Align PTS system fructose-specific EIIB component; EIIB-Fru; Fructose-specific phosphotransferase enzyme IIB component; EC 2.7.1.202 (characterized)
to candidate AO356_07325 AO356_07325 PTS fructose transporter subunit IIBC
Query= SwissProt::D4GYE1 (158 letters) >FitnessBrowser__pseudo5_N2C3_1:AO356_07325 Length = 580 Score = 94.7 bits (234), Expect = 2e-24 Identities = 51/122 (41%), Positives = 79/122 (64%), Gaps = 3/122 (2%) Query: 2 KLVAVTSCPTGIAHSQMAAENLLQAGERLGHDIDVEVQGAMGTQDELASDAIAEADAVII 61 +LVA+T+CPTG+AH+ MAAE L QA +LG+D+ VE QG++G ++ L+++AIAEAD V++ Sbjct: 122 RLVAITACPTGVAHTFMAAEALQQAATKLGYDLQVETQGSVGARNPLSAEAIAEADVVLL 181 Query: 62 TSDTSVSRDRFDGKLVLKGTVKDGVNNAEAVVQKAVELAEAGKTGSVTFGSGDDGEDADV 121 +D V+ +RF GK + + + AEA + KA L EA + S + G+ + Sbjct: 182 ATDIEVATERFAGKKIYRCGTGIALKQAEATLNKA--LVEA-RQESASSGASAPAKSEKT 238 Query: 122 GA 123 GA Sbjct: 239 GA 240 Score = 55.5 bits (132), Expect = 1e-12 Identities = 38/118 (32%), Positives = 60/118 (50%), Gaps = 4/118 (3%) Query: 1 MKLVAVTSCPTGIAHSQMAAENLLQAGERLGHDIDVEVQGAMGTQDELASDAIAEADAVI 60 MKL VT+CP G+ S + A L A +R G VEV A + +L++ + A+ V+ Sbjct: 1 MKLAIVTACPNGMVTSVLCARLLDAAAQRQGWSTSVEVHDAAHPERQLSAATLEAAEWVL 60 Query: 61 ITSDTSVSRDRFDGKLVLKGTVKDGVNNAEAVVQK-AVE---LAEAGKTGSVTFGSGD 114 + + V RF GK V + T + + +AV+++ AVE L EA + V S + Sbjct: 61 LVASGPVDLSRFVGKRVFRSTPALALQDVDAVLRRGAVEAEVLGEADASAQVPAASAE 118 Lambda K H 0.309 0.128 0.345 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: 155 Number of extensions: 6 Number of successful extensions: 2 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 158 Length of database: 580 Length adjustment: 26 Effective length of query: 132 Effective length of database: 554 Effective search space: 73128 Effective search space used: 73128 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.1 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 42 (21.7 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