Align L-alanine and D-alanine permease (characterized)
to candidate WP_033100257.1 JG50_RS0106285 amino acid permease
Query= reanno::pseudo5_N2C3_1:AO356_17670 (473 letters) >NCBI__GCF_000763315.1:WP_033100257.1 Length = 446 Score = 305 bits (780), Expect = 3e-87 Identities = 164/436 (37%), Positives = 251/436 (57%), Gaps = 9/436 (2%) Query: 18 LKRELGERHIRLMALGACIGVGLFLGSAKAIEMAGPAIMLSYIIGGLAILVIMRALGEMA 77 L+++L RH+++MALG IG G+F GSA+ I AGP ++ SY + G+ + ++M A+ EMA Sbjct: 5 LQKQLLPRHVQMMALGGAIGAGIFQGSAETISAAGPGVIFSYALAGILLYIVMSAMAEMA 64 Query: 78 VHNPVAGSFSR-YAQDYLGPLAGFLTGWNYWFLWLVTCVAEITAVAVYMGIWFPDVPRWI 136 + AG+ R G F+ GW Y+ W++ EI ++ WF VP W+ Sbjct: 65 LG--FAGTDLRGLVHKAFGTRVSFILGWLYFIQWVLVMAVEIVTAGTFLQYWF-SVPVWL 121 Query: 137 WALAALVSMGSINLIAVKAFGEFEFWFALIKIVTIIAMVIGGVGIIAFGFGNDGVALGIS 196 +L + + +INL +V+ FGE E+W +KIVT+I VI G ++ FG A G++ Sbjct: 122 LSLIVTLVIIAINLFSVRLFGEIEYWLTSVKIVTLIVFVILGA-LLLFGIIPSAQAPGLT 180 Query: 197 NLWAHGGFMPNGVSGVLMSLQMVMFAYLGVEMIGLTAGEAKNPQKTIPNAIGSVFWRILL 256 N HGGF P G GVL SL +V+F+Y G EMIGLT E K+ +KT+P I V RI L Sbjct: 181 NYRVHGGFFPLGWQGVLSSLLIVIFSYGGTEMIGLTITEMKDAKKTLPRVIKGVILRICL 240 Query: 257 FYVGALFVILSIYPWNEIGTQGSPFVMTFERLGIKTAAGIINFVVITAALSSCNGGIFST 316 FYV L +I + PW+++ + GSPFV +G+K A I+NF+++TA +S+ N G+++T Sbjct: 241 FYVLPLLIITGLIPWDQVKSSGSPFVEVLSAVGLKGVANIMNFILLTAVISAANSGMYAT 300 Query: 317 GRMLYSLAQNGQAPAGFAKTSTNGVPRRALLLSIAALLLGVLLNYLVPEKVFVWVTSIAT 376 RMLYSLA +APA F + GVP AL S L LG L+ ++ PE VF ++ I Sbjct: 301 TRMLYSLAGEKEAPAFFTRLGKRGVPIYALAASSVCLFLGSLVAFIAPESVFQYLMGIPG 360 Query: 377 FGAIWTWVMILLAQLKFRKSLSASERAALKYRMWLYPVSSYLALAFLVLVVGLMAYFPDT 436 + I TW++I L+ LK R + +R+ +P ++ + L L ++ + P Sbjct: 361 YTVILTWILICLSHLKLRGKYERTP----DFRLSFFPFTTGITLIVLAAIMIFVLLSPKN 416 Query: 437 RVALYVGPAFLVLLTV 452 + V A +++LT+ Sbjct: 417 LINTIVYLAIILVLTI 432 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: 504 Number of extensions: 25 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: 473 Length of database: 446 Length adjustment: 33 Effective length of query: 440 Effective length of database: 413 Effective search space: 181720 Effective search space used: 181720 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 24 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