GapMind for catabolism of small carbon sources

 

Alignments for a candidate for dadA in Sphingomonas koreensis DSMZ 15582

Align D-alanine dehydrogenase (EC 1.4.99.-) (characterized)
to candidate Ga0059261_3351 Ga0059261_3351 Glycine/D-amino acid oxidases (deaminating)

Query= reanno::azobra:AZOBR_RS08020
         (436 letters)



>FitnessBrowser__Korea:Ga0059261_3351
          Length = 405

 Score =  229 bits (585), Expect = 9e-65
 Identities = 140/401 (34%), Positives = 205/401 (51%), Gaps = 6/401 (1%)

Query: 3   VIVLGSGVIGVSTAYFLAKAGHEVTVVDRQPGPALETSYANAGEVSPGYSAPWAAPGLMA 62
           +IVLG+GV+G++TA  LA  GH VTVVD   GP L TS+AN  ++S  Y+   A+P ++ 
Sbjct: 7   IIVLGAGVVGMATALTLAGRGHRVTVVDGAGGPGLGTSFANGAQLSYAYTDALASPSVLR 66

Query: 63  KAVKWMLMKHSPLVIRPKMDPAMWSWCLKLLANANERSYEINKGRMVRLAEYSRDCLRVL 122
           +    +L     L  +P +DP    W +  L N    S+  N    + LA  SR  L  L
Sbjct: 67  QIPHILLGLDPALRFQPHLDPDFLRWSIAFLRNCGAGSFRRNTLAGLALAARSRLALDQL 126

Query: 123 RDETGIRYDERAKGTLQVFRTQKQVDAAATDMAVLDRFKVPYSLLDVEGCAAVEPALRLV 182
            +   + Y +   G + ++RT     AA   +A+     +  +LLD +   A+EP L  V
Sbjct: 127 TERHALEYGQSVPGKIHIYRTAASFAAAEAMVALKRANGITQTLLDPDAAVALEPMLAPV 186

Query: 183 KEKIVGGLLLPGDETGDCFRFTNALAAMATELGVEFRYNTGIRKLESDGRRVTGVVTDAG 242
           +++I G L  PG+  GD  RF +         G    ++  + ++E+ G +   +VT  G
Sbjct: 187 RDEIAGALHTPGEAVGDPHRFCSGAHDALIRAGGSSMFDLPVERIETQGSQ-PAIVTRCG 245

Query: 243 T-LTADSYVVAMGSYSPTLVKPFGLDLPVYPVKGYSLTLPIVDAAGAPESTVMDETHKIA 301
           T + AD  V+A G  +P L +  G+ LPV P+KGYS+T P    A AP +++ D  +++ 
Sbjct: 246 TRVPADRIVLAAGPGAPRLARSLGVYLPVQPMKGYSITAP--TGAAAPRASITDVANRVV 303

Query: 302 VTRLGDRIRVGGTAELTGFDLTLRPGRRGPLDHVVSDLFPTGGDLSKAE-FWTGLRPNTP 360
             RLG+R+R+ G AE+   D  + P R   L        P   D    E  W GLRP TP
Sbjct: 304 FARLGNRMRIAGLAEVGRRDTRVEPDRLRALTDSARAALPQAADYDNIESSWAGLRPMTP 363

Query: 361 DGTPIVGPTPVRNLFLNTGHGTLGWTMAAGSGRVVADVVGG 401
           D  PI   T    +  NTGHG LGWT AAGS   VA ++ G
Sbjct: 364 DSLPIT-RTIAPGVIANTGHGGLGWTYAAGSAERVAQIIEG 403


Lambda     K      H
   0.319    0.136    0.408 

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: 424
Number of extensions: 16
Number of successful extensions: 4
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: 436
Length of database: 405
Length adjustment: 32
Effective length of query: 404
Effective length of database: 373
Effective search space:   150692
Effective search space used:   150692
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 (21.7 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