GapMind for catabolism of small carbon sources

 

Alignments for a candidate for hpcD in Pontibacillus litoralis JSM 072002

Align 3-hydroxypropionyl-CoA dehydratase (EC 4.2.1.116) (characterized)
to candidate WP_036834013.1 N784_RS08155 enoyl-CoA hydratase

Query= BRENDA::A4YI89
         (259 letters)



>NCBI__GCF_000775615.1:WP_036834013.1
          Length = 257

 Score =  158 bits (400), Expect = 9e-44
 Identities = 89/256 (34%), Positives = 142/256 (55%), Gaps = 1/256 (0%)

Query: 3   FETIETKKEGNLFWITLNRPDKLNALNAKLLEELDRAVSQAESDPEIRVIIITGKGKAFC 62
           +ETI+      +  ITL+RP KLNA+  +L  EL +A+ QA    ++RVII+TG+G+AFC
Sbjct: 2   YETIQYDVIQQVATITLHRPAKLNAITLQLNAELSKALKQASHSDDVRVIILTGEGRAFC 61

Query: 63  AGADITQFNQLTPAEAWKFSKKGREIMDKIEALSKPTIAMINGYALGGGLELALACDIRI 122
           +G D+T  +          +  G  ++  +E   KP IA +NG A G G  LALACD R+
Sbjct: 62  SGQDLTLASDDVDYGDVLRTSYG-PVVRAMEECEKPIIAAVNGVAAGAGFSLALACDFRL 120

Query: 123 AAEEAQLGLPEINLGIYPGYGGTQRLTRVIGKGRALEMMMTGDRIPGKDAEKYGLVNRVV 182
            +E+A      + +G+ P  G    L++++G  +ALE+ + G ++  ++A+   L  +V+
Sbjct: 121 MSEKASFVQAFVQIGLIPDAGNLYYLSKLVGHAKALELSLLGGKVTAEEAKALHLATKVI 180

Query: 183 PLANLEQETRKLAEKIAKKSPISLALIKEVVNRGLDSPLLSGLALESVGWGVVFSTEDKK 242
           P    E++    A ++A     ++ LIK  +    +S L   L  E+ G  +   T D K
Sbjct: 181 PEEQWEEQVNAFAHQLANMPTKTMGLIKRNLKASWNSTLPEFLEAEANGQKIAGLTNDHK 240

Query: 243 EGVSAFLEKREPTFKG 258
           EGV AFL+KR P F+G
Sbjct: 241 EGVQAFLDKRPPLFQG 256


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: 143
Number of extensions: 5
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: 257
Length adjustment: 24
Effective length of query: 235
Effective length of database: 233
Effective search space:    54755
Effective search space used:    54755
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