Align D-trehalose PTS system, I, HPr, and IIA components (characterized)
to candidate CCNA_00892 CCNA_00892 phosphoenolpyruvate-protein phosphotransferase PtsP
Query= reanno::WCS417:GFF4500 (838 letters) >FitnessBrowser__Caulo:CCNA_00892 Length = 754 Score = 238 bits (607), Expect = 1e-66 Identities = 179/540 (33%), Positives = 252/540 (46%), Gaps = 18/540 (3%) Query: 271 LRGVCASPGSAFGQVVQVTDPELVITEQGTGGATERAALTRGLLAANEALQVLQDKAAGS 330 L+G + G A+G V P T E A LT + EALQ D+ Sbjct: 187 LKGSRFAEGLAYGVAVLHEQPVAPETLLSDDALAEEARLTYAI----EALQTQIDQML-E 241 Query: 331 AQAEIFRAHQELLEDPTLLEHA---HRLLGEGKSAAFAWNSATLATVTLFQG-LGNA--- 383 Q + A E+LE L H +R L E + +A + + LG A Sbjct: 242 GQHGLVGASYEVLETYRLFAHDRGWNRSLQEAVRSGLTAEAAVERVRSEHRARLGQARDP 301 Query: 384 LIAERAADLADVGQRVLKLILGIQDSAWDLPERAILIAEQLTPSQTASLDTRKVLGFVTV 443 + ER DL D+ R+L+ + G LPE AILIA L P+ D K+ G + Sbjct: 302 YLRERLHDLEDLNDRLLRHLSGDVHHVRQLPEDAILIARNLGPADLLEYDRTKLKGILLE 361 Query: 444 AGGATSHVAILARALGLPAICGVPAQVLALANGKQVLLDADKGELHLEPNLAEIEQLEAA 503 G A SH I+ARAL +P + + + G V++DA+ E L P ++ L+A Sbjct: 362 EGSAASHAGIVARALDIPCVGRLVGLRDRVNEGDPVVVDAETQEAWLRPRPDVVKALKAR 421 Query: 504 RKHQVLRHQRDVAQASLPATTRDGHHVEVTANVASLQEVEHALTLGGEGVGLLRSEFLYL 563 + + R P T+DG V + N +++ G EG+GL R+EF ++ Sbjct: 422 MEVRAQRKAEFARLRDTPPITKDGSKVTLLMNAGLAVDLDILGETGAEGIGLFRTEFQFM 481 Query: 564 DRNRAPSPEEQAGTYTAIARALGTERNLVVRTLDVGGDKPLAYVPMDAETNPFLGLRGIR 623 P E Q Y + A + RTLD+GGDK L Y+ ++ E NP LG R +R Sbjct: 482 VAEELPRLEAQTALYEKVLDA-ANGMPVTFRTLDLGGDKLLPYMELEREDNPALGWRAVR 540 Query: 624 LCLERPQLLREQFRAILASAGFARLHIMLPMVSLLSELHLARKILEEE---ALALGLTEL 680 + L+RP LLR Q RA++ +A L IM P+V+ + E AR +++E AL G Sbjct: 541 MGLDRPALLRMQIRALIKAANGRPLRIMFPLVANVDEFRAARSFVDQEVAWALKRGRPAP 600 Query: 681 PKL--GIMIEVPSAALMADVFAPHVDFFSIGTNDLTQYTLAMDRDHPRLANQADSFHPAV 738 +L G MIE PS D P DF S+GTNDL QY A DR +PR++++ D PA Sbjct: 601 ARLDVGAMIEAPSLLWHLDALLPMTDFVSVGTNDLMQYMFAADRGNPRVSDRYDPLSPAA 660 Query: 739 LRLIATTVKAAHAHGKWVGVCGALASEALAVPVLIGLGVDELSVSVPLIPTIKATVRELD 798 LR + T +A G V VCG +A L L+ LG D LS+ I +K V LD Sbjct: 661 LRALKTIQQACADTGTQVSVCGEMAGRPLEAFALVALGFDRLSMPPAGIGPVKQMVLSLD 720 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: 1228 Number of extensions: 65 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: 838 Length of database: 754 Length adjustment: 41 Effective length of query: 797 Effective length of database: 713 Effective search space: 568261 Effective search space used: 568261 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