Align N-acetylglucosamine-specific PTS system, I, HPr, and IIA components (nagF) (characterized)
to candidate WP_106711077.1 CU102_RS10565 phosphoenolpyruvate--protein phosphotransferase
Query= reanno::pseudo3_N2E3:AO353_04460 (838 letters) >NCBI__GCF_003010955.1:WP_106711077.1 Length = 746 Score = 253 bits (645), Expect = 4e-71 Identities = 153/507 (30%), Positives = 259/507 (51%), Gaps = 9/507 (1%) Query: 313 QLQALDRALEQVRSEIRETLSHAKKHKHTEEEQIFAAHLALLEDPALLEAAIQSIDQGSA 372 ++ L+ +L +R I + LS E ++ A+ D + ++I G Sbjct: 207 EIDRLESSLGSLRISIDDMLSRRDVAFEGEHREVLEAYRMFAHDTGWVRRLEEAIRNGLT 266 Query: 373 ATHAWSQSIEAQCEVLQQLGNPLLAERANDLRDLRQRVLRALLGQDWHY---DVPAGAIV 429 A A + + L +P + ER +D DL R+LR L+G+D + A++ Sbjct: 267 AEAAVEKVQSDTRARMMHLTDPYMRERLSDFDDLANRLLRQLMGRDVKTMAGSLAKDAVI 326 Query: 430 AAHELTPSDLLQLSQQGVAGLCMAEGGATSHVAILARGKGLPCLVALSASLLQQPQGQSV 489 A + ++LL ++ + GL + +G ATSHV I+AR G+P + + +V Sbjct: 327 IARSMGAAELLDYPRERLRGLVLEDGAATSHVVIVARAMGIPVAGQVKGVVSMAENNDAV 386 Query: 490 VLDADGGRLELTPDSQRLEQVAQAQREHLQRRERQQAQAHTPAHTRDGLRIEVAANVASS 549 ++D D GR+ L P S ++ R +R+ + P+ ++DG+ I + N Sbjct: 387 IVDGDDGRVHLRPQSDVEAAYSEKVRFRAKRQALYRELRDKPSVSKDGISISLLMNAGLL 446 Query: 550 NEAADALKGGADGVGLLRTEFLFVDRQTAPDEQEQRQAYQAVLDAMGDKSVIIRTIDVGG 609 + + GA G+GL RTE F+ T P ++Q + Y++VL+A GD+ V RT+D+GG Sbjct: 447 VDLPQLAEAGAAGIGLFRTELQFMVASTFPRAEQQERLYRSVLEAAGDRPVTFRTLDIGG 506 Query: 610 DKQLDYLPLPA-EANPVLGLRGIRMAQVRPELLDQQLRALLQVSPLQRCRILLPMVTEVD 668 DK L Y E NP +G R +R+ RP LL Q+RALL+ + + R++LPMVTEV Sbjct: 507 DKVLPYFRSNVKEENPAMGWRALRLTLDRPGLLRTQVRALLKAAGGRELRLMLPMVTEVA 566 Query: 669 ELLYIRQRLDALCAELA-----LTQRLELGVMIEVPAAALLAEQLAEHADFLSIGTNDLS 723 E+ + ++ L+ L R+++G M+EVP+ ++L DF+S+G+NDL Sbjct: 567 EVRKASELINREVQHLSRFAYDLPTRVKIGAMVEVPSLLWQLDELMSVVDFVSVGSNDLF 626 Query: 724 QYTLAMDRDHAGLAARVDALHPALLRLIAQTCIGAAKHQRWVGVCGALASDPLATPVLIG 783 Q+ +A+DR ++ + R D L LR++ Q ++ V +CG +A PL+ L+G Sbjct: 627 QFVMAVDRGNSMITNRFDNLSVPFLRVLRQISEAGERNHTDVTLCGEMAGKPLSAMALLG 686 Query: 784 LGISELSVSPPQVGEIKERVRQLDAAD 810 LG +S+SP +G +K + LD + Sbjct: 687 LGFRSISMSPAAIGPVKAMLGTLDIGE 713 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: 1115 Number of extensions: 46 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: 838 Length of database: 746 Length adjustment: 41 Effective length of query: 797 Effective length of database: 705 Effective search space: 561885 Effective search space used: 561885 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 24 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