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 N515DRAFT_0484 N515DRAFT_0484 glutaryl-CoA dehydrogenase
Query= BRENDA::Q18AQ1 (378 letters) >FitnessBrowser__Dyella79:N515DRAFT_0484 Length = 389 Score = 213 bits (541), Expect = 9e-60 Identities = 126/368 (34%), Positives = 196/368 (53%), Gaps = 6/368 (1%) Query: 9 QMLKELYVSFAENEVKPLATELDEEERFPYETVEKMAKAGMMGIPYPKEYGGEGGDTVGY 68 +M+++ F + V P+ + ++ RFP E + ++A G++G P++YG G + V Y Sbjct: 22 RMVQDTVGRFVDERVLPIIGDAFDQGRFPKELIPEIAGLGLLGATLPEQYGCAGMNGVSY 81 Query: 69 IMAVEELSRVCGTTGVILSAHTSLGSWPIYQYGNEEQKQKFLRPLASGEKLGAFGLTEPN 128 + +EL R S +SL +PIY YG EEQK +L +A+GE +G FGLTEP+ Sbjct: 82 GLICQELERGDSGLRSFASVQSSLCMYPIYAYGTEEQKLHYLPKMAAGEIIGCFGLTEPH 141 Query: 129 AGTDASGQQTTAVLDGDEYILNGSKIFITNAIAGDIYVVMAMTDKSKGNKGISAFIVEKG 188 G+D + +T A DG ++I+NG+K++ITN I +V A T+ GI FIV Sbjct: 142 GGSDPANMKTNARKDGGDWIINGAKMWITNGNLAHIAIVWAQTE-----DGIQGFIVPTD 196 Query: 189 TPGFSFGVKEKKMGIRGSATSELIFEDCRIPKENLLGKEGQGFKIAMSTLDGGRIGIAAQ 248 + GF+ KKM +R S TS L F+ R+P+ N L +G K + L R GI Sbjct: 197 SQGFTAQEVHKKMSLRASVTSALFFDSVRVPEANRL-PNVKGLKGPLGCLTQARYGITWG 255 Query: 249 ALGLAQGALDETVKYVKERVQFGRPLSKFQNTQFQLADMEVKVQAARHLVYQAAINKDLG 308 +G AQ L E + Y +ERV FGRPL+ Q Q +LA+M ++ A+ L Q KD G Sbjct: 256 PIGAAQACLKEVLDYTQERVLFGRPLASNQAIQLKLAEMARRITMAQLLSLQLGRLKDAG 315 Query: 309 KPYGVEAAMAKLFAAETAMEVTTKAVQLHGGYGYTRDYPVERMMRDAKITEIYEGTSEVQ 368 + ++AK A+++ + + GG G T ++ R + + YEGT V Sbjct: 316 NMQPTQVSLAKWNNCRIAIDIARECRDILGGAGITTEHVAIRHALNLESVITYEGTETVH 375 Query: 369 RMVISGKL 376 ++V+ +L Sbjct: 376 QLVVGREL 383 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: 327 Number of extensions: 15 Number of successful extensions: 3 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: 389 Length adjustment: 30 Effective length of query: 348 Effective length of database: 359 Effective search space: 124932 Effective search space used: 124932 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