Align PTS system fructose-specific EIIB component; EIIB-Fru; Fructose-specific phosphotransferase enzyme IIB component; EC 2.7.1.202 (characterized)
to candidate Pf1N1B4_1144 PTS system, fructose-specific IIB component (EC 2.7.1.69) / PTS system, fructose-specific IIC component (EC 2.7.1.69)
Query= SwissProt::D4GYE1 (158 letters) >FitnessBrowser__pseudo1_N1B4:Pf1N1B4_1144 Length = 579 Score = 97.4 bits (241), Expect = 3e-25 Identities = 53/121 (43%), Positives = 80/121 (66%), Gaps = 3/121 (2%) Query: 2 KLVAVTSCPTGIAHSQMAAENLLQAGERLGHDIDVEVQGAMGTQDELASDAIAEADAVII 61 +LVAVT+CPTG+AH+ MAAE L QA +RLG+D+ VE QG++G ++ L+++AIA+AD V++ Sbjct: 121 RLVAVTACPTGVAHTFMAAEALQQAAKRLGYDLQVETQGSVGARNPLSAEAIADADVVLL 180 Query: 62 TSDTSVSRDRFDGKLVLKGTVKDGVNNAEAVVQKAVELAEAGKTGSVTFGSGDDGEDADV 121 +D V+ +RF GK + + + AEA + KA LAE GK S + G+ + Sbjct: 181 AADIEVATERFAGKKIYRCGTGIALKQAEATLNKA--LAE-GKQESASTGAKGPAKQEKT 237 Query: 122 G 122 G Sbjct: 238 G 238 Score = 62.4 bits (150), Expect = 1e-14 Identities = 36/101 (35%), Positives = 54/101 (53%) Query: 1 MKLVAVTSCPTGIAHSQMAAENLLQAGERLGHDIDVEVQGAMGTQDELASDAIAEADAVI 60 MKL VT+CP G+ S + A L A +R G VEV A + +L++ I A+ V+ Sbjct: 1 MKLAIVTACPNGMVTSVLCARLLDAAAQRQGWSTSVEVVDAAHPERQLSAATIEAAEWVL 60 Query: 61 ITSDTSVSRDRFDGKLVLKGTVKDGVNNAEAVVQKAVELAE 101 + + V RF GK V + T + + EAV+++ VE AE Sbjct: 61 LVTSAPVDMSRFVGKRVFQSTPAQALQDVEAVLRRGVEEAE 101 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: 152 Number of extensions: 4 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: 579 Length adjustment: 26 Effective length of query: 132 Effective length of database: 553 Effective search space: 72996 Effective search space used: 72996 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