GapMind for catabolism of small carbon sources

 

Aligments for a candidate for paaJ1 in Shewanella loihica PV-4

Align 3-oxoadipyl-CoA/3-oxo-5,6-dehydrosuberyl-CoA thiolase; EC 2.3.1.174; EC 2.3.1.223 (characterized)
to candidate 5207484 Shew_0018 3-ketoacyl-CoA thiolase (RefSeq)

Query= SwissProt::P0C7L2
         (401 letters)



>lcl|FitnessBrowser__PV4:5207484 Shew_0018 3-ketoacyl-CoA thiolase
           (RefSeq)
          Length = 387

 Score =  317 bits (813), Expect = 3e-91
 Identities = 184/405 (45%), Positives = 250/405 (61%), Gaps = 24/405 (5%)

Query: 1   MREAFICDGIRTPIGRY-GGALSSVRADDLAAIPLRELLVRNPRLDAECIDDVILGCANQ 59
           M++A I D IRTP+GR   G   ++RA+ L+A  ++ LLVRNP+LD   I+DVI GC  Q
Sbjct: 1   MKQAVIVDCIRTPMGRSKAGVFRNMRAESLSAELMKALLVRNPQLDPNTIEDVIWGCVQQ 60

Query: 60  AGEDNRNVARMATLLAGLPQSVSGTTINRLCGSGLDALGFAARAIKAGDGDLLIAGGVES 119
             E   N+AR A LLAG+P+     T+NRLCGS ++A+  AARAI  G GD  I GGVE 
Sbjct: 61  TLEQGFNIARNAALLAGIPKQAGAVTVNRLCGSSMEAIHQAARAIMTGMGDTFIVGGVEH 120

Query: 120 MSRAPFVMGKAASAFSRQAEMFDTTIGWRFVNPLMAQQFGTDS--MPETAENVAELLKIS 177
           M   P   G                      +P +A      S  M  TAE + ++  I+
Sbjct: 121 MGHVPMNHGVD-------------------FHPGLATNVAKASGMMGLTAEMLGKMHGIT 161

Query: 178 REDQDSFALRSQQRTAKAQSSGILAEEIVPVVLKNKKGVVTEIQHDEHLRPETTLEQLRG 237
           R+ QD FA+RS QR   A   G  A EI  +   +  G + ++ HDE +RPET+LE L  
Sbjct: 162 RQQQDEFAVRSHQRAHAATVEGRFANEIHAIEGHDANGALIKVMHDEVIRPETSLESLAT 221

Query: 238 LKAPFR-ANGVITAGNASGVNDGAAALIIASEQMAAAQGLTPRARIVAMATAGVEPRLMG 296
           L+  F  ANG +TAG +S ++DGA+A+++  E+ A A GL  RARI +MA AG +  +MG
Sbjct: 222 LRPVFDPANGTVTAGTSSALSDGASAMLVMEEEKAKALGLPIRARIRSMAVAGCDAAIMG 281

Query: 297 LGPVPATRRVLERAGLSIHDMDVIELNEAFAAQALGVLRELGLPDDAPH-VNPNGGAIAL 355
            GPVPAT++ L+RAGL+++D+D+IELNEAFAAQ+L  +++LGL D     VN NGGAIAL
Sbjct: 282 YGPVPATQKALQRAGLTMNDIDLIELNEAFAAQSLPCVKDLGLMDLVDEKVNLNGGAIAL 341

Query: 356 GHPLGMSGARLALAASHELHRRNGRYALCTMCIGVGQGIAMILER 400
           GHPLG SGAR++    + +  ++    L TMCIG+GQGIA + ER
Sbjct: 342 GHPLGCSGARISTTLINLMESKDATLGLATMCIGLGQGIATVFER 386


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: 417
Number of extensions: 16
Number of successful extensions: 5
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 2
Length of query: 401
Length of database: 387
Length adjustment: 31
Effective length of query: 370
Effective length of database: 356
Effective search space:   131720
Effective search space used:   131720
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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 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