GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__Dino:3607892
          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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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