Align PTS system, fructose-specific, IIB subunnit, component of Fructose Enzyme II complex (IIAFru - IIBFru - IICFru) (based on homology) (characterized)
to candidate GFF3783 HP15_3725 PTS system, fructose-specific IIBC component
Query= TCDB::D2RXA4 (150 letters) >FitnessBrowser__Marino:GFF3783 Length = 587 Score = 89.7 bits (221), Expect = 7e-23 Identities = 48/115 (41%), Positives = 70/115 (60%), Gaps = 4/115 (3%) Query: 2 KFVAVTSCPTGIAHSQMAAENLEQTATDRGHEIDVEVQGAMGQENELSSDAIAEADAVII 61 + VAVT+CPTG+AH+ MAAE L A GH+I VE QG++G ++ L+ + IA AD VI+ Sbjct: 128 RIVAVTACPTGVAHTFMAAEALTAAAQSAGHKIRVETQGSVGAQDPLTEEEIAAADVVIL 187 Query: 62 AADTSVNQDRFEGKPV----VTAPVKDAVNDVEDLLERAIAAADGETSTADSAQS 112 A D V+ RF GK V A +K + + D LE+A+ G+ T+ ++ S Sbjct: 188 ACDIEVDPGRFSGKRVWRTSTGAALKKPADTIRDALEQAVVLNAGQKKTSGASGS 242 Score = 66.2 bits (160), Expect = 8e-16 Identities = 43/122 (35%), Positives = 63/122 (51%), Gaps = 1/122 (0%) Query: 1 MKFVAVTSCPTGIAHSQMAAENLEQTATDRGHEIDVEVQGAMGQ-ENELSSDAIAEADAV 59 M + VT+CP G+A +AA LE+ A RG + + +G G+ +N+ S AI +AD V Sbjct: 1 MNLIIVTACPQGVATRFLAARALERAANRRGWSVTTDTRGPDGKTDNKPSEAAIQQADLV 60 Query: 60 IIAADTSVNQDRFEGKPVVTAPVKDAVNDVEDLLERAIAAADGETSTADSAQSEGAADAS 119 I A VN D + GK ++ PV A+ D + +L RA A A S +S + A Sbjct: 61 IAAVGIPVNLDVYAGKRLLQIPVTAALPDPDAILTRAQAEATPWDPAMASQESIATSTAV 120 Query: 120 AS 121 S Sbjct: 121 GS 122 Lambda K H 0.307 0.122 0.323 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: 150 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: 150 Length of database: 587 Length adjustment: 26 Effective length of query: 124 Effective length of database: 561 Effective search space: 69564 Effective search space used: 69564 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 (21.6 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