Align Short-chain acyl-CoA dehydrogenase (EC 1.3.8.1) (characterized)
to candidate AZOBR_RS22300 AZOBR_RS22300 acyl-CoA dehydrogenase
Query= reanno::pseudo13_GW456_L13:PfGW456L13_2983 (375 letters) >FitnessBrowser__azobra:AZOBR_RS22300 Length = 377 Score = 533 bits (1374), Expect = e-156 Identities = 264/371 (71%), Positives = 314/371 (84%) Query: 5 DDQQQIRDMARDFAQERLKPFAAEWDREHRFPKEAIGEMAGLGFFGMLVPEQWGGCDTGY 64 ++Q+ +RDMARDFA ERL P AAE DR FPKE + EM LG GMLVPE++ G T + Sbjct: 5 EEQRMVRDMARDFAAERLAPTAAERDRTGAFPKEELAEMGRLGLMGMLVPEEFDGAGTDH 64 Query: 65 LAYAMALEEIAAGDGACSTIMSVHNSVGCVPILNYGTDEQKERFLKPLASGAMLGAFALT 124 +AYA+A+EEIAAGDGA STIMSVHNSVGC+PIL +G+ EQKERFLKP+A G LG F LT Sbjct: 65 IAYALAIEEIAAGDGAISTIMSVHNSVGCMPILKFGSAEQKERFLKPMARGEQLGCFCLT 124 Query: 125 EPQAGSDASGLKTRARLEGDHYVLNGCKQFITSGQNAGVVIVFAVTDPSAGKRGISAFIV 184 EPQAGSDA+ +KTRAR +G+H+VLNG KQFITSG+NA V IVFAV+DP AGK+GI+AF+V Sbjct: 125 EPQAGSDAAAIKTRARRDGNHWVLNGTKQFITSGKNADVAIVFAVSDPEAGKKGITAFVV 184 Query: 185 PTDSPGYKVARVEDKLGQHASDTCQILFEDVKVPLANRLGEEGEGYRIALANLEGGRVGI 244 PTD+PG++VARVE+KLGQ SDTCQI+ ED ++P LG EG GYR+ALANLEGGR+GI Sbjct: 185 PTDTPGFQVARVEEKLGQSCSDTCQIVLEDCRIPADLMLGAEGGGYRVALANLEGGRIGI 244 Query: 245 ASQSVGMARAAFEAARDYARERESFGKPIIEHQAVAFRLADMATQIAVARQMVHYAAALR 304 ASQSVGMARAA + A YA+ER+S G PII+HQAVAFRLADMAT++ ARQ+V +AA+LR Sbjct: 245 ASQSVGMARAALDHATRYAQERQSMGLPIIQHQAVAFRLADMATKVEAARQLVLHAASLR 304 Query: 305 DSGKPALVEASMAKLFASEMAEKVCSSALQTLGGYGYLNDFPVERIYRDVRVCQIYEGTS 364 D+G+P L EA+MAKLFASE+AE+VCS A+Q GGYGYLNDFPVERIYRDVRVCQIYEGTS Sbjct: 305 DAGEPCLKEAAMAKLFASEIAERVCSDAIQIHGGYGYLNDFPVERIYRDVRVCQIYEGTS 364 Query: 365 DIQRMVISRNL 375 DIQR+VISR L Sbjct: 365 DIQRLVISRAL 375 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: 478 Number of extensions: 16 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: 377 Length adjustment: 30 Effective length of query: 345 Effective length of database: 347 Effective search space: 119715 Effective search space used: 119715 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