Align Short-chain acyl-CoA dehydrogenase (EC 1.3.8.1) (characterized)
to candidate GFF1190 PGA1_c12060 acyl-CoA dehydrogenase
Query= reanno::pseudo13_GW456_L13:PfGW456L13_2983 (375 letters) >FitnessBrowser__Phaeo:GFF1190 Length = 383 Score = 224 bits (571), Expect = 3e-63 Identities = 130/373 (34%), Positives = 207/373 (55%), Gaps = 3/373 (0%) Query: 5 DDQQQIRDMARDFAQERLKPFAAEWDREHRFPKEAIGEMAGLGFFGMLVPEQWGGCDTGY 64 D+ Q + DM F P W ++ + E LG VPE++GG + Sbjct: 12 DEHQMLADMTAQFITREWAPKFETWRKQGMMDRSTWNEAGALGLLCPSVPEEYGGVGGDF 71 Query: 65 LAYAMALEEIAAGDGACSTIMSVHNSVGCVPILNYGTDEQKERFLKPLASGAMLGAFALT 124 A L E + + A S +H+ + +L+YGT+EQK+R+L + +G ++GA A+T Sbjct: 72 GHEAAILIEGSRANLA-SWGHGIHSGIVAHYVLSYGTEEQKQRWLPKMITGELVGALAMT 130 Query: 125 EPQAGSDASGLKTRARLEGDHYVLNGCKQFITSGQNAGVVIVFAVTDPSAGKRGISAFIV 184 EP GSD +KT+A +G+ Y L+G K FIT+GQ+A +++V A TDPS G +GIS V Sbjct: 131 EPSTGSDVQRIKTKAVKDGNAYRLSGQKTFITNGQHANLILVAAKTDPSQGSKGISLVAV 190 Query: 185 PTD-SPGYKVARVEDKLGQHASDTCQILFEDVKVPLANRL-GEEGEGYRIALANLEGGRV 242 TD + G+ R DK+G HA+DT ++ F++V++ N L G EG+G+ + L R+ Sbjct: 191 ETDGADGFSRGRNLDKIGLHAADTSELFFDNVEIAPENILGGTEGQGFYQMMQQLPQERL 250 Query: 243 GIASQSVGMARAAFEAARDYARERESFGKPIIEHQAVAFRLADMATQIAVARQMVHYAAA 302 IA +VG A E Y +ERE+FG P+ + Q F+L + T+ VAR + Sbjct: 251 IIACGAVGAMEGAVERTITYCKEREAFGGPLTQFQNTRFKLVECQTKTKVARAFLDECMV 310 Query: 303 LRDSGKPALVEASMAKLFASEMAEKVCSSALQTLGGYGYLNDFPVERIYRDVRVCQIYEG 362 GK + +A+MAK + ++ V +Q GGYG++ ++ V ++ D RV +IY G Sbjct: 311 EHLQGKLTVEKAAMAKYWITDTQGDVLDECVQLHGGYGFMQEYAVAEMWTDARVQRIYGG 370 Query: 363 TSDIQRMVISRNL 375 T++I + +I+R+L Sbjct: 371 TNEIMKELIARSL 383 Lambda K H 0.320 0.135 0.394 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: 352 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: 375 Length of database: 383 Length adjustment: 30 Effective length of query: 345 Effective length of database: 353 Effective search space: 121785 Effective search space used: 121785 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 Apr 09 2024. 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