Align Amino acid transporter (characterized, see rationale)
to candidate RR42_RS01585 RR42_RS01585 amino acid permease
Query= uniprot:A0A0H3C3Q5 (483 letters) >FitnessBrowser__Cup4G11:RR42_RS01585 Length = 464 Score = 347 bits (889), Expect = e-100 Identities = 198/471 (42%), Positives = 271/471 (57%), Gaps = 21/471 (4%) Query: 13 RRKAIDTITAGHADSHQLKKTLSWPHLVALGVGAIVGTGIYTLTGVGAGLAGPGVILSFL 72 R K I+ + A D LKK L L+ +G+GAI+GTGI+ LTG GA AGP + +SF+ Sbjct: 5 RTKNIEAMLAAARDDG-LKKVLGPVDLILMGIGAIIGTGIFVLTGTGALTAGPALTVSFV 63 Query: 73 IAGAVCACAALCYAELSTMIPASGSAYTYSYAAMGEPVAWFVGWSLILEYTLVCAAVAVG 132 IA C AALCYAE ++ IP SGS YTYSYA +GE VAW +GW L+LEY L +AV+VG Sbjct: 64 IAALACGFAALCYAEFASAIPVSGSIYTYSYATLGEIVAWMIGWDLLLEYGLATSAVSVG 123 Query: 133 WSAHAHGLFKMIGF--PDALLAGPHQ----GGLINMPAVFISMAVAGLLALGTRESATVN 186 WS + L G P L A P L N+PA I + + +++ G RESA +N Sbjct: 124 WSGYFQSLMAGFGIHLPAMLTAAPGAVPGVQTLFNLPAAVIMLLITWVVSYGVRESARLN 183 Query: 187 MVLVFVKIIALIVFVVLCLPAFNLAHFTPFMPNGFQAHVPEGAAADAAKVGVMAAASLIF 246 V+V VKI +++F+ + + A++ PF P G GV AA+L+F Sbjct: 184 NVMVAVKIAVVLLFIGVGVWHVKPANWHPFAPFGLD--------------GVFNAAALVF 229 Query: 247 FAFYGFDAVSTAAEETKNPKRDLTIGIVGSMAVCTAIYMIVAAVSIGASRTEVFSKSEAP 306 FAF GFDAV++AAEE +NP+RDL IGI+GS+AVCT +Y+ VAA+ G F+ + P Sbjct: 230 FAFIGFDAVTSAAEEVRNPRRDLPIGIIGSLAVCTVLYVTVAAIMTGIVPFAKFAGIDHP 289 Query: 307 LVFILESLNHGKIAQLVALAAVIALPTVILAFMYGQSRIFFVMARDGLLPRALSKVNAKT 366 + L+ +A V L A++ + TVIL +GQ+RI F M+RDGLLP LS V+ Sbjct: 290 VSLALQYAGENWVAGFVDLGAILGMTTVILVMTFGQTRIIFAMSRDGLLPERLSTVHPVH 349 Query: 367 GTPVMMTLLTGVLAAVISGLLSLKDIAELANAGTLWAFIAVGASVILLRLREPNRPRVFS 426 TP T G++ A I+ + L +AEL N GTL AF + +V++LR P+ PR F Sbjct: 350 ATPFFATWTVGIVFAFIAAFVPLNVLAELINIGTLSAFTLISVAVLVLRKTRPDLPRAFR 409 Query: 427 TPLWPIVAPAGILGCLYLFLSLPGKTQLYFLYAHLIGAVVYLAYGMRKSVL 477 P P+V + CL+L L T + FL IG +Y Y R +VL Sbjct: 410 CPGVPVVPLLSVGFCLFLMAHLQALTWVAFLAWLAIGLAIYFLYARRNAVL 460 Lambda K H 0.326 0.138 0.415 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: 616 Number of extensions: 32 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: 483 Length of database: 464 Length adjustment: 33 Effective length of query: 450 Effective length of database: 431 Effective search space: 193950 Effective search space used: 193950 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 (21.7 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