = 6e-91 Identities = 166/455 (36%), Positives = 277/455 (60%), Gaps = 24/455 (5%) Query: 28 KAMGNRQVQMIAIGGAIGTGLFLGAGARLQMAGPALALVYLICGIFSFFILRALGELVLH 87 + + NR +Q+IA+GGAIGTGLFLG+ L+ AGP++ L Y I G +F I+R LGE+++ Sbjct: 13 RGLKNRHIQLIALGGAIGTGLFLGSAGVLKSAGPSMILGYAIAGFIAFLIMRQLGEMIVE 72 Query: 88 RPSSGSFVSYAREFLGEKAAYVAGWMYFINWAMTGIVDITAVALYMHYWGAFGDVPQWVF 147 P +GSF +A ++ G A +++GW Y++ + + G+ ++TAV Y+ +W + +VP WV Sbjct: 73 EPVAGSFSHFAHKYWGGYAGFLSGWNYWVLYVLVGMAELTAVGKYVQFW--WPEVPSWVS 130 Query: 148 ALGALTIVGTMNMIGVKWFAEMEFWFALIKVLAIVIFLVVG--TIFLGTGQPLEGNATGF 205 A +V +NM+ VK F EMEFWFA+IKV+AI+ + +G +F GTG P + Sbjct: 131 AAVFFVLVNLINMMNVKVFGEMEFWFAIIKVVAIIGMIALGCYMLFSGTGGPQASVSN-- 188 Query: 206 HLITDNGGFFPHGLLPALVLIQGVVFAFASIELVGTAAGECKDPQKMVPKAINSVIWRIG 265 + D+GGFFP+G L+ + ++F+F +ELVG A E +P K++PKAIN V++R+ Sbjct: 189 --LWDHGGFFPNGYSGLLMAMAFIMFSFGGLELVGITAAEASEPGKVIPKAINQVVYRVL 246 Query: 266 LFYVGSVVLLVLLLPW-----------NAYQAGQSPFVTFFSKLGVPYIGSIMNIVVLTA 314 +FYVG++ +L+ L PW +AY G SPFV FS +G I+N VVLTA Sbjct: 247 IFYVGALTVLLSLYPWDQLLQTLGASGDAY--GGSPFVQIFSLIGSDTAAHILNFVVLTA 304 Query: 315 ALSSLNSGLYCTGRILRSMSMGGSAPKFMAKMSRQHVPYAGILATLVVYVVGVFLNYLVP 374 ALS NSG+YC R+L ++ G APK + K+++Q VP + + ++ ++ V +NYL P Sbjct: 305 ALSVYNSGVYCNSRMLYGLAEQGDAPKALMKLNKQGVPLLALGVSALITLLSVLVNYLAP 364 Query: 375 SRVFEIVLNFASLGIIASWAFIMVCQMRLRQAIKEGKAADVSFKLPGAPFTSWLTLLFLL 434 E++ ++ +WA I + ++ R+ + + + FK PF+++L L F++ Sbjct: 365 HEALELLFALVVASLMINWAMISLTHLKFRKIMSQ-QGIVPGFKSFWFPFSNYLCLAFMV 423 Query: 435 SVLVLMAFDYPNGTYTIASLPLIAILLVAGWFGVR 469 ++ +M P ++ ++P + +L++ G++ +R Sbjct: 424 MIVCVMLM-IPGIRASVFAIP-VWVLIIFGFYRMR 456 Lambda K H 0.328 0.140 0.434 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: 634 Number of extensions: 35 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: 497 Length of database: 467 Length adjustment: 34 Effective length of query: 463 Effective length of database: 433 Effective search space: 200479 Effective search space used: 200479 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