GapMind for catabolism of small carbon sources

 

Alignments for a candidate for hpcD in Paraburkholderia bryophila 376MFSha3.1

Align 3-hydroxypropionyl-CoA dehydratase (EC 4.2.1.116) (characterized)
to candidate H281DRAFT_01179 H281DRAFT_01179 short chain enoyl-CoA hydratase

Query= BRENDA::A4YI89
         (259 letters)



>FitnessBrowser__Burk376:H281DRAFT_01179
          Length = 257

 Score =  154 bits (388), Expect = 2e-42
 Identities = 92/260 (35%), Positives = 136/260 (52%), Gaps = 4/260 (1%)

Query: 1   MEFETIETKKEGNLFWITLNRPDKLNALNAKLLEELDRAVSQAESDPEIRVIIITGKGKA 60
           MEF T+  +    +  +TLNRP+K NA N+++  E+        +  ++ VI++TG G A
Sbjct: 1   MEFNTLLVEINNKIAVVTLNRPEKRNAQNSEMRNEIIDCFDVLGARDDVSVIVVTGAGSA 60

Query: 61  FCAGADITQFNQLTPAEAW-KFSKKGREIMDKIEALSKPTIAMINGYALGGGLELALACD 119
           F AGAD+T    L+   A+ K  +  RE    I    KP IA ING A+G G  + +  D
Sbjct: 61  FSAGADLTDRKDLSQPGAFPKHHRIVRESAYAIRECPKPIIAAINGAAMGAGFGIVMNSD 120

Query: 120 IRIAAEEAQLGLPEINLGIYPGYGGTQRLTRVIGKGRALEMMMTGDRIPGKDAEKYGLVN 179
           I +A+EEA + +PEIN+G+    GG   L R+  + RA  M  TG ++ G++  + GLV 
Sbjct: 121 IWVASEEAYVSMPEINVGLA---GGVSFLNRIFSQSRARRMFYTGMKVTGRELYRLGLVE 177

Query: 180 RVVPLANLEQETRKLAEKIAKKSPISLALIKEVVNRGLDSPLLSGLALESVGWGVVFSTE 239
                  L     ++A +IA KSP++L L KE      + PL      E      +  TE
Sbjct: 178 ACTTKEELLPFAMEIAREIASKSPVALRLAKEAAGLTENMPLREAYRYEQGNTEFLSKTE 237

Query: 240 DKKEGVSAFLEKREPTFKGK 259
           D KE   AF+EKR P + G+
Sbjct: 238 DSKEAQRAFIEKRAPVYVGR 257


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: 145
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: 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 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