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_036833410.1 N784_RS16575 enoyl-CoA hydratase

Query= BRENDA::A4YI89
         (259 letters)



>NCBI__GCF_000775615.1:WP_036833410.1
          Length = 260

 Score =  196 bits (497), Expect = 5e-55
 Identities = 101/252 (40%), Positives = 160/252 (63%), Gaps = 1/252 (0%)

Query: 9   KKEGNLFWITLNRPDKLNALNAKLLEELDRAVSQAESDPEIRVIIITGKG-KAFCAGADI 67
           +K  ++  +TLNR +  NA + +L++++ +A  +     +IR ++ITG G KAFCAGAD+
Sbjct: 9   RKGDHIILLTLNRQEAANAFSLQLMDDVIQATKEINKMDDIRCVVITGAGDKAFCAGADL 68

Query: 68  TQFNQLTPAEAWKFSKKGREIMDKIEALSKPTIAMINGYALGGGLELALACDIRIAAEEA 127
            + + +   +      K  + ++ +E +  P +A ING A GGG+ELALACDIR +++ A
Sbjct: 69  KERSTMNERQVVDAVHKIGQTVNAVEQIRVPVVAAINGVAFGGGMELALACDIRYSSDMA 128

Query: 128 QLGLPEINLGIYPGYGGTQRLTRVIGKGRALEMMMTGDRIPGKDAEKYGLVNRVVPLANL 187
           ++GL E++LGI PG GGTQRL R++G G+A E++ +  RI   +A   G+V RV+P   L
Sbjct: 129 KMGLTEVSLGIIPGAGGTQRLPRLVGVGKAKELIYSAKRIDAHEAYHIGIVERVIPQQLL 188

Query: 188 EQETRKLAEKIAKKSPISLALIKEVVNRGLDSPLLSGLALESVGWGVVFSTEDKKEGVSA 247
             E   LA +IA  +PISL   K+ + +G +  L +GL+LE + +     TED+ EG+ A
Sbjct: 189 MNEVLTLASQIASNAPISLIQAKKAIQKGQEVGLTTGLSLEWMCYEATIPTEDRLEGLRA 248

Query: 248 FLEKREPTFKGK 259
           F EKR+P ++GK
Sbjct: 249 FKEKRKPVYQGK 260


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: 139
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: 260
Length adjustment: 24
Effective length of query: 235
Effective length of database: 236
Effective search space:    55460
Effective search space used:    55460
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