Align NAD-specific glutamate dehydrogenase A; NAD-GDH A; EC 1.4.1.2 (characterized)
to candidate WP_062736531.1 AYX06_RS15495 Glu/Leu/Phe/Val dehydrogenase
Query= SwissProt::P29051 (435 letters) >NCBI__GCF_001580365.1:WP_062736531.1 Length = 431 Score = 385 bits (988), Expect = e-111 Identities = 207/420 (49%), Positives = 265/420 (63%), Gaps = 4/420 (0%) Query: 17 EAADSTEPESALETARRQLYHAASYLDIDQNIVERLKYPKKVHEVTIPIERDDGTVEVFT 76 EAA T P L A+ QL A L + + L P++ V+IP+ RDDG+VEV T Sbjct: 15 EAAAGTGP---LADAQAQLAAAVRALGYETGLHALLARPRREMTVSIPLRRDDGSVEVLT 71 Query: 77 GYRAQHDSVRGPYKGGLRYHPDVTRDECVGLGMWMTWKCAVMDLPFGGAKGGVAVNPKEL 136 G+R QH+ RGP KGGLR+ P V DE L MWMTWKCA++D+P+GGAKGG+ ++P+ Sbjct: 72 GHRVQHNFSRGPAKGGLRFSPAVDLDEVRALAMWMTWKCALLDVPYGGAKGGITIDPRRY 131 Query: 137 SPEEKERLTRRFTQEIRDVIGPNQDIPAPDMGTDPQTMAWLMDAYSMQEGETTPGVVTGK 196 S EE ER+TRR+T EI +IGP +DIPAPD+GTD QTMAW+MD YS+ G T PGVVTGK Sbjct: 132 SREELERVTRRYTSEILPIIGPERDIPAPDIGTDEQTMAWMMDTYSVSVGYTVPGVVTGK 191 Query: 197 PPVVGGSEGREEAPGRSVAIITQLVCEYYDQPLDETTVAVQGYGSVGANAARLLDKWGAT 256 P VGGS GR A R V I + T AVQG+G VGA AA L + G Sbjct: 192 PVSVGGSLGRSSATSRGVVHIALAALAHRGITPAGATAAVQGFGKVGAGAALFLAEAGVE 251 Query: 257 IVAISDVNGAMYEPDGIDTASVPSHDEEPEAVTTYADT-VISNEELLTLDVDVLIPAALG 315 +VA+SD GA++ G+D ++ H +V +A + E LL L VD+L+PAA+ Sbjct: 252 VVAVSDQYGAVHRAGGLDVPALQQHVAATGSVVGFAGADPLPAERLLGLAVDLLVPAAVE 311 Query: 316 NVITKENAEAIAADLVVEGANGPTTSTADSILADRDVAVIPDILANAGGVTVSYFEWLQD 375 V+ NA +AA +VVEGANGPTT+ AD ILA V V+PDILANAGGV VSYFEW+Q Sbjct: 312 GVLHAGNAAEVAASVVVEGANGPTTAAADEILAAHGVLVVPDILANAGGVIVSYFEWVQS 371 Query: 376 INRRAWSLERVNDELEAEMQAAWRAVKDEYENRDVTWRDAAYIVALSRIAEAHEARGLWP 435 WS V+ LEA M AAW V + R ++ R+AA + A+ R+A+AH RGL+P Sbjct: 372 DQAYWWSAAEVDARLEARMLAAWGKVLEVAAERGLSLREAATVTAVQRVADAHLTRGLYP 431 Lambda K H 0.313 0.131 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: 513 Number of extensions: 26 Number of successful extensions: 3 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: 435 Length of database: 431 Length adjustment: 32 Effective length of query: 403 Effective length of database: 399 Effective search space: 160797 Effective search space used: 160797 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.2 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 42 (21.9 bits) S2: 51 (24.3 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