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 RR42_RS28565 RR42_RS28565 acyl-CoA dehydrogenase
Query= BRENDA::Q18AQ1 (378 letters) >FitnessBrowser__Cup4G11:RR42_RS28565 Length = 377 Score = 341 bits (875), Expect = 2e-98 Identities = 171/372 (45%), Positives = 247/372 (66%) Query: 5 SKKYQMLKELYVSFAENEVKPLATELDEEERFPYETVEKMAKAGMMGIPYPKEYGGEGGD 64 S++ M+++ +FA + P A E D + P E V +M G++G+ P+E+GG D Sbjct: 6 SEQQTMIRDTARTFASERLAPCAAEWDRAGQLPAEVVAEMGALGLLGMIVPEEWGGTYTD 65 Query: 65 TVGYIMAVEELSRVCGTTGVILSAHTSLGSWPIYQYGNEEQKQKFLRPLASGEKLGAFGL 124 + Y +A+EE++ C ++S H S+G PI YG + QK+++L LASGE +GAF L Sbjct: 66 YIAYALAIEEIAAGCAACATLMSVHNSVGCGPILHYGTQAQKERYLPRLASGEIIGAFCL 125 Query: 125 TEPNAGTDASGQQTTAVLDGDEYILNGSKIFITNAIAGDIYVVMAMTDKSKGNKGISAFI 184 TEP AG++A +T A + ++L+GSK F+TN + +V A T+ ++G +G+SAF+ Sbjct: 126 TEPQAGSEAHNLRTRARATDNGWVLSGSKQFVTNGQRAGVAIVFAATEPAQGKRGLSAFV 185 Query: 185 VEKGTPGFSFGVKEKKMGIRGSATSELIFEDCRIPKENLLGKEGQGFKIAMSTLDGGRIG 244 V TPGFS E+KMGIR S T + +DC++P + LLG+ G+G +IA+S L+GGRIG Sbjct: 186 VPTDTPGFSVHTPERKMGIRASDTCAITLDDCQVPHDALLGEPGEGLRIALSNLEGGRIG 245 Query: 245 IAAQALGLAQGALDETVKYVKERVQFGRPLSKFQNTQFQLADMEVKVQAARHLVYQAAIN 304 IAAQALG+A+ A + +Y ERVQFGRPL + LADM ++ AAR LV++AA Sbjct: 246 IAAQALGIARSAFEAACRYAAERVQFGRPLREHAPIANMLADMATELNAARLLVHRAAHM 305 Query: 305 KDLGKPYGVEAAMAKLFAAETAMEVTTKAVQLHGGYGYTRDYPVERMMRDAKITEIYEGT 364 + G+P EA+ AKL+A+E A V +KA+Q+HGGYGY DYPVER RDA+IT+IYEGT Sbjct: 306 RTAGQPCLSEASQAKLYASELAERVCSKALQIHGGYGYLEDYPVERHYRDARITQIYEGT 365 Query: 365 SEVQRMVISGKL 376 SE+QRM+I+ L Sbjct: 366 SEIQRMLIARTL 377 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: 315 Number of extensions: 8 Number of successful extensions: 1 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: 377 Length adjustment: 30 Effective length of query: 348 Effective length of database: 347 Effective search space: 120756 Effective search space used: 120756 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 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