GapMind for catabolism of small carbon sources

 

Alignments for a candidate for hpcD in Pseudomonas stutzeri RCH2

Align 3-hydroxypropionyl-CoA dehydratase (EC 4.2.1.116) (characterized)
to candidate GFF2604 Psest_2654 fatty oxidation complex, alpha subunit FadB

Query= BRENDA::A4YI89
         (259 letters)



>FitnessBrowser__psRCH2:GFF2604
          Length = 715

 Score =  118 bits (296), Expect = 3e-31
 Identities = 73/219 (33%), Positives = 113/219 (51%), Gaps = 12/219 (5%)

Query: 23  DKLNALNAKLLEELDRAVSQAESDPEIRVIIITGKGKAFCAGADITQFN---QLTPAEAW 79
           + +N  N   L +L +AV   ++D  ++ +I+T     F  GADIT+F    ++   E  
Sbjct: 27  ESVNKFNRLTLNDLRQAVDAIKADASVKGVIVTSGKDVFIVGADITEFVDNFKMADEELV 86

Query: 80  KFSKKGREIMDKIEALSKPTIAMINGYALGGGLELALACDIRIAAEEAQLGLPEINLGIY 139
             + +  +I    E L  PT+A ING ALGGG E+ +A D R+ +  A++GLPE+ LGIY
Sbjct: 87  AGNLEANKIFSDFEDLGVPTVAAINGIALGGGFEMCMAADYRVMSTTAKVGLPEVKLGIY 146

Query: 140 PGYGGTQRLTRVIGKGRALEMMMTGDRIPGKDAEKYGLVNRVVPLANLEQETRKLAEKIA 199
           PG+GGT RL R+IG   A+E + +G     +DA K   V+ VV    L+     L ++  
Sbjct: 147 PGFGGTVRLPRLIGVDNAVEWIASGKENRAEDALKVHAVDAVVAPDKLQAAALDLVKR-- 204

Query: 200 KKSPISLALIKEVVNRGLDSPLLSGLALESVGWGVVFST 238
                  A+  E+  +    P L  L L ++   + F T
Sbjct: 205 -------AISGELDYKAKRQPKLDKLKLNAIEQMMAFET 236


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: 370
Number of extensions: 20
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: 715
Length adjustment: 32
Effective length of query: 227
Effective length of database: 683
Effective search space:   155041
Effective search space used:   155041
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: 51 (24.3 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