Align Short-chain acyl-CoA dehydrogenase (EC 1.3.8.1) (characterized)
to candidate RR42_RS28565 RR42_RS28565 acyl-CoA dehydrogenase
Query= reanno::pseudo13_GW456_L13:PfGW456L13_2983 (375 letters) >FitnessBrowser__Cup4G11:RR42_RS28565 Length = 377 Score = 468 bits (1203), Expect = e-136 Identities = 232/372 (62%), Positives = 287/372 (77%) Query: 4 NDDQQQIRDMARDFAQERLKPFAAEWDREHRFPKEAIGEMAGLGFFGMLVPEQWGGCDTG 63 ++ Q IRD AR FA ERL P AAEWDR + P E + EM LG GM+VPE+WGG T Sbjct: 6 SEQQTMIRDTARTFASERLAPCAAEWDRAGQLPAEVVAEMGALGLLGMIVPEEWGGTYTD 65 Query: 64 YLAYAMALEEIAAGDGACSTIMSVHNSVGCVPILNYGTDEQKERFLKPLASGAMLGAFAL 123 Y+AYA+A+EEIAAG AC+T+MSVHNSVGC PIL+YGT QKER+L LASG ++GAF L Sbjct: 66 YIAYALAIEEIAAGCAACATLMSVHNSVGCGPILHYGTQAQKERYLPRLASGEIIGAFCL 125 Query: 124 TEPQAGSDASGLKTRARLEGDHYVLNGCKQFITSGQNAGVVIVFAVTDPSAGKRGISAFI 183 TEPQAGS+A L+TRAR + +VL+G KQF+T+GQ AGV IVFA T+P+ GKRG+SAF+ Sbjct: 126 TEPQAGSEAHNLRTRARATDNGWVLSGSKQFVTNGQRAGVAIVFAATEPAQGKRGLSAFV 185 Query: 184 VPTDSPGYKVARVEDKLGQHASDTCQILFEDVKVPLANRLGEEGEGYRIALANLEGGRVG 243 VPTD+PG+ V E K+G ASDTC I +D +VP LGE GEG RIAL+NLEGGR+G Sbjct: 186 VPTDTPGFSVHTPERKMGIRASDTCAITLDDCQVPHDALLGEPGEGLRIALSNLEGGRIG 245 Query: 244 IASQSVGMARAAFEAARDYARERESFGKPIIEHQAVAFRLADMATQIAVARQMVHYAAAL 303 IA+Q++G+AR+AFEAA YA ER FG+P+ EH +A LADMAT++ AR +VH AA + Sbjct: 246 IAAQALGIARSAFEAACRYAAERVQFGRPLREHAPIANMLADMATELNAARLLVHRAAHM 305 Query: 304 RDSGKPALVEASMAKLFASEMAEKVCSSALQTLGGYGYLNDFPVERIYRDVRVCQIYEGT 363 R +G+P L EAS AKL+ASE+AE+VCS ALQ GGYGYL D+PVER YRD R+ QIYEGT Sbjct: 306 RTAGQPCLSEASQAKLYASELAERVCSKALQIHGGYGYLEDYPVERHYRDARITQIYEGT 365 Query: 364 SDIQRMVISRNL 375 S+IQRM+I+R L Sbjct: 366 SEIQRMLIARTL 377 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: 419 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: 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