GapMind for catabolism of small carbon sources

 

Alignments for a candidate for pimC in Cupriavidus basilensis 4G11

Align pimeloyl-CoA dehydrogenase small subunit (EC 1.3.1.62) (characterized)
to candidate RR42_RS05600 RR42_RS05600 acyl-CoA dehydrogenase

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



>FitnessBrowser__Cup4G11:RR42_RS05600
          Length = 372

 Score =  290 bits (743), Expect = 3e-83
 Identities = 167/382 (43%), Positives = 228/382 (59%), Gaps = 15/382 (3%)

Query: 1   MDFDLSEEQRLLKESVEGLLKGSYDFDSRKKYAKEKGGWSRAVWGKFAEQGLLGLPFSEE 60
           M+F+LS+EQ+ L ++V   +   YDF++RKK  K + G S A WG   E GL  LP  E 
Sbjct: 1   MNFNLSDEQKQLADAVHRFIDKDYDFETRKKGIKAEAGHSDAAWGALVELGLTALPVPEA 60

Query: 61  DGGFGAGAVETMIVMEALGHSLVLEPYLPTVVIGGGFLRRAGSAAQKAAHLPGIIDGSKT 120
            GGF    ++ M+VM+ LG  LV+EPY  TVV     L+ AG    + A L  +  G   
Sbjct: 61  QGGFSGTPIDMMVVMQELGRGLVVEPYFATVVAAYA-LKLAGG---QDALLEQVAGGELK 116

Query: 121 FAFAQLEKNSRWDLGDVSTTAKKSGDGWVIDGEKFVVLNGEAADTLIVTARTKGGQRDRT 180
            A A  E ++R+ L DV  TAK    G  ++G K V ++G  A  L+V+ART G   D +
Sbjct: 117 LATAFNEPHARYALNDVRVTAK----GGKLNGRKVVTIHGAQAGKLVVSARTSGADADTS 172

Query: 181 GVGVFLVPADAKGITRKGYPTQDGLHAADITFTGVQVGADAAIGDPENALELIEAVVDDA 240
           G+ +FLV   A G++   Y T D L AADITF   Q      +G    A  LIE V D A
Sbjct: 173 GISLFLVDPKAAGVSITDYRTIDNLRAADITFKDAQ---GELLGTEGAAFALIEQVADYA 229

Query: 241 RTALCAEAVGLMDESLTTTVEYIKTRKQFGVPIGSFQVLQHRAADMFVATEQARSMAMFA 300
              LCAEAVG++D     T+EY KTR+QFGVPI  FQ LQHR  +MF+  EQ+RS+ + A
Sbjct: 230 AVLLCAEAVGVIDTLNAATLEYAKTRQQFGVPIARFQALQHRMVEMFIHAEQSRSITLLA 289

Query: 301 TMAAEFDDA--KERAGAIAAAKVQIGKSGKFVGQQSIQLHGGIGMTMEAKIGHYFKRLTM 358
             AA+FD+A  +ER    +AAK ++G++ + VGQ+++Q+HGG+G+T E    H FKRLT+
Sbjct: 290 --AAKFDEASPEERRRFASAAKARVGQAARSVGQEAVQIHGGMGVTDELPAAHMFKRLTL 347

Query: 359 IEQTFGDTDHHLARVSAGGGLI 380
           I  TFGD DHHL+R +   G +
Sbjct: 348 INTTFGDVDHHLSRFATQPGFL 369


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: 375
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: 372
Length adjustment: 30
Effective length of query: 350
Effective length of database: 342
Effective search space:   119700
Effective search space used:   119700
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 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