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_26740 AO353_26740 choline dehydrogenase

Query= BRENDA::Q76HN6
         (526 letters)



>lcl|FitnessBrowser__pseudo3_N2E3:AO353_26740 AO353_26740 choline
           dehydrogenase
          Length = 550

 Score =  423 bits (1088), Expect = e-123
 Identities = 237/526 (45%), Positives = 317/526 (60%), Gaps = 8/526 (1%)

Query: 3   FDYLIVGAGSAGCVLANRLSADPSVTVCLLEAGPEDRSPLIHTPLGLAAILPTRHVNWAF 62
           +DY++VGAG AGC+LANRLSA+P   V LLEAG  D  P IH P+G    +     +W F
Sbjct: 8   YDYIVVGAGPAGCLLANRLSANPQHRVLLLEAGGRDNYPWIHIPVGYLYCIGNPRTDWCF 67

Query: 63  KTTPQPGLGGRVGYQPRGKVLGGSSSINGMIYIRGHQDDFNDWQALGNEGWGFDDVLPYF 122
           KT  Q GL GR    PRGKVLGGSSSINGMIY+RG   D++ W A GN GW ++DVLP F
Sbjct: 68  KTEAQTGLQGRSLSYPRGKVLGGSSSINGMIYMRGQAGDYDRWAAEGNPGWSWNDVLPLF 127

Query: 123 RKSEMHHGGSSEYHGGDGELYVSPAN-RHAASEAFVESALRAGHSYNPDFNGATQEGAGY 181
           ++SE H  G S +HG  GE  V          +AF  +A ++G +   DFN    EG GY
Sbjct: 128 KQSENHFAGDSAFHGAAGEWRVERQRLSWPILDAFRSAAEQSGIASVDDFNQGDNEGCGY 187

Query: 182 YDVTIRDGRRWSTATAFLKPVRHRSNLTVLTHTHVESIVLLGKQATGVQALIKGSRVHLR 241
           + V  + G RW+ A AFLKPVRHR NLTVLT   V+ ++L   +A+ V A  +G      
Sbjct: 188 FQVNQKAGVRWNAAKAFLKPVRHRPNLTVLTSVDVDRVLLENGRASRVSARWQGQVNIFA 247

Query: 242 ARKEVILSAGAFGSPHLLMLSGIGSAAELEPQGIAPRHELPGVGQNLQDHADVVLCYKSN 301
           AR+E+ILSAG+ GSP +L  SGIG    L+  GI   HEL GVG+NLQDH  + L YK  
Sbjct: 248 ARREIILSAGSVGSPSILQRSGIGPGDLLKRLGIGVAHELNGVGRNLQDHLQLRLIYKLE 307

Query: 302 DTSLL---GFSLSGGVKMGKAMFDYARHRNGPVASNCAEAGAFLKTDPGLERPDIQLHSV 358
           +   L     SL G + MG     Y   R+GP++   ++ GAF ++ P     +++ H  
Sbjct: 308 NARTLNQIAGSLWGKIGMG---LRYLYDRSGPLSMAPSQLGAFARSGPEQTSANLEYHVQ 364

Query: 359 IGTVDDHNRKLHWGHGFSCHVCVLRPKSIGSVGLASPDPRKAPRIDPNFLAHDDDVATLL 418
             +++     LH    F+  VC LRP+S G V + S DP++ P I PN+L+H +D+    
Sbjct: 365 PLSLERFGEPLHAFPAFTASVCDLRPQSRGRVEIRSADPQQPPLIQPNYLSHPEDLRVAA 424

Query: 419 KGYRITRDIIAQTPMASFG-LRDMYSAGLHNDEQLIELLRKRTDTIYHPIGTCKMGQDEM 477
           +  R+TR I+A   +  F  +  +  A L ++EQL E   +   TI+HP+GTC+MG D  
Sbjct: 425 EAIRLTRRIVAAPALQPFNPVEYLPGAALQSEEQLHEAAARIGTTIFHPVGTCRMGNDAD 484

Query: 478 AVVDSQLRVHGIEGLRVVDASIMPTLVGGNTNAAAIMIAERAAEWI 523
           AVVD+QLRVHGI GLR+ DASIMP +  GNT +  +MIAE+AA+ I
Sbjct: 485 AVVDAQLRVHGIPGLRIADASIMPHITSGNTCSPTLMIAEKAAQLI 530


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: 760
Number of extensions: 32
Number of successful extensions: 4
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: 550
Length adjustment: 35
Effective length of query: 491
Effective length of database: 515
Effective search space:   252865
Effective search space used:   252865
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