Align PTS system glucose-specific EIIA component; EIIA-Glc; EIII-Glc; Glucose-specific phosphotransferase enzyme IIA component (characterized)
to candidate BWI76_RS08220 BWI76_RS08220 PTS N-acetyl glucosamine transporter subunit IIABC
Query= SwissProt::P0A283 (169 letters) >FitnessBrowser__Koxy:BWI76_RS08220 Length = 650 Score = 163 bits (413), Expect = 5e-45 Identities = 79/151 (52%), Positives = 108/151 (71%), Gaps = 2/151 (1%) Query: 20 TIE-IVAPLSGEIVNIEDVPDVVFAEKIVGDGIAIKPTGNKMVAPVDGTIGKIFETNHAF 78 T+E +V+P++G+IV +E VPD FA K VGDG+A+KPT +VAP GT+ KIF TNHAF Sbjct: 498 TVEALVSPITGDIVALEQVPDEAFASKAVGDGVAVKPTDKIVVAPAAGTVVKIFNTNHAF 557 Query: 79 SIESDSGIELFVHFGIDTVELKGEGFKRIAEEGQRVKVGDPVIEFDLPLLEEKAKSTLTP 138 +E+++G E+ VH GIDTV L G+GFKR+ EEG VK G+P++E DL L A+S ++P Sbjct: 558 CLETENGAEIVVHMGIDTVALNGQGFKRLVEEGAEVKAGEPILELDLEFLNANARSMISP 617 Query: 139 VVISNMDEIKEL-IKLSGSVTVGETPVIRIK 168 VV SN D+ L I+ +G V G+TP+ IK Sbjct: 618 VVCSNSDDYSALVIQATGKVVAGQTPLYEIK 648 Lambda K H 0.315 0.139 0.377 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: 266 Number of extensions: 12 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: 169 Length of database: 650 Length adjustment: 28 Effective length of query: 141 Effective length of database: 622 Effective search space: 87702 Effective search space used: 87702 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 (21.9 bits) S2: 48 (23.1 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