GapMind for catabolism of small carbon sources

 

Alignments for a candidate for fadA in Sphingomonas koreensis DSMZ 15582

Align 3-ketoacyl-CoA thiolase 1, peroxisomal; Acetyl-CoA acyltransferase 1; Beta-ketothiolase 1; Peroxisomal 3-oxoacyl-CoA thiolase 1; EC 2.3.1.16 (characterized)
to candidate Ga0059261_2160 Ga0059261_2160 acetyl-CoA acetyltransferases

Query= SwissProt::Q8LF48
         (443 letters)



>FitnessBrowser__Korea:Ga0059261_2160
          Length = 398

 Score =  293 bits (749), Expect = 9e-84
 Identities = 178/403 (44%), Positives = 241/403 (59%), Gaps = 25/403 (6%)

Query: 43  DVVIVAAQRTALCKAKRGSFKDTFPDELLASVLRALIEKTNVNPSEVGDIVVGTVLGPGS 102
           +  IV+  RT + KA RG+F  T    L   V+ A +E+  V+P+ + DI  G     G+
Sbjct: 3   EAAIVSTARTGIGKAYRGAFNTTEAPVLAGHVMNAAVERAGVDPARIDDIFWGVGNQWGT 62

Query: 103 QRASECRMAAFYAGFPETVPIRTVNRQCSSGLQAVADVAAAIKAGFYDIGIGAGLESMTT 162
           Q  +  RMA F AG P++VP  T++R+C SGL A+A  A +I AG  DI +  G+ES++ 
Sbjct: 63  QGGNAGRMAVFAAGLPQSVPAFTLDRKCGSGLTALALAARSIIAGDIDIALSGGMESISL 122

Query: 163 N-----PRGWKGSVNPNVKKFEQAHNCLLPMGITSENVAHRFNVSREEQDQAAVDSHRKA 217
                 PR    SV  N        +  +PM  T+E VA R+ +SR  QD+    S ++A
Sbjct: 123 TVTKDAPRYANQSVLANEP------HAYMPMIETAEIVAERYGISRARQDEYGAMSQQRA 176

Query: 218 ASATASGKFKDEITPVKTK--IVDP---KTGDEKPITVSVDDGIRPNTTLSGLAKLKPVF 272
            +  ASG F +EI P+  +  I D    +TG E+ +TV+ D+GIR  TT   LA LK V+
Sbjct: 177 EAGLASGAFAEEIAPITVEKAIFDKEGNRTGSER-VTVTQDEGIRAGTTAEALAGLKTVW 235

Query: 273 KEDGTT------TAGNSSQLSDGAGAVLLMRRNVAMQKGLPILGVFRTFSAVGVDPAIMG 326
           K+          TAGN+SQLSDGA A ++M R +A  +G  ILG++R F A G  P  MG
Sbjct: 236 KDGQVVKEGRHITAGNASQLSDGAAAQIVMDRAIAEAEGKEILGIYRGFQAAGCAPDEMG 295

Query: 327 VGPAVAIPAAVKAAGLELNDVDLFEINEAFASQFVYCRNKLGLDAEKINVNGGAIAIGHP 386
           +GP  AIP  +  AGLE+ D+ L+E+NEAFASQ +YCR+ LG+D EK NVNGGAIAIGHP
Sbjct: 296 IGPVFAIPKLLGRAGLEVADIGLWELNEAFASQCLYCRDTLGIDPEKYNVNGGAIAIGHP 355

Query: 387 LGATGARCVATLLHEMKRRGKDCRFGVVSMCIGSGMGAAAVFE 429
            G TGAR +   L E ++RG   R+ VVSMC   GMGAA +FE
Sbjct: 356 FGMTGARLIGHALIEGRKRG--VRWVVVSMCTAGGMGAAGLFE 396


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: 402
Number of extensions: 16
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: 443
Length of database: 398
Length adjustment: 32
Effective length of query: 411
Effective length of database: 366
Effective search space:   150426
Effective search space used:   150426
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