Align N-acetylglucosamine-specific PTS system, I, HPr, and IIA components (nagF) (characterized)
to candidate H281DRAFT_01852 H281DRAFT_01852 Phosphocarrier protein HPr/phosphoenolpyruvate--protein phosphotransferase (EC 2.7.3.9)/PTS system IIA component, Glc family (TC 4.A.1)
Query= reanno::pseudo3_N2E3:AO353_04460 (838 letters) >FitnessBrowser__Burk376:H281DRAFT_01852 Length = 851 Score = 611 bits (1576), Expect = e-179 Identities = 358/841 (42%), Positives = 494/841 (58%), Gaps = 27/841 (3%) Query: 8 LTLSAPLSGPVLTLAKVPDPVFASGAMGDGIAIDPLNNTLHAPCAGVVVHVARTGHAVTL 67 + L APLSG ++ L VPDPVFA +GDGI+IDP ++ L +P G V + + HAVT+ Sbjct: 10 IELVAPLSGVMVPLETVPDPVFAQKMVGDGISIDPTSHELLSPLPGKVTQLHSSSHAVTI 69 Query: 68 RADNGAELLLHLGLDTVELQGEGFSMLVKEGTRVSNGQALLRFDLDQVAQGCKSLVSLLV 127 +G E+LLH+GLDTV L+GEGF+ LVKEG V+ GQ L+RFD V SL++ +V Sbjct: 70 TGASGLEVLLHIGLDTVLLRGEGFTPLVKEGDTVATGQPLIRFDPVYVGAKAASLLTQMV 129 Query: 128 LTNSEDF-QVLPITLKSVKVGEPLLHIVPRTTHSAQVEADSSGAEVHGHIRIIHRGGLHA 186 + N + + +P G+ L + + A ++GA V + + + G+HA Sbjct: 130 IANGDRVTRYVPAEGLVTAAGDVALTVELADDTAKDQTARTTGAIVSDEVTLPNPAGMHA 189 Query: 187 RPAALIRQTAHLFNSKSQLHFAGKSASCDSLIGLMGLGIGEQDEVQVSCKGADAKAALQA 246 RPAA+ A + S+ +L SA+ S++ +MGL D V++ G DA A Sbjct: 190 RPAAVFVGAAKKYESEIRLLHGSNSANAKSIVSIMGLATKFGDRVRIQATGPDAGEAASV 249 Query: 247 LLNALSTAVND---DSHAAAPTPIA------------QRTRTAEAGVLNGVCAAPGLVGG 291 L L+ + D+ A PT +A +R + A+ L GV A+PGL G Sbjct: 250 LARLLAEGSGEKPADAPAFPPTSLAPASGSSGEPAVVKRAQPADVNELTGVSASPGLAVG 309 Query: 292 PLFQLAAIPLPEDTGKHNAEEQLQALDRALEQVRSEIRETLSHAKKHKHTE--EEQIFAA 349 + Q + + + + L+ A + R I A K K T+ + QI A Sbjct: 310 KIVQFRQQVIDVKEAGESPQRERVRLEAAHHEARQNIE-----ALKAKLTDPSKAQILDA 364 Query: 350 HLALLEDPALLEAAIQSIDQGSAATHAWSQSIEAQCEVLQQLGNPLLAERANDLRDLRQR 409 HL LLEDP L AI SI +G +A AW + E Q L++L NPLL ERA D+RD+ +R Sbjct: 365 HLELLEDPDLNGMAIGSISEGKSAGFAWRAAFEQQAATLEKLDNPLLRERAGDVRDVGRR 424 Query: 410 VLRALLG-QDWHYDVPAGAIVAAHELTPSDLLQLSQQGVAGLCMAEGGATSHVAILARGK 468 VL L G Q DVPAG+I+ A EL+PSD L + V G C GGATSHVAILAR Sbjct: 425 VLALLAGMQQAQIDVPAGSILIAEELSPSDTASLDRTKVLGFCTTTGGATSHVAILARSL 484 Query: 469 GLPCLVALSASLLQQPQGQSVVLDADGGRLELTPDSQRLEQVAQAQREHLQRRERQQAQA 528 G+P + + LQ G VVLD G L P + +E+ + ++RE ++ A Sbjct: 485 GIPAICGIDEDALQLADGTLVVLDGSHGSLRRNPSAGEVEKARERISRQAEKREEEKLAA 544 Query: 529 HTPAHTRDGLRIEVAANVASSNEAADALKGGADGVGLLRTEFLFVDRQTAPDEQEQRQAY 588 A T DG R+EV AN+ ++ EA DA+ GA+GVGLLR+EFLF DR TAP E EQ Y Sbjct: 545 SKLAMTADGHRVEVVANIRNAKEARDAVAAGAEGVGLLRSEFLFDDRDTAPSEDEQASEY 604 Query: 589 QAVLDAMG-DKSVIIRTIDVGGDKQLDYLPLPAEANPVLGLRGIRMAQVRPELLDQQLRA 647 AV +A+G ++ ++IRT+D GGDK L Y+PLP E NP LGLRG+R++ RP++ QLRA Sbjct: 605 CAVAEALGRERPLVIRTLDAGGDKPLSYMPLPKEDNPFLGLRGVRVSLDRPDIFRTQLRA 664 Query: 648 LLQVSPLQRCRILLPMVTEVDELLYIRQRLDALCAELALTQRLELGVMIEVPAAALLAEQ 707 +L+ +P+ ++ PMV ++E+L ++ L + A +++GVMIEVPAAAL+AE Sbjct: 665 ILRAAPIGNLHVMFPMVAAIEEVLAAKKILLEEAGDRA--NSIKVGVMIEVPAAALIAEP 722 Query: 708 LAEHADFLSIGTNDLSQYTLAMDRDHAGLAARVDALHPALLRLIAQTCIGAAKHQRWVGV 767 LA DF SIGTNDL+QYTLAMDR H LA + DALHPA+LRLI T GA KH +WVGV Sbjct: 723 LAREVDFFSIGTNDLTQYTLAMDRGHPKLARQADALHPAVLRLIGMTVEGAHKHGKWVGV 782 Query: 768 CGALASDPLATPVLIGLGISELSVSPPQVGEIKERVRQLDAADCRRFSATLLNLSSATAV 827 CG +ASD +A PVL+GLG+ ELSVS P VG IK ++ +L A R+ +A ++ L +A V Sbjct: 783 CGGIASDAIAVPVLVGLGVDELSVSVPAVGSIKAQLARLTMAQARQLAAEVVRLGTAAEV 842 Query: 828 R 828 R Sbjct: 843 R 843 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: 1539 Number of extensions: 74 Number of successful extensions: 6 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: 851 Length adjustment: 42 Effective length of query: 796 Effective length of database: 809 Effective search space: 643964 Effective search space used: 643964 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: 56 (26.2 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