Align glutaryl-CoA dehydrogenase (EC 1.3.8.6) (characterized)
to candidate 6938693 Sama_2796 acyl-CoA dehydrogenase-like protein (RefSeq)
Query= metacyc::G1G01-166-MONOMER (393 letters) >FitnessBrowser__SB2B:6938693 Length = 391 Score = 561 bits (1446), Expect = e-164 Identities = 278/391 (71%), Positives = 318/391 (81%), Gaps = 1/391 (0%) Query: 2 VGKASFNWIDPLLLDQQLTEEERMVRDSAYQFAQDKLAPRVLEAFRHEQTDPAIFREMGE 61 + + F+W DPL + LTEEERM+RD +++AQDKL RVL A R E D I E+GE Sbjct: 1 MARVQFDWQDPLNFNSLLTEEERMIRDMVHEYAQDKLMARVLMANRDEHFDREIMNELGE 60 Query: 62 VGLLGATIPEQYGGSGLNYVCYGLIAREVERIDSGYRSMMSVQSSLVMVPINEFGTEAQK 121 +GLLGAT+PE+YG + NYV YGL+ARE+ER+DSGYRS MSVQSSLVM PI +GTEAQ+ Sbjct: 61 LGLLGATLPEEYGCANANYVSYGLVAREIERVDSGYRSAMSVQSSLVMHPIYTYGTEAQR 120 Query: 122 QKYLPKLASGEWIGCFGLTEPNHGSDPGSMITRARKVDGGYRLTGSKMWITNSPIADVFV 181 +KYLPKLA+GEW+GCFGLTEP+ GSDP M TRA ++DGGYR+TG+KMWITNSPIADVFV Sbjct: 121 RKYLPKLATGEWVGCFGLTEPDVGSDPAGMKTRAERIDGGYRITGAKMWITNSPIADVFV 180 Query: 182 VWAKDDAGDIRGFVLEKGWQGLSAPAIHGKVGLRASITGEIVMDNVFVPEENIFPDVRGL 241 VWAK D G IRGFVLEKG +GLSAP I GK LRASITGEIVMDNV V E+ + P+V GL Sbjct: 181 VWAKLD-GAIRGFVLEKGMKGLSAPKIEGKFSLRASITGEIVMDNVEVGEDALLPNVEGL 239 Query: 242 KGPFTCLNSARYGISWGALGAAEACWHTARQYTLDRQQFGRPLAANQLIQKKLADMQTEI 301 KGPF CLN ARYGI+WGALGAAE CWH ARQY LDR QF RPLAANQL QKKLADMQTEI Sbjct: 240 KGPFGCLNKARYGIAWGALGAAEFCWHAARQYGLDRIQFNRPLAANQLYQKKLADMQTEI 299 Query: 302 TLALQGCLRLGRMKDEGTAAVEITSIMKRNSCGKALDIARMARDMLGGNGISDEFGVARH 361 T L CL+ GR+ D VE S++KRNSCGKALDIAR+ARDM GGNGISDEF V RH Sbjct: 300 TTGLFACLQAGRLMDVDALPVEAISLIKRNSCGKALDIARIARDMHGGNGISDEFHVIRH 359 Query: 362 LVNLEVVNTYEGTHDVHALILGRAQTGIQAF 392 ++NLE VNTYEGTHD+HALILGRAQT +QAF Sbjct: 360 VMNLEAVNTYEGTHDIHALILGRAQTDLQAF 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: 524 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: 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 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