GapMind for catabolism of small carbon sources

 

Alignments for a candidate for dddA in Pseudomonas fluorescens FW300-N1B4

Align 3-hydroxypropionate dehydrogenase (EC 1.1.1.59) (characterized)
to candidate Pf1N1B4_2416 Choline dehydrogenase (EC 1.1.99.1)

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



>FitnessBrowser__pseudo1_N1B4:Pf1N1B4_2416
          Length = 567

 Score =  333 bits (854), Expect = 1e-95
 Identities = 208/543 (38%), Positives = 297/543 (54%), Gaps = 23/543 (4%)

Query: 36  FDYIVVGAGTAGCLLANRLSADPANRVLLIEAGGRDNY--HWIHIPVGYLYCINNPRTDW 93
           FDYI++GAG+AG  LA RL+ D    VLL+EAGG D        +P    + +   R +W
Sbjct: 5   FDYIIIGAGSAGNTLATRLTEDEGVTVLLLEAGGPDYRLDFRTQMPAALAFPLQGRRYNW 64

Query: 94  RFRTEPDPGLNGRSLIYPRGKTLGGCSSINGMLYLRGQARDYDGWAELTGDDAWRWDNCL 153
            + T+P+P ++GR +   RGK LGG S INGM Y+RG A DYD W++L G + W + +CL
Sbjct: 65  AYETDPEPHMDGRRMECGRGKGLGGSSLINGMCYIRGNAMDYDNWSKLPGLEDWTYLDCL 124

Query: 154 PDFMRHEDHYRLDEGGDADPDHYKFHGHGGEWRIEKQRLKW---QVLADFATAAVEAGVP 210
           P       ++R  E  D  P+ Y    HGG+  +     K     +      A V+AG P
Sbjct: 125 P-------YFRKAETRDIGPNDY----HGGDGPVSVTTPKAGNNPLFHAMVEAGVQAGYP 173

Query: 211 RTRDFNRGDNEGVDAFE-VNQRSGWRWNASKAFLRGVEQRGNLTVWHSTQVLKLDFASGE 269
           RT D N    EG    +     +G R + ++ +L   ++R  LT+       K+ F   E
Sbjct: 174 RTEDLNGYQQEGFGPMDRTVTPNGRRASTARGYLDVAKKRSTLTIVTHALTDKILF---E 230

Query: 270 GSEPRCCGVTVERAGKKVVTTARCEVVLSAGAIGSPQLLQLSGIGPTALLAEHAIPVVAD 329
           G         +  A ++V   AR EV+L +GAI SPQ+LQ SG+GP  LL +  IPVV D
Sbjct: 231 GKRAVGVRYLIGAAEERVEVRARKEVLLCSGAIASPQILQRSGVGPAELLKKLDIPVVHD 290

Query: 330 LPGVGENLQDHLQIRSIYKVKGAKTLNTMANSLIGKAKIGLEYILKRSGPMSMAPSQLCI 389
           LPGVGENLQDHL++   Y      +L   +  L  +  IG E++   +G  +    +   
Sbjct: 291 LPGVGENLQDHLELYLQYACTQPVSLYP-SLLLHNQPAIGAEWLFNGTGIGASNQFEAGG 349

Query: 390 FTRSSKEYEHPNLEYHVQPLSLEAFGQPLHDFPAITASVCNLNPTSRGTVRIKSGNPRQA 449
           F R+  E++ PN++YH  P+++   G          A + ++   SRG ++ KS +PR+ 
Sbjct: 350 FIRTRPEFDWPNIQYHFLPVAINYNGSNGVKEHGFQAHMGSMRSPSRGRIQAKSKDPREY 409

Query: 450 PAISPNYLSTEEDRQVAADSLRVTRHIASQPAFAKYDPEEFKPGVQYQSDEDLARLAGDI 509
           P+I  NY++TE+D Q   D +R+TR I  QPA   +   E  PG+  Q+DE L +   + 
Sbjct: 410 PSILFNYMATEQDWQEFRDGIRLTREIMQQPALDAFRGREISPGIDVQTDEQLDKFIREH 469

Query: 510 GTTIFHPVGTAKMGRDDDPMAVVDSHLRVRGVTGLRVVDASIMPTITSGNTNSPTLMIAE 569
             T FHP  + KMG D+  MAVVD   RV G+  LRVVDASIMP IT+GN N+PT+M+AE
Sbjct: 470 AETAFHPSCSCKMGTDE--MAVVDGEGRVHGMQALRVVDASIMPIITTGNLNAPTIMMAE 527

Query: 570 KAA 572
           K A
Sbjct: 528 KIA 530


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: 974
Number of extensions: 53
Number of successful extensions: 7
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: 567
Length adjustment: 36
Effective length of query: 543
Effective length of database: 531
Effective search space:   288333
Effective search space used:   288333
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 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