Align Aromatic amino acid transporter AroP (characterized, see rationale)
to candidate RR42_RS28305 RR42_RS28305 proline-specific permease
Query= uniprot:A0A2Z5MFR8 (461 letters) >FitnessBrowser__Cup4G11:RR42_RS28305 Length = 472 Score = 419 bits (1078), Expect = e-122 Identities = 202/449 (44%), Positives = 299/449 (66%), Gaps = 5/449 (1%) Query: 6 QQDGLKRGLKNRHIQLIALGGAIGTGLFLGSASVLQAAGPSMILGYAIGGVIAFMIMRQL 65 ++ L RGLK+RHIQ+IA+GGAIG GLFLG+ + AGP ++L YAIGGV F IMR L Sbjct: 15 EEKDLHRGLKDRHIQMIAIGGAIGVGLFLGAGRAIAIAGPGLMLSYAIGGVAIFFIMRAL 74 Query: 66 GEMVAQEPVAGSFSHFAYKYWGDFPGFLSGWNYWVLYVLVSMAELTAVGTYVHYWWPGVP 125 GE++ PV+GSF+ +A ++ G F GF +GW+YW ++V+ MAE+TAV YVHYW+P VP Sbjct: 75 GELLLYRPVSGSFATYAEEFVGPFAGFATGWSYWFMWVVTGMAEITAVAVYVHYWFPDVP 134 Query: 126 TWVSALVCFAGINAINLANVKAYGETEFWFAIIKVVAVIGMILFGGYLLVSGHG--GPQA 183 W+ AL A + +N V +GE EFWFA+IKVV ++ MI+ G ++ G GP A Sbjct: 135 QWIPALATLAVLYLVNCVAVAVFGELEFWFALIKVVTIVAMIVIGLAIIFFGVTPLGPTA 194 Query: 184 SISNLWSHGGFFPHGFHGLFTMLAVIMFSFGGLELIGITAAEADEPQKSIPKAVNQVIYR 243 S SNLW+HGGF P G G+ L ++MF++ G+ELIG+TA EA P+K +P A N V++R Sbjct: 195 SFSNLWTHGGFMPFGTLGVVLTLQIVMFAYQGVELIGVTAGEAQNPEKVLPHATNGVVWR 254 Query: 244 ILIFYICSLAVLLSLYPWNEVAAGGSPFVMIFSQIGSTLTANVLNVVVLTAALSVYNSGV 303 ILIFY+ +L ++++L PWNE+ G SPFV +F +IG A ++N+VV+TAA S NSG+ Sbjct: 255 ILIFYVGALIIMMALVPWNELKPGVSPFVYVFERIGVPGAAAIVNLVVITAAASSCNSGI 314 Query: 304 YANSRMLYGLAEQGNAPRALMKVDRRGVPYMAIGLSALATFTCVIVNYLIPAEALGLLMA 363 ++ RMLY LA+ G APRA +V + VP +AI SA V++NY++P + + + Sbjct: 315 FSTGRMLYTLAQFGQAPRAFGRVSSKHVPSIAITFSAALMGIGVLLNYIVPEQVFVWVTS 374 Query: 364 LVVAALVLNWALISLTHLKSRRAMVAAG--ETLVFKSFWFPVSNWICLAFMALILVILAM 421 + + + W++I + HL R+A +AAG + + F+ P +NW+ +AFM + V+L++ Sbjct: 375 ISLVGSLWTWSIIMIAHLGYRKA-IAAGRVKAVAFRMPGAPYANWLVVAFMIAVAVLLSL 433 Query: 422 TPGLSVSVLLVPLWLVVMWAGYAFKRRRA 450 PG V++ + P+W ++ GY F + RA Sbjct: 434 DPGTRVALYVAPVWFALLGIGYRFTKSRA 462 Lambda K H 0.327 0.140 0.440 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: 569 Number of extensions: 22 Number of successful extensions: 4 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: 461 Length of database: 472 Length adjustment: 33 Effective length of query: 428 Effective length of database: 439 Effective search space: 187892 Effective search space used: 187892 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