Align Methylcrotonyl-CoA carboxylase biotin-containing subunit (EC 6.4.1.4) (characterized)
to candidate WP_050656086.1 C1M55_RS09265 acetyl/propionyl/methylcrotonyl-CoA carboxylase subunit alpha
Query= reanno::pseudo1_N1B4:Pf1N1B4_3984 (651 letters) >NCBI__GCF_002893965.1:WP_050656086.1 Length = 679 Score = 533 bits (1373), Expect = e-155 Identities = 308/658 (46%), Positives = 404/658 (61%), Gaps = 22/658 (3%) Query: 6 LTTLLVANRGEIACRVMRTAKALGLTTVAVHSATDRDARHSREADIRVDLGGSKAADSYL 65 + T+LVANRGEIA RV+RT + LG+ +VAV+S D +ARH READ V++G + A +SYL Sbjct: 7 IDTVLVANRGEIAVRVIRTLRELGIRSVAVYSDADANARHVREADTAVNIGPAAARESYL 66 Query: 66 QIDKLIAAAKASGAQAIHPGYGFLSENAGFARAIEAAGLIFLGPPASAIDAMGSKSAAKA 125 IDK+I AAK++GAQ IHPGYGFLSEN+ F+ A AAG+ FLGP AI+ MG K AK Sbjct: 67 VIDKVIDAAKSTGAQGIHPGYGFLSENSAFSAACAAAGIAFLGPSEHAIEVMGDKITAKN 126 Query: 126 LMETAGVPLVPGYHGEAQDLETFRDACERIGYPVLLKATAGGGGKGMKVVEDVSQLAEAL 185 + VP+VPG E A E IGYPVL+K +AGGGGKGM++VED + LAEAL Sbjct: 127 SVAAFDVPVVPGIARPNLTDEELIAAAEDIGYPVLVKPSAGGGGKGMRLVEDPANLAEAL 186 Query: 186 ASAQREALSSFGDSRMLVEKYLLKPRHVEIQVFADQHGNCLYLNERDCSIQRRHQKVVEE 245 SA+REA SSFGD + +E+++L+PRH+E+QV ADQHGN ++L ER+CS+QRRHQKV+EE Sbjct: 187 RSARREAASSFGDDTLFLERFVLRPRHIEVQVLADQHGNVVHLGERECSLQRRHQKVIEE 246 Query: 246 APAPGLSPELRRAMGEAAVRSAQAIGYVGAGTVEFLL--DARGEFFFMEMNTRLQVEHPV 303 AP+P L R +G AA +A+++ Y GAGTVEF++ D EFFFMEMNTRLQVEHPV Sbjct: 247 APSPLLDQVTRDRIGAAACNTARSVDYTGAGTVEFIVSADKPDEFFFMEMNTRLQVEHPV 306 Query: 304 TEAITGLDLVAWQIRVARGEALPMTQDQVPLIGHAIEVRLYAEDPGNDFLPATGRLALYR 363 TE +TGLDLV WQ+RVA GE L +Q + L GHAIE R+YAEDPG FLP GR+ Sbjct: 307 TEMVTGLDLVEWQVRVAAGEKLAFSQSDITLTGHAIEARVYAEDPGRGFLPTGGRVVDLV 366 Query: 364 ESAAGPGRRVDSGVEEGDEISPFYDPMLGKLIAWGEDREQARLRLLSMLDEFAIGGLKTN 423 E +G G RVDSG+ G + YDPML K+IA DR A +L L + A+ G+ TN Sbjct: 367 E-PSGSGVRVDSGLLAGTVVGSDYDPMLSKVIAHAPDRAGALRKLDRALGDTAVLGVVTN 425 Query: 424 INFLRRIIGHPAFAAAELDTGFIPRYQEQLLPAPSDLSDEFWQAAAQAFAQSQSSTTRAD 483 I F R ++ P A LDTG + R E + A D SDE AAA S+ +T+ Sbjct: 426 IEFARFLLADPDVIAGNLDTGLLDRRVEDFVAA--DASDEVLIAAAAYRWLSRWTTSERF 483 Query: 484 DLSSPWGIGNGFRAGLPTEITLHLSCEEQDRALTL-------------GDADAHTAQLKG 530 D PW + +G+R G P ++ LS + + + A +A L G Sbjct: 484 D---PWDVPSGWRVGTPAPTSIRLSAGTRTAHVAIVGVPAAAKVEVEGSQPRAFSATLTG 540 Query: 531 EYLLTEHNGLRRQHRAIRRGDTLYLQWDGELRRIESYDPISAVEASHSHQGGLTAPMNGS 590 L +G RR L+L G E + E H+ + +PM G+ Sbjct: 541 SELAVVIDGRRRTFVVAETDGGLWLAGGGTWHVREVAEVSVRGEDKHAGDAEIASPMPGA 600 Query: 591 IVRVLVEAGQTVEAGAQLVVLEAMKMEHSIRAPHAGIIKALYCQEGEMVSEGSALVEL 648 ++ V VE G V AG LVV+EAMKMEHS+ +P GI++ L ++G+ V L + Sbjct: 601 VIAVNVENGAAVSAGQPLVVVEAMKMEHSLTSPIDGIVEVL-VRQGDQVMVDQVLARV 657 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: 1039 Number of extensions: 43 Number of successful extensions: 6 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: 679 Length adjustment: 38 Effective length of query: 613 Effective length of database: 641 Effective search space: 392933 Effective search space used: 392933 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 24 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