GapMind for catabolism of small carbon sources

 

Alignments for a candidate for hpcD in Shewanella loihica PV-4

Align 3-hydroxypropionyl-CoA dehydratase (EC 4.2.1.116) (characterized)
to candidate 5209977 Shew_2425 multifunctional fatty acid oxidation complex subunit alpha (RefSeq)

Query= BRENDA::A4YI89
         (259 letters)



>FitnessBrowser__PV4:5209977
          Length = 706

 Score =  140 bits (353), Expect = 7e-38
 Identities = 85/197 (43%), Positives = 127/197 (64%), Gaps = 8/197 (4%)

Query: 17  ITLNRP-DKLNALNAKLLEELDRAVSQAESDPEIR-VIIITGKGKAFCAGADITQFNQLT 74
           +T++ P + +N L A+   E+   +++ ++D  IR V+II+GK  +F AGADI+  +   
Sbjct: 17  LTMDVPGETMNTLRAEFGPEICEMLAEIKADAGIRGVVIISGKKDSFVAGADISMLDACA 76

Query: 75  PAE-AWKFSKKGREIMDKIEALSKPTIAMINGYALGGGLELALACDIRIAAE--EAQLGL 131
            AE A + SK+G E+   +E+LS P +A ING  LGGGLELALAC  R+  +  +  LGL
Sbjct: 77  TAEDARELSKQGHEVFFALESLSIPVVAAINGACLGGGLELALACHQRVCTDSNKTMLGL 136

Query: 132 PEINLGIYPGYGGTQRLTRVIGKGRALEMMMTGDRIPGKDAEKYGLVNRVVPLANLEQET 191
           PE+ LG+ PG GGTQRL R++G  ++L+MM+TG ++  K A K GLV+ VVP + L Q  
Sbjct: 137 PEVQLGLLPGGGGTQRLPRLVGIAKSLDMMLTGKQLRAKQALKMGLVDDVVPESILLQTA 196

Query: 192 RKLA---EKIAKKSPIS 205
            ++A    + AKK  +S
Sbjct: 197 IEMALAGARPAKKPKLS 213


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: 373
Number of extensions: 24
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: 706
Length adjustment: 32
Effective length of query: 227
Effective length of database: 674
Effective search space:   152998
Effective search space used:   152998
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: 50 (23.9 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