Align PTS system N-acetylglucosamine-specific EIIB component; PTS system GlcNAc-specific EIIB component; N-acetylglucosamine-specific phosphotransferase enzyme IIB component; GlcNAc-specific phosphotransferase enzyme IIB component; EC 2.7.1.193 (characterized)
to candidate 15742 b1621 fused maltose and glucose-specific PTS enzymes: IIB component -! IIC component (NCBI)
Query= SwissProt::Q9S2H6 (77 letters) >FitnessBrowser__Keio:15742 Length = 530 Score = 55.5 bits (132), Expect = 6e-13 Identities = 38/93 (40%), Positives = 48/93 (51%), Gaps = 16/93 (17%) Query: 1 MASKAEKIVAG---------------LGGIDNIDEIEGCITRLRTEVNDPALVNEAALKA 45 +AS EK VAG LGG DNI ++ CITRLR V D +LVN ALK Sbjct: 433 VASSIEKAVAGAPGKSGYNVPAILEALGGADNIVSLDNCITRLRLSVKDMSLVNVQALKD 492 Query: 46 AGAHGVVKMGT-AIQVVIGTDADPIAAEIEDMM 77 A GVV++ +QVVIG + E+ +M Sbjct: 493 NRAIGVVQLNQHNLQVVIGPQVQSVKDEMAGLM 525 Lambda K H 0.315 0.133 0.360 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: 101 Number of extensions: 10 Number of successful extensions: 1 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: 77 Length of database: 530 Length adjustment: 20 Effective length of query: 57 Effective length of database: 510 Effective search space: 29070 Effective search space used: 29070 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 42 (22.0 bits) S2: 44 (21.6 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