Align D-serine/D-alanine/glycine transporter (characterized, see rationale)
to candidate PfGW456L13_4291 Aromatic amino acid transport protein AroP
Query= uniprot:A0A0C4YRF7 (472 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_4291 Length = 467 Score = 408 bits (1049), Expect = e-118 Identities = 200/464 (43%), Positives = 304/464 (65%), Gaps = 14/464 (3%) Query: 11 ERVHEEKDLHRGLKDRHIQMIAIGGAIGVGLFLGAGRAIAIAGPGLMLSYAIGGVAIFFI 70 + + + +L RGLK+RHIQ+IA+GGAIG GLFLG+ + AGP ++L YAI G F I Sbjct: 3 DEILRQGELKRGLKNRHIQLIALGGAIGTGLFLGSAGVLKSAGPSMILGYAIAGFIAFLI 62 Query: 71 MRALGELLLYRPVSGSFATYAEEFVGPFAGFATGWSYWFMWVVTGMAEITAVAVYVHYWF 130 MR LGE+++ PV+GSF+ +A ++ G +AGF +GW+YW ++V+ GMAE+TAV YV +W+ Sbjct: 63 MRQLGEMIVEEPVAGSFSHFAHKYWGGYAGFLSGWNYWVLYVLVGMAELTAVGKYVQFWW 122 Query: 131 PDVPQWIPALATLAVLYLVNCVAVAVFGELEFWFALIKVVTIVAMIVIGLAIIFFGVTPL 190 P+VP W+ A ++ L+N + V VFGE+EFWFA+IKVV I+ MI +G ++F G Sbjct: 123 PEVPSWVSAAVFFVLVNLINMMNVKVFGEMEFWFAIIKVVAIIGMIALGCYMLFSGTG-- 180 Query: 191 GPTASFSNLWTHGGFMPFGTLGVVLTLQIVMFAYQGVELIGVTAGEAQNPEKVLPHATNG 250 GP AS SNLW HGGF P G G+++ + +MF++ G+EL+G+TA EA P KV+P A N Sbjct: 181 GPQASVSNLWDHGGFFPNGYSGLLMAMAFIMFSFGGLELVGITAAEASEPGKVIPKAINQ 240 Query: 251 VVWRILIFYVGALIIMMALVPWNELKP---------GVSPFVYVFERIGVPGAAAIVNLV 301 VV+R+LIFYVGAL ++++L PW++L G SPFV +F IG AA I+N V Sbjct: 241 VVYRVLIFYVGALTVLLSLYPWDQLLQTLGASGDAYGGSPFVQIFSLIGSDTAAHILNFV 300 Query: 302 VITAAASSCNSGIFSTGRMLYTLAQFGQAPRAFGRVSSKHVPSIAITFSAALMGIGVLLN 361 V+TAA S NSG++ RMLY LA+ G AP+A +++ + VP +A+ SA + + VL+N Sbjct: 301 VLTAALSVYNSGVYCNSRMLYGLAEQGDAPKALMKLNKQGVPLLALGVSALITLLSVLVN 360 Query: 362 YIVPEQVFVWVTSISLVGSLWTWSIIMIAHLGYRKAIAAGRVKAVAFRMPGAPYANWLVV 421 Y+ P + + ++ + + W++I + HL +RK ++ + F+ P++N+L + Sbjct: 361 YLAPHEALELLFALVVASLMINWAMISLTHLKFRKIMSQQGI-VPGFKSFWFPFSNYLCL 419 Query: 422 AFMIAVAVLLSLDPGTRVALYVAPVWFALLGIGY--RFTKSRAL 463 AFM+ + ++ + PG R +++ PVW ++ Y R K RAL Sbjct: 420 AFMVMIVCVMLMIPGIRASVFAIPVWVLIIFGFYRMRMAKDRAL 463 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: 743 Number of extensions: 40 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: 472 Length of database: 467 Length adjustment: 33 Effective length of query: 439 Effective length of database: 434 Effective search space: 190526 Effective search space used: 190526 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