Align Asparagine permease (AnsP) of 497 aas and 12 TMSs (characterized)
to candidate Pf6N2E2_4959 S-methylmethionine permease
Query= TCDB::P40812 (497 letters) >FitnessBrowser__pseudo6_N2E2:Pf6N2E2_4959 Length = 476 Score = 270 bits (690), Expect = 8e-77 Identities = 151/448 (33%), Positives = 240/448 (53%), Gaps = 8/448 (1%) Query: 15 KRRWLNAHEEGYHKAMGNRQVQMIAIGGAIGTGLFLGAGARLQMAGPALALV-YLICGIF 73 K + LN G+ + M R + M+A+GG IGTGLFL +G + AGP A++ Y+I + Sbjct: 4 KEQQLNTRA-GFKQEMQTRHIVMLALGGVIGTGLFLTSGYTVNQAGPMGAVIAYIIGALM 62 Query: 74 SFFILRALGELVLHRPSSGSFVSYAREFLGEKAAYVAGWMYFINWAMTGIVDITAVALYM 133 + ++ LGEL + P +GSF +YA FLG Y W+Y++ W + + TA + M Sbjct: 63 VYMVMMCLGELAVQMPETGSFSTYATRFLGPGTGYTVAWLYWLTWTVAIGSEFTAAGILM 122 Query: 134 HYWGAFGDVPQWVFALGALTIVGTMNMIGVKWFAEMEFWFALIKVLAIVIFLVVGT-IFL 192 W F D P W+++ +V N+I V+ FAE EFW +LIKVL +V+FL++G L Sbjct: 123 SRW--FPDTPVWIWSALFAGVVFLSNVISVRLFAETEFWLSLIKVLTVVVFLLIGGGAIL 180 Query: 193 GTGQPLEGNATGFHLITDNGGFFPHGLLPALVLIQGVVFAFASIELVGTAAGECKDPQKM 252 G + ++ G T G FP G +P + + V FAF+ EL+G AAGE KDPQ+ Sbjct: 181 GLLNIDQAHSIGLSNFTREG-LFPTGFMPIAMTLLAVSFAFSGTELIGIAAGETKDPQRN 239 Query: 253 VPKAINSVIWRIGLFYVGSVVLLVLLLPWNAYQAGQSPFVTFFSKLGVPYIGSIMNIVVL 312 VP+AI + + R+ +F+VG++ +L LLP +SPFVT F+ +G+PY IMN V++ Sbjct: 240 VPRAIRTTVLRLAVFFVGTIFVLATLLPREQAGLVESPFVTVFTYIGIPYSADIMNFVII 299 Query: 313 TAALSSLNSGLYCTGRILRSMSMGGSAPKFMAKMSRQHVPYAGILATLVVYVVGVFLNYL 372 +A LS+ NSGLY R+L ++S G PK + ++R P I+ ++ + + Sbjct: 300 SALLSAANSGLYAASRMLWTLSDQGHLPKQFSALTRMGTPLNAIIVSMAGGAASLLSSVF 359 Query: 373 VPSRVFEIVLNFASLGIIASWAFIMVCQMRLRQ--AIKEGKAADVSFKLPGAPFTSWLTL 430 ++ +++ + L ++ W I Q+ R+ G + F++ G P+ L Sbjct: 360 AADTIYLALVSISGLAVVVVWMSIAASQIAFRRHYVANGGDIRKLKFRVRGYPWVPLGAL 419 Query: 431 LFLLSVLVLMAFDYPNGTYTIASLPLIA 458 + + +AFD LP IA Sbjct: 420 VCCSLACIGIAFDPEQRVALYFGLPFIA 447 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: 661 Number of extensions: 39 Number of successful extensions: 5 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