GapMind for catabolism of small carbon sources

 

Alignments for a candidate for dch in Pseudomonas stutzeri RCH2

Align cyclohexa-1,5-dienecarbonyl-CoA hydratase monomer (EC 4.2.1.100) (characterized)
to candidate GFF2389 Psest_2437 Enoyl-CoA hydratase/carnithine racemase

Query= metacyc::MONOMER-18320
         (256 letters)



>FitnessBrowser__psRCH2:GFF2389
          Length = 257

 Score =  139 bits (349), Expect = 8e-38
 Identities = 86/259 (33%), Positives = 133/259 (51%), Gaps = 5/259 (1%)

Query: 1   MGFNTILFEKKDKVATITLNVPNS-NWLTIPMMKEINEALMDVKKDPTIQLLVFDHAGDK 59
           M F T+L + +++VA ITLN P + N L   ++ E+N+AL  ++ DP I  +V   +  K
Sbjct: 1   MTFETLLVDIQERVALITLNRPQALNALNGQLISELNQALGQLEADPQIGCIVLTGSA-K 59

Query: 60  AFCDGVDVADHVPEKVDEM-IDLFHGMFRNMAAMDVTSVCLVNGRSLGGGCELMAFCDIV 118
           AF  G D+ +       ++ +D F      +A      +  V G +LGGGCEL   CD++
Sbjct: 60  AFAAGADIKEMAELTYPQIYLDDFFADADRIATRRKPLIAAVAGYALGGGCELALLCDMI 119

Query: 119 IASEKAKIGQPEINLAVFPPVAAAW-FPKIMGLKKAMELILTGKIISAKEAEAIGLVNVV 177
            A++ A+ GQPE+NL V P +       + +G  KAM++ LTG+ + A EAE  GLV  V
Sbjct: 120 FAADNARFGQPEVNLGVLPGIGGTQRLTRAVGKAKAMDMCLTGRQMDAAEAERAGLVARV 179

Query: 178 LPVEGFREAAQKFMADFTSKSRPVAMWARRAIMAGLNLDFLQALKASEIIYMQGCMATED 237
            P E   E   K       KS P  M  + ++         + ++    ++     AT D
Sbjct: 180 FPAESLLEETLKAARVIAEKSLPATMMIKESVNRAFETTLAEGIRFERRVF-HAVFATAD 238

Query: 238 ANEGLASFLEKRKPVFKDK 256
             EG+A+F EKRKP F ++
Sbjct: 239 QKEGMAAFSEKRKPEFTNR 257


Lambda     K      H
   0.322    0.136    0.401 

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: 156
Number of extensions: 12
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: 256
Length of database: 257
Length adjustment: 24
Effective length of query: 232
Effective length of database: 233
Effective search space:    54056
Effective search space used:    54056
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 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