Align Methylcrotonyl-CoA carboxylase biotin-containing subunit (EC 6.4.1.4) (characterized)
to candidate PP_4067 PP_4067 methylcrotonyl-CoA carboxylase biotin-containing subunit alpha
Query= reanno::pseudo1_N1B4:Pf1N1B4_3984 (651 letters) >FitnessBrowser__Putida:PP_4067 Length = 650 Score = 1062 bits (2747), Expect = 0.0 Identities = 539/648 (83%), Positives = 581/648 (89%) Query: 1 MSAPVLTTLLVANRGEIACRVMRTAKALGLTTVAVHSATDRDARHSREADIRVDLGGSKA 60 MS P LTTLLVANRGEIACRVMRTAKA+GLTTVAVHSATDRDARHSREADIRVDLGG+KA Sbjct: 1 MSRPALTTLLVANRGEIACRVMRTAKAMGLTTVAVHSATDRDARHSREADIRVDLGGTKA 60 Query: 61 ADSYLQIDKLIAAAKASGAQAIHPGYGFLSENAGFARAIEAAGLIFLGPPASAIDAMGSK 120 A+SYL +DKL+AAAKASGAQAIHPGYGFLSENAGFARAIE AGLIFLGPPASAIDAMGSK Sbjct: 61 AESYLLVDKLLAAAKASGAQAIHPGYGFLSENAGFARAIEQAGLIFLGPPASAIDAMGSK 120 Query: 121 SAAKALMETAGVPLVPGYHGEAQDLETFRDACERIGYPVLLKATAGGGGKGMKVVEDVSQ 180 SAAKALME AGVPLVPGYHGEAQDL+TFR A ERIGYPVLLKA+AGGGGKGMKVVE+ SQ Sbjct: 121 SAAKALMEAAGVPLVPGYHGEAQDLDTFRAAAERIGYPVLLKASAGGGGKGMKVVEEESQ 180 Query: 181 LAEALASAQREALSSFGDSRMLVEKYLLKPRHVEIQVFADQHGNCLYLNERDCSIQRRHQ 240 LA+ALASAQREA SSFGD+RMLVEKY+LKPRHVEIQVFADQHGNCLYLNERDCSIQRRHQ Sbjct: 181 LADALASAQREAQSSFGDARMLVEKYVLKPRHVEIQVFADQHGNCLYLNERDCSIQRRHQ 240 Query: 241 KVVEEAPAPGLSPELRRAMGEAAVRSAQAIGYVGAGTVEFLLDARGEFFFMEMNTRLQVE 300 KVVEEAPAPGLSPELRRAMGEAAVR+AQAIGYVGAGTVEFLLDARGEFFFMEMNTRLQVE Sbjct: 241 KVVEEAPAPGLSPELRRAMGEAAVRAAQAIGYVGAGTVEFLLDARGEFFFMEMNTRLQVE 300 Query: 301 HPVTEAITGLDLVAWQIRVARGEALPMTQDQVPLIGHAIEVRLYAEDPGNDFLPATGRLA 360 HPVTEAITGLDLVAWQIRVA GEALP+TQ+QVPLIGHAIEVRLYAEDP NDFLPATG+LA Sbjct: 301 HPVTEAITGLDLVAWQIRVACGEALPITQEQVPLIGHAIEVRLYAEDPANDFLPATGKLA 360 Query: 361 LYRESAAGPGRRVDSGVEEGDEISPFYDPMLGKLIAWGEDREQARLRLLSMLDEFAIGGL 420 LYRESA G GRRVDSGV EGD +SPFYDPMLGKLIAWGEDREQARLRLL+MLDEFAIGGL Sbjct: 361 LYRESAPGEGRRVDSGVSEGDVVSPFYDPMLGKLIAWGEDREQARLRLLAMLDEFAIGGL 420 Query: 421 KTNINFLRRIIGHPAFAAAELDTGFIPRYQEQLLPAPSDLSDEFWQAAAQAFAQSQSSTT 480 KTNI FLRRI+ HPAFAAAELDTGFIPR+Q+ LLPAP L FW+AAA+A+ Q Q+ Sbjct: 421 KTNIAFLRRILAHPAFAAAELDTGFIPRHQDVLLPAPRALPAAFWEAAAEAWLQGQAGHQ 480 Query: 481 RADDLSSPWGIGNGFRAGLPTEITLHLSCEEQDRALTLGDADAHTAQLKGEYLLTEHNGL 540 R DD SPW NG R GLP +LHL QD+A+ L + A T QL+GE L+ + NG+ Sbjct: 481 REDDRHSPWSGSNGLRLGLPARSSLHLVSAGQDQAVALERSAASTWQLQGEQLVHDQNGV 540 Query: 541 RRQHRAIRRGDTLYLQWDGELRRIESYDPISAVEASHSHQGGLTAPMNGSIVRVLVEAGQ 600 RRQH AIRRG TLYL W+GE+ IE++DPI+ EASHSHQGGL APMNGSIVRVLVE GQ Sbjct: 541 RRQHLAIRRGGTLYLHWEGEMHAIEAFDPIAEAEASHSHQGGLGAPMNGSIVRVLVEPGQ 600 Query: 601 TVEAGAQLVVLEAMKMEHSIRAPHAGIIKALYCQEGEMVSEGSALVEL 648 VEAG L+VLEAMKMEHSIRAPHAG +KAL+C EG+MVSEG+ LVEL Sbjct: 601 VVEAGTALLVLEAMKMEHSIRAPHAGTVKALFCLEGDMVSEGTVLVEL 648 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: 1376 Number of extensions: 45 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: 650 Length adjustment: 38 Effective length of query: 613 Effective length of database: 612 Effective search space: 375156 Effective search space used: 375156 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