Align D-serine/D-alanine/glycine transporter (characterized, see rationale)
to candidate BPHYT_RS07280 BPHYT_RS07280 amino acid permease
Query= uniprot:A0A0C4YRF7 (472 letters) >FitnessBrowser__BFirm:BPHYT_RS07280 Length = 466 Score = 330 bits (847), Expect = 5e-95 Identities = 173/452 (38%), Positives = 266/452 (58%), Gaps = 6/452 (1%) Query: 13 VHEEKDLHRGLKDRHIQMIAIGGAIGVGLFLGAGRAIAIAGPGLMLSYAIGGVAIFFIMR 72 V EK L RGL + MIAIGGAIG GLFLG+G AI AGP +++SYAIG + +M Sbjct: 12 VEREKGLQRGLSTGQLSMIAIGGAIGTGLFLGSGFAIGFAGPSVLVSYAIGALIALLLMG 71 Query: 73 ALGELLLYRPVSGSFATYAEEFVGPFAGFATGWSYWFMWVVTGMAEITAVAVYVHYWFPD 132 L E+ + P SGSF YAE ++ P+AGF ++YW V E+TA+AVY+ YWFP Sbjct: 72 CLAEMTVAHPTSGSFGAYAEHYIAPWAGFLVRYAYWSSIVFAVGTEVTAIAVYMKYWFPA 131 Query: 133 VPQWIPALATLAVLYLVNCVAVAVFGELEFWFALIKVVTIVAMIVIGLAIIFFGVTPLGP 192 VP W + A L +N V+V VFG +E+ F+++K+V IV I++G ++F P Sbjct: 132 VPGWYWIVGFSAALIGINSVSVKVFGAVEYVFSMLKIVAIVGFILLGAYVVF--GAPADS 189 Query: 193 TASFSNLWTHGGFMPFGTLGVVLTLQIVMFAYQGVELIGVTAGEAQNPEKVLPHATNGVV 252 T F+N +HGGF P G G+ + + + +F+Y +E+I V AGEA++P+K + A + Sbjct: 190 TIGFANYTSHGGFFPKGVWGMWVAVIVSIFSYLSIEMIAVAAGEARDPQKAITRAFRATM 249 Query: 253 WRILIFYVGALIIMMALVPWNELKPGVSPFVYVFERIGVPGAAAIVNLVVITAAASSCNS 312 +R++ FY+ L +M+A+VPWN SPFV V VPGAA ++N V++ AA S+ NS Sbjct: 250 FRLVFFYLLTLALMLAIVPWNAAGTDESPFVRVMAATHVPGAAGVINFVILVAALSAMNS 309 Query: 313 GIFSTGRMLYTLAQFGQAPRAFGRVSSKHVPSIAITFSAALMGIGVLLNYIVPEQVFVWV 372 ++ T RM+++L++ G APR G ++ K VP A+ S + + +LN + P+ FV + Sbjct: 310 QLYITTRMMFSLSRAGYAPRKLGALNGKGVPVAALWLSTIGIALATVLNVVYPDASFVLM 369 Query: 373 TSISLVGSLWTWSIIMIAHLGYRKAIAAGRVKAVAFRMPGAPYANWLVVAFMIAVAVLLS 432 S+S+ G+++TW +I + H +R +AFRM G P + L M++ V Sbjct: 370 MSVSMFGAMFTWLMIFVTHFFFRHRHQGA---PLAFRMWGYPGTSALGAGLMVSALVTTW 426 Query: 433 LDPGTRVALYV-APVWFALLGIGYRFTKSRAL 463 R+ L + P +LL + + + + RA+ Sbjct: 427 FTREFRMTLVIGVPFIVSLLVVYFVWYRKRAV 458 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: 792 Number of extensions: 57 Number of successful extensions: 3 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 472 Length of database: 466 Length adjustment: 33 Effective length of query: 439 Effective length of database: 433 Effective search space: 190087 Effective search space used: 190087 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