GapMind for catabolism of small carbon sources

 

Alignments for a candidate for dhaD in Lactobacillus silagei IWT126

Align Glycerol dehydrogenase; GDH; GLDH; GlyDH; EC 1.1.1.6 (characterized)
to candidate WP_089136115.1 CES79_RS01700 glycerol dehydrogenase

Query= SwissProt::P32816
         (370 letters)



>NCBI__GCF_002217945.1:WP_089136115.1
          Length = 368

 Score =  368 bits (945), Expect = e-106
 Identities = 196/361 (54%), Positives = 250/361 (69%), Gaps = 2/361 (0%)

Query: 5   RVFISPAKYVQGKNVITKIANYLEGIGNKTVVIADEIVWKIAGHTIVNELKKGNIAAEEV 64
           ++F SP+ YVQG   +   A  L  +G+K +V+AD  V+KI G   ++ L +      +V
Sbjct: 3   KIFGSPSTYVQGSGALFDSAEALHKLGSKPIVMADTTVYKIVGKKFIDYLGQQKFDVRKV 62

Query: 65  VFSGEASRNEVERIANIARKAEAAIVIGVGGGKTLDTAKAVADELDAYIVIVPTAASTDA 124
            F GEAS  E++RI  I +   A ++IG+GGGKTLD+AKA+AD L   + I+PT ASTDA
Sbjct: 63  TFKGEASDKEIDRITGIGQDFGADLIIGLGGGKTLDSAKAIADNLKLPVAILPTLASTDA 122

Query: 125 PTSALSVIYSDDGVFESYRFYKKNPDLVLVDTKIIANAPPRLLASGIADALATWVEARSV 184
           P S LSVIY+ DG FE YRFY KNPDLVLVDT+++ANAP RLLASGIADALAT VEA++V
Sbjct: 123 PCSRLSVIYTPDGGFEKYRFYSKNPDLVLVDTQLVANAPTRLLASGIADALATNVEAQAV 182

Query: 185 IKSGGKTMAGGIPTIAAEAIAEKCEQTLFKYGKLAYESVKAKVVTPALEAVVEANTLLSG 244
            K+ G+TM     T+   AIAEKCE+TLF YG  A ++     VTPALE +VEANTL+SG
Sbjct: 183 AKANGQTMLNAKQTLVGNAIAEKCEETLFAYGLQAIDAAGVHAVTPALEKIVEANTLMSG 242

Query: 245 LGFESGGLAAAHAIHNGFTALEGE-IHHLTHGEKVAFGTLVQLALEEHSQQEIERYIELY 303
           +GFESGGLAAAHAIHNG T+L  E +H  THGEKVAFGTL QL LE    ++I  Y+   
Sbjct: 243 VGFESGGLAAAHAIHNGLTSLPNEALHAKTHGEKVAFGTLTQLFLEGRETEDIHTYLAFD 302

Query: 304 LSLDLPVTLEDIKLKDASREDILKVAKAATAEGETI-HNAFNVTADDVADAIFAADQYAK 362
           L+L LP T +D+ + D S ED+LKV +AATA  +T+    F VT  DV  A+  AD Y++
Sbjct: 303 LALGLPTTFDDLGIADISDEDLLKVGQAATAPADTMTEMPFEVTPADVVAAMKGADAYSR 362

Query: 363 A 363
           A
Sbjct: 363 A 363


Lambda     K      H
   0.314    0.131    0.357 

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: 331
Number of extensions: 7
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: 370
Length of database: 368
Length adjustment: 30
Effective length of query: 340
Effective length of database: 338
Effective search space:   114920
Effective search space used:   114920
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: 42 (22.0 bits)
S2: 49 (23.5 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