GapMind for catabolism of small carbon sources

 

Alignments for a candidate for etoh-dh-nad in Algoriphagus aquaeductus T4

Align alcohol dehydrogenase (EC 1.1.1.1) (characterized)
to candidate WP_111392030.1 CLV31_RS05425 zinc-dependent alcohol dehydrogenase family protein

Query= BRENDA::D4GSN2
         (353 letters)



>NCBI__GCF_003253485.1:WP_111392030.1
          Length = 346

 Score =  260 bits (664), Expect = 4e-74
 Identities = 142/349 (40%), Positives = 204/349 (58%), Gaps = 10/349 (2%)

Query: 1   MRAAVLREHGEPLDVTEVPDPTCDADGVVVEVEACGICRSDWHSWMGHGEWADDAVPSGQ 60
           M+A ++    E   +T+VPDP     GVV+EV+A G+CRSDWH WMGH    D  +    
Sbjct: 1   MKAILVESFQEKPIITQVPDPQVPDYGVVLEVKATGLCRSDWHGWMGH----DSDIRLPH 56

Query: 61  ILGHEPAGRVVEAGDRVETIREGDRVALPFNLACGSCGYCQTGHGNVCTGDHPHALGFEP 120
           + GHE AG + E G  V+  + GDRV +PF  ACG+C  CQ+G+  +C  D     GF  
Sbjct: 57  VPGHEFAGVIREVGKGVKNWKAGDRVTVPFVCACGTCPTCQSGNQQIC--DDQFQPGF-- 112

Query: 121 AAQGAFAELVHLPSADYNAIQLPEDVLPTDVAALGCRFMTAYNALDARAGLRAGQWVAVH 180
              G+FAE V +  A+ N ++LP+ V     A+LGCRF T++  + A+  +  GQWVAVH
Sbjct: 113 THWGSFAEYVAVHRAEANLVRLPDSVSFEAAASLGCRFATSFRGVVAQGKVTGGQWVAVH 172

Query: 181 GCGGVGLSTIQVANVLGARVVAVDVRESALDAAADLGADAVVDGSAE-DPVDAIRGLTDG 239
           GCGGVGLS I +A  LGA+V+AVD+ E  L  A   GAD +++G    D  +AI  LT G
Sbjct: 173 GCGGVGLSAIMIAAALGAQVIAVDISEEKLALAKAAGADILLNGKINPDIPEAILELTKG 232

Query: 240 GAHVSLDALGVAETCRNSVRSVRPRGSHVQVGLTTEAEKGNVSLPTDWMTRHEVSFLGAR 299
           GAHVS+DALG   TC NS+  +R RG H+Q+GL    ++ N  +P   +   E+  LG+ 
Sbjct: 233 GAHVSIDALGSKITCYNSIACLRKRGKHIQIGLMA-GDQTNPQVPMHLVIAQELELLGSH 291

Query: 300 GMPPTNADDLLSLLASDAVDPGSLVTKTVSLDEVPERLAAMTDYDTVGV 348
           GM      +++ ++    + P +L+ + + LDE  E L +M  +   G+
Sbjct: 292 GMQAHAYPEMMQMILQGKIAPQTLIGRRIGLDEAVEALTSMDRFQENGM 340


Lambda     K      H
   0.317    0.134    0.412 

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: 406
Number of extensions: 19
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: 353
Length of database: 346
Length adjustment: 29
Effective length of query: 324
Effective length of database: 317
Effective search space:   102708
Effective search space used:   102708
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