Align Glutaryl-CoA dehydrogenase, mitochondrial; GCD; EC 1.3.8.6 (characterized)
to candidate WP_073035809.1 BUB04_RS00225 acyl-CoA dehydrogenase family protein
Query= SwissProt::P81140 (408 letters) >NCBI__GCF_900129305.1:WP_073035809.1 Length = 382 Score = 176 bits (447), Expect = 8e-49 Identities = 127/383 (33%), Positives = 194/383 (50%), Gaps = 18/383 (4%) Query: 28 QLTADEILIRDTFRTYCQEHLMPRIVLANRNEVFHREIIS----EMGELGVLGPTIKG-Y 82 +LT ++ +I+DT + + L P V A + +REI+ ++ ELG +G + Y Sbjct: 4 ELTEEQKIIQDTAAKFAKNELEP--VAAELDRTKNREILKRNLKKLAELGFMGLNVDPEY 61 Query: 83 GCAGVSSVAYGLLARELERVDSGYRSAMSVQSSLVMHPIYAYGSEEQQQQKYLPRLAKGE 142 G G VA+ L EL R + SV +++V I A G+EEQ++ KY+P L GE Sbjct: 62 GGTGAGVVAFSLAMTELGRACASTTVTTSV-TNMVAEVIQAVGTEEQKR-KYIPPLCSGE 119 Query: 143 LL-GCFGLTEPNHGSDPGSMETRALHNPSNRSYTLNGAKTWITNSPVADLFVVWARCEDN 201 G FGL+E GSDP SM T A+ + + LNG+K WIT++ A +FVVWA + Sbjct: 120 FAAGSFGLSEAGAGSDPASMRTSAVQDGDY--WVLNGSKMWITSAEYAGVFVVWAVTDKE 177 Query: 202 CIRG-----FLLEKGMRGLSAPKIEGKFSLRASATGMIIMDDVEVPEENVLPKASS-LAV 255 +G FL+E G G + K E K S+T ++ +D V ++NVL K + + Sbjct: 178 APKGKGITCFLVEPGTPGFTIGKDEKKLGQHGSSTNELLFEDCRVHKDNVLGKVNDGFRI 237 Query: 256 PFGCLNNARYGISWGVLGAAEFCLHTARQYTLDRIQFGVPLAKNQLIQRKLADMLTEITL 315 L R GI LG + A Y+ +RIQFGVP+AK+Q IQ +AD T + Sbjct: 238 AVSELAGGRIGIGSMALGIGLAAMDFATNYSKERIQFGVPIAKHQAIQWMIADNYTRLEA 297 Query: 316 GLHACLQLGRLKDQDKVTPEMVSLLKRNNCGKALDIARQARDMLGGNGISDEYHVIRHAM 375 L+ LK+Q + + S+ K A A +LGG G + ++ + R+ Sbjct: 298 ARLLLLRAAYLKEQGRPYSKEASMGKVYATEAANKACYDALQILGGYGYTQDFPIERYYR 357 Query: 376 NLEAVNTYEGTHDIHALILGRAI 398 ++ + YEGT +I LI+ R + Sbjct: 358 DVRVTSIYEGTSEIQRLIIAREL 380 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: 378 Number of extensions: 22 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: 382 Length adjustment: 31 Effective length of query: 377 Effective length of database: 351 Effective search space: 132327 Effective search space used: 132327 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 Apr 09 2024. 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