GapMind for catabolism of small carbon sources

 

Alignments for a candidate for etoh-dh-nad in Cupriavidus basilensis 4G11

Align alcohol dehydrogenase (EC 1.1.1.1) (characterized)
to candidate RR42_RS24700 RR42_RS24700 glucose-methanol-choline oxidoreductase

Query= BRENDA::Q76HN6
         (526 letters)



>FitnessBrowser__Cup4G11:RR42_RS24700
          Length = 560

 Score =  562 bits (1448), Expect = e-164
 Identities = 280/524 (53%), Positives = 363/524 (69%), Gaps = 2/524 (0%)

Query: 2   EFDYLIVGAGSAGCVLANRLSADPSVTVCLLEAGPEDRSPLIHTPLGLAAILPTRHVNWA 61
           +FDY++VG GS GCV+A RLS DP+++VC+LEAG      ++  P G  A++PTR  NWA
Sbjct: 4   QFDYIVVGGGSGGCVVAGRLSEDPNLSVCVLEAGGHGDGMVVKVPAGAVAMMPTRLNNWA 63

Query: 62  FKTTPQPGLGGRVGYQPRGKVLGGSSSINGMIYIRGHQDDFNDWQALGNEGWGFDDVLPY 121
           F T PQ GLGGR+GYQPRGK+LGGSS+IN M+YIRGH+ D++ W +LGN GW +DDVLPY
Sbjct: 64  FDTVPQAGLGGRIGYQPRGKMLGGSSAINAMVYIRGHRSDYDRWASLGNSGWSYDDVLPY 123

Query: 122 FRKSEMHHGGSSEYHGGDGELYVSPANRHAASEA-FVESALRAGHSYNPDFNGATQEGAG 180
           FR SE +    + +HG +G L VS        +A ++E+A +AG     DFNGA QEG G
Sbjct: 124 FRLSEHNERFDNAWHGRNGPLNVSDLRTDNPFQARYLEAARQAGLPLTDDFNGAQQEGIG 183

Query: 181 YYDVTIRDGRRWSTATAFLKP-VRHRSNLTVLTHTHVESIVLLGKQATGVQALIKGSRVH 239
            Y VT + G RWS A A+L P +  R+NLTV TH  V  I+L GK+A GV+ L  G    
Sbjct: 184 IYQVTQKQGERWSAARAYLHPHIGRRANLTVETHAQVRRILLEGKRAVGVEVLQHGVIRT 243

Query: 240 LRARKEVILSAGAFGSPHLLMLSGIGSAAELEPQGIAPRHELPGVGQNLQDHADVVLCYK 299
           LRAR+EV+L+AGA  +P LLMLSG+G A EL   GI     LPGVG+NLQDH D V  Y+
Sbjct: 244 LRARREVVLAAGALQTPQLLMLSGVGPAQELARVGIQTVQHLPGVGRNLQDHPDFVFGYR 303

Query: 300 SNDTSLLGFSLSGGVKMGKAMFDYARHRNGPVASNCAEAGAFLKTDPGLERPDIQLHSVI 359
           +     +G SL G V++   +  + R R G + +N AE G FLKT P LE PDIQLH V+
Sbjct: 304 TGSLDTMGVSLLGSVRILSEILRFRRERRGMLTTNFAEGGGFLKTRPELEAPDIQLHFVV 363

Query: 360 GTVDDHNRKLHWGHGFSCHVCVLRPKSIGSVGLASPDPRKAPRIDPNFLAHDDDVATLLK 419
             VD+H R++  GHGFSCHVC+LRP+S GSV L S DP  AP IDP F     DV  ++ 
Sbjct: 364 AMVDNHARRMRLGHGFSCHVCLLRPRSTGSVTLHSNDPLTAPLIDPAFFDDPLDVEDMVA 423

Query: 420 GYRITRDIIAQTPMASFGLRDMYSAGLHNDEQLIELLRKRTDTIYHPIGTCKMGQDEMAV 479
           G++ITR ++    +A +  RD++++ +  D+ +  +LR+RTDT+YHP+GTC+MGQDEMAV
Sbjct: 424 GFKITRRLMQTPALAKWATRDLFTSHVKTDDDIRAVLRQRTDTVYHPVGTCRMGQDEMAV 483

Query: 480 VDSQLRVHGIEGLRVVDASIMPTLVGGNTNAAAIMIAERAAEWI 523
           VD QLRVHG++GLRVVDASIMPTL+GGNTNA  IMI E+A + I
Sbjct: 484 VDPQLRVHGLDGLRVVDASIMPTLIGGNTNAPTIMIGEKAVDLI 527


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: 908
Number of extensions: 42
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: 526
Length of database: 560
Length adjustment: 35
Effective length of query: 491
Effective length of database: 525
Effective search space:   257775
Effective search space used:   257775
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: 52 (24.6 bits)

This GapMind analysis is from Sep 17 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