GapMind for catabolism of small carbon sources

 

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

Align 2-(1,2-epoxy-1,2-dihydrophenyl)acetyl-CoA isomerase (EC 5.3.3.18) (characterized)
to candidate 5210229 Shew_2672 carnitinyl-CoA dehydratase (RefSeq)

Query= BRENDA::Q5SLK3
         (254 letters)



>FitnessBrowser__PV4:5210229
          Length = 261

 Score =  131 bits (329), Expect = 2e-35
 Identities = 96/257 (37%), Positives = 136/257 (52%), Gaps = 12/257 (4%)

Query: 6   RQDGVLVLTLNRPEKLNAITGELLDALYAALKEGEEDREVRALLLTGAG-RAFSAGQDLT 64
           R   +L + L+RP K NAI  +    +        +D E+R  ++TGAG R FSAG DL 
Sbjct: 9   RNGSILEIVLDRP-KANAIDAKTSYEMGEVFLAFRDDPELRVAIITGAGARFFSAGWDLK 67

Query: 65  EFGDRK-PDYEAHLRRYNRVVEALSGLEKPLVVAVNGVAAGAGMSLALWGDLRLAAVGAS 123
              + + PD +     +  + E L  L+KP++ AVNG A G G  LAL  DL + A  AS
Sbjct: 68  AAAEGEAPDADFGPGGFAGLTE-LFDLDKPVIAAVNGYAFGGGFELALAADLIVCADNAS 126

Query: 124 FTTAFVRIGLVPDSGLSFLLPRLVGLAKAQELLLLSPRLSAEEALALGLVHRVVPAEKLM 183
           F     ++G+VPDSG    LP+L+      EL++    + A+EAL  G+V+RVV  E LM
Sbjct: 127 FALPEAKLGIVPDSGGMLRLPKLLPAPIVNELMMTGRSMDAQEALRWGVVNRVVEQEALM 186

Query: 184 EEALSLAKELAQGPTRAYALTKKLLLETYRLSLTEALALEAVLQGQAG------QTQDHE 237
           E A  LA E++Q    A A  K++  ET  LS+ +  A   +  GQ         ++D  
Sbjct: 187 ETARELANEISQSAPLALAAIKEIYRETGELSVEQGYA--HIRGGQLKHYPSVLHSEDAL 244

Query: 238 EGVRAFREKRPPRFQGR 254
           EG  AF EKR P +QG+
Sbjct: 245 EGPAAFAEKRDPVWQGK 261


Lambda     K      H
   0.318    0.135    0.371 

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: 172
Number of extensions: 11
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: 254
Length of database: 261
Length adjustment: 24
Effective length of query: 230
Effective length of database: 237
Effective search space:    54510
Effective search space used:    54510
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: 41 (21.7 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