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 7025094 Shewana3_2257 phosphoenolpyruvate--protein phosphotransferase (RefSeq)
Query= TCDB::Q9HXN5 (842 letters) >FitnessBrowser__ANA3:7025094 Length = 567 Score = 280 bits (717), Expect = 1e-79 Identities = 195/543 (35%), Positives = 282/543 (51%), Gaps = 22/543 (4%) Query: 282 TLAGVCASPGLASGPLARLGAISLPADDGRHRP------EEQHLALDQALQRVRDDVQGS 335 ++ G+ S G+A G L D +RP +Q +ALQ ++ + S Sbjct: 2 SITGIIVSSGIAFGQALHLTQAEHHLD---YRPIPLSRIPQQQSKFVKALQALQQQLSHS 58 Query: 336 LQQARLGGDENEAAIFSAHLALLEDPGLLDAADMLIDQ-GVGAAHAWHRAIQAQCEILQA 394 Q +L + A L LLED L+D I + A+ A R Q L++ Sbjct: 59 --QTKLDPQSENYQLIEADLLLLEDEELIDQVKEAIRTLQLSASVAVERIFAHQANELES 116 Query: 395 LGNLLLAERANDLRDLEKRVLRVLLG--DTAPLRVPAGAIVAAREITPSDLAPLVDAGAA 452 L + LA RA D+R L +R++ + G D ++ I+ A+++TP++ A L + Sbjct: 117 LDDPYLANRAQDVRCLGQRLVTAINGRLDQGLAQLTEPTILLAQDLTPAEFALLPKEQLS 176 Query: 453 GLCMAEGGATSHVAILARSKGLPCLVALGAGLLELEEGRQVVLDAGQGRLELSPDARRLE 512 G+ + GG TSH AILAR+ G+P +++ + G +VLDA G L ++P Sbjct: 177 GIVLKTGGLTSHTAILARAAGIPAILSCQFDAEFIPNGTPLVLDALSGELFVNPAPEL-- 234 Query: 513 QVALQVAQREEQRRRQQADAQRE--ALTRDGRRIEIGANVASPREAAEAFANGADGVGLL 570 Q L V EQ RR A R+ A T+DG + + ANV + + GADG+GL Sbjct: 235 QARLTVTLHHEQARRAALQAYRDVPAKTQDGHLVGLMANVGNLNDITHVGDVGADGIGLF 294 Query: 571 RTEFLFLERRAAPDEEEQRNAYQEVLDAMGQRKVIIRTIDVGGDKHLDYLPLPVEENPAL 630 RTEF+ + PDE+ Q N Y E L A+G + IRT+D+G DK L L VE+NPAL Sbjct: 295 RTEFMLMHTSTLPDEKAQYNLYCEALHALGGKTFTIRTLDIGADKELPCLCQEVEDNPAL 354 Query: 631 GLRGIHLGQARPELLDQQLRALLRVEPLERCRILLPMVSEVDELRAIRRRLGELATQLGI 690 GLRG+ A PEL QLRA+LR R++ PMV++V+EL I + E L Sbjct: 355 GLRGVRYTLAHPELFKTQLRAILRAANHGPIRLMFPMVNQVEELDQIFALIAECQDALEE 414 Query: 691 ER--LPEL--GVMIEVPSAALLADQLAEHADFLSIGTNDLSQYALAMDRCHAGLADRIDA 746 E EL G+++E P+A + + DF+SIGTNDL+QYA+A DR + L + Sbjct: 415 EEKGFGELSYGIVVETPAAVMNLASMLPRLDFVSIGTNDLTQYAMAADRTNPQLTRDYPS 474 Query: 747 LHPALLRLIAQTCAGAARHGRWVGVCGALASDPLATPVLVGLGVEELSVGPNLVGEIKTR 806 L PA+L LI T A G V +CG LAS PL P+L+G+G++ELSV + + E+K Sbjct: 475 LSPAILGLIKMTVDQAKAAGVKVSLCGELASSPLMVPLLIGMGLDELSVNLSALLEVKAA 534 Query: 807 VRQ 809 V Q Sbjct: 535 VCQ 537 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: 1063 Number of extensions: 46 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: 842 Length of database: 567 Length adjustment: 39 Effective length of query: 803 Effective length of database: 528 Effective search space: 423984 Effective search space used: 423984 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