GapMind for catabolism of small carbon sources

 

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

Align acetyl-CoA:acetyl-CoA C-acetyltransferase / acetyl-CoA:propanoyl-CoA 2-C-acetyltransferase (EC 2.3.1.9; EC 2.3.1.16) (characterized)
to candidate Pf1N1B4_4786 3-ketoacyl-CoA thiolase (EC 2.3.1.16)

Query= reanno::pseudo3_N2E3:AO353_25685
         (397 letters)



>lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_4786 3-ketoacyl-CoA
           thiolase (EC 2.3.1.16)
          Length = 397

 Score =  736 bits (1899), Expect = 0.0
 Identities = 374/397 (94%), Positives = 388/397 (97%)

Query: 1   MTMSHDPIVIVSAVRTPMGGFQGELKSLSAPQLGAAAIRAAVERAGVAADAVEEVLFGCV 60
           MT+S+DPIVIVSAVRTPMGGFQGELKSL+APQLGAAAIRAAVERAG+A ++VEEVLFGCV
Sbjct: 1   MTLSNDPIVIVSAVRTPMGGFQGELKSLTAPQLGAAAIRAAVERAGIAPESVEEVLFGCV 60

Query: 61  LSAGLGQAPARQAALGAGLDKSTRCTTLNKMCGSGMEAAILAHDMLLAGSADVVVAGGME 120
           LSAGLGQAPARQAALGAGLDKSTRCTTLNKMCGSGMEA ILAHDML+AGSADVVVAGGME
Sbjct: 61  LSAGLGQAPARQAALGAGLDKSTRCTTLNKMCGSGMEATILAHDMLIAGSADVVVAGGME 120

Query: 121 SMSNAPYLLDRARSGYRMGHGKVLDHMFLDGLEDAYDKGRLMGTFAEDCAEANGFTREAQ 180
           SMSNAP+LLDRARSGYRMGHG+VLDHMFLDGLEDAYDKGRLMGTFAEDCAE NGFTREAQ
Sbjct: 121 SMSNAPFLLDRARSGYRMGHGRVLDHMFLDGLEDAYDKGRLMGTFAEDCAETNGFTREAQ 180

Query: 181 DEFAIASTTRAQQAIKDGSFNAEIVPLQVIVGKEQKLITDDEQPPKAKLDKIASLKPAFR 240
           D FAIASTTRAQQAIKDGSFNAEIVPL V VGKEQ LI+ DEQPPKAKLDKIASLKPAFR
Sbjct: 181 DAFAIASTTRAQQAIKDGSFNAEIVPLTVTVGKEQVLISHDEQPPKAKLDKIASLKPAFR 240

Query: 241 DGGTVTAANSSSISDGAAALLLMRRSEAEKRGLKPLAVIHGHAAFADTPGLFPVAPVGAI 300
           DGGTVTAANSSSISDGAAAL+LMRRSEAEK+GLKPLAVIHGHAAFADTPGLFPVAPVGAI
Sbjct: 241 DGGTVTAANSSSISDGAAALVLMRRSEAEKQGLKPLAVIHGHAAFADTPGLFPVAPVGAI 300

Query: 301 KKLLKKTGWSLDEVELFEVNEAFAVVSLVTMTKLEIPHSKVNVHGGACALGHPIGASGAR 360
           KKL+KKTGWSLDEVELFEVNEAFAVVSLVTMTKLEIPH K+NVHGGACALGHPIGASGAR
Sbjct: 301 KKLMKKTGWSLDEVELFEVNEAFAVVSLVTMTKLEIPHEKINVHGGACALGHPIGASGAR 360

Query: 361 ILVTLLSALRQKGLKRGVAAICIGGGEATAMAVECLY 397
           ILVTLLSALRQKGLKRGVAAICIGGGEATAMAVECLY
Sbjct: 361 ILVTLLSALRQKGLKRGVAAICIGGGEATAMAVECLY 397


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: 635
Number of extensions: 9
Number of successful extensions: 1
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: 397
Length of database: 397
Length adjustment: 31
Effective length of query: 366
Effective length of database: 366
Effective search space:   133956
Effective search space used:   133956
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 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