Align high affinity cationic amino acid transporter 1 (characterized)
to candidate WP_057509036.1 ABB28_RS13110 amino acid permease
Query= CharProtDB::CH_091324 (622 letters) >NCBI__GCF_001431535.1:WP_057509036.1 Length = 475 Score = 225 bits (574), Expect = 3e-63 Identities = 147/430 (34%), Positives = 220/430 (51%), Gaps = 39/430 (9%) Query: 13 MLRRKVVDCSREES---RLSRCLNTYDLVALGVGSTLGAGVYVLAGAVARENAGPAIVIS 69 +LRRK +D +L R L+ L+ALG+G+ +G G+Y L G V AGPA++IS Sbjct: 3 LLRRKSLDTVTVHEAGRQLVRTLSWPHLIALGIGAIVGTGIYTLIG-VGANLAGPAVLIS 61 Query: 70 FLIAALASVLAGLCYGEFGARVPKTGSAYLYSYVTVGELWAFITGWNLILSYIIGTSSVA 129 F IA A L Y E +P +GSAY YSY +GE++A++ GW+LIL Y + S+VA Sbjct: 62 FAIAGAVCACAALSYAELATMMPASGSAYTYSYTALGEIFAWVVGWSLILEYSLVVSTVA 121 Query: 130 RAWSATFD---ELIGKPIGEFSRQHMALNA-PGVLAQTPDIFAVIIIIILTGLLTLGVKE 185 WS F E + +G R +AL+A P V ++ AV+I ++ G L LG KE Sbjct: 122 VGWSGYFVGFLEWVNSQMGIDIRLPLALSAGPHVEGGVFNLPAVLITWLVAGGLMLGTKE 181 Query: 186 SAMVNKIFTCINVLVLCFIVVSGFVKGSIKNWQLTEKNFSCNNNDTNVKYGEGGFMPFGF 245 SA +N + + ++ L + N Q FMP+GF Sbjct: 182 SATLNAVLVVLKLIALGVFIAVALPAFDSANLQ--------------------PFMPYGF 221 Query: 246 S----------GVLSGAATCFYAFVGFDCIATTGEEVKNPQKAIPVGIVASLLICFIAYF 295 + GV++ AA F+AF GFD IAT EE KNP + + +GI+ S++ C I Y Sbjct: 222 AKSLGPDGLERGVMAAAAIIFFAFYGFDAIATAAEETKNPGRDLSIGIIGSMVGCTIVYM 281 Query: 296 GVSAALTLMMPYFCLDIDS-PLPGAFKHQGWEEAKYAVAIGSLCALSTSLLGSMFPMPRV 354 V+ A M Y + PL + G A + + ++ AL T LL MF RV Sbjct: 282 LVALAAVGAMSYAVFGSSAEPLALIMRQLGHPTAALIIGVVAIVALPTVLLAFMFGQSRV 341 Query: 355 IYAMAEDGLLFKFLAKINNRTKTPVIATVTSGAIAAVMAFLFELKDLVDLMSIGTLLAYS 414 + M DG+L + L+ ++ RT TPV T+ S + + +A + L ++ L + GTL A++ Sbjct: 342 FFVMGRDGMLPRRLSNVSKRTGTPVATTLFSALLVSALAGVARLDEIAALANAGTLAAFT 401 Query: 415 LVAACVLVLR 424 V C++V+R Sbjct: 402 AVGVCLVVMR 411 Lambda K H 0.324 0.138 0.417 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: 712 Number of extensions: 47 Number of successful extensions: 5 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 622 Length of database: 475 Length adjustment: 35 Effective length of query: 587 Effective length of database: 440 Effective search space: 258280 Effective search space used: 258280 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.0 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.6 bits) S2: 52 (24.6 bits)
This GapMind analysis is from Sep 24 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