Align Fructose-specific PTS system, I, HPr, and IIA components (characterized)
to candidate WP_007154627.1 MDG893_RS14835 phosphoenolpyruvate--protein phosphotransferase
Query= reanno::pseudo3_N2E3:AO353_05485 (953 letters) >NCBI__GCF_000170835.1:WP_007154627.1 Length = 768 Score = 330 bits (845), Expect = 3e-94 Identities = 211/593 (35%), Positives = 325/593 (54%), Gaps = 20/593 (3%) Query: 376 LPTVSAQSEVIDEITDVVVA--PASGCVIQAVAAAPGIAIGPAHIQVLQAIDYPLRGEST 433 L V A SE I+ + + A+ V APG+AIG + V A D + E Sbjct: 151 LAGVIAHSEATGAISGLSLTGEEATDVSFSGVPGAPGVAIGKG-VVVYPAADLDVVPEKP 209 Query: 434 AIERERLKTSLAD-----VRRDIEGLIQRSKAKAIRE---IFITHQEMLDDPELTDEVDT 485 + E L+ SL D VR DIE + R ++ E +F + ML D + EV Sbjct: 210 TDDVE-LELSLFDGAVTAVREDIERVAARLASQLRPEEQALFDVYLRMLGDDAMPGEVGN 268 Query: 486 RLKQGESAEAAWMAVIDAAARQQESLQDALLAERAADLRDIGRRVLAQLC-GIETPSEPD 544 R+K+G A+ A V+ R E + D L ERA D+RD+GRR+L+ L G + + Sbjct: 269 RIKEGFWAQGALKQVVQQYVRHFEMMDDHYLQERAVDIRDLGRRLLSHLQEGEQKDTVYP 328 Query: 545 QPYILVMDEVGPSDVARLDPTRVAGILTARGGATAHSAIVARALGIPALVGAGAAVLRLA 604 + +LV +E+ P+ + + ++ G+++ +G + +H AI+ARA+G+P ++G + Sbjct: 329 ENTVLVSEELTPAMLGEVPKGQLVGLVSVKGSSNSHVAILARAMGVPTVMGLVDIPVNQL 388 Query: 605 SGTPLLLDGQRGRLHVDADAATLQRAAEERDNREQRLQAAAAQRHQPALTTDGHAVEVFA 664 G L++DG G++ E D ++ ++ A R P TTD H V + Sbjct: 389 DGKDLIVDGFEGQIFASPSTDLRNFYQEICDEEDELVKGLEALRDLPCETTDNHRVSLLV 448 Query: 665 NIGESAGVVSAVEQGAEGIGLLRTELIFMAHQQAPDEATQEVEYRRVLDGLAGRPLVVRT 724 N G VV ++ GAEGIGL RTE+ FM + P E Q YR L+ A P+ +RT Sbjct: 449 NTGLMTDVVRSLSHGAEGIGLYRTEVPFMIKDRFPSEQEQREYYREQLEAFAPNPVTMRT 508 Query: 725 LDVGGDKPLPYWPIAKEENPFLGVRGIRLTLQRPQIMEAQLRALLRAADN-RPLRIMFPM 783 LD+GGDK L Y+PI +EENPFLG RGIR+TL P+I Q+RA+L+A++ L+IM PM Sbjct: 509 LDIGGDKALTYFPI-QEENPFLGWRGIRVTLDHPEIFLVQVRAMLKASEGLNNLQIMLPM 567 Query: 784 VGSVDEWRQARDMTERLRLEI-----PVADLQLGIMIEVPSAALLAPVLAKEVDFFSVGT 838 + ++ E ++ + R+ E+ + ++G+M+E+P+A LA VDF SVG+ Sbjct: 568 ISNISEVEESLHLIYRVYHEVREEGYNIHMPKVGVMVEIPAAVYQIRELADRVDFLSVGS 627 Query: 839 NDLTQYTLAIDRGHPTLSAQADGLHPAVLQLIDITVRAAHAHGKWVGVCGELAADPLAVP 898 NDLTQY LA+DR +P ++ HPAVLQ + + AHA GK VG+CGELA DP Sbjct: 628 NDLTQYLLAVDRNNPRVAQLYHSYHPAVLQALVRVAQDAHAVGKPVGICGELAGDPGGAL 687 Query: 899 VLVGLGVDELSVSARSIGEVKARVRELSLAQVKHLAQLALAVGSANEVRALVE 951 +L+ +G D LS++A S+ +VK+ +R +S L + L + S + +++ V+ Sbjct: 688 LLMAMGYDSLSMNAASLPKVKSVIRSVSREWSAQLLEDVLLLDSPHVIKSCVD 740 Lambda K H 0.319 0.135 0.383 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: 1355 Number of extensions: 58 Number of successful extensions: 4 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: 953 Length of database: 768 Length adjustment: 42 Effective length of query: 911 Effective length of database: 726 Effective search space: 661386 Effective search space used: 661386 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 (21.7 bits) S2: 56 (26.2 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