Align Short-chain acyl-CoA dehydrogenase (EC 1.3.8.1) (characterized)
to candidate WP_011443795.1 SARO_RS00655 acyl-CoA dehydrogenase
Query= reanno::pseudo13_GW456_L13:PfGW456L13_2983 (375 letters) >NCBI__GCF_000013325.1:WP_011443795.1 Length = 384 Score = 244 bits (622), Expect = 4e-69 Identities = 131/374 (35%), Positives = 218/374 (58%), Gaps = 3/374 (0%) Query: 4 NDDQQQIRDMARDFAQERLKPFAAEWDREHRFPKEAIGEMAGLGFFGMLVPEQWGGCDTG 63 N+D + R R F QE + P A +W + PK + LG VPE++GG Sbjct: 12 NEDHEAFRQTVRRFLQEEIAPNAEKWGDDGIVPKSIWPKAGELGMLCPTVPEEYGGLGLD 71 Query: 64 YLAYAMALEEIAAGDGACSTIMSVHNSVGCVPILNYGTDEQKERFLKPLASGAMLGAFAL 123 + Y ++E ++ G +T S+ + + +++YG++EQK+++L + SG ++ A A+ Sbjct: 72 F-GYNAIVDEESSYYGRVATGFSLQSDIVANYLVSYGSEEQKKKWLPKMVSGEVITAIAM 130 Query: 124 TEPQAGSDASGLKTRARLEGDHYVLNGCKQFITSGQNAGVVIVFAVTDPSAGK--RGISA 181 TEP GSD G++T A+ +G+HYV+NG K +IT+GQNA +++V TD +G+S Sbjct: 131 TEPGTGSDLQGMRTTAKKDGNHYVINGSKTYITNGQNADLILVCCKTDTEIQPAWKGVSI 190 Query: 182 FIVPTDSPGYKVARVEDKLGQHASDTCQILFEDVKVPLANRLGEEGEGYRIALANLEGGR 241 +V D G+K R DK+GQ +DT ++ FEDV+VP+ N LGEEG+G+ ++ L R Sbjct: 191 VLVEADREGFKRGRNLDKIGQDEADTSELFFEDVRVPITNCLGEEGKGFIYLMSELPQER 250 Query: 242 VGIASQSVGMARAAFEAARDYARERESFGKPIIEHQAVAFRLADMATQIAVARQMVHYAA 301 + IA + A+ AF+ ++ RER++FGKPI++ Q F LAD+ ++ V + +A Sbjct: 251 LSIAVGAQASAQKAFDDTVEFTRERKAFGKPILDFQNTRFTLADIKAKLQVGWAHLDWAL 310 Query: 302 ALRDSGKPALVEASMAKLFASEMAEKVCSSALQTLGGYGYLNDFPVERIYRDVRVCQIYE 361 + + E + AKL+ +E+ +V LQ GG GY+N++ + R +R RV +I+ Sbjct: 311 SRHLRKELTPEEGAAAKLWHTELQWEVMDKCLQLHGGAGYMNEYAIARAWRGARVTRIFG 370 Query: 362 GTSDIQRMVISRNL 375 GT++I + +I R L Sbjct: 371 GTNEIMKELIGRKL 384 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: 338 Number of extensions: 14 Number of successful extensions: 4 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: 384 Length adjustment: 30 Effective length of query: 345 Effective length of database: 354 Effective search space: 122130 Effective search space used: 122130 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