Align Methylcrotonoyl-CoA carboxylase (EC 6.4.1.4) (characterized)
to candidate WP_086510405.1 BZY95_RS13295 methylcrotonoyl-CoA carboxylase
Query= reanno::SB2B:6937191 (535 letters) >NCBI__GCF_002151265.1:WP_086510405.1 Length = 535 Score = 810 bits (2092), Expect = 0.0 Identities = 397/535 (74%), Positives = 454/535 (84%) Query: 1 MTQLTSRVNPRSDEFKQKHDAMAALVADLKDKLAHIEQGGGLVAMERHLSRGKLAPRARV 60 M L ++VNPRSD F+ AM V L++ A I QGGG A RH SRGKL R R+ Sbjct: 1 MAILNTQVNPRSDGFQANDKAMRQEVMKLRELTAAISQGGGEKARARHESRGKLFVRDRI 60 Query: 61 EKLLDPGSPFLELSQFAAFEVYDEDVPAAGIIAGIGRVSGVECMIIANDATVKGGTYYPI 120 + L+D GSPFLE S AA EVY+ DVPAAG++ GIGRVSGVEC+I+ANDATVKGGTYYP+ Sbjct: 61 DHLIDEGSPFLEFSALAAHEVYESDVPAAGVVTGIGRVSGVECVIVANDATVKGGTYYPL 120 Query: 121 TVKKHLRAQAIAERCHLPCIYLVDSGGANLPRQDEVFPDRDHFGRIFFNQARMSAKGIPQ 180 TVKKH+RAQ IA + LPCIYLVDSGGA LPRQDEVFPDRDHFGRIF+NQA +SA+GIPQ Sbjct: 121 TVKKHIRAQEIARKHRLPCIYLVDSGGAFLPRQDEVFPDRDHFGRIFYNQATLSAEGIPQ 180 Query: 181 IAVVMGLCTAGGAYVPAMADESIIVREQGTIFLAGPPLVKAATGEEVSAEELGGGDVHTK 240 IAVVMG CTAGGAYVPAMADESIIV++QGTIFL GPPLVKAATGE +SAE+LGG DVH K Sbjct: 181 IAVVMGSCTAGGAYVPAMADESIIVKQQGTIFLGGPPLVKAATGETISAEDLGGADVHAK 240 Query: 241 ISGVADHLAQNDEHALELARKAVSRLNHQKQVELQLSKVKPPKYDINELYGIVGTDLKKP 300 SGVADH A+ND HAL+LAR VSRLN QK+ +L++ KPP+ D +E+YGIVGTDLKKP Sbjct: 241 KSGVADHYAENDAHALQLARACVSRLNWQKRGQLKMQAPKPPRLDPSEIYGIVGTDLKKP 300 Query: 301 FDVKEVIARIVDDSDFDEFKANYGTTLVCGFARIHGYPVGIVANNGILFSESAQKGAHFI 360 FDV+EVI RIVDDSDFDEFK YG TLV GFA IHGYPVGIVANNG+LFSESA KGAHFI Sbjct: 301 FDVREVIGRIVDDSDFDEFKRYYGDTLVTGFAHIHGYPVGIVANNGVLFSESAVKGAHFI 360 Query: 361 ELCCQRKIPLVFLQNITGFMVGKKYEHEGIAKHGAKMVTAVSCATVPKFTVLIGGSYGAG 420 ELC QRKIPLVFLQNITGFMVG KYEHEGIAKHGAK+VTAV+CA VPKFTVLIGGS+GAG Sbjct: 361 ELCAQRKIPLVFLQNITGFMVGSKYEHEGIAKHGAKLVTAVACAKVPKFTVLIGGSFGAG 420 Query: 421 NYGMCGRAFEPTLMWMWPNARISVMGGEQAAGVLATVRKDGLARKGETMSAEEEAKFKAP 480 NYGMCGRA++P L++MWPNARISVMGGEQAAGVLA V+++ R+G SAEEE FK P Sbjct: 421 NYGMCGRAYDPNLLFMWPNARISVMGGEQAAGVLAQVKREQYEREGREWSAEEEEAFKQP 480 Query: 481 IIAQYDKEGHPYHASARLWDDGIIDPAQTRDVLGLAISAALNAPIEETRFGVFRM 535 QY+++GHPY+ASARLWDDG+IDPAQTRDVLGL+++AA+NA +++TRFGVFRM Sbjct: 481 TREQYERQGHPYYASARLWDDGVIDPAQTRDVLGLSLAAAMNAEVQDTRFGVFRM 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: 1014 Number of extensions: 41 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 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