GapMind for catabolism of small carbon sources

 

Alignments for a candidate for liuC in Pseudomonas fluorescens FW300-N2E3

Align Methylglutaconyl-CoA hydratase (EC 4.2.1.18) (characterized)
to candidate AO353_20340 AO353_20340 gamma-carboxygeranoyl-CoA hydratase

Query= reanno::pseudo6_N2E2:Pf6N2E2_2193
         (272 letters)



>FitnessBrowser__pseudo3_N2E3:AO353_20340
          Length = 271

 Score =  472 bits (1214), Expect = e-138
 Identities = 240/271 (88%), Positives = 254/271 (93%)

Query: 1   MDNFNTLELHSDPRGVATLWLSRESKNNAFNAEMIRELILALDHVSSDPNLRFLLIRGRG 60
           M +FNTLEL +DPRG ATLWLSRE+KNNAFNAEMIRELILALD V S+P+LRFLL+RGRG
Sbjct: 1   MSDFNTLELLTDPRGFATLWLSREAKNNAFNAEMIRELILALDKVQSNPSLRFLLVRGRG 60

Query: 61  KHFSAGADLAWMQQSAELDYHTNLDDARELAELMYNLAKLKIPTLAVVQGAAFGGALGLI 120
           KHFSAGADLAWMQQSAELDYHTNLDDARELAELMYNLAKLKIPTLAVVQGAA+GGALGLI
Sbjct: 61  KHFSAGADLAWMQQSAELDYHTNLDDARELAELMYNLAKLKIPTLAVVQGAAYGGALGLI 120

Query: 121 SACDMAIGADEAQFCLSEVRIGLAPAVISPFVVQAIGERAARRYALTAERFDGQRAKEIG 180
           S CDMAIGAD+AQFCLSEVRIGLAPAVISPFVVQAIGERAARRYALTAERF GQRA+EIG
Sbjct: 121 SCCDMAIGADDAQFCLSEVRIGLAPAVISPFVVQAIGERAARRYALTAERFSGQRAQEIG 180

Query: 181 LLSESYPAEVLDQQVEQWIDNLLLNSPAAMRASKELLREVGNGALTPALRRYTENAIARI 240
           LLSESYPA  L+ QVEQWI+NLLLNSP AMR+SKELLREVGNGAL PALRRY ENAIARI
Sbjct: 181 LLSESYPASELESQVEQWINNLLLNSPHAMRSSKELLREVGNGALNPALRRYCENAIARI 240

Query: 241 RVSPEGQEGLRAFLQKRAPNWQAESNNKEPR 271
           RVSPEGQEGLRAFLQKR P+WQ+ES  KE R
Sbjct: 241 RVSPEGQEGLRAFLQKRPPSWQSESTTKELR 271


Lambda     K      H
   0.318    0.133    0.382 

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: 383
Number of extensions: 8
Number of successful extensions: 1
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: 272
Length of database: 271
Length adjustment: 25
Effective length of query: 247
Effective length of database: 246
Effective search space:    60762
Effective search space used:    60762
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: 47 (22.7 bits)

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

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