Align Methylcrotonoyl-CoA carboxylase (EC 6.4.1.4) (characterized)
to candidate GFF1015 PGA1_c10320 methylcrotonoyl-CoA carboxylase beta chain
Query= reanno::Smeli:SM_b21122 (535 letters) >FitnessBrowser__Phaeo:GFF1015 Length = 527 Score = 845 bits (2183), Expect = 0.0 Identities = 412/526 (78%), Positives = 460/526 (87%) Query: 10 PSSEEFKANRAAMTEAIATIEDAVRLAAAGGGETARERHVSRGKLLPRDRLATLIDPGTP 69 PSSE FK NR A +A+ I +A A GGGE +R RH SRGK+LPR R+A L+DPG+P Sbjct: 2 PSSEGFKQNREAHLDALGQISEAAETARMGGGEKSRARHESRGKMLPRRRVANLLDPGSP 61 Query: 70 FLEVGATAAYGMYNDDAPGAGLITGIGRISARECMIVCNDPTVKGGTYYPLTVKKHLRAQ 129 FLE+GATAA+ MY+ APGAG++ GIGR+ +E M+VCND TVKGGTY+P+TVKKHLRAQ Sbjct: 62 FLEIGATAAHAMYDGAAPGAGVVAGIGRVHGQEVMVVCNDATVKGGTYFPMTVKKHLRAQ 121 Query: 130 EIAAENRLPCVYLVDSGGANLPNQDEVFPDRDHFGRIFYNQANMSAAGIPQIAVVMGSCT 189 EIA ENRLPC+YLVDSGGANLP QDEVFPDRDHFGRIFYNQA MSA GI QIAVVMGSCT Sbjct: 122 EIAEENRLPCIYLVDSGGANLPQQDEVFPDRDHFGRIFYNQARMSAKGIAQIAVVMGSCT 181 Query: 190 AGGAYVPAMSDEAIIVEKQGTIFLAGPPLVRAATGEVVSAEDLGGADVHTRLSGVADHLA 249 AGGAYVPAMSD IIV++QGTIFLAGPPLV+AATGEVVSAEDLGG DVHTRLSGVAD+LA Sbjct: 182 AGGAYVPAMSDVTIIVKEQGTIFLAGPPLVKAATGEVVSAEDLGGGDVHTRLSGVADYLA 241 Query: 250 RDDAHALALARRAVSALNREKPWTVERIEPEPPLYDPEEIAGIVPADLKTPYEIREVIAR 309 DDAHALALARRAV +LN KP TV PE P YDPEEI G+VP DL+TPY+IREVIAR Sbjct: 242 EDDAHALALARRAVQSLNITKPLTVNWASPEEPAYDPEEILGVVPGDLRTPYDIREVIAR 301 Query: 310 LVDGSRFDEFKARFGTTLVCGFAHVHGIPVGIVANNGVLFSESAVKGAHFVELCAQRRIP 369 LVDGSRFDEFK RFG TLV GFAHV G PVGI+ANNGVLFSE+A KGAHFVELC+QR+IP Sbjct: 302 LVDGSRFDEFKPRFGETLVTGFAHVKGCPVGIIANNGVLFSEAAQKGAHFVELCSQRKIP 361 Query: 370 LVFLQNITGFMVGRKYETEGIAKHGAKLVTAVATVKVPKITMLVGGSFGAGNYGMCGRAF 429 LVFLQNITGFMVGRKYE EGIA+HGAK+VTAVAT VPK+TMLVGGSFGAGNYGM GRA+ Sbjct: 362 LVFLQNITGFMVGRKYENEGIARHGAKMVTAVATTNVPKVTMLVGGSFGAGNYGMSGRAY 421 Query: 430 SPRFLWTWPNSRISVMGGEQAAGVLSSVRGEALKRSGKPWSEEEEARFRQPVLDLFERQS 489 PRFLW+WPNSRISVMGGEQAAGVL++V+ +A++R G WS EEEA F+QP +D+FE QS Sbjct: 422 QPRFLWSWPNSRISVMGGEQAAGVLATVKRDAIERQGGSWSTEEEASFKQPTIDMFEEQS 481 Query: 490 HPLYASARLWDDGVIDPRKSRDVLALSLSAALNAPIEETRFGLFRM 535 HPLYASARLWDDG+IDPRKSRDVLALSLSAALNAPIE+TRFG+FRM Sbjct: 482 HPLYASARLWDDGIIDPRKSRDVLALSLSAALNAPIEDTRFGVFRM 527 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: 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: 527 Length adjustment: 35 Effective length of query: 500 Effective length of database: 492 Effective search space: 246000 Effective search space used: 246000 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