Align butanoyl-CoA dehydrogenase (NAD+, ferredoxin) (subunit 1/3) (EC 1.3.1.109) (characterized)
to candidate N515DRAFT_4319 N515DRAFT_4319 electron transfer flavoprotein alpha subunit apoprotein
Query= BRENDA::Q18AQ5 (336 letters) >FitnessBrowser__Dyella79:N515DRAFT_4319 Length = 314 Score = 161 bits (407), Expect = 2e-44 Identities = 105/329 (31%), Positives = 169/329 (51%), Gaps = 29/329 (8%) Query: 1 MGNVLVVIEQRENVIQTVSLELLGKATEIAKDYDTKVSALLLGSKVEGLIDTLAHY-GAD 59 M +LVV E + + + + A + D + L+L V+ + A G Sbjct: 1 MSKILVVAEHLNGKLNSSTARAVSAAAAVKGD---SIDVLVLADSVDAIAAEAAKIDGVG 57 Query: 60 EVIVV----DDEALAVYTTEPYTKAAYEAIKAADPIVVLFGATSIGRDLAPRVSARIHTG 115 +V+ + + LA KAA A V F +T+ G+D+APRV+A + Sbjct: 58 KVLTIARAENAHPLAAVLAPQVAKAA------AGYSHVFFPSTTFGKDVAPRVAALLGVS 111 Query: 116 LTADCTGLAVAEDTKLLLMTRPAFGGNIMATIVCKDFRPQMSTVR----PGVMKKNEPDE 171 +D + A K RP + GN + T+ ++T+R P + + Sbjct: 112 QVSDVMSVEGAHSFK-----RPIYAGNAIVTVEANPAHAVVATIRTASWPAAGSRGDSAA 166 Query: 172 TKEAVINRFKVEFNDADKLVQVVQVIKEAKKQVKIEDAKILVSAGRGMGGKENLDILYEL 231 + ++ + V++ + + ++ A +VS GRG+G KEN +++Y+L Sbjct: 167 VEALAVDAALPAHT------RFVELQQGKSDRPDLQGAGKVVSGGRGVGSKENFEVIYKL 220 Query: 232 AEIIGGEVSGSRATIDAGWLDKARQVGQTGKTVRPDLYIACGISGAIQHIAGMEDAEFIV 291 A+ IG V SRA +DAG++ QVGQTGK + P+LY+A GISGAIQH+ G++DA IV Sbjct: 221 ADKIGAAVGASRAAVDAGYVPNELQVGQTGKIIAPELYMAFGISGAIQHLTGIKDAGTIV 280 Query: 292 AINKNPEAPIFKYADVGIVGDVHKVLPEL 320 AINK+ EAPIF+ AD+G+VGD+ K++PE+ Sbjct: 281 AINKDGEAPIFEIADIGLVGDLFKLIPEI 309 Lambda K H 0.316 0.135 0.371 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: 254 Number of extensions: 12 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: 336 Length of database: 314 Length adjustment: 28 Effective length of query: 308 Effective length of database: 286 Effective search space: 88088 Effective search space used: 88088 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 (21.6 bits) S2: 48 (23.1 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