GapMind for catabolism of small carbon sources

 

Aligments for a candidate for lysDH in Azospirillum brasilense Sp245

Align lysine 6-dehydrogenase (EC 1.4.1.18) (characterized)
to candidate AZOBR_RS29980 AZOBR_RS29980 saccharopine dehydrogenase

Query= BRENDA::Q5LX24
         (368 letters)



>lcl|FitnessBrowser__azobra:AZOBR_RS29980 AZOBR_RS29980 saccharopine
           dehydrogenase
          Length = 375

 Score =  379 bits (972), Expect = e-110
 Identities = 194/365 (53%), Positives = 255/365 (69%), Gaps = 1/365 (0%)

Query: 4   NICVVGAGKIGQMIAALLKTSSNYSVTVADHDLAALAVL-NRMGVATKQVDAKDEAGLAK 62
           +I ++G GKIG+ I   LK + +Y VTVAD    AL  L     + T+ VDA D A LA+
Sbjct: 3   DILLMGGGKIGETIGDFLKATGDYRVTVADRSAEALERLPTHPRMETRVVDAADPAELAE 62

Query: 63  ALGGFDAVISAAPFFLTPIIAKAAKAAGAHYFDLTEDVAATNAVRALAEDSQTAFMPQCG 122
           A+ G  AV+SA P+ LT  +A+AA+ AG HY DLTEDVA+T  V+ LA+ +  AF+PQCG
Sbjct: 63  AMRGKFAVLSALPYHLTVGVAEAARDAGTHYLDLTEDVASTRRVKELADGAPCAFIPQCG 122

Query: 123 LAPGFVGIAGAALAAEFDEIDSLHMRVGALPLYPTNALKYNLTWSTDGLINEYCNPCDAI 182
           LAPGF+ I    +A+ FD +D++ MRVGALP YP+NAL YNLTWST+G+INEY  PC+AI
Sbjct: 123 LAPGFISIVANDVASRFDTLDTVRMRVGALPKYPSNALNYNLTWSTEGVINEYLEPCEAI 182

Query: 183 VNGERVKTAPLEDYEILGHDGVEYECFNTSGGLGTLPETLDGKARSVSYRSIRYPGHRDI 242
           V G  V   PLE+ E    DGV YE FNTSGGLGTL ETL GK R+++YRS+RYPGHRD+
Sbjct: 183 VEGRLVSVPPLEEREEFSLDGVLYEAFNTSGGLGTLCETLAGKVRTLNYRSVRYPGHRDL 242

Query: 243 LRLLLNDLGLERRRDLLKDIFETALPRTDQDVVLVYCTAKGRIGGQLREKSLINKSYSRV 302
           ++ LL+DL L  RR+LLKDI E ++P T QDVVL++ T  G   G+L +++  NK Y R 
Sbjct: 243 MKALLHDLRLGSRRELLKDILEHSIPATLQDVVLIFVTVTGTKRGRLLQETYANKIYGRE 302

Query: 303 IDGQVWSAIQVTTAAGVLGVVDLMRAGTLPAKGFVRQEQVKFADFLETEFGRLYRAGDLT 362
           I G  ++ IQ+TTA+G+  V+DL+  GTLP +GFV+QE+V++ADF+   FGR Y   D  
Sbjct: 303 IGGTFYNGIQITTASGMCAVLDLLADGTLPQRGFVKQEEVRYADFIANRFGRNYAMTDAA 362

Query: 363 AQNKA 367
            Q  A
Sbjct: 363 PQQGA 367


Lambda     K      H
   0.320    0.136    0.397 

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: 351
Number of extensions: 13
Number of successful extensions: 2
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: 368
Length of database: 375
Length adjustment: 30
Effective length of query: 338
Effective length of database: 345
Effective search space:   116610
Effective search space used:   116610
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 (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