Align NAD-specific glutamate dehydrogenase; NAD-GDH; EC 1.4.1.2 (uncharacterized)
to candidate WP_086508080.1 BZY95_RS00680 Glu/Leu/Phe/Val dehydrogenase
Query= curated2:Q5HHC7 (414 letters) >NCBI__GCF_002151265.1:WP_086508080.1 Length = 432 Score = 368 bits (945), Expect = e-106 Identities = 187/424 (44%), Positives = 263/424 (62%), Gaps = 15/424 (3%) Query: 2 TENNNLVTSTQGIIKEALHKLGFDEGMYDLIKEPLRMLQVRIPVRMDDGTVKTFTGYRAQ 61 T++ NL + ++E + + + +P LQV +PVRMDDG++K F G+R Q Sbjct: 5 TDHANLFDDARSRLEEVCQAIDIQGDARERLMQPSLSLQVSVPVRMDDGSLKVFPGWRVQ 64 Query: 62 HNDAVGPTKGGVRFHPDVDEEEVKALSMWMTLKCGIVNLPYGGGKGGIVCDPRQMSIHEV 121 +N +GP KGG+RFHPDV++EEV LS WM +KC +V+LPYGGGKGG+ DP+Q+S E+ Sbjct: 65 YNTTLGPAKGGIRFHPDVNQEEVTTLSFWMAVKCAVVDLPYGGGKGGVKVDPKQLSKLEL 124 Query: 122 ERLSRGYVRAISQFVGPNKDIPAPDVFTNSQIMAWMMDEYSALDKFNSPGFITGKPIVLG 181 ERL+RGYVRAI+ +GP++DIPAPDV TN+ +M WM DE+ L + P ITGKP LG Sbjct: 125 ERLARGYVRAIADIMGPDRDIPAPDVNTNATVMGWMADEFDHLARGKVPAAITGKPPELG 184 Query: 182 GSHGRDRSTALGVVIAIEQAAKRRNMQIEGAKVVIQGFGNAGSFLAKFLYDLGAKIVGIS 241 GS GR +T G + ++ A R + E V IQGFGNA A+ +D G +IV +S Sbjct: 185 GSLGRVAATGRGALHVLDLWAAREKRKPEETTVAIQGFGNAAYHFARLAHDQGYRIVAVS 244 Query: 242 DAYGALHDPNGLDIDYLLDRR-------------DSFGTVTNLFEETISNKELFELDCDI 288 D+ GA++ GLD D +++++ DS ++ E + EL L+ D+ Sbjct: 245 DSKGAIYSEEGLDPDAIMEQKQRNMRLHEMVYCDDSVCIAEDV--EKLDRDELLTLEVDV 302 Query: 289 LVPAAISNQITEDNAHDIKASIVVEAANGPTTPEATRILTERGILLVPDVLASAGGVTVS 348 L AA+ NQ+ EDN +KA ++E ANGP + A L ERG+ ++PDVLA+ GGV VS Sbjct: 303 LALAALENQVHEDNVDQVKAGALLEIANGPVSSRADERLEERGVPVLPDVLANTGGVIVS 362 Query: 349 YFEWVQNNQGYYWSEEEVNEKLREKLEAAFDTIYELSQNRKIDMRLAAYIIGIKRTAEAA 408 Y+EWVQN G W EEE+N +L E LE + ++E ++ +I R AAY GI+R A A Sbjct: 363 YYEWVQNRSGERWPEEEINRRLAEHLERQSELVFERAEQEEISYRRAAYRQGIERIAHAI 422 Query: 409 RYRG 412 RG Sbjct: 423 ELRG 426 Lambda K H 0.318 0.137 0.401 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: 498 Number of extensions: 17 Number of successful extensions: 2 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: 414 Length of database: 432 Length adjustment: 32 Effective length of query: 382 Effective length of database: 400 Effective search space: 152800 Effective search space used: 152800 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: 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