GapMind for catabolism of small carbon sources

 

Alignments for a candidate for dddA in Novosphingobium fuchskuhlense FNE08-7

Align 3-hydroxypropionate dehydrogenase (EC 1.1.1.59) (characterized)
to candidate WP_067911515.1 AQZ52_RS13155 choline dehydrogenase

Query= metacyc::MONOMER-15202
         (579 letters)



>NCBI__GCF_001519075.1:WP_067911515.1
          Length = 555

 Score =  384 bits (986), Expect = e-111
 Identities = 228/541 (42%), Positives = 310/541 (57%), Gaps = 16/541 (2%)

Query: 36  FDYIVVGAGTAGCLLANRLSADPANRVLLIEAGGRDNYHWIHIPVGYLYCINNPRTDWRF 95
           FDYI+VGAG+AGC+LA+RLSAD  ++VL++E GG D   +I +P      +N  R +W +
Sbjct: 8   FDYIIVGAGSAGCVLADRLSADGKHKVLVLEFGGSDQSIYIQMPSALAIPMNTTRWNWHY 67

Query: 96  RTEPDPGLNGRSLIYPRGKTLGGCSSINGMLYLRGQARDYDGWAELTGDDAWRWDNCLPD 155
            +EP+PGL+GR L  PRGK LGG SSING++Y+RG   D++ W E  G   W + + LP 
Sbjct: 68  ESEPEPGLDGRVLHTPRGKGLGGSSSINGLVYIRGNPLDFERWEE-EGARGWNYASVLPY 126

Query: 156 FMRHEDHYRLDEGGDADPDHYKFHGHGGEWRIEKQRLKWQVLADFATAAVEAGVPRTRDF 215
           F R E   R DEGGD      ++ G  G        L+  +   +  AA +AG   T D 
Sbjct: 127 FKRAE---RRDEGGD------EYRGSDGPLDTRYGTLENPLNQAWLDAASQAGYALTDDV 177

Query: 216 NRGDNEGVDAFEVNQRSGWRWNASKAFLRGVEQRGNLTVWHSTQVLKLDFASGEGSEPRC 275
           N    EG    ++  R+G R +A+KA+LR   +R NLTV   T   ++     EG   R 
Sbjct: 178 NGYRQEGFGRMDMTVRNGERCSAAKAYLRPAMRRSNLTVLQHTLATRVVM---EGK--RA 232

Query: 276 CGVTVERAGKKVVTTARCEVVLSAGAIGSPQLLQLSGIGPTALLAEHAIPVVADLPGVGE 335
            GV +ER GK+ +  A  EV+L+ G I SPQLL+LSGIGP A LA+H I VVAD PGVG 
Sbjct: 233 VGVEIERYGKRSIVKAGREVILAGGPINSPQLLKLSGIGPAAELAQHGIAVVADRPGVGA 292

Query: 336 NLQDHLQIRSIYKVKGAKTLNTMANSLIGKAKIGLEYILKRSGPMSMAPSQLCIFTRSSK 395
           NLQDHL+           TL   AN L GK  +G  ++  +SG  +    + C F RS  
Sbjct: 293 NLQDHLEFYFQMACTQPVTLYKYAN-LFGKGLVGARWLFLKSGLGATNHFETCGFIRSKA 351

Query: 396 EYEHPNLEYHVQPLSLEAFGQPLHDFPAITASVCNLNPTSRGTVRIKSGNPRQAPAISPN 455
              +P+++YH  P+++   G  L       A V  +   SRGTV ++S +P   P I  N
Sbjct: 352 GIRYPDIQYHFFPMAVSYDGNSLASEHGFQAHVGPMRSKSRGTVTLRSADPADKPVIRFN 411

Query: 456 YLSTEEDRQVAADSLRVTRHIASQPAFAKYDPEEFKPGVQYQSDEDLARLAGDIGTTIFH 515
           Y++  +D +     +R+TR I  QPAFA +   E +PG    SDE +         + +H
Sbjct: 412 YMTHPDDIEEMRACVRLTREIFQQPAFAPWRGREIQPGADVTSDEAIDAFIRQKVESAYH 471

Query: 516 PVGTAKMGRDDDPMAVVDSHLRVRGVTGLRVVDASIMPTITSGNTNSPTLMIAEKAAGWI 575
           P  T KMG  +DPMAVVD  LRV GV GLRVVD+S+MP++T+GN N+PT+MI EK A  I
Sbjct: 472 PSCTCKMGAVNDPMAVVDPELRVIGVEGLRVVDSSVMPSVTTGNLNAPTIMIGEKGADHI 531

Query: 576 L 576
           L
Sbjct: 532 L 532


Lambda     K      H
   0.318    0.135    0.418 

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: 944
Number of extensions: 39
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: 579
Length of database: 555
Length adjustment: 36
Effective length of query: 543
Effective length of database: 519
Effective search space:   281817
Effective search space used:   281817
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 53 (25.0 bits)

This GapMind analysis is from Sep 24 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