Align Short-chain acyl-CoA dehydrogenase (EC 1.3.8.1) (characterized)
to candidate GFF2713 PS417_13840 acyl-CoA dehydrogenase
Query= reanno::pseudo13_GW456_L13:PfGW456L13_2983 (375 letters) >FitnessBrowser__WCS417:GFF2713 Length = 383 Score = 449 bits (1155), Expect = e-131 Identities = 222/371 (59%), Positives = 278/371 (74%) Query: 5 DDQQQIRDMARDFAQERLKPFAAEWDREHRFPKEAIGEMAGLGFFGMLVPEQWGGCDTGY 64 ++Q IRDMARDFA+ + P+A W++ + +M LG GM+VPE+WGG Y Sbjct: 8 EEQVMIRDMARDFARGEIAPYAQAWEKAGWIDDALVAKMGELGLLGMVVPEEWGGTYVDY 67 Query: 65 LAYAMALEEIAAGDGACSTIMSVHNSVGCVPILNYGTDEQKERFLKPLASGAMLGAFALT 124 +AYA+A+EEI+AGDGA +MS+HNSVGC PILNYGT+ QK+ +L LASG +G F LT Sbjct: 68 VAYALAVEEISAGDGATGALMSIHNSVGCGPILNYGTESQKQTWLADLASGQAIGCFCLT 127 Query: 125 EPQAGSDASGLKTRARLEGDHYVLNGCKQFITSGQNAGVVIVFAVTDPSAGKRGISAFIV 184 EPQAGS+A L+TRA L H+V+ G KQF+++G+ A + IVFA+TDP GK+GISAF+V Sbjct: 128 EPQAGSEAHNLRTRAELRDGHWVITGAKQFVSNGKRAKLAIVFAITDPELGKKGISAFLV 187 Query: 185 PTDSPGYKVARVEDKLGQHASDTCQILFEDVKVPLANRLGEEGEGYRIALANLEGGRVGI 244 PT +PG+ V R E K+G ASDTC + VP AN LGE G+G IAL+NLEGGR+GI Sbjct: 188 PTATPGFVVDRTEHKMGIRASDTCAVTLNQCTVPEANLLGERGKGLAIALSNLEGGRIGI 247 Query: 245 ASQSVGMARAAFEAARDYARERESFGKPIIEHQAVAFRLADMATQIAVARQMVHYAAALR 304 A+Q++G+ARAAFEAA YAR+R F K IIEHQ+VA LADM TQ+ AR ++ +AA LR Sbjct: 248 AAQALGIARAAFEAALAYARDRVQFDKAIIEHQSVANLLADMQTQLNAARLLILHAARLR 307 Query: 305 DSGKPALVEASMAKLFASEMAEKVCSSALQTLGGYGYLNDFPVERIYRDVRVCQIYEGTS 364 +GKP L EAS AKLFASEMAEKVCSSA+Q GGYGYL D+PVER YRD R+ QIYEGTS Sbjct: 308 SAGKPCLSEASQAKLFASEMAEKVCSSAMQIHGGYGYLEDYPVERYYRDARITQIYEGTS 367 Query: 365 DIQRMVISRNL 375 +IQRMVI+R L Sbjct: 368 EIQRMVIAREL 378 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: 397 Number of extensions: 10 Number of successful extensions: 1 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 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