GapMind for catabolism of small carbon sources

 

Alignments for a candidate for etoh-dh-nad in Sphingopyxis indica DS15

Align NADP-retinol dehydrogenase (EC 1.1.1.300); alcohol dehydrogenase [NAD(P)+] (EC 1.1.1.71) (characterized)
to candidate WP_089217430.1 CHB69_RS18510 SDR family NAD(P)-dependent oxidoreductase

Query= BRENDA::Q9HBH5
         (336 letters)



>NCBI__GCF_900188185.1:WP_089217430.1
          Length = 306

 Score =  176 bits (445), Expect = 9e-49
 Identities = 119/303 (39%), Positives = 159/303 (52%), Gaps = 32/303 (10%)

Query: 43  GKTVLITGANSGLGRATAAELLRLGARVIMGCRDRARAEEAAGQLRRELRQAAECGPEPG 102
           GK +++TGANSG+G   A+ L    ARV++ CRD ++A  A  ++R+             
Sbjct: 17  GKCLIVTGANSGVGFEVASALAARRARVLLACRDESKARAAMDKIRQR------------ 64

Query: 103 VSGVGELIVRELDLASLRSVRAFCQEMLQEEPRLDVLINNAGIFQCPYMKTEDGFEMQFG 162
            S   +L    LDLA L SVR    E+  +EPR+DVLINNAG+       T  GFE+ FG
Sbjct: 65  -SSGADLAFLPLDLADLASVRK-AAEVAAKEPRIDVLINNAGVTVPTRQTTRQGFELLFG 122

Query: 163 VNHLGHFLLTNLLLGLLKSSAPSRIVVVSSKLYKYGDINFDDLNSEQSYNKSFCYSRSKL 222
           VNHLG F LT L+L  L+ +  SRIV+ SS  +K   I +DDLN+E++YN    Y  SKL
Sbjct: 123 VNHLGSFALTALMLPKLRETPGSRIVITSSGQHKGAKIEWDDLNAEKNYNWLSRYGASKL 182

Query: 223 ANILFTRELARRLEGTNVTVNVL--HPGIVRTNLGRHIHIPLLVKPLFNLVSWAFFKTPV 280
           AN+LF  EL RRL+   + V  +  HPG  RTN GR      L   L   V    F TP 
Sbjct: 183 ANLLFMLELNRRLQAAEMPVTTVGCHPGFARTNFGR----ASLAGRLAVGVGGLLFNTPA 238

Query: 281 EGAQTSIYLASSPEVEGVSGRYFGDCKEEEL---------LPKAMDESVARKLWDISEVM 331
            GA  ++  A+        G Y+G     EL            A +  +AR+LWD+S  M
Sbjct: 239 MGAWPTLQAATG---NVKPGGYYGPTAFAELRGPSFECTPSDDARNPQLARRLWDVSIEM 295

Query: 332 VGL 334
            G+
Sbjct: 296 TGI 298


Lambda     K      H
   0.322    0.138    0.403 

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: 248
Number of extensions: 11
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: 336
Length of database: 306
Length adjustment: 28
Effective length of query: 308
Effective length of database: 278
Effective search space:    85624
Effective search space used:    85624
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 (21.9 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