Align Proline-specific permease (ProY) (characterized)
to candidate BPHYT_RS15500 BPHYT_RS15500 aromatic amino acid transporter
Query= TCDB::P37460 (456 letters) >FitnessBrowser__BFirm:BPHYT_RS15500 Length = 461 Score = 397 bits (1020), Expect = e-115 Identities = 196/448 (43%), Positives = 292/448 (65%), Gaps = 3/448 (0%) Query: 2 ESNNKLKRGLSTRHIRFMALGSAIGTGLFYGSADAIKMAGPSVLLAYIIGGVAAYIIMRA 61 + + LKRGL RHI+ +ALG AIGTGLF GSA ++ AGPS++L Y IGG+ A++IMR Sbjct: 5 QQQDGLKRGLKNRHIQLIALGGAIGTGLFLGSASVLQAAGPSMILGYAIGGIIAFMIMRQ 64 Query: 62 LGEMSVHNPAASSFSRYAQENLGPLAGYITGWTYCFEILIVAIADVTAFGIYMGVWFPAV 121 LGEM P A SFS +A + G G+++GW Y ++V++A++TA G Y+ W+P V Sbjct: 65 LGEMVAQEPVAGSFSHFAYKYWGDFPGFLSGWNYWVLYVLVSMAELTAVGTYIHYWWPGV 124 Query: 122 PHWIWVLSVVLIICAINLMSVKVFGELEFWFSFFKVATIIIMIVAGIGIIVWGIGNGGQP 181 P W+ L +I AINL +VK +GE EFWF+ KV +I MIV G +++ G+GG Sbjct: 125 PTWVSALVCFALINAINLANVKAYGETEFWFAIIKVVAVIGMIVFGGYLLI--SGHGGPQ 182 Query: 182 TGIHNLWSNGGFFSNGWLGMIMSLQMVMFAYGGIEIIGITAGEAKDPEKSIPRAINSVPM 241 I NLWS+GGFF +G+ G+ M L ++MF++GG+E+IGITA EA P+KSIP+A+N V Sbjct: 183 ASITNLWSHGGFFPHGFHGLFMMLAVIMFSFGGLELIGITAAEADQPQKSIPKAVNQVIY 242 Query: 242 RILVFYVGTLFVIMSIYPWNQVGTNGSPFVLTFQHMGITFAASILNFVVLTASLSAINSD 301 RIL+FY+ +L V++S+YPWN+V GSPFV+ F +G T A++LN VVLTA+LS NS Sbjct: 243 RILIFYICSLTVLLSLYPWNEVAAGGSPFVMIFSQIGSTLTANVLNVVVLTAALSVYNSG 302 Query: 302 VFGVGRMLHGMAEQGSAPKVFAKTSRRGIPWVTVLVMTIALLFAVYLNYIMPENVFLVIA 361 V+ RML+G+AEQG+AP+ K RRG+P++ + + +A V +NY++P ++ Sbjct: 303 VYANSRMLYGLAEQGNAPRALMKVDRRGVPYMAIGLSALATFTCVIVNYLIPAEALGLLM 362 Query: 362 SLATFATVWVWIMILLSQIAFRRRLPPEEVKALKFKVPGGVVTTIAGLIFLVFIIALIGY 421 +L A V W +I L+ + R+ + + L FK V+ L F+ I+ ++ Sbjct: 363 ALVVAALVLNWALISLTHLKSRKAMVAAG-ETLVFKSFWFPVSNWICLAFMALILVILAM 421 Query: 422 HPDTRISLYVGFAWIVLLLIGWIFKRRR 449 P +S+++ AW+V++ G++FKRRR Sbjct: 422 TPGLSVSVWLVPAWLVVMWAGYVFKRRR 449 Lambda K H 0.329 0.143 0.449 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: 597 Number of extensions: 30 Number of successful extensions: 3 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: 456 Length of database: 461 Length adjustment: 33 Effective length of query: 423 Effective length of database: 428 Effective search space: 181044 Effective search space used: 181044 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 (21.8 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