GapMind for catabolism of small carbon sources

 

Aligments for a candidate for atoB in Pseudomonas fluorescens FW300-N2E2

Align acetyl-CoA C-acetyltransferase (EC 2.3.1.9) (characterized)
to candidate Pf6N2E2_1851 3-ketoacyl-CoA thiolase (EC 2.3.1.16) @ Acetyl-CoA acetyltransferase (EC 2.3.1.9)

Query= BRENDA::Q0KAI3
         (392 letters)



>lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_1851 3-ketoacyl-CoA
           thiolase (EC 2.3.1.16) @ Acetyl-CoA acetyltransferase
           (EC 2.3.1.9)
          Length = 402

 Score =  278 bits (711), Expect = 2e-79
 Identities = 172/405 (42%), Positives = 237/405 (58%), Gaps = 16/405 (3%)

Query: 1   MQQAVIV-DAIRSPMGRSKPGSAFTELHATELLAQVIKGLVERNKLDPGLVDDVITGCVT 59
           M QAV + DA+R+P G+ K   A   +    + A ++  L +R  LD   VDDV+ GC  
Sbjct: 1   MSQAVFIYDAVRTPRGKGKKDGALYSVKPVHMAAGLLTELQQRYDLDTSRVDDVVLGCGQ 60

Query: 60  QAGEQSAGPGRVAWLAAGFPDHVPATTIDRKCGSSQQAVHFAAQGIMAGAYDIVIACGIE 119
             GEQ     +     AG+ + VP   IDR C S  +AV+ AA  I +G  D+++A G+E
Sbjct: 61  PVGEQGGDVAKCVVQYAGWDESVPGVQIDRFCASGLEAVNQAASRIASGWEDLIVAGGVE 120

Query: 120 SMSRVPMGSARIGQNPYGPSMEARYAPGLVSQGVAAELVAAKYELSRHDMDSYSARSHEL 179
           SMSR+PMG+A  GQ  +    E  +    V QG+ A+L+AA    SR D+D ++  S + 
Sbjct: 121 SMSRLPMGAA--GQ-AWIQDPEIAFKLQSVPQGIGADLLAALDGYSREDVDRFALVSQQR 177

Query: 180 AATARESGAFRREILGISTPNGLV--EQDETIRPGTSVEKLGTLQASFR-------NDEL 230
           AA AR+SG F R ++ +   NGLV  E+DE I+P T++E L  L+ SF        +D  
Sbjct: 178 AAHARDSGYFDRSVVPVRDLNGLVVLERDEFIKPATTLEALSQLKPSFAAMGKLGYSDVA 237

Query: 231 SARFPQIGWNV---TAGNASQISDGASAMLLMSESMAQRLGLKPRARFVAFDVCGDDPVM 287
             ++PQ+       TAGN+S I DGASA LL SE + Q+LGL PR R +A  V   +P +
Sbjct: 238 LRKYPQVARIEPIHTAGNSSGIVDGASATLLGSERIGQQLGLAPRGRIIATAVLSTEPTL 297

Query: 288 MLTAPIPASQRAIKKSGLKLDQIDHYEINEAFACVPLAWQRALGADPARLNPRGGAIALG 347
           ML  P PA+++A+ K+GL +  ID +EINEAFA V L + R L   P   N  GGAIALG
Sbjct: 298 MLAGPGPAAKKALAKAGLSVQDIDLFEINEAFASVVLRFMRDLDISPEITNVNGGAIALG 357

Query: 348 HPLGASGVRLMTTMLHALEDSGQRYGLQSMCEAGGMANATIIERL 392
           HP+GA+G  L+ T+L  LE    + GL ++C  GGM  ATIIERL
Sbjct: 358 HPIGATGAMLVGTVLDELERRNLKRGLIALCVGGGMGIATIIERL 402


Lambda     K      H
   0.318    0.132    0.384 

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: 456
Number of extensions: 21
Number of successful extensions: 4
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: 392
Length of database: 402
Length adjustment: 31
Effective length of query: 361
Effective length of database: 371
Effective search space:   133931
Effective search space used:   133931
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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, 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