Align Asparagine permease (AnsP) of 497 aas and 12 TMSs (characterized)
to candidate BPHYT_RS21680 BPHYT_RS21680 amino acid permease-associated protein
Query= TCDB::P40812 (497 letters) >FitnessBrowser__BFirm:BPHYT_RS21680 Length = 476 Score = 273 bits (697), Expect = 1e-77 Identities = 157/447 (35%), Positives = 248/447 (55%), Gaps = 14/447 (3%) Query: 33 RQVQMIAIGGAIGTGLFLGAGARLQMAGPALALVYLICGIFSFFILRALGELVLHRPSSG 92 R + MIA+GG IG GLF+G+G +Q AGPA L +LI G ++R LGE+ P+ G Sbjct: 17 RHMTMIALGGVIGAGLFVGSGVVVQQAGPAAVLSFLITGALVVLVMRMLGEMACAMPAVG 76 Query: 93 SFVSYAREFLGEK------AAYVAGWMYFINWAMTGIVDITAVALYMHYWGAFGDVPQWV 146 SF YAR G K A ++ GWMY+ W + V+ A A + +W DVP W Sbjct: 77 SFYEYARLAFGGKRASGNLAGFLTGWMYWYFWVIVVAVEAVAGAKLVQFW--LPDVPAWA 134 Query: 147 FALGALTIVGTMNMIGVKWFAEMEFWFALIKVLAIVIFLVVGTIFLGTGQPLEGNATG-F 205 +L L + N++ V + E EFWFA IKV AI++FL +G +++ P + T Sbjct: 135 ISLVLLVTLTATNLVSVGSYGEFEFWFASIKVAAIMVFLFLGGMYVLGLWPAAKHVTAVL 194 Query: 206 HLITDNGGFFPHGLLPALVLIQGVVFAFASIELVGTAAGECKDPQKMVPKAINSVIWRIG 265 + +GG P G+ P L + E+V AA E ++P K V KA NSVI R+ Sbjct: 195 PTLLSHGGLMPKGIGPVLSGAVAATGFYFGAEIVTIAAAEAQEPAKAVAKATNSVITRVL 254 Query: 266 LFYVGSVVLLVLLLPWNAYQAGQSPFVTFFSKLGVPYIGSIMNIVVLTAALSSLNSGLYC 325 +FYVGS++L+V L+PWN+ + +P+V+ +G+P S+MN +VLTA LS+LNSGLY Sbjct: 255 VFYVGSILLVVALVPWNSPKMA-TPYVSALDAMGIPAAASVMNAIVLTAVLSALNSGLYA 313 Query: 326 TGRILRSMSMGGSAPKFMAKMSRQHVPYAGILATLVVYVVGVFLNYLVPSRVFEIVLNFA 385 R++ +++ G AP +AK++R+ VP IL V V ++Y+ P VF ++N Sbjct: 314 ASRMIFALTRHGDAPAALAKVNRRGVPVRAILIGTVFGYASVVMSYVSPDTVFAFLVN-- 371 Query: 386 SLGIIASWAFIMVC--QMRLRQAIKEGKAADVSFKLPGAPFTSWLTLLFLLSVLVLMAFD 443 S G +A + ++++ Q++LR I+ + ++ P+ +W+ ++ ++ +LV MAF Sbjct: 372 SYGTVAIFVYVLIAISQLKLRARIERDAPEKLRVRMWCYPYLTWVAIIGMVGILVAMAFI 431 Query: 444 YPNGTYTIASLPLIAILLVAGWFGVRR 470 + + +LL+A VR+ Sbjct: 432 PEQRQPLWFGVASLGVLLLAYLLRVRK 458 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: 690 Number of extensions: 41 Number of successful extensions: 6 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: 476 Length adjustment: 34 Effective length of query: 463 Effective length of database: 442 Effective search space: 204646 Effective search space used: 204646 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