Align D-serine/D-alanine/glycine transporter (characterized, see rationale)
to candidate BPHYT_RS21680 BPHYT_RS21680 amino acid permease-associated protein
Query= uniprot:A0A0C4YRF7 (472 letters) >FitnessBrowser__BFirm:BPHYT_RS21680 Length = 476 Score = 308 bits (789), Expect = 3e-88 Identities = 165/453 (36%), Positives = 252/453 (55%), Gaps = 17/453 (3%) Query: 11 ERVHEEKDLHRGLKDRHIQMIAIGGAIGVGLFLGAGRAIAIAGPGLMLSYAIGGVAIFFI 70 +R + +L GLK RH+ MIA+GG IG GLF+G+G + AGP +LS+ I G + + Sbjct: 2 QRSTDTTELKAGLKQRHMTMIALGGVIGAGLFVGSGVVVQQAGPAAVLSFLITGALVVLV 61 Query: 71 MRALGELLLYRPVSGSFATYA------EEFVGPFAGFATGWSYWFMWVVTGMAEITAVAV 124 MR LGE+ P GSF YA + G AGF TGW YW+ WV+ E A A Sbjct: 62 MRMLGEMACAMPAVGSFYEYARLAFGGKRASGNLAGFLTGWMYWYFWVIVVAVEAVAGAK 121 Query: 125 YVHYWFPDVPQWIPALATLAVLYLVNCVAVAVFGELEFWFALIKVVTIVAMIVIGLAIIF 184 V +W PDVP W +L L L N V+V +GE EFWFA IKV I+ + +G + Sbjct: 122 LVQFWLPDVPAWAISLVLLVTLTATNLVSVGSYGEFEFWFASIKVAAIMVFLFLG-GMYV 180 Query: 185 FGVTPLGP--TASFSNLWTHGGFMPFGTLGVVLTLQIVMFA-YQGVELIGVTAGEAQNPE 241 G+ P TA L +HGG MP G +G VL+ + Y G E++ + A EAQ P Sbjct: 181 LGLWPAAKHVTAVLPTLLSHGGLMPKG-IGPVLSGAVAATGFYFGAEIVTIAAAEAQEPA 239 Query: 242 KVLPHATNGVVWRILIFYVGALIIMMALVPWNELKPGVSPFVYVFERIGVPGAAAIVNLV 301 K + ATN V+ R+L+FYVG++++++ALVPWN K +P+V + +G+P AA+++N + Sbjct: 240 KAVAKATNSVITRVLVFYVGSILLVVALVPWNSPKMA-TPYVSALDAMGIPAAASVMNAI 298 Query: 302 VITAAASSCNSGIFSTGRMLYTLAQFGQAPRAFGRVSSKHVPSIAITFSAALMGIGVLLN 361 V+TA S+ NSG+++ RM++ L + G AP A +V+ + VP AI V+++ Sbjct: 299 VLTAVLSALNSGLYAASRMIFALTRHGDAPAALAKVNRRGVPVRAILIGTVFGYASVVMS 358 Query: 362 YIVPEQVFVWVTSISLVGSLWTWSIIMIAHLGYRKAIAAGRVKAVAFRMPGAPYANWLVV 421 Y+ P+ VF ++ + +++ + +I I+ L R I + + RM PY W+ + Sbjct: 359 YVSPDTVFAFLVNSYGTVAIFVYVLIAISQLKLRARIERDAPEKLRVRMWCYPYLTWVAI 418 Query: 422 AFMIAVAVLLSLDPGTRVALYVAPVWFALLGIG 454 M+ + V ++ P R P+WF + +G Sbjct: 419 IGMVGILVAMAFIPEQR-----QPLWFGVASLG 446 Lambda K H 0.328 0.142 0.445 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: 733 Number of extensions: 45 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: 472 Length of database: 476 Length adjustment: 33 Effective length of query: 439 Effective length of database: 443 Effective search space: 194477 Effective search space used: 194477 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 (21.8 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