GapMind for catabolism of small carbon sources

 

Aligments for a candidate for galdh in Desulfovibrio vulgaris Hildenborough

Align L-arabinose 1-dehydrogenase / D-galactose 1-dehydrogenase (EC 1.1.1.46; EC 1.1.1.48) (characterized)
to candidate 206645 3-oxoacyl-(acyl-carrier-protein) reductase

Query= reanno::pseudo13_GW456_L13:PfGW456L13_2119
         (272 letters)



>lcl|MicrobesOnline__882:206645 3-oxoacyl-(acyl-carrier-protein)
           reductase
          Length = 259

 Score =  122 bits (306), Expect = 8e-33
 Identities = 80/242 (33%), Positives = 124/242 (51%), Gaps = 7/242 (2%)

Query: 25  LLTGAAQGIGEAIVATFASQQARLIISDI-QGEKVEKVAAHWRDQGADVVAIKADVSRQQ 83
           ++TG ++GIG+A+  T A    ++ ++ + + ++ E VAA  RD G    A + DVS   
Sbjct: 21  IVTGGSRGIGKAVAETLARAGLQVFLTYVSKPDEAEAVAAGIRDAGGSATAFRLDVSDAA 80

Query: 84  DLHAMARLAIDLHGRIDVLVNCAGVNVFRDPLEMTEEDWRRCFAIDLDGAWYGCKAVLPQ 143
            + A  +  I    R+DVLVN AG+      + M +ED+ R   ++L GA+   +     
Sbjct: 81  AVAAFFQSEIKDKVRLDVLVNNAGITKDGLIMRMKDEDFERVLDVNLCGAFTCLREASKL 140

Query: 144 MIEQGIGSIINIASTHSTHIIPGCFPYPVAKHGLLGLTRALGIEYAPKGVRVNAIAPGYI 203
           M  Q +G IINI S        G   Y  AK GL+GLT++   E A + V VNA+APG+I
Sbjct: 141 MTRQRLGRIINITSVVGQMGNAGQANYCAAKAGLIGLTKSAAKELAARNVTVNAVAPGFI 200

Query: 204 ETQLNVDYWNGFADPHAERQRAFDLHPPRRIGQPIEVAMTAVFLASDEAPFINASCITID 263
           ET +          P   R+   +  P RR+G   ++A    FLAS+ A +I    + ++
Sbjct: 201 ETDMTAGL------PEEVRKAYVEAIPLRRLGSAQDIADAVAFLASERASYITGQVLAVN 254

Query: 264 GG 265
           GG
Sbjct: 255 GG 256


Lambda     K      H
   0.322    0.138    0.426 

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: 5
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: 259
Length adjustment: 25
Effective length of query: 247
Effective length of database: 234
Effective search space:    57798
Effective search space used:    57798
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 17 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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.

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