GapMind for catabolism of small carbon sources

 

Alignments for a candidate for pimD in Sphingomonas koreensis DSMZ 15582

Align pimeloyl-CoA dehydrogenase large subunit (EC 1.3.1.62) (characterized)
to candidate Ga0059261_0839 Ga0059261_0839 Acyl-CoA dehydrogenases

Query= metacyc::MONOMER-20676
         (396 letters)



>FitnessBrowser__Korea:Ga0059261_0839
          Length = 393

 Score =  263 bits (671), Expect = 8e-75
 Identities = 156/396 (39%), Positives = 219/396 (55%), Gaps = 22/396 (5%)

Query: 12  FRDEVRQFFKDNVPAKTRQKLIE-------GRHNTK--EEMVEWYRILNKKGWAVTHWPK 62
           FR E R + ++N PA  R+ +         GR  +    +   W   +  +GW V  WPK
Sbjct: 7   FRAETRAWLEENCPASMREPVRSEKDTVWGGRDQSALTPDQKTWMDRMAARGWTVPDWPK 66

Query: 63  EYGGTGWSSVQHYIFNEELQAAPAPQPLA-FGVSMVGPVIYTFGSEEQKKRFLPRIANVD 121
            YGG G S  +  I  EE++A     PL+ FG+SM+GP +  +G+EEQK   LPRIA  +
Sbjct: 67  AYGGGGLSPAESKILREEMRALGCRNPLSSFGISMLGPALLKYGNEEQKLEHLPRIARGE 126

Query: 122 DWWCQGFSEPGSGSDLASLKTKAEKKGDKWIINGQKTWTTLAQHADWIFCLCRTDPAAKK 181
             WCQG+SEP +GSDLA+L T AE  GD +++NGQK WT+ A  ADWIFCL RTD +  K
Sbjct: 127 IRWCQGYSEPNAGSDLAALATSAEDMGDHYLVNGQKVWTSYADKADWIFCLVRTDKSV-K 185

Query: 182 QEGISFILVDMKTKGITVRPIQTIDGGHEVNEVFFDDVEVPLENLVGQENKGWDYAKFLL 241
           Q GISF+L DM + G++ +PI  I G     E FFDDV+VP  NLVG+ NKGWD AK+LL
Sbjct: 186 QAGISFLLFDMASPGVSTKPILLISGYSPFCETFFDDVKVPKANLVGELNKGWDVAKYLL 245

Query: 242 GNERTGIARVGMS-KERIRRIKQLAAQVESGGKPVIEDPKFRDKLAAVEIELKALELTQL 300
           G+ER  I+ +G+        I    A++  G    + DP  R ++A  E+  +A      
Sbjct: 246 GHEREMISGMGLGLSSGGTLIGNAVARMGLGDDGRLADPLLRGQIALHEVRARAFAAMSE 305

Query: 301 RVVADEGKHGKGKPNPASSVLKIKGSEIQQATTELLMEVIGPFAAPYDVHGDDDSNETMD 360
           R + DE K G+  P    S++K  G+E+ +A  EL M   G  +  ++    ++      
Sbjct: 306 RFL-DELKTGRAHP-AQPSMMKYYGTELNKARHELEMAAGGSDSLEWESAASNNGAAPRA 363

Query: 361 WTAQIAPGYFNNRKVSIYGGSNEIQRNIICKAVLGL 396
           W           +  SI GG++E+Q NII K +L L
Sbjct: 364 W--------LRTKANSIEGGTSEVQLNIIAKRILEL 391


Lambda     K      H
   0.317    0.135    0.411 

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: 441
Number of extensions: 24
Number of successful extensions: 5
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: 396
Length of database: 393
Length adjustment: 31
Effective length of query: 365
Effective length of database: 362
Effective search space:   132130
Effective search space used:   132130
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 (21.6 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