Align 2-amino-3,7-dideoxy-D-threo-hept-6-ulosonate synthase (EC 2.2.1.10) (characterized)
to candidate BWI76_RS14880 BWI76_RS14880 putative fructose-bisphosphate aldolase, class 1
Query= BRENDA::Q57843 (273 letters) >FitnessBrowser__Koxy:BWI76_RS14880 Length = 262 Score = 115 bits (289), Expect = 7e-31 Identities = 78/260 (30%), Positives = 135/260 (51%), Gaps = 7/260 (2%) Query: 10 LGKLVRLERIFNRESEKTVIVPMDHGVSNGPIKGLIDIRKTVNDVAEGGANAVLLHKGIV 69 + K RL RIF ++ K+V + +D + G+ + K + + E G + L+ G++ Sbjct: 1 MSKERRLSRIFAKDG-KSVTLALDGYYFSSNTNGIDNTIKQLPVLVENGLDCALVTWGML 59 Query: 70 RHGHRGYGKDVGLIIHLSGGTAISPNPLKKVI-VTTVEEAIRMGADAVSIHVNVGSDEDW 128 ++ R V +++ + +I N + V ++E+A+++ AD V G+ + Sbjct: 60 KN-FREIFNSVPVVLRVDSTVSIFDNTVPDTTPVFSIEDALKVAADGVVCMTFPGAFNEE 118 Query: 129 EAYRDLGMIAETCEYWGMPLIAMMYPRGKHIQNE--RDPELVAHAARLGAELGADIVKTS 186 + + +A+ + W MPLI P G + ++ +P ++A +AR+ ELGAD++KT Sbjct: 119 KTHIMAMQLAQAADRWSMPLIVESLPYGYPVTSDDSNNPAIIAASARVAVELGADVIKTR 178 Query: 187 YTGDIDSFRDVVKGCPAPVVVAGGPKTNTDEEFLQMIKDAMEAGAAGVAVGRNIFQHDDV 246 +TG D R +V+ PV+ GGPKT D F + + M+ GA GVAVGRNI Q Sbjct: 179 FTGTEDD-RLIVEAAGVPVLALGGPKTGIDGYF-KFVHHCMQVGAKGVAVGRNITQDPRP 236 Query: 247 VGITRAVCKIVHENADVEEA 266 + + I+HENA E+A Sbjct: 237 EKVVAGLNAIIHENATAEDA 256 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: 167 Number of extensions: 7 Number of successful extensions: 4 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: 262 Length adjustment: 25 Effective length of query: 248 Effective length of database: 237 Effective search space: 58776 Effective search space used: 58776 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 Apr 09 2024. The underlying query database was built on Apr 09 2024.
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