Align glutaryl-CoA dehydrogenase (ETF) (EC 1.3.8.6) (characterized)
to candidate N515DRAFT_0484 N515DRAFT_0484 glutaryl-CoA dehydrogenase
Query= BRENDA::B0EVL5 (395 letters) >FitnessBrowser__Dyella79:N515DRAFT_0484 Length = 389 Score = 383 bits (984), Expect = e-111 Identities = 196/376 (52%), Positives = 254/376 (67%), Gaps = 1/376 (0%) Query: 18 SQLTDTERMVRDSARAYSQERLLPRVQEAFRHEKTDRAIFNEMGELGLLGATIPEQYGGS 77 S LTD ERMV+D+ + ER+LP + +AF + + + E+ LGLLGAT+PEQYG + Sbjct: 15 SLLTDEERMVQDTVGRFVDERVLPIIGDAFDQGRFPKELIPEIAGLGLLGATLPEQYGCA 74 Query: 78 GMNYVCYGLIAREVERVDSGYRSMMSVQSSLVMVPINEFGSEETKQKYLPKLATGEWVGC 137 GMN V YGLI +E+ER DSG RS SVQSSL M PI +G+EE K YLPK+A GE +GC Sbjct: 75 GMNGVSYGLICQELERGDSGLRSFASVQSSLCMYPIYAYGTEEQKLHYLPKMAAGEIIGC 134 Query: 138 FGLTEPNHGSDPGSMVTRARKVDGGYSLSGAKMWITNSPIADVFVVWAKDDAGDIRGFVL 197 FGLTEP+ GSDP +M T ARK G + ++GAKMWITN +A + +VWA+ + G I+GF++ Sbjct: 135 FGLTEPHGGSDPANMKTNARKDGGDWIINGAKMWITNGNLAHIAIVWAQTEDG-IQGFIV 193 Query: 198 EKGWKGLSAPAIHGKVGLRASITGEIVMDEVFCPEENAFPTVRGLKGPFTCLNSARYGIA 257 +G +A +H K+ LRAS+T + D V PE N P V+GLKGP CL ARYGI Sbjct: 194 PTDSQGFTAQEVHKKMSLRASVTSALFFDSVRVPEANRLPNVKGLKGPLGCLTQARYGIT 253 Query: 258 WGALGAAEACYETARQYTMDRKQFGRPLAANQLIQKKLADMLTEITLGLQGCLRLGRLKD 317 WG +GAA+AC + YT +R FGRPLA+NQ IQ KLA+M IT+ L+LGRLKD Sbjct: 254 WGPIGAAQACLKEVLDYTQERVLFGRPLASNQAIQLKLAEMARRITMAQLLSLQLGRLKD 313 Query: 318 EGNAPVELTSIMKRNSCGKSLDIARVARDMLGGNGISDEFCIARHLVNLEVVNTYEGTHD 377 GN S+ K N+C ++DIAR RD+LGG GI+ E RH +NLE V TYEGT Sbjct: 314 AGNMQPTQVSLAKWNNCRIAIDIARECRDILGGAGITTEHVAIRHALNLESVITYEGTET 373 Query: 378 IHALILGRAITGLAAF 393 +H L++GR +TG+ AF Sbjct: 374 VHQLVVGRELTGINAF 389 Lambda K H 0.319 0.136 0.409 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: 392 Number of extensions: 13 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: 389 Length adjustment: 31 Effective length of query: 364 Effective length of database: 358 Effective search space: 130312 Effective search space used: 130312 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