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

GapMind for catabolism of small carbon sources

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

Align 3-hydroxypropionate dehydrogenase (EC 1.1.1.59) (characterized)
to candidate 3608021 Dshi_1428 glucose-methanol-choline oxidoreductase (RefSeq)

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



>FitnessBrowser__Dino:3608021
          Length = 544

 Score =  230 bits (587), Expect = 1e-64
 Identities = 173/547 (31%), Positives = 264/547 (48%), Gaps = 53/547 (9%)

Query: 36  FDYIVVGAGTAGCLLANRLSADPANRVLLIEAGGRDNYHWIHIPVGYLYCINNPRTDWRF 95
           +D+IV+G G+AG     +L+   A R+L++EAG  D+   +H    +   +    T W F
Sbjct: 46  YDFIVIGTGSAGAACVYQLAQTGA-RILVLEAGRNDDLEEVHDSRLWAASLGTDATKW-F 103

Query: 96  RTEPDPGLNGRSLIYPRGKTLGGCSSINGMLYLRGQARDYDGWAELTGDDAWRWDNCLPD 155
            T P    +GR+ ++PRG  LGG S++N M+Y RG   D+D W E  G   W +++ LP 
Sbjct: 104 ETLPSSHTDGRNHMWPRGNVLGGTSALNAMVYARGHRTDFDVW-ETMGATGWSYEDVLPH 162

Query: 156 FMRHEDHYRLDEGGDADPDHYKFHGHGGEWRIEKQR--LKWQVLADFATAAVEAGVPRTR 213
           FM  E +   + GG+         G  G   + + +   + +    F  AA   G   T 
Sbjct: 163 FMAMESY---EPGGEN-------RGTSGPIFVSQPQDPHRHEGAVAFMDAAAGLGYKETP 212

Query: 214 DFNRGDNEGVDAFEVNQRSGWRWNASKAFLRGVEQRGNLTVWHSTQVLKLDFASGEGSEP 273
            FN     G    + N +   R +++ AFLR   + GN+T+     V KL     EG+  
Sbjct: 213 SFNSDRMSGQAWIDFNIKDQRRQSSAVAFLRPAIENGNITLLTDAPVQKLTL---EGT-- 267

Query: 274 RCCGVTVERAGKKVVTTARCEVVLSAGAIGSPQLLQLSGIGPTALLAEHAIPVVADLPGV 333
           +C GVT    G  V   A  EV+LSAGAI SP+LL LSGIG  + L +  I  V DLP V
Sbjct: 268 KCTGVTYLHNGAPVSVRAANEVILSAGAIDSPRLLMLSGIGIASDLRQVGIDAVVDLP-V 326

Query: 334 GENLQDHLQIRSI-YKVKGAKTLNTMANSLIGKAKIGLEYILKRSGPMSMAPSQLCIFTR 392
           G  LQDH+    + Y+ KG   ++   +S +        Y+ +RS P   +P  + ++  
Sbjct: 327 GVGLQDHILGAGVNYEAKGPVPVSHYNHSEV--------YMWERSDPGLRSPDMIALYVS 378

Query: 393 SSKEYEHPNLEYHVQPLSLEAFGQPLHDFPAITASVCNLNPTSRGTVRIKSGNPRQAPAI 452
                    L+Y              H +  ++       P SRG V++ S +   AP I
Sbjct: 379 VPFASTGHKLDYE-------------HGYCILSGVA---TPQSRGYVKLASDDIADAPII 422

Query: 453 SPNYLSTEEDRQVAADSLRVTRHIASQPAFAKYDPEEFKPGVQYQ-SDEDLARLAGDIGT 511
             NYL+ E+D +    +  + R + +  A+A++   E  P    + +D +          
Sbjct: 423 ETNYLAEEQDWKSYRAATELCRELGASDAYAEFRKRESLPQKDGELTDAEWRDFLSASVN 482

Query: 512 TIFHPVGTAKMGRDDDPMAVVDSHLRVRGVTGLRVVDASIMPTITSGNTNSPTLMIAEKA 571
           T FHP  T ++G+      VV+  LRV+G+ GLRV DAS+MP IT+ NTN+PT+MI  +A
Sbjct: 483 TYFHPTSTCQIGK------VVEPDLRVKGIEGLRVADASVMPQITTSNTNAPTMMIGWRA 536

Query: 572 AGWILKS 578
              I K+
Sbjct: 537 GDMISKA 543


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: 848
Number of extensions: 52
Number of successful extensions: 9
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: 544
Length adjustment: 36
Effective length of query: 543
Effective length of database: 508
Effective search space:   275844
Effective search space used:   275844
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, 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

GapMind for catabolism of small carbon sources