GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gdhA in Echinicola vietnamensis KMM 6221, DSM 17526

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.

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About GapMind

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:

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

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