Align glutaryl-CoA dehydrogenase (ETF) (EC 1.3.8.6) (characterized)
to candidate YP_427092.1 Rru_A2005 glutaryl-CoA dehydrogenase
Query= BRENDA::Q3JP94 (395 letters) >NCBI__GCF_000013085.1:YP_427092.1 Length = 395 Score = 568 bits (1463), Expect = e-166 Identities = 283/389 (72%), Positives = 322/389 (82%), Gaps = 1/389 (0%) Query: 7 HWDDPLLLDQQLADDERMVRDAAHAYAQGKLAPRVTEAFRHETTDAAIFREMGEIGLLGP 66 +WDD L LD LA+DERM+RD+A AY Q KL PRV EA RHE D AI EMG +GLLGP Sbjct: 8 NWDDLLDLDGALAEDERMIRDSARAYCQDKLMPRVVEANRHEHFDRAIMTEMGALGLLGP 67 Query: 67 TIPEQYGGPGLDYVSYGLIAREVERVDSGYRSMMSVQSSLVMVPIFEFGSDAQKEKYLPK 126 TIPE+YGGPG+++V+YGLIAREVERVDSGYRS MSVQSSLVM PI+ +GSDAQK +LP Sbjct: 68 TIPEEYGGPGVNHVAYGLIAREVERVDSGYRSAMSVQSSLVMHPIYAYGSDAQKATWLPA 127 Query: 127 LATGEWIGCFGLTEPNHGSDPGSMVTRARKVPGGYSLSGSKMWITNSPIADVFVVWAKLD 186 LA+GE IGCFGLTEP+HGSDPGSM TRA K GGY L+G+KMWITNSPIAD+ VVWAK Sbjct: 128 LASGEKIGCFGLTEPDHGSDPGSMKTRATKTAGGYRLNGAKMWITNSPIADLAVVWAK-S 186 Query: 187 EDGRDEIRGFILEKGCKGLSAPAIHGKVGLRASITGEIVLDEAFVPEENILPHVKGLRGP 246 E D+IRGF++E+G KG S P I GK LRAS+TGEIVLD+ VPE N+LP +GL GP Sbjct: 187 EAHDDKIRGFLVERGMKGFSTPKIEGKFSLRASLTGEIVLDDCVVPEANLLPLAEGLAGP 246 Query: 247 FTCLNSARYGIAWGALGAAESCWHIARQYVLDRKQFGRPLAANQLIQKKLADMQTEITLG 306 F CLN ARYGI+WGA+GAAE CWH ARQY LDR QFGRPLAA QLIQKKLADMQTEITLG Sbjct: 247 FGCLNKARYGISWGAMGAAEFCWHAARQYTLDRLQFGRPLAATQLIQKKLADMQTEITLG 306 Query: 307 LQGVLRLGRMKDEGTAAVEITSIMKRNSCGKALDIARLARDMLGGNGISDEFGVARHLVN 366 L G LR+GR+ DEG A E S++KRN+ GKALDIAR+ARDM GGNGI+DEF V RH++N Sbjct: 307 LLGSLRVGRLLDEGKARPEAISLVKRNNAGKALDIARVARDMHGGNGIADEFHVIRHVMN 366 Query: 367 LEVVNTYEGTHDIHALILGRAQTGIQAFF 395 LE VNTYEGTHD+HALILGRAQTG+QAFF Sbjct: 367 LESVNTYEGTHDVHALILGRAQTGLQAFF 395 Lambda K H 0.320 0.138 0.414 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: 529 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: 395 Length of database: 395 Length adjustment: 31 Effective length of query: 364 Effective length of database: 364 Effective search space: 132496 Effective search space used: 132496 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 24 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