Align glutaryl-CoA dehydrogenase (ETF) (EC 1.3.8.6) (characterized)
to candidate WP_011385596.1 AMB_RS16315 acyl-CoA dehydrogenase
Query= BRENDA::Q3JP94 (395 letters) >NCBI__GCF_000009985.1:WP_011385596.1 Length = 392 Score = 574 bits (1480), Expect = e-168 Identities = 278/389 (71%), Positives = 327/389 (84%), Gaps = 1/389 (0%) Query: 6 FHWDDPLLLDQQLADDERMVRDAAHAYAQGKLAPRVTEAFRHETTDAAIFREMGEIGLLG 65 F WDDP LL+ QL++DE+++RD+AHAY Q KL PRV +AFR ET D I EMGE+GLLG Sbjct: 4 FKWDDPFLLEDQLSEDEKLIRDSAHAYCQEKLQPRVMKAFRDETFDREIMNEMGEMGLLG 63 Query: 66 PTIPEQYGGPGLDYVSYGLIAREVERVDSGYRSMMSVQSSLVMVPIFEFGSDAQKEKYLP 125 PTIPE+YGGPG+++V+YGLI+REVERVDSGYRS MSVQSSLVM PIF +G++ QK+KYLP Sbjct: 64 PTIPEEYGGPGVNHVAYGLISREVERVDSGYRSAMSVQSSLVMHPIFSYGTEEQKKKYLP 123 Query: 126 KLATGEWIGCFGLTEPNHGSDPGSMVTRARKVPGGYSLSGSKMWITNSPIADVFVVWAKL 185 +LATGE IGCFGLTEP+ GSDPG M TRA+KV GGY L+GSKMWITNSPI+D+ +VWAK Sbjct: 124 RLATGEIIGCFGLTEPDAGSDPGGMRTRAKKVDGGYLLTGSKMWITNSPISDIAIVWAKS 183 Query: 186 DEDGRDEIRGFILEKGCKGLSAPAIHGKVGLRASITGEIVLDEAFVPEENILPHVKGLRG 245 D +I+GFI+EKG KG + P I GK+ LRASITGEIVLDEAFVP+E ++P+ GL G Sbjct: 184 DAH-EGKIKGFIVEKGIKGFTTPKIEGKLSLRASITGEIVLDEAFVPDEALMPNASGLGG 242 Query: 246 PFTCLNSARYGIAWGALGAAESCWHIARQYVLDRKQFGRPLAANQLIQKKLADMQTEITL 305 PF CLN ARYGIAWG +GAAE CWH ARQY+LDRKQFGRPLAANQ+ Q KLA+M TEITL Sbjct: 243 PFGCLNKARYGIAWGVIGAAEFCWHAARQYMLDRKQFGRPLAANQIPQLKLANMMTEITL 302 Query: 306 GLQGVLRLGRMKDEGTAAVEITSIMKRNSCGKALDIARLARDMLGGNGISDEFGVARHLV 365 GLQ +R+GRM D+ T A E S++KRN+CGKALDIAR+ARDM GGNGIS+EF V RH+V Sbjct: 303 GLQACVRVGRMMDDHTWAPEAVSLIKRNNCGKALDIARMARDMHGGNGISEEFHVIRHMV 362 Query: 366 NLEVVNTYEGTHDIHALILGRAQTGIQAF 394 NLE VNTYEG HD+HALILGRA TGIQAF Sbjct: 363 NLETVNTYEGAHDVHALILGRAMTGIQAF 391 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: 534 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: 395 Length of database: 392 Length adjustment: 31 Effective length of query: 364 Effective length of database: 361 Effective search space: 131404 Effective search space used: 131404 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