Align 2-amino-3,7-dideoxy-D-threo-hept-6-ulosonate synthase (EC 2.2.1.10) (characterized)
to candidate YP_004144350.1 Mesci_5202 deoxyribose-phosphate aldolase/phospho-2-dehydro-3-deoxyheptonate aldolase
Query= BRENDA::Q57843 (273 letters) >NCBI__GCF_000185905.1:YP_004144350.1 Length = 266 Score = 151 bits (381), Expect = 2e-41 Identities = 92/263 (34%), Positives = 138/263 (52%), Gaps = 7/263 (2%) Query: 9 NLGKLVRLERIFNRESEKTVIVPMDHGVSNGPIK--GLIDIRKTVNDVAEGGANAVLLHK 66 +LG VRL R+F+ S +DH V G ++ GL D+ + V G + V + Sbjct: 2 SLGTKVRLARLFSHPSGNLFGGAVDHFVGYGDVRKGGLADLPGALARVMVGKPDYVSIQP 61 Query: 67 GIVRHGHRGYGKDVGLIIHLSGGTAISPNPLKKVIVTTVEEAIRMGADAVSIHVNVGSDE 126 G RH Y L+I +P+ ++ T E+A+R GADA+++ + V Sbjct: 62 GTARHLWPQYAGKASLVIQAG---CFTPDDRISELIATPEDAVRAGADALAVAIPVRGAT 118 Query: 127 DWEAYRDLGMIAETCEYWGMPLIAMMYPRG--KHIQNERDPELVAHAARLGAELGADIVK 184 + + R L +GMP++A +YPR + P+ +A+AAR+G E G D++K Sbjct: 119 EGKYIRWLTDSVNAAARYGMPVVAHIYPRDFTDGAKIVFTPDEIAYAARIGYESGVDVIK 178 Query: 185 TSYTGDIDSFRDVVKGCPAPVVVAGGPKTNTDEEFLQMIKDAMEAGAAGVAVGRNIFQHD 244 YTGD +SFR+ V+ CP PVV+AGGPKT+T LQ DA+ AGA G VGRN++ H Sbjct: 179 IGYTGDFESFRETVRTCPVPVVIAGGPKTDTLLGALQQTADAIRAGARGAVVGRNLWGHG 238 Query: 245 DVVGITRAVCKIVHENADVEEAL 267 D A ++HE ++AL Sbjct: 239 DPEKAAIAFRGVIHEGLSAQDAL 261 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: 206 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: 266 Length adjustment: 25 Effective length of query: 248 Effective length of database: 241 Effective search space: 59768 Effective search space used: 59768 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 10 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