GapMind for catabolism of small carbon sources

 

Alignments for a candidate for prpB in Azospirillum brasilense Sp245

Align 2-methylisocitrate lyase; 2-MIC; MICL; EC 4.1.3.30; (2R,3S)-2-methylisocitrate lyase (uncharacterized)
to candidate AZOBR_RS27785 AZOBR_RS27785 carboxyvinyl-carboxyphosphonate phosphorylmutase

Query= curated2:Q9YFM7
         (308 letters)



>FitnessBrowser__azobra:AZOBR_RS27785
          Length = 292

 Score =  214 bits (546), Expect = 1e-60
 Identities = 119/281 (42%), Positives = 166/281 (59%), Gaps = 6/281 (2%)

Query: 16  LRELIEKRDIVVAPGVYNPAVALLAERMGFEALYLSG-AAITGSLAMPDLGLITLSELAM 74
           L++ + +  ++ APGV++   A +A+ MGF+ LY++G   +   L +PD GL T S++  
Sbjct: 10  LKQRLSQPGLISAPGVFDMISAKVADGMGFDTLYMTGYGTVASHLGLPDAGLATFSDMVG 69

Query: 75  FTSYITRVVRVPVIVDADTGFGEAINVERTVRELERAGAAAIQIEDQVMPKKCGHLQGKA 134
               I R    P++ D DTG+G  +NV+ T+R  E AGAAAIQ+EDQ  PKKCGH  G+ 
Sbjct: 70  RVRAIARGTSTPLVADGDTGYGGLLNVDFTIRGYEEAGAAAIQLEDQEFPKKCGHTPGRR 129

Query: 135 LISPEDMVKKIIAAVGARR--DALIVARTDARGVEGFEKAVERAQLYVEAGADIIFPEAL 192
           +I   DMV+KI  A  AR   D LI+ARTDAR   G ++A+ RA  Y EAGADIIF E+ 
Sbjct: 130 VIPMADMVRKIRVACEARSSSDFLIIARTDARTTLGLDEALRRADAYAEAGADIIFVESP 189

Query: 193 TSLEEFREFARRVKAPLLANMTEFGKTPYITVDQFREAGYKIVIFPVTTFRASLKASETV 252
            S  E     R +  PL+ANM E G+TP +T  Q    GY+I IFP T F A   A  + 
Sbjct: 190 ESEAEMERICRTIGKPLIANMVEGGRTPVMTGAQLESLGYRIAIFPATGFLAMAAALRSA 249

Query: 253 LREIMEKGTQKDILDKLYTRTEFYDLIGYH---DYEKRDAE 290
             EI+ KG+  +   +LY   +F  L+G+    ++EKR  E
Sbjct: 250 YGEILAKGSSAEYRGELYPFPDFTRLMGFERVWEFEKRHPE 290


Lambda     K      H
   0.321    0.137    0.378 

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: 274
Number of extensions: 7
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: 308
Length of database: 292
Length adjustment: 27
Effective length of query: 281
Effective length of database: 265
Effective search space:    74465
Effective search space used:    74465
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: 48 (23.1 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