GapMind for catabolism of small carbon sources

 

Alignments for a candidate for paaH in Haloglycomyces albus DSM 45210

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_025272362.1 HALAL_RS0101795 3-oxoacyl-ACP reductase FabG

Query= SwissProt::O18404
         (255 letters)



>NCBI__GCF_000527155.1:WP_025272362.1
          Length = 236

 Score =  105 bits (262), Expect = 8e-28
 Identities = 79/248 (31%), Positives = 119/248 (47%), Gaps = 20/248 (8%)

Query: 6   VSLVTGGASGLGRATAERLAKQGASVILADLPSSKGNEVAKELGDKVVFVPVDVTSEKDV 65
           V L+TGG  G+GRA A+RL   G +V +A    S+    A+   D V    VDV+     
Sbjct: 5   VVLITGGTRGIGRAAAQRLKDDGFTVAVA----SRSIPDAENRLD-VHHYQVDVSDGNAC 59

Query: 66  SAALQTAKDKFGRLDLTVNCAGTATAVKTFNFNKNVAHRLEDFQRVININTVGTFNVIRL 125
              + T +D+ G +D+ +N AG                  +D+  VI  N  GT+N+ R 
Sbjct: 60  KDLITTVEDEVGDIDVLINSAGIVRDSPLLTMTG------DDWNDVIRTNLDGTYNMCRS 113

Query: 126 SAGLMGANEPNQDGQRGVIVNTASVAAFDGQIGQAAYSASKAAVVGMTLPIARDLSTQGI 185
            A  M         + G I+N +SVA   G   Q+ YSASKA ++G +  ++++L    I
Sbjct: 114 MAFSM------MKRKNGSIINLSSVAGIQGNPTQSNYSASKAGIIGFSKALSKELGRFNI 167

Query: 186 RICTIAPGLFNTPMLAALPEKVRTFLAKSIPFPQRLGEPSEYAHLV--QAIYENPLLNGE 243
           R+  +APG   T M A L E V+    ++IP   R+G   + AHLV   A      + G 
Sbjct: 168 RVNVVAPGFIETDMTADLAESVKKKAVENIPL-GRMGSVDDVAHLVGFLASPRATYMTGA 226

Query: 244 VIRIDGAL 251
           V+ +DG +
Sbjct: 227 VVPVDGGI 234


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: 171
Number of extensions: 9
Number of successful extensions: 2
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: 236
Length adjustment: 24
Effective length of query: 231
Effective length of database: 212
Effective search space:    48972
Effective search space used:    48972
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: 46 (22.3 bits)

This GapMind analysis is from Apr 09 2024. 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