Align Catabolic NAD-specific glutamate dehydrogenase RocG; NAD-GDH; Glutamate dehydrogenase; GlutDH; Trigger enzyme RocG; EC 1.4.1.2 (characterized)
to candidate WP_011320799.1 AVA_RS20865 Glu/Leu/Phe/Val dehydrogenase
Query= SwissProt::P39633 (424 letters) >NCBI__GCF_000204075.1:WP_011320799.1 Length = 365 Score = 187 bits (474), Expect = 6e-52 Identities = 118/320 (36%), Positives = 178/320 (55%), Gaps = 17/320 (5%) Query: 77 GPTKGGVRFHPEVNEEEVKALSIWMTLKCGIANLPYGGGKGGIICDPRTMSFGELERLSR 136 GP GGVR +V EEV L+ MTLK A+LP+GGGK I+ DP+ + ERL R Sbjct: 38 GPAIGGVRMATDVTTEEVFRLARAMTLKNAAADLPHGGGKSAILADPK-QPLADKERLVR 96 Query: 137 GYVRAISQIVGPTKDIPAPDVYTNSQIMAWMMDEYSRLREFDSPGFITGKPLVLGGSQGR 196 + RAI + T+ IP PD+ T+ Q MAW+ +E R G P +GG Sbjct: 97 TFARAIRDV---TEYIPGPDMGTDEQCMAWIKEEIGRA---------VGLPKAIGGIPLD 144 Query: 197 ET-ATAQGVTICIEEAVKKKGIKLQNARIIIQGFGNAGSFLAKFMHDAGAKVIGISDANG 255 E AT G++IC E A K + L+ ARI+IQGFG+ G A+F+ GA +IG +D+ G Sbjct: 145 EIGATGFGLSICAEIASKFCHLNLEGARIVIQGFGSVGKNAARFLTAKGALLIGAADSQG 204 Query: 256 GLYNPDGLDIPYLLD-KRDSFGMVTNLFTDVITNEELLEKDCDILVPAAISNQITAKNAH 314 L+NP G+D+ L+ K +++ D + + +++ +CDI +PAA + I A N Sbjct: 205 TLFNPLGIDVKQLIKLKNSGKSVISYPQGDKLDRDAVIDIECDIWIPAARPDIIHADNVD 264 Query: 315 NIQASIVVEAANGPTTIDATKILNERGVLLVPDILASAGGVTVSYFEWVQNNQGYYWSEE 374 ++ +V+ AN P T A +I +ER +++VPD +A+AGGV + E+ NQ + E Sbjct: 265 RLKTQLVISGANIPFTEAAERICHERNIIVVPDFIANAGGVICAAVEYDGGNQTTAF--E 322 Query: 375 EVAEKLRSVMVSSFETIYQT 394 +A+K+R E + +T Sbjct: 323 TIAKKIRYNTTLVLEQVAKT 342 Lambda K H 0.317 0.134 0.390 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: 385 Number of extensions: 31 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: 424 Length of database: 365 Length adjustment: 31 Effective length of query: 393 Effective length of database: 334 Effective search space: 131262 Effective search space used: 131262 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 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