Align Glutaryl-CoA dehydrogenase, mitochondrial; GCD; EC 1.3.8.6 (characterized)
to candidate PP_3492 PP_3492 short-chain acyl-CoA dehydrogenase
Query= SwissProt::P81140 (408 letters) >FitnessBrowser__Putida:PP_3492 Length = 383 Score = 176 bits (445), Expect = 1e-48 Identities = 116/377 (30%), Positives = 186/377 (49%), Gaps = 9/377 (2%) Query: 28 QLTADEILIRDTFRTYCQEHLMPRIVLANRNEVFHREIISEMGELGVLGPTI-KGYGCAG 86 +L+ ++I+IRD R + + + P + ++ +MGELG+LG + + +G + Sbjct: 5 ELSEEQIMIRDMARDFARGEIAPHAQAWEKAGWIDDGVVRKMGELGLLGMVVPEDFGGSY 64 Query: 87 VSSVAYGLLARELERVDSGYRSAMSVQSSLVMHPIYAYGSEEQQQQKYLPRLAKGELLGC 146 VAY L E+ + MS+ +S+ P+ AYG+ EQQQQ +LPRLA GE++GC Sbjct: 65 TDYVAYALAVEEISAGCGATGAMMSIHNSVGCGPLLAYGTAEQQQQ-WLPRLASGEVIGC 123 Query: 147 FGLTEPNHGSDPGSMETRALHNPSNRSYTLNGAKTWITNSPVADLFVVWARCEDNC---- 202 F LTEP GS+ ++ TRA + + +NGAK +++N+ A L +V+A + Sbjct: 124 FCLTEPQAGSEAHNLRTRA--ELVDGQWVINGAKQFVSNARRAGLAIVFAVTDPELGKKG 181 Query: 203 IRGFLLEKGMRGLSAPKIEGKFSLRASATGMIIMDDVEVPEENVL-PKASSLAVPFGCLN 261 + FL+ G + E K +RAS T + D+ +P N+L + LA+ L Sbjct: 182 LSAFLVPTDNPGFKVDRSEHKMGIRASDTCAVTFDNCRIPAANILGERGKGLAIALSNLE 241 Query: 262 NARYGISWGVLGAAEFCLHTARQYTLDRIQFGVPLAKNQLIQRKLADMLTEITLGLHACL 321 R GI+ LG A A Y+ DRIQFG P+ ++Q I LADM ++ L Sbjct: 242 GGRIGIAAQALGIARAAFEAALVYSRDRIQFGKPINEHQSIANLLADMQVQVNAARLLIL 301 Query: 322 QLGRLKDQDKVTPEMVSLLKRNNCGKALDIARQARDMLGGNGISDEYHVIRHAMNLEAVN 381 RL+ K S K A + A + GG G ++Y V R+ + Sbjct: 302 HAARLRSAGKPCLSEASQAKLFASEMAERVCSMAIQVHGGYGYLEDYPVERYYRDARITQ 361 Query: 382 TYEGTHDIHALILGRAI 398 YEG+ +I +++ R + Sbjct: 362 IYEGSSEIQRMLIAREL 378 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: 386 Number of extensions: 19 Number of successful extensions: 5 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: 383 Length adjustment: 31 Effective length of query: 377 Effective length of database: 352 Effective search space: 132704 Effective search space used: 132704 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 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