GapMind for catabolism of small carbon sources

 

Alignments for a candidate for fahA in Phaeobacter inhibens BS107

Align fumarylacetoacetase (EC 3.7.1.2) (characterized)
to candidate GFF442 PGA1_c04530 ureidoglycolate lyase

Query= BRENDA::A0A076VF18
         (308 letters)



>FitnessBrowser__Phaeo:GFF442
          Length = 282

 Score =  146 bits (368), Expect = 6e-40
 Identities = 97/242 (40%), Positives = 131/242 (54%), Gaps = 35/242 (14%)

Query: 66  QTLLSPLAPTDVPAIRG----------------MGLQYSGDPANPQ---DKPPVACLFFK 106
           Q  L+ L   D+P IRG                +GL Y       +    K P+  LF K
Sbjct: 43  QAKLASLPLADLPIIRGEPRLAPCVGNVGKFLCIGLNYRDHAEEAELAIPKHPI--LFLK 100

Query: 107 ASQALAGPGDDIVLPRLARDEKNDYEVELCVVLGKDAKDVDEKDAMSFVGGYCVVNDVSS 166
           A+ A++GP D +VLPR A  EK D+EVEL VV+GK AK V  +DA+  V GYCVVNDVS 
Sbjct: 101 ANSAISGPNDPVVLPRGA--EKVDWEVELGVVIGKTAKYVGAEDALDHVAGYCVVNDVSE 158

Query: 167 RGL-CAKGGQWGMGKSYDTWCPFGPCLVSPSALGADPHKLTITTHVNGKLAQKGNTADLV 225
           R       GQW  GKS D++ P GP LV+P  +  DP +L +   VNGK  Q+G++  ++
Sbjct: 159 RSFQMDLSGQWTKGKSCDSFGPIGPWLVTPDEV-PDPQQLALYCDVNGKRMQQGHSGTMI 217

Query: 226 LKIPELIARLSHGTTLQAGSLILTGSPIALGRKAPGDAVEQSP---FMKDGDEIRCFVEG 282
             + E+I+ LS   TL  G LI TG+P       PG  + Q P   ++K GD +R  ++G
Sbjct: 218 FSVAEIISHLSQLMTLHPGDLIATGTP-------PGVGMGQKPVPVYLKAGDTLRLGIDG 270

Query: 283 CG 284
            G
Sbjct: 271 LG 272


Lambda     K      H
   0.316    0.135    0.411 

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: 246
Number of extensions: 12
Number of successful extensions: 4
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: 282
Length adjustment: 26
Effective length of query: 282
Effective length of database: 256
Effective search space:    72192
Effective search space used:    72192
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 48 (23.1 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