Align methylcrotonoyl-CoA carboxylase (EC 6.4.1.4) (characterized)
to candidate WP_011386592.1 AMB_RS21450 acyl-CoA carboxylase subunit beta
Query= BRENDA::Q9LDD8 (587 letters) >NCBI__GCF_000009985.1:WP_011386592.1 Length = 512 Score = 247 bits (631), Expect = 7e-70 Identities = 167/518 (32%), Positives = 257/518 (49%), Gaps = 36/518 (6%) Query: 68 MEGILSELRSHIKKVLAGGGEEAVKRNRSRNKLLPRERIDRLLDPGSSFLELSQLAGH-- 125 M I+ +L + GGGE+ + R KL RERI+ LLDP SF E H Sbjct: 1 MHEIIQQLEEKREGARMGGGEKRIAAQHKRGKLTARERIELLLDP-DSFEEWDMFKEHRC 59 Query: 126 -----ELYEEPLPSGGIITGIGPIHGRICMFMANDPTVKGGTYYPITIKKHLRAQEIAAR 180 + + +P G++TG G I+GR+ + D TV GG+ +K + + A + Sbjct: 60 TDFGMDSEDNMIPGDGVVTGYGTINGRLVFVFSQDFTVFGGSLSEAHAEKICKIMDKAVQ 119 Query: 181 CRLPCIYLVDSGGAYLPKQAEVFPDKENFGRVFYNESVMSSDGIPQIAIVLGSCTAGGAY 240 P I L DSGGA + E + VF +VM+S +PQI++++G C G Y Sbjct: 120 VGAPVIGLNDSGGARIQ---EGVASLAGYAEVF-QRNVMASGVVPQISMIMGPCAGGAVY 175 Query: 241 IPAMADESVMVKGNGTIFLAGPPLVKAATGEEVSAEDLGGATVHCTVSGVSDYFAQDELH 300 PAM D MVK + +F+ GP +VK T E V+AE+LGGA H T SGV+D ++++ Sbjct: 176 SPAMTDYIFMVKDSSYMFVTGPDVVKTVTHETVTAEELGGAVTHSTKSGVADLAFENDVE 235 Query: 301 GLAIGRNIVKNLHMAAKQGMEGTFGSKNLVYKEPLYDINELRSIAPVDHKQQFDVRSIIA 360 L R + L + ++ S P L ++ P + + +D++ +I Sbjct: 236 ALLQLRRFMDFLPSSNREKPPVRPTSDG-----PERIETSLDTLIPDNANKPYDMKELIL 290 Query: 361 RIVDGSEFDEFKKQYGTTLVTGFARIYGQTVGIIGNN-----GILFNESALKGAHFIELC 415 ++VD +F E + Y ++ GFAR+ G+TVGI+ N G L S++KGA F+ C Sbjct: 291 KVVDEGDFFEVQPGYAGNIIVGFARMEGRTVGIVANQPMVLAGCLDISSSIKGARFVRFC 350 Query: 416 SQRKIPLVFLQNITGFMVGSRAEANGIAKAGAKMVMAVSCAKVPKITIITGASFGAGNYA 475 IP+V ++ GF+ G+ E GI K GAK++ A + VPKIT+IT ++G Sbjct: 351 DAFNIPIVTFVDVPGFLPGTSQEYGGIIKHGAKLLYAYAECTVPKITVITRKAYGGAYDV 410 Query: 476 MCGRAYSPDFMFIWPNARIGIMGGAQAAGVLTQIERATKKRQGIKWTEEEEEAFKKKTVD 535 M + D F WP A I +MG A ++ + + ++ + TEE + F Sbjct: 411 MSSKHLRGDVNFAWPTAEIAVMGPKGAVEIIFRSDIGDAEKIAAR-TEEYRQKF------ 463 Query: 536 AYEREANPYYSTARLWDDGVIDPCDTRKVLGLCLSAAL 573 ANP+ + R + D VI P +TRK +C S A+ Sbjct: 464 -----ANPFIAGHRGFIDDVIMPRNTRK--RICRSLAM 494 Lambda K H 0.320 0.138 0.408 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: 728 Number of extensions: 38 Number of successful extensions: 6 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: 587 Length of database: 512 Length adjustment: 36 Effective length of query: 551 Effective length of database: 476 Effective search space: 262276 Effective search space used: 262276 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: 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