Align Cryptic catabolic NAD-specific glutamate dehydrogenase GudB; NAD-GDH; EC 1.4.1.2 (characterized)
to candidate Echvi_1535 Echvi_1535 Glutamate dehydrogenase/leucine dehydrogenase
Query= SwissProt::P50735 (427 letters) >FitnessBrowser__Cola:Echvi_1535 Length = 425 Score = 377 bits (968), Expect = e-109 Identities = 187/417 (44%), Positives = 272/417 (65%), Gaps = 6/417 (1%) Query: 12 EDKLDVLKSTQTVIHKALEKLGYPEEVYELLKEPMRLLTVKIPVRMDDGSVKIFTGYRAQ 71 +DK + L+S + A EKLG EEVY +LK P + + V +P+ MD+G +K+F G R Sbjct: 10 KDKENPLESMMERFNIAAEKLGLSEEVYNVLKNPAKQVIVSLPITMDNGKIKVFEGIRVV 69 Query: 72 HNDSVGPTKGGIRFHPNVTEKEVKAVKALSIWMSLKCGIIDLPYGGGKGGIVCDPRDMSF 131 H++ +GP KGGIRF P+V + V+AL+ WM+ KC ++D+PYGGGKGG+ C+PR+MS Sbjct: 70 HSNILGPAKGGIRFAPDV---HIDEVRALAAWMTWKCAVVDIPYGGGKGGVRCNPREMSP 126 Query: 132 RELERLSRGYVRAISQIVGPTKDVPAPDVFTNSQIMAWMMDEYSRIDEFNSPGFITGKPL 191 E+ERL R Y A+ + GP KD+PAPD+ T + MAW+MDEYS+ +TGKPL Sbjct: 127 GEIERLVRAYTLAMIDVFGPDKDIPAPDMGTGPKEMAWLMDEYSKAKGTTVNAVVTGKPL 186 Query: 192 VLGGSHGRESATAKGVTICIKEAAKKRGIDIKGARVVVQGFGNAGSYLAKFMHDAGAKVV 251 VLGGS GR AT +GV + A +K I+ A VQGFGN GS+ + + + G KVV Sbjct: 187 VLGGSLGRTEATGRGVMVSALAAMEKLKINPFQATCAVQGFGNVGSWASALLEERGLKVV 246 Query: 252 GISDAYGGLYDPEGLDIDYLLDRRDSFGTVTKLFNDT---ITNQELLELDCDILVPAAIE 308 +SD G Y+ G++I + RD + F+ ELLEL D+LVPAA+E Sbjct: 247 AVSDISGAYYNANGINIQKAIAYRDGNKGTLEGFDGAEKLSDPMELLELKVDVLVPAAVE 306 Query: 309 NQITEENAHNIRAKIVVEAANGPTTLEGTKILSDRDILLVPDVLASAGGVTVSYFEWVQN 368 + IT+ N I A+++VE ANGPT+ KI++D+ I++VPD+LA+AGGVTVSYFEWVQN Sbjct: 307 DVITKANVDKINARLIVEGANGPTSFNADKIINDKGIMVVPDILANAGGVTVSYFEWVQN 366 Query: 369 NQGFYWSEEEVEEKLEKMMVKSFNNIYEMANNRRIDMRLAAYMVGVRKMAEASRFRG 425 G+ W+ E V + +++M ++F+ +Y+++ + MR+AAY+V + K+A+ +FRG Sbjct: 367 RLGYKWTAERVNRRSDRIMKEAFDQVYKVSVKHGVPMRIAAYIVAIDKVAQTYQFRG 423 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: 527 Number of extensions: 19 Number of successful extensions: 3 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: 425 Length adjustment: 32 Effective length of query: 395 Effective length of database: 393 Effective search space: 155235 Effective search space used: 155235 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: 51 (24.3 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