Align Catabolic NAD-specific glutamate dehydrogenase RocG; NAD-GDH; Glutamate dehydrogenase; GlutDH; Trigger enzyme RocG; EC 1.4.1.2 (characterized)
to candidate WP_008623896.1 C943_RS02640 Glu/Leu/Phe/Val dehydrogenase
Query= SwissProt::P39633 (424 letters) >NCBI__GCF_000330725.2:WP_008623896.1 Length = 425 Score = 379 bits (973), Expect = e-110 Identities = 189/398 (47%), Positives = 262/398 (65%), Gaps = 3/398 (0%) Query: 28 ALRKLGYPGDMYELMKEPQRMLTVRIPVKMDNGSVKVFTGYRSQHNDAVGPTKGGVRFHP 87 A +KLG ++Y ++K P + + V +P+ MDNG +KVF G R H++ +GP KGG+RF P Sbjct: 26 AAQKLGLSEEVYNVLKNPAKQVIVSLPITMDNGKIKVFEGIRVIHSNILGPAKGGIRFAP 85 Query: 88 EVNEEEVKALSIWMTLKCGIANLPYGGGKGGIICDPRTMSFGELERLSRGYVRAISQIVG 147 +V+ +EV+AL+ WMT KC + ++PYGGGKGG+ C+PR MS GE+ERL R Y A+ + G Sbjct: 86 DVHLDEVRALAAWMTWKCAVVDIPYGGGKGGVRCNPREMSAGEIERLVRAYTLAMIDVFG 145 Query: 148 PTKDIPAPDVYTNSQIMAWMMDEYSRLREFDSPGFITGKPLVLGGSQGRETATAQGVTIC 207 P KDIPAPD+ T + MAW+MDEYS+ +TGKPLVLGGS GR AT +GV + Sbjct: 146 PDKDIPAPDMGTGPREMAWLMDEYSKAHGMTVNAVVTGKPLVLGGSLGRTEATGRGVMVT 205 Query: 208 IEEAVKKKGIKLQNARIIIQGFGNAGSFLAKFMHDAGAKVIGISDANGGLYNPDGLDIPY 267 A++K I A +QGFGN GS+ A+ + + G KV+ ISD +G YN +G++I Sbjct: 206 ALAAMQKLKINPFQATCAVQGFGNVGSWAAQLLEERGLKVVSISDISGAYYNSNGINIQE 265 Query: 268 LLDKRDSFGMVTNLF--TDVITNE-ELLEKDCDILVPAAISNQITAKNAHNIQASIVVEA 324 + RD + + ++N ELLE + D+LVPAA+ + IT NA I+A ++VE Sbjct: 266 AIAYRDGNKGTLEGYQGAEKLSNPMELLELEVDVLVPAAVEDVITIGNADKIKAKLIVEG 325 Query: 325 ANGPTTIDATKILNERGVLLVPDILASAGGVTVSYFEWVQNNQGYYWSEEEVAEKLRSVM 384 ANGPT+ A ILNE+G++ VPDILA+AGGVTVSYFEWVQN GY W+ E V + +M Sbjct: 326 ANGPTSAKADAILNEKGIMAVPDILANAGGVTVSYFEWVQNRLGYKWTAERVNRRSDRIM 385 Query: 385 VSSFETIYQTAATHKVDMRLAAYMTGIRKSAEASRFRG 422 +F+ +YQ A + V MR+AAY+ I K A+ FRG Sbjct: 386 KDAFDHVYQAAVKYDVPMRIAAYIVAIDKVAKTYTFRG 423 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: 509 Number of extensions: 15 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: 425 Length adjustment: 32 Effective length of query: 392 Effective length of database: 393 Effective search space: 154056 Effective search space used: 154056 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: 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