GapMind for catabolism of small carbon sources

 

Alignments for a candidate for etoh-dh-nad in Gracilibacillus halophilus YIM-C55.5

Align L-threonine 3-dehydrogenase; TDH; L-threonine dehydrogenase; EC 1.1.1.103 (characterized)
to candidate WP_003468267.1 J416_RS08060 erythritol/L-threitol dehydrogenase

Query= SwissProt::Q8U259
         (348 letters)



>NCBI__GCF_000359605.1:WP_003468267.1
          Length = 358

 Score =  177 bits (450), Expect = 3e-49
 Identities = 116/336 (34%), Positives = 181/336 (53%), Gaps = 19/336 (5%)

Query: 1   MSEKMVAIMKTKPE-YGAELVEVDVPKPGPGEVLIKILATSICGTDLHIYEWNE--WA-- 55
           + E M A++   PE Y  E  EV+ P  GPGE++IK+ A  ICG+DL +Y   +  WA  
Sbjct: 4   LPETMKAVVCHGPEDYRVE--EVNTPTAGPGEIVIKVKACGICGSDLKVYHGADMYWAGD 61

Query: 56  QTRIRPPQIMGHEVAGEVVEVGPGV---EGIEVGDYVSVETHIVCGKCYACKRGQYHVCQ 112
              ++ P I GHE  GEV E+G G      +++GD ++ +    CG C  C  G+Y +CQ
Sbjct: 62  DPWLKAPVIPGHEFYGEVAELGEGAAETHDLQIGDRITTDQINPCGNCMYCNSGKYWMCQ 121

Query: 113 NTKIFGVD---TDGVFAEYAVV-PAQNVWKNPKNIPPEYATLQEPLGNAVDTVLAGPIAG 168
              ++G      +G  AEY    P   ++K P+ +    A+L EP+  AV  V    I  
Sbjct: 122 VHNMYGFQREVAEGAMAEYMKFSPQSKIYKVPEGVNDYEASLLEPMACAVHAVQRATIEF 181

Query: 169 KS-VLITGAGPLGLLGIAVAKASGAYPVIVSEPSEFRRNLAKKVGADYVINPFEEDVVKE 227
           +  V++ GAG LGL  I + K      ++V + ++ R  LAKK GAD  +NP +EDV+++
Sbjct: 182 EDFVVMAGAGTLGLCMIQLIKLKTPKTLVVLDANDRRLELAKKYGADICMNPTKEDVIQK 241

Query: 228 VMDITDGNGVDVFLEFSGAPKALEQGLQAVTPAGRVSLLGLFPGKVSIDFNNLIIFKALT 287
           V D+T+G G DV++E +G PK + QGL+ V   GR     +F  + + D++ +   K L 
Sbjct: 242 VKDLTNGYGCDVYIEATGNPKGVTQGLEMVRKLGRYVEFSVFGKETTTDWSVIGDKKEL- 300

Query: 288 VYGITGRHLWETWYTVS-RLLQSGKLNIDPIITHKY 322
              I G HL    Y ++  L + G ++ + I+TH +
Sbjct: 301 --DIRGSHLGPYTYPIAIDLFERGLVSAEGIVTHTF 334


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: 310
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: 358
Length adjustment: 29
Effective length of query: 319
Effective length of database: 329
Effective search space:   104951
Effective search space used:   104951
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