Align N-acetylglucosamine-specific PTS system, I, HPr, and IIA components (nagF) (characterized)
to candidate 206257 DVU0829 phosphoenolpyruvate-protein phosphotransferase
Query= reanno::BFirm:BPHYT_RS02740 (854 letters) >MicrobesOnline__882:206257 Length = 590 Score = 322 bits (826), Expect = 3e-92 Identities = 200/571 (35%), Positives = 293/571 (51%), Gaps = 9/571 (1%) Query: 288 LAPNTLAGVCAAPGVAVGKLVRWDDADIDPPEKANGTSAAESRL--LDKAIATVDADLDT 345 +A L G+ + G+++GK D + AAES + LD+A A V +DLD Sbjct: 1 MARGILYGIAVSSGISIGKAFFMDRSRQSAAHDIIQPGAAESEVARLDEAAAQVASDLDR 60 Query: 346 TVRDASQRGAVGEAGIFSVHRVLLEDPTLL-DAARDLISLGKSAGFAWREAIRAQIAILT 404 R A I HR++ DP L+ DAAR + SA +A +A+ A Sbjct: 61 A-RAQVPADLRDHAAIIDSHRMICRDPKLMGDAARRIREQNISAPWALEQAVDAIAQAFR 119 Query: 405 NIEDALLAERAADLRDIEKRVLRALGYTSATARTLPEEAVLAAEEFTPSDLSTLDRSRVT 464 I+D + ER D+R + +R+L L + ++ E VL A + TP+D L SR+ Sbjct: 120 AIDDPYIRERVQDVRAVAERILSRLAGNARELKSTGERMVLLAHDLTPADTIELQVSRIM 179 Query: 465 ALVMARGGATSHAAILARQAGIPALVAVGDALHAIPEGTQVVVNATTGRLEFAPTELDVE 524 + A GG TSH ILAR IPA+V V A +G V+++A GR+ P E ++ Sbjct: 180 SFATAEGGKTSHTGILARSLQIPAVVGVSGLEEATADGDLVIIDALRGRILIDPDEHELA 239 Query: 525 RARLERTRLADVREANRRTSQQAAVTSDGRAIEVAANIATLDDAKTAVENGADSVGLLRT 584 + + + + RR S A T DG IEV +NI L++ +++GAD VGL RT Sbjct: 240 EYTELKYQFESYQRSIRRQSTLPAETLDGYRIEVQSNIELLEEVPQVLDSGADGVGLYRT 299 Query: 585 ELLFIHRAAAPTTDEHRQSYQAIVDALSGRTAIIRTLDVGADKEVDYLTLPPEPNPALGL 644 E F+ R P+ + Y + +S R + RTLDVGADK + EPNPALGL Sbjct: 300 EYAFLARRQPPSEQDLCDEYSQVAALMSPRQVVFRTLDVGADKMLREQVRMEEPNPALGL 359 Query: 645 RGIRLAQVRPDLLDDQLRGLLAVQPLGAVRILLPMVTDVGELIRIRKRIDEFARELG--- 701 R IR D+ QLR +L G V +L PM++ + EL + R + E +EL Sbjct: 360 RAIRFCLRHQDVFRTQLRAILRASVHGNVALLFPMISGIQELRQARHILQEVRQELDAEG 419 Query: 702 --RTEPIEVGVMIEVPSAALLADQLAQHADFLSIGTNDLTQYTLAMDRCQADLAAQADGL 759 + VG+M+E+PSA L+AD LA DF SIGTNDL QY+L +DR ++ L Sbjct: 420 IPHAPDMPVGIMVELPSAVLIADALAHEVDFFSIGTNDLIQYSLGIDRGNRHVSYLYQPL 479 Query: 760 HPAVLRLIAATVQGADKHGKWVGVCGALAGDPLAMPLLVGLGVTELSVDPVSVPGIKARV 819 HPA++R I V A + G V VCG +A DP +P+L+G+ + +S+ P +VPGIK + Sbjct: 480 HPAIVRSIKLVVDSAHRAGISVSVCGEVASDPFCLPILMGMQIDSISIAPQAVPGIKHII 539 Query: 820 RNLDYQLCRQRAQDALALESAQAVRAASRET 850 R + + C+ +D L + + +ET Sbjct: 540 RKTNMEECKTLTRDVLNATTVSTINRMVKET 570 Lambda K H 0.317 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: 1018 Number of extensions: 41 Number of successful extensions: 3 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: 854 Length of database: 590 Length adjustment: 39 Effective length of query: 815 Effective length of database: 551 Effective search space: 449065 Effective search space used: 449065 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