Align Fructose PTS system (E-I, HPr, and E-IIA components) (characterized)
to candidate 206257 DVU0829 phosphoenolpyruvate-protein phosphotransferase
Query= reanno::azobra:AZOBR_RS32325 (846 letters) >MicrobesOnline__882:206257 Length = 590 Score = 325 bits (833), Expect = 5e-93 Identities = 198/573 (34%), Positives = 310/573 (54%), Gaps = 28/573 (4%) Query: 283 GIAASPGLAIGPVHVLPRAAVSVPDEPVPLIEGGDRLHEALSLTRQNLKALAD-DTARRL 341 GIA S G++IG + R+ S + +I+ G E L + +D D AR Sbjct: 8 GIAVSSGISIGKAFFMDRSRQSAAHD---IIQPGAAESEVARLDEAAAQVASDLDRARAQ 64 Query: 342 GPSE----AAIFAAQAEILNDTDLVTLACQLMVEGH-GVAWSWHQAVERTAAGLAALDNP 396 P++ AAI + I D L+ A + + E + W+ QAV+ A A+D+P Sbjct: 65 VPADLRDHAAIIDSHRMICRDPKLMGDAARRIREQNISAPWALEQAVDAIAQAFRAIDDP 124 Query: 397 VLAARAADLRDVGQRVLARIDPALRTGGAPDLPDTP--CILIAEDLSPSDTAALDMARVI 454 + R D+R V +R+L+R+ G A +L T +L+A DL+P+DT L ++R++ Sbjct: 125 YIRERVQDVRAVAERILSRL-----AGNARELKSTGERMVLLAHDLTPADTIELQVSRIM 179 Query: 455 GLATAQGGPTSHTAILARTLGLPAMVAGGAALMELANGTPAILDGQSGRLHLSPAAADIA 514 ATA+GG TSHT ILAR+L +PA+V A+G I+D GR+ + P ++A Sbjct: 180 SFATAEGGKTSHTGILARSLQIPAVVGVSGLEEATADGDLVIIDALRGRILIDPDEHELA 239 Query: 515 DARAWIAREEARKAEEEARRGLPARTRDGHEVEIGANVNRPDQVAVALSQGAESVGLMRT 574 + + E+ + + LPA T DG+ +E+ +N+ ++V L GA+ VGL RT Sbjct: 240 EYTELKYQFESYQRSIRRQSTLPAETLDGYRIEVQSNIELLEEVPQVLDSGADGVGLYRT 299 Query: 575 EFLFLERGDAPGEDEQYETYRGMLTALEGRPLIVRALDIGGDKQVPHLQLPHEENPFLGV 634 E+ FL R P E + + Y + + R ++ R LD+G DK + E NP LG+ Sbjct: 300 EYAFLARRQPPSEQDLCDEYSQVAALMSPRQVVFRTLDVGADKMLREQVRMEEPNPALGL 359 Query: 635 RGARLLLRRPELLETQLRALYRAAKDGGAKDGGALSIMFPMITALGEVQALRAACERIRA 694 R R LR ++ TQLRA+ RA+ G ++++FPMI+ + E++ R + +R Sbjct: 360 RAIRFCLRHQDVFRTQLRAILRASVHGN------VALLFPMISGIQELRQARHILQEVRQ 413 Query: 695 ELD------APAVPLGIMVEVPAAAIQADVLARHVDFFSIGTNDLTQYALAIDRQHPELA 748 ELD AP +P+GIMVE+P+A + AD LA VDFFSIGTNDL QY+L IDR + ++ Sbjct: 414 ELDAEGIPHAPDMPVGIMVELPSAVLIADALAHEVDFFSIGTNDLIQYSLGIDRGNRHVS 473 Query: 749 AEADSLHPAVLRLIRLTVEGAERHGRWVGVCGGIAGDPFGAALLTGLGVRELSMTPRDIP 808 LHPA++R I+L V+ A R G V VCG +A DPF +L G+ + +S+ P+ +P Sbjct: 474 YLYQPLHPAIVRSIKLVVDSAHRAGISVSVCGEVASDPFCLPILMGMQIDSISIAPQAVP 533 Query: 809 AVKDRLRGSDLSALKDAAQRALDCETADAVRAL 841 +K +R +++ K + L+ T + + Sbjct: 534 GIKHIIRKTNMEECKTLTRDVLNATTVSTINRM 566 Lambda K H 0.319 0.134 0.387 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: 951 Number of extensions: 42 Number of successful extensions: 5 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: 846 Length of database: 590 Length adjustment: 39 Effective length of query: 807 Effective length of database: 551 Effective search space: 444657 Effective search space used: 444657 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 54 (25.4 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