Align PTS system glucose-specific EIIA component; EIIA-Glc; EIII-Glc; Glucose-specific phosphotransferase enzyme IIA component (characterized)
to candidate AO356_17540 AO356_17540 PTS N-acetyl-D-glucosamine transporter
Query= SwissProt::P0A283 (169 letters) >FitnessBrowser__pseudo5_N2C3_1:AO356_17540 Length = 837 Score = 114 bits (284), Expect = 5e-30 Identities = 57/143 (39%), Positives = 89/143 (62%), Gaps = 1/143 (0%) Query: 25 APLSGEIVNIEDVPDVVFAEKIVGDGIAIKPTGNKMVAPVDGTIGKIFETNHAFSIESDS 84 APLSG ++ + +VPD VFA +GDGIAI P + + AP D + + T HA ++ +D+ Sbjct: 12 APLSGPVLTLANVPDAVFASGAMGDGIAIDPLNDTLYAPCDAEVIHVARTGHAVTLRADN 71 Query: 85 GIELFVHFGIDTVELKGEGFKRIAEEGQRVKVGDPVIEFDLPLLEEKAKSTLTPVVISNM 144 G EL +H G+DTVEL+GEGF + +EG RV G P++ +D+ + + KS ++ +VI+N Sbjct: 72 GAELLLHLGLDTVELQGEGFSMLVKEGARVSHGQPLLRYDVDKVALRCKSLVSLLVITNG 131 Query: 145 DEIKELIKLSGSVTVGETPVIRI 167 + + V VGE P++ I Sbjct: 132 EHFQARPITLKGVKVGE-PLLHI 153 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: 305 Number of extensions: 17 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: 837 Length adjustment: 30 Effective length of query: 139 Effective length of database: 807 Effective search space: 112173 Effective search space used: 112173 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: 49 (23.5 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