GapMind for catabolism of small carbon sources

 

Aligments for a candidate for etoh-dh-nad in Dinoroseobacter shibae DFL-12

Align alcohol dehydrogenase (EC 1.1.1.1) (characterized)
to candidate 3608021 Dshi_1428 glucose-methanol-choline oxidoreductase (RefSeq)

Query= BRENDA::Q76HN6
         (526 letters)



>lcl|FitnessBrowser__Dino:3608021 Dshi_1428 glucose-methanol-choline
           oxidoreductase (RefSeq)
          Length = 544

 Score =  301 bits (772), Expect = 3e-86
 Identities = 198/531 (37%), Positives = 274/531 (51%), Gaps = 42/531 (7%)

Query: 2   EFDYLIVGAGSAGCVLANRLSADPSVTVCLLEAGPEDRSPLIHTPLGLAAILPTRHVNWA 61
           E+D++++G GSAG     +L A     + +LEAG  D    +H     AA L T    W 
Sbjct: 45  EYDFIVIGTGSAGAACVYQL-AQTGARILVLEAGRNDDLEEVHDSRLWAASLGTDATKW- 102

Query: 62  FKTTPQPGLGGRVGYQPRGKVLGGSSSINGMIYIRGHQDDFNDWQALGNEGWGFDDVLPY 121
           F+T P     GR    PRG VLGG+S++N M+Y RGH+ DF+ W+ +G  GW ++DVLP+
Sbjct: 103 FETLPSSHTDGRNHMWPRGNVLGGTSALNAMVYARGHRTDFDVWETMGATGWSYEDVLPH 162

Query: 122 FRKSEMHHGGSSEYHGGDGELYVSPA---NRHAASEAFVESALRAGHSYNPDFNGATQEG 178
           F   E +  G  E  G  G ++VS     +RH  + AF+++A   G+   P FN     G
Sbjct: 163 FMAMESYEPGG-ENRGTSGPIFVSQPQDPHRHEGAVAFMDAAAGLGYKETPSFNSDRMSG 221

Query: 179 AGYYDVTIRDGRRWSTATAFLKPVRHRSNLTVLTHTHVESIVLLGKQATGVQALIKGSRV 238
             + D  I+D RR S+A AFL+P     N+T+LT   V+ + L G + TGV  L  G+ V
Sbjct: 222 QAWIDFNIKDQRRQSSAVAFLRPAIENGNITLLTDAPVQKLTLEGTKCTGVTYLHNGAPV 281

Query: 239 HLRARKEVILSAGAFGSPHLLMLSGIGSAAELEPQGIAPRHELPGVGQNLQDHADVVLCY 298
            +RA  EVILSAGA  SP LLMLSGIG A++L   GI    +LP VG  LQDH       
Sbjct: 282 SVRAANEVILSAGAIDSPRLLMLSGIGIASDLRQVGIDAVVDLP-VGVGLQDH------- 333

Query: 299 KSNDTSLLGFSLSGGVKMGKAMFDYARHRNGPVA---SNCAEAGAFLKTDPGLERPDIQL 355
                 +LG  ++   K             GPV     N +E   + ++DPGL  PD+  
Sbjct: 334 ------ILGAGVNYEAK-------------GPVPVSHYNHSEVYMWERSDPGLRSPDMIA 374

Query: 356 HSVIGTVDDHNRKLHWGHGFSCHVCVLRPKSIGSVGLASPDPRKAPRIDPNFLAHDDDVA 415
             V         KL + HG+     V  P+S G V LAS D   AP I+ N+LA + D  
Sbjct: 375 LYVSVPFASTGHKLDYEHGYCILSGVATPQSRGYVKLASDDIADAPIIETNYLAEEQDWK 434

Query: 416 TLLKGYRITRDIIAQTPMASFGLRDM--YSAGLHNDEQLIELLRKRTDTIYHPIGTCKMG 473
           +      + R++ A    A F  R+      G   D +  + L    +T +HP  TC++G
Sbjct: 435 SYRAATELCRELGASDAYAEFRKRESLPQKDGELTDAEWRDFLSASVNTYFHPTSTCQIG 494

Query: 474 QDEMAVVDSQLRVHGIEGLRVVDASIMPTLVGGNTNAAAIMIAERAAEWIA 524
           +    VV+  LRV GIEGLRV DAS+MP +   NTNA  +MI  RA + I+
Sbjct: 495 K----VVEPDLRVKGIEGLRVADASVMPQITTSNTNAPTMMIGWRAGDMIS 541


Lambda     K      H
   0.319    0.137    0.419 

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: 744
Number of extensions: 43
Number of successful extensions: 8
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: 526
Length of database: 544
Length adjustment: 35
Effective length of query: 491
Effective length of database: 509
Effective search space:   249919
Effective search space used:   249919
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 52 (24.6 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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint 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