Align lysine-specific permease (characterized)
to candidate H281DRAFT_01668 H281DRAFT_01668 gamma-aminobutyrate:proton symporter, AAT family
Query= CharProtDB::CH_003129 (489 letters) >FitnessBrowser__Burk376:H281DRAFT_01668 Length = 459 Score = 280 bits (716), Expect = 8e-80 Identities = 157/422 (37%), Positives = 242/422 (57%), Gaps = 12/422 (2%) Query: 13 LRRELKARHLTMIAIGGSIGTGLFVASGATISQAGPGGALLSYMLIGLMVYFLMTSLGEL 72 L++ LK RH+TMIA+GG IG GLFV SG+ I+ AGP A+LSY++ G+MV +M LGE+ Sbjct: 6 LKKSLKQRHITMIALGGVIGAGLFVGSGSIIATAGPA-AILSYLIGGVMVTLVMFMLGEM 64 Query: 73 AAYMPVSGSFATYGQNYVEEGFGFALGWNYWYNWAVTIAVDLVAAQLVMSWWFPDTPGWI 132 A+ P SGSF+TY +Y+ E GFA+GW YW+ +TI V+ + ++ + P P Sbjct: 65 ASRNPDSGSFSTYANSYLGEWAGFAVGWLYWFKSMITITVEAILLGAILHDFLPWLPVPA 124 Query: 133 WSALFLGVIFLLNYISVRGFGEAEYWFSLIKVTTVIVFIIVGVLMIIGIFKGAQPAGWSN 192 + L + N SVR FGEAEYW S KV T+IVF+++G ++ G+ G G N Sbjct: 125 GALFMLIALMATNAYSVRAFGEAEYWLSFAKVATIIVFMVLGASILFGLQPGIPAPGLLN 184 Query: 193 WTIGEAPFAGGFAAMIGVAMIVGFSFQGTELIGIAAGESEDPAKNIPRAVRQVFWRILLF 252 T G + +I M+V FS G+E+ +AAGESE+P+KN+ RA++ V R+++F Sbjct: 185 LTDHGGFMPNGISPVISGVMVVIFSLGGSEIAAVAAGESENPSKNVIRAIKSVILRVMVF 244 Query: 253 YVFAILIISLIIPYTDPSLLRNDVKDISVSPFTLVFQHAGLLSAAAVMNAVILTAVLSAG 312 YV ++ I+ L +P+TD + L+ SP+ +F AG AA M V+ + +S Sbjct: 245 YVGSVSILILCMPWTDKANLK--------SPYVSLFSMAGFTGAAVAMKIVLFVSFMSVM 296 Query: 313 NSGMYASTRMLYTLACDGKAPRIFAKLSRGGVPRNALYATTVIAGLCFLTSMFGNQTVYL 372 NS +++++RML++L+ G AP +F + + GVP NAL V+ ++L Sbjct: 297 NSFLFSNSRMLFSLSQRGHAPAMFGRTNAKGVPMNALVLCLVVCVSILGIHFLSGGDLFL 356 Query: 373 WLLNTSGMTGFIAWLGIAISHYRFRRGYVLQGHDINDLPYRSGFFPLGPIFAFILCLIIT 432 L +SG I W+ I ++H+ RR + D +R+ F+P+ A +L L+ Sbjct: 357 MLAKSSGAFVMIVWIFIIVAHFAMRRQTKHEQRD--PASFRAWFYPVSNWVA-LLALVAV 413 Query: 433 LG 434 LG Sbjct: 414 LG 415 Lambda K H 0.327 0.142 0.451 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: 674 Number of extensions: 37 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: 489 Length of database: 459 Length adjustment: 33 Effective length of query: 456 Effective length of database: 426 Effective search space: 194256 Effective search space used: 194256 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 (21.7 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