Align Methylcrotonoyl-CoA carboxylase (EC 6.4.1.4) (characterized)
to candidate 201058 SO1896 3-methylcrotonyl CoA carboxylase, beta subunit (NCBI ptt file)
Query= reanno::SB2B:6937191 (535 letters) >FitnessBrowser__MR1:201058 Length = 535 Score = 990 bits (2559), Expect = 0.0 Identities = 489/535 (91%), Positives = 512/535 (95%) Query: 1 MTQLTSRVNPRSDEFKQKHDAMAALVADLKDKLAHIEQGGGLVAMERHLSRGKLAPRARV 60 MTQL+SR+N RSDEFK K D MAALVADLK KLA IE GGG VA+ERHLSRGK PR RV Sbjct: 1 MTQLSSRINARSDEFKAKSDDMAALVADLKTKLAKIELGGGPVALERHLSRGKRLPRQRV 60 Query: 61 EKLLDPGSPFLELSQFAAFEVYDEDVPAAGIIAGIGRVSGVECMIIANDATVKGGTYYPI 120 EKLLD GSPFLELSQFAAFEVYDE+VPAAGIIAGIGRVSGVECMIIANDATVKGGTYYPI Sbjct: 61 EKLLDAGSPFLELSQFAAFEVYDEEVPAAGIIAGIGRVSGVECMIIANDATVKGGTYYPI 120 Query: 121 TVKKHLRAQAIAERCHLPCIYLVDSGGANLPRQDEVFPDRDHFGRIFFNQARMSAKGIPQ 180 TVKKH+RAQ IA RCHLPCIYLVDSGGANLPRQDEVFPDRDHFGRIF+NQA+MSAKGIPQ Sbjct: 121 TVKKHIRAQEIASRCHLPCIYLVDSGGANLPRQDEVFPDRDHFGRIFYNQAQMSAKGIPQ 180 Query: 181 IAVVMGLCTAGGAYVPAMADESIIVREQGTIFLAGPPLVKAATGEEVSAEELGGGDVHTK 240 IAVVMGLCTAGGAYVPAMADESIIV++QGTIFLAGPPLVKAATGEEVSAEELGG DVHTK Sbjct: 181 IAVVMGLCTAGGAYVPAMADESIIVKDQGTIFLAGPPLVKAATGEEVSAEELGGADVHTK 240 Query: 241 ISGVADHLAQNDEHALELARKAVSRLNHQKQVELQLSKVKPPKYDINELYGIVGTDLKKP 300 ISGVADHLAQNDEHALELAR+AVSRLNHQK++ L+LS VKPPK+DI+ELYGIVGTDLKKP Sbjct: 241 ISGVADHLAQNDEHALELARRAVSRLNHQKEITLRLSPVKPPKFDISELYGIVGTDLKKP 300 Query: 301 FDVKEVIARIVDDSDFDEFKANYGTTLVCGFARIHGYPVGIVANNGILFSESAQKGAHFI 360 FDVKEVIARIVDDSDFDEFKANYG TLVCGFARIHGYPVGIVANNGILFSESAQKGAHFI Sbjct: 301 FDVKEVIARIVDDSDFDEFKANYGATLVCGFARIHGYPVGIVANNGILFSESAQKGAHFI 360 Query: 361 ELCCQRKIPLVFLQNITGFMVGKKYEHEGIAKHGAKMVTAVSCATVPKFTVLIGGSYGAG 420 ELCCQRKIPL+FLQNITGFMVGKKYEHEGIAKHGAKMVTAVSCA VPKFTV+IGGSYGAG Sbjct: 361 ELCCQRKIPLLFLQNITGFMVGKKYEHEGIAKHGAKMVTAVSCANVPKFTVIIGGSYGAG 420 Query: 421 NYGMCGRAFEPTLMWMWPNARISVMGGEQAAGVLATVRKDGLARKGETMSAEEEAKFKAP 480 NYGMCGRAFEPT+MWMWPNARISVMGGEQAAGVLATVR+DGLARKGE SAE+E FKAP Sbjct: 421 NYGMCGRAFEPTMMWMWPNARISVMGGEQAAGVLATVRRDGLARKGEEWSAEDEKAFKAP 480 Query: 481 IIAQYDKEGHPYHASARLWDDGIIDPAQTRDVLGLAISAALNAPIEETRFGVFRM 535 IIAQYDKEGHPYHASARLWDDGIIDPAQTRDV+GLA+SAALNAPIE+TRFGVFRM Sbjct: 481 IIAQYDKEGHPYHASARLWDDGIIDPAQTRDVVGLALSAALNAPIEDTRFGVFRM 535 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: 1125 Number of extensions: 44 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: 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