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 BPHYT_RS15500 BPHYT_RS15500 aromatic amino acid transporter
Query= TCDB::P15993 (457 letters) >FitnessBrowser__BFirm:BPHYT_RS15500 Length = 461 Score = 654 bits (1687), Expect = 0.0 Identities = 314/450 (69%), Positives = 369/450 (82%) Query: 2 MEGQQHGEQLKRGLKNRHIQLIALGGAIGTGLFLGSASVIQSAGPGIILGYAIAGFIAFL 61 M Q + LKRGLKNRHIQLIALGGAIGTGLFLGSASV+Q+AGP +ILGYAI G IAF+ Sbjct: 1 MNSAQQQDGLKRGLKNRHIQLIALGGAIGTGLFLGSASVLQAAGPSMILGYAIGGIIAFM 60 Query: 62 IMRQLGEMVVEEPVAGSFSHFAYKYWGSFAGFASGWNYWVLYVLVAMAELTAVGKYIQFW 121 IMRQLGEMV +EPVAGSFSHFAYKYWG F GF SGWNYWVLYVLV+MAELTAVG YI +W Sbjct: 61 IMRQLGEMVAQEPVAGSFSHFAYKYWGDFPGFLSGWNYWVLYVLVSMAELTAVGTYIHYW 120 Query: 122 YPEIPTWVSAAVFFVVINAINLTNVKVFGEMEFWFAIIKVIAVVAMIIFGGWLLFSGNGG 181 +P +PTWVSA V F +INAINL NVK +GE EFWFAIIKV+AV+ MI+FGG+LL SG+GG Sbjct: 121 WPGVPTWVSALVCFALINAINLANVKAYGETEFWFAIIKVVAVIGMIVFGGYLLISGHGG 180 Query: 182 PQATVSNLWDQGGFLPHGFTGLVMMMAIIMFSFGGLELVGITAAEADNPEQSIPKATNQV 241 PQA+++NLW GGF PHGF GL MM+A+IMFSFGGLEL+GITAAEAD P++SIPKA NQV Sbjct: 181 PQASITNLWSHGGFFPHGFHGLFMMLAVIMFSFGGLELIGITAAEADQPQKSIPKAVNQV 240 Query: 242 IYRILIFYIGSLAVLLSLMPWTRVTADTSPFVLIFHELGDTFVANALNIVVLTAALSVYN 301 IYRILIFYI SL VLLSL PW V A SPFV+IF ++G T AN LN+VVLTAALSVYN Sbjct: 241 IYRILIFYICSLTVLLSLYPWNEVAAGGSPFVMIFSQIGSTLTANVLNVVVLTAALSVYN 300 Query: 302 SCVYCNSRMLFGLAQQGNAPKALASVDKRGVPVNTILVSALVTALCVLINYLAPESAFGL 361 S VY NSRML+GLA+QGNAP+AL VD+RGVP I +SAL T CV++NYL P A GL Sbjct: 301 SGVYANSRMLYGLAEQGNAPRALMKVDRRGVPYMAIGLSALATFTCVIVNYLIPAEALGL 360 Query: 362 LMALVVSALVINWAMISLAHMKFRRAKQEQGVVTRFPALLYPLGNWICLLFMAAVLVIML 421 LMALVV+ALV+NWA+ISL H+K R+A G F + +P+ NWICL FMA +LVI+ Sbjct: 361 LMALVVAALVLNWALISLTHLKSRKAMVAAGETLVFKSFWFPVSNWICLAFMALILVILA 420 Query: 422 MTPGMAISVYLIPVWLIVLGIGYLFKEKTA 451 MTPG+++SV+L+P WL+V+ GY+FK + A Sbjct: 421 MTPGLSVSVWLVPAWLVVMWAGYVFKRRRA 450 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: 749 Number of extensions: 38 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: 461 Length adjustment: 33 Effective length of query: 424 Effective length of database: 428 Effective search space: 181472 Effective search space used: 181472 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