Align Cryptic catabolic NAD-specific glutamate dehydrogenase GudB; NAD-GDH; EC 1.4.1.2 (characterized)
to candidate WP_086511351.1 BZY95_RS18440 Glu/Leu/Phe/Val dehydrogenase
Query= SwissProt::P50735 (427 letters) >NCBI__GCF_002151265.1:WP_086511351.1 Length = 345 Score = 111 bits (277), Expect = 4e-29 Identities = 92/295 (31%), Positives = 141/295 (47%), Gaps = 40/295 (13%) Query: 70 AQHNDSVGPTKGGIRFHPNVTEKEVKA-VKALSIWMSLKCGIIDLPYGGGKGGIVCDPR- 127 A H+ GP GG+R +P +E + V LS M+ K + DLP GGGK I+ DPR Sbjct: 30 AIHDTRRGPALGGLRIYPYASEADALTDVLRLSRGMTYKSALADLPLGGGKAVIIADPRR 89 Query: 128 DMSFRELERLSRGYVRAISQIVGPTKDVPAPDVFTNSQIMAWMMDEYSRIDEFNSPGFIT 187 D + L + R + + G + + A D + + M + E S + G + Sbjct: 90 DKTPAMLYAMGR----LVESLGG--RYITAEDSGSGEEDMRLIRQETSHVSGLGHDGN-S 142 Query: 188 GKPLVLGGSHGRESATAKGVTICIKEAAKKR--GIDIKGARVVVQGFGNAGSYLAKFMHD 245 G P TA GV +K A + R D++G RV +QG G+ G++LA+ +H+ Sbjct: 143 GDP---------SPFTAHGVFCALKSAVRHRLGRSDLQGLRVAIQGVGHVGAHLARELHE 193 Query: 246 AGAKVVGISDAYGGLYDPEGLDIDYLLDRRDSFG-TVTKLFNDTITNQELLELDCDILVP 304 AGAK+V D+D RDS G V++L +++ + + D D+ P Sbjct: 194 AGAKLV-------------LTDVD-----RDSLGMLVSELSAESVAPDAIFDADVDVFAP 235 Query: 305 AAIENQITEENAHNIRAKIVVEAANGP-TTLEGTKILSDRDILLVPDVLASAGGV 358 A+ +T+E A ++AK++ AAN T L R IL PD +A+AGGV Sbjct: 236 CALGAVLTDEVAERLKAKVICGAANNQLATAAVAGRLQARGILYTPDYVANAGGV 290 Lambda K H 0.318 0.136 0.398 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: 301 Number of extensions: 15 Number of successful extensions: 5 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: 427 Length of database: 345 Length adjustment: 30 Effective length of query: 397 Effective length of database: 315 Effective search space: 125055 Effective search space used: 125055 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