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 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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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