Align butanoyl-CoA dehydrogenase (NAD+, ferredoxin) (subunit 3/3) (EC 1.3.1.109); short-chain acyl-CoA dehydrogenase (EC 1.3.8.1) (characterized)
to candidate WP_043917997.1 jaqu_RS05745 acyl-CoA dehydrogenase
Query= BRENDA::Q18AQ1 (378 letters) >NCBI__GCF_000877395.1:WP_043917997.1 Length = 402 Score = 203 bits (516), Expect = 8e-57 Identities = 124/371 (33%), Positives = 194/371 (52%), Gaps = 6/371 (1%) Query: 2 DLNSKKYQMLKELYVSFAENEVKPLATELDEEERFPYETVEKMAKAGMMGIPYPKEYGGE 61 D S+ +ML++ +FAE E+ P T +E E +M AG++G+ P+EYGG Sbjct: 27 DQLSEDERMLRDAARAFAEAELAPGVTRAARDEVVDPEVFRRMGAAGLLGVTIPEEYGGL 86 Query: 62 GGDTVGYIMAVEELSRVCGTTGVILSAHTSLGSWPIYQYGNEEQKQKFLRPLASGEKLGA 121 G V Y + E+ RV ++S +SL +PI+ YG+E QK ++L LASGE +G Sbjct: 87 GAGYVTYGLVAREIERVDSGYRSMMSVQSSLVMYPIHAYGSEAQKARWLPQLASGEAIGC 146 Query: 122 FGLTEPNAGTDASGQQTTAVLDGDEYILNGSKIFITNAIAGDIYVVMAMTDKSKGNKGIS 181 FGLTEP+AG+D G +T A Y + G+K +I+NA D++VV A D I Sbjct: 147 FGLTEPDAGSDPGGMKTRAEKTATGYRITGTKTWISNAPIADVFVVWAKLDGV-----IR 201 Query: 182 AFIVEKGTPGFSFGVKEKKMGIRGSATSELIFEDCRIPKENLLGKEGQGFKIAMSTLDGG 241 F++E+GTPG S K+ +R S T E++ + +P+E LL +G K L+ Sbjct: 202 GFLIERGTPGLSAPKIGGKLSLRASVTGEIVMDGVEVPEEALL-PGVEGLKGPFGCLNRA 260 Query: 242 RIGIAAQALGLAQGALDETVKYVKERVQFGRPLSKFQNTQFQLADMEVKVQAARHLVYQA 301 R GI+ +G A+ +Y +R QFGRPL++ Q Q +LADM+ + + Sbjct: 261 RYGISWGVMGAAEACWHAARQYGLDRKQFGRPLAQTQLYQKKLADMQTAIGLGLQGSLRL 320 Query: 302 AINKDLGKPYGVEAAMAKLFAAETAMEVTTKAVQLHGGYGYTRDYPVERMMRDAKITEIY 361 + G +M K A++V +A +HGG G + ++ V R M + + Y Sbjct: 321 GRMMEAGTASPELVSMMKRNNCGAALDVARQARDMHGGNGISEEFGVMRHMINLETVNTY 380 Query: 362 EGTSEVQRMVI 372 EGT +V +++ Sbjct: 381 EGTHDVHALIL 391 Lambda K H 0.315 0.133 0.373 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: 374 Number of extensions: 18 Number of successful extensions: 4 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: 378 Length of database: 402 Length adjustment: 30 Effective length of query: 348 Effective length of database: 372 Effective search space: 129456 Effective search space used: 129456 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: 42 (22.0 bits) S2: 50 (23.9 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