Align general amino acid permease AGP1 (characterized)
to candidate WP_034528194.1 LOSG293_RS05955 amino acid permease
Query= CharProtDB::CH_091105 (633 letters) >NCBI__GCF_000740055.1:WP_034528194.1 Length = 485 Score = 283 bits (725), Expect = 9e-81 Identities = 165/490 (33%), Positives = 262/490 (53%), Gaps = 26/490 (5%) Query: 113 SDSLKKTIQPRHVLMIALGTGIGTGLLVGNGTALVHAGPAGLLIGYAIMGSILYCIIQAC 172 S +K+ ++ RHV MIALG IGTGL V +G+A+ AGP G L+ Y MG ++Y ++ + Sbjct: 7 SHQVKRELKTRHVSMIALGGSIGTGLFVASGSAISTAGPGGALVAYTAMGLMVYFLMTSL 66 Query: 173 GEMALVYSNLTGGYNAYPSFLVDDGFGFAVAWVYCLQWLCVCPLELVTASMTIKYWTTSV 232 GEMA Y ++G + AY + VD GFA+ W Y W +++ TA++ +K+W + Sbjct: 67 GEMA-TYMPVSGSFAAYATKYVDPAMGFAMGWNYWFNWAITLAVDISTAALVMKFWLPDI 125 Query: 233 NPDVFVIIFYVLVITINIFGARGYAEAEFFFNCCKILMMTGFFILGIIIDVGGAGNDGFI 292 ++ ++ V++ +N + + E+E++ K++ + F +G+ A G + Sbjct: 126 PGWIWSVLVLVIIFMLNALTVKAFGESEYWMAMIKVVTVFIFLAVGV------ATIFGIM 179 Query: 293 GGKYWHDPGAFNGKHAIDRFKG----VAATLVTAAFAFGGSEFIAITTAEQSNPRKAIPG 348 GG H G N F G + + V A F+F G+E + IT E +P K+IP Sbjct: 180 GG---HATGLENFTRKEAPFVGGIPTILSVFVVAGFSFQGTELVGITAGESKDPEKSIPK 236 Query: 349 AAKQMIYRILFLFLATIILLGFLVPYNSDQLLGSTGGGTKASPYVIAVASHGVRVVPHFI 408 A Q+ +RI+ ++ +I ++ ++PY S QLLGS+ SP+ + G+ + Sbjct: 237 AINQVFWRIILFYILSIFVIACIIPYTSPQLLGSSASDIAISPFTLVFQRAGLAAAASVM 296 Query: 409 NAVILLSVLSMANSSFYSSARLFLTLSEQGYAPKVFSYIDRAGRPLIAMGVSALFAVIAF 468 NAVIL SV+S ANS Y+S+R+ +L+ QGYA K F+ R G PL A ++ + + F Sbjct: 297 NAVILTSVISAANSGMYASSRMLYSLAVQGYASKAFTKTTRTGVPLNAQIMTTVVGALTF 356 Query: 469 CA--ASPKEEQVFTWLLAISGLSQLFTWTAICLSHLRFRRAMKVQGRSLGELGFKSQTGV 526 A A PK ++ WL+A SGL+ W I LSH RFRRA QG + EL + ++ Sbjct: 357 IASIAGPK---IYIWLVAASGLTGFIAWLGIALSHFRFRRAFIKQGHHISELKYHAKLFP 413 Query: 527 WGSAYACIMMILILIAQFWVAIAPIGEGKLDAQAFFENYLAMPILIALYVGYKVWHKDWK 586 G +A I+ +LI++ Q A + Q YL++PI I LY YK+ ++ Sbjct: 414 IGPIFALILCLLIIVGQDLDAFT-----NFNWQQISITYLSVPIFIGLYSYYKIRYR--T 466 Query: 587 LFIRADKIDL 596 I +KIDL Sbjct: 467 KLISLEKIDL 476 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: 705 Number of extensions: 38 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: 485 Length adjustment: 36 Effective length of query: 597 Effective length of database: 449 Effective search space: 268053 Effective search space used: 268053 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