GapMind for catabolism of small carbon sources

 

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

Align acetyl-CoA C-acetyltransferase (EC 2.3.1.9) (characterized)
to candidate AO353_00505 AO353_00505 3-ketoacyl-CoA thiolase

Query= BRENDA::Q0K368
         (391 letters)



>FitnessBrowser__pseudo3_N2E3:AO353_00505
          Length = 391

 Score =  262 bits (670), Expect = 1e-74
 Identities = 162/397 (40%), Positives = 234/397 (58%), Gaps = 20/397 (5%)

Query: 3   EAYIVAAVRTAGGR-KGGKLSGWHPADLAAQVLDALVERT-GADPALVEDVIMGCVSQVG 60
           +  IV   RT  GR KGG        D++A ++  L+ER    DP+ VEDVI GCV+Q  
Sbjct: 7   DVVIVDFGRTPMGRSKGGMHRNTRAEDMSAHLISKLLERNVKVDPSEVEDVIWGCVNQTL 66

Query: 61  EQAGNVARNAILASRLPESVPGTSVDRQCGSSQQALHFAAQAVMSGAMDIVIAAGVESMT 120
           EQ  N+AR A L +++P +  G +V R CGSS  ALH AAQA+M+G  D+ +  GVE M 
Sbjct: 67  EQGWNIARMASLMTQIPHTAAGQTVSRLCGSSMSALHTAAQAIMTGNGDVFVVGGVEHMG 126

Query: 121 RVPMGLSSQLPAKNGFGVPKSPGIEARYPGVQFSQFTGAEMIARKYDLSREQLDAYALQS 180
            V M            GV  +P +              AEM+ + + ++REQ DA+ ++S
Sbjct: 127 HVSMM----------HGVDPNPHMSLYAAKASGMMGLTAEMLGKMHGITREQQDAFGVRS 176

Query: 181 HQRAIAATKSGRFTAEILPVEVRTADGANGEMHTTDEGVRYDATLESIGSVK--LIAEGG 238
           HQ A  AT  G+F  EI+P++    +G   ++   DE +R + TLES+ ++K     +GG
Sbjct: 177 HQLAHKATVEGKFKDEIIPMQGYDENGFL-KLFDYDETIRPETTLESLAALKPAFNPKGG 235

Query: 239 RVTAASASQICDGAAGLMVVNEAGLKKLGVKPLARVHAMTVIGHDPVVMLEAPLPATEVA 298
            VTA ++SQI DGA+ ++V++    + LG++P+A + +M V G DP +M   P+PAT+ A
Sbjct: 236 TVTAGTSSQITDGASCMIVMSAQRAQDLGIQPMAVIRSMAVAGVDPAIMGYGPVPATQKA 295

Query: 299 LKKAGLRIGDIDLFEVNEAFA----PVPLAWLKATGADPARLNVHGGAIALGHPLGGSGA 354
           LK+AGL I DID FE+NEAFA    PV L  LK       ++N+HGGAIALGHP G SGA
Sbjct: 296 LKRAGLGIADIDFFELNEAFAAQALPV-LKDLKVLDKMNEKVNLHGGAIALGHPFGCSGA 354

Query: 355 KLMTTLVHALHTHGKRYGLQTMCEGGGLANVTIVERL 391
           ++  TL++ +  +G  +G+ TMC G G    T+ ER+
Sbjct: 355 RISGTLLNVMKQNGGTFGVSTMCIGLGQGIATVFERV 391


Lambda     K      H
   0.317    0.132    0.379 

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: 412
Number of extensions: 23
Number of successful extensions: 4
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: 391
Length of database: 391
Length adjustment: 31
Effective length of query: 360
Effective length of database: 360
Effective search space:   129600
Effective search space used:   129600
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