Align Methylcrotonoyl-CoA carboxylase subunit alpha, mitochondrial; MCCase subunit alpha; 3-methylcrotonyl-CoA carboxylase 1; 3-methylcrotonyl-CoA:carbon dioxide ligase subunit alpha; EC 6.4.1.4 (characterized)
to candidate H281DRAFT_06283 H281DRAFT_06283 biotin carboxylase
Query= SwissProt::Q2QMG2 (737 letters) >FitnessBrowser__Burk376:H281DRAFT_06283 Length = 455 Score = 402 bits (1034), Expect = e-116 Identities = 212/444 (47%), Positives = 289/444 (65%), Gaps = 7/444 (1%) Query: 40 EKVLVANRGEIACRVMRTARRLGIPTVAVYSDADRGALHVRAADEAVRLGPPPARESYLN 99 EK+L+ANRGEIA R+ R R LG+ TV VYS+AD+ A +V+ ADEAV +GP P+ SYLN Sbjct: 3 EKILIANRGEIALRIQRACRELGVKTVVVYSEADKEAKYVKLADEAVCIGPAPSNLSYLN 62 Query: 100 ASAIVDAALRTGAKAIHPGYGFLSESADFAQLCKAEGLTFIGPPPSAIRDMGDKSASKRI 159 A++ AA T A+AIHPGYGFLSE+ADFA+ + G TFIGP P IR MGDK +K+ Sbjct: 63 MPALISAAEVTDAEAIHPGYGFLSENADFAERVEQSGFTFIGPRPETIRMMGDKVTAKQT 122 Query: 160 MGAAGVPLVPGYHGA--EQDIELLKLEANKIGYPVLIKPTHGGGGKGMRIVQRPEDFVDS 217 M GVP VPG GA E E++K+ A ++GYPV+IK GGGG+GMR+V V++ Sbjct: 123 MIKTGVPCVPGSEGALPEDPKEIVKI-ARQVGYPVIIKAAGGGGGRGMRVVHTEAALVNA 181 Query: 218 VLSAQREAAASFGINTLLVEKYITQPRHIEVQIFGDQHGNVIHLYERDCSLQRRHQKIIE 277 V + EA +FG + +EK++ PRHIE+Q+ D N + L ERDCS+QRRHQK+IE Sbjct: 182 VNMTREEAGRAFGNPQVYMEKFLENPRHIEIQVLSDSFKNAVWLGERDCSMQRRHQKVIE 241 Query: 278 EAPAPNVTAQFRSHIGEAAVSAAKAVGYYSAGTVEFIVDTLSGEFYFMEMNTRLQVEHPV 337 EAPAP + + IG+ A K +GY AGT EF+ + +GEFYF+EMNTR+QVEHPV Sbjct: 242 EAPAPGIARRLIDRIGDRCADACKKMGYLGAGTFEFLYE--NGEFYFIEMNTRVQVEHPV 299 Query: 338 TEMIVGQDLVEWQIRIANGECLPLSQEQVPLNGHAFEARIYAENVPRGFLPATGTLHHYR 397 TE+I G D+V+ QIRIA GE L Q + GHA E RI AE+ P F+P+ G L + Sbjct: 300 TELITGVDIVQEQIRIAAGEKLAFRQRDIVFKGHAIECRINAED-PFKFIPSPGRLTSWH 358 Query: 398 PVPSTATVRVETGVEEGDTVSMHYDPMIAKLVVWGESRNAALVKLKNSLSNFQIAGLPTN 457 +P +RV++ G V +YD MI KL+ +G +R A+ +++ +LS + G+ TN Sbjct: 359 -MPGGPGIRVDSHAYNGYFVPPNYDSMIGKLIAYGATREQAIKRMRIALSEMVVEGIQTN 417 Query: 458 VGFLQELAGHSAFEKGLVDTHFIE 481 + +EL + F +G H++E Sbjct: 418 IPLHRELMLDAKFVEGGTSIHYLE 441 Lambda K H 0.317 0.133 0.389 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: 746 Number of extensions: 35 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: 737 Length of database: 455 Length adjustment: 36 Effective length of query: 701 Effective length of database: 419 Effective search space: 293719 Effective search space used: 293719 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: 53 (25.0 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