Align general amino acid permease AGP1 (characterized)
to candidate 16265 b2156 lysine transporter (NCBI)
Query= CharProtDB::CH_091105 (633 letters) >FitnessBrowser__Keio:16265 Length = 489 Score = 261 bits (667), Expect = 5e-74 Identities = 139/472 (29%), Positives = 245/472 (51%), Gaps = 14/472 (2%) Query: 112 KSDSLKKTIQPRHVLMIALGTGIGTGLLVGNGTALVHAGPAGLLIGYAIMGSILYCIIQA 171 ++ L++ ++ RH+ MIA+G IGTGL V +G + AGP G L+ Y ++G ++Y ++ + Sbjct: 9 EAPGLRRELKARHLTMIAIGGSIGTGLFVASGATISQAGPGGALLSYMLIGLMVYFLMTS 68 Query: 172 CGEMALVYSNLTGGYNAYPSFLVDDGFGFAVAWVYCLQWLCVCPLELVTASMTIKYWTTS 231 GE+A Y ++G + Y V++GFGFA+ W Y W ++LV A + + +W Sbjct: 69 LGELA-AYMPVSGSFATYGQNYVEEGFGFALGWNYWYNWAVTIAVDLVAAQLVMSWWFPD 127 Query: 232 VNPDVFVIIFYVLVITINIFGARGYAEAEFFFNCCKILMMTGFFILGIIIDVG---GAGN 288 ++ +F ++ +N RG+ EAE++F+ K+ + F I+G+++ +G GA Sbjct: 128 TPGWIWSALFLGVIFLLNYISVRGFGEAEYWFSLIKVTTVIVFIIVGVLMIIGIFKGAQP 187 Query: 289 DGFIGGKYWHDPGAFNGKHAIDRFKGVAATLVTAAFAFGGSEFIAITTAEQSNPRKAIPG 348 G+ P A F + + F+F G+E I I E +P K IP Sbjct: 188 AGWSNWTIGEAPFAGG-------FAAMIGVAMIVGFSFQGTELIGIAAGESEDPAKNIPR 240 Query: 349 AAKQMIYRILFLFLATIILLGFLVPYNSDQLLGSTGGGTKASPYVIAVASHGVRVVPHFI 408 A +Q+ +RIL ++ I+++ ++PY LL + SP+ + G+ + Sbjct: 241 AVRQVFWRILLFYVFAILIISLIIPYTDPSLLRNDVKDISVSPFTLVFQHAGLLSAAAVM 300 Query: 409 NAVILLSVLSMANSSFYSSARLFLTLSEQGYAPKVFSYIDRAGRPLIAMGVSALFAVIAF 468 NAVIL +VLS NS Y+S R+ TL+ G AP++F+ + R G P A+ + + A + F Sbjct: 301 NAVILTAVLSAGNSGMYASTRMLYTLACDGKAPRIFAKLSRGGVPRNALYATTVIAGLCF 360 Query: 469 CAASPKEEQVFTWLLAISGLSQLFTWTAICLSHLRFRRAMKVQGRSLGELGFKSQTGVWG 528 + + V+ WLL SG++ W I +SH RFRR +QG + +L ++S G Sbjct: 361 LTSMFGNQTVYLWLLNTSGMTGFIAWLGIAISHYRFRRGYVLQGHDINDLPYRSGFFPLG 420 Query: 529 SAYACIMMILILIAQFWVAIAPIGEGKLDAQAFFENYLAMPILIALYVGYKV 580 +A I+ ++I + Q + A + +D Y+ +P+ + ++ GYK+ Sbjct: 421 PIFAFILCLIITLGQNYEAFL---KDTIDWGGVAATYIGIPLFLIIWFGYKL 469 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: 721 Number of extensions: 29 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: 633 Length of database: 489 Length adjustment: 36 Effective length of query: 597 Effective length of database: 453 Effective search space: 270441 Effective search space used: 270441 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 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