Align PTS system, IIABC components (characterized, see rationale)
to candidate GFF4494 PS417_23000 PTS N-acetyl-D-glucosamine transporter
Query= uniprot:Q836Y6 (722 letters) >FitnessBrowser__WCS417:GFF4494 Length = 568 Score = 204 bits (520), Expect = 7e-57 Identities = 170/556 (30%), Positives = 260/556 (46%), Gaps = 104/556 (18%) Query: 11 QKFGKALMVVVAVMPAAGLMISIGKSLPLIDPNLGLLVTTGGVLESIGWAIIGNLHLLFA 70 Q+ G+ALM+ +A++P AGL++ +G + L N+ V+ G AI NL L+FA Sbjct: 10 QRLGRALMLPIAILPIAGLLLRLGDTDLL---NIA-------VMHDAGQAIFANLALIFA 59 Query: 71 LAIGGSWAKDRAGGAFAAGISFVLINRITGAIFGVTNEMLADEQAFTHTLFGTKIMVKGF 130 + I +A+D G A AG G +MV Sbjct: 60 IGIAVGFARDNNGTAGLAGA------------------------------IGYLVMVS-- 87 Query: 131 FTSVLEAPALNMGVFVGIIAGFVGAMAYNKYYNYRKLPDALSFFNGKRFVPFVVILWSTI 190 T + ++NMG+ GI +G + YN++ + KLP+ L+FF G+RFVP V + Sbjct: 88 -TLKVMDTSINMGMLAGIASGLMAGGLYNRFKDI-KLPEYLAFFGGRRFVPIVTGFSAVG 145 Query: 191 VSIALALIWPNIQAGINNFGLWIAQSQDSAPILAPFLYGTLERLLLPFGLHHMLTIPINY 250 + + LIWP IQ GIN+FG+ + +S L F++G RLL+ GLHH+L Sbjct: 146 LGVIFGLIWPPIQHGINSFGVLLMESGS----LGAFVFGVFNRLLIVTGLHHILN----- 196 Query: 251 TQLGGTYEILSGAQAGTQVFGQ--DPLWLAWATDLVNLKGAGDMSKYQFVLENWTPARFK 308 VFG DP+ A T + AGD QF+ + F Sbjct: 197 -------------NMAWFVFGSFTDPVTGAVVTGDLTRYFAGDPKGGQFMTGMFPVMLFG 243 Query: 309 VGQMIGSSGILMGMALAMYRNVDADKKAKYKSMYFSAALAVFLTGVTEPLEFMFMFAAVP 368 L LAMYRN +++ ++ S AL FLTGVTEP+EF FMF A Sbjct: 244 ----------LPAACLAMYRNALPERRKVMGGIFLSMALTSFLTGVTEPIEFAFMFLAPF 293 Query: 369 LYVIYAVIQGAAFAMADILPLRV---HSFGNIELLTRTPLAIKAGLGGDLINFVLMVI-- 423 LY+I+AV+ G + A+ ++L + + S G I+++ G G +++ + Sbjct: 294 LYLIHAVLTGLSMAVTNMLNIHLGFTFSGGFIDMV--------LGWGKSTNGWLVFPVGL 345 Query: 424 IFGVVTYFLANFLIKKFNYATPGRNGNYDNDNSEEIASGAAGSGVVDQQIAQIVYLLGGK 483 + ++ Y + N+ I+ FN TPGR ++++ + + A +Q+ + LGG Sbjct: 346 AYALIYYSVFNYCIRHFNLKTPGR------EDTQVVQAEAMSD---NQRATAYIQALGGA 396 Query: 484 QNIKEVDACMTRLRVSVKDREKVGSEEAWKRAGAMGLIVKDNG--VQAVYGPKADVLKSD 541 QN+ V AC TRLR+ + DR K E K GAM ++ NG +Q V GP AD + + Sbjct: 397 QNLLSVGACTTRLRLDMVDRNKAVDAEL-KALGAMAVVRPGNGGSLQVVVGPMADSIADE 455 Query: 542 IEDLLASGVDIPEPVI 557 I L G PV+ Sbjct: 456 IR-LAMPGFVAAAPVV 470 Lambda K H 0.322 0.138 0.404 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: 948 Number of extensions: 49 Number of successful extensions: 7 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: 722 Length of database: 568 Length adjustment: 38 Effective length of query: 684 Effective length of database: 530 Effective search space: 362520 Effective search space used: 362520 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 (21.9 bits) S2: 54 (25.4 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