GapMind for catabolism of small carbon sources

 

Aligments for a candidate for glcE in Sphingomonas koreensis DSMZ 15582

Align D-lactate oxidase, FAD binding subunit (EC 1.1.3.15) (characterized)
to candidate Ga0059261_2632 Ga0059261_2632 FAD binding domain

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



>lcl|FitnessBrowser__Korea:Ga0059261_2632 Ga0059261_2632 FAD binding
           domain
          Length = 364

 Score =  277 bits (709), Expect = 3e-79
 Identities = 166/372 (44%), Positives = 207/372 (55%), Gaps = 28/372 (7%)

Query: 27  LAVVGGGTRAGLGNPVRADRTLSTRRLSGIVTYDPAEMTMSALAGTPVAEVEAALHAKGQ 86
           L + GGG++  +G P  A + +  R  SGIV YDP E+ ++  AGTP+A++EA +  +GQ
Sbjct: 20  LRLRGGGSKDAIGAPCDA-QVVDMRGFSGIVDYDPPELVLTVGAGTPLAQIEALVVGEGQ 78

Query: 87  MLSFEPMDHRPIFATTGEPTIGGVFAANVSGPRRYVAGAARDSLLGVRFVNGRGEPIKAG 146
           ML+F+P DH  +    G  TIGGV AA V+GP R   G ARD LLG   V+GRGE   AG
Sbjct: 79  MLAFDPFDHGAMLGNDGGATIGGVVAAGVAGPARLSRGGARDHLLGFTAVSGRGERFVAG 138

Query: 147 GRVMKNVTGLDLVKLMAGSYGTLGILTEVTFKVLPLPPAAATVVVSGLNDAEAAAVMAEA 206
            +V+KNVTG DL KLMAGS+G L  LTEVT KVLP P    T+ + GL+ A A A MA A
Sbjct: 139 AKVVKNVTGYDLPKLMAGSWGRLAALTEVTLKVLPAPRTRLTLAMRGLDAAGAVAAMARA 198

Query: 207 MAQPVEVSGASHLPESVRSRFLDGALPDGAATVLRLEGLAASVAIRAEKLGEKLSRFGRI 266
           +    EV+ A+HLP+              A T LRL+G A SVA RA  L E    F  I
Sbjct: 199 LGSAAEVTAAAHLPD----------WRGEAVTALRLDGFAESVAARAAMLPE----FDAI 244

Query: 267 SQLDEAQTRTLWAEIRDVKPYADGTRRPLWRISVAPSAGHQLVAALRLQTGVDAFYDWQG 326
              D      LW  +RD  P       PLWR+ VAP     ++AAL          DW G
Sbjct: 245 EDAD-----ALWRAVRDASPLP--REWPLWRLIVAPGKAPGVIAAL---PDAQWLLDWAG 294

Query: 327 GLVWLRMEADPEAELLRRYIGAVGGGHAALLRAGEEARGRIPAFEPQPPAVARLSERIRA 386
           GL+WL  +A P A    R      GGHA L RA E  R  +PA  PQP A+A +  R+R 
Sbjct: 295 GLIWLTSDAGPVA---IRTAAEAAGGHATLWRASEAMRRAVPALHPQPGALAAIEARVRR 351

Query: 387 QFDPSGIFNPGR 398
            FDP G+F  GR
Sbjct: 352 AFDPGGVFETGR 363


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: 498
Number of extensions: 28
Number of successful extensions: 6
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: 364
Length adjustment: 30
Effective length of query: 375
Effective length of database: 334
Effective search space:   125250
Effective search space used:   125250
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 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