GapMind for catabolism of small carbon sources

 

Alignments for a candidate for D-LDH in Limnohabitans curvus MWH-C5

Align D-lactate dehydrogenase (EC 1.1.1.28) (characterized)
to candidate WP_108360123.1 B9Z44_RS13000 D-glycerate dehydrogenase

Query= BRENDA::A0A0M3KL04
         (335 letters)



>NCBI__GCF_003063475.1:WP_108360123.1
          Length = 324

 Score =  117 bits (294), Expect = 3e-31
 Identities = 94/284 (33%), Positives = 133/284 (46%), Gaps = 22/284 (7%)

Query: 57  SNPAVYETLQK-NGLRQLTSRTAGYDMIDLEQASERGLVVTNVPAYSPNSVAELA---LT 112
           S+P   E L+    L+ + +   GY+  D+   +  G+  +N P     + A+     L 
Sbjct: 54  SDPVDAEVLKACPNLKAVANMAVGYNNFDVPAMTAHGVQASNTPDVLTETTADFGFALLM 113

Query: 113 QTMRLIRNLPLFDARGAEQDFRWAGLMAREIRSLTVGIIGAGRIG-GTVARLFKALGATV 171
            T R I     +  RG    +R+      E+   T+GI+G GRIG G   R     G  V
Sbjct: 114 ATARRITESEHYLRRGEWTQWRYDMFAGAEVHGSTIGILGMGRIGQGIARRAAHGFGMKV 173

Query: 172 IAND---IVERVELKDIVTYVSKEELLQAADVVTLHVPLMDSTTQLIDADALALMKNDAV 228
           I ++   +    E +   TYVSKEELL+ AD V L VP   ++   I A  LA MK  A 
Sbjct: 174 IYHNRSRLSAESEAECKATYVSKEELLKTADHVMLVVPYSAASHHTIGAAELAQMKPTAT 233

Query: 229 LINASRGPVVDTDALIAALQNKQIAGAALDTLNGEEHFFNQDLCGKELPSEQLKVLRTLP 288
           LIN +RG +VD  AL  AL+ KQIA A LD   GE          K  P      L T+P
Sbjct: 234 LINIARGGIVDDAALAVALREKQIAAAGLDVFEGEP---------KVHPD-----LLTVP 279

Query: 289 NVLITPHIGFYTNKAVQNMVEISLNDVLAILKTGTSEHQLNKVA 332
           NV++TPHI   +      M  ++ +++++    G S   LN VA
Sbjct: 280 NVVLTPHIASASIPTRMAMANLAADNLISYFTQGKSLTPLNTVA 323


Lambda     K      H
   0.317    0.133    0.364 

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: 212
Number of extensions: 13
Number of successful extensions: 4
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: 335
Length of database: 324
Length adjustment: 28
Effective length of query: 307
Effective length of database: 296
Effective search space:    90872
Effective search space used:    90872
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: 41 (21.7 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