Align Methylcrotonyl-CoA carboxylase biotin-containing subunit (EC 6.4.1.4) (characterized)
to candidate AO353_20335 AO353_20335 3-methylcrotonyl-CoA carboxylase
Query= reanno::pseudo1_N1B4:Pf1N1B4_3984 (651 letters) >FitnessBrowser__pseudo3_N2E3:AO353_20335 Length = 649 Score = 1167 bits (3018), Expect = 0.0 Identities = 589/649 (90%), Positives = 616/649 (94%) Query: 1 MSAPVLTTLLVANRGEIACRVMRTAKALGLTTVAVHSATDRDARHSREADIRVDLGGSKA 60 MSAPVLTTLLVANRGEIACRVMRTAKALGLTTVAVHSATDRDARHSREADIRVDLGGSKA Sbjct: 1 MSAPVLTTLLVANRGEIACRVMRTAKALGLTTVAVHSATDRDARHSREADIRVDLGGSKA 60 Query: 61 ADSYLQIDKLIAAAKASGAQAIHPGYGFLSENAGFARAIEAAGLIFLGPPASAIDAMGSK 120 ADSYLQIDKL+AAAKASGAQAIHPGYGFLSENAGFARAIEAAGLIFLGPPASAIDAMGSK Sbjct: 61 ADSYLQIDKLLAAAKASGAQAIHPGYGFLSENAGFARAIEAAGLIFLGPPASAIDAMGSK 120 Query: 121 SAAKALMETAGVPLVPGYHGEAQDLETFRDACERIGYPVLLKATAGGGGKGMKVVEDVSQ 180 SAAKALMETAGVPLVPGYHGEAQDLETFRDA ERIGYPVLLKATAGGGGKGMKVVEDVSQ Sbjct: 121 SAAKALMETAGVPLVPGYHGEAQDLETFRDAAERIGYPVLLKATAGGGGKGMKVVEDVSQ 180 Query: 181 LAEALASAQREALSSFGDSRMLVEKYLLKPRHVEIQVFADQHGNCLYLNERDCSIQRRHQ 240 LAEALASAQREA SSFGDSRMLVEKYLLKPRHVEIQVFADQHGNCLYLNERDCSIQRRHQ Sbjct: 181 LAEALASAQREAQSSFGDSRMLVEKYLLKPRHVEIQVFADQHGNCLYLNERDCSIQRRHQ 240 Query: 241 KVVEEAPAPGLSPELRRAMGEAAVRSAQAIGYVGAGTVEFLLDARGEFFFMEMNTRLQVE 300 KVVEEAPAPGLS +LR+AMGEAAVR+AQAIGYVGAGTVEFLLD+RGEFFFMEMNTRLQVE Sbjct: 241 KVVEEAPAPGLSAQLRKAMGEAAVRAAQAIGYVGAGTVEFLLDSRGEFFFMEMNTRLQVE 300 Query: 301 HPVTEAITGLDLVAWQIRVARGEALPMTQDQVPLIGHAIEVRLYAEDPGNDFLPATGRLA 360 HPVTEAITGLDLVAWQIRVA+GE LPMTQ QVPL+GHAIEVRLYAEDP NDFLPATG LA Sbjct: 301 HPVTEAITGLDLVAWQIRVAQGEPLPMTQAQVPLLGHAIEVRLYAEDPSNDFLPATGHLA 360 Query: 361 LYRESAAGPGRRVDSGVEEGDEISPFYDPMLGKLIAWGEDREQARLRLLSMLDEFAIGGL 420 LYRESAAGPGRRVDSGVEEGD ISPFYDPMLGKLIAWG DREQARLRLLSML+EFAIGGL Sbjct: 361 LYRESAAGPGRRVDSGVEEGDSISPFYDPMLGKLIAWGVDREQARLRLLSMLEEFAIGGL 420 Query: 421 KTNINFLRRIIGHPAFAAAELDTGFIPRYQEQLLPAPSDLSDEFWQAAAQAFAQSQSSTT 480 KTNINFLRRIIGHPAFAAAELDTGFIPRYQ+QLLPAP++LSD FWQAAAQAFAQSQ+ Sbjct: 421 KTNINFLRRIIGHPAFAAAELDTGFIPRYQDQLLPAPNELSDAFWQAAAQAFAQSQAHHV 480 Query: 481 RADDLSSPWGIGNGFRAGLPTEITLHLSCEEQDRALTLGDADAHTAQLKGEYLLTEHNGL 540 RADD SPW +G+GFRAGLP E TLHLSCE+QDRA+TL A+ +L GE LL EH+GL Sbjct: 481 RADDPGSPWAVGSGFRAGLPAETTLHLSCEDQDRAITLATAETRNTELNGEQLLVEHHGL 540 Query: 541 RRQHRAIRRGDTLYLQWDGELRRIESYDPISAVEASHSHQGGLTAPMNGSIVRVLVEAGQ 600 RRQHRAIR+ +TLYLQW+GELR I+ YDPI+AVEASHSHQGGLTAPMNGSIVRVLV GQ Sbjct: 541 RRQHRAIRQAETLYLQWEGELRCIKLYDPIAAVEASHSHQGGLTAPMNGSIVRVLVTPGQ 600 Query: 601 TVEAGAQLVVLEAMKMEHSIRAPHAGIIKALYCQEGEMVSEGSALVELE 649 TVE GAQLVVLEAMKMEHSIRAPHAG++KALYCQEGEMV+EGSALVELE Sbjct: 601 TVETGAQLVVLEAMKMEHSIRAPHAGVVKALYCQEGEMVNEGSALVELE 649 Lambda K H 0.318 0.134 0.386 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: 1425 Number of extensions: 37 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: 651 Length of database: 649 Length adjustment: 38 Effective length of query: 613 Effective length of database: 611 Effective search space: 374543 Effective search space used: 374543 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 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