Align L-2-keto-3-deoxyarabonate dehydratase (EC 4.2.1.43) (characterized)
to candidate WP_011653798.1 RL_RS22810 dihydrodipicolinate synthase family protein
Query= reanno::BFirm:BPHYT_RS22715 (310 letters) >NCBI__GCF_000009265.1:WP_011653798.1 Length = 310 Score = 134 bits (336), Expect = 4e-36 Identities = 94/278 (33%), Positives = 148/278 (53%), Gaps = 10/278 (3%) Query: 11 RGVFPVAPTIFDDAGRLDLEGQKRCIDFMIDAGSNGLCILANFSEQFALSDDERNTLMHV 70 +GV+ +A T F D G LDL +DF AG GL +L E L+ +E T++ Sbjct: 9 KGVYVIAVTPFTDDGALDLASIDSMVDFYEGAGVTGLTVLGQLGEAPKLTAEESRTVVER 68 Query: 71 VLEHVAGRVPVIVTTTHFSSYQCAERSRSAQAAGAAMVMVMPPYHGATIRIGERGIYEFY 130 VL+ + GR+PV+V + +E + + GAA VMV PP+ T++ ++ + FY Sbjct: 69 VLKRLDGRLPVVVGVSAPGLAPMSELAEAVMDQGAAGVMVAPPW---TVKTDDQA-FAFY 124 Query: 131 RTVSDAIG-IPIMIQDAPVSGTPLSAP-FLARMAREIDNVSYFKIEVPQAANK---LREL 185 ++V +A+G P ++QD P++ AP + R+ E+ N K E +K LR Sbjct: 125 QSVGEALGNTPFVLQDYPLTTNVTIAPKVIERIVNEVPNCVMLKHEDWPGLSKISALRAA 184 Query: 186 IELGGDAIVGPWDGEEAITLMADLDAGATGSMTGGGYADGIRLIVDAYAAGDTEAAAAHY 245 + G + G + L ++ GA G+MTG Y + + +VDAYAAG+ + A A + Sbjct: 185 SDKGTMRRISILCGNGGLFLPEEMGRGADGAMTGFCYPEMMVGVVDAYAAGNPDRAHAIF 244 Query: 246 QQWLPLINYENRQG-GLASCKALMKEGGVIRSDAVRHP 282 +LPL YE +QG GLAS K ++ + GVI+S +R P Sbjct: 245 DAYLPLARYEQQQGIGLASRKYVLAKRGVIKSATLRKP 282 Lambda K H 0.321 0.136 0.407 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: 223 Number of extensions: 17 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: 310 Length of database: 310 Length adjustment: 27 Effective length of query: 283 Effective length of database: 283 Effective search space: 80089 Effective search space used: 80089 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.9 bits) S2: 48 (23.1 bits)
This GapMind analysis is from Sep 24 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