GapMind for catabolism of small carbon sources

 

Alignments for a candidate for hpcD in Cupriavidus basilensis 4G11

Align 3-hydroxypropionyl-CoA dehydratase (EC 4.2.1.116) (characterized)
to candidate RR42_RS28550 RR42_RS28550 enoyl-CoA hydratase

Query= BRENDA::A4YI89
         (259 letters)



>FitnessBrowser__Cup4G11:RR42_RS28550
          Length = 256

 Score =  159 bits (401), Expect = 7e-44
 Identities = 98/254 (38%), Positives = 146/254 (57%), Gaps = 3/254 (1%)

Query: 6   IETKKEGNLFWITLNRPDKLNALNAKLLEELDRAVSQAESDPEIRVIIITGKG-KAFCAG 64
           IE   +G++  +TL RP   NA NA+ L +L + V+   +D  +R I+ITG G + F AG
Sbjct: 2   IEHVIDGHIARLTLKRPPA-NAFNAEGLAQLQQLVATLNADTRVRAIVITGDGSRFFSAG 60

Query: 65  ADITQFNQLTPAEAWKFSKKGREIMDKIEALSKPTIAMINGYALGGGLELALACDIRIAA 124
           AD+  F     A A   +++     + ++      IA INGYA+GGGLE ALACD+RIA 
Sbjct: 61  ADLNGFADGDRAHARLMAQRFGAAFEALQNARPLVIAAINGYAMGGGLECALACDVRIAE 120

Query: 125 EEAQLGLPEINLGIYPGYGGTQRLTRVIGKGRALEMMMTGDRIPGKDAEKYGLVNRVVPL 184
           E+AQ+ LPE  +G+ P   GTQ L  ++G+G A  M++  +RI    A + GLV  +VP 
Sbjct: 121 EQAQMALPEAGVGLLPCGCGTQTLPWLVGEGWAKRMILANERIDAATALRIGLVEEMVPT 180

Query: 185 ANLEQETRKLAEKIAKKSPISLALIKEVVNRGLDS-PLLSGLALESVGWGVVFSTEDKKE 243
                   +LAE+ +  SP + A  K++V+      P    LALE   +  +F  ED++E
Sbjct: 181 GQALDAALRLAERASNVSPRAAAYSKQLVHLARQGVPRGPALALERERFVDLFDGEDQRE 240

Query: 244 GVSAFLEKREPTFK 257
           GV+AFL+KR P ++
Sbjct: 241 GVNAFLQKRAPQWR 254


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: 123
Number of extensions: 9
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: 256
Length adjustment: 24
Effective length of query: 235
Effective length of database: 232
Effective search space:    54520
Effective search space used:    54520
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.

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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