Align D-trehalose PTS system, I, HPr, and IIA components (characterized)
to candidate PP_5145 PP_5145 phosphoenolpyruvate-dependent regulator (with NPR and NTR proteins)
Query= reanno::WCS417:GFF4500 (838 letters) >FitnessBrowser__Putida:PP_5145 Length = 759 Score = 294 bits (753), Expect = 1e-83 Identities = 189/569 (33%), Positives = 300/569 (52%), Gaps = 27/569 (4%) Query: 273 GVCASPGSAFGQVVQVTDP---ELVITEQGTGGATERAALTRGLLAANEALQVLQDKAAG 329 GV SPG+A G+ V + P E+V + E L + ++ L K A Sbjct: 180 GVPGSPGAAVGRAVVMLPPADLEVVPDKTVDDIDAELKLFQNALEGVRDDMRKLSAKLAT 239 Query: 330 SAQAE---IFRAHQELLEDPTLLEHAHRLLGEGKSAAFAWNSATLATVTLFQGLGNALIA 386 + E +F + +LED L ++ G+ A A V F+ + + + Sbjct: 240 QLRPEERALFDVYLMMLEDAALGGEVTEVIKTGQWAQGALRQVVGEHVNRFELMDDDYLR 299 Query: 387 ERAADLADVGQRVLKLILGIQDSAWDLPERAILIAEQLTPSQTASLDTRKVLGFVTVAGG 446 ERA+D+ D+G+R+L + + + + IL++E+LTP+ + K++G V+V G Sbjct: 300 ERASDVKDLGRRLLAYLQEARSQSLVYADNTILVSEELTPAMLGEVPEGKLVGLVSVLGS 359 Query: 447 ATSHVAILARALGLPAICGVPAQVLALANGKQVLLDADKGELHLEPNLAEIEQLEAARKH 506 SHVAILARA+G+P + G+ + +G ++++D KGE+ P+ E RK Sbjct: 360 GNSHVAILARAMGIPTVMGLVDLPYSKVDGIELIVDGYKGEVFTNPS-------EVLRKQ 412 Query: 507 --QVLRHQRDVAQA-----SLPATTRDGHHVEVTANVASLQEVEHALTLGGEGVGLLRSE 559 +V+ +R +AQ LP T DGH + + N L +V A G EGVGL R+E Sbjct: 413 YSEVVEEERQLAQGLDALRELPCVTPDGHRMPLWVNTGLLADVARAQQRGAEGVGLYRTE 472 Query: 560 FLYLDRNRAPSPEEQAGTYTAIARALGTERNLVVRTLDVGGDKPLAYVPMDAETNPFLGL 619 ++ R PS +EQ Y A + +RTLD+GGDK L+Y P+ E NPFLG Sbjct: 473 VPFMINQRFPSEKEQLAIYREQLAAFHP-LPVTMRTLDIGGDKALSYFPIKEE-NPFLGW 530 Query: 620 RGIRLCLERPQLLREQFRAIL-ASAGFARLHIMLPMVSLLSEL----HLARKILEEEALA 674 RGIR+ L+ P++ Q RA+L AS G L I+LPM+S + EL HL + E Sbjct: 531 RGIRVTLDHPEIFLVQTRAMLKASEGLNNLRILLPMISGIHELEEALHLIHRAWGEVRDE 590 Query: 675 LGLTELPKLGIMIEVPSAALMADVFAPHVDFFSIGTNDLTQYTLAMDRDHPRLANQADSF 734 +P +G+M+E+P+A A VDF S+G+NDLTQY LA+DR++PR+A+ D Sbjct: 591 GTDVPMPPVGVMVEIPAAVYQTKELARQVDFLSVGSNDLTQYLLAVDRNNPRVADLYDYL 650 Query: 735 HPAVLRLIATTVKAAHAHGKWVGVCGALASEALAVPVLIGLGVDELSVSVPLIPTIKATV 794 HPAVL+ + T V+ AH GK V +CG +A + A +L+ +G D LS++ +P +K + Sbjct: 651 HPAVLQALNTVVRDAHGEGKPVSICGEMAGDPAAAVLLMAMGFDSLSMNATNLPKVKWML 710 Query: 795 RELDLADCQIIARQVLGLEEAAEVREALR 823 R++++ + + + L + + +L+ Sbjct: 711 RQINMGKAKELLAEALSHDNPQVIHSSLQ 739 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: 1217 Number of extensions: 65 Number of successful extensions: 8 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: 759 Length adjustment: 41 Effective length of query: 797 Effective length of database: 718 Effective search space: 572246 Effective search space used: 572246 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