GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__Burk376:H281DRAFT_03365
          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.

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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