GapMind for catabolism of small carbon sources

 

Alignments for a candidate for fahA in Sinorhizobium meliloti 1021

Align fumarylacetoacetase (EC 3.7.1.2) (characterized)
to candidate SM_b21112 SM_b21112 bifunctional 2-hydroxyhepta-2,4-diene-1, 7-dioatesomerase/5-carboxymethyl-2-oxo-hex-3-ene-1, 7-dioatedecarboxylase

Query= BRENDA::A0A076VF18
         (308 letters)



>FitnessBrowser__Smeli:SM_b21112
          Length = 281

 Score =  147 bits (371), Expect = 3e-40
 Identities = 108/287 (37%), Positives = 150/287 (52%), Gaps = 25/287 (8%)

Query: 22  YGEPQQDGDLGLLYSNG--ERITARVV-AAPWTSSPASTSSPRVLTVQTLLSPLA-PTDV 77
           YGEP Q+   GLL S+G    ++  V   A     P+       L V+TL +    P   
Sbjct: 6   YGEPGQEKP-GLLGSDGIIRDLSGHVSDLAAGALDPSKLDELANLDVETLPAVSGNPRLG 64

Query: 78  PAIRG------MGLQYSGDPANP-QDKPPVACLFFKASQALAGPGDDIVLPRLARDEKND 130
           P + G      +GL YS   A      PP   +F KA+ A+ GP DD+VLPR    EK D
Sbjct: 65  PCVAGTGKFICIGLNYSDHAAETGATVPPEPIIFMKATSAIVGPNDDLVLPR--GSEKTD 122

Query: 131 YEVELCVVLGKDAKDVDEKDAMSFVGGYCVVNDVSSRGL-CAKGGQWGMGKSYDTWCPFG 189
           +EVEL +V+GK AK V E +A+ +V GYC V+DVS R     + GQW  GKS DT+ P G
Sbjct: 123 WEVELGIVIGKTAKYVSEAEALDYVAGYCTVHDVSERAFQTERHGQWTKGKSCDTFGPTG 182

Query: 190 PCLVSPSALGADPHKLTITTHVNGKLAQKGNTADLVLKIPELIARLSHGTTLQAGSLILT 249
           P LV+   + ADP  L +   VNG+  Q G+T  +V     L++ LS   +L+ G +I T
Sbjct: 183 PWLVTKDEV-ADPQDLAMWLKVNGETMQDGSTKTMVYGAAHLVSYLSQFMSLRPGDIIST 241

Query: 250 GSP--IALGRKAPGDAVEQSPFMKDGDEIRCFVEGCGTLINSVRDEA 294
           G+P  + +G K P        ++K GD +   +EG G+    VR +A
Sbjct: 242 GTPPGVGMGMKPP-------RYLKAGDVVELGIEGLGSQKQRVRADA 281


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: 273
Number of extensions: 14
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: 281
Length adjustment: 26
Effective length of query: 282
Effective length of database: 255
Effective search space:    71910
Effective search space used:    71910
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.

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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