Align glutamate dehydrogenase [NAD(P)+] (EC 1.4.1.3) (characterized)
to candidate N515DRAFT_0947 N515DRAFT_0947 leucine dehydrogenase
Query= BRENDA::Q38946 (411 letters) >FitnessBrowser__Dyella79:N515DRAFT_0947 Length = 367 Score = 111 bits (277), Expect = 4e-29 Identities = 99/292 (33%), Positives = 139/292 (47%), Gaps = 40/292 (13%) Query: 58 HDNARGPMKGGIRYHP-EVDPDEVNALAQL---MTWKTAVADIPYGGAKGGIGCSPRDLS 113 H+ GP GG+R P + + D VN + +L MT+K AVA + GG K I P S Sbjct: 31 HNTVLGPALGGLRMWPYKTEQDAVNDVLRLSRGMTYKNAVAGLNLGGGKAVIIGDP---S 87 Query: 114 LSELERLTRVFTQKIHDLIGIHTDVPAPDMGTNAQTMAWILDEYSKFHGHSPAVVTGKPI 173 + E L R F + ++ L G + + A D+G + M ++ E VTG Sbjct: 88 KDKSEALFRAFGRFVNSLNGRY--ITAEDVGIDVNDMEYVFRETE--------YVTGVHQ 137 Query: 174 DLGGSLGREAATGRGVVFATEALL-AEYGKSIQG-LTFVIQGFGNVGTWAAKLIHEKGGK 231 GGS T G + A L ++G G ++ +QG G+VG+ KL+ E+G K Sbjct: 138 VHGGSGDPSPFTAFGTLQGLMAALQVKHGNEDVGKYSYAVQGCGHVGSEFIKLLREQGAK 197 Query: 232 VVAVSDITGAIRNPEGIDINALIKHKDATGSLNDFNGGDAMNSDELLIHECDVLIPCALG 291 V DIN KDA D G +A+ DE+ + DV PCALG Sbjct: 198 VFVT-------------DIN-----KDAVQRCVDELGCEAVGLDEIYDVDADVYSPCALG 239 Query: 292 GVLNKENAGDVKAKFIVEAANH--PTDPDADEILSKKGVIILPDIYANAGGV 341 G LN++ +KAK I AAN+ TD DE L+++GV+ PD NAGGV Sbjct: 240 GTLNEQTIDRIKAKIICGAANNQLATDAIGDE-LTRRGVLYAPDYAVNAGGV 290 Lambda K H 0.319 0.137 0.413 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: 424 Number of extensions: 25 Number of successful extensions: 4 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: 411 Length of database: 367 Length adjustment: 30 Effective length of query: 381 Effective length of database: 337 Effective search space: 128397 Effective search space used: 128397 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 (21.7 bits) S2: 50 (23.9 bits)
This GapMind analysis is from Sep 17 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