GapMind for catabolism of small carbon sources

 

Alignments for a candidate for pimC in Novosphingobium barchaimii LL02

Align pimeloyl-CoA dehydrogenase small subunit (EC 1.3.1.62) (characterized)
to candidate WP_059149579.1 V474_RS00150 acyl-CoA dehydrogenase

Query= metacyc::MONOMER-20677
         (380 letters)



>NCBI__GCF_001046635.1:WP_059149579.1
          Length = 373

 Score =  212 bits (540), Expect = 1e-59
 Identities = 131/361 (36%), Positives = 185/361 (51%), Gaps = 5/361 (1%)

Query: 1   MDFDLSEEQRLLKESVEGLLKGSYDFDSRKKYAKEKGGWSRAVWGKFAEQGLLGLPFSEE 60
           M+FDL+E++ +LK   E  +   YD DSR+ +  E GG+S A W    E GL+  PF EE
Sbjct: 1   MNFDLNEDEEMLKALTERFVTDHYDHDSRRAFLAEPGGFSGANWQLLGELGLIAAPFPEE 60

Query: 61  DGGFGAGAVETMIVMEALGHSLVLEPYLPTVVIGGGFLRRAGSAAQKAAHLPGIIDGSKT 120
            GG G  A     V EALG  LV+EP    VV+ G         A +   L  ++ G K 
Sbjct: 61  LGGLGLDATGIATVFEALGRGLVVEPLAEAVVMAGRLFASTAPEALQGEWLGALMAGEKR 120

Query: 121 FAFAQLEKNSRWDLGDVSTTAKKSGDGWVIDGEKFVVLNGEAADTLIVTARTKGGQRDRT 180
            A A +E  +R  L  V T+A     G+ + G K     G  AD  IV+AR  G   D  
Sbjct: 121 LALAHVEARARDGLVWVQTSATAQDGGYCLSGTKPYCAVGGGADGFIVSARLSGEPGDAD 180

Query: 181 GVGVFLVPADAKGITRKGYPTQDGLHAADITFTGVQVGADAAIGDPENALELIEAVVDDA 240
           GV +FLVPA   G + + +   DG  A  +   GV + A   +GD  + L  I +  D A
Sbjct: 181 GVALFLVPAGTPGASTRDWTMADGSVATSLDLEGVVLPAGNRLGD--DGLAAIASTSDLA 238

Query: 241 RTALCAEAVGLMDESLTTTVEYIKTRKQFGVPIGSFQVLQHRAADMFVATEQARSMAMFA 300
             A  AEA+G+M+  L  T+ Y+KTR QFG  +G+FQ +QHR    +   EQ+R++   A
Sbjct: 239 SLARSAEALGIMERLLHETIGYLKTRDQFGSALGAFQAIQHRMVAQYAVIEQSRALLNLA 298

Query: 301 TMAAEFDDAKERAGAIAAAKVQIGKSGKFVGQQSIQLHGGIGMTMEAKIGHYFKRLTMIE 360
            ++ E D   E A A+   +  I  +   +G + IQ HGG+G+T E  IG   KRL ++ 
Sbjct: 299 LVSWESD---EFAQAVHGVRAFIADASVELGHEMIQFHGGMGVTDELAIGGGHKRLLVLS 355

Query: 361 Q 361
           +
Sbjct: 356 R 356


Lambda     K      H
   0.318    0.135    0.388 

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: 405
Number of extensions: 17
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: 380
Length of database: 373
Length adjustment: 30
Effective length of query: 350
Effective length of database: 343
Effective search space:   120050
Effective search space used:   120050
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: 50 (23.9 bits)

This GapMind analysis is from Sep 24 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