Align Methylcrotonoyl-CoA carboxylase (EC 6.4.1.4) (characterized)
to candidate WP_073037629.1 BUB04_RS05245 acyl-CoA carboxylase subunit beta
Query= reanno::SB2B:6937191 (535 letters) >NCBI__GCF_900129305.1:WP_073037629.1 Length = 518 Score = 265 bits (676), Expect = 4e-75 Identities = 175/517 (33%), Positives = 271/517 (52%), Gaps = 30/517 (5%) Query: 22 MAALVADLKDKL----AHIEQGGGLVAMERHLSRGKLAPRARVEKLLDPGSPFLELSQFA 77 MAA +LK+KL + GGG E+ ++GKL R R++ L DPG+ F E+ FA Sbjct: 1 MAADWKELKEKLEAERVRLRAGGGPALQEKEHAKGKLTARERIDLLFDPGT-FEEIDLFA 59 Query: 78 A-----FEVYDEDVPAAGIIAGIGRVSGVECMIIANDATVKGGTYYPITVKKHLRAQAIA 132 + + ++VPA G+I G G V+G CM+ A D TV GT+ +K + +A Sbjct: 60 KHIGRDYGLDKKEVPADGVIIGYGEVNGRGCMVYAEDFTVIAGTFGERHGRKICKIIDMA 119 Query: 133 ERCHLPCIYLVDSGGANLPRQDEVFPDRDHFGRIFFNQARMSAKGIPQIAVVMGLCTAGG 192 + P + + DSGGA + Q +G++F+ S +PQIA++MG G Sbjct: 120 RKYGFPVVGINDSGGARVTEQMGAL---SQYGQLFYRHVAASGV-VPQIALIMGPVAGGQ 175 Query: 193 AYVPAMADESIIVREQGTIFLAGPPLVKAATGEEVSAEELGGGDVHTKISGVADHLAQND 252 AY PA+ D +V + +F+AGPPLV+A E+ + LGG VH +I+GV+D +D Sbjct: 176 AYSPALMDFIFMVEKTSAMFIAGPPLVEAVVYEKTDEQSLGGPKVHGRITGVSDGTMADD 235 Query: 253 EHALELARKAVSRLN-HQKQVELQLSKVKPPKYDINELYGIVGTDLKKPFDVKEVIARIV 311 LE R+ +S L + K + + P + EL I+ TD K+ +++++VI + Sbjct: 236 RQCLEQTRRLLSYLPLNNKDLPPYEAPEDSPDRETVELEEIIPTDQKRLYNMRKVIECVF 295 Query: 312 DDSDFDEFKANYGTTLVCGFARIHGYPVGIVANN-----GILFSESAQKGAHFIELCCQR 366 D F E K + L+ G AR++G+ VG+VANN G L +A KG+ FI C Sbjct: 296 DRGSFFELKKEFAQNLIIGLARLNGHVVGVVANNPVKYNGALDYNAADKGSRFIRFCNAF 355 Query: 367 KIPLVFLQNITGFMVGKKYEHEGIAKHGAKMVTAVSCATVPKFTVLIGGSYGAGNYGMCG 426 IPL+ LQ++ GF++G + EH I +HGAKM+ A + ATVPK T ++ +Y G MC Sbjct: 356 NIPLINLQDVPGFLIGTRSEHNAIIRHGAKMLYAYAEATVPKITCVLRKAYAGGYLAMCS 415 Query: 427 RAFEPTLMWMWPNARISVMGGEQAAGVLATVRKD-GLARKGETMSAEEEAKFKAPIIAQY 485 + +++ P A I +MG + A +L RK+ + E A+ EA+F Sbjct: 416 KDLGADVVFALPTAEICLMGPQGAVNIL--FRKEIASSENPEETRAQREAEF-------M 466 Query: 486 DKEGHPYHASARLWDDGIIDPAQTRDVLGLAISAALN 522 +K +P +A+ D II P + R L A+ L+ Sbjct: 467 EKYVNPTYAAGLQHVDDIIMPGELRRRLIRALEMTLD 503 Lambda K H 0.320 0.137 0.405 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: 722 Number of extensions: 36 Number of successful extensions: 5 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: 518 Length adjustment: 35 Effective length of query: 500 Effective length of database: 483 Effective search space: 241500 Effective search space used: 241500 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 24 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