GapMind for catabolism of small carbon sources

 

Aligments for a candidate for dddA in Paraburkholderia bryophila 376MFSha3.1

Align 3-hydroxypropionate dehydrogenase (EC 1.1.1.59) (characterized)
to candidate H281DRAFT_03365 H281DRAFT_03365 choline dehydrogenase

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



>lcl|FitnessBrowser__Burk376:H281DRAFT_03365 H281DRAFT_03365 choline
           dehydrogenase
          Length = 546

 Score =  355 bits (912), Expect = e-102
 Identities = 216/547 (39%), Positives = 317/547 (57%), Gaps = 24/547 (4%)

Query: 33  THAFDYIVVGAGTAGCLLANRLSADPANRVLLIEAGGRDNYHWIHIPVGYLYCINNPRTD 92
           ++  DY++VGAGTAGC+LANRL+ DPA +V+L+EAG RD + +IH+P G++  +++P   
Sbjct: 3   SYTADYVIVGAGTAGCVLANRLTEDPAIKVILVEAGERDRHPFIHVPAGFVRLLDHPTVT 62

Query: 93  WRFRTEPDPGLNGRSLIYPRGKTLGGCSSINGMLYLRGQARDYDGWAELTGDDAWRWDNC 152
           WR+RTE D G +GR++++PRG+ LGG S+ING+LY+R  A D D W E +G + W + NC
Sbjct: 63  WRYRTEADAGTSGRAILFPRGRGLGGSSAINGLLYVRPFAEDIDSW-EQSGANGWNFKNC 121

Query: 153 LPDFMRHEDHYRLDEGGDADPDHYKFHGHGGEWRIEKQRLKWQVLADFATAAVEAGVPRT 212
           LP + R E      EG           G  G  ++ + +   ++      AA   G+   
Sbjct: 122 LPFYSRSE---TWTEGSSPQ------RGTHGPIQVSRVKNPPEICGAVVEAAQRTGLDFV 172

Query: 213 RDFNRGDNEGVDAFEVNQ-RSG-WRWNASKAFLRGVEQRGNLTVWHSTQVLKLDFASGEG 270
            D N  D  G   +   Q R G  R +A++ +LR    R NLTV    QV  L+      
Sbjct: 173 DDPN-SDTRGPSIWYYQQTRDGRRRSSAARGYLRPAMARPNLTVVTGLQVSTLEMNGTHV 231

Query: 271 SEPRCCGVT-VERAGKKVVTTARCEVVLSAGAIGSPQLLQLSGIGPTALLAEHAIPVVAD 329
           S     G+     AG  V   A  EV+LSAG +G+P+LL++SGIG  A+L    +     
Sbjct: 232 S-----GINGTTGAGIPVQIRATREVILSAGVVGTPRLLEMSGIGDKAVLDNAGVKTRIA 286

Query: 330 LPGVGENLQDHLQIRSIYKVKGAKTLNTMANSLIGKAKIGLEYILKRSGPMSMAPSQLCI 389
           LPGVG NLQDH  +R  Y+V+GA T N  A+ L   A+  + Y++  +G ++ + + +  
Sbjct: 287 LPGVGNNLQDHYVVRLGYRVRGAGTANERAHGL-ALAREMMRYVVSGTGVLTYSAALVGG 345

Query: 390 FTRSSKEYEHPNLEYHVQPLSL-EAFGQPLHDFPAITASVCNLNPTSRGTVRIKSGNPRQ 448
           F + ++    P++++ + P S  E     L   P ++  V  + P SRG V I S     
Sbjct: 346 FAQ-TRLATRPDVQFVIAPGSFAEGRIGVLESEPGVSCGVWQMRPESRGHVHITSSEITA 404

Query: 449 APAISPNYLSTEEDRQVAADSLRVTRHIASQPAFAKYDPEEFKPGVQYQSDEDLARLAGD 508
           AP I+P+YLS+E DR    + L++ R I +QP  A+Y  +E  PG Q  +DE L +   D
Sbjct: 405 APTIAPSYLSSELDRNTMVEGLKIGRRIFAQPEVARYIVDETVPGRQADTDEALLQYVRD 464

Query: 509 IGTTIFHPVGTAKMGRDDDPMAVVDSHLRVRGVTGLRVVDASIMPTITSGNTNSPTLMIA 568
            G+T++H VGT +MG D+  M+VVDS +RVRG TGLRVVD S+MP+ITS NTN+  LM+A
Sbjct: 465 NGSTVYHAVGTCRMGEDE--MSVVDSEMRVRGTTGLRVVDGSVMPSITSTNTNATVLMLA 522

Query: 569 EKAAGWI 575
           E+AA  I
Sbjct: 523 ERAADMI 529


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: 859
Number of extensions: 36
Number of successful extensions: 6
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: 546
Length adjustment: 36
Effective length of query: 543
Effective length of database: 510
Effective search space:   276930
Effective search space used:   276930
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.

Links

Downloads

Related tools

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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 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