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.
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:
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