GapMind for catabolism of small carbon sources

 

Alignments for a candidate for etoh-dh-nad in Mariniradius saccharolyticus AK6

Align NADP-retinol dehydrogenase (EC 1.1.1.300); alcohol dehydrogenase [NAD(P)+] (EC 1.1.1.71) (characterized)
to candidate WP_008628641.1 C943_RS13225 SDR family NAD(P)-dependent oxidoreductase

Query= BRENDA::Q9HBH5
         (336 letters)



>NCBI__GCF_000330725.2:WP_008628641.1
          Length = 277

 Score =  130 bits (326), Expect = 5e-35
 Identities = 90/291 (30%), Positives = 143/291 (49%), Gaps = 24/291 (8%)

Query: 46  VLITGANSGLGRATAAELLRLGARVIMGCRDRARAEEAAGQLRRELRQAAECGPEPGVSG 105
           + ITGA SG+G  T   ++    +V +  R++ +A+     L  +  Q            
Sbjct: 3   IAITGATSGIGWVTLKRIIPDAEQVFLLARNKDKADVLLKSLPSDQSQKVR--------- 53

Query: 106 VGELIVRELDLASLRSVRAFCQEMLQEEPRLDVLINNAGIFQCPYMKTEDGFEMQFGVNH 165
                    DLA   SV A  + +  +   LD L+NNAG        T+DG EM    NH
Sbjct: 54  -----FVACDLADFDSVSAAAKTIQSQTTHLDCLVNNAGGIFDKKEFTKDGVEMSLAANH 108

Query: 166 LGHFLLTNLLLGLLKSSAPSRIVVVSSKLYKYGDINFDDLN-SEQSYNKSFCYSRSKLAN 224
           LGHFLLTN L+ LL ++   +++ VSS+ ++    +FDDLN  ++SY+    Y+  KL N
Sbjct: 109 LGHFLLTNRLIPLLLAAKNPKVINVSSEAHRMAKPDFDDLNFVKKSYSSFLAYANVKLFN 168

Query: 225 ILFTRELARRLEGTNVTVNVLHPGIVRTNLGRHIHIPLLVKPLFNL---VSWAFFKTPVE 281
           ILF++ L  R     +    LHPG+V+TN G+        K +F+L   ++  F  +  +
Sbjct: 169 ILFSKSLVDRYGKKGLRSYSLHPGVVKTNFGKE------TKGIFSLFWKMAAPFMISADD 222

Query: 282 GAQTSIYLASSPEVEGVSGRYFGDCKEEELLPKAMDESVARKLWDISEVMV 332
           GA+ S++L  S      +G YF + K ++    A       +LW++SE M+
Sbjct: 223 GAKNSLFLIKSDFSAEQNGNYFKNQKPKKPSSLARSVKTREQLWEVSEKML 273


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: 149
Number of extensions: 6
Number of successful extensions: 5
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: 277
Length adjustment: 27
Effective length of query: 309
Effective length of database: 250
Effective search space:    77250
Effective search space used:    77250
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.

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