Align 2-methylbutanoyl-CoA dehydrogenase (EC 1.3.8.5) (characterized)
to candidate WP_015817809.1 TERTU_RS02185 acyl-CoA dehydrogenase
Query= reanno::pseudo6_N2E2:Pf6N2E2_1146 (375 letters) >NCBI__GCF_000023025.1:WP_015817809.1 Length = 591 Score = 132 bits (332), Expect = 2e-35 Identities = 114/396 (28%), Positives = 182/396 (45%), Gaps = 68/396 (17%) Query: 37 REAIDEMAELGFFGMLVPEQWGG-----CDTGYLAYAMTLEE---------IAAGD---- 78 REA ++ +L + VP+ + CD G+ + + E +AA D Sbjct: 59 READEQGCQLQEGNVAVPQGFADAYQLLCDGGWCSLSGNPEYGGMGLPKSLVAAVDEMVQ 118 Query: 79 GACST--IMSVHNSVGCVPILKFGNDEQKAKFLTPLASGAMLGAFALTEPQAGSDASSLK 136 GAC + ++ + + C+ I G+D K+ +L + SGA GA LTEP AG+D ++ Sbjct: 119 GACMSFGLLPMLTAGACLAIDAHGSDALKSTYLEKMYSGAWSGAMDLTEPHAGTDLGLIR 178 Query: 137 TRAR-LEGDHYVLNGCKQFITSGQ-----NAGVVIVFAVTDPSAGKRGISAFIVPTDSPG 190 TRA L D Y + G K FIT G+ N +++ + D AG RGIS F+VP P Sbjct: 179 TRAEPLADDSYAVTGTKIFITWGEHQLAENIIHLVLAKLPDAPAGSRGISMFLVPKYIPD 238 Query: 191 ----------YSVARVEDKLGQHASDTCQILFEDLKVPVGNRLGEEGEGYKIALANLEGG 240 +S +E K+G AS TC + F+ + G +GE +G + + Sbjct: 239 AQGEPGERNRFSCGGLEKKMGIKASPTCVMNFDGAR---GWLVGEPHKGLQAMFTMMNYE 295 Query: 241 RVGIAAQAVGMARAAFEAARDYARERSSFGKPIIEHQAVAFRLADMATQIAVARQMVHYA 300 R+ + Q VG A A+++ A YARER P+ H + AD R+M+ Sbjct: 296 RLVVGIQGVGAAEASYQNAVSYARERLQGRSPVGAHSPE--KEADNLLVHPDVRRMLLTM 353 Query: 301 AALRDSGQPALVEAS---------------------------MAKLFASEMAEKVCSMAL 333 AL ++G+ + S +AK F ++ A +V + Sbjct: 354 RALNEAGRAFYIYVSQWLDIAKFSDDQQRKTQAEALVALLTPVAKGFMTDRAFEVAVLGQ 413 Query: 334 QTLGGYGYLNDFPLERIYRDVRVCQIYEGTSDIQRM 369 Q GG+G++ ++ E++ RD R+ QIYEGT+ +Q M Sbjct: 414 QVYGGHGFIREWGQEQLVRDTRITQIYEGTNGVQAM 449 Lambda K H 0.320 0.134 0.388 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: 445 Number of extensions: 22 Number of successful extensions: 5 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: 375 Length of database: 591 Length adjustment: 33 Effective length of query: 342 Effective length of database: 558 Effective search space: 190836 Effective search space used: 190836 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: 51 (24.3 bits)
This GapMind analysis is from Sep 24 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