GapMind for catabolism of small carbon sources

 

Alignments for a candidate for lysDH in Paraburkholderia bryophila 376MFSha3.1

Align lysine 6-dehydrogenase (EC 1.4.1.18) (characterized)
to candidate H281DRAFT_05221 H281DRAFT_05221 Saccharopine dehydrogenase, NADP-dependent

Query= BRENDA::Q5LX24
         (368 letters)



>FitnessBrowser__Burk376:H281DRAFT_05221
          Length = 368

 Score =  379 bits (972), Expect = e-110
 Identities = 194/364 (53%), Positives = 243/364 (66%)

Query: 5   ICVVGAGKIGQMIAALLKTSSNYSVTVADHDLAALAVLNRMGVATKQVDAKDEAGLAKAL 64
           + +VGAG IG  IA +L+ + +Y V   D D  AL  L   G++T++VD+ D A L  A+
Sbjct: 3   VAIVGAGLIGHTIAHMLRETGDYDVVAFDRDQHALDKLAAQGISTRRVDSADAAALRAAV 62

Query: 65  GGFDAVISAAPFFLTPIIAKAAKAAGAHYFDLTEDVAATNAVRALAEDSQTAFMPQCGLA 124
            GFDA+I+A P++L   +A AAK AG HYFDLTEDV AT+A+RA+A+D+  AFMPQCGLA
Sbjct: 63  HGFDALINALPYYLAVNVAAAAKGAGVHYFDLTEDVRATHAIRAIADDADHAFMPQCGLA 122

Query: 125 PGFVGIAGAALAAEFDEIDSLHMRVGALPLYPTNALKYNLTWSTDGLINEYCNPCDAIVN 184
           PGF+GIA   LA  F EI  + MRVGALP +PTNALKYNLTWS DGLINEYC PC+AI +
Sbjct: 123 PGFIGIAAHELANRFTEIRDVKMRVGALPQFPTNALKYNLTWSVDGLINEYCQPCEAIRD 182

Query: 185 GERVKTAPLEDYEILGHDGVEYECFNTSGGLGTLPETLDGKARSVSYRSIRYPGHRDILR 244
                  PLE  E    DG EYE FNTSGGLGTL ETL G+  S+ Y+S+RYPGHR++++
Sbjct: 183 SRTQWVQPLEGLEHFSLDGTEYEAFNTSGGLGTLCETLSGRVESLDYKSVRYPGHRNLMQ 242

Query: 245 LLLNDLGLERRRDLLKDIFETALPRTDQDVVLVYCTAKGRIGGQLREKSLINKSYSRVID 304
            LL DL L   RD LK I   ++P T QDVVLV+ T  G   GQL ++    K +++ I 
Sbjct: 243 FLLEDLRLSSDRDTLKTIMRRSVPSTAQDVVLVFITVSGMRDGQLVQEVFTRKIFAKTIC 302

Query: 305 GQVWSAIQVTTAAGVLGVVDLMRAGTLPAKGFVRQEQVKFADFLETEFGRLYRAGDLTAQ 364
           G   SAIQ+TTA  +  V+DL R   LP +GFVRQEQV   DFL   FG+LY    L + 
Sbjct: 303 GVPMSAIQITTAGAMCAVLDLFREKKLPQRGFVRQEQVSLRDFLGNRFGQLYEGQALESL 362

Query: 365 NKAA 368
             AA
Sbjct: 363 QSAA 366


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: 340
Number of extensions: 7
Number of successful extensions: 1
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: 368
Length adjustment: 30
Effective length of query: 338
Effective length of database: 338
Effective search space:   114244
Effective search space used:   114244
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:

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