Align methylcrotonoyl-CoA carboxylase (subunit 2/2) (EC 6.4.1.4) (characterized)
to candidate GFF3827 PS417_19595 3-methylcrotonyl-CoA carboxylase
Query= BRENDA::Q9I299 (655 letters) >FitnessBrowser__WCS417:GFF3827 Length = 627 Score = 580 bits (1494), Expect = e-170 Identities = 319/645 (49%), Positives = 415/645 (64%), Gaps = 22/645 (3%) Query: 7 SIQRLLVANRGEIACRVMRSARALGIGSVAVHSDIDRHARHVAEADIAVDLGGAKPADSY 66 + ++L+ANRGEIACR+ R+A+ALG +VAV+SD D A HV AD AV +G A SY Sbjct: 3 AFSKILIANRGEIACRIQRTAQALGYRTVAVYSDADAQALHVQMADEAVHIGPAPVQQSY 62 Query: 67 LRGDRIIAAALASGAQAIHPGYGFLSENADFARACEEAGLLFLGPPAAAIDAMGSKSAAK 126 L D I+ AA + A AI PGYGFLSEN DFARAC++AGL F+GP AI+ MGSK +K Sbjct: 63 LNIDAILNAARVTSADAIPPGYGFLSENPDFARACQQAGLTFIGPSPEAIELMGSKRLSK 122 Query: 127 ALMEEAGVPLVPGYHGEAQDLETFRREAGRIGYPVLLKAAAGGGGKGMKVVEREAELAEA 186 M +AGVP + GY G AQD T +REA IGYP+++KA+AGGGG+GM++V+ EL + Sbjct: 123 LAMLDAGVPCIAGYQGSAQDDSTLQREADAIGYPLMIKASAGGGGRGMRLVQHPEELLDN 182 Query: 187 LSSAQREAKAAFGDARMLVEKYLLKPRHVEIQVFADRHGHCLYLNERDCSIQRRHQKVVE 246 L +A+ EAK AFG +++E+ L+ PRHVEIQ+F D HGH +YL ERDCSIQRRHQK++E Sbjct: 183 LHTARSEAKNAFGSGELILEQALIDPRHVEIQLFGDSHGHLIYLGERDCSIQRRHQKIIE 242 Query: 247 EAPAPGLGAELRRAMGEAAVRAAQAIGYVGAGTVEFLLDERGQFFFMEMNTRLQVEHPVT 306 EAP P + ELR+AMGEAA+ A +A+ YVGAGTVEFLLD G+F+F+EMNTRLQVEHPVT Sbjct: 243 EAPCPVMTPELRQAMGEAALNAGRAVNYVGAGTVEFLLDRNGRFYFLEMNTRLQVEHPVT 302 Query: 307 EAITGLDLVAWQIRVARGEALPLTQEQVPLNGHAIEVRLYAEDPEGDFLPASGRLMLYRE 366 E ITGLDLV WQ+++A G+ LPLTQ V LNGHA+EVRLYAEDP FLP +G ++ + Sbjct: 303 ELITGLDLVDWQLQIAAGQPLPLTQPDVSLNGHAMEVRLYAEDPAQGFLPQTGEVLRWDP 362 Query: 367 AAAGPGRRVDSGVREGDEVSPFYDPMLAKLIAWGETREEARQRLLAMLAETSVGGLRTNL 426 AA G R+D GV EG +SPFYDPML K+IA+G TREEAR++LL + +T + G+ TN Sbjct: 363 AA---GVRIDHGVTEGQRISPFYDPMLGKIIAYGATREEARRKLLRAVEDTVLLGVTTNQ 419 Query: 427 AFLRRILGHPAFAAAELDTGFIARHQDDLLP-APQALPEHFWQAAAEAWLQSEPGHRRDD 485 L +L HP F + TGFIA H ++ P P A EH AAA + S H + Sbjct: 420 PLLVDLLKHPDFVGGDFSTGFIAEHFSEIRPLTPSA--EHLALAAALFYQHSANQHPQG- 476 Query: 486 DPHSPWSRNDGWRSALARESDLMLRCRDERRCVRLRHASPSQYRLDGDDLVSRVDGVTRR 545 GWR+ + L + V +A+P DG +G+ RR Sbjct: 477 --------LAGWRNNTSAPCTYRLEVNGDTHTV---NAAPLPLTTDGRHANHVFNGIRRR 525 Query: 546 SAALRRGRQLFLEWEGELLAIEAVDPIAEAEAAHAHQGGLSAPMNGSIVRVLVEPGQTVE 605 +A G QL W L + +A + A+ G + APM+G+IV V V G +V Sbjct: 526 TAYHLVGNQL---WLPGLTVTDRTQQVASRQ-ANVSSGTVKAPMDGAIVDVRVSAGDSVT 581 Query: 606 AGATLVVLEAMKMEHSIRAPHAGVVKALYCSEGELVEEGTPLVEL 650 G L+VLEAMKMEH + A GV+K + G+ V L+E+ Sbjct: 582 KGQLLLVLEAMKMEHPLTAGIDGVIKGVQVIAGDQVRNRQVLLEI 626 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: 1010 Number of extensions: 41 Number of successful extensions: 4 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: 655 Length of database: 627 Length adjustment: 38 Effective length of query: 617 Effective length of database: 589 Effective search space: 363413 Effective search space used: 363413 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 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