GapMind for catabolism of small carbon sources

 

Alignments for a candidate for ligU in Azospirillum brasilense Sp245

Align 4-oxalomesaconate tautomerase; Gallate degradation protein D; EC 5.3.2.8 (characterized)
to candidate AZOBR_RS28105 AZOBR_RS28105 hypothetical protein

Query= SwissProt::Q88JY0
         (361 letters)



>FitnessBrowser__azobra:AZOBR_RS28105
          Length = 374

 Score =  304 bits (778), Expect = 3e-87
 Identities = 170/356 (47%), Positives = 223/356 (62%), Gaps = 12/356 (3%)

Query: 3   QTRIPCLLMRGGTSKGAYFLHDDLPAPGPLRDRVLLAVMGSPDARQIDGIGGADSLTSKV 62
           Q  IPC++MRGGTS+G +FL  DLPA    RD +LL+VMG+ +   IDGIGG + LTSKV
Sbjct: 8   QIGIPCVMMRGGTSRGPFFLASDLPASPAERDALLLSVMGAGNDLGIDGIGGGNPLTSKV 67

Query: 63  AIIRASQRDDADVDYLFAQVVVDEARVDYGQNCGNILAGVGPFALERGLVAASGASTPVR 122
           AI+  +    ADVDYLFAQV V E  VD   NCGN+LA V PFA+E GLV A+   T VR
Sbjct: 68  AIVGPATLAGADVDYLFAQVRVQEGIVDTSPNCGNMLAAVAPFAIEAGLVPATDGVTVVR 127

Query: 123 IFMENTGQIAVAQVPTADGQVEYAGDTRIDGVPGRAAALVVTFADVAGASCGALLPTGNS 182
           I   NTG++  A+V T DG+V Y G+  IDGVPG AA + + F D AGA+ G LLPTG  
Sbjct: 128 IHNVNTGKLIEARVQTPDGRVTYEGEAVIDGVPGTAAPIHLAFLDAAGANTGRLLPTGAP 187

Query: 183 RDCV------EGVEVTCIDNGMPVVLLCAEDLGVTGYEPCETLEADSALKTRLEAIRLQL 236
            D +      +G+EV+CID  +PV+L+ A DLG TG+EP ++   D     RLEA+R++ 
Sbjct: 188 VDRIIGIDGTDGIEVSCIDAAIPVMLVRAADLGKTGHEPMDSYRLDRVFMARLEALRVEA 247

Query: 237 GPRMNLGDVSQRNVPKMCLLSAPRNGGTVNTRSFIPHRCHASIGVFGAVSVATACLIEGS 296
           G RM   + +   +PK  LL+ P  GGT+  R F+PH CH ++ + GAV+ ATAC I G+
Sbjct: 248 GRRMGFPNAAGMVIPKPVLLAPPTRGGTLAVRYFMPHDCHRAMAITGAVATATACTIPGT 307

Query: 297 VAQGLASTSG--GDRQRLAVEHPSGEFTVEISLEHG-VIKGCGLVRTARLLFDGVV 349
           VA  LA      GD   +  EHP+G  TV +    G       ++RT+R LF+G V
Sbjct: 308 VASALAGRMALPGD---VTFEHPAGRLTVRLDPGAGQSAPTASILRTSRRLFEGTV 360


Lambda     K      H
   0.320    0.138    0.412 

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: 486
Number of extensions: 25
Number of successful extensions: 2
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: 361
Length of database: 374
Length adjustment: 30
Effective length of query: 331
Effective length of database: 344
Effective search space:   113864
Effective search space used:   113864
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: 49 (23.5 bits)

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

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