GapMind for catabolism of small carbon sources

 

Alignments for a candidate for fucA in Azospirillum brasilense Sp245

Align L-fuculose-phosphate aldolase (EC 4.1.2.17) (characterized)
to candidate AZOBR_RS05280 AZOBR_RS05280 fuculose phosphate aldolase

Query= BRENDA::P0AB87
         (215 letters)



>FitnessBrowser__azobra:AZOBR_RS05280
          Length = 232

 Score =  191 bits (484), Expect = 1e-53
 Identities = 101/210 (48%), Positives = 138/210 (65%), Gaps = 3/210 (1%)

Query: 8   RQIIDTCLEMTRLGLNQGTAGNVSVRYQDGMLITPTGIPYEKLTESHIVFIDGNGKHEEG 67
           R IIDTCL M   G+NQG++GN+SVR + G LITP+ +PY++     IV +  +G +   
Sbjct: 11  RAIIDTCLAMNGAGINQGSSGNLSVRVEGGFLITPSSLPYDETAPEDIVEMGFDGTYVGR 70

Query: 68  KLPSSEWRFHMAAYQSRPDANAVVHNHAVHCTAVSILNRSIPAIHYMIAAAGGNSIPCAP 127
           + PSSEWRFH    ++RPD + V+H H+   TA+++  R IP+ HYM+A AGG+SI CAP
Sbjct: 71  RRPSSEWRFHRDILKARPDVDVVLHTHSTFATALAVHGRGIPSFHYMVALAGGDSIRCAP 130

Query: 128 YATFGTRELSEHVALALKNRKATLLQHHGLIACEVNLEKALWLAHEVEVLAQLYLTTLAI 187
           YATFG++ELS+H   AL+ R A LL +HG+I      + AL LA EVE LA+ YL    +
Sbjct: 131 YATFGSQELSDHAVAALEGRLACLLANHGMIVLGKTPKGALALAVEVETLARQYLHAHLL 190

Query: 188 TDPVPVLSDEEIAVVLEKFK--TYGLRIEE 215
            +PV +L  EEIA V EK +   YGL  +E
Sbjct: 191 GEPV-ILPPEEIARVAEKMRRMKYGLPPDE 219


Lambda     K      H
   0.319    0.134    0.394 

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: 155
Number of extensions: 7
Number of successful extensions: 1
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: 215
Length of database: 232
Length adjustment: 22
Effective length of query: 193
Effective length of database: 210
Effective search space:    40530
Effective search space used:    40530
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: 46 (22.3 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