Align Amino-acid permease RocE (characterized)
to candidate BPHYT_RS15500 BPHYT_RS15500 aromatic amino acid transporter
Query= SwissProt::P39137 (467 letters) >FitnessBrowser__BFirm:BPHYT_RS15500 Length = 461 Score = 296 bits (759), Expect = 7e-85 Identities = 157/461 (34%), Positives = 262/461 (56%), Gaps = 10/461 (2%) Query: 1 MNTNQDNGNQLQRTMKSRHLFMISLGGVIGTGFFLGTGFTINQAGPLGAVLSYLVGGFIM 60 MN+ Q L+R +K+RH+ +I+LGG IGTG FLG+ + AGP +L Y +GG I Sbjct: 1 MNSAQQQDG-LKRGLKNRHIQLIALGGAIGTGLFLGSASVLQAAGP-SMILGYAIGGIIA 58 Query: 61 FLTMLCLGELAVAFPVSGSFQTYATKFISPAFGFAFGWLYWLGWAVTCAIEFLSAGQLMQ 120 F+ M LGE+ PV+GSF +A K+ GF GW YW+ + + E + G + Sbjct: 59 FMIMRQLGEMVAQEPVAGSFSHFAYKYWGDFPGFLSGWNYWVLYVLVSMAELTAVGTYIH 118 Query: 121 RWFPHIDVWIWCLVFAALMFILNAITTKAFAESEFWFSGIKILIILLFIILGGAAMFGLI 180 W+P + W+ LV AL+ +N KA+ E+EFWF+ IK++ ++ I+ GG + LI Sbjct: 119 YWWPGVPTWVSALVCFALINAINLANVKAYGETEFWFAIIKVVAVIGMIVFGG---YLLI 175 Query: 181 DLKGGEQAPFLTHFYEDGLFPNGIKAMLITMITVNFAFQGTELIGVAAGESEDPEKTIPR 240 GG QA + G FP+G + + + + F+F G ELIG+ A E++ P+K+IP+ Sbjct: 176 SGHGGPQASITNLWSHGGFFPHGFHGLFMMLAVIMFSFGGLELIGITAAEADQPQKSIPK 235 Query: 241 SIKQTVWRTLVFFVLSIIVIAGMIPWKQAGVVESPFVAVFEQIGIPYAADIMNFVILIAL 300 ++ Q ++R L+F++ S+ V+ + PW + SPFV +F QIG A+++N V+L A Sbjct: 236 AVNQVIYRILIFYICSLTVLLSLYPWNEVAAGGSPFVMIFSQIGSTLTANVLNVVVLTAA 295 Query: 301 LSVANSGLYASTRILYAMANEGQAFKALGKTNQRGVPMYSLIVTMAVACLSLLTKFAQAE 360 LSV NSG+YA++R+LY +A +G A +AL K ++RGVP ++ ++ ++ + Sbjct: 296 LSVYNSGVYANSRMLYGLAEQGNAPRALMKVDRRGVPYMAIGLSALATFTCVIVNYLIPA 355 Query: 361 TVYMVLLSLAGMSAQVGWITISLSQIMFRRKYIREGGKIEDLKFKTPLYPVLPLIGLTLN 420 +L++L + + W ISL+ + R+ + G E L FK+ +PV I L Sbjct: 356 EALGLLMALVVAALVLNWALISLTHLKSRKAMVAAG---ETLVFKSFWFPVSNWICLAFM 412 Query: 421 TVVLISLAFDPEQRIALYCGVPFMIICYIIYHVVIKKRQQA 461 ++L+ LA P ++++ ++++ + Y V K+R+ A Sbjct: 413 ALILVILAMTPGLSVSVWLVPAWLVVMWAGY--VFKRRRAA 451 Lambda K H 0.329 0.142 0.438 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: 548 Number of extensions: 27 Number of successful extensions: 4 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: 467 Length of database: 461 Length adjustment: 33 Effective length of query: 434 Effective length of database: 428 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 (21.8 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