Align Amino acid permease (characterized, see rationale)
to candidate RR42_RS05070 RR42_RS05070 amino acid permease
Query= uniprot:A0A0N9WG97 (470 letters) >FitnessBrowser__Cup4G11:RR42_RS05070 Length = 466 Score = 621 bits (1601), Expect = 0.0 Identities = 317/455 (69%), Positives = 367/455 (80%), Gaps = 6/455 (1%) Query: 13 REHGLRRQLTSGQMSMIAIGGAIGTGLFMGSAYAIGYAGPSVLLSYAIGAVITLLLMGCL 72 RE GL R L Q++MIAIGGAIGTGLFMGS +AIG+AGP VLLSYAIGA++TLLLMGCL Sbjct: 4 REQGLHRSLKPAQLAMIAIGGAIGTGLFMGSGFAIGFAGPGVLLSYAIGALVTLLLMGCL 63 Query: 73 AEMTVAHSTSGSFGAYAEFYISPLAGFLVRYAYWAAIVLAVGTEVTAVAMYMKYWFANVP 132 AEMTVAH TSGSFGAYAE Y+SPLAGFLVRYAYWA+IVLAVGTEVTAVA+YM YWF VP Sbjct: 64 AEMTVAHPTSGSFGAYAEHYVSPLAGFLVRYAYWASIVLAVGTEVTAVALYMGYWFPQVP 123 Query: 133 EWIWIVSFSSILIVLNAISVKTFGTFEYWFSTIKIGAIVGFIILAVYVVFG------SGN 186 W WIVSFS+ LI++N + V FG EY FS +KI AIV FI++A Y+VFG SG Sbjct: 124 AWFWIVSFSAALILINLVGVGIFGAVEYLFSMVKIVAIVAFILVAAYIVFGAPGSTGSGA 183 Query: 187 PEYGVHHYTSHGGFFPNGLQGMWVAVIVSIFSYLSVEMIAVAAGEAEDPERAVKKAFRAT 246 G HHYT+HGGF PNGL GMWVAVIVSIFSYLS+EMIAVAAGEA+DPERAV +AFR+T Sbjct: 184 AGAGFHHYTAHGGFLPNGLWGMWVAVIVSIFSYLSIEMIAVAAGEAQDPERAVLQAFRST 243 Query: 247 IVRLVVFYLLTLALMLAIVPWVQAGHAQSPFVTVMQTIGIPGATGVMNFVILIAALSAMN 306 ++RL +FYLLTLALMLAIVPW QAG +SPFV VM+ I +PGA ++NFV+LIAALSAMN Sbjct: 244 MIRLGLFYLLTLALMLAIVPWNQAGAQKSPFVQVMEAIHVPGAAAIINFVVLIAALSAMN 303 Query: 307 SQLYITTRMMFSLSRGGYAPKAMGALSKSGIPLNALLLSSSGIALATLLNVMYPESSFTL 366 SQLYITTR MFSL+R G AP++ G +SK GIP+ ALLLSS GIALAT LNV YP ++F L Sbjct: 304 SQLYITTRTMFSLARAGQAPRSFGEVSKRGIPVRALLLSSIGIALATGLNVFYPGNAFLL 363 Query: 367 MMAISMFGAIFTWFMIFLTHYCFRRYHQRHGERKLSFRMRLFPYTTLLGLVLMGAVMITT 426 MMAISMFGA+FTWFMIF+THY FRR G R L+FRMR FP TLLG +M A+M+TT Sbjct: 364 MMAISMFGALFTWFMIFVTHYRFRRQWAAAGNRPLAFRMRGFPLLTLLGAGMMLAIMLTT 423 Query: 427 YFTEAFKMTLVFGVPFLLILSLVYGVFFRKTRALA 461 T+AF+MTL+ G+PFL LS+ Y + FR A A Sbjct: 424 LLTDAFRMTLITGIPFLAALSVAYLLRFRHRAAPA 458 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: 824 Number of extensions: 42 Number of successful extensions: 2 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