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_084198396.1 C0029_RS13540 acyl-CoA dehydrogenase
Query= BRENDA::Q18AQ1 (378 letters) >NCBI__GCF_002869505.1:WP_084198396.1 Length = 385 Score = 247 bits (630), Expect = 4e-70 Identities = 136/376 (36%), Positives = 217/376 (57%), Gaps = 4/376 (1%) Query: 5 SKKYQMLKELYVSFAENEVKPLATELDEEERFPYETVEKMAKAGMMGIPYPKEYGGEGGD 64 +++ +ML + + F E E+ P + + + AG++ P EYGG GGD Sbjct: 10 NEELRMLHDSALKFTEQELGPNRERWEAQGMCDRDAWRTTGAAGLLCASIPVEYGGAGGD 69 Query: 65 TVGYIMAVEELSR--VCGTTGVILSAHTSLGSWPIYQYGNEEQKQKFLRPLASGEKLGAF 122 + + + R + G + H+ + + I YG E+QK K+L +A+GE +GA Sbjct: 70 YTHEAVIYDAMIRGGAAASVGGGNTVHSQIVAHYILDYGTEDQKHKWLPAMAAGELVGAI 129 Query: 123 GLTEPNAGTDASGQQTTAVLDGDEYILNGSKIFITNAIAGDIYVVMAMTDKSKGNKGISA 182 +TEP AG+D G +TTAV +GDEYI+NG+K FI+N ++ +V+A TD + G KG S Sbjct: 130 AMTEPGAGSDLQGVKTTAVREGDEYIINGAKTFISNGQHAELIIVVAKTDPAAGAKGTSL 189 Query: 183 FIVE-KGTPGFSFGVKEKKMGIRGSATSELIFEDCRIPKENLLGK-EGQGFKIAMSTLDG 240 +VE +G GF+ G K+G++ + TSEL F + R+P NLLG EGQGF M L Sbjct: 190 IVVETEGLDGFARGRNLDKVGLKDADTSELFFNNVRVPTANLLGDPEGQGFIQLMMQLPQ 249 Query: 241 GRIGIAAQALGLAQGALDETVKYVKERVQFGRPLSKFQNTQFQLADMEVKVQAARHLVYQ 300 R+GIA +A+ A++ T++Y ++R FG+ + FQNT+F+LA+ + + AR V Q Sbjct: 250 ERLGIACAGATIAEMAVETTLEYTRDRAAFGKSVFDFQNTRFKLAECKTEATIARSFVDQ 309 Query: 301 AAINKDLGKPYGVEAAMAKLFAAETAMEVTTKAVQLHGGYGYTRDYPVERMMRDAKITEI 360 G+ EA+MAK + + ++ + +QLHGGYGY +YP+ RM D+++ +I Sbjct: 310 CIAKHINGELSAEEASMAKWWCTQKQCDIVDECLQLHGGYGYMWEYPIARMYADSRVQKI 369 Query: 361 YEGTSEVQRMVISGKL 376 Y GT+E+ + +I+ L Sbjct: 370 YGGTNEIMKELIARSL 385 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: 346 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: 385 Length adjustment: 30 Effective length of query: 348 Effective length of database: 355 Effective search space: 123540 Effective search space used: 123540 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