GapMind for catabolism of small carbon sources

 

Aligments for a candidate for etoh-dh-nad in Pseudomonas fluorescens FW300-N2E3

Align alcohol dehydrogenase (EC 1.1.1.1) (characterized)
to candidate AO353_07810 AO353_07810 choline dehydrogenase

Query= BRENDA::Q76HN6
         (526 letters)



>lcl|FitnessBrowser__pseudo3_N2E3:AO353_07810 AO353_07810 choline
           dehydrogenase
          Length = 567

 Score =  373 bits (958), Expect = e-108
 Identities = 230/532 (43%), Positives = 311/532 (58%), Gaps = 12/532 (2%)

Query: 2   EFDYLIVGAGSAGCVLANRLSADPSVTVCLLEAGPEDRSPLIHT--PLGLAAILPTRHVN 59
           E+DY+I+GAGSAG  LA RL+ D  VTV LLEAG  D      T  P  LA  L  R  N
Sbjct: 4   EYDYIIIGAGSAGNTLATRLTEDAGVTVLLLEAGGPDYRLDFRTQMPAALAFPLQGRRYN 63

Query: 60  WAFKTTPQPGLGGRVGYQPRGKVLGGSSSINGMIYIRGHQDDFNDW-QALGNEGWGFDDV 118
           WA++T P+P + GR     RGK LGGSS INGM YIRG+  D++ W +  G E W + D 
Sbjct: 64  WAYETDPEPHMDGRRMECGRGKGLGGSSLINGMCYIRGNAMDYDGWAKNPGLEDWTYLDC 123

Query: 119 LPYFRKSEMHHGGSSEYHGGDGELYVSP--ANRHAASEAFVESALRAGHSYNPDFNGATQ 176
           LPYFRK+E    G ++YHGG+G + V+   A  +    A VE+ ++AG+    D NG  Q
Sbjct: 124 LPYFRKAETRDIGPNDYHGGEGPVSVTTPKAGNNPLFHAMVEAGVQAGYPRTEDLNGYQQ 183

Query: 177 EGAGYYDVTIRD-GRRWSTATAFLKPVRHRSNLTVLTHTHVESIVLLGKQATGVQALIKG 235
           EG G  D T+   GRR STA  +L   + RS L ++TH   + I+  GK+A GV+ L+  
Sbjct: 184 EGFGPMDRTVTPKGRRSSTARGYLDIAKKRSTLNIVTHALTDKILFEGKRAIGVRYLVGS 243

Query: 236 SR--VHLRARKEVILSAGAFGSPHLLMLSGIGSAAELEPQGIAPRHELPGVGQNLQDHAD 293
           +   V  RARKEV+L +GA  SP +L  SG+G A  L+   I   H+LPGVG+NLQDH +
Sbjct: 244 AEEPVEARARKEVLLCSGAIASPQILQRSGVGPAKLLKSLDIPVVHDLPGVGENLQDHLE 303

Query: 294 VVLCYKSNDTSLLGFSLSGGVKMGKAMFDYARHRNGPVASNCAEAGAFLKTDPGLERPDI 353
           + L Y       L  SL           ++  +  G  ASN  EAG F++T P  E P+I
Sbjct: 304 LYLQYACTQPVSLYPSLLW-YNQPAIGAEWLFNGTGIGASNQFEAGGFIRTRPDFEWPNI 362

Query: 354 QLHSVIGTVDDHNRKLHWGHGFSCHVCVLRPKSIGSVGLASPDPRKAPRIDPNFLAHDDD 413
           Q H +   ++ +       HGF  H+  +R  S G + + S DPR+ P I  N++A + D
Sbjct: 363 QYHFLPVAINYNGSNGVKEHGFQAHMGSMRSPSRGRIQVKSKDPRQHPSILFNYMATEQD 422

Query: 414 VATLLKGYRITRDIIAQTPMASFGLRDMYSAGLH--NDEQLIELLRKRTDTIYHPIGTCK 471
                 G R+TR+I+ Q  + +F  R++ S G+    DEQL + +R+  +T +HP  +CK
Sbjct: 423 WQEFRDGIRLTREIMQQPALDAFRGREL-SPGIEVQTDEQLDKFIREHAETAFHPSCSCK 481

Query: 472 MGQDEMAVVDSQLRVHGIEGLRVVDASIMPTLVGGNTNAAAIMIAERAAEWI 523
           MG DEMAVVD Q RVHG++GLRVVDASIMP +  GN NA  IMIAE+ A+ I
Sbjct: 482 MGTDEMAVVDGQGRVHGMQGLRVVDASIMPLITTGNLNAPTIMIAEKIADKI 533


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: 865
Number of extensions: 46
Number of successful extensions: 9
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: 567
Length adjustment: 36
Effective length of query: 490
Effective length of database: 531
Effective search space:   260190
Effective search space used:   260190
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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code.

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