Align Asparagine permease (AnsP) of 497 aas and 12 TMSs (characterized)
to candidate N515DRAFT_3653 N515DRAFT_3653 amino acid/polyamine/organocation transporter, APC superfamily (TC 2.A.3)
Query= TCDB::P40812 (497 letters) >FitnessBrowser__Dyella79:N515DRAFT_3653 Length = 453 Score = 330 bits (846), Expect = 6e-95 Identities = 168/435 (38%), Positives = 260/435 (59%), Gaps = 20/435 (4%) Query: 33 RQVQMIAIGGAIGTGLFLGAGARLQMAGPALALVYLICGIFSFFILRALGELVLHRPSSG 92 R + +A+G AIG GLFLG+ + +AGP++ YL G F I+RALGE+ +H P +G Sbjct: 12 RHITFMALGMAIGAGLFLGSANAINLAGPSVLFAYLFGGAMIFIIMRALGEMAVHDPVAG 71 Query: 93 SFVSYAREFLGEKAAYVAGWMYFINWAMTGIVDITAVALYMHYWGAFGDVPQWVFALGAL 152 SF +YA +LG A Y+ GW Y+I G+ + TAV +YM W F ++PQW++ G++ Sbjct: 72 SFSTYAHRYLGPFAGYLTGWNYWILMVGVGMAESTAVGIYMRQW--FPELPQWIWVFGSV 129 Query: 153 TIVGTMNMIGVKWFAEMEFWFALIKVLAIVIFLV--VGTIFLGTGQPLEGNATGFHLITD 210 ++G +N++ VK + EMEFWF LIKV+ +V+ ++ G I+LG G G G + Sbjct: 130 AMIGGLNLMAVKVYGEMEFWFTLIKVVTVVLMILGGAGMIWLGWGN--GGQPVGLANLWS 187 Query: 211 NGGFFPHGLLPALVLIQGVVFAFASIELVGTAAGECKDPQKMVPKAINSVIWRIGLFYVG 270 +GG+FPHG ++ + VVFAF IE +G AAGE P++ +P+A+NSV+WRI +FYVG Sbjct: 188 HGGWFPHGFTGMVLALPVVVFAFGGIETIGMAAGEAAQPERTIPRAVNSVLWRILIFYVG 247 Query: 271 SVVLLVLLLPWNAYQAGQSPFVTFFSKLGVPYIGSIMNIVVLTAALSSLNSGLYCTGRIL 330 ++ +++ + PW+ SPFVT F KLG+P ++N VV+TAALS NS + R+L Sbjct: 248 ALFVIMAIYPWDQLGTQGSPFVTTFGKLGIPQAAGLINFVVITAALSGFNSTTFSGSRML 307 Query: 331 RSMSMGGSAPKFMAKMSRQHVPYAGILATLVVYVVGVFLNYLVPSRVFEIVLNFASLGII 390 S+S AP F+ ++S VP +L TL V GV LNYL+P R+F ++++ + + Sbjct: 308 YSLSTKAQAPAFLGQVSEHGVPVRAVLVTLACLVFGVVLNYLLPERIFAMMMSILAFNTV 367 Query: 391 ASWAFIMVCQMRLRQAIKEGKAADVSFKLPGAPFTSWLTLLFLLSVLVLMAFDYPNGTYT 450 +W +++ R+ + G A F L P TS + LLFL VL ++ + Sbjct: 368 WTWMMVLIAHYSFRR--RHGATA---FPLRAWPLTSVVCLLFLAFVLFMLGY-------- 414 Query: 451 IASLPLIAILLVAGW 465 ++ +A+ + AGW Sbjct: 415 -SADTRVALYVGAGW 428 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: 666 Number of extensions: 33 Number of successful extensions: 2 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: 453 Length adjustment: 33 Effective length of query: 464 Effective length of database: 420 Effective search space: 194880 Effective search space used: 194880 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: 51 (24.3 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