Align Methylcrotonyl-CoA carboxylase carboxyl transferase subunit (EC 6.4.1.4) (characterized)
to candidate N515DRAFT_0936 N515DRAFT_0936 3-methylcrotonyl-CoA carboxylase beta subunit
Query= reanno::psRCH2:GFF1050 (535 letters) >FitnessBrowser__Dyella79:N515DRAFT_0936 Length = 535 Score = 782 bits (2019), Expect = 0.0 Identities = 383/535 (71%), Positives = 445/535 (83%) Query: 1 MAILHTQINIRSPEFAANSAAMLEQVNDLRALLGRVSEGGGATAQQRHVSRGKLLVRERI 60 M+++ +Q++ RSPEF A SA++ V+DL L +EGGG A+++H +RGKLL RERI Sbjct: 1 MSVIASQLDTRSPEFQAGSASLRALVDDLHRQLAHSAEGGGEKAREKHTARGKLLPRERI 60 Query: 61 DTLLDAGSAFLELAPLAAHEVYGEDVAAAGVVAGIGRVEGIECMIIANDATVKGGTYYPL 120 LLD GS FLEL+PLAAH +Y + AAG++ GIGRV GIE +++ANDATVKGGTY+P+ Sbjct: 61 RALLDPGSPFLELSPLAAHGMYDDAAPAAGIITGIGRVHGIEVVVVANDATVKGGTYFPM 120 Query: 121 TVKKHLRAQTVARENRLPCIYLVDSGGANLPRQDEVFPDREHFGRIFFNQANMSAMGIPQ 180 TVKKHLRAQ VA ENRLPC+YLVDSGGA LP QDEVFPD+EHFGRIF+NQA MS +GIPQ Sbjct: 121 TVKKHLRAQEVALENRLPCVYLVDSGGAFLPLQDEVFPDKEHFGRIFYNQARMSGLGIPQ 180 Query: 181 IAVVMGSCTAGGAYVPAMADETIMVRNQATIFLAGPPLVKAATGEVVTAEELGGADVHCK 240 IAVVMGSCTAGGAYVPAM+DETI+VR Q TIFL GPPLVKAATGEVV AE LGGADVH Sbjct: 181 IAVVMGSCTAGGAYVPAMSDETIIVREQGTIFLGGPPLVKAATGEVVDAEALGGADVHTS 240 Query: 241 TSGVADHYAENDEHALSIARRCVANLNWRKLGQLQTREPRAPLYAADELYGVIPAQAKQP 300 SGVADH+AEND HALSIAR VA+LN RK L R P P YAA+ELYGVIP ++P Sbjct: 241 VSGVADHFAENDAHALSIARDIVASLNRRKDIPLALRAPAEPRYAAEELYGVIPQDTRRP 300 Query: 301 YDVREVIARLVDGSEFDEFKALFGTTLVCGFAHLHGYPIAILANNGILFAEAAQKGAHFI 360 +D+REVIAR+VDGSEF EFKA +G TLVCGFAH+HGYP+ I+ANNGILFAE+A KGAHFI Sbjct: 301 FDIREVIARIVDGSEFHEFKARYGKTLVCGFAHIHGYPVGIVANNGILFAESALKGAHFI 360 Query: 361 ELACQRGIPLLFLQNITGFMVGQKYEAGGIAKHGAKLVTAVACAQVPKFTVLIGGSFGAG 420 EL QR +PL+FLQNITGFMVG+KYE GIAK GAK+VTAVAC+ VPKFTV+IGGSFGAG Sbjct: 361 ELCNQRNVPLVFLQNITGFMVGRKYENAGIAKDGAKMVTAVACSHVPKFTVVIGGSFGAG 420 Query: 421 NYGMCGRAYDPRFLWMWPNARIAVMGGEQAAGVLAQVKQEQSERAGKSLGDDEVAAIKQP 480 NY MCGRAY RFLWMWPNARI+VMGGEQA+ VLA V+++ E +GKS ++ A K P Sbjct: 421 NYAMCGRAYGARFLWMWPNARISVMGGEQASSVLATVRRDGLEASGKSWSAEDEEAFKAP 480 Query: 481 ILEQYERQGHPYYSSARLWDDGVIDPAQTREVLGLALSAALNAPIEPTRFGVFRM 535 I EQYERQGHPYY+SARLWDDG+IDPA TR VLGLA+SA+LNAPIEP R+GVFRM Sbjct: 481 IREQYERQGHPYYASARLWDDGIIDPADTRRVLGLAISASLNAPIEPQRYGVFRM 535 Lambda K H 0.321 0.136 0.405 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: 959 Number of extensions: 33 Number of successful extensions: 2 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 (21.8 bits) S2: 52 (24.6 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