GapMind for catabolism of small carbon sources

 

Alignments for a candidate for hpcD in Shewanella amazonensis SB2B

Align 3-hydroxypropionyl-CoA dehydratase (EC 4.2.1.116) (characterized)
to candidate 6938034 Sama_2167 multifunctional fatty acid oxidation complex subunit alpha (RefSeq)

Query= BRENDA::A4YI89
         (259 letters)



>FitnessBrowser__SB2B:6938034
          Length = 706

 Score =  137 bits (346), Expect = 5e-37
 Identities = 86/242 (35%), Positives = 143/242 (59%), Gaps = 20/242 (8%)

Query: 8   TKKEGNLFWITLNRP-DKLNALNAKLLEELDRAVSQAESDPEIR-VIIITGKGKAFCAGA 65
           ++++  +  +T++ P + +N L A+   E+   + + ++D  I+ +++I+GK  +F AGA
Sbjct: 8   SRRDDGIALLTMDVPGETMNTLKAQFAPEITAILQEIKADSSIKGLVLISGKADSFVAGA 67

Query: 66  DITQFNQLTPAE-AWKFSKKGREIMDKIEALSKPTIAMINGYALGGGLELALACDIRIAA 124
           DI+  +    AE A   S++G  +  ++E L+ P +A I+G  LGGGLELALAC  R+ +
Sbjct: 68  DISMLDACETAEDARLLSRQGHHVFAELEGLNIPVVAAIHGACLGGGLELALACHQRVCS 127

Query: 125 EEAQ--LGLPEINLGIYPGYGGTQRLTRVIGKGRALEMMMTGDRIPGKDAEKYGLVNRVV 182
           + ++  LG+PE+ LG+ PG GGTQRL R+IG  +AL++M+TG ++  K A K GLV+ VV
Sbjct: 128 DSSKTMLGVPEVQLGLLPGGGGTQRLPRLIGIAKALDLMLTGKQVRPKQAVKMGLVDDVV 187

Query: 183 PLANLEQETRKLAEKIAKKSPISLALIKEVVNRGLDSPLLSGLALES--VGWGVVFSTED 240
           P            E I   + I +AL  +   + L  PL++ L LE   VG  ++F    
Sbjct: 188 P------------ESILLDTAIEMALAGKKTRKPLKQPLVTKL-LEGTPVGRNIMFDQAT 234

Query: 241 KK 242
           K+
Sbjct: 235 KQ 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: 361
Number of extensions: 14
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.

Links

Downloads

Related tools

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