Align short-chain acyl-CoA dehydrogenase monomer (EC 1.3.8.1) (characterized)
to candidate WP_012966055.1 FERP_RS07810 acyl-CoA dehydrogenase
Query= metacyc::MONOMER-17424 (375 letters) >NCBI__GCF_000025505.1:WP_012966055.1 Length = 395 Score = 275 bits (702), Expect = 2e-78 Identities = 151/378 (39%), Positives = 229/378 (60%), Gaps = 9/378 (2%) Query: 2 LVNDEQQQIADAVRAFAQERLKPFAEQWDKDHRFPKEAIDEMAELGLFGMLVPEQWGGSD 61 ++ +EQ++I +A R FA++ +AE++DK FP E + A+LG G+ PE++GG+ Sbjct: 6 ILTEEQKEIKEAAREFAEKEFPKYAEEFDKKEEFPFELWKKAAKLGFIGLFFPEEYGGAG 65 Query: 62 TGYVAYAMALEEIAAGDGACSTIMSVHNSVGCVPILRFGNEQQKEQFLTPLATGAMLGAF 121 G Y +A+EE D I+S ++ G IL FG E QKE++L PLA G + Sbjct: 66 YGITEYCLAVEEFWRVDAGLGLILS--STFGSEMILLFGREDQKEKYLPPLAKGEAISCA 123 Query: 122 ALTEPQAGSDASSLKTRARLEGDHYVLNGSKQFITSGQNAGVVIVFAVTDP-EAGKRGIS 180 TEPQ+GSD + +KT AR E +H+V+NG+K FIT+G A IV A TD E G+S Sbjct: 124 CFTEPQSGSDLAGIKTTAREENEHFVINGNKIFITNGSIADFYIVLARTDKGEKRHHGLS 183 Query: 181 AFIVPTDSPGYQVARVEDKLGQHASDTCQIVFDNVQVPVANRLGAEGEGYKIALANLEGG 240 F+V + G + +++DKLG ASDT ++ F NV+VP N +G G G+ A+ Sbjct: 184 VFVVERGTEGLEARKMKDKLGIRASDTAEVFFKNVKVPKENLIGERGRGFYQAVEFFNVT 243 Query: 241 RIGIASQAVGMARAAFEVARDYANERQSFGKPLIEHQAVAFRLADMATKISVARQMVLHA 300 RI +A QAVG+A+ AFE+A +YA R+ F + LI+ Q +LA M T+I AR + A Sbjct: 244 RIHVAFQAVGIAQGAFELALEYAKNRELFERKLIDFQMTREKLAKMRTEIEAARLLAYQA 303 Query: 301 AALRDAGR---PALVEASMAKLFASEMAEKVCSDALQTLGGYGYLSDFPLERIYRDVRVC 357 A D P L +MAK + +++A+K ++ALQ GG+G++S + R+YRDVRV Sbjct: 304 ALYYDKNHKSDPGL--TAMAKYYTAKIAQKAVTEALQIFGGHGFVSS-AISRMYRDVRVL 360 Query: 358 QIYEGTSDIQRMVIARNL 375 +IYEGT +++ ++A ++ Sbjct: 361 EIYEGTREVELEIVANSI 378 Lambda K H 0.319 0.134 0.382 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: 327 Number of extensions: 12 Number of successful extensions: 5 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: 395 Length adjustment: 30 Effective length of query: 345 Effective length of database: 365 Effective search space: 125925 Effective search space used: 125925 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