GapMind for catabolism of small carbon sources

 

Alignments for a candidate for D-LDH in Carboxydothermus pertinax Ug1

Align D-lactate dehydrogenase (EC 1.1.1.28) (characterized)
to candidate WP_075858559.1 cpu_RS03150 phosphoglycerate dehydrogenase

Query= BRENDA::F8A9V0
         (325 letters)



>NCBI__GCF_001950255.1:WP_075858559.1
          Length = 525

 Score =  172 bits (435), Expect = 2e-47
 Identities = 104/298 (34%), Positives = 163/298 (54%), Gaps = 21/298 (7%)

Query: 10  PYEEEFLGPILPSDWDVEMTPDFLDETTVEKAKGAQVVSLFVSDKADGPVLEALHSYGVG 69
           P  E+ L  +    + VE      +E  ++       + +    K    ++EA  +  + 
Sbjct: 8   PVSEKGLNILREEGFIVEEKTKLSEEELIKIISEFDALIVRSETKVTARIIEAAEN--LK 65

Query: 70  LLALRSAGYDHIDIETAKRLGIKVVNVPAYSPHAIADHTLAIMLALIRRLHRAHDKVRLG 129
           ++     G D+ID+  A + GI VVN P  +  A A+HT A+M+AL+R + +AH  ++ G
Sbjct: 66  IIGRAGVGVDNIDLAAASKKGIIVVNSPEGNTIAAAEHTFALMMALLRNIPQAHAALKEG 125

Query: 130 DFDLDGLMGFDLNGKVAGVIGLGKIGRLVATRLKAFGCKVLGYDPYIQPEI-----VENV 184
            +      G++L GK  G+IGLG+IG  VA R+KAF  KV+GYDP+I  E      +  +
Sbjct: 126 KWLRKEFTGYELRGKTVGIIGLGRIGTAVAKRVKAFETKVIGYDPFISEERAHMLGITLM 185

Query: 185 DLDTLITQADIISIHCPLTRENFHMFNEETFKRMKPGAILVNTARGGLIDTKALLEALKS 244
            L+ L+ +ADI+++H PL  E  ++ N E  K MK  A ++N ARGG+ID +AL EALK+
Sbjct: 186 SLEELLQKADIVTMHLPLNNETRNLINRERLKLMKKSAFIINCARGGIIDEEALYEALKT 245

Query: 245 GKLGGAALDVYEYERGLFFKNHQKEGIKDPYLAQLLGLANVVLTGHQAFLTREAVKNI 302
           G++ GAALDV+            KE + +   + L  L NV++T H    T+EA  N+
Sbjct: 246 GEIAGAALDVF-----------SKEPLTE---SPLFELPNVIVTPHLGASTKEAQVNV 289


Lambda     K      H
   0.321    0.140    0.407 

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: 392
Number of extensions: 19
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: 325
Length of database: 525
Length adjustment: 31
Effective length of query: 294
Effective length of database: 494
Effective search space:   145236
Effective search space used:   145236
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: 50 (23.9 bits)

This GapMind analysis is from Apr 09 2024. 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