Align 2-amino-3,7-dideoxy-D-threo-hept-6-ulosonate synthase (EC 2.2.1.10) (characterized)
to candidate 8501014 DvMF_1751 fructose-bisphosphate aldolase (RefSeq)
Query= BRENDA::Q57843 (273 letters) >FitnessBrowser__Miya:8501014 Length = 265 Score = 324 bits (831), Expect = 1e-93 Identities = 153/258 (59%), Positives = 202/258 (78%) Query: 10 LGKLVRLERIFNRESEKTVIVPMDHGVSNGPIKGLIDIRKTVNDVAEGGANAVLLHKGIV 69 +GK +R+ERIFNR++ + VIVP+DHGVS GPI GL+D+R+TVN VAEGGA+AVL+HKG+V Sbjct: 3 IGKRIRMERIFNRKTGRAVIVPLDHGVSVGPIYGLVDMRETVNQVAEGGADAVLMHKGLV 62 Query: 70 RHGHRGYGKDVGLIIHLSGGTAISPNPLKKVIVTTVEEAIRMGADAVSIHVNVGSDEDWE 129 R GHR G+DVGLI+HLS T++SP P K +V TVE+A++ GAD VS+HVN+G + + + Sbjct: 63 RCGHREGGRDVGLIVHLSASTSLSPRPNAKTLVATVEDALKHGADGVSVHVNLGDETERD 122 Query: 130 AYRDLGMIAETCEYWGMPLIAMMYPRGKHIQNERDPELVAHAARLGAELGADIVKTSYTG 189 DLG +A WGMPL+AMMY RG I+NE DPE+VAHAAR+G ELGAD+VK +YTG Sbjct: 123 MLADLGRVATVANDWGMPLLAMMYARGPRIKNEYDPEVVAHAARVGVELGADVVKVAYTG 182 Query: 190 DIDSFRDVVKGCPAPVVVAGGPKTNTDEEFLQMIKDAMEAGAAGVAVGRNIFQHDDVVGI 249 D+DSF VV C PVV+AGGPK ++ FLQM+ DA+ AGAAG++VGRNIFQH+ + Sbjct: 183 DMDSFAHVVASCCVPVVIAGGPKLDSTRSFLQMVHDAVRAGAAGLSVGRNIFQHERTPAL 242 Query: 250 TRAVCKIVHENADVEEAL 267 +A+ +VHE+ DVE+A+ Sbjct: 243 VKALRGLVHEDWDVEQAM 260 Lambda K H 0.318 0.138 0.401 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: 12 Number of successful extensions: 3 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: 273 Length of database: 265 Length adjustment: 25 Effective length of query: 248 Effective length of database: 240 Effective search space: 59520 Effective search space used: 59520 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: 41 (21.7 bits) S2: 47 (22.7 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