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_075619666.1 GY23_RS13105 SDR family oxidoreductase

Query= BRENDA::Q1J2J0
         (255 letters)



>NCBI__GCF_001939075.1:WP_075619666.1
          Length = 245

 Score =  176 bits (445), Expect = 5e-49
 Identities = 103/248 (41%), Positives = 150/248 (60%), Gaps = 16/248 (6%)

Query: 15  RLDGRHALVTGGAQGIGFEIARGLAQAGARVTIADLNPDVGEGAAREL-----DGTFERL 69
           +L  + A++TGGA GIG   A+     GA+V + DLN + G+    EL     +  F + 
Sbjct: 3   KLQNKVAIITGGASGIGAATAKLFVSEGAKVVLVDLNEEKGKAFEAELKALNAEALFVKA 62

Query: 70  NVTDADAVADLARRLPD----VDVLVNNAGIVRNAPAEDTPDDDWRAVLSVNLDGVFWCC 125
           N+T  + VA++ ++  +    VDV+ NNAGI R  P+ +    +WR  ++V+LDGVF   
Sbjct: 63  NITSEEDVANIFKQTIEAFGKVDVVFNNAGIGRVHPSHELEYSEWRNTVNVDLDGVFLVA 122

Query: 126 REFGRTMLARGRGAIVSTASMSGLISNHPQPQAAYNASKAAVIHLTRSLAGEWASRGVRV 185
           RE  R ML  G G IV+TASM G + +     AAYNA+K  VI+LTRSLA E+A + +RV
Sbjct: 123 REAIREMLKAGGGTIVNTASMYGWVGS--PGSAAYNAAKGGVINLTRSLALEYADQNIRV 180

Query: 186 NAVAPGYTATPLTRRGLETPEWRETWLKETPLGRLAEPREIAPAVLYLASDAASFVTGHT 245
           N++ PG+  TP+        E ++     TP+ RL    E+A AVL++ASD +SF+TG++
Sbjct: 181 NSLCPGFIDTPII-----PEESKQVLASMTPMKRLGRSEEMAKAVLFMASDDSSFMTGNS 235

Query: 246 LVVDGGYT 253
           L VDGGYT
Sbjct: 236 LTVDGGYT 243


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: 169
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: 255
Length of database: 245
Length adjustment: 24
Effective length of query: 231
Effective length of database: 221
Effective search space:    51051
Effective search space used:    51051
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