GapMind for catabolism of small carbon sources

 

Alignments for a candidate for sdh in Paenisporosarcina indica PN2

Align L-iditol 2-dehydrogenase (EC 1.1.1.14) (characterized)
to candidate WP_075617526.1 GY23_RS01955 3-oxoacyl-[acyl-carrier-protein] reductase

Query= BRENDA::Q1J2J0
         (255 letters)



>NCBI__GCF_001939075.1:WP_075617526.1
          Length = 248

 Score =  156 bits (395), Expect = 3e-43
 Identities = 99/250 (39%), Positives = 147/250 (58%), Gaps = 20/250 (8%)

Query: 15  RLDGRHALVTGGAQGIGFEIARGLAQAGARVTIADLNPDVGEGAARELDGTFE------- 67
           +L+G+ A+VTG ++GIG EIA+ LA+ GARV +   N    +  A E+    E       
Sbjct: 3   KLNGKTAIVTGASRGIGAEIAKYLAKEGARVIV---NYSGSQSKAEEVVKEIEAFGGEAL 59

Query: 68  --RLNVTDADAVADLA----RRLPDVDVLVNNAGIVRNAPAEDTPDDDWRAVLSVNLDGV 121
             + +V+DAD+V  L          +D+LVNNAGI R+       +++W  V++ NL GV
Sbjct: 60  AVQASVSDADSVTALISATMEHFGSIDILVNNAGITRDNLIMRMKENEWDDVINTNLKGV 119

Query: 122 FWCCREFGRTMLARGRGAIVSTASMSGLISNHPQPQAAYNASKAAVIHLTRSLAGEWASR 181
           F C +   R M+ +  G IV+ AS+ G+  N    QA Y A+KA VI LT++ A E ASR
Sbjct: 120 FLCTKAVTRQMMKQRAGRIVNIASIVGVSGN--AGQANYVAAKAGVIGLTKTTAKELASR 177

Query: 182 GVRVNAVAPGYTATPLTRRGLETPEWRETWLKETPLGRLAEPREIAPAVLYLASDAASFV 241
            + VNA+APG+ +T +T    E  E +   L + PL +L  P ++A AV++LASD ++++
Sbjct: 178 NINVNAIAPGFISTEMTADLPE--EVKAQMLTQIPLAKLGNPEDVAKAVIFLASDDSNYI 235

Query: 242 TGHTLVVDGG 251
           TG TL VDGG
Sbjct: 236 TGQTLHVDGG 245


Lambda     K      H
   0.319    0.134    0.408 

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: 150
Number of extensions: 5
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: 255
Length of database: 248
Length adjustment: 24
Effective length of query: 231
Effective length of database: 224
Effective search space:    51744
Effective search space used:    51744
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: 46 (22.3 bits)

This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

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