GapMind for catabolism of small carbon sources

 

Alignments for a candidate for D-LDH in Dyella japonica UNC79MFTsu3.2

Align D-lactate dehydrogenase (EC 1.1.1.28) (characterized)
to candidate N515DRAFT_3581 N515DRAFT_3581 D-3-phosphoglycerate dehydrogenase

Query= BRENDA::A0A0M3KL04
         (335 letters)



>FitnessBrowser__Dyella79:N515DRAFT_3581
          Length = 410

 Score =  137 bits (345), Expect = 5e-37
 Identities = 95/262 (36%), Positives = 139/262 (53%), Gaps = 20/262 (7%)

Query: 50  IQQRSHISNPAVYETLQKNGLRQLTSRTAGYDMIDLEQASERGLVVTNVPAYSPNSVAEL 109
           I+ RSH++   +    Q   L  +     G + +DLE A ++G+ V N P  +  SVAEL
Sbjct: 58  IRSRSHLTADVLE---QARRLIAVGCFCIGTNQVDLETARQQGVPVFNAPYSNTRSVAEL 114

Query: 110 ALTQTMRLIRNLPLFDARGAEQDFRWAGLMAREIRSLTVGIIGAGRIGGTVARLFKALGA 169
            + + + L+R +P  +A      +  +   + E+R   +GI+G G IG  V  L ++LG 
Sbjct: 115 VIAEAIMLLRGIPQKNALCHRGGWTKSAAGSFEVRDKVLGIVGYGHIGTQVGVLAESLGM 174

Query: 170 TVIANDIVERVELKDIVTYVSKEELLQAADVVTLHVPLMDSTTQLIDADALALMKNDAVL 229
            VI +DI  ++ L +     S ++LL+ ADVVTLHVP   +T  +I A  LA M+  A L
Sbjct: 175 RVIFHDIETKLSLGNARAAGSLDDLLERADVVTLHVPETPATKLMIGATELAKMRKGAAL 234

Query: 230 INASRGPVVDTDALIAALQNKQIAGAALDTL----NGEEHFFNQDLCGKELPSEQLKVLR 285
           INASRG VVD DAL AAL+   +AGAA+D       G +  F   L G            
Sbjct: 235 INASRGTVVDIDALAAALRTGHVAGAAVDVFPLEPKGNDDPFVSPLVG------------ 282

Query: 286 TLPNVLITPHIGFYTNKAVQNM 307
            + NV++TPHIG  T +A  N+
Sbjct: 283 -MDNVILTPHIGGSTLEAQDNI 303


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: 275
Number of extensions: 14
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: 335
Length of database: 410
Length adjustment: 30
Effective length of query: 305
Effective length of database: 380
Effective search space:   115900
Effective search space used:   115900
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 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