Align glutaryl-CoA dehydrogenase (ETF) (EC 1.3.8.6) (characterized)
to candidate N515DRAFT_0492 N515DRAFT_0492 hypothetical protein
Query= BRENDA::B0EVL5 (395 letters) >FitnessBrowser__Dyella79:N515DRAFT_0492 Length = 386 Score = 214 bits (545), Expect = 3e-60 Identities = 130/385 (33%), Positives = 206/385 (53%), Gaps = 10/385 (2%) Query: 16 LDSQLTDTERMVRDSARAYSQERLLPRVQEAFRHEKTDRAIFNEMGELGLLGATIPEQYG 75 +D T+ + ++ AR ++Q+R++P E + EMG+LGL+G +P +YG Sbjct: 1 MDFSFTEDQLSIQSIARDFAQKRIVPVAAELDAKGEFPLENIREMGQLGLMGIEVPHEYG 60 Query: 76 GSGMNYVCYGLIAREVERVDSGYRSMMSVQSSLVMVPINEFGSEETKQKYLPKLATGEWV 135 G+GM+ + Y L E+ D+ ++MSV +SL I + G+EE KQKY+ +A GE + Sbjct: 61 GAGMDPIAYVLAMIEIAAADAATSTVMSVNNSLFCNGILKHGNEEQKQKYVRAIAQGEAI 120 Query: 136 GCFGLTEPNHGSDPGSMVTRARK-VDGGYSLSGAKMWITNSPIADVFVVWAKDDAG---- 190 G + LTEP GSD +M TRA K DG + ++G K WIT+ P+A V++A G Sbjct: 121 GAYALTEPQSGSDASAMHTRATKNADGDWVINGKKSWITSGPVARYIVLFAISTPGIGAR 180 Query: 191 DIRGFVLEKGWKGLSAPAIHGKVGLRASITGEIVMDEVFCPEENAF-PTVRGLKGPFTCL 249 + F+++ G +A K+G+RAS T EI + CP+EN +G L Sbjct: 181 GVSAFIIDTQLPGFAAGKTEPKLGIRASATCEIEFSDYVCPKENLLGEEGKGFSIAMGVL 240 Query: 250 NSARYGIAWGALGAAEACYETARQYTMDRKQFGRPLAANQLIQKKLADMLTEI----TLG 305 ++ R GIA ++G A A YE Q++ DRK FG+ + + Q+ Q K+ADM ++ L Sbjct: 241 DAGRIGIASQSVGIARAAYEATLQWSRDRKAFGQAIGSFQMTQAKIADMKCKLDAATLLT 300 Query: 306 LQGCLRLGRLKDEGNAPVELTSIMKRNSCGKSLDIARVARDMLGGNGISDEFCIARHLVN 365 L+ G+ + G S+ K + ++ IA A + GG G S E + R+ + Sbjct: 301 LRAAWTKGQAEKNGGRFGTEASVAKLVASEAAMWIAHQAVQIHGGMGYSKEMPLERYFRD 360 Query: 366 LEVVNTYEGTHDIHALILGRAITGL 390 ++ YEGT +I L++ RA TGL Sbjct: 361 AKITEIYEGTSEIQRLVIARAETGL 385 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: 352 Number of extensions: 17 Number of successful extensions: 5 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: 386 Length adjustment: 31 Effective length of query: 364 Effective length of database: 355 Effective search space: 129220 Effective search space used: 129220 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