Align Aromatic amino acid transporter AroP (characterized, see rationale)
to candidate PP_0927 PP_0927 aromatic amino acid transport protein
Query= uniprot:A0A2Z5MFR8 (461 letters) >FitnessBrowser__Putida:PP_0927 Length = 453 Score = 624 bits (1610), Expect = 0.0 Identities = 298/451 (66%), Positives = 364/451 (80%) Query: 1 MDNALQQDGLKRGLKNRHIQLIALGGAIGTGLFLGSASVLQAAGPSMILGYAIGGVIAFM 60 M + + L+RGLKNRHIQLIALGGAIGTGLFLG A +Q AGPS++LGYAI G++AF+ Sbjct: 1 MQDQSTPERLQRGLKNRHIQLIALGGAIGTGLFLGIAQTIQLAGPSVLLGYAIAGLMAFL 60 Query: 61 IMRQLGEMVAQEPVAGSFSHFAYKYWGDFPGFLSGWNYWVLYVLVSMAELTAVGTYVHYW 120 IMRQLGEMV +EPVAGSFSHFA++YW +F GF+SGWNYWV+YVLV MAELTAVG YV YW Sbjct: 61 IMRQLGEMVVEEPVAGSFSHFAHQYWSEFAGFVSGWNYWVVYVLVGMAELTAVGIYVQYW 120 Query: 121 WPGVPTWVSALVCFAGINAINLANVKAYGETEFWFAIIKVVAVIGMILFGGYLLVSGHGG 180 WP PTW +A + F IN INL VK YGE EFWFA++KVVA++ MI FG +LL SGHGG Sbjct: 121 WPDFPTWATAAIFFVVINLINLTQVKVYGEMEFWFALVKVVAIVSMIGFGAWLLGSGHGG 180 Query: 181 PQASISNLWSHGGFFPHGFHGLFTMLAVIMFSFGGLELIGITAAEADEPQKSIPKAVNQV 240 P AS++NLW +GGFFP+G GL LAVIMFSFGGLEL+GITAAEAD P++SIPKA NQV Sbjct: 181 PDASVANLWQYGGFFPNGVTGLVMALAVIMFSFGGLELVGITAAEADNPRESIPKATNQV 240 Query: 241 IYRILIFYICSLAVLLSLYPWNEVAAGGSPFVMIFSQIGSTLTANVLNVVVLTAALSVYN 300 +YRILIFYI +LAVLLSLYPW +V GGSPFVMIF ++ S L A +LN+VVLTAALSVYN Sbjct: 241 VYRILIFYIGALAVLLSLYPWQKVVQGGSPFVMIFHELDSDLVATILNIVVLTAALSVYN 300 Query: 301 SGVYANSRMLYGLAEQGNAPRALMKVDRRGVPYMAIGLSALATFTCVIVNYLIPAEALGL 360 S VYANSRML+GLA QG+APR L+KV R GVP A+ +SA AT CV++NYL+P A GL Sbjct: 301 SCVYANSRMLFGLASQGDAPRQLLKVSRSGVPLTALAVSAFATGLCVLINYLMPGGAFGL 360 Query: 361 LMALVVAALVLNWALISLTHLKSRRAMVAAGETLVFKSFWFPVSNWICLAFMALILVILA 420 LMAL V+ALV+NWA IS+THLK R+A +AAG T +KS P++N++CLAF+ LILV++ Sbjct: 361 LMALAVSALVINWASISITHLKFRKAKLAAGITPFYKSLGHPLTNYLCLAFIVLILVVMY 420 Query: 421 MTPGLSVSVLLVPLWLVVMWAGYAFKRRRAA 451 +TP + +SV+L+P W+ V+W + K+ R A Sbjct: 421 LTPPIRISVMLIPAWIAVLWVAFKLKKARQA 451 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: 594 Number of extensions: 26 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: 453 Length adjustment: 33 Effective length of query: 428 Effective length of database: 420 Effective search space: 179760 Effective search space used: 179760 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