Align Short-chain acyl-CoA dehydrogenase (EC 1.3.8.1) (characterized)
to candidate WP_028321426.1 H567_RS0110890 acyl-CoA dehydrogenase
Query= reanno::pseudo13_GW456_L13:PfGW456L13_2983 (375 letters) >NCBI__GCF_000422285.1:WP_028321426.1 Length = 382 Score = 348 bits (894), Expect = e-100 Identities = 174/372 (46%), Positives = 250/372 (67%), Gaps = 1/372 (0%) Query: 5 DDQQQIRDMARDFAQERLKPFAAEWDREHRFPKEAIGEMAGLGFFGMLVPEQWGGCDTGY 64 D+QQ +R+MAR FA+ +KP AAE D H P + E+ L G+ VPE++GG Y Sbjct: 7 DEQQMVREMARRFAEAEIKPKAAELDATHAHPAAIVRELGELKMLGIAVPEEYGGGGMDY 66 Query: 65 LAYAMALEEIAAGDGACSTIMSVHNSVGCVPILNYGTDEQKERFLKPLASGAMLGAFALT 124 ++Y +AL E++ + IMSV+NS+ C P++ YGT EQK+++L+P ASG LG + LT Sbjct: 67 VSYVLALIEVSKACASTGVIMSVNNSLYCFPVMAYGTHEQKKKYLEPCASGEKLGCYGLT 126 Query: 125 EPQAGSDASGLKTRARLEGDHYVLNGCKQFITSGQNAGVVIVFAVTDPSAGKRGISAFIV 184 E AGSD S + T A +GD +++NG K+FIT+G A ++ AVTD G +GIS F+ Sbjct: 127 EAGAGSDPSAMLTTAVRDGDQWIINGEKKFITNGNVASYCVLAAVTDKGKGYKGISTFVA 186 Query: 185 PT-DSPGYKVARVEDKLGQHASDTCQILFEDVKVPLANRLGEEGEGYRIALANLEGGRVG 243 D+PG+KV RVE+KLG AS T +++FED ++P LG+EGEG++ L+ L+GGR+G Sbjct: 187 DLEDTPGFKVGRVEEKLGILASGTAELVFEDARLPADALLGQEGEGFKQMLSTLDGGRIG 246 Query: 244 IASQSVGMARAAFEAARDYARERESFGKPIIEHQAVAFRLADMATQIAVARQMVHYAAAL 303 IASQ++G+ RA E + YAR RE F KPI QA+ ++LADMAT++ A + AA L Sbjct: 247 IASQAIGIGRAVLEESLAYARTREQFNKPISSFQAIQWKLADMATELDAAELLTLRAAWL 306 Query: 304 RDSGKPALVEASMAKLFASEMAEKVCSSALQTLGGYGYLNDFPVERIYRDVRVCQIYEGT 363 D P EA+MAK+FAS++ + +Q LGGYGY ++P+ER RD ++CQIYEGT Sbjct: 307 EDHHMPYEKEAAMAKMFASDITMRASIEGVQILGGYGYSREYPMERHMRDAKICQIYEGT 366 Query: 364 SDIQRMVISRNL 375 ++I R+V++RNL Sbjct: 367 NEIMRLVVARNL 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: 394 Number of extensions: 13 Number of successful extensions: 3 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: 382 Length adjustment: 30 Effective length of query: 345 Effective length of database: 352 Effective search space: 121440 Effective search space used: 121440 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 24 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