GapMind for catabolism of small carbon sources

 

Alignments for a candidate for xacB in Azospirillum brasilense Sp245

Align L-arabinose 1-dehydrogenase / D-galactose 1-dehydrogenase (EC 1.1.1.46; EC 1.1.1.48) (characterized)
to candidate AZOBR_RS24695 AZOBR_RS24695 3-oxoacyl-ACP reductase

Query= reanno::pseudo6_N2E2:Pf6N2E2_5967
         (272 letters)



>FitnessBrowser__azobra:AZOBR_RS24695
          Length = 256

 Score =  155 bits (391), Expect = 1e-42
 Identities = 92/251 (36%), Positives = 136/251 (54%), Gaps = 13/251 (5%)

Query: 18  RLKNKVVLLTGAAQGIGEAIVAAFASQQARLVISDIQAEKVETVAAHWRERGADVHALKA 77
           RL  +V  +TG   GIG A+    A++ A +V++DI AE  ETVAA  R  GA  HA   
Sbjct: 10  RLAGRVAFVTGGGGGIGRAVCERLAAEGAAVVVADIGAEVAETVAAALRAEGAQAHATAL 69

Query: 78  DVSNQQDLHAMARHAVERHGRIDVLVNCAGVNVFRDPLEMTEEDWRRCFAIDLDGAWYGC 137
           +V++++   A      E    +D++VN AG+   R   +MT+ +W     ++L G W GC
Sbjct: 70  NVADRESWGAAVTGLPEAFRGVDIMVNVAGIVRDRSLPKMTDAEWSAVIDVNLRGTWLGC 129

Query: 138 KAVLPQMIEQGVGSIINIASTHSSHIIPGCF---PYPVAKHGLLGLTRALGIEYAPKGVR 194
           +     + ++G G I+NIAST     I G F    Y  +K G++GLTR   +E A +G+ 
Sbjct: 130 QTAFRLVGDRGWGRIVNIAST----AILGTFGQANYSASKAGVVGLTRTAALEGARRGIL 185

Query: 195 VNAIAPGYIETQLNVDYWNGFADPYAERQRALDLHPPRRIGQPIEVAMTAVFLASDEAPF 254
           VNA+APG +ET +          P A R + L+  P  R+G+P E+A    FLASD+A +
Sbjct: 186 VNAVAPGVVETAIVEGV------PDAVRSQWLEKTPIGRLGKPAEIAAVVAFLASDDAAY 239

Query: 255 INASCITIDGG 265
           +    I  DGG
Sbjct: 240 VTGQTIVADGG 250


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: 181
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: 272
Length of database: 256
Length adjustment: 25
Effective length of query: 247
Effective length of database: 231
Effective search space:    57057
Effective search space used:    57057
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 (21.8 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 (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