GapMind for catabolism of small carbon sources

 

Alignments for a candidate for etoh-dh-nad in Pseudomonas fluorescens GW456-L13

Align alcohol dehydrogenase (EC 1.1.1.1) (characterized)
to candidate PfGW456L13_3561 Choline dehydrogenase (EC 1.1.99.1)

Query= BRENDA::Q76HN6
         (526 letters)



>FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3561
          Length = 548

 Score =  416 bits (1070), Expect = e-121
 Identities = 231/526 (43%), Positives = 314/526 (59%), Gaps = 6/526 (1%)

Query: 2   EFDYLIVGAGSAGCVLANRLSADPSVTVCLLEAGPEDRSPLIHTPLGLAAILPTRHVNWA 61
           EFDY++VGAG AGC+LANRLSAD    V LLEAG  D    IH P+G    +     +W 
Sbjct: 7   EFDYIVVGAGPAGCLLANRLSADAQHRVLLLEAGGRDNYAWIHIPVGYLFCIGNPRTDWC 66

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

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

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

Query: 241 RARKEVILSAGAFGSPHLLMLSGIGSAAELEPQGIAPRHELPGVGQNLQDHADVVLCYKS 300
           +ARKE++L AG+ GSP +L  SGIG    LE  GI   HEL G G NLQDH  + L YK 
Sbjct: 247 KARKEIVLCAGSVGSPSILQRSGIGPRPLLERLGIGVAHELSGAGGNLQDHLQLRLIYKL 306

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

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

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

Query: 478 AVVDSQLRVHGIEGLRVVDASIMPTLVGGNTNAAAIMIAERAAEWI 523
           AVVD+QL+VHGI GLR+ DASIMP +  GNT +  +MIAE+AA+ I
Sbjct: 485 AVVDAQLKVHGIPGLRIADASIMPRITSGNTCSPTLMIAEKAAQLI 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: 754
Number of extensions: 29
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: 548
Length adjustment: 35
Effective length of query: 491
Effective length of database: 513
Effective search space:   251883
Effective search space used:   251883
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