GapMind for catabolism of small carbon sources

 

Alignments for a candidate for D-LDH in Pleomorphomonas diazotrophica R5-392

Align D-lactate dehydrogenase (EC 1.1.1.28) (characterized)
to candidate WP_101287199.1 CXZ10_RS01560 2-hydroxyacid dehydrogenase

Query= BRENDA::Q9I530
         (329 letters)



>NCBI__GCF_002844595.1:WP_101287199.1
          Length = 338

 Score =  347 bits (890), Expect = e-100
 Identities = 177/322 (54%), Positives = 231/322 (71%), Gaps = 1/322 (0%)

Query: 1   MRILFFSSQAYDSESFQASNHRHGFELHFQQAHLQADTAVLAQGFEVVCAFVNDDLSRPV 60
           MR+  FS++ YD      +   HG EL F +  L   TA LA+GF  VCAFVND L   V
Sbjct: 1   MRVAIFSTKPYDRTFLSRAAASHGHELTFFEPRLDRTTARLAEGFPAVCAFVNDTLDAEV 60

Query: 61  LERLAAGGTRLVALRSAGYNHVDLAAAEALGLPVVHVPAYSPHAVAEHAVGLILTLNRRL 120
           +  L++GGTR+VALR+AG+N+V L AAE  G+ V+ VPAYSPHAVAE +VGL+L L+RR+
Sbjct: 61  IATLSSGGTRIVALRAAGFNNVALDAAEEKGVTVLRVPAYSPHAVAEFSVGLLLALDRRI 120

Query: 121 HRAYNRTREGDFSLHGLTGFDLHGKRVGVIGTGQIGETFARIMA-GFGCELLAYDPYPNP 179
           HRA+ R RE +F+L GL G DLHG+ VG++GTG+IG   AR    GFGCE++A+D Y   
Sbjct: 121 HRAWARVRENNFALEGLLGHDLHGRTVGIVGTGRIGALVARAYRLGFGCEVVAHDRYEVD 180

Query: 180 RIQALGGRYLALDALLAESDIVSLHCPLTADTRHLIDAQRLATMKPGAMLINTGRGALVN 239
            ++A+G  Y+  D L+  SDI+SLHCPLT +T +LID   +A  K G +LINT RGAL+N
Sbjct: 181 DLKAIGVTYVDRDELIERSDIISLHCPLTPETHYLIDEAAIARAKQGFLLINTSRGALIN 240

Query: 240 AAALIEALKSGQLGYLGLDVYEEEADIFFEDRSDQPLQDDVLARLLSFPNVVVTAHQAFL 299
           A A+I  LKSG++G + LDVYE+EAD+FFED S + +QDDV  RLL+FPNV++T HQAF 
Sbjct: 241 AEAVIGGLKSGRIGGVALDVYEQEADLFFEDLSSEIIQDDVFQRLLTFPNVLITGHQAFF 300

Query: 300 TREALAAIADTTLDNIAAWQDG 321
           T EAL AIA+TT+ NIA  + G
Sbjct: 301 TEEALLAIAETTMGNIADEEAG 322


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: 373
Number of extensions: 15
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: 338
Length adjustment: 28
Effective length of query: 301
Effective length of database: 310
Effective search space:    93310
Effective search space used:    93310
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: 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