Align Asparagine permease (AnsP) of 497 aas and 12 TMSs (characterized)
to candidate GFF4342 PS417_22235 aromatic amino acid transporter
Query= TCDB::P40812 (497 letters) >FitnessBrowser__WCS417:GFF4342 Length = 473 Score = 324 bits (830), Expect = 5e-93 Identities = 171/467 (36%), Positives = 282/467 (60%), Gaps = 20/467 (4%) Query: 28 KAMGNRQVQMIAIGGAIGTGLFLGAGARLQMAGPALALVYLICGIFSFFILRALGELVLH 87 + + NR +Q+IA+GGAIGTGLFLG+ L+ AGP++ L Y ICG +F I+R LGE+++ Sbjct: 13 RGLKNRHIQLIALGGAIGTGLFLGSAGVLKSAGPSMILGYAICGFIAFMIMRQLGEMIVE 72 Query: 88 RPSSGSFVSYAREFLGEKAAYVAGWMYFINWAMTGIVDITAVALYMHYWGAFGDVPQWVF 147 P +GSF +A ++ G A +++GW +I + + G+ ++TAV Y+HYW + ++P WV Sbjct: 73 EPVAGSFSHFAHKYWGGFAGFLSGWNCWILYILVGMSELTAVGKYVHYW--WPEIPTWVS 130 Query: 148 ALGALTIVGTMNMIGVKWFAEMEFWFALIKVLAIVIFLVVGTIFL--GTGQPLEGNATGF 205 A ++ +N+ VK F E EFWFA+IKV+AIV + +G+ L GTG P + + T Sbjct: 131 AAAFFVLINLINLANVKVFGEAEFWFAIIKVVAIVGMIALGSYLLVSGTGGP-QASVTN- 188 Query: 206 HLITDNGGFFPHGLLPALVLIQGVVFAFASIELVGTAAGECKDPQKMVPKAINSVIWRIG 265 + ++GGFFPHG+ ++ + ++F+F +E++G A E P+ ++PKAIN VI+RI Sbjct: 189 --LWEHGGFFPHGVGGLVMAMAIIMFSFGGLEMLGFTAAEADKPRTVIPKAINQVIYRIL 246 Query: 266 LFYVGSVVLLVLLLPWNAYQA---------GQSPFVTFFSKLGVPYIGSIMNIVVLTAAL 316 +FY+G++V+L+ L PW++ A SPFV FS LG I+N VVLTAAL Sbjct: 247 IFYIGALVVLLSLTPWDSLLATLNASGDAYSGSPFVQVFSMLGSDTAAHILNFVVLTAAL 306 Query: 317 SSLNSGLYCTGRILRSMSMGGSAPKFMAKMSRQHVPYAGILATLVVYVVGVFLNYLVPSR 376 S NSG YC R+L M+ G APK +AK+ ++ VP ILA+ + +V V +NYL+P Sbjct: 307 SVYNSGTYCNSRMLLGMAEQGDAPKALAKIDKRGVPVRSILASAAITLVAVLMNYLIPQH 366 Query: 377 VFEIVLNFASLGIIASWAFIMVCQMRLRQAIKEGKAADVSFKLPGAPFTSWLTLLFLLSV 436 E++++ ++ +WA I + RQ + + FK P+ +++ L F++ + Sbjct: 367 ALELLMSLVVATLVINWAMISFSHFKFRQHMNRTGQVPL-FKALWYPYGNYVCLAFVVFI 425 Query: 437 LVLMAFDYPNGTYTIASLPLIAILLVAGWFGVRRRVAEIHRTAPVTA 483 LV+M P ++ ++P + ++ +A +G++ + + AP + Sbjct: 426 LVIMLM-IPGIQVSVFAIP-VWVMFMAVCYGIKNKRSAQQALAPAAS 470 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: 623 Number of extensions: 31 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: 473 Length adjustment: 34 Effective length of query: 463 Effective length of database: 439 Effective search space: 203257 Effective search space used: 203257 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