GapMind for catabolism of small carbon sources

 

Alignments for a candidate for atoB in Novosphingobium fuchskuhlense FNE08-7

Align acetyl-CoA C-acetyltransferase (EC 2.3.1.9) (characterized)
to candidate WP_067912752.1 AQZ52_RS15020 acetyl-CoA C-acyltransferase

Query= BRENDA::Q0K368
         (391 letters)



>NCBI__GCF_001519075.1:WP_067912752.1
          Length = 390

 Score =  509 bits (1310), Expect = e-149
 Identities = 256/392 (65%), Positives = 313/392 (79%), Gaps = 3/392 (0%)

Query: 1   MAEAYIVAAVRTAGGRKGGKLSGWHPADLAAQVLDALVERTGADPALVEDVIMGCVSQVG 60
           MA AYIV AVRTAGGR+ G+L+G HP DL+A  LDAL+ERTG D A VEDVIMGCVSQ G
Sbjct: 1   MATAYIVDAVRTAGGRRNGRLAGVHPVDLSAATLDALIERTGIDGAAVEDVIMGCVSQGG 60

Query: 61  EQAGNVARNAILASR-LPESVPGTSVDRQCGSSQQALHFAAQAVMSGAMDIVIAAGVESM 119
           +QAG V RNA+LA+R LP+SVP  ++DRQCGSSQQA+ FAAQAV+SG  DIVIAAGVESM
Sbjct: 61  QQAGQVGRNAVLAARRLPDSVPAVTIDRQCGSSQQAIQFAAQAVLSGTQDIVIAAGVESM 120

Query: 120 TRVPMGLSSQLPAKNGFGVPKSPGIEARYPGVQFSQFTGAEMIARKYDLSREQLDAYALQ 179
           TRVPMG ++    K G G  KSP +E +YPG+ FSQF GAEMI +K+  +++QLDA+AL 
Sbjct: 121 TRVPMGSTAIFHMKEGLGNYKSPRLEEKYPGIMFSQFMGAEMIVKKHGFTKDQLDAFALS 180

Query: 180 SHQRAIAATKSGRFTAEILPVEVRTADGANGEMHTTDEGVRYDATLESIGSVKLIAEGGR 239
           SH +AIAAT +  F  EI+P+ + T DG    MHT DEG+R+DATLESI  VKL++  G 
Sbjct: 181 SHLKAIAATNANAFAGEIVPIAIETPDGP--AMHTVDEGIRFDATLESIAGVKLLSPEGL 238

Query: 240 VTAASASQICDGAAGLMVVNEAGLKKLGVKPLARVHAMTVIGHDPVVMLEAPLPATEVAL 299
           +TAAS+SQICDGA+  ++V+EA LK   + PLAR+H +TV   DPV+MLE PL AT+ AL
Sbjct: 239 LTAASSSQICDGASAALIVSEAALKAHNLTPLARIHNLTVTAGDPVIMLEEPLFATDRAL 298

Query: 300 KKAGLRIGDIDLFEVNEAFAPVPLAWLKATGADPARLNVHGGAIALGHPLGGSGAKLMTT 359
           ++AG++IGDIDL+EVNEAFA VP+AWLK TGADP +LNV+GGAIALGHPLG SG KLM+T
Sbjct: 299 QRAGMKIGDIDLYEVNEAFASVPMAWLKHTGADPEKLNVNGGAIALGHPLGASGTKLMST 358

Query: 360 LVHALHTHGKRYGLQTMCEGGGLANVTIVERL 391
           L+HAL   G +YGLQTMCEGGG+ANVTIVE +
Sbjct: 359 LLHALKARGLKYGLQTMCEGGGVANVTIVEMM 390


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: 536
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: 391
Length of database: 390
Length adjustment: 31
Effective length of query: 360
Effective length of database: 359
Effective search space:   129240
Effective search space used:   129240
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 24 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