GapMind for catabolism of small carbon sources

 

Alignments for a candidate for xacB in Dethiosulfovibrio salsuginis USBA 82

Align L-arabinose 1-dehydrogenase (EC 1.1.1.46) (characterized)
to candidate WP_085543521.1 B9Y55_RS01195 3-oxoacyl-[acyl-carrier-protein] reductase

Query= reanno::pseudo5_N2C3_1:AO356_20240
         (272 letters)



>NCBI__GCF_900177735.1:WP_085543521.1
          Length = 248

 Score =  119 bits (299), Expect = 5e-32
 Identities = 81/249 (32%), Positives = 124/249 (49%), Gaps = 7/249 (2%)

Query: 22  KVVLLTGAAQGIGEAIVAAFASQQARLVIS-DIQAQKVEAVAAHWRERGADVHALQADVS 80
           +VVL+TG A+GIG+AI    AS   ++ ++    AQ    +       G    A+  DVS
Sbjct: 6   RVVLVTGGAKGIGKAISLKLASAGYQVAVNYRSSAQSASELVEEINASGGVAMAVSGDVS 65

Query: 81  KQQDLQAMARRAVELHGRIDVLVNCAGVNVFRDPLEMTEEDWRRCFAIDLDGAWYGCKAV 140
              D++ +     +  G ++VLVN AGV      + M EEDW      +L  A+   K  
Sbjct: 66  SSDDVKGIFSSVAKELGPVEVLVNNAGVTRDGLLMRMKEEDWDTVIDGNLKSAFLCSKEA 125

Query: 141 LPQMIEQGVGSIINIASVHSSHIIPGCFPYPVAKHGLLGLTRALGIEYAPKGVRVNAIAP 200
           +  M +   G I+N+ASV      PG   Y  +K GL+GLT+++  EYA +G+ VNA+AP
Sbjct: 126 IKAMSKGRWGRIVNMASVVGLIGNPGQANYCSSKAGLIGLTKSVAREYAQRGITVNAVAP 185

Query: 201 GYIETQLNVDYWNGFADPHAERQRALDLHPPRRVGQPIEVAMTAVFLASDEAPFINASCI 260
           G+I T +          P + +   +   P  R G   +VA    FL SDEA +I    +
Sbjct: 186 GFIVTDMTE------VLPQSVKDGMVSSIPSGRPGTVEDVASAVAFLVSDEASYITGQVL 239

Query: 261 TIDGGRSVM 269
            +DGG +++
Sbjct: 240 AVDGGMTMV 248


Lambda     K      H
   0.321    0.137    0.419 

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: 137
Number of extensions: 4
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: 272
Length of database: 248
Length adjustment: 24
Effective length of query: 248
Effective length of database: 224
Effective search space:    55552
Effective search space used:    55552
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 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