Align methylcrotonoyl-CoA carboxylase (EC 6.4.1.4) (characterized)
to candidate WP_029133982.1 A3GO_RS0114360 carboxyl transferase domain-containing protein
Query= BRENDA::Q9I297 (535 letters) >NCBI__GCF_000428045.1:WP_029133982.1 Length = 535 Score = 780 bits (2015), Expect = 0.0 Identities = 372/535 (69%), Positives = 439/535 (82%) Query: 1 MAILHTQINPRSAEFAANAATMLEQVNALRTLLGRIHEGGGSAAQARHSARGKLLVRERI 60 M+++ + IN +S ++ N M V LR + I EGGG A+ +H RGKLL RERI Sbjct: 1 MSVIKSSINRKSEQYRENQVFMQALVADLRERVEVIAEGGGERAREKHLKRGKLLPRERI 60 Query: 61 NRLLDPGSPFLELSALAAHEVYGEEVAAAGIVAGIGRVEGVECMIVGNDATVKGGTYYPL 120 LLD GSPFLELS AA +Y EV AAG++ GIGRV G ECMI+ NDATVKGG+Y+P+ Sbjct: 61 RVLLDTGSPFLELSQFAAFGMYNNEVPAAGVITGIGRVCGQECMIIANDATVKGGSYFPM 120 Query: 121 TVKKHLRAQAIALENRLPCIYLVDSGGANLPRQDEVFPDREHFGRIFFNQANMSARGIPQ 180 TVKKH+RAQ IA ENRLPCIYLVDSGGANLP QDEVFPDREHFGRIF+NQANMSA+GIPQ Sbjct: 121 TVKKHIRAQEIARENRLPCIYLVDSGGANLPTQDEVFPDREHFGRIFYNQANMSAQGIPQ 180 Query: 181 IAVVMGSCTAGGAYVPAMSDETVMVREQATIFLAGPPLVKAATGEVVSAEELGGADVHCK 240 +AVVMGSCTAGGAYVPAMSDE+++V+EQ TIFL GPPLVKAATG VV+AEELGGADVH + Sbjct: 181 VAVVMGSCTAGGAYVPAMSDESIIVKEQGTIFLGGPPLVKAATGAVVTAEELGGADVHSR 240 Query: 241 VSGVADHYAEDDDHALAIARRCVANLNWRKQGQLQCRAPRAPLYPAEELYGVIPADSKQP 300 SGV DHYA +D HAL +ARR V LN K+ ++ R P PLYP E++YG++P D ++P Sbjct: 241 TSGVTDHYAMNDSHALGLARRVVNTLNRDKRPEVTLRQPVEPLYPKEDIYGIVPTDLRKP 300 Query: 301 YDVREVIARLVDGSEFDEFKALFGTTLVCGFAHLHGYPIAILANNGILFAEAAQKGAHFI 360 +D+REVIAR+VDGSE DEFK L+GTTL+CGFAH+HGYP+ I+ANNGILF+E+AQKGAHF+ Sbjct: 301 FDIREVIARVVDGSELDEFKKLYGTTLICGFAHIHGYPVGIVANNGILFSESAQKGAHFV 360 Query: 361 ELACQRGIPLLFLQNITGFMVGQKYEAGGIAKHGAKLVTAVACARVPKFTVLIGGSFGAG 420 EL QRGIPL+FLQN+TGFMVG+KYEAGGIAK GAK+VTAVACA+VPKFT+++GGSFGAG Sbjct: 361 ELCAQRGIPLVFLQNVTGFMVGKKYEAGGIAKDGAKMVTAVACAKVPKFTIIVGGSFGAG 420 Query: 421 NYGMCGRAYDPRFLWMWPNARIGVMGGEQAAGVLAQVKREQAERAGQQLGVEEEAKIKAP 480 NY MCGRAY RFLWMWPNAR+ VMGGEQAA VL Q+KR+ E G+ +E KAP Sbjct: 421 NYAMCGRAYGSRFLWMWPNARVSVMGGEQAANVLGQIKRDALEARGESWAAADEEAFKAP 480 Query: 481 ILEQYEHQGHPYYSSARLWDDGVIDPAQTREVLALALSAALNAPIEPTAFGVFRM 535 I +QYEHQGHPYY+SARLWDDG+IDPA TR VL L LSAALNAP+E T FG+FRM Sbjct: 481 IRDQYEHQGHPYYASARLWDDGIIDPADTRTVLGLGLSAALNAPVEKTTFGIFRM 535 Lambda K H 0.321 0.137 0.409 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: 939 Number of extensions: 36 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: 535 Length of database: 535 Length adjustment: 35 Effective length of query: 500 Effective length of database: 500 Effective search space: 250000 Effective search space used: 250000 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 (21.9 bits) S2: 52 (24.6 bits)
This GapMind analysis is from Apr 09 2024. 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