Align N-acetylglucosamine-specific PTS system, I, HPr, and IIA components (nagF) (characterized)
to candidate PfGW456L13_4832 PTS system, glucose-specific IIA component / Phosphotransferase system, phosphocarrier protein HPr / Phosphoenolpyruvate-protein phosphotransferase of PTS system (EC 2.7.3.9)
Query= reanno::pseudo3_N2E3:AO353_04460 (838 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_4832 Length = 838 Score = 1364 bits (3530), Expect = 0.0 Identities = 704/838 (84%), Positives = 748/838 (89%) Query: 1 MHNNNKDLTLSAPLSGPVLTLAKVPDPVFASGAMGDGIAIDPLNNTLHAPCAGVVVHVAR 60 MHNNNK+LTLSAPLSGPVLTLAKVPD VFASGAMGDGIAIDPLN+TLHAPCAGVVVHVAR Sbjct: 1 MHNNNKELTLSAPLSGPVLTLAKVPDAVFASGAMGDGIAIDPLNDTLHAPCAGVVVHVAR 60 Query: 61 TGHAVTLRADNGAELLLHLGLDTVELQGEGFSMLVKEGTRVSNGQALLRFDLDQVAQGCK 120 TGHAVTLRADNGAELLLHLGLDTVELQG+GFSMLVKEG RVSNGQ LLR+DLD+VAQ CK Sbjct: 61 TGHAVTLRADNGAELLLHLGLDTVELQGQGFSMLVKEGARVSNGQPLLRYDLDKVAQQCK 120 Query: 121 SLVSLLVLTNSEDFQVLPITLKSVKVGEPLLHIVPRTTHSAQVEADSSGAEVHGHIRIIH 180 SLVSLL+LTNS+DFQ PITLKSVKVGEPLLHI+ R AQ + + +G EV GHIRI H Sbjct: 121 SLVSLLILTNSQDFQARPITLKSVKVGEPLLHIIRRQGVGAQADVELAGEEVVGHIRIAH 180 Query: 181 RGGLHARPAALIRQTAHLFNSKSQLHFAGKSASCDSLIGLMGLGIGEQDEVQVSCKGADA 240 RGGLHARPAALIRQTA F SKSQLHFAGKSA+CDSLIGLMGL IGEQ EVQVSC+G DA Sbjct: 181 RGGLHARPAALIRQTAQGFKSKSQLHFAGKSATCDSLIGLMGLAIGEQAEVQVSCQGPDA 240 Query: 241 KAALQALLNALSTAVNDDSHAAAPTPIAQRTRTAEAGVLNGVCAAPGLVGGPLFQLAAIP 300 +AALQALL ALSTA+ +DSHAAAPT IAQR R AEAGVL+GVCAAPGLVGGPLF L AI Sbjct: 241 EAALQALLTALSTALAEDSHAAAPTTIAQRNRPAEAGVLHGVCAAPGLVGGPLFHLNAIS 300 Query: 301 LPEDTGKHNAEEQLQALDRALEQVRSEIRETLSHAKKHKHTEEEQIFAAHLALLEDPALL 360 LP D G H+ ++Q Q LD AL QVRSEI TL AKKHK T EE IFAAHLALLEDPALL Sbjct: 301 LPVDAGHHDPQQQQQVLDAALSQVRSEIERTLVLAKKHKDTAEEAIFAAHLALLEDPALL 360 Query: 361 EAAIQSIDQGSAATHAWSQSIEAQCEVLQQLGNPLLAERANDLRDLRQRVLRALLGQDWH 420 +AAIQ++ QG+AATHAWSQ+I+ QCEVLQQ G+ LLAERANDLRDL+QRVLRALLG WH Sbjct: 361 DAAIQTVAQGTAATHAWSQAIDVQCEVLQQTGSTLLAERANDLRDLKQRVLRALLGDTWH 420 Query: 421 YDVPAGAIVAAHELTPSDLLQLSQQGVAGLCMAEGGATSHVAILARGKGLPCLVALSASL 480 YDVPAGAIVAAHELTPSDLLQLSQQGVAGLCMAEGGATSHVAILARGKGLPC+VAL ++L Sbjct: 421 YDVPAGAIVAAHELTPSDLLQLSQQGVAGLCMAEGGATSHVAILARGKGLPCMVALGSTL 480 Query: 481 LQQPQGQSVVLDADGGRLELTPDSQRLEQVAQAQREHLQRRERQQAQAHTPAHTRDGLRI 540 L Q QGQ VVLDADGGRLELTP ++RL V Q Q++ QRR QQAQAHTPA T DGLRI Sbjct: 481 LDQQQGQPVVLDADGGRLELTPSAERLADVRQLQQQQQQRRAEQQAQAHTPALTTDGLRI 540 Query: 541 EVAANVASSNEAADALKGGADGVGLLRTEFLFVDRQTAPDEQEQRQAYQAVLDAMGDKSV 600 EVAANVASS EAADAL GADGVGLLRTEFLFVDR TAPDEQEQ AYQAVLDAMGDKSV Sbjct: 541 EVAANVASSTEAADALANGADGVGLLRTEFLFVDRHTAPDEQEQHHAYQAVLDAMGDKSV 600 Query: 601 IIRTIDVGGDKQLDYLPLPAEANPVLGLRGIRMAQVRPELLDQQLRALLQVSPLQRCRIL 660 IIRTIDVGGDKQLDYLPLPAEANPVLGLRGIR+AQ RPELLDQQLRALL + PL RCRIL Sbjct: 601 IIRTIDVGGDKQLDYLPLPAEANPVLGLRGIRLAQARPELLDQQLRALLHLRPLSRCRIL 660 Query: 661 LPMVTEVDELLYIRQRLDALCAELALTQRLELGVMIEVPAAALLAEQLAEHADFLSIGTN 720 LPMVTEVDELL+I QRLDALC EL L QR ELGVMIEVPAAALLAEQLAEHADFLSIGTN Sbjct: 661 LPMVTEVDELLHIHQRLDALCGELGLAQRPELGVMIEVPAAALLAEQLAEHADFLSIGTN 720 Query: 721 DLSQYTLAMDRDHAGLAARVDALHPALLRLIAQTCIGAAKHQRWVGVCGALASDPLATPV 780 DLSQYTLAMDRDHAGLAARVDALHPALLRLIAQTC GAA+H RWVGVCGALASDPLATPV Sbjct: 721 DLSQYTLAMDRDHAGLAARVDALHPALLRLIAQTCAGAAQHNRWVGVCGALASDPLATPV 780 Query: 781 LIGLGISELSVSPPQVGEIKERVRQLDAADCRRFSATLLNLSSATAVRHACHQHWPLS 838 LIGLG+SELSVSP QVGEIK+RVR LDA++CRR S LL LSSA+AVRHACHQHWPLS Sbjct: 781 LIGLGVSELSVSPVQVGEIKDRVRHLDASECRRISQGLLKLSSASAVRHACHQHWPLS 838 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: 2100 Number of extensions: 83 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: 838 Length adjustment: 42 Effective length of query: 796 Effective length of database: 796 Effective search space: 633616 Effective search space used: 633616 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