Align glutaryl-CoA dehydrogenase (EC 1.3.8.6) (characterized)
to candidate GFF3996 HP15_3936 acyl-CoA dehydrogenase domain protein
Query= metacyc::G1G01-166-MONOMER (393 letters) >FitnessBrowser__Marino:GFF3996 Length = 389 Score = 538 bits (1386), Expect = e-157 Identities = 269/389 (69%), Positives = 311/389 (79%), Gaps = 3/389 (0%) Query: 5 ASFNWIDPLLLDQQLTEEERMVRDSAYQFAQDKLAPRVLEAFRHEQTDPAIFREMGEVGL 64 AS W D L D QL E ER VRDS F ++L P + EA RHE+ D +IF +MGE+G+ Sbjct: 2 ASAPWNDLLGFDAQLDETERQVRDSIRSFCDEQLMPGITEANRHEKFDRSIFNQMGELGM 61 Query: 65 LGATIPEQYGGSGLNYVCYGLIAREVERIDSGYRSMMSVQSSLVMVPINEFGTEAQKQKY 124 LGAT+PE+YGG GLN+VCYGLIAREVER+DS YRS +SVQSSLVM PI +G EA K++ Sbjct: 62 LGATLPEEYGGPGLNHVCYGLIAREVERVDSAYRSALSVQSSLVMYPIYSYGKEAMKKRI 121 Query: 125 LPKLASGEWIGCFGLTEPNHGSDPGSMITRARKVDGGYRLTGSKMWITNSPIADVFVVWA 184 LPKLASGE++GCFGLTEPNHGSDP M TRA+KVDGGY L+GSK WITNSPIADV VVWA Sbjct: 122 LPKLASGEYVGCFGLTEPNHGSDPSGMETRAKKVDGGYLLSGSKTWITNSPIADVCVVWA 181 Query: 185 KDDAGDIRGFVLEK-GWQGLSAPAIHGKVGLRASITGEIVMDNVFVPEENIFPDVRGLKG 243 K D G + GFV+E+ G GL P I GK LRAS TG I MD VFVP+EN +V GLKG Sbjct: 182 KLD-GKVNGFVIEREGATGLETPKIQGKFSLRASETGSIFMDEVFVPDENHL-EVEGLKG 239 Query: 244 PFTCLNSARYGISWGALGAAEACWHTARQYTLDRQQFGRPLAANQLIQKKLADMQTEITL 303 PF+CLN AR+GISWG+LGAAE CWH AR YTL+R+QFG+PLAANQLIQKKL DMQTEIT+ Sbjct: 240 PFSCLNKARFGISWGSLGAAEFCWHAARNYTLERKQFGKPLAANQLIQKKLVDMQTEITI 299 Query: 304 ALQGCLRLGRMKDEGTAAVEITSIMKRNSCGKALDIARMARDMLGGNGISDEFGVARHLV 363 LQ L+LGRM D GT + S++KRN+CGKALDIAR+ARDM GGNGI+DE+ V RH++ Sbjct: 300 GLQAVLQLGRMMDAGTVTPDAISLLKRNNCGKALDIARVARDMHGGNGIADEYHVIRHVM 359 Query: 364 NLEVVNTYEGTHDVHALILGRAQTGIQAF 392 NLE VNTYEGTHDVHALILGR QTGIQAF Sbjct: 360 NLEAVNTYEGTHDVHALILGRGQTGIQAF 388 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: 485 Number of extensions: 17 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: 389 Length adjustment: 31 Effective length of query: 362 Effective length of database: 358 Effective search space: 129596 Effective search space used: 129596 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