GapMind for catabolism of small carbon sources

 

Aligments for a candidate for glcE in Burkholderia phytofirmans PsJN

Align D-lactate oxidase, FAD binding subunit (EC 1.1.3.15) (characterized)
to candidate BPHYT_RS03505 BPHYT_RS03505 FAD-binding protein

Query= reanno::Cup4G11:RR42_RS17310
         (374 letters)



>lcl|FitnessBrowser__BFirm:BPHYT_RS03505 BPHYT_RS03505 FAD-binding
           protein
          Length = 362

 Score =  421 bits (1082), Expect = e-122
 Identities = 210/368 (57%), Positives = 268/368 (72%), Gaps = 13/368 (3%)

Query: 7   DQQATLTAFRDAIRHATGTRTPLRLRGGGSKDFYGQHPQGTLLDTRAYSGIVDYDPPELV 66
           ++   +  + + +R A+     LR+RGGG+KD+YGQ  +G +LDTRAY GI+ YDP ELV
Sbjct: 2   EEDDIVAVWSERVRSASAEGHALRIRGGGTKDWYGQTLEGDILDTRAYRGIIAYDPAELV 61

Query: 67  ITARCGTPLAQIEAALAERRQMLAFEPPHFSTGADGSDVATIGGAVAAGLSGPRRQAVGA 126
           ITAR GTPL +IEAALAE  QMLAFEPPHF   A      T GG +AAG++GPRR + GA
Sbjct: 62  ITARAGTPLLEIEAALAEHHQMLAFEPPHFGPQA------TFGGCIAAGIAGPRRPSAGA 115

Query: 127 LRDFVLGTRVMDGRGDVLSFGGQVMKNVAGYDVSRLMSGSLGTLGLILEVSLKVLPVPFD 186
            RDFVLG  +M+G+G  L FGGQV+KNVAGYDVSRLM+GSLGTLGLILE+S+KVLP+P  
Sbjct: 116 ARDFVLGAVIMNGQGQKLHFGGQVVKNVAGYDVSRLMAGSLGTLGLILELSIKVLPLPQA 175

Query: 187 DATLRFALDEAAALDRLNDWGGQPLPIAASAWHDGVLHLRLSGAAAALRAARARLGGEAV 246
           +ATL+F ++   A+ +LN+WGG+PLPI ASAW  G L +RL+GA AA+++A+  LGGE V
Sbjct: 176 EATLKFDMNGTDAVRKLNEWGGRPLPITASAWRHGTLVVRLAGAEAAVKSAKMALGGEVV 235

Query: 247 DAAQADALWRALREHSHAFFAPVQAGRALWRIAVPTTAAPLALPGGQLIEWGGGQRWWLG 306
           DA +A+  W  LRE + +FFA +    ALWR+A+P+   PL LPG QL+EWGGGQRWW+ 
Sbjct: 236 DAVEAERFWAGLREQTDSFFAAIPPRAALWRLALPSITEPLQLPGAQLMEWGGGQRWWI- 294

Query: 307 GSDSAADSAIVRAAAKAAGGHATLFRNG---DKAVGVFTPLSAPVAAIHQRLKATFDPAG 363
              +  D+  VR +AK AGGHAT+FR G   D+  GVFTPL AP+  IH+ LK  FDPA 
Sbjct: 295 ---TDTDAQTVRISAKQAGGHATIFRAGHGYDRGAGVFTPLPAPLMKIHRGLKTAFDPAR 351

Query: 364 IFNPQRMY 371
           IFN  R+Y
Sbjct: 352 IFNRGRLY 359


Lambda     K      H
   0.321    0.136    0.414 

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: 474
Number of extensions: 20
Number of successful extensions: 3
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: 374
Length of database: 362
Length adjustment: 30
Effective length of query: 344
Effective length of database: 332
Effective search space:   114208
Effective search space used:   114208
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: 49 (23.5 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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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, 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