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 HSERO_RS12750 HSERO_RS12750 acyl-CoA dehydrogenase
Query= BRENDA::Q18AQ1 (378 letters) >FitnessBrowser__HerbieS:HSERO_RS12750 Length = 386 Score = 305 bits (780), Expect = 2e-87 Identities = 161/361 (44%), Positives = 225/361 (62%), Gaps = 3/361 (0%) Query: 18 FAENEVKPLATELDEEERFPYETVEKMAKAGMMGIPYPKEYGGEGGDTVGYIMAVEELSR 77 FA E+ P A + DEE FP + + K + G G+ P+ GG G + + EEL+R Sbjct: 19 FAAGEMAPFAAKWDEEAHFPLDVIAKAGELGFCGLYTPEADGGLGLSRLDATVVFEELAR 78 Query: 78 VCGTTGVILSAHTSLGSWPIYQYGNEEQKQKFLRPLASGEKLGAFGLTEPNAGTDASGQQ 137 C +T L+ H + SW I +G K ++ LA+G K+G++ LTEP +G+DA+ + Sbjct: 79 ACTSTAAYLTIHNMV-SWMIASWGQPSLKAQWCEQLAAGRKIGSYCLTEPGSGSDAASLK 137 Query: 138 TTAVLDGDEYILNGSKIFITNAIAGDIYVVMAMTDKSKGNKGISAFIVEKGTPGFSFGVK 197 TTA L+ Y+LNGSK FI+ A + D+ VVMA T +G +G+SA +V PG S+G K Sbjct: 138 TTARLEDGHYVLNGSKAFISGAGSTDVLVVMARTG-GEGARGVSAIVVPGNAPGVSYGKK 196 Query: 198 EKKMGIRGSATSELIFEDCRIPKENLLGKEGQGFKIAMSTLDGGRIGIAAQALGLAQGAL 257 E KMG T + F++ ++P ++LLG+EGQGF AM LDGGRI IA ++G AQ AL Sbjct: 197 ESKMGWNSQPTRTISFDNVKVPADHLLGQEGQGFIFAMKGLDGGRINIATCSVGAAQAAL 256 Query: 258 DETVKYVKERVQFGRPLSKFQNTQFQLADMEVKVQAARHLVYQAAINKDLGKPYGVE-AA 316 D Y+KER QFGRP++ FQ QF+LADM+ ++ AAR +V AA D G P A Sbjct: 257 DAAHAYMKERKQFGRPIADFQALQFKLADMQTELVAARQMVRLAATKLDAGSPEATTYCA 316 Query: 317 MAKLFAAETAMEVTTKAVQLHGGYGYTRDYPVERMMRDAKITEIYEGTSEVQRMVISGKL 376 MAK A + V +A+QLHGGYGY R+YP+ER RD ++ +I EGT+E+ R++IS KL Sbjct: 317 MAKRLATDLGFRVCNEALQLHGGYGYIREYPLERYFRDVRVHQILEGTNEIMRVIISRKL 376 Query: 377 L 377 L Sbjct: 377 L 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: 328 Number of extensions: 15 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: 386 Length adjustment: 30 Effective length of query: 348 Effective length of database: 356 Effective search space: 123888 Effective search space used: 123888 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