GapMind for catabolism of small carbon sources

 

Alignments for a candidate for fadA in Cupriavidus basilensis 4G11

Align 3-oxo-acyl CoA thiolase (EC 2.3.1.16) (characterized)
to candidate RR42_RS36320 RR42_RS36320 acetyl-CoA acetyltransferase

Query= metacyc::G185E-7833-MONOMER
         (386 letters)



>FitnessBrowser__Cup4G11:RR42_RS36320
          Length = 392

 Score =  399 bits (1024), Expect = e-115
 Identities = 206/394 (52%), Positives = 276/394 (70%), Gaps = 10/394 (2%)

Query: 1   MTEAYVIDAVRTAVGKRGGALAGIHPVDLGALAWRGLLDRTDIDPAAVDDVIAGCVDAIG 60
           M EAY++ A RTA G++GG LAG HP DL A     L+ R+  DPA +DDVI GCV   G
Sbjct: 1   MAEAYIVAAARTAGGRKGGKLAGWHPADLAAQVLNALVARSGADPALIDDVIMGCVGQAG 60

Query: 61  GQAGNIARLSWLAAGYPEEVPGVTVDRQCGSSQQAISFGAQAIMSGTADVIVAGGVQNMS 120
            QAGN+AR + LA+  P+ VPG +VDRQCGSSQQA+ F AQA+MSGT D+++A GV++M+
Sbjct: 61  EQAGNVARNAVLASKLPQSVPGTSVDRQCGSSQQALHFAAQAVMSGTMDIVIAAGVESMT 120

Query: 121 QIPISSAMTVGEQFGFTSPTNESKQWLHRYGDQEISQFRGSELIAEKWNLSREEMERYSL 180
           ++P+    T+  + GF S  + + Q   RY   + SQF G+E+++ K+ L+R++++RY+L
Sbjct: 121 RVPMGLPSTLPFKNGFGSSMSPAMQ--ERYPGVKFSQFTGAEMMSRKYGLTRDDLDRYAL 178

Query: 181 TSHERAFAAIRAGHFENEIITVETESGP-------FRVDEGPR-ESSLEKMAGLQPLVEG 232
            SH RA AA +AG F++EI+ V   +           VDEG R E+SLE ++ ++ + EG
Sbjct: 179 ESHRRAIAATQAGRFKDEIVPVAVRAADGSANGELHTVDEGIRFEASLESISSVKLIEEG 238

Query: 233 GRLTAAMASQISDGASAVLLASERAVKDHGLRPRARIHHISARAADPVFMLTGPIPATRY 292
           G +TAA ASQI DGA+ +++ +E  +K  G++P ARIHH+S    DPV ML  P+PAT  
Sbjct: 239 GTVTAASASQICDGAAGLMVVNEAGLKKLGVKPLARIHHMSVLGHDPVIMLEAPLPATLR 298

Query: 293 ALDKTGLAIDDIDTVEINEAFAPVVMAWLKEIKADPAKVNPNGGAIALGHPLGATGAKLF 352
           ALDK G+ I DID  EINEAFAPV +AWL+   ADPA++N NGGAIALGHPLG +GAKL 
Sbjct: 299 ALDKAGMKIGDIDLFEINEAFAPVPLAWLQTTGADPARMNVNGGAIALGHPLGGSGAKLM 358

Query: 353 TTMLGELERIGGRYGLQTMCEGGGTANVTIIERL 386
           TT++  L   G RYGLQTMCEGGG ANVTI+ERL
Sbjct: 359 TTLVHALHAQGKRYGLQTMCEGGGMANVTIVERL 392


Lambda     K      H
   0.317    0.134    0.389 

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: 466
Number of extensions: 18
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: 386
Length of database: 392
Length adjustment: 30
Effective length of query: 356
Effective length of database: 362
Effective search space:   128872
Effective search space used:   128872
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