GapMind for catabolism of small carbon sources

 

Alignments for a candidate for dhaD in Streptococcus massiliensis 4401825

Align Glycerol dehydrogenase; GDH; GLDH; GlyDH; EC 1.1.1.6 (characterized)
to candidate WP_018371638.1 BN415_RS08265 glycerol dehydrogenase

Query= SwissProt::P32816
         (370 letters)



>NCBI__GCF_000341525.1:WP_018371638.1
          Length = 363

 Score =  400 bits (1027), Expect = e-116
 Identities = 201/362 (55%), Positives = 266/362 (73%), Gaps = 1/362 (0%)

Query: 5   RVFISPAKYVQGKNVITKIANYLEGIGNKTVVIADEIVWKIAGHTIVNELKKGNIAAEEV 64
           + F SP++YVQG+N + + A  L  +GN  +++ D++V+++ G      L +       V
Sbjct: 2   KYFASPSRYVQGENALFENAKPLLKLGNHPLLLCDDLVYELVGERFEEYLIRYGFQVHHV 61

Query: 65  VFSGEASRNEVERIANIARKAEAAIVIGVGGGKTLDTAKAVADELDAYIVIVPTAASTDA 124
            F+GEAS  E+ R+  +A + +  ++IG+GGGKT+D+AKA+AD L   +VI PT ASTDA
Sbjct: 62  AFNGEASEKEITRVVALAEEKKNDMIIGLGGGKTIDSAKAIADMLKVPVVIAPTIASTDA 121

Query: 125 PTSALSVIYSDDGVFESYRFYKKNPDLVLVDTKIIANAPPRLLASGIADALATWVEARSV 184
           PTSALSVIY++DG FE Y FY +NPDLVLVD+ +IA AP RLLASGIADALATWVEAR+V
Sbjct: 122 PTSALSVIYTEDGAFEKYIFYSRNPDLVLVDSAVIAKAPKRLLASGIADALATWVEARAV 181

Query: 185 IKSGGKTMAGGIPTIAAEAIAEKCEQTLFKYGKLAYESVKAKVVTPALEAVVEANTLLSG 244
            ++ G+ M G   T+A  AIA+KCE+TLF  G  A  + + +VVTPAL+ ++EANTLLSG
Sbjct: 182 KEAHGQNMLGAKQTLAGLAIAQKCEETLFADGLQAMAACEVQVVTPALDNIIEANTLLSG 241

Query: 245 LGFESGGLAAAHAIHNGFTALEGEIHHLTHGEKVAFGTLVQLALEEHSQQEIERYIELYL 304
           +GFESGGLAAAHAIHNGFTAL G+IHHLTHGEKVA+GTLVQL LE   ++E+++YI  Y 
Sbjct: 242 VGFESGGLAAAHAIHNGFTALTGDIHHLTHGEKVAYGTLVQLFLENRPKEELDKYIRFYQ 301

Query: 305 SLDLPVTLEDIKLKDASREDILKVAKAATAEGETIHN-AFNVTADDVADAIFAADQYAKA 363
            + +P TL ++ L++AS +D+LKV K AT EGETIH   F VTA D+A+AI A D Y K 
Sbjct: 302 KIQMPTTLAELHLENASYQDLLKVGKQATIEGETIHQMPFKVTATDIANAILAVDAYVKT 361

Query: 364 YK 365
            K
Sbjct: 362 LK 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: 348
Number of extensions: 9
Number of successful extensions: 1
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: 363
Length adjustment: 30
Effective length of query: 340
Effective length of database: 333
Effective search space:   113220
Effective search space used:   113220
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