Align Glutaryl-CoA dehydrogenase, mitochondrial; GCD; EC 1.3.8.6 (characterized)
to candidate WP_090274985.1 BLU11_RS15705 isovaleryl-CoA dehydrogenase
Query= SwissProt::P81140 (408 letters) >NCBI__GCF_900105005.1:WP_090274985.1 Length = 387 Score = 172 bits (436), Expect = 2e-47 Identities = 111/370 (30%), Positives = 190/370 (51%), Gaps = 9/370 (2%) Query: 35 LIRDTFRTYCQEHLMPRIVLANRNEVFHREIISEMGELGVLGPTI-KGYGCAGVSSVAYG 93 ++R+ + + L PR + + +F ++ + G++G+LG T+ + YG AG+ +A+ Sbjct: 16 MLREQVQAFAAAELAPRAAAIDSDNLFPSDMWRKFGDMGLLGVTVSEEYGGAGLGYLAHV 75 Query: 94 LLARELERVDSGYRSAMSVQSSLVMHPIYAYGSEEQQQQKYLPRLAKGELLGCFGLTEPN 153 + E+ R + + S+L ++ I G+ EQ+ +YLP+L GE +G ++EPN Sbjct: 76 VAMEEISRYSASVGLSYGAHSNLCVNQINRNGTAEQKT-RYLPKLISGEHIGALAMSEPN 134 Query: 154 HGSDPGSMETRALHNPSNRSYTLNGAKTWITNSPVADLFVVWARCE----DNCIRGFLLE 209 GSD SM+ RA + Y LNG+KTWITN P A+ +V++A+ + + I F++E Sbjct: 135 AGSDVVSMKLRA--DKKGDRYILNGSKTWITNGPDANTYVIYAKTDLEKGPHGITAFIVE 192 Query: 210 KGMRGLSAPKIEGKFSLRASATGMIIMDDVEVPEENVLPKASS-LAVPFGCLNNARYGIS 268 + +G S K +R S T + DDVEVP EN+L + + V L+ R ++ Sbjct: 193 RDWKGFSRGNKFDKLGMRGSNTCELFFDDVEVPAENILGSENGGVKVLMSGLDYERAVLA 252 Query: 269 WGVLGAAEFCLHTARQYTLDRIQFGVPLAKNQLIQRKLADMLTEITLGLHACLQLGRLKD 328 G G + CL Y DR QFG + + Q IQ K+ADM T++ + + D Sbjct: 253 GGPTGIMQACLDVVVPYIHDRKQFGQSIGEFQFIQGKVADMYTQLNASRAYLYTVAQACD 312 Query: 329 QDKVTPEMVSLLKRNNCGKALDIARQARDMLGGNGISDEYHVIRHAMNLEAVNTYEGTHD 388 + + T + + + A +A QA +LGGNG +E+ R + + GT + Sbjct: 313 RGETTRKDAAGVILYTAENATQMALQAIQILGGNGYINEFSTGRLLRDAKLYEIGAGTSE 372 Query: 389 IHALILGRAI 398 I +++GR + Sbjct: 373 IRRMLIGREL 382 Lambda K H 0.319 0.136 0.404 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: 366 Number of extensions: 16 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: 408 Length of database: 387 Length adjustment: 31 Effective length of query: 377 Effective length of database: 356 Effective search space: 134212 Effective search space used: 134212 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: 50 (23.9 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