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_0861 Ga0059261_0861 Acyl-CoA dehydrogenases

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



>FitnessBrowser__Korea:Ga0059261_0861
          Length = 403

 Score =  259 bits (663), Expect = 7e-74
 Identities = 153/395 (38%), Positives = 224/395 (56%), Gaps = 21/395 (5%)

Query: 12  FRDEVRQFFKDNVPAKTRQK-----LIEGRHNTKEEMVEWYRILNKKGWAVTHWPKEYGG 66
           FR EVR++   N PA  + K      +EG      +   W + + +KGW V  WP+EYGG
Sbjct: 16  FRTEVREWLAANFPASLKGKDNTMSAVEGPTEETPDQAAWRKAMGEKGWGVPTWPREYGG 75

Query: 67  TGWSSVQHYIFNEELQAAPAPQPLA-FGVSMVGPVIYTFGSEEQKKRFLPRIANVDDWWC 125
            G S  +  +  +E+  A A  P+   GV M GP +  +G+E QK+  +P IA  +  WC
Sbjct: 76  GGLSRAEAKVLADEMAKAGAWNPIGGMGVMMFGPTLLEYGNEAQKREHIPAIAKGEVRWC 135

Query: 126 QGFSEPGSGSDLASLKTKAEKKGDKWIINGQKTWTTLAQHADWIFCLCRTDPAAKKQEGI 185
           QG+SEP +GSDLA+L+  AE KGD +++NGQKTWT+  Q AD  FC+ RTD   +KQ GI
Sbjct: 136 QGYSEPNAGSDLANLQCFAEDKGDHYLVNGQKTWTSGGQWADKCFCIVRTD-KTQKQGGI 194

Query: 186 SFILVDMKTKGITVRPIQTIDGGHEVNEVFFDDVEVPLENLVGQENKGWDYAKFLLGNER 245
           +F+L+DM T G+ V+PIQ I G     E FF +V+VP EN VG+E +GW   K LL +ER
Sbjct: 195 TFLLIDMDTPGVEVKPIQMISGMSPFCETFFTNVKVPKENRVGEEGQGWTIGKRLLQHER 254

Query: 246 T----GIARVGMSKERIRRIKQLAAQVESGGKPVIEDPKFRDKLAAVEIELKALELTQLR 301
           T    G +R+  S   +  I +     ++ G+  + DP  R ++A  E++ +A  LT +R
Sbjct: 255 TNLSGGGSRLMPSGPSLADIAKNYVGADAEGR--VADPDLRARIAKWEMDWRAFLLTAMR 312

Query: 302 VVADEGKHGKGKPNPASSVLKIKGSEIQQATTELLMEVIGPFAAPYDVHGDDDSNETMDW 361
           V A+      G  +  SS+LK  G+++ Q   ELL+E+ G     ++  G+  S   +  
Sbjct: 313 VQAE--SKAAGGVSEVSSILKTVGTKLGQERAELLIEIQGHEGLGWE--GEGFSEAQLKG 368

Query: 362 TAQIAPGYFNNRKVSIYGGSNEIQRNIICKAVLGL 396
           T      +   +  +IYGGS EIQ NII K +LG+
Sbjct: 369 TR----AWLFGKATTIYGGSTEIQNNIIAKRILGM 399


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: 492
Number of extensions: 23
Number of successful extensions: 7
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: 403
Length adjustment: 31
Effective length of query: 365
Effective length of database: 372
Effective search space:   135780
Effective search space used:   135780
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