Align Predicted dapE by GapMind curators (no experimental data)
to candidate WP_012709239.1 NGR_RS24810 M20 aminoacylase family protein
Query= predicted:L0FXC2 (397 letters) >NCBI__GCF_000018545.1:WP_012709239.1 Length = 387 Score = 243 bits (621), Expect = 5e-69 Identities = 151/385 (39%), Positives = 198/385 (51%), Gaps = 11/385 (2%) Query: 10 AADQLNQTIAIRRHIHAHPELSFEEHQTCAFVEKHLQEIGITNIQRK-ANTGLVALIEGK 68 AA+ N+ RRH+H +PEL F T AFVEK L+E G+ I TG+V LI G Sbjct: 7 AAELQNEVTEWRRHLHMNPELLFAVENTAAFVEKKLREFGVDEIVTGLGRTGVVGLIRGN 66 Query: 69 NPSKKVIALRADMDALPIVEQNDVPYKSNKEGVMHACGHDVHTSSLLGAASILHAVKDQF 128 + + I LRADMDALPI E + + S G MHACGHD HT+ LLGAA L ++ F Sbjct: 67 LGAGRTIGLRADMDALPITETSGKAWSSTTPGKMHACGHDGHTAMLLGAAKYLAETRN-F 125 Query: 129 EGTVKLIFQPGEEKIPGGASLMIKDKALENPRPSGIVGQHVMPLIDAGKVGFRKGMYMAS 188 G V +IFQP EE GG + M+KD +E + G H MP + G G R G MAS Sbjct: 126 SGNVAVIFQPAEEG-GGGGNEMVKDGMMERFAIEEVYGMHNMPGMPVGHFGSRVGPIMAS 184 Query: 189 ADELYLKVIGKGGHGAMPETLVDPVLIASHIIVALQQVISRNASPKVPSVLSFGRIEALG 248 DE + V G+GGH A P +DP+ I + I+ ALQ + SR P V+S + A Sbjct: 185 TDEFTITVKGRGGHAAQPHKTIDPIAIGAQIVNALQTIASRTVDPLASIVVSVTKFNAGF 244 Query: 249 ATNVIPNEVNIQGTFRTLDETWRAEAHQKMVKIAEGIAEGMGGSVDFEVRKGYPFLQNAP 308 A NVIP + + GT R L R ++ +IAE IA G +VD + YP N Sbjct: 245 AHNVIPEQAVLAGTVRALTPQVRDTGEARIRQIAESIAGAYGATVDVWYGRNYPVTVNHA 304 Query: 309 ELTDRAYKAAQAYLGEENVE-DLDIWMAAEDFSYYTQEMDGCFYRLGIRNEEKGITSGVH 367 T A A GE NV LD M EDFSY G F +G G ++G+H Sbjct: 305 TETGHALAVAATVAGEGNVNAALDPMMGGEDFSYMLLARPGAFVFIG-----NGESAGLH 359 Query: 368 TPTFDIDESALEVGAGLMAWIAINE 392 P +D ++ + G+ W+ + E Sbjct: 360 HPAYDFNDDV--IPHGISYWVKLTE 382 Lambda K H 0.317 0.134 0.387 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: 400 Number of extensions: 26 Number of successful extensions: 5 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: 397 Length of database: 387 Length adjustment: 31 Effective length of query: 366 Effective length of database: 356 Effective search space: 130296 Effective search space used: 130296 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 (21.6 bits) S2: 50 (23.9 bits)
This GapMind analysis is from Jul 25 2024. The underlying query database was built on Jul 25 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