Align Predicted dapE by GapMind curators (no experimental data)
to candidate WP_106711061.1 CU102_RS09815 amidohydrolase
Query= predicted:L0FXC2 (397 letters) >NCBI__GCF_003010955.1:WP_106711061.1 Length = 387 Score = 252 bits (643), Expect = 1e-71 Identities = 150/385 (38%), Positives = 211/385 (54%), Gaps = 12/385 (3%) Query: 11 ADQLNQTIAI-RRHIHAHPELSFEEHQTCAFVEKHLQEIGITNIQRK-ANTGLVALIEGK 68 A ++ Q +A R H+H +PE+ ++ HQT AFV + L+E G I+ TG+V L+ G+ Sbjct: 7 AHEMQQHVAEWRHHLHENPEILYDVHQTSAFVAEKLREFGCDTIETGIGQTGVVGLVRGR 66 Query: 69 NPSKKVIALRADMDALPIVEQNDVPYKSNKEGVMHACGHDVHTSSLLGAASILHAVKDQF 128 + VI RADMDALPI E + P+ S G MHACGHD HT+ LLGAA L ++ F Sbjct: 67 HGEGPVIGFRADMDALPITEASGKPWASKTLGKMHACGHDGHTAMLLGAAQYLAETRN-F 125 Query: 129 EGTVKLIFQPGEEKIPGGASLMIKDKALENPRPSGIVGQHVMPLIDAGKVGFRKGMYMAS 188 GT+ LIFQP EE GA MI D ++ + G H P + G+ RKG MA+ Sbjct: 126 RGTIVLIFQPAEEG-GAGARAMIDDGLMDRFAIGEVYGMHNAPGLPVGQFATRKGSIMAA 184 Query: 189 ADELYLKVIGKGGHGAMPETLVDPVLIASHIIVALQQVISRNASPKVPSVLSFGRIEALG 248 +E + V G+ GH A P T +DPV+I++HII+ALQ ++SR P V+S ++ Sbjct: 185 TNEFEITVTGRSGHAAKPHTAIDPVVISAHIILALQSIVSRETDPLKALVVSVTQLNGGD 244 Query: 249 ATNVIPNEVNIQGTFRTLDETWRAEAHQKMVKIAEGIAEGMGGSVDFEVRKGYPFLQNAP 308 ATNVIP+ + + GT RTL R A +++ +I E A GG + +GYP N Sbjct: 245 ATNVIPDVIKLGGTVRTLVPEIREFAQKRLTEIVESTAAVFGGKAEVVYHQGYPVTFNHD 304 Query: 309 ELTDRAYKAAQAYLGEENVE-DLDIWMAAEDFSYYTQEMDGCFYRLGIRNEEKGITSGVH 367 TD A AQ +GE V + M AEDFSY + G F LG G T G+H Sbjct: 305 RETDFAIGIAQTIVGEAAVNTTMPPVMGAEDFSYMLESRPGAFVFLG-----NGDTPGLH 359 Query: 368 TPTFDIDESALEVGAGLMAWIAINE 392 +D ++ A+ G+ W+++ E Sbjct: 360 NSAYDFNDDAIPY--GISYWVSLAE 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: 402 Number of extensions: 27 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 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