Align glutaryl-CoA dehydrogenase (EC 1.3.8.6) (characterized)
to candidate Ac3H11_2720 Acyl-CoA dehydrogenase, short-chain specific (EC 1.3.99.2)
Query= metacyc::G1G01-166-MONOMER (393 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_2720 Length = 384 Score = 141 bits (355), Expect = 4e-38 Identities = 112/372 (30%), Positives = 180/372 (48%), Gaps = 12/372 (3%) Query: 21 EEERMVRDSAYQFAQDKLAPRVLEAFRHEQTDP-AIFREMGEVGLLGATIPEQYGGSGLN 79 E+ R+ A +F + ++ P L A+ E P +++ + GE GLL +T+PE YGG+G + Sbjct: 17 EDHEQFREQARRFIEREIVPH-LHAWEAEGIVPKSVWLKAGEAGLLCSTVPEAYGGAGGD 75 Query: 80 YVCYGLIAREVERIDSGYRSMMSVQSSLVMVPINEFGTEAQKQKYLPKLASGEWIGCFGL 139 + ++ E+ R+++ + S +V I +GTE QKQ++LPK+ SGE IG + Sbjct: 76 FGHSAVMIEELARVNATAVGF-TTHSEIVAPYIVAYGTEEQKQRWLPKMVSGETIGVIAM 134 Query: 140 TEPNHGSDPGSMITRARKVDGGYRLTGSKMWITNSPIADVFVVWAKDD--AGDIRGFVLE 197 +EP GSD SM T A + + Y + G K +ITN AD+ V K D A ++ +E Sbjct: 135 SEPGIGSDLRSMRTTAVRGEDIYTINGQKTFITNGGNADLAVTATKLDPAAKELTLICVE 194 Query: 198 KGWQGLSAPAIHGKVGLRASITGEIVMDNVFVPEEN-IFPDVRGLKGPFTCLNSARYGIS 256 G S K+GL+ T E+ DNV VP N + + +G K L R I Sbjct: 195 TDQPGFSKGRRLEKIGLKGQDTSELFFDNVSVPMANRLGEEGQGFKYLTHQLAWERTIIG 254 Query: 257 WGALGAAEACWHTARQYTLDRQQFGRPLAANQLIQKKLADMQTEITLA---LQGCLRLGR 313 A + ++ QYT DR+ FG+ + Q + KLA+ + + T+ + CL Sbjct: 255 IRAAASIDSLIEQTIQYTRDRKVFGKTVFDFQNTKFKLAECKAQATMLRVFVDDCLAKAM 314 Query: 314 MKDEGTAAVEITSIMKRNSCGKALDIARMARDMLGGNGISDEFGVARHLVNLEVVNTYEG 373 + + +M GK LD + GG G E+ ++R V+ V Y G Sbjct: 315 RGELSAEVGAMCKLMGSEMQGKILD---ELLQLHGGYGFMSEYMISRAWVDARVARIYGG 371 Query: 374 THDVHALILGRA 385 T ++ I+ R+ Sbjct: 372 TSEIMKEIISRS 383 Lambda K H 0.320 0.137 0.413 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: 322 Number of extensions: 17 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: 393 Length of database: 384 Length adjustment: 30 Effective length of query: 363 Effective length of database: 354 Effective search space: 128502 Effective search space used: 128502 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: 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