Align isobutyryl-CoA dehydrogenase (EC 1.3.8.5) (characterized)
to candidate N515DRAFT_0492 N515DRAFT_0492 hypothetical protein
Query= reanno::WCS417:GFF2713 (383 letters) >FitnessBrowser__Dyella79:N515DRAFT_0492 Length = 386 Score = 350 bits (898), Expect = e-101 Identities = 184/379 (48%), Positives = 257/379 (67%), Gaps = 5/379 (1%) Query: 3 DIEYTEEQVMIRDMARDFARGEIAPYAQAWEKAGWIDDALVAKMGELGLLGMVVPEEWGG 62 D +TE+Q+ I+ +ARDFA+ I P A + G + +MG+LGL+G+ VP E+GG Sbjct: 2 DFSFTEDQLSIQSIARDFAQKRIVPVAAELDAKGEFPLENIREMGQLGLMGIEVPHEYGG 61 Query: 63 TYVDYVAYALAVEEISAGDGATGALMSIHNSVGCGPILNYGTESQKQTWLADLASGQAIG 122 +D +AY LA+ EI+A D AT +MS++NS+ C IL +G E QKQ ++ +A G+AIG Sbjct: 62 AGMDPIAYVLAMIEIAAADAATSTVMSVNNSLFCNGILKHGNEEQKQKYVRAIAQGEAIG 121 Query: 123 CFCLTEPQAGSEAHNLRTRAELR-DGHWVITGAKQFVSNGKRAKLAIVFAITDPELGKKG 181 + LTEPQ+GS+A + TRA DG WVI G K ++++G A+ ++FAI+ P +G +G Sbjct: 122 AYALTEPQSGSDASAMHTRATKNADGDWVINGKKSWITSGPVARYIVLFAISTPGIGARG 181 Query: 182 ISAFLVPTATPGFVVDRTEHKMGIRASDTCAVTLNQCTVPEANLLGERGKGLAIALSNLE 241 +SAF++ T PGF +TE K+GIRAS TC + + P+ NLLGE GKG +IA+ L+ Sbjct: 182 VSAFIIDTQLPGFAAGKTEPKLGIRASATCEIEFSDYVCPKENLLGEEGKGFSIAMGVLD 241 Query: 242 GGRIGIAAQALGIARAAFEAALAYARDRVQFDKAIIEHQSVANLLADMQTQLNAARLLIL 301 GRIGIA+Q++GIARAA+EA L ++RDR F +AI Q +ADM+ +L+AA LL L Sbjct: 242 AGRIGIASQSVGIARAAYEATLQWSRDRKAFGQAIGSFQMTQAKIADMKCKLDAATLLTL 301 Query: 302 HAA----RLRSAGKPCLSEASQAKLFASEMAEKVCSSAMQIHGGYGYLEDYPVERYYRDA 357 AA + G +EAS AKL ASE A + A+QIHGG GY ++ P+ERY+RDA Sbjct: 302 RAAWTKGQAEKNGGRFGTEASVAKLVASEAAMWIAHQAVQIHGGMGYSKEMPLERYFRDA 361 Query: 358 RITQIYEGTSEIQRMVIAR 376 +IT+IYEGTSEIQR+VIAR Sbjct: 362 KITEIYEGTSEIQRLVIAR 380 Lambda K H 0.319 0.133 0.390 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: 345 Number of extensions: 13 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: 383 Length of database: 386 Length adjustment: 30 Effective length of query: 353 Effective length of database: 356 Effective search space: 125668 Effective search space used: 125668 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