Align butanoyl-CoA dehydrogenase (NAD+, ferredoxin) (subunit 2/3) (EC 1.3.1.109) (characterized)
to candidate HSERO_RS07555 HSERO_RS07555 electron transfer flavoprotein subunit beta
Query= BRENDA::Q18AQ6 (260 letters) >FitnessBrowser__HerbieS:HSERO_RS07555 Length = 251 Score = 96.7 bits (239), Expect = 4e-25 Identities = 85/257 (33%), Positives = 127/257 (49%), Gaps = 33/257 (12%) Query: 1 MNIVVCIKQVPD-TTEVKLDPNTGTLIRDGVPSIINPDDKAGLEEAIKLKEEMGAHVT-- 57 M ++V +K+V D +V++ + + V +NP D+ +EEA++LKE G VT Sbjct: 1 MKVLVPVKRVVDYNVKVRVKSDGSGVDIANVKMSMNPFDEIAVEEAVRLKE--GGKVTEV 58 Query: 58 -VITMGPPQADMALKEALAMGADRGILLTDRAFAGADTWATSSALAGALKNI----DFDI 112 ++ G Q L+ A+A+GADRGIL A GAD A+A LK + + Sbjct: 59 IAVSAGVTQCQETLRTAMAIGADRGIL----AEVGADVELQPLAVAKILKALAEKEQPQL 114 Query: 113 IIAGRQAIDGDTAQVGPQIAEHLNLPSITYAEEIKTEGEYVLVKRQFEDCCHDLKVKMPC 172 II G+QAID D Q G +A L P T+A ++ E V V R+ + L + +P Sbjct: 115 IILGKQAIDDDCNQTGQMLAALLGWPQATFASKVVLEEGKVTVTREVDGGLETLALTLPA 174 Query: 173 LITTLKDMNTPRYMKVGRIYDAFENDVVETWTVKDIEVDPSNLGLKGSPTSVFKSFTKSV 232 +ITT +N PRY+ + I A + + TVK P LG+ +P K++ Sbjct: 175 IITTDLRLNEPRYVTLPNIMKAKKKQLD---TVK-----PEELGVDVAPR------VKTL 220 Query: 233 KPAGTIYNEDAKTSAGI 249 K A E AK SAG+ Sbjct: 221 KVA-----EPAKRSAGV 232 Lambda K H 0.316 0.135 0.386 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: 168 Number of extensions: 8 Number of successful extensions: 2 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: 260 Length of database: 251 Length adjustment: 24 Effective length of query: 236 Effective length of database: 227 Effective search space: 53572 Effective search space used: 53572 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: 47 (22.7 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