Align Predicted dapE by GapMind curators (no experimental data)
to candidate HSERO_RS04135 HSERO_RS04135 amidohydrolase
Query= predicted:L0FXC2 (397 letters) >FitnessBrowser__HerbieS:HSERO_RS04135 Length = 402 Score = 255 bits (652), Expect = 1e-72 Identities = 153/398 (38%), Positives = 221/398 (55%), Gaps = 15/398 (3%) Query: 1 MLKDTIKKLAADQLNQTIAIRRHIHAHPELSFEEHQTCAFVEKHLQEIGITNIQRKANTG 60 ++ D IK+L + ++IRRH+HAHPEL FEE +T +FV L+ G+T + G Sbjct: 3 IVNDGIKELPKEM--DLVSIRRHLHAHPELRFEEKRTASFVADMLRSYGLTVAENIGGYG 60 Query: 61 LVALIEGKNPSKKVIALRADMDALPIVEQNDVPYKSNKEGVMHACGHDVHTSSLLGAASI 120 +VA + K S + IALRADMDALP+ EQND + S G MHACGHD HT+ LLGAA Sbjct: 61 VVATLR-KGKSTRAIALRADMDALPMSEQNDFSHISTCAGKMHACGHDGHTTMLLGAARR 119 Query: 121 LHAVKDQFEGTVKLIFQPGEEKIPGGASLMIKDKALENPRPSGIVGQHVMPLIDAGKVGF 180 L + +F+GTV +FQP EE GA LMI+D E I G H P + AG G Sbjct: 120 LSR-EVEFDGTVHFVFQPAEEG-GAGARLMIEDGLFERFPADAIFGVHNWPGLPAGSFGL 177 Query: 181 RKGMYMASADELYLKVIGKGGHGAMPETLVDPVLIASHIIVALQQVISRNASPKVPSVLS 240 R G MAS++ + G+G HGA P +DPVL A+ + +A Q +++RN +P +V+S Sbjct: 178 RPGPLMASSNTFSATLFGRGAHGAQPHRSIDPVLAAAQLTLAWQSIVTRNINPNHRAVIS 237 Query: 241 FGRIEALGATNVIPNEVNIQGTFRTLDETWRAEAHQKMVKIAEGIAEGMGGSVDFEVRKG 300 ++ A NVIP + + GT R+ D +M IAE I + V F + Sbjct: 238 VTQLHTGTADNVIPEQATLSGTVRSFDAETLDLIEHRMAAIAEAIGQMFDLRVQFHFERL 297 Query: 301 YPFLQNAPELTDRAYKAAQAYLGEENVE-DLDIWMAAEDFSYYTQEMDGCFYRLGIRNEE 359 YP + N PE T +A +A A +G E V+ D + A+EDF++Y Q GC+ LG Sbjct: 298 YPAVVNHPEATQQAMQAMMAAVGAEQVDGDTEPAFASEDFAFYLQHKPGCYAFLGNGVIA 357 Query: 360 KGITSG-------VHTPTFDIDESALEVGAGLMAWIAI 390 G +G +H+P +D ++ ++ AG+ W+++ Sbjct: 358 DGKQAGSQATSRELHSPFYDFNDDIID--AGVAYWVSL 393 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: 365 Number of extensions: 17 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: 402 Length adjustment: 31 Effective length of query: 366 Effective length of database: 371 Effective search space: 135786 Effective search space used: 135786 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