GapMind for catabolism of small carbon sources

 

Alignments for a candidate for LRA1 in Methylocystis bryophila S285

Align NAD(P)+-dependent L-rhamnose 1-dehydrogenase (EC 1.1.1.378; EC 1.1.1.173) (characterized)
to candidate WP_085770280.1 B1812_RS02990 3-oxoacyl-[acyl-carrier-protein] reductase

Query= metacyc::MONOMER-16231
         (254 letters)



>NCBI__GCF_002117405.1:WP_085770280.1
          Length = 246

 Score =  122 bits (306), Expect = 7e-33
 Identities = 76/246 (30%), Positives = 135/246 (54%), Gaps = 7/246 (2%)

Query: 4   LEGKTVLVTGASTGIGRAAAIGAAQHGADVAINYAHSDGPAQSCVAEIEALGQRAIAVKG 63
           L GKT LVTGAS+G+G A A    Q GA V ++    +   ++   E++   +RA  +  
Sbjct: 4   LTGKTALVTGASSGLGLAIARTLHQAGATVGLSGTRREA-LETLAGELK---ERAHILPC 59

Query: 64  DVADPQTAQDFVAKAVETFGKVDVMVSNAGICPFHAFLDMPVDVVERTFKVNLHGAYFMV 123
           +++D       +  A    G VD++V+NAGI     F+ M  +  +    VNL  A+ + 
Sbjct: 60  NLSDRAETDKLIPAAEGAMGGVDILVNNAGITRDMLFMRMKDEDWDAVLAVNLTAAFRLS 119

Query: 124 QAAAQQMVRQGHGGSIVAVSSISALVGGEYQTHYTPTKAGVHSLMQSTAIALGKHGIRCN 183
           +A  + M+R+ HG  I+ ++S++  VG   Q +Y+  KAG+  + +S A  +   G+  N
Sbjct: 120 RAVLRGMMRKRHG-RIINITSVAGAVGNPGQANYSAAKAGLTGMTKSLANEVASRGVTVN 178

Query: 184 SVLPGTILTEINKDDLADQEKREYMEARTPLGRLGAPEDLAGPIVFLASDMAAYVTGAAL 243
            V PG I + + +  + ++ +RE +    P+ R G+ +++   +++LASD AA++TG  L
Sbjct: 179 CVAPGVIESPMTQ--VLNEAQRERLLKLIPMERFGSADEIGAAVLYLASDEAAFITGQTL 236

Query: 244 LVDGGM 249
            ++GGM
Sbjct: 237 HINGGM 242


Lambda     K      H
   0.318    0.133    0.379 

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: 99
Number of extensions: 5
Number of successful extensions: 4
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: 254
Length of database: 246
Length adjustment: 24
Effective length of query: 230
Effective length of database: 222
Effective search space:    51060
Effective search space used:    51060
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