GapMind for catabolism of small carbon sources

 

Alignments for a candidate for tdh in Dyella japonica UNC79MFTsu3.2

Align L-threonine 3-dehydrogenase; TDH; EC 1.1.1.103 (uncharacterized)
to candidate N515DRAFT_2489 N515DRAFT_2489 alcohol dehydrogenase, propanol-preferring

Query= curated2:Q67N85
         (351 letters)



>FitnessBrowser__Dyella79:N515DRAFT_2489
          Length = 343

 Score =  141 bits (355), Expect = 3e-38
 Identities = 116/350 (33%), Positives = 167/350 (47%), Gaps = 17/350 (4%)

Query: 1   MAETMRALRKLEAGPGATLQEVPIPTIGPRDVLVKVRAASICGTDYHIYTWDPWSAGRVK 60
           M++TM+A      G   ++ EVP+PT G  +VLVK+ A  +C TD H    D W   + K
Sbjct: 1   MSKTMKAAVVRAFGQPLSIDEVPVPTPGLGEVLVKIEACGVCHTDLHAVDGD-WPV-KPK 58

Query: 61  PPLTIGHELAGEVVAVGREVTACKVGDYVSAE-THIVCNRCPRCHMGEYHLCENTKILGV 119
           PP   GHE  G VVA+G  VT  K GD V     +  C  C  C  G   LCE+ +  G 
Sbjct: 59  PPFIPGHEGVGYVVAIGPGVTHLKEGDRVGIPWLYSACGHCEHCLGGWETLCESQQNTGY 118

Query: 120 DTDGAFAEYVAVPEQNIWVNDKDIPFELQSIQEPLGNAVHTALNGDLT--ARSVLITGCG 177
             +G FAEY       +      I F   +     G  V+  L    T     V+I+G G
Sbjct: 119 SVNGGFAEYALAAADYVGHLPDGIGFVEIAPVLCAGVTVYKGLKVTDTRPGNWVVISGIG 178

Query: 178 PIGIMSVPVAKMAGAEIVMAMDINEYRLQLAGQLGADVLINPTKQDPVEVVRSYTRGYGA 237
            +G M+V  A   G   V A+DI++ +L LA +LGA ++IN    DPV VV+    G   
Sbjct: 179 GLGHMAVQYAAAMGLN-VAAVDIDDAKLDLARRLGAQLIINARHADPVAVVKKEIGGAHG 237

Query: 238 DVVLEMSGNPTAIRQGLKAARNGARISLLGLPGRPLELDLAADVIMRGLVLQG-ITGRRM 296
            +V  +S  P A  Q +   R G  +SL GLP    +L +  D+++ G+ ++G I G R+
Sbjct: 238 ALVTAVS--PKAFGQAMNMVRRGGTVSLNGLPPGSFDLSI-FDMVLNGVTVRGSIVGTRL 294

Query: 297 WQTWYQVRSLYRAGLAERLRPLVTHRMPLEQIDAAMELMGSGQ-SGKIVL 345
                 ++       A +++  VT    LE I+     M  GQ  G++VL
Sbjct: 295 -----DLQESLDFAKAGKVKATVTTDR-LENINEVFRRMHQGQIEGRVVL 338


Lambda     K      H
   0.320    0.137    0.415 

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: 307
Number of extensions: 24
Number of successful extensions: 5
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: 351
Length of database: 343
Length adjustment: 29
Effective length of query: 322
Effective length of database: 314
Effective search space:   101108
Effective search space used:   101108
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.

Links

Downloads

Related tools

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