GapMind for catabolism of small carbon sources

 

Aligments for a candidate for paaJ2 in Pseudomonas stutzeri RCH2

Align 3-oxoadipyl-CoA/3-oxo-5,6-dehydrosuberyl-CoA thiolase; EC 2.3.1.174; EC 2.3.1.223 (characterized)
to candidate GFF2603 Psest_2653 fatty oxidation complex, beta subunit FadA

Query= SwissProt::P0C7L2
         (401 letters)



>lcl|FitnessBrowser__psRCH2:GFF2603 Psest_2653 fatty oxidation
           complex, beta subunit FadA
          Length = 391

 Score =  291 bits (745), Expect = 2e-83
 Identities = 170/405 (41%), Positives = 244/405 (60%), Gaps = 24/405 (5%)

Query: 2   REAFICDGIRTPIGRY-GGALSSVRADDLAAIPLRELLVRNPRLDAECIDDVILGCANQA 60
           R+A I D  RTP+GR  GG   + RA+ ++A  +  +L RNP++D   ++DVI GC NQ 
Sbjct: 6   RDAVIVDFGRTPMGRSKGGMHRNTRAETMSAHLIDGVLARNPKIDPAEVEDVIWGCVNQT 65

Query: 61  GEDNRNVARMATLLAGLPQSVSGTTINRLCGSGLDALGFAARAIKAGDGDLLIAGGVESM 120
            E   N+ARMA+L+  +P + +G T++RLCGS + AL  A +AI+  +GD+ + GGVE M
Sbjct: 66  LEQGWNIARMASLMTRIPHTSAGQTVSRLCGSSMSALHTAVQAIQTNNGDVFVIGGVEHM 125

Query: 121 SRAPFVMGKAASAFSRQAEMFDTTIGWRFVNPLMAQQFGTDS--MPETAENVAELLKISR 178
                + G                      NP ++      S  M  TAE + ++  I+R
Sbjct: 126 GHVSMMHGVDP-------------------NPQLSLYAAKASGMMGLTAEMLGKMHGITR 166

Query: 179 EDQDSFALRSQQRTAKAQSSGILAEEIVPVVLKNKKGVVTEIQHDEHLRPETTLEQLRGL 238
           E QD+F  RS +   KA   G   +EI+P+   ++ G +    +DE +RP+TTLE L  L
Sbjct: 167 EQQDAFGERSHRLAHKATLEGNFKDEIIPMEGYDEDGFLKVFDYDETIRPDTTLESLAAL 226

Query: 239 KAPFRANG-VITAGNASGVNDGAAALIIASEQMAAAQGLTPRARIVAMATAGVEPRLMGL 297
           K  F   G  +TAG +S + DGA+ +I+ S Q A   G+ P A + AMA AGV+P +MG 
Sbjct: 227 KPAFNPKGGTVTAGTSSQITDGASCMIVMSAQRAKDLGIQPLAVVRAMALAGVDPAIMGY 286

Query: 298 GPVPATRRVLERAGLSIHDMDVIELNEAFAAQALGVLRELGLPDDAPH-VNPNGGAIALG 356
           GPVP+T++VL+RAGL++ D+  +ELNEAFAAQAL VL++L L D     VN +GGAIALG
Sbjct: 287 GPVPSTQKVLKRAGLTMDDISHVELNEAFAAQALPVLKDLKLLDKMEEKVNLHGGAIALG 346

Query: 357 HPLGMSGARLALAASHELHRRNGRYALCTMCIGVGQGIAMILERV 401
           HP G SGAR++    + + + NG   + TMCIG+GQGI+ + ERV
Sbjct: 347 HPFGCSGARISGTLLNVMKQNNGTIGVATMCIGLGQGISTVFERV 391


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: 432
Number of extensions: 20
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: 391
Length adjustment: 31
Effective length of query: 370
Effective length of database: 360
Effective search space:   133200
Effective search space used:   133200
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 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