GapMind for catabolism of small carbon sources

 

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

Align Acetyl-CoA C-acetyltransferase (EC 2.3.1.9) (characterized)
to candidate Pf1N1B4_5133 3-ketoacyl-CoA thiolase (EC 2.3.1.16) @ Acetyl-CoA acetyltransferase (EC 2.3.1.9)

Query= reanno::pseudo13_GW456_L13:PfGW456L13_2411
         (393 letters)



>lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_5133 3-ketoacyl-CoA
           thiolase (EC 2.3.1.16) @ Acetyl-CoA acetyltransferase
           (EC 2.3.1.9)
          Length = 394

 Score =  563 bits (1451), Expect = e-165
 Identities = 285/394 (72%), Positives = 321/394 (81%), Gaps = 1/394 (0%)

Query: 1   MNTPEIYVVSAARTAIGTFGGSLKDVPLADLATTAVKAALERAAVDPALVGHLVMGNVIP 60
           MN  +I+VVSA R+AIG+FGGSLKDVP   LAT   +AA+ER+ + P  +GH VMG+VIP
Sbjct: 1   MNHSDIFVVSAVRSAIGSFGGSLKDVPPIQLATDVCRAAIERSGLAPEHIGHAVMGHVIP 60

Query: 61  TETRDAYISRVAAMNAGIPKETPAYNVNRLCGSGLQAIINAAQTLMLGDADIVVGAGAES 120
           TE RDAYISR  A+NAG+ KETPA+NVNRLCGSGLQAI++AAQ+LMLGDA   +  G ES
Sbjct: 61  TEARDAYISRAVAINAGLTKETPAFNVNRLCGSGLQAIVSAAQSLMLGDAGAALAGGVES 120

Query: 121 MSRGPYLMPAARWGSRMGNAQVIDYMLGILHDPFHGIHMGITAENVAARNGITREMQDAL 180
           MSRG YL+P ARWG+RMG+ Q IDYMLG+L DPF G HMGITAEN+A   GITR+ QD L
Sbjct: 121 MSRGAYLLPQARWGARMGDMQAIDYMLGVLQDPFAGFHMGITAENIAEHYGITRQAQDEL 180

Query: 181 AFEDQQRAAHAIANGYFSEQIATVEIQDRKGVKLFSVDEHPRA-TSLEQLAAMKPAFKKD 239
           A   QQRAA AIA G F+ QI  +EI+ RKG   F+ DEH RA  + EQL+ MKPAFKKD
Sbjct: 181 ALLSQQRAARAIAEGRFAGQIVPIEIETRKGTVTFATDEHVRAEVNAEQLSRMKPAFKKD 240

Query: 240 GSVTAGNASGLNDGAAALVMASGNAVQANNLKPLARLVSYAHAGVEPEFMGLGPIPATRL 299
           GSVTAGNASGLNDGA AL+MA+G  VQ   LKP+ARLV YAHAGVEP  MGLGPIPATRL
Sbjct: 241 GSVTAGNASGLNDGAGALIMATGQVVQEQGLKPMARLVGYAHAGVEPSMMGLGPIPATRL 300

Query: 300 ALKRAGLTVADLDVIEANIAFAAQACAVSQELDLDPAKVNPNGSGIALGHPVGATGAIIA 359
            LKRAGLTVADLDVIE+N AFAAQACAV+QEL  DP KVNPNGSGI+LGHPVGATGAIIA
Sbjct: 301 VLKRAGLTVADLDVIESNEAFAAQACAVAQELGFDPQKVNPNGSGISLGHPVGATGAIIA 360

Query: 360 TKAIHELHRTGGRYALVTMCIGGGQGIAAIFERV 393
           TKAIHELHR  GRYAL TMCIGGGQGIA +FERV
Sbjct: 361 TKAIHELHRCQGRYALATMCIGGGQGIAVLFERV 394


Lambda     K      H
   0.318    0.133    0.378 

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: 537
Number of extensions: 15
Number of successful extensions: 2
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: 393
Length of database: 394
Length adjustment: 31
Effective length of query: 362
Effective length of database: 363
Effective search space:   131406
Effective search space used:   131406
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.

Links

Downloads

Related tools

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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 the paper from 2019 on GapMind for amino acid biosynthesis, or view the source code.

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