Align glutaryl-CoA dehydrogenase (EC 1.3.8.6) (characterized)
to candidate 5208388 Shew_0900 acyl-CoA dehydrogenase domain-containing protein (RefSeq)
Query= metacyc::G1G01-166-MONOMER (393 letters) >FitnessBrowser__PV4:5208388 Length = 391 Score = 559 bits (1441), Expect = e-164 Identities = 276/391 (70%), Positives = 317/391 (81%), Gaps = 1/391 (0%) Query: 2 VGKASFNWIDPLLLDQQLTEEERMVRDSAYQFAQDKLAPRVLEAFRHEQTDPAIFREMGE 61 + + F+W DPL D L+E+ERM+RD + +AQ+KL RVL A R+E D I E+GE Sbjct: 1 MARVKFDWQDPLQFDALLSEDERMIRDMVHDYAQEKLMTRVLMANRNEHFDREIMNELGE 60 Query: 62 VGLLGATIPEQYGGSGLNYVCYGLIAREVERIDSGYRSMMSVQSSLVMVPINEFGTEAQK 121 +GLLGAT+PE YG + NYV YGL+ARE+ER+DSGYRS MSVQSSLVM PI +G E Q+ Sbjct: 61 LGLLGATLPEAYGCANANYVSYGLVAREIERVDSGYRSAMSVQSSLVMHPIYAYGNEQQR 120 Query: 122 QKYLPKLASGEWIGCFGLTEPNHGSDPGSMITRARKVDGGYRLTGSKMWITNSPIADVFV 181 QKYLPKLA+GEW+GCFGLTEP+ GSDPG M TRA ++DGGYRL G+KMWITNSPIADVFV Sbjct: 121 QKYLPKLATGEWVGCFGLTEPDVGSDPGGMKTRAERIDGGYRLNGAKMWITNSPIADVFV 180 Query: 182 VWAKDDAGDIRGFVLEKGWQGLSAPAIHGKVGLRASITGEIVMDNVFVPEENIFPDVRGL 241 VWAK D G IRGF+LEKG +GLSAP I GK LRASITGEIVMDNV V EE + P+V GL Sbjct: 181 VWAKLD-GVIRGFILEKGMKGLSAPKIEGKFSLRASITGEIVMDNVEVGEEALLPNVEGL 239 Query: 242 KGPFTCLNSARYGISWGALGAAEACWHTARQYTLDRQQFGRPLAANQLIQKKLADMQTEI 301 KGPF CLN ARYGI+WGALGAAE CWH ARQY+LDR QF RPLAA QLIQKKLADMQTEI Sbjct: 240 KGPFGCLNKARYGIAWGALGAAEFCWHAARQYSLDRIQFNRPLAATQLIQKKLADMQTEI 299 Query: 302 TLALQGCLRLGRMKDEGTAAVEITSIMKRNSCGKALDIARMARDMLGGNGISDEFGVARH 361 T L CL+ GR+ D+ VE S++KRNSCGKAL+IAR +RDM GGNGISDEF V RH Sbjct: 300 TTGLFACLQAGRLMDQDALPVEAISLIKRNSCGKALEIARTSRDMHGGNGISDEFHVIRH 359 Query: 362 LVNLEVVNTYEGTHDVHALILGRAQTGIQAF 392 ++NLE VNTYEGTHD+HALILGRAQTGIQAF Sbjct: 360 VMNLEAVNTYEGTHDIHALILGRAQTGIQAF 390 Lambda K H 0.320 0.137 0.413 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: 510 Number of extensions: 14 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: 393 Length of database: 391 Length adjustment: 31 Effective length of query: 362 Effective length of database: 360 Effective search space: 130320 Effective search space used: 130320 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