Align Methylcrotonoyl-CoA carboxylase (EC 6.4.1.4) (characterized)
to candidate GFF3326 PS417_17020 methylcrotonoyl-CoA carboxylase
Query= reanno::pseudo6_N2E2:Pf6N2E2_2192 (535 letters) >FitnessBrowser__WCS417:GFF3326 Length = 535 Score = 1001 bits (2588), Expect = 0.0 Identities = 501/535 (93%), Positives = 511/535 (95%) Query: 1 MATLHTQLNPRSPEFIANRDAMLGHVEALRTLLAQIRQGGGPKAQERHTSRGKLLPRERI 60 MATLHTQLNPRS EF AN AM V+AL +LLA ++QGGG KAQERHTSRGKLLPRERI Sbjct: 1 MATLHTQLNPRSAEFAANSAAMRQQVDALHSLLAHVQQGGGAKAQERHTSRGKLLPRERI 60 Query: 61 NRLLDPGSPFLEISPLAAHEVYGEDVPAAGVIAGIGRVEGVECMIVANDATVKGGSYYPL 120 NRLLDPGSPFLE+S LAAH+VYGEDVPAAGVIAGIGRVEGVECMIVANDATVKGGSYYPL Sbjct: 61 NRLLDPGSPFLELSQLAAHQVYGEDVPAAGVIAGIGRVEGVECMIVANDATVKGGSYYPL 120 Query: 121 TVKKHLRAQTIAQQNRLPCIYLVDSGGANLPRQDEVFPDREHFGRIFFNQANMSAQGIPQ 180 TVKKHLRAQTIA+QNRLPCIYLVDSGGANLPRQDEVFPDREHFGRIFFNQANMSAQGIPQ Sbjct: 121 TVKKHLRAQTIAEQNRLPCIYLVDSGGANLPRQDEVFPDREHFGRIFFNQANMSAQGIPQ 180 Query: 181 IAVVMGSCTAGGAYVPAMADEAIMVRQQATIFLAGPPLVKAATGEVVSAEDLGGADVHCK 240 IAVVMGSCTAGGAYVPAMADEAIMVRQQATIFLAGPPLVKAATGEVVSAEDLGGADVHCK Sbjct: 181 IAVVMGSCTAGGAYVPAMADEAIMVRQQATIFLAGPPLVKAATGEVVSAEDLGGADVHCK 240 Query: 241 ISGVADHYADSDEHALALARRSVANLNWRKQGELQHRLPIAPLYSGEELYGVVSADAKQP 300 ISGVADHYADSDEHALALARRSVANLNWRKQG L R P+APLYS EELYGV+ ADAKQP Sbjct: 241 ISGVADHYADSDEHALALARRSVANLNWRKQGGLLQRTPVAPLYSSEELYGVIPADAKQP 300 Query: 301 FDVREVIARLVDGSVFDEFKALFGTTLVCGFAHLHGYPIAILANNGILFAEAAQKGAHFI 360 FDVREVIARLVDGSVFDEFKALFGTTLVCGFAHLHGYPIAILANNGILFAEAAQKGAHFI Sbjct: 301 FDVREVIARLVDGSVFDEFKALFGTTLVCGFAHLHGYPIAILANNGILFAEAAQKGAHFI 360 Query: 361 ELACQRGIPLLFLQNITGFMVGQKYEAGGIAKHGAKLVTAVACAKVPKFTVIIGGSFGAG 420 ELACQRGIPLLFLQNITGFMVGQKYEAGGIAKHGAKLVTAVACAKVPKFTVIIGGSFGAG Sbjct: 361 ELACQRGIPLLFLQNITGFMVGQKYEAGGIAKHGAKLVTAVACAKVPKFTVIIGGSFGAG 420 Query: 421 NYGMCGRAYDPRFLWMWPNARIGVMGAEQAAGVLVQVKREQAERSGHPFSAEQEAEIKQP 480 NYGMCGRAYDPRFLWMWPNARIGVMGAEQAAGVLVQVKREQAER G FSAE+EA IKQP Sbjct: 421 NYGMCGRAYDPRFLWMWPNARIGVMGAEQAAGVLVQVKREQAERVGVGFSAEEEAAIKQP 480 Query: 481 ILDQYEEQGHPYYSSARLWDDGVIDPAQTRDVLGLALSASLNAPIEPSRFGVFRM 535 ILDQYE QGHPYYSSARLWDDGVIDP QTRDVL LALSASLNAPIEPSRFGVFRM Sbjct: 481 ILDQYETQGHPYYSSARLWDDGVIDPLQTRDVLALALSASLNAPIEPSRFGVFRM 535 Lambda K H 0.321 0.137 0.411 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: 1146 Number of extensions: 28 Number of successful extensions: 2 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: 535 Length adjustment: 35 Effective length of query: 500 Effective length of database: 500 Effective search space: 250000 Effective search space used: 250000 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