GapMind for catabolism of small carbon sources

 

Alignments for a candidate for D-LDH in Alkalitalea saponilacus SC/BZ-SP2

Align D-lactate dehydrogenase (EC 1.1.1.28) (characterized)
to candidate WP_079557862.1 CDL62_RS17635 hydroxyacid dehydrogenase

Query= BRENDA::O66939
         (334 letters)



>NCBI__GCF_002201795.1:WP_079557862.1
          Length = 334

 Score =  161 bits (407), Expect = 2e-44
 Identities = 98/283 (34%), Positives = 158/283 (55%), Gaps = 27/283 (9%)

Query: 45  LISVFVYDKLTEELLSKMPRLKLIHTRSVGFDHIDLDYCKKKGILVTHIPAYSPESVAEH 104
           L+SVF  +K+TEE++SK P+LKLI    VG+D++D+DY   +GI+VT+ P+   E  AE 
Sbjct: 48  LVSVFG-NKVTEEMMSKAPKLKLIANYGVGYDNVDVDYATSQGIVVTNTPSPVTEPTAEL 106

Query: 105 TFAMILTLVKRLKRIEDRVKKLNFSQDS--EILARELNRLTLGVIGTGRIGSRVAMYGLA 162
              ++L L + +  + + + + +  + +    L+  L   TLG+IG G IG  +A    A
Sbjct: 107 AMLLMLALARNIIGLHNGILENSLPEWNVRNNLSTTLYNKTLGIIGMGAIGQALARRAKA 166

Query: 163 FGMKVL-----CYDVVKREDLKEKGCVYTSLDELLKESDVISLHVPYTKETHHMINEERI 217
           FGMK++     C D    E  +     Y S  ELL++SD +S+HVP+++ET+H+I +E +
Sbjct: 167 FGMKIIYHNRACLDSAIEEKYE---ATYVSKTELLQKSDYVSIHVPFSQETYHLIGKEEL 223

Query: 218 SLMKDGVYLINTARGKVVDTDALYRAYQRGKFSGLGLDVFEDEEILILKKYTEGKATDKN 277
            LMK+  +LINT+RGKV+    L +A +  + +G GLDVF +E I+           D  
Sbjct: 224 KLMKNSAFLINTSRGKVIHEKVLIKALKNREIAGAGLDVFSNEPIV----------PD-- 271

Query: 278 LKILELACKDNVIITPHIAYYTDKSLERIREETVKVVKAFVKG 320
               EL     V++TPH+   T ++   + +    V+  F  G
Sbjct: 272 ----ELKNSPYVVLTPHVGSGTHEARAEMSQFVADVISNFFNG 310


Lambda     K      H
   0.319    0.138    0.383 

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: 279
Number of extensions: 9
Number of successful extensions: 4
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 1
Length of query: 334
Length of database: 334
Length adjustment: 28
Effective length of query: 306
Effective length of database: 306
Effective search space:    93636
Effective search space used:    93636
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 (21.7 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