Align methylcrotonoyl-CoA carboxylase (subunit 2/2) (EC 6.4.1.4) (characterized)
to candidate WP_090447226.1 BLS63_RS18330 acetyl/propionyl/methylcrotonyl-CoA carboxylase subunit alpha
Query= BRENDA::Q9I299 (655 letters) >NCBI__GCF_900100495.1:WP_090447226.1 Length = 660 Score = 580 bits (1496), Expect = e-170 Identities = 333/662 (50%), Positives = 438/662 (66%), Gaps = 25/662 (3%) Query: 7 SIQRLLVANRGEIACRVMRSARALGIGSVAVHSDIDRHARHVAEADIAVDLGGAKPADSY 66 + ++L+ANRGEIACRVMR+A LG +VAV+S D ARHV AD AV +G A+ SY Sbjct: 3 AFNKILIANRGEIACRVMRTAMDLGYRTVAVYSVADADARHVQLADEAVCIGPAQVNQSY 62 Query: 67 LRGDRIIAAALASGAQAIHPGYGFLSENADFARACEEAGLLFLGPPAAAIDAMGSKSAAK 126 L D II AA +GA AIHPGYGFLSENA+FARACE AG++F+GP AI MGSK +K Sbjct: 63 LLIDAIIEAAQKTGADAIHPGYGFLSENAEFARACEAAGIVFIGPTVEAIRLMGSKRLSK 122 Query: 127 ALMEEAGVPLVPGYHGEAQDLETFRREAGRIGYPVLLKAAAGGGGKGMKVVEREAELAEA 186 M EAGVP +PGY G AQD T EA RIGYP+++KA+AGGGG+GM++V+ AELA Sbjct: 123 LAMLEAGVPCIPGYEGAAQDDATLSGEAERIGYPLMIKASAGGGGRGMRLVDNAAELAAQ 182 Query: 187 LSSAQREAKAAFGDARMLVEKYLLKPRHVEIQVFADRHGHCLYLNERDCSIQRRHQKVVE 246 L SA+ EA+ AFG +++E+ L++PRHVEIQVF D HG+ +YL ERDCS+QRRHQKVVE Sbjct: 183 LRSARSEAQNAFGCGELILERALIQPRHVEIQVFGDAHGNLVYLGERDCSVQRRHQKVVE 242 Query: 247 EAPAPGLGAELRRAMGEAAVRAAQAIGYVGAGTVEFLLDERGQFFFMEMNTRLQVEHPVT 306 EAP P + AELR+AMG AAV+AA ++ Y+GAGTVEFLL+ G+FFF+EMNTRLQVEHPVT Sbjct: 243 EAPCPLMTAELRQAMGAAAVKAAASVNYIGAGTVEFLLEPSGEFFFLEMNTRLQVEHPVT 302 Query: 307 EAITGLDLVAWQIRVARGEALPLTQEQVPLNGHAIEVRLYAEDPEGDFLPASGRLMLYRE 366 E ITG DLVAWQIRVA G+ LPL QE++ L+GHA+EVRLYAED FLP +G+++ + E Sbjct: 303 ELITGQDLVAWQIRVAEGQPLPLRQEEIQLSGHAMEVRLYAEDSAAGFLPQTGQVLRW-E 361 Query: 367 AAAGPGRRVDSGVREGDEVSPFYDPMLAKLIAWGETREEARQRLLAMLAETSVGGLRTNL 426 AA G R+D G+ EG V+PFYDP+LAK+IA+G +R+EAR++LL + + + G++ N Sbjct: 362 PAALEGIRIDHGLLEGQAVTPFYDPLLAKVIAYGASRDEARRKLLRAVEDCVLLGVKGNQ 421 Query: 427 AFLRRILGHPAFAAAELDTGFIARH-QDDLLPAPQALPEHFWQAAAEAWLQSEPGHRRDD 485 FL +L HP FAA + T FI +H +D +PQA P A+A A L ++ Sbjct: 422 RFLANLLRHPQFAAGQATTAFIEQHFANDPSLSPQA-PAASELASAAALL-----YQASA 475 Query: 486 DPHSPWSRNDGWRSALARESDLMLRCRDERRCVRLR-HASPSQYRLD---GDDLVS---- 537 + + GWRSA + +L+ ++R V L S Q RLD GD+ V Sbjct: 476 QASAHQAGLAGWRSAGSAPWRFILKQGEQRFAVELAVLQSGQQPRLDARIGDEQVQLRLL 535 Query: 538 ---------RVDGVTRRSAALRRGRQLFLEWEGELLAIEAVDPIAEAEAAHAHQGGLSAP 588 VDG+ RR A G +L+L L + + A + G + AP Sbjct: 536 ASDGRWASLEVDGIRRRLAYHLAGDRLWLYGSDGNLEFTDITHAPVSGAEGSGTGTVKAP 595 Query: 589 MNGSIVRVLVEPGQTVEAGATLVVLEAMKMEHSIRAPHAGVVKALYCSEGELVEEGTPLV 648 M+G+IV VLV G V G L+VLEAMKMEH ++A G+++ + S+G+ V+ LV Sbjct: 596 MDGAIVEVLVTEGDRVGKGQLLLVLEAMKMEHPLKATIDGIIRRVQVSKGDQVKNRQLLV 655 Query: 649 EL 650 E+ Sbjct: 656 EV 657 Lambda K H 0.319 0.135 0.397 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: 1006 Number of extensions: 37 Number of successful extensions: 4 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 655 Length of database: 660 Length adjustment: 38 Effective length of query: 617 Effective length of database: 622 Effective search space: 383774 Effective search space used: 383774 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: 54 (25.4 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