GapMind for catabolism of small carbon sources

 

Aligments for a candidate for glcD in Pseudomonas putida KT2440

Align D-lactate oxidase and glycolate oxidase, FAD-linked subunit (EC 1.1.3.15) (characterized)
to candidate PP_3745 PP_3745 glycolate oxidase, putative FAD-linked subunit

Query= reanno::psRCH2:GFF3772
         (499 letters)



>lcl|FitnessBrowser__Putida:PP_3745 PP_3745 glycolate oxidase,
           putative FAD-linked subunit
          Length = 499

 Score =  892 bits (2304), Expect = 0.0
 Identities = 441/499 (88%), Positives = 468/499 (93%)

Query: 1   MNILYDERVDGALPKVDKAALLAELQAQLPDLDILHRSEDLKPYECDGLSAYRTTPLLVV 60
           MNILYDERVDGALP VD AALL  L+  LPDL+ILHR EDLKPYECDGLSAYRT PLLV 
Sbjct: 1   MNILYDERVDGALPNVDLAALLQALRDALPDLEILHRDEDLKPYECDGLSAYRTVPLLVA 60

Query: 61  LPERIEQVETLLKLCHQRGVPVVARGAGTGLSGGALPLEQGILLVMARFNKILEVDPAGR 120
           LPER+EQV+TLLKLCHQRGVPVVARGAGTGLSGGALPL +GILLVMARFN+ILEV+P GR
Sbjct: 61  LPERLEQVQTLLKLCHQRGVPVVARGAGTGLSGGALPLAKGILLVMARFNRILEVNPQGR 120

Query: 121 FARVQPGVRNLAISQAAAPYELYYAPDPSSQIACSIGGNVAENAGGVHCLKYGLTVHNLL 180
           +ARVQPGVRNLAISQAAAP+ +YYAPDPSSQIACSIGGNVAENAGGVHCLKYGLTVHN+L
Sbjct: 121 YARVQPGVRNLAISQAAAPHGMYYAPDPSSQIACSIGGNVAENAGGVHCLKYGLTVHNVL 180

Query: 181 KVDILTVEGERMTLGSDALDSPGFDLLALFTGSEGMLGIVTEVTVKLLPKPQVAKVLLAA 240
           KVDILTVEGER++LGSDALDSPGFDLLALF GSEGMLGIVTEVTVKLLPKPQVA+V+LA+
Sbjct: 181 KVDILTVEGERLSLGSDALDSPGFDLLALFIGSEGMLGIVTEVTVKLLPKPQVARVILAS 240

Query: 241 FDSVEKAGRAVGDIIAAGIIPGGLEMMDNLSIRAAEDFIHAGYPVDAEAILLCELDGVEA 300
           FDSVE AGRAV DIIAAGIIPGGLEMMDNL+IRAAEDFIHAGYPVDA AILLCELDGVEA
Sbjct: 241 FDSVEDAGRAVADIIAAGIIPGGLEMMDNLAIRAAEDFIHAGYPVDAAAILLCELDGVEA 300

Query: 301 DVHDDCARVSEVLKLAGATEVRLAKDEAERVRFWAGRKNAFPAVGRISPDYYCMDGTIPR 360
           DV+DDC RV+ VL  AGA EV LA DEAER RFWAGRKNAFPAVGRISPDYYCMDGTIPR
Sbjct: 301 DVYDDCERVAAVLTQAGAREVHLACDEAERARFWAGRKNAFPAVGRISPDYYCMDGTIPR 360

Query: 361 RELPGVLKGISDLSEQFGLRVANVFHAGDGNMHPLILFDANQPGELERAEDLGGKILELC 420
           RELP VLKGISDLS ++GLRVANVFHAGDGNMHPLILFDAN PGELERAE +GGKILELC
Sbjct: 361 RELPRVLKGISDLSAEYGLRVANVFHAGDGNMHPLILFDANLPGELERAEAIGGKILELC 420

Query: 421 VKVGGSITGEHGVGREKINQMCSQFNADELTLFHAVKAAFDPSGLLNPGKNIPTLHRCAE 480
           VKVGGSITGEHGVGREKINQMC+QFN+DE+TLFHAVKAAFDP GLLNPGKNIPTLHRCAE
Sbjct: 421 VKVGGSITGEHGVGREKINQMCAQFNSDEITLFHAVKAAFDPQGLLNPGKNIPTLHRCAE 480

Query: 481 FGRMHIHNGQLPFPELERF 499
           FG +H+H GQLPFPELERF
Sbjct: 481 FGALHVHQGQLPFPELERF 499


Lambda     K      H
   0.320    0.140    0.412 

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: 979
Number of extensions: 28
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: 499
Length of database: 499
Length adjustment: 34
Effective length of query: 465
Effective length of database: 465
Effective search space:   216225
Effective search space used:   216225
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: 52 (24.6 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