Alignments for a candidate for aldox-large in Dinoroseobacter shibae DFL-12

GapMind for catabolism of small carbon sources

Alignments for a candidate for aldox-large in Dinoroseobacter shibae DFL-12

Align glycolaldehyde oxidoreductase large subunit (characterized)
to candidate 3609273 Dshi_2659 aldehyde oxidase and xanthine dehydrogenase molybdopterin binding (RefSeq)

Query= metacyc::MONOMER-18071
         (749 letters)



>FitnessBrowser__Dino:3609273
          Length = 791

 Score =  442 bits (1138), Expect = e-128
 Identities = 279/788 (35%), Positives = 422/788 (53%), Gaps = 46/788 (5%)

Query: 4   VGKPVKRIYDDKFVTGRSTYVDDIRIP-ALYAGFVRSTYPHAIIKRIDVSDALKVNGIVA 62
           +G   KR  D +F+TGR  Y DDI +    YA F+RS   H  I  ID + A  ++G++ 
Sbjct: 7   IGASSKRREDVRFLTGRGRYTDDINLNNQTYAYFLRSEVAHGKINGIDTAAAEGMDGVIR 66

Query: 63  VFTAKEINPLLKGGIRPWPTYIDIRSFRYSERK--AFPENKVKYVGEPVAIVLGQDKYSV 120
           VFTAK+   +  GG+       DI      E K     E KV++VG+P+A+V+ +     
Sbjct: 67  VFTAKDFEGV--GGVPCGWQVTDIHGQPMKEPKHPVLAEGKVRHVGDPIAVVVAESLEQA 124

Query: 121 RDAIDKVVVEYEPLKPVIRMEEAEKDQVI-IHEELKTNISYKIPF---KAGEVDKAFSES 176
           RDA + + ++ E L  V+ M+ A  +    +H++L  N+ Y+  F       VD+A   +
Sbjct: 125 RDAAEAIELDIEELPAVMDMKAALAEGATKVHDDLDDNLCYEWGFVEENRAAVDEAIKNA 184

Query: 177 DKVVRVEAINERLIPNPMEPRGIVSRFEAGT--LSIWYSTQVPHYMRSEF-ARILGIPES 233
             V  +E  N RL+ NPMEPR  V  +  GT   +++ ++Q PH +R    A +LGIPE 
Sbjct: 185 HHVTTLELTNNRLVANPMEPRVAVGDYHPGTQDYTLYTTSQNPHVIRLLMGAFVLGIPEH 244

Query: 234 KIKVSMPDVGGAFGAKVHLMPEELAVVASSIILGRPVRWTATRSEEMLA-SEARHNVFTG 292
           K++V  PDVGG FG+K++   EE  V  +S  +GRPV+WT++RSE  ++ +  R +V   
Sbjct: 245 KLRVVAPDVGGGFGSKIYHYAEEAFVTFASGQIGRPVKWTSSRSEAFVSDAHGRDHVTKI 304

Query: 293 EVAVKRDGTILGIKGKLLLDLGAYITVTA-GIQPLIIPMMIPGPYKIRNLDIESVAVYTN 351
           E+A+  +     ++     ++GAY++  A  I   +   ++ G Y    +     AV+T 
Sbjct: 305 ELALDENHKFTALRCDTYANMGAYLSTFAPSIPTWLHGTLLAGNYTTPLIYTNVKAVFTT 364

Query: 352 TPPITMYRGASRPEATYIIERIMSTVADELGLDDVSIREKNLVT--ELPYTNPFGLRYDS 409
           T P+  YRGA RPEAT+ +ER++   A ELG+D   +R  N +   + PY  P  + YD+
Sbjct: 365 TTPVDAYRGAGRPEATFQLERVVDKAARELGVDPAELRRINFIKPEQFPYDTPVAVTYDT 424

Query: 410 GDYVGLLREGVKRLGYYELKKWAEEERKKGHRVGVGLAYYLEICSFGP------------ 457
           G+Y   L +G++  G    +  A E + +G   G GLA+++E C   P            
Sbjct: 425 GNYHATLEKGLEMAGADTFEARAAESKARGKLRGFGLAHFIEACGIAPSNLVGQLGARAG 484

Query: 458 -WEYAEVRVDERGDVLVVTGTTPHGQGTETAIAQIVADALQIDISRVRVIWGDTDTVAAS 516
            +E A VRV+  G + V+TG+  HGQG ETA  Q+VA+ L ID + + ++ GDT      
Sbjct: 485 LYESATVRVNATGSISVMTGSHSHGQGHETAFPQVVAEMLGIDENMIEIVHGDTANTPMG 544

Query: 517 MGTYGSRSVTIGGSAAIKVAEKILDKMKRIAASTWNVDVQEVQYEKGEFKLKNDPSKKMS 576
           MGTYGSRS+ +GGSA ++  EKI++K K+IAA        +++ + G F +     K ++
Sbjct: 545 MGTYGSRSIAVGGSAMVRATEKIINKAKKIAAHLLEAAEGDIELKDGAFTVAG-TDKSVA 603

Query: 577 WDDVASIAYRSH-------DPGLVEKIIYE-NDVTFPYGVHIATVEVD-DTGVARVLEYR 627
           W DV   AY  H       +PGL E   Y+ ++ T+P G +I  VEVD DTG   VL + 
Sbjct: 604 WGDVTLAAYVPHNYPLEDIEPGLEETAFYDPSNFTYPSGAYICEVEVDPDTGKVDVLAFT 663

Query: 628 AYDDIGKVVNPALAEAQIHGGGVQAVGQALYEQALLNENGQLIV-TYADYYVPTAVEAPK 686
           A DD G V+NP + E Q+HGG  Q +GQAL E    + +GQL+  +Y DY +P A + P 
Sbjct: 664 AADDFGNVINPMIVEGQVHGGVAQGIGQALLENCSYDADGQLLSGSYMDYTMPRADDLPM 723

Query: 687 FTSVFADQYHPSNYPTGSKGVGEAALIVGPAVIIRALEDAI----GTRFT--KTPTTPEE 740
           F    +     ++ P G KG GEA  I  P  ++ A+ DA+     T  T    P TP  
Sbjct: 724 FEVDHSCITPCTHNPLGVKGCGEAGAIGSPPAVVNAVIDALHRAGQTHVTHIDMPLTPSR 783

Query: 741 ILRAIASK 748
           +  AI  K
Sbjct: 784 VWAAIHGK 791


Lambda     K      H
   0.317    0.136    0.394 

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: 1444
Number of extensions: 83
Number of successful extensions: 12
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: 749
Length of database: 791
Length adjustment: 41
Effective length of query: 708
Effective length of database: 750
Effective search space:   531000
Effective search space used:   531000
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: 55 (25.8 bits)

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

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Rules (tab-delimited)
Protein sequences (fasta format)
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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