GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gdhA in Kocuria turfanensis HO-9042

Align NAD-specific glutamate dehydrogenase A; NAD-GDH A; EC 1.4.1.2 (characterized)
to candidate WP_062736531.1 AYX06_RS15495 Glu/Leu/Phe/Val dehydrogenase

Query= SwissProt::P29051
         (435 letters)



>NCBI__GCF_001580365.1:WP_062736531.1
          Length = 431

 Score =  385 bits (988), Expect = e-111
 Identities = 207/420 (49%), Positives = 265/420 (63%), Gaps = 4/420 (0%)

Query: 17  EAADSTEPESALETARRQLYHAASYLDIDQNIVERLKYPKKVHEVTIPIERDDGTVEVFT 76
           EAA  T P   L  A+ QL  A   L  +  +   L  P++   V+IP+ RDDG+VEV T
Sbjct: 15  EAAAGTGP---LADAQAQLAAAVRALGYETGLHALLARPRREMTVSIPLRRDDGSVEVLT 71

Query: 77  GYRAQHDSVRGPYKGGLRYHPDVTRDECVGLGMWMTWKCAVMDLPFGGAKGGVAVNPKEL 136
           G+R QH+  RGP KGGLR+ P V  DE   L MWMTWKCA++D+P+GGAKGG+ ++P+  
Sbjct: 72  GHRVQHNFSRGPAKGGLRFSPAVDLDEVRALAMWMTWKCALLDVPYGGAKGGITIDPRRY 131

Query: 137 SPEEKERLTRRFTQEIRDVIGPNQDIPAPDMGTDPQTMAWLMDAYSMQEGETTPGVVTGK 196
           S EE ER+TRR+T EI  +IGP +DIPAPD+GTD QTMAW+MD YS+  G T PGVVTGK
Sbjct: 132 SREELERVTRRYTSEILPIIGPERDIPAPDIGTDEQTMAWMMDTYSVSVGYTVPGVVTGK 191

Query: 197 PPVVGGSEGREEAPGRSVAIITQLVCEYYDQPLDETTVAVQGYGSVGANAARLLDKWGAT 256
           P  VGGS GR  A  R V  I      +        T AVQG+G VGA AA  L + G  
Sbjct: 192 PVSVGGSLGRSSATSRGVVHIALAALAHRGITPAGATAAVQGFGKVGAGAALFLAEAGVE 251

Query: 257 IVAISDVNGAMYEPDGIDTASVPSHDEEPEAVTTYADT-VISNEELLTLDVDVLIPAALG 315
           +VA+SD  GA++   G+D  ++  H     +V  +A    +  E LL L VD+L+PAA+ 
Sbjct: 252 VVAVSDQYGAVHRAGGLDVPALQQHVAATGSVVGFAGADPLPAERLLGLAVDLLVPAAVE 311

Query: 316 NVITKENAEAIAADLVVEGANGPTTSTADSILADRDVAVIPDILANAGGVTVSYFEWLQD 375
            V+   NA  +AA +VVEGANGPTT+ AD ILA   V V+PDILANAGGV VSYFEW+Q 
Sbjct: 312 GVLHAGNAAEVAASVVVEGANGPTTAAADEILAAHGVLVVPDILANAGGVIVSYFEWVQS 371

Query: 376 INRRAWSLERVNDELEAEMQAAWRAVKDEYENRDVTWRDAAYIVALSRIAEAHEARGLWP 435
                WS   V+  LEA M AAW  V +    R ++ R+AA + A+ R+A+AH  RGL+P
Sbjct: 372 DQAYWWSAAEVDARLEARMLAAWGKVLEVAAERGLSLREAATVTAVQRVADAHLTRGLYP 431


Lambda     K      H
   0.313    0.131    0.387 

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: 513
Number of extensions: 26
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: 435
Length of database: 431
Length adjustment: 32
Effective length of query: 403
Effective length of database: 399
Effective search space:   160797
Effective search space used:   160797
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.9 bits)
S2: 51 (24.3 bits)

This GapMind analysis is from Sep 24 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