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

GapMind for catabolism of small carbon sources

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

Align Methylcrotonoyl-CoA carboxylase (EC 6.4.1.4) (characterized)
to candidate 3607892 Dshi_1300 Propionyl-CoA carboxylase (RefSeq)

Query= reanno::Smeli:SM_b21122
         (535 letters)



>lcl|FitnessBrowser__Dino:3607892 Dshi_1300 Propionyl-CoA
           carboxylase (RefSeq)
          Length = 534

 Score =  810 bits (2091), Expect = 0.0
 Identities = 395/524 (75%), Positives = 451/524 (86%)

Query: 12  SEEFKANRAAMTEAIATIEDAVRLAAAGGGETARERHVSRGKLLPRDRLATLIDPGTPFL 71
           + E  ANRAA   A+A +     LAAAGGGE AR RHV+RGK+LPRDR+A L+DPG+PFL
Sbjct: 11  TSEGAANRAAHLAALAQVSQVAALAAAGGGEAARARHVARGKMLPRDRVANLLDPGSPFL 70

Query: 72  EVGATAAYGMYNDDAPGAGLITGIGRISARECMIVCNDPTVKGGTYYPLTVKKHLRAQEI 131
           EVGATA +G+++  AP  G I G+GR+  ++ M+VCND TVKGGTYYP+TVKKHLRAQEI
Sbjct: 71  EVGATAGHGLHDGAAPCGGAIAGVGRVHGQDVMVVCNDATVKGGTYYPITVKKHLRAQEI 130

Query: 132 AAENRLPCVYLVDSGGANLPNQDEVFPDRDHFGRIFYNQANMSAAGIPQIAVVMGSCTAG 191
           AAE  LPC+YLVDSGGANLPNQDEVFPDRDHFGRIFYNQA MSAAGIPQIAVVMGSCTAG
Sbjct: 131 AAECHLPCIYLVDSGGANLPNQDEVFPDRDHFGRIFYNQARMSAAGIPQIAVVMGSCTAG 190

Query: 192 GAYVPAMSDEAIIVEKQGTIFLAGPPLVRAATGEVVSAEDLGGADVHTRLSGVADHLARD 251
           GAYVPAMSD  IIV+ QGTIFLAGPPLV+AATGEVVSAEDLGG DVHTRLSGVAD LA D
Sbjct: 191 GAYVPAMSDVTIIVKAQGTIFLAGPPLVKAATGEVVSAEDLGGGDVHTRLSGVADALAED 250

Query: 252 DAHALALARRAVSALNREKPWTVERIEPEPPLYDPEEIAGIVPADLKTPYEIREVIARLV 311
           DAHALALAR+AV++LNR  P +V    PE P YDPEE+  +VPA L  PY+I EVIAR+V
Sbjct: 251 DAHALALARQAVASLNRAAPSSVVWQSPEAPAYDPEELLELVPASLSVPYDIHEVIARIV 310

Query: 312 DGSRFDEFKARFGTTLVCGFAHVHGIPVGIVANNGVLFSESAVKGAHFVELCAQRRIPLV 371
           DGSRFD FK RFG TLV GFAH+ G PVGIVANNGVLFSE+A KGAHFVELC+QR+IPLV
Sbjct: 311 DGSRFDAFKPRFGETLVTGFAHIEGCPVGIVANNGVLFSEAAQKGAHFVELCSQRKIPLV 370

Query: 372 FLQNITGFMVGRKYETEGIAKHGAKLVTAVATVKVPKITMLVGGSFGAGNYGMCGRAFSP 431
           FLQNITGFMVGR+YE EGIA+HGAK+VTAVAT  VPKITM+VGGSFGAGNYGM GRA+ P
Sbjct: 371 FLQNITGFMVGRQYENEGIARHGAKMVTAVATTAVPKITMVVGGSFGAGNYGMAGRAYQP 430

Query: 432 RFLWTWPNSRISVMGGEQAAGVLSSVRGEALKRSGKPWSEEEEARFRQPVLDLFERQSHP 491
           RF+W+WP+SRISVMGG QAAGVL++V+ +A++R G  WS +EEA F+QP +++FE QSHP
Sbjct: 431 RFMWSWPSSRISVMGGAQAAGVLATVKRDAIERKGGSWSAQEEAAFKQPTIEMFEAQSHP 490

Query: 492 LYASARLWDDGVIDPRKSRDVLALSLSAALNAPIEETRFGLFRM 535
           LYASARLWDDG++DPRKSR VL+LSL AALNAPIEETRFG+FRM
Sbjct: 491 LYASARLWDDGIVDPRKSRAVLSLSLRAALNAPIEETRFGVFRM 534


Lambda     K      H
   0.320    0.136    0.404 

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: 883
Number of extensions: 36
Number of successful extensions: 1
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: 535
Length of database: 534
Length adjustment: 35
Effective length of query: 500
Effective length of database: 499
Effective search space:   249500
Effective search space used:   249500
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 (21.8 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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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 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

GapMind for catabolism of small carbon sources