GapMind for catabolism of small carbon sources

 

Alignments for a candidate for hpcD in Pseudomonas fluorescens FW300-N1B4

Align 3-hydroxypropionyl-CoA dehydratase (EC 4.2.1.116) (characterized)
to candidate Pf1N1B4_4777 Enoyl-CoA hydratase [valine degradation] (EC 4.2.1.17)

Query= BRENDA::A4YI89
         (259 letters)



>FitnessBrowser__pseudo1_N1B4:Pf1N1B4_4777
          Length = 270

 Score =  135 bits (341), Expect = 7e-37
 Identities = 81/266 (30%), Positives = 134/266 (50%), Gaps = 11/266 (4%)

Query: 2   EFETIETKKEGNLFWITLNRPDKLNALNAKLLEELDRAVSQAESDPEIRVIIITGKGKAF 61
           ++     +   N+  + +NRP+K+N++NA    E+       +   E+RV++++G GK F
Sbjct: 3   QYTAFSVELADNIAHVQINRPEKINSMNAAFWSEIIEIFQWIDDTDEVRVVVLSGAGKHF 62

Query: 62  CAGADITQFNQLTPAEAWKFSKKGREIMDKIEALS----------KPTIAMINGYALGGG 111
            +G D+     +        S+  R +   I  L           KP +A I GY LGG 
Sbjct: 63  SSGIDLMMMAGMLNELGKDVSRNARLLRRTILTLQASFNAVDNCRKPVLAAIQGYCLGGA 122

Query: 112 LELALACDIRIAAEEAQLGLPEINLGIYPGYGGTQRLTRVIGKGRALEMMMTGDRIPGKD 171
           ++L  ACD+R AAE+AQ  + EI++G+    G  QRL R+IG G   E+  TG      +
Sbjct: 123 IDLISACDMRYAAEDAQFSIKEIDIGMAADVGTLQRLPRIIGDGMLRELAYTGRTFGADE 182

Query: 172 AEKYGLVNRVV-PLANLEQETRKLAEKIAKKSPISLALIKEVVNRGLDSPLLSGLALESV 230
           A   GLVNRV    A+L +    +A +IA KSPI++   KE+++   D  +  GL   + 
Sbjct: 183 ARSIGLVNRVYSDAASLLEGVMGIAREIAGKSPIAVTGTKEMISYMRDHRIDDGLEYVAT 242

Query: 231 GWGVVFSTEDKKEGVSAFLEKREPTF 256
               +  + D +  ++A + K++P F
Sbjct: 243 WNAAMLQSTDLRVAMAAHMSKQKPEF 268


Lambda     K      H
   0.315    0.135    0.382 

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: 147
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: 259
Length of database: 270
Length adjustment: 25
Effective length of query: 234
Effective length of database: 245
Effective search space:    57330
Effective search space used:    57330
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: 42 (22.0 bits)
S2: 47 (22.7 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