GapMind for catabolism of small carbon sources

 

Alignments for a candidate for etoh-dh-nad in Neptunomonas antarctica S3-22

Align alcohol dehydrogenase (EC 1.1.1.1) (characterized)
to candidate WP_054343390.1 Nant_RS19700 choline dehydrogenase

Query= BRENDA::Q76HN6
         (526 letters)



>NCBI__GCF_001305295.1:WP_054343390.1
          Length = 579

 Score =  381 bits (979), Expect = e-110
 Identities = 221/542 (40%), Positives = 313/542 (57%), Gaps = 22/542 (4%)

Query: 3   FDYLIVGAGSAGCVLANRLSADPSVTVCLLEAGPEDRSPLIHTPLGLAAILPTRHVNWAF 62
           +DY+IVGAGSAGCVLANRL+ D   TV LLEAG  D+S  I  P  L+  + T    W F
Sbjct: 7   YDYIIVGAGSAGCVLANRLTEDGQHTVLLLEAGGSDKSIFIQMPTALSYPMNTPKYAWQF 66

Query: 63  KTTPQPGLGGRVGYQPRGKVLGGSSSINGMIYIRGHQDDFNDWQALGNEGWGFDDVLPYF 122
            T  +P L GR  + PRGKVLGGSSSINGM+Y+RGH  DF++W   G  GWG+   LPYF
Sbjct: 67  HTEGEPFLDGRSMHCPRGKVLGGSSSINGMVYVRGHACDFDEWSEKGATGWGYQQCLPYF 126

Query: 123 RKSEMHHGGSSEYHGGDGELYVSPAN---RHAASEAFVESALRAGHSYNPDFNGATQEGA 179
           +K+E    GS +Y GG G L+    N    +   +AF+++   AG+    D+NG  QEG 
Sbjct: 127 KKAETWAKGSDDYRGGSGPLFTCNGNDMKLNPLYQAFIDAGEDAGYPTTDDYNGYRQEGF 186

Query: 180 GYYDVTIRDGRRWSTATAFLKPVRHRSNLTVLTHTHVESIVLLGKQATGVQ--------- 230
           G   +T++ G R ST+ A+L+    R NLT+++      +++ GK+A G++         
Sbjct: 187 GAMHMTVKAGVRASTSNAYLRDAMQRPNLTLISGVLTRKVIMEGKRAVGIEYEKMDSEKK 246

Query: 231 -----ALIKGSRV-HLRARKEVILSAGAFGSPHLLMLSGIGSAAELEPQGIAPRHELPGV 284
                +  K +RV +  A KEVIL+AG+ GSPHLL LSGIG A  LE  G+A  H+LPGV
Sbjct: 247 SSEKKSSDKSARVINATANKEVILAAGSIGSPHLLQLSGIGPAKVLEEAGVALVHDLPGV 306

Query: 285 GQNLQDHADVVLCYKSNDTSLLGFSLSGGVKMGKAMFDYARHRNGPVASNCAEAGAFLKT 344
           G+NLQDH ++   Y       L   L   V  G     +   ++G  A+N  E+  F+++
Sbjct: 307 GENLQDHLEIYFQYHCKQPITLNGKLD-LVSKGLIGARWMLFKDGLGATNHFESCGFIRS 365

Query: 345 DPGLERPDIQLHSVIGTVDDHNRKLHWGHGFSCHVCVLRPKSIGSVGLASPDPRKAPRID 404
             GL+ P+IQ H +   +     K   GHGF  HV   +P+S G V + S DP+  P I 
Sbjct: 366 RKGLKWPNIQYHFLPAAMRYDGGKAIEGHGFQVHVGPNKPQSRGRVWIKSADPKAKPSIV 425

Query: 405 PNFLAHDDDVATLLKGYRITRDIIAQTPMASF-GLRDMYSAGLHNDEQLIELLRKRTDTI 463
            N++  + D        R+TR+I+ Q  + ++ G      A + +D  +   +R+  ++ 
Sbjct: 426 FNYIGTEQDKQDWRDCIRLTREILKQPALDAYRGDEVQPGAQVSSDIDVDRWVRENVESA 485

Query: 464 YHPIGTCKMGQDE--MAVVDSQLRVHGIEGLRVVDASIMPTLVGGNTNAAAIMIAERAAE 521
           YHP  TCK+G D+  MAV+D+Q RV G+E LRVVD+S+ PT+  GN NA  IM+AE+AA+
Sbjct: 486 YHPSCTCKIGADDDAMAVLDTQCRVRGVESLRVVDSSVFPTIPNGNLNAPTIMVAEKAAD 545

Query: 522 WI 523
            I
Sbjct: 546 MI 547


Lambda     K      H
   0.319    0.137    0.419 

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: 832
Number of extensions: 47
Number of successful extensions: 6
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: 526
Length of database: 579
Length adjustment: 36
Effective length of query: 490
Effective length of database: 543
Effective search space:   266070
Effective search space used:   266070
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 (21.7 bits)
S2: 53 (25.0 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