Align L-alanine and D-alanine permease (characterized)
to candidate Pf6N2E2_4959 S-methylmethionine permease
Query= reanno::pseudo5_N2C3_1:AO356_17670 (473 letters) >FitnessBrowser__pseudo6_N2E2:Pf6N2E2_4959 Length = 476 Score = 306 bits (783), Expect = 1e-87 Identities = 163/441 (36%), Positives = 254/441 (57%), Gaps = 5/441 (1%) Query: 19 KRELGERHIRLMALGACIGVGLFLGSAKAIEMAGP-AIMLSYIIGGLAILVIMRALGEMA 77 K+E+ RHI ++ALG IG GLFL S + AGP +++YIIG L + ++M LGE+A Sbjct: 15 KQEMQTRHIVMLALGGVIGTGLFLTSGYTVNQAGPMGAVIAYIIGALMVYMVMMCLGELA 74 Query: 78 VHNPVAGSFSRYAQDYLGPLAGFLTGWNYWFLWLVTCVAEITAVAVYMGIWFPDVPRWIW 137 V P GSFS YA +LGP G+ W YW W V +E TA + M WFPD P WIW Sbjct: 75 VQMPETGSFSTYATRFLGPGTGYTVAWLYWLTWTVAIGSEFTAAGILMSRWFPDTPVWIW 134 Query: 138 ALAALVSMGSINLIAVKAFGEFEFWFALIKIVTIIA-MVIGGVGIIAFGFGNDGVALGIS 196 + + N+I+V+ F E EFW +LIK++T++ ++IGG I+ + ++G+S Sbjct: 135 SALFAGVVFLSNVISVRLFAETEFWLSLIKVLTVVVFLLIGGGAILGLLNIDQAHSIGLS 194 Query: 197 NLWAHGGFMPNGVSGVLMSLQMVMFAYLGVEMIGLTAGEAKNPQKTIPNAIGSVFWRILL 256 N G F P G + M+L V FA+ G E+IG+ AGE K+PQ+ +P AI + R+ + Sbjct: 195 NFTREGLF-PTGFMPIAMTLLAVSFAFSGTELIGIAAGETKDPQRNVPRAIRTTVLRLAV 253 Query: 257 FYVGALFVILSIYPWNEIGTQGSPFVMTFERLGIKTAAGIINFVVITAALSSCNGGIFST 316 F+VG +FV+ ++ P + G SPFV F +GI +A I+NFV+I+A LS+ N G+++ Sbjct: 254 FFVGTIFVLATLLPREQAGLVESPFVTVFTYIGIPYSADIMNFVIISALLSAANSGLYAA 313 Query: 317 GRMLYSLAQNGQAPAGFAKTSTNGVPRRALLLSIAALLLGVLLNYLVPEKVFVWVTSIAT 376 RML++L+ G P F+ + G P A+++S+A +L + + +++ + SI+ Sbjct: 314 SRMLWTLSDQGHLPKQFSALTRMGTPLNAIIVSMAGGAASLLSSVFAADTIYLALVSISG 373 Query: 377 FGAIWTWVMILLAQLKFRKSLSAS--ERAALKYRMWLYPVSSYLALAFLVLVVGLMAYFP 434 + W+ I +Q+ FR+ A+ + LK+R+ YP AL L +A+ P Sbjct: 374 LAVVVVWMSIAASQIAFRRHYVANGGDIRKLKFRVRGYPWVPLGALVCCSLACIGIAFDP 433 Query: 435 DTRVALYVGPAFLVLLTVLFY 455 + RVALY G F+ ++Y Sbjct: 434 EQRVALYFGLPFIAWCYFVYY 454 Lambda K H 0.328 0.142 0.444 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: 606 Number of extensions: 25 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: 473 Length of database: 476 Length adjustment: 33 Effective length of query: 440 Effective length of database: 443 Effective search space: 194920 Effective search space used: 194920 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