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

GapMind for catabolism of small carbon sources

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

Align 3D-(3,5/4)-trihydroxycyclohexane-1,2-dione acylhydrolase (ring-opening) (EC 3.7.1.22) (characterized)
to candidate 3607861 Dshi_1269 thiamine pyrophosphate protein central region (RefSeq)

Query= BRENDA::Q9L3I0
         (626 letters)



>FitnessBrowser__Dino:3607861
          Length = 621

 Score =  553 bits (1425), Expect = e-162
 Identities = 301/629 (47%), Positives = 398/629 (63%), Gaps = 17/629 (2%)

Query: 6   LREDPMGKTIRLTMAQAVAHFLKVQMTIVDGKKVPIFGGVWAIFGHGNVAGIGEALYQVR 65
           +RED    TIRLT AQA+  +L  Q    DG +  + GG + IFGHGNV  +GEAL+  R
Sbjct: 1   MRED----TIRLTTAQAIIRYLNAQFIETDGTRQRVCGGGFGIFGHGNVTCLGEALHDHR 56

Query: 66  EELTTYRAHNEQGMAHAAIAYAKANFRTRFMACTSSIGPGALNMVTAAGVAHVNRIPVLF 125
           E L  YR  NEQ M  AA AYAK + R RFM CT+S GPG  N++TA+ +AH NR+P+L 
Sbjct: 57  ETLPLYRGQNEQSMGFAAAAYAKYHLRRRFMFCTASAGPGTANLLTASALAHANRLPMLM 116

Query: 126 LPGDVFANRAPDPVLQQIEDSATASVSANDAFRSVSRYFDRITRPEQIITALKRAMQVLT 185
           L GD F  R PDPVLQQ+E     ++  NDAF +V+RY+DRIT P Q+I +L  A+  + 
Sbjct: 117 LCGDTFLTRLPDPVLQQLEHYGNPALGLNDAFHAVTRYWDRITHPAQVIQSLPAALATML 176

Query: 186 DPLDCGPVTLSLCQDVQAEAYDYPESLFAEKVWTTRRPQPDADELANAIALIKASQKPVI 245
           DP DCGP  L+L QDVQ  AYDYP + F EK    RR  PDADE+A A AL++++++PVI
Sbjct: 177 DPADCGPAFLALPQDVQGWAYDYPRAFFEEKTHRIRRITPDADEVAEAAALLRSAERPVI 236

Query: 246 VAGGGVLYSQATKELAAFAEAHGIPVVVSQAGKSAINETHPLALGSVGVTGTSAANAIAE 305
           +AGGGV YS A  EL  FAEAHGIPV+ + AG++ +   HPL +G VGVTG+ +ANAIAE
Sbjct: 237 IAGGGVQYSGAVAELTGFAEAHGIPVIETIAGRANLLADHPLNIGPVGVTGSDSANAIAE 296

Query: 306 ETDLVIAVGTRCQDFTTGSWALFKNDSLKMIGLNIAAYDAVKHDSHPLVADAREGLKALS 365
           + D+++AVGTR QDFTTGSW  F  ++ + I LN A +DA KH + P+V DA+ GL AL 
Sbjct: 297 QADVILAVGTRLQDFTTGSWTAFAQEA-RFIALNAARHDAGKHRALPIVGDAKLGLVALE 355

Query: 366 AGLSGWKAPAALAEKAAAEKKIWMEAAARAMATTNAALPSDAQVIGAVARTIGGENTTVL 425
           A L  ++ P A    A  E+K W    A  +   N    S AQ IG V   +      V+
Sbjct: 356 AALGDYRCPEAWRNYAQTERKGWDAYVADNVRPGNRP-NSYAQAIG-VVNALCEPRDRVV 413

Query: 426 CAAGGLPGELHKLWPATAPGSYHMEYGFSCMGYEIAGGLGAKMAR----PERDVVVMVGD 481
            AAGGLP E+   W     G+  +E+GFSCMGYEIAGG GA++A+    PE D +V  GD
Sbjct: 414 AAAGGLPAEVTANWRTLDIGTVDVEFGFSCMGYEIAGGWGARIAQTEVEPEADTIVFCGD 473

Query: 482 GSYMMMNSELATSVMLGLKLNIIVLDNRGYGCINRLQMGTGGANFNNLLKDSYHEVMPE- 540
           GSY++MNS++ +SV+   K+ ++VLDN G+  IN+LQ  TG  +FNNLL D+    +PE 
Sbjct: 474 GSYLLMNSDIYSSVLTRKKMIVLVLDNGGFAVINKLQNNTGNESFNNLLADA--PTIPEA 531

Query: 541 --IDFRAHAESMGAIAVKVASIAELEQALADSRKNDRTSVFVIDTDPLITTEAGGH-WWD 597
             +DF AHA +MGA A +VA+  EL +A   ++ +D+T+V V+  D        GH WW+
Sbjct: 532 FGVDFVAHAAAMGAEATQVANADELAEAFKAAKASDKTTVIVMSVDAYDGWTTQGHTWWE 591

Query: 598 VAVPEVSSRSEVNRAHEAYVKARAAQRVG 626
           V  P V+   +V   H      RA QR G
Sbjct: 592 VGTPHVTDNPKVREKHLEIEAERAKQRRG 620


Lambda     K      H
   0.318    0.131    0.382 

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: 960
Number of extensions: 36
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: 626
Length of database: 621
Length adjustment: 37
Effective length of query: 589
Effective length of database: 584
Effective search space:   343976
Effective search space used:   343976
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: 54 (25.4 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