Align glutamate dehydrogenase (EC 1.4.1.2) (characterized)
to candidate WP_008626729.1 C943_RS08810 Glu/Leu/Phe/Val dehydrogenase
Query= BRENDA::P00366 (558 letters) >NCBI__GCF_000330725.2:WP_008626729.1 Length = 472 Score = 447 bits (1150), Expect = e-130 Identities = 232/455 (50%), Positives = 304/455 (66%), Gaps = 14/455 (3%) Query: 103 RSILRIIKPCNHVLSLSFPIRRDDGSWEVIEGYRAQHSQHRTPCKGGIRYSTDVSVDEVK 162 + +L IK CN + FPIR +DG++EV+ GYR QHS H+ P KGGIR+S+ V +EVK Sbjct: 28 QGLLDQIKACNSIYKFHFPIRHEDGTYEVLTGYRIQHSHHKLPVKGGIRFSSFVDEEEVK 87 Query: 163 ALASLMTYKCAVVDVPFGGAKAGVKINPKNYTDNELEKITRRFTMELAKKGFIGPGVDVP 222 LA+LMTYKCA+V+VPFGGAK GV + PKNY + LEKITRR+T EL KK FIGP +DVP Sbjct: 88 GLAALMTYKCALVNVPFGGAKGGVSVEPKNYNERMLEKITRRYTSELIKKKFIGPAIDVP 147 Query: 223 APDMSTGEREMSWIADTYASTIGHYDINAHACVTGKPISQGGIHGRISATGRGVFHGIEN 282 APD TG REM+WI DTY INA CVTGKP+SQ GI GR ATG+GVF GI Sbjct: 148 APDYGTGAREMAWIVDTY-EAFNPEVINAKGCVTGKPLSQHGIEGRTEATGQGVFFGIRE 206 Query: 283 FINEASYMSILGMTPGFGDKTFVVQGFGNVGLHSMRYLHRFGAKCITVGESDGSIWNPDG 342 + M LG+T G+ KT +VQG GNVG +S +Y+ GAK I V E +G IW+ G Sbjct: 207 ALAVEEDMRELGLTTGYRGKTVIVQGLGNVGYYSAKYIAEAGAKVIGVAEWNGGIWDEKG 266 Query: 343 IDPKELEDFKLQHGTILGFPKAKIYEGSI--LEVDCDILIPAASEKQLTKSNAPRVKAKI 400 ID + L++++L++ GFPK + E SI L CDILIPAA E Q+TK NAP+++AKI Sbjct: 267 IDIEALKEYQLKNKGFKGFPKGEFIENSIEMLTYPCDILIPAALENQITKDNAPKIQAKI 326 Query: 401 IAEGANGPTTPEADKIFLERNIMVIPDLYLNAGGVTVSYFEWLNNLNHVSYGRLTFKYER 460 I E ANGP T EA+KI LE+ IMVIPD+YLNAGGVTVSYFEWL NL+ VS+G+L +Y++ Sbjct: 327 IGEAANGPVTKEAEKILLEKGIMVIPDMYLNAGGVTVSYFEWLKNLSRVSFGKLERRYDQ 386 Query: 461 DSNYHLLMSVQESLERKFGKHGGTIPIVPTAEFQDRISGASEKDIVHSGLAYTMERSARQ 520 + LL +++ + +F + E I GASE+D+V SGL TM + Sbjct: 387 EKFRRLLGTIENATGEEFTED----------EKTQLIQGASERDLVLSGLEETMVTAYHA 436 Query: 521 IMRTAMKYNLGLDLRTAAYVNAIEKVFRVYNEAGV 555 I R + N+ LRTA ++ A++++ + Y + G+ Sbjct: 437 INRVRKEKNI-KSLRTAGFILALQRIAQSYTDLGI 470 Lambda K H 0.318 0.136 0.404 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: 707 Number of extensions: 20 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: 558 Length of database: 472 Length adjustment: 35 Effective length of query: 523 Effective length of database: 437 Effective search space: 228551 Effective search space used: 228551 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 (21.7 bits) S2: 52 (24.6 bits)
This GapMind analysis is from Sep 24 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