Align D-trehalose PTS system, I, HPr, and IIA components (characterized)
to candidate WP_086509481.1 BZY95_RS08245 phosphoenolpyruvate-protein phosphotransferase PtsP
Query= reanno::WCS417:GFF4500 (838 letters) >NCBI__GCF_002151265.1:WP_086509481.1 Length = 753 Score = 303 bits (776), Expect = 2e-86 Identities = 203/612 (33%), Positives = 327/612 (53%), Gaps = 35/612 (5%) Query: 234 EDAEAAIKALVALLAEGCGEAVV--NVAEPVATQSSATLLRGVCASPGSAFGQVVQVTD- 290 E+ EA + + A LA A+ ++++P A + GV ASPG A G+VV V Sbjct: 137 EEDEAFLITMGAQLAGVLAHALATGSLSKPTLPGGQA-MFTGVPASPGMAIGEVVVVAPL 195 Query: 291 ------PELVITEQGTGGATERAALTRGLLAANEALQVLQDKAAGSAQAE---IFRAHQE 341 P+L+ T+ E A L + E ++ ++ A A+ +F +Q+ Sbjct: 196 ADLDSVPDLIPTDV----EHEIARLKEAIERVREEIRAAGERLANRISAQELALFEVYQQ 251 Query: 342 LLEDPTLLEHAHRLLGEGKSAAFAWNSATLATVTLFQGLGNALIAERAADLADVGQRVLK 401 +L + L + + + EG+ A A V + + + + ERAAD+ D+G+RVL Sbjct: 252 MLSEAALSQEVEKRIREGQWAPGALADVVRRHVQYLERVDDDYLRERAADVRDLGRRVLA 311 Query: 402 -LILGIQDSAWDLPERAILIAEQLTPSQTASLDTRKVLGFVTVAGGATSHVAILARALGL 460 L + + PE IL+ ++++ + + ++ G V+V G +TSHVAI+ARA+G+ Sbjct: 312 HLQEETPQTPANFPESTILVGDEISVAMLGEVPRERLAGLVSVRGSSTSHVAIVARAMGI 371 Query: 461 PAICGVPAQVLALANGKQVLLDADKGELHLEPN---LAEIEQL--EAARKHQVLRHQRDV 515 P + G+ L +G +V+LD +G L + P+ A L E A +VL H++D Sbjct: 372 PTVSGMVDLPLPRLSGAEVVLDGHRGRLFVRPSDELKARYSSLIAEEAALTEVLEHEQD- 430 Query: 516 AQASLPATTRDGHHVEVTANVASLQEVEHALTLGGEGVGLLRSEFLYLDRNRAPSPEEQA 575 LP+ T DGH + + N + +L GVGL R+E ++ R P +EQA Sbjct: 431 ----LPSETPDGHVMPLMVNTGLAIDTAASLKKRISGVGLYRTEVPFMIAERFPGEQEQA 486 Query: 576 GTYTAIARALGTERNLVVRTLDVGGDKPLAYVPMDAETNPFLGLRGIRLCLERPQLLREQ 635 Y + +V+RTLD+GGDK L Y P++ E NPFLG RGIR+ L+ P++L Q Sbjct: 487 RLYRDQLESFAP-LPVVMRTLDIGGDKDLPYFPIE-EANPFLGWRGIRVTLDHPEVLMVQ 544 Query: 636 FRAILASA-GFARLHIMLPMVSLLSELHLARKILEEEALALG----LTELPKLGIMIEVP 690 RA+L +A G L I+LPMV+ + E+ A ++L+ LG ++ P++G+M+EVP Sbjct: 545 LRAMLRAAQGLDNLQILLPMVTNVDEVDDALRLLDRAIRELGEEGVVSPRPRVGVMLEVP 604 Query: 691 SAALMADVFAPHVDFFSIGTNDLTQYTLAMDRDHPRLANQADSFHPAVLRLIATTVKAAH 750 + D A VDFFS+G+NDLTQY LA+DR++PR+A+ DS HPAVL +A + + Sbjct: 605 ATLYQLDALAERVDFFSVGSNDLTQYLLAVDRNNPRVASLYDSCHPAVLCAMARLAEESR 664 Query: 751 AHGKWVGVCGALASEALAVPVLIGLGVDELSVSVPLIPTIKATVRELDLADCQIIARQVL 810 K + VCG LA + +L+G+G D LS++ P +P ++A +R + + + + ++ L Sbjct: 665 RLKKPISVCGELAGDPAGALLLMGMGFDSLSMNAPSLPRVRAAIRRVSIDAAKALVQETL 724 Query: 811 GLEEAAEVREAL 822 L VR L Sbjct: 725 ALNTPVAVRSHL 736 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: 1205 Number of extensions: 55 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: 753 Length adjustment: 41 Effective length of query: 797 Effective length of database: 712 Effective search space: 567464 Effective search space used: 567464 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 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