Align N-acetylglucosamine-specific PTS system, I, HPr, and IIA components (nagF) (characterized)
to candidate 6936677 Sama_0864 phosphoenolpyruvate-protein phosphotransferase PtsP (RefSeq)
Query= reanno::pseudo5_N2C3_1:AO356_17540 (837 letters) >FitnessBrowser__SB2B:6936677 Length = 744 Score = 278 bits (710), Expect = 1e-78 Identities = 191/556 (34%), Positives = 292/556 (52%), Gaps = 14/556 (2%) Query: 280 GVCAAPGLVTGPLVRLSGIQLPEDIGGHAIEEQRQRLSDALAQVRGEIHLTLEHARARQH 339 GV A LV G + L + PE ++ + RL A+ + R + L H Sbjct: 178 GVAIAHALVIGGEISL---EQPEACATD-VDAEVNRLRLAMGRSRDAL-TALAQKFENDH 232 Query: 340 RDE-EAIFSAHLALLEDPVLLDAADLFIEQGSAAPHAWSRSIDTQCQVLQQLGSTLLAER 398 DE +IF++ +LLED L + G +A A SR + + L ER Sbjct: 233 DDELSSIFTSLQSLLEDASLGGEYQREVLAGWSAETAVSRVSLRYVAQFETMEDAYLRER 292 Query: 399 ANDLRDLRQRVLRVLLGEA-WQFDVAAGAIVAAQELTPSDLLQLSAQGVAGVCMVEGGAT 457 A+D+RDL QRVLR L+ D I+ +E S L + Q +AG+ GG Sbjct: 293 ASDIRDLGQRVLRQLIEPGRMMLDPDKPVILVTREADTSMLAEFPRQKLAGIVTEAGGVN 352 Query: 458 SHVAILARGKGLPCLVALGDELLAQEQGQAVVLDADGGRLELTPTVERLAQVRQAQTRRT 517 SH AILAR G+P ++ + L A Q +VL+A G L ++P+ + + R + + Sbjct: 353 SHAAILARALGVPAIMGVEQVLQANLDKQLLVLNASRGILMVSPSPTVVDEYRNLISAQK 412 Query: 518 ALRAQQQSLAHTPARTVDGVEVEVAANVASSAEAGESLANGADGVGLLRTEFLFVDRHTA 577 AL Q PA T+DG + + N + +A+GADGVGL RTE F+ + Sbjct: 413 ALDRQYAEELKEPALTLDGHRIHLYLNAGLMSGVSSEIADGADGVGLYRTEIPFMLQQRF 472 Query: 578 PDEEEQRQAYQAVLEAMGDKPVIIRTIDVGGDKQLDYLPLPSEANPVLGLRGIRLAQVRP 637 P E EQ + Y++VL++ +PV++RT+DVGGDK L Y P+ SE NP LG RGIRL+ P Sbjct: 473 PSESEQIKVYRSVLQSAAGRPVVMRTLDVGGDKPLPYFPI-SEENPFLGWRGIRLSLDHP 531 Query: 638 DLLDQQLRALLQTR-PLDRCRILLPMVTEVDELLHIRKRLDALGSELGLS-----ERPQL 691 +L QLRA+LQ D +ILLPMV+ +DE+ LD SEL RP + Sbjct: 532 ELFLVQLRAMLQAAGDTDNLKILLPMVSSLDEIDEALLYLDQAFSELRADVNPSLARPPV 591 Query: 692 GVMVEVPAAALLAEQLAEHADFLSIGTNDLSQYTLAMDRDHAGLAARVDALHPALLRLIA 751 GVM+EVPA ++A+ +F+S+G+NDL+QY LA+DR++ +++ D+ HP +LR + Sbjct: 592 GVMLEVPALLYQLREVAQRVEFVSVGSNDLTQYLLAVDRNNPRVSSLYDSYHPGVLRALQ 651 Query: 752 QTCAGAAKHGRWVGVCGALASDPLATPVLIGLGVRELSVSPPQIGEIKDRVRHLDAAQCA 811 +H V VCG LA +P+ +L+ +G ELS++ + +I +R ++ ++ Sbjct: 652 LALQECRQHKLDVSVCGELAGEPMGALLLVAMGYDELSMNQGSLAKINYLLRRVERSELE 711 Query: 812 RLSNELLNLGSALAVR 827 +L ++ + + VR Sbjct: 712 QLLALVMQMSNGQDVR 727 Lambda K H 0.319 0.134 0.386 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: 1031 Number of extensions: 41 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: 837 Length of database: 744 Length adjustment: 41 Effective length of query: 796 Effective length of database: 703 Effective search space: 559588 Effective search space used: 559588 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 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