Align Methylcrotonoyl-CoA carboxylase (EC 6.4.1.4) (characterized)
to candidate Pf6N2E2_2194 Methylcrotonyl-CoA carboxylase biotin-containing subunit (EC 6.4.1.4)
Query= reanno::pseudo6_N2E2:Pf6N2E2_2194 (649 letters) >FitnessBrowser__pseudo6_N2E2:Pf6N2E2_2194 Length = 649 Score = 1276 bits (3301), Expect = 0.0 Identities = 649/649 (100%), Positives = 649/649 (100%) Query: 1 MSAPALTTLLVANRGEIACRVMRTAKAMGLTTVAVHSATDRDARHSREADIRVDLGGSKA 60 MSAPALTTLLVANRGEIACRVMRTAKAMGLTTVAVHSATDRDARHSREADIRVDLGGSKA Sbjct: 1 MSAPALTTLLVANRGEIACRVMRTAKAMGLTTVAVHSATDRDARHSREADIRVDLGGSKA 60 Query: 61 ADSYLQIDKLIAAAKASGAQAIHPGYGFLSENAGFARAIENAGLIFLGPPASAIDAMGSK 120 ADSYLQIDKLIAAAKASGAQAIHPGYGFLSENAGFARAIENAGLIFLGPPASAIDAMGSK Sbjct: 61 ADSYLQIDKLIAAAKASGAQAIHPGYGFLSENAGFARAIENAGLIFLGPPASAIDAMGSK 120 Query: 121 SAAKALMETAGVPLVPGYHGEAQDLETFRDAAERIGYPVLLKATAGGGGKGMKVVEDVSQ 180 SAAKALMETAGVPLVPGYHGEAQDLETFRDAAERIGYPVLLKATAGGGGKGMKVVEDVSQ Sbjct: 121 SAAKALMETAGVPLVPGYHGEAQDLETFRDAAERIGYPVLLKATAGGGGKGMKVVEDVSQ 180 Query: 181 LAEALASAQREAQSSFGDSRMLVEKYLLKPRHVEIQVFADQHGNCLYLNERDCSIQRRHQ 240 LAEALASAQREAQSSFGDSRMLVEKYLLKPRHVEIQVFADQHGNCLYLNERDCSIQRRHQ Sbjct: 181 LAEALASAQREAQSSFGDSRMLVEKYLLKPRHVEIQVFADQHGNCLYLNERDCSIQRRHQ 240 Query: 241 KVVEEAPAPGLTAQLRQAMGEAAVRAAQAIGYVGAGTVEFLLDARGEFFFMEMNTRLQVE 300 KVVEEAPAPGLTAQLRQAMGEAAVRAAQAIGYVGAGTVEFLLDARGEFFFMEMNTRLQVE Sbjct: 241 KVVEEAPAPGLTAQLRQAMGEAAVRAAQAIGYVGAGTVEFLLDARGEFFFMEMNTRLQVE 300 Query: 301 HPVTEAITGLDLVAWQIRVAQGEPLPITQAQVPLLGHAIEVRLYAEDPVNDFLPATGRLA 360 HPVTEAITGLDLVAWQIRVAQGEPLPITQAQVPLLGHAIEVRLYAEDPVNDFLPATGRLA Sbjct: 301 HPVTEAITGLDLVAWQIRVAQGEPLPITQAQVPLLGHAIEVRLYAEDPVNDFLPATGRLA 360 Query: 361 LYRESAKGPGRRVDSGVEEGDEISPFYDPMLGKLIAWGENREQARLRLLSMLDEFAIGGL 420 LYRESAKGPGRRVDSGVEEGDEISPFYDPMLGKLIAWGENREQARLRLLSMLDEFAIGGL Sbjct: 361 LYRESAKGPGRRVDSGVEEGDEISPFYDPMLGKLIAWGENREQARLRLLSMLDEFAIGGL 420 Query: 421 KTNIGFLRRIVAHPAFAAAELDTGFIPRYQAQLLPEPGELDDAFWLAAAQGFALSLAPHI 480 KTNIGFLRRIVAHPAFAAAELDTGFIPRYQAQLLPEPGELDDAFWLAAAQGFALSLAPHI Sbjct: 421 KTNIGFLRRIVAHPAFAAAELDTGFIPRYQAQLLPEPGELDDAFWLAAAQGFALSLAPHI 480 Query: 481 RGDDAGSPWASTTGMRLGLSRETTLHLSCEGQDRALTLDVTAHCAELKGERLTIEHHGVR 540 RGDDAGSPWASTTGMRLGLSRETTLHLSCEGQDRALTLDVTAHCAELKGERLTIEHHGVR Sbjct: 481 RGDDAGSPWASTTGMRLGLSRETTLHLSCEGQDRALTLDVTAHCAELKGERLTIEHHGVR 540 Query: 541 RSHRAIRQGDSLYLHWAGDLHRIDLYDPLAAAEASHSHQGGLAAPMNGSIVRVLVSVGQP 600 RSHRAIRQGDSLYLHWAGDLHRIDLYDPLAAAEASHSHQGGLAAPMNGSIVRVLVSVGQP Sbjct: 541 RSHRAIRQGDSLYLHWAGDLHRIDLYDPLAAAEASHSHQGGLAAPMNGSIVRVLVSVGQP 600 Query: 601 VDAGAQLVVLEAMKMEHSIRAPKAGVIKALYCQEGEMVSEGSALVAFEE 649 VDAGAQLVVLEAMKMEHSIRAPKAGVIKALYCQEGEMVSEGSALVAFEE Sbjct: 601 VDAGAQLVVLEAMKMEHSIRAPKAGVIKALYCQEGEMVSEGSALVAFEE 649 Lambda K H 0.319 0.134 0.389 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: 1546 Number of extensions: 38 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: 649 Length of database: 649 Length adjustment: 38 Effective length of query: 611 Effective length of database: 611 Effective search space: 373321 Effective search space used: 373321 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 (21.7 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