Align 3-methyl-2-oxobutanoate dehydrogenase (2-methylpropanoyl-transferring) (EC 1.2.4.4) (characterized)
to candidate WP_047093915.1 AAV99_RS08480 alpha-ketoacid dehydrogenase subunit beta
Query= reanno::WCS417:GFF3430 (352 letters) >NCBI__GCF_001013305.1:WP_047093915.1 Length = 355 Score = 484 bits (1247), Expect = e-141 Identities = 222/332 (66%), Positives = 273/332 (82%) Query: 19 MTMIQALRSAMDVMLERDDNVVVFGQDVGYFGGVFRCTEGLQTKYGSSRVFDAPISESGI 78 M MI+A+ SA+DVML RD +V + G+D+GYFGGVFRCT GLQ K+G +RVFD PISE GI Sbjct: 22 MNMIEAINSALDVMLTRDSDVTLLGEDIGYFGGVFRCTAGLQEKHGKTRVFDTPISECGI 81 Query: 79 VGVAVGMGAYGLRPVAEIQFADYVYPATDQIISEAARLRYRSAGQFTAPLTMRMPCGGGI 138 +GVAVGMGAYGLRPV EIQFADY+YP DQ+ISEAARLRYRSA +F AP+T+R P GGGI Sbjct: 82 IGVAVGMGAYGLRPVPEIQFADYIYPGLDQLISEAARLRYRSAAEFIAPMTVRSPFGGGI 141 Query: 139 YGGQTHSQSIEAVFTQVCGLRTVMPSNPYDAKGLLIASIENDDPVIFLEPKRLYNGPFDG 198 +GGQTHSQS E++FT VCGL+TV+P+ PYDAKGLLI+ IE++DPVIF EPKR+YNGPFDG Sbjct: 142 FGGQTHSQSPESIFTHVCGLKTVIPATPYDAKGLLISCIEDNDPVIFFEPKRIYNGPFDG 201 Query: 199 HHDRPVTPWSKHPQAQVPDGYYTVPLDVAAIVRPGSAVTVLTYGTTVYVSQVAAEETGID 258 ++DRP W AQVPDGYY +PL A V G A+T+L YGT V+V++ E G+ Sbjct: 202 YYDRPAKNWKGREDAQVPDGYYKIPLGKARTVTEGDAMTILAYGTMVHVAESVCREKGVA 261 Query: 259 AEVIDLRSLWPLDLETIVKSVKKTGRCVVVHEATRTCGFGAELVSLVQEHCFHHLEAPIE 318 AE++DLR+L PLD+E I SVK+TGRC++VHEATRT GFGAEL +LV E CF+HLEAP+E Sbjct: 262 AEILDLRTLVPLDIEAIEASVKRTGRCLIVHEATRTSGFGAELSALVTERCFYHLEAPVE 321 Query: 319 RVTGWDTPYPHAQEWAYFPGPSRVGAALKRVM 350 RVTG+DTPYPH+ EWAYFPGP R+G A+ +++ Sbjct: 322 RVTGFDTPYPHSLEWAYFPGPVRIGEAIDKIL 353 Lambda K H 0.320 0.136 0.414 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: 456 Number of extensions: 15 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: 352 Length of database: 355 Length adjustment: 29 Effective length of query: 323 Effective length of database: 326 Effective search space: 105298 Effective search space used: 105298 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: 49 (23.5 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