GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__pseudo1_N1B4:Pf1N1B4_4786
          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 (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