Align Methylcrotonyl-CoA carboxylase biotin-containing subunit (EC 6.4.1.4) (characterized)
to candidate PfGW456L13_2588 Methylcrotonyl-CoA carboxylase biotin-containing subunit (EC 6.4.1.4)
Query= reanno::pseudo1_N1B4:Pf1N1B4_3984 (651 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_2588 Length = 651 Score = 1216 bits (3145), Expect = 0.0 Identities = 618/651 (94%), Positives = 629/651 (96%) Query: 1 MSAPVLTTLLVANRGEIACRVMRTAKALGLTTVAVHSATDRDARHSREADIRVDLGGSKA 60 MSAPVLTTLLVANRGEIACRVMRTAKALGLTTVAVHSATDRDARHSREADIRVDLGGSKA Sbjct: 1 MSAPVLTTLLVANRGEIACRVMRTAKALGLTTVAVHSATDRDARHSREADIRVDLGGSKA 60 Query: 61 ADSYLQIDKLIAAAKASGAQAIHPGYGFLSENAGFARAIEAAGLIFLGPPASAIDAMGSK 120 DSYLQIDKLIAAAKASGAQAIHPGYGFLSENAGFARAIEAAGLIFLGPPASAIDAMGSK Sbjct: 61 VDSYLQIDKLIAAAKASGAQAIHPGYGFLSENAGFARAIEAAGLIFLGPPASAIDAMGSK 120 Query: 121 SAAKALMETAGVPLVPGYHGEAQDLETFRDACERIGYPVLLKATAGGGGKGMKVVEDVSQ 180 SAAKALMETAGVPLVPGYHGEAQDLETFR ACERIGYPVLLKATAGGGGKGMKVVEDVSQ Sbjct: 121 SAAKALMETAGVPLVPGYHGEAQDLETFRAACERIGYPVLLKATAGGGGKGMKVVEDVSQ 180 Query: 181 LAEALASAQREALSSFGDSRMLVEKYLLKPRHVEIQVFADQHGNCLYLNERDCSIQRRHQ 240 LAEALASAQREA SSFGDSRMLVEKYLLKPRHVEIQVFADQHGNCLYLNERDCSIQRRHQ Sbjct: 181 LAEALASAQREAQSSFGDSRMLVEKYLLKPRHVEIQVFADQHGNCLYLNERDCSIQRRHQ 240 Query: 241 KVVEEAPAPGLSPELRRAMGEAAVRSAQAIGYVGAGTVEFLLDARGEFFFMEMNTRLQVE 300 KVVEEAPAPGLSPELRRAMGEAAVRSAQAIGYVGAGTVEFLLDARGEFFFMEMNTRLQVE Sbjct: 241 KVVEEAPAPGLSPELRRAMGEAAVRSAQAIGYVGAGTVEFLLDARGEFFFMEMNTRLQVE 300 Query: 301 HPVTEAITGLDLVAWQIRVARGEALPMTQDQVPLIGHAIEVRLYAEDPGNDFLPATGRLA 360 HPVTEAITGLDLVAWQIRVARGEALPMTQDQVPL+GHAIEVRLYAEDPGNDFLPATGRL Sbjct: 301 HPVTEAITGLDLVAWQIRVARGEALPMTQDQVPLVGHAIEVRLYAEDPGNDFLPATGRLE 360 Query: 361 LYRESAAGPGRRVDSGVEEGDEISPFYDPMLGKLIAWGEDREQARLRLLSMLDEFAIGGL 420 LYRESA GPGRRVDSGVEEGDEISPFYDPMLGKLIAWGEDREQARLRLLSMLDEFAIGGL Sbjct: 361 LYRESAQGPGRRVDSGVEEGDEISPFYDPMLGKLIAWGEDREQARLRLLSMLDEFAIGGL 420 Query: 421 KTNINFLRRIIGHPAFAAAELDTGFIPRYQEQLLPAPSDLSDEFWQAAAQAFAQSQSSTT 480 KTNINFLRRIIGHPAFA AELDTGFIPRYQEQLLP P++LSD+FWQAAAQAFAQSQ T Sbjct: 421 KTNINFLRRIIGHPAFATAELDTGFIPRYQEQLLPTPAELSDDFWQAAAQAFAQSQPHAT 480 Query: 481 RADDLSSPWGIGNGFRAGLPTEITLHLSCEEQDRALTLGDADAHTAQLKGEYLLTEHNGL 540 RADD SSPW NG RAGLP EITLHLSCE QDRALTLGD +AH+A+LKGE LLTEH G+ Sbjct: 481 RADDPSSPWAAPNGLRAGLPREITLHLSCEGQDRALTLGDINAHSARLKGEQLLTEHEGV 540 Query: 541 RRQHRAIRRGDTLYLQWDGELRRIESYDPISAVEASHSHQGGLTAPMNGSIVRVLVEAGQ 600 RRQHRAIRRGD +YLQWDGELRRIESYDPISAVEASHSHQGGLTAPMNGSIVRVLVEAGQ Sbjct: 541 RRQHRAIRRGDYVYLQWDGELRRIESYDPISAVEASHSHQGGLTAPMNGSIVRVLVEAGQ 600 Query: 601 TVEAGAQLVVLEAMKMEHSIRAPHAGIIKALYCQEGEMVSEGSALVELEHA 651 +VEAGAQLVVLEAMKMEHSIRAPHAG+IKALYCQEGEMVSEGSALVELE A Sbjct: 601 SVEAGAQLVVLEAMKMEHSIRAPHAGVIKALYCQEGEMVSEGSALVELEEA 651 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: 1444 Number of extensions: 47 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: 651 Length adjustment: 38 Effective length of query: 613 Effective length of database: 613 Effective search space: 375769 Effective search space used: 375769 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