GapMind for catabolism of small carbon sources

 

Alignments for a candidate for D-LDH in Geotalea uraniireducens Rf4

Align D-lactate dehydrogenase (EC 1.1.1.28) (characterized)
to candidate WP_011938637.1 GURA_RS08815 phosphoglycerate dehydrogenase

Query= BRENDA::F8A9V0
         (325 letters)



>NCBI__GCF_000016745.1:WP_011938637.1
          Length = 541

 Score =  160 bits (404), Expect = 9e-44
 Identities = 95/249 (38%), Positives = 140/249 (56%), Gaps = 16/249 (6%)

Query: 70  LLALRSAGYDHIDIETAKRLGIKVVNVPAYSPHAIADHTLAIMLALIRRLHRAHDKVRLG 129
           ++A    G D++DI+ A   G+ VVN P  + ++ A+H +A++L+  R + +A+  ++ G
Sbjct: 67  MVARAGVGIDNVDIDYASSKGVIVVNAPFGNTNSAAEHAMALLLSFCRNITKANASLKSG 126

Query: 130 DFDLDGLMGFDLNGKVAGVIGLGKIGRLVATRLKAFGCKVLGYDPYIQPEI-----VENV 184
           ++      G +L GK AGVIGLGK+G  VATRLKAF C VLG DPYI  +      V+ V
Sbjct: 127 EWKRAPFTGVELKGKTAGVIGLGKVGGRVATRLKAFECDVLGCDPYIAVKRAHDLGVKLV 186

Query: 185 DLDTLITQADIISIHCPLTRENFHMFNEETFKRMKPGAILVNTARGGLIDTKALLEALKS 244
             + +    DII+ H PL  E  +M  E+    MK G IL+N ARGG+I+ +ALL ALK 
Sbjct: 187 SHEEIYKNCDIITFHTPLNEETRNMVGEKEIAMMKDGVILINAARGGIINEQALLNALKG 246

Query: 245 GKLGGAALDVYEYERGLFFKNHQKEGIKDPYLAQLLGLANVVLTGHQAFLTREAVKNIEE 304
           GK+ GAA+DV+            +E  K   L +L+    +V+T H    T EA  N+  
Sbjct: 247 GKVFGAAMDVW-----------SEEPPKSETLKELISQDKLVVTPHLGANTFEAQINVAV 295

Query: 305 TTVENILEW 313
              + IL +
Sbjct: 296 DVSKEILNY 304


Lambda     K      H
   0.321    0.140    0.407 

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: 375
Number of extensions: 17
Number of successful extensions: 2
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: 325
Length of database: 541
Length adjustment: 32
Effective length of query: 293
Effective length of database: 509
Effective search space:   149137
Effective search space used:   149137
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 (21.8 bits)
S2: 50 (23.9 bits)

This GapMind analysis is from Apr 09 2024. 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