Align butyryl-CoA dehydrogenase; EC 1.3.99.2 (characterized)
to candidate N515DRAFT_0492 N515DRAFT_0492 hypothetical protein
Query= CharProtDB::CH_091785 (379 letters) >FitnessBrowser__Dyella79:N515DRAFT_0492 Length = 386 Score = 343 bits (880), Expect = 5e-99 Identities = 177/379 (46%), Positives = 256/379 (67%), Gaps = 5/379 (1%) Query: 1 MDFNLTREQELVRQMVREFAENEVKPIAAEIDETERFPMENVKKMGQYGMMGIPFSKEYG 60 MDF+ T +Q ++ + R+FA+ + P+AAE+D FP+EN+++MGQ G+MGI EYG Sbjct: 1 MDFSFTEDQLSIQSIARDFAQKRIVPVAAELDAKGEFPLENIREMGQLGLMGIEVPHEYG 60 Query: 61 GAGGDVLSYIIAVEELSKVCGTTGVILSAHTSLCASLINEHGTEEQKQKYLVPLAKGEKI 120 GAG D ++Y++A+ E++ T ++S + SL + I +HG EEQKQKY+ +A+GE I Sbjct: 61 GAGMDPIAYVLAMIEIAAADAATSTVMSVNNSLFCNGILKHGNEEQKQKYVRAIAQGEAI 120 Query: 121 GAYGLTEPNAGTDSGAQQTVAVLEGD-HYVINGSKIFITNGGVADTFVIFAMTDRTKGTK 179 GAY LTEP +G+D+ A T A D +VING K +IT+G VA V+FA++ G + Sbjct: 121 GAYALTEPQSGSDASAMHTRATKNADGDWVINGKKSWITSGPVARYIVLFAISTPGIGAR 180 Query: 180 GISAFIIEKGFKGFSIGKVEQKLGIRASSTTELVFEDMIVPVENMIGKEGKGFPIAMKTL 239 G+SAFII+ GF+ GK E KLGIRAS+T E+ F D + P EN++G+EGKGF IAM L Sbjct: 181 GVSAFIIDTQLPGFAAGKTEPKLGIRASATCEIEFSDYVCPKENLLGEEGKGFSIAMGVL 240 Query: 240 DGGRIGIAAQALGIAEGAFNEARAYMKERKQFGRSLDKFQGLAWMMADMDVAIESARYLV 299 D GRIGIA+Q++GIA A+ + ++RK FG+++ FQ +ADM +++A L Sbjct: 241 DAGRIGIASQSVGIARAAYEATLQWSRDRKAFGQAIGSFQMTQAKIADMKCKLDAATLLT 300 Query: 300 YKAAYLK----QAGLPYTVDAARAKLHAANVAMDVTTKAVQLFGGYGYTKDYPVERMMRD 355 +AA+ K + G + +A+ AKL A+ AM + +AVQ+ GG GY+K+ P+ER RD Sbjct: 301 LRAAWTKGQAEKNGGRFGTEASVAKLVASEAAMWIAHQAVQIHGGMGYSKEMPLERYFRD 360 Query: 356 AKITEIYEGTSEVQKLVIS 374 AKITEIYEGTSE+Q+LVI+ Sbjct: 361 AKITEIYEGTSEIQRLVIA 379 Lambda K H 0.317 0.135 0.377 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: 421 Number of extensions: 15 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: 379 Length of database: 386 Length adjustment: 30 Effective length of query: 349 Effective length of database: 356 Effective search space: 124244 Effective search space used: 124244 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