Align general amino acid permease AGP1 (characterized)
to candidate BPHYT_RS15500 BPHYT_RS15500 aromatic amino acid transporter
Query= CharProtDB::CH_091105 (633 letters) >FitnessBrowser__BFirm:BPHYT_RS15500 Length = 461 Score = 217 bits (553), Expect = 8e-61 Identities = 140/437 (32%), Positives = 222/437 (50%), Gaps = 20/437 (4%) Query: 108 NTGHKSDSLKKTIQPRHVLMIALGTGIGTGLLVGNGTALVHAGPAGLLIGYAIMGSILYC 167 N+ + D LK+ ++ RH+ +IALG IGTGL +G+ + L AGP+ +++GYAI G I + Sbjct: 2 NSAQQQDGLKRGLKNRHIQLIALGGAIGTGLFLGSASVLQAAGPS-MILGYAIGGIIAFM 60 Query: 168 IIQACGEMALVYSNLTGGYNAYPSFLVDDGFGFAVAWVYCLQWLCVCPLELVTASMTIKY 227 I++ GEM + + G ++ + D GF W Y + ++ V EL I Y Sbjct: 61 IMRQLGEM-VAQEPVAGSFSHFAYKYWGDFPGFLSGWNYWVLYVLVSMAELTAVGTYIHY 119 Query: 228 WTTSVNPDVFVIIFYVLVITINIFGARGYAEAEFFFNCCKILMMTGFFILGIIIDVGGAG 287 W V V ++ + L+ IN+ + Y E EF+F K++ + G + G + + G G Sbjct: 120 WWPGVPTWVSALVCFALINAINLANVKAYGETEFWFAIIKVVAVIGMIVFGGYLLISGHG 179 Query: 288 NDGFIGGKYWHDPGAFNGKHAIDRFKGVAATLVTAAFAFGGSEFIAITTAEQSNPRKAIP 347 W G F H F G+ L F+FGG E I IT AE P+K+IP Sbjct: 180 GPQASITNLWSHGGFF--PHG---FHGLFMMLAVIMFSFGGLELIGITAAEADQPQKSIP 234 Query: 348 GAAKQMIYRILFLFLATIILLGFLVPYNSDQLLGSTGGGTKASPYVIAVASHGVRVVPHF 407 A Q+IYRIL ++ ++ +L L P+N + GG SP+V+ + G + + Sbjct: 235 KAVNQVIYRILIFYICSLTVLLSLYPWNEV----AAGG----SPFVMIFSQIGSTLTANV 286 Query: 408 INAVILLSVLSMANSSFYSSARLFLTLSEQGYAPKVFSYIDRAGRPLIAMGVSAL--FAV 465 +N V+L + LS+ NS Y+++R+ L+EQG AP+ +DR G P +A+G+SAL F Sbjct: 287 LNVVVLTAALSVYNSGVYANSRMLYGLAEQGNAPRALMKVDRRGVPYMAIGLSALATFTC 346 Query: 466 IAFCAASPKEEQVFTWLLAISGLSQLFTWTAICLSHLRFRRAMKVQGRSLGELGFKSQTG 525 + P E L ++ L + W I L+HL+ R+AM G +L F Sbjct: 347 VIVNYLIPAEALGLLMALVVAAL--VLNWALISLTHLKSRKAMVAAGETLVFKSFWFPVS 404 Query: 526 VWGSAYACIMMILILIA 542 W A + +IL+++A Sbjct: 405 NW-ICLAFMALILVILA 420 Lambda K H 0.324 0.138 0.424 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: 712 Number of extensions: 31 Number of successful extensions: 6 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: 633 Length of database: 461 Length adjustment: 35 Effective length of query: 598 Effective length of database: 426 Effective search space: 254748 Effective search space used: 254748 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.0 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (22.0 bits) S2: 52 (24.6 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