Align Aromatic amino acid transporter AroP (characterized, see rationale)
to candidate GFF4632 PS417_23700 aromatic amino acid transporter
Query= uniprot:A0A2Z5MFR8 (461 letters) >FitnessBrowser__WCS417:GFF4632 Length = 467 Score = 635 bits (1639), Expect = 0.0 Identities = 308/465 (66%), Positives = 376/465 (80%), Gaps = 9/465 (1%) Query: 2 DNALQQDGLKRGLKNRHIQLIALGGAIGTGLFLGSASVLQAAGPSMILGYAIGGVIAFMI 61 D+ + GLKRGLKNRHIQLIALGGAIGTGLFLGSA VL++AGPSMILGYAI G IAF+I Sbjct: 3 DDMVNPVGLKRGLKNRHIQLIALGGAIGTGLFLGSAGVLKSAGPSMILGYAIAGFIAFLI 62 Query: 62 MRQLGEMVAQEPVAGSFSHFAYKYWGDFPGFLSGWNYWVLYVLVSMAELTAVGTYVHYWW 121 MRQLGEM+ +EPVAGSFSHFA+KYWG + GFL+GWNYWVLYVLV MAELTAVG Y+ +WW Sbjct: 63 MRQLGEMIVEEPVAGSFSHFAHKYWGGYAGFLAGWNYWVLYVLVGMAELTAVGKYIQFWW 122 Query: 122 PGVPTWVSALVCFAGINAINLANVKAYGETEFWFAIIKVVAVIGMILFGGYLLVSGHGGP 181 P +PTWVSALV F +N IN NVK +GETEFWFAIIKVVA++GMI+ G YLL SG GGP Sbjct: 123 PDIPTWVSALVFFVAVNLINTLNVKFFGETEFWFAIIKVVAIVGMIVLGCYLLFSGTGGP 182 Query: 182 QASISNLWSHGGFFPHGFHGLFTMLAVIMFSFGGLELIGITAAEADEPQKSIPKAVNQVI 241 QAS+SNLWSHGGFFP+G GL +A IMFSFGGLEL+GITAAEA EP+K IPKA+NQV+ Sbjct: 183 QASVSNLWSHGGFFPNGGMGLLMSMAFIMFSFGGLELVGITAAEASEPRKVIPKAINQVV 242 Query: 242 YRILIFYICSLAVLLSLYPWNEV---------AAGGSPFVMIFSQIGSTLTANVLNVVVL 292 YRILIFY+ +L VLLSLYPW+++ A GSPFV IFS IG+ A++LN VVL Sbjct: 243 YRILIFYVGALTVLLSLYPWDQLLQTLGASGDAYSGSPFVQIFSLIGNDTAAHILNFVVL 302 Query: 293 TAALSVYNSGVYANSRMLYGLAEQGNAPRALMKVDRRGVPYMAIGLSALATFTCVIVNYL 352 TAALSVYNSGVY NSRML+GLAEQG+AP++LMK++++GVP A+ +SAL T CV+VNY+ Sbjct: 303 TAALSVYNSGVYCNSRMLFGLAEQGDAPKSLMKLNKQGVPIRALAISALVTMLCVVVNYV 362 Query: 353 IPAEALGLLMALVVAALVLNWALISLTHLKSRRAMVAAGETLVFKSFWFPVSNWICLAFM 412 P AL LL ALVVA+L++NWALIS+TH+K R+AM G T FK+FWFP SN++CLAFM Sbjct: 363 APQSALELLFALVVASLMINWALISITHIKFRKAMGEQGVTPSFKTFWFPFSNYLCLAFM 422 Query: 413 ALILVILAMTPGLSVSVLLVPLWLVVMWAGYAFKRRRAAAHVAAR 457 +I+ ++ PG+S SV +P+W+ +++ Y + RR+ A V A+ Sbjct: 423 VMIISVMLAIPGISESVYAMPVWVGIIYVAYRLRVRRSHAVVNAQ 467 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: 678 Number of extensions: 28 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