GapMind for catabolism of small carbon sources

 

Alignments for a candidate for ivdG in Kocuria flava HO-9041

Align 3-hydroxyacyl-CoA dehydrogenase type-2; 17-beta-hydroxysteroid dehydrogenase 10; 17-beta-HSD 10; 3-hydroxy-2-methylbutyryl-CoA dehydrogenase; 3-hydroxyacyl-CoA dehydrogenase type II; Mitochondrial ribonuclease P protein 2; Mitochondrial RNase P protein 2; Scully protein; Type II HADH; EC 1.1.1.35; EC 1.1.1.51; EC 1.1.1.178 (characterized)
to candidate WP_058857809.1 AS188_RS04270 acetoin reductase

Query= SwissProt::O18404
         (255 letters)



>NCBI__GCF_001482365.1:WP_058857809.1
          Length = 259

 Score = 98.6 bits (244), Expect = 1e-25
 Identities = 81/261 (31%), Positives = 119/261 (45%), Gaps = 26/261 (9%)

Query: 6   VSLVTGGASGLGRATAERLAKQGASVILADLPSSKGNEVAKEL---GDKVVFVPVDVTSE 62
           V+LVTG   G+G+A A RLA+ G  V L DL      EV  E+   G +   V  DV+  
Sbjct: 7   VALVTGAGRGIGKAIALRLAQDGFDVGLVDLRDELTREVLGEIEATGRRACAVTADVSDR 66

Query: 63  KDVSAALQTAKDKFGRLDLTVNCAGTATAVKTFNFNKNVAHRLEDFQRVININTVGTFNV 122
             V AA+Q   ++ GRLD+ VN AG A          +    +E     +NIN V  + +
Sbjct: 67  DSVRAAVQEVAERLGRLDVMVNNAGIAQVQPILEVTPDEVETIER----VNINGV-LWGI 121

Query: 123 IRLSAGLMGANEPNQDGQRGVIVNTASVAAFDGQIGQAAYSASKAAVVGMTLPIARDLST 182
              +A  +      + G RG I+N AS+A  +G      YSA+K AV G+T   A++L+ 
Sbjct: 122 QAAAARFL------EQGTRGKIINAASIAGHEGFAVLGVYSATKFAVRGLTQAAAKELAP 175

Query: 183 QGIRICTIAPGLFNTPMLAALPEKVR--TFLAKSIPFPQRLG--------EPSEYAHLVQ 232
            GI +    PG+  T M   + E+    T   K   + Q +G         P + A  V 
Sbjct: 176 HGITVNAYCPGVVGTDMWVEIDERFAELTGAEKGATYEQYVGGIALGRAQTPEDVAAFVS 235

Query: 233 AIY--ENPLLNGEVIRIDGAL 251
            +   +   + G+   IDG L
Sbjct: 236 YLAGPDADYMTGQAPLIDGGL 256


Lambda     K      H
   0.317    0.133    0.369 

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: 148
Number of extensions: 9
Number of successful extensions: 3
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: 259
Length adjustment: 24
Effective length of query: 231
Effective length of database: 235
Effective search space:    54285
Effective search space used:    54285
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 47 (22.7 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