Align Methylcrotonoyl-CoA carboxylase (EC 6.4.1.4) (characterized)
to candidate GFF926 PGA1_c09420 pyruvate carboxylase Pyc
Query= reanno::SB2B:6937189 (673 letters) >FitnessBrowser__Phaeo:GFF926 Length = 1188 Score = 378 bits (970), Expect = e-108 Identities = 197/449 (43%), Positives = 290/449 (64%), Gaps = 9/449 (2%) Query: 2 FNKLLIANRGEIACRVIRTARDMGIKTVAVYSDADRDARHVALADESFYLGES-APASSY 60 F K+LIANRGEIA RV+R A +MG KTVAVY++ D+ H ADE++ +GE P ++Y Sbjct: 46 FKKILIANRGEIAIRVMRAANEMGKKTVAVYAEEDKLGLHRFKADEAYRIGEGMGPVAAY 105 Query: 61 LRGELIIDIAKKCGAEAIHPGYGFLSENAAFARACEASGIAFVGPGSDAIDAMGSKSAAK 120 L + II +AK+CGA+AIHPGYG LSEN F AC +GI F+GP ++ + A+G K++A+ Sbjct: 106 LSIDEIIRVAKECGADAIHPGYGLLSENPDFVDACARNGITFIGPKAETMRALGDKASAR 165 Query: 121 LIMEKAGVPLVPGYHGDDQSDATLLAEAKKIGYPLLIKAAYGGGGKGMRIVESESELKAA 180 + A VP++P + EA ++GYPL++KA++GGGG+GMR + SE EL+ Sbjct: 166 RVAIDADVPVIPATEVLGNDMDAIRKEAAEVGYPLMLKASWGGGGRGMRPIHSEDELEEK 225 Query: 181 IDSARREAASSFGNDKLLMERYLRQPRHVEVQVFADSQGNCVYLSDRDCSIQRRHQKVVE 240 + RREA ++FGN + +E+ + + RHVEVQ+ D G +L +RDCS+QRR+QKVVE Sbjct: 226 VLEGRREAEAAFGNGEGYLEKMITRARHVEVQILGDKHGEIYHLYERDCSVQRRNQKVVE 285 Query: 241 EAPAPGLPDSLRKQMGEAAVAAAKAIDYRGAGTVEFLLDV-DMSFFFMEMNTRLQVEHPV 299 APAP L + R ++ + + ++Y AGTVEFL+D+ D F+F+E+N R+QVEH V Sbjct: 286 RAPAPYLTEEQRTEICDLGRKICQHVNYECAGTVEFLMDMNDGKFYFIEVNPRVQVEHTV 345 Query: 300 TEMVTGQDLVKWQLLVAAGAQL-----PLEQHEIQIHGHAFEVRIYAEDPNNEFLPASGK 354 TE VTG D+V+ Q+L+A G + Q EIQ++GHA + R+ EDP N F+P G+ Sbjct: 346 TEEVTGIDIVQAQILIAEGKTIAEATGKASQDEIQLNGHALQTRVTTEDPLNNFIPDYGR 405 Query: 355 LTFLREPEPSRHVRIDSGVR-ENDVISNYYDPMIAKLIVWDESRPRALARLTRALGDYRV 413 +T R +R+D G VI+ YYD ++ K+ + +A+AR+ RAL ++RV Sbjct: 406 ITAYRS-ATGMGIRLDGGTAYAGGVITRYYDSLLTKVTAKAPTPEKAIARMDRALREFRV 464 Query: 414 GGLKHNIEFLSNIAEHPAFAQANFSTDFI 442 G+ NI F+ N+ +HP F ++T FI Sbjct: 465 RGVSTNIAFVENLLKHPTFLSNEYTTKFI 493 Score = 45.4 bits (106), Expect = 2e-08 Identities = 28/65 (43%), Positives = 32/65 (49%) Query: 596 APMNGTVVTHLVAAGDKVSAGQGLLVMEAMKMEYTIEAPFDGVVSEFFFAPGELVSDGTL 655 APM G V + V G V G LL +EAMKME I A D VV PG + L Sbjct: 1124 APMPGVVASVAVQVGQPVHEGDMLLTIEAMKMETGIHAERDAVVKAVHVQPGGQIDAKDL 1183 Query: 656 LLALE 660 L+ LE Sbjct: 1184 LIELE 1188 Lambda K H 0.317 0.134 0.380 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: 1755 Number of extensions: 76 Number of successful extensions: 8 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 3 Number of HSP's successfully gapped: 2 Length of query: 673 Length of database: 1188 Length adjustment: 43 Effective length of query: 630 Effective length of database: 1145 Effective search space: 721350 Effective search space used: 721350 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 56 (26.2 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