GapMind for catabolism of small carbon sources

 

Alignments for a candidate for atoB in Pseudomonas fluorescens FW300-N1B4

Align acetyl-CoA C-acetyltransferase (EC 2.3.1.9) (characterized)
to candidate Pf1N1B4_3904 3-ketoacyl-CoA thiolase (EC 2.3.1.16) @ Acetyl-CoA acetyltransferase (EC 2.3.1.9)

Query= BRENDA::Q0K368
         (391 letters)



>FitnessBrowser__pseudo1_N1B4:Pf1N1B4_3904
          Length = 383

 Score =  261 bits (666), Expect = 3e-74
 Identities = 162/394 (41%), Positives = 233/394 (59%), Gaps = 20/394 (5%)

Query: 6   IVAAVRTAGGR-KGGKLSGWHPADLAAQVLDALVERT-GADPALVEDVIMGCVSQVGEQA 63
           IV   RT  GR KGG        D++A ++  L+ER    DP+ VEDVI GCV+Q  EQ 
Sbjct: 2   IVDFGRTPMGRSKGGMHRNTRAEDMSAHLISKLLERNVKVDPSEVEDVIWGCVNQTLEQG 61

Query: 64  GNVARNAILASRLPESVPGTSVDRQCGSSQQALHFAAQAVMSGAMDIVIAAGVESMTRVP 123
            N+AR A L +++P +  G +V R CGSS  ALH AAQA+M+G  D+ +  GVE M  V 
Sbjct: 62  WNIARMASLMTQIPHTAAGQTVSRLCGSSMSALHTAAQAIMTGNGDVFVVGGVEHMGHVS 121

Query: 124 MGLSSQLPAKNGFGVPKSPGIEARYPGVQFSQFTGAEMIARKYDLSREQLDAYALQSHQR 183
           M            GV  +P +              AEM+ + + ++REQ DA+ ++SHQ 
Sbjct: 122 MM----------HGVDPNPHMSLYAAKASGMMGLTAEMLGKMHGITREQQDAFGVRSHQL 171

Query: 184 AIAATKSGRFTAEILPVEVRTADGANGEMHTTDEGVRYDATLESIGSVK--LIAEGGRVT 241
           A  AT  G+F  EI+P++    +G   ++   DE +R + TLES+ ++K     +GG VT
Sbjct: 172 AHKATLEGKFKDEIIPMQGYDENGFL-KLFDYDETIRPETTLESLAALKPAFNPKGGTVT 230

Query: 242 AASASQICDGAAGLMVVNEAGLKKLGVKPLARVHAMTVIGHDPVVMLEAPLPATEVALKK 301
           A ++SQI DGA+ ++V++    + LG++P+A + +M V G DP +M   P+PAT+ ALK+
Sbjct: 231 AGTSSQITDGASCMIVMSAQRAQDLGIQPMAVIRSMAVAGVDPAIMGYGPVPATQKALKR 290

Query: 302 AGLRIGDIDLFEVNEAFA----PVPLAWLKATGADPARLNVHGGAIALGHPLGGSGAKLM 357
           AGL I DID FE+NEAFA    PV L  LK       ++N+HGGAIALGHP G SGA++ 
Sbjct: 291 AGLGINDIDFFELNEAFAAQALPV-LKDLKVLDKMNEKVNLHGGAIALGHPFGCSGARIS 349

Query: 358 TTLVHALHTHGKRYGLQTMCEGGGLANVTIVERL 391
            TL++ +  +G  +G+ TMC G G    T+ ER+
Sbjct: 350 GTLLNVMKQNGGTFGVATMCIGLGQGISTVFERV 383


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: 21
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: 383
Length adjustment: 30
Effective length of query: 361
Effective length of database: 353
Effective search space:   127433
Effective search space used:   127433
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