Align Catabolic NAD-specific glutamate dehydrogenase RocG; NAD-GDH; Glutamate dehydrogenase; GlutDH; Trigger enzyme RocG; EC 1.4.1.2 (characterized)
to candidate AZOBR_RS22625 AZOBR_RS22625 glutamate dehydrogenase
Query= SwissProt::P39633 (424 letters) >FitnessBrowser__azobra:AZOBR_RS22625 Length = 419 Score = 375 bits (964), Expect = e-108 Identities = 188/401 (46%), Positives = 262/401 (65%), Gaps = 3/401 (0%) Query: 25 IKEALRKLGYPGDMYELMKEPQRMLTVRIPVKMDNGSVKVFTGYRSQHNDAVGPTKGGVR 84 + EA + + ++ E +K + L+VR+ V+MD+GS + F +R +++D GPTKGG+R Sbjct: 12 LDEAAKHVEVDSEVLEKLKYAKETLSVRLSVRMDDGSRRSFPAWRCRYDDTRGPTKGGIR 71 Query: 85 FHPEVNEEEVKALSIWMTLKCGIANLPYGGGKGGIICDPRTMSFGELERLSRGYVRAISQ 144 FHP N EEV L+ WMT KC + NLPYGGGKG + DP ++S ELERLSR YV+A + Sbjct: 72 FHPSSNVEEVTTLAFWMTFKCAVMNLPYGGGKGAVKVDPHSLSKSELERLSRAYVQAFAG 131 Query: 145 IVGPTKDIPAPDVYTNSQIMAWMMDEYSRLREFDSPGFITGKPLVLGGSQGRETATAQGV 204 ++GP +DIPAPDVYTNS IM WM DEYS + SP ITGKPL LGGS GR+ ATA+G Sbjct: 132 MIGPDRDIPAPDVYTNSMIMGWMADEYSSIVRQPSPAVITGKPLPLGGSLGRDDATARGG 191 Query: 205 TICIEEAVKKKGIKLQNARIIIQGFGNAGSFLAKFMHDAGAKVIGISDANGGLYNPDGLD 264 I+ + + R++IQG+GNAG +A+ +H G +++G+SD+ G + DGLD Sbjct: 192 YYLIKHLEEDLRLSGSARRVVIQGYGNAGFHIARLLHADGYRIVGLSDSRGAIVCEDGLD 251 Query: 265 IPYLLDKRDSFGMVTNLFTD---VITNEELLEKDCDILVPAAISNQITAKNAHNIQASIV 321 + ++ G VT + +T +ELL C+ILVPAA+ +QI NA I+A +V Sbjct: 252 PQAVQTAKEHGGSVTAYTGNGARAVTGDELLGTPCEILVPAALEDQIHKGNAGLIKARVV 311 Query: 322 VEAANGPTTIDATKILNERGVLLVPDILASAGGVTVSYFEWVQNNQGYYWSEEEVAEKLR 381 +E ANGP T DA +ILNE GV+++PDILA+AGGVTVSYFEWVQN QGYYW +E+ E+LR Sbjct: 312 LELANGPVTPDADRILNEAGVIVLPDILANAGGVTVSYFEWVQNRQGYYWGLDEIHERLR 371 Query: 382 SVMVSSFETIYQTAATHKVDMRLAAYMTGIRKSAEASRFRG 422 +M + ++ T + MR AAY + + ++A G Sbjct: 372 VIMETEGRRVWDMGTTKDIPMRTAAYAHALERLSKAIAAHG 412 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: 497 Number of extensions: 20 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: 424 Length of database: 419 Length adjustment: 32 Effective length of query: 392 Effective length of database: 387 Effective search space: 151704 Effective search space used: 151704 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 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