Align D-trehalose PTS system, I, HPr, and IIA components (characterized)
to candidate GFF475 HP15_463 fused phosphoenolpyruvate-protein phosphotransferase PtsP/GAF domain protein
Query= reanno::WCS417:GFF4500 (838 letters) >FitnessBrowser__Marino:GFF475 Length = 768 Score = 288 bits (738), Expect = 6e-82 Identities = 184/545 (33%), Positives = 297/545 (54%), Gaps = 31/545 (5%) Query: 273 GVCASPGSAFGQ-VVQVTDPEL-VITEQGTGGATERAALT-RGLLAANEALQVLQDKAAG 329 GV +PG A G VV +L V+ E+ T + AL + A E ++ + + A Sbjct: 181 GVPGAPGVAIGNGVVVYPSADLDVVPEKPTDDIDQELALFGASVKAVREDIERVAKRLAS 240 Query: 330 SAQAE---IFRAHQELLEDPTLLEHAHRLLGEGKSAAFAWNSATLATVTLFQGLGNALIA 386 + E +F + +L D + + EG A A + F+ + + + Sbjct: 241 QLRPEEQALFDVYLRMLGDDAMPGEVSNKIREGIWAQGALKQVVQQYIRHFEMMDDHYLQ 300 Query: 387 ERAADLADVGQRVLKLILGIQDSAWDLPERAILIAEQLTPSQTASLDTRKVLGFVTVAGG 446 ERA D+ D+G+R+L + + + PER +L++E+LTP+ + +++G V+V G Sbjct: 301 ERAVDIRDLGRRLLSHLQEGEQKHLNYPERTVLVSEELTPAMLGEVPKGQLVGLVSVKGS 360 Query: 447 ATSHVAILARALGLPAICGVPAQVLALANGKQVLLDADKGELHLEPNLAEI--------- 497 + SHVAILARA+G+P + G+ + +GK++++D +G++ P+ A++ Sbjct: 361 SNSHVAILARAMGVPTVMGLVDIPVNQLDGKELIVDGFEGQIFASPS-ADLRSYYQAICD 419 Query: 498 EQLEAARKHQVLRHQRDVAQASLPATTRDGHHVEVTANVASLQEVEHALTLGGEGVGLLR 557 E+ E R +VL+ + P T D H V + N + +V +L+ G EG+GL R Sbjct: 420 EEDELIRGLEVLKDK--------PCETTDHHRVSLLVNTGLMTDVVRSLSHGAEGIGLYR 471 Query: 558 SEFLYLDRNRAPSPEEQAGTYTAIARALGTERNLVVRTLDVGGDKPLAYVPMDAETNPFL 617 +E ++ ++R PS +EQ Y A + +RTLD+GGDK L Y P+ E NPFL Sbjct: 472 TEVPFMIKDRFPSEQEQREYYREQLEAFAPSP-VTMRTLDIGGDKALTYFPIQEE-NPFL 529 Query: 618 GLRGIRLCLERPQLLREQFRAIL-ASAGFARLHIMLPMVSLLSE----LHLARKILEEEA 672 G RGIR+ L+ P++ Q RA+L AS G L IMLPM+S +SE LHL ++ E Sbjct: 530 GWRGIRVTLDHPEIFLVQVRAMLKASEGLNNLQIMLPMISNISEVEESLHLIYRVYHEVR 589 Query: 673 LALGLTELPKLGIMIEVPSAALMADVFAPHVDFFSIGTNDLTQYTLAMDRDHPRLANQAD 732 +PK+G+M+E+P+A A VDF S+G+NDLTQY LA+DR++PR+A Sbjct: 590 EEGYDIHMPKVGVMVEIPAAVYQIRELADRVDFLSVGSNDLTQYLLAVDRNNPRVAQLYH 649 Query: 733 SFHPAVLRLIATTVKAAHAHGKWVGVCGALASEALAVPVLIGLGVDELSVSVPLIPTIKA 792 S+HPAVL+ + + AH+ GK VG+CG LA + +L+ +G D LS++ +P +K+ Sbjct: 650 SYHPAVLQALVRIAQDAHSVGKPVGICGELAGDPGGALLLMAMGYDSLSMNAASLPKVKS 709 Query: 793 TVREL 797 +R + Sbjct: 710 VIRSV 714 Lambda K H 0.318 0.133 0.371 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: 1194 Number of extensions: 60 Number of successful extensions: 7 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: 838 Length of database: 768 Length adjustment: 41 Effective length of query: 797 Effective length of database: 727 Effective search space: 579419 Effective search space used: 579419 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 55 (25.8 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