GapMind for catabolism of small carbon sources

 

Alignments for a candidate for paaJ1 in Pseudomonas fluorescens FW300-N2C3

Align 3-oxoadipyl-CoA/3-oxo-5,6-dehydrosuberyl-CoA thiolase; EC 2.3.1.174; EC 2.3.1.223 (characterized)
to candidate AO356_20395 AO356_20395 acetyl-CoA acetyltransferase

Query= SwissProt::P0C7L2
         (401 letters)



>FitnessBrowser__pseudo5_N2C3_1:AO356_20395
          Length = 401

 Score =  271 bits (692), Expect = 3e-77
 Identities = 169/423 (39%), Positives = 234/423 (55%), Gaps = 44/423 (10%)

Query: 1   MREAFICDGIRTPIGR--YGGALSSVRADDLAAIPLRELLVRNPRLDAECIDDVILGCAN 58
           M +A I D +RTP G+    GAL SV+  +L    L  L  R   LD   +DD++LGC  
Sbjct: 1   MTQALIFDALRTPRGKGKADGALHSVKPVNLMGGLLSALRQRMD-LDTSQVDDIVLGCVT 59

Query: 59  QAGEDNRNVARMATLLAGLPQSVSGTTINRLCGSGLDALGFAARAIKAGDGDLLIAGGVE 118
             GE   ++A+ A L+A    SV+G  +NR C SGL+A+  AA  +++G  DL++AGGVE
Sbjct: 60  PVGEQGADIAKTAALVANWDVSVAGVQLNRFCASGLEAVNLAAMKVRSGFEDLVVAGGVE 119

Query: 119 SMSRAPFVMGKAASAFSRQAEMFDTTIGWRFVNPLMAQQFGTDSMPETAENVAELLKISR 178
           SMSR P      A A   Q+ +             + Q  G D        +A L   SR
Sbjct: 120 SMSRVPMGSDGGAWALDPQSNL---------QGHFIPQGIGADL-------IATLEGFSR 163

Query: 179 EDQDSFALRSQQRTAKAQSSGILAEEIVPVVLKNKKGVVTEIQHDEHLRPETTLEQLRGL 238
           ED D +AL SQQ+ A+A++ G   + +V V  +++ G+V  + HDE +R ++TLE L  L
Sbjct: 164 EDVDRYALHSQQKAARARADGSFDKSLVAV--RDQNGIVL-LDHDEFIRADSTLEGLGKL 220

Query: 239 KAPFRANG--------------------VITAGNASGVNDGAAALIIASEQMAAAQGLTP 278
           K  F A G                    V T GN+SG+ DGAA ++I SE    A GL P
Sbjct: 221 KPSFEAMGQMGFDGTALRVYSHVERIHHVHTPGNSSGIVDGAALMLIGSEAKGRAMGLQP 280

Query: 279 RARIVAMATAGVEPRLMGLGPVPATRRVLERAGLSIHDMDVIELNEAFAAQALGVLRELG 338
           RARIVA A    +P +M  GP PATR+ L +AGL + D+D+ E+NEAFA+  L  +R++ 
Sbjct: 281 RARIVATAVTSTDPTIMLTGPAPATRKALAKAGLRVEDIDLFEVNEAFASVVLKFIRDMA 340

Query: 339 LPDDAPHVNPNGGAIALGHPLGMSGARLALAASHELHRRNGRYALCTMCIGVGQGIAMIL 398
           +  D   VN NGG+IALGHPLG +G  +      EL  R  RY L T+C+G G GIA ++
Sbjct: 341 I--DPAKVNVNGGSIALGHPLGATGCAILGTLLDELEARRLRYGLATLCVGGGMGIATVI 398

Query: 399 ERV 401
           ER+
Sbjct: 399 ERL 401


Lambda     K      H
   0.319    0.135    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: 424
Number of extensions: 18
Number of successful extensions: 5
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: 401
Length of database: 401
Length adjustment: 31
Effective length of query: 370
Effective length of database: 370
Effective search space:   136900
Effective search space used:   136900
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 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