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_089303231.1 CHB84_RS20145 acyl-CoA dehydrogenase
Query= BRENDA::Q18AQ1 (378 letters) >NCBI__GCF_900188115.1:WP_089303231.1 Length = 383 Score = 328 bits (842), Expect = 1e-94 Identities = 174/372 (46%), Positives = 236/372 (63%), Gaps = 3/372 (0%) Query: 8 YQMLKELYVSFAENEVKPLATELDEEERFPYETVEKMAKAGMMGIPYPKEYGGEGGDTVG 67 Y+ L++ FA +EV P+ E E ERFPY+ V +M + G+ G+P+P+ YGG GGD Sbjct: 10 YEDLRKTVEDFARSEVAPVIGEYYEHERFPYDLVAQMGRMGLFGLPFPESYGGMGGDYFA 69 Query: 68 YIMAVEELSRVCGTTGVILSAHTSLGSWPIYQYGNEEQKQKFLRPLASGEKLGAFGLTEP 127 +A+EEL+RV + + L A SLG+ PIY++G +EQ++++L L SGE LGAFGLTEP Sbjct: 70 LCVALEELARVDSSVAITLEAGVSLGAMPIYRFGTDEQRRQWLPRLCSGEMLGAFGLTEP 129 Query: 128 NAGTDASGQQTTAVLDGDEYILNGSKIFITNA---IAGDIYVVMAMTDKSKGNKGISAFI 184 G+DA T+A E+++NGSK FITN+ I G + V K+ G K IS I Sbjct: 130 GGGSDAGATVTSATARDGEWVINGSKAFITNSGTDITGFVTVTAVTGTKAGGGKEISTII 189 Query: 185 VEKGTPGFSFGVKEKKMGIRGSATSELIFEDCRIPKENLLGKEGQGFKIAMSTLDGGRIG 244 V GTPGF+ K K+G S T L F D R+P+ENLLG G+G+ +S LD GRI Sbjct: 190 VPSGTPGFTVDAKYSKVGWNCSDTHGLAFSDVRVPEENLLGTRGKGYNQFLSILDEGRIA 249 Query: 245 IAAQALGLAQGALDETVKYVKERVQFGRPLSKFQNTQFQLADMEVKVQAARHLVYQAAIN 304 IAA +GLAQG +DE ++YV ER FG + FQ QF++ADME + AR Y AA Sbjct: 250 IAAIGVGLAQGCVDECLRYVAEREAFGHKIGDFQAIQFKVADMESRTHTARLAYYAAASK 309 Query: 305 KDLGKPYGVEAAMAKLFAAETAMEVTTKAVQLHGGYGYTRDYPVERMMRDAKITEIYEGT 364 G+P+ EAA+AKL ++ AM+ +A Q+ GGYG+ ++PV R RDAKI E+ EGT Sbjct: 310 MLRGEPFKREAAIAKLTSSNAAMDNAREATQIFGGYGFMNEFPVGRFYRDAKILEVGEGT 369 Query: 365 SEVQRMVISGKL 376 SEVQRM+I+ L Sbjct: 370 SEVQRMLIARDL 381 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: 356 Number of extensions: 10 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: 378 Length of database: 383 Length adjustment: 30 Effective length of query: 348 Effective length of database: 353 Effective search space: 122844 Effective search space used: 122844 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