GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__pseudo3_N2E3:AO353_26740
          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:

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