Align glutaryl-CoA dehydrogenase (ETF) (EC 1.3.8.6) (characterized)
to candidate GFF3754 HP15_3696 acyl-CoA dehydrogenase domain protein
Query= BRENDA::Q60759 (438 letters) >FitnessBrowser__Marino:GFF3754 Length = 689 Score = 74.7 bits (182), Expect = 8e-18 Identities = 102/369 (27%), Positives = 151/369 (40%), Gaps = 62/369 (16%) Query: 113 YGCAGVSSVAYGLLTRELERVDSGYRSMMSVQSSLVMHPIYTYGSEEQRQKYLPGLAKGE 172 YG G+ + + GLL +E+ + SM S M+ I+ +G+E+Q+Q YL L +G Sbjct: 183 YGGQGLPA-SMGLLKQEMMGTANWPFSMYPGLSLGAMNTIFLHGTEDQKQTYLAPLTEGR 241 Query: 173 LLGCFGLTEPNHGSDPGGMETRARHNPSNQSYTLSGTKTWITNSPVADL-----FIVWAR 227 G LTEP G+D G ++T+A ++ SY L+GTK +I++ DL IV AR Sbjct: 242 WAGTMCLTEPQCGTDLGQVKTKAEPQ-ADGSYRLTGTKIFISSGD-HDLTENIVHIVLAR 299 Query: 228 CED-----NCIRGFILEKGM----------RGLSAPRIEGKFSLRASATGMIIMDSVEVP 272 D I FI+ K + G+ +E K ++ASAT ++ D Sbjct: 300 LPDAPKGTRGISLFIVPKFLPDSNGDVGERNGVVCGSLEKKMGIKASATCVLNFDG--AT 357 Query: 273 EENVLPNVSSLAGPFGCLNTARYGITWGVLGAAEFCLHTARQYALDR------------- 319 + P L F +NTAR G +G AE A YA DR Sbjct: 358 GFLIGPENDGLNCMFTFMNTARIGTAIQGVGPAELSYQWALAYAKDRRSMRALSGKKEPD 417 Query: 320 -----IQFGVPLARNQLVQKKLAD-----MLTEITLGLHAC--LQLGRLKDQDK------ 361 + + R L QK +A+ + L H G K DK Sbjct: 418 QVADSLIHHADVRRMLLTQKAIAEGGRAMLYYAARLADHMVEGFTEGDEKKADKYDDKLG 477 Query: 362 -ATPEMVSMLKRNNCGKALDIARQARDILGGNGISDEYHVIRHAMNLEAVNTYEGTHDIH 420 TP + L C + A + GG+G E+ + + + YEGT I Sbjct: 478 FLTPILKGFLTELGC----EAANLGVQVFGGHGYIREHGMEQIVRDTRIATLYEGTTGIQ 533 Query: 421 AL-ILGRAI 428 AL +LGR + Sbjct: 534 ALDLLGRKV 542 Lambda K H 0.320 0.136 0.408 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: 600 Number of extensions: 30 Number of successful extensions: 2 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 438 Length of database: 689 Length adjustment: 36 Effective length of query: 402 Effective length of database: 653 Effective search space: 262506 Effective search space used: 262506 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 bits) S2: 53 (25.0 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