Align Isovaleryl-CoA dehydrogenase (EC 1.3.8.4) (characterized)
to candidate N515DRAFT_0492 N515DRAFT_0492 hypothetical protein
Query= reanno::Phaeo:GFF1011 (386 letters) >FitnessBrowser__Dyella79:N515DRAFT_0492 Length = 386 Score = 292 bits (747), Expect = 1e-83 Identities = 163/380 (42%), Positives = 232/380 (61%), Gaps = 5/380 (1%) Query: 6 MTFDLGEDVNALRDMVHRWAQERVRPMAQEIDQKNEFPAELWQEMGELGLLGITVPEEFG 65 M F ED +++ + +AQ+R+ P+A E+D K EFP E +EMG+LGL+GI VP E+G Sbjct: 1 MDFSFTEDQLSIQSIARDFAQKRIVPVAAELDAKGEFPLENIREMGQLGLMGIEVPHEYG 60 Query: 66 GAGMSYLAHTVAVEEIARASASVSLSYGAHSNLCVNQIKLNGNAEQKAKYLPRLVSGEHV 125 GAGM +A+ +A+ EIA A A+ S +++L N I +GN EQK KY+ + GE + Sbjct: 61 GAGMDPIAYVLAMIEIAAADAATSTVMSVNNSLFCNGILKHGNEEQKQKYVRAIAQGEAI 120 Query: 126 GALAMSEAGAGSDVVSMSLRAEKRND-HYRLNGNKYWITNGPDADTLVVYAKTDPDAGSK 184 GA A++E +GSD +M RA K D + +NG K WIT+GP A +V++A + P G++ Sbjct: 121 GAYALTEPQSGSDASAMHTRATKNADGDWVINGKKSWITSGPVARYIVLFAISTPGIGAR 180 Query: 185 GMTAFLIEKEFKGFSTSQHFDKLGMRGSNTAELVFEDVEVPFENVLGEEGKGVRVLMSGL 244 G++AF+I+ + GF+ + KLG+R S T E+ F D P EN+LGEEGKG + M L Sbjct: 181 GVSAFIIDTQLPGFAAGKTEPKLGIRASATCEIEFSDYVCPKENLLGEEGKGFSIAMGVL 240 Query: 245 DYERVVLAGIGTGIMAACMDEMMPYMKERKQFGQPIGNFQLMQGKIADMYTAMNTARAYV 304 D R+ +A GI A + + + ++RK FGQ IG+FQ+ Q KIADM ++ A Sbjct: 241 DAGRIGIASQSVGIARAAYEATLQWSRDRKAFGQAIGSFQMTQAKIADMKCKLDAATLLT 300 Query: 305 YEVA----KACDKGTVTRQDAAACCLYASEVAMTQAHQAVQAFGGAGYLSDNPVGRIFRD 360 A +A G +A+ L ASE AM AHQAVQ GG GY + P+ R FRD Sbjct: 301 LRAAWTKGQAEKNGGRFGTEASVAKLVASEAAMWIAHQAVQIHGGMGYSKEMPLERYFRD 360 Query: 361 AKLMEIGAGTSEIRRMLIGR 380 AK+ EI GTSEI+R++I R Sbjct: 361 AKITEIYEGTSEIQRLVIAR 380 Lambda K H 0.318 0.132 0.382 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: 375 Number of extensions: 19 Number of successful extensions: 3 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: 386 Length of database: 386 Length adjustment: 30 Effective length of query: 356 Effective length of database: 356 Effective search space: 126736 Effective search space used: 126736 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 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