Align N-Acetyl-D-Glucosamine phosphotransferase system transporter, component of N-acetyl glucosamine-specific PTS permease, GlcNAc IIBC/GlcNAc I-HPr-IIA (characterized)
to candidate AZOBR_RS30470 AZOBR_RS30470 phosphoenolpyruvate-protein phosphotransferase
Query= TCDB::Q9HXN5 (842 letters) >FitnessBrowser__azobra:AZOBR_RS30470 Length = 590 Score = 331 bits (848), Expect = 8e-95 Identities = 218/570 (38%), Positives = 318/570 (55%), Gaps = 24/570 (4%) Query: 276 PAAVAG-TLAGVCASPGLASGP--LARLGAISLPADD-GRHRPEEQHLALDQALQRVRDD 331 PAA G +L G+ SPG+A GP + GAI +P + E + A + R Sbjct: 6 PAAGQGRSLRGLGVSPGIAIGPAHVVESGAIRVPEYTLTADQVEAEAARFADACGKARRQ 65 Query: 332 VQGSLQQARL---GGDENEAAIFSAHLALLEDPGLLDAADMLIDQGVGAAHAWHRAIQAQ 388 ++ +A + E + AHLA++ + L + I Q + A A A+QA+ Sbjct: 66 IRKLKAKALVLPGSASEEIGFLLDAHLAMVTNSRLTRGVERRIQQELVNAEA---AVQAE 122 Query: 389 ----CEILQALGNLLLAERANDLRDLEKRVLRVLLGDT--APLRVPAGAIVAAREITPSD 442 + ++ + LA R D+R++ +R++R L+ A + GA++ A E+TP+D Sbjct: 123 IATIAQTFASMEDSYLAGRIADVREVGRRLIRNLMRHEYQAFSMLNPGAVILAEELTPAD 182 Query: 443 LAPLVDAGAAGLCMAEGGATSHVAILARSKGLPCLVALGAGLLELEEGRQVVLDAGQGRL 502 A L AG GGA H AI+ARS G+P ++ +G L L+ G V++D QGR+ Sbjct: 183 TALLDPRRVAGFATVLGGAEGHTAIMARSLGIPAVLGVGGLLAGLKNGITVIVDGVQGRV 242 Query: 503 ELSPDARRLEQVALQVAQREEQRRRQQADAQREALTRDGRRIEIGANVASPREAAEAFAN 562 + P LE + A+RE +R + + + A+TRD + + AN+ PR+ A N Sbjct: 243 IIDPTPEVLEDYRQRRAEREREREQLKGLRKLPAVTRDNTAVTLQANLELPRDLDHALEN 302 Query: 563 GADGVGLLRTEFLFLERRAAPDEEEQRNAYQEVLDAMGQRKVIIRTIDVGGDKHLDYLPL 622 GA G+GLLRTEFLF+ R PDE+EQ + +++ MG R V RT+DVGG+K ++ Sbjct: 303 GAQGIGLLRTEFLFMNRDQLPDEDEQYTVLRSIVEGMGGRTVTARTMDVGGEKLAGWMAG 362 Query: 623 PVEE--NPALGLRGIHLGQARPELLDQQLRALLRVEPLERCRILLPMVSEVDELRAIRRR 680 E NPALGLR + LG P+LL+ QL A+LR RILLPM+ V E++ +R Sbjct: 363 RYGEPANPALGLRAVRLGLREPKLLETQLAAMLRAGVHGPLRILLPMICSVAEVQRVREM 422 Query: 681 LGELATQL---GI---ERLPELGVMIEVPSAALLADQLAEHADFLSIGTNDLSQYALAMD 734 +G++A +L G+ + LP +GVM+EVP AAL AD LA ADF SIGTNDL+QY LA+D Sbjct: 423 MGQVARRLRRRGVPIADPLPPVGVMVEVPGAALSADALAYAADFFSIGTNDLTQYTLAID 482 Query: 735 RCHAGLADRIDALHPALLRLIAQTCAGAARHGRWVGVCGALASDPLATPVLVGLGVEELS 794 R +A D LHPA+LRLI T A R V VCG +A D T +L+GLGV +LS Sbjct: 483 RGDEQVASLYDPLHPAVLRLIQFTIEAALRARIPVSVCGEIAGDSRYTALLLGLGVRDLS 542 Query: 795 VGPNLVGEIKTRVRQLDAAECRRHAQALLD 824 + P + +K R+R+LD E R A+ ++D Sbjct: 543 MVPPAIPLVKRRIRKLDLQEATRRARVIMD 572 Lambda K H 0.319 0.136 0.390 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: 1157 Number of extensions: 45 Number of successful extensions: 5 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 842 Length of database: 590 Length adjustment: 39 Effective length of query: 803 Effective length of database: 551 Effective search space: 442453 Effective search space used: 442453 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: 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