GapMind for catabolism of small carbon sources

 

Alignments for a candidate for badH in Rhodobacter maris JA276

Align BadH (characterized)
to candidate WP_097069992.1 CRO22_RS09910 3-oxoacyl-[acyl-carrier-protein] reductase

Query= metacyc::MONOMER-893
         (255 letters)



>NCBI__GCF_900217815.1:WP_097069992.1
          Length = 245

 Score =  164 bits (414), Expect = 2e-45
 Identities = 96/253 (37%), Positives = 139/253 (54%), Gaps = 9/253 (3%)

Query: 1   MARLQNKTAVITGGGGGIGGATCRRFAQEGAKIAVFDLNLDAAEKVAGAIRDAGGTAEAV 60
           M  L  KTA++TG  GGIGG   +     GAK+A+    ++  E +A  +   G  A   
Sbjct: 1   MFDLTGKTALVTGASGGIGGEIAKALHGAGAKVALSGTRVEPLEALAAEL---GAGAFVC 57

Query: 61  RCDIADRTSVDAAIATTTTTLGPVDILVNNAGWDIFKPFTKTEPGEWERLIAINLTGALH 120
             +++D  SV+A        +G +DILVNNAG      F +    EW+ +I +NLT +  
Sbjct: 58  PANLSDPDSVEALPKAAAAAMGSLDILVNNAGITRDNLFMRMSDDEWQSVIDVNLTSSFR 117

Query: 121 MHHAVLPGMVERRHGRIVNIASDAARVGSSGEAVYAACKGGLVAFSKTLAREHARHGITV 180
           +   VL GM++ R GRIV I S   + G+ G+  YAA K GLV  SK+LA E A  GITV
Sbjct: 118 LMRGVLRGMMKARWGRIVTITSVVGQTGNPGQGNYAAAKAGLVGMSKSLAYEVASRGITV 177

Query: 181 NVVCPGPTDTALLADVTSGAANPEKLIEAFTKAIPLGRLGKPDDLAGAIAFFGSDDAGFI 240
           N V PG      +A   +   N E+  +   + IP GR+G P+++A A+ +  S +AG++
Sbjct: 178 NCVAPG-----FIATAMTDKLNDEQKGKILGQ-IPAGRMGLPEEIAAAVLYLASPEAGYV 231

Query: 241 TGQVLSVSGGLTM 253
           TG  LSV+GG+ M
Sbjct: 232 TGATLSVNGGMAM 244


Lambda     K      H
   0.318    0.135    0.398 

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: 175
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: 245
Length adjustment: 24
Effective length of query: 231
Effective length of database: 221
Effective search space:    51051
Effective search space used:    51051
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 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