GapMind for catabolism of small carbon sources

 

Alignments for a candidate for D-LDH in Methanosarcina acetivorans C2A

Align D-lactate dehydrogenase (EC 1.1.1.28) (characterized)
to candidate WP_011021352.1 MA_RS06920 NAD(P)-dependent oxidoreductase

Query= BRENDA::Q9I530
         (329 letters)



>NCBI__GCF_000007345.1:WP_011021352.1
          Length = 319

 Score =  182 bits (462), Expect = 1e-50
 Identities = 109/259 (42%), Positives = 156/259 (60%), Gaps = 14/259 (5%)

Query: 70  RLVALRSAGYNHVDLAAAEALGLPVVHVPAYSPHAVAEHAVGLILTLNRRLHRAYNRTRE 129
           ++++L   G+++VDL  A   G+ V +VP+Y+  +VAE    L L L RR+H A    RE
Sbjct: 67  KMISLWQTGFDNVDLEEATDHGVIVSNVPSYAFESVAEFVFALTLNLLRRVHLADMNLRE 126

Query: 130 GDFSLHGLTGFDLHGKRVGVIGTGQIGETFARIMAGFGCELLAYDPYPNP-RIQALGGRY 188
           G F      G  L  K +GV+GTG+IG+   +I  GF   +L+   +P+P R +ALG ++
Sbjct: 127 GLFDWKYYVGNQLMSKTIGVLGTGEIGKRVIQIAHGFNMNVLSVTAHPSPERAKALGVKF 186

Query: 189 LALDALLAESDIVSLHCPLTADTRHLIDAQRLATMKPGAMLINTGRGALVNAAALIEALK 248
           + LD LL+ESDIV+LH PLT +T H+I A+ LA MKP A+LINT RG +V  AAL+EALK
Sbjct: 187 VDLDTLLSESDIVTLHVPLTPETEHMIGARELAKMKPTAILINTARGKVVEEAALMEALK 246

Query: 249 SGQLGYLGLDVYEEEADIFFEDRSDQPLQDDVLARLLSFPNVVVTAHQAFLTREALAAIA 308
             ++   GLDV+E E           PL  D  + LL   NVV+T H AFL+ E+L    
Sbjct: 247 EKKIAGAGLDVFERE-----------PLSMD--SPLLEMHNVVLTPHIAFLSEESLDECT 293

Query: 309 DTTLDNIAAWQDGTPRNRV 327
             +++N+  +  G P+N V
Sbjct: 294 YISIENVEMFAKGKPQNVV 312


Lambda     K      H
   0.323    0.137    0.402 

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: 243
Number of extensions: 5
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: 329
Length of database: 319
Length adjustment: 28
Effective length of query: 301
Effective length of database: 291
Effective search space:    87591
Effective search space used:    87591
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.5 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (22.0 bits)
S2: 48 (23.1 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