Align Methylcrotonoyl-CoA carboxylase (EC 6.4.1.4) (characterized)
to candidate GFF1025 HP15_1004 3-methylcrotonyl CoA carboxylase, beta subunit
Query= reanno::SB2B:6937191 (535 letters) >FitnessBrowser__Marino:GFF1025 Length = 535 Score = 837 bits (2163), Expect = 0.0 Identities = 402/535 (75%), Positives = 466/535 (87%) Query: 1 MTQLTSRVNPRSDEFKQKHDAMAALVADLKDKLAHIEQGGGLVAMERHLSRGKLAPRARV 60 MT L S++NPRS+EF+ ++MA VADL+DK++ I+QGGG ERH++RGKL PR R+ Sbjct: 1 MTILQSKINPRSEEFQANQESMAQAVADLRDKVSTIQQGGGPSYQERHIARGKLLPRERI 60 Query: 61 EKLLDPGSPFLELSQFAAFEVYDEDVPAAGIIAGIGRVSGVECMIIANDATVKGGTYYPI 120 +LLD GSPFLE+ QFAA+ VYDE+VPAAG+IAG+GRVSG ECMIIANDATVKGG+YYP+ Sbjct: 61 NRLLDDGSPFLEIGQFAAYNVYDEEVPAAGVIAGVGRVSGTECMIIANDATVKGGSYYPL 120 Query: 121 TVKKHLRAQAIAERCHLPCIYLVDSGGANLPRQDEVFPDRDHFGRIFFNQARMSAKGIPQ 180 TVKKHLRAQ IA + LPCIYLVDSGGANLPRQDEVFPDR+HFGRIF+NQARMSA IPQ Sbjct: 121 TVKKHLRAQEIALQNRLPCIYLVDSGGANLPRQDEVFPDREHFGRIFYNQARMSADDIPQ 180 Query: 181 IAVVMGLCTAGGAYVPAMADESIIVREQGTIFLAGPPLVKAATGEEVSAEELGGGDVHTK 240 IAVVMGLCTAGGAYVPAMADESIIVR QGTIFLAGPPLVKAATGE V+AE+LGG DVH K Sbjct: 181 IAVVMGLCTAGGAYVPAMADESIIVRNQGTIFLAGPPLVKAATGEVVTAEDLGGADVHCK 240 Query: 241 ISGVADHLAQNDEHALELARKAVSRLNHQKQVELQLSKVKPPKYDINELYGIVGTDLKKP 300 ISGVADH A+ND HALE+AR++VS LN +K ++++ K K P YD E+YGIVGTDL+K Sbjct: 241 ISGVADHYAENDAHALEIARRSVSNLNRRKPTDVEIRKPKAPLYDAEEIYGIVGTDLRKQ 300 Query: 301 FDVKEVIARIVDDSDFDEFKANYGTTLVCGFARIHGYPVGIVANNGILFSESAQKGAHFI 360 FDV++VIAR VD S+FDEFK YG TLV GFA IHGYPVGI+ANNGILFSE+AQKGAHF+ Sbjct: 301 FDVRDVIARTVDGSEFDEFKRYYGQTLVTGFAHIHGYPVGIIANNGILFSEAAQKGAHFV 360 Query: 361 ELCCQRKIPLVFLQNITGFMVGKKYEHEGIAKHGAKMVTAVSCATVPKFTVLIGGSYGAG 420 ELCCQR IPL+FLQNITGFMVG+KYE EGIAKHGAKMV AV+CA VPK TVLIGGS+GAG Sbjct: 361 ELCCQRNIPLLFLQNITGFMVGQKYESEGIAKHGAKMVMAVACANVPKITVLIGGSFGAG 420 Query: 421 NYGMCGRAFEPTLMWMWPNARISVMGGEQAAGVLATVRKDGLARKGETMSAEEEAKFKAP 480 NYGMCGRA+ P +WMWPNARISVMGGEQAAGV+ATVR++G+ RKG+ SAEEEA+FK P Sbjct: 421 NYGMCGRAYSPDFLWMWPNARISVMGGEQAAGVMATVRREGMERKGQEWSAEEEAEFKKP 480 Query: 481 IIAQYDKEGHPYHASARLWDDGIIDPAQTRDVLGLAISAALNAPIEETRFGVFRM 535 II Y+ +GHPY+ASARLWDDG+IDPAQTR+V+ L++SA LN P + TRFGVFRM Sbjct: 481 IIDTYEHQGHPYYASARLWDDGVIDPAQTREVVALSLSATLNRPAKPTRFGVFRM 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: 1022 Number of extensions: 45 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