Align Aromatic amino acid transporter AroP (characterized, see rationale)
to candidate PfGW456L13_318 Histidine transport protein (permease)
Query= uniprot:A0A2Z5MFR8 (461 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_318 Length = 468 Score = 396 bits (1017), Expect = e-115 Identities = 197/457 (43%), Positives = 288/457 (63%), Gaps = 12/457 (2%) Query: 7 QDGLKRGLKNRHIQLIALGGAIGTGLFLGSASVLQAAGPSMILGYAIGGVIAFMIMRQLG 66 + GLKRGL RHI+ +ALG AIGTGLF GSAS +Q AGP+++L Y IGG FM+MR LG Sbjct: 5 EKGLKRGLSARHIRFMALGSAIGTGLFYGSASAIQMAGPAVLLAYLIGGAAVFMVMRALG 64 Query: 67 EMVAQEPVAGSFSHFAYKYWGDFPGFLSGWNYWVLYVLVSMAELTAVGTYVHYWWPGVPT 126 EM PVAGSF +A Y G GF+ GW Y V+V MA++TA G Y+ +W+P V Sbjct: 65 EMAVHNPVAGSFGQYASTYLGPMAGFILGWTYAFEMVIVGMADVTAFGIYMGFWFPEVSR 124 Query: 127 WVSALVCFAGINAINLANVKAYGETEFWFAIIKVVAVIGMILFGGYLL---VSGHGGPQA 183 W+ L + + +NL NVK +GE EFW +++KV A++ MIL G ++ +S G Sbjct: 125 WIWVLGVVSIVGGLNLCNVKVFGEMEFWLSLLKVAAIVAMILGGFGIMWFGISSAPGQAT 184 Query: 184 SISNLWSHGGFFPHGFHGLFTMLAVIMFSFGGLELIGITAAEADEPQKSIPKAVNQVIYR 243 ISNLWSHGGF P+G GL AV+MF+FGG+E+IG+TA EA +PQ +P+A+N V R Sbjct: 185 DISNLWSHGGFMPNGMGGLIASFAVVMFAFGGIEIIGVTAGEAKDPQHVLPRAINAVPLR 244 Query: 244 ILIFYICSLAVLLSLYPWNEVAAGGSPFVMIFSQIGSTLTANVLNVVVLTAALSVYNSGV 303 IL+FY+ ++ VL+S++PW ++ + GSPFV IF ++G + A +LN+VV+TAA+S NS + Sbjct: 245 ILLFYVLTMLVLMSIFPWQQIGSQGSPFVQIFDKLGISSAATILNIVVITAAISAINSDI 304 Query: 304 YANSRMLYGLAEQGNAPRALMKVDRRGVPYMAIGLSALATFTCVIVNYLIPAEALGLLMA 363 + RM++GLA+QG+AP+ ++ R GVP+M + + + A V++NYLIP L+ + Sbjct: 305 FGAGRMMFGLAQQGHAPKGFARLSRNGVPWMTVVVMSAALLLGVLLNYLIPENVFLLIAS 364 Query: 364 LVVAALVLNWALISLTHLKSRRAMVAAGETLVFKSFWFPVSNW-----ICLAFMALILVI 418 + A V W +I +T + RR+M +A + K FPV W +AFM I + Sbjct: 365 VATFATVWVWLMILVTQVAMRRSM-SAEQVAQLK---FPVPLWPYAPAAAIAFMLFIFGV 420 Query: 419 LAMTPGLSVSVLLVPLWLVVMWAGYAFKRRRAAAHVA 455 L P ++++ +W+V++ Y + AA A Sbjct: 421 LGYFPDTQAALIVGVVWIVLLVLAYLTWVKPAAGQAA 457 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: 29 Number of successful extensions: 2 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: 468 Length adjustment: 33 Effective length of query: 428 Effective length of database: 435 Effective search space: 186180 Effective search space used: 186180 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