GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__Keio:17057
          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:

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