Align Aromatic amino acid transporter AroP (characterized, see rationale)
to candidate PfGW456L13_4291 Aromatic amino acid transport protein AroP
Query= uniprot:A0A2Z5MFR8 (461 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_4291 Length = 467 Score = 634 bits (1636), Expect = 0.0 Identities = 314/467 (67%), Positives = 373/467 (79%), Gaps = 12/467 (2%) Query: 2 DNALQQDGLKRGLKNRHIQLIALGGAIGTGLFLGSASVLQAAGPSMILGYAIGGVIAFMI 61 D L+Q LKRGLKNRHIQLIALGGAIGTGLFLGSA VL++AGPSMILGYAI G IAF+I Sbjct: 3 DEILRQGELKRGLKNRHIQLIALGGAIGTGLFLGSAGVLKSAGPSMILGYAIAGFIAFLI 62 Query: 62 MRQLGEMVAQEPVAGSFSHFAYKYWGDFPGFLSGWNYWVLYVLVSMAELTAVGTYVHYWW 121 MRQLGEM+ +EPVAGSFSHFA+KYWG + GFLSGWNYWVLYVLV MAELTAVG YV +WW Sbjct: 63 MRQLGEMIVEEPVAGSFSHFAHKYWGGYAGFLSGWNYWVLYVLVGMAELTAVGKYVQFWW 122 Query: 122 PGVPTWVSALVCFAGINAINLANVKAYGETEFWFAIIKVVAVIGMILFGGYLLVSGHGGP 181 P VP+WVSA V F +N IN+ NVK +GE EFWFAIIKVVA+IGMI G Y+L SG GGP Sbjct: 123 PEVPSWVSAAVFFVLVNLINMMNVKVFGEMEFWFAIIKVVAIIGMIALGCYMLFSGTGGP 182 Query: 182 QASISNLWSHGGFFPHGFHGLFTMLAVIMFSFGGLELIGITAAEADEPQKSIPKAVNQVI 241 QAS+SNLW HGGFFP+G+ GL +A IMFSFGGLEL+GITAAEA EP K IPKA+NQV+ Sbjct: 183 QASVSNLWDHGGFFPNGYSGLLMAMAFIMFSFGGLELVGITAAEASEPGKVIPKAINQVV 242 Query: 242 YRILIFYICSLAVLLSLYPWNEV---------AAGGSPFVMIFSQIGSTLTANVLNVVVL 292 YR+LIFY+ +L VLLSLYPW+++ A GGSPFV IFS IGS A++LN VVL Sbjct: 243 YRVLIFYVGALTVLLSLYPWDQLLQTLGASGDAYGGSPFVQIFSLIGSDTAAHILNFVVL 302 Query: 293 TAALSVYNSGVYANSRMLYGLAEQGNAPRALMKVDRRGVPYMAIGLSALATFTCVIVNYL 352 TAALSVYNSGVY NSRMLYGLAEQG+AP+ALMK++++GVP +A+G+SAL T V+VNYL Sbjct: 303 TAALSVYNSGVYCNSRMLYGLAEQGDAPKALMKLNKQGVPLLALGVSALITLLSVLVNYL 362 Query: 353 IPAEALGLLMALVVAALVLNWALISLTHLKSRRAMVAAGETLVFKSFWFPVSNWICLAFM 412 P EAL LL ALVVA+L++NWA+ISLTHLK R+ M G FKSFWFP SN++CLAFM Sbjct: 363 APHEALELLFALVVASLMINWAMISLTHLKFRKIMSQQGIVPGFKSFWFPFSNYLCLAFM 422 Query: 413 ALILVILAMTPGLSVSVLLVPLWLVVMWAGYAFKRRRAAAHVAARVV 459 +I+ ++ M PG+ SV +P+W++++ + F R R A A VV Sbjct: 423 VMIVCVMLMIPGIRASVFAIPVWVLII---FGFYRMRMAKDRALPVV 466 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: 667 Number of extensions: 27 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: 467 Length adjustment: 33 Effective length of query: 428 Effective length of database: 434 Effective search space: 185752 Effective search space used: 185752 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