Align methylcrotonoyl-CoA carboxylase (EC 6.4.1.4) (characterized)
to candidate WP_099019486.1 CCS90_RS10290 methylcrotonoyl-CoA carboxylase
Query= BRENDA::Q9I297 (535 letters) >NCBI__GCF_002591915.1:WP_099019486.1 Length = 535 Score = 710 bits (1832), Expect = 0.0 Identities = 346/535 (64%), Positives = 421/535 (78%) Query: 1 MAILHTQINPRSAEFAANAATMLEQVNALRTLLGRIHEGGGSAAQARHSARGKLLVRERI 60 M I+ TQI+ S +F N M + V+ L L + GG ++ +H+ RGKLLVR+RI Sbjct: 1 MKIIKTQIDASSTQFDENRHFMGQLVDDLNLKLTQTSLGGSERSRIKHTDRGKLLVRDRI 60 Query: 61 NRLLDPGSPFLELSALAAHEVYGEEVAAAGIVAGIGRVEGVECMIVGNDATVKGGTYYPL 120 N LLDPGSPFLE++ +AA +Y AAG+V GIG V G + ++V NDATVKGGTY+P+ Sbjct: 61 NLLLDPGSPFLEIAPMAAEGMYQNAAPAAGVVVGIGLVHGQQVVVVANDATVKGGTYFPM 120 Query: 121 TVKKHLRAQAIALENRLPCIYLVDSGGANLPRQDEVFPDREHFGRIFFNQANMSARGIPQ 180 TVKKHLRAQ +ALEN LPC+YLVDSGGA LP QDEVFPD+EHFGRIF+NQAN+SA+ IPQ Sbjct: 121 TVKKHLRAQEVALENHLPCVYLVDSGGAFLPLQDEVFPDKEHFGRIFYNQANLSAQNIPQ 180 Query: 181 IAVVMGSCTAGGAYVPAMSDETVMVREQATIFLAGPPLVKAATGEVVSAEELGGADVHCK 240 IAVVMGSCTAGGAYVPAM DE ++V+EQ TIFL GPPLVKAATGEVV AE LGGA+VH Sbjct: 181 IAVVMGSCTAGGAYVPAMCDEAIIVKEQGTIFLGGPPLVKAATGEVVDAESLGGAEVHSS 240 Query: 241 VSGVADHYAEDDDHALAIARRCVANLNWRKQGQLQCRAPRAPLYPAEELYGVIPADSKQP 300 SGV DH+AE+D HAL +AR + LN K L+ + PR PLYPA ELYG+IP ++ P Sbjct: 241 QSGVTDHFAENDQHALQMARNSLQFLNRPKHNWLERKTPRKPLYPAHELYGIIPQSTRTP 300 Query: 301 YDVREVIARLVDGSEFDEFKALFGTTLVCGFAHLHGYPIAILANNGILFAEAAQKGAHFI 360 Y+V+E+IAR+VDGSEF EFKA +GTTL+CGFAH++GYP+ I+ANNGILFAE+A KGAHF+ Sbjct: 301 YEVKEIIARIVDGSEFQEFKAKYGTTLICGFAHINGYPVGIVANNGILFAESALKGAHFV 360 Query: 361 ELACQRGIPLLFLQNITGFMVGQKYEAGGIAKHGAKLVTAVACARVPKFTVLIGGSFGAG 420 EL QR IPL+FLQNITGFMVGQKYE GIAK GAK+VTAVACA+VPKFTV+IGGSFGAG Sbjct: 361 ELCNQRKIPLVFLQNITGFMVGQKYENAGIAKDGAKMVTAVACAQVPKFTVVIGGSFGAG 420 Query: 421 NYGMCGRAYDPRFLWMWPNARIGVMGGEQAAGVLAQVKREQAERAGQQLGVEEEAKIKAP 480 NY M GRAY RFLWMWPNARI VMGG+QAA VL +K++ +++ Q+ EE+ Sbjct: 421 NYAMNGRAYQARFLWMWPNARISVMGGDQAASVLTTIKQDGFDQSDQKWDSEEKESFYQN 480 Query: 481 ILEQYEHQGHPYYSSARLWDDGVIDPAQTREVLALALSAALNAPIEPTAFGVFRM 535 I QY+ QGHPYYS+ARLWDDGVIDPA TR++L+LA+ A+ A ++ +GVFRM Sbjct: 481 IKNQYDQQGHPYYSTARLWDDGVIDPADTRQILSLAIEASTCADVKKVQYGVFRM 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: 852 Number of extensions: 28 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 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