Align Aromatic amino acid transporter AroP (characterized, see rationale)
to candidate GFF344 PS417_01755 proline-specific permease
Query= uniprot:A0A2Z5MFR8 (461 letters) >FitnessBrowser__WCS417:GFF344 Length = 469 Score = 392 bits (1008), Expect = e-113 Identities = 199/455 (43%), Positives = 286/455 (62%), Gaps = 5/455 (1%) Query: 6 QQDGLKRGLKNRHIQLIALGGAIGTGLFLGSASVLQAAGPSMILGYAIGGVIAFMIMRQL 65 Q+ GLKRGL RHI+ +ALG AIGTGLF GSAS +Q AGP+++L Y IGG FM+MR L Sbjct: 4 QEKGLKRGLSARHIRFMALGSAIGTGLFYGSASAIQMAGPAVLLAYLIGGAAVFMVMRAL 63 Query: 66 GEMVAQEPVAGSFSHFAYKYWGDFPGFLSGWNYWVLYVLVSMAELTAVGTYVHYWWPGVP 125 GEM PVAGSF +A Y G GF+ GW Y ++V +A++TA G Y+ +W+P V Sbjct: 64 GEMAVHNPVAGSFGQYASTYLGPMAGFILGWTYAFEMIIVCLADVTAFGIYMGFWFPDVA 123 Query: 126 TWVSALVCFAGINAINLANVKAYGETEFWFAIIKVVAVIGMILFG-GYLLVSGH--GGPQ 182 WV L I +NL NVK +GE EFW +++KV A++ MIL G G +L H G Q Sbjct: 124 RWVWVLGIVLLIGGLNLCNVKVFGEMEFWLSLLKVGAIVAMILGGFGIMLFGIHSAGETQ 183 Query: 183 AS-ISNLWSHGGFFPHGFHGLFTMLAVIMFSFGGLELIGITAAEADEPQKSIPKAVNQVI 241 AS +SNLW+HGGF P+G GL AV+MF+FGG+E+IGITA EA +PQ+ IPKA+N V Sbjct: 184 ASGLSNLWAHGGFMPNGIGGLIASFAVVMFAFGGIEIIGITAGEAKDPQRVIPKAINAVP 243 Query: 242 YRILIFYICSLAVLLSLYPWNEVAAGGSPFVMIFSQIGSTLTANVLNVVVLTAALSVYNS 301 RIL+FY+ +L VL+++YPW ++ + GSPFV IFS +G A +LN+VV++AA+S NS Sbjct: 244 LRILLFYVLTLFVLMAIYPWPQIGSQGSPFVQIFSNLGIGSAATILNIVVISAAVSAINS 303 Query: 302 GVYANSRMLYGLAEQGNAPRALMKVDRRGVPYMAIGLSALATFTCVIVNYLIPAEALGLL 361 ++ RM+YGLA+QG AP+ ++ ++GVP+M + + A V++NYLIP ++ Sbjct: 304 DIFGAGRMMYGLAQQGQAPKGFAQLSKQGVPWMTVVVMGAALLGGVVLNYLIPENVFLVI 363 Query: 362 MALVVAALVLNWALISLTHLKSRRAMVAAG-ETLVFKSFWFPVSNWICLAFMALILVILA 420 ++ A V W +I T + RR+M L F ++P + + FM + +L Sbjct: 364 ASIATFATVWVWLMILFTQVAMRRSMTKEQVAELKFPVPFWPYAPAAAIVFMLFVFGVLG 423 Query: 421 MTPGLSVSVLLVPLWLVVMWAGYAFKRRRAAAHVA 455 P ++L+ +W+V++ Y + +A A Sbjct: 424 YFPDTQAALLVGAVWIVLLVVAYLLWVKPSAGQAA 458 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: 596 Number of extensions: 28 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: 461 Length of database: 469 Length adjustment: 33 Effective length of query: 428 Effective length of database: 436 Effective search space: 186608 Effective search space used: 186608 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