Align general amino acid permease AGP1 (characterized)
to candidate WP_033101984.1 JG50_RS0115245 amino acid permease
Query= CharProtDB::CH_091105 (633 letters) >NCBI__GCF_000763315.1:WP_033101984.1 Length = 484 Score = 288 bits (738), Expect = 3e-82 Identities = 151/489 (30%), Positives = 268/489 (54%), Gaps = 11/489 (2%) Query: 111 HKSDSLKKTIQPRHVLMIALGTGIGTGLLVGNGTALVHAGPAGLLIGYAIMGSILYCIIQ 170 ++S LK+ ++ RH+ MIA+G IGTG+ + +G ++ AGP G L+ Y +G ++Y ++ Sbjct: 5 NRSPELKRGLKARHLSMIAIGGSIGTGVFLASGASISEAGPGGALVAYLAIGIMVYFLMT 64 Query: 171 ACGEMALVYSNLTGGYNAYPSFLVDDGFGFAVAWVYCLQWLCVCPLELVTASMTIKYWTT 230 + GEMA + + G ++ Y VD GFA+ W Y W +EL S+ + YW Sbjct: 65 SLGEMA-TFMPVAGSFSTYAGRFVDPALGFAMGWNYWYNWAITIAVELSAGSLIMDYWFP 123 Query: 231 SVNPDVFVIIFYVLVITINIFGARGYAEAEFFFNCCKILMMTGFFILGIIIDVGGAGNDG 290 ++ +F +L+ +N +GY E+E++F+ K+ + F ++G+++ G G + Sbjct: 124 HSPSILWSALFLLLMFGLNALSVKGYGESEYWFSFIKVATVIIFIVIGLLMIFGIMGGEA 183 Query: 291 FIGGKYWHDPGAFNGKHAIDRFKGVAATLVTAAFAFGGSEFIAITTAEQSNPRKAIPGAA 350 IG K + N + G+ + + A F+F G+E + + E NPRK +P A Sbjct: 184 -IGFKNF----TINDAPFHHGWLGILSVFMIAGFSFQGTELVGVAAGESENPRKNVPKAI 238 Query: 351 KQMIYRILFLFLATIILLGFLVPYNSDQLLGSTGGGTKASPYVIAVASHGVRVVPHFINA 410 +Q+ +RIL + I+++G ++PY + L+G SP+ I G+ +NA Sbjct: 239 RQVFWRILLFYALAILVMGLVLPYTNPNLVGGDVNQIAKSPFTIIFEKAGLAFAASVMNA 298 Query: 411 VILLSVLSMANSSFYSSARLFLTLSEQGYAPKVFSYIDRAGRPLIAMGVSALFAVIAFCA 470 VIL SVLS NS Y+S R+ ++++G APK+F+ ++R G P+ A+ ++ +AF A Sbjct: 299 VILTSVLSAGNSGMYASTRMLWQMAKEGKAPKLFAKVNRRGVPVFALLLTTAVGAVAFLA 358 Query: 471 ASPKEEQVFTWLLAISGLSQLFTWTAICLSHLRFRRAMKVQGRSLGELGFKSQTGVWGSA 530 + + +++ WLL SGLS W I +SH RFRRA QGR L L ++++ +G Sbjct: 359 SLVGQGKIYIWLLNASGLSGFIAWLGIAISHYRFRRAYVAQGRDLNHLVYRAKWFPFGPL 418 Query: 531 YACIMMILILIAQFWVAIAPIGEGKLDAQAFFENYLAMPILIALYVGYKVWHKDWKLFIR 590 +A ++ +++++ Q + A +D +Y+ +P+ I L++GYK W K K+ I Sbjct: 419 FALVLCVIVIVGQNYQAFT---GNTIDWNGILVSYIGLPLFILLWLGYK-WVKKTKV-IP 473 Query: 591 ADKIDLDSH 599 ++DL+S+ Sbjct: 474 LKEVDLESN 482 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: 737 Number of extensions: 40 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: 633 Length of database: 484 Length adjustment: 36 Effective length of query: 597 Effective length of database: 448 Effective search space: 267456 Effective search space used: 267456 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: 53 (25.0 bits)
This GapMind analysis is from Sep 24 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