GapMind for catabolism of small carbon sources

 

Alignments for a candidate for etoh-dh-nad in Paenisporosarcina indica PN2

Align L-threonine 3-dehydrogenase; TDH; L-threonine dehydrogenase; EC 1.1.1.103 (characterized)
to candidate WP_084544078.1 GY23_RS09030 alcohol dehydrogenase catalytic domain-containing protein

Query= SwissProt::Q8U259
         (348 letters)



>NCBI__GCF_001939075.1:WP_084544078.1
          Length = 349

 Score =  185 bits (470), Expect = 1e-51
 Identities = 111/335 (33%), Positives = 185/335 (55%), Gaps = 15/335 (4%)

Query: 18  ELVEVDVPKPGPGEVLIKILATSICGTDLHIYEWNEWAQTRIRPPQIMGHEVAGEVVEVG 77
           ++VEV +P     E+L+++    +CGTD  IY+  +     I  P+I+GHE +G + +VG
Sbjct: 17  KVVEVPIPVINEDELLVRVSYAGVCGTDNRIYQGTKI----IEGPRIIGHEFSGVIEKVG 72

Query: 78  PGVEGIEVGDYVSVETHIVCGKCYACKRGQYHVCQNTKIFGVDTDGVFAEYAVVP----- 132
             V+   VGD+V+V   I CG CY CK G+ ++C N K  G + DG FA+Y  +P     
Sbjct: 73  TNVQSFSVGDHVTVYPMISCGDCYTCKTGRKNICVNRKTIGYEIDGGFAQYIKIPKIAIN 132

Query: 133 AQNVWKNPKNIPPEYATLQEPLGNAVDTVLAGPI-AGKSVLITGAGPLGLLGIAVAKASG 191
             NV+K   N+  +   + EP+  A++ +    I  G  V+I GAGP+GL  + +AK   
Sbjct: 133 MGNVFKVSSNLDQKVVAITEPIAAALNGIKRANIQQGDCVVIIGAGPIGLFHVQLAKLKE 192

Query: 192 AYPVIVSEPSEFRRNLAKKVGADYVINPFEEDVVKEVMDITDGNGVDVFLEFSGAPKALE 251
              ++V EP   +R +A K+GA + INPF+E+    + ++TDG G DV +   G PK +E
Sbjct: 193 PGILVVIEPDHAKREIALKLGATHTINPFDENPEIRLKELTDGEGADVVIIDVGIPKIIE 252

Query: 252 QGLQAVTPAGRVSLLGLFP--GKVSIDFNNLIIFKALTVYGITGRHLWETWYTVSRLLQS 309
           + ++ V   G   +    P   K+S+D  NLI +K + + G +     E    V  L++S
Sbjct: 253 ESIEYVKKGGTYVIFAGAPHGSKISLD-PNLIHYKEINLTG-SSAATPELHQEVLDLVES 310

Query: 310 GKLNIDPIITHKYKGFDKYEEAFELMRAGKTGKVV 344
           G++++  +I+ +  G D++E A E+  + +  KV+
Sbjct: 311 GQVDVTLLIS-EVVGLDEWERALEMKNSFQKIKVI 344


Lambda     K      H
   0.318    0.138    0.417 

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: 306
Number of extensions: 15
Number of successful extensions: 3
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: 348
Length of database: 349
Length adjustment: 29
Effective length of query: 319
Effective length of database: 320
Effective search space:   102080
Effective search space used:   102080
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: 49 (23.5 bits)

This GapMind analysis is from Sep 24 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