Align Amino acid transporter (characterized, see rationale)
to candidate BPHYT_RS01785 BPHYT_RS01785 amino acid permease
Query= uniprot:A0A0H3C3Q5 (483 letters) >FitnessBrowser__BFirm:BPHYT_RS01785 Length = 463 Score = 367 bits (941), Expect = e-106 Identities = 200/473 (42%), Positives = 282/473 (59%), Gaps = 20/473 (4%) Query: 13 RRKAIDTITAGHADSHQLKKTLSWPHLVALGVGAIVGTGIYTLTGVGAGLAGPGVILSFL 72 R+K ++ + A A + LKK L L LGVGAI+GTGI+ LTG GA AGP +++SFL Sbjct: 5 RKKNVEHMIAASAQNAGLKKALGALDLTFLGVGAIIGTGIFVLTGTGAVQAGPALMISFL 64 Query: 73 IAGAVCACAALCYAELSTMIPASGSAYTYSYAAMGEPVAWFVGWSLILEYTLVCAAVAVG 132 IA C AAL YAE ++ IP +GS YTYSYA +GE AW +GW L+LEY L +AV+VG Sbjct: 65 IAAIACGFAALAYAEFASTIPVAGSIYTYSYATLGELAAWIIGWDLMLEYGLATSAVSVG 124 Query: 133 WSAHAHGLFKMIG--FPDALLAGPH----QGGLINMPAVFISMAVAGLLALGTRESATVN 186 WS + L G P AL A P L N+PA + MA+ LL++G RESA +N Sbjct: 125 WSGYLQSLLSGFGVSLPVALTAAPGALPGHDTLFNLPAFLVMMAITALLSVGVRESARIN 184 Query: 187 MVLVFVKIIALIVFVVLCLPAFNLAHFTPFMPNGFQAHVPEGAAADAAKVGVMAAASLIF 246 V+V +K++ +++ + + + A++ PFMPNG+ GV AA+++F Sbjct: 185 NVMVAIKVVVVLLVIGVGVFHVTPANWHPFMPNGWN--------------GVFGAAAVMF 230 Query: 247 FAFYGFDAVSTAAEETKNPKRDLTIGIVGSMAVCTAIYMIVAAVSIGASRTEVFSKSEAP 306 FAF GFD+VS+AAEE K+PKRDL IGI+ S+ VC +Y+ VAAV G + F+ P Sbjct: 231 FAFIGFDSVSSAAEEVKDPKRDLPIGIIASLGVCAVLYVAVAAVVTGIVPSAQFANISHP 290 Query: 307 LVFILESLNHGKIAQLVALAAVIALPTVILAFMYGQSRIFFVMARDGLLPRALSKVNAKT 366 + + L+ +A + L AV+ + TVIL YGQ+R+ F M+RDGLLP LS+V+ + Sbjct: 291 VSYALQVAGEKWVAGFIDLGAVLGMLTVILVMAYGQTRVIFAMSRDGLLPERLSRVHPRF 350 Query: 367 GTPVMMTLLTGVLAAVISGLLSLKDIAELANAGTLWAFIAVGASVILLRLREPNRPRVFS 426 TP T L G+ +I L+ L +AEL N GTL AF V +V++LR P+ PR F Sbjct: 351 ATPFFTTWLVGIFFGLIGALVPLNVLAELINIGTLAAFSMVSIAVLVLRKTHPDLPRAFR 410 Query: 427 TPLWPIVAPAGILGCLYLFLSLPGKTQLYFLYAHLIGAVVYLAYGMRKSVLAQ 479 P P+V + CL+L ++L T + F+ L+G V+Y Y R S L++ Sbjct: 411 CPGVPVVPVLAVAACLFLMVNLQAVTWVAFVVWLLVGMVIYFGYSRRHSKLSK 463 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: 639 Number of extensions: 34 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: 463 Length adjustment: 33 Effective length of query: 450 Effective length of database: 430 Effective search space: 193500 Effective search space used: 193500 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