Alignments for a candidate for dddA in Dinoroseobacter shibae DFL-12

GapMind for catabolism of small carbon sources

Alignments for a candidate for dddA in Dinoroseobacter shibae DFL-12

Align 3-hydroxypropionate dehydrogenase (EC 1.1.1.59) (characterized)
to candidate 3607390 Dshi_0804 glucose-methanol-choline oxidoreductase (RefSeq)

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



>FitnessBrowser__Dino:3607390
          Length = 540

 Score =  439 bits (1129), Expect = e-127
 Identities = 244/544 (44%), Positives = 330/544 (60%), Gaps = 21/544 (3%)

Query: 37  DYIVVGAGTAGCLLANRLSADPANRVLLIEAGGRDNYHWIHIPVGYLYCINNPRTDWRFR 96
           DY+V+GAG+AGC++ANRLS D  N+V+L+EAG  D   WIHIPVGY   ++NP  DW ++
Sbjct: 4   DYVVIGAGSAGCVVANRLSTDARNKVVLLEAGPPDTNPWIHIPVGYFKTMHNPTVDWCYK 63

Query: 97  TEPDPGLNGRSLIYPRGKTLGGCSSINGMLYLRGQARDYDGWAELTGDDAWRWDNCLPDF 156
           T+ DPGLNGRS+ +PRGK LGG SS+NG+LY+RGQ  DYD W ++ G+  W WD+ LP F
Sbjct: 64  TQADPGLNGRSIDWPRGKVLGGSSSLNGLLYVRGQPEDYDRWRQM-GNAGWGWDDVLPLF 122

Query: 157 MRHEDHYRLDEGGDADPDHYKFHGHGGEWRIEKQRLKWQVLADFATAAVEAGVPRTRDFN 216
            R E + R      ADP    +HG  G   +   R++  +   +  AA   G P   D+N
Sbjct: 123 RRAEANER-----GADP----WHGDDGPLAVSNMRIQRPICDAWVAAAQAMGYPFNPDYN 173

Query: 217 RGDNEGVDAFEVNQRSGWRWNASKAFLRGVEQRGNLTVWHSTQVLKLDFASGEGSEPRCC 276
               EGV  F++  R+G R +A+ A+L+   +R NL++     V +++    EG   R  
Sbjct: 174 GASQEGVGYFQLTTRNGRRCSAAVAYLKPARKRPNLSIITRALVTRIEM---EGK--RVT 228

Query: 277 GVTVERAGKKVVT-TARCEVVLSAGAIGSPQLLQLSGIGPTALLAEHAIPVVADLPGVGE 335
           GVT   AG +  T +AR EV+LS GAI SP +L LSGIG    L  H I     LPGVG+
Sbjct: 229 GVTYTDAGGRAHTVSARREVILSGGAINSPHILMLSGIGDPDQLQAHGITPRHALPGVGK 288

Query: 336 NLQDHLQIRSIYKVKGAKTLNTMANSLIGKAKIGLEYILKRSGPMSMAPSQLCIFTRSSK 395
           NLQDHLQ R ++K     TLN    SL+ +A+I L+Y L R+GPM+MA S    F ++  
Sbjct: 289 NLQDHLQARLVFKC-NEPTLNDEVRSLVNQARIALKYALFRAGPMTMAASLATGFLKTRP 347

Query: 396 EYEHPNLEYHVQPLSLEAFGQPLHDFPAITASVCNLNPTSRGTVRIKSGNPRQAPAISPN 455
           +   P++++HVQP S ++ G+ +H F A T SVC L P SRG +R+   +PR  P I PN
Sbjct: 348 DIATPDIQFHVQPWSADSPGEGVHPFSAFTMSVCQLRPESRGEIRLAGPDPRTYPTIHPN 407

Query: 456 YLSTEEDRQVAADSLRVTRHIASQPAFAKYDPEEFKPGVQYQSDEDLARL--AGDIGTTI 513
           YLSTE D     + +++ R IA     A    EEF+P      D+D A L  A     +I
Sbjct: 408 YLSTETDCATLTEGVKIARRIARADPLAGKIAEEFRPPANLALDDDAATLDWARSNSVSI 467

Query: 514 FHPVGTAKMGRDDDPMAVVDSHLRVRGVTGLRVVDASIMPTITSGNTNSPTLMIAEKAAG 573
           +HP GT KMG    P AVVD+ LRV G++GLRV D SIMP I SGNTN+P +MI EK + 
Sbjct: 468 YHPTGTCKMG--TGPGAVVDARLRVHGLSGLRVADCSIMPEIVSGNTNAPAIMIGEKLSD 525

Query: 574 WILK 577
            +L+
Sbjct: 526 MVLE 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: 935
Number of extensions: 46
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: 540
Length adjustment: 36
Effective length of query: 543
Effective length of database: 504
Effective search space:   273672
Effective search space used:   273672
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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Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

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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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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
the source code
instructions for running GapMind on your computer

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

GapMind for catabolism of small carbon sources