Aligments for a candidate for etoh-dh-nad in Pseudomonas fluorescens FW300-N1B4

GapMind for catabolism of small carbon sources

Aligments for a candidate for etoh-dh-nad in Pseudomonas fluorescens FW300-N1B4

Align alcohol dehydrogenase (EC 1.1.1.1) (characterized)
to candidate Pf1N1B4_4450 Choline dehydrogenase (EC 1.1.99.1)

Query= BRENDA::Q76HN6
         (526 letters)



>lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_4450 Choline dehydrogenase
           (EC 1.1.99.1)
          Length = 549

 Score =  429 bits (1102), Expect = e-124
 Identities = 233/524 (44%), Positives = 319/524 (60%), Gaps = 6/524 (1%)

Query: 2   EFDYLIVGAGSAGCVLANRLSADPSVTVCLLEAGPEDRSPLIHTPLGLAAILPTRHVNWA 61
           E+DY++VGAG AGC+LANRLSA+P   V LLEAG  D  P IH P+G    +     +W 
Sbjct: 7   EYDYIVVGAGPAGCLLANRLSANPQHRVLLLEAGGRDNYPWIHIPVGYLFCIGNPRTDWC 66

Query: 62  FKTTPQPGLGGRVGYQPRGKVLGGSSSINGMIYIRGHQDDFNDWQALGNEGWGFDDVLPY 121
           FKT  QPGL GR    PRGKVLGG SSINGMIY+RG   D++ W A GN GWG+ DVLP 
Sbjct: 67  FKTETQPGLQGRALSYPRGKVLGGCSSINGMIYMRGQAGDYDGWAAEGNAGWGWQDVLPL 126

Query: 122 FRKSEMHHGGSSEYHGGDGELYVSPAN-RHAASEAFVESALRAGHSYNPDFNGATQEGAG 180
           F++SE H  G SE+HG  G+  V          +AF  +A ++G +   DFN    EG G
Sbjct: 127 FKQSENHFAGDSEFHGAAGQWRVERQRLSWPILDAFRTAAEQSGIASIDDFNQGDNEGCG 186

Query: 181 YYDVTIRDGRRWSTATAFLKPVRHRSNLTVLTHTHVESIVLLGKQATGVQALIKGSRVHL 240
           Y+ V  + G RW+ A AFLKP+R R+NLTVLT   V+ ++L   +A+ V A  +      
Sbjct: 187 YFQVNQKAGIRWNAAKAFLKPIRQRANLTVLTDVEVDRVLLENGRASAVSARWQDQAKTF 246

Query: 241 RARKEVILSAGAFGSPHLLMLSGIGSAAELEPQGIAPRHELPGVGQNLQDHADVVLCYKS 300
           +ARKE++L AGA GSP +L  SGIG    L+  GI   HELPGVG NLQDH  + L YK 
Sbjct: 247 KARKEIVLCAGAVGSPGILQRSGIGPRPLLQKLGIGVTHELPGVGGNLQDHLQLRLIYKL 306

Query: 301 NDTSLLGFSLSGGV--KMGKAMFDYARHRNGPVASNCAEAGAFLKTDPGLERPDIQLHSV 358
            +   L   ++G +  KMG  +  Y   R+GP++   ++ GAF ++ P     +++ H  
Sbjct: 307 ENARTLN-QIAGTLWGKMGMGL-RYLYDRSGPLSMAPSQLGAFARSGPEQTSANLEYHVQ 364

Query: 359 IGTVDDHNRKLHWGHGFSCHVCVLRPKSIGSVGLASPDPRKAPRIDPNFLAHDDDVATLL 418
             +++     LH    F+  VC LRP+S G + + S DPR+AP I PN+L+H +D+    
Sbjct: 365 PLSLERFGEPLHAFPAFTASVCDLRPQSRGRIDIRSADPREAPLIQPNYLSHPEDLRVAA 424

Query: 419 KGYRITRDIIAQTPMASF-GLRDMYSAGLHNDEQLIELLRKRTDTIYHPIGTCKMGQDEM 477
              R+TR I++   + +F  +  +    L ++EQL E   +   TI+HP+GTC+MG D  
Sbjct: 425 DAIRLTRRIVSAPALQAFKPVEYLPGDSLQSEEQLHEAAARIGTTIFHPVGTCRMGNDAH 484

Query: 478 AVVDSQLRVHGIEGLRVVDASIMPTLVGGNTNAAAIMIAERAAE 521
           AVVD++LRVHGI GLR+ DASIMP +  GNT +  +MIAE+AA+
Sbjct: 485 AVVDAELRVHGIPGLRIADASIMPRITSGNTCSPTLMIAEKAAQ 528


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: 746
Number of extensions: 30
Number of successful extensions: 5
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: 549
Length adjustment: 35
Effective length of query: 491
Effective length of database: 514
Effective search space:   252374
Effective search space used:   252374
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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Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

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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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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 preprint 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

GapMind for catabolism of small carbon sources