GapMind for catabolism of small carbon sources

 

Alignments for a candidate for glcE in Azospirillum brasilense Sp245

Align D-lactate oxidase, FAD binding subunit (EC 1.1.3.15) (characterized)
to candidate AZOBR_RS05730 AZOBR_RS05730 2-hydroxy-acid oxidase

Query= reanno::Smeli:SMc00833
         (405 letters)



>FitnessBrowser__azobra:AZOBR_RS05730
          Length = 417

 Score =  298 bits (763), Expect = 2e-85
 Identities = 173/414 (41%), Positives = 239/414 (57%), Gaps = 23/414 (5%)

Query: 6   EPASEEGIASVVRSAAAERVTLAVVGGGTRAGLGNPVRADRTLSTRRLSGIVTYDPAEMT 65
           +P S    A  VR A +E   L V G G++ GLG P++   TL    LSG+V Y+  E+ 
Sbjct: 7   KPDSAAQAADAVRWALSEGTPLDVAGSGSKRGLGRPIQTAYTLDLSGLSGVVAYEAEELV 66

Query: 66  MSALAGTPVAEVEAALHAKGQMLSFEPMDHRPIFATT-GEPTIGGVFAANVSGPRRYVAG 124
           ++A AGTP+AE+   L  + Q  +FEP D  P+F    G+ T+GGV +  ++GPRR  AG
Sbjct: 67  LTARAGTPMAEILPMLAERRQQFAFEPQDLGPLFGRPEGQGTLGGVISCGLAGPRRISAG 126

Query: 125 AARDSLLGVRFVNGRGEPIKAGGRVMKNVTGLDLVKLMAGSYGTLGILTEVTFKVLPLPP 184
           +ARD  LG+  VNGRG+  K GG+V+KNVTG D+ KLMAGS+GTL +LTE+T KVLP   
Sbjct: 127 SARDHTLGIEGVNGRGDLYKGGGKVVKNVTGYDVPKLMAGSFGTLTVLTELTVKVLPASE 186

Query: 185 AAATVVVSGLNDAEAAAVMAEAMAQPVEVSGASHLPESV--RSRFLDGALPDGAATVLRL 242
              T++++G  DA A A +  A+  P +VSGA+HLP +V  RS     A   GA T++R+
Sbjct: 187 DVRTLLLAGREDAGAVAALTAALQSPYDVSGAAHLPAAVAARSHVRAVAAVGGAVTLVRV 246

Query: 243 EGLAASVAIRAEKLGEKLSRFGRISQLDEAQTRTLWAEIRDV-------KPYADG----- 290
           EG   SV  R   L E+L   G  + LD  ++  +W E+RDV        P + G     
Sbjct: 247 EGFGPSVIARVAALKEEL---GADAVLDRDESLAVWKEVRDVAYFGPTPSPASAGEGWGG 303

Query: 291 --TRRPLWRISVAPSAGHQLVAALRLQTGVDAFYDWQGGLVWLRMEADPEAELLRRYIGA 348
               R +W+ISV PS G ++  ++R     + ++DW GGL+W  +   P+A    R  GA
Sbjct: 304 GEDSRHIWKISVQPSEGPRVAESIRWALDAELYFDWGGGLIWAAVAPTPDAASAIR--GA 361

Query: 349 VG-GGHAALLRAGEEARGRIPAFEPQPPAVARLSERIRAQFDPSGIFNPGRAAA 401
           +G  GHA L+RA E+ R     F P P  V  LS R++  FDP GI NPGR  A
Sbjct: 362 LGTAGHATLVRAPEDVRTTTEVFHPLPDPVKALSRRVKESFDPCGILNPGRMYA 415


Lambda     K      H
   0.318    0.134    0.387 

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: 538
Number of extensions: 31
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: 405
Length of database: 417
Length adjustment: 31
Effective length of query: 374
Effective length of database: 386
Effective search space:   144364
Effective search space used:   144364
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 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