GapMind for catabolism of small carbon sources

 

Alignments for a candidate for D-LDH in Megamonas funiformis YIT 11815

Align D-lactate dehydrogenase (EC 1.1.1.28) (characterized)
to candidate WP_008540147.1 HMPREF9454_RS12055 hydroxyacid dehydrogenase

Query= BRENDA::Q9I530
         (329 letters)



>NCBI__GCF_000245775.1:WP_008540147.1
          Length = 326

 Score =  133 bits (334), Expect = 7e-36
 Identities = 82/261 (31%), Positives = 136/261 (52%), Gaps = 16/261 (6%)

Query: 70  RLVALRSAGYNHVDLAAAEALGLPVVHVPAYSPHAVAEHAVGLILTLNRRLHRAYNRTRE 129
           +++     G + VD+ AA  LG+PVV  P  +  +VAEHA+ ++    + + R     R+
Sbjct: 65  KVIGRPGVGVDDVDVEAATELGIPVVIAPGANTRSVAEHAMAMMFACAKDMVRCDKEMRK 124

Query: 130 GDFSLHG-LTGFDLHGKRVGVIGTGQIGETFARIMAGFGCELLAYDPYPNPRI-QALGGR 187
           G+F++      ++L+GK +G+IG G IG   A +  G G ++L YDP+    + +A G  
Sbjct: 125 GNFAIRSEYKAYELNGKVLGLIGCGHIGNILAEMATGIGMKVLVYDPFVKAEVVEAKGYG 184

Query: 188 YLA-LDALLAESDIVSLHCPLTADTRHLIDAQRLATMKPGAMLINTGRGALVNAAALIEA 246
           Y A ++ +L E+D+VS+H PLT  T+++I  + L  MK   +LIN  RG ++N  AL +A
Sbjct: 185 YRAEMEDILKEADVVSIHTPLTPKTKNMIGEKELKLMKSTGILINCARGGIINEEALCKA 244

Query: 247 LKSGQLGYLGLDVYEEEADIFFEDRSDQPLQDDVLARLLSFPNVVVTAHQAFLTREALAA 306
           L    +     DV   E           P+  D    L    N++VT H A  T+EA + 
Sbjct: 245 LSENWIHSAATDVVVHE-----------PISVD--DPLFMHENIIVTPHMAGQTKEAASG 291

Query: 307 IADTTLDNIAAWQDGTPRNRV 327
           +A    + + A  +G   ++V
Sbjct: 292 VATMAAEGVMAVINGQKWDKV 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: 242
Number of extensions: 12
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: 329
Length of database: 326
Length adjustment: 28
Effective length of query: 301
Effective length of database: 298
Effective search space:    89698
Effective search space used:    89698
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 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