Align Predicted dapE by GapMind curators (no experimental data)
to candidate WP_106710957.1 CU102_RS10055 amidohydrolase
Query= predicted:L0FXC2 (397 letters) >NCBI__GCF_003010955.1:WP_106710957.1 Length = 389 Score = 246 bits (629), Expect = 6e-70 Identities = 140/375 (37%), Positives = 204/375 (54%), Gaps = 9/375 (2%) Query: 21 RRHIHAHPELSFEEHQTCAFVEKHLQEIGITNIQRK-ANTGLVALIEGKNPSKKVIALRA 79 RRH+HA+PEL F+ H+T FV L + G ++ TG+V +I G++ + LR+ Sbjct: 18 RRHLHANPELMFDVHETARFVTDKLHQFGCDIVETGIGRTGVVGVIRGRHGEGPTVGLRS 77 Query: 80 DMDALPIVEQNDVPYKSNKEGVMHACGHDVHTSSLLGAASILHAVKDQFEGTVKLIFQPG 139 DMDALP+ E P+ S+ G MHACGHD HT+ LLGAA L ++ F+G++ +IFQP Sbjct: 78 DMDALPLTEITGKPWASHAAGKMHACGHDGHTAMLLGAAQYLAETRN-FKGSIAVIFQPA 136 Query: 140 EEKIPGGASLMIKDKALENPRPSGIVGQHVMPLIDAGKVGFRKGMYMASADELYLKVIGK 199 EE GG M+KD +E S + G H +P + G+ RKG MA+ DE + + G+ Sbjct: 137 EEG-GGGGREMVKDGMMERFSISEVYGMHNVPGLPVGEFAIRKGPIMAATDEFTITIEGR 195 Query: 200 GGHGAMPETLVDPVLIASHIIVALQQVISRNASPKVPSVLSFGRIEALGATNVIPNEVNI 259 GGH A P +DPV+I S ++ ALQ ++SR P VLS + A A N+IP + Sbjct: 196 GGHAAQPHRTIDPVVIGSQLVNALQTIVSRGTDPLDSVVLSVTQFHAGDAHNIIPQRAEL 255 Query: 260 QGTFRTLDETWRAEAHQKMVKIAEGIAEGMGGSVDFEVRKGYPFLQNAPELTDRAYKAAQ 319 GT RTL R A +++ ++AEG+A +G S + + YP N T+ A + A+ Sbjct: 256 AGTVRTLRPEMRDFAERRLTEVAEGVANALGASANVHYARNYPVTFNHERETEFAAQTAR 315 Query: 320 AYLGEENVE-DLDIWMAAEDFSYYTQEMDGCFYRLGIRNEEKGITSGVHTPTFDIDESAL 378 G V D+ MA EDFSY + G F +G G ++ +H P +D ++ A+ Sbjct: 316 NVAGGGAVNTDVAPMMAGEDFSYMLEARPGAFIFIG-----NGDSASLHNPAYDFNDDAI 370 Query: 379 EVGAGLMAWIAINEL 393 G IA N L Sbjct: 371 VYGISYWVQIAENAL 385 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: 406 Number of extensions: 23 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: 389 Length adjustment: 31 Effective length of query: 366 Effective length of database: 358 Effective search space: 131028 Effective search space used: 131028 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 26 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