Align Aromatic amino acid:H+ symporter, AroP of 457 aas and 12 TMSs (Cosgriff and Pittard 1997). Transports phenylalanine, tyrosine and tryptophan (characterized)
to candidate PP_0927 PP_0927 aromatic amino acid transport protein
Query= TCDB::P15993 (457 letters) >FitnessBrowser__Putida:PP_0927 Length = 453 Score = 641 bits (1654), Expect = 0.0 Identities = 314/454 (69%), Positives = 368/454 (81%), Gaps = 2/454 (0%) Query: 2 MEGQQHGEQLKRGLKNRHIQLIALGGAIGTGLFLGSASVIQSAGPGIILGYAIAGFIAFL 61 M+ Q E+L+RGLKNRHIQLIALGGAIGTGLFLG A IQ AGP ++LGYAIAG +AFL Sbjct: 1 MQDQSTPERLQRGLKNRHIQLIALGGAIGTGLFLGIAQTIQLAGPSVLLGYAIAGLMAFL 60 Query: 62 IMRQLGEMVVEEPVAGSFSHFAYKYWGSFAGFASGWNYWVLYVLVAMAELTAVGKYIQFW 121 IMRQLGEMVVEEPVAGSFSHFA++YW FAGF SGWNYWV+YVLV MAELTAVG Y+Q+W Sbjct: 61 IMRQLGEMVVEEPVAGSFSHFAHQYWSEFAGFVSGWNYWVVYVLVGMAELTAVGIYVQYW 120 Query: 122 YPEIPTWVSAAVFFVVINAINLTNVKVFGEMEFWFAIIKVIAVVAMIIFGGWLLFSGNGG 181 +P+ PTW +AA+FFVVIN INLT VKV+GEMEFWFA++KV+A+V+MI FG WLL SG+GG Sbjct: 121 WPDFPTWATAAIFFVVINLINLTQVKVYGEMEFWFALVKVVAIVSMIGFGAWLLGSGHGG 180 Query: 182 PQATVSNLWDQGGFLPHGFTGLVMMMAIIMFSFGGLELVGITAAEADNPEQSIPKATNQV 241 P A+V+NLW GGF P+G TGLVM +A+IMFSFGGLELVGITAAEADNP +SIPKATNQV Sbjct: 181 PDASVANLWQYGGFFPNGVTGLVMALAVIMFSFGGLELVGITAAEADNPRESIPKATNQV 240 Query: 242 IYRILIFYIGSLAVLLSLMPWTRVTADTSPFVLIFHELGDTFVANALNIVVLTAALSVYN 301 +YRILIFYIG+LAVLLSL PW +V SPFV+IFHEL VA LNIVVLTAALSVYN Sbjct: 241 VYRILIFYIGALAVLLSLYPWQKVVQGGSPFVMIFHELDSDLVATILNIVVLTAALSVYN 300 Query: 302 SCVYCNSRMLFGLAQQGNAPKALASVDKRGVPVNTILVSALVTALCVLINYLAPESAFGL 361 SCVY NSRMLFGLA QG+AP+ L V + GVP+ + VSA T LCVLINYL P AFGL Sbjct: 301 SCVYANSRMLFGLASQGDAPRQLLKVSRSGVPLTALAVSAFATGLCVLINYLMPGGAFGL 360 Query: 362 LMALVVSALVINWAMISLAHMKFRRAKQEQGVVTRFPALLYPLGNWICLLFMAAVLVIML 421 LMAL VSALVINWA IS+ H+KFR+AK G+ + +L +PL N++CL F+ +LV+M Sbjct: 361 LMALAVSALVINWASISITHLKFRKAKLAAGITPFYKSLGHPLTNYLCLAFIVLILVVMY 420 Query: 422 MTPGMAISVYLIPVWLIVLGIGYLFKEKTAKAVK 455 +TP + ISV LIP W+ VL + FK K A+ K Sbjct: 421 LTPPIRISVMLIPAWIAVLWVA--FKLKKARQAK 452 Lambda K H 0.328 0.141 0.434 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: 720 Number of extensions: 26 Number of successful extensions: 1 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: 457 Length of database: 453 Length adjustment: 33 Effective length of query: 424 Effective length of database: 420 Effective search space: 178080 Effective search space used: 178080 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