Align Amino acid permease (characterized, see rationale)
to candidate BPHYT_RS07280 BPHYT_RS07280 amino acid permease
Query= uniprot:A0A0N9WG97 (470 letters) >FitnessBrowser__BFirm:BPHYT_RS07280 Length = 466 Score = 612 bits (1579), Expect = e-180 Identities = 312/458 (68%), Positives = 376/458 (82%), Gaps = 5/458 (1%) Query: 6 GFETISNREHGLRRQLTSGQMSMIAIGGAIGTGLFMGSAYAIGYAGPSVLLSYAIGAVIT 65 GF+TI RE GL+R L++GQ+SMIAIGGAIGTGLF+GS +AIG+AGPSVL+SYAIGA+I Sbjct: 7 GFDTIVEREKGLQRGLSTGQLSMIAIGGAIGTGLFLGSGFAIGFAGPSVLVSYAIGALIA 66 Query: 66 LLLMGCLAEMTVAHSTSGSFGAYAEFYISPLAGFLVRYAYWAAIVLAVGTEVTAVAMYMK 125 LLLMGCLAEMTVAH TSGSFGAYAE YI+P AGFLVRYAYW++IV AVGTEVTA+A+YMK Sbjct: 67 LLLMGCLAEMTVAHPTSGSFGAYAEHYIAPWAGFLVRYAYWSSIVFAVGTEVTAIAVYMK 126 Query: 126 YWFANVPEWIWIVSFSSILIVLNAISVKTFGTFEYWFSTIKIGAIVGFIILAVYVVFGS- 184 YWF VP W WIV FS+ LI +N++SVK FG EY FS +KI AIVGFI+L YVVFG+ Sbjct: 127 YWFPAVPGWYWIVGFSAALIGINSVSVKVFGAVEYVFSMLKIVAIVGFILLGAYVVFGAP 186 Query: 185 GNPEYGVHHYTSHGGFFPNGLQGMWVAVIVSIFSYLSVEMIAVAAGEAEDPERAVKKAFR 244 + G +YTSHGGFFP G+ GMWVAVIVSIFSYLS+EMIAVAAGEA DP++A+ +AFR Sbjct: 187 ADSTIGFANYTSHGGFFPKGVWGMWVAVIVSIFSYLSIEMIAVAAGEARDPQKAITRAFR 246 Query: 245 ATIVRLVVFYLLTLALMLAIVPWVQAGHAQSPFVTVMQTIGIPGATGVMNFVILIAALSA 304 AT+ RLV FYLLTLALMLAIVPW AG +SPFV VM +PGA GV+NFVIL+AALSA Sbjct: 247 ATMFRLVFFYLLTLALMLAIVPWNAAGTDESPFVRVMAATHVPGAAGVINFVILVAALSA 306 Query: 305 MNSQLYITTRMMFSLSRGGYAPKAMGALSKSGIPLNALLLSSSGIALATLLNVMYPESSF 364 MNSQLYITTRMMFSLSR GYAP+ +GAL+ G+P+ AL LS+ GIALAT+LNV+YP++SF Sbjct: 307 MNSQLYITTRMMFSLSRAGYAPRKLGALNGKGVPVAALWLSTIGIALATVLNVVYPDASF 366 Query: 365 TLMMAISMFGAIFTWFMIFLTHYCFRRYHQRHGERKLSFRMRLFPYTTLLGLVLMGAVMI 424 LMM++SMFGA+FTW MIF+TH+ FR RH L+FRM +P T+ LG LM + ++ Sbjct: 367 VLMMSVSMFGAMFTWLMIFVTHFFFR---HRHQGAPLAFRMWGYPGTSALGAGLMVSALV 423 Query: 425 TTYFTEAFKMTLVFGVPFLLILSLVYGVFFRKTRALAG 462 TT+FT F+MTLV GVPF++ L +VY V++RK RA+ G Sbjct: 424 TTWFTREFRMTLVIGVPFIVSLLVVYFVWYRK-RAVEG 460 Lambda K H 0.328 0.140 0.422 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: 852 Number of extensions: 42 Number of successful extensions: 3 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: 470 Length of database: 466 Length adjustment: 33 Effective length of query: 437 Effective length of database: 433 Effective search space: 189221 Effective search space used: 189221 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