GapMind for catabolism of small carbon sources

 

Alignments for a candidate for hpcD in Novosphingobium barchaimii LL02

Align 3-hydroxypropionyl-CoA dehydratase (EC 4.2.1.116) (characterized)
to candidate WP_059150767.1 V474_RS04200 crotonase/enoyl-CoA hydratase family protein

Query= BRENDA::A4YI89
         (259 letters)



>NCBI__GCF_001046635.1:WP_059150767.1
          Length = 267

 Score =  153 bits (386), Expect = 4e-42
 Identities = 98/250 (39%), Positives = 136/250 (54%), Gaps = 8/250 (3%)

Query: 17  ITLNRPDKLNALN-AKLLEELDRAVSQAESDPEIRVIIITGKGKAFCAGADITQF----- 70
           +TLNRP   N ++  +++E L  A++  E+DP  RV I+TG GK F +G DI Q      
Sbjct: 17  LTLNRPALRNPISDPEVIEALLAALAYLEADPAARVAILTGAGKGFSSGGDINQMKPGGN 76

Query: 71  -NQLTPAEAWKFSKKGREIMD-KIEALSKPTIAMINGYALGGGLELALACDIRIAAEEAQ 128
            N  +PA      K+G + +     AL  P IA +NG A+G G +L   CD+RIA E A+
Sbjct: 77  LNSGSPAVTRLNYKRGIQRLPLAFAALEVPVIAAVNGAAMGAGCDLTCMCDLRIAGESAK 136

Query: 129 LGLPEINLGIYPGYGGTQRLTRVIGKGRALEMMMTGDRIPGKDAEKYGLVNRVVPLANLE 188
                + LG+  G GG+  L RV+G  +A EM +TGD I   +A   GLV+RVVP   L 
Sbjct: 137 FAESFVKLGLIAGDGGSWLLPRVVGWSKAAEMALTGDPIDAAEALACGLVSRVVPDGELM 196

Query: 189 QETRKLAEKIAKKSPISLALIKEVVNRGLDSPLLSGLALESVGWGVVFSTEDKKEGVSAF 248
              R LA +IA   P ++ + K ++  G  + L S L + S       +T D  E V+AF
Sbjct: 197 NAARALALRIAVNPPHAVRMTKRLLWEGRRADLASLLEMASAMQAAAHATADHAEAVTAF 256

Query: 249 LEKREPTFKG 258
           LEKR P FKG
Sbjct: 257 LEKRPPEFKG 266


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: 156
Number of extensions: 6
Number of successful extensions: 2
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: 267
Length adjustment: 25
Effective length of query: 234
Effective length of database: 242
Effective search space:    56628
Effective search space used:    56628
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 24 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