Align N-acetylglucosamine-specific PTS system, I, HPr, and IIA components (nagF) (characterized)
to candidate 5209394 Shew_1865 phosphoenolpyruvate-protein phosphotransferase (RefSeq)
Query= reanno::pseudo3_N2E3:AO353_04460 (838 letters) >FitnessBrowser__PV4:5209394 Length = 568 Score = 297 bits (761), Expect = 1e-84 Identities = 192/535 (35%), Positives = 287/535 (53%), Gaps = 17/535 (3%) Query: 310 AEEQLQALDRALEQVRSEIRETLSHAKKHKHTEEEQIFAAHLALLEDPALLEAAIQSIDQ 369 A EQ Q L+RAL+ + + + AK ++ Q+ A L LLED LL +I + Sbjct: 38 AREQ-QRLNRALKTLIKQSQACA--AKLDPESDNYQLIEADLLLLEDEELLAELSDTIGK 94 Query: 370 GS-AATHAWSQSIEAQCEVLQQLGNPLLAERANDLRDLRQRVLRALLGQDWHYD----VP 424 +A A S Q + +Q+ +P LA RA D+ L QR++R LL H D +P Sbjct: 95 RQFSAALAVEHSFAKQAQAMQEADSPYLARRAEDVLSLGQRLIRTLL--TGHCDNLSRLP 152 Query: 425 AGAIVAAHELTPSDLLQLSQQGVAGLCMAEGGATSHVAILARGKGLPCLVALSASLLQQP 484 AIV A ++TP++ L + V+ L + GG TSH AILAR G+P L++ L+ Sbjct: 153 ENAIVLAKDITPAEFATLPLERVSALVLQTGGVTSHTAILARSAGIPTLMSCPWQTLEVT 212 Query: 485 QGQSVVLDADGGRLELTPDSQRLEQVAQAQREHLQRRERQQAQAHTPAHTRDGLRIEVAA 544 G + +DA G L L PD +++ + +++ +R+ A T T+DG I + A Sbjct: 213 DGMVLAVDAINGELYLEPDETQIDDLNAQKQQADERKSALLALKGTVTQTKDGRSIPLLA 272 Query: 545 NVASSNEAADALKGGADGVGLLRTEFLFVDRQTAPDEQEQRQAYQAVLDAMGDKSVIIRT 604 NV +E GA+GVGL RTEFLF++ PDE Q Q Y L + K + IR+ Sbjct: 273 NVGCISEINHLADVGAEGVGLFRTEFLFMNNHELPDENRQYQLYCDALQLLDGKPLTIRS 332 Query: 605 IDVGGDKQLDYLPLPAEANPVLGLRGIRMAQVRPELLDQQLRALLQVSPLQRCRILLPMV 664 +D+G DK++ L + +E NP LGLRG+R P+L QL+A+L+ + R++ PMV Sbjct: 333 MDLGADKEVPTLAMDSEENPALGLRGVRYTLAHPKLFSAQLKAILRAANHGPIRLMFPMV 392 Query: 665 TEVDELLYIRQRLDALCAELALTQR----LELGVMIEVPAAALLAEQLAEHADFLSIGTN 720 +V+EL + L+ EL ++ LELG+++E PAA + DF+SIGTN Sbjct: 393 NQVEELEAVLALLELCKQELVEAEKGFGELELGIVVETPAAVFNLASMLPLLDFVSIGTN 452 Query: 721 DLSQYTLAMDRDHAGLAARVDALHPALLRLIAQTCIGAAKHQRWVGVCGALASDPLATPV 780 DL+QYT+A DR + L + L P ++RLIAQ A + V +CG LAS+P AT + Sbjct: 453 DLTQYTMAADRANPLLIDQYPVLSPVIIRLIAQIIEQAKAAKVRVSMCGELASNPSATAL 512 Query: 781 LIGLGISELSVSPPQVGEIKERVRQLDAADCRRFSATLLNLSSATAVRHA---CH 832 LIGLG+ E SV+ + E+K+ + + DC + L +S A+ CH Sbjct: 513 LIGLGLEEFSVNLASLLEVKQALSRWSYPDCVELAHKALQISRIDALNQLLTHCH 567 Lambda K H 0.318 0.133 0.379 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: 932 Number of extensions: 31 Number of successful extensions: 2 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: 568 Length adjustment: 39 Effective length of query: 799 Effective length of database: 529 Effective search space: 422671 Effective search space used: 422671 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: 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