GapMind for catabolism of small carbon sources

 

Aligments for a candidate for D-LDH in Escherichia coli BW25113

Align Probable D-lactate dehydrogenase, mitochondrial; DLD; Lactate dehydrogenase D; EC 1.1.2.4 (characterized)
to candidate 17057 b2979 glycolate oxidase subunit, FAD-linked (NCBI)

Query= SwissProt::F1QXM5
         (497 letters)



>lcl|FitnessBrowser__Keio:17057 b2979 glycolate oxidase subunit,
           FAD-linked (NCBI)
          Length = 499

 Score =  199 bits (505), Expect = 2e-55
 Identities = 131/433 (30%), Positives = 210/433 (48%), Gaps = 21/433 (4%)

Query: 63  SVHRCRPPDVVVFPRSVEEVSALAKICHHYRLPIIPFGTGTGLEGGVGALQGGVCFSLRK 122
           S +R RP  +VV P+ +E+V+A+  +CH  R+P++  G GTGL GG   L+ GV   + +
Sbjct: 50  SAYRTRPL-LVVLPKQMEQVTAILAVCHRLRVPVVTRGAGTGLSGGALPLEKGVLLVMAR 108

Query: 123 MEQVVDLHQEDFDVTVEPGVTRKSLNSYLRDTGLWFPVDPGAD--ASLCGMAATSASGTN 180
            ++++D++       V+PGV   +++  +    L++  DP +    S+ G  A +A G +
Sbjct: 109 FKEILDINPVGRRARVQPGVRNLAISQAVAPHNLYYAPDPSSQIACSIGGNVAENAGGVH 168

Query: 181 AVRYGTMRENVLNLEVVLADGTILHTAGKGRRPRKTAAGYNLTNLFVGSEGTLGIITKAT 240
            ++YG    N+L +EV   DG  L T G        + G++L  LF GSEG LG+ T+ T
Sbjct: 169 CLKYGLTVHNLLKIEVQTLDGEAL-TLGS---DALDSPGFDLLALFTGSEGMLGVTTEVT 224

Query: 241 LRLYGVPESMVSAVCSFPSVQSAVDSTVQILQAGVPIARIEFLDDVMINACNRFNNLSYA 300
           ++L   P      + SF SV+ A  +   I+  G+    +E +D++ I A   F +  Y 
Sbjct: 225 VKLLPKPPVARVLLASFDSVEKAGLAVGDIIANGIIPGGLEMMDNLSIRAAEDFIHAGYP 284

Query: 301 V--TPTLFLEFHGSSKSMEEQVSVTEEITRDNGGSDFAWAEDEETRSRLWKARHDAWYAA 358
           V     L  E  G    ++E      +I    G +D   A+DE  R R W  R +A+ A 
Sbjct: 285 VDAEAILLCELDGVESDVQEDCERVNDILLKAGATDVRLAQDEAERVRFWAGRKNAFPAV 344

Query: 359 MALRPGCKAYSTDVCVPISRLPQII-----VETKADLISNNITGPIAGHVGDGNFHCLIV 413
             + P    Y  D  +P   LP ++     +  + DL   N+      H GDGN H LI+
Sbjct: 345 GRISP--DYYCMDGTIPRRALPGVLEGIARLSQQYDLRVANVF-----HAGDGNMHPLIL 397

Query: 414 LDPNDTDEVQRVHSFTERLARRALAMDGTCTGEHGIGLGKRALLREEVGPLAIEVMKGLK 473
            D N+  E  R      ++    + + G+ +GEHGIG  K   +  +     I     +K
Sbjct: 398 FDANEPGEFARAEELGGKILELCVEVGGSISGEHGIGREKINQMCAQFNSDEITTFHAVK 457

Query: 474 ASLDPRNLMNPGK 486
           A+ DP  L+NPGK
Sbjct: 458 AAFDPDGLLNPGK 470


Lambda     K      H
   0.319    0.135    0.399 

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: 558
Number of extensions: 27
Number of successful extensions: 5
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: 497
Length of database: 499
Length adjustment: 34
Effective length of query: 463
Effective length of database: 465
Effective search space:   215295
Effective search space used:   215295
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 52 (24.6 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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code.

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