Align Methylcrotonoyl-CoA carboxylase (EC 6.4.1.4) (characterized)
to candidate Ga0059261_4055 Ga0059261_4055 Acetyl-CoA carboxylase, carboxyltransferase component (subunits alpha and beta)
Query= reanno::Smeli:SM_b21122 (535 letters) >FitnessBrowser__Korea:Ga0059261_4055 Length = 533 Score = 739 bits (1908), Expect = 0.0 Identities = 360/534 (67%), Positives = 429/534 (80%), Gaps = 6/534 (1%) Query: 3 VLRSHISPSSEEFKANRAAMTEAIATIEDAVRLAAAGGGETARERHVSRGKLLPRDRLAT 62 VLRS +SP E F+ N A + V AA GG E +RERH SRGKLLPR+R+ Sbjct: 5 VLRSALSPEDEGFRTNAAHNRALAEKLHADVAQAALGGNEKSRERHTSRGKLLPRERVER 64 Query: 63 LIDPGTPFLEVGATAAYGMYNDDAPGAGLITGIGRISARECMIVCNDPTVKGGTYYPLTV 122 L+DPG+PFLE+G AA MY + PGAG+I GIGR+S R+CMIVCND TVKGGTYYP+TV Sbjct: 65 LLDPGSPFLEIGQLAACDMYEGEVPGAGMIAGIGRVSGRQCMIVCNDATVKGGTYYPMTV 124 Query: 123 KKHLRAQEIAAENRLPCVYLVDSGGANLPNQDEVFPDRDHFGRIFYNQANMSAAGIPQIA 182 KKHLRAQEIA NRLPC+YLVDSGGANLP+Q EVFPD++HFGRIF+NQANMSA GIPQIA Sbjct: 125 KKHLRAQEIAEANRLPCIYLVDSGGANLPHQAEVFPDKEHFGRIFFNQANMSAKGIPQIA 184 Query: 183 VVMGSCTAGGAYVPAMSDEAIIVEKQGTIFLAGPPLVRAATGEVVSAEDLGGADVHTRLS 242 VMGSCTAGGAYVPAMSDE++IV QGTIFLAGPPLV+AATGE +SAEDLGG D+H R S Sbjct: 185 CVMGSCTAGGAYVPAMSDESVIVRNQGTIFLAGPPLVKAATGEEISAEDLGGGDLHGRKS 244 Query: 243 GVADHLARDDAHALALARRAVSALNREKPWTVERIEPEPPLYDPEEIAGIVPADLKTPYE 302 GV DH+A +D HAL + R VS L R++ V ++P PP +D EE+ GIVP D++ PY+ Sbjct: 245 GVVDHVAENDEHALTIVRDIVSHLPRDRTPDVAILDPRPPKFDAEELYGIVPTDVRAPYD 304 Query: 303 IREVIARLVDGSRFDEFKARFGTTLVCGFAHVHGIPVGIVANNGVLFSESAVKGAHFVEL 362 + EVIAR+VDGS F EFKA +G+TLVCGFAH+ G+PV I+ANNGVLFSESAVKGAHF+EL Sbjct: 305 VHEVIARIVDGSEFHEFKAPYGSTLVCGFAHIWGMPVAILANNGVLFSESAVKGAHFIEL 364 Query: 363 CAQRRIPLVFLQNITGFMVGRKYETEGIAKHGAKLVTAVATVKVPKITMLVGGSFGAGNY 422 QRRIPL+FLQNI+GFMVG KYE EGIAKHGAKLVTAVAT VPKIT+L+GGSFGAGNY Sbjct: 365 ACQRRIPLLFLQNISGFMVGGKYEAEGIAKHGAKLVTAVATASVPKITVLIGGSFGAGNY 424 Query: 423 GMCGRAFSPRFLWTWPNSRISVMGGEQAAGVLSSVRGEALKRSGKPWSEEEEARFRQPVL 482 GMCGRA+SPRFL++WPNSRISVMGGEQAA VL++V R W+ E+ F+ P+ Sbjct: 425 GMCGRAYSPRFLFSWPNSRISVMGGEQAASVLATVH-----RDADSWTPEQAETFKAPIR 479 Query: 483 DLFERQSHPLYASARLWDDGVIDPRKSRDVLALSLSAALNAPIEE-TRFGLFRM 535 +E + +P +A+ARLWDDG+IDP ++RDVL L+ +A LNAP+EE TRFG+FRM Sbjct: 480 QKYEDEGNPWHATARLWDDGIIDPAQTRDVLGLAFAATLNAPVEEGTRFGVFRM 533 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: 908 Number of extensions: 33 Number of successful extensions: 4 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: 533 Length adjustment: 35 Effective length of query: 500 Effective length of database: 498 Effective search space: 249000 Effective search space used: 249000 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