GapMind for catabolism of small carbon sources

 

Alignments for a candidate for mt2d in Haloglycomyces albus DSM 45210

Align NADP-dependent mannitol dehydrogenase; MtDH; Mannitol 2-dehydrogenase [NADP(+)]; EC 1.1.1.138 (characterized)
to candidate WP_025272362.1 HALAL_RS0101795 3-oxoacyl-ACP reductase FabG

Query= SwissProt::O93868
         (262 letters)



>NCBI__GCF_000527155.1:WP_025272362.1
          Length = 236

 Score =  127 bits (320), Expect = 2e-34
 Identities = 81/248 (32%), Positives = 127/248 (51%), Gaps = 17/248 (6%)

Query: 14  IIVTGGNRGIGLAFTRAVAAAGANVAVIYRSAKDAVEVTEKVGKEFGVKTKAYQCDVSNT 73
           +++TGG RGIG A  + +   G  VAV  RS  DA         E  +    YQ DVS+ 
Sbjct: 6   VLITGGTRGIGRAAAQRLKDDGFTVAVASRSIPDA---------ENRLDVHHYQVDVSDG 56

Query: 74  DIVTKTIQQIDADLGAISGLIANAGVSVVKPATELTHEDFKFVYDVNVFGVFNTCRAVAK 133
           +     I  ++ ++G I  LI +AG+    P   +T +D+  V   N+ G +N CR++A 
Sbjct: 57  NACKDLITTVEDEVGDIDVLINSAGIVRDSPLLTMTGDDWNDVIRTNLDGTYNMCRSMA- 115

Query: 134 LWLQKQQKGSIVVTSSMSSQIINQSSLNGSLTQVFYNSSKAACSNLVKGLAAEWASAGIR 193
             + K++ GSI+  SS++        + G+ TQ  Y++SKA      K L+ E     IR
Sbjct: 116 FSMMKRKNGSIINLSSVAG-------IQGNPTQSNYSASKAGIIGFSKALSKELGRFNIR 168

Query: 194 VNALSPGYVNTDQTAHMDKKIRDHQASNIPLNRFAQPEEMTGQAILLLSDHATYMTGGEY 253
           VN ++PG++ TD TA + + ++     NIPL R    +++      L S  ATYMTG   
Sbjct: 169 VNVVAPGFIETDMTADLAESVKKKAVENIPLGRMGSVDDVAHLVGFLASPRATYMTGAVV 228

Query: 254 FIDGGQLI 261
            +DGG ++
Sbjct: 229 PVDGGIIL 236


Lambda     K      H
   0.317    0.130    0.372 

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: 134
Number of extensions: 6
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: 262
Length of database: 236
Length adjustment: 24
Effective length of query: 238
Effective length of database: 212
Effective search space:    50456
Effective search space used:    50456
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.

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